data/last-align-1145/ChangeLog.txt:5793: seqeunce ==> sequence
data/last-align-1145/ChangeLog.txt:5800: seqeunce ==> sequence
data/last-align-1145/ChangeLog.txt:5961: progam ==> program
data/last-align-1145/examples/multiMito.maf:106: BA ==> BY, BE
data/last-align-1145/examples/multiMito.maf:142: ba ==> by, be
data/last-align-1145/doc/last-map-probs.html:411: Wan ==> Want
data/last-align-1145/doc/last-matrices.txt:42: Asai ==> Asia
data/last-align-1145/doc/last-matrices.txt:59: Asai ==> Asia
data/last-align-1145/doc/last-seeds.html:361: Asai ==> Asia
data/last-align-1145/doc/last-seeds.html:380: Asai ==> Asia
data/last-align-1145/doc/last-seeds.txt:48: Asai ==> Asia
data/last-align-1145/doc/last-seeds.txt:69: Asai ==> Asia
data/last-align-1145/doc/last-map-probs.txt:87: Wan ==> Want
data/last-align-1145/doc/last-matrices.html:356: Asai ==> Asia
data/last-align-1145/doc/last-matrices.html:372: Asai ==> Asia
data/last-align-1145/doc/last-papers.txt:11: Wan ==> Want
data/last-align-1145/doc/last-papers.txt:18: Wan ==> Want
data/last-align-1145/doc/last-papers.txt:53: Asai ==> Asia
data/last-align-1145/doc/last-papers.txt:62: Asai ==> Asia
data/last-align-1145/doc/last-papers.txt:104: Asai ==> Asia
data/last-align-1145/doc/last-papers.html:328: Wan ==> Want
data/last-align-1145/doc/last-papers.html:332: Wan ==> Want
data/last-align-1145/doc/last-papers.html:355: Asai ==> Asia
data/last-align-1145/doc/last-papers.html:361: Asai ==> Asia
data/last-align-1145/doc/last-papers.html:388: Asai ==> Asia
data/last-align-1145/scripts/last-map-probs:28: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/last-map-probs:29: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:103: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:105: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:113: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:130: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:136: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:137: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:145: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:212: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:227: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:243: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:247: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:274: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:277: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:535: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:549: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:652: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:666: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:720: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:735: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:754: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:760: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:875: aLine ==> align, a line, line, saline
data/last-align-1145/scripts/maf-convert:878: aLine ==> align, a line, line, saline
data/last-align-1145/src/AlignmentWrite.cc:30: Ser ==> Set
data/last-align-1145/src/AlignmentWrite.cc:30: ser ==> set
data/last-align-1145/src/AlignmentWrite.cc:118: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:126: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:130: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:306: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:308: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:311: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:316: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:317: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:319: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:339: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:362: aLine ==> align, a line, line, saline
data/last-align-1145/src/AlignmentWrite.cc:363: aLine ==> align, a line, line, saline
data/last-align-1145/src/AlignmentWrite.cc:364: aLine ==> align, a line, line, saline
data/last-align-1145/src/AlignmentWrite.cc:387: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:398: aLine ==> align, a line, line, saline
data/last-align-1145/src/AlignmentWrite.cc:401: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:407: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:413: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:443: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:464: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:609: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:611: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:612: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:616: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:625: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:636: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:643: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:660: alph ==> alpha
data/last-align-1145/src/AlignmentWrite.cc:666: alph ==> alpha
data/last-align-1145/src/QualityPssmMaker.cc:52: wee ==> we
data/last-align-1145/src/MultiSequence.cc:12: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.cc:39: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.cc:80: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.cc:105: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.cc:105: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.cc:106: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.cc:123: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.cc:147: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.cc:148: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.cc:149: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.cc:150: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:41: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:43: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:43: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:43: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:55: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:55: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:89: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:89: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:101: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:102: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:104: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:105: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:106: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:108: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:116: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:116: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:118: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:118: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:118: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:120: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:120: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:120: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:124: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:124: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:130: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:130: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:134: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:134: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:134: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:138: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:138: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:138: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:159: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:167: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:171: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:171: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:171: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:174: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:174: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:174: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:177: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:177: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:177: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:180: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:180: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:180: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:183: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:183: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:183: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:184: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:186: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:192: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:192: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:195: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:195: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:210: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:210: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:220: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:220: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:227: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:227: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:234: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:234: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:238: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:238: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:242: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:242: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:244: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:245: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:251: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:251: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:253: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:254: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:260: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.hh:261: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:10: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:10: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:24: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:25: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:35: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:36: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:43: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:44: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:96: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:97: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:98: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:99: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:109: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:132: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:132: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:138: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:159: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:161: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:177: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:179: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:190: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:190: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:195: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:209: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:210: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:210: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:213: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:223: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:224: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:224: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:227: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:237: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:237: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:251: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:252: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:296: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:297: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:297: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:303: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:304: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:330: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:331: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:331: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:337: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySearch.cc:338: indexT ==> index, indent
data/last-align-1145/src/SegmentPair.hh:14: indexT ==> index, indent
data/last-align-1145/src/SegmentPair.hh:19: indexT ==> index, indent
data/last-align-1145/src/SegmentPair.hh:19: indexT ==> index, indent
data/last-align-1145/src/SegmentPair.hh:19: indexT ==> index, indent
data/last-align-1145/src/SegmentPair.hh:28: indexT ==> index, indent
data/last-align-1145/src/SegmentPair.hh:29: indexT ==> index, indent
data/last-align-1145/src/SegmentPair.hh:30: indexT ==> index, indent
data/last-align-1145/src/SegmentPair.hh:31: indexT ==> index, indent
data/last-align-1145/src/SegmentPair.hh:32: indexT ==> index, indent
data/last-align-1145/src/SegmentPair.hh:40: indexT ==> index, indent
data/last-align-1145/src/SegmentPair.hh:41: indexT ==> index, indent
data/last-align-1145/src/SegmentPair.hh:42: indexT ==> index, indent
data/last-align-1145/src/DiagonalTable.cc:7: indexT ==> index, indent
data/last-align-1145/src/DiagonalTable.cc:7: indexT ==> index, indent
data/last-align-1145/src/DiagonalTable.cc:9: indexT ==> index, indent
data/last-align-1145/src/DiagonalTable.cc:10: indexT ==> index, indent
data/last-align-1145/src/DiagonalTable.cc:25: indexT ==> index, indent
data/last-align-1145/src/DiagonalTable.cc:25: indexT ==> index, indent
data/last-align-1145/src/DiagonalTable.cc:27: indexT ==> index, indent
data/last-align-1145/src/DiagonalTable.cc:28: indexT ==> index, indent
data/last-align-1145/src/Centroid.cc:135: partion ==> partition, portion
data/last-align-1145/src/lastdb.cc:28: alph ==> alpha
data/last-align-1145/src/lastdb.cc:29: alph ==> alpha
data/last-align-1145/src/lastdb.cc:30: alph ==> alpha
data/last-align-1145/src/lastdb.cc:30: alph ==> alpha
data/last-align-1145/src/lastdb.cc:31: alph ==> alpha
data/last-align-1145/src/lastdb.cc:31: alph ==> alpha
data/last-align-1145/src/lastdb.cc:35: alph ==> alpha
data/last-align-1145/src/lastdb.cc:40: alph ==> alpha
data/last-align-1145/src/lastdb.cc:41: alph ==> alpha
data/last-align-1145/src/lastdb.cc:42: alph ==> alpha
data/last-align-1145/src/lastdb.cc:42: alph ==> alpha
data/last-align-1145/src/lastdb.cc:51: alph ==> alpha
data/last-align-1145/src/lastdb.cc:57: alph ==> alpha
data/last-align-1145/src/lastdb.cc:58: alph ==> alpha
data/last-align-1145/src/lastdb.cc:67: alph ==> alpha
data/last-align-1145/src/lastdb.cc:68: alph ==> alpha
data/last-align-1145/src/lastdb.cc:71: alph ==> alpha
data/last-align-1145/src/lastdb.cc:77: alph ==> alpha
data/last-align-1145/src/lastdb.cc:84: alph ==> alpha
data/last-align-1145/src/lastdb.cc:88: alph ==> alpha
data/last-align-1145/src/lastdb.cc:88: alph ==> alpha
data/last-align-1145/src/lastdb.cc:91: alph ==> alpha
data/last-align-1145/src/lastdb.cc:107: alph ==> alpha
data/last-align-1145/src/lastdb.cc:118: alph ==> alpha
data/last-align-1145/src/lastdb.cc:151: indexT ==> index, indent
data/last-align-1145/src/lastdb.cc:191: alph ==> alpha
data/last-align-1145/src/lastdb.cc:200: alph ==> alpha
data/last-align-1145/src/lastdb.cc:204: alph ==> alpha
data/last-align-1145/src/lastdb.cc:210: alph ==> alpha
data/last-align-1145/src/lastdb.cc:219: alph ==> alpha
data/last-align-1145/src/lastdb.cc:223: alph ==> alpha
data/last-align-1145/src/lastdb.cc:282: indexT ==> index, indent
data/last-align-1145/src/lastdb.cc:288: indexT ==> index, indent
data/last-align-1145/src/lastdb.cc:288: indexT ==> index, indent
data/last-align-1145/src/lastdb.cc:289: numer ==> number
data/last-align-1145/src/lastdb.cc:292: numer ==> number
data/last-align-1145/src/lastdb.cc:297: numer ==> number
data/last-align-1145/src/lastdb.cc:301: numer ==> number
data/last-align-1145/src/lastdb.cc:303: indexT ==> index, indent
data/last-align-1145/src/lastdb.cc:304: indexT ==> index, indent
data/last-align-1145/src/lastdb.cc:329: alph ==> alpha
data/last-align-1145/src/lastdb.cc:330: alph ==> alpha
data/last-align-1145/src/lastdb.cc:333: alph ==> alpha
data/last-align-1145/src/lastdb.cc:334: alph ==> alpha
data/last-align-1145/src/lastdb.cc:334: alph ==> alpha
data/last-align-1145/src/lastdb.cc:336: alph ==> alpha
data/last-align-1145/src/lastdb.cc:339: alph ==> alpha
data/last-align-1145/src/lastdb.cc:341: alph ==> alpha
data/last-align-1145/src/lastdb.cc:347: alph ==> alpha
data/last-align-1145/src/lastdb.cc:350: alph ==> alpha
data/last-align-1145/src/lastdb.cc:351: indexT ==> index, indent
data/last-align-1145/src/lastdb.cc:360: openIn ==> opening
data/last-align-1145/src/lastdb.cc:363: alph ==> alpha
data/last-align-1145/src/lastdb.cc:369: alph ==> alpha
data/last-align-1145/src/lastdb.cc:384: alph ==> alpha
data/last-align-1145/src/lastdb.cc:391: alph ==> alpha
data/last-align-1145/src/lastdb.cc:397: alph ==> alpha
data/last-align-1145/src/lastdb.cc:407: alph ==> alpha
data/last-align-1145/src/lastdb.cc:413: alph ==> alpha
data/last-align-1145/src/lastdb.cc:417: alph ==> alpha
data/last-align-1145/src/SegmentPair.cc:14: indexT ==> index, indent
data/last-align-1145/src/SegmentPair.cc:15: indexT ==> index, indent
data/last-align-1145/src/SegmentPair.cc:29: indexT ==> index, indent
data/last-align-1145/src/MultiSequenceQual.cc:15: indexT ==> index, indent
data/last-align-1145/src/MultiSequenceQual.cc:36: indexT ==> index, indent
data/last-align-1145/src/MultiSequenceQual.cc:86: indexT ==> index, indent
data/last-align-1145/src/MultiSequenceQual.cc:165: indexT ==> index, indent
data/last-align-1145/src/zio.hh:16: openIn ==> opening
data/last-align-1145/src/zio.hh:30: openIn ==> opening
data/last-align-1145/src/SegmentPairPot.hh:24: indexT ==> index, indent
data/last-align-1145/src/SegmentPairPot.hh:24: indexT ==> index, indent
data/last-align-1145/src/Alignment.hh:32: indexT ==> index, indent
data/last-align-1145/src/Alignment.hh:33: indexT ==> index, indent
data/last-align-1145/src/Alignment.hh:34: indexT ==> index, indent
data/last-align-1145/src/Alignment.hh:36: indexT ==> index, indent
data/last-align-1145/src/Alignment.hh:37: indexT ==> index, indent
data/last-align-1145/src/Alignment.hh:94: alph ==> alpha
data/last-align-1145/src/Alignment.hh:122: alph ==> alpha
data/last-align-1145/src/Alignment.hh:149: alph ==> alpha
data/last-align-1145/src/Alignment.hh:159: alph ==> alpha
data/last-align-1145/src/Alignment.hh:166: alph ==> alpha
data/last-align-1145/src/Alignment.hh:173: alph ==> alpha
data/last-align-1145/src/Alignment.hh:176: alph ==> alpha
data/last-align-1145/src/lastal.cc:75: alph ==> alpha
data/last-align-1145/src/lastal.cc:101: alph ==> alpha
data/last-align-1145/src/lastal.cc:101: alph ==> alpha
data/last-align-1145/src/lastal.cc:110: alph ==> alpha
data/last-align-1145/src/lastal.cc:114: alph ==> alpha
data/last-align-1145/src/lastal.cc:115: alph ==> alpha
data/last-align-1145/src/lastal.cc:117: alph ==> alpha
data/last-align-1145/src/lastal.cc:117: alph ==> alpha
data/last-align-1145/src/lastal.cc:121: alph ==> alpha
data/last-align-1145/src/lastal.cc:133: alph ==> alpha
data/last-align-1145/src/lastal.cc:142: alph ==> alpha
data/last-align-1145/src/lastal.cc:147: alph ==> alpha
data/last-align-1145/src/lastal.cc:158: alph ==> alpha
data/last-align-1145/src/lastal.cc:160: alph ==> alpha
data/last-align-1145/src/lastal.cc:181: alph ==> alpha
data/last-align-1145/src/lastal.cc:184: alph ==> alpha
data/last-align-1145/src/lastal.cc:189: alph ==> alpha
data/last-align-1145/src/lastal.cc:189: alph ==> alpha
data/last-align-1145/src/lastal.cc:192: alph ==> alpha
data/last-align-1145/src/lastal.cc:195: alph ==> alpha
data/last-align-1145/src/lastal.cc:240: alph ==> alpha
data/last-align-1145/src/lastal.cc:246: alph ==> alpha
data/last-align-1145/src/lastal.cc:249: alph ==> alpha
data/last-align-1145/src/lastal.cc:256: alph ==> alpha
data/last-align-1145/src/lastal.cc:260: alph ==> alpha
data/last-align-1145/src/lastal.cc:312: alph ==> alpha
data/last-align-1145/src/lastal.cc:318: alph ==> alpha
data/last-align-1145/src/lastal.cc:351: alph ==> alpha
data/last-align-1145/src/lastal.cc:367: alph ==> alpha
data/last-align-1145/src/lastal.cc:378: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:387: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:387: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:409: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:486: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:486: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:492: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:492: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:498: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:498: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:504: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:504: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:504: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:510: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:510: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:510: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:516: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:516: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:516: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:522: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:522: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:522: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:543: alph ==> alpha
data/last-align-1145/src/lastal.cc:573: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:574: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:579: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:585: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:604: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:605: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:606: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:694: alph ==> alpha
data/last-align-1145/src/lastal.cc:695: alph ==> alpha
data/last-align-1145/src/lastal.cc:716: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:717: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:718: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:749: alph ==> alpha
data/last-align-1145/src/lastal.cc:789: alph ==> alpha
data/last-align-1145/src/lastal.cc:793: alph ==> alpha
data/last-align-1145/src/lastal.cc:817: alph ==> alpha
data/last-align-1145/src/lastal.cc:966: alph ==> alpha
data/last-align-1145/src/lastal.cc:979: alph ==> alpha
data/last-align-1145/src/lastal.cc:1070: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:1076: alph ==> alpha
data/last-align-1145/src/lastal.cc:1076: alph ==> alpha
data/last-align-1145/src/lastal.cc:1079: alph ==> alpha
data/last-align-1145/src/lastal.cc:1079: alph ==> alpha
data/last-align-1145/src/lastal.cc:1085: alph ==> alpha
data/last-align-1145/src/lastal.cc:1128: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:1128: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:1129: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:1129: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:1218: alph ==> alpha
data/last-align-1145/src/lastal.cc:1218: alph ==> alpha
data/last-align-1145/src/lastal.cc:1219: alph ==> alpha
data/last-align-1145/src/lastal.cc:1256: alph ==> alpha
data/last-align-1145/src/lastal.cc:1256: alph ==> alpha
data/last-align-1145/src/lastal.cc:1269: alph ==> alpha
data/last-align-1145/src/lastal.cc:1272: alph ==> alpha
data/last-align-1145/src/lastal.cc:1277: alph ==> alpha
data/last-align-1145/src/lastal.cc:1304: indexT ==> index, indent
data/last-align-1145/src/lastal.cc:1313: openIn ==> opening
data/last-align-1145/src/last.hh:15: indexT ==> index, indent
data/last-align-1145/src/last.hh:15: indexT ==> index, indent
data/last-align-1145/src/last.hh:21: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.cc:37: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.cc:37: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.cc:69: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.cc:217: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.cc:218: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.cc:219: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.cc:223: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.cc:224: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.cc:229: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.cc:244: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.cc:257: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.cc:261: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArray.cc:285: indexT ==> index, indent
data/last-align-1145/src/DiagonalTable.hh:26: indexT ==> index, indent
data/last-align-1145/src/DiagonalTable.hh:27: indexT ==> index, indent
data/last-align-1145/src/DiagonalTable.hh:27: indexT ==> index, indent
data/last-align-1145/src/DiagonalTable.hh:33: indexT ==> index, indent
data/last-align-1145/src/DiagonalTable.hh:33: indexT ==> index, indent
data/last-align-1145/src/DiagonalTable.hh:36: indexT ==> index, indent
data/last-align-1145/src/DiagonalTable.hh:36: indexT ==> index, indent
data/last-align-1145/src/last-pair-probs.cc:392: aLine ==> align, a line, line, saline
data/last-align-1145/src/last-pair-probs.cc:393: aLine ==> align, a line, line, saline
data/last-align-1145/src/last-pair-probs.cc:631: openIn ==> opening
data/last-align-1145/src/last-pair-probs.cc:633: openIn ==> opening
data/last-align-1145/src/last-pair-probs.cc:643: openIn ==> opening
data/last-align-1145/src/last-pair-probs.cc:645: openIn ==> opening
data/last-align-1145/src/SubsetSuffixArraySort.cc:17: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:17: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:22: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:22: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:22: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:30: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:30: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:31: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:33: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:34: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:43: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:44: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:72: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:72: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:72: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:73: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:74: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:77: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:104: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:104: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:104: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:105: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:106: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:107: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:110: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:146: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:146: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:146: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:147: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:148: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:149: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:150: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:153: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:198: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:198: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:198: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:199: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:200: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:201: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:202: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:203: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:206: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:262: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:262: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:262: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:263: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:264: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:269: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:281: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:283: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:294: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:302: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:310: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:312: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:350: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:398: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:399: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:400: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:404: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:454: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:455: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:457: indexT ==> index, indent
data/last-align-1145/src/SubsetSuffixArraySort.cc:459: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:24: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:27: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:39: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:48: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:51: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:57: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:61: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:65: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:73: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:79: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:79: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:81: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:81: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:82: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:82: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:83: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:83: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:84: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:84: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:85: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:85: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:86: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:86: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:88: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:90: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:91: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:96: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:98: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:99: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:122: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:124: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:127: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:129: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:131: indexT ==> index, indent
data/last-align-1145/src/MultiSequence.hh:175: indexT ==> index, indent
data/last-align-1145/src/Alignment.cc:51: alph ==> alpha
data/last-align-1145/src/Alignment.cc:69: alph ==> alpha
data/last-align-1145/src/Alignment.cc:75: indexT ==> index, indent
data/last-align-1145/src/Alignment.cc:76: indexT ==> index, indent
data/last-align-1145/src/Alignment.cc:89: alph ==> alpha
data/last-align-1145/src/Alignment.cc:95: indexT ==> index, indent
data/last-align-1145/src/Alignment.cc:96: indexT ==> index, indent
data/last-align-1145/src/Alignment.cc:285: alph ==> alpha
data/last-align-1145/src/Alignment.cc:355: alph ==> alpha
data/last-align-1145/src/Alignment.cc:360: alph ==> alpha
data/last-align-1145/src/Alignment.cc:365: alph ==> alpha
data/last-align-1145/src/Alignment.cc:381: alph ==> alpha
data/last-align-1145/src/Alignment.cc:432: alph ==> alpha
data/last-align-1145/src/alp/njn_root.hpp:12: offical ==> official
data/last-align-1145/src/alp/njn_localmaxstatutil.hpp:12: offical ==> official
data/last-align-1145/src/alp/sls_fsa1.cpp:9: offical ==> official
data/last-align-1145/src/alp/sls_fsa1.cpp:280: additonal ==> additional
data/last-align-1145/src/alp/sls_fsa1.cpp:364: additonal ==> additional
data/last-align-1145/src/alp/sls_fsa1.cpp:977: dimention ==> dimension
data/last-align-1145/src/alp/sls_fsa1.cpp:1020: dimention ==> dimension
data/last-align-1145/src/alp/sls_fsa1.cpp:1419: dimention ==> dimension
data/last-align-1145/src/alp/sls_fsa1.cpp:1891: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:1892: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:3589: alingment ==> alignment
data/last-align-1145/src/alp/sls_fsa1.cpp:3597: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:3598: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:3781: alingment ==> alignment
data/last-align-1145/src/alp/sls_fsa1.cpp:5081: adjusment ==> adjustment
data/last-align-1145/src/alp/sls_fsa1.cpp:5691: acheived ==> achieved
data/last-align-1145/src/alp/sls_fsa1.cpp:6533: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:6534: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:6644: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:6645: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:6688: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:6689: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:6954: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:6955: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:6958: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:6959: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:7040: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:7041: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:7067: weigths ==> weights
data/last-align-1145/src/alp/sls_fsa1.cpp:8409: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:8410: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:8414: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:8415: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:8549: alingment ==> alignment
data/last-align-1145/src/alp/sls_fsa1.cpp:8596: wheter ==> whether
data/last-align-1145/src/alp/sls_fsa1.cpp:8761: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:8762: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:8837: weigths ==> weights
data/last-align-1145/src/alp/sls_fsa1.cpp:10341: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:10342: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:10457: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:10458: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:11298: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:11299: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:11363: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.cpp:11364: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1_parameters.hpp:12: offical ==> official
data/last-align-1145/src/alp/sls_alp_sim.hpp:12: offical ==> official
data/last-align-1145/src/alp/sls_alp.hpp:12: offical ==> official
data/last-align-1145/src/alp/sls_alp.hpp:114: weigths ==> weights
data/last-align-1145/src/alp/sls_alp.hpp:142: upto ==> up to
data/last-align-1145/src/alp/sls_alp.hpp:145: upto ==> up to
data/last-align-1145/src/alp/sls_alp.hpp:168: weigths ==> weights
data/last-align-1145/src/alp/sls_alp_regression.hpp:12: offical ==> official
data/last-align-1145/src/alp/sls_fsa1_utils.hpp:12: offical ==> official
data/last-align-1145/src/alp/sls_fsa1_utils.hpp:129: ot ==> to, of, or
data/last-align-1145/src/alp/sls_fsa1_utils.hpp:132: ot ==> to, of, or
data/last-align-1145/src/alp/sls_fsa1.hpp:12: offical ==> official
data/last-align-1145/src/alp/sls_fsa1.hpp:75: weigths ==> weights
data/last-align-1145/src/alp/sls_fsa1.hpp:192: additonal ==> additional
data/last-align-1145/src/alp/sls_fsa1.hpp:198: additonal ==> additional
data/last-align-1145/src/alp/sls_fsa1.hpp:337: dimention ==> dimension
data/last-align-1145/src/alp/sls_fsa1.hpp:392: dimentions ==> dimensions
data/last-align-1145/src/alp/sls_fsa1.hpp:393: dimentions ==> dimensions
data/last-align-1145/src/alp/sls_fsa1.hpp:865: desinged ==> designed
data/last-align-1145/src/alp/sls_fsa1.hpp:888: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.hpp:889: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.hpp:894: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.hpp:894: exeeds ==> exceeds
data/last-align-1145/src/alp/sls_fsa1.hpp:895: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.hpp:929: alingment ==> alignment
data/last-align-1145/src/alp/sls_fsa1.hpp:992: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.hpp:993: upto ==> up to
data/last-align-1145/src/alp/sls_fsa1.hpp:1032: dimention ==> dimension
data/last-align-1145/src/alp/sls_fsa1.hpp:1197: alingment ==> alignment
data/last-align-1145/src/alp/njn_localmaxstatmatrix.hpp:12: offical ==> official
data/last-align-1145/src/alp/njn_doubletype.hpp:12: offical ==> official
data/last-align-1145/src/alp/sls_basic.hpp:12: offical ==> official
data/last-align-1145/src/alp/sls_alp.cpp:9: offical ==> official
data/last-align-1145/src/alp/sls_alp.cpp:934: weigths ==> weights
data/last-align-1145/src/alp/sls_alp.cpp:2191: weigths ==> weights
data/last-align-1145/src/alp/sls_alp.cpp:2338: upto ==> up to
data/last-align-1145/src/alp/sls_alp.cpp:2352: upto ==> up to
data/last-align-1145/src/alp/sls_falp_alignment_evaluer.hpp:12: offical ==> official
data/last-align-1145/src/alp/njn_random.hpp:12: offical ==> official
data/last-align-1145/src/alp/njn_localmaxstatutil.cpp:9: offical ==> official
data/last-align-1145/src/alp/sls_alp_sim.cpp:9: offical ==> official
data/last-align-1145/src/alp/njn_dynprogprob.hpp:12: offical ==> official
data/last-align-1145/src/alp/njn_integer.hpp:12: offical ==> official
data/last-align-1145/src/alp/njn_function.hpp:12: offical ==> official
data/last-align-1145/src/alp/njn_ioutil.hpp:12: offical ==> official
data/last-align-1145/src/alp/sls_alp_data.cpp:9: offical ==> official
data/last-align-1145/src/alp/sls_alp_data.cpp:1076: ot ==> to, of, or
data/last-align-1145/src/alp/sls_alp_data.cpp:1112: ot ==> to, of, or
data/last-align-1145/src/alp/sls_normal_distr_array.hpp:12: offical ==> official
data/last-align-1145/src/alp/njn_dynprogproblim.hpp:12: offical ==> official
data/last-align-1145/src/alp/njn_localmaxstat.hpp:12: offical ==> official
data/last-align-1145/src/alp/njn_dynprogproblim.cpp:9: offical ==> official
data/last-align-1145/src/alp/sls_fsa1_utils.cpp:9: offical ==> official
data/last-align-1145/src/alp/sls_fsa1_utils.cpp:1008: ot ==> to, of, or
data/last-align-1145/src/alp/sls_fsa1_utils.cpp:1044: ot ==> to, of, or
data/last-align-1145/src/alp/sls_fsa1_utils.cpp:1529: errro ==> error
data/last-align-1145/src/alp/sls_alignment_evaluer.hpp:12: offical ==> official
data/last-align-1145/src/alp/njn_uniform.hpp:12: offical ==> official
data/last-align-1145/src/alp/njn_dynprogprobproto.cpp:9: offical ==> official
data/last-align-1145/src/alp/njn_memutil.hpp:12: offical ==> official
data/last-align-1145/src/alp/sls_basic.cpp:9: offical ==> official
data/last-align-1145/src/alp/njn_dynprogprob.cpp:9: offical ==> official
data/last-align-1145/src/alp/sls_alp_data.hpp:12: offical ==> official
data/last-align-1145/src/alp/sls_alp_data.hpp:84: calclation ==> calculation
data/last-align-1145/src/alp/sls_alp_data.hpp:401: ot ==> to, of, or
data/last-align-1145/src/alp/sls_alp_data.hpp:404: ot ==> to, of, or
data/last-align-1145/src/alp/sls_alignment_evaluer.cpp:9: offical ==> official
data/last-align-1145/src/alp/njn_approx.hpp:12: offical ==> official
data/last-align-1145/src/alp/sls_fsa1_parameters.cpp:9: offical ==> official
data/last-align-1145/src/alp/njn_random.cpp:9: offical ==> official
data/last-align-1145/src/alp/njn_matrix.hpp:12: offical ==> official
data/last-align-1145/src/alp/sls_fsa1_pvalues.cpp:9: offical ==> official
data/last-align-1145/src/alp/njn_vector.hpp:12: offical ==> official
data/last-align-1145/src/alp/sls_pvalues.cpp:9: offical ==> official
data/last-align-1145/src/alp/sls_falp_alignment_evaluer.cpp:9: offical ==> official
data/last-align-1145/src/alp/sls_falp_alignment_evaluer.cpp:510: alingment ==> alignment
data/last-align-1145/src/alp/sls_falp_alignment_evaluer.cpp:548: alingment ==> alignment
data/last-align-1145/src/alp/njn_dynprogprobproto.hpp:12: offical ==> official
data/last-align-1145/src/alp/njn_ioutil.cpp:9: offical ==> official
data/last-align-1145/src/alp/njn_localmaxstat.cpp:9: offical ==> official
data/last-align-1145/src/alp/sls_alp_regression.cpp:9: offical ==> official
data/last-align-1145/src/alp/njn_localmaxstatmatrix.cpp:9: offical ==> official
data/last-align-1145/src/split/last-split.cc:22: openIn ==> opening
data/last-align-1145/src/split/last-split.cc:312: openIn ==> opening
data/last-align-1145/src/split/cbrc_split_aligner.cc:1318: indexT ==> index, indent
data/last-align-1145/data/gc.prt:68: instaed ==> instead
data/last-align-1145/data/BISR.mat:2: Asai ==> Asia
data/last-align-1145/data/BISR.seed:3: Asai ==> Asia
data/last-align-1145/data/BISF.seed:3: Asai ==> Asia
data/last-align-1145/data/BISF.mat:2: Asai ==> Asia
data/last-align-1145/debian/changelog:574: debain ==> debian
data/last-align-1145/debian/changelog:690: informations ==> information
data/last-align-1145/debian/rules:5: developpers ==> developers
data/last-align-1145/debian/rules:5: acces ==> access
data/last-align-1145/debian/rules:127: droped ==> dropped
data/last-align-1145/debian/patches/simde:363: alph ==> alpha
data/last-align-1145/debian/upstream/metadata:2: Wan ==> Want
data/last-align-1145/.pc/2to3.patch/scripts/last-map-probs:28: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/last-map-probs:29: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:103: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:105: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:113: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:130: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:136: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:137: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:145: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:212: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:227: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:243: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:247: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:274: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:277: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:535: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:549: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:652: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:666: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:720: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:735: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:754: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:760: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:875: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/2to3.patch/scripts/maf-convert:878: aLine ==> align, a line, line, saline
data/last-align-1145/.pc/simde/src/Alignment.cc:51: alph ==> alpha
data/last-align-1145/.pc/simde/src/Alignment.cc:69: alph ==> alpha
data/last-align-1145/.pc/simde/src/Alignment.cc:75: indexT ==> index, indent
data/last-align-1145/.pc/simde/src/Alignment.cc:76: indexT ==> index, indent
data/last-align-1145/.pc/simde/src/Alignment.cc:89: alph ==> alpha
data/last-align-1145/.pc/simde/src/Alignment.cc:95: indexT ==> index, indent
data/last-align-1145/.pc/simde/src/Alignment.cc:96: indexT ==> index, indent
data/last-align-1145/.pc/simde/src/Alignment.cc:285: alph ==> alpha
data/last-align-1145/.pc/simde/src/Alignment.cc:355: alph ==> alpha
data/last-align-1145/.pc/simde/src/Alignment.cc:360: alph ==> alpha
data/last-align-1145/.pc/simde/src/Alignment.cc:365: alph ==> alpha
data/last-align-1145/.pc/simde/src/Alignment.cc:382: alph ==> alpha
data/last-align-1145/.pc/simde/src/Alignment.cc:436: alph ==> alpha