Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005526.1 Corchorus capsularis cultivar CVL-1 contig05544, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3916
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Found at i:859 original size:322 final size:320
Alignment explanation
Indices: 5--971 Score: 1367
Period size: 322 Copynumber: 3.0 Consensus size: 320
1 GTTA
5 GTTAGTACTCGATTTCGGCTATAAATTAACTCGAAAAG-CTTTTTACCCAATTTTATGCAGAACA
1 GTTAGTACTCGATTTCGGCTATAAATTAACTCGAAAAGACTTTTT-CCCAATTTTATGCAGAACA
69 TTCAGAAAAATATATAATTAAAAACCAAAAAATTGACGGGCTTTTCACGCTTCTAATATCGTTTT
65 TTCAGAAAAATATATAATTAAAAACCAAAAAATTGACGGGCTTTTCACGCTTCTAATATCG-TTT
134 TTTTTATTTTTTTCGAATTTATTTCAAATTAAATCGAAACACGATTCCGATGCTAGTAAAAACAA
129 TTTTTA-TTTTTTCGAATTTATTTCAAATTAAATCGAAACACGATTCCGATGCTAGTAAAAACAA
*
199 ATCCTTAAATCCATTGTGATTGAGATTTTGATAGATGAATATAGATATTTCAAGCAGTCTTTCTG
193 ATCCTTAAATCCATTGTGATTGAGATTTGGATAGATGAATATAGATATTTCAAGCAGTCTTTCTG
264 TCAAAAATCATGAAAAACAGAGCCGGAGCCCCGAAACACGTTTTTAGCCAAAAAACCGTGATG
258 TCAAAAATCATGAAAAACAGAGCCGGAGCCCCGAAACACGTTTTTAGCCAAAAAACCGTGATG
* * * * * * ** * * * *
327 GTTAGTACACGATTTTCGGCTAAAAACTGACGCG--AAGAGTTTTTCTTAATTTTTTTGGAAAAT
1 GTTAGTACTCGA-TTTCGGCTATAAATTAACTCGAAAAGACTTTTTCCCAA-TTTTATGCAGAAC
* * * * *
390 ATTCAGAAAAAATATATAATTCAACAA-CAAAAAGATTGACTGGCTTTTCACACTTTTAACATCG
64 ATTCAG-AAAAATATATAATT-AAAAACCAAAAA-ATTGACGGGCTTTTCACGCTTCTAATATCG
* * * * * * **
454 TTTTTCTTT-TTTTTT-TACTTTATTTAAAATTAAATCGAAACAAGATTCAGATTCGCGTAAAAA
126 TTTTT-TTTATTTTTTCGAATTTATTTCAAATTAAATCGAAACACGATTCCGATGCTAGTAAAAA
* * * * *
517 CAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATA-TTAAAGGAGTCGTT
190 CAAATCCTTAAATCCATTGTGATTGAGATTTGGATAGATGAATATAGATATTTCAAGCAGTCTTT
* * * ** * * *
581 CTGCCAAATATCATGCAAAACTA-AGAAGGGGCCCCGAAACGCGTTTTTAGCC-AAAAATCGTGA
255 CTGTCAAAAATCATGAAAAAC-AGAGCCGGAGCCCCGAAACACGTTTTTAGCCAAAAAACCGTGA
644 TG
319 TG
*
646 GTTAGTACTCGATTTCGGCTATAAATTAACTCGAAAAGATTTTTTCCCCAATTTTATGCAGAACA
1 GTTAGTACTCGATTTCGGCTATAAATTAACTCGAAAAGACTTTTT-CCCAATTTTATGCAGAACA
711 TTCAGAAAAATATATAATTAAAAACCAAAAATATTGACGGGCTTTTCACGCTTCTAATATCGTTT
65 TTCAGAAAAATATATAATTAAAAACCAAAAA-ATTGACGGGCTTTTCACGCTTCTAATATCGTTT
776 TTTTAATATTTTTTCGAATTTATTTCAAATTAAATCGAAACACGATTCCGATGCTAGTAAAAACA
129 TTTT--TATTTTTTCGAATTTATTTCAAATTAAATCGAAACACGATTCCGATGCTAGTAAAAACA
*
841 AATCCTTAAATCCATTGTGATTGAGATTTGAATAGATGAATATAGATATTTCAAGCAGTCTTTCT
192 AATCCTTAAATCCATTGTGATTGAGATTTGGATAGATGAATATAGATATTTCAAGCAGTCTTTCT
*
906 GTCAAAAATCATGAAAAACAGAGCCGGAGCCCCGAAACACGATTTTAGCCAAAAAACCGTGATG
257 GTCAAAAATCATGAAAAACAGAGCCGGAGCCCCGAAACACGTTTTTAGCCAAAAAACCGTGATG
970 GT
1 GT
972 ACACGATTTC
Statistics
Matches: 546, Mismatches: 80, Indels: 36
0.82 0.12 0.05
Matches are distributed among these distances:
318 23 0.04
319 74 0.14
320 79 0.14
321 103 0.19
322 125 0.23
323 95 0.17
324 47 0.09
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (320 bp):
GTTAGTACTCGATTTCGGCTATAAATTAACTCGAAAAGACTTTTTCCCAATTTTATGCAGAACAT
TCAGAAAAATATATAATTAAAAACCAAAAAATTGACGGGCTTTTCACGCTTCTAATATCGTTTTT
TTTATTTTTTCGAATTTATTTCAAATTAAATCGAAACACGATTCCGATGCTAGTAAAAACAAATC
CTTAAATCCATTGTGATTGAGATTTGGATAGATGAATATAGATATTTCAAGCAGTCTTTCTGTCA
AAAATCATGAAAAACAGAGCCGGAGCCCCGAAACACGTTTTTAGCCAAAAAACCGTGATG
Found at i:2087 original size:320 final size:320
Alignment explanation
Indices: 1050--3916 Score: 3236
Period size: 320 Copynumber: 9.0 Consensus size: 320
1040 TATATAATTC
* * *
1050 AACAAAACCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAATGAGTTG
1 AACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCG
* * * * *
1115 TTCTACCAAAAATCATGCAAAACAGAGCCGGAGCACTGAAACGCGTTTCTAG-CAAAAAACAATG
66 TTCTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCCAAAAATC-GTG
* ** * * * **
1179 ATGGTTACTACACGATTTCTTCTAAAAATTATCCCGAAAAGTTTTTTTTATCAATTTTT-TAAAA
130 ATGGTTAGTACACGATTTCAGCTAAAAACTAACCCGAAAAG--TTTTTTCTCAATTTTTCTGCAA
* * * * * * * *
1243 AATGTTCAG-AAAAATATGTAATTCAAAGCCAAAAAGATTGACTGGCTTTTCACACTTTTCACAT
193 AATATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGA-TGGTTTTTCACGCTTCTAATAT
* * * *
1307 CG-TTTTT-TTTTTTTT--ACTTTATTTCAAATTAAATCGAAATAAGATTCAGATTCGCGTAAA
257 CGTTTTTTCTTTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * *
1367 AACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATACATAATTAAAGGAGTCT
1 AACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCG
* * ** * * *
1432 TTCTGCCAAAAATCATACAAAACTGAGAAGGGGCCCCGAAACGCATTTCTAACCAAAAATCGTGA
66 TTCTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCCAAAAATCGTGA
* * * * * * * * *
1497 TGG-TAATACACGATTTCGGCTAAAAATTAACTCGAAAAGATTTTTCCCAA-TTTTATGCAGAAC
131 TGGTTAGTACACGATTTCAGCTAAAAACTAACCCGAAAAGTTTTTTCTCAATTTTTCTGCAAAAT
* * * * *
1560 ATTCAGAAAAAAAAATATAATTAAACACCAAAAAGATTGACGTGTTTTTCACGCTTCTAATATCA
196 ATTCAG-AAAAAATATATAATTCAACGCCAAAAAGATTGATG-GTTTTTCACGCTTCTAATATCG
* * * *
1625 TTTTTTTTATTTTTTTCGAATTTATTTCAAATTAAATCGAAACACGATTCCGATGCTAGTAAA
259 TTTTTTCT-TTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * * *
1688 CACAAATCCTTAAATCCATTGTGATTGAGATTTTGATAGATGAATATAGATATTTCAAGGAGTCT
1 AACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCG
* * * * * *
1753 TTCTGTCAAAAATCATGAAAAATAGAGCCGGAACCCCGAAACACGTTTATAGCCAAAAATCGTGA
66 TTCTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCCAAAAATCGTGA
* * * * *
1818 TGGTTAGTACACGATTTCAGCTAAAAACTGACGCGAAGAG-TTTTTCTTAATTTTTCTGGAAAAT
131 TGGTTAGTACACGATTTCAGCTAAAAACTAACCCGAAAAGTTTTTTCTCAATTTTTCTGCAAAAT
* *
1882 ATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGATGGATTTTTCACGCTTTTAAAATCGT
196 ATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGATGG-TTTTTCACGCTTCTAATATCGT
* *
1947 TTTTTCTTTTTTTTCGAATTTATTTCAGATTAAATCGAAACAAGATTAAGATGCTCGTAAA
260 TTTTTCTTTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * * *
2008 AACAAATCCTTAAATCCGTTGTGACTGAGATTTTGTTAAATAAATATAGATATTTCAAGGTGTCG
1 AACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCG
* * * * *
2073 TCCTGCCCAAAATCATGCAAAACAGAGTCGGAGCCCCGAAACGCGTTT-TAAGGCGAAAATCGTG
66 TTCTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCT-AGCCAAAAATCGTG
* * * * * *
2137 ATGGTTAGTACACGATTTCAGCTAATATCTGACCCGAAGAG-TTTTTCTCAATTTTTCCGGAAAA
130 ATGGTTAGTACACGATTTCAGCTAAAAACTAACCCGAAAAGTTTTTTCTCAATTTTTCTGCAAAA
* *
2201 TATTCTGAAAAAATATATAATTGAACGCCAAAAAGATT-ATTGGGTTTTTTCACGCTTCTAATAT
195 TATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGA-T-GG-TTTTTCACGCTTCTAATAT
* * * * *
2265 CGTTTTTTCATTTTTTTTCAAATTTATTTCAAATTAAATAGAAATAAGTTTTAAGATGCTCGTAA
257 CGTTTTTTC-TTTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAG-ATTCAGATGCTCGTAA
2330 A
320 A
** *
2331 AACAAAAACTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTG
1 AACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCG
* * *
2396 TTCTACCAAAAATCATGCAAAACAGAGCCGGAGCACCGAAACGCGTTTCTAG-CAAAAAACGGTG
66 TTCTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCCAAAAATC-GTG
* * * *
2460 ATGGTTTGTACACGATTTCTGCTAAAAATTAACCCGAAAAGTTTTTTCTCAATTTTT-TCCAAAA
130 ATGGTTAGTACACGATTTCAGCTAAAAACTAACCCGAAAAGTTTTTTCTCAATTTTTCTGCAAAA
* * * * * *
2524 TGTTCA-AAAAAATATGTAATTCAAAGCCAAAAAGATTGATTGGCTTTTCACGCTTTTAACATCG
195 TATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGA-TGGTTTTTCACGCTTCTAATATCG
* * * *
2588 TTTTTTCATTTTTTTCGACTTTATTTCAAATTAAATCGAAACAAGATTCAGATTCGCGTAAA
259 TTTTTTCTTTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * *
2650 AACAAATCCTTAAATCCATTGTGACTTAAATTTGGTTAGATGAATATAGATATTTAAAGGAGTCT
1 AACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCG
* ** * *
2715 TTCTGCCAAAAATCATGCAAAACTGAGAAAGG-GCCTCGAAACGCGTTTCTAGCCATAAATCGTG
66 TTCTGCCAAAAATCATGCAAAACAGAG-CCGGAGCCCCGAAACGCGTTTCTAGCCAAAAATCGTG
* * * * * * * *
2779 ATAGTTAGTACACGATCTCAGCAAAAAATTAACTCGAAAAGCTTTTTTCCCAA-TTTTATGCAGA
130 ATGGTTAGTACACGATTTCAGCTAAAAACTAACCCGAAAAG-TTTTTTCTCAATTTTTCTGCAAA
* * * * *
2843 ACATTCAG-AAAAATATATAATTCAACACCAAAAAGATTGACGGGCTTTTAACGCTTCTAATATC
194 ATATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGA-TGGTTTTTCACGCTTCTAATATC
* * *
2907 G-----T-TTTTTTTTCGAATTTATTTCAAATTAAATCGAAACACGATTCTGATGCTCATAAA
258 GTTTTTTCTTTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * * *
2964 AACAAATCCTTAAAACCATTATGATTGAGATTTGGATAGATGGATATAGATATTTCAAGGAG-CA
1 AACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC-
* * * * * *
3028 TTTCTGTCAAAAATCATGCAAAACAGAGTCGGAGCCCCGAAACGGGTTTTTAGCCAAAAACCGTG
65 GTTCTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCCAAAAATCGTG
* * * * * * *
3093 ATGGTTAGTACACGATTACGGCTAAAAACTGACGCGAAGAG-TTTTTCTCAATTTTCCTGGAAAA
130 ATGGTTAGTACACGATTTCAGCTAAAAACTAACCCGAAAAGTTTTTTCTCAATTTTTCTGCAAAA
*
3157 TATTCAGAAAAAAATATATAATTCAACGACAAAAAGATTGATGGGTTTTTCACGCTTCTAATATC
195 TATTCAG-AAAAAATATATAATTCAACGCCAAAAAGATTGAT-GGTTTTTCACGCTTCTAATATC
* * *
3222 GTTTTTTCATTTTTTTTTCCGAATTTATTTCATATTAAATCGAAACAAGATTTATATGCTCGTAA
258 GTTTTTTC--TTTTTTTT-CGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAA
3287 A
320 A
* * * * * *
3288 AACAAATCTTTAAATCCATTGTAACTGAGATTTGGTTAAATAAATATAGATATTTCAATGAGTCA
1 AACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCG
** * * * *
3353 TTCTGCCAAAAATCATGCAAAACAGATTCGGAACCCCGAAACGCGTTT-TAAGGCGAAAACCGTG
66 TTCTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCT-AGCCAAAAATCGTG
* * * * *
3417 ATGGTTAGTACACGATTTCCGCTAATATCTGATCCGAAAAG-TTTTTCTCAATTTTTCCTG-AAA
130 ATGGTTAGTACACGATTTCAGCTAAAAACTAACCCGAAAAGTTTTTTCTCAATTTTT-CTGCAAA
* * * *
3480 ATATTCAGAAAAAATATATAATTCAACACCAAAAATATTAAGGGGTTTTTCACGCTTCTAATATC
194 ATATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGA-TGGTTTTTCACGCTTCTAATATC
* * *
3545 ATTTTTTTTCATTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTAAGATGCTCGTAAA
258 --GTTTTTTCTTTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * * * *
3610 AATAAAACCTTAAATGCATTGTGACTGAGATTTTGTTAGATGAATAAAGATATTTCAAGGAGTTG
1 AACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCG
* *
3675 TTTTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAG-CAAAAAACAGTG
66 TTCTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCCAAAAATC-GTG
* * * *
3739 A-----CGTACACGATTTCTGCTAAAAATTAACCCGAAAAGTTTTTTTCTCAATTTTT-TCCAAA
130 ATGGTTAGTACACGATTTCAGCTAAAAACTAACCCGAAAAG-TTTTTTCTCAATTTTTCTGCAAA
* * * * * * * *
3798 ATGTT-AAAAAAAATATGTAATTCAAAGCCAAAAAGATTGACTGGCTTTTCACACTTTTAACATC
194 ATATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGA-TGGTTTTTCACGCTTCTAATATC
* * *
3862 GTTTTTTCATTCTTTTTCGACTTTATTTCAAATTAAATCGACACAAGATTCAGAT
258 GTTTTTTC-TTTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGAT
Statistics
Matches: 2161, Mismatches: 335, Indels: 109
0.83 0.13 0.04
Matches are distributed among these distances:
312 9 0.00
313 21 0.01
314 204 0.09
315 60 0.03
316 115 0.05
317 187 0.09
318 15 0.01
319 180 0.08
320 365 0.17
321 274 0.13
322 262 0.12
323 234 0.11
324 224 0.10
325 11 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (320 bp):
AACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCG
TTCTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCCAAAAATCGTGA
TGGTTAGTACACGATTTCAGCTAAAAACTAACCCGAAAAGTTTTTTCTCAATTTTTCTGCAAAAT
ATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGATGGTTTTTCACGCTTCTAATATCGTT
TTTTCTTTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
Found at i:2602 original size:642 final size:638
Alignment explanation
Indices: 1050--3916 Score: 3514
Period size: 638 Copynumber: 4.5 Consensus size: 638
1040 TATATAATTC
*
1050 AACAAAACCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAATGAGTTG
1 AACAAAACCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTG
* * * *
1115 TTCTACCAAAAATCATGCAAAACAGAGCCGGAGCACTGAAACGCGTTTCTAGCAAAAAACAATGA
66 TTCTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCAAAAAACAGTGA
* * * * **
1180 TGGTTACTACACGATTTCTTCTAAAAATTATCCCGAAAAGTTTTTTTTATCAATTTTTTAAAAAA
131 TGGTTAGTACACGATTTCTGCTAAAAATTAACCCGAAAAG--TTTTTTCTCAATTTTTTCCAAAA
* * *
1245 TGTTCAGAAAAATATGTAATTCAAAGCCAAAAAGATTGACTGGCTTTTCACACTTTTCACATCGT
194 TGTTCAAAAAAATATGTAATTCAAAGCCAAAAAGATTGACTGGCTTTTCACGCTTTTAACATCGT
* *
1310 TTTTT--TTTTTTT--ACTTTATTTCAAATTAAATCGAAATAAGATTCAGATTCGCGTAAAAACA
259 TTTTTCATTTTTTTCGACTTTATTTCAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACA
* * * *
1371 AATCCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATACATAATTAAAGGAGTCTTTCT
324 AATCCTTAAATCCATTGTGACTGAGATTTGGTTAAATAAATATAGATATTTAAAGGAGTCTTTCT
* * * * * *
1436 GCCAAAAATCATACAAAACTGAGAAGGGGCCCCGAAACGCATTTCTAACCAAAAATCGTGATGG-
389 GCCAAAAATCATGCAAAACAGAGAAGGAGCCCCGAAACGCGTTTCTAAGCGAAAATCGTGATGGT
* * * *
1500 TAATACACGATTTCGGCTAAAAATTAACTCGAAAAGATTTTTCCCAATTTTATGCAGAACATTCA
454 TAGTACACGATTTCAGCT-AAAATTAACCCGAAAAGATTTTTCCCAATTTTATGCAAAACATTCA
* * * *
1565 GAAAAAAAAATATAATTAAACACCAAAAAGATTGACGTGTTTTTCACGCTTCTAATATCATTTTT
518 G-AAAAAATATATAATTCAACACCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCGTTTTT
* * ** *
1630 TTTATTTTTTTCGAATTTATTTCAAATTAAATCGAAACACGATTCCGATGCTAGTAAA
582 TAT-TTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTAAGATGCTCGTAAA
* * * * *
1688 CACAAATCCTTAAATCCATTGTGATTGAGATTTTGATAGATGAATATAGATATTTCAAGGAGTCT
1 AACAAAACCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT-T
* * * * * * *
1753 -TTCTGTCAAAAATCATGAAAAATAGAGCCGGAACCCCGAAACACGTTTATAGCCAAAAATC-GT
65 GTTCTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAG-CAAAAAACAGT
* * * * * * **
1816 GATGGTTAGTACACGATTTCAGCTAAAAACTGACGCGAAGAG-TTTTTCTTAATTTTTCTGGAAA
129 GATGGTTAGTACACGATTTCTGCTAAAAATTAACCCGAAAAGTTTTTTCTCAATTTTT-TCCAAA
* * * * *
1880 ATATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGA-TGGATTTTTCACGCTTTTAAAAT
193 ATGTTCA-AAAAAATATGTAATTCAAAGCCAAAAAGATTGACTGG-CTTTTCACGCTTTTAACAT
* * * * *
1944 CGTTTTTTCTTTTTTTTCGAATTTATTTCAGATTAAATCGAAACAAGATTAAGATGCTCGTAAAA
256 CGTTTTTTCATTTTTTTCGACTTTATTTCAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAA
* * * * *
2009 ACAAATCCTTAAATCCGTTGTGACTGAGATTTTGTTAAATAAATATAGATATTTCAAGGTGTCGT
321 ACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAAATAAATATAGATATTTAAAGGAGTCTT
* * **
2074 CCTGCCCAAAATCATGCAAAACAGAGTCGGAGCCCCGAAACGCGTTT-TAAGGCGAAAATCGTGA
386 TCTGCCAAAAATCATGCAAAACAGAGAAGGAGCCCCGAAACGCGTTTCTAA-GCGAAAATCGTGA
* * * * *
2138 TGGTTAGTACACGATTTCAGCTAATATCTGACCCGAAGAG-TTTTTCTCAATTTT-TCCGGAAAA
450 TGGTTAGTACACGATTTCAGCTAAAAT-TAACCCGAAAAGATTTTTCCCAATTTTAT--GCAAAA
* * * * *
2201 TATTCTGAAAAAATATATAATTGAACGCCAAAAAGATT-ATTGGGTTTTTTCACGCTTCTAATAT
512 CATTCAGAAAAAATATATAATTCAACACCAAAAAGATTGA-CGGG-TTTTTCACGCTTCTAATAT
* * * *
2265 CGTTTTTTCATTTTTTTTCAAATTTATTTCAAATTAAATAGAAATAAGTTTTAAGATGCTCGTAA
575 CGTTTTTT-ATTTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAG-ATTAAGATGCTCGTAA
2330 A
638 A
*
2331 AACAAAAACTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTG
1 AACAAAACCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTG
* * *
2396 TTCTACCAAAAATCATGCAAAACAGAGCCGGAGCACCGAAACGCGTTTCTAGCAAAAAACGGTGA
66 TTCTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCAAAAAACAGTGA
*
2461 TGGTTTGTACACGATTTCTGCTAAAAATTAACCCGAAAAGTTTTTTCTCAATTTTTTCCAAAATG
131 TGGTTAGTACACGATTTCTGCTAAAAATTAACCCGAAAAGTTTTTTCTCAATTTTTTCCAAAATG
*
2526 TTCAAAAAAATATGTAATTCAAAGCCAAAAAGATTGATTGGCTTTTCACGCTTTTAACATCGTTT
196 TTCAAAAAAATATGTAATTCAAAGCCAAAAAGATTGACTGGCTTTTCACGCTTTTAACATCGTTT
*
2591 TTTCATTTTTTTCGACTTTATTTCAAATTAAATCGAAACAAGATTCAGATTCGCGTAAAAACAAA
261 TTTCATTTTTTTCGACTTTATTTCAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAA
* * * *
2656 TCCTTAAATCCATTGTGACTTAAATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGC
326 TCCTTAAATCCATTGTGACTGAGATTTGGTTAAATAAATATAGATATTTAAAGGAGTCTTTCTGC
* * * *
2721 CAAAAATCATGCAAAACTGAGAAAGG-GCCTCGAAACGCGTTTCT-AGCCATAAATCGTGATAGT
391 CAAAAATCATGCAAAACAGAG-AAGGAGCCCCGAAACGCGTTTCTAAGCGA-AAATCGTGATGGT
* * * * *
2784 TAGTACACGATCTCAGCAAAAAATTAACTCGAAAAGCTTTTTTCCCAATTTTATGCAGAACATTC
454 TAGTACACGATTTCAGC-TAAAATTAACCCGAAAAG-ATTTTTCCCAATTTTATGCAAAACATTC
* *
2849 AG-AAAAATATATAATTCAACACCAAAAAGATTGACGGGCTTTTAACGCTTCTAATATCG-----
517 AGAAAAAATATATAATTCAACACCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCGTTTTT
* ** *
2908 T-TTTTTTTTCGAATTTATTTCAAATTAAATCGAAACACGATTCTGATGCTCATAAA
582 TATTTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTAAGATGCTCGTAAA
* * * * * * *
2964 AACAAATCCTTAAAACCATTATGATTGAGATTTGGATAGATGGATATAGATATTTCAAGGAGCAT
1 AACAAAACCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG-TT
* * * * * *
3029 -TTCTGTCAAAAATCATGCAAAACAGAGTCGGAGCCCCGAAACGGGTTTTTAGCCAAAAACCGTG
65 GTTCTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCAAAAAACAGTG
* * * * * * * **
3093 ATGGTTAGTACACGATTACGGCTAAAAACTGACGCGAAGAG-TTTTTCTCAATTTTCCTGGAAAA
130 ATGGTTAGTACACGATTTCTGCTAAAAATTAACCCGAAAAGTTTTTTCTCAATTTT-TTCCAAAA
* * * * * * *
3157 TATTCAGAAAAAAATATATAATTCAACGACAAAAAGATTGA-TGGGTTTTTCACGCTTCTAATAT
194 TGTTC--AAAAAAATATGTAATTCAAAGCCAAAAAGATTGACT-GGCTTTTCACGCTTTTAACAT
* * * * *
3221 CGTTTTTTCATTTTTTTTTCCGAATTTATTTCATATTAAATCGAAACAAGATTTATATGCTCGTA
256 CGTTTTTTCA--TTTTTTT-CGACTTTATTTCAAATTAAATCGAAACAAGATTCAGATGCGCGTA
* * * *
3286 AAAACAAATCTTTAAATCCATTGTAACTGAGATTTGGTTAAATAAATATAGATATTTCAATGAGT
318 AAAACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTAAATAAATATAGATATTTAAAGGAGT
* *** * *
3351 CATTCTGCCAAAAATCATGCAAAACAGATTCGGAACCCCGAAACGCGTTT-TAAGGCGAAAACCG
383 CTTTCTGCCAAAAATCATGCAAAACAGAGAAGGAGCCCCGAAACGCGTTTCTAA-GCGAAAATCG
* * * * * *
3415 TGATGGTTAGTACACGATTTCCGCTAATATCTGATCCGAAAAG-TTTTTCTCAATTTT-TCCTGA
447 TGATGGTTAGTACACGATTTCAGCTAAAAT-TAACCCGAAAAGATTTTTCCCAATTTTATGC--A
* * * *
3478 AAATATTCAGAAAAAATATATAATTCAACACCAAAAATATTAAGGGGTTTTTCACGCTTCTAATA
509 AAACATTCAGAAAAAATATATAATTCAACACCAAAAAGATTGACGGGTTTTTCACGCTTCTAATA
* *
3543 TCATTTTTTTTCATTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTAAGATGCTCGTA
574 TCGTTTTTTAT--TTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTAAGATGCTCGTA
3608 AA
637 AA
* * * *
3610 AATAAAACCTTAAATGCATTGTGACTGAGATTTTGTTAGATGAATAAAGATATTTCAAGGAGTTG
1 AACAAAACCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTG
*
3675 TTTTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCAAAAAACAGTGA
66 TTCTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCAAAAAACAGTGA
*
3740 -----CGTACACGATTTCTGCTAAAAATTAACCCGAAAAGTTTTTTTCTCAATTTTTTCCAAAAT
131 TGGTTAGTACACGATTTCTGCTAAAAATTAACCCGAAAAG-TTTTTTCTCAATTTTTTCCAAAAT
* *
3800 GTTAAAAAAAATATGTAATTCAAAGCCAAAAAGATTGACTGGCTTTTCACACTTTTAACATCGTT
195 GTTCAAAAAAATATGTAATTCAAAGCCAAAAAGATTGACTGGCTTTTCACGCTTTTAACATCGTT
*
3865 TTTTCATTCTTTTTCGACTTTATTTCAAATTAAATCGACACAAGATTCAGAT
260 TTTTCATT-TTTTTCGACTTTATTTCAAATTAAATCGAAACAAGATTCAGAT
Statistics
Matches: 1887, Mismatches: 284, Indels: 116
0.83 0.12 0.05
Matches are distributed among these distances:
632 14 0.01
633 167 0.09
634 36 0.02
635 74 0.04
636 27 0.01
637 76 0.04
638 393 0.21
639 23 0.01
640 63 0.03
641 247 0.13
642 379 0.20
643 198 0.10
644 28 0.01
645 2 0.00
646 160 0.08
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (638 bp):
AACAAAACCTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTG
TTCTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCAAAAAACAGTGA
TGGTTAGTACACGATTTCTGCTAAAAATTAACCCGAAAAGTTTTTTCTCAATTTTTTCCAAAATG
TTCAAAAAAATATGTAATTCAAAGCCAAAAAGATTGACTGGCTTTTCACGCTTTTAACATCGTTT
TTTCATTTTTTTCGACTTTATTTCAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAA
TCCTTAAATCCATTGTGACTGAGATTTGGTTAAATAAATATAGATATTTAAAGGAGTCTTTCTGC
CAAAAATCATGCAAAACAGAGAAGGAGCCCCGAAACGCGTTTCTAAGCGAAAATCGTGATGGTTA
GTACACGATTTCAGCTAAAATTAACCCGAAAAGATTTTTCCCAATTTTATGCAAAACATTCAGAA
AAAATATATAATTCAACACCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCGTTTTTTATT
TTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTAAGATGCTCGTAAA
Done.