Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010858.1 Corchorus capsularis cultivar CVL-1 contig10879, 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: 21442
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1712 original size:109 final size:108
Alignment explanation
Indices: 1565--1854 Score: 449
Period size: 109 Copynumber: 2.6 Consensus size: 108
1555 ATGGTAAAAA
*
1565 TAAAAATAAA-AATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAAT
1 TAAAAATAAATAATTATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAAT
1628 AAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTTGG
64 AAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTTGG
1673 TAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATA
1 TAAAAATAAA-TAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATA
*
1738 AAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTTTGG
65 AAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTTGG
* *
1782 TAAAAATAAAATAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGTA
1 TAAAAAT-AAATAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTA
1847 GAATAAAA
60 GAATAAAA
1855 CTATAATAGT
Statistics
Matches: 169, Mismatches: 4, Indels: 12
0.91 0.02 0.06
Matches are distributed among these distances:
108 10 0.06
109 117 0.69
110 13 0.08
111 1 0.01
114 28 0.17
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (108 bp):
TAAAAATAAATAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAA
AATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTTGG
Found at i:4054 original size:19 final size:19
Alignment explanation
Indices: 4026--4070 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
4016 GCATTTGCGA
*
4026 TTAATTTACCTACAAAATT
1 TTAATCTACCTACAAAATT
*
4045 TTAATCTACCTACAAACTT
1 TTAATCTACCTACAAAATT
4064 TTGAATC
1 TT-AATC
4071 ATTGGTATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40
Consensus pattern (19 bp):
TTAATCTACCTACAAAATT
Found at i:9604 original size:78 final size:75
Alignment explanation
Indices: 9522--9694 Score: 191
Period size: 70 Copynumber: 2.3 Consensus size: 75
9512 TTGTTTAGGT
* *
9522 TTTTATAGTTTTACTTAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-T-A-TA
1 TTTTATA-TTTTACTTAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACTA
*
9583 AT-TATTTTA-
65 TTATATTTTAC
* *
9592 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTA-TATTTTACTTAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACTA
9657 TTATATTTTACC
65 TTATATTTTA-C
*
9669 ATTTTACTATTTTAATTAA--AAAAACT
1 -TTTTA-TATTTTACTTAACTAAAAACT
9695 TGATATATTA
Statistics
Matches: 87, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
70 47 0.54
71 5 0.06
72 1 0.01
73 1 0.01
74 3 0.03
75 7 0.08
76 7 0.08
78 16 0.18
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.50
Consensus pattern (75 bp):
TTTTATATTTTACTTAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACTAT
TATATTTTAC
Found at i:9605 original size:70 final size:70
Alignment explanation
Indices: 9522--9676 Score: 222
Period size: 70 Copynumber: 2.2 Consensus size: 70
9512 TTGTTTAGGT
* * * * *
9522 TTTTA-TAGTTTTACTTAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACT
*
9586 ATTTTA
65 ATTATA
*
9592 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACTA
9657 TTATA
66 TTATA
*
9662 TTTTACCATTTTACT
1 TTTTACTATTTTACT
9677 ATTTTAATTA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
70 74 0.97
71 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.51
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACTA
TTATA
Found at i:9806 original size:23 final size:23
Alignment explanation
Indices: 9777--9820 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
9767 AAACTTTTGC
*
9777 AATTGAAAACACTATTTTTATTT
1 AATTGAAAACAATATTTTTATTT
**
9800 AATTGAATTCAATATTTTTAT
1 AATTGAAAACAATATTTTTAT
9821 AATATTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (23 bp):
AATTGAAAACAATATTTTTATTT
Found at i:20129 original size:320 final size:319
Alignment explanation
Indices: 18809--21430 Score: 2756
Period size: 321 Copynumber: 8.2 Consensus size: 319
18799 TTACAAGGAG
* * * *
18809 TCATGCAAAATTGAG-CTGGCACTCCGAAACACGTTTTTAA-CCTAAAACCGTGATGGTTAGTAC
1 TCATGCAAAATTGAGTC-GG-ACTCCGAAACGCGTTTTTAACCCAAAAACTGTGATGATTAGTAC
* * *
18872 ACGATGTCGGCTAAAAACTGACCCAGAAA-TTTTTTTCATGAAATTTTAGCCACAATACTCAGAA
64 ACAATGTCGGCTAAAAACTGACCC-GAAATTTTTTTTCATGAAATTTTTGCCACAATACTAAGAA
* ** * ** *
18936 AAA-ATATATAAATCAACGTAAAAAAGATTGA-AGGAATTTCACGCCTCTAATATCGTTTTTCAT
128 AAATA-ATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAT
* * * * * *
18999 TATTT-TGAATTAATTTCTAATTAAATGGAAACAAGACTAAGATGCTCATAAAATAAATCCTTAT
192 T-TTTCCGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAACAAATCCTTAT
* ** * * * *
19063 ATCCAATCCGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAGAAA
256 ATACAATGTGGCTGAAATTTGGTTAGATGAATATATATATTTCAAGGAGTCTTGCTGCCAAAAA
* ** * * *
19127 TCATGCAAAACTGAGTCGGGGTCCCGAAACGCGTTTTTAGCCCAAAAACTATGATAATTAGTACA
1 TCATGCAAAATTGAGTCGGACT-CCGAAACGCGTTTTTAACCCAAAAACTGTGATGATTAGTACA
* * ** * * * * *
19192 CAATTTCGGCTAACAACAAATCTGAAATTTGTTTTTTTTTTTTTATGAATTTTTTACCACAATAC
65 CAATGTCGGCTAAAAACTGACCCGAAA--------TTTTTTTTCATGAAATTTTTGCCACAATAC
* * * * *
19257 TAAGAAAAATAATATAATTTACCGCCAAAAATATTAACGGGCTTTTCACGCTTCTAAAATCGTTT
122 TAAGAAAAATAATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTT
* *
19322 TTCCATTTTTCCGAATTAATTTCTAATTAACTAGAAACAAGATTCAGATGTTCGTAAAAACAAAT
187 TT-CATTTTTCCGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGT-AAAACAAAT
19387 CCTTATATACAATGTGGCTGAAATTTGGTTCA-ATGAATATATATATTTCAAGGAGTCATTGC-G
250 CCTTATATACAATGTGGCTGAAATTTGGTT-AGATGAATATATATATTTCAAGGAGTC-TTGCTG
* *
19450 CCAGAAG
313 CCAAAAA
* * * * *
19457 TCATGCAAAATTGAGCCGGAACTCCG-AACGTGTTTTTAACCCAAAACCTGTGATGGTTACTACA
1 TCATGCAAAATTGAGTCGG-ACTCCGAAACGCGTTTTTAACCCAAAAACTGTGATGATTAGTACA
* * * *
19521 CAATGTCGGCTAAAAACTGACCCGAAAATTTTGTTCATGAAATTTTTGTCACAATACTCAGAAAA
65 CAATGTCGGCTAAAAACTGACCCGAAATTTTTTTTCATGAAATTTTTGCCACAATACTAAG-AAA
* * *
19586 AATAA-ATAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGCTTATAATATCGTTTTTCATTT
129 AATAATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCA-TT
*** * * *
19650 TTTTAAAATTAATTTCTAATTAAATGGAAACAACATTCAGATGCTCGTAAAACAAATCATTATAT
193 TTTCCGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAACAAATCCTTATAT
* ** * * * *
19715 CCAATCCGACT-AAGATTTAGTTAGATG-ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAA
258 ACAATGTGGCTGAA-ATTTGGTTAGATGAATATATATATTTCAAGGAGTCTTGCTGCCAAAAA
* ** * * * *
19776 TCATGCAAAACTGAGTCGGGGTCCCGAAACGCATTTTTAGCTCAAAAACTATGATGATTAGTACA
1 TCATGCAAAATTGAGTCGGACT-CCGAAACGCGTTTTTAACCCAAAAACTGTGATGATTAGTACA
* ** *
19841 CAATTTCGGCTAAAAACTGTTCCGAAATTTTTTTTAATG-AATTTTTGCCACAATACTAAGAAAA
65 CAATGTCGGCTAAAAACTGACCCGAAATTTTTTTTCATGAAATTTTTGCCACAATACTAAGAAAA
* ** * * *
19905 ATAATATAATT-AACCGCCAAAAATATTGACTAGCTTTTCACGCTTCTAAAACCGTTTTTCCA-A
130 ATAATATAATTCAA-CGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTT-CATT
* * *
19968 TTTCCGAATTAATTTCTAATTAACTAGAAACAATATTCAGATGTTCGTAAAAACAAATCCTTATA
193 TTTCCGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGT-AAAACAAATCCTTATA
* * *
20033 TACAATGTAGCTGAAATTTGGTTCA-ATGAATATATCTATTTCAAGGAGT-TAGTGC-GTCAAAA
257 TACAATGTGGCTGAAATTTGGTT-AGATGAATATATATATTTCAAGGAGTCT--TGCTGCCAAAA
20095 A
319 A
* * * * *
20096 TCATGCAAAATTGAGCCAGGACTCCGAAACGCATTTTTAACCTAAAAACCGTGATGGTTAGTACA
1 TCATGCAAAATTGAGTC-GGACTCCGAAACGCGTTTTTAACCCAAAAACTGTGATGATTAGTACA
**
20161 CAATGTCGGCTAAAAACTGACCCGAAAATTTTTTTTCCATGAAATTTTTGCCACAATACTCGGAA
65 CAATGTCGGCTAAAAACTGACCCG-AAATTTTTTTT-CATGAAATTTTTGCCACAATACTAAGAA
** ** * *
20226 AAGATAA-ATAATTCAACGTAAAAAAGATTGAAAGGTTTTTCACGCTTCTAATATAGTTTTTCAT
128 AA-ATAATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCA-
*** * * *
20290 TTTTTTAAAATTAATTTCTAATTAAATGGAATCAAGATTCGGATGCTCGTAAAACAAATCCTTAT
191 TTTTTCCGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAACAAATCCTTAT
* ** * * * * *
20355 ATCCAATCCGGTTGAGATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAA
256 ATACAATGTGGCTGAAATTTGGTTAGATGAATATATATATTTCAAGGAGTCTTGCTGCCAAAAA
* * * *
20419 TCATGCAAAACTGAGTCGGGGC-CACGAAACGCGTTTTTAGCTCC-AAAACTATGATGATTAGTA
1 TCATGCAAAATTGAGTC-GGACTC-CGAAACGCGTTTTTAAC-CCAAAAACTGTGATGATTAGTA
* ** * * *
20482 CACAATTTCGGCTAAAAACTGTTCTGAAATTTTTTTTTATGAATTTTTTGCCACAATACTAAGAA
63 CACAATGTCGGCTAAAAACTGACCCGAAATTTTTTTTCATGAAATTTTTGCCACAATACTAAGAA
* * * * *
20547 AAATAATAAAATTCAATGCCAAAAATATAGACGGGCTTTTCACGCTTCTAATATCGTTTTCCCAT
128 AAATAATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTT-TCA-
* *
20612 TTTTTTCCGAATTAATTTCTAATTAAATAGAAACAATATTCAGATGTTCGTAAAAGCAAATCCTT
191 -TTTTTCCGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAA-CAAATCCTT
* *
20677 ATATACAATGTGGATGAAATTTGGTTCA-ATG-A-ATATATATTTCAAGGAGTCATTGC-GCCAG
254 ATATACAATGTGGCTGAAATTTGGTT-AGATGAATATATATATTTCAAGGAGTC-TTGCTGCCAA
20738 AAA
317 AAA
* * * * * *
20741 TCATGCAAAATTGAGCCGGAACTCCGAAACGTG-TTTTAAACTAAAACCTGTGATGGTTAGTACA
1 TCATGCAAAATTGAGTCGG-ACTCCGAAACGCGTTTTTAACCCAAAAACTGTGATGATTAGTACA
* * * *
20805 CGATGTCGGCTAAAAACTGACCCGAAAATTTTGTTCATGAAATTTTTGCCACAATACTCAGAAAA
65 CAATGTCGGCTAAAAACTGACCCGAAATTTTTTTTCATGAAATTTTTGCCACAATACTAAG-AAA
** * *
20870 AATAA-ATAATTCAACATCAAAAAGATTGAAGGGCATTTCACGCTTCTAATATCGTTTTTCATTT
129 AATAATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCA--T
* * * * *
20934 TTTTCCGAATTAATTTCTAATTAAATGGAAACAAGACTAAGGTGCTCATAAAACAAATCCTTATA
192 TTTTCCGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAACAAATCCTTATA
* ** * * * * *
20999 TCCAATCCGGCTGAGATTTGGTTATATGAATGTATATATTTTAAGGAGTCTTTCTGCCAAAAA
257 TACAATGTGGCTGAAATTTGGTTAGATGAATATATATATTTCAAGGAGTCTTGCTGCCAAAAA
* * * * *
21062 TCATGCGAAACTGAGTCGGGGCCCCGAAACGCG-TTTTAGCCCAAAAACTGTGATGATTAGTACA
1 TCATGCAAAATTGAGTC-GGACTCCGAAACGCGTTTTTAACCCAAAAACTGTGATGATTAGTACA
* * * * *
21126 CAATTTCGGCTAAAAACTAATCC-AAATTTTTTTT-AAGAATTTTTTTGCCACAATACTAAGAAA
65 CAATGTCGGCTAAAAACTGACCCGAAATTTTTTTTCATGAA-ATTTTTGCCACAATACTAAGAAA
* * * *
21189 AATAATAAAATT-AACTGCCAAAAATATTGACGGGTTTTTCACGCTTCTAAAATCGTTTTTCCAT
129 AATAATATAATTCAAC-GCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTT-CAT
* * * *
21253 TTTTCTGAATTAATTTCTAATTAACTAGAAACAAGATTCAAATGTTCGTAAAAACAAATCCTTAT
192 TTTTCCGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGT-AAAACAAATCCTTAT
* * *
21318 ATACAATGTGGCTGAAATTTGATTCA-ATGAATATATCTATTTCAAGGAGT-TAGTGC-GCCAAG
256 ATACAATGTGGCTGAAATTTGGTT-AGATGAATATATATATTTCAAGGAGTCT--TGCTGCCAAA
21380 AA
318 AA
*
21382 TCATGCAAAATTGAGTCGGGACTCCGAAACGCATTTTTAACCCAAAAAC
1 TCATGCAAAATTGAGTC-GGACTCCGAAACGCGTTTTTAACCCAAAAAC
21431 CATGATGGTT
Statistics
Matches: 1895, Mismatches: 336, Indels: 143
0.80 0.14 0.06
Matches are distributed among these distances:
317 1 0.00
318 91 0.05
319 270 0.14
320 419 0.22
321 434 0.23
322 89 0.05
323 248 0.13
324 79 0.04
325 1 0.00
327 52 0.03
328 28 0.01
329 93 0.05
330 85 0.04
331 5 0.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (319 bp):
TCATGCAAAATTGAGTCGGACTCCGAAACGCGTTTTTAACCCAAAAACTGTGATGATTAGTACAC
AATGTCGGCTAAAAACTGACCCGAAATTTTTTTTCATGAAATTTTTGCCACAATACTAAGAAAAA
TAATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTT
CCGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAACAAATCCTTATATACA
ATGTGGCTGAAATTTGGTTAGATGAATATATATATTTCAAGGAGTCTTGCTGCCAAAAA
Found at i:20962 original size:643 final size:634
Alignment explanation
Indices: 18266--21441 Score: 4329
Period size: 642 Copynumber: 4.9 Consensus size: 634
18256 ACTTGAATTT
* * * *
18266 TTTTTTTCATGAAATTTTTGCCACAATACTTAGAAAAAAAAATATAATTTAAGGTCAAAAAGATT
1 TTTTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATAA-ATAATTCAACGTCAAAAAGATT
* *
18331 AAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTCTGAATTAATTTCTAATTAAATGG
65 GAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTT-AGAATTAATTTCTAATTAAATGG
* * * * *
18396 AAAGAAGATTCAGATGCTCGTAAAACAAATTCTTATATCCAATCCCGCGGAAATTTGGTTAGATG
129 AAACAAGATTCAGATGCTCGTAAAACAAATCCTTATATCCAATCCGGCTGAGATTTGGTTAGATG
* * * * *
18461 AATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTCAAAACTGAGTTGTGGCCATGAAAA
194 AATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCC-CGAAAC
* ** * *
18526 ACGTTTTTAGCCCAAGAACCGTGAT-AGTTAGTACAAAATTTCGGCTAAAAACTGATACGAATTT
258 GCGTTTTTAGCCCAA-AACTATGATGA-TTAGTACACAATTTCGGCTAAAAACTG-TTCGAA---
* * *
18590 TATTATTTTTTT-TGAATTTTTTGCCACAAAACTCAGAAAAA-ATATATAATTCAACACCAAAAA
317 -ATT-TTTTTTTATGAATTTTTTGCCACAATACTAAGAAAAATA-ATATAATT-AACGCCAAAAA
* ** * * * *
18653 TATTGACGGGCATTTCACATTTCTAATATCGCTTTTCCATTTTTTTCAGAAATAATTTCTAATTA
378 TATTGACGGGCTTTTCACGCTTCTAAAATCGTTTTTCCA--TTTTTCCGAATTAATTTCTAATTA
* * * *
18718 AATAGAAACAAGATTCAAATGTTCGTAAAAACAAATCCTTATATACAATGTGACTGAAATTTGAT
441 ACTAGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTATATACAATGTGGCTGAAATTTGGT
* * *
18783 TCAATGAATATATATATT-----A--CA-AG-G--AG---TCATGCAAAATTGAGCTGGCACTCC
506 TCAATGAATATATAT-TTCAAGGAGTCAGTGCGCCAGAAATCATGCAAAATTGAGCCGGAACTCC
*
18834 GAAACACGTTTTTAACCTAAAACCGTGATGGTTAGTACACGATGTCGGCTAAAAACTGACCC-AG
570 G-AA-ACGTTTTTAACCTAAAACCGTGATGGTTAGTACACAATGTCGGCTAAAAACTGACCCGA-
18898 AAA
632 AAA
* * * *
18901 TTTTTTTCATGAAATTTTAGCCACAATACTCAGAAAAAATATATAAATCAACGTAAAAAAGATTG
1 TTTTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATAAATAATTCAACGTCAAAAAGATTG
** * *
18966 AA-GGAATTTCACGCCTCTAATATCGTTTTTCATTATTTT-GAATTAATTTCTAATTAAATGGAA
66 AAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTAGAATTAATTTCTAATTAAATGGAA
* * * *
19029 ACAAGACTAAGATGCTCATAAAATAAATCCTTATATCCAATCCGGCTGAGATTTGGTTAGATGAA
131 ACAAGATTCAGATGCTCGTAAAACAAATCCTTATATCCAATCCGGCTGAGATTTGGTTAGATGAA
*
19094 TATAGATATTTCAAGGAGTCTTTCTGCCAGAAATCATGCAAAACTGAGTCGGGGTCCCGAAACGC
196 TATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGG-CCCGAAACGC
* *
19159 GTTTTTAGCCCAAAAACTATGATAATTAGTACACAATTTCGGCTAACAACAAATCTGAAATTTGT
260 GTTTTTAGCCC-AAAACTATGATGATTAGTACACAATTTCGGCT---AA-AAA-CTG---TTCG-
*** * *
19224 TTTTTTTTTTTTATGAATTTTTTACCACAATACTAAGAAAAATAATATAATTTACCGCCAAAAAT
315 AAATTTTTTTTTATGAATTTTTTGCCACAATACTAAGAAAAATAATATAA-TTAACGCCAAAAAT
*
19289 ATTAACGGGCTTTTCACGCTTCTAAAATCGTTTTTCCATTTTTCCGAATTAATTTCTAATTAACT
379 ATTGACGGGCTTTTCACGCTTCTAAAATCGTTTTTCCATTTTTCCGAATTAATTTCTAATTAACT
19354 AGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTATATACAATGTGGCTGAAATTTGGTTCA
444 AGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTATATACAATGTGGCTGAAATTTGGTTCA
* *
19419 ATGAATATATATATTTCAAGGAGTCATTGCGCCAGAAGTCATGCAAAATTGAGCCGGAACTCCG-
509 ATG-A-ATATATATTTCAAGGAGTCAGTGCGCCAGAAATCATGCAAAATTGAGCCGGAACTCCGA
* *
19483 AACGTGTTTTTAACCCAAAACCTGTGATGGTTACTACACAATGTCGGCTAAAAACTGACCCGAAA
572 AAC--GTTTTTAACCTAAAACC-GTGATGGTTAGTACACAATGTCGGCTAAAAACTGACCCGAAA
19548 A
634 A
* *
19549 TTTTGTTCATGAAATTTTTGTCACAATACTCAGAAAAAATAAATAATTCAACGTCAAAAAGATTG
1 TTTTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATAAATAATTCAACGTCAAAAAGATTG
* *
19614 AAGGGCTTTTCACGCTTATAATATCGTTTTTCATTTTTTTAAAATTAATTTCTAATTAAATGGAA
66 AAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTAGAATTAATTTCTAATTAAATGGAA
* * * * *
19679 ACAACATTCAGATGCTCGTAAAACAAATCATTATATCCAATCCGACTAAGATTTAGTTAGATG-A
131 ACAAGATTCAGATGCTCGTAAAACAAATCCTTATATCCAATCCGGCTGAGATTTGGTTAGATGAA
19743 TATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGTCCCGAAACGC
196 TATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGG-CCCGAAACGC
* *
19808 ATTTTTAGCTCAAAAACTATGATGATTAGTACACAATTTCGGCTAAAAACTGTTCCGAAATTTTT
260 GTTTTTAGC-CCAAAACTATGATGATTAGTACACAATTTCGGCTAAAAACTGTT-CGAAATTTTT
* **
19873 TTTAATGAA-TTTTTGCCACAATACTAAGAAAAATAATATAATTAACCGCCAAAAATATTGACTA
323 TTTTATGAATTTTTTGCCACAATACTAAGAAAAATAATATAATTAA-CGCCAAAAATATTGACGG
* *
19937 GCTTTTCACGCTTCTAAAACCGTTTTTCCA-ATTTCCGAATTAATTTCTAATTAACTAGAAACAA
387 GCTTTTCACGCTTCTAAAATCGTTTTTCCATTTTTCCGAATTAATTTCTAATTAACTAGAAACAA
* *
20001 TATTCAGATGTTCGTAAAAACAAATCCTTATATACAATGTAGCTGAAATTTGGTTCAATGAATAT
452 GATTCAGATGTTCGTAAAAACAAATCCTTATATACAATGTGGCTGAAATTTGGTTCAATGAATAT
* * *
20066 ATCTATTTCAAGGAGTTAGTGCGTCAAAAATCATGCAAAATTGAGCCAGG-ACTCCGAAACGCAT
517 A--TATTTCAAGGAGTCAGTGCGCCAGAAATCATGCAAAATTGAGCC-GGAACTCCGAAACG--T
20130 TTTTAACCTAAAAACCGTGATGGTTAGTACACAATGTCGGCTAAAAACTGACCCGAAAA
577 TTTTAACCT-AAAACCGTGATGGTTAGTACACAATGTCGGCTAAAAACTGACCCGAAAA
* * *
20189 TTTTTTTTCCATGAAATTTTTGCCACAATACTCGGAAAAGATAAATAATTCAACGTAAAAAAGAT
1 -TTTTTTT-CATGAAATTTTTGCCACAATACTCAGAAAAAATAAATAATTCAACGTCAAAAAGAT
* * * *
20254 TGAAAGGTTTTTCACGCTTCTAATATAGTTTTTCATTTTTTTAAAATTAATTTCTAATTAAATGG
64 TGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTAGAATTAATTTCTAATTAAATGG
* * * *
20319 AATCAAGATTCGGATGCTCGTAAAACAAATCCTTATATCCAATCCGGTTGAGATTTAGTTAGATG
129 AAACAAGATTCAGATGCTCGTAAAACAAATCCTTATATCCAATCCGGCTGAGATTTGGTTAGATG
20384 AATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCACGAAAC
194 AATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCC-CGAAAC
20449 GCGTTTTTAGCTCCAAAACTATGATGATTAGTACACAATTTCGGCTAAAAACTGTTCTGAAATTT
258 GCGTTTTTAGC-CCAAAACTATGATGATTAGTACACAATTTCGGCTAAAAACTGTTC-GAAATTT
* * *
20514 TTTTTTATGAATTTTTTGCCACAATACTAAGAAAAATAATAAAATTCAATGCCAAAAATATAGAC
321 TTTTTTATGAATTTTTTGCCACAATACTAAGAAAAATAATATAATT-AACGCCAAAAATATTGAC
* * *
20579 GGGCTTTTCACGCTTCTAATATCGTTTTCCCATTTTTTTCCGAATTAATTTCTAATTAAATAGAA
385 GGGCTTTTCACGCTTCTAAAATCGTTTTTCCA--TTTTTCCGAATTAATTTCTAATTAACTAGAA
* * *
20644 ACAATATTCAGATGTTCGTAAAAGCAAATCCTTATATACAATGTGGATGAAATTTGGTTCAATGA
448 ACAAGATTCAGATGTTCGTAAAAACAAATCCTTATATACAATGTGGCTGAAATTTGGTTCAATGA
*
20709 ATATATATTTCAAGGAGTCATTGCGCCAGAAATCATGCAAAATTGAGCCGGAACTCCGAAACGTG
513 ATATATATTTCAAGGAGTCAGTGCGCCAGAAATCATGCAAAATTGAGCCGGAACTCCGAAACGT-
* *
20774 TTTTAAACTAAAACCTGTGATGGTTAGTACACGATGTCGGCTAAAAACTGACCCGAAAA
577 TTTTAACCTAAAACC-GTGATGGTTAGTACACAATGTCGGCTAAAAACTGACCCGAAAA
* *
20833 TTTTGTTCATGAAATTTTTGCCACAATACTCAGAAAAAATAAATAATTCAACATCAAAAAGATTG
1 TTTTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATAAATAATTCAACGTCAAAAAGATTG
* *
20898 AAGGGCATTTCACGCTTCTAATATCGTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAATGGA
66 AAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTT-AGAATTAATTTCTAATTAAATGGA
* * * * *
20963 AACAAGACTAAGGTGCTCATAAAACAAATCCTTATATCCAATCCGGCTGAGATTTGGTTATATGA
130 AACAAGATTCAGATGCTCGTAAAACAAATCCTTATATCCAATCCGGCTGAGATTTGGTTAGATGA
* * * *
21028 ATGTATATATTTTAAGGAGTCTTTCTGCCAAAAATCATGCGAAACTGAGTCGGGGCCCCGAAACG
195 ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGG-CCCGAAACG
* ** *
21093 CG-TTTTAGCCCAAAAACTGTGATGATTAGTACACAATTTCGGCTAAAAACTAATCCAAA-TTTT
259 CGTTTTTAGCCC-AAAACTATGATGATTAGTACACAATTTCGGCTAAAAACTGTTCGAAATTTTT
* *
21156 TTTTAAGAATTTTTTTGCCACAATACTAAGAAAAATAATAAAATTAACTGCCAAAAATATTGACG
323 TTTTATGAA-TTTTTTGCCACAATACTAAGAAAAATAATATAATTAAC-GCCAAAAATATTGACG
* *
21221 GGTTTTTCACGCTTCTAAAATCGTTTTTCCATTTTTCTGAATTAATTTCTAATTAACTAGAAACA
386 GGCTTTTCACGCTTCTAAAATCGTTTTTCCATTTTTCCGAATTAATTTCTAATTAACTAGAAACA
* *
21286 AGATTCAAATGTTCGTAAAAACAAATCCTTATATACAATGTGGCTGAAATTTGATTCAATGAATA
451 AGATTCAGATGTTCGTAAAAACAAATCCTTATATACAATGTGGCTGAAATTTGGTTCAATGAATA
* * *
21351 TATCTATTTCAAGGAGTTAGTGCGCCA-AGAATCATGCAAAATTGAGTCGGGACTCCGAAACGCA
516 TA--TATTTCAAGGAGTCAGTGCGCCAGA-AATCATGCAAAATTGAGCCGGAACTCCGAAACG--
* *
21415 TTTTTAACCCAAAAACCATGATGGTTA
576 TTTTTAA-CCTAAAACCGTGATGGTTA
21442 T
Statistics
Matches: 2279, Mismatches: 192, Indels: 133
0.88 0.07 0.05
Matches are distributed among these distances:
631 171 0.08
632 5 0.00
633 122 0.05
634 32 0.01
635 125 0.05
636 6 0.00
637 5 0.00
638 5 0.00
639 234 0.10
640 146 0.06
641 164 0.07
642 328 0.14
643 292 0.13
644 131 0.06
645 60 0.03
646 3 0.00
647 111 0.05
648 124 0.05
649 137 0.06
650 78 0.03
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (634 bp):
TTTTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATAAATAATTCAACGTCAAAAAGATTG
AAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTAGAATTAATTTCTAATTAAATGGAA
ACAAGATTCAGATGCTCGTAAAACAAATCCTTATATCCAATCCGGCTGAGATTTGGTTAGATGAA
TATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCGAAACGCG
TTTTTAGCCCAAAACTATGATGATTAGTACACAATTTCGGCTAAAAACTGTTCGAAATTTTTTTT
TATGAATTTTTTGCCACAATACTAAGAAAAATAATATAATTAACGCCAAAAATATTGACGGGCTT
TTCACGCTTCTAAAATCGTTTTTCCATTTTTCCGAATTAATTTCTAATTAACTAGAAACAAGATT
CAGATGTTCGTAAAAACAAATCCTTATATACAATGTGGCTGAAATTTGGTTCAATGAATATATAT
TTCAAGGAGTCAGTGCGCCAGAAATCATGCAAAATTGAGCCGGAACTCCGAAACGTTTTTAACCT
AAAACCGTGATGGTTAGTACACAATGTCGGCTAAAAACTGACCCGAAAA
Done.