Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010707.1 Corchorus capsularis cultivar CVL-1 contig10728, 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: 33102
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:360 original size:21 final size:21
Alignment explanation
Indices: 336--515 Score: 227
Period size: 21 Copynumber: 8.6 Consensus size: 21
326 TGTTTACATA
*
336 TTGATACTCAAACCCCAAATT
1 TTGATAGTCAAACCCCAAATT
* *
357 TTGATAGTCAACCCCCGAATT
1 TTGATAGTCAAACCCCAAATT
* *
378 TTGATAGTCAAATCCCGAATT
1 TTGATAGTCAAACCCCAAATT
*
399 TTGATAGTCAAACCCCAAAGT
1 TTGATAGTCAAACCCCAAATT
*
420 TTGATAGTCAAACCCCCAAAGT
1 TTGATAGTCAAA-CCCCAAATT
* * *
442 TTAATAGTCAAACCCTAAAAT
1 TTGATAGTCAAACCCCAAATT
463 TTGATAGTC-AACCCCAAATT
1 TTGATAGTCAAACCCCAAATT
** *
483 TAAATAGTCAAACCCCAAAAT
1 TTGATAGTCAAACCCCAAATT
504 TTGATAGTCAAA
1 TTGATAGTCAAA
516 TCACAAGAAA
Statistics
Matches: 138, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 16 0.12
21 102 0.74
22 20 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (21 bp):
TTGATAGTCAAACCCCAAATT
Found at i:573 original size:21 final size:21
Alignment explanation
Indices: 543--638 Score: 113
Period size: 21 Copynumber: 4.5 Consensus size: 21
533 CTATACAAGC
543 ATAGTCAAACCCCAAAGTTTA
1 ATAGTCAAACCCCAAAGTTTA
*
564 ATAGTTAAACCCCCCAAAGTTTA
1 ATAGTCAAA--CCCCAAAGTTTA
* * *
587 ATAGTCAAACACTAAAGTTTG
1 ATAGTCAAACCCCAAAGTTTA
* *
608 ATAGTC-AACCCCAAAATTTG
1 ATAGTCAAACCCCAAAGTTTA
628 ATAGTCAAACC
1 ATAGTCAAACC
639 ACGTTAAACC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
20 17 0.27
21 27 0.42
23 20 0.31
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (21 bp):
ATAGTCAAACCCCAAAGTTTA
Found at i:606 original size:44 final size:41
Alignment explanation
Indices: 543--637 Score: 109
Period size: 44 Copynumber: 2.2 Consensus size: 41
533 CTATACAAGC
* *
543 ATAGTCAAACCCCAAAGTTTAATAGTTAAACCCCCCAAAGTTTA
1 ATAGTCAAACACCAAAGTTTAATAG-TAAA--CCCCAAAATTTA
* * * *
587 ATAGTCAAACACTAAAGTTTGATAGTCAACCCCAAAATTTG
1 ATAGTCAAACACCAAAGTTTAATAGTAAACCCCAAAATTTA
628 ATAGTCAAAC
1 ATAGTCAAAC
638 CACGTTAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 20 0.44
43 3 0.07
44 22 0.49
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (41 bp):
ATAGTCAAACACCAAAGTTTAATAGTAAACCCCAAAATTTA
Found at i:4220 original size:2 final size:2
Alignment explanation
Indices: 4185--4209 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4175 CCAACTTTTG
4185 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4210 AGTCGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5309 original size:103 final size:103
Alignment explanation
Indices: 5136--5334 Score: 328
Period size: 103 Copynumber: 1.9 Consensus size: 103
5126 TACACATTCG
* * *
5136 TTTACTTGATTTATTATTTTTTCTCTAACTTTTTTACGTTTAGGCATTTGGGTTGGTGATCTAGT
1 TTTACTTGATTTATTATTTTTTCTCTAACTTTTTTACGTTTAAGCATTTGGGTTAGTGATCCAGT
5201 TAGGGCTCAAAGCAAG-AAACGAAGAAGAAAAAACATTT
66 TAGGGCTCAAAG-AAGAAAACGAAGAAGAAAAAACATTT
*
5239 TTTACTTGATTTATTATTTTTTCTCTAACTTTTTTACGTTTAAGCATTTGGGTTATTGATCCAGT
1 TTTACTTGATTTATTATTTTTTCTCTAACTTTTTTACGTTTAAGCATTTGGGTTAGTGATCCAGT
**
5304 TAGGGCTCAAAGTGGAAAACGAAGAAGAAAA
66 TAGGGCTCAAAGAAGAAAACGAAGAAGAAAA
5335 GAAATGGATA
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 1 0.01
103 88 0.99
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (103 bp):
TTTACTTGATTTATTATTTTTTCTCTAACTTTTTTACGTTTAAGCATTTGGGTTAGTGATCCAGT
TAGGGCTCAAAGAAGAAAACGAAGAAGAAAAAACATTT
Found at i:6299 original size:13 final size:13
Alignment explanation
Indices: 6281--6305 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6271 GAAAACGTCA
6281 AAATTTTCTCAAT
1 AAATTTTCTCAAT
6294 AAATTTTCTCAA
1 AAATTTTCTCAA
6306 CAAAAGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTTTCTCAAT
Found at i:7846 original size:30 final size:30
Alignment explanation
Indices: 7717--8133 Score: 483
Period size: 30 Copynumber: 13.7 Consensus size: 30
7707 ATAAATCTCC
* *
7717 ATTGACACCAGAAGTTGTCAATGGTCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATTTTACA
* **
7748 ATTGAAACCAGAAGTTGTCAATGACCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATTTTACA
**
7779 ATTGACACCAGAAGTTGTCAATGACCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATTTTACA
*
7810 ATTGACACCATAAGTTGTCATGATTTTACA
1 ATTGACACCAGAAGTTGTCATGATTTTACA
* *
7840 AATGACACCAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTACA
* *
7870 ATTGACACCAGAAGTTGTCATGAGTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTACA
** ** ** *
7900 ATTGACACTTGAAAATGTCATGACCTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTACA
* * *
7930 ATTGACACTAGAAGTTGTCATGGTATTACA
1 ATTGACACCAGAAGTTGTCATGATTTTACA
* *
7960 AATGACACCAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTACA
* *
7990 ATTGACACAAGAAGTTGTCAATGATCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATTTTACA
* * *
8021 AATGACACTAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTACA
*
8051 ATTGACACCAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTACA
** *
8081 ATTGACACTTGAAGATGTCATGATTTTATTCA
1 ATTGACACCAGAAGTTGTCATGATTTTA--CA
8113 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
8134 ATACACCATG
Statistics
Matches: 336, Mismatches: 47, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
30 214 0.64
31 102 0.30
32 20 0.06
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (30 bp):
ATTGACACCAGAAGTTGTCATGATTTTACA
Found at i:8022 original size:181 final size:183
Alignment explanation
Indices: 7746--8133 Score: 575
Period size: 181 Copynumber: 2.1 Consensus size: 183
7736 AATGGTCTTA
* * *
7746 CAATTGAAACCAGAAGTTGTCAATGACCTTACAATTGACACCAGAAGTTGTCAATGACCTTACAA
1 CAATTGACACCAGAAGTTGTC-ATGACATTACAAATGACACCAGAAGTTGTCAATGACCTTACAA
* * *
7811 TTGACACCATAAGTTGTCATGATTTTACAAATGACACCAGAAGTTGTCATGATTTTGCAATTGAC
65 TTGACACAAGAAGTTGTCATGATCTTACAAATGACACCAGAAGTTGTCATGATTTTGCAATTGAC
7876 ACCAGAAGTTGTCATGAGTTTGCAATTGACACTTGAAAATGTCATGA-CCT-TG
130 ACCAGAAGTTGTCATGAGTTTGCAATTGACACTTGAAAATGTCATGATCCTATG
* ** ** *
7928 CAATTGACACTAGAAGTTGTCATGGTATTACAAATGACACCAGAAGTTGTC-ATGATTTTGCAAT
1 CAATTGACACCAGAAGTTGTCATGACATTACAAATGACACCAGAAGTTGTCAATGACCTTACAAT
*
7992 TGACACAAGAAGTTGTCAATGATCTTACAAATGACACTAGAAGTTGTCATGATTTTGCAATTGAC
66 TGACACAAGAAGTTGTC-ATGATCTTACAAATGACACCAGAAGTTGTCATGATTTTGCAATTGAC
* * ** *
8057 ACCAGAAGTTGTCATGATTTTGCAATTGACACTTGAAGATGTCATGATTTTATT
130 ACCAGAAGTTGTCATGAGTTTGCAATTGACACTTGAAAATGTCATGATCCTATG
8111 CAATTGACACCAGAAGTTGTCAT
1 CAATTGACACCAGAAGTTGTCAT
8134 ATACACCATG
Statistics
Matches: 184, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
180 25 0.14
181 116 0.63
182 20 0.11
183 23 0.12
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (183 bp):
CAATTGACACCAGAAGTTGTCATGACATTACAAATGACACCAGAAGTTGTCAATGACCTTACAAT
TGACACAAGAAGTTGTCATGATCTTACAAATGACACCAGAAGTTGTCATGATTTTGCAATTGACA
CCAGAAGTTGTCATGAGTTTGCAATTGACACTTGAAAATGTCATGATCCTATG
Found at i:13149 original size:24 final size:23
Alignment explanation
Indices: 13121--13205 Score: 71
Period size: 24 Copynumber: 3.6 Consensus size: 23
13111 GGTTCATTTA
13121 TGTTCACGAACACGTTCGATTAG
1 TGTTCACGAACACGTTCGATTAG
* ** *
13144 TTGTTCACAAACATTTTCGATAAAG
1 -TGTTCACGAACACGTTCGAT-TAG
* ** *
13169 TGTTCATGAACGTGTTCGATATGG
1 TGTTCACGAACACGTTCGAT-TAG
13193 TGTTCACGAACAC
1 TGTTCACGAACAC
13206 ATGTATTATA
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
24 45 0.96
25 2 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (23 bp):
TGTTCACGAACACGTTCGATTAG
Found at i:13491 original size:13 final size:13
Alignment explanation
Indices: 13473--13497 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13463 ACTCTCTACA
13473 TCATCTTCTTTGT
1 TCATCTTCTTTGT
13486 TCATCTTCTTTG
1 TCATCTTCTTTG
13498 ATTAATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.24, G:0.08, T:0.60
Consensus pattern (13 bp):
TCATCTTCTTTGT
Found at i:18424 original size:16 final size:15
Alignment explanation
Indices: 18383--18426 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
18373 GGGACTATAC
18383 ATCAAAATAAAAGTA
1 ATCAAAATAAAAGTA
18398 AT---AAT-AAAGTA
1 ATCAAAATAAAAGTA
18409 TATCAAAATAAAAGTA
1 -ATCAAAATAAAAGTA
18425 AT
1 AT
18427 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
11 6 0.25
12 5 0.21
15 7 0.29
16 6 0.25
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.25
Consensus pattern (15 bp):
ATCAAAATAAAAGTA
Found at i:19570 original size:122 final size:122
Alignment explanation
Indices: 19415--19664 Score: 455
Period size: 122 Copynumber: 2.0 Consensus size: 122
19405 TTTTCCCTTG
* *
19415 CAGGTTAGAGGGTTAGTGAAGCAACACTTGGATTCATTTAACTACTTTGTTAAGATTGGGATAAA
1 CAGGTTAGAGGGTTAGTGAAGCAACACTTGGATTCATTTAACTACTTTGTTAAAACTGGGATAAA
*
19480 GAAGATTGTTAGTGACAATTACTGGATTGCATCGGATGTTGACCCCACTATTTACAT
66 GAACATTGTTAGTGACAATTACTGGATTGCATCGGATGTTGACCCCACTATTTACAT
19537 CAGGTTAGAGGGTTAGTGAAGCAACACTTGGATTCATTTAACTACTTTGTTAAAACTGGGATAAA
1 CAGGTTAGAGGGTTAGTGAAGCAACACTTGGATTCATTTAACTACTTTGTTAAAACTGGGATAAA
* *
19602 GAACATTGTTAGTGATAATTACTGGATTGCATTGGATGTTGACCCCACTATTTACAT
66 GAACATTGTTAGTGACAATTACTGGATTGCATCGGATGTTGACCCCACTATTTACAT
19659 CAGGTT
1 CAGGTT
19665 TGAAAGCATT
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
122 123 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (122 bp):
CAGGTTAGAGGGTTAGTGAAGCAACACTTGGATTCATTTAACTACTTTGTTAAAACTGGGATAAA
GAACATTGTTAGTGACAATTACTGGATTGCATCGGATGTTGACCCCACTATTTACAT
Found at i:22523 original size:16 final size:16
Alignment explanation
Indices: 22502--22534 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
22492 TGCTAAACTT
22502 AAAAAAG-AGAATGAGA
1 AAAAAAGAAGAA-GAGA
22518 AAAAAAGAAGAAGAGA
1 AAAAAAGAAGAAGAGA
22534 A
1 A
22535 TTCCGTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (16 bp):
AAAAAAGAAGAAGAGA
Found at i:23275 original size:17 final size:17
Alignment explanation
Indices: 23255--23303 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
23245 TTATCGAGTT
23255 AGTTTTTTTATAGTCTC
1 AGTTTTTTTATAGTCTC
*
23272 AGTTCTTTTTGA-A-TCTG
1 AGTT-TTTTT-ATAGTCTC
23289 AGTTTTTTT-TAGTCT
1 AGTTTTTTTATAGTCT
23304 GAATCTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
15 1 0.04
16 8 0.30
17 11 0.41
18 6 0.22
19 1 0.04
ACGTcount: A:0.16, C:0.10, G:0.14, T:0.59
Consensus pattern (17 bp):
AGTTTTTTTATAGTCTC
Found at i:25685 original size:21 final size:21
Alignment explanation
Indices: 25659--25701 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
25649 CCTTCGGGAA
25659 TTACTAAATACCGCCCCCTTT
1 TTACTAAATACCGCCCCCTTT
**
25680 TTACTAGCTACCGCCCCCTTT
1 TTACTAAATACCGCCCCCTTT
25701 T
1 T
25702 GACACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.40, G:0.07, T:0.35
Consensus pattern (21 bp):
TTACTAAATACCGCCCCCTTT
Found at i:26997 original size:45 final size:41
Alignment explanation
Indices: 26916--27014 Score: 110
Period size: 45 Copynumber: 2.3 Consensus size: 41
26906 TCGAGGAGGC
* *
26916 GAAGCAGAAGTACAGAAAGAGATAGGCCTTCGAGGAGGCGAAGCA
1 GAAGCAGGAGTACAGAAAGAGATAGG-CATCGAGGAGGC--AG-A
*
26961 GAAGCAGGAGTACAGAAAGAGATAGAG-ATGGAAGGAGGCAGA
1 GAAGCAGGAGTACAGAAAGAGATAG-GCATCG-AGGAGGCAGA
27003 GAAGCAGGAGTA
1 GAAGCAGGAGTA
27015 GGTCACCGCG
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
42 13 0.27
43 2 0.04
44 2 0.04
45 31 0.63
46 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.38, T:0.08
Consensus pattern (41 bp):
GAAGCAGGAGTACAGAAAGAGATAGGCATCGAGGAGGCAGA
Found at i:30569 original size:51 final size:51
Alignment explanation
Indices: 30493--30595 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
30483 TGGATAACTC
30493 TTACAAGTGGCCCTCTCAACTAGCCAATCAGATTAAAAATAACAATAATAA
1 TTACAAGTGGCCCTCTCAACTAGCCAATCAGATTAAAAATAACAATAATAA
*
30544 TTACAAGTTGCCCTCTCAACTAGCCAATCAGATTAAAAATAACAATAATAA
1 TTACAAGTGGCCCTCTCAACTAGCCAATCAGATTAAAAATAACAATAATAA
30595 T
1 T
30596 AATAATTTCT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.25
Consensus pattern (51 bp):
TTACAAGTGGCCCTCTCAACTAGCCAATCAGATTAAAAATAACAATAATAA
Found at i:30991 original size:5 final size:5
Alignment explanation
Indices: 30981--31008 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
30971 TAAAGTGGTA
30981 GATCT GATCT GATCT GATCT GATCT GAT
1 GATCT GATCT GATCT GATCT GATCT GAT
31009 GACATAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (5 bp):
GATCT
Found at i:32834 original size:21 final size:23
Alignment explanation
Indices: 32808--32852 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
32798 ATTTACTGAA
32808 TTGCTAAACACCG-CCC-TATTT
1 TTGCTAAACACCGTCCCATATTT
**
32829 TTGCTATTCACCGTCCCATATTT
1 TTGCTAAACACCGTCCCATATTT
32852 T
1 T
32853 ACATTTTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 3 0.15
23 6 0.30
ACGTcount: A:0.20, C:0.31, G:0.09, T:0.40
Consensus pattern (23 bp):
TTGCTAAACACCGTCCCATATTT
Done.