Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009857.1 Corchorus capsularis cultivar CVL-1 contig09878, 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: 56648
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1630 original size:2 final size:2
Alignment explanation
Indices: 1617--1646 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1607 TTCCAAGGAA
*
1617 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1647 CTTGTTCTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5837 original size:31 final size:31
Alignment explanation
Indices: 5802--5863 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
5792 AGAAAATAAA
*
5802 ACTGGGTTTCGCGAAGAGAACAAAAGAATTT
1 ACTGGGTTTCGCAAAGAGAACAAAAGAATTT
5833 ACTGGGTTTCGCAAAGAGAACAAAAGAATTT
1 ACTGGGTTTCGCAAAGAGAACAAAAGAATTT
5864 TATATGAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (31 bp):
ACTGGGTTTCGCAAAGAGAACAAAAGAATTT
Found at i:8414 original size:60 final size:61
Alignment explanation
Indices: 8321--8442 Score: 210
Period size: 60 Copynumber: 2.0 Consensus size: 61
8311 AGAAATCTTG
*
8321 CCTCGGCATTGTTACTTCACTTTAGACTGACTAGC-TATATATTGTAGTAATTGGTGGTTC
1 CCTCGGCATTGTTACTTCACTTTAGACTCACTAGCATATATATTGTAGTAATTGGTGGTTC
*
8381 CCTCGGCATTGTTGCTTCACTTTAGACTCACTAGCTATATATATTGTAGTAATTGGTGGTTC
1 CCTCGGCATTGTTACTTCACTTTAGACTCACTAGC-ATATATATTGTAGTAATTGGTGGTTC
8443 AAATATAAGT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
60 33 0.57
62 25 0.43
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (61 bp):
CCTCGGCATTGTTACTTCACTTTAGACTCACTAGCATATATATTGTAGTAATTGGTGGTTC
Found at i:20559 original size:33 final size:33
Alignment explanation
Indices: 20523--20816 Score: 250
Period size: 33 Copynumber: 8.9 Consensus size: 33
20513 AAGGGGAAAG
* *
20523 GCTCAAAGGGGCCCAAGGGGTGACTCGAGAAGG
1 GCTCAAAGGGGCCCAAGGGGTGACTGGAGAAGC
* * * *
20556 GCTCGAAGAGGCCCAAGGGGTGACTAGAGAAAC
1 GCTCAAAGGGGCCCAAGGGGTGACTGGAGAAGC
* * *
20589 GCT-AAACGGCGTCGAAGGGGTGACTGGAGAAGC
1 GCTCAAA-GGGGCCCAAGGGGTGACTGGAGAAGC
* * * *
20622 GCTCAAAGGGACCCAATGGGTGACTCGAGAAGG
1 GCTCAAAGGGGCCCAAGGGGTGACTGGAGAAGC
* ** *
20655 GCTCGAAGGGAG-CCAAGGGGTGACTATAAAAGC
1 GCTCAAAGGG-GCCCAAGGGGTGACTGGAGAAGC
* * * * * *
20688 ACTGAAAAGGGCTCAAGGGGTGATTGGAGAAAC
1 GCTCAAAGGGGCCCAAGGGGTGACTGGAGAAGC
** * *
20721 GCTCAAAGACGCCGAAGGGTTGACTGGAGAAGC
1 GCTCAAAGGGGCCCAAGGGGTGACTGGAGAAGC
** * *
20754 GCTCAAAGGCACCCAAGGGGTTACTAGAGAAGC
1 GCTCAAAGGGGCCCAAGGGGTGACTGGAGAAGC
** *
20787 GCTCAAAGGCACCCAAGAGGTGACTGGAGA
1 GCTCAAAGGGGCCCAAGGGGTGACTGGAGA
20817 GCTCGATAGG
Statistics
Matches: 202, Mismatches: 55, Indels: 8
0.76 0.21 0.03
Matches are distributed among these distances:
32 3 0.01
33 196 0.97
34 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.37, T:0.12
Consensus pattern (33 bp):
GCTCAAAGGGGCCCAAGGGGTGACTGGAGAAGC
Found at i:20706 original size:99 final size:98
Alignment explanation
Indices: 20518--20784 Score: 294
Period size: 99 Copynumber: 2.7 Consensus size: 98
20508 TGATAAAGGG
* *
20518 GAAAGGCTCAAAGGGGCCCAAGGGGTGACTCGAGAAGGGCTCGAAGAGG-CCCAAGGGGTGACTA
1 GAAACGCTCAAAGGGACCCAA-GGGTGACTCGAGAAGGGCTCGAAG-GGACCCAAGGGGTGACTA
*
20582 GAGAAACGCTAAACGGCGTCGAAGGGGTGACTGGA
64 GAGAAACACTAAACGGCGTCGAAGGGGTGACTGGA
* * *
20617 GAAGCGCTCAAAGGGACCCAATGGGTGACTCGAGAAGGGCTCGAAGGGAGCCAAGGGGTGACTAT
1 GAAACGCTCAAAGGGACCCAA-GGGTGACTCGAGAAGGGCTCGAAGGGACCCAAGGGGTGACTAG
* *
20682 A-AAAGCACTGAAAAGG-GCTC-AAGGGGTGATTGGA
65 AGAAA-CACT-AAACGGCG-TCGAAGGGGTGACTGGA
* * * * *
20716 GAAACGCTCAAA--GACGCCGAAGGGTTGACTGGAGAAGCGCTCAAAGGCACCCAAGGGGTTACT
1 GAAACGCTCAAAGGGAC-CC-AAGGG-TGACTCGAGAAGGGCTCGAAGGGACCCAAGGGGTGACT
20779 AGAGAA
63 AGAGAA
20785 GCGCTCAAAG
Statistics
Matches: 143, Mismatches: 17, Indels: 15
0.82 0.10 0.09
Matches are distributed among these distances:
97 3 0.02
98 10 0.07
99 121 0.85
100 9 0.06
ACGTcount: A:0.32, C:0.19, G:0.37, T:0.12
Consensus pattern (98 bp):
GAAACGCTCAAAGGGACCCAAGGGTGACTCGAGAAGGGCTCGAAGGGACCCAAGGGGTGACTAGA
GAAACACTAAACGGCGTCGAAGGGGTGACTGGA
Found at i:20759 original size:132 final size:132
Alignment explanation
Indices: 20569--20811 Score: 344
Period size: 132 Copynumber: 1.8 Consensus size: 132
20559 CGAAGAGGCC
* * *
20569 CAAGGGGTGACTAGAGAAACGCTAAACGGCGTCGAAGGGGTGACTGGAGAAGCGCTCAAAGGGAC
1 CAAGGGGTGACTAGAGAAACGCTAAACGACGCCGAAGGGGTGACTGGAGAAGCGCTCAAAGGCAC
* * * * * * *
20634 CCAATGGGTGACTCGAGAAGGGCTCGAAGGGAGCCAAGGGGTGACTATAAAAGCACTGAAAAGGG
66 CCAAGGGGTGACTAGAGAAGCGCTCAAAGGCACCCAAGAGGTGACTATAAAAGCACTGAAAAGGG
20699 CT
131 CT
* * *
20701 CAAGGGGTGATTGGAGAAACGCTCAAA-GACGCCGAAGGGTTGACTGGAGAAGCGCTCAAAGGCA
1 CAAGGGGTGACTAGAGAAACGCT-AAACGACGCCGAAGGGGTGACTGGAGAAGCGCTCAAAGGCA
*
20765 CCCAAGGGGTTACTAGAGAAGCGCTCAAAGGCACCCAAGAGGTGACT
65 CCCAAGGGGTGACTAGAGAAGCGCTCAAAGGCACCCAAGAGGTGACT
20812 GGAGAGCTCG
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
132 93 0.97
133 3 0.03
ACGTcount: A:0.33, C:0.20, G:0.35, T:0.12
Consensus pattern (132 bp):
CAAGGGGTGACTAGAGAAACGCTAAACGACGCCGAAGGGGTGACTGGAGAAGCGCTCAAAGGCAC
CCAAGGGGTGACTAGAGAAGCGCTCAAAGGCACCCAAGAGGTGACTATAAAAGCACTGAAAAGGG
CT
Found at i:23377 original size:16 final size:16
Alignment explanation
Indices: 23356--23389 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
23346 TTAAAGACAC
23356 CTACATACTTGGTCGA
1 CTACATACTTGGTCGA
23372 CTACATACTTGGTCGA
1 CTACATACTTGGTCGA
23388 CT
1 CT
23390 TCTAGTCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (16 bp):
CTACATACTTGGTCGA
Found at i:24139 original size:33 final size:33
Alignment explanation
Indices: 24078--24465 Score: 481
Period size: 33 Copynumber: 11.8 Consensus size: 33
24068 AAAGGAGTGT
24078 TCGAAGGGGCCAAA-GGGTGACTGGAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* *
24110 TTGAAGGGGCCAAAGGGGTCACTGGAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* **
24143 TCGAAGGGGCCAAAGGTGTGACTAAAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* *
24176 TCGACGGGGCCAAAGAGGTGACTGGAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* **
24209 TCGAAGGGGCCAAAGGTGTGACTAAAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* ** *
24242 TAGTTGGGGCCAAAGGGGTGACTGGAACAATGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* * *
24275 TCGAAGGGGCCAAAAGGGTGACCGGAATAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* * ** *
24308 TCGAAGAGGCCAAAGGCGTGACTAAAATAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* * *
24341 TTGACGGGGCCAAAGAGGTGACTGGAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
* * *
24374 TCGAAGGGGCCAAAGGCGTGAGTGGAACAACAC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
** *
24407 TCGAAGGGGCCAAAGATGTAACTGGAACAACGC
1 TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
*
24440 TCGAAGGGACCAAAGGGGTGACTGGA
1 TCGAAGGGGCCAAAGGGGTGACTGGA
24466 GGATTGTTCA
Statistics
Matches: 295, Mismatches: 60, Indels: 1
0.83 0.17 0.00
Matches are distributed among these distances:
32 13 0.04
33 282 0.96
ACGTcount: A:0.33, C:0.21, G:0.35, T:0.12
Consensus pattern (33 bp):
TCGAAGGGGCCAAAGGGGTGACTGGAACAACGC
Found at i:30888 original size:27 final size:27
Alignment explanation
Indices: 30858--30911 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
30848 AATACTTTTA
30858 AGAAAATTCAGTTAAGAAATGAAATTT
1 AGAAAATTCAGTTAAGAAATGAAATTT
30885 AGAAAATTCAGTTAAGAAATGAAATTT
1 AGAAAATTCAGTTAAGAAATGAAATTT
30912 TGTTGTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.30
Consensus pattern (27 bp):
AGAAAATTCAGTTAAGAAATGAAATTT
Found at i:30904 original size:13 final size:14
Alignment explanation
Indices: 30855--30903 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
30845 ATAAATACTT
30855 TTAAGAAAATTCAG
1 TTAAGAAAATTCAG
** *
30869 TTAAG-AAATGAAA
1 TTAAGAAAATTCAG
*
30882 TTTAGAAAATTCAG
1 TTAAGAAAATTCAG
30896 TTAAGAAA
1 TTAAGAAA
30904 TGAAATTTTG
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (14 bp):
TTAAGAAAATTCAG
Found at i:31230 original size:11 final size:11
Alignment explanation
Indices: 31216--31253 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
31206 ATTCATAACA
31216 AATTTATAATT
1 AATTTATAATT
31227 AATTTATAATT
1 AATTTATAATT
31238 -ATTTGATAATT
1 AATTT-ATAATT
*
31249 TATTT
1 AATTT
31254 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:34059 original size:32 final size:32
Alignment explanation
Indices: 34013--34104 Score: 139
Period size: 32 Copynumber: 2.9 Consensus size: 32
34003 GCGGTATTGC
*
34013 TGACGTGGCAATGCCACATCAGACCAAGGCAA
1 TGACGTGGCAATGCCACGTCAGACCAAGGCAA
* * **
34045 TGACATGGCAATGCCACGTCAGACAAAGGTGA
1 TGACGTGGCAATGCCACGTCAGACCAAGGCAA
34077 TGACGTGGCAATGCCACGTCAGACCAAG
1 TGACGTGGCAATGCCACGTCAGACCAAG
34105 TGCCACATCA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.33, C:0.26, G:0.27, T:0.14
Consensus pattern (32 bp):
TGACGTGGCAATGCCACGTCAGACCAAGGCAA
Found at i:34538 original size:4 final size:4
Alignment explanation
Indices: 34529--34564 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
34519 CCTCTTTATT
* *
34529 ATAA ATAA ATAT ATAA ATAA ATAA ATAA ATTA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
34565 TAATAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (4 bp):
ATAA
Found at i:36235 original size:18 final size:19
Alignment explanation
Indices: 36199--36236 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
36189 AATTTGGTTG
36199 AAAAGTTTTAATTGCACTAA
1 AAAAGTTTTAATT-CACTAA
36219 AAAAGTTTTAATT-ACTAA
1 AAAAGTTTTAATTCACTAA
36237 TTGTTAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
20 13 0.72
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (19 bp):
AAAAGTTTTAATTCACTAA
Found at i:37627 original size:2 final size:2
Alignment explanation
Indices: 37620--37657 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
37610 TACAGTTTTA
37620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37658 GTATGTATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38346 original size:33 final size:33
Alignment explanation
Indices: 38304--38371 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
38294 ATTAGACACC
*
38304 TTGTCATCAAAATGATCCTTTATAGCCTTGGCA
1 TTGTCATCAAAATGATCCTTTATAGCCTTGACA
**
38337 TTGTCATCAATCTGATCCTTTATAGCCTTGACA
1 TTGTCATCAAAATGATCCTTTATAGCCTTGACA
38370 TT
1 TT
38372 CTTATCAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (33 bp):
TTGTCATCAAAATGATCCTTTATAGCCTTGACA
Found at i:38379 original size:33 final size:33
Alignment explanation
Indices: 38307--38382 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
38297 AGACACCTTG
** * *
38307 TCATCAAAATGATCCTTTATAGCCTTGGCATTG
1 TCATCAATCTGATCCTTTATAGCCTTGACATTC
38340 TCATCAATCTGATCCTTTATAGCCTTGACATTC
1 TCATCAATCTGATCCTTTATAGCCTTGACATTC
*
38373 TTATCAATCT
1 TCATCAATCT
38383 CATCTTCTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (33 bp):
TCATCAATCTGATCCTTTATAGCCTTGACATTC
Found at i:38836 original size:60 final size:60
Alignment explanation
Indices: 38700--38815 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
38690 TACAAAGAGA
* * * *
38700 AGAAGAGAAGACGAGAAGACAATAAACACTCCATACAGTGAGAGCAATGAAATCCAAAAG
1 AGAAGACAAGACGAGAAGACAATAAACACTCCACACAGAGAGAGCAATCAAATCCAAAAG
* *
38760 AGAAGAGAAGACGAGAAGACAATAAACACTCCACACTCAGAGAGAGTAATCAAATC
1 AGAAGACAAGACGAGAAGACAATAAACACTCCACA--CAGAGAGAGCAATCAAATC
38816 AAATCGCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 34 0.68
62 16 0.32
ACGTcount: A:0.51, C:0.18, G:0.21, T:0.10
Consensus pattern (60 bp):
AGAAGACAAGACGAGAAGACAATAAACACTCCACACAGAGAGAGCAATCAAATCCAAAAG
Found at i:39001 original size:31 final size:31
Alignment explanation
Indices: 38963--39022 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
38953 AACCAGAACA
38963 GAGATTGAGATGTGATTCAAGATATAAAGAT
1 GAGATTGAGATGTGATTCAAGATATAAAGAT
*
38994 GAGATTGAGATGTGATTCGAGATATAAAG
1 GAGATTGAGATGTGATTCAAGATATAAAG
39023 TGATATAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.03, G:0.28, T:0.28
Consensus pattern (31 bp):
GAGATTGAGATGTGATTCAAGATATAAAGAT
Found at i:40459 original size:30 final size:30
Alignment explanation
Indices: 40425--40482 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
40415 AAAGTTGGAG
*
40425 GGCTT-TTTGGTCATTCTGAAAAAAGTAGTT
1 GGCTTATTTAGTCATTCTG-AAAAAGTAGTT
*
40455 GGCTTATTTAGTCATTTTGAAAAAGTAG
1 GGCTTATTTAGTCATTCTGAAAAAGTAG
40483 AGGGCCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (30 bp):
GGCTTATTTAGTCATTCTGAAAAAGTAGTT
Found at i:42793 original size:2 final size:2
Alignment explanation
Indices: 42786--42814 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42776 TGTTTAAGCG
42786 AT AT 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 AT AT A
42815 GAAGATTGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.