Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015891.1 Corchorus capsularis cultivar CVL-1 contig15912, 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: 28650
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:191 original size:38 final size:37
Alignment explanation
Indices: 127--219 Score: 109
Period size: 38 Copynumber: 2.5 Consensus size: 37
117 AATTTGACTT
*
127 TTTGTTTCTAACGTCCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCTAACGTCCTATTTAATTTTGCATTTTGTC
**
164 TTTGTTTCTAATCGTTGTATTTAATTTTGCATTTTTGT-
1 TTTGTTTCTAA-CGTCCTATTTAATTTTGCA-TTTTGTC
202 TTTCGTCTTC-AACGTCCT
1 TTT-GT-TTCTAACGTCCT
220 GTTTGGGCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
37 11 0.23
38 23 0.49
39 10 0.21
40 3 0.06
ACGTcount: A:0.14, C:0.17, G:0.12, T:0.57
Consensus pattern (37 bp):
TTTGTTTCTAACGTCCTATTTAATTTTGCATTTTGTC
Found at i:309 original size:22 final size:22
Alignment explanation
Indices: 281--403 Score: 108
Period size: 22 Copynumber: 5.6 Consensus size: 22
271 TGATCCAATT
* *
281 TCAAAATTTCAAAGCGCGGTTA
1 TCAAAATTTCAAAGAGAGGTTA
* *
303 TCAAAATTACATAATGTGA--TTA
1 TCAAAATTTCA-AA-GAGAGGTTA
* *
325 TCAAAATTTCATAGAGGGGTTA
1 TCAAAATTTCAAAGAGAGGTTA
* * *
347 ACAAAATTTTATAGAGAGGTTA
1 TCAAAATTTCAAAGAGAGGTTA
369 TCAAAATTTCATAA-AGAGGTTA
1 TCAAAATTTCA-AAGAGAGGTTA
*
391 TCAAATTTTCAAA
1 TCAAAATTTCAAA
404 ATATAATTAC
Statistics
Matches: 82, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.02
21 3 0.04
22 72 0.88
23 3 0.04
24 2 0.02
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.33
Consensus pattern (22 bp):
TCAAAATTTCAAAGAGAGGTTA
Found at i:346 original size:44 final size:44
Alignment explanation
Indices: 281--426 Score: 141
Period size: 44 Copynumber: 3.3 Consensus size: 44
271 TGATCCAATT
* * * *
281 TCAAAATTTCAAAGCGCGGTTATCAAAATTACATAATGTGATTA
1 TCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGATTA
* * * * *
325 TCAAAATTTCATAGAGGGGTTAACAAAATTTTATAGA-GAGGTTA
1 TCAAAATTTCATAGAGAGGTTATCAAAATTTCATA-ATGTGATTA
* * * * *
369 TCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATATAATTA
1 TCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGATTA
*
413 CCAAAATTTCATAG
1 TCAAAATTTCATAG
427 TGGTATTTCT
Statistics
Matches: 80, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
43 1 0.01
44 78 0.98
45 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (44 bp):
TCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGATTA
Found at i:744 original size:23 final size:22
Alignment explanation
Indices: 714--815 Score: 98
Period size: 23 Copynumber: 4.5 Consensus size: 22
704 TTTCATGCGG
*
714 TTATCAAAATTTTACAGGGAGTT
1 TTATCAAAATTTTATAGGGAG-T
* *
737 TTATCAAAATTTTATTGGAAGGT
1 TTATCAAAATTTTATAGGGA-GT
* *
760 TTATCAAAATTTTATAGCGAGG
1 TTATCAAAATTTTATAGGGAGT
* * *
782 TTATCACAATTTTATA-GTATGA
1 TTATCAAAATTTTATAGGGA-GT
804 TTATCAAAATTT
1 TTATCAAAATTT
816 CAGACTGTGA
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
21 1 0.02
22 28 0.43
23 35 0.54
24 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGAGT
Found at i:792 original size:22 final size:21
Alignment explanation
Indices: 439--815 Score: 138
Period size: 22 Copynumber: 17.8 Consensus size: 21
429 GTATTTCTGG
*
439 GGAGGTTATCAAAATTTCATA
1 GGAGGTTATCAAAATTTTATA
* *
460 GTATGGTTA-CCAAA---T-TA
1 GGA-GGTTATCAAAATTTTATA
* *
477 GGAAGGTTATTAAACTTTTATTA
1 GG-AGGTTATCAAAATTTTA-TA
* * *
500 TGGA-GTAATCAAAATTTCA-G
1 -GGAGGTTATCAAAATTTTATA
* *
520 GGAGGATATCAAAATTTCATA
1 GGAGGTTATCAAAATTTTATA
*
541 TGAAGGTTATC-AAATTTTCATA
1 -GGAGGTTATCAAAATTTT-ATA
* *
563 GTTTA-GTTTTCAAAATTTTATAA
1 G--GAGGTTATCAAAATTTTAT-A
* *
586 GAAGGTTATCAAAATTTCATA
1 GGAGGTTATCAAAATTTTATA
* * * *
607 GTATGTAGATCAAAATTTCATA
1 GGAGGT-TATCAAAATTTTATA
* * *
629 GGGAGATTAACAAAATTTCATAA
1 -GGAGGTTATCAAAATTTTAT-A
* * ** *
652 TGAGGTTATAAAAAAATCATA
1 GGAGGTTATCAAAATTTTATA
673 GGAAGGTTATCAAAA--TT-T-
1 GG-AGGTTATCAAAATTTTATA
* * *
691 GTA-GTTATCAAGATTTCAT-
1 GGAGGTTATCAAAATTTTATA
* *
710 -GCGGTTATCAAAATTTTACA
1 GGAGGTTATCAAAATTTTATA
* *
730 GGGAGTTTTATCAAAATTTTATT
1 -GGAG-GTTATCAAAATTTTATA
753 GGAAGGTTTATCAAAATTTTATA
1 GG-AGG-TTATCAAAATTTTATA
*
776 GCGAGGTTATCACAATTTTATA
1 G-GAGGTTATCAAAATTTTATA
* *
798 GTATGATTATCAAAATTT
1 GGA-GGTTATCAAAATTT
816 CAGACTGTGA
Statistics
Matches: 264, Mismatches: 58, Indels: 67
0.68 0.15 0.17
Matches are distributed among these distances:
16 9 0.03
17 9 0.03
18 5 0.02
19 18 0.07
20 14 0.05
21 23 0.09
22 131 0.50
23 52 0.20
24 3 0.01
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.37
Consensus pattern (21 bp):
GGAGGTTATCAAAATTTTATA
Found at i:1004 original size:22 final size:22
Alignment explanation
Indices: 978--1026 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
968 TTCCTTAAGG
*
978 AGGTT-AATAAAATTTCATAAAA
1 AGGTTAAAAAAAATTT-ATAAAA
*
1000 TGGTTAAAAAAAATTTATAAAA
1 AGGTTAAAAAAAATTTATAAAA
1022 AGGTT
1 AGGTT
1027 CTCGAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (22 bp):
AGGTTAAAAAAAATTTATAAAA
Found at i:1072 original size:22 final size:22
Alignment explanation
Indices: 1028--1084 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
1018 AAAAAGGTTC
* *
1028 TCGAAATTTCATAGTATCGTTA
1 TCGAAATTTCATAGGATAGTTA
*
1050 TTGAAATTTCATAGGA-AGATTA
1 TCGAAATTTCATAGGATAG-TTA
*
1072 TCAAAATTTCATA
1 TCGAAATTTCATA
1085 AAGACGTCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.39
Consensus pattern (22 bp):
TCGAAATTTCATAGGATAGTTA
Found at i:1150 original size:40 final size:39
Alignment explanation
Indices: 1068--1175 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 39
1058 TCATAGGAAG
* * *
1068 ATTATCAAAATTTCATAAAGACGTCAT-AAAAATAGTGTA
1 ATTATCATAATTTCATAAA-AGGTTATCAAAAATAGTGTA
1107 ATTATCATAATTTCATAAGAAGGTTATCAAAAATAGTGTA
1 ATTATCATAATTTCATAA-AAGGTTATCAAAAATAGTGTA
*
1147 ATTATCATAATTTAATAAAAAGGTTATCA
1 ATTATCATAATTTCAT-AAAAGGTTATCA
1176 TAATTTCGTA
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
39 22 0.35
40 38 0.61
41 2 0.03
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.34
Consensus pattern (39 bp):
ATTATCATAATTTCATAAAAGGTTATCAAAAATAGTGTA
Found at i:1969 original size:12 final size:12
Alignment explanation
Indices: 1952--1986 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1942 TCAAGATGAT
1952 TCTTCTTCTTCA
1 TCTTCTTCTTCA
*
1964 TCTTCTTCTGCA
1 TCTTCTTCTTCA
*
1976 TCTTCATCTTC
1 TCTTCTTCTTC
1987 CCCTGGTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.34, G:0.03, T:0.54
Consensus pattern (12 bp):
TCTTCTTCTTCA
Found at i:5362 original size:2 final size:2
Alignment explanation
Indices: 5355--5386 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5345 CAGTTCAGAA
5355 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
5387 TGGCAAGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6023 original size:16 final size:18
Alignment explanation
Indices: 5982--6025 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
5972 GAAGGATTGG
5982 CTCTTCCCACCTCTTAGC
1 CTCTTCCCACCTCTTAGC
*
6000 CTCCTCCC-CCTC-TAGC
1 CTCTTCCCACCTCTTAGC
*
6016 TTCTTCCCAC
1 CTCTTCCCAC
6026 TTCACTACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 10 0.45
17 5 0.23
18 7 0.32
ACGTcount: A:0.09, C:0.55, G:0.05, T:0.32
Consensus pattern (18 bp):
CTCTTCCCACCTCTTAGC
Found at i:13029 original size:29 final size:30
Alignment explanation
Indices: 12996--13065 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
12986 GACGTTTTTT
* *
12996 CCCCTGAACTTTAATCTT-GGACATTTTGC
1 CCCCTGAACTTCAATCTTGGGACATTTTAC
* *
13025 CCCCTGAACTTCAATTTTGGGACGTTTTAC
1 CCCCTGAACTTCAATCTTGGGACATTTTAC
*
13055 CCCCTTAACTT
1 CCCCTGAACTT
13066 AACGGCTCCG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 16 0.46
30 19 0.54
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (30 bp):
CCCCTGAACTTCAATCTTGGGACATTTTAC
Found at i:13065 original size:30 final size:29
Alignment explanation
Indices: 12986--13065 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
12976 GTAGCGTTTA
** *
12986 GACGTTTTTTCCCCTGAACTTTAATCTTG
1 GACGTTTTACCCCCTGAACTTCAATCTTG
* * *
13015 GACATTTTGCCCCCTGAACTTCAATTTTGG
1 GACGTTTTACCCCCTGAACTTCAATCTT-G
*
13045 GACGTTTTACCCCCTTAACTT
1 GACGTTTTACCCCCTGAACTT
13066 AACGGCTCCG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 23 0.55
30 19 0.45
ACGTcount: A:0.19, C:0.28, G:0.14, T:0.40
Consensus pattern (29 bp):
GACGTTTTACCCCCTGAACTTCAATCTTG
Found at i:19589 original size:19 final size:19
Alignment explanation
Indices: 19565--19602 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
19555 ATCGGTGCTT
19565 ATCGGT-TTAGTTGGCTTTA
1 ATCGGTGTTAGTTGG-TTTA
19584 ATCGGTGTTAGTTGGTTTA
1 ATCGGTGTTAGTTGGTTTA
19603 CAATTGCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.16, C:0.08, G:0.29, T:0.47
Consensus pattern (19 bp):
ATCGGTGTTAGTTGGTTTA
Found at i:24455 original size:28 final size:28
Alignment explanation
Indices: 24419--24490 Score: 126
Period size: 28 Copynumber: 2.6 Consensus size: 28
24409 CTAGGACGTC
*
24419 TCCCTCTGATGTATCAGGCGTAAAATTG
1 TCCCTCTGATGTATCAGGCGTAAAATCG
*
24447 TCCTTCTGATGTATCAGGCGTAAAATCG
1 TCCCTCTGATGTATCAGGCGTAAAATCG
24475 TCCCTCTGATGTATCA
1 TCCCTCTGATGTATCA
24491 CATGGCATGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (28 bp):
TCCCTCTGATGTATCAGGCGTAAAATCG
Found at i:25811 original size:49 final size:49
Alignment explanation
Indices: 25758--26122 Score: 302
Period size: 49 Copynumber: 7.6 Consensus size: 49
25748 AAAAAGCGAC
** ***
25758 GCCTTCCGTCCGGGAAGGAGTGTTTTAGGAAA-AACAAATAAAAATTGGT
1 GCCTTCCGTCCGGGAAGG-GCATTTTAGGAAATAACAAATAAAAACAAGT
* * * *
25807 GCCTTCTGTCCGGGAAGGGCATTTTGGGAAATAGCAGATAAAAACAAGT
1 GCCTTCCGTCCGGGAAGGGCATTTTAGGAAATAACAAATAAAAACAAGT
* * * *
25856 GCCTTCCGTCCGGGAAGGGCATTTT-GGGAATAGCAGAT---GA-AAGT
1 GCCTTCCGTCCGGGAAGGGCATTTTAGGAAATAACAAATAAAAACAAGT
* ** ** * *
25900 GCCTTCCGTCCGGGAA-GGCATTTTTGGAAAATAGTAGGTAAAAATAAAT
1 GCCTTCCGTCCGGGAAGGGCATTTTAGG-AAATAACAAATAAAAACAAGT
* * *
25949 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGATAAAAACAAGT
1 GCCTTCCGTCCGGGAAGGGCATTTTAGGAAATAACAAATAAAAACAAGT
* * * * * *
25998 GCCTTCCGTCTGGGAAGGGCATTTTGGGAAATAGCAGATAAAATCAAAT
1 GCCTTCCGTCCGGGAAGGGCATTTTAGGAAATAACAAATAAAAACAAGT
* * * * * * *
26047 TCCTTCCATCTGGGAAGGGCATTTTGGGAAATAGCAGAT---GA-AAGT
1 GCCTTCCGTCCGGGAAGGGCATTTTAGGAAATAACAAATAAAAACAAGT
*
26092 GCCTTCCGTCCGGGAAGGGCATTTTTGGAAA
1 GCCTTCCGTCCGGGAAGGGCATTTTAGGAAA
26123 ATAGCAAGTG
Statistics
Matches: 274, Mismatches: 34, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
43 8 0.03
44 22 0.08
45 39 0.14
48 23 0.08
49 172 0.63
50 10 0.04
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (49 bp):
GCCTTCCGTCCGGGAAGGGCATTTTAGGAAATAACAAATAAAAACAAGT
Found at i:26145 original size:98 final size:94
Alignment explanation
Indices: 25805--26128 Score: 456
Period size: 98 Copynumber: 3.4 Consensus size: 94
25795 ATAAAAATTG
* * * *
25805 GTGCCTTCTGTCCGGGAAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
1 GTGCCTTCCGTCCGGGAAGGGCATTTTGGAAAATAGCAGATAAAAATAAATGCCTTCCGTCCGGG
25870 AAGGGCATTTTGGG-AATAGCAGATGAAA
66 AAGGGCATTTTGGGAAATAGCAGATGAAA
* *
25898 GTGCCTTCCGTCCGGGAA-GGCATTTTTGGAAAATAGTAGGTAAAAATAAATGCCTTCCGTCCGG
1 GTGCCTTCCGTCCGGGAAGGGCA-TTTTGGAAAATAGCAGATAAAAATAAATGCCTTCCGTCCGG
*
25962 GAAGGGCATTTTGGGAAATAGCAGATAAAAACAA
65 GAAGGGCATTTTGGGAAATAGCAGAT---GA-AA
* * * * *
25996 GTGCCTTCCGTCTGGGAAGGGCATTTTGGGAAATAGCAGAT-AAAATCAAATTCCTTCCATCTGG
1 GTGCCTTCCGTCCGGGAAGGGCATTTTGGAAAATAGCAGATAAAAAT-AAATGCCTTCCGTCCGG
26060 GAAGGGCATTTTGGGAAATAGCAGATGAAA
65 GAAGGGCATTTTGGGAAATAGCAGATGAAA
26090 GTGCCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCA
1 GTGCCTTCCGTCCGGGAAGGGCA-TTTTGGAAAATAGCA
26129 AGTGAGAACT
Statistics
Matches: 205, Mismatches: 17, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
92 4 0.02
93 68 0.33
94 34 0.17
95 15 0.07
97 6 0.03
98 74 0.36
99 4 0.02
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (94 bp):
GTGCCTTCCGTCCGGGAAGGGCATTTTGGAAAATAGCAGATAAAAATAAATGCCTTCCGTCCGGG
AAGGGCATTTTGGGAAATAGCAGATGAAA
Done.