Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010986.1 Corchorus capsularis cultivar CVL-1 contig11007, 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: 24570
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2845 original size:82 final size:81
Alignment explanation
Indices: 2634--2878 Score: 322
Period size: 78 Copynumber: 3.0 Consensus size: 81
2624 ATATGGACTA
* * * *
2634 TTGAAATTAATGATGAATTATTTGAATTAATAATTAATGGAGGTCATTTGGTTAGTATTATTGAT
1 TTGAAATTAATGATAAATTATTAGAATTAATAATTGATGGAGGTCATTTGATTAGTATTATTGAT
* * *
2699 TAGCT----ATGGACTA-
66 T-GGTAAAAATTG-TTAT
2712 TTGAAATTAATGATAAATTATTAGAATTAATAATTGATGGAGGTCATTTGATTAGTATTATTGAT
1 TTGAAATTAATGATAAATTATTAGAATTAATAATTGATGGAGGTCATTTGATTAGTATTATTGAT
2777 TGGTAAAAATTGTTAT
66 TGGTAAAAATTGTTAT
* * *
2793 TTGAATTTTATGATAAATTTTTAGAAATTAATAATTGATGGAGGTCCA-TTGATTAGTATTATTG
1 TTGAAATTAATGATAAATTATTAG-AATTAATAATTGATGGAGGT-CATTTGATTAGTATTATTG
2857 ATTGGTAAAAATTGTTAT
64 ATTGGTAAAAATTGTTAT
2875 TTGA
1 TTGA
2879 TCTGTGTTAG
Statistics
Matches: 150, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
77 2 0.01
78 62 0.41
80 2 0.01
81 24 0.16
82 58 0.39
83 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.44
Consensus pattern (81 bp):
TTGAAATTAATGATAAATTATTAGAATTAATAATTGATGGAGGTCATTTGATTAGTATTATTGAT
TGGTAAAAATTGTTAT
Found at i:3045 original size:3 final size:3
Alignment explanation
Indices: 3037--3069 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3027 GGATTTATCT
3037 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3070 TATTACTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6615 original size:183 final size:183
Alignment explanation
Indices: 6306--6663 Score: 680
Period size: 183 Copynumber: 2.0 Consensus size: 183
6296 TTGAGCAAAC
6306 TTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGATTGTGATTGCTTAATTGTTTGTG
1 TTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGATTGTGATTGCTTAATTGTTTGTG
*
6371 AATCTTGTGATCTTAAGAGTTCAAGTGCAGATCGACTTGGAGGTCTAAGGCCGACGAACAAAGGA
66 AATCTTGTGATCTAAAGAGTTCAAGTGCAGATCGACTTGGAGGTCTAAGGCCGACGAACAAAGGA
6436 AGATTTATCAAGTGAAGATTATCGACATACTCATCTAGAAGTTTGTATTAGGG
131 AGATTTATCAAGTGAAGATTATCGACATACTCATCTAGAAGTTTGTATTAGGG
*
6489 TTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTGATTGCTTAATTGTTTGTG
1 TTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGATTGTGATTGCTTAATTGTTTGTG
* *
6554 AATCTTGTGATCTAAAGTGTTCAAGTGCAGATCGACTTGGAGGTCTAAGGCCGATGAACAAAGGA
66 AATCTTGTGATCTAAAGAGTTCAAGTGCAGATCGACTTGGAGGTCTAAGGCCGACGAACAAAGGA
6619 AGATTTATCAAGTGAAGATTATCGACATACTCATCTAGAAGTTTG
131 AGATTTATCAAGTGAAGATTATCGACATACTCATCTAGAAGTTTG
6664 GTGATTCAAG
Statistics
Matches: 171, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
183 171 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (183 bp):
TTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGATTGTGATTGCTTAATTGTTTGTG
AATCTTGTGATCTAAAGAGTTCAAGTGCAGATCGACTTGGAGGTCTAAGGCCGACGAACAAAGGA
AGATTTATCAAGTGAAGATTATCGACATACTCATCTAGAAGTTTGTATTAGGG
Found at i:7250 original size:10 final size:10
Alignment explanation
Indices: 7235--7269 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
7225 CTGGTCGAAA
7235 TTTTTTTTAT
1 TTTTTTTTAT
7245 TTTTTTTTAT
1 TTTTTTTTAT
*
7255 TTTTTCTATAT
1 TTTTT-TTTAT
7266 TTTT
1 TTTT
7270 CGATATAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:8714 original size:2 final size:2
Alignment explanation
Indices: 8702--8734 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
8692 TTCTACATGA
8702 AT AT GAT 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
8735 CATTATTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9953 original size:32 final size:32
Alignment explanation
Indices: 9917--9978 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
9907 GGCATTAGCA
*
9917 TTAGCAGTTTGGCATTGTCTTATATGAAATGG
1 TTAGCAGTTTGGCATTGTCTTACATGAAATGG
9949 TTAGCAGTTTGGCATTGTCTTACATGAAAT
1 TTAGCAGTTTGGCATTGTCTTACATGAAAT
9979 CGTTTTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (32 bp):
TTAGCAGTTTGGCATTGTCTTACATGAAATGG
Found at i:10007 original size:22 final size:22
Alignment explanation
Indices: 9982--10026 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
9972 ATGAAATCGT
9982 TTTAATAATATAATTTGGTTCA
1 TTTAATAATATAATTTGGTTCA
*
10004 TTTAGTAATATAATTTGGTTCA
1 TTTAATAATATAATTTGGTTCA
10026 T
1 T
10027 ATTAGTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (22 bp):
TTTAATAATATAATTTGGTTCA
Found at i:10108 original size:31 final size:31
Alignment explanation
Indices: 10070--10134 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
10060 AGTCTACATC
*
10070 TAAATAGAACTGGCATTAGAATTATTTTGGT
1 TAAATAGAACTGGCATTAGAATCATTTTGGT
* *
10101 TAAATAGAATTGGCATTAGAGTCATTTTGGT
1 TAAATAGAACTGGCATTAGAATCATTTTGGT
10132 TAA
1 TAA
10135 TTAGCTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.38
Consensus pattern (31 bp):
TAAATAGAACTGGCATTAGAATCATTTTGGT
Found at i:13485 original size:29 final size:28
Alignment explanation
Indices: 13420--13487 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
13410 AAGTTTTCAA
*
13420 AGTTTT-AGATTTAGTGAAAGATCCCGCC
1 AGTTTTCA-ATTTAGGGAAAGATCCCGCC
*
13448 A-TATCTTCAATTTAGGGAAAGATCCCATCC
1 AGT-T-TTCAATTTAGGGAAAGATCCC-GCC
13478 AGTTTTCAAT
1 AGTTTTCAAT
13488 GTTTTCAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
27 1 0.03
28 2 0.06
29 24 0.73
30 5 0.15
31 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (28 bp):
AGTTTTCAATTTAGGGAAAGATCCCGCC
Found at i:14327 original size:35 final size:35
Alignment explanation
Indices: 14263--14404 Score: 151
Period size: 35 Copynumber: 4.1 Consensus size: 35
14253 ATTCGGTGAA
* * *
14263 TCAGATGACTCGGTGCAACATCTTT-AAAGTTGGAT
1 TCAGATGACTCAGTGTAGCAT-TTTCAAAGTTGGAT
* *
14298 TTAGATGACTCAATGTAGCATTTTCAAAGTTGGAT
1 TCAGATGACTCAGTGTAGCATTTTCAAAGTTGGAT
* * * *
14333 TCAAATAACTCAGTGTAGCATTTTCAATGTTGGAA
1 TCAGATGACTCAGTGTAGCATTTTCAAAGTTGGAT
* * **
14368 TCAGTTGACTCGGTGTAGCATCATCAAAGTTGGAT
1 TCAGATGACTCAGTGTAGCATTTTCAAAGTTGGAT
14403 TC
1 TC
14405 GTTGAGCTCG
Statistics
Matches: 87, Mismatches: 19, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
34 3 0.03
35 84 0.97
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (35 bp):
TCAGATGACTCAGTGTAGCATTTTCAAAGTTGGAT
Found at i:14578 original size:91 final size:91
Alignment explanation
Indices: 14393--14618 Score: 307
Period size: 91 Copynumber: 2.5 Consensus size: 91
14383 TAGCATCATC
* * *
14393 AAAG-TTGGATTCGTTGAGCTCGGTACAGCACATTTTCAAACAG-TCAGGATGATCCAGTGAATC
1 AAAGATTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAAGATGATCCAGTGAATC
*
14456 ATGTTAGTGCGGTGCATTATTTCTTA
66 ATGTTAGTGCGGTGCATAATTTCTTA
* *
14482 AAAGATTTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAAGATGATTCGGTGAAT
1 AAAGA-TTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAAGATGATCCAGTGAAT
*
14547 CATGTTGAG-GCGGTGCCTAATTTCTT-
65 CATGTT-AGTGCGGTGCATAATTTCTTA
* * * *
14573 CAAGATTGGATTCAGTGAGCTCGGTGTAGCAAATTTTCAAACAGTT
1 AAAGATTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTT
14619 TAGACTTGAT
Statistics
Matches: 122, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
89 4 0.03
90 38 0.31
91 41 0.34
92 37 0.30
93 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (91 bp):
AAAGATTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAAGATGATCCAGTGAATC
ATGTTAGTGCGGTGCATAATTTCTTA
Found at i:15853 original size:31 final size:31
Alignment explanation
Indices: 15818--15879 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
15808 CACAAGAGAA
* *
15818 CTCTTGATTCATGAATAATTACAATATTCAT
1 CTCTTGATTCATGAATAATCACAATACTCAT
15849 CTCTTGATTCATGAATAATCACAATACTCAT
1 CTCTTGATTCATGAATAATCACAATACTCAT
15880 TAATGACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (31 bp):
CTCTTGATTCATGAATAATCACAATACTCAT
Found at i:17984 original size:41 final size:42
Alignment explanation
Indices: 17920--18004 Score: 127
Period size: 41 Copynumber: 2.0 Consensus size: 42
17910 AAATAAAAAG
*
17920 GAGATCCTTAAAGCTAAATAATTGAACTTGTGATTAATTAAT
1 GAGATCCTTAAAGCTAAAAAATTGAACTTGTGATTAATTAAT
* * *
17962 GAGATCCTT-GAGCTAAAAAATTGAACTTGTGGTTAATTTAT
1 GAGATCCTTAAAGCTAAAAAATTGAACTTGTGATTAATTAAT
18003 GA
1 GA
18005 TAAGAATGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 30 0.77
42 9 0.23
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (42 bp):
GAGATCCTTAAAGCTAAAAAATTGAACTTGTGATTAATTAAT
Found at i:17990 original size:93 final size:91
Alignment explanation
Indices: 17882--18049 Score: 230
Period size: 93 Copynumber: 1.8 Consensus size: 91
17872 CTTCTTAAGT
*
17882 TAAAAGATTGAACTTGTGGTTAATTTATAAATAAAAAGGAGATCCTT-AAAGCTAAATAATTGAA
1 TAAAAAATTGAACTTGTGGTTAATTTAT-AATAAAAAGGAGATCCTTGAAA--TAAATAATTGAA
*
17946 CTTGTGATTAATTAATGAGATCCTTGAGC
63 CTTGTGATCAATTAATGAGATCCTTGAGC
* * * * *
17975 TAAAAAATTGAACTTGTGGTTAATTTATGATAAGAATGAGATCTTTGAAATAAATGATTGAACTT
1 TAAAAAATTGAACTTGTGGTTAATTTATAATAAAAAGGAGATCCTTGAAATAAATAATTGAACTT
*
18040 TTGATCAATT
66 GTGATCAATT
18050 TGTAATAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
91 22 0.33
92 14 0.21
93 30 0.45
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (91 bp):
TAAAAAATTGAACTTGTGGTTAATTTATAATAAAAAGGAGATCCTTGAAATAAATAATTGAACTT
GTGATCAATTAATGAGATCCTTGAGC
Found at i:18686 original size:48 final size:48
Alignment explanation
Indices: 18589--19069 Score: 585
Period size: 48 Copynumber: 10.0 Consensus size: 48
18579 AATTCAAGAG
* * * *
18589 ATTTT-AGATGTCAATTCCCTGTTTTGCCCTTCTCGGTCGGAAGGCGCT
1 ATTTTCAG-TGTCTATTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
* * * * *
18637 ATATTCAGTGTTTCTTTCCTATTTTGCCCTTCCCGATCGGAAGGTGCT
1 ATTTTCAGTGTCTATTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
* *
18685 ATTTTCAGTATCTATTTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGCT
1 ATTTTCAGTGTCTATTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
** * *
18733 ACCTTCAGTGTTTCTTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
1 ATTTTCAGTGTCTATTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
* * *
18781 ATTTTCAGTATCTATTTCCCGTTTTGCCCTTCCCAGTCGGAAGGTGCT
1 ATTTTCAGTGTCTATTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
*** * * *
18829 ACCATCAGTGTCAATTTCCTGTTTTGCCCTTCCCAGTTGGAAGGTGC-
1 ATTTTCAGTGTCTATTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
* *
18876 AGTTTTCAGTGTCTATTTCCAGTTTTGCCCTTCCCGGTCGAAAGGTGCT
1 A-TTTTCAGTGTCTATTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
* * *
18925 ATCTTCAGTGTTTATTTCCAT-TTTTGCCCTTCCCGGTCCGAAGGTG-T
1 ATTTTCAGTGTCTATTTCC-TGTTTTGCCCTTCCCGGTCGGAAGGTGCT
* *
18972 AGTCTTT-AGTGTTTATTTCCTGTTTTGTCCTTCCCGGTCGGAAGGTGCT
1 A-T-TTTCAGTGTCTATTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
* *
19021 ATTTTCAGTGTCTATTTCCAGTTTTGCCCTTCCCAGTCGGAAGGTGCT
1 ATTTTCAGTGTCTATTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
19069 A
1 A
19070 GATTTGTCTT
Statistics
Matches: 368, Mismatches: 56, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
47 7 0.02
48 354 0.96
49 7 0.02
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.40
Consensus pattern (48 bp):
ATTTTCAGTGTCTATTTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT
Found at i:19618 original size:20 final size:19
Alignment explanation
Indices: 19593--19635 Score: 77
Period size: 20 Copynumber: 2.2 Consensus size: 19
19583 AGAAGAGTTC
19593 GCCTTCCTCAGCAAGTAAA
1 GCCTTCCTCAGCAAGTAAA
19612 TGCCTTCCTCAGCAAGTAAA
1 -GCCTTCCTCAGCAAGTAAA
19632 GCCT
1 GCCT
19636 GCCAGTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (19 bp):
GCCTTCCTCAGCAAGTAAA
Found at i:22086 original size:33 final size:33
Alignment explanation
Indices: 22044--22111 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
22034 ATAAGTACTC
22044 ATGATTTGCACTCAAGAATAGTACTTGGTACAA
1 ATGATTTGCACTCAAGAATAGTACTTGGTACAA
22077 ATGATTTGCACTCAAGAATAGTACTTGGTACAA
1 ATGATTTGCACTCAAGAATAGTACTTGGTACAA
22110 AT
1 AT
22112 ATAAGGGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (33 bp):
ATGATTTGCACTCAAGAATAGTACTTGGTACAA
Found at i:23675 original size:1 final size:1
Alignment explanation
Indices: 23671--23698 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
23661 CCCCCACCAA
23671 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
23699 TCAAATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:24335 original size:21 final size:21
Alignment explanation
Indices: 24309--24353 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
24299 AAAAATTCCA
24309 TAATTTA-CTAAATATGTATTT
1 TAATTTATCTAAAT-TGTATTT
* *
24330 TAATTTATTTAAATTGTGTTT
1 TAATTTATCTAAATTGTATTT
24351 TAA
1 TAA
24354 GGCCCTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (21 bp):
TAATTTATCTAAATTGTATTT
Done.