Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007569.1 Corchorus capsularis cultivar CVL-1 contig07590, 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: 39873
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:551 original size:22 final size:22
Alignment explanation
Indices: 526--1127 Score: 188
Period size: 22 Copynumber: 27.9 Consensus size: 22
516 ATGATCTCAT
526 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* * *
548 TATGAAATTTTAATAATAC-TAC
1 TATGAAATTTTGATAA-CCTTCC
* * * **
570 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* ** *
592 TAT-AATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* *
613 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
635 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
657 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * **
679 AATTAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
702 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
723 ATTTG--A-TAT-AT-ACCTTCA
1 -TATGAAATTTTGATAACCTTCC
741 TATG-AATTGTT-AGTAA--TTGCAC
1 TATGAAATT-TTGA-TAACCTT-C-C
* * *
763 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
785 TATG-AATTTGTGATAACC-TCGC
1 TATGAAATTT-TGATAACCTTC-C
*
807 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
830 TATAAAATTTTGATGAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* *
853 TATAAAATTTTGATAACTTTCC
1 TATGAAATTTTGATAACCTTCC
* *
875 TATGAAATCTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
897 TAT-CATTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
918 TATGGAAATTTTTGTTAATCTCCC
1 TAT-GAAA-TTTTGATAACCTTCC
*** * *
942 TATGAAATTTTGATCTTCGTAC
1 TATGAAATTTTGATAACCTTCC
* *
964 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
** * **
986 TAAAAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* * *
1008 TATGGAATTTTAATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
1029 -CTGAAATTTTGATATCC-T-C
1 TATGAAATTTTGATAACCTTCC
* *
1048 TCTGAAATTTTGATTA-C-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
1068 ATAATAAAAGTTTAATAACCTTCC
1 -T-ATGAAATTTTGATAACCTTCC
* * *
1092 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCC
1109 TATGAAATTTTGATAACCT
1 TATGAAATTTTGATAACCT
1128 CCCCAAAATG
Statistics
Matches: 419, Mismatches: 116, Indels: 90
0.67 0.19 0.14
Matches are distributed among these distances:
17 16 0.04
18 7 0.02
19 6 0.01
20 36 0.09
21 47 0.11
22 215 0.51
23 74 0.18
24 17 0.04
25 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:861 original size:46 final size:44
Alignment explanation
Indices: 789--899 Score: 150
Period size: 46 Copynumber: 2.5 Consensus size: 44
779 TCACACTATG
* *
789 AATTTGTGATAACCTCGCTATGAAATTTTGATAAATCTTCCTATAA
1 AATTT-TGATAACCTCCCTATAAAATTTTGATAAAT-TTCCTATAA
* *
835 AATTTTGATGAACCTCCCTATAAAATTTTGATAACTTTCCTATGA
1 AATTTTGAT-AACCTCCCTATAAAATTTTGATAAATTTCCTATAA
*
880 AATCTTGATAACCTCCCTAT
1 AATTTTGATAACCTCCCTAT
900 CATTTTTGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
44 11 0.19
45 20 0.34
46 28 0.47
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (44 bp):
AATTTTGATAACCTCCCTATAAAATTTTGATAAATTTCCTATAA
Found at i:1059 original size:20 final size:20
Alignment explanation
Indices: 1013--1061 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1003 TAAACTATGG
*
1013 AATTTTAATATCCTCCCTGA
1 AATTTTGATATCCTCCCTGA
*
1033 AATTTTGATATCCTCTCTGA
1 AATTTTGATATCCTCCCTGA
1053 AATTTTGAT
1 AATTTTGAT
1062 TACTCCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (20 bp):
AATTTTGATATCCTCCCTGA
Found at i:2713 original size:25 final size:25
Alignment explanation
Indices: 2685--2734 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
2675 AGATAAAAAG
2685 CAAA-ATTAAATACAACGATTGGAAA
1 CAAAGATTAAATACAACG-TTGGAAA
*
2710 CAAAGATTAAATAGAACGTTGGAAA
1 CAAAGATTAAATACAACGTTGGAAA
2735 ATACCAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.54, C:0.10, G:0.16, T:0.20
Consensus pattern (25 bp):
CAAAGATTAAATACAACGTTGGAAA
Found at i:4623 original size:30 final size:32
Alignment explanation
Indices: 4580--4657 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 32
4570 TTTAATAATG
* *
4580 ACAATTTAGAAATATATGTTAAAAA-ATGGGT
1 ACAATTGAGAAATATATGTTAAAAATAAGGGT
*
4611 ACAATTG-GAAATATATTTTAAAAATAAGGGT
1 ACAATTGAGAAATATATGTTAAAAATAAGGGT
*
4642 ACAATTGAAAAATATA
1 ACAATTGAGAAATATA
4658 AAATTTCTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
30 16 0.39
31 18 0.44
32 7 0.17
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.31
Consensus pattern (32 bp):
ACAATTGAGAAATATATGTTAAAAATAAGGGT
Found at i:5086 original size:2 final size:2
Alignment explanation
Indices: 5079--5122 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
5069 CAGAGTCCAG
*
5079 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
5122 T
1 T
5123 TAAAGTACGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5411 original size:109 final size:109
Alignment explanation
Indices: 5215--5509 Score: 457
Period size: 109 Copynumber: 2.7 Consensus size: 109
5205 ACTATTATAG
* *
5215 TTTTATTCTACTAGAAACTCTATTTTTATTTAATTAAATTAAATCTAATATATTTATAATTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCA--T--TT-AATTAAATCTAATATATTTATAATTATTT
5280 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* *
5329 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATATTTATAATTATTTTATTT
*
5394 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* *
5438 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTAT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATATT-TATAATTATTTTAT
5502 TTTTACCA
64 TTTTACCA
5510 TTTTAATTTA
Statistics
Matches: 171, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
108 1 0.01
109 121 0.71
110 22 0.13
112 1 0.01
114 26 0.15
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.51
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATATTTATAATTATTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:9644 original size:133 final size:133
Alignment explanation
Indices: 9406--9678 Score: 537
Period size: 133 Copynumber: 2.1 Consensus size: 133
9396 AAATGAAATG
9406 TATTTGACTTTTGTTTTGATGTTTCAATTTAGGGGTTTATCAAAGAAAAAATTTAGAGTTTCCAA
1 TATTTGACTTTTGTTTTGATGTTTCAATTTAGGGGTTTATCAAAGAAAAAATTTAGAGTTTCCAA
9471 AACGGGGATTTTCGAAGAATGGTTGAAATTGAGCTGATTTATGAGTTGGGTTTGAGTTAGAGTTT
66 AACGGGGATTTTCGAAGAATGGTTGAAATTGAGCTGATTTATGAGTTGGGTTTGAGTTAGAGTTT
9536 CCT
131 CCT
9539 TATTTGACTTTTGTTTTGATGTTTCAATTTAGGGGTTTATCAAAGAAAAAATTTAGAGTTTCCAA
1 TATTTGACTTTTGTTTTGATGTTTCAATTTAGGGGTTTATCAAAGAAAAAATTTAGAGTTTCCAA
9604 AACGGGGATTTTCGAAGAATGGTTGAAATTGAGCTGATTTATGAGTTGGGTTTGAGTTAGAGTTT
66 AACGGGGATTTTCGAAGAATGGTTGAAATTGAGCTGATTTATGAGTTGGGTTTGAGTTAGAGTTT
9669 CCT
131 CCT
*
9672 TAATTGA
1 TATTTGA
9679 AAGCTACCTT
Statistics
Matches: 139, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 139 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (133 bp):
TATTTGACTTTTGTTTTGATGTTTCAATTTAGGGGTTTATCAAAGAAAAAATTTAGAGTTTCCAA
AACGGGGATTTTCGAAGAATGGTTGAAATTGAGCTGATTTATGAGTTGGGTTTGAGTTAGAGTTT
CCT
Found at i:10695 original size:5 final size:5
Alignment explanation
Indices: 10663--10697 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
10653 AAAAAACTTC
* *
10663 CCTTC CCTTT CCTTT CCTTT CCCTT CCTTT CCTTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT
10698 AAAAACTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (5 bp):
CCTTT
Found at i:10697 original size:15 final size:16
Alignment explanation
Indices: 10660--10697 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
10650 TTCAAAAAAC
*
10660 TTCCCTTCCCTTTCCT
1 TTCCTTTCCCTTTCCT
10676 TTCCTTTCCC-TTCCT
1 TTCCTTTCCCTTTCCT
10691 TTCCTTT
1 TTCCTTT
10698 AAAAACTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (16 bp):
TTCCTTTCCCTTTCCT
Found at i:13540 original size:21 final size:21
Alignment explanation
Indices: 13501--13540 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13491 AGGGGGCTGT
*
13501 TAAATACCGTCCTAGTTTTGC
1 TAAATACCGTCCCAGTTTTGC
*
13522 TAAATACCGTCCCATTTTT
1 TAAATACCGTCCCAGTTTT
13541 TACACTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (21 bp):
TAAATACCGTCCCAGTTTTGC
Found at i:13716 original size:21 final size:21
Alignment explanation
Indices: 13677--13716 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13667 GTTAGACCAA
** *
13677 ATTTTTTTTTTAAATAATATT
1 ATTTTTTTTAAAAAAAATATT
13698 ATTTTTTTTAAAAAAAATA
1 ATTTTTTTTAAAAAAAATA
13717 GCCGAGCTGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTTTTAAAAAAAATATT
Found at i:14078 original size:80 final size:80
Alignment explanation
Indices: 13945--14106 Score: 270
Period size: 80 Copynumber: 2.0 Consensus size: 80
13935 GATAGTTTCA
* ** * **
13945 AGATTAGAAAATGAAGTAAAGGGCAAAAGCGTAAAAAATGGGGCGGTGAATAGCAAAAATGGGGC
1 AGATTAGAAAATGAAGCAAAGAACAAAAGCGTAAAAAATGAGGCAATGAATAGCAAAAATGGGGC
14010 GGTATTTAGCAATCC
66 GGTATTTAGCAATCC
14025 AGATTAGAAAATGAAGCAAAGAACAAAAGCGTAAAAAATGAGGCAATGAATAGCAAAAATGGGGC
1 AGATTAGAAAATGAAGCAAAGAACAAAAGCGTAAAAAATGAGGCAATGAATAGCAAAAATGGGGC
14090 GGTATTTAGCAATCC
66 GGTATTTAGCAATCC
14105 AG
1 AG
14107 TTTTTTAATC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.46, C:0.10, G:0.27, T:0.17
Consensus pattern (80 bp):
AGATTAGAAAATGAAGCAAAGAACAAAAGCGTAAAAAATGAGGCAATGAATAGCAAAAATGGGGC
GGTATTTAGCAATCC
Found at i:14955 original size:25 final size:25
Alignment explanation
Indices: 14927--14975 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
14917 TTTTGAATTA
14927 ATTATTTA-TTATTTAAAATATATTT
1 ATTATTTATTTA-TTAAAATATATTT
*
14952 ATTATTTATTTATTAATATATATT
1 ATTATTTATTTATTAAAATATATT
14976 ATATCTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTATTTATTTATTAAAATATATTT
Found at i:14956 original size:21 final size:24
Alignment explanation
Indices: 14898--14977 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 24
14888 TTAATAATTG
* *
14898 AATATATATTGTTTATTTATTT-TG
1 AATATATATT-ATTATTTATTTATA
14922 AAT-TA-ATTATT-TATTATTTA-A
1 AATATATATTATTAT-TTATTTATA
*
14943 AATATAT-TTATTATTTATTTATT
1 AATATATATTATTATTTATTTATA
14966 AATATATATTAT
1 AATATATATTAT
14978 ATCTAAGATA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
20 1 0.02
21 11 0.24
22 17 0.37
23 10 0.22
24 7 0.15
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (24 bp):
AATATATATTATTATTTATTTATA
Found at i:21724 original size:27 final size:28
Alignment explanation
Indices: 21694--21763 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
21684 CGATTGAGAT
* * *
21694 TGAGTATAAATTACATGAACTCCGC-GA
1 TGAGTATAAACTAAATGAACTCCGCTAA
*
21721 TGAGTATAAACTAAATGGACTCCGCTAA
1 TGAGTATAAACTAAATGAACTCCGCTAA
21749 TGAGTATAAACTAAA
1 TGAGTATAAACTAAA
21764 ATGACGAACG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (28 bp):
TGAGTATAAACTAAATGAACTCCGCTAA
Found at i:25266 original size:24 final size:24
Alignment explanation
Indices: 25239--25288 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
25229 CAACAGTGCA
25239 ACCAAGTAGCAATATCAAACAATG
1 ACCAAGTAGCAATATCAAACAATG
25263 ACCAAGTAGCAATATCAAACAATG
1 ACCAAGTAGCAATATCAAACAATG
25287 AC
1 AC
25289 TGAAACTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.22, G:0.12, T:0.16
Consensus pattern (24 bp):
ACCAAGTAGCAATATCAAACAATG
Found at i:28926 original size:1 final size:1
Alignment explanation
Indices: 28920--28962 Score: 68
Period size: 1 Copynumber: 43.0 Consensus size: 1
28910 GTGTGGATAA
**
28920 TTTTTTTTTTTTTTTAATTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28963 CCAGTTTGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.05, C:0.00, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:28939 original size:17 final size:17
Alignment explanation
Indices: 28917--28962 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
28907 TCAGTGTGGA
28917 TAATTTTTTTTTTTTTT
1 TAATTTTTTTTTTTTTT
28934 TAATTTTTTTTTTTTTT
1 TAATTTTTTTTTTTTTT
28951 T--TTTTTTTTTTT
1 TAATTTTTTTTTTT
28963 CCAGTTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.38
17 18 0.62
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (17 bp):
TAATTTTTTTTTTTTTT
Found at i:39448 original size:71 final size:71
Alignment explanation
Indices: 39241--39453 Score: 365
Period size: 71 Copynumber: 3.0 Consensus size: 71
39231 AATGAGTTCA
*
39241 AAACCCACCAACTACAAATATTCTTCAGC-ATTGTTTCAAATATAAAACCACCGGTTCAAATGGT
1 AAACCCACCAACTACAAATATTCTTCAACAATT-TTTCAAATATAAAACCACCGGTTCAAATGGT
* *
39305 CCAGGTC
65 TCGGGTC
* *
39312 AAACCCACCAACTACAAATATTCTTCAACATTTTTTCAAATATAAAACCACCGGTTCAAACGGTT
1 AAACCCACCAACTACAAATATTCTTCAACAATTTTTCAAATATAAAACCACCGGTTCAAATGGTT
39377 CGGGTC
66 CGGGTC
39383 AAACCCACCAACTACAAATATTCTTCAACAATTTTTCAAATATAAAACCACCGGTTCAAATGGTT
1 AAACCCACCAACTACAAATATTCTTCAACAATTTTTCAAATATAAAACCACCGGTTCAAATGGTT
39448 CGGGTC
66 CGGGTC
39454 CGAGCTAACT
Statistics
Matches: 134, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
71 132 0.99
72 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.10, T:0.26
Consensus pattern (71 bp):
AAACCCACCAACTACAAATATTCTTCAACAATTTTTCAAATATAAAACCACCGGTTCAAATGGTT
CGGGTC
Done.