Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009935.1 Corchorus capsularis cultivar CVL-1 contig09956, 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: 87145
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:664 original size:332 final size:332
Alignment explanation
Indices: 50--2378 Score: 2426
Period size: 332 Copynumber: 7.0 Consensus size: 332
40 CGAAATCATG
* ** ** **
50 ATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCATCTCAATTTTTAATGATTTTTGGCACC
1 ATCACGGTTTTTGGCTAAAAACGCGTTTCGAGGCCCCGGCTCAATTTTGCATGATTTTTGGTGCC
* * * * * * *
115 AACACTCCTTGAAATATCTATATTCATCTAACCAAATTTTAGCCACATTGGATTTAATGAATTGT
66 AAGACTCCTTAAAATATCTATATTCGTCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGT
* *
180 TTTTACAATCATCTGAATCATGTTTCGAGTTAATTAGATATTTATTCGGAAAAAATACGAAAAAC
131 TTTTACAATCATCTGAATAATGTTTCGAGTTAATTAGATATTTATTCAGAAAAAATACGAAAAAC
* * * * *
245 GATATTAGAAGCGTGAAATGCTCATCAATCTTTATGGCGTTAAATTATATACTTTTTAGGAGTGT
196 GATATTAGAAGCGTGAAAAGCTCATCAATCTTTTTGGTGTTAAATTATATATTTTTTATGAGTGT
* * *
310 TGTAGCAAGAAATTTAGAAAAAAA-ATTCGGGTCAATTTTTTGCAAAATTTAAATCGAAATCATG
261 TGTAGCAAAAAATTGAGAAAAAAATTTTCGGGTCAA-TTTTTGCAAAATTTAAATCGAAATCATG
*
374 TAATAACT
325 TACTAACT
* * * * * * *
382 GTCACGGTTTTTTGCTAAAAACGCATTCCTAGGCCCCGGCTCAATTTTGTACGATTTTTGGTGCC
1 ATCACGGTTTTTGGCTAAAAACGCGTTTCGAGGCCCCGGCTCAATTTTGCATGATTTTTGGTGCC
* * * *
447 AAGAGTCCTTAAAATATCTATATTCGTCTTACCAAATCTCAGCCACATTGCATTTAAGGATTAGT
66 AAGACTCCTTAAAATATCTATATTCGTCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGT
* * * * * * **
512 TTTTACGAGT-ATCTGAATAATGTTTCGATTTAACTA-AAATTAATTTAGAAAAAATAATAAAAA
131 TTTTAC-AATCATCTGAATAATGTTTCGAGTTAATTAGATATTTATTCAGAAAAAATACGAAAAA
* * * * * * *
575 GGATATTAGAAACGTGAAAAACTCTTCAATTTTTTTGGTGTCAAATTATAGATTTTTTATGAGTG
195 CGATATTAGAAGCGTGAAAAGCTCATCAATCTTTTTGGTGTTAAATTATATATTTTTTATGAGTG
* * **
640 TTGTGGCAAAAAATTGAGGAAAAAAATTTTCGGGTCAGTTTTTGCAATCAATTTTGTCAAATTAA
260 TTGTAGCAAAAAATTGA-GAAAAAAATTTTCGGGTCAATTTTTGCAA--AA--TT-T-AAATCGA
*
705 TTTAGATTTTTTATGTACTAGA-T
318 ---A-A----TCATGTACTA-ACT
* * * * * * * *
728 ATCACGGTTTTTTGCTAGAAACACGTTCCTG-GGCACCTGCTCCATTTTGCACGATTTTTGGTGC
1 ATCACGGTTTTTGGCTAAAAACGCGTTTC-GAGGCCCCGGCTCAATTTTGCATGATTTTTGGTGC
* * ** *
792 CAAGACTCTTTAAAATATCTATATTCGTCTAACCAGATCTTGGCCACATTGGATTTGAA-TATTT
65 CAAGACTCCTTAAAATATCTATATTCGTCTAACCAAATCTCAGCCACATTGGATTT-AAGGATTT
* ** * * * * * * * *
856 CTTTTTATGAGCATCTGAATAATGTGTCGATTTAACTA-AAATTAATTCAGAAAATATAAGAAAA
129 GTTTTTACAATCATCTGAATAATGTTTCGAGTTAATTAGATATTTATTCAGAAAAAATACGAAAA
* * * * * * *
920 ATGATACTAGAAGCGTTAAAAACTCTTCAATATTTTTGGTGTTAAATTAAATATTTTTTATGAGT
194 ACGATATTAGAAGCGTGAAAAGCTCATCAATCTTTTTGGTGTTAAATTATATATTTTTTATGAGT
* ** * ** *
985 GTTGTGGCAAAAAATTGAGGAAAAAAATTTTCGCCTTAATTTTTGC-AAATTTTCAGCAGAAATC
259 GTTGTAGCAAAAAATTGA-GAAAAAAATTTTCGGGTCAATTTTTGCAAAATTTAAATC-GAAATC
*
1049 ATGTACTAACC
322 ATGTACTAACT
* * * * * *
1060 ATCACGGTTTTTGGCTAAAAACGCGTTTCAAGGCCCTGGCACAATTTTGCATTATTTTTAGCGCC
1 ATCACGGTTTTTGGCTAAAAACGCGTTTCGAGGCCCCGGCTCAATTTTGCATGATTTTTGGTGCC
* * ** * * * *
1125 AAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAATCATATTGTATTTAACGATTTGG
66 AAGACTCCTTAAAATATCTATATTCGTCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGT
* *
1190 TTTTACAATCATCTGAA-ACATGTTTTGAGTTAATTAGATATTTATTCGGAAAAAATACGAAAAA
131 TTTTACAATCATCTGAATA-ATGTTTCGAGTTAATTAGATATTTATTCAGAAAAAATACGAAAAA
* * * * *
1254 CGATATTAGAAGCGTGAAATGCTCATCAATCTTTTTTGCGTTAAATTATATATTTCTTATGGGTG
195 CGATATTAGAAGCGTGAAAAGCTCATCAATCTTTTTGGTGTTAAATTATATATTTTTTATGAGTG
* * * **
1319 TTGTAGCAAAAAATTGAG-AAATAATCTTTCAGGTCAATTTTTTCCAAAATTTAAGCCGAAATCA
260 TTGTAGCAAAAAATTGAGAAAAAAAT-TTTCGGGTCAA-TTTTTGCAAAATTTAAATCGAAATCA
*
1383 CGTACTAACT
323 TGTACTAACT
* * * *
1393 ATAACGGTTTTTGGCTAAAAACGCGTTCCCAGGCCCCGGCTCAATTTTGCACGA-TTTTGGTGCC
1 ATCACGGTTTTTGGCTAAAAACGCGTTTCGAGGCCCCGGCTCAATTTTGCATGATTTTTGGTGCC
* * * *
1457 AAGACTCCTTAAGATATCTATATTCGTCTTACCAAATCTC-GGC-CATTGGATTTAAGAATTTGT
66 AAGACTCCTTAAAATATCTATATTCGTCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGT
* *
1520 TTTTACAATCATCTGAATCATGTTTCGAGTTAATTAGATATTTATTCGGAAAAAATACGAAAAAC
131 TTTTACAATCATCTGAATAATGTTTCGAGTTAATTAGATATTTATTCAGAAAAAATACGAAAAAC
* ** * * * * *
1585 GATATTAAAATTGGGAAACGCTCATCAATCTTTTTGGAGTTAAATTATATA-TTTTTATGGGTGC
196 GATATTAGAAGCGTGAAAAGCTCATCAATCTTTTTGGTGTTAAATTATATATTTTTTATGAGTGT
* * * * *
1649 TATAGCAAAAACTTGAGAAAAAAATCTTCGGGTCAA-TTTTGCAAAATTTAAGTGGAAATCGA-G
261 TGTAGCAAAAAATTGAGAAAAAAATTTTCGGGTCAATTTTTGCAAAATTTAAATCGAAATC-ATG
1712 TACTAACT
325 TACTAACT
* * * * *
1720 ATTACGGTTTTTTGCTAAAAACGCATTTC-AGGGACCCGGCTCAATTTTGCATGATTTTCGGTGC
1 ATCACGGTTTTTGGCTAAAAACGCGTTTCGA-GGCCCCGGCTCAATTTTGCATGATTTTTGGTGC
*
1784 CAAGACTCCTTAAAATATCTATATTCGTCTAACCAAATCTCGGCCACATTGGATTTAAGGATTTG
65 CAAGACTCCTTAAAATATCTATATTCGTCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTG
* * * * * * ** *
1849 TTTTTACAAGT-ACCTGAATAATATTTCGATTTAACTA-AAATTAATTCAGAAAAAATAATAATA
130 TTTTTACAA-TCATCTGAATAATGTTTCGAGTTAATTAGATATTTATTCAGAAAAAATACGAAAA
* * * * *
1912 ACGATATTAGAAGCGTGAAAAACTCTTTAATATTTTTGGTGTTAAATTATAGATTTTTTATGAGT
194 ACGATATTAGAAGCGTGAAAAGCTCATCAATCTTTTTGGTGTTAAATTATATATTTTTTATGAGT
* * * * * **
1977 GTTGTCGCCAAAAATTGAGGAAAAAAATTTTCGGGTCAATTTATGTAAAATTTTAGCCGAAATCA
259 GTTGTAGCAAAAAATTGA-GAAAAAAATTTTCGGGTCAATTTTTGCAAAATTTAAATCGAAATCA
2042 TG---TAAC-
323 TGTACTAACT
* ** *
2048 ATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTTCTGGCTCAATTTTGCATGATTTTTGGCT-C
1 ATCACGGTTTTTGGCTAAAAACGCGTTTCGAGGCCCCGGCTCAATTTTGCATGATTTTTGG-TGC
* * * * *
2112 CAAGACTCCTTGAAATATCTATATTCATCTAACTAAATCTCAACCACATTGGATTTAAAGATTTG
65 CAAGACTCCTTAAAATATCTATATTCGTCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTG
2177 TTTTTACAATCATCTGAA-ACATGTTTCGAGTTAATTAGATATTTATTC-GAAAAAAATACGAAA
130 TTTTTACAATCATCTGAATA-ATGTTTCGAGTTAATTAGATATTTATTCAG-AAAAAATACGAAA
* * * * * *
2240 AACGACATTAGAAGTGTGAAATGCTAATCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAG
193 AACGATATTAGAAGCGTGAAAAGCTCATCAATCTTTTTGGTGTTAAATTATATATTTTTTATGAG
** * **
2305 TGTTGTAGCAAAAAATTGAGAAAAAAA-AATCGGGTCAATTATTTGCAAAATATAAGCCGAAATC
258 TGTTGTAGCAAAAAATTGAGAAAAAAATTTTCGGGTCAATT-TTTGCAAAATTTAAATCGAAATC
* *
2369 GTGTGCTAAC
322 ATGTACTAAC
2379 AACAAGTTTC
Statistics
Matches: 1653, Mismatches: 292, Indels: 105
0.81 0.14 0.05
Matches are distributed among these distances:
326 1 0.00
327 89 0.05
328 219 0.13
329 193 0.12
330 198 0.12
331 124 0.08
332 359 0.22
333 170 0.10
334 9 0.01
336 3 0.00
337 2 0.00
338 5 0.00
339 1 0.00
340 2 0.00
341 3 0.00
342 1 0.00
343 2 0.00
345 1 0.00
346 268 0.16
347 3 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (332 bp):
ATCACGGTTTTTGGCTAAAAACGCGTTTCGAGGCCCCGGCTCAATTTTGCATGATTTTTGGTGCC
AAGACTCCTTAAAATATCTATATTCGTCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGT
TTTTACAATCATCTGAATAATGTTTCGAGTTAATTAGATATTTATTCAGAAAAAATACGAAAAAC
GATATTAGAAGCGTGAAAAGCTCATCAATCTTTTTGGTGTTAAATTATATATTTTTTATGAGTGT
TGTAGCAAAAAATTGAGAAAAAAATTTTCGGGTCAATTTTTGCAAAATTTAAATCGAAATCATGT
ACTAACT
Found at i:3335 original size:48 final size:48
Alignment explanation
Indices: 3283--3400 Score: 137
Period size: 48 Copynumber: 2.5 Consensus size: 48
3273 AAATCGTGTA
* ** *
3283 CTAACCATCACGACTTTCGGGGGCCAAAATTTTCCTAAAATCTAAAGG
1 CTAACCATCACGACTTTCGGGGGCCAAAAATGGCCTAAAATCCAAAGG
* ****
3331 CTAACCGTCACGACTTTCAAATGCCAAAAATGGCCTAAAATCCAAAGG
1 CTAACCATCACGACTTTCGGGGGCCAAAAATGGCCTAAAATCCAAAGG
* *
3379 CTAACCATCACAACTTCCGGGG
1 CTAACCATCACGACTTTCGGGG
3401 CTCAAATGGC
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (48 bp):
CTAACCATCACGACTTTCGGGGGCCAAAAATGGCCTAAAATCCAAAGG
Found at i:7420 original size:2 final size:2
Alignment explanation
Indices: 7378--7411 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
7368 AAAAAAATCG
7378 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7412 TCTTATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15793 original size:17 final size:18
Alignment explanation
Indices: 15767--15813 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
15757 ATCATGCTTA
*
15767 ATAATCATGA-AATTTCC
1 ATAATTATGAGAATTTCC
* *
15784 ATAATTATGAGATTTTCT
1 ATAATTATGAGAATTTCC
15802 ATAATTAT-AGAA
1 ATAATTATGAGAA
15814 GTGCCTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (18 bp):
ATAATTATGAGAATTTCC
Found at i:17574 original size:33 final size:33
Alignment explanation
Indices: 17532--17599 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
17522 TCTATTAAAT
17532 CATCACATACAATAACAAAACCAAACACCAAGA
1 CATCACATACAATAACAAAACCAAACACCAAGA
17565 CATCACATACAATAACAAAACCAAACACCAAGA
1 CATCACATACAATAACAAAACCAAACACCAAGA
17598 CA
1 CA
17600 ATAAGGGACA
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:0.57, C:0.31, G:0.03, T:0.09
Consensus pattern (33 bp):
CATCACATACAATAACAAAACCAAACACCAAGA
Found at i:23765 original size:12 final size:13
Alignment explanation
Indices: 23748--23780 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
23738 CGCCAAACAA
23748 AGAAGTAGAA-GT
1 AGAAGTAGAACGT
23760 AGAAGTAGAACTGT
1 AGAAGTAGAAC-GT
23774 AGAAGTA
1 AGAAGTA
23781 ATCGTAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
14 9 0.47
ACGTcount: A:0.48, C:0.03, G:0.30, T:0.18
Consensus pattern (13 bp):
AGAAGTAGAACGT
Found at i:24476 original size:6 final size:6
Alignment explanation
Indices: 24467--24495 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
24457 TGACTTTAGC
24467 TTTGAT TTTGAT TTTGAT TTTGAT TTTGA
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGA
24496 ATGAATGCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTGAT
Found at i:24476 original size:18 final size:18
Alignment explanation
Indices: 24453--24495 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
24443 CAGCTCAGGT
24453 ATTTTGACTTTAG-CTTTG
1 ATTTTGA-TTTAGACTTTG
* *
24471 ATTTTGATTTTGATTTTG
1 ATTTTGATTTAGACTTTG
24489 ATTTTGA
1 ATTTTGA
24496 ATGAATGCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.19, C:0.05, G:0.16, T:0.60
Consensus pattern (18 bp):
ATTTTGATTTAGACTTTG
Found at i:34075 original size:2 final size:2
Alignment explanation
Indices: 34068--34104 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
34058 GGGCCCCCAA
34068 AT AT AT AT 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 AT AT AT AT A
34105 AGCTGAGCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53050 original size:2 final size:2
Alignment explanation
Indices: 53014--53038 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53004 TGCAATTTGC
53014 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
53039 GTTCCTATAT
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:77416 original size:84 final size:84
Alignment explanation
Indices: 77275--77440 Score: 323
Period size: 84 Copynumber: 2.0 Consensus size: 84
77265 AATGATAGTT
77275 AGTGCTTTTGGTTTTGAGATGCTCAAACCTCAGTTACCATAAATTTAAGCATAGCTAATTAATCT
1 AGTGCTTTTGGTTTTGAGATGCTCAAACCTCAGTTACCATAAATTTAAGCATAGCTAATTAATCT
77340 GGATCGGATCATCAATACA
66 GGATCGGATCATCAATACA
*
77359 AGTGCTTTTGGTTTTGAGATGCTCAAACCTCAGTTATCATAAATTTAAGCATAGCTAATTAATCT
1 AGTGCTTTTGGTTTTGAGATGCTCAAACCTCAGTTACCATAAATTTAAGCATAGCTAATTAATCT
77424 GGATCGGATCATCAATA
66 GGATCGGATCATCAATA
77441 TAACCCCAAG
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (84 bp):
AGTGCTTTTGGTTTTGAGATGCTCAAACCTCAGTTACCATAAATTTAAGCATAGCTAATTAATCT
GGATCGGATCATCAATACA
Found at i:86128 original size:2 final size:2
Alignment explanation
Indices: 86121--86151 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
86111 ATATACACTA
86121 AT 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 AT A
86152 ACGTCATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.