Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006507.1 Corchorus capsularis cultivar CVL-1 contig06528, 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: 53946
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Found at i:1876 original size:15 final size:17
Alignment explanation
Indices: 1855--1894 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
1845 GGTGTTTTTT
1855 TATATATATATTGT-TGA
1 TATATATATA-TGTATGA
1872 TATAT-TATATGTATG-
1 TATATATATATGTATGA
1887 TATATATA
1 TATATATA
1895 ACATTGATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.38
16 8 0.38
17 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (17 bp):
TATATATATATGTATGA
Found at i:2075 original size:14 final size:14
Alignment explanation
Indices: 2056--2083 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2046 TATTAGTTGG
2056 CCGATCCGATTCGA
1 CCGATCCGATTCGA
2070 CCGATCCGATTCGA
1 CCGATCCGATTCGA
2084 ACAAGATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (14 bp):
CCGATCCGATTCGA
Found at i:13756 original size:2 final size:2
Alignment explanation
Indices: 13749--13778 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13739 TAAGCAGGAA
13749 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
13779 GAACTCCACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23423 original size:101 final size:101
Alignment explanation
Indices: 23292--23596 Score: 452
Period size: 101 Copynumber: 3.0 Consensus size: 101
23282 GACGTGGTGG
* * *
23292 AAACTACTTGGTTTTTGCTCCATAGAGAGAGCAAGGTGAGAGAT-AGATAGACAACAAATTGGGT
1 AAACTACTTGGTTCTTGCTCTATAGAGAGAGCAAGGTGAGAGATAAG-TGGACAACAAATTGGGT
23356 TCTTTTGGGGTTGATTTCTTGATGATTCAAAGAGGGA
65 TCTTTTGGGGTTGATTTCTTGATGATTCAAAGAGGGA
* *
23393 AAACTACTTGGTTCTTGCTCTATAGAGAGAGCAAGGTGAGAGATAAGTGGACAATAAATTAGGTT
1 AAACTACTTGGTTCTTGCTCTATAGAGAGAGCAAGGTGAGAGATAAGTGGACAACAAATTGGGTT
23458 CTTTTGGGGTTGATTTCTTGATGATTCAAAGAGGGA
66 CTTTTGGGGTTGATTTCTTGATGATTCAAAGAGGGA
* *** ** *
23494 AAACTACTTGGTTCTTGCT-TCCTAGAGAGAGCAAGCCAAGAGATAAGTGGGTAACAAACTGGGT
1 AAACTACTTGGTTCTTGCTCT-ATAGAGAGAGCAAGGTGAGAGATAAGTGGACAACAAATTGGGT
* *
23558 TCTTTTAGGGTTGATTTCTTGATGATTCAAAAAGGGA
65 TCTTTTGGGGTTGATTTCTTGATGATTCAAAGAGGGA
23595 AA
1 AA
23597 TCTTTGTATT
Statistics
Matches: 186, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
100 1 0.01
101 183 0.98
102 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.30
Consensus pattern (101 bp):
AAACTACTTGGTTCTTGCTCTATAGAGAGAGCAAGGTGAGAGATAAGTGGACAACAAATTGGGTT
CTTTTGGGGTTGATTTCTTGATGATTCAAAGAGGGA
Found at i:24704 original size:19 final size:19
Alignment explanation
Indices: 24682--24718 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
24672 AGGCCAAAAT
24682 TAATAATTAAATTAATTAA
1 TAATAATTAAATTAATTAA
*
24701 TAATAATTATATTAATTA
1 TAATAATTAAATTAATTA
24719 TTTTTGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAATAATTAAATTAATTAA
Found at i:26007 original size:17 final size:18
Alignment explanation
Indices: 25975--26012 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
25965 GTTATCCAGC
*
25975 ACCTCATGCTACCTA-GT
1 ACCTCATGCTAACTAGGT
*
25992 ACCTCATGTTAACTAGGT
1 ACCTCATGCTAACTAGGT
26010 ACC
1 ACC
26013 ATGAGGAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.29
Consensus pattern (18 bp):
ACCTCATGCTAACTAGGT
Found at i:26404 original size:17 final size:17
Alignment explanation
Indices: 26369--26421 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
26359 TTTGTTCAAT
*
26369 CTCATGCTATCC-AGCAC
1 CTCATGCTA-CCTAGTAC
26386 CTCATGCTACCTAGTAC
1 CTCATGCTACCTAGTAC
* *
26403 CTTATGTTACCTAGGTAC
1 CTCATGCTACCTA-GTAC
26421 C
1 C
26422 ATGAGGAGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 2 0.06
17 24 0.77
18 5 0.16
ACGTcount: A:0.23, C:0.34, G:0.13, T:0.30
Consensus pattern (17 bp):
CTCATGCTACCTAGTAC
Found at i:26726 original size:409 final size:409
Alignment explanation
Indices: 25967--26780 Score: 1412
Period size: 409 Copynumber: 2.0 Consensus size: 409
25957 CATCAGATGT
25967 TATCCAGCACCTCATGCTACCTAGTACCTCATGTTAACTAGGTACCATGAGGAGGGAATCGCCTA
1 TATCCAGCACCTCATGCTACCTAGTACCTCATGTTAACTAGGTACCATGAGGAGGGAATCGCCTA
* * *
26032 TCACCATGAGGGACGCCTCATCCTCCTCTTCTCACCCTCATATCACCTGCTGCAGTAACTAGAAG
66 TCACCATGAGGGACGCCTCATCCTCCTCTCCTCACCCTCATATCACCTGCTGCAGCAACCAGAAG
* * *
26097 AAGAGGGAAGCTTCACTGCAACTTCCTGTAAAATTCCTCCGACCAATAAGAAGAGTTCGACTTCT
131 AAGAGGGAAGCTTCACTGCAACTTCCTGGAAAATTCCTCCGACCAACAAGAAGAGTTCGACTTCC
* * *
26162 TCAGCAAGTAAAGCCCACCAGATTTCTAGGCCCATGCTGCCCCCTATATAAAGGAACCAGTTCAA
196 TCAACAAGTAAAACCCACCAGATTTCTAGGCCCATGCAGCCCCCTATATAAAGGAACCAGTTCAA
26227 GAGTTTCAAATCAAGTCATGCACTTCACAACTTGCTCCGTGCAAAAAACCAAGCTCCGTGCTTAT
261 GAGTTTCAAATCAAGTCATGCACTTCACAACTTGCTCCGTGCAAAAAACCAAGCTCCGTGCTTAT
* *
26292 TTTCTCTTTAGCTCCGCGCCTTTTTACTCTTGTTCATCACGAGTTCTTACTCGTTCTTCAAATTT
326 TTTCTCTCTAGCTCCGCGCCTTTTTACTCTTGGTCATCACGAGTTCTTACTCGTTCTTCAAATTT
26357 CCTTTGTTCAATCTCATGC
391 CCTTTGTTCAATCTCATGC
* * *
26376 TATCCAGCACCTCATGCTACCTAGTACCTTATGTTACCTAGGTACCATGAGGAGGGAGTCGCCTA
1 TATCCAGCACCTCATGCTACCTAGTACCTCATGTTAACTAGGTACCATGAGGAGGGAATCGCCTA
*
26441 TCACCATGAGGGACGCCTCATCCTCCTCTCCTCACCCTCCTATCACCTGCTGCAGCAACCAGAAG
66 TCACCATGAGGGACGCCTCATCCTCCTCTCCTCACCCTCATATCACCTGCTGCAGCAACCAGAAG
* * *
26506 GAGAGGGAAGCTTCACTGCAACTTCCTGGAAATTTCCTCCGACCAACCAGAAGAGTTCGACTTCC
131 AAGAGGGAAGCTTCACTGCAACTTCCTGGAAAATTCCTCCGACCAACAAGAAGAGTTCGACTTCC
* *
26571 TCAACAAGTAAAACCCACCAGATTTCTAGGCCCATGCAGCCCCCTATATAAAGGAACTAGTTCCA
196 TCAACAAGTAAAACCCACCAGATTTCTAGGCCCATGCAGCCCCCTATATAAAGGAACCAGTTCAA
* *
26636 GAGTTTCAAATCAAGTCCTGCACTTCACAACTTGCTCCGTGCAAAAAACCAAGCTCTGTGCTTAT
261 GAGTTTCAAATCAAGTCATGCACTTCACAACTTGCTCCGTGCAAAAAACCAAGCTCCGTGCTTAT
* *
26701 TTTCTCTCTGGCTCCGCGCCTTTTTACTCTTGGTCATCACGAGTTCTTACTCGTTCTTTAAATTT
326 TTTCTCTCTAGCTCCGCGCCTTTTTACTCTTGGTCATCACGAGTTCTTACTCGTTCTTCAAATTT
26766 CCTTTGTTCAATCTC
391 CCTTTGTTCAATCTC
26781 GTCCAAGGAC
Statistics
Matches: 381, Mismatches: 24, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
409 381 1.00
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.28
Consensus pattern (409 bp):
TATCCAGCACCTCATGCTACCTAGTACCTCATGTTAACTAGGTACCATGAGGAGGGAATCGCCTA
TCACCATGAGGGACGCCTCATCCTCCTCTCCTCACCCTCATATCACCTGCTGCAGCAACCAGAAG
AAGAGGGAAGCTTCACTGCAACTTCCTGGAAAATTCCTCCGACCAACAAGAAGAGTTCGACTTCC
TCAACAAGTAAAACCCACCAGATTTCTAGGCCCATGCAGCCCCCTATATAAAGGAACCAGTTCAA
GAGTTTCAAATCAAGTCATGCACTTCACAACTTGCTCCGTGCAAAAAACCAAGCTCCGTGCTTAT
TTTCTCTCTAGCTCCGCGCCTTTTTACTCTTGGTCATCACGAGTTCTTACTCGTTCTTCAAATTT
CCTTTGTTCAATCTCATGC
Found at i:36292 original size:22 final size:21
Alignment explanation
Indices: 36262--36320 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 21
36252 GATTCTTGCT
*
36262 TCTTGAAATAATTCTTCAATA
1 TCTTCAAATAATTCTTCAATA
* **
36283 GTCTTCAAAT-GTTC-AAAATA
1 -TCTTCAAATAATTCTTCAATA
36303 TCTTCAAATAA-TCTTCAA
1 TCTTCAAATAATTCTTCAA
36321 ACACGAACTT
Statistics
Matches: 28, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
19 11 0.39
20 6 0.21
21 3 0.11
22 8 0.29
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTTCAAATAATTCTTCAATA
Found at i:37407 original size:16 final size:18
Alignment explanation
Indices: 37373--37407 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
37363 TCCTCTTGTC
37373 ATGAAAACACTTCTTTTT
1 ATGAAAACACTTCTTTTT
37391 ATGAAAACA-TT-TTTTT
1 ATGAAAACACTTCTTTTT
37407 A
1 A
37408 ACTACCCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 9 0.53
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
ATGAAAACACTTCTTTTT
Found at i:44308 original size:25 final size:25
Alignment explanation
Indices: 44280--44364 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 25
44270 TCACATTTTG
44280 TTTGGGCCTTGGTTTCTTAGCAAGA
1 TTTGGGCCTTGGTTTCTTAGCAAGA
** * * ** *
44305 TTTGGGTTTTGTTTGTTTATGTGGTTACA
1 TTTGGGCCTTG---GTTTCT-TAGCAAGA
44334 TTTGGGCCTTGGTTTCTTAGCAAGA
1 TTTGGGCCTTGGTTTCTTAGCAAGA
44359 TTTGGG
1 TTTGGG
44365 TTTTGTTTGT
Statistics
Matches: 42, Mismatches: 14, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
25 19 0.45
26 5 0.12
28 5 0.12
29 13 0.31
ACGTcount: A:0.13, C:0.11, G:0.29, T:0.47
Consensus pattern (25 bp):
TTTGGGCCTTGGTTTCTTAGCAAGA
Found at i:44336 original size:29 final size:29
Alignment explanation
Indices: 44304--44393 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
44294 TCTTAGCAAG
44304 ATTTGGGTTTTGTTTGTTTATGTGGTTAC
1 ATTTGGGTTTTGTTTGTTTATGTGGTTAC
** * * ** *
44333 ATTTGGGCCTTG---GTTTCT-TAGCAAG
1 ATTTGGGTTTTGTTTGTTTATGTGGTTAC
44358 ATTTGGGTTTTGTTTGTTTATGTGGTTAC
1 ATTTGGGTTTTGTTTGTTTATGTGGTTAC
44387 ATTTGGG
1 ATTTGGG
44394 CCTTGATGAA
Statistics
Matches: 43, Mismatches: 14, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
25 13 0.30
26 5 0.12
28 5 0.12
29 20 0.47
ACGTcount: A:0.12, C:0.07, G:0.29, T:0.52
Consensus pattern (29 bp):
ATTTGGGTTTTGTTTGTTTATGTGGTTAC
Found at i:44341 original size:54 final size:54
Alignment explanation
Indices: 44280--44398 Score: 238
Period size: 54 Copynumber: 2.2 Consensus size: 54
44270 TCACATTTTG
44280 TTTGGGCCTTGGTTTCTTAGCAAGATTTGGGTTTTGTTTGTTTATGTGGTTACA
1 TTTGGGCCTTGGTTTCTTAGCAAGATTTGGGTTTTGTTTGTTTATGTGGTTACA
44334 TTTGGGCCTTGGTTTCTTAGCAAGATTTGGGTTTTGTTTGTTTATGTGGTTACA
1 TTTGGGCCTTGGTTTCTTAGCAAGATTTGGGTTTTGTTTGTTTATGTGGTTACA
44388 TTTGGGCCTTG
1 TTTGGGCCTTG
44399 ATGAATTATG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.12, C:0.10, G:0.29, T:0.50
Consensus pattern (54 bp):
TTTGGGCCTTGGTTTCTTAGCAAGATTTGGGTTTTGTTTGTTTATGTGGTTACA
Found at i:48577 original size:22 final size:21
Alignment explanation
Indices: 48547--48605 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 21
48537 AATTCTTGTT
*
48547 TCTTGAAATAATTCTTCAATA
1 TCTTCAAATAATTCTTCAATA
* **
48568 GTCTTCAAAT-GTTC-AAAATA
1 -TCTTCAAATAATTCTTCAATA
48588 TCTTCAAATAA-TCTTCAA
1 TCTTCAAATAATTCTTCAA
48606 ACACGAACTT
Statistics
Matches: 28, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
19 11 0.39
20 6 0.21
21 3 0.11
22 8 0.29
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTTCAAATAATTCTTCAATA
Found at i:49690 original size:16 final size:18
Alignment explanation
Indices: 49656--49690 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
49646 TCCTCTTGTC
49656 ATGAAAACACTTCTTTTT
1 ATGAAAACACTTCTTTTT
49674 ATGAAAACA-TT-TTTTT
1 ATGAAAACACTTCTTTTT
49690 A
1 A
49691 ACTACCCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 9 0.53
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
ATGAAAACACTTCTTTTT
Found at i:50324 original size:16 final size:16
Alignment explanation
Indices: 50299--50330 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
50289 AGGAATAGAC
50299 AATCAATCAAAGCAAT
1 AATCAATCAAAGCAAT
*
50315 AATCATTCAAAGCAAT
1 AATCAATCAAAGCAAT
50331 GTGATCGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.19, G:0.06, T:0.22
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Found at i:51833 original size:11 final size:11
Alignment explanation
Indices: 51815--51848 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
51805 AATGATCTTC
51815 AAATCTTCAAA
1 AAATCTTCAAA
**
51826 TTATCTTCAAA
1 AAATCTTCAAA
51837 AAATCTTCAAA
1 AAATCTTCAAA
51848 A
1 A
51849 CACGAACTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATCTTCAAA
Found at i:51833 original size:19 final size:18
Alignment explanation
Indices: 51800--51836 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
51790 TTGAAATAAT
51800 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
51818 TCTTCAAATTATCTTCAAA
1 TCTTC-AATGATCTTCAAA
51837 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.