Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015412.1 Corchorus capsularis cultivar CVL-1 contig15433, 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: 31259
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:1375 original size:10 final size:10
Alignment explanation
Indices: 1357--1397 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1347 ACTAGTAGTT
*
1357 ATATCAAAAA
1 ATATAAAAAA
1367 ATATAAAAAA
1 ATATAAAAAA
1377 A-ATAAAATAA
1 ATATAAAA-AA
1387 A-ATAAAAAA
1 ATATAAAAAA
1396 AT
1 AT
1398 TTTCGACCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 9 0.32
10 19 0.68
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (10 bp):
ATATAAAAAA
Found at i:8821 original size:12 final size:12
Alignment explanation
Indices: 8804--8835 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
8794 CATTGATGAC
8804 TCTGATGAGGAA
1 TCTGATGAGGAA
8816 TCTGATGAGGAA
1 TCTGATGAGGAA
8828 TCTGATGA
1 TCTGATGA
8836 AGAGACTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.28
Consensus pattern (12 bp):
TCTGATGAGGAA
Found at i:13430 original size:50 final size:50
Alignment explanation
Indices: 13371--13468 Score: 178
Period size: 50 Copynumber: 2.0 Consensus size: 50
13361 TATTAAATTA
* *
13371 TGAAAATTCCATGCTGGCATACATGTGTCATCCACGTCAGCATATCAGTG
1 TGAAAATTCCATGCTGGCATACATGTATCATCCACATCAGCATATCAGTG
13421 TGAAAATTCCATGCTGGCATACATGTATCATCCACATCAGCATATCAG
1 TGAAAATTCCATGCTGGCATACATGTATCATCCACATCAGCATATCAG
13469 ATTGCGTGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (50 bp):
TGAAAATTCCATGCTGGCATACATGTATCATCCACATCAGCATATCAGTG
Found at i:18524 original size:21 final size:21
Alignment explanation
Indices: 18485--18533 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
18475 TCAATGCTTT
** *
18485 AGGAATGCAAGAGGGATTTCTA
1 AGGAA-GCAAGAGCCATTTCCA
18507 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCCA
18528 A-GAAGC
1 AGGAAGC
18534 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.39, C:0.16, G:0.29, T:0.16
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCCA
Found at i:26269 original size:19 final size:19
Alignment explanation
Indices: 26245--26281 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
26235 AGCTGAAAAT
*
26245 TGAAAAGTTGTTGGAATGC
1 TGAAAAATTGTTGGAATGC
26264 TGAAAAATTGTTGGAATG
1 TGAAAAATTGTTGGAATG
26282 GCCTCCCTTG
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:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (19 bp):
TGAAAAATTGTTGGAATGC
Found at i:26346 original size:19 final size:19
Alignment explanation
Indices: 26322--26358 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
26312 AGTTGTAAAT
*
26322 TGAAAAGTTGTTGGAATGC
1 TGAAAAATTGTTGGAATGC
*
26341 TGAAAAATTGTTGTAATG
1 TGAAAAATTGTTGGAATG
26359 GCCTCCCTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (19 bp):
TGAAAAATTGTTGGAATGC
Found at i:26368 original size:77 final size:78
Alignment explanation
Indices: 26241--26418 Score: 304
Period size: 77 Copynumber: 2.3 Consensus size: 78
26231 GAGCAGCTGA
*
26241 AAATTGAAAAGTTGTTGGAATGCTGAAAAATTGTTGGAATGGCCTCCCTTGGGAGCAACTGGAAA
1 AAATTGAAAAGTTGTTGGAATGCTGAAAAATTGTTGGAATGGCCTCCCTTGGGAGCAACTGAAAA
*
26306 CT-GTAAAGTTGT
66 CTACTAAAGTTGT
*
26318 AAATTGAAAAGTTGTTGGAATGCTGAAAAATTGTTGTAATGGCCTCCCTTGGGAGCAACTGAAAA
1 AAATTGAAAAGTTGTTGGAATGCTGAAAAATTGTTGGAATGGCCTCCCTTGGGAGCAACTGAAAA
*
26383 CTACTGAAGTTGT
66 CTACTAAAGTTGT
*
26396 AATTTGAAAAGTTGTTGGAATGC
1 AAATTGAAAAGTTGTTGGAATGC
26419 CCCCCTTGGG
Statistics
Matches: 95, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
77 65 0.68
78 30 0.32
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (78 bp):
AAATTGAAAAGTTGTTGGAATGCTGAAAAATTGTTGGAATGGCCTCCCTTGGGAGCAACTGAAAA
CTACTAAAGTTGT
Found at i:26494 original size:37 final size:38
Alignment explanation
Indices: 26442--26515 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 38
26432 AACCGAAAAC
*
26442 TGCTGAAAGATGACCTGTTTCCAGTC-AACTTGATAAG
1 TGCTGAAAGACGACCTGTTTCCAGTCGAACTTGATAAG
*
26479 TGCTGAAAGACGACCTGTTTCCAGTCGATCTTGATAA
1 TGCTGAAAGACGACCTGTTTCCAGTCGAACTTGATAA
26516 CTACTAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 25 0.74
38 9 0.26
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (38 bp):
TGCTGAAAGACGACCTGTTTCCAGTCGAACTTGATAAG
Found at i:26526 original size:38 final size:37
Alignment explanation
Indices: 26447--26526 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
26437 AAAACTGCTG
* * * *
26447 AAAGATGACCTGTTTCCAGTCAACTTGATAAGTGCTG
1 AAAGACGACCTGTTTCCAGTCAACTTGATAACTACTA
*
26484 AAAGACGACCTGTTTCCAGTCGATCTTGATAACTACTA
1 AAAGACGACCTGTTTCCAGTC-AACTTGATAACTACTA
26522 AAAGA
1 AAAGA
26527 TAACCTCTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 20 0.54
38 17 0.46
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (37 bp):
AAAGACGACCTGTTTCCAGTCAACTTGATAACTACTA
Found at i:26598 original size:22 final size:22
Alignment explanation
Indices: 26570--26612 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
26560 CAGTCAACTT
*
26570 TGATAATTTGGAAGATGACCTC
1 TGATAATTTGAAAGATGACCTC
26592 TGATAATTTGAAAGATGACCT
1 TGATAATTTGAAAGATGACCT
26613 GTTTTCAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (22 bp):
TGATAATTTGAAAGATGACCTC
Found at i:26608 original size:58 final size:58
Alignment explanation
Indices: 26482--26708 Score: 292
Period size: 58 Copynumber: 3.8 Consensus size: 58
26472 TGATAAGTGC
* * * * * *
26482 TGAAAGACGACCTGTTTCCAGTCGATCTTGATAACTACTAAAAGATAACCTCTGATAATT
1 TGAAAGATGACCTGTTTCCAGTCAACCTTGATAA-T-TTGAAAGATGACCTCTGATAATT
* *
26542 TGAAAGATGACCTGTTTCCAGTCAACTTTGATAATTTGGAAGATGACCTCTGATAATT
1 TGAAAGATGACCTGTTTCCAGTCAACCTTGATAATTTGAAAGATGACCTCTGATAATT
* * * *
26600 TGAAAGATGACCTGTTTTCAGTCAACCTTGATTATTTGGAAGATGACCTCTGATAATC
1 TGAAAGATGACCTGTTTCCAGTCAACCTTGATAATTTGAAAGATGACCTCTGATAATT
* *
26658 TGAAAGATGACTTGTTTCCAGTCAACCTTGATTATTGCTGAAAGATGACCT
1 TGAAAGATGACCTGTTTCCAGTCAACCTTGATAATT--TGAAAGATGACCT
26709 GTTTCCAGTC
Statistics
Matches: 150, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
58 107 0.71
59 1 0.01
60 42 0.28
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (58 bp):
TGAAAGATGACCTGTTTCCAGTCAACCTTGATAATTTGAAAGATGACCTCTGATAATT
Found at i:26653 original size:22 final size:21
Alignment explanation
Indices: 26624--26668 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
26614 TTTTCAGTCA
* * *
26624 ACCTTGATTATTTGGAAGATG
1 ACCTTGATAATCTGAAAGATG
26645 ACCTCTGATAATCTGAAAGATG
1 ACCT-TGATAATCTGAAAGATG
26667 AC
1 AC
26669 TTGTTTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (21 bp):
ACCTTGATAATCTGAAAGATG
Found at i:26756 original size:48 final size:48
Alignment explanation
Indices: 26685--26867 Score: 330
Period size: 48 Copynumber: 3.8 Consensus size: 48
26675 CCAGTCAACC
* * *
26685 TTGATTATTGCTGAAAGATGACCTGTTTCCAGTCATCTTTGATAAACT
1 TTGATGATTGCTGAAAGGTGACCTGTTTCCAGTCAACTTTGATAAACT
*
26733 TTGATGATTGCTGAAAGGTGACCTATTTCCAGTCAACTTTGATAAACT
1 TTGATGATTGCTGAAAGGTGACCTGTTTCCAGTCAACTTTGATAAACT
26781 TTGATGATTGCTGAAAGGTGACCTGTTTCCAGTCAACTTTGATAAACT
1 TTGATGATTGCTGAAAGGTGACCTGTTTCCAGTCAACTTTGATAAACT
26829 TTGATGATTGCTGAAAGGTGACCTGTTTCCAGTCAACTT
1 TTGATGATTGCTGAAAGGTGACCTGTTTCCAGTCAACTT
26868 CGATGACTTC
Statistics
Matches: 130, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 130 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (48 bp):
TTGATGATTGCTGAAAGGTGACCTGTTTCCAGTCAACTTTGATAAACT
Found at i:27171 original size:37 final size:37
Alignment explanation
Indices: 27124--27234 Score: 93
Period size: 37 Copynumber: 3.0 Consensus size: 37
27114 TTGATCTTTA
*
27124 AGAAGCGACCAATCCGTGGTCAGTTGTTTGAGACTCG
1 AGAAGAGACCAATCCGTGGTCAGTTGTTTGAGACTCG
* * * * *
27161 AGGAGAGACCAGTCCGTGATC-GATTG-TTGA-TCTTTG
1 AGAAGAGACCAATCCGTGGTCAG-TTGTTTGAGAC-TCG
* * * *
27197 TGAAGCGACCAATCTGTCGTCAGTTGTTTGAGACTCG
1 AGAAGAGACCAATCCGTGGTCAGTTGTTTGAGACTCG
27234 A
1 A
27235 ATAGAGATCA
Statistics
Matches: 53, Mismatches: 16, Indels: 10
0.67 0.20 0.13
Matches are distributed among these distances:
35 1 0.02
36 24 0.45
37 27 0.51
38 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (37 bp):
AGAAGAGACCAATCCGTGGTCAGTTGTTTGAGACTCG
Found at i:27269 original size:73 final size:73
Alignment explanation
Indices: 27111--27273 Score: 236
Period size: 73 Copynumber: 2.2 Consensus size: 73
27101 CGTGGTCAAC
** * *
27111 TTGTTGATCTTTAAGAAGCGACCAATCCGTGGTCAGTTGTTTGAGACTCGAGGAGAGACCAGTCC
1 TTGTTGATCTTTGTGAAGCGACCAATCCGTCGTCAGTTGTTTGAGACTCGAAGAGAGACCAGTCC
27176 GTGATCGA
66 GTGATCGA
* * * *
27184 TTGTTGATCTTTGTGAAGCGACCAATCTGTCGTCAGTTGTTTGAGACTCGAATAGAGATCAGTTC
1 TTGTTGATCTTTGTGAAGCGACCAATCCGTCGTCAGTTGTTTGAGACTCGAAGAGAGACCAGTCC
* *
27249 TTGGTCGA
66 GTGATCGA
27257 TTGTTGATCTTTGTGAA
1 TTGTTGATCTTTGTGAA
27274 TTTTGTTAAG
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 80 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.34
Consensus pattern (73 bp):
TTGTTGATCTTTGTGAAGCGACCAATCCGTCGTCAGTTGTTTGAGACTCGAAGAGAGACCAGTCC
GTGATCGA
Found at i:28120 original size:18 final size:17
Alignment explanation
Indices: 28084--28125 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
28074 TTTGCTTGTT
28084 TTTTTTTC--TTTCTTC
1 TTTTTTTCATTTTCTTC
28099 -TTTTTTCATTTTCTCTC
1 TTTTTTTCATTTTCT-TC
28116 TTTTTTTCAT
1 TTTTTTTCAT
28126 GCGCTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.30
16 5 0.22
17 2 0.09
18 9 0.39
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTTCATTTTCTTC
Found at i:29758 original size:27 final size:27
Alignment explanation
Indices: 29717--29792 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
29707 GCATCAGGGT
* *
29717 CATCTAGGGGCATTTTGGTCATTTGCA
1 CATCCAGGGACATTTTGGTCATTTGCA
*
29744 CATCCAGGGATATTTTGGTCATTTGCA
1 CATCCAGGGACATTTTGGTCATTTGCA
**
29771 CATTTAGGGACATTTTGGTCAT
1 CATCCAGGGACATTTTGGTCAT
29793 CTCAAGTCTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (27 bp):
CATCCAGGGACATTTTGGTCATTTGCA
Done.