Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012655.1 Corchorus capsularis cultivar CVL-1 contig12676, 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: 27666
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:20842 original size:2 final size:2
Alignment explanation
Indices: 20837--20863 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20827 ATATATATAG
20837 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
20864 ACAACTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:21040 original size:12 final size:12
Alignment explanation
Indices: 21022--21052 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21012 TCCTCCTCCA
21022 CCGCCTCATCCT
1 CCGCCTCATCCT
*
21034 CCTCCTCATCCT
1 CCGCCTCATCCT
21046 CCGCCTC
1 CCGCCTC
21053 TTCTTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.06, C:0.61, G:0.06, T:0.26
Consensus pattern (12 bp):
CCGCCTCATCCT
Found at i:21619 original size:135 final size:135
Alignment explanation
Indices: 21372--21731 Score: 468
Period size: 135 Copynumber: 2.7 Consensus size: 135
21362 TCACTGCCCT
* * * * * *
21372 TTTGAAGGTTAGCGCTTTCAAAGACGAATCCCATGAAATCTCCCATGTTTTAAAATTGAGAATCA
1 TTTGAAGGTGAACGCTTTCAAAGAGGAATCCCTTGAAATCTCCCCTGTTTTAAACTTGAGAATCA
* ** * * * *
21437 TCCCAAAGGGAGGCTGTTGGTATTTGTTCAATCGCTGTTCCAATGTTTTCTTTCAGAAGCATCAA
66 TCACAAAGGGAGGCCCTTGGTATTTGTTAAATCGCTATTCCAATGTTTTCTTCCAGAAGCATAAA
21502 TCTTC
131 TCTTC
* * *
21507 TTTGAAGGTGAACACTTTCAAAGAGGAATCCCTTGAATTCTCCCCTGTTTTAAACTTGAAAATCA
1 TTTGAAGGTGAACGCTTTCAAAGAGGAATCCCTTGAAATCTCCCCTGTTTTAAACTTGAGAATCA
* * * ** *
21572 TCACAAAGGGAGGCCCTTGGTATTTGTTAAATCGTTATTTCAGTGTTTTCTTCCATCAGTATAAA
66 TCACAAAGGGAGGCCCTTGGTATTTGTTAAATCGCTATTCCAATGTTTTCTTCCAGAAGCATAAA
21637 TCTTC
131 TCTTC
* *
21642 TTTGAAGGTGAAGGCTTTCAAAGAGGAATCCCTTGAAATCTTCCCTGTTTTAAACTTGAGAATCA
1 TTTGAAGGTGAACGCTTTCAAAGAGGAATCCCTTGAAATCTCCCCTGTTTTAAACTTGAGAATCA
** * *
21707 TCTTAAAGGAAGGCCCATGGTATTT
66 TCACAAAGGGAGGCCCTTGGTATTT
21732 TTTCAATCCC
Statistics
Matches: 194, Mismatches: 31, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
135 194 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (135 bp):
TTTGAAGGTGAACGCTTTCAAAGAGGAATCCCTTGAAATCTCCCCTGTTTTAAACTTGAGAATCA
TCACAAAGGGAGGCCCTTGGTATTTGTTAAATCGCTATTCCAATGTTTTCTTCCAGAAGCATAAA
TCTTC
Found at i:22546 original size:30 final size:31
Alignment explanation
Indices: 22499--22569 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 31
22489 TGTTTTCCGC
*
22499 TTGTACCCTTATTTTTAAAACATATTTCCAA
1 TTGTACCATTATTTTTAAAACATATTTCCAA
*
22530 TTGTACCATT-TTTTTAAAACATATTTCTAA
1 TTGTACCATTATTTTTAAAACATATTTCCAA
*
22560 AT-TACCATTA
1 TTGTACCATTA
22570 CTAAATAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.19
30 20 0.56
31 9 0.25
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (31 bp):
TTGTACCATTATTTTTAAAACATATTTCCAA
Found at i:22758 original size:38 final size:37
Alignment explanation
Indices: 22677--22774 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 37
22667 TCAATGTGAC
*
22677 TTTTTATTTCCAACGTCCTATTTAATTTTGCCTTCTG
1 TTTTTGTTTCCAACGTCCTATTTAATTTTGCCTTCTG
* ** * *
22714 TCTTTGTTTCCAATCGTTGTATTTAATTTTGCTTTTTG
1 TTTTTGTTTCCAA-CGTCCTATTTAATTTTGCCTTCTG
* * *
22752 TTTTTGTCTCAAACATCCTATTT
1 TTTTTGTTTCCAACGTCCTATTT
22775 GGGCTTAGAT
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
37 18 0.38
38 30 0.62
ACGTcount: A:0.16, C:0.18, G:0.09, T:0.56
Consensus pattern (37 bp):
TTTTTGTTTCCAACGTCCTATTTAATTTTGCCTTCTG
Found at i:23821 original size:26 final size:27
Alignment explanation
Indices: 23790--23854 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 27
23780 ATAATTTTAG
23790 TTTTAATTTATAAT-TTATAT-ATAAGT
1 TTTTAATTTATAATGTTATATAATAA-T
*
23816 TTTTAATTT-TAATGTTTTATAATAAT
1 TTTTAATTTATAATGTTATATAATAAT
*
23842 TTATATATTTATA
1 TTTTA-ATTTATA
23855 TTCAACATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 4 0.12
26 19 0.58
27 8 0.24
28 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (27 bp):
TTTTAATTTATAATGTTATATAATAAT
Found at i:23968 original size:10 final size:10
Alignment explanation
Indices: 23942--23979 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
23932 AAATATAAAT
23942 CAAAACCG-C
1 CAAAACCGAC
23951 CAAAACCGAC
1 CAAAACCGAC
*
23961 CGAAACCGAC
1 CAAAACCGAC
23971 CAAAACCGA
1 CAAAACCGA
23980 TTAGTCGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.47, C:0.39, G:0.13, T:0.00
Consensus pattern (10 bp):
CAAAACCGAC
Found at i:24614 original size:22 final size:21
Alignment explanation
Indices: 24543--24726 Score: 129
Period size: 22 Copynumber: 8.3 Consensus size: 21
24533 TTGTCTCTAT
24543 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATCAAAATTTCAT-AG
* * * *
24565 ATGATTATTACAATTTCATGAG
1 GTGGTTATCAAAATTTCAT-AG
*
24587 GAGGTTATCAAAATTTCATAG
1 GTGGTTATCAAAATTTCATAG
* *
24608 TGTGGTTACCAAAATTTTATA-
1 -GTGGTTATCAAAATTTCATAG
*
24629 -TGGAATATCAAAATTTCATAG
1 GTGG-TTATCAAAATTTCATAG
*
24650 TGTGGTTTACCAAAATTTCATAG
1 -GTGG-TTATCAAAATTTCATAG
* * *
24673 GATCATGTTATTAAAATTTCTTAG
1 G-T--GGTTATCAAAATTTCATAG
**
24697 GTTGGTTATTGAAATTTCATAGG
1 G-TGGTTATCAAAATTTCATA-G
24720 GTGGTTA
1 GTGGTTA
24727 ATTATCACAA
Statistics
Matches: 126, Mismatches: 27, Indels: 18
0.74 0.16 0.11
Matches are distributed among these distances:
19 3 0.02
20 13 0.10
21 2 0.02
22 70 0.56
23 21 0.17
24 16 0.13
25 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.40
Consensus pattern (21 bp):
GTGGTTATCAAAATTTCATAG
Found at i:24820 original size:22 final size:22
Alignment explanation
Indices: 24766--24888 Score: 88
Period size: 22 Copynumber: 5.5 Consensus size: 22
24756 AAGAGATTAT
* *
24766 CAAAATGTCATAGTGAGGTTTA
1 CAAAATTTCATAGTGAGGTTAA
* *
24788 TAAGAATTTCATAGTGTGGTTAA
1 CAA-AATTTCATAGTGAGGTTAA
24811 CAAAATTTCATTAG-GAGGTT-A
1 CAAAATTTCA-TAGTGAGGTTAA
* * * * *
24832 CTAATATTTGATGGGGAGGTTAT
1 C-AAAATTTCATAGTGAGGTTAA
* * * *
24855 CAAAATTTTATAGTGTGATTAT
1 CAAAATTTCATAGTGAGGTTAA
24877 CAAAATTTCATA
1 CAAAATTTCATA
24889 TGAAGTTTAT
Statistics
Matches: 79, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
21 4 0.05
22 53 0.67
23 22 0.28
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAA
Found at i:25027 original size:14 final size:14
Alignment explanation
Indices: 25008--25034 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24998 ATAGGAAGAT
25008 TATCAAAATTTCAG
1 TATCAAAATTTCAG
25022 TATCAAAATTTCA
1 TATCAAAATTTCA
25035 AAACAAGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (14 bp):
TATCAAAATTTCAG
Found at i:25118 original size:22 final size:22
Alignment explanation
Indices: 25022--25146 Score: 117
Period size: 22 Copynumber: 5.6 Consensus size: 22
25012 AAAATTTCAG
*
25022 TATCAAAATTTCA-AAACAAGGT
1 TATCAAAATTTCATAAA-GAGGT
* * *
25044 TATCAAAATTACATAATGTGTGAT
1 TATCAAAATTTCATAAAGAG-G-T
* * *
25068 TATCAGAATTTCATAGAGGGGT
1 TATCAAAATTTCATAAAGAGGT
* * *
25090 CAACAAAATTTTATAAAGAGGT
1 TATCAAAATTTCATAAAGAGGT
25112 TATCAAAATTTCATAAAGAGGT
1 TATCAAAATTTCATAAAGAGGT
*
25134 TATCAAATTTTCA
1 TATCAAAATTTCA
25147 AAATGTGATT
Statistics
Matches: 81, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
22 61 0.75
23 4 0.05
24 16 0.20
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
TATCAAAATTTCATAAAGAGGT
Found at i:25299 original size:22 final size:22
Alignment explanation
Indices: 25271--25766 Score: 105
Period size: 22 Copynumber: 22.5 Consensus size: 22
25261 TCAGGGAGGA
*
25271 TATCAAAATTCCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
25293 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
25315 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
25337 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * ** * * **
25358 AGATCAAGATTTGGTAGGGACAT
1 -TATCAAAATTTCATATGAAGGT
*
25381 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
25403 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
25425 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
25441 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
25463 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* *
25486 TATCAAAGATTTC-TAGGAAGATT
1 TATCAAA-ATTTCATATGAAG-GT
* * *
25509 TATCAAAATTTTATA-GCGAGAT
1 TATCAAAATTTCATATG-AAGGT
** * ** *
25531 TATCTCAATTTCATAGGGTGAT
1 TATCAAAATTTCATATGAAGGT
* * * *
25553 TATTAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
25575 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * *
25597 T-TTAAAATTTTCATAACG-TGGT
1 TATCAAAA-TTTCAT-ATGAAGGT
* * * *
25619 TATCGATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* *
25641 TATCAACATCTCATAT-ATAGTGTTCGT
1 TATCAAAATTTCATATGA-A--G---GT
*
25668 TATCAAAATTTCATTAGGAA-GT
1 TATCAAAATTTCA-TATGAAGGT
25690 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * *
25712 CT-TCAAAATTCCATAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* * *
25734 TAACAGAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
25756 TAAAAAAATTT
1 TATCAAAATTT
25767 ATAAAAAGGT
Statistics
Matches: 347, Mismatches: 86, Indels: 82
0.67 0.17 0.16
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 2 0.01
20 4 0.01
21 18 0.05
22 247 0.71
23 43 0.12
24 5 0.01
27 13 0.04
28 3 0.01
29 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:25490 original size:23 final size:23
Alignment explanation
Indices: 25440--25524 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
25430 AAATTTGTAG
* * * *
25440 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
* *
25462 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGAT
*
25485 TTATCAAAGA-TTTCTAGGAAGAT
1 TTATCAAA-ATTTTATAGGAAGAT
25508 TTATCAAAATTTTATAG
1 TTATCAAAATTTTATAG
25525 CGAGATTATC
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
22 17 0.34
23 32 0.64
24 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:25775 original size:21 final size:22
Alignment explanation
Indices: 25730--25777 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
25720 TTCCATAGGG
* * *
25730 AGGTTAACAGAATTTCATAAGA
1 AGGTTAAAAAAATTTCATAAAA
25752 AGGTTAAAAAAATTT-ATAAAA
1 AGGTTAAAAAAATTTCATAAAA
25773 AGGTT
1 AGGTT
25778 CTCGAAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.29
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCATAAAA
Done.