Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008159.1 Corchorus capsularis cultivar CVL-1 contig08180, 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: 51166
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7645 original size:2 final size:2
Alignment explanation
Indices: 7640--7677 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
7630 ACTCTCTAGC
7640 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7678 GGAGGGGTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11649 original size:17 final size:17
Alignment explanation
Indices: 11625--11659 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11615 TCTGGTCGAA
*
11625 ATTTTTTTTATTTATTTT
1 ATTTTTTTT-TATATTTT
11643 ATTTTTTTTTATATTTT
1 ATTTTTTTTTATATTTT
11660 TCGATATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (17 bp):
ATTTTTTTTTATATTTT
Found at i:12702 original size:30 final size:30
Alignment explanation
Indices: 12668--12730 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
12658 AATGGGTCGA
*
12668 ATGGCCGGTTATGGCCGGATGGCCCGTGCG
1 ATGGCCGGTTATGGCCGGATGGCCCATGCG
* *
12698 ATGGCCGGTTGTGGCCGGATGGCTCATGCG
1 ATGGCCGGTTATGGCCGGATGGCCCATGCG
12728 ATG
1 ATG
12731 TCCCGTGCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.11, C:0.24, G:0.43, T:0.22
Consensus pattern (30 bp):
ATGGCCGGTTATGGCCGGATGGCCCATGCG
Found at i:12739 original size:12 final size:12
Alignment explanation
Indices: 12722--12751 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12712 CCGGATGGCT
12722 CATGCGATGTCC
1 CATGCGATGTCC
*
12734 CGTGCGATGTCC
1 CATGCGATGTCC
12746 CATGCG
1 CATGCG
12752 TTGGCCGGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.13, C:0.33, G:0.30, T:0.23
Consensus pattern (12 bp):
CATGCGATGTCC
Found at i:14343 original size:24 final size:24
Alignment explanation
Indices: 14311--14359 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
14301 GAGACAACTG
*
14311 AGCCGAACCACCACCCCTCGGAAC
1 AGCCGAACCACCACCCCTCGAAAC
14335 AGCCGAACCACCACCCCTCGAAAC
1 AGCCGAACCACCACCCCTCGAAAC
14359 A
1 A
14360 ACAGGTCCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.49, G:0.14, T:0.04
Consensus pattern (24 bp):
AGCCGAACCACCACCCCTCGAAAC
Found at i:15738 original size:35 final size:35
Alignment explanation
Indices: 15699--16323 Score: 988
Period size: 35 Copynumber: 17.9 Consensus size: 35
15689 TTCTTACTAA
15699 ACTTAACTT-CCCTGAATTAAGTTGATTACTGACTC
1 ACTTAA-TTACCCTGAATTAAGTTGATTACTGACTC
* *
15734 ACTTAATTACCCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
*
15769 ACTTAATTACCTTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * * *
15804 GCTTAATTACCTTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
15839 ACTTAATTACCCTGAATTAAGTTGATCACTCACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
15874 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
15909 ACTTAATTACCCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
15944 ACTTAATTACCCTAAATTAAGTTGATTACTG-CATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAC-TC
15979 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
16014 ACTTAATTACCCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
16049 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
*
16084 ACTTAATTACCCTGAATTAAGTGGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
*
16119 ACTTAATTACCCTGAATTAAGTGGATTACT--CTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
16152 ACTTAATTACCCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
16187 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * *
16222 AGTTAATTACCCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* *
16257 ACTTAATTACCCTTAATTAAGTTGATTACTAACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
16292 ACTTAATTACCCTGAATTAAGTTGATTACTGA
1 ACTTAATTACCCTGAATTAAGTTGATTACTGA
16324 AAACCTTTTC
Statistics
Matches: 543, Mismatches: 42, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
33 32 0.06
34 2 0.00
35 508 0.94
36 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.38
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
Found at i:17060 original size:30 final size:30
Alignment explanation
Indices: 17026--17084 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
17016 AAAAGAAAAC
17026 CAATCCTCATACACAACTTACTTAAAAATT
1 CAATCCTCATACACAACTTACTTAAAAATT
* * *
17056 CAATCTTTATATACAACTTACTTAAAAAT
1 CAATCCTCATACACAACTTACTTAAAAAT
17085 CCCACCTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (30 bp):
CAATCCTCATACACAACTTACTTAAAAATT
Found at i:17132 original size:20 final size:20
Alignment explanation
Indices: 17075--17133 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
17065 TATACAACTT
* * *
17075 ACTTAAAAATCCCACCTTTC
1 ACTTAAAAATTCAATCTTTC
*
17095 ACTTAAAAATTCAGTCTTTC
1 ACTTAAAAATTCAATCTTTC
* *
17115 ACTTAAACATTTAATCTTT
1 ACTTAAAAATTCAATCTTT
17134 ATTTATAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.39
Consensus pattern (20 bp):
ACTTAAAAATTCAATCTTTC
Found at i:17192 original size:30 final size:30
Alignment explanation
Indices: 17115--17193 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
17105 TCAGTCTTTC
*
17115 ACTTAAACATTTAATCTTTATTTATAAATT
1 ACTTAAAAATTTAATCTTTATTTATAAATT
* ** *
17145 ACTCAAAAATACAATCTTTGTTTATAAATT
1 ACTTAAAAATTTAATCTTTATTTATAAATT
* * *
17175 ATTTAAAGATTTTATCTTT
1 ACTTAAAAATTTAATCTTT
17194 CAACACAATG
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (30 bp):
ACTTAAAAATTTAATCTTTATTTATAAATT
Found at i:19306 original size:26 final size:26
Alignment explanation
Indices: 19272--19323 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
19262 GTTTTATTTG
*
19272 AGTTTTTTTTTAGTCGGTTT-GAGTC
1 AGTTTTTTTTTAGTCAGTTTCGAGTC
19297 AGTTTGTTTTTTAGTCAGTTTCGAGTC
1 AGTTT-TTTTTTAGTCAGTTTCGAGTC
19324 TAGTCTCAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 5 0.21
26 14 0.58
27 5 0.21
ACGTcount: A:0.13, C:0.10, G:0.23, T:0.54
Consensus pattern (26 bp):
AGTTTTTTTTTAGTCAGTTTCGAGTC
Found at i:25616 original size:27 final size:28
Alignment explanation
Indices: 25586--25659 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 28
25576 GGTCACCTAA
* *
25586 GGGCATTTTGGTCATTTTCATATTC-TG
1 GGGCATTTTGGTCATTTTCACATTCAGG
**
25613 GGGCATTTTGGTCATTTTTGCATTCAAGG
1 GGGCATTTTGGTCATTTTCACATTC-AGG
25642 GGGCATTTTGGTCATTTT
1 GGGCATTTTGGTCATTTT
25660 GAGTCCATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 22 0.54
29 19 0.46
ACGTcount: A:0.15, C:0.14, G:0.26, T:0.46
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTTCACATTCAGG
Found at i:35872 original size:176 final size:176
Alignment explanation
Indices: 35578--35926 Score: 644
Period size: 176 Copynumber: 2.0 Consensus size: 176
35568 AGATGTGTTC
* *
35578 GCATGGTCGTATCAGGATATGTCGGGATTGAATCCTAAGGTAGCAGTTCACAGATTACCGATTAG
1 GCATGGTCGTATCAGGATATGCCGGGATTGAATCCTAAGGTAGCAGATCACAGATTACCGATTAG
*
35643 ACTTGAATGCAAGCCAGTACAACAAAAGTTAAGAAGGATGAAGCCGGATATGCTTTTGAAAATAA
66 ACTTGAATGCAAGCCAGTACAACAAAAGTTAAGAAGGATGAAGCCGGATATGCTTTGGAAAATAA
35708 AAGAAGAAGTCAAGAAACAGTTTGATGCCGATTTTCTTAAGGATAT
131 AAGAAGAAGTCAAGAAACAGTTTGATGCCGATTTTCTTAAGGATAT
*
35754 GCATGGTCGTATCAGGATATGCCGGGATTGAATCCTGAGGTAGCAGATCACAGATTACCGATTAG
1 GCATGGTCGTATCAGGATATGCCGGGATTGAATCCTAAGGTAGCAGATCACAGATTACCGATTAG
35819 ACTTGAATGCAAGCCAGTACAACAAAAGTTAAGAAGGATGAAGCCGGATATGCTTTGGAAAATAA
66 ACTTGAATGCAAGCCAGTACAACAAAAGTTAAGAAGGATGAAGCCGGATATGCTTTGGAAAATAA
* *
35884 AAGAAGAAGTCAAGAAACAGTTTGATGCCGGTTTTCTTGAGGA
131 AAGAAGAAGTCAAGAAACAGTTTGATGCCGATTTTCTTAAGGA
35927 GATTAGGTAT
Statistics
Matches: 167, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
176 167 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (176 bp):
GCATGGTCGTATCAGGATATGCCGGGATTGAATCCTAAGGTAGCAGATCACAGATTACCGATTAG
ACTTGAATGCAAGCCAGTACAACAAAAGTTAAGAAGGATGAAGCCGGATATGCTTTGGAAAATAA
AAGAAGAAGTCAAGAAACAGTTTGATGCCGATTTTCTTAAGGATAT
Found at i:37650 original size:22 final size:22
Alignment explanation
Indices: 37622--37667 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
37612 AATTGGACCA
37622 AATCCACCGTAGAGACCCGCCT
1 AATCCACCGTAGAGACCCGCCT
37644 AATCCACCGTAGAGACCCGCCT
1 AATCCACCGTAGAGACCCGCCT
37666 AA
1 AA
37668 GATCAACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.39, G:0.17, T:0.13
Consensus pattern (22 bp):
AATCCACCGTAGAGACCCGCCT
Found at i:44488 original size:21 final size:21
Alignment explanation
Indices: 44455--44503 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
44445 AAGAATTGTA
**
44455 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
44475 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
44496 GCATTCCT
1 GC-TTCCT
44504 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:45704 original size:28 final size:28
Alignment explanation
Indices: 45631--45704 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 28
45621 AAGTAACTTG
*
45631 GAAAATAAAAAG-TAAGGAAAAATTAAC
1 GAAAATAAAAAGATAAAGAAAAATTAAC
* *
45658 TAAACTAAAAATTGA-AAAGAAAAA-TAAC
1 GAAAATAAAAA--GATAAAGAAAAATTAAC
45686 GAAAATATAAAAGATAAAG
1 GAAAATA-AAAAGATAAAG
45705 GTAAGAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
27 11 0.30
28 13 0.35
29 13 0.35
ACGTcount: A:0.68, C:0.04, G:0.12, T:0.16
Consensus pattern (28 bp):
GAAAATAAAAAGATAAAGAAAAATTAAC
Found at i:49184 original size:27 final size:27
Alignment explanation
Indices: 49129--49184 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
49119 TTGTCTCAAT
* **
49129 TCGAGAGTTTCTTGTCTCAATCTCTAG
1 TCGAGAGTTTCCTGTCTCAATCTAAAG
* *
49156 TCGAGAGTTTCCTGTTTCAATTTAAAG
1 TCGAGAGTTTCCTGTCTCAATCTAAAG
49183 TC
1 TC
49185 TTGTTTTGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (27 bp):
TCGAGAGTTTCCTGTCTCAATCTAAAG
Found at i:49227 original size:63 final size:63
Alignment explanation
Indices: 49149--49484 Score: 423
Period size: 63 Copynumber: 5.3 Consensus size: 63
49139 CTTGTCTCAA
*
49149 TCTCTAGTCGAGAGTTTCCTGTTTCAATTTAAAGTCTTGTTTTGCTTCAAATCCTAGTTGAGG
1 TCTCTAGTCGAGAGTTTCTTGTTTCAATTTAAAGTCTTGTTTTGCTTCAAATCCTAGTTGAGG
49212 TCTCTAGTCGAGAGTTTCTTGTTTCAATTTAAAGTCTTGTTTTGCTTCAAATCCTAGTTGAGG
1 TCTCTAGTCGAGAGTTTCTTGTTTCAATTTAAAGTCTTGTTTTGCTTCAAATCCTAGTTGAGG
* * * *
49275 TCTCTAGTCGAGAGTTTCTTGTTTCAATTCAAGGTCTTGTTTAGCTTCAAATCCTAATTGAGG
1 TCTCTAGTCGAGAGTTTCTTGTTTCAATTTAAAGTCTTGTTTTGCTTCAAATCCTAGTTGAGG
* * * *
49338 TCTCTAGTC-AGAGTTTTCTTGTTTCAATTCCAAAATCATGCTCTT--TTCAAATCCT-GCTTGA
1 TCTCTAGTCGAGAG-TTTCTTGTTTCAATT-TAAAGTCTTG-TTTTGCTTCAAATCCTAG-TTGA
49399 GG
62 GG
* * * * * * *
49401 TTTCTAGTCGAGGGTTTCTTATTTCAATCTAAAGACTTG-TTT-CTTTCCAAATCCTAATCGAGG
1 TCTCTAGTCGAGAGTTTCTTGTTTCAATTTAAAGTCTTGTTTTGC-TT-CAAATCCTAGTTGAGG
*
49464 TCTCTAGTCGAGGGTTTCTTG
1 TCTCTAGTCGAGAGTTTCTTG
49485 CTCCAGTTCT
Statistics
Matches: 240, Mismatches: 24, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
60 2 0.01
62 12 0.05
63 214 0.89
64 10 0.04
65 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (63 bp):
TCTCTAGTCGAGAGTTTCTTGTTTCAATTTAAAGTCTTGTTTTGCTTCAAATCCTAGTTGAGG
Found at i:49520 original size:126 final size:123
Alignment explanation
Indices: 49151--49543 Score: 404
Period size: 126 Copynumber: 3.1 Consensus size: 123
49141 TGTCTCAATC
* *
49151 TCTAGTCGAGAGTTTCCTGTTTCAATTTAAAGTCTTGTTT-TGCTTCAAATCCTAGTTGAGGTCT
1 TCTAGTCGAGAGTTTCTTGTTTCAA-TTAAAGTCTTGTTTCT--TTCAAATCCTAATTGAGGTCT
* * *
49215 CTAGTCGAGAGTTTCTTGTTTCAATT-TAAAGTCTTGTTTTGCTTCAAATCCTAG-TTGAGGTC
63 CTAGTCGAGGGTTTCTTGTTTCAATTCTAAA-TCTTGTTTT-TTTCAAATCCT-GCTTGAGGTT
*
49277 TCTAGTCGAGAGTTTCTTGTTTCAATTCAAGGTCTTGTTTAGC-TTCAAATCCTAATTGAGGTCT
1 TCTAGTCGAGAGTTTCTTGTTTCAATT-AAAGTCTTGTTT--CTTTCAAATCCTAATTGAGGTCT
* * * * *
49341 CTAGTC-AGAGTTTTCTTGTTTCAATTCCAAAATCATGCTCTTTTCAAATCCTGCTTGAGGTT
63 CTAGTCGAG-GGTTTCTTGTTTCAATT-CTAAATCTTGTTTTTTTCAAATCCTGCTTGAGGTT
* * * *
49403 TCTAGTCGAGGGTTTCTTATTTCAATCTAAAGACTTGTTTCTTTCCAAATCCTAATCGAGGTCTC
1 TCTAGTCGAGAGTTTCTTGTTTCAAT-TAAAGTCTTGTTTCTTT-CAAATCCTAATTGAGGTCTC
* * * * * *
49468 TAGTCGAGGGTTTCTTGCTCCAGTTCTAAATTTTGTTTTATTTCGAGA-CCTGCTCGAGGTT
64 TAGTCGAGGGTTTCTTGTTTCAATTCTAAATCTTGTTTT-TTTC-AAATCCTGCTTGAGGTT
49529 TCT-GTTCGAGAGTTT
1 TCTAG-TCGAGAGTTT
49544 GGTTTCAAAA
Statistics
Matches: 224, Mismatches: 28, Indels: 30
0.79 0.10 0.11
Matches are distributed among these distances:
124 1 0.00
125 17 0.08
126 192 0.86
127 11 0.05
128 3 0.01
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (123 bp):
TCTAGTCGAGAGTTTCTTGTTTCAATTAAAGTCTTGTTTCTTTCAAATCCTAATTGAGGTCTCTA
GTCGAGGGTTTCTTGTTTCAATTCTAAATCTTGTTTTTTTCAAATCCTGCTTGAGGTT
Found at i:49821 original size:26 final size:27
Alignment explanation
Indices: 49792--49865 Score: 98
Period size: 26 Copynumber: 2.7 Consensus size: 27
49782 GGGTCACCCA
*
49792 GGGGCATTTTGGTCATTTTAT-ATTC-T
1 GGGGCATTTTGGTCATTTT-TCATTCAG
49818 GGGGCATTTTGGTCATTTTTGCATTCAAG
1 GGGGCATTTTGGTCATTTTT-CATTC-AG
49847 GGGGCATTTTGGTCATTTT
1 GGGGCATTTTGGTCATTTT
49866 GAGTCCATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 1 0.02
26 19 0.44
27 4 0.09
29 19 0.44
ACGTcount: A:0.15, C:0.12, G:0.27, T:0.46
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTTTCATTCAG
Done.