Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014396.1 Corchorus capsularis cultivar CVL-1 contig14417, 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: 30609
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:361 original size:78 final size:78
Alignment explanation
Indices: 275--436 Score: 254
Period size: 78 Copynumber: 2.1 Consensus size: 78
265 GATTTTTATA
* *
275 ATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATA-TTTATAACTATTATAT
1 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATA-ACCTTATAACTATTATAT
*
339 TTTACCATTTTACT
65 TTTAACATTTTACT
* *
353 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTATTAACCTTATAACTATTATATT
1 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAACCTTATAACTATTATATT
*
418 TTAATATTTTACT
66 TTAACATTTTACT
431 ATTTTA
1 ATTTTA
437 ATTAAAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
77 1 0.01
78 76 0.99
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (78 bp):
ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAACCTTATAACTATTATATT
TTAACATTTTACT
Found at i:555 original size:23 final size:23
Alignment explanation
Indices: 528--571 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
518 AAACTTTTGC
*
528 AATTGAAAACACTATTTTTATTT
1 AATTGAAAACAATATTTTTATTT
**
551 AATTGAATTCAATATTTTTAT
1 AATTGAAAACAATATTTTTAT
572 AATTATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (23 bp):
AATTGAAAACAATATTTTTATTT
Found at i:1150 original size:13 final size:13
Alignment explanation
Indices: 1132--1166 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1122 TCCTTAATGG
1132 AATCGATATGGTT
1 AATCGATATGGTT
1145 AATCGATATGGTT
1 AATCGATATGGTT
*
1158 AATCAATAT
1 AATCGATAT
1167 AGTATTCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (13 bp):
AATCGATATGGTT
Found at i:4145 original size:14 final size:13
Alignment explanation
Indices: 4126--4153 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4116 ACCTCGAGGG
4126 AGAAAAATATTAA
1 AGAAAAATATTAA
4139 AGAAAAATATTAA
1 AGAAAAATATTAA
4152 AG
1 AG
4154 GAGAGGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (13 bp):
AGAAAAATATTAA
Found at i:11067 original size:16 final size:17
Alignment explanation
Indices: 11035--11067 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11025 AAGAGAAGTA
*
11035 TATATGTTTAGCATTTT
1 TATATCTTTAGCATTTT
11052 TATATCTTTA-CATTTT
1 TATATCTTTAGCATTTT
11068 CAGGACATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.61
Consensus pattern (17 bp):
TATATCTTTAGCATTTT
Found at i:13265 original size:40 final size:39
Alignment explanation
Indices: 13210--13286 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 39
13200 AGATAATATG
* *
13210 ATATATCTGCTTCTTTCTTTTTCTTTTTCTTTTTTGAAAA
1 ATATATCTGCTTCTTTCTTCTTCTTTTT-TTTGTTGAAAA
13250 ATATATCTGCTTCTTTCTTCTTCTTTTTTTTGTTGAA
1 ATATATCTGCTTCTTTCTTCTTCTTTTTTTTGTTGAA
13287 TGGCAAGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 8 0.23
40 27 0.77
ACGTcount: A:0.16, C:0.16, G:0.06, T:0.62
Consensus pattern (39 bp):
ATATATCTGCTTCTTTCTTCTTCTTTTTTTTGTTGAAAA
Found at i:13412 original size:2 final size:2
Alignment explanation
Indices: 13394--13435 Score: 59
Period size: 2 Copynumber: 20.5 Consensus size: 2
13384 GCATGTAATC
13394 AT AT CAT AT AT -T CAT 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 AT AT A
13436 AACTGAGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 1 0.03
2 33 0.89
3 3 0.08
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14167 original size:20 final size:20
Alignment explanation
Indices: 14130--14167 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
14120 TTAGTATGGC
* *
14130 AAAATTTTTGTTTTTTTAGG
1 AAAATTTTTATTTATTTAGG
14150 AAAATTTTTATTTATTTA
1 AAAATTTTTATTTATTTA
14168 AGAACTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (20 bp):
AAAATTTTTATTTATTTAGG
Found at i:14344 original size:13 final size:13
Alignment explanation
Indices: 14328--14359 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
14318 TTTTTCATTC
14328 TTATGTTCTTAAA
1 TTATGTTCTTAAA
14341 TTATGTTCTTAAA
1 TTATGTTCTTAAA
14354 TTATGT
1 TTATGT
14360 ATTGTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.56
Consensus pattern (13 bp):
TTATGTTCTTAAA
Found at i:15827 original size:138 final size:139
Alignment explanation
Indices: 15589--15858 Score: 355
Period size: 138 Copynumber: 1.9 Consensus size: 139
15579 CCAAAAGCTA
* *
15589 ATGATTATTTAATTTTGCCACAAATAAATGAATCAATTAGTATTATATTACAAAAAAATAAATTG
1 ATGATTATTTAATTTTGCCACAAATAAATAAATCAATTAATATTATATTAC-AAAAAATAAATTG
* * * *
15654 ATTGAACATCCAAAATAAGTAAATGAATCAAGTTAGCCATTAGTTAACTTTGCCAATAAAAGTTA
65 ATTGAACAACCAAAATAAATAAATGAATCAAGTTAGCCATTAATCAACTTTGCCAATAAAAGTTA
15719 TAAATGATGG
130 TAAATGATGG
* ** * *
15729 ATGATTATTTAATTTTTCCATGAATAAATAAATCAATTAATAATTATGTTAC-CAAAA-AAATTG
1 ATGATTATTTAATTTTGCCACAAATAAATAAATCAATTAAT-ATTATATTACAAAAAATAAATTG
* * * * * *
15792 ATTGAACAAGCTAAATAAATAAATGAATCAAGTTAGTCGTTAATCAACTTTGTCAATCAAAGTTA
65 ATTGAACAACCAAAATAAATAAATGAATCAAGTTAGCCATTAATCAACTTTGCCAATAAAAGTTA
15857 TA
130 TA
15859 TGTCACGCCC
Statistics
Matches: 112, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
138 63 0.56
139 4 0.04
140 36 0.32
141 9 0.08
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (139 bp):
ATGATTATTTAATTTTGCCACAAATAAATAAATCAATTAATATTATATTACAAAAAATAAATTGA
TTGAACAACCAAAATAAATAAATGAATCAAGTTAGCCATTAATCAACTTTGCCAATAAAAGTTAT
AAATGATGG
Found at i:16932 original size:26 final size:27
Alignment explanation
Indices: 16879--16938 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
16869 TAATGCACCC
* * *
16879 AAAACATTTTAATAAAAATCATTTATA
1 AAAACAATTTAATAAAAATCAGTAATA
*
16906 AAAACAATTTATTAAAAAT-AGTAATA
1 AAAACAATTTAATAAAAATCAGTAATA
16932 AAAACAA
1 AAAACAA
16939 GTCACTCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAACAATTTAATAAAAATCAGTAATA
Found at i:18721 original size:16 final size:16
Alignment explanation
Indices: 18702--18732 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18692 TTCTGTTTTC
*
18702 TGTTTTTGTTTCGTTT
1 TGTTTTTGTTGCGTTT
18718 TGTTTTTGTTGCGTT
1 TGTTTTTGTTGCGTT
18733 GTCAATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.06, G:0.23, T:0.71
Consensus pattern (16 bp):
TGTTTTTGTTGCGTTT
Found at i:19399 original size:141 final size:142
Alignment explanation
Indices: 19114--19444 Score: 531
Period size: 141 Copynumber: 2.3 Consensus size: 142
19104 AAGTCAGTGA
* * *
19114 TCGTTAGTTAATTTT-TCCAATCAAAGTCGTAATTGATTGATAATTATTTAATTTTACCATAAAT
1 TCGTTAGTTAATTTTGT-CAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAA-
*
19178 GATCACTACCAAAAAAATTAACATAAAGAAATAAATCAATTAGTAATTATGTTACCAAAAAAATA
64 GATCACCACCAAAAAAATTAACATAAAGAAATAAATCAATTAGTAATTATGTTACCAAAAAAATA
19243 AATTATTGAACATG
129 AATTATTGAACATG
19257 TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAA-A
1 TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAGA
* * * *
19321 TCGCCACCAAAAAAATTACCATAAATAAATAAATCAGTTAGTAATTATGTTACCAAAAAAATAAA
66 TCACCACCAAAAAAATTAACATAAAGAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAA
*
19386 TTATTGAATATG
131 TTATTGAACATG
* *
19398 TCGTTAGTTAATTTTGCCAATCAAAGTTGTAATTCATTGATGATTAT
1 TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTAT
19445 GTAACCAAAG
Statistics
Matches: 176, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
141 117 0.66
143 58 0.33
144 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.37
Consensus pattern (142 bp):
TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAGA
TCACCACCAAAAAAATTAACATAAAGAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAA
TTATTGAACATG
Found at i:21291 original size:36 final size:35
Alignment explanation
Indices: 21224--21292 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 35
21214 AGGAATATAA
* *
21224 TACAATTATGTTTGGTATCTTTCTTTTTTTTTCGG
1 TACAATTATGTTTGGTATCTTTCTCTCTTTTTCGG
21259 TACATATTATGTTTGGTATCTTAT-TCTCTTTTTC
1 TACA-ATTATGTTTGGTATCTT-TCTCTCTTTTTC
21293 CTTTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 4 0.13
36 25 0.83
37 1 0.03
ACGTcount: A:0.16, C:0.13, G:0.12, T:0.59
Consensus pattern (35 bp):
TACAATTATGTTTGGTATCTTTCTCTCTTTTTCGG
Found at i:23233 original size:12 final size:12
Alignment explanation
Indices: 23202--23235 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
23192 AATTTTCTAC
23202 AAATTTATTCTG
1 AAATTTATTCTG
*
23214 AGAATTTATTCTT
1 A-AATTTATTCTG
23227 AAATTTATT
1 AAATTTATT
23236 GGAGATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (12 bp):
AAATTTATTCTG
Found at i:23602 original size:16 final size:16
Alignment explanation
Indices: 23581--23614 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
23571 ACAATTCAGA
23581 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
23597 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
23613 AA
1 AA
23615 CTATTTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:25902 original size:63 final size:61
Alignment explanation
Indices: 25818--25952 Score: 216
Period size: 63 Copynumber: 2.2 Consensus size: 61
25808 ATAAAAAATT
*
25818 AAAAAAAAAAACTCACTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGC
1 AAAAAAAAAAACTCACTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGC
* *
25879 AAAAAAAAAAAGTCTCGCTAAGTTGAAAATCCTGCAAATGACGGCTTAGGCAAAACTTAGAGC
1 AAAAAAAAAAA--CTCACTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGC
*
25942 ACAAAAAAAAA
1 AAAAAAAAAAA
25953 TGAACTACGT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 11 0.16
63 57 0.84
ACGTcount: A:0.50, C:0.16, G:0.18, T:0.16
Consensus pattern (61 bp):
AAAAAAAAAAACTCACTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGC
Found at i:26705 original size:16 final size:16
Alignment explanation
Indices: 26684--26718 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
26674 ACAATTCAGA
26684 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
26700 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
26716 AAG
1 AAG
26719 TATTTCAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:28626 original size:53 final size:54
Alignment explanation
Indices: 28558--28668 Score: 197
Period size: 53 Copynumber: 2.1 Consensus size: 54
28548 TCGCCGCGGG
* *
28558 CTTGTGTCTCTAAACGGGACTTGTAAAATTGTTGGGCAATTATTGAATTAGGAA
1 CTTGTGTCTCTAAACGGGAATTGTAAAATTGTTGGGCAATTATTGAATTAGAAA
28612 CTTG-GTCTCTAAACGGGAATTGTAAAATTGTTGGGCAATTATTGAATTAGAAA
1 CTTGTGTCTCTAAACGGGAATTGTAAAATTGTTGGGCAATTATTGAATTAGAAA
28665 CTTG
1 CTTG
28669 ACATGAAAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
53 51 0.93
54 4 0.07
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (54 bp):
CTTGTGTCTCTAAACGGGAATTGTAAAATTGTTGGGCAATTATTGAATTAGAAA
Done.