Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015270.1 Corchorus capsularis cultivar CVL-1 contig15291, 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: 77825
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Found at i:4296 original size:21 final size:21
Alignment explanation
Indices: 4257--4305 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
4247 TCAATGCTTT
**
4257 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
4279 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
4300 A-GAAGC
1 AGGAAGC
4306 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:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:23731 original size:29 final size:27
Alignment explanation
Indices: 23699--23772 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
23689 AAGTGGACTT
*
23699 AAAATGACCAAAATGCCCTTTGAATGCAA
1 AAAATGACCAAAATGCCC-ATGAATG-AA
**
23728 AAAATGACCAAAATGCCCATGAATGTG
1 AAAATGACCAAAATGCCCATGAATGAA
23755 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
23773 CTGGGTGACC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
27 18 0.43
28 6 0.14
29 18 0.43
ACGTcount: A:0.46, C:0.22, G:0.15, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCATGAATGAA
Found at i:44012 original size:33 final size:33
Alignment explanation
Indices: 43915--44019 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 33
43905 TTGCAAAGAG
* * *
43915 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
** * *
43948 TAATTT-GAGTGTTGTTTGCAATGACACTAAATC
1 TGTTTTAG-GTGTTGTTTGCGATGAAACTAAATC
*
43981 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
44014 TGTTTT
1 TGTTTT
44020 GGATGCTAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 1 0.02
33 57 0.97
34 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.45
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
Found at i:44033 original size:33 final size:32
Alignment explanation
Indices: 43968--44055 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 32
43958 GTTGTTTGCA
* * **
43968 ATGACACTAAATCTGTTTTAGGTGTTGTTTGTG
1 ATGAAACTAAATCTGTTTT-GGTGCTAATTGTG
44001 ATGAAACTAAATCTGTTTTGGATGCTAATTGTG
1 ATGAAACTAAATCTGTTTTGG-TGCTAATTGTG
*
44034 ATGAAAAC-AAATTTGTTTTGGT
1 ATG-AAACTAAATCTGTTTTGGT
44056 TGATCATAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
32 3 0.06
33 41 0.85
34 4 0.08
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (32 bp):
ATGAAACTAAATCTGTTTTGGTGCTAATTGTG
Found at i:46074 original size:45 final size:44
Alignment explanation
Indices: 46025--46111 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 44
46015 TCGCATTTGA
* *
46025 CCGGCCACACCGGCTAGATGACCCGGCCATGCCGATCGCACAAGC
1 CCGGCCACACCGGCCAGATGACCCGGCCATGCCCAT-GCACAAGC
*
46070 CCGGCCACACCGGCCATATGACCCGGCCATGCCCATGCACAA
1 CCGGCCACACCGGCCAGATGACCCGGCCATGCCCATGCACAA
46112 TCGGCCATGC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 6 0.15
45 33 0.85
ACGTcount: A:0.23, C:0.44, G:0.24, T:0.09
Consensus pattern (44 bp):
CCGGCCACACCGGCCAGATGACCCGGCCATGCCCATGCACAAGC
Found at i:46097 original size:22 final size:22
Alignment explanation
Indices: 46025--46098 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
46015 TCGCATTTGA
* *
46025 CCGGCCACACCGGCTAGATGAC
1 CCGGCCACACCGGCCACATGAC
** * *
46047 CCGGCCATGCCGATCGCACAAG-C
1 CCGGCCACACCG-GC-CACATGAC
*
46070 CCGGCCACACCGGCCATATGAC
1 CCGGCCACACCGGCCACATGAC
46092 CCGGCCA
1 CCGGCCA
46099 TGCCCATGCA
Statistics
Matches: 38, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
21 4 0.11
22 19 0.50
23 12 0.32
24 3 0.08
ACGTcount: A:0.22, C:0.45, G:0.26, T:0.08
Consensus pattern (22 bp):
CCGGCCACACCGGCCACATGAC
Found at i:47163 original size:13 final size:12
Alignment explanation
Indices: 47144--47173 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
47134 GAAAAATATC
47144 AAAAAAATAAAA
1 AAAAAAATAAAA
47156 ATAAAAAATAAAA
1 A-AAAAAATAAAA
47169 AAAAA
1 AAAAA
47174 TTTCGACCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAAAATAAAA
Found at i:57118 original size:207 final size:207
Alignment explanation
Indices: 56758--57166 Score: 728
Period size: 207 Copynumber: 2.0 Consensus size: 207
56748 AAGGTGATTT
*
56758 GCCAAAGGCTTATCATGGTTTTGAAGAGCACAATGGAGCTAATGAAGATCATGTCTCGGATAAAC
1 GCCAAAGGCTTATCATGGTTTTGAAGAGCACAATGGAGCTAATGAAGATCATGTCTCCGATAAAC
* *
56823 TTGGAGATGTCTCGGATATTCAAGAAGTTGCTACGGTTGATCCCGGATTGAGAGGAAGCATGGAG
66 TTGGAGATGTCTCGGATATTCAAGAAGTTGCTACAGTTGATCCCGGATTGAAAGGAAGCATGGAG
* * ** *
56888 GAGCTTGGAGAGGATGTCATCGCACAAGACCTTCCATTGCTTGGAAGGATCGCACAAGACCGGGC
131 GAGCTTGGAGAGGACGCCATCGCACAAGACCGACCACTGCTTGGAAGGATCGCACAAGACCGGGC
56953 ACATGATGATGG
196 ACATGATGATGG
56965 GCCAAAGGCTTATCATGGTTTTGAAGAGCACAATGGAGCTAATGAAGATCATGTCTCCGATAAAC
1 GCCAAAGGCTTATCATGGTTTTGAAGAGCACAATGGAGCTAATGAAGATCATGTCTCCGATAAAC
57030 TTGGAGATGTCTCGGATATTCAAGAAGTTGCTACAGTTGATCCCGGATTGAAAGGAAGCATGGAG
66 TTGGAGATGTCTCGGATATTCAAGAAGTTGCTACAGTTGATCCCGGATTGAAAGGAAGCATGGAG
**
57095 GAGCTTGGAGAGGACGCCATCGCACAAGACCGACCACTGCTTGGAAGGATCGCACAAGACCGGTT
131 GAGCTTGGAGAGGACGCCATCGCACAAGACCGACCACTGCTTGGAAGGATCGCACAAGACCGGGC
57160 ACATGAT
196 ACATGAT
57167 CGGGCACATG
Statistics
Matches: 192, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
207 192 1.00
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (207 bp):
GCCAAAGGCTTATCATGGTTTTGAAGAGCACAATGGAGCTAATGAAGATCATGTCTCCGATAAAC
TTGGAGATGTCTCGGATATTCAAGAAGTTGCTACAGTTGATCCCGGATTGAAAGGAAGCATGGAG
GAGCTTGGAGAGGACGCCATCGCACAAGACCGACCACTGCTTGGAAGGATCGCACAAGACCGGGC
ACATGATGATGG
Found at i:58254 original size:13 final size:14
Alignment explanation
Indices: 58236--58266 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
58226 AGTTATATCG
58236 AAAAAT-ATAAAAA
1 AAAAATAATAAAAA
58249 AAAAATAATAAAAA
1 AAAAATAATAAAAA
58263 AAAA
1 AAAA
58267 GTTTCGACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAATAATAAAAA
Found at i:64975 original size:33 final size:33
Alignment explanation
Indices: 64935--65050 Score: 171
Period size: 33 Copynumber: 3.5 Consensus size: 33
64925 TGATGAAAAC
*
64935 AAATCTGTTTTGGTTTATCATAGCATTGCAAAT
1 AAATCTGTTTTGGTTGATCATAGCATTGCAAAT
*
64968 AATTCTGTTTTGGTTGATCATAGCATTGCAAAT
1 AAATCTGTTTTGGTTGATCATAGCATTGCAAAT
* *
65001 AAATCTGTTTTGGTTGATAATAGCATTGAAAAT
1 AAATCTGTTTTGGTTGATCATAGCATTGCAAAT
*
65034 AGGA-CTGTTTTGGTTGA
1 A-AATCTGTTTTGGTTGA
65051 AAAGAAAGAG
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
33 75 0.99
34 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.41
Consensus pattern (33 bp):
AAATCTGTTTTGGTTGATCATAGCATTGCAAAT
Found at i:74428 original size:53 final size:53
Alignment explanation
Indices: 74365--74857 Score: 649
Period size: 53 Copynumber: 9.6 Consensus size: 53
74355 AAAGAGTAAA
* *
74365 CAGTAAATAGGTTTCATTCAGAGTAATTAAGCTAAGCAGTAAAAGGAGAAAAT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAAT
* *
74418 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGTAGTAAAAGGGGAAAAT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAAT
**
74471 CAG----TA-G--TAATT-AGCTTAATTAACCTAAGCAGTAAAAGGAGAAAAT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAAT
* * *
74516 CAGTAAATAGGTTTAATTCCGAGTAATTAACCTAAGTAGTAAAAGGGGAAAAT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAAT
**
74569 CAGTAAATAGGTTTAATTCAGAGTAATTAATGTAAGCAGTAAAAGGAGAAAAT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAAT
* * *
74622 CAGTAAATAGGTTTAATTCCGAGTAATTAACCTAAGTAGTAAAAGGGGAAAAT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAAT
*
74675 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAAGAGAAAAT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAAT
* * *
74728 TAGTAAATAGGTTTAATTCAGAGTATTTAACCTAAGAAGT-AAA--AG----T
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAAT
* * * *
74774 -AGTAAAGAGGTTTAATTTAGAGTAGTTAACCTAAGCAGTAAAAAGAGAAAAT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAAT
* * *
74826 TAGTAAACAGGTCTAATTCAGAGTAATTAACC
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACC
74858 AACAAGGGGT
Statistics
Matches: 386, Mismatches: 38, Indels: 32
0.85 0.08 0.07
Matches are distributed among these distances:
45 68 0.18
46 9 0.02
48 3 0.01
49 4 0.01
50 3 0.01
52 9 0.02
53 290 0.75
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.26
Consensus pattern (53 bp):
CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAAT
Found at i:74787 original size:204 final size:198
Alignment explanation
Indices: 74365--74857 Score: 668
Period size: 204 Copynumber: 2.4 Consensus size: 198
74355 AAAGAGTAAA
*
74365 CAGTAAATAGGTTTCATTCAGAGTAATTAAGCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAAG-TAAGCAGTAAAAGGAGAAAATCAGTAAATAGGT
**
74430 TTAATTCAGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAGTAATTAGCTTAATTAACC
65 TTAATTCAGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAGTAATTAGAGTAATTAACC
* * *
74495 TAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCCGAGTAATTAACCTAAGTAGTAAAA
130 TAAGCAGTAAAAAGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGAAGTAAAA
74560 GGGGAAAAT
195 --GG---AT
74569 CAGTAAATAGGTTTAATTCAGAGTAATTAATGTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAA-GTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGT
*
74634 TTAATTCCGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAAATAGGTTTAATTCAGAGT
65 TTAATTCAGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAG----TA-G--TAATT-AGAGT
* *
74699 AATTAACCTAAGCAGTAAAAAGAGAAAATTAGTAAATAGGTTTAATTCAGAGTATTTAACCTAAG
122 AATTAACCTAAGCAGTAAAAAGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAG
74764 AAGTAAAA-G-T
187 AAGTAAAAGGAT
* * * * * * *
74774 -AGTAAAGAGGTTTAATTTAGAGTAGTTAACCTAAGCAGTAAAAAGAGAAAATTAGTAAACAGGT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAA-GTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGT
*
74838 CTAATTCAGAGTAATTAACC
65 TTAATTCAGAGTAATTAACC
74858 AACAAGGGGT
Statistics
Matches: 261, Mismatches: 19, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
204 179 0.69
205 2 0.01
208 2 0.01
209 2 0.01
211 5 0.02
212 71 0.27
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.26
Consensus pattern (198 bp):
CAGTAAATAGGTTTAATTCAGAGTAATTAAGTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTT
TAATTCAGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAGTAATTAGAGTAATTAACCT
AAGCAGTAAAAAGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGAAGTAAAAG
GAT
Found at i:76161 original size:30 final size:30
Alignment explanation
Indices: 76125--76186 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
76115 GGTCAAGTGG
*
76125 CCGGTTGTGGCCGGATGGCCCGTGCGATGT
1 CCGGTTGTGGCCGGATAGCCCGTGCGATGT
* *
76155 CCGGTTGTGTCCGGATATCCCGTGCGATGT
1 CCGGTTGTGGCCGGATAGCCCGTGCGATGT
76185 CC
1 CC
76187 CATGCATTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.08, C:0.29, G:0.37, T:0.26
Consensus pattern (30 bp):
CCGGTTGTGGCCGGATAGCCCGTGCGATGT
Done.