Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011398.1 Corchorus capsularis cultivar CVL-1 contig11419, 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: 27459
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:6029 original size:2 final size:2
Alignment explanation
Indices: 6022--6070 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
6012 CTCATGAACA
* * *
6022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT CT AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6064 ACT AT AT
1 A-T AT AT
6071 TAAAAAGTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8146 original size:22 final size:22
Alignment explanation
Indices: 8088--8152 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
8078 GAAAACCTTA
*
8088 ATATGAAATTTTGATAACCAAC
1 ATATGAAATATTGATAACCAAC
* * **
8110 ACTATGAGATGTTGATAACCTCC
1 A-TATGAAATATTGATAACCAAC
*
8133 ATATGATATATTGATAACCA
1 ATATGAAATATTGATAACCA
8153 CTTTATAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (22 bp):
ATATGAAATATTGATAACCAAC
Found at i:8216 original size:22 final size:22
Alignment explanation
Indices: 8182--8237 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
8172 CCTCCATACG
* *
8182 AATTGTTAGTAATCACACTTTAA
1 AATTGTGA-TAATCACACTATAA
* *
8205 AATTTTGATAATCACACTATGA
1 AATTGTGATAATCACACTATAA
8227 AATTGTGATAA
1 AATTGTGATAA
8238 CCTCTCTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (22 bp):
AATTGTGATAATCACACTATAA
Found at i:8246 original size:22 final size:22
Alignment explanation
Indices: 8204--8513 Score: 125
Period size: 22 Copynumber: 14.5 Consensus size: 22
8194 TCACACTTTA
* * *
8204 AAATTTTGATAATCACACTATG
1 AAATTTTGATAACCTCTCTATG
*
8226 AAATTGTGATAACCTCTCTATG
1 AAATTTTGATAACCTCTCTATG
* *
8248 AAATTTTGATAA-ATCTTCCTATA
1 AAATTTTGATAACCTC-T-CTATG
* * *
8271 AAATTTTAATAAACCTCCCTATA
1 AAATTTTGAT-AACCTCTCTATG
*
8294 AAATTTTGATAA-CTTTCTTATG
1 AAATTTTGATAACCTCTC-TATG
* *
8316 AAATCTTGATAA-----CTA-C
1 AAATTTTGATAACCTCTCTATG
* *
8332 AAATTTTGATAAGCTCCCTATG
1 AAATTTTGATAACCTCTCTATG
*
8354 AATTTTTTGATAACCTCAT-TATG
1 AA-ATTTTGATAACCTC-TCTATG
* * * *
8377 CAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCTCTATG
* * *
8399 AAATTTTGATCTACAT-ACTATG
1 AAATTTTGAT-AACCTCTCTATG
* ** *
8421 AAATTTTGA-AAACTAAACCATG
1 AAATTTTGATAACCT-CTCTATG
*
8443 CAAA-CTTGATAACCT-TCATATG
1 -AAATTTTGATAACCTCTC-TATG
* *
8465 AAATTTTGATATCCTC-C-CTG
1 AAATTTTGATAACCTCTCTATG
* *
8485 -AATTTTGGTATCCTCT-T-TG
1 AAATTTTGATAACCTCTCTATG
8504 AAATTTTGAT
1 AAATTTTGAT
8514 TACTCCATCA
Statistics
Matches: 218, Mismatches: 45, Indels: 52
0.69 0.14 0.17
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
18 1 0.00
19 16 0.07
20 12 0.06
21 12 0.06
22 107 0.49
23 53 0.24
24 2 0.01
25 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACCTCTCTATG
Found at i:8299 original size:46 final size:45
Alignment explanation
Indices: 8202--8305 Score: 122
Period size: 46 Copynumber: 2.3 Consensus size: 45
8192 AATCACACTT
* * *
8202 TAAAATTTTGAT-AATCACACTATGAAATTGTGATAACCTCTCTA
1 TAAAATTTTGATAAATCACACTATAAAATTGTAATAACCTCCCTA
* * *
8246 TGAAATTTTGATAAATCTTC-CTATAAAATTTTAATAAACCTCCCTA
1 TAAAATTTTGATAAATC-ACACTATAAAATTGTAAT-AACCTCCCTA
8292 TAAAATTTTGATAA
1 TAAAATTTTGATAA
8306 CTTTCTTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 11 0.22
45 16 0.32
46 23 0.46
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.38
Consensus pattern (45 bp):
TAAAATTTTGATAAATCACACTATAAAATTGTAATAACCTCCCTA
Found at i:8510 original size:20 final size:20
Alignment explanation
Indices: 8463--8513 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
8453 AACCTTCATA
8463 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
* **
8483 TG-AATTTTGGTATCCTCTT
1 TGAAATTTTGATATCCTCCC
8502 TGAAATTTTGAT
1 TGAAATTTTGAT
8514 TACTCCATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.47
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:8650 original size:22 final size:22
Alignment explanation
Indices: 8624--8864 Score: 113
Period size: 22 Copynumber: 11.0 Consensus size: 22
8614 ATTTTGAGAA
8624 TTTGATAACCTCTTTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
* * *
8646 TTTGATAACATTTTTATAAAAT
1 TTTGATAACCTCTTTATGAAAT
* * * * *
8668 TTTGTTGACCCCTCTATTAAAT
1 TTTGATAACCTCTTTATGAAAT
* * * **
8690 TTTGATAATCACATTATTTAAT
1 TTTGATAACCTCTTTATGAAAT
8712 TTTGATAACCT-TGCTT-TGAAAT
1 TTTGATAACCTCT--TTATGAAAT
*****
8734 TTTGATAACAAAACTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
8756 TTTGATAA--TCTTCATAT-AAAT
1 TTTGATAACCTCTT--TATGAAAT
8777 TTTGATAATCCTATCTTTATGAAAT
1 TTTGATAA-CC--TCTTTATGAAAT
* * * * *
8802 TTCGATAATCACTCTATGAGA-
1 TTTGATAACCTCTTTATGAAAT
* *
8823 TTTGATAACCT-TCTATCAAAT
1 TTTGATAACCTCTTTATGAAAT
* *
8844 TTTGGT-A-CTCCTTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
8864 T
1 T
8865 GAGACTTTTA
Statistics
Matches: 161, Mismatches: 44, Indels: 30
0.69 0.19 0.13
Matches are distributed among these distances:
19 2 0.01
20 16 0.10
21 26 0.16
22 96 0.60
23 2 0.01
24 4 0.02
25 11 0.07
26 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (22 bp):
TTTGATAACCTCTTTATGAAAT
Found at i:8756 original size:88 final size:88
Alignment explanation
Indices: 8593--8759 Score: 198
Period size: 88 Copynumber: 1.9 Consensus size: 88
8583 AGAAATACCA
**
8593 CTATGAAATTTTTGTAATCACATTTTGAGAATTTGATAACCTCTTTATGAAATTTTGATAACATT
1 CTATGAAATTTTTGTAATCACATTTTGAGAATTTGATAACCTCTTTATGAAATTTTGATAACAAA
**
8658 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* * *
8681 CTATTAAA-TTTTGATAATCACATTATTTA-ATTTTGATAACCT-TGCTT-TGAAATTTTGATAA
1 CTATGAAATTTTTG-TAATCACATT-TTGAGAATTTGATAACCTCT--TTATGAAATTTTGATAA
*
8742 CAAAACTATGAAATTTTG
62 CAAAACTATAAAATTTTG
8760 ATAATCTTCA
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
87 6 0.09
88 56 0.84
89 5 0.07
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (88 bp):
CTATGAAATTTTTGTAATCACATTTTGAGAATTTGATAACCTCTTTATGAAATTTTGATAACAAA
ACTATAAAATTTTGTTGACCCCT
Found at i:8802 original size:25 final size:23
Alignment explanation
Indices: 8748--8921 Score: 93
Period size: 22 Copynumber: 7.7 Consensus size: 23
8738 ATAACAAAAC
8748 TATGAAATTTTGATAAT-CTTCA
1 TATGAAATTTTGATAATCCTTCA
*
8770 TAT-AAATTTTGATAATCCTATCTT
1 TATGAAATTTTGATAATCCT-TC-A
*
8794 TATGAAATTTCGATAATCAC-TC-
1 TATGAAATTTTGATAATC-CTTCA
*
8816 TATGAGA-TTTGATAA-CCTTC-
1 TATGAAATTTTGATAATCCTTCA
* * *
8836 TATCAAATTTTGGTACTCCTT-A
1 TATGAAATTTTGATAATCCTTCA
*
8858 TGAAATTGAGACTTTT-ATAA-CCTTCA
1 T---A-TGA-AATTTTGATAATCCTTCA
* *
8884 TATGAAAATTTGATAA-CC-ACA
1 TATGAAATTTTGATAATCCTTCA
*
8905 CTATAAAATTTTGATAA
1 -TATGAAATTTTGATAA
8922 CCTCCCGATG
Statistics
Matches: 118, Mismatches: 17, Indels: 34
0.70 0.10 0.20
Matches are distributed among these distances:
19 1 0.01
20 8 0.07
21 32 0.27
22 39 0.33
23 3 0.03
24 5 0.04
25 18 0.15
26 7 0.06
27 5 0.04
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (23 bp):
TATGAAATTTTGATAATCCTTCA
Found at i:8976 original size:22 final size:22
Alignment explanation
Indices: 8884--8980 Score: 72
Period size: 22 Copynumber: 4.4 Consensus size: 22
8874 ATAACCTTCA
*
8884 TATGAAAATTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
* * *
8906 TATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACAC
* * * **
8928 GATGAAGTATT-AGTAACC-TTC
1 TATGAAATTTTGA-TAACCACAC
*
8949 TAATGAAATTTTGTTAACCACAC
1 T-ATGAAATTTTGATAACCACAC
8972 TATGAAATT
1 TATGAAATT
8981 CGTATACATA
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
21 2 0.04
22 51 0.93
23 2 0.04
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.34
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:9113 original size:24 final size:22
Alignment explanation
Indices: 9055--9096 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9045 AATTAGCCAC
* *
9055 CCTACGAAATTTCAATAACCAG
1 CCTAAGAAATTTTAATAACCAG
9077 CCTAAGAAATTTTAATAACC
1 CCTAAGAAATTTTAATAACC
9097 TGATCCTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (22 bp):
CCTAAGAAATTTTAATAACCAG
Found at i:9130 original size:22 final size:22
Alignment explanation
Indices: 9102--9276 Score: 187
Period size: 22 Copynumber: 8.0 Consensus size: 22
9092 TAACCTGATC
9102 CTATGAAATTTTGGTAACCACT
1 CTATGAAATTTTGGTAACCACT
*
9124 CTATGAAATTTTGGTAACTACAT
1 CTATGAAATTTTGGTAACCAC-T
*
9147 -TATGAAATTTTGGTAACTACAT
1 CTATGAAATTTTGGTAACCAC-T
*
9169 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACT
*
9190 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACT
* *
9212 CTATGAAATTTTGATAACCTC-
1 CTATGAAATTTTGGTAACCACT
* * **
9233 CTCATGGAATTATAATAACCA-T
1 CT-ATGAAATTTTGGTAACCACT
*
9255 CTTATGAAATTTTGATAACCAC
1 C-TATGAAATTTTGGTAACCAC
9277 ATAGAGACAA
Statistics
Matches: 135, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
21 2 0.01
22 131 0.97
23 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACT
Found at i:9183 original size:66 final size:66
Alignment explanation
Indices: 9103--9229 Score: 218
Period size: 66 Copynumber: 1.9 Consensus size: 66
9093 AACCTGATCC
* * * *
9103 TATGAAATTTTGGTAACCACTCTATGAAATTTTGGTAACTACATTATGAAATTTTGGTAACTACA
1 TATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTACA
9168 T
66 T
9169 TATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACCACACTATGAAATTTTGATAAC
1 TATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACCACACTATGAAATTTTGATAAC
9230 CTCCTCATGG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (66 bp):
TATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTACA
T
Found at i:9610 original size:31 final size:31
Alignment explanation
Indices: 9545--9610 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
9535 TGGTAATTTA
*
9545 GAAATATGTTTTAAATAAAAAGGTAAAATTG
1 GAAATATGTTTTAAATAAAAAGGTAAAATCG
* *
9576 GAAATATGTTTTAAA-AATAAGGGTACAATCG
1 GAAATATGTTTTAAATAA-AAAGGTAAAATCG
9607 GAAA
1 GAAA
9611 CTTTATGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.50, C:0.03, G:0.18, T:0.29
Consensus pattern (31 bp):
GAAATATGTTTTAAATAAAAAGGTAAAATCG
Found at i:9993 original size:31 final size:32
Alignment explanation
Indices: 9941--10003 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
9931 AAACACAAAC
*
9941 AAAACCCATATCTTTTTTTTTCAAATTACTAAG
1 AAAACCCAAATC-TTTTTTTTCAAATTACTAAG
*
9974 AAAACCCAAATC-TTTTTTTCAAATTTCTAA
1 AAAACCCAAATCTTTTTTTTCAAATTACTAA
10004 CATCATTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 17 0.61
33 11 0.39
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.41
Consensus pattern (32 bp):
AAAACCCAAATCTTTTTTTTCAAATTACTAAG
Found at i:12262 original size:68 final size:65
Alignment explanation
Indices: 12175--12306 Score: 183
Period size: 68 Copynumber: 2.0 Consensus size: 65
12165 TTTGAAGACA
*
12175 TAGAACCCTTTGAAAACATTCAAAAAGGAGATGATGAAAATATGGAGGAAGCCCAAGATTTTGAT
1 TAGAACCCCTTGAAAACATTCAAAAAGGAGATGATGAAAATATGGAGG--G-CCAAGATTTTGAT
12240 GAT
63 GAT
* ** * *
12243 TAGAACCCCTTGAAGACATTCATGAAGGAGATGATGAAAATGTGTAGGGCCAAGATTTTGATGA
1 TAGAACCCCTTGAAAACATTCAAAAAGGAGATGATGAAAATATGGAGGGCCAAGATTTTGATGA
12307 CATCGATTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
65 15 0.26
66 1 0.02
68 42 0.72
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (65 bp):
TAGAACCCCTTGAAAACATTCAAAAAGGAGATGATGAAAATATGGAGGGCCAAGATTTTGATGAT
Found at i:20282 original size:42 final size:42
Alignment explanation
Indices: 20225--20306 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
20215 TTTCTTTTTC
* *
20225 TTTCAGATTTTGCCGCAGCTTCTCTACTTCAGCATTTTGGTT
1 TTTCAGATTTTGCCGCAACTTCTCTAATTCAGCATTTTGGTT
*
20267 TTTCAGATTTTGCCGCAACTTGTCTAATTCAGCATTTTGG
1 TTTCAGATTTTGCCGCAACTTCTCTAATTCAGCATTTTGG
20307 GTTTCTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (42 bp):
TTTCAGATTTTGCCGCAACTTCTCTAATTCAGCATTTTGGTT
Done.