Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016290.1 Corchorus capsularis cultivar CVL-1 contig16311, 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: 10890
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:938 original size:46 final size:46
Alignment explanation
Indices: 871--962 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
861 CAGAGCATTA
871 GCACTCTGTTTCTTCCTATTTACGAATTTGCTCGTCAATGATTTCT
1 GCACTCTGTTTCTTCCTATTTACGAATTTGCTCGTCAATGATTTCT
*
917 GCACTCTGTTTCTTCCTATTTACGAATTTGCTTGTCAATGATTTCT
1 GCACTCTGTTTCTTCCTATTTACGAATTTGCTCGTCAATGATTTCT
963 TGCAAATTCT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.17, C:0.23, G:0.13, T:0.47
Consensus pattern (46 bp):
GCACTCTGTTTCTTCCTATTTACGAATTTGCTCGTCAATGATTTCT
Found at i:4052 original size:62 final size:61
Alignment explanation
Indices: 3891--4045 Score: 195
Period size: 62 Copynumber: 2.5 Consensus size: 61
3881 GAAATATTCA
* * * * *
3891 TATGAAATTGTGATAACCTTCCCATTAAATTATGATAATTATACTATTTTTGGAGACATACT
1 TATG-AATTTTGATAACCTTCCTATGAAATTATAATAATTACACTATTTTTGGAGACATACT
* * *
3953 TATGACATTTTGATAACCTTCCTATGAAATTATAATAATTACACTATTTTT-TATGACGTCCT
1 TATGA-ATTTTGATAACCTTCCTATGAAATTATAATAATTACACTATTTTTGGA-GACATACT
4015 TATGAAGTTTTGATAACCTTCCTATGAAATT
1 TATGAA-TTTTGATAACCTTCCTATGAAATT
4046 TCAATAACGA
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
61 3 0.04
62 79 0.96
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (61 bp):
TATGAATTTTGATAACCTTCCTATGAAATTATAATAATTACACTATTTTTGGAGACATACT
Found at i:4177 original size:23 final size:23
Alignment explanation
Indices: 4144--4187 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4134 TTGAAGACCT
* *
4144 CACTATGAAATTTTGATAACCAA
1 CACTATAAAATGTTGATAACCAA
4167 CACTATAAAATGTTGATAACC
1 CACTATAAAATGTTGATAACC
4188 TCCATATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (23 bp):
CACTATAAAATGTTGATAACCAA
Found at i:4205 original size:45 final size:44
Alignment explanation
Indices: 4133--4241 Score: 114
Period size: 45 Copynumber: 2.5 Consensus size: 44
4123 TCTAAGGAAT
* *
4133 TTTGAAGACCT-CACTATGAAATTTTGATAACCAACACTAT-AAAA
1 TTTGAAAACCTCCA-TATGAAATATTGATAACC-ACACTATGAAAA
* * **
4177 TGTTGATAACCTCCATATGATATATTGATAACCACGTTATGAAAA
1 T-TTGAAAACCTCCATATGAAATATTGATAACCACACTATGAAAA
*
4222 TTTTAAAACCTCCATATGAA
1 TTTGAAAACCTCCATATGAA
4242 TTGTCAGTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
44 22 0.42
45 29 0.55
46 2 0.04
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.32
Consensus pattern (44 bp):
TTTGAAAACCTCCATATGAAATATTGATAACCACACTATGAAAA
Found at i:4308 original size:44 final size:43
Alignment explanation
Indices: 4103--4755 Score: 187
Period size: 44 Copynumber: 15.3 Consensus size: 43
4093 TTAACCTTCT
* * * * *
4103 TATGAAATTTTGTTAATCTCTCTAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATAACCTC-CTATGAAATTTTGATA-ACCACAC
* * * *
4147 TATGAAATTTTGATAACCAACACTATAAAATGTTGATAACCTC-C
1 TATGAAATTTTGATAACC-TC-CTATGAAATTTTGATAACCACAC
* * * * * *
4191 ATATGATATATTGATAACCACGTTATGAAAATTTT-AAAACCTC-C
1 -TATGAAATTTTGATAACCTC-CTATG-AAATTTTGATAACCACAC
* * * * * *
4235 ATATG-AATTGTCAGTAATCACACTCTGAAATTTTGATAATCACAC
1 -TATGAAATTTTGA-TAACCTC-CTATGAAATTTTGATAACCACAC
* *
4280 TATGAAATTGTGATAACCTCGCTATGAAATTTTAATAA--AC-C
1 TATGAAATTTTGATAACCTC-CTATGAAATTTTGATAACCACAC
*** * * * * *
4321 T-TCCTA-TAT-A-AATCTCTCTATAAAATTTTAATAACCTC-C
1 TATGAAATTTTGATAACCTC-CTATGAAATTTTGATAACCACAC
* ** * *
4360 TTATGAAATCTTGATAACCTCCCTATGATTTTTTGATAACCTCAT
1 -TATGAAATTTTGATAACCT-CCTATGAAATTTTGATAACCACAC
* * * *
4405 TATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGATAACCT-CCTATGAAATTTTGAT-AACCACAC
* * * *
4449 TATGAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTAAAC
1 TATGAAATTTTGATAA-CCTCCTATGAAATTTTGATAACCACAC
* *
4493 TATGAAATTTTGATAACCTTCATATGAAATTTTTGATTACTC-CA-
1 TATGAAATTTTGATAACC-TCCTATGAAA-TTTTGATAAC-CACAC
* * * * * * *
4537 TAATAAAAGTTTAATAACCTTCT-T--AATCTAG-TAACCATAC
1 T-ATGAAATTTTGATAACCTCCTATGAAATTTTGATAACCACAC
*
4577 TATGAAATTTTGATAACCTTCCCA-G-AA----G-T-A-C-CAC
1 TATGAAATTTTGATAACC-TCCTATGAAATTTTGATAACCACAC
* * * * * * * **
4611 TATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCTC-CTATGAAATTTTGATAACCACAC
* * * * * *
4655 TACGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCTC-CTATGAAATTTTGATAACCACAC
* * * * * *
4699 TATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACCTC-CTATGAAATTTTGATAACCACAC
*
4743 TTTGAAATTTTGA
1 TATGAAATTTTGA
4756 AATTGGACCA
Statistics
Matches: 449, Mismatches: 120, Indels: 80
0.69 0.18 0.12
Matches are distributed among these distances:
33 1 0.00
34 18 0.04
35 2 0.00
36 3 0.01
37 23 0.05
38 2 0.00
39 22 0.05
40 10 0.02
41 9 0.02
42 4 0.01
43 17 0.04
44 264 0.59
45 73 0.16
46 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (43 bp):
TATGAAATTTTGATAACCTCCTATGAAATTTTGATAACCACAC
Found at i:4317 original size:22 final size:22
Alignment explanation
Indices: 4103--4317 Score: 116
Period size: 22 Copynumber: 9.7 Consensus size: 22
4093 TTAACCTTCT
* * * *
4103 TATGAAATTTTGTTAATCTCTC
1 TATGAAATTTTGATAACCACAC
* * *
4125 TAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATA-ACCACAC
4147 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-ACAC
* * *
4170 TATAAAATGTTGATAACCTC-C
1 TATGAAATTTTGATAACCACAC
* * **
4191 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCACAC
* *
4214 TATGAAAATTTT-AAAACCTC-C
1 TATG-AAATTTTGATAACCACAC
* * *
4235 ATATG-AATTGTCAGTAATCACAC
1 -TATGAAATTTTGA-TAACCACAC
* *
4258 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCACAC
* * *
4280 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCACAC
*
4302 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
4318 ACCTTCCTAT
Statistics
Matches: 147, Mismatches: 35, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
20 5 0.03
21 3 0.02
22 107 0.73
23 32 0.22
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:4368 original size:22 final size:22
Alignment explanation
Indices: 4343--4525 Score: 158
Period size: 22 Copynumber: 8.3 Consensus size: 22
4333 TCTCTCTATA
*
4343 AAATTTTAATAACCTCCTTATG
1 AAATTTTGATAACCTCCTTATG
* *
4365 AAATCTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCCTTATG
** *
4387 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCCTTATG
* * *
4409 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCTTATG
* * *
4431 AAATTTTGATCTACATAC-TATG
1 AAATTTTGAT-AACCTCCTTATG
4453 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTC-CTTATG
* *
4475 AAATTTTGA-AAACTAAAC-TATG
1 AAATTTTGATAACCT--CCTTATG
* *
4497 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACCTCCTTATG
4519 AAATTTT
1 AAATTTT
4526 TGATTACTCC
Statistics
Matches: 127, Mismatches: 26, Indels: 16
0.75 0.15 0.09
Matches are distributed among these distances:
21 7 0.06
22 112 0.88
23 8 0.06
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTCCTTATG
Found at i:4538 original size:22 final size:22
Alignment explanation
Indices: 4343--4556 Score: 150
Period size: 22 Copynumber: 9.7 Consensus size: 22
4333 TCTCTCTATA
* *
4343 AAATTTTAATAACCTCCTTATG
1 AAATTTTGATAACCTCCATATG
* *
4365 AAATCTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCCATATG
**
4387 ATTTTTTGATAACCT-CATTATG
1 AAATTTTGATAACCTCCA-TATG
* * *
4409 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCATATG
* * *
4431 AAATTTTGATCTACATAC-TATG
1 AAATTTTGAT-AACCTCCATATG
*
4453 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTC-CATATG
* **
4475 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCTCCA-TATG
*
4497 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACCTCCATATG
* *
4519 AAATTTTTGATTA-CTCCATAATA
1 AAA-TTTTGATAACCTCCAT-ATG
* *
4542 AAAGTTTAATAACCT
1 AAATTTTGATAACCT
4557 TCTTAATCTA
Statistics
Matches: 148, Mismatches: 33, Indels: 21
0.73 0.16 0.10
Matches are distributed among these distances:
21 7 0.05
22 117 0.79
23 24 0.16
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACCTCCATATG
Found at i:4684 original size:22 final size:22
Alignment explanation
Indices: 4635--4755 Score: 118
Period size: 22 Copynumber: 5.5 Consensus size: 22
4625 AATCACATTT
* *
4635 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
*
4657 CGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
4679 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
4701 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * *
4723 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTCTCTA
4745 TGAAATTTTGA
1 TGAAATTTTGA
4756 AATTGGACCA
Statistics
Matches: 78, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
22 77 0.99
23 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:4905 original size:37 final size:37
Alignment explanation
Indices: 4813--4908 Score: 113
Period size: 38 Copynumber: 2.6 Consensus size: 37
4803 ATCTAAACCC
* *
4813 AAATAGGACGTTGGAGACGAAGACAAAAAGCAAAATT
1 AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
**
4850 AAATACAACGATTGGAAACAAAGAC-AAAAGACAAAATT
1 AAATAGGACG-TTGGAAACAAAGACAAAAAG-CAAAATT
**
4888 AAATAGGACGTCAGAAACAAA
1 AAATAGGACGTTGGAAACAAA
4909 AAGCCAAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 22 0.45
38 27 0.55
ACGTcount: A:0.56, C:0.12, G:0.19, T:0.12
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
Done.