Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018495.1 Corchorus olitorius cultivar O-4 contig18528, 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: 6725
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2028 original size:22 final size:21
Alignment explanation
Indices: 1985--2028 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1975 GGGGGTCAGA
*
1985 ATGAGATGCAGAAAAATGACT
1 ATGAGATGCAGAAAAAGGACT
* *
2006 ATGAGGTGCTGAATAAAGGACT
1 ATGAGATGCAGAA-AAAGGACT
2028 A
1 A
2029 AAAGATATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.43, C:0.09, G:0.27, T:0.20
Consensus pattern (21 bp):
ATGAGATGCAGAAAAAGGACT
Found at i:3695 original size:9 final size:9
Alignment explanation
Indices: 3653--3695 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
3643 TTTCCCATAA
3653 AAAAAGAATG
1 AAAAA-AATG
3663 -AAAAAATG
1 AAAAAAATG
*
3671 GAAAAAATG
1 AAAAAAATG
3680 AAAAAAATG
1 AAAAAAATG
3689 AAAAAAA
1 AAAAAAA
3696 AAGCACTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
8 4 0.13
9 27 0.87
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (9 bp):
AAAAAAATG
Found at i:3795 original size:14 final size:13
Alignment explanation
Indices: 3748--3796 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
3738 AAAAAGAATC
3748 ATGGTTTTCAAAA
1 ATGGTTTTCAAAA
* *
3761 TTGCTTTTCAAAA
1 ATGGTTTTCAAAA
*
3774 ATGTTTTTCAAAAA
1 ATGGTTTTC-AAAA
3788 ATGGTTTTC
1 ATGGTTTTC
3797 GGAAACTCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 18 0.60
14 12 0.40
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (13 bp):
ATGGTTTTCAAAA
Found at i:5557 original size:69 final size:69
Alignment explanation
Indices: 5475--5615 Score: 201
Period size: 69 Copynumber: 2.0 Consensus size: 69
5465 TTGCATAAGT
* * **
5475 CAAACTCGTTTCCATACGAGTTAGTTCAAGTTTTGGTTCCATCCAAACAGCTTGGGCTTTTCCAC
1 CAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAACAGCAAGGGCTTTTCCAC
5540 AAGC
66 AAGC
* * * * *
5544 CAAACTCGTTTCCATATGAGATAGTTTAAGCTTTGGTTCCATCCAACCATCAAGGGCTTTTCCAT
1 CAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAACAGCAAGGGCTTTTCCAC
5609 AAGC
66 AAGC
5613 CAA
1 CAA
5616 GTTAAACGAG
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (69 bp):
CAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAACAGCAAGGGCTTTTCCAC
AAGC
Found at i:6075 original size:149 final size:150
Alignment explanation
Indices: 5883--6190 Score: 456
Period size: 149 Copynumber: 2.1 Consensus size: 150
5873 ATTAATAAAA
* *
5883 CCTCCGGGTATCATGTCATTTCATCAAAAATTTTTCATCAAAGATTCATGTTTAAGTTTAAAATC
1 CCTCCGGGTACCATGTCATTTCATC-AAAATTTTTCATCAAAGATTCATGTTTAAGTTCAAAATC
* * * *
5948 CTTGGTCAAGGTCTCTATTTAAAGTTTGCATTAGTAAGTCCTCCCGGCGCAAATTCAGAAACCTC
65 CTTGGTCAAGGTCTCTATTCAAAGTTTGCATTAGTAAGACCTCCAGGCACAAATTCAGAAACCTC
6013 CAGGTATTAATTCTGATAAGT
130 CAGGTATTAATTCTGATAAGT
* *
6034 CCTCCGGGTACCATTTCATTTCATC-AAGTTTTTCATCAAAGATTCATGTTTAAGTTCAAAATCC
1 CCTCCGGGTACCATGTCATTTCATCAAAATTTTTCATCAAAGATTCATGTTTAAGTTCAAAATCC
* * * * *
6098 TTGTTCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGACCTCCAGGCACAATTTCAGAAGCCTCC
66 TTGGTCAAGGTCTCTATTCAAAGTTTGCATTAGTAAGACCTCCAGGCACAAATTCAGAAACCTCC
* * *
6163 GGGTATTAGTTTTGATAAGT
131 AGGTATTAATTCTGATAAGT
6183 CCTCCGGG
1 CCTCCGGG
6191 CATTTCATAT
Statistics
Matches: 141, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
149 118 0.84
151 23 0.16
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (150 bp):
CCTCCGGGTACCATGTCATTTCATCAAAATTTTTCATCAAAGATTCATGTTTAAGTTCAAAATCC
TTGGTCAAGGTCTCTATTCAAAGTTTGCATTAGTAAGACCTCCAGGCACAAATTCAGAAACCTCC
AGGTATTAATTCTGATAAGT
Found at i:6287 original size:38 final size:38
Alignment explanation
Indices: 6235--6691 Score: 290
Period size: 38 Copynumber: 12.2 Consensus size: 38
6225 ATCGGTTTCT
* * *
6235 TTTCGAATCCTGGTTTAGGATCATTGCTTTATGACTTAA
1 TTTC-AATCCTGATTTAGGATCATTGCTTTATCAGTTAA
* * * * *
6274 TTTCAGTCTTGGTTTAGGATCATTGTTTTATGAGTTAA
1 TTTCAATCCTGATTTAGGATCATTGCTTTATCAGTTAA
* *
6312 TTTCAATCCCGATTTAGGATCTTTGC-TT-T-A-TT-A
1 TTTCAATCCTGATTTAGGATCATTGCTTTATCAGTTAA
* *
6345 GTT-AATCCTGATTTAGGATCATTGCTTCATCAGTTAA
1 TTTCAATCCTGATTTAGGATCATTGCTTTATCAGTTAA
* *
6382 TTTCAATCCTGATTTAGGATTATTGGTTTATCAGTTAA
1 TTTCAATCCTGATTTAGGATCATTGCTTTATCAGTTAA
* *
6420 TTTCAGAATCCT-ATTGAGGATCATCGC-TTAGT-AGTTAA
1 TTTC--AATCCTGATTTAGGATCATTGCTTTA-TCAGTTAA
* * * *
6458 TTTCATAT--TTATAATCAAGTTCATTG-TTT-TC--TTAA
1 TTTCA-ATCCTGAT--TTAGGATCATTGCTTTATCAGTTAA
*
6493 TTTCAAAAT-CTCG-TTTAGGATCATTGCTTTATCAGTTTAC
1 TTTC--AATCCT-GATTTAGGATCATTGCTTTATCAG-TTAA
* * * *
6533 TTTCAATCTTGATTTAGGATTATCGCATTT-TGAGTTAA
1 TTTCAATCCTGATTTAGGATCATTGC-TTTATCAGTTAA
* *
6571 TTTCGATCCTGATTTAGGATCATTG-TTATATGAGTTAAA
1 TTTCAATCCTGATTTAGGATCATTGCTT-TATCAGTT-AA
* * * * * *
6610 TTTCAATCCTG-TTGAAGATCATTGCGTTATTAATTGA
1 TTTCAATCCTGATTTAGGATCATTGCTTTATCAGTTAA
* * * *
6647 TTTCAAAATCCTG-TTCAAGATTATTGCTTTGTCAGTTAA
1 TTTC--AATCCTGATTTAGGATCATTGCTTTATCAGTTAA
6686 TTTCAA
1 TTTCAA
6692 AGTCTTGGTT
Statistics
Matches: 331, Mismatches: 54, Indels: 68
0.73 0.12 0.15
Matches are distributed among these distances:
32 20 0.06
33 4 0.01
34 3 0.01
35 20 0.06
36 14 0.04
37 20 0.06
38 159 0.48
39 75 0.23
40 16 0.05
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (38 bp):
TTTCAATCCTGATTTAGGATCATTGCTTTATCAGTTAA
Found at i:6358 original size:32 final size:32
Alignment explanation
Indices: 6316--6382 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
6306 AGTTAATTTC
* * *
6316 AATCCCGATTTAGGATCTTTGCTTTATTAGTT
1 AATCCCGATTTAGGATCATTGCTTCATCAGTT
*
6348 AATCCTGATTTAGGATCATTGCTTCATCAGTT
1 AATCCCGATTTAGGATCATTGCTTCATCAGTT
6380 AAT
1 AAT
6383 TTCAATCCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.43
Consensus pattern (32 bp):
AATCCCGATTTAGGATCATTGCTTCATCAGTT
Found at i:6390 original size:70 final size:70
Alignment explanation
Indices: 6286--6420 Score: 200
Period size: 70 Copynumber: 1.9 Consensus size: 70
6276 TCAGTCTTGG
* * * *
6286 TTTAGGATCATTGTTTTATGAGTTAATTTCAATCCCGATTTAGGATCT-TTGCTTTATTAGTTAA
1 TTTAGGATCATTGCTTCATCAGTTAATTTCAATCCCGATTTAGGAT-TATTGCTTTATCAGTTAA
6350 TCCTGA
65 TCCTGA
* *
6356 TTTAGGATCATTGCTTCATCAGTTAATTTCAATCCTGATTTAGGATTATTGGTTTATCAGTTAAT
1 TTTAGGATCATTGCTTCATCAGTTAATTTCAATCCCGATTTAGGATTATTGCTTTATCAGTTAAT
6421 TTCAGAATCC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
69 1 0.02
70 57 0.98
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.47
Consensus pattern (70 bp):
TTTAGGATCATTGCTTCATCAGTTAATTTCAATCCCGATTTAGGATTATTGCTTTATCAGTTAAT
CCTGA
Found at i:6455 original size:108 final size:108
Alignment explanation
Indices: 6240--6458 Score: 271
Period size: 108 Copynumber: 2.0 Consensus size: 108
6230 TTTCTTTTCG
* * * * * * *
6240 AATCCTGGTTTAGGATCATTGCTTTATGACTTAATTTCAGTCTTGGTTTAGGATCATTGTTTTAT
1 AATCCTGATTTAGGATCATTGCTTCATCACTTAATTTCAATCCTGATTTAGGATCATTGGTTTAT
* * * * *
6305 GAGTTAATTTCAATCCCGATTTAGGATCTTTGCTTTATTAGTT
66 CAGTTAATTTCAATCCCGATTGAGGATCATCGCTTTAGTAGTT
* *
6348 AATCCTGATTTAGGATCATTGCTTCATCAGTTAATTTCAATCCTGATTTAGGATTATTGGTTTAT
1 AATCCTGATTTAGGATCATTGCTTCATCACTTAATTTCAATCCTGATTTAGGATCATTGGTTTAT
*
6413 CAGTTAATTTCAGAAT-CCTATTGAGGATCATCGC-TTAGTAGTT
66 CAGTTAATTTC--AATCCCGATTGAGGATCATCGCTTTAGTAGTT
6456 AAT
1 AAT
6459 TTCATATTTA
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
108 77 0.82
109 14 0.15
110 3 0.03
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (108 bp):
AATCCTGATTTAGGATCATTGCTTCATCACTTAATTTCAATCCTGATTTAGGATCATTGGTTTAT
CAGTTAATTTCAATCCCGATTGAGGATCATCGCTTTAGTAGTT
Found at i:6689 original size:39 final size:39
Alignment explanation
Indices: 6614--6692 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
6604 GTTAAATTTC
* * *
6614 AATCCTGTTGAAGATCATTGCGTTATTAATTGATTTCAA
1 AATCCTGTTCAAGATCATTGCGTTATCAATTAATTTCAA
* * * *
6653 AATCCTGTTCAAGATTATTGCTTTGTCAGTTAATTTCAA
1 AATCCTGTTCAAGATCATTGCGTTATCAATTAATTTCAA
6692 A
1 A
6693 GTCTTGGTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (39 bp):
AATCCTGTTCAAGATCATTGCGTTATCAATTAATTTCAA
Done.