Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012037.1 Corchorus olitorius cultivar O-4 contig12070, 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: 29282
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4708 original size:19 final size:18
Alignment explanation
Indices: 4684--4719 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4674 TGAAGATTTA
4684 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
4703 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
4720 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:7712 original size:16 final size:15
Alignment explanation
Indices: 7690--7733 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
7680 TTAAAGTTTG
*
7690 AATTCAGTACTTATGA
1 AATTCAGTACTTA-AA
*
7706 GATTCAGTA-TTAAA
1 AATTCAGTACTTAAA
7720 AATTCAGTACTTAA
1 AATTCAGTACTTAA
7734 TCTTTCAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 9 0.38
15 7 0.29
16 8 0.33
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (15 bp):
AATTCAGTACTTAAA
Found at i:7755 original size:14 final size:15
Alignment explanation
Indices: 7722--7755 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
7712 GTATTAAAAA
*
7722 TTCAGTACTTAATCT
1 TTCAGCACTTAATCT
7737 TTCAGCACTTAAT-T
1 TTCAGCACTTAATCT
7751 TTCAG
1 TTCAG
7756 TTTTATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (15 bp):
TTCAGCACTTAATCT
Found at i:9519 original size:20 final size:21
Alignment explanation
Indices: 9489--9534 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
9479 TGGAAATACA
*
9489 AGGCCTTTGATTTACAAATTG
1 AGGCATTTGATTTACAAATTG
*
9510 -GGCATTTGATTTGCAAATTG
1 AGGCATTTGATTTACAAATTG
9530 AGGCA
1 AGGCA
9535 CTTTTTCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (21 bp):
AGGCATTTGATTTACAAATTG
Found at i:15585 original size:16 final size:16
Alignment explanation
Indices: 15561--15599 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
15551 TAAGAGACGT
**
15561 TTTTC-AAGAAAATTG
1 TTTTCAAAGAAAAAGG
15576 TTTTCAAAGAAAAAGG
1 TTTTCAAAGAAAAAGG
15592 TTTTCAAA
1 TTTTCAAA
15600 AATGAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.36
Consensus pattern (16 bp):
TTTTCAAAGAAAAAGG
Found at i:19550 original size:64 final size:64
Alignment explanation
Indices: 19464--20076 Score: 865
Period size: 64 Copynumber: 9.6 Consensus size: 64
19454 TGATAGAAAT
*
19464 AATTTTCA-AATGTTGATTGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAA-GTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
*
19528 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * * *
19592 AGTTTTAAGGAGTTGATCGGAAGACGATCTTGTTAA-AAGTACACCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* *
19655 AATTTTCAGAAGTTGATTGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * * * *
19719 AGTTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* **
19783 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTTAA-AAGTACTGCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * *
19846 AATTTTCAGAAGTTGATCGGAAGACAATCTTGTCAAGTAGTACACCAGAAGATGGTTTCTCAAG
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * * ** * * *
19910 AGTTTTCAGGAGTTGATCAGAAGACGATCTTGTCAAGAAGTATGCCAGAAGATGCTTTTTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * * *
19974 AATTTTCAGAAGTTGATCGGAAGAGGATCTTGTTAAAAAGTACACCAGAAGATAGTTTCTCGAA-
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC-AAC
* * *
20038 AACATTTCAGAAGTTGATCGGAAGATGATCTTGTTAAGA
1 AA-TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGA
20077 GATGCACCGG
Statistics
Matches: 488, Mismatches: 56, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
63 114 0.23
64 337 0.69
65 37 0.08
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (64 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
Found at i:19662 original size:127 final size:128
Alignment explanation
Indices: 19464--20076 Score: 874
Period size: 127 Copynumber: 4.8 Consensus size: 128
19454 TGATAGAAAT
*
19464 AATTTTCA-AATGTTGATTGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAA-GTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
19528 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
65 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
* * * *
19592 AGTTTTAAGGAGTTGATCGGAAGACGATCTTGTTAA-AAGTACACCAGAAGATGGTTTCTCAACA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAACA
*
19656 ATTTTCAGAAGTTGATTGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
66 ATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
* * * * *
19719 AGTTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTCAAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAACA
* ** *
19784 ATTTTCAGAAGTTGATCGGAAGACGATCTTGTTAA-AAGTACTGCAGAAGATGGTTTCTCAAC
66 ATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
* * *
19846 AATTTTCAGAAGTTGATCGGAAGACAATCTTGTCAAGTAGTACACCAGAAGATGGTTTCTCAAGA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAACA
* * * ** * * *
19911 GTTTTCAGGAGTTGATCAGAAGACGATCTTGTCAAGAAGTATGCCAGAAGATGCTTTTTCAAA
66 ATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
* * * *
19974 AATTTTCAGAAGTTGATCGGAAGAGGATCTTGTTAAAAAGTACACCAGAAGATAGTTTCTCGAA-
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC-AAC
* * *
20038 AACATTTCAGAAGTTGATCGGAAGATGATCTTGTTAAGA
65 AA-TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGA
20077 GATGCACCGG
Statistics
Matches: 435, Mismatches: 45, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
127 237 0.54
128 164 0.38
129 34 0.08
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (128 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAACA
ATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
Found at i:19799 original size:191 final size:191
Alignment explanation
Indices: 19464--20076 Score: 969
Period size: 191 Copynumber: 3.2 Consensus size: 191
19454 TGATAGAAAT
* *
19464 AATTTTCA-AATGTTGATTGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAA-GTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
* * * * *
19528 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGA
65 AGTTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTCAAAA
* * *
19593 GTTTTAAGGAGTTGATCGGAAGACGATCTTGTTAAAAGTACACCAGAAGATGGTTTCTCAAC
130 ATTTTCAGAAGTTGATCGGAAGACGATCTTGTTAAAAGTACACCAGAAGATGGTTTCTCAAC
*
19655 AATTTTCAGAAGTTGATTGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGA
19720 GTTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTCAAAAA
66 GTTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTCAAAAA
**
19785 TTTTCAGAAGTTGATCGGAAGACGATCTTGTTAAAAGTACTGCAGAAGATGGTTTCTCAAC
131 TTTTCAGAAGTTGATCGGAAGACGATCTTGTTAAAAGTACACCAGAAGATGGTTTCTCAAC
* *
19846 AATTTTCAGAAGTTGATCGGAAGACAATCTTGTCAAGTAGTACACCAGAAGATGGTTTCTCAAGA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGA
* * *
19911 GTTTTCAGGAGTTGATCAGAAGACGATCTTGTCAAGAAGTATGCCAGAAGATGCTTTTTCAAAAA
66 GTTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTCAAAAA
* *
19976 TTTTCAGAAGTTGATCGGAAGAGGATCTTGTTAAAAAGTACACCAGAAGATAGTTTCTCGAA-
131 TTTTCAGAAGTTGATCGGAAGACGATCTTGTT-AAAAGTACACCAGAAGATGGTTTCTC-AAC
* * *
20038 AACATTTCAGAAGTTGATCGGAAGATGATCTTGTTAAGA
1 AA-TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGA
20077 GATGCACCGG
Statistics
Matches: 392, Mismatches: 26, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
191 332 0.85
192 27 0.07
193 33 0.08
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (191 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGA
GTTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACGCCAGAAGATGGTTTTTCAAAAA
TTTTCAGAAGTTGATCGGAAGACGATCTTGTTAAAAGTACACCAGAAGATGGTTTCTCAAC
Found at i:22082 original size:16 final size:15
Alignment explanation
Indices: 22061--22099 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
22051 CCATACACCT
*
22061 AAGGAAAATAAAATTG
1 AAGGAAAATAAAA-AG
22077 AAGGAAAAATAAAAAG
1 AAGG-AAAATAAAAAG
22093 AAGGAAA
1 AAGGAAA
22100 TTACCTCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 9 0.43
17 9 0.43
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (15 bp):
AAGGAAAATAAAAAG
Found at i:25081 original size:132 final size:132
Alignment explanation
Indices: 24844--25375 Score: 762
Period size: 132 Copynumber: 4.0 Consensus size: 132
24834 GACTTCTATT
* * * * * * *
24844 AGTCGTTGCGAATTCATAGTCTTTTCACAACGACT-TCTGTTAGTCGTTGTTTAATATATTTTAC
1 AGTCGCTGCGAAATCTTACTCTTTTCGCAATGACTAT-TGTTAGTCGTTGCTTAATATATTTTAC
* * * * * *
24908 AAATTGATTTTCTCAGCGACCTTGAAAGTCGCTACAAAAAACATGATTACTTTTGAAACGACAGA
65 AAATTGATTTTCGCAACGACCTTGAAAGTCGCTACAAAAAACATAATTACTTTTGAAGCCACAAA
24973 TTA
130 TTA
* * *
24976 AGTCGCTGTGAAATCTTACTCTTTTCGCAATTACTTTTGTTAGTCGTTGCTTAATATATTTTACA
1 AGTCGCTGCGAAATCTTACTCTTTTCGCAATGACTATTGTTAGTCGTTGCTTAATATATTTTACA
* * * *
25041 AATTGATTCTCGCAACGACCTTGAAAGTAGCTACAAAAAACATGATTACTTTCGAAGCCACAAAT
66 AATTGATTTTCGCAACGACCTTGAAAGTCGCTACAAAAAACATAATTACTTTTGAAGCCACAAAT
25106 TA
131 TA
****
25108 AGTCGCTGCGAAATCTTACTCTTTTCGCAATGACTAACAATAGTCGTTGCTTAATATATTTTACA
1 AGTCGCTGCGAAATCTTACTCTTTTCGCAATGACTATTGTTAGTCGTTGCTTAATATATTTTACA
*
25173 AATTAATTTTCGCAACGACCTTGAAAGTCGCTACAAAAAACATAATTACTTTTGAAGCCACAAAT
66 AATTGATTTTCGCAACGACCTTGAAAGTCGCTACAAAAAACATAATTACTTTTGAAGCCACAAAT
25238 TA
131 TA
*
25240 AGTCGCTGCGAAATCTTACTCTTTTCGCAACGACTATTGTTAGTCGTTGCTTAATATATTTTTAC
1 AGTCGCTGCGAAATCTTACTCTTTTCGCAATGACTATTGTTAGTCGTTGCTTAATATA-TTTTAC
* * *
25305 TAAA-TGATTTTCGCAGCGACCTTGAAAGTCGTTACAAAAAACGTAATTACTTTTGAAGCCACAA
65 -AAATTGATTTTCGCAACGACCTTGAAAGTCGCTACAAAAAACATAATTACTTTTGAAGCCACAA
25369 ATTA
129 ATTA
25373 AGT
1 AGT
25376 GGCAATGACA
Statistics
Matches: 359, Mismatches: 38, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
132 286 0.80
133 70 0.19
134 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (132 bp):
AGTCGCTGCGAAATCTTACTCTTTTCGCAATGACTATTGTTAGTCGTTGCTTAATATATTTTACA
AATTGATTTTCGCAACGACCTTGAAAGTCGCTACAAAAAACATAATTACTTTTGAAGCCACAAAT
TA
Found at i:25962 original size:17 final size:17
Alignment explanation
Indices: 25935--25989 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
25925 AACCCATGTA
*
25935 ATCTTTGATCACTGGTG
1 ATCTTAGATCACTGGTG
25952 ATCTT-GCATCACTGGTG
1 ATCTTAG-ATCACTGGTG
*
25969 ATCTTAGATCACTAGTG
1 ATCTTAGATCACTGGTG
25986 ATCT
1 ATCT
25990 GGGGAGTGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
16 1 0.03
17 33 0.94
18 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (17 bp):
ATCTTAGATCACTGGTG
Found at i:26890 original size:65 final size:65
Alignment explanation
Indices: 26804--26934 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
26794 GTATAGTGTT
26804 ATGAAATGATAACAAAATAAAGCAAGGGAGTAGAGAATTGAAGTATGGAAAAGATAAGAGAATAG
1 ATGAAATGATAACAAAATAAAGCAAGGGAGTAGAGAATTGAAGTATGGAAAAGATAAGAGAATAG
26869 ATGAAATGATAACAAAATAAAGCAAGGGAGTAGAGAATTGAAGTATGGAAAAGATAAGAGAATAG
1 ATGAAATGATAACAAAATAAAGCAAGGGAGTAGAGAATTGAAGTATGGAAAAGATAAGAGAATAG
26934 A
1 A
26935 GAGAACAAGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.54, C:0.03, G:0.26, T:0.17
Consensus pattern (65 bp):
ATGAAATGATAACAAAATAAAGCAAGGGAGTAGAGAATTGAAGTATGGAAAAGATAAGAGAATAG
Done.