Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023215.1 Corchorus olitorius cultivar O-4 contig23248, 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: 27836
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1740 original size:109 final size:109
Alignment explanation
Indices: 1549--1766 Score: 391
Period size: 109 Copynumber: 2.0 Consensus size: 109
1539 CTATTATATA
*
1549 TATTATTATTAATTTTGTGGTTTATTCAATTGAACCTATCAAATAAACACACATACCAAACAATA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATCAAATAAACACACATACCAAACAATA
*
1614 CAAAATGTAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
* *
1658 TATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAACACACATACCAAACAATA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATCAAATAAACACACATACCAAACAATA
*
1723 CAAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
1767 AAAATGACTA
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 104 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (109 bp):
TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATCAAATAAACACACATACCAAACAATA
CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
Found at i:7641 original size:76 final size:78
Alignment explanation
Indices: 7490--7641 Score: 209
Period size: 76 Copynumber: 2.0 Consensus size: 78
7480 TTTACAGCAT
* *
7490 TCCATGGTCATTTGGTGTTAATTACTATTATGGATTGTGTTTCTATTCCAAATTATTGCAATGCT
1 TCCATGGTCATTTGGTGTTAAGTA-TATTATGAATTGTGTTTCTATTCCAAATTATTGCAATGCT
**
7555 TGAAGATAAAACTA
65 CCAAGATAAAACTA
* * *
7569 TCCATTGTCATTTGGTGTT-AGT-TATTATGAATTGTGTTTCTATTCCAAATTCTTGTAATGCTC
1 TCCATGGTCATTTGGTGTTAAGTATATTATGAATTGTGTTTCTATTCCAAATTATTGCAATGCTC
*
7632 CAAGGTAAAA
66 CAAGATAAAA
7642 TGATGATTCT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
76 45 0.69
78 2 0.03
79 18 0.28
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (78 bp):
TCCATGGTCATTTGGTGTTAAGTATATTATGAATTGTGTTTCTATTCCAAATTATTGCAATGCTC
CAAGATAAAACTA
Found at i:7884 original size:16 final size:17
Alignment explanation
Indices: 7857--7892 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
7847 GGTTAAGCTA
7857 TTCCCTTTTAAGTAATT
1 TTCCCTTTTAAGTAATT
7874 TTCCC-TTTAAGTAATT
1 TTCCCTTTTAAGTAATT
7890 TTC
1 TTC
7893 TTTCCTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (17 bp):
TTCCCTTTTAAGTAATT
Found at i:9390 original size:38 final size:38
Alignment explanation
Indices: 9339--9414 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
9329 GGCTGCAAAA
9339 TAATGGCCAAAATCCCGCGGCATCGTGCGGGCTCAACT
1 TAATGGCCAAAATCCCGCGGCATCGTGCGGGCTCAACT
9377 TAATGGCCAAAATCCCGCGGCATCGTGCGGGCTCAACT
1 TAATGGCCAAAATCCCGCGGCATCGTGCGGGCTCAACT
9415 AACTAGTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.32, G:0.26, T:0.18
Consensus pattern (38 bp):
TAATGGCCAAAATCCCGCGGCATCGTGCGGGCTCAACT
Found at i:9819 original size:23 final size:24
Alignment explanation
Indices: 9784--9829 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
9774 TTGCTTGGGT
9784 TTAGGGTGGTAATCCAGATCACCA
1 TTAGGGTGGTAATCCAGATCACCA
9808 TTAGGG-GGTAATCCAGATCACC
1 TTAGGGTGGTAATCCAGATCACC
9830 CTCATGGGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (24 bp):
TTAGGGTGGTAATCCAGATCACCA
Found at i:9838 original size:23 final size:23
Alignment explanation
Indices: 9786--9838 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
9776 GCTTGGGTTT
*
9786 AGGGTGGTAATCCAGATCACCATT
1 AGGG-GGTAATCCAGATCACCATC
*
9810 AGGGGGTAATCCAGATCACCCTC
1 AGGGGGTAATCCAGATCACCATC
*
9833 ATGGGG
1 AGGGGG
9839 CGTTTGGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (23 bp):
AGGGGGTAATCCAGATCACCATC
Found at i:14683 original size:2 final size:2
Alignment explanation
Indices: 14676--14706 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14666 ATTATTACTA
14676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14707 CTAATTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16368 original size:30 final size:31
Alignment explanation
Indices: 16317--16425 Score: 211
Period size: 31 Copynumber: 3.5 Consensus size: 31
16307 GTAGTTTCTC
16317 AAATTCGAATTCAGTTTTTTTTTGGATACAT
1 AAATTCGAATTCAGTTTTTTTTTGGATACAT
16348 AAATTCGAATTCAG-TTTTTTTTGGATACAT
1 AAATTCGAATTCAGTTTTTTTTTGGATACAT
16378 AAATTCGAATTCAGTTTTTTTTTGGATACAT
1 AAATTCGAATTCAGTTTTTTTTTGGATACAT
16409 AAATTCGAATTCAGTTT
1 AAATTCGAATTCAGTTT
16426 AGCACTTCAA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
30 30 0.39
31 47 0.61
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (31 bp):
AAATTCGAATTCAGTTTTTTTTTGGATACAT
Found at i:16995 original size:51 final size:51
Alignment explanation
Indices: 16939--17046 Score: 198
Period size: 51 Copynumber: 2.1 Consensus size: 51
16929 TTTATTTTAT
*
16939 ATATAAAAGGGGATGCATGTTTTTTAATTTTTTCAAACTAAATGAATACAA
1 ATATAAAAGGGGATGCATGTTTTTTAATTTTTCCAAACTAAATGAATACAA
*
16990 ATATAAAAGGGGATGTATGTTTTTTAATTTTTCCAAACTAAATGAATACAA
1 ATATAAAAGGGGATGCATGTTTTTTAATTTTTCCAAACTAAATGAATACAA
17041 ATATAA
1 ATATAA
17047 TAAACAAAAC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (51 bp):
ATATAAAAGGGGATGCATGTTTTTTAATTTTTCCAAACTAAATGAATACAA
Found at i:22097 original size:28 final size:28
Alignment explanation
Indices: 22065--22233 Score: 320
Period size: 28 Copynumber: 6.0 Consensus size: 28
22055 TCTGCAACAA
22065 CCTTACACTCGGGTTCATGCCACTAAGC
1 CCTTACACTCGGGTTCATGCCACTAAGC
22093 CCTTACACTCGGGTTCATGCCACTAAGC
1 CCTTACACTCGGGTTCATGCCACTAAGC
*
22121 CCTTACACTCAGGTTCATGCCACTAAGC
1 CCTTACACTCGGGTTCATGCCACTAAGC
22149 CCTTACACTCGGGTTCATGCCACTAAGC
1 CCTTACACTCGGGTTCATGCCACTAAGC
*
22177 CCTTACACTCAGGTTCATGCCACTAAGC
1 CCTTACACTCGGGTTCATGCCACTAAGC
22205 CCTTACACTCGGGTTCATGCCACTAAGC
1 CCTTACACTCGGGTTCATGCCACTAAGC
22233 C
1 C
22234 ATCTTGTAGA
Statistics
Matches: 137, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 137 1.00
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (28 bp):
CCTTACACTCGGGTTCATGCCACTAAGC
Found at i:22292 original size:10 final size:10
Alignment explanation
Indices: 22277--22310 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
22267 AACCAAGCCA
22277 TTTTCTTTTT
1 TTTTCTTTTT
22287 TTTTCTTTTT
1 TTTTCTTTTT
*
22297 TTCT-TTTTT
1 TTTTCTTTTT
22306 TTTTC
1 TTTTC
22311 ATTATACCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:23463 original size:15 final size:15
Alignment explanation
Indices: 23443--23472 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23433 GTGATCTCTG
*
23443 TAGATCTCCTCCCTA
1 TAGATCACCTCCCTA
23458 TAGATCACCTCCCTA
1 TAGATCACCTCCCTA
23473 GTCTCCGAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.40, G:0.07, T:0.30
Consensus pattern (15 bp):
TAGATCACCTCCCTA
Found at i:26130 original size:58 final size:56
Alignment explanation
Indices: 26023--26130 Score: 153
Period size: 57 Copynumber: 1.9 Consensus size: 56
26013 ATTAATCAAA
* *
26023 TATCAAGTGACATGTTCTTTATTAGATGCATAAATAAACGTTTTCGGACCAAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAACGTTTTAGGACCAAGACT
* * *
26079 TATCGAGTGACATGTTTTTTTATTAGATGCCTAAAAAAGACGTTTTAGGACC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAA-ACGTTTTAGGACC
26131 GAGGCATGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
56 13 0.29
57 20 0.44
58 12 0.27
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (56 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAACGTTTTAGGACCAAGACT
Done.