Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017753.1 Corchorus olitorius cultivar O-4 contig17786, 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: 20424
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:3043 original size:32 final size:32
Alignment explanation
Indices: 3002--3069 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
2992 TGAAAAATTC
3002 GTGATTTTTGACAATCTCTTTCTAATAAACTA
1 GTGATTTTTGACAATCTCTTTCTAATAAACTA
3034 GTGATTTTTGACAATCTCTTTCTAATAAACTA
1 GTGATTTTTGACAATCTCTTTCTAATAAACTA
3066 GTGA
1 GTGA
3070 ATGACGCCCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.43
Consensus pattern (32 bp):
GTGATTTTTGACAATCTCTTTCTAATAAACTA
Found at i:8124 original size:9 final size:9
Alignment explanation
Indices: 8110--8138 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
8100 CTTTTGCAGT
8110 ATAGGGTTG
1 ATAGGGTTG
8119 ATAGGGTTG
1 ATAGGGTTG
8128 ATAGGGTTG
1 ATAGGGTTG
8137 AT
1 AT
8139 TCATTGTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.34
Consensus pattern (9 bp):
ATAGGGTTG
Found at i:11065 original size:27 final size:29
Alignment explanation
Indices: 11018--11075 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 29
11008 AAAGTTACCT
11018 TTCCTTACCAGCCCTTGAACCC-TTGCCC
1 TTCCTTACCAGCCCTTGAACCCTTTGCCC
11046 TTCCTTACCA-CCCTTGAACCCTTTGCCC
1 TTCCTTACCAGCCCTTGAACCCTTTGCCC
11074 TT
1 TT
11076 AAAGTTTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.14, C:0.45, G:0.09, T:0.33
Consensus pattern (29 bp):
TTCCTTACCAGCCCTTGAACCCTTTGCCC
Found at i:11469 original size:20 final size:20
Alignment explanation
Indices: 11433--11470 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11423 GACTCGAGAA
*
11433 AAATTCGAGTTCGGCTCGGG
1 AAATTCGAGTCCGGCTCGGG
11453 AAATTCGAG-CCGAGCTCG
1 AAATTCGAGTCCG-GCTCG
11471 AGCTCGTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.21
Consensus pattern (20 bp):
AAATTCGAGTCCGGCTCGGG
Found at i:14344 original size:93 final size:93
Alignment explanation
Indices: 14241--14417 Score: 284
Period size: 93 Copynumber: 1.9 Consensus size: 93
14231 ACTTTTTAAT
* * * *
14241 TAAATTAGTAATATCGTTAAAATAAAATAGA-TATAAGGATATTAGATTTAATTAAATAAAAATA
1 TAAAATAGTAAAATCGTAAAAATAAAA-AAATTATAAGGATATTAGATTTAATTAAATAAAAATA
*
14305 GAGTTTTTAGTTGAGTAAAACTATAAAAG
65 GAGTTTTTAGTTGACTAAAACTATAAAAG
*
14334 TAAAATAGTAAAATGGTAAAAATAAAAAAATTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAAAAATTATAAGGATATTAGATTTAATTAAATAAAAATAG
14399 AGTTTTTAGTTGACTAAAA
66 AGTTTTTAGTTGACTAAAA
14418 TAAGGATATG
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
92 2 0.03
93 75 0.97
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (93 bp):
TAAAATAGTAAAATCGTAAAAATAAAAAAATTATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG
Found at i:14463 original size:31 final size:31
Alignment explanation
Indices: 14416--14477 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
14406 AGTTGACTAA
*
14416 AATAAGGATATGATAGGCGATTCAAAAGTTT
1 AATAAGGATATAATAGGCGATTCAAAAGTTT
*
14447 AATAAGGGTATAATAGGCGATTCAAAAGTTT
1 AATAAGGATATAATAGGCGATTCAAAAGTTT
14478 TACAAAACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (31 bp):
AATAAGGATATAATAGGCGATTCAAAAGTTT
Found at i:18798 original size:21 final size:21
Alignment explanation
Indices: 18766--18821 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
18756 GTGTCGTGAA
18766 CAAAATTTTATACG-AAGGTTAT
1 CAAAA-TTTATA-GTAAGGTTAT
**
18788 CAAAATTTATAGTGTGGTTAT
1 CAAAATTTATAGTAAGGTTAT
18809 CAAAATTTCATAG
1 CAAAATTT-ATAG
18822 GGAGGGAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 1 0.03
21 20 0.67
22 9 0.30
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (21 bp):
CAAAATTTATAGTAAGGTTAT
Found at i:18843 original size:26 final size:26
Alignment explanation
Indices: 18803--18852 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
18793 TTTATAGTGT
18803 GGTTATCAAAATTTCATAGGGAGGGA
1 GGTTATCAAAATTTCATAGGGAGGGA
* *
18829 GGTTATCAAAGTTTCCTAGGGAGG
1 GGTTATCAAAATTTCATAGGGAGG
18853 TTAACAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.30, C:0.10, G:0.32, T:0.28
Consensus pattern (26 bp):
GGTTATCAAAATTTCATAGGGAGGGA
Found at i:18882 original size:21 final size:22
Alignment explanation
Indices: 18608--18907 Score: 147
Period size: 22 Copynumber: 13.3 Consensus size: 22
18598 TCAATCAAAC
*
18608 CAAAATTACATAGGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
18630 CAAATTTTCATAGTG-TGGTTAT
1 CAAAATTTCATAG-GAAGGTTAT
*
18652 TAAAATTTCATATGG-AGGTTAT
1 CAAAATTTCATA-GGAAGGTTAT
** *
18674 CAAAACGTCATAGTGTA-GTTAT
1 CAAAATTTCATAG-GAAGGTTAT
* * *
18696 CAAAATTCCATACAGACA--TTAC
1 CAAAATTTCATA-GGA-AGGTTAT
* **
18718 CAAAATTTTATAAAAAGGTTAAT
1 CAAAATTTCATAGGAAGGTT-AT
*
18741 CAAAAATTTCATA-G-AGTGTCGTGAA
1 C-AAAATTTCATAGGAAG-GT--T-AT
* *
18766 CAAAATTTTATACGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
*
18788 CAAAATTT-ATAGTG-TGGTTAT
1 CAAAATTTCATAG-GAAGGTTAT
18809 CAAAATTTCATAGGGAGGGAGGTTAT
1 CAAAATTTCATA-GGA---AGGTTAT
* * * *
18835 CAAAGTTTCCTAGGGAGGTTAA
1 CAAAATTTCATAGGAAGGTTAT
18857 CAAAATTTCATAGGAAGGTTA-
1 CAAAATTTCATAGGAAGGTTAT
*
18878 CAAAAACTTT-AT-GGAGATGTTAT
1 C-AAAA-TTTCATAGGA-AGGTTAT
18901 CAAAATT
1 CAAAATT
18908 AAATAAAGAG
Statistics
Matches: 216, Mismatches: 36, Indels: 53
0.71 0.12 0.17
Matches are distributed among these distances:
20 1 0.00
21 26 0.12
22 129 0.60
23 14 0.06
24 20 0.09
25 8 0.04
26 18 0.08
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:19023 original size:22 final size:22
Alignment explanation
Indices: 18952--19089 Score: 136
Period size: 22 Copynumber: 6.3 Consensus size: 22
18942 GAAGGGAAAC
*
18952 TTCATTGTGTGGTTATCAAAATT
1 TTCATAGTGTGGTTATCAAAA-T
* * *
18975 TTCATAATGCGGTTA-C-CAAT
1 TTCATAGTGTGGTTATCAAAAT
* *
18995 TTTATAGTGTGATTATCAAAAT
1 TTCATAGTGTGGTTATCAAAAT
* * *
19017 TTCATAGGGAGATTATCAAAAT
1 TTCATAGTGTGGTTATCAAAAT
19039 TTCATAGTGTGGTTATCAAAAT
1 TTCATAGTGTGGTTATCAAAAT
* * * *
19061 TTCACAGTGCGTTTATCAAATT
1 TTCATAGTGTGGTTATCAAAAT
19083 TTCATAG
1 TTCATAG
19090 CTTATCGAAA
Statistics
Matches: 93, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
20 12 0.13
21 3 0.03
22 66 0.71
23 12 0.13
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (22 bp):
TTCATAGTGTGGTTATCAAAAT
Found at i:19086 original size:66 final size:65
Alignment explanation
Indices: 18964--19089 Score: 155
Period size: 66 Copynumber: 1.9 Consensus size: 65
18954 CATTGTGTGG
* * * *
18964 TTATCAAAATTTTCATAATGCGGTTACCAATTTTATAGTGTGATTATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTTCATAATGCGGTTACAAATTTCACAGTGCGATTATCAAAATTTCATAGGGAGA
* * * *
19029 TTATCAAAA-TTTCATAGTGTGGTTATCAAAATTTCACAGTGCGTTTATCAAATTTTCATAG
1 TTATCAAAATTTTCATAATGCGGTTA-C-AAATTTCACAGTGCGATTATCAAAATTTCATAG
19090 CTTATCGAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
64 14 0.27
65 10 0.20
66 27 0.53
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (65 bp):
TTATCAAAATTTTCATAATGCGGTTACAAATTTCACAGTGCGATTATCAAAATTTCATAGGGAGA
Found at i:19125 original size:22 final size:21
Alignment explanation
Indices: 18952--19125 Score: 108
Period size: 22 Copynumber: 8.1 Consensus size: 21
18942 GAAGGGAAAC
*
18952 TTCATTGTGTGGTTATCAAAATT
1 TTCATAGTGT-GTTATC-AAATT
* * *
18975 TTCATAATGCGGTTA-CCAATT
1 TTCATAGTG-TGTTATCAAATT
*
18996 TT-ATAGTGTGATTATCAAAAT
1 TTCATAGTGTG-TTATCAAATT
* * *
19017 TTCATAGGGAGATTATCAAAAT
1 TTCATAGTGTG-TTATCAAATT
*
19039 TTCATAGTGTGGTTATCAAAAT
1 TTCATAGTGT-GTTATCAAATT
* *
19061 TTCACAGTGCGTTTATCAAATT
1 TTCATAGTGTG-TTATCAAATT
*
19083 TTCATA--G-CTTATCGAAA-T
1 TTCATAGTGTGTTATC-AAATT
*
19101 TTCATAATGATGTTATCAAATT
1 TTCATAGTG-TGTTATCAAATT
19123 TTC
1 TTC
19126 GCATCATTAT
Statistics
Matches: 121, Mismatches: 18, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
18 12 0.10
19 4 0.03
20 10 0.08
21 16 0.13
22 67 0.55
23 12 0.10
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (21 bp):
TTCATAGTGTGTTATCAAATT
Found at i:19755 original size:12 final size:11
Alignment explanation
Indices: 19698--19756 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
19688 CAAAATCTAA
*
19698 AATTATCTTTT
1 AATTATTTTTT
19709 AATTATTTTTT
1 AATTATTTTTT
*
19720 TATTGATTTTTAT
1 AATT-ATTTTT-T
* *
19733 AATTTAATTTTC
1 AA-TTATTTTTT
19745 AATTATTTTTT
1 AATTATTTTTT
19756 A
1 A
19757 TTTAAATATT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
11 21 0.55
12 8 0.21
13 7 0.18
14 2 0.05
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (11 bp):
AATTATTTTTT
Done.