Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016476.1 Corchorus olitorius cultivar O-4 contig16509, 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: 105982
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1825 original size:36 final size:36
Alignment explanation
Indices: 1776--1854 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 36
1766 TGAGTGGGGA
1776 ATTAT-ATGATGATCATCATCATCTTAATATAATAT
1 ATTATGATGATGATCATCATCATCTTAATATAATAT
1811 ATTATGATGATGATCATCATCATCTTAATATAATAT
1 ATTATGATGATGATCATCATCATCTTAATATAATAT
1847 ATTATGAT
1 ATTATGAT
1855 ATATATGGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 5 0.12
36 38 0.88
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (36 bp):
ATTATGATGATGATCATCATCATCTTAATATAATAT
Found at i:3693 original size:18 final size:18
Alignment explanation
Indices: 3670--3723 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
3660 GAGTTAATGT
3670 CGATGGGGATTCAAAAAC
1 CGATGGGGATTCAAAAAC
*
3688 CGATGGGAATTCAAAAAC
1 CGATGGGGATTCAAAAAC
3706 CGATGGGGATTCAAAAAC
1 CGATGGGGATTCAAAAAC
3724 ATACAAGGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.41, C:0.17, G:0.26, T:0.17
Consensus pattern (18 bp):
CGATGGGGATTCAAAAAC
Found at i:6374 original size:16 final size:16
Alignment explanation
Indices: 6353--6384 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6343 AGTTGTTAAA
6353 TCTACAATGTTGACAT
1 TCTACAATGTTGACAT
6369 TCTACAATGTTGACAT
1 TCTACAATGTTGACAT
6385 CCACATTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
TCTACAATGTTGACAT
Found at i:12600 original size:19 final size:19
Alignment explanation
Indices: 12576--12615 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
12566 TAATATTGTC
12576 TTTATTCATAATCA-AATTA
1 TTTATTCA-AATCATAATTA
*
12595 TTTATTTAAATCATAATTA
1 TTTATTCAAATCATAATTA
12614 TT
1 TT
12616 AATAAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTATTCAAATCATAATTA
Found at i:12606 original size:18 final size:17
Alignment explanation
Indices: 12585--12629 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
12575 CTTTATTCAT
* *
12585 AATCAAATTATTTATTTA
1 AATCAAATTA-TTAATAA
12603 AATCATAATTATTAATAA
1 AATCA-AATTATTAATAA
12621 AATCAAATT
1 AATCAAATT
12630 GGTCCAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 15 0.62
19 5 0.21
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (17 bp):
AATCAAATTATTAATAA
Found at i:15789 original size:23 final size:23
Alignment explanation
Indices: 15759--15805 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
15749 ACTTACAACT
15759 TTCCCTTATTAAAAATAATTCTA
1 TTCCCTTATTAAAAATAATTCTA
*
15782 TTCCCTTATTAAAAATGATTCTA
1 TTCCCTTATTAAAAATAATTCTA
15805 T
1 T
15806 GGTGTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.17, G:0.02, T:0.45
Consensus pattern (23 bp):
TTCCCTTATTAAAAATAATTCTA
Found at i:43054 original size:4 final size:4
Alignment explanation
Indices: 43047--43095 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
43037 TGTCTCTCTC
* * *
43047 TTCT TTCT TTCT TTTT TTGT GTCT CTTC- TTCT TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT
43095 T
1 T
43096 ACATTCTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
3 3 0.08
4 33 0.87
5 2 0.05
ACGTcount: A:0.00, C:0.22, G:0.04, T:0.73
Consensus pattern (4 bp):
TTCT
Found at i:43092 original size:32 final size:29
Alignment explanation
Indices: 43033--43088 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 29
43023 TGAGCACTCA
43033 TTTGTGTCTCTCTCTTCTTTCTTTCTTTT
1 TTTGTGTCTCTCTCTTCTTTCTTTCTTTT
43062 TTTGTGTCTCT-TCTTCTTTCTTTCTTT
1 TTTGTGTCTCTCTCTTCTTTCTTTCTTT
43089 CTTTCTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.00, C:0.23, G:0.07, T:0.70
Consensus pattern (29 bp):
TTTGTGTCTCTCTCTTCTTTCTTTCTTTT
Found at i:49707 original size:3 final size:3
Alignment explanation
Indices: 49701--49735 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
49691 TTGGGGGTGG
* *
49701 TGC TGC TGC TGC TGG TGC TGC TGC TGC TGG TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
49736 GGGGTGGTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.26, G:0.40, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:49716 original size:15 final size:15
Alignment explanation
Indices: 49698--49735 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
49688 TGTTTGGGGG
49698 TGGTGCTGCTGCTGC
1 TGGTGCTGCTGCTGC
49713 TGGTGCTGCTGCTGC
1 TGGTGCTGCTGCTGC
49728 TGGTGCTG
1 TGGTGCTG
49736 GGGGTGGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.00, C:0.24, G:0.42, T:0.34
Consensus pattern (15 bp):
TGGTGCTGCTGCTGC
Found at i:69411 original size:12 final size:12
Alignment explanation
Indices: 69394--69423 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
69384 AGGATGGCAG
69394 TATCGAGGATAA
1 TATCGAGGATAA
69406 TATCGAGGATAA
1 TATCGAGGATAA
69418 TATCGA
1 TATCGA
69424 TGAGATAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (12 bp):
TATCGAGGATAA
Found at i:86336 original size:27 final size:27
Alignment explanation
Indices: 86304--86365 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
86294 GGAGGAGAAG
86304 AAGGAGAAAGTGGAAGCTGGAGAAAAC
1 AAGGAGAAAGTGGAAGCTGGAGAAAAC
* * *
86331 AAGGAGAGAGTGGGAGCTGGAGAAAAG
1 AAGGAGAAAGTGGAAGCTGGAGAAAAC
86358 AAGGAGAA
1 AAGGAGAA
86366 GAAGGCAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.47, C:0.05, G:0.42, T:0.06
Consensus pattern (27 bp):
AAGGAGAAAGTGGAAGCTGGAGAAAAC
Found at i:87877 original size:20 final size:20
Alignment explanation
Indices: 87852--87891 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
87842 CCAATCTGAT
87852 CTTTTGTTTTACACACAAAA
1 CTTTTGTTTTACACACAAAA
87872 CTTTTGTTTTACACACAAAA
1 CTTTTGTTTTACACACAAAA
87892 TTTGATCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (20 bp):
CTTTTGTTTTACACACAAAA
Found at i:88455 original size:24 final size:24
Alignment explanation
Indices: 88411--88471 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
88401 AAGAAAAGGA
*
88411 GGAGAAGAAGGAGAAAGTGGAAGCT
1 GGAGAA-AAGAAGAAAGTGGAAGCT
*
88436 GGAGAAAAGAAGAGAGTGGAAGCT
1 GGAGAAAAGAAGAAAGTGGAAGCT
88460 GGAGAAAAGAAG
1 GGAGAAAAGAAG
88472 GAGAAGAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 28 0.82
25 6 0.18
ACGTcount: A:0.48, C:0.03, G:0.43, T:0.07
Consensus pattern (24 bp):
GGAGAAAAGAAGAAAGTGGAAGCT
Found at i:88910 original size:16 final size:16
Alignment explanation
Indices: 88889--88928 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
88879 TTGGCATCTA
88889 GGTTTTGATTGGATTT
1 GGTTTTGATTGGATTT
*
88905 GGTTTTTA-TGGATTT
1 GGTTTTGATTGGATTT
88920 -G-TTTGATTG
1 GGTTTTGATTG
88929 AATTCATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
13 4 0.19
14 3 0.14
15 7 0.33
16 7 0.33
ACGTcount: A:0.12, C:0.00, G:0.30, T:0.57
Consensus pattern (16 bp):
GGTTTTGATTGGATTT
Found at i:94767 original size:17 final size:17
Alignment explanation
Indices: 94745--94794 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
94735 TCATTTGAGG
*
94745 GGTGATCTTAGATTACT
1 GGTGATCTTAGATTACA
*
94762 GGTGATCTTAGATCACA
1 GGTGATCTTAGATTACA
*
94779 GGTGATCTTTGATTAC
1 GGTGATCTTAGATTAC
94795 CTGGGTTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (17 bp):
GGTGATCTTAGATTACA
Found at i:99737 original size:335 final size:329
Alignment explanation
Indices: 98908--100239 Score: 1374
Period size: 335 Copynumber: 4.0 Consensus size: 329
98898 AACAATAGCT
* *
98908 GATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTCAGCGC-CAAAAATCATGCAAAACTGAA
1 GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC-G-GCACAAAAATCATGCAAAACTGAA
* * *
98972 TC-GGGCCCCAGAACACGTTTTTAGCCAAAAACCGTGATGATTATTATACGATTTCCGGA-TAAA
64 TCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTT-C-GACTAAA
* * * *
99035 ATTTTGCAAAAATTGACCCAAAAGATATTTCCTCAAATTTTAGCCACAATACTCATAAAAATATA
127 ATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCTAAAATACTCAT-AAAA-ATA
* *
99100 TATAATTCT-ACACTAAAAAGA-TAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTT
190 TATAATT-TAACACCAAAAAGATTAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTT
* ** * *
99163 CAGAATTAATTT-TTAATTAAATTAAAACAAGATTCAGATGCTCGTGAAAACAAATCCTTAAATG
254 CTGAATTAATTTATTAATTAAATCGAAACAAGATTTAGATGCTCGT-AAAACAAATCCTTAAATC
* *
99227 CAATGTGGCTAA
318 CAATGTAGCTGA
* * * *
99239 GATTTTATTAGATGAATATAAAAATTTCAAGGAGTCTCGACGC-CAAAAATCATGCAAAACTGAG
1 GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCG--GCACAAAAATCATGCAAAACTGAA
* * * * *
99303 TCGGGGCCCTGAAACGCGTTTTTAGCCAAAAAACTGTGATGATTAGTACACGATTTCGGCTAAAA
64 TCGGGGCCCCGGAACGCGTTTTTAGCC-AAAAACCGTGATGATTATTACACGATTTCGACTAAAA
* * * * * *
99368 TTTTGTAAAAAAAAATGAACTGAAA-ATTTTTCCTCAATTTTTAGATAAAATACTCATAAAATAT
128 TTTTG---CAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCTAAAATACTCATAAAA-AT
*
99432 ATATAATTTAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTTCATATTTT
189 ATATAATTTAACACCAAAAAGATT-AAGGACTTTTCACGCTTTTAATATCG-TTTTTCATATTTT
* *
99497 TT-TGAATTAATTTCTAATTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAA-AAATTTCTT
252 TTCTGAATTAA-TT-T-ATTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAACAAA-TCCTT
99560 AAATCCAATGTAGCTGA
313 AAATCCAATGTAGCTGA
* * * * * * *
99577 GATTTGATTAAATGAATATGGATATCTCAAGGAGTTTTGGCACAAAAAATCATACAAAACTGAAC
1 GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCAC-AAAAATCATGCAAAACTGAAT
* * ** *
99642 CGGGGCCCCGGAACGCTTTTTTAGACAAAAATTGTGATGGTTATTACACGATTTCGACTAAAATT
65 CGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTTCGACTAAAATT
* * * *
99707 TTGTAAAAATGGGCCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAATATAT-A
130 TTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCTAAAATACTCATAAAAATATATAA
* * * * *
99771 TTTCAACGCCAAAAATATTGAAGGGCTTTTGACG-TTTCTAATATTGTTTTTTC-TATTTTTTTC
195 TTT-AACACCAAAAAGATT-AAGGACTTTTCACGCTTT-TAATATCG-TTTTTCATA-TTTTTTC
*
99834 TGAATTAATTTA-TAATTAAATCGAAACAAGATTAAGATGCTCGTAAAATCAAATCCTTAAATCC
255 TGAATTAATTTATTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAA-CAAATCCTTAAATCC
* * *
99898 TATGTGGTTGA
319 AATGTAGCTGA
* * * *
99909 GATTTGATTAGATGAATATAGATATTTCAAGTAGCCTCGG-AGTCAAAAATCATGCAAAATTGAG
1 GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCA--CAAAAATCATGCAAAACTGAA
* ** * * * * *
99973 GCGGATCCCCGGAACGCATTTTTAGCCAAAAACCGTTATGGTTAGTTAGTACACGATTTCG-GTT
64 TCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-G--A-TTATTACACGATTTCGACTA
* * *
100037 AAATTTTGCAAAAATTGACACGAAAGA-ATTCTCCTCAATTTTTGGCTAAAAAACTCATAAAAAT
125 AAATTTTGCAAAAATTGACCCGAAAGATATT-TCCTCAATTTTTAGCTAAAATACTCATAAAAAT
* * * * * ** *
100101 ATATAATTCAACGCCTAAAAAGATT-GGGAGCCTTTCACGCTTTTTATATCGCATTTCTTATTTT
189 ATATAATTTAACACC-AAAAAGATTAAGGA-CTTTTCACGCTTTTAATATCGTTTTTCATATTTT
* *
100165 TTCT-ATATTAA--AATCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTTA
252 TTCTGA-ATTAATTTAT-TAATTAAATCGAAACAAGATTTAGATGCTCGT-AAAACAAATCCTTA
*
100227 AATGCAATGTAGC
314 AATCCAATGTAGC
100240 AAGCCTGAGA
Statistics
Matches: 840, Mismatches: 120, Indels: 79
0.81 0.12 0.08
Matches are distributed among these distances:
330 1 0.00
331 94 0.11
332 133 0.16
333 67 0.08
334 163 0.19
335 169 0.20
336 48 0.06
337 43 0.05
338 93 0.11
339 29 0.03
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (329 bp):
GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCACAAAAATCATGCAAAACTGAATC
GGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTTCGACTAAAATTT
TGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCTAAAATACTCATAAAAATATATAAT
TTAACACCAAAAAGATTAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATT
AATTTATTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAACAAATCCTTAAATCCAATGTAG
CTGA
Found at i:100761 original size:27 final size:27
Alignment explanation
Indices: 100721--100774 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
100711 CATAATTAAT
* *
100721 AAAAAAGTTGAATGATCTAAAAA-AATA
1 AAAAAAATTAAATGA-CTAAAAAGAATA
100748 AAAAAAATTAAATGACTAAAAAGAATA
1 AAAAAAATTAAATGACTAAAAAGAATA
100775 CTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.20
Consensus pattern (27 bp):
AAAAAAATTAAATGACTAAAAAGAATA
Done.