Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016957.1 Corchorus olitorius cultivar O-4 contig16990, 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: 34399
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:409 original size:17 final size:17
Alignment explanation
Indices: 387--419 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
377 AATTTTATTA
387 TTTTATTGTTTATTTAT
1 TTTTATTGTTTATTTAT
*
404 TTTTATTGTTTCTTTA
1 TTTTATTGTTTATTTA
420 ATTCAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTATTGTTTATTTAT
Found at i:2032 original size:26 final size:26
Alignment explanation
Indices: 1975--2032 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
1965 TGTTGAAAAT
*
1975 AAAATCTTTCTAATTCTTTTTTATCA
1 AAAATCTTTCTAATTCTTTTTTAGCA
*
2001 AAAATCTTTCTAATT-TTTTTTAGGA
1 AAAATCTTTCTAATTCTTTTTTAGCA
2026 AATAATC
1 AA-AATC
2033 ATTTTTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 10 0.34
26 19 0.66
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.50
Consensus pattern (26 bp):
AAAATCTTTCTAATTCTTTTTTAGCA
Found at i:12696 original size:111 final size:107
Alignment explanation
Indices: 12512--12807 Score: 384
Period size: 111 Copynumber: 2.7 Consensus size: 107
12502 ATAAAATTTT
* * *
12512 AATTTTAATTT-GGCCTAAACTTAGTG-AATTAGTTATATATATTATTTCTAAAACCCTATAACA
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACA
* * * *
12575 ATAACTTATTAATTATGGAATTTACGCTTAAAA-TAAAAACAA
66 ATAAATTATTAATT-TGGAAATTACCCTTAAAACAAAAAACAA
*
12617 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAACCCTTTATAT
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCC----TAT
* *
12682 AACAATAAATTATTAATTTTGAAATTACCCTTAAAACAAAAAATAA
62 AACAATAAATTATTAATTTGGAAATTACCCTTAAAACAAAAAACAA
* * *
12728 AATTTTAATTTGGGGCTAAATTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACTCTATAATA
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACA
*
12793 AAAAATCT-TTAATTT
66 ATAAAT-TATTAATTT
12808 CATGTAACGT
Statistics
Matches: 168, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
105 11 0.07
106 14 0.08
107 45 0.27
108 1 0.01
110 15 0.09
111 82 0.49
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (107 bp):
AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACA
ATAAATTATTAATTTGGAAATTACCCTTAAAACAAAAAACAA
Found at i:13047 original size:23 final size:22
Alignment explanation
Indices: 13003--13047 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
12993 TGCATAATCA
*
13003 GGACTCTTTGTGAGAGCATTTG
1 GGACTCTTTGTGAGAACATTTG
*
13025 GGACTCCTTTGTGAGAACGTTTG
1 GGACT-CTTTGTGAGAACATTTG
13048 TCTTGCTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.36
Consensus pattern (22 bp):
GGACTCTTTGTGAGAACATTTG
Found at i:15323 original size:42 final size:42
Alignment explanation
Indices: 15264--15346 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
15254 GCTAAGTCTT
15264 GAAAATTCTCTGTAAATTAAGAAATACTCAACACAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACACAAATCATA
* *
15306 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCAT
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACACAAATCAT
15347 GATCCTTAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.29
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACACAAATCATA
Found at i:15484 original size:57 final size:60
Alignment explanation
Indices: 15414--15530 Score: 204
Period size: 57 Copynumber: 2.0 Consensus size: 60
15404 TTTTGTAGAT
*
15414 TAATTAAGTAGAGATAGGGGGGATAGG-AT-TT-GTTATAACATTTATTGTGTGAAAGAA
1 TAATTAAGTAGAGATAGGGGGGATAGGAATATTAATTATAACATTTATTGTGTGAAAGAA
15471 TAATTAAGTAGAGATAGGGGGGATAGGAATATTAATTATAACATTTATTGTGTGAAAGAA
1 TAATTAAGTAGAGATAGGGGGGATAGGAATATTAATTATAACATTTATTGTGTGAAAGAA
15531 AACATATAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
57 27 0.48
58 2 0.04
59 2 0.04
60 25 0.45
ACGTcount: A:0.39, C:0.02, G:0.26, T:0.32
Consensus pattern (60 bp):
TAATTAAGTAGAGATAGGGGGGATAGGAATATTAATTATAACATTTATTGTGTGAAAGAA
Found at i:17304 original size:111 final size:113
Alignment explanation
Indices: 17107--17317 Score: 313
Period size: 111 Copynumber: 1.9 Consensus size: 113
17097 TCGAATTTGC
*
17107 TAACCACCTACTCACATATATGATAAGAACCGAGAGAAAAAAAAAACTCTATAACTAAATCAAAT
1 TAACCACCTACTCACATATATGATAAGAACCGAGAGAAAAAAAAAACTCTATAAC-AAATAAAAT
* *
17172 AATTTTCTAGCCACATATCAAGAATGCTCAACGCGCCAACACGATCCGA
65 AATTTGCTAGCCACAAATCAAGAATGCTCAACGCGCCAACACGATCCGA
* * *
17221 TAACCACCTACTCACATATATATGATAAGAACTGAGAG-AAAAAAAAGCT-T-TAA-AACTAAAA
1 TAACCACCTACTCAC--ATATATGATAAGAACCGAGAGAAAAAAAAAACTCTATAACAAATAAAA
17282 TAATTTGCTAGCCACAAATCAAGAATGCTCAACGCG
64 TAATTTGCTAGCCACAAATCAAGAATGCTCAACGCG
17318 TCAGCATGAG
Statistics
Matches: 89, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
111 40 0.45
113 3 0.03
114 16 0.18
115 10 0.11
116 20 0.22
ACGTcount: A:0.45, C:0.22, G:0.11, T:0.21
Consensus pattern (113 bp):
TAACCACCTACTCACATATATGATAAGAACCGAGAGAAAAAAAAAACTCTATAACAAATAAAATA
ATTTGCTAGCCACAAATCAAGAATGCTCAACGCGCCAACACGATCCGA
Found at i:17463 original size:30 final size:31
Alignment explanation
Indices: 17404--17473 Score: 117
Period size: 30 Copynumber: 2.3 Consensus size: 31
17394 CAACTTTCAC
*
17404 AAAG-TTTAGTCCCAAATTTTTGTTTTAAAA
1 AAAGATTTATTCCCAAATTTTTGTTTTAAAA
17434 AAAGATTTATTCCCAAATTTTTG-TTTAAAA
1 AAAGATTTATTCCCAAATTTTTGTTTTAAAA
17464 AAAGATTTAT
1 AAAGATTTAT
17474 AGGGTAAGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
30 21 0.55
31 17 0.45
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (31 bp):
AAAGATTTATTCCCAAATTTTTGTTTTAAAA
Found at i:17884 original size:18 final size:18
Alignment explanation
Indices: 17861--17895 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17851 ATTTGAGTTA
*
17861 AACAAACTGAACTGACTC
1 AACAAACTAAACTGACTC
17879 AACAAACTAAACTGACT
1 AACAAACTAAACTGACT
17896 GAAATATCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.26, G:0.09, T:0.17
Consensus pattern (18 bp):
AACAAACTAAACTGACTC
Found at i:18622 original size:29 final size:31
Alignment explanation
Indices: 18550--18623 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 31
18540 AAATAGCCCA
*
18550 TTTGCCCTCTGAACTTTGCAAATTTAGTCCAG
1 TTTGCCCTCTGAACTTT-CAAATTTAGTCCAC
* *
18582 ATTGCCCCCTGAACTTT-AAA-TT-GTGCCAC
1 TTTGCCCTCTGAACTTTCAAATTTAGT-CCAC
18611 TTTGCCCTCTGAA
1 TTTGCCCTCTGAA
18624 TTTGTAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.06
29 16 0.44
30 3 0.08
32 15 0.42
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (31 bp):
TTTGCCCTCTGAACTTTCAAATTTAGTCCAC
Found at i:28947 original size:29 final size:29
Alignment explanation
Indices: 28568--28944 Score: 448
Period size: 29 Copynumber: 13.0 Consensus size: 29
28558 TTCGCACGCT
* *
28568 CAGGGGAATTTTGGTCATTTTTGCATATT
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * * *
28597 CAAGGGCATTTTGGTCATTTTCGCACATT
1 CAGGGGCATTTTGGTCATTTTTGCATATC
*
28626 CAGGGGCATTTTGGTCATTTTTGCATATA
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* *
28655 CAGGGGCATTTTGGTCATTTATGCATATA
1 CAGGGGCATTTTGGTCATTTTTGCATATC
*
28684 CGGGGGCATTTTGGTCATTTTTGCATATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * **
28713 CGGGGGGCATTTTGATCATTTTTGCGCATC
1 C-AGGGGCATTTTGGTCATTTTTGCATATC
* *
28743 CAGGGGCATTTCGGTCATTTTTGCACATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * * *
28772 CAGGGGCATTTTAGTCATCTTTACACATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
*
28801 CAGGGGCATTTTGGTCATTTTTGCATATA
1 CAGGGGCATTTTGGTCATTTTTGCATATC
*
28830 CAGGGGCATTTTGGTCATTTTTGCATATT
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * * *
28859 CGGGGGCATTTTGTTCATTTTTACACATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * * * *
28888 CAGGGGCATTTCGGTCATCTTTACACATT
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* *
28917 CTGGGGCAGTTTGGTCATTTTTGCATAT
1 CAGGGGCATTTTGGTCATTTTTGCATAT
28945 TCTAGGTTCT
Statistics
Matches: 302, Mismatches: 45, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
29 276 0.91
30 26 0.09
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.40
Consensus pattern (29 bp):
CAGGGGCATTTTGGTCATTTTTGCATATC
Done.