Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011419.1 Corchorus olitorius cultivar O-4 contig11452, 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: 61404
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:10748 original size:103 final size:102
Alignment explanation
Indices: 10569--10778 Score: 384
Period size: 103 Copynumber: 2.0 Consensus size: 102
10559 GGAGCGTTAC
10569 AATTCATCTCCAGACATATTATTGCATAACGTCCACGATCCTTATTGCCAATATGCACATCGATT
1 AATTCATCTCCAGACATATTATTGCATAACGTCCACGATCCTTATTGCCAATATGCACATCGATT
10634 TTTATAGGTTTTCCAATAATACACCCTATCCGAAATAG
66 TTTATAGGTTTT-CAATAATACACCCTATCCGAAATAG
* *
10672 AATTCATCTCCAGACATATTATTGCATAACGTCCACGATCCTTATTGCCAGTATGCACATTGATT
1 AATTCATCTCCAGACATATTATTGCATAACGTCCACGATCCTTATTGCCAATATGCACATCGATT
*
10737 TTTATAGGTTTTCAATAATGCACCCTATCCGAAATAG
66 TTTATAGGTTTTCAATAATACACCCTATCCGAAATAG
10774 AATTC
1 AATTC
10779 CCGAATCATA
Statistics
Matches: 104, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
102 29 0.28
103 75 0.72
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (102 bp):
AATTCATCTCCAGACATATTATTGCATAACGTCCACGATCCTTATTGCCAATATGCACATCGATT
TTTATAGGTTTTCAATAATACACCCTATCCGAAATAG
Found at i:13324 original size:30 final size:29
Alignment explanation
Indices: 13244--13326 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
13234 ATCCTAGCAC
* *
13244 TCGTCGTTCCTGTGGCAAAGTCCAGGACGA
1 TCGTCGTTCATGT-GCAATGTCCAGGACGA
* *
13274 TCGT-GTTCTAATG-GCAATGTCCAGGGCGT
1 TCGTCGTTC--ATGTGCAATGTCCAGGACGA
13303 TCGTCGTTCATGTGTCAATGTCCA
1 TCGTCGTTCATGTG-CAATGTCCA
13327 AGACAAAACC
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
28 3 0.07
29 22 0.50
30 17 0.39
31 2 0.05
ACGTcount: A:0.18, C:0.24, G:0.28, T:0.30
Consensus pattern (29 bp):
TCGTCGTTCATGTGCAATGTCCAGGACGA
Found at i:17857 original size:32 final size:33
Alignment explanation
Indices: 17800--17872 Score: 121
Period size: 32 Copynumber: 2.2 Consensus size: 33
17790 AATTGATGTA
17800 AAGTTAATAAAAAAAATAGAAGGGTAAATTGGAG
1 AAGTTAATAAAAAAAATAG-AGGGTAAATTGGAG
*
17834 AAGTTAATAAAAAATATAG-GGGTAAATTGGAG
1 AAGTTAATAAAAAAAATAGAGGGTAAATTGGAG
17866 AAGTTAA
1 AAGTTAA
17873 ATGTGAGTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 20 0.53
34 18 0.47
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (33 bp):
AAGTTAATAAAAAAAATAGAGGGTAAATTGGAG
Found at i:23023 original size:25 final size:24
Alignment explanation
Indices: 22995--23056 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
22985 GTGGATTGTA
*
22995 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
23020 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
*
23044 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
23057 CTGACCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 17 0.50
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:25104 original size:22 final size:22
Alignment explanation
Indices: 25062--25105 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
25052 CATTGTTAAG
* *
25062 TCTCGCATCTAGTCGAGCTCAA
1 TCTCGCATCTAGTCAAACTCAA
*
25084 TCTCGTATCTAGTCAAACTCAA
1 TCTCGCATCTAGTCAAACTCAA
25106 ACTGCATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.30
Consensus pattern (22 bp):
TCTCGCATCTAGTCAAACTCAA
Found at i:26383 original size:11 final size:11
Alignment explanation
Indices: 26355--26388 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
26345 AGCATGTGAA
*
26355 TTTCTTTTTGT
1 TTTCTTTTTCT
26366 TTT-TTTTTCT
1 TTTCTTTTTCT
26376 TTTCTTTTTCT
1 TTTCTTTTTCT
26387 TT
1 TT
26389 CTACGGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:39291 original size:12 final size:12
Alignment explanation
Indices: 39274--39312 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
39264 GTACAGATAT
39274 CGGATATATCGA
1 CGGATATATCGA
39286 CGGATATATCGA
1 CGGATATATCGA
39298 --G--ATATCGA
1 CGGATATATCGA
39306 CGGATAT
1 CGGATAT
39313 TTAATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.30
10 2 0.09
12 14 0.61
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:43882 original size:2 final size:2
Alignment explanation
Indices: 43875--43901 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43865 TTAACCATTC
43875 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
43902 TTCAAGACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47501 original size:21 final size:19
Alignment explanation
Indices: 47457--47515 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
47447 CTGTTTGGCA
47457 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
* *
47476 ACTGTACATATTAGATTAGGT
1 ACTGTACAGATGAGATTA--T
47497 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
47516 TAGAGCAGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAT
Found at i:49343 original size:30 final size:30
Alignment explanation
Indices: 49307--49384 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
49297 CATCAGAAAA
49307 GGGCTTATTTGGCCTTTTTAA-AGAGTTCAG
1 GGGCTTATTTGGCC-TTTTAATAGAGTTCAG
**
49337 GGGCTTATTTGG-C-TGCAATTAGAGTTCAG
1 GGGCTTATTTGGCCTTTTAA-TAGAGTTCAG
49366 GGGCTTATTTGGCCGTTTT
1 GGGCTTATTTGGCC-TTTT
49385 GTGTAAGTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.08
29 22 0.56
30 13 0.33
32 1 0.03
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40
Consensus pattern (30 bp):
GGGCTTATTTGGCCTTTTAATAGAGTTCAG
Found at i:50645 original size:9 final size:9
Alignment explanation
Indices: 50633--50666 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
50623 TTGCAAAAAA
50633 AAAAAAACT
1 AAAAAAACT
50642 AAAAAAACT
1 AAAAAAACT
50651 AAAAAAACT
1 AAAAAAACT
50660 AAAAAAA
1 AAAAAAA
50667 AGTGTAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.82, C:0.09, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAAAAACT
Found at i:52117 original size:43 final size:44
Alignment explanation
Indices: 52056--52158 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 44
52046 CATAGTTAGG
* * * * *
52056 TTATCAAAGTTTCTTATGGAGTTTATCACAATTTTA-TAGGTAA
1 TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATTAGGTAA
* * * *
52099 TTATCAAAATTTGATATGGTGGTTATCAAAATTTAATTGGGTGA
1 TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATTAGGTAA
52143 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
52159 AAAATATTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
43 29 0.59
44 20 0.41
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.43
Consensus pattern (44 bp):
TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATTAGGTAA
Found at i:52125 original size:22 final size:22
Alignment explanation
Indices: 52078--52154 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
52068 CTTATGGAGT
* * *
52078 TTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTAATATGGTGA
* *
52099 TTATCAAAATTTGATATGGTGG
1 TTATCAAAATTTAATATGGTGA
52121 TTATCAAAATTTAAT-TGGGTGA
1 TTATCAAAATTTAATAT-GGTGA
52143 TTATCAAAATTT
1 TTATCAAAATTT
52155 CATAAAAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 15 0.31
22 33 0.69
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTAATATGGTGA
Found at i:52184 original size:43 final size:43
Alignment explanation
Indices: 52128--52213 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
52118 TGGTTATCAA
* *
52128 AATTTAATTGGGTGATTATCAAAATTTCATAAAAATATTTAAT
1 AATTTAATAGGGTGATCATCAAAATTTCATAAAAATATTTAAT
*
52171 AATTTAATAGGGTGATCATCAAAATTTTATAAAAATATTTAAT
1 AATTTAATAGGGTGATCATCAAAATTTCATAAAAATATTTAAT
52214 TGAAACATGC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (43 bp):
AATTTAATAGGGTGATCATCAAAATTTCATAAAAATATTTAAT
Found at i:52306 original size:24 final size:25
Alignment explanation
Indices: 52279--52334 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
52269 AACCAATTAA
52279 CAAAA-CCCCAAAAGAAAAGTGAAT
1 CAAAATCCCCAAAAGAAAAGTGAAT
** * *
52303 CAAAATCCCCTTAATAAAATTGAAT
1 CAAAATCCCCAAAAGAAAAGTGAAT
52328 CAAAATC
1 CAAAATC
52335 GCGAGAGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.54, C:0.21, G:0.07, T:0.18
Consensus pattern (25 bp):
CAAAATCCCCAAAAGAAAAGTGAAT
Found at i:53117 original size:17 final size:17
Alignment explanation
Indices: 53095--53127 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
53085 CTTCTGCATA
53095 AGGAATGCCTAATTTTG
1 AGGAATGCCTAATTTTG
53112 AGGAATGCCTAATTTT
1 AGGAATGCCTAATTTT
53128 TTGTAGTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36
Consensus pattern (17 bp):
AGGAATGCCTAATTTTG
Found at i:54201 original size:42 final size:44
Alignment explanation
Indices: 54150--54243 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
54140 AGTGCATTAC
*
54150 CTAA-ATTCTACT-T-CATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
*
54191 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATATAG
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAG
54236 CTAATATT
1 CTAATATT
54244 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
44 1 0.02
45 34 0.72
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:55951 original size:15 final size:16
Alignment explanation
Indices: 55926--55955 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55916 AAAAAAAGAG
55926 AAGAAGAAAGATTAGA
1 AAGAAGAAAGATTAGA
55942 AAGAAG-AAGATTAG
1 AAGAAGAAAGATTAG
55956 GAAGGAACGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.27, T:0.13
Consensus pattern (16 bp):
AAGAAGAAAGATTAGA
Found at i:56905 original size:27 final size:28
Alignment explanation
Indices: 56837--56905 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
56827 TTAAGATGTC
* *
56837 AAAATTACTGTTTTACCCTTGGTAAGCT
1 AAAATTACAGTTTTACCCCTGGTAAGCT
*
56865 AAAATTACCA-TTTTACCCCTGGT-TGACT
1 AAAATTA-CAGTTTTACCCCTGGTAAG-CT
56893 -AAATTACAGTTTT
1 AAAATTACAGTTTT
56906 GCCCTTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
26 2 0.06
27 11 0.31
28 21 0.60
29 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (28 bp):
AAAATTACAGTTTTACCCCTGGTAAGCT
Done.