Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024763.1 Corchorus olitorius cultivar O-4 contig24796, 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: 40501
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:433 original size:30 final size:29
Alignment explanation
Indices: 360--435 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
350 TTTGGTGCCG
*
360 TTGCCGGGGAAGGGTAACTTTTTCTGGTTT
1 TTGCCGGGGAA-GGAAACTTTTTCTGGTTT
390 TTGCCGGGGAAGGAAACTTTTTCTGGTTT
1 TTGCCGGGGAAGGAAACTTTTTCTGGTTT
419 TTGCCAGGGGAAGGAAA
1 TTGCC-GGGGAAGGAAA
436 AATAGACTCA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 22 0.50
30 22 0.50
ACGTcount: A:0.20, C:0.13, G:0.34, T:0.33
Consensus pattern (29 bp):
TTGCCGGGGAAGGAAACTTTTTCTGGTTT
Found at i:585 original size:22 final size:22
Alignment explanation
Indices: 554--597 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
544 CTGAAAAAAA
* *
554 AATTTGTTGTTTTTGCGTTTTT
1 AATTTGTTGTGTTTGCCTTTTT
*
576 AATTTTTTGTGTTTGCCTTTTT
1 AATTTGTTGTGTTTGCCTTTTT
598 TTTGAAAAAA
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:0.09, C:0.07, G:0.16, T:0.68
Consensus pattern (22 bp):
AATTTGTTGTGTTTGCCTTTTT
Found at i:648 original size:21 final size:21
Alignment explanation
Indices: 622--668 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
612 TCTGTTTGTT
622 TTTTGCGTCGA-AAAAAAAAAA
1 TTTTGCGTC-ATAAAAAAAAAA
643 TTTTGCGTCATAAAAAAAAAA
1 TTTTGCGTCATAAAAAAAAAA
664 TTTTG
1 TTTTG
669 TCCTTGCGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.32
Consensus pattern (21 bp):
TTTTGCGTCATAAAAAAAAAA
Found at i:11812 original size:110 final size:110
Alignment explanation
Indices: 11674--11896 Score: 428
Period size: 110 Copynumber: 2.0 Consensus size: 110
11664 GGAGACCAAC
11674 TTAGAGTCTAAACTGTCCTACACTATCCTAATTCTATTAGGATTCTTATTTTTCCACTATAAATA
1 TTAGAGTCTAAACTGTCCTACACTATCCTAATTCTATTAGGATTCTTATTTTTCCACTATAAATA
* *
11739 GCCACCTTAGGTCTAGGTTTTTATTATTATTGTATTGTTGAATTA
66 GCCACCTTAGATCTAGGTTTTTATTATTATTGTATTGTAGAATTA
11784 TTAGAGTCTAAACTGTCCTACACTATCCTAATTCTATTAGGATTCTTATTTTTCCACTATAAATA
1 TTAGAGTCTAAACTGTCCTACACTATCCTAATTCTATTAGGATTCTTATTTTTCCACTATAAATA
11849 GCCACCTTAGATCTAGGTTTTTATTATTATTGTATTGTAGAATTA
66 GCCACCTTAGATCTAGGTTTTTATTATTATTGTATTGTAGAATTA
11894 TTA
1 TTA
11897 TAATTGTTTG
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 111 1.00
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.44
Consensus pattern (110 bp):
TTAGAGTCTAAACTGTCCTACACTATCCTAATTCTATTAGGATTCTTATTTTTCCACTATAAATA
GCCACCTTAGATCTAGGTTTTTATTATTATTGTATTGTAGAATTA
Found at i:24818 original size:38 final size:34
Alignment explanation
Indices: 24739--24827 Score: 124
Period size: 38 Copynumber: 2.5 Consensus size: 34
24729 GAAAACCTTC
24739 AAGCCATGAATCATGATGAATTCATATAACTCTT
1 AAGCCATGAATCATGATGAATTCATATAACTCTT
* *
24773 AAACCATGAATCATGATGCATTCATATATAGTACTCTT
1 AAGCCATGAATCATGATGAATTC--ATATA--ACTCTT
24811 AAGCCATGAATCATGAT
1 AAGCCATGAATCATGAT
24828 AATACTCTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
34 21 0.44
36 5 0.10
38 22 0.46
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (34 bp):
AAGCCATGAATCATGATGAATTCATATAACTCTT
Found at i:28123 original size:12 final size:12
Alignment explanation
Indices: 28106--28131 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28096 TCTCTTAAAA
28106 ATAAAAATAATT
1 ATAAAAATAATT
28118 ATAAAAATAATT
1 ATAAAAATAATT
28130 AT
1 AT
28132 TATTTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAAAAATAATT
Found at i:29149 original size:15 final size:15
Alignment explanation
Indices: 29126--29185 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
29116 AGTCAGGTTG
*
29126 GGTTGAATTTGGGTCA
1 GGTT-AATTCGGGTCA
*
29142 GGTTAATTCGGGTTCG
1 GGTTAATTCGGG-TCA
*
29158 GGTTAATTTGGGTCA
1 GGTTAATTCGGGTCA
29173 GGTTAATTCGGGT
1 GGTTAATTCGGGT
29186 TCGATCTGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
15 21 0.55
16 17 0.45
ACGTcount: A:0.17, C:0.08, G:0.37, T:0.38
Consensus pattern (15 bp):
GGTTAATTCGGGTCA
Found at i:29161 original size:16 final size:16
Alignment explanation
Indices: 29121--29188 Score: 70
Period size: 15 Copynumber: 4.4 Consensus size: 16
29111 GCTTGAGTCA
*
29121 GGTT-GGGTTGAATTTG
1 GGTTCGGGTT-AATTCG
*
29137 GG-TCAGGTTAATTCG
1 GGTTCGGGTTAATTCG
*
29152 GGTTCGGGTTAATTTG
1 GGTTCGGGTTAATTCG
*
29168 GG-TCAGGTTAATTCG
1 GGTTCGGGTTAATTCG
29183 GGTTCG
1 GGTTCG
29189 ATCTGGGTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
15 21 0.50
16 21 0.50
ACGTcount: A:0.15, C:0.09, G:0.38, T:0.38
Consensus pattern (16 bp):
GGTTCGGGTTAATTCG
Found at i:29169 original size:31 final size:32
Alignment explanation
Indices: 29121--29188 Score: 122
Period size: 31 Copynumber: 2.2 Consensus size: 32
29111 GCTTGAGTCA
29121 GGTT-GGGTTGAATTTGGGTCAGGTTAATTCG
1 GGTTCGGGTTGAATTTGGGTCAGGTTAATTCG
29152 GGTTCGGGTT-AATTTGGGTCAGGTTAATTCG
1 GGTTCGGGTTGAATTTGGGTCAGGTTAATTCG
29183 GGTTCG
1 GGTTCG
29189 ATCTGGGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 31 0.86
32 5 0.14
ACGTcount: A:0.15, C:0.09, G:0.38, T:0.38
Consensus pattern (32 bp):
GGTTCGGGTTGAATTTGGGTCAGGTTAATTCG
Found at i:30513 original size:32 final size:32
Alignment explanation
Indices: 30472--30532 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
30462 TGTAAAACTT
*
30472 TTGAATCGACTATTATACCCTTATTTTTCTAA
1 TTGAATCGACCATTATACCCTTATTTTTCTAA
30504 TTGAATCGACCATTATACCCTTATTTTTC
1 TTGAATCGACCATTATACCCTTATTTTTC
30533 AAACATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (32 bp):
TTGAATCGACCATTATACCCTTATTTTTCTAA
Found at i:32357 original size:6 final size:6
Alignment explanation
Indices: 32336--32374 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
32326 TATGTTAAGC
*
32336 TTTTC- TTTTC- TTTTCT TTTTCT TTTTCT TTTTTT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
32375 AACGAATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:32357 original size:16 final size:16
Alignment explanation
Indices: 32336--32371 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
32326 TATGTTAAGC
32336 TTTTC-TTTTCTTTTCT
1 TTTTCTTTTTCTTTT-T
32352 TTTTCTTTTTCTTTTT
1 TTTTCTTTTTCTTTTT
32368 TTTT
1 TTTT
32372 TTCAACGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTT
Found at i:35701 original size:44 final size:43
Alignment explanation
Indices: 35638--35724 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 43
35628 CATTAAATTT
* *
35638 TCTGCAAAATATGCATAATGCCAATAGTTGTTCAACTACATTG
1 TCTGCAAAATATGCATAATGCCAATAGCTATTCAACTACATTG
* * *
35681 TCTGCAAAATGTGGCCTAATGCCAATAGCTATTCAAGTACATTG
1 TCTGCAAAATAT-GCATAATGCCAATAGCTATTCAACTACATTG
35725 CCCAATATAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
43 11 0.29
44 27 0.71
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (43 bp):
TCTGCAAAATATGCATAATGCCAATAGCTATTCAACTACATTG
Found at i:36658 original size:24 final size:23
Alignment explanation
Indices: 36630--36686 Score: 60
Period size: 27 Copynumber: 2.3 Consensus size: 23
36620 ATGTGCAGGT
36630 TCTTGCTCATTACCAGCATCTACA
1 TCTTGCTCATTACCAGC-TCTACA
*
36654 TCTTGTTGCACATTACCAGCTCTACA
1 TC---TTGCTCATTACCAGCTCTACA
*
36680 TTTTGCT
1 TCTTGCT
36687 GCTCAACATC
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
23 4 0.15
24 2 0.07
26 7 0.26
27 14 0.52
ACGTcount: A:0.21, C:0.30, G:0.11, T:0.39
Consensus pattern (23 bp):
TCTTGCTCATTACCAGCTCTACA
Found at i:36662 original size:27 final size:26
Alignment explanation
Indices: 36632--36691 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
36622 GTGCAGGTTC
36632 TTGCTCATTACCAGCATCTACATCTTG
1 TTGCTCATTACCAGC-TCTACATCTTG
* *
36659 TTGCACATTACCAGCTCTACATTTTG
1 TTGCTCATTACCAGCTCTACATCTTG
*
36685 CTGCTCA
1 TTGCTCA
36692 ACATCTACCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 15 0.52
27 14 0.48
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.37
Consensus pattern (26 bp):
TTGCTCATTACCAGCTCTACATCTTG
Found at i:39048 original size:11 final size:11
Alignment explanation
Indices: 39032--39057 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39022 AGATAATTTC
39032 TTTTCTTCTAG
1 TTTTCTTCTAG
39043 TTTTCTTCTAG
1 TTTTCTTCTAG
39054 TTTT
1 TTTT
39058 TTAGGCAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:40137 original size:29 final size:29
Alignment explanation
Indices: 40104--40189 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
40094 GTTTTCCCTA
40104 AAAAAAAAAATTCTTTTGCGTTTTTAATT
1 AAAAAAAAAATTCTTTTGCGTTTTTAATT
* ** *
40133 GAAAAAAAAATTC---TGCGTTTTTTCTAA
1 AAAAAAAAAATTCTTTTGCGTTTTTAAT-T
*
40160 AAAAAAAAAATTAGTTTTGCGTTTTTAATT
1 AAAAAAAAAATT-CTTTTGCGTTTTTAATT
40190 CTAAAAATTT
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
26 10 0.23
27 11 0.26
29 12 0.28
31 10 0.23
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (29 bp):
AAAAAAAAAATTCTTTTGCGTTTTTAATT
Found at i:40196 original size:57 final size:55
Alignment explanation
Indices: 40090--40196 Score: 151
Period size: 57 Copynumber: 1.9 Consensus size: 55
40080 CTCTTGAGTC
*
40090 CTGCGTTTTCCCTAAAAAAAAAAATTCTTTTGCGTTTTTAATTGAAAAAAAAATT
1 CTGCGTTTTCCCTAAAAAAAAAAATTCTTTTGCGTTTTTAATTCAAAAAAAAATT
** * *
40145 CTGCGTTTTTTCTAAAAAAAAAAAATTAGTTTTGCGTTTTTAATTCTAAAAA
1 CTGCGTTTTCCCT-AAAAAAAAAAATT-CTTTTGCGTTTTTAATTCAAAAAA
40197 TTTTTTTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 11 0.24
56 13 0.29
57 21 0.47
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.40
Consensus pattern (55 bp):
CTGCGTTTTCCCTAAAAAAAAAAATTCTTTTGCGTTTTTAATTCAAAAAAAAATT
Done.