Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009823.1 Corchorus capsularis cultivar CVL-1 contig09844, 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: 72979
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:138 original size:6 final size:6
Alignment explanation
Indices: 129--170 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
119 TGAGTTGCCG
129 CCTTAC CCTTAC CCTTAC CCTTAC CCTTAC CCTTAC CCTTAC
1 CCTTAC CCTTAC CCTTAC CCTTAC CCTTAC CCTTAC CCTTAC
171 AAAGTTGTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
CCTTAC
Found at i:18052 original size:26 final size:26
Alignment explanation
Indices: 18015--18066 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
18005 TCCATAAACA
* *
18015 CTAACAATCAGTTAACGTATTTTCCT
1 CTAACAAACAGTTAACGTACTTTCCT
18041 CTAACAAACAGTTAACGTACTTTCCT
1 CTAACAAACAGTTAACGTACTTTCCT
18067 ATCTTTCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.35
Consensus pattern (26 bp):
CTAACAAACAGTTAACGTACTTTCCT
Found at i:20078 original size:34 final size:34
Alignment explanation
Indices: 20035--20103 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
20025 CAAGCGATGC
20035 CAAACGGCCCCTAAGTTATTAGTTTTTTCCTATT
1 CAAACGGCCCCTAAGTTATTAGTTTTTTCCTATT
20069 CAAACGGCCCCTAAGTTATTAGTTTTTTCCTATT
1 CAAACGGCCCCTAAGTTATTAGTTTTTTCCTATT
20103 C
1 C
20104 TTTTTCCGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.41
Consensus pattern (34 bp):
CAAACGGCCCCTAAGTTATTAGTTTTTTCCTATT
Found at i:23247 original size:24 final size:24
Alignment explanation
Indices: 23215--23262 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
23205 TGTTCTTCGA
23215 ATGAACATATAGCTATCAGAAAGT
1 ATGAACATATAGCTATCAGAAAGT
23239 ATGAACATATAGCTATCAGAAAGT
1 ATGAACATATAGCTATCAGAAAGT
23263 TTACTCAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (24 bp):
ATGAACATATAGCTATCAGAAAGT
Found at i:25960 original size:28 final size:29
Alignment explanation
Indices: 25883--25959 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
25873 ATGGTGTTCA
* *
25883 AGGAGACAAAACGTTCTAAAATTGAAGTTG
1 AGGAAACAAAACGTTC-AAAATTAAAGTTG
* * * *
25913 AGG-AATAAAATGTCCAAAATTAAAGTTT
1 AGGAAACAAAACGTTCAAAATTAAAGTTG
25941 AGGAAACAAAACGTTCAAA
1 AGGAAACAAAACGTTCAAA
25960 TCTACAAGTT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
28 14 0.38
29 20 0.54
30 3 0.08
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.22
Consensus pattern (29 bp):
AGGAAACAAAACGTTCAAAATTAAAGTTG
Found at i:35857 original size:12 final size:12
Alignment explanation
Indices: 35821--35857 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
35811 CAAATCCCTT
35821 TCTGTCAACTTCC
1 TCTG-CAACTTCC
35834 TCTGCAAC-TCC
1 TCTGCAACTTCC
35845 TCTGCAACTTCC
1 TCTGCAACTTCC
35857 T
1 T
35858 TATTGGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
12 8 0.35
13 4 0.17
ACGTcount: A:0.16, C:0.41, G:0.08, T:0.35
Consensus pattern (12 bp):
TCTGCAACTTCC
Found at i:45438 original size:13 final size:13
Alignment explanation
Indices: 45422--45446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45412 ACAATTCTAG
45422 CAAACATTTAGTC
1 CAAACATTTAGTC
45435 CAAACATTTAGT
1 CAAACATTTAGT
45447 GCAGTATTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
CAAACATTTAGTC
Found at i:48087 original size:31 final size:31
Alignment explanation
Indices: 48052--48112 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
48042 AAAAGCGATT
*
48052 TTAGTCCATATACTCACAAAATTTGGTCAAG
1 TTAGTCCATATACTCACAAAATTAGGTCAAG
* *
48083 TTAGTCCCTATTCTCACAAAATTAGGTCAA
1 TTAGTCCATATACTCACAAAATTAGGTCAA
48113 CTAAGTCCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.33
Consensus pattern (31 bp):
TTAGTCCATATACTCACAAAATTAGGTCAAG
Found at i:48120 original size:31 final size:31
Alignment explanation
Indices: 48054--48120 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
48044 AAGCGATTTT
* * *
48054 AGTCCATATACTCACAAAATTTGGTCAAGTT
1 AGTCCATATACTCACAAAATTAGGTCAACTA
* *
48085 AGTCCCTATTCTCACAAAATTAGGTCAACTA
1 AGTCCATATACTCACAAAATTAGGTCAACTA
48116 AGTCC
1 AGTCC
48121 TCAGTTGTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (31 bp):
AGTCCATATACTCACAAAATTAGGTCAACTA
Found at i:48203 original size:31 final size:31
Alignment explanation
Indices: 48162--48222 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
48152 TTATCGATTA
* *
48162 GATTCAATTGAC-CTAATCATGTAAGTATATG
1 GATTAAATTGACTC-AATCATATAAGTATATG
*
48193 GATTAAATTGACTCAATCTTATAAGTATAT
1 GATTAAATTGACTCAATCATATAAGTATAT
48223 ATGCGCTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (31 bp):
GATTAAATTGACTCAATCATATAAGTATATG
Found at i:54813 original size:1 final size:1
Alignment explanation
Indices: 54807--54831 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
54797 GTTCTTTTGC
54807 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
54832 CAAACAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:65055 original size:21 final size:21
Alignment explanation
Indices: 65031--65073 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
65021 TTGTTCATCT
65031 TTCTTCTT-GCTTTCCTCTTTC
1 TTCTTCTTAG-TTTCCTCTTTC
*
65052 TTCTTTTTAGTTTCCTCTTTC
1 TTCTTCTTAGTTTCCTCTTTC
65073 T
1 T
65074 CTTTTGGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.02, C:0.28, G:0.05, T:0.65
Consensus pattern (21 bp):
TTCTTCTTAGTTTCCTCTTTC
Found at i:69406 original size:15 final size:15
Alignment explanation
Indices: 69388--69438 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
69378 CTAAAAACTG
69388 AATTGAACTAACAAA
1 AATTGAACTAACAAA
*
69403 AATTG-CCTAA-AAA
1 AATTGAACTAACAAA
69416 CTGAATTGAACTAACAAA
1 ---AATTGAACTAACAAA
69434 AATTG
1 AATTG
69439 CGTTTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 3 0.10
14 4 0.14
15 10 0.34
16 5 0.17
17 4 0.14
18 3 0.10
ACGTcount: A:0.53, C:0.14, G:0.10, T:0.24
Consensus pattern (15 bp):
AATTGAACTAACAAA
Found at i:69416 original size:31 final size:31
Alignment explanation
Indices: 69378--69439 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
69368 ATAAGAATGA
69378 CTAAAAACTGAATTGAACTAACAAAAATTGC
1 CTAAAAACTGAATTGAACTAACAAAAATTGC
69409 CTAAAAACTGAATTGAACTAACAAAAATTGC
1 CTAAAAACTGAATTGAACTAACAAAAATTGC
69440 GTTTTTACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.23
Consensus pattern (31 bp):
CTAAAAACTGAATTGAACTAACAAAAATTGC
Found at i:69713 original size:6 final size:6
Alignment explanation
Indices: 69698--69744 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
69688 ACAAGAGCGC
*
69698 TGTTGT TGTTGA TGTTGA TGTTGA TGTTGA TGTTGA TGTTGA TGTTG
1 TGTTGA TGTTGA TGTTGA TGTTGA TGTTGA TGTTGA TGTTGA TGTTG
69745 TTGGATGGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.13, C:0.00, G:0.34, T:0.53
Consensus pattern (6 bp):
TGTTGA
Found at i:72143 original size:26 final size:26
Alignment explanation
Indices: 72114--72235 Score: 115
Period size: 26 Copynumber: 4.7 Consensus size: 26
72104 TCGCACGCGC
72114 GAGGTCACGTGTGGAGTTGTAC-TTCG
1 GAGGTCACGTGTGGAGTTGTACGTT-G
* * * *
72140 GAGGTCACGTGTTGAAGGTATCCGTTG
1 GAGGTCACGTG-TGGAGTTGTACGTTG
72167 GAGGTCACGTGTGGAGTTGTAC-TTCG
1 GAGGTCACGTGTGGAGTTGTACGTT-G
* * *
72193 AAGATCACGTGTGG-GATCGTACGTTG
1 GAGGTCACGTGTGGAG-TTGTACGTTG
*
72219 GAGGTTACGTGTGGAGT
1 GAGGTCACGTGTGGAGT
72236 ACCAGCTGGC
Statistics
Matches: 76, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
25 3 0.04
26 49 0.64
27 22 0.29
28 2 0.03
ACGTcount: A:0.18, C:0.14, G:0.39, T:0.30
Consensus pattern (26 bp):
GAGGTCACGTGTGGAGTTGTACGTTG
Found at i:72201 original size:53 final size:52
Alignment explanation
Indices: 72114--72235 Score: 165
Period size: 53 Copynumber: 2.3 Consensus size: 52
72104 TCGCACGCGC
* * * *
72114 GAGGTCACGTGTGGAGTTGTACTTCGGAGGTCACGTGT-TGAAGGTATCCGTTG
1 GAGGTCACGTGTGGAGTTGTACTTCGAAGATCACGTGTGGGAACGTA--CGTTG
*
72167 GAGGTCACGTGTGGAGTTGTACTTCGAAGATCACGTGTGGGATCGTACGTTG
1 GAGGTCACGTGTGGAGTTGTACTTCGAAGATCACGTGTGGGAACGTACGTTG
*
72219 GAGGTTACGTGTGGAGT
1 GAGGTCACGTGTGGAGT
72236 ACCAGCTGGC
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
52 21 0.34
53 36 0.58
54 5 0.08
ACGTcount: A:0.18, C:0.14, G:0.39, T:0.30
Consensus pattern (52 bp):
GAGGTCACGTGTGGAGTTGTACTTCGAAGATCACGTGTGGGAACGTACGTTG
Found at i:72296 original size:15 final size:15
Alignment explanation
Indices: 72276--72320 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
72266 TTGTGGTCAT
*
72276 AGGTGGTCGATCGCC
1 AGGTGGTCGAGCGCC
72291 AGGTGGTCGAGCGCC
1 AGGTGGTCGAGCGCC
*
72306 AGGTGGTCGGGCGCC
1 AGGTGGTCGAGCGCC
72321 GGGCTTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.11, C:0.27, G:0.47, T:0.16
Consensus pattern (15 bp):
AGGTGGTCGAGCGCC
Found at i:72426 original size:15 final size:15
Alignment explanation
Indices: 72406--72435 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
72396 TTGTGGTCAT
72406 AGGTGGTCGAGCGCC
1 AGGTGGTCGAGCGCC
*
72421 AGGTGGTCGGGCGCC
1 AGGTGGTCGAGCGCC
72436 GGGCTTTGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.27, G:0.50, T:0.13
Consensus pattern (15 bp):
AGGTGGTCGAGCGCC
Done.