Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007612.1 Corchorus capsularis cultivar CVL-1 contig07633, 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: 17495
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:560 original size:156 final size:155
Alignment explanation
Indices: 276--647 Score: 418
Period size: 156 Copynumber: 2.4 Consensus size: 155
266 TGACCGATCA
* * *
276 GTTTCACACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCA-CCTTAAGTCTGATT
1 GTTTCACACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCC-TAAGTCTCAAT
* * *
340 GAGCTGAAACTTTGCCAAGGGACTTAAATTCTCTCCACGAGACTATGGAAACAATTCTAAGTAAA
65 GAGCTG-AACTTTGCCAAGGGACTTAAATTATCTCCACAAGACTATGGAAACAAATCTAAGTAAA
* * *
405 ACCGAGCTCCCCT-TGATGGT-GAACTAG
129 ACCGAACT-CCCTATCAT-ATAGAACTAG
* * * *
432 GTTTCTCTCCCTAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAATG
1 GTTTCACACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCCTAAGTCTCAATG
* * * *
496 AAGCTG-A-TTTTCCACCAGTAGG-CTTAGATTATCTCCATAAGGCTATGGGAAA-AAATCTAAG
66 -AGCTGAACTTTGCCA--AG--GGACTTAAATTATCTCCACAAGACTAT-GGAAACAAATCTAAG
* *
557 TAAAACCGAACTCCCTATCATATAGAAGTGG
125 TAAAACCGAACTCCCTATCATATAGAACTAG
*
588 GTTTCACACCCCAAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATCCTAAGTCT
1 GTTTCACACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCCTAAGTCT
648 GTTTGAGATG
Statistics
Matches: 182, Mismatches: 24, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
153 6 0.03
154 1 0.01
155 10 0.05
156 157 0.86
157 8 0.04
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (155 bp):
GTTTCACACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCCTAAGTCTCAATG
AGCTGAACTTTGCCAAGGGACTTAAATTATCTCCACAAGACTATGGAAACAAATCTAAGTAAAAC
CGAACTCCCTATCATATAGAACTAG
Found at i:8055 original size:31 final size:31
Alignment explanation
Indices: 8019--8086 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
8009 AAAAAGGGGC
8019 AATCAGCAATTAAAGTTCAATAAGAAA-AAGT
1 AATCAGCAATT-AAGTTCAATAAGAAAGAAGT
** *
8050 AATCAGTGATTAAGTTCAATAAGAAAGATGT
1 AATCAGCAATTAAGTTCAATAAGAAAGAAGT
8081 AATCAG
1 AATCAG
8087 TAAAAGGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (31 bp):
AATCAGCAATTAAGTTCAATAAGAAAGAAGT
Found at i:8106 original size:22 final size:23
Alignment explanation
Indices: 8081--8140 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
8071 AGAAAGATGT
*
8081 AATCAGTAAAAG-GTAAAGCGGC
1 AATCAGTAAAAGAGTAAAGCGAC
* *
8103 AATCAGT-AAAGAGTAAAGTGAT
1 AATCAGTAAAAGAGTAAAGCGAC
8125 AATCAGT-AAAGAGTAA
1 AATCAGTAAAAGAGTAA
8141 TAAAAATCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 4 0.12
22 30 0.88
ACGTcount: A:0.50, C:0.08, G:0.23, T:0.18
Consensus pattern (23 bp):
AATCAGTAAAAGAGTAAAGCGAC
Found at i:8169 original size:51 final size:52
Alignment explanation
Indices: 8117--8274 Score: 196
Period size: 51 Copynumber: 3.0 Consensus size: 52
8107 AGTAAAGAGT
*
8117 AAAGTGATAATCAGTAAAGAGTAATAAAAATCAGTAAATCAGTAATTAAGTAA
1 AAAGTGATAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGT-A
* ** * * *
8170 AAATTGACCA-GAGTCAAG-GTAATAGAAATCAGTAAATCAATAATTAAGTGA
1 AAAGTGATAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGT-A
8221 AAAGAT-ATTAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTA
1 AAAG-TGA-TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTA
8274 A
1 A
8275 TTAAGTAAAA
Statistics
Matches: 87, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
51 34 0.39
52 8 0.09
53 15 0.17
54 30 0.34
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.25
Consensus pattern (52 bp):
AAAGTGATAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTA
Found at i:8259 original size:54 final size:51
Alignment explanation
Indices: 8124--8274 Score: 198
Period size: 54 Copynumber: 2.9 Consensus size: 51
8114 AGTAAAGTGA
*
8124 TAATCAGTAAAGAGTAATAAAAATCAGTAAATCAGTAATTAAGTAAAAATT
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAATT
* * * *
8175 GACCA-GAGTCAAG-GTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGATAT
1 TA--ATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGT-AAAA-AT-T
8229 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAA
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAA
8275 TTAAGTAAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
51 30 0.36
52 11 0.13
53 11 0.13
54 32 0.38
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.25
Consensus pattern (51 bp):
TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAATT
Found at i:8331 original size:63 final size:62
Alignment explanation
Indices: 8195--8334 Score: 178
Period size: 62 Copynumber: 2.2 Consensus size: 62
8185 AAGGTAATAG
* * *
8195 AAATCAGTAAATCAA-TAATTAAGTGAAAAGATATTAATCAGTAAAGAGTAATAGAAATCAGT
1 AAATCAGT-AATTAAGTAATTAAGTAAAAAGAGATTAATCAGTAAAGAGTAATAGAAATCAGT
* *
8257 AAATCAGTAATTAAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA-AGTAATAGTAATCAGT
1 AAATCAGTAATTAAGTAATTAAGTAAAAAGAGATTAATC--AGTAAAGAGTAATAGAAATCAGT
8320 AAATC-GATAATTAAG
1 AAATCAG-TAATTAAG
8335 AGTTCAAATG
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
61 5 0.07
62 31 0.45
63 28 0.41
64 5 0.07
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.26
Consensus pattern (62 bp):
AAATCAGTAATTAAGTAATTAAGTAAAAAGAGATTAATCAGTAAAGAGTAATAGAAATCAGT
Found at i:8580 original size:22 final size:22
Alignment explanation
Indices: 8555--8681 Score: 118
Period size: 22 Copynumber: 5.8 Consensus size: 22
8545 GAAAGGGTAA
8555 AAAAAGTAATCAGTAAAAAAGT
1 AAAAAGTAATCAGTAAAAAAGT
*
8577 AAAATAGTAATCAGT-AAAAATT
1 AAAA-AGTAATCAGTAAAAAAGT
* * *
8599 AAGAAGGTAATCA--ACAAGAGT
1 AA-AAAGTAATCAGTAAAAAAGT
*
8620 AAAATAGTAGTCAGT-AAAAAGT
1 AAAA-AGTAATCAGTAAAAAAGT
*
8642 AAATAGTAATCAGTAAAAAAGT
1 AAAAAGTAATCAGTAAAAAAGT
* **
8664 AATAAGTAAGAAGTAAAA
1 AAAAAGTAATCAGTAAAA
8682 GGAAATCGGT
Statistics
Matches: 83, Mismatches: 15, Indels: 14
0.74 0.13 0.12
Matches are distributed among these distances:
20 2 0.02
21 21 0.25
22 48 0.58
23 12 0.14
ACGTcount: A:0.59, C:0.05, G:0.16, T:0.20
Consensus pattern (22 bp):
AAAAAGTAATCAGTAAAAAAGT
Found at i:8606 original size:66 final size:64
Alignment explanation
Indices: 8519--8913 Score: 213
Period size: 65 Copynumber: 6.3 Consensus size: 64
8509 AATAGCAGGC
* * *
8519 AATCAGTAAAAAGTAAAAAGGT-ACCTGA-AAGGGTAAAAAAAGTAATCAGTAAAAAAGTAAAAT
1 AATCAGTAAAAAGTAAAAAGGTAATC-AACAAGAGT-AAAAAAGTAATCAGT-AAAAAGT-AAAT
8582 AGT
62 AGT
* * * *
8585 AATCAGTAAAAATTAAGAAGGTAATCAACAAGAGTAAAATAGTAGTCAGTAAAAAGTAAATAGT
1 AATCAGTAAAAAGTAAAAAGGTAATCAACAAGAGTAAAAAAGTAATCAGTAAAAAGTAAATAGT
* * * * * * *
8649 AATCAGTAAAAAAGTAATAA-G---T-AA-GA-AGT-AAAAGGAAATCGGT-AAGAGTAAAAAGG
1 AATCAGT-AAAAAGTAAAAAGGTAATCAACAAGAGTAAAAAAGTAATCAGTAAAAAGTAAATA-G
8705 T
64 T
* * * * * *
8706 GATCAGTAAAGAGTAAAAAGCTAATCAGCAAGAAGTAAAAAGGTAATCAGTAAAAAGCAAA-AGG
1 AATCAGTAAAAAGTAAAAAGGTAATCAACAAG-AGTAAAAAAGTAATCAGTAAAAAGTAAATA-G
*
8770 C
64 T
** * * *
8771 AATCAGTAAAAAGT-AAAAGAGTAATCAGTAA-A--AAAAAAG-GAGCAG-AAAATAGTAAAGAG
1 AATCAGTAAAAAGTAAAAAG-GTAATCAACAAGAGTAAAAAAGTAATCAGTAAAA-AGTAAATAG
8830 T
64 T
* * * *
8831 AATCAGTAAAAGAGTAAAACA-GTAATCAGTA-AAAAGTAAGAAGGTAATCA--ACAAGAGTAAA
1 AATCAGTAAAA-AGTAAAA-AGGTAATCA--ACAAGAGTAAAAAAGTAATCAGTA-AAAAGT-AA
8892 ATAGT
60 ATAGT
*
8897 AATCAGTACAAAGTAAA
1 AATCAGTAAAAAGTAAA
8914 GAATAATCAG
Statistics
Matches: 256, Mismatches: 45, Indels: 57
0.72 0.13 0.16
Matches are distributed among these distances:
56 19 0.07
57 17 0.07
58 3 0.01
59 5 0.02
60 24 0.09
61 19 0.07
62 6 0.02
63 3 0.01
64 23 0.09
65 68 0.27
66 62 0.24
67 7 0.03
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.17
Consensus pattern (64 bp):
AATCAGTAAAAAGTAAAAAGGTAATCAACAAGAGTAAAAAAGTAATCAGTAAAAAGTAAATAGT
Found at i:8624 original size:43 final size:41
Alignment explanation
Indices: 8574--8858 Score: 171
Period size: 43 Copynumber: 6.9 Consensus size: 41
8564 TCAGTAAAAA
*
8574 AGTAAAATAGTAATCAGTAAAAATTAAGAAGGTAATCAACAAG
1 AGTAAAA-AGTAATCAGTAAAAAGTAA-AAGGTAATCAACAAG
*
8617 AGTAAAATAGTAGTCAGTAAAAAGTAAATA-GTAAT---C---
1 AGTAAAA-AGTAATCAGTAAAAAGTAAA-AGGTAATCAACAAG
* * * ***
8653 AGTAAAAAAGTAATAAGTAAGAAGTAAAAGGAAATCGGTAAG
1 AGT-AAAAAGTAATCAGTAAAAAGTAAAAGGTAATCAACAAG
* * * *
8695 AGTAAAAAGGTGATCAGTAAAGAGTAAAAAGCTAATCAGCAAG
1 AGTAAAAA-GTAATCAGTAAAAAGT-AAAAGGTAATCAACAAG
* * *
8738 AAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGCAATCAGTA-AAA
1 -AGTAAAAA-GTAATCAGTAAAAAGTAAAAGGTAATCA--ACAAG
* * *
8782 AGTAAAAGAGTAATCAGTAAAAA--AAAAGG--AGCAGAAAAT
1 AGTAAAA-AGTAATCAGTAAAAAGTAAAAGGTAATCA-ACAAG
* *
8821 AGTAAAGAGTAATCAGTAAAAGAGTAAAACAGTAATCA
1 AGTAAAAAGTAATCAGTAAAA-AGTAAAA-GGTAATCA
8859 GTAAAAAGTA
Statistics
Matches: 192, Mismatches: 28, Indels: 43
0.73 0.11 0.16
Matches are distributed among these distances:
35 1 0.01
36 24 0.12
37 4 0.02
38 15 0.08
39 13 0.07
41 15 0.08
42 22 0.11
43 70 0.36
44 28 0.15
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.18
Consensus pattern (41 bp):
AGTAAAAAGTAATCAGTAAAAAGTAAAAGGTAATCAACAAG
Found at i:8720 original size:22 final size:22
Alignment explanation
Indices: 8702--8927 Score: 151
Period size: 22 Copynumber: 10.6 Consensus size: 22
8692 AAGAGTAAAA
*
8702 AGGTGATCAGTAAAGAGTAAAA
1 AGGTAATCAGTAAAGAGTAAAA
* *
8724 AGCTAATCAG-CAAGAAGTAAAA
1 AGGTAATCAGTAAAG-AGTAAAA
* *
8746 AGGTAATCAGTAAAAAG-CAAA
1 AGGTAATCAGTAAAGAGTAAAA
* *
8767 AGGCAATCAGTAAAAAGT-AAA
1 AGGTAATCAGTAAAGAGTAAAA
8788 AGAGTAATCAGTAAA-A--AAAA
1 AG-GTAATCAGTAAAGAGTAAAA
* * * *
8808 AGG--AGCAGAAAATAGTAAAG
1 AGGTAATCAGTAAAGAGTAAAA
8828 A-GTAATCAGTAAAAGAGTAAAA
1 AGGTAATCAGT-AAAGAGTAAAA
* *
8850 CA-GTAATCAGTAAAAAGTAAGA
1 -AGGTAATCAGTAAAGAGTAAAA
8872 AGGTAATCA--ACAAGAGTAAAA
1 AGGTAATCAGTA-AAGAGTAAAA
8893 TA-GTAATCAGTACAA-AGTAAAGA
1 -AGGTAATCAGTA-AAGAGTAAA-A
8916 A--TAATCAGTAAA
1 AGGTAATCAGTAAA
8928 ATAGTGATGC
Statistics
Matches: 166, Mismatches: 20, Indels: 38
0.74 0.09 0.17
Matches are distributed among these distances:
17 7 0.04
18 1 0.01
19 2 0.01
20 12 0.07
21 57 0.34
22 70 0.42
23 17 0.10
ACGTcount: A:0.56, C:0.08, G:0.19, T:0.16
Consensus pattern (22 bp):
AGGTAATCAGTAAAGAGTAAAA
Found at i:8829 original size:38 final size:41
Alignment explanation
Indices: 8738--8841 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 41
8728 AATCAGCAAG
*
8738 AAGTAAAA-AGGTAATCAGTAAAAAGCAAAAGGCAATCAGTAAA
1 AAGTAAAAGA-GTAATCAGTAAAAA-CAAAAGG-AAGCAGTAAA
8781 AAGTAAAAGAGTAATCAGTAAAAA-AAAAGG-AGCAG-AAA
1 AAGTAAAAGAGTAATCAGTAAAAACAAAAGGAAGCAGTAAA
8819 ATAGT-AAAGAGTAATCAGTAAAA
1 A-AGTAAAAGAGTAATCAGTAAAA
8842 GAGTAAAACA
Statistics
Matches: 58, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
38 22 0.38
39 7 0.12
41 6 0.10
43 22 0.38
44 1 0.02
ACGTcount: A:0.60, C:0.07, G:0.19, T:0.14
Consensus pattern (41 bp):
AAGTAAAAGAGTAATCAGTAAAAACAAAAGGAAGCAGTAAA
Found at i:10485 original size:42 final size:42
Alignment explanation
Indices: 10432--10530 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
10422 TTGTATATGG
* * * **
10432 TGCATCCATCATGTATTGTCCATTTC-TTTGTATATATGTTCA
1 TGCATCCATCATGCATTATCC-TTTCATTGGTATATATGCCCA
* *
10474 TGCATCGATCATGCATTATCCTTTCATTGGTATATGTGCCCA
1 TGCATCCATCATGCATTATCCTTTCATTGGTATATATGCCCA
10516 TGCATCCATCATGCA
1 TGCATCCATCATGCA
10531 CTCACTTGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 4 0.08
42 44 0.92
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.40
Consensus pattern (42 bp):
TGCATCCATCATGCATTATCCTTTCATTGGTATATATGCCCA
Found at i:11664 original size:28 final size:29
Alignment explanation
Indices: 11634--11687 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
11624 ATATCTCTCA
* *
11634 AAAAATTA-TTTTC-AAGAAAAGGTTTTT
1 AAAAATGAGTTTTCAAAAAAAAGGTTTTT
11661 AAAAATGAGTTTTCAAAAAAAAGGTTT
1 AAAAATGAGTTTTCAAAAAAAAGGTTT
11688 ATGAGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 5 0.22
29 11 0.48
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (29 bp):
AAAAATGAGTTTTCAAAAAAAAGGTTTTT
Found at i:14107 original size:53 final size:55
Alignment explanation
Indices: 14000--14126 Score: 204
Period size: 53 Copynumber: 2.3 Consensus size: 55
13990 TAACCGAGTC
*
14000 TCAAGTGATCCAGTGCGGTCAATCAAGAAAGCTTCCAGTGGTATTGAGTTTATCT
1 TCAAGTGATCCAGTGCGGTCAATCAAGAAAGCTTCCAGTGGTATTAAGTTTATCT
* *
14055 TCAGGTGATCCAGTGCGGTCAATC-A-AAAGTTTCCAGTGGTATTAAGTTTATCT
1 TCAAGTGATCCAGTGCGGTCAATCAAGAAAGCTTCCAGTGGTATTAAGTTTATCT
*
14108 TCAAGTGAACCAGTGCGGT
1 TCAAGTGATCCAGTGCGGT
14127 TAGTCAACGA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
53 43 0.64
54 1 0.01
55 23 0.34
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (55 bp):
TCAAGTGATCCAGTGCGGTCAATCAAGAAAGCTTCCAGTGGTATTAAGTTTATCT
Done.