Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005985.1 Corchorus capsularis cultivar CVL-1 contig06003, 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: 13787
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Found at i:1987 original size:68 final size:68
Alignment explanation
Indices: 1911--2156 Score: 331
Period size: 68 Copynumber: 3.7 Consensus size: 68
1901 ACGAGTAAGT
* * *
1911 TCAAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACATGAGC
1 TCAAGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACAAGCCAAACTCGTTTTCACATGAGT
1976 CAA
66 CAA
* *
1979 TCAAGCCTTGGTTCTATCCAAGCAGCAAGGGC--TTCCACCAGCCAAACTCGTTTTCACATGAGT
1 TCAAGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACAAGCCAAACTCGTTTTCACATGAGT
2042 CAA
66 CAA
** * *
2045 TTTAGCCTTTGTTCCATCCAAGCAGCAAGGGCTTTTCCACAAGCCAAACTCGTTTTCATATGAGT
1 TCAAGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACAAGCCAAACTCGTTTTCACATGAGT
* *
2110 TAT
66 CAA
** *
2113 TTTAGCCTTGGTTCCATCCAAGCAG---GGGCTTTTCCATAAGCCAA
1 TCAAGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACAAGCCAA
2157 GTTCATTTCC
Statistics
Matches: 161, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
65 18 0.11
66 59 0.37
68 84 0.52
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (68 bp):
TCAAGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACAAGCCAAACTCGTTTTCACATGAGT
CAA
Found at i:2177 original size:134 final size:132
Alignment explanation
Indices: 1914--2177 Score: 323
Period size: 134 Copynumber: 2.0 Consensus size: 132
1904 AGTAAGTTCA
*
1914 AGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACATGAGCCAA
1 AGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCACATGAGCCAA
* * * *
1979 TCAAGCCTTGGTTCTATCCAAGCAGCAAGGGCTTCCACCAGCCAAACTCGTTTTCACATGAGTCA
66 TCAAGCCTTGGTTCCATCCAAGCAG--AGGGCTTCCACAAGCCAAACTCATTTCCACATGAGTCA
2044 ATTT
129 ATTT
* * * ** *
2048 AGCCTTTGTTCCATCCAAGCAGCAAGGGCTTTTCCACAAGCCAAACTCGTTTTCATATGAGTTAT
1 AGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCACATGAGCCAA
** * ** *
2113 TTTAGCCTTGGTTCCATCCAAGCAG-GGGCTTTTCCATAAGCCAAGTTCATTTCCATATGAAGTC
66 TCAAGCCTTGGTTCCATCCAAGCAGAGGGC--TTCCACAAGCCAAACTCATTTCCACATG-AGTC
2177 A
128 A
2178 GTCTTCCAAG
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
131 4 0.04
133 21 0.19
134 85 0.77
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (132 bp):
AGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCACATGAGCCAA
TCAAGCCTTGGTTCCATCCAAGCAGAGGGCTTCCACAAGCCAAACTCATTTCCACATGAGTCAAT
TT
Found at i:5078 original size:12 final size:14
Alignment explanation
Indices: 5049--5081 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
5039 GTGGCAGAGG
5049 GAAGAAGCGTTGAA
1 GAAGAAGCGTTGAA
5063 GAAGAAG-GTT-AA
1 GAAGAAGCGTTGAA
5075 GAAGAAG
1 GAAGAAG
5082 AGTACGGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 3 0.16
14 7 0.37
ACGTcount: A:0.48, C:0.03, G:0.36, T:0.12
Consensus pattern (14 bp):
GAAGAAGCGTTGAA
Found at i:6647 original size:26 final size:26
Alignment explanation
Indices: 6618--6704 Score: 88
Period size: 26 Copynumber: 3.2 Consensus size: 26
6608 AAAAAGGGGC
6618 AATCAGTAATTAAGTAAAAAGAGATT
1 AATCAGTAATTAAGTAAAAAGAGATT
* * *
6644 AATCAG-AGTTAAGGTAATAGTAATCAG-TA
1 AATCAGTAATTAA-GTAA-A--AA-GAGATT
6673 AATCAGTAATTAAGTAAAAAGAGATT
1 AATCAGTAATTAAGTAAAAAGAGATT
6699 AATCAG
1 AATCAG
6705 AGTCAAGGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
25 7 0.15
26 19 0.40
27 1 0.02
28 1 0.02
29 13 0.27
30 7 0.15
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (26 bp):
AATCAGTAATTAAGTAAAAAGAGATT
Found at i:6715 original size:26 final size:26
Alignment explanation
Indices: 6618--6715 Score: 76
Period size: 26 Copynumber: 3.7 Consensus size: 26
6608 AAAAAGGGGC
*
6618 AATCAGTAATTAA-GTAAAAAGAGATT
1 AATCAG-AGTTAAGGTAAAAAGAGATT
* *
6644 AATCAGAGTTAAGGTAATAGTAATCAG-TA
1 AATCAGAGTTAAGGTAA-A--AA-GAGATT
*
6673 AATCAGTAATTAA-GTAAAAAGAGATT
1 AATCAG-AGTTAAGGTAAAAAGAGATT
*
6699 AATCAGAGTCAAGGTAA
1 AATCAGAGTTAAGGTAA
6716 TAGTAATCAG
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
25 11 0.20
26 23 0.41
27 1 0.02
28 1 0.02
29 13 0.23
30 7 0.12
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (26 bp):
AATCAGAGTTAAGGTAAAAAGAGATT
Found at i:6747 original size:55 final size:55
Alignment explanation
Indices: 6618--6737 Score: 231
Period size: 55 Copynumber: 2.2 Consensus size: 55
6608 AAAAAGGGGC
*
6618 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
6673 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
6728 AATCAGTAAT
1 AATCAGTAAT
6738 CAGGAAAAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
Found at i:7070 original size:22 final size:21
Alignment explanation
Indices: 7045--7086 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
7035 TGAAAGGGTA
* *
7045 AAATGGTAATTAGTAAAGAGTG
1 AAATAGTAATCAGT-AAGAGTG
7067 AAATAGTAATCAGTAAGAGT
1 AAATAGTAATCAGTAAGAGT
7087 AAAAGAGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.48, C:0.02, G:0.24, T:0.26
Consensus pattern (21 bp):
AAATAGTAATCAGTAAGAGTG
Found at i:7176 original size:35 final size:34
Alignment explanation
Indices: 7088--7181 Score: 93
Period size: 35 Copynumber: 2.7 Consensus size: 34
7078 AGTAAGAGTA
* * *
7088 AAAGAGCAAAGAGTAACCAATAAAGAAAAAAATGT
1 AAAGAGTAAAGAG-AATCAGTAAAGAAAAAAATGT
7123 AAAGAGTAAAGAGTAATCAGTAAAG-AAAAAATAGT
1 AAAGAGTAAAGAG-AATCAGTAAAGAAAAAAAT-GT
*
7158 AAGGAGTGAGAAGA-AATCAGTAAA
1 AAAGAGT-A-AAGAGAATCAGTAAA
7182 ATATTAATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
34 7 0.13
35 40 0.77
36 1 0.02
37 4 0.08
ACGTcount: A:0.60, C:0.05, G:0.21, T:0.14
Consensus pattern (34 bp):
AAAGAGTAAAGAGAATCAGTAAAGAAAAAAATGT
Found at i:9138 original size:3 final size:3
Alignment explanation
Indices: 9132--9157 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9122 ATCATTAGAA
9132 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
9158 ACTTCCTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:11081 original size:24 final size:25
Alignment explanation
Indices: 11025--11079 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
11015 AACCCTAAAT
*
11025 TTCATTTCTAACAACTTCTTCAAAC
1 TTCATTTCTAACAACATCTTCAAAC
11050 TTCATTTCTAACAA-ATCTTCAAA-
1 TTCATTTCTAACAACATCTTCAAAC
11073 TTCATTT
1 TTCATTT
11080 TCCTTCATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 7 0.24
24 8 0.28
25 14 0.48
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.44
Consensus pattern (25 bp):
TTCATTTCTAACAACATCTTCAAAC
Found at i:11113 original size:11 final size:11
Alignment explanation
Indices: 11099--11171 Score: 56
Period size: 11 Copynumber: 5.9 Consensus size: 11
11089 TTAATCATAA
11099 ACTAATTAAAT
1 ACTAATTAAAT
11110 ACTAATTAATAAT
1 ACTAATT-A-AAT
*
11123 AAACTAATTAGAT
1 --ACTAATTAAAT
11136 ACTAATTAAACAT
1 ACTAATT-AA-AT
*
11149 AAACTAATTAGAT
1 --ACTAATTAAAT
11162 ACTAATTAAA
1 ACTAATTAAA
11172 CATAAACTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
11 23 0.46
12 2 0.04
13 9 0.18
14 2 0.04
15 14 0.28
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (11 bp):
ACTAATTAAAT
Found at i:11118 original size:26 final size:26
Alignment explanation
Indices: 11089--11182 Score: 154
Period size: 26 Copynumber: 3.6 Consensus size: 26
11079 TTCCTTCATT
* *
11089 TTAATCATAAACTAATTAAATACTAA
1 TTAAACATAAACTAATTAGATACTAA
11115 TTAATA-ATAAACTAATTAGATACTAA
1 TTAA-ACATAAACTAATTAGATACTAA
11141 TTAAACATAAACTAATTAGATACTAA
1 TTAAACATAAACTAATTAGATACTAA
11167 TTAAACATAAACTAAT
1 TTAAACATAAACTAAT
11183 AAACTAAGTA
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
25 1 0.02
26 63 0.98
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (26 bp):
TTAAACATAAACTAATTAGATACTAA
Found at i:11279 original size:9 final size:9
Alignment explanation
Indices: 11266--11307 Score: 75
Period size: 9 Copynumber: 4.6 Consensus size: 9
11256 AAATTTTGAA
11266 AAAAAAAATT
1 AAAAAAAA-T
11276 AAAAAAAAT
1 AAAAAAAAT
11285 AAAAAAAAT
1 AAAAAAAAT
11294 AAAAAAAAT
1 AAAAAAAAT
11303 AAAAA
1 AAAAA
11308 GAAAATGGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 24 0.75
10 8 0.25
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:11279 original size:10 final size:10
Alignment explanation
Indices: 11266--11313 Score: 64
Period size: 9 Copynumber: 4.9 Consensus size: 10
11256 AAATTTTGAA
11266 AAAAAAAATT
1 AAAAAAAATT
11276 AAAAAAAA-T
1 AAAAAAAATT
11285 AAAAAAAA-T
1 AAAAAAAATT
*
11294 AAAAAAAATA
1 AAAAAAAATT
11304 AAAAGAAAAT
1 AAAA-AAAAT
11314 GGCCAAGCTG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
9 18 0.51
10 12 0.34
11 5 0.14
ACGTcount: A:0.85, C:0.00, G:0.02, T:0.12
Consensus pattern (10 bp):
AAAAAAAATT
Found at i:11424 original size:19 final size:19
Alignment explanation
Indices: 11391--11436 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
11381 CGGCTCGGCC
* *
11391 ATTTTCTTTACTTTTTTTTA
1 ATTTT-TTTAATTTTTTTAA
11411 ATTTTTTTAATTTTTTTAA
1 ATTTTTTTAATTTTTTTAA
11430 ATTTTTT
1 ATTTTTT
11437 AAAAGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (19 bp):
ATTTTTTTAATTTTTTTAA
Found at i:11432 original size:10 final size:9
Alignment explanation
Indices: 11403--11438 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
11393 TTTCTTTACT
11403 TTTTTTTAA
1 TTTTTTTAA
11412 TTTTTTTAA
1 TTTTTTTAA
11421 TTTTTTTAA
1 TTTTTTTAA
*
11430 ATTTTTTAA
1 TTTTTTTAA
11439 AAGATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:11618 original size:21 final size:21
Alignment explanation
Indices: 11577--11621 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11567 AAAAATTATA
**
11577 AAAAGGGGGGCGATATTTAGC
1 AAAAGGGGGGCGATAAATAGC
*
11598 AAAAGGGGGGCGGTAAATAGC
1 AAAAGGGGGGCGATAAATAGC
11619 AAA
1 AAA
11622 CCCCATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.38, T:0.13
Consensus pattern (21 bp):
AAAAGGGGGGCGATAAATAGC
Done.