Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009079.1 Corchorus capsularis cultivar CVL-1 contig09100, 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: 87443
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:165 original size:6 final size:6
Alignment explanation
Indices: 156--188 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
146 AAAGCAAAGC
156 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
189 GCAGATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:200 original size:12 final size:13
Alignment explanation
Indices: 185--229 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
175 AATCTAAATC
185 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
197 TAAAGCAAATTAA
1 TAAAGCAGATTAA
210 TAAAGCAGATTAA
1 TAAAGCAGATTAA
223 TAAAGCA
1 TAAAGCA
230 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:236 original size:25 final size:25
Alignment explanation
Indices: 185--237 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
175 AATCTAAATC
*
185 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
210 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
235 TAA
1 TAA
238 TTATAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Found at i:1870 original size:16 final size:16
Alignment explanation
Indices: 1849--1879 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1839 TTCGTATCAC
1849 AATCAATCAAAGCAAT
1 AATCAATCAAAGCAAT
1865 AATCAATCAAAGCAA
1 AATCAATCAAAGCAA
1880 AGCAATGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.19, G:0.06, T:0.16
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Found at i:4121 original size:21 final size:20
Alignment explanation
Indices: 4075--4121 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
4065 TAAAGAGATT
* *
4075 AATT-AAAAGAAAGCAATTA
1 AATTAAAAACAAAGCAAGTA
*
4094 AACTAAAAACAAAGCAAAGTA
1 AATTAAAAACAAAGC-AAGTA
4115 AATTAAA
1 AATTAAA
4122 TCTAAATCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (20 bp):
AATTAAAAACAAAGCAAGTA
Found at i:5517 original size:19 final size:18
Alignment explanation
Indices: 5480--5519 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
5470 TTCTTGAAAT
*
5480 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
5498 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
5517 AAT
1 AAT
5520 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:7142 original size:41 final size:41
Alignment explanation
Indices: 7096--7369 Score: 272
Period size: 41 Copynumber: 6.7 Consensus size: 41
7086 ACCCAATATC
* *
7096 CAAAGTGCC-CAAACACAATCCTAACACAGGGGCAACTATTT
1 CAAAGT-CCTCAAACACAATCTTAACACAGAGGCAACTATTT
* * **
7137 CAAAGTCCTCAAACACATTCTTAACACAGAGGCATCTACAT
1 CAAAGTCCTCAAACACAATCTTAACACAGAGGCAACTATTT
* *
7178 CAAAGTGCC-CAAACACAATCCTAACACAGGGGCAACTATTT
1 CAAAGT-CCTCAAACACAATCTTAACACAGAGGCAACTATTT
* * **
7219 CAAAGTCCTCAAACACATTCTTAACACAGAGGCATCTACAT
1 CAAAGTCCTCAAACACAATCTTAACACAGAGGCAACTATTT
* * * *
7260 CAAAGTCCCCAAGCACAAT-TATAACACAGGGGCAATTATCTTT
1 CAAAGTCCTCAAACACAATCT-TAACACAGAGGCAACTA--TTT
* **
7303 CAAAGTCCTCAAACACATTCTTAACACAGAGGCAACTACAT
1 CAAAGTCCTCAAACACAATCTTAACACAGAGGCAACTATTT
*
7344 CAAATTCC-CTAAACAC-AT-TTAACACA
1 CAAAGTCCTC-AAACACAATCTTAACACA
7370 AGGGCAATTT
Statistics
Matches: 190, Mismatches: 35, Indels: 18
0.78 0.14 0.07
Matches are distributed among these distances:
39 8 0.04
40 7 0.04
41 140 0.74
42 2 0.01
43 32 0.17
44 1 0.01
ACGTcount: A:0.40, C:0.29, G:0.11, T:0.20
Consensus pattern (41 bp):
CAAAGTCCTCAAACACAATCTTAACACAGAGGCAACTATTT
Found at i:7187 original size:82 final size:82
Alignment explanation
Indices: 7096--7376 Score: 433
Period size: 82 Copynumber: 3.4 Consensus size: 82
7086 ACCCAATATC
7096 CAAAGTGCCCAAACACAATCCTAACACAGGGGCAACTATTTCAAAGTCCTCAAACACATTCTTAA
1 CAAAGTGCCCAAACACAATCCTAACACAGGGGCAACTATTTCAAAGTCCTCAAACACATTCTTAA
7161 CACAGAGGCATCTACAT
66 CACAGAGGCATCTACAT
7178 CAAAGTGCCCAAACACAATCCTAACACAGGGGCAACTATTTCAAAGTCCTCAAACACATTCTTAA
1 CAAAGTGCCCAAACACAATCCTAACACAGGGGCAACTATTTCAAAGTCCTCAAACACATTCTTAA
7243 CACAGAGGCATCTACAT
66 CACAGAGGCATCTACAT
* * ** *
7260 CAAAGTCCCCAAGCACAATTATAACACAGGGGCAATTATCTTTCAAAGTCCTCAAACACATTCTT
1 CAAAGTGCCCAAACACAATCCTAACACAGGGGCAACTA--TTTCAAAGTCCTCAAACACATTCTT
*
7325 AACACAGAGGCAACTACAT
64 AACACAGAGGCATCTACAT
* * *
7344 CAAA-TTCCCTAAACAC-AT-TTAACACAAGGGCAA
1 CAAAGTGCCC-AAACACAATCCTAACACAGGGGCAA
7377 TTTCCTCTAC
Statistics
Matches: 186, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
82 128 0.69
83 6 0.03
84 52 0.28
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.20
Consensus pattern (82 bp):
CAAAGTGCCCAAACACAATCCTAACACAGGGGCAACTATTTCAAAGTCCTCAAACACATTCTTAA
CACAGAGGCATCTACAT
Found at i:9872 original size:19 final size:18
Alignment explanation
Indices: 9835--9874 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
9825 TTCTTGAAAT
*
9835 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
9853 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
9872 AAT
1 AAT
9875 AAATCTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:12758 original size:33 final size:33
Alignment explanation
Indices: 12650--12746 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 33
12640 TGAAAACGAA
* * *
12650 TCTGTTTTGGTTGATAATAGCATGGAAATTAAT
1 TCTGTTTTGGTTGATCATAGCATTGAAAATAAT
*
12683 TTTGTTTTGGTTGATCATAGCATTGAAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGAAAATAAT
*
12716 TCTATTTTGGTTGATCATAGCATTGAAAATA
1 TCTGTTTTGGTTGATCATAGCATTGAAAATA
12747 GGACTGTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGAAAATAAT
Found at i:22591 original size:30 final size:30
Alignment explanation
Indices: 22555--22619 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
22545 CCATCACATG
22555 GGCCATCGCATGGAGCAACCG-GCCACAACC
1 GGCCATCGCATGGAGCAACCGCG-CACAACC
* *
22585 GGCCATCGCATGGGGCATCCGCGCACAACC
1 GGCCATCGCATGGAGCAACCGCGCACAACC
22615 GGCCA
1 GGCCA
22620 AAGGACCCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.23, C:0.40, G:0.29, T:0.08
Consensus pattern (30 bp):
GGCCATCGCATGGAGCAACCGCGCACAACC
Found at i:26563 original size:12 final size:12
Alignment explanation
Indices: 26543--26572 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
26533 AACCGACCAA
*
26543 CGCATGGGACAT
1 CGCACGGGACAT
26555 CGCACGGGACAT
1 CGCACGGGACAT
26567 CGCACG
1 CGCACG
26573 AGCCATCCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.33, G:0.33, T:0.10
Consensus pattern (12 bp):
CGCACGGGACAT
Found at i:26600 original size:42 final size:42
Alignment explanation
Indices: 26552--26638 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
26542 ACGCATGGGA
26552 CATCGCACGGGACATCGCAC-GAGCCATCCGGCCACAACCGAC
1 CATCGCACGGGACATCGCACTG-GCCATCCGGCCACAACCGAC
* * * *
26594 CATCGCATGGGCCATCGCACTGGCCATCTGGCCACAACCGGC
1 CATCGCACGGGACATCGCACTGGCCATCCGGCCACAACCGAC
26636 CAT
1 CAT
26639 TCGACCCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 39 0.98
43 1 0.03
ACGTcount: A:0.23, C:0.41, G:0.24, T:0.11
Consensus pattern (42 bp):
CATCGCACGGGACATCGCACTGGCCATCCGGCCACAACCGAC
Found at i:33078 original size:42 final size:42
Alignment explanation
Indices: 33045--33132 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
33035 GCCATGACTG
*
33045 GCCAACGCATGGGACATCGCACGGGACATCCGGCCACAACCA
1 GCCAACGCACGGGACATCGCACGGGACATCCGGCCACAACCA
** * *
33087 GCCATTGCACGGGCCATCGCACGGGCCATCCGGCCACAACCA
1 GCCAACGCACGGGACATCGCACGGGACATCCGGCCACAACCA
33129 GCCA
1 GCCA
33133 TTCGACCCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.25, C:0.41, G:0.26, T:0.08
Consensus pattern (42 bp):
GCCAACGCACGGGACATCGCACGGGACATCCGGCCACAACCA
Found at i:33108 original size:12 final size:12
Alignment explanation
Indices: 33087--33116 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
33077 GCCACAACCA
*
33087 GCCATTGCACGG
1 GCCATCGCACGG
33099 GCCATCGCACGG
1 GCCATCGCACGG
33111 GCCATC
1 GCCATC
33117 CGGCCACAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.40, G:0.30, T:0.13
Consensus pattern (12 bp):
GCCATCGCACGG
Found at i:37584 original size:30 final size:30
Alignment explanation
Indices: 37538--37615 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 30
37528 CGCACAACAT
37538 CGGCCACATGACCGGCCATCGCATGGAGCAAC
1 CGGCCACA--ACCGGCCATCGCATGGAGCAAC
* *
37570 CGGCCACAACCGGCCATCGCATGGGGCATC
1 CGGCCACAACCGGCCATCGCATGGAGCAAC
*
37600 C-GCGCACAACCTGCCA
1 CGGC-CACAACCGGCCA
37616 AAGGACCGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 2 0.05
30 32 0.76
32 8 0.19
ACGTcount: A:0.23, C:0.41, G:0.27, T:0.09
Consensus pattern (30 bp):
CGGCCACAACCGGCCATCGCATGGAGCAAC
Found at i:70041 original size:89 final size:89
Alignment explanation
Indices: 69931--70099 Score: 338
Period size: 89 Copynumber: 1.9 Consensus size: 89
69921 AACACCATTG
69931 GATCTCTTCATTCTGCTAATGGTGATAAGTTGGAAACTTTCCAACAAATATCTAATGAGGCCATT
1 GATCTCTTCATTCTGCTAATGGTGATAAGTTGGAAACTTTCCAACAAATATCTAATGAGGCCATT
69996 CATTTCTATGAAAATATCTCTTCA
66 CATTTCTATGAAAATATCTCTTCA
70020 GATCTCTTCATTCTGCTAATGGTGATAAGTTGGAAACTTTCCAACAAATATCTAATGAGGCCATT
1 GATCTCTTCATTCTGCTAATGGTGATAAGTTGGAAACTTTCCAACAAATATCTAATGAGGCCATT
70085 CATTTCTATGAAAAT
66 CATTTCTATGAAAAT
70100 CTGCTTGGGA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 80 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (89 bp):
GATCTCTTCATTCTGCTAATGGTGATAAGTTGGAAACTTTCCAACAAATATCTAATGAGGCCATT
CATTTCTATGAAAATATCTCTTCA
Done.