Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010649.1 Corchorus capsularis cultivar CVL-1 contig10670, 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: 35865
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Found at i:7663 original size:19 final size:18
Alignment explanation
Indices: 7630--7665 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7620 TTGAAATAAT
7630 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
7648 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
7666 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:9681 original size:33 final size:33
Alignment explanation
Indices: 9611--9723 Score: 122
Period size: 33 Copynumber: 3.4 Consensus size: 33
9601 GCCGCGCAAC
* *
9611 ACCGGCCACGTGACATGGACATGTCTGGCCATC-
1 ACCGGCCACGCGACATGGACATGTCCGGCCA-CA
*
9644 ACCGGCCACGCGACATGGACATGTCCGGCTACA
1 ACCGGCCACGCGACATGGACATGTCCGGCCACA
** * * *
9677 ACCGGCCAAACGAC-TCGGCCATGCCCAGCCACA
1 ACCGGCCACGCGACAT-GGACATGTCCGGCCACA
9710 ACCGGCCACGCGAC
1 ACCGGCCACGCGAC
9724 CCTTTATCTA
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 2 0.03
33 65 0.97
ACGTcount: A:0.24, C:0.40, G:0.26, T:0.11
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGACATGTCCGGCCACA
Found at i:15807 original size:53 final size:53
Alignment explanation
Indices: 15709--15971 Score: 314
Period size: 53 Copynumber: 4.8 Consensus size: 53
15699 CATTTATAAG
* * * *
15709 TCCCTAAACACAGAGGCAATTCTATATCAAAAGACCTCGAGCACAAGGGTGTTCA
1 TCCCTAAACACAGAGGC-A-TCTATATCAAAAGTCCTCAAACACAAGGGTATTCA
15764 TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGGTATTCA
1 TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGGTATTCA
* * *
15817 TCCCTAAACACAGAGGCACCTCTCTCAAAAGTCCTCAAACACAAGGGTATTCA
1 TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGGTATTCA
* * *
15870 TCCCTAAACACAGAGGCATCTACATC-AAAGTCCTCAAGCACAAGGGCATTCATACTAAA
1 TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGG---T-AT--T-CA
* *
15929 GTCCCTAAACACAGAGGCATCTATA-CTAAAGTCCCCAAACACA
1 -TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACA
15972 TGTAACACAG
Statistics
Matches: 183, Mismatches: 16, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
52 19 0.10
53 103 0.56
54 1 0.01
55 18 0.10
56 2 0.01
58 1 0.01
59 2 0.01
60 37 0.20
ACGTcount: A:0.38, C:0.29, G:0.14, T:0.19
Consensus pattern (53 bp):
TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGGTATTCA
Found at i:15875 original size:106 final size:107
Alignment explanation
Indices: 15679--15922 Score: 321
Period size: 106 Copynumber: 2.3 Consensus size: 107
15669 CCCAATAATT
* * *
15679 AAAGCCCTCAAACACAAGGGCATTTATAAGTCCCTAAACACAGAGGCAATTCTATATCAAAAGAC
1 AAAGTCCTCAAACACAAGGGCA--T-TCA-TCCCTAAACACAGAGGCAATCCTATATCAAAAGAC
* * * *
15744 CTCGAGCACAAGGGTGTTCATCCCTAAACACAGAGGCATCTATATC
62 CTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCATCTACATC
* * * *
15790 AAAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGC-A-CCTCTCTCAAAAGTCCTC
1 -AAAGTCCTCAAACACAAGGGCATTCATCCCTAAACACAGAGGCAATCCTATATCAAAAGACCTC
15853 AAACACAAGGGTATTCATCCCTAAACACAGAGGCATCTACATC
65 AAACACAAGGGTATTCATCCCTAAACACAGAGGCATCTACATC
*
15896 AAAGTCCTCAAGCACAAGGGCATTCAT
1 AAAGTCCTCAAACACAAGGGCATTCAT
15923 ACTAAAGTCC
Statistics
Matches: 119, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
105 25 0.21
106 53 0.45
107 1 0.01
108 17 0.14
109 2 0.02
110 1 0.01
112 20 0.17
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.19
Consensus pattern (107 bp):
AAAGTCCTCAAACACAAGGGCATTCATCCCTAAACACAGAGGCAATCCTATATCAAAAGACCTCA
AACACAAGGGTATTCATCCCTAAACACAGAGGCATCTACATC
Found at i:15930 original size:30 final size:30
Alignment explanation
Indices: 15870--15971 Score: 97
Period size: 30 Copynumber: 3.4 Consensus size: 30
15860 AGGGTATTCA
*
15870 TCCCTAAACAC-AGAGGCATCTACA-TCAAAG
1 TCCC-AAACACAAGAGGCATCTATACT-AAAG
*
15900 TCCTCAAGCACAAG-GGCAT-TCATACTAAAG
1 TCC-CAAACACAAGAGGCATCT-ATACTAAAG
15930 TCCCTAAACAC-AGAGGCATCTATACTAAAG
1 TCCC-AAACACAAGAGGCATCTATACTAAAG
15960 TCCCCAAACACA
1 T-CCCAAACACA
15972 TGTAACACAG
Statistics
Matches: 60, Mismatches: 3, Indels: 17
0.75 0.04 0.21
Matches are distributed among these distances:
29 4 0.07
30 48 0.80
31 8 0.13
ACGTcount: A:0.39, C:0.30, G:0.13, T:0.18
Consensus pattern (30 bp):
TCCCAAACACAAGAGGCATCTATACTAAAG
Found at i:17810 original size:33 final size:33
Alignment explanation
Indices: 17759--17844 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
17749 CTAATTGTGA
* * *
17759 TGAAAACAAATCTATTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
*
17792 TGCAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
17825 TGAAAATAATTCTGTTTTGG
1 TGAAAATAATTCTGTTTTGG
17845 GTGAAAAGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (33 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
Found at i:18259 original size:30 final size:30
Alignment explanation
Indices: 18223--18281 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
18213 CAAGGGGGAG
18223 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
*
18253 GGAATGATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
18282 CTTGAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Found at i:21580 original size:21 final size:21
Alignment explanation
Indices: 21556--21604 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
21546 TCTCACTAAG
*
21556 TCTGATTTGAAT-TTGAAAACC
1 TCTGATTTAAATCTTGAAAA-C
21577 TCTGA-TTAAATCTTGAAAAC
1 TCTGATTTAAATCTTGAAAAC
21597 TCTTGATT
1 TC-TGATT
21605 ACCAATTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (21 bp):
TCTGATTTAAATCTTGAAAAC
Found at i:23038 original size:31 final size:31
Alignment explanation
Indices: 23003--23070 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
22993 TTTATCATAA
* * *
23003 AAACATAAATATGCCTCCAATTGAAACAATC
1 AAACATAAACAAGCCTCAAATTGAAACAATC
*
23034 AAACATAAACAAGCTTCAAATTGAAACAATC
1 AAACATAAACAAGCCTCAAATTGAAACAATC
23065 AAACAT
1 AAACAT
23071 GACCAGTCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.53, C:0.21, G:0.06, T:0.21
Consensus pattern (31 bp):
AAACATAAACAAGCCTCAAATTGAAACAATC
Found at i:27716 original size:21 final size:21
Alignment explanation
Indices: 27690--27749 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
27680 GCAAATCTTG
*
27690 GAATCGATTGGAATATTCCTA
1 GAATCGATTGGAATATTCATA
* * **
27711 GAATCGATTGTAGTACACATA
1 GAATCGATTGGAATATTCATA
27732 GAATCGATTGGAATATTC
1 GAATCGATTGGAATATTC
27750 TTGCTCCAAG
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (21 bp):
GAATCGATTGGAATATTCATA
Found at i:28642 original size:2 final size:2
Alignment explanation
Indices: 28635--28662 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28625 TTATTTTTAT
28635 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28663 CTAATTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28792 original size:21 final size:21
Alignment explanation
Indices: 28761--28811 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
28751 TACCTATCAT
28761 AAATAAAACTA-CTCATTTTAAA
1 AAAT-AAACTACCT-ATTTTAAA
*
28783 AAATAAACTACCTGTTTTAAA
1 AAATAAACTACCTATTTTAAA
28804 AAA-AAACT
1 AAATAAACT
28812 GTCATAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 5 0.19
21 16 0.59
22 6 0.22
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (21 bp):
AAATAAACTACCTATTTTAAA
Found at i:29861 original size:1 final size:1
Alignment explanation
Indices: 29855--29881 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
29845 TTTCTTTGTC
29855 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
29882 CCATTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:30423 original size:16 final size:18
Alignment explanation
Indices: 30388--30425 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
30378 TTCAACAAAT
30388 TAAATAAAAAATATTATA
1 TAAATAAAAAATATTATA
30406 TAAATAAAAAATATTATA
1 TAAATAAAAAATATTATA
30424 TA
1 TA
30426 TTAAGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAATAAAAAATATTATA
Found at i:30725 original size:74 final size:74
Alignment explanation
Indices: 30619--30768 Score: 264
Period size: 74 Copynumber: 2.0 Consensus size: 74
30609 ATTTATAACC
* * *
30619 TTTTCTCTTTATATTACTTATAATCAACTTTTTTTTGAGATAAGAATTATTTTCATTTCTTGAAG
1 TTTTCTCTTTATATTACTTATAATCAACTTTTTTTTGAGATAAAAATCATTTTCATTTCTTGAAA
30684 AAATTGAGA
66 AAATTGAGA
30693 TTTTCTCTTTATATTACTTATAATCAACTTTTTTTTGAGATAAAAATCATTTTCATTTCTTGAAA
1 TTTTCTCTTTATATTACTTATAATCAACTTTTTTTTGAGATAAAAATCATTTTCATTTCTTGAAA
*
30758 AAATTGGGA
66 AAATTGAGA
30767 TT
1 TT
30769 ACAAACGCAC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (74 bp):
TTTTCTCTTTATATTACTTATAATCAACTTTTTTTTGAGATAAAAATCATTTTCATTTCTTGAAA
AAATTGAGA
Found at i:30980 original size:62 final size:62
Alignment explanation
Indices: 30911--31031 Score: 226
Period size: 62 Copynumber: 2.0 Consensus size: 62
30901 ACCATAAACT
30911 ACCTACCTACCAAATAAACAAACAAATTACAAACAAACTCACA-TTCGGTGAGAGTTGAACCC
1 ACCTACCTACCAAATAAACAAACAAATTACAAACAAACTCACATTTC-GTGAGAGTTGAACCC
30973 ACCTACCTACCAAATAAACAAACAAATTACAAACAAACTCACATTTCGTGAGAGTTGAA
1 ACCTACCTACCAAATAAACAAACAAATTACAAACAAACTCACATTTCGTGAGAGTTGAA
31032 TCAAAGACCT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
62 55 0.95
63 3 0.05
ACGTcount: A:0.46, C:0.26, G:0.09, T:0.19
Consensus pattern (62 bp):
ACCTACCTACCAAATAAACAAACAAATTACAAACAAACTCACATTTCGTGAGAGTTGAACCC
Found at i:33135 original size:58 final size:58
Alignment explanation
Indices: 33065--33181 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
33055 GACATGAGGT
33065 AAATTCAGTGGTTGGACTACACTCTATAAGAGAAACCCTCCTTTTGAAAGATAAGGCC
1 AAATTCAGTGGTTGGACTACACTCTATAAGAGAAACCCTCCTTTTGAAAGATAAGGCC
* *
33123 AAATTCAGTGGTTGGACTACACTCTATAAGAGAGAGCCTCCTTTTGAAAGATAAGGCC
1 AAATTCAGTGGTTGGACTACACTCTATAAGAGAAACCCTCCTTTTGAAAGATAAGGCC
33181 A
1 A
33182 CTTCTATTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (58 bp):
AAATTCAGTGGTTGGACTACACTCTATAAGAGAAACCCTCCTTTTGAAAGATAAGGCC
Found at i:34763 original size:21 final size:21
Alignment explanation
Indices: 34737--34779 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
34727 GACAGAAGGA
*
34737 AAGCAGGAAATTAAATGCTTC
1 AAGCAGGAAATTAAACGCTTC
34758 AAGCAGGAAATTAAACGCTTC
1 AAGCAGGAAATTAAACGCTTC
34779 A
1 A
34780 TTAAGAGGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGCAGGAAATTAAACGCTTC
Done.