Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011632.1 Corchorus capsularis cultivar CVL-1 contig11653, 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: 36325
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--74 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
43 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
75 TTTTTGTGGG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:459 original size:30 final size:30
Alignment explanation
Indices: 400--459 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
390 AACACGCGCT
*
400 GACGTGGATGACACGTGGAAGAAATGTGTA
1 GACGTGGATGACACGTGGAAGAAACGTGTA
*
430 GACGTGGATGACACGTGGAAGATACGTGTA
1 GACGTGGATGACACGTGGAAGAAACGTGTA
460 TGCAAACATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.12, G:0.37, T:0.20
Consensus pattern (30 bp):
GACGTGGATGACACGTGGAAGAAACGTGTA
Found at i:596 original size:33 final size:33
Alignment explanation
Indices: 554--622 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
544 CCTATTTTAT
*
554 CATGAACTATTATGAACACTAAGAACATTCAAA
1 CATGAACTATTATGAACACCAAGAACATTCAAA
587 CATGAACTATTATGAACACCAAGAACATTCAAA
1 CATGAACTATTATGAACACCAAGAACATTCAAA
620 CAT
1 CAT
623 TGCAGCCACC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.23
Consensus pattern (33 bp):
CATGAACTATTATGAACACCAAGAACATTCAAA
Found at i:823 original size:13 final size:13
Alignment explanation
Indices: 805--829 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
795 TCAGAAACAG
805 AAAAAAATTCCCC
1 AAAAAAATTCCCC
818 AAAAAAATTCCC
1 AAAAAAATTCCC
830 TCCGTTTTGT
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:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAAATTCCCC
Found at i:1485 original size:22 final size:22
Alignment explanation
Indices: 1457--1500 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1447 AAAAACTAAA
*
1457 TTGCATTGTGTCTTCTTTACTT
1 TTGCATTGTGTCTTCTCTACTT
1479 TTGCATTGTGTCTTCTCTACTT
1 TTGCATTGTGTCTTCTCTACTT
1501 ATGGTCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.20, G:0.14, T:0.57
Consensus pattern (22 bp):
TTGCATTGTGTCTTCTCTACTT
Found at i:1644 original size:13 final size:13
Alignment explanation
Indices: 1626--1652 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1616 ATTAGATACT
1626 TCTTTTCATTGCA
1 TCTTTTCATTGCA
1639 TCTTTTCATTGCA
1 TCTTTTCATTGCA
1652 T
1 T
1653 ACATAGGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.56
Consensus pattern (13 bp):
TCTTTTCATTGCA
Found at i:4603 original size:35 final size:35
Alignment explanation
Indices: 4530--5113 Score: 687
Period size: 35 Copynumber: 16.7 Consensus size: 35
4520 TCATAATAAG
4530 CAACTTAATTCAGGGT-A--AA-TAAGTCAGTAAGT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA-T
* * *
4562 -AGCTTAATTCAGGGTAATTAAGTGAGTCAGTTAGT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAG-TAAT
* * *
4597 -AACTTAA-TCTAGGGTAATTAGGTGAGCCAGTAAT
1 CAACTTAATTC-AGGGTAATTAAGTAAGTCAGTAAT
*
4631 CAACTTTAATTCAGGGTAATTAAGTCAGTCAGTAAT
1 CAAC-TTAATTCAGGGTAATTAAGTAAGTCAGTAAT
*
4667 CAACTTAATTCAGGGTAATTAAGTAAATCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* *
4702 CAACTTAATTCAGGGCAATTAAGTAGGTCAGTGAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGT-AAT
*
4738 -AACTTAATTCAGGGTAATTAAGTAAATCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
*
4772 CAGCTTAATTCAGGGTAATTAAGTAAGTCAGTAATAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAG---TAAT
*
4810 CAACTTAATTCAGGGTAATTAAGTAAATCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
4845 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAG---TAAT
*
4883 CAACTTAATTCAGGGTAATTAAGTAAATCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
*
4918 CAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* * *
4953 CAACTTAATTCAGGGCAATCAAGTAGGTCAGTGAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGT-AAT
4989 -AACTTAATTCAGGGTAA-T---TAAGTCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* ** * * *
5019 CAACTTTAATTCGGGGTAATTAAGTGGGTTAATGAGT
1 CAAC-TTAATTCAGGGTAATTAAGTAAGTCAGT-AAT
*
5056 -AACTTAATTCAGGGTAATTAAGT-AGTTCAATAAGT
1 CAACTTAATTCAGGGTAATTAAGTAAG-TCAGTAA-T
5091 -AACTTAATTCAGGGTAATTAAGT
1 CAACTTAATTCAGGGTAATTAAGT
5114 TTAGTAAGAA
Statistics
Matches: 482, Mismatches: 43, Indels: 51
0.84 0.07 0.09
Matches are distributed among these distances:
30 3 0.01
31 25 0.05
32 14 0.03
33 1 0.00
34 12 0.02
35 311 0.65
36 45 0.09
37 4 0.01
38 67 0.14
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Consensus pattern (35 bp):
CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
Found at i:5070 original size:67 final size:66
Alignment explanation
Indices: 4636--5078 Score: 302
Period size: 73 Copynumber: 6.3 Consensus size: 66
4626 GTAATCAACT
* * ** *
4636 TTAATTCAGGGTAATTAAGTCAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAATCAGT-A
1 TTAATTCAGGGTAATT-A---AGTCAGTAATCAACTTAATTCAGGGCAATCAAGTAGGTCAATGA
4700 ATCAAC
62 AT-AAC
* * * ** *
4706 TTAATTCAGGGCAATTAAGTAGGTCAGTGAAT-AACTTAATTCAGGGTAATTAAGTAAATCAGT-
1 TTAATTCAGGGTAATT-A--A-GTCAGT-AATCAACTTAATTCAGGGCAATCAAGTAGGTCAATG
*
4769 AATCAGC
61 AAT-AAC
* * ** *
4776 TTAATTCAGGGTAATTAAGTAAGTCAGTAATAATCAACTTAATTCAGGGTAATTAAGTAAATCAG
1 TTAATTCAGGGTAA-T---TAAGTCAG---TAATCAACTTAATTCAGGGCAATCAAGTAGGTCAA
4841 T-AATCAAC
59 TGAAT-AAC
* * ** *
4849 TTAATTCAGGGTAATTAAGTAAGTCAGTAATAATCAACTTAATTCAGGGTAATTAAGTAAATCAG
1 TTAATTCAGGGTAA-T---TAAGTCAG---TAATCAACTTAATTCAGGGCAATCAAGTAGGTCAA
4914 T-AATCAAC
59 TGAAT-AAC
*
4922 TTAATTCAGGGTAATTAAGTGAGTCAGTAATCAACTTAATTCAGGGCAATCAAGTAGGTCAGTGA
1 TTAATTCAGGGTAATT-A---AGTCAGTAATCAACTTAATTCAGGGCAATCAAGTAGGTCAATGA
4987 ATAAC
62 ATAAC
* * * * * *
4992 TTAATTCAGGGTAATTAAGTCAGTAATCAACTTTAATTCGGGGTAATTAAGTGGGTTAATGAGTA
1 TTAATTCAGGGTAATTAAGTCAGTAATCAAC-TTAATTCAGGGCAATCAAGTAGGTCAATGAATA
5057 AC
65 AC
5059 TTAATTCAGGGTAATTAAGT
1 TTAATTCAGGGTAATTAAGT
5079 AGTTCAATAA
Statistics
Matches: 340, Mismatches: 17, Indels: 35
0.87 0.04 0.09
Matches are distributed among these distances:
66 14 0.04
67 48 0.14
69 3 0.01
70 130 0.38
71 8 0.02
72 4 0.01
73 132 0.39
74 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (66 bp):
TTAATTCAGGGTAATTAAGTCAGTAATCAACTTAATTCAGGGCAATCAAGTAGGTCAATGAATAA
C
Found at i:7037 original size:31 final size:31
Alignment explanation
Indices: 7002--7060 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
6992 TACTATAAGA
* * *
7002 AACTTTTGAAATGCCTATTGTACCCTTATTT
1 AACTTTTAAAATACCTATTATACCCTTATTT
*
7033 AACTTTTAAAATACCTATTATATCCTTA
1 AACTTTTAAAATACCTATTATACCCTTA
7061 CTTATCTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (31 bp):
AACTTTTAAAATACCTATTATACCCTTATTT
Found at i:14745 original size:16 final size:16
Alignment explanation
Indices: 14712--14760 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
14702 TAAAAGAAGA
*
14712 GTATCGTGTATATGTAT
1 GTAT-GTGTATATATAT
*
14729 GTATGTGTCTATATAT
1 GTATGTGTATATATAT
*
14745 GTGTGTGTATATATAT
1 GTATGTGTATATATAT
14761 ATGTCTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 24 0.86
17 4 0.14
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.49
Consensus pattern (16 bp):
GTATGTGTATATATAT
Found at i:14755 original size:14 final size:14
Alignment explanation
Indices: 14732--14773 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
14722 TATGTATGTA
14732 TGTGTCTATATATG
1 TGTGTCTATATATG
* *
14746 TGTGTGTATATATA
1 TGTGTCTATATATG
*
14760 TATGTCTA-ATATG
1 TGTGTCTATATATG
14773 T
1 T
14774 TGCTACTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.50
Consensus pattern (14 bp):
TGTGTCTATATATG
Found at i:16207 original size:29 final size:30
Alignment explanation
Indices: 16174--16230 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
16164 TTAACTGATC
* *
16174 TATTTATAGAGCCTAAG-ATTTTTTTAGGG
1 TATTTATAGAGCCCAAGAATTTATTTAGGG
16203 TATTTATAGAGCCCAAGAATTTATTTAG
1 TATTTATAGAGCCCAAGAATTTATTTAG
16231 AATTAACTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.42
Consensus pattern (30 bp):
TATTTATAGAGCCCAAGAATTTATTTAGGG
Found at i:21839 original size:20 final size:20
Alignment explanation
Indices: 21814--21861 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
21804 CGGCCACTTG
21814 ACCGGCCATCGCATGGAGCA
1 ACCGGCCATCGCATGGAGCA
21834 ACCGGCCATCGCATGGAGCA
1 ACCGGCCATCGCATGGAGCA
21854 ACCGGCCA
1 ACCGGCCA
21862 CAACCGGCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.38, G:0.29, T:0.08
Consensus pattern (20 bp):
ACCGGCCATCGCATGGAGCA
Found at i:27968 original size:30 final size:30
Alignment explanation
Indices: 27932--28026 Score: 181
Period size: 30 Copynumber: 3.2 Consensus size: 30
27922 CCATCGCATG
*
27932 GGCCATCACATGGAGCAACCGGCCACAACC
1 GGCCATCGCATGGAGCAACCGGCCACAACC
27962 GGCCATCGCATGGAGCAACCGGCCACAACC
1 GGCCATCGCATGGAGCAACCGGCCACAACC
27992 GGCCATCGCATGGAGCAACCGGCCACAACC
1 GGCCATCGCATGGAGCAACCGGCCACAACC
28022 GGCCA
1 GGCCA
28027 ATGGACCCTT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.27, C:0.40, G:0.26, T:0.06
Consensus pattern (30 bp):
GGCCATCGCATGGAGCAACCGGCCACAACC
Found at i:32507 original size:20 final size:20
Alignment explanation
Indices: 32482--32528 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
32472 AAATCATTAG
32482 AGAAATCTGATACCATAACA
1 AGAAATCTGATACCATAACA
32502 AGAAATCTGATACCATAACA
1 AGAAATCTGATACCATAACA
32522 AGAAATC
1 AGAAATC
32529 AATACAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.51, C:0.19, G:0.11, T:0.19
Consensus pattern (20 bp):
AGAAATCTGATACCATAACA
Done.