Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009288.1 Corchorus capsularis cultivar CVL-1 contig09309, 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: 45036
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:87 original size:4 final size:4
Alignment explanation
Indices: 80--106 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
70 TATATATATA
80 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
107 TTTTGACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:970 original size:17 final size:17
Alignment explanation
Indices: 948--1004 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
938 TTATGTGTGA
*
948 TTAGTGATATAGTGATT
1 TTAGTGATTTAGTGATT
*
965 TTAGTGATTTAGCGACTT
1 TTAGTGATTTAGTGA-TT
*
983 GATTAGTGATTTAGTAATT
1 --TTAGTGATTTAGTGATT
1002 TTA
1 TTA
1005 TTTAACACAC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 16 0.48
18 2 0.06
19 2 0.06
20 13 0.39
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (17 bp):
TTAGTGATTTAGTGATT
Found at i:990 original size:20 final size:19
Alignment explanation
Indices: 945--996 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 19
935 TACTTATGTG
* *
945 TGATTAGTGATATAGTGAT
1 TGATTAGTGATTTAGCGAT
964 T--TTAGTGATTTAGCGACT
1 TGATTAGTGATTTAGCGA-T
982 TGATTAGTGATTTAG
1 TGATTAGTGATTTAG
997 TAATTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 13 0.46
18 2 0.07
19 1 0.04
20 12 0.43
ACGTcount: A:0.27, C:0.04, G:0.25, T:0.44
Consensus pattern (19 bp):
TGATTAGTGATTTAGCGAT
Found at i:3915 original size:13 final size:14
Alignment explanation
Indices: 3887--3931 Score: 74
Period size: 13 Copynumber: 3.2 Consensus size: 14
3877 ACCCTAGCCG
3887 CTCCTCTCTCCCCTT
1 CTCC-CTCTCCCCTT
3902 CTCCCTCT-CCCTT
1 CTCCCTCTCCCCTT
3915 CTCCCTCTCCCCTT
1 CTCCCTCTCCCCTT
3929 CTC
1 CTC
3932 GTTGGTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.45
14 12 0.41
15 4 0.14
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (14 bp):
CTCCCTCTCCCCTT
Found at i:6289 original size:35 final size:35
Alignment explanation
Indices: 6247--7081 Score: 1098
Period size: 35 Copynumber: 23.9 Consensus size: 35
6237 CAGTCATTCT
* *
6247 AAGAAGTTTTCGAAGACCAGAGTTGATCTCATTCC
1 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
* * * *
6282 AACAAG-TTTCTAACGATCAGAGTTGATCTTATTCC
1 AAGAAGTTTTCGAA-GATCAGAGTTGATCTCATTTC
*
6317 AAGAAGTTTTTGAAGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
* * * *
6352 AAGAAG-TTACCAACGATCTGAGTTGATCTCATTCC
1 AAGAAGTTTTCGAA-GATCAGAGTTGATCTCATTTC
6387 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
* * * *
6422 AAGAAG-TTACCAACGATCTGAGTTGATCTCATTCC
1 AAGAAGTTTTCGAA-GATCAGAGTTGATCTCATTTC
6457 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
*
6492 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
* * *
6527 AAGAAGTTTTCCATGATCCGAGTTGATCTCATTTC
1 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
* * *
6562 AAGAAGTTTTCCACGATCAGAGTTGATCTCATTTT
1 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
* * *
6597 AAGAAG-TTACCAACGATCAGAGTTGATCTCATTCC
1 AAGAAGTTTTCGAA-GATCAGAGTTGATCTCATTTC
*
6632 AAGAAGTTTTTGAAGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
*
6667 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
*
6702 AAGAAGTTTTC-AGAGGTCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGA-AGATCAGAGTTGATCTCATTTC
* * *
6737 AAGAA-ATTTCCAACGATCAGAGTTGATCTCATTCC
1 AAGAAGTTTTCGAA-GATCAGAGTTGATCTCATTTC
6772 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
*
6807 AAGAAGTTTTC-AGAGGTCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGA-AGATCAGAGTTGATCTCATTTC
* * *
6842 AAGAAG-TTTCCAACTATCAGAGTTGATCTCATTCC
1 AAGAAGTTTTCGAA-GATCAGAGTTGATCTCATTTC
6877 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
*
6912 AAGAAGTTTTC-AGAGATCAGAGTTGATCTCATTCC
1 AAGAAGTTTTCGA-AGATCAGAGTTGATCTCATTTC
* *
6947 AAGAAGTTTTCGATGATCATAGTTGATCTCATTTC
1 AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
* * *
6982 AAGAAGTTTTC-AGAGATCATAGTTGATTTCATTCC
1 AAGAAGTTTTCGA-AGATCAGAGTTGATCTCATTTC
*
7017 AAGAAGTTTTC-AATGATCAGAGTTGATCTCAGTTC
1 AAGAAGTTTTCGAA-GATCAGAGTTGATCTCATTTC
* *
7052 AAGAGGTTTTCGATGATCAGAGTTGATCTC
1 AAGAAGTTTTCGAAGATCAGAGTTGATCTC
7082 TAATTGATCC
Statistics
Matches: 709, Mismatches: 70, Indels: 42
0.86 0.09 0.05
Matches are distributed among these distances:
34 35 0.05
35 641 0.90
36 33 0.05
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (35 bp):
AAGAAGTTTTCGAAGATCAGAGTTGATCTCATTTC
Found at i:14768 original size:1 final size:1
Alignment explanation
Indices: 14762--14815 Score: 81
Period size: 1 Copynumber: 54.0 Consensus size: 1
14752 CTTGTGCCAC
** *
14762 AAAAAAAAAAAAAAAAAAAAAAATTAAAAAAAAAAAAAAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
14816 CGCTGCACAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.94, C:0.02, G:0.00, T:0.04
Consensus pattern (1 bp):
A
Found at i:14795 original size:24 final size:24
Alignment explanation
Indices: 14763--14808 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
14753 TTGTGCCACA
14763 AAAAAAAAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAAAAAAAATT
14787 AAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAA
14809 CAAAAAACGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.96, C:0.00, G:0.00, T:0.04
Consensus pattern (24 bp):
AAAAAAAAAAAAAAAAAAAAAATT
Found at i:33437 original size:24 final size:24
Alignment explanation
Indices: 33410--33456 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
33400 AACTAAACTT
33410 TCTCACAAGTAATAATTCAAATCA
1 TCTCACAAGTAATAATTCAAATCA
*
33434 TCTCATAAGTAATAATTCAAATC
1 TCTCACAAGTAATAATTCAAATC
33457 CTTGACAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (24 bp):
TCTCACAAGTAATAATTCAAATCA
Found at i:36758 original size:21 final size:23
Alignment explanation
Indices: 36719--36762 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
36709 AAGGTAATTT
36719 TCATTCATGAAAATGAAATTACA
1 TCATTCATGAAAATGAAATTACA
*
36742 TCATTCAT-AACAT-AAATTACA
1 TCATTCATGAAAATGAAATTACA
36763 ATAGATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 4 0.20
23 8 0.40
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.32
Consensus pattern (23 bp):
TCATTCATGAAAATGAAATTACA
Found at i:38043 original size:23 final size:22
Alignment explanation
Indices: 38017--38089 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 22
38007 TTGGCCAAGC
* *
38017 TTTTGTAGTGTATTAATTTTATT
1 TTTTTTAGTATATTAATTTTA-T
* *
38040 TTTTTTGGCACTAATTAATTTTAT
1 TTTTTTAGTA-T-ATTAATTTTAT
*
38064 TTTTTTAGTATATATATTTTTAT
1 TTTTTTAGTATAT-TAATTTTAT
38087 TTT
1 TTT
38090 GTTTTGTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
22 2 0.05
23 18 0.45
24 10 0.25
25 10 0.25
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.66
Consensus pattern (22 bp):
TTTTTTAGTATATTAATTTTAT
Found at i:38645 original size:16 final size:16
Alignment explanation
Indices: 38624--38685 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
38614 AAATCAACGT
*
38624 CCCGAACCCGCCCGAA
1 CCCGAACCCACCCGAA
***
38640 CCCGAAAATACCCGAA
1 CCCGAACCCACCCGAA
*
38656 CCCGAGA-CAACCCGAA
1 CCCGA-ACCCACCCGAA
38672 CCCGAACCCGACCC
1 CCCGAACCC-ACCC
38686 CGACCCGAGC
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
15 1 0.03
16 30 0.83
17 5 0.14
ACGTcount: A:0.32, C:0.50, G:0.16, T:0.02
Consensus pattern (16 bp):
CCCGAACCCACCCGAA
Found at i:38691 original size:17 final size:18
Alignment explanation
Indices: 38666--38699 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38656 CCCGAGACAA
38666 CCCGAACCCGAACCCGAC
1 CCCGAACCCGAACCCGAC
*
38684 CCCG-ACCCGAGCCCGA
1 CCCGAACCCGAACCCGA
38700 GATCAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.56, G:0.21, T:0.00
Consensus pattern (18 bp):
CCCGAACCCGAACCCGAC
Found at i:39182 original size:4 final size:4
Alignment explanation
Indices: 39173--39197 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39163 GATGAGACAC
39173 TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT T
39198 ATTTTCTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Done.