Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011836.1 Corchorus capsularis cultivar CVL-1 contig11857, 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: 24626
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:421 original size:11 final size:11
Alignment explanation
Indices: 407--452 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
397 AATATTTATT
*
407 GCCATGTCATA
1 GCCACGTCATA
*
418 GCCACATCATA
1 GCCACGTCATA
429 GCCACGTCATA
1 GCCACGTCATA
*
440 GCCACATCATA
1 GCCACGTCATA
451 GC
1 GC
453 TTAACGGTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.30, C:0.35, G:0.15, T:0.20
Consensus pattern (11 bp):
GCCACGTCATA
Found at i:437 original size:22 final size:22
Alignment explanation
Indices: 407--452 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
397 AATATTTATT
*
407 GCCATGTCATAGCCACATCATA
1 GCCACGTCATAGCCACATCATA
429 GCCACGTCATAGCCACATCATA
1 GCCACGTCATAGCCACATCATA
451 GC
1 GC
453 TTAACGGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.35, G:0.15, T:0.20
Consensus pattern (22 bp):
GCCACGTCATAGCCACATCATA
Found at i:2417 original size:53 final size:53
Alignment explanation
Indices: 2359--2495 Score: 231
Period size: 52 Copynumber: 2.6 Consensus size: 53
2349 ATTTGAATGT
* *
2359 TTTGAAAAGACTTAAATTGAACATTTTGAAAAACTTGATGGGAACTTTCCCAA
1 TTTGAAAAGACCTAAATTGAACACTTTGAAAAACTTGATGGGAACTTTCCCAA
*
2412 TTTGAAAAAACCTAAATTGAACACTTTG-AAAACTTGATGGGAACTTTCCCAA
1 TTTGAAAAGACCTAAATTGAACACTTTGAAAAACTTGATGGGAACTTTCCCAA
*
2464 TTTAAAAAGACCTAAATTGAACACTTTGAAAA
1 TTTGAAAAGACCTAAATTGAACACTTTGAAAA
2496 TTTGATGAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
52 50 0.64
53 28 0.36
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (53 bp):
TTTGAAAAGACCTAAATTGAACACTTTGAAAAACTTGATGGGAACTTTCCCAA
Found at i:5816 original size:24 final size:25
Alignment explanation
Indices: 5788--5843 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
5778 TTGATCAATC
* *
5788 AAGAAACCCAAAGA-CTAAAAGTGA
1 AAGAAAACCAAAAAGCTAAAAGTGA
*
5812 AAGAAAATCAAAAAGCTAAAAGTGA
1 AAGAAAACCAAAAAGCTAAAAGTGA
*
5837 AATAAAA
1 AAGAAAA
5844 GGCCACATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.64, C:0.11, G:0.14, T:0.11
Consensus pattern (25 bp):
AAGAAAACCAAAAAGCTAAAAGTGA
Found at i:5953 original size:22 final size:23
Alignment explanation
Indices: 5907--5953 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
5897 AAAGAAACTT
5907 AAGAATTATTCTAAAAAGGAGGA
1 AAGAATTATTCTAAAAAGGAGGA
*
5930 AAGAATTATTCTAAAGA-GAGGA
1 AAGAATTATTCTAAAAAGGAGGA
5952 AA
1 AA
5954 TGATTCATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.21
Consensus pattern (23 bp):
AAGAATTATTCTAAAAAGGAGGA
Found at i:6504 original size:18 final size:17
Alignment explanation
Indices: 6481--6519 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
6471 TAATCATTTG
6481 TGAATAATGGACTTTTAA
1 TGAATAATGGAC-TTTAA
* *
6499 TGAATAGTGGGCTTTAA
1 TGAATAATGGACTTTAA
6516 TGAA
1 TGAA
6520 ATAGTGCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (17 bp):
TGAATAATGGACTTTAA
Found at i:14539 original size:134 final size:134
Alignment explanation
Indices: 14299--14563 Score: 530
Period size: 134 Copynumber: 2.0 Consensus size: 134
14289 GTTTAAAAGC
14299 TGTTATTAAGAAGGTCATACAACTTTGCTCTAGTTTCTTTTGGAAAGGAAAAGCTGGCAGTTCCT
1 TGTTATTAAGAAGGTCATACAACTTTGCTCTAGTTTCTTTTGGAAAGGAAAAGCTGGCAGTTCCT
14364 CTTGAACTAGAAACAAATGGGACGACATATGCAAACCGAAGGCTGAAGGGGGACTTGGCTTGAAA
66 CTTGAACTAGAAACAAATGGGACGACATATGCAAACCGAAGGCTGAAGGGGGACTTGGCTTGAAA
14429 CTAG
131 CTAG
14433 TGTTATTAAGAAGGTCATACAACTTTGCTCTAGTTTCTTTTGGAAAGGAAAAGCTGGCAGTTCCT
1 TGTTATTAAGAAGGTCATACAACTTTGCTCTAGTTTCTTTTGGAAAGGAAAAGCTGGCAGTTCCT
14498 CTTGAACTAGAAACAAATGGGACGACATATGCAAACCGAAGGCTGAAGGGGGACTTGGCTTGAAA
66 CTTGAACTAGAAACAAATGGGACGACATATGCAAACCGAAGGCTGAAGGGGGACTTGGCTTGAAA
14563 C
131 C
14564 ATGCAAAAGA
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 131 1.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (134 bp):
TGTTATTAAGAAGGTCATACAACTTTGCTCTAGTTTCTTTTGGAAAGGAAAAGCTGGCAGTTCCT
CTTGAACTAGAAACAAATGGGACGACATATGCAAACCGAAGGCTGAAGGGGGACTTGGCTTGAAA
CTAG
Found at i:15957 original size:22 final size:22
Alignment explanation
Indices: 15932--15977 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
15922 AAACCTTTTT
*
15932 TTTTTAAATCAAAAAAATGTAA
1 TTTTTAAATCAAAAAAATGAAA
* * *
15954 TTTTTCATTCATAAAAATGAAA
1 TTTTTAAATCAAAAAAATGAAA
15976 TT
1 TT
15978 ACATTAAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TTTTTAAATCAAAAAAATGAAA
Found at i:17638 original size:2 final size:2
Alignment explanation
Indices: 17631--17662 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17621 TCAAAGTTAC
17631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17663 TTCAATACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20855 original size:16 final size:16
Alignment explanation
Indices: 20831--20889 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
20821 GGCAATTGGG
*
20831 CGGGTTCGGGTTCTGT
1 CGGGTTCGGGTTATGT
* *
20847 CGGGATCGGGCTATGT
1 CGGGTTCGGGTTATGT
*
20863 TGGGTTCGGGTTATGT
1 CGGGTTCGGGTTATGT
20879 CGGGTTCGGGT
1 CGGGTTCGGGT
20890 ATTTTTGGGT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.05, C:0.15, G:0.46, T:0.34
Consensus pattern (16 bp):
CGGGTTCGGGTTATGT
Found at i:20871 original size:32 final size:32
Alignment explanation
Indices: 20832--20901 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
20822 GCAATTGGGC
*
20832 GGGTTCGGGTTCTGTCGGGATCGGGCTA-TGTT
1 GGGTTCGGGTTATGTCGGGATCGGG-TATTGTT
* *
20864 GGGTTCGGGTTATGTCGGGTTCGGGTATTTTT
1 GGGTTCGGGTTATGTCGGGATCGGGTATTGTT
20896 GGGTTC
1 GGGTTC
20902 CTTCTCGGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 2 0.06
32 32 0.94
ACGTcount: A:0.06, C:0.13, G:0.43, T:0.39
Consensus pattern (32 bp):
GGGTTCGGGTTATGTCGGGATCGGGTATTGTT
Found at i:21102 original size:21 final size:20
Alignment explanation
Indices: 21057--21104 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
21047 TTTATTGATA
* *
21057 ATATATAATATAATAATATT
1 ATATATAACATAATAATAAT
*
21077 A-ATATAACATAATTATCAAT
1 ATATATAACATAATAAT-AAT
21097 ATATATAA
1 ATATATAA
21105 AGATTGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 13 0.57
20 4 0.17
21 6 0.26
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATATAACATAATAATAAT
Found at i:21648 original size:2 final size:2
Alignment explanation
Indices: 21641--21680 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
21631 TGTTTTAAGT
* *
21641 TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21681 ATTTAGTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Done.