Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009373.1 Corchorus capsularis cultivar CVL-1 contig09394, 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: 42529
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Found at i:70 original size:11 final size:12
Alignment explanation
Indices: 53--90 Score: 62
Period size: 11 Copynumber: 3.3 Consensus size: 12
43 ACTTATAACT
53 TATATATACATA
1 TATATATACATA
65 TA-ATATACATA
1 TATATATACATA
76 TATATATA-ATA
1 TATATATACATA
87 TATA
1 TATA
91 AAAAAAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 18 0.72
12 7 0.28
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATACATA
Found at i:76 original size:17 final size:17
Alignment explanation
Indices: 56--88 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
46 TATAACTTAT
56 ATATACATATAATATAC
1 ATATACATATAATATAC
*
73 ATATATATATAATATA
1 ATATACATATAATATA
89 TAAAAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATACATATAATATAC
Found at i:1493 original size:78 final size:77
Alignment explanation
Indices: 1364--1581 Score: 321
Period size: 78 Copynumber: 2.8 Consensus size: 77
1354 TTTTACCTTA
*
1364 GAGGTTCCTCCAGTTTCTAAAGATGATGATATTTCATTGATGTTGGCATCCTTCATAGAAGATGA
1 GAGGTTCCTCAAGTTTCT-AAGATGATGATATTTCATTGATGTTGGCATCCTTCATAGAAGATGA
* *
1429 GGCAGCATTTATT
65 GACAGCATTCATT
* *
1442 GAGGTTCCTCAAGTTTCTGAAGATGATGATATTTCATTGATGTTGGCATCCTTCGTAGGAGATGA
1 GAGGTTCCTCAAGTTTCT-AAGATGATGATATTTCATTGATGTTGGCATCCTTCATAGAAGATGA
*
1507 TACAGCATTCATT
65 GACAGCATTCATT
* *
1520 GAGGTTCCTCAAGATTCTAGAGATGATGATA-TTCAATTGATGTTGGCATCGTTCATAGAAGA
1 GAGGTTCCTCAAGTTTCTA-AGATGATGATATTTC-ATTGATGTTGGCATCCTTCATAGAAGA
1582 GGAAGATTGG
Statistics
Matches: 127, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
77 4 0.03
78 123 0.97
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (77 bp):
GAGGTTCCTCAAGTTTCTAAGATGATGATATTTCATTGATGTTGGCATCCTTCATAGAAGATGAG
ACAGCATTCATT
Found at i:2555 original size:50 final size:50
Alignment explanation
Indices: 2498--2595 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
2488 TTAGCAAAAC
*
2498 AATATTTTACAACCAATTTCTCAATCATGATCAACAATAAAAACATTTCA
1 AATATTTTACAACCAATTTCTCAATCACGATCAACAATAAAAACATTTCA
2548 AATATTTTACAACCAATTTCTCAATCACGATCAACAATAAAAACATTT
1 AATATTTTACAACCAATTTCTCAATCACGATCAACAATAAAAACATTT
2596 TAATAGAGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (50 bp):
AATATTTTACAACCAATTTCTCAATCACGATCAACAATAAAAACATTTCA
Found at i:4575 original size:7 final size:7
Alignment explanation
Indices: 4563--4599 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
4553 ACATCGAAAC
4563 CTTGAGA
1 CTTGAGA
4570 CTTGAGA
1 CTTGAGA
4577 CTTGAGA
1 CTTGAGA
4584 CTTGAGA
1 CTTGAGA
4591 CTTGAGA
1 CTTGAGA
4598 CT
1 CT
4600 AATAATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (7 bp):
CTTGAGA
Found at i:14536 original size:30 final size:31
Alignment explanation
Indices: 14500--14570 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
14490 ACATGGCACA
* * *
14500 TGGCATGCCATGTGTCCT-TTTTTATACACG
1 TGGCATGCCATGTGGCATATTTTGATACACG
*
14530 TGGCATGCCATGTGGCATATTTTGGTACACG
1 TGGCATGCCATGTGGCATATTTTGATACACG
14561 TGGCATGCCA
1 TGGCATGCCA
14571 CGTCGGATGC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 16 0.44
31 20 0.56
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (31 bp):
TGGCATGCCATGTGGCATATTTTGATACACG
Found at i:17725 original size:7 final size:7
Alignment explanation
Indices: 17713--17737 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17703 AATCTTGGGG
17713 GGCCAAT
1 GGCCAAT
17720 GGCCAAT
1 GGCCAAT
17727 GGCCAAT
1 GGCCAAT
17734 GGCC
1 GGCC
17738 CTGCTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.32, T:0.12
Consensus pattern (7 bp):
GGCCAAT
Found at i:20077 original size:2 final size:2
Alignment explanation
Indices: 20070--20101 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20060 TAAGGTCAAC
20070 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
20102 TCTAGTGATT
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:23685 original size:122 final size:124
Alignment explanation
Indices: 23549--23782 Score: 321
Period size: 122 Copynumber: 1.9 Consensus size: 124
23539 ATTTCATCAT
* * * ** *
23549 TGTTGGGAATCTTCACAAAAGATGATGCAGCATTCATTACTTGTAA-CAATGGTCAAATTTCTGG
1 TGTTGGAAATCTTCACAAAAGATGATGCAGAATTCATTACTT-AAATCAATGGTCAAATGACAGG
*
23613 TAATGGTAATGA-TTTACCTTT-GAGGTTCCTCAAGTTTTTGAAGATGATGGTATTTCAA
65 TAATGCTAATGATTTTACCTTTGGAGGTTCCTCAAGTTTTTGAAGATGATGGTATTTCAA
* * * *
23671 TGTTGGAAATCTTCACAGAAGTTGATGCCGAATTCATTACTTAAATCGATGGTCAAATGACAGGT
1 TGTTGGAAATCTTCACAAAAGATGATGCAGAATTCATTACTTAAATCAATGGTCAAATGACAGGT
23736 AATGCTAATGATTTTACCTTTGAGGAGGTTCCTCAAGTTTTTGAAGA
66 AATGCTAATGATTTTACCTTT--GGAGGTTCCTCAAGTTTTTGAAGA
23783 CGATTATATT
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
121 2 0.02
122 62 0.65
123 9 0.09
126 23 0.24
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (124 bp):
TGTTGGAAATCTTCACAAAAGATGATGCAGAATTCATTACTTAAATCAATGGTCAAATGACAGGT
AATGCTAATGATTTTACCTTTGGAGGTTCCTCAAGTTTTTGAAGATGATGGTATTTCAA
Found at i:23849 original size:78 final size:78
Alignment explanation
Indices: 23760--23943 Score: 289
Period size: 78 Copynumber: 2.4 Consensus size: 78
23750 TACCTTTGAG
* * *
23760 GAGGTTCCTCAAGTTTTTGAAGACGATTATATTTCATTGATGCTGGCATTCTTCATAGAAGATGA
1 GAGGTTCCTCAAGTTTCTGAAGACGATGATATTTCATTGATGCTGACATTCTTCATAGAAGATGA
*
23825 TGCAGCTTCCATT
66 TGCAGCATCCATT
*
23838 GAGGTTCCTCAAGTTTCT-AGAGATGATGATATTTCATTGATGCTGACATTCTTCATAGAAGATG
1 GAGGTTCCTCAAGTTTCTGA-AGACGATGATATTTCATTGATGCTGACATTCTTCATAGAAGATG
*
23902 ATGCATCATCCATT
65 ATGCAGCATCCATT
*
23916 GAGGTTCCTCAAGTTTCTGAAGATGATG
1 GAGGTTCCTCAAGTTTCTGAAGACGATG
23944 CAGCATCCAT
Statistics
Matches: 98, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
77 1 0.01
78 96 0.98
79 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (78 bp):
GAGGTTCCTCAAGTTTCTGAAGACGATGATATTTCATTGATGCTGACATTCTTCATAGAAGATGA
TGCAGCATCCATT
Found at i:23863 original size:39 final size:40
Alignment explanation
Indices: 23815--23982 Score: 163
Period size: 39 Copynumber: 4.3 Consensus size: 40
23805 GCATTCTTCA
*
23815 TAGAAGATGATGCAGCTTCCATTGAGGTTCCTCAAGTTTC
1 TAGAAGATGATGCAGCATCCATTGAGGTTCCTCAAGTTTC
* * * * *
23855 TAG-AGATGATG-A-TATTTCATTGA---TGCTGACATTCTTC
1 TAGAAGATGATGCAGCA-TCCATTGAGGTTCCTCA-AGT-TTC
*
23892 ATAGAAGATGATGCATCATCCATTGAGGTTCCTCAAGTTTC
1 -TAGAAGATGATGCAGCATCCATTGAGGTTCCTCAAGTTTC
*
23933 T-GAAGATGATGCAGCATCCATTGAGGTTCCTGAAGTTTC
1 TAGAAGATGATGCAGCATCCATTGAGGTTCCTCAAGTTTC
*
23972 CA-AAGATGATG
1 TAGAAGATGATG
23983 ATATTTCATT
Statistics
Matches: 103, Mismatches: 14, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
35 4 0.04
36 2 0.02
37 3 0.03
38 11 0.11
39 61 0.59
40 12 0.12
41 4 0.04
42 2 0.02
43 4 0.04
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (40 bp):
TAGAAGATGATGCAGCATCCATTGAGGTTCCTCAAGTTTC
Found at i:36032 original size:24 final size:25
Alignment explanation
Indices: 35972--36030 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
35962 TTCAAACCCT
*
35972 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACATCTTC
35997 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
36021 AAA-TTCATTT
1 AAACTTCATTT
36031 TCCTTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 18 0.55
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.41
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:36069 original size:26 final size:26
Alignment explanation
Indices: 36040--36107 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
36030 TTCCTTCATT
*
36040 TTAATCATAAACTAATTAAATATTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
36066 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
36092 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
36108 AAACTAAGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Done.