Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008911.1 Corchorus capsularis cultivar CVL-1 contig08932, 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: 20860
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:633 original size:13 final size:14
Alignment explanation
Indices: 599--635 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
589 ATATGGAAAG
599 TTCAAAAATCATCA
1 TTCAAAAATCATCA
613 TTCAAAAATCATCA
1 TTCAAAAATCATCA
627 TTCAAAAAT
1 TTCAAAAAT
636 TAATTATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (14 bp):
TTCAAAAATCATCA
Found at i:672 original size:24 final size:24
Alignment explanation
Indices: 645--722 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
635 TTAATTATCA
645 TATAATAATCAATAATCCAGAAAT
1 TATAATAATCAATAATCCAGAAAT
* * * *
669 TATAA-ATTTCAAAAAT-TA-ATTAT
1 TATAATA-ATCAATAATCCAGA-AAT
692 CATATAATAATCAATAATCCAGAAAT
1 --TATAATAATCAATAATCCAGAAAT
718 TATAA
1 TATAA
723 CAAAAATAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 14
0.64 0.13 0.23
Matches are distributed among these distances:
22 1 0.03
23 4 0.10
24 17 0.44
25 12 0.31
26 4 0.10
27 1 0.03
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (24 bp):
TATAATAATCAATAATCCAGAAAT
Found at i:684 original size:49 final size:49
Alignment explanation
Indices: 627--722 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
617 AAAATCATCA
627 TTCAAAAATTAATTATCATATAATAATCAATAATCCAGAAATTATAAAT
1 TTCAAAAATTAATTATCATATAATAATCAATAATCCAGAAATTATAAAT
676 TTCAAAAATTAATTATCATATAATAATCAATAATCCAGAAATTATAA
1 TTCAAAAATTAATTATCATATAATAATCAATAATCCAGAAATTATAA
723 CAAAAATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.34
Consensus pattern (49 bp):
TTCAAAAATTAATTATCATATAATAATCAATAATCCAGAAATTATAAAT
Found at i:2223 original size:66 final size:63
Alignment explanation
Indices: 2095--2219 Score: 162
Period size: 66 Copynumber: 2.0 Consensus size: 63
2085 TTAACTAAAA
* ** * *
2095 AGAGTAAATTTTAGTAAGGAATTTAGAAAAAGAGTCGAATCTTTAGATAAGAAATCCCTTGAT
1 AGAGTAAAATTTAAAAAGCAATTTAGAAAAAGAGTCGAACCTTTAGATAAGAAATCCCTTGAT
*
2158 AGAGTAAAATTTAAAAAGCAATTTAGAAATAGAAGAGTCGAACCTTTAGATAAGGAA-CCCTT
1 AGAGTAAAATTTAAAAAGCAATTTAG-AA-A-AAGAGTCGAACCTTTAGATAAGAAATCCCTT
2220 TGATCTGGGC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 22 0.42
64 2 0.04
65 6 0.11
66 23 0.43
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (63 bp):
AGAGTAAAATTTAAAAAGCAATTTAGAAAAAGAGTCGAACCTTTAGATAAGAAATCCCTTGAT
Found at i:2789 original size:22 final size:22
Alignment explanation
Indices: 2650--2789 Score: 126
Period size: 22 Copynumber: 6.4 Consensus size: 22
2640 AAATTGAGAC
2650 TTTT-ATAACCTTCA-TATGAAA
1 TTTTAATAACC-TCACTATGAAA
* * *
2671 TTTTGATAACCACACTATAAAA
1 TTTTAATAACCTCACTATGAAA
* *
2693 TTTTAATAACCTCCCCATGAAA
1 TTTTAATAACCTCACTATGAAA
* *
2715 TATTAGTAACCTC-CTAATGAAA
1 TTTTAATAACCTCACT-ATGAAA
** *
2737 TTTTGTTAACCACACTATGAAA
1 TTTTAATAACCTCACTATGAAA
*
2759 TTCTT-ATAACCTCACTATGACA
1 TT-TTAATAACCTCACTATGAAA
2781 TTTTAATAA
1 TTTTAATAA
2790 TCTCTTTGAT
Statistics
Matches: 96, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
21 9 0.09
22 83 0.86
23 4 0.04
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (22 bp):
TTTTAATAACCTCACTATGAAA
Found at i:2964 original size:22 final size:22
Alignment explanation
Indices: 2832--2964 Score: 117
Period size: 22 Copynumber: 6.0 Consensus size: 22
2822 AATCAATTAC
* *
2832 CCTATGAAATTTCAATAACCAA
1 CCTATGAAATTTTAATAACCAT
* *
2854 CCTAAGAAATTTTAATAACATGAT
1 CCTATGAAATTTTAATAAC--CAT
**
2878 CCTATGAAATTTTGGTAACCA-
1 CCTATGAAATTTTAATAACCAT
* *
2899 CACTATGGAATTTTGATAACC-T
1 C-CTATGAAATTTTAATAACCAT
*
2921 CCTCATGAAATTATAATAACCAT
1 CCT-ATGAAATTTTAATAACCAT
* *
2944 CTTATGAAATTTTGATAACCA
1 CCTATGAAATTTTAATAACCA
2965 CATAGAGACA
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
21 3 0.03
22 66 0.74
23 3 0.03
24 17 0.19
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (22 bp):
CCTATGAAATTTTAATAACCAT
Found at i:3150 original size:19 final size:20
Alignment explanation
Indices: 3128--3166 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3118 TTATTGACAT
3128 TTAAAA-ATTGAAATT-AAAA
1 TTAAAATATT-AAATTCAAAA
3147 TTAAAATATTAAATTCAAAA
1 TTAAAATATTAAATTCAAAA
3167 ACTAATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (20 bp):
TTAAAATATTAAATTCAAAA
Found at i:3545 original size:30 final size:31
Alignment explanation
Indices: 3511--3575 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
3501 TGGCAATTTA
* * *
3511 GAAATATGTTTTGAAAA-AAGGATACAATTG
1 GAAATATATTTTAAAAATAAGGATACAATCG
*
3541 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGGATACAATCG
3572 GAAA
1 GAAA
3576 ACATAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.28
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGATACAATCG
Found at i:3610 original size:2 final size:2
Alignment explanation
Indices: 3603--3627 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3593 ATTCGTACTT
3603 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3628 TTAAAATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4557 original size:33 final size:32
Alignment explanation
Indices: 4520--4626 Score: 108
Period size: 33 Copynumber: 3.2 Consensus size: 32
4510 CGCCAAGCGA
* *
4520 TGGCCGGTTG-TGGCCGGACATGTCCATGTCGCG
1 TGGCCGG-TGATGGCCGGGCATCTCCA-GTCGCG
*
4553 TGGCCGGTGATGGCCGGGCATCTCCGAGTCGTG
1 TGGCCGGTGATGGCCGGGCATCTCC-AGTCGCG
* * * *
4586 TGGCCAGTGTTGGCCGGGCTTCTCCAAGTCGCA
1 TGGCCGGTGATGGCCGGGCATCTCC-AGTCGCG
4619 TGGCCGGT
1 TGGCCGGT
4627 CACTCGCGCC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 2 0.03
33 59 0.95
34 1 0.02
ACGTcount: A:0.09, C:0.28, G:0.39, T:0.23
Consensus pattern (32 bp):
TGGCCGGTGATGGCCGGGCATCTCCAGTCGCG
Found at i:10634 original size:5 final size:5
Alignment explanation
Indices: 10624--10649 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
10614 TCATCTTTTG
10624 GTTGA GTTGA GTTGA GTTGA GTTGA G
1 GTTGA GTTGA GTTGA GTTGA GTTGA G
10650 GCTGGTTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.38
Consensus pattern (5 bp):
GTTGA
Found at i:18685 original size:2 final size:2
Alignment explanation
Indices: 18678--18702 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18668 AGATAGATAA
18678 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
18703 AGCTTAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18767 original size:7 final size:7
Alignment explanation
Indices: 18755--18781 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
18745 TTGCCCATCC
18755 ATTCATA
1 ATTCATA
18762 ATTCATA
1 ATTCATA
18769 ATTCATA
1 ATTCATA
18776 ATTCAT
1 ATTCAT
18782 TCAAAGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTCATA
Found at i:19187 original size:2 final size:2
Alignment explanation
Indices: 19180--19211 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
19170 TATTACAATC
19180 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19212 ACTATTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19438 original size:14 final size:14
Alignment explanation
Indices: 19419--19446 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19409 AATATCCTCT
19419 AAATTAGATCAAAC
1 AAATTAGATCAAAC
19433 AAATTAGATCAAAC
1 AAATTAGATCAAAC
19447 CCACTTACGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
AAATTAGATCAAAC
Done.