Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011092.1 Corchorus capsularis cultivar CVL-1 contig11113, 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: 48004
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:555 original size:33 final size:31
Alignment explanation
Indices: 484--623 Score: 104
Period size: 31 Copynumber: 4.5 Consensus size: 31
474 TCCTTTTGTG
** * * **
484 CACGTGGCATGCCACGTGCCATTTTTTGAAA
1 CACGTGGCATGCCATATGTCACTTTTTGGTA
*
515 CATGTGGCATATGCCACT-TGTCACTTTTTGGTA
1 CACGTGGC--ATGCCA-TATGTCACTTTTTGGTA
** *
548 CACGTGGCGA-GATATGTGTCACTTTTTGGTA
1 CACGTGGC-ATGCCATATGTCACTTTTTGGTA
* * *
579 CATGTGGCGTGTCATATGTCACTTTTTGGTA
1 CACGTGGCATGCCATATGTCACTTTTTGGTA
*
610 CACGTGGCGTGCCA
1 CACGTGGCATGCCA
624 CGTCGGACAC
Statistics
Matches: 87, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
30 1 0.01
31 61 0.70
32 1 0.01
33 24 0.28
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (31 bp):
CACGTGGCATGCCATATGTCACTTTTTGGTA
Found at i:619 original size:31 final size:31
Alignment explanation
Indices: 533--620 Score: 133
Period size: 31 Copynumber: 2.8 Consensus size: 31
523 ATATGCCACT
* *
533 TGTCACTTTTTGGTACACGTGGCGAGATATG
1 TGTCACTTTTTGGTACACGTGGCGTGATATA
*
564 TGTCACTTTTTGGTACATGTGGCGTG-TCATA
1 TGTCACTTTTTGGTACACGTGGCGTGAT-ATA
595 TGTCACTTTTTGGTACACGTGGCGTG
1 TGTCACTTTTTGGTACACGTGGCGTG
621 CCACGTCGGA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
30 1 0.02
31 51 0.98
ACGTcount: A:0.16, C:0.17, G:0.28, T:0.39
Consensus pattern (31 bp):
TGTCACTTTTTGGTACACGTGGCGTGATATA
Found at i:3500 original size:29 final size:29
Alignment explanation
Indices: 3460--3558 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
3450 CCAAAATGCT
3460 CAAATAAGGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTGATCTTTTAATTTGGC
* * * ** **
3489 CAAATAAGGGCCTAATGTTATCGAAAATGTT
1 CAAATAAGGGCCTGATCTT-T-TAATTTGGC
* *
3520 CAAATAAGAGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTGATCTTTTAATTTGGC
3549 CAAATAAGGG
1 CAAATAAGGG
3559 TCTAACGTTA
Statistics
Matches: 51, Mismatches: 17, Indels: 4
0.71 0.24 0.06
Matches are distributed among these distances:
29 30 0.59
30 2 0.04
31 19 0.37
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (29 bp):
CAAATAAGGGCCTGATCTTTTAATTTGGC
Found at i:3523 original size:60 final size:60
Alignment explanation
Indices: 3430--3588 Score: 239
Period size: 60 Copynumber: 2.6 Consensus size: 60
3420 CTAATTACTT
*
3430 AAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGCC
1 AAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGCC
* * * *
3490 AAATAAGGGCCTAATGTTATCGAAAATGTTCAAATAAGAGTCTGATCTTTTAATTTGGCC
1 AAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGCC
* *
3550 AAATAAGGGTCTAACGTTATTGAAAATGCTCAAATAAGG
1 AAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGG
3589 ATCTAACGTT
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
60 87 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (60 bp):
AAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGCC
Found at i:3527 original size:31 final size:31
Alignment explanation
Indices: 3489--3620 Score: 128
Period size: 31 Copynumber: 4.3 Consensus size: 31
3479 TTAATTTGGC
* * *
3489 CAAATAAGGGCCTAATGTTATCGAAAATGTT
1 CAAATAAGGGTCTAACGTTATCGAAAATGCT
* * * **
3520 CAAATAAGAGTCTGATC-TT-T-TAATTTGGC-
1 CAAATAAGGGTCT-AACGTTATCGAAAAT-GCT
*
3549 CAAATAAGGGTCTAACGTTATTGAAAATGCT
1 CAAATAAGGGTCTAACGTTATCGAAAATGCT
*
3580 CAAATAAGGATCTAACGTTATCGAAAATGCT
1 CAAATAAGGGTCTAACGTTATCGAAAATGCT
3611 CAAATAAGGG
1 CAAATAAGGG
3621 CCTGGTTTCA
Statistics
Matches: 79, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
28 2 0.03
29 17 0.22
30 5 0.06
31 54 0.68
32 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (31 bp):
CAAATAAGGGTCTAACGTTATCGAAAATGCT
Found at i:3685 original size:31 final size:30
Alignment explanation
Indices: 3650--3818 Score: 143
Period size: 31 Copynumber: 5.6 Consensus size: 30
3640 ACGTATGAGA
*
3650 TAGGCCTTTATTTGAGCATTTTGGCAAATGT
1 TAGGCCCTTATTTGAGCATTTTGGCAAA-GT
** *
3681 TAGGCCCTTATTTG-GCCAAATT--CAAAGA
1 TAGGCCCTTATTTGAG-CATTTTGGCAAAGT
*
3709 TCGGACCCTTATTTGAGCATTTTGGCAAACGT
1 TAGG-CCCTTATTTGAGCATTTTGGCAAA-GT
** *
3741 TAGGCCCTTATTTG-GCCAAATT--CAAAGA
1 TAGGCCCTTATTTGAG-CATTTTGGCAAAGT
*
3769 TCGGACCCTTATTTGAGCATTTTGGCAAACGT
1 TAGG-CCCTTATTTGAGCATTTTGGCAAA-GT
*
3801 TAGGCCCTTATTTAAGCA
1 TAGGCCCTTATTTGAGCA
3819 ATTAGCCATG
Statistics
Matches: 108, Mismatches: 18, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
28 8 0.07
29 36 0.33
30 4 0.04
31 52 0.48
32 8 0.07
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (30 bp):
TAGGCCCTTATTTGAGCATTTTGGCAAAGT
Found at i:3717 original size:29 final size:29
Alignment explanation
Indices: 3685--3783 Score: 112
Period size: 29 Copynumber: 3.3 Consensus size: 29
3675 AAATGTTAGG
3685 CCCTTATTTGGCCAAATTCAAAGATCGGA
1 CCCTTATTTGGCCAAATTCAAAGATCGGA
** * *
3714 CCCTTATTTGAG-CATTTTGGCAAACGTTAGG-
1 CCCTTATTTG-GCCAAATT--CAAA-GATCGGA
3745 CCCTTATTTGGCCAAATTCAAAGATCGGA
1 CCCTTATTTGGCCAAATTCAAAGATCGGA
3774 CCCTTATTTG
1 CCCTTATTTG
3784 AGCATTTTGG
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
28 4 0.07
29 28 0.50
30 2 0.04
31 18 0.32
32 4 0.07
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTCAAAGATCGGA
Found at i:3725 original size:60 final size:60
Alignment explanation
Indices: 3657--3813 Score: 305
Period size: 60 Copynumber: 2.6 Consensus size: 60
3647 AGATAGGCCT
*
3657 TTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTCAAAGATCGGACCC
1 TTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATCGGACCC
3717 TTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATCGGACCC
1 TTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATCGGACCC
3777 TTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTT
1 TTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTT
3814 AAGCAATTAG
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 96 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (60 bp):
TTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATCGGACCC
Found at i:23390 original size:1 final size:1
Alignment explanation
Indices: 23384--23420 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
23374 CTAGAGGTAG
23384 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23421 GATCTCACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:27936 original size:147 final size:143
Alignment explanation
Indices: 27607--27903 Score: 472
Period size: 147 Copynumber: 2.1 Consensus size: 143
27597 GAATCTCATT
** *
27607 ATCAGAATCGGACGAGTTGTCTTGGAGCGCAGCTTCTTTTCTAGCCGTTCTGGCGGATTGATGGC
1 ATCAGAATCGGACGAGCCGTCTTGGAGCGCAGCTTCTTTTCTAGCCGTTCCGGCGGATTGATGGC
* * *
27672 TGGTTTCATCGGCAATGGAATGATGGCTAGTTTCATCGGCGTTGCCACCTCCATCGCCACCGGAA
66 TGGTTTCATCGGCAATGGAATGATGGCTAGCTTCATCGGCATCGCCA---CCA-CGCCACCGGAA
27737 TCATTATCATCGTCACC
127 TCATTATCATCGTCACC
27754 ATCAGAATCGGACGAGCCGTCTTGGAGCGCAGCTTCTTTTCTAGCCGTTCCGGCGGATTGATGGC
1 ATCAGAATCGGACGAGCCGTCTTGGAGCGCAGCTTCTTTTCTAGCCGTTCCGGCGGATTGATGGC
*
27819 TGGTTTCATCGGCGATGGAATGATGGCTAGCTTCATCGGCATCGCCA-C-CGCCACCGGAATCAT
66 TGGTTTCATCGGCAATGGAATGATGGCTAGCTTCATCGGCATCGCCACCACGCCACCGGAATCAT
27882 TATCATCGTCACC
131 TATCATCGTCACC
*
27895 ATCCGAATC
1 ATCAGAATC
27904 ATTGTCATCG
Statistics
Matches: 142, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
141 36 0.25
143 1 0.01
147 105 0.74
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.27
Consensus pattern (143 bp):
ATCAGAATCGGACGAGCCGTCTTGGAGCGCAGCTTCTTTTCTAGCCGTTCCGGCGGATTGATGGC
TGGTTTCATCGGCAATGGAATGATGGCTAGCTTCATCGGCATCGCCACCACGCCACCGGAATCAT
TATCATCGTCACC
Found at i:28724 original size:28 final size:28
Alignment explanation
Indices: 28673--28726 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
28663 GCATTGGACA
*
28673 ATTTAATCATGGTCATAATGGATACAAT
1 ATTTAATCATGGTCAGAATGGATACAAT
28701 ATTTAATCATGGTCAGAA-GAGATACA
1 ATTTAATCATGGTCAGAATG-GATACA
28727 GTATCACTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (28 bp):
ATTTAATCATGGTCAGAATGGATACAAT
Found at i:28924 original size:2 final size:2
Alignment explanation
Indices: 28917--28947 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28907 GGTAAATTAC
28917 AT AT AT 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 AT AT AT A
28948 CCATGTGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35150 original size:2 final size:2
Alignment explanation
Indices: 35143--35170 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35133 TTAGGCTACC
35143 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
35171 TTCTGTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:42331 original size:1 final size:1
Alignment explanation
Indices: 42325--42353 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
42315 GGTTAATACC
42325 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
42354 CTCAAAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.