Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014607.1 Corchorus capsularis cultivar CVL-1 contig14628, 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: 22414
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3510 original size:41 final size:40
Alignment explanation
Indices: 3426--3510 Score: 91
Period size: 41 Copynumber: 2.1 Consensus size: 40
3416 ATTTGATTTT
* * *
3426 ATTTGATTCAAGGGTCGAATGACTTAGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCGAACGACTTAGTCTTGAATTGAGA
* * *
3466 ATTTAATTCAAGGGTCGTGACGACTT-GATCTTGACTTGGGA
1 ATTTAATTCAAGGGTCG-AACGACTTAG-TCTTGAATTGAGA
3507 ATTT
1 ATTT
3511 GATTTGATTC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
40 17 0.46
41 20 0.54
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.38
Consensus pattern (40 bp):
ATTTAATTCAAGGGTCGAACGACTTAGTCTTGAATTGAGA
Found at i:3778 original size:68 final size:68
Alignment explanation
Indices: 3695--3821 Score: 218
Period size: 68 Copynumber: 1.9 Consensus size: 68
3685 GAAGAAGATC
* * *
3695 CTCCACATACGTGGATCTTCTTTCAATAATTTCCCAATAACTGGGTCTTCAGTAATTCTGCAAGA
1 CTCCACATACATGGATCTTCTTTCAATAACTCCCCAATAACTGGGTCTTCAGTAATTCTGCAAGA
3760 ATA
66 ATA
*
3763 CTCCACCTACATGGATCTTCTTTCAATAACTCCCCAATAACTGGGTCTTCAGTAATTCT
1 CTCCACATACATGGATCTTCTTTCAATAACTCCCCAATAACTGGGTCTTCAGTAATTCT
3822 CCAATTGAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 55 1.00
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.34
Consensus pattern (68 bp):
CTCCACATACATGGATCTTCTTTCAATAACTCCCCAATAACTGGGTCTTCAGTAATTCTGCAAGA
ATA
Found at i:3943 original size:16 final size:16
Alignment explanation
Indices: 3922--3956 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
3912 ATCTGAAATA
3922 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
3938 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
3954 CTT
1 CTT
3957 TCTGAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:4783 original size:62 final size:63
Alignment explanation
Indices: 4706--4843 Score: 224
Period size: 64 Copynumber: 2.2 Consensus size: 63
4696 ACGTAGTTCA
4706 TTTTTTTTTTGTGCTCTAA-GTTGCCTAAGCCGTCCTTAGCAGGATTTTCAACTTAGCGAGCCC
1 TTTTTTTTTT-TGCTCTAACGTTGCCTAAGCCGTCCTTAGCAGGATTTTCAACTTAGCGAGCCC
* * *
4769 TTTTTTTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTCGCAGGATTTTCAACTTAGCGAGCCT
1 TTTTTTTTTTTGCTCTAAC-GTTGCCTAAGCCGTCCTTAGCAGGATTTTCAACTTAGCGAGCCC
4833 TTTTTTTTTTT
1 TTTTTTTTTTT
4844 TGGGTTGACT
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
62 8 0.11
63 10 0.14
64 52 0.74
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (63 bp):
TTTTTTTTTTTGCTCTAACGTTGCCTAAGCCGTCCTTAGCAGGATTTTCAACTTAGCGAGCCC
Found at i:6452 original size:2 final size:2
Alignment explanation
Indices: 6439--6470 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6429 TCTCAAGTAA
*
6439 AT AT AT AA 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
6471 TAAAACCACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12562 original size:2 final size:2
Alignment explanation
Indices: 12555--12583 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12545 TATTATCTAA
12555 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12584 TTTTAATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15339 original size:124 final size:122
Alignment explanation
Indices: 15098--15464 Score: 614
Period size: 124 Copynumber: 3.0 Consensus size: 122
15088 AAATACATGC
*
15098 TTTTTCCCTATATGATCATCATAATGAGCTAACTCATAACATTACTTGTCTAACTAACTCATATT
1 TTTTTCCCTATATGATCATCATAATGAGCTAACTCATAATATTACTTGTCTAACTAACTCATATT
* *
15163 ATTTGTTAGAGTTTTAAAAATATAACCTCTTCATCTAAAAGGCTACTCCTAACATCA
66 ATTTGTTAGAGTTTTAAAAATATAACATCTTCATCTAAAAGGCTATTCCTAACATCA
* * *
15220 TTTTTCCCTATATGGTCATCATAATAAGCTAACTCGTAATATTACTTGTCTAACTAACTCACATA
1 TTTTTCCCTATATGATCATCATAATGAGCTAACTCATAATATTACTTGTCTAACTAACT--CATA
15285 TTATTT-TTCAGAGTTTTAAAAATATAACATCTTCATCTAAAAGGCTATTCCTAACATCA
64 TTATTTGTT-AGAGTTTTAAAAATATAACATCTTCATCTAAAAGGCTATTCCTAACATCA
*
15344 TTTTTCCCTATATGATCATCATAATGAGCTAACTCATAATAGTACTTGTCTAACTAACT--TATT
1 TTTTTCCCTATATGATCATCATAATGAGCTAACTCATAATATTACTTGTCTAACTAACTCATATT
15407 ATTTGTTAGAGTTTTAAAAAATATAACATCTTCATCTAAAAGGCTATTCCTAACATCA
66 ATTTGTTAGAGTTTT-AAAAATATAACATCTTCATCTAAAAGGCTATTCCTAACATCA
15465 ATTATAATTT
Statistics
Matches: 230, Mismatches: 10, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
120 16 0.07
121 44 0.19
122 55 0.24
123 2 0.01
124 113 0.49
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (122 bp):
TTTTTCCCTATATGATCATCATAATGAGCTAACTCATAATATTACTTGTCTAACTAACTCATATT
ATTTGTTAGAGTTTTAAAAATATAACATCTTCATCTAAAAGGCTATTCCTAACATCA
Done.