Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005638.1 Corchorus capsularis cultivar CVL-1 contig05656, 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: 5681
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Found at i:611 original size:23 final size:22
Alignment explanation
Indices: 585--627 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
575 TTTTTTTGTT
*
585 TTATCTATTTACTATTTATTTTC
1 TTATCTATTTA-TAATTATTTTC
608 TTATCTATTTATAATTATTT
1 TTATCTATTTATAATTATTT
628 ATTATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATCTATTTATAATTATTTTC
Found at i:642 original size:27 final size:28
Alignment explanation
Indices: 597--659 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 28
587 ATCTATTTAC
*
597 TATTTATTTTCTTATCTATTTA-TA-AT
1 TATTTATTTTATTATCTATTTAGTACAT
623 TATTTATTATTATTATCTATTTAGTACTAT
1 TATTTATT-TTATTATCTATTTAGTAC-AT
653 TATTTAT
1 TATTTAT
660 CTATCTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 8 0.25
27 13 0.41
28 2 0.06
30 9 0.28
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (28 bp):
TATTTATTTTATTATCTATTTAGTACAT
Found at i:3231 original size:15 final size:15
Alignment explanation
Indices: 3211--3239 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3201 GGCATTATCT
3211 TTTATGAGTTTGGGG
1 TTTATGAGTTTGGGG
3226 TTTATGAGTTTGGG
1 TTTATGAGTTTGGG
3240 CTTGTAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.38, T:0.48
Consensus pattern (15 bp):
TTTATGAGTTTGGGG
Found at i:3850 original size:16 final size:16
Alignment explanation
Indices: 3788--3852 Score: 69
Period size: 16 Copynumber: 4.1 Consensus size: 16
3778 GGTAATCAAG
*
3788 AGAAGTAATCAATAAA
1 AGAAGTAATCAGTAAA
*
3804 GGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
** * *
3820 AGGGGCAA-AAGTAAA
1 AGAAGTAATCAGTAAA
3835 AGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
3851 AG
1 AG
3853 TAAAAGAACA
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
15 11 0.30
16 26 0.70
ACGTcount: A:0.55, C:0.06, G:0.23, T:0.15
Consensus pattern (16 bp):
AGAAGTAATCAGTAAA
Found at i:3867 original size:14 final size:14
Alignment explanation
Indices: 3848--3874 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3838 AGTAATCAGT
3848 AAAAGTAAAAGAAC
1 AAAAGTAAAAGAAC
3862 AAAAGTAAAAGAA
1 AAAAGTAAAAGAA
3875 GTGATCAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.15, T:0.07
Consensus pattern (14 bp):
AAAAGTAAAAGAAC
Found at i:3871 original size:36 final size:38
Alignment explanation
Indices: 3825--3926 Score: 136
Period size: 40 Copynumber: 2.7 Consensus size: 38
3815 GTAAAAGGGG
3825 CAAAAGTAAAAGAAGTAATCAGTAAAA-GTAA-AAGAA
1 CAAAAGTAAAAGAAGTAATCAGTAAAAGGTAATAAGAA
* * *
3861 CAAAAGTAAAAGAAGTGATCAATAAAATGGTAATTAAGAG
1 CAAAAGTAAAAGAAGTAATCAGTAAAA-GGTAA-TAAGAA
*
3901 TAAAAGTAAAAGAAGTAATCAGTAAA
1 CAAAAGTAAAAGAAGTAATCAGTAAA
3927 TCGGTAAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
36 25 0.45
38 4 0.07
40 27 0.48
ACGTcount: A:0.60, C:0.05, G:0.18, T:0.18
Consensus pattern (38 bp):
CAAAAGTAAAAGAAGTAATCAGTAAAAGGTAATAAGAA
Found at i:4075 original size:29 final size:28
Alignment explanation
Indices: 4020--4080 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
4010 AGGGTAAAAT
4020 AGTAATCAGTAAAGAGGAAAAAGCAAAG
1 AGTAATCAGTAAAGAGGAAAAAGCAAAG
* *
4048 AGTAATCAGTGAA-AGTAAAAATGGCAAAG
1 AGTAATCAGTAAAGAGGAAAAA--GCAAAG
4077 AGTA
1 AGTA
4081 GTAAAAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 7 0.24
28 12 0.41
29 10 0.34
ACGTcount: A:0.54, C:0.07, G:0.25, T:0.15
Consensus pattern (28 bp):
AGTAATCAGTAAAGAGGAAAAAGCAAAG
Found at i:4144 original size:21 final size:21
Alignment explanation
Indices: 4118--4175 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
4108 AGTAAAAGGT
4118 AATCAGTAAGAGTAAAATAGC
1 AATCAGTAAGAGTAAAATAGC
* * *
4139 AATCAGTAAGAGCAAAATGGT
1 AATCAGTAAGAGTAAAATAGC
*
4160 AATTAGTAAGGAGTAA
1 AATCAGTAA-GAGTAA
4176 TCAGTAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 26 0.84
22 5 0.16
ACGTcount: A:0.50, C:0.07, G:0.22, T:0.21
Consensus pattern (21 bp):
AATCAGTAAGAGTAAAATAGC
Found at i:4300 original size:27 final size:27
Alignment explanation
Indices: 4255--4314 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
4245 GGTAACAAGT
4255 GGTAATCAATAAAAGAGAGTAAGGAAAA
1 GGTAATCAATAAAAGAGAGTAA-GAAAA
* *
4283 GGTAATTAGTAAAA-AGAGTAAGAAAA
1 GGTAATCAATAAAAGAGAGTAAGAAAA
4309 GAGTAA
1 G-GTAA
4315 AAATGATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 6 0.21
27 11 0.38
28 12 0.41
ACGTcount: A:0.57, C:0.02, G:0.25, T:0.17
Consensus pattern (27 bp):
GGTAATCAATAAAAGAGAGTAAGAAAA
Found at i:5542 original size:3 final size:3
Alignment explanation
Indices: 5534--5585 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
5524 AACAGTCTGC
* *
5534 GAA GAA GAA GAG GAA G-A GTAA GAG GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA
5579 GAA GAA G
1 GAA GAA G
5586 GAGGAGGATG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (3 bp):
GAA
Done.