Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014634.1 Corchorus capsularis cultivar CVL-1 contig14655, 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: 43101
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:567 original size:16 final size:16
Alignment explanation
Indices: 546--576 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
536 AAAAATGTTG
546 TATATATATATATAAT
1 TATATATATATATAAT
562 TATATATATATATAA
1 TATATATATATATAA
577 AGTTTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATATATATATAAT
Found at i:1184 original size:17 final size:17
Alignment explanation
Indices: 1162--1197 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1152 TATAATAAAC
1162 AAAACATTTAGAAAATT
1 AAAACATTTAGAAAATT
1179 AAAACATTTAGAAAATT
1 AAAACATTTAGAAAATT
1196 AA
1 AA
1198 CTATTGACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (17 bp):
AAAACATTTAGAAAATT
Found at i:12069 original size:20 final size:22
Alignment explanation
Indices: 12039--12100 Score: 74
Period size: 20 Copynumber: 2.9 Consensus size: 22
12029 AAAAATAATT
12039 TATTATATATATCATAAATATA
1 TATTATATATATCATAAATATA
** *
12061 -ATT-TATATATTTTACATATA
1 TATTATATATATCATAAATATA
*
12081 TTTTATATATATCATAAATA
1 TATTATATATATCATAAATA
12101 ATTAAATATA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 14 0.45
21 5 0.16
22 12 0.39
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
TATTATATATATCATAAATATA
Found at i:22219 original size:20 final size:20
Alignment explanation
Indices: 22194--22235 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
22184 TTTATTGGTA
22194 AGACTGTCAATGGACCCTTC
1 AGACTGTCAATGGACCCTTC
*
22214 AGACTGTCAATGGACCTTTC
1 AGACTGTCAATGGACCCTTC
22234 AG
1 AG
22236 TTGCATTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
AGACTGTCAATGGACCCTTC
Found at i:30779 original size:60 final size:60
Alignment explanation
Indices: 30713--30908 Score: 295
Period size: 60 Copynumber: 3.3 Consensus size: 60
30703 TTTGTCAAAT
* * **
30713 TGCTCAAATAAGGGTCTGATCTTTTAATTTGGCCAAATAAAGGCCTAACGCTATCGAAAA
1 TGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAAGGCCTAACATTATCGAAAA
* *
30773 TGCTCAAATAAGGACCCGGTCTTTTAATTTGGCCAAAT-AAGGACCTAACATTATCGAAAA
1 TGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAAGG-CCTAACATTATCGAAAA
* * *
30833 TGCTCAAATAAGAGCCCGATCTTTTAATTTAGCCAAATAAGGGCCTAACATTATCGAAAA
1 TGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAAGGCCTAACATTATCGAAAA
30893 TGCTCAAATAAGGGCC
1 TGCTCAAATAAGGGCC
30909 TAGTGTCAGT
Statistics
Matches: 122, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
59 4 0.03
60 115 0.94
61 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (60 bp):
TGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAAGGCCTAACATTATCGAAAA
Found at i:30844 original size:31 final size:31
Alignment explanation
Indices: 30806--30910 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 31
30796 TTAATTTGGC
*
30806 CAAATAAGGACCTAACATTATCGAAAATGCT
1 CAAATAAGGGCCTAACATTATCGAAAATGCT
* * * * **
30837 CAAATAAGAGCCCGATC-TT-T-TAATTTAGC-
1 CAAATAAG-GGCCTAACATTATCGAAAAT-GCT
30866 CAAATAAGGGCCTAACATTATCGAAAATGCT
1 CAAATAAGGGCCTAACATTATCGAAAATGCT
30897 CAAATAAGGGCCTA
1 CAAATAAGGGCCTA
30911 GTGTCAGTTT
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
28 5 0.09
29 13 0.23
30 6 0.11
31 27 0.48
32 5 0.09
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (31 bp):
CAAATAAGGGCCTAACATTATCGAAAATGCT
Found at i:30976 original size:31 final size:29
Alignment explanation
Indices: 30941--31039 Score: 94
Period size: 31 Copynumber: 3.3 Consensus size: 29
30931 TGAGACAAGT
30941 CCTTATTTGAGCATTTTGACAAACGTTAGGC
1 CCTTATTTGAGCATTTTG-CAAA-GTTAGGC
** * *
30972 CCTTATTTG-GCCAAATT-CAAAGATCGAGC
1 CCTTATTTGAG-CATTTTGCAAAGTTAG-GC
31001 CCTTATTTGAGCATTTTGGCAAATGTTAGGC
1 CCTTATTTGAGCATTTT-GCAAA-GTTAGGC
31032 CCTTATTT
1 CCTTATTT
31040 AACCAAATTA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
28 3 0.06
29 19 0.35
30 2 0.04
31 27 0.50
32 3 0.06
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (29 bp):
CCTTATTTGAGCATTTTGCAAAGTTAGGC
Found at i:31014 original size:60 final size:60
Alignment explanation
Indices: 30941--31101 Score: 207
Period size: 60 Copynumber: 2.7 Consensus size: 60
30931 TGAGACAAGT
* * *
30941 CCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATCGA-GC
1 CCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATC-ATAC
* * *
31001 CCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTAACCAAATTAAAAGATCATAC
1 CCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCATAC
* * * * *
31061 TCTTATTTAAACATTTTGTCAAACGTTAGGTCCTTATTTGA
1 CCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGA
31102 ACAATTAGCC
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
59 1 0.01
60 86 0.99
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCATAC
Done.