Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008477.1 Corchorus capsularis cultivar CVL-1 contig08498, 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: 34992
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:907 original size:16 final size:15
Alignment explanation
Indices: 870--926 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
860 CGTTCACATG
*
870 TCGGGTCATTTGGGT
1 TCGGGTCATTTTGGT
**
885 TTTGGTCAATTTTGGT
1 TCGGGTC-ATTTTGGT
*
901 TCGGGTCTTTTTCGGTT
1 TCGGGTCATTTT-GG-T
918 TCGGGTCAT
1 TCGGGTCAT
927 ATGCTTCTGA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 9 0.28
16 14 0.44
17 9 0.28
ACGTcount: A:0.07, C:0.14, G:0.32, T:0.47
Consensus pattern (15 bp):
TCGGGTCATTTTGGT
Found at i:18172 original size:37 final size:37
Alignment explanation
Indices: 18131--18202 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 37
18121 GACATAATTA
*
18131 TTCATAAAGTTATGTCTAT-TTAGAAAGACATGTATTG
1 TTCATAAAGTTATGTCTATATGA-AAAGACATGTATTG
18168 TTCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TTCATAAAGTTATGTCTATATGAAAAGACATGTAT
18203 GTTGATCAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
37 31 0.94
38 2 0.06
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (37 bp):
TTCATAAAGTTATGTCTATATGAAAAGACATGTATTG
Found at i:21821 original size:17 final size:17
Alignment explanation
Indices: 21799--21831 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21789 AGGCATATTG
21799 CTTGGTGGACAAGAATA
1 CTTGGTGGACAAGAATA
*
21816 CTTGGTGTACAAGAAT
1 CTTGGTGGACAAGAAT
21832 CCTAGTAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (17 bp):
CTTGGTGGACAAGAATA
Found at i:22632 original size:24 final size:25
Alignment explanation
Indices: 22594--22641 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
22584 AGTGAACAAC
*
22594 AAAATAAATAAACAAGA-AAATAAG
1 AAAATAAAGAAACAAGATAAATAAG
*
22618 AAAATAAAGAGACAAGATAAATAA
1 AAAATAAAGAAACAAGATAAATAA
22642 ATACTCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.73, C:0.04, G:0.10, T:0.12
Consensus pattern (25 bp):
AAAATAAAGAAACAAGATAAATAAG
Found at i:29410 original size:24 final size:24
Alignment explanation
Indices: 29378--29426 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
29368 GCCCTTTTTA
29378 AATAGTTGTTTGAACACAATAGCT
1 AATAGTTGTTTGAACACAATAGCT
* *
29402 AATATTTGTTTGAACAGAATAGCT
1 AATAGTTGTTTGAACACAATAGCT
29426 A
1 A
29427 TTGAAGGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (24 bp):
AATAGTTGTTTGAACACAATAGCT
Found at i:32125 original size:23 final size:24
Alignment explanation
Indices: 32085--32141 Score: 98
Period size: 23 Copynumber: 2.4 Consensus size: 24
32075 ACATATTGAA
32085 GAACATATTGAGGAGCACCATGGG
1 GAACATATTGAGGAGCACCATGGG
32109 GAACATATT-AGGAGCACCATGGG
1 GAACATATTGAGGAGCACCATGGG
*
32132 TAACATATTG
1 GAACATATTG
32142 TTGAATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 22 0.71
24 9 0.29
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (24 bp):
GAACATATTGAGGAGCACCATGGG
Found at i:32188 original size:30 final size:33
Alignment explanation
Indices: 32113--32191 Score: 110
Period size: 36 Copynumber: 2.4 Consensus size: 33
32103 CATGGGGAAC
32113 ATATTAGGAGCACCATGGGTAACATATTGTTGAAT
1 ATATTAGGAGCACCATGGGTAACATA-T-TTGAAT
32148 ATATTGAGGAGCACCATGGGTAACATA-TTG-AT
1 ATATT-AGGAGCACCATGGGTAACATATTTGAAT
32180 AT-TTAGGAGCAC
1 ATATTAGGAGCAC
32192 AACCGGAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
30 8 0.19
31 2 0.05
32 4 0.09
33 3 0.07
35 5 0.12
36 21 0.49
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (33 bp):
ATATTAGGAGCACCATGGGTAACATATTTGAAT
Found at i:32266 original size:22 final size:21
Alignment explanation
Indices: 32235--32278 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
32225 GAATCGTGAC
*
32235 CTAACGTAGAAAGATGAGAAAA
1 CTAACCTAGAAAGATGA-AAAA
*
32257 CTAACCTAGAATGATGAAAAA
1 CTAACCTAGAAAGATGAAAAA
32278 C
1 C
32279 AAAGATAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.52, C:0.14, G:0.18, T:0.16
Consensus pattern (21 bp):
CTAACCTAGAAAGATGAAAAA
Found at i:33109 original size:8 final size:7
Alignment explanation
Indices: 33091--33120 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
33081 TCAAAGGGCC
33091 TTTTTCA
1 TTTTTCA
33098 TTTTTCA
1 TTTTTCA
33105 TTTTTCA
1 TTTTTCA
33112 TTTTCTCA
1 TTTT-TCA
33120 T
1 T
33121 AAACTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTTCA
Found at i:34964 original size:2 final size:2
Alignment explanation
Indices: 34957--34992 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
34947 ACAGCTAATC
34957 AT AT AT AT AT AT 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 AT AT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.