Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008476.1 Corchorus capsularis cultivar CVL-1 contig08497, 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: 13727
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Found at i:624 original size:31 final size:31
Alignment explanation
Indices: 560--634 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
550 GTCGGGTTGA
* * *
560 TCGGGTTCGGGTCAT-TTTGGGTTTGGGTCATT
1 TCGGGTTCGGGT--TGTTTGGATTCGGGTAATT
*
592 TCGGGTTTGGGTTGTTTGGATTCGGGTAATT
1 TCGGGTTCGGGTTGTTTGGATTCGGGTAATT
623 TCGGGTTCGGGT
1 TCGGGTTCGGGT
635 ACCCCAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 1 0.03
31 25 0.68
32 11 0.30
ACGTcount: A:0.07, C:0.11, G:0.40, T:0.43
Consensus pattern (31 bp):
TCGGGTTCGGGTTGTTTGGATTCGGGTAATT
Found at i:635 original size:16 final size:16
Alignment explanation
Indices: 560--635 Score: 73
Period size: 16 Copynumber: 4.8 Consensus size: 16
550 GTCGGGTTGA
*
560 TCGGGTTCGGGTCATT
1 TCGGGTTCGGGTAATT
* * *
576 TTGGGTTTGGGTCATT
1 TCGGGTTCGGGTAATT
* **
592 TCGGGTTTGGGTTGTT
1 TCGGGTTCGGGTAATT
*
608 T-GGATTCGGGTAATT
1 TCGGGTTCGGGTAATT
623 TCGGGTTCGGGTA
1 TCGGGTTCGGGTA
636 CCCCAAAAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
15 11 0.22
16 38 0.78
ACGTcount: A:0.08, C:0.11, G:0.39, T:0.42
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:7609 original size:6 final size:6
Alignment explanation
Indices: 7598--7622 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
7588 CAGGCTGAAC
7598 CACAAT CACAAT CACAAT CACAAT C
1 CACAAT CACAAT CACAAT CACAAT C
7623 TAGCCAACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:7679 original size:38 final size:38
Alignment explanation
Indices: 7626--8003 Score: 569
Period size: 38 Copynumber: 9.9 Consensus size: 38
7616 CACAATCTAG
* * *
7626 CCAACAG-TTAACCCCCTGAGGCACAGATCCACTTTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* *
7663 CCAACAGTTTAACCCCCTGAGACACAGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
7701 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAA-CAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
7740 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAA-CAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * *
7779 CCATCAGTTTAACCCCCTAAGGCACCGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
*
7817 CCATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
**
7855 CCAATCAGTTTAACCCCCTGAGAAACGGGTCCACTCTTA
1 CCAA-CAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
*
7894 CCAACAGTTTAACCCCCTGAGGCATGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * *
7932 CCATCAGTTTAACCCCCTGAGGCGCGGGTCCGCTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* *
7970 CCATCAGTTTAACCCCCTGAGGCGCGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
8004 ATGCACAGCC
Statistics
Matches: 317, Mismatches: 21, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
37 7 0.02
38 200 0.63
39 110 0.35
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:7726 original size:77 final size:77
Alignment explanation
Indices: 7626--8003 Score: 584
Period size: 77 Copynumber: 4.9 Consensus size: 77
7616 CACAATCTAG
* * * * *
7626 CCAA-CAG-TTAACCCCCTGAGGCACAGATCCACTTTTACCAACAGTTTAACCCCCTGAGACACA
1 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACG
7689 GGTCCACTCTTA
66 GGTCCACTCTTA
7701 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAATCAGTTTAACCCCCTGAGGCAC
1 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAA-CAGTTTAACCCCCTGAGGCAC
7766 GGGTCCACTCTTA
65 GGGTCCACTCTTA
* * *
7779 CC-ATCAGTTTAACCCCCTAAGGCACCGGTCCACTCTTACCATCAGTTTAACCCCCTGAGGCACG
1 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACG
7843 GGTCCACTCTTA
66 GGTCCACTCTTA
** *
7855 CCAATCAGTTTAACCCCCTGAGAAACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCATG
1 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACG
7920 GGTCCACTCTTA
66 GGTCCACTCTTA
* * * *
7932 CC-ATCAGTTTAACCCCCTGAGGCGCGGGTCCGCTCTTACCATCAGTTTAACCCCCTGAGGCGCG
1 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACG
7996 GGTCCACT
66 GGTCCACT
8004 ATGCACAGCC
Statistics
Matches: 278, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
75 4 0.01
76 102 0.37
77 138 0.50
78 34 0.12
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23
Consensus pattern (77 bp):
CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACG
GGTCCACTCTTA
Found at i:7859 original size:115 final size:115
Alignment explanation
Indices: 7626--8003 Score: 600
Period size: 115 Copynumber: 3.3 Consensus size: 115
7616 CACAATCTAG
* * * *
7626 CCAA-CAG-TTAACCCCCTGAGGCACAGATCCACTTTTACCAACAGTTTAACCCCCTGAGACACA
1 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACA
7689 GGTCCACTCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
66 GGTCCACTCTTACC-ATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * *
7740 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCATCAGTTTAACCCCCTAAGGCACC
1 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACA
7805 GGTCCACTCTTACCATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
66 GGTCCACTCTTACCATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
** **
7855 CCAATCAGTTTAACCCCCTGAGAAACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCATG
1 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACA
* *
7920 GGTCCACTCTTACCATCAGTTTAACCCCCTGAGGCGCGGGTCCGCTCTTA
66 GGTCCACTCTTACCATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
*
7970 CC-ATCAGTTTAACCCCCTGAGGCGCGGGTCCACT
1 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACT
8004 ATGCACAGCC
Statistics
Matches: 244, Mismatches: 18, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
114 33 0.14
115 148 0.61
116 63 0.26
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23
Consensus pattern (115 bp):
CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACA
GGTCCACTCTTACCATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:8137 original size:20 final size:20
Alignment explanation
Indices: 8112--8152 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
8102 CGATTTTACG
* *
8112 AAAACAACAATACTCTTTCA
1 AAAACAACAAAACACTTTCA
8132 AAAACAACAAAACACTTTCA
1 AAAACAACAAAACACTTTCA
8152 A
1 A
8153 TCATTTATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAACAACAAAACACTTTCA
Found at i:13491 original size:12 final size:13
Alignment explanation
Indices: 13462--13491 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13452 AGCACCAGAT
13462 GAAAAAAAAAAAC
1 GAAAAAAAAAAAC
13475 GAAAAAAAAAAAC
1 GAAAAAAAAAAAC
13488 -AAAA
1 GAAAA
13492 GATCCTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.87, C:0.07, G:0.07, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAAAAC
Done.