Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006230.1 Corchorus capsularis cultivar CVL-1 contig06249, 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: 17773
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1843 original size:15 final size:15
Alignment explanation
Indices: 1823--1859 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1813 TTTAAGTTGT
*
1823 TCATCTTCTTGTGGC
1 TCATCTTCTGGTGGC
1838 TCATCTTCTGGTGGC
1 TCATCTTCTGGTGGC
1853 TCATCTT
1 TCATCTT
1860 TTGGCTTAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.27, G:0.19, T:0.46
Consensus pattern (15 bp):
TCATCTTCTGGTGGC
Found at i:3326 original size:6 final size:6
Alignment explanation
Indices: 3310--3346 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
3300 CAAAGCAAAA
*
3310 TAAAT- TAAATC TAAATC TAAATC TAAATA TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TA
3347 TGGCAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:4711 original size:22 final size:21
Alignment explanation
Indices: 4681--4739 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
4671 AATTCTTGCT
* *
4681 TCTTGAAATAATTCTTCAATTG
1 TCTTCAAATAA-TCTTCAATTA
4703 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTC-AATTA
4722 TCTTCAAATAATCTTCAA
1 TCTTCAAATAATCTTCAA
4740 ACACGAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 1 0.03
21 3 0.10
22 11 0.35
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (21 bp):
TCTTCAAATAATCTTCAATTA
Found at i:4726 original size:11 final size:11
Alignment explanation
Indices: 4709--4740 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
4699 ATTGTCTTCA
4709 AATCTTCAAAT
1 AATCTTCAAAT
*
4720 TATCTTCAAAT
1 AATCTTCAAAT
4731 AATCTTCAAA
1 AATCTTCAAA
4741 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:4740 original size:22 final size:22
Alignment explanation
Indices: 4681--4740 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
4671 AATTCTTGCT
* *
4681 TCTTGAAATAATTCTTC-AATTG
1 TCTTCAAATAA-TCTTCAAATTA
4703 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTCAAATTA
4722 TCTTCAAATAATCTTCAAA
1 TCTTCAAATAATCTTCAAA
4741 CACGAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.16
19 11 0.34
20 1 0.03
21 1 0.03
22 14 0.44
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATTA
Found at i:5343 original size:31 final size:29
Alignment explanation
Indices: 5286--5351 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
5276 AAATCGCTCT
*
5286 GATCTTTTAATCTGCTGATACGTGCACCCTA
1 GATCTTTTAATCTGCTGACACGTGCA-CC-A
* *
5317 GATCTTTTAATCTGCTG-CGCTTTGCACCA
1 GATCTTTTAATCTGCTGACAC-GTGCACCA
5346 GATCTT
1 GATCTT
5352 GTTGTTTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 7 0.23
30 3 0.10
31 21 0.68
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.38
Consensus pattern (29 bp):
GATCTTTTAATCTGCTGACACGTGCACCA
Found at i:5434 original size:31 final size:31
Alignment explanation
Indices: 5396--5458 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
5386 TGATTGGCAC
*
5396 GCCCCTATGCTGTCATTAAGTAGTTTTCGCA
1 GCCCCTATGCTGTCATTAAGTAATTTTCGCA
* *
5427 GCCCCTATGTTGTCCTTAAGTAATTTTCGCA
1 GCCCCTATGCTGTCATTAAGTAATTTTCGCA
5458 G
1 G
5459 AAACTCTTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (31 bp):
GCCCCTATGCTGTCATTAAGTAATTTTCGCA
Found at i:10898 original size:42 final size:42
Alignment explanation
Indices: 10851--10932 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
10841 TATTGACACA
10851 TACCCCACCTGATAATTAACTATGTATTTAATATTCAAAACC
1 TACCCCACCTGATAATTAACTATGTATTTAATATTCAAAACC
* *
10893 TACCCCACCTGATTATTAAGTATGTATTTAATATTCAAAA
1 TACCCCACCTGATAATTAACTATGTATTTAATATTCAAAA
10933 TTAATATCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (42 bp):
TACCCCACCTGATAATTAACTATGTATTTAATATTCAAAACC
Found at i:12966 original size:42 final size:44
Alignment explanation
Indices: 12915--13008 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
12905 AGTGCATTAC
* *
12915 CTAA-ATTCTACT-C-CATCTCTAGGTAATACATCAAAATAAAG
1 CTAATATTCTACTCCTCATCTCTAGATAATACATCAAAATAAAA
*
12956 CTAATATTCTACTCCTTCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTACTCC-TCATCTCTAGATAATACATCAAAATAAAA
13001 CTAATATT
1 CTAATATT
13009 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
43 1 0.02
45 33 0.72
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.34
Consensus pattern (44 bp):
CTAATATTCTACTCCTCATCTCTAGATAATACATCAAAATAAAA
Found at i:13507 original size:15 final size:15
Alignment explanation
Indices: 13487--13524 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
13477 TTCAACTGAA
*
13487 GGAGGGGTGGGGTGG
1 GGAGGGGTGGGGTAG
13502 GGAGGGGTGGGGTAG
1 GGAGGGGTGGGGTAG
13517 GGAGGGGT
1 GGAGGGGT
13525 TTTAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.11, C:0.00, G:0.76, T:0.13
Consensus pattern (15 bp):
GGAGGGGTGGGGTAG
Found at i:13973 original size:19 final size:20
Alignment explanation
Indices: 13949--13997 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
13939 ATGGGAAAGA
13949 AATAAAAATATA-AATTATT
1 AATAAAAATATATAATTATT
13968 AATAAAAATA-ATAATTATT
1 AATAAAAATATATAATTATT
* *
13987 ATTATAAATAT
1 AATAAAAATAT
13998 TGTATCAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 25 0.96
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATAAAAATATATAATTATT
Done.