Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006181.1 Corchorus capsularis cultivar CVL-1 contig06199, 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: 46096
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:5349 original size:23 final size:23
Alignment explanation
Indices: 5295--5349 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
5285 AGGTACGAGT
*
5295 GACCGGCCATGCGACTTGGAGAA
1 GACCGGCCATGCGACTCGGAGAA
* *
5318 GACCAGCCATGCGACTCGGAGAT
1 GACCGGCCATGCGACTCGGAGAA
*
5341 GCCCGGCCA
1 GACCGGCCA
5350 CCACCGGCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.33, G:0.33, T:0.11
Consensus pattern (23 bp):
GACCGGCCATGCGACTCGGAGAA
Found at i:9084 original size:22 final size:22
Alignment explanation
Indices: 9056--9109 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
9046 ATCGCAAACC
9056 CTAATTTGAACCCTTAAGAACA
1 CTAATTTGAACCCTTAAGAACA
*
9078 CTAATTTGAACCCTTAAGAACC
1 CTAATTTGAACCCTTAAGAACA
9100 CTAATTTGAA
1 CTAATTTGAA
9110 TTTTGATGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (22 bp):
CTAATTTGAACCCTTAAGAACA
Found at i:13031 original size:28 final size:28
Alignment explanation
Indices: 13000--13068 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
12990 TGACAGGTTC
*
13000 AGCGCGTCCGTACAGCGTTGAT-ATTTTT
1 AGCGCGTCCGTACAACGTTGATGA-TTTT
13028 AGCGCGTCCGTACAACGTTGATGATTTT
1 AGCGCGTCCGTACAACGTTGATGATTTT
13056 AGCGCGTCCGTAC
1 AGCGCGTCCGTAC
13069 TGTTTGTCGT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 38 0.97
29 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (28 bp):
AGCGCGTCCGTACAACGTTGATGATTTT
Found at i:14936 original size:22 final size:22
Alignment explanation
Indices: 14881--14937 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
14871 AATTGTTACA
* *
14881 AAATTGATTGTAAAATAATTCC
1 AAATTGATGGTGAAATAATTCC
14903 AAATTGATGGTGAAATAATTCC
1 AAATTGATGGTGAAATAATTCC
14925 AAATTGATGGTGA
1 AAATTGATGGTGA
14938 CCGATTTGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (22 bp):
AAATTGATGGTGAAATAATTCC
Found at i:18499 original size:2 final size:2
Alignment explanation
Indices: 18492--18520 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18482 AGTAACTAAT
18492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18521 CCTATTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24350 original size:30 final size:31
Alignment explanation
Indices: 24314--24404 Score: 123
Period size: 30 Copynumber: 2.9 Consensus size: 31
24304 ATCCATTGGT
*
24314 CGGTTGTGCG-TGGATGCTCCATCCGATGGC
1 CGGTTGTGCGCTGGATGCTCCATGCGATGGC
*
24344 CGGTTGTGGCCGCTTGATGCTCCATGCGATGGC
1 CGGTTGT-G-CGCTGGATGCTCCATGCGATGGC
*
24377 CGGTTGTG-GCTGGTTGCTCCATGCGATG
1 CGGTTGTGCGCTGGATGCTCCATGCGATG
24405 TCGCATGCGA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
30 25 0.46
31 1 0.02
32 3 0.06
33 25 0.46
ACGTcount: A:0.09, C:0.25, G:0.37, T:0.29
Consensus pattern (31 bp):
CGGTTGTGCGCTGGATGCTCCATGCGATGGC
Found at i:25233 original size:33 final size:33
Alignment explanation
Indices: 25187--25253 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
25177 TGGCTGCAAA
25187 GTTTGAATCTTCTTAGTGTTCATAA-TAGTTCAT
1 GTTTGAATCTTCTTAGTGTTCATAATTA-TTCAT
*
25220 GTTTGAATGTTCTTAGTGTTCATAATTATTCAT
1 GTTTGAATCTTCTTAGTGTTCATAATTATTCAT
25253 G
1 G
25254 ATAAACTAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.49
Consensus pattern (33 bp):
GTTTGAATCTTCTTAGTGTTCATAATTATTCAT
Found at i:27752 original size:22 final size:22
Alignment explanation
Indices: 27686--27756 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
27676 CACTTGACCA
* *
27686 GCCACACCGGCTACATGACCCT
1 GCCACACCGGCCACATGACCCG
** * *
27708 GCCATGCCGATCGCACAAG-CCCG
1 GCCACACCG-GC-CACATGACCCG
27731 GCCACACCGGCCACATGACCCG
1 GCCACACCGGCCACATGACCCG
27753 GCCA
1 GCCA
27757 TGCGATCCTT
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
21 5 0.14
22 16 0.44
23 11 0.31
24 4 0.11
ACGTcount: A:0.23, C:0.46, G:0.23, T:0.08
Consensus pattern (22 bp):
GCCACACCGGCCACATGACCCG
Found at i:33177 original size:33 final size:33
Alignment explanation
Indices: 33139--33203 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
33129 CCGAATCATG
* * *
33139 TGGCCGGGCATGTCCATGTCGCGTGGCCGGTGA
1 TGGCCGGGCATCTCCAAGTCGCGTGGCAGGTGA
33172 TGGCCGGGCATCTCCAAGTCGCGTGGCAGGTG
1 TGGCCGGGCATCTCCAAGTCGCGTGGCAGGTG
33204 TTGCGCGGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.11, C:0.28, G:0.42, T:0.20
Consensus pattern (33 bp):
TGGCCGGGCATCTCCAAGTCGCGTGGCAGGTGA
Found at i:35302 original size:33 final size:32
Alignment explanation
Indices: 35232--35339 Score: 119
Period size: 33 Copynumber: 3.3 Consensus size: 32
35222 AAAGGATCAT
* * **
35232 GTGGCCGGTTGTGGCCGGGCATGGCCGAATCAT
1 GTGGCCGGTTGTGGCCGGGCATGTCC-AGTCGC
*
35265 GTGGCCGGTTGTGTCCGGGCATGTCCATGTCGC
1 GTGGCCGGTTGTGGCCGGGCATGTCCA-GTCGC
*
35298 GTGGCCGG-TGATGGCCGGGCATCTCCAAGTCGC
1 GTGGCCGGTTG-TGGCCGGGCATGTCC-AGTCGC
35331 GTGGCCGGT
1 GTGGCCGGT
35340 GTTGCGTGCC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
32 3 0.05
33 60 0.94
34 1 0.02
ACGTcount: A:0.09, C:0.27, G:0.42, T:0.22
Consensus pattern (32 bp):
GTGGCCGGTTGTGGCCGGGCATGTCCAGTCGC
Found at i:45050 original size:5 final size:5
Alignment explanation
Indices: 45033--45068 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
45023 GTTATATCGA
45033 AAAAT ATAAAT AAAAT AAAAT AAAAT AAAA- AAAAT A
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
45069 TTTCAACCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 20 0.69
6 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Done.