Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017155.1 Corchorus olitorius cultivar O-4 contig17188, 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: 20401
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:982 original size:19 final size:19
Alignment explanation
Indices: 962--998 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
952 AATTAATTAT
962 TTTA-ATATTATATTTTTA
1 TTTATATATTATATTTTTA
980 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
999 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:1009 original size:19 final size:19
Alignment explanation
Indices: 968--1009 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
958 TTATTTTAAT
* * *
968 ATTATATTTTTATTTATAT
1 ATTATATTTTTACTTAAAA
987 ATTATATTTTTACTTAAAA
1 ATTATATTTTTACTTAAAA
1006 ATTA
1 ATTA
1010 CTCCTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATATTTTTACTTAAAA
Found at i:1540 original size:16 final size:15
Alignment explanation
Indices: 1515--1573 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
1505 ATTTCCAAAA
* *
1515 TTCTTATTTTCTTTA
1 TTCTTTTTTTCTTTC
1530 TT-TCTTTTTT-TTTC
1 TTCT-TTTTTTCTTTC
1544 TTCTTTTTTTTCTTTC
1 TTC-TTTTTTTCTTTC
*
1560 TTCTTTTCTTCTTT
1 TTCTTTTTTTCTTT
1574 TGGGCCAGGC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 6 0.16
15 23 0.62
16 8 0.22
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (15 bp):
TTCTTTTTTTCTTTC
Found at i:1547 original size:13 final size:13
Alignment explanation
Indices: 1531--1574 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
1521 TTTTCTTTAT
1531 TTCTTTTTTTTTC
1 TTCTTTTTTTTTC
1544 TTC-TTTTTTTTC
1 TTCTTTTTTTTTC
* *
1556 TT-TCTTCTTTTC
1 TTCTTTTTTTTTC
1568 TTCTTTT
1 TTCTTTT
1575 GGGCCAGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTCTTTTTTTTTC
Found at i:1675 original size:18 final size:18
Alignment explanation
Indices: 1654--1752 Score: 53
Period size: 18 Copynumber: 5.2 Consensus size: 18
1644 TGCTAAGCCA
1654 GGCCGCTGGGCCTGCGCT
1 GGCCGCTGGGCCTGCGCT
**
1672 GGCCCGC-AAGCCTG-GCCT
1 GG-CCGCTGGGCCTGCG-CT
*
1690 GGCGCGCCTGGGCCTGCACT
1 GGC-CG-CTGGGCCTGCGCT
*
1710 GGCCCGC-GTGCCTG-GCCT
1 GG-CCGCTGGGCCTGCG-CT
1728 GGCACGCCTGGGCCTGCGCT
1 GGC-CG-CTGGGCCTGCGCT
1748 AGGCC
1 -GGCC
1753 CGCGTGCTTG
Statistics
Matches: 60, Mismatches: 8, Indels: 24
0.65 0.09 0.26
Matches are distributed among these distances:
17 3 0.05
18 25 0.42
19 7 0.12
20 20 0.33
21 5 0.08
ACGTcount: A:0.05, C:0.41, G:0.39, T:0.14
Consensus pattern (18 bp):
GGCCGCTGGGCCTGCGCT
Found at i:1702 original size:38 final size:38
Alignment explanation
Indices: 1659--1755 Score: 149
Period size: 38 Copynumber: 2.5 Consensus size: 38
1649 AGCCAGGCCG
*
1659 CTGGGCCTGCGCTGGCCCGCAAGCCTGGCCTGGCGCGC
1 CTGGGCCTGCGCTGGCCCGCAAGCCTGGCCTGGCACGC
* **
1697 CTGGGCCTGCACTGGCCCGCGTGCCTGGCCTGGCACGC
1 CTGGGCCTGCGCTGGCCCGCAAGCCTGGCCTGGCACGC
1735 CTGGGCCTGCGCTAGGCCCGC
1 CTGGGCCTGCGCT-GGCCCGC
1756 GTGCTTGGGC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 46 0.87
39 7 0.13
ACGTcount: A:0.05, C:0.42, G:0.38, T:0.14
Consensus pattern (38 bp):
CTGGGCCTGCGCTGGCCCGCAAGCCTGGCCTGGCACGC
Found at i:5001 original size:21 final size:21
Alignment explanation
Indices: 4977--5041 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
4967 AATTCTCTGT
4977 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
4998 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
5019 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
5040 AA
1 AA
5042 GTCATGATTC
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
20 6 0.20
21 18 0.60
22 6 0.20
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:5023 original size:42 final size:42
Alignment explanation
Indices: 4964--5046 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
4954 GCTAAGTCTT
4964 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
* *
5006 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAGTCAT
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCAT
5047 GATTCTTAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:5209 original size:55 final size:56
Alignment explanation
Indices: 5110--5222 Score: 192
Period size: 55 Copynumber: 2.0 Consensus size: 56
5100 TTTATTTTAT
* * *
5110 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGATAAGATTTATTATAACATTTATTGTATGAA
5166 AGAATAATTAAGTAGAAATA-GGGGATAAGATTTATTATAACATTTATTGTATGAA
1 AGAATAATTAAGTAGAAATAGGGGGATAAGATTTATTATAACATTTATTGTATGAA
5221 AG
1 AG
5223 GAAATGGATA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
55 35 0.65
56 19 0.35
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.34
Consensus pattern (56 bp):
AGAATAATTAAGTAGAAATAGGGGGATAAGATTTATTATAACATTTATTGTATGAA
Found at i:17501 original size:22 final size:22
Alignment explanation
Indices: 17473--17530 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
17463 TATTAACGGT
17473 AGTTTTCTTTTTTGGCACAATA
1 AGTTTTCTTTTTTGGCACAATA
17495 AGTTTTCTTTTTTGGCACAATA
1 AGTTTTCTTTTTTGGCACAATA
*
17517 AGTTTTTTTTTTTG
1 AGTTTTCTTTTTTG
17531 TTAAATGGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.19, C:0.10, G:0.14, T:0.57
Consensus pattern (22 bp):
AGTTTTCTTTTTTGGCACAATA
Found at i:17562 original size:25 final size:24
Alignment explanation
Indices: 17517--17575 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
17507 TGGCACAATA
* *
17517 AGTTTTTTTTTTTGTTAAATGGTG
1 AGTTTTTTTTTTTGTAAAATGATG
*
17541 AGTTTTTTCTTTTT-TAATAATGATT
1 AGTTTTTT-TTTTTGTAA-AATGATG
17566 AGTTTTTTTT
1 AGTTTTTTTT
17576 AAAATGATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 12 0.40
25 18 0.60
ACGTcount: A:0.19, C:0.02, G:0.14, T:0.66
Consensus pattern (24 bp):
AGTTTTTTTTTTTGTAAAATGATG
Found at i:18174 original size:2 final size:2
Alignment explanation
Indices: 18167--18191 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18157 TTATGATGAA
18167 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
18192 ATCGAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19270 original size:21 final size:21
Alignment explanation
Indices: 19229--19271 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
19219 CTTGTAATCT
*
19229 AAAGTTACTAAAAAGTTTATA
1 AAAGTTACTAAAAAGTCTATA
*
19250 AAAGTTATTAAAATAG-CTATA
1 AAAGTTACTAAAA-AGTCTATA
19271 A
1 A
19272 TGTTTTTCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (21 bp):
AAAGTTACTAAAAAGTCTATA
Done.