Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022424.1 Corchorus olitorius cultivar O-4 contig22457, 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: 59421
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:3973 original size:41 final size:42
Alignment explanation
Indices: 3916--4020 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
3906 GACTAAAATG
3916 ATTAAGTGATTTGCGTTCTATTCTTTTGT-TTTTTGTTCTTA
1 ATTAAGTGATTTGCGTTCTATTCTTTTGTATTTTTGTTCTTA
3957 ATTAAGTGATTTGCGTTCTATTCTTTTGTATTTTTGTTCTTA
1 ATTAAGTGATTTGCGTTCTATTCTTTTGTATTTTTGTTCTTA
3999 ATTAAGTGATTTGCGTTCTATT
1 ATTAAGTGATTTGCGTTCTATT
4021 ATTGCAGCTA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 29 0.46
42 34 0.54
ACGTcount: A:0.17, C:0.10, G:0.15, T:0.58
Consensus pattern (42 bp):
ATTAAGTGATTTGCGTTCTATTCTTTTGTATTTTTGTTCTTA
Found at i:3974 original size:21 final size:21
Alignment explanation
Indices: 3950--4017 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
3940 TTTGTTTTTT
3950 GTTCTTAATTAAGTGATTTGC
1 GTTCTTAATTAAGTGATTTGC
** ** **
3971 GTTCTATTCTTTTGT-ATTTTT
1 GTTCT-TAATTAAGTGATTTGC
3992 GTTCTTAATTAAGTGATTTGC
1 GTTCTTAATTAAGTGATTTGC
4013 GTTCT
1 GTTCT
4018 ATTATTGCAG
Statistics
Matches: 33, Mismatches: 12, Indels: 4
0.67 0.24 0.08
Matches are distributed among these distances:
20 5 0.15
21 23 0.70
22 5 0.15
ACGTcount: A:0.18, C:0.10, G:0.16, T:0.56
Consensus pattern (21 bp):
GTTCTTAATTAAGTGATTTGC
Found at i:8433 original size:15 final size:15
Alignment explanation
Indices: 8410--8443 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
8400 TTCCCAATGG
*
8410 AAAGGAAAGGAAAGC
1 AAAGCAAAGGAAAGC
*
8425 AAAGCAAAGGATAGC
1 AAAGCAAAGGAAAGC
8440 AAAG
1 AAAG
8444 AAAAAGAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.29, T:0.03
Consensus pattern (15 bp):
AAAGCAAAGGAAAGC
Found at i:9030 original size:20 final size:20
Alignment explanation
Indices: 9005--9042 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
8995 CTTGTAGCAG
* *
9005 CCAATGGTAGTATGCTACAA
1 CCAATGCTAATATGCTACAA
9025 CCAATGCTAATATGCTAC
1 CCAATGCTAATATGCTAC
9043 TAGAGTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (20 bp):
CCAATGCTAATATGCTACAA
Found at i:11521 original size:37 final size:37
Alignment explanation
Indices: 11475--11565 Score: 119
Period size: 37 Copynumber: 2.5 Consensus size: 37
11465 GGAGATTCAT
* *
11475 CCATTATAACTAGGTGCGCGACGCAAGTCGGACTCAC
1 CCATCATAACTAGGTGCGCGACGCAAGTCAGACTCAC
* * ** *
11512 CCATCATAACTAGATGTGCGACGCGGGTTAGACTCAC
1 CCATCATAACTAGGTGCGCGACGCAAGTCAGACTCAC
11549 CCATCATAACTAGGTGC
1 CCATCATAACTAGGTGC
11566 ACAAACGGGT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (37 bp):
CCATCATAACTAGGTGCGCGACGCAAGTCAGACTCAC
Found at i:13266 original size:19 final size:19
Alignment explanation
Indices: 13242--13299 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
13232 TTGTTTAGCA
13242 ACTGTACAGATGAAATTAC
1 ACTGTACAGATGAAATTAC
* *
13261 ACTGTACAGATTGAATTATAT
1 ACTGTACAGA-TGAAAT-TAC
*
13282 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAAATTA
13300 TTAGAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.36
20 9 0.27
21 12 0.36
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAAATTAC
Found at i:13287 original size:21 final size:20
Alignment explanation
Indices: 13242--13300 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
13232 TTGTTTAGCA
*
13242 ACTGTACAGATGAAAT-TAC
1 ACTGTACAGATGAATTATAC
*
13261 ACTGTACAGATTGAATTATAT
1 ACTGTACAGA-TGAATTATAC
13282 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGA-ATTAT
13301 TAGAGCAGCG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.29
20 8 0.23
21 17 0.49
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (20 bp):
ACTGTACAGATGAATTATAC
Found at i:27272 original size:17 final size:17
Alignment explanation
Indices: 27250--27283 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
27240 GTTTCTTGAA
27250 GAAACAGACTTAGGTCC
1 GAAACAGACTTAGGTCC
27267 GAAACAGACTTAGGTCC
1 GAAACAGACTTAGGTCC
27284 CACCGATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (17 bp):
GAAACAGACTTAGGTCC
Found at i:35576 original size:16 final size:15
Alignment explanation
Indices: 35555--35594 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
35545 CTTGACTTCT
*
35555 GACAATTAAAGGCACC
1 GACAATTAAAGACA-C
35571 GACAATTAAAGACAC
1 GACAATTAAAGACAC
35586 GACTAATTA
1 GAC-AATTA
35595 GAAATTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.17
Consensus pattern (15 bp):
GACAATTAAAGACAC
Found at i:41376 original size:21 final size:21
Alignment explanation
Indices: 41350--41392 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
41340 TATTCTAACT
41350 AATTTAGAGTCAAATCGTGTC
1 AATTTAGAGTCAAATCGTGTC
41371 AATTTAGAGTCAAATCGTGTC
1 AATTTAGAGTCAAATCGTGTC
41392 A
1 A
41393 CTTTGTGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
AATTTAGAGTCAAATCGTGTC
Found at i:49740 original size:16 final size:16
Alignment explanation
Indices: 49719--49752 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
49709 AGAGTTGAAT
49719 TCAAAGTTGAATTGTG
1 TCAAAGTTGAATTGTG
49735 TCAAAGTTGAATTGTG
1 TCAAAGTTGAATTGTG
49751 TC
1 TC
49753 GGATTTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (16 bp):
TCAAAGTTGAATTGTG
Found at i:50764 original size:21 final size:22
Alignment explanation
Indices: 50740--50780 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
50730 AGTAGTTTGA
50740 CTAATCTT-ATTATTT-GTAAAC
1 CTAAT-TTAATTATTTAGTAAAC
50761 CTAATTTAATTATTTAGTAA
1 CTAATTTAATTATTTAGTAA
50781 CTTACCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 12 0.67
22 4 0.22
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.49
Consensus pattern (22 bp):
CTAATTTAATTATTTAGTAAAC
Found at i:55676 original size:21 final size:19
Alignment explanation
Indices: 55651--55708 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
55641 GCTATTCTAA
55651 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
55672 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
55691 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
55709 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Done.