Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015096.1 Corchorus olitorius cultivar O-4 contig15129, 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: 30051
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:13358 original size:19 final size:18
Alignment explanation
Indices: 13321--13360 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
13311 TTCTTGAAAT
*
13321 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
13339 AATTCTTCTAATTATCTTC
1 AATTCTTC-AATGATCTTC
13358 AAT
1 AAT
13361 AAATCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:18988 original size:29 final size:28
Alignment explanation
Indices: 18930--19022 Score: 102
Period size: 27 Copynumber: 3.4 Consensus size: 28
18920 AAGTAGGGGA
* * *
18930 CCAAATGGCCAAAATGCCCCTCTAA-ATG
1 CCAAATGACCAAAATGCCCC-CGAATGTG
18958 CACAAATGACCAAAATGCCCCCGAATGTG
1 C-CAAATGACCAAAATGCCCCCGAATGTG
* *
18987 -CAATTGACTAAAATGCCCCCGAATGTG
1 CCAAATGACCAAAATGCCCCCGAATGTG
19014 CC-AATGACC
1 CCAAATGACC
19023 GAATGACCCC
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
27 30 0.55
28 5 0.09
29 20 0.36
ACGTcount: A:0.35, C:0.31, G:0.16, T:0.17
Consensus pattern (28 bp):
CCAAATGACCAAAATGCCCCCGAATGTG
Found at i:19032 original size:27 final size:25
Alignment explanation
Indices: 18962--19032 Score: 79
Period size: 27 Copynumber: 2.7 Consensus size: 25
18952 TAAATGCACA
18962 AATGACCAAAATGCCCCCGAATGTGC
1 AATGACC-AAATGCCCCCGAATGTGC
*
18988 AATTGACTAAAATGCCCCCGAATGTGCC
1 AA-TGAC-CAAATGCCCCCGAATGTG-C
* *
19016 AATGACCGAATGACCCC
1 AATGACCAAATGCCCCC
19033 TAGGTGATCC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
26 10 0.26
27 25 0.66
28 3 0.08
ACGTcount: A:0.34, C:0.31, G:0.18, T:0.17
Consensus pattern (25 bp):
AATGACCAAATGCCCCCGAATGTGC
Found at i:27305 original size:7 final size:8
Alignment explanation
Indices: 27281--27305 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
27271 TTCCTAGAAT
27281 AACTCAAA
1 AACTCAAA
27289 AACTCAAA
1 AACTCAAA
27297 AACTCAAA
1 AACTCAAA
27305 A
1 A
27306 GAAAATTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.24, G:0.00, T:0.12
Consensus pattern (8 bp):
AACTCAAA
Found at i:27397 original size:30 final size:30
Alignment explanation
Indices: 27363--27422 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
27353 GAAAATAAAG
27363 GAAAATATATTTTTTTT-AGAAAACGCAAAA
1 GAAAATATATTTTTTTTCA-AAAACGCAAAA
* *
27393 GAAAATCTTTTTTTTTTCAAAAACGCAAAA
1 GAAAATATATTTTTTTTCAAAAACGCAAAA
27423 CACTAAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (30 bp):
GAAAATATATTTTTTTTCAAAAACGCAAAA
Found at i:27476 original size:16 final size:18
Alignment explanation
Indices: 27446--27478 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
27436 TTTTTAAATT
27446 AAAAGAAAATGTAGAAAC
1 AAAAGAAAATGTAGAAAC
27464 AAAA-AAAAT-TAGAAA
1 AAAAGAAAATGTAGAAA
27479 AAATGCAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (18 bp):
AAAAGAAAATGTAGAAAC
Found at i:27483 original size:27 final size:29
Alignment explanation
Indices: 27441--27500 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
27431 AATTTTTTTT
*
27441 AAATTAAAAGAAAATGTAGAAACAA-AAA
1 AAATTAAAAGAAAATGCAGAAACAAGAAA
*
27469 AAATTAGAA-AAAATGCAGAAACAAGAAA
1 AAATTAAAAGAAAATGCAGAAACAAGAAA
27497 AAAT
1 AAAT
27501 ATTTTTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.13
Consensus pattern (29 bp):
AAATTAAAAGAAAATGCAGAAACAAGAAA
Found at i:28630 original size:32 final size:32
Alignment explanation
Indices: 28563--28676 Score: 140
Period size: 32 Copynumber: 3.5 Consensus size: 32
28553 TAAAAGCAGT
* *
28563 TAAATATAGCGGCATTTTGTTCTGA-AGACGTCGC
1 TAAATA-AG-GGCGTTTTGTTCT-ATAGACGCCGC
* *
28597 TAAATAAGGGCGTTTTTTTCTTTAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
* *
28629 TAAATAAGGGTGTTTTGTTCTATAAACGCCGC
1 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
28661 TAAATAAGGGCGTTTT
1 TAAATAAGGGCGTTTT
28677 CTTTTCACAC
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
32 62 0.89
33 2 0.03
34 6 0.09
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (32 bp):
TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
Found at i:29452 original size:27 final size:26
Alignment explanation
Indices: 29400--29462 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 26
29390 AAATTACCAA
* *
29400 GGGCATTTTCGTCATTTTCATCTCAG
1 GGGCATTTTGGTCATTTTCACCTCAG
*
29426 GGGCATTTTGGTCATTTTTCGCCTCAG
1 GGGCATTTTGGTCA-TTTTCACCTCAG
*
29453 GGGGATTTTG
1 GGGCATTTTG
29463 ATCAAAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 13 0.41
27 19 0.59
ACGTcount: A:0.13, C:0.19, G:0.27, T:0.41
Consensus pattern (26 bp):
GGGCATTTTGGTCATTTTCACCTCAG
Done.