Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019537.1 Corchorus olitorius cultivar O-4 contig19570, 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: 14680
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:2835 original size:19 final size:19
Alignment explanation
Indices: 2808--2844 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2798 CGGTGGAGAA
2808 AACAAAAATGAAGAAAATT
1 AACAAAAATGAAGAAAATT
*
2827 AACACAAATGAAGAAAAT
1 AACAAAAATGAAGAAAAT
2845 GAAGTAACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.08, G:0.11, T:0.14
Consensus pattern (19 bp):
AACAAAAATGAAGAAAATT
Found at i:3503 original size:30 final size:27
Alignment explanation
Indices: 3470--3552 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 27
3460 ATACCACTAA
* *
3470 TAATTATTATTATTATAATAATAAGTT
1 TAATAATTATTATAATAATAATAAGTT
*
3497 TAATAATTATAATACCACTAATAATAAGTT
1 TAATAATTATTATA--A-TAATAATAAGTT
3527 TAATAATTATTATAATAATAATAAGT
1 TAATAATTATTATAATAATAATAAGT
3553 CTAAATTAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 22 0.45
28 1 0.02
29 1 0.02
30 25 0.51
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (27 bp):
TAATAATTATTATAATAATAATAAGTT
Found at i:3836 original size:2 final size:2
Alignment explanation
Indices: 3824--3857 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
3814 AGTTTAGACT
3824 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3858 CTACATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6086 original size:19 final size:19
Alignment explanation
Indices: 6062--6098 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6052 GTACAATACC
*
6062 TAATCTAATCTGTACAGTG
1 TAATCTAATCTATACAGTG
6081 TAATCTAATCTATACAGT
1 TAATCTAATCTATACAGT
6099 TGCTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTATACAGTG
Found at i:12678 original size:37 final size:36
Alignment explanation
Indices: 12628--12772 Score: 166
Period size: 37 Copynumber: 3.9 Consensus size: 36
12618 ATTGAAGACT
12628 AAAACTTGATGGGAACTTTCCCAATTTAAAAACTTTG
1 AAAAC-TGATGGGAACTTTCCCAATTTAAAAACTTTG
* * * ***
12665 AAAACTGAATGGGAACCTTCCTAA-TTGAAAACTAAAA
1 AAAACTG-ATGGGAACTTTCCCAATTTAAAAACT-TTG
*
12702 AAAACTGGTGGGAACTTTCCCAATTTAAAAACTTTG
1 AAAACTGATGGGAACTTTCCCAATTTAAAAACTTTG
* *
12738 AAAAATGGATGGGAACTTTCCCAATTTGAAAACTT
1 AAAACT-GATGGGAACTTTCCCAATTTAAAAACTT
12773 AAACCTGATG
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
36 28 0.32
37 60 0.68
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (36 bp):
AAAACTGATGGGAACTTTCCCAATTTAAAAACTTTG
Found at i:12714 original size:36 final size:37
Alignment explanation
Indices: 12565--12771 Score: 133
Period size: 37 Copynumber: 5.6 Consensus size: 37
12555 TGCTTTTGAC
* ** **
12565 GGGAACTTTCCCATTTTGAAAACTAAGACTGAAA-TGAC
1 GGGAACTTTCCCAATTTGAAAACTAA-A-AAAAACTGGT
* * *
12603 GGGAACTTTCCCTAAATTGAAGACT----AAAACTTGAT
1 GGGAACTTTCCC-AATTTGAAAACTAAAAAAAAC-TGGT
* *** *
12638 GGGAACTTTCCCAATTTAAAAACT-TTGAAAACTGAAT
1 GGGAACTTTCCCAATTTGAAAACTAAAAAAAACTG-GT
* *
12675 GGGAACCTTCCTAA-TTGAAAACTAAAAAAAACTGGT
1 GGGAACTTTCCCAATTTGAAAACTAAAAAAAACTGGT
* ***
12711 GGGAACTTTCCCAATTTAAAAACTTTGAAAAA-TGGAT
1 GGGAACTTTCCCAATTTGAAAACTAAAAAAAACTGG-T
12748 GGGAACTTTCCCAATTTGAAAACT
1 GGGAACTTTCCCAATTTGAAAACT
12772 TAAACCTGAT
Statistics
Matches: 137, Mismatches: 22, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
33 3 0.02
34 9 0.07
35 15 0.11
36 26 0.19
37 63 0.46
38 12 0.09
39 9 0.07
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (37 bp):
GGGAACTTTCCCAATTTGAAAACTAAAAAAAACTGGT
Found at i:12714 original size:73 final size:75
Alignment explanation
Indices: 12628--12771 Score: 229
Period size: 73 Copynumber: 1.9 Consensus size: 75
12618 ATTGAAGACT
* *
12628 AAAACTTGATGGGAACTTTCCCAATTTAAAAACTTTGAAAACTGAATGGGAACCTTCCTAA-TTG
1 AAAACTTGATGGGAACTTTCCCAATTTAAAAACTTTGAAAAATGAATGGGAACCTTCCCAATTTG
12692 AAAACTAAAA
66 AAAACTAAAA
* * *
12702 AAAAC-TGGTGGGAACTTTCCCAATTTAAAAACTTTGAAAAATGGATGGGAACTTTCCCAATTTG
1 AAAACTTGATGGGAACTTTCCCAATTTAAAAACTTTGAAAAATGAATGGGAACCTTCCCAATTTG
12766 AAAACT
66 AAAACT
12772 TAAACCTGAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 50 0.78
74 14 0.22
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (75 bp):
AAAACTTGATGGGAACTTTCCCAATTTAAAAACTTTGAAAAATGAATGGGAACCTTCCCAATTTG
AAAACTAAAA
Found at i:14368 original size:48 final size:47
Alignment explanation
Indices: 14281--14373 Score: 116
Period size: 48 Copynumber: 2.0 Consensus size: 47
14271 GAGCGTGCCA
* *
14281 ATCAATTTTGTCAAAAAATTGATAAAAAGTACAAAGAAAATTAAAAG
1 ATCAATTTTGTCAAAAAATTGAGAAAAAGTACAAAGAAAAGTAAAAG
* **
14328 ATCAATTTTGT-AGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGTCA--AAAAATTGAGAAAAAGTACAAAGAAAAGTAAA
14374 GGGTTGCTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.03
47 11 0.28
48 27 0.69
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.26
Consensus pattern (47 bp):
ATCAATTTTGTCAAAAAATTGAGAAAAAGTACAAAGAAAAGTAAAAG
Found at i:14652 original size:10 final size:10
Alignment explanation
Indices: 14637--14669 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
14627 TAGAACTTGA
14637 TGAACAATAT
1 TGAACAATAT
14647 TGAACAATAT
1 TGAACAATAT
14657 TGAGA-AATAT
1 TGA-ACAATAT
14667 TGA
1 TGA
14670 TGAAAGCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 21 0.95
11 1 0.05
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.30
Consensus pattern (10 bp):
TGAACAATAT
Done.