Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001516.1 Corchorus olitorius cultivar O-4 contig01516, 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: 9955
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2588 original size:95 final size:95
Alignment explanation
Indices: 2447--2626 Score: 335
Period size: 95 Copynumber: 1.9 Consensus size: 95
2437 AGACTACACA
2447 AGCGAGTCCTGAAGAGTGACATGTGTCCTCTAGGAACTAGATTGAAATATTTAAAACTTAATTAA
1 AGCGAGTCCTGAAGAGTGACATGTGTCCTCTAGGAACTAGATTGAAATATTTAAAACTTAATTAA
2512 TTCAAAAAATGGACATGTGTGACATGTGTC
66 TTCAAAAAATGGACATGTGTGACATGTGTC
*
2542 AGCGAGTCCTGAAGAGTGACATGTGTCCTCTAAGG-ACTAGATTGAAATATTTAAAATTTAATTA
1 AGCGAGTCCTGAAGAGTGACATGTGTCCTCT-AGGAACTAGATTGAAATATTTAAAACTTAATTA
2606 ATTCAAAAAATGGACATGTGT
65 ATTCAAAAAATGGACATGTGT
2627 CATCTCCACA
Statistics
Matches: 83, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
95 80 0.96
96 3 0.04
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (95 bp):
AGCGAGTCCTGAAGAGTGACATGTGTCCTCTAGGAACTAGATTGAAATATTTAAAACTTAATTAA
TTCAAAAAATGGACATGTGTGACATGTGTC
Found at i:2695 original size:2 final size:2
Alignment explanation
Indices: 2688--2713 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2678 AATAATTACC
2688 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2714 TGTTTCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6045 original size:14 final size:13
Alignment explanation
Indices: 6015--6052 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
6005 TTTTGCAAGG
*
6015 AACAGAGGAAGGA
1 AACAGAGGAAAGA
6028 AACAGAGGAATAGA
1 AACAGAGGAA-AGA
6042 AACAGAGGAAA
1 AACAGAGGAAA
6053 ACAGAGGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.58, C:0.08, G:0.32, T:0.03
Consensus pattern (13 bp):
AACAGAGGAAAGA
Found at i:6833 original size:19 final size:18
Alignment explanation
Indices: 6806--6844 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
6796 CCTAGTGTGC
*
6806 AAAAAAAAAGGAAAAAAG
1 AAAAAAAAAAGAAAAAAG
6824 AAAAAGAAAAAGAAAAAAG
1 AAAAA-AAAAAGAAAAAAG
6843 AA
1 AA
6845 TAAGGGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAGAAAAAAG
Found at i:9365 original size:24 final size:23
Alignment explanation
Indices: 9314--9365 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
9304 AAGACTAAAG
*
9314 TAAATAATAAAAAATAAATTTAC
1 TAAATAATAAAAAATAAATATAC
*
9337 TAATAGTAA-AAATAATAAATAT-C
1 TAA-A-TAATAAAAAATAAATATAC
9360 TAAATA
1 TAAATA
9366 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.08
22 1 0.04
23 7 0.28
24 12 0.48
25 3 0.12
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (23 bp):
TAAATAATAAAAAATAAATATAC
Found at i:9907 original size:1 final size:1
Alignment explanation
Indices: 9901--9955 Score: 110
Period size: 1 Copynumber: 55.0 Consensus size: 1
9891 AGGTTTTAGG
9901 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.