Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023997.1 Corchorus olitorius cultivar O-4 contig24030, 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: 9756
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:2748 original size:31 final size:31
Alignment explanation
Indices: 2713--2771 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
2703 AAATGACTGA
2713 CCGGAATTTGGAAAATTCCAGATTCCGGATT
1 CCGGAATTTGGAAAATTCCAGATTCCGGATT
2744 CCGGAATTTGGAAAATTCCAGATTCCGG
1 CCGGAATTTGGAAAATTCCAGATTCCGG
2772 TGCTGGAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (31 bp):
CCGGAATTTGGAAAATTCCAGATTCCGGATT
Found at i:2973 original size:6 final size:6
Alignment explanation
Indices: 2959--3031 Score: 73
Period size: 6 Copynumber: 12.8 Consensus size: 6
2949 GACCAACTTT
* *
2959 AAAAA- AAAAAG -AAAAG AGAAAG GAAAAG -AAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* * *
3004 AAAAAG GAAAGG GAAAAG -AAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
3032 AAATAAATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
5 20 0.34
6 38 0.66
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2987 original size:17 final size:17
Alignment explanation
Indices: 2965--3027 Score: 83
Period size: 17 Copynumber: 3.6 Consensus size: 17
2955 CTTTAAAAAA
2965 AAAAGAAAAGAGAAAGG
1 AAAAGAAAAGAGAAAGG
* *
2982 AAAAGAAAAGAAAAAGA
1 AAAAGAAAAGAGAAAGG
2999 AAAAGAAAA-AGGAAAGGG
1 AAAAGAAAAGA-GAAA-GG
3017 AAAAGAAAAGA
1 AAAAGAAAAGA
3028 AAAAAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
16 1 0.03
17 27 0.69
18 10 0.26
19 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAGAGAAAGG
Found at i:2990 original size:23 final size:22
Alignment explanation
Indices: 2960--3031 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 22
2950 ACCAACTTTA
2960 AAAAA-AAAAGA-AAAGAGAAAG
1 AAAAAGAAAAGAGAAAGA-AAAG
* *
2981 GAAAAGAAAAGAAAAAGAAAAAG
1 AAAAAGAAAAGAGAAAG-AAAAG
* *
3004 AAAAAGGAAAGGGAAAAGAAAAG
1 AAAAAGAAAAGAG-AAAGAAAAG
3027 AAAAA
1 AAAAA
3032 AAATAAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
21 4 0.10
22 6 0.14
23 27 0.64
24 5 0.12
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAGAGAAAGAAAAG
Found at i:3049 original size:25 final size:25
Alignment explanation
Indices: 3021--3069 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
3011 AAAGGGAAAA
*
3021 GAAAAGAAAAAAAATAAATAAATAG
1 GAAAAGAAAAAAAATAAAGAAATAG
* * *
3046 GAAAATAAGAAAATTAAAGAAATA
1 GAAAAGAAAAAAAATAAAGAAATA
3070 TTTGGAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.14
Consensus pattern (25 bp):
GAAAAGAAAAAAAATAAAGAAATAG
Found at i:5740 original size:15 final size:15
Alignment explanation
Indices: 5701--5755 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
5691 CAGTAATGGT
5701 TCCACCTATGCCGTA
1 TCCACCTATGCCGTA
* *
5716 TCCGCGTATGCCGT-
1 TCCACCTATGCCGTA
*
5730 TGCCACCTATGCCATA
1 T-CCACCTATGCCGTA
5746 -CCAACCTATG
1 TCC-ACCTATG
5756 ACTTTTCCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 3 0.09
15 29 0.91
ACGTcount: A:0.20, C:0.38, G:0.16, T:0.25
Consensus pattern (15 bp):
TCCACCTATGCCGTA
Found at i:8729 original size:6 final size:6
Alignment explanation
Indices: 8714--8803 Score: 82
Period size: 6 Copynumber: 15.8 Consensus size: 6
8704 CCTAACCTTT
* * *
8714 AAAAAA AAAAAG -AAAAG -AAAAG AAAAAG AGAAAG GAAAAG -AAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* * * *
8759 AAAAAG AAAAAG GAAAAG GAAAGG GAAAAG -AAAAG -AAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
8804 AATAAATAGT
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
5 25 0.34
6 49 0.66
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:8751 original size:5 final size:5
Alignment explanation
Indices: 8716--8802 Score: 84
Period size: 5 Copynumber: 15.8 Consensus size: 5
8706 TAACCTTTAA
*
8716 AAAAA AAAAG AAAAG AAAAG AAAAAG AGAAAGG AAAAG AAAAG AAAAAG
1 AAAAG AAAAG AAAAG AAAAG -AAAAG A-AAA-G AAAAG AAAAG -AAAAG
*
8765 AAAAAGG AAAAGG AAAGGG AAAAG AAAAG AAAAG AAAA
1 -AAAA-G AAAA-G AAA-AG AAAAG AAAAG AAAAG AAAA
8803 AAATAAATAG
Statistics
Matches: 73, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
5 36 0.49
6 34 0.47
7 3 0.04
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:8751 original size:23 final size:22
Alignment explanation
Indices: 8714--8802 Score: 108
Period size: 23 Copynumber: 4.0 Consensus size: 22
8704 CCTAACCTTT
* *
8714 AAAAAAAAAAAGAAAAGAAAAG
1 AAAAAGAAAAGGAAAAGAAAAG
8736 AAAAAGAGAAAGGAAAAGAAAAG
1 AAAAAGA-AAAGGAAAAGAAAAG
*
8759 AAAAAGAAAAAGGAAAAGGAAAGG
1 AAAAAG-AAAAGGAAAA-GAAAAG
*
8783 GAAAAGAAAA-GAAAAGAAAA
1 AAAAAGAAAAGGAAAAGAAAA
8803 AAATAAATAG
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.07
22 11 0.19
23 33 0.56
24 11 0.19
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAGGAAAAGAAAAG
Found at i:8931 original size:28 final size:28
Alignment explanation
Indices: 8875--8931 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
8865 TTGGAAAGTG
** *
8875 AAATTACTAGTTTACCCTTGGAGGGGTA
1 AAATTACTAAATTACCCTTGGAGGAGTA
* *
8903 AAATTACTAAATTACCCTTTGATGAGTA
1 AAATTACTAAATTACCCTTGGAGGAGTA
8931 A
1 A
8932 TTTTAAGAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (28 bp):
AAATTACTAAATTACCCTTGGAGGAGTA
Done.