Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024040.1 Corchorus olitorius cultivar O-4 contig24073, 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: 34239
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1064 original size:41 final size:41
Alignment explanation
Indices: 1019--1113 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
1009 TCTCTAAAAC
* * *
1019 CAGGGACCAAATTGAATTAAAAAGTAACTAAAATCCTAAAT
1 CAGGGACTAAATTGAATCAAAAAGTAAATAAAATCCTAAAT
* * * *
1060 CAGGGACTAAATTGCATCAAATAGTAAATAGAATCTTAAAT
1 CAGGGACTAAATTGAATCAAAAAGTAAATAAAATCCTAAAT
1101 CAGGGACTAAATT
1 CAGGGACTAAATT
1114 AAAGAAATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (41 bp):
CAGGGACTAAATTGAATCAAAAAGTAAATAAAATCCTAAAT
Found at i:13070 original size:25 final size:24
Alignment explanation
Indices: 13036--13090 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
13026 TTAATACAGG
* *
13036 TATCCATGGATATATCGAACGGATA
1 TATCGATGGATATATCG-ACAGATA
13061 TATCGATGGATATATCGACAGATA
1 TATCGATGGATATATCGACAGATA
13085 TATCGA
1 TATCGA
13091 GGTATCGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (24 bp):
TATCGATGGATATATCGACAGATA
Found at i:13073 original size:12 final size:12
Alignment explanation
Indices: 13043--13090 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
13033 AGGTATCCAT
13043 GGATATATCGAAC
1 GGATATATCG-AC
*
13056 GGATATATCGAT
1 GGATATATCGAC
13068 GGATATATCGAC
1 GGATATATCGAC
*
13080 AGATATATCGA
1 GGATATATCGA
13091 GGTATCGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
12 22 0.69
13 10 0.31
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (12 bp):
GGATATATCGAC
Found at i:14097 original size:10 final size:10
Alignment explanation
Indices: 14078--14113 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
14068 AATTTAATAT
14078 GGATATTTAC
1 GGATATTTAC
* *
14088 AGATACTTAC
1 GGATATTTAC
14098 GGATATTTAC
1 GGATATTTAC
14108 GGATAT
1 GGATAT
14114 ATCGAGAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.36
Consensus pattern (10 bp):
GGATATTTAC
Found at i:14627 original size:8 final size:8
Alignment explanation
Indices: 14614--14661 Score: 57
Period size: 8 Copynumber: 6.2 Consensus size: 8
14604 GAAAACAAAT
14614 TATATTTA
1 TATATTTA
14622 TATATTTA
1 TATATTTA
14630 TATA-TT-
1 TATATTTA
14636 TATATTTA
1 TATATTTA
14644 TAT-TTATA
1 TATATT-TA
*
14652 TATATCTA
1 TATATTTA
14660 TA
1 TA
14662 ACAAATAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
6 4 0.11
7 6 0.17
8 24 0.69
9 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (8 bp):
TATATTTA
Found at i:14632 original size:14 final size:14
Alignment explanation
Indices: 14613--14654 Score: 68
Period size: 14 Copynumber: 3.0 Consensus size: 14
14603 AGAAAACAAA
14613 TTATATTTATATAT
1 TTATATTTATATAT
14627 TTATATATT-TATAT
1 TTATAT-TTATATAT
14641 TTATATTTATATAT
1 TTATATTTATATAT
14655 ATCTATAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATATTTATATAT
Found at i:14638 original size:22 final size:22
Alignment explanation
Indices: 14613--14661 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
14603 AGAAAACAAA
14613 TTATATTTATATATT-TATATAT
1 TTATATTTATAT-TTATATATAT
14635 TTATATTTATATTTATATATAT
1 TTATATTTATATTTATATATAT
*
14657 CTATA
1 TTATA
14662 ACAAATAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATATTTATATTTATATATAT
Found at i:14661 original size:6 final size:6
Alignment explanation
Indices: 14613--14652 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
14603 AGAAAACAAA
14613 TTATAT TTATA- -TAT-T TATATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT T-TATAT TTATAT TTATAT TTATAT
14653 ATATCTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
4 3 0.10
6 25 0.83
7 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TTATAT
Found at i:14991 original size:20 final size:20
Alignment explanation
Indices: 14968--15006 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
14958 TTTTCCCATC
14968 TTTTCCTCTTTTTTTTCTTT
1 TTTTCCTCTTTTTTTTCTTT
* *
14988 TTTTTCTTTTTTTTTTCTT
1 TTTTCCTCTTTTTTTTCTT
15007 CAACTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTCCTCTTTTTTTTCTTT
Found at i:15002 original size:10 final size:9
Alignment explanation
Indices: 14974--15001 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
14964 CATCTTTTCC
14974 TCTTTTTTT
1 TCTTTTTTT
14983 TCTTTTTTT
1 TCTTTTTTT
14992 TCTTTTTTT
1 TCTTTTTTT
15001 T
1 T
15002 TTCTTCAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:17949 original size:2 final size:2
Alignment explanation
Indices: 17942--17984 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
17932 AGTCCCGCAT
*
17942 TC TC TC TC TC TC TC TC TC TC TC TC TA TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
17984 T
1 T
17985 ATATATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:17989 original size:2 final size:2
Alignment explanation
Indices: 17984--18011 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17974 TCTCTCTCTC
17984 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18012 AATCTACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19064 original size:2 final size:2
Alignment explanation
Indices: 19057--19119 Score: 65
Period size: 2 Copynumber: 31.0 Consensus size: 2
19047 CATATGGCCA
* *
19057 AT AT AT AT AT CT AT ACT AT AA AT AT AT AT AT AT AT AT AT A- ACT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T
**
19100 CC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
19120 CAAACTAATG
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
1 1 0.02
2 47 0.94
3 2 0.04
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:19967 original size:14 final size:14
Alignment explanation
Indices: 19948--19975 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19938 AAGAGAGATT
19948 GCTATAAAACTTTC
1 GCTATAAAACTTTC
19962 GCTATAAAACTTTC
1 GCTATAAAACTTTC
19976 AGTAGACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
GCTATAAAACTTTC
Done.