Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009512.1 Corchorus capsularis cultivar CVL-1 contig09533, 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: 35900
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10126 original size:2 final size:2
Alignment explanation
Indices: 10121--10146 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10111 TTGTTCTCTC
10121 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
10147 TGTGATTTTC
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:15830 original size:12 final size:12
Alignment explanation
Indices: 15813--15837 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15803 AATCCTTATT
15813 AACAAAGAAAGA
1 AACAAAGAAAGA
15825 AACAAAGAAAGA
1 AACAAAGAAAGA
15837 A
1 A
15838 GAAGAGATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (12 bp):
AACAAAGAAAGA
Found at i:17536 original size:2 final size:2
Alignment explanation
Indices: 17529--17553 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17519 GGGCGCCATT
17529 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
17554 TCGGTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:19488 original size:1 final size:1
Alignment explanation
Indices: 19482--19507 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
19472 ATTCTGATGC
19482 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
19508 CTCACATTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29802 original size:12 final size:12
Alignment explanation
Indices: 29770--29808 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
29760 ATGGAATTAA
29770 ATATCCGTCG--
1 ATATCCGTCGAT
29780 ATA-CC-TCGAT
1 ATATCCGTCGAT
29790 ATATCCGTCGAT
1 ATATCCGTCGAT
29802 ATATCCG
1 ATATCCG
29809 ATATCTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.12
9 2 0.08
10 6 0.24
11 2 0.08
12 12 0.48
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:30954 original size:13 final size:13
Alignment explanation
Indices: 30936--31029 Score: 149
Period size: 13 Copynumber: 7.5 Consensus size: 13
30926 CATCGATACC
30936 TCGATATATCCGT
1 TCGATATATCCGT
30949 TCGATATATCCG-
1 TCGATATATCCGT
30961 TCGATATATCCGT
1 TCGATATATCCGT
*
30974 TCGACATATCCG-
1 TCGATATATCCGT
30986 TCGATATATCCGT
1 TCGATATATCCGT
*
30999 TCGACATATCCGT
1 TCGATATATCCGT
31012 TCGATATATCCG-
1 TCGATATATCCGT
31024 TCGATA
1 TCGATA
31030 CCTATATTTA
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
12 29 0.39
13 46 0.61
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (13 bp):
TCGATATATCCGT
Found at i:31025 original size:38 final size:38
Alignment explanation
Indices: 30936--31029 Score: 122
Period size: 38 Copynumber: 2.5 Consensus size: 38
30926 CATCGATACC
*
30936 TCGATATATCCGTTCGATATATCCG-TCGATATATCCG
1 TCGACATATCCGTTCGATATATCCGTTCGATATATCCG
*
30973 TTCGACATATCCG-TCGATATATCCGTTCGACATATCCG
1 -TCGACATATCCGTTCGATATATCCGTTCGATATATCCG
*
31011 TTCGATATATCCG-TCGATA
1 -TCGACATATCCGTTCGATA
31030 CCTATATTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
37 12 0.23
38 40 0.77
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (38 bp):
TCGACATATCCGTTCGATATATCCGTTCGATATATCCG
Found at i:31027 original size:25 final size:25
Alignment explanation
Indices: 30936--31024 Score: 160
Period size: 25 Copynumber: 3.5 Consensus size: 25
30926 CATCGATACC
*
30936 TCGATATATCCGTTCGATATATCCG
1 TCGATATATCCGTTCGACATATCCG
30961 TCGATATATCCGTTCGACATATCCG
1 TCGATATATCCGTTCGACATATCCG
30986 TCGATATATCCGTTCGACATATCCG
1 TCGATATATCCGTTCGACATATCCG
31011 TTCGATATATCCGT
1 -TCGATATATCCGT
31025 CGATACCTAT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
25 49 0.79
26 13 0.21
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.35
Consensus pattern (25 bp):
TCGATATATCCGTTCGACATATCCG
Done.