Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013005.1 Corchorus capsularis cultivar CVL-1 contig13026, 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: 24306
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:119 original size:22 final size:23
Alignment explanation
Indices: 89--134 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
79 AAAATAGGGT
*
89 AGTCAACGGAAAATA-ACATAAA
1 AGTCAACGGAAAATATACACAAA
*
111 AGTCCACGGAAAATATACACAAA
1 AGTCAACGGAAAATATACACAAA
134 A
1 A
135 CACGGGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (23 bp):
AGTCAACGGAAAATATACACAAA
Found at i:1915 original size:2 final size:2
Alignment explanation
Indices: 1910--1936 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1900 CTTAGCTAAT
1910 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1937 GATGTGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2061 original size:11 final size:11
Alignment explanation
Indices: 2042--2075 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2032 CATTTTATAC
*
2042 TAATGTATCAT
1 TAATTTATCAT
2053 TAATTTATCAT
1 TAATTTATCAT
2064 TAATTTAT-AT
1 TAATTTATCAT
2074 TA
1 TA
2076 CTCATTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (11 bp):
TAATTTATCAT
Found at i:2315 original size:21 final size:21
Alignment explanation
Indices: 2286--2334 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2276 GTTTAACATT
* * *
2286 GTTTAACTATCAAACTTTGGG
1 GTTTGACTATCAAAATTTGAG
*
2307 GTTTGACTATTAAAATTTGAG
1 GTTTGACTATCAAAATTTGAG
2328 GTTTGAC
1 GTTTGAC
2335 CATGAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (21 bp):
GTTTGACTATCAAAATTTGAG
Found at i:8966 original size:1 final size:1
Alignment explanation
Indices: 8960--8984 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
8950 CACTATTCTG
8960 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
8985 GGGAAAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:10594 original size:5 final size:5
Alignment explanation
Indices: 10584--10629 Score: 67
Period size: 5 Copynumber: 9.0 Consensus size: 5
10574 ATATAAACCC
10584 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ACTAATT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAA-T ATAAT
10630 GTGAACTCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 3 0.08
5 29 0.76
6 4 0.11
7 2 0.05
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:11705 original size:3 final size:3
Alignment explanation
Indices: 11695--11728 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
11685 CTATAATAAG
11695 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
11729 AAATTACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:17608 original size:17 final size:17
Alignment explanation
Indices: 17583--17623 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
17573 TTAAAACTAG
*
17583 TAAATATAAACATATAA
1 TAAACATAAACATATAA
17600 TAAACATAAACATATAA
1 TAAACATAAACATATAA
*
17617 TAGACAT
1 TAAACAT
17624 GGTTGTCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAACATAAACATATAA
Found at i:18297 original size:2 final size:2
Alignment explanation
Indices: 18292--18317 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18282 TTTTTATTGA
18292 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
18318 GTACTGTTGA
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
Done.