Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010563.1 Corchorus capsularis cultivar CVL-1 contig10584, 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: 64782
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:175 original size:33 final size:32
Alignment explanation
Indices: 132--218 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 32
122 CCATGGTAGT
*
132 GCCGTCCCCCTGGTGCGGCATTACCATGGC-CA
1 GCCGCCCCCCTGG-GCGGCATTACCATGGCTCA
* **
164 GGCCGCTCCCCTGGGGCGGCCCTACCATGGCTCA
1 -GCCGCCCCCCT-GGGCGGCATTACCATGGCTCA
198 GCCGCCCCCCTAGGGCGGCAT
1 GCCGCCCCCCT-GGGCGGCAT
219 GAGCAATTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
33 40 0.91
34 4 0.09
ACGTcount: A:0.10, C:0.44, G:0.31, T:0.15
Consensus pattern (32 bp):
GCCGCCCCCCTGGGCGGCATTACCATGGCTCA
Found at i:955 original size:2 final size:2
Alignment explanation
Indices: 948--980 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
938 GTCCTCATGG
*
948 GT GT GT GT GT GT GT GT GT GT GT AT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
981 ATCGTTTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.48, T:0.48
Consensus pattern (2 bp):
GT
Found at i:2338 original size:2 final size:2
Alignment explanation
Indices: 2331--2356 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2321 TATTGAAGTT
2331 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
2357 CACACACACA
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):
TA
Found at i:21842 original size:22 final size:22
Alignment explanation
Indices: 21808--21850 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
21798 CATGGTTTTT
21808 ATGGGTAATAGGAAATCTGTTG
1 ATGGGTAATAGGAAATCTGTTG
*
21830 ATGGGTTAA-AGGAACTCTGTT
1 ATGGG-TAATAGGAAATCTGTT
21851 TTAGGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (22 bp):
ATGGGTAATAGGAAATCTGTTG
Found at i:24408 original size:2 final size:2
Alignment explanation
Indices: 24401--24429 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24391 ATGGGGTAGC
24401 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24430 ATTTTCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34895 original size:2 final size:2
Alignment explanation
Indices: 34850--34876 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34840 CAGAAAAGGG
34850 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
34877 TGTGTAGCAC
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:44110 original size:20 final size:20
Alignment explanation
Indices: 44085--44122 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
44075 GAGGATCAGC
44085 GCTTAGTTTAGTTTAATTGT
1 GCTTAGTTTAGTTTAATTGT
44105 GCTTAGTTTAGTTTAATT
1 GCTTAGTTTAGTTTAATT
44123 ATATTGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.18, T:0.55
Consensus pattern (20 bp):
GCTTAGTTTAGTTTAATTGT
Found at i:47064 original size:17 final size:18
Alignment explanation
Indices: 47029--47067 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
47019 TGAAGTTTCA
47029 TTTCTATGGCTTCCTCTT
1 TTTCTATGGCTTCCTCTT
*
47047 TTTC-ATGG-TTCCTCCT
1 TTTCTATGGCTTCCTCTT
47063 TTTCT
1 TTTCT
47068 GCTGTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 11 0.58
17 4 0.21
18 4 0.21
ACGTcount: A:0.05, C:0.28, G:0.10, T:0.56
Consensus pattern (18 bp):
TTTCTATGGCTTCCTCTT
Found at i:50934 original size:1 final size:1
Alignment explanation
Indices: 50930--50956 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
50920 TTTTGGGATG
50930 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
50957 CTTTTTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.