Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002216.1 Corchorus capsularis cultivar CVL-1 contig02221, 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, 781
Length: 1302
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Found at i:174 original size:13 final size:13
Alignment explanation
Indices: 156--202 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
146 CATCCATCAG
156 CAAGTGCCGATGC
1 CAAGTGCCGATGC
169 CAAGTGCC-AT-C
1 CAAGTGCCGATGC
180 AGCAAGTGCCGATGC
1 --CAAGTGCCGATGC
195 CAAGTGCC
1 CAAGTGCC
203 ATCGGAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 1 0.03
12 2 0.07
13 24 0.80
14 2 0.07
15 1 0.03
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.15
Consensus pattern (13 bp):
CAAGTGCCGATGC
Found at i:217 original size:26 final size:26
Alignment explanation
Indices: 149--205 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
139 CAAGTGCCAT
149 CCATCAGCAAGTGCCGATGCCAAGTG
1 CCATCAGCAAGTGCCGATGCCAAGTG
175 CCATCAGCAAGTGCCGATGCCAAGTG
1 CCATCAGCAAGTGCCGATGCCAAGTG
201 CCATC
1 CCATC
206 GGAGAATGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.26, C:0.33, G:0.25, T:0.16
Consensus pattern (26 bp):
CCATCAGCAAGTGCCGATGCCAAGTG
Found at i:222 original size:26 final size:26
Alignment explanation
Indices: 160--283 Score: 81
Period size: 32 Copynumber: 4.3 Consensus size: 26
150 CATCAGCAAG
*
160 TGCCGATGCCAAGTGCCATC--AGCAA
1 TGCCGACGCCAAGTGCCATCGGAG-AA
*
185 GTGCCGATGCCAAGTGCCATCGGAGAA
1 -TGCCGACGCCAAGTGCCATCGGAGAA
*
212 TGCCGACGCCAAGGCCAAGATCCATCGGAGAA
1 TGCCGACGCCAA-G---TG--CCATCGGAGAA
244 TGCCGACGCCAAGGTCAAGTGCCATCGGAGAA
1 TGCCGACG-C-----CAAGTGCCATCGGAGAA
276 TGCCGACG
1 TGCCGACG
284 AAGGGTGTCC
Statistics
Matches: 81, Mismatches: 3, Indels: 22
0.76 0.03 0.21
Matches are distributed among these distances:
26 31 0.38
27 3 0.04
28 2 0.02
30 1 0.01
32 38 0.47
33 1 0.01
34 1 0.01
37 1 0.01
38 3 0.04
ACGTcount: A:0.27, C:0.30, G:0.30, T:0.13
Consensus pattern (26 bp):
TGCCGACGCCAAGTGCCATCGGAGAA
Found at i:229 original size:32 final size:32
Alignment explanation
Indices: 193--283 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 32
183 AAGTGCCGAT
193 GCCAAGTGCCATCGGAGAATGCCGACGCCAAG
1 GCCAAGTGCCATCGGAGAATGCCGACGCCAAG
225 GCCAAGAT-CCATCGGAGAATGCCGACGCCAAG
1 GCCAAG-TGCCATCGGAGAATGCCGACGCCAAG
*
257 GTCAAGTGCCATCGGAGAATGCCGACG
1 GCCAAGTGCCATCGGAGAATGCCGACG
284 AAGGGTGTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
31 1 0.02
32 54 0.96
33 1 0.02
ACGTcount: A:0.29, C:0.30, G:0.31, T:0.11
Consensus pattern (32 bp):
GCCAAGTGCCATCGGAGAATGCCGACGCCAAG
Found at i:634 original size:77 final size:78
Alignment explanation
Indices: 501--655 Score: 197
Period size: 77 Copynumber: 2.0 Consensus size: 78
491 AGGTGTTCGC
* **** *
501 TGAGTTTCGGGGGCAAAAAATGGGCCAAAATGCATTAGGTTTTGTATCATGAGTTCCAGACCCAA
1 TGAGCTTCGGGGGCAAAAAATGGGCCAAAATGCATTAGGTTAACCATCAAGAGTTCCAGACCCAA
*
566 AAAATGGCCGAAA
66 AAAATGGCAGAAA
* *
579 TGAGCTTCGGGGGC-AAAAATTGGCCAAAATGCCA-TAGGTTAACCATCAAGAGTTCCGGACCCA
1 TGAGCTTCGGGGGCAAAAAATGGGCCAAAATG-CATTAGGTTAACCATCAAGAGTTCCAGACCCA
*
642 AAAATTGGCAGAAA
65 AAAAATGGCAGAAA
656 AGCCGTAGGT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
77 51 0.77
78 15 0.23
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (78 bp):
TGAGCTTCGGGGGCAAAAAATGGGCCAAAATGCATTAGGTTAACCATCAAGAGTTCCAGACCCAA
AAAATGGCAGAAA
Found at i:665 original size:48 final size:47
Alignment explanation
Indices: 592--703 Score: 161
Period size: 48 Copynumber: 2.3 Consensus size: 47
582 GCTTCGGGGG
*
592 CAAAAATTGGCCAAAATGCCATAGGTTAACCATCAAGAGTTCCGGACC
1 CAAAAATTGG-CAAAAAGCCATAGGTTAACCATCAAGAGTTCCGGACC
* *
640 CAAAAATTGGCAGAAAAGCCGTAGGTTAACCATCATGAGTTCCGGACC
1 CAAAAATTGGCA-AAAAGCCATAGGTTAACCATCAAGAGTTCCGGACC
* *
688 CAATAATTGGCCAAAA
1 CAAAAATTGGCAAAAA
704 TTAGAAATCC
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
47 6 0.10
48 52 0.90
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (47 bp):
CAAAAATTGGCAAAAAGCCATAGGTTAACCATCAAGAGTTCCGGACC
Done.