Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001630.1 Corchorus capsularis cultivar CVL-1 contig01630, 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: 3752
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34
Found at i:376 original size:29 final size:31
Alignment explanation
Indices: 312--378 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
302 TCCGTTTAAA
* *
312 TATATCCTGATTTGGTCATTTCATGTAACGT
1 TATATCCTGAATTGGTCATTTCATGGAACGT
*
343 TATATCCTGAATTGG-CGTTTC-TGGAACGT
1 TATATCCTGAATTGGTCATTTCATGGAACGT
372 TATATCC
1 TATATCC
379 CAAATTGATC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 14 0.42
30 5 0.15
31 14 0.42
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (31 bp):
TATATCCTGAATTGGTCATTTCATGGAACGT
Found at i:1071 original size:11 final size:11
Alignment explanation
Indices: 1057--1094 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1047 ATTCATAACA
1057 AATTTATAATT
1 AATTTATAATT
1068 AATTTATAATT
1 AATTTATAATT
1079 -ATTTGATAATT
1 AATTT-ATAATT
*
1090 TATTT
1 AATTT
1095 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:1386 original size:13 final size:13
Alignment explanation
Indices: 1368--1395 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1358 TTTGTTTGTC
1368 AGATAGTTTGTAA
1 AGATAGTTTGTAA
1381 AGATAGTTTGTAA
1 AGATAGTTTGTAA
1394 AG
1 AG
1396 TATGTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (13 bp):
AGATAGTTTGTAA
Found at i:2198 original size:161 final size:161
Alignment explanation
Indices: 1933--2256 Score: 576
Period size: 161 Copynumber: 2.0 Consensus size: 161
1923 AGGAGACCGA
*
1933 AACAATATTAATGGAAGCATCACCTAAAACTATATGTTGAATTGAATAGAATCGATATAAGGAAG
1 AACAATATTAATGGAAGCAGCACCTAAAACTATATGTTGAATTGAATAGAATCGATATAAGGAAG
1998 CAACAGAAAAACCATGATCTTATACAAATCTAACAAGTAAATGGGTACACCCATAAGAAATCTAA
66 CAACAGAAAAACCATGATCTTATACAAATCTAACAAGTAAATGGGTACACCCATAAGAAATCTAA
2063 TTCAGTTTAACTCCACAACTCTAGTTTCTGC
131 TTCAGTTTAACTCCACAACTCTAGTTTCTGC
** * * *
2094 AACAATATTAATGGAAGCAGCACCTAAAACTATATGTTGAATTTTATAGAATTGTTATAGGGAAG
1 AACAATATTAATGGAAGCAGCACCTAAAACTATATGTTGAATTGAATAGAATCGATATAAGGAAG
* *
2159 CAACAGAAAAACCATGATCTTATTCAAATCTAACAAGTAAATGGGTACAGCCATAAGAAATCTAA
66 CAACAGAAAAACCATGATCTTATACAAATCTAACAAGTAAATGGGTACACCCATAAGAAATCTAA
2224 TTCAGTTTAACTCCACAACTCTAGTTTCTGC
131 TTCAGTTTAACTCCACAACTCTAGTTTCTGC
2255 AA
1 AA
2257 TTCCTCTGCT
Statistics
Matches: 155, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
161 155 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (161 bp):
AACAATATTAATGGAAGCAGCACCTAAAACTATATGTTGAATTGAATAGAATCGATATAAGGAAG
CAACAGAAAAACCATGATCTTATACAAATCTAACAAGTAAATGGGTACACCCATAAGAAATCTAA
TTCAGTTTAACTCCACAACTCTAGTTTCTGC
Found at i:3667 original size:15 final size:15
Alignment explanation
Indices: 3647--3680 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3637 TTTTATTTAT
3647 TATAACATATATATA
1 TATAACATATATATA
3662 TATAACATATATATA
1 TATAACATATATATA
3677 TATA
1 TATA
3681 CACACACAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (15 bp):
TATAACATATATATA
Done.