Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010807.1 Corchorus capsularis cultivar CVL-1 contig10828, 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: 17967
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:10030 original size:126 final size:126
Alignment explanation
Indices: 9804--10057 Score: 490
Period size: 126 Copynumber: 2.0 Consensus size: 126
9794 GTTGCCTAGT
9804 TATCAGCTCTCATTTCCTGTTTAGTCAAGCCTTTGTATTTGATATGTGCTACTCCATGGTTTTTC
1 TATCAGCTCTCATTTCCTGTTTAGTCAAGCCTTTGTATTTGATATGTGCTACTCCATGGTTTTTC
*
9869 CAGTAAAGCTGGTAAATTTTAGTATAAAATGTAAGCGTTTTTATTGTTTTCTGTAACTAAC
66 CAGTAAAGCTGGTAAATTTTAGTATAAAATATAAGCGTTTTTATTGTTTTCTGTAACTAAC
9930 TATCAGCTCTCATTTCCTGTTTAGTCAAGCCTTTGTATTTGATATGTGCTACTCCATGGTTTTTC
1 TATCAGCTCTCATTTCCTGTTTAGTCAAGCCTTTGTATTTGATATGTGCTACTCCATGGTTTTTC
*
9995 CAGTAAAGCTGGTAAATTTTAGTATCAAATATAAGCGTTTTTATTGTTTTCTGTAACTAAC
66 CAGTAAAGCTGGTAAATTTTAGTATAAAATATAAGCGTTTTTATTGTTTTCTGTAACTAAC
10056 TA
1 TA
10058 GCAAACCTGT
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 126 1.00
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (126 bp):
TATCAGCTCTCATTTCCTGTTTAGTCAAGCCTTTGTATTTGATATGTGCTACTCCATGGTTTTTC
CAGTAAAGCTGGTAAATTTTAGTATAAAATATAAGCGTTTTTATTGTTTTCTGTAACTAAC
Found at i:14481 original size:12 final size:12
Alignment explanation
Indices: 14464--14489 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
14454 TGGTTTAATG
14464 AAAAAAAAAAAC
1 AAAAAAAAAAAC
14476 AAAAAAAAAAAC
1 AAAAAAAAAAAC
14488 AA
1 AA
14490 GTAGCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:17823 original size:174 final size:174
Alignment explanation
Indices: 17520--17871 Score: 579
Period size: 174 Copynumber: 2.0 Consensus size: 174
17510 GTTTTCAAGG
*
17520 GTTCGGTTATTCTTCGCTTATTCAATATGTTGCTAAGATAAAAAGCTTATTAGAGGTCTCTATTG
1 GTTCGGTTATTCTTCACTTATTCAATATGTTGCTAAGATAAAAAGCTTATTAGAGGTCTCTATTG
*
17585 ACCATGCTTTGGACTACGTAGTCCATTGGTACCACTAAGATCTAAGCTGGAGCATATAGCTGCAA
66 ACCATGCTTTGGACTAC--ACTCCATTGGTACCACTAAGATCTAAGCTGGAGCATATAGCTGCAA
17650 AGTTACATTATATTTTAATTATTTATACAAAACTATAAGAAAACATTTTAT
129 AGTTACA-T-TA---TAATTATTTATACAAAACTATAAGAAAACATTTTAT
17701 GTTCGGTTATTCTTCACTTATTC-A-ATGTTGCTAAGAT-AAAAGCTTATTAGAGGTCTCTATTG
1 GTTCGGTTATTCTTCACTTATTCAATATGTTGCTAAGATAAAAAGCTTATTAGAGGTCTCTATTG
*
17763 ACCATGCTTTGGACT-C-CTCCATTGGTACCACTAAGATCTAAGCTGGAGCATATGGCTGCAAAG
66 ACCATGCTTTGGACTACACTCCATTGGTACCACTAAGATCTAAGCTGGAGCATATAGCTGCAAAG
17826 TTACATTATAATTATTTATACAAAACTATAAGAAAACATTTTAT
131 TTACATTATAATTATTTATACAAAACTATAAGAAAACATTTTAT
17870 GT
1 GT
17872 AATTCTTTTT
Statistics
Matches: 168, Mismatches: 3, Indels: 12
0.92 0.02 0.07
Matches are distributed among these distances:
169 38 0.23
172 2 0.01
173 1 0.01
174 50 0.30
177 1 0.01
178 40 0.24
179 13 0.08
180 1 0.01
181 22 0.13
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (174 bp):
GTTCGGTTATTCTTCACTTATTCAATATGTTGCTAAGATAAAAAGCTTATTAGAGGTCTCTATTG
ACCATGCTTTGGACTACACTCCATTGGTACCACTAAGATCTAAGCTGGAGCATATAGCTGCAAAG
TTACATTATAATTATTTATACAAAACTATAAGAAAACATTTTAT
Done.