Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014532.1 Corchorus olitorius cultivar O-4 contig14565, 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: 10059
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:8043 original size:29 final size:30
Alignment explanation
Indices: 7983--8062 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 30
7973 GCTAAATACC
* *
7983 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTCGGGA
8014 CAAAATAATCCCTTATGTTTT-TTTCGGGA
1 CAAAATAATCCCTTATGTTTTCTTTCGGGA
* *
8043 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
8063 CAAAAATGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.56
31 20 0.44
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTCGGGA
Found at i:8161 original size:28 final size:28
Alignment explanation
Indices: 8129--8185 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
8119 GCTTTTCCAC
*
8129 GTCAGC-AAGGGAGTGGATTTGTCCCAAA
1 GTCAGCAAAGGGACT-GATTTGTCCCAAA
8157 GTCAGCATAAGGGACTGATTTGTCCCAAA
1 GTCAGCA-AAGGGACTGATTTGTCCCAAA
8186 AGCAAAACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 6 0.23
29 13 0.50
30 7 0.27
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (28 bp):
GTCAGCAAAGGGACTGATTTGTCCCAAA
Found at i:8200 original size:31 final size:31
Alignment explanation
Indices: 8162--8229 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
8152 CCAAAGTCAG
* *
8162 CATAAGGGACTGATTTGTCCCAAAAGCAAAA
1 CATAAGGGACTCATTTGTCCCAAAAGAAAAA
* *
8193 CATAAGGGATTCTTTTGTCCCAAAAGAAAAA
1 CATAAGGGACTCATTTGTCCCAAAAGAAAAA
*
8224 TATAAG
1 CATAAG
8230 AGAATTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.24
Consensus pattern (31 bp):
CATAAGGGACTCATTTGTCCCAAAAGAAAAA
Found at i:9035 original size:49 final size:49
Alignment explanation
Indices: 8933--9036 Score: 149
Period size: 49 Copynumber: 2.1 Consensus size: 49
8923 AAATACTATT
* *
8933 TTATTTTTACCATTTTATTATTTTAATTAAATATATTTTTAATATACTT
1 TTATTTTTACCATTTTACTATTTTAATTAAATATATTTTTAATATACTA
*
8982 TTATTTTTATCATTTTACTATTTTAATTAAATATATTTCTTAA-ATGAC-A
1 TTATTTTTACCATTTTACTATTTTAATTAAATATATTT-TTAATAT-ACTA
9031 TTATTT
1 TTATTT
9037 AAACTTTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
49 44 0.88
50 6 0.12
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.60
Consensus pattern (49 bp):
TTATTTTTACCATTTTACTATTTTAATTAAATATATTTTTAATATACTA
Found at i:9226 original size:7 final size:7
Alignment explanation
Indices: 9214--9247 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
9204 GAAGGGGAAG
9214 GAAAAAA
1 GAAAAAA
9221 GAAAAAA
1 GAAAAAA
9228 GAAAAAA
1 GAAAAAA
9235 G-AAAAA
1 GAAAAAA
9241 GAAAAAA
1 GAAAAAA
9248 ATCAATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:9248 original size:14 final size:14
Alignment explanation
Indices: 9214--9247 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
9204 GAAGGGGAAG
9214 GAAAAAAGAAAAAA
1 GAAAAAAGAAAAAA
9228 GAAAAAAG-AAAAA
1 GAAAAAAGAAAAAA
9241 GAAAAAA
1 GAAAAAA
9248 ATCAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
GAAAAAAGAAAAAA
Found at i:9397 original size:31 final size:31
Alignment explanation
Indices: 9290--9387 Score: 142
Period size: 32 Copynumber: 3.1 Consensus size: 31
9280 ACTAAATACT
* * *
9290 AAAAAAATTCTCTTATATTTTTCTTTTGAGAC
1 AAAAAAA-TCCCTTATGTTTTTCTTTTGGGAC
9322 AAAAAAATCCCTTATGTTTTTCTTTTGGGCAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGG-AC
*
9354 AAAAAAATCCCTTATGTTTTTTTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
9385 AAA
1 AAA
9388 TCAGTCCCTT
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
31 24 0.39
32 37 0.61
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:9563 original size:29 final size:30
Alignment explanation
Indices: 9516--9588 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 30
9506 TTTTGAGACG
* * *
9516 TAAGGGATTAATTTGTCCCGAAA-AAAACA
1 TAAGGGATTATTTTATCCCAAAACAAAACA
9545 TAAGGGATTATTTTATCCCAAAACAAAACA
1 TAAGGGATTATTTTATCCCAAAACAAAACA
*
9575 TAAGGGATTTTTTT
1 TAAGGGATTATTTT
9589 GGGTATTTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 20 0.51
30 19 0.49
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (30 bp):
TAAGGGATTATTTTATCCCAAAACAAAACA
Done.