Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019488.1 Corchorus olitorius cultivar O-4 contig19521, 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: 26591
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:423 original size:3 final size:3
Alignment explanation
Indices: 415--462 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
405 GTGACAAGTG
415 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
463 GGAGGAATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:13234 original size:31 final size:31
Alignment explanation
Indices: 13192--13351 Score: 137
Period size: 31 Copynumber: 5.3 Consensus size: 31
13182 ATGTCCGACG
* * *
13192 GTGGCATGCCACGTGTACCAAAAAGCGACAT
1 GTGGCACGCCACGTGTACCAAAAAGTGACAC
13223 GTGGCACGCCACGTGTACCAAAAAGTGACAC
1 GTGGCACGCCACGTGTACCAAAAAGTGACAC
* ** *
13254 ATATCACGCCATGTGTACCAAAAAGTGACAC
1 GTGGCACGCCACGTGTACCAAAAAGTGACAC
* * * ** *
13285 ATGGCATGCCATGTGTTTCAAAAAATGACAC
1 GTGGCACGCCACGTGTACCAAAAAGTGACAC
* * * *
13316 ATGGCATGCCACATGCA-C-AAAAG-GACAC
1 GTGGCACGCCACGTGTACCAAAAAGTGACAC
*
13344 GTGCCACG
1 GTGGCACG
13352 TGTCATTTTT
Statistics
Matches: 108, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
28 10 0.09
29 4 0.04
30 1 0.01
31 93 0.86
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (31 bp):
GTGGCACGCCACGTGTACCAAAAAGTGACAC
Found at i:13307 original size:62 final size:62
Alignment explanation
Indices: 13199--13317 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 62
13189 ACGGTGGCAT
** *
13199 GCCACGTGTACCAAAAAGCGACATGTGGCACGCCACGTGTACCAAAAAGTGACACATATCAC
1 GCCACGTGTACCAAAAAGCGACACATGGCACGCCACGTGTACCAAAAAATGACACATATCAC
* * * * **
13261 GCCATGTGTACCAAAAAGTGACACATGGCATGCCATGTGTTTCAAAAAATGACACAT
1 GCCACGTGTACCAAAAAGCGACACATGGCACGCCACGTGTACCAAAAAATGACACAT
13318 GGCATGCCAC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 48 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (62 bp):
GCCACGTGTACCAAAAAGCGACACATGGCACGCCACGTGTACCAAAAAATGACACATATCAC
Found at i:14243 original size:17 final size:18
Alignment explanation
Indices: 14217--14251 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
14207 TGAGTTCCTC
*
14217 CATCATCTTCA-ACTCAT
1 CATCAGCTTCATACTCAT
14234 CATCAGCTTCATACTCAT
1 CATCAGCTTCATACTCAT
14252 AATTTCTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (18 bp):
CATCAGCTTCATACTCAT
Found at i:15863 original size:45 final size:43
Alignment explanation
Indices: 15812--15896 Score: 143
Period size: 45 Copynumber: 1.9 Consensus size: 43
15802 GGGAATCTAA
*
15812 TGGGTATTATTGCAATAGAATGGAGATGGGTAGGAAAAAGAATAG
1 TGGGTATCATTGCAATAGAAT-G-GATGGGTAGGAAAAAGAATAG
15857 TGGGTATCATTGCAATAGAATGGATGGGTAGGAAAAAGAA
1 TGGGTATCATTGCAATAGAATGGATGGGTAGGAAAAAGAA
15897 AAGTAGAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
43 18 0.46
44 1 0.03
45 20 0.51
ACGTcount: A:0.40, C:0.04, G:0.33, T:0.24
Consensus pattern (43 bp):
TGGGTATCATTGCAATAGAATGGATGGGTAGGAAAAAGAATAG
Found at i:18425 original size:2 final size:2
Alignment explanation
Indices: 18418--18442 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18408 CAAAGGTAAC
18418 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
18443 GAAGTTGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19793 original size:31 final size:31
Alignment explanation
Indices: 19755--19820 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
19745 CAATAAACGA
* *
19755 TCAATTTAGTTCC-TATACTCACGAGATTTGG
1 TCAATTTAG-TCCATATACTCACAAGATTGGG
19786 TCAATTTAGTCCATATACTCACAAGATTGGG
1 TCAATTTAGTCCATATACTCACAAGATTGGG
19817 TCAA
1 TCAA
19821 ATATTGAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (31 bp):
TCAATTTAGTCCATATACTCACAAGATTGGG
Found at i:19946 original size:29 final size:29
Alignment explanation
Indices: 19891--19957 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
19881 CCAATCTTAC
* * *
19891 GAGTACATGGATTAAATTGATCGTTTTTT
1 GAGTACATGGATGAAATTGAACATTTTTT
*
19920 GAGTATATGGATGAAATTGAACATTTTTGT
1 GAGTACATGGATGAAATTGAACATTTTT-T
19950 GTAGTACA
1 G-AGTACA
19958 AAGACCTCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 24 0.77
30 2 0.06
31 5 0.16
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.40
Consensus pattern (29 bp):
GAGTACATGGATGAAATTGAACATTTTTT
Done.