Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014841.1 Corchorus olitorius cultivar O-4 contig14874, 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: 18331
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:8393 original size:23 final size:23
Alignment explanation
Indices: 8367--8414 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
8357 GGGGTAAAAC
*
8367 TCTCTCAACAATGGTTCTTTCAT
1 TCTCTCAACAATGGTTCTTCCAT
8390 TCTCTCAACAATGGTTCTTCCAT
1 TCTCTCAACAATGGTTCTTCCAT
8413 TC
1 TC
8415 ACAAGACTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.29, G:0.08, T:0.42
Consensus pattern (23 bp):
TCTCTCAACAATGGTTCTTCCAT
Found at i:12838 original size:209 final size:209
Alignment explanation
Indices: 12478--12870 Score: 732
Period size: 209 Copynumber: 1.9 Consensus size: 209
12468 GACCAATATT
* *
12478 TACAGTGTGTTTGGATAAATTTTTTGAGGGATCAGTAAAGGACAGGATAGGATGTGAAATGAGGG
1 TACAGTGTGTTTGGATAAATTTTTTGAGGGATCAGTAAAGGACAGGATAGGATGGGAAAAGAGGG
*
12543 TTTTTTAAAGAAAAGGAAGGGAAGGACCAATCCTTGTTTGGATTTTTTAAAATATAAAAAGTAAG
66 TTTTTTAAAGAAAAGGAAGGGAAGGACCAATCCTTGTTTGGATTGTTTAAAATATAAAAAGTAAG
12608 GAACACGAGGGATCACCTAACATTTAATAAATAAAAACTTTGTTGGTCCTTGTTTGGAGTACCAA
131 GAACACGAGGGATCACCTAACATTTAATAAATAAAAACTTTGTTGGTCCTTGTTTGGAGTACCAA
12673 AAAAGGTGGACTTA
196 AAAAGGTGGACTTA
12687 TACAGTGTGTTTGGATAAATTTTTTGAGGGATCAGTAAAGGACAGGATAGGATGGGAAAAGAGGG
1 TACAGTGTGTTTGGATAAATTTTTTGAGGGATCAGTAAAGGACAGGATAGGATGGGAAAAGAGGG
*
12752 TTTTTTAAAGGAAAGGAAGGGAAGGACCAATCCTTGTTTGGATTGTTTAAAATATAAAAAGTAAG
66 TTTTTTAAAGAAAAGGAAGGGAAGGACCAATCCTTGTTTGGATTGTTTAAAATATAAAAAGTAAG
* *
12817 GAACATGAGGGATCACCTAACATTTAATGAATAAAAACTTTGTTGGTCCTTGTT
131 GAACACGAGGGATCACCTAACATTTAATAAATAAAAACTTTGTTGGTCCTTGTT
12871 GGTACTCCAA
Statistics
Matches: 178, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
209 178 1.00
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (209 bp):
TACAGTGTGTTTGGATAAATTTTTTGAGGGATCAGTAAAGGACAGGATAGGATGGGAAAAGAGGG
TTTTTTAAAGAAAAGGAAGGGAAGGACCAATCCTTGTTTGGATTGTTTAAAATATAAAAAGTAAG
GAACACGAGGGATCACCTAACATTTAATAAATAAAAACTTTGTTGGTCCTTGTTTGGAGTACCAA
AAAAGGTGGACTTA
Found at i:14533 original size:49 final size:49
Alignment explanation
Indices: 14472--14594 Score: 153
Period size: 49 Copynumber: 2.6 Consensus size: 49
14462 ATCTTTTACA
14472 TTTCC-TGCACCTTTTTCTCAATTTTTACAACAAAATTGAATC-TTTAAT
1 TTTCCTTGCACCTTTTTCTCAATTTTTACAACAAAATTGAA-CATTTAAT
** *
14520 TTTCCTTGCACCTTTTTCTCAATTTTTATGACAAAATTGAACATTTACT
1 TTTCCTTGCACCTTTTTCTCAATTTTTACAACAAAATTGAACATTTAAT
** * *
14569 TTTTATTGCA-CTTTTTATCATTTTTT
1 TTTCCTTGCACCTTTTTCTCAATTTTT
14595 TGACAAAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
48 20 0.30
49 46 0.70
ACGTcount: A:0.25, C:0.19, G:0.05, T:0.51
Consensus pattern (49 bp):
TTTCCTTGCACCTTTTTCTCAATTTTTACAACAAAATTGAACATTTAAT
Found at i:16729 original size:78 final size:78
Alignment explanation
Indices: 16595--16755 Score: 295
Period size: 78 Copynumber: 2.1 Consensus size: 78
16585 GTTTTCTACT
* *
16595 TAAAATAGTAAAATGGTAAACTGAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGA
16660 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
*
16673 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGA
16738 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
16751 TAAAA
1 TAAAA
16756 CTATAAATCT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.51, C:0.01, G:0.14, T:0.34
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGA
GTTTTTAGTTGAG
Found at i:17157 original size:60 final size:60
Alignment explanation
Indices: 17093--17231 Score: 208
Period size: 60 Copynumber: 2.3 Consensus size: 60
17083 AAAGTTTGTC
* *
17093 AAAATGCTCAAATAAGGGTTTGAT-ATTTTAATTTGGCCAAATAAGGACCTAACGTTATCG
1 AAAATGCTCAAATAAGGGTCTGATCA-TTTAATTTAGCCAAATAAGGACCTAACGTTATCG
* * *
17153 AAAATACTCAAATAAGGGTCTGGTCATTTAATTTAGCCAAATAAGGGCCTAACGTTATCG
1 AAAATGCTCAAATAAGGGTCTGATCATTTAATTTAGCCAAATAAGGACCTAACGTTATCG
*
17213 AAAATGCTAAAATAAGGGT
1 AAAATGCTCAAATAAGGGT
17232 ATAGTGTCGA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
60 70 0.99
61 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGTCTGATCATTTAATTTAGCCAAATAAGGACCTAACGTTATCG
Found at i:17365 original size:60 final size:59
Alignment explanation
Indices: 17272--17435 Score: 186
Period size: 60 Copynumber: 2.7 Consensus size: 59
17262 AACTGATGCT
* *
17272 AGGCCCTTATTTGAGCATTGTCG-ATAACGTTAGGCTCTTATTTGGCCAAACTAAAAGATC
1 AGGCCCTTATTTGAGCATTGTGGCA-AACGTTAGGC-CTTATTTGGCCAAACTAAAAAATC
* * * *
17332 AGGCCCTTATTTGAGCATTTTGGCAAACATTAGGCCTTTATTTGGCCAAATTAAAAAATT
1 AGGCCCTTATTTGAGCATTGTGGCAAACGTTAGGCC-TTATTTGGCCAAACTAAAAAATC
* * * * *
17392 AGACTCTCATTTGAGTATTGTGGCAAATGTTAGGCCCTTATTTG
1 AGGCCCTTATTTGAGCATTGTGGCAAACGTTAGG-CCTTATTTG
17436 AGTAATTAAC
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 1 0.01
60 84 0.95
61 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (59 bp):
AGGCCCTTATTTGAGCATTGTGGCAAACGTTAGGCCTTATTTGGCCAAACTAAAAAATC
Done.