Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013752.1 Corchorus olitorius cultivar O-4 contig13785, 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: 30151
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1156 original size:20 final size:20
Alignment explanation
Indices: 1128--1165 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1118 GTCCAAATTA
1128 GAAATATTCAAAACAAAAAGG
1 GAAATATTC-AAACAAAAAGG
*
1149 GAAA-ATTCGAACAAAAA
1 GAAATATTCAAACAAAAA
1166 ACAAACAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.50
20 4 0.25
21 4 0.25
ACGTcount: A:0.63, C:0.11, G:0.13, T:0.13
Consensus pattern (20 bp):
GAAATATTCAAACAAAAAGG
Found at i:8629 original size:14 final size:14
Alignment explanation
Indices: 8606--8635 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
8596 TGTAAACAGA
*
8606 AACTTTAAAAAGAG
1 AACTTCAAAAAGAG
8620 AACTTCAAAAAGAG
1 AACTTCAAAAAGAG
8634 AA
1 AA
8636 AATGTGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.10, G:0.13, T:0.17
Consensus pattern (14 bp):
AACTTCAAAAAGAG
Found at i:15955 original size:42 final size:42
Alignment explanation
Indices: 15909--16017 Score: 200
Period size: 42 Copynumber: 2.6 Consensus size: 42
15899 GGTATTTATT
*
15909 ATCGGGATCGGGTAGGGTTCGGGTATTACATAATAAATTTTA
1 ATCGGGTTCGGGTAGGGTTCGGGTATTACATAATAAATTTTA
15951 ATCGGGTTCGGGTAGGGTTCGGGTATTACATAATAAATTTTA
1 ATCGGGTTCGGGTAGGGTTCGGGTATTACATAATAAATTTTA
*
15993 ATCGGGTTCGAGTAGGGTTCGGGTA
1 ATCGGGTTCGGGTAGGGTTCGGGTA
16018 GTGTATTTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.25, C:0.10, G:0.32, T:0.33
Consensus pattern (42 bp):
ATCGGGTTCGGGTAGGGTTCGGGTATTACATAATAAATTTTA
Found at i:17283 original size:35 final size:34
Alignment explanation
Indices: 17235--17367 Score: 149
Period size: 35 Copynumber: 3.8 Consensus size: 34
17225 CTCCTCGATT
* * ** *
17235 CTTAACTAAACCGAATTAAGTTGATTGTAGATTTA
1 CTTAATTACACCGAATTAAGTTGATTACA-ATTTC
17270 CTTAATTACACCGAATTAAGTTGATTACCAATTTC
1 CTTAATTACACCGAATTAAGTTGATTA-CAATTTC
* * * *
17305 CTCAATTATACCGAATTAAGTTGAATACCTATTTC
1 CTTAATTACACCGAATTAAGTTGATTA-CAATTTC
*
17340 CTTAATTACATCGAATTAAGTTGATTAC
1 CTTAATTACACCGAATTAAGTTGATTAC
17368 CAAAGTTGAA
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
34 1 0.01
35 82 0.98
36 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.38
Consensus pattern (34 bp):
CTTAATTACACCGAATTAAGTTGATTACAATTTC
Found at i:22866 original size:28 final size:29
Alignment explanation
Indices: 22797--22868 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
22787 TAAATGTGTG
* * *
22797 AATGATCAAAATACCCCTGAATATGCAAA
1 AATGACCAAAATGCCACTGAATATGCAAA
* *
22826 AATGACCATAATGCCACTGAATGTG-AAA
1 AATGACCAAAATGCCACTGAATATGCAAA
*
22854 AATGACTAAAATGCC
1 AATGACCAAAATGCC
22869 CCTGGATTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 16 0.44
29 20 0.56
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (29 bp):
AATGACCAAAATGCCACTGAATATGCAAA
Found at i:22883 original size:29 final size:28
Alignment explanation
Indices: 22768--22868 Score: 87
Period size: 28 Copynumber: 3.6 Consensus size: 28
22758 TAAATGGACC
* * *
22768 AAATGACCAAAATGCCCCCTAAATGTG-T
1 AAATGACCAAAATG-CCACTGAATGTGAA
* * * * *
22796 GAATGATCAAAATACCCCTGAATATGCAA
1 AAATGACCAAAATGCCACTGAATGTG-AA
*
22825 AAATGACCATAATGCCACTGAATGTGAA
1 AAATGACCAAAATGCCACTGAATGTGAA
*
22853 AAATGACTAAAATGCC
1 AAATGACCAAAATGCC
22869 CCTGGATTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
27 10 0.18
28 27 0.47
29 20 0.35
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (28 bp):
AAATGACCAAAATGCCACTGAATGTGAA
Found at i:23049 original size:14 final size:14
Alignment explanation
Indices: 23030--23059 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
23020 GCTCAACTTA
*
23030 ATTTATCTATATAT
1 ATTTATATATATAT
23044 ATTTATATATATAT
1 ATTTATATATATAT
23058 AT
1 AT
23060 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTATATATATAT
Done.