Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012540.1 Corchorus olitorius cultivar O-4 contig12573, 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: 28738
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Found at i:8778 original size:2 final size:2
Alignment explanation
Indices: 8771--8802 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8761 AGTTAGTATA
8771 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
8803 ACCGAACATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:12403 original size:2 final size:2
Alignment explanation
Indices: 12398--12445 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
12388 TATTTTAAAA
* *
12398 AC AC AC AC AA AC AC AC AC GC AC AC AC AC AC AC AC AC A- AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
12439 AC AC AC A
1 AC AC AC A
12446 ACAACAACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.46, G:0.02, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12451 original size:3 final size:3
Alignment explanation
Indices: 12432--12488 Score: 96
Period size: 3 Copynumber: 18.3 Consensus size: 3
12422 ACACACACAC
12432 ACA ACA CACA CACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA -ACA -ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
12479 ACA ACA ACA A
1 ACA ACA ACA A
12489 AGTCATCAGT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.87
4 7 0.13
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:17164 original size:14 final size:14
Alignment explanation
Indices: 17145--17171 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17135 TGCAGGGTTT
17145 TTCTCCTAAAACCC
1 TTCTCCTAAAACCC
17159 TTCTCCTAAAACC
1 TTCTCCTAAAACC
17172 GCCTTGATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.41, G:0.00, T:0.30
Consensus pattern (14 bp):
TTCTCCTAAAACCC
Found at i:18714 original size:22 final size:22
Alignment explanation
Indices: 18689--18734 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
18679 GCAGGCTTGC
18689 AGCGCAGAAGCAGAAGAGAAGG
1 AGCGCAGAAGCAGAAGAGAAGG
*
18711 AGCGCAGAAGCAGAAGAGGAGG
1 AGCGCAGAAGCAGAAGAGAAGG
18733 AG
1 AG
18735 TGGGGAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.43, T:0.00
Consensus pattern (22 bp):
AGCGCAGAAGCAGAAGAGAAGG
Found at i:21475 original size:216 final size:216
Alignment explanation
Indices: 21101--21533 Score: 814
Period size: 216 Copynumber: 2.0 Consensus size: 216
21091 TCACAATACA
21101 TTAACTATCAAATAGAAACAGATCAATCACAAATTAACCTTTTAAATTAAAATAGTAAAAATAAA
1 TTAACTATCAAATAGAAACAGATCAATCACAAATTAACCTTTTAAATTAAAATAGTAAAAATAAA
* *
21166 ATGATTATAAAAATATTTAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAGCTGTATA
66 ATGATCATAAAAATATTTAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAACTGTATA
21231 TTAAATTTTTTTTAATATATCCAAGTTTTTAATGAAAAATAGTAACATGGTAAAAATAAAGTAAT
131 TTAAATTTTTTTTAATATATCCAAGTTTTTAATGAAAAATAGTAACATGGTAAAAATAAAGTAAT
21296 TATAATGATATTCGATTTAAT
196 TATAATGATATTCGATTTAAT
* *
21317 TTAACTATCAAATAGAAACAGATCAATCACAAATTGACCTTTTAAATTAAAATAGTAAAAGTAAA
1 TTAACTATCAAATAGAAACAGATCAATCACAAATTAACCTTTTAAATTAAAATAGTAAAAATAAA
21382 ATGATCATAAAAAATATTTAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAACTGTAT
66 ATGATCAT-AAAAATATTTAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAACTGTAT
21447 ATTAAA-TTTTTTTAATATATCCAAGTTTTTAATGAAAAATAGTAACATGGTAAAAATAAAGTAA
130 ATTAAATTTTTTTTAATATATCCAAGTTTTTAATGAAAAATAGTAACATGGTAAAAATAAAGTAA
21511 TTATAATGATATTCGATTTAAT
195 TTATAATGATATTCGATTTAAT
21533 T
1 T
21534 AAATAAAAAT
Statistics
Matches: 212, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
216 151 0.71
217 61 0.29
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (216 bp):
TTAACTATCAAATAGAAACAGATCAATCACAAATTAACCTTTTAAATTAAAATAGTAAAAATAAA
ATGATCATAAAAATATTTAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAACTGTATA
TTAAATTTTTTTTAATATATCCAAGTTTTTAATGAAAAATAGTAACATGGTAAAAATAAAGTAAT
TATAATGATATTCGATTTAAT
Found at i:22534 original size:19 final size:19
Alignment explanation
Indices: 22508--22557 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
22498 CGTGTACCTG
22508 TAACCGTTTCACCACCGTT
1 TAACCGTTTCACCACCGTT
* *
22527 TGACCGTTTCATCACCGTT
1 TAACCGTTTCACCACCGTT
22546 TAACCGTTTCAC
1 TAACCGTTTCAC
22558 TTAAGCTCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (19 bp):
TAACCGTTTCACCACCGTT
Found at i:24854 original size:18 final size:18
Alignment explanation
Indices: 24831--24867 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
24821 CGTTTTAAGT
24831 TGCATTTAGCATATTCCA
1 TGCATTTAGCATATTCCA
24849 TGCATTTAGCATATTCCA
1 TGCATTTAGCATATTCCA
24867 T
1 T
24868 TTTAAGAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (18 bp):
TGCATTTAGCATATTCCA
Done.