Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012504.1 Corchorus olitorius cultivar O-4 contig12537, 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: 44437
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:12521 original size:1 final size:1
Alignment explanation
Indices: 12515--12539 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
12505 CAAGAATTGG
12515 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
12540 AAAATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:22540 original size:6 final size:6
Alignment explanation
Indices: 22529--22554 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
22519 GCAGCCATGC
22529 GCATTT GCATTT GCATTT GCATTT GC
1 GCATTT GCATTT GCATTT GCATTT GC
22555 GAAAAATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.46
Consensus pattern (6 bp):
GCATTT
Found at i:25560 original size:1 final size:1
Alignment explanation
Indices: 25556--25586 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
25546 GGGCCCCCCC
25556 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25587 CTCGAACTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:26277 original size:7 final size:7
Alignment explanation
Indices: 26265--26291 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
26255 AGGCGCCACG
26265 TTTGAAC
1 TTTGAAC
26272 TTTGAAC
1 TTTGAAC
26279 TTTGAAC
1 TTTGAAC
26286 TTTGAA
1 TTTGAA
26292 TTCTATGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (7 bp):
TTTGAAC
Found at i:30253 original size:18 final size:18
Alignment explanation
Indices: 30230--30265 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
30220 TAAAAGGCCT
*
30230 AAAGAGAGGTTACAATTC
1 AAAGAGAGATTACAATTC
30248 AAAGAGAGATTACAATTC
1 AAAGAGAGATTACAATTC
30266 TAGATAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.22
Consensus pattern (18 bp):
AAAGAGAGATTACAATTC
Found at i:31284 original size:2 final size:2
Alignment explanation
Indices: 31277--31308 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31267 AGAGGGTTTG
31277 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31309 TAATGGGGAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32298 original size:44 final size:45
Alignment explanation
Indices: 32234--32350 Score: 155
Period size: 44 Copynumber: 2.6 Consensus size: 45
32224 GGCAGTTATA
* *
32234 ATAATATAATATAAGATGATTTGTCATTTTCTATCAGACTACACTT
1 ATAATAT-ATATAAGATGATTTGTCATTTTCTATCAGACGACAATT
* * *
32280 ATAAT-TTTATAAGATGATTTGTCTTTTTCTATCAGACGGCAATT
1 ATAATATATATAAGATGATTTGTCATTTTCTATCAGACGACAATT
*
32324 ATAATAATATATAAGATGATCTGTCAT
1 ATAAT-ATATATAAGATGATTTGTCAT
32351 GACATATTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
44 38 0.62
45 1 0.02
46 22 0.36
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (45 bp):
ATAATATATATAAGATGATTTGTCATTTTCTATCAGACGACAATT
Found at i:32495 original size:97 final size:99
Alignment explanation
Indices: 32322--32517 Score: 308
Period size: 97 Copynumber: 2.0 Consensus size: 99
32312 CAGACGGCAA
* * *
32322 TTATAATAATATATAAGATGATCTGTCATGACATATTTATAATGTAATCCCTTTTCAAGAGTCAA
1 TTATAATAATATATAAGATGATCTGTCAAGACACATTTATAATGTAACCCCTTTTCAAGAGTCAA
32387 TATTCAAGCTGAACAACTTAAAATTGTGTGACCC
66 TATTCAAGCTGAACAACTTAAAATTGTGTGACCC
* *
32421 TTATAA-AA-ATATAAGATGATCTGTCAAGTCACATTTATAATGTAACCCCTTTTTAAG-GTCCA
1 TTATAATAATATATAAGATGATCTGTCAAGACACATTTATAATGTAACCCCTTTTCAAGAGT-CA
*
32483 ATATTCACGCTGAACAACTTAAAATTGTGTGACCC
65 ATATTCAAGCTGAACAACTTAAAATTGTGTGACCC
32518 AATGTCAATC
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
96 2 0.02
97 80 0.89
98 2 0.02
99 6 0.07
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (99 bp):
TTATAATAATATATAAGATGATCTGTCAAGACACATTTATAATGTAACCCCTTTTCAAGAGTCAA
TATTCAAGCTGAACAACTTAAAATTGTGTGACCC
Found at i:40671 original size:12 final size:11
Alignment explanation
Indices: 40648--40684 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
40638 TACCTCGTAC
40648 TATTATATTAT
1 TATTATATTAT
40659 TATTATCATTAT
1 TATTAT-ATTAT
40671 TATTA-ATTA-
1 TATTATATTAT
40680 TATTA
1 TATTA
40685 GACTTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 5 0.20
10 4 0.16
11 6 0.24
12 10 0.40
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTATATTAT
Found at i:42394 original size:6 final size:6
Alignment explanation
Indices: 42383--42412 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
42373 AATTGCACCT
*
42383 AATCAA AATCAA AATCAA GATCAA AATCAA
1 AATCAA AATCAA AATCAA AATCAA AATCAA
42413 GAGCACTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.63, C:0.17, G:0.03, T:0.17
Consensus pattern (6 bp):
AATCAA
Done.