Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012259.1 Corchorus olitorius cultivar O-4 contig12292, 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: 21069
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Found at i:1210 original size:56 final size:57
Alignment explanation
Indices: 1136--1249 Score: 140
Period size: 57 Copynumber: 2.0 Consensus size: 57
1126 GTTAAAGAGT
* * * *
1136 ACTTATTACGAACGATAG-AAACCTGTAATGAGATGTCTGATAAAAGAAATAAATTC
1 ACTTATTACAAACAATAGAAAACCTATAATGAGATGTCTAATAAAAGAAATAAATTC
* * * * *
1192 ACTTATTACAAACAATAGAAAATCTATAATTAGATGTCTAATCAAATAAATATATTC
1 ACTTATTACAAACAATAGAAAACCTATAATGAGATGTCTAATAAAAGAAATAAATTC
1249 A
1 A
1250 TGTATTTCTA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
56 16 0.33
57 32 0.67
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (57 bp):
ACTTATTACAAACAATAGAAAACCTATAATGAGATGTCTAATAAAAGAAATAAATTC
Found at i:5358 original size:4 final size:4
Alignment explanation
Indices: 5349--5384 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
5339 AAGATTAATA
5349 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
5385 AATGTATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:5398 original size:10 final size:10
Alignment explanation
Indices: 5383--5416 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
5373 GTATGTATGT
5383 ATAATGTATA
1 ATAATGTATA
5393 ATAATGTATAA
1 ATAATGTAT-A
5404 TATAATGTATA
1 -ATAATGTATA
5415 AT
1 AT
5417 TATATTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 11 0.50
11 2 0.09
12 9 0.41
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (10 bp):
ATAATGTATA
Found at i:9507 original size:22 final size:22
Alignment explanation
Indices: 9482--9558 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
9472 TATTTTTATG
*
9482 AAATTTTGATAACTACCCTATT
1 AAATTTTGATAACTACCCTATA
** *
9504 AAATTTTGATAACTACTATATG
1 AAATTTTGATAACTACCCTATA
*
9526 AAATTTTGATAATTA-CCTATA
1 AAATTTTGATAACTACCCTATA
*
9547 AAATTGTGATAA
1 AAATTTTGATAA
9559 ATTCCATAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
21 14 0.30
22 33 0.70
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACTACCCTATA
Found at i:9577 original size:43 final size:44
Alignment explanation
Indices: 9481--9581 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 44
9471 ATATTTTTAT
* * * * *
9481 GAAATTTTGATAACTACCCTATTAAATTTTGATAACTACTATAT
1 GAAATTTTGATAACTACCCTATAAAATTGTGATAAATACCATAA
* *
9525 GAAATTTTGATAATTA-CCTATAAAATTGTGATAAATTCCATAA
1 GAAATTTTGATAACTACCCTATAAAATTGTGATAAATACCATAA
*
9568 GAAACTTTGATAAC
1 GAAATTTTGATAAC
9582 CTAACAATGA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
43 33 0.69
44 15 0.31
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.38
Consensus pattern (44 bp):
GAAATTTTGATAACTACCCTATAAAATTGTGATAAATACCATAA
Found at i:9616 original size:22 final size:20
Alignment explanation
Indices: 9591--9632 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
9581 CCTAACAATG
9591 AAATTTTAATAAACTTTCCTAT
1 AAATTTT-AT-AACTTTCCTAT
*
9613 AAATTTTGTAACTTTCCTAT
1 AAATTTTATAACTTTCCTAT
9633 GATTTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (20 bp):
AAATTTTATAACTTTCCTAT
Found at i:14440 original size:26 final size:26
Alignment explanation
Indices: 14404--14457 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
14394 ACAAACCCCT
14404 TCCCCCAACAAACAAACCCAGTGAAA
1 TCCCCCAACAAACAAACCCAGTGAAA
14430 TCCCCCAACAAACAAACCCAGTGAAA
1 TCCCCCAACAAACAAACCCAGTGAAA
14456 TC
1 TC
14458 TCATTACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.39, G:0.07, T:0.09
Consensus pattern (26 bp):
TCCCCCAACAAACAAACCCAGTGAAA
Found at i:15613 original size:7 final size:7
Alignment explanation
Indices: 15603--15635 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
15593 GTTAGAAGTT
*
15603 AGAAATG
1 AGAAATC
15610 AGAAATC
1 AGAAATC
15617 AGAAATC
1 AGAAATC
15624 AGAAATC
1 AGAAATC
15631 AGAAA
1 AGAAA
15636 CCAAGTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.61, C:0.09, G:0.18, T:0.12
Consensus pattern (7 bp):
AGAAATC
Found at i:18198 original size:50 final size:50
Alignment explanation
Indices: 18139--18237 Score: 198
Period size: 50 Copynumber: 2.0 Consensus size: 50
18129 AATATCATAA
18139 AGTTATAAATAGAATCACCACACTAAGAAACAGAATCACCACACTTATAT
1 AGTTATAAATAGAATCACCACACTAAGAAACAGAATCACCACACTTATAT
18189 AGTTATAAATAGAATCACCACACTAAGAAACAGAATCACCACACTTATA
1 AGTTATAAATAGAATCACCACACTAAGAAACAGAATCACCACACTTATA
18238 AATAGAATCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.48, C:0.22, G:0.08, T:0.21
Consensus pattern (50 bp):
AGTTATAAATAGAATCACCACACTAAGAAACAGAATCACCACACTTATAT
Found at i:18250 original size:42 final size:43
Alignment explanation
Indices: 18191--18298 Score: 139
Period size: 42 Copynumber: 2.5 Consensus size: 43
18181 ACTTATATAG
*
18191 TTATAAATAGAATCACCACACTAAGAAACA-GA-ATCACCACAC
1 TTATAAATAGAATCACCACACTAAGAAACAGGATATCA-CAAAC
* * * *
18233 TTATAAATAGAATCACCACACTAATAGACATGGATATCATAAAG
1 TTATAAATAGAATCACCACACTAAGAAACA-GGATATCACAAAC
18277 TTATAAATAGAATCACCACACT
1 TTATAAATAGAATCACCACACT
18299 TATATAGAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
42 28 0.48
44 26 0.45
45 4 0.07
ACGTcount: A:0.48, C:0.21, G:0.08, T:0.22
Consensus pattern (43 bp):
TTATAAATAGAATCACCACACTAAGAAACAGGATATCACAAAC
Found at i:18301 original size:21 final size:21
Alignment explanation
Indices: 18191--18302 Score: 118
Period size: 21 Copynumber: 5.2 Consensus size: 21
18181 ACTTATATAG
18191 TTATAAATAGAATCACCACAC
1 TTATAAATAGAATCACCACAC
* * *
18212 TAAGAAACAGAATCACCACAC
1 TTATAAATAGAATCACCACAC
18233 TTATAAATAGAATCACCACAC
1 TTATAAATAGAATCACCACAC
* * * * *
18254 TAATAGACATGGATATCA-TAAAG
1 TTATA-A-ATAGA-ATCACCACAC
18277 TTATAAATAGAATCACCACAC
1 TTATAAATAGAATCACCACAC
18298 TTATA
1 TTATA
18303 TAGAATAGAA
Statistics
Matches: 71, Mismatches: 16, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
20 4 0.06
21 51 0.72
22 2 0.03
23 10 0.14
24 4 0.06
ACGTcount: A:0.48, C:0.21, G:0.08, T:0.23
Consensus pattern (21 bp):
TTATAAATAGAATCACCACAC
Done.