Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017473.1 Corchorus olitorius cultivar O-4 contig17506, 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: 26772
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:19824 original size:29 final size:29
Alignment explanation
Indices: 19789--19864 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
19779 ACCGAATCGT
*
19789 CAAATAAGCCCTTGAACTTTTATTTCGGC
1 CAAATAAGCCCCTGAACTTTTATTTCGGC
* *
19818 CAAATAAACCCCTGAATTTTTATTTCGGC
1 CAAATAAGCCCCTGAACTTTTATTTCGGC
19847 CAAATAAGCCCCTGAACT
1 CAAATAAGCCCCTGAACT
19865 CTTAAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTTTTATTTCGGC
Found at i:20871 original size:21 final size:21
Alignment explanation
Indices: 20846--20887 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
20836 ATTTACTGTT
20846 GTGTCATTTTATTTATCTCTA
1 GTGTCATTTTATTTATCTCTA
20867 GTGTCATTTTATTTATCTCTA
1 GTGTCATTTTATTTATCTCTA
20888 ATTAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (21 bp):
GTGTCATTTTATTTATCTCTA
Found at i:21127 original size:45 final size:46
Alignment explanation
Indices: 21062--21150 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 46
21052 GGAGGATTAT
*
21062 TGAAAGAAGATCCACATATGTGGATCATTA-TTATCAAAAAAGATC
1 TGAAAGAAGATCCACATATGTGGAGCATTATTTATCAAAAAAGATC
* * *
21107 TGAAAGAAGATCCACGTATGTGGAGGATTATTTATCAAAGAAGA
1 TGAAAGAAGATCCACATATGTGGAGCATTATTTATCAAAAAAGA
21151 AATTTATTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 27 0.69
46 12 0.31
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (46 bp):
TGAAAGAAGATCCACATATGTGGAGCATTATTTATCAAAAAAGATC
Found at i:21409 original size:62 final size:62
Alignment explanation
Indices: 21326--21488 Score: 265
Period size: 62 Copynumber: 2.6 Consensus size: 62
21316 CTCCCAAGTT
21326 ATCAA-TTCAAGATCAAGTCATTCGACCCTTGAATCAAATTAAATCAAACTCTCAAATTATC
1 ATCAAGTTCAAGATCAAGTCATTCGACCCTTGAATCAAATTAAATCAAACTCTCAAATTATC
* *
21387 ATCAAGTTCAAGATCAAGTCATTAGACCCTTGGATCAAATTAAATCAAACTCTCAAATTATC
1 ATCAAGTTCAAGATCAAGTCATTCGACCCTTGAATCAAATTAAATCAAACTCTCAAATTATC
* * * *
21449 GTTAAGTTCAAGATCAAGTCATTCGACCCTTAAAGCAAAT
1 ATCAAGTTCAAGATCAAGTCATTCGACCCTTGAATCAAAT
21489 CTTGAAGTAG
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
61 5 0.05
62 88 0.95
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (62 bp):
ATCAAGTTCAAGATCAAGTCATTCGACCCTTGAATCAAATTAAATCAAACTCTCAAATTATC
Found at i:23333 original size:15 final size:15
Alignment explanation
Indices: 23309--23339 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
23299 TTGAAATTTT
*
23309 ATAATTAATTTTTAA
1 ATAATAAATTTTTAA
23324 ATAATAAATTTTTAA
1 ATAATAAATTTTTAA
23339 A
1 A
23340 ATGTCAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATAAATTTTTAA
Found at i:24460 original size:21 final size:22
Alignment explanation
Indices: 24377--24513 Score: 143
Period size: 22 Copynumber: 6.2 Consensus size: 22
24367 TTGCTATATT
*
24377 ATTTTGATAACCTCTCTAAGAA
1 ATTTTGATAACCTCTCTATGAA
* *
24399 ATTGTGATAACCTCTCTGTGAA
1 ATTTTGATAACCTCTCTATGAA
* * *
24421 ACTTTGATAACCACACTATGAA
1 ATTTTGATAACCTCTCTATGAA
24443 ATTTTGAT-ACCAT-TCTATGAA
1 ATTTTGATAACC-TCTCTATGAA
* * *
24464 ATTTTGATAACCACACTATAAA
1 ATTTTGATAACCTCTCTATGAA
* *
24486 ATTGTGATAACCTCTATATGAA
1 ATTTTGATAACCTCTCTATGAA
24508 ACTTTT
1 A-TTTT
24514 TTTGATGACT
Statistics
Matches: 91, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
21 18 0.20
22 70 0.77
23 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (22 bp):
ATTTTGATAACCTCTCTATGAA
Found at i:24476 original size:43 final size:43
Alignment explanation
Indices: 24377--24513 Score: 159
Period size: 43 Copynumber: 3.1 Consensus size: 43
24367 TTGCTATATT
* * * *
24377 ATTTTGATAACCTCTCTAAGAAATTGTGATAACCTCTCTGTGAA
1 ATTTTGATAACCACACTATGAAATTGTGAT-ACCTCTCTATGAA
* *
24421 ACTTTGATAACCACACTATGAAATTTTGATACCAT-TCTATGAA
1 ATTTTGATAACCACACTATGAAATTGTGATACC-TCTCTATGAA
* *
24464 ATTTTGATAACCACACTATAAAATTGTGATAACCTCTATATGAA
1 ATTTTGATAACCACACTATGAAATTGTGAT-ACCTCTCTATGAA
24508 ACTTTT
1 A-TTTT
24514 TTTGATGACT
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
43 38 0.48
44 37 0.47
45 4 0.05
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (43 bp):
ATTTTGATAACCACACTATGAAATTGTGATACCTCTCTATGAA
Found at i:24603 original size:22 final size:22
Alignment explanation
Indices: 24575--24616 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
24565 GATTTGGTAC
24575 ACTATGAAATTTGGATAACCAT
1 ACTATGAAATTTGGATAACCAT
*
24597 ACTATGAAATTTTGATAACC
1 ACTATGAAATTTGGATAACC
24617 TCCTTATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (22 bp):
ACTATGAAATTTGGATAACCAT
Found at i:24633 original size:22 final size:22
Alignment explanation
Indices: 24608--24650 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
24598 CTATGAAATT
*
24608 TTGATAACCTCCTTATAGAATG
1 TTGATAACCTCCCTATAGAATG
*
24630 TTGATAACTTCCCTATAGAAT
1 TTGATAACCTCCCTATAGAAT
24651 TTCATGAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (22 bp):
TTGATAACCTCCCTATAGAATG
Found at i:24690 original size:22 final size:22
Alignment explanation
Indices: 24665--24786 Score: 103
Period size: 22 Copynumber: 5.7 Consensus size: 22
24655 TGAATCTCAC
*
24665 TATGAAATTTTGATAAGCACAA
1 TATGAAATTTTGATAAGCACAT
*
24687 TATGAAATTTTGATTAG----T
1 TATGAAATTTTGATAAGCACAT
* *
24705 TTTGAAATTTTTG-TAACCACAT
1 TATGAAA-TTTTGATAAGCACAT
* *
24727 TATGAAATTTTGACAACCACAT
1 TATGAAATTTTGATAAGCACAT
* *
24749 TATGAAATTTCGAT-AGCTACAC
1 TATGAAATTTTGATAAGC-ACAT
*
24771 TATGAAATTTCGATAA
1 TATGAAATTTTGATAA
24787 TCTGCAAAGT
Statistics
Matches: 81, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
18 8 0.10
19 5 0.06
21 7 0.09
22 60 0.74
23 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAAGCACAT
Found at i:25459 original size:22 final size:22
Alignment explanation
Indices: 25333--25483 Score: 121
Period size: 22 Copynumber: 6.9 Consensus size: 22
25323 TGAATATTTT
*
25333 TATGAAATTTTGAT-AACTACCC
1 TATGAAATTTTGATAAACTA-AC
* *
25355 TATTAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAAACTA-AC
** *
25377 TATGAAATTTTGATAATTTAGC
1 TATGAAATTTTGATAAACTAAC
* *
25399 TATGAAATTGTGATAAACT-TC
1 TATGAAATTTTGATAAACTAAC
*
25420 ATATGAAACTTTGATAAACTAAC
1 -TATGAAATTTTGATAAACTAAC
* **
25443 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGATAAA-CTAAC
*
25466 TATGAAAATTTG-TAAACT
1 TATGAAATTTTGATAAACT
25484 TCCTATGATT
Statistics
Matches: 105, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
21 3 0.03
22 85 0.81
23 17 0.16
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAAACTAAC
Found at i:26667 original size:7 final size:7
Alignment explanation
Indices: 26650--26762 Score: 105
Period size: 6 Copynumber: 18.4 Consensus size: 7
26640 GATTTAAACT
26650 TAAA-AA
1 TAAATAA
*
26656 TAAATCA
1 TAAATAA
26663 TAAATAA
1 TAAATAA
26670 T-AATAA
1 TAAATAA
26676 T-AATAA
1 TAAATAA
26682 T-AATAA
1 TAAATAA
26688 T-AATAA
1 TAAATAA
26694 T-AATAA
1 TAAATAA
26700 T-AATAA
1 TAAATAA
26706 T-AATAA
1 TAAATAA
26712 T-AATAA
1 TAAATAA
26718 T-AATAA
1 TAAATAA
26724 T-AATAA
1 TAAATAA
26730 T-AATAA
1 TAAATAA
26736 T-AATAA
1 TAAATAA
26742 T-AATAA
1 TAAATAA
26748 T-AATAA
1 TAAATAA
26754 T-AATAA
1 TAAATAA
26760 TAA
1 TAA
26763 TATAGTAGAA
Statistics
Matches: 103, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
6 94 0.91
7 9 0.09
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (7 bp):
TAAATAA
Found at i:26673 original size:3 final size:3
Alignment explanation
Indices: 26665--26764 Score: 200
Period size: 3 Copynumber: 33.3 Consensus size: 3
26655 ATAAATCATA
26665 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
26713 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
26761 AAT A
1 AAT A
26765 TAGTAGAA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 97 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.