Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010866.1 Corchorus olitorius cultivar O-4 contig10898, 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: 18914
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:238 original size:22 final size:23
Alignment explanation
Indices: 213--259 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
203 CAAGTACAAC
*
213 AACAAG-AATCAGCATGA-AACAT
1 AACAAGAAATAAGCA-GATAACAT
235 AACAAGAAATAAGCAGATAACAT
1 AACAAGAAATAAGCAGATAACAT
258 AA
1 AA
260 AGTAGAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.60, C:0.15, G:0.13, T:0.13
Consensus pattern (23 bp):
AACAAGAAATAAGCAGATAACAT
Found at i:11613 original size:78 final size:76
Alignment explanation
Indices: 11524--11788 Score: 250
Period size: 78 Copynumber: 3.4 Consensus size: 76
11514 AAACAACACT
* *
11524 CTAAGCAGGTTTACTCAAACGACAACTT-TAAATAGGGACCTAAGCAGGCGTACTTACACGAAAC
1 CTAAGCAGGTTTACT-AAATGA-AA-TTCTAAATAGGGACCTAAGCAGGCGTACTTAAACGAAAC
* *
11588 ACGAAGCAGAGATC
63 TCTAAGCAGAGATC
* * * * ** * *
11602 CTAAGCAGGTTTACTTAAATGATAATTCTAAGTAGAGAGCTAAGCGGGTTTTCATAAACGAAACT
1 CTAAGCAGGTTTAC-TAAATGA-AATTCTAAATAGGGACCTAAGCAGGCGTACTTAAACGAAACT
11667 CTAAGCAGAGATC
64 CTAAGCAGAGATC
** * * *
11680 CTAATTAGGTTTGACTAAATGAAAATTCTAAATGGGGACCTAAGTAGGTTCG-A-TTAAATGAAA
1 CTAAGCAGGTTT-ACTAAATG-AAATTCTAAATAGGGACCTAAGCAGG--CGTACTTAAACGAAA
11743 CTCTAAGCAGAGA-C
62 CTCTAAGCAGAGATC
11757 CTAAGCAGGTTTACTTAAATGGAAATTCTAAA
1 CTAAGCAGGTTTAC-TAAAT-GAAATTCTAAA
11789 CGAGGACGAA
Statistics
Matches: 151, Mismatches: 28, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
76 2 0.01
77 28 0.19
78 117 0.77
79 4 0.03
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (76 bp):
CTAAGCAGGTTTACTAAATGAAATTCTAAATAGGGACCTAAGCAGGCGTACTTAAACGAAACTCT
AAGCAGAGATC
Found at i:11645 original size:39 final size:38
Alignment explanation
Indices: 11524--11787 Score: 174
Period size: 39 Copynumber: 6.8 Consensus size: 38
11514 AAACAACACT
* * ** *
11524 CTAAGCAGGTTTACTCAAACGACAACTT-TAAATAGGGAC
1 CTAAGCAGGTTTACTTAAATGA-AA-TTCTAAGCAGAGAC
** * * ** *
11563 CTAAGCAGGCGTACTTACACGAAACACGAAGCAGAGATC
1 CTAAGCAGGTTTACTTAAATGAAATTCTAAGCAGAGA-C
* *
11602 CTAAGCAGGTTTACTTAAATGATAATTCTAAGTAGAGAG
1 CTAAGCAGGTTTACTTAAATGA-AATTCTAAGCAGAGAC
* * * * *
11641 CTAAGCGGGTTTTCATAAACGAAACTCTAAGCAGAGATC
1 CTAAGCAGGTTTACTTAAATGAAATTCTAAGCAGAGA-C
** *** *
11680 CTAATTAGGTTTGAC-TAAATGAAAATTCTAAATGGGGAC
1 CTAAGCAGGTTT-ACTTAAATG-AAATTCTAAGCAGAGAC
* * *
11719 CTAAGTAGGTTCGA-TTAAATGAAACTCTAAGCAGAGAC
1 CTAAGCAGGTT-TACTTAAATGAAATTCTAAGCAGAGAC
11757 CTAAGCAGGTTTACTTAAATGGAAATTCTAA
1 CTAAGCAGGTTTACTTAAAT-GAAATTCTAA
11788 ACGAGGACGA
Statistics
Matches: 169, Mismatches: 46, Indels: 20
0.72 0.20 0.09
Matches are distributed among these distances:
37 1 0.01
38 49 0.29
39 96 0.57
40 23 0.14
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (38 bp):
CTAAGCAGGTTTACTTAAATGAAATTCTAAGCAGAGAC
Found at i:11827 original size:57 final size:57
Alignment explanation
Indices: 11739--11910 Score: 299
Period size: 57 Copynumber: 3.0 Consensus size: 57
11729 TCGATTAAAT
11739 GAAACTCTAAGCAGAGACCTAAGCAGGTTTACTTAAATGGAAATTCTAAACGAGGAC
1 GAAACTCTAAGCAGAGACCTAAGCAGGTTTACTTAAATGGAAATTCTAAACGAGGAC
* * *
11796 GAAACTCTAAGCAGAGACCTAAACAGGTTTACTTAAATGGAAATTCTAAACAAGGAT
1 GAAACTCTAAGCAGAGACCTAAGCAGGTTTACTTAAATGGAAATTCTAAACGAGGAC
*
11853 GAAACTCTAAGCAGAGATCCTAAGCAGGTTTACTTAAATGGAAATTCTAAATGAGGAC
1 GAAACTCTAAGCAGAGA-CCTAAGCAGGTTTACTTAAATGGAAATTCTAAACGAGGAC
11911 CTAAGCAGGC
Statistics
Matches: 107, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
57 71 0.66
58 36 0.34
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (57 bp):
GAAACTCTAAGCAGAGACCTAAGCAGGTTTACTTAAATGGAAATTCTAAACGAGGAC
Found at i:11846 original size:27 final size:27
Alignment explanation
Indices: 11814--11903 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
11804 AAGCAGAGAC
11814 CTAAACAGGTTTACTTAAATGGAAATT
1 CTAAACAGGTTTACTTAAATGGAAATT
** *** * *
11841 CTAAACAAGGATGAAACTCTAAGCAGAGATC
1 CTAAAC-AGG-T-TTACT-TAAATGGAAATT
*
11872 CTAAGCAGGTTTACTTAAATGGAAATT
1 CTAAACAGGTTTACTTAAATGGAAATT
11899 CTAAA
1 CTAAA
11904 TGAGGACCTA
Statistics
Matches: 43, Mismatches: 16, Indels: 8
0.64 0.24 0.12
Matches are distributed among these distances:
27 17 0.40
28 6 0.14
29 2 0.05
30 6 0.14
31 12 0.28
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (27 bp):
CTAAACAGGTTTACTTAAATGGAAATT
Found at i:17586 original size:20 final size:20
Alignment explanation
Indices: 17563--17603 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
17553 ACAAGGATAA
*
17563 TTAAACGTGTTAGTCGTGTT
1 TTAAACGTGTTAGCCGTGTT
*
17583 TTAATCGTGTTAGCCGTGTT
1 TTAAACGTGTTAGCCGTGTT
17603 T
1 T
17604 GACACGGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.12, G:0.24, T:0.46
Consensus pattern (20 bp):
TTAAACGTGTTAGCCGTGTT
Found at i:18602 original size:22 final size:21
Alignment explanation
Indices: 18577--18908 Score: 149
Period size: 22 Copynumber: 15.3 Consensus size: 21
18567 AAATTTTTTT
18577 TAACCTCCTTATGAAATTTTGA
1 TAACCTCC-TATGAAATTTTGA
* * *
18599 TAACCTCCCTAAGGAATTTTAA
1 TAACCT-CCTATGAAATTTTGA
*
18621 AAACCTCACTATGAAATTTTGA
1 TAACCTC-CTATGAAATTTTGA
* *
18643 TAACTTCCGAATGAAATTTTGA
1 TAACCTCC-TATGAAATTTTGA
* * *
18665 TAACCAACACTATGAGATGTTGA
1 TAACC-TC-CTATGAAATTTTGA
* * * *
18688 TACCCTTCATATGATATATTGA
1 TAACC-TCCTATGAAATTTTGA
* * * *
18710 TAACCACGTTATGAAAATTTAA
1 TAACCTC-CTATGAAATTTTGA
* *
18732 GAACCTCCATTTG-AATTGTT-A
1 TAACCTCC-TATGAAATT-TTGA
* * *
18753 GTAATCACACTCTGAAATTTTGA
1 -TAACCTC-CTATGAAATTTTGA
* * *
18776 TAATCACACTATGAAATTGTGA
1 TAACCTC-CTATGAAATTTTGA
* *
18798 TAACCTTGCTATAAAATTTTGA
1 TAACC-TCCTATGAAATTTTGA
*
18820 TAAACCTCCTTATAAAATTTT-A
1 T-AACCTCC-TATGAAATTTTGA
* *
18842 TAACCTTCTTATGAAATCTTGA
1 TAACC-TCCTATGAAATTTTGA
*
18864 TAA----CTA-CAAATTTTGA
1 TAACCTCCTATGAAATTTTGA
**
18880 TAACCTCCCTATGATTTTTTGA
1 TAACCT-CCTATGAAATTTTGA
18902 TAACCTC
1 TAACCTC
18909 ATTATG
Statistics
Matches: 233, Mismatches: 54, Indels: 47
0.70 0.16 0.14
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
21 24 0.10
22 156 0.67
23 39 0.17
24 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (21 bp):
TAACCTCCTATGAAATTTTGA
Done.