Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019583.1 Corchorus olitorius cultivar O-4 contig19616, 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: 8412
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Found at i:613 original size:12 final size:12
Alignment explanation
Indices: 596--640 Score: 72
Period size: 12 Copynumber: 3.6 Consensus size: 12
586 ATCTTCTTCT
596 TTTTTTTGTTTG
1 TTTTTTTGTTTG
608 TTTTTTTGTTTG
1 TTTTTTTGTTTG
620 TTTTTTTGTTGTTG
1 TTTTTTTG-T-TTG
634 TTTTTTT
1 TTTTTTT
641 TTTCTTAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 20 0.65
13 1 0.03
14 10 0.32
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (12 bp):
TTTTTTTGTTTG
Found at i:3020 original size:8 final size:8
Alignment explanation
Indices: 3009--3056 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
2999 ATTTGAGGCC
*
3009 TTGAATAA
1 TTGAAGAA
3017 TTGAAGAA
1 TTGAAGAA
*
3025 TTGAAGCA
1 TTGAAGAA
* *
3033 TCGAATAA
1 TTGAAGAA
*
3041 CTGAAGAA
1 TTGAAGAA
3049 TTGAAGAA
1 TTGAAGAA
3057 AGACCACCCT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.25
Consensus pattern (8 bp):
TTGAAGAA
Found at i:3089 original size:36 final size:35
Alignment explanation
Indices: 3050--3549 Score: 494
Period size: 35 Copynumber: 14.1 Consensus size: 35
3040 ACTGAAGAAT
* **
3050 TGAAGAAAGACCACCCTGGGTCATTCTGAAATAAGT
1 TGAAGAAAGACCACCCTGGGTCA-ACTGAAATAAAC
* *
3086 TGAAGCAAGACCACCCTGGGTC-ACTTGAAATACAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATAAAC
* * * * * *
3121 TGAA-AAATGACCACCCTCGATCATTCCGACACAAAC
1 TGAAGAAA-GACCACCCTGGGTCA-ACTGAAATAAAC
* *
3157 TAAAGACAGACCACCCTGGGTCAACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
*
3192 TGAAGGAAA-ACCACCCTGGGTCAACTGAAATATAC
1 TGAA-GAAAGACCACCCTGGGTCAACTGAAATAAAC
3227 TG-AGAAAGGACCACCCTGGGTCAACTGAAATAAAC
1 TGAAGAAA-GACCACCCTGGGTCAACTGAAATAAAC
* *
3262 TGAAAAAAGACCACCCTGGGTCAACTGAAATATAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
*
3297 TG-AGAAAAGACCACCCTGGGTCAACTGAAATAAAT
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
* * * * *
3332 TGAAAAAAGACCACCCTGGATCAATCCGAACTGAAC
1 TGAAGAAAGACCACCCTGGGTCAA-CTGAAATAAAC
* * *** * * * *
3368 TGAGGAACA-ACCACTCTCAATCATTCCGACACAAAC
1 TGAAGAA-AGACCACCCTGGGTCA-ACTGAAATAAAC
*
3404 TGAAGGAAGACCACCCTGGGTC-ACTTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATAAAC
*
3439 TGAAGAAAAGACCACCCTGGGTCAACTGACATAAAC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
*
3475 TGAAGAAAAGACCACCCTGGGTCGAA-TGAAATAAGC
1 TGAAG-AAAGACCACCCTGGGTC-AACTGAAATAAAC
* *
3511 TGAAGAACGACCACCCTAGGTCAACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
3546 TGAA
1 TGAA
3550 TAATCGCCCT
Statistics
Matches: 381, Mismatches: 63, Indels: 41
0.79 0.13 0.08
Matches are distributed among these distances:
33 4 0.01
34 8 0.02
35 205 0.54
36 156 0.41
37 8 0.02
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (35 bp):
TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
Found at i:3255 original size:70 final size:70
Alignment explanation
Indices: 3050--3549 Score: 454
Period size: 71 Copynumber: 7.1 Consensus size: 70
3040 ACTGAAGAAT
* * *
3050 TGAAG-AAAGACCACCCTGGGTCATTCTGAAATAAGTTGA-AGCAAGACCACCCTGGGTC-ACTT
1 TGAAGAAAAGACCACCCTGGGTCA-ACTGAAATAA-CTGAGA-AAAGACCACCCTGGGTCAAC-T
*
3112 GAAATACAC
62 GAAATAAAC
* * * * *
3121 TGAA-AAATGACCACCCTCGATCATTCCGACACA-AACT-A-AAGACAGACCACCCTGGGTCAAC
1 TGAAGAAAAGACCACCCTGGGTCA-ACTGA-A-ATAACTGAGAA-A-AGACCACCCTGGGTCAAC
3182 TGAAATAAAC
61 TGAAATAAAC
* *
3192 TGAAGGAAA-ACCACCCTGGGTCAACTGAAATATACTGAGAAAGGACCACCCTGGGTCAACTGAA
1 TGAAGAAAAGACCACCCTGGGTCAACTGAAATA-ACTGAGAAAAGACCACCCTGGGTCAACTGAA
3256 ATAAAC
65 ATAAAC
3262 TGAA-AAAAGACCACCCTGGGTCAACTGAAATATACTGAGAAAAGACCACCCTGGGTCAACTGAA
1 TGAAGAAAAGACCACCCTGGGTCAACTGAAATA-ACTGAGAAAAGACCACCCTGGGTCAACTGAA
*
3326 ATAAAT
65 ATAAAC
* * * * * *** * *
3332 TGAA-AAAAGACCACCCTGGATCAATCCGAACTGAACTGAGGAACA-ACCACTCTCAATCATTCC
1 TGAAGAAAAGACCACCCTGGGTCAA-CTGAAAT-AACTGA-GAAAAGACCACCCTGGGTCA-ACT
* *
3395 GACACAAAC
62 GAAATAAAC
*
3404 TGAAG-GAAGACCACCCTGGGTC-ACTTGAAATAAACTGAAGAAAAGACCACCCTGGGTCAACTG
1 TGAAGAAAAGACCACCCTGGGTCAAC-TGAAAT-AACTG-AGAAAAGACCACCCTGGGTCAACTG
*
3467 ACATAAAC
63 AAATAAAC
* *
3475 TGAAGAAAAGACCACCCTGGGTCGAA-TGAAATAAGCTGA-AGAACGACCACCCTAGGTCAACTG
1 TGAAGAAAAGACCACCCTGGGTC-AACTGAAATAA-CTGAGA-AAAGACCACCCTGGGTCAACTG
3538 AAATAAAC
63 AAATAAAC
3546 TGAA
1 TGAA
3550 TAATCGCCCT
Statistics
Matches: 357, Mismatches: 47, Indels: 50
0.79 0.10 0.11
Matches are distributed among these distances:
68 1 0.00
69 5 0.01
70 124 0.35
71 149 0.42
72 76 0.21
73 1 0.00
74 1 0.00
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (70 bp):
TGAAGAAAAGACCACCCTGGGTCAACTGAAATAACTGAGAAAAGACCACCCTGGGTCAACTGAAA
TAAAC
Found at i:5354 original size:14 final size:14
Alignment explanation
Indices: 5332--5364 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5322 TGAAAACAAA
5332 TTTTG-GAAACCAT
1 TTTTGAGAAACCAT
*
5345 TTTTGAGAAATCAT
1 TTTTGAGAAACCAT
5359 TTTTGA
1 TTTTGA
5365 AAAATCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.45
Consensus pattern (14 bp):
TTTTGAGAAACCAT
Found at i:5745 original size:2 final size:2
Alignment explanation
Indices: 5738--5778 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
5728 GAATAGTAGA
* * *
5738 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT TT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5779 CTAAAGGGCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Done.