Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018538.1 Corchorus olitorius cultivar O-4 contig18571, 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: 7613
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:90 original size:39 final size:39
Alignment explanation
Indices: 10--91 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 39
1 GATAAAGCG
** ** **
10 ATAATCCTAAACCAGGATTGGTATAAAACTGTTAAGGCA
1 ATAATCCTAAACCAGGATTGAAATAAAACTGACAACACA
* *
49 ATAATCCTAGATCAGGATTGAAATAAAACTGACAACACA
1 ATAATCCTAAACCAGGATTGAAATAAAACTGACAACACA
88 ATAA
1 ATAA
92 CCAAACATCA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.46, C:0.16, G:0.15, T:0.23
Consensus pattern (39 bp):
ATAATCCTAAACCAGGATTGAAATAAAACTGACAACACA
Found at i:357 original size:81 final size:82
Alignment explanation
Indices: 255--471 Score: 265
Period size: 90 Copynumber: 2.6 Consensus size: 82
245 AATCAAATGG
* * *
255 TACCCGGAGGTTTTATCAATTGCCCGGAGAACTTAACAGAATTAAT-TTTGATCCAATGCCCGGA
1 TACCCGGAGGTTTTATCAATTGCCCTGAGGACTTATCAGAATTAATGTTTGATCCAATGCCCGGA
319 GGACTTATCAGAATTAA
66 GGACTTATCAGAATTAA
* * * *
336 TACCCGGAGGTTTTATCAATTGCCCTGAGGACTTATCGGAATTAATACCCGGAGGTTTTATCGAT
1 TACCCGGAGGTTTTATCAATTGCCCTGAGGACTTATCAGAATTAAT--------GTTTGATCCAA
* *
401 TGCCCTGAGGACTTATCGGAATTAA
58 TGCCCGGAGGACTTATCAGAATTAA
*
426 TACCCGGAGGTTTTATCAATTGCCCTGAGGACTTATCAAAATTAAT
1 TACCCGGAGGTTTTATCAATTGCCCTGAGGACTTATCAGAATTAAT
472 ACCCAGAGGT
Statistics
Matches: 116, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
81 42 0.36
90 74 0.64
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (82 bp):
TACCCGGAGGTTTTATCAATTGCCCTGAGGACTTATCAGAATTAATGTTTGATCCAATGCCCGGA
GGACTTATCAGAATTAA
Found at i:371 original size:20 final size:20
Alignment explanation
Indices: 348--507 Score: 68
Period size: 20 Copynumber: 7.2 Consensus size: 20
338 CCCGGAGGTT
348 TTATCAATTGCCCTGAGGAC
1 TTATCAATTGCCCTGAGGAC
* * **
368 TTATCGGAATTAATACCCGGAGGTT
1 TTATC--AA-T--TGCCCTGAGGAC
*
393 TTATCGATTGCCCTGAGGAC
1 TTATCAATTGCCCTGAGGAC
* * **
413 TTATCGGAATTAATACCCGGAGGTT
1 TTATC--AA-T--TGCCCTGAGGAC
438 TTATCAATTGCCCTGAGGAC
1 TTATCAATTGCCCTGAGGAC
* * **
458 TTATCAAAATTAATACCCAGAGGTT
1 TTATC--AA-T--TGCCCTGAGGAC
483 TTATCAATTGCCCTGAGGAC
1 TTATCAATTGCCCTGAGGAC
503 TTATC
1 TTATC
508 GGAATTAATA
Statistics
Matches: 99, Mismatches: 26, Indels: 30
0.64 0.17 0.19
Matches are distributed among these distances:
20 44 0.44
22 8 0.08
23 8 0.08
25 39 0.39
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (20 bp):
TTATCAATTGCCCTGAGGAC
Found at i:378 original size:45 final size:45
Alignment explanation
Indices: 311--528 Score: 373
Period size: 45 Copynumber: 4.8 Consensus size: 45
301 TTTGATCCAA
* *
311 TGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTTATCAAT
1 TGCCCTGAGGACTTATCGGAATTAATACCCGGAGGTTTTATCAAT
*
356 TGCCCTGAGGACTTATCGGAATTAATACCCGGAGGTTTTATCGAT
1 TGCCCTGAGGACTTATCGGAATTAATACCCGGAGGTTTTATCAAT
401 TGCCCTGAGGACTTATCGGAATTAATACCCGGAGGTTTTATCAAT
1 TGCCCTGAGGACTTATCGGAATTAATACCCGGAGGTTTTATCAAT
** *
446 TGCCCTGAGGACTTATCAAAATTAATACCCAGAGGTTTTATCAAT
1 TGCCCTGAGGACTTATCGGAATTAATACCCGGAGGTTTTATCAAT
*
491 TGCCCTGAGGACTTATCGGAATTAATACCAGGAGGTTT
1 TGCCCTGAGGACTTATCGGAATTAATACCCGGAGGTTT
529 CTAAATTTGT
Statistics
Matches: 162, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 162 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (45 bp):
TGCCCTGAGGACTTATCGGAATTAATACCCGGAGGTTTTATCAAT
Found at i:759 original size:102 final size:101
Alignment explanation
Indices: 554--802 Score: 392
Period size: 103 Copynumber: 2.4 Consensus size: 101
544 GAGGACCTAC
* *
554 CAATGCAAACTCTGAATAGAGACCTTGACCAAGGATTTTGAACTTAAACATGAATTTTTGATGAA
1 CAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTT-AACTTAAACATGAATCTTTGATGAA
* *
619 AAACTTGATGAAATGAAATGATACCTGGAGGTTTTAT
65 AAACTTGATAAAATGAAATGATACCCGGAGGTTTTAT
656 CAATGCAAAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTTGATG-
1 CAATGC-AAACTCTGAATAGAGACCTTGAACAAGGATTTT-AACTTAAACATGAATCTTTGATGA
* *
720 AGAACTTGATAAAATGAAATGGTACCCGGAGGTTTTAT
64 AAAACTTGATAAAATGAAATGATACCCGGAGGTTTTAT
* *
758 CAATGCAAATTCTGAATTGAGACCTTGAACAAGGATTTTAACTTA
1 CAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTTAACTTA
803 CATAGAAATA
Statistics
Matches: 137, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
100 6 0.04
101 31 0.23
102 46 0.34
103 54 0.39
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (101 bp):
CAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTTAACTTAAACATGAATCTTTGATGAAA
AACTTGATAAAATGAAATGATACCCGGAGGTTTTAT
Found at i:2666 original size:15 final size:15
Alignment explanation
Indices: 2626--2669 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2616 TGGGATTGTT
*
2626 TTTTTGTATTTTTGA
1 TTTTTGTTTTTTTGA
2641 TTTTTGATTTTTTTG-
1 TTTTTG-TTTTTTTGA
2656 TTCTTTGTTTTTTT
1 TT-TTTGTTTTTTT
2670 TTTGGAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.07, C:0.02, G:0.11, T:0.80
Consensus pattern (15 bp):
TTTTTGTTTTTTTGA
Found at i:2669 original size:24 final size:24
Alignment explanation
Indices: 2624--2668 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2614 TTTGGGATTG
*
2624 TTTTTTTGTATTTTTGATTTTTGA
1 TTTTTTTGTATCTTTGATTTTTGA
*
2648 TTTTTTTGT-TCTTTGTTTTTT
1 TTTTTTTGTATCTTTGATTTTT
2669 TTTTGGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.07, C:0.02, G:0.11, T:0.80
Consensus pattern (24 bp):
TTTTTTTGTATCTTTGATTTTTGA
Found at i:7592 original size:14 final size:15
Alignment explanation
Indices: 7563--7592 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7553 AGAACATGAC
7563 TTGAAAAAACCTTTT
1 TTGAAAAAACCTTTT
*
7578 TTGAAAATACCTTTT
1 TTGAAAAAACCTTTT
7593 ATTGCTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (15 bp):
TTGAAAAAACCTTTT
Done.