Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020821.1 Corchorus olitorius cultivar O-4 contig20854, 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: 64991
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:561 original size:12 final size:12
Alignment explanation
Indices: 546--570 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
536 CTGACCCGAA
546 AAATTTTTTTCC
1 AAATTTTTTTCC
558 AAATTTTTTTCC
1 AAATTTTTTTCC
570 A
1 A
571 TAATACTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATTTTTTTCC
Found at i:593 original size:2 final size:2
Alignment explanation
Indices: 586--618 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
576 CTAAACAAAC
586 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
619 GTAACAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2000 original size:23 final size:23
Alignment explanation
Indices: 1973--2017 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1963 GTTGGTTAAC
*
1973 AGTTAATTAGTT-GTTACTAAGTT
1 AGTTAATTAATTAGTT-CTAAGTT
*
1996 AGTTACTTAATTAGTTCTAAGT
1 AGTTAATTAATTAGTTCTAAGT
2018 AACTAACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.47
Consensus pattern (23 bp):
AGTTAATTAATTAGTTCTAAGTT
Found at i:4792 original size:30 final size:30
Alignment explanation
Indices: 4753--4809 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
4743 TTATCTTGAC
4753 TTTCCTCTTATACCCTCAAATTTTAATGAA
1 TTTCCTCTTATACCCTCAAATTTTAATGAA
*
4783 TTTCTTCTTATACCCTCAAATTTTAAT
1 TTTCCTCTTATACCCTCAAATTTTAAT
4810 ATCTTATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.02, T:0.47
Consensus pattern (30 bp):
TTTCCTCTTATACCCTCAAATTTTAATGAA
Found at i:7829 original size:22 final size:23
Alignment explanation
Indices: 7792--7839 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
7782 AAGTTTCCTC
*
7792 TATTTTATTTTTTTGGGTATATT
1 TATTTTATCTTTTTGGGTATATT
7815 TATTTTA-CTTTTTGGGTATATT
1 TATTTTATCTTTTTGGGTATATT
7837 TAT
1 TAT
7840 AAGTTAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.19, C:0.02, G:0.12, T:0.67
Consensus pattern (23 bp):
TATTTTATCTTTTTGGGTATATT
Found at i:30783 original size:21 final size:19
Alignment explanation
Indices: 30738--30795 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
30728 CTATTTAATA
30738 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
30757 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
30778 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
30796 TTAGAACAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:39365 original size:6 final size:6
Alignment explanation
Indices: 39354--39378 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39344 ATGAAACAAC
39354 TTCTAG TTCTAG TTCTAG TTCTAG T
1 TTCTAG TTCTAG TTCTAG TTCTAG T
39379 ATAATTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TTCTAG
Found at i:44330 original size:21 final size:19
Alignment explanation
Indices: 44305--44362 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
44295 GTTGCTCTAA
44305 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
44326 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
*
44345 TAATCTCATATGTACAGT
1 TAATCTCATCTGTACAGT
44363 TACTAAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:45045 original size:21 final size:20
Alignment explanation
Indices: 45020--45074 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
45010 GCTGCTCTAA
45020 TAATCTCATCTGTACAGTAGC
1 TAATCTCATCTGTACAGT-GC
* * *
45041 TAATCTAATTTGTACAATG-
1 TAATCTCATCTGTACAGTGC
45060 TAATCTCATCTGTAC
1 TAATCTCATCTGTAC
45075 GGTTGCTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 13 0.45
20 1 0.03
21 15 0.52
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTGC
Found at i:58758 original size:20 final size:20
Alignment explanation
Indices: 58733--58785 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
58723 CTATGTCCCT
58733 CCATTTTTAAAGTGCAGTAA
1 CCATTTTTAAAGTGCAGTAA
58753 CCATTTTTAAAGTGCAGTAA
1 CCATTTTTAAAGTGCAGTAA
58773 CCATTTTTAAAGT
1 CCATTTTTAAAGT
58786 ACTATTACAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (20 bp):
CCATTTTTAAAGTGCAGTAA
Done.