Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401628.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4746.0, 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, 676
Length: 1128
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Found at i:534 original size:45 final size:44
Alignment explanation
Indices: 481--747 Score: 199
Period size: 45 Copynumber: 6.1 Consensus size: 44
471 ATATGACATA
* *
481 TAACAACCTAACCATTACGTGTCACATATTTTTGTATATGCCGTG
1 TAACAACCTAACCATGACGTGTCACATGTTTTTGTATATG-CGTG
* **
526 TAATAACCTAACCATGATATGTCACATGTTTTTGTATATG-GTG
1 TAACAACCTAACCATGACGTGTCACATGTTTTTGTATATGCGTG
* *
569 T------GT-ACCATGACGTGTCACATGTTTTTGTATATAACGTG
1 TAACAACCTAACCATGACGTGTCACATGTTTTTGTATAT-GCGTG
** ** * *
607 TAACAATTTAATTATAACATGTCACATGTTTTTGTATATAGCGTG
1 TAACAACCTAACCATGACGTGTCACATGTTTTTGTATAT-GCGTG
* * ** * ** * *
652 CAACAACTTAATTATAACGTGTCATGTGCTTTTGTATATGACCTG
1 TAACAACCTAACCATGACGTGTCACATGTTTTTGTATATG-CGTG
* * * *
697 TAACAACCTAACTATGACGTGTCACATATTTTTGTACATAACGTG
1 TAACAACCTAACCATGACGTGTCACATGTTTTTGTATAT-GCGTG
742 TAACAA
1 TAACAA
748 TTTAACTATA
Statistics
Matches: 178, Mismatches: 33, Indels: 22
0.76 0.14 0.09
Matches are distributed among these distances:
36 27 0.15
37 1 0.01
38 4 0.02
43 4 0.02
44 2 0.01
45 140 0.79
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (44 bp):
TAACAACCTAACCATGACGTGTCACATGTTTTTGTATATGCGTG
Found at i:594 original size:81 final size:81
Alignment explanation
Indices: 491--645 Score: 211
Period size: 81 Copynumber: 1.9 Consensus size: 81
481 TAACAACCTA
* ** * * *
491 ACCATTACGTGTCACATATTTTTGTATATGCCGTGTAATAACCTAACCATGATATGTCACATGTT
1 ACCATGACGTGTCACATATTTTTGTATATAACGTGTAACAACCTAACCATAACATGTCACATGTT
556 TTTGTATATGGTGTGT
66 TTTGTATATGGTGTGT
* ** **
572 ACCATGACGTGTCACATGTTTTTGTATATAACGTGTAACAATTTAATTATAACATGTCACATGTT
1 ACCATGACGTGTCACATATTTTTGTATATAACGTGTAACAACCTAACCATAACATGTCACATGTT
637 TTTGTATAT
66 TTTGTATAT
646 AGCGTGCAAC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 63 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (81 bp):
ACCATGACGTGTCACATATTTTTGTATATAACGTGTAACAACCTAACCATAACATGTCACATGTT
TTTGTATATGGTGTGT
Found at i:605 original size:24 final size:24
Alignment explanation
Indices: 578--651 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
568 GTGTACCATG
578 ACGTGTCACATGTTTTTGTATATA
1 ACGTGTCACATGTTTTTGTATATA
* * **
602 ACGTGTAACA--ATTTAAT-TATA
1 ACGTGTCACATGTTTTTGTATATA
*
623 ACATGTCACATGTTTTTGTATATA
1 ACGTGTCACATGTTTTTGTATATA
*
647 GCGTG
1 ACGTG
652 CAACAACTTA
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
21 12 0.33
22 4 0.11
23 4 0.11
24 16 0.44
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (24 bp):
ACGTGTCACATGTTTTTGTATATA
Found at i:608 original size:36 final size:36
Alignment explanation
Indices: 536--608 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
526 TAATAACCTA
* ***
536 ACCATGATATGTCACATGTTTTTGTATATGGTGTGT
1 ACCATGACATGTCACATGTTTTTGTATATAACGTGT
*
572 ACCATGACGTGTCACATGTTTTTGTATATAACGTGT
1 ACCATGACATGTCACATGTTTTTGTATATAACGTGT
608 A
1 A
609 ACAATTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.41
Consensus pattern (36 bp):
ACCATGACATGTCACATGTTTTTGTATATAACGTGT
Found at i:624 original size:21 final size:21
Alignment explanation
Indices: 598--673 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
588 TGTTTTTGTA
598 TATAACGTGTAACAATTTAAT
1 TATAACGTGTAACAATTTAAT
* * **
619 TATAACATGTCAC-ATGTTTTT
1 TATAACGTGTAACAAT-TTAAT
* *
640 GTATATAGCGTGCAACAACTTAAT
1 -TATA-A-CGTGTAACAATTTAAT
664 TATAACGTGT
1 TATAACGTGT
674 CATGTGCTTT
Statistics
Matches: 39, Mismatches: 11, Indels: 10
0.65 0.18 0.17
Matches are distributed among these distances:
20 2 0.05
21 18 0.46
22 5 0.13
23 5 0.13
24 8 0.21
25 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (21 bp):
TATAACGTGTAACAATTTAAT
Found at i:754 original size:45 final size:45
Alignment explanation
Indices: 578--759 Score: 220
Period size: 45 Copynumber: 4.0 Consensus size: 45
568 GTGTACCATG
* *
578 ACGTGTCACATGTTTTTGTATATAACGTGTAACAATTTAATTATA
1 ACGTGTCACATGTTTTTGTATATAACGTGTAACAACTTAACTATA
* * * *
623 ACATGTCACATGTTTTTGTATATAGCGTGCAACAACTTAATTATA
1 ACGTGTCACATGTTTTTGTATATAACGTGTAACAACTTAACTATA
** * * * * *
668 ACGTGTCATGTGCTTTTGTATATGACCTGTAACAACCTAACTATG
1 ACGTGTCACATGTTTTTGTATATAACGTGTAACAACTTAACTATA
* * *
713 ACGTGTCACATATTTTTGTACATAACGTGTAACAATTTAACTATA
1 ACGTGTCACATGTTTTTGTATATAACGTGTAACAACTTAACTATA
758 AC
1 AC
760 ATGCACTACA
Statistics
Matches: 112, Mismatches: 25, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 112 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (45 bp):
ACGTGTCACATGTTTTTGTATATAACGTGTAACAACTTAACTATA
Done.