Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399824.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3062.0, 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, 1000
Length: 7786
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.32
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:3512 original size:2 final size:2
Alignment explanation
Indices: 3498--3542 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
3488 ACTCAGTCCC
3498 CT CT CT CGT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT C-T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3540 CT C
1 CT C
3543 GGGGGCTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
CT
Found at i:6602 original size:27 final size:27
Alignment explanation
Indices: 6541--6621 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 27
6531 AAAAATACCT
* * *
6541 TTTA-TTATAATATATAATTATTT-TAT
1 TTTATTTAAAATAT-TAATAATTTATAA
6567 TTTATTTTAAAATATTAATAATTTATAA
1 TTTA-TTTAAAATATTAATAATTTATAA
*
6595 TTTATTTAAAATATTAATAATTAATAA
1 TTTATTTAAAATATTAATAATTTATAA
6622 CTTAACTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 4 0.08
27 30 0.62
28 14 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTATTTAAAATATTAATAATTTATAA
Found at i:6646 original size:15 final size:16
Alignment explanation
Indices: 6623--6654 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
6613 AATTAATAAC
6623 TTAACTATTAATATTT
1 TTAACTATTAATATTT
6639 TTAA-TATTAATATTT
1 TTAACTATTAATATTT
6654 T
1 T
6655 ATTTATAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAACTATTAATATTT
Found at i:6764 original size:15 final size:16
Alignment explanation
Indices: 6697--6777 Score: 51
Period size: 15 Copynumber: 5.0 Consensus size: 16
6687 TAATATTTTA
*
6697 TTTATAATTTAAGATT
1 TTTATAATTTAAAATT
* *
6713 TATTATGA-TTAAAATA
1 T-TTATAATTTAAAATT
* *
6729 TTAATAATTTTTATTAATT
1 TTTATAA--TTTA-AAATT
6748 TTTA-AATTTAAAA-T
1 TTTATAATTTAAAATT
*
6762 TTTATAATTTATAATT
1 TTTATAATTTAAAATT
6778 AAAATTTTAG
Statistics
Matches: 48, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
14 5 0.10
15 14 0.29
16 13 0.27
17 5 0.10
18 5 0.10
19 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TTTATAATTTAAAATT
Found at i:6779 original size:21 final size:23
Alignment explanation
Indices: 6728--6786 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 23
6718 TGATTAAAAT
*
6728 ATTAATAATTTTTATTAATTTTTAA
1 ATTAA-AA-TTTTATTAATTTATAA
6753 ATTTAAAATTTTA-TAATTTAT-A
1 A-TTAAAATTTTATTAATTTATAA
6775 ATTAAAATTTTA
1 ATTAAAATTTTA
6787 GTCTTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 11 0.34
22 2 0.06
23 7 0.22
24 5 0.16
25 3 0.09
26 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTAAAATTTTATTAATTTATAA
Found at i:7008 original size:23 final size:23
Alignment explanation
Indices: 6985--7034 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
6975 TATATTTTAA
6985 TTAAAAATTTAAAATATTAATAAT
1 TTAAAAATTT-AAATATTAATAAT
** *
7009 TTAATCATTTAAATATTAATATT
1 TTAAAAATTTAAATATTAATAAT
7032 TTA
1 TTA
7035 TTCATAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAAAATTTAAATATTAATAAT
Found at i:7039 original size:23 final size:24
Alignment explanation
Indices: 6991--7039 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
6981 TTAATTAAAA
6991 ATTTAAAATATTAATAATTTAATC
1 ATTTAAAATATTAATAATTTAATC
* *
7015 ATTT-AAATATTAATATTTTATTC
1 ATTTAAAATATTAATAATTTAATC
7038 AT
1 AT
7040 AATTTGAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTTAAAATATTAATAATTTAATC
Found at i:7534 original size:21 final size:21
Alignment explanation
Indices: 7486--7534 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
7476 GAAAGTGAAA
7486 ATACTATATAACAATACTATT
1 ATACTATATAACAATACTATT
*
7507 ATGCTATACTAAC-ATACTA-T
1 ATACTATA-TAACAATACTATT
7527 ATCACTAT
1 AT-ACTAT
7535 TTATTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.43, C:0.18, G:0.02, T:0.37
Consensus pattern (21 bp):
ATACTATATAACAATACTATT
Done.