Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402456.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5533.0, 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, 648
Length: 1080
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Found at i:286 original size:171 final size:171
Alignment explanation
Indices: 1--622 Score: 851
Period size: 171 Copynumber: 3.6 Consensus size: 171
* * **
1 TTTTAATCAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAGATTAT-AAACTCCTAAAAA
1 TTTTAATCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACT-ATTTAAA
* * * * * * *
65 ACGGGTAATAAGCCTTTTGAAGGGATGAGTGACTATAAATGAATTTTTCTTCTCAATGAATGGCT
65 GCGAGTAATAAGCCTTTTGAAGGAATGAGTGACTCTAAATGGACTTTTCTTGTCAATGAAT-GCT
*
130 T-TTT-TTGCACGTTTCTTGAGGTAGACAATT-AATTATAGTCTG
129 TGTTTCTT-CACGTTTCTTGAGGTAGAC-ATTCAATTATAGTATG
*
172 TTTTAAT-AAAAAGTGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAA
1 TTTTAATCAAAAA-TATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAA
* * * *
236 GCGAGTAATAAGCCTTTTGAAAGAAAG-GCTGACTCTAAATAGACTTTTCTTGTCAATGAATACT
65 GCGAGTAATAAGCCTTTTGAAGGAATGAG-TGACTCTAAATGGACTTTTCTTGTCAATGAATGCT
* * * *
300 TGTTTCTTCATGTTTCATGAGGAATACATTCAATTATAGTATG
129 TGTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTATG
*
343 TTTTAATCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
1 TTTTAATCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAG
* * *
408 TGAGTAATAAACTTTTTGAAGGAATGAGTGACTCTAAATGGACTTTTCTTGTCAATGAATGCTTG
66 CGAGTAATAAGCCTTTTGAAGGAATGAGTGACTCTAAATGGACTTTTCTTGTCAATGAATGCTTG
* *
473 TTTCTTCACGTGTCTCGAGGTAGACATTCAATTATAGTATG
131 TTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTATG
* * * * *
514 TTCTAATAAAAAATGTAAAAAAATTAAACTTAAAATTAATTATGAGATTATAAAACTATTTAAAG
1 TTTTAATCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAG
*
579 CGAGTAATAAGCTTTTTGAAGGAATGAGTGACTCTAAATGGACT
66 CGAGTAATAAGCCTTTTGAAGGAATGAGTGACTCTAAATGGACT
623 ATTTAAAGCG
Statistics
Matches: 399, Mismatches: 44, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
170 12 0.03
171 374 0.94
172 13 0.03
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (171 bp):
TTTTAATCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAG
CGAGTAATAAGCCTTTTGAAGGAATGAGTGACTCTAAATGGACTTTTCTTGTCAATGAATGCTTG
TTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTATG
Found at i:630 original size:52 final size:53
Alignment explanation
Indices: 568--675 Score: 200
Period size: 53 Copynumber: 2.1 Consensus size: 53
558 AGATTATAAA
*
568 ACTATTTAAAGCGAGTAATAAGC-TTTTTGAAGGAATGAGTGACTCTAAATGG
1 ACTATTTAAAGCGAGTAATAAGCTTTTTTAAAGGAATGAGTGACTCTAAATGG
620 ACTATTTAAAGCGAGTAATAAGCTTTTTTAAAGGAATGAGTGACTCTAAATGG
1 ACTATTTAAAGCGAGTAATAAGCTTTTTTAAAGGAATGAGTGACTCTAAATGG
673 ACT
1 ACT
676 TTTTTTGCAC
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 23 0.43
53 31 0.57
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (53 bp):
ACTATTTAAAGCGAGTAATAAGCTTTTTTAAAGGAATGAGTGACTCTAAATGG
Found at i:1053 original size:170 final size:171
Alignment explanation
Indices: 673--1053 Score: 430
Period size: 170 Copynumber: 2.2 Consensus size: 171
663 CTCTAAATGG
* * * *
673 ACTTTTTTTGCACGTTTCTTGAGGTAGACAATCAAA-TA-AAGTCTGTTTTAATAAAAACTGTAA
1 ACTTCTTTTGCACGTTTCTTGAGGTAGAC-ATTAAATTATAAGTATGTTTTAATAAAAACTATAA
* * * * * *
736 AACAATTAAACTTAAAATCGATTATGAGATTATAAAACCGTTTAAAGTGAGTAATAAGCTTTTTG
65 AACAATTAAACTTAAAATCAATTATAAGATTATAAAACCATTAAAAGCGAGTAATAAGCCTTTTG
* * * * * *
801 AAGGGATGGGTGACTCTAAATGGACTTTTTTTATCAATGAGT
130 AAGGAATGAGTGACTATAAATGAACTTTTCTTATCAATGAAT
* * * * * *
843 ACTTGTTTCTTCATGTTTCTTGAGGTAAAGATTCAATTATAA-TATGTTTTAATCAAAAA-TATA
1 ACTTCTTT-TGCACGTTTCTTGAGGTAGACATTAAATTATAAGTATGTTTTAAT-AAAAACTATA
* * *
906 AAA-AATTCAACTTAAAATCAATTATAAGATTATAAAATCATTAAAAGCGGGTAATAAGCCTTTT
64 AAACAATTAAACTTAAAATCAATTATAAGATTATAAAACCATTAAAAGCGAGTAATAAGCCTTTT
*
970 GAAGGAATGAGTGACTATAAATGAACTTTTCTTCTCAATGAAT
129 GAAGGAATGAGTGACTATAAATGAACTTTTCTTATCAATGAAT
* **
1013 GCCTTCTTTTGCACGTTTCCAGAGGTAGACATTAAATTATA
1 -ACTTCTTTTGCACGTTTCTTGAGGTAGACATTAAATTATA
1054 GACTGTTTGA
Statistics
Matches: 172, Mismatches: 34, Indels: 10
0.80 0.16 0.05
Matches are distributed among these distances:
170 124 0.72
171 41 0.24
172 7 0.04
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (171 bp):
ACTTCTTTTGCACGTTTCTTGAGGTAGACATTAAATTATAAGTATGTTTTAATAAAAACTATAAA
ACAATTAAACTTAAAATCAATTATAAGATTATAAAACCATTAAAAGCGAGTAATAAGCCTTTTGA
AGGAATGAGTGACTATAAATGAACTTTTCTTATCAATGAAT
Done.