Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400496.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3691.0, 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, 732
Length: 1221
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.23
Warning! 412 characters in sequence are not A, C, G, or T
Found at i:1079 original size:170 final size:168
Alignment explanation
Indices: 548--1155 Score: 656
Period size: 171 Copynumber: 3.6 Consensus size: 168
538 ATGGGTGATA
* * * * * **
548 ATAAATGGACTTTTTTTGTCAACGAATACCTTTTTTTGGATGTTTCTCGAGGTAAGCATTTAATT
1 ATAAATGGACTTTTCTTCTCAATGAAT-GC-TTTTTTGTATGTTTCTCGAGGTAAAAATTTAATT
* * *
613 ATAGTCAGTTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACC
64 ATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACT
* *
678 ATTTAGAGC-GAGTAATAAGCTTTTTGAAGGAATTGGTGACT
129 ATTTAAAGCAG-GTAATAAGCCTTTTGAAGGAA-TGGTGACT
* * * *
719 CTAAATGGACTTTTCTTATCAATGAATG-TTTGTTTCT-TCCCAG-TTCCCGAGGTAAAAATTTA
1 ATAAATGGACTTTTCTTCTCAATGAATGCTTT-TTTGTAT----GTTTCTCGAGGTAAAAATTTA
* * * *
781 ATTATAGTTTGTTTTAACAAAAAATGTAAAAAAATTCAATTTAAAATCAATTGTGAGATTATAAA
61 ATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * *
846 ACTATTTAAAGCTA-GTAAAAAGCCATTTGAAAGAATGGGTGATT
126 ACTATTTAAAGC-AGGTAATAAGCCTTTTGAAGGAAT-GGTGACT
890 ATAAATGGACTTTTCTTCTCAATGAATCGCTTTTTATGTATGTTTCTCGA-GTCAAAAATTTAAT
1 ATAAATGGACTTTTCTTCTCAATGAAT-GCTTTTT-TGTATGTTTCTCGAGGT-AAAAATTTAAT
* * *
954 AATAGTCTGTTTTAACAAAAAATAT-AAAAAATTCAGCTTAAAATCGATTATGAGATTATAAAAC
63 TATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* *
1018 TATTAAAAGCAGGTAATAAGCCTTTTGAAGGAACGAGTGACT
128 TATTTAAAGCAGGTAATAAGCCTTTTGAAGGAATG-GTGACT
* * * * * * **
1060 ATCAATGAACTTATCTTCTCAATGAATGCCTTTTTTGCATGTTTTTCGAGGTAGACAA-TCGATT
1 ATAAATGGACTTTTCTTCTCAATGAATG-CTTTTTTGTATGTTTCTCGAGGTA-AAAATTTAATT
*
1124 ATAGTCTATTTTAACAAAAAATATAACAAAAA
64 ATAGTCTGTTTTAACAAAAAATATAA-AAAAA
1156 ATATAACAAA
Statistics
Matches: 366, Mismatches: 50, Indels: 42
0.80 0.11 0.09
Matches are distributed among these distances:
168 4 0.01
169 45 0.12
170 107 0.29
171 200 0.55
172 4 0.01
173 5 0.01
174 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (168 bp):
ATAAATGGACTTTTCTTCTCAATGAATGCTTTTTTGTATGTTTCTCGAGGTAAAAATTTAATTAT
AGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTAT
TTAAAGCAGGTAATAAGCCTTTTGAAGGAATGGTGACT
Found at i:1152 original size:12 final size:12
Alignment explanation
Indices: 1135--1166 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1125 TAGTCTATTT
1135 TAACAAAAAATA
1 TAACAAAAAATA
1147 TAACAAAAAATA
1 TAACAAAAAATA
1159 TAACAAAA
1 TAACAAAA
1167 GTCAACTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (12 bp):
TAACAAAAAATA
Done.