Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397274.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_228.0, 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: 2969030
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 66526 characters in sequence are not A, C, G, or T
File 8 of 8
Found at i:2955573 original size:13 final size:14
Alignment explanation
Indices: 2955555--2955587 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2955545 ATTTTATTTT
2955555 TTATTTAT-AATAA
1 TTATTTATAAATAA
2955568 TTATTTATAAATAA
1 TTATTTATAAATAA
*
2955582 ATATTT
1 TTATTT
2955588 TTATAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTATTTATAAATAA
Found at i:2958059 original size:21 final size:21
Alignment explanation
Indices: 2958033--2958109 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
2958023 TACAGAAATA
*
2958033 TGTTACATGCCATGGTTAGGT
1 TGTTACACGCCATGGTTAGGT
*
2958054 TGTTACACGCCATGGTTAAGT
1 TGTTACACGCCATGGTTAGGT
*
2958075 TGTTACATGCCATGGTTAGGT
1 TGTTACACGCCATGGTTAGGT
*
2958096 AGTTACACGCCATG
1 TGTTACACGCCATG
2958110 TTAAAAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (21 bp):
TGTTACACGCCATGGTTAGGT
Found at i:2958080 original size:42 final size:41
Alignment explanation
Indices: 2958033--2958113 Score: 144
Period size: 42 Copynumber: 2.0 Consensus size: 41
2958023 TACAGAAATA
*
2958033 TGTTACATGCCATGGTTAGGTTGTTACACGCCATGGTTAAGT
1 TGTTACATGCCATGGTTAGGTAGTTACACGCCAT-GTTAAGT
2958075 TGTTACATGCCATGGTTAGGTAGTTACACGCCATGTTAA
1 TGTTACATGCCATGGTTAGGTAGTTACACGCCATGTTAA
2958114 AAAAATACTA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 5 0.13
42 33 0.87
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (41 bp):
TGTTACATGCCATGGTTAGGTAGTTACACGCCATGTTAAGT
Found at i:2958163 original size:24 final size:28
Alignment explanation
Indices: 2958097--2958163 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 28
2958087 TGGTTAGGTA
2958097 GTTACACGCCATGTTAAAAAAATACTATT
1 GTTACACGCCATG-TAAAAAAATACTATT
* * *
2958126 GTTACACACTATGT-ACAAAA-AC-A-T
1 GTTACACGCCATGTAAAAAAATACTATT
2958150 GTTACACGCCATGT
1 GTTACACGCCATGT
2958164 TGAGTCTACT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
24 13 0.39
25 1 0.03
26 2 0.06
27 5 0.15
28 1 0.03
29 11 0.33
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (28 bp):
GTTACACGCCATGTAAAAAAATACTATT
Found at i:2960012 original size:18 final size:19
Alignment explanation
Indices: 2959984--2960022 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
2959974 ATATATATAT
2959984 TATTATGTTTATTAAA-AAA
1 TATTATGTTTA-TAAATAAA
2960003 TATT-TGTTTATAAATAAA
1 TATTATGTTTATAAATAAA
2960021 TA
1 TA
2960023 AAAGTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 11 0.58
19 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
TATTATGTTTATAAATAAA
Found at i:2963220 original size:2 final size:2
Alignment explanation
Indices: 2963213--2963248 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2963203 AAGAATAGAG
*
2963213 CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2963249 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Done.