Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400837.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4008.0, 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, 659
Length: 1099
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.38
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:39 original size:27 final size:26
Alignment explanation
Indices: 1--57 Score: 105
Period size: 27 Copynumber: 2.2 Consensus size: 26
1 AAATTATTAATTATTAATATTTAAAA
1 AAATTATTAATTATTAATATTTAAAA
27 TAAATTATTAATTATTAATATTTAAAA
1 -AAATTATTAATTATTAATATTTAAAA
54 AAAT
1 AAAT
58 AATCATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATTATTAATTATTAATATTTAAAA
Found at i:778 original size:24 final size:24
Alignment explanation
Indices: 751--898 Score: 59
Period size: 25 Copynumber: 5.7 Consensus size: 24
741 TACAAGAATC
751 AAAAATTAAAATAAAATAAAATATA
1 AAAA-TTAAAATAAAATAAAATATA
** *
776 AAAAGTTAAAATTTATATAATATAGGTAAA
1 AAAA-TTAAAA--TA-A-AATA-AAATATA
806 ATAAATTAAAATAAAATATATAATATAA
1 A-AAATTAAAATAAAATA-A-AATAT-A
* * * *
834 AAAATTATATTAAAAGAAATAAATA
1 AAAATTAAAATAAAATAAA-ATATA
*
859 AAAA-T-ATATAAGAATTAAAATA-A
1 AAAATTAAAATAA-AA-TAAAATATA
* *
882 TAAATGAAAATAAAATA
1 AAAATTAAAATAAAATA
899 TATGACATTA
Statistics
Matches: 91, Mismatches: 19, Indels: 28
0.66 0.14 0.20
Matches are distributed among these distances:
23 9 0.10
24 7 0.08
25 24 0.26
26 10 0.11
27 18 0.20
28 5 0.05
29 4 0.04
30 11 0.12
31 3 0.03
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (24 bp):
AAAATTAAAATAAAATAAAATATA
Found at i:847 original size:27 final size:26
Alignment explanation
Indices: 808--862 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
798 TAGGTAAAAT
* *
808 AAATTAAAATAAAATATATAATATAAA
1 AAATTAAAATAAAAGAAATAA-ATAAA
* *
835 AAATTATATTAAAAGAAATAAATAAA
1 AAATTAAAATAAAAGAAATAAATAAA
861 AA
1 AA
863 TATATAAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (26 bp):
AAATTAAAATAAAAGAAATAAATAAA
Found at i:861 original size:55 final size:55
Alignment explanation
Indices: 753--861 Score: 123
Period size: 55 Copynumber: 2.0 Consensus size: 55
743 CAAGAATCAA
* * * * **
753 AAATTAAAATAAAATAAAATATAAAAAGTTAAAATTTATATAATATAGGTAAAAT
1 AAATTAAAATAAAATAAAATATAAAAAATTAAAATTAAAAGAATATAAATAAAAT
*
808 AAATTAAAATAAAATATATAATATAAAAAATT-ATATTAAAAGAA-ATAAATAAAA
1 AAATTAAAATAAAATA-A-AATATAAAAAATTAAAATTAAAAGAATATAAATAAAA
862 ATATATAAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
55 24 0.53
56 9 0.20
57 12 0.27
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (55 bp):
AAATTAAAATAAAATAAAATATAAAAAATTAAAATTAAAAGAATATAAATAAAAT
Found at i:869 original size:14 final size:14
Alignment explanation
Indices: 814--893 Score: 51
Period size: 14 Copynumber: 5.8 Consensus size: 14
804 AAATAAATTA
814 AAAT-AAAATATAT
1 AAATAAAAATATAT
827 AATATAAAAA-AT-T
1 AA-ATAAAAATATAT
* * * *
840 ATATTAAAAGAAAT
1 AAATAAAAATATAT
854 AAATAAAAATATAT
1 AAATAAAAATATAT
*
868 AAGAATTAAAATA-AT
1 -A-AATAAAAATATAT
*
883 AAATGAAAATA
1 AAATAAAAATA
894 AAATATATGA
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
12 6 0.12
13 14 0.27
14 16 0.31
15 7 0.13
16 9 0.17
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (14 bp):
AAATAAAAATATAT
Found at i:903 original size:15 final size:16
Alignment explanation
Indices: 854--917 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 16
844 TAAAAGAAAT
854 AAATAAAAATATAT-A
1 AAATAAAAATATATGA
*
869 AGAATTAAAATAATAAATGA
1 A-AA-T-AAA-AATATATGA
889 AAAT-AAAATATATGA
1 AAATAAAAATATATGA
* *
904 CATTAAAAATATAT
1 AAATAAAAATATAT
918 TTAAGAGCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
15 11 0.28
16 13 0.33
17 1 0.03
18 4 0.10
19 8 0.21
20 2 0.05
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (16 bp):
AAATAAAAATATATGA
Done.