Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402717.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_578.0, 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: 18507
ACGTcount: A:0.22, C:0.07, G:0.08, T:0.22
Warning! 7577 characters in sequence are not A, C, G, or T
Found at i:4013 original size:47 final size:48
Alignment explanation
Indices: 3944--4037 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 48
3934 CTTGGAACTG
3944 ATATTTAATTATAATATATTTTAACCAAAAATGT-AAAAAAATTTAAA
1 ATATTTAATTATAATATATTTTAACCAAAAATGTCAAAAAAATTTAAA
3991 ATATTTAATTATAATATATTTTAACCAAAAATGTCAAAAAAATTTAA
1 ATATTTAATTATAATATATTTTAACCAAAAATGTCAAAAAAATTTAA
4038 CTTAAAACAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 34 0.74
48 12 0.26
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.38
Consensus pattern (48 bp):
ATATTTAATTATAATATATTTTAACCAAAAATGTCAAAAAAATTTAAA
Found at i:10079 original size:23 final size:22
Alignment explanation
Indices: 10045--10116 Score: 82
Period size: 21 Copynumber: 3.4 Consensus size: 22
10035 ATATGATATT
10045 ATATAAAA-ATTAATAATAAAA
1 ATATAAAATATTAATAATAAAA
10066 ATATAAATATATTACA-AAT-AAA
1 ATATAAA-ATATTA-ATAATAAAA
*
10088 ATATAAAATATT-ATAATAATA
1 ATATAAAATATTAATAATAAAA
10109 A-ATAAAAT
1 ATATAAAAT
10117 TAAAATATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
19 1 0.02
20 10 0.22
21 15 0.33
22 11 0.24
23 7 0.16
24 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (22 bp):
ATATAAAATATTAATAATAAAA
Found at i:10138 original size:27 final size:27
Alignment explanation
Indices: 10040--10139 Score: 77
Period size: 27 Copynumber: 3.7 Consensus size: 27
10030 TTAAAATATG
10040 ATATTAT-A-TAAAAATTAATAATA-AAA
1 ATATTATAATTAAAAA-TAA-AATATAAA
* *
10066 ATATAAATATATTACAAATAAAATATAAA
1 ATAT-TATA-ATTAAAAATAAAATATAAA
10095 ATATTATAA-TAATAAATAAAAT-TAAA
1 ATATTATAATTAA-AAATAAAATATAAA
10121 ATA-TATGACATTAAAAATA
1 ATATTAT-A-ATTAAAAATA
10140 TATTTAAGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
25 3 0.05
26 14 0.23
27 18 0.30
28 10 0.16
29 11 0.18
30 5 0.08
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (27 bp):
ATATTATAATTAAAAATAAAATATAAA
Found at i:13386 original size:170 final size:169
Alignment explanation
Indices: 12785--13502 Score: 633
Period size: 170 Copynumber: 4.2 Consensus size: 169
12775 NNNNNNNNNN
* * *
12785 AAATATAAAAAAATTCAACTTAAAATCAAGTATGAGATTATAAAACCATTTAAA-TCGAGCAATA
1 AAATATAAAAAAA-TCAACTTAAAATCAATTATGAGATTAGAAAACCATTTAAAGT-GAGTAATA
* *
12849 AGGCTTTCTAAGGCTT-GAGTGATTATAAATGGACTTTTCTTGCCAATGGATGATTTTTGCTTCA
64 AGGCTTTCAAAGGCTTAG-GTGACTATAAATGGACTTTTCTTGCCAATGGATG-TTTTTGCTTCA
* * * * *
12913 TATTTCCCAAGGCAGACATTTAATTATAATATATTTTAACAAA
127 TGTTTCCTAAGGCAGATATTCAATTATAATATATTTTAACTAA
* * * * *
12956 AAATATAAAAACAAATCAACTTAAAATTAATTATGAGATTATG-AACCCACTTATAGTGATTAAT
1 AAATAT-AAAA-AAATCAACTTAAAATCAATTATGAGATTA-GAAAACCATTTAAAGTGAGTAAT
** * * * *
13020 AATACTTTCGAAGGCATAAGTGACTACAAATGGACTTTTCTCT-CCAATGGATGTCTTTTGCTTC
63 AAGGCTTTCAAAGGCTTAGGTGACTATAAATGGACTTTTCT-TGCCAATGGATGT-TTTTGCTTC
* *
13084 ATGTGT-CTAGAGGCAGATGTTCAATTATAATATATTTTAACTAA
126 ATGTTTCCTA-AGGCAGATATTCAATTATAATATATTTTAACTAA
* * * * * * *
13128 AACATA-AAAATATTCAACTTATAATCAATTATGAGTTTATAAAGCTATTTAAAGTGAGTAATAA
1 AA-ATATAAAAAAATCAACTTAAAATCAATTATGAGATTAGAAAACCATTTAAAGTGAGTAATAA
* ********** * * *
13192 GGCTTCCANNNNNNNNNNTGACTATAAATGGACTTTTATTGCCAATGAATAGTTTTTGCTTTATG
65 GGCTTTCAAAGGCTTAGGTGACTATAAATGGACTTTTCTTGCCAATGGAT-GTTTTTGCTTCATG
* * * *
13257 TTTCCTAAGGTAAATATTCAATTATAATATGTTTTAATTAA
129 TTTCCTAAGGCAGATATTCAATTATAATATATTTTAACTAA
* * * *
13298 AAATGTAAAAAAATAAAGTTAAAATCAATTTTGAGATTAGAAAACCATTTAAAGTGAGTAATAAG
1 AAATATAAAAAAATCAACTTAAAATCAATTATGAGATTAGAAAACCATTTAAAGTGAGTAATAAG
* ********** **
13363 CCTTTCAAAGGCTTAGGTGACTATAAATGGACTTTTCTTGCNNNNNNNNNNCTTTTGCACCATGT
66 GCTTTCAAAGGCTTAGGTGACTATAAATGGACTTTTCTTGC-CAATGGATGTTTTTGCTTCATGT
* *
13428 TTCATGAA-GCAGACATTCAATTATAATATATTTTAA-TCAA
130 TTCCT-AAGGCAGATATTCAATTATAATATATTTTAACT-AA
13468 AAATATAGAAAAAATCAACTTAAAATCAATTATGA
1 AAATATA-AAAAAATCAACTTAAAATCAATTATGA
13503 NNNNNNNNNN
Statistics
Matches: 426, Mismatches: 103, Indels: 36
0.75 0.18 0.06
Matches are distributed among these distances:
169 4 0.01
170 240 0.56
171 44 0.10
172 130 0.31
173 8 0.02
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.34
Consensus pattern (169 bp):
AAATATAAAAAAATCAACTTAAAATCAATTATGAGATTAGAAAACCATTTAAAGTGAGTAATAAG
GCTTTCAAAGGCTTAGGTGACTATAAATGGACTTTTCTTGCCAATGGATGTTTTTGCTTCATGTT
TCCTAAGGCAGATATTCAATTATAATATATTTTAACTAA
Done.