Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400464.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3660.0, 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: 3290
ACGTcount: A:0.29, C:0.09, G:0.10, T:0.27
Warning! 819 characters in sequence are not A, C, G, or T
Found at i:374 original size:171 final size:170
Alignment explanation
Indices: 190--653 Score: 445
Period size: 171 Copynumber: 2.7 Consensus size: 170
180 TTTCTACACT
* * *
190 TTTCTTAAGGTAGACAATT-AATTATAGTCTGTTTTAATAAAAAATAGAAAAAAATTCAACTTAA
1 TTTCTCAAGGTAGAC-ATTCAATTATA-TATGTTTTAATAAAAAATATAAAAAAATTCAACTTAA
********** * *
254 AATNNNNNNNNNNATT-ATAAAACTATTTAAAGCGAGTAGTAAGCCTTTTGAAGGAATGAACG-A
64 AATAAATTATGACATTGA-AAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATG--CGTA
* * * * *
317 -CTCTACATGGACTTTTCTTGTCAATGAATGTTTGTTTCTTTATG
126 TCTCTAAATGGACTTTTCTTATCAATGAATGCTTGCTTCTTCATG
* ********
361 TTTCTCGAGGTAGACATTCAATTATA-ANNNNNNNNNNTAAAAAATATAAAAAAATTCAACTTAA
1 TTTCTCAAGGTAGACATTCAATTATATA--TGTTTTAATAAAAAATATAAAAAAATTCAACTTAA
* * *
425 AATAAATTATGACATTGAAAAACCATTTAAAGCGAGTAATAAGCTTTTTGAAGGAATGGGTATTT
64 AATAAATTATGACATTGAAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGCGTATCT
490 CTAAATGGACTTTTCTTATCAATGAATGCTTGCTTCTTCATG
129 CTAAATGGACTTTTCTTATCAATGAATGCTTGCTTCTTCATG
* * *
532 TTTCTCAACGTAGACATTCAATTATTATATTTTTTAGTAAAAAATATAAAAAAATTCAACTTAAA
1 TTTCTCAAGGTAGACATTCAATTA-TATATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAA
** * * *
597 ACCAATTATGAAATT-ATAAAACTATTTAAAGCGAGTGATAAGCCTTTTGAAGGAATG
65 ATAAATTATGACATTGA-AAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATG
654 NNNNNNNNNN
Statistics
Matches: 236, Mismatches: 48, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
169 1 0.00
170 5 0.02
171 226 0.96
172 3 0.01
173 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.34
Consensus pattern (170 bp):
TTTCTCAAGGTAGACATTCAATTATATATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAA
TAAATTATGACATTGAAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGCGTATCTCT
AAATGGACTTTTCTTATCAATGAATGCTTGCTTCTTCATG
Found at i:724 original size:171 final size:170
Alignment explanation
Indices: 398--797 Score: 430
Period size: 171 Copynumber: 2.3 Consensus size: 170
388 NNNNNNNNNN
* * *
398 TAAAAAATATAAAAAAATTCAACTTAAAATAAATTATGACATTGA-AAAACCATTTAAAGCGAGT
1 TAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAAATT-ATAAAACTATTTAAAGCGAGT
* * *
462 AATAAGCTTTTTGAAGGAATGGGTATTTCTAAATGGACTTTTCTTATCAATGAATGCTTGCTTCT
65 AATAAGCCTTTTGAAGGAATGGGTATTTCTAAATGAACTTTTCTTATCAATCAATGCTTGCTTCT
* ** * *
527 TCATGTTTCTCAACGTAGACATTCAATTATTATATTTTTTA
130 GCACATTTCTCAACGTAAACATTCAATTATTATATATTTTA
*
568 GTAAAAAATATAAAAAAATTCAACTTAAAACCAATTATGAAATTATAAAACTATTTAAAGCGAGT
1 -TAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAACTATTTAAAGCGAGT
* ********** * *
633 GATAAGCCTTTTGAAGGAATGNNNNNNNNNNAATGAACTTTTCTTCTCAATCAATGGCTT-TTTC
65 AATAAGCCTTTTGAAGGAATGGGTATTTCTAAATGAACTTTTCTTATCAATCAAT-GCTTGCTTC
* * *
697 TGCACATTTCTTAA-GATAAAGATTCAATTATTGTATATTTTA
129 TGCACATTTCTCAACG-TAAACATTCAATTATTATATATTTTA
* * * *
739 AAGAAAAATATAAAAAATTTCAACTTGAAATCAATTATGAGATTATAAAA-TCATTTAAA
1 TA-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAACT-ATTTAAA
798 NNNNNNNNNN
Statistics
Matches: 191, Mismatches: 33, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
170 4 0.02
171 183 0.96
172 4 0.02
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.35
Consensus pattern (170 bp):
TAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAACTATTTAAAGCGAGTA
ATAAGCCTTTTGAAGGAATGGGTATTTCTAAATGAACTTTTCTTATCAATCAATGCTTGCTTCTG
CACATTTCTCAACGTAAACATTCAATTATTATATATTTTA
Found at i:1155 original size:171 final size:172
Alignment explanation
Indices: 827--1166 Score: 389
Period size: 171 Copynumber: 2.0 Consensus size: 172
817 NNNNNNNNNG
* * *** *
827 TGACTATAAATGGACTTTTCTTCTCAATGAATAGGCTTTTTCTACATGTTTCCTAGGGCATGTAT
1 TGACTATAAATGGACTTTTCTTCTCAATGAATAGGCTTTTTCCACATGTTTCCTAAGGCAAACAA
** * * *
892 TCAATTATTGTCTGTTTTAACAAAAAAGGCAAAAAAATTCCACTTAAAATCAATTATGAGATTAT
66 TCAATTACAGTCTATTTGAACAAAAAAGGCAAAAAAATTCCAATTAAAATCAATTATGAGATTAT
********** *
957 AAANNNNNNNNNNGCGGGTAATAAGCCTTTTGAAGGAATGAA
131 AAAACTATTTGAAGCGAGTAATAAGCCTTTTGAAGGAATGAA
* * *
999 TGACTATCAATGGACTTTTCTTCTCAATGAAT-GGTTTTTTCCACATGTTT-CTGAAGGTAAACA
1 TGACTATAAATGGACTTTTCTTCTCAATGAATAGGCTTTTTCCACATGTTTCCT-AAGGCAAACA
* *
1062 ATCAATTACAGTCTATTTGAACAAAAAATGTAAAAAAATT-CAATGTAAAATCAATTATGAGATT
65 ATCAATTACAGTCTATTTGAACAAAAAAGGCAAAAAAATTCCAAT-TAAAATCAATTATGAGATT
*
1126 ATAAAACTATTTGAAGCGAGTAGTAAGCCTTTTGAAGGAAT
129 ATAAAACTATTTGAAGCGAGTAATAAGCCTTTTGAAGGAAT
1167 NNNNNNNNNN
Statistics
Matches: 138, Mismatches: 28, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
170 5 0.04
171 102 0.74
172 31 0.22
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.33
Consensus pattern (172 bp):
TGACTATAAATGGACTTTTCTTCTCAATGAATAGGCTTTTTCCACATGTTTCCTAAGGCAAACAA
TCAATTACAGTCTATTTGAACAAAAAAGGCAAAAAAATTCCAATTAAAATCAATTATGAGATTAT
AAAACTATTTGAAGCGAGTAATAAGCCTTTTGAAGGAATGAA
Done.