Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403072.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_737.0, 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: 3368
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.25
Warning! 1140 characters in sequence are not A, C, G, or T
Found at i:1840 original size:171 final size:170
Alignment explanation
Indices: 1128--1849 Score: 458
Period size: 171 Copynumber: 4.2 Consensus size: 170
1118 NNNNNNNNNN
*
1128 AAATGGTTTTATAATCTCATAATTGATTTTATGTTGAATTTTTTTACATTTTT-TTTAAAACAAA
1 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTATTTAAAACAAA
* ** ** * * * **
1192 CTATAATTGGAAGCCTGCCTC-AGGAAAGGTGTAGAAAAAGCCATTCATTGAGAAAGAAAATTTA
66 CTATAATTGAAATTCTAACTCGA-GAAACGTGTAAAAAAAGCCATTTATTGAGAAA-AAAATCCA
* * ** **
1256 TTTTTAGTCACCCATTCTTTCAAAACCCTTATTACTC-GGTT
129 TTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCTATTT
********* * * * *
1297 AANNNNNNNNNNTAGTCTCATAATTGATTTTAAGTTGAAATTTTTTATATTTTTCTTTAAAACAA
1 AA-ATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTATTTAAAACAA
* * * * *********
1362 ACAATAATT-AAATGTCTAACTCGAGAAACGTGCAGAAAAAGCCATTGATTGANNNNNNNNNNCC
65 ACTATAATTGAAAT-TCTAACTCGAGAAACGTGTAAAAAAAGCCATTTATTGA-GAAAAAAATCC
* *
1426 ATTTATAGTCACTCATTCCTTCAAAAGGCTTATTAGTCGT-TTT
128 ATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTC-TATTT
* * ** * * * *
1469 AAATAGTTTCATAATCTCATAATTGATTTCCAGATGAATTTTGTTATATTTTT-TATTAAAACAT
1 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTAT-TTAAAACAA
********* * * *
1533 ACTATAATTG-AATNNNNNNNNNNAGAAACGT-AAAGAAACAAG-TATTCT-TTGACAAGAAAAA
65 ACTATAATTGAAAT-TCTAACTCGAGAAACGTGTAA-AAA-AAGCCATT-TATTGAGAA-AAAAA
* * *
1594 ACCATTTAGAGTCACCCATTCCTTCAAAAGGCTTATTACTCGATTT
125 TCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCTATTT
************** * *
1640 AAATGGTTTNNNNNNNNNNNNNNTGATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAACAGA
1 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTATTTAAAACAAA
* *
1705 CTATAA-TGAAATTCTTATCTCGAGAAACGTGTAAAAAAAGCCATTTATTGAGAAAAAAAGTCTA
66 CTATAATTGAAATTC-TAACTCGAGAAACGTGTAAAAAAAGCCATTTATTGAGAAAAAAA-TCCA
*
1769 TTTATAGTCACCCCTTCCTTCAAAAGGCTTATTACTCTATTT
129 TTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCTATTT
1811 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAT
1 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAT
1850 NNNNNNNNNN
Statistics
Matches: 395, Mismatches: 137, Indels: 40
0.69 0.24 0.07
Matches are distributed among these distances:
169 2 0.01
170 53 0.13
171 330 0.84
172 10 0.03
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.36
Consensus pattern (170 bp):
AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTATTTAAAACAAA
CTATAATTGAAATTCTAACTCGAGAAACGTGTAAAAAAAGCCATTTATTGAGAAAAAAATCCATT
TATAGTCACCCATTCCTTCAAAAGGCTTATTACTCTATTT
Done.