Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399330.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2599.0, 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: 2095
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.28
Warning! 542 characters in sequence are not A, C, G, or T
Found at i:909 original size:172 final size:169
Alignment explanation
Indices: 525--1229 Score: 514
Period size: 170 Copynumber: 4.1 Consensus size: 169
515 NNNNNNNNNN
* * * ** * *
525 GTTTTATAATCTCATAATTGATTTTAGGTTGAATTTTTTTACATCTTCAGCTAAAACAAATTATA
1 GTTTTATAATCTCATAATTGATTTTAAGATGAA-TTTTTTACATTTTTGGTTAAAACATATTATA
* * * * * ** * * *
590 ATTGATTCTTTACCTTGAGAAGCATTTAGAAAAATAC-ATTCATTTG-CAAAAAAA-CCCATTTG
65 AATGACTGTTT-CCTTGAGAAACGTGAAGAAAAA-ACTATTGA-TTGACAAAAAAAGCACATTTA
* * ** * * *
652 TAGTCACCCA-AGCTTTTGAATGCCTTATTACTCCCTTT-CAAT-
127 TAGTCACTCATA-CCTTAAAAAGCCTTATTACT-ACTTTAAAATA
* * * * *
694 GATTTTACAAACTCATAATTGATTTTAGGATGAATGTTTTTACATTTTTGGTTAAAATATATAAT
1 G-TTTTATAATCTCATAATTGATTTTAAGATGAAT-TTTTTACATTTTTGGTTAAAACATATTAT
* * * *
759 AAATGACTGTTTACCTTGAGAAACGTGAAGGAAAAGCTATTGATTGAGAAAAAAAGCTCATTTAT
64 AAATGACTGTTT-CCTTGAGAAACGTGAAGAAAAAACTATTGATTGACAAAAAAAGCACATTTAT
824 AGTCACTCATACCTTAAAAAGCCTTATTACTAACTTTAAAATA
128 AGTCACTCATACCTTAAAAAGCCTTATTACT-ACTTTAAAATA
********** * ** *
867 GTTTTATAATCTCATAATTGATNNNNNNNNNNCATTTTTTACATCTTCAGTTAAAACATATTATT
1 GTTTTATAATCTCATAATTGAT-TTTAAGATGAATTTTTTACATTTTTGGTTAAAACATATTATA
* * * * * * * * * *
932 ATTAATTCTTTCCGTCAGGTAACGTGTAGAAAAATA-TATTCATTTG-CAAAAAAAGCACATTTG
65 AATGACTGTTTCCTTGA-GAAACGTGAAGAAAAA-ACTATTGA-TTGACAAAAAAAGCACATTTA
* * * * *
995 TAGTCACCCA-AGCCTTTAAAAGCCTTATTACTCCCTTAAAATT
127 TAGTCACTCATA-CCTTAAAAAGCCTTATTACTACTTTAAAATA
* * *
1038 GTTTTACAAACTCATAATTGATTTTAAGATGAATTTTTTATATTTTTGGTTAAAACATATTATAA
1 GTTTTATAATCTCATAATTGATTTTAAGATGAATTTTTTACATTTTTGGTTAAAACATATTATAA
* * * * *
1103 ATGACTGTCTGCCTTGAGAAACGTGAA-AAAAAACCATTGATTGATAAGAAAAGCCCATTTATAG
66 ATGACTGT-TTCCTTGAGAAACGTGAAGAAAAAACTATTGATTGACAAAAAAAGCACATTTATAG
* * * *
1167 TCACTCATACCTTCAAAGGCTTTATTACTCGCTTT-AAATA
130 TCACTCATACCTTAAAAAGCCTTATTACT-ACTTTAAAATA
1207 GTTTTATAATCTCATAATTGATT
1 GTTTTATAATCTCATAATTGATT
1230 NNNNNNNNNN
Statistics
Matches: 409, Mismatches: 109, Indels: 36
0.74 0.20 0.06
Matches are distributed among these distances:
168 4 0.01
169 79 0.19
170 133 0.33
171 73 0.18
172 114 0.28
173 6 0.01
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (169 bp):
GTTTTATAATCTCATAATTGATTTTAAGATGAATTTTTTACATTTTTGGTTAAAACATATTATAA
ATGACTGTTTCCTTGAGAAACGTGAAGAAAAAACTATTGATTGACAAAAAAAGCACATTTATAGT
CACTCATACCTTAAAAAGCCTTATTACTACTTTAAAATA
Found at i:1223 original size:169 final size:167
Alignment explanation
Indices: 673--1229 Score: 494
Period size: 172 Copynumber: 3.3 Consensus size: 167
663 GCTTTTGAAT
* *
673 GCCTTATTACTCCCTTTCAAT-GATTTTACAAACTCATAATTGATTTTAGGATGAATGTTTTTAC
1 GCCTTATTACTCCCTTTAAATAG-TTTTACAAACTCATAATTGATTTTAAGATGAAT-TTTTTAC
* * * * *
737 ATTTTTGGTTAAAATATATAATAAATGACTGTTTACCTTGAGAAACGTGAAGGAAAAGCTATTGA
64 ATTTTTGGTTAAAACATATTATAAATGACTGTCTACCTTGAGAAACGTGAA-AAAAAACTATTGA
*
802 TTGAGAAAAAAAGCTCATTTATAGTCACTCATACCTTAAAAA
128 TT--GAAAAAAAGCACATTTATAGTCACTCATACCTTAAAAA
** * * **********
844 GCCTTATTACTAACTTTAAAATAGTTTTATAATCTCATAATTGATNNNNNNNNNNCATTTTTTAC
1 GCCTTATTACTCCCTTT-AAATAGTTTTACAAACTCATAATTGAT-TTTAAGATGAATTTTTTAC
* ** * * * * * * * *
909 ATCTTCAGTTAAAACATATTAT-TATTAAT-TCTTTCCGTCAGGTAACGTGTAGAAAAATA-TAT
64 ATTTTTGGTTAAAACATATTATAAATGACTGTC-TACCTTGA-GAAACGTG-A-AAAAAAACTAT
* * * *
971 TCATTTGCAAAAAAAGCACATTTGTAGTCACCCA-AGCCTTTAAAA
125 TGA-TTG-AAAAAAAGCACATTTATAGTCACTCATA-CCTTAAAAA
* * *
1016 GCCTTATTACTCCCTTAAAATTGTTTTACAAACTCATAATTGATTTTAAGATGAATTTTTTATAT
1 GCCTTATTACTCCCTTTAAATAGTTTTACAAACTCATAATTGATTTTAAGATGAATTTTTTACAT
* *
1081 TTTTGGTTAAAACATATTATAAATGACTGTCTGCCTTGAGAAACGTGAAAAAAAACCATTGATTG
66 TTTTGGTTAAAACATATTATAAATGACTGTCTACCTTGAGAAACGTGAAAAAAAACTATTGATTG
* * *
1146 ATAAGAAAAGCCCATTTATAGTCACTCATACCTTCAAAG
131 A-AA-AAAAGCACATTTATAGTCACTCATACCTTAAAAA
* * * *
1185 GCTTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATT
1 GCCTTATTACTCCCTTTAAATAGTTTTACAAACTCATAATTGATT
1230 NNNNNNNNNN
Statistics
Matches: 293, Mismatches: 77, Indels: 34
0.73 0.19 0.08
Matches are distributed among these distances:
167 1 0.00
168 11 0.04
169 71 0.24
170 36 0.12
171 59 0.20
172 105 0.36
173 9 0.03
174 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.37
Consensus pattern (167 bp):
GCCTTATTACTCCCTTTAAATAGTTTTACAAACTCATAATTGATTTTAAGATGAATTTTTTACAT
TTTTGGTTAAAACATATTATAAATGACTGTCTACCTTGAGAAACGTGAAAAAAAACTATTGATTG
AAAAAAAGCACATTTATAGTCACTCATACCTTAAAAA
Done.