Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399335.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2603.0, 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: 3353
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.30
Warning! 773 characters in sequence are not A, C, G, or T
Found at i:1073 original size:172 final size:171
Alignment explanation
Indices: 895--1309 Score: 430
Period size: 171 Copynumber: 2.4 Consensus size: 171
885 NNNNNNNNNC
895 CATTCCTTCAAAAGCCTTATTATCT-ATTTCAAATGATTTTATTATCTCAAAATTGATTTT-GAG
1 CATTCCTTCAAAAGCCTTATTATCTCATTT-AAATG-TTTTATTATCTCAAAATTGATTTTAG-G
* * * * * * *
958 TTCAATTATTTTT-ATATT-TTTACTTAAGACAAACTATAATTGAACGTCTTCCCTAAGAATCGT
63 TTCAATT-TTTTTAACATTATTGAC-TAAAACAAACTACAATTGAACGTCTGCCCTAAGAAACAT
* *
1021 GAATAAAAAAACATTCATTAAAAAGAAAAATCCATTTGTAGTCTCA
126 GAAGAAAAAAACATTCATTAAAAAGAAAAATCCATTTATAGTCTCA
* * * *
1067 CATTCCTTCAAAAGCCTTATTA-CTCACTTTAAATGTTTTGTTATCTTAAAATTGATTTCATGTT
1 CATTCCTTCAAAAGCCTTATTATCTCA-TTTAAATGTTTTATTATCTCAAAATTGATTTTAGGTT
* * * * * *
1131 CAGTTTTTTTAACATTATTGGCTAAAACATACTACAATTGAATGTCTGCCTTGAGAAACATGAAG
65 CAATTTTTTTAACATTATTGACTAAAACAAACTACAATTGAACGTCTGCCCTAAGAAACATGAAG
* * * * * *
1196 AAAAAAGCATTCATTGACAAGAAAAGTCCATTTATTGTCTCC
130 AAAAAAACATTCATTAAAAAGAAAAATCCATTTATAGTCTCA
* * * * *
1238 CATTCGTTCAAAAG-CTTCATT-TCTCGCTTTAAATGGCTTTATAATCTCATAATTGATTTTAGG
1 CATTCCTTCAAAAGCCTT-ATTATCTC-ATTTAAAT-GTTTTATTATCTCAAAATTGATTTTAGG
1301 TTCAATTTT
63 TTCAATTTT
1310 NNNNNNNNNN
Statistics
Matches: 199, Mismatches: 35, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
170 8 0.04
171 128 0.64
172 60 0.30
173 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (171 bp):
CATTCCTTCAAAAGCCTTATTATCTCATTTAAATGTTTTATTATCTCAAAATTGATTTTAGGTTC
AATTTTTTTAACATTATTGACTAAAACAAACTACAATTGAACGTCTGCCCTAAGAAACATGAAGA
AAAAAACATTCATTAAAAAGAAAAATCCATTTATAGTCTCA
Found at i:1731 original size:169 final size:169
Alignment explanation
Indices: 589--1959 Score: 419
Period size: 171 Copynumber: 8.1 Consensus size: 169
579 NNNNNTGAAT
* * * * * * * *
589 GGTTTCATAATCTCATAATTGATTCTAAGTTGAATTTTTTATATTTTTTATTAAAACATACTATA
1 GGTTTTATAATATCATAATTGATTTTAAGTTGAA-TTTTTACATATTTTGTTAAAAAAGACTATA
* * * * * * *
654 ATTGAATGTTTATCTCGAGAAACGTGTAGAAAAACTCATTTATATGAAAGAAAACTCTATTTATA
65 ATTGAATGCTTACCTTGAGAAACGTGTAGAAAAAATCATTTATTTAAAAGAAAAGTCTATTTATA
* * * * * * * *
719 GTCTCCCATTACTTCAAAAGCCTTATTCCTCGC-TTAAAT
130 GCCACGCATTCCTTCAAAAGCTTTATTACTCACTTTAAAG
* ********** **
758 GGTTTTATAATCTCATAATTGNNNNNNNNNNGAATTTTTTTATATTTTTGGTTAAAACAA-A-TC
1 GGTTTTATAATATCATAATTGATTTTAAGTTGAATTTTTACATA-TTTT-GTTAAAA-AAGACT-
* * * * * * *
821 ATAATTGAATG-TCTACCTTGTGAAACATG-AAAAAACAAGCATTCA-TTAGCAACAAAAGTCTA
62 ATAATTGAATGCT-TACCTTGAGAAACGTGTAGAAAA-AATCATTTATTTA-AAAGAAAAGTCTA
********* * *
883 TNNNNNNNNNNC-CATTCCTTCAAAAGCCTTATTA-TCTA-TTTCAAAT
124 T-TTATAGCCACGCATTCCTTCAAAAGCTTTATTACTC-ACTTT-AAAG
* * * * * * ** * *
929 GATTTTATTATCTCAAAATTGATTTTGAGTTCAATTATTTTTATATTTTTACTTAAGACAA-ACT
1 GGTTTTATAATATCATAATTGATTTTAAGTTGAATT-TTTACATA-TTTT-GTTAA-AAAAGACT
* * * * * * * * * * *
993 ATAATTGAACGTCTT-CCCTAAGAATCGTGAATAAAAAAACATTCATTAAAAAGAAAAATCCATT
62 ATAATTGAATG-CTTACCTTGAGAAACGTGTAGAAAAAATCATTTATTTAAAAGAAAAGTCTATT
* * * * *
1057 TGTAGTCTCACATTCCTTCAAAAGCCTTATTACTCACTTTAAA-
126 TATAGCCACGCATTCCTTCAAAAGCTTTATTACTCACTTTAAAG
* * * * * * * * ** * * * *
1100 TGTTTTGTTATCTTAAAATTGATTTCATGTTCAGTTTTTTTAACAT-TATTGGCTAAAACATACT
1 GGTTTTATAATATCATAATTGATTTTAAGTT--GAATTTTT-ACATAT-TTTGTTAAAAAAGACT
* * * * * * * * *
1164 ACAATTGAATG-TCTGCCTTGAGAAACATGAAGAAAAAAGCATTCATTGACAAGAAAAGTCCATT
62 ATAATTGAATGCT-TACCTTGAGAAACGTGTAGAAAAAATCATTTATTTAAAAGAAAAGTCTATT
* * * * * * * * *
1228 TATTGTCTCCCATTCGTTCAAAAGCTTCATTTCTCGCTTTAAAT
126 TATAGCCACGCATTCCTTCAAAAGCTTTATTACTCACTTTAAAG
* * * * ******** * * *
1272 GGCTTTATAATCTCATAATTGATTTTAGGTTCAATTTTNNNNNNNNNNTGGTTAAAACAGATTAT
1 GGTTTTATAATATCATAATTGATTTTAAGTTGAATTTT--TACATATTTTGTTAAAAAAGACTAT
* *
1337 AATTGAATG-TCTACCTTGAGAAACGTG-AGGAAAAAGA-CATTTA-CTAGCAAGAAAAGT-TCA
64 AATTGAATGCT-TACCTTGAGAAACGTGTA-GAAAAA-ATCATTTATTTA-AAAGAAAAGTCT-A
** * ** * * * * *
1397 TTTATAATCGCTTATTCTTTCAAAAGCCTTATTATTCACTCTAAAT
124 TTTATAGCCACGCATTCCTTCAAAAGCTTTATTACTCACTTTAAAG
* * * * * * * * *
1443 GGTTTTATAATCTCA-ACTT--TTTTAAGTTCATTTTTTAAAAAATTTTGATTAAAATAGATTAC
1 GGTTTTATAATATCATAATTGATTTTAAGTTGAATTTTT-ACATATTTTG-TTAAAAAAGACTAT
* ** * **
1505 AATTGAATG-TCTACCTCATG-G---CATGTAGGGAAAAAGGCATTCATTGGCAAA-AAAAGTCT
64 AATTGAATGCT-TACCT--TGAGAAACGTGTA--GAAAAAATCATTTATT-TAAAAGAAAAGTCT
* * * *
1564 ATTTATTGCCACGCATTCCTTCAAAAGCTTTATTGCTC-GTTTAAAT
123 ATTTATAGCCACGCATTCCTTCAAAAGCTTTATTACTCACTTTAAAG
* * * * *
1610 GGTTTTATCATCTCATAATTGATTTTAAGTTGACTTTTTTACATATTTTGTTAAAACAA-ATTGT
1 GGTTTTATAATATCATAATTGATTTTAAGTTGA-ATTTTTACATATTTTGTTAAAA-AAGACTAT
*
1674 AATTGAATGCTTACCTTGAGAAACGTGT-GAAAAAATCTATTTATTTAAAAGAAAAGTCCATTTA
64 AATTGAATGCTTACCTTGAGAAACGTGTAGAAAAAATC-ATTTATTTAAAAGAAAAGTCTATTTA
* * * **********
1738 TAGTCTCTCATTCCTTCANNNNNNNNNNTACTCACTTTAAAG
128 TAGCCACGCATTCCTTCAAAAGCTTTATTACTCACTTTAAAG
* * *
1780 GGTTTTATAATATCATAATTGATTTTAAGTTTAATTTTTATATTTTTTGTTAAAAAAGACTATAA
1 GGTTTTATAATATCATAATTGATTTTAAGTTGAATTTTTACATATTTTGTTAAAAAAGACTATAA
* * * ** *
1845 TTGAATGCTTACCTTGAGAAATGTGTAGATAAACTCATTTATTTGGAAGAAAACTCTATTTATAG
66 TTGAATGCTTACCTTGAGAAACGTGTAGAAAAAATCATTTATTTAAAAGAAAAGTCTATTTATAG
* * * ** * * *
1910 TCTCCCATTATTTCAAAAGCCTTATTCCTCACTTTAAAT
131 CCACGCATTCCTTCAAAAGCTTTATTACTCACTTTAAAG
*
1949 GATTTTATAAT
1 GGTTTTATAAT
1960 CNNNNNNNNN
Statistics
Matches: 889, Mismatches: 252, Indels: 122
0.70 0.20 0.10
Matches are distributed among these distances:
166 3 0.00
167 25 0.03
168 112 0.13
169 209 0.24
170 146 0.16
171 262 0.29
172 112 0.13
173 19 0.02
174 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.38
Consensus pattern (169 bp):
GGTTTTATAATATCATAATTGATTTTAAGTTGAATTTTTACATATTTTGTTAAAAAAGACTATAA
TTGAATGCTTACCTTGAGAAACGTGTAGAAAAAATCATTTATTTAAAAGAAAAGTCTATTTATAG
CCACGCATTCCTTCAAAAGCTTTATTACTCACTTTAAAG
Done.