Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400526.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3721.0, 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, 835
Length: 1392
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.33
Warning! 201 characters in sequence are not A, C, G, or T
Found at i:323 original size:171 final size:160
Alignment explanation
Indices: 146--456 Score: 331
Period size: 171 Copynumber: 1.9 Consensus size: 160
136 NNATTACTCA
* * ** *
146 CTTTAAATTGCTTTATAATCTCATAATTGAATTTAAGTT-AATTTTTTTTGAATTTTTGGTTAAA
1 CTTTAAATGGCTTTATAAACTCATAATTGAATTTAAGTTGAA-TTTTTTAAAATTTTTGATTAAA
*
210 ACAGACTATAATTGAATGCCTGCCTT-GAGAAA-TGTACAACAAAAGCTATTCATCGAGAAGAAA
65 ACAGACTATAATTGAATGCCTGCCTTAGA-AAACTGT-CAA-AAAAGCCATTCATCGAGAAGAAA
273 AGTCCATTTATAGTCACCCATTCNNNNNNNNNNCTTATTACTTG
127 AGTCCATTTATAGTCACCCATTC----------CTTATTACTTG
* * * *
317 CTTTAAATGGTTTTATAAACTCATAATTTATTTTAAGTTGAATTTTTTAAAATTTTTTATTAAAA
1 CTTTAAATGGCTTTATAAACTCATAATTGAATTTAAGTTGAATTTTTTAAAATTTTTGATTAAAA
* * * *
382 CAGATTATAATTTAATGCCTGTCTTAGAAAACGTGTCAAAAAAGCCATTCATTGAGAAGAAAAGT
66 CAGACTATAATTGAATGCCTGCCTTAGAAAAC-TGTCAAAAAAGCCATTCATCGAGAAGAAAAGT
*
447 TCATTTATAG
130 CCATTTATAG
457 NNNNNNNNNN
Statistics
Matches: 121, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
171 111 0.92
172 7 0.06
173 3 0.02
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.38
Consensus pattern (160 bp):
CTTTAAATGGCTTTATAAACTCATAATTGAATTTAAGTTGAATTTTTTAAAATTTTTGATTAAAA
CAGACTATAATTGAATGCCTGCCTTAGAAAACTGTCAAAAAAGCCATTCATCGAGAAGAAAAGTC
CATTTATAGTCACCCATTCCTTATTACTTG
Found at i:1377 original size:171 final size:171
Alignment explanation
Indices: 630--1391 Score: 751
Period size: 169 Copynumber: 4.5 Consensus size: 171
620 TTTTAACTTG
* * * *
630 AATTTTTTTACATTTATGATTAAAATAAACTATAATTGAATGCTTACTTTGAGAAATGTGTAAAA
1 AATTTTTTTACATTTTTGATTAAAACAAACTATAATTGAATGCTTACCTTGAGAAACGTGTAAAA
* * ** *
695 AAAGCATTCATT-A-AGAAAAAA-TCCATTTATAGTCATTCATTCCTTTAAAAGCGTTATTACTC
66 AAACCATTCATTGAGAAAAAAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACTC
* * *
757 ACTTTAAATTGTTTTATAATCTCATAATT-ATTTTAAAGTTG
131 ACTTTAAATTGTTTTATAATCTCAAAATTGA-TTTGAAGTTA
* * * * * *
798 ATTTTTTTTACATTTTAGGTTAAAACAAACAATAATTGAATGTTTACCTTGAGAAA--TATAAAA
1 AATTTTTTTACATTTTTGATTAAAACAAACTATAATTGAATGCTTACCTTGAGAAACGTGT-AAA
* * * * * ******
861 AAAAGCATTCGTTG-GCAAGAAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGTCTTNNNNNN
65 AAAACCATTCATTGAGAAAAAAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACT
****
925 NNNNTTAAATTGTTTTATAATCTCAAAATTGATTTGAAGTTA
130 CACTTTAAATTGTTTTATAATCTCAAAATTGATTTGAAGTTA
* * * *
967 ATTTTTTTTGA-ATTTTTG-TTAAAACATACTATAATTGAATGCCTACCTTGAGAAACATGTAAA
1 AATTTTTTT-ACATTTTTGATTAAAACAAACTATAATTGAATGCTTACCTTGAGAAACGTGTAAA
* **
1030 AAAACCATTCATTGAG-AAAAAAAGTCCATTTATAGTCATCCATTCCTTCGAAAGCCTTATTACT
65 AAAACCATTCATTGAGAAAAAAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACT
* * *
1094 -AGCTTTAAATTATTTTATAATCCCAAAATTGATATT-AAGTTG
130 CA-CTTTAAATTGTTTTATAATCTCAAAATTGAT-TTGAAGTTA
********** * * * * ***
1136 AATTTTTTTACATTTNNNNNNNNNNCAGACTATAA-TGAATGCCTACCTCGAGAAATGCAAAAAG
1 AATTTTTTTACATTTTTGATTAAAACAAACTATAATTGAATGCTTACCTTGAGAAACGTGTAAA-
* *
1200 AAAACCATTCATTGAGAAAAAAAAGTCTATTTATAGTCACCCATTCCTTTAAAACCCTTATTACT
65 AAAACCATTCATTGAGAAAAAAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACT
* * *
1265 CTCTTTAAATTGTTTTGTAATCTCATAATTGATTTGAAGTTA
130 CACTTTAAATTGTTTTATAATCTCAAAATTGATTTGAAGTTA
* * *
1307 AATTTTTTTGA-ATTTTTGATTCAAACAGACTTTAATTGAATGCTTACCTTGAGAAACGTGTAAA
1 AATTTTTTT-ACATTTTTGATTAAAACAAACTATAATTGAATGCTTACCTTGAGAAACGTGTAAA
1371 AAAACCATTCATTGAGAAAAA
65 AAAACCATTCATTGAGAAAAA
1392 T
Statistics
Matches: 475, Mismatches: 100, Indels: 35
0.78 0.16 0.06
Matches are distributed among these distances:
166 2 0.00
167 15 0.03
168 87 0.18
169 196 0.41
170 34 0.07
171 118 0.25
172 23 0.05
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.37
Consensus pattern (171 bp):
AATTTTTTTACATTTTTGATTAAAACAAACTATAATTGAATGCTTACCTTGAGAAACGTGTAAAA
AAACCATTCATTGAGAAAAAAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACTC
ACTTTAAATTGTTTTATAATCTCAAAATTGATTTGAAGTTA
Done.