Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398453.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1751.0, 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: 2719
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.24
Warning! 1014 characters in sequence are not A, C, G, or T
Found at i:1431 original size:171 final size:162
Alignment explanation
Indices: 1252--1612 Score: 389
Period size: 170 Copynumber: 2.1 Consensus size: 162
1242 NNNNNNTTGG
* * * **
1252 AAGAAAAGTCTATTTATAGTCCCTCATTCTTTCAAAAGCCTTATTACTCACTTNNNNNNNNNNTA
1 AAGAAAAGTCCATTTATAGTCCCTCATTCCTTCAAAAGCCTTATCACTCACTT--------TTTA
*
1317 TAATCTCATAATTGATTTTAGATTAAATGTTTTTACATCCTTTATTAAGACAGACTATAATTGAA
58 TAATCTCATAATTGATTTTAGATT-AATGTTTTTACATCCTTTATTAAGACAAACTATAATTGAA
* * **
1382 TGCCTGTCTTAAGAAACATGTAGAAAATGCCATTCATTAGA
122 TGCCTGCCTCAAGAAACATGTAGAAAACACCATTCATTAGA
** * **
1423 AAGAAAAGTCCATTTATAGTGTCTCATTCCTTCAAAAGCCTTATCACTCGCNNNNNNNNNNTTTA
1 AAGAAAAGTCCATTTATAGTCCCTCATTCCTTCAAAAGCCTTATCACTCAC--------TTTTTA
* *
1488 TAATCTCATAATTGATTTTAGGTTAATGTTTTTACATCTTTTATTAAGACAAACTATAATTGAAT
58 TAATCTCATAATTGATTTTAGATTAATGTTTTTACATCCTTTATTAAGACAAACTATAATTGAAT
* * *
1553 GCCTGCCTCAGGAAACATGTAGAAAACATCATTCATTTGA
123 GCCTGCCTCAAGAAACATGTAGAAAACACCATTCATTAGA
1593 AAGAAAAGTCCATTTATAGT
1 AAGAAAAGTCCATTTATAGT
1613 NNNNNNNNNN
Statistics
Matches: 162, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
170 92 0.57
171 70 0.43
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.35
Consensus pattern (162 bp):
AAGAAAAGTCCATTTATAGTCCCTCATTCCTTCAAAAGCCTTATCACTCACTTTTTATAATCTCA
TAATTGATTTTAGATTAATGTTTTTACATCCTTTATTAAGACAAACTATAATTGAATGCCTGCCT
CAAGAAACATGTAGAAAACACCATTCATTAGA
Found at i:1665 original size:170 final size:170
Alignment explanation
Indices: 1318--1785 Score: 397
Period size: 170 Copynumber: 2.7 Consensus size: 170
1308 NNNNNNNTAT
* *
1318 AATCTCATAATTGATTTTAGATTAAATGTTTTTACATCCTTTATTAAGACAGACTATAATTGAAT
1 AATCTCATAATTGATTTTAGGTTAAATGTTTTTACATCTTTTATTAAGACAGACTATAATTGAAT
* * * * *
1383 GCCTGTCTTAAGAAACATGTAGAAAATGCCATTCATTAGAAAGAAAAGTCCATTTATAGTGTCTC
66 GCCTGCCTCAGGAAACATGTAGAAAA-ACCATTCATTTGAAAGAAAAGTCCATTTATAGTGTCTC
* * ********** *
1448 ATTCCTTCAAAAGCCTTATCACTCGCNNNNNNNNNNTTTAT
130 ATTCCTTCAAAAGCCTTATCACCCACTTTAAACGGTTTTAC
*
1489 AATCTCATAATTGATTTTAGGTT-AATGTTTTTACATCTTTTATTAAGACAAACTATAATTGAAT
1 AATCTCATAATTGATTTTAGGTTAAATGTTTTTACATCTTTTATTAAGACAGACTATAATTGAAT
* *****
1553 GCCTGCCTCAGGAAACATGTAGAAAACATCATTCATTTGAAAGAAAAGTCCATTTATAGTNNNNN
66 GCCTGCCTCAGGAAACATGTAGAAAA-ACCATTCATTTGAAAGAAAAGTCCATTTATAGTGTCTC
***** * *
1618 NNNNNTTTAAAAGCCTTATTACCCACTTTAAACGGTTTTAC
130 ATTCCTTCAAAAGCCTTATCACCCACTTTAAACGGTTTTAC
* * * * * * **
1659 AATCTCAAAATT-ATTTATAAGTTCAATTTTTTTAAAAT-TTTTAGTTAAAACAGTTTATAATTG
1 AATCTCATAATTGATTT-TAGGTTAAATGTTTTT-ACATCTTTTA-TTAAGACAGACTATAATTG
* * * * * *
1722 AATGTCTACCTC-GAGAAACATGAAGAAAAAGGCATTTA-TTGACAGGAAAAGTCCATTTATAGT
63 AATGCCTGCCTCAG-GAAACATGTAGAAAAA-CCATTCATTTGA-AAGAAAAGTCCATTTATAGT
1785 G
125 G
1786 ACCTATTCNN
Statistics
Matches: 240, Mismatches: 50, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
169 4 0.02
170 129 0.54
171 41 0.17
172 66 0.28
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.35
Consensus pattern (170 bp):
AATCTCATAATTGATTTTAGGTTAAATGTTTTTACATCTTTTATTAAGACAGACTATAATTGAAT
GCCTGCCTCAGGAAACATGTAGAAAAACCATTCATTTGAAAGAAAAGTCCATTTATAGTGTCTCA
TTCCTTCAAAAGCCTTATCACCCACTTTAAACGGTTTTAC
Done.