Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400551.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3744.0, 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: 10218
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.27
Warning! 3060 characters in sequence are not A, C, G, or T
Found at i:799 original size:171 final size:169
Alignment explanation
Indices: 503--1079 Score: 408
Period size: 171 Copynumber: 3.4 Consensus size: 169
493 NNNNNNNNNN
* * * * * *
503 TTTATAATCTCATAATTGATTTAAAGTTAAATTTTTTTACATTTTTAGTTAAAACAGACAATAAT
1 TTTATAATCTCATAATTGATTTTAAGTTAAA-TTTTTTATATTTTTAGCTAAAAGAGACTATAAA
* * * * * *********
568 TGAATGTCTTCCTCAGGAAACATG-AAGAAAAAGGC-ATTCATTG-GNNNNNNNNNNCCATTTAT
65 TGAATGCCTACCTTAAGAAACGTGCAA-AAAAA-GCTATTCATTGAG-AGAAAAAGTCCATTTAT
* *
630 AGTCACCCATTCCTTTAAATGTCTTATTACTCGCTTTAAATTGT
127 AGTCACCCATTCATTCAAA-GTCTTATTACTCGCTTTAAATTGT
* * ********* *
674 TTTATAATCTCAAAAGTGATTTTAAGTTAAATTTTTTNNNNNNNNNNGTTAAAAGAGACTATAAA
1 TTTATAATCTCATAATTGATTTTAAGTTAAATTTTTT-ATATTTTTAGCTAAAAGAGACTATAAA
* * * * *
739 TGAATGCCTGCCTTACGAAACGTTCAAAAAAAGCTATTGATTGAGA-AGAAAAGTCCATTTATGG
65 TGAATGCCTACCTTAAGAAACGTGCAAAAAAAGCTATTCATTGAGAGA-AAAAGTCCATTTATAG
* * * ***
803 TCACCCATTCATTGAAAAGCCTTATTACTCGCTTTTAATNNN
129 TCACCCATTCATT-CAAAGTCTTATTACTCGCTTTAAATTGT
******* * * *
845 NNNNNNNTCTCATAATTGATTTTAAGTTGAATATTTTTATATTTTTAGCTAAAATAGACTATAAT
1 TTTATAATCTCATAATTGATTTTAAGTTAAAT-TTTTTATATTTTTAGCTAAAAGAGACTATAAA
** *
910 TGAATTTCTACCTTAAGAAACGTGCAAAAAAAGCTGTTCATTGAGAGAAAAAGTCCATTTATAGT
65 TGAATGCCTACCTTAAGAAACGTGCAAAAAAAGCTATTCATTGAGAGAAAAAGTCCATTTATAGT
* * **
975 CACCCATTCGTTCAAAATCTTTATTACTCATTTTAAATTGT
130 CACCCATTCATTCAAAGTC-TTATTACTCGCTTTAAATTGT
* * * * *
1016 TTTATAATCTCATCATTGATTTTAAGTTTAATTTTTTTACACTTTCT-GCTAAAACAGACTATAA
1 TTTATAATCTCATAATTGATTTTAAG-TTAAATTTTTTATA-TTTTTAGCTAAAAGAGACTATAA
1080 NNNNNNNNNN
Statistics
Matches: 304, Mismatches: 91, Indels: 22
0.73 0.22 0.05
Matches are distributed among these distances:
170 12 0.04
171 272 0.89
172 20 0.07
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.37
Consensus pattern (169 bp):
TTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTATATTTTTAGCTAAAAGAGACTATAAAT
GAATGCCTACCTTAAGAAACGTGCAAAAAAAGCTATTCATTGAGAGAAAAAGTCCATTTATAGTC
ACCCATTCATTCAAAGTCTTATTACTCGCTTTAAATTGT
Found at i:7149 original size:171 final size:161
Alignment explanation
Indices: 6864--7196 Score: 364
Period size: 171 Copynumber: 2.0 Consensus size: 161
6854 NNNNNNNNNT
*
6864 TAAATTGTTTTATAATCTCAAAATTGATTTTAAGTTAAATTTTTTTATATTTACGGTTAAAACAG
1 TAAATTGTTTTATAATCACAAAATTGATTTTAAGTTAAATTTTTTTATATTTACGGTTAAAACAG
* * ** * *
6929 ACTATAATTGAATGCCTGCCTTTAGAAATGTGTAAAAACAGTCATTCATTGAGAAAAAAAGTCCA
66 ACTATAATTGAATGCCTACCTTAAGAAACATGCAAAAAAAGTCATTCATTGAGAAAAAAAGTCCA
* * *
6994 TTTATAGTCATCTATTCCTTCAAAAGCCTTNNNNNNNNNNA
131 CTTATAGTCACCCATTCCTTCAAAAGCCTT----------A
* * * ***
7035 TAAATTGTTTTAT-ATCACATAATTGATTTTTAGTTGAATTTTTTTATATTGTTTTGTTAAAACA
1 TAAATTGTTTTATAATCACAAAATTGATTTTAAGTTAAATTTTTTTATATT-TACGGTTAAAACA
* *
7099 GACTATAGTTGAATGCCTACCTTAAGAAACATGCAAAAAAAG-CTATTCATTGAGAAGAAAAGTC
65 GACTATAATTGAATGCCTACCTTAAGAAACATGCAAAAAAAGTC-ATTCATTGAGAAAAAAAGTC
**
7163 CACTTATAGTCACCCATTTTTTCAAAAGCCTTA
129 CACTTATAGTCACCCATTCCTTCAAAAGCCTTA
7196 T
1 T
7197 TACTCGCTGN
Statistics
Matches: 140, Mismatches: 20, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
161 2 0.01
170 34 0.24
171 104 0.74
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.38
Consensus pattern (161 bp):
TAAATTGTTTTATAATCACAAAATTGATTTTAAGTTAAATTTTTTTATATTTACGGTTAAAACAG
ACTATAATTGAATGCCTACCTTAAGAAACATGCAAAAAAAGTCATTCATTGAGAAAAAAAGTCCA
CTTATAGTCACCCATTCCTTCAAAAGCCTTA
Found at i:9475 original size:170 final size:162
Alignment explanation
Indices: 9286--9606 Score: 317
Period size: 172 Copynumber: 1.9 Consensus size: 162
9276 NNNNNNNNNG
* * * *
9286 CCTTATTACTCATTTTAAATTATTTTATAATCACATAATTAATTTTAAGTTGAAT-TTTTTT-AC
1 CCTTATTACTCACTTTAAATTATTTTATAATCACAAAATTAATTTTAAGTTAAATATTTTTTGAA
* * *
9349 ATTTTTGCTAAAACAGACTATAATCGAATGTCTAAC-TCAAGAAACGTGAAAAAAAA-ATCATTC
66 ATTTTAGCTAAAACAGACTATAATCGAATGTCT-ACTTCAAGAAACATGAAAAAAAAGCT-ATTC
*
9412 ATTGGGAAGAAAAGTCCATTTATAGTCACCCATT
129 ATTGAGAAGAAAAGTCCATTTATAGTCACCCATT
* * * *
9446 CNNNNNNNNNNCTTATTACTCGCTTTAAATTGTTTTATAATCTCAAAATTGATTTTAAGTTAAAT
1 C----------CTTATTACTCACTTTAAATTATTTTATAATCACAAAATTAATTTTAAGTTAAAT
* * * * * * **
9511 ATTTTTTGAAATTTTAGTTGAAATAGACTATAATTGAATGTCTGCTTTAAGAAACATGCCAAAAA
56 ATTTTTTGAAATTTTAGCTAAAACAGACTATAATCGAATGTCTACTTCAAGAAACATGAAAAAAA
*
9576 AGCTATTCATTGAGAATAAAAGTCCATTTAT
121 AGCTATTCATTGAGAAGAAAAGTCCATTTAT
9607 GGNNNNNNNN
Statistics
Matches: 126, Mismatches: 21, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
160 1 0.01
170 47 0.37
171 7 0.06
172 70 0.56
173 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.38
Consensus pattern (162 bp):
CCTTATTACTCACTTTAAATTATTTTATAATCACAAAATTAATTTTAAGTTAAATATTTTTTGAA
ATTTTAGCTAAAACAGACTATAATCGAATGTCTACTTCAAGAAACATGAAAAAAAAGCTATTCAT
TGAGAAGAAAAGTCCATTTATAGTCACCCATT
Done.