Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398538.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1830.0, 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: 2183
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.20
Warning! 926 characters in sequence are not A, C, G, or T
Found at i:647 original size:171 final size:173
Alignment explanation
Indices: 342--920 Score: 544
Period size: 171 Copynumber: 3.4 Consensus size: 173
332 ATTTTAAGTA
* * * * *
342 GAATTGTTTTTATATTTTTGGTT-AAACATACTCTA--ATTGATTGTCTACCTTGAG-AA-ATGT
1 GAATTCTTTGTATATTTTTGGTTAAAACAGA-T-TAGGATTGAATGTCTA-CTTCAGAAACATG-
* * * * * * *
402 AA-AGAAAAAAGTGCTCATTGACAAAAGAAGTCCATTTATAGTCACTTATTCCTCCAAAGGCCTT
62 AAGAGAAAAAGGTACTAATTGGCAAGAGAAGTCCAATTATAGTCACTTATTCCTTCAAAGGCCTT
466 ATTACTCACTTTAAACGGTTTTACAATCTCAAAATTGATTTAAATTT
127 ATTACTCACTTTAAACGGTTTTACAATCTCAAAATTGATTTAAATTT
*
513 GAATTCTTTGTATATCTTT-GTTAAAACAGATTAGGATTGAATGTCTACTTTCAGAAACATGAAG
1 GAATTCTTTGTATATTTTTGGTTAAAACAGATTAGGATTGAATGTCTAC-TTCAGAAACATGAAG
* ********** *
577 AG-AAAA-GTATTAATTGGCAAGAGAAGTCCAATTATAGTCNNNNNNNNNNTCAAAAGCCTTATT
65 AGAAAAAGGTACTAATTGGCAAGAGAAGTCCAATTATAGTCACTTATTCCTTCAAAGGCCTTATT
* * * * * * *
640 ACTCACTTTAAATGGTTTTGTA-AAGC-CATAATTCATTTTAAGTA
130 ACTCACTTTAAACGG-TTT-TACAATCTCAAAATTGATTTAAATTT
* * * * *
684 GAATTTTTTTTATATTTTTGGTT-AAACAAACTCTA--ATTGATTGTCTACCTC-GAGAA-ATGC
1 GAATTCTTTGTATATTTTTGGTTAAAACAGA-T-TAGGATTGAATGTCTACTTCAGA-AACATG-
* * *
744 AA-AGAAAAAGGTGCTCATTGGCAAGAGAAGTCCATTTATAGTCACTTATTCCTTCAAAGGCCTT
62 AAGAGAAAAAGGTACTAATTGGCAAGAGAAGTCCAATTATAGTCACTTATTCCTTCAAAGGCCTT
*
808 ATTACTCACTTTAAACAGTTTTACAATCTCAAAATTGATTTAAATTT
127 ATTACTCACTTTAAACGGTTTTACAATCTCAAAATTGATTTAAATTT
* *
855 GAATTCTTTGTATATTTTTGGTTAAAACTGACTAGGATTGAATGTCTACCTTCAGAAACATGAAG
1 GAATTCTTTGTATATTTTTGGTTAAAACAGATTAGGATTGAATGTCTA-CTTCAGAAACATGAAG
920 A
65 A
921 ANNNNNNNNN
Statistics
Matches: 316, Mismatches: 67, Indels: 47
0.73 0.16 0.11
Matches are distributed among these distances:
169 11 0.03
170 23 0.07
171 226 0.72
172 34 0.11
173 16 0.05
174 6 0.02
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.36
Consensus pattern (173 bp):
GAATTCTTTGTATATTTTTGGTTAAAACAGATTAGGATTGAATGTCTACTTCAGAAACATGAAGA
GAAAAAGGTACTAATTGGCAAGAGAAGTCCAATTATAGTCACTTATTCCTTCAAAGGCCTTATTA
CTCACTTTAAACGGTTTTACAATCTCAAAATTGATTTAAATTT
Found at i:666 original size:342 final size:333
Alignment explanation
Indices: 296--920 Score: 1027
Period size: 342 Copynumber: 1.8 Consensus size: 333
286 NNNNNNNNNN
*
296 TTACTCGCTTTAAATGGTTTTGTAAAGCCATAATTCATTTTAAGTAGAATTGTTTTTATATTTTT
1 TTACTCACTTTAAATGGTTTTGTAAAGCCATAATTCATTTTAAGTAGAATTGTTTTTATATTTTT
* * *
361 GGTTAAACATACTCTAATTGATTGTCTACCTTGAGAAATGTAAAGAAAAAAGTGCTCATTGACAA
66 GGTTAAACAAACTCTAATTGATTGTCTACCTCGAGAAATGCAAAGAAAAAAGTGCTCATTGACAA
*
426 AAGAAGTCCATTTATAGTCACTTATTCCTCCAAAGGCCTTATTACTCACTTTAAACGGTTTTACA
131 AAGAAGTCCATTTATAGTCACTTATTCCTCCAAAGGCCTTATTACTCACTTTAAACAGTTTTACA
*
491 ATCTCAAAATTGATTTAAATTTGAATTCTTTGTATATCTTT-GTTAAAACAGATTAGGATTGAAT
196 ATCTCAAAATTGATTTAAATTTGAATTCTTTGTATATCTTTGGTTAAAACAGACTAGGATTGAAT
*
555 GTCTACTTTCAGAAACATGAAGAGAAAAGTATTAATTGGCAAGAGAAGTCCAATTATAGTCNNNN
261 GTCTACCTTCAGAAACATGAAGAGAAAAGTATTAATTGGCAAGAGAAGTCCAATTATAGTC----
620 NNNNNNTCAAAAGCCTTA
322 ------TCAAAAGCCTTA
*
638 TTACTCACTTTAAATGGTTTTGTAAAGCCATAATTCATTTTAAGTAGAATTTTTTTTATATTTTT
1 TTACTCACTTTAAATGGTTTTGTAAAGCCATAATTCATTTTAAGTAGAATTGTTTTTATATTTTT
* *
703 GGTTAAACAAACTCTAATTGATTGTCTACCTCGAGAAATGCAAAGAAAAAGGTGCTCATTGGCAA
66 GGTTAAACAAACTCTAATTGATTGTCTACCTCGAGAAATGCAAAGAAAAAAGTGCTCATTGACAA
* *
768 GAGAAGTCCATTTATAGTCACTTATTCCTTCAAAGGCCTTATTACTCACTTTAAACAGTTTTACA
131 AAGAAGTCCATTTATAGTCACTTATTCCTCCAAAGGCCTTATTACTCACTTTAAACAGTTTTACA
* *
833 ATCTCAAAATTGATTTAAATTTGAATTCTTTGTATATTTTTGGTTAAAACTGACTAGGATTGAAT
196 ATCTCAAAATTGATTTAAATTTGAATTCTTTGTATATCTTTGGTTAAAACAGACTAGGATTGAAT
898 GTCTACCTTCAGAAACATGAAGA
261 GTCTACCTTCAGAAACATGAAGA
921 ANNNNNNNNN
Statistics
Matches: 268, Mismatches: 14, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
342 225 0.84
343 43 0.16
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (333 bp):
TTACTCACTTTAAATGGTTTTGTAAAGCCATAATTCATTTTAAGTAGAATTGTTTTTATATTTTT
GGTTAAACAAACTCTAATTGATTGTCTACCTCGAGAAATGCAAAGAAAAAAGTGCTCATTGACAA
AAGAAGTCCATTTATAGTCACTTATTCCTCCAAAGGCCTTATTACTCACTTTAAACAGTTTTACA
ATCTCAAAATTGATTTAAATTTGAATTCTTTGTATATCTTTGGTTAAAACAGACTAGGATTGAAT
GTCTACCTTCAGAAACATGAAGAGAAAAGTATTAATTGGCAAGAGAAGTCCAATTATAGTCTCAA
AAGCCTTA
Done.