Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402464.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5540.0, 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: 3714
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.26
Warning! 1144 characters in sequence are not A, C, G, or T
Found at i:403 original size:172 final size:162
Alignment explanation
Indices: 225--770 Score: 403
Period size: 171 Copynumber: 3.2 Consensus size: 162
215 NNNATACAAT
* * *
225 TATAATCTGTTTTAATAATAAATATAAAAAAAATTTAGCTTAAAATTAATTATGAGATTAAAAAN
1 TATAATCTATTTTAATAA-AAATATAAAAAAAGTTTAACTTAAAATTAATTATGAGATTAAAAA-
** * * * *
290 NNNNNNNNNGTGAGTAATAAGGCTTTCGCAGGTATGAGTGACTATAAATGGACATTTCTTACCAA
64 -------AAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTACAAATGGACATTTCTTA-CAA
*
355 TGGATATCCTTTTCTTTACGTTTCTCAAGGCAGACATTCAAC
121 TGGATATCCTTTTCTTTACATTTCTCAAGGCAGACATTCAAC
* * * *
397 TATAATCTCTTTTAATAAAAAAATATAAAAAAGTTCAACTTAAAACTAATTATGAGATTAAANNN
1 TATAATCTATTTTAATAAAAATATA-AAAAAAGTTTAACTTAAAATTAATTATGAGATTAAA---
** * *
462 NNNNNNNAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTACAAATGGACTTTTCTTACAAT
62 -----AAAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTACAAATGGACATTTCTTACAAT
* * * *
527 GGATATCTTTTTCTTTACATTTCTCAAGGTAGATATTCAAT
122 GGATATCCTTTTCTTTACATTTCTCAAGGCAGACATTCAAC
* **
568 TATAATCTATTTTAATAGAAAATAT-AAAAAAGTTTAACTTAAAATCAATTATGANNNNNNNNNN
1 TATAATCTATTTTAATA-AAAATATAAAAAAAGTTTAACTTAAAATTAATTATGA--------GA
* *** * * * * * *
632 TCATTTAAAGCGAGTACTAAAGCTTTTGAAGACATGAGTGACTATAAATGGACTTTTCTTGACAA
57 TTAAAAAAAGCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTACAAATGGACATTTCTT-ACAA
* * * ** * * *
697 TCGATATCTTTTTCTTTACGTTT-TCTGGGGCAAATATTCAAT
121 TGGATATCCTTTTCTTTACATTTCTC-AAGGCAGACATTCAAC
*
739 TATAATCTATTTTAATAAAAAATATGAAAAAA
1 TATAATCTATTTTAAT-AAAAATATAAAAAAA
771 TTTCAATCAA
Statistics
Matches: 307, Mismatches: 45, Indels: 44
0.78 0.11 0.11
Matches are distributed among these distances:
170 75 0.24
171 122 0.40
172 108 0.35
178 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.34
Consensus pattern (162 bp):
TATAATCTATTTTAATAAAAATATAAAAAAAGTTTAACTTAAAATTAATTATGAGATTAAAAAAA
GCGAGTAATAAGGCTTTCGAAGGCATGAGTGACTACAAATGGACATTTCTTACAATGGATATCCT
TTTCTTTACATTTCTCAAGGCAGACATTCAAC
Found at i:850 original size:170 final size:166
Alignment explanation
Indices: 301--792 Score: 497
Period size: 171 Copynumber: 2.9 Consensus size: 166
291 NNNNNNNNGT
* * * *
301 GAGTAATAAGGCTTTCGCAGGTATGAGTGACTATAAATGGACATTTCTTACCAATGGATATCCTT
1 GAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTTTCTTA-CAATGGATATCTTT
* * * *
366 TTCTTTACGTTTCTCAAGGCAGACATTCAACTATAATCTCTTTTAATAAAAAAATATAAAAAAGT
65 TTCTTTACGTTTCTCAAGGCAGATATTCAATTATAATCTATTTTAAT-AAAAAATATAAAAAATT
*******
431 TCAACTTAAAA-CTAATTATGAGATTAAANNNNNNNNNNAAGC
129 TCAAC-TAAAATC-AATTATGAGATTAAA---TCATTTAAAGC
* *
473 GAGTAATAAGGCTTTCGAAGGCATGGGTGACTACAAATGGACTTTTCTTACAATGGATATCTTTT
1 GAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTTTCTTACAATGGATATCTTTT
* * *
538 TCTTTACATTTCTCAAGGTAGATATTCAATTATAATCTATTTTAATAGAAAATATAAAAAAGTTT
66 TCTTTACGTTTCTCAAGGCAGATATTCAATTATAATCTATTTTAATAAAAAATATAAAAAA-TTT
*******
603 -AACTTAAAATCAATTATGANNNNNNNNNNTCATTTAAAGC
130 CAAC-TAAAATCAATTATGA---GATTAAATCATTTAAAGC
* * * * *
643 GAGTACTAAAGCTTTTGAAGACATGAGTGACTATAAATGGACTTTTCTTGACAATCGATATCTTT
1 GAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTTTCTT-ACAATGGATATCTTT
** *
708 TTCTTTACGTTT-TCTGGGGCAAATATTCAATTATAATCTATTTTAATAAAAAATATGAAAAAAT
65 TTCTTTACGTTTCTC-AAGGCAGATATTCAATTATAATCTATTTTAATAAAAAATAT-AAAAAAT
*
772 TTCAA-TCAAATCAATTATGAG
128 TTCAACTAAAATCAATTATGAG
793 GTTATANNNN
Statistics
Matches: 269, Mismatches: 42, Indels: 23
0.81 0.13 0.07
Matches are distributed among these distances:
170 94 0.35
171 122 0.45
172 53 0.20
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.34
Consensus pattern (166 bp):
GAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTTTCTTACAATGGATATCTTTT
TCTTTACGTTTCTCAAGGCAGATATTCAATTATAATCTATTTTAATAAAAAATATAAAAAATTTC
AACTAAAATCAATTATGAGATTAAATCATTTAAAGC
Found at i:1417 original size:160 final size:159
Alignment explanation
Indices: 1120--1441 Score: 346
Period size: 160 Copynumber: 2.0 Consensus size: 159
1110 NATTCAAATT
* * * *
1120 AAAATCAATTATGAGCTTCAAAAATCATTTAAAGCGAGTACTAAAGCTTTTGAAGGTATGAGTGA
1 AAAATCAATTATGAGCTTCAAAAATCATTTAAAGCAAGTAATAAAGCTTTTGAAGGCATCAGTGA
* **********
1185 CTATAAATAGACTTTTCTTGTCAATGGATATCTTTTTCTTCATGTTNNNNNNNNNNAACATTCAA
66 CTATAAATAGACTTTTCTTGTCAATAGATATCTTTTTCTTCATGTTTCTCGAGGTAAACATTCAA
* * *
1250 TTATAATCTGTTTTAATTAAAAATATAAA
131 ATATAATCAGTTTTAATGAAAAATATAAA
* * *
1279 AAAATTCAATTATGAGGTT-ATAAAATCATTTAAAGCAAGTAATAAGGTTTTTGAAGGCATCAGT
1 AAAA-TCAATTATGAGCTTCA-AAAATCATTTAAAGCAAGTAATAAAGCTTTTGAAGGCATCAGT
* *
1343 GTCTATAAATAGACTTCTT-TTG-CTAATAGATATCTTTTTCTTTATGTTTCTCGAGGTAAACAT
64 GACTATAAATAGACTT-TTCTTGTC-AATAGATATCTTTTTCTTCATGTTTCTCGAGGTAAACAT
* *
1406 AT-AAATATAATCAGTTTTTATGACAAATATAAA
127 -TCAAATATAATCAGTTTTAATGAAAAATATAAA
1439 AAA
1 AAA
1442 GTTTAACTTA
Statistics
Matches: 133, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
159 6 0.05
160 124 0.93
161 3 0.02
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.37
Consensus pattern (159 bp):
AAAATCAATTATGAGCTTCAAAAATCATTTAAAGCAAGTAATAAAGCTTTTGAAGGCATCAGTGA
CTATAAATAGACTTTTCTTGTCAATAGATATCTTTTTCTTCATGTTTCTCGAGGTAAACATTCAA
ATATAATCAGTTTTAATGAAAAATATAAA
Done.