Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400810.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3984.0, 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: 6090
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.26
Warning! 1851 characters in sequence are not A, C, G, or T
Found at i:1492 original size:341 final size:342
Alignment explanation
Indices: 992--1856 Score: 827
Period size: 341 Copynumber: 2.5 Consensus size: 342
982 NNNNNNNNNN
** * ** * * *
992 ACTATAAATGGACTTTTCTTGCCAATGAATTCCATTT-T-TTCATATTTCTTGAGGTAAACATTC
1 ACTATAAATAAACTTTTCTAGCCAATGAATGAC-TTTGTCTTCACATTTCCTAAGGTAAACATTC
* * * * * * *
1055 AATTAAAATATGTTTTAACTAAAAATATGAAAAAATTCAACTTGAAATCAATAATGAGATTACAA
65 AATTATAATTTGTTTTAACTAAAAATGTGAAAAAATTCAACTTAAAATAAATTATGAGATTATAA
* * * * * **
1120 AGCAATTTAAAGCGAGGAATAAGGGTTTTGAAAGAATTAGTGACTATAAGTAGACTTTTCTTGTA
130 AACAATTTAAAGCGAGGAATAAGGCTTTTGAAAGAATGAGTGACTATAAATAGACTTTCCTTACA
* * * * * * ** * *
1185 -AATGAATGGCTTTTTCTTCACGTTTCCT-ACGGCAGATGATT-AATTATA-TTTTTTTTCGA-T
195 GAA-GAATAGCATTTTCTTCACATTT-CTAAAGACAGA-CATTCAATTATAGCCTGTTTT-AACT
*
1245 AAAAAATATAAAAAAATTCAACTCAAAATC-A-TATGCGAGATTATAAAACCATTTAAACCGAGT
256 AAAAAA-ATAAAAAAATTCAACTCAAAATCAATTAT--GAGATTACAAAACCATTTAAACCGAGT
* **
1308 AGTAAAGCTTTCGTAGGAATGGGTG
318 AATAAAGCTTTCAAAGGAATGGGTG
* * * * *
1333 ACTATAAATAAACTTTTCTAGTCAATGAATGACTTTGTGTTCACGTTTCCCT-AGGTATACATTT
1 ACTATAAATAAACTTTTCTAGCCAATGAATGACTTTGTCTTCACATTT-CCTAAGGTAAACATTC
*
1397 AATTATAATTTGTTTTAACTAATAATGTGAAAAAATTCAACTTAAAATAAATTATGAGATTATAA
65 AATTATAATTTGTTTTAACTAAAAATGTGAAAAAATTCAACTTAAAATAAATTATGAGATTATAA
* * * * * *
1462 AACCATTTAAAGCGAGTAATAA-GCTTTTGAAGGTATGAGTGGCTATAAATGGACTTTCCTTACA
130 AACAATTTAAAGCGAGGAATAAGGCTTTTGAAAGAATGAGTGACTATAAATAGACTTTCCTTACA
* *
1526 GAAGAATAGCATTTTCTTTACATTTTTAAAGACAGACATTCAATTATAGCCTGTTTTAACTAAAA
195 GAAGAATAGCATTTTCTTCACATTTCTAAAGACAGACATTCAATTATAGCCTGTTTTAACTAAAA
* * * * * *
1591 AAGTAAAAAAATTTAACTTAAAATCAATTATGAGATTACAAAACTATTTAAAGCGAGTAATAAGG
260 AAATAAAAAAATTCAACTCAAAATCAATTATGAGATTACAAAACCATTTAAACCGAGTAATAAAG
*
1656 CTTTCAAAGGTATGGGTG
325 CTTTCAAAGGAATGGGTG
* *** * * * * *
1674 ATTATAAATGGGCTTTTCTAGCCAATGTATGGCTTTTTCTTCACATTTTCTAAGGTAGACATTCA
1 ACTATAAATAAACTTTTCTAGCCAATGAATGACTTTGTCTTCACATTTCCTAAGGTAAACATTCA
* * * * * *
1739 ATTATAATTTATTTGAACCAAAAATGTAAAAACAAATCAACTTAAAATGAATTATGAGATTATAA
66 ATTATAATTTGTTTTAACTAAAAATGTGAAAA-AATTCAACTTAAAATAAATTATGAGATTATAA
* ** * * * * *
1804 AACTATTTAAAGCTTGTACTAATG-TTTTGGAAAGAATGGGTGACTACAAATAG
130 AACAATTTAAAGCGAGGAATAAGGCTTTT-GAAAGAATGAGTGACTATAAATAG
1857 TATTTTCTCA
Statistics
Matches: 425, Mismatches: 85, Indels: 26
0.79 0.16 0.05
Matches are distributed among these distances:
340 9 0.02
341 232 0.55
342 160 0.38
343 24 0.06
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (342 bp):
ACTATAAATAAACTTTTCTAGCCAATGAATGACTTTGTCTTCACATTTCCTAAGGTAAACATTCA
ATTATAATTTGTTTTAACTAAAAATGTGAAAAAATTCAACTTAAAATAAATTATGAGATTATAAA
ACAATTTAAAGCGAGGAATAAGGCTTTTGAAAGAATGAGTGACTATAAATAGACTTTCCTTACAG
AAGAATAGCATTTTCTTCACATTTCTAAAGACAGACATTCAATTATAGCCTGTTTTAACTAAAAA
AATAAAAAAATTCAACTCAAAATCAATTATGAGATTACAAAACCATTTAAACCGAGTAATAAAGC
TTTCAAAGGAATGGGTG
Found at i:1770 original size:171 final size:171
Alignment explanation
Indices: 992--1816 Score: 713
Period size: 171 Copynumber: 4.8 Consensus size: 171
982 NNNNNNNNNN
* ** * * * *
992 ACTATAAATGGACTTTTCTTGCCAATGAATTCCATTTT-TTCATA-TTTCTTGAGGTAAACATTC
1 ACTATAAATGGACTTTTCTAGCCAATGAATGGCTTTTTCTTCACATTTTC-TAAGGTAGACATTC
* * * * * * *
1055 AATTAAAATATGTTTTAACTAAAAATATGAAAAAATTCAACTTGAAATCAATAATGAGATTACAA
65 AATTATAATTTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * * * *
1120 AGCAATTTAAAGCGAGGAATAAGGGTTTTGAAA-GAATTAGTG
130 AACCATTTAAAGCGAGTAATAA-GGCTTTCAAAGGAATGAGTG
* * * ** * * * * *
1162 ACTATAAGTAGACTTTTCTTGTAAATGAATGGCTTTTTCTTCACGTTTCCTACGGCAGATGATT-
1 ACTATAAATGGACTTTTCTAGCCAATGAATGGCTTTTTCTTCACATTTTCTAAGGTAGA-CATTC
* * * *
1226 AATTAT-ATTTTTTTTCGA-TAAAAAATATAAAAAAATTCAACTCAAAATC-A-TATGCGAGATT
65 AATTATAATTTGTTTT-AACT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTAT--GAGATT
* * * ** *
1287 ATAAAACCATTTAAACCGAGTAGTAAAGCTTTCGTAGGAATGGGTG
126 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGAATGAGTG
** * * * * * * * *
1333 ACTATAAATAAACTTTTCTAGTCAATGAATGACTTTGTGTTCACGTTTCCCT-AGGTATACATTT
1 ACTATAAATGGACTTTTCTAGCCAATGAATGGCTTTTTCTTCACATTT-TCTAAGGTAGACATTC
* * *
1397 AATTATAATTTGTTTTAACTAATAATGTGAAAAAATTCAACTTAAAATAAATTATGAGATTATAA
65 AATTATAATTTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
** *
1462 AACCATTTAAAGCGAGTAATAA-GCTTTTGAAGGTATGAGTG
130 AACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGAATGAGTG
* * * * * * **
1503 GCTATAAATGGACTTTCCTTA--CAGAAGAATAGCATTTTCTTTACATTTT-TAAAGACAGACAT
1 ACTATAAATGGACTTTTC-TAGCCA-ATGAATGGCTTTTTCTTCACATTTTCT-AAGGTAGACAT
*** * * *
1565 TCAATTATAGCCTGTTTTAACTAAAAAAGTAAAAAAATTTAACTTAAAATCAATTATGAGATTAC
63 TCAATTATAATTTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * *
1630 AAAACTATTTAAAGCGAGTAATAAGGCTTTCAAAGGTATGGGTG
128 AAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGAATGAGTG
* * *
1674 ATTATAAATGGGCTTTTCTAGCCAATGTATGGCTTTTTCTTCACATTTTCTAAGGTAGACATTCA
1 ACTATAAATGGACTTTTCTAGCCAATGAATGGCTTTTTCTTCACATTTTCTAAGGTAGACATTCA
* * * * *
1739 ATTATAATTTATTTGAACCAAAAATGTAAAAACAAATCAACTTAAAATGAATTATGAGATTATAA
66 ATTATAATTTGTTTTAACTAAAAATGTAAAAA-AATTCAACTTAAAATCAATTATGAGATTATAA
*
1804 AACTATTTAAAGC
130 AACCATTTAAAGC
1817 TTGTACTAAT
Statistics
Matches: 520, Mismatches: 112, Indels: 44
0.77 0.17 0.07
Matches are distributed among these distances:
168 1 0.00
169 4 0.01
170 180 0.35
171 269 0.52
172 63 0.12
173 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (171 bp):
ACTATAAATGGACTTTTCTAGCCAATGAATGGCTTTTTCTTCACATTTTCTAAGGTAGACATTCA
ATTATAATTTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
ACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGAATGAGTG
Done.