Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398164.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1468.0, 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: 2496
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.28
Warning! 573 characters in sequence are not A, C, G, or T
Found at i:472 original size:171 final size:171
Alignment explanation
Indices: 180--993 Score: 688
Period size: 171 Copynumber: 4.8 Consensus size: 171
170 NNNNNNNNNN
** * **
180 ACTATAAATGGACTTTTCTCATCAATGAAT-GCTTTTTTCTTCACGTTTCTTGAGGTAGGCATTC
1 ACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTTTCTACACGTTTCTCAAGGTAGGCATTC
* * * * * *
244 AATTATAGTCTGTTTTAACCAAAATTATAAAAAAATTCAGCTCAAA-ATCAGTTATGAGATTATA
66 AATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAATCAACTTAAATA-CAATTATGAGATTATA
* *
308 AAATCATTTAAAGCGAGTAATAAGGCTTTCGAATGAATAGTTG
130 AAA-CATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATAGTAG
* * * * **
351 ACTATAAATAGACTTTTCTTGTCAATGAATGGC-TTTTTCTACATGTTTTTCAAGATAAACATTC
1 ACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTTTCTACACGTTTCTCAAGGTAGGCATTC
** * ****
415 AATTATAGTCTGTTTTAATGAAAATTGTAAAAAAAATCAACTTAAATACAATTATGAGATNNNNN
66 AATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAATCAACTTAAATACAATTATGAGAT-TATA
***** * * * * * *
480 NNNNNTTTAAGGCTAGTAATAAGGCTTTTC-AAGGTATGGAAA
130 AAACATTTAAAGCGAGTAATAAGGC-TTTCGAAGGAATAGTAG
* * * *
522 ACTGTAAATGGACTTTTCTT-CCAAATAAATGGC-TTTCTCTACACGTTATCT-AAGGTAGGCAT
1 ACTATAAATGGACTTTTCTTGTC-AATGAATGGCTTTTTTCTACACGTT-TCTCAAGGTAGGCAT
** *
584 TCAATTATAGTCTGTTTTAAAGAAAAATGTAAAAAAAATTTAACTTAAGATA-AATTATGAGATT
64 TCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAA-TCAACTTAA-ATACAATTATGAGATT
* * *
648 ATAAAACCATTTAAAGTGAGTAATAAGGCCTTT-GGAGGAATAGGAG
127 ATAAAA-CATTTAAAGCGAGTAATAAGG-CTTTCGAAGGAATAGTAG
** * * * *
694 ACTATAAATCAACTTTTCTTGACAATGAAT-GCTTTTTTCTTCAAC-TTTCTCGAGGTAGGCGTT
1 ACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTTTCTAC-ACGTTTCTCAAGGTAGGCATT
* * * *
757 CAATTAT-GTTTGTTTTAACCAAAAGTGTAAAAAAATTCAACTTATAAT-CAATTATAAGATTAT
65 CAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAATCAACTTA-AATACAATTATGAGATTAT
* * ** * *
820 AAAACTATTTAAAGCGAGTAATAAGACTTTTGAAAAAATGGGT-T
129 AAAAC-ATTTAAAGCGAGTAATAAGGCTTTCGAAGGAAT-AGTAG
* * * * ** *
864 ACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTTCT-CACATTTCTCGATGTAAACATTT
1 ACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTTTCTACACGTTTCTCAAGGTAGGCATTC
* * * * * *
928 AATTATAATTTTTTTTAACCAAAAATATAAAAAAAATTAAACTTAAA-ATCAATTTTGAGATTAT
66 AATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAA-TCAACTTAAATA-CAATTATGAGATTAT
992 AA
129 AA
994 NNNNNNNNNN
Statistics
Matches: 511, Mismatches: 106, Indels: 51
0.76 0.16 0.08
Matches are distributed among these distances:
169 7 0.01
170 98 0.19
171 274 0.54
172 125 0.24
173 7 0.01
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (171 bp):
ACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTTTCTACACGTTTCTCAAGGTAGGCATTC
AATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAATCAACTTAAATACAATTATGAGATTATAA
AACATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATAGTAG
Found at i:874 original size:342 final size:342
Alignment explanation
Indices: 180--993 Score: 770
Period size: 342 Copynumber: 2.4 Consensus size: 342
170 NNNNNNNNNN
* * * *
180 ACTATAAATGGACTTTTC-TCATCAATGAATGCTTTTTTCTTCACGTTTCTTGAGGTAGGCATTC
1 ACTATAAATGGACTTTTCTTCA-CAATAAATGCTTTTCTCTACACGTTTCTTAAGGTAGGCATTC
* * * *
244 AATTATAGTCTGTTTTAACCAAAATTATAAAAAAATTCAGCTCAAAATCAGTTATGAGATTATAA
65 AATTATAGTCTGTTTTAACAAAAATTATAAAAAAATTCAACTCAAAATAAATTATGAGATTATAA
* * ** *
309 AATCATTTAAAGCGAGTAATAAGGCTTTCGAATGAATAGTTGACTATAAATAGACTTTTCTTGTC
130 AACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATAGGAGACTATAAATAGACTTTTCTTGAC
** * **
374 AATGAATGGCTTTTTCTACATGTTTTTCAAGATAAACATTCAATTATAGTCTGTTTTAATGAAAA
195 AATGAATGGCTTTTTCTACAACTTTCTCAAGATAAACATTCAATTATAGTCTGTTTTAACCAAAA
* * ********** * * *
439 TTGTAAAAAAAATCAACTTAAATACAATTATGAGATNNNNNNNNNNTTTAAGGCTAGTAATAAGG
260 GTGTAAAAAAAATCAACTTAAATACAATTATAAGATTATAAAACTATTTAAAGCGAGTAATAAGA
***
504 CTTTTCAAGGTATGGAAA
325 CTTTTCAAAAAATGGAAA
*
522 ACTGTAAATGGACTTTTCTTC-CAAATAAATGGC-TTTCTCTACACGTTATC-TAAGGTAGGCAT
1 ACTATAAATGGACTTTTCTTCAC-AATAAAT-GCTTTTCTCTACACGTT-TCTTAAGGTAGGCAT
* * * *
584 TCAATTATAGTCTGTTTTAAAGAAAAATGTA-AAAAAAATTTAACTTAAGATAAATTATGAGATT
63 TCAATTATAGTCTGTTTT-AACAAAAAT-TATAAAAAAATTCAACTCAAAATAAATTATGAGATT
* *
648 ATAAAACCATTTAAAGTGAGTAATAAGGCCTTT-GGAGGAATAGGAGACTATAAATCA-ACTTTT
126 ATAAAACCATTTAAAGCGAGTAATAAGG-CTTTCGAAGGAATAGGAGACTATAAAT-AGACTTTT
* * * ** * *
711 CTTGACAATGAAT-GCTTTTTTCTTCAACTTTCTCGAGGTAGGCGTTCAATTAT-GTTTGTTTTA
189 CTTGACAATGAATGGC-TTTTTCTACAACTTTCTCAAGATAAACATTCAATTATAGTCTGTTTTA
*
774 ACCAAAAGTGTAAAAAAATTCAACTTATAAT-CAATTATAAGATTATAAAACTATTTAAAGCGAG
253 ACCAAAAGTGTAAAAAAAATCAACTTA-AATACAATTATAAGATTATAAAACTATTTAAAGCGAG
* ***
838 TAATAAGACTTTTGAAAAAATGGGTT
317 TAATAAGACTTTTCAAAAAATGGAAA
** * * * ** * ** *
864 ACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTTCT-CACATTTCTCGATGTAAACATTT
1 ACTATAAATGGACTTTTCTTCACAATAAATG-CTTTTCTCTACACGTTTCTTAAGGTAGGCATTC
* * * * * * *
928 AATTATAATTTTTTTTAACCAAAAA-TATAAAAAAAATTAAACTTAAAATCAATTTTGAGATTAT
65 AATTATAGTCTGTTTTAA-CAAAAATTAT-AAAAAAATTCAACTCAAAATAAATTATGAGATTAT
992 AA
128 AA
994 NNNNNNNNNN
Statistics
Matches: 381, Mismatches: 74, Indels: 34
0.78 0.15 0.07
Matches are distributed among these distances:
340 2 0.01
341 6 0.02
342 226 0.59
343 140 0.37
344 7 0.02
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (342 bp):
ACTATAAATGGACTTTTCTTCACAATAAATGCTTTTCTCTACACGTTTCTTAAGGTAGGCATTCA
ATTATAGTCTGTTTTAACAAAAATTATAAAAAAATTCAACTCAAAATAAATTATGAGATTATAAA
ACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGAATAGGAGACTATAAATAGACTTTTCTTGACA
ATGAATGGCTTTTTCTACAACTTTCTCAAGATAAACATTCAATTATAGTCTGTTTTAACCAAAAG
TGTAAAAAAAATCAACTTAAATACAATTATAAGATTATAAAACTATTTAAAGCGAGTAATAAGAC
TTTTCAAAAAATGGAAA
Found at i:1538 original size:171 final size:168
Alignment explanation
Indices: 1213--1687 Score: 505
Period size: 171 Copynumber: 2.8 Consensus size: 168
1203 TCTTGAGGTT
* ** * *
1213 GACATTCAATTATAGTCTGTTTTAACCAAAAGCGCAAAAAAAAAATCAACTTAAAATCAATTATG
1 GACATTCAATTACAGTCTGTTTTAA-CAAAAATG--TAAAAAAATTCAACTTAAAATCAATTATG
* * * * *
1278 AGATTGTAAAACTATTTAAAGTGTGTAATAAGGCTTTTGAAGGAAT-AGGAGACTATTAATAGAC
63 AGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGAGG-GACTATAAATGGAC
* * *
1342 TTTTTTTCCAAATAAATTATTTTTTTACACATTTCCCAAGGCAA
127 TTTTCTTACAAATAAACTATTTTTTT-CACATTTCCCAAGG-AA
** * *
1386 G-CATT-GGTGTACAGTCTGTTTTAACTAAAAATGTAAAAAAACTTCAGCTTAAAATCCATTATG
1 GACATTCAAT-TACAGTCTGTTTTAAC-AAAAATGTAAAAAAA-TTCAACTTAAAATCAATTATG
* *
1449 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAAGAATGAGGGAC-ATAAATGGACT
63 AGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGAGGGACTATAAATGGACT
* * * **
1513 TTTCTTACAAGTGAATACT-TTTTTTTCACGTTTCTCAAGGTT
128 TTTCTTACAAAT-AA-ACTATTTTTTTCACATTTCCCAAGGAA
* * *
1555 GACATTCAATTATAGTCTATTTTAAACAAAAATGT-AATAAATTCAACTTAAAATCAATTATGAG
1 GACATTCAATTACAGTCTGTTTT-AACAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
* * * * *
1619 ATTATAAAA-TATTTAAAGTGAGTAATAAAGTTTTTGAAAGAATGAGAGACTATAAATGAATTTT
65 ATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGAGGGACTATAAATGGACTTT
1683 TCTTA
130 TCTTA
1688 NNNNNNNNNN
Statistics
Matches: 254, Mismatches: 38, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
167 36 0.14
168 46 0.18
169 6 0.02
170 60 0.24
171 77 0.30
172 28 0.11
173 1 0.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (168 bp):
GACATTCAATTACAGTCTGTTTTAACAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGA
TTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGAGGGACTATAAATGGACTTTT
CTTACAAATAAACTATTTTTTTCACATTTCCCAAGGAA
Done.