Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398182.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1486.0, 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: 3213
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.26
Warning! 909 characters in sequence are not A, C, G, or T
Found at i:865 original size:171 final size:170
Alignment explanation
Indices: 313--1153 Score: 851
Period size: 171 Copynumber: 4.9 Consensus size: 170
303 NNNNNNNNNN
* * * **
313 AAAAACTCAACTTAAAATGAATTATGACATTATAAAACCATTTAAAGTGAGTAATCGGGCTTTTG
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
* * * ** * * * *
378 AAGGAATAGGTGACTATAAATGGACTTTTCTTGATACTGAATACT-TGTTCCTTCATATTTC-TC
66 AAGGAAT-GGAGGCTATAAATAGACTTTTCTTGCCAATGAATGCTCT-TTTCTTCACATTTCTTC
* *
441 AAGATAGACATTCAATTATTGTCTATTTTAATCAAAAATATAAA
129 AA-ATAGACATTCAATTATAGTCTGTTTTAATCAAAAATAT-AA
* * * *
485 AAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGCGAATAATAGGGCTTTTG
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
* * * *
550 AAGGAATTGGAGGCTATAAATAGACTTTTCTTGCCAATGAATG-TTTTTTCTTCAAAATTCTCCA
66 AAGGAA-TGGAGGCTATAAATAGACTTTTCTTGCCAATGAATGCTCTTTTCTTCACATTTCTTCA
** * * * *
614 GGTAAACATTCAATTATAGCCCGTTTTAA-CAAAAAATGTAA
130 AATAGACATTCAATTATAGTCTGTTTTAATC-AAAAATATAA
* *
655 AAAAAATCAACTTAAAATCAATTATGAGATTAGAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
* * * * *
720 AAGGAGTGGAAGGTTATAAATAGACTTTTCTTGCCAATGAACGCTATTTTCTTCACATTTCTTGA
66 AAGGAATGG-AGGCTATAAATAGACTTTTCTTGCCAATGAATGCTCTTTTCTTCACATTTCTTCA
*
785 AATAGACATTCAATTATTA-ACTGTTTTAAT-AATAAATATAA
130 AATAGACATTCAATTA-TAGTCTGTTTTAATCAA-AAATATAA
* **
826 AAAAATTCAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGAT-AGTAATAAACCTTTT
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG-TGAGTAATAAGGCTTTT
*
890 GAAGG-ATGGGGAGGCTATAAAT-GAACTTTTCTTGCCAATGAATGCTCTTTTCTTCTCATTTCT
65 GAAGGAAT--GGAGGCTATAAATAG-ACTTTTCTTGCCAATGAATGCTCTTTTCTTCACATTTCT
** * *
953 TGC-GTTCA-ACATTCAATTATAGTCTGTTTTAATGAAAAATGTAA
127 T-CAAAT-AGACATTCAATTATAGTCTGTTTTAATCAAAAATATAA
* * * * * *** *
997 AAAAATTCAACTTGAAATTAATTACGAGATTAGAAAACTATTTAAAGCCTGTAATTAGGCTTTTG
1 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
* ** * * * **
1062 AAGAAATAGCTGACTATAAATGGACTTTTCTTGTCAATGAATGCTCTTTTCTTCATGTTT-TTCG
66 AAGGAAT-GGAGGCTATAAATAGACTTTTCTTGCCAATGAATGCTCTTTTCTTCACATTTCTTC-
* * *
1126 AGATATATATTCAATTATAGTCTGTTTT
129 AAATAGACATTCAATTATAGTCTGTTTT
1154 NNNNNNNNNN
Statistics
Matches: 563, Mismatches: 83, Indels: 47
0.81 0.12 0.07
Matches are distributed among these distances:
169 4 0.01
170 107 0.19
171 345 0.61
172 106 0.19
173 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (170 bp):
AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
AAGGAATGGAGGCTATAAATAGACTTTTCTTGCCAATGAATGCTCTTTTCTTCACATTTCTTCAA
ATAGACATTCAATTATAGTCTGTTTTAATCAAAAATATAA
Found at i:1153 original size:342 final size:341
Alignment explanation
Indices: 313--1153 Score: 1014
Period size: 342 Copynumber: 2.5 Consensus size: 341
303 NNNNNNNNNN
* * * * **
313 AAAAACTCAACTTAAAATGAATTATGACATTATAAAACCATTTAAAGTGAGTAATCGGGCTTTTG
1 AAAAAATCAACTTAAAATCAATTATGAGATTAGAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
* * * * * *
378 AAGGAATAGGTGACTATAAATGGACTTTTCTTGAT-ACTGAATACTTGTTCCTTCATATTTCTCA
66 AAGGAATAGATGACTATAAATGGACTTTTCTTG-TCAATGAATGCTT-TTTCTTCATATTTTTCG
* *
442 AGATAGACATTCAATTATTGTCTATTTTAATCAAAAATATAAAAAAAATTCAACTTAAAATCAAT
129 AGATAGACATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAAATTCAACTTAAAATCAAT
* *** *
507 TATTAGATTATAAAACCATTTAAAGCGAATAATAGGGCTTTTGAAGGAATTGGAGGCTATAAATA
194 TATTAGATTATAAAACCATTTAAAGAGAATAATAAACCTTTTGAAGGAATGGGAGGCTATAAATA
*
572 GACTTTTCTTGCCAATGAATGTTTTTTCTTCAAAATTCTCCAGGTAAACATTCAATTATAGCCCG
259 GACTTTTCTTGCCAATGAATGTCTTTTCTTCAAAATTCTCCAGGTAAACATTCAATTATAGCCCG
637 TTTTAACAAAAAATGTAA
324 TTTTAACAAAAAATGTAA
655 AAAAAATCAACTTAAAATCAATTATGAGATTAGAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
1 AAAAAATCAACTTAAAATCAATTATGAGATTAGAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
* * * ** * * * *
720 AAGGAGTGGAAGGTTATAAATAGACTTTTCTTGCCAATGAACGCTATTTTCTTCACATTTCTT-G
66 AAGGAATAGATGACTATAAATGGACTTTTCTTGTCAATGAATGCT-TTTTCTTCATATTT-TTCG
* *
784 AAATAGACATTCAATTATTA-ACTGTTTTAAT-AATAAATAT-AAAAAAATTCAACTTAAAATCA
129 AGATAGACATTCAATTA-TAGTCTGTTTTAATCAA-AAATATAAAAAAAATTCAACTTAAAATCA
* *
846 ATTATTAGATTATAAAACCATTTAAAGATAGTAATAAACCTTTTGAAGG-ATGGGGAGGCTATAA
192 ATTATTAGATTATAAAACCATTTAAAGAGAATAATAAACCTTTTGAAGGAAT-GGGAGGCTATAA
** * * * *
910 AT-GAACTTTTCTTGCCAATGAATGCTCTTTTCTTCTCATTTCTTGC-GTTCAACATTCAATTAT
256 ATAG-ACTTTTCTTGCCAATGAATG-TCTTTTCTTCAAAATTC-TCCAGGTAAACATTCAATTAT
* * **
973 AGTCTGTTTTAATGAAAAATGTAA
318 AGCCCGTTTTAACAAAAAATGTAA
* * * * * *** *
997 AAAAATTCAACTTGAAATTAATTACGAGATTAGAAAACTATTTAAAGCCTGTAATTAGGCTTTTG
1 AAAAAATCAACTTAAAATCAATTATGAGATTAGAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
* * *
1062 AAGAAATAGCTGACTATAAATGGACTTTTCTTGTCAATGAATGCTCTTTTCTTCATGTTTTTCGA
66 AAGGAATAGATGACTATAAATGGACTTTTCTTGTCAATGAATGCT-TTTTCTTCATATTTTTCGA
* *
1127 GATATATATTCAATTATAGTCTGTTTT
130 GATAGACATTCAATTATAGTCTGTTTT
1154 NNNNNNNNNN
Statistics
Matches: 419, Mismatches: 69, Indels: 22
0.82 0.14 0.04
Matches are distributed among these distances:
340 3 0.01
341 104 0.25
342 307 0.73
343 5 0.01
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (341 bp):
AAAAAATCAACTTAAAATCAATTATGAGATTAGAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
AAGGAATAGATGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTCTTCATATTTTTCGAG
ATAGACATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAAATTCAACTTAAAATCAATTA
TTAGATTATAAAACCATTTAAAGAGAATAATAAACCTTTTGAAGGAATGGGAGGCTATAAATAGA
CTTTTCTTGCCAATGAATGTCTTTTCTTCAAAATTCTCCAGGTAAACATTCAATTATAGCCCGTT
TTAACAAAAAATGTAA
Done.