Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398342.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1641.0, 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: 1747
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.31
Warning! 269 characters in sequence are not A, C, G, or T
Found at i:1244 original size:340 final size:339
Alignment explanation
Indices: 503--1747 Score: 1209
Period size: 341 Copynumber: 3.7 Consensus size: 339
493 NNNNNNNNNN
* *
503 ATTCAACTTAAAATCAATTATGAGATTAT-AAACCATTTAAAGCAAGTAATAAGGGTTTTAAACG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAA-G
* ** * * * *
567 -AATGGGTGACTATGAATAGACTTTTTTTCTCTATGAATGTCTTTTTC-T-ACATGTTCTCGAGG
65 AAATAGAAGACTATAAATGGACTTTTTTTGTCAATGAATGTCTTTTTCTTCACAT-TTCTCGAGG
* * * * * * * *
629 CAGACATTAAATTATAGTTTGTTTTAATGAAAAATATAAAAAAATTCAA-TGTAAAATCAATTAT
129 AAGACATTCAATTATAATCTGTTTTAATCAAAAATATAAAAAAATTGAACT-TAAAGTCAATTTT
* * * * * *
693 GAGATTTTAAAACCATTTAAAGCGAGCAATAGAGCTTTTGAAGAAATGAGTGATTATAAATGTAC
193 GAGATTATAAAACCATTTAAAGTGAGTAATA-ACCTTTTGAAGAAATGAGTGACTATAAATGGAC
* * *** * * *
758 TTTTTTTCTCAATGAATG-GTTTTTTTTGCACTTTTCTTGAGGTAGACATTCAATTATAGTCCGT
257 TTTTCTTCTCAATGAATGAG--TTTTTTGCACATTTCCCAAGGTAAACAATCAATTATAGTCTGT
**********
822 NNNNNNNNNNAATGTAAAAAA
320 TTTAACTAAAAATGT-AAAAA
* * * * *
843 ATTCAACTTAAAATCAATTAAGATATTATAAAACCATTTAAAGTGAGTAATATGACTTTTAAAG-
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGA
*
907 AATAGAAGACTATAAATGGACTTTTTTTGTCAATGAATGTCTTTTTCTTCACATTTCACGAGGAA
66 AATAGAAGACTATAAATGGACTTTTTTTGTCAATGAATGTCTTTTTCTTCACATTTCTCGAGGAA
* * *
972 GATATTCAATTATAATATGTTTT-ATCCAAAAATATAAAATAAATTGAACTTGAAGTCAATTTTG
131 GACATTCAATTATAATCTGTTTTAAT-CAAAAATATAAAA-AAATTGAACTTAAAGTCAATTTTG
********* *
1036 AGATTATAAAACCATTTAAAGTGAGTAATAANNNNNNNNNNGGAATGAGTGACTATAAATGGACT
194 AGATTATAAAACCATTTAAAGTGAGTAATAA-CCTTTTGAAGAAATGAGTGACTATAAATGGACT
* *
1101 TTTCTTCTCAATGAATGAGTTTTTTGCACGTTTCCCAAAGTAAACAATCAATTATAGTCTGTTTT
258 TTTCTTCTCAATGAATGAGTTTTTTGCACATTTCCCAAGGTAAACAATCAATTATAGTCTGTTTT
**
1166 AACTAAAAACATAAAAA
323 AACTAAAAATGTAAAAA
* *
1183 ATTCAACTTAAAATAAATTATGAGATTATAAAACCATTTAAAGCGTGTAATAAGGCTTTTAAAGA
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGA
* * * * *
1248 AATAGGAGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCACATTTTTTGA-GAA
66 AATAGAAGACTATAAATGGACTTTTTTTGTCAATGAATGTCTTTTTCTTCACATTTCTCGAGGAA
* * * *
1312 AAGCATTCAATTATAATCTGTTTTGA-CAAAAAATGTAAAAAAATTAAACTTAAAGTCAATTTTG
131 GA-CATTCAATTATAATCTGTTTTAATC-AAAAATATAAAAAAATTGAACTTAAAGTCAATTTTG
* ********** * *
1376 AGATTATAAAACAATTTAAAGNNNNNNNNNNGCTTTTTGAAGAAATGGGTGACTATAAATGGACT
194 AGATTATAAAACCATTTAAAG-TGAGTAATAACCTTTTGAAGAAATGAGTGACTATAAATGGACT
* * * * *
1441 TTTCTTCTCAACGAATAAGTTTTCTGCACATTTTCCAAGGTAAACAATCAATTATAGTTTGTTTT
258 TTTCTTCTCAATGAATGAGTTTTTTGCACATTTCCCAAGGTAAACAATCAATTATAGTCTGTTTT
1506 AACTAAAAATGTAAAAA
323 AACTAAAAATGTAAAAA
* * ************* *
1523 CATTTAACTTAAAATTAATNNNNNNNNNNNNNAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
1 -ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAG
* * *
1588 AAATA-AGAGACTATAAATGGA-TTTTTCTTGTCAATGAATATCTTTTTCTTCACATCTCTCAAG
65 AAATAGA-AGACTATAAATGGACTTTTT-TTGTCAATGAATGTCTTTTTCTTCACATTTCTCGAG
* * **
1651 GAAGACATTCAATTATAATCTATTTTCATCAAAAATGCAAAACAAATTGAACTTAAAGTCAATTT
128 GAAGACATTCAATTATAATCTGTTTTAATCAAAAATATAAAA-AAATTGAACTTAAAGTCAATTT
1716 TGAGATTATAAAACCATTTAAAGTGAGTAATA
192 TGAGATTATAAAACCATTTAAAGTGAGTAATA
Statistics
Matches: 735, Mismatches: 151, Indels: 37
0.80 0.16 0.04
Matches are distributed among these distances:
340 278 0.38
341 320 0.44
342 135 0.18
343 2 0.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (339 bp):
ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGA
AATAGAAGACTATAAATGGACTTTTTTTGTCAATGAATGTCTTTTTCTTCACATTTCTCGAGGAA
GACATTCAATTATAATCTGTTTTAATCAAAAATATAAAAAAATTGAACTTAAAGTCAATTTTGAG
ATTATAAAACCATTTAAAGTGAGTAATAACCTTTTGAAGAAATGAGTGACTATAAATGGACTTTT
CTTCTCAATGAATGAGTTTTTTGCACATTTCCCAAGGTAAACAATCAATTATAGTCTGTTTTAAC
TAAAAATGTAAAAA
Found at i:1396 original size:171 final size:171
Alignment explanation
Indices: 503--1747 Score: 930
Period size: 171 Copynumber: 7.3 Consensus size: 171
493 NNNNNNNNNN
* *
503 ATTCAACTTAAAATCAATTATGAGATTAT-AAACCATTTAAAGCAAGTAATAAGGGTTTTAAACG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAA-G
* * * * *
567 -AATGGGTGACTATGAATAGACTTTTTTTCTCTATGAATGTCTTTTTC-T-ACATGTTCTCGAGG
65 AAATAGGTGACTATAAATGGACTTTTCTTCTCAATGAATGTCTTTTTCTTCACAT-TTCTCGAGG
* * * *
629 CAGACATTAAATTATAGTTTGTTTTAA-TGAAAAATATAAAAAA
129 AAGACATTCAATTATAGTCTGTTTTAACT-AAAAATGTAAAAAA
* * *
672 ATTCAA-TGTAAAATCAATTATGAGATTTTAAAACCATTTAAAGCGAGCAAT-AGAGCTTTTGAA
1 ATTCAACT-TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG-GCTTTTAAA
* * * * *
735 GAAAT-GAGTGATTATAAATGTACTTTTTTTCTCAATGAATGGT-TTTTT-TTGCACTTTTCTTG
64 GAAATAG-GTGACTATAAATGGACTTTTCTTCTCAATGAAT-GTCTTTTTCTT-CACATTTCTCG
* * **********
797 AGGTAGACATTCAATTATAGTCCGTNNNNNNNNNNAATGTAAAAAA
126 AGGAAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAA
* * * * *
843 ATTCAACTTAAAATCAATTAAGATATTATAAAACCATTTAAAGTGAGTAATATGACTTTTAAAG-
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGA
** * * *
907 AATAGAAGACTATAAATGGACTTTTTTTGTCAATGAATGTCTTTTTCTTCACATTTCACGAGGAA
66 AATAGGTGACTATAAATGGACTTTTCTTCTCAATGAATGTCTTTTTCTTCACATTTCTCGAGGAA
* * * * * *
972 GATATTCAATTATAATATGTTTTATCCAAAAATATAAAATAA
131 GACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAA-AA
* * * * * ********** *
1014 ATTGAACTTGAAGTCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAANNNNNNNNNNGG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGA
** * * * * *
1079 AAT-GAGTGACTATAAATGGACTTTTCTTCTCAATGAATGAGTTTTT-TGCACGTTTCCCAAAGT
66 AATAG-GTGACTATAAATGGACTTTTCTTCTCAATGAATGTCTTTTTCTTCACATTTCTC-GAGG
* **
1142 AA-ACAATCAATTATAGTCTGTTTTAACTAAAAACAT-AAAAA
129 AAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAA
* *
1183 ATTCAACTTAAAATAAATTATGAGATTATAAAACCATTTAAAGCGTGTAATAAGGCTTTTAAAGA
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGA
* * * * *
1248 AATAGGAGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCACATTTTTTGA-GAA
66 AATAGGTGACTATAAATGGACTTTTCTTCTCAATGAATGTCTTTTTCTTCACATTTCTCGAGGAA
* * * *
1312 AAGCATTCAATTATAATCTGTTTTGACAAAAAATGTAAAAAA
131 GA-CATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAA
* * * * ********** *
1354 ATTAAACTTAAAGTCAATTTTGAGATTATAAAACAATTTAAAG-NNNNNNNNNNGCTTTTTGAAG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGC-TTTTAAAG
* * *** * *
1418 AAATGGGTGACTATAAATGGACTTTTCTTCTCAACGAAT-AAGTTTTCTGCACATTT-TCCAAGG
65 AAATAGGTGACTATAAATGGACTTTTCTTCTCAATGAATGTCTTTTTCTTCACATTTCT-CGAGG
* * *
1481 TAA-ACAATCAATTATAGTTTGTTTTAACTAAAAATGTAAAAAC
129 -AAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAA
* * ************* *
1524 ATTTAACTTAAAATTAATNNNNNNNNNNNNNAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGA
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGA
* * * * * * *
1589 AATAAGAGACTATAAATGGATTTTTCTTGTCAATGAATATCTTTTTCTTCACATCTCTCAAGGAA
66 AATAGGTGACTATAAATGGACTTTTCTTCTCAATGAATGTCTTTTTCTTCACATTTCTCGAGGAA
* * * *
1654 GACATTCAATTATAATCTATTTTCA-TCAAAAATGCAAAACAA
131 GACATTCAATTATAGTCTGTTTTAACT-AAAAATGTAAAA-AA
* * * *
1696 ATTGAACTTAAAGTCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATA
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
Statistics
Matches: 820, Mismatches: 222, Indels: 65
0.74 0.20 0.06
Matches are distributed among these distances:
168 3 0.00
169 124 0.15
170 292 0.36
171 315 0.38
172 86 0.10
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (171 bp):
ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGA
AATAGGTGACTATAAATGGACTTTTCTTCTCAATGAATGTCTTTTTCTTCACATTTCTCGAGGAA
GACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAA
Done.