Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399708.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2953.0, 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: 6950
ACGTcount: A:0.19, C:0.07, G:0.08, T:0.20
Warning! 3183 characters in sequence are not A, C, G, or T
Found at i:1047 original size:169 final size:169
Alignment explanation
Indices: 735--1128 Score: 475
Period size: 169 Copynumber: 2.3 Consensus size: 169
725 NNNNNNNNNT
* * * * * ***
735 AAAACTATGTAAAGCGAGTAATAAGGCTTTTTGAAGGAATGGGTGACTATTAACGGACTTTTCTT
1 AAAACCATTTAAAGTGAGTAATAAGGC-TTTTGAAGGAATAGGTGACTATAAATAAACTTTTCTT
* * *** * * * * *
800 GCCAATGACTACCTTTACCTTCATGTTTCTGGAGGTTGACATTGAATTATAATCTTTTTGATGAA
65 ACCAATGA--AACTTTTTTTTCATGTTTCTAGAGGTTGACAGTCAATTATAATCTTTTTAAAGAA
* *
865 CAATGTACAAAGAAGTCAAATTTCAATCAATTTAGAGATTAC
128 AAATGTACAAAGAAGTCAAATTTAAATCAATTTAGAGATTAC
* * *
907 AAAACCATTTAAAGTGAGTGATAAGGCTTTTGGAGGAATAGGTGATTATAAATAAACTTTTCTTA
1 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAAACTTTTCTTA
972 CCAATGAAACTTTTTTTTCATG-TTCTAGAGGTTGACAGTCAATTATAATCTATTTTAAAGAAAA
66 CCAATGAAACTTTTTTTTCATGTTTCTAGAGGTTGACAGTCAATTATAATCT-TTTTAAAGAAAA
* ** *
1036 ATGTACAAAGAATTCAAATTTAAATCAATTTTTAGATTAT
130 ATGTACAAAGAAGTCAAATTTAAATCAATTTAGAGATTAC
* * *
1076 AAAACGATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTTACTATAAAT
1 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAAT
1129 GGACTCNNNN
Statistics
Matches: 188, Mismatches: 33, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
168 26 0.14
169 102 0.54
171 37 0.20
172 23 0.12
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (169 bp):
AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAAACTTTTCTTA
CCAATGAAACTTTTTTTTCATGTTTCTAGAGGTTGACAGTCAATTATAATCTTTTTAAAGAAAAA
TGTACAAAGAAGTCAAATTTAAATCAATTTAGAGATTAC
Found at i:5481 original size:171 final size:171
Alignment explanation
Indices: 5170--5483 Score: 377
Period size: 171 Copynumber: 1.8 Consensus size: 171
5160 CAATTTTGAG
* * * *
5170 ATTATAAAATCATTTAAAGTGAGTATTAAGGCTTTTTGAAAGAATTGGTGACTATAAATGAACTT
1 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTTGAAAGAATGGGTGACTATAAACGAACTT
* *
5235 TTTTTGTCAACAAATACCTTTTTCTCTATGTTTCTTAAGATTGACATTCAATTATAGTTTTTATT
66 TTTTTGTCAACAAATACATTTTTCTCTACGTTTCTTAAGATTGACATTCAATTATA-TTTTTATT
*
5300 AACCAAAAATGTAAAAAACTTCAACTAAAAATCACTTATGAC
130 AACAAAAAATGTAAAAAACTTCAACTAAAAATCACTTATGAC
* * *
5342 ATTATACAACCATTTAAAGTGAGTAATGAGGC-TTTTG-AAGAAATGGGTGACTATAAACGGA-T
1 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTTGAAAG-AATGGGTGACTATAAACGAACT
*** * * * *
5404 TTTTCTTGTCAATGTATGCATTTTTCT-TCACGTTTCTTGAGGTTGACTTTCAATTAT-TTTCTG
65 TTTT-TTGTCAACAAATACATTTTTCTCT-ACGTTTCTTAAGATTGACATTCAATTATATTT-T-
*
5467 TTTTAACAAAAAATGTA
126 TATTAACAAAAAATGTA
5484 CAAAGAATTC
Statistics
Matches: 119, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
169 3 0.03
170 10 0.08
171 78 0.66
172 28 0.24
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (171 bp):
ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTTGAAAGAATGGGTGACTATAAACGAACTT
TTTTTGTCAACAAATACATTTTTCTCTACGTTTCTTAAGATTGACATTCAATTATATTTTTATTA
ACAAAAAATGTAAAAAACTTCAACTAAAAATCACTTATGAC
Done.