Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399462.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2725.0, 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: 1931
ACGTcount: A:0.20, C:0.07, G:0.08, T:0.19
Warning! 884 characters in sequence are not A, C, G, or T
Found at i:1305 original size:170 final size:169
Alignment explanation
Indices: 1128--1611 Score: 391
Period size: 171 Copynumber: 2.8 Consensus size: 169
1118 NNNNNNNNNG
* *
1128 AAACTAAAAATGTGAAAAAGTTCAACTTAAAATCAATAATGAGATTATAAACAATTTAAAGTGTG
1 AAACTAAAAATATGAAAAA-TTCAACTTAAAATCAATTATGAGATTATAAACAATTTAAAGTGTG
********** *
1193 TAATAAGGCTTTTGAAGGAATAGGAGACTANNNNNNNNNNTGTCTTGCCAATAAATGCTTGTTTC
65 TAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGCACTTGTCTTGCAAATAAATGCTTGTTTC
* *
1258 TTCATGTGTCTCGAGGTAAATATTTAATTATAGTTTGTTT
130 TTCATGTGTCTCGAGGTAAAGATTCAATTATAGTTTGTTT
* ********* * * * **
1298 TAACTAAAAATATNNNNNNNNNNAACTTAAAATCAATTATTAGATTACAAAACCATTTAAAACGT
1 AAACTAAAAATAT-GAAAAATTCAACTTAAAATCAATTATGAGATTA-TAAACAATTTAAAGTGT
* * * * * *
1363 GTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGCACTTTTCTTGCAAATGAATTCTTTTTT
64 GTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGCACTTGTCTTGCAAATAAATGCTTGTTT
* *
1428 CTTTATGTTTCTCGAGGTAAAGATTCAATTATAGTTTGTTT
129 CTTCATGTGTCTCGAGGTAAAGATTCAATTATAGTTTGTTT
* * * * *
1469 AAATTAAAAATCTAGAAATATTCAACTTAAAA-CAAATTTTGAGATTATAAAACTATTTAAAGCT
1 AAACTAAAAATAT-GAAAAATTCAACTTAAAATC-AATTATGAGATTAT-AAACAATTTAAAG-T
* * * * * * * *
1533 -AGTATTAAGGCTTTTGAAGGAATAAGTGACTATAAATAG-ACTTTTTTTGCCAATGAATGCCTT
62 GTGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAAT-GCACTTGTCTTGCAAATAAATG-CTT
*
1596 -TTTCTTCATGTTTCTC
125 GTTTCTTCATGTGTCTC
1612 NNNNNNNNNN
Statistics
Matches: 242, Mismatches: 65, Indels: 13
0.76 0.20 0.04
Matches are distributed among these distances:
170 34 0.14
171 204 0.84
172 4 0.02
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.36
Consensus pattern (169 bp):
AAACTAAAAATATGAAAAATTCAACTTAAAATCAATTATGAGATTATAAACAATTTAAAGTGTGT
AATAAGGCTTTTGAAGGAATAGGAGACTATAAATGCACTTGTCTTGCAAATAAATGCTTGTTTCT
TCATGTGTCTCGAGGTAAAGATTCAATTATAGTTTGTTT
Found at i:1443 original size:171 final size:171
Alignment explanation
Indices: 1235--1611 Score: 429
Period size: 171 Copynumber: 2.2 Consensus size: 171
1225 NNNNNNNNTG
* * * * * *
1235 TCTTGCCAATAAATGCTTGTTTCTTCATGTGTCTCGAGGTAAATATTTAATTATAGTTTGTTTTA
1 TCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCGAGGTAAAGATTCAATTATAGTTTGTTTAA
**********
1300 ACTAAAAATATNNNNNNNNNNAACTTAAAATC-AATTATT-AGATTACAAAACCATTTAAAACGT
66 ACTAAAAATATAGAAATATTCAACTTAAAA-CAAATT-TTGAGATTACAAAACCATTTAAAAC-T
**
1363 -GTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GCACTTT
128 AGTAATAAGGCTTTTGAAGGAATAAGTGACTATAAATAG-ACTTT
* * *
1406 TCTTGCAAATGAATTCTTTTTTCTTTATGTTTCTCGAGGTAAAGATTCAATTATAGTTTGTTTAA
1 TCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCGAGGTAAAGATTCAATTATAGTTTGTTTAA
* * * * *
1471 ATTAAAAATCTAGAAATATTCAACTTAAAACAAATTTTGAGATTATAAAACTATTTAAAGCTAGT
66 ACTAAAAATATAGAAATATTCAACTTAAAACAAATTTTGAGATTACAAAACCATTTAAAACTAGT
*
1536 ATTAAGGCTTTTGAAGGAATAAGTGACTATAAATAGACTTT
131 AATAAGGCTTTTGAAGGAATAAGTGACTATAAATAGACTTT
* *
1577 TTTTGCCAATGAATGCCTTTTTCTTCATGTTTCTC
1 TCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTC
1612 NNNNNNNNNN
Statistics
Matches: 170, Mismatches: 32, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
170 4 0.02
171 165 0.97
172 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.39
Consensus pattern (171 bp):
TCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCGAGGTAAAGATTCAATTATAGTTTGTTTAA
ACTAAAAATATAGAAATATTCAACTTAAAACAAATTTTGAGATTACAAAACCATTTAAAACTAGT
AATAAGGCTTTTGAAGGAATAAGTGACTATAAATAGACTTT
Done.