Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400445.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3642.0, 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: 3948
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.31
Warning! 639 characters in sequence are not A, C, G, or T
Found at i:647 original size:172 final size:171
Alignment explanation
Indices: 352--843 Score: 410
Period size: 172 Copynumber: 2.9 Consensus size: 171
342 NNNNNNNNNN
* * *
352 AATAGACTTTTCTTGCTAATGAATGCCTTTTTTTCATGTTTCTCAAGATAAACAGTCAATTATTG
1 AATAGACTTTTCTTGCTAATGAATGCCTTTTTTTCATGTTTCTAAAGACAAACAGTCAATTATAG
* * *
417 TCTGTTTTAACAAAAAGTGTAAAAAAAATTCAAATCAAAATCTATTATGAGTTTATAAAACTATT
66 TCTGTTTTAACAAAAAGTGTAAAAAAAATTCAAATCAAAATCAATTATGAGATTATAAAACAATT
482 AAAAGCGAGTAATGAGGCTTTCGAAGGAATGGGTGATCATA
131 AAAAGCGAGTAATGAGGCTTTCGAAGGAATGGGTGATCATA
* ** *
523 AATAGACTTTTCTT-CTCAATTAATAG-CTTTTTTTGCATGTTTCTTAAAG-CAGGCATTCAATT
1 AATAGACTTTTCTTGCT-AATGAAT-GCCTTTTTTT-CATGTTTC-TAAAGACAAACAGTCAATT
* * * *
585 ATAGTCTGTTTTAACTAAAA-TTTCAAAAAAAAATT-AACTCAAAATCAATTTTGAGATTATAAA
62 ATAGTCTGTTTTAACAAAAAGTGT--AAAAAAAATTCAAATCAAAATCAATTATGAGATTATAAA
* *********
648 ACAATTTAAAGCGAGTAAT-ANNNNNNNNNNAGGAATGGGTGA-CTATA
125 ACAATTAAAAGCGAGTAATGA-GGCTTTCGAAGGAATGGGTGATC-ATA
*** * * * * * * *
695 AATAGACTTTTCTTG-TCAATGAATAATTTTTTTTTTCACGTTTCTTGATG-TAGACATTCGATT
1 AATAGACTTTTCTTGCT-AATGAAT--GCCTTTTTTTCATGTTTC-TAAAGACAAACAGTCAATT
* * * * * ** *
758 ATAGTCTGTTTTAAAAAAAAATGT-AAAAAAATTCAACTTAAAATTAATTATCTGATTATAAAAT
62 ATAGTCTGTTTTAACAAAAAGTGTAAAAAAAATTCAAATCAAAATCAATTATGAGATTATAAAAC
* *
822 AATTTAAAGCGAGTAATAAGGC
127 AATTAAAAGCGAGTAATGAGGC
844 NNNNNNNNNN
Statistics
Matches: 262, Mismatches: 45, Indels: 27
0.78 0.13 0.08
Matches are distributed among these distances:
170 2 0.01
171 41 0.16
172 155 0.59
173 55 0.21
174 9 0.03
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.36
Consensus pattern (171 bp):
AATAGACTTTTCTTGCTAATGAATGCCTTTTTTTCATGTTTCTAAAGACAAACAGTCAATTATAG
TCTGTTTTAACAAAAAGTGTAAAAAAAATTCAAATCAAAATCAATTATGAGATTATAAAACAATT
AAAAGCGAGTAATGAGGCTTTCGAAGGAATGGGTGATCATA
Found at i:864 original size:172 final size:161
Alignment explanation
Indices: 686--1014 Score: 322
Period size: 171 Copynumber: 2.0 Consensus size: 161
676 NNAGGAATGG
* * * * *
686 GTGACTATAAATAGACTTTTCTTGTCAATGAAT-AATTTTTTTTTTCACGTTTCT-TGATGTAGA
1 GTGACTATAAATAGACTTTTCTTATAAACGAATGAA-TTTTTCTTT-ACGTTTCTCT-AAGTAGA
* * * * *
749 CATTCGATTATAGTCTGTTTTAAAAAAAAATGTAAAAAAATTCAACTTAAAATTAATTATCTGAT
63 AATTCAATTATAGTCTGTTTTAAAAAAAAATATAAAAAAATTCAACTTAAAATCAATTATCAGAT
814 TATAAAATAA-TTTAAAGCGAGTAATAAGGCNNNNNNNNNNATGA
128 TATAAAA-AACTTTAAAGCGAGTAATAAGGC----------ATGA
* * *
858 GTGACTATAAATGGACTTTTCTTATAAACGAATGCATTTTTCTTTATGTTTCTCTAAGTAGAAAT
1 GTGACTATAAATAGACTTTTCTTATAAACGAATGAATTTTTCTTTACGTTTCTCTAAGTAGAAAT
* *** * * *
923 TTAATTATAGTCTGTTTTAGCTAAAACTATACAAAAATTCAACTTAAAATCAATTATGAGATTAT
66 TCAATTATAGTCTGTTTTAAAAAAAAATATAAAAAAATTCAACTTAAAATCAATTATCAGATTAT
*
988 AAAAAACTTTAAAGTGAGTAATAAGGC
131 AAAAAACTTTAAAGCGAGTAATAAGGC
1015 TTTTGAAGGN
Statistics
Matches: 133, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
170 2 0.02
171 92 0.69
172 38 0.29
173 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.37
Consensus pattern (161 bp):
GTGACTATAAATAGACTTTTCTTATAAACGAATGAATTTTTCTTTACGTTTCTCTAAGTAGAAAT
TCAATTATAGTCTGTTTTAAAAAAAAATATAAAAAAATTCAACTTAAAATCAATTATCAGATTAT
AAAAAACTTTAAAGCGAGTAATAAGGCATGA
Found at i:1692 original size:170 final size:161
Alignment explanation
Indices: 1507--2015 Score: 388
Period size: 171 Copynumber: 3.0 Consensus size: 161
1497 TATAAAATAA
* * *
1507 TTTAAGGCGAGTAATAAGGCTTTTGAAGGAATAGGGGACTATAAATGGACTT-TTTTTCTCAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGAGGACTACAAATGGA-TTCTTTTTCTCAATG
* * * * * *
1571 AGTAGTCTTTTTGTGCATGT-TCCTTAAGGCA-GACATTCAATTATAGTTTATTTTAA-TAAAAA
65 AATAGT-TTTTTGTGCATGTCT-CTCAAGGCATG-CAATCAATTATAGTCTATTGTAACAAAAAA
*
1633 -ATAAAAAAATTCAACTTAAAATCAATTATGAGAT
127 TATAAAAAAATTCAACTTAAAATCAATTATAAGAT
* *
1667 TNNNNNNNNNNTTAAAGCGAGTAATAAGGCTTTTGAAGGAATTGATGACTACAAATGGATTCTTT
1 T----------TTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGAGGACTACAAATGGATTCTTT
* *
1732 TTCTCAATGAATAGTTTTTTTTGCATGTCTCTCAAGGCATGCAATCAATTATAGTCTGTTGTAAC
56 TTCTCAATGAATAGTTTTTTGTGCATGTCTCTCAAGGCATGCAATCAATTATAGTCTATTGTAAC
**
1797 AAAAAATATAAAAAAATTCATTTTAAAATCAATTATAAGAT
121 AAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAGAT
* * * * *
1838 TATAANNNNNNNNNNAGTGAGTAATAAGGCTTTTGAAGGGATAG-GTGACTATAAATGAATT-TG
1 TTTAA----------AGCGAGTAATAAGGCTTTTGAAGGAATAGAG-GACTACAAATGGATTCT-
* * * * * * * * * * *
1901 TTTTCTCAATGAAT-GATTTTTTTTACATATTTCTGAAGACAGGCAATCACTTTTAGTCTGTTTT
54 TTTTCTCAATGAATAG-TTTTTTGTGCATGTCTCTCAAGGCATGCAATCAATTATAGTCTATTGT
*
1965 AACAAAAAATGA-AAAATAAATTCAACTTAAAATCAATTATGAGAT
118 AACAAAAAAT-ATAAAA-AAATTCAACTTAAAATCAATTATAAGAT
*
2010 TATAAA
1 TTTAAA
2016 ACAATTTAAA
Statistics
Matches: 284, Mismatches: 35, Indels: 58
0.75 0.09 0.15
Matches are distributed among these distances:
160 1 0.00
161 3 0.01
162 1 0.00
169 41 0.14
170 69 0.24
171 138 0.49
172 31 0.11
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.35
Consensus pattern (161 bp):
TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGAGGACTACAAATGGATTCTTTTTCTCAATGA
ATAGTTTTTTGTGCATGTCTCTCAAGGCATGCAATCAATTATAGTCTATTGTAACAAAAAATATA
AAAAAATTCAACTTAAAATCAATTATAAGAT
Found at i:3647 original size:170 final size:161
Alignment explanation
Indices: 3471--3799 Score: 333
Period size: 171 Copynumber: 2.0 Consensus size: 161
3461 NNNNNNAGAG
* * * *
3471 AGTAATAAGGCTTTTAAAGGAATTGTTGACTATAAATGGACTTTTCTT-TCCAATGAATG-ATTT
1 AGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTAT-AAACGAATGCATTT
* * * * *
3534 TTTTTCACGTTTCT-TGAGGAAGACATTCGATTATAGTGTGTTTTAG-TAAAAAATATAAAAAAA
65 TTCTTCACGTTTCTCT-AAGAAGAAATTCAATTATAGTCTGTTTTAGCT-AAAAATATAAAAAAA
* * *
3597 TTCAACTTAAAATTAATTATGTGATTATAAAACA
128 GTCAACTTAAAATCAATTATGAGATTATAAAACA
* *
3631 NNNNNNNNNNAGTAATAAGGTTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTATAAACG
1 ----------AGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTATAAACG
* * * * *
3696 AATGCATTTTTCTTCATGTTTGTCTAAGTAGAAATTTAATTATAGTCTGTTTTAGCTAAAAATGT
56 AATGCATTTTTCTTCACGTTTCTCTAAGAAGAAATTCAATTATAGTCTGTTTTAGCTAAAAATAT
*
3761 ACAAAAAGTCAACTTAAAATCAATTATGAGATTATAAAA
121 AAAAAAAGTCAACTTAAAATCAATTATGAGATTATAAAA
3800 AAATTTAAAG
Statistics
Matches: 135, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
170 51 0.38
171 82 0.61
172 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.37
Consensus pattern (161 bp):
AGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTATAAACGAATGCATTTT
TCTTCACGTTTCTCTAAGAAGAAATTCAATTATAGTCTGTTTTAGCTAAAAATATAAAAAAAGTC
AACTTAAAATCAATTATGAGATTATAAAACA
Done.