Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_927.0, 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: 3693
ACGTcount: A:0.24, C:0.07, G:0.08, T:0.23
Warning! 1399 characters in sequence are not A, C, G, or T
Found at i:299 original size:171 final size:169
Alignment explanation
Indices: 1--480 Score: 532
Period size: 171 Copynumber: 2.8 Consensus size: 169
* * * *
1 TTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACCATAAATGGACTTTTATTTCCAATGA
1 TTTAAAACGAGTAATAAGGATTTTG-AAGAATGGGTGACTATAAATGGACTTTTATTACCAATGA
* * * **** * *
66 ATGCCTTTTTCTTCACGTTTCCCAAGAAAAATATTCAATTATAATTTGTTTTAACTAAAAATGTA
65 ATGTCTTTTTCTTCATGTTTCTCAAGGTCGACATTCAATTA-AATCTGTTTTAACTAAAAATGTA
*
131 AAAAAACTTAAACTTAAAATCAATT-TTGATATTATAAAAC-C
129 AAAAAA-TTAAACTTAAAATCAATTATT-AGATTATAAAACTC
* * **
172 ATTTAAAACGAGTAATAAAGATTTTGAAGAATGAGTGACTATAAATGGACTTTCCTTACCAATGA
1 -TTTAAAACGAGTAATAAGGATTTTGAAGAATGGGTGACTATAAATGGACTTTTATTACCAATGA
* * * *
237 ATGTCTTTTTCTTCATGTTTGTCGAGGTCGACATTCAATTAAACTCTGTTTTATCCAAAAATGTA
65 ATGTCTTTTTCTTCATGTTTCTCAAGGTCGACATTCAATTAAA-TCTGTTTTAACTAAAAATGTA
* * * *
302 AACAAATTCAAGTTAAAATCAATTATTAGATTATAATACTC
129 AAAAAATTAAACTTAAAATCAATTATTAGATTATAAAACTC
* * * *
343 TTGAAAACGAGTAATAAGGTTTTTAAAGGAATGGGTGACTATAAATGGACTTTTTTTACCAATGA
1 TTTAAAACGAGTAATAAGGATTTTGAA-GAATGGGTGACTATAAATGGACTTTTATTACCAATGA
* * * * * * * *
408 ATCTCTTGTTCTTTATGTTTTTTAAGGTCGACATTCAATTATAGTCTTTTTTAACTAAAAATATA
65 ATGTCTTTTTCTTCATGTTTCTCAAGGTCGACATTCAATTA-AATCTGTTTTAACTAAAAATGTA
473 AAAAAATT
129 AAAAAATT
481 TNNNNNNNNN
Statistics
Matches: 258, Mismatches: 45, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
170 51 0.20
171 184 0.71
172 23 0.09
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (169 bp):
TTTAAAACGAGTAATAAGGATTTTGAAGAATGGGTGACTATAAATGGACTTTTATTACCAATGAA
TGTCTTTTTCTTCATGTTTCTCAAGGTCGACATTCAATTAAATCTGTTTTAACTAAAAATGTAAA
AAAATTAAACTTAAAATCAATTATTAGATTATAAAACTC
Found at i:2058 original size:173 final size:171
Alignment explanation
Indices: 1743--2071 Score: 405
Period size: 173 Copynumber: 1.9 Consensus size: 171
1733 GAAGAAATGG
* * * *
1743 GTGACTATAAGTGGACTTTTCTTCTTAATGAATGACTTTTTTTACACGTTTCATAAGGCAGACAA
1 GTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTTTTTTACACGTTTCATAACGCAGACAA
* * * * * *
1808 TCAATTATAGTTTGTTTTAATAAAAAATGTAAACAAATTTCACTTGAAAGCAATTATTAGATTAT
66 TCAAATATAATCTGTTTTAATAAAAAATGTAAAAAAATTTAACTTAAAAGCAATTATTAGATTAT
1873 AAAACCATTTAAAGC-GAGTAATAAGGATTTAGAAAGGATGA
131 AAAACCATTTAAA-CTGAGTAATAAGGATTTAGAAAGGATGA
* * * * * *
1914 GTGACTATAAATAGACTTTTCTTGC-CAGTGAATGTCTTTTTTTTTCATGTTTCATGACGTAGAC
1 GTGACTATAAATAGACTTTTCTT-CTCAATGAATGAC-TTTTTTTACACGTTTCATAACGCAGAC
* *
1978 ATTCAAATATAATCTGTTTTAACTAAAAAA-GTAAAAAAAATTTAACTTAAAATCAATT-TTGAG
64 AATCAAATATAATCTGTTTTAA-TAAAAAATGT-AAAAAAATTTAACTTAAAAGCAATTATT-AG
*
2041 ATTATAAAACTATTTAAACTGAGTAATAAGG
126 ATTATAAAACCATTTAAACTGAGTAATAAGG
2072 CTTNNNNNNN
Statistics
Matches: 133, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
171 29 0.22
172 46 0.35
173 58 0.44
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (171 bp):
GTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTTTTTTACACGTTTCATAACGCAGACAA
TCAAATATAATCTGTTTTAATAAAAAATGTAAAAAAATTTAACTTAAAAGCAATTATTAGATTAT
AAAACCATTTAAACTGAGTAATAAGGATTTAGAAAGGATGA
Found at i:3671 original size:171 final size:170
Alignment explanation
Indices: 3194--3693 Score: 435
Period size: 171 Copynumber: 2.9 Consensus size: 170
3184 NNGAGTGACT
* * *
3194 ATAAATGGACTTTTCTTG-CTAATGAATACTTTTTTCTTCATGTTTCATGAA-GT-AGACATTCA
1 ATAAATGGACTTTTCTTGTC-AATGAATGCCTTTTTCTTCATGTTTC-TCAAGGTAAG-CATTCA
* * * ** *
3256 TTTATAATCTGTTTTAACCAAAAATGTAATAAAATTTAACTTAAAATGAATTACAGGATAATAAA
63 ATTATAGTCTATTTTAATAAAAAATGTAAAAAAATTTAACTTAAAATGAATTACA-GATAATAAA
* * * * * *
3321 TCTATTTAAAGCGAGTAATAAGGCTTTT-ATAGGAATGTGTGACT
127 ACCATTTAAAGCGAGTAATAAGGCTTTTGA-AGAAATGGGTCACA
* * * * * *
3365 ATAAATGGACCTTTCTTCTCAATGAATGACTTTTT-TT-ATGTATT-TCCTGAGGTAGGCATTTA
1 ATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCATGT-TTCT-C-AAGGTAAGCATTCA
* * * * *********
3427 ATTAGAGTC-AGTTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAANNNNNNNNNNATAA
63 ATTATAGTCTA-TTTTAATAAAAAATGTAAAAAAATTTAACTTAAAATGAA-TTACAGATAATAA
* *
3491 AAGCATTTAAAACGAGTAATAAGGCTTTTGAAGAAATGGGTCACA
126 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGGGTCACA
*
3536 ATAAATAGACTTTTCTTGTCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAAGCATTCAATT
1 ATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAAGCATTCAATT
* * * *
3601 ATAGCCTATTTTATTAAAAAATG-AAAACAAATTTAACTTAAAATGAATTATGAGATTATAAAAC
66 ATAGTCTATTTTAATAAAAAATGTAAAA-AAATTTAACTTAAAATGAATTA-CAGATAATAAAAC
*
3665 CATTTAAAGCGAATAATCAA-GCTTTTGAA
129 CATTTAAAGCGAGTAAT-AAGGCTTTTGAA
Statistics
Matches: 253, Mismatches: 60, Indels: 32
0.73 0.17 0.09
Matches are distributed among these distances:
168 1 0.00
169 4 0.02
170 9 0.04
171 223 0.88
172 11 0.04
173 5 0.02
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.36
Consensus pattern (170 bp):
ATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAAGCATTCAATT
ATAGTCTATTTTAATAAAAAATGTAAAAAAATTTAACTTAAAATGAATTACAGATAATAAAACCA
TTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGGGTCACA
Done.