Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399278.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2547.0, 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, 978
Length: 1630
ACGTcount: A:0.25, C:0.09, G:0.10, T:0.26
Warning! 483 characters in sequence are not A, C, G, or T
Found at i:1051 original size:171 final size:169
Alignment explanation
Indices: 603--1630 Score: 1233
Period size: 171 Copynumber: 6.0 Consensus size: 169
593 NNNNNNNNAT
* * *
603 GTTTCTCGAGTTAGACATTCAATTATTGTCTGTTTTAA-AGAAAGATGTACAAAAATTCAACTTA
1 GTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACA-AAA-ATGTAAAAAAATTCAACTTA
* * * *
667 AAATCAATTATGAGATTTTAAAATCATTTAAACCGAGTAATAAGGC-TTTCGAAAGAATGGGTGA
64 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCATTT-GAAAGAATGGGTGA
* * * * *
731 CTAAAAATAGATTTTTCTTCTCAATGAATATCTTTTTCTACAC
128 CTATAAATGGACTTTTCTTCTCAATGAAT-GCTTTTTCTTCAC
* * * *
774 GTTTCTCGAGGTAAAAATTCAATTATAGTCTATTTTTAA-AAAAATGTAAAAATATTCAACTTAA
1 GTTTCTCGAGGTAGACATTCAATTATAGTCT-GTTTTAACAAAAATGTAAAAAAATTCAACTTAA
* * * * *
838 AATCAATTATGGGATTATAAAACTATTTAAAGCGAGTAATAAGCCAATTGAAGGAATAGGTGACT
65 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCATTTGAAAGAATGGGTGACT
* *
903 CTAAATGCACTTTTCTTCTCAATGAATGCTTATTTCTTCAC
130 ATAAATGGACTTTTCTTCTCAATGAATGCTT-TTTCTTCAC
* * * * * *
944 GTTTTTTGACGTAGACATTCAATTATAGTATGTTTTAATCAAAAATGTGAAAACATTCAACTTAA
1 GTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAA-CAAAAATGTAAAAAAATTCAACTTAA
* **
1009 AATCAATTATGAGATTATAAAACCATTTAAAGCGATTAATAAGCTTTTTGAAAGAATGGGTGACT
65 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCATTTGAAAGAATGGGTGACT
* *
1074 CTAAATGGACTTTTCTTGTCAATGAATGCTTGTTTCTTCAC
130 ATAAATGGACTTTTCTTCTCAATGAATGCTT-TTTCTTCAC
* * *
1115 GTTTCTCGAGGTAGATATTCAATTATAGTCTGTTTTAATAAAAAATGTAAACAAATTCAACTTAA
1 GTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAA-CAAAAATGTAAAAAAATTCAACTTAA
* * * * *
1180 AATCAATTATGAGATTCTAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACT
65 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCATTTGAAAGAATGGGTGACT
* * **
1245 ATAAATGGACTTTTCTTCTCAATCAATGGCTTTTTCTGCTT
130 ATAAATGGACTTTTCTTCTCAATGAAT-GCTTTTTCTTCAC
* *
1286 GTTTCTCGAGTTAGACATTCAATTATTGTCTGTTTTAA-AGAAAGATGTAAAAAAATTCAACTTA
1 GTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACA-AAA-ATGTAAAAAAATTCAACTTA
* * * * * *
1350 AAATCAATTATGAGATTATCAAATCTTTTATATCGTGTAATAAG--ATTTTCGAAAGAATGGGTG
64 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCA-TTT-GAAAGAATGGGTG
* * * *
1413 ACTAAAAATGAATTTTTCTTCTCAATGAATGTCTTTTTCTACAC
127 ACTATAAATGGACTTTTCTTCTCAATGAATG-CTTTTTCTTCAC
* * * * * *
1457 GTTTTTCGAGGCAAAAATTCAATTATATTCTATTTT-ACAAAAAATGTAAAAAAATTCAACTTAA
1 GTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAAC-AAAAATGTAAAAAAATTCAACTTAA
* * * *
1521 AATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGCCAATTGAAGGAATGGGTGACT
65 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCATTTGAAAGAATGGGTGACT
*
1586 CTAAATGGACTTTTCTTCTCAATGAATGCTTATTTCTTCAC
130 ATAAATGGACTTTTCTTCTCAATGAATGCTT-TTTCTTCAC
1627 GTTT
1 GTTT
Statistics
Matches: 733, Mismatches: 108, Indels: 33
0.84 0.12 0.04
Matches are distributed among these distances:
169 13 0.02
170 242 0.33
171 465 0.63
172 13 0.02
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (169 bp):
GTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAATGTAAAAAAATTCAACTTAAA
ATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCATTTGAAAGAATGGGTGACTA
TAAATGGACTTTTCTTCTCAATGAATGCTTTTTCTTCAC
Found at i:1580 original size:512 final size:510
Alignment explanation
Indices: 603--1630 Score: 1397
Period size: 512 Copynumber: 2.0 Consensus size: 510
593 NNNNNNNNAT
* * *
603 GTTTCTCGAGTTAGACATTCAATTATTGTCTGTTTTAAAGAAAGATGTACAAAAATTCAACTTAA
1 GTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAAAGAAAAATGTACAAAAATTCAACTTAA
*
668 AATCAATTATGAGATTTTAAAATCATTTAAACCGAGTAATAAGGCTTTCGAAAGAATGGGTGACT
66 AATCAATTATGAGATTCTAAAATCATTTAAACCGAGTAATAAGGCTTTCGAAAGAATGGGTGACT
* * *
733 AAAAATAGATTTTTCTTCTCAATGAATATCTTTTTCTACACGTTTCTCGAGGTAAAAATTCAATT
131 AAAAATAGACTTTTCTTCTCAATCAATAGCTTTTTCTACACGTTTCTCGAGGTAAAAATTCAATT
* * *
798 ATAGTCTATTTTTAAAAAAATGTAAAAATATTCAACTTAAAATCAATTATGGGATTATAAAACTA
196 ATAGTCTAGTTTTAAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
* ** *
863 TTTAAAGCGAGTAATAAGCCAATTGAAGGAATAGGTGACTCTAAATGCACTTTTCTTCTCAATGA
261 TTTAAAGCGAGTAATAAG-CAATTGAAAGAATAGGTGACTAAAAATGAACTTTTCTTCTCAATGA
* * * * * * *
928 ATGCTTATTTCTTCACGTTTTTTGACGTAGACATTCAATTATAGTATGTTTTAATCAAAAATGTG
325 ATGCTTATTTCTACACGTTTTTCGACGCAAAAATTCAATTATAGTATATTTTAA-CAAAAATGTA
* * ***
993 AAAACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGATTAATAAGCTTTTT
389 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCAATT
* *
1058 GAAAGAATGGGTGACTCTAAATGGACTTTTCTTGTCAATGAATGCTTGTTTCTTCAC
454 GAAAGAATGGGTGACTCTAAATGGACTTTTCTTCTCAATGAATGCTTATTTCTTCAC
*
1115 GTTTCTCGAGGTAGATATTCAATTATAGTCTGTTTTAATA-AAAAATGTA-AACAAATTCAACTT
1 GTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAA-AGAAAAATGTACAA-AAATTCAACTT
* * *
1178 AAAATCAATTATGAGATTCTAAAA-CTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTG
64 AAAATCAATTATGAGATTCTAAAATC-ATTTAAACCGAGTAATAAGGCTTTCGAAAGAATGGGTG
* * * * ** * * *
1242 ACTATAAATGGACTTTTCTTCTCAATCAATGGCTTTTTCTGCTTGTTTCTCGAGTTAGACATTCA
128 ACTAAAAATAGACTTTTCTTCTCAATCAATAGCTTTTTCTACACGTTTCTCGAGGTAAAAATTCA
*
1307 ATTATTGTCT-GTTTTAAAGAAAGATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATCA
193 ATTATAGTCTAGTTTTAAA-AAA-ATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT-A
* * * * * * *
1371 AATCT-TTTATATCGTGTAATAAG-ATTTTCGAAAGAATGGGTGACTAAAAATGAATTTTTCTTC
255 AAACTATTTAAAGCGAGTAATAAGCA-ATT-GAAAGAATAGGTGACTAAAAATGAACTTTTCTTC
* * *
1434 TCAATGAATGTCTT-TTTCTACACGTTTTTCGAGGCAAAAATTCAATTATATTCTATTTT-ACAA
318 TCAATGAATG-CTTATTTCTACACGTTTTTCGACGCAAAAATTCAATTATAGTATATTTTAAC-A
* *
1497 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATA
381 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
*
1562 AGCCAATTGAAGGAATGGGTGACTCTAAATGGACTTTTCTTCTCAATGAATGCTTATTTCTTCAC
446 AGCCAATTGAAAGAATGGGTGACTCTAAATGGACTTTTCTTCTCAATGAATGCTTATTTCTTCAC
1627 GTTT
1 GTTT
Statistics
Matches: 451, Mismatches: 55, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
511 12 0.03
512 304 0.67
513 127 0.28
514 8 0.02
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (510 bp):
GTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAAAGAAAAATGTACAAAAATTCAACTTAA
AATCAATTATGAGATTCTAAAATCATTTAAACCGAGTAATAAGGCTTTCGAAAGAATGGGTGACT
AAAAATAGACTTTTCTTCTCAATCAATAGCTTTTTCTACACGTTTCTCGAGGTAAAAATTCAATT
ATAGTCTAGTTTTAAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
TTTAAAGCGAGTAATAAGCAATTGAAAGAATAGGTGACTAAAAATGAACTTTTCTTCTCAATGAA
TGCTTATTTCTACACGTTTTTCGACGCAAAAATTCAATTATAGTATATTTTAACAAAAATGTAAA
AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCAATTGA
AAGAATGGGTGACTCTAAATGGACTTTTCTTCTCAATGAATGCTTATTTCTTCAC
Done.