Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401757.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4870.0, 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: 2313
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.28
Warning! 427 characters in sequence are not A, C, G, or T
Found at i:730 original size:171 final size:168
Alignment explanation
Indices: 443--1471 Score: 768
Period size: 171 Copynumber: 6.0 Consensus size: 168
433 NNNNNNNNNN
*
443 GTAATAAGGCTTTTGAAAGA-ATAGGTGACTATAAATGGACTTTTCT-TGCCAATTAATGACTTT
1 GTAATAAGGCTTTTG-AAGACATAGGTGACTATAAATGGACTTTTCTAT--CAATAAATGACTTT
* ** * ** * *
506 TTCTTTACATTTCTTGAGGTAGACACTT-AATTATAACCCGTTTTATCCAAAAATGCAAGAAAAT
63 TTCTTCACATTT-TCAAGGTAGACA-TTCAATTATAATCTATTTTAACCAAAAATGTAA-AAAAT
* * * *
570 ACAACCTAAAATCAATTATGAGTTTATAAAACTATTTAAAGAGA
125 TCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGA
* * * * *
614 GAAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGATTTTTGCTATTAATAAATGACTTTTT
1 GTAATAAGGCTTTTGAAGACATAGGTGACTATAAATGGACTTTT-CTATCAATAAATGACTTTTT
** *
679 CTTCACATTTTCAGAGACAGACATTCAATTACAATCTATTTTAACCAAAAATGTAAAAACATTCA
65 CTTCACATTTTCA-AGGTAGACATTCAATTATAATCTATTTTAACCAAAAATGTAAAAA-ATTCA
* *
744 ACTTAAAATCAATT-TGGAGGTTATAAAA-TCATTTAAAGGGA
128 ACTTAAAATCAATTAT-GAGATTATAAAACT-ATTTAAAGCGA
* * * * * *
785 GCAATAAGGCTTTTGAAGACAT-GGATAATTATAAATGGACTTTTCTTGTCAATGAATGGCTTTT
1 GTAATAAGGCTTTTGAAGACATAGG-TGACTATAAATGGACTTTTC-TATCAATAAATGACTTTT
* * * * * *
849 TCATT-ACGTTTCCTAAGGTAGACATTTAACTATAATCTATTTCAACTAAAAATGTAAAAAAATT
64 TC-TTCACATTTTC-AAGGTAGACATTCAATTATAATCTATTTTAACCAAAAATGT-AAAAAATT
* * * * *
913 TAGCTTAAAATCAATTATAAGATAATAAAACTATTTAAGGCGA
126 CAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGA
* * * * * * * * * *
956 GTAATAAAGCTTTTGAAGGCTTAAGTGACAACAAATAGACTTTT-TGCACCAATGAATGGCTTTT
1 GTAATAAGGCTTTTGAAGACATAGGTGACTATAAATGGACTTTTCT--ATCAATAAATGACTTTT
* * * * * * *
1020 GT-TTCACGTTTCTCAAGGCAAATATTCAATTGTAATATATTTTAA-CAAAAATATAAAATAATT
64 -TCTTCACATTT-TCAAGGTAGACATTCAATTATAATCTATTTTAACCAAAAATGTAAAA-AATT
* * *
1083 CAACTTAAAATTAAGTATGAGATTGTAAAA-TCATTTAAAGCGA
126 CAACTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAGCGA
* * * * * * * * *
1126 GTAATAAGGCTTTCGAATG-CTTGGGTGATTACAAATGGGCTTCTCTTACCAATAAATGAGTTTT
1 GTAATAAGGCTTTTGAA-GACATAGGTGACTATAAATGGACTTTTC-TATCAATAAATGA--CTT
* * * * * *
1190 TTTTTTCATATTTCTCAAGGTAAACATTTAATTACAATCTGTTTTAACCAAAAATGTAAAAAAAA
62 TTTCTTCACATTT-TCAAGGTAGACATTCAATTATAATCTATTTTAACCAAAAATGT--AAAAAA
* * * *
1255 ATCAACGTAAAATCAATTATGGGATTATAAAACTATTTAAAGTGA
124 TTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGA
* * * * * * *
1300 GGAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGAACTTTTTCCATCAATGAGTGGCTTTTT
1 GTAATAAGGCTTTTGAAGACATAGGTGACTATAAATGGAC-TTTTCTATCAATAAATGACTTTTT
** * * * * * * * * *
1365 CTTCATGTTTTTTAAGGAAGACAGTCAATTATATTCTGTTTGAACTAAAAATATAAAAAATATTT
65 CTTCA-CATTTTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAAAATGT-AAAAA-ATTC
* * * *
1430 AACCTAAAATCAATTGTGAGATTGTAAAACCATTTAAAGCGA
127 AACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGA
1472 NNNNNNNNNN
Statistics
Matches: 680, Mismatches: 141, Indels: 73
0.76 0.16 0.08
Matches are distributed among these distances:
169 6 0.01
170 104 0.15
171 338 0.50
172 134 0.20
173 13 0.02
174 76 0.11
175 9 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (168 bp):
GTAATAAGGCTTTTGAAGACATAGGTGACTATAAATGGACTTTTCTATCAATAAATGACTTTTTC
TTCACATTTTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAAAATGTAAAAAATTCAACT
TAAAATCAATTATGAGATTATAAAACTATTTAAAGCGA
Found at i:2235 original size:171 final size:160
Alignment explanation
Indices: 1997--2313 Score: 314
Period size: 170 Copynumber: 1.9 Consensus size: 160
1987 TTTAAAACTA
* ***
1997 ATTTAAAGTGAGTAATAAGACTTTCGAAGGATTAGGTGATGATAAATGGACTTTTCTTGTTAATG
1 ATTTAAAGCGAGTAATAAGACTTTCGAAGGATTAGGTGATGATAAATGGACTTTTCTTACAAATG
* * * * * *
2062 AATAGCTTTTTCTTCACATTTCCCAAGGTAGACATTCAATTACAATTTGTTTTAACCAAAAATGT
66 AATAG-GTTTTCTTCACATTTCCCAAAGCAAACATTCAATTACAATCTGTTTTAACAAAAAATGT
*
2127 AAAAAAATTTAACCTAAAATCANNNNNNNNNNTATAAAACC
130 AAAAAAATTCAACCTAAAATCA----------TATAAAACC
* * * *
2168 ATTTAAAGCGAGTAATAAGGA-TTTTGAAGGTTTGGGTGACT-ATAAATGGGCTTTTCTTACAAA
1 ATTTAAAGCGAGTAATAA-GACTTTCGAAGGATTAGGTGA-TGATAAATGGACTTTTCTTACAAA
* *** * *
2231 TGAATTGGTTTTCTTCTTGTTTCCTAAAGCAAACATTCAATTATAATCTGTTTTAACAAAAAATG
64 TGAATAGGTTTTCTTCACATTTCCCAAAGCAAACATTCAATTACAATCTGTTTTAACAAAAAATG
2296 TAAAAAAATTCAACCTAA
129 TAAAAAAATTCAACCTAA
Statistics
Matches: 123, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
170 64 0.52
171 56 0.46
172 3 0.02
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34
Consensus pattern (160 bp):
ATTTAAAGCGAGTAATAAGACTTTCGAAGGATTAGGTGATGATAAATGGACTTTTCTTACAAATG
AATAGGTTTTCTTCACATTTCCCAAAGCAAACATTCAATTACAATCTGTTTTAACAAAAAATGTA
AAAAAATTCAACCTAAAATCATATAAAACC
Done.