Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400885.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4051.0, 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: 1839
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.34
Warning! 104 characters in sequence are not A, C, G, or T
Found at i:311 original size:170 final size:172
Alignment explanation
Indices: 99--453 Score: 448
Period size: 170 Copynumber: 2.1 Consensus size: 172
89 NNNNNNNNNN
* * *
99 TGAGATTATAAAACCAATTAAAGCGAGTAATAAAGTTTTCGAAGGCTTCAGTGACTATAAATGGA
1 TGAGATTATAAAACCAATTAAAACGAGTAATAAAGCTTTCGAAGCCTTCAGTGACTATAAATGGA
* * * *
164 CTTTTCATATCAACGAATGGCTTTTGCTTCACATTTCTTAGGGAAAACATTCAATTATAATATAT
66 CCTTTCATACCAACGAATGGCTTTTGCTTCACATTTCTTAAGGAAAACATTCAATTACAATATAT
*
229 TTTAATGAAAAAA-ATAA-A-AAATTC-ACCTTAAAATGAATTA
131 TTTAAT-AAAAAATATAATAGAAATTCAACC-TAAAATCAATTA
* * * *
269 TGAGATTATAAAACGATTTAAAACGAGTAATAAGGCTTTCGAAGCCTTCAGTGACTATAAATGGG
1 TGAGATTATAAAACCAATTAAAACGAGTAATAAAGCTTTCGAAGCCTTCAGTGACTATAAATGGA
* * * * * ** * *
334 CCTTTCTTACCAATGAATGGGTTTTTCTTTATGTTTCTTAAGGCAAGCATTCAATTACAATATAT
66 CCTTTCATACCAACGAATGGCTTTTGCTTCACATTTCTTAAGGAAAACATTCAATTACAATATAT
* * *
399 TTTAATAAAAAATGTAATAGAATTTCAACCTCAAATCAATTA
131 TTTAATAAAAAATATAATAGAAATTCAACCTAAAATCAATTA
441 TGAGATTATAAAA
1 TGAGATTATAAAA
454 NNNNNNNNNN
Statistics
Matches: 157, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
169 6 0.04
170 119 0.76
171 1 0.01
172 28 0.18
173 3 0.02
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (172 bp):
TGAGATTATAAAACCAATTAAAACGAGTAATAAAGCTTTCGAAGCCTTCAGTGACTATAAATGGA
CCTTTCATACCAACGAATGGCTTTTGCTTCACATTTCTTAAGGAAAACATTCAATTACAATATAT
TTTAATAAAAAATATAATAGAAATTCAACCTAAAATCAATTA
Found at i:644 original size:170 final size:170
Alignment explanation
Indices: 243--792 Score: 389
Period size: 170 Copynumber: 3.2 Consensus size: 170
233 ATGAAAAAAA
* * * * *
243 TAAAAAATTC-ACCTTAAAATGAATTATGAGATTATAAAACGATTTAAAACGAGTAATAAGGCTT
1 TAAAAAATTCAACC-TAAAATCAATTATGAGATTATAAAGCCATTTAAAACTAATAATAAGGCTT
* * * * * *** * ** * * * *
307 TCGAAGCCTTCAGTGACTATAAATGGGCCTTTCTTACCAATGAATGGGTTTTTCTTTATG-TTTC
65 TCAAAGGCATGAGTGACTACAAATAATCTTTTCTTGTCAATAAATGAGATTTTCTTCATGTTTTC
* ** * ** *
371 TTAAGGCA-AGCATTCAATTACAATATATTTTAATAAAAAATG
130 -TAAGGCAGAG-AATCAATTACAATATGCTTTCACCAAAAATC
* * ***********
413 TAATAGAATTTCAACCTCAAATCAATTATGAGATTATAAAANNNNNNNNNNC-AAGTAATAAGGC
1 TAA-A-AAATTCAACCTAAAATCAATTATGAGATTATAAAGCCATTTAAAACTAA-TAATAAGGC
* * * * * *
477 TTTTAAAGGCAT-ATGTGACTATAAATGGAT-TTTTCTTGTCAATGAAT-AGCTTTTCTTCTTG-
63 TTTCAAAGGCATGA-GTGACTACAAAT-AATCTTTTCTTGTCAATAAATGAGATTTTCTTCATGT
* * *
538 TTTCTCGAGGTAGAGAATCAATTACAATATG-TTTCAACCAAAAGTC
126 TTTCT-AAGGCAGAGAATCAATTACAATATGCTTTC-ACCAAAAATC
*
584 TGAAAGAATTCAACCTAAAATCAATTATGAGATTATAAAGCCATTTAAAACTAATAATAAGGCTT
1 T-AAAAAATTCAACCTAAAATCAATTATGAGATTATAAAGCCATTTAAAACTAATAATAAGGCTT
* * *
649 TCGAAGGCATGAGTGACTACAAATAATCTTTTCTTGTGAATAAATGGGATTTTCTTCATGTTTTC
65 TCAAAGGCATGAGTGACTACAAATAATCTTTTCTTGTCAATAAATGAGATTTTCTTCATGTTTTC
* * ** * *
714 TAAGGCAGATATTCAATTTTAATATGCTTTCATCAAAAATG
130 TAAGGCAGAGAATCAATTACAATATGCTTTCACCAAAAATC
* *
755 TAAAAAATTCAACTTAAATTCAATTATGAGATTATAAA
1 TAAAAAATTCAACCTAAAATCAATTATGAGATTATAAA
793 ACAATTNNNN
Statistics
Matches: 293, Mismatches: 71, Indels: 32
0.74 0.18 0.08
Matches are distributed among these distances:
169 2 0.01
170 118 0.40
171 84 0.29
172 85 0.29
173 4 0.01
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.34
Consensus pattern (170 bp):
TAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAGCCATTTAAAACTAATAATAAGGCTTT
CAAAGGCATGAGTGACTACAAATAATCTTTTCTTGTCAATAAATGAGATTTTCTTCATGTTTTCT
AAGGCAGAGAATCAATTACAATATGCTTTCACCAAAAATC
Found at i:1359 original size:172 final size:172
Alignment explanation
Indices: 873--1835 Score: 524
Period size: 171 Copynumber: 5.6 Consensus size: 172
863 CTATAAATGG
* * * * * *
873 ACTTTTCTTGTCAATGAATGGTTTTTTCTTCATGTTT-TTCAAGGTAGACATTCAATTAT-A-AT
1 ACTTTTTTTCTCAATGAATGGCTTTTTCTTCATGTTTCCT-GAGGTAGACATTAAATTATAATAT
* * * * * * *
935 GTCTTAACCAAAAATGAAAAAAAAATCAACTTAAAATAAATTATGAAATTATAAAACTATTTAAA
65 ATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGATATTATAAAACCATTTAAA
* * * * * **
1000 GCGAGCAATAAGG-TTTTCGAAGGTATAGGTGACAATAAGTGG
130 GTGAGTAATAAGGCTTTTCGAAAGAATAGGTGACAATAAATAA
* ** * * * *
1042 ACTTTTTTTGTCAATGAATGGCTTTTTCTTCACATTTCCTGGGGTAAACACTAAATTATAATCTA
1 ACTTTTTTTCTCAATGAATGGCTTTTTCTTCATGTTTCCTGAGGTAGACATTAAATTATAATATA
** * ** *
1107 TTTTAACCAAAAATGTAAGGAAATTTAACCCAAAATCAGTTATGATATTATAAAACCATTTAAAG
66 TTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGATATTATAAAACCATTTAAAG
* * *
1172 TGAGTAGTAAGGCTTTT-GAAAGAAT-GAGTTACTATAAATAA
131 TGAGTAATAAGGCTTTTCGAAAGAATAG-GTGACAATAAATAA
*
1213 ACTTTTTTTACT-AATGAATGGCTTTTTCTTCATGTTTCCTGAGGTAGACATTTAATTATAATAT
1 ACTTTTTTT-CTCAATGAATGGCTTTTTCTTCATGTTTCCTGAGGTAGACATTAAATTATAATA-
* * * * * *
1277 TTTTTTTACAAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGATATTGTTAAACCATTTAA
64 TATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGATATTATAAAACCATTTAA
********** * **
1342 AGTGAGTAATAAGGC-TTTCGAANNNNNNNNNNACTATAAATGG
129 AGTGAGTAATAAGGCTTTTCGAAAGAATAGGTGACAATAAATAA
* * * * * * * * * *
1385 ACTTTTCTTATCAATGAATGGCATTTTGTTCATGTTT-TTAGAGGCAGACAATCAATTACAATCT
1 ACTTTTTTTCTCAATGAATGGCTTTTTCTTCATGTTTCCT-GAGGTAGACATTAAATTATAATAT
* * * * ********** **
1449 GTTTTAACCAATAATATAAAAAAATTCAACCTAAAATCAATNNNNNNNNNNTAAAATTATTTAAA
65 ATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGATATTATAAAACCATTTAAA
** * * * * *
1514 GTGAGTAATAAATC-TTTCGAAGGCATGGGTGACTATAAATAC
130 GTGAGTAATAAGGCTTTTCGAAAGAATAGGTGACAATAAATAA
* * * * * * * * *
1556 ACTTTTCTTATCAATGAATGGCTTTGTCTTTATGTTTCC-CATTGTAAACATTCAATTATAATCT
1 ACTTTTTTTCTCAATGAATGGCTTTTTCTTCATGTTTCCTGA-GGTAGACATTAAATTATAATAT
* ** * * * * * * *
1620 GTTTTAA-TGAAAA-GTATAAAAACTTCAGCCTAAATTCTATTGTGAGATTATAAAACCATTTAA
65 ATTTTAACCAAAAATGTA-AAAAAATTCAACTTAAAATCAATTATGATATTATAAAACCATTTAA
** * ** * ** *
1683 AGCAAGTAATAAGGCTTTTC-AAGGCTTGGGTGACTGTAAATGGA
129 AGTGAGTAATAAGGCTTTTCGAAAGAATAGGTGACAATAAAT-AA
* * ** * *
1727 A-TTTTCTTGCT-AATGAATGGGTTTTTCTTCACATTT-CTCGAGGTCA-ACACT-CATGTATAA
1 ACTTTT-TTTCTCAATGAATGGCTTTTTCTTCATGTTTCCT-GAGGT-AGACATTAAAT-TATAA
* * * * * *
1787 TATGTTTTAACCCAAAATGTTAGAAAATTCAACCTAAAATCAACTATGA
62 TATATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA
1836 GATT
Statistics
Matches: 599, Mismatches: 172, Indels: 44
0.73 0.21 0.05
Matches are distributed among these distances:
169 52 0.09
170 111 0.19
171 301 0.50
172 135 0.23
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.36
Consensus pattern (172 bp):
ACTTTTTTTCTCAATGAATGGCTTTTTCTTCATGTTTCCTGAGGTAGACATTAAATTATAATATA
TTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGATATTATAAAACCATTTAAAG
TGAGTAATAAGGCTTTTCGAAAGAATAGGTGACAATAAATAA
Done.