Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400559.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3751.0, 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, 695
Length: 1159
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.33
Warning! 104 characters in sequence are not A, C, G, or T
Found at i:204 original size:87 final size:87
Alignment explanation
Indices: 48--216 Score: 234
Period size: 87 Copynumber: 1.9 Consensus size: 87
38 AAGGCTTTCG
* * *
48 AAGGTATTGGTGACTATAAATAGACTTTTCTCACCAATGGATATCTTTTTCTTCACGTTTCTTGA
1 AAGGTATGGGAGACTATAAATAGACTTTTCTCACCAATGGATATCTTTTTCTTCACGTTTCTTCA
113 GGTAGACACTCAATTATTACTC
66 GGTAGACACTCAATTATTACTC
** *
135 AAGGTATGGGAGACTATAAACT-GACTTTTCTTGCCAATGGATATCTTTTTTTTCACGTTTC-TC
1 AAGGTATGGGAGACTATAAA-TAGACTTTTCTCACCAATGGATATCTTTTTCTTCACGTTTCTTC
* *
198 ATGGTAGACATTTAATTAT
65 A-GGTAGACACTCAATTAT
217 AATCTTTTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
86 2 0.03
87 69 0.96
88 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (87 bp):
AAGGTATGGGAGACTATAAATAGACTTTTCTCACCAATGGATATCTTTTTCTTCACGTTTCTTCA
GGTAGACACTCAATTATTACTC
Found at i:703 original size:171 final size:170
Alignment explanation
Indices: 265--946 Score: 435
Period size: 171 Copynumber: 4.0 Consensus size: 170
255 NNNNNNNNNN
* * * *
265 ATAAGATTATAAAACCATTTAAAACGAGTAATAAGGCTTCTGAAGGTATGACTGACTATAAATAG
1 ATAAGATTATAAAACCATTCAAAACGAGTAATAAGGCTTC-GAAGGCATGACTGATTATAAATGG
* * ** * *
330 ACTTTTCTTTCCAATGGATATCTTTTTCTTCATGTTTCTCAAGGTACACATTCAATTATAATATG
65 ACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTCCCAAGAAACACATTCAATTACAATATA
*
395 TTTTAATAAAAACTATAAAAAAATTTAACTTAAAACCAATT
130 TTTTAATAAAAAATATAAAAAAATTTAACTTAAAACCAATT
********** * **
436 ATAAGATTATAAAACCATTNNNNNNNNNNAATAAGGCTTTTGAAGGCATGGGTGATTATAAATGG
1 ATAAGATTATAAAACCATTCAAAACGAGTAATAAGGC-TTCGAAGGCATGACTGATTATAAATGG
*** * ** * * * *
501 ACTTTTCTTGTGAATGAATGGCTTCTTCTTCATGTTTCCCGAGAAAGACATTCAATTACAATCTA
65 ACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTCCCAAGAAACACATTCAATTACAATATA
********** *
566 TTTTAATAAAAAATATAAAAAANNNNNNNNNNAAATCAATT
130 TTTTAATAAAAAATATAAAAAAATTTAACTTAAAACCAATT
* * * *
607 ATGAGATTGTAAAACTATTCAAAGCGAGTAATAAGGCTTACGAAGGCATGACTGATTATAAATGG
1 ATAAGATTATAAAACCATTCAAAACGAGTAATAAGGCTT-CGAAGGCATGACTGATTATAAATGG
* ** ** * * * * *
672 ACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTACTGAGCCAGACATTC-ATT-TATTTTT
65 ACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTCCCAAGAAACACATTCAATTACAATATA
* * * * * * *
735 TGTTTCAGACAAAAATGTAATAAAATTCAGCTTAAAATCAATT
130 T-TTTAATA-AAAAATATAAAAAAATTTAACTTAAAACCAATT
* * * * * * ***
778 ATAAGATTAT-AAACATATTTAAAGCGACTAATAAGGCTTTTGAAGGCATGAGTGGCAATAAATG
1 ATAAGATTATAAAAC-CATTCAAAACGAGTAATAAGGC-TTCGAAGGCATGACTGATTATAAATG
* * * * * ** * *
842 CAC-TTT-GT--CAATGGATATCTTTTTCTTTACGTTTCCTAAGGCAGACATTCAATTA-ATATC
64 GACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTCCCAAGAAACACATTCAATTACA-ATA
* * * * *
902 TGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATT
128 TATTTTAATAAAAAATATAAAAAAATTTAACTTAAAACCAATT
945 AT
1 AT
947 NNNNNNNNNN
Statistics
Matches: 390, Mismatches: 112, Indels: 22
0.74 0.21 0.04
Matches are distributed among these distances:
167 70 0.18
168 8 0.02
169 8 0.02
170 17 0.04
171 283 0.73
172 4 0.01
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.34
Consensus pattern (170 bp):
ATAAGATTATAAAACCATTCAAAACGAGTAATAAGGCTTCGAAGGCATGACTGATTATAAATGGA
CTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTCCCAAGAAACACATTCAATTACAATATAT
TTTAATAAAAAATATAAAAAAATTTAACTTAAAACCAATT
Found at i:929 original size:167 final size:170
Alignment explanation
Indices: 598--946 Score: 420
Period size: 167 Copynumber: 2.1 Consensus size: 170
588 NNNNNNNNNN
* * * *
598 AAATCAATTATGAGATTGTAAAACTATTCAAAGCGAGTAATAAGGCTTACGAAGGCATGACTGAT
1 AAATCAATTATAAGATTATAAAACTATTCAAAGCGACTAATAAGGCTTACGAAGGCATGACTGAC
* * * * * *
663 TATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTACTGAGCCAGACATTCATT
66 AATAAATGCACTTTTCGTA-CAATGGATATCTTTTTCTTCACGTTTACTAAGCCAGACATTCAAT
* * * * *
728 TATTTTTTGTTTCAGACAAAAATGTAATAAAATTCAGCTTA
130 TAATATCTGTTTCAGACAAAAATGTAAAAAAATTCAACTTA
* ** * *
769 AAATCAATTATAAGATTAT-AAACATATTTAAAGCGACTAATAAGGCTTTTGAAGGCATGAGTGG
1 AAATCAATTATAAGATTATAAAAC-TATTCAAAGCGACTAATAAGGCTTACGAAGGCATGACTGA
* * *
833 CAATAAATGCAC-TTT-GT-CAATGGATATCTTTTTCTTTACGTTTCCTAAGGCAGACATTCAAT
65 CAATAAATGCACTTTTCGTACAATGGATATCTTTTTCTTCACGTTTACTAAGCCAGACATTCAAT
*
895 TAATATCTGTTTTA-ATCAAAAATGTAAAAAAATTCAACTTA
130 TAATATCTGTTTCAGA-CAAAAATGTAAAAAAATTCAACTTA
936 AAATCAATTAT
1 AAATCAATTAT
947 NNNNNNNNNN
Statistics
Matches: 152, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
166 1 0.01
167 83 0.55
169 1 0.01
170 7 0.05
171 60 0.39
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (170 bp):
AAATCAATTATAAGATTATAAAACTATTCAAAGCGACTAATAAGGCTTACGAAGGCATGACTGAC
AATAAATGCACTTTTCGTACAATGGATATCTTTTTCTTCACGTTTACTAAGCCAGACATTCAATT
AATATCTGTTTCAGACAAAAATGTAAAAAAATTCAACTTA
Done.