Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398983.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2264.1, 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: 3394
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.34
Warning! 158 characters in sequence are not A, C, G, or T
Found at i:2779 original size:171 final size:170
Alignment explanation
Indices: 1972--2927 Score: 544
Period size: 171 Copynumber: 5.6 Consensus size: 170
1962 TTTAACTAAA
* * * * ** *
1972 AATGTAAAAAAGAATTGAGCTTAAAATCAACTATAAGATTATAAAACCATTTAAAGTTAGTAACA
1 AATGT-AAAAACAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * * * * ** *
2037 AGGCATTTGAAGGAATGGGTGACTAATAATGGACTTTGCTAGCCATTGAAT-GCATTTTCTTCAC
65 AGGCTTTTGAAGGAATGGGTGACT-ATAATTGACTTTTCT-TCCAATGAATAGCTTTTTCTGAAT
* * * * * * *
2101 GTTTCTTGAGGTAGAAAATCAATTATAGTATGTTTTAACTACA-
128 ATTTCTTAAGGTAGAAATTCAATTATAGTCTATTTGAACCA-AT
* * * **********
2144 AATGTAAAAA-ACTTCAACTTAAAATCAATTGTGAGANNNNNNNNNNATTTAAAGCGAGTAATAA
1 AATGTAAAAACAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
* * * * * * * ** **
2208 GGC-TTTGAAAGAATGGGAGAATATAAATGGACTTTTCTTCCAAATAAATGGATTTTTCTTCACG
66 GGCTTTTGAAGGAATGGGTGACTAT-AATTGACTTTTCTTCC-AATGAATAGCTTTTTCTGAATA
* * * * * * **
2272 TTTCCTAAGGCA-AGCATTCAATTATTGTCTGTTTTAA-TGAT
129 TTTCTTAAGGTAGA-AATTCAATTATAGTCTATTTGAACCAAT
* * * * * * * *
2313 AAATGT--AAACCATTCAAGTTAAAATCAATTTTGAGATTATAAAATCGTGTAAAGTGAGTAATA
1 -AATGTAAAAACAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * *
2376 AGGCTTTTGAAGGAATGGGTGTCTATATATAGACTTTTCTTGCATATGAAT-GCCTTTTTCTGAA
65 AGGCTTTTGAAGGAATGGGTGACTATA-ATTGACTTTTCTTCCA-ATGAATAG-CTTTTTCTGAA
* *
2440 TGTTTCTTAAGGTAGAAATTCAATTATAGTCTATTTTAACCAAT
127 TATTTCTTAAGGTAGAAATTCAATTATAGTCTATTTGAACCAAT
* ********** *
2484 AATGTAAAAACAATTGAACCTNNNNNNNNNNATGAGATTATAAAACCATTTAAAGC-ATGTAGTA
1 AATGTAAAAACAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGA-GTAATA
* * * **
2548 GGGCTTTTGAAGGAATGGGGGACTATAAATGAACTTTTCTTGCCAATGAA-AGCTTTTTTCTTCA
65 AGGCTTTTGAAGGAATGGGTGACTATAATTG-ACTTTTCTT-CCAATGAATAGC-TTTTTCTGAA
* *
2612 TATTTCTTGAGGTAGACATTCAATTATAGTCTATTTGAACCAA-
127 TATTTCTTAAGGTAGAAATTCAATTATAGTCTATTTGAACCAAT
* * *
2655 AAGTGT-AAAACTATTTAACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGCGAGTAATA
1 AA-TGTAAAAACAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * *
2719 ACGCTTTTGAAGGAATGAGTGACTATGAATTGAGTTTTCTTCTCAACGAATAGCTTTTTCT--AT
65 AGGCTTTTGAAGGAATGGGTGACTAT-AATTGACTTTTCTTC-CAATGAATAGCTTTTTCTGAAT
* * * * * * **
2782 ATGTT-TTCCAAGGTAGGAGTTTAATTATACTCTGTTTTAATGAGA-
128 AT-TTCTT--AAGGTAGAAATTCAATTATAGTCTATTTGAACCA-AT
* * * ** * ** *
2827 AATGTAAAAA-AAATCAACTTAAAATTAATTAAAAAATTATAAAATTATTTAAAGTGAGTAATAA
1 AATGTAAAAACAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
* ** *
2891 GGCTTTTCAAAAAATGGGTGACTATAAATGGACTTTT
66 GGCTTTTGAAGGAATGGGTGACTAT-AATTGACTTTT
2928 GTTGTCAATG
Statistics
Matches: 600, Mismatches: 154, Indels: 61
0.74 0.19 0.07
Matches are distributed among these distances:
168 8 0.01
169 84 0.14
170 165 0.28
171 197 0.33
172 144 0.24
173 2 0.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.34
Consensus pattern (170 bp):
AATGTAAAAACAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
GGCTTTTGAAGGAATGGGTGACTATAATTGACTTTTCTTCCAATGAATAGCTTTTTCTGAATATT
TCTTAAGGTAGAAATTCAATTATAGTCTATTTGAACCAAT
Found at i:3299 original size:170 final size:161
Alignment explanation
Indices: 3064--3391 Score: 288
Period size: 170 Copynumber: 2.0 Consensus size: 161
3054 AGTAATAAGA
* *
3064 CTTTTGAAAGAATGGGAGACTATAAATGGACTTTTCTTCTAAATAAATGTATATTTTCACACA-T
1 CTTTTGAAAGAATGGGAGACGATAAATGGACTTTTCTTCTAAATAAATGTACATTTTCACACATT
* *** ***
3128 TTCCCATGGCAGGCATTCAATTATAGTTTATTTTAATGGAAAATAT-AAAAA-ATTCAACTTAAA
66 TTACCA-GGCA-GCATTCAATTATAACATATTTTAACAAAAAATATAAAAAACATTCAACTTAAA
*
3191 ATCAATTATGAGATTATAAAACTATTTAANNNNNNNNNNAAGG
129 ATCAATTATGAGATTATAAAACCATTTAA----------AAGG
* * * * * *
3234 CTTTTGAAGGAATGGGTGACGATAAATGGACTTTTCTTGC-CAATGAATGT-CGTTTTCTTCACA
1 CTTTTGAAAGAATGGGAGACGATAAATGGACTTTTCTT-CTAAATAAATGTACATTTTC-ACACA
* * * * * *
3297 TTTTACGAGGTAGCATTCGATTATAACATGTTTTAACAAAAAATGTAAAAAACATTGAACTTAAA
64 TTTTACCAGGCAGCATTCAATTATAACATATTTTAACAAAAAATATAAAAAACATTCAACTTAAA
*
3362 ATCAATTTTGAGATTATAAAACCATTTAAA
129 ATCAATTATGAGATTATAAAACCATTTAAA
3392 GTG
Statistics
Matches: 130, Mismatches: 23, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
161 1 0.01
169 30 0.23
170 55 0.42
171 44 0.34
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (161 bp):
CTTTTGAAAGAATGGGAGACGATAAATGGACTTTTCTTCTAAATAAATGTACATTTTCACACATT
TTACCAGGCAGCATTCAATTATAACATATTTTAACAAAAAATATAAAAAACATTCAACTTAAAAT
CAATTATGAGATTATAAAACCATTTAAAAGG
Done.