Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399428.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2693.0, 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, 732
Length: 1220
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.33
Warning! 80 characters in sequence are not A, C, G, or T
Found at i:502 original size:171 final size:162
Alignment explanation
Indices: 325--656 Score: 339
Period size: 171 Copynumber: 2.0 Consensus size: 162
315 NNNNNNACTT
* * * * * * *
325 AAAATCAATTATGGGATTATAAAACTATTTAAAGCGGGTAATGAGGCTTTTGAAGG-AATGAATG
1 AAAATCAATTATGAGATTAT-AAACCATTTAAACCGAGTAATAAGGCTTTTAAAGGAAACG-ATG
* * * ***
389 ACTATAAATAGACTTTTCTTCTAAATGAA-TGGCTTTTTTTGCACGCTTCCTA-AGGTGGACATT
64 ACTATAAATAGACTTTTCTTCTAAATGAACAGGCTTTTTCTACACGCTTCCTAGAGCAAG-CATT
452 CAATTATAGTCTGTTTTAACAAAAAATG-TAAAANNNNNNNNNNC
128 CAATTATAGTCTGTTTTAACAAAAAATGATAAAA----------C
* *
496 AAAATCAATTATGAGATTATAAACCATTTAAACCGAGTAATAAGGCTTTTAAAGGAAACGGTGGC
1 AAAATCAATTATGAGATTATAAACCATTTAAACCGAGTAATAAGGCTTTTAAAGGAAACGATGAC
* * * *
561 TATAAATAGACTTTTCTTCTCAATGAACAGGCTTTTTCTACACGTTTTCTAGAGCAAGTATTCAA
66 TATAAATAGACTTTTCTTCTAAATGAACAGGCTTTTTCTACACGCTTCCTAGAGCAAGCATTCAA
*
626 TTATAGTCTGTTTTAATAAAAAATGATAAAA
131 TTATAGTCTGTTTTAACAAAAAATGATAAAA
657 AATTCAACTT
Statistics
Matches: 137, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
170 59 0.43
171 70 0.51
172 8 0.06
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.33
Consensus pattern (162 bp):
AAAATCAATTATGAGATTATAAACCATTTAAACCGAGTAATAAGGCTTTTAAAGGAAACGATGAC
TATAAATAGACTTTTCTTCTAAATGAACAGGCTTTTTCTACACGCTTCCTAGAGCAAGCATTCAA
TTATAGTCTGTTTTAACAAAAAATGATAAAAC
Found at i:1094 original size:170 final size:169
Alignment explanation
Indices: 702--1096 Score: 483
Period size: 168 Copynumber: 2.3 Consensus size: 169
692 NNNNNNNNGG
* * * * *
702 GTAACAAGCCTTTTGAAGGAATGAGTGACTA-AAATAGACTTTTCTTCTCAATGAATAGCTTTTT
1 GTAATAAGTCTTTCGAAGGAATGAGTAACTATAAATGGACTTTTCTTCTCAATGAATAGCTTTTT
* * *
766 TTGCACGTTTCTCAAGATAGACAATCAATTATAGTCTGTTTTAAAGAAAAATGTAAAAAATTCAA
66 CTGCACGTTTCTCAAGACAGACAATCAATTATAGTCTGTTTTAAAGAAAAATATAAAAAATTCAA
* *
831 CTTAAAATAAATTATGAGATTATAAACTATTTAAAGCGA
131 CTTAAAATAAATTATGAGATTATAAACCATTTAAACCGA
* * *
870 GTAATAAGTCTTTTGAAGGAATGAGTAACTATAAATGGACTTTTTTTCTCAATGACTAGC-TTTT
1 GTAATAAGTCTTTCGAAGGAATGAGTAACTATAAATGGACTTTTCTTCTCAATGAATAGCTTTTT
* * * * *
934 CTGCATGTTTTTCAAGGCAGACATTGAATTATAGTCTGTTTTAACA-AAAAATATAAAAAATTTC
66 CTGCACGTTTCTCAAGACAGACAATCAATTATAGTCTGTTTTAA-AGAAAAATATAAAAAA-TTC
* * *
998 AATTTAAAATCAATTATGAGATTATAAAACCATTTCAACCGA
129 AACTTAAAATAAATTATGAGATTAT-AAACCATTTAAACCGA
* ** * * *
1040 GTAATAAAG-CTTTCGAAGGAATGGGTGGCTCTGAATGGACTTTTCTTGTCAATGAAT
1 GTAAT-AAGTCTTTCGAAGGAATGAGTAACTATAAATGGACTTTTCTTCTCAATGAAT
1097 NNNNNNNNNN
Statistics
Matches: 194, Mismatches: 28, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
168 82 0.42
169 52 0.27
170 57 0.29
171 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (169 bp):
GTAATAAGTCTTTCGAAGGAATGAGTAACTATAAATGGACTTTTCTTCTCAATGAATAGCTTTTT
CTGCACGTTTCTCAAGACAGACAATCAATTATAGTCTGTTTTAAAGAAAAATATAAAAAATTCAA
CTTAAAATAAATTATGAGATTATAAACCATTTAAACCGA
Found at i:1185 original size:171 final size:169
Alignment explanation
Indices: 711--1217 Score: 522
Period size: 171 Copynumber: 3.0 Consensus size: 169
701 GGTAACAAGC
* * * *
711 CTTTTGAAGGAATGAGTGACTA-AAATAGACTTTTCTTCTCAATGAATAGCTTTTTTTGCACGTT
1 CTTTCGAAGGAATGAGTAACTATAAATGGACTTTTCTTCTCAATGAATAGC-TTTTCTGCACGTT
* * * * *
775 TCTCAAGATAGACAATCAATTATAGTCTGTTTTAAAGAAAAATGTAAAAAATTCAACTTAAAATA
65 TCTTAAGGTAGACATTCAATTATAGTCTGTTTT-AACAAAAATGTAAAAAATTCAACTTAAAATC
* *
840 AATTATGAGATTAT-AAACTATTTAAAGCGAGTAAT-AAGT
129 AATTATGAGATTATAAAACCATTTAAACCGAGTAATAAAGT
* * * *
879 CTTTTGAAGGAATGAGTAACTATAAATGGACTTTTTTTCTCAATGACTAGCTTTTCTGCATGTTT
1 CTTTCGAAGGAATGAGTAACTATAAATGGACTTTTCTTCTCAATGAATAGCTTTTCTGCACGTTT
* * * *
944 -TTCAAGGCAGACATTGAATTATAGTCTGTTTTAACAAAAAATATAAAAAATTTCAATTTAAAAT
66 CTT-AAGGTAGACATTCAATTATAGTCTGTTTTAAC-AAAAATGTAAAAAA-TTCAACTTAAAAT
*
1008 CAATTATGAGATTATAAAACCATTTCAACCGAGTAATAAAG-
128 CAATTATGAGATTATAAAACCATTTAAACCGAGTAATAAAGT
* ** * * * ********
1049 CTTTCGAAGGAATGGGTGGCTCTGAATGGACTTTTCTTGTCAATGAATNNNNNNNNNNT-CACGT
1 CTTTCGAAGGAATGAGTAACTATAAATGGACTTTTCTTCTCAATGAAT--AGCTTTTCTGCACGT
* * * *
1113 TTCTTGAGGTAGACATTCCATTACAGTATGTTTTAATCAAAAATGTAAAAAATGTCAACTTAAAA
64 TTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAA-CAAAAATGTAAAAAAT-TCAACTTAAAA
* * *
1178 TCAATTATGATATTATAAAAACATTTAAATCGAGTAATAA
127 TCAATTATGAGATTATAAAACCATTTAAACCGAGTAATAA
1218 GCT
Statistics
Matches: 280, Mismatches: 48, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
167 3 0.01
168 71 0.25
169 51 0.18
170 58 0.21
171 93 0.33
172 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (169 bp):
CTTTCGAAGGAATGAGTAACTATAAATGGACTTTTCTTCTCAATGAATAGCTTTTCTGCACGTTT
CTTAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAATGTAAAAAATTCAACTTAAAATCAA
TTATGAGATTATAAAACCATTTAAACCGAGTAATAAAGT
Done.