Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397701.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_10.0, 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: 2776
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.27
Warning! 769 characters in sequence are not A, C, G, or T
Found at i:726 original size:172 final size:165
Alignment explanation
Indices: 351--1020 Score: 544
Period size: 169 Copynumber: 3.9 Consensus size: 165
341 GTTGAATTTC
* * * * * *
351 TTTTACATTTTTTGTTAAAACAGATTATAATTAAATATCTACTTCCAGAA-ATGTCAAGAAAATG
1 TTTTACGTTTTTGGTTAAAACAGATTATAATTGAATGTCTACTT-GAGAACATG--AAGAAAAAG
* * * * * * * * * *
415 GCATTCATTGGCAAAAAAAAGTCTATTTATAATCGCTCATTGCTTCAAAAACCTTTTTGCTAACT
63 GCATTCATTGGC-AAGAAAAG-CCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACT
* * * * * ** *
480 TCAAATGGTTTCA-CA-CTCAAAATTAATTTTAAGTTCAAATT
126 TTAAATGGTTTTATAATCTCAAAATTGA-TTTCA--TGGAATA
** *
521 TATTTATATATTTT--TTAAAACAGATTATAATTGAATGTCTATTTCGAGAAGCATGAAGAAAAA
1 T-TTTACGT-TTTTGGTTAAAACAGATTATAATTGAATGTCTACTT-GAGAA-CATGAAGAAAAA
* * * *
584 GGCATTCATTGGTAAGAAAAGCCAATTTATAGTTACCCATTCCTTTATAAGCCTTATTACTCACT
62 GGCATTCATTGGCAAGAAAAGCC-ATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACT
* * * *
649 TGAAATGGTTTTAAAATCTCAAAATTGATTTCAATTTGAATTC
126 TTAAATGGTTTTATAATCTCAAAATTGATTTC-A-TGGAA-TA
* *
692 TTTGTACGTTTTTGGTTAAAACAGATTGTAATTGAATGTCTACCTAGAGGAACATGAAGAAAAAG
1 TTT-TACGTTTTTGGTTAAAACAGATTATAATTGAATGTCTA-CTTGA-GAACATGAAGAAAAAG
* * * * ** * *
757 TCTTTCGTTGGCAAGAAAAGTCTATTTATAGTCACTTATTCCATCAAAAGCCTTATTACTGACTT
63 GCATTCATTGGCAAGAAAAG-CCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTT
*
822 TAAATGGTTTTATAATCTCATAATTGATTTTTCATGGAATA
127 TAAATGGTTTTATAATCTCAAAATTGA--TTTCATGGAATA
* * * * * * *
863 TTTTACGTTTTTGGTTAGAATAGTTTATAACTGAATATCTACCTTGGGAAACGTGAAG-AAAAGG
1 TTTTACGTTTTTGGTTAAAACAGATTATAATTGAATGTCTA-CTTGAG-AACATGAAGAAAAAGG
* * *
927 CATTCATAGGCAAGAAGAGTCCATTTATCA-TCACCCATTCCTTCAAAAGGCTTATTACTCACTT
64 CATTCATTGGCAAGAAAAG-CCATTTAT-AGTCACCCATTCCTTCAAAAGCCTTATTACTCACTT
*
991 TAAATGGCTTTATAATCTCAAAATTGATTT
127 TAAATGGTTTTATAATCTCAAAATTGATTT
1021 TANNNNNNNN
Statistics
Matches: 409, Mismatches: 72, Indels: 41
0.78 0.14 0.08
Matches are distributed among these distances:
167 3 0.01
168 1 0.00
169 131 0.32
170 111 0.27
171 26 0.06
172 127 0.31
173 6 0.01
174 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.37
Consensus pattern (165 bp):
TTTTACGTTTTTGGTTAAAACAGATTATAATTGAATGTCTACTTGAGAACATGAAGAAAAAGGCA
TTCATTGGCAAGAAAAGCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAA
TGGTTTTATAATCTCAAAATTGATTTCATGGAATA
Found at i:993 original size:169 final size:174
Alignment explanation
Indices: 219--1021 Score: 576
Period size: 172 Copynumber: 4.7 Consensus size: 174
209 NNNNNNNNNN
* * * * * *
219 ACCTCGAGAAACATGAAG-AAAAGGATATTCATTGGCAAGAAATGTCCATTTATGGTCACCCTTT
1 ACCTAGAGGAACATGAAGAAAAAGG-CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATT
* ** * * ********** * *
283 CCTTCACAAGCCTTATTACTTGCTGTAAAAGGTTTTATAATC-NNNNNNNNNNTTTTGAGTT-GA
65 CCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTTCAATTGGA
* * * * *
346 ATT-TCTTTTACATTTTTTGTTAAAACAGATTATAATTAAATATCT
130 ATTAT-TTGTACGTTTTTGGTTAAAACAGATTATAACTGAATATCT
* ** * * * * * *
391 ACTTCCA-GAA-ATGTCAAGAAAATGGCATTCATTGGCAAAAAAAAGTCTATTTATAATCGCTCA
1 ACCTAGAGGAACATG--AAGAAAAAGGCATTCATTGGC-AAGAAAAGTCCATTTATAGTCACCCA
* * * * * * * * *
454 TTGCTTCAAAAACCTTTTTGCTAACTTCAAATGGTTTCA-CA-CTCAAAATT-AATTTT-AAGTT
63 TTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTTCAA-TT
** * * *
515 CAAATTTATTTATA--TATTTT--TTAAAACAGATTATAATTGAATGTCT
127 GGAA-TTATTTGTACGT-TTTTGGTTAAAACAGATTATAACTGAATATCT
** * * *
561 ATTTCGA-GAAGCATGAAGAAAAAGGCATTCATTGGTAAGAAAAG-CCAATTTATAGTTACCCAT
1 ACCTAGAGGAA-CATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCC-ATTTATAGTCACCCAT
* * * * *
624 TCCTTTATAAGCCTTATTACTCACTTGAAATGGTTTTAAAATCTCAAAATTGA--TTTCAATTTG
64 TCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTTCAATTGG
* * * *
687 AATTCTTTGTACGTTTTTGGTTAAAACAGATTGTAATTGAATGTCT
129 AATTATTTGTACGTTTTTGGTTAAAACAGATTATAACTGAATATCT
* * * * **
733 ACCTAGAGGAACATGAAGAAAAAGTCTTTCGTTGGCAAGAAAAGTCTATTTATAGTCACTTATTC
1 ACCTAGAGGAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTC
* * *
798 CATCAAAAGCCTTATTACTGACTTTAAATGGTTTTATAATCTCATAATTGATTTTTC-A-TGGAA
66 CTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTTCAATTGGAA
* * *
861 -TATTT-TACGTTTTTGGTTAGAATAGTTTATAACTGAATATCT
131 TTATTTGTACGTTTTTGGTTAAAACAGATTATAACTGAATATCT
* * * *
903 ACCTTG-GGAAACGTGAAG-AAAAGGCATTCATAGGCAAGAAGAGTCCATTTATCA-TCACCCAT
1 ACCTAGAGG-AACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTAT-AGTCACCCAT
* *
965 TCCTTCAAAAGGCTTATTACTCACTTTAAATGGCTTTATAATCTCAAAATTGATTTT
64 TCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTT
1022 ANNNNNNNNN
Statistics
Matches: 499, Mismatches: 105, Indels: 57
0.75 0.16 0.09
Matches are distributed among these distances:
168 1 0.00
169 143 0.29
170 112 0.22
171 26 0.05
172 150 0.30
173 62 0.12
174 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.36
Consensus pattern (174 bp):
ACCTAGAGGAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTC
CTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTTCAATTGGAA
TTATTTGTACGTTTTTGGTTAAAACAGATTATAACTGAATATCT
Done.