Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397528.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1335.0, 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: 9980
ACGTcount: A:0.20, C:0.07, G:0.08, T:0.20
Warning! 4410 characters in sequence are not A, C, G, or T
Found at i:3837 original size:174 final size:173
Alignment explanation
Indices: 3529--4030 Score: 476
Period size: 173 Copynumber: 2.9 Consensus size: 173
3519 ATTTTAAGTT
* * * *** *
3529 AAAATAGACTATAATTGAATGTCTACTTGAAGAAACATGAAGAAAAATTAATTCATTGGCAGGAA
1 AAAACAGACTATAATTGAATGTCTACCTCAAGAAACATGAAGAAAAAACCATTCATTGGCAAGAA
* * * * * * * * **********
3594 AAATCTATTTATAGTCACTCATTCCTTCAAAAGCC-TTATTACTCACATTAAATNNNNNNNNNNT
66 AAGTCCAGTTATAGTTACCCATTCCTT-AAAAACCTTTATTACCCACTTTAAATAATTTTATAAT
* * *
3658 CTCAAAATAGATTTTAAGTTCAATTTTTTTTT-TACTTTTTTAGTA
130 CTCAAAATTGATTTTATGTTCAATTTTTTTTTGTA-TTTTTGA-TA
* * ** * **
3703 AAAACAGATTATAATTGAATGTTTATGTCGAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAA
1 AAAACAGACTATAATTGAATGTCTACCTCAAGAAACATGAAGAAAAAACCATTCATTGGCAAGAA
* * * *
3768 AAGTCCA-TTATAGTCT-CCTATTTCTTCAAAAAGCC-TTATTACCCACTTTAAATATTTTTATT
66 AAGTCCAGTTATAGT-TACCCATTCCTT-AAAAA-CCTTTATTACCCACTTTAAATAATTTTATA
* * *
3830 ATCTCAAAATTCATTTTATGTTTAATTTTTTTTTGTATTTTTGATT
128 ATCTCAAAATTGATTTTATGTTCAATTTTTTTTTGTATTTTTGATA
* * *
3876 AAAATAGACTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAAAAACCATTCATTGGCAAGAA
1 AAAACAGACTATAATTGAATGTCTACCTCAAGAAACATGAAGAAAAAACCATTCATTGGCAAGAA
* *
3941 AAGTCCAGTTATAGTTACCCATTCCTTTAAAACCTTTATTACTCACTTTAAATAATTTTATAATC
66 AAGTCCAGTTATAGTTACCCATTCCTTAAAAACCTTTATTACCCACTTTAAATAATTTTATAATC
4006 -CTAAAATTGATTTTATGTTCAATTT
131 TC-AAAATTGATTTTATGTTCAATTT
4031 ATTCTACTTT
Statistics
Matches: 267, Mismatches: 54, Indels: 15
0.79 0.16 0.04
Matches are distributed among these distances:
172 3 0.01
173 135 0.51
174 127 0.48
175 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (173 bp):
AAAACAGACTATAATTGAATGTCTACCTCAAGAAACATGAAGAAAAAACCATTCATTGGCAAGAA
AAGTCCAGTTATAGTTACCCATTCCTTAAAAACCTTTATTACCCACTTTAAATAATTTTATAATC
TCAAAATTGATTTTATGTTCAATTTTTTTTTGTATTTTTGATA
Found at i:3921 original size:173 final size:173
Alignment explanation
Indices: 3520--4292 Score: 531
Period size: 174 Copynumber: 4.5 Consensus size: 173
3510 NNNNNNNATA
* ***
3520 TTTTAAGTTAAAATAGACTATAATTGAATGTCTACTTGAAGAAACATGAAGAAAAATTAATTCAT
1 TTTTGAGTTAAAATAGACTATAATTGAATGTCTACTT-AAGAAACATGAAGAAAAAACCATTCAT
* * * * * * **
3585 TGGCAGGAAAAATCTATTTATAGTC-ACTCATTCCTTCAAAAGCCTTATTACTCACATTAAATNN
65 TGGCAAGAAAAGTCCAGTTATAGTCTCCT-ATTCCTTCAAAAGCCTTATTACTCACTTTAAATAA
******** * *
3649 NNNNNNNNTCTCAAAATAGATTTTAAGTTCAATTTTTTTTTTACT
129 TTTTATAATCTCAAAATTGATTTTATGTTCAATTTTTTTTTTACT
* * * * * * **
3694 TTTTTAGTAAAAACAGATTATAATTGAATGTTTA-TGTCGAGAAACATGAAGAAAAAGGCATTCA
1 TTTTGAGTTAAAATAGACTATAATTGAATGTCTACT-T-AAGAAACATGAAGAAAAAACCATTCA
* *
3758 TTGGCAAGAAAAGTCCA-TTATAGTCTCCTATTTCTTCAAAAAGCCTTATTACCCACTTTAAATA
64 TTGGCAAGAAAAGTCCAGTTATAGTCTCCTATTCCTTC-AAAAGCCTTATTACTCACTTTAAATA
* * * *
3822 TTTTTATTATCTCAAAATTCATTTTATGTTTAATTTTTTTTTGTA-T
128 ATTTTATAATCTCAAAATTGATTTTATGTTCAATTTTTTTTT-TACT
*
3868 TTTTGA-TTAAAATAGACTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAAAAACCATTCAT
1 TTTTGAGTTAAAATAGACTATAATTGAATGTCTA-CTTAAGAAACATGAAGAAAAAACCATTCAT
* *
3932 TGGCAAGAAAAGTCCAGTTATAGT-TACCCATTCCTTTAAAA-CCTTTATTACTCACTTTAAATA
65 TGGCAAGAAAAGTCCAGTTATAGTCT-CCTATTCCTTCAAAAGCC-TTATTACTCACTTTAAATA
* *
3995 ATTTTATAATC-CTAAAATTGATTTTATGTTCAA--TTTATTCTACT
128 ATTTTATAATCTC-AAAATTGATTTTATGTTCAATTTTTTTTTTACT
********** * * ** * *
4039 TTNNNNNNNNNNACAGATTATAATTGAATAACTACATTAAGAAACGTGAAG-AAAAACACATTCG
1 TTTTGAGTTAAAATAGACTATAATTGAATGTCTAC-TTAAGAAACATGAAGAAAAAAC-CATTCA
* * ********** *
4103 TT-GCTAAAAAAAGTCCA-TTATAGT-TACCCATTCCTTCAAAAGCCTTANNNNNNNNNNTGAAT
64 TTGGC-AAGAAAAGTCCAGTTATAGTCT-CCTATTCCTTCAAAAGCCTTATTACTCACTTTAAAT
* * * * **
4165 AGTTTTATAATCTCATAATTGATTTTAAGTT-GA-TTTTTTAATA-T
127 AATTTTATAATCTCAAAATTGATTTTATGTTCAATTTTTTTTTTACT
* * * * * **
4209 TTTTGA-CTAAAACAGACTATAATTGAATGCCTACATTGAGAAATATGAAGAAAAATGCATTCAT
1 TTTTGAGTTAAAATAGACTATAATTGAATGTCTAC-TTAAGAAACATGAAGAAAAAACCATTCAT
4273 TGGCAAGAAAAGTCCA-TTAT
65 TGGCAAGAAAAGTCCAGTTAT
4293 NNNNNNNNNN
Statistics
Matches: 476, Mismatches: 103, Indels: 45
0.76 0.17 0.07
Matches are distributed among these distances:
169 55 0.12
170 12 0.03
171 79 0.17
172 57 0.12
173 128 0.27
174 142 0.30
175 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.36
Consensus pattern (173 bp):
TTTTGAGTTAAAATAGACTATAATTGAATGTCTACTTAAGAAACATGAAGAAAAAACCATTCATT
GGCAAGAAAAGTCCAGTTATAGTCTCCTATTCCTTCAAAAGCCTTATTACTCACTTTAAATAATT
TTATAATCTCAAAATTGATTTTATGTTCAATTTTTTTTTTACT
Done.