Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402788.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5846.0, 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, 611
Length: 1019
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.38
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:403 original size:170 final size:171
Alignment explanation
Indices: 1--406 Score: 450
Period size: 171 Copynumber: 2.4 Consensus size: 171
* * *
1 ATCTCATAATTGATTTTAAGTTCAATTATTTTTACGTTTTTGGTTAAAACAGA-TATAGTTGAAT
1 ATCTCATAATTGATTTTAAGTTGAATT-TTTTTACGTTTTTTGTTAAAACAGACTATAATTGAAT
* * * * *
65 GTCTACATTGAGAAACATGAAGAAAAAAGTATTCATTGATAAGAAAAGGCTATTTGTAGTCACCC
65 GTCTACATTGAAAAACATGAAGAAAAAACTATTCATTGATAAGAAAACGCCATTTATAGTCACCC
* * * * *
130 ATTCTTTCCAAAGCCTTATTATTCGTTTTAAATAGTTTTATA
130 ATTCCTTCAAAAGCCCTATTACTCGCTTTAAATAGTTTTATA
* * * * *
172 ATCTCATAATTGATTTAAAGTTGAATTTTTTTACATTTCTTATTAAAACAAACTATAATTGAATG
1 ATCTCATAATTGATTTTAAGTTGAATTTTTTTACGTTTTTTGTTAAAACAGACTATAATTGAATG
* * * * *
237 TCTATC-TTGAAAAACGTGTA-AAAAAACTCATTTATTTGGA-AA-ACAACTCCATTTATAGTC-
66 TCTA-CATTGAAAAACATGAAGAAAAAACT-ATTCA-TT-GATAAGAAAACGCCATTTATAGTCA
*
297 CCTCATTCCTTCAAAAGCCCTATTACTCGCTTTAAAT-GCTTTTCTA
127 CC-CATTCCTTCAAAAGCCCTATTACTCGCTTTAAATAG-TTTTATA
* * *
343 ATCTTATAATTAATTTTAAGTAGAA-TTTTTTACGTTTTTTGTTAAAACAGACTATAATTGAATG
1 ATCTCATAATTGATTTTAAGTTGAATTTTTTTACGTTTTTTGTTAAAACAGACTATAATTGAATG
407 CCTGCCTCAG
Statistics
Matches: 196, Mismatches: 32, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
170 65 0.33
171 124 0.63
172 5 0.03
173 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (171 bp):
ATCTCATAATTGATTTTAAGTTGAATTTTTTTACGTTTTTTGTTAAAACAGACTATAATTGAATG
TCTACATTGAAAAACATGAAGAAAAAACTATTCATTGATAAGAAAACGCCATTTATAGTCACCCA
TTCCTTCAAAAGCCCTATTACTCGCTTTAAATAGTTTTATA
Found at i:440 original size:170 final size:171
Alignment explanation
Indices: 1--827 Score: 603
Period size: 170 Copynumber: 4.9 Consensus size: 171
* ** * ** *
1 ATCTCATAATTGATTTTAAGTTCAATTATTTTTACGTTTTTGGTTAAAACAGA-TATAGTTGAAT
1 ATCTTATAATTGATTTTAAGTAGAA-T-TTTTTACATTTTTTATTAAAACAGACTATAATTGAAT
* * * * * * * * ** * *
65 GTCTACAT-TGAGAAACATGAAGAAAAAAGT-ATTCA-TTGATAAGAAAAGGCTATTTGTAGTCA
64 GCCTGCCTCAGAGAAACATGTAG-AAAAACTCATTTATTTG-GAAGAAAACTCCATTTATAGTC-
* * *
127 CC-CATTCTTTCCAAAGCCTTATTATTCGTTTTAAAT-AGTTTTATA
126 CCTCATTCTTTCAAAAGCCTTATTACTCGCTTTAAATGA-TTTTATA
* * * * *
172 ATCTCATAATTGATTTAAAGTTGAATTTTTTTACATTTCTTATTAAAACAAACTATAATTGAATG
1 ATCTTATAATTGATTTTAAGTAGAA-TTTTTTACATTTTTTATTAAAACAGACTATAATTGAATG
* ** * * * *
237 TCTATCT-TGAAAAACGTGTAAAAAAACTCATTTATTTGGAA-AACAACTCCATTTATAGTCCCT
65 CCTGCCTCAGAGAAACATGTAGAAAAACTCATTTATTTGGAAGAA-AACTCCATTTATAGTCCCT
* * * *
300 CATTCCTTCAAAAGCCCTATTACTCGCTTTAAATGCTTTTCTA
129 CATTCTTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTATA
* * *
343 ATCTTATAATTAATTTTAAGTAGAATTTTTTACGTTTTTTGTTAAAACAGACTATAATTGAATGC
1 ATCTTATAATTGATTTTAAGTAGAATTTTTTACATTTTTTATTAAAACAGACTATAATTGAATGC
* * * * ********
408 CTGCCTCAG-GAGACATGTGGAAAAAGTCATTTATTTGGAAGAAAAGTCCATTTATANNNNNNNN
66 CTGCCTCAGAGAAACATGTAGAAAAACTCATTTATTTGGAAGAAAACTCCATTTATAGTCCCTCA
** * * *
472 NNCTTTCAAAAGCCTTATTAGTCACTTTAAATAATTTTATA
131 TTCTTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTATA
* * * * **
513 ATCTTATAATTGATTTGAAGTTGAATTTTTTACATTTTTCATTAAAAGAGACTATAATTGAACAC
1 ATCTTATAATTGATTTTAAGTAGAATTTTTTACATTTTTTATTAAAACAGACTATAATTGAATGC
* ********** * *
578 TTGCCTCA-AGAAACATGTAGAAAAACTCNNNNNNNNNNAAGAAAAGTCCATTTATAGTCTCTCA
66 CTGCCTCAGAGAAACATGTAGAAAAACTCATTTATTTGGAAGAAAACTCCATTTATAGTCCCTCA
* * * * *
642 TTATTTAAAAAGCCATATTATTTGCTTTAAATGATTTTATA
131 TTCTTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTATA
* * * *
683 ATCTGATAATTGATTTTAAG-ATGAA---TTT---TTTTTTGTTAAAACAGATTACAATTGAATG
1 ATCTTATAATTGATTTTAAGTA-GAATTTTTTACATTTTTTATTAAAACAGACTATAATTGAATG
* ** * * *
741 CATGCCTC-GAGAAACATGTAGAAAAACTCATTTATTTTCAA-AAAACATCTATTTATAGTCTCA
65 CCTGCCTCAGAGAAACATGTAGAAAAACTCATTTATTTGGAAGAAAAC-TCCATTTATAGTCCCT
804 CATTCTTTCAAAAGCCTTATTACT
129 CATTCTTTCAAAAGCCTTATTACT
828 NNNNNNNNNN
Statistics
Matches: 512, Mismatches: 132, Indels: 31
0.76 0.20 0.05
Matches are distributed among these distances:
163 4 0.01
164 86 0.17
167 3 0.01
170 288 0.56
171 128 0.25
172 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.38
Consensus pattern (171 bp):
ATCTTATAATTGATTTTAAGTAGAATTTTTTACATTTTTTATTAAAACAGACTATAATTGAATGC
CTGCCTCAGAGAAACATGTAGAAAAACTCATTTATTTGGAAGAAAACTCCATTTATAGTCCCTCA
TTCTTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTATA
Done.