Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401157.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_431.0, 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: 19472
ACGTcount: A:0.19, C:0.07, G:0.06, T:0.20
Warning! 9255 characters in sequence are not A, C, G, or T
Found at i:748 original size:171 final size:171
Alignment explanation
Indices: 4--753 Score: 586
Period size: 171 Copynumber: 4.4 Consensus size: 171
1 AAT
* * * * * * *
4 GATATCCATT-GACAAGAGAAGTCCATTTATAGTCACCCATACCTTCGAAAGTCTTATTAGTCAC
1 GATATCCATTAG-CAAAAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATGACTCGC
* ********** *
68 CTTAAAT-ATTTTTATAATCTCATAATTGATTTTAANNNNNNNNNNTTTATAATTTTTATTAAAA
65 TTTAAATGATTTTT-TAATCTCATAATTGATTTTAAGTTGAACTTTTTTATATTTTTTATTAAAA
* *
132 TAGATTATAATTAAATGTCTATCTTGAGAAACAT---GAAAAA
129 TAGATTATAATTAAATGTCTACCTCGAGAAACATGAAGAAAAA
* * *
172 GATATCCATT-GACAAAAAAAATCCATTTATAGTCACCCATGCCTTCGAAAGTCTTATGACTCTC
1 GATATCCATTAG-CAAAAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATGACTCGC
* * * * * *
236 TTTAAATGGTTTTTTAATCTCACAATTGTTTTTCAGTTGAACTTTTTTATATTTTTTATTGAAAC
65 TTTAAATGATTTTTTAATCTCATAATTGATTTTAAGTTGAACTTTTTTATATTTTTTATTAAAAT
* * * *
301 AGATTATAATTAAATCTTTACCTCCAGAAACATGACGAAAAA
130 AGATTATAATTAAATGTCTACCTCGAGAAACATGAAGAAAAA
* * * * ***********
343 GATTTCCATTAGCAAGAAAAGTCCATTTATAGCCACCCATGGCTTC-AANNNNNNNNNNNNTCGC
1 GATATCCATTAGCAAAAAAAGTCCATTTATAGTCACCCATGCCTTCGAA-AGCCTTATGACTCGC
* * * *
407 TTTAAATGATTTTATAACCTCATAATTGATTTTAATTTGAA-TTTTTT-TACTTTTTATTAAAAT
65 TTTAAATGATTTTTTAATCTCATAATTGATTTTAAGTTGAACTTTTTTATATTTTTTATTAAAAT
* * * **
470 AAATTATAATTGAATGTCTATCTTAAGAAACATGAAGAAAAA
130 AGATTATAATTAAATGTCTACCTCGAGAAACATGAAGAAAAA
* * * *********** * *
512 GGTATCCATTGGTAAAAAAAGTCCATTTATAGTCACCTNNNNNNNNNNAAGCCTTTTTACTCGCT
1 GATATCCATTAGCAAAAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATGACTCGCT
* * * *
577 TTAAATGCTTTTTTAATCTCAT-ATTTAGTTTAAAGTT-AACTTTTTTATATTTTTTTCTTAAAA
66 TTAAATGATTTTTTAATCTCATAATTGA-TTTTAAGTTGAACTTTTTTATA-TTTTTTATTAAAA
* * * * * *
640 TAGATTATAATTGAATGTCTGCCTCGAGGAACGTTAAGAACAA
129 TAGATTATAATTAAATGTCTACCTCGAGAAACATGAAGAAAAA
* **
683 GATATCCATTAGCAAGAGTAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATGACTCGCT
1 GATATCCATTAGCAAAAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATGACTCGCT
748 TTAAAT
66 TTAAAT
754 ANNNNNNNNN
Statistics
Matches: 443, Mismatches: 128, Indels: 19
0.75 0.22 0.03
Matches are distributed among these distances:
168 132 0.30
169 120 0.27
170 11 0.02
171 179 0.40
172 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.37
Consensus pattern (171 bp):
GATATCCATTAGCAAAAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATGACTCGCT
TTAAATGATTTTTTAATCTCATAATTGATTTTAAGTTGAACTTTTTTATATTTTTTATTAAAATA
GATTATAATTAAATGTCTACCTCGAGAAACATGAAGAAAAA
Found at i:749 original size:340 final size:338
Alignment explanation
Indices: 4--754 Score: 713
Period size: 340 Copynumber: 2.2 Consensus size: 338
1 AAT
* * * * *
4 GATATCCATT-GACAAGAGAAGTCCATTTATAGTCACCCATACCTTCGAAAGTCTTATTAGTCAC
1 GATATCCATTAG-CAAGAGAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATGACTCGC
* * *********
68 CTTAAATATTTTTATAATCTCATAATTGATTTTAANNNNNNNNNNTTTATAATTTTTATTAAAAT
65 TTTAAATATTTTTATAACCTCATAATTGATTTTAA-ATTTGAATTTTTATAATTTTTATTAAAAT
* *
133 AGATTATAATTAAATGTCTATCTTGAGAAACATGAAAAAGATATCCATTGACAAAAAAAATCCAT
129 AAATTATAATTAAATGTCTATCTTAAGAAACATGAAAAAGATATCCATTGACAAAAAAAATCCAT
* * *
198 TTATAGTCACCCATGCCTTCGAAAGTCTTATGACTCTCTTTAAATGGTTTTTTAATCTCACAATT
194 TTATAGTCACCCATGCCTTCGAAAGCCTTATGACTCGCTTTAAATGCTTTTTTAATCTCACAATT
** * *
263 GTTTTTCAGTTGAACTTTTTTATATTTTTTATTGAAACAGATTATAATTAAATCTTTACCTCCAG
259 GTTTTAAAGTTGAACTTTTTTATATTTTTTATTAAAACAGATTATAATTAAATCTCTACCTCCAG
*
328 AAACATGACGAAAAA
324 AAACATGAAGAAAAA
* * * * ***********
343 GATTTCCATTAGCAAGAAAAGTCCATTTATAGCCACCCATGGCTTC-AANNNNNNNNNNNNTCGC
1 GATATCCATTAGCAAGAGAAGTCCATTTATAGTCACCCATGCCTTCGAA-AGCCTTATGACTCGC
* *
407 TTTAAATGA-TTTTATAACCTCATAATTGATTTT-AATTTGAATTTTTTTACTTTTTATTAAAAT
65 TTTAAAT-ATTTTTATAACCTCATAATTGATTTTAAATTTGAATTTTTATAATTTTTATTAAAAT
* * ** *
470 AAATTATAATTGAATGTCTATCTTAAGAAACATGAAGAAAAAGGTATCCATTGGTAAAAAAAGTC
129 AAATTATAATTAAATGTCTATCTTAAGAAACAT---GAAAAAGATATCCATTGACAAAAAAAATC
*********** * * *
535 CATTTATAGTCACCTNNNNNNNNNNAAGCCTTTTTACTCGCTTTAAATGCTTTTTTAATCTCATA
191 CATTTATAGTCACCCATGCCTTCGAAAGCCTTATGACTCGCTTTAAATGCTTTTTTAATCTCACA
* * * * * *
600 TTTAG-TTTAAAGTT-AACTTTTTTATATTTTTTTCTTAAAATAGATTATAATTGAATGTCTGCC
256 ATT-GTTTTAAAGTTGAACTTTTTTATA-TTTTTTATTAAAACAGATTATAATTAAATCTCTACC
* * * * *
663 TCGAGGAACGTTAAGAACAA
319 TCCAGAAACATGAAGAAAAA
*
683 GATATCCATTAGCAAGAGTAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATGACTCGCT
1 GATATCCATTAGCAAGAGAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATGACTCGCT
748 TTAAATA
66 TTAAATA
755 NNNNNNNNNN
Statistics
Matches: 317, Mismatches: 86, Indels: 18
0.75 0.20 0.04
Matches are distributed among these distances:
337 48 0.15
338 3 0.01
339 84 0.26
340 179 0.56
341 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.37
Consensus pattern (338 bp):
GATATCCATTAGCAAGAGAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATGACTCGCT
TTAAATATTTTTATAACCTCATAATTGATTTTAAATTTGAATTTTTATAATTTTTATTAAAATAA
ATTATAATTAAATGTCTATCTTAAGAAACATGAAAAAGATATCCATTGACAAAAAAAATCCATTT
ATAGTCACCCATGCCTTCGAAAGCCTTATGACTCGCTTTAAATGCTTTTTTAATCTCACAATTGT
TTTAAAGTTGAACTTTTTTATATTTTTTATTAAAACAGATTATAATTAAATCTCTACCTCCAGAA
ACATGAAGAAAAA
Found at i:11693 original size:171 final size:171
Alignment explanation
Indices: 11192--11696 Score: 433
Period size: 171 Copynumber: 2.9 Consensus size: 171
11182 NNNNNGTTTA
* * * ** * *
11192 AAGTTAAACTTTTTTATATTTTTTTATTAAAATAGATTATAATTGAATACCTGCCTAGAGGAACG
1 AAGTTGAACATTTTTATA-TTTTTTATTAAAATTGATTATAATTGAATGTCTACCTAGAGAAACG
* *
11257 TGAAGAAAATGATATCCATTGGCAAGAATAGTCCATTTATAGTCACCTATGCCTTCGAAAGCCTT
65 TGAAGAAAATGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCTATGCCTTCGAAAGCCTT
** * ********** *
11322 AGGACTCGCTCTNNNNNNNNNNTTAATCTCATAATTGTTTTT
130 ATTACTCGCTTTAAATGGTTTTTTAATCTCATAATTGATTTT
* * * * * *
11364 AAGTTGAACGTTTTTATATTTTTTATTAAAACAT-ATTATAATTGAACGTCTATCTCA-AAAAAT
1 AAGTTGAACATTTTTATATTTTTTATTAAAA-TTGATTATAATTGAATGTCTACCT-AGAGAAAC
* * * * * * *
11427 ATAAAGAAAATGATATCCATTGGA-AAGAGAAGTCTATTTATAGTCACCCATACCTTCAAAAGCC
64 GTGAAGAAAATGATATCCATT-GACAAGAAAAGTCCATTTATAGTCACCTATGCCTTCGAAAGCC
* * ********** *
11491 TTATTACTCACCTNNNNNNNNNNTATAATCTCATAATTGATTTT
128 TTATTACTCGCTTTAAATGGTTTTTTAATCTCATAATTGATTTT
* * * *
11535 AAGTTGAATATTTTTATAATTTTTATTAAAATTGATTATAATTAAATGTCTACCTTGAGAAACGT
1 AAGTTGAACATTTTTATATTTTTTATTAAAATTGATTATAATTGAATGTCTACCTAGAGAAACGT
* * *
11600 GAAGAACAA-GATATCCATTGACAAGAAAAGTCCATCTATAGTAACCTATGCCTTCGAAAGTCTT
66 GAAGAA-AATGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCTATGCCTTCGAAAGCCTT
11664 ATTACTCGCTTTAAATGGTTTTTTAATCTCATA
130 ATTACTCGCTTTAAATGGTTTTTTAATCTCATA
11697 NNNNNNNNNN
Statistics
Matches: 263, Mismatches: 63, Indels: 15
0.77 0.18 0.04
Matches are distributed among these distances:
170 3 0.01
171 240 0.91
172 20 0.08
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.36
Consensus pattern (171 bp):
AAGTTGAACATTTTTATATTTTTTATTAAAATTGATTATAATTGAATGTCTACCTAGAGAAACGT
GAAGAAAATGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCTATGCCTTCGAAAGCCTTA
TTACTCGCTTTAAATGGTTTTTTAATCTCATAATTGATTTT
Found at i:13970 original size:171 final size:168
Alignment explanation
Indices: 13644--14132 Score: 549
Period size: 171 Copynumber: 2.9 Consensus size: 168
13634 NNNNNNNNNC
* * *
13644 AATTATGAGGTTATAAAATTATTTAAAGCGAGTAATAATGTTGTT-GAAGGCATGGACGACTATA
1 AATTATGAGATTACAAAACTATTTAAAGCGAGTAATAA-G-TGTTCGAAGGCATGG-CGACTATA
* * * **
13708 AATAGACTTTTCTTACTAATGAATATCTTTTTTCTTCACGTTTCTCAAGGTAAACATTCAATTAT
63 AATGGACTTTTCTTGCTAATG-ATATCATTTTTCTTCACGTTTCT-AAGACAAACATTCAATTAT
*
13773 AATCT-ATTTAATTAAAAATTATAAAAATA-TTTAACTTAAAACT
126 AATCTGTTTTAA-TAAAAATTATAAAAA-AGTTTAACTTAAAACT
* * * * *
13816 AATTATGAGATTACAAAACTCTTTAAAGTGAGTAATAAGAGTTACGAAGGCATAGGCGAGTACAA
1 AATTATGAGATTACAAAACTATTTAAAGCGAGTAATAAGTGTT-CGAAGGCAT-GGCGACTATAA
*
13881 ATGGACTTTTCTTGCTAGTAGATAT-ATTTTTCTTCACGTTTCCTAAGACAAACATTCAATTATA
64 ATGGACTTTTCTTGCTAAT-GATATCATTTTTCTTCACGTTT-CTAAGACAAACATTCAATTATA
13945 ATCTGTTTTAATAATAAA-TATAAAAAAGTTTAACTTAAAACT
127 ATCTGTTTTAATAA-AAATTATAAAAAAGTTTAACTTAAAACT
* * * *
13987 AATTATGAGTTTACAAAACTATTTAAAGCGAGTAATAAGTCTTTCGAAGGCATGAGTGACAATAA
1 AATTATGAGATTACAAAACTATTTAAAGCGAGTAATAAGT-GTTCGAAGGCATG-GCGACTATAA
* * * ** * * *
14052 ATGGACTTCTCTTGCCAATGGATATCA-TTTTCTTTATATTTTTTGAGACAGACATTCAATTATA
64 ATGGACTTTTCTTGCTAAT-GATATCATTTTTCTTCA-CGTTTCTAAGACAAACATTCAATTATA
14116 ATCTGTTTTAATAAAAA
127 ATCTGTTTTAATAAAAA
14133 AATTAAAATT
Statistics
Matches: 271, Mismatches: 34, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
170 8 0.03
171 176 0.65
172 84 0.31
173 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.37
Consensus pattern (168 bp):
AATTATGAGATTACAAAACTATTTAAAGCGAGTAATAAGTGTTCGAAGGCATGGCGACTATAAAT
GGACTTTTCTTGCTAATGATATCATTTTTCTTCACGTTTCTAAGACAAACATTCAATTATAATCT
GTTTTAATAAAAATTATAAAAAAGTTTAACTTAAAACT
Done.