Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401215.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4362.0, 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, 664
Length: 1108
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.30
Warning! 195 characters in sequence are not A, C, G, or T
Found at i:972 original size:172 final size:171
Alignment explanation
Indices: 367--1106 Score: 490
Period size: 172 Copynumber: 4.3 Consensus size: 171
357 NNNNNNNNNN
* * * *
367 ATGCCTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTG-TTTAACAAACAAAT-T
1 ATGCTTTTTTCTTTATGTTTCTC-ATGTAGACATTCAATTCTAGTCTGTTTTAACAAA-AAATGT
* * ********** *
430 AACAAAAAAATTCAACTTAAAATCAATTACGGNNNNNNNNNNCCATTTAAAGTGAGTAATAATGC
64 -AC-AAAGAATTCAA-TTTAAATCAATTACGGCATTAAAAAACCATTTAAAGTGAGTAATAAGGC
* * * * *
495 TGTTGTAGGTATGAG-TGACTATAAATGGACATTTCTTGCCAATCA
126 TGTTGAAGGAATGGGTTGACTATAAATGGACTTTTCTTGCCAATAA
* *
540 ATG-TTTTTTCCTTTATGTTTCTCATGCTAGACATTCAATTCTGGTCTGTTTTAACTAAAAATGT
1 ATGCTTTTTT-CTTTATGTTTCTCATG-TAGACATTCAATTCTAGTCTGTTTTAACAAAAAATGT
************ * *
604 ACAAAGAATTCAAATTTAAATCAACNNNNNNNNNNTAAAACCATTTAAAGTGAGTAATAAGGGTT
64 ACAAAGAATTC-AATTTAAATCAATTACGGCATTAAAAAACCATTTAAAGTGAGTAATAAGGCTG
* *
669 TTGAAGGAATGGGTTGACTATAAATGGACTTCTCTTACCAATAA
128 TTGAAGGAATGGGTTGACTATAAATGGACTTTTCTTGCCAATAA
* * * * * *
713 ATGCCTTTTTCTTTACGTTTCTCGAGGTAGACGTTCAATTATAGTCT-CTTTAACAAAAAAAT-T
1 ATGCTTTTTTCTTTATGTTTCTC-ATGTAGACATTCAATTCTAGTCTGTTTTAAC-AAAAAATGT
* * * *
776 AAAAAAAATTCAACTTAAAATCAATTACGGCATTAAAAAACCATTTAAAGTGAGTAATAATGCTG
64 ACAAAGAATTCAA-TTTAAATCAATTACGGCATTAAAAAACCATTTAAAGTGAGTAATAAGGCTG
* ********** *
841 TTGAAGGTATGGG-TGNNNNNNNNNNGACTTTTCTTGCCAATGA
128 TTGAAGGAATGGGTTGACTATAAATGGACTTTTCTTGCCAATAA
* *
884 ATGCTTTTTTCTTTATGTTTCTCATTGTAGACATTCAATTCTAGTATGTTTTAACCAAAAATGTA
1 ATGCTTTTTTCTTTATGTTTCTCA-TGTAGACATTCAATTCTAGTCTGTTTTAACAAAAAATGTA
** ********** *
949 CAAAGAATTCACATTTAAATCAATTTTGAG-ATTANNNNNNNNNNTAAAGTGAGTAATAAGGCTT
65 CAAAGAATTCA-ATTTAAATCAATTACG-GCATTAAAAAACCATTTAAAGTGAGTAATAAGGCTG
* * * **
1013 TTGAAGGAATGGG-TGACTATAAATAGACTTCTCGTATCAATAA
128 TTGAAGGAATGGGTTGACTATAAATGGACTTTTCTTGCCAATAA
* * * * * *
1056 ATGCCTTTTTCTTTACGTTTCTTGAGGTAGACATTCAATTATAGTTTGTTT
1 ATGCTTTTTTCTTTATGTTTC-TCATGTAGACATTCAATTCTAGTCTGTTT
1107 AA
Statistics
Matches: 435, Mismatches: 116, Indels: 33
0.74 0.20 0.06
Matches are distributed among these distances:
170 1 0.00
171 64 0.15
172 244 0.56
173 110 0.25
174 16 0.04
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.35
Consensus pattern (171 bp):
ATGCTTTTTTCTTTATGTTTCTCATGTAGACATTCAATTCTAGTCTGTTTTAACAAAAAATGTAC
AAAGAATTCAATTTAAATCAATTACGGCATTAAAAAACCATTTAAAGTGAGTAATAAGGCTGTTG
AAGGAATGGGTTGACTATAAATGGACTTTTCTTGCCAATAA
Found at i:999 original size:344 final size:344
Alignment explanation
Indices: 367--1100 Score: 893
Period size: 344 Copynumber: 2.1 Consensus size: 344
357 NNNNNNNNNN
* * *
367 ATGCCTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTAACAAACAAATTAA
1 ATGCCTTTTTCTTTACGTTTCTCGAGGTAGACATTCAATTATAGTCTCTTTAACAAAAAAATTAA
**********
432 CAAAAAAATTCAACTTAAAATCAATTACGGNNNNNNNNNNCCATTTAAAGTGAGTAATAATGCTG
66 CAAAAAAATTCAACTTAAAATCAATTACGGCATTAAAAAACCATTTAAAGTGAGTAATAATGCTG
*
497 TTGTAGGTATGAGTGACTATAAATGGACATTTCTTGCCAATCAATGTTTTTTCCTTTATGTTTCT
131 TTGAAGGTATGAGTGACTATAAATGGACATTTCTTGCCAATCAATGTTTTTTCCTTTATGTTTCT
* * *
562 CATGCTAGACATTCAATTCTGGTCTGTTTTAACTAAAAATGTACAAAGAATTCAAATTTAAATCA
196 CATGCTAGACATTCAATTCTAGTATGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCA
********* *
627 ACNNNNNNNNNNTAAAACCATTTAAAGTGAGTAATAAGGGTTTTGAAGGAATGGGTTGACTATAA
261 AC-TTTTGAGATTAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGG-TGACTATAA
* *
692 ATGGACTTCTCTTACCAATAA
324 ATAGACTTCTCGTACCAATAA
*
713 ATGCCTTTTTCTTTACGTTTCTCGAGGTAGACGTTCAATTATAGTCTCTTTAACAAAAAAATT-A
1 ATGCCTTTTTCTTTACGTTTCTCGAGGTAGACATTCAATTATAGTCTCTTTAACAAAAAAATTAA
777 -AAAAAAATTCAACTTAAAATCAATTACGGCATTAAAAAACCATTTAAAGTGAGTAATAATGCTG
66 CAAAAAAATTCAACTTAAAATCAATTACGGCATTAAAAAACCATTTAAAGTGAGTAATAATGCTG
* ********** * *
841 TTGAAGGTATGGGTGNNNNNNNNNNGACTTTTCTTGCCAATGAATGCTTTTTT-CTTTATGTTTC
131 TTGAAGGTATGAGTGACTATAAATGGACATTTCTTGCCAATCAATG-TTTTTTCCTTTATGTTTC
*
905 TCATTG-TAGACATTCAATTCTAGTATGTTTTAACCAAAAATGTACAAAGAATTCACATTTAAAT
195 TCA-TGCTAGACATTCAATTCTAGTATGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAAT
********
969 CAA-TTTTGAGATTANNNNNNNNNNTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
259 CAACTTTTGAGATTA--AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
*
1033 AAATAGACTTCTCGTATCAATAA
322 AAATAGACTTCTCGTACCAATAA
*
1056 ATGCCTTTTTCTTTACGTTTCTTGAGGTAGACATTCAATTATAGT
1 ATGCCTTTTTCTTTACGTTTCTCGAGGTAGACATTCAATTATAGT
1101 TTGTTTAA
Statistics
Matches: 329, Mismatches: 55, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
342 2 0.01
343 70 0.21
344 189 0.57
345 9 0.03
346 59 0.18
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.35
Consensus pattern (344 bp):
ATGCCTTTTTCTTTACGTTTCTCGAGGTAGACATTCAATTATAGTCTCTTTAACAAAAAAATTAA
CAAAAAAATTCAACTTAAAATCAATTACGGCATTAAAAAACCATTTAAAGTGAGTAATAATGCTG
TTGAAGGTATGAGTGACTATAAATGGACATTTCTTGCCAATCAATGTTTTTTCCTTTATGTTTCT
CATGCTAGACATTCAATTCTAGTATGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCA
ACTTTTGAGATTAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT
AGACTTCTCGTACCAATAA
Done.