Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397709.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1008.0, 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: 3285
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.30
Warning! 557 characters in sequence are not A, C, G, or T
Found at i:1432 original size:70 final size:70
Alignment explanation
Indices: 1309--1453 Score: 186
Period size: 70 Copynumber: 2.1 Consensus size: 70
1299 AAAATAAACT
*
1309 CAAA-ATCAATTTTGAGATTACAAAATCATTTAAAGCAAGTAATAAGGCCTTTGAAGGAATGAGA
1 CAAATATCAATTTTGAGATTACAAAATCATTTAAAGCAAGTAATAAAGCCTTTGAAGGAATGAGA
1373 GACAA
66 GACAA
* * * * * *
1378 CAAATATCAATTTTTAGATTA-TAAAGCTATTTAAAGCAGGTAATAAAGCTTTTGAAGGAATGGG
1 CAAATATCAATTTTGAGATTACAAAATC-ATTTAAAGCAAGTAATAAAGCCTTTGAAGGAATGAG
*
1442 TGACAA
65 AGACAA
*
1448 TAAATA
1 CAAATA
1454 GACTTTTCGT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
69 8 0.12
70 57 0.88
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (70 bp):
CAAATATCAATTTTGAGATTACAAAATCATTTAAAGCAAGTAATAAAGCCTTTGAAGGAATGAGA
GACAA
Found at i:1977 original size:172 final size:171
Alignment explanation
Indices: 1383--2197 Score: 453
Period size: 171 Copynumber: 4.7 Consensus size: 171
1373 GACAACAAAT
* * * * * *
1383 ATCAATTTTTAGATTATAAAGCTATTTAAAGC-AGGTAATAAAG-CTTTTGAAGGAATGGGTGAC
1 ATCAATTTTGAGATTATAAAACCATTTAAAGCGA-GCAAT-AAGCCTTTTGACGGAATGGGAGAC
* * * * * * * *
1446 AATAAATAGACTTTTCGTGCCAATGAATGTTTTTTTCTTTACGTTTCTCAATGTACACATTCAAT
64 TATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTTTTAA-GTAAACATTCAAT
* * * * * * **********
1511 TGTAGTCTGTTTTAACCAAAAATGT-AAAACANNNNNNNNNNAA
128 TATAATCTATTTTAACTAAAAAAGTAAAAAAAATTAACACTAAA
* * * * * * * *
1554 ATCAGTTATGAGATTATAAAACCATTTAAAGTGAGTAGTAAGCCTTTTAAAGGAAT-AGATGA-T
1 ATCAATTTTGAGATTATAAAACCATTTAAAGCGAGCAATAAGCCTTTTGACGGAATGGGA-GACT
* * * * ** * * *
1617 GATGAATGGATTTTTCTTGCCAATGAATGCTTTTTTTTTCATGTTTCTTGAGGTACACATTCAAC
65 -ATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTT-TTTAAGTAAACATTCAA-
* * ** * *** *
1682 TT-TAGTCTGTTTTAAAGAAAAATGT-AAAACGTTTCAAC-TTAAA
127 TTATAATCTATTTTAACTAAAAAAGTAAAAAAAATT-AACACTAAA
** * ** ** **********
1725 ATCAATTAAGAGATTATAAAACCATTTAAAGCGAGTAATAAGGGTTTTGAAAGANNNNNNNNNNA
1 ATCAATTTTGAGATTATAAAACCATTTAAAGCGAGCAATAAGCCTTTTGACGGAATGGGAGACTA
* * *
1790 TAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCACATTTTTTAATGTATACATTCAATTA
66 TAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTTTTAA-GTAAACATTCAATTA
*
1855 TAATCTATTTTAACTAAAAAAGTAAAAAAAA-TAGACATTAAA
130 TAATCTATTTTAACTAAAAAAGTAAAAAAAATTA-ACACTAAA
* * *
1897 ATCCATTTTGAGATTATGAAACCATTTAAAGCGAGCAGTTAAG-CTTTTGACGGAATGGGAGACT
1 ATCAATTTTGAGATTATAAAACCATTTAAAGCGAGCA-ATAAGCCTTTTGACGGAATGGGAGACT
* * ** * ** ** * * *
1961 ATAAATAGAATTTTCTTGCCAATAAATATTTTTTTCTTGATGTTTCTCGAGGTAAAAATTTAATT
65 ATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTT-TTTAAGTAAACATTCAATT
** * *
2026 ATTGTCTGTTTTAACTAAAAATGTAAAAAAAATTAACACTAAA
129 ATAATCTATTTTAACTAAAAAAGTAAAAAAAATTAACACTAAA
* ********** *
2069 ATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTNNNNNNNNNNTGGGTGACTA
1 ATCAATTTTGAGATTATAAAACCATTTAAAGCGAGCAATAAGCCTTTTGACGGAATGGGAGACTA
* *
2134 TAAATAGACTTTTCTTGCCACTGAATGCTTTTTTCTTCACATTTTTTGAAGTACACATTCAATT
66 TAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTTTT-AAGTAAACATTCAATT
2198 GCAGTCTGTT
Statistics
Matches: 490, Mismatches: 135, Indels: 37
0.74 0.20 0.06
Matches are distributed among these distances:
170 10 0.02
171 243 0.50
172 229 0.47
173 8 0.02
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.36
Consensus pattern (171 bp):
ATCAATTTTGAGATTATAAAACCATTTAAAGCGAGCAATAAGCCTTTTGACGGAATGGGAGACTA
TAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTTTTAAGTAAACATTCAATTAT
AATCTATTTTAACTAAAAAAGTAAAAAAAATTAACACTAAA
Found at i:2207 original size:172 final size:172
Alignment explanation
Indices: 1383--2255 Score: 545
Period size: 172 Copynumber: 5.1 Consensus size: 172
1373 GACAACAAAT
* * * * * *
1383 ATCAATTTTTAGATTATAAAGCTATTTAAAGC-AGGTA-ATAAAGCTTTTGAAGGAATGGGTGAC
1 ATCAATTTTGAGATTATAAAACCATTTAAAGCGA-GCAGAT-AAGCTTTTGACGGAATGGGAGAC
* * * * * * * *
1446 AATAAATAGACTTTTCGTGCCAATGAATGTTTTTTTCTTTAC-GTTTCTCAATGTACACATTCAA
64 TATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTTTTGAA-GTAAACATTCAA
* * * **********
1510 TTGTAGTCTGTTTTAACCAAAAATGT-AAAACANNNNNNNNNNAA
128 TTATAGTCTGTTTTAACTAAAAATGTAAAAAAAATTAACATTAAA
* * * * * * *
1554 ATCAGTTATGAGATTATAAAACCATTTAAAGTGAGTAG-TAAGCCTTTTAAAGGAAT-AGATGA-
1 ATCAATTTTGAGATTATAAAACCATTTAAAGCGAGCAGATAAG-CTTTTGACGGAATGGGA-GAC
* * * * ** * * *
1616 TGATGAATGGATTTTTCTTGCCAATGAATGCTTTTTTTTTCATGTTTCTTGAGGTACACATTCAA
64 T-ATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTTTTGAAGTAAACATTCAA
** ***
1681 CTT-TAGTCTGTTTTAAAGAAAAATGT-AAAACGTTTCAAC-TTAAA
128 -TTATAGTCTGTTTTAACTAAAAATGTAAAAAAAATT-AACATTAAA
** * * ** **********
1725 ATCAATTAAGAGATTATAAAACCATTTAAAGCGAGTA-ATAAGGGTTTTGAAAGANNNNNNNNNN
1 ATCAATTTTGAGATTATAAAACCATTTAAAGCGAGCAGATAA-GCTTTTGACGGAATGGGAGACT
* * *
1789 ATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCACATTTTTT-AATGTATACATTCAAT
65 ATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTTTTGAA-GTAAACATTCAAT
* * *
1853 TATAATCTATTTTAACTAAAAAAGTAAAAAAAA-TAGACATTAAA
129 TATAGTCTGTTTTAACTAAAAATGTAAAAAAAATTA-ACATTAAA
* * *
1897 ATCCATTTTGAGATTATGAAACCATTTAAAGCGAGCAGTTAAGCTTTTGACGGAATGGGAGACTA
1 ATCAATTTTGAGATTATAAAACCATTTAAAGCGAGCAGATAAGCTTTTGACGGAATGGGAGACTA
* * ** * ** * * * * *
1962 TAAATAGAATTTTCTTGCCAATAAATATTTTTTTCTTGATGTTTCTCGAGGTAAAAATTTAATTA
66 TAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTTTTGAAGTAAACATTCAATTA
* *
2027 TTGTCTGTTTTAACTAAAAATGTAAAAAAAATTAACACTAAA
131 TAGTCTGTTTTAACTAAAAATGTAAAAAAAATTAACATTAAA
* ********** *
2069 ATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTA-ATAAGCCTNNNNNNNNNNTGGGTGACT
1 ATCAATTTTGAGATTATAAAACCATTTAAAGCGAGCAGATAAG-CTTTTGACGGAATGGGAGACT
* *
2133 ATAAATAGACTTTTCTTGCCACTGAATGCTTTTTTCTTCACATTTTTTGAAGTACACATTCAATT
65 ATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTTTTGAAGTAAACATTCAATT
** * * *
2198 GCAGTCTGTTTTAA-TGAAAAATGTTAAACAATTTAAC-TTAAA
130 ATAGTCTGTTTTAACT-AAAAATGTAAAAAAAATTAACATTAAA
**
2240 ATCAATTAGGAGATTA
1 ATCAATTTTGAGATTA
2256 NNNNNNNNNN
Statistics
Matches: 537, Mismatches: 143, Indels: 44
0.74 0.20 0.06
Matches are distributed among these distances:
170 8 0.01
171 258 0.48
172 265 0.49
173 6 0.01
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.36
Consensus pattern (172 bp):
ATCAATTTTGAGATTATAAAACCATTTAAAGCGAGCAGATAAGCTTTTGACGGAATGGGAGACTA
TAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTTTTGAAGTAAACATTCAATTA
TAGTCTGTTTTAACTAAAAATGTAAAAAAAATTAACATTAAA
Done.