Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400351.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3552.0, 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: 2122
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.30
Warning! 369 characters in sequence are not A, C, G, or T
Found at i:1048 original size:170 final size:170
Alignment explanation
Indices: 735--2122 Score: 1136
Period size: 170 Copynumber: 8.2 Consensus size: 170
725 NNNNNNAACT
* * * *
735 ATTTAAAGC-ATGTAACATGGCTTTTGAAGGAATAAGAGACTATAAATGGACTTTTCTT-TCAAG
1 ATTTAAAGCGA-GTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAA-
* *** * * * * * * *
798 TAAATGGGATTTTCTACATGTTTCTCGGGGTAGACACTT-AACTATAGCCTATTTTAATAAAAAA
64 TGAATGCTTTTTTCTTCATGTTTCTCGAGGCAGACA-TTCAATTATAGTCTGTTTTAATGAAAAA
* * *
862 TCTAAAATATTCAACTTAAAATCAATTATGAGATTATAAAACC
128 TGTAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACC
* * * * *
905 ATTTCAAGCGAGTCATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCTAGTG
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATG
* * ** * * * *
970 AAAGCTTTTTTCTTCATGTTTATCGAGAAAGACAATCAATTCTAGTCTGTTTTAATCAAAAAGGT
66 AATGCTTTTTTCTTCATGTTTCTCGAGGCAGACATTCAATTATAGTCTGTTTTAATGAAAAATGT
* *
1035 AAAAAAATCAACTTAAAATCAATTATTAGATTTTAAAACC
131 AAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACC
* * * *
1075 ATTTAAAGCGAGTAATAAGGCATTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCATTC
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATG
* * * * * **
1140 AATG-TTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAGTATAGTCTTTTTTAATGAGAAATAC
66 AATGCTTTTTTCTTCATGTTTCTCGAGGCAGACATTCAATTATAGTCTGTTTTAATGAAAAATGT
* * *
1204 ACAAAAATTCAAC-TAAAATTAATTATGAGATTATAAAACT
131 A-AAAAAATCAACTTAAAATCAATTATGAGATTATAAAACC
* * * * *
1244 ATTTAAAGTC-AGTAATAAGGCTTTTGAAGGAATAGAAGACTATGAATTGACTTTTCTTACCCAT
1 ATTTAAAG-CGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAAT
* * * * * * **
1308 GACTGCTTTTTTTCTTTAGGTTTCTTGAGGCATACATTCAATTATAGTTTGTTTTAACAAAAAAT
65 GAATGC-TTTTTTCTTCATGTTTCTCGAGGCAGACATTCAATTATAGTCTGTTTTAATGAAAAAT
* *
1373 GTAAAAAAATTCAAGTTAAAATTAATTATGAGATTATAAAACC
129 GTAAAAAAA-TCAACTTAAAATCAATTATGAGATTATAAAACC
** ** * * * * *
1416 ATTTAAAAAGAGTAATAAAACTTTTAAAGAAAT-GCGTGTCTATAAATGGACTTTTCTTACCAAT
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAG-GAGACTATAAATGGACTTTTCTTGCCAAT
* *** * * * * *
1480 GAATGCATTTTTT-TACATGTTTCTCGATATAGATATTCAATTATTGTCTGTTTTAGTCAAAATT
65 GAATGC-TTTTTTCTTCATGTTTCTCGAGGCAGACATTCAATTATAGTCTGTTTTAATGAAAAAT
* ** * *
1544 ATAAAAAAATTCAGTTTAAAATCAATTATG-GTTATATAAAACT
129 GTAAAAAAA-TCAACTTAAAATCAATTATGAGAT-TATAAAACC
* * * * * * ***
1587 ATTTAAAGC-ATGTAACATGGCTTTTGAAAGAAT-GAGAGAATATAAATAGATTTTTCTTTTAAA
1 ATTTAAAGCGA-GTAATAAGGCTTTTGAAGGAATAG-GAGACTATAAATGGACTTTTCTTGCCAA
* ** * * *
1650 TAAATGGATTTTTCTACATGTTTCTCTGA-GCAGACATTTAATTATATTCTGTTTTAATGAAAAA
64 TGAATGCTTTTTTCTTCATGTTTCTC-GAGGCAGACATTCAATTATAGTCTGTTTTAATGAAAAA
* * *
1714 TCTAAAATATTCAACTTAAAATCAATTATGAGATTATAAAACC
128 TGTAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACC
* ** * * * * * *
1757 ATTTAAAGTGAGTAATAAGTATTCTAAAGGAATGGGTGGCTATAAATGGACTTTTTTTGCCAATG
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATG
* ** ** * * * * **
1822 AATGCTTTTTT-TTCACGTTTCTTAAGATAAACATTTAATTATTA-TCCGTTTTAAAGAAAAACA
66 AATGCTTTTTTCTTCATGTTTCTCGAGGCAGACATTCAATTA-TAGTCTGTTTTAATGAAAAATG
********** **
1885 TAAAACANNNNNNNNNNAAATCAATTATTG-GATTATAAAATT
130 TAAAA-AAATCAACTTAAAATCAATTA-TGAGATTATAAAACC
* * * *** *
1927 ATTTCAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATTGACTTTTCTTATGATTG
1 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATG
* * * * * *
1992 AATGCTTTTTTCATCATGTTTCTCAAGGCATATATTGAATTATAGTCT-TTTTAATGAAAAATGC
66 AATGCTTTTTTCTTCATGTTTCTCGAGGCAGACATTCAATTATAGTCTGTTTTAATGAAAAATGT
* * *
2056 AAAAAAGTTCAAC-CAAAATCAGTTATGAGATTATAAAACC
131 AAAAAA-ATCAACTTAAAATCAATTATGAGATTATAAAACC
2096 ATTTAAAGCGAGTAATAAGGCTTTTGA
1 ATTTAAAGCGAGTAATAAGGCTTTTGA
Statistics
Matches: 951, Mismatches: 241, Indels: 53
0.76 0.19 0.04
Matches are distributed among these distances:
168 3 0.00
169 216 0.23
170 397 0.42
171 247 0.26
172 88 0.09
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (170 bp):
ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATG
AATGCTTTTTTCTTCATGTTTCTCGAGGCAGACATTCAATTATAGTCTGTTTTAATGAAAAATGT
AAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACC
Found at i:1982 original size:511 final size:510
Alignment explanation
Indices: 849--2122 Score: 1194
Period size: 511 Copynumber: 2.5 Consensus size: 510
839 CTATAGCCTA
* * *
849 TTTTAATAAAAAATC-T-AAAATATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTCAA
1 TTTTAACAAAAAA-CATAAAAAAATTCAAGTTAAAATCAATTATGAGATTATAAAACCATTTCAA
* * * * * *
912 GCGAGTCATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCTAGTGAAAGCTT
65 GCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGCTT
* * * *
977 TTTTCTTCATGTTTATCGAGAAAGACAATCAATTCTAGTCTGTTTTAATCAAAAAGGTAAAAAAA
130 TTTT-TACATGTTTCTCGAGAAAGACAATCAATTATAGTCTGTTTTAATCAAAAAGATAAAAAAA
* *
1042 TCAACTTAAAATCAATTATTAGATTTTAAAACCATTTAAAGCGAGTAATAAGGCATTTGAAGGAA
194 TCAACTTAAAATCAATTATTAGATTTTAAAACCATTTAAAGCGAGTAACAAGGCATTTGAAAGAA
* * * * * * * * *
1107 TGGGAGACTATAAATGGACTTTTCTTGCCATTCAATGTTTTTTCTTCATGTTTCTCAAGGTAGAC
259 TGAGAGAATATAAATAGACTTTTCTTGCAAATAAATGATTTTTCTACATGTTTCTCAAGGCAGAC
* * *
1172 ATTCAAGTATAGTCTTTTTTAATGAGAAATACACAAAAATTCAACTAAAATTAATTATGAGATTA
324 ATTCAAGTATAGTCTGTTTTAATGAAAAATACACAAAAATTCAACTAAAATCAATTATGAGATTA
* * * * * *
1237 TAAAACTATTTAAAGTCAGTAATAAGGCTTTTGAAGGAATAGAAGACTATGAATTGACTTTTCTT
389 TAAAACCATTTAAAGTCAGTAATAAGGATTCTAAAGGAATAGAAGACTATAAATGGACTTTTCTT
* * * * * * * **
1302 ACCCATGACTGCTTTTTTTCTTTAGGTTTCTTGAGGCATACATTCAATTATAGTTTG
454 ACCAATGAATGCTTTTTTTCTTCACGTTTCTTAAGACAAACATTCAATTATAGTCCG
** * * *
1359 TTTTAACAAAAAATGTAAAAAAATTCAAGTTAAAATTAATTATGAGATTATAAAACCATTTAAAA
1 TTTTAACAAAAAACATAAAAAAATTCAAGTTAAAATCAATTATGAGATTATAAAACCATTTCAAG
* ** * * * *
1424 AGAGTAATAAAACTTTTAAAGAAATGCGTGTCTATAAATGGACTTTTCTTACCAATGAATGCATT
66 CGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGC-TT
* * * * * * **
1489 TTTTTACATGTTTCTCGATATAGATATTCAATTATTGTCTGTTTTAGTCAAAATTATAAAAAAAT
130 TTTTTACATGTTTCTCGAGAAAGACAATCAATTATAGTCTGTTTTAATCAAAAAGATAAAAAAA-
** * * * *
1554 TCAGTTTAAAATCAATTA-T-GGTTATATAAAACTATTTAAAGC-ATGTAACATGGCTTTTGAAA
194 TCAACTTAAAATCAATTATTAGATT-T-TAAAACCATTTAAAGCGA-GTAACAAGGCATTTGAAA
* ** *
1616 GAATGAGAGAATATAAATAGATTTTTCTTTTAAATAAATGGATTTTTCTACATGTTTCTC-TGAG
256 GAATGAGAGAATATAAATAGACTTTTCTTGCAAATAAAT-GATTTTTCTACATGTTTCTCAAG-G
* * * *
1680 CAGACATTTAATTATATTCTGTTTTAATGAAAAAT-CTA-AAATATTCAACTTAAAATCAATTAT
319 CAGACATTCAAGTATAGTCTGTTTTAATGAAAAATAC-ACAAAAATTCAAC-TAAAATCAATTAT
* * * ** *
1743 GAGATTATAAAACCATTTAAAGTGAGTAATAAGTATTCTAAAGGAATGGGTGGCTATAAATGGAC
382 GAGATTATAAAACCATTTAAAGTCAGTAATAAGGATTCTAAAGGAATAGAAGACTATAAATGGAC
* * * *
1808 TTTTTTTGCCAATGAATGC-TTTTTT-TTCACGTTTCTTAAGATAAACATTTAATTATTA-TCCG
447 TTTTCTTACCAATGAATGCTTTTTTTCTTCACGTTTCTTAAGACAAACATTCAATTA-TAGTCCG
* ********** **
1870 TTTTAA-AGAAAAACATAAAACANNNNNNNNNNAAATCAATTATTG-GATTATAAAATTATTTCA
1 TTTTAACA-AAAAACATAAAAAAATTCAAGTTAAAATCAATTA-TGAGATTATAAAACCATTTCA
* * ** *
1933 AGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATTGACTTTTCTTATGATTGAATGCT
64 AGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGCT
* * ** * * * * *
1998 TTTTTCATCATGTTTCTCAAGGCATATATTGAATTATAGTCT-TTTTAATGAAAAATGCA-AAAA
129 TTTTTTA-CATGTTTCTCGAGAAAGACAATCAATTATAGTCTGTTTTAATCAAAAA-G-ATAAAA
** * * * * * *
2061 AGTTCAAC-CAAAATCAGTTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGA
191 AAATCAACTTAAAATCAATTATTAGATTTTAAAACCATTTAAAGCGAGTAACAAGGCATTTGA
Statistics
Matches: 605, Mismatches: 139, Indels: 41
0.77 0.18 0.05
Matches are distributed among these distances:
509 39 0.06
510 38 0.06
511 295 0.49
512 104 0.17
513 129 0.21
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (510 bp):
TTTTAACAAAAAACATAAAAAAATTCAAGTTAAAATCAATTATGAGATTATAAAACCATTTCAAG
CGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGCTTT
TTTTACATGTTTCTCGAGAAAGACAATCAATTATAGTCTGTTTTAATCAAAAAGATAAAAAAATC
AACTTAAAATCAATTATTAGATTTTAAAACCATTTAAAGCGAGTAACAAGGCATTTGAAAGAATG
AGAGAATATAAATAGACTTTTCTTGCAAATAAATGATTTTTCTACATGTTTCTCAAGGCAGACAT
TCAAGTATAGTCTGTTTTAATGAAAAATACACAAAAATTCAACTAAAATCAATTATGAGATTATA
AAACCATTTAAAGTCAGTAATAAGGATTCTAAAGGAATAGAAGACTATAAATGGACTTTTCTTAC
CAATGAATGCTTTTTTTCTTCACGTTTCTTAAGACAAACATTCAATTATAGTCCG
Done.