Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402937.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5983.0, 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: 1772
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.34
Warning! 132 characters in sequence are not A, C, G, or T
Found at i:1516 original size:340 final size:332
Alignment explanation
Indices: 607--1621 Score: 935
Period size: 341 Copynumber: 3.0 Consensus size: 332
597 ATGATAAAAC
* *
607 CATTTAAAGCGTGTAATAAGGC-TTTGAAGAAGTGGGTAAATATAAATAGACTTTTCTT-CCTAA
1 CATTTAAAGCGTGTAATAAGGCTTTTGAAGAAAT-GGTGAATATAAATAGACTTTTCTTGCC-AA
** * * * *
670 TGAATACCTTTTTCTTCCTGTTTTTAGAGGTAGACATTCAATTATAGTTTGTTTTATCTAAAAAT
64 TGAATGTCTTTTTCTTCATGTTTCTAGAGGTAGACATTCAATTATAGTCTGTTTTAACT-AAAAT
* * * *
735 TTTAAAAAATTTAACTTAAAATCAAATATGAGATTATAAAACAATTTAAAGCGAGCGATAATGCT
128 TTTAAAAAAATTAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGCGATAAGGCT
* ********* *
800 TTTGAAGGAATAGGTGACTATAAATGGANNNNNNNNNNCAATGAATAACTTTTTCTACATGTTTC
193 TTTGAAGGAATGGGTGACTATAAATGGA-CTTTTTTTCCAATGAATAACTTTTTCTACACGTTTC
* * * *
865 TCGAGGCAGGCATTTAATTATAGTCTGTTTTAACAAAAAATGTAAAAAACTTCAACTTAAAATCA
257 TCTAGGTAGGCATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCA
* *
930 ATTTTGAGATNNNNNNNN
322 ATTATGAGAT-------T
** * * * * *
948 NNTTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAA-AGACTTTTCTTGCAAAT
1 CATTTAAAGCGTGTAATAAGGCTTTTGAAGAAATG-GTGAATATAAATAGACTTTTCTTGCCAAT
* * * * * * * *
1012 GAATGTTTTTTTCTTCATGTTTCTTGAGGTAAACATTCAATTATACTCTATTTTACCCAAAAATA
65 GAATGTCTTTTTCTTCATGTTTCTAGAGGTAGACATTCAATTATAGTCTGTTTTA-ACTAAAATT
* **********
1077 TAAAAAAAATTAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCNNNNNNNNNNGCTT
129 TTAAAAAAATTAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGCGATAAGGCTT
* *
1142 TTGAAGGAATGAGTGACTATAAGTGGACTTTTTTTCTCAATGAATAACTTTTTCTACACGTTTCT
194 TTGAAGGAATGGGTGACTATAAATGGACTTTTTTTC-CAATGAATAACTTTTTCTACACGTTTCT
* * **
1207 CTAGGTAGGCATTCAATTATAGCCTGTTTGAAGTAAAAATGTAAAAAAATTCAACTTAAAATCAA
258 CTAGGTAGGCATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAA
***
1272 TTATGANNNNNNNNNNT
323 TTATGA-------GATT
* *
1289 CATTTAAAGCGTGTAATAAGGCTTTTGAAGAAAT-GTGAGTATAAATAGACTTTTCTTGCCAATT
1 CATTTAAAGCGTGTAATAAGGCTTTTGAAGAAATGGTGAATATAAATAGACTTTTCTTGCCAATG
* * *
1353 AATGTCTTTTTCTTCATGTTCCTCGAAGTAGACATTCAATTATAGTCTGTTTTAACTAAAATTGT
66 AATGTCTTTTTCTTCATGTTTCTAGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAATT-T
**********
1418 TAAAAAAATTAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGNNNNNNNNNNGGCTTT
130 TAAAAAAATTAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGCGATAAGGCTTT
* * * *** * *
1483 TGAAGGAATGGGTGACTATAAATAGATTTTTTTTGCCAATAAATGTTTTTTTCTTCACATTTCT-
195 TGAAGGAATGGGTGACTATAAATGGACTTTTTTT-CCAATGAATAACTTTTTCTACACGTTTCTC
* * * * *
1547 TGAGGTAGGCATTCAATTATAGTC-GATTTTAACCAAAAATGTAAAACATTTTAACTTAAAATTA
259 T-AGGTAGGCATTCAATTATAGTCTG-TTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCA
1611 ATTATGAGATT
322 ATTATGAGATT
1622 ATAAAACAAT
Statistics
Matches: 553, Mismatches: 104, Indels: 42
0.79 0.15 0.06
Matches are distributed among these distances:
333 1 0.00
339 18 0.03
340 237 0.43
341 277 0.50
342 20 0.04
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.36
Consensus pattern (332 bp):
CATTTAAAGCGTGTAATAAGGCTTTTGAAGAAATGGTGAATATAAATAGACTTTTCTTGCCAATG
AATGTCTTTTTCTTCATGTTTCTAGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAATTTT
AAAAAAATTAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGCGATAAGGCTTTT
GAAGGAATGGGTGACTATAAATGGACTTTTTTTCCAATGAATAACTTTTTCTACACGTTTCTCTA
GGTAGGCATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
TGAGATT
Found at i:1654 original size:171 final size:164
Alignment explanation
Indices: 577--1772 Score: 642
Period size: 171 Copynumber: 7.0 Consensus size: 164
567 NNNNNNNNNC
* *
577 AACTTAAAATTC-ATTATGAGATGATAAAACCATTTAAAGCGTGTAATAAGGC-TTTGAA-GAAG
1 AACTTAAAA-TCAATTATGAGATTATAAAACAATTTAAA----G-AATAAGGCTTTTGAAGGAA-
* * * ***
639 TGGGTAAATATAAATAGACTTTTCTT-CCTAATGAATACCTTTTTCTTC-CTGTTT-TTAGAGGT
59 TGGGTGACTATAAATAGA-TTTTCTTGCC-AATAAATGTTTTTTTCTTCAC-GTTTCTT-GAGGT
* * * *
701 AGACATTCAATTATAGTTTGTTTTATCTAAAAATTTTAAAAAATTT
120 AGGCATTCAATTATAGTCTGTTTTAACTAAAAA-TGTAAAAAATTT
* * *
747 AACTTAAAATCAAATATGAGATTATAAAACAATTTAAAGCGAGCGATAATGCTTTTGAAGGAATA
1 AACTTAAAATCAATTATGAGATTATAAAACAATTTAAA--GA---ATAAGGCTTTTGAAGGAATG
* ********* * *** * * * *
812 GGTGACTATAAATGGANNNNNNNNNNCAATGAATAACTTTTTCTACATGTTTCTCGAGGCAGGCA
61 GGTGACTATAAATAGA-TTTTCTTGCCAATAAATGTTTTTTTCTTCACGTTTCTTGAGGTAGGCA
* * *
877 TTTAATTATAGTCTGTTTTAACAAAAAATGTAAAAAACTTC
125 TTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAA-TTT
* **********
918 AACTTAAAATCAATTTTGAGATNNNNNNNNNNTTTAAAGTGAGTAATAAGGCTTTTGAAGGAATG
1 AACTTAAAATCAATTATGAGATTATAAAACAATTT-AA---AG-AATAAGGCTTTTGAAGGAATG
* * * * **
983 AGTGACTATAAA-AGACTTTTCTTGCAAATGAATGTTTTTTTCTTCATGTTTCTTGAGGTAAACA
61 GGTGACTATAAATAGA-TTTTCTTGCCAATAAATGTTTTTTTCTTCACGTTTCTTGAGGTAGGCA
* * * * * *
1047 TTCAATTATACTCTATTTTACCCAAAAATATAAAAAAAATT
125 TTCAATTATAGTCTGTTTTAACTAAAAATGT-AAAAAATTT
* ******
1088 AACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCNNNNNNNNNNGCTTTTGAAGGAATG
1 AACTTAAAATCAATTATGAGATTATAAAACAATTTAAAG-----AATAAGGCTTTTGAAGGAATG
* * * * * *** *
1153 AGTGACTATAAGTGGACTTTT-TTTCTCAATGAATAACTTTTTCTACACGTTTCTCT-AGGTAGG
61 GGTGACTATAAATAGA-TTTTCTTGC-CAATAAATGTTTTTTTCTTCACGTTTCT-TGAGGTAGG
* * * *
1216 CATTCAATTATAGCCTGTTTGAAGTAAAAATGTAAAAAAATTC
123 CATTCAATTATAGTCTGTTTTAACTAAAAATGT-AAAAAATTT
********** *
1259 AACTTAAAATCAATTATGANNNNNNNNNNTC-ATTTAAAGCGTGTAATAAGGCTTTTGAAGAAAT
1 AACTTAAAATCAATTATGA-GATTATAAAACAATTTAAA----G-AATAAGGCTTTTGAAGGAAT
* * * * * * * *
1323 --GTGAGTATAAATAGACTTTTCTTGCCAATTAATGTCTTTTTCTTCATGTTCCTCGAAGTAGAC
60 GGGTGACTATAAATAGA-TTTTCTTGCCAATAAATGTTTTTTTCTTCACGTTTCTTGAGGTAGGC
* *
1386 ATTCAATTATAGTCTGTTTTAACTAAAATTGTTAAAAAAATT
124 ATTCAATTATAGTCTGTTTTAACTAAAAATG-TAAAAAATTT
* *****
1428 AACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGNNNNNNNNNNGGCTTTTGAAGGAATG
1 AACTTAAAATCAATTATGAGATTATAAAACAATTTAAAG-----AATAAGGCTTTTGAAGGAATG
* *
1493 GGTGACTATAAATAGATTTTTTTTGCCAATAAATGTTTTTTTCTTCACATTTCTTGAGGTAGGCA
61 GGTGACTATAAATAGA-TTTTCTTGCCAATAAATGTTTTTTTCTTCACGTTTCTTGAGGTAGGCA
* *
1558 TTCAATTATAGTC-GATTTTAACCAAAAATGTAAAACATTTT
125 TTCAATTATAGTCTG-TTTTAACTAAAAATGTAAAA-AATTT
* *****
1599 AACTTAAAATTAATTATGAGATTATAAAACAATTNNNNNNNNNNAATAAGGCTTTTGAAGGAATG
1 AACTTAAAATCAATTATGAGATTATAAAACAATT-----TAAAGAATAAGGCTTTTGAAGGAATG
* ** * *
1664 GGTGACTATAAATCA-ATTTTCTT-CTCAATGAATAATTTTTTCTACACGTTT-TTCGAGGCAGG
61 GGTGACTATAAAT-AGATTTTCTTGC-CAATAAATGTTTTTTTCTTCACGTTTCTT-GAGGTAGG
*
1726 CATTTAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTT
123 CATTCAATTATAGTCTGTTTTAACTAAAAATGT-AAAAAATTT
1769 AACT
1 AACT
Statistics
Matches: 771, Mismatches: 205, Indels: 100
0.72 0.19 0.09
Matches are distributed among these distances:
165 1 0.00
166 2 0.00
167 1 0.00
168 2 0.00
169 126 0.16
170 238 0.31
171 388 0.50
172 9 0.01
173 1 0.00
174 1 0.00
175 2 0.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.35
Consensus pattern (164 bp):
AACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGAATAAGGCTTTTGAAGGAATGGGTGA
CTATAAATAGATTTTCTTGCCAATAAATGTTTTTTTCTTCACGTTTCTTGAGGTAGGCATTCAAT
TATAGTCTGTTTTAACTAAAAATGTAAAAAATTT
Done.