Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399202.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2470.0, 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: 2331
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.26
Warning! 614 characters in sequence are not A, C, G, or T
Found at i:2124 original size:344 final size:340
Alignment explanation
Indices: 929--2331 Score: 1454
Period size: 344 Copynumber: 4.1 Consensus size: 340
919 NNNNNNNNNN
* * * *
929 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCCT-CACTATGAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGC-CAATGAAT
* ** * * * * *
993 AGCTTTTTCTTTACGTTACTTGAGCAAGACATTCAATTATAATCTTTTTTAACCGATAATGTAAA
65 -GCTTTTTCTTTACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGCAAA
* * * **
1058 AAAATTTGAGCAC-TAAAA-CAAATTTTTAGATTATAAAA-CTATTTAAAGCGAGTAATAAGGCT
129 AAAA-TTCA--ACTTAAAATC-AATTATGAGATTATAAAATC-ATTTAAAATGAGTAATAAGGCT
* * *
1120 TTTGAAGGAGTAGATGACTATAAATGGACTTATCTTGCCAATGAATG-CTTGTTTCTTCACGTTT
189 TTTGAAGGAATAGGTGACTATAAATGGACTTTTCTT-CCAATGAATGCCTT-TTTCTTCACGTTT
* * ** * *
1184 CTCAAGGTAGACACTCAATTAT-AGCTTGTTTTAAAGAAAAATGTAGAAAAATTTAA-CTTAAAA
252 CTCAAGGTAGACATTCAATTATAATC-TGTTTTAACCAAAAATGTA-AAAAAATTAACCCTAAAA
1247 TCAATTATGAGATTATAAAACTATTT
315 TCAATTATGAGATTATAAAACTATTT
* * * * * *
1273 AAATCAAGTAATAAAGCTTTTCAAGGAAT-GGATCACTATAAATGGACTTTTCTTTCCAATGAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATAGG-TGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * * *
1337 GTCTTTTTCCTCACGTTTCTTGAGGTAGACATCCAATGATAGTCTGTTTTAATCAAAAATGCAAA
65 G-CTTTTTCTTTACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGCAAA
* * * *
1402 ACAATTCAACTTAAAACCAATTATGAGATTATAAAATCATTTAAAGA-GAGTAATAAAGCTTTTA
129 AAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAA-ATGAGTAATAAGGCTTTTG
* * * * * * *
1466 AAGGAATGGGTGACTATAAATGGACATTTT-TTGCTAGTGTATGCCTTTTTCTTTACATTTCTCG
193 AAGGAATAGGTGACTATAAATGGAC-TTTTCTT-CCAATGAATGCCTTTTTCTTCACGTTTCTCA
** ** * * *
1530 AGGTAGATGTTCAATTATTGTCCGTTTTAACCAAAAAAGTAAAAAAATTAA-ACTCAAAATCAAT
256 AGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTAACCCT-AAAATCAAT
* *
1594 TATGAGATTATAAAACAATGT
320 TATGAGATTATAAAACTATTT
* * * * * *
1615 AAAGCGAGTAATAAGGCTTTTGAGGGAATATGAGACAATAAATGGACTTTTCTTGCCAATGTACG
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
* * *
1680 ATTTCTTTTTTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAA
66 CTTT-TTCTTT-ACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGCAAA
* *
1745 AAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAATGAGTAATAAGGCATTTGA
129 AAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAATGAGTAATAAGGCTTTTGA
* * * * * **
1810 AGGAATGGGTGACTATAAATGGACTTTTCTTCACTATGAATAG-CTTTTTCTTTATGTTACTGGA
194 AGGAATAGGTGACTATAAATGGACTTTTCTTC-CAATGAAT-GCCTTTTTCTTCACGTTTCTCAA
* * * * *
1874 GCTAGACATTCAATTATAATCTTTTTTAACTAATAATGTAAAACAAATTGAGCCCTAAAA-CTAA
257 GGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAA-AAATT-AACCCTAAAATC-AA
* * *
1938 TTTTTAGATTATAAAAGTATTT
319 TTATGAGATTATAAAACTATTT
* * *
1960 CAAA-CGACTAATAAGGCTTTTGAAGGAGTAGGTGACTATAAATGGACTTATCTTGCCAATGAAT
1 -AAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* ** **
2024 GCTTGTTTCTTTATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAAAGAAAAATGCAAA
65 GCTT-TTTCTTTACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGCAAA
*
2089 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT-AAATCGAGTAATAAGGCTTTTG
129 AAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAAT-GAGTAATAAGGCTTTTG
* * * * *
2153 AAGGAATATGTCACTATAAATGAACTTTTCTTCCCAACGAATGCCTTTTTCTTCATGTTTCTCAA
193 AAGGAATAGGTGACTATAAATGGACTTTTCTT-CCAATGAATGCCTTTTTCTTCACGTTTCTCAA
* * * * * * *
2218 GATAGACATTCAGTTATAGTCTGTTTTAACCAAAAATATGAAAAAATTCAA-CTTAAAA-CTAGT
257 GGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATT-AACCCTAAAATC-AAT
* *
2281 TATGAGATTACAAAACCATTT
320 TATGAGATTATAAAACTATTT
*
2302 AAAGCGAGTAATAAGGCTTTTAAAGGAATA
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATA
Statistics
Matches: 878, Mismatches: 153, Indels: 58
0.81 0.14 0.05
Matches are distributed among these distances:
341 18 0.02
342 256 0.29
343 213 0.24
344 300 0.34
345 85 0.10
346 6 0.01
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (340 bp):
AAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
CTTTTTCTTTACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGCAAAAA
AATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAATGAGTAATAAGGCTTTTGAAG
GAATAGGTGACTATAAATGGACTTTTCTTCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTA
GACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTAACCCTAAAATCAATTATGAG
ATTATAAAACTATTT
Found at i:2331 original size:171 final size:170
Alignment explanation
Indices: 929--2331 Score: 1485
Period size: 171 Copynumber: 8.2 Consensus size: 170
919 NNNNNNNNNN
* * * *
929 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCCT-CACTATGAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGC-CAATGAAT
* * * ** * * * *
993 AGCTTTTTCTTTACGTTACTTGAGCAAGACATTCAATTATAATCTTTTTTAACCGATAATGTAAA
65 -GCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAA
* * * *
1058 AAAATTTGAGCAC-TAAAA-CAAATTTTTAGATTATAAAACTATTT
129 AAAA-TTCA--ACTTAAAATC-AATTATGAGATTATAAAACCATTT
* * *
1102 AAAGCGAGTAATAAGGCTTTTGAAGGAGTAGATGACTATAAATGGACTTATCTTGCCAATGAATG
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
* * ** *
1167 CTTGTTTCTTCACGTTTCTCAAGGTAGACACTCAATTATAG-CTTGTTTTAAAGAAAAATGTAGA
66 CTT-TTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTC-TGTTTTAACCAAAAATGTAAA
* *
1231 AAAATTTAACTTAAAATCAATTATGAGATTATAAAACTATTT
129 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * * * * *
1273 AAATCAAGTAATAAAGCTTTTCAAGGAAT-GGATCACTATAAATGGACTTTTCTTTCCAATGAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATAGG-TGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * * * *
1337 GTCTTTTTCCTCACGTTTCTTGAGGTAGACATCCAATGATAGTCTGTTTTAATCAAAAATGCAAA
65 G-CTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAA
* * *
1402 ACAATTCAACTTAAAACCAATTATGAGATTATAAAATCATTT
129 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * * * * * *
1444 AAAGAGAGTAATAAAGCTTTTAAAGGAATGGGTGACTATAAATGGACATTTT-TTGCTAGTGTAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGAC-TTTTCTTGCCAATGAAT
* * ** * * *
1508 GCCTTTTTCTTTACATTTCTCGAGGTAGATGTTCAATTATTGTCCGTTTTAACCAAAAAAGTAAA
65 G-CTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAA
* * * *
1573 AAAATTAAACTCAAAATCAATTATGAGATTATAAAACAATGT
129 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * * * * *
1615 AAAGCGAGTAATAAGGCTTTTGAGGGAATATGAGACAATAAATGGACTTTTCTTGCCAATGTACG
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
* * *
1680 ATTTCTTTTTTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAA
66 -CTT-TTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAA
**
1745 AAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTT
129 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
** * * *
1787 AAAATGAGTAATAAGGCATTTGAAGGAATGGGTGACTATAAATGGACTTTTCTT-CACTATGAAT
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGC-CAATGAAT
* * * * * * * * *
1851 AGCTTTTTCTTTATGTTACTGGAGCTAGACATTCAATTATAATCTTTTTTAACTAATAATGTAAA
65 -GCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAA
* * * * * **
1916 ACAAATTGAGCCCTAAAA-CTAATTTTTAGATTATAAAAGTATTT
129 A-AAATTCA-ACTTAAAATC-AATTATGAGATTATAAAACCATTT
* * *
1960 CAAA-CGACTAATAAGGCTTTTGAAGGAGTAGGTGACTATAAATGGACTTATCTTGCCAATGAAT
1 -AAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * ** *
2024 GCTTGTTTCTTTATGTTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAAAGAAAAATGCAAA
65 GCTT-TTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAA
2089 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
129 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * * * * *
2131 AAATCGAGTAATAAGGCTTTTGAAGGAATATGTCACTATAAATGAACTTTTCTTCCCAACGAATG
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
* * * * * *
2196 CCTTTTTCTTCATGTTTCTCAAGATAGACATTCAGTTATAGTCTGTTTTAACCAAAAATATGAAA
66 -CTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAA
* *
2261 AAATTCAACTTAAAA-CTAGTTATGAGATTACAAAACCATTT
130 AAATTCAACTTAAAATC-AATTATGAGATTATAAAACCATTT
*
2302 AAAGCGAGTAATAAGGCTTTTAAAGGAATA
1 AAAGCGAGTAATAAGGCTTTTGAAGGAATA
Statistics
Matches: 1029, Mismatches: 177, Indels: 50
0.82 0.14 0.04
Matches are distributed among these distances:
170 11 0.01
171 599 0.58
172 182 0.18
173 232 0.23
174 5 0.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (170 bp):
AAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
CTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAA
AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
Done.