Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400387.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3587.0, 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, 990
Length: 1650
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.34
Warning! 180 characters in sequence are not A, C, G, or T
Found at i:686 original size:171 final size:170
Alignment explanation
Indices: 509--998 Score: 481
Period size: 171 Copynumber: 2.9 Consensus size: 170
499 ATTTAGGTTG
* * *
509 AATTTTTTTATATAGTTAGTTAAAATAAATTGTAATTGAATGTCTGCCTCAAGAAACATAGAACA
1 AATTTTTTTATATTGTTTGTTAAAATAAATTATAATTGAATGTCTGCCTCAAGAAACATAGAACA
* * * *
574 AAAGCCATCTATTGGAGAGAAACGTCCATTTATATTCACTCATAG-CTTTGAAATCATTATTGCT
66 AAAGCCATCTATTGGA-AGAAAAGTCCATTTATAGTCACTCAT-GCCTTTGAAAGCATTATTACT
* * * *
638 CGTTTTAAATGATTTTATAATCTCATAATTGATTTTAAATCA
129 CGCTTTAAATGGTTTTATAATCTAATAATCGATTTTAAATCA
** * * * * ** **
680 AATTTTTTTACCTTTTTTGTTAAAATATATTATAATTGAATATCTACCTTGAGAAAC-GGGAAGC
1 AATTTTTTTATATTGTTTGTTAAAATAAATTATAATTGAATGTCTGCCTCAAGAAACATAGAA-C
* * *
744 AAAAGCCAT-TCATTGGCAAGAAAAGTCTATTTATAGCCA-TCCATGCCTTTGAAAGCCTTATTA
65 AAAAGCCATCT-ATTGG-AAGAAAAGTCCATTTATAGTCACT-CATGCCTTTGAAAGCATTATTA
* * * **
807 CTTGCTTTAAATGGTTTTACAATCTAATAATCGATTTTAAGTTG
127 CTCGCTTTAAATGGTTTTATAATCTAATAATCGATTTTAAATCA
* * * * *
851 AATTCTTTTATATTGTTTGTTAAAATAGATTATAATTAAATGTC-GCC-CTTAGAAA-ATGTGAA
1 AATTTTTTTATATTGTTTGTTAAAATAAATTATAATTGAATGTCTGCCTC-AAGAAACAT-AG-A
* * * * * *
913 ACAAAAGCCATCCATTGGAAAGAAAAGTTCATTAATGGTCACTCATGTCTTTGAAAGCATCATTA
63 ACAAAAGCCATCTATTGG-AAGAAAAGTCCATTTATAGTCACTCATGCCTTTGAAAGCATTATTA
978 CTCGCTTTAAATGGTTTTATA
127 CTCGCTTTAAATGGTTTTATA
999 TTTGTGGTTA
Statistics
Matches: 255, Mismatches: 53, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
170 13 0.05
171 238 0.93
172 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (170 bp):
AATTTTTTTATATTGTTTGTTAAAATAAATTATAATTGAATGTCTGCCTCAAGAAACATAGAACA
AAAGCCATCTATTGGAAGAAAAGTCCATTTATAGTCACTCATGCCTTTGAAAGCATTATTACTCG
CTTTAAATGGTTTTATAATCTAATAATCGATTTTAAATCA
Found at i:957 original size:342 final size:342
Alignment explanation
Indices: 302--998 Score: 765
Period size: 342 Copynumber: 2.0 Consensus size: 342
292 NNNNNNNNNN
** ** * *
302 AAATGGTTTTATAATCTCATAACTGATTTTAGGTTGAATTTTTTTATATTTTTAATTCAAACATA
1 AAATGGTTTTATAATCTCATAACTGATTTTAAATCAAATTTTTTTACATTTTTAATTAAAACATA
* * * * * * * *
367 TTATAATTGAATGTCTGCTTTAGGAAATGTGATGCAAGAGCCATCCATTGGTAAGAAAAGTCTAT
66 TTATAATTGAATATCTCCTTGAGGAAACGGGAAGCAAAAGCCATCCATTGGCAAGAAAAGTCTAT
* *********** *
432 TTATAGTCACCCATACCTTCCAAACCCTTATTACTCGCTTTAAATGGTTTTATNNNNNNNNNNTT
131 TTATAGCCACCCATACCTTCCAAACCCTTATTACTCGCTTTAAATGGTTTTACAATCTAATAATC
* * * *
497 GAATTTAGGTTGAATTTTTTTATATAGTTAGTTAAAATAAATTGTAATTGAATGTCTGCCTCAAG
196 GAATTTAAGTTGAATTCTTTTATATAGTTAGTTAAAATAAATTATAATTAAATGTCTGCCTCAAG
* * * * *
562 AAACATAGAACAAAAGCCATCTATTGGAGAGAAACGTCCATTTATATTCACTCATAG-CTTTGAA
261 AAACATAGAACAAAAGCCATCCATTGGAAAGAAAAGTCCATTAATAGTCACTCAT-GTCTTTGAA
* * * *
626 ATCATTATTGCTCGTTTT
325 AGCATCATTACTCGCTTT
* * * ** *
644 AAATGATTTTATAATCTCATAATTGATTTTAAATCAAATTTTTTTACCTTTTTTGTTAAAATATA
1 AAATGGTTTTATAATCTCATAACTGATTTTAAATCAAATTTTTTTACATTTTTAATTAAAACATA
*
709 TTATAATTGAATATCTACCTTGA-GAAACGGGAAGCAAAAGCCATTCATTGGCAAGAAAAGTCTA
66 TTATAATTGAATATCT-CCTTGAGGAAACGGGAAGCAAAAGCCATCCATTGGCAAGAAAAGTCTA
* * ** * *
773 TTTATAGCCATCCATGCCTTTGAAAGCCTTATTACTTGCTTTAAATGGTTTTACAATCTAATAAT
130 TTTATAGCCACCCATACCTTCCAAACCCTTATTACTCGCTTTAAATGGTTTTACAATCTAATAAT
* * * * *
838 CGATTTTAAGTTGAATTCTTTTATATTGTTTGTTAAAATAGATTATAATTAAATGTC-GCC-CTT
195 CGAATTTAAGTTGAATTCTTTTATATAGTTAGTTAAAATAAATTATAATTAAATGTCTGCCTC-A
* * *
901 AGAAA-ATGTGAAACAAAAGCCATCCATTGGAAAGAAAAGTTCATTAATGGTCACTCATGTCTTT
259 AGAAACAT-AG-AACAAAAGCCATCCATTGGAAAGAAAAGTCCATTAATAGTCACTCATGTCTTT
965 GAAAGCATCATTACTCGCTTT
322 GAAAGCATCATTACTCGCTTT
986 AAATGGTTTTATA
1 AAATGGTTTTATA
999 TTTGTGGTTA
Statistics
Matches: 288, Mismatches: 62, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
340 3 0.01
341 10 0.03
342 271 0.94
343 4 0.01
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.38
Consensus pattern (342 bp):
AAATGGTTTTATAATCTCATAACTGATTTTAAATCAAATTTTTTTACATTTTTAATTAAAACATA
TTATAATTGAATATCTCCTTGAGGAAACGGGAAGCAAAAGCCATCCATTGGCAAGAAAAGTCTAT
TTATAGCCACCCATACCTTCCAAACCCTTATTACTCGCTTTAAATGGTTTTACAATCTAATAATC
GAATTTAAGTTGAATTCTTTTATATAGTTAGTTAAAATAAATTATAATTAAATGTCTGCCTCAAG
AAACATAGAACAAAAGCCATCCATTGGAAAGAAAAGTCCATTAATAGTCACTCATGTCTTTGAAA
GCATCATTACTCGCTTT
Done.