Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399829.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3067.0, 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, 814
Length: 1358
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.33
Warning! 221 characters in sequence are not A, C, G, or T
Found at i:374 original size:171 final size:165
Alignment explanation
Indices: 5--421 Score: 459
Period size: 171 Copynumber: 2.5 Consensus size: 165
1 TTGG
*
5 CAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGGAAGCCTTATTAC-TCACTTTAAATATTTT
1 CAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTTC-CTTTAAATATTTT
* * * * * * * *
69 CTAATCTCAGAAATGATTTTAAGTTGAACATTTCTACATTTTTTTAAATATATTATAATTGAATG
65 ATAATCTCATAATTGATTGTAAGTTAAACATTTATACATTTTTTTAAATAGATTATAATTGAATA
134 TCTGCCACAGGAAACATGAAGAAAAAACAATTCATTGA
130 TCT--CACAGGAAACATGAAGAAAAAACAATTCATTGA
* *
172 -ATAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTTCCTTTAAATGATTG
1 CA-AGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTTCCTTTAAAT-ATTT
** * *
236 TATAATCTCATAATTGATTGTAAGTTAAAGTTTTTATATATTTTTAGTTAAAATAGATTATATTT
64 TATAATCTCATAATTGATTGTAAGTTAAA-CATTTATACATTTTT--TT-AAATAGATTATAATT
* * *
301 GAATATCT-ACTTGGAGAA-ATGTAA-AAAAATATC-TTTTATTGA
125 GAATATCTCAC-AGGA-AACATG-AAGAAAAA-A-CAATTCATTGA
** * *
343 CAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGTATTATTACTTACTCTAAATAGTTTT
1 CAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTTCCTTTAAATA-TTTT
408 ATAATCTCATAATT
65 ATAATCTCATAATT
422 AATNNNNNNN
Statistics
Matches: 212, Mismatches: 24, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
166 1 0.00
167 52 0.25
168 29 0.14
169 13 0.06
170 12 0.06
171 83 0.39
172 22 0.10
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.38
Consensus pattern (165 bp):
CAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTTCCTTTAAATATTTTA
TAATCTCATAATTGATTGTAAGTTAAACATTTATACATTTTTTTAAATAGATTATAATTGAATAT
CTCACAGGAAACATGAAGAAAAAACAATTCATTGA
Found at i:1271 original size:171 final size:170
Alignment explanation
Indices: 814--1358 Score: 629
Period size: 171 Copynumber: 3.2 Consensus size: 170
804 NNNNNNNNNN
* *
814 TTTTTTATATTTTTAGTTAAAATAGATTATAATTCAATGTCTGCCTTGAGAAACATGAAGAAAAA
1 TTTTTTATATTTTTA-TTAAAATAGATTATAATTGAATGTCTGCCTTAAGAAACATGAAGAAAAA
* * *
879 G-CTAGTCATTGACAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTA-TATCTCA
65 GTC-ATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGTCTTATTA-CTCG
* * * *
942 CTTTAAATGATTTTTTAATCTCAGAATTGATTTTAAGTTAAAC
128 CTTTAAATGGTTTTATAATCTCAGAATTGATTTTAAGTTGAAT
* * * * * * * *
985 TTTTTCACATTTTT-CT-AAATATATTATAATTGAATGTGTGCATTAGGAAACATGAAGAAAAAA
1 TTTTTTATATTTTTATTAAAATAGATTATAATTGAATGTCTGCCTTAAGAAACATGAAGAAAAAG
* * * ** *
1048 TCATTCATTGACGAGAAAAGTCCATTTATAATTACTAATGCCTTCGAAAGTCTTATTACTTGCTT
66 TCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGTCTTATTACTCGCTT
* * *
1113 TAAATGGTTTTATAATCTCATAATTCATTTTAATTTGAAT
131 TAAATGGTTTTATAATCTCAGAATTGATTTTAAGTTGAAT
* *
1153 TTTTTTATATTTTTAGTTAAAATAGATTATATTTGAATGTCTACCTTAAG-AA-ATGTAA-AACA
1 TTTTTTATATTTTTA-TTAAAATAGATTATAATTGAATGTCTGCCTTAAGAAACATG-AAGAA-A
** * *
1215 AATGTCATTCATTGGA-AAGAAAAGTAGATTTATAGTCACCCATACCTTCAAAAGTCTTATTACT
63 AA-GTCATTCATT-GACAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGTCTTATTACT
* * *
1279 CGTTTTAAATGGTTTTCTAATCTCAGAATTGATTTTACGTTGAAT
126 CGCTTTAAATGGTTTTATAATCTCAGAATTGATTTTAAGTTGAAT
*
1324 TTTTTTATATTTTTTATTAAAATATATTATAATTG
1 TTTTTTATA-TTTTTATTAAAATAGATTATAATTG
Statistics
Matches: 310, Mismatches: 54, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
168 136 0.44
169 9 0.03
170 8 0.03
171 149 0.48
172 8 0.03
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.41
Consensus pattern (170 bp):
TTTTTTATATTTTTATTAAAATAGATTATAATTGAATGTCTGCCTTAAGAAACATGAAGAAAAAG
TCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGTCTTATTACTCGCTT
TAAATGGTTTTATAATCTCAGAATTGATTTTAAGTTGAAT
Done.