Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399382.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2648.0, 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: 2047
ACGTcount: A:0.22, C:0.08, G:0.06, T:0.24
Warning! 813 characters in sequence are not A, C, G, or T
Found at i:1319 original size:170 final size:168
Alignment explanation
Indices: 595--1488 Score: 696
Period size: 171 Copynumber: 5.3 Consensus size: 168
585 NNNNNNNNNN
* *
595 CTTATTACTTGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAATTCTTTTATATTT
1 CTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAATTTTTTTATA-TT
* * * * *
660 TTTATT-AAACAGAATATAATTGAATATCTACC-CGAGAAATGT-AAAAAAAACGATATACATT-
65 TTTATTAAAACAGATTATAATTGAATATCTACCTCAAGAAACGTGAAGAAAAA-GATATCCATTG
* *
721 AGCAAAAAAAGTCTATTTATAGTCACCCATGACTTCAAAAGC
129 A-CAAAAAAAGTCCATTTATAGTCACCCATG-CTTCGAAAGC
* * * * *
763 CTTATTAGTCACTTTAAAT-GTTTTGATAATCTCATAATTAAATTTAAGTTGAATTTTTTTACAT
1 CTTATTACTCGCTTTAAATGGTTTT-ATAATCTCATAATTGATTTTAAGTT-AATTTTTTTATAT
* * * * * *
827 TTTTGGTTGAAACA-AATAGTAATTGAATATCTGCCAT-ATGAAACGTAAAGAAAAAGATATCCA
64 TTTT-ATTAAAACAGATTA-TAATTGAATATCTACC-TCAAGAAACGTGAAGAAAAAGATATCCA
* * * * * *
890 -TCAGTAAGAAAAGTCCATTTATAATCAGCCATGGCTTCGAAAGT
126 TTGA-CAAAAAAAGTCCATTTATAGTCACCCAT-GCTTCGAAAGC
* * * * *********
934 CTTATTAC-CTGCTTTGAATAGTTTTACAATCTCATAATAGATTTTAAGNNNNNNNNNNTTATAT
1 CTTATTACTC-GCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAG-TTAATTTTTTTATA-
* * * * * * *
998 TTTTTATTCAAACAAATTATAATTTAATATGTACCTCTAGAAACATGAAGAAAAATATATCCATT
63 TTTTTATTAAAACAGATTATAATTGAATATCTACCTCAAGAAACGTGAAGAAAAAGATATCCATT
** * * **
1063 GTTAAAAAAAATCCACTTATAGTCACCCAAACTTTCGAAAGC
128 GACAAAAAAAGTCCATTTATAGTCACCCATGC-TTCGAAAGC
* **********
1105 CTTATTACTCGCTTTAAATGATTTNNNNNNNNNNTAATTGATTTTAAGTTAATTTTTTTTATATT
1 CTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAA-TTTTTTTATATT
* * * *
1170 TTTATTAAAATAGATTATAATTAAATAACTACCTCAAGAAACGTGAAGAAAAAGATATCTATTGA
65 TTTATTAAAACAGATTATAATTGAATATCTACCTCAAGAAACGTGAAGAAAAAGATATCCATTGA
* * * * *
1235 CAAAAAAAGTCTATTTATAGTGACCTATCGCTTCGGAATC
130 CAAAAAAAGTCCATTTATAGTCACCCAT-GCTTCGAAAGC
* * * * *
1275 CTTATTACTCACTTTAAATGGTTTTACAATCTTATAACTGATTTTAAGTTGATTTTTTT-TATTT
1 CTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAATTTTTTTATATTT
* * * ** * * *
1339 TTATTAAAACATATTATAATTGAATATTTACTTTGAGAAA-GTGAAGCAGAA-ATATCCATTGGC
66 TTATTAAAACAGATTATAATTGAATATCTACCTCAAGAAACGTGAAGAAAAAGATATCCATTGAC
* * * *
1402 AAGAAAAGCCCATATATAGTGACCCATGCCTTCGAAAGC
131 AAAAAAAGTCCATTTATAGTCACCCATG-CTTCGAAAGC
* ** * *
1441 CTTATTACTCGGTTTAAATATTTTTATAATCTAATAATAGATTTTAAG
1 CTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAG
1489 CNNNNNNNNN
Statistics
Matches: 560, Mismatches: 144, Indels: 46
0.75 0.19 0.06
Matches are distributed among these distances:
165 1 0.00
166 80 0.14
167 14 0.03
168 81 0.14
169 23 0.04
170 146 0.26
171 192 0.34
172 23 0.04
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38
Consensus pattern (168 bp):
CTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAATTTTTTTATATTT
TTATTAAAACAGATTATAATTGAATATCTACCTCAAGAAACGTGAAGAAAAAGATATCCATTGAC
AAAAAAAGTCCATTTATAGTCACCCATGCTTCGAAAGC
Done.