Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402302.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5384.0, 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, 781
Length: 1302
ACGTcount: A:0.26, C:0.08, G:0.09, T:0.24
Warning! 429 characters in sequence are not A, C, G, or T
Found at i:287 original size:171 final size:172
Alignment explanation
Indices: 2--405 Score: 499
Period size: 171 Copynumber: 2.4 Consensus size: 172
1 T
2 ATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATAGGTGACTATAAATGGACTTCTCTTGCCTATG
1 ATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATAGGTGACTATAAATGGACTTCTCTTGCCTATG
* * *
67 AATGCCTTTTTCATCACGTTTCAGGCGATAGACAGTCAATTATAATCTGTTTCAA-CAAAAAAAT
66 AATACCTTTTTCATCACGTTTCACGCGATAGACAATCAATTATAATCTGTTTCAACCAAAAAAAT
*
131 ACAAAGAATTTAAATTAAAA-CTAATTTTGAGATTATAAAATC-
131 ACAAAGAATTCAAATTAAAATC-AATTTTGAGATTATAAAA-CA
** * *
173 ATTTAAAATGAGTAATAAGGCTTTTAAAGGAATATGTGACTATAAATGGACTTGTCTTGCCTATG
1 ATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATAGGTGACTATAAATGGACTTCTCTTGCCTATG
* * * * * * ***
238 AATACCTTTTTTATCATGTTTCTCGTGGTAGACAATCAATTATAATCTGTTTTAACCAAAAANNN
66 AATACCTTTTTCATCACGTTTCACGCGATAGACAATCAATTATAATCTGTTTCAACCAAAAAAAT
******* *
303 NNNNNNNATTCAAATTAAAATCAATTTTGAGATTATAACACA
131 ACAAAGAATTCAAATTAAAATCAATTTTGAGATTATAAAACA
* * * * *
345 ATTTGAAGCGAGTAATATGACTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCC
1 ATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATAGGTGACTATAAATGGACTTCTCTTGCC
406 AATATATCCC
Statistics
Matches: 197, Mismatches: 33, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
171 108 0.55
172 88 0.45
173 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.34
Consensus pattern (172 bp):
ATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATAGGTGACTATAAATGGACTTCTCTTGCCTATG
AATACCTTTTTCATCACGTTTCACGCGATAGACAATCAATTATAATCTGTTTCAACCAAAAAAAT
ACAAAGAATTCAAATTAAAATCAATTTTGAGATTATAAAACA
Found at i:1274 original size:171 final size:168
Alignment explanation
Indices: 831--1302 Score: 441
Period size: 171 Copynumber: 2.8 Consensus size: 168
821 NNNNNNNNAG
* *
831 CGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTTTTGTTAATGAATACCTT
1 CGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCTAAT-AATACCTT
* * * * * *
896 TTTCTTCACTTTTATCAAGGCAAACATTCAATTATTATCTGTTTTA-ATAAAAAATATACAAAAA
65 TTTTTTCACGTTTCTCAAGGTAGACATT-AATTATAATCTGTTTTACA-AAAAAATATA-AAAAA
* * * *
960 TTTCAAAGTAAAATCAATTTTGAGATTATAAAATCATTGAAA
127 ATTAAAAGTAAAATCAATTTTGAGAATATAAAACCATTGAAA
********** * *
1002 TCGAGTAATAAGGCTTTT-AAAGGAANNNNNNNNNNTAAATGGACTTTTCTTGCCAATGACTACC
1 -CGAGTAATAAGGCTTTTGAAA-GAATGGGTGACTATAAATGGACTTTTCTTGCTAAT-AATACC
* * * ** * * * *
1066 TTATTCTTT-ATGGTTCTTGAGATAGACTATCAATTATAATCTATTTTACACAAAAATATAAAAA
63 TT-TTTTTTCACGTTTCTCAAGGTAGAC-ATTAATTATAATCTGTTTTACAAAAAAATATAAAAA
* *
1130 AATTAAAATTAAAATCAATTTTGAGAATATAAAACCTTTTGAAGA
126 AATTAAAAGTAAAATCAATTTTGAGAATATAAAACC-ATTGAA-A
* * *
1175 -GAGTGATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCTAATAAGTGCATT
1 CGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCTAATAA-TACCTT
1239 TTTTTTCACGTTTCTCAAGGTAGACAGTTAATTATAATCTGTTTT-CAATAAAAATATAAAAAAA
65 TTTTTTCACGTTTCTCAAGGTAGACA-TTAATTATAATCTGTTTTACAA-AAAAATATAAAAAAA
Statistics
Matches: 230, Mismatches: 59, Indels: 23
0.74 0.19 0.07
Matches are distributed among these distances:
170 9 0.04
171 125 0.54
172 88 0.38
173 8 0.03
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.36
Consensus pattern (168 bp):
CGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCTAATAATACCTTT
TTTTTCACGTTTCTCAAGGTAGACATTAATTATAATCTGTTTTACAAAAAAATATAAAAAAATTA
AAAGTAAAATCAATTTTGAGAATATAAAACCATTGAAA
Done.