Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400355.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3556.0, 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: 1764
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.28
Warning! 496 characters in sequence are not A, C, G, or T
Found at i:1192 original size:171 final size:170
Alignment explanation
Indices: 650--1194 Score: 444
Period size: 171 Copynumber: 3.2 Consensus size: 170
640 NNNNNNNNNN
* * * * * *
650 ATAATTAATTTTAAGTTGAATTTTTTTACGTTTTTGC-TTAAAATAGACTATAATTGAATGTTTA
1 ATAATTGATTTTAAG-TGAATTTTTTTACATTCTT-CATTAAAACAGACAATAATTGAATGCTTA
* ** * * * * **
714 GCTCGAGAAACATA-AAGAAAAGGACATTGATTGACAAGAAAAGTTTATTTATAGTCACCCATTC
64 CCTTAAGAAACGTACAA-AAAAAGACATTCATTGACAAAAAAAGTCCATTTATAGTCACCCATT-
**********
778 CTTT-AAAAGC-CTTATNNNNNNNNNNAAA-TAGTTTTATAATCTC
127 CTTTCAAAA-CTCTTATTACTCACTTTAAATTA-TTTTATAATCTC
* * * *
821 ATAATTAATTTTAAGTCGAATTTTTTTACATTCTTCATTAAAACAGTCTATAATTGAATGCTTGC
1 ATAATTGATTTTAAGT-GAATTTTTTTACATTCTTCATTAAAACAGACAATAATTGAATGCTTAC
*
886 CTTAAGAAACGTACAAAAAAAGACATTCATTGAGAAAAAAAGTCCATTTATAGTCACCCATTCTT
65 CTTAAGAAACGTACAAAAAAAGACATTCATTGACAAAAAAAGTCCATTTATAGTCACCCATTCTT
* ***********
951 TCAAAAGTCTTATTACTCNNNNNNNNNNGTTTTATAATCTC
130 TCAAAACTCTTATTACTCACTTTAAATTATTTTATAATCTC
* *
992 ATAATTGATTTTAAGGTGAATTGTTTTACATT-TTTAGTTAAAACAGACAATAATTGAATG-TCT
1 ATAATTGATTTTAA-GTGAATTTTTTTACATTCTTCA-TTAAAACAGACAATAATTGAATGCT-T
* * * *
1055 ACC-TAGAGAAATGTGA-AGAAAAATG-TATTGATTGACAAAAAAAGTCCATTTATAGTCACCCA
63 ACCTTA-AGAAACGT-ACA-AAAAAAGACATTCATTGACAAAAAAAGTCCATTTATAGTCACCCA
1117 TTCTTTCAAAACTCTTATTACTCACTTTAAATTATTTTATAATCTC
125 TTCTTTCAAAACTCTTATTACTCACTTTAAATTATTTTATAATCTC
* *
1163 ATAATTGATTTTCAGTTAATTTTTTTTACATT
1 ATAATTGATTTTAAGTGAA-TTTTTTTACATT
1195 NNNNNNNNNN
Statistics
Matches: 308, Mismatches: 53, Indels: 26
0.80 0.14 0.07
Matches are distributed among these distances:
170 16 0.05
171 281 0.91
172 11 0.04
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.38
Consensus pattern (170 bp):
ATAATTGATTTTAAGTGAATTTTTTTACATTCTTCATTAAAACAGACAATAATTGAATGCTTACC
TTAAGAAACGTACAAAAAAAGACATTCATTGACAAAAAAAGTCCATTTATAGTCACCCATTCTTT
CAAAACTCTTATTACTCACTTTAAATTATTTTATAATCTC
Done.