Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401854.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_496.0, 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: 3134
ACGTcount: A:0.21, C:0.08, G:0.07, T:0.23
Warning! 1263 characters in sequence are not A, C, G, or T
Found at i:1700 original size:170 final size:170
Alignment explanation
Indices: 1466--1791 Score: 390
Period size: 170 Copynumber: 1.9 Consensus size: 170
1456 NNNNNNNNNN
* *
1466 TTATAATCTCATAATTGATTTAAGTTGAATTTTTTTATATTTTTCTTTAAAACAAACTATAATTG
1 TTATAATCTCATAATTGATTTAAGTTGAATTTTTTAACATTTTTCTTTAAAACAAACTATAATTG
** * *
1531 AAAG-CTTGCCTCAG-GAAAAGTGTAGAAAAAGTCATTCATTGAGAAGAAAAATCCATTT-TAGT
66 AAAGTC-TAACT-AGAGAAAAGTGCAGAAAAAGCCATTCATTGAGAAGAAAAATCCATTTATAGT
* * *
1593 CACTCATTCATTCGAAAGCCTTATTACTCGGTTTAACTGATT
129 CACCCAATCATTCAAAAGCCTTATTACTCGGTTTAACTGATT
** * ***
1635 TTATAATCTTTTAGTTGATTTTAAGTTGAATTTTTTAACATTTTTCTTTAAAATTGA-TAATAAT
1 TTATAATCTCATAATTGA-TTTAAGTTGAATTTTTTAACATTTTTCTTTAAAACAAACT-ATAAT
* * * * *
1699 TGAATGTCTAACTAGAGAAACGTGCAGAAAAAGCCATTGATTGAGAGGAAAAGTCCATTTATAGT
64 TGAAAGTCTAACTAGAGAAAAGTGCAGAAAAAGCCATTCATTGAGAAGAAAAATCCATTTATAGT
* *
1764 CACCCAATCCTTCAAAAGGCTTATTACT
129 CACCCAATCATTCAAAAGCCTTATTACT
1792 NNNNNNNNNN
Statistics
Matches: 130, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
169 18 0.14
170 84 0.65
171 28 0.22
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (170 bp):
TTATAATCTCATAATTGATTTAAGTTGAATTTTTTAACATTTTTCTTTAAAACAAACTATAATTG
AAAGTCTAACTAGAGAAAAGTGCAGAAAAAGCCATTCATTGAGAAGAAAAATCCATTTATAGTCA
CCCAATCATTCAAAAGCCTTATTACTCGGTTTAACTGATT
Found at i:2404 original size:169 final size:169
Alignment explanation
Indices: 2096--2408 Score: 407
Period size: 169 Copynumber: 1.9 Consensus size: 169
2086 NNNTAAATAG
* ** *
2096 TTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTACATTTTTTGTTAAAATAGACTATAAT
1 TTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTACACTTTTAATTAAAACAGACTATAAT
* * * * ** * *
2161 TGATTGTTTTCCTTGAGAAACATGTAAAAAAGCCATTTATTGAGAAGAAAAGTCAATCTATAGTC
66 TGAATGTCTACCTCGAGAAACATGTAAAAAAAACATTCATTGAGAAGAAAAGTCAATCTAGAGTC
2226 ACTCATTCCTTCAAAACGCTTATTACTCGCTTTTAATGA
131 ACTCATTCCTTCAAAACGCTTATTACTCGCTTTTAATGA
* * * * *
2265 TTTTATAATCTCATAATTGATTTTAAGTTGATTTTTTTATACTTTTAATTAAAACATATTATAAT
1 TTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTACACTTTTAATTAAAACAGACTATAAT
* *
2330 TGAATGTCTACCTCGAGAAACGTG-AAGAAACAAACATTCATT-AGCAAGAAAAGTCAATTTAGA
66 TGAATGTCTACCTCGAGAAACATGTAA-AAA-AAACATTCATTGAG-AAGAAAAGTCAATCTAGA
2393 GTCAC-CATTCCTTCAA
128 GTCACTCATTCCTTCAA
2409 TACTCACTTT
Statistics
Matches: 122, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
168 2 0.02
169 91 0.75
170 29 0.24
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (169 bp):
TTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTACACTTTTAATTAAAACAGACTATAAT
TGAATGTCTACCTCGAGAAACATGTAAAAAAAACATTCATTGAGAAGAAAAGTCAATCTAGAGTC
ACTCATTCCTTCAAAACGCTTATTACTCGCTTTTAATGA
Done.