Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399717.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2962.0, 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: 2302
ACGTcount: A:0.26, C:0.10, G:0.09, T:0.25
Warning! 698 characters in sequence are not A, C, G, or T
Found at i:678 original size:30 final size:30
Alignment explanation
Indices: 644--705 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
634 ATATAATTGA
644 ATGTCTGCCTAATGAAACATGAAGCAAAAG
1 ATGTCTGCCTAATGAAACATGAAGCAAAAG
674 ATGTCTGCCTAATGAAACATGAAGCAAAAG
1 ATGTCTGCCTAATGAAACATGAAGCAAAAG
704 AT
1 AT
706 ATCCATTGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (30 bp):
ATGTCTGCCTAATGAAACATGAAGCAAAAG
Found at i:1792 original size:171 final size:171
Alignment explanation
Indices: 1401--2302 Score: 681
Period size: 171 Copynumber: 5.3 Consensus size: 171
1391 TTTGGTCTCA
* * * * * *
1401 AGAAACATGAAGAAAAAGATATCTAATGGCAAGAAAAGCCCATTTATAGTCACCCATACCTTCGA
1 AGAAACGTGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGA
* * * * * * * *
1466 AAACTTTATTAGTCGCTTTAAATGGTTATGTAATCTCATAATTTG-TTTTAAGTTGAATTTTTTT
66 AAACTTTATTACTCACTTTAAATGATTTTATAACCTCATAA-TTGAATTTAATTTGAATTTTTTT
********** * * *
1530 ATNNNNNNNNNNAAAACAGATTGTAATTGAATGTC-ACCCTCG
130 ATTATTTTTATTAAAATAAATTATAATTGAATGTCTA-CCTCG
* * * * **********
1572 AAAAACTTGGAGAAAAAGATATCCATTGGCAAGNNNNNNNNNNTTATAGTCACCCATGCCTTCGA
1 AGAAACGTGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGA
* * * ****
1637 AAACTTTGTTACTCCCTTTAAATGATTTTATAACCTCATAGTTGAATTTAATTTGAATTTTNNNN
66 AAACTTTATTACTCACTTTAAATGATTTTATAACCTCATAATTGAATTTAATTTGAATTTTTTTA
****** *
1702 NNNNNNTTATTAAAATAAATTATAATTGAATGTCTACCTCA
131 TTATTTTTATTAAAATAAATTATAATTGAATGTCTACCTCG
* * * * **********
1743 AGACACTTGATGAAAAAGATATCCATTGTCAAGAAAAGTCCATTTATAGTCACNNNNNNNNNNGA
1 AGAAACGTGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGA
* * * *
1808 AAGCTATATTACTCACTTTAAATGATTTTATAACCTCATAACTGATTTTAATTTGAATTTTTTTA
66 AAACTTTATTACTCACTTTAAATGATTTTATAACCTCATAATTGAATTTAATTTGAATTTTTTTA
* * *
1873 -TATTTTTTATTACAATAGATTATAATTGAATGTCTTCCTCG
131 TTA-TTTTTATTAAAATAAATTATAATTGAATGTCTACCTCG
* * * * *
1914 AGAAACGTGAAGAAAAAGATATCCATTGACAAGAAAAGTACATTTATAGTTACGCATACCTTTGA
1 AGAAACGTGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGA
**
1979 AAA-TCTTATTACTTGCTTTAAATGATTTTATAACCTCATAATTG-ATTTGACA-TTGAATTTTT
66 AAACT-TTATTACTCACTTTAAATGATTTTATAACCTCATAATTGAATTT-A-ATTTGAATTTTT
**
2041 TTA-TATTTTT-TATAAAGA-AGGTTATAATTGAATGTCTACCTCG
128 TTATTATTTTTAT-TAAA-ATAAATTATAATTGAATGTCTACCTCG
********** * * *
2084 AGAAACNNNNNNNNNNAGATATCCATTGAAAAGAAAAGTCCATATATAGTAACCCATGCCTTCGA
1 AGAAACGTGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGA
* * * * * *
2149 AAGCCTTATTACTCTCTCTAAATGATTTTATAACCTTATAATTGATTTTAATTTG-ATTTTTTTA
66 AAACTTTATTACTCACTTTAAATGATTTTATAACCTCATAATTGAATTTAATTTGAATTTTTTTA
* * * *
2213 ATATTTTTATTAAAATATATTATAATTGAATATCTATCTCG
131 TTATTTTTATTAAAATAAATTATAATTGAATGTCTACCTCG
*
2254 AGAAACGTAAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAG
1 AGAAACGTGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAG
Statistics
Matches: 567, Mismatches: 150, Indels: 29
0.76 0.20 0.04
Matches are distributed among these distances:
169 12 0.02
170 196 0.35
171 357 0.63
172 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.35
Consensus pattern (171 bp):
AGAAACGTGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGA
AAACTTTATTACTCACTTTAAATGATTTTATAACCTCATAATTGAATTTAATTTGAATTTTTTTA
TTATTTTTATTAAAATAAATTATAATTGAATGTCTACCTCG
Done.