Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400676.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3861.0, 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: 1684
ACGTcount: A:0.25, C:0.10, G:0.07, T:0.26
Warning! 533 characters in sequence are not A, C, G, or T
Found at i:925 original size:171 final size:168
Alignment explanation
Indices: 514--1039 Score: 510
Period size: 171 Copynumber: 3.1 Consensus size: 168
504 NNNNNNNNNN
*
514 ATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGATTTAAATTATTTTATAATATCATAATTGA
1 ATAGTCACCCATTCCTTTAAAAGCCTTATTACTCGATTTAAATTATTTTATAATATCATAATTGA
* * * * * * *
579 TTTTAAGTTGAATTTTTTTACATTTGTGGCT-AAACATACTATAATTGAATTTTTA-CTTGAAGA
66 TTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAACAAACTATAATTGAA-TGTCACCTT-AGGA
* ** *
642 AACGTGAAGAAACACA-CATTTGTTGGTAAGAAAAGT-CTATTT
129 AACATGAAGAAA-A-AGCATTCATTAG-AAGAAAAGTCCT-TTT
* * **********
684 ATAATCACCCATTCCTTTAAAAGCCTTATTACTCGTTTTAAATTATTTNNNNNNNNNNTAATTGA
1 ATAGTCACCCATTCCTTTAAAAGCCTTATTACTCGATTTAAATTATTTTATAATATCATAATTGA
* * *
749 TTTTAAGTTGAATTGTTTTACATTTTTAATTAAAACAAACAATAATTGAATGTCAACCTTAGGAA
66 TTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAACAAACTATAATTGAATGTC-ACCTTAGGAA
*
814 ACATGAAGAAAAAGGCAATCATTAGCAAGAAAAGTCCTTTT
130 ACATGAAGAAAAA-GCATTCATTAG-AAGAAAAGTCCTTTT
* * * * * * *
855 ATAGTCACACATTCCTTTAAAAGCTTTATTACTCGCTTTAAATTATTTTATAATTTTAAAATTAA
1 ATAGTCACCCATTCCTTTAAAAGCCTTATTACTCGATTTAAATTATTTTATAATATCATAATTGA
* * *
920 TTTTAAGTT--ATTTTTTTAAATTTTTAGTTAAAACAAACTATAATTGAATG-CCCGCTTTGAGA
66 TTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAACAAACTATAATTGAATGTCAC-CTTAG-GA
*
982 AACATGTAA-AAAAAGCTATTCATTGAGAAGAAAAGTCCATTT
129 AACATG-AAGAAAAAGC-ATTCATT-AGAAGAAAAGTCCTTTT
*
1024 ATAGTAACCCATTCCT
1 ATAGTCACCCATTCCT
1040 NNNNNNNNNN
Statistics
Matches: 290, Mismatches: 55, Indels: 23
0.79 0.15 0.06
Matches are distributed among these distances:
167 1 0.00
168 7 0.02
169 85 0.29
170 85 0.29
171 107 0.37
172 5 0.02
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.38
Consensus pattern (168 bp):
ATAGTCACCCATTCCTTTAAAAGCCTTATTACTCGATTTAAATTATTTTATAATATCATAATTGA
TTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAACAAACTATAATTGAATGTCACCTTAGGAAA
CATGAAGAAAAAGCATTCATTAGAAGAAAAGTCCTTTT
Done.