Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399584.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2838.0, 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: 2802
ACGTcount: A:0.24, C:0.09, G:0.08, T:0.25
Warning! 935 characters in sequence are not A, C, G, or T
Found at i:2093 original size:171 final size:169
Alignment explanation
Indices: 1715--2234 Score: 431
Period size: 171 Copynumber: 3.0 Consensus size: 169
1705 NNNNNNNNNT
* * * * *
1715 AGTCACCCATTCC-TTCAAAAGCCTTTTTACTCGGTTTAAATTGTTTTATAATCACATAATTGAT
1 AGTCACCCATTCCTTTAAAAAG-CTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGAT
* * * * *
1779 TTTAAGTTGAATTTTTCTACATTTTT-AGTTAGAACAGAC-ATTAATTAAATGCTTGCCTTGAGA
65 TTTAAGTTGAATTTTTC-ACATTTTTGA-TTAAAACAG-CTA-TAATTGAATGTTTACCTTAAGA
* * * * * *
1842 AACATGCAA-AAAAAGTAATTTATTGAGAAAAAAAGTCCATTTAT
126 AACATG-AAGAAACAGTCATTCATTGACAAGAAAAGTCCATTTAG
********** *
1886 AGTCACCCATTCCTTTAAAANNNNNNNNNNTCGCTTTAAATGGTTTTATAGTCTCATAATTGATT
1 AGTCACCCATTCCTTTAAAAAGCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATT
* *
1951 TTATGTTGAATGTTTTCACATTTTTGATTAAAACATGCTATAATTGAATGTTTACCTCAAGAAAC
66 TTAAGTTGAAT-TTTTCACATTTTTGATTAAAACA-GCTATAATTGAATGTTTACCTTAAGAAAC
* **
2016 ATGAAGAAACAGTCATTCATTGATAAGAAAAGTGTATTTAG
129 ATGAAGAAACAGTCATTCATTGACAAGAAAAGTCCATTTAG
***********
2057 AGTCACCCATTCCTTTAAAAAGCTTATTACTCGCTTTNNNNNNNNNNNTAATCTCATAATTGATT
1 AGTCACCCATTCCTTTAAAAAGCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATT
* * * * **
2122 TTAAGTT-AATTTTTTTTACATTTTTGATTAAAATAAACTATAATTGAATGTCTATTTTAAGAAA
66 TTAAGTTGAA--TTTTTCACATTTTTGATTAAAA-CAGCTATAATTGAATGTTTACCTTAAGAAA
* *
2186 CGTGTAGAAACAAG-CATTCATTGACAAGAAAAGTCCATTTAG
128 CATGAAGAAAC-AGTCATTCATTGACAAGAAAAGTCCATTTAG
2228 AGTCACC
1 AGTCACC
2235 NNNNNNNNNN
Statistics
Matches: 274, Mismatches: 65, Indels: 20
0.76 0.18 0.06
Matches are distributed among these distances:
170 4 0.01
171 253 0.92
172 17 0.06
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.37
Consensus pattern (169 bp):
AGTCACCCATTCCTTTAAAAAGCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATT
TTAAGTTGAATTTTTCACATTTTTGATTAAAACAGCTATAATTGAATGTTTACCTTAAGAAACAT
GAAGAAACAGTCATTCATTGACAAGAAAAGTCCATTTAG
Found at i:2660 original size:171 final size:161
Alignment explanation
Indices: 2483--2802 Score: 313
Period size: 171 Copynumber: 1.9 Consensus size: 161
2473 ATTTTTTAAT
* ** * *
2483 ATTTTTCTTTAAAATAGACTTTAATTGAAAGCCTGCCT-TAGGAAAGGTGTAGAAAAAGCCATTA
1 ATTTTTCTTTAAAACAGACAATAATTGAAAGCCTACCTCTA-GAAAGGTGAAGAAAAAGCCATTA
* * **
2547 ATTGAGAAGAAAAATCTATTTTTAGTCACCCATTCTTTCAAAAGCCTCATT-ACTCGATTTAAAT
65 ATTGACAAGAAAAATCCATTTAGAGTCACCCATTCTTTCAAAAGCCT-ATTCACTCGATTTAAAT
2611 -GATTTTATAATCTCATAATTGATTNNNNNNNNNNCGTTTTTAC
129 AG-TTTTATAATCTCATAATTGATT----------CGTTTTTAC
* * * * * *
2654 ATTTTTCTTTAAAACAGACAATAATTGAATGTCTATCTCTAGAAATGTGAAGAAAAAGTCATTCA
1 ATTTTTCTTTAAAACAGACAATAATTGAAAGCCTACCTCTAGAAAGGTGAAGAAAAAGCCATTAA
* * * * * *
2719 TTGACATGAAAAGTCCATTTAGAGTCACCGATTCTTTCAAAAGGCTTTTCACTCGCTTTAAATAG
66 TTGACAAGAAAAATCCATTTAGAGTCACCCATTCTTTCAAAAGCCTATTCACTCGATTTAAATAG
2784 TTTTATAATCTCATAATTG
131 TTTTATAATCTCATAATTG
Statistics
Matches: 125, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
170 2 0.02
171 120 0.96
172 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.36
Consensus pattern (161 bp):
ATTTTTCTTTAAAACAGACAATAATTGAAAGCCTACCTCTAGAAAGGTGAAGAAAAAGCCATTAA
TTGACAAGAAAAATCCATTTAGAGTCACCCATTCTTTCAAAAGCCTATTCACTCGATTTAAATAG
TTTTATAATCTCATAATTGATTCGTTTTTAC
Done.