Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402652.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5720.0, 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, 804
Length: 1340
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.34
Warning! 157 characters in sequence are not A, C, G, or T
Found at i:516 original size:171 final size:169
Alignment explanation
Indices: 1--832 Score: 516
Period size: 171 Copynumber: 4.9 Consensus size: 169
* * * * *
1 TTTAAGTTGAATTTTTTTACATTTTTTATTAAAACAGACTATAATTGCATGTCTACCAT-AAGAA
1 TTTAAGTTGAATTTTTTTATA-TTTTCATTAAAACAGACTATAATTGAATGTTTACC-TCGAGAA
* * ** * * * * *
65 ACATTAATAAAAGAA-CATTCATTGGCAAGAAAACTCTATTTATAGTCTCCCAGTCCTTCAAAAG
64 ACATGAAGAAAA-AAGCATTCATTGATAAGAAAAGTCCATTTATAGCCTCACATTCCTTCAAAAG
********
129 CCTTNNNNNNNNNNT-TAAAT-GATTTTATAATCTAATAATTGAT
128 CCTT--TTGCTCGTTCTAAATAG-TTTTATAATCTAATAATTGAT
* * * * * * * * * * *
172 TTTATGTTAAATGTTTTTACATTTTTGATTGAAATAGA-TAATAATTGATTGTCTATCTCAAGAA
1 TTTAAGTTGAATTTTTTTATA-TTTTCATTAAAACAGACT-ATAATTGAATGTTTACCTCGAGAA
* * * * ** *
236 ACATGAAGAAAAAA-CATTCATTTG-TAAGAAAAGTCCATTTATAGTCACCCATTTCACCAAAAC
64 ACATGAAGAAAAAAGCATTCA-TTGATAAGAAAAGTCCATTTATAGCCTCACATTCCTTCAAAAG
* * **********
299 CCTTATTACTCACTT-TAAATCA-TTTTATANNNNNNNNNNTGAT
128 CCTT-TTGCTC-GTTCTAAAT-AGTTTTATAATCTAATAATTGAT
* * * * * *
342 TTTAGGTTGAATTTTTTTATATTTTCCCTTAAAACAGACTACAATTAAATGTTTGCCTTGAGAAA
1 TTTAAGTTGAATTTTTTTATATTTT-CATTAAAACAGACTATAATTGAATGTTTACCTCGAGAAA
* *
407 CATGAAGAAAAAAGCATTCATTTGATAAGAAAAGTCTATTTATAGCCTCACATTCCTTCAACAGC
65 CATGAAGAAAAAAGCATTCA-TTGATAAGAAAAGTCCATTTATAGCCTCACATTCCTTCAAAAGC
472 CTTTTGCTCGTTCTAAATAGTTTTATAATCTAATAATTGAT
129 CTTTTGCTCGTTCTAAATAGTTTTATAATCTAATAATTGAT
* * * * * * *
513 TTTAAGTTAAATTTTTGTATATTCTTGATGAAAACAGACAATAATTGAATGTTTATCTCAAGAAA
1 TTTAAGTTGAATTTTTTTATATT-TTCATTAAAACAGACTATAATTGAATGTTTACCTCGAGAAA
* * ** ********** *
578 -ATTGAAGAAAAAAGTATTAATTGGCAAGAAAAGTCCATTTATNNNNNNNNNNTGCTTCAAAAGC
65 CA-TGAAGAAAAAAGCATTCATTGATAAGAAAAGTCCATTTATAGCCTCACATTCCTTCAAAAGC
** * * *
642 CTTATCACTCGCTT-TAAATGGTTTTATACTCTTATAATTGAT
129 CTT-TTGCTCG-TTCTAAATAGTTTTATAATCTAATAATTGAT
* * * * * * *
684 TTTAAGTTGACTTTTTTTATATTTTTTATTAAAGCAGGCTATAATTGAATATCTCCCTCGAGAAA
1 TTTAAGTTGAATTTTTTTATA-TTTTCATTAAAACAGACTATAATTGAATGTTTACCTCGAGAAA
* * * * *
749 CATGAAGAAAAAAGCATTCATTAATAAGATAAGTCCATTTATAGCCTCTCATTCCTTTAATAGCC
65 CATGAAGAAAAAAGCATTCATTGATAAGAAAAGTCCATTTATAGCCTCACATTCCTTCAAAAGCC
814 TTTTTGCTCGTTCTAAATA
130 -TTTTGCTCGTTCTAAATA
833 NNNNNNNNNN
Statistics
Matches: 495, Mismatches: 146, Indels: 40
0.73 0.21 0.06
Matches are distributed among these distances:
169 4 0.01
170 154 0.31
171 294 0.59
172 43 0.09
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (169 bp):
TTTAAGTTGAATTTTTTTATATTTTCATTAAAACAGACTATAATTGAATGTTTACCTCGAGAAAC
ATGAAGAAAAAAGCATTCATTGATAAGAAAAGTCCATTTATAGCCTCACATTCCTTCAAAAGCCT
TTTGCTCGTTCTAAATAGTTTTATAATCTAATAATTGAT
Found at i:1267 original size:170 final size:170
Alignment explanation
Indices: 960--1340 Score: 464
Period size: 170 Copynumber: 2.2 Consensus size: 170
950 NNNNNNNNNN
* * * * * *
960 AAAAGCATTTATTGGCAAGAAAAGTCTATTTACAGCCTCTCATTCCTTCAAAAGTACCTTATTAC
1 AAAAGCATTCATTGGCAAGAAAAGTCAATTTATAGTCACTCATTCCTTCAAAAG-ACCTTATTAA
* * * *
1025 CCATTTTAAATGATTTTATAATCTAACAACTAATTTTTAGTTGATTTTTTTACATTTTTTATTAA
65 CCACTTTAAATGATTTTATAATCTAACAACTAATTTTAAGTTGATTTTATTACATTTTTGATTAA
* *
1090 AACAAATAATAATTGAATGTTTATCTCA-AGAAACATGAAGA
130 AACAAATAATAATTAAATGTCTATCT-AGAGAAACATGAAGA
*
1131 GAAAAGCATTCATTGGCAAAAAAAGTCAATTTATAGTCAC-CAATTCCTTCAAAAG-CCTTATTA
1 -AAAAGCATTCATTGGCAAGAAAAGTCAATTTATAGTCACTC-ATTCCTTCAAAAGACCTTATTA
* * * * * * *
1194 ATCGCTTTAAATGA-TTTCTAATCTCATAATTGATTTTAAGTTGAATTTTATTACATTTTTGATT
64 ACCACTTTAAATGATTTTATAATCTAACAACTAATTTTAAGTTG-ATTTTATTACATTTTTGATT
* * *
1258 AACACAAATAATAATTAAATGTCTGTCTAGAGAAACGTGAAGA
128 AAAACAAATAATAATTAAATGTCTATCTAGAGAAACATGAAGA
* *
1301 AAAAGTATTCATTGGCAAGAAAAGTCCATTTATAGTCACT
1 AAAAGCATTCATTGGCAAGAAAAGTCAATTTATAGTCACT
Statistics
Matches: 179, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
169 60 0.34
170 72 0.40
171 1 0.01
172 46 0.26
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.37
Consensus pattern (170 bp):
AAAAGCATTCATTGGCAAGAAAAGTCAATTTATAGTCACTCATTCCTTCAAAAGACCTTATTAAC
CACTTTAAATGATTTTATAATCTAACAACTAATTTTAAGTTGATTTTATTACATTTTTGATTAAA
ACAAATAATAATTAAATGTCTATCTAGAGAAACATGAAGA
Done.