Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401684.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_48.0, 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: 3343
ACGTcount: A:0.26, C:0.10, G:0.09, T:0.25
Warning! 951 characters in sequence are not A, C, G, or T
Found at i:1757 original size:172 final size:172
Alignment explanation
Indices: 977--2062 Score: 776
Period size: 172 Copynumber: 6.3 Consensus size: 172
967 AACATATAAT
* * * * * * * *
977 AATTGAACGTCTAC-CTCGAGAAACATAAAGAAGAGAGCATTCATTAGAAAGAAAAGTCCAATTA
1 AATTGAATGTCTACATTC-AGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTA
*
1041 TAGTCAGCC-TTCCCTTCAAAAGCCTTATTACTCACTTTAAATGTTTTTATAATCTCAAAATTGA
65 TAGTCACCCATT-CCTTCAAAAGCCTTATTACTCACTTTAAATGTTTTTATAATCTCAAAATTGA
********** * *
1105 NNNNNNNNNNAATTCTTTGTATATTTTTGATTAAAACAGACTACG
129 TTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTA-G
* * * *
1150 -ATTGAATGTCTACATTCAGAAACATGAAG-AAAAAGTATTTATTGGTAAGAAAAGTCCATTTAA
1 AATTGAATGTCTACATTCAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTAT
**********
1213 AGTCACCCATTCCTTCAAAAGCCTTNNNNNNNNNNTTAAATGTTTTTATAATCTCAAAATTGATT
66 AGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGTTTTTATAATCTCAAAATTGATT
* * *
1278 TAAATTTGAATTCTTTGTCCAGTTTTGGTTCAAACAGACTAG
131 TAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAG
* * * * * * *
1320 AATTGAATGTCTACCTTAAGAAACATAAAGAAAAAAGTAGTCATTGGTAAGAAAAGTCCATTGAT
1 AATTGAATGTCTACATTCAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTAT
* * * * * * ** ****
1385 AGTCACCCATACCATCAAAGGCCTTATTACTCGCTTTAAATGGTTTTGTAATGC-CGTAATNNNN
66 AGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGTTTTTATAAT-CTCAAAATTGAT
****** * * * * * *
1449 NNNNNNTTGAATTTTTTTTATATTTTTTGTT-AAACAAACTAT
130 TTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAG
* * * * * * *
1491 AATTGAATGTTTAC-CT-AGAAAATATAAAGAAAAATGCATTCATTAGCAAGAAATGTCCATTTA
1 AATTGAATGTCTACATTCAG-AAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTA
********* * *
1554 TAGTCACCCATT-CTTNNNNNNNNNNTATTACTCACTTTAAATAG-TTTTATAATCTTAAAATTA
65 TAGTCACCCATTCCTT-CAAAAGCCTTATTACTCACTTTAAAT-GTTTTTATAATCTCAAAATTG
* ** *
1617 ATTTAAATTTGAATTCTTTGTGCATTTTTTATTAAAACTGACTAG
128 ATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAG
* * * *
1662 GATTGAATGTCTACATTCAGAAACATGAAGAAAAAGGCATTCATTGGCATGAGAAGTCCATTTAT
1 AATTGAATGTCTACATTCAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTAT
* * * * ******
1727 AGTCACCCATTCCCTCAAAAGCCTTATTACTCACATTAAATGGTTTTATAATGTCAAAANNNNNN
66 AGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGTTTTTATAATCTCAAAATTGATT
**** * *
1792 NNNNTTTGAATTCTTTGTACATTTTTTGTTAACA-AGAACTAG
131 TAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAG-ACTAG
* * * **********
1834 GATTGAGTGTCTACCTTCAGAAACATGAAGAAANNNNNNNNNNTTGGCAAGAAAAGTCCATTTAT
1 AATTGAATGTCTACATTCAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTAT
* * * * * *
1899 AGTCGCCCATTCCTTCAAGAGCCTTATTACTCAGTTTAAATGATTTTACAGTCTCAAAATTGATT
66 AGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGTTTTTATAATCTCAAAATTGATT
* * *
1964 TAAATTTGAATGT-TTTGAACATTTTTGGTTAAAATAGAGTAG
131 TAAATTTGAAT-TCTTTGTACATTTTTGGTTAAAACAGACTAG
* *
2006 AACTGAATGTCTACCATT-AGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGT
1 AATTGAATGTCTA-CATTCAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGT
2063 NNNNNNNNNN
Statistics
Matches: 684, Mismatches: 211, Indels: 37
0.73 0.23 0.04
Matches are distributed among these distances:
169 5 0.01
170 96 0.14
171 174 0.25
172 396 0.58
173 13 0.02
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.33
Consensus pattern (172 bp):
AATTGAATGTCTACATTCAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTAT
AGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGTTTTTATAATCTCAAAATTGATT
TAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAG
Found at i:3080 original size:172 final size:171
Alignment explanation
Indices: 2781--3277 Score: 593
Period size: 172 Copynumber: 2.9 Consensus size: 171
2771 TTTTTTTTGC
* * * * * * ** * * *
2781 TTTTCTGGTTAAAACATATTATAATTGAGTATCTACCCCGAGAAACAAAAAGAAAAGAGCATTCG
1 TTTT-TGGTTAAAACAGACTAGAATTGAATGTCTACCACGAGAAACATGAAGAAAAAAGTATTCA
* * * * **
2846 TTGGCAAGAAAAGTCCATTTATAGTCACCCTTTCCTTCAAAACCTTTATTACTCACTTTAAATAT
65 TTGGGAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAGCC-TTATTACTCACTTTAAATGG
2911 TTTTATAATCTCAAAATTGATTTAAATTTCAAT-TCTTCGTACA
129 TTTTATAATCTCAAAATTGATTTAAATTTCAATAT-TTCGTACA
* *
2954 TTTTTGGTTAAAACAGACTAGGATTGAATGTCTACCTTC-AGAAACATGAAGAAAAAAGTATTCA
1 TTTTTGGTTAAAACAGACTAGAATTGAATGTCTACC-ACGAGAAACATGAAGAAAAAAGTATTCA
* * * *
3018 TTGGGAACAAAAGTCTATTTATACTCACCCATTCCTTCAAGAGCCTTATTACTAAGTTTAAATGG
65 TTGGGAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAA-AGCCTTATTACTCACTTTAAATGG
* * **
3083 TTTTATAATCTCAAAATTGATTTAAATTTTAATATTTTGTGTA
129 TTTTATAATCTCAAAATTGATTTAAATTTCAATATTTCGTACA
* * *
3126 TTTTTGGTTAAAATAGACTAGAATTGATTGTCTACCACGAGATACATGAAGAAAAAAGTATTCAT
1 TTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCACGAGAAACATGAAGAAAAAAGTATTCAT
* * * * * *
3191 TGAGAAGAACAGTCTTTTTATAGTCACCCACTGCTTCAAAAGCCTTATTAATCACTTTAAATGGT
66 TGGGAAGAAAAGTCTATTTATAGTCACCCATTCCTTC-AAAGCCTTATTACTCACTTTAAATGGT
*
3256 TTTATAATCTTAAAATTGATTT
130 TTTATAATCTCAAAATTGATTT
3278 TAAGTCCATT
Statistics
Matches: 277, Mismatches: 42, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
171 1 0.00
172 265 0.96
173 11 0.04
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (171 bp):
TTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCACGAGAAACATGAAGAAAAAAGTATTCAT
TGGGAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAGCCTTATTACTCACTTTAAATGGTT
TTATAATCTCAAAATTGATTTAAATTTCAATATTTCGTACA
Done.