Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399156.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_243.0, 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: 11504
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.21
Warning! 4809 characters in sequence are not A, C, G, or T
Found at i:1769 original size:172 final size:171
Alignment explanation
Indices: 1475--2371 Score: 1028
Period size: 172 Copynumber: 5.2 Consensus size: 171
1465 NNNNNNNNNN
* *
1475 AAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTATTTGTACGTTTTTGGTTAAAACAG
1 AAAT-GTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAG
* * * *
1540 ACTAGAATCGAATGTCTACCATGAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGACCA
65 ACTAGAATTGAATGTCTACCATAAGAAACATGAAGAAAAAAGCATTCATTAGCAAGAAAAGTCCA
* * *
1605 TTTATAGTCACCCATACCTTTAAAAGCCTTAGTACTCACTTT
130 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTT
*
1647 AAATGTTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTTGTTAAAACAG
1 AAATG-TTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAG
* * * * *
1712 ACTAGGATTGAATGTCTACCTTCAGAAACATGAAGAAAAAAGTATTCATTAGCAAGAAAAGTCTA
65 ACTAGAATTGAATGTCTACCATAAGAAACATGAAGAAAAAAGCATTCATTAGCAAGAAAAGTCCA
* * * * * *
1777 TTTGTAGTCACTCATTCCTTCAAGAGCATTATTACTTAGTTT
130 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTT
*** ** *
1819 AAATAGTTTTATAATCTCAAAATTGATTTAAATTTGAATGT-TTCAAACATTTTTTATTAAAATA
1 AAAT-GTTTTATAATCTCAAAATTGATTTAAATTTGAAT-TCTTTGTACATTTTTGGTTAAAACA
* * * ** *
1883 GACAAGAATTAAATGTCTACCATAAGAAACATGAAAAAAAAAGTTTTCATTAGCAAGAAAAGTCT
64 GACTAGAATTGAATGTCTACCATAAGAAACATGAAGAAAAAAGCATTCATTAGCAAGAAAAGTCC
** * *
1948 ATTTATAGTCACCCATTGGTTCGAAAA-CCTTATTAATCACTTC
129 ATTTATAGTCACCCATTCCTTC-AAAAGCCTTATTACTCACTTT
* * * * * * * * *
1991 AAATAGTTTTATAATCTTAAAATTCATTTTAAGTTCAATTTTTTTTTC-TTTTCTAGTTAAAACA
1 AAAT-GTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTT-TGGTTAAAACA
* * * * * * * * * *
2055 TATTATAATTCAATGTCTACCCTAAGAAACATAAAGAAGAAAGCATTAATTGGCAAGAGAAGTCC
64 GACTAGAATTGAATGTCTACCATAAGAAACATGAAGAAAAAAGCATTCATTAGCAAGAAAAGTCC
** * *
2120 ATTTATAGTCATTCATTCCTTCAGAAGCCTTATTACTGACTTT
129 ATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTT
* ** *
2163 AAATGGTTTTATAATCTCAAAATTAATTTAAATTTGAATTCTTTGTATGTTTTTGGTTAAAA-AA
1 AAAT-GTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAG
* * * * * *
2227 ACTAGATTTGAATATCTACCATGAGAAACATAAAGAAAAAAGCATTCATTCGCAAGAAAAGACCA
65 ACTAGAATTGAATGTCTACCATAAGAAACATGAAGAAAAAAGCATTCATTAGCAAGAAAAGTCCA
* * *
2292 TTTATAGTCACCCATACCTTCAAAACCCCTATTACTCACTTT
130 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTT
2334 AAATGTTTTTATAATCTCAAAATTGATTTAAATTTGAA
1 AAATG-TTTTATAATCTCAAAATTGATTTAAATTTGAA
2372 NNNNNNNNNN
Statistics
Matches: 607, Mismatches: 109, Indels: 19
0.83 0.15 0.03
Matches are distributed among these distances:
170 1 0.00
171 133 0.22
172 464 0.76
173 9 0.01
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (171 bp):
AAATGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTAAAACAGA
CTAGAATTGAATGTCTACCATAAGAAACATGAAGAAAAAAGCATTCATTAGCAAGAAAAGTCCAT
TTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTT
Found at i:4236 original size:157 final size:155
Alignment explanation
Indices: 3947--4248 Score: 354
Period size: 157 Copynumber: 1.9 Consensus size: 155
3937 ATTTGAATTC
* * *
3947 TTTCTACATTTTTGGTTAAAACATACTAGAATTGAAGTCTACCTTGAAAAACATGAAGAAAAAAG
1 TTTCTACATTTTTGGTTAAAACAGACTAGAATCGAAGCCTACCTTGAAAAACATGAAGAAAAAAG
* * * *********** * * *
4012 CATTCGTTGGCAAGAAAAGTCCATTNNNNNNNNNNNATGCCTTCAAAAGCCTTATTACTCGCTTT
66 CATTCATTAGCAAGAAAAGACCATTTATAGTTACGCATACCTTCAAAAGCCTTATTACCCACTTT
*
4077 AAATGGTTTTGTAATGCCGTACTTG
131 AAATGGTTTTATAATGCCGTACTTG
*
4102 TTTCGTACATTTTTGGTTAAAACAGACTAGAATCGAATGCCTACCATT-AGAAACATGAAGAAAA
1 TTTC-TACATTTTTGGTTAAAACAGACTAGAATCGAA-GCCTACC-TTGAAAAACATGAAGAAAA
*
4166 AAGCATTCATTAGCAAGAAAAGACCATTTATAGTTACGCATATCTTCAAAAGCCTTATTACCCAC
63 AAGCATTCATTAGCAAGAAAAGACCATTTATAGTTACGCATACCTTCAAAAGCCTTATTACCCAC
*
4231 TTTAAATGTTTTTATAAT
128 TTTAAATGGTTTTATAAT
4249 CTCAAAATTG
Statistics
Matches: 120, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
155 4 0.03
156 30 0.25
157 84 0.70
158 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.31
Consensus pattern (155 bp):
TTTCTACATTTTTGGTTAAAACAGACTAGAATCGAAGCCTACCTTGAAAAACATGAAGAAAAAAG
CATTCATTAGCAAGAAAAGACCATTTATAGTTACGCATACCTTCAAAAGCCTTATTACCCACTTT
AAATGGTTTTATAATGCCGTACTTG
Found at i:4910 original size:172 final size:172
Alignment explanation
Indices: 4579--4910 Score: 358
Period size: 172 Copynumber: 1.9 Consensus size: 172
4569 NNNNNNNNNN
* * * * * *
4579 AATGTACAAAACATTCCAATTTAAATCAATTTTGAGATTATAAAACCATTTAAATTGTGTAATAA
1 AATGTACAAAAAATTCAAATTTAAATCAATTTTGAGATTATAAAACAATTGAAAGTGAGTAATAA
* * ************ *
4644 GACTCTTGAAGGAATAGGTGACTATAAATAGACTTTTCTTGCCAATGNNNNNNNNNNNNTTCATG
66 GACTCTTCAAGGAATAGGTGACTATAAATAGACTTTTCTTACCAATGAATACTTTTTTCTGCATG
* * *
4709 TTTCTGAAGGAAGACTTTCAATCCTAGTCTATTTTAACCAAA
131 TTTCTCAAGGAAGACATTAAATCCTAGTCTATTTTAACCAAA
* *
4751 AATGTATAAAAAATTCAAATTTAAATCAATTTTTAGATTATAAAACAATTGAAAGTGAGTAATAA
1 AATGTACAAAAAATTCAAATTTAAATCAATTTTGAGATTATAAAACAATTGAAAGTGAGTAATAA
* * * * *
4816 GGCTTTTCAAGGGATGGGTGACTATAAATGGACTTTTCTTACCAATGAATACTTTTTTCTGCATG
66 GACTCTTCAAGGAATAGGTGACTATAAATAGACTTTTCTTACCAATGAATACTTTTTTCTGCATG
* * *
4881 TTTCTCATGGTAGACATTAAATTCTAGTCT
131 TTTCTCAAGGAAGACATTAAATCCTAGTCT
4911 NNNNNNNNNN
Statistics
Matches: 126, Mismatches: 34, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
172 126 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (172 bp):
AATGTACAAAAAATTCAAATTTAAATCAATTTTGAGATTATAAAACAATTGAAAGTGAGTAATAA
GACTCTTCAAGGAATAGGTGACTATAAATAGACTTTTCTTACCAATGAATACTTTTTTCTGCATG
TTTCTCAAGGAAGACATTAAATCCTAGTCTATTTTAACCAAA
Done.