Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402560.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5632.0, 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: 2624
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.30
Warning! 597 characters in sequence are not A, C, G, or T
Found at i:716 original size:171 final size:170
Alignment explanation
Indices: 182--822 Score: 506
Period size: 171 Copynumber: 3.7 Consensus size: 170
172 TTTTTTATAT
* * * ***
182 TTTTTTACATTTTTTATGAAAATAGATTATAATTGAATGTTTGCCTCAAGAAACGTGAAGAANNN
1 TTTTTTATATTTTATATTAAAATAGATTATAATTGAATGTTTGCCTCAAGAAACGTGAAGAAAAA
******** **
247 NNNNNNNNTTGGCAAGAAAAGTCTATTTATAGTCACCCATGCTTTCAAAAGCTTTATTACTCCCT
66 GATATCCATTGGCAAGAAAAGTCTATTTATAGTCACCCATGCTTTCAAAAGCTTTATTACTAGCT
312 CCGAAGGATTTTATAACCTCATAATTGATTTTAATTTGAA
131 CCGAAGGATTTTATAACCTCATAATTGATTTTAATTTGAA
******* *
352 TTTTTNNNNNNNNNNT-TATTAAAATAGATTATAATTGAATGTTTGCCTCTAGAAACGTGAAGAA
1 TTTTT---TATATTTTATATTAAAATAGATTATAATTGAATGTTTGCCTCAAGAAACGTGAAGAA
* * ** ** *
416 GAAGATATCCATTGGTAAGAAAAGTCCGTTTATAGTCACTAATGCCTTT-GAAAGAC-TTATTAC
63 AAAGATATCCATTGGCAAGAAAAGTCTATTTATAGTCACCCATG-CTTTCAAAAG-CTTTATTAC
*** ** * * *
479 TAG-TTTTAAATAGTTTT-TTACTCTCATAGTT-ACTTTTAAGTTGAA
126 TAGCTCCGAAGGA-TTTTATAAC-CTCATAATTGA-TTTTAATTTGAA
* ********** * * * *
524 CTNNNNNNNNNNTATTATTAAAACAGATTATAATT-ATATATTTACCTCAAGAAACGTAAAGAAA
1 TTTTTTATATTTTA-TATTAAAATAGATTATAATTGA-ATGTTTGCCTCAAGAAACGTGAAGAAA
* *
588 AAGATATCTATTGGCAAGAAAAGTCTATTTATAGTCACCCATGCTTTCAAAAGCTTTATTACTTG
64 AAGATATCCATTGGCAAGAAAAGTCTATTTATAGTCACCCATGCTTTCAAAAGCTTTATTACTAG
653 CTCCGAAGGATTTTATAACCTCATAATTGATTTTAATTTGAAA
129 CTCCGAAGGATTTTATAACCTCATAATTGATTTTAATTTG-AA
* * *
696 TTTTTTATATTTTATATTAAAATAGATTATAATTGAATGTTTGCCTCCAGAAATGTGAAGTAAAA
1 TTTTTTATATTTTATATTAAAATAGATTATAATTGAATGTTTGCCTCAAGAAACGTGAAGAAAAA
** * * * * * *
761 GATATCCATTAGTAAAAAAAAGT-TCATTTATAGTTACCCACGCCTTCCAAAGCCTTATTACT
66 GATATCCATT-GGCAAGAAAAGTCT-ATTTATAGTCACCCATGCTTTCAAAAGCTTTATTACT
823 CGCTTTNNNN
Statistics
Matches: 362, Mismatches: 89, Indels: 38
0.74 0.18 0.08
Matches are distributed among these distances:
169 8 0.02
170 11 0.03
171 172 0.48
172 165 0.46
173 6 0.02
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.36
Consensus pattern (170 bp):
TTTTTTATATTTTATATTAAAATAGATTATAATTGAATGTTTGCCTCAAGAAACGTGAAGAAAAA
GATATCCATTGGCAAGAAAAGTCTATTTATAGTCACCCATGCTTTCAAAAGCTTTATTACTAGCT
CCGAAGGATTTTATAACCTCATAATTGATTTTAATTTGAA
Found at i:2008 original size:171 final size:170
Alignment explanation
Indices: 1448--2624 Score: 886
Period size: 171 Copynumber: 6.9 Consensus size: 170
1438 NNNNNNNNNC
* * * *
1448 CTCATAATT-GATTTTAATTTAAACTTTTTTATATTTTTTACTAAAACAGATTACAACTGAATGT
1 CTCATAATTAG-TTTTAATTTGAA-TTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGT
** * * * * **
1512 CTGCCTTGAGAAACGTGAAGAAAAAGATATCCA-TGGCAAAAAAAGTCCATTTATAGTAACGTAT
64 CTGCCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTTCATTTATAGTCACCCAT
** *
1576 GCCTTCCGAAGCCTTATTACTCGCTTTAAATGCTTTTTTAAT
129 GCCTTCAAAAGCTTTATTACTCGCTTTAAATGCTTTTTTAAT
* * **
1618 CTTATAATTAGGTTTAGGTTGAACTTTTTTATATATTTTT-TTAAAACAGATTATAATTGAATGT
1 CTCATAATTAGTTTTAATTTGAA-TTTTTTATAT-TTTTTATTAAAACAGATTATAATTGAATGT
********** * * * * * *
1682 CNNNNNNNNNNAACATAAAGAAAAAGATATCAATTGGCAAGAAAAGTCCATTTACAGTCATCTAT
64 CTGCCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTTCATTTATAGTCACCCAT
* * ** **
1747 GCCTTCGAAAGCCTTATTACTCTTTTTAAATAATTTTTTAAT
129 GCCTTCAAAAGCTTTATTACTCGCTTTAAATGCTTTTTTAAT
* * * ********** * * *
1789 CTCATACTTAATTTT-TTGTTGAACNNNNNNNNNNTTATTATTAAAACAGATCATAATTGTATGT
1 CTCATAATTAGTTTTAAT-TTGAA-TTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGT
* ** *
1853 TTAACTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTTGATTTATAGTCACCCAT
64 CTGCCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTTCATTTATAGTCACCCAT
*
1918 GCTTTCAAAAGCTTTATTACTCGCTTTAAATGCTTTTTTAAT
129 GCCTTCAAAAGCTTTATTACTCGCTTTAAATGCTTTTTTAAT
* * * *
1960 CTTATAATTAGTTTTAATTTGAATTTGTTTCTATTTTTTATGAAAACAGATTATAATTGAATGTT
1 CTCATAATTAGTTTTAATTTGAATTT-TTTATATTTTTTATTAAAACAGATTATAATTGAATGTC
* *
2025 TGGCC-CGAGAAACATGAAGAAAAAGATATCCATTGGCAAGGAAAGTTCATTTATAGTCACCCAT
65 T-GCCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTTCATTTATAGTCACCCAT
* * * * *
2089 GCTTTCAAAAGCTTTATTACTCGCTCTAAAGGAC-TTTATAAC
129 GCCTTCAAAAGCTTTATTACTCGCTTTAAATG-CTTTTTTAAT
**********
2131 CTCATAATNNNNNNNNNNTTGAATTTTTTATA-TTTTTATTAAAACAGATTATAATTGAATGTCT
1 CTCATAATTAGTTTTAATTTGAATTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCT
* * * * *
2195 GCCTCGAGAAGCTTGAGGAAAAAGATATCCATTGGCAAGAAAAGTTCATTTATAGTCACCCTTGC
66 GCCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTTCATTTATAGTCACCCATGC
* * * * *
2260 TTTCAAAAGCTTTATTACTCGCTCTAAAGGAC-TTTATAAC
131 CTTCAAAAGCTTTATTACTCGCTTTAAATG-CTTTTTTAAT
********** *
2300 CTCATNNNNNNNNNNAATTTTAATTTTTTATA-TTTTTATTAAAACAGATTATAATTGAATGTCT
1 CTCATAATTAGTTTTAATTTGAATTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCT
* * * ** *
2364 GTCTCAAGAAGCTTGAAGAAAAAGATATCCATTGGCAAGAAAAG-TCTATTTATAGTTGCCCATA
66 GCCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTTC-ATTTATAGTCACCCATG
* * * **********
2428 CCTTCGAAAGCTTTATCACTCGCCTTAAATNNNNNNNNNNT
130 CCTTCAAAAGCTTTATTACTCGCTTTAAATGCTTTTTTAAT
* * * * *
2469 CTCATAGTTACTTTTAAGTTGAATTTTTTTATATTTATTATTAAAATAGATTATAATT-ACATGT
1 CTCATAATTAGTTTTAATTTGAA-TTTTTTATATTTTTTATTAAAACAGATTATAATTGA-ATGT
* * * * * * * *
2533 TTACCTTAAGAAACGT-AAGGAAAAAGATATTCATTAGAAAGAAAAG-TCTATTTATAGTCACCG
64 CTGCCTCAAGAAACATGAA-GAAAAAGATATCCATTGGCAAGAAAAGTTC-ATTTATAGTCACCC
* *
2596 ATACCTTCAAAAGCCTTATTACTCGCTTT
127 ATGCCTTCAAAAGCTTTATTACTCGCTTT
Statistics
Matches: 809, Mismatches: 182, Indels: 31
0.79 0.18 0.03
Matches are distributed among these distances:
168 5 0.01
169 272 0.34
170 89 0.11
171 440 0.54
172 3 0.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.36
Consensus pattern (170 bp):
CTCATAATTAGTTTTAATTTGAATTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCT
GCCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTTCATTTATAGTCACCCATGC
CTTCAAAAGCTTTATTACTCGCTTTAAATGCTTTTTTAAT
Found at i:2278 original size:340 final size:328
Alignment explanation
Indices: 1826--2450 Score: 732
Period size: 340 Copynumber: 1.9 Consensus size: 328
1816 NNNNNNNTTA
* *
1826 TTATTAAAACAGATCATAATTGTATGTTTAACTCAAGAAACATGAAGAAAAAGATATCCATTGGC
1 TTATTAAAACAGATCATAATTGAATGTCTAACTCAAGAAACATGAAGAAAAAGATATCCATTGGC
* * *
1891 AAGAAAAGTTGATTTATAGTCACCCATGCTTTCAAAAGCTTTATTACTCGCTTTAAATG-CTTTT
66 AAGAAAAGTTCATTTATAGTCACCCATGCTTTCAAAAGCTTTATTACTCGCTCTAAAGGAC-TTT
* * * *
1955 TTAATCTTATAATTAGTTTTAATTTGAATTTGTTTCTATTTTTTATGAAAACAGATTATAATTGA
130 ATAACCTCATAATTAGTTTTAATTTGAATTT-TTTATA-TTTTTATGAAAACAGATTATAATTGA
* * *
2020 ATGTTTGGCCCGAGAAACATGAAGAAAAAGATATCCATTGGCAAGGAAAGT-TCATTTATAGTCA
193 ATGTCTGGCCCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCT-ATTTATAGTCA
* * *
2084 CCCATGCTTTCAAAAGCTTTATTACTCGCTCTAAAGGACTTTATAACCTCATAATNNNNNNNNNN
257 CCCATACCTTCAAAAGCTTTATCACTCGCTCTAAAGGACTTTATAACCTCATAAT----------
2149 TTGAATTTTTTATATTT
312 TTGAATTTTTTATATTT
* ** * * * *
2166 TTATTAAAACAGATTATAATTGAATGTCTGCCTCGAGAAGCTTGAGGAAAAAGATATCCATTGGC
1 TTATTAAAACAGATCATAATTGAATGTCTAACTCAAGAAACATGAAGAAAAAGATATCCATTGGC
*
2231 AAGAAAAGTTCATTTATAGTCACCCTTGCTTTCAAAAGCTTTATTACTCGCTCTAAAGGACTTTA
66 AAGAAAAGTTCATTTATAGTCACCCATGCTTTCAAAAGCTTTATTACTCGCTCTAAAGGACTTTA
********** * *
2296 TAACCTCATNNNNNNNNNNAATTTTAATTTTTTATATTTTTATTAAAACAGATTATAATTGAATG
131 TAACCTCATAATTAGTTTTAATTTGAATTTTTTATATTTTTATGAAAACAGATTATAATTGAATG
* * * * **
2361 TCTGTCTCAAGAAGCTTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCTATTTATAGTTGCCCA
196 TCTGGCCCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCTATTTATAGTCACCCA
*
2426 TACCTTCGAAAGCTTTATCACTCGC
261 TACCTTCAAAAGCTTTATCACTCGC
2451 CTTAAATNNN
Statistics
Matches: 241, Mismatches: 42, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
338 103 0.43
339 6 0.02
340 131 0.54
341 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.35
Consensus pattern (328 bp):
TTATTAAAACAGATCATAATTGAATGTCTAACTCAAGAAACATGAAGAAAAAGATATCCATTGGC
AAGAAAAGTTCATTTATAGTCACCCATGCTTTCAAAAGCTTTATTACTCGCTCTAAAGGACTTTA
TAACCTCATAATTAGTTTTAATTTGAATTTTTTATATTTTTATGAAAACAGATTATAATTGAATG
TCTGGCCCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTCTATTTATAGTCACCCA
TACCTTCAAAAGCTTTATCACTCGCTCTAAAGGACTTTATAACCTCATAATTTGAATTTTTTATA
TTT
Done.