Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402346.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5427.0, 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: 4434
ACGTcount: A:0.26, C:0.10, G:0.09, T:0.28
Warning! 1192 characters in sequence are not A, C, G, or T
Found at i:308 original size:170 final size:159
Alignment explanation
Indices: 187--504 Score: 185
Period size: 170 Copynumber: 1.9 Consensus size: 159
177 NNNNNNNNNN
*
187 TTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCTCAAAAAATATGAAGAAAAAGA
1 TTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACATCAAAAAATATGAAGAAAAAGA
* * **********
252 TATCTATTGGCAAGAAAAGTCCATTTATAATCNNNNNNNNNNTCGAAA-GCCTTATTACTCGCTT
66 TATCCATCGGCAAGAAAAGTCCATTTATAATCACCCATGCCTTC-AAATG-CTTATTACTCGCTT
*
316 TAAATGATTTTATAATCTCATATTTGATTTTAGGTTGAATTT
129 TAAATGATTTTATAATCTC--A--T-A----A--TTGATTTT
* * * * * * * *
358 TTTTATGTTTTTTTATTAAAACTGATTATAATTGAATGTTTACCTCGAGAAATGTGAAAAAAAAG
1 TTTTAT-ATTTTTTATTAAAACAGATTATAATTGAATGTCTACATCAAAAAATATGAAGAAAAAG
* * * * * * * *
423 -TATTCATTGACAA-AAAAGCCCATTTATAGTCACCCATGCCTTTGAAA-GCCTTATTACTTGTT
65 ATATCCATCGGCAAGAAAAGTCCATTTATAATCACCCATGCC-TTCAAATG-CTTATTACTCGCT
*
485 TTAAATGGTTTTATAATCTC
128 TTAAATGATTTTATAATCTC
505 NNNNNNNNNN
Statistics
Matches: 119, Mismatches: 26, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
170 51 0.43
171 17 0.14
172 51 0.43
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.39
Consensus pattern (159 bp):
TTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACATCAAAAAATATGAAGAAAAAGA
TATCCATCGGCAAGAAAAGTCCATTTATAATCACCCATGCCTTCAAATGCTTATTACTCGCTTTA
AATGATTTTATAATCTCATAATTGATTTT
Found at i:2020 original size:170 final size:159
Alignment explanation
Indices: 1824--2136 Score: 306
Period size: 169 Copynumber: 1.9 Consensus size: 159
1814 ATTTTAAATG
* * * *
1824 TTTTTATAATCTCATAATTAATTTTAAGTTGAATTTTT-TACATTTTCAGTTAAAATAAATAATA
1 TTTTTATAATCTCATAATTAATTTTAAATTAAATTTTTATA-ATTTTCA-TCAAAACAAATAATA
* * * *
1888 ATTGAATGTCTAACTCTAAAAACGTAAAGAAAAAGATATCCATTGGCAAAAAAAGTCTATTTATA
64 ATTGAATATCTAACTCGAAAAACATAAAGAAAAAGATATCCATTGGCAAAAAAAGTCCATTTAT-
*
1953 T-TTACCCATGCCTTCAAAAGCCTTATTACTC
128 TGTCACCCATGCCTTCAAAAGCCTTATTACTC
* * * *
1984 NNNNNNNNNNTTTTTATAATCTTATAATTGATTTTAAATTAAATTTTTATATTTTTTATCAAAAC
1 ----------TTTTTATAATCTCATAATTAATTTTAAATTAAATTTTTATAATTTTCATCAAAAC
* * * * * * * *
2049 AGATTATAATTGTATATCTACCTCGAGAAACATTAAGAAAAAGATATCCATTGGTAAGAAAAGTC
56 AAATAATAATTGAATATCTAACTCGAAAAACATAAAGAAAAAGATATCCATTGGCAAAAAAAGTC
2114 CATTTATTGTCACCCATGCCTTC
121 CATTTATTGTCACCCATGCCTTC
2137 NNNNNNNNNN
Statistics
Matches: 120, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
168 1 0.01
169 78 0.65
170 39 0.32
171 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.38
Consensus pattern (159 bp):
TTTTTATAATCTCATAATTAATTTTAAATTAAATTTTTATAATTTTCATCAAAACAAATAATAAT
TGAATATCTAACTCGAAAAACATAAAGAAAAAGATATCCATTGGCAAAAAAAGTCCATTTATTGT
CACCCATGCCTTCAAAAGCCTTATTACTC
Found at i:3008 original size:171 final size:160
Alignment explanation
Indices: 2810--3134 Score: 339
Period size: 171 Copynumber: 2.0 Consensus size: 160
2800 TGATTTTAAA
* ** * * * *
2810 TTAAATTTTTTTACATGTTTCATTAAAACTGATAATTATTGAATGTCTGCCTCAGGAAAC-ATGA
1 TTAAATTATTTTACATGTTTCATTAAAACAAATAATAATTCAATGTCTACCTCAAGAAACGA-GA
* * * * *
2874 AGAAAAAGATATTTATTGGCAAGAGAAGTCCATTTATAGTCA-CTCATACCTTCAAAAGCCTTAT
65 AGAAAAAGATATTCATTGCCAAGAAAAGTCCATCTACAGTCACCT-ATACCTTCAAAAGCCTTAT
*
2938 TACTTGCTTTAAATGTTTTTATAATCTTATAAT
129 TACTT-ATTTAAATGTTTTTATAATCTTATAAT
* * * *
2971 TNNNNNNNNNNTAAATTATTTTATATTTTTTATTAAAACAAATTATAATTCAATGTCTACCTCAA
1 T----------TAAATTATTTTACATGTTTCATTAAAACAAATAATAATTCAATGTCTACCTCAA
* *
3036 GAAACGAGAAGAAAAAGATATTCATTGCCAAGAAAAGTCCATCTACAGTTACCTATACCTTCGAA
56 GAAACGAGAAGAAAAAGATATTCATTGCCAAGAAAAGTCCATCTACAGTCACCTATACCTTCAAA
*
3101 AGCCTTATTACTTATTTAAATGTTTTTCTAATCT
121 AGCCTTATTACTTATTTAAATGTTTTTATAATCT
3135 AATNNNNNNN
Statistics
Matches: 132, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
161 1 0.01
170 19 0.14
171 109 0.83
172 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.37
Consensus pattern (160 bp):
TTAAATTATTTTACATGTTTCATTAAAACAAATAATAATTCAATGTCTACCTCAAGAAACGAGAA
GAAAAAGATATTCATTGCCAAGAAAAGTCCATCTACAGTCACCTATACCTTCAAAAGCCTTATTA
CTTATTTAAATGTTTTTATAATCTTATAAT
Found at i:4189 original size:171 final size:172
Alignment explanation
Indices: 4006--4434 Score: 449
Period size: 171 Copynumber: 2.5 Consensus size: 172
3996 NNNNNNNNNT
*
4006 TTTTATATTTTTTATTAAAACAGATTATAATTGAATGTTTACCTCGAAACACATGAAGAAAAAGA
1 TTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCTCGAAACACATGAAGAAAAAGA
* * * * * * *
4071 TATCCACTGGCAAGAAAAGTCCA-TTTATAATCACCCATGACTTTGAAAGCCTTATTACTCGCTT
66 TATCCATTGGCAAGAAAAGTCCACATAATAATCACCCATGACTTCGAAAGCCTTATTACGCACCT
********** * *
4135 TAAATGA-TTTNNNNNNNNNNTAATTGACTTTAAGTTGAATTG
131 TAAAT-ATTTTTATCATGTTATAATTGACTTTAAATTAAATTG
* * * *
4177 TTTTACATTTTTT-TTAAAATAGATTGTAATTGAATGTCTACCTCGTGAAAC-GA-GAAGAAAAA
1 TTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCTC--GAAACACATGAAGAAAAA
* *** ** **
4239 GATATTCATTCATAAGAAAAGTCCACATAATTTTCACCCATTCCTTCGAAAGCCTTATTACGCAC
64 GATATCCATTGGCAAGAAAAGTCCACATAATAATCACCCATGACTTCGAAAGCCTTATTACGCAC
* *
4304 CTTAAATATTTTTATCATGTTATAATTGATTTTAAATTAAATTT
129 CTTAAATATTTTTATCATGTTATAATTGACTTTAAATTAAATTG
* *
4348 TTTTATATTTTTTATTAAAACAGTTTATAATTGTATGTCTA-CTCGAGAA-ACATGAAGAAAAAG
1 TTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCTCGA-AACACATGAAGAAAAAG
4411 ATATCCATTGGCAAGAAAAGTCCA
65 ATATCCATTGGCAAGAAAAGTCCA
Statistics
Matches: 206, Mismatches: 44, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
169 2 0.01
170 61 0.30
171 115 0.56
172 28 0.14
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.36
Consensus pattern (172 bp):
TTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCTCGAAACACATGAAGAAAAAGA
TATCCATTGGCAAGAAAAGTCCACATAATAATCACCCATGACTTCGAAAGCCTTATTACGCACCT
TAAATATTTTTATCATGTTATAATTGACTTTAAATTAAATTG
Done.