Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403109.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_776.0, 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: 4515
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.28
Warning! 1011 characters in sequence are not A, C, G, or T
Found at i:2268 original size:170 final size:167
Alignment explanation
Indices: 1972--2560 Score: 539
Period size: 170 Copynumber: 3.5 Consensus size: 167
1962 NNNNNNNNGC
* * * * * * * *
1972 AGACATTTAATTATAATCTGTATTAATAAAAAATGTAAAAAAGTTCAACTGACAACCAATTATGA
1 AGACATTCAATTATAATCTGTTTTAAT-AAAAATATAAAAAA-TTCAAATTAAAATCAAGTATGA
* * ** * * *
2037 GATTA-AAAAACTACTTAAAGTGAGTAATAAGGCTTTTGAAGGTATAGGTGACTACAAATGGACC
64 GGTTATAAAATC-A-TT-AAGCAAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATGGACC
* * *
2101 TTTTTTGCCAATGGATATCTTTTTCTTCATATTTGTCAAGGT
126 TTTTTTACCAATGGATATCTTTTTCTTCATATTTCTCGAGGT
* *
2143 AGACATTCAAGTATAATATGTTTTAATAAAAATATAATAAAATTCAAATTAAAATCAAGTATGAG
1 AGACATTCAATTATAATCTGTTTTAATAAAAATATAA-AAAATTCAAATTAAAATCAAGTATGAG
********* *
2208 GTTATAAAATCAGTTANNNNNNNNNNTAAGGCTTTCAAAGGCATAGGTGACTATAAATGGA-CTT
65 GTTATAAAATCA-TTA-AGCAAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATGGACCTT
* * * * *
2272 TTCTTACTAATGGATATCTTTTTCTTTACATGTCTGGAGGT
128 TT-TTACCAATGGATATCTTTTTCTTCATATTTCTCGAGGT
* * * *
2313 AAACATTCAATTATAATCTTTTTTAATAACATATTATAAAAAAATTTAAATTAAAATCAAGGTAT
1 AGACATTCAATTATAATCTGTTTTAATAA-A-AATAT-AAAAAATTCAAATTAAAATCAA-GTAT
*
2378 GAAGTTATAAAATCATTAAGCAAGTAATAAGGCTTTCGAA-GCATA-GTGGAC-ATAAATGGACC
62 GAGGTTATAAAATCATTAAGCAAGTAATAAGGCTTTCGAAGGCATAGGT-GACTATAAATGGACC
* * *
2440 ----TTACCTATGGATATCTTTTTCTTCATGTTTCTCGAGGC
126 TTTTTTACCAATGGATATCTTTTTCTTCATATTTCTCGAGGT
* * * *
2478 AGACATTTAATTATGATCTGTTTTAATAAAAAATATTAAACAATTCAAATTAAAATCAATTATGA
1 AGACATTCAATTATAATCTGTTTTAAT-AAAAATA-TAAAAAATTCAAATTAAAATCAAGTATGA
2543 GGTTATAAAATCACTTAA
64 GGTTATAAAATCA-TTAA
2561 AGCGAGNNNN
Statistics
Matches: 337, Mismatches: 68, Indels: 33
0.77 0.16 0.08
Matches are distributed among these distances:
163 17 0.05
164 27 0.08
165 55 0.16
166 2 0.01
169 17 0.05
170 128 0.38
171 45 0.13
172 26 0.08
173 20 0.06
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (167 bp):
AGACATTCAATTATAATCTGTTTTAATAAAAATATAAAAAATTCAAATTAAAATCAAGTATGAGG
TTATAAAATCATTAAGCAAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATGGACCTTTTT
TACCAATGGATATCTTTTTCTTCATATTTCTCGAGGT
Found at i:3126 original size:170 final size:172
Alignment explanation
Indices: 2937--3251 Score: 408
Period size: 170 Copynumber: 1.8 Consensus size: 172
2927 NNNNNNNNNA
* * *
2937 TGGACTTTTCTTGCCAATGGATATCTTTTTCTTCC-CGTTTCTAAATGCAGAAATTAAATTATAA
1 TGGACTTTTCTTACCAATGGATATCTTTTT-GTCCACGTTTCTAAAGGCAGAAATTAAATTATAA
*
3001 TC-TATTTTAATGAAAAA-TAT-AAAAAAA-TAAAATTAAAA-TCAATTCTGAGGTTATAAAATC
65 TCGTATTTTAA--AAAAATTATAAAAAAAATTAAAATTAAAACT-AATTATGAGGTTATAAAATC
*
3061 ATTTAAAGCGAGTAATAAAACTTTTGAAGGCGTGGGTGACTATAAG
127 ATTTAAAGCAAGTAATAAAACTTTTGAAGGCGTGGGTGACTATAAG
* ** ** *
3107 TGGACTTTTCTTACCAATGGATATCTTTTTGTCCAGGTTTCTTGAGGCAGACGTTTAATTATAAT
1 TGGACTTTTCTTACCAATGGATATCTTTTTGTCCACGTTTCTAAAGGCAGAAATTAAATTATAAT
* * * *
3172 CTGTTTTTTAAAAAAATTATAAAAAAAATTCAACTTAAAACTAATTATGAGGTTATACAATCATT
66 C-GTATTTTAAAAAAATTATAAAAAAAATTAAAATTAAAACTAATTATGAGGTTATAAAATCATT
3237 TAAAGCAAGTAATAA
130 TAAAGCAAGTAATAA
3252 GGCTTTNNNN
Statistics
Matches: 123, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
169 3 0.02
170 58 0.47
171 3 0.02
172 14 0.11
173 44 0.36
174 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (172 bp):
TGGACTTTTCTTACCAATGGATATCTTTTTGTCCACGTTTCTAAAGGCAGAAATTAAATTATAAT
CGTATTTTAAAAAAATTATAAAAAAAATTAAAATTAAAACTAATTATGAGGTTATAAAATCATTT
AAAGCAAGTAATAAAACTTTTGAAGGCGTGGGTGACTATAAG
Found at i:4173 original size:171 final size:169
Alignment explanation
Indices: 3887--4320 Score: 494
Period size: 171 Copynumber: 2.5 Consensus size: 169
3877 NNNTTCAACT
** * * * *
3887 TAAAATCAATTATGAGGCTATAAAAACATTTAAGCCGAGTAATAAGGATTTAGAAGGCATGGATA
1 TAAAATCAATTATGAGATTATAAAATCATTTAAG-CAAGTAATAAGG-TTTCGAAGGCATGGATG
* * * * * *
3952 ACCATAAATAGACTTTTCTTACCAATGGATATCTATTTCTTCTCGTTTCTCGAGGTAGACATTCT
64 ACTATAAATGGACTTTTCTTGCCAATGGATATCTATCTCTTCTCGTTTCTCGAGGCAGACATTCA
* * *
4017 ATTATAATCTGATATAATAAAAAATATAAAAAAATTTAAAT
129 ATTATAATCTGATATAATAAAAAATATAAAAAAACTCAAAC
* *
4058 TAAAATCTATTAT-ACGATTATAAAATCATTTAAAGCAAGTAATAAGGCTTTCGAAAGCATGGAT
1 TAAAATCAATTATGA-GATTATAAAATCATTT-AAGCAAGTAATAAGG-TTTCGAAGGCATGGAT
*
4122 GACTATAAATGGACATTTCTTGCCAATGGATATCTATCTCTTCAT-GTTTCTCGAGGCAGACATT
63 GACTATAAATGGACTTTTCTTGCCAATGGATATCTATCTCTTC-TCGTTTCTCGAGGCAGACATT
********** *
4186 CAATTANNNNNNNNNNTTATAAAAAATATAAAAAAACTCAAAC
127 CAATTATAATCTGATATAATAAAAAATATAAAAAAACTCAAAC
* * *
4229 TAAAATCAATTATGAGGTTATAAAATTATTTGAAGCAAGTAATAAGGTTTCGAAGGCATGGGTGA
1 TAAAATCAATTATGAGATTATAAAATCATTT-AAGCAAGTAATAAGGTTTCGAAGGCATGGATGA
*
4294 CTATAAATGGACTTTTCTTGTCAATGG
65 CTATAAATGGACTTTTCTTGCCAATGG
4321 TAAACATTCA
Statistics
Matches: 221, Mismatches: 38, Indels: 9
0.82 0.14 0.03
Matches are distributed among these distances:
170 42 0.19
171 174 0.79
172 5 0.02
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.32
Consensus pattern (169 bp):
TAAAATCAATTATGAGATTATAAAATCATTTAAGCAAGTAATAAGGTTTCGAAGGCATGGATGAC
TATAAATGGACTTTTCTTGCCAATGGATATCTATCTCTTCTCGTTTCTCGAGGCAGACATTCAAT
TATAATCTGATATAATAAAAAATATAAAAAAACTCAAAC
Done.