Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400797.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3972.0, 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: 3185
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.28
Warning! 749 characters in sequence are not A, C, G, or T
Found at i:1265 original size:171 final size:171
Alignment explanation
Indices: 976--1284 Score: 404
Period size: 171 Copynumber: 1.8 Consensus size: 171
966 NNNNNNNNNN
* *
976 AAAATAGACAATAATTCAATGTCTACTTAGAGAAACGCGAAGAAAAATGCATTCATTGGAAAAAA
1 AAAATAGACAATAATTCAATGTCTACTTAGAGAAACGCGAAGAAAAAAGCATTCATTCGAAAAAA
* ********** *
1041 AAGTCCCTTTATAGTTACCCATTCCTTCAAAAGCCTTNNNNNNNNNNTTAAATTGTTTTATAATC
66 AAGTCCCTTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCATTTTAAATTATTTTATAATC
1106 TCATAATTGATTTCAAGTTGATTTTTTTTATATTTTTGATT
131 TCATAATTGATTTCAAGTTGATTTTTTTTATATTTTTGATT
* * * * * * *
1147 AAAATATACTATAATTCAATGTTTACTTAGAGAAACGTGAAGAAAAACAG-ATTTATTCGCAAGA
1 AAAATAGACAATAATTCAATGTCTACTTAGAGAAACGCGAAGAAAAA-AGCATTCATTCGAAAAA
*
1211 AAAGTCCCTTTATAGTCACGCATTCCTTCAAAAGCCTTATTACTCATTTTAAATTATTTTATAAT
65 AAAGTCCCTTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCATTTTAAATTATTTTATAAT
1276 CTCATAATT
130 CTCATAATT
1285 NNNNNNNNNN
Statistics
Matches: 115, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
171 114 0.99
172 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.36
Consensus pattern (171 bp):
AAAATAGACAATAATTCAATGTCTACTTAGAGAAACGCGAAGAAAAAAGCATTCATTCGAAAAAA
AAGTCCCTTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCATTTTAAATTATTTTATAATC
TCATAATTGATTTCAAGTTGATTTTTTTTATATTTTTGATT
Found at i:3057 original size:171 final size:167
Alignment explanation
Indices: 2523--3080 Score: 482
Period size: 171 Copynumber: 3.3 Consensus size: 167
2513 NNNNNNNNNN
* *
2523 TACTTAGAGAAACGTGAAG-AAAAGGGATTCATTGGCAAGAAAAGTCTATTTATAATT-ACCCAT
1 TACTTAGAGAAACGTGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCTATTTAT-ATTCA-CTAT
* * * ** *
2586 TCCTTCAAATGCTTTATTACTCGCTTTAAATTATTTATAATCTCATAATTGATTTTACGTTGAAT
64 TCCTTCAAAAGCCTTATTACTCGCTTAAAAGGATTTATAATCTCATAATTGA-TTTAAGTTGAA-
* * * *
2651 TTTTTTATGTTTTTGATTAAAATAGACTATAATTGAATGTT
127 TTTTTTATATTTTTCATTAAAACAGACTATAATTGAATGTC
* * * ** *
2692 TACCTT-GTGAAATGTGAAGAAAAAGGCATTCATTGGTAAGAAAAGTCCGTTTATAGTCAGCTAT
1 TA-CTTAGAGAAACGTGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCTATTTATATTCA-CTAT
* * * * * * * *
2756 TCCTTCCAAAGCCTTATTATTTGTTTTAAATGGTTTTATAAACACATAATTGATTCTAAGTTGAA
64 TCCTTCAAAAGCCTTATTACTCG-CTTAAAAGGATTTATAATCTCATAATTGATT-TAAGTTGAA
2821 TTTTTGTATATTTTTCATTAAAACAGACTATAATTGAATGTC
127 TTTTT-TATATTTTTCATTAAAACAGACTATAATTGAATGTC
* * *
2863 TGTA-TCAG-GAAACCT-ATAGAAAAAGTCATTCATTGAG-AAGAAAAGTCTATTTATATTCACT
1 --TACTTAGAGAAACGTGA-AGAAAAAGGCATTCATTG-GCAAGAAAAGTCTATTTATATTCACT
********* *
2924 AATTCCTTCAAAAGCCTTATTACTCGCTNNNNNNNNNNTTATAATCTCATAATTGATTTAAAATT
62 -ATTCCTTCAAAAGCCTTATTACTCGCT-TAAAAGGATTTATAATCTCATAATTGATTT-AAGTT
* * * * *
2989 AAATTATTTTATATTTTTTATTAAAACATACTATAATTCAATATC
124 GAATT-TTTTATATTTTTCATTAAAACAGACTATAATTGAATGTC
*** *
3034 TACTTAGAGAAACGTGAAGAAAAACATATTCGTTGGCAAGAAAAGTC
1 TACTTAGAGAAACGTGAAGAAAAAGGCATTCATTGGCAAGAAAAGTC
3081 CCTTNNNNNN
Statistics
Matches: 309, Mismatches: 61, Indels: 36
0.76 0.15 0.09
Matches are distributed among these distances:
169 17 0.06
170 71 0.23
171 213 0.69
172 6 0.02
173 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.38
Consensus pattern (167 bp):
TACTTAGAGAAACGTGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCTATTTATATTCACTATTC
CTTCAAAAGCCTTATTACTCGCTTAAAAGGATTTATAATCTCATAATTGATTTAAGTTGAATTTT
TTATATTTTTCATTAAAACAGACTATAATTGAATGTC
Done.