Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401945.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5044.0, 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: 1766
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.33
Warning! 195 characters in sequence are not A, C, G, or T
Found at i:324 original size:170 final size:169
Alignment explanation
Indices: 1--1290 Score: 853
Period size: 170 Copynumber: 7.6 Consensus size: 169
* * * * * * *
1 TAAGTTAAATTTTTTTACATTTTTAGTTAAAATAGACAATAATTGAATGTTTACTTTG-AGAAAC
1 TAAGTTGAATTTTTTTACATTTTTAGCTAAAACAGACTATAATTGAATG-CTGCCTTGAAGAAAC
* * * *
65 ATGAAAAAAATACATTCATTGGCAAGAAAAGTC-ATTTTATAGTCACTCATTCCTTT-AAAAGCC
65 GTGAAAAAAA-CCATTCATTGGCAA-AAAAGTCTA-TTTATAGTCACCCATTACTTTCAAAAGCC
********** * *
128 TTATTNNNNNNNNNNAATTATTTTATAATCCCAAAATTGATTT
127 TTATTACTCGCTTTAAATTATTTTATAATCTCATAATTGATTT
* * * * *
171 TAAGTTGAATTTTTTCATATTTTTAGTTAAAATAGACTATAATTGAATGACTGTCTT-AAGAAAC
1 TAAGTTGAATTTTTTTACATTTTTAGCTAAAACAGACTATAATTGAATG-CTGCCTTGAAGAAAC
* * * *
235 ATGTAAAAGAAACCATTCATTAAG-AAAAAAATCTATTTATAGTCATCCATT-CTTTCAAAAGCC
65 GTG-AAAA-AAACCATTCATT-GGCAAAAAAGTCTATTTATAGTCACCCATTACTTTCAAAAGCC
** * * *
298 TTATTACTAACTTTAAATTGTTTTATAATATTATAATTGATTT
127 TTATTACTCGCTTTAAATTATTTTATAATCTCATAATTGATTT
** * * * *
341 TAAGTCAAATTTTTTTACATTGTT-GCTCAAACAAACTATAATTGAATGACTGCCTT-AAGAAAT
1 TAAGTTGAATTTTTTTACATTTTTAGCTAAAACAGACTATAATTGAATG-CTGCCTTGAAGAAAC
* * * * * * *
404 GTGCAAAAAGAGCTACTCATTAAGAAAAAAAGTCTATTTATAGTCACCCATTGC-TTCAAAAGCT
65 GTG-AAAAA-AACCATTCATT-GGCAAAAAAGTCTATTTATAGTCACCCATTACTTTCAAAAGCC
********** *
468 TTATTACTCGCTTTAAATTATTTTATANNNNNNNNNNTAATTT
127 TTATTACTCGCTTTAAATTATTTTATAATCTCATAATTGATTT
* * ** *
511 TAAGTTGAATTTTTTTACATTTTTAGCTAAAACAGACTATAATTAAAT-TTTTCTTGGAGAAACG
1 TAAGTTGAATTTTTTTACATTTTTAGCTAAAACAGACTATAATTGAATGCTGCCTTGAAGAAACG
* ** * *
575 TGAAGAAAAATGCATTTGTTGGTAAGAAAAGTCTATTTATAGTCACCCATT-CTTTCAAAAGGCT
66 TGAA-AAAAA-CCATTCATTGGCAA-AAAAGTCTATTTATAGTCACCCATTACTTTCAAAAGCCT
*
639 TATTATTCGCTTTAAATTATTTTATAATCTCATAATTGATTT
128 TATTACTCGCTTTAAATTATTTTATAATCTCATAATTGATTT
* * * * ** ** *
681 GAAGTTGAAGTTTTTTACACTTTTTA-CTAAAACAGACTACAATTAAATTTTTACTTGGAGAAAC
1 TAAGTTGAATTTTTTTACA-TTTTTAGCTAAAACAGACTATAATTGAATGCTGCCTTGAAGAAAC
* * * *
745 GTGACGAAAAACACAATT-GTTGGCAGGAAAAGTCTATTTATAGTCACCCATT-CCTTCAAAAGC
65 GTGA--AAAAA-ACCATTCATTGGCA-AAAAAGTCTATTTATAGTCACCCATTACTTTCAAAAGC
* ********** * *
808 TTTATNNNNNNNNNNAAATTGTGTTATAATCTCATAATTGATTT
126 CTTATTACTCGCTTTAAATTATTTTATAATCTCATAATTGATTT
* * * * *
852 TAAGTTGAATTTTATTTACATTTTTGGC-AAAACAAACTATAATCGAATGTCTACC-TCAAGAAA
1 TAAGTTGAATTTT-TTTACATTTTTAGCTAAAACAGACTATAATTGAATG-CTGCCTTGAAGAAA
* * * * * *
915 CATGAAAAAAAAGCATTCATTGGCAAGAGAGGTCCATTTATAGTCACCCATTCCTTT-AAAAGCC
64 CGTG-AAAAAAACCATTCATTGGCAA-AAAAGTCTATTTATAGTCACCCATTACTTTCAAAAGCC
* * *
979 TTATTACTCGTTTTAAATTATGTTATAATC-CTAAAATTGATTT
127 TTATTACTCGCTTTAAATTATTTTATAATCTC-ATAATTGATTT
* *** * * * * * *
1022 TAAGTTGACTTTTTTTTACATTTACGGTTAAAA-ACACTATAACTGAATGCCGGCCTTGAACAAC
1 TAAGTTGA-ATTTTTTTACATTTTTAGCTAAAACAGACTATAATTGAATG-CTGCCTTGAAGAAA
* *
1086 CGTGCAAAAAAAACCATTCATTGAGGAAAAAAGTCCATTTATAGTCACCCATTAC-TTCAAAAGC
64 CGTG--AAAAAAACCATTCATTG-GCAAAAAAGTCTATTTATAGTCACCCATTACTTTCAAAAGC
* * * ** * *
1150 CCTATTACTCCCTTTAGATTGCTTTACAATCTCATAATTGACTT
126 CTTATTACTCGCTTTAAATTATTTTATAATCTCATAATTGATTT
* * ** ** *
1194 TAAGTTGAATTTATTTATAC-TTTTTA-CTGAAACAGACTATAATTAAATTTTTACTAG-AGAAA
1 TAAGTTGAATTT-TTT-TACATTTTTAGCTAAAACAGACTATAATTGAATGCTGCCTTGAAGAAA
*
1256 CGTGAAGAAAAACACATTCGTTGGCAAGAAAAGTC
64 CGTGAA-AAAAAC-CATTCATTGGCAA-AAAAGTC
1291 CANNNNNNNN
Statistics
Matches: 877, Mismatches: 201, Indels: 84
0.75 0.17 0.07
Matches are distributed among these distances:
168 3 0.00
169 79 0.09
170 457 0.52
171 203 0.23
172 126 0.14
173 9 0.01
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.36
Consensus pattern (169 bp):
TAAGTTGAATTTTTTTACATTTTTAGCTAAAACAGACTATAATTGAATGCTGCCTTGAAGAAACG
TGAAAAAAACCATTCATTGGCAAAAAAGTCTATTTATAGTCACCCATTACTTTCAAAAGCCTTAT
TACTCGCTTTAAATTATTTTATAATCTCATAATTGATTT
Found at i:1235 original size:172 final size:171
Alignment explanation
Indices: 919--1235 Score: 372
Period size: 172 Copynumber: 1.8 Consensus size: 171
909 AAGAAACATG
* * * * * *
919 AAAAAAAAGCATTCATTGGCAAGAGAGGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATT
1 AAAAAAAACCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTACTTCAAAAGCCCTATT
** * * * *
984 ACTCGTTTTAAATTATGTTATAATCCTAAAATTGATTTTAAGTTGACTTTTTTTTACATTTACGG
66 ACTCCCTTTAAATTATGTTACAATCCTAAAATTGACTTTAAGTTGAATTTTTTATACATTTAC-G
*
1049 TTAAAAACACTATAACTGAATGCCGGCCTTGAACAACCGTGC
130 TGAAAAACACTATAACTGAATGCCGGCCTTGAACAACCGTGC
*
1091 AAAAAAAACCATTCATTGAGGAA-AAAAGTCCATTTATAGTCACCCATTACTTCAAAAGCCCTAT
1 AAAAAAAACCATTCATTG-GCAAGAAAAGTCCATTTATAGTCACCCATTACTTCAAAAGCCCTAT
* * * *
1155 TACTCCCTTTAGATTGCT-TTACAAT-CTCATAATTGACTTTAAGTTGAATTTATTTATACTTTT
65 TACTCCCTTTAAATT-ATGTTACAATCCT-AAAATTGACTTTAAGTTGAATTT-TTTATAC-ATT
* *
1218 TAC-TGAAACAGACTATAA
126 TACGTGAAAAACACTATAA
1236 TTAAATTTTT
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
171 2 0.02
172 103 0.86
173 10 0.08
174 5 0.04
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.35
Consensus pattern (171 bp):
AAAAAAAACCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTACTTCAAAAGCCCTATT
ACTCCCTTTAAATTATGTTACAATCCTAAAATTGACTTTAAGTTGAATTTTTTATACATTTACGT
GAAAAACACTATAACTGAATGCCGGCCTTGAACAACCGTGC
Done.