Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401655.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4772.0, 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: 4232
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.23
Warning! 1619 characters in sequence are not A, C, G, or T
Found at i:671 original size:171 final size:172
Alignment explanation
Indices: 335--671 Score: 430
Period size: 172 Copynumber: 2.0 Consensus size: 172
325 NNAGCGAGTA
* * * * *
335 ATAAGCCTTTTGAAGGAATGGGTGGCTGTAAATGGACTTTTTTTATTAAAGAATGCTTGTTTCTT
1 ATAAGCATTTCGAAAGAAAGGGTGGCTGTAAATGGACTTTTTTTATTAAAGAATGCTTCTTTCTT
* * *
400 TATATTTCTCCAGGTAAACATATAATTATACTCTCTTTTAATTCAAAATGTAAAAACAATTCAAC
66 CACATTTCTCCAGGTAAACATATAATTATACTCTCTTTTAATTAAAAATGTAAAAACAATTCAAC
465 TTAAAATCAATTACAAGATTATAAAAACATTTAAAGATAGTG
131 TTAAAATCAATTACAAGATTATAAAAACATTTAAAGATAGTG
* *
507 ATAAGCATTTCGAAAGAAAGGGTGGCTGTAAATGGACTTTTTTCTGTTAATGAATGCTTCTTTCT
1 ATAAGCATTTCGAAAGAAAGGGTGGCTGTAAATGGACTTTTTT-TATTAAAGAATGCTTCTTTCT
* ** * * * *
572 TCACGTTTCT-CATGGTAGGCAT-TCAATTATAGTCTGTTTTAA-TAAAAATGTTAAAA-AATTT
65 TCACATTTCTCCA-GGTAAACATAT-AATTATACTCTCTTTTAATTAAAAATGTAAAAACAATTC
** * *
633 AACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAG
128 AACTTAAAATCAATTACAAGATTATAAAAACATTTAAAG
672 CGAGNNNNNN
Statistics
Matches: 141, Mismatches: 21, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
171 39 0.28
172 54 0.38
173 48 0.34
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.38
Consensus pattern (172 bp):
ATAAGCATTTCGAAAGAAAGGGTGGCTGTAAATGGACTTTTTTTATTAAAGAATGCTTCTTTCTT
CACATTTCTCCAGGTAAACATATAATTATACTCTCTTTTAATTAAAAATGTAAAAACAATTCAAC
TTAAAATCAATTACAAGATTATAAAAACATTTAAAGATAGTG
Found at i:1264 original size:171 final size:171
Alignment explanation
Indices: 802--1265 Score: 495
Period size: 171 Copynumber: 2.7 Consensus size: 171
792 NNNNNNNNNN
* * *
802 TGTTTCTTAAGATAGACATTCAATTATA-CTCTGTTTTAATCAAAAATGTAAAAATATTCAATTT
1 TGTTTCTCAAGGTAGACATTCAATTATAGCTCTGTTTTAATCAAAAATGTAAAAA-ATTCAACTT
* *
866 AAAATCAATTATGAGATTATAAAACTATCTAATGAGAGTAATAAGCCTTTTGAAGAAATGAGTGA
65 AAAATCAATTATGAGATTATAAAACTATCTAAAGAGAGTAATAAGCCTTTTGAAGGAATGAGTGA
*
931 CTGTAAATGGACTTTTCTTATCAATGAATGTTTGTTTCTTCA
130 CTGTAAATGGACTTTTCTTATCAATGAATGCTTGTTTCTTCA
* * * *
973 TGTTTCTCTAGGGAAACTTTCAATTAT-GCTCTGTTTTAATCAAAAATGTAAAAAATTCAACTTA
1 TGTTTCTCAAGGTAGACATTCAATTATAGCTCTGTTTTAATCAAAAATGTAAAAAATTCAACTTA
***************** * * **
1037 AAATCAATTATGAGATTANNNNNNNNNNNNNNNNNAGTAATAAGCCTTTCGAAGGAATGGGTGGT
66 AAATCAATTATGAGATTATAAAACTATCTAAAGAGAGTAATAAGCCTTTTGAAGGAATGAGTGAC
* * * *
1102 TGTAAATGGACTTTCTTTTGTTAATGTATGCTTGTTTCTTCA
131 TGTAAATGGACTTT-TCTTATCAATGAATGCTTGTTTCTTCA
* *
1144 TGTTTCTCAAGGTAGACATTCAATTATAGCT-TGTTTTAATAAAAAATATAAAAAA-TCTAACTT
1 TGTTTCTCAAGGTAGACATTCAATTATAGCTCTGTTTTAATCAAAAATGTAAAAAATTC-AACTT
* * * * *
1207 AAAATCAATTATGAGATTATAAAACTATTTAAAGTGTGTAGTAAGGCTTTTGAAGGAAT
65 AAAATCAATTATGAGATTATAAAACTATCTAAAGAGAGTAATAAGCCTTTTGAAGGAAT
1266 AGNNNNNNNN
Statistics
Matches: 228, Mismatches: 61, Indels: 8
0.77 0.21 0.03
Matches are distributed among these distances:
170 68 0.30
171 157 0.69
172 3 0.01
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.37
Consensus pattern (171 bp):
TGTTTCTCAAGGTAGACATTCAATTATAGCTCTGTTTTAATCAAAAATGTAAAAAATTCAACTTA
AAATCAATTATGAGATTATAAAACTATCTAAAGAGAGTAATAAGCCTTTTGAAGGAATGAGTGAC
TGTAAATGGACTTTTCTTATCAATGAATGCTTGTTTCTTCA
Done.