Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399043.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2319.0, 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: 7746
ACGTcount: A:0.18, C:0.07, G:0.06, T:0.19
Warning! 3847 characters in sequence are not A, C, G, or T
Found at i:629 original size:171 final size:170
Alignment explanation
Indices: 326--710 Score: 459
Period size: 171 Copynumber: 2.2 Consensus size: 170
316 NNNNNNNNNN
* * * * *
326 TTTTTTTATATTTTTCATTAAAACAGACTATAATTGAATGTCTGCCTTGACAATTATGAAGAAAA
1 TTTTTTTA-ATTTTTCATTAAAACAGACAATAATTAAATGTCTCCCTTGACAATAAGGAAGAAAA
* * * * * * * *
391 AAGCATTCATTGATAAGAAAAGTTGATTTATAGCCTTCTATTCCTTTAATAGCCTTTTTACTCAT
65 AACCATTCATTGACAAGAAAAGTTGATTTATAGCCTCCCATTCCATCAAAAGCCTTATTACTCAT
* *
456 TTTAAATAATTTTATATTCTCATAATTAAATTTAAGTTCAA
130 TTTAAATAATTTTATAATCTAATAATTAAATTTAAGTTCAA
* * *
497 TTTTTTTACATTTTTCATTAAAACAAACAATAGTTAAATGTCTCCCTTGAGAA-AAGGGAAGAAA
1 TTTTTTTA-ATTTTTCATTAAAACAGACAATAATTAAATGTCTCCCTTGACAATAA-GGAAGAAA
*
561 AAACCATTCATTGACAAGAAAAGTCT-ATTTATAGCCTCCCATTCCATCAAAAGCCTTATTATTC
64 AAACCATTCATTGACAAGAAAAGT-TGATTTATAGCCTCCCATTCCATCAAAAGCCTTATTACTC
* * * * *
625 ATTTTAAATGATTTTCTAATCTAATAATTGATTTTAAGTTGAA
128 ATTTTAAATAATTTTATAATCTAATAATTAAATTTAAGTTCAA
* * * *
668 TTTTTTTAACTTTTTGATCAAAACAGACAACAATTAATTGTCT
1 TTTTTTTAA-TTTTTCATTAAAACAGACAATAATTAAATGTCT
711 ATCNNNNNNN
Statistics
Matches: 180, Mismatches: 31, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
170 2 0.01
171 177 0.98
172 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.41
Consensus pattern (170 bp):
TTTTTTTAATTTTTCATTAAAACAGACAATAATTAAATGTCTCCCTTGACAATAAGGAAGAAAAA
ACCATTCATTGACAAGAAAAGTTGATTTATAGCCTCCCATTCCATCAAAAGCCTTATTACTCATT
TTAAATAATTTTATAATCTAATAATTAAATTTAAGTTCAA
Found at i:3428 original size:170 final size:161
Alignment explanation
Indices: 3142--3474 Score: 366
Period size: 170 Copynumber: 2.0 Consensus size: 161
3132 TTAAGTTGAA
* * *
3142 TTTTTTTACATTTTTGATTAAAACAGATAATAATTGACTGACTATCTCAAGAAACATCAAGACAA
1 TTTTTTTACATTTTTGATTAAAACAAACAACAATTGACTGACTATCTCAAGAAACATCAAGACAA
* ** ***
3207 AAGTATTCAATGGCAAGAAAAGTCTATTTATAATCTTTCATTCCCTCAAAAGCCTTATTACTC-A
66 AAGCATTCAATCACAAGAAAAGTCTATTTATAATCACGCATTCCCTCAAAAGCCTTATTACTCGA
*
3271 TTTAAATAGTTTTTTAATCTAATAATTGATT
131 TTTAAATAGTCTTTTAATCTAATAATTGATT
* *
3302 TNNNNNNNNNNTTTTTTACATTTTTGATTAAAACAAACAACACTTGACT-ATCTATCTCGAGAAA
1 T----------TTTTTTACATTTTTGATTAAAACAAACAACAATTGACTGA-CTATCTCAAGAAA
* ** * *
3366 CATGAAGACAAAAGCATTCCTTCACAAGAAAAGTCT-TTTGATAGTCACGCATTCCTTCAAAAGC
55 CATCAAGACAAAAGCATTCAATCACAAGAAAAGTCTATTT-ATAATCACGCATTCCCTCAAAAGC
* *
3430 CTTATTACTCGCTTTAAATAGTCTTTTAATCTCATAATTGATT
119 CTTATTACTCGATTTAAATAGTCTTTTAATCTAATAATTGATT
3473 TT
1 TT
3475 AGGTTGAATT
Statistics
Matches: 141, Mismatches: 19, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
160 1 0.01
161 1 0.01
169 4 0.03
170 105 0.74
171 30 0.21
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.37
Consensus pattern (161 bp):
TTTTTTTACATTTTTGATTAAAACAAACAACAATTGACTGACTATCTCAAGAAACATCAAGACAA
AAGCATTCAATCACAAGAAAAGTCTATTTATAATCACGCATTCCCTCAAAAGCCTTATTACTCGA
TTTAAATAGTCTTTTAATCTAATAATTGATT
Found at i:6114 original size:170 final size:161
Alignment explanation
Indices: 5859--6176 Score: 275
Period size: 170 Copynumber: 1.9 Consensus size: 161
5849 AACAGACTAT
* * *
5859 AATTGAATATTTTCCTCGAGAAACGTAAAGAAAAAAGTATTCCTTGACAAGAAAAGCCCATTTAT
1 AATTGAATATTTACCTCGAGAAACGTAAAGAAAAAAGTATTCATTGACAAAAAAAGCCCATTTAT
* * * * * *
5924 AGTCACCCTTTTCTTCAAAAGTCATATTAGTA-ACTTCAAAT-GGTTTATAATCTCATATTTGAT
66 AGTCACCCTTTCCTTCAAAAGCCATATT-GCATACTTCAAATAGGTTTATAAACTAATAATTGAT
5987 CTTAAGTTGAATATTTTTACATTTTTCATTAA
130 CTTAAGTTGAATATTTTTACATTTTTCATTAA
* * * * * *
6019 NNNNNNNNNNAATTGAATGTTTACCTCTAGAAATGTGAAGAGAAAAGTATTCATTGGCAAAAAAA
1 ----------AATTGAATATTTACCTCGAGAAACGTAAAGAAAAAAGTATTCATTGACAAAAAAA
* * * * * * *
6084 GTCTATTTATAG-C-CTCTAATTCCTTCAAAAGCCTTATTGCATGCTTTAAATAGTTTTATAAAC
56 GCCCATTTATAGTCACCCT--TTCCTTCAAAAGCCATATTGCATACTTCAAATAGGTTTATAAAC
* *
6147 TAATAATTGATTTTAAGTTGAATTTTTTTA
119 TAATAATTGATCTTAAGTTGAATATTTTTA
6177 NNNNNNNNNN
Statistics
Matches: 120, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
168 3 0.03
169 3 0.03
170 79 0.66
171 35 0.29
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37
Consensus pattern (161 bp):
AATTGAATATTTACCTCGAGAAACGTAAAGAAAAAAGTATTCATTGACAAAAAAAGCCCATTTAT
AGTCACCCTTTCCTTCAAAAGCCATATTGCATACTTCAAATAGGTTTATAAACTAATAATTGATC
TTAAGTTGAATATTTTTACATTTTTCATTAA
Done.