Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402427.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5506.0, 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, 894
Length: 1490
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.35
Warning! 424 characters in sequence are not A, C, G, or T
Found at i:77 original size:20 final size:21
Alignment explanation
Indices: 52--91 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
42 TGTAGATAAT
*
52 TTTAAAATTTATTT-AGTTTA
1 TTTAAAAGTTATTTAAGTTTA
72 TTTAAAAGTTATTTAAGTTT
1 TTTAAAAGTTATTTAAGTTT
92 TAATTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAAAAGTTATTTAAGTTTA
Found at i:102 original size:17 final size:17
Alignment explanation
Indices: 80--116 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
70 TATTTAAAAG
*
80 TTATTTAAGTTTTAATT
1 TTATTTAAGTTTTAACT
*
97 TTATTTTAGTTTTAACT
1 TTATTTAAGTTTTAACT
114 TTA
1 TTA
117 AACTATAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (17 bp):
TTATTTAAGTTTTAACT
Found at i:898 original size:209 final size:199
Alignment explanation
Indices: 528--935 Score: 498
Period size: 209 Copynumber: 2.0 Consensus size: 199
518 NNNNNNNCAC
* * * *
528 ATATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTATAACAATTGTTACA
1 ATATTTACGTTAAGATTTAAAATTTAATCACTCCACCTTTATAAGTTTTTACAACAATTGTTACA
** * * *
593 GTTTTACGTTAAGATTTATCTATGACAATTTTGAGCTATAATTATTATTATTATTATTATTGTTT
66 GTTTTACGACAAGATTTATCTATGACAATTTTGAACTATAAATATTATTATTATTATTATTATTT
* * * *
658 ATTTAAAAATTAAATTTTATATATCGTTAAACACATTTAG-TCAAAGAATATATATTTAAATATT
131 ATTTAAAAAATAAAATTTACATATAGTTAAACACATTTAGTTC-AAGAATATATATTTAAATATT
722 TATTT
195 TATTT
* **
727 NNNNNNNNNNATATTTACGTTAAGATTTGAAATTTAATCACTCCACCTTTATAAGTTTTTACGTC
1 ----------ATATTTACGTTAAGATTTAAAATTTAATCACTCCACCTTTATAAGTTTTTACAAC
*
792 -ATCTGTTACAGTTTTACGACAAGATTTATCTAT-ACCAATTTTGAACTATAAATATTTTTATTA
56 AAT-TGTTACAGTTTTACGACAAGATTTATCTATGA-CAATTTTGAACTATAAATATTATTATTA
* *
855 TTATTATTATTTATTTAAAAAATAAAATTTACATATAGTTAAACACTTTTAGTTCGAGAATATAT
119 TTATTATTATTTATTTAAAAAATAAAATTTACATATAGTTAAACACATTTAGTTCAAGAATATAT
*
920 ATTTATATATTTATTT
184 ATTTAAATATTTATTT
936 TTTACTAAAA
Statistics
Matches: 176, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
208 3 0.02
209 171 0.97
210 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.46
Consensus pattern (199 bp):
ATATTTACGTTAAGATTTAAAATTTAATCACTCCACCTTTATAAGTTTTTACAACAATTGTTACA
GTTTTACGACAAGATTTATCTATGACAATTTTGAACTATAAATATTATTATTATTATTATTATTT
ATTTAAAAAATAAAATTTACATATAGTTAAACACATTTAGTTCAAGAATATATATTTAAATATTT
ATTT
Found at i:1280 original size:248 final size:232
Alignment explanation
Indices: 951--1402 Score: 537
Period size: 248 Copynumber: 1.9 Consensus size: 232
941 TAAAATTAGA
* * *
951 TTTTTTTTATTTAATTGACTTATTACGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAA
1 TTTTTTTTACTTAATTAACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAA
* * * * *
1016 TTATTCTACGTTTATAAGTTTTTACATCAATTCTAACAGTTTTACGTTAAAACTTATTTCTGTCA
66 TTATTCTACGTTTATAAGTTTTTACATAAATTCTAACAGTTTTACATCAAAACTTATCTATGTCA
* * *
1081 ATTTTATAGTATAATTATTTTTATCCTTATTATTTTTATTTAAAAATTAAAATTTGTGTA-TCGT
131 ATTTTAAAGTATAATTATTTTTATCCTTATTATTTTTATATAAAAATTAAAATTTGTATATTC-T
*
1145 TACATACTTTTAGCTCGATAATATAAATATAAATACTT
195 TAAATACTTTTAGCTCGATAATATAAATATAAATACTT
* *
1183 TTTTNNNNNNNNNNNNNNNNTTTTACTTAATTAATTTATTACGTTAACTCTCACATATTTACGTT
1 TTTT----------------TTTTACTTAATTAACTTATTACGTTAACTCTCACACATTTACGTT
* ** * * *
1248 AAGATTTAAAATTTAGTTATTCTATTTTTATAAGTTTTTACGTAAATTCTTATAGTTTTACATCA
50 AAGATTTAAAATTTAATTATTCTACGTTTATAAGTTTTTACATAAATTCTAACAGTTTTACATCA
* * *
1313 ATACTTATCTATGTCAATTTTAAATTATAATTATTTTTATCTTTATTATTTTTATATAAAAATTA
115 AAACTTATCTATGTCAATTTTAAAGTATAATTATTTTTATCCTTATTATTTTTATATAAAAATTA
1378 AAATTTGTATATTCTTAAATACTTT
180 AAATTTGTATATTCTTAAATACTTT
1403 AATTCCAAGA
Statistics
Matches: 180, Mismatches: 23, Indels: 18
0.81 0.10 0.08
Matches are distributed among these distances:
232 4 0.02
248 174 0.97
249 2 0.01
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.50
Consensus pattern (232 bp):
TTTTTTTTACTTAATTAACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAA
TTATTCTACGTTTATAAGTTTTTACATAAATTCTAACAGTTTTACATCAAAACTTATCTATGTCA
ATTTTAAAGTATAATTATTTTTATCCTTATTATTTTTATATAAAAATTAAAATTTGTATATTCTT
AAATACTTTTAGCTCGATAATATAAATATAAATACTT
Found at i:1445 original size:21 final size:20
Alignment explanation
Indices: 1415--1453 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1405 TTCCAAGAAT
*
1415 ATAAATTTAAATATTTTTTCA
1 ATAAAATTAAAT-TTTTTTCA
1436 ATAAAATTAAATTTTTTT
1 ATAAAATTAAATTTTTTT
1454 ACTTCATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
ATAAAATTAAATTTTTTTCA
Done.