Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397822.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1124.0, 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: 10443
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.19
Warning! 4850 characters in sequence are not A, C, G, or T
Found at i:2367 original size:18 final size:20
Alignment explanation
Indices: 2341--2377 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
2331 AAAAATGCAA
2341 AAATAATCA-ATT-TAAAAT
1 AAATAATCAGATTATAAAAT
*
2359 AAATTATCAGATTATAAAA
1 AAATAATCAGATTATAAAA
2378 CCATTTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 3 0.19
20 5 0.31
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (20 bp):
AAATAATCAGATTATAAAAT
Found at i:5176 original size:170 final size:160
Alignment explanation
Indices: 4871--5194 Score: 296
Period size: 170 Copynumber: 2.0 Consensus size: 160
4861 NNNNNATTCA
* *
4871 ATTATAATCTGTTTTAACCAATAATGTAAAAAAATTGAACCTAAAATCATTTTTGAGGTTATAAA
1 ATTATAATCTGTTTTAACCAATAATGTAAAAAAATTGAACCTAAAATCATTATTGAGATTATAAA
* * ** * * *
4936 ACTACTTAAAGCGAGTAAAAAGGGTTTTGAAGGAATAGAAGACTATGAATGGACTTTTTTTGCCA
66 ACAACTTAAAGCAAGTAAAAAGCCTTTTGAAAGAATAGAAGACTATAAATGGACTTTTTCTG-CA
** *
5001 ATGAAT-TCTTTTTTTTCATGTTTCTCAAGG
130 ATGAATGGATTTTTTTGCATGTTTCTCAAGG
* * *
5031 NNNNNNNNNNATTATAATCTGTTTTAATCAATAATGTAATAAAAA-TGTACTTAAAATCAATTAT
1 ----------ATTATAATCTGTTTTAACCAATAATGTAA-AAAAATTGAACCTAAAATC-ATTAT
* * * * **
5095 T-AGATTATAAAACAATTTACAGCAAGTAATAAGCCTTTTGAAAGAATGGGTGACTATAAATGGA
54 TGAGATTATAAAACAACTTAAAGCAAGTAAAAAGCCTTTTGAAAGAATAGAAGACTATAAATGGA
5159 CTTTTCCTCTG-AATGAATGGATTTTTTTGCATGTTT
119 CTTTT--TCTGCAATGAATGGATTTTTTTGCATGTTT
5195 TCCAAGGTAG
Statistics
Matches: 128, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
170 101 0.79
171 24 0.19
172 3 0.02
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.36
Consensus pattern (160 bp):
ATTATAATCTGTTTTAACCAATAATGTAAAAAAATTGAACCTAAAATCATTATTGAGATTATAAA
ACAACTTAAAGCAAGTAAAAAGCCTTTTGAAAGAATAGAAGACTATAAATGGACTTTTTCTGCAA
TGAATGGATTTTTTTGCATGTTTCTCAAGG
Found at i:7563 original size:172 final size:171
Alignment explanation
Indices: 7209--7682 Score: 564
Period size: 172 Copynumber: 2.8 Consensus size: 171
7199 NNNNNNNNGC
* * * *
7209 ATTCAATTATAGTCTTTTTTAACTAAAAATGTGAAAACAGTT-AGCTTAAAATCAATTATGA-TA
1 ATTCAATTATAGTCTGTTTTAACTAAAAAAGTGAAAA-AATTCAACTTAAAATCAATTATGAGT-
* * * * *
7272 TTAT-AAAATAATTTAAAGCGACTAATAAAGCTTTTAAAGGAATAAGAGACAATAAATAGACTTT
64 TTATAAAAAT-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATGGACTTT
7336 TCTTGCCAATGAATGCTTGTTTCTTCACGTTTCTCAATAAAAAT
128 TCTTGCCAATGAATGCTTGTTTCTTCACGTTTCTCAATAAAAAT
* *
7380 ATTCAATTATAGTCTGTTTTAACTAAAAAAGTGAAAAAATTCACCTCAAAATCAATTATGAGTTT
1 ATTCAATTATAGTCTGTTTTAACTAAAAAAGTGAAAAAATTCAACTTAAAATCAATTATGAGTTT
* *
7445 ATAAAAATATTTTAAAGCGAGTAACAAGGCTTTTGAAGGAATATGAGACTATAAATGGACTTTTC
66 ATAAAAATA-TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATGGACTTTTC
* * * * *
7510 TTGCCAATGTATTCTTTTTTCTTCACGTTTCTCGAGGTAAACAT
130 TTGCCAATGAATGCTTGTTTCTTCACGTTTCTC-A-ATAAAAAT
* * * * *
7554 -TT-TATTATAGTCTGTTTTAACCAACAAA-TAAAAAAAATTCAACTTAAAATCAATTATGAGAT
1 ATTCAATTATAGTCTGTTTTAACTAAAAAAGT-GAAAAAATTCAACTTAAAATCAATTATGAGTT
* * * * * ** *
7616 TATAAAACTATTTCAAGTGAGTAATAAGACTTTTGAAGGATTGGGTGACTATAAATGGACTTTTC
65 TATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATGGACTTTTC
7681 TT
130 TT
7683 CACTATAAAT
Statistics
Matches: 263, Mismatches: 33, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
170 3 0.01
171 107 0.41
172 144 0.55
173 3 0.01
174 6 0.02
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (171 bp):
ATTCAATTATAGTCTGTTTTAACTAAAAAAGTGAAAAAATTCAACTTAAAATCAATTATGAGTTT
ATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATGGACTTTTCT
TGCCAATGAATGCTTGTTTCTTCACGTTTCTCAATAAAAAT
Done.