Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400138.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3353.0, 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: 3849
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.33
Warning! 491 characters in sequence are not A, C, G, or T
Found at i:883 original size:133 final size:132
Alignment explanation
Indices: 723--965 Score: 346
Period size: 132 Copynumber: 1.8 Consensus size: 132
713 NNNNNNNNNN
* *
723 AGGAATGGGTGACTATAAATAGACTTTTCTTT-TCAATGAATAGTTTTTTTTACACG-TTTCTTA
1 AGGAATGGGTGACTATAAATAGACTTTT-TTTCTCAATGAAT-GATTTTTTTA-ACGATTTCTAA
** * *
786 AGGCAAGCATTCAATTATAGTCTGTTTTAGTAAAACATGTAAAAAAATGAGTGAGTAATAAGGCT
63 AGGCAAGCATTCAATTATAGTCTGTTTTAACAAAAAATGAAAAAAAATGAGTGAGTAATAAGGCT
851 TTTGA
128 TTTGA
* * **
856 AGGAATGGGTGACTGTAAATGGACTTTTTTTCTCAATGAATGATTTTTTTATGGATTTCTAAAGG
1 AGGAATGGGTGACTATAAATAGACTTTTTTTCTCAATGAATGATTTTTTTAACGATTTCTAAAGG
*
921 CAGGCATTCAATTATAGTCTGTTTTAACAAAAAATGAAAAAAAAT
66 CAAGCATTCAATTATAGTCTGTTTTAACAAAAAATGAAAAAAAAT
966 TCAAATTAAA
Statistics
Matches: 97, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
131 1 0.01
132 61 0.63
133 35 0.36
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.37
Consensus pattern (132 bp):
AGGAATGGGTGACTATAAATAGACTTTTTTTCTCAATGAATGATTTTTTTAACGATTTCTAAAGG
CAAGCATTCAATTATAGTCTGTTTTAACAAAAAATGAAAAAAAATGAGTGAGTAATAAGGCTTTT
GA
Found at i:1371 original size:167 final size:160
Alignment explanation
Indices: 1161--1472 Score: 307
Period size: 167 Copynumber: 1.9 Consensus size: 160
1151 NAAAACAATT
*
1161 TAAAGCGAGTAATAAGGCTTTTACAGGAATGGGTGACTATAAATAGA-TTTGTTTTGC-TAATAA
1 TAAAGCGAGTAATAAGGCTTTTACAGGAATGGCTGACTATAAATAGACTTT-TTTT-CTTAATAA
* * *
1224 AT-GTCTTTTTTT-CATGTTTCTCAAGGTA-ACATTCAATTAT-TTCCTATTTTAACCAAAAATA
64 ATAG-CTTTTTTTACACGTTTCTCAAGGTAGACATTCAATTATAAT-CTATTTTAACAAAAAATA
*
1285 TAAAAAAATT-AATTTAAATCAATTATGAGATTA
127 TAAAAAAATTCAACTTAAATCAATTATGAGATTA
* * *
1318 TAANNNNNNNNNNAGCGAGTATTAAGGCTTTTGA-AGGTATGGCTGATTATAAATAGACTTTTTT
1 TAA----------AGCGAGTAATAAGGCTTTT-ACAGGAATGGCTGACTATAAATAGACTTTTTT
* * ** * *
1382 TCTTAATGAATAGCTTTTTTTACACGTTTCTGAAGGTAGGTATTCAATTATAATCTGTTTTAATA
55 TCTTAATAAATAGCTTTTTTTACACGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACA
1447 AAAAATATAAAAAAATTCAACTTAAA
120 AAAAATATAAAAAAATTCAACTTAAA
1473 ATCNNNNNNN
Statistics
Matches: 123, Mismatches: 14, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
157 3 0.02
166 1 0.01
167 57 0.46
168 19 0.15
169 35 0.28
170 8 0.07
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.38
Consensus pattern (160 bp):
TAAAGCGAGTAATAAGGCTTTTACAGGAATGGCTGACTATAAATAGACTTTTTTTCTTAATAAAT
AGCTTTTTTTACACGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACAAAAAATATAAA
AAAATTCAACTTAAATCAATTATGAGATTA
Found at i:2094 original size:171 final size:173
Alignment explanation
Indices: 1917--2533 Score: 474
Period size: 171 Copynumber: 3.6 Consensus size: 173
1907 NNNNNTTTTG
* *
1917 CACATTTCTCAAGGCA-AACATTTAATTATAGTCTGTTTTACCCAAAAATTTAAAAAAATCTAAC
1 CACATTTCTCAAGGCAGAACATTTAATTATAGTCTGTTTTAACCAAAAATTTAAAAAAATTTAAC
* *
1981 CTAAAATCAATTTTGAGATTATAAAACAATTTAAAACGAGTAATAAAGCTTTTGAAGG-ATTGAG
66 TTAAAATCAATTTTGAGATTATAAAACAATTTAAAACGAGTAATAAAGCTTTTGAAGGAATAG-G
2045 TGACTATAAATGGACTTTTCTTACCAATAAATG-CATTTTTCTT
130 TGACTATAAATGGACTTTTCTTACCAATAAATGTCATTTTTCTT
* * **********
2088 CACATTTCTCTAA-GTAGAA-ATTCAATTATAG-CATGTTTTANNNNNNNNNNTAAAAAAATTTA
1 CACATTTCTC-AAGGCAGAACATTTAATTATAGTC-TGTTTTAACCAAAAATTTAAAAAAATTTA
* * * * *
2150 ACTTAAAATCAAATATGAGATTATAAAATAATTTAGAACGAGTAATAAGGCTTTTGAAGGAATAG
64 ACTTAAAATCAATTTTGAGATTATAAAACAATTTAAAACGAGTAATAAAGCTTTTGAAGGAATAG
* * * * * *
2215 GTGATTATAATTGGACTTTTCTTATCAATGAATGTCTTTTTTTTT
129 GTGACTATAAATGGACTTTTCTTACCAATAAATGTCATTTTTCTT
* * * * * *
2260 CAC-TTT-TCTAGGGATAGAC-TTTCAATTATAGTCTCTTTTAACTAAAAATTCAAAAAAATTTA
1 CACATTTCTCAAGGCAGA-ACATTT-AATTATAGTCTGTTTTAACCAAAAATTTAAAAAAATTTA
* * * *********** *
2322 AATTAAAATCAATTTTGGGATTATAAAACAATTTAAAGCGAGTAATATNNNNNNNNNNGGAATGG
64 ACTTAAAATCAATTTTGAGATTATAAAACAATTTAAAACGAGTAATAAAGCTTTTGAAGGAATAG
* *
2387 GTGACTATAAATGGACTTTTCTTAGCAATGAAA-G-CCTTTTTCTT
129 GTGACTATAAATGGACTTTTCTTACCAAT-AAATGTCATTTTTCTT
* ** * * * * * ** *
2431 TATGTTTC-CTGAGGTA-TACATTCAATTATTGTCTGTTTTAATTAAAAA--T-AAAAAATTCAA
1 CACATTTCTC-AAGGCAGAACATTTAATTATAGTCTGTTTTAACCAAAAATTTAAAAAAATTTAA
* * * *
2491 CTTAAAATCGATTATGAGATTATAAAATAATTTAAAACAAGTA
65 CTTAAAATCAATTTTGAGATTATAAAACAATTTAAAACGAGTA
2534 NNNNNNNNNN
Statistics
Matches: 346, Mismatches: 85, Indels: 33
0.75 0.18 0.07
Matches are distributed among these distances:
168 46 0.13
169 1 0.00
170 6 0.02
171 164 0.47
172 122 0.35
173 7 0.02
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.36
Consensus pattern (173 bp):
CACATTTCTCAAGGCAGAACATTTAATTATAGTCTGTTTTAACCAAAAATTTAAAAAAATTTAAC
TTAAAATCAATTTTGAGATTATAAAACAATTTAAAACGAGTAATAAAGCTTTTGAAGGAATAGGT
GACTATAAATGGACTTTTCTTACCAATAAATGTCATTTTTCTT
Done.