Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399977.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3204.0, 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: 3434
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.30
Warning! 595 characters in sequence are not A, C, G, or T
Found at i:2007 original size:170 final size:158
Alignment explanation
Indices: 1778--2084 Score: 273
Period size: 170 Copynumber: 1.9 Consensus size: 158
1768 NAGTAATAAG
* *
1778 GCTTTTGAAGGAATTGGTAACTATAAATAGACTTTTATTACCAATGGATACACTTTTCTTCACGT
1 GCTTTTGAAGGAATTGG-AACTATAAATAGACTTTTATTACCAAT-GAAACACTTTTCTTAACGT
* * * *
1843 TTCTCGAGCA-A-ACATTTAATTATAGTTTGTTGTAACAAAAAATGTAAAAAAATTCAACCTAAA
64 TTCTC-AACATAGACATTCAATTATAGTCTGTTGTAA-AAAAAATATAAAAAAATTCAACCTAAA
1906 ATCAATTATAAGATGATAAAACCATTTAAAGC
127 ATCAATTATAAGATGATAAAACCATTTAAAGC
*
1938 NNNNNNNNNNGCTTTTGAAGGAA-TGTGAGACTATAAATGGACTTTTCA-TACCAAT-AAACACT
1 ----------GCTTTTGAAGGAATTG-GA-ACTATAAATAGACTTTT-ATTACCAATGAAACAC-
* * * * ** *
2000 TTTTTCTTAATGTTTCTCAATATAGACATTCGATTATAGTCTGTTTTAATGAAAATATAAAGAAA
52 -TTTTCTTAACGTTTCTCAACATAGACATTCAATTATAGTCTGTTGTAAAAAAAATATAAAAAAA
*
2065 TTCAACTTAAAATCAATTAT
116 TTCAACCTAAAATCAATTAT
2085 GAGANNNNNN
Statistics
Matches: 115, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
168 5 0.04
169 5 0.04
170 84 0.73
171 21 0.18
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.35
Consensus pattern (158 bp):
GCTTTTGAAGGAATTGGAACTATAAATAGACTTTTATTACCAATGAAACACTTTTCTTAACGTTT
CTCAACATAGACATTCAATTATAGTCTGTTGTAAAAAAAATATAAAAAAATTCAACCTAAAATCA
ATTATAAGATGATAAAACCATTTAAAGC
Found at i:2124 original size:170 final size:163
Alignment explanation
Indices: 1948--2263 Score: 307
Period size: 170 Copynumber: 1.9 Consensus size: 163
1938 NNNNNNNNNN
** * *
1948 GCTTTTGAAGGAATGTGA-GACTATAAATGGACTTTTCATACCAATAAACACTTTTTTCTTAATG
1 GCTTTTGAAAAAATG-GATGACTATAAATGAACTTTTCATACCAATAAACACCTTTTTCTTAATG
* * * * * * *
2012 TTTCTCAATATAGACATTCGATTATAGTCTGTTTTAA-T-GAAAA-TATAAAGAAATTCAACTTA
65 TTTCTCAATATAGACATTCAATTATAATATGTTTTAACTAAAAAAGTAAAAAAAAATTAAACTTA
2074 AAATCAATTATGAGANNNNNNNNNNTTTTAAAGCGAGTAATAAA
130 AAATCAATTATGAGA----------TTTTAAAGCGAGTAATAAA
* * ** *
2118 GCTTTTGAAAAAATGGATGACTATAAATGAACTTTTCTTACCAATGAATGCCTTTTTCTTCATGT
1 GCTTTTGAAAAAATGGATGACTATAAATGAACTTTTCATACCAATAAACACCTTTTTCTTAATGT
* ** * *
2183 TTTTTGATGTAGACATTTAATTATAATATGTTTTAACTAAAAAAGTAAAAAAAAATTAAACTTAA
66 TTCTCAATATAGACATTCAATTATAATATGTTTTAACTAAAAAAGTAAAAAAAAATTAAACTTAA
*
2248 AATCAATTTTGAGATT
131 AATCAATTATGAGATT
2264 ATAAGACCAT
Statistics
Matches: 120, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
163 2 0.02
169 2 0.02
170 81 0.68
171 1 0.01
172 4 0.03
173 30 0.25
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.37
Consensus pattern (163 bp):
GCTTTTGAAAAAATGGATGACTATAAATGAACTTTTCATACCAATAAACACCTTTTTCTTAATGT
TTCTCAATATAGACATTCAATTATAATATGTTTTAACTAAAAAAGTAAAAAAAAATTAAACTTAA
AATCAATTATGAGATTTTAAAGCGAGTAATAAA
Found at i:2354 original size:137 final size:135
Alignment explanation
Indices: 2148--2414 Score: 356
Period size: 137 Copynumber: 2.0 Consensus size: 135
2138 CTATAAATGA
* * * * * *
2148 ACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTTTTGATGTAGACATTTAATTATAATATG
1 ACTTTTATTACCAATGAATGCATTTCTCTTCATGTTTCTTAATGTAGACATTTAATTATAATATA
** *
2213 TTTTAACTAAAAAAGTAAAAAAAAATTAAACTTAAAATCAATTTTGAGATTATAAGACCATTTAA
66 TTTTAAC-AAAAAA-TAAAAAAAAATTAAACTTAAAATCAATTACGAGATTATAAAACCATTTAA
2278 AGTGAGT
129 AGTGAGT
** *
2285 ACTTTTATTACCAATGAATGCATTTCTCTTCATGTTTCTTAATGCT-GACATTTAATTATTGTTT
1 ACTTTTATTACCAATGAATGCATTTCTCTTCATGTTTCTTAATG-TAGACATTTAATTATAATAT
* * * *
2349 ATTTTAACAAAAAATATAAAAAAATTTAACTTAAAATCGATTACGCGATTATAAAACCATTTAAA
65 ATTTTAACAAAAAATAAAAAAAAATTAAACTTAAAATCAATTACGAGATTATAAAACCATTTAAA
2414 G
130 G
2415 CTAGTAATAA
Statistics
Matches: 113, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
135 45 0.40
136 6 0.05
137 61 0.54
138 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (135 bp):
ACTTTTATTACCAATGAATGCATTTCTCTTCATGTTTCTTAATGTAGACATTTAATTATAATATA
TTTTAACAAAAAATAAAAAAAAATTAAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAG
TGAGT
Found at i:2656 original size:172 final size:170
Alignment explanation
Indices: 2285--3182 Score: 660
Period size: 172 Copynumber: 5.2 Consensus size: 170
2275 TAAAGTGAGT
* * * * * * ** *
2285 ACTTTTATTACCAATGAATGCATTTCTCTTCATGTTTCTTAATGCT-GACATTTAATTATTGTTT
1 ACTTTTCTT-CCAATGAATGCCTTTTTCTTCATGTTTCTCAA-GGTAGACATTCAATTATAATCT
* * * * * * *
2349 ATTTTAAC-AAAAAAT-ATAAAAAAATTTAACTTAAAATC-GATTACGCGATTATAAAACCATTT
64 GTTTT-ACTAGAAAATGA-AAAAAAATTAAACTTAAAAGCAAATT-TGAGATTATAAAACCATTT
** * *
2411 AAAGCT-AGTAATAAGGCTTTTGAAGGAATGAGGGACTATAAATGG
126 AAAG-TGAGTAATAAGGCTTTTGAAACAATGAGTGACTATAAATAG
** * ** *
2456 GTTTTTCTTCCAAATAAATGGGTTTTTCTAT-ATGTTTCTCAATGTAGACATTCAATTATAATCT
1 ACTTTTCTTCC-AATGAATGCCTTTTTCT-TCATGTTTCTCAAGGTAGACATTCAATTATAATCT
* * * *
2520 GTTTTAGCTAGAAAAGTGAAAAAAAACTAAACTTAATAGCAAATTTGAAATTATAAAACCA-TAA
64 GTTTTA-CTAGAAAA-TGAAAAAAAATTAAACTTAAAAGCAAATTTGAGATTATAAAACCATTTA
*
2584 AAGTGAGTAATAAGGCTTTTGAAGA-AATTG-CTGACTATAAATAG
127 AAGTGAGTAATAAGGCTTTTGAA-ACAA-TGAGTGACTATAAATAG
* * *
2628 ACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCACTAGGTAGACATTCAATTATAGTCTG
1 ACTTTTCTT-CCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTG
* * * * *
2693 TTTTAAT-GAACAATGTAAAAAAAATTCAAGTTAAAATG--AATTATGAGATTATGAAAGCATTT
65 TTTTACTAGAA-AATG-AAAAAAAATTAAACTTAAAA-GCAAATT-TGAGATTATAAAACCATTT
* * *
2755 AAAGCGAGTAATAAGGCTTTTGAAAGAATAAGTGACTATAAATAG
126 AAAGTGAGTAATAAGGCTTTTGAAACAATGAGTGACTATAAATAG
* * **
2800 ACTTTTCTTTCCAGTGAAAGCCTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAATCTG
1 ACTTTTC-TTCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTG
* * * * * ********** *
2865 TCTTAACTA-AAAATCCAAAAAAAATTGAACTTAAAATCAATTTTGAGATNNNNNNNNNNTTTGA
65 T-TTTACTAGAAAAT-GAAAAAAAATTAAACTTAAAAGCAAATTTGAGATTATAAAACCATTTAA
*
2929 AGTGAGTAATAAGGCTTTTGAAACAATGAGTGACTATAAATGG
128 AGTGAGTAATAAGGCTTTTGAAACAATGAGTGACTATAAATAG
* * * * *
2972 ACTTTTCTTACCAATGAATGCGTTTTTCTTTACT-CTTCTCAAGGTAGACATTCAATTATAGTTT
1 ACTTTTCTT-CCAATGAATGCCTTTTTCTTCA-TGTTTCTCAAGGTAGACATTCAATTATAATCT
* * ** * *
3036 GTTTTA--AAAAAATTGTAAAAAAAATTCAACTTAAAA-TTAGTTATGAGATTATAAAAACTATT
64 GTTTTACTAGAAAA-TG-AAAAAAAATTAAACTTAAAAGCAAATT-TGAGATTAT-AAAACCATT
** * * ** * * *
3098 TAAAGCAAGTAATAAGGTTTTTCAAGGAATGGGTGACCATAAATGG
125 TAAAGTGAGTAATAAGGCTTTTGAAACAATGAGTGACTATAAATAG
* * *
3144 ACTTTTCTTACCAATGAATACCCTTTTCTTCATATTTCT
1 ACTTTTCTT-CCAATGAATGCCTTTTTCTTCATGTTTCT
3183 TNNNNNNNNN
Statistics
Matches: 576, Mismatches: 117, Indels: 67
0.76 0.15 0.09
Matches are distributed among these distances:
169 1 0.00
170 20 0.03
171 116 0.20
172 389 0.68
173 46 0.08
174 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (170 bp):
ACTTTTCTTCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGT
TTTACTAGAAAATGAAAAAAAATTAAACTTAAAAGCAAATTTGAGATTATAAAACCATTTAAAGT
GAGTAATAAGGCTTTTGAAACAATGAGTGACTATAAATAG
Done.