Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399311.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_258.0, 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: 3471
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.26
Warning! 1054 characters in sequence are not A, C, G, or T
Found at i:1602 original size:171 final size:169
Alignment explanation
Indices: 1296--2187 Score: 606
Period size: 171 Copynumber: 5.2 Consensus size: 169
1286 NNNNNNNNNN
* * ** * **
1296 CTTTTGAAGGAATGAGTGACTATAAATGAACTTTTCTTG-CTAATAAATGCCTTTCTTTTCATGT
1 CTTTTGAAGGAATGAGTGACTATAAATGGACTTTGCTTGTC-AAGGAATGCATTT-TTCCCATGT
* * ** * *********
1360 TTCTCGAGGTAGACATTCAATTATTA-TCTGTTTTAATAAAAATTGTAAAAATAATNNNNNNNNN
64 TTCTCAAGGTAGACATTCAATTA-TAGTCTGTTTTAACAAAAAAAGTAAAAA-ATTCAACTTAAA
* * *
1424 NTCAATTATGAGATTATAAAACCATTTAAAGCGAGTAACAAGG
127 ATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGG
* * * *
1467 GTTTTGAAGGAATGAGTTACTATAAATAGACTTTGCTTGTCAAGGAATGCATTTGTGCCCATGTT
1 CTTTTGAAGGAATGAGTGACTATAAATGGACTTTGCTTGTCAAGGAATGCATTT-TTCCCATGTT
** *
1532 TCTCGGGGTAGACATTCAATTATTGTCTGTTTTAACAAAAAAAGTAAAAAGATTCAACTTAAAAT
65 TCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAAAGTAAAAA-ATTCAACTTAAAAT
* * *
1597 CAATTATGGGATTATAAAACTATTTAAAGTGAGTAAAAAGG
129 CAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGG
* ** * * * * *
1638 CTTTTGAAGGAATAAAAGACTATAAATGGACTTTTCTTG-CTAGTGAATCCCTTTTTCTTCATGT
1 CTTTTGAAGGAATGAGTGACTATAAATGGACTTTGCTTGTCAAG-GAATGCATTTTTC-CCATGT
** * * * * * * *
1702 TTCTCAAGACAAATATTCAATTATAATCAGTTTTAACAAAAAATGTAAAAAATAAAATTGAACAT
64 TTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAAAGT----AA-AAAATTCAACTT
* **********
1767 AAAATCAATTTTGAGATTATAAAACCATTTNNNNNNNNNNATAAGG
124 AAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGG
* * * * *
1813 CTTTTGAAGGAATGGGTGAGTATAAATGGACTTT-TTTTTCAACGAATGC-TTTTTCCTTCATGT
1 CTTTTGAAGGAATGAGTGACTATAAATGGACTTTGCTTGTCAAGGAATGCATTTTTCC--CATGT
** *
1876 TTCTTGAGGTAGACAATCAATTATAGTCTGTTTTAA-ACAAAAAAGTAAAAAACTTCAA-TTCAA
64 TTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACA-AAAAAAGTAAAAAA-TTCAACTT-AA
* * *
1939 AATCAATTTTTAAATTATAAAACCATTT--A--GAGTAATAAGG
126 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGG
* ********** * * * ** *
1979 CTTTTGAAGAAATGNNNNNNNNNNAATGGACTTTTCTTGTCAATGAATAG-TTTTTTTTCACGTT
1 CTTTTGAAGGAATGAGTGACTATAAATGGACTTTGCTTGTCAAGGAAT-GCATTTTTCCCATGTT
* * * *
2043 TCTCATGGTAGACATTCAATTATAGTCTGTTTTAATAAAAAATGTAAACATAA-TCAATTTAAAA
65 TCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAAAGTAAA-A-AATTCAACTTAAAA
* * *
2107 TTAATTATGAGATTATAAAACCGTTTAAAATGAGTAATAAGG
128 TCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGG
*
2149 CTTTTGAAGGAATG-GATGACTATAAATAGACTTTGCTTG
1 CTTTTGAAGGAATGAG-TGACTATAAATGGACTTTGCTTG
2188 CCAATGANNN
Statistics
Matches: 553, Mismatches: 141, Indels: 55
0.74 0.19 0.07
Matches are distributed among these distances:
166 104 0.19
167 14 0.03
168 9 0.02
169 5 0.01
170 77 0.14
171 215 0.39
172 1 0.00
173 7 0.01
174 46 0.08
175 72 0.13
176 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.35
Consensus pattern (169 bp):
CTTTTGAAGGAATGAGTGACTATAAATGGACTTTGCTTGTCAAGGAATGCATTTTTCCCATGTTT
CTCAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAAAGTAAAAAATTCAACTTAAAATCA
ATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGG
Found at i:3041 original size:171 final size:168
Alignment explanation
Indices: 2364--3087 Score: 571
Period size: 171 Copynumber: 4.2 Consensus size: 168
2354 NNNNNNNNNN
* *
2364 TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGAAGACTATAAATTAACTTTTTTT
1 TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAAAGACTATAAATTAACTTTTCTT
** * * * * **
2429 GTCAATGAATGCTTTTTTTTTCACATTTCTTGAGGTAGACATTTAATTATTGTCTATTTTAATGA
66 GTCAATGAATGCTTTTTTTTTCATGTTT-TTGAGATAGACATTCAATTATTATCTGTTTTAACCA
*
2494 AAAATGTAAAAATAATT-AACTTAAAATCAATTATGAGAATA
130 AAAAT-T-AAAA-AATTCAACTTAAAATCAATTATGAGATTA
*********** *** *
2535 TAAAACTATTTAAAGTNNNNNNNNNNGCTTTTGAAGGAATAGGTGACTATAAATAAACTTTTCTT
1 TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAAAGACTATAAATTAACTTTTCTT
* *
2600 -ACTAATGAATG-TTTTTTTTTCATGTCTCTTGAGATAGACATTCAATTA-TAGTCTGTTTTAA-
66 GTC-AATGAATGCTTTTTTTTTCATGT-TTTTGAGATAGACATTCAATTATTA-TCTGTTTTAAC
*
2661 CAAAAGTTAGGAAAAATTCAACTTAAAATCAATTATGAGATTA
128 CAAAAATTA--AAAAATTCAACTTAAAATCAATTATGAGATTA
********** * ** * *
2704 TAAANNNNNNNNNNGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTAT-AAGTAGACTTTGCT
1 TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAAAGACTATAAATTA-ACTTTTCT
* * * * * * * * *
2768 TGCCAACGAATGCATTTTTGTCCATGTTTATCGATATAGACATTCAATTATTGTCTGTTTTAACT
65 TGTCAATGAATGCTTTTTTTTTCATGTTT-TTGAGATAGACATTCAATTATTATCTGTTTTAACC
******** * *
2833 ANNNNNNNNNNAAAATTCAACTTGAAATCAATTTTGAGATTA
129 A--AAAATTAAAAAATTCAACTTAAAATCAATTATGAGATTA
* * * *
2875 TATAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGTAATAAAAAACTATAAATTAACTTTTTTT
1 TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAAAGACTATAAATTAACTTTTCTT
* * * *
2940 GTCAATGAATACTTTTCTCTTCATGTTTTTCGAGGTAGACATTCAATTATTATCTGTTTTAACCA
66 GTCAATGAATGCTTTTTTTTTCATGTTTTT-GAGATAGACATTCAATTATTATCTGTTTTAACCA
* *
3005 AAAATATAAAAAATTCAAATTAAAATCAATTTTTGAGATTA
130 AAAAT-TAAAAAATTCAACTTAAAATCAA-TTATGAGATTA
**
3046 TAAAACCGTTTCAAA-CGAGTAATAAGGCTTTTGAAGGAATAA
1 TAAAACTATTT-AAAGCGAGTAATAAGGCTTTTGAAGGAATAA
3088 GAGNNNNNNN
Statistics
Matches: 417, Mismatches: 117, Indels: 38
0.73 0.20 0.07
Matches are distributed among these distances:
167 1 0.00
168 8 0.02
169 75 0.18
170 99 0.24
171 227 0.54
172 7 0.02
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.36
Consensus pattern (168 bp):
TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAAAGACTATAAATTAACTTTTCTT
GTCAATGAATGCTTTTTTTTTCATGTTTTTGAGATAGACATTCAATTATTATCTGTTTTAACCAA
AAATTAAAAAATTCAACTTAAAATCAATTATGAGATTA
Found at i:3220 original size:72 final size:71
Alignment explanation
Indices: 3104--3237 Score: 241
Period size: 72 Copynumber: 1.9 Consensus size: 71
3094 NNNNNNNGAC
* *
3104 TTTTCTTTCCAATGAATGCTTTTTTCTTCATGTTTCTTGACGTAGACATTTAATTATAGTCTATA
1 TTTTCTTCCCAATGAATGCTTTTTTCTTCATATTTCTTGACGTAGACATTTAATTATAGTCTATA
3169 AATGGA
66 AATGGA
3175 TTTTCCTTCCCAATGAATGCTTTTTTCTTCATATTTCTTGACGTAGACATTTAATTATAGTCT
1 TTTT-CTTCCCAATGAATGCTTTTTTCTTCATATTTCTTGACGTAGACATTTAATTATAGTCT
3238 GTTTTAACAA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
71 4 0.07
72 56 0.93
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (71 bp):
TTTTCTTCCCAATGAATGCTTTTTTCTTCATATTTCTTGACGTAGACATTTAATTATAGTCTATA
AATGGA
Done.