Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397868.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1172.0, 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: 17028
ACGTcount: A:0.19, C:0.06, G:0.07, T:0.18
Warning! 8506 characters in sequence are not A, C, G, or T
Found at i:278 original size:20 final size:20
Alignment explanation
Indices: 253--299 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
243 TATAAATGGA
253 CTTTTCTTCTCAAGAAAAGG
1 CTTTTCTTCTCAAGAAAAGG
273 CTTTTCTTCTCAAGAAAAGG
1 CTTTTCTTCTCAAGAAAAGG
293 CTTTTCT
1 CTTTTCT
300 ATATGTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (20 bp):
CTTTTCTTCTCAAGAAAAGG
Found at i:15145 original size:170 final size:170
Alignment explanation
Indices: 14809--15227 Score: 438
Period size: 170 Copynumber: 2.5 Consensus size: 170
14799 NNNNNNNNNN
* *
14809 AGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC-ACTAAATGAAC
1 AGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGG-ATTGGTGACTA-TAAATGGAC
* * * *** * * *
14873 TTTGT-TT-CTCAATGAATGGCTTTTTCTATACGTTTCTTGAGATAGGCGTTCAATTATAGTCTG
64 TTT-TCTTGC-CAATGAATGACCTTATCTATACGTTTCACAAGATAGGCATTCAATAATAGTCTA
** * *
14936 TTTCAATGAAAAATGTAAAGAAATTTAACTTAAAATCAATTCTG
127 TTTCAACCAAAAATGTAAAGAAATTAAACTTAAAATCAATTATG
* * *
14980 AGTTTATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGATTGAGTGACTATAAATGGACT
1 AGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGATTG-GTGACTATAAATGGACT
* *
15045 TTTCTTGCCATTGAAT-ACCTTAT-TATCACGTTTCACAAGGT-GGACATTCAATAATAGTCTAT
65 TTTCTTGCCAATGAATGACCTTATCTAT-ACGTTTCACAAGATAGG-CATTCAATAATAGTCTAT
*
15107 TTTAACCAAAAATGTAAA-AATATTAAACTTAAAATCAATTATG
128 TTCAACCAAAAATGTAAAGAA-ATTAAACTTAAAATCAATTATG
* * * * ** * **
15150 AGACTATAAAATAATTTAAAGCAAGTAATAGGGCTTTTGAAAAAATCGGTGACTATAAAAAGACT
1 AGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTG-AAGGATTGGTGACTATAAATGGACT
15215 TTTCTTGCCAATG
65 TTTCTTGCCAATG
15228 GATGTTTATT
Statistics
Matches: 206, Mismatches: 34, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
169 7 0.03
170 127 0.62
171 70 0.34
172 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.34
Consensus pattern (170 bp):
AGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGATTGGTGACTATAAATGGACTT
TTCTTGCCAATGAATGACCTTATCTATACGTTTCACAAGATAGGCATTCAATAATAGTCTATTTC
AACCAAAAATGTAAAGAAATTAAACTTAAAATCAATTATG
Found at i:15360 original size:120 final size:120
Alignment explanation
Indices: 15136--15371 Score: 303
Period size: 120 Copynumber: 2.0 Consensus size: 120
15126 ATATTAAACT
* * * * *
15136 TAAAATCAATTATGAGACTATAAAATAATTTAAAGCAAGTAATAGGGCTTTTGAAAAAATCGGTG
1 TAAAATCAATTATGAAACTATAAAACAACTTAAAGCAAGTAATAAGGCTTTTGAAAAAATAGGTG
* * * *
15201 ACTATAAAAAGACTTTTCTTGCCAATGGATGTTTATTTCTTCATATTTCTCGAGG
66 ACTATAAAAAGACTTTACTTGCCAACGAATGGTTATTTCTTCATATTTCTCGAGG
* ** *
15256 TAAAATCAATTATGAAATTATAAAACAACTTAAAGTGAGTAATAAGGCTTTTGAAGAAATAGGTG
1 TAAAATCAATTATGAAACTATAAAACAACTTAAAGCAAGTAATAAGGCTTTTGAAAAAATAGGTG
** * *
15321 ACTATAAAGGGACTTTACTTGCCAACGAATGCGTT-TTTCTTTATGTTTCTC
66 ACTATAAAAAGACTTTACTTGCCAACGAATG-GTTATTTCTTCATATTTCTC
15372 TAAGTAGACA
Statistics
Matches: 98, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
120 96 0.98
121 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (120 bp):
TAAAATCAATTATGAAACTATAAAACAACTTAAAGCAAGTAATAAGGCTTTTGAAAAAATAGGTG
ACTATAAAAAGACTTTACTTGCCAACGAATGGTTATTTCTTCATATTTCTCGAGG
Found at i:16391 original size:171 final size:171
Alignment explanation
Indices: 15850--16610 Score: 517
Period size: 171 Copynumber: 4.5 Consensus size: 171
15840 NNNNNNNNNN
* * * * * *
15850 AGATTATAAAACCACTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTCTGAATGGGCT
1 AGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACT
* * *
15915 TTTC-TTCTCAATGAATGG-TTTTTCTAAATGTTTCTTG-GAGTAGACATTCAATTATTGTCTAT
66 TTTCTTTC-CAATGAATGGCTTTTTCTATACGTTTCTTGAGAGTAGACATTCAATTATAGTCTAT
* ********* *
15977 TTTANNNNNNNNNNTAAAAAAATTCAACTTAAAATCAATTATG
130 TTCA-ATAAAAATGTAAAAAAATTAAACTTAAAATCAATTATG
* *
16020 AGATTATAAAACATATTTCAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAAGGGAC
1 AGATTATAAAAC-TATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGAC
* ** * ******** *
16085 TTTTCTTACCAACAAAT-GCATTTCTCT-T-CNNNNNNNNNNA-AGTAGACATTTAATTATAGTC
65 TTTTCTTTCCAATGAATGGC-TTTTTCTATAC--GTTTCTTGAGAGTAGACATTCAATTATAGTC
* * * *
16146 TATTTTGACTAAAAATGAAAAAAAATTAAACTTAAAATCAAATATG
127 TA-TTTCAATAAAAATGTAAAAAAATTAAACTTAAAATCAATTATG
********** * *
16192 AGATTATAAAACNNNNNNNNNNGAGTAATAAGGCTTTTGAAAGAATGGGTGAC-ACTAAATGGAC
1 AGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTA-TAAATGGAC
* *
16256 TTTT-TTTCTCAATGAATGGCTTTTTCTATACGTTTCTTGAGA-TGGGCATTCAATTATAGTCTA
65 TTTTCTTTC-CAATGAATGGCTTTTTCTATACGTTTCTTGAGAGTAGACATTCAATTATAGTCTA
* *
16319 TTTCAATGAAAAATGTAAAGAAATTTAACTTAAAATCAATTATG
129 TTTCAAT-AAAAATGTAAAAAAATTAAACTTAAAATCAATTATG
* * *
16363 AGTTTATAAAACTATTTAAATCGAGTAATAGGGCTTTTGAAGGAATGAGTGACTATAAATGGACT
1 AGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACT
* ** * * * *** * *
16428 TTTCTTTCCATTGAATACCTTATTAT-TATGTTTCACAAG-GCAGACATTCAATAATAGTCTATT
66 TTTCTTTCCAATGAATGGCTTTTTCTATACGTTTCTTGAGAGTAGACATTCAATTATAGTCTATT
* *********
16491 TTAANNNNNNNNNNAAAAAAATTAAACTTAAAATCAATTATTG
131 TCAA-TAAAAATGTAAAAAAATTAAACTTAAAATCAATTA-TG
** * * **
16534 -GGCTATAAAA-TAATTTAAAGCAAGTAATAGGGCTTTTGAAGGAATCGA-TGACTATAAAAAGA
1 AGATTATAAAACT-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GAGTGACTATAAATGGA
*
16596 CTTTTCTTGCCAATG
64 CTTTTCTTTCCAATG
16611 GATGTTTATT
Statistics
Matches: 451, Mismatches: 118, Indels: 44
0.74 0.19 0.07
Matches are distributed among these distances:
169 1 0.00
170 141 0.31
171 228 0.51
172 76 0.17
173 5 0.01
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.33
Consensus pattern (171 bp):
AGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACT
TTTCTTTCCAATGAATGGCTTTTTCTATACGTTTCTTGAGAGTAGACATTCAATTATAGTCTATT
TCAATAAAAATGTAAAAAAATTAAACTTAAAATCAATTATG
Found at i:16743 original size:120 final size:120
Alignment explanation
Indices: 16537--16754 Score: 294
Period size: 120 Copynumber: 1.8 Consensus size: 120
16527 ATTATTGGGC
* * * * * *
16537 TATAAAATAATTTAAAGCAAGTAATAGGGCTTTTGAAGGAATCGATGACTATAAAAAGACTTTTC
1 TATAAAATAACTAAAAGCAAGTAATAAGGCTTCTGAAGAAATAGATGACTATAAAAAGACTTTTC
* * *
16602 TTGCCAATGGATGTTTATTTCTTCATGTTTCTCGAGGTAAAATCAATTATGAAAT
66 TTGCCAACGAATGGTTATTTCTTCATGTTTCTCGAGGTAAAATCAATTATGAAAT
** * **
16657 TATAAAATAACTAAAAGTGAGTAATAAGGCTTCTGAAGAAATAGGTGACTATAAAGGGACTTTTC
1 TATAAAATAACTAAAAGCAAGTAATAAGGCTTCTGAAGAAATAGATGACTATAAAAAGACTTTTC
16722 TTGCCAACGAATGCGTT-TTTCTTCATGTTTCTC
66 TTGCCAACGAATG-GTTATTTCTTCATGTTTCTC
16755 TAANNNNNNN
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
120 81 0.98
121 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (120 bp):
TATAAAATAACTAAAAGCAAGTAATAAGGCTTCTGAAGAAATAGATGACTATAAAAAGACTTTTC
TTGCCAACGAATGGTTATTTCTTCATGTTTCTCGAGGTAAAATCAATTATGAAAT
Done.