Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399204.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2472.0, 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: 8939
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.25
Warning! 2847 characters in sequence are not A, C, G, or T
Found at i:1132 original size:22 final size:21
Alignment explanation
Indices: 1102--1142 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1092 GAATGGGTGA
1102 CTATAAATGGACTTTTTTTTAC
1 CTATAAAT-GACTTTTTTTTAC
* *
1124 CTATGAATGCCTTTTTTTT
1 CTATAAATGACTTTTTTTT
1143 CACGTTTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.22, C:0.15, G:0.10, T:0.54
Consensus pattern (21 bp):
CTATAAATGACTTTTTTTTAC
Found at i:1432 original size:167 final size:171
Alignment explanation
Indices: 1095--1420 Score: 380
Period size: 167 Copynumber: 1.9 Consensus size: 171
1085 TTTGAAAGAA
* * * * *
1095 TGGGTGACTATAAATGGACTTTTTTTTACCTATGAATGCCTTTTTTTTCACGTTTCTAGACGTAA
1 TGGGTGACTAGAAATGGACTTTTTCTTACCAATGAATGCCTTTCTCTTCACGTTTCTAGACGTAA
* * *
1160 ACATTCAATTATAATCTATTTAAACCAAAAAAGTAAATATAATTGAACTTAAAATCAATTATAAA
66 ACAGT-AATTATAATCTATTTAAACCAAAAAAGTAAATAAAATTAAACTTAAAATCAATTATAAA
* *
1225 ATAATAAAACTATTTAAATCGTGTAATAAGAATTTTGAAGGT
130 ATAATAAAACTATTTAAAGCGAGTAATAAGAATTTTGAAGGT
1267 TGGGTGACTAGAAAT-GAGC-TTTTCTTACCAATGAATGCCTTTCTCTTCACGTTTCATAGA-GT
1 TGGGTGACTAGAAATGGA-CTTTTTCTTACCAATGAATGCCTTTCTCTTCACGTTTC-TAGACGT
* * * * * * *
1329 AGAC-GT-GTTATAATCTGTTTTAACCAAAAATA-TAAA-AAAATTAAACTTAAAATTAATTTTG
64 AAACAGTAATTATAATCTATTTAAACCAAAAA-AGTAAATAAAATTAAACTTAAAATCAATTATA
* *
1390 ATATTATAAAA-TCATTTAAAGCGAGTAATAA
128 AAATAATAAAACT-ATTTAAAGCGAGTAATAA
1421 TGCTTTTGAA
Statistics
Matches: 131, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
166 1 0.01
167 45 0.34
168 25 0.19
169 1 0.01
170 1 0.01
171 39 0.30
172 19 0.15
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (171 bp):
TGGGTGACTAGAAATGGACTTTTTCTTACCAATGAATGCCTTTCTCTTCACGTTTCTAGACGTAA
ACAGTAATTATAATCTATTTAAACCAAAAAAGTAAATAAAATTAAACTTAAAATCAATTATAAAA
TAATAAAACTATTTAAAGCGAGTAATAAGAATTTTGAAGGT
Found at i:4274 original size:171 final size:172
Alignment explanation
Indices: 3837--4279 Score: 448
Period size: 172 Copynumber: 2.6 Consensus size: 172
3827 AAAAATATAA
* *
3837 AAAATCTAAA-TTAAAATCAATTATGAGATTATAAAACCATTTAATA-CGAGTAATAAGACTTTT
1 AAAAT-TAAACTTAAAATCAATTATGAAATTATAAAACTATTTAA-AGCGAGTAATAAGACTTTT
* * * * *
3900 GAAGGAATGTGTGACTATAAATGGACTTTTTTTGCCTATGAATGCCTTTTTCTTCACGTTTCTAG
64 GAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTCTCTTCACGTCTCTAG
3965 ACATAAACATTCAATTATAATCTATTTAAACCAAAAAACCAAAT
129 ACATAAACATTCAATTATAATCTATTTAAACCAAAAAACCAAAT
* * * * * *
4009 ATAATTGAACTTAAAATCAATTATAAAATAATAAAACTATTTAAAGCGATTAATAAGAATTTTGA
1 AAAATTAAACTTAAAATCAATTATGAAATTATAAAACTATTTAAAGCGAGTAATAAGACTTTTGA
* * * *
4074 AGGATTGGGTGACTAGAAAT-GAGCTTTTCTTGCCAATGAATGCCTTTCTCTTCACGTCTCATGG
66 AGGAATGAGTGACTATAAATGGA-CTTTTCTTGCCAATGAATGCCTTTCTCTTCACGTCTC-TAG
* * * * * **********
4138 A-GTAGACGTTCAATTATAATCTGTTTTAA-CAANNNNNNNNNN
129 ACATAAACATTCAATTATAATCTATTTAAACCAAAAAACCAAAT
* * * *
4180 AAAATTAAACTTAAAATCAATTTTGATATTATAAAACTATTTAAAGCAAGTAATACTG-CTTTTG
1 AAAATTAAACTTAAAATCAATTATGAAATTATAAAACTATTTAAAGCGAGTAATA-AGACTTTTG
** *
4244 AAGGAATGAAAGACTATTAATGGACTTTTCTTGCCA
65 AAGGAATGAGTGACTATAAATGGACTTTTCTTGCCA
4280 GTAAATGTTT
Statistics
Matches: 218, Mismatches: 47, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
171 88 0.40
172 127 0.58
173 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.34
Consensus pattern (172 bp):
AAAATTAAACTTAAAATCAATTATGAAATTATAAAACTATTTAAAGCGAGTAATAAGACTTTTGA
AGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTCTCTTCACGTCTCTAGAC
ATAAACATTCAATTATAATCTATTTAAACCAAAAAACCAAAT
Found at i:5373 original size:171 final size:171
Alignment explanation
Indices: 5196--5546 Score: 368
Period size: 172 Copynumber: 2.1 Consensus size: 171
5186 NNNNNNNNAT
5196 GTAAAAAAATTTAACTTAAAATCAATTACGAGATTATAAAA-CTATTTAAAGAGAATAATAAGGC
1 GTAAAAAAATTTAACTTAAAATCAATTACGAGATTATAAAATC-ATTTAAAGAGAATAATAAGGC
* * *
5260 TTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCCTATAAATGTCT-TTTTCTTCACGTT
65 TTTTGAAAGAATGGGTGACTATAAATGAACTTTTCTTACCAATAAAT-T-TATTTTCTTCACGTT
5324 TCTAAACATAGACATTCAATTATAATCTGTTTTAACTAAAAA-A
128 TCTAAACATAGACATTCAATTATAATCTGTTTTAACTAAAAATA
********** * * * **
5367 GTAAAAATAATNNNNNNNNNNATCAATTATGAGATTATAAAATCATTTATAGTGTGTAATAAGGC
1 GTAAAAA-AATTTAACTTAAAATCAATTACGAGATTATAAAATCATTTAAAGAGAATAATAAGGC
* * * * *
5432 TTTTGAAGGATTTGGTGACTATAAATGAACTTTTCTTACCAATGAATTTATTTTCTTTACGTTTC
65 TTTTGAAAGAATGGGTGACTATAAATGAACTTTTCTTACCAATAAATTTATTTTCTTCACGTTTC
** ** * * *
5497 TTGAGGTAGACATTTAATTATAGTCTGTTTTAATTAAAAATA
130 TAAACATAGACATTCAATTATAATCTGTTTTAACTAAAAATA
5539 -TAAAAAAA
1 GTAAAAAAA
5547 NNNNNNNNNN
Statistics
Matches: 146, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
170 3 0.02
171 61 0.42
172 81 0.55
173 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.37
Consensus pattern (171 bp):
GTAAAAAAATTTAACTTAAAATCAATTACGAGATTATAAAATCATTTAAAGAGAATAATAAGGCT
TTTGAAAGAATGGGTGACTATAAATGAACTTTTCTTACCAATAAATTTATTTTCTTCACGTTTCT
AAACATAGACATTCAATTATAATCTGTTTTAACTAAAAATA
Found at i:8121 original size:170 final size:170
Alignment explanation
Indices: 7732--8260 Score: 439
Period size: 170 Copynumber: 3.1 Consensus size: 170
7722 NNNNNNNNNN
* * * * * * * ** *
7732 AATTTTGAGATAATAAAACTATTTAAAGTGAGTAATAAGGCTTTTCAAGGAATAAGAGACTATAA
1 AATTATGAGATAATAAAACCATTTAAAGCGAGCAATAAGACTTTTGAAAGAATGGGAGACAATAA
* * * * * * *
7797 ATAGATTTTTCTTGCTAAAT-AATGCCTTTTTCTTCATGTTTCTCGATTTAGACAT--TT-AGTT
66 ATAGACTTTTCTTGC-AAATAAATACATTTTTCTACATGTTTC-C---TGAGGCATGATTCAATT
*
7858 AT-GATC-GATTTTAGTCAAAAAAAGTAAAAAAATTAAACTTAAAATC
126 ATAG-TCTG-TTTTACTC-AAAAAAGTAAAAAAATTAAACTTAAAATC
* * * * * ** * * * *
7904 AATTTTGAGATTATAAAACTATTTCAAGTGAGCAATAAGGTTTTTGAAGGAATTGGTGACTATAA
1 AATTATGAGATAATAAAACCATTTAAAGCGAGCAATAAGACTTTTGAAAGAATGGGAGACAATAA
* * * * * * *
7969 ATAGACTTTTCTTGCAAATGAATTCATTTTT-TTCTTGTTT-TTGAAGGTA-GATGTTCAATTGT
66 ATAGACTTTTCTTGCAAATAAATACATTTTTCTACATGTTTCCTG-AGGCATGA--TTCAATTAT
* * *
8031 AGTCTGTTTTAACT-AAAAATGTAAAAAAATTTAACTTAAAATT
128 AGTCTGTTTT-ACTCAAAAAAGTAAAAAAATTAAACTTAAAATC
** *
8074 AATTATGAGATAATAAAACCATTTAAAGCGAGTTATATGACTTTTGAAAGAATGGGAGACAATAA
1 AATTATGAGATAATAAAACCATTTAAAGCGAGCAATAAGACTTTTGAAAGAATGGGAGACAATAA
* * **
8139 ATGGACTTTTCTTTCAAATAAATAGGTTTTTCTACATGTTTCCTGAGGCATGCATTCAATTATAG
66 ATAGACTTTTCTTGCAAATAAATACATTTTTCTACATGTTTCCTGAGGCATG-ATTCAATTATAG
* *
8204 TCTGTTTTACTCAAAAAAGTCAAAAAATTCAACTTAAAATC
130 TCTGTTTTACTCAAAAAAGTAAAAAAATTAAACTTAAAATC
8245 AATTATGAGATAATAA
1 AATTATGAGATAATAA
8261 GGCTTTTGAA
Statistics
Matches: 291, Mismatches: 51, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
166 1 0.00
167 3 0.01
170 107 0.37
171 92 0.32
172 87 0.30
173 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (170 bp):
AATTATGAGATAATAAAACCATTTAAAGCGAGCAATAAGACTTTTGAAAGAATGGGAGACAATAA
ATAGACTTTTCTTGCAAATAAATACATTTTTCTACATGTTTCCTGAGGCATGATTCAATTATAGT
CTGTTTTACTCAAAAAAGTAAAAAAATTAAACTTAAAATC
Done.