Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399378.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2643.0, 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: 5448
ACGTcount: A:0.24, C:0.08, G:0.09, T:0.23
Warning! 2008 characters in sequence are not A, C, G, or T
Found at i:3207 original size:171 final size:169
Alignment explanation
Indices: 2911--3542 Score: 611
Period size: 171 Copynumber: 3.8 Consensus size: 169
2901 NNNNNNNNNN
* *
2911 TAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATA-AGAGACTATAAATAGACTTTTAT
1 TAAAACCATTTAAAGCGAGTAATAAGCCTTTTTAAGGAATAGAGAGACTATAAATAGACTTTTCT
* * ** * *
2975 GGCCAATGATTGCTTGTTTCTTCATGTTTCTCAAAGTAGACATTCAATTATAGTTTGTTTTAACC
66 TGCCAATGAATGCTTGTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACC
3040 AAAATGAAAAAAAAATTGAACCTAAAATAAATTTTGAGATTA
131 AAAATGAAAAAAAAATTGAACCT-AAAT-AATTTTGA-ATTA
* *
3082 TAAAACTATTTAAAGCGAGTAATAAGCCTTTTTAAGGAATAGA-AGACTATAAATGGACTTTTCT
1 TAAAACCATTTAAAGCGAGTAATAAGCCTTTTTAAGGAATAGAGAGACTATAAATAGACTTTTCT
* * * * *
3146 TGCCAATGAATGCTTGTTTCTTCACATTTCTCAATGTAGGCAATCAATTATAGTATGTTTTAATG
66 TGCCAATGAATGCTTGTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAA-C
* ** * *
3211 AAAAATGTAAAAAAAAATT-AATTTACAATCAATTATGTTATTA
130 CAAAATG-AAAAAAAAATTGAACCTA-AAT-AATTTTG-AATTA
* * *
3254 TAAAACCATTTAAAGCGAGTAATAAG-GTTTTTGAAGGAAT-GAGTGACTATAAATGGACTTTTC
1 TAAAACCATTTAAAGCGAGTAATAAGCCTTTTT-AAGGAATAGAGAGACTATAAATAGACTTTTC
* * * * ** * *
3317 TTACTAATGAATCCCTT-TTTCTTTATGTTTCTCAAGGTAAACATTCAATTATAATCTGTTTTTA
65 TTGCCAATGAAT-GCTTGTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAGTCTG-TTTTA
* * **
3381 ACTAATAACG-TTAAAAAA--G--CC------A-TTT-AATTA
128 ACCAA-AATGAAAAAAAAATTGAACCTAAATAATTTTGAATTA
* * * ** *
3411 TAAAGCCATTTAAAACGAGTAATAAGGCTTTGAAAGGAATA-AAAGACTATAAATAGACTTTTCT
1 TAAAACCATTTAAAGCGAGTAATAAGCCTTTTTAAGGAATAGAGAGACTATAAATAGACTTTTCT
* * * *
3475 TGCCAATGAATACTTTTTTTTTCACATTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACC
66 TGCCAATGAATGCTTGTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACC
3540 AAA
131 AAA
3543 NNNNNNNNNN
Statistics
Matches: 385, Mismatches: 62, Indels: 44
0.78 0.13 0.09
Matches are distributed among these distances:
155 1 0.00
156 12 0.03
157 98 0.25
158 3 0.01
159 2 0.01
160 1 0.00
171 127 0.33
172 118 0.31
173 23 0.06
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (169 bp):
TAAAACCATTTAAAGCGAGTAATAAGCCTTTTTAAGGAATAGAGAGACTATAAATAGACTTTTCT
TGCCAATGAATGCTTGTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACC
AAAATGAAAAAAAAATTGAACCTAAATAATTTTGAATTA
Found at i:3314 original size:172 final size:170
Alignment explanation
Indices: 2911--3538 Score: 560
Period size: 172 Copynumber: 3.7 Consensus size: 170
2901 NNNNNNNNNN
* * * *
2911 TAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATAAGAGACTATAAATAGACTTTTATG
1 TAAAACCATTTAAAGCGAGTAATAAGCTTTTTGAAGGAAT-AGAGACTATAAATGGACTTTTCTT
* ** * * *
2976 GCCAATGATTGCTTGTTTCTTCATGTTTCTCAAAGTAGACATTCAATTATAGTTTGTTTTAACCA
65 GCCAATGAATGCTTGTTTCTTCACATTTCTCAAAGTAGACAATCAATTATAGTATGTTTTAACAA
*
3041 AAATGAAAAAAAAATTGAACCTAAAATAAATTTTGAGATTA
130 AAATGAAAAAAAAATTGAACCTAAAATAAATTATGAGATTA
*
3082 TAAAACTATTTAAAGCGAGTAATAAGCCTTTTT-AAGGAATAGAAGACTATAAATGGACTTTTCT
1 TAAAACCATTTAAAGCGAGTAATAAG-CTTTTTGAAGGAATAG-AGACTATAAATGGACTTTTCT
* * *
3146 TGCCAATGAATGCTTGTTTCTTCACATTTCTCAATGTAGGCAATCAATTATAGTATGTTTTAATG
64 TGCCAATGAATGCTTGTTTCTTCACATTTCTCAAAGTAGACAATCAATTATAGTATGTTTTAA-C
** * * **
3211 AAAAATGTAAAAAAAAATT-AATTTACAATCAATTATGTTATTA
128 AAAAATG-AAAAAAAAATTGAACCTAAAATAAATTATGAGATTA
* *
3254 TAAAACCATTTAAAGCGAGTAATAAGGTTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTT
1 TAAAACCATTTAAAGCGAGTAATAAGCTTTTTGAAGGAAT-AGAGACTATAAATGGACTTTTCTT
* * * * ** * * * * *
3319 ACTAATGAATCCCTT-TTTCTTTATGTTTCTCAAGGTAAACATTCAATTATAATCTGTTTTTAAC
65 GCCAATGAAT-GCTTGTTTCTTCACATTTCTCAAAGTAGACAATCAATTATAGTATG-TTTTAAC
* * **
3383 TAATAACG-TTAAAAAA--G--CC--------ATT-T-A-ATTA
128 -AAAAATGAAAAAAAAATTGAACCTAAAATAAATTATGAGATTA
* * * *
3411 TAAAGCCATTTAAAACGAGTAATAAGGC--TTTGAAAGGAATAAAAGACTATAAATAGACTTTTC
1 TAAAACCATTTAAAGCGAGTAATAA-GCTTTTTG-AAGGAAT-AGAGACTATAAATGGACTTTTC
* * * * * * *
3474 TTGCCAATGAATACTTTTTTTTTCACATTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAAC
63 TTGCCAATGAATGCTTGTTTCTTCACATTTCTCAAAGTAGACAATCAATTATAGTATGTTTTAAC
3539 CAAANNNNNN
Statistics
Matches: 383, Mismatches: 61, Indels: 41
0.79 0.13 0.08
Matches are distributed among these distances:
156 14 0.04
157 97 0.25
158 1 0.00
159 1 0.00
160 3 0.01
170 2 0.01
171 117 0.31
172 121 0.32
173 27 0.07
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (170 bp):
TAAAACCATTTAAAGCGAGTAATAAGCTTTTTGAAGGAATAGAGACTATAAATGGACTTTTCTTG
CCAATGAATGCTTGTTTCTTCACATTTCTCAAAGTAGACAATCAATTATAGTATGTTTTAACAAA
AATGAAAAAAAAATTGAACCTAAAATAAATTATGAGATTA
Found at i:5401 original size:170 final size:172
Alignment explanation
Indices: 4693--5419 Score: 608
Period size: 171 Copynumber: 4.3 Consensus size: 172
4683 CTCAAGATAG
* * * * * * * * *
4693 ACATTCAATTATAATCTATTTTAACCAATAATGTAATAA-AAATTGAGCCTAAAATGAATTTTTA
1 ACATTCAATTATAATCTGTTTTAACAAAAAATGTAA-AACAAATTCAACTTAAAATCAATTATGA
* * * *
4757 GATCATAAAACCATTTAAAGCGAGTAACAAGGCTTTTGAAGGAATTG-GAGACTATAAATAGAGT
65 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA-TGAGAGACTATAAATGGACT
* * * * * ** * *
4821 TCTCTTACCAATGAAT-GCTTTTTTCCTAATGTTTC-TCAAGGTAG
129 TTTCTTGCCAATGAATACCTTTTTT-TTCACATTTCATGAA-GTAC
* ** *
4865 ACATTTAATTATTGTCTGTTTTAACCAAAACA--TAAAACAAA-TCGAACTTAAAATCAATTATG
1 ACATTCAATTATAATCTGTTTTAA-CAAAAAATGTAAAACAAATTC-AACTTAAAATCAATTATG
* * * *
4927 CA-TTTATAAAGA-CATTTAAAGCGAGTAATAAGGCTTTTGAATGAATGAGTGACTATAAATGAA
64 -AGATTATAAA-ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGA
* * *
4990 CTTTTCTTGCAAATGAATGCCTTTTTTTTCACGTTTCACATGACAG---
127 CTTTTCTTGCCAATGAATACCTTTTTTTTCACATTT--CATGA-AGTAC
* * * * *
5036 ACATTTAATTATAATCTGTTTTAAGCAAAAAA-GGAAAACAAATTAAACTTAAAATGAATTTTGA
1 ACATTCAATTATAATCTGTTTTAA-CAAAAAATGTAAAACAAATTCAACTTAAAATCAATTATGA
* * * * * * * *
5100 GATTATAATACCATTTCAAG-TAGTAATAAGGCCTTCGGAGGACT-AGAAGACTATGAATGGACT
65 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAG-AGACTATAAATGGACT
* ** * * * * * * *
5163 TTTGTTTTCAAAGAATAACTTTTTCTTCATATTTCTTGAGGTAG
129 TTTCTTGCCAATGAATACCTTTTTTTTCACATTTCATGAAGTAC
* *
5207 ACATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAA-AACTTCAACTTAAAATCAATTATGAG
1 ACATTCAATTATAATCTGTTTTAACAAAAAATGTAAAACAAATTCAACTTAAAATCAATTATGAG
* * * * *
5271 GTTATAAAACTATTTAAAGCGAGTAATAAGACTTTTGAAGGAATGAGCGACAATAAATGGACTTT
66 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTT
5336 TCTTGCCAATGAAT-CCTTTTTTTTCACATTTCATGAAGTAC
131 TCTTGCCAATGAATACCTTTTTTTTCACATTTCATGAAGTAC
* * * *
5377 ATATTCAATTATAATCTATTTTAACCAATAATGT-AAACAAATT
1 ACATTCAATTATAATCTGTTTTAACAAAAAATGTAAAACAAATT
5420 GTACCTAAAA
Statistics
Matches: 435, Mismatches: 97, Indels: 48
0.75 0.17 0.08
Matches are distributed among these distances:
168 1 0.00
169 7 0.02
170 105 0.24
171 243 0.56
172 69 0.16
173 6 0.01
174 3 0.01
175 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (172 bp):
ACATTCAATTATAATCTGTTTTAACAAAAAATGTAAAACAAATTCAACTTAAAATCAATTATGAG
ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTT
TCTTGCCAATGAATACCTTTTTTTTCACATTTCATGAAGTAC
Done.