Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403146.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_813.0, 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: 5635
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.33
Warning! 626 characters in sequence are not A, C, G, or T
Found at i:832 original size:340 final size:338
Alignment explanation
Indices: 4--1042 Score: 1195
Period size: 340 Copynumber: 3.1 Consensus size: 338
1 ATA
* *
4 GAATGGGTGACTATAAATGGACTTTTTTAGCCAATGAATGTCTTTCTT-TT-ATGTTTCTTGAGG
1 GAATGGGTGACTATAAATGGACTTTTTT-GCCAATGAATGCCTTT-TTCTTCATGTTTCTTAAGG
* * ** *
67 TAGACATCCAATTATTGTCTGTTTTAACAAAAATGTAAAAAAATTCAACTT-AACGTAAGTTATA
64 TAGACATTCAATTATAGTCTGTTTTAACAAAAATGTAAAAAAATTCAACTTAAAATTAA-TTATG
* * * * *
131 AGATTATAAAACCATTTAAAGCGTGTAATAAGCCTTTTAGAA-GAATGGGTGATTATAAGTGGGC
128 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT-GAAGGAAT-GGTGAATATAAATGGAC
* * * *
195 TTTTCTTCTCAATGTAATAC-TTTTTT-TACATGTTTCTTGAGGTAGACATTCCATTATAGCCTG
191 TTTTCTGC-CAATG-AAGACTTTTTTTCTACATGTTTCTTGAGGTAGACATTCAATTATAGTCTG
* ** * * * * *
258 TTTTTATGAGAA-GTATAAAACAATTCAACTTAAAATTAATTTTGAGACTATAAAACCTTTTAAA
254 TTTTAACAAAAATGTA-AAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
**
322 ACGAGTAATAAGACTTTTGAAG
317 GTGAGTAATAAGACTTTTGAAG
* * * * * *
344 AAATGGGTGACTATAAGTAGACTTTTTTTGTCAATGAATGCCATTTTCTTCATGTTTCTGAAGGT
1 GAATGGGTGACTATAAATGGAC-TTTTTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTAAGGT
* ** *
409 AGACATTCATTTATAGTCAATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA
65 AGACATTCAATTATAGTCTGTTTTAA-CAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGA
* *
474 GATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTT
129 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGTGAATATAAATGGACTT
* * * ** * * * *
539 TTCTAGCCAAAGAAGGCTTTTTTTCTTCATGTTTCTCAATGTAGACATTTAATTACAGTATGTTT
193 TTCT-GCCAATGAAGACTTTTTTTCTACATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTT
*
604 TAACAAAAATGTAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAG
257 TAACAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAG
*
669 TAATAAGGCTTTTGAAG
322 TAATAAGACTTTTGAAG
*
686 GAATGGGTGACTATAAATGGACTTTTTT-CCAATGAATGCCTTTTTCTTCACGTTTCTTAAGGTA
1 GAATGGGTGACTATAAATGGACTTTTTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTAAGGTA
* *
750 GACATTCAATTATAGTCTGTTTTAATAAAAAATGTAAAAAACTTCAACTTAAAATTAATTATGAG
66 GACATTCAATTATAGTCTGTTTTAA-CAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGAG
* * * * *
815 ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGATGGAATGAATGAATATAAATAGAATTT
130 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG-GTGAATATAAATGGACTTT
* *
880 TCTTGCCAATGAATGACTTTTTTTC-ACA--TTTCTTGAGGTAGACATCCAGA-TATTA-TCTAT
194 TC-TGCCAATGAA-GACTTTTTTTCTACATGTTTCTTGAGGTAGACATTCA-ATTA-TAGTCTGT
* * * * * * *
940 TTTAATGAAAAATGTAAAAATATTCACCTTAAAATCAATTATAACATTCTAAAACTATTTAAAGT
255 TTTAA-CAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGT
*
1005 GAGTAATAAGCCTTTTGAAG
319 GAGTAATAAGACTTTTGAAG
*
1025 GAATGAGTGACTATAAAT
1 GAATGGGTGACTATAAAT
1043 NNNNNNNNNN
Statistics
Matches: 592, Mismatches: 91, Indels: 33
0.83 0.13 0.05
Matches are distributed among these distances:
338 25 0.04
339 92 0.16
340 192 0.32
341 62 0.10
342 173 0.29
343 45 0.08
344 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (338 bp):
GAATGGGTGACTATAAATGGACTTTTTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTAAGGTA
GACATTCAATTATAGTCTGTTTTAACAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGAGA
TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGTGAATATAAATGGACTTTTC
TGCCAATGAAGACTTTTTTTCTACATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAAC
AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAAT
AAGACTTTTGAAG
Found at i:1002 original size:170 final size:170
Alignment explanation
Indices: 4--1042 Score: 1029
Period size: 171 Copynumber: 6.1 Consensus size: 170
1 ATA
* * **
4 GAATGGGTGACTATAAATGGACTTTT-TTAGCCAATGAATGTCTTTCTTTT-ATGTTTCTTGAGG
1 GAATGAGTGACTATAAATGGACTTTTCTT-GCCAATGAATGACTTT-TTTTCACATTTCTTGAGG
**
67 TAGACATCCAATTATT-GTCTGTTTTAA-CAAAAATGTAAAAAAATTCAACTTAACGT-AAGTTA
64 TAGACATCCAA-TATTAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAA-TTA
* * *
129 TAAGATTATAAAACCATTTAAAGCGTGTAATAAGCCTTTTAGAA-
127 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT-GAAG
* * * *
173 GAATGGGTGATTATAAGTGGGCTTTTCTT-CTCAATGTAAT-ACTTTTTTT-ACATGTTTCTTGA
1 GAATGAGTGACTATAAATGGACTTTTCTTGC-CAATG-AATGACTTTTTTTCACA--TTTCTTGA
* * * * * * * * *
235 GGTAGACATTCCATTA-TAGCCTGTTTTTATGAGAAGTATAAAACAATTCAACTTAAAATTAATT
62 GGTAGACA-TCCAATATTAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATT
* * * * *
299 TTGAGACTATAAAACCTTTTAAAACGAGTAATAAGACTTTTGAAG
126 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
* * * * * * * * **
344 AAATGGGTGACTATAAGTAGACTTTTTTTGTCAATGAATGCCATTTTCTTCATGTTTC-TGAAGG
1 GAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGAC-TTTTTTTCACATTTCTTG-AGG
* * ** *
408 TAGACATTC-ATTTATAGTCAATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTAT
64 TAGACATCCAATAT-TAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTAT
*
472 GAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAG
128 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
* * * * **
515 GAAT-AGGTGACTATAAATGGACTTTTCTAGCCAAAGAA-GGCTTTTTTTCTTCATGTTTCTCAA
1 GAATGA-GTGACTATAAATGGACTTTTCTTGCCAATGAATGACTTTTTTTC-ACA--TTTCTTGA
* ** * * *
578 TGTAGACATTTAAT-TACAGTATGTTTTAA-CAAAAATGTAAAAAAAATCAACTTAAAATCAATT
62 GGTAGACATCCAATAT-TAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATT
*
641 ATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
126 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
* * * *
686 GAATGGGTGACTATAAATGGACTTTT-TT-CCAATGAATGCCTTTTTCTTCACGTTTCTTAAGGT
1 GAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGACTTTTT-TTCACATTTCTTGAGGT
* * * *
749 AGACATTCAAT-TATAGTCTGTTTTAATAAAAAATGTAAAAAACTTCAACTTAAAATTAATTATG
65 AGACATCCAATAT-TAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATG
* *
813 AGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGATG
129 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
* * * *
855 GAATGAATGAATATAAATAGAATTTTCTTGCCAATGAATGACTTTTTTTCACATTTCTTGAGGTA
1 GAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGACTTTTTTTCACATTTCTTGAGGTA
* * * * *
920 GACATCCAGATATTA-TCTATTTTAATGAAAAATGTAAAAATATTCACCTTAAAATCAATTATAA
66 GACATCCA-ATATTAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA
* * * * *
984 CATTCTAAAACTATTTAAAGTGAGTAATAAGCCTTTTGAAG
130 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
1025 GAATGAGTGACTATAAAT
1 GAATGAGTGACTATAAAT
1043 NNNNNNNNNN
Statistics
Matches: 719, Mismatches: 120, Indels: 61
0.80 0.13 0.07
Matches are distributed among these distances:
168 38 0.05
169 141 0.20
170 170 0.24
171 333 0.46
172 34 0.05
173 3 0.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (170 bp):
GAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGACTTTTTTTCACATTTCTTGAGGTA
GACATCCAATATTAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
Found at i:4315 original size:169 final size:169
Alignment explanation
Indices: 4096--5253 Score: 534
Period size: 171 Copynumber: 6.8 Consensus size: 169
4086 TTTCTCGATA
* * *
4096 TAGACATTTAATTATAGTCTGTTTT-AGCAAAAATGTAAAAACAATTCAACTTAAAATCAATTAT
1 TAGACATTCAAATATAGTCTGTTTTAAG-AAAAATGTAAAAA-AATTCAACTTAAAATTAATTAT
* ********** * *
4160 GAGATTATAAAANNNNNNNNNNCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC
64 GAAATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGAC
* * * *
4225 -TTT-TTACCAATGAATACCTTTTTCT-TCATGTTTCTTAAGG
129 TTTTCTTACCAATGAATA-ATTTTT-TATCACGTTTCTCAACG
* *
4265 TAGACATTCAAATATAGTCTGTTTTAATGAAAAATATAAAAAAGTTCAACTTAAAATTAATTATG
1 TAGACATTCAAATATAGTCTGTTTTAA-GAAAAATGTAAAAAAATTCAACTTAAAATTAATTATG
* **
4330 AAATTATAAAACCATTTAAAGGGAGTAATAAGGCTTTTGGTGGAATGAGTGACTATAAATAGACT
65 AAATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACT
*
4395 TTTCTTGCCAATGAATAATTTTTTATCACGTTTCTCAACG
130 TTTCTTACCAATGAATAATTTTTTATCACGTTTCTCAACG
* ** ** * *
4435 TAGACATCCTGATATTTTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATTAATTCT-
1 TAGACATTCAAATATAGTCTGTTTTAA-GAAAAATGTAAAAAAATTCAACTTAAAATTAATTATG
* * ********** * *
4499 AACATTATAAAATCGTTTAAAGCGAGTAATAAGNNNNNNNNNNGAAT-AGGTGACTATAAATGGG
65 AA-ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA-GTGACTATAAATAGA
* * * *
4563 CTTTTCTT-CTCAATGTATGACTTTTTCTA-CATGTTT-TCTAAGG
128 CTTTTCTTAC-CAATGAAT-AATTTTT-TATCACGTTTCTC-AACG
* * * * * *
4606 CAGGCATTCAATTATAGCCTGTTTTAATGAGAAATAT-AAAAAATGTCAA-TTCAAAATTAATT-
1 TAGACATTCAAATATAGTCTGTTTTAA-GAAAAATGTAAAAAAAT-TCAACTT-AAAATTAATTA
* * * * ** *
4668 TTAAGATTATAAAGCTATCTAAAGCGAGTAACCAGGCTTTTGAAGGAATGGGTGACTATAAACT-
63 TGAA-ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAA-TA
* * * * ** * * *
4732 GACTTTTTTTGCCTACGAATGTCTTTTTCTTTCTA--TTTCTCTATG
126 GACTTTTCTTACCAATGAAT-AATTTTT-TATC-ACGTTTCTCAACG
* * * * * ** *
4777 TAAACATTCAATTATAGTCTGTTTTAATAAAAAATATAAACAAATTTTACTTAAAATCAATTATG
1 TAGACATTCAAATATAGTCTGTTTTAA-GAAAAATGTAAAAAAATTCAACTTAAAATTAATTATG
* * ************ *
4842 AGATTACAAAACCATTTAAAGCGAGTAATAAGGCTTNNNNNNNNNNNNGTGACTATAAATGGACT
65 AAATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACT
** * ** * * * *
4907 TTTCTTGTCAATTAATGCTTTTTTCTTCACATTTCTCGATG
130 TTTCTTACCAATGAATAATTTTTT-ATCACGTTTCTCAACG
* ** * ** ********** * *
4948 AAGACATTCATTTATAGTCAT-TTTTGATCANNNNNNNNNNAAATTCAACTCAAAATCAATTATG
1 TAGACATTCAAATATAGTC-TGTTTTAAGAAAAATGTAAAAAAATTCAACTTAAAATTAATTATG
* * * **********
5012 ATATTATAAAGCCAGTTAAAGCGAGTAATAAGGCTTTTGAAGGAATNNNNNNNNNNAAATAGACT
65 AAATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACT
* * * * * * *
5077 TTTCTTGCCAATAAATACCTTTTTCT-TTATGTTTCTCGAGG
130 TTTCTTACCAATGAATA-ATTTTT-TATCACGTTTCTCAACG
* * * * * * * * *
5118 TAGAGATTTAATTACAGTCTGTTTTAATAAAAAATATAAAAACAA-TCCACTTAAAATTAACTAC
1 TAGACATTCAAATATAGTCTGTTTTAA-GAAAAATGTAAAAA-AATTCAACTTAAAATTAATTAT
* * * * *
5182 GATATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAAGAGCGACAATAAATTGAC
64 GAAATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGAC
5247 TTTTCTT
129 TTTTCTT
5254 GTCAACGAAT
Statistics
Matches: 737, Mismatches: 219, Indels: 64
0.72 0.21 0.06
Matches are distributed among these distances:
169 100 0.14
170 276 0.37
171 339 0.46
172 21 0.03
173 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (169 bp):
TAGACATTCAAATATAGTCTGTTTTAAGAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGA
AATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTT
TTCTTACCAATGAATAATTTTTTATCACGTTTCTCAACG
Found at i:4724 original size:171 final size:165
Alignment explanation
Indices: 4182--4877 Score: 548
Period size: 171 Copynumber: 4.1 Consensus size: 165
4172 NNNNNNNNNN
*
4182 CGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTT-TACCAATGAATACCTTT
1 CGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCCAATGAATA-CTTT
*
4246 TTCTTCATGTTTCTTAAGGTAGACATTCAAATATAGTCTGTTTTAATGAAAAATATAAAAAA-GT
65 TTCTACATGTTTC-TAAGGTAGACATTC-AATATAGTCTGTTTTAATGAAAAATATAAAAAATG-
* *
4310 TCAACTTAAAATTAATTATGAAATTATAAAACCATTTAAAG
127 TCAACTTAAAATTAATT-TTAAATTATAAAACTA-TTAAAG
* ** * * *
4351 GGAGTAATAAGGCTTTTGGTGGAATGAGTGACTATAAATAGACTTTTCTTGCCAATGAATAATTT
1 CGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTT-CCAATGAATACTTT
* * * * ** ** *
4416 TT-TATCACGTTTCTCAACGTAGACATCCTGATATTTTCTGTTTTAACAAAAAATGTAAAAAAAT
65 TTCTA-CATGTTTCT-AAGGTAGACATTC-AATATAGTCTGTTTTAATGAAAAATAT-AAAAAAT
*
4480 -TCAACTTAAAATTAATTCTAACATTATAAAATCGT-TTAAAG
126 GTCAACTTAAAATTAATTTTAA-ATTATAAAA-C-TATTAAAG
********** * * *
4521 CGAGTAATAAGNNNNNNNNNNGAATAGGTGACTATAAATGGGCTTTTCTTCTCAATGTATGACTT
1 CGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTC-CAATGAAT-ACTT
* * * *
4586 TTTCTACATGTTTTCTAAGGCAGGCATTCAATTATAGCCTGTTTTAATGAGAAATATAAAAAATG
64 TTTCTACATG-TTTCTAAGGTAGACATTCAA-TATAGTCTGTTTTAATGAAAAATATAAAAAATG
*
4651 TCAA-TTCAAAATTAATTTTAAGATTATAAAGCTATCTAAAG
127 TCAACTT-AAAATTAATTTTAA-ATTATAAAACTAT-TAAAG
** * * * *
4692 CGAGTAACCAGGCTTTTGAAGGAATGGGTGACTATAAACT-GACTTTTTTTGCCTACGAATGTCT
1 CGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAA-TGGACTTTTCTT-CCAATGAAT-ACT
* * * *
4756 TTTTCTTTCTAT-TTCTCT-ATGTAAACATTCAATTATAGTCTGTTTTAATAAAAAATATAAACA
63 TTTTC-TAC-ATGTT-TCTAAGGTAGACATTCAA-TATAGTCTGTTTTAATGAAAAATATAAA-A
** * * * * *
4819 AAT-TTTACTTAAAATCAATTATGAGATTACAAAACCATTTAAAG
123 AATGTCAACTTAAAATTAATT-TTAAATTATAAAACTA-TTAAAG
4863 CGAGTAATAAGGCTT
1 CGAGTAATAAGGCTT
4878 NNNNNNNNNN
Statistics
Matches: 409, Mismatches: 91, Indels: 52
0.74 0.16 0.09
Matches are distributed among these distances:
169 48 0.12
170 131 0.32
171 205 0.50
172 23 0.06
173 2 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (165 bp):
CGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCCAATGAATACTTTT
TCTACATGTTTCTAAGGTAGACATTCAATATAGTCTGTTTTAATGAAAAATATAAAAAATGTCAA
CTTAAAATTAATTTTAAATTATAAAACTATTAAAG
Done.