Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399503.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2763.0, 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: 5560
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.31
Warning! 793 characters in sequence are not A, C, G, or T
Found at i:289 original size:171 final size:169
Alignment explanation
Indices: 72--1000 Score: 953
Period size: 171 Copynumber: 5.4 Consensus size: 169
62 TGTTTTAGCT
*
72 AAAAATGTAAAACAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAAT
1 AAAAATGTAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * *
137 AAGACATTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTCTCAATGAATGGCTTTTTCTAT-
65 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTC-CAATGAATGCCTTTTTCT-TC
* *
201 ATGTTTTTCAAGGCAACCTTTTAATTATAGTCTATTTTAATG
128 ATGTTTCTCAAGGTAACCTTTTAATTATAGTCTATTTTAATG
* * ** *
243 AAAAATGCAACAAAATTTAACTTAAAATCAATTATGAGGCTATAAAACTATTTAAAGCGAGTAAT
1 AAAAATGTAA-AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* *
308 AAGGCTTTT-ATA-AAATGGGTGACTATAAATGGAC-TTTTCTCACGAATGAATGCCTTTTT-TT
65 AAGGCTTTTGA-AGGAATGGGTGACTATAAATGGACTTTTTTTC-C-AATGAATGCCTTTTTCTT
* * * * * *
369 CACGTTTCTCAAGGTAAACATTCAATTATAGTTTGTTTTAACT-
127 CATGTTTCTCAAGGTAACCTTTTAATTATAGTCTATTTTAA-TG
*
412 AAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATA
1 AAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * * * * * *
477 AGGCTTTTGAAGGAATGAGCGAATATTAATAGAATTTTCTTACCAATGAATGCCTTTCTCTTCAT
66 AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTT-TTTCCAATGAATGCCTTTTTCTTCAT
* * ** * * * *
542 GTTTCTCAAAG-CAGGTATTCAATTATATTCCATTTTTATG
130 GTTTCTCAAGGTAACCT-TTTAATTATAGTCTATTTTAATG
* * * * *
582 AAAAATATAAAAGCATTCAACTTAAAATGAATCATGAGATTATAAAACCATTTAAAGCGAATAAT
1 AAAAATGTAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * * *
647 AAGGCTTTTCAAGGAATGGATGACAATAAATAGACTTTTTTTACCAATGAATCCCTTTTTCTTCA
65 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTT-CCAATGAATGCCTTTTTCTTCA
* * * * *
712 CGTTTCTCGATGTAA-ATATTTAATTATAATCTATTTTAATG
129 TGTTTCTCAAGGTAACCT-TTTAATTATAGTCTATTTTAATG
* * * * **
753 AAAAAAT-TAAAAAAAAATTGAACTTAAAATCAATTTTGAGAGTAGAAAACCATTTAAAGTAAGT
1 -AAAAATGT---AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGT
* * *
817 AATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTTTCT
62 AATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTT-TTTCCAATGAATGCCTTTTTCT
* ** * ** * **
881 TTATGTTTCTTGAGGTAGCCAATTAATTATAGTCTGTTTTAACC
126 TCATGTTTCTCAAGGTAACCTTTTAATTATAGTCTATTTTAATG
* * *
925 AAAAATGTAAAAAAAATTTAAGTTAAAATTAATTATGAGATTAT-AAACCATTTAAAGCGAGTAA
1 AAAAATGT--AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
989 TAAGGCTTTTGA
64 TAAGGCTTTTGA
1001 NNNNNNNNNN
Statistics
Matches: 629, Mismatches: 107, Indels: 45
0.81 0.14 0.06
Matches are distributed among these distances:
168 62 0.10
169 81 0.13
170 114 0.18
171 233 0.37
172 49 0.08
173 84 0.13
174 6 0.01
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (169 bp):
AAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTCCAATGAATGCCTTTTTCTTCATG
TTTCTCAAGGTAACCTTTTAATTATAGTCTATTTTAATG
Found at i:869 original size:344 final size:336
Alignment explanation
Indices: 21--998 Score: 1086
Period size: 339 Copynumber: 2.9 Consensus size: 336
11 AATAAATGCA
* * * * ** * * * *
21 TTTTTCTTTACGTGTCTCATGGTAGACATTCAATTATTGTTTGTTTTAGCTAAAAATGTAAAACA
1 TTTTT-TTCACGTTTCTCAAGGTAAACATTCAATTATAATCTATTTTAACTAAAAATGTAAAAAA
* *
86 ATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGACATTTGAAGG
65 ATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGG
* * * *
151 AATGGGTGACTATAAATGGACTTTT-TTTCTCAATGAATGGCTTTTTCTATATGTTTTTCAAGGC
130 AATGAGAGACTATAAATGGACTTTTCTTAC-CAATGAAT-GCTTTTTCT-TATGTTTCTCAAGGC
* * *
215 AACCTTTTAATTATAGTCTATTTTAATGAAAAATGCAACAAAATTTAACTTAAAATCAATTATGA
192 -AGCTATTAATTATAGTCTATTTTAATGAAAAATGTAA-AAAATTTAACTTAAAATCAATTATGA
** * * * *
280 GGCTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTATAAAATGGGTGACTATAAATGGACTTT
255 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTATAAAATGGATGACAATAAATAGACTTT
* *
345 TCTCACGAATGAATGCC
320 TCTCACCAATGAATCCC
* * *
362 TTTTTTTCACGTTTCTCAAGGTAAACATTCAATTATAGTTTGTTTTAACTAAAAATGT-AAAAAA
1 TTTTTTTCACGTTTCTCAAGGTAAACATTCAATTATAATCTATTTTAACTAAAAATGTAAAAAAA
426 TTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
66 TTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
* * * * * * *
491 ATGAGCGAATATTAATAGAATTTTCTTACCAATGAATGCCTTTCTCTTCATGTTTCTCAAAGCAG
131 ATGAGAGACTATAAATGGACTTTTCTTACCAATGAATG-CTTTTTCTT-ATGTTTCTCAAGGCAG
* * * * * * * * *
556 GTATTCAATTATATTCCATTTTTATGAAAAATATAAAAGCATTCAACTTAAAATGAATCATGAGA
194 CTATT-AATTATAGTCTATTTTAATGAAAAATGTAAAA-AATTTAACTTAAAATCAATTATGAGA
* *
621 TTATAAAACCATTTAAAGCGAATAATAAGGCTTTTCA-AGGAATGGATGACAATAAATAGACTTT
257 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT-ATA-AAATGGATGACAATAAATAGACTTT
* *
685 TTTTACCAATGAATCCC
320 TCTCACCAATGAATCCC
* * * *
702 TTTTTCTTCACGTTTCTCGATGTAAATATTTAATTATAATCTATTTTAA-TGAAAAAAT-TAAAA
1 TTTTT-TTCACGTTTCTCAAGGTAAACATTCAATTATAATCTATTTTAACT--AAAAATGT--AA
* * * * * **
765 AAAAATTGAACTTAAAATCAATTTTGAGAGTAGAAAACCATTTAAAGTAAGTAATAAGGCTTTTG
61 AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTG
* **
830 AAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTTATGTTTCTTGAG
126 AAGGAATGAGAGACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTC-TTATGTTTCTCAAG
* * * ** * *
895 GTAGCCAATTAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAATTTAAGTTAAAATTAATTA
190 GCAG-CTATTAATTATAGTCTATTTTAATGAAAAATGT--AAAAAATTTAACTTAAAATCAATTA
960 TGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTT
252 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
999 GANNNNNNNN
Statistics
Matches: 537, Mismatches: 83, Indels: 32
0.82 0.13 0.05
Matches are distributed among these distances:
338 8 0.01
339 192 0.36
340 91 0.17
341 42 0.08
342 6 0.01
343 68 0.13
344 126 0.23
345 4 0.01
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (336 bp):
TTTTTTTCACGTTTCTCAAGGTAAACATTCAATTATAATCTATTTTAACTAAAAATGTAAAAAAA
TTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
ATGAGAGACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTCTTATGTTTCTCAAGGCAGCT
ATTAATTATAGTCTATTTTAATGAAAAATGTAAAAAATTTAACTTAAAATCAATTATGAGATTAT
AAAACCATTTAAAGCGAGTAATAAGGCTTTTATAAAATGGATGACAATAAATAGACTTTTCTCAC
CAATGAATCCC
Found at i:2928 original size:171 final size:169
Alignment explanation
Indices: 1938--3379 Score: 603
Period size: 171 Copynumber: 8.4 Consensus size: 169
1928 NNNNNNNNNN
* * * * * * *
1938 ACTTAAAATCAATTATGGGATTATAAAACAATTTAAAGTGAATAATAAGGCTTTCGAAGGAGTGG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAGAGCGAGTAATAAGGCTTTTGAAGGAATGG
* * * ** ** ** * * * *
2003 GTGACTATAAATGGACTTTTTTTTGCTAAAAAATATCTTTTTCTTCTTGTTTCT-TGATATATAC
66 GTGACTATAAA-GGAC-TTTTCTTACCAATGAATGCCTTTTTCTTCACGTTTCTCAGATGTAGAT
* * * ** *
2067 ATTCAATTATAACCTGTTTTGACCAAAAATGTCAAAAAAATTGA
129 ATTTAATTATAATCTATTTT-AATAAAAATAT--AAAAAATTGA
********** * * * * * * *
2111 ACTTAAANNNNNNNNNNAGATTATAAAACTATTTAAAGTGAGTAATAAGGATTTTAAAGAAATGA
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAGAGCGAGTAATAAGGCTTTTGAAGGAATGG
* * * * * *
2176 GTGACTATAATGGA-TTTTTTTGCCAATGAATG-CTATTTCTTCACGTTTCTC-GAGGTAGACAT
66 GTGACTATAAAGGACTTTTCTTACCAATGAATGCCTTTTTCTTCACGTTTCTCAGATGTAGATAT
* ** * **
2238 TTAATTATTATCTGCTTTAACTAAAAATGTAAAACAATTNN
131 TTAATTATAATCTATTTTAA-TAAAAATATAAAA-AATTGA
******** * * * * * *
2279 NNNNNNNNTCAATTATGGGATTATAAAACCATTTAAAACGAGTAATAAAG-TATTTGAAAGAATT
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAGAGCGAGTAATAAGGCT-TTTGAAGGAATG
* * * * *
2343 GGTGACTATTAATA-GACTTATT-TT-CTCAATGAATGGC-TTTTCTACATGTTTCTCA-AGGCA
65 GGTGACTA-TAA-AGGACTT-TTCTTAC-CAATGAATGCCTTTTTCTTCACGTTTCTCAGATGTA
* * * * * * *
2403 -AGTACTCAATTATAGTATATTTTAATGAAAATGTAAAAAAATTTA
126 GA-TATTTAATTATAATCTATTTTAATAAAAATAT-AAAAAATTGA
* * ********** *
2448 ACGTAAAATCAATTATGAGATTATAAAACTATTTANNNNNNNNNNTAAGGTTTTTGAAGGAATGG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAGAGCGAGTAATAAGGCTTTTGAAGGAATGG
* * ** * * *
2513 GTGACTATAAATGAACTTTTTTTGTCAATGAATGTCTTTTTCTTCACGTTTTTCA-A-GATAGAC
66 GTGACTATAAA-GGACTTTTCTTACCAATGAATGCCTTTTTCTTCACGTTTCTCAGATG-TAGAT
* * * *
2576 ATTCT-ATTATAGTCTGTTTTAATAAAAAATAGAAAAAAATTTA
129 ATT-TAATTATAATCTATTTTAAT-AAAAATA-TAAAAAATTGA
* * * * * * * * * * * *
2619 ACTTAAAATCAATTATCAGATTATAAAACTATTTAAAGCAAATAAAAAAGTTTTTAAAAGAGTAG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAGAGCGAGTAATAAGGCTTTTGAAGGAATGG
* * ********** * * *
2684 GTGACTATAAATGGACTTTTCTT-CTTAATGAATGGCTTTNNNNNNNNNNTTCCCA-AGGCA-AG
66 GTGACTATAAA-GGACTTTTCTTAC-CAATGAATGCCTTTTTCTTCACGTTTCTCAGATGTAGA-
* * *
2746 CATTCAATTATAGTCTATTTTAATGAAAAATATAATAAAATTGA
128 TATTTAATTATAATCTATTTTAAT-AAAAATATAA-AAAATTGA
* *
2790 ACATAAAATCAATTATGAGATTATAAAACCATTTAGAGCGAGTAATAAGGCTTTTGGAGGAATGG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAGAGCGAGTAATAAGGCTTTTGAAGGAATGG
* *
2855 GTGACTATAAACGGACCTTTT-TTATCAATGAATCCCTTTTTCTTCACGTTTCT-AGATGTAGAT
66 GTGACTATAAA-GGA-CTTTTCTTACCAATGAATGCCTTTTTCTTCACGTTTCTCAGATGTAGAT
* *******
2918 ATTTAATTATAATCTGTTTTAACTAAAAATNNNNNNNNNNATTGA
129 ATTTAATTATAATCTATTTTAA-TAAAAAT---ATAAAAAATTGA
* * * * *
2963 ACTTAAAATCAATTTTGAGAGTATAAAACCATTTAGAGTGAGTAAGAAGGCTTTTGAAGGAATGA
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAGAGCGAGTAATAAGGCTTTTGAAGGAATGG
* * * * *
3028 GAGACTATAAATGAACTTTTCTTACCAAAGAATGCCTTTTTCTTCATGTTTCTCA-AAGTAGATA
66 GTGACTATAAA-GGACTTTTCTTACCAATGAATGCCTTTTTCTTCACGTTTCTCAGATGTAGATA
* * * ******** * *
3092 ATTAATTATAGTCTGTTTTAATAAANNNNNNNNNNATATTCA
130 TTTAATTATAATCTATTTTAATAAA--AATATAAAAAATTGA
* * * * * * **
3134 ACTTAAAATCAATTATGTGATTATAAAACTATTTAAACCGAGTAATAAGGGTCTTGAAAAAATGG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAGAGCGAGTAATAAGGCTTTTGAAGGAATGG
* * * * * * *
3199 TTTACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTTAC--TTCTTGAGATGCACAT
66 GTGACTATAAA-GGACTTTTCTTACCAATGAATGCCTTTTTCTTCACGTTTC-TCAGATGTAGAT
* * *
3262 -TCT-ATTATAATCTATTTTGACTAAAAATGTCAAAATATATTGA
129 ATTTAATTATAATCTATTTT-AATAAAAATAT-AAAA-A-ATTGA
* * * * *
3305 ACTTAAAATCAATTTTAAGATTAAAAAACCATTTA-AACTGAGTAATAAGGCTTTTGAAGGAATA
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAGAGC-GAGTAATAAGGCTTTTGAAGGAATG
*
3369 GGCGACTATAA
65 GGTGACTATAA
3380 NNNNNNNNNN
Statistics
Matches: 942, Mismatches: 279, Indels: 98
0.71 0.21 0.07
Matches are distributed among these distances:
167 6 0.01
168 54 0.06
169 145 0.15
170 114 0.12
171 416 0.44
172 20 0.02
173 186 0.20
174 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.35
Consensus pattern (169 bp):
ACTTAAAATCAATTATGAGATTATAAAACCATTTAGAGCGAGTAATAAGGCTTTTGAAGGAATGG
GTGACTATAAAGGACTTTTCTTACCAATGAATGCCTTTTTCTTCACGTTTCTCAGATGTAGATAT
TTAATTATAATCTATTTTAATAAAAATATAAAAAATTGA
Found at i:2991 original size:173 final size:162
Alignment explanation
Indices: 2777--3116 Score: 380
Period size: 173 Copynumber: 2.0 Consensus size: 162
2767 AATGAAAAAT
* *
2777 ATAATAAA-ATTGAACATAAAATCAATTATGAGATTATAAAACCATTTAGAGCGAGTAATAAGGC
1 ATAA-AAATATTGAACATAAAATCAATTATGAGAGTATAAAACCATTTAGAGCGAGTAAGAAGGC
* * * * * *
2841 TTTTGGAGGAATGGGTGACTATAAACGGACCTTTT-TTATCAATGAATCCCTTTTTCTTCACGTT
65 TTTTGAAGGAATGAGAGACTATAAA-GGAACTTTTCTTACCAAAGAATCCCTTTTTCTTCACGTT
* *
2905 TCT-AGATGTAGATATTTAATTATAATCTGTTTTA
129 TCTCA-AAGTAGATAATTAATTATAATCTGTTTTA
* * *
2939 ACTAAAAATNNNNNNNNNNATTGAACTTAAAATCAATTTTGAGAGTATAAAACCATTTAGAGTGA
1 A-TAAAAAT----------ATTGAACATAAAATCAATTATGAGAGTATAAAACCATTTAGAGCGA
* *
3004 GTAAGAAGGCTTTTGAAGGAATGAGAGACTATAAATGAACTTTTCTTACCAAAGAATGCCTTTTT
55 GTAAGAAGGCTTTTGAAGGAATGAGAGACTATAAAGGAACTTTTCTTACCAAAGAATCCCTTTTT
* *
3069 CTTCATGTTTCTCAAAGTAGATAATTAATTATAGTCTGTTTTA
120 CTTCACGTTTCTCAAAGTAGATAATTAATTATAATCTGTTTTA
3112 ATAAA
1 ATAAA
3117 NNNNNNNNNN
Statistics
Matches: 147, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
162 4 0.03
163 3 0.02
172 11 0.07
173 128 0.87
174 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.35
Consensus pattern (162 bp):
ATAAAAATATTGAACATAAAATCAATTATGAGAGTATAAAACCATTTAGAGCGAGTAAGAAGGCT
TTTGAAGGAATGAGAGACTATAAAGGAACTTTTCTTACCAAAGAATCCCTTTTTCTTCACGTTTC
TCAAAGTAGATAATTAATTATAATCTGTTTTA
Done.