Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398363.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1660.0, 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, 766
Length: 1278
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:307 original size:171 final size:171
Alignment explanation
Indices: 1--1275 Score: 598
Period size: 171 Copynumber: 7.5 Consensus size: 171
*
1 GTTTTAATC-AAAAATATAAAAAAATCT-AACTTAAAATTAATTATGAGATTATAATACAGTTTA
1 GTTTTAA-CAAAAAATATAAAAAAAT-TAAACTTAAAATCAATTATGAGATTATAATACAGTTTA
*** * * * * * *********** *
64 AAATGAGTAACAAGGCTTTCTAAGGAGTAAGTGACTATAAATGGACTTTTCNNNNNNNNNNATGC
64 AAGCCAGTAACAAGGCTTTCAAAGGAATAGGTAACTATAAAAGGACTTTTTTTGCCAAGGAATGT
* *
129 ATTTTTCTTCATGTTTCTCGAGGTAAACATTTAATTATAGTCT
129 GTTTTTCTTCATGTTTCTCGAGGTAAACATTCAATTATAGTCT
* * **********
172 GTTTTAAGAAAAAATATAAAATAATTAAACTTAAAATCAATTATGAGATTATNNNNNNNNNNAAA
1 GTTTTAACAAAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGATTATAATACAGTTTAAA
* * * * * *
237 GCGAGTAATAAGGCTTTTGAAA-GAATGGGTAACTATAAATGGACTTTTTTTGCCAATGAATGTG
66 GCCAGTAACAAGGC-TTTCAAAGGAATAGGTAACTATAAAAGGACTTTTTTTGCCAAGGAATGTG
* *
301 TTTTTCTTTATGTTACTCGAGGTAAACATTCAATTATTA-TCT
130 TTTTTCTTCATGTTTCTCGAGGTAAACATTCAATTA-TAGTCT
* * *
343 GTTTTAACTAGAAATATAAAAAAATTTATA-TTAAAATCAATTATGAGATTATAATACAGTTTAA
1 GTTTTAACAAAAAATATAAAAAAA-TTAAACTTAAAATCAATTATGAGATTATAATACAGTTTAA
* * *
407 AGCCAGTAACAAGGCTTTCAAAGGAATAGGTGACTGTAAAAGGACTTTTTTTTCCAAGGAATGTG
65 AGCCAGTAACAAGGCTTTCAAAGGAATAGGTAACTATAAAAGGACTTTTTTTGCCAAGGAATGTG
* * *
472 TTTTTCTTCATGTTTCTTGAGCTAGACATTCAATTATAGTCT
130 TTTTTCTTCATGTTTCTCGAGGTAAACATTCAATTATAGTCT
* * * ********** * * *
514 GTTTTATCCAAAAATATAAAAAAATTTAACTTNNNNNNNNNNATAAGATTATAAAACAATTTAAA
1 GTTTTAACAAAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGATTATAATACAGTTTAAA
*** * * * * * ** * *
579 ATGAATAATAAGGCTATTGAAA-GAATGGGTGACTATAAATTGACTTTTTGT-CTCAATGAATAG
66 GCCAGTAACAAGGCT-TTCAAAGGAATAGGTAACTATAAAAGGACTTTTTTTGC-CAAGGAAT-G
* * * * * *
642 CT-TTTTT-TAT-ACGTTTCTCAAGGCAAGCATTTAATTATAATCT
128 -TGTTTTTCT-TCATGTTTCTCGAGGTAAACATTCAATTATAGTCT
** ** * * * ********** *
685 GTTTTAATGAAAAATGCAAAACAATTCAGCTTAAAATCAATTNNNNNNNNNNAAAACCA-TTTAA
1 GTTTTAACAAAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGATTATAATA-CAGTTTAA
** * * * * * * * *
749 AGTGAATAATAAGACTTTTGAAA-GAAT-GAGTGACTATAAATGGACTTTTCTTGACC-ATG-AT
65 AGCCAGTAACAAGGC-TTTCAAAGGAATAG-GTAACTATAAAAGGACTTTTTTTG-CCAAGGAAT
* * * * *
810 GTATTTTTCTTCATGTTTCTCAATGTACACATTCCATTATAGTCT
127 GTGTTTTTCTTCATGTTTCTCGAGGTAAACATTCAATTATAGTCT
* * * * * *
855 ATTTTATCCAAAAATATAAAAAAATTCAGCTTAAAATCAATTATGAGATGATGAA-ACCA-TTTA
1 GTTTTAACAAAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGATTAT-AATA-CAGTTTA
* * ** ********** * * * *
918 AAGCAAGTAATAAGGCTTTTGAAGGAATNNNNNNNNNNAAATGGACTTTTCTTGCCAATGAATGC
64 AAGCCAGTAACAAGGCTTTCAAAGGAATAGGTAACTATAAAAGGACTTTTTTTGCCAAGGAATGT
* ** * * * *
983 ATTTTTCTTCACATTTCGCAAGGTAGACATTCATTTATTA-TCT
129 GTTTTTCTTCATGTTTCTCGAGGTAAACATTCAATTA-TAGTCT
* * * * * *
1026 GTTTTAACCAAAAATATAAAAAAATTTAGCTTAAAATTAATTATGAGATTATAATATATTTTAAA
1 GTTTTAACAAAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGATTATAATACAGTTTAAA
** * * * * * * * *
1091 GTAAATAACAAGGCTTTCGAAA-GAATAGGTGACTACAAATGGACTTTTCTTGTCAATGAATGCG
66 GCCAGTAACAAGGCTTTC-AAAGGAATAGGTAACTATAAAAGGACTTTTTTTGCCAAGGAATGTG
* * * * * *
1155 TTTTTCTTCACGTTTCTTGAGGGAGACATTCAGTTGCT-GTCT
130 TTTTTCTTCATGTTTCTCGAGGTAAACATTCAATT-ATAGTCT
* * * * * *
1197 ATTTTAACCAAAAATATAAAAAAATTTAACTTAAAATC-A--ATGAGATTATAAAATAATTTAAA
1 GTTTTAACAAAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGATTATAATACAGTTTAAA
* *
1259 GCGAGTAATAAGGCTTT
66 GCCAGTAACAAGGCTTT
1276 TGA
Statistics
Matches: 846, Mismatches: 226, Indels: 67
0.74 0.20 0.06
Matches are distributed among these distances:
168 35 0.04
169 14 0.02
170 124 0.15
171 640 0.76
172 31 0.04
173 2 0.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (171 bp):
GTTTTAACAAAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGATTATAATACAGTTTAAA
GCCAGTAACAAGGCTTTCAAAGGAATAGGTAACTATAAAAGGACTTTTTTTGCCAAGGAATGTGT
TTTTCTTCATGTTTCTCGAGGTAAACATTCAATTATAGTCT
Found at i:1170 original size:512 final size:503
Alignment explanation
Indices: 242--1171 Score: 989
Period size: 512 Copynumber: 1.8 Consensus size: 503
232 NNAAAGCGAG
* * * *
242 TAATAAGGCTTTTGAAAGAATGGGTAACTATAAATGGACTTTTTTTGCCAATGAATGTGTTTTTC
1 TAATAAGACTTTTGAAAGAATGAGTAACTATAAATGGACTTTTCTTGCCAATGAATGTATTTTTC
* * * * * * *
307 TTTATGTTACTCGAGGTAAACATTCAATTATTATCTGTTTTAACTAGAAATATAAAAAAATTTAT
66 TTCATGTTACTCAAGGTAAACATTCAATTATTATCTATTTTAACCAAAAATATAAAAAAATTCAG
* *
372 ATTAAAATCAATTATGAGATTATAATACAGTTTAAAGCCAGTAACAAGGCTTTCAAAGGAATAGG
131 ATTAAAATCAATTATGAGATGATAATACAGTTTAAAGCAAGTAACAAGGCTTTCAAAGGAATAGG
* * ** ** ***
437 TGACTGTAAAAGGACTTTTTTTTCCAAGGAATGTGTTTTTCTTCATGTTTCTTGAGCTAGACATT
196 TGACTGTAAAAGGACTTTTCTTGCCAAGGAATGCATTTTTCTTCACATTTCGCAAGCTAGACATT
* **********
502 CAATTATAGTCTGTTTTATCCAAAAATATAAAAAAATTTAACTTNNNNNNNNNNATAAGATTATA
261 CAATTATAGTCTGTTTTAACCAAAAATATAAAAAAATTTAACTTAAAATTAATTATAAGATTATA
* * * * *
567 AAACAATTTAAAATGAATAATAAGGCTATTGAAAGAATGGGTGACTATAAATTGACTTTTTGTCT
326 AAACAATTTAAAATAAATAACAAGGCTATTGAAAGAATAGGTGACTACAAATGGACTTTTTGTCT
*
632 CAATGAATAGCTTTTTTTATACGTTTCTCAAGGCAAGCATTTAATTATAATCTGTTTTAATGAAA
391 CAATGAATAGCTTTTTTTACACGTTTCTCAAGGCAAGCATTTAATTATAATCTGTTTTAATGAAA
697 AATGCAAAACAATTCAGCTTAAAATCAATTNNNNNNNNNNAAAACCATTTAAAGTGAA
456 AATGCAAAACAATTCAGCTTAAAATCAATT----------AAAACCATTTAAAGTGAA
*
755 TAATAAGACTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTGACC-ATG-ATGTATTTTT
1 TAATAAGACTTTTGAAAGAATGAGTAACTATAAATGGACTTTTCTTG-CCAATGAATGTATTTTT
* * * * *
818 CTTCATGTTTCTCAATGTACACATTCCATTA-TAGTCTATTTTATCCAAAAATATAAAAAAATTC
65 CTTCATGTTACTCAAGGTAAACATTCAATTATTA-TCTATTTTAACCAAAAATATAAAAAAATTC
* * **
882 AGCTTAAAATCAATTATGAGATGATGAA-ACCA-TTTAAAGCAAGTAATAAGGCTTTTGAAGGAA
129 AGATTAAAATCAATTATGAGATGAT-AATA-CAGTTTAAAGCAAGTAACAAGGCTTTCAAAGGAA
********** * * *
945 TNNNNNNNNNNAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCACATTTCGCAAGGTAGA
192 TAGGTGACTGTAAAAGGACTTTTCTTGCCAAGGAATGCATTTTTCTTCACATTTCGCAAGCTAGA
* * *
1010 CATTCATTTATTA-TCTGTTTTAACCAAAAATATAAAAAAATTTAGCTTAAAATTAATTATGAGA
257 CATTCAATTA-TAGTCTGTTTTAACCAAAAATATAAAAAAATTTAACTTAAAATTAATTATAAGA
* * * *
1074 TTATAATATATTTTAAAGTAAATAACAAGGCT-TTCGAAAGAATAGGTGACTACAAATGGACTTT
321 TTATAAAACAATTTAAAATAAATAACAAGGCTATT-GAAAGAATAGGTGACTACAAATGGACTTT
*
1138 TCT-TGTCAATGAAT-GCGTTTTTCTT-CACGTTTCT
385 T-TGTCTCAATGAATAGC-TTTTT-TTACACGTTTCT
1172 TGAGGGAGAC
Statistics
Matches: 338, Mismatches: 70, Indels: 19
0.79 0.16 0.04
Matches are distributed among these distances:
511 6 0.02
512 275 0.81
513 55 0.16
514 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.36
Consensus pattern (503 bp):
TAATAAGACTTTTGAAAGAATGAGTAACTATAAATGGACTTTTCTTGCCAATGAATGTATTTTTC
TTCATGTTACTCAAGGTAAACATTCAATTATTATCTATTTTAACCAAAAATATAAAAAAATTCAG
ATTAAAATCAATTATGAGATGATAATACAGTTTAAAGCAAGTAACAAGGCTTTCAAAGGAATAGG
TGACTGTAAAAGGACTTTTCTTGCCAAGGAATGCATTTTTCTTCACATTTCGCAAGCTAGACATT
CAATTATAGTCTGTTTTAACCAAAAATATAAAAAAATTTAACTTAAAATTAATTATAAGATTATA
AAACAATTTAAAATAAATAACAAGGCTATTGAAAGAATAGGTGACTACAAATGGACTTTTTGTCT
CAATGAATAGCTTTTTTTACACGTTTCTCAAGGCAAGCATTTAATTATAATCTGTTTTAATGAAA
AATGCAAAACAATTCAGCTTAAAATCAATTAAAACCATTTAAAGTGAA
Done.