Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400911.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4074.0, 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: 2527
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.27
Warning! 622 characters in sequence are not A, C, G, or T
Found at i:1777 original size:343 final size:332
Alignment explanation
Indices: 1375--2139 Score: 713
Period size: 343 Copynumber: 2.2 Consensus size: 332
1365 NNNNNNNNNN
* * *
1375 TTTTTCTTCATGTTTCTCGAGGTAAGCATTCAATTATATTCTATTTTAAAGAAAAATATAAAAAA
1 TTTTTCTTCATGTTTCTCAAGGTAAGCATTCAATTATAGTCTATTTTAAACAAAAATATAAAAAA
* * * * * * * *
1440 ATTTAACTTAAAATCGA-TTATTACATTATAACACTATTTCAAGCGATTAACAAGGCTTTTGAAG
66 AGTCAACTTAAAAT-GACTTATCACATTATAAAACTATTTAAAGCGAGTAACAAGACTTTTGAAA
* * * * * ** *
1504 GAATGGGTGACTATAAATAGAATTTTTTTTGCCAATGAATCCCTTTCTCTTCATGTTGCTCGAGG
130 GAATGGATGACTATAAAT-GAACTTTTCTTGCCAATAAATACCTTTCTCTTCACATTGCTCAAGG
* * * *
1569 TAGACATTCAATTATAATCTATTTTGACT-AAAAATGTAAACAAATTTGAACTTAAAATCAATTT
194 TAAACATTCAATTATAATCTATTTTAACTAAAAAATGTAAA-AAAATTCAACTTAAAATCAATTT
* *
1633 TGAAATTATAAAACCATTTAAAGGGAGTAATAAGGCTTTTGAAGAAATAGNNNNNNNNNNTAGAC
258 TGAAATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATAG----------TAGAC
1698 TTTTCTTGCCAATGAATGCA
313 TTTTCTTGCCAATGAATGCA
* * *
1718 TTTTTCTTCATTTTTCTCAAGGT-AG-ATAGTCAATTAGT-GTCTGTTTTAACCAAAAATATAAA
1 TTTTTCTTCATGTTTCTCAAGGTAAGCAT--TCAATTA-TAGTCTATTTTAAACAAAAATATAAA
* * * *
1780 AAAGGTCAACTTAAAATTACTTATCAGATTATAAAACTATTTAAAGCGAGTAATAAGACTTTTGA
63 AAAAGTCAACTTAAAATGACTTATCACATTATAAAACTATTTAAAGCGAGTAACAAGACTTTTGA
* * * * **
1845 AAGAATGGATGACTATAAGTGGACTTTTCTTGCCAATAAATATCTTTTTCTTCACATTTTTCAAG
128 AAGAATGGATGACTATAAATGAACTTTTCTTGCCAATAAATACCTTTCTCTTCACATTGCTCAAG
* * * *
1910 GTAAACATTCAATTATAGTCTGTTTTAACTAAAAAAATGTAAAAAAATTCAATTTAAAATTAATT
193 GTAAACATTCAATTATAATCTATTTTAACT-AAAAAATGTAAAAAAATTCAACTTAAAATCAATT
* * * *
1975 TTGAGATTATAAAATAATTTAAAGCGAGTTATAAGGCTTTTGAAGGAATAGGT-GACTATNNNNN
257 TTGAAATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATA-GTAGACT-T-----
*
2039 NNNNNTTCTTGTCAATGAATGGC-
315 -----TTCTTGCCAATGAAT-GCA
* * *
2062 TTTTTCTACATGTTTC-CTAAGGTAAGCATTCAATTATTGTCTATTTTAATA-AAAAATGT-AAA
1 TTTTTCTTCATGTTTCTC-AAGGTAAGCATTCAATTATAGTCTATTTTAA-ACAAAAATATAAAA
*
2124 AAATTCAACTTAAAAT
64 AAAGTCAACTTAAAAT
2140 CANNNNNNNN
Statistics
Matches: 344, Mismatches: 54, Indels: 48
0.77 0.12 0.11
Matches are distributed among these distances:
333 4 0.01
334 2 0.01
341 2 0.01
342 62 0.18
343 198 0.58
344 70 0.20
345 4 0.01
346 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.36
Consensus pattern (332 bp):
TTTTTCTTCATGTTTCTCAAGGTAAGCATTCAATTATAGTCTATTTTAAACAAAAATATAAAAAA
AGTCAACTTAAAATGACTTATCACATTATAAAACTATTTAAAGCGAGTAACAAGACTTTTGAAAG
AATGGATGACTATAAATGAACTTTTCTTGCCAATAAATACCTTTCTCTTCACATTGCTCAAGGTA
AACATTCAATTATAATCTATTTTAACTAAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGA
AATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATAGTAGACTTTTCTTGCCAAT
GAATGCA
Found at i:1878 original size:171 final size:172
Alignment explanation
Indices: 1695--2033 Score: 429
Period size: 173 Copynumber: 2.0 Consensus size: 172
1685 NNNNNNNNTA
* * * *
1695 GACTTTTCTTGCCAATGAAT-GCATTTTTCTTCA-TTTTTCTCAAGGTAGATAGTCAATTAGT-G
1 GACTTTTCTTGCCAATAAATAGC-TTTTTCTTCACATTTT-TCAAGGTAAACAGTCAATTA-TAG
* * *
1757 TCTGTTTTAAC-CAAAAATATAAAAAAGGTCAACTTAAAATTACTTATCAGATTATAAAACT-AT
63 TCTGTTTTAACAAAAAAATATAAAAAAAGTCAACTTAAAATTAATTATCAGATTATAAAA-TAAT
1820 TTAAAGCGAGTAATAAGACTTTTGAAAGAAT-GGATGACTATAAGTG
127 TTAAAGCGAGTAATAAGACTTTTGAAAGAATAGG-TGACTATAAGTG
* *
1866 GACTTTTCTTGCCAATAAATATCTTTTTCTTCACATTTTTCAAGGTAAACATTCAATTATAGTCT
1 GACTTTTCTTGCCAATAAATAGCTTTTTCTTCACATTTTTCAAGGTAAACAGTCAATTATAGTCT
* * * * *
1931 GTTTTAACTAAAAAAATGTAAAAAAATTCAATTTAAAATTAATTTTGAGATTATAAAATAATTTA
66 GTTTTAAC-AAAAAAATATAAAAAAAGTCAACTTAAAATTAATTATCAGATTATAAAATAATTTA
* * *
1996 AAGCGAGTTATAAGGCTTTTGAAGGAATAGGTGACTAT
130 AAGCGAGTAATAAGACTTTTGAAAGAATAGGTGACTAT
2034 NNNNNNNNNN
Statistics
Matches: 144, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
170 1 0.01
171 58 0.40
172 6 0.04
173 77 0.53
174 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.37
Consensus pattern (172 bp):
GACTTTTCTTGCCAATAAATAGCTTTTTCTTCACATTTTTCAAGGTAAACAGTCAATTATAGTCT
GTTTTAACAAAAAAATATAAAAAAAGTCAACTTAAAATTAATTATCAGATTATAAAATAATTTAA
AGCGAGTAATAAGACTTTTGAAAGAATAGGTGACTATAAGTG
Found at i:2017 original size:173 final size:167
Alignment explanation
Indices: 1248--2141 Score: 583
Period size: 171 Copynumber: 5.2 Consensus size: 167
1238 TGTAATCTGG
* * * * * * *
1248 TTTAACCAATAATATAAAAAAATTAAACCTAAAATCAATTTTAATATTATAAAATTATTTAATGT
1 TTTAA-CAAAAATATAAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAA-TATTTAAAGC
* *** * *********
1313 GAGTAATAAGGCTTTTGAAGGAATACAAGACTATAAATGGACTTTTCTTTCCNNNNNNNNNNTTT
64 GAGTAATAAGGCTTTTGAAAGAAT-GGTGACTATAAATGGACTTTTCTTGCC-AATGAATCCTTT
* * *
1378 TTCTTCATGTTTCTCGAGGTAAGCATTCAATTATATTCTAT
127 TTCTTCATGTTTCTCAAGGTAAACATTCAATTATAGTCTAT
* * * * * *
1419 TTTAAAGAAAAATATAAAAAAATTTAACTTAAAATCGATTATT-ACATTATAACACTATTTCAAG
1 TTT-AACAAAAATATAAAAAAATTCAACTTAAAATCAATT-TTGAGATTATAA-AATATTTAAAG
* * * * * *
1483 CGATTAACAAGGCTTTTGAAGGAATGGGTGACTATAAATAGAATTTTTTTTGCCAATGAATCCCT
63 CGAGTAATAAGGCTTTTGAAAGAAT-GGTGACTATAAAT-GGACTTTTCTTGCCAATGAAT-CCT
* * * * *
1548 TTCTCTTCATGTTGCTCGAGGTAGACATTCAATTATAATCTAT
125 TTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATAGTCTAT
* * * * * *
1591 TTTGACTAAAAATGTAAACAAATTTGAACTTAAAATCAATTTTGAAATTATAAAACCATTTAAAG
1 TTTAAC-AAAAATATAAA-AAAATTCAACTTAAAATCAATTTTGAGATTATAAAA-TATTTAAAG
* * ********** * *
1656 GGAGTAATAAGGCTTTTG-AAGAAATAGNNNNNNNNNNTAGACTTTTCTTGCCAATGAATGCATT
63 CGAGTAATAAGGCTTTTGAAAG-AATGGTGACTATAAATGGACTTTTCTTGCCAATGAAT-CCTT
* * * * *
1720 TTTCTTCATTTTTCTCAAGGTAGATAGTCAATTAGT-GTCTGT
126 TTTCTTCATGTTTCTCAAGGTAAACATTCAATTA-TAGTCTAT
** * * * *
1762 TTTAACCAAAAATATAAAAAAGGTCAACTTAAAATTACTTATCAGATTATAAAACTATTTAAAGC
1 TTTAA-CAAAAATATAAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAA-TATTTAAAGC
* * * *
1827 GAGTAATAAGACTTTTGAAAGAATGGATGACTATAAGTGGACTTTTCTTGCCAATAAATATCTTT
64 GAGTAATAAGGCTTTTGAAAGAATGG-TGACTATAAATGGACTTTTCTTGCCAATGAAT-CCTTT
** * *
1892 TTCTTCACATTTTTCAAGGTAAACATTCAATTATAGTCTGT
127 TTCTTCATGTTTCTCAAGGTAAACATTCAATTATAGTCTAT
* * *
1933 TTTAACTAAAAAAATGTAAAAAAATTCAATTTAAAATTAATTTTGAGATTATAAAATAATTTAAA
1 TTTAAC---AAAAATATAAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAAT-ATTTAAA
* * ********** * *
1998 GCGAGTTATAAGGCTTTTGAAGGAATAGGTGACTATNNNNNNNNNNTTCTTGTCAATGAATGGCT
62 GCGAGTAATAAGGCTTTTGAAAGAAT-GGTGACTATAAATGGACTTTTCTTGCCAATGAAT-CCT
* * *
2063 TTTTCTACATGTTTC-CTAAGGTAAGCATTCAATTATTGTCTAT
125 TTTTCTTCATGTTTCTC-AAGGTAAACATTCAATTATAGTCTAT
* *
2106 TTTAATAAAAA-ATGTAAAAAATTCAACTTAAAATCA
1 TTTAACAAAAATAT-AAAAAAATTCAACTTAAAATCA
2142 NNNNNNNNNN
Statistics
Matches: 557, Mismatches: 144, Indels: 45
0.75 0.19 0.06
Matches are distributed among these distances:
169 1 0.00
170 83 0.15
171 210 0.38
172 78 0.14
173 183 0.33
174 2 0.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.36
Consensus pattern (167 bp):
TTTAACAAAAATATAAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAATATTTAAAGCGA
GTAATAAGGCTTTTGAAAGAATGGTGACTATAAATGGACTTTTCTTGCCAATGAATCCTTTTTCT
TCATGTTTCTCAAGGTAAACATTCAATTATAGTCTAT
Done.