Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401071.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_423.0, 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: 5131
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.25
Warning! 1581 characters in sequence are not A, C, G, or T
Found at i:622 original size:171 final size:169
Alignment explanation
Indices: 8--1088 Score: 705
Period size: 171 Copynumber: 6.5 Consensus size: 169
1 AAAACCT
* * ** * * * *
8 TTTAAAGCGAGTACTAAGGCTTTCGAAGGCGTGGGTAACTATAAATAGACTTTTTTTGCCAATGT
1 TTTAAAGTGAGTAATAAGG-TTTTAAAGGCGTGGGTTACTATAAATGGACTTTTCTTGCCAATGG
* * ** ** *
73 ATATATTTTTCTTCATGTTTCCCAAGGTAAACATTCAATTATTATCTGTTTCCACCGAAAATGTA
65 ATATCTTTTTCTTCATGTTTCCCAAGATAAACATTCAATTATTATCTGTTTTAACTAAAAAAGT-
* *
138 AAAAAAATTCAACTTAAAATCAATTATAAAGCTATAAAAACA
129 AAAAAAATTCAACTTAAAATCAATTATAGA-TTATAAAAACA
* * **** ** *
180 TTTAAAGTGAGTAATAAGGCTTTTGAAGACAACAGTTACTATAAATGGACTTTTCTTGAAAATAG
1 TTTAAAGTGAGTAATAAGG-TTTTAAAGGCGTGGGTTACTATAAATGGACTTTTCTTGCCAATGG
* * * * * *
245 ATACCTTTTT-TTCATGTTTCTCAAGGTAGACATTCAAGTATAATCTGTTTTAA-TAAAAAA-TA
65 ATATCTTTTTCTTCATGTTTCCCAAGATAAACATTCAATTATTATCTGTTTTAACTAAAAAAGTA
**
307 AAAAAAGTT-AACGAAAAATCAATTATAAGATTATAAAAACA
130 AAAAAA-TTCAACTTAAAATCAATTAT-AGATTATAAAAACA
* * * * *
348 TTTAAAGTGAGCAATAATGCTTTTAAAGGCTTGGGTTTCTATAAATGGACTTTTCTTGGCAATGG
1 TTTAAAGTGAGTAATAA-GGTTTTAAAGGCGTGGGTTACTATAAATGGACTTTTCTTGCCAATGG
* ** * *
413 ATATCATTTTCTTCATGTTTTTCAAGGA-AGACATTCAATTATTATCTATTTTAACTAAAAAAGT
65 ATATCTTTTTCTTCATGTTTCCCAA-GATAAACATTCAATTATTATCTGTTTTAACTAAAAAAGT
* * * *
477 AAAAAAATTCAGCTTAAAGTGAATTATGAGATTATAAAAATA
129 AAAAAAATTCAACTTAAAATCAATTAT-AGATTATAAAAACA
* *
519 TTTAAAGTGAGTAATAAGGTGTTTAAAGGGGTGGGTGACTATAAATGGACTTTTCTTGCCAATGG
1 TTTAAAGTGAGTAATAAGGT-TTTAAAGGCGTGGGTTACTATAAATGGACTTTTCTTGCCAATGG
* * * ** *
584 ATGTCTTTTTCTTCATGTTTCCCATGATAAATATTCAATTACAATATGTTTTAA-TAAAAAA-T-
65 ATATCTTTTTCTTCATGTTTCCCAAGATAAACATTCAATTATTATCTGTTTTAACTAAAAAAGTA
** * * *
646 --TCAATTGAA---AAAGT-AATTATGAGGTTAT-AAAACTA
130 AAAAAATTCAACTTAAAATCAATTAT-AGATTATAAAAAC-A
* * * * ** * *
681 TTTAAAGTAAATAACATGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTT-TT-----T--
1 TTTAAAGTGAGTAATAAGG-TTTTAAAGGCGTGGGTTACTATAAATGGACTTTTCTTGCCAATGG
* *** * * * * * ** *
738 -TAT-TTTTT-TTTATGTTTCTTTAGGTAGACATTCAAATATAACCAATTTTAA-TAAAAACTGT
65 ATATCTTTTTCTTCATGTTTCCCAAGATAAACATTCAATTATTATCTGTTTTAACTAAAAA-AGT
* * * * *
799 AAAAAACTTCAACTCAAAATTAATTATGAGATTGTAAAAATA
129 AAAAAAATTCAACTTAAAATCAATTAT-AGATTATAAAAACA
* ** * * * * * *
841 TTTAAAGTGAGTAATAAGACTTTCGAAGGCATGGGTGACTATAAATGGATTTTTTTTGCCTATTG
1 TTTAAAGTGAGTAATAAG-GTTTTAAAGGCGTGGGTTACTATAAATGGACTTTTCTTGCCAATGG
** * * * * * *
906 ATATCTTTTTCTTCACATTTTCTAAGGTAGACATTCAATTATAATCTGTTTTAA-TAAAAAATAT
65 ATATCTTTTTCTTCATGTTTCCCAAGATAAACATTCAATTATTATCTGTTTTAACTAAAAAA-GT
* * * * *
970 AAAAAAAGTAAACTTAAAATCAATTATGAAATTTTAAAAGCA
129 AAAAAAATTCAACTTAAAATCAATTAT-AGATTATAAAAACA
* ** * * * * *
1012 TTTAAACT-AGGTAA-ACAGGATTTCGAAGGCATGGGTAACTATGAACGGATTTTTCTTGCCAAT
1 TTTAAAGTGA-GTAATA-AGG-TTTTAAAGGCGTGGGTTACTATAAATGGACTTTTCTTGCCAAT
1075 --ATATCTTTTTCTTC
63 GGATATCTTTTTCTTC
1089 GCATTTTCTA
Statistics
Matches: 725, Mismatches: 146, Indels: 79
0.76 0.15 0.08
Matches are distributed among these distances:
151 35 0.05
152 5 0.01
153 3 0.00
156 6 0.01
159 4 0.01
160 60 0.08
161 12 0.02
162 58 0.08
163 6 0.01
166 6 0.01
168 91 0.13
169 60 0.08
170 32 0.04
171 289 0.40
172 58 0.08
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (169 bp):
TTTAAAGTGAGTAATAAGGTTTTAAAGGCGTGGGTTACTATAAATGGACTTTTCTTGCCAATGGA
TATCTTTTTCTTCATGTTTCCCAAGATAAACATTCAATTATTATCTGTTTTAACTAAAAAAGTAA
AAAAATTCAACTTAAAATCAATTATAGATTATAAAAACA
Found at i:2256 original size:171 final size:170
Alignment explanation
Indices: 1358--2480 Score: 878
Period size: 171 Copynumber: 6.6 Consensus size: 170
1348 TTTTCTAGGG
* * * *
1358 TAGACATTCAATTATAATCTGTTGTAGT-AAAAAGTATAAAAAAATCAACTTAAAATGAATTATG
1 TAGACATTCAATTATAATCTGTTTTAATAAAAAAATATAAAAAAATCAACTTAAAATCAATTATG
* ** * * * * *
1422 AGATTATAAAAATATTTAAAGCAAGTAA-ATAGGCTTTCGAAGGCATAGGTTACTATAGACGGAT
66 AGATTATAAAAACATTTAAAGTGAGTAATA-AGGCTTTCGAAGGCATGGGTGACTATAAATGGAC
* * * ** *
1486 TTTTCTTGCCAATGGATGTTTTTTTCTTCACGTTTCTTAACA
130 TTTTCTTG-CAATGGATATCTTTTTCTTCATGTTTCTCGAGA
* * * * *
1528 TAGACATGCAATTATAATCTGTTTTAAT-AAAAAATATCAAGAAATTAAACTCAAAATCAATTAT
1 TAGACATTCAATTATAATCTGTTTTAATAAAAAAATAT-AAAAAAATCAACTTAAAATCAATTAT
* ** * * * * * *
1592 GAGATTGTTTAACCATTTAAAGTGTGTAACAAGGTTTTTC-AATGGCATAGGTGACTATAAATCG
65 GAGATTATAAAAACATTTAAAGTGAGTAATAAGG-CTTTCGAA-GGCATGGGTGACTATAAATGG
* * * * *
1656 ACTTTTTTTTCAATGGATATCTTTTTCTTCATGTTCCCCGAGG
128 ACTTTTCTTGCAATGGATATCTTTTTCTTCATGTTTCTCGAGA
* * * * * ***
1699 TAAATATTTAATTATAATCTGTTTTAAT-AAAAAATATAAAAAAATTCAAGTTAAAATTAATNNN
1 TAGACATTCAATTATAATCTGTTTTAATAAAAAAATATAAAAAAA-TCAACTTAAAATCAATTAT
******* * * * * *
1763 NNNNNNNT-AAAACTATTTAAAGCGAGTAGTAAGGCTTTTGAAGGAATGGGTGACTATAAATTGA
65 GAGATTATAAAAAC-ATTTAAAGTGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGA
* * * *
1827 CTTATCTTGCCAAAGGATATCTTTTTCTTTACAT-TTTCT-AAGG
129 CTTTTCTTG-CAATGGATATCTTTTTC-TT-CATGTTTCTCGAGA
* * * *
1870 TAGATATTCGATTATTATCTGTTTTAACT--AAAAATATAAGAAAATTCAACTTAAAATCAATTA
1 TAGACATTCAATTATAATCTGTTTTAA-TAAAAAAATATAA-AAAAATCAACTTAAAATCAATTA
****************** *
1933 TNNNNNNNNNNNNNNNNNNAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGA
64 TGAGATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGA
*
1998 C-TTTCTTGTCAATGGATATCTTTTTCTTCAAGTTT-TCTGAGA
129 CTTTTCTTG-CAATGGATATCTTTTTCTTCATGTTTCTC-GAGA
* * * * *
2040 TAGACATTCAATTATAATCTTTTTTTATAAAAATATGA-AAAAAAATCAACTTAGAGTCAATTAT
1 TAGACATTCAATTATAATCTGTTTTAATAAAAAAAT-ATAAAAAAATCAACTTAAAATCAATTAT
* * * * * * *
2104 GAGATTATAAAAGCATTTAAAGTTAGCAATAAGGCTGTCGAAGGTATGAGTGACTATAAATAGAC
65 GAGATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGAC
*
2169 TTTTCTTAGCAATGGATATCTTTTTCTTCATGTTTCTCGAGG
130 TTTTCTT-GCAATGGATATCTTTTTCTTCATGTTTCTCGAGA
* * * **
2211 CAGATATTCAATTGTAATCTGTTTTAATAAAAAAATATAAAAAAATTCAACACAAAATCAATTAT
1 TAGACATTCAATTATAATCTGTTTTAATAAAAAAATATAAAAAAA-TCAACTTAAAATCAATTAT
* * * **
2276 AAGATTATAAAATCATTTAAAGTGAGTAATAAGAG-TTTCGAAGGCATGGGTGTCTACCAATGGA
65 GAGATTATAAAAACATTTAAAGTGAGTAATAAG-GCTTTCGAAGGCATGGGTGACTATAAATGGA
* * * *
2340 CTTTTCTTGCTAATGAATATCTTCTTCTTTATGTTTCTCGAGT
129 CTTTTCTTGC-AATGGATATCTTTTTCTTCATGTTTCTCGAGA
* * * * *
2383 TAGCCATTCAATTTTAATTTGTTTTAAT---AAAA-ATAAAAAAATAAACTTAAAATTAATTATG
1 TAGACATTCAATTATAATCTGTTTTAATAAAAAAATATAAAAAAATCAACTTAAAATCAATTATG
* *
2444 AGATTATAAAAAAATTTAAAGCGAGTAATAAGGCTTT
66 AGATTATAAAAACATTTAAAGTGAGTAATAAGGCTTT
2481 TGAANNNNNN
Statistics
Matches: 750, Mismatches: 176, Indels: 57
0.76 0.18 0.06
Matches are distributed among these distances:
166 1 0.00
167 47 0.06
168 12 0.02
169 10 0.01
170 177 0.24
171 331 0.44
172 168 0.22
173 4 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (170 bp):
TAGACATTCAATTATAATCTGTTTTAATAAAAAAATATAAAAAAATCAACTTAAAATCAATTATG
AGATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACT
TTTCTTGCAATGGATATCTTTTTCTTCATGTTTCTCGAGA
Found at i:3939 original size:171 final size:169
Alignment explanation
Indices: 3528--4050 Score: 611
Period size: 170 Copynumber: 3.1 Consensus size: 169
3518 NNNNNNACCA
* * * *
3528 TTTAAAACAAGTAATAAGGCTTTCGAAGGCACAGGTGACTATAAATGGATTTTTCTTACCAACAG
1 TTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATGGACTTTTCTTACCAATAG
* * *
3593 ATATCTTTTTCTTTACGTTTCCCAAGGCATACATTGAATTATTATCTATTTTAGCAAAAAATATA
66 ATATCTTTTTCTTTACGTTTCCCAAGGCA-AAATTCAATTATTATCTATTTTAACAAAAAATATA
3658 AAAAAATTAACTTAAAA-CAAATTATGAGATTATAAAACCG
130 AAAAAATTAACTTAAAATC-AATTATGAGATTATAAAACCG
* * ** * * *
3698 TTTAAAGCGAGTAATAAGGTTTTTTAAGGCATAGGCGACTATAAATAGACTTTTCTTACCAATGG
1 TTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATGGACTTTTCTTACCAATAG
** * * * * *
3763 ATATCTTTTTCTGCATGTGTT-CCATGGCAGAAATTCAATTATTATCTGTTTTAACTAAAAATGT
66 ATATCTTTTTCTTTACGT-TTCCCAAGGCA-AAATTCAATTATTATCTATTTTAACAAAAAATAT
** *****
3827 AAAAAAATTCAGGTTAAAATCAATTATGAGATTATAANNNNN
129 AAAAAAATT-AACTTAAAATCAATTATGAGATTATAAAACCG
***** * * *
3869 NNNNNAGCAAGTAATAAGGCTTTCGAAGGCATGGGTGACGATAAATGGACTTTTCTTACTAATAG
1 TTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATGGACTTTTCTTACCAATAG
* * *
3934 ATATCTTTTTGTTTACGTTTCCCAAGGTAAATATTCAATTATTATCTATTTTAACCAAAAATATA
66 ATATCTTTTTCTTTACGTTTCCCAAGGCAAA-ATTCAATTATTATCTATTTTAACAAAAAATATA
3999 AAAAAATTAACTTAAAATCAATTATGA-ATTATAAAACCG
130 AAAAAATTAACTTAAAATCAATTATGAGATTATAAAACCG
*
4038 TTTAAAGCGAGTA
1 TTTAAAGCAAGTA
4051 NNNNNNNNNN
Statistics
Matches: 282, Mismatches: 66, Indels: 11
0.79 0.18 0.03
Matches are distributed among these distances:
169 14 0.05
170 134 0.48
171 133 0.47
172 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (169 bp):
TTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATGGACTTTTCTTACCAATAG
ATATCTTTTTCTTTACGTTTCCCAAGGCAAAATTCAATTATTATCTATTTTAACAAAAAATATAA
AAAAATTAACTTAAAATCAATTATGAGATTATAAAACCG
Found at i:4274 original size:335 final size:337
Alignment explanation
Indices: 3528--4312 Score: 819
Period size: 335 Copynumber: 2.3 Consensus size: 337
3518 NNNNNNACCA
** * *
3528 TTTAAAACAAGTAATAAGGCTTTCGAAGGCACAGGTGACTATAAATGGATTTTTCTTACCAACAG
1 TTTAAAACAAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATAG
* * *
3593 ATATCTTTTTCTTTACGTTTCCCAAGGCATACATTGAATTATTATCTATTTTAGCAAAAAATATA
66 ATATCTTTTTCTTTACGTTTCCCAAGGCAAACATTCAATTATTATCTATTTTAACAAAAAATATA
**
3658 AAAAAATTAACTTAAAACAAATTATGAGATTATAAAACCGTTTAAAGCGAGTAATAAGGTTTTTT
131 AAAAAATTAACTTAAAACAAATTATGAGATTATAAAACCGTTTAAAGCGAGTAATAAGGTTTTCA
*
3723 AAGGCATAGGCGACTATAAATAGACTTTTCTTACCAATGGATATCTTTTTCTGCATGTGTTCCAT
196 AAGGCATAGGCGACTATAAATAGA----TCTTACCAATGGATACCTTTTTCTGCATGTGTTCCAT
* * ** *
3788 GGCAGAAATTCAATTATTATCTGTTTTAACTAAAAATGTAAAAAAATTCAGGTTAAAATCAATTA
257 GGCAGAAATTCAATTATAATCTATTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAACTA
* *****
3853 TGAGATTATAANNNNN
322 TAAGATTATAAAACTC
***** * * *
3869 NNNNNAGCAAGTAATAAGGCTTTCGAAGGCATGGGTGACGATAAATGGACTTTTCTTACTAATAG
1 TTTAAAACAAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATAG
* * * *
3934 ATATCTTTTTGTTTACGTTTCCCAAGGTAAATATTCAATTATTATCTATTTTAACCAAAAATATA
66 ATATCTTTTTCTTTACGTTTCCCAAGGCAAACATTCAATTATTATCTATTTTAACAAAAAATATA
**********
3999 AAAAAATTAACTTAAAATC-AATTATGA-ATTATAAAACCGTTTAAAGCGAGTANNNNNNNNNNC
131 AAAAAATTAACTTAAAA-CAAATTATGAGATTATAAAACCGTTTAAAGCGAGTAATAAGGTTTTC
* * * * *
4062 AAAGGCATAGGTGACTATAAATAGA-CTTGCCAATGGCTACCTTTTTCTTCATGT-TT-CTTGAG
195 AAAGGCATAGGCGACTATAAATAGATCTTACCAATGGATACCTTTTTCTGCATGTGTTCCAT--G
* *********
4124 GCAG-ACTCTCAATTATAATCTATTTTAA-TAANNNNNNNNNNAAAATTCAACTTAAAATCAACT
258 GCAGAAAT-TCAATTATAATCTATTTTAACTAA-AAATGTAAAAAAATTCAACTTAAAATCAACT
4187 ATAAGATTATAAAACTC
321 ATAAGATTATAAAACTC
* * * * *
4204 TTTAAAACGAGTAATAAGGCTTTTGAAGGCATGGGTGACTCTAAATGGACTTTTATTACCAATGG
1 TTTAAAACAAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATAG
* * *** *
4269 ATATCTTTTTCTTCATGTTTCTTGAGGCAGACATTCAATTATTA
66 ATATCTTTTTCTTTACGTTTCCCAAGGCAAACATTCAATTATTA
4313 NNNNNNNNNN
Statistics
Matches: 359, Mismatches: 80, Indels: 16
0.79 0.18 0.04
Matches are distributed among these distances:
333 2 0.01
334 7 0.02
335 165 0.46
340 48 0.13
341 136 0.38
342 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.34
Consensus pattern (337 bp):
TTTAAAACAAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATAG
ATATCTTTTTCTTTACGTTTCCCAAGGCAAACATTCAATTATTATCTATTTTAACAAAAAATATA
AAAAAATTAACTTAAAACAAATTATGAGATTATAAAACCGTTTAAAGCGAGTAATAAGGTTTTCA
AAGGCATAGGCGACTATAAATAGATCTTACCAATGGATACCTTTTTCTGCATGTGTTCCATGGCA
GAAATTCAATTATAATCTATTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAACTATAAG
ATTATAAAACTC
Done.