Multiple sequence alignment - TraesCS7A01G189800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G189800 chr7A 100.000 2849 0 0 1 2849 147053522 147050674 0.000000e+00 5262
1 TraesCS7A01G189800 chr7A 91.424 653 45 4 2198 2849 191204452 191205094 0.000000e+00 885
2 TraesCS7A01G189800 chr7D 87.051 2116 136 68 120 2184 146236726 146234698 0.000000e+00 2263
3 TraesCS7A01G189800 chr7D 89.940 666 43 7 2190 2849 168420189 168419542 0.000000e+00 837
4 TraesCS7A01G189800 chr7D 97.826 92 2 0 1 92 146236813 146236722 2.940000e-35 159
5 TraesCS7A01G189800 chr7B 93.391 923 43 11 995 1907 108558490 108557576 0.000000e+00 1351
6 TraesCS7A01G189800 chr7B 90.813 849 47 15 3 844 108559751 108558927 0.000000e+00 1107
7 TraesCS7A01G189800 chr7B 84.116 277 15 10 1940 2189 108555654 108555380 1.020000e-59 241
8 TraesCS7A01G189800 chr3D 93.185 631 30 4 2211 2840 300145931 300146549 0.000000e+00 915
9 TraesCS7A01G189800 chr4A 91.441 666 47 3 2186 2849 428153223 428152566 0.000000e+00 905
10 TraesCS7A01G189800 chr2D 91.317 668 44 6 2185 2849 32461423 32462079 0.000000e+00 900
11 TraesCS7A01G189800 chr2D 90.259 657 40 7 2185 2840 300425668 300426301 0.000000e+00 837
12 TraesCS7A01G189800 chr1D 91.541 662 38 3 2189 2849 464785512 464786156 0.000000e+00 896
13 TraesCS7A01G189800 chr5D 91.403 663 37 5 2189 2849 26740974 26740330 0.000000e+00 891
14 TraesCS7A01G189800 chr5D 91.536 638 35 4 2213 2849 318491241 318490622 0.000000e+00 861
15 TraesCS7A01G189800 chr5D 93.128 422 20 2 2429 2849 264616624 264616211 6.750000e-171 610
16 TraesCS7A01G189800 chr5D 91.606 274 14 2 2577 2849 208189640 208189375 1.250000e-98 370
17 TraesCS7A01G189800 chr5B 91.031 669 45 6 2182 2849 123797487 123796833 0.000000e+00 889
18 TraesCS7A01G189800 chr6D 92.138 636 39 4 2215 2849 80593266 80593891 0.000000e+00 887
19 TraesCS7A01G189800 chr1A 90.937 662 49 4 2187 2847 573697912 573698563 0.000000e+00 880
20 TraesCS7A01G189800 chr4D 90.772 661 47 5 2190 2849 21476097 21475450 0.000000e+00 870
21 TraesCS7A01G189800 chr6A 90.299 670 47 8 2189 2849 256751918 256751258 0.000000e+00 861
22 TraesCS7A01G189800 chr6A 90.181 662 49 8 2190 2849 10057857 10058504 0.000000e+00 848
23 TraesCS7A01G189800 chr6B 91.094 640 39 4 2211 2849 649810106 649809484 0.000000e+00 850


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G189800 chr7A 147050674 147053522 2848 True 5262.000000 5262 100.0000 1 2849 1 chr7A.!!$R1 2848
1 TraesCS7A01G189800 chr7A 191204452 191205094 642 False 885.000000 885 91.4240 2198 2849 1 chr7A.!!$F1 651
2 TraesCS7A01G189800 chr7D 146234698 146236813 2115 True 1211.000000 2263 92.4385 1 2184 2 chr7D.!!$R2 2183
3 TraesCS7A01G189800 chr7D 168419542 168420189 647 True 837.000000 837 89.9400 2190 2849 1 chr7D.!!$R1 659
4 TraesCS7A01G189800 chr7B 108555380 108559751 4371 True 899.666667 1351 89.4400 3 2189 3 chr7B.!!$R1 2186
5 TraesCS7A01G189800 chr3D 300145931 300146549 618 False 915.000000 915 93.1850 2211 2840 1 chr3D.!!$F1 629
6 TraesCS7A01G189800 chr4A 428152566 428153223 657 True 905.000000 905 91.4410 2186 2849 1 chr4A.!!$R1 663
7 TraesCS7A01G189800 chr2D 32461423 32462079 656 False 900.000000 900 91.3170 2185 2849 1 chr2D.!!$F1 664
8 TraesCS7A01G189800 chr2D 300425668 300426301 633 False 837.000000 837 90.2590 2185 2840 1 chr2D.!!$F2 655
9 TraesCS7A01G189800 chr1D 464785512 464786156 644 False 896.000000 896 91.5410 2189 2849 1 chr1D.!!$F1 660
10 TraesCS7A01G189800 chr5D 26740330 26740974 644 True 891.000000 891 91.4030 2189 2849 1 chr5D.!!$R1 660
11 TraesCS7A01G189800 chr5D 318490622 318491241 619 True 861.000000 861 91.5360 2213 2849 1 chr5D.!!$R4 636
12 TraesCS7A01G189800 chr5B 123796833 123797487 654 True 889.000000 889 91.0310 2182 2849 1 chr5B.!!$R1 667
13 TraesCS7A01G189800 chr6D 80593266 80593891 625 False 887.000000 887 92.1380 2215 2849 1 chr6D.!!$F1 634
14 TraesCS7A01G189800 chr1A 573697912 573698563 651 False 880.000000 880 90.9370 2187 2847 1 chr1A.!!$F1 660
15 TraesCS7A01G189800 chr4D 21475450 21476097 647 True 870.000000 870 90.7720 2190 2849 1 chr4D.!!$R1 659
16 TraesCS7A01G189800 chr6A 256751258 256751918 660 True 861.000000 861 90.2990 2189 2849 1 chr6A.!!$R1 660
17 TraesCS7A01G189800 chr6A 10057857 10058504 647 False 848.000000 848 90.1810 2190 2849 1 chr6A.!!$F1 659
18 TraesCS7A01G189800 chr6B 649809484 649810106 622 True 850.000000 850 91.0940 2211 2849 1 chr6B.!!$R1 638

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
818 877 0.108709 GCCGAACGTGTGGTACCATA 60.109 55.0 19.72 13.49 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2291 4590 0.322098 TGTATTGGAGTTGTGGCCCG 60.322 55.0 0.0 0.0 0.0 6.13 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 7.169140 ACTTTGTTTTCCATTTCGTTTAGCATC 59.831 33.333 0.00 0.00 0.00 3.91
92 125 2.093500 ACGGCGCATCATGGATATGTAT 60.093 45.455 10.83 0.00 35.73 2.29
93 126 2.286025 CGGCGCATCATGGATATGTATG 59.714 50.000 10.83 0.00 35.73 2.39
94 127 3.273434 GGCGCATCATGGATATGTATGT 58.727 45.455 10.83 0.00 35.73 2.29
95 128 3.064408 GGCGCATCATGGATATGTATGTG 59.936 47.826 10.83 0.00 36.51 3.21
96 129 3.486375 GCGCATCATGGATATGTATGTGC 60.486 47.826 0.30 10.02 43.02 4.57
97 130 3.685756 CGCATCATGGATATGTATGTGCA 59.314 43.478 15.40 0.00 35.73 4.57
98 131 4.154556 CGCATCATGGATATGTATGTGCAA 59.845 41.667 0.00 0.00 35.73 4.08
99 132 5.163693 CGCATCATGGATATGTATGTGCAAT 60.164 40.000 0.00 0.00 35.73 3.56
100 133 6.037391 CGCATCATGGATATGTATGTGCAATA 59.963 38.462 0.00 0.00 35.73 1.90
101 134 7.415229 GCATCATGGATATGTATGTGCAATAG 58.585 38.462 0.00 0.00 35.73 1.73
102 135 6.990341 TCATGGATATGTATGTGCAATAGC 57.010 37.500 0.00 0.00 37.12 2.97
103 136 6.714278 TCATGGATATGTATGTGCAATAGCT 58.286 36.000 0.00 0.00 37.33 3.32
104 137 6.596497 TCATGGATATGTATGTGCAATAGCTG 59.404 38.462 0.00 0.00 37.33 4.24
105 138 5.247862 TGGATATGTATGTGCAATAGCTGG 58.752 41.667 0.00 0.00 42.74 4.85
106 139 4.637534 GGATATGTATGTGCAATAGCTGGG 59.362 45.833 0.00 0.00 42.74 4.45
107 140 3.582998 ATGTATGTGCAATAGCTGGGT 57.417 42.857 0.00 0.00 42.74 4.51
108 141 4.705110 ATGTATGTGCAATAGCTGGGTA 57.295 40.909 0.00 0.00 42.74 3.69
109 142 4.071961 TGTATGTGCAATAGCTGGGTAG 57.928 45.455 0.00 0.00 42.74 3.18
110 143 3.454447 TGTATGTGCAATAGCTGGGTAGT 59.546 43.478 0.00 0.00 42.74 2.73
111 144 2.401583 TGTGCAATAGCTGGGTAGTG 57.598 50.000 0.00 3.39 42.74 2.74
112 145 1.905894 TGTGCAATAGCTGGGTAGTGA 59.094 47.619 10.68 0.00 42.74 3.41
113 146 2.280628 GTGCAATAGCTGGGTAGTGAC 58.719 52.381 10.68 3.97 42.74 3.67
114 147 1.134818 TGCAATAGCTGGGTAGTGACG 60.135 52.381 10.68 0.00 42.74 4.35
115 148 1.134788 GCAATAGCTGGGTAGTGACGT 60.135 52.381 10.68 0.00 37.91 4.34
116 149 2.677037 GCAATAGCTGGGTAGTGACGTT 60.677 50.000 10.68 0.00 37.91 3.99
117 150 3.429822 GCAATAGCTGGGTAGTGACGTTA 60.430 47.826 10.68 0.00 37.91 3.18
118 151 4.110482 CAATAGCTGGGTAGTGACGTTAC 58.890 47.826 1.53 1.53 0.00 2.50
119 152 1.624336 AGCTGGGTAGTGACGTTACA 58.376 50.000 13.41 0.00 0.00 2.41
120 153 2.176889 AGCTGGGTAGTGACGTTACAT 58.823 47.619 13.41 0.83 0.00 2.29
121 154 2.094182 AGCTGGGTAGTGACGTTACATG 60.094 50.000 13.41 0.00 0.00 3.21
122 155 2.353406 GCTGGGTAGTGACGTTACATGT 60.353 50.000 13.41 2.69 0.00 3.21
123 156 3.119388 GCTGGGTAGTGACGTTACATGTA 60.119 47.826 13.41 0.08 0.00 2.29
128 161 3.505464 AGTGACGTTACATGTAGGAGC 57.495 47.619 13.41 0.00 0.00 4.70
156 189 3.797451 TTTTGTGCTGCACATTCAAGA 57.203 38.095 33.25 16.60 44.16 3.02
169 202 7.366513 TGCACATTCAAGATTTGATTTCGTTA 58.633 30.769 0.00 0.00 39.84 3.18
170 203 7.864882 TGCACATTCAAGATTTGATTTCGTTAA 59.135 29.630 0.00 0.00 39.84 2.01
244 278 4.736793 GCATTTCATTTGATCGTGATGGTC 59.263 41.667 0.00 0.00 0.00 4.02
245 279 5.676837 GCATTTCATTTGATCGTGATGGTCA 60.677 40.000 0.00 0.00 0.00 4.02
246 280 4.944962 TTCATTTGATCGTGATGGTCAC 57.055 40.909 0.07 0.07 43.65 3.67
255 289 1.303309 GTGATGGTCACATAGGCTGC 58.697 55.000 0.00 0.00 46.22 5.25
259 293 0.181114 TGGTCACATAGGCTGCATCC 59.819 55.000 0.00 0.00 0.00 3.51
350 385 4.992381 GCTAGGGCGAAGTTTATATGTG 57.008 45.455 0.00 0.00 0.00 3.21
351 386 4.377897 GCTAGGGCGAAGTTTATATGTGT 58.622 43.478 0.00 0.00 0.00 3.72
360 395 8.433126 GGCGAAGTTTATATGTGTATATGTGTC 58.567 37.037 0.00 0.00 31.97 3.67
361 396 8.974408 GCGAAGTTTATATGTGTATATGTGTCA 58.026 33.333 0.00 0.00 31.97 3.58
371 406 5.581874 TGTGTATATGTGTCAATGTCTGCAG 59.418 40.000 7.63 7.63 0.00 4.41
380 415 1.271379 CAATGTCTGCAGTGCAATGGT 59.729 47.619 20.22 3.07 38.41 3.55
386 421 1.535028 CTGCAGTGCAATGGTTCGTTA 59.465 47.619 20.22 0.00 38.41 3.18
387 422 1.950216 TGCAGTGCAATGGTTCGTTAA 59.050 42.857 17.26 0.00 34.76 2.01
465 505 6.904626 AGCCTTTTGGTACTGAATCTGATAT 58.095 36.000 0.00 0.00 42.99 1.63
467 507 8.494433 AGCCTTTTGGTACTGAATCTGATATTA 58.506 33.333 0.00 0.00 42.99 0.98
496 537 8.143193 TGATTTTTAGCATGTGAACTCAATGTT 58.857 29.630 0.00 0.00 42.38 2.71
540 588 3.808728 TGGCCTTGCAGTTAGTATGATC 58.191 45.455 3.32 0.00 0.00 2.92
544 592 5.470368 GCCTTGCAGTTAGTATGATCGATA 58.530 41.667 0.00 0.00 0.00 2.92
597 645 3.067106 CCATGGAACTAGACACACACAC 58.933 50.000 5.56 0.00 0.00 3.82
643 691 4.778213 TCTGATAGTTCTTTGATGGGGG 57.222 45.455 0.00 0.00 0.00 5.40
644 692 4.111577 TCTGATAGTTCTTTGATGGGGGT 58.888 43.478 0.00 0.00 0.00 4.95
646 694 3.202151 TGATAGTTCTTTGATGGGGGTCC 59.798 47.826 0.00 0.00 0.00 4.46
695 745 3.764434 GGGAAGGGGATTTTTGTTCTCTC 59.236 47.826 0.00 0.00 0.00 3.20
740 797 3.197790 CCGTGATGAAGCAGGGCG 61.198 66.667 0.00 0.00 37.05 6.13
789 846 3.857665 CACATGCTTGGTACAGTACGTAG 59.142 47.826 4.58 5.65 42.39 3.51
790 847 3.119245 ACATGCTTGGTACAGTACGTAGG 60.119 47.826 4.58 0.00 42.39 3.18
818 877 0.108709 GCCGAACGTGTGGTACCATA 60.109 55.000 19.72 13.49 0.00 2.74
852 1180 0.442310 GCACGACATACGCATGTGTT 59.558 50.000 18.51 0.00 45.58 3.32
877 1205 4.457496 ACTGCGCTCCACATCGGG 62.457 66.667 9.73 0.00 34.36 5.14
906 1234 1.478510 AGCAATGTACAGCTAGCTCGT 59.521 47.619 16.15 18.13 39.78 4.18
907 1235 1.590238 GCAATGTACAGCTAGCTCGTG 59.410 52.381 16.15 7.67 0.00 4.35
932 1265 0.251634 CTCCTTGGTTCTCAGCCTCC 59.748 60.000 0.00 0.00 0.00 4.30
933 1266 0.473694 TCCTTGGTTCTCAGCCTCCA 60.474 55.000 0.00 0.00 0.00 3.86
934 1267 0.322008 CCTTGGTTCTCAGCCTCCAC 60.322 60.000 0.00 0.00 0.00 4.02
935 1268 0.397941 CTTGGTTCTCAGCCTCCACA 59.602 55.000 0.00 0.00 0.00 4.17
936 1269 0.843309 TTGGTTCTCAGCCTCCACAA 59.157 50.000 0.00 0.00 0.00 3.33
937 1270 0.397941 TGGTTCTCAGCCTCCACAAG 59.602 55.000 0.00 0.00 0.00 3.16
938 1271 0.398318 GGTTCTCAGCCTCCACAAGT 59.602 55.000 0.00 0.00 0.00 3.16
939 1272 1.202818 GGTTCTCAGCCTCCACAAGTT 60.203 52.381 0.00 0.00 0.00 2.66
940 1273 1.876156 GTTCTCAGCCTCCACAAGTTG 59.124 52.381 0.00 0.00 0.00 3.16
941 1274 1.131638 TCTCAGCCTCCACAAGTTGT 58.868 50.000 1.64 1.64 0.00 3.32
973 1306 2.037367 TCCCAGTCTCCTCCCACG 59.963 66.667 0.00 0.00 0.00 4.94
991 1324 4.999939 CAACACAAAGCGGCCGGC 63.000 66.667 29.38 21.18 44.05 6.13
1059 1433 2.126031 GTCGCCGTCCTTGTCCTC 60.126 66.667 0.00 0.00 0.00 3.71
1260 1637 0.798389 TCTTCGCGCTCAACATCTCG 60.798 55.000 5.56 0.00 0.00 4.04
1519 1896 4.681978 AGTTCGGCAGCGTGGACC 62.682 66.667 0.00 0.00 0.00 4.46
1539 1916 3.050275 GCCGACAACCAGCTCACC 61.050 66.667 0.00 0.00 0.00 4.02
1683 2060 1.396996 GACCACAACATGATGTACGGC 59.603 52.381 8.43 0.49 30.84 5.68
1742 2119 1.714460 GTTCGACGTGAGCTACAACAG 59.286 52.381 0.00 0.00 0.00 3.16
1753 2130 0.033504 CTACAACAGTCTGTGCGGGT 59.966 55.000 6.18 5.77 0.00 5.28
1848 2225 4.819761 CTCGCGCCCTGCAGCTAA 62.820 66.667 8.66 0.00 46.97 3.09
1851 2228 4.785453 GCGCCCTGCAGCTAAGGT 62.785 66.667 8.66 0.00 45.45 3.50
1852 2229 2.821366 CGCCCTGCAGCTAAGGTG 60.821 66.667 8.66 7.07 32.45 4.00
1873 2250 2.172483 CTTAGGTGGCCGCTCACTGT 62.172 60.000 17.49 0.00 37.75 3.55
1874 2251 2.449031 TTAGGTGGCCGCTCACTGTG 62.449 60.000 17.49 0.17 37.75 3.66
1875 2252 4.314440 GGTGGCCGCTCACTGTGA 62.314 66.667 17.49 10.50 37.75 3.58
1876 2253 3.044305 GTGGCCGCTCACTGTGAC 61.044 66.667 9.68 3.58 34.98 3.67
1877 2254 4.662961 TGGCCGCTCACTGTGACG 62.663 66.667 19.00 19.00 0.00 4.35
1904 2281 1.196354 GCCTCGCTGATGATGTATTGC 59.804 52.381 0.00 0.00 0.00 3.56
1907 2284 4.502016 CCTCGCTGATGATGTATTGCTAT 58.498 43.478 0.00 0.00 0.00 2.97
1908 2285 4.934001 CCTCGCTGATGATGTATTGCTATT 59.066 41.667 0.00 0.00 0.00 1.73
1911 2288 4.153655 CGCTGATGATGTATTGCTATTGCT 59.846 41.667 0.00 0.00 40.48 3.91
1912 2289 5.349543 CGCTGATGATGTATTGCTATTGCTA 59.650 40.000 0.00 0.00 40.48 3.49
1913 2290 6.455246 CGCTGATGATGTATTGCTATTGCTAG 60.455 42.308 0.00 0.00 40.48 3.42
1915 2292 7.547019 GCTGATGATGTATTGCTATTGCTAGTA 59.453 37.037 0.00 0.00 40.48 1.82
1917 2294 8.588472 TGATGATGTATTGCTATTGCTAGTACT 58.412 33.333 0.00 0.00 40.48 2.73
1918 2295 9.429359 GATGATGTATTGCTATTGCTAGTACTT 57.571 33.333 0.00 0.30 40.48 2.24
1919 2296 9.784531 ATGATGTATTGCTATTGCTAGTACTTT 57.215 29.630 0.00 0.00 40.48 2.66
1920 2297 9.045223 TGATGTATTGCTATTGCTAGTACTTTG 57.955 33.333 0.00 0.00 40.48 2.77
1922 2299 5.757850 ATTGCTATTGCTAGTACTTTGGC 57.242 39.130 0.00 4.47 40.48 4.52
1923 2300 4.214986 TGCTATTGCTAGTACTTTGGCA 57.785 40.909 0.00 7.23 40.48 4.92
1925 2302 4.192317 GCTATTGCTAGTACTTTGGCAGT 58.808 43.478 0.00 9.21 36.06 4.40
1926 2303 4.034510 GCTATTGCTAGTACTTTGGCAGTG 59.965 45.833 16.97 12.33 36.06 3.66
1965 4231 4.083003 CCACGCCTTTGAGTTAGCAATAAA 60.083 41.667 0.00 0.00 0.00 1.40
1981 4256 7.573968 AGCAATAAAGCCCTTCTTAATGTAG 57.426 36.000 0.00 0.00 33.88 2.74
1990 4265 6.097839 AGCCCTTCTTAATGTAGTTCGTGATA 59.902 38.462 0.00 0.00 0.00 2.15
1991 4266 6.421202 GCCCTTCTTAATGTAGTTCGTGATAG 59.579 42.308 0.00 0.00 0.00 2.08
1992 4267 7.490000 CCCTTCTTAATGTAGTTCGTGATAGT 58.510 38.462 0.00 0.00 0.00 2.12
1993 4268 8.627403 CCCTTCTTAATGTAGTTCGTGATAGTA 58.373 37.037 0.00 0.00 0.00 1.82
2004 4279 6.091437 AGTTCGTGATAGTAAGTACAAGTGC 58.909 40.000 0.00 0.00 0.00 4.40
2010 4285 5.715279 TGATAGTAAGTACAAGTGCCACTCT 59.285 40.000 0.00 0.00 0.00 3.24
2033 4308 1.268743 GCCAATTAATCACGAGCTGGC 60.269 52.381 8.83 8.83 40.93 4.85
2036 4311 1.959042 ATTAATCACGAGCTGGCCAG 58.041 50.000 29.34 29.34 0.00 4.85
2046 4322 3.023949 GCTGGCCAGGTCGATCAGT 62.024 63.158 33.46 0.00 0.00 3.41
2291 4590 8.368962 ACCTCAATTATATAAGACTAGGAGGC 57.631 38.462 16.77 0.00 41.38 4.70
2396 4725 4.457834 CAGATAGACTGGACCGAAACTT 57.542 45.455 0.00 0.00 42.39 2.66
2603 4933 1.002544 GCAGTAGACAAGAGTGGCCTT 59.997 52.381 3.32 0.00 30.22 4.35
2604 4934 2.693069 CAGTAGACAAGAGTGGCCTTG 58.307 52.381 3.32 1.98 46.61 3.61
2803 5147 4.403137 CGTCGCGTGTCGGGGTAA 62.403 66.667 5.77 0.00 40.17 2.85
2818 5162 1.369091 GGTAACCAGCCATGTCAGCG 61.369 60.000 0.00 0.00 34.64 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.525912 ATGGAAAACAAAGTGGAGCATC 57.474 40.909 0.00 0.00 0.00 3.91
61 62 1.864082 TGATGCGCCGTGTTATACATG 59.136 47.619 4.18 0.00 34.96 3.21
92 125 1.905894 TCACTACCCAGCTATTGCACA 59.094 47.619 1.12 0.00 42.74 4.57
93 126 2.280628 GTCACTACCCAGCTATTGCAC 58.719 52.381 1.12 0.00 42.74 4.57
94 127 1.134818 CGTCACTACCCAGCTATTGCA 60.135 52.381 1.12 0.00 42.74 4.08
95 128 1.134788 ACGTCACTACCCAGCTATTGC 60.135 52.381 0.00 0.00 40.05 3.56
96 129 2.961526 ACGTCACTACCCAGCTATTG 57.038 50.000 0.00 0.00 0.00 1.90
97 130 3.765511 TGTAACGTCACTACCCAGCTATT 59.234 43.478 0.00 0.00 0.00 1.73
98 131 3.359033 TGTAACGTCACTACCCAGCTAT 58.641 45.455 0.00 0.00 0.00 2.97
99 132 2.794103 TGTAACGTCACTACCCAGCTA 58.206 47.619 0.00 0.00 0.00 3.32
100 133 1.624336 TGTAACGTCACTACCCAGCT 58.376 50.000 0.00 0.00 0.00 4.24
101 134 2.268298 CATGTAACGTCACTACCCAGC 58.732 52.381 0.00 0.00 0.00 4.85
102 135 3.587797 ACATGTAACGTCACTACCCAG 57.412 47.619 0.00 0.00 0.00 4.45
103 136 3.444742 CCTACATGTAACGTCACTACCCA 59.555 47.826 7.06 0.00 0.00 4.51
104 137 3.696051 TCCTACATGTAACGTCACTACCC 59.304 47.826 7.06 0.00 0.00 3.69
105 138 4.732938 GCTCCTACATGTAACGTCACTACC 60.733 50.000 7.06 0.00 0.00 3.18
106 139 4.349501 GCTCCTACATGTAACGTCACTAC 58.650 47.826 7.06 0.00 0.00 2.73
107 140 3.064408 CGCTCCTACATGTAACGTCACTA 59.936 47.826 7.06 0.00 0.00 2.74
108 141 2.159421 CGCTCCTACATGTAACGTCACT 60.159 50.000 7.06 0.00 0.00 3.41
109 142 2.182825 CGCTCCTACATGTAACGTCAC 58.817 52.381 7.06 0.00 0.00 3.67
110 143 1.468565 GCGCTCCTACATGTAACGTCA 60.469 52.381 7.06 0.00 0.00 4.35
111 144 1.197910 GCGCTCCTACATGTAACGTC 58.802 55.000 7.06 2.57 0.00 4.34
112 145 0.815734 AGCGCTCCTACATGTAACGT 59.184 50.000 2.64 0.00 0.00 3.99
113 146 1.202256 TGAGCGCTCCTACATGTAACG 60.202 52.381 33.23 9.47 0.00 3.18
114 147 2.194271 GTGAGCGCTCCTACATGTAAC 58.806 52.381 33.23 17.82 0.00 2.50
115 148 1.822371 TGTGAGCGCTCCTACATGTAA 59.178 47.619 33.23 9.65 0.00 2.41
116 149 1.470051 TGTGAGCGCTCCTACATGTA 58.530 50.000 33.23 10.44 0.00 2.29
117 150 0.826715 ATGTGAGCGCTCCTACATGT 59.173 50.000 31.32 16.92 32.90 3.21
118 151 1.945387 AATGTGAGCGCTCCTACATG 58.055 50.000 32.07 0.00 34.28 3.21
119 152 2.679837 CAAAATGTGAGCGCTCCTACAT 59.320 45.455 33.23 30.42 35.43 2.29
120 153 2.076100 CAAAATGTGAGCGCTCCTACA 58.924 47.619 33.23 29.67 0.00 2.74
121 154 2.076863 ACAAAATGTGAGCGCTCCTAC 58.923 47.619 33.23 25.25 0.00 3.18
122 155 2.472695 ACAAAATGTGAGCGCTCCTA 57.527 45.000 33.23 22.35 0.00 2.94
123 156 3.329300 ACAAAATGTGAGCGCTCCT 57.671 47.368 33.23 16.06 0.00 3.69
255 289 6.539826 TGTCTGTTTCTATTACATGCAGGATG 59.460 38.462 4.84 0.00 38.15 3.51
259 293 6.726258 TGTGTCTGTTTCTATTACATGCAG 57.274 37.500 0.00 0.00 0.00 4.41
292 326 5.045286 AGGAGAGAAAAAGATGCATGTAGGT 60.045 40.000 2.46 0.00 0.00 3.08
343 378 9.423061 GCAGACATTGACACATATACACATATA 57.577 33.333 0.00 0.00 0.00 0.86
344 379 7.933033 TGCAGACATTGACACATATACACATAT 59.067 33.333 0.00 0.00 0.00 1.78
345 380 7.271511 TGCAGACATTGACACATATACACATA 58.728 34.615 0.00 0.00 0.00 2.29
346 381 6.114767 TGCAGACATTGACACATATACACAT 58.885 36.000 0.00 0.00 0.00 3.21
347 382 5.486526 TGCAGACATTGACACATATACACA 58.513 37.500 0.00 0.00 0.00 3.72
348 383 5.582269 ACTGCAGACATTGACACATATACAC 59.418 40.000 23.35 0.00 0.00 2.90
349 384 5.581874 CACTGCAGACATTGACACATATACA 59.418 40.000 23.35 0.00 0.00 2.29
350 385 5.503031 GCACTGCAGACATTGACACATATAC 60.503 44.000 23.35 0.00 0.00 1.47
351 386 4.571984 GCACTGCAGACATTGACACATATA 59.428 41.667 23.35 0.00 0.00 0.86
360 395 1.271379 ACCATTGCACTGCAGACATTG 59.729 47.619 23.35 21.07 40.61 2.82
361 396 1.624336 ACCATTGCACTGCAGACATT 58.376 45.000 23.35 11.44 40.61 2.71
362 397 1.542915 GAACCATTGCACTGCAGACAT 59.457 47.619 23.35 3.25 40.61 3.06
366 401 0.311790 AACGAACCATTGCACTGCAG 59.688 50.000 13.48 13.48 40.61 4.41
367 402 1.598882 TAACGAACCATTGCACTGCA 58.401 45.000 0.00 0.00 36.47 4.41
371 406 5.746721 AGAAACTTTTAACGAACCATTGCAC 59.253 36.000 0.00 0.00 0.00 4.57
380 415 8.555166 CATTACTGCAAGAAACTTTTAACGAA 57.445 30.769 0.00 0.00 37.43 3.85
467 507 9.715121 ATTGAGTTCACATGCTAAAAATCAAAT 57.285 25.926 13.20 4.51 38.63 2.32
496 537 0.466543 ATGTTCATACCCGCCGCTAA 59.533 50.000 0.00 0.00 0.00 3.09
520 568 2.802816 CGATCATACTAACTGCAAGGCC 59.197 50.000 0.00 0.00 39.30 5.19
540 588 3.321968 TGTGACCCTGATCTCCATTATCG 59.678 47.826 0.00 0.00 0.00 2.92
544 592 1.561542 GGTGTGACCCTGATCTCCATT 59.438 52.381 0.00 0.00 30.04 3.16
555 603 0.535102 CCACTCTGTTGGTGTGACCC 60.535 60.000 0.00 0.00 40.61 4.46
557 605 1.583054 GTCCACTCTGTTGGTGTGAC 58.417 55.000 0.00 0.00 40.61 3.67
643 691 0.472161 GAGGGAGAGGGGGTATGGAC 60.472 65.000 0.00 0.00 0.00 4.02
644 692 1.675936 GGAGGGAGAGGGGGTATGGA 61.676 65.000 0.00 0.00 0.00 3.41
646 694 1.152008 GGGAGGGAGAGGGGGTATG 60.152 68.421 0.00 0.00 0.00 2.39
647 695 1.311928 AGGGAGGGAGAGGGGGTAT 60.312 63.158 0.00 0.00 0.00 2.73
648 696 2.019272 GAGGGAGGGAGAGGGGGTA 61.019 68.421 0.00 0.00 0.00 3.69
649 697 3.369388 GAGGGAGGGAGAGGGGGT 61.369 72.222 0.00 0.00 0.00 4.95
651 699 4.179599 GGGAGGGAGGGAGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
652 700 1.705450 TAGGGAGGGAGGGAGAGGG 60.705 68.421 0.00 0.00 0.00 4.30
653 701 1.297409 TGTAGGGAGGGAGGGAGAGG 61.297 65.000 0.00 0.00 0.00 3.69
654 702 0.187361 CTGTAGGGAGGGAGGGAGAG 59.813 65.000 0.00 0.00 0.00 3.20
655 703 1.297409 CCTGTAGGGAGGGAGGGAGA 61.297 65.000 0.00 0.00 37.23 3.71
657 705 3.452123 CCTGTAGGGAGGGAGGGA 58.548 66.667 0.00 0.00 37.23 4.20
740 797 2.300152 TCTGCCCTCGTCAATGATATCC 59.700 50.000 0.00 0.00 0.00 2.59
789 846 2.108362 CGTTCGGCATCCCTACCC 59.892 66.667 0.00 0.00 0.00 3.69
790 847 1.520787 CACGTTCGGCATCCCTACC 60.521 63.158 0.00 0.00 0.00 3.18
818 877 3.923864 TGCGCTCTGTTGGTCGGT 61.924 61.111 9.73 0.00 0.00 4.69
877 1205 2.670414 GCTGTACATTGCTGACTGAGAC 59.330 50.000 0.00 0.00 0.00 3.36
906 1234 0.603569 GAGAACCAAGGAGTCGAGCA 59.396 55.000 0.00 0.00 0.00 4.26
907 1235 0.603569 TGAGAACCAAGGAGTCGAGC 59.396 55.000 0.00 0.00 0.00 5.03
909 1237 0.603569 GCTGAGAACCAAGGAGTCGA 59.396 55.000 0.00 0.00 0.00 4.20
911 1239 0.980423 AGGCTGAGAACCAAGGAGTC 59.020 55.000 0.00 0.00 0.00 3.36
915 1243 0.322008 GTGGAGGCTGAGAACCAAGG 60.322 60.000 0.00 0.00 34.11 3.61
916 1244 0.397941 TGTGGAGGCTGAGAACCAAG 59.602 55.000 0.00 0.00 34.11 3.61
939 1272 0.107410 GGAGTGTGTTGTGGTCCACA 60.107 55.000 21.21 21.21 43.02 4.17
940 1273 0.818040 GGGAGTGTGTTGTGGTCCAC 60.818 60.000 15.64 15.64 34.56 4.02
941 1274 1.275421 TGGGAGTGTGTTGTGGTCCA 61.275 55.000 0.00 0.00 0.00 4.02
942 1275 0.535102 CTGGGAGTGTGTTGTGGTCC 60.535 60.000 0.00 0.00 0.00 4.46
943 1276 0.180406 ACTGGGAGTGTGTTGTGGTC 59.820 55.000 0.00 0.00 0.00 4.02
944 1277 0.180406 GACTGGGAGTGTGTTGTGGT 59.820 55.000 0.00 0.00 0.00 4.16
945 1278 0.469917 AGACTGGGAGTGTGTTGTGG 59.530 55.000 0.00 0.00 0.00 4.17
946 1279 1.541233 GGAGACTGGGAGTGTGTTGTG 60.541 57.143 0.00 0.00 0.00 3.33
947 1280 0.759346 GGAGACTGGGAGTGTGTTGT 59.241 55.000 0.00 0.00 0.00 3.32
948 1281 1.001406 GAGGAGACTGGGAGTGTGTTG 59.999 57.143 0.00 0.00 44.43 3.33
949 1282 1.343069 GAGGAGACTGGGAGTGTGTT 58.657 55.000 0.00 0.00 44.43 3.32
950 1283 0.543174 GGAGGAGACTGGGAGTGTGT 60.543 60.000 0.00 0.00 44.43 3.72
973 1306 4.999939 CCGGCCGCTTTGTGTTGC 63.000 66.667 22.85 0.00 0.00 4.17
991 1324 0.110056 GTGAGCTGCATGTTGGTTCG 60.110 55.000 1.02 0.00 0.00 3.95
992 1325 0.110056 CGTGAGCTGCATGTTGGTTC 60.110 55.000 1.02 0.00 0.00 3.62
993 1326 0.534877 TCGTGAGCTGCATGTTGGTT 60.535 50.000 1.02 0.00 35.00 3.67
995 1328 0.952497 ACTCGTGAGCTGCATGTTGG 60.952 55.000 1.02 0.00 35.00 3.77
998 1366 1.079543 GGACTCGTGAGCTGCATGT 60.080 57.895 1.02 0.00 35.00 3.21
1113 1490 2.266055 GACTTGACGGCCAGGAGG 59.734 66.667 2.24 0.00 38.23 4.30
1640 2017 2.586079 CCAGTATGTCCAGCGCCG 60.586 66.667 2.29 0.00 0.00 6.46
1662 2039 2.694213 CCGTACATCATGTTGTGGTCA 58.306 47.619 17.80 0.00 0.00 4.02
1742 2119 2.202756 GGATCGACCCGCACAGAC 60.203 66.667 0.00 0.00 0.00 3.51
1853 2230 2.125106 GTGAGCGGCCACCTAAGG 60.125 66.667 2.24 0.00 0.00 2.69
1854 2231 1.448540 CAGTGAGCGGCCACCTAAG 60.449 63.158 2.24 0.00 37.76 2.18
1855 2232 2.214216 ACAGTGAGCGGCCACCTAA 61.214 57.895 2.24 0.00 37.76 2.69
1856 2233 2.603473 ACAGTGAGCGGCCACCTA 60.603 61.111 2.24 0.00 37.76 3.08
1857 2234 4.320456 CACAGTGAGCGGCCACCT 62.320 66.667 2.24 0.00 37.76 4.00
1865 2242 3.938112 GTCACCGTCACAGTGAGC 58.062 61.111 2.53 0.00 44.57 4.26
1877 2254 4.148825 ATCAGCGAGGCGGTCACC 62.149 66.667 0.00 0.00 34.62 4.02
1886 2263 5.670588 GCAATAGCAATACATCATCAGCGAG 60.671 44.000 0.00 0.00 41.58 5.03
1888 2265 4.153655 AGCAATAGCAATACATCATCAGCG 59.846 41.667 0.00 0.00 45.49 5.18
1889 2266 5.624344 AGCAATAGCAATACATCATCAGC 57.376 39.130 0.00 0.00 45.49 4.26
1904 2281 4.034510 GCACTGCCAAAGTACTAGCAATAG 59.965 45.833 14.05 7.34 36.83 1.73
1907 2284 2.151202 GCACTGCCAAAGTACTAGCAA 58.849 47.619 14.05 2.25 36.83 3.91
1908 2285 1.347707 AGCACTGCCAAAGTACTAGCA 59.652 47.619 12.88 12.88 36.83 3.49
1911 2288 3.319137 CAGAGCACTGCCAAAGTACTA 57.681 47.619 0.00 0.00 36.83 1.82
1912 2289 2.175878 CAGAGCACTGCCAAAGTACT 57.824 50.000 0.00 0.00 36.83 2.73
1922 2299 3.181468 TGGAGATATTCAGCAGAGCACTG 60.181 47.826 6.80 6.80 45.91 3.66
1923 2300 3.036819 TGGAGATATTCAGCAGAGCACT 58.963 45.455 0.00 0.00 0.00 4.40
1925 2302 2.223900 CGTGGAGATATTCAGCAGAGCA 60.224 50.000 0.00 0.00 0.00 4.26
1926 2303 2.402305 CGTGGAGATATTCAGCAGAGC 58.598 52.381 0.00 0.00 0.00 4.09
1928 2305 1.069204 GGCGTGGAGATATTCAGCAGA 59.931 52.381 0.00 0.00 0.00 4.26
1935 4201 3.914426 ACTCAAAGGCGTGGAGATATT 57.086 42.857 12.00 0.00 33.00 1.28
1965 4231 4.222145 TCACGAACTACATTAAGAAGGGCT 59.778 41.667 0.00 0.00 0.00 5.19
1981 4256 5.287992 GGCACTTGTACTTACTATCACGAAC 59.712 44.000 0.00 0.00 0.00 3.95
1990 4265 4.503296 CCAAGAGTGGCACTTGTACTTACT 60.503 45.833 22.98 8.51 41.88 2.24
1991 4266 3.746492 CCAAGAGTGGCACTTGTACTTAC 59.254 47.826 22.98 6.08 41.88 2.34
1992 4267 4.002906 CCAAGAGTGGCACTTGTACTTA 57.997 45.455 22.98 0.00 41.88 2.24
1993 4268 2.851195 CCAAGAGTGGCACTTGTACTT 58.149 47.619 22.98 16.73 41.88 2.24
2010 4285 2.423185 CAGCTCGTGATTAATTGGCCAA 59.577 45.455 23.00 23.00 0.00 4.52
2033 4308 9.452065 CGATATTATATTAACTGATCGACCTGG 57.548 37.037 0.00 0.00 37.49 4.45
2169 4461 4.216257 CACACCATTGGACTAGGAAAAGTG 59.784 45.833 10.37 0.00 0.00 3.16
2273 4572 4.021916 GCCCGCCTCCTAGTCTTATATAA 58.978 47.826 0.00 0.00 0.00 0.98
2278 4577 1.457079 GGCCCGCCTCCTAGTCTTA 60.457 63.158 0.00 0.00 0.00 2.10
2291 4590 0.322098 TGTATTGGAGTTGTGGCCCG 60.322 55.000 0.00 0.00 0.00 6.13
2346 4652 2.757099 GCTTCGACTACCGGGGGA 60.757 66.667 6.32 0.00 39.14 4.81
2368 4697 2.421670 GGTCCAGTCTATCTGTCTCCGA 60.422 54.545 0.00 0.00 42.19 4.55
2377 4706 4.674475 GAGAAGTTTCGGTCCAGTCTATC 58.326 47.826 0.00 0.00 0.00 2.08
2396 4725 0.747283 GCCTACTCCCGTCTTCGAGA 60.747 60.000 0.00 0.00 39.71 4.04
2632 4962 0.741326 GATACGTCAGCTGCTCCAGA 59.259 55.000 9.47 0.00 32.44 3.86
2801 5145 0.391130 GACGCTGACATGGCTGGTTA 60.391 55.000 7.64 0.00 0.00 2.85
2803 5147 2.046892 GACGCTGACATGGCTGGT 60.047 61.111 7.64 3.57 0.00 4.00
2810 5154 2.005960 GCCTACTCGGACGCTGACAT 62.006 60.000 0.00 0.00 33.16 3.06
2811 5155 2.697761 GCCTACTCGGACGCTGACA 61.698 63.158 0.00 0.00 33.16 3.58
2818 5162 2.772691 CCTCGTGGCCTACTCGGAC 61.773 68.421 3.32 0.00 43.30 4.79


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.