Multiple sequence alignment - TraesCS5A01G404900

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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 TraesCS5A01G404900 chr5A 100.000 2468 0 0 1 2468 596551839 596554306 0.000000e+00 4558.0
1 TraesCS5A01G404900 chr5D 89.842 1644 82 38 326 1933 477320604 477322198 0.000000e+00 2032.0
2 TraesCS5A01G404900 chr5D 84.116 554 51 19 1948 2468 477322469 477323018 3.660000e-138 501.0
3 TraesCS5A01G404900 chr5D 83.492 315 27 13 9 311 477320122 477320423 1.120000e-68 270.0
4 TraesCS5A01G404900 chr5B 88.281 1681 94 45 192 1819 584898637 584900267 0.000000e+00 1917.0
5 TraesCS5A01G404900 chr5B 81.013 395 54 11 2091 2468 584900706 584901096 6.670000e-76 294.0
6 TraesCS5A01G404900 chr5B 89.873 158 11 4 1919 2074 584900395 584900549 5.380000e-47 198.0
7 TraesCS5A01G404900 chr4A 88.525 61 4 3 2340 2398 661320334 661320275 1.220000e-08 71.3


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 TraesCS5A01G404900 chr5A 596551839 596554306 2467 False 4558.000000 4558 100.000000 1 2468 1 chr5A.!!$F1 2467
1 TraesCS5A01G404900 chr5D 477320122 477323018 2896 False 934.333333 2032 85.816667 9 2468 3 chr5D.!!$F1 2459
2 TraesCS5A01G404900 chr5B 584898637 584901096 2459 False 803.000000 1917 86.389000 192 2468 3 chr5B.!!$F1 2276

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
725 930 0.178888 TCACCTACCATCCACACCCA 60.179 55.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1763 1999 0.097674 CCGCGCTTTCAATCTCTTGG 59.902 55.0 5.56 0.0 32.95 3.61 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
25 26 8.424274 AAACTTTGATCAAACTGAAATGGTTC 57.576 30.769 16.91 0.00 0.00 3.62
34 35 7.414436 TCAAACTGAAATGGTTCGAGTTAAAG 58.586 34.615 0.00 0.00 35.70 1.85
67 68 2.706339 ATCAGATTGACCAGACCAGC 57.294 50.000 0.00 0.00 0.00 4.85
99 100 6.519679 TCAGATTGTGCAGCTCAATAAAAT 57.480 33.333 20.10 6.73 35.94 1.82
102 103 8.522003 TCAGATTGTGCAGCTCAATAAAATAAA 58.478 29.630 20.10 2.87 35.94 1.40
105 106 9.962759 GATTGTGCAGCTCAATAAAATAAAAAG 57.037 29.630 20.10 0.00 35.94 2.27
106 107 9.709495 ATTGTGCAGCTCAATAAAATAAAAAGA 57.291 25.926 18.96 0.00 34.34 2.52
107 108 9.539825 TTGTGCAGCTCAATAAAATAAAAAGAA 57.460 25.926 5.77 0.00 0.00 2.52
108 109 9.195411 TGTGCAGCTCAATAAAATAAAAAGAAG 57.805 29.630 0.00 0.00 0.00 2.85
109 110 8.164790 GTGCAGCTCAATAAAATAAAAAGAAGC 58.835 33.333 0.00 0.00 0.00 3.86
125 126 1.262151 GAAGCGCTAAAACGTGGTTCA 59.738 47.619 12.05 0.00 45.88 3.18
145 146 6.183360 GGTTCATCAAAGGGTCCTTCAATATG 60.183 42.308 2.37 5.33 34.84 1.78
146 147 6.078456 TCATCAAAGGGTCCTTCAATATGT 57.922 37.500 2.37 0.00 34.84 2.29
147 148 7.206789 TCATCAAAGGGTCCTTCAATATGTA 57.793 36.000 2.37 0.00 34.84 2.29
150 151 8.917088 CATCAAAGGGTCCTTCAATATGTAATT 58.083 33.333 2.37 0.00 34.84 1.40
153 154 9.627123 CAAAGGGTCCTTCAATATGTAATTCTA 57.373 33.333 2.37 0.00 34.84 2.10
157 158 8.936864 GGGTCCTTCAATATGTAATTCTAATCG 58.063 37.037 0.00 0.00 0.00 3.34
158 159 9.490379 GGTCCTTCAATATGTAATTCTAATCGT 57.510 33.333 0.00 0.00 0.00 3.73
214 227 6.803154 AAAGATACTGTAAGCAGGTGAAAC 57.197 37.500 0.00 0.00 46.62 2.78
226 239 3.311596 GCAGGTGAAACGTACTCAAAGTT 59.688 43.478 2.06 0.00 38.12 2.66
232 245 8.092687 AGGTGAAACGTACTCAAAGTTATGTAT 58.907 33.333 2.06 0.00 38.12 2.29
233 246 9.357652 GGTGAAACGTACTCAAAGTTATGTATA 57.642 33.333 2.06 0.00 38.12 1.47
273 293 5.991933 ATAGTAGGAGCACGAATCATGAT 57.008 39.130 1.18 1.18 0.00 2.45
277 297 1.002033 GGAGCACGAATCATGATTGGC 60.002 52.381 25.37 22.44 30.89 4.52
312 332 2.093152 CCGTCCGTCGTTATCTTTTTGG 59.907 50.000 0.00 0.00 37.94 3.28
313 333 2.473376 CGTCCGTCGTTATCTTTTTGGC 60.473 50.000 0.00 0.00 34.52 4.52
314 334 2.481185 GTCCGTCGTTATCTTTTTGGCA 59.519 45.455 0.00 0.00 0.00 4.92
317 337 4.095610 CCGTCGTTATCTTTTTGGCATTC 58.904 43.478 0.00 0.00 0.00 2.67
318 338 4.095610 CGTCGTTATCTTTTTGGCATTCC 58.904 43.478 0.00 0.00 0.00 3.01
319 339 4.095610 GTCGTTATCTTTTTGGCATTCCG 58.904 43.478 0.00 0.00 34.14 4.30
320 340 2.851824 CGTTATCTTTTTGGCATTCCGC 59.148 45.455 0.00 0.00 41.28 5.54
321 341 2.842208 TATCTTTTTGGCATTCCGCG 57.158 45.000 0.00 0.00 43.84 6.46
443 629 2.979814 AAAGGCCAGCGTTTCTTTTT 57.020 40.000 5.01 0.00 29.44 1.94
446 632 0.319555 GGCCAGCGTTTCTTTTTCCC 60.320 55.000 0.00 0.00 0.00 3.97
491 678 1.661341 GCTCACAGGATCATCACACC 58.339 55.000 0.00 0.00 0.00 4.16
515 702 4.742201 CCGGTGCACCAGACCTCG 62.742 72.222 34.16 18.29 35.14 4.63
522 709 2.524394 ACCAGACCTCGTGGCTGT 60.524 61.111 19.47 10.08 38.83 4.40
552 739 2.590092 GCCAACTCACGCCCCTAT 59.410 61.111 0.00 0.00 0.00 2.57
553 740 1.523938 GCCAACTCACGCCCCTATC 60.524 63.158 0.00 0.00 0.00 2.08
555 742 1.227263 CAACTCACGCCCCTATCCG 60.227 63.158 0.00 0.00 0.00 4.18
557 744 2.838225 CTCACGCCCCTATCCGGT 60.838 66.667 0.00 0.00 0.00 5.28
558 745 3.151710 TCACGCCCCTATCCGGTG 61.152 66.667 0.00 0.00 36.92 4.94
559 746 3.151710 CACGCCCCTATCCGGTGA 61.152 66.667 0.00 0.00 34.82 4.02
560 747 2.122989 ACGCCCCTATCCGGTGAT 60.123 61.111 0.00 0.00 34.82 3.06
561 748 2.343758 CGCCCCTATCCGGTGATG 59.656 66.667 0.00 0.00 32.29 3.07
562 749 2.507854 CGCCCCTATCCGGTGATGT 61.508 63.158 0.00 0.00 32.29 3.06
583 784 2.029290 TGTCTAGAAGACCGGAGCAAAC 60.029 50.000 9.46 0.00 44.44 2.93
595 796 1.724582 GAGCAAACCAACGTGCACCT 61.725 55.000 12.15 0.00 43.42 4.00
646 847 2.550830 CGGAAGGAATACAGGGGATG 57.449 55.000 0.00 0.00 0.00 3.51
647 848 1.543429 CGGAAGGAATACAGGGGATGC 60.543 57.143 0.00 0.00 0.00 3.91
648 849 1.202940 GGAAGGAATACAGGGGATGCC 60.203 57.143 0.00 0.00 0.00 4.40
649 850 1.494721 GAAGGAATACAGGGGATGCCA 59.505 52.381 5.30 0.00 0.00 4.92
650 851 0.846693 AGGAATACAGGGGATGCCAC 59.153 55.000 5.30 0.00 0.00 5.01
651 852 0.846693 GGAATACAGGGGATGCCACT 59.153 55.000 5.30 0.00 38.09 4.00
725 930 0.178888 TCACCTACCATCCACACCCA 60.179 55.000 0.00 0.00 0.00 4.51
796 1023 1.300697 ACCACAGACGCTCGAAACC 60.301 57.895 0.00 0.00 0.00 3.27
848 1075 5.955355 TCATCCCCACCTTATTAAACCAAAG 59.045 40.000 0.00 0.00 0.00 2.77
902 1130 1.153823 ACAGCGTCCGTGATAGTGC 60.154 57.895 0.00 0.00 0.00 4.40
980 1208 1.304547 CAGGGAGAGTGGGTCGAGT 60.305 63.158 0.00 0.00 0.00 4.18
987 1215 2.005960 GAGTGGGTCGAGTGATCGGG 62.006 65.000 0.00 0.00 0.00 5.14
1395 1623 2.361357 ACGCTCTACTCCCGCAGT 60.361 61.111 0.00 0.00 39.41 4.40
1505 1738 1.606480 CCTCAACTGCTCGTGTGTGAT 60.606 52.381 0.00 0.00 0.00 3.06
1506 1739 1.723542 CTCAACTGCTCGTGTGTGATC 59.276 52.381 0.00 0.00 0.00 2.92
1507 1740 1.068434 TCAACTGCTCGTGTGTGATCA 59.932 47.619 0.00 0.00 0.00 2.92
1508 1741 1.458445 CAACTGCTCGTGTGTGATCAG 59.542 52.381 0.00 0.00 37.94 2.90
1509 1742 0.037882 ACTGCTCGTGTGTGATCAGG 60.038 55.000 0.00 0.00 36.63 3.86
1510 1743 0.037882 CTGCTCGTGTGTGATCAGGT 60.038 55.000 0.00 0.00 30.40 4.00
1511 1744 0.392706 TGCTCGTGTGTGATCAGGTT 59.607 50.000 0.00 0.00 0.00 3.50
1542 1775 4.197750 TGCTTGCCAAAAATTGTTCATGT 58.802 34.783 0.00 0.00 0.00 3.21
1572 1805 6.211515 CGATCCATCTGAAATTGGGATTTTC 58.788 40.000 0.00 0.00 38.43 2.29
1610 1846 1.340248 CAGGGAGGAATTCATGCATGC 59.660 52.381 22.25 11.82 0.00 4.06
1619 1855 4.209703 GGAATTCATGCATGCGTAATTTGG 59.790 41.667 22.25 0.00 0.00 3.28
1627 1863 3.122780 GCATGCGTAATTTGGTTGTTTCC 59.877 43.478 0.00 0.00 0.00 3.13
1630 1866 4.363999 TGCGTAATTTGGTTGTTTCCTTG 58.636 39.130 0.00 0.00 0.00 3.61
1634 1870 6.146898 CGTAATTTGGTTGTTTCCTTGTAGG 58.853 40.000 0.00 0.00 36.46 3.18
1678 1914 2.050144 GGGCTCCATGGTCATTCTCTA 58.950 52.381 12.58 0.00 0.00 2.43
1681 1917 3.898123 GGCTCCATGGTCATTCTCTAGTA 59.102 47.826 12.58 0.00 0.00 1.82
1682 1918 4.262249 GGCTCCATGGTCATTCTCTAGTAC 60.262 50.000 12.58 0.00 0.00 2.73
1693 1929 4.617253 TTCTCTAGTACCTTGCTTGCAA 57.383 40.909 7.83 7.83 0.00 4.08
1719 1955 2.837498 TGCCGGAATGATCATACAGTG 58.163 47.619 9.04 0.00 0.00 3.66
1735 1971 8.648557 TCATACAGTGTAGATATTTGCAACTC 57.351 34.615 9.25 0.00 0.00 3.01
1837 2074 3.006940 GGCGACATGATTTTCCAGTACA 58.993 45.455 0.00 0.00 0.00 2.90
1855 2092 0.379316 CATGGACCATGTCACATGCG 59.621 55.000 24.15 8.35 37.12 4.73
1866 2103 1.020861 TCACATGCGGCAGACATCAC 61.021 55.000 9.25 0.00 0.00 3.06
1907 2153 2.420129 GCCACATTTGATACTCTCGGGT 60.420 50.000 0.00 0.00 0.00 5.28
1933 2193 9.914131 TCTATATTGATATTCCAGTCGAGTTTG 57.086 33.333 0.00 0.00 0.00 2.93
1935 2195 3.186909 TGATATTCCAGTCGAGTTTGCG 58.813 45.455 0.00 0.00 0.00 4.85
1939 2199 2.060326 TCCAGTCGAGTTTGCGTTAG 57.940 50.000 0.00 0.00 0.00 2.34
1941 2201 2.132762 CCAGTCGAGTTTGCGTTAGTT 58.867 47.619 0.00 0.00 0.00 2.24
1942 2202 2.542595 CCAGTCGAGTTTGCGTTAGTTT 59.457 45.455 0.00 0.00 0.00 2.66
1944 2204 4.375706 CCAGTCGAGTTTGCGTTAGTTTAC 60.376 45.833 0.00 0.00 0.00 2.01
1957 2473 1.425412 AGTTTACAACGCTGCTACCG 58.575 50.000 0.00 0.00 36.23 4.02
1967 2483 1.234615 GCTGCTACCGCCAAAGTTCA 61.235 55.000 0.00 0.00 34.43 3.18
2074 2593 8.035394 ACTCCGTACCTTATAATTGCATCATAG 58.965 37.037 0.00 0.00 0.00 2.23
2119 2778 7.192148 TCTATTCTACTGAGTTCAGATACGC 57.808 40.000 15.63 0.00 46.59 4.42
2135 2794 6.478016 TCAGATACGCTCATTGAAAGAGAATG 59.522 38.462 1.05 0.00 35.09 2.67
2166 2829 2.423185 CGGCTTAGATTGCATTGGACAA 59.577 45.455 0.00 0.00 0.00 3.18
2214 2883 6.824305 AAATAAAGAGTTGTCCTGGACATG 57.176 37.500 28.76 0.00 42.40 3.21
2216 2885 2.847327 AGAGTTGTCCTGGACATGTG 57.153 50.000 28.76 0.00 42.40 3.21
2256 2931 0.460987 CTGGAGTTCAGATGTCGGCC 60.461 60.000 0.00 0.00 46.18 6.13
2286 2961 8.194769 TCATTTTGGTGAAGTTAGAAAAAGGTC 58.805 33.333 0.00 0.00 0.00 3.85
2311 2986 5.431179 TTAACCTACTCCACTTGATTCCC 57.569 43.478 0.00 0.00 0.00 3.97
2318 2993 1.308069 CCACTTGATTCCCGCACCTG 61.308 60.000 0.00 0.00 0.00 4.00
2323 2998 1.971167 GATTCCCGCACCTGCACAA 60.971 57.895 0.00 0.00 42.21 3.33
2325 3000 0.899717 ATTCCCGCACCTGCACAATT 60.900 50.000 0.00 0.00 42.21 2.32
2326 3001 0.250945 TTCCCGCACCTGCACAATTA 60.251 50.000 0.00 0.00 42.21 1.40
2327 3002 0.034574 TCCCGCACCTGCACAATTAT 60.035 50.000 0.00 0.00 42.21 1.28
2329 3004 0.381801 CCGCACCTGCACAATTATCC 59.618 55.000 0.00 0.00 42.21 2.59
2330 3005 0.381801 CGCACCTGCACAATTATCCC 59.618 55.000 0.00 0.00 42.21 3.85
2331 3006 1.473258 GCACCTGCACAATTATCCCA 58.527 50.000 0.00 0.00 41.59 4.37
2332 3007 1.824230 GCACCTGCACAATTATCCCAA 59.176 47.619 0.00 0.00 41.59 4.12
2333 3008 2.159198 GCACCTGCACAATTATCCCAAG 60.159 50.000 0.00 0.00 41.59 3.61
2335 3010 3.129287 CACCTGCACAATTATCCCAAGTC 59.871 47.826 0.00 0.00 0.00 3.01
2336 3011 2.689983 CCTGCACAATTATCCCAAGTCC 59.310 50.000 0.00 0.00 0.00 3.85
2337 3012 3.624777 CTGCACAATTATCCCAAGTCCT 58.375 45.455 0.00 0.00 0.00 3.85
2338 3013 4.019174 CTGCACAATTATCCCAAGTCCTT 58.981 43.478 0.00 0.00 0.00 3.36
2340 3015 3.763897 GCACAATTATCCCAAGTCCTTGT 59.236 43.478 6.31 0.00 38.85 3.16
2341 3016 4.220602 GCACAATTATCCCAAGTCCTTGTT 59.779 41.667 6.31 0.00 38.85 2.83
2342 3017 5.713025 CACAATTATCCCAAGTCCTTGTTG 58.287 41.667 6.31 5.56 38.85 3.33
2345 3020 4.993705 TTATCCCAAGTCCTTGTTGAGT 57.006 40.909 6.31 0.00 38.85 3.41
2352 3039 2.221299 TCCTTGTTGAGTCCCCCGG 61.221 63.158 0.00 0.00 0.00 5.73
2400 3088 8.468349 CGCAACCATTGTTATGATTATTAAACG 58.532 33.333 0.00 0.00 33.37 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.222611 CGAACCATTTCAGTTTGATCAAAGTTT 59.777 33.333 23.08 14.21 32.02 2.66
1 2 6.697019 CGAACCATTTCAGTTTGATCAAAGTT 59.303 34.615 23.08 18.29 32.02 2.66
2 3 6.039270 TCGAACCATTTCAGTTTGATCAAAGT 59.961 34.615 21.05 20.78 33.60 2.66
3 4 6.437928 TCGAACCATTTCAGTTTGATCAAAG 58.562 36.000 21.05 10.76 33.60 2.77
4 5 6.039270 ACTCGAACCATTTCAGTTTGATCAAA 59.961 34.615 16.91 16.91 37.09 2.69
5 6 5.530915 ACTCGAACCATTTCAGTTTGATCAA 59.469 36.000 3.38 3.38 37.09 2.57
6 7 5.063204 ACTCGAACCATTTCAGTTTGATCA 58.937 37.500 0.00 0.00 37.09 2.92
7 8 5.613358 ACTCGAACCATTTCAGTTTGATC 57.387 39.130 0.00 0.00 37.09 2.92
20 21 9.615295 GCAATTAATTAACTTTAACTCGAACCA 57.385 29.630 0.00 0.00 0.00 3.67
21 22 9.836076 AGCAATTAATTAACTTTAACTCGAACC 57.164 29.630 0.00 0.00 0.00 3.62
43 44 3.519107 TGGTCTGGTCAATCTGATAGCAA 59.481 43.478 0.00 0.00 0.00 3.91
61 62 1.981256 TCTGAAAACTTGGGCTGGTC 58.019 50.000 0.00 0.00 0.00 4.02
67 68 3.645884 CTGCACAATCTGAAAACTTGGG 58.354 45.455 0.00 0.00 0.00 4.12
99 100 4.035441 ACCACGTTTTAGCGCTTCTTTTTA 59.965 37.500 18.68 0.00 34.88 1.52
102 103 1.944709 ACCACGTTTTAGCGCTTCTTT 59.055 42.857 18.68 0.00 34.88 2.52
105 106 1.262151 TGAACCACGTTTTAGCGCTTC 59.738 47.619 18.68 2.82 34.88 3.86
106 107 1.301423 TGAACCACGTTTTAGCGCTT 58.699 45.000 18.68 0.00 34.88 4.68
107 108 1.463444 GATGAACCACGTTTTAGCGCT 59.537 47.619 17.26 17.26 34.88 5.92
108 109 1.195900 TGATGAACCACGTTTTAGCGC 59.804 47.619 0.00 0.00 34.88 5.92
109 110 3.529634 TTGATGAACCACGTTTTAGCG 57.470 42.857 0.00 0.00 37.94 4.26
125 126 9.136323 GAATTACATATTGAAGGACCCTTTGAT 57.864 33.333 2.43 3.51 36.26 2.57
145 146 8.727910 ACTTCCTTCCAAAACGATTAGAATTAC 58.272 33.333 0.00 0.00 0.00 1.89
146 147 8.857694 ACTTCCTTCCAAAACGATTAGAATTA 57.142 30.769 0.00 0.00 0.00 1.40
147 148 7.761038 ACTTCCTTCCAAAACGATTAGAATT 57.239 32.000 0.00 0.00 0.00 2.17
150 151 6.996282 AGAAACTTCCTTCCAAAACGATTAGA 59.004 34.615 0.00 0.00 0.00 2.10
153 154 6.465439 AAGAAACTTCCTTCCAAAACGATT 57.535 33.333 0.00 0.00 0.00 3.34
154 155 6.073327 GAAGAAACTTCCTTCCAAAACGAT 57.927 37.500 0.00 0.00 35.26 3.73
163 176 3.223674 TGTGGGGAAGAAACTTCCTTC 57.776 47.619 23.72 17.88 38.61 3.46
235 248 9.472361 GCTCCTACTATTTTACATGAATTCGTA 57.528 33.333 0.00 0.00 0.00 3.43
236 249 7.985184 TGCTCCTACTATTTTACATGAATTCGT 59.015 33.333 0.00 0.00 0.00 3.85
238 251 8.276325 CGTGCTCCTACTATTTTACATGAATTC 58.724 37.037 0.00 0.00 0.00 2.17
239 252 7.985184 TCGTGCTCCTACTATTTTACATGAATT 59.015 33.333 0.00 0.00 0.00 2.17
240 253 7.497595 TCGTGCTCCTACTATTTTACATGAAT 58.502 34.615 0.00 0.00 0.00 2.57
241 254 6.869695 TCGTGCTCCTACTATTTTACATGAA 58.130 36.000 0.00 0.00 0.00 2.57
242 255 6.459670 TCGTGCTCCTACTATTTTACATGA 57.540 37.500 0.00 0.00 0.00 3.07
246 259 7.652105 TCATGATTCGTGCTCCTACTATTTTAC 59.348 37.037 0.72 0.00 0.00 2.01
257 277 1.002033 GCCAATCATGATTCGTGCTCC 60.002 52.381 18.16 0.00 0.00 4.70
277 297 1.883084 GACGGTAATGGAGGCAGCG 60.883 63.158 0.00 0.00 38.99 5.18
283 303 4.704007 CGACGGACGGTAATGGAG 57.296 61.111 0.00 0.00 38.46 3.86
313 333 3.554692 GTCGGTGCTCGCGGAATG 61.555 66.667 6.13 0.00 39.05 2.67
353 539 2.713154 GCGTGACTGTTTGGCGTT 59.287 55.556 0.00 0.00 0.00 4.84
379 565 4.467084 GGATGGTTCCGCTGCCGA 62.467 66.667 0.00 0.00 36.29 5.54
443 629 2.026262 CCTTTCCGGATTTGAGAAGGGA 60.026 50.000 18.85 0.00 38.64 4.20
446 632 1.398390 CGCCTTTCCGGATTTGAGAAG 59.602 52.381 4.15 4.43 33.16 2.85
491 678 4.293648 TGGTGCACCGGTGAGACG 62.294 66.667 38.30 12.09 39.43 4.18
515 702 0.601311 GGTGTGACTCAGACAGCCAC 60.601 60.000 8.48 0.00 36.11 5.01
522 709 1.069090 GTTGGCGGTGTGACTCAGA 59.931 57.895 0.00 0.00 0.00 3.27
552 739 2.753452 GTCTTCTAGACACATCACCGGA 59.247 50.000 9.46 0.00 44.45 5.14
553 740 2.159226 GGTCTTCTAGACACATCACCGG 60.159 54.545 0.00 0.00 46.79 5.28
555 742 2.159226 CCGGTCTTCTAGACACATCACC 60.159 54.545 8.89 0.00 46.79 4.02
557 744 3.017442 CTCCGGTCTTCTAGACACATCA 58.983 50.000 0.00 0.00 46.79 3.07
558 745 2.223618 GCTCCGGTCTTCTAGACACATC 60.224 54.545 0.00 0.00 46.79 3.06
559 746 1.751924 GCTCCGGTCTTCTAGACACAT 59.248 52.381 0.00 0.00 46.79 3.21
560 747 1.174783 GCTCCGGTCTTCTAGACACA 58.825 55.000 0.00 0.00 46.79 3.72
561 748 1.174783 TGCTCCGGTCTTCTAGACAC 58.825 55.000 0.00 0.00 46.79 3.67
562 749 1.919240 TTGCTCCGGTCTTCTAGACA 58.081 50.000 0.00 0.00 46.79 3.41
583 784 3.773630 CGCGTAGGTGCACGTTGG 61.774 66.667 18.35 10.86 43.79 3.77
628 829 1.202940 GGCATCCCCTGTATTCCTTCC 60.203 57.143 0.00 0.00 0.00 3.46
629 830 1.494721 TGGCATCCCCTGTATTCCTTC 59.505 52.381 0.00 0.00 0.00 3.46
630 831 1.215423 GTGGCATCCCCTGTATTCCTT 59.785 52.381 0.00 0.00 0.00 3.36
631 832 0.846693 GTGGCATCCCCTGTATTCCT 59.153 55.000 0.00 0.00 0.00 3.36
632 833 0.846693 AGTGGCATCCCCTGTATTCC 59.153 55.000 0.00 0.00 0.00 3.01
633 834 1.212935 ACAGTGGCATCCCCTGTATTC 59.787 52.381 6.69 0.00 39.40 1.75
634 835 1.064463 CACAGTGGCATCCCCTGTATT 60.064 52.381 8.00 0.00 39.26 1.89
635 836 0.548031 CACAGTGGCATCCCCTGTAT 59.452 55.000 8.00 0.00 39.26 2.29
636 837 1.561769 CCACAGTGGCATCCCCTGTA 61.562 60.000 6.67 0.00 39.26 2.74
637 838 2.759114 CACAGTGGCATCCCCTGT 59.241 61.111 2.90 2.90 40.82 4.00
638 839 2.044650 CCACAGTGGCATCCCCTG 60.045 66.667 6.67 0.00 36.24 4.45
639 840 2.532715 ACCACAGTGGCATCCCCT 60.533 61.111 20.48 0.00 42.67 4.79
640 841 2.361610 CACCACAGTGGCATCCCC 60.362 66.667 20.48 0.00 42.67 4.81
641 842 2.756400 TCACCACAGTGGCATCCC 59.244 61.111 20.48 0.00 42.67 3.85
796 1023 1.554617 GATGGATTTGGTTGGGTTGGG 59.445 52.381 0.00 0.00 0.00 4.12
1488 1721 1.458445 CTGATCACACACGAGCAGTTG 59.542 52.381 0.00 0.00 42.99 3.16
1489 1722 1.606480 CCTGATCACACACGAGCAGTT 60.606 52.381 5.57 0.00 45.79 3.16
1505 1738 2.507484 CAAGCATGACCTGAAACCTGA 58.493 47.619 0.00 0.00 0.00 3.86
1506 1739 1.068055 GCAAGCATGACCTGAAACCTG 60.068 52.381 0.00 0.00 0.00 4.00
1507 1740 1.251251 GCAAGCATGACCTGAAACCT 58.749 50.000 0.00 0.00 0.00 3.50
1508 1741 0.244721 GGCAAGCATGACCTGAAACC 59.755 55.000 0.00 0.00 0.00 3.27
1509 1742 0.961019 TGGCAAGCATGACCTGAAAC 59.039 50.000 0.00 0.00 31.48 2.78
1510 1743 1.702182 TTGGCAAGCATGACCTGAAA 58.298 45.000 0.00 0.00 31.48 2.69
1511 1744 1.702182 TTTGGCAAGCATGACCTGAA 58.298 45.000 0.00 0.00 31.48 3.02
1542 1775 3.565764 ATTTCAGATGGATCGGAGCAA 57.434 42.857 0.00 0.00 32.80 3.91
1572 1805 6.652481 CCTCCCTGTATCATATTTACAAGCTG 59.348 42.308 0.00 0.00 0.00 4.24
1585 1818 3.459227 TGCATGAATTCCTCCCTGTATCA 59.541 43.478 2.27 0.00 0.00 2.15
1610 1846 6.146898 CCTACAAGGAAACAACCAAATTACG 58.853 40.000 0.00 0.00 37.67 3.18
1619 1855 2.762745 TCGAGCCTACAAGGAAACAAC 58.237 47.619 0.00 0.00 37.67 3.32
1627 1863 4.371786 TGAAGCATAATCGAGCCTACAAG 58.628 43.478 0.00 0.00 0.00 3.16
1630 1866 5.734855 TTTTGAAGCATAATCGAGCCTAC 57.265 39.130 0.00 0.00 0.00 3.18
1634 1870 6.143438 CCATGATTTTTGAAGCATAATCGAGC 59.857 38.462 0.00 0.00 31.29 5.03
1678 1914 4.856922 GCATTTCATTGCAAGCAAGGTACT 60.857 41.667 17.47 1.77 41.47 2.73
1681 1917 2.419667 GCATTTCATTGCAAGCAAGGT 58.580 42.857 17.47 0.00 42.31 3.50
1682 1918 1.735571 GGCATTTCATTGCAAGCAAGG 59.264 47.619 12.73 12.73 44.59 3.61
1693 1929 5.072055 TGTATGATCATTCCGGCATTTCAT 58.928 37.500 14.65 12.06 0.00 2.57
1761 1997 0.179153 GCGCTTTCAATCTCTTGGGC 60.179 55.000 0.00 0.00 32.95 5.36
1763 1999 0.097674 CCGCGCTTTCAATCTCTTGG 59.902 55.000 5.56 0.00 32.95 3.61
1795 2031 3.254654 CATCGTGTGCCCGCTACG 61.255 66.667 9.67 9.67 39.04 3.51
1837 2074 0.749091 CCGCATGTGACATGGTCCAT 60.749 55.000 25.22 0.00 0.00 3.41
1866 2103 4.154015 TGGCAATACGAATGTCAAGACAAG 59.846 41.667 7.02 4.83 45.41 3.16
1907 2153 9.914131 CAAACTCGACTGGAATATCAATATAGA 57.086 33.333 0.00 0.00 0.00 1.98
1935 2195 3.181537 CGGTAGCAGCGTTGTAAACTAAC 60.182 47.826 0.00 0.00 46.99 2.34
1939 2199 0.179233 GCGGTAGCAGCGTTGTAAAC 60.179 55.000 0.00 0.00 43.19 2.01
1941 2201 3.864944 GCGGTAGCAGCGTTGTAA 58.135 55.556 0.00 0.00 41.74 2.41
1997 2513 8.002984 TGACACGTTCATAGACCTATTTATGA 57.997 34.615 0.00 0.00 35.18 2.15
2003 2519 6.282199 AGTTTGACACGTTCATAGACCTAT 57.718 37.500 0.00 0.00 32.84 2.57
2006 2522 4.510340 ACAAGTTTGACACGTTCATAGACC 59.490 41.667 0.00 0.00 32.84 3.85
2074 2593 0.249238 TGTTGGCGGATGTTGTTTGC 60.249 50.000 0.00 0.00 0.00 3.68
2119 2778 3.760151 TGGTGGCATTCTCTTTCAATGAG 59.240 43.478 0.00 0.00 33.69 2.90
2196 2863 2.439507 ACACATGTCCAGGACAACTCTT 59.560 45.455 26.53 6.60 45.96 2.85
2197 2864 2.050144 ACACATGTCCAGGACAACTCT 58.950 47.619 26.53 7.01 45.96 3.24
2214 2883 2.610374 TCACCAAAACGTGAAGCTACAC 59.390 45.455 0.00 0.00 39.78 2.90
2216 2885 3.955771 TTCACCAAAACGTGAAGCTAC 57.044 42.857 0.17 0.00 45.49 3.58
2237 2906 0.460987 GGCCGACATCTGAACTCCAG 60.461 60.000 0.00 0.00 44.27 3.86
2245 2914 1.742761 AATGAACTGGCCGACATCTG 58.257 50.000 0.00 0.00 0.00 2.90
2252 2927 0.958091 TCACCAAAATGAACTGGCCG 59.042 50.000 0.00 0.00 36.03 6.13
2256 2931 8.925161 TTTTCTAACTTCACCAAAATGAACTG 57.075 30.769 0.00 0.00 34.84 3.16
2286 2961 5.753921 GGAATCAAGTGGAGTAGGTTAATCG 59.246 44.000 0.00 0.00 0.00 3.34
2311 2986 0.381801 GGGATAATTGTGCAGGTGCG 59.618 55.000 0.00 0.00 45.83 5.34
2318 2993 3.763897 ACAAGGACTTGGGATAATTGTGC 59.236 43.478 15.72 0.00 44.45 4.57
2323 2998 5.501156 GACTCAACAAGGACTTGGGATAAT 58.499 41.667 15.72 3.26 44.45 1.28
2325 3000 3.263425 GGACTCAACAAGGACTTGGGATA 59.737 47.826 15.72 0.00 44.45 2.59
2326 3001 2.040412 GGACTCAACAAGGACTTGGGAT 59.960 50.000 15.72 0.10 44.45 3.85
2327 3002 1.420138 GGACTCAACAAGGACTTGGGA 59.580 52.381 15.72 11.40 44.45 4.37
2329 3004 1.545651 GGGGACTCAACAAGGACTTGG 60.546 57.143 15.72 1.47 44.45 3.61
2330 3005 1.545651 GGGGGACTCAACAAGGACTTG 60.546 57.143 10.34 10.34 45.58 3.16
2331 3006 0.771755 GGGGGACTCAACAAGGACTT 59.228 55.000 0.00 0.00 0.00 3.01
2332 3007 1.481056 CGGGGGACTCAACAAGGACT 61.481 60.000 0.00 0.00 0.00 3.85
2333 3008 1.003718 CGGGGGACTCAACAAGGAC 60.004 63.158 0.00 0.00 0.00 3.85
2335 3010 2.351276 CCGGGGGACTCAACAAGG 59.649 66.667 0.00 0.00 0.00 3.61
2336 3011 2.359975 GCCGGGGGACTCAACAAG 60.360 66.667 2.18 0.00 0.00 3.16
2337 3012 3.961414 GGCCGGGGGACTCAACAA 61.961 66.667 2.18 0.00 0.00 2.83
2338 3013 4.974438 AGGCCGGGGGACTCAACA 62.974 66.667 2.18 0.00 35.03 3.33
2340 3015 2.856988 AAAGGCCGGGGGACTCAA 60.857 61.111 2.18 0.00 42.44 3.02
2341 3016 3.646715 CAAAGGCCGGGGGACTCA 61.647 66.667 2.18 0.00 42.44 3.41
2345 3020 4.440829 GATGCAAAGGCCGGGGGA 62.441 66.667 2.18 0.00 40.13 4.81
2375 3062 8.751335 CCGTTTAATAATCATAACAATGGTTGC 58.249 33.333 0.00 0.00 37.88 4.17
2400 3088 6.642950 CGTGATTGTCTTTCATCCTATACTCC 59.357 42.308 0.00 0.00 0.00 3.85
2406 3094 4.676986 CGACCGTGATTGTCTTTCATCCTA 60.677 45.833 0.00 0.00 0.00 2.94
2409 3097 3.250744 TCGACCGTGATTGTCTTTCATC 58.749 45.455 0.00 0.00 0.00 2.92
2411 3099 2.798283 GTTCGACCGTGATTGTCTTTCA 59.202 45.455 0.00 0.00 0.00 2.69
2412 3100 2.157085 GGTTCGACCGTGATTGTCTTTC 59.843 50.000 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.