Multiple sequence alignment - TraesCS1A01G299300

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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 TraesCS1A01G299300 chr1A 100.000 2377 0 0 1 2377 494393287 494390911 0.000000e+00 4390
1 TraesCS1A01G299300 chr1A 100.000 73 0 0 2624 2696 494390664 494390592 4.680000e-28 135
2 TraesCS1A01G299300 chr1D 92.674 1597 54 23 760 2327 397055304 397053742 0.000000e+00 2242
3 TraesCS1A01G299300 chr1D 82.888 187 20 6 512 690 397055808 397055626 9.990000e-35 158
4 TraesCS1A01G299300 chr1D 98.413 63 1 0 2315 2377 397053219 397053157 7.890000e-21 111
5 TraesCS1A01G299300 chr1B 90.986 1664 55 29 749 2370 532066388 532064778 0.000000e+00 2154
6 TraesCS1A01G299300 chr1B 87.500 104 7 2 511 612 532066873 532066774 6.100000e-22 115
7 TraesCS1A01G299300 chr7A 87.814 517 61 1 1 515 238883999 238884515 2.970000e-169 604


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 TraesCS1A01G299300 chr1A 494390592 494393287 2695 True 2262.5 4390 100.000 1 2696 2 chr1A.!!$R1 2695
1 TraesCS1A01G299300 chr1D 397053157 397055808 2651 True 837.0 2242 91.325 512 2377 3 chr1D.!!$R1 1865
2 TraesCS1A01G299300 chr1B 532064778 532066873 2095 True 1134.5 2154 89.243 511 2370 2 chr1B.!!$R1 1859
3 TraesCS1A01G299300 chr7A 238883999 238884515 516 False 604.0 604 87.814 1 515 1 chr7A.!!$F1 514

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
614 625 0.109597 GGATCGCTTGTTGGTTGCAG 60.11 55.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 2744 0.737367 TGCAAGCGGAGATCAAGACG 60.737 55.0 0.0 0.0 0.0 4.18 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
23 24 1.375326 GGAGCCCCGACAAGTCTTT 59.625 57.895 0.00 0.00 0.00 2.52
32 33 2.028112 CCGACAAGTCTTTGATGGAGGA 60.028 50.000 0.00 0.00 37.73 3.71
33 34 3.257393 CGACAAGTCTTTGATGGAGGAG 58.743 50.000 0.00 0.00 37.73 3.69
36 37 3.009916 ACAAGTCTTTGATGGAGGAGCAT 59.990 43.478 0.00 0.00 37.73 3.79
39 40 3.522750 AGTCTTTGATGGAGGAGCATTCT 59.477 43.478 0.00 0.00 0.00 2.40
68 69 3.079578 TGATGTTAAGAGAGTCGACCGT 58.920 45.455 13.01 0.00 0.00 4.83
85 86 1.007734 GTCGACCAGACGTCAGCAA 60.008 57.895 19.50 0.00 42.07 3.91
86 87 1.007734 TCGACCAGACGTCAGCAAC 60.008 57.895 19.50 4.17 42.07 4.17
88 89 0.874175 CGACCAGACGTCAGCAACAA 60.874 55.000 19.50 0.00 42.07 2.83
105 106 4.573900 CAACAATAGAGCAGTGGAGAAGT 58.426 43.478 0.00 0.00 0.00 3.01
113 114 1.555075 GCAGTGGAGAAGTATGTGGGA 59.445 52.381 0.00 0.00 0.00 4.37
116 117 0.535335 TGGAGAAGTATGTGGGACGC 59.465 55.000 0.00 0.00 40.62 5.19
124 125 2.236146 AGTATGTGGGACGCTGATTCAA 59.764 45.455 0.00 0.00 40.97 2.69
126 127 1.452110 TGTGGGACGCTGATTCAATG 58.548 50.000 0.00 0.00 40.97 2.82
150 151 0.745486 TGCAGAATGGGCATGAGTCG 60.745 55.000 0.00 0.00 36.11 4.18
160 161 0.814457 GCATGAGTCGGAGTCTGTCT 59.186 55.000 13.63 0.00 0.00 3.41
169 170 1.174783 GGAGTCTGTCTAGTTCCGCA 58.825 55.000 0.00 0.00 0.00 5.69
180 183 1.058903 GTTCCGCAAATCGACGCTC 59.941 57.895 0.00 0.00 41.67 5.03
185 188 1.491563 GCAAATCGACGCTCGTTGT 59.508 52.632 9.22 0.00 41.35 3.32
188 191 1.070843 CAAATCGACGCTCGTTGTTGT 60.071 47.619 9.22 0.00 41.35 3.32
202 205 1.694844 TGTTGTACAGTCTCCCACGA 58.305 50.000 0.00 0.00 0.00 4.35
211 214 2.434884 CTCCCACGATGCGCAAGT 60.435 61.111 17.11 15.75 41.68 3.16
256 259 2.304761 AGTCGCATAGTTCTTTCCCCAA 59.695 45.455 0.00 0.00 0.00 4.12
267 270 7.855784 AGTTCTTTCCCCAAATAAAATCTGT 57.144 32.000 0.00 0.00 0.00 3.41
273 276 6.985653 TCCCCAAATAAAATCTGTGAACAA 57.014 33.333 0.00 0.00 0.00 2.83
283 286 0.804989 CTGTGAACAAATCCTCCGGC 59.195 55.000 0.00 0.00 0.00 6.13
289 292 1.123928 ACAAATCCTCCGGCCTAGAG 58.876 55.000 11.74 11.74 0.00 2.43
290 293 1.343075 ACAAATCCTCCGGCCTAGAGA 60.343 52.381 18.62 8.01 32.86 3.10
300 303 1.662517 GGCCTAGAGAAGAAAGCAGC 58.337 55.000 0.00 0.00 0.00 5.25
301 304 1.662517 GCCTAGAGAAGAAAGCAGCC 58.337 55.000 0.00 0.00 0.00 4.85
350 353 5.408604 GGCTTATCGTTGACCCTACATAATG 59.591 44.000 0.00 0.00 0.00 1.90
353 356 7.115947 GCTTATCGTTGACCCTACATAATGTAC 59.884 40.741 0.00 0.00 0.00 2.90
378 381 4.940463 TCAGGTATGTGCGGTATTAAGTC 58.060 43.478 0.00 0.00 0.00 3.01
390 393 5.172934 CGGTATTAAGTCAACAGTGGCTAA 58.827 41.667 0.00 0.00 39.37 3.09
395 398 1.768870 AGTCAACAGTGGCTAACAGGT 59.231 47.619 0.00 0.00 38.16 4.00
401 404 2.048597 TGGCTAACAGGTCACGCG 60.049 61.111 3.53 3.53 0.00 6.01
402 405 2.813908 GGCTAACAGGTCACGCGG 60.814 66.667 12.47 0.00 0.00 6.46
404 407 2.654877 CTAACAGGTCACGCGGGT 59.345 61.111 8.89 0.00 0.00 5.28
409 412 1.079405 CAGGTCACGCGGGTATTGT 60.079 57.895 8.89 0.00 0.00 2.71
422 425 3.490419 CGGGTATTGTAGTTCGGAGGAAG 60.490 52.174 0.00 0.00 31.49 3.46
438 441 1.295792 GAAGCAACGTTGGACAGACA 58.704 50.000 28.33 0.00 0.00 3.41
464 467 2.224695 TGTAACGAGAGACAGAGGTCCA 60.225 50.000 0.00 0.00 45.48 4.02
467 470 0.808125 CGAGAGACAGAGGTCCACAG 59.192 60.000 0.00 0.00 45.48 3.66
469 472 0.114168 AGAGACAGAGGTCCACAGCT 59.886 55.000 0.00 0.00 45.48 4.24
482 485 1.372251 ACAGCTGAGAGCACGAACG 60.372 57.895 23.35 0.00 45.56 3.95
484 487 2.734723 GCTGAGAGCACGAACGCA 60.735 61.111 0.00 0.00 41.89 5.24
485 488 2.310233 GCTGAGAGCACGAACGCAA 61.310 57.895 0.00 0.00 41.89 4.85
496 499 0.179215 CGAACGCAACAGAGGCATTC 60.179 55.000 0.00 0.00 30.72 2.67
504 507 1.244019 ACAGAGGCATTCGGTTTGGC 61.244 55.000 0.00 0.00 39.77 4.52
554 559 4.775236 AGCTAGATCACAAATCAGGGTTC 58.225 43.478 0.00 0.00 0.00 3.62
572 579 4.505039 GGGTTCCACATTGTCACTCTAACT 60.505 45.833 0.00 0.00 0.00 2.24
573 580 5.279809 GGGTTCCACATTGTCACTCTAACTA 60.280 44.000 0.00 0.00 0.00 2.24
574 581 6.407202 GGTTCCACATTGTCACTCTAACTAT 58.593 40.000 0.00 0.00 0.00 2.12
575 582 7.364408 GGGTTCCACATTGTCACTCTAACTATA 60.364 40.741 0.00 0.00 0.00 1.31
587 594 8.109391 GTCACTCTAACTATATATGCTCGTACG 58.891 40.741 9.53 9.53 0.00 3.67
614 625 0.109597 GGATCGCTTGTTGGTTGCAG 60.110 55.000 0.00 0.00 0.00 4.41
619 630 1.726865 CTTGTTGGTTGCAGCGTGA 59.273 52.632 0.00 0.00 0.00 4.35
620 631 0.592247 CTTGTTGGTTGCAGCGTGAC 60.592 55.000 0.00 0.00 0.00 3.67
633 644 1.087501 GCGTGACCCTCCTTTCATTC 58.912 55.000 0.00 0.00 0.00 2.67
636 647 2.939103 CGTGACCCTCCTTTCATTCATC 59.061 50.000 0.00 0.00 0.00 2.92
644 657 4.157289 CCTCCTTTCATTCATCACCTTGTG 59.843 45.833 0.00 0.00 34.45 3.33
651 664 0.684535 TCATCACCTTGTGAGCGGAA 59.315 50.000 3.11 0.00 46.04 4.30
658 671 1.737793 CCTTGTGAGCGGAATGTAACC 59.262 52.381 0.00 0.00 0.00 2.85
661 674 2.181125 TGTGAGCGGAATGTAACCCTA 58.819 47.619 0.00 0.00 0.00 3.53
665 678 3.452990 TGAGCGGAATGTAACCCTATTGA 59.547 43.478 0.00 0.00 0.00 2.57
693 706 9.831682 ATGGAATAAAACTCCCCTTTACTAAAA 57.168 29.630 0.00 0.00 31.32 1.52
694 707 9.657728 TGGAATAAAACTCCCCTTTACTAAAAA 57.342 29.630 0.00 0.00 31.32 1.94
733 989 1.661197 GACCCGTCGTGCGTTTGTA 60.661 57.895 0.00 0.00 39.32 2.41
734 990 1.005867 ACCCGTCGTGCGTTTGTAT 60.006 52.632 0.00 0.00 39.32 2.29
735 991 0.243365 ACCCGTCGTGCGTTTGTATA 59.757 50.000 0.00 0.00 39.32 1.47
736 992 0.641783 CCCGTCGTGCGTTTGTATAC 59.358 55.000 0.00 0.00 39.32 1.47
737 993 1.338765 CCGTCGTGCGTTTGTATACA 58.661 50.000 0.08 0.08 39.32 2.29
738 994 1.921887 CCGTCGTGCGTTTGTATACAT 59.078 47.619 6.36 0.00 39.32 2.29
739 995 3.107407 CCGTCGTGCGTTTGTATACATA 58.893 45.455 6.36 0.00 39.32 2.29
846 1421 1.533033 TGACCACCGAGCAAGAGGA 60.533 57.895 0.00 0.00 0.00 3.71
847 1422 1.216710 GACCACCGAGCAAGAGGAG 59.783 63.158 0.00 0.00 0.00 3.69
848 1423 2.125350 CCACCGAGCAAGAGGAGC 60.125 66.667 0.00 0.00 0.00 4.70
849 1424 2.507992 CACCGAGCAAGAGGAGCG 60.508 66.667 0.00 0.00 37.01 5.03
850 1425 2.676822 ACCGAGCAAGAGGAGCGA 60.677 61.111 0.00 0.00 37.01 4.93
851 1426 2.202676 CCGAGCAAGAGGAGCGAC 60.203 66.667 0.00 0.00 37.01 5.19
957 1532 1.543690 CCTCCCCCATTCCATTCCC 59.456 63.158 0.00 0.00 0.00 3.97
968 1543 2.186903 CATTCCCTCCGTCCACCG 59.813 66.667 0.00 0.00 0.00 4.94
995 1570 4.221703 CACCTACCCAGAGATCATACCATC 59.778 50.000 0.00 0.00 0.00 3.51
1557 2144 4.079850 AGCAGCTGCCTGGACGAG 62.080 66.667 34.39 0.00 43.38 4.18
1811 2407 3.741805 TGTCTATCGACACGACTTGAG 57.258 47.619 10.65 0.00 44.85 3.02
1853 2462 2.125326 CCTGCCTCGATCCGGTGTA 61.125 63.158 0.00 0.00 0.00 2.90
1878 2487 1.539388 CCTGCGTCTGATAGCTCTAGG 59.461 57.143 0.00 4.75 0.00 3.02
1928 2537 1.154727 CGTTTAGCGTTGGCGTGTC 60.155 57.895 0.00 0.00 46.35 3.67
1980 2589 4.983090 CGAGCATGTCGCCATTTC 57.017 55.556 5.07 0.00 43.03 2.17
2014 2624 3.275617 TTGTTGCTGTTGTCTAGTGGT 57.724 42.857 0.00 0.00 0.00 4.16
2118 2746 3.236632 GGAACTAATCCCACGTTACGT 57.763 47.619 3.95 3.95 43.00 3.57
2119 2747 3.182182 GGAACTAATCCCACGTTACGTC 58.818 50.000 7.67 0.00 43.00 4.34
2120 2748 3.119352 GGAACTAATCCCACGTTACGTCT 60.119 47.826 7.67 0.00 43.00 4.18
2153 2781 6.456718 CGCTTGCATTTTATAATTGTTTGGGG 60.457 38.462 0.00 0.00 0.00 4.96
2162 2790 0.977108 ATTGTTTGGGGGCGCATGAT 60.977 50.000 10.83 0.00 0.00 2.45
2243 2871 3.604875 ACATCGACGGTGGACTAATTT 57.395 42.857 13.58 0.00 0.00 1.82
2245 2873 5.075858 ACATCGACGGTGGACTAATTTTA 57.924 39.130 13.58 0.00 0.00 1.52
2249 2877 4.022068 TCGACGGTGGACTAATTTTACACT 60.022 41.667 0.00 0.00 32.88 3.55
2259 2887 6.533367 GGACTAATTTTACACTGCTCTCAGAG 59.467 42.308 0.00 0.00 42.95 3.35
2261 2889 7.846066 ACTAATTTTACACTGCTCTCAGAGAT 58.154 34.615 5.62 0.00 42.95 2.75
2302 2930 1.134788 GCTGCGTAGTGGACCAATACT 60.135 52.381 25.16 9.11 33.52 2.12
2649 3812 8.935844 CACACACACATTTATCATGTAGTAACT 58.064 33.333 0.00 0.00 0.00 2.24
2650 3813 9.502091 ACACACACATTTATCATGTAGTAACTT 57.498 29.630 0.00 0.00 0.00 2.66
2651 3814 9.759259 CACACACATTTATCATGTAGTAACTTG 57.241 33.333 0.00 0.00 33.22 3.16
2652 3815 9.719355 ACACACATTTATCATGTAGTAACTTGA 57.281 29.630 0.00 0.00 42.15 3.02
2654 3817 9.944376 ACACATTTATCATGTAGTAACTTGAGT 57.056 29.630 0.00 0.00 41.50 3.41
2656 3819 8.883731 ACATTTATCATGTAGTAACTTGAGTGC 58.116 33.333 0.00 0.00 41.50 4.40
2657 3820 8.882736 CATTTATCATGTAGTAACTTGAGTGCA 58.117 33.333 0.00 0.00 41.50 4.57
2658 3821 8.840833 TTTATCATGTAGTAACTTGAGTGCAA 57.159 30.769 0.00 0.00 41.50 4.08
2659 3822 8.840833 TTATCATGTAGTAACTTGAGTGCAAA 57.159 30.769 0.00 0.00 41.50 3.68
2660 3823 6.785488 TCATGTAGTAACTTGAGTGCAAAG 57.215 37.500 0.00 0.00 35.50 2.77
2661 3824 6.521162 TCATGTAGTAACTTGAGTGCAAAGA 58.479 36.000 3.66 0.00 35.50 2.52
2662 3825 6.423905 TCATGTAGTAACTTGAGTGCAAAGAC 59.576 38.462 3.66 0.00 35.50 3.01
2663 3826 4.743151 TGTAGTAACTTGAGTGCAAAGACG 59.257 41.667 3.66 0.00 32.73 4.18
2664 3827 2.544267 AGTAACTTGAGTGCAAAGACGC 59.456 45.455 3.66 0.00 32.73 5.19
2665 3828 0.304705 AACTTGAGTGCAAAGACGCG 59.695 50.000 3.53 3.53 32.73 6.01
2666 3829 1.439365 CTTGAGTGCAAAGACGCGC 60.439 57.895 5.73 0.00 42.82 6.86
2667 3830 2.104770 CTTGAGTGCAAAGACGCGCA 62.105 55.000 5.73 0.00 44.95 6.09
2668 3831 2.104770 TTGAGTGCAAAGACGCGCAG 62.105 55.000 5.73 2.42 44.95 5.18
2669 3832 2.588877 AGTGCAAAGACGCGCAGT 60.589 55.556 5.73 6.37 44.95 4.40
2670 3833 1.282248 GAGTGCAAAGACGCGCAGTA 61.282 55.000 5.73 0.00 44.95 2.74
2671 3834 1.130613 GTGCAAAGACGCGCAGTAG 59.869 57.895 5.73 0.00 42.07 2.57
2672 3835 1.300620 TGCAAAGACGCGCAGTAGT 60.301 52.632 5.73 0.00 33.34 2.73
2673 3836 0.038983 TGCAAAGACGCGCAGTAGTA 60.039 50.000 5.73 0.00 33.34 1.82
2674 3837 1.065358 GCAAAGACGCGCAGTAGTAA 58.935 50.000 5.73 0.00 0.00 2.24
2675 3838 1.659098 GCAAAGACGCGCAGTAGTAAT 59.341 47.619 5.73 0.00 0.00 1.89
2676 3839 2.093783 GCAAAGACGCGCAGTAGTAATT 59.906 45.455 5.73 0.00 0.00 1.40
2677 3840 3.781280 GCAAAGACGCGCAGTAGTAATTC 60.781 47.826 5.73 0.00 0.00 2.17
2678 3841 1.823828 AGACGCGCAGTAGTAATTCG 58.176 50.000 5.73 0.00 0.00 3.34
2679 3842 0.226484 GACGCGCAGTAGTAATTCGC 59.774 55.000 5.73 4.55 42.05 4.70
2680 3843 1.143969 ACGCGCAGTAGTAATTCGCC 61.144 55.000 5.73 0.00 42.44 5.54
2681 3844 0.870307 CGCGCAGTAGTAATTCGCCT 60.870 55.000 8.75 0.00 42.44 5.52
2682 3845 1.598676 CGCGCAGTAGTAATTCGCCTA 60.599 52.381 8.75 0.00 42.44 3.93
2683 3846 1.785430 GCGCAGTAGTAATTCGCCTAC 59.215 52.381 0.30 0.00 39.91 3.18
2684 3847 2.797087 GCGCAGTAGTAATTCGCCTACA 60.797 50.000 0.30 0.00 39.91 2.74
2685 3848 3.639538 CGCAGTAGTAATTCGCCTACAT 58.360 45.455 10.65 0.00 36.77 2.29
2686 3849 4.049186 CGCAGTAGTAATTCGCCTACATT 58.951 43.478 10.65 0.00 36.77 2.71
2687 3850 4.506654 CGCAGTAGTAATTCGCCTACATTT 59.493 41.667 10.65 0.00 36.77 2.32
2688 3851 5.556382 CGCAGTAGTAATTCGCCTACATTTG 60.556 44.000 10.65 4.24 36.77 2.32
2689 3852 5.738370 CAGTAGTAATTCGCCTACATTTGC 58.262 41.667 10.65 0.00 36.77 3.68
2694 3857 2.701006 CGCCTACATTTGCGTCGG 59.299 61.111 0.00 0.00 45.43 4.79
2695 3858 2.403586 GCCTACATTTGCGTCGGC 59.596 61.111 0.00 0.00 40.13 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.831652 AAGACTTGTCGGGGCTCCAG 61.832 60.000 1.96 0.00 0.00 3.86
6 7 0.034896 TCAAAGACTTGTCGGGGCTC 59.965 55.000 0.00 0.00 33.94 4.70
18 19 3.626670 CAGAATGCTCCTCCATCAAAGAC 59.373 47.826 0.00 0.00 0.00 3.01
36 37 4.041567 TCTCTTAACATCAACCCTGCAGAA 59.958 41.667 17.39 0.00 0.00 3.02
39 40 3.327757 ACTCTCTTAACATCAACCCTGCA 59.672 43.478 0.00 0.00 0.00 4.41
82 83 2.977914 TCTCCACTGCTCTATTGTTGC 58.022 47.619 0.00 0.00 0.00 4.17
85 86 5.423610 ACATACTTCTCCACTGCTCTATTGT 59.576 40.000 0.00 0.00 0.00 2.71
86 87 5.752472 CACATACTTCTCCACTGCTCTATTG 59.248 44.000 0.00 0.00 0.00 1.90
88 89 4.343526 CCACATACTTCTCCACTGCTCTAT 59.656 45.833 0.00 0.00 0.00 1.98
105 106 3.205338 CATTGAATCAGCGTCCCACATA 58.795 45.455 0.00 0.00 0.00 2.29
113 114 1.078709 CACGTCCATTGAATCAGCGT 58.921 50.000 0.00 0.00 0.00 5.07
116 117 2.349590 TCTGCACGTCCATTGAATCAG 58.650 47.619 0.00 0.00 0.00 2.90
124 125 1.750399 GCCCATTCTGCACGTCCAT 60.750 57.895 0.00 0.00 0.00 3.41
126 127 1.750399 ATGCCCATTCTGCACGTCC 60.750 57.895 0.00 0.00 42.38 4.79
150 151 1.174783 TGCGGAACTAGACAGACTCC 58.825 55.000 0.00 0.00 0.00 3.85
160 161 0.108992 AGCGTCGATTTGCGGAACTA 60.109 50.000 0.00 0.00 41.33 2.24
169 170 1.214367 ACAACAACGAGCGTCGATTT 58.786 45.000 13.06 2.27 43.74 2.17
180 183 2.132762 GTGGGAGACTGTACAACAACG 58.867 52.381 0.00 0.00 0.00 4.10
185 188 1.067142 GCATCGTGGGAGACTGTACAA 60.067 52.381 0.00 0.00 0.00 2.41
188 191 1.807226 CGCATCGTGGGAGACTGTA 59.193 57.895 0.00 0.00 31.21 2.74
202 205 3.119849 GGTTGTTTATCTGACTTGCGCAT 60.120 43.478 12.75 0.00 0.00 4.73
211 214 2.076100 CGCTGCAGGTTGTTTATCTGA 58.924 47.619 17.12 0.00 0.00 3.27
250 253 6.985653 TTGTTCACAGATTTTATTTGGGGA 57.014 33.333 0.00 0.00 0.00 4.81
256 259 7.538575 CGGAGGATTTGTTCACAGATTTTATT 58.461 34.615 0.00 0.00 0.00 1.40
283 286 2.499289 TGAGGCTGCTTTCTTCTCTAGG 59.501 50.000 0.00 0.00 0.00 3.02
289 292 2.947652 TGCATATGAGGCTGCTTTCTTC 59.052 45.455 6.97 0.00 39.16 2.87
290 293 3.008835 TGCATATGAGGCTGCTTTCTT 57.991 42.857 6.97 0.00 39.16 2.52
316 319 3.650942 TCAACGATAAGCCCCTATCCATT 59.349 43.478 0.00 0.00 0.00 3.16
318 321 2.367567 GTCAACGATAAGCCCCTATCCA 59.632 50.000 0.00 0.00 0.00 3.41
322 325 1.125633 GGGTCAACGATAAGCCCCTA 58.874 55.000 0.00 0.00 33.40 3.53
353 356 2.839486 ATACCGCACATACCTGATGG 57.161 50.000 0.00 0.00 40.18 3.51
363 366 3.743911 CACTGTTGACTTAATACCGCACA 59.256 43.478 0.00 0.00 0.00 4.57
370 373 6.170506 CCTGTTAGCCACTGTTGACTTAATA 58.829 40.000 0.00 0.00 0.00 0.98
378 381 1.873591 GTGACCTGTTAGCCACTGTTG 59.126 52.381 0.00 0.00 0.00 3.33
390 393 1.079405 CAATACCCGCGTGACCTGT 60.079 57.895 4.92 0.00 0.00 4.00
395 398 1.467883 CGAACTACAATACCCGCGTGA 60.468 52.381 4.92 0.00 0.00 4.35
401 404 3.740452 GCTTCCTCCGAACTACAATACCC 60.740 52.174 0.00 0.00 0.00 3.69
402 405 3.118884 TGCTTCCTCCGAACTACAATACC 60.119 47.826 0.00 0.00 0.00 2.73
404 407 4.501071 GTTGCTTCCTCCGAACTACAATA 58.499 43.478 0.00 0.00 0.00 1.90
409 412 0.963962 ACGTTGCTTCCTCCGAACTA 59.036 50.000 0.00 0.00 0.00 2.24
422 425 1.275657 CGTGTCTGTCCAACGTTGC 59.724 57.895 22.93 10.71 32.79 4.17
438 441 0.522180 CTGTCTCTCGTTACAGCCGT 59.478 55.000 0.00 0.00 36.96 5.68
447 450 0.110678 TGTGGACCTCTGTCTCTCGT 59.889 55.000 0.00 0.00 41.47 4.18
448 451 0.808125 CTGTGGACCTCTGTCTCTCG 59.192 60.000 0.00 0.00 41.47 4.04
464 467 1.372251 CGTTCGTGCTCTCAGCTGT 60.372 57.895 14.67 0.00 42.97 4.40
467 470 2.310233 TTGCGTTCGTGCTCTCAGC 61.310 57.895 0.00 0.00 42.82 4.26
469 472 1.215014 CTGTTGCGTTCGTGCTCTCA 61.215 55.000 0.00 0.00 35.36 3.27
482 485 0.598065 AAACCGAATGCCTCTGTTGC 59.402 50.000 0.00 0.00 32.40 4.17
484 487 1.247567 CCAAACCGAATGCCTCTGTT 58.752 50.000 0.00 0.00 33.32 3.16
485 488 1.244019 GCCAAACCGAATGCCTCTGT 61.244 55.000 0.00 0.00 0.00 3.41
496 499 4.939368 TCCCACACCGCCAAACCG 62.939 66.667 0.00 0.00 0.00 4.44
504 507 2.882137 ACATGTTTAAACTCCCACACCG 59.118 45.455 18.72 0.00 0.00 4.94
554 559 9.144747 GCATATATAGTTAGAGTGACAATGTGG 57.855 37.037 0.00 0.00 0.00 4.17
587 594 1.654105 CAACAAGCGATCCTACGTGTC 59.346 52.381 0.00 0.00 35.59 3.67
596 607 0.730494 GCTGCAACCAACAAGCGATC 60.730 55.000 0.00 0.00 0.00 3.69
598 609 2.721231 GCTGCAACCAACAAGCGA 59.279 55.556 0.00 0.00 0.00 4.93
614 625 1.087501 GAATGAAAGGAGGGTCACGC 58.912 55.000 0.00 0.00 0.00 5.34
619 630 2.922283 AGGTGATGAATGAAAGGAGGGT 59.078 45.455 0.00 0.00 0.00 4.34
620 631 3.659183 AGGTGATGAATGAAAGGAGGG 57.341 47.619 0.00 0.00 0.00 4.30
633 644 1.399440 CATTCCGCTCACAAGGTGATG 59.601 52.381 0.00 0.00 41.94 3.07
636 647 2.093306 TACATTCCGCTCACAAGGTG 57.907 50.000 0.00 0.00 34.45 4.00
644 657 4.067972 TCAATAGGGTTACATTCCGCTC 57.932 45.455 0.00 0.00 0.00 5.03
658 671 8.394040 AGGGGAGTTTTATTCCATATCAATAGG 58.606 37.037 0.00 0.00 36.40 2.57
703 716 1.796459 CGACGGGTCAGTTCGATTTTT 59.204 47.619 0.00 0.00 0.00 1.94
704 717 1.269936 ACGACGGGTCAGTTCGATTTT 60.270 47.619 0.00 0.00 0.00 1.82
710 723 3.103911 CGCACGACGGGTCAGTTC 61.104 66.667 0.00 0.00 38.44 3.01
733 989 8.615211 CAATCAGTGCTTGTGTGTATTATGTAT 58.385 33.333 0.00 0.00 0.00 2.29
734 990 7.065683 CCAATCAGTGCTTGTGTGTATTATGTA 59.934 37.037 6.01 0.00 0.00 2.29
735 991 6.127925 CCAATCAGTGCTTGTGTGTATTATGT 60.128 38.462 6.01 0.00 0.00 2.29
736 992 6.260377 CCAATCAGTGCTTGTGTGTATTATG 58.740 40.000 6.01 0.00 0.00 1.90
737 993 5.163622 GCCAATCAGTGCTTGTGTGTATTAT 60.164 40.000 6.01 0.00 0.00 1.28
738 994 4.155826 GCCAATCAGTGCTTGTGTGTATTA 59.844 41.667 6.01 0.00 0.00 0.98
739 995 3.057315 GCCAATCAGTGCTTGTGTGTATT 60.057 43.478 6.01 0.00 0.00 1.89
848 1423 0.611062 TATATGCGGGAGGAGGGTCG 60.611 60.000 0.00 0.00 0.00 4.79
849 1424 1.640917 TTATATGCGGGAGGAGGGTC 58.359 55.000 0.00 0.00 0.00 4.46
850 1425 2.105993 GTTTTATATGCGGGAGGAGGGT 59.894 50.000 0.00 0.00 0.00 4.34
851 1426 2.779506 GTTTTATATGCGGGAGGAGGG 58.220 52.381 0.00 0.00 0.00 4.30
968 1543 0.466124 GATCTCTGGGTAGGTGGTGC 59.534 60.000 0.00 0.00 0.00 5.01
995 1570 2.025767 CTCTCGCCCTCTCATGGTGG 62.026 65.000 0.00 0.00 34.09 4.61
1101 1679 3.307445 CTCTCCCTGGTGAGCAGG 58.693 66.667 23.17 23.17 39.48 4.85
1286 1873 3.842126 CGTACGACGACGCCGAGA 61.842 66.667 10.44 0.00 46.05 4.04
1350 1937 3.889134 CTTGCAGCTCCTGTCGCCA 62.889 63.158 0.00 0.00 33.43 5.69
1600 2187 4.925861 GAGGCAGAGCATCCCCGC 62.926 72.222 0.00 0.00 32.93 6.13
1811 2407 2.287915 CCAATGGAACGATCGATCAACC 59.712 50.000 24.34 21.34 0.00 3.77
1853 2462 1.759445 AGCTATCAGACGCAGGAACAT 59.241 47.619 0.00 0.00 0.00 2.71
1950 2559 1.806461 ATGCTCGTGTCGTGTGTCCT 61.806 55.000 0.00 0.00 0.00 3.85
1951 2560 1.372997 ATGCTCGTGTCGTGTGTCC 60.373 57.895 0.00 0.00 0.00 4.02
1952 2561 0.939577 ACATGCTCGTGTCGTGTGTC 60.940 55.000 0.00 0.00 32.89 3.67
1953 2562 0.939577 GACATGCTCGTGTCGTGTGT 60.940 55.000 6.49 0.00 39.12 3.72
1980 2589 1.923864 GCAACAAACGTTCCAAAGGTG 59.076 47.619 0.00 0.00 0.00 4.00
2014 2624 8.049117 ACAACAAGCATTCTATTTCTCCATAGA 58.951 33.333 0.00 0.00 34.50 1.98
2115 2743 0.737715 GCAAGCGGAGATCAAGACGT 60.738 55.000 0.00 0.00 0.00 4.34
2116 2744 0.737367 TGCAAGCGGAGATCAAGACG 60.737 55.000 0.00 0.00 0.00 4.18
2117 2745 1.661341 ATGCAAGCGGAGATCAAGAC 58.339 50.000 0.00 0.00 0.00 3.01
2118 2746 2.408271 AATGCAAGCGGAGATCAAGA 57.592 45.000 0.00 0.00 0.00 3.02
2119 2747 3.498927 AAAATGCAAGCGGAGATCAAG 57.501 42.857 0.00 0.00 0.00 3.02
2120 2748 6.691754 TTATAAAATGCAAGCGGAGATCAA 57.308 33.333 0.00 0.00 0.00 2.57
2153 2781 1.195448 CGTCCTCAATAATCATGCGCC 59.805 52.381 4.18 0.00 0.00 6.53
2162 2790 3.066291 ACATGGCAACGTCCTCAATAA 57.934 42.857 0.00 0.00 42.51 1.40
2243 2871 5.929058 ATCAATCTCTGAGAGCAGTGTAA 57.071 39.130 13.50 0.00 42.84 2.41
2245 2873 4.467082 AGAATCAATCTCTGAGAGCAGTGT 59.533 41.667 13.50 0.00 42.84 3.55
2249 2877 6.297080 AGAAAGAATCAATCTCTGAGAGCA 57.703 37.500 13.50 0.00 37.42 4.26
2259 2887 6.036953 AGCTGATGAACGAGAAAGAATCAATC 59.963 38.462 0.00 0.00 0.00 2.67
2261 2889 5.121298 CAGCTGATGAACGAGAAAGAATCAA 59.879 40.000 8.42 0.00 0.00 2.57
2302 2930 9.959749 GTATTTCAAACATTTGGAGAAGTTACA 57.040 29.630 4.58 0.00 38.66 2.41
2327 2955 8.677148 ATGAGAAAGTACAACAAATAGTGTGT 57.323 30.769 0.00 0.00 40.60 3.72
2623 3786 8.935844 AGTTACTACATGATAAATGTGTGTGTG 58.064 33.333 0.00 0.00 33.76 3.82
2624 3787 9.502091 AAGTTACTACATGATAAATGTGTGTGT 57.498 29.630 0.00 0.00 33.76 3.72
2625 3788 9.759259 CAAGTTACTACATGATAAATGTGTGTG 57.241 33.333 0.00 0.00 33.76 3.82
2626 3789 9.719355 TCAAGTTACTACATGATAAATGTGTGT 57.281 29.630 0.00 3.51 33.76 3.72
2628 3791 9.944376 ACTCAAGTTACTACATGATAAATGTGT 57.056 29.630 0.00 3.34 32.14 3.72
2630 3793 8.883731 GCACTCAAGTTACTACATGATAAATGT 58.116 33.333 0.00 0.00 32.14 2.71
2631 3794 8.882736 TGCACTCAAGTTACTACATGATAAATG 58.117 33.333 0.00 0.00 32.14 2.32
2632 3795 9.448438 TTGCACTCAAGTTACTACATGATAAAT 57.552 29.630 0.00 0.00 32.14 1.40
2633 3796 8.840833 TTGCACTCAAGTTACTACATGATAAA 57.159 30.769 0.00 0.00 32.14 1.40
2634 3797 8.840833 TTTGCACTCAAGTTACTACATGATAA 57.159 30.769 0.00 0.00 32.14 1.75
2635 3798 8.311109 TCTTTGCACTCAAGTTACTACATGATA 58.689 33.333 0.00 0.00 32.14 2.15
2636 3799 7.118390 GTCTTTGCACTCAAGTTACTACATGAT 59.882 37.037 0.00 0.00 32.14 2.45
2637 3800 6.423905 GTCTTTGCACTCAAGTTACTACATGA 59.576 38.462 0.00 0.00 33.12 3.07
2638 3801 6.593978 GTCTTTGCACTCAAGTTACTACATG 58.406 40.000 0.00 0.00 33.12 3.21
2639 3802 5.405571 CGTCTTTGCACTCAAGTTACTACAT 59.594 40.000 0.00 0.00 33.12 2.29
2640 3803 4.743151 CGTCTTTGCACTCAAGTTACTACA 59.257 41.667 0.00 0.00 33.12 2.74
2641 3804 4.376109 GCGTCTTTGCACTCAAGTTACTAC 60.376 45.833 0.00 0.00 33.12 2.73
2642 3805 3.739300 GCGTCTTTGCACTCAAGTTACTA 59.261 43.478 0.00 0.00 33.12 1.82
2643 3806 2.544267 GCGTCTTTGCACTCAAGTTACT 59.456 45.455 0.00 0.00 33.12 2.24
2644 3807 2.659291 CGCGTCTTTGCACTCAAGTTAC 60.659 50.000 0.00 0.00 33.12 2.50
2645 3808 1.525197 CGCGTCTTTGCACTCAAGTTA 59.475 47.619 0.00 0.00 33.12 2.24
2646 3809 0.304705 CGCGTCTTTGCACTCAAGTT 59.695 50.000 0.00 0.00 33.12 2.66
2647 3810 1.934463 CGCGTCTTTGCACTCAAGT 59.066 52.632 0.00 0.00 33.12 3.16
2648 3811 1.439365 GCGCGTCTTTGCACTCAAG 60.439 57.895 8.43 0.00 33.12 3.02
2649 3812 2.104770 CTGCGCGTCTTTGCACTCAA 62.105 55.000 8.43 0.00 35.90 3.02
2650 3813 2.587473 TGCGCGTCTTTGCACTCA 60.587 55.556 8.43 0.00 35.90 3.41
2651 3814 1.282248 TACTGCGCGTCTTTGCACTC 61.282 55.000 8.43 0.00 35.90 3.51
2652 3815 1.284982 CTACTGCGCGTCTTTGCACT 61.285 55.000 8.43 0.00 35.90 4.40
2653 3816 1.130613 CTACTGCGCGTCTTTGCAC 59.869 57.895 8.43 0.00 35.90 4.57
2654 3817 0.038983 TACTACTGCGCGTCTTTGCA 60.039 50.000 8.43 0.00 39.13 4.08
2655 3818 1.065358 TTACTACTGCGCGTCTTTGC 58.935 50.000 8.43 0.00 0.00 3.68
2656 3819 3.539592 CGAATTACTACTGCGCGTCTTTG 60.540 47.826 8.43 0.00 0.00 2.77
2657 3820 2.597305 CGAATTACTACTGCGCGTCTTT 59.403 45.455 8.43 0.00 0.00 2.52
2658 3821 2.182825 CGAATTACTACTGCGCGTCTT 58.817 47.619 8.43 0.00 0.00 3.01
2659 3822 1.823828 CGAATTACTACTGCGCGTCT 58.176 50.000 8.43 0.00 0.00 4.18
2660 3823 0.226484 GCGAATTACTACTGCGCGTC 59.774 55.000 8.43 0.00 38.24 5.19
2661 3824 2.285154 GCGAATTACTACTGCGCGT 58.715 52.632 8.43 6.51 38.24 6.01
2663 3826 1.785430 GTAGGCGAATTACTACTGCGC 59.215 52.381 0.00 0.00 46.20 6.09
2664 3827 3.074504 TGTAGGCGAATTACTACTGCG 57.925 47.619 12.76 0.00 40.11 5.18
2665 3828 5.738370 CAAATGTAGGCGAATTACTACTGC 58.262 41.667 12.76 0.22 40.11 4.40
2666 3829 5.738370 GCAAATGTAGGCGAATTACTACTG 58.262 41.667 12.76 6.79 40.11 2.74
2667 3830 5.986004 GCAAATGTAGGCGAATTACTACT 57.014 39.130 12.76 0.00 40.11 2.57


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

AutoCloner maintained by Alex Coulton.