Multiple sequence alignment - TraesCS4D01G267500

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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 TraesCS4D01G267500 chr4D 100.000 2846 0 0 1 2846 438152023 438154868 0.000000e+00 5256
1 TraesCS4D01G267500 chr4D 88.050 159 19 0 2586 2744 71288630 71288472 3.740000e-44 189
2 TraesCS4D01G267500 chr4A 91.206 2752 161 37 1 2715 27588308 27591015 0.000000e+00 3666
3 TraesCS4D01G267500 chr4B 92.027 1781 103 25 976 2731 541910469 541912235 0.000000e+00 2466
4 TraesCS4D01G267500 chr4B 95.238 441 16 5 553 988 541910007 541910447 0.000000e+00 693
5 TraesCS4D01G267500 chr6A 84.314 255 38 2 1329 1582 535403371 535403118 6.090000e-62 248
6 TraesCS4D01G267500 chr7A 83.137 255 41 2 1331 1584 135689646 135689393 6.130000e-57 231
7 TraesCS4D01G267500 chr6D 83.137 255 41 2 1329 1582 388951404 388951151 6.130000e-57 231
8 TraesCS4D01G267500 chr6D 88.679 159 18 0 2586 2744 402874932 402874774 8.050000e-46 195
9 TraesCS4D01G267500 chr6B 82.353 255 43 2 1329 1582 581867820 581867567 1.330000e-53 220
10 TraesCS4D01G267500 chr5D 85.437 206 27 3 1304 1509 304163201 304162999 7.990000e-51 211
11 TraesCS4D01G267500 chr5D 86.792 159 21 0 2586 2744 412592831 412592989 8.100000e-41 178
12 TraesCS4D01G267500 chr5D 86.792 159 21 0 2586 2744 438386598 438386440 8.100000e-41 178
13 TraesCS4D01G267500 chr5B 84.951 206 28 3 1304 1509 348571425 348571223 3.720000e-49 206
14 TraesCS4D01G267500 chr5A 84.951 206 28 3 1304 1509 393917954 393918156 3.720000e-49 206
15 TraesCS4D01G267500 chr3B 91.333 150 13 0 2595 2744 588861337 588861188 3.720000e-49 206
16 TraesCS4D01G267500 chr2B 87.421 159 18 1 2586 2744 28628895 28629051 6.260000e-42 182
17 TraesCS4D01G267500 chr3D 86.000 150 21 0 2595 2744 543018777 543018926 8.160000e-36 161
18 TraesCS4D01G267500 chr1D 84.277 159 25 0 2586 2744 74283632 74283790 3.800000e-34 156


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 TraesCS4D01G267500 chr4D 438152023 438154868 2845 False 5256.0 5256 100.0000 1 2846 1 chr4D.!!$F1 2845
1 TraesCS4D01G267500 chr4A 27588308 27591015 2707 False 3666.0 3666 91.2060 1 2715 1 chr4A.!!$F1 2714
2 TraesCS4D01G267500 chr4B 541910007 541912235 2228 False 1579.5 2466 93.6325 553 2731 2 chr4B.!!$F1 2178

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
324 325 0.109319 GCCACAAATTGCCCGTGTAG 60.109 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 2006 0.251077 AAACCAAGCAGAGCAGGGAG 60.251 55.0 6.05 0.0 31.81 4.3 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
17 18 2.927864 TAGAGCGGGAGGAGGAGG 59.072 66.667 0.00 0.00 0.00 4.30
23 24 4.851214 GGGAGGAGGAGGAGCGCT 62.851 72.222 11.27 11.27 0.00 5.92
24 25 3.535962 GGAGGAGGAGGAGCGCTG 61.536 72.222 18.48 0.00 0.00 5.18
49 50 0.971447 GGTAGGCACGAGAGAAGGGT 60.971 60.000 0.00 0.00 0.00 4.34
59 60 2.032071 AGAAGGGTCGGTTTGCGG 59.968 61.111 0.00 0.00 0.00 5.69
153 154 2.280404 TAGGTCCGATCTCCGTGGCT 62.280 60.000 0.00 0.00 36.31 4.75
193 194 5.237996 TGTCTCTGCCGTATACAGTACATAC 59.762 44.000 3.32 0.00 36.50 2.39
208 209 3.438297 ACATACGGTATCACTGTCTGC 57.562 47.619 0.00 0.00 38.84 4.26
256 257 6.318112 AGGAACATCTTTCTGGAAGGAAAAT 58.682 36.000 0.00 0.00 35.22 1.82
261 262 6.210185 ACATCTTTCTGGAAGGAAAATGAAGG 59.790 38.462 0.00 0.00 35.22 3.46
266 267 2.833338 TGGAAGGAAAATGAAGGCCATG 59.167 45.455 5.01 0.00 35.24 3.66
269 270 2.181975 AGGAAAATGAAGGCCATGGTG 58.818 47.619 14.67 0.00 35.24 4.17
273 274 0.251922 AATGAAGGCCATGGTGTGCT 60.252 50.000 14.67 0.00 35.24 4.40
282 283 2.927871 GCCATGGTGTGCTCACATTTTC 60.928 50.000 19.67 3.54 45.45 2.29
293 294 5.414454 GTGCTCACATTTTCCAATGGTACTA 59.586 40.000 0.00 0.00 43.82 1.82
297 298 7.520614 GCTCACATTTTCCAATGGTACTATAGC 60.521 40.741 0.00 0.00 43.82 2.97
301 302 9.860650 ACATTTTCCAATGGTACTATAGCATAA 57.139 29.630 0.00 0.00 45.32 1.90
323 324 1.857318 CGCCACAAATTGCCCGTGTA 61.857 55.000 0.00 0.00 0.00 2.90
324 325 0.109319 GCCACAAATTGCCCGTGTAG 60.109 55.000 0.00 0.00 0.00 2.74
348 349 4.094887 ACCATCGCTCATAAACAATGACAC 59.905 41.667 0.00 0.00 39.77 3.67
384 385 2.764967 ATGTACGGGCGGCCCTTA 60.765 61.111 33.80 26.79 42.67 2.69
404 405 3.358707 ACATCGCCATCGTATCGTTAA 57.641 42.857 0.00 0.00 36.96 2.01
423 424 5.052172 CGTTAAATCGACACCACTATTACCG 60.052 44.000 0.00 0.00 0.00 4.02
424 425 3.447918 AATCGACACCACTATTACCGG 57.552 47.619 0.00 0.00 0.00 5.28
440 441 0.179056 CCGGCCCTCGATGTTGTATT 60.179 55.000 0.00 0.00 42.43 1.89
505 513 8.664798 AGACAAACAACAGTATATACGTACGTA 58.335 33.333 28.62 28.62 34.87 3.57
514 522 9.476202 ACAGTATATACGTACGTACAATCTACA 57.524 33.333 28.99 7.24 33.01 2.74
591 599 1.290955 CGGAGACCGTAGCAACCAA 59.709 57.895 1.80 0.00 42.73 3.67
593 601 0.320697 GGAGACCGTAGCAACCAAGT 59.679 55.000 0.00 0.00 0.00 3.16
678 686 0.684153 AATCACCCCTTGGCCAATCG 60.684 55.000 20.85 12.18 33.59 3.34
682 690 2.282039 CCCCTTGGCCAATCGCAAA 61.282 57.895 20.85 0.00 40.31 3.68
716 724 4.626081 GTGTCACCGCCACCTGCT 62.626 66.667 0.00 0.00 38.05 4.24
900 908 2.594303 CCCAACAGCTCGCACCAA 60.594 61.111 0.00 0.00 0.00 3.67
913 925 0.322816 GCACCAAGCTCCCATTCTCA 60.323 55.000 0.00 0.00 41.15 3.27
915 927 2.421952 GCACCAAGCTCCCATTCTCATA 60.422 50.000 0.00 0.00 41.15 2.15
925 937 4.129380 TCCCATTCTCATAGCAAATCGTG 58.871 43.478 0.00 0.00 0.00 4.35
1146 1194 1.218047 CATCTCGTTCGCCTTCCCA 59.782 57.895 0.00 0.00 0.00 4.37
1701 1749 1.153249 CTCCGTCTCCGAGAGCTCT 60.153 63.158 18.28 18.28 35.63 4.09
1911 1981 5.801350 TCTGCTTTCATTAGGTTTGATCG 57.199 39.130 0.00 0.00 0.00 3.69
1926 1996 5.229469 GGTTTGATCGAGTATTCGTGTGTAG 59.771 44.000 7.56 0.00 46.72 2.74
1933 2003 4.027621 CGAGTATTCGTGTGTAGCATCAAC 60.028 45.833 0.00 0.00 41.84 3.18
1934 2004 4.181578 AGTATTCGTGTGTAGCATCAACC 58.818 43.478 0.00 0.00 0.00 3.77
1935 2005 1.803334 TTCGTGTGTAGCATCAACCC 58.197 50.000 0.00 0.00 0.00 4.11
1936 2006 0.036765 TCGTGTGTAGCATCAACCCC 60.037 55.000 0.00 0.00 0.00 4.95
2060 2131 5.638234 ACTTTGGTAGTACTCGAAATTGCTC 59.362 40.000 0.00 0.00 34.56 4.26
2061 2132 3.766151 TGGTAGTACTCGAAATTGCTCG 58.234 45.455 0.00 0.00 40.25 5.03
2075 2149 6.740905 CGAAATTGCTCGTATGTGTTTTGTAT 59.259 34.615 0.00 0.00 34.08 2.29
2085 2159 6.519761 CGTATGTGTTTTGTATTGCAGAACTC 59.480 38.462 9.05 6.52 41.25 3.01
2087 2161 6.060028 TGTGTTTTGTATTGCAGAACTCTC 57.940 37.500 9.05 2.45 41.25 3.20
2097 2172 9.066892 TGTATTGCAGAACTCTCTTTATTGTTT 57.933 29.630 2.66 0.00 0.00 2.83
2123 2198 6.711194 AGAATAGCATGACAGAAATGAGATGG 59.289 38.462 0.00 0.00 0.00 3.51
2142 2217 8.792633 TGAGATGGAAATTTTATTATAAGGCGG 58.207 33.333 0.00 0.00 0.00 6.13
2230 2305 7.648039 ACTAACCTCAGGACTATGAAGTAAG 57.352 40.000 0.00 0.00 35.56 2.34
2243 2318 9.232473 GACTATGAAGTAAGAAAAATCCCACTT 57.768 33.333 0.00 0.00 35.56 3.16
2278 2353 7.439381 ACTTGAAGATTTTGATGTTCTTGCAT 58.561 30.769 0.00 0.00 30.11 3.96
2298 2373 5.532032 TGCATGAATTTGACTTTCAGAGACA 59.468 36.000 0.00 0.00 36.60 3.41
2314 2389 0.950555 GACAACACTGCATGAGCCGA 60.951 55.000 0.00 0.00 41.13 5.54
2322 2397 1.353103 GCATGAGCCGATTTCCACG 59.647 57.895 0.00 0.00 33.58 4.94
2534 2610 4.458989 TGTTTGCAAGGACCTGTGATAATC 59.541 41.667 0.00 0.00 0.00 1.75
2561 2637 7.557724 AGCCTTTAGAGAACAATAAGGTACTC 58.442 38.462 0.00 0.00 38.49 2.59
2562 2638 6.762187 GCCTTTAGAGAACAATAAGGTACTCC 59.238 42.308 0.00 0.00 38.49 3.85
2564 2640 9.198475 CCTTTAGAGAACAATAAGGTACTCCTA 57.802 37.037 0.00 0.00 44.35 2.94
2566 2642 9.765295 TTTAGAGAACAATAAGGTACTCCTACT 57.235 33.333 0.00 0.00 44.35 2.57
2567 2643 9.765295 TTAGAGAACAATAAGGTACTCCTACTT 57.235 33.333 0.00 0.00 44.35 2.24
2568 2644 8.068892 AGAGAACAATAAGGTACTCCTACTTG 57.931 38.462 0.00 0.00 44.35 3.16
2569 2645 7.894364 AGAGAACAATAAGGTACTCCTACTTGA 59.106 37.037 12.44 0.00 44.35 3.02
2570 2646 7.838884 AGAACAATAAGGTACTCCTACTTGAC 58.161 38.462 12.44 8.06 44.35 3.18
2582 2658 6.177610 ACTCCTACTTGACAACAGTTTGAAA 58.822 36.000 0.00 0.00 36.48 2.69
2584 2660 7.083875 TCCTACTTGACAACAGTTTGAAAAG 57.916 36.000 0.00 0.00 36.48 2.27
2616 2692 4.559300 CGATGTTGGAATTCTTGCTGGTTT 60.559 41.667 5.23 0.00 0.00 3.27
2637 2713 1.135315 CATTGCCGCTCTTGGTTCG 59.865 57.895 0.00 0.00 0.00 3.95
2662 2738 1.296727 GGTAGGTTTAGCCGTGATGC 58.703 55.000 0.00 0.00 43.70 3.91
2667 2743 1.378531 GTTTAGCCGTGATGCATCCA 58.621 50.000 23.67 9.30 0.00 3.41
2678 2754 0.038166 ATGCATCCACTGTTCGGGTT 59.962 50.000 0.00 0.00 0.00 4.11
2681 2757 1.442769 CATCCACTGTTCGGGTTGAG 58.557 55.000 0.00 0.00 0.00 3.02
2687 2763 1.002624 TGTTCGGGTTGAGCATCCC 60.003 57.895 6.56 6.56 40.26 3.85
2708 2784 0.598562 TGTCTCTCTGCTTCGGACAC 59.401 55.000 0.00 0.00 32.91 3.67
2716 2792 0.107643 TGCTTCGGACACCATGTTCA 59.892 50.000 0.00 0.00 0.00 3.18
2724 2800 2.112928 ACCATGTTCACGCCTGCA 59.887 55.556 0.00 0.00 0.00 4.41
2726 2802 0.035534 ACCATGTTCACGCCTGCATA 60.036 50.000 0.00 0.00 0.00 3.14
2731 2807 1.336980 TGTTCACGCCTGCATACGTTA 60.337 47.619 11.05 1.78 41.32 3.18
2732 2808 1.323534 GTTCACGCCTGCATACGTTAG 59.676 52.381 11.05 2.68 41.32 2.34
2733 2809 0.528924 TCACGCCTGCATACGTTAGT 59.471 50.000 11.05 0.00 41.32 2.24
2734 2810 0.645355 CACGCCTGCATACGTTAGTG 59.355 55.000 11.05 0.73 41.32 2.74
2735 2811 0.245539 ACGCCTGCATACGTTAGTGT 59.754 50.000 8.21 0.00 40.09 3.55
2736 2812 0.921347 CGCCTGCATACGTTAGTGTC 59.079 55.000 0.00 0.00 0.00 3.67
2737 2813 1.734377 CGCCTGCATACGTTAGTGTCA 60.734 52.381 0.00 0.00 0.00 3.58
2738 2814 2.550978 GCCTGCATACGTTAGTGTCAT 58.449 47.619 0.00 0.00 0.00 3.06
2739 2815 2.285220 GCCTGCATACGTTAGTGTCATG 59.715 50.000 0.00 0.00 0.00 3.07
2740 2816 3.521560 CCTGCATACGTTAGTGTCATGT 58.478 45.455 0.00 0.00 0.00 3.21
2741 2817 3.306973 CCTGCATACGTTAGTGTCATGTG 59.693 47.826 0.00 0.00 0.00 3.21
2742 2818 3.920446 TGCATACGTTAGTGTCATGTGT 58.080 40.909 0.00 0.00 0.00 3.72
2743 2819 4.311606 TGCATACGTTAGTGTCATGTGTT 58.688 39.130 0.00 0.00 0.00 3.32
2744 2820 4.752604 TGCATACGTTAGTGTCATGTGTTT 59.247 37.500 0.00 0.00 0.00 2.83
2745 2821 5.237561 TGCATACGTTAGTGTCATGTGTTTT 59.762 36.000 0.00 0.00 0.00 2.43
2746 2822 6.140110 GCATACGTTAGTGTCATGTGTTTTT 58.860 36.000 0.00 0.00 0.00 1.94
2770 2846 8.568732 TTTATGCTAAAATTATTTGTAGCGCC 57.431 30.769 2.29 0.00 34.32 6.53
2771 2847 5.568685 TGCTAAAATTATTTGTAGCGCCA 57.431 34.783 2.29 0.00 34.32 5.69
2772 2848 6.142818 TGCTAAAATTATTTGTAGCGCCAT 57.857 33.333 2.29 0.00 34.32 4.40
2773 2849 5.976534 TGCTAAAATTATTTGTAGCGCCATG 59.023 36.000 2.29 0.00 34.32 3.66
2774 2850 6.183360 TGCTAAAATTATTTGTAGCGCCATGA 60.183 34.615 2.29 0.00 34.32 3.07
2775 2851 6.863126 GCTAAAATTATTTGTAGCGCCATGAT 59.137 34.615 2.29 0.00 0.00 2.45
2776 2852 7.382218 GCTAAAATTATTTGTAGCGCCATGATT 59.618 33.333 2.29 0.00 0.00 2.57
2777 2853 9.248291 CTAAAATTATTTGTAGCGCCATGATTT 57.752 29.630 2.29 1.27 0.00 2.17
2778 2854 8.491331 AAAATTATTTGTAGCGCCATGATTTT 57.509 26.923 2.29 7.19 0.00 1.82
2779 2855 7.467557 AATTATTTGTAGCGCCATGATTTTG 57.532 32.000 2.29 0.00 0.00 2.44
2780 2856 4.717233 ATTTGTAGCGCCATGATTTTGA 57.283 36.364 2.29 0.00 0.00 2.69
2781 2857 4.511617 TTTGTAGCGCCATGATTTTGAA 57.488 36.364 2.29 0.00 0.00 2.69
2782 2858 4.717233 TTGTAGCGCCATGATTTTGAAT 57.283 36.364 2.29 0.00 0.00 2.57
2783 2859 4.031418 TGTAGCGCCATGATTTTGAATG 57.969 40.909 2.29 0.00 0.00 2.67
2784 2860 1.930567 AGCGCCATGATTTTGAATGC 58.069 45.000 2.29 0.00 0.00 3.56
2785 2861 1.205179 AGCGCCATGATTTTGAATGCA 59.795 42.857 2.29 0.00 0.00 3.96
2786 2862 2.159014 AGCGCCATGATTTTGAATGCAT 60.159 40.909 2.29 0.00 0.00 3.96
2787 2863 2.610374 GCGCCATGATTTTGAATGCATT 59.390 40.909 12.83 12.83 0.00 3.56
2788 2864 3.064271 GCGCCATGATTTTGAATGCATTT 59.936 39.130 14.33 0.00 0.00 2.32
2789 2865 4.437659 GCGCCATGATTTTGAATGCATTTT 60.438 37.500 14.33 0.00 0.00 1.82
2790 2866 5.632959 CGCCATGATTTTGAATGCATTTTT 58.367 33.333 14.33 0.00 0.00 1.94
2791 2867 5.735427 CGCCATGATTTTGAATGCATTTTTC 59.265 36.000 14.33 2.12 0.00 2.29
2792 2868 6.402766 CGCCATGATTTTGAATGCATTTTTCT 60.403 34.615 14.33 0.00 0.00 2.52
2793 2869 7.309920 GCCATGATTTTGAATGCATTTTTCTT 58.690 30.769 14.33 0.00 0.00 2.52
2794 2870 8.452534 GCCATGATTTTGAATGCATTTTTCTTA 58.547 29.630 14.33 0.00 0.00 2.10
2808 2884 9.033481 TGCATTTTTCTTATTATGTAAGCATGC 57.967 29.630 10.51 10.51 36.58 4.06
2809 2885 9.033481 GCATTTTTCTTATTATGTAAGCATGCA 57.967 29.630 21.98 0.00 36.58 3.96
2813 2889 9.518906 TTTTCTTATTATGTAAGCATGCATGTG 57.481 29.630 26.79 5.68 36.58 3.21
2814 2890 7.806409 TCTTATTATGTAAGCATGCATGTGT 57.194 32.000 26.79 17.24 36.58 3.72
2815 2891 8.224389 TCTTATTATGTAAGCATGCATGTGTT 57.776 30.769 26.79 21.38 36.58 3.32
2816 2892 8.685427 TCTTATTATGTAAGCATGCATGTGTTT 58.315 29.630 26.79 19.70 36.58 2.83
2817 2893 8.631676 TTATTATGTAAGCATGCATGTGTTTG 57.368 30.769 26.79 3.24 36.58 2.93
2818 2894 4.524316 ATGTAAGCATGCATGTGTTTGT 57.476 36.364 26.79 8.05 33.37 2.83
2819 2895 3.640592 TGTAAGCATGCATGTGTTTGTG 58.359 40.909 26.79 1.63 0.00 3.33
2820 2896 3.317430 TGTAAGCATGCATGTGTTTGTGA 59.683 39.130 26.79 4.60 0.00 3.58
2821 2897 2.717580 AGCATGCATGTGTTTGTGAG 57.282 45.000 26.79 0.00 0.00 3.51
2822 2898 1.271379 AGCATGCATGTGTTTGTGAGG 59.729 47.619 26.79 0.00 0.00 3.86
2823 2899 1.270274 GCATGCATGTGTTTGTGAGGA 59.730 47.619 26.79 0.00 0.00 3.71
2824 2900 2.923605 GCATGCATGTGTTTGTGAGGAC 60.924 50.000 26.79 2.60 0.00 3.85
2825 2901 1.317613 TGCATGTGTTTGTGAGGACC 58.682 50.000 0.00 0.00 0.00 4.46
2826 2902 1.133823 TGCATGTGTTTGTGAGGACCT 60.134 47.619 0.00 0.00 0.00 3.85
2827 2903 1.267806 GCATGTGTTTGTGAGGACCTG 59.732 52.381 0.00 0.00 0.00 4.00
2828 2904 2.575532 CATGTGTTTGTGAGGACCTGT 58.424 47.619 0.00 0.00 0.00 4.00
2829 2905 2.325583 TGTGTTTGTGAGGACCTGTC 57.674 50.000 0.00 0.00 0.00 3.51
2830 2906 1.557371 TGTGTTTGTGAGGACCTGTCA 59.443 47.619 0.00 0.00 0.00 3.58
2831 2907 2.172505 TGTGTTTGTGAGGACCTGTCAT 59.827 45.455 0.00 0.00 0.00 3.06
2832 2908 3.389656 TGTGTTTGTGAGGACCTGTCATA 59.610 43.478 0.00 0.00 0.00 2.15
2833 2909 3.746492 GTGTTTGTGAGGACCTGTCATAC 59.254 47.826 0.00 4.13 0.00 2.39
2834 2910 3.646162 TGTTTGTGAGGACCTGTCATACT 59.354 43.478 0.00 0.00 0.00 2.12
2835 2911 4.102524 TGTTTGTGAGGACCTGTCATACTT 59.897 41.667 0.00 0.00 0.00 2.24
2836 2912 3.961480 TGTGAGGACCTGTCATACTTG 57.039 47.619 0.00 0.00 0.00 3.16
2837 2913 3.506398 TGTGAGGACCTGTCATACTTGA 58.494 45.455 0.00 0.00 0.00 3.02
2838 2914 3.511540 TGTGAGGACCTGTCATACTTGAG 59.488 47.826 0.00 0.00 30.85 3.02
2839 2915 2.497675 TGAGGACCTGTCATACTTGAGC 59.502 50.000 0.00 0.00 30.85 4.26
2840 2916 1.834263 AGGACCTGTCATACTTGAGCC 59.166 52.381 0.00 0.00 30.85 4.70
2841 2917 1.834263 GGACCTGTCATACTTGAGCCT 59.166 52.381 0.00 0.00 30.85 4.58
2842 2918 2.237392 GGACCTGTCATACTTGAGCCTT 59.763 50.000 0.00 0.00 30.85 4.35
2843 2919 3.307762 GGACCTGTCATACTTGAGCCTTT 60.308 47.826 0.00 0.00 30.85 3.11
2844 2920 4.081087 GGACCTGTCATACTTGAGCCTTTA 60.081 45.833 0.00 0.00 30.85 1.85
2845 2921 5.091261 ACCTGTCATACTTGAGCCTTTAG 57.909 43.478 0.00 0.00 30.85 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.507102 CGTGCCTACCGCTGTCAG 60.507 66.667 0.00 0.00 38.78 3.51
23 24 2.986979 TCGTGCCTACCGCTGTCA 60.987 61.111 0.00 0.00 38.78 3.58
24 25 2.202623 CTCGTGCCTACCGCTGTC 60.203 66.667 0.00 0.00 38.78 3.51
33 34 2.344203 CGACCCTTCTCTCGTGCCT 61.344 63.158 0.00 0.00 0.00 4.75
44 45 0.752376 TTTTCCGCAAACCGACCCTT 60.752 50.000 0.00 0.00 40.02 3.95
67 68 2.248280 TACGGACACACAACATGCTT 57.752 45.000 0.00 0.00 0.00 3.91
68 69 2.472695 ATACGGACACACAACATGCT 57.527 45.000 0.00 0.00 0.00 3.79
69 70 2.607635 CCTATACGGACACACAACATGC 59.392 50.000 0.00 0.00 33.16 4.06
81 82 5.871396 AGAAGATTGAAAGCCTATACGGA 57.129 39.130 0.00 0.00 33.16 4.69
83 84 9.745880 TTACTAAGAAGATTGAAAGCCTATACG 57.254 33.333 0.00 0.00 0.00 3.06
130 131 0.838608 ACGGAGATCGGACCTACTCT 59.161 55.000 0.00 0.00 44.45 3.24
193 194 2.196749 GACATGCAGACAGTGATACCG 58.803 52.381 0.00 0.00 0.00 4.02
208 209 3.190118 GCTCTTCCAGAAACAAGGACATG 59.810 47.826 0.00 0.00 32.62 3.21
230 231 4.655963 TCCTTCCAGAAAGATGTTCCTTG 58.344 43.478 0.00 0.00 37.12 3.61
256 257 1.303561 GAGCACACCATGGCCTTCA 60.304 57.895 13.04 0.00 0.00 3.02
261 262 0.604578 AAATGTGAGCACACCATGGC 59.395 50.000 13.04 0.00 45.05 4.40
266 267 3.319755 CATTGGAAAATGTGAGCACACC 58.680 45.455 11.92 3.45 45.05 4.16
269 270 3.665745 ACCATTGGAAAATGTGAGCAC 57.334 42.857 10.37 0.00 0.00 4.40
273 274 7.342581 TGCTATAGTACCATTGGAAAATGTGA 58.657 34.615 10.37 0.00 0.00 3.58
282 283 6.037172 GGCGAATTATGCTATAGTACCATTGG 59.963 42.308 0.00 0.00 0.00 3.16
293 294 4.984161 GCAATTTGTGGCGAATTATGCTAT 59.016 37.500 0.00 0.00 0.00 2.97
323 324 4.572389 GTCATTGTTTATGAGCGATGGTCT 59.428 41.667 2.35 0.00 43.78 3.85
324 325 4.332543 TGTCATTGTTTATGAGCGATGGTC 59.667 41.667 2.35 0.00 43.78 4.02
348 349 3.058016 ACATCGCTTTGATTTGGTGACAG 60.058 43.478 0.00 0.00 37.01 3.51
384 385 3.358707 TTAACGATACGATGGCGATGT 57.641 42.857 0.00 0.00 41.64 3.06
404 405 2.482490 GCCGGTAATAGTGGTGTCGATT 60.482 50.000 1.90 0.00 0.00 3.34
423 424 0.663153 GCAATACAACATCGAGGGCC 59.337 55.000 0.69 0.00 0.00 5.80
424 425 0.663153 GGCAATACAACATCGAGGGC 59.337 55.000 0.69 0.00 0.00 5.19
440 441 6.656632 TTTCCAATTTTGTACTGTATGGCA 57.343 33.333 0.00 0.00 0.00 4.92
477 485 9.489393 CGTACGTATATACTGTTGTTTGTCTTA 57.511 33.333 7.22 0.00 0.00 2.10
478 486 8.023128 ACGTACGTATATACTGTTGTTTGTCTT 58.977 33.333 21.41 0.00 0.00 3.01
490 498 9.698309 AGTGTAGATTGTACGTACGTATATACT 57.302 33.333 29.05 23.89 32.82 2.12
493 501 9.144747 CCTAGTGTAGATTGTACGTACGTATAT 57.855 37.037 29.05 23.63 32.82 0.86
498 506 4.521943 GCCTAGTGTAGATTGTACGTACG 58.478 47.826 20.18 15.01 0.00 3.67
499 507 4.521943 CGCCTAGTGTAGATTGTACGTAC 58.478 47.826 18.90 18.90 0.00 3.67
505 513 0.464452 GGCCGCCTAGTGTAGATTGT 59.536 55.000 0.71 0.00 0.00 2.71
514 522 1.452108 GATTGCAAGGCCGCCTAGT 60.452 57.895 13.73 0.00 31.13 2.57
591 599 0.179134 GACTGATCTACGCGGCAACT 60.179 55.000 12.47 0.00 0.00 3.16
593 601 0.457853 GTGACTGATCTACGCGGCAA 60.458 55.000 12.47 0.00 0.00 4.52
899 907 3.939740 TTGCTATGAGAATGGGAGCTT 57.060 42.857 0.00 0.00 34.19 3.74
900 908 3.939740 TTTGCTATGAGAATGGGAGCT 57.060 42.857 0.00 0.00 34.19 4.09
925 937 4.884164 AGCTGGTAATTTAGGATGAACTGC 59.116 41.667 0.00 0.00 0.00 4.40
1058 1106 1.023513 GTCTCTGCTGTCCACCATGC 61.024 60.000 0.00 0.00 0.00 4.06
1190 1238 4.208686 GCGCGGGAGTGAGGTAGG 62.209 72.222 8.83 0.00 44.85 3.18
1911 1981 4.267928 GGTTGATGCTACACACGAATACTC 59.732 45.833 0.00 0.00 0.00 2.59
1919 1989 1.679032 GGAGGGGTTGATGCTACACAC 60.679 57.143 0.00 0.00 0.00 3.82
1926 1996 2.440980 GCAGGGAGGGGTTGATGC 60.441 66.667 0.00 0.00 0.00 3.91
1933 2003 3.013932 AAGCAGAGCAGGGAGGGG 61.014 66.667 0.00 0.00 0.00 4.79
1934 2004 2.271497 CAAGCAGAGCAGGGAGGG 59.729 66.667 0.00 0.00 0.00 4.30
1935 2005 2.134630 AACCAAGCAGAGCAGGGAGG 62.135 60.000 6.05 0.00 31.81 4.30
1936 2006 0.251077 AAACCAAGCAGAGCAGGGAG 60.251 55.000 6.05 0.00 31.81 4.30
2045 2116 4.561606 ACACATACGAGCAATTTCGAGTAC 59.438 41.667 6.54 0.00 43.03 2.73
2050 2121 4.909305 ACAAAACACATACGAGCAATTTCG 59.091 37.500 0.00 0.00 45.70 3.46
2060 2131 6.370593 AGTTCTGCAATACAAAACACATACG 58.629 36.000 0.00 0.00 0.00 3.06
2061 2132 7.584987 AGAGTTCTGCAATACAAAACACATAC 58.415 34.615 0.00 0.00 0.00 2.39
2075 2149 8.902540 TCTAAACAATAAAGAGAGTTCTGCAA 57.097 30.769 0.00 0.00 32.79 4.08
2097 2172 7.876582 CCATCTCATTTCTGTCATGCTATTCTA 59.123 37.037 0.00 0.00 0.00 2.10
2123 2198 9.589111 TTTGAACCCGCCTTATAATAAAATTTC 57.411 29.630 0.00 0.00 0.00 2.17
2132 2207 5.071370 TCAACTTTTGAACCCGCCTTATAA 58.929 37.500 0.00 0.00 36.59 0.98
2230 2305 9.764363 AAGTTTCTATCAAAAGTGGGATTTTTC 57.236 29.630 0.00 0.00 30.01 2.29
2278 2353 6.599244 AGTGTTGTCTCTGAAAGTCAAATTCA 59.401 34.615 0.00 0.00 35.60 2.57
2298 2373 1.470098 GAAATCGGCTCATGCAGTGTT 59.530 47.619 0.00 0.00 41.91 3.32
2322 2397 3.502211 AGATTTGTGTGACGGTGATTTCC 59.498 43.478 0.00 0.00 0.00 3.13
2332 2407 7.099764 TCTAGATGGAAAGAGATTTGTGTGAC 58.900 38.462 0.00 0.00 0.00 3.67
2335 2410 7.180051 AGACTCTAGATGGAAAGAGATTTGTGT 59.820 37.037 6.36 0.00 41.51 3.72
2534 2610 7.824779 AGTACCTTATTGTTCTCTAAAGGCTTG 59.175 37.037 0.00 0.00 40.33 4.01
2561 2637 6.265577 CCTTTTCAAACTGTTGTCAAGTAGG 58.734 40.000 0.00 0.00 36.07 3.18
2562 2638 6.265577 CCCTTTTCAAACTGTTGTCAAGTAG 58.734 40.000 0.00 0.00 36.07 2.57
2563 2639 5.393678 GCCCTTTTCAAACTGTTGTCAAGTA 60.394 40.000 0.00 0.00 36.07 2.24
2564 2640 4.620567 GCCCTTTTCAAACTGTTGTCAAGT 60.621 41.667 0.00 0.00 36.07 3.16
2565 2641 3.865164 GCCCTTTTCAAACTGTTGTCAAG 59.135 43.478 0.00 0.00 36.07 3.02
2566 2642 3.513515 AGCCCTTTTCAAACTGTTGTCAA 59.486 39.130 0.00 0.00 36.07 3.18
2567 2643 3.096092 AGCCCTTTTCAAACTGTTGTCA 58.904 40.909 0.00 0.00 36.07 3.58
2568 2644 3.801114 AGCCCTTTTCAAACTGTTGTC 57.199 42.857 0.00 0.00 36.07 3.18
2569 2645 3.369366 CCAAGCCCTTTTCAAACTGTTGT 60.369 43.478 0.00 0.00 36.07 3.32
2570 2646 3.197265 CCAAGCCCTTTTCAAACTGTTG 58.803 45.455 0.00 0.00 35.95 3.33
2582 2658 1.978617 CAACATCGCCCAAGCCCTT 60.979 57.895 0.00 0.00 34.57 3.95
2584 2660 3.451894 CCAACATCGCCCAAGCCC 61.452 66.667 0.00 0.00 34.57 5.19
2655 2731 0.371301 CGAACAGTGGATGCATCACG 59.629 55.000 27.25 18.67 39.86 4.35
2662 2738 1.442769 CTCAACCCGAACAGTGGATG 58.557 55.000 0.00 0.00 0.00 3.51
2667 2743 0.321653 GGATGCTCAACCCGAACAGT 60.322 55.000 0.00 0.00 0.00 3.55
2678 2754 1.829849 CAGAGAGACAAGGGATGCTCA 59.170 52.381 0.00 0.00 35.76 4.26
2681 2757 0.540923 AGCAGAGAGACAAGGGATGC 59.459 55.000 0.00 0.00 0.00 3.91
2687 2763 1.270826 TGTCCGAAGCAGAGAGACAAG 59.729 52.381 0.00 0.00 0.00 3.16
2708 2784 0.378257 GTATGCAGGCGTGAACATGG 59.622 55.000 11.29 0.00 0.00 3.66
2716 2792 0.245539 ACACTAACGTATGCAGGCGT 59.754 50.000 11.77 11.77 43.64 5.68
2744 2820 9.026074 GGCGCTACAAATAATTTTAGCATAAAA 57.974 29.630 7.64 0.00 29.45 1.52
2745 2821 8.191446 TGGCGCTACAAATAATTTTAGCATAAA 58.809 29.630 7.64 0.00 29.45 1.40
2746 2822 7.708051 TGGCGCTACAAATAATTTTAGCATAA 58.292 30.769 7.64 0.00 29.45 1.90
2747 2823 7.265647 TGGCGCTACAAATAATTTTAGCATA 57.734 32.000 7.64 0.00 29.45 3.14
2748 2824 6.142818 TGGCGCTACAAATAATTTTAGCAT 57.857 33.333 7.64 0.00 29.45 3.79
2749 2825 5.568685 TGGCGCTACAAATAATTTTAGCA 57.431 34.783 7.64 0.00 29.45 3.49
2750 2826 6.205784 TCATGGCGCTACAAATAATTTTAGC 58.794 36.000 7.64 0.00 0.00 3.09
2751 2827 8.801715 AATCATGGCGCTACAAATAATTTTAG 57.198 30.769 7.64 0.00 0.00 1.85
2752 2828 9.593134 AAAATCATGGCGCTACAAATAATTTTA 57.407 25.926 7.64 0.00 0.00 1.52
2753 2829 8.389603 CAAAATCATGGCGCTACAAATAATTTT 58.610 29.630 7.64 5.69 0.00 1.82
2754 2830 7.763528 TCAAAATCATGGCGCTACAAATAATTT 59.236 29.630 7.64 0.00 0.00 1.82
2755 2831 7.264221 TCAAAATCATGGCGCTACAAATAATT 58.736 30.769 7.64 0.00 0.00 1.40
2756 2832 6.804677 TCAAAATCATGGCGCTACAAATAAT 58.195 32.000 7.64 0.00 0.00 1.28
2757 2833 6.201226 TCAAAATCATGGCGCTACAAATAA 57.799 33.333 7.64 0.00 0.00 1.40
2758 2834 5.826601 TCAAAATCATGGCGCTACAAATA 57.173 34.783 7.64 0.00 0.00 1.40
2759 2835 4.717233 TCAAAATCATGGCGCTACAAAT 57.283 36.364 7.64 0.00 0.00 2.32
2760 2836 4.511617 TTCAAAATCATGGCGCTACAAA 57.488 36.364 7.64 0.00 0.00 2.83
2761 2837 4.422840 CATTCAAAATCATGGCGCTACAA 58.577 39.130 7.64 0.00 0.00 2.41
2762 2838 3.734597 GCATTCAAAATCATGGCGCTACA 60.735 43.478 7.64 0.00 0.00 2.74
2763 2839 2.791004 GCATTCAAAATCATGGCGCTAC 59.209 45.455 7.64 0.00 0.00 3.58
2764 2840 2.426381 TGCATTCAAAATCATGGCGCTA 59.574 40.909 7.64 0.00 0.00 4.26
2765 2841 1.205179 TGCATTCAAAATCATGGCGCT 59.795 42.857 7.64 0.00 0.00 5.92
2766 2842 1.642728 TGCATTCAAAATCATGGCGC 58.357 45.000 0.00 0.00 0.00 6.53
2767 2843 4.868450 AAATGCATTCAAAATCATGGCG 57.132 36.364 13.38 0.00 0.00 5.69
2768 2844 6.848451 AGAAAAATGCATTCAAAATCATGGC 58.152 32.000 13.38 0.00 0.00 4.40
2782 2858 9.033481 GCATGCTTACATAATAAGAAAAATGCA 57.967 29.630 11.37 0.00 33.67 3.96
2783 2859 9.033481 TGCATGCTTACATAATAAGAAAAATGC 57.967 29.630 20.33 0.00 33.67 3.56
2787 2863 9.518906 CACATGCATGCTTACATAATAAGAAAA 57.481 29.630 26.53 0.00 33.67 2.29
2788 2864 8.685427 ACACATGCATGCTTACATAATAAGAAA 58.315 29.630 26.53 0.00 33.67 2.52
2789 2865 8.224389 ACACATGCATGCTTACATAATAAGAA 57.776 30.769 26.53 0.00 33.67 2.52
2790 2866 7.806409 ACACATGCATGCTTACATAATAAGA 57.194 32.000 26.53 0.00 33.67 2.10
2791 2867 8.748582 CAAACACATGCATGCTTACATAATAAG 58.251 33.333 26.53 0.00 33.67 1.73
2792 2868 8.249638 ACAAACACATGCATGCTTACATAATAA 58.750 29.630 26.53 0.00 33.67 1.40
2793 2869 7.701501 CACAAACACATGCATGCTTACATAATA 59.298 33.333 26.53 0.00 33.67 0.98
2794 2870 6.532302 CACAAACACATGCATGCTTACATAAT 59.468 34.615 26.53 0.28 33.67 1.28
2795 2871 5.862860 CACAAACACATGCATGCTTACATAA 59.137 36.000 26.53 0.00 33.67 1.90
2796 2872 5.182760 TCACAAACACATGCATGCTTACATA 59.817 36.000 26.53 3.73 33.67 2.29
2797 2873 4.022155 TCACAAACACATGCATGCTTACAT 60.022 37.500 26.53 2.71 36.79 2.29
2798 2874 3.317430 TCACAAACACATGCATGCTTACA 59.683 39.130 26.53 0.00 0.00 2.41
2799 2875 3.899734 TCACAAACACATGCATGCTTAC 58.100 40.909 26.53 0.00 0.00 2.34
2800 2876 3.057386 CCTCACAAACACATGCATGCTTA 60.057 43.478 26.53 0.00 0.00 3.09
2801 2877 2.288579 CCTCACAAACACATGCATGCTT 60.289 45.455 26.53 14.83 0.00 3.91
2802 2878 1.271379 CCTCACAAACACATGCATGCT 59.729 47.619 26.53 11.04 0.00 3.79
2803 2879 1.270274 TCCTCACAAACACATGCATGC 59.730 47.619 26.53 11.82 0.00 4.06
2804 2880 2.352030 GGTCCTCACAAACACATGCATG 60.352 50.000 25.09 25.09 0.00 4.06
2805 2881 1.888512 GGTCCTCACAAACACATGCAT 59.111 47.619 0.00 0.00 0.00 3.96
2806 2882 1.133823 AGGTCCTCACAAACACATGCA 60.134 47.619 0.00 0.00 0.00 3.96
2807 2883 1.267806 CAGGTCCTCACAAACACATGC 59.732 52.381 0.00 0.00 0.00 4.06
2808 2884 2.549754 GACAGGTCCTCACAAACACATG 59.450 50.000 0.00 0.00 0.00 3.21
2809 2885 2.172505 TGACAGGTCCTCACAAACACAT 59.827 45.455 0.00 0.00 0.00 3.21
2810 2886 1.557371 TGACAGGTCCTCACAAACACA 59.443 47.619 0.00 0.00 0.00 3.72
2811 2887 2.325583 TGACAGGTCCTCACAAACAC 57.674 50.000 0.00 0.00 0.00 3.32
2812 2888 3.646162 AGTATGACAGGTCCTCACAAACA 59.354 43.478 0.00 0.00 0.00 2.83
2813 2889 4.273148 AGTATGACAGGTCCTCACAAAC 57.727 45.455 0.00 0.00 0.00 2.93
2814 2890 4.346709 TCAAGTATGACAGGTCCTCACAAA 59.653 41.667 0.00 0.00 0.00 2.83
2815 2891 3.901222 TCAAGTATGACAGGTCCTCACAA 59.099 43.478 0.00 0.00 0.00 3.33
2816 2892 3.506398 TCAAGTATGACAGGTCCTCACA 58.494 45.455 0.00 0.00 0.00 3.58
2817 2893 3.677424 GCTCAAGTATGACAGGTCCTCAC 60.677 52.174 0.00 0.00 0.00 3.51
2818 2894 2.497675 GCTCAAGTATGACAGGTCCTCA 59.502 50.000 0.00 0.00 0.00 3.86
2819 2895 2.159028 GGCTCAAGTATGACAGGTCCTC 60.159 54.545 0.00 0.00 0.00 3.71
2820 2896 1.834263 GGCTCAAGTATGACAGGTCCT 59.166 52.381 0.00 0.00 0.00 3.85
2821 2897 1.834263 AGGCTCAAGTATGACAGGTCC 59.166 52.381 0.00 0.00 0.00 4.46
2822 2898 3.618690 AAGGCTCAAGTATGACAGGTC 57.381 47.619 0.00 0.00 0.00 3.85
2823 2899 5.091261 CTAAAGGCTCAAGTATGACAGGT 57.909 43.478 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.