Multiple sequence alignment - TraesCS7A01G138500

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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 TraesCS7A01G138500 chr7A 100.000 3029 0 0 1 3029 90650834 90653862 0.000000e+00 5594
1 TraesCS7A01G138500 chr7D 94.320 2729 106 23 1 2698 89721619 89724329 0.000000e+00 4135
2 TraesCS7A01G138500 chr7D 92.121 330 26 0 2700 3029 594017006 594017335 1.640000e-127 466
3 TraesCS7A01G138500 chr7D 91.496 341 26 2 2690 3029 610654803 610655141 1.640000e-127 466
4 TraesCS7A01G138500 chr7B 95.831 2087 72 7 1 2082 40399206 40401282 0.000000e+00 3358
5 TraesCS7A01G138500 chr7B 83.826 643 46 22 2066 2698 40401303 40401897 2.640000e-155 558
6 TraesCS7A01G138500 chr3D 93.884 327 19 1 2703 3029 41801947 41801622 2.710000e-135 492
7 TraesCS7A01G138500 chr3D 93.333 330 22 0 2700 3029 324765366 324765037 3.510000e-134 488
8 TraesCS7A01G138500 chr3D 92.447 331 24 1 2700 3029 485199179 485198849 3.530000e-129 472
9 TraesCS7A01G138500 chr2D 92.727 330 24 0 2700 3029 43291232 43290903 7.600000e-131 477
10 TraesCS7A01G138500 chr1D 92.447 331 24 1 2700 3029 782948 783278 3.530000e-129 472
11 TraesCS7A01G138500 chrUn 92.145 331 24 2 2700 3029 325812400 325812729 1.640000e-127 466
12 TraesCS7A01G138500 chr5D 92.145 331 25 1 2700 3029 443062022 443061692 1.640000e-127 466


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 TraesCS7A01G138500 chr7A 90650834 90653862 3028 False 5594 5594 100.0000 1 3029 1 chr7A.!!$F1 3028
1 TraesCS7A01G138500 chr7D 89721619 89724329 2710 False 4135 4135 94.3200 1 2698 1 chr7D.!!$F1 2697
2 TraesCS7A01G138500 chr7B 40399206 40401897 2691 False 1958 3358 89.8285 1 2698 2 chr7B.!!$F1 2697

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
807 832 2.572556 TGGACGTGCCTAGGGAAATAAA 59.427 45.455 11.72 0.0 37.63 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2713 2796 0.178938 TGGAATGCAAAGCAGGGGAA 60.179 50.0 0.0 0.0 43.65 3.97 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
56 57 4.740902 AGCCCTTAATTTTGTCTGTCCTT 58.259 39.130 0.00 0.00 0.00 3.36
57 58 5.147767 AGCCCTTAATTTTGTCTGTCCTTT 58.852 37.500 0.00 0.00 0.00 3.11
157 176 8.897752 GCAAACTCTCTTATCATATTTGTTCCT 58.102 33.333 0.00 0.00 0.00 3.36
167 186 9.513906 TTATCATATTTGTTCCTTCACTTGACA 57.486 29.630 0.00 0.00 0.00 3.58
182 201 7.136289 TCACTTGACATAAAATTACCGAACC 57.864 36.000 0.00 0.00 0.00 3.62
201 221 4.546829 ACCACCGTTGCTAGAAATTAGA 57.453 40.909 0.00 0.00 0.00 2.10
306 326 9.173021 TCAAAGCGAAAAGGATTCAGATATTTA 57.827 29.630 0.00 0.00 0.00 1.40
412 435 5.885230 TCTCAAAAGTGTATTGGCAGATG 57.115 39.130 0.00 0.00 0.00 2.90
431 454 7.118101 GGCAGATGAATTATTGTCTCAGAGATC 59.882 40.741 2.64 0.00 0.00 2.75
575 599 6.592607 TGGCTTAAACTACTACAAGTACATGC 59.407 38.462 0.00 0.00 0.00 4.06
654 678 8.777865 TGTTCTACCTTCATTGAGATGTTTAG 57.222 34.615 0.00 0.00 34.77 1.85
677 701 4.081642 GCTGTAGATTGTAGGAGGTGTTCA 60.082 45.833 0.00 0.00 0.00 3.18
807 832 2.572556 TGGACGTGCCTAGGGAAATAAA 59.427 45.455 11.72 0.00 37.63 1.40
909 934 5.014228 AGCAGTTTTTCTGTTAGTCCCCTAT 59.986 40.000 0.00 0.00 45.23 2.57
912 937 6.940298 CAGTTTTTCTGTTAGTCCCCTATCAA 59.060 38.462 0.00 0.00 39.17 2.57
974 999 8.092687 TGTAGACTCCCTTTTCTTACATTGTAC 58.907 37.037 0.00 0.00 0.00 2.90
1191 1216 1.840635 GGTTTCCTCTACCATGAGCCT 59.159 52.381 0.00 0.00 35.67 4.58
1205 1230 2.851195 TGAGCCTTTCAACTTCCAGAC 58.149 47.619 0.00 0.00 31.34 3.51
1353 1378 2.741092 GCTGACACCACCTTCCGA 59.259 61.111 0.00 0.00 0.00 4.55
1404 1429 6.884472 TTCTTGTCCCTGGTGATTATCTTA 57.116 37.500 0.00 0.00 0.00 2.10
1413 1438 2.329379 GTGATTATCTTAGGAGGCGCG 58.671 52.381 0.00 0.00 0.00 6.86
1611 1636 1.149854 GTTTGGGGTTCTGACGGGT 59.850 57.895 0.00 0.00 0.00 5.28
1746 1771 1.896660 TTTCGCGGCAAGGAAAGCT 60.897 52.632 6.13 0.00 0.00 3.74
1878 1903 1.002868 CTTCACTCTGGCAGGTGGG 60.003 63.158 25.63 16.66 34.57 4.61
1915 1940 6.719365 CAGTCTGTCAAAAGTAAAGGAAGTG 58.281 40.000 0.00 0.00 0.00 3.16
1959 1984 0.872388 CTAACAAAGGCCGTGGTGAC 59.128 55.000 10.06 0.00 0.00 3.67
2071 2133 6.679327 ACTCAGTTTTGTCCTTTTGTCTAC 57.321 37.500 0.00 0.00 0.00 2.59
2128 2190 9.601217 AACTATGTAATACAGACAATTCAGGAC 57.399 33.333 0.00 0.00 0.00 3.85
2131 2193 5.867174 TGTAATACAGACAATTCAGGACGTG 59.133 40.000 0.00 0.00 0.00 4.49
2246 2312 9.327628 TGCAACTACTATTGTGTTGTTTACTAA 57.672 29.630 16.88 0.00 41.93 2.24
2258 2324 7.230510 TGTGTTGTTTACTAAAATCATCTGCCT 59.769 33.333 0.00 0.00 0.00 4.75
2297 2363 7.255569 TGTAGTCGTTTAGTGATGTCTATTGG 58.744 38.462 0.00 0.00 0.00 3.16
2299 2365 5.105310 AGTCGTTTAGTGATGTCTATTGGCT 60.105 40.000 0.00 0.00 0.00 4.75
2309 2377 7.677745 AGTGATGTCTATTGGCTCTCCTTATAT 59.322 37.037 0.00 0.00 0.00 0.86
2312 2380 9.415008 GATGTCTATTGGCTCTCCTTATATAGA 57.585 37.037 0.00 0.00 0.00 1.98
2315 2383 8.691797 GTCTATTGGCTCTCCTTATATAGAAGG 58.308 40.741 18.44 18.44 46.48 3.46
2316 2384 6.882768 ATTGGCTCTCCTTATATAGAAGGG 57.117 41.667 22.88 14.80 45.35 3.95
2317 2385 5.355670 TGGCTCTCCTTATATAGAAGGGT 57.644 43.478 22.88 0.00 45.35 4.34
2318 2386 5.727630 TGGCTCTCCTTATATAGAAGGGTT 58.272 41.667 22.88 0.00 45.35 4.11
2323 2391 7.304497 TCTCCTTATATAGAAGGGTTTCTGC 57.696 40.000 22.88 0.00 45.35 4.26
2329 2397 8.777578 TTATATAGAAGGGTTTCTGCTGTCTA 57.222 34.615 0.26 0.00 43.41 2.59
2431 2501 2.143925 GCAGCGTAAACCTCAGTCTTT 58.856 47.619 0.00 0.00 0.00 2.52
2432 2502 2.548480 GCAGCGTAAACCTCAGTCTTTT 59.452 45.455 0.00 0.00 0.00 2.27
2433 2503 3.003378 GCAGCGTAAACCTCAGTCTTTTT 59.997 43.478 0.00 0.00 0.00 1.94
2435 2505 4.272504 CAGCGTAAACCTCAGTCTTTTTGA 59.727 41.667 0.00 0.00 0.00 2.69
2438 2508 5.220796 GCGTAAACCTCAGTCTTTTTGAGTT 60.221 40.000 2.05 0.00 40.32 3.01
2443 2514 4.823989 ACCTCAGTCTTTTTGAGTTGATGG 59.176 41.667 2.05 0.00 40.32 3.51
2497 2579 8.463456 ACTCTCTTTTACAATACTTTAGTCGC 57.537 34.615 0.00 0.00 0.00 5.19
2498 2580 8.086522 ACTCTCTTTTACAATACTTTAGTCGCA 58.913 33.333 0.00 0.00 0.00 5.10
2499 2581 8.997621 TCTCTTTTACAATACTTTAGTCGCAT 57.002 30.769 0.00 0.00 0.00 4.73
2502 2584 9.865321 TCTTTTACAATACTTTAGTCGCATAGT 57.135 29.630 0.00 0.00 0.00 2.12
2548 2631 5.449177 GCTTCATGCATTGGTACTTTACTCC 60.449 44.000 0.00 0.00 42.31 3.85
2574 2657 5.878406 AGTATATCTCTTTGGTGGAGTGG 57.122 43.478 0.00 0.00 33.06 4.00
2662 2745 5.011125 TGGCTCTTAATACTATCTGGACAGC 59.989 44.000 0.00 0.00 0.00 4.40
2679 2762 5.476752 GACAGCTGTCCAAATGAATAGAC 57.523 43.478 32.55 6.14 39.07 2.59
2698 2781 4.730657 AGACCATGACGACTAAGTTTACG 58.269 43.478 0.00 0.00 0.00 3.18
2699 2782 4.217118 AGACCATGACGACTAAGTTTACGT 59.783 41.667 0.00 0.00 41.57 3.57
2700 2783 5.412594 AGACCATGACGACTAAGTTTACGTA 59.587 40.000 0.00 0.00 39.04 3.57
2701 2784 5.393962 ACCATGACGACTAAGTTTACGTAC 58.606 41.667 0.00 0.00 39.04 3.67
2702 2785 4.795278 CCATGACGACTAAGTTTACGTACC 59.205 45.833 0.00 0.00 39.04 3.34
2703 2786 4.065423 TGACGACTAAGTTTACGTACCG 57.935 45.455 0.00 0.00 39.04 4.02
2704 2787 3.743911 TGACGACTAAGTTTACGTACCGA 59.256 43.478 0.00 0.00 39.04 4.69
2705 2788 4.212425 TGACGACTAAGTTTACGTACCGAA 59.788 41.667 0.00 0.00 39.04 4.30
2706 2789 5.103290 ACGACTAAGTTTACGTACCGAAA 57.897 39.130 0.00 0.00 37.22 3.46
2707 2790 5.516090 ACGACTAAGTTTACGTACCGAAAA 58.484 37.500 0.00 0.00 37.22 2.29
2708 2791 5.974751 ACGACTAAGTTTACGTACCGAAAAA 59.025 36.000 0.00 0.00 37.22 1.94
2725 2808 3.558931 AAAAAGGTTTCCCCTGCTTTG 57.441 42.857 0.00 0.00 45.47 2.77
2726 2809 0.758734 AAAGGTTTCCCCTGCTTTGC 59.241 50.000 0.00 0.00 45.47 3.68
2727 2810 0.398381 AAGGTTTCCCCTGCTTTGCA 60.398 50.000 0.00 0.00 45.47 4.08
2728 2811 0.178924 AGGTTTCCCCTGCTTTGCAT 60.179 50.000 0.00 0.00 44.08 3.96
2729 2812 0.686789 GGTTTCCCCTGCTTTGCATT 59.313 50.000 0.00 0.00 38.13 3.56
2730 2813 1.338105 GGTTTCCCCTGCTTTGCATTC 60.338 52.381 0.00 0.00 38.13 2.67
2731 2814 0.975887 TTTCCCCTGCTTTGCATTCC 59.024 50.000 0.00 0.00 38.13 3.01
2732 2815 0.178938 TTCCCCTGCTTTGCATTCCA 60.179 50.000 0.00 0.00 38.13 3.53
2733 2816 0.178938 TCCCCTGCTTTGCATTCCAA 60.179 50.000 0.00 0.00 38.13 3.53
2734 2817 0.686224 CCCCTGCTTTGCATTCCAAA 59.314 50.000 0.00 0.00 40.97 3.28
2735 2818 1.072015 CCCCTGCTTTGCATTCCAAAA 59.928 47.619 0.00 0.00 42.51 2.44
2736 2819 2.145536 CCCTGCTTTGCATTCCAAAAC 58.854 47.619 0.00 0.00 42.51 2.43
2737 2820 2.485124 CCCTGCTTTGCATTCCAAAACA 60.485 45.455 0.00 0.00 42.51 2.83
2738 2821 3.204526 CCTGCTTTGCATTCCAAAACAA 58.795 40.909 0.00 0.00 42.51 2.83
2739 2822 3.002553 CCTGCTTTGCATTCCAAAACAAC 59.997 43.478 0.00 0.00 42.51 3.32
2740 2823 2.941720 TGCTTTGCATTCCAAAACAACC 59.058 40.909 0.00 0.00 42.51 3.77
2741 2824 2.941720 GCTTTGCATTCCAAAACAACCA 59.058 40.909 0.00 0.00 42.51 3.67
2742 2825 3.376546 GCTTTGCATTCCAAAACAACCAA 59.623 39.130 0.00 0.00 42.51 3.67
2743 2826 4.730324 GCTTTGCATTCCAAAACAACCAAC 60.730 41.667 0.00 0.00 42.51 3.77
2744 2827 3.616956 TGCATTCCAAAACAACCAACA 57.383 38.095 0.00 0.00 0.00 3.33
2745 2828 3.265791 TGCATTCCAAAACAACCAACAC 58.734 40.909 0.00 0.00 0.00 3.32
2746 2829 2.611751 GCATTCCAAAACAACCAACACC 59.388 45.455 0.00 0.00 0.00 4.16
2747 2830 2.656560 TTCCAAAACAACCAACACCG 57.343 45.000 0.00 0.00 0.00 4.94
2748 2831 1.835494 TCCAAAACAACCAACACCGA 58.165 45.000 0.00 0.00 0.00 4.69
2749 2832 2.168496 TCCAAAACAACCAACACCGAA 58.832 42.857 0.00 0.00 0.00 4.30
2750 2833 2.761208 TCCAAAACAACCAACACCGAAT 59.239 40.909 0.00 0.00 0.00 3.34
2751 2834 3.952323 TCCAAAACAACCAACACCGAATA 59.048 39.130 0.00 0.00 0.00 1.75
2752 2835 4.045783 CCAAAACAACCAACACCGAATAC 58.954 43.478 0.00 0.00 0.00 1.89
2753 2836 4.440250 CCAAAACAACCAACACCGAATACA 60.440 41.667 0.00 0.00 0.00 2.29
2754 2837 4.985538 AAACAACCAACACCGAATACAA 57.014 36.364 0.00 0.00 0.00 2.41
2755 2838 4.985538 AACAACCAACACCGAATACAAA 57.014 36.364 0.00 0.00 0.00 2.83
2756 2839 5.523438 AACAACCAACACCGAATACAAAT 57.477 34.783 0.00 0.00 0.00 2.32
2757 2840 6.636562 AACAACCAACACCGAATACAAATA 57.363 33.333 0.00 0.00 0.00 1.40
2758 2841 6.827586 ACAACCAACACCGAATACAAATAT 57.172 33.333 0.00 0.00 0.00 1.28
2759 2842 6.848451 ACAACCAACACCGAATACAAATATC 58.152 36.000 0.00 0.00 0.00 1.63
2760 2843 5.728351 ACCAACACCGAATACAAATATCG 57.272 39.130 0.00 0.00 0.00 2.92
2761 2844 4.034742 ACCAACACCGAATACAAATATCGC 59.965 41.667 0.00 0.00 0.00 4.58
2762 2845 4.272504 CCAACACCGAATACAAATATCGCT 59.727 41.667 0.00 0.00 0.00 4.93
2763 2846 5.197549 CAACACCGAATACAAATATCGCTG 58.802 41.667 0.00 0.00 0.00 5.18
2764 2847 4.439057 ACACCGAATACAAATATCGCTGT 58.561 39.130 0.00 0.00 0.00 4.40
2765 2848 4.270084 ACACCGAATACAAATATCGCTGTG 59.730 41.667 0.00 0.00 0.00 3.66
2766 2849 3.807622 ACCGAATACAAATATCGCTGTGG 59.192 43.478 0.00 0.00 0.00 4.17
2767 2850 3.363970 CCGAATACAAATATCGCTGTGGC 60.364 47.826 0.00 0.00 0.00 5.01
2784 2867 2.633657 CGAGCAGCACAACACACC 59.366 61.111 0.00 0.00 0.00 4.16
2785 2868 2.179547 CGAGCAGCACAACACACCA 61.180 57.895 0.00 0.00 0.00 4.17
2786 2869 1.713937 CGAGCAGCACAACACACCAA 61.714 55.000 0.00 0.00 0.00 3.67
2787 2870 0.455410 GAGCAGCACAACACACCAAA 59.545 50.000 0.00 0.00 0.00 3.28
2788 2871 0.894141 AGCAGCACAACACACCAAAA 59.106 45.000 0.00 0.00 0.00 2.44
2789 2872 1.135024 AGCAGCACAACACACCAAAAG 60.135 47.619 0.00 0.00 0.00 2.27
2790 2873 1.135141 GCAGCACAACACACCAAAAGA 60.135 47.619 0.00 0.00 0.00 2.52
2791 2874 2.673610 GCAGCACAACACACCAAAAGAA 60.674 45.455 0.00 0.00 0.00 2.52
2792 2875 3.583806 CAGCACAACACACCAAAAGAAA 58.416 40.909 0.00 0.00 0.00 2.52
2793 2876 3.993081 CAGCACAACACACCAAAAGAAAA 59.007 39.130 0.00 0.00 0.00 2.29
2794 2877 4.450419 CAGCACAACACACCAAAAGAAAAA 59.550 37.500 0.00 0.00 0.00 1.94
2795 2878 4.690280 AGCACAACACACCAAAAGAAAAAG 59.310 37.500 0.00 0.00 0.00 2.27
2796 2879 4.688413 GCACAACACACCAAAAGAAAAAGA 59.312 37.500 0.00 0.00 0.00 2.52
2797 2880 5.178438 GCACAACACACCAAAAGAAAAAGAA 59.822 36.000 0.00 0.00 0.00 2.52
2798 2881 6.618379 GCACAACACACCAAAAGAAAAAGAAG 60.618 38.462 0.00 0.00 0.00 2.85
2799 2882 6.644592 CACAACACACCAAAAGAAAAAGAAGA 59.355 34.615 0.00 0.00 0.00 2.87
2800 2883 7.170658 CACAACACACCAAAAGAAAAAGAAGAA 59.829 33.333 0.00 0.00 0.00 2.52
2801 2884 7.384932 ACAACACACCAAAAGAAAAAGAAGAAG 59.615 33.333 0.00 0.00 0.00 2.85
2802 2885 7.227049 ACACACCAAAAGAAAAAGAAGAAGA 57.773 32.000 0.00 0.00 0.00 2.87
2803 2886 7.666623 ACACACCAAAAGAAAAAGAAGAAGAA 58.333 30.769 0.00 0.00 0.00 2.52
2804 2887 8.147704 ACACACCAAAAGAAAAAGAAGAAGAAA 58.852 29.630 0.00 0.00 0.00 2.52
2805 2888 8.435430 CACACCAAAAGAAAAAGAAGAAGAAAC 58.565 33.333 0.00 0.00 0.00 2.78
2806 2889 8.147704 ACACCAAAAGAAAAAGAAGAAGAAACA 58.852 29.630 0.00 0.00 0.00 2.83
2807 2890 8.987890 CACCAAAAGAAAAAGAAGAAGAAACAA 58.012 29.630 0.00 0.00 0.00 2.83
2808 2891 9.554395 ACCAAAAGAAAAAGAAGAAGAAACAAA 57.446 25.926 0.00 0.00 0.00 2.83
2812 2895 7.834068 AGAAAAAGAAGAAGAAACAAAAGCC 57.166 32.000 0.00 0.00 0.00 4.35
2813 2896 7.386059 AGAAAAAGAAGAAGAAACAAAAGCCA 58.614 30.769 0.00 0.00 0.00 4.75
2814 2897 7.877612 AGAAAAAGAAGAAGAAACAAAAGCCAA 59.122 29.630 0.00 0.00 0.00 4.52
2815 2898 6.968131 AAAGAAGAAGAAACAAAAGCCAAC 57.032 33.333 0.00 0.00 0.00 3.77
2816 2899 5.011090 AGAAGAAGAAACAAAAGCCAACC 57.989 39.130 0.00 0.00 0.00 3.77
2817 2900 4.466015 AGAAGAAGAAACAAAAGCCAACCA 59.534 37.500 0.00 0.00 0.00 3.67
2818 2901 4.123497 AGAAGAAACAAAAGCCAACCAC 57.877 40.909 0.00 0.00 0.00 4.16
2819 2902 2.577449 AGAAACAAAAGCCAACCACG 57.423 45.000 0.00 0.00 0.00 4.94
2820 2903 1.136110 AGAAACAAAAGCCAACCACGG 59.864 47.619 0.00 0.00 0.00 4.94
2828 2911 3.673484 CCAACCACGGCAGCTTGG 61.673 66.667 11.07 11.07 39.00 3.61
2829 2912 4.347453 CAACCACGGCAGCTTGGC 62.347 66.667 12.26 1.16 39.85 4.52
2830 2913 4.892965 AACCACGGCAGCTTGGCA 62.893 61.111 12.26 0.00 43.94 4.92
2831 2914 4.892965 ACCACGGCAGCTTGGCAA 62.893 61.111 12.26 0.00 43.94 4.52
2832 2915 3.604667 CCACGGCAGCTTGGCAAA 61.605 61.111 0.00 0.00 43.94 3.68
2833 2916 2.049802 CACGGCAGCTTGGCAAAG 60.050 61.111 0.00 0.00 43.94 2.77
2841 2924 2.202518 CTTGGCAAAGCGCGGATG 60.203 61.111 8.83 3.48 43.84 3.51
2842 2925 2.671276 TTGGCAAAGCGCGGATGA 60.671 55.556 8.83 0.00 43.84 2.92
2843 2926 2.855728 CTTGGCAAAGCGCGGATGAC 62.856 60.000 8.83 10.99 43.84 3.06
2844 2927 4.179579 GGCAAAGCGCGGATGACC 62.180 66.667 8.83 9.91 43.84 4.02
2845 2928 4.179579 GCAAAGCGCGGATGACCC 62.180 66.667 8.83 0.00 0.00 4.46
2871 2954 4.910585 GGCGCCCACCGGATACAG 62.911 72.222 18.11 0.00 37.44 2.74
2872 2955 3.845259 GCGCCCACCGGATACAGA 61.845 66.667 9.46 0.00 37.44 3.41
2873 2956 2.106332 CGCCCACCGGATACAGAC 59.894 66.667 9.46 0.00 0.00 3.51
2874 2957 2.504519 GCCCACCGGATACAGACC 59.495 66.667 9.46 0.00 0.00 3.85
2875 2958 2.363975 GCCCACCGGATACAGACCA 61.364 63.158 9.46 0.00 0.00 4.02
2876 2959 1.520666 CCCACCGGATACAGACCAC 59.479 63.158 9.46 0.00 0.00 4.16
2877 2960 1.520666 CCACCGGATACAGACCACC 59.479 63.158 9.46 0.00 0.00 4.61
2878 2961 1.261938 CCACCGGATACAGACCACCA 61.262 60.000 9.46 0.00 0.00 4.17
2879 2962 0.108329 CACCGGATACAGACCACCAC 60.108 60.000 9.46 0.00 0.00 4.16
2880 2963 0.543410 ACCGGATACAGACCACCACA 60.543 55.000 9.46 0.00 0.00 4.17
2881 2964 0.175760 CCGGATACAGACCACCACAG 59.824 60.000 0.00 0.00 0.00 3.66
2882 2965 1.182667 CGGATACAGACCACCACAGA 58.817 55.000 0.00 0.00 0.00 3.41
2883 2966 1.135083 CGGATACAGACCACCACAGAC 60.135 57.143 0.00 0.00 0.00 3.51
2884 2967 1.207329 GGATACAGACCACCACAGACC 59.793 57.143 0.00 0.00 0.00 3.85
2885 2968 0.895530 ATACAGACCACCACAGACCG 59.104 55.000 0.00 0.00 0.00 4.79
2886 2969 0.178984 TACAGACCACCACAGACCGA 60.179 55.000 0.00 0.00 0.00 4.69
2887 2970 1.290324 CAGACCACCACAGACCGAG 59.710 63.158 0.00 0.00 0.00 4.63
2888 2971 1.908793 AGACCACCACAGACCGAGG 60.909 63.158 0.00 0.00 0.00 4.63
2889 2972 3.591254 GACCACCACAGACCGAGGC 62.591 68.421 0.00 0.00 0.00 4.70
2890 2973 3.314331 CCACCACAGACCGAGGCT 61.314 66.667 0.00 0.00 0.00 4.58
2891 2974 2.262915 CACCACAGACCGAGGCTC 59.737 66.667 3.87 3.87 0.00 4.70
2892 2975 2.997897 ACCACAGACCGAGGCTCC 60.998 66.667 9.32 0.00 0.00 4.70
2893 2976 4.135153 CCACAGACCGAGGCTCCG 62.135 72.222 9.32 4.97 0.00 4.63
2894 2977 3.062466 CACAGACCGAGGCTCCGA 61.062 66.667 9.32 0.00 0.00 4.55
2895 2978 2.282958 ACAGACCGAGGCTCCGAA 60.283 61.111 9.32 0.00 0.00 4.30
2896 2979 2.182030 CAGACCGAGGCTCCGAAC 59.818 66.667 9.32 3.22 0.00 3.95
2897 2980 3.069318 AGACCGAGGCTCCGAACC 61.069 66.667 9.32 0.00 0.00 3.62
2898 2981 4.493747 GACCGAGGCTCCGAACCG 62.494 72.222 9.32 0.00 0.00 4.44
2910 2993 3.484547 GAACCGCCGCGTACCAAG 61.485 66.667 12.58 0.00 0.00 3.61
2916 2999 3.788766 CCGCGTACCAAGCAGCAC 61.789 66.667 4.92 0.00 34.19 4.40
2917 3000 3.788766 CGCGTACCAAGCAGCACC 61.789 66.667 0.00 0.00 34.19 5.01
2918 3001 2.358737 GCGTACCAAGCAGCACCT 60.359 61.111 0.00 0.00 34.19 4.00
2919 3002 2.391389 GCGTACCAAGCAGCACCTC 61.391 63.158 0.00 0.00 34.19 3.85
2920 3003 1.741770 CGTACCAAGCAGCACCTCC 60.742 63.158 0.00 0.00 0.00 4.30
2921 3004 1.374947 GTACCAAGCAGCACCTCCA 59.625 57.895 0.00 0.00 0.00 3.86
2922 3005 0.250727 GTACCAAGCAGCACCTCCAA 60.251 55.000 0.00 0.00 0.00 3.53
2923 3006 0.036732 TACCAAGCAGCACCTCCAAG 59.963 55.000 0.00 0.00 0.00 3.61
2924 3007 1.073722 CCAAGCAGCACCTCCAAGA 59.926 57.895 0.00 0.00 0.00 3.02
2925 3008 0.538057 CCAAGCAGCACCTCCAAGAA 60.538 55.000 0.00 0.00 0.00 2.52
2926 3009 1.321474 CAAGCAGCACCTCCAAGAAA 58.679 50.000 0.00 0.00 0.00 2.52
2927 3010 1.268899 CAAGCAGCACCTCCAAGAAAG 59.731 52.381 0.00 0.00 0.00 2.62
2928 3011 0.251077 AGCAGCACCTCCAAGAAAGG 60.251 55.000 0.00 0.00 39.96 3.11
2929 3012 0.250901 GCAGCACCTCCAAGAAAGGA 60.251 55.000 0.00 0.00 37.35 3.36
2930 3013 1.615384 GCAGCACCTCCAAGAAAGGAT 60.615 52.381 0.00 0.00 36.99 3.24
2931 3014 2.089980 CAGCACCTCCAAGAAAGGATG 58.910 52.381 0.00 0.00 36.99 3.51
2932 3015 0.813821 GCACCTCCAAGAAAGGATGC 59.186 55.000 0.00 0.00 36.99 3.91
2933 3016 1.089920 CACCTCCAAGAAAGGATGCG 58.910 55.000 0.00 0.00 36.99 4.73
2934 3017 0.984230 ACCTCCAAGAAAGGATGCGA 59.016 50.000 0.00 0.00 36.99 5.10
2935 3018 1.561542 ACCTCCAAGAAAGGATGCGAT 59.438 47.619 0.00 0.00 36.99 4.58
2936 3019 1.945394 CCTCCAAGAAAGGATGCGATG 59.055 52.381 0.00 0.00 36.99 3.84
2937 3020 1.332997 CTCCAAGAAAGGATGCGATGC 59.667 52.381 0.00 0.00 36.99 3.91
2938 3021 0.383231 CCAAGAAAGGATGCGATGCC 59.617 55.000 0.00 0.00 0.00 4.40
2939 3022 0.028505 CAAGAAAGGATGCGATGCCG 59.971 55.000 0.00 0.00 39.16 5.69
2940 3023 0.107703 AAGAAAGGATGCGATGCCGA 60.108 50.000 0.00 0.00 38.22 5.54
2941 3024 0.811616 AGAAAGGATGCGATGCCGAC 60.812 55.000 0.00 0.00 38.22 4.79
2942 3025 2.094126 GAAAGGATGCGATGCCGACG 62.094 60.000 0.00 0.00 38.22 5.12
2943 3026 2.572095 AAAGGATGCGATGCCGACGA 62.572 55.000 0.00 0.00 38.22 4.20
2944 3027 2.356313 GGATGCGATGCCGACGAT 60.356 61.111 0.00 0.00 38.22 3.73
2945 3028 2.661566 GGATGCGATGCCGACGATG 61.662 63.158 0.00 0.00 38.22 3.84
2946 3029 3.287121 GATGCGATGCCGACGATGC 62.287 63.158 0.00 0.00 38.22 3.91
2947 3030 3.797225 ATGCGATGCCGACGATGCT 62.797 57.895 0.00 0.00 38.22 3.79
2948 3031 3.993234 GCGATGCCGACGATGCTG 61.993 66.667 0.00 0.00 38.22 4.41
2949 3032 3.993234 CGATGCCGACGATGCTGC 61.993 66.667 0.00 0.00 38.22 5.25
2950 3033 2.587194 GATGCCGACGATGCTGCT 60.587 61.111 0.00 0.00 0.00 4.24
2951 3034 2.879070 GATGCCGACGATGCTGCTG 61.879 63.158 0.00 0.00 0.00 4.41
2963 3046 4.803426 CTGCTGCCCGGACGAGTC 62.803 72.222 0.73 0.00 0.00 3.36
2984 3067 4.941309 GGGTTTCCCCGTGCACGT 62.941 66.667 34.81 0.00 42.41 4.49
2985 3068 3.656045 GGTTTCCCCGTGCACGTG 61.656 66.667 34.81 25.85 37.74 4.49
2986 3069 3.656045 GTTTCCCCGTGCACGTGG 61.656 66.667 31.68 31.68 38.26 4.94
2987 3070 3.862991 TTTCCCCGTGCACGTGGA 61.863 61.111 35.03 35.03 43.86 4.02
2988 3071 3.818121 TTTCCCCGTGCACGTGGAG 62.818 63.158 35.76 26.26 45.92 3.86
2992 3075 4.742201 CCGTGCACGTGGAGGGAG 62.742 72.222 36.37 15.82 42.90 4.30
2993 3076 4.742201 CGTGCACGTGGAGGGAGG 62.742 72.222 30.50 0.00 34.11 4.30
2994 3077 3.626924 GTGCACGTGGAGGGAGGT 61.627 66.667 18.88 0.00 0.00 3.85
2995 3078 3.625897 TGCACGTGGAGGGAGGTG 61.626 66.667 18.88 0.00 35.32 4.00
2996 3079 4.394712 GCACGTGGAGGGAGGTGG 62.395 72.222 18.88 0.00 33.29 4.61
2997 3080 3.706373 CACGTGGAGGGAGGTGGG 61.706 72.222 7.95 0.00 0.00 4.61
3017 3100 3.680842 GGTGGATACCATCGACACC 57.319 57.895 3.66 3.66 46.71 4.16
3018 3101 0.106149 GGTGGATACCATCGACACCC 59.894 60.000 7.67 0.00 46.71 4.61
3019 3102 1.120530 GTGGATACCATCGACACCCT 58.879 55.000 0.00 0.00 37.84 4.34
3020 3103 1.068741 GTGGATACCATCGACACCCTC 59.931 57.143 0.00 0.00 37.84 4.30
3021 3104 1.063190 TGGATACCATCGACACCCTCT 60.063 52.381 0.00 0.00 0.00 3.69
3022 3105 2.176148 TGGATACCATCGACACCCTCTA 59.824 50.000 0.00 0.00 0.00 2.43
3023 3106 2.820787 GGATACCATCGACACCCTCTAG 59.179 54.545 0.00 0.00 0.00 2.43
3024 3107 2.359981 TACCATCGACACCCTCTAGG 57.640 55.000 0.00 0.00 43.78 3.02
3025 3108 0.629596 ACCATCGACACCCTCTAGGA 59.370 55.000 0.00 0.00 39.89 2.94
3026 3109 1.006758 ACCATCGACACCCTCTAGGAA 59.993 52.381 0.00 0.00 39.89 3.36
3027 3110 1.683917 CCATCGACACCCTCTAGGAAG 59.316 57.143 0.00 0.00 39.89 3.46
3028 3111 1.683917 CATCGACACCCTCTAGGAAGG 59.316 57.143 0.00 0.00 39.89 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 3.598299 GAAAATGGGCTTGCTGCATAAA 58.402 40.909 1.84 0.00 45.15 1.40
57 58 2.093553 GGAAAATGGGCTTGCTGCATAA 60.094 45.455 1.84 0.00 45.15 1.90
157 176 7.228906 TGGTTCGGTAATTTTATGTCAAGTGAA 59.771 33.333 0.00 0.00 0.00 3.18
167 186 4.379708 GCAACGGTGGTTCGGTAATTTTAT 60.380 41.667 0.90 0.00 32.98 1.40
182 201 6.721571 TTCTTCTAATTTCTAGCAACGGTG 57.278 37.500 0.00 0.00 0.00 4.94
201 221 9.703892 GCTCTACATACAATATGTGAGATTCTT 57.296 33.333 20.54 0.00 33.31 2.52
258 278 6.061441 TGACCGGCATGAAAGATATGTTAAT 58.939 36.000 0.00 0.00 0.00 1.40
260 280 5.029807 TGACCGGCATGAAAGATATGTTA 57.970 39.130 0.00 0.00 0.00 2.41
336 359 4.219725 GCAAAGGCTTGAAGGGTGTTAATA 59.780 41.667 0.00 0.00 34.14 0.98
412 435 5.292765 TGCCGATCTCTGAGACAATAATTC 58.707 41.667 10.00 0.90 0.00 2.17
431 454 9.478019 GATTAAAAGTATGATAATCGATTGCCG 57.522 33.333 20.87 0.00 40.25 5.69
482 505 5.104569 TGGTGACATGGCTATTATCAGACAA 60.105 40.000 0.00 0.00 37.04 3.18
654 678 4.081642 TGAACACCTCCTACAATCTACAGC 60.082 45.833 0.00 0.00 0.00 4.40
697 722 4.639310 AGAACAATTCTGCAATCAGGCTAG 59.361 41.667 0.00 0.00 40.69 3.42
974 999 6.302269 AGGAAAGATTTATCTGCATGGTAGG 58.698 40.000 0.00 0.00 37.19 3.18
1191 1216 2.727123 TGGCAGTCTGGAAGTTGAAA 57.273 45.000 1.14 0.00 33.76 2.69
1205 1230 0.527565 AGGCGCATACTTTTTGGCAG 59.472 50.000 10.83 0.00 0.00 4.85
1353 1378 1.999648 TTGAAGGACATGGCTGCTTT 58.000 45.000 0.00 0.00 0.00 3.51
1413 1438 3.266510 TCTGTCATCACATAGCCAACC 57.733 47.619 0.00 0.00 0.00 3.77
1455 1480 0.602905 AAGCAACTGCCCACGAGTAC 60.603 55.000 0.00 0.00 43.38 2.73
1611 1636 1.277273 CTGAAGATGGACAGGTGCTCA 59.723 52.381 0.00 0.00 0.00 4.26
1623 1648 5.221067 CCTTGATTCAATGGCTCTGAAGATG 60.221 44.000 0.00 1.46 36.30 2.90
1624 1649 4.888239 CCTTGATTCAATGGCTCTGAAGAT 59.112 41.667 0.00 0.00 36.30 2.40
1746 1771 2.089887 TAAACGCCGTGGCAGAGACA 62.090 55.000 12.06 0.00 42.06 3.41
1878 1903 6.384258 TTGACAGACTGCTGATAGAGTATC 57.616 41.667 1.25 0.00 45.17 2.24
1915 1940 1.812922 CCTCACGATGTGCTGGAGC 60.813 63.158 0.00 0.00 42.50 4.70
1923 1948 1.763968 TAGCTACAGCCTCACGATGT 58.236 50.000 0.00 0.00 43.38 3.06
1959 1984 4.025061 GGATCAAACTCAGCTTCATCATCG 60.025 45.833 0.00 0.00 0.00 3.84
2109 2171 6.032956 ACACGTCCTGAATTGTCTGTATTA 57.967 37.500 0.00 0.00 0.00 0.98
2128 2190 3.796178 CCATCCTTCAACAACAAAACACG 59.204 43.478 0.00 0.00 0.00 4.49
2131 2193 3.555547 GTGCCATCCTTCAACAACAAAAC 59.444 43.478 0.00 0.00 0.00 2.43
2154 2216 4.570772 GTGTGTAACTTGTGATGTGAGTGT 59.429 41.667 0.00 0.00 38.04 3.55
2309 2377 4.157246 TGTAGACAGCAGAAACCCTTCTA 58.843 43.478 0.00 0.00 40.05 2.10
2312 2380 3.409026 CTGTAGACAGCAGAAACCCTT 57.591 47.619 0.00 0.00 37.15 3.95
2323 2391 2.478134 GAGTTGTTGCTGCTGTAGACAG 59.522 50.000 5.26 5.26 46.40 3.51
2329 2397 2.213499 GTACAGAGTTGTTGCTGCTGT 58.787 47.619 0.00 0.00 42.04 4.40
2431 2501 3.491792 GCCGGAAAAACCATCAACTCAAA 60.492 43.478 5.05 0.00 38.90 2.69
2432 2502 2.035321 GCCGGAAAAACCATCAACTCAA 59.965 45.455 5.05 0.00 38.90 3.02
2433 2503 1.611491 GCCGGAAAAACCATCAACTCA 59.389 47.619 5.05 0.00 38.90 3.41
2435 2505 0.596082 CGCCGGAAAAACCATCAACT 59.404 50.000 5.05 0.00 38.90 3.16
2438 2508 0.808125 CATCGCCGGAAAAACCATCA 59.192 50.000 5.05 0.00 38.90 3.07
2443 2514 4.095610 CAATTCTACATCGCCGGAAAAAC 58.904 43.478 5.05 0.00 0.00 2.43
2487 2569 8.888579 AAGCAATATTACTATGCGACTAAAGT 57.111 30.769 0.00 0.00 0.00 2.66
2492 2574 8.230486 GCATAAAAGCAATATTACTATGCGACT 58.770 33.333 6.28 0.00 33.20 4.18
2493 2575 8.230486 AGCATAAAAGCAATATTACTATGCGAC 58.770 33.333 12.91 0.00 43.02 5.19
2494 2576 8.322906 AGCATAAAAGCAATATTACTATGCGA 57.677 30.769 12.91 0.00 43.02 5.10
2500 2582 9.512588 AGCTGATAGCATAAAAGCAATATTACT 57.487 29.630 3.43 0.00 45.56 2.24
2503 2585 8.853126 TGAAGCTGATAGCATAAAAGCAATATT 58.147 29.630 3.43 0.00 45.56 1.28
2548 2631 7.382110 CACTCCACCAAAGAGATATACTATGG 58.618 42.308 0.00 0.00 35.27 2.74
2566 2649 0.533491 TATGTACACCGCCACTCCAC 59.467 55.000 0.00 0.00 0.00 4.02
2574 2657 7.575332 AAATGTTCAAAATTATGTACACCGC 57.425 32.000 0.00 0.00 34.14 5.68
2662 2745 5.007039 CGTCATGGTCTATTCATTTGGACAG 59.993 44.000 0.00 0.00 0.00 3.51
2679 2762 4.795278 GGTACGTAAACTTAGTCGTCATGG 59.205 45.833 0.00 0.00 37.66 3.66
2710 2793 0.686789 AATGCAAAGCAGGGGAAACC 59.313 50.000 0.00 0.00 46.34 3.27
2711 2794 1.338105 GGAATGCAAAGCAGGGGAAAC 60.338 52.381 0.00 0.00 43.65 2.78
2712 2795 0.975887 GGAATGCAAAGCAGGGGAAA 59.024 50.000 0.00 0.00 43.65 3.13
2713 2796 0.178938 TGGAATGCAAAGCAGGGGAA 60.179 50.000 0.00 0.00 43.65 3.97
2714 2797 0.178938 TTGGAATGCAAAGCAGGGGA 60.179 50.000 0.00 0.00 43.65 4.81
2715 2798 0.686224 TTTGGAATGCAAAGCAGGGG 59.314 50.000 0.00 0.00 43.65 4.79
2716 2799 2.145536 GTTTTGGAATGCAAAGCAGGG 58.854 47.619 8.96 0.00 43.65 4.45
2717 2800 2.836262 TGTTTTGGAATGCAAAGCAGG 58.164 42.857 12.11 0.00 43.65 4.85
2718 2801 3.002553 GGTTGTTTTGGAATGCAAAGCAG 59.997 43.478 15.03 0.00 43.65 4.24
2719 2802 2.941720 GGTTGTTTTGGAATGCAAAGCA 59.058 40.909 12.11 12.11 44.86 3.91
2720 2803 2.941720 TGGTTGTTTTGGAATGCAAAGC 59.058 40.909 7.09 7.09 0.00 3.51
2721 2804 4.394300 TGTTGGTTGTTTTGGAATGCAAAG 59.606 37.500 0.00 0.00 0.00 2.77
2722 2805 4.154918 GTGTTGGTTGTTTTGGAATGCAAA 59.845 37.500 0.00 0.00 0.00 3.68
2723 2806 3.686726 GTGTTGGTTGTTTTGGAATGCAA 59.313 39.130 0.00 0.00 0.00 4.08
2724 2807 3.265791 GTGTTGGTTGTTTTGGAATGCA 58.734 40.909 0.00 0.00 0.00 3.96
2725 2808 2.611751 GGTGTTGGTTGTTTTGGAATGC 59.388 45.455 0.00 0.00 0.00 3.56
2726 2809 2.863137 CGGTGTTGGTTGTTTTGGAATG 59.137 45.455 0.00 0.00 0.00 2.67
2727 2810 2.761208 TCGGTGTTGGTTGTTTTGGAAT 59.239 40.909 0.00 0.00 0.00 3.01
2728 2811 2.168496 TCGGTGTTGGTTGTTTTGGAA 58.832 42.857 0.00 0.00 0.00 3.53
2729 2812 1.835494 TCGGTGTTGGTTGTTTTGGA 58.165 45.000 0.00 0.00 0.00 3.53
2730 2813 2.656560 TTCGGTGTTGGTTGTTTTGG 57.343 45.000 0.00 0.00 0.00 3.28
2731 2814 4.673441 TGTATTCGGTGTTGGTTGTTTTG 58.327 39.130 0.00 0.00 0.00 2.44
2732 2815 4.985538 TGTATTCGGTGTTGGTTGTTTT 57.014 36.364 0.00 0.00 0.00 2.43
2733 2816 4.985538 TTGTATTCGGTGTTGGTTGTTT 57.014 36.364 0.00 0.00 0.00 2.83
2734 2817 4.985538 TTTGTATTCGGTGTTGGTTGTT 57.014 36.364 0.00 0.00 0.00 2.83
2735 2818 6.402766 CGATATTTGTATTCGGTGTTGGTTGT 60.403 38.462 0.00 0.00 0.00 3.32
2736 2819 5.963004 CGATATTTGTATTCGGTGTTGGTTG 59.037 40.000 0.00 0.00 0.00 3.77
2737 2820 5.448089 GCGATATTTGTATTCGGTGTTGGTT 60.448 40.000 0.00 0.00 0.00 3.67
2738 2821 4.034742 GCGATATTTGTATTCGGTGTTGGT 59.965 41.667 0.00 0.00 0.00 3.67
2739 2822 4.272504 AGCGATATTTGTATTCGGTGTTGG 59.727 41.667 0.00 0.00 33.24 3.77
2740 2823 5.197549 CAGCGATATTTGTATTCGGTGTTG 58.802 41.667 13.65 0.00 44.06 3.33
2741 2824 5.403897 CAGCGATATTTGTATTCGGTGTT 57.596 39.130 13.65 0.00 44.06 3.32
2744 2827 3.807622 CCACAGCGATATTTGTATTCGGT 59.192 43.478 0.00 0.00 34.83 4.69
2745 2828 3.363970 GCCACAGCGATATTTGTATTCGG 60.364 47.826 0.00 0.00 0.00 4.30
2746 2829 3.799035 GCCACAGCGATATTTGTATTCG 58.201 45.455 0.00 0.00 0.00 3.34
2761 2844 2.974148 TTGTGCTGCTCGCCACAG 60.974 61.111 0.00 0.00 38.05 3.66
2762 2845 3.279116 GTTGTGCTGCTCGCCACA 61.279 61.111 0.00 0.00 38.05 4.17
2763 2846 3.279116 TGTTGTGCTGCTCGCCAC 61.279 61.111 0.00 0.00 38.05 5.01
2764 2847 3.279116 GTGTTGTGCTGCTCGCCA 61.279 61.111 0.00 0.00 38.05 5.69
2765 2848 3.279116 TGTGTTGTGCTGCTCGCC 61.279 61.111 0.00 0.00 38.05 5.54
2766 2849 2.051882 GTGTGTTGTGCTGCTCGC 60.052 61.111 0.00 0.00 39.77 5.03
2767 2850 1.713937 TTGGTGTGTTGTGCTGCTCG 61.714 55.000 0.00 0.00 0.00 5.03
2768 2851 0.455410 TTTGGTGTGTTGTGCTGCTC 59.545 50.000 0.00 0.00 0.00 4.26
2769 2852 0.894141 TTTTGGTGTGTTGTGCTGCT 59.106 45.000 0.00 0.00 0.00 4.24
2770 2853 1.135141 TCTTTTGGTGTGTTGTGCTGC 60.135 47.619 0.00 0.00 0.00 5.25
2771 2854 2.937469 TCTTTTGGTGTGTTGTGCTG 57.063 45.000 0.00 0.00 0.00 4.41
2772 2855 3.951775 TTTCTTTTGGTGTGTTGTGCT 57.048 38.095 0.00 0.00 0.00 4.40
2773 2856 4.688413 TCTTTTTCTTTTGGTGTGTTGTGC 59.312 37.500 0.00 0.00 0.00 4.57
2774 2857 6.644592 TCTTCTTTTTCTTTTGGTGTGTTGTG 59.355 34.615 0.00 0.00 0.00 3.33
2775 2858 6.754193 TCTTCTTTTTCTTTTGGTGTGTTGT 58.246 32.000 0.00 0.00 0.00 3.32
2776 2859 7.598493 TCTTCTTCTTTTTCTTTTGGTGTGTTG 59.402 33.333 0.00 0.00 0.00 3.33
2777 2860 7.666623 TCTTCTTCTTTTTCTTTTGGTGTGTT 58.333 30.769 0.00 0.00 0.00 3.32
2778 2861 7.227049 TCTTCTTCTTTTTCTTTTGGTGTGT 57.773 32.000 0.00 0.00 0.00 3.72
2779 2862 8.435430 GTTTCTTCTTCTTTTTCTTTTGGTGTG 58.565 33.333 0.00 0.00 0.00 3.82
2780 2863 8.147704 TGTTTCTTCTTCTTTTTCTTTTGGTGT 58.852 29.630 0.00 0.00 0.00 4.16
2781 2864 8.532977 TGTTTCTTCTTCTTTTTCTTTTGGTG 57.467 30.769 0.00 0.00 0.00 4.17
2782 2865 9.554395 TTTGTTTCTTCTTCTTTTTCTTTTGGT 57.446 25.926 0.00 0.00 0.00 3.67
2786 2869 8.721478 GGCTTTTGTTTCTTCTTCTTTTTCTTT 58.279 29.630 0.00 0.00 0.00 2.52
2787 2870 7.877612 TGGCTTTTGTTTCTTCTTCTTTTTCTT 59.122 29.630 0.00 0.00 0.00 2.52
2788 2871 7.386059 TGGCTTTTGTTTCTTCTTCTTTTTCT 58.614 30.769 0.00 0.00 0.00 2.52
2789 2872 7.595311 TGGCTTTTGTTTCTTCTTCTTTTTC 57.405 32.000 0.00 0.00 0.00 2.29
2790 2873 7.094805 GGTTGGCTTTTGTTTCTTCTTCTTTTT 60.095 33.333 0.00 0.00 0.00 1.94
2791 2874 6.371548 GGTTGGCTTTTGTTTCTTCTTCTTTT 59.628 34.615 0.00 0.00 0.00 2.27
2792 2875 5.874810 GGTTGGCTTTTGTTTCTTCTTCTTT 59.125 36.000 0.00 0.00 0.00 2.52
2793 2876 5.046663 TGGTTGGCTTTTGTTTCTTCTTCTT 60.047 36.000 0.00 0.00 0.00 2.52
2794 2877 4.466015 TGGTTGGCTTTTGTTTCTTCTTCT 59.534 37.500 0.00 0.00 0.00 2.85
2795 2878 4.566759 GTGGTTGGCTTTTGTTTCTTCTTC 59.433 41.667 0.00 0.00 0.00 2.87
2796 2879 4.503910 GTGGTTGGCTTTTGTTTCTTCTT 58.496 39.130 0.00 0.00 0.00 2.52
2797 2880 3.428862 CGTGGTTGGCTTTTGTTTCTTCT 60.429 43.478 0.00 0.00 0.00 2.85
2798 2881 2.857748 CGTGGTTGGCTTTTGTTTCTTC 59.142 45.455 0.00 0.00 0.00 2.87
2799 2882 2.418060 CCGTGGTTGGCTTTTGTTTCTT 60.418 45.455 0.00 0.00 0.00 2.52
2800 2883 1.136110 CCGTGGTTGGCTTTTGTTTCT 59.864 47.619 0.00 0.00 0.00 2.52
2801 2884 1.566404 CCGTGGTTGGCTTTTGTTTC 58.434 50.000 0.00 0.00 0.00 2.78
2802 2885 3.750828 CCGTGGTTGGCTTTTGTTT 57.249 47.368 0.00 0.00 0.00 2.83
2812 2895 4.347453 GCCAAGCTGCCGTGGTTG 62.347 66.667 18.16 6.69 41.91 3.77
2813 2896 4.892965 TGCCAAGCTGCCGTGGTT 62.893 61.111 18.16 0.00 41.91 3.67
2814 2897 4.892965 TTGCCAAGCTGCCGTGGT 62.893 61.111 18.16 0.00 41.91 4.16
2815 2898 3.562779 CTTTGCCAAGCTGCCGTGG 62.563 63.158 14.06 14.06 42.66 4.94
2816 2899 2.049802 CTTTGCCAAGCTGCCGTG 60.050 61.111 0.00 0.00 0.00 4.94
2824 2907 2.202518 CATCCGCGCTTTGCCAAG 60.203 61.111 5.56 0.00 42.08 3.61
2825 2908 2.671276 TCATCCGCGCTTTGCCAA 60.671 55.556 5.56 0.00 42.08 4.52
2826 2909 3.430862 GTCATCCGCGCTTTGCCA 61.431 61.111 5.56 0.00 42.08 4.92
2827 2910 4.179579 GGTCATCCGCGCTTTGCC 62.180 66.667 5.56 2.72 42.08 4.52
2828 2911 4.179579 GGGTCATCCGCGCTTTGC 62.180 66.667 5.56 0.00 41.47 3.68
2854 2937 4.910585 CTGTATCCGGTGGGCGCC 62.911 72.222 21.18 21.18 0.00 6.53
2855 2938 3.845259 TCTGTATCCGGTGGGCGC 61.845 66.667 0.00 0.00 0.00 6.53
2856 2939 2.106332 GTCTGTATCCGGTGGGCG 59.894 66.667 0.00 0.00 0.00 6.13
2857 2940 2.363975 TGGTCTGTATCCGGTGGGC 61.364 63.158 0.00 0.00 0.00 5.36
2858 2941 1.520666 GTGGTCTGTATCCGGTGGG 59.479 63.158 0.00 0.00 0.00 4.61
2859 2942 1.261938 TGGTGGTCTGTATCCGGTGG 61.262 60.000 0.00 0.00 0.00 4.61
2860 2943 0.108329 GTGGTGGTCTGTATCCGGTG 60.108 60.000 0.00 0.00 0.00 4.94
2861 2944 0.543410 TGTGGTGGTCTGTATCCGGT 60.543 55.000 0.00 0.00 0.00 5.28
2862 2945 0.175760 CTGTGGTGGTCTGTATCCGG 59.824 60.000 0.00 0.00 0.00 5.14
2863 2946 1.135083 GTCTGTGGTGGTCTGTATCCG 60.135 57.143 0.00 0.00 0.00 4.18
2864 2947 1.207329 GGTCTGTGGTGGTCTGTATCC 59.793 57.143 0.00 0.00 0.00 2.59
2865 2948 1.135083 CGGTCTGTGGTGGTCTGTATC 60.135 57.143 0.00 0.00 0.00 2.24
2866 2949 0.895530 CGGTCTGTGGTGGTCTGTAT 59.104 55.000 0.00 0.00 0.00 2.29
2867 2950 0.178984 TCGGTCTGTGGTGGTCTGTA 60.179 55.000 0.00 0.00 0.00 2.74
2868 2951 1.456892 TCGGTCTGTGGTGGTCTGT 60.457 57.895 0.00 0.00 0.00 3.41
2869 2952 1.290324 CTCGGTCTGTGGTGGTCTG 59.710 63.158 0.00 0.00 0.00 3.51
2870 2953 1.908793 CCTCGGTCTGTGGTGGTCT 60.909 63.158 0.00 0.00 0.00 3.85
2871 2954 2.657237 CCTCGGTCTGTGGTGGTC 59.343 66.667 0.00 0.00 0.00 4.02
2872 2955 3.626924 GCCTCGGTCTGTGGTGGT 61.627 66.667 1.82 0.00 33.61 4.16
2873 2956 3.302347 GAGCCTCGGTCTGTGGTGG 62.302 68.421 1.82 0.00 33.61 4.61
2874 2957 2.262915 GAGCCTCGGTCTGTGGTG 59.737 66.667 1.82 0.00 33.61 4.17
2875 2958 2.997897 GGAGCCTCGGTCTGTGGT 60.998 66.667 1.82 0.00 33.61 4.16
2876 2959 4.135153 CGGAGCCTCGGTCTGTGG 62.135 72.222 0.00 0.00 32.48 4.17
2877 2960 2.636412 TTCGGAGCCTCGGTCTGTG 61.636 63.158 0.00 0.00 37.64 3.66
2878 2961 2.282958 TTCGGAGCCTCGGTCTGT 60.283 61.111 0.00 0.00 37.64 3.41
2879 2962 2.182030 GTTCGGAGCCTCGGTCTG 59.818 66.667 0.00 0.00 37.73 3.51
2880 2963 3.069318 GGTTCGGAGCCTCGGTCT 61.069 66.667 3.33 0.00 0.00 3.85
2881 2964 4.493747 CGGTTCGGAGCCTCGGTC 62.494 72.222 9.30 0.00 0.00 4.79
2893 2976 3.484547 CTTGGTACGCGGCGGTTC 61.485 66.667 27.37 15.19 0.00 3.62
2899 2982 3.788766 GTGCTGCTTGGTACGCGG 61.789 66.667 12.47 0.00 36.84 6.46
2900 2983 3.788766 GGTGCTGCTTGGTACGCG 61.789 66.667 3.53 3.53 0.00 6.01
2901 2984 2.358737 AGGTGCTGCTTGGTACGC 60.359 61.111 0.00 0.00 0.00 4.42
2902 2985 1.741770 GGAGGTGCTGCTTGGTACG 60.742 63.158 0.00 0.00 0.00 3.67
2903 2986 0.250727 TTGGAGGTGCTGCTTGGTAC 60.251 55.000 0.00 0.00 0.00 3.34
2904 2987 0.036732 CTTGGAGGTGCTGCTTGGTA 59.963 55.000 0.00 0.00 0.00 3.25
2905 2988 1.228367 CTTGGAGGTGCTGCTTGGT 60.228 57.895 0.00 0.00 0.00 3.67
2906 2989 0.538057 TTCTTGGAGGTGCTGCTTGG 60.538 55.000 0.00 0.00 0.00 3.61
2907 2990 1.268899 CTTTCTTGGAGGTGCTGCTTG 59.731 52.381 0.00 0.00 0.00 4.01
2908 2991 1.613836 CTTTCTTGGAGGTGCTGCTT 58.386 50.000 0.00 0.00 0.00 3.91
2909 2992 0.251077 CCTTTCTTGGAGGTGCTGCT 60.251 55.000 0.00 0.00 0.00 4.24
2910 2993 0.250901 TCCTTTCTTGGAGGTGCTGC 60.251 55.000 0.00 0.00 35.71 5.25
2911 2994 2.089980 CATCCTTTCTTGGAGGTGCTG 58.910 52.381 0.00 0.00 39.78 4.41
2912 2995 1.615384 GCATCCTTTCTTGGAGGTGCT 60.615 52.381 0.00 0.00 39.79 4.40
2913 2996 0.813821 GCATCCTTTCTTGGAGGTGC 59.186 55.000 0.00 0.00 39.79 5.01
2914 2997 1.089920 CGCATCCTTTCTTGGAGGTG 58.910 55.000 0.00 0.00 41.04 4.00
2915 2998 0.984230 TCGCATCCTTTCTTGGAGGT 59.016 50.000 0.00 0.00 39.79 3.85
2916 2999 1.945394 CATCGCATCCTTTCTTGGAGG 59.055 52.381 0.00 0.00 39.78 4.30
2917 3000 1.332997 GCATCGCATCCTTTCTTGGAG 59.667 52.381 0.00 0.00 39.78 3.86
2918 3001 1.382522 GCATCGCATCCTTTCTTGGA 58.617 50.000 0.00 0.00 40.82 3.53
2919 3002 0.383231 GGCATCGCATCCTTTCTTGG 59.617 55.000 0.00 0.00 0.00 3.61
2920 3003 0.028505 CGGCATCGCATCCTTTCTTG 59.971 55.000 0.00 0.00 0.00 3.02
2921 3004 0.107703 TCGGCATCGCATCCTTTCTT 60.108 50.000 0.00 0.00 36.13 2.52
2922 3005 0.811616 GTCGGCATCGCATCCTTTCT 60.812 55.000 0.00 0.00 36.13 2.52
2923 3006 1.643832 GTCGGCATCGCATCCTTTC 59.356 57.895 0.00 0.00 36.13 2.62
2924 3007 2.173669 CGTCGGCATCGCATCCTTT 61.174 57.895 0.00 0.00 36.13 3.11
2925 3008 2.369257 ATCGTCGGCATCGCATCCTT 62.369 55.000 0.00 0.00 36.13 3.36
2926 3009 2.861101 ATCGTCGGCATCGCATCCT 61.861 57.895 0.00 0.00 36.13 3.24
2927 3010 2.356313 ATCGTCGGCATCGCATCC 60.356 61.111 0.00 0.00 36.13 3.51
2928 3011 2.849007 CATCGTCGGCATCGCATC 59.151 61.111 0.00 0.00 36.13 3.91
2929 3012 3.341043 GCATCGTCGGCATCGCAT 61.341 61.111 0.00 0.00 36.13 4.73
2930 3013 4.512961 AGCATCGTCGGCATCGCA 62.513 61.111 0.00 0.00 36.13 5.10
2931 3014 3.993234 CAGCATCGTCGGCATCGC 61.993 66.667 0.00 0.00 36.13 4.58
2932 3015 3.993234 GCAGCATCGTCGGCATCG 61.993 66.667 0.00 0.00 37.82 3.84
2933 3016 2.587194 AGCAGCATCGTCGGCATC 60.587 61.111 0.00 0.00 0.00 3.91
2934 3017 2.893895 CAGCAGCATCGTCGGCAT 60.894 61.111 0.00 0.00 0.00 4.40
2946 3029 4.803426 GACTCGTCCGGGCAGCAG 62.803 72.222 6.96 0.12 0.00 4.24
2975 3058 4.742201 CTCCCTCCACGTGCACGG 62.742 72.222 39.21 27.67 44.95 4.94
2976 3059 4.742201 CCTCCCTCCACGTGCACG 62.742 72.222 35.99 35.99 46.33 5.34
2977 3060 3.626924 ACCTCCCTCCACGTGCAC 61.627 66.667 10.91 6.82 0.00 4.57
2978 3061 3.625897 CACCTCCCTCCACGTGCA 61.626 66.667 10.91 0.00 0.00 4.57
2979 3062 4.394712 CCACCTCCCTCCACGTGC 62.395 72.222 10.91 0.00 0.00 5.34
2980 3063 3.706373 CCCACCTCCCTCCACGTG 61.706 72.222 9.08 9.08 0.00 4.49
2996 3079 1.052124 TGTCGATGGTATCCACCCCC 61.052 60.000 0.00 0.00 45.11 5.40
2997 3080 0.106149 GTGTCGATGGTATCCACCCC 59.894 60.000 0.00 0.00 45.11 4.95
2998 3081 0.106149 GGTGTCGATGGTATCCACCC 59.894 60.000 7.67 0.00 45.11 4.61
2999 3082 0.106149 GGGTGTCGATGGTATCCACC 59.894 60.000 9.91 9.91 46.00 4.61
3000 3083 1.068741 GAGGGTGTCGATGGTATCCAC 59.931 57.143 0.00 0.00 35.80 4.02
3001 3084 1.063190 AGAGGGTGTCGATGGTATCCA 60.063 52.381 0.00 0.00 38.19 3.41
3002 3085 1.705873 AGAGGGTGTCGATGGTATCC 58.294 55.000 0.00 0.00 0.00 2.59
3003 3086 2.820787 CCTAGAGGGTGTCGATGGTATC 59.179 54.545 0.00 0.00 0.00 2.24
3004 3087 2.445905 TCCTAGAGGGTGTCGATGGTAT 59.554 50.000 0.00 0.00 36.25 2.73
3005 3088 1.848388 TCCTAGAGGGTGTCGATGGTA 59.152 52.381 0.00 0.00 36.25 3.25
3006 3089 0.629596 TCCTAGAGGGTGTCGATGGT 59.370 55.000 0.00 0.00 36.25 3.55
3007 3090 1.683917 CTTCCTAGAGGGTGTCGATGG 59.316 57.143 0.00 0.00 36.25 3.51
3008 3091 1.683917 CCTTCCTAGAGGGTGTCGATG 59.316 57.143 0.00 0.00 36.25 3.84
3009 3092 2.074729 CCTTCCTAGAGGGTGTCGAT 57.925 55.000 0.00 0.00 36.25 3.59
3010 3093 3.590643 CCTTCCTAGAGGGTGTCGA 57.409 57.895 0.00 0.00 36.25 4.20


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

AutoCloner maintained by Alex Coulton.