Multiple sequence alignment - TraesCS4D01G118000

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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 TraesCS4D01G118000 chr4D 100.000 2984 0 0 1 2984 98480373 98483356 0.000000e+00 5511
1 TraesCS4D01G118000 chr4D 98.854 611 7 0 1 611 98472497 98473107 0.000000e+00 1090
2 TraesCS4D01G118000 chr4A 90.234 2048 99 44 634 2642 477834840 477832855 0.000000e+00 2580
3 TraesCS4D01G118000 chr4A 86.512 215 21 3 1869 2083 477792913 477792707 2.310000e-56 230
4 TraesCS4D01G118000 chr4A 92.857 112 8 0 1408 1519 477830667 477830556 2.380000e-36 163
5 TraesCS4D01G118000 chr4B 91.257 1933 91 37 740 2651 139768376 139770251 0.000000e+00 2562
6 TraesCS4D01G118000 chr7D 98.854 611 7 0 1 611 105669967 105670577 0.000000e+00 1090
7 TraesCS4D01G118000 chr7D 97.557 614 12 2 1 611 160895217 160895830 0.000000e+00 1048
8 TraesCS4D01G118000 chr7D 97.386 612 13 3 1 611 160903491 160904100 0.000000e+00 1038
9 TraesCS4D01G118000 chr7D 96.900 613 17 2 1 611 408966214 408966826 0.000000e+00 1026
10 TraesCS4D01G118000 chr7D 96.405 612 21 1 1 611 408974189 408974800 0.000000e+00 1007
11 TraesCS4D01G118000 chr7D 96.260 615 20 3 1 613 347859092 347858479 0.000000e+00 1005
12 TraesCS4D01G118000 chr3D 97.097 620 16 2 1 619 420481955 420482573 0.000000e+00 1044
13 TraesCS4D01G118000 chr5D 96.248 613 13 7 1 611 118223973 118223369 0.000000e+00 996
14 TraesCS4D01G118000 chr5D 94.702 302 16 0 1389 1690 231321890 231322191 1.250000e-128 470
15 TraesCS4D01G118000 chr5B 94.702 302 16 0 1389 1690 275173535 275173234 1.250000e-128 470
16 TraesCS4D01G118000 chr5A 95.222 293 14 0 1398 1690 325996548 325996256 5.830000e-127 464
17 TraesCS4D01G118000 chr5A 90.173 346 24 8 2640 2976 95786414 95786758 2.730000e-120 442
18 TraesCS4D01G118000 chr2D 87.283 346 33 9 2647 2984 568314616 568314274 4.670000e-103 385


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 TraesCS4D01G118000 chr4D 98480373 98483356 2983 False 5511.0 5511 100.0000 1 2984 1 chr4D.!!$F2 2983
1 TraesCS4D01G118000 chr4D 98472497 98473107 610 False 1090.0 1090 98.8540 1 611 1 chr4D.!!$F1 610
2 TraesCS4D01G118000 chr4A 477830556 477834840 4284 True 1371.5 2580 91.5455 634 2642 2 chr4A.!!$R2 2008
3 TraesCS4D01G118000 chr4B 139768376 139770251 1875 False 2562.0 2562 91.2570 740 2651 1 chr4B.!!$F1 1911
4 TraesCS4D01G118000 chr7D 105669967 105670577 610 False 1090.0 1090 98.8540 1 611 1 chr7D.!!$F1 610
5 TraesCS4D01G118000 chr7D 160895217 160895830 613 False 1048.0 1048 97.5570 1 611 1 chr7D.!!$F2 610
6 TraesCS4D01G118000 chr7D 160903491 160904100 609 False 1038.0 1038 97.3860 1 611 1 chr7D.!!$F3 610
7 TraesCS4D01G118000 chr7D 408966214 408966826 612 False 1026.0 1026 96.9000 1 611 1 chr7D.!!$F4 610
8 TraesCS4D01G118000 chr7D 408974189 408974800 611 False 1007.0 1007 96.4050 1 611 1 chr7D.!!$F5 610
9 TraesCS4D01G118000 chr7D 347858479 347859092 613 True 1005.0 1005 96.2600 1 613 1 chr7D.!!$R1 612
10 TraesCS4D01G118000 chr3D 420481955 420482573 618 False 1044.0 1044 97.0970 1 619 1 chr3D.!!$F1 618
11 TraesCS4D01G118000 chr5D 118223369 118223973 604 True 996.0 996 96.2480 1 611 1 chr5D.!!$R1 610

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
616 622 0.736325 CTCGGGGCGTTACAGTCTTG 60.736 60.0 0.0 0.0 0.0 3.02 F
1042 1053 0.729478 CATCGTCTTGCTCGTCGTGT 60.729 55.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 1840 0.179089 CAGGAGTCGGGAATCTGCTG 60.179 60.0 0.0 0.0 41.88 4.41 R
2908 4371 0.029035 CGCTCATCTGCTGGCAAATC 59.971 55.0 0.0 0.0 0.00 2.17 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
88 91 9.780413 GCAGAATGGTATTAGAGAAAAGAAAAG 57.220 33.333 0.00 0.00 35.86 2.27
613 619 1.153881 GTCTCGGGGCGTTACAGTC 60.154 63.158 0.00 0.00 0.00 3.51
614 620 1.303888 TCTCGGGGCGTTACAGTCT 60.304 57.895 0.00 0.00 0.00 3.24
615 621 0.896940 TCTCGGGGCGTTACAGTCTT 60.897 55.000 0.00 0.00 0.00 3.01
616 622 0.736325 CTCGGGGCGTTACAGTCTTG 60.736 60.000 0.00 0.00 0.00 3.02
617 623 2.388232 CGGGGCGTTACAGTCTTGC 61.388 63.158 0.00 0.00 0.00 4.01
618 624 1.003718 GGGGCGTTACAGTCTTGCT 60.004 57.895 0.00 0.00 0.00 3.91
631 637 5.611796 CAGTCTTGCTGTACATGCTTTAA 57.388 39.130 15.28 4.52 40.27 1.52
632 638 6.000891 CAGTCTTGCTGTACATGCTTTAAA 57.999 37.500 15.28 0.00 40.27 1.52
658 664 3.460103 CATATTTGCACATCAAAGGCCC 58.540 45.455 0.00 0.00 46.68 5.80
714 720 9.547753 AGTACAAAATGATAATGTGCTACCTAG 57.452 33.333 0.00 0.00 38.08 3.02
722 728 8.263940 TGATAATGTGCTACCTAGTTTTTGTC 57.736 34.615 0.00 0.00 0.00 3.18
784 791 4.630111 TGGCTTTGCATTTCTTTACAAGG 58.370 39.130 0.00 0.00 0.00 3.61
869 877 1.758280 TGCATGAATTGAGGCAATCCC 59.242 47.619 0.64 0.00 32.43 3.85
908 916 1.002087 GGAGGAAGAAGAAGACGGCAA 59.998 52.381 0.00 0.00 0.00 4.52
909 917 2.070028 GAGGAAGAAGAAGACGGCAAC 58.930 52.381 0.00 0.00 0.00 4.17
910 918 1.416401 AGGAAGAAGAAGACGGCAACA 59.584 47.619 0.00 0.00 0.00 3.33
911 919 2.039084 AGGAAGAAGAAGACGGCAACAT 59.961 45.455 0.00 0.00 0.00 2.71
912 920 2.814336 GGAAGAAGAAGACGGCAACATT 59.186 45.455 0.00 0.00 0.00 2.71
924 932 2.284150 CGGCAACATTACATCGATCGTT 59.716 45.455 15.94 3.47 0.00 3.85
953 961 2.248487 CATTTGCTCTTGCGCTTCTTC 58.752 47.619 9.73 0.00 43.34 2.87
955 963 1.527034 TTGCTCTTGCGCTTCTTCAT 58.473 45.000 9.73 0.00 43.34 2.57
968 976 4.095483 CGCTTCTTCATACTCCAATTTGCT 59.905 41.667 0.00 0.00 0.00 3.91
971 979 6.238593 GCTTCTTCATACTCCAATTTGCTAGG 60.239 42.308 0.00 0.00 0.00 3.02
1012 1020 1.835483 GATAGCAATGGCAGCGTCGG 61.835 60.000 0.00 0.00 44.61 4.79
1042 1053 0.729478 CATCGTCTTGCTCGTCGTGT 60.729 55.000 0.00 0.00 0.00 4.49
1715 1729 2.896685 CGCCATTAATCTCTCTCCCTCT 59.103 50.000 0.00 0.00 0.00 3.69
1717 1731 3.900601 GCCATTAATCTCTCTCCCTCTCA 59.099 47.826 0.00 0.00 0.00 3.27
1719 1733 5.147032 CCATTAATCTCTCTCCCTCTCACT 58.853 45.833 0.00 0.00 0.00 3.41
1722 1736 3.864789 ATCTCTCTCCCTCTCACTCTC 57.135 52.381 0.00 0.00 0.00 3.20
1723 1737 2.845659 TCTCTCTCCCTCTCACTCTCT 58.154 52.381 0.00 0.00 0.00 3.10
1724 1738 2.771943 TCTCTCTCCCTCTCACTCTCTC 59.228 54.545 0.00 0.00 0.00 3.20
1725 1739 1.484653 TCTCTCCCTCTCACTCTCTCG 59.515 57.143 0.00 0.00 0.00 4.04
1765 1779 7.832685 TCTTTCTCACTCATGATGGATTGATTT 59.167 33.333 0.00 0.00 33.22 2.17
1766 1780 6.937436 TCTCACTCATGATGGATTGATTTG 57.063 37.500 0.00 0.00 33.22 2.32
1767 1781 6.655930 TCTCACTCATGATGGATTGATTTGA 58.344 36.000 0.00 0.00 33.22 2.69
1777 1792 7.666623 TGATGGATTGATTTGATTGATGATGG 58.333 34.615 0.00 0.00 0.00 3.51
1788 1803 6.009908 TGATTGATGATGGTCTTGGAATCT 57.990 37.500 0.00 0.00 0.00 2.40
1789 1804 7.140522 TGATTGATGATGGTCTTGGAATCTA 57.859 36.000 0.00 0.00 0.00 1.98
1790 1805 6.994496 TGATTGATGATGGTCTTGGAATCTAC 59.006 38.462 0.00 0.00 0.00 2.59
1791 1806 6.566079 TTGATGATGGTCTTGGAATCTACT 57.434 37.500 0.00 0.00 0.00 2.57
1883 1898 4.215908 TCAGGTCAACTACTCACTCACTT 58.784 43.478 0.00 0.00 0.00 3.16
1884 1899 4.278669 TCAGGTCAACTACTCACTCACTTC 59.721 45.833 0.00 0.00 0.00 3.01
1885 1900 4.279671 CAGGTCAACTACTCACTCACTTCT 59.720 45.833 0.00 0.00 0.00 2.85
1886 1901 4.279671 AGGTCAACTACTCACTCACTTCTG 59.720 45.833 0.00 0.00 0.00 3.02
1889 1904 6.273825 GTCAACTACTCACTCACTTCTGAAA 58.726 40.000 0.00 0.00 0.00 2.69
1890 1905 6.419413 GTCAACTACTCACTCACTTCTGAAAG 59.581 42.308 0.00 0.00 38.54 2.62
1891 1906 6.096987 TCAACTACTCACTCACTTCTGAAAGT 59.903 38.462 0.00 0.00 46.80 2.66
1907 1943 8.463930 TTCTGAAAGTGAAAAATCCATACTGT 57.536 30.769 0.00 0.00 33.76 3.55
1908 1944 8.099364 TCTGAAAGTGAAAAATCCATACTGTC 57.901 34.615 0.00 0.00 33.76 3.51
1910 1946 6.775142 TGAAAGTGAAAAATCCATACTGTCCA 59.225 34.615 0.00 0.00 0.00 4.02
1933 1969 2.540361 GCATGGTTAAGCTCGATTGCTG 60.540 50.000 6.19 0.00 43.24 4.41
1935 1971 2.076100 TGGTTAAGCTCGATTGCTGTG 58.924 47.619 6.19 0.00 43.24 3.66
1953 1989 4.505808 CTGTGAGCTGAATTCTGATGTCT 58.494 43.478 15.79 3.57 0.00 3.41
2117 2162 1.318576 ACTACCAACTTTGCAGCCAC 58.681 50.000 0.00 0.00 0.00 5.01
2120 2165 1.364901 CCAACTTTGCAGCCACCAG 59.635 57.895 0.00 0.00 0.00 4.00
2121 2166 1.108727 CCAACTTTGCAGCCACCAGA 61.109 55.000 0.00 0.00 0.00 3.86
2122 2167 0.963962 CAACTTTGCAGCCACCAGAT 59.036 50.000 0.00 0.00 0.00 2.90
2123 2168 1.068055 CAACTTTGCAGCCACCAGATC 60.068 52.381 0.00 0.00 0.00 2.75
2265 2312 5.538053 TGCATCAAAGGGAGTATTGTTTCAA 59.462 36.000 0.00 0.00 0.00 2.69
2312 2359 5.997843 TGATGATCCTATAATGCCCATCTG 58.002 41.667 0.00 0.00 32.53 2.90
2328 2375 1.833934 CTGGCCCTGGCTTGTGTTT 60.834 57.895 8.29 0.00 41.60 2.83
2330 2377 0.825840 TGGCCCTGGCTTGTGTTTAC 60.826 55.000 8.29 0.00 41.60 2.01
2401 2448 5.107683 CGTTTCTGTCTAGTCAAAGAGCTTG 60.108 44.000 0.00 0.00 36.25 4.01
2413 2460 4.225942 TCAAAGAGCTTGGACCATCTACAT 59.774 41.667 0.00 0.00 35.56 2.29
2414 2461 4.851639 AAGAGCTTGGACCATCTACATT 57.148 40.909 0.00 0.00 0.00 2.71
2421 2468 6.891908 AGCTTGGACCATCTACATTACATTTT 59.108 34.615 0.00 0.00 0.00 1.82
2424 2471 7.864108 TGGACCATCTACATTACATTTTCTG 57.136 36.000 0.00 0.00 0.00 3.02
2541 2593 2.551504 GGGACCCACGCTTAAAAAGAGA 60.552 50.000 5.33 0.00 32.24 3.10
2576 2628 1.886542 CCTTCCCACACTTTTACAGGC 59.113 52.381 0.00 0.00 0.00 4.85
2604 2656 6.112734 ACCCACCTAAAAAGCAAAAGAAAAG 58.887 36.000 0.00 0.00 0.00 2.27
2665 2717 4.734398 TTTTGAACTGTCCAACATTGCT 57.266 36.364 0.00 0.00 0.00 3.91
2666 2718 3.713858 TTGAACTGTCCAACATTGCTG 57.286 42.857 0.00 0.00 0.00 4.41
2667 2719 1.955778 TGAACTGTCCAACATTGCTGG 59.044 47.619 0.00 0.00 35.05 4.85
2668 2720 1.270550 GAACTGTCCAACATTGCTGGG 59.729 52.381 6.26 0.00 34.46 4.45
2670 2722 1.331214 CTGTCCAACATTGCTGGGTT 58.669 50.000 6.26 0.00 34.46 4.11
2671 2723 1.688197 CTGTCCAACATTGCTGGGTTT 59.312 47.619 6.26 0.00 34.46 3.27
2672 2724 1.686052 TGTCCAACATTGCTGGGTTTC 59.314 47.619 6.26 0.00 34.46 2.78
2673 2725 1.686052 GTCCAACATTGCTGGGTTTCA 59.314 47.619 6.26 0.00 34.46 2.69
2674 2726 2.299867 GTCCAACATTGCTGGGTTTCAT 59.700 45.455 6.26 0.00 34.46 2.57
2676 2728 4.021544 GTCCAACATTGCTGGGTTTCATTA 60.022 41.667 6.26 0.00 34.46 1.90
2677 2729 4.220382 TCCAACATTGCTGGGTTTCATTAG 59.780 41.667 6.26 0.00 34.46 1.73
2678 2730 3.874392 ACATTGCTGGGTTTCATTAGC 57.126 42.857 0.00 0.00 36.72 3.09
2679 2731 3.434309 ACATTGCTGGGTTTCATTAGCT 58.566 40.909 0.00 0.00 37.10 3.32
2680 2732 3.834231 ACATTGCTGGGTTTCATTAGCTT 59.166 39.130 0.00 0.00 37.10 3.74
2681 2733 5.016173 ACATTGCTGGGTTTCATTAGCTTA 58.984 37.500 0.00 0.00 37.10 3.09
2682 2734 5.126061 ACATTGCTGGGTTTCATTAGCTTAG 59.874 40.000 0.00 0.00 37.10 2.18
2683 2735 3.016736 TGCTGGGTTTCATTAGCTTAGC 58.983 45.455 0.00 0.00 37.10 3.09
2684 2736 3.016736 GCTGGGTTTCATTAGCTTAGCA 58.983 45.455 7.07 0.00 33.53 3.49
2685 2737 3.065925 GCTGGGTTTCATTAGCTTAGCAG 59.934 47.826 7.07 0.00 33.53 4.24
2686 2738 4.517285 CTGGGTTTCATTAGCTTAGCAGA 58.483 43.478 7.07 0.00 0.00 4.26
2689 2741 4.336713 GGGTTTCATTAGCTTAGCAGAAGG 59.663 45.833 7.07 2.01 0.00 3.46
2690 2742 4.336713 GGTTTCATTAGCTTAGCAGAAGGG 59.663 45.833 7.07 0.00 0.00 3.95
2691 2743 5.186198 GTTTCATTAGCTTAGCAGAAGGGA 58.814 41.667 7.07 0.00 0.00 4.20
2692 2744 4.679373 TCATTAGCTTAGCAGAAGGGAG 57.321 45.455 7.07 0.00 0.00 4.30
2693 2745 4.033709 TCATTAGCTTAGCAGAAGGGAGT 58.966 43.478 7.07 0.00 0.00 3.85
2694 2746 3.895232 TTAGCTTAGCAGAAGGGAGTG 57.105 47.619 7.07 0.00 0.00 3.51
2695 2747 1.944177 AGCTTAGCAGAAGGGAGTGA 58.056 50.000 7.07 0.00 0.00 3.41
2698 2750 2.289694 GCTTAGCAGAAGGGAGTGACAA 60.290 50.000 0.00 0.00 0.00 3.18
2699 2751 3.594134 CTTAGCAGAAGGGAGTGACAAG 58.406 50.000 0.00 0.00 0.00 3.16
2700 2752 1.722034 AGCAGAAGGGAGTGACAAGA 58.278 50.000 0.00 0.00 0.00 3.02
2701 2753 1.622811 AGCAGAAGGGAGTGACAAGAG 59.377 52.381 0.00 0.00 0.00 2.85
2702 2754 1.346068 GCAGAAGGGAGTGACAAGAGT 59.654 52.381 0.00 0.00 0.00 3.24
2704 2756 3.745797 GCAGAAGGGAGTGACAAGAGTTT 60.746 47.826 0.00 0.00 0.00 2.66
2705 2757 3.812053 CAGAAGGGAGTGACAAGAGTTTG 59.188 47.826 0.00 0.00 40.24 2.93
2709 2761 3.648067 AGGGAGTGACAAGAGTTTGATCA 59.352 43.478 0.00 0.00 37.73 2.92
2710 2762 4.103153 AGGGAGTGACAAGAGTTTGATCAA 59.897 41.667 3.38 3.38 37.73 2.57
2712 2764 5.059833 GGAGTGACAAGAGTTTGATCAAGT 58.940 41.667 8.41 1.75 37.73 3.16
2713 2765 5.049818 GGAGTGACAAGAGTTTGATCAAGTG 60.050 44.000 8.41 6.03 37.73 3.16
2714 2766 5.674525 AGTGACAAGAGTTTGATCAAGTGA 58.325 37.500 8.41 0.00 37.73 3.41
2715 2767 6.294473 AGTGACAAGAGTTTGATCAAGTGAT 58.706 36.000 8.41 0.00 37.73 3.06
2723 2775 2.695314 GATCAAGTGATCGGTGGGC 58.305 57.895 5.57 0.00 41.15 5.36
2724 2776 1.153369 ATCAAGTGATCGGTGGGCG 60.153 57.895 0.00 0.00 0.00 6.13
2726 2778 1.375396 CAAGTGATCGGTGGGCGAA 60.375 57.895 0.00 0.00 0.00 4.70
2727 2779 0.953471 CAAGTGATCGGTGGGCGAAA 60.953 55.000 0.00 0.00 0.00 3.46
2729 2781 1.079405 GTGATCGGTGGGCGAAAGA 60.079 57.895 0.00 0.00 0.00 2.52
2734 4197 0.948678 TCGGTGGGCGAAAGAAAAAG 59.051 50.000 0.00 0.00 0.00 2.27
2736 4199 1.324383 GGTGGGCGAAAGAAAAAGGA 58.676 50.000 0.00 0.00 0.00 3.36
2738 4201 2.545113 GGTGGGCGAAAGAAAAAGGAAC 60.545 50.000 0.00 0.00 0.00 3.62
2744 4207 5.450171 GGCGAAAGAAAAAGGAACTAGAAC 58.550 41.667 0.00 0.00 38.49 3.01
2746 4209 6.459161 GGCGAAAGAAAAAGGAACTAGAACAA 60.459 38.462 0.00 0.00 38.49 2.83
2758 4221 8.103948 AGGAACTAGAACAAATCTCAAACATG 57.896 34.615 0.00 0.00 39.71 3.21
2759 4222 7.175641 AGGAACTAGAACAAATCTCAAACATGG 59.824 37.037 0.00 0.00 39.71 3.66
2760 4223 7.040409 GGAACTAGAACAAATCTCAAACATGGT 60.040 37.037 0.00 0.00 39.71 3.55
2761 4224 7.206981 ACTAGAACAAATCTCAAACATGGTG 57.793 36.000 0.00 0.00 39.71 4.17
2762 4225 6.998074 ACTAGAACAAATCTCAAACATGGTGA 59.002 34.615 0.00 0.00 39.71 4.02
2763 4226 6.906157 AGAACAAATCTCAAACATGGTGAT 57.094 33.333 0.00 0.00 30.46 3.06
2764 4227 9.166173 CTAGAACAAATCTCAAACATGGTGATA 57.834 33.333 0.00 0.00 39.71 2.15
2765 4228 8.585471 AGAACAAATCTCAAACATGGTGATAT 57.415 30.769 0.00 0.00 30.46 1.63
2766 4229 8.680903 AGAACAAATCTCAAACATGGTGATATC 58.319 33.333 0.00 0.00 30.46 1.63
2767 4230 8.585471 AACAAATCTCAAACATGGTGATATCT 57.415 30.769 3.98 0.00 0.00 1.98
2769 4232 7.830697 ACAAATCTCAAACATGGTGATATCTCA 59.169 33.333 3.98 3.22 0.00 3.27
2771 4234 7.981102 ATCTCAAACATGGTGATATCTCATG 57.019 36.000 24.68 24.68 42.65 3.07
2772 4235 6.293698 TCTCAAACATGGTGATATCTCATGG 58.706 40.000 27.29 17.50 41.64 3.66
2774 4237 5.132480 TCAAACATGGTGATATCTCATGGGA 59.868 40.000 27.29 21.65 41.64 4.37
2775 4238 4.630644 ACATGGTGATATCTCATGGGAC 57.369 45.455 27.29 10.13 41.64 4.46
2776 4239 3.007290 ACATGGTGATATCTCATGGGACG 59.993 47.826 27.29 13.55 41.64 4.79
2777 4240 2.677914 TGGTGATATCTCATGGGACGT 58.322 47.619 0.00 0.00 32.98 4.34
2778 4241 3.038280 TGGTGATATCTCATGGGACGTT 58.962 45.455 0.00 0.00 32.98 3.99
2779 4242 3.069586 TGGTGATATCTCATGGGACGTTC 59.930 47.826 0.00 0.00 32.98 3.95
2781 4244 2.296190 TGATATCTCATGGGACGTTCCG 59.704 50.000 8.75 0.00 37.43 4.30
2782 4245 1.037493 TATCTCATGGGACGTTCCGG 58.963 55.000 8.75 2.85 37.43 5.14
2783 4246 0.686441 ATCTCATGGGACGTTCCGGA 60.686 55.000 8.75 0.00 37.43 5.14
2785 4248 0.460284 CTCATGGGACGTTCCGGAAG 60.460 60.000 19.50 14.20 37.43 3.46
2798 4261 1.153349 CGGAAGGGGTGCTCTAAGC 60.153 63.158 0.00 0.00 42.82 3.09
2829 4292 2.706636 CGATCCGCCATTGTTCCAT 58.293 52.632 0.00 0.00 0.00 3.41
2830 4293 0.308684 CGATCCGCCATTGTTCCATG 59.691 55.000 0.00 0.00 0.00 3.66
2831 4294 1.392589 GATCCGCCATTGTTCCATGT 58.607 50.000 0.00 0.00 0.00 3.21
2832 4295 1.334869 GATCCGCCATTGTTCCATGTC 59.665 52.381 0.00 0.00 0.00 3.06
2833 4296 0.679640 TCCGCCATTGTTCCATGTCC 60.680 55.000 0.00 0.00 0.00 4.02
2834 4297 1.429021 CGCCATTGTTCCATGTCCG 59.571 57.895 0.00 0.00 0.00 4.79
2835 4298 1.024046 CGCCATTGTTCCATGTCCGA 61.024 55.000 0.00 0.00 0.00 4.55
2837 4300 0.734889 CCATTGTTCCATGTCCGAGC 59.265 55.000 0.00 0.00 0.00 5.03
2838 4301 0.374758 CATTGTTCCATGTCCGAGCG 59.625 55.000 0.00 0.00 0.00 5.03
2840 4303 3.195698 GTTCCATGTCCGAGCGGC 61.196 66.667 3.59 0.00 34.68 6.53
2842 4305 3.664025 TTCCATGTCCGAGCGGCAG 62.664 63.158 1.45 0.00 34.68 4.85
2855 4318 2.515523 GGCAGCCGCTGATGATGT 60.516 61.111 24.80 0.00 38.60 3.06
2856 4319 2.117156 GGCAGCCGCTGATGATGTT 61.117 57.895 24.80 0.00 38.60 2.71
2857 4320 1.063649 GCAGCCGCTGATGATGTTG 59.936 57.895 24.80 0.00 32.44 3.33
2858 4321 1.725665 CAGCCGCTGATGATGTTGG 59.274 57.895 15.74 0.00 32.44 3.77
2860 4323 3.113745 CCGCTGATGATGTTGGCC 58.886 61.111 0.00 0.00 0.00 5.36
2861 4324 2.711311 CGCTGATGATGTTGGCCG 59.289 61.111 0.00 0.00 0.00 6.13
2863 4326 2.484062 GCTGATGATGTTGGCCGGG 61.484 63.158 2.18 0.00 0.00 5.73
2864 4327 2.440065 TGATGATGTTGGCCGGGC 60.440 61.111 23.42 23.42 0.00 6.13
2866 4329 1.754234 GATGATGTTGGCCGGGCTT 60.754 57.895 29.87 11.25 0.00 4.35
2868 4331 3.451894 GATGTTGGCCGGGCTTGG 61.452 66.667 29.87 0.00 0.00 3.61
2878 4341 4.372999 GGGCTTGGCTGCTTCCCT 62.373 66.667 0.00 0.00 34.19 4.20
2879 4342 2.283460 GGCTTGGCTGCTTCCCTT 60.283 61.111 0.00 0.00 0.00 3.95
2880 4343 1.910276 GGCTTGGCTGCTTCCCTTT 60.910 57.895 0.00 0.00 0.00 3.11
2883 4346 1.331214 CTTGGCTGCTTCCCTTTGAA 58.669 50.000 0.00 0.00 0.00 2.69
2891 4354 0.600057 CTTCCCTTTGAAGGTGCAGC 59.400 55.000 8.11 8.11 45.66 5.25
2892 4355 0.106268 TTCCCTTTGAAGGTGCAGCA 60.106 50.000 19.63 0.00 44.98 4.41
2894 4357 0.825010 CCCTTTGAAGGTGCAGCAGT 60.825 55.000 19.63 5.10 44.98 4.40
2896 4359 1.000938 CCTTTGAAGGTGCAGCAGTTC 60.001 52.381 19.63 14.20 41.41 3.01
2897 4360 1.000938 CTTTGAAGGTGCAGCAGTTCC 60.001 52.381 19.63 0.00 0.00 3.62
2898 4361 0.183492 TTGAAGGTGCAGCAGTTCCT 59.817 50.000 19.63 1.42 0.00 3.36
2899 4362 0.250467 TGAAGGTGCAGCAGTTCCTC 60.250 55.000 19.63 5.10 0.00 3.71
2900 4363 0.036022 GAAGGTGCAGCAGTTCCTCT 59.964 55.000 19.63 0.00 0.00 3.69
2902 4365 1.376553 GGTGCAGCAGTTCCTCTCC 60.377 63.158 11.86 0.00 0.00 3.71
2903 4366 1.372683 GTGCAGCAGTTCCTCTCCA 59.627 57.895 0.00 0.00 0.00 3.86
2904 4367 0.035630 GTGCAGCAGTTCCTCTCCAT 60.036 55.000 0.00 0.00 0.00 3.41
2905 4368 0.251354 TGCAGCAGTTCCTCTCCATC 59.749 55.000 0.00 0.00 0.00 3.51
2907 4370 0.907486 CAGCAGTTCCTCTCCATCCA 59.093 55.000 0.00 0.00 0.00 3.41
2908 4371 1.134461 CAGCAGTTCCTCTCCATCCAG 60.134 57.143 0.00 0.00 0.00 3.86
2909 4372 1.198713 GCAGTTCCTCTCCATCCAGA 58.801 55.000 0.00 0.00 0.00 3.86
2910 4373 1.767681 GCAGTTCCTCTCCATCCAGAT 59.232 52.381 0.00 0.00 0.00 2.90
2911 4374 2.172293 GCAGTTCCTCTCCATCCAGATT 59.828 50.000 0.00 0.00 0.00 2.40
2913 4376 4.197750 CAGTTCCTCTCCATCCAGATTTG 58.802 47.826 0.00 0.00 0.00 2.32
2914 4377 2.948315 GTTCCTCTCCATCCAGATTTGC 59.052 50.000 0.00 0.00 0.00 3.68
2915 4378 1.492176 TCCTCTCCATCCAGATTTGCC 59.508 52.381 0.00 0.00 0.00 4.52
2917 4380 2.573369 CTCTCCATCCAGATTTGCCAG 58.427 52.381 0.00 0.00 0.00 4.85
2918 4381 1.030457 CTCCATCCAGATTTGCCAGC 58.970 55.000 0.00 0.00 0.00 4.85
2919 4382 0.332293 TCCATCCAGATTTGCCAGCA 59.668 50.000 0.00 0.00 0.00 4.41
2920 4383 0.744874 CCATCCAGATTTGCCAGCAG 59.255 55.000 0.00 0.00 0.00 4.24
2921 4384 1.683938 CCATCCAGATTTGCCAGCAGA 60.684 52.381 0.00 0.00 0.00 4.26
2923 4386 1.758936 TCCAGATTTGCCAGCAGATG 58.241 50.000 0.00 0.00 0.00 2.90
2924 4387 1.282738 TCCAGATTTGCCAGCAGATGA 59.717 47.619 0.00 0.00 0.00 2.92
2925 4388 1.676529 CCAGATTTGCCAGCAGATGAG 59.323 52.381 0.00 0.00 0.00 2.90
2926 4389 1.065701 CAGATTTGCCAGCAGATGAGC 59.934 52.381 0.00 0.00 0.00 4.26
2927 4390 0.029035 GATTTGCCAGCAGATGAGCG 59.971 55.000 0.00 0.00 40.15 5.03
2928 4391 2.001361 ATTTGCCAGCAGATGAGCGC 62.001 55.000 0.00 0.00 40.15 5.92
2931 4394 2.478890 GCCAGCAGATGAGCGCAAT 61.479 57.895 11.47 1.82 40.15 3.56
2932 4395 1.647629 CCAGCAGATGAGCGCAATC 59.352 57.895 11.47 12.77 40.15 2.67
2933 4396 1.093496 CCAGCAGATGAGCGCAATCA 61.093 55.000 20.92 12.96 40.15 2.57
2934 4397 0.945099 CAGCAGATGAGCGCAATCAT 59.055 50.000 20.92 16.80 42.62 2.45
2935 4398 0.945099 AGCAGATGAGCGCAATCATG 59.055 50.000 16.02 14.35 40.02 3.07
2936 4399 0.040336 GCAGATGAGCGCAATCATGG 60.040 55.000 16.02 9.46 40.02 3.66
2937 4400 1.589803 CAGATGAGCGCAATCATGGA 58.410 50.000 16.02 0.00 40.02 3.41
2938 4401 2.152016 CAGATGAGCGCAATCATGGAT 58.848 47.619 16.02 0.78 40.02 3.41
2941 4404 2.855660 TGAGCGCAATCATGGATTTG 57.144 45.000 11.47 0.00 28.87 2.32
2942 4405 2.367486 TGAGCGCAATCATGGATTTGA 58.633 42.857 11.47 0.00 28.87 2.69
2943 4406 2.097954 TGAGCGCAATCATGGATTTGAC 59.902 45.455 11.47 1.02 28.87 3.18
2944 4407 1.064505 AGCGCAATCATGGATTTGACG 59.935 47.619 11.47 10.19 28.87 4.35
2945 4408 1.469917 CGCAATCATGGATTTGACGC 58.530 50.000 7.77 0.00 28.87 5.19
2946 4409 1.843992 GCAATCATGGATTTGACGCC 58.156 50.000 7.77 0.00 28.87 5.68
2950 4413 4.107622 CAATCATGGATTTGACGCCTTTC 58.892 43.478 0.00 0.00 28.87 2.62
2951 4414 2.091541 TCATGGATTTGACGCCTTTCC 58.908 47.619 0.00 0.00 0.00 3.13
2952 4415 2.094675 CATGGATTTGACGCCTTTCCT 58.905 47.619 0.00 0.00 0.00 3.36
2953 4416 1.533625 TGGATTTGACGCCTTTCCTG 58.466 50.000 0.00 0.00 0.00 3.86
2954 4417 0.811281 GGATTTGACGCCTTTCCTGG 59.189 55.000 0.00 0.00 0.00 4.45
2956 4419 2.617021 GGATTTGACGCCTTTCCTGGTA 60.617 50.000 0.00 0.00 0.00 3.25
2958 4421 0.035739 TTGACGCCTTTCCTGGTACC 59.964 55.000 4.43 4.43 0.00 3.34
2959 4422 1.447314 GACGCCTTTCCTGGTACCG 60.447 63.158 7.57 1.95 0.00 4.02
2960 4423 2.818274 CGCCTTTCCTGGTACCGC 60.818 66.667 7.57 1.27 0.00 5.68
2961 4424 2.818274 GCCTTTCCTGGTACCGCG 60.818 66.667 7.57 0.00 0.00 6.46
2962 4425 2.125269 CCTTTCCTGGTACCGCGG 60.125 66.667 26.86 26.86 0.00 6.46
2963 4426 2.818274 CTTTCCTGGTACCGCGGC 60.818 66.667 28.58 10.15 0.00 6.53
2964 4427 4.745751 TTTCCTGGTACCGCGGCG 62.746 66.667 28.58 16.78 0.00 6.46
2981 4444 2.246739 CGGCGGCAATGACGATCAT 61.247 57.895 14.82 0.00 45.34 2.45
2983 4446 0.381801 GGCGGCAATGACGATCATTT 59.618 50.000 14.82 0.00 44.03 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 91 4.778427 TCCTTTCTCTAACCCTCTCTTTCC 59.222 45.833 0.00 0.00 0.00 3.13
396 402 7.565029 TGACTTCTCTTGATAACATATCCTCCA 59.435 37.037 0.00 0.00 0.00 3.86
613 619 5.163513 CCCTTTTAAAGCATGTACAGCAAG 58.836 41.667 16.27 11.21 0.00 4.01
614 620 4.560513 GCCCTTTTAAAGCATGTACAGCAA 60.561 41.667 16.27 3.43 0.00 3.91
615 621 3.056891 GCCCTTTTAAAGCATGTACAGCA 60.057 43.478 16.27 0.00 0.00 4.41
616 622 3.056891 TGCCCTTTTAAAGCATGTACAGC 60.057 43.478 0.33 5.47 0.00 4.40
617 623 4.782019 TGCCCTTTTAAAGCATGTACAG 57.218 40.909 0.33 0.00 0.00 2.74
618 624 7.416964 AATATGCCCTTTTAAAGCATGTACA 57.583 32.000 18.62 0.00 46.30 2.90
619 625 7.254421 GCAAATATGCCCTTTTAAAGCATGTAC 60.254 37.037 18.62 6.59 46.30 2.90
620 626 6.760770 GCAAATATGCCCTTTTAAAGCATGTA 59.239 34.615 18.62 5.22 46.30 2.29
621 627 5.585844 GCAAATATGCCCTTTTAAAGCATGT 59.414 36.000 18.62 12.02 46.30 3.21
622 628 6.051646 GCAAATATGCCCTTTTAAAGCATG 57.948 37.500 18.62 8.50 46.30 4.06
654 660 8.270744 AGTGAGAATATGATTATATGAAGGGCC 58.729 37.037 0.00 0.00 30.00 5.80
655 661 9.107177 CAGTGAGAATATGATTATATGAAGGGC 57.893 37.037 0.00 0.00 30.00 5.19
697 703 8.100791 AGACAAAAACTAGGTAGCACATTATCA 58.899 33.333 0.00 0.00 0.00 2.15
714 720 8.911247 AAACTGAGAAATACACAGACAAAAAC 57.089 30.769 0.00 0.00 39.04 2.43
722 728 6.483307 TGTTCCAGAAACTGAGAAATACACAG 59.517 38.462 0.00 0.00 41.66 3.66
784 791 7.440856 TGCTTAAACATTCCATCTTTGGTTTTC 59.559 33.333 0.00 0.00 44.06 2.29
869 877 5.047021 TCCTCCTGCCATTTTATATCTCTCG 60.047 44.000 0.00 0.00 0.00 4.04
908 916 4.112634 CACAGGAACGATCGATGTAATGT 58.887 43.478 24.34 14.65 0.00 2.71
909 917 4.359706 TCACAGGAACGATCGATGTAATG 58.640 43.478 24.34 14.04 0.00 1.90
910 918 4.611943 CTCACAGGAACGATCGATGTAAT 58.388 43.478 24.34 0.00 0.00 1.89
911 919 3.733988 GCTCACAGGAACGATCGATGTAA 60.734 47.826 24.34 6.19 0.00 2.41
912 920 2.223502 GCTCACAGGAACGATCGATGTA 60.224 50.000 24.34 8.62 0.00 2.29
953 961 6.238593 GCTTCTTCCTAGCAAATTGGAGTATG 60.239 42.308 0.00 0.00 38.51 2.39
955 963 5.186198 GCTTCTTCCTAGCAAATTGGAGTA 58.814 41.667 0.00 0.00 38.51 2.59
968 976 2.949177 TGGCTGTTTGCTTCTTCCTA 57.051 45.000 0.00 0.00 42.39 2.94
971 979 5.713025 TCAAATATGGCTGTTTGCTTCTTC 58.287 37.500 5.38 0.00 42.39 2.87
994 1002 1.889105 CCGACGCTGCCATTGCTAT 60.889 57.895 0.00 0.00 38.71 2.97
1012 1020 3.188786 GACGATGACGCTGCACCC 61.189 66.667 0.00 0.00 43.96 4.61
1021 1029 0.454620 ACGACGAGCAAGACGATGAC 60.455 55.000 0.00 0.00 33.85 3.06
1022 1030 0.454452 CACGACGAGCAAGACGATGA 60.454 55.000 0.00 0.00 33.85 2.92
1715 1729 2.456948 CGAGCGAGCGAGAGAGTGA 61.457 63.158 0.00 0.00 0.00 3.41
1717 1731 3.871574 GCGAGCGAGCGAGAGAGT 61.872 66.667 1.41 0.00 0.00 3.24
1719 1733 3.568743 GAGCGAGCGAGCGAGAGA 61.569 66.667 1.41 0.00 43.00 3.10
1722 1736 3.506312 GAGAGAGCGAGCGAGCGAG 62.506 68.421 1.41 0.00 43.00 5.03
1723 1737 3.568743 GAGAGAGCGAGCGAGCGA 61.569 66.667 1.41 0.00 43.00 4.93
1724 1738 2.591129 AAAGAGAGAGCGAGCGAGCG 62.591 60.000 0.00 0.00 43.00 5.03
1725 1739 0.865639 GAAAGAGAGAGCGAGCGAGC 60.866 60.000 0.00 0.00 37.41 5.03
1765 1779 6.009908 AGATTCCAAGACCATCATCAATCA 57.990 37.500 0.00 0.00 0.00 2.57
1766 1780 7.222872 AGTAGATTCCAAGACCATCATCAATC 58.777 38.462 0.00 0.00 0.00 2.67
1767 1781 7.146715 AGTAGATTCCAAGACCATCATCAAT 57.853 36.000 0.00 0.00 0.00 2.57
1777 1792 5.236047 CAGCTGCATAAGTAGATTCCAAGAC 59.764 44.000 0.00 0.00 0.00 3.01
1788 1803 3.786656 CTGCCCAGCTGCATAAGTA 57.213 52.632 8.66 0.00 41.16 2.24
1789 1804 4.651867 CTGCCCAGCTGCATAAGT 57.348 55.556 8.66 0.00 41.16 2.24
1825 1840 0.179089 CAGGAGTCGGGAATCTGCTG 60.179 60.000 0.00 0.00 41.88 4.41
1827 1842 1.144936 CCAGGAGTCGGGAATCTGC 59.855 63.158 0.00 0.00 0.00 4.26
1829 1844 1.007238 TCTTCCAGGAGTCGGGAATCT 59.993 52.381 13.48 0.00 44.16 2.40
1883 1898 7.174946 GGACAGTATGGATTTTTCACTTTCAGA 59.825 37.037 0.00 0.00 43.62 3.27
1884 1899 7.040478 TGGACAGTATGGATTTTTCACTTTCAG 60.040 37.037 0.00 0.00 43.62 3.02
1885 1900 6.775142 TGGACAGTATGGATTTTTCACTTTCA 59.225 34.615 0.00 0.00 43.62 2.69
1886 1901 7.214467 TGGACAGTATGGATTTTTCACTTTC 57.786 36.000 0.00 0.00 43.62 2.62
1889 1904 5.126061 GCATGGACAGTATGGATTTTTCACT 59.874 40.000 0.00 0.00 43.62 3.41
1890 1905 5.105797 TGCATGGACAGTATGGATTTTTCAC 60.106 40.000 0.00 0.00 43.62 3.18
1891 1906 5.015515 TGCATGGACAGTATGGATTTTTCA 58.984 37.500 0.00 0.00 43.62 2.69
1892 1907 5.581126 TGCATGGACAGTATGGATTTTTC 57.419 39.130 0.00 0.00 43.62 2.29
1910 1946 2.033801 GCAATCGAGCTTAACCATGCAT 59.966 45.455 0.00 0.00 33.00 3.96
1933 1969 4.332268 GGAAGACATCAGAATTCAGCTCAC 59.668 45.833 8.44 0.00 0.00 3.51
1935 1971 4.511527 TGGAAGACATCAGAATTCAGCTC 58.488 43.478 8.44 0.00 0.00 4.09
2117 2162 1.078759 GCGTTGACCACTCGATCTGG 61.079 60.000 7.57 7.57 34.62 3.86
2120 2165 0.924090 GATGCGTTGACCACTCGATC 59.076 55.000 0.00 0.00 0.00 3.69
2121 2166 0.246360 TGATGCGTTGACCACTCGAT 59.754 50.000 0.00 0.00 0.00 3.59
2122 2167 0.246360 ATGATGCGTTGACCACTCGA 59.754 50.000 0.00 0.00 0.00 4.04
2123 2168 0.371301 CATGATGCGTTGACCACTCG 59.629 55.000 0.00 0.00 0.00 4.18
2155 2200 9.423427 GCTATTACATCGATCAGTAATACTACG 57.577 37.037 17.81 12.35 40.38 3.51
2224 2271 9.745880 CTTTGATGCAATCTGCTCTTATAATTT 57.254 29.630 0.00 0.00 45.81 1.82
2225 2272 8.358148 CCTTTGATGCAATCTGCTCTTATAATT 58.642 33.333 0.00 0.00 45.81 1.40
2226 2273 7.039923 CCCTTTGATGCAATCTGCTCTTATAAT 60.040 37.037 0.00 0.00 45.81 1.28
2227 2274 6.263842 CCCTTTGATGCAATCTGCTCTTATAA 59.736 38.462 0.00 0.00 45.81 0.98
2265 2312 6.904463 AACGGAAAACCCATGTAAATAGTT 57.096 33.333 0.00 0.00 34.14 2.24
2312 2359 0.539669 AGTAAACACAAGCCAGGGCC 60.540 55.000 6.70 0.00 43.17 5.80
2375 2422 4.149046 GCTCTTTGACTAGACAGAAACGTG 59.851 45.833 0.00 0.00 0.00 4.49
2401 2448 7.012421 GTCCAGAAAATGTAATGTAGATGGTCC 59.988 40.741 0.00 0.00 0.00 4.46
2528 2578 9.072294 TGAGTTTTCTTTTTCTCTTTTTAAGCG 57.928 29.630 0.00 0.00 0.00 4.68
2541 2593 4.161565 GTGGGAAGGGTGAGTTTTCTTTTT 59.838 41.667 0.00 0.00 0.00 1.94
2576 2628 0.250989 TGCTTTTTAGGTGGGTCCCG 60.251 55.000 2.65 0.00 36.75 5.14
2651 2703 1.331214 AACCCAGCAATGTTGGACAG 58.669 50.000 17.94 3.59 37.96 3.51
2652 2704 1.686052 GAAACCCAGCAATGTTGGACA 59.314 47.619 17.94 0.00 37.96 4.02
2653 2705 1.686052 TGAAACCCAGCAATGTTGGAC 59.314 47.619 17.94 6.65 37.96 4.02
2659 2711 4.460948 AAGCTAATGAAACCCAGCAATG 57.539 40.909 0.00 0.00 36.47 2.82
2660 2712 4.098501 GCTAAGCTAATGAAACCCAGCAAT 59.901 41.667 0.00 0.00 36.47 3.56
2662 2714 3.016736 GCTAAGCTAATGAAACCCAGCA 58.983 45.455 0.00 0.00 36.47 4.41
2663 2715 3.016736 TGCTAAGCTAATGAAACCCAGC 58.983 45.455 0.00 0.00 0.00 4.85
2665 2717 4.568072 TCTGCTAAGCTAATGAAACCCA 57.432 40.909 0.00 0.00 0.00 4.51
2666 2718 4.336713 CCTTCTGCTAAGCTAATGAAACCC 59.663 45.833 0.00 0.00 0.00 4.11
2667 2719 4.336713 CCCTTCTGCTAAGCTAATGAAACC 59.663 45.833 0.00 0.00 0.00 3.27
2668 2720 5.186198 TCCCTTCTGCTAAGCTAATGAAAC 58.814 41.667 0.00 0.00 0.00 2.78
2670 2722 4.471386 ACTCCCTTCTGCTAAGCTAATGAA 59.529 41.667 0.00 0.00 0.00 2.57
2671 2723 4.033709 ACTCCCTTCTGCTAAGCTAATGA 58.966 43.478 0.00 0.00 0.00 2.57
2672 2724 4.125703 CACTCCCTTCTGCTAAGCTAATG 58.874 47.826 0.00 0.00 0.00 1.90
2673 2725 4.033709 TCACTCCCTTCTGCTAAGCTAAT 58.966 43.478 0.00 0.00 0.00 1.73
2674 2726 3.195825 GTCACTCCCTTCTGCTAAGCTAA 59.804 47.826 0.00 0.00 0.00 3.09
2676 2728 1.552792 GTCACTCCCTTCTGCTAAGCT 59.447 52.381 0.00 0.00 0.00 3.74
2677 2729 1.276421 TGTCACTCCCTTCTGCTAAGC 59.724 52.381 0.00 0.00 0.00 3.09
2678 2730 3.259374 TCTTGTCACTCCCTTCTGCTAAG 59.741 47.826 0.00 0.00 0.00 2.18
2679 2731 3.239449 TCTTGTCACTCCCTTCTGCTAA 58.761 45.455 0.00 0.00 0.00 3.09
2680 2732 2.828520 CTCTTGTCACTCCCTTCTGCTA 59.171 50.000 0.00 0.00 0.00 3.49
2681 2733 1.622811 CTCTTGTCACTCCCTTCTGCT 59.377 52.381 0.00 0.00 0.00 4.24
2682 2734 1.346068 ACTCTTGTCACTCCCTTCTGC 59.654 52.381 0.00 0.00 0.00 4.26
2683 2735 3.760580 AACTCTTGTCACTCCCTTCTG 57.239 47.619 0.00 0.00 0.00 3.02
2684 2736 3.711704 TCAAACTCTTGTCACTCCCTTCT 59.288 43.478 0.00 0.00 33.94 2.85
2685 2737 4.073293 TCAAACTCTTGTCACTCCCTTC 57.927 45.455 0.00 0.00 33.94 3.46
2686 2738 4.103153 TGATCAAACTCTTGTCACTCCCTT 59.897 41.667 0.00 0.00 33.94 3.95
2689 2741 5.049818 CACTTGATCAAACTCTTGTCACTCC 60.050 44.000 9.88 0.00 33.94 3.85
2690 2742 5.755375 TCACTTGATCAAACTCTTGTCACTC 59.245 40.000 9.88 0.00 33.94 3.51
2691 2743 5.674525 TCACTTGATCAAACTCTTGTCACT 58.325 37.500 9.88 0.00 33.94 3.41
2692 2744 5.991328 TCACTTGATCAAACTCTTGTCAC 57.009 39.130 9.88 0.00 33.94 3.67
2705 2757 1.154205 CGCCCACCGATCACTTGATC 61.154 60.000 8.90 8.90 45.60 2.92
2709 2761 0.673644 CTTTCGCCCACCGATCACTT 60.674 55.000 0.00 0.00 46.81 3.16
2710 2762 1.079127 CTTTCGCCCACCGATCACT 60.079 57.895 0.00 0.00 46.81 3.41
2712 2764 0.035598 TTTCTTTCGCCCACCGATCA 59.964 50.000 0.00 0.00 46.81 2.92
2713 2765 1.161843 TTTTCTTTCGCCCACCGATC 58.838 50.000 0.00 0.00 46.81 3.69
2714 2766 1.539827 CTTTTTCTTTCGCCCACCGAT 59.460 47.619 0.00 0.00 46.81 4.18
2715 2767 0.948678 CTTTTTCTTTCGCCCACCGA 59.051 50.000 0.00 0.00 45.77 4.69
2717 2769 1.324383 TCCTTTTTCTTTCGCCCACC 58.676 50.000 0.00 0.00 0.00 4.61
2718 2770 2.361119 AGTTCCTTTTTCTTTCGCCCAC 59.639 45.455 0.00 0.00 0.00 4.61
2719 2771 2.661718 AGTTCCTTTTTCTTTCGCCCA 58.338 42.857 0.00 0.00 0.00 5.36
2720 2772 4.070009 TCTAGTTCCTTTTTCTTTCGCCC 58.930 43.478 0.00 0.00 0.00 6.13
2721 2773 5.008316 TGTTCTAGTTCCTTTTTCTTTCGCC 59.992 40.000 0.00 0.00 0.00 5.54
2722 2774 6.056428 TGTTCTAGTTCCTTTTTCTTTCGC 57.944 37.500 0.00 0.00 0.00 4.70
2723 2775 9.170584 GATTTGTTCTAGTTCCTTTTTCTTTCG 57.829 33.333 0.00 0.00 0.00 3.46
2726 2778 9.408648 TGAGATTTGTTCTAGTTCCTTTTTCTT 57.591 29.630 0.00 0.00 33.74 2.52
2727 2779 8.980481 TGAGATTTGTTCTAGTTCCTTTTTCT 57.020 30.769 0.00 0.00 33.74 2.52
2729 2781 9.803315 GTTTGAGATTTGTTCTAGTTCCTTTTT 57.197 29.630 0.00 0.00 33.74 1.94
2734 4197 7.040409 ACCATGTTTGAGATTTGTTCTAGTTCC 60.040 37.037 0.00 0.00 33.74 3.62
2736 4199 7.502226 TCACCATGTTTGAGATTTGTTCTAGTT 59.498 33.333 0.00 0.00 33.74 2.24
2738 4201 7.439157 TCACCATGTTTGAGATTTGTTCTAG 57.561 36.000 0.00 0.00 33.74 2.43
2739 4202 9.685276 ATATCACCATGTTTGAGATTTGTTCTA 57.315 29.630 0.00 0.00 33.74 2.10
2744 4207 8.217131 TGAGATATCACCATGTTTGAGATTTG 57.783 34.615 5.32 0.00 0.00 2.32
2746 4209 7.447545 CCATGAGATATCACCATGTTTGAGATT 59.552 37.037 24.25 0.00 36.77 2.40
2751 4214 5.240183 GTCCCATGAGATATCACCATGTTTG 59.760 44.000 24.25 16.94 36.77 2.93
2758 4221 3.555168 GGAACGTCCCATGAGATATCACC 60.555 52.174 5.32 0.00 0.00 4.02
2759 4222 3.654414 GGAACGTCCCATGAGATATCAC 58.346 50.000 5.32 0.00 0.00 3.06
2776 4239 1.262640 TAGAGCACCCCTTCCGGAAC 61.263 60.000 14.35 1.95 0.00 3.62
2777 4240 0.545787 TTAGAGCACCCCTTCCGGAA 60.546 55.000 17.73 17.73 0.00 4.30
2778 4241 0.976073 CTTAGAGCACCCCTTCCGGA 60.976 60.000 0.00 0.00 0.00 5.14
2779 4242 1.522569 CTTAGAGCACCCCTTCCGG 59.477 63.158 0.00 0.00 0.00 5.14
2781 4244 4.966123 GCTTAGAGCACCCCTTCC 57.034 61.111 0.00 0.00 41.89 3.46
2790 4253 1.010685 GGCGCGAAATGCTTAGAGC 60.011 57.895 12.10 0.00 43.27 4.09
2791 4254 1.643832 GGGCGCGAAATGCTTAGAG 59.356 57.895 12.10 0.00 43.27 2.43
2794 4257 3.871574 GCGGGCGCGAAATGCTTA 61.872 61.111 28.66 0.00 43.27 3.09
2810 4273 2.112198 TGGAACAATGGCGGATCGC 61.112 57.895 3.48 3.48 45.25 4.58
2819 4282 2.928676 CCGCTCGGACATGGAACAATG 61.929 57.143 1.35 0.00 39.15 2.82
2821 4284 1.375396 CCGCTCGGACATGGAACAA 60.375 57.895 1.35 0.00 39.15 2.83
2822 4285 2.264480 CCGCTCGGACATGGAACA 59.736 61.111 1.35 0.00 39.93 3.18
2823 4286 3.195698 GCCGCTCGGACATGGAAC 61.196 66.667 13.11 0.00 37.50 3.62
2825 4288 4.147449 CTGCCGCTCGGACATGGA 62.147 66.667 13.11 0.00 37.50 3.41
2838 4301 2.117156 AACATCATCAGCGGCTGCC 61.117 57.895 24.78 9.11 44.31 4.85
2840 4303 1.725665 CCAACATCATCAGCGGCTG 59.274 57.895 23.72 23.72 0.00 4.85
2842 4305 2.410469 GCCAACATCATCAGCGGC 59.590 61.111 0.00 0.00 0.00 6.53
2843 4306 2.827051 CGGCCAACATCATCAGCGG 61.827 63.158 2.24 0.00 0.00 5.52
2844 4307 2.711311 CGGCCAACATCATCAGCG 59.289 61.111 2.24 0.00 0.00 5.18
2845 4308 2.484062 CCCGGCCAACATCATCAGC 61.484 63.158 2.24 0.00 0.00 4.26
2846 4309 2.484062 GCCCGGCCAACATCATCAG 61.484 63.158 2.24 0.00 0.00 2.90
2848 4311 1.754234 AAGCCCGGCCAACATCATC 60.754 57.895 5.55 0.00 0.00 2.92
2849 4312 2.053865 CAAGCCCGGCCAACATCAT 61.054 57.895 5.55 0.00 0.00 2.45
2850 4313 2.676121 CAAGCCCGGCCAACATCA 60.676 61.111 5.55 0.00 0.00 3.07
2851 4314 3.451894 CCAAGCCCGGCCAACATC 61.452 66.667 5.55 0.00 0.00 3.06
2861 4324 3.893961 AAGGGAAGCAGCCAAGCCC 62.894 63.158 0.00 0.00 39.12 5.19
2863 4326 1.181098 TCAAAGGGAAGCAGCCAAGC 61.181 55.000 0.00 0.00 0.00 4.01
2864 4327 1.271656 CTTCAAAGGGAAGCAGCCAAG 59.728 52.381 0.00 0.00 45.99 3.61
2866 4329 3.040965 CTTCAAAGGGAAGCAGCCA 57.959 52.632 0.00 0.00 45.99 4.75
2877 4340 1.000938 GGAACTGCTGCACCTTCAAAG 60.001 52.381 14.20 0.00 0.00 2.77
2878 4341 1.032014 GGAACTGCTGCACCTTCAAA 58.968 50.000 14.20 0.00 0.00 2.69
2879 4342 0.183492 AGGAACTGCTGCACCTTCAA 59.817 50.000 14.20 0.00 37.18 2.69
2880 4343 0.250467 GAGGAACTGCTGCACCTTCA 60.250 55.000 11.11 0.00 41.55 3.02
2883 4346 1.676384 GAGAGGAACTGCTGCACCT 59.324 57.895 9.77 9.77 41.55 4.00
2886 4349 0.251354 GATGGAGAGGAACTGCTGCA 59.749 55.000 0.88 0.88 41.55 4.41
2887 4350 0.463474 GGATGGAGAGGAACTGCTGC 60.463 60.000 0.00 0.00 41.55 5.25
2888 4351 0.907486 TGGATGGAGAGGAACTGCTG 59.093 55.000 0.00 0.00 41.55 4.41
2889 4352 1.202330 CTGGATGGAGAGGAACTGCT 58.798 55.000 0.00 0.00 41.55 4.24
2890 4353 1.198713 TCTGGATGGAGAGGAACTGC 58.801 55.000 0.00 0.00 41.55 4.40
2891 4354 4.197750 CAAATCTGGATGGAGAGGAACTG 58.802 47.826 0.00 0.00 41.55 3.16
2894 4357 2.092212 GGCAAATCTGGATGGAGAGGAA 60.092 50.000 0.00 0.00 0.00 3.36
2896 4359 1.213678 TGGCAAATCTGGATGGAGAGG 59.786 52.381 0.00 0.00 0.00 3.69
2897 4360 2.573369 CTGGCAAATCTGGATGGAGAG 58.427 52.381 0.00 0.00 0.00 3.20
2898 4361 1.409241 GCTGGCAAATCTGGATGGAGA 60.409 52.381 0.00 0.00 0.00 3.71
2899 4362 1.030457 GCTGGCAAATCTGGATGGAG 58.970 55.000 0.00 0.00 0.00 3.86
2900 4363 0.332293 TGCTGGCAAATCTGGATGGA 59.668 50.000 0.00 0.00 0.00 3.41
2902 4365 1.758936 TCTGCTGGCAAATCTGGATG 58.241 50.000 0.00 0.00 0.00 3.51
2903 4366 2.092049 TCATCTGCTGGCAAATCTGGAT 60.092 45.455 0.00 0.00 0.00 3.41
2904 4367 1.282738 TCATCTGCTGGCAAATCTGGA 59.717 47.619 0.00 0.00 0.00 3.86
2905 4368 1.676529 CTCATCTGCTGGCAAATCTGG 59.323 52.381 0.00 0.00 0.00 3.86
2907 4370 1.390565 GCTCATCTGCTGGCAAATCT 58.609 50.000 0.00 0.00 0.00 2.40
2908 4371 0.029035 CGCTCATCTGCTGGCAAATC 59.971 55.000 0.00 0.00 0.00 2.17
2909 4372 2.001361 GCGCTCATCTGCTGGCAAAT 62.001 55.000 0.00 0.00 0.00 2.32
2910 4373 2.693762 GCGCTCATCTGCTGGCAAA 61.694 57.895 0.00 0.00 0.00 3.68
2911 4374 3.129502 GCGCTCATCTGCTGGCAA 61.130 61.111 0.00 0.00 0.00 4.52
2913 4376 2.389866 GATTGCGCTCATCTGCTGGC 62.390 60.000 9.73 0.00 0.00 4.85
2914 4377 1.093496 TGATTGCGCTCATCTGCTGG 61.093 55.000 9.73 0.00 0.00 4.85
2915 4378 0.945099 ATGATTGCGCTCATCTGCTG 59.055 50.000 9.73 0.00 29.85 4.41
2917 4380 0.040336 CCATGATTGCGCTCATCTGC 60.040 55.000 9.73 0.00 33.59 4.26
2918 4381 1.589803 TCCATGATTGCGCTCATCTG 58.410 50.000 9.73 9.98 33.59 2.90
2919 4382 2.563261 ATCCATGATTGCGCTCATCT 57.437 45.000 9.73 0.00 33.59 2.90
2920 4383 3.004002 TCAAATCCATGATTGCGCTCATC 59.996 43.478 9.73 11.07 33.59 2.92
2921 4384 2.953648 TCAAATCCATGATTGCGCTCAT 59.046 40.909 9.73 7.75 36.29 2.90
2923 4386 2.724349 GTCAAATCCATGATTGCGCTC 58.276 47.619 9.73 0.00 32.14 5.03
2924 4387 1.064505 CGTCAAATCCATGATTGCGCT 59.935 47.619 9.73 0.00 32.14 5.92
2925 4388 1.469917 CGTCAAATCCATGATTGCGC 58.530 50.000 0.00 0.00 32.14 6.09
2926 4389 1.469917 GCGTCAAATCCATGATTGCG 58.530 50.000 0.00 6.35 32.14 4.85
2927 4390 1.406539 AGGCGTCAAATCCATGATTGC 59.593 47.619 0.00 0.00 32.14 3.56
2928 4391 3.788333 AAGGCGTCAAATCCATGATTG 57.212 42.857 0.00 0.00 32.14 2.67
2931 4394 2.091541 GGAAAGGCGTCAAATCCATGA 58.908 47.619 0.00 0.00 0.00 3.07
2932 4395 2.094675 AGGAAAGGCGTCAAATCCATG 58.905 47.619 8.22 0.00 32.47 3.66
2933 4396 2.094675 CAGGAAAGGCGTCAAATCCAT 58.905 47.619 8.22 0.00 32.47 3.41
2934 4397 1.533625 CAGGAAAGGCGTCAAATCCA 58.466 50.000 8.22 0.00 32.47 3.41
2935 4398 0.811281 CCAGGAAAGGCGTCAAATCC 59.189 55.000 0.00 0.00 0.00 3.01
2936 4399 1.534729 ACCAGGAAAGGCGTCAAATC 58.465 50.000 0.00 0.00 0.00 2.17
2937 4400 2.433436 GTACCAGGAAAGGCGTCAAAT 58.567 47.619 0.00 0.00 0.00 2.32
2938 4401 1.543871 GGTACCAGGAAAGGCGTCAAA 60.544 52.381 7.15 0.00 0.00 2.69
2941 4404 1.447314 CGGTACCAGGAAAGGCGTC 60.447 63.158 13.54 0.00 0.00 5.19
2942 4405 2.660802 CGGTACCAGGAAAGGCGT 59.339 61.111 13.54 0.00 0.00 5.68
2943 4406 2.818274 GCGGTACCAGGAAAGGCG 60.818 66.667 13.54 0.00 0.00 5.52
2944 4407 2.818274 CGCGGTACCAGGAAAGGC 60.818 66.667 13.54 4.09 0.00 4.35
2945 4408 2.125269 CCGCGGTACCAGGAAAGG 60.125 66.667 19.50 4.11 0.00 3.11
2946 4409 2.818274 GCCGCGGTACCAGGAAAG 60.818 66.667 28.70 2.93 0.00 2.62
2962 4425 4.299316 GATCGTCATTGCCGCCGC 62.299 66.667 0.00 0.00 0.00 6.53
2963 4426 1.775039 AATGATCGTCATTGCCGCCG 61.775 55.000 10.97 0.00 44.68 6.46
2964 4427 0.381801 AAATGATCGTCATTGCCGCC 59.618 50.000 12.06 0.00 45.57 6.13
2965 4428 3.924238 AAATGATCGTCATTGCCGC 57.076 47.368 12.06 0.00 45.57 6.53


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

AutoCloner maintained by Alex Coulton.