Multiple sequence alignment - TraesCS3A01G344800

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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 TraesCS3A01G344800 chr3A 100.000 3146 0 0 1 3146 594491193 594494338 0.000000e+00 5810.0
1 TraesCS3A01G344800 chr3A 93.750 48 3 0 1094 1141 170658715 170658762 4.350000e-09 73.1
2 TraesCS3A01G344800 chr3D 92.825 2648 83 50 1 2622 451708843 451711409 0.000000e+00 3738.0
3 TraesCS3A01G344800 chr3D 87.217 2206 99 63 504 2689 451884909 451886951 0.000000e+00 2342.0
4 TraesCS3A01G344800 chr3D 97.826 46 1 0 2889 2934 408647436 408647481 2.600000e-11 80.5
5 TraesCS3A01G344800 chr3D 91.667 48 4 0 1094 1141 157540740 157540693 2.030000e-07 67.6
6 TraesCS3A01G344800 chr3B 91.730 2648 83 50 1 2624 593162602 593165137 0.000000e+00 3552.0
7 TraesCS3A01G344800 chr3B 89.138 2007 85 57 676 2670 593540782 593542667 0.000000e+00 2375.0
8 TraesCS3A01G344800 chr3B 79.927 274 33 14 2637 2889 593165751 593166023 6.930000e-42 182.0
9 TraesCS3A01G344800 chr3B 93.750 48 3 0 1094 1141 228750902 228750855 4.350000e-09 73.1
10 TraesCS3A01G344800 chr1B 88.961 308 34 0 1839 2146 533324012 533323705 6.370000e-102 381.0
11 TraesCS3A01G344800 chr1B 86.111 324 43 2 1277 1599 533324652 533324330 6.460000e-92 348.0
12 TraesCS3A01G344800 chr1A 88.961 308 34 0 1839 2146 495192326 495192019 6.370000e-102 381.0
13 TraesCS3A01G344800 chr1A 87.037 324 40 2 1277 1599 495192933 495192611 6.410000e-97 364.0
14 TraesCS3A01G344800 chr1A 97.826 46 1 0 2889 2934 554474463 554474508 2.600000e-11 80.5
15 TraesCS3A01G344800 chr1D 88.636 308 35 0 1839 2146 397973287 397972980 2.960000e-100 375.0
16 TraesCS3A01G344800 chr1D 85.890 326 42 4 1277 1600 397973932 397973609 8.350000e-91 344.0
17 TraesCS3A01G344800 chr1D 97.826 46 1 0 2889 2934 77984747 77984702 2.600000e-11 80.5
18 TraesCS3A01G344800 chr1D 97.826 46 1 0 2889 2934 111546426 111546471 2.600000e-11 80.5
19 TraesCS3A01G344800 chr1D 97.826 46 1 0 2889 2934 491425089 491425134 2.600000e-11 80.5
20 TraesCS3A01G344800 chr2D 84.709 327 33 15 1277 1590 27837049 27837371 8.470000e-81 311.0
21 TraesCS3A01G344800 chr2A 84.756 328 31 14 1277 1590 29989773 29990095 8.470000e-81 311.0
22 TraesCS3A01G344800 chr2B 83.537 328 35 14 1277 1590 44159063 44159385 3.970000e-74 289.0
23 TraesCS3A01G344800 chr6A 82.712 295 43 6 1838 2128 542430362 542430072 4.030000e-64 255.0
24 TraesCS3A01G344800 chr6B 81.849 292 51 2 1838 2128 592464283 592463993 8.720000e-61 244.0
25 TraesCS3A01G344800 chr5D 97.826 46 1 0 2889 2934 6173086 6173131 2.600000e-11 80.5
26 TraesCS3A01G344800 chr5D 97.826 46 1 0 2889 2934 6272157 6272202 2.600000e-11 80.5
27 TraesCS3A01G344800 chr5D 97.826 46 1 0 2889 2934 512413091 512413046 2.600000e-11 80.5
28 TraesCS3A01G344800 chr4D 97.826 46 1 0 2889 2934 427508415 427508460 2.600000e-11 80.5


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 TraesCS3A01G344800 chr3A 594491193 594494338 3145 False 5810.0 5810 100.0000 1 3146 1 chr3A.!!$F2 3145
1 TraesCS3A01G344800 chr3D 451708843 451711409 2566 False 3738.0 3738 92.8250 1 2622 1 chr3D.!!$F2 2621
2 TraesCS3A01G344800 chr3D 451884909 451886951 2042 False 2342.0 2342 87.2170 504 2689 1 chr3D.!!$F3 2185
3 TraesCS3A01G344800 chr3B 593540782 593542667 1885 False 2375.0 2375 89.1380 676 2670 1 chr3B.!!$F1 1994
4 TraesCS3A01G344800 chr3B 593162602 593166023 3421 False 1867.0 3552 85.8285 1 2889 2 chr3B.!!$F2 2888
5 TraesCS3A01G344800 chr1B 533323705 533324652 947 True 364.5 381 87.5360 1277 2146 2 chr1B.!!$R1 869
6 TraesCS3A01G344800 chr1A 495192019 495192933 914 True 372.5 381 87.9990 1277 2146 2 chr1A.!!$R1 869
7 TraesCS3A01G344800 chr1D 397972980 397973932 952 True 359.5 375 87.2630 1277 2146 2 chr1D.!!$R2 869


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
975 992 0.03563 AGCTAGAAAGGCACCAGCTG 60.036 55.0 6.78 6.78 40.92 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2837 3709 0.03601 AGTACAGTGGTGGCTGCATC 60.036 55.0 0.5 0.0 39.96 3.91 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
71 72 5.402464 GGTTACAACCGACGAAAAGTTAA 57.598 39.130 0.00 0.00 39.66 2.01
72 73 5.197549 GGTTACAACCGACGAAAAGTTAAC 58.802 41.667 0.00 0.00 39.66 2.01
73 74 5.006649 GGTTACAACCGACGAAAAGTTAACT 59.993 40.000 1.12 1.12 39.66 2.24
160 161 2.079925 GAGGAACATGCTTCACACTCC 58.920 52.381 0.00 0.00 0.00 3.85
197 198 4.840005 CGCCCTCTTTCCGCTCCC 62.840 72.222 0.00 0.00 0.00 4.30
240 241 4.152607 TGATCGATCGAGCATCACTAAG 57.847 45.455 30.45 0.00 35.47 2.18
304 305 3.269347 AAACTGTTGCGCGCGACT 61.269 55.556 41.74 26.56 0.00 4.18
306 307 2.695712 AAACTGTTGCGCGCGACTTC 62.696 55.000 41.74 23.74 0.00 3.01
325 326 1.222936 GACATCCTGTCCCTGCCAG 59.777 63.158 0.00 0.00 41.37 4.85
402 406 2.824041 GGCGACGGGAACATGCAT 60.824 61.111 0.00 0.00 0.00 3.96
404 408 1.498865 GGCGACGGGAACATGCATAG 61.499 60.000 0.00 0.00 0.00 2.23
483 493 5.487433 TCACACGATCACATGGTTAATCTT 58.513 37.500 0.00 0.00 0.00 2.40
556 566 1.434696 CAGTGGCGAAATCCATGGC 59.565 57.895 6.96 0.00 38.57 4.40
615 625 2.289002 CGAGCTTAATCTGGCCATGAAC 59.711 50.000 5.51 0.00 0.00 3.18
631 641 1.602877 GAACTGTACGCACACGACCG 61.603 60.000 0.00 0.00 43.93 4.79
760 772 4.016706 CGGGCCGGGGATGGATAC 62.017 72.222 20.56 0.00 0.00 2.24
761 773 4.016706 GGGCCGGGGATGGATACG 62.017 72.222 2.18 0.00 42.51 3.06
762 774 4.699522 GGCCGGGGATGGATACGC 62.700 72.222 2.18 0.00 42.51 4.42
801 813 0.974383 TCTCCGACTTTTGTCCCCTC 59.026 55.000 0.00 0.00 46.25 4.30
937 954 1.611673 CCATCGGTTCCTCAGCAAGTT 60.612 52.381 0.00 0.00 0.00 2.66
975 992 0.035630 AGCTAGAAAGGCACCAGCTG 60.036 55.000 6.78 6.78 40.92 4.24
1161 1180 3.132646 GTGAGCTCATCTTCATCAGGAGT 59.867 47.826 21.47 0.00 0.00 3.85
1162 1181 4.340666 GTGAGCTCATCTTCATCAGGAGTA 59.659 45.833 21.47 0.00 0.00 2.59
1163 1182 5.010922 GTGAGCTCATCTTCATCAGGAGTAT 59.989 44.000 21.47 0.00 0.00 2.12
1181 1200 7.549134 CAGGAGTATTATTACACTGTTGAAGCA 59.451 37.037 9.53 0.00 33.98 3.91
1223 1251 8.229605 ACCTATACCTACCTGTATTGTATGTGA 58.770 37.037 8.66 0.00 33.58 3.58
1243 1271 0.320374 GTGGTTCCCGACATGAGTGA 59.680 55.000 0.00 0.00 0.00 3.41
1244 1272 1.052617 TGGTTCCCGACATGAGTGAA 58.947 50.000 0.00 0.00 0.00 3.18
1245 1273 1.628340 TGGTTCCCGACATGAGTGAAT 59.372 47.619 0.00 0.00 0.00 2.57
1246 1274 2.009774 GGTTCCCGACATGAGTGAATG 58.990 52.381 0.00 0.00 0.00 2.67
1250 1278 3.361786 TCCCGACATGAGTGAATGTAGA 58.638 45.455 0.00 0.00 40.87 2.59
1642 1686 4.435121 CGCGTGTACAAACTTCCTTAATCC 60.435 45.833 0.00 0.00 0.00 3.01
1778 1917 3.058016 CACTTGACCACCATGATGTGTTC 60.058 47.826 0.00 0.00 34.35 3.18
1779 1918 2.198827 TGACCACCATGATGTGTTCC 57.801 50.000 0.00 0.00 34.35 3.62
1780 1919 1.423161 TGACCACCATGATGTGTTCCA 59.577 47.619 0.00 0.00 34.35 3.53
1781 1920 2.158549 TGACCACCATGATGTGTTCCAA 60.159 45.455 0.00 0.00 34.35 3.53
1782 1921 2.228822 GACCACCATGATGTGTTCCAAC 59.771 50.000 0.00 0.00 34.35 3.77
1836 2062 2.483583 TTGTGTTTCACCGATTGTGC 57.516 45.000 0.00 0.00 45.03 4.57
1917 2143 2.111043 AACCTGGTGCTGGTGACG 59.889 61.111 0.00 0.00 35.88 4.35
2163 2389 1.515304 GCGAGCTGGACGACTTCTC 60.515 63.158 0.00 0.00 0.00 2.87
2215 2447 2.469274 TTGGAGCTTGAGCAAGAGAG 57.531 50.000 14.04 0.00 45.16 3.20
2277 2510 0.392729 ATTCTGAGGCTGCTGCTGAC 60.393 55.000 15.64 7.58 39.59 3.51
2304 2537 1.833606 GCTTAGGCCTCCCCTTCTC 59.166 63.158 9.68 0.00 43.06 2.87
2429 2664 5.437060 GCAAGGTGATCTTATTCAAGGGTA 58.563 41.667 0.00 0.00 33.68 3.69
2478 2715 7.066887 TGTTTTGTATTCATGTGTGAGAGTGTT 59.933 33.333 0.00 0.00 35.39 3.32
2497 2734 5.861787 AGTGTTTTGTAACTTCTGTTGTTGC 59.138 36.000 0.00 0.00 37.59 4.17
2503 2740 4.630505 TGTAACTTCTGTTGTTGCGTTGTA 59.369 37.500 0.00 0.00 37.59 2.41
2543 2791 1.993956 TGGTTGGGAGATGTTTGTGG 58.006 50.000 0.00 0.00 0.00 4.17
2666 3521 1.145738 AGCTGACCTTTGTCCCATGTT 59.854 47.619 0.00 0.00 41.01 2.71
2672 3527 0.604578 CTTTGTCCCATGTTGCCTGG 59.395 55.000 0.00 0.00 0.00 4.45
2711 3569 6.951198 TGTAACACTTGGATTGATTGGGTATT 59.049 34.615 0.00 0.00 0.00 1.89
2732 3590 1.250840 GCCCCTCGAAAAATGCCACT 61.251 55.000 0.00 0.00 0.00 4.00
2735 3593 1.613437 CCCTCGAAAAATGCCACTGTT 59.387 47.619 0.00 0.00 0.00 3.16
2770 3641 4.400961 GCCACTCCAAGCTCGCCT 62.401 66.667 0.00 0.00 0.00 5.52
2773 3644 4.749310 ACTCCAAGCTCGCCTGCG 62.749 66.667 4.92 4.92 41.35 5.18
2774 3645 4.749310 CTCCAAGCTCGCCTGCGT 62.749 66.667 11.68 0.00 40.74 5.24
2778 3649 2.046892 AAGCTCGCCTGCGTGATT 60.047 55.556 16.69 13.70 40.74 2.57
2795 3666 1.961180 ATTGCTCTCCCGAGAACCCG 61.961 60.000 0.00 0.00 39.74 5.28
2829 3701 1.601419 CGCCTTCAAGGAGGGTACGA 61.601 60.000 7.98 0.00 37.67 3.43
2830 3702 0.108281 GCCTTCAAGGAGGGTACGAC 60.108 60.000 7.98 0.00 37.67 4.34
2834 3706 0.963962 TCAAGGAGGGTACGACACAC 59.036 55.000 0.00 0.00 0.00 3.82
2836 3708 0.677842 AAGGAGGGTACGACACACAC 59.322 55.000 0.00 0.00 30.42 3.82
2837 3709 1.080974 GGAGGGTACGACACACACG 60.081 63.158 0.00 0.00 30.42 4.49
2838 3710 1.518056 GGAGGGTACGACACACACGA 61.518 60.000 0.00 0.00 30.42 4.35
2840 3712 0.242825 AGGGTACGACACACACGATG 59.757 55.000 0.00 0.00 30.42 3.84
2841 3713 1.349259 GGGTACGACACACACGATGC 61.349 60.000 0.00 0.00 34.70 3.91
2843 3715 0.708370 GTACGACACACACGATGCAG 59.292 55.000 0.00 0.00 34.70 4.41
2844 3716 1.006825 TACGACACACACGATGCAGC 61.007 55.000 0.00 0.00 34.70 5.25
2845 3717 2.863153 GACACACACGATGCAGCC 59.137 61.111 0.00 0.00 0.00 4.85
2847 3719 2.175184 GACACACACGATGCAGCCAC 62.175 60.000 0.00 0.00 0.00 5.01
2849 3721 2.669229 CACACGATGCAGCCACCA 60.669 61.111 0.00 0.00 0.00 4.17
2850 3722 2.669569 ACACGATGCAGCCACCAC 60.670 61.111 0.00 0.00 0.00 4.16
2851 3723 2.359107 CACGATGCAGCCACCACT 60.359 61.111 0.00 0.00 0.00 4.00
2852 3724 2.359107 ACGATGCAGCCACCACTG 60.359 61.111 0.00 0.00 40.80 3.66
2853 3725 2.359107 CGATGCAGCCACCACTGT 60.359 61.111 0.00 0.00 39.96 3.55
2854 3726 1.079197 CGATGCAGCCACCACTGTA 60.079 57.895 0.00 0.00 39.96 2.74
2858 3734 1.121407 TGCAGCCACCACTGTACTCT 61.121 55.000 0.00 0.00 39.96 3.24
2863 3739 1.132643 GCCACCACTGTACTCTAGTCG 59.867 57.143 0.00 0.00 0.00 4.18
2889 3765 3.838244 TGGATTTTCACCCGAGATAGG 57.162 47.619 0.00 0.00 0.00 2.57
2890 3766 3.112263 TGGATTTTCACCCGAGATAGGT 58.888 45.455 0.00 0.00 38.48 3.08
2891 3767 3.521937 TGGATTTTCACCCGAGATAGGTT 59.478 43.478 0.00 0.00 34.56 3.50
2892 3768 4.018779 TGGATTTTCACCCGAGATAGGTTT 60.019 41.667 0.00 0.00 34.56 3.27
2893 3769 4.948004 GGATTTTCACCCGAGATAGGTTTT 59.052 41.667 0.00 0.00 34.56 2.43
2894 3770 5.066117 GGATTTTCACCCGAGATAGGTTTTC 59.934 44.000 0.00 0.00 34.56 2.29
2895 3771 3.622166 TTCACCCGAGATAGGTTTTCC 57.378 47.619 0.00 0.00 34.56 3.13
2896 3772 1.479323 TCACCCGAGATAGGTTTTCCG 59.521 52.381 0.00 0.00 46.35 4.30
2897 3773 1.206371 CACCCGAGATAGGTTTTCCGT 59.794 52.381 0.00 0.00 46.35 4.69
2898 3774 1.904537 ACCCGAGATAGGTTTTCCGTT 59.095 47.619 0.00 0.00 46.35 4.44
2899 3775 2.303890 ACCCGAGATAGGTTTTCCGTTT 59.696 45.455 0.00 0.00 46.35 3.60
2900 3776 2.934553 CCCGAGATAGGTTTTCCGTTTC 59.065 50.000 0.00 0.00 46.35 2.78
2901 3777 2.934553 CCGAGATAGGTTTTCCGTTTCC 59.065 50.000 0.00 0.00 46.35 3.13
2902 3778 2.601763 CGAGATAGGTTTTCCGTTTCCG 59.398 50.000 0.00 0.00 46.35 4.30
2919 3795 5.975939 CGTTTCCGGAGACTAGTAAAATAGG 59.024 44.000 21.62 0.00 0.00 2.57
2920 3796 5.526506 TTCCGGAGACTAGTAAAATAGGC 57.473 43.478 3.34 0.00 0.00 3.93
2921 3797 3.567164 TCCGGAGACTAGTAAAATAGGCG 59.433 47.826 0.00 0.00 35.80 5.52
2922 3798 3.305199 CCGGAGACTAGTAAAATAGGCGG 60.305 52.174 0.00 0.00 35.80 6.13
2923 3799 3.567164 CGGAGACTAGTAAAATAGGCGGA 59.433 47.826 0.00 0.00 35.80 5.54
2924 3800 4.217983 CGGAGACTAGTAAAATAGGCGGAT 59.782 45.833 0.00 0.00 35.80 4.18
2925 3801 5.278858 CGGAGACTAGTAAAATAGGCGGATT 60.279 44.000 0.00 0.00 35.80 3.01
2926 3802 6.157904 GGAGACTAGTAAAATAGGCGGATTC 58.842 44.000 0.00 0.00 35.80 2.52
2927 3803 6.015265 GGAGACTAGTAAAATAGGCGGATTCT 60.015 42.308 0.00 0.00 35.80 2.40
2928 3804 6.750148 AGACTAGTAAAATAGGCGGATTCTG 58.250 40.000 0.00 0.00 35.80 3.02
2929 3805 5.855045 ACTAGTAAAATAGGCGGATTCTGG 58.145 41.667 0.00 0.00 0.00 3.86
2930 3806 5.601313 ACTAGTAAAATAGGCGGATTCTGGA 59.399 40.000 0.00 0.00 0.00 3.86
2931 3807 5.367945 AGTAAAATAGGCGGATTCTGGAA 57.632 39.130 0.00 0.00 0.00 3.53
2932 3808 5.123936 AGTAAAATAGGCGGATTCTGGAAC 58.876 41.667 0.00 0.00 0.00 3.62
2933 3809 2.640316 AATAGGCGGATTCTGGAACC 57.360 50.000 0.00 0.00 0.00 3.62
2935 3811 1.682451 TAGGCGGATTCTGGAACCGG 61.682 60.000 6.79 0.00 45.66 5.28
2936 3812 2.513897 GCGGATTCTGGAACCGGG 60.514 66.667 6.32 0.00 45.66 5.73
2937 3813 2.987125 CGGATTCTGGAACCGGGT 59.013 61.111 6.32 0.00 42.48 5.28
2938 3814 1.449601 CGGATTCTGGAACCGGGTG 60.450 63.158 6.32 0.00 42.48 4.61
2939 3815 1.077716 GGATTCTGGAACCGGGTGG 60.078 63.158 6.32 0.00 42.84 4.61
2940 3816 1.559065 GGATTCTGGAACCGGGTGGA 61.559 60.000 6.32 0.00 39.21 4.02
2941 3817 0.546598 GATTCTGGAACCGGGTGGAT 59.453 55.000 6.32 0.00 39.21 3.41
2942 3818 1.766496 GATTCTGGAACCGGGTGGATA 59.234 52.381 6.32 0.00 39.21 2.59
2943 3819 1.200519 TTCTGGAACCGGGTGGATAG 58.799 55.000 6.32 0.00 39.21 2.08
2944 3820 0.337082 TCTGGAACCGGGTGGATAGA 59.663 55.000 6.32 0.00 39.21 1.98
2945 3821 0.753262 CTGGAACCGGGTGGATAGAG 59.247 60.000 6.32 0.00 39.21 2.43
2946 3822 0.689745 TGGAACCGGGTGGATAGAGG 60.690 60.000 6.32 0.00 39.21 3.69
2947 3823 1.408453 GGAACCGGGTGGATAGAGGG 61.408 65.000 6.32 0.00 39.21 4.30
2948 3824 1.384082 AACCGGGTGGATAGAGGGG 60.384 63.158 6.32 0.00 39.21 4.79
2949 3825 1.893588 AACCGGGTGGATAGAGGGGA 61.894 60.000 6.32 0.00 39.21 4.81
2950 3826 1.837499 CCGGGTGGATAGAGGGGAC 60.837 68.421 0.00 0.00 37.49 4.46
2963 3839 2.430367 GGGACCTCAACGGCAACT 59.570 61.111 0.00 0.00 35.61 3.16
2964 3840 1.671379 GGGACCTCAACGGCAACTC 60.671 63.158 0.00 0.00 35.61 3.01
2965 3841 1.671379 GGACCTCAACGGCAACTCC 60.671 63.158 0.00 0.00 35.61 3.85
2966 3842 1.070786 GACCTCAACGGCAACTCCA 59.929 57.895 0.00 0.00 35.61 3.86
2967 3843 0.534203 GACCTCAACGGCAACTCCAA 60.534 55.000 0.00 0.00 35.61 3.53
2968 3844 0.535102 ACCTCAACGGCAACTCCAAG 60.535 55.000 0.00 0.00 35.61 3.61
2969 3845 1.237285 CCTCAACGGCAACTCCAAGG 61.237 60.000 0.00 0.00 34.01 3.61
2970 3846 0.250295 CTCAACGGCAACTCCAAGGA 60.250 55.000 0.00 0.00 34.01 3.36
2971 3847 0.250295 TCAACGGCAACTCCAAGGAG 60.250 55.000 14.44 14.44 46.91 3.69
2972 3848 1.073199 AACGGCAACTCCAAGGAGG 59.927 57.895 19.62 4.72 45.88 4.30
2973 3849 1.415672 AACGGCAACTCCAAGGAGGA 61.416 55.000 19.62 0.00 45.88 3.71
2983 3859 3.154827 TCCAAGGAGGAAAATGACACC 57.845 47.619 0.00 0.00 45.65 4.16
2984 3860 2.171003 CCAAGGAGGAAAATGACACCC 58.829 52.381 0.00 0.00 41.22 4.61
2985 3861 2.171003 CAAGGAGGAAAATGACACCCC 58.829 52.381 0.00 0.00 0.00 4.95
2986 3862 1.760405 AGGAGGAAAATGACACCCCT 58.240 50.000 0.00 0.00 0.00 4.79
2987 3863 1.636003 AGGAGGAAAATGACACCCCTC 59.364 52.381 0.00 0.00 41.92 4.30
2988 3864 1.679032 GGAGGAAAATGACACCCCTCG 60.679 57.143 0.00 0.00 43.19 4.63
2989 3865 0.328258 AGGAAAATGACACCCCTCGG 59.672 55.000 0.00 0.00 0.00 4.63
2990 3866 1.313091 GGAAAATGACACCCCTCGGC 61.313 60.000 0.00 0.00 0.00 5.54
2991 3867 0.322546 GAAAATGACACCCCTCGGCT 60.323 55.000 0.00 0.00 0.00 5.52
2992 3868 0.112412 AAAATGACACCCCTCGGCTT 59.888 50.000 0.00 0.00 0.00 4.35
2993 3869 0.112412 AAATGACACCCCTCGGCTTT 59.888 50.000 0.00 0.00 0.00 3.51
2994 3870 0.609131 AATGACACCCCTCGGCTTTG 60.609 55.000 0.00 0.00 0.00 2.77
2995 3871 1.779061 ATGACACCCCTCGGCTTTGT 61.779 55.000 0.00 0.00 0.00 2.83
2996 3872 1.671379 GACACCCCTCGGCTTTGTC 60.671 63.158 0.00 0.00 0.00 3.18
2997 3873 2.742372 CACCCCTCGGCTTTGTCG 60.742 66.667 0.00 0.00 0.00 4.35
2998 3874 3.239253 ACCCCTCGGCTTTGTCGT 61.239 61.111 0.00 0.00 30.45 4.34
2999 3875 2.434359 CCCCTCGGCTTTGTCGTC 60.434 66.667 0.00 0.00 30.45 4.20
3000 3876 2.809601 CCCTCGGCTTTGTCGTCG 60.810 66.667 0.00 0.00 30.45 5.12
3001 3877 2.049433 CCTCGGCTTTGTCGTCGT 60.049 61.111 0.00 0.00 33.02 4.34
3002 3878 2.087009 CCTCGGCTTTGTCGTCGTC 61.087 63.158 0.00 0.00 33.02 4.20
3003 3879 1.371267 CTCGGCTTTGTCGTCGTCA 60.371 57.895 0.00 0.00 33.02 4.35
3004 3880 1.337817 CTCGGCTTTGTCGTCGTCAG 61.338 60.000 0.00 0.00 33.02 3.51
3005 3881 2.372690 CGGCTTTGTCGTCGTCAGG 61.373 63.158 0.00 0.00 0.00 3.86
3006 3882 2.668280 GGCTTTGTCGTCGTCAGGC 61.668 63.158 9.57 9.57 0.00 4.85
3007 3883 2.668280 GCTTTGTCGTCGTCAGGCC 61.668 63.158 0.00 0.00 0.00 5.19
3008 3884 2.355363 TTTGTCGTCGTCAGGCCG 60.355 61.111 0.00 0.00 0.00 6.13
3009 3885 3.851845 TTTGTCGTCGTCAGGCCGG 62.852 63.158 0.00 0.00 0.00 6.13
3011 3887 4.773117 GTCGTCGTCAGGCCGGAC 62.773 72.222 24.44 24.44 34.42 4.79
3025 3901 2.044551 GGACGGACCGACTAGGGT 60.045 66.667 23.38 0.00 46.96 4.34
3026 3902 1.680314 GGACGGACCGACTAGGGTT 60.680 63.158 23.38 0.00 46.96 4.11
3027 3903 1.253593 GGACGGACCGACTAGGGTTT 61.254 60.000 23.38 0.00 46.96 3.27
3028 3904 0.172127 GACGGACCGACTAGGGTTTC 59.828 60.000 23.38 0.00 46.96 2.78
3029 3905 1.253593 ACGGACCGACTAGGGTTTCC 61.254 60.000 23.38 0.00 46.96 3.13
3030 3906 1.903294 GGACCGACTAGGGTTTCCC 59.097 63.158 0.00 0.00 46.96 3.97
3040 3916 4.843624 GGTTTCCCCTGTCCCTTG 57.156 61.111 0.00 0.00 0.00 3.61
3041 3917 1.606601 GGTTTCCCCTGTCCCTTGC 60.607 63.158 0.00 0.00 0.00 4.01
3042 3918 1.606601 GTTTCCCCTGTCCCTTGCC 60.607 63.158 0.00 0.00 0.00 4.52
3043 3919 2.088096 TTTCCCCTGTCCCTTGCCA 61.088 57.895 0.00 0.00 0.00 4.92
3044 3920 2.080336 TTTCCCCTGTCCCTTGCCAG 62.080 60.000 0.00 0.00 0.00 4.85
3045 3921 4.748144 CCCCTGTCCCTTGCCAGC 62.748 72.222 0.00 0.00 0.00 4.85
3046 3922 3.655211 CCCTGTCCCTTGCCAGCT 61.655 66.667 0.00 0.00 0.00 4.24
3047 3923 2.045536 CCTGTCCCTTGCCAGCTC 60.046 66.667 0.00 0.00 0.00 4.09
3048 3924 2.045536 CTGTCCCTTGCCAGCTCC 60.046 66.667 0.00 0.00 0.00 4.70
3049 3925 2.853542 TGTCCCTTGCCAGCTCCA 60.854 61.111 0.00 0.00 0.00 3.86
3050 3926 2.360475 GTCCCTTGCCAGCTCCAC 60.360 66.667 0.00 0.00 0.00 4.02
3051 3927 3.650950 TCCCTTGCCAGCTCCACC 61.651 66.667 0.00 0.00 0.00 4.61
3052 3928 4.748144 CCCTTGCCAGCTCCACCC 62.748 72.222 0.00 0.00 0.00 4.61
3069 3945 2.819595 CGCACCCGGGTTCATCAG 60.820 66.667 27.83 13.42 0.00 2.90
3070 3946 2.668632 GCACCCGGGTTCATCAGA 59.331 61.111 27.83 0.00 0.00 3.27
3071 3947 1.450312 GCACCCGGGTTCATCAGAG 60.450 63.158 27.83 11.68 0.00 3.35
3072 3948 1.450312 CACCCGGGTTCATCAGAGC 60.450 63.158 27.83 0.00 0.00 4.09
3073 3949 2.190578 CCCGGGTTCATCAGAGCC 59.809 66.667 14.18 0.00 43.80 4.70
3076 3952 4.522971 GGGTTCATCAGAGCCGTC 57.477 61.111 0.00 0.00 45.33 4.79
3077 3953 1.596934 GGGTTCATCAGAGCCGTCA 59.403 57.895 0.00 0.00 45.33 4.35
3078 3954 0.036388 GGGTTCATCAGAGCCGTCAA 60.036 55.000 0.00 0.00 45.33 3.18
3079 3955 1.079503 GGTTCATCAGAGCCGTCAAC 58.920 55.000 0.00 0.00 35.33 3.18
3080 3956 1.079503 GTTCATCAGAGCCGTCAACC 58.920 55.000 0.00 0.00 0.00 3.77
3081 3957 0.389817 TTCATCAGAGCCGTCAACCG 60.390 55.000 0.00 0.00 0.00 4.44
3082 3958 1.215382 CATCAGAGCCGTCAACCGA 59.785 57.895 0.00 0.00 39.56 4.69
3083 3959 0.803768 CATCAGAGCCGTCAACCGAG 60.804 60.000 0.00 0.00 39.56 4.63
3084 3960 1.949847 ATCAGAGCCGTCAACCGAGG 61.950 60.000 0.00 0.00 39.56 4.63
3086 3962 3.692406 GAGCCGTCAACCGAGGGT 61.692 66.667 3.41 0.00 46.88 4.34
3087 3963 3.644399 GAGCCGTCAACCGAGGGTC 62.644 68.421 3.41 0.00 46.88 4.46
3097 3973 2.434359 CGAGGGTCGGAAGCAACC 60.434 66.667 0.00 0.00 36.00 3.77
3105 3981 3.882025 GGAAGCAACCGAGAGCAG 58.118 61.111 0.00 0.00 0.00 4.24
3106 3982 2.394563 GGAAGCAACCGAGAGCAGC 61.395 63.158 0.00 0.00 0.00 5.25
3107 3983 2.734673 GAAGCAACCGAGAGCAGCG 61.735 63.158 0.00 0.00 0.00 5.18
3108 3984 3.226429 AAGCAACCGAGAGCAGCGA 62.226 57.895 0.00 0.00 0.00 4.93
3109 3985 3.184683 GCAACCGAGAGCAGCGAG 61.185 66.667 0.00 0.00 0.00 5.03
3110 3986 2.568612 CAACCGAGAGCAGCGAGA 59.431 61.111 0.00 0.00 0.00 4.04
3111 3987 1.515952 CAACCGAGAGCAGCGAGAG 60.516 63.158 0.00 0.00 0.00 3.20
3112 3988 1.675972 AACCGAGAGCAGCGAGAGA 60.676 57.895 0.00 0.00 0.00 3.10
3113 3989 1.653094 AACCGAGAGCAGCGAGAGAG 61.653 60.000 0.00 0.00 0.00 3.20
3114 3990 1.817520 CCGAGAGCAGCGAGAGAGA 60.818 63.158 0.00 0.00 0.00 3.10
3115 3991 1.643292 CGAGAGCAGCGAGAGAGAG 59.357 63.158 0.00 0.00 0.00 3.20
3116 3992 0.809636 CGAGAGCAGCGAGAGAGAGA 60.810 60.000 0.00 0.00 0.00 3.10
3117 3993 0.657840 GAGAGCAGCGAGAGAGAGAC 59.342 60.000 0.00 0.00 0.00 3.36
3118 3994 0.253044 AGAGCAGCGAGAGAGAGACT 59.747 55.000 0.00 0.00 0.00 3.24
3119 3995 0.378257 GAGCAGCGAGAGAGAGACTG 59.622 60.000 0.00 0.00 0.00 3.51
3120 3996 1.031571 AGCAGCGAGAGAGAGACTGG 61.032 60.000 0.00 0.00 0.00 4.00
3121 3997 1.029408 GCAGCGAGAGAGAGACTGGA 61.029 60.000 0.00 0.00 0.00 3.86
3122 3998 1.016627 CAGCGAGAGAGAGACTGGAG 58.983 60.000 0.00 0.00 0.00 3.86
3123 3999 0.908910 AGCGAGAGAGAGACTGGAGA 59.091 55.000 0.00 0.00 0.00 3.71
3124 4000 1.490490 AGCGAGAGAGAGACTGGAGAT 59.510 52.381 0.00 0.00 0.00 2.75
3125 4001 1.603802 GCGAGAGAGAGACTGGAGATG 59.396 57.143 0.00 0.00 0.00 2.90
3126 4002 2.744823 GCGAGAGAGAGACTGGAGATGA 60.745 54.545 0.00 0.00 0.00 2.92
3127 4003 3.540617 CGAGAGAGAGACTGGAGATGAA 58.459 50.000 0.00 0.00 0.00 2.57
3128 4004 3.944650 CGAGAGAGAGACTGGAGATGAAA 59.055 47.826 0.00 0.00 0.00 2.69
3129 4005 4.035558 CGAGAGAGAGACTGGAGATGAAAG 59.964 50.000 0.00 0.00 0.00 2.62
3130 4006 5.191727 AGAGAGAGACTGGAGATGAAAGA 57.808 43.478 0.00 0.00 0.00 2.52
3131 4007 5.195940 AGAGAGAGACTGGAGATGAAAGAG 58.804 45.833 0.00 0.00 0.00 2.85
3132 4008 3.701040 AGAGAGACTGGAGATGAAAGAGC 59.299 47.826 0.00 0.00 0.00 4.09
3133 4009 2.765699 AGAGACTGGAGATGAAAGAGCC 59.234 50.000 0.00 0.00 0.00 4.70
3134 4010 2.499289 GAGACTGGAGATGAAAGAGCCA 59.501 50.000 0.00 0.00 0.00 4.75
3135 4011 3.113824 AGACTGGAGATGAAAGAGCCAT 58.886 45.455 0.00 0.00 0.00 4.40
3136 4012 3.118334 AGACTGGAGATGAAAGAGCCATG 60.118 47.826 0.00 0.00 0.00 3.66
3137 4013 2.575279 ACTGGAGATGAAAGAGCCATGT 59.425 45.455 0.00 0.00 0.00 3.21
3138 4014 3.776969 ACTGGAGATGAAAGAGCCATGTA 59.223 43.478 0.00 0.00 0.00 2.29
3139 4015 4.125703 CTGGAGATGAAAGAGCCATGTAC 58.874 47.826 0.00 0.00 0.00 2.90
3140 4016 3.118261 TGGAGATGAAAGAGCCATGTACC 60.118 47.826 0.00 0.00 0.00 3.34
3141 4017 3.135530 GGAGATGAAAGAGCCATGTACCT 59.864 47.826 0.00 0.00 0.00 3.08
3142 4018 4.376146 GAGATGAAAGAGCCATGTACCTC 58.624 47.826 0.00 0.00 0.00 3.85
3143 4019 3.135530 AGATGAAAGAGCCATGTACCTCC 59.864 47.826 0.00 0.00 0.00 4.30
3144 4020 2.265367 TGAAAGAGCCATGTACCTCCA 58.735 47.619 0.00 0.00 0.00 3.86
3145 4021 2.846206 TGAAAGAGCCATGTACCTCCAT 59.154 45.455 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.403766 CCTGTCGCTCTGCTAAAGTTATATG 59.596 44.000 0.00 0.00 0.00 1.78
70 71 5.501897 CGAAACTTGCGTTCTTCAGTTAGTT 60.502 40.000 0.00 0.00 31.66 2.24
71 72 4.025979 CGAAACTTGCGTTCTTCAGTTAGT 60.026 41.667 0.00 0.00 31.66 2.24
72 73 4.208460 TCGAAACTTGCGTTCTTCAGTTAG 59.792 41.667 0.00 0.00 31.66 2.34
73 74 4.114073 TCGAAACTTGCGTTCTTCAGTTA 58.886 39.130 0.00 0.00 31.66 2.24
160 161 0.726827 CATGACAACCAATCGTCCCG 59.273 55.000 0.00 0.00 0.00 5.14
197 198 7.477144 TCAAGTTGCACGTAGATTAATATGG 57.523 36.000 0.00 0.00 0.00 2.74
325 326 3.490526 TGCCAAACTTTTACTACGACGTC 59.509 43.478 2.43 5.18 0.00 4.34
402 406 4.412796 AGATGCTGCTGCTAATGAACTA 57.587 40.909 17.00 0.00 40.48 2.24
404 408 3.376234 TCAAGATGCTGCTGCTAATGAAC 59.624 43.478 17.00 0.00 40.48 3.18
501 511 7.997773 ACAATATGGATCCTCTTGATTGATG 57.002 36.000 20.98 7.84 32.41 3.07
583 593 0.394216 TTAAGCTCGCATGCCCACAT 60.394 50.000 13.15 0.00 36.79 3.21
584 594 0.394216 ATTAAGCTCGCATGCCCACA 60.394 50.000 13.15 0.00 0.00 4.17
585 595 0.308993 GATTAAGCTCGCATGCCCAC 59.691 55.000 13.15 0.75 0.00 4.61
586 596 0.181114 AGATTAAGCTCGCATGCCCA 59.819 50.000 13.15 0.00 0.00 5.36
587 597 0.590195 CAGATTAAGCTCGCATGCCC 59.410 55.000 13.15 0.38 0.00 5.36
588 598 0.590195 CCAGATTAAGCTCGCATGCC 59.410 55.000 13.15 0.00 0.00 4.40
592 602 0.181114 ATGGCCAGATTAAGCTCGCA 59.819 50.000 13.05 0.00 0.00 5.10
615 625 2.803670 CCGGTCGTGTGCGTACAG 60.804 66.667 6.58 1.60 37.52 2.74
631 641 0.304705 CACACAACGAGACAGCAACC 59.695 55.000 0.00 0.00 0.00 3.77
762 774 1.218316 GGAAGTGGGGACTGCGTAG 59.782 63.158 0.00 0.00 0.00 3.51
801 813 3.731295 GGAACGGCAGAGAGAGAAG 57.269 57.895 0.00 0.00 0.00 2.85
829 841 1.006832 CTGGCCGTTGGAATCGTTAG 58.993 55.000 0.00 0.00 0.00 2.34
858 870 1.549170 AGGTATTTATAGGCGAGCCGG 59.451 52.381 8.63 0.00 41.95 6.13
860 872 3.430513 GGCTAGGTATTTATAGGCGAGCC 60.431 52.174 5.89 5.89 40.13 4.70
937 954 2.568090 GGTAAAGCGACCGACCGA 59.432 61.111 0.72 0.00 0.00 4.69
1013 1032 0.740516 GAAGAGCAGGAGCAGAGCAC 60.741 60.000 0.00 0.00 45.49 4.40
1188 1207 4.523558 CAGGTAGGTATAGGTAGGTGCTTC 59.476 50.000 0.00 0.00 0.00 3.86
1203 1222 5.128827 CCACTCACATACAATACAGGTAGGT 59.871 44.000 0.00 0.00 36.30 3.08
1204 1223 5.128827 ACCACTCACATACAATACAGGTAGG 59.871 44.000 0.00 0.00 0.00 3.18
1780 1919 7.701579 TGATTGGATCATGCAACTTGGAAGTT 61.702 38.462 0.00 0.00 41.09 2.66
1781 1920 3.159213 TGGATCATGCAACTTGGAAGT 57.841 42.857 0.00 0.00 42.04 3.01
1782 1921 4.158949 TGATTGGATCATGCAACTTGGAAG 59.841 41.667 0.00 0.00 33.59 3.46
2215 2447 5.975282 ACTATAACGAAGAGGTTTCCTTCC 58.025 41.667 0.00 0.00 37.36 3.46
2262 2495 3.243816 TGGTCAGCAGCAGCCTCA 61.244 61.111 0.00 0.00 43.56 3.86
2304 2537 8.767085 GTCTACTACTGTGCTACTAGTATGAAG 58.233 40.741 2.33 2.28 0.00 3.02
2429 2664 5.877012 CACTCCATGCATGTACTTCTAAAGT 59.123 40.000 24.58 10.41 45.40 2.66
2478 2715 4.688511 ACGCAACAACAGAAGTTACAAA 57.311 36.364 0.00 0.00 35.85 2.83
2497 2734 1.089112 GGATTCGGGGGTTTACAACG 58.911 55.000 0.00 0.00 0.00 4.10
2503 2740 1.874299 ATGGCAGGATTCGGGGGTTT 61.874 55.000 0.00 0.00 0.00 3.27
2682 3540 6.405065 CCCAATCAATCCAAGTGTTACATGAG 60.405 42.308 0.00 0.00 0.00 2.90
2689 3547 6.700352 CAAATACCCAATCAATCCAAGTGTT 58.300 36.000 0.00 0.00 0.00 3.32
2691 3549 5.111293 GCAAATACCCAATCAATCCAAGTG 58.889 41.667 0.00 0.00 0.00 3.16
2711 3569 0.829602 TGGCATTTTTCGAGGGGCAA 60.830 50.000 0.00 0.00 0.00 4.52
2716 3574 3.369546 AAACAGTGGCATTTTTCGAGG 57.630 42.857 0.00 0.00 0.00 4.63
2735 3593 6.866248 GGAGTGGCTTTTTCGAATGATAAAAA 59.134 34.615 0.00 0.00 34.39 1.94
2739 3597 4.584874 TGGAGTGGCTTTTTCGAATGATA 58.415 39.130 0.00 0.00 0.00 2.15
2742 3600 3.568538 CTTGGAGTGGCTTTTTCGAATG 58.431 45.455 0.00 0.00 0.00 2.67
2770 3641 2.125552 CGGGAGAGCAATCACGCA 60.126 61.111 0.00 0.00 39.59 5.24
2795 3666 3.680786 GCGTTGCCTGGGGGAAAC 61.681 66.667 0.00 0.00 45.55 2.78
2829 3701 2.110835 TGGCTGCATCGTGTGTGT 59.889 55.556 0.50 0.00 0.00 3.72
2830 3702 2.557805 GTGGCTGCATCGTGTGTG 59.442 61.111 0.50 0.00 0.00 3.82
2834 3706 2.359107 AGTGGTGGCTGCATCGTG 60.359 61.111 0.50 0.00 0.00 4.35
2836 3708 1.079197 TACAGTGGTGGCTGCATCG 60.079 57.895 0.50 0.00 39.96 3.84
2837 3709 0.036010 AGTACAGTGGTGGCTGCATC 60.036 55.000 0.50 0.00 39.96 3.91
2838 3710 0.036010 GAGTACAGTGGTGGCTGCAT 60.036 55.000 0.50 0.00 39.96 3.96
2840 3712 0.895530 TAGAGTACAGTGGTGGCTGC 59.104 55.000 0.00 0.00 39.96 5.25
2841 3713 2.164624 GACTAGAGTACAGTGGTGGCTG 59.835 54.545 0.00 0.00 41.92 4.85
2843 3715 1.132643 CGACTAGAGTACAGTGGTGGC 59.867 57.143 0.00 0.00 0.00 5.01
2844 3716 2.434428 ACGACTAGAGTACAGTGGTGG 58.566 52.381 0.00 0.00 34.21 4.61
2845 3717 5.814764 AATACGACTAGAGTACAGTGGTG 57.185 43.478 8.99 0.00 35.95 4.17
2847 3719 6.034591 CCAAAATACGACTAGAGTACAGTGG 58.965 44.000 0.00 5.36 0.00 4.00
2849 3721 7.642082 ATCCAAAATACGACTAGAGTACAGT 57.358 36.000 0.00 0.00 0.00 3.55
2850 3722 8.928270 AAATCCAAAATACGACTAGAGTACAG 57.072 34.615 0.00 0.00 0.00 2.74
2851 3723 9.362539 GAAAATCCAAAATACGACTAGAGTACA 57.637 33.333 0.00 0.00 0.00 2.90
2852 3724 9.362539 TGAAAATCCAAAATACGACTAGAGTAC 57.637 33.333 0.00 0.00 0.00 2.73
2853 3725 9.362539 GTGAAAATCCAAAATACGACTAGAGTA 57.637 33.333 0.00 0.71 0.00 2.59
2854 3726 7.333672 GGTGAAAATCCAAAATACGACTAGAGT 59.666 37.037 0.00 0.00 0.00 3.24
2858 3734 5.352016 CGGGTGAAAATCCAAAATACGACTA 59.648 40.000 0.00 0.00 0.00 2.59
2863 3739 5.890424 TCTCGGGTGAAAATCCAAAATAC 57.110 39.130 0.00 0.00 0.00 1.89
2896 3772 5.752472 GCCTATTTTACTAGTCTCCGGAAAC 59.248 44.000 5.23 1.28 0.00 2.78
2897 3773 5.450965 CGCCTATTTTACTAGTCTCCGGAAA 60.451 44.000 5.23 0.00 0.00 3.13
2898 3774 4.037208 CGCCTATTTTACTAGTCTCCGGAA 59.963 45.833 5.23 0.00 0.00 4.30
2899 3775 3.567164 CGCCTATTTTACTAGTCTCCGGA 59.433 47.826 2.93 2.93 0.00 5.14
2900 3776 3.305199 CCGCCTATTTTACTAGTCTCCGG 60.305 52.174 0.00 0.00 0.00 5.14
2901 3777 3.567164 TCCGCCTATTTTACTAGTCTCCG 59.433 47.826 0.00 0.00 0.00 4.63
2902 3778 5.725325 ATCCGCCTATTTTACTAGTCTCC 57.275 43.478 0.00 0.00 0.00 3.71
2903 3779 6.864165 CAGAATCCGCCTATTTTACTAGTCTC 59.136 42.308 0.00 0.00 0.00 3.36
2904 3780 6.239345 CCAGAATCCGCCTATTTTACTAGTCT 60.239 42.308 0.00 0.00 0.00 3.24
2905 3781 5.927115 CCAGAATCCGCCTATTTTACTAGTC 59.073 44.000 0.00 0.00 0.00 2.59
2906 3782 5.601313 TCCAGAATCCGCCTATTTTACTAGT 59.399 40.000 0.00 0.00 0.00 2.57
2907 3783 6.097915 TCCAGAATCCGCCTATTTTACTAG 57.902 41.667 0.00 0.00 0.00 2.57
2908 3784 6.285990 GTTCCAGAATCCGCCTATTTTACTA 58.714 40.000 0.00 0.00 0.00 1.82
2909 3785 5.123936 GTTCCAGAATCCGCCTATTTTACT 58.876 41.667 0.00 0.00 0.00 2.24
2910 3786 4.275196 GGTTCCAGAATCCGCCTATTTTAC 59.725 45.833 0.00 0.00 0.00 2.01
2911 3787 4.457466 GGTTCCAGAATCCGCCTATTTTA 58.543 43.478 0.00 0.00 0.00 1.52
2912 3788 3.288092 GGTTCCAGAATCCGCCTATTTT 58.712 45.455 0.00 0.00 0.00 1.82
2913 3789 2.745152 CGGTTCCAGAATCCGCCTATTT 60.745 50.000 7.96 0.00 37.90 1.40
2914 3790 1.202651 CGGTTCCAGAATCCGCCTATT 60.203 52.381 7.96 0.00 37.90 1.73
2915 3791 0.393077 CGGTTCCAGAATCCGCCTAT 59.607 55.000 7.96 0.00 37.90 2.57
2916 3792 1.682451 CCGGTTCCAGAATCCGCCTA 61.682 60.000 12.84 0.00 42.48 3.93
2917 3793 2.584608 CGGTTCCAGAATCCGCCT 59.415 61.111 7.96 0.00 37.90 5.52
2918 3794 2.513897 CCGGTTCCAGAATCCGCC 60.514 66.667 12.84 0.00 42.48 6.13
2919 3795 2.513897 CCCGGTTCCAGAATCCGC 60.514 66.667 0.00 0.00 42.48 5.54
2920 3796 1.449601 CACCCGGTTCCAGAATCCG 60.450 63.158 0.00 11.86 43.30 4.18
2921 3797 1.077716 CCACCCGGTTCCAGAATCC 60.078 63.158 0.00 0.00 0.00 3.01
2922 3798 0.546598 ATCCACCCGGTTCCAGAATC 59.453 55.000 0.00 0.00 0.00 2.52
2923 3799 1.768870 CTATCCACCCGGTTCCAGAAT 59.231 52.381 0.00 0.00 0.00 2.40
2924 3800 1.200519 CTATCCACCCGGTTCCAGAA 58.799 55.000 0.00 0.00 0.00 3.02
2925 3801 0.337082 TCTATCCACCCGGTTCCAGA 59.663 55.000 0.00 0.00 0.00 3.86
2926 3802 0.753262 CTCTATCCACCCGGTTCCAG 59.247 60.000 0.00 0.00 0.00 3.86
2927 3803 0.689745 CCTCTATCCACCCGGTTCCA 60.690 60.000 0.00 0.00 0.00 3.53
2928 3804 1.408453 CCCTCTATCCACCCGGTTCC 61.408 65.000 0.00 0.00 0.00 3.62
2929 3805 1.408453 CCCCTCTATCCACCCGGTTC 61.408 65.000 0.00 0.00 0.00 3.62
2930 3806 1.384082 CCCCTCTATCCACCCGGTT 60.384 63.158 0.00 0.00 0.00 4.44
2931 3807 2.285868 CCCCTCTATCCACCCGGT 59.714 66.667 0.00 0.00 0.00 5.28
2932 3808 1.837499 GTCCCCTCTATCCACCCGG 60.837 68.421 0.00 0.00 0.00 5.73
2933 3809 1.837499 GGTCCCCTCTATCCACCCG 60.837 68.421 0.00 0.00 0.00 5.28
2934 3810 0.472161 GAGGTCCCCTCTATCCACCC 60.472 65.000 2.98 0.00 46.41 4.61
2935 3811 3.151048 GAGGTCCCCTCTATCCACC 57.849 63.158 2.98 0.00 46.41 4.61
2944 3820 2.852075 TTGCCGTTGAGGTCCCCT 60.852 61.111 0.00 0.00 43.70 4.79
2945 3821 2.671963 GTTGCCGTTGAGGTCCCC 60.672 66.667 0.00 0.00 43.70 4.81
2946 3822 1.671379 GAGTTGCCGTTGAGGTCCC 60.671 63.158 0.00 0.00 43.70 4.46
2947 3823 1.671379 GGAGTTGCCGTTGAGGTCC 60.671 63.158 0.00 0.00 43.70 4.46
2948 3824 0.534203 TTGGAGTTGCCGTTGAGGTC 60.534 55.000 0.00 0.00 43.70 3.85
2949 3825 0.535102 CTTGGAGTTGCCGTTGAGGT 60.535 55.000 0.00 0.00 43.70 3.85
2950 3826 1.237285 CCTTGGAGTTGCCGTTGAGG 61.237 60.000 0.00 0.00 44.97 3.86
2951 3827 0.250295 TCCTTGGAGTTGCCGTTGAG 60.250 55.000 0.00 0.00 40.66 3.02
2952 3828 0.250295 CTCCTTGGAGTTGCCGTTGA 60.250 55.000 8.45 0.00 40.66 3.18
2953 3829 1.237285 CCTCCTTGGAGTTGCCGTTG 61.237 60.000 14.77 0.00 40.66 4.10
2954 3830 1.073199 CCTCCTTGGAGTTGCCGTT 59.927 57.895 14.77 0.00 40.66 4.44
2955 3831 1.841556 TCCTCCTTGGAGTTGCCGT 60.842 57.895 14.77 0.00 40.56 5.68
2956 3832 3.068881 TCCTCCTTGGAGTTGCCG 58.931 61.111 14.77 0.51 40.56 5.69
2963 3839 2.225017 GGGTGTCATTTTCCTCCTTGGA 60.225 50.000 0.00 0.00 44.51 3.53
2964 3840 2.171003 GGGTGTCATTTTCCTCCTTGG 58.829 52.381 0.00 0.00 37.10 3.61
2965 3841 2.171003 GGGGTGTCATTTTCCTCCTTG 58.829 52.381 0.00 0.00 0.00 3.61
2966 3842 2.041755 GAGGGGTGTCATTTTCCTCCTT 59.958 50.000 0.00 0.00 38.36 3.36
2967 3843 1.636003 GAGGGGTGTCATTTTCCTCCT 59.364 52.381 0.00 0.00 38.36 3.69
2968 3844 1.679032 CGAGGGGTGTCATTTTCCTCC 60.679 57.143 0.00 0.00 40.50 4.30
2969 3845 1.679032 CCGAGGGGTGTCATTTTCCTC 60.679 57.143 0.00 0.00 40.28 3.71
2970 3846 0.328258 CCGAGGGGTGTCATTTTCCT 59.672 55.000 0.00 0.00 0.00 3.36
2971 3847 1.313091 GCCGAGGGGTGTCATTTTCC 61.313 60.000 0.00 0.00 34.97 3.13
2972 3848 0.322546 AGCCGAGGGGTGTCATTTTC 60.323 55.000 0.00 0.00 34.97 2.29
2973 3849 0.112412 AAGCCGAGGGGTGTCATTTT 59.888 50.000 0.00 0.00 31.90 1.82
2974 3850 0.112412 AAAGCCGAGGGGTGTCATTT 59.888 50.000 0.00 0.00 31.90 2.32
2975 3851 0.609131 CAAAGCCGAGGGGTGTCATT 60.609 55.000 0.00 0.00 31.90 2.57
2976 3852 1.002134 CAAAGCCGAGGGGTGTCAT 60.002 57.895 0.00 0.00 31.90 3.06
2977 3853 2.391724 GACAAAGCCGAGGGGTGTCA 62.392 60.000 0.00 0.00 37.01 3.58
2978 3854 1.671379 GACAAAGCCGAGGGGTGTC 60.671 63.158 0.00 0.00 31.95 3.67
2979 3855 2.430367 GACAAAGCCGAGGGGTGT 59.570 61.111 0.00 0.00 31.90 4.16
2980 3856 2.742372 CGACAAAGCCGAGGGGTG 60.742 66.667 0.00 0.00 31.90 4.61
2981 3857 3.236003 GACGACAAAGCCGAGGGGT 62.236 63.158 0.00 0.00 34.97 4.95
2982 3858 2.434359 GACGACAAAGCCGAGGGG 60.434 66.667 0.00 0.00 0.00 4.79
2983 3859 2.809601 CGACGACAAAGCCGAGGG 60.810 66.667 0.00 0.00 0.00 4.30
2984 3860 2.049433 ACGACGACAAAGCCGAGG 60.049 61.111 0.00 0.00 0.00 4.63
2985 3861 1.337817 CTGACGACGACAAAGCCGAG 61.338 60.000 0.00 0.00 0.00 4.63
2986 3862 1.371267 CTGACGACGACAAAGCCGA 60.371 57.895 0.00 0.00 0.00 5.54
2987 3863 2.372690 CCTGACGACGACAAAGCCG 61.373 63.158 0.00 0.00 0.00 5.52
2988 3864 2.668280 GCCTGACGACGACAAAGCC 61.668 63.158 0.00 0.00 0.00 4.35
2989 3865 2.668280 GGCCTGACGACGACAAAGC 61.668 63.158 0.00 7.63 0.00 3.51
2990 3866 2.372690 CGGCCTGACGACGACAAAG 61.373 63.158 0.00 0.00 35.47 2.77
2991 3867 2.355363 CGGCCTGACGACGACAAA 60.355 61.111 0.00 0.00 35.47 2.83
2992 3868 4.351938 CCGGCCTGACGACGACAA 62.352 66.667 0.00 0.00 35.47 3.18
2994 3870 4.773117 GTCCGGCCTGACGACGAC 62.773 72.222 11.85 0.00 35.47 4.34
3008 3884 1.253593 AAACCCTAGTCGGTCCGTCC 61.254 60.000 11.88 3.31 33.98 4.79
3009 3885 0.172127 GAAACCCTAGTCGGTCCGTC 59.828 60.000 11.88 5.68 33.98 4.79
3010 3886 1.253593 GGAAACCCTAGTCGGTCCGT 61.254 60.000 11.88 0.00 33.98 4.69
3011 3887 1.514553 GGAAACCCTAGTCGGTCCG 59.485 63.158 4.39 4.39 33.98 4.79
3024 3900 1.606601 GGCAAGGGACAGGGGAAAC 60.607 63.158 0.00 0.00 0.00 2.78
3025 3901 2.088096 TGGCAAGGGACAGGGGAAA 61.088 57.895 0.00 0.00 0.00 3.13
3026 3902 2.451493 TGGCAAGGGACAGGGGAA 60.451 61.111 0.00 0.00 0.00 3.97
3032 3908 2.853542 TGGAGCTGGCAAGGGACA 60.854 61.111 0.00 0.00 0.00 4.02
3033 3909 2.360475 GTGGAGCTGGCAAGGGAC 60.360 66.667 0.00 0.00 0.00 4.46
3034 3910 3.650950 GGTGGAGCTGGCAAGGGA 61.651 66.667 0.00 0.00 0.00 4.20
3035 3911 4.748144 GGGTGGAGCTGGCAAGGG 62.748 72.222 0.00 0.00 0.00 3.95
3051 3927 4.402528 TGATGAACCCGGGTGCGG 62.403 66.667 31.05 0.00 0.00 5.69
3052 3928 2.819595 CTGATGAACCCGGGTGCG 60.820 66.667 31.05 8.66 0.00 5.34
3053 3929 1.450312 CTCTGATGAACCCGGGTGC 60.450 63.158 31.05 28.67 0.00 5.01
3054 3930 1.450312 GCTCTGATGAACCCGGGTG 60.450 63.158 31.05 14.22 0.00 4.61
3055 3931 2.670148 GGCTCTGATGAACCCGGGT 61.670 63.158 24.16 24.16 0.00 5.28
3056 3932 2.190578 GGCTCTGATGAACCCGGG 59.809 66.667 22.25 22.25 0.00 5.73
3057 3933 2.202932 CGGCTCTGATGAACCCGG 60.203 66.667 0.00 0.00 35.11 5.73
3058 3934 1.519455 GACGGCTCTGATGAACCCG 60.519 63.158 0.00 0.00 40.63 5.28
3059 3935 0.036388 TTGACGGCTCTGATGAACCC 60.036 55.000 0.00 0.00 0.00 4.11
3060 3936 1.079503 GTTGACGGCTCTGATGAACC 58.920 55.000 0.00 0.00 0.00 3.62
3061 3937 1.079503 GGTTGACGGCTCTGATGAAC 58.920 55.000 0.00 0.00 0.00 3.18
3062 3938 0.389817 CGGTTGACGGCTCTGATGAA 60.390 55.000 0.00 0.00 39.42 2.57
3063 3939 1.215382 CGGTTGACGGCTCTGATGA 59.785 57.895 0.00 0.00 39.42 2.92
3064 3940 0.803768 CTCGGTTGACGGCTCTGATG 60.804 60.000 0.00 0.00 44.45 3.07
3065 3941 1.513158 CTCGGTTGACGGCTCTGAT 59.487 57.895 0.00 0.00 44.45 2.90
3066 3942 2.636412 CCTCGGTTGACGGCTCTGA 61.636 63.158 0.00 0.00 44.45 3.27
3067 3943 2.125912 CCTCGGTTGACGGCTCTG 60.126 66.667 0.00 0.00 44.45 3.35
3068 3944 3.382832 CCCTCGGTTGACGGCTCT 61.383 66.667 0.00 0.00 44.45 4.09
3069 3945 3.644399 GACCCTCGGTTGACGGCTC 62.644 68.421 0.00 0.00 44.45 4.70
3070 3946 3.692406 GACCCTCGGTTGACGGCT 61.692 66.667 0.00 0.00 44.45 5.52
3080 3956 2.434359 GGTTGCTTCCGACCCTCG 60.434 66.667 0.00 0.00 39.29 4.63
3088 3964 2.394563 GCTGCTCTCGGTTGCTTCC 61.395 63.158 0.00 0.00 0.00 3.46
3089 3965 2.734673 CGCTGCTCTCGGTTGCTTC 61.735 63.158 0.00 0.00 0.00 3.86
3090 3966 2.740055 CGCTGCTCTCGGTTGCTT 60.740 61.111 0.00 0.00 0.00 3.91
3091 3967 3.639541 CTCGCTGCTCTCGGTTGCT 62.640 63.158 0.00 0.00 0.00 3.91
3092 3968 3.184683 CTCGCTGCTCTCGGTTGC 61.185 66.667 0.00 0.00 0.00 4.17
3093 3969 1.515952 CTCTCGCTGCTCTCGGTTG 60.516 63.158 0.00 0.00 0.00 3.77
3094 3970 1.653094 CTCTCTCGCTGCTCTCGGTT 61.653 60.000 0.00 0.00 0.00 4.44
3095 3971 2.045829 TCTCTCGCTGCTCTCGGT 60.046 61.111 0.00 0.00 0.00 4.69
3096 3972 1.775039 CTCTCTCTCGCTGCTCTCGG 61.775 65.000 0.00 0.00 0.00 4.63
3097 3973 0.809636 TCTCTCTCTCGCTGCTCTCG 60.810 60.000 0.00 0.00 0.00 4.04
3098 3974 0.657840 GTCTCTCTCTCGCTGCTCTC 59.342 60.000 0.00 0.00 0.00 3.20
3099 3975 0.253044 AGTCTCTCTCTCGCTGCTCT 59.747 55.000 0.00 0.00 0.00 4.09
3100 3976 0.378257 CAGTCTCTCTCTCGCTGCTC 59.622 60.000 0.00 0.00 0.00 4.26
3101 3977 1.031571 CCAGTCTCTCTCTCGCTGCT 61.032 60.000 0.00 0.00 0.00 4.24
3102 3978 1.029408 TCCAGTCTCTCTCTCGCTGC 61.029 60.000 0.00 0.00 0.00 5.25
3103 3979 1.016627 CTCCAGTCTCTCTCTCGCTG 58.983 60.000 0.00 0.00 0.00 5.18
3104 3980 0.908910 TCTCCAGTCTCTCTCTCGCT 59.091 55.000 0.00 0.00 0.00 4.93
3105 3981 1.603802 CATCTCCAGTCTCTCTCTCGC 59.396 57.143 0.00 0.00 0.00 5.03
3106 3982 3.192541 TCATCTCCAGTCTCTCTCTCG 57.807 52.381 0.00 0.00 0.00 4.04
3107 3983 5.192927 TCTTTCATCTCCAGTCTCTCTCTC 58.807 45.833 0.00 0.00 0.00 3.20
3108 3984 5.191727 TCTTTCATCTCCAGTCTCTCTCT 57.808 43.478 0.00 0.00 0.00 3.10
3109 3985 4.202050 GCTCTTTCATCTCCAGTCTCTCTC 60.202 50.000 0.00 0.00 0.00 3.20
3110 3986 3.701040 GCTCTTTCATCTCCAGTCTCTCT 59.299 47.826 0.00 0.00 0.00 3.10
3111 3987 3.181476 GGCTCTTTCATCTCCAGTCTCTC 60.181 52.174 0.00 0.00 0.00 3.20
3112 3988 2.765699 GGCTCTTTCATCTCCAGTCTCT 59.234 50.000 0.00 0.00 0.00 3.10
3113 3989 2.499289 TGGCTCTTTCATCTCCAGTCTC 59.501 50.000 0.00 0.00 0.00 3.36
3114 3990 2.544721 TGGCTCTTTCATCTCCAGTCT 58.455 47.619 0.00 0.00 0.00 3.24
3115 3991 3.204526 CATGGCTCTTTCATCTCCAGTC 58.795 50.000 0.00 0.00 0.00 3.51
3116 3992 2.575279 ACATGGCTCTTTCATCTCCAGT 59.425 45.455 0.00 0.00 0.00 4.00
3117 3993 3.278668 ACATGGCTCTTTCATCTCCAG 57.721 47.619 0.00 0.00 0.00 3.86
3118 3994 3.118261 GGTACATGGCTCTTTCATCTCCA 60.118 47.826 0.00 0.00 0.00 3.86
3119 3995 3.135530 AGGTACATGGCTCTTTCATCTCC 59.864 47.826 0.00 0.00 0.00 3.71
3120 3996 4.376146 GAGGTACATGGCTCTTTCATCTC 58.624 47.826 0.00 0.00 0.00 2.75
3121 3997 3.135530 GGAGGTACATGGCTCTTTCATCT 59.864 47.826 0.00 0.00 0.00 2.90
3122 3998 3.118261 TGGAGGTACATGGCTCTTTCATC 60.118 47.826 0.00 0.00 0.00 2.92
3123 3999 2.846206 TGGAGGTACATGGCTCTTTCAT 59.154 45.455 0.00 0.00 0.00 2.57
3124 4000 2.265367 TGGAGGTACATGGCTCTTTCA 58.735 47.619 0.00 0.00 0.00 2.69
3125 4001 3.567478 ATGGAGGTACATGGCTCTTTC 57.433 47.619 0.00 0.00 0.00 2.62



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

AutoCloner maintained by Alex Coulton.