Multiple sequence alignment - TraesCS4D01G190100

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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 TraesCS4D01G190100 chr4D 100.000 3011 0 0 1 3011 333012872 333009862 0.000000e+00 5561
1 TraesCS4D01G190100 chr4D 96.522 115 4 0 2897 3011 310113771 310113657 1.100000e-44 191
2 TraesCS4D01G190100 chr4A 89.775 2670 95 53 57 2609 140306045 140308653 0.000000e+00 3254
3 TraesCS4D01G190100 chr4A 93.143 175 10 1 2617 2789 140309023 140309197 3.850000e-64 255
4 TraesCS4D01G190100 chr4B 91.706 2315 86 33 541 2789 411490234 411487960 0.000000e+00 3114
5 TraesCS4D01G190100 chr4B 90.659 364 15 9 25 373 411491093 411490734 1.630000e-127 466
6 TraesCS4D01G190100 chr4B 87.958 191 14 6 370 552 411490462 411490273 1.820000e-52 217
7 TraesCS4D01G190100 chr2D 96.667 120 4 0 2892 3011 629478132 629478013 1.830000e-47 200
8 TraesCS4D01G190100 chr2D 96.610 118 4 0 2894 3011 49614451 49614568 2.370000e-46 196
9 TraesCS4D01G190100 chr2D 96.552 116 4 0 2896 3011 110637281 110637166 3.060000e-45 193
10 TraesCS4D01G190100 chr5D 96.491 114 4 0 2898 3011 499958785 499958898 3.960000e-44 189
11 TraesCS4D01G190100 chr5D 76.140 285 43 21 1159 1426 536694366 536694642 3.150000e-25 126
12 TraesCS4D01G190100 chr3D 95.690 116 5 0 2896 3011 179916663 179916778 1.430000e-43 187
13 TraesCS4D01G190100 chr7D 94.783 115 6 0 2897 3011 563845967 563845853 2.380000e-41 180
14 TraesCS4D01G190100 chr1B 93.043 115 8 0 2897 3011 671524320 671524206 5.160000e-38 169
15 TraesCS4D01G190100 chr6D 91.667 120 10 0 2892 3011 408944645 408944526 1.860000e-37 167


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 TraesCS4D01G190100 chr4D 333009862 333012872 3010 True 5561.000000 5561 100.000000 1 3011 1 chr4D.!!$R2 3010
1 TraesCS4D01G190100 chr4A 140306045 140309197 3152 False 1754.500000 3254 91.459000 57 2789 2 chr4A.!!$F1 2732
2 TraesCS4D01G190100 chr4B 411487960 411491093 3133 True 1265.666667 3114 90.107667 25 2789 3 chr4B.!!$R1 2764

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
55 57 0.179129 TAAAGCGACGGATCCGGTTC 60.179 55.0 35.87 24.23 45.29 3.62 F
659 1021 0.250945 AGAGACAGTGTCGCTCTCCA 60.251 55.0 22.16 0.00 38.21 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1392 1791 0.939577 TGTTGCAGAAGACGTCGAGC 60.940 55.0 10.46 13.01 34.07 5.03 R
2615 3075 0.108615 GCTTCTTCCGCTGCACTCTA 60.109 55.0 0.00 0.00 0.00 2.43 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
41 42 7.860918 AGGCTACAAAGGTTAGTATTAAAGC 57.139 36.000 0.00 0.00 0.00 3.51
42 43 6.537660 AGGCTACAAAGGTTAGTATTAAAGCG 59.462 38.462 0.00 0.00 0.00 4.68
43 44 6.536224 GGCTACAAAGGTTAGTATTAAAGCGA 59.464 38.462 0.00 0.00 0.00 4.93
44 45 7.397194 GCTACAAAGGTTAGTATTAAAGCGAC 58.603 38.462 0.00 0.00 0.00 5.19
45 46 6.399204 ACAAAGGTTAGTATTAAAGCGACG 57.601 37.500 0.00 0.00 0.00 5.12
48 49 5.526506 AGGTTAGTATTAAAGCGACGGAT 57.473 39.130 0.00 0.00 0.00 4.18
49 50 5.527033 AGGTTAGTATTAAAGCGACGGATC 58.473 41.667 0.00 0.00 0.00 3.36
50 51 4.683320 GGTTAGTATTAAAGCGACGGATCC 59.317 45.833 0.00 0.00 0.00 3.36
55 57 0.179129 TAAAGCGACGGATCCGGTTC 60.179 55.000 35.87 24.23 45.29 3.62
162 167 1.002087 CTACCCAGCCAGAAAAGTCGT 59.998 52.381 0.00 0.00 0.00 4.34
197 202 4.540824 GAAGCAAACACAATGTCTTCTCC 58.459 43.478 5.00 0.00 32.80 3.71
202 207 3.971245 ACACAATGTCTTCTCCTCTCC 57.029 47.619 0.00 0.00 0.00 3.71
203 208 3.515562 ACACAATGTCTTCTCCTCTCCT 58.484 45.455 0.00 0.00 0.00 3.69
206 211 3.245948 ACAATGTCTTCTCCTCTCCTCCT 60.246 47.826 0.00 0.00 0.00 3.69
216 222 2.285180 CTCCTCCTCCCCCTCCTG 59.715 72.222 0.00 0.00 0.00 3.86
241 247 1.662044 GGTTGACCCAGCAAGCAAG 59.338 57.895 0.00 0.00 43.66 4.01
250 256 2.202570 GCAAGCAAGCCTCGCATG 60.203 61.111 0.00 0.00 0.00 4.06
334 363 2.808543 GTTTCGTGCTCCTCAATCTTGT 59.191 45.455 0.00 0.00 0.00 3.16
413 717 1.370609 CATCAGCTCAAGACAGCCAG 58.629 55.000 0.00 0.00 40.65 4.85
421 725 0.393537 CAAGACAGCCAGGACCATCC 60.394 60.000 0.00 0.00 36.58 3.51
521 832 2.106131 CAATCCGATCCGTCCGCA 59.894 61.111 0.00 0.00 0.00 5.69
631 993 0.253894 TCGTGGACCGGAGACATCTA 59.746 55.000 9.46 0.00 37.11 1.98
659 1021 0.250945 AGAGACAGTGTCGCTCTCCA 60.251 55.000 22.16 0.00 38.21 3.86
672 1034 1.756408 CTCTCCATGCTGATCCGCCT 61.756 60.000 6.66 0.00 0.00 5.52
790 1180 4.976619 GCTTGGCTAATCGCGAAC 57.023 55.556 15.24 2.68 40.44 3.95
794 1184 0.800012 TTGGCTAATCGCGAACCAAC 59.200 50.000 23.80 12.52 40.44 3.77
929 1325 0.896226 CCGGCCCTCCTATAAGTAGC 59.104 60.000 0.00 0.00 0.00 3.58
980 1376 2.099756 GCAAGCTTCACACACTTCCTTT 59.900 45.455 0.00 0.00 0.00 3.11
1015 1414 2.490148 TACATGCGCGCTAGCCTCT 61.490 57.895 33.29 10.65 41.18 3.69
1248 1647 3.959975 GTCAAGCACGGCGCCAAA 61.960 61.111 28.98 0.00 44.04 3.28
2108 2517 4.992381 ATAACTGCACTCAAGTTCGTTC 57.008 40.909 0.00 0.00 0.00 3.95
2261 2682 7.001674 AGATACGATCTGAGATGGAAAGTACT 58.998 38.462 11.52 0.00 38.44 2.73
2264 2685 5.039984 CGATCTGAGATGGAAAGTACTGTG 58.960 45.833 0.00 0.00 0.00 3.66
2266 2687 6.611613 ATCTGAGATGGAAAGTACTGTGAA 57.388 37.500 0.00 0.00 0.00 3.18
2268 2689 6.634805 TCTGAGATGGAAAGTACTGTGAATC 58.365 40.000 0.00 0.00 0.00 2.52
2269 2690 6.211384 TCTGAGATGGAAAGTACTGTGAATCA 59.789 38.462 0.00 0.00 0.00 2.57
2386 2828 2.691674 AATTTTGGGCCGCACACACG 62.692 55.000 0.00 0.00 0.00 4.49
2406 2854 1.333619 GCTCTCTCTTCCGCTAGAGTG 59.666 57.143 10.60 8.95 41.91 3.51
2422 2870 4.280789 AGAGTGGGGATGGTTGATAGTA 57.719 45.455 0.00 0.00 0.00 1.82
2423 2871 4.227197 AGAGTGGGGATGGTTGATAGTAG 58.773 47.826 0.00 0.00 0.00 2.57
2424 2872 3.967987 GAGTGGGGATGGTTGATAGTAGT 59.032 47.826 0.00 0.00 0.00 2.73
2425 2873 4.371681 AGTGGGGATGGTTGATAGTAGTT 58.628 43.478 0.00 0.00 0.00 2.24
2501 2952 8.023706 TGCGATCTATCTGTAGATTTGACATAC 58.976 37.037 0.00 0.00 45.47 2.39
2512 2963 9.623000 TGTAGATTTGACATACTAGTAGTAGCA 57.377 33.333 15.08 10.22 33.66 3.49
2516 2967 8.693120 ATTTGACATACTAGTAGTAGCAGCTA 57.307 34.615 15.08 0.00 33.66 3.32
2517 2968 7.731882 TTGACATACTAGTAGTAGCAGCTAG 57.268 40.000 15.08 0.00 33.66 3.42
2520 2971 7.774157 TGACATACTAGTAGTAGCAGCTAGTTT 59.226 37.037 15.20 7.07 41.62 2.66
2551 3002 3.497932 GCGAGCAGAGGCAGCAAG 61.498 66.667 0.00 0.00 44.61 4.01
2552 3003 2.818714 CGAGCAGAGGCAGCAAGG 60.819 66.667 0.00 0.00 44.61 3.61
2559 3010 0.980231 AGAGGCAGCAAGGAGGGTAG 60.980 60.000 0.00 0.00 0.00 3.18
2610 3070 8.998377 TCTATCTGTCGATTGAAACAATTTTGA 58.002 29.630 0.00 0.00 30.29 2.69
2612 3072 7.026631 TCTGTCGATTGAAACAATTTTGAGT 57.973 32.000 0.00 0.00 0.00 3.41
2613 3073 8.148807 TCTGTCGATTGAAACAATTTTGAGTA 57.851 30.769 0.00 0.00 0.00 2.59
2615 3075 7.925993 TGTCGATTGAAACAATTTTGAGTAGT 58.074 30.769 0.00 0.00 0.00 2.73
2616 3076 9.047371 TGTCGATTGAAACAATTTTGAGTAGTA 57.953 29.630 0.00 0.00 0.00 1.82
2617 3077 9.530129 GTCGATTGAAACAATTTTGAGTAGTAG 57.470 33.333 0.00 0.00 0.00 2.57
2618 3078 9.483916 TCGATTGAAACAATTTTGAGTAGTAGA 57.516 29.630 0.00 0.00 0.00 2.59
2619 3079 9.746711 CGATTGAAACAATTTTGAGTAGTAGAG 57.253 33.333 0.00 0.00 0.00 2.43
2622 3082 7.861630 TGAAACAATTTTGAGTAGTAGAGTGC 58.138 34.615 0.00 0.00 0.00 4.40
2626 3448 2.921634 TTGAGTAGTAGAGTGCAGCG 57.078 50.000 0.00 0.00 0.00 5.18
2634 3456 0.108615 TAGAGTGCAGCGGAAGAAGC 60.109 55.000 0.00 0.00 0.00 3.86
2743 3569 7.913674 GAAAAGATCGAAGGGCAGAATATAT 57.086 36.000 0.00 0.00 0.00 0.86
2789 3615 2.253603 GCCTAAAAGTTGAATGCAGCG 58.746 47.619 0.00 0.00 0.00 5.18
2790 3616 2.351738 GCCTAAAAGTTGAATGCAGCGT 60.352 45.455 0.00 0.00 0.00 5.07
2791 3617 3.119990 GCCTAAAAGTTGAATGCAGCGTA 60.120 43.478 0.00 0.00 0.00 4.42
2792 3618 4.651994 CCTAAAAGTTGAATGCAGCGTAG 58.348 43.478 0.00 0.00 0.00 3.51
2805 3631 4.692129 CGTAGCCGTCTAGTGCAG 57.308 61.111 0.00 0.00 0.00 4.41
2806 3632 1.064296 CGTAGCCGTCTAGTGCAGG 59.936 63.158 0.00 0.00 0.00 4.85
2807 3633 1.437986 GTAGCCGTCTAGTGCAGGG 59.562 63.158 0.00 0.00 0.00 4.45
2808 3634 1.035932 GTAGCCGTCTAGTGCAGGGA 61.036 60.000 0.00 0.00 0.00 4.20
2809 3635 1.035932 TAGCCGTCTAGTGCAGGGAC 61.036 60.000 0.00 0.00 0.00 4.46
2810 3636 2.893398 CCGTCTAGTGCAGGGACC 59.107 66.667 0.00 0.00 0.00 4.46
2811 3637 1.682684 CCGTCTAGTGCAGGGACCT 60.683 63.158 0.00 0.00 0.00 3.85
2812 3638 1.668101 CCGTCTAGTGCAGGGACCTC 61.668 65.000 0.00 0.00 0.00 3.85
2813 3639 0.965866 CGTCTAGTGCAGGGACCTCA 60.966 60.000 0.00 0.00 0.00 3.86
2814 3640 1.267121 GTCTAGTGCAGGGACCTCAA 58.733 55.000 0.00 0.00 0.00 3.02
2815 3641 1.834263 GTCTAGTGCAGGGACCTCAAT 59.166 52.381 0.00 0.00 0.00 2.57
2816 3642 1.833630 TCTAGTGCAGGGACCTCAATG 59.166 52.381 0.00 0.00 0.00 2.82
2817 3643 0.253044 TAGTGCAGGGACCTCAATGC 59.747 55.000 0.00 0.00 39.14 3.56
2818 3644 2.046023 TGCAGGGACCTCAATGCG 60.046 61.111 0.00 0.00 41.58 4.73
2819 3645 3.512516 GCAGGGACCTCAATGCGC 61.513 66.667 0.00 0.00 0.00 6.09
2820 3646 2.046023 CAGGGACCTCAATGCGCA 60.046 61.111 14.96 14.96 0.00 6.09
2821 3647 1.452651 CAGGGACCTCAATGCGCAT 60.453 57.895 19.28 19.28 0.00 4.73
2822 3648 1.033746 CAGGGACCTCAATGCGCATT 61.034 55.000 29.36 29.36 0.00 3.56
2823 3649 0.546122 AGGGACCTCAATGCGCATTA 59.454 50.000 33.44 20.32 0.00 1.90
2824 3650 0.663153 GGGACCTCAATGCGCATTAC 59.337 55.000 33.44 20.62 0.00 1.89
2838 3664 2.804421 CATTACGCAATGCTCACGAA 57.196 45.000 2.94 0.00 35.44 3.85
2839 3665 2.697363 CATTACGCAATGCTCACGAAG 58.303 47.619 2.94 0.00 35.44 3.79
2849 3675 3.521995 CTCACGAAGCTCACCACAT 57.478 52.632 0.00 0.00 0.00 3.21
2850 3676 1.354040 CTCACGAAGCTCACCACATC 58.646 55.000 0.00 0.00 0.00 3.06
2851 3677 0.388520 TCACGAAGCTCACCACATCG 60.389 55.000 0.37 0.37 39.30 3.84
2852 3678 1.079819 ACGAAGCTCACCACATCGG 60.080 57.895 6.66 0.00 37.81 4.18
2865 3691 3.706698 CCACATCGGTCATACTGTAGTG 58.293 50.000 0.00 0.00 33.48 2.74
2866 3692 3.490933 CCACATCGGTCATACTGTAGTGG 60.491 52.174 13.78 13.78 40.79 4.00
2867 3693 3.130516 CACATCGGTCATACTGTAGTGGT 59.869 47.826 0.00 0.00 31.65 4.16
2868 3694 4.337274 CACATCGGTCATACTGTAGTGGTA 59.663 45.833 0.00 0.00 31.65 3.25
2869 3695 4.951715 ACATCGGTCATACTGTAGTGGTAA 59.048 41.667 0.00 0.00 0.00 2.85
2870 3696 5.597182 ACATCGGTCATACTGTAGTGGTAAT 59.403 40.000 0.00 0.00 0.00 1.89
2871 3697 6.774170 ACATCGGTCATACTGTAGTGGTAATA 59.226 38.462 0.00 0.00 0.00 0.98
2872 3698 7.286087 ACATCGGTCATACTGTAGTGGTAATAA 59.714 37.037 0.00 0.00 0.00 1.40
2873 3699 7.828508 TCGGTCATACTGTAGTGGTAATAAT 57.171 36.000 0.00 0.00 0.00 1.28
2874 3700 7.879070 TCGGTCATACTGTAGTGGTAATAATC 58.121 38.462 0.00 0.00 0.00 1.75
2875 3701 7.722728 TCGGTCATACTGTAGTGGTAATAATCT 59.277 37.037 0.00 0.00 0.00 2.40
2876 3702 7.808381 CGGTCATACTGTAGTGGTAATAATCTG 59.192 40.741 0.00 0.00 0.00 2.90
2877 3703 8.088981 GGTCATACTGTAGTGGTAATAATCTGG 58.911 40.741 0.00 0.00 0.00 3.86
2878 3704 8.088981 GTCATACTGTAGTGGTAATAATCTGGG 58.911 40.741 0.00 0.00 0.00 4.45
2879 3705 5.888982 ACTGTAGTGGTAATAATCTGGGG 57.111 43.478 0.00 0.00 0.00 4.96
2880 3706 4.658901 ACTGTAGTGGTAATAATCTGGGGG 59.341 45.833 0.00 0.00 0.00 5.40
2881 3707 4.637600 TGTAGTGGTAATAATCTGGGGGT 58.362 43.478 0.00 0.00 0.00 4.95
2882 3708 5.790642 TGTAGTGGTAATAATCTGGGGGTA 58.209 41.667 0.00 0.00 0.00 3.69
2883 3709 6.395598 TGTAGTGGTAATAATCTGGGGGTAT 58.604 40.000 0.00 0.00 0.00 2.73
2884 3710 5.843019 AGTGGTAATAATCTGGGGGTATG 57.157 43.478 0.00 0.00 0.00 2.39
2885 3711 4.601857 AGTGGTAATAATCTGGGGGTATGG 59.398 45.833 0.00 0.00 0.00 2.74
2886 3712 3.332485 TGGTAATAATCTGGGGGTATGGC 59.668 47.826 0.00 0.00 0.00 4.40
2887 3713 3.332485 GGTAATAATCTGGGGGTATGGCA 59.668 47.826 0.00 0.00 0.00 4.92
2888 3714 4.202631 GGTAATAATCTGGGGGTATGGCAA 60.203 45.833 0.00 0.00 0.00 4.52
2889 3715 4.551215 AATAATCTGGGGGTATGGCAAA 57.449 40.909 0.00 0.00 0.00 3.68
2890 3716 2.938428 AATCTGGGGGTATGGCAAAA 57.062 45.000 0.00 0.00 0.00 2.44
2891 3717 2.938428 ATCTGGGGGTATGGCAAAAA 57.062 45.000 0.00 0.00 0.00 1.94
2910 3736 5.793026 AAAAAGAACGAAATTGCTTTGCA 57.207 30.435 0.00 0.00 36.47 4.08
2911 3737 4.777140 AAAGAACGAAATTGCTTTGCAC 57.223 36.364 0.00 0.00 38.71 4.57
2912 3738 3.435105 AGAACGAAATTGCTTTGCACA 57.565 38.095 0.00 0.00 38.71 4.57
2913 3739 3.115554 AGAACGAAATTGCTTTGCACAC 58.884 40.909 0.00 0.00 38.71 3.82
2914 3740 1.476074 ACGAAATTGCTTTGCACACG 58.524 45.000 0.00 0.00 38.71 4.49
2915 3741 1.064803 ACGAAATTGCTTTGCACACGA 59.935 42.857 0.00 0.00 38.71 4.35
2916 3742 2.287547 ACGAAATTGCTTTGCACACGAT 60.288 40.909 0.00 0.00 38.71 3.73
2917 3743 2.339400 CGAAATTGCTTTGCACACGATC 59.661 45.455 0.00 0.00 38.71 3.69
2918 3744 3.568538 GAAATTGCTTTGCACACGATCT 58.431 40.909 0.00 0.00 38.71 2.75
2919 3745 3.648339 AATTGCTTTGCACACGATCTT 57.352 38.095 0.00 0.00 38.71 2.40
2920 3746 3.648339 ATTGCTTTGCACACGATCTTT 57.352 38.095 0.00 0.00 38.71 2.52
2921 3747 2.404265 TGCTTTGCACACGATCTTTG 57.596 45.000 0.00 0.00 31.71 2.77
2922 3748 1.675483 TGCTTTGCACACGATCTTTGT 59.325 42.857 0.00 0.00 31.71 2.83
2923 3749 2.875317 TGCTTTGCACACGATCTTTGTA 59.125 40.909 0.00 0.00 31.71 2.41
2924 3750 3.226347 GCTTTGCACACGATCTTTGTAC 58.774 45.455 0.00 0.00 0.00 2.90
2925 3751 3.303725 GCTTTGCACACGATCTTTGTACA 60.304 43.478 0.00 0.00 0.00 2.90
2926 3752 4.613622 GCTTTGCACACGATCTTTGTACAT 60.614 41.667 0.00 0.00 0.00 2.29
2927 3753 5.390461 GCTTTGCACACGATCTTTGTACATA 60.390 40.000 0.00 0.00 0.00 2.29
2928 3754 5.524511 TTGCACACGATCTTTGTACATAC 57.475 39.130 0.00 0.00 0.00 2.39
2929 3755 3.610677 TGCACACGATCTTTGTACATACG 59.389 43.478 0.00 1.53 0.00 3.06
2930 3756 3.855379 GCACACGATCTTTGTACATACGA 59.145 43.478 0.00 0.00 0.00 3.43
2931 3757 4.503007 GCACACGATCTTTGTACATACGAT 59.497 41.667 0.00 0.00 0.00 3.73
2932 3758 5.331607 GCACACGATCTTTGTACATACGATC 60.332 44.000 14.66 14.66 0.00 3.69
2933 3759 5.971792 CACACGATCTTTGTACATACGATCT 59.028 40.000 19.00 9.63 0.00 2.75
2934 3760 5.971792 ACACGATCTTTGTACATACGATCTG 59.028 40.000 19.00 17.55 0.00 2.90
2935 3761 6.183360 ACACGATCTTTGTACATACGATCTGA 60.183 38.462 19.00 2.20 0.00 3.27
2936 3762 6.140895 CACGATCTTTGTACATACGATCTGAC 59.859 42.308 19.00 3.66 0.00 3.51
2937 3763 5.337251 CGATCTTTGTACATACGATCTGACG 59.663 44.000 19.00 9.26 39.31 4.35
2939 3765 5.329493 TCTTTGTACATACGATCTGACGTG 58.671 41.667 13.06 3.41 46.02 4.49
2940 3766 4.690184 TTGTACATACGATCTGACGTGT 57.310 40.909 13.06 6.06 46.02 4.49
2941 3767 4.268767 TGTACATACGATCTGACGTGTC 57.731 45.455 13.06 0.00 46.02 3.67
2942 3768 3.937079 TGTACATACGATCTGACGTGTCT 59.063 43.478 13.06 1.07 46.02 3.41
2943 3769 4.393990 TGTACATACGATCTGACGTGTCTT 59.606 41.667 13.06 2.46 46.02 3.01
2944 3770 4.017380 ACATACGATCTGACGTGTCTTC 57.983 45.455 13.06 0.00 46.02 2.87
2945 3771 3.439129 ACATACGATCTGACGTGTCTTCA 59.561 43.478 13.06 0.00 46.02 3.02
2946 3772 2.333389 ACGATCTGACGTGTCTTCAC 57.667 50.000 0.00 0.00 44.84 3.18
2947 3773 1.880675 ACGATCTGACGTGTCTTCACT 59.119 47.619 0.00 0.00 44.84 3.41
2948 3774 3.072211 ACGATCTGACGTGTCTTCACTA 58.928 45.455 0.00 0.00 44.84 2.74
2949 3775 3.125487 ACGATCTGACGTGTCTTCACTAG 59.875 47.826 0.00 0.00 44.84 2.57
2950 3776 3.371285 CGATCTGACGTGTCTTCACTAGA 59.629 47.826 0.00 0.00 41.89 2.43
2951 3777 7.088627 ACGATCTGACGTGTCTTCACTAGAC 62.089 48.000 0.00 0.00 44.84 2.59
2961 3787 4.607293 TCTTCACTAGACAACATGCTGT 57.393 40.909 0.26 0.26 0.00 4.40
2962 3788 4.309933 TCTTCACTAGACAACATGCTGTG 58.690 43.478 6.45 0.00 0.00 3.66
2963 3789 3.751479 TCACTAGACAACATGCTGTGT 57.249 42.857 6.45 5.21 44.84 3.72
2974 3800 4.470334 ACATGCTGTGTTGGTTTTCTTT 57.530 36.364 0.00 0.00 38.01 2.52
2975 3801 4.831107 ACATGCTGTGTTGGTTTTCTTTT 58.169 34.783 0.00 0.00 38.01 2.27
2976 3802 4.869861 ACATGCTGTGTTGGTTTTCTTTTC 59.130 37.500 0.00 0.00 38.01 2.29
2977 3803 3.855858 TGCTGTGTTGGTTTTCTTTTCC 58.144 40.909 0.00 0.00 0.00 3.13
2978 3804 3.194861 GCTGTGTTGGTTTTCTTTTCCC 58.805 45.455 0.00 0.00 0.00 3.97
2979 3805 3.368948 GCTGTGTTGGTTTTCTTTTCCCA 60.369 43.478 0.00 0.00 0.00 4.37
2980 3806 4.826556 CTGTGTTGGTTTTCTTTTCCCAA 58.173 39.130 0.00 0.00 34.69 4.12
2981 3807 5.427378 CTGTGTTGGTTTTCTTTTCCCAAT 58.573 37.500 0.00 0.00 39.05 3.16
2982 3808 5.181748 TGTGTTGGTTTTCTTTTCCCAATG 58.818 37.500 0.00 0.00 39.05 2.82
2983 3809 4.574421 GTGTTGGTTTTCTTTTCCCAATGG 59.426 41.667 0.00 0.00 39.05 3.16
2984 3810 4.471386 TGTTGGTTTTCTTTTCCCAATGGA 59.529 37.500 0.00 0.00 39.05 3.41
2985 3811 4.953940 TGGTTTTCTTTTCCCAATGGAG 57.046 40.909 0.00 0.00 43.07 3.86
2986 3812 3.070878 TGGTTTTCTTTTCCCAATGGAGC 59.929 43.478 0.00 0.00 43.07 4.70
2987 3813 3.324846 GGTTTTCTTTTCCCAATGGAGCT 59.675 43.478 0.00 0.00 43.07 4.09
2988 3814 4.309933 GTTTTCTTTTCCCAATGGAGCTG 58.690 43.478 0.00 0.00 43.07 4.24
2989 3815 2.220653 TCTTTTCCCAATGGAGCTGG 57.779 50.000 0.00 0.00 43.07 4.85
2990 3816 1.428912 TCTTTTCCCAATGGAGCTGGT 59.571 47.619 0.00 0.00 43.07 4.00
2991 3817 2.158325 TCTTTTCCCAATGGAGCTGGTT 60.158 45.455 0.00 0.00 43.07 3.67
2992 3818 1.631405 TTTCCCAATGGAGCTGGTTG 58.369 50.000 0.00 0.00 43.07 3.77
2993 3819 0.776810 TTCCCAATGGAGCTGGTTGA 59.223 50.000 0.00 0.00 43.07 3.18
2994 3820 1.002069 TCCCAATGGAGCTGGTTGAT 58.998 50.000 0.00 0.00 35.03 2.57
2995 3821 1.358787 TCCCAATGGAGCTGGTTGATT 59.641 47.619 0.00 0.00 35.03 2.57
2996 3822 1.479323 CCCAATGGAGCTGGTTGATTG 59.521 52.381 0.00 0.00 31.45 2.67
2997 3823 1.479323 CCAATGGAGCTGGTTGATTGG 59.521 52.381 13.20 13.20 37.72 3.16
2998 3824 2.449464 CAATGGAGCTGGTTGATTGGA 58.551 47.619 0.00 0.00 0.00 3.53
2999 3825 2.134789 ATGGAGCTGGTTGATTGGAC 57.865 50.000 0.00 0.00 0.00 4.02
3000 3826 0.321564 TGGAGCTGGTTGATTGGACG 60.322 55.000 0.00 0.00 0.00 4.79
3001 3827 0.036388 GGAGCTGGTTGATTGGACGA 60.036 55.000 0.00 0.00 0.00 4.20
3002 3828 1.610624 GGAGCTGGTTGATTGGACGAA 60.611 52.381 0.00 0.00 0.00 3.85
3003 3829 2.151202 GAGCTGGTTGATTGGACGAAA 58.849 47.619 0.00 0.00 0.00 3.46
3004 3830 2.154462 AGCTGGTTGATTGGACGAAAG 58.846 47.619 0.00 0.00 0.00 2.62
3005 3831 1.200020 GCTGGTTGATTGGACGAAAGG 59.800 52.381 0.00 0.00 0.00 3.11
3006 3832 2.778299 CTGGTTGATTGGACGAAAGGA 58.222 47.619 0.00 0.00 0.00 3.36
3007 3833 2.484264 CTGGTTGATTGGACGAAAGGAC 59.516 50.000 0.00 0.00 0.00 3.85
3008 3834 2.158740 TGGTTGATTGGACGAAAGGACA 60.159 45.455 0.00 0.00 0.00 4.02
3009 3835 3.081804 GGTTGATTGGACGAAAGGACAT 58.918 45.455 0.00 0.00 0.00 3.06
3010 3836 3.119849 GGTTGATTGGACGAAAGGACATG 60.120 47.826 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.093458 ACCTTTGTAGCCTTTTACTAGTAGTAA 57.907 33.333 17.12 17.12 38.79 2.24
4 5 8.655935 ACCTTTGTAGCCTTTTACTAGTAGTA 57.344 34.615 5.90 5.90 0.00 1.82
5 6 7.550597 ACCTTTGTAGCCTTTTACTAGTAGT 57.449 36.000 8.14 8.14 0.00 2.73
6 7 9.583765 CTAACCTTTGTAGCCTTTTACTAGTAG 57.416 37.037 2.23 0.00 0.00 2.57
7 8 9.093458 ACTAACCTTTGTAGCCTTTTACTAGTA 57.907 33.333 0.00 0.00 0.00 1.82
8 9 7.971201 ACTAACCTTTGTAGCCTTTTACTAGT 58.029 34.615 0.00 0.00 0.00 2.57
15 16 8.737175 GCTTTAATACTAACCTTTGTAGCCTTT 58.263 33.333 0.00 0.00 0.00 3.11
16 17 7.065443 CGCTTTAATACTAACCTTTGTAGCCTT 59.935 37.037 0.00 0.00 0.00 4.35
17 18 6.537660 CGCTTTAATACTAACCTTTGTAGCCT 59.462 38.462 0.00 0.00 0.00 4.58
18 19 6.536224 TCGCTTTAATACTAACCTTTGTAGCC 59.464 38.462 0.00 0.00 0.00 3.93
19 20 7.397194 GTCGCTTTAATACTAACCTTTGTAGC 58.603 38.462 0.00 0.00 0.00 3.58
20 21 7.253883 CCGTCGCTTTAATACTAACCTTTGTAG 60.254 40.741 0.00 0.00 0.00 2.74
21 22 6.531240 CCGTCGCTTTAATACTAACCTTTGTA 59.469 38.462 0.00 0.00 0.00 2.41
22 23 5.349543 CCGTCGCTTTAATACTAACCTTTGT 59.650 40.000 0.00 0.00 0.00 2.83
23 24 5.577945 TCCGTCGCTTTAATACTAACCTTTG 59.422 40.000 0.00 0.00 0.00 2.77
35 36 0.247185 AACCGGATCCGTCGCTTTAA 59.753 50.000 31.22 0.00 37.81 1.52
36 37 0.179129 GAACCGGATCCGTCGCTTTA 60.179 55.000 31.22 0.00 37.81 1.85
37 38 1.447314 GAACCGGATCCGTCGCTTT 60.447 57.895 31.22 16.02 37.81 3.51
38 39 1.033746 TAGAACCGGATCCGTCGCTT 61.034 55.000 31.22 16.75 37.81 4.68
39 40 1.445716 CTAGAACCGGATCCGTCGCT 61.446 60.000 31.22 24.45 37.81 4.93
40 41 1.008767 CTAGAACCGGATCCGTCGC 60.009 63.158 31.22 19.25 37.81 5.19
41 42 0.816825 TCCTAGAACCGGATCCGTCG 60.817 60.000 31.22 19.88 37.81 5.12
42 43 0.953003 CTCCTAGAACCGGATCCGTC 59.047 60.000 31.22 22.88 37.81 4.79
43 44 0.467659 CCTCCTAGAACCGGATCCGT 60.468 60.000 31.22 15.45 37.81 4.69
44 45 0.178998 TCCTCCTAGAACCGGATCCG 60.179 60.000 27.65 27.65 39.44 4.18
45 46 1.896465 CATCCTCCTAGAACCGGATCC 59.104 57.143 9.46 0.00 34.15 3.36
48 49 0.635009 ACCATCCTCCTAGAACCGGA 59.365 55.000 9.46 0.00 0.00 5.14
49 50 0.753262 CACCATCCTCCTAGAACCGG 59.247 60.000 0.00 0.00 0.00 5.28
50 51 1.486211 ACACCATCCTCCTAGAACCG 58.514 55.000 0.00 0.00 0.00 4.44
55 57 0.537188 ACGCAACACCATCCTCCTAG 59.463 55.000 0.00 0.00 0.00 3.02
162 167 0.249699 TTGCTTCGACTTTCGGCTCA 60.250 50.000 0.00 0.00 40.88 4.26
197 202 2.018086 AGGAGGGGGAGGAGGAGAG 61.018 68.421 0.00 0.00 0.00 3.20
202 207 0.980231 CTTCACAGGAGGGGGAGGAG 60.980 65.000 0.00 0.00 0.00 3.69
203 208 1.081092 CTTCACAGGAGGGGGAGGA 59.919 63.158 0.00 0.00 0.00 3.71
241 247 1.817099 CCTTGAGACCATGCGAGGC 60.817 63.158 0.00 0.00 0.00 4.70
250 256 1.466856 TGCATTGCATCCTTGAGACC 58.533 50.000 7.38 0.00 31.71 3.85
334 363 0.176910 TTCAACAGTGTGGACGCTCA 59.823 50.000 0.00 0.00 33.88 4.26
413 717 3.793888 GGGGTCGGTGGATGGTCC 61.794 72.222 0.00 0.00 36.96 4.46
482 793 4.653888 CGGCTTCGGGTTTGGGGT 62.654 66.667 0.00 0.00 0.00 4.95
631 993 0.178987 ACACTGTCTCTGACCGGACT 60.179 55.000 9.46 0.00 34.01 3.85
659 1021 0.105593 CAGTACAGGCGGATCAGCAT 59.894 55.000 19.63 9.95 39.27 3.79
672 1034 6.850752 TCTGGTGTGAGATTATTCAGTACA 57.149 37.500 0.00 0.00 0.00 2.90
790 1180 4.693566 TGTTGCTAGTTCTTTATCGGTTGG 59.306 41.667 0.00 0.00 0.00 3.77
794 1184 6.481954 AAGTTGTTGCTAGTTCTTTATCGG 57.518 37.500 0.00 0.00 0.00 4.18
837 1230 2.755836 ACGTAGTTGTTGCTTGCTTG 57.244 45.000 0.00 0.00 37.78 4.01
917 1313 0.543646 GGCGGGGGCTACTTATAGGA 60.544 60.000 0.00 0.00 0.00 2.94
942 1338 0.323360 TGCTGGTTTATGCAGGGGAC 60.323 55.000 0.00 0.00 34.84 4.46
980 1376 1.267121 GTACAGGAGCCACAGGAAGA 58.733 55.000 0.00 0.00 0.00 2.87
1015 1414 2.707849 GGTCTTGCGCGTAGGAGGA 61.708 63.158 9.68 0.00 0.00 3.71
1248 1647 1.141881 GATGTCCGCGATCACCACT 59.858 57.895 8.23 0.00 0.00 4.00
1389 1788 2.876645 CAGAAGACGTCGAGCCGC 60.877 66.667 10.46 0.00 0.00 6.53
1392 1791 0.939577 TGTTGCAGAAGACGTCGAGC 60.940 55.000 10.46 13.01 34.07 5.03
1570 1969 2.419198 GACGCTGGCGATGGAGAT 59.581 61.111 21.77 0.00 42.83 2.75
1620 2019 1.741770 GTGCTTGGAGGCGGTGTAG 60.742 63.158 0.00 0.00 34.52 2.74
1947 2346 4.003788 ACGAGGTTGTGGCCGGAG 62.004 66.667 5.05 0.00 0.00 4.63
2015 2414 1.888436 ATGCGAGGTCGGTCATGTGT 61.888 55.000 0.89 0.00 40.23 3.72
2094 2499 1.850441 ACGAACGAACGAACTTGAGTG 59.150 47.619 11.97 0.00 37.03 3.51
2108 2517 3.059733 TCAACCAATTAACCGAACGAACG 60.060 43.478 0.00 0.00 0.00 3.95
2261 2682 3.515502 AGGCTAGTGCTAACTGATTCACA 59.484 43.478 0.00 0.00 37.19 3.58
2264 2685 4.038642 AGCTAGGCTAGTGCTAACTGATTC 59.961 45.833 21.92 1.57 36.99 2.52
2266 2687 3.571590 AGCTAGGCTAGTGCTAACTGAT 58.428 45.455 21.92 0.00 36.99 2.90
2268 2689 3.452474 CAAGCTAGGCTAGTGCTAACTG 58.548 50.000 21.92 7.34 38.25 3.16
2269 2690 2.159028 GCAAGCTAGGCTAGTGCTAACT 60.159 50.000 22.87 9.75 38.77 2.24
2270 2691 2.205911 GCAAGCTAGGCTAGTGCTAAC 58.794 52.381 22.87 9.83 38.77 2.34
2271 2692 1.831106 TGCAAGCTAGGCTAGTGCTAA 59.169 47.619 27.33 13.18 41.34 3.09
2386 2828 1.333619 CACTCTAGCGGAAGAGAGAGC 59.666 57.143 17.29 0.00 44.93 4.09
2388 2830 1.408961 CCCACTCTAGCGGAAGAGAGA 60.409 57.143 17.29 0.00 44.93 3.10
2406 2854 4.881850 CACAAACTACTATCAACCATCCCC 59.118 45.833 0.00 0.00 0.00 4.81
2422 2870 4.701765 TGCCAATTGTAAATGCACAAACT 58.298 34.783 4.43 0.00 41.50 2.66
2423 2871 5.007528 AGTTGCCAATTGTAAATGCACAAAC 59.992 36.000 4.43 2.38 41.50 2.93
2424 2872 5.121811 AGTTGCCAATTGTAAATGCACAAA 58.878 33.333 4.43 0.00 41.50 2.83
2425 2873 4.701765 AGTTGCCAATTGTAAATGCACAA 58.298 34.783 4.43 0.00 42.32 3.33
2501 2952 9.562583 GCATATAAAACTAGCTGCTACTACTAG 57.437 37.037 5.02 0.00 39.44 2.57
2503 2954 7.379750 GGCATATAAAACTAGCTGCTACTACT 58.620 38.462 5.02 0.00 0.00 2.57
2505 2956 6.269077 TGGGCATATAAAACTAGCTGCTACTA 59.731 38.462 5.02 0.00 0.00 1.82
2506 2957 5.071788 TGGGCATATAAAACTAGCTGCTACT 59.928 40.000 5.02 0.00 0.00 2.57
2507 2958 5.305585 TGGGCATATAAAACTAGCTGCTAC 58.694 41.667 5.02 0.00 0.00 3.58
2508 2959 5.560722 TGGGCATATAAAACTAGCTGCTA 57.439 39.130 9.34 9.34 0.00 3.49
2509 2960 4.437682 TGGGCATATAAAACTAGCTGCT 57.562 40.909 7.57 7.57 0.00 4.24
2510 2961 5.464168 CAATGGGCATATAAAACTAGCTGC 58.536 41.667 0.00 0.00 0.00 5.25
2610 3070 1.746220 CTTCCGCTGCACTCTACTACT 59.254 52.381 0.00 0.00 0.00 2.57
2612 3072 2.124277 TCTTCCGCTGCACTCTACTA 57.876 50.000 0.00 0.00 0.00 1.82
2613 3073 1.203523 CTTCTTCCGCTGCACTCTACT 59.796 52.381 0.00 0.00 0.00 2.57
2615 3075 0.108615 GCTTCTTCCGCTGCACTCTA 60.109 55.000 0.00 0.00 0.00 2.43
2616 3076 1.375268 GCTTCTTCCGCTGCACTCT 60.375 57.895 0.00 0.00 0.00 3.24
2617 3077 1.633852 CTGCTTCTTCCGCTGCACTC 61.634 60.000 0.00 0.00 0.00 3.51
2618 3078 1.670406 CTGCTTCTTCCGCTGCACT 60.670 57.895 0.00 0.00 0.00 4.40
2619 3079 2.866028 CTGCTTCTTCCGCTGCAC 59.134 61.111 0.00 0.00 0.00 4.57
2622 3082 3.036783 GCTGCTGCTTCTTCCGCTG 62.037 63.158 8.53 0.00 36.03 5.18
2657 3479 0.605319 ATCGCGTCTTTTTCCTGGCA 60.605 50.000 5.77 0.00 0.00 4.92
2742 3568 5.598417 GCCATCCCTTTTGTCCAGTTTATAT 59.402 40.000 0.00 0.00 0.00 0.86
2743 3569 4.953579 GCCATCCCTTTTGTCCAGTTTATA 59.046 41.667 0.00 0.00 0.00 0.98
2789 3615 1.035932 TCCCTGCACTAGACGGCTAC 61.036 60.000 0.00 0.00 0.00 3.58
2790 3616 1.035932 GTCCCTGCACTAGACGGCTA 61.036 60.000 0.00 0.00 0.00 3.93
2791 3617 2.037367 TCCCTGCACTAGACGGCT 59.963 61.111 0.00 0.00 0.00 5.52
2792 3618 2.184579 GTCCCTGCACTAGACGGC 59.815 66.667 0.00 0.00 0.00 5.68
2793 3619 1.668101 GAGGTCCCTGCACTAGACGG 61.668 65.000 0.00 0.00 0.00 4.79
2794 3620 0.965866 TGAGGTCCCTGCACTAGACG 60.966 60.000 0.00 0.00 0.00 4.18
2795 3621 1.267121 TTGAGGTCCCTGCACTAGAC 58.733 55.000 0.00 0.00 0.00 2.59
2796 3622 1.833630 CATTGAGGTCCCTGCACTAGA 59.166 52.381 0.00 0.00 0.00 2.43
2797 3623 1.745141 GCATTGAGGTCCCTGCACTAG 60.745 57.143 0.00 0.00 34.77 2.57
2798 3624 0.253044 GCATTGAGGTCCCTGCACTA 59.747 55.000 0.00 0.00 34.77 2.74
2799 3625 1.001641 GCATTGAGGTCCCTGCACT 60.002 57.895 0.00 0.00 34.77 4.40
2800 3626 2.401766 CGCATTGAGGTCCCTGCAC 61.402 63.158 0.00 0.00 34.29 4.57
2801 3627 2.046023 CGCATTGAGGTCCCTGCA 60.046 61.111 0.00 0.00 34.29 4.41
2802 3628 3.512516 GCGCATTGAGGTCCCTGC 61.513 66.667 0.30 0.00 0.00 4.85
2803 3629 1.033746 AATGCGCATTGAGGTCCCTG 61.034 55.000 33.48 0.00 0.00 4.45
2804 3630 0.546122 TAATGCGCATTGAGGTCCCT 59.454 50.000 38.81 17.14 32.50 4.20
2805 3631 0.663153 GTAATGCGCATTGAGGTCCC 59.337 55.000 38.81 17.16 32.50 4.46
2806 3632 0.304705 CGTAATGCGCATTGAGGTCC 59.695 55.000 38.81 20.30 32.50 4.46
2807 3633 3.806257 CGTAATGCGCATTGAGGTC 57.194 52.632 38.81 23.13 32.50 3.85
2819 3645 2.697363 CTTCGTGAGCATTGCGTAATG 58.303 47.619 20.37 20.37 45.17 1.90
2831 3657 1.354040 GATGTGGTGAGCTTCGTGAG 58.646 55.000 0.00 0.00 0.00 3.51
2832 3658 0.388520 CGATGTGGTGAGCTTCGTGA 60.389 55.000 0.00 0.00 0.00 4.35
2833 3659 1.354337 CCGATGTGGTGAGCTTCGTG 61.354 60.000 0.00 0.00 33.51 4.35
2834 3660 1.079819 CCGATGTGGTGAGCTTCGT 60.080 57.895 0.00 0.00 33.51 3.85
2835 3661 3.786101 CCGATGTGGTGAGCTTCG 58.214 61.111 0.00 0.00 34.62 3.79
2844 3670 3.490933 CCACTACAGTATGACCGATGTGG 60.491 52.174 0.00 0.00 39.69 4.17
2845 3671 3.130516 ACCACTACAGTATGACCGATGTG 59.869 47.826 0.00 0.00 39.69 3.21
2846 3672 3.362706 ACCACTACAGTATGACCGATGT 58.637 45.455 0.00 0.00 39.69 3.06
2847 3673 5.509716 TTACCACTACAGTATGACCGATG 57.490 43.478 0.00 0.00 39.69 3.84
2848 3674 7.828508 TTATTACCACTACAGTATGACCGAT 57.171 36.000 0.00 0.00 39.69 4.18
2849 3675 7.722728 AGATTATTACCACTACAGTATGACCGA 59.277 37.037 0.00 0.00 39.69 4.69
2850 3676 7.808381 CAGATTATTACCACTACAGTATGACCG 59.192 40.741 0.00 0.00 39.69 4.79
2851 3677 8.088981 CCAGATTATTACCACTACAGTATGACC 58.911 40.741 0.00 0.00 39.69 4.02
2852 3678 8.088981 CCCAGATTATTACCACTACAGTATGAC 58.911 40.741 0.00 0.00 39.69 3.06
2853 3679 7.234782 CCCCAGATTATTACCACTACAGTATGA 59.765 40.741 0.00 0.00 39.69 2.15
2854 3680 7.386851 CCCCAGATTATTACCACTACAGTATG 58.613 42.308 0.00 0.00 46.00 2.39
2855 3681 6.500751 CCCCCAGATTATTACCACTACAGTAT 59.499 42.308 0.00 0.00 0.00 2.12
2856 3682 5.842328 CCCCCAGATTATTACCACTACAGTA 59.158 44.000 0.00 0.00 0.00 2.74
2857 3683 4.658901 CCCCCAGATTATTACCACTACAGT 59.341 45.833 0.00 0.00 0.00 3.55
2858 3684 4.658901 ACCCCCAGATTATTACCACTACAG 59.341 45.833 0.00 0.00 0.00 2.74
2859 3685 4.637600 ACCCCCAGATTATTACCACTACA 58.362 43.478 0.00 0.00 0.00 2.74
2860 3686 6.296259 CCATACCCCCAGATTATTACCACTAC 60.296 46.154 0.00 0.00 0.00 2.73
2861 3687 5.788533 CCATACCCCCAGATTATTACCACTA 59.211 44.000 0.00 0.00 0.00 2.74
2862 3688 4.601857 CCATACCCCCAGATTATTACCACT 59.398 45.833 0.00 0.00 0.00 4.00
2863 3689 4.809691 GCCATACCCCCAGATTATTACCAC 60.810 50.000 0.00 0.00 0.00 4.16
2864 3690 3.332485 GCCATACCCCCAGATTATTACCA 59.668 47.826 0.00 0.00 0.00 3.25
2865 3691 3.332485 TGCCATACCCCCAGATTATTACC 59.668 47.826 0.00 0.00 0.00 2.85
2866 3692 4.650972 TGCCATACCCCCAGATTATTAC 57.349 45.455 0.00 0.00 0.00 1.89
2867 3693 5.671463 TTTGCCATACCCCCAGATTATTA 57.329 39.130 0.00 0.00 0.00 0.98
2868 3694 4.551215 TTTGCCATACCCCCAGATTATT 57.449 40.909 0.00 0.00 0.00 1.40
2869 3695 4.551215 TTTTGCCATACCCCCAGATTAT 57.449 40.909 0.00 0.00 0.00 1.28
2870 3696 4.338795 TTTTTGCCATACCCCCAGATTA 57.661 40.909 0.00 0.00 0.00 1.75
2871 3697 2.938428 TTTTGCCATACCCCCAGATT 57.062 45.000 0.00 0.00 0.00 2.40
2872 3698 2.938428 TTTTTGCCATACCCCCAGAT 57.062 45.000 0.00 0.00 0.00 2.90
2888 3714 5.121454 TGTGCAAAGCAATTTCGTTCTTTTT 59.879 32.000 0.00 0.00 41.47 1.94
2889 3715 4.629200 TGTGCAAAGCAATTTCGTTCTTTT 59.371 33.333 0.00 0.00 41.47 2.27
2890 3716 4.032786 GTGTGCAAAGCAATTTCGTTCTTT 59.967 37.500 0.00 0.00 41.47 2.52
2891 3717 3.551485 GTGTGCAAAGCAATTTCGTTCTT 59.449 39.130 0.00 0.00 41.47 2.52
2892 3718 3.115554 GTGTGCAAAGCAATTTCGTTCT 58.884 40.909 0.00 0.00 41.47 3.01
2893 3719 2.097925 CGTGTGCAAAGCAATTTCGTTC 60.098 45.455 0.00 0.00 41.47 3.95
2894 3720 1.851666 CGTGTGCAAAGCAATTTCGTT 59.148 42.857 0.00 0.00 41.47 3.85
2895 3721 1.064803 TCGTGTGCAAAGCAATTTCGT 59.935 42.857 0.00 0.00 41.47 3.85
2896 3722 1.752753 TCGTGTGCAAAGCAATTTCG 58.247 45.000 0.00 0.00 41.47 3.46
2897 3723 3.568538 AGATCGTGTGCAAAGCAATTTC 58.431 40.909 0.00 0.00 41.47 2.17
2898 3724 3.648339 AGATCGTGTGCAAAGCAATTT 57.352 38.095 0.00 0.00 41.47 1.82
2899 3725 3.648339 AAGATCGTGTGCAAAGCAATT 57.352 38.095 0.00 0.00 41.47 2.32
2900 3726 3.243501 ACAAAGATCGTGTGCAAAGCAAT 60.244 39.130 4.49 0.00 41.47 3.56
2901 3727 2.098934 ACAAAGATCGTGTGCAAAGCAA 59.901 40.909 4.49 0.00 41.47 3.91
2902 3728 1.675483 ACAAAGATCGTGTGCAAAGCA 59.325 42.857 4.49 0.00 35.60 3.91
2903 3729 2.405892 ACAAAGATCGTGTGCAAAGC 57.594 45.000 4.49 0.00 0.00 3.51
2904 3730 4.466567 TGTACAAAGATCGTGTGCAAAG 57.533 40.909 16.84 0.00 38.44 2.77
2905 3731 5.388994 CGTATGTACAAAGATCGTGTGCAAA 60.389 40.000 20.87 5.66 43.40 3.68
2906 3732 4.090786 CGTATGTACAAAGATCGTGTGCAA 59.909 41.667 20.87 11.58 43.40 4.08
2907 3733 3.610677 CGTATGTACAAAGATCGTGTGCA 59.389 43.478 19.84 19.84 44.12 4.57
2908 3734 3.855379 TCGTATGTACAAAGATCGTGTGC 59.145 43.478 13.51 12.63 32.80 4.57
2909 3735 5.971792 AGATCGTATGTACAAAGATCGTGTG 59.028 40.000 21.89 4.03 41.65 3.82
2910 3736 5.971792 CAGATCGTATGTACAAAGATCGTGT 59.028 40.000 21.89 9.62 41.65 4.49
2911 3737 6.140895 GTCAGATCGTATGTACAAAGATCGTG 59.859 42.308 21.89 19.94 41.65 4.35
2912 3738 6.200100 GTCAGATCGTATGTACAAAGATCGT 58.800 40.000 21.89 13.57 41.65 3.73
2913 3739 5.337251 CGTCAGATCGTATGTACAAAGATCG 59.663 44.000 21.89 18.41 41.65 3.69
2914 3740 6.140895 CACGTCAGATCGTATGTACAAAGATC 59.859 42.308 21.20 21.20 42.27 2.75
2915 3741 5.971792 CACGTCAGATCGTATGTACAAAGAT 59.028 40.000 0.00 5.21 42.27 2.40
2916 3742 5.106436 ACACGTCAGATCGTATGTACAAAGA 60.106 40.000 0.00 0.00 42.27 2.52
2917 3743 5.093457 ACACGTCAGATCGTATGTACAAAG 58.907 41.667 0.00 0.00 42.27 2.77
2918 3744 5.050644 ACACGTCAGATCGTATGTACAAA 57.949 39.130 0.00 0.00 42.27 2.83
2919 3745 4.393990 AGACACGTCAGATCGTATGTACAA 59.606 41.667 0.00 0.00 42.27 2.41
2920 3746 3.937079 AGACACGTCAGATCGTATGTACA 59.063 43.478 0.00 0.00 42.27 2.90
2921 3747 4.533225 AGACACGTCAGATCGTATGTAC 57.467 45.455 0.00 0.00 42.27 2.90
2922 3748 4.632688 TGAAGACACGTCAGATCGTATGTA 59.367 41.667 0.00 0.00 42.27 2.29
2923 3749 3.439129 TGAAGACACGTCAGATCGTATGT 59.561 43.478 0.00 0.00 42.27 2.29
2924 3750 3.786576 GTGAAGACACGTCAGATCGTATG 59.213 47.826 0.00 0.00 42.27 2.39
2925 3751 4.017380 GTGAAGACACGTCAGATCGTAT 57.983 45.455 0.00 0.00 42.27 3.06
2926 3752 3.466712 GTGAAGACACGTCAGATCGTA 57.533 47.619 0.00 0.00 42.27 3.43
2927 3753 2.333389 GTGAAGACACGTCAGATCGT 57.667 50.000 0.00 0.00 45.10 3.73
2954 3780 4.270808 GGAAAAGAAAACCAACACAGCATG 59.729 41.667 0.00 0.00 46.00 4.06
2955 3781 4.441792 GGAAAAGAAAACCAACACAGCAT 58.558 39.130 0.00 0.00 0.00 3.79
2956 3782 3.368948 GGGAAAAGAAAACCAACACAGCA 60.369 43.478 0.00 0.00 0.00 4.41
2957 3783 3.194861 GGGAAAAGAAAACCAACACAGC 58.805 45.455 0.00 0.00 0.00 4.40
2958 3784 4.464069 TGGGAAAAGAAAACCAACACAG 57.536 40.909 0.00 0.00 0.00 3.66
2959 3785 4.891992 TTGGGAAAAGAAAACCAACACA 57.108 36.364 0.00 0.00 38.02 3.72
2960 3786 4.574421 CCATTGGGAAAAGAAAACCAACAC 59.426 41.667 0.00 0.00 44.89 3.32
2961 3787 4.471386 TCCATTGGGAAAAGAAAACCAACA 59.529 37.500 2.09 0.00 44.89 3.33
2962 3788 5.029807 TCCATTGGGAAAAGAAAACCAAC 57.970 39.130 2.09 0.00 44.89 3.77
2963 3789 4.444164 GCTCCATTGGGAAAAGAAAACCAA 60.444 41.667 2.09 0.00 44.38 3.67
2964 3790 3.070878 GCTCCATTGGGAAAAGAAAACCA 59.929 43.478 2.09 0.00 44.38 3.67
2965 3791 3.324846 AGCTCCATTGGGAAAAGAAAACC 59.675 43.478 2.09 0.00 44.38 3.27
2966 3792 4.309933 CAGCTCCATTGGGAAAAGAAAAC 58.690 43.478 2.09 0.00 44.38 2.43
2967 3793 3.324556 CCAGCTCCATTGGGAAAAGAAAA 59.675 43.478 2.09 0.00 44.38 2.29
2968 3794 2.899256 CCAGCTCCATTGGGAAAAGAAA 59.101 45.455 2.09 0.00 44.38 2.52
2969 3795 2.158325 ACCAGCTCCATTGGGAAAAGAA 60.158 45.455 2.09 0.00 44.38 2.52
2970 3796 1.428912 ACCAGCTCCATTGGGAAAAGA 59.571 47.619 2.09 0.00 44.38 2.52
2971 3797 1.928868 ACCAGCTCCATTGGGAAAAG 58.071 50.000 2.09 0.00 44.38 2.27
2972 3798 1.969923 CAACCAGCTCCATTGGGAAAA 59.030 47.619 2.09 0.00 44.38 2.29
2973 3799 1.146774 TCAACCAGCTCCATTGGGAAA 59.853 47.619 2.09 0.00 44.38 3.13
2974 3800 0.776810 TCAACCAGCTCCATTGGGAA 59.223 50.000 2.09 0.00 44.38 3.97
2975 3801 1.002069 ATCAACCAGCTCCATTGGGA 58.998 50.000 2.09 0.00 42.29 4.37
2976 3802 1.479323 CAATCAACCAGCTCCATTGGG 59.521 52.381 2.09 0.00 40.11 4.12
2977 3803 1.479323 CCAATCAACCAGCTCCATTGG 59.521 52.381 0.00 0.00 38.06 3.16
2978 3804 2.165030 GTCCAATCAACCAGCTCCATTG 59.835 50.000 0.00 0.00 0.00 2.82
2979 3805 2.450476 GTCCAATCAACCAGCTCCATT 58.550 47.619 0.00 0.00 0.00 3.16
2980 3806 1.679944 CGTCCAATCAACCAGCTCCAT 60.680 52.381 0.00 0.00 0.00 3.41
2981 3807 0.321564 CGTCCAATCAACCAGCTCCA 60.322 55.000 0.00 0.00 0.00 3.86
2982 3808 0.036388 TCGTCCAATCAACCAGCTCC 60.036 55.000 0.00 0.00 0.00 4.70
2983 3809 1.808411 TTCGTCCAATCAACCAGCTC 58.192 50.000 0.00 0.00 0.00 4.09
2984 3810 2.154462 CTTTCGTCCAATCAACCAGCT 58.846 47.619 0.00 0.00 0.00 4.24
2985 3811 1.200020 CCTTTCGTCCAATCAACCAGC 59.800 52.381 0.00 0.00 0.00 4.85
2986 3812 2.484264 GTCCTTTCGTCCAATCAACCAG 59.516 50.000 0.00 0.00 0.00 4.00
2987 3813 2.158740 TGTCCTTTCGTCCAATCAACCA 60.159 45.455 0.00 0.00 0.00 3.67
2988 3814 2.500229 TGTCCTTTCGTCCAATCAACC 58.500 47.619 0.00 0.00 0.00 3.77
2989 3815 4.083581 CATGTCCTTTCGTCCAATCAAC 57.916 45.455 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.