Multiple sequence alignment - TraesCS7A01G316800

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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 TraesCS7A01G316800 chr7A 100.000 4091 0 0 1 4091 452758082 452753992 0.000000e+00 7555.0
1 TraesCS7A01G316800 chr7A 80.915 634 96 19 1064 1682 450965815 450966438 1.030000e-130 477.0
2 TraesCS7A01G316800 chr7A 96.923 65 2 0 2739 2803 125703015 125703079 4.320000e-20 110.0
3 TraesCS7A01G316800 chr7A 100.000 32 0 0 308 339 47153546 47153577 4.420000e-05 60.2
4 TraesCS7A01G316800 chr7B 96.167 2009 60 11 687 2685 400924945 400926946 0.000000e+00 3267.0
5 TraesCS7A01G316800 chr7B 94.133 750 19 7 2814 3542 400926963 400927708 0.000000e+00 1118.0
6 TraesCS7A01G316800 chr7B 89.301 458 37 8 27 478 400924452 400924903 7.680000e-157 564.0
7 TraesCS7A01G316800 chr7B 80.507 631 96 22 1067 1682 400637579 400638197 3.730000e-125 459.0
8 TraesCS7A01G316800 chr7B 87.925 265 27 2 3646 3910 400927831 400928090 1.430000e-79 307.0
9 TraesCS7A01G316800 chr7B 93.151 146 9 1 3946 4091 400928090 400928234 3.200000e-51 213.0
10 TraesCS7A01G316800 chr7B 90.141 71 2 2 3580 3645 400927711 400927781 2.030000e-13 87.9
11 TraesCS7A01G316800 chr7D 93.973 1825 77 20 75 1876 397194587 397196401 0.000000e+00 2730.0
12 TraesCS7A01G316800 chr7D 94.401 768 32 5 1916 2678 397196408 397197169 0.000000e+00 1170.0
13 TraesCS7A01G316800 chr7D 93.325 794 26 9 2804 3577 397197176 397197962 0.000000e+00 1147.0
14 TraesCS7A01G316800 chr7D 81.417 635 91 22 1064 1682 396985142 396985765 1.020000e-135 494.0
15 TraesCS7A01G316800 chr7D 88.068 352 24 10 3741 4086 397197981 397198320 6.370000e-108 401.0
16 TraesCS7A01G316800 chr7D 93.151 73 4 1 2739 2810 591399317 591399245 5.590000e-19 106.0
17 TraesCS7A01G316800 chr7D 100.000 35 0 0 1 35 397194519 397194553 9.490000e-07 65.8
18 TraesCS7A01G316800 chr2A 85.246 122 16 2 2681 2801 356709469 356709349 1.540000e-24 124.0
19 TraesCS7A01G316800 chr4B 98.485 66 1 0 2739 2804 24837201 24837136 2.580000e-22 117.0
20 TraesCS7A01G316800 chr3B 100.000 63 0 0 2739 2801 452550960 452551022 2.580000e-22 117.0
21 TraesCS7A01G316800 chr3D 90.698 86 7 1 2739 2823 610540042 610539957 3.340000e-21 113.0
22 TraesCS7A01G316800 chr5D 96.923 65 1 1 2745 2808 408791795 408791859 1.550000e-19 108.0
23 TraesCS7A01G316800 chr5D 96.825 63 2 0 2739 2801 385720479 385720541 5.590000e-19 106.0
24 TraesCS7A01G316800 chr1D 95.522 67 3 0 2739 2805 452843 452909 1.550000e-19 108.0
25 TraesCS7A01G316800 chr5B 77.692 130 19 10 234 355 527067523 527067396 2.040000e-08 71.3
26 TraesCS7A01G316800 chr4A 76.000 125 21 9 242 359 407483458 407483336 5.710000e-04 56.5
27 TraesCS7A01G316800 chr6A 84.483 58 5 4 298 354 17403061 17403115 2.000000e-03 54.7
28 TraesCS7A01G316800 chr6A 94.444 36 1 1 297 332 96774019 96773985 2.000000e-03 54.7


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 TraesCS7A01G316800 chr7A 452753992 452758082 4090 True 7555.00 7555 100.0000 1 4091 1 chr7A.!!$R1 4090
1 TraesCS7A01G316800 chr7A 450965815 450966438 623 False 477.00 477 80.9150 1064 1682 1 chr7A.!!$F3 618
2 TraesCS7A01G316800 chr7B 400924452 400928234 3782 False 926.15 3267 91.8030 27 4091 6 chr7B.!!$F2 4064
3 TraesCS7A01G316800 chr7B 400637579 400638197 618 False 459.00 459 80.5070 1067 1682 1 chr7B.!!$F1 615
4 TraesCS7A01G316800 chr7D 397194519 397198320 3801 False 1102.76 2730 93.9534 1 4086 5 chr7D.!!$F2 4085
5 TraesCS7A01G316800 chr7D 396985142 396985765 623 False 494.00 494 81.4170 1064 1682 1 chr7D.!!$F1 618

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
671 706 1.069358 GCGAATAAGTGGGAGAGGAGG 59.931 57.143 0.00 0.0 0.00 4.30 F
1907 1990 0.606130 TGTCGTCAATGCATGCCACT 60.606 50.000 16.68 0.0 0.00 4.00 F
2691 2781 0.244721 GGCAAACGTACTACCTCCGT 59.755 55.000 0.00 0.0 36.17 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 2110 0.664761 CCAATTAGCAGCACATCCGG 59.335 55.0 0.00 0.00 0.00 5.14 R
2770 2860 0.036306 TCCGGAAAAGCTTGTCCCTC 59.964 55.0 26.94 5.77 0.00 4.30 R
3963 4130 0.032813 ATGAGGATGTTGCCAAGGGG 60.033 55.0 0.00 0.00 37.18 4.79 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
416 440 7.692908 TTGTTTCCAGATTTCGAAAATTGTC 57.307 32.000 15.66 7.88 30.18 3.18
418 442 7.488322 TGTTTCCAGATTTCGAAAATTGTCTT 58.512 30.769 15.66 0.00 30.18 3.01
579 614 5.500645 AACAGAGAGAAAAAGGAAAACCG 57.499 39.130 0.00 0.00 0.00 4.44
580 615 4.777463 ACAGAGAGAAAAAGGAAAACCGA 58.223 39.130 0.00 0.00 0.00 4.69
581 616 5.377478 ACAGAGAGAAAAAGGAAAACCGAT 58.623 37.500 0.00 0.00 0.00 4.18
582 617 5.828328 ACAGAGAGAAAAAGGAAAACCGATT 59.172 36.000 0.00 0.00 0.00 3.34
597 632 1.342819 CCGATTTGCCCAAAACCAGAA 59.657 47.619 0.00 0.00 33.56 3.02
598 633 2.224161 CCGATTTGCCCAAAACCAGAAA 60.224 45.455 0.00 0.00 33.56 2.52
644 679 4.759782 CAGTTCTACTTCACCCTATGTGG 58.240 47.826 0.00 0.00 45.48 4.17
671 706 1.069358 GCGAATAAGTGGGAGAGGAGG 59.931 57.143 0.00 0.00 0.00 4.30
691 726 2.943033 GGTATGCGTTTGGTTGCTATCT 59.057 45.455 0.00 0.00 0.00 1.98
753 788 2.642171 TCCCTGTTGGACTAGGACAT 57.358 50.000 0.00 0.00 38.61 3.06
816 853 3.583276 TAGCCCAGTCCACGTTGCG 62.583 63.158 0.00 0.00 0.00 4.85
1028 1074 3.131478 GCACAGCCGCGGGTAATT 61.131 61.111 31.92 14.71 0.00 1.40
1043 1089 2.172082 GGTAATTCTCACCCCCTACACC 59.828 54.545 0.00 0.00 0.00 4.16
1046 1092 3.000819 CTCACCCCCTACACCGCA 61.001 66.667 0.00 0.00 0.00 5.69
1050 1096 3.642503 CCCCCTACACCGCAACCA 61.643 66.667 0.00 0.00 0.00 3.67
1096 1142 2.561885 CGTCTCCGCGACTCTGTT 59.438 61.111 8.23 0.00 40.59 3.16
1191 1237 2.464865 CCGATGTAAGAAGAAGCCTCG 58.535 52.381 0.00 0.00 0.00 4.63
1689 1772 6.919775 AAGTAGTAAGTCACTCACTTCCAT 57.080 37.500 0.00 0.00 42.07 3.41
1756 1839 5.277345 GGCCTTATCAGTTTAGTACGCAATG 60.277 44.000 0.00 0.00 0.00 2.82
1783 1866 0.806241 AGCGGTTCGTTGTTTGTGTT 59.194 45.000 0.00 0.00 0.00 3.32
1784 1867 1.200484 AGCGGTTCGTTGTTTGTGTTT 59.800 42.857 0.00 0.00 0.00 2.83
1802 1885 5.643348 TGTGTTTCACTTGCTACATATGAGG 59.357 40.000 10.38 2.61 35.11 3.86
1842 1925 7.425224 ACATATAGCTTGTTGAGTAGGAGTT 57.575 36.000 0.00 0.00 0.00 3.01
1843 1926 8.534954 ACATATAGCTTGTTGAGTAGGAGTTA 57.465 34.615 0.00 0.00 0.00 2.24
1848 1931 4.924462 GCTTGTTGAGTAGGAGTTAGTGTC 59.076 45.833 0.00 0.00 0.00 3.67
1907 1990 0.606130 TGTCGTCAATGCATGCCACT 60.606 50.000 16.68 0.00 0.00 4.00
1914 1997 2.092484 TCAATGCATGCCACTTAGCCTA 60.092 45.455 16.68 0.00 0.00 3.93
1924 2008 7.011857 GCATGCCACTTAGCCTATATTTAGATC 59.988 40.741 6.36 0.00 0.00 2.75
2009 2093 8.265055 AGCTACTTAGTTATGCCTGTGATTAAA 58.735 33.333 0.00 0.00 0.00 1.52
2026 2110 7.486551 TGTGATTAAACTTAGTTGTGTTTGTGC 59.513 33.333 0.00 0.00 37.06 4.57
2066 2150 2.676342 GTGTTAGTAAGGCATTCCCGTG 59.324 50.000 0.00 0.00 39.21 4.94
2122 2206 7.790861 GTGTGCACACCAAAATTATAAGTAC 57.209 36.000 34.94 7.51 40.85 2.73
2236 2320 8.243426 CACCTATGCATTTTGTGTGTTACTAAT 58.757 33.333 3.54 0.00 0.00 1.73
2395 2479 3.138304 TGCAACTGGTTGTGATACTGAC 58.862 45.455 13.85 0.00 42.31 3.51
2416 2500 5.545063 ACATATGTGTCATTATCCCACGA 57.455 39.130 7.78 0.00 31.41 4.35
2515 2600 5.461516 TCCTACTCAGTGGTGGTCTATTA 57.538 43.478 0.00 0.00 0.00 0.98
2651 2741 6.817765 TGAGGGTGCATTTTAGTCTTTTAG 57.182 37.500 0.00 0.00 0.00 1.85
2688 2778 2.344025 CCAAGGCAAACGTACTACCTC 58.656 52.381 0.00 0.00 0.00 3.85
2689 2779 2.344025 CAAGGCAAACGTACTACCTCC 58.656 52.381 0.00 0.00 0.00 4.30
2690 2780 0.529378 AGGCAAACGTACTACCTCCG 59.471 55.000 0.00 0.00 0.00 4.63
2691 2781 0.244721 GGCAAACGTACTACCTCCGT 59.755 55.000 0.00 0.00 36.17 4.69
2693 2783 1.733718 GCAAACGTACTACCTCCGTCC 60.734 57.143 0.00 0.00 32.95 4.79
2694 2784 1.541147 CAAACGTACTACCTCCGTCCA 59.459 52.381 0.00 0.00 32.95 4.02
2695 2785 1.909700 AACGTACTACCTCCGTCCAA 58.090 50.000 0.00 0.00 32.95 3.53
2715 2805 2.845363 AAAAGCTTGGCCCTCAAATG 57.155 45.000 0.00 0.00 34.56 2.32
2716 2806 2.014010 AAAGCTTGGCCCTCAAATGA 57.986 45.000 0.00 0.00 34.56 2.57
2717 2807 2.014010 AAGCTTGGCCCTCAAATGAA 57.986 45.000 0.00 0.00 34.56 2.57
2718 2808 2.242882 AGCTTGGCCCTCAAATGAAT 57.757 45.000 0.00 0.00 34.56 2.57
2719 2809 1.829222 AGCTTGGCCCTCAAATGAATG 59.171 47.619 0.00 0.00 34.56 2.67
2720 2810 1.551883 GCTTGGCCCTCAAATGAATGT 59.448 47.619 0.00 0.00 34.56 2.71
2721 2811 2.760092 GCTTGGCCCTCAAATGAATGTA 59.240 45.455 0.00 0.00 34.56 2.29
2722 2812 3.181483 GCTTGGCCCTCAAATGAATGTAG 60.181 47.826 0.00 0.00 34.56 2.74
2723 2813 2.378038 TGGCCCTCAAATGAATGTAGC 58.622 47.619 0.00 0.00 0.00 3.58
2724 2814 1.683385 GGCCCTCAAATGAATGTAGCC 59.317 52.381 0.00 0.00 0.00 3.93
2725 2815 1.683385 GCCCTCAAATGAATGTAGCCC 59.317 52.381 0.00 0.00 0.00 5.19
2726 2816 2.949963 GCCCTCAAATGAATGTAGCCCA 60.950 50.000 0.00 0.00 0.00 5.36
2727 2817 3.364549 CCCTCAAATGAATGTAGCCCAA 58.635 45.455 0.00 0.00 0.00 4.12
2728 2818 3.382546 CCCTCAAATGAATGTAGCCCAAG 59.617 47.826 0.00 0.00 0.00 3.61
2729 2819 4.272489 CCTCAAATGAATGTAGCCCAAGA 58.728 43.478 0.00 0.00 0.00 3.02
2730 2820 4.096984 CCTCAAATGAATGTAGCCCAAGAC 59.903 45.833 0.00 0.00 0.00 3.01
2731 2821 4.661222 TCAAATGAATGTAGCCCAAGACA 58.339 39.130 0.00 0.00 0.00 3.41
2732 2822 5.076182 TCAAATGAATGTAGCCCAAGACAA 58.924 37.500 0.00 0.00 0.00 3.18
2733 2823 5.538053 TCAAATGAATGTAGCCCAAGACAAA 59.462 36.000 0.00 0.00 0.00 2.83
2734 2824 6.211184 TCAAATGAATGTAGCCCAAGACAAAT 59.789 34.615 0.00 0.00 0.00 2.32
2735 2825 5.587388 ATGAATGTAGCCCAAGACAAATG 57.413 39.130 0.00 0.00 0.00 2.32
2736 2826 3.763360 TGAATGTAGCCCAAGACAAATGG 59.237 43.478 0.00 0.00 37.71 3.16
2744 2834 1.818674 CCAAGACAAATGGGTAGCACC 59.181 52.381 0.00 0.00 37.60 5.01
2745 2835 2.513753 CAAGACAAATGGGTAGCACCA 58.486 47.619 7.49 2.77 46.24 4.17
2746 2836 2.890311 CAAGACAAATGGGTAGCACCAA 59.110 45.455 7.49 0.00 45.13 3.67
2747 2837 2.795329 AGACAAATGGGTAGCACCAAG 58.205 47.619 7.49 0.97 45.13 3.61
2748 2838 2.108250 AGACAAATGGGTAGCACCAAGT 59.892 45.455 7.49 3.65 45.13 3.16
2749 2839 2.890945 GACAAATGGGTAGCACCAAGTT 59.109 45.455 7.49 0.00 45.13 2.66
2750 2840 4.076394 GACAAATGGGTAGCACCAAGTTA 58.924 43.478 7.49 0.00 45.13 2.24
2751 2841 4.079253 ACAAATGGGTAGCACCAAGTTAG 58.921 43.478 7.49 1.34 45.13 2.34
2752 2842 4.079253 CAAATGGGTAGCACCAAGTTAGT 58.921 43.478 7.49 0.00 45.13 2.24
2753 2843 2.851263 TGGGTAGCACCAAGTTAGTG 57.149 50.000 7.49 0.00 41.02 2.74
2765 2855 7.470289 CACCAAGTTAGTGCTAGATACATTC 57.530 40.000 0.00 0.00 0.00 2.67
2766 2856 7.041721 CACCAAGTTAGTGCTAGATACATTCA 58.958 38.462 0.00 0.00 0.00 2.57
2767 2857 7.712639 CACCAAGTTAGTGCTAGATACATTCAT 59.287 37.037 0.00 0.00 0.00 2.57
2768 2858 8.267894 ACCAAGTTAGTGCTAGATACATTCATT 58.732 33.333 0.00 0.00 0.00 2.57
2769 2859 9.113838 CCAAGTTAGTGCTAGATACATTCATTT 57.886 33.333 0.00 0.00 0.00 2.32
2770 2860 9.926751 CAAGTTAGTGCTAGATACATTCATTTG 57.073 33.333 0.00 0.00 0.00 2.32
2771 2861 9.890629 AAGTTAGTGCTAGATACATTCATTTGA 57.109 29.630 0.00 0.00 0.00 2.69
2772 2862 9.539825 AGTTAGTGCTAGATACATTCATTTGAG 57.460 33.333 0.00 0.00 0.00 3.02
2773 2863 8.768955 GTTAGTGCTAGATACATTCATTTGAGG 58.231 37.037 0.00 0.00 0.00 3.86
2774 2864 6.294473 AGTGCTAGATACATTCATTTGAGGG 58.706 40.000 0.00 0.00 0.00 4.30
2775 2865 6.100279 AGTGCTAGATACATTCATTTGAGGGA 59.900 38.462 0.00 0.00 0.00 4.20
2776 2866 6.203723 GTGCTAGATACATTCATTTGAGGGAC 59.796 42.308 0.00 0.00 0.00 4.46
2777 2867 6.126796 TGCTAGATACATTCATTTGAGGGACA 60.127 38.462 0.00 0.00 0.00 4.02
2778 2868 6.767902 GCTAGATACATTCATTTGAGGGACAA 59.232 38.462 0.00 0.00 36.65 3.18
2779 2869 7.041508 GCTAGATACATTCATTTGAGGGACAAG 60.042 40.741 0.00 0.00 39.77 3.16
2780 2870 5.591877 AGATACATTCATTTGAGGGACAAGC 59.408 40.000 0.00 0.00 39.77 4.01
2781 2871 3.771216 ACATTCATTTGAGGGACAAGCT 58.229 40.909 0.00 0.00 39.77 3.74
2782 2872 4.154942 ACATTCATTTGAGGGACAAGCTT 58.845 39.130 0.00 0.00 39.77 3.74
2783 2873 4.590222 ACATTCATTTGAGGGACAAGCTTT 59.410 37.500 0.00 0.00 39.77 3.51
2784 2874 5.070847 ACATTCATTTGAGGGACAAGCTTTT 59.929 36.000 0.00 0.00 39.77 2.27
2785 2875 4.853924 TCATTTGAGGGACAAGCTTTTC 57.146 40.909 3.91 3.91 39.77 2.29
2786 2876 3.573967 TCATTTGAGGGACAAGCTTTTCC 59.426 43.478 21.34 21.34 39.77 3.13
2787 2877 1.604604 TTGAGGGACAAGCTTTTCCG 58.395 50.000 22.30 2.85 34.20 4.30
2788 2878 0.250727 TGAGGGACAAGCTTTTCCGG 60.251 55.000 22.30 0.00 32.00 5.14
2789 2879 0.036306 GAGGGACAAGCTTTTCCGGA 59.964 55.000 22.30 0.00 32.00 5.14
2790 2880 0.250770 AGGGACAAGCTTTTCCGGAC 60.251 55.000 22.30 11.02 32.00 4.79
2791 2881 1.574702 GGGACAAGCTTTTCCGGACG 61.575 60.000 22.30 0.00 32.00 4.79
2792 2882 1.574702 GGACAAGCTTTTCCGGACGG 61.575 60.000 15.65 3.96 0.00 4.79
2793 2883 0.601841 GACAAGCTTTTCCGGACGGA 60.602 55.000 1.83 9.76 43.52 4.69
2794 2884 0.602905 ACAAGCTTTTCCGGACGGAG 60.603 55.000 13.64 3.27 46.06 4.63
2795 2885 1.003718 AAGCTTTTCCGGACGGAGG 60.004 57.895 13.64 9.30 46.06 4.30
2796 2886 2.436115 GCTTTTCCGGACGGAGGG 60.436 66.667 13.64 8.97 46.06 4.30
2797 2887 2.951101 GCTTTTCCGGACGGAGGGA 61.951 63.158 13.64 1.83 46.06 4.20
2798 2888 1.218316 CTTTTCCGGACGGAGGGAG 59.782 63.158 13.64 9.15 46.06 4.30
2799 2889 1.534717 TTTTCCGGACGGAGGGAGT 60.535 57.895 13.64 0.00 46.06 3.85
2800 2890 0.251742 TTTTCCGGACGGAGGGAGTA 60.252 55.000 13.64 0.00 46.06 2.59
2801 2891 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
2802 2892 1.856539 TTCCGGACGGAGGGAGTACT 61.857 60.000 13.64 0.00 46.06 2.73
2803 2893 0.982852 TCCGGACGGAGGGAGTACTA 60.983 60.000 9.76 0.00 39.76 1.82
2804 2894 0.107017 CCGGACGGAGGGAGTACTAA 60.107 60.000 4.40 0.00 37.50 2.24
2805 2895 1.020437 CGGACGGAGGGAGTACTAAC 58.980 60.000 0.00 0.00 0.00 2.34
2806 2896 1.407989 CGGACGGAGGGAGTACTAACT 60.408 57.143 0.00 0.00 39.21 2.24
2807 2897 2.158900 CGGACGGAGGGAGTACTAACTA 60.159 54.545 0.00 0.00 35.56 2.24
2808 2898 3.682718 CGGACGGAGGGAGTACTAACTAA 60.683 52.174 0.00 0.00 35.56 2.24
2809 2899 4.273318 GGACGGAGGGAGTACTAACTAAA 58.727 47.826 0.00 0.00 35.56 1.85
2810 2900 4.097135 GGACGGAGGGAGTACTAACTAAAC 59.903 50.000 0.00 0.00 35.56 2.01
2811 2901 4.019858 ACGGAGGGAGTACTAACTAAACC 58.980 47.826 0.00 0.00 35.56 3.27
2812 2902 3.065925 CGGAGGGAGTACTAACTAAACCG 59.934 52.174 0.00 3.19 35.56 4.44
2867 2957 5.505173 CCGAAGGCAGTTCAATGATAATT 57.495 39.130 0.00 0.00 46.14 1.40
2873 2963 6.112734 AGGCAGTTCAATGATAATTGTACGA 58.887 36.000 2.59 0.00 37.06 3.43
2933 3026 6.566564 GCCTGGATGAATTTGTACACATATCG 60.567 42.308 0.00 0.00 0.00 2.92
2938 3031 7.870954 GGATGAATTTGTACACATATCGGACTA 59.129 37.037 0.00 0.00 0.00 2.59
3003 3099 9.860650 TTATAGTATTCCTGTATGTTGCCAATT 57.139 29.630 0.00 0.00 0.00 2.32
3362 3458 4.485024 TCCGCTGAAGATCGTATACTTC 57.515 45.455 0.56 0.00 41.67 3.01
3429 3540 5.629020 GCATTCAAATACTTGAGCGTTTTCA 59.371 36.000 0.00 0.00 42.48 2.69
3453 3564 6.423776 AATTGAAATGTTGACCACATCCTT 57.576 33.333 0.00 0.00 46.23 3.36
3456 3567 5.009631 TGAAATGTTGACCACATCCTTAGG 58.990 41.667 0.00 0.00 46.23 2.69
3461 3572 6.381498 TGTTGACCACATCCTTAGGAAATA 57.619 37.500 4.56 0.00 34.34 1.40
3462 3573 6.177610 TGTTGACCACATCCTTAGGAAATAC 58.822 40.000 4.56 0.00 34.34 1.89
3463 3574 6.177610 GTTGACCACATCCTTAGGAAATACA 58.822 40.000 4.56 0.00 34.34 2.29
3464 3575 6.575244 TGACCACATCCTTAGGAAATACAT 57.425 37.500 4.56 0.00 34.34 2.29
3577 3688 4.940463 CATTCCTTTATGAATGGTGCAGG 58.060 43.478 5.97 0.00 45.04 4.85
3578 3689 2.378038 TCCTTTATGAATGGTGCAGGC 58.622 47.619 0.00 0.00 0.00 4.85
3631 3746 6.176975 TGTTGCATTTAAACTCGGTATCAG 57.823 37.500 0.00 0.00 0.00 2.90
3633 3748 4.257731 TGCATTTAAACTCGGTATCAGCA 58.742 39.130 0.00 0.00 0.00 4.41
3636 3751 5.237344 GCATTTAAACTCGGTATCAGCAGAT 59.763 40.000 0.00 0.00 38.29 2.90
3637 3752 6.564873 GCATTTAAACTCGGTATCAGCAGATC 60.565 42.308 0.00 0.00 35.67 2.75
3638 3753 5.592104 TTAAACTCGGTATCAGCAGATCA 57.408 39.130 0.00 0.00 35.67 2.92
3639 3754 4.679373 AAACTCGGTATCAGCAGATCAT 57.321 40.909 0.00 0.00 35.67 2.45
3640 3755 3.932545 ACTCGGTATCAGCAGATCATC 57.067 47.619 0.00 0.00 35.67 2.92
3641 3756 3.495331 ACTCGGTATCAGCAGATCATCT 58.505 45.455 0.00 0.00 35.67 2.90
3642 3757 3.505680 ACTCGGTATCAGCAGATCATCTC 59.494 47.826 0.00 0.00 35.67 2.75
3644 3759 2.824936 CGGTATCAGCAGATCATCTCCT 59.175 50.000 0.00 0.00 35.67 3.69
3652 3817 4.032310 AGCAGATCATCTCCTCTCAAAGT 58.968 43.478 0.00 0.00 0.00 2.66
3655 3820 3.134442 AGATCATCTCCTCTCAAAGTGCC 59.866 47.826 0.00 0.00 0.00 5.01
3658 3823 3.265221 TCATCTCCTCTCAAAGTGCCAAT 59.735 43.478 0.00 0.00 0.00 3.16
3674 3839 6.331061 AGTGCCAATAAAGTCGTAAGTAGAG 58.669 40.000 0.00 0.00 39.48 2.43
3685 3850 8.937634 AAGTCGTAAGTAGAGAAGTTTTTCAA 57.062 30.769 0.00 0.00 35.51 2.69
3689 3854 9.977762 TCGTAAGTAGAGAAGTTTTTCAAAAAC 57.022 29.630 16.67 16.67 35.51 2.43
3690 3855 9.983804 CGTAAGTAGAGAAGTTTTTCAAAAACT 57.016 29.630 20.53 20.53 41.82 2.66
3701 3866 8.234887 AGTTTTTCAAAAACTTACCTCGTTTG 57.765 30.769 20.53 0.00 37.18 2.93
3707 3872 5.684550 AAAACTTACCTCGTTTGTCCATC 57.315 39.130 0.00 0.00 35.00 3.51
3715 3880 2.872245 CTCGTTTGTCCATCAAGTGTGT 59.128 45.455 0.00 0.00 37.35 3.72
3716 3881 2.611751 TCGTTTGTCCATCAAGTGTGTG 59.388 45.455 0.00 0.00 37.35 3.82
3717 3882 2.731217 GTTTGTCCATCAAGTGTGTGC 58.269 47.619 0.00 0.00 37.35 4.57
3725 3890 1.939974 TCAAGTGTGTGCTGTCTGAC 58.060 50.000 0.00 0.00 0.00 3.51
3729 3894 1.069204 AGTGTGTGCTGTCTGACGAAT 59.931 47.619 2.98 0.00 0.00 3.34
3737 3902 4.561606 GTGCTGTCTGACGAATAATAACGT 59.438 41.667 2.98 0.00 45.32 3.99
3739 3904 4.561606 GCTGTCTGACGAATAATAACGTGT 59.438 41.667 2.98 0.00 42.74 4.49
3774 3939 5.986741 TGCGTTCGTATTATGTTACATGGAT 59.013 36.000 8.26 4.89 0.00 3.41
3775 3940 6.074034 TGCGTTCGTATTATGTTACATGGATG 60.074 38.462 8.26 0.00 0.00 3.51
3776 3941 6.617741 GCGTTCGTATTATGTTACATGGATGG 60.618 42.308 8.26 0.00 0.00 3.51
3778 3943 7.358931 CGTTCGTATTATGTTACATGGATGGAC 60.359 40.741 8.26 2.97 0.00 4.02
3779 3944 7.056844 TCGTATTATGTTACATGGATGGACA 57.943 36.000 8.26 0.00 34.23 4.02
3780 3945 7.501844 TCGTATTATGTTACATGGATGGACAA 58.498 34.615 8.26 0.00 33.72 3.18
3782 3947 8.783093 CGTATTATGTTACATGGATGGACAAAT 58.217 33.333 8.26 0.00 33.72 2.32
3796 3961 6.983890 GGATGGACAAATTATAAATTGGCGTT 59.016 34.615 15.86 5.44 35.33 4.84
3815 3980 4.024387 GCGTTCTTGTTCCTCAACATGTTA 60.024 41.667 11.53 0.00 42.28 2.41
3819 3984 7.466725 CGTTCTTGTTCCTCAACATGTTAAAGA 60.467 37.037 11.53 5.18 42.28 2.52
3831 3996 5.460646 ACATGTTAAAGATGCAAAAGTCGG 58.539 37.500 0.00 0.00 0.00 4.79
3856 4021 6.738649 GCTGAAGAGCTAAAGAAAACATAACG 59.261 38.462 0.00 0.00 42.52 3.18
3864 4029 9.174166 AGCTAAAGAAAACATAACGTATCCAAT 57.826 29.630 0.00 0.00 0.00 3.16
3910 4075 4.943705 CCACCTATGTCAAACAATGTAGCT 59.056 41.667 0.00 0.00 0.00 3.32
3950 4117 3.125316 GCATGAAAAACTAGTGTCCCTCG 59.875 47.826 0.00 0.00 0.00 4.63
3953 4120 5.223449 TGAAAAACTAGTGTCCCTCGAAT 57.777 39.130 0.00 0.00 0.00 3.34
3961 4128 2.492484 AGTGTCCCTCGAATCTGTACAC 59.508 50.000 0.00 0.00 36.79 2.90
3962 4129 2.230508 GTGTCCCTCGAATCTGTACACA 59.769 50.000 0.00 0.00 36.60 3.72
3963 4130 2.230508 TGTCCCTCGAATCTGTACACAC 59.769 50.000 0.00 0.00 0.00 3.82
4010 4177 5.070847 ACACATGATCACTATGGCAGTATGA 59.929 40.000 0.00 0.00 39.69 2.15
4068 4235 1.048601 TGACCTCAAGGACTCCACAC 58.951 55.000 2.30 0.00 38.94 3.82
4077 4244 1.064017 AGGACTCCACACCAAGCAAAA 60.064 47.619 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 213 9.645059 GGGAATTTTGAAATTTTCCAAAAACAA 57.355 25.926 16.96 2.33 42.97 2.83
192 214 8.806146 TGGGAATTTTGAAATTTTCCAAAAACA 58.194 25.926 16.96 12.44 42.97 2.83
193 215 9.645059 TTGGGAATTTTGAAATTTTCCAAAAAC 57.355 25.926 18.21 14.22 42.28 2.43
204 226 9.531942 GCTTTTGAAATTTGGGAATTTTGAAAT 57.468 25.926 0.00 0.00 43.61 2.17
381 405 8.642020 CGAAATCTGGAAACAATTCTGAATTTC 58.358 33.333 12.74 9.17 42.06 2.17
528 562 8.579863 CCTTGTCAGTTTTATCTGGATTTTTCT 58.420 33.333 0.00 0.00 36.25 2.52
537 571 7.930217 TCTGTTTTCCTTGTCAGTTTTATCTG 58.070 34.615 0.00 0.00 36.85 2.90
579 614 3.402110 CCTTTCTGGTTTTGGGCAAATC 58.598 45.455 0.00 0.00 0.00 2.17
580 615 2.106338 CCCTTTCTGGTTTTGGGCAAAT 59.894 45.455 0.00 0.00 0.00 2.32
581 616 1.488393 CCCTTTCTGGTTTTGGGCAAA 59.512 47.619 0.00 0.00 0.00 3.68
582 617 1.127343 CCCTTTCTGGTTTTGGGCAA 58.873 50.000 0.00 0.00 0.00 4.52
597 632 7.669722 TGCTTGTATTTTTATGAAGACTCCCTT 59.330 33.333 0.00 0.00 37.93 3.95
598 633 7.175104 TGCTTGTATTTTTATGAAGACTCCCT 58.825 34.615 0.00 0.00 0.00 4.20
644 679 0.451783 CCCACTTATTCGCTTGGTGC 59.548 55.000 0.00 0.00 38.57 5.01
653 688 4.262678 GCATACCTCCTCTCCCACTTATTC 60.263 50.000 0.00 0.00 0.00 1.75
671 706 3.788797 GCAGATAGCAACCAAACGCATAC 60.789 47.826 0.00 0.00 44.79 2.39
753 788 1.605971 TAACGACTGCGGCCCACATA 61.606 55.000 0.00 0.00 43.17 2.29
816 853 3.630148 CCATGATCACGCCGCGTC 61.630 66.667 17.16 5.74 38.32 5.19
1028 1074 2.682494 GCGGTGTAGGGGGTGAGA 60.682 66.667 0.00 0.00 0.00 3.27
1039 1085 2.258013 CGGATTGTGGTTGCGGTGT 61.258 57.895 0.00 0.00 0.00 4.16
1043 1089 1.511318 TTCACCGGATTGTGGTTGCG 61.511 55.000 9.46 0.00 37.72 4.85
1046 1092 3.895041 AGAAAATTCACCGGATTGTGGTT 59.105 39.130 9.46 0.00 37.72 3.67
1050 1096 3.496331 ACCAGAAAATTCACCGGATTGT 58.504 40.909 9.46 0.00 0.00 2.71
1096 1142 1.823295 GAGATGCCCTTCCTGCGTA 59.177 57.895 0.00 0.00 0.00 4.42
1756 1839 0.782384 CAACGAACCGCTCACTGTAC 59.218 55.000 0.00 0.00 0.00 2.90
1765 1848 1.580256 GAAACACAAACAACGAACCGC 59.420 47.619 0.00 0.00 0.00 5.68
1767 1850 3.828786 AGTGAAACACAAACAACGAACC 58.171 40.909 4.75 0.00 41.43 3.62
1783 1866 5.420725 ACACCTCATATGTAGCAAGTGAA 57.579 39.130 1.90 0.00 0.00 3.18
1784 1867 5.891551 TCTACACCTCATATGTAGCAAGTGA 59.108 40.000 1.90 0.00 46.12 3.41
1826 1909 6.085555 TGACACTAACTCCTACTCAACAAG 57.914 41.667 0.00 0.00 0.00 3.16
1842 1925 6.718294 TCATCTGAAGTAGTACCTGACACTA 58.282 40.000 0.00 0.00 0.00 2.74
1843 1926 5.571285 TCATCTGAAGTAGTACCTGACACT 58.429 41.667 0.00 0.00 0.00 3.55
1848 1931 3.957497 AGCCTCATCTGAAGTAGTACCTG 59.043 47.826 0.00 0.00 0.00 4.00
1914 1997 9.646522 ACAGCCAACAAATTAGGATCTAAATAT 57.353 29.630 0.00 0.00 0.00 1.28
1924 2008 4.321230 GGACAGAACAGCCAACAAATTAGG 60.321 45.833 0.00 0.00 0.00 2.69
1930 2014 1.476833 GGAGGACAGAACAGCCAACAA 60.477 52.381 0.00 0.00 0.00 2.83
2009 2093 1.673920 CCGGCACAAACACAACTAAGT 59.326 47.619 0.00 0.00 0.00 2.24
2026 2110 0.664761 CCAATTAGCAGCACATCCGG 59.335 55.000 0.00 0.00 0.00 5.14
2066 2150 1.207089 TGTCCACTACAGTATGCCAGC 59.793 52.381 0.00 0.00 42.53 4.85
2140 2224 9.430623 TCACTTCATAACATCGATCTTTACAAA 57.569 29.630 0.00 0.00 0.00 2.83
2151 2235 7.761249 TGGCTATATCATCACTTCATAACATCG 59.239 37.037 0.00 0.00 0.00 3.84
2192 2276 9.120538 GCATAGGTGTTTTCCATTTAGATCTTA 57.879 33.333 0.00 0.00 0.00 2.10
2236 2320 3.321396 TCATGCTGGCAAATTGAAGTCAA 59.679 39.130 0.00 0.00 40.51 3.18
2395 2479 6.128200 CCATTCGTGGGATAATGACACATATG 60.128 42.308 0.00 0.00 35.53 1.78
2490 2575 3.100671 AGACCACCACTGAGTAGGAATC 58.899 50.000 7.84 3.33 0.00 2.52
2515 2600 4.954202 AGAATGACATGATTCAGCCAACAT 59.046 37.500 0.00 0.00 35.16 2.71
2540 2625 9.471084 TGCAATTTCATCATTATAGATTTGCTG 57.529 29.630 10.52 0.00 38.18 4.41
2678 2768 3.302365 TTTTTGGACGGAGGTAGTACG 57.698 47.619 0.00 0.00 0.00 3.67
2695 2785 2.705127 TCATTTGAGGGCCAAGCTTTTT 59.295 40.909 6.18 0.00 35.94 1.94
2699 2789 1.829222 CATTCATTTGAGGGCCAAGCT 59.171 47.619 6.18 0.00 35.94 3.74
2700 2790 1.551883 ACATTCATTTGAGGGCCAAGC 59.448 47.619 6.18 0.00 35.94 4.01
2701 2791 3.181483 GCTACATTCATTTGAGGGCCAAG 60.181 47.826 6.18 0.00 35.94 3.61
2702 2792 2.760092 GCTACATTCATTTGAGGGCCAA 59.240 45.455 6.18 0.00 0.00 4.52
2703 2793 2.378038 GCTACATTCATTTGAGGGCCA 58.622 47.619 6.18 0.00 0.00 5.36
2704 2794 1.683385 GGCTACATTCATTTGAGGGCC 59.317 52.381 0.00 0.00 0.00 5.80
2705 2795 1.683385 GGGCTACATTCATTTGAGGGC 59.317 52.381 0.00 0.00 0.00 5.19
2706 2796 3.017048 TGGGCTACATTCATTTGAGGG 57.983 47.619 0.00 0.00 0.00 4.30
2707 2797 4.096984 GTCTTGGGCTACATTCATTTGAGG 59.903 45.833 0.00 0.00 0.00 3.86
2708 2798 4.701651 TGTCTTGGGCTACATTCATTTGAG 59.298 41.667 0.00 0.00 0.00 3.02
2709 2799 4.661222 TGTCTTGGGCTACATTCATTTGA 58.339 39.130 0.00 0.00 0.00 2.69
2710 2800 5.389859 TTGTCTTGGGCTACATTCATTTG 57.610 39.130 0.00 0.00 0.00 2.32
2711 2801 6.400568 CATTTGTCTTGGGCTACATTCATTT 58.599 36.000 0.00 0.00 0.00 2.32
2712 2802 5.105228 CCATTTGTCTTGGGCTACATTCATT 60.105 40.000 0.00 0.00 0.00 2.57
2713 2803 4.403432 CCATTTGTCTTGGGCTACATTCAT 59.597 41.667 0.00 0.00 0.00 2.57
2714 2804 3.763360 CCATTTGTCTTGGGCTACATTCA 59.237 43.478 0.00 0.00 0.00 2.57
2715 2805 4.376340 CCATTTGTCTTGGGCTACATTC 57.624 45.455 0.00 0.00 0.00 2.67
2724 2814 1.818674 GGTGCTACCCATTTGTCTTGG 59.181 52.381 0.00 0.00 30.04 3.61
2725 2815 2.513753 TGGTGCTACCCATTTGTCTTG 58.486 47.619 3.33 0.00 37.50 3.02
2726 2816 2.969821 TGGTGCTACCCATTTGTCTT 57.030 45.000 3.33 0.00 37.50 3.01
2727 2817 2.108250 ACTTGGTGCTACCCATTTGTCT 59.892 45.455 3.33 0.00 37.50 3.41
2728 2818 2.514803 ACTTGGTGCTACCCATTTGTC 58.485 47.619 3.33 0.00 37.50 3.18
2729 2819 2.675658 ACTTGGTGCTACCCATTTGT 57.324 45.000 3.33 0.00 37.50 2.83
2730 2820 4.079253 ACTAACTTGGTGCTACCCATTTG 58.921 43.478 3.33 0.52 37.50 2.32
2731 2821 4.079253 CACTAACTTGGTGCTACCCATTT 58.921 43.478 3.33 0.00 37.50 2.32
2732 2822 3.686016 CACTAACTTGGTGCTACCCATT 58.314 45.455 3.33 0.00 37.50 3.16
2733 2823 3.350219 CACTAACTTGGTGCTACCCAT 57.650 47.619 3.33 0.00 37.50 4.00
2734 2824 2.851263 CACTAACTTGGTGCTACCCA 57.149 50.000 3.33 0.00 37.50 4.51
2741 2831 7.041721 TGAATGTATCTAGCACTAACTTGGTG 58.958 38.462 0.97 0.97 37.70 4.17
2742 2832 7.182817 TGAATGTATCTAGCACTAACTTGGT 57.817 36.000 0.00 0.00 0.00 3.67
2743 2833 8.668510 AATGAATGTATCTAGCACTAACTTGG 57.331 34.615 0.00 0.00 0.00 3.61
2744 2834 9.926751 CAAATGAATGTATCTAGCACTAACTTG 57.073 33.333 0.00 0.00 0.00 3.16
2745 2835 9.890629 TCAAATGAATGTATCTAGCACTAACTT 57.109 29.630 0.00 0.00 0.00 2.66
2746 2836 9.539825 CTCAAATGAATGTATCTAGCACTAACT 57.460 33.333 0.00 0.00 0.00 2.24
2747 2837 8.768955 CCTCAAATGAATGTATCTAGCACTAAC 58.231 37.037 0.00 0.00 0.00 2.34
2748 2838 7.933577 CCCTCAAATGAATGTATCTAGCACTAA 59.066 37.037 0.00 0.00 0.00 2.24
2749 2839 7.290014 TCCCTCAAATGAATGTATCTAGCACTA 59.710 37.037 0.00 0.00 0.00 2.74
2750 2840 6.100279 TCCCTCAAATGAATGTATCTAGCACT 59.900 38.462 0.00 0.00 0.00 4.40
2751 2841 6.203723 GTCCCTCAAATGAATGTATCTAGCAC 59.796 42.308 0.00 0.00 0.00 4.40
2752 2842 6.126796 TGTCCCTCAAATGAATGTATCTAGCA 60.127 38.462 0.00 0.00 0.00 3.49
2753 2843 6.291377 TGTCCCTCAAATGAATGTATCTAGC 58.709 40.000 0.00 0.00 0.00 3.42
2754 2844 7.041508 GCTTGTCCCTCAAATGAATGTATCTAG 60.042 40.741 0.00 0.00 35.48 2.43
2755 2845 6.767902 GCTTGTCCCTCAAATGAATGTATCTA 59.232 38.462 0.00 0.00 35.48 1.98
2756 2846 5.591877 GCTTGTCCCTCAAATGAATGTATCT 59.408 40.000 0.00 0.00 35.48 1.98
2757 2847 5.591877 AGCTTGTCCCTCAAATGAATGTATC 59.408 40.000 0.00 0.00 35.48 2.24
2758 2848 5.513233 AGCTTGTCCCTCAAATGAATGTAT 58.487 37.500 0.00 0.00 35.48 2.29
2759 2849 4.922206 AGCTTGTCCCTCAAATGAATGTA 58.078 39.130 0.00 0.00 35.48 2.29
2760 2850 3.771216 AGCTTGTCCCTCAAATGAATGT 58.229 40.909 0.00 0.00 35.48 2.71
2761 2851 4.796038 AAGCTTGTCCCTCAAATGAATG 57.204 40.909 0.00 0.00 35.48 2.67
2762 2852 5.279657 GGAAAAGCTTGTCCCTCAAATGAAT 60.280 40.000 23.49 0.00 35.48 2.57
2763 2853 4.039124 GGAAAAGCTTGTCCCTCAAATGAA 59.961 41.667 23.49 0.00 35.48 2.57
2764 2854 3.573967 GGAAAAGCTTGTCCCTCAAATGA 59.426 43.478 23.49 0.00 35.48 2.57
2765 2855 3.612479 CGGAAAAGCTTGTCCCTCAAATG 60.612 47.826 26.94 9.69 35.48 2.32
2766 2856 2.558359 CGGAAAAGCTTGTCCCTCAAAT 59.442 45.455 26.94 0.00 35.48 2.32
2767 2857 1.953686 CGGAAAAGCTTGTCCCTCAAA 59.046 47.619 26.94 0.00 35.48 2.69
2768 2858 1.604604 CGGAAAAGCTTGTCCCTCAA 58.395 50.000 26.94 0.00 34.61 3.02
2769 2859 0.250727 CCGGAAAAGCTTGTCCCTCA 60.251 55.000 26.94 0.00 0.00 3.86
2770 2860 0.036306 TCCGGAAAAGCTTGTCCCTC 59.964 55.000 26.94 5.77 0.00 4.30
2771 2861 0.250770 GTCCGGAAAAGCTTGTCCCT 60.251 55.000 26.94 0.00 0.00 4.20
2772 2862 1.574702 CGTCCGGAAAAGCTTGTCCC 61.575 60.000 26.94 13.97 0.00 4.46
2773 2863 1.574702 CCGTCCGGAAAAGCTTGTCC 61.575 60.000 24.00 24.00 37.50 4.02
2774 2864 0.601841 TCCGTCCGGAAAAGCTTGTC 60.602 55.000 5.23 8.23 42.05 3.18
2775 2865 0.602905 CTCCGTCCGGAAAAGCTTGT 60.603 55.000 5.23 0.00 44.66 3.16
2776 2866 1.298859 CCTCCGTCCGGAAAAGCTTG 61.299 60.000 5.23 0.00 44.66 4.01
2777 2867 1.003718 CCTCCGTCCGGAAAAGCTT 60.004 57.895 5.23 0.00 44.66 3.74
2778 2868 2.663196 CCTCCGTCCGGAAAAGCT 59.337 61.111 5.23 0.00 44.66 3.74
2779 2869 2.436115 CCCTCCGTCCGGAAAAGC 60.436 66.667 5.23 0.00 44.66 3.51
2780 2870 1.218316 CTCCCTCCGTCCGGAAAAG 59.782 63.158 5.23 3.59 44.66 2.27
2781 2871 0.251742 TACTCCCTCCGTCCGGAAAA 60.252 55.000 5.23 0.00 44.66 2.29
2782 2872 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2783 2873 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2784 2874 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
2785 2875 0.107017 TTAGTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
2786 2876 1.020437 GTTAGTACTCCCTCCGTCCG 58.980 60.000 0.00 0.00 0.00 4.79
2787 2877 2.433662 AGTTAGTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
2788 2878 4.097135 GGTTTAGTTAGTACTCCCTCCGTC 59.903 50.000 0.00 0.00 35.78 4.79
2789 2879 4.019858 GGTTTAGTTAGTACTCCCTCCGT 58.980 47.826 0.00 0.00 35.78 4.69
2790 2880 3.065925 CGGTTTAGTTAGTACTCCCTCCG 59.934 52.174 0.00 2.57 35.78 4.63
2791 2881 4.019858 ACGGTTTAGTTAGTACTCCCTCC 58.980 47.826 0.00 0.00 35.78 4.30
2792 2882 4.676459 GCACGGTTTAGTTAGTACTCCCTC 60.676 50.000 0.00 0.00 35.78 4.30
2793 2883 3.194329 GCACGGTTTAGTTAGTACTCCCT 59.806 47.826 0.00 0.00 35.78 4.20
2794 2884 3.056607 TGCACGGTTTAGTTAGTACTCCC 60.057 47.826 0.00 0.00 35.78 4.30
2795 2885 4.178545 TGCACGGTTTAGTTAGTACTCC 57.821 45.455 0.00 0.00 35.78 3.85
2796 2886 5.648572 AGATGCACGGTTTAGTTAGTACTC 58.351 41.667 0.00 0.00 35.78 2.59
2797 2887 5.656213 AGATGCACGGTTTAGTTAGTACT 57.344 39.130 0.00 0.00 38.44 2.73
2798 2888 6.976925 ACATAGATGCACGGTTTAGTTAGTAC 59.023 38.462 0.00 0.00 0.00 2.73
2799 2889 7.104043 ACATAGATGCACGGTTTAGTTAGTA 57.896 36.000 0.00 0.00 0.00 1.82
2800 2890 5.974108 ACATAGATGCACGGTTTAGTTAGT 58.026 37.500 0.00 0.00 0.00 2.24
2801 2891 7.997107 TTACATAGATGCACGGTTTAGTTAG 57.003 36.000 0.00 0.00 0.00 2.34
2802 2892 7.982919 ACATTACATAGATGCACGGTTTAGTTA 59.017 33.333 0.00 0.00 0.00 2.24
2803 2893 6.821665 ACATTACATAGATGCACGGTTTAGTT 59.178 34.615 0.00 0.00 0.00 2.24
2804 2894 6.346096 ACATTACATAGATGCACGGTTTAGT 58.654 36.000 0.00 0.00 0.00 2.24
2805 2895 6.844696 ACATTACATAGATGCACGGTTTAG 57.155 37.500 0.00 0.00 0.00 1.85
2806 2896 8.605746 GTTTACATTACATAGATGCACGGTTTA 58.394 33.333 0.00 0.00 0.00 2.01
2807 2897 7.119992 TGTTTACATTACATAGATGCACGGTTT 59.880 33.333 0.00 0.00 0.00 3.27
2808 2898 6.596106 TGTTTACATTACATAGATGCACGGTT 59.404 34.615 0.00 0.00 0.00 4.44
2809 2899 6.110033 TGTTTACATTACATAGATGCACGGT 58.890 36.000 0.00 0.00 0.00 4.83
2810 2900 6.597262 TGTTTACATTACATAGATGCACGG 57.403 37.500 0.00 0.00 0.00 4.94
2811 2901 8.122330 ACAATGTTTACATTACATAGATGCACG 58.878 33.333 7.72 0.00 44.10 5.34
2812 2902 9.787532 AACAATGTTTACATTACATAGATGCAC 57.212 29.630 7.72 0.00 44.10 4.57
2867 2957 7.823665 ACAGAGTGAATATAAACTGTCGTACA 58.176 34.615 0.00 0.00 34.21 2.90
2873 2963 7.928307 ATGCAACAGAGTGAATATAAACTGT 57.072 32.000 0.00 0.00 39.70 3.55
2933 3026 7.095523 TGCTTTACGTATGACAAAAAGTAGTCC 60.096 37.037 0.00 0.00 33.89 3.85
2938 3031 9.389570 GTAAATGCTTTACGTATGACAAAAAGT 57.610 29.630 0.00 0.00 36.51 2.66
2963 3056 9.364653 AGGAATACTATAAGATAAGTCCAACGT 57.635 33.333 0.00 0.00 0.00 3.99
3170 3266 2.715046 CATCTGCTTGGCTCCAAACTA 58.285 47.619 2.69 0.00 35.33 2.24
3204 3300 0.323178 AGCATCCTCCAGGCAAACAG 60.323 55.000 0.00 0.00 34.44 3.16
3362 3458 1.800586 TGAGTAAGAGCAAAGCAAGCG 59.199 47.619 0.00 0.00 37.01 4.68
3453 3564 9.725019 CTTTGATGCCATACTATGTATTTCCTA 57.275 33.333 0.00 0.00 0.00 2.94
3456 3567 8.621532 TCCTTTGATGCCATACTATGTATTTC 57.378 34.615 0.00 0.00 0.00 2.17
3461 3572 5.894298 TCTCCTTTGATGCCATACTATGT 57.106 39.130 0.00 0.00 0.00 2.29
3462 3573 7.756395 AATTCTCCTTTGATGCCATACTATG 57.244 36.000 0.00 0.00 0.00 2.23
3463 3574 8.636213 CAAAATTCTCCTTTGATGCCATACTAT 58.364 33.333 0.00 0.00 36.12 2.12
3464 3575 7.833682 TCAAAATTCTCCTTTGATGCCATACTA 59.166 33.333 0.00 0.00 37.76 1.82
3558 3669 2.025037 AGCCTGCACCATTCATAAAGGA 60.025 45.455 0.00 0.00 0.00 3.36
3577 3688 6.183360 GCAAAGCTAGACTAAAGGAAGTTAGC 60.183 42.308 0.00 0.00 36.91 3.09
3578 3689 7.064016 CAGCAAAGCTAGACTAAAGGAAGTTAG 59.936 40.741 0.00 0.00 36.40 2.34
3631 3746 4.121317 CACTTTGAGAGGAGATGATCTGC 58.879 47.826 5.76 5.76 34.82 4.26
3633 3748 3.134442 GGCACTTTGAGAGGAGATGATCT 59.866 47.826 0.00 0.00 0.00 2.75
3636 3751 2.259917 TGGCACTTTGAGAGGAGATGA 58.740 47.619 0.00 0.00 0.00 2.92
3637 3752 2.775911 TGGCACTTTGAGAGGAGATG 57.224 50.000 0.00 0.00 0.00 2.90
3638 3753 5.441718 TTATTGGCACTTTGAGAGGAGAT 57.558 39.130 0.00 0.00 0.00 2.75
3639 3754 4.908601 TTATTGGCACTTTGAGAGGAGA 57.091 40.909 0.00 0.00 0.00 3.71
3640 3755 5.006386 ACTTTATTGGCACTTTGAGAGGAG 58.994 41.667 0.00 0.00 0.00 3.69
3641 3756 4.985538 ACTTTATTGGCACTTTGAGAGGA 58.014 39.130 0.00 0.00 0.00 3.71
3642 3757 4.142816 CGACTTTATTGGCACTTTGAGAGG 60.143 45.833 0.00 0.00 0.00 3.69
3644 3759 4.385825 ACGACTTTATTGGCACTTTGAGA 58.614 39.130 0.00 0.00 0.00 3.27
3652 3817 6.519679 TCTCTACTTACGACTTTATTGGCA 57.480 37.500 0.00 0.00 0.00 4.92
3674 3839 8.456904 AACGAGGTAAGTTTTTGAAAAACTTC 57.543 30.769 37.27 29.13 44.50 3.01
3682 3847 4.942483 TGGACAAACGAGGTAAGTTTTTGA 59.058 37.500 0.00 0.00 39.50 2.69
3685 3850 5.127491 TGATGGACAAACGAGGTAAGTTTT 58.873 37.500 0.00 0.00 39.50 2.43
3689 3854 4.152402 CACTTGATGGACAAACGAGGTAAG 59.848 45.833 0.00 0.00 38.08 2.34
3690 3855 4.062293 CACTTGATGGACAAACGAGGTAA 58.938 43.478 0.00 0.00 38.08 2.85
3696 3861 2.854424 GCACACACTTGATGGACAAACG 60.854 50.000 0.00 0.00 38.08 3.60
3701 3866 1.532868 GACAGCACACACTTGATGGAC 59.467 52.381 0.00 0.00 37.20 4.02
3707 3872 0.578683 CGTCAGACAGCACACACTTG 59.421 55.000 0.41 0.00 0.00 3.16
3715 3880 4.561213 CACGTTATTATTCGTCAGACAGCA 59.439 41.667 0.41 0.00 38.23 4.41
3716 3881 4.561606 ACACGTTATTATTCGTCAGACAGC 59.438 41.667 0.41 0.00 38.23 4.40
3717 3882 5.229469 GGACACGTTATTATTCGTCAGACAG 59.771 44.000 0.41 0.00 38.23 3.51
3725 3890 5.403897 AGCAATGGACACGTTATTATTCG 57.596 39.130 0.00 0.00 0.00 3.34
3729 3894 5.277106 CGCATTAGCAATGGACACGTTATTA 60.277 40.000 9.81 0.00 42.27 0.98
3737 3902 1.396648 CGAACGCATTAGCAATGGACA 59.603 47.619 9.81 0.00 42.27 4.02
3739 3904 1.732941 ACGAACGCATTAGCAATGGA 58.267 45.000 9.81 0.00 42.27 3.41
3774 3939 7.164230 AGAACGCCAATTTATAATTTGTCCA 57.836 32.000 15.43 0.00 0.00 4.02
3775 3940 7.544217 ACAAGAACGCCAATTTATAATTTGTCC 59.456 33.333 15.43 7.95 0.00 4.02
3776 3941 8.460831 ACAAGAACGCCAATTTATAATTTGTC 57.539 30.769 15.43 5.54 0.00 3.18
3778 3943 8.379902 GGAACAAGAACGCCAATTTATAATTTG 58.620 33.333 11.49 11.49 0.00 2.32
3779 3944 8.311109 AGGAACAAGAACGCCAATTTATAATTT 58.689 29.630 0.00 0.00 0.00 1.82
3780 3945 7.836842 AGGAACAAGAACGCCAATTTATAATT 58.163 30.769 0.00 0.00 0.00 1.40
3782 3947 6.431543 TGAGGAACAAGAACGCCAATTTATAA 59.568 34.615 0.00 0.00 0.00 0.98
3796 3961 7.522073 GCATCTTTAACATGTTGAGGAACAAGA 60.522 37.037 21.42 11.33 45.23 3.02
3815 3980 2.229792 TCAGCCGACTTTTGCATCTTT 58.770 42.857 0.00 0.00 0.00 2.52
3819 3984 1.808945 CTCTTCAGCCGACTTTTGCAT 59.191 47.619 0.00 0.00 0.00 3.96
3864 4029 8.782144 GTGGCCATTTGATTTTTATCTCAAAAA 58.218 29.630 9.72 0.00 42.72 1.94
3874 4039 5.248020 TGACATAGGTGGCCATTTGATTTTT 59.752 36.000 9.72 0.00 29.75 1.94
3879 4044 3.448093 TTGACATAGGTGGCCATTTGA 57.552 42.857 9.72 0.00 29.75 2.69
3910 4075 8.954950 TTTCATGCCAAAATTTGAGAACTTTA 57.045 26.923 7.37 0.00 0.00 1.85
3950 4117 2.711542 CCAAGGGGTGTGTACAGATTC 58.288 52.381 0.00 0.00 0.00 2.52
3953 4120 1.057275 TGCCAAGGGGTGTGTACAGA 61.057 55.000 0.00 0.00 36.17 3.41
3961 4128 0.967380 GAGGATGTTGCCAAGGGGTG 60.967 60.000 0.00 0.00 36.17 4.61
3962 4129 1.384191 GAGGATGTTGCCAAGGGGT 59.616 57.895 0.00 0.00 36.17 4.95
3963 4130 0.032813 ATGAGGATGTTGCCAAGGGG 60.033 55.000 0.00 0.00 37.18 4.79
4038 4205 7.310485 GGAGTCCTTGAGGTCAATAAAGTCTTA 60.310 40.741 0.41 0.00 35.02 2.10


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

AutoCloner maintained by Alex Coulton.