Multiple sequence alignment - TraesCS4A01G249000

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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 TraesCS4A01G249000 chr4A 100.000 2839 0 0 461 3299 559951519 559948681 0.000000e+00 5243.0
1 TraesCS4A01G249000 chr4A 97.238 181 4 1 2754 2933 464567612 464567432 4.140000e-79 305.0
2 TraesCS4A01G249000 chr4A 97.701 174 4 0 2757 2930 594145383 594145210 1.920000e-77 300.0
3 TraesCS4A01G249000 chr4A 100.000 97 0 0 1 97 559951979 559951883 2.620000e-41 180.0
4 TraesCS4A01G249000 chr4D 91.733 2141 67 25 461 2519 40113243 40115355 0.000000e+00 2872.0
5 TraesCS4A01G249000 chr4D 94.118 255 15 0 2514 2768 40115405 40115659 3.990000e-104 388.0
6 TraesCS4A01G249000 chr4D 90.909 110 10 0 3088 3197 40115722 40115831 7.380000e-32 148.0
7 TraesCS4A01G249000 chr4D 91.209 91 8 0 2995 3085 503153844 503153934 1.240000e-24 124.0
8 TraesCS4A01G249000 chr4D 95.775 71 3 0 2927 2997 40115656 40115726 7.480000e-22 115.0
9 TraesCS4A01G249000 chr4D 87.629 97 12 0 1 97 40113095 40113191 2.690000e-21 113.0
10 TraesCS4A01G249000 chr4B 90.721 2080 98 55 493 2517 58564676 58566715 0.000000e+00 2684.0
11 TraesCS4A01G249000 chr4B 90.714 280 20 1 2514 2793 58566767 58567040 5.200000e-98 368.0
12 TraesCS4A01G249000 chr4B 88.119 101 12 0 2993 3093 640979252 640979152 1.610000e-23 121.0
13 TraesCS4A01G249000 chr5A 97.238 181 3 2 2752 2932 361454807 361454629 4.140000e-79 305.0
14 TraesCS4A01G249000 chr6B 98.824 170 2 0 2764 2933 114057034 114057203 1.490000e-78 303.0
15 TraesCS4A01G249000 chr6B 83.654 208 31 2 3088 3294 663019667 663019872 3.360000e-45 193.0
16 TraesCS4A01G249000 chr6B 91.837 49 3 1 2950 2997 663019623 663019671 2.120000e-07 67.6
17 TraesCS4A01G249000 chr1A 97.714 175 4 0 2756 2930 322177184 322177358 5.350000e-78 302.0
18 TraesCS4A01G249000 chr1A 89.000 100 11 0 2996 3095 340015098 340014999 1.240000e-24 124.0
19 TraesCS4A01G249000 chr3A 97.701 174 4 0 2757 2930 89152575 89152748 1.920000e-77 300.0
20 TraesCS4A01G249000 chr7B 95.628 183 7 1 2767 2949 705489055 705489236 3.220000e-75 292.0
21 TraesCS4A01G249000 chr7B 96.111 180 4 3 2764 2941 685246308 685246486 1.160000e-74 291.0
22 TraesCS4A01G249000 chr7B 90.000 90 9 0 2996 3085 741719801 741719712 2.080000e-22 117.0
23 TraesCS4A01G249000 chr3B 95.082 183 7 2 2767 2949 45447695 45447515 1.500000e-73 287.0
24 TraesCS4A01G249000 chr3B 86.111 108 15 0 2987 3094 607809458 607809351 2.080000e-22 117.0
25 TraesCS4A01G249000 chr5D 87.923 207 22 2 3089 3294 109565972 109565768 1.180000e-59 241.0
26 TraesCS4A01G249000 chr5D 92.500 40 3 0 2953 2992 109566013 109565974 1.280000e-04 58.4
27 TraesCS4A01G249000 chr3D 86.047 215 28 2 3086 3299 15699587 15699374 2.560000e-56 230.0
28 TraesCS4A01G249000 chr5B 88.889 99 11 0 2987 3085 68902501 68902403 4.470000e-24 122.0
29 TraesCS4A01G249000 chr5B 90.000 90 9 0 2996 3085 418373521 418373432 2.080000e-22 117.0
30 TraesCS4A01G249000 chr5B 90.805 87 8 0 2996 3082 582392571 582392657 2.080000e-22 117.0
31 TraesCS4A01G249000 chr7A 87.037 108 13 1 2988 3094 60728633 60728526 1.610000e-23 121.0
32 TraesCS4A01G249000 chr6D 97.674 43 1 0 2955 2997 51195670 51195628 1.270000e-09 75.0


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 TraesCS4A01G249000 chr4A 559948681 559951979 3298 True 2711.5 5243 100.0000 1 3299 2 chr4A.!!$R3 3298
1 TraesCS4A01G249000 chr4D 40113095 40115831 2736 False 727.2 2872 92.0328 1 3197 5 chr4D.!!$F2 3196
2 TraesCS4A01G249000 chr4B 58564676 58567040 2364 False 1526.0 2684 90.7175 493 2793 2 chr4B.!!$F1 2300

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
80 81 0.307146 GATCTTCATCGCTGCTTGGC 59.693 55.0 0.0 0.0 0.0 4.52 F
1741 1796 0.390472 CACCTTCCTGAGAGCGAACC 60.390 60.0 0.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2053 2141 1.519455 CATCAACGGCGTCCTCCTC 60.519 63.158 15.17 0.0 0.00 3.71 R
3254 3434 0.177373 TGCTATGCAGAGCTGTCAGG 59.823 55.000 31.40 0.0 43.27 3.86 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
43 44 0.322277 ACCTCGACTCGCTCAACCTA 60.322 55.000 0.00 0.00 0.00 3.08
45 46 0.803117 CTCGACTCGCTCAACCTACA 59.197 55.000 0.00 0.00 0.00 2.74
80 81 0.307146 GATCTTCATCGCTGCTTGGC 59.693 55.000 0.00 0.00 0.00 4.52
482 483 2.031870 GAGGAGAGAGGAAGAGGAAGC 58.968 57.143 0.00 0.00 0.00 3.86
484 485 1.470051 GAGAGAGGAAGAGGAAGCGT 58.530 55.000 0.00 0.00 0.00 5.07
519 520 2.831565 AGAGAGGAAGAGCAAGACCAT 58.168 47.619 0.00 0.00 0.00 3.55
599 601 1.672356 GTGTGCAACGCTCTCCCAT 60.672 57.895 0.00 0.00 45.72 4.00
629 631 1.422024 GGGATAAGGAGGAAAGGGAGC 59.578 57.143 0.00 0.00 0.00 4.70
631 633 0.470341 ATAAGGAGGAAAGGGAGCGC 59.530 55.000 0.00 0.00 0.00 5.92
710 714 4.204891 GCCACGTCGAATTCGCGG 62.205 66.667 32.10 24.72 40.89 6.46
717 721 1.373622 TCGAATTCGCGGTCAAGCA 60.374 52.632 22.90 0.00 39.60 3.91
883 896 9.828852 GACATATTATTAGAGAGTAGGTTCGTG 57.171 37.037 0.00 0.00 0.00 4.35
923 938 5.687285 CGGGAAGTGTCAATCAAAAGAAAAG 59.313 40.000 0.00 0.00 0.00 2.27
925 940 7.436933 GGGAAGTGTCAATCAAAAGAAAAGAT 58.563 34.615 0.00 0.00 0.00 2.40
926 941 8.576442 GGGAAGTGTCAATCAAAAGAAAAGATA 58.424 33.333 0.00 0.00 0.00 1.98
927 942 9.965824 GGAAGTGTCAATCAAAAGAAAAGATAA 57.034 29.630 0.00 0.00 0.00 1.75
967 982 1.890041 GCGCGCTCTCCTCTCTCTA 60.890 63.158 26.67 0.00 0.00 2.43
1161 1216 1.976474 GTTCTTGGCCGGCATGGAA 60.976 57.895 30.85 23.48 42.00 3.53
1299 1354 2.997315 CGCCAGGTCCAGTCTCCA 60.997 66.667 0.00 0.00 0.00 3.86
1351 1406 1.915769 AAGAAGCGTGAGGAGGCCT 60.916 57.895 3.86 3.86 36.03 5.19
1356 1411 3.699894 CGTGAGGAGGCCTGCACT 61.700 66.667 27.56 13.99 31.76 4.40
1362 1417 2.343758 GAGGCCTGCACTTCGTCA 59.656 61.111 12.00 0.00 0.00 4.35
1741 1796 0.390472 CACCTTCCTGAGAGCGAACC 60.390 60.000 0.00 0.00 0.00 3.62
2033 2121 3.924013 ATGCCCCACACGAGGAGGA 62.924 63.158 0.00 0.00 0.00 3.71
2034 2122 4.083862 GCCCCACACGAGGAGGAC 62.084 72.222 0.00 0.00 0.00 3.85
2035 2123 3.760035 CCCCACACGAGGAGGACG 61.760 72.222 0.00 0.00 0.00 4.79
2036 2124 4.436998 CCCACACGAGGAGGACGC 62.437 72.222 0.00 0.00 0.00 5.19
2037 2125 4.436998 CCACACGAGGAGGACGCC 62.437 72.222 0.00 0.00 0.00 5.68
2038 2126 4.778415 CACACGAGGAGGACGCCG 62.778 72.222 0.00 0.00 0.00 6.46
2040 2128 4.052229 CACGAGGAGGACGCCGTT 62.052 66.667 0.00 0.00 32.58 4.44
2041 2129 4.052229 ACGAGGAGGACGCCGTTG 62.052 66.667 0.00 0.00 31.24 4.10
2042 2130 3.744719 CGAGGAGGACGCCGTTGA 61.745 66.667 0.00 0.00 0.00 3.18
2043 2131 2.893398 GAGGAGGACGCCGTTGAT 59.107 61.111 0.00 0.00 0.00 2.57
2044 2132 1.519455 GAGGAGGACGCCGTTGATG 60.519 63.158 0.00 0.00 0.00 3.07
2045 2133 3.195698 GGAGGACGCCGTTGATGC 61.196 66.667 0.00 0.00 0.00 3.91
2046 2134 3.195698 GAGGACGCCGTTGATGCC 61.196 66.667 0.00 0.00 0.00 4.40
2047 2135 4.778143 AGGACGCCGTTGATGCCC 62.778 66.667 0.00 0.00 0.00 5.36
2052 2140 3.747976 GCCGTTGATGCCCCACAC 61.748 66.667 0.00 0.00 0.00 3.82
2053 2141 3.430862 CCGTTGATGCCCCACACG 61.431 66.667 0.00 0.00 0.00 4.49
2054 2142 2.358125 CGTTGATGCCCCACACGA 60.358 61.111 0.00 0.00 0.00 4.35
2055 2143 2.390599 CGTTGATGCCCCACACGAG 61.391 63.158 0.00 0.00 0.00 4.18
2056 2144 2.040544 GTTGATGCCCCACACGAGG 61.041 63.158 0.00 0.00 0.00 4.63
2057 2145 2.220586 TTGATGCCCCACACGAGGA 61.221 57.895 0.00 0.00 0.00 3.71
2058 2146 2.184020 TTGATGCCCCACACGAGGAG 62.184 60.000 0.00 0.00 0.00 3.69
2059 2147 3.391665 GATGCCCCACACGAGGAGG 62.392 68.421 0.00 0.00 0.00 4.30
2060 2148 3.924013 ATGCCCCACACGAGGAGGA 62.924 63.158 0.00 0.00 0.00 3.71
2211 2301 0.673985 ATCGATCGATTTCCAGGCGA 59.326 50.000 24.60 2.12 38.51 5.54
2256 2346 6.875195 ACAAGAAACATTATTTGGCATCTTGG 59.125 34.615 19.78 7.59 42.06 3.61
2313 2403 8.193438 AGACTCTTAATTGGAATGCAATTTAGC 58.807 33.333 17.37 6.22 36.07 3.09
2342 2434 3.668447 TCTCCATGAGTTTCTTCAGTGC 58.332 45.455 0.00 0.00 0.00 4.40
2347 2439 4.094590 CCATGAGTTTCTTCAGTGCAGATC 59.905 45.833 0.00 0.00 0.00 2.75
2351 2443 4.573900 AGTTTCTTCAGTGCAGATCGATT 58.426 39.130 0.00 0.00 0.00 3.34
2352 2444 4.391216 AGTTTCTTCAGTGCAGATCGATTG 59.609 41.667 0.00 1.24 0.00 2.67
2353 2445 3.874392 TCTTCAGTGCAGATCGATTGA 57.126 42.857 0.00 0.00 0.00 2.57
2354 2446 3.515630 TCTTCAGTGCAGATCGATTGAC 58.484 45.455 0.00 0.00 0.00 3.18
2355 2447 3.194329 TCTTCAGTGCAGATCGATTGACT 59.806 43.478 0.00 0.00 0.00 3.41
2373 2492 6.583912 TTGACTCGTTCTGTTTTCAGTTAG 57.416 37.500 0.00 0.00 46.98 2.34
2375 2494 5.518847 TGACTCGTTCTGTTTTCAGTTAGTG 59.481 40.000 0.00 0.00 46.98 2.74
2378 2497 5.593968 TCGTTCTGTTTTCAGTTAGTGCTA 58.406 37.500 0.00 0.00 46.98 3.49
2379 2498 6.220930 TCGTTCTGTTTTCAGTTAGTGCTAT 58.779 36.000 0.00 0.00 46.98 2.97
2380 2499 6.145534 TCGTTCTGTTTTCAGTTAGTGCTATG 59.854 38.462 0.00 0.00 46.98 2.23
2521 2701 6.375455 CAGCACTTTTTAGTGATCCATACCTT 59.625 38.462 9.35 0.00 42.02 3.50
2612 2792 8.397906 GGAATCAACAATGATATCTTCGAAACA 58.602 33.333 3.98 0.00 45.60 2.83
2634 2814 8.507470 AACAAACTTTTTAGATGATTTCTCGC 57.493 30.769 0.00 0.00 35.79 5.03
2690 2870 9.819267 AAAACCATTTTCCGTTTTATTACAGAA 57.181 25.926 0.00 0.00 39.70 3.02
2759 2939 4.569966 TGCGATGCAAATTGAAAGTTTGTT 59.430 33.333 0.00 0.00 38.49 2.83
2764 2944 8.113062 CGATGCAAATTGAAAGTTTGTTACAAA 58.887 29.630 6.41 6.41 38.49 2.83
2765 2945 9.424659 GATGCAAATTGAAAGTTTGTTACAAAG 57.575 29.630 11.07 0.00 38.49 2.77
2766 2946 8.316640 TGCAAATTGAAAGTTTGTTACAAAGT 57.683 26.923 11.07 11.52 38.49 2.66
2767 2947 9.424319 TGCAAATTGAAAGTTTGTTACAAAGTA 57.576 25.926 17.17 3.81 38.49 2.24
2768 2948 9.683651 GCAAATTGAAAGTTTGTTACAAAGTAC 57.316 29.630 17.17 14.35 38.49 2.73
2771 2951 9.797556 AATTGAAAGTTTGTTACAAAGTACTCC 57.202 29.630 17.17 8.43 0.00 3.85
2772 2952 7.324354 TGAAAGTTTGTTACAAAGTACTCCC 57.676 36.000 17.17 1.98 0.00 4.30
2773 2953 7.114095 TGAAAGTTTGTTACAAAGTACTCCCT 58.886 34.615 17.17 4.16 0.00 4.20
2774 2954 7.281549 TGAAAGTTTGTTACAAAGTACTCCCTC 59.718 37.037 17.17 7.88 0.00 4.30
2775 2955 5.618236 AGTTTGTTACAAAGTACTCCCTCC 58.382 41.667 15.58 0.00 0.00 4.30
2776 2956 3.947910 TGTTACAAAGTACTCCCTCCG 57.052 47.619 0.00 0.00 0.00 4.63
2777 2957 3.233507 TGTTACAAAGTACTCCCTCCGT 58.766 45.455 0.00 0.00 0.00 4.69
2778 2958 3.256631 TGTTACAAAGTACTCCCTCCGTC 59.743 47.826 0.00 0.00 0.00 4.79
2779 2959 1.264295 ACAAAGTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
2780 2960 0.535797 CAAAGTACTCCCTCCGTCCC 59.464 60.000 0.00 0.00 0.00 4.46
2781 2961 0.412640 AAAGTACTCCCTCCGTCCCT 59.587 55.000 0.00 0.00 0.00 4.20
2782 2962 1.302907 AAGTACTCCCTCCGTCCCTA 58.697 55.000 0.00 0.00 0.00 3.53
2783 2963 1.302907 AGTACTCCCTCCGTCCCTAA 58.697 55.000 0.00 0.00 0.00 2.69
2784 2964 1.642762 AGTACTCCCTCCGTCCCTAAA 59.357 52.381 0.00 0.00 0.00 1.85
2785 2965 2.246849 AGTACTCCCTCCGTCCCTAAAT 59.753 50.000 0.00 0.00 0.00 1.40
2786 2966 3.464833 AGTACTCCCTCCGTCCCTAAATA 59.535 47.826 0.00 0.00 0.00 1.40
2787 2967 2.675583 ACTCCCTCCGTCCCTAAATAC 58.324 52.381 0.00 0.00 0.00 1.89
2788 2968 2.246849 ACTCCCTCCGTCCCTAAATACT 59.753 50.000 0.00 0.00 0.00 2.12
2789 2969 3.306613 CTCCCTCCGTCCCTAAATACTT 58.693 50.000 0.00 0.00 0.00 2.24
2790 2970 3.036091 TCCCTCCGTCCCTAAATACTTG 58.964 50.000 0.00 0.00 0.00 3.16
2791 2971 2.770232 CCCTCCGTCCCTAAATACTTGT 59.230 50.000 0.00 0.00 0.00 3.16
2792 2972 3.181468 CCCTCCGTCCCTAAATACTTGTC 60.181 52.174 0.00 0.00 0.00 3.18
2793 2973 3.705072 CCTCCGTCCCTAAATACTTGTCT 59.295 47.826 0.00 0.00 0.00 3.41
2794 2974 4.161754 CCTCCGTCCCTAAATACTTGTCTT 59.838 45.833 0.00 0.00 0.00 3.01
2795 2975 5.338137 CCTCCGTCCCTAAATACTTGTCTTT 60.338 44.000 0.00 0.00 0.00 2.52
2796 2976 5.727434 TCCGTCCCTAAATACTTGTCTTTC 58.273 41.667 0.00 0.00 0.00 2.62
2797 2977 5.482878 TCCGTCCCTAAATACTTGTCTTTCT 59.517 40.000 0.00 0.00 0.00 2.52
2798 2978 6.664816 TCCGTCCCTAAATACTTGTCTTTCTA 59.335 38.462 0.00 0.00 0.00 2.10
2799 2979 6.979238 CCGTCCCTAAATACTTGTCTTTCTAG 59.021 42.308 0.00 0.00 0.00 2.43
2800 2980 6.979238 CGTCCCTAAATACTTGTCTTTCTAGG 59.021 42.308 0.00 0.00 0.00 3.02
2801 2981 6.762187 GTCCCTAAATACTTGTCTTTCTAGGC 59.238 42.308 0.00 0.00 0.00 3.93
2802 2982 6.442564 TCCCTAAATACTTGTCTTTCTAGGCA 59.557 38.462 0.00 0.00 33.22 4.75
2803 2983 7.127339 TCCCTAAATACTTGTCTTTCTAGGCAT 59.873 37.037 0.00 0.00 35.56 4.40
2804 2984 7.775561 CCCTAAATACTTGTCTTTCTAGGCATT 59.224 37.037 0.00 0.00 35.56 3.56
2805 2985 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
2807 2987 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
2808 2988 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
2809 2989 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
2810 2990 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
2811 2991 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
2812 2992 6.317789 TGTCTTTCTAGGCATTTCAACAAG 57.682 37.500 0.00 0.00 29.10 3.16
2813 2993 5.827797 TGTCTTTCTAGGCATTTCAACAAGT 59.172 36.000 0.00 0.00 29.10 3.16
2814 2994 6.145535 GTCTTTCTAGGCATTTCAACAAGTG 58.854 40.000 0.00 0.00 0.00 3.16
2815 2995 6.017109 GTCTTTCTAGGCATTTCAACAAGTGA 60.017 38.462 0.00 0.00 0.00 3.41
2816 2996 5.689383 TTCTAGGCATTTCAACAAGTGAC 57.311 39.130 0.00 0.00 35.39 3.67
2817 2997 4.973168 TCTAGGCATTTCAACAAGTGACT 58.027 39.130 0.00 0.00 40.60 3.41
2818 2998 6.109156 TCTAGGCATTTCAACAAGTGACTA 57.891 37.500 0.00 0.00 38.51 2.59
2819 2999 5.932303 TCTAGGCATTTCAACAAGTGACTAC 59.068 40.000 0.00 0.00 38.51 2.73
2820 3000 4.460263 AGGCATTTCAACAAGTGACTACA 58.540 39.130 0.00 0.00 35.84 2.74
2821 3001 5.072741 AGGCATTTCAACAAGTGACTACAT 58.927 37.500 0.00 0.00 35.84 2.29
2822 3002 6.237901 AGGCATTTCAACAAGTGACTACATA 58.762 36.000 0.00 0.00 35.84 2.29
2823 3003 6.149474 AGGCATTTCAACAAGTGACTACATAC 59.851 38.462 0.00 0.00 35.84 2.39
2824 3004 6.015504 GCATTTCAACAAGTGACTACATACG 58.984 40.000 0.00 0.00 35.39 3.06
2825 3005 6.534059 CATTTCAACAAGTGACTACATACGG 58.466 40.000 0.00 0.00 35.39 4.02
2826 3006 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2827 3007 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2828 3008 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2829 3009 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2830 3010 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2831 3011 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2832 3012 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2833 3013 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2834 3014 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2835 3015 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2836 3016 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2837 3017 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2838 3018 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2839 3019 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2840 3020 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2841 3021 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2842 3022 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2843 3023 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2844 3024 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2845 3025 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2846 3026 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2847 3027 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2890 3070 7.342769 ACATCCGTATGTAGTAGTCATTTGA 57.657 36.000 0.00 0.00 44.66 2.69
2891 3071 7.778083 ACATCCGTATGTAGTAGTCATTTGAA 58.222 34.615 0.00 0.00 44.66 2.69
2892 3072 8.255206 ACATCCGTATGTAGTAGTCATTTGAAA 58.745 33.333 0.00 0.00 44.66 2.69
2893 3073 9.261180 CATCCGTATGTAGTAGTCATTTGAAAT 57.739 33.333 0.00 0.00 0.00 2.17
2894 3074 8.642908 TCCGTATGTAGTAGTCATTTGAAATG 57.357 34.615 11.54 11.54 0.00 2.32
2895 3075 8.255206 TCCGTATGTAGTAGTCATTTGAAATGT 58.745 33.333 16.62 2.38 0.00 2.71
2896 3076 8.540492 CCGTATGTAGTAGTCATTTGAAATGTC 58.460 37.037 16.62 11.74 0.00 3.06
2897 3077 9.302345 CGTATGTAGTAGTCATTTGAAATGTCT 57.698 33.333 18.62 18.62 0.00 3.41
2921 3101 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2922 3102 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2923 3103 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2924 3104 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2925 3105 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2964 3144 1.378514 AATCACACGACCCCATGGC 60.379 57.895 6.09 0.00 33.59 4.40
2971 3151 2.594592 GACCCCATGGCCGTATGC 60.595 66.667 6.09 0.00 40.16 3.14
3009 3189 0.257039 TGTACTACTCCCTCCGTCCC 59.743 60.000 0.00 0.00 0.00 4.46
3010 3190 0.257039 GTACTACTCCCTCCGTCCCA 59.743 60.000 0.00 0.00 0.00 4.37
3016 3196 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3017 3197 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3018 3198 1.064979 TCCCTCCGTCCCAAAATAAGC 60.065 52.381 0.00 0.00 0.00 3.09
3022 3202 1.276989 TCCGTCCCAAAATAAGCGTCT 59.723 47.619 0.00 0.00 0.00 4.18
3023 3203 2.081462 CCGTCCCAAAATAAGCGTCTT 58.919 47.619 0.00 0.00 0.00 3.01
3024 3204 2.159572 CCGTCCCAAAATAAGCGTCTTG 60.160 50.000 2.86 0.00 0.00 3.02
3025 3205 2.739913 CGTCCCAAAATAAGCGTCTTGA 59.260 45.455 2.86 0.00 0.00 3.02
3026 3206 3.424433 CGTCCCAAAATAAGCGTCTTGAC 60.424 47.826 2.86 0.00 0.00 3.18
3027 3207 3.078837 TCCCAAAATAAGCGTCTTGACC 58.921 45.455 2.86 0.00 0.00 4.02
3028 3208 3.081804 CCCAAAATAAGCGTCTTGACCT 58.918 45.455 2.86 0.00 0.00 3.85
3029 3209 3.506067 CCCAAAATAAGCGTCTTGACCTT 59.494 43.478 2.86 8.65 0.00 3.50
3030 3210 4.698304 CCCAAAATAAGCGTCTTGACCTTA 59.302 41.667 11.29 11.29 0.00 2.69
3031 3211 5.357032 CCCAAAATAAGCGTCTTGACCTTAT 59.643 40.000 13.60 13.60 34.25 1.73
3032 3212 6.127730 CCCAAAATAAGCGTCTTGACCTTATT 60.128 38.462 19.52 19.52 41.18 1.40
3033 3213 7.066525 CCCAAAATAAGCGTCTTGACCTTATTA 59.933 37.037 22.33 9.15 39.53 0.98
3034 3214 7.908601 CCAAAATAAGCGTCTTGACCTTATTAC 59.091 37.037 22.33 0.00 39.53 1.89
3035 3215 8.447833 CAAAATAAGCGTCTTGACCTTATTACA 58.552 33.333 22.33 6.11 39.53 2.41
3036 3216 8.556213 AAATAAGCGTCTTGACCTTATTACAA 57.444 30.769 22.33 0.00 39.53 2.41
3037 3217 5.857822 AAGCGTCTTGACCTTATTACAAC 57.142 39.130 0.00 0.00 0.00 3.32
3038 3218 5.148651 AGCGTCTTGACCTTATTACAACT 57.851 39.130 0.00 0.00 0.00 3.16
3039 3219 5.548406 AGCGTCTTGACCTTATTACAACTT 58.452 37.500 0.00 0.00 0.00 2.66
3040 3220 5.995897 AGCGTCTTGACCTTATTACAACTTT 59.004 36.000 0.00 0.00 0.00 2.66
3041 3221 6.073222 AGCGTCTTGACCTTATTACAACTTTG 60.073 38.462 0.00 0.00 0.00 2.77
3042 3222 6.293244 GCGTCTTGACCTTATTACAACTTTGT 60.293 38.462 0.00 0.00 44.86 2.83
3043 3223 7.095523 GCGTCTTGACCTTATTACAACTTTGTA 60.096 37.037 0.00 0.00 42.35 2.41
3044 3224 8.219105 CGTCTTGACCTTATTACAACTTTGTAC 58.781 37.037 1.18 0.00 42.84 2.90
3045 3225 9.269453 GTCTTGACCTTATTACAACTTTGTACT 57.731 33.333 1.18 0.00 42.84 2.73
3046 3226 9.485206 TCTTGACCTTATTACAACTTTGTACTC 57.515 33.333 1.18 0.00 42.84 2.59
3047 3227 7.878477 TGACCTTATTACAACTTTGTACTCG 57.122 36.000 1.18 0.00 42.84 4.18
3048 3228 7.660112 TGACCTTATTACAACTTTGTACTCGA 58.340 34.615 1.18 0.00 42.84 4.04
3049 3229 7.811236 TGACCTTATTACAACTTTGTACTCGAG 59.189 37.037 11.84 11.84 42.84 4.04
3050 3230 7.664758 ACCTTATTACAACTTTGTACTCGAGT 58.335 34.615 23.66 23.66 42.84 4.18
3051 3231 8.146412 ACCTTATTACAACTTTGTACTCGAGTT 58.854 33.333 25.44 8.09 42.84 3.01
3052 3232 9.630098 CCTTATTACAACTTTGTACTCGAGTTA 57.370 33.333 25.44 10.82 42.84 2.24
3083 3263 7.653767 AGTTAAGACACTTATTTTGAGACGG 57.346 36.000 0.00 0.00 0.00 4.79
3084 3264 7.439381 AGTTAAGACACTTATTTTGAGACGGA 58.561 34.615 0.00 0.00 0.00 4.69
3085 3265 8.095169 AGTTAAGACACTTATTTTGAGACGGAT 58.905 33.333 0.00 0.00 0.00 4.18
3086 3266 9.362539 GTTAAGACACTTATTTTGAGACGGATA 57.637 33.333 0.00 0.00 0.00 2.59
3089 3269 9.751542 AAGACACTTATTTTGAGACGGATATAG 57.248 33.333 0.00 0.00 0.00 1.31
3090 3270 8.915036 AGACACTTATTTTGAGACGGATATAGT 58.085 33.333 0.00 0.00 0.00 2.12
3105 3285 9.286946 GACGGATATAGTATTTCATTAAGGACG 57.713 37.037 3.44 0.00 0.00 4.79
3123 3303 1.150560 ACGCCAATCCTATAGGGGGTA 59.849 52.381 18.97 0.00 43.73 3.69
3173 3353 6.723298 TGTTCCAATCCAAATTTGTACACT 57.277 33.333 16.73 0.00 0.00 3.55
3177 3357 8.357402 GTTCCAATCCAAATTTGTACACTACTT 58.643 33.333 16.73 0.00 0.00 2.24
3264 3444 2.427320 TGGCACACCTGACAGCTC 59.573 61.111 0.00 0.00 36.63 4.09
3265 3445 2.142761 TGGCACACCTGACAGCTCT 61.143 57.895 0.00 0.00 36.63 4.09
3266 3446 1.670406 GGCACACCTGACAGCTCTG 60.670 63.158 0.00 0.00 0.00 3.35
3267 3447 2.323580 GCACACCTGACAGCTCTGC 61.324 63.158 0.00 0.00 0.00 4.26
3268 3448 1.070275 CACACCTGACAGCTCTGCA 59.930 57.895 0.00 0.00 0.00 4.41
3269 3449 0.321387 CACACCTGACAGCTCTGCAT 60.321 55.000 0.00 0.00 0.00 3.96
3270 3450 1.066645 CACACCTGACAGCTCTGCATA 60.067 52.381 0.00 0.00 0.00 3.14
3271 3451 1.206610 ACACCTGACAGCTCTGCATAG 59.793 52.381 0.00 0.00 0.00 2.23
3272 3452 0.177604 ACCTGACAGCTCTGCATAGC 59.822 55.000 15.84 15.84 43.11 2.97
3273 3453 0.177373 CCTGACAGCTCTGCATAGCA 59.823 55.000 24.15 4.44 45.30 3.49
3286 3466 2.813754 TGCATAGCAGAGTGAACAAACC 59.186 45.455 0.00 0.00 33.32 3.27
3287 3467 2.813754 GCATAGCAGAGTGAACAAACCA 59.186 45.455 0.00 0.00 0.00 3.67
3288 3468 3.253188 GCATAGCAGAGTGAACAAACCAA 59.747 43.478 0.00 0.00 0.00 3.67
3289 3469 4.614535 GCATAGCAGAGTGAACAAACCAAG 60.615 45.833 0.00 0.00 0.00 3.61
3290 3470 1.678101 AGCAGAGTGAACAAACCAAGC 59.322 47.619 0.00 0.00 0.00 4.01
3291 3471 1.405105 GCAGAGTGAACAAACCAAGCA 59.595 47.619 0.00 0.00 0.00 3.91
3292 3472 2.159254 GCAGAGTGAACAAACCAAGCAA 60.159 45.455 0.00 0.00 0.00 3.91
3293 3473 3.491447 GCAGAGTGAACAAACCAAGCAAT 60.491 43.478 0.00 0.00 0.00 3.56
3294 3474 4.685924 CAGAGTGAACAAACCAAGCAATT 58.314 39.130 0.00 0.00 0.00 2.32
3295 3475 4.505191 CAGAGTGAACAAACCAAGCAATTG 59.495 41.667 0.00 0.00 0.00 2.32
3296 3476 3.197265 AGTGAACAAACCAAGCAATTGC 58.803 40.909 23.05 23.05 42.49 3.56
3297 3477 2.935201 GTGAACAAACCAAGCAATTGCA 59.065 40.909 30.89 3.86 45.16 4.08
3298 3478 3.373439 GTGAACAAACCAAGCAATTGCAA 59.627 39.130 30.89 0.00 45.16 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.153939 CGAGGTCGAGCTCCAACAG 60.154 63.158 32.56 18.08 43.02 3.16
43 44 4.626081 GTGGTGCTGCCCTCGTGT 62.626 66.667 0.00 0.00 36.04 4.49
76 77 4.243008 TGAGTTGGACCGCGCCAA 62.243 61.111 13.34 13.34 45.28 4.52
460 461 0.548989 TCCTCTTCCTCTCTCCTCCG 59.451 60.000 0.00 0.00 0.00 4.63
461 462 2.666317 CTTCCTCTTCCTCTCTCCTCC 58.334 57.143 0.00 0.00 0.00 4.30
462 463 2.031870 GCTTCCTCTTCCTCTCTCCTC 58.968 57.143 0.00 0.00 0.00 3.71
463 464 1.684869 CGCTTCCTCTTCCTCTCTCCT 60.685 57.143 0.00 0.00 0.00 3.69
484 485 0.756294 TCTCTTCTTTGTCGTGCCCA 59.244 50.000 0.00 0.00 0.00 5.36
498 499 2.614259 TGGTCTTGCTCTTCCTCTCTT 58.386 47.619 0.00 0.00 0.00 2.85
556 558 4.402192 CTCGATCGACGTGCCATT 57.598 55.556 15.15 0.00 43.13 3.16
562 564 0.861866 CACAATCGCTCGATCGACGT 60.862 55.000 27.03 11.26 41.62 4.34
565 567 0.170339 ACACACAATCGCTCGATCGA 59.830 50.000 18.32 18.32 43.09 3.59
599 601 2.158097 CCTCCTTATCCCATCCTCCTCA 60.158 54.545 0.00 0.00 0.00 3.86
629 631 3.892740 TTCACCACCACCATCCGCG 62.893 63.158 0.00 0.00 0.00 6.46
631 633 1.377202 CCTTCACCACCACCATCCG 60.377 63.158 0.00 0.00 0.00 4.18
680 684 1.529438 GACGTGGCAAAGAAATGACGA 59.471 47.619 0.00 0.00 0.00 4.20
710 714 5.557891 AGATGCACTAAAGATTGCTTGAC 57.442 39.130 0.00 0.00 39.62 3.18
717 721 6.182627 TCCATGACAAGATGCACTAAAGATT 58.817 36.000 0.00 0.00 0.00 2.40
731 735 4.578871 TCACAGTGGTAATCCATGACAAG 58.421 43.478 0.00 0.00 46.20 3.16
842 848 8.934023 AATAATATGTCACCGGGAATGTTTAT 57.066 30.769 6.32 0.00 0.00 1.40
923 938 3.363970 CGCATGGATACCAGCGTTTTATC 60.364 47.826 18.60 0.00 42.00 1.75
925 940 1.937223 CGCATGGATACCAGCGTTTTA 59.063 47.619 18.60 0.00 42.00 1.52
926 941 0.732571 CGCATGGATACCAGCGTTTT 59.267 50.000 18.60 0.00 42.00 2.43
927 942 2.393557 CGCATGGATACCAGCGTTT 58.606 52.632 18.60 0.00 42.00 3.60
928 943 4.124910 CGCATGGATACCAGCGTT 57.875 55.556 18.60 0.00 42.00 4.84
1299 1354 4.648626 TTGCTTGCTCTGGCCGCT 62.649 61.111 0.00 0.00 37.74 5.52
1714 1769 3.655211 CAGGAAGGTGCCCCAGCT 61.655 66.667 0.00 0.00 44.48 4.24
1741 1796 4.796231 CTTCCCCACGACGAGGCG 62.796 72.222 5.72 0.00 37.29 5.52
2035 2123 3.747976 GTGTGGGGCATCAACGGC 61.748 66.667 0.00 0.00 0.00 5.68
2036 2124 3.430862 CGTGTGGGGCATCAACGG 61.431 66.667 0.00 0.00 0.00 4.44
2037 2125 2.358125 TCGTGTGGGGCATCAACG 60.358 61.111 0.00 0.00 0.00 4.10
2038 2126 2.040544 CCTCGTGTGGGGCATCAAC 61.041 63.158 0.00 0.00 0.00 3.18
2039 2127 2.184020 CTCCTCGTGTGGGGCATCAA 62.184 60.000 0.00 0.00 0.00 2.57
2040 2128 2.606213 TCCTCGTGTGGGGCATCA 60.606 61.111 0.00 0.00 0.00 3.07
2041 2129 2.187946 CTCCTCGTGTGGGGCATC 59.812 66.667 0.00 0.00 0.00 3.91
2042 2130 3.402681 CCTCCTCGTGTGGGGCAT 61.403 66.667 0.00 0.00 0.00 4.40
2043 2131 4.631740 TCCTCCTCGTGTGGGGCA 62.632 66.667 0.00 0.00 0.00 5.36
2044 2132 4.083862 GTCCTCCTCGTGTGGGGC 62.084 72.222 0.00 0.00 0.00 5.80
2045 2133 3.760035 CGTCCTCCTCGTGTGGGG 61.760 72.222 0.00 0.00 0.00 4.96
2046 2134 4.436998 GCGTCCTCCTCGTGTGGG 62.437 72.222 0.00 0.00 0.00 4.61
2047 2135 4.436998 GGCGTCCTCCTCGTGTGG 62.437 72.222 0.00 0.00 0.00 4.17
2048 2136 4.778415 CGGCGTCCTCCTCGTGTG 62.778 72.222 0.00 0.00 0.00 3.82
2050 2138 4.052229 AACGGCGTCCTCCTCGTG 62.052 66.667 15.17 0.00 35.93 4.35
2051 2139 4.052229 CAACGGCGTCCTCCTCGT 62.052 66.667 15.17 0.00 37.45 4.18
2052 2140 3.064987 ATCAACGGCGTCCTCCTCG 62.065 63.158 15.17 0.00 0.00 4.63
2053 2141 1.519455 CATCAACGGCGTCCTCCTC 60.519 63.158 15.17 0.00 0.00 3.71
2054 2142 2.579201 CATCAACGGCGTCCTCCT 59.421 61.111 15.17 0.00 0.00 3.69
2055 2143 3.195698 GCATCAACGGCGTCCTCC 61.196 66.667 15.17 0.00 0.00 4.30
2056 2144 3.195698 GGCATCAACGGCGTCCTC 61.196 66.667 15.17 0.83 0.00 3.71
2057 2145 4.778143 GGGCATCAACGGCGTCCT 62.778 66.667 15.17 0.00 0.00 3.85
2176 2266 4.908730 CGATCGATCTACACTGAACTCATG 59.091 45.833 22.43 0.00 0.00 3.07
2211 2301 2.744202 GTGTCGTGCCAAGAATCAATCT 59.256 45.455 0.00 0.00 41.32 2.40
2313 2403 3.390639 AGAAACTCATGGAGATAGGCCTG 59.609 47.826 17.99 0.00 33.32 4.85
2351 2443 5.518847 CACTAACTGAAAACAGAACGAGTCA 59.481 40.000 0.00 0.00 0.00 3.41
2352 2444 5.556570 GCACTAACTGAAAACAGAACGAGTC 60.557 44.000 0.00 0.00 0.00 3.36
2353 2445 4.270325 GCACTAACTGAAAACAGAACGAGT 59.730 41.667 0.00 0.00 0.00 4.18
2354 2446 4.508124 AGCACTAACTGAAAACAGAACGAG 59.492 41.667 0.00 0.00 0.00 4.18
2355 2447 4.439057 AGCACTAACTGAAAACAGAACGA 58.561 39.130 0.00 0.00 0.00 3.85
2375 2494 7.649306 CCAAGGATAAAACATGCTTTACATAGC 59.351 37.037 3.48 0.00 36.64 2.97
2378 2497 7.716799 TCCAAGGATAAAACATGCTTTACAT 57.283 32.000 3.48 0.00 40.66 2.29
2379 2498 7.375053 GTTCCAAGGATAAAACATGCTTTACA 58.625 34.615 3.48 0.00 0.00 2.41
2380 2499 6.526674 CGTTCCAAGGATAAAACATGCTTTAC 59.473 38.462 3.48 0.00 0.00 2.01
2612 2792 5.795441 GCGCGAGAAATCATCTAAAAAGTTT 59.205 36.000 12.10 0.00 38.96 2.66
2622 2802 4.458951 ACAAATAGCGCGAGAAATCATC 57.541 40.909 12.10 0.00 0.00 2.92
2688 2868 6.238593 GCCTGAAGATAATCACATCAAGGTTC 60.239 42.308 0.00 0.00 30.63 3.62
2690 2870 5.104193 AGCCTGAAGATAATCACATCAAGGT 60.104 40.000 0.00 0.00 30.63 3.50
2735 2915 4.751098 ACAAACTTTCAATTTGCATCGCAT 59.249 33.333 0.00 0.00 40.10 4.73
2739 2919 9.424659 CTTTGTAACAAACTTTCAATTTGCATC 57.575 29.630 0.00 0.00 40.10 3.91
2759 2939 2.450476 GGACGGAGGGAGTACTTTGTA 58.550 52.381 0.00 0.00 0.00 2.41
2764 2944 1.302907 TTAGGGACGGAGGGAGTACT 58.697 55.000 0.00 0.00 0.00 2.73
2765 2945 2.149973 TTTAGGGACGGAGGGAGTAC 57.850 55.000 0.00 0.00 0.00 2.73
2766 2946 3.464833 AGTATTTAGGGACGGAGGGAGTA 59.535 47.826 0.00 0.00 0.00 2.59
2767 2947 2.246849 AGTATTTAGGGACGGAGGGAGT 59.753 50.000 0.00 0.00 0.00 3.85
2768 2948 2.960163 AGTATTTAGGGACGGAGGGAG 58.040 52.381 0.00 0.00 0.00 4.30
2769 2949 3.036091 CAAGTATTTAGGGACGGAGGGA 58.964 50.000 0.00 0.00 0.00 4.20
2770 2950 2.770232 ACAAGTATTTAGGGACGGAGGG 59.230 50.000 0.00 0.00 0.00 4.30
2771 2951 3.705072 AGACAAGTATTTAGGGACGGAGG 59.295 47.826 0.00 0.00 0.00 4.30
2772 2952 5.340439 AAGACAAGTATTTAGGGACGGAG 57.660 43.478 0.00 0.00 0.00 4.63
2773 2953 5.482878 AGAAAGACAAGTATTTAGGGACGGA 59.517 40.000 0.00 0.00 0.00 4.69
2774 2954 5.731591 AGAAAGACAAGTATTTAGGGACGG 58.268 41.667 0.00 0.00 0.00 4.79
2775 2955 6.979238 CCTAGAAAGACAAGTATTTAGGGACG 59.021 42.308 0.00 0.00 0.00 4.79
2776 2956 6.762187 GCCTAGAAAGACAAGTATTTAGGGAC 59.238 42.308 9.79 0.00 0.00 4.46
2777 2957 6.442564 TGCCTAGAAAGACAAGTATTTAGGGA 59.557 38.462 9.79 5.62 0.00 4.20
2778 2958 6.650120 TGCCTAGAAAGACAAGTATTTAGGG 58.350 40.000 9.79 6.40 0.00 3.53
2779 2959 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
2781 2961 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
2782 2962 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
2783 2963 8.515414 GTTGAAATGCCTAGAAAGACAAGTATT 58.485 33.333 0.00 0.00 0.00 1.89
2784 2964 7.665559 TGTTGAAATGCCTAGAAAGACAAGTAT 59.334 33.333 0.00 0.00 0.00 2.12
2785 2965 6.995686 TGTTGAAATGCCTAGAAAGACAAGTA 59.004 34.615 0.00 0.00 0.00 2.24
2786 2966 5.827797 TGTTGAAATGCCTAGAAAGACAAGT 59.172 36.000 0.00 0.00 0.00 3.16
2787 2967 6.317789 TGTTGAAATGCCTAGAAAGACAAG 57.682 37.500 0.00 0.00 0.00 3.16
2788 2968 6.321181 ACTTGTTGAAATGCCTAGAAAGACAA 59.679 34.615 0.00 0.00 0.00 3.18
2789 2969 5.827797 ACTTGTTGAAATGCCTAGAAAGACA 59.172 36.000 0.00 0.00 0.00 3.41
2790 2970 6.017109 TCACTTGTTGAAATGCCTAGAAAGAC 60.017 38.462 0.00 0.00 0.00 3.01
2791 2971 6.017109 GTCACTTGTTGAAATGCCTAGAAAGA 60.017 38.462 0.00 0.00 35.39 2.52
2792 2972 6.016777 AGTCACTTGTTGAAATGCCTAGAAAG 60.017 38.462 0.00 0.00 35.39 2.62
2793 2973 5.827797 AGTCACTTGTTGAAATGCCTAGAAA 59.172 36.000 0.00 0.00 35.39 2.52
2794 2974 5.376625 AGTCACTTGTTGAAATGCCTAGAA 58.623 37.500 0.00 0.00 35.39 2.10
2795 2975 4.973168 AGTCACTTGTTGAAATGCCTAGA 58.027 39.130 0.00 0.00 35.39 2.43
2796 2976 5.700832 TGTAGTCACTTGTTGAAATGCCTAG 59.299 40.000 0.00 0.00 35.39 3.02
2797 2977 5.616270 TGTAGTCACTTGTTGAAATGCCTA 58.384 37.500 0.00 0.00 35.39 3.93
2798 2978 4.460263 TGTAGTCACTTGTTGAAATGCCT 58.540 39.130 0.00 0.00 35.39 4.75
2799 2979 4.829064 TGTAGTCACTTGTTGAAATGCC 57.171 40.909 0.00 0.00 35.39 4.40
2800 2980 6.015504 CGTATGTAGTCACTTGTTGAAATGC 58.984 40.000 0.00 0.00 35.39 3.56
2801 2981 6.367695 TCCGTATGTAGTCACTTGTTGAAATG 59.632 38.462 0.00 0.00 35.39 2.32
2802 2982 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2803 2983 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2804 2984 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
2805 2985 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
2806 2986 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2807 2987 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2808 2988 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2809 2989 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2810 2990 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2811 2991 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2812 2992 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2813 2993 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2814 2994 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2815 2995 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2816 2996 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2817 2997 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2818 2998 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2819 2999 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2820 3000 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2821 3001 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2822 3002 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2823 3003 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2824 3004 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2825 3005 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2864 3044 9.074576 TCAAATGACTACTACATACGGATGTAT 57.925 33.333 20.64 13.02 45.42 2.29
2865 3045 8.454570 TCAAATGACTACTACATACGGATGTA 57.545 34.615 19.32 19.32 44.77 2.29
2867 3047 8.642908 TTTCAAATGACTACTACATACGGATG 57.357 34.615 5.94 5.94 39.16 3.51
2868 3048 9.261180 CATTTCAAATGACTACTACATACGGAT 57.739 33.333 3.82 0.00 0.00 4.18
2869 3049 8.255206 ACATTTCAAATGACTACTACATACGGA 58.745 33.333 17.30 0.00 0.00 4.69
2870 3050 8.420374 ACATTTCAAATGACTACTACATACGG 57.580 34.615 17.30 0.00 0.00 4.02
2871 3051 9.302345 AGACATTTCAAATGACTACTACATACG 57.698 33.333 17.30 0.00 0.00 3.06
2895 3075 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2896 3076 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2897 3077 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2898 3078 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2899 3079 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2900 3080 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2901 3081 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2902 3082 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2903 3083 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2904 3084 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2905 3085 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2906 3086 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2907 3087 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
2908 3088 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2909 3089 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2910 3090 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2911 3091 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2912 3092 3.525199 ACTACTACTCCCTCCGTTCCTAA 59.475 47.826 0.00 0.00 0.00 2.69
2913 3093 3.118531 ACTACTACTCCCTCCGTTCCTA 58.881 50.000 0.00 0.00 0.00 2.94
2914 3094 1.921748 ACTACTACTCCCTCCGTTCCT 59.078 52.381 0.00 0.00 0.00 3.36
2915 3095 2.433662 ACTACTACTCCCTCCGTTCC 57.566 55.000 0.00 0.00 0.00 3.62
2916 3096 6.295249 ACTTATACTACTACTCCCTCCGTTC 58.705 44.000 0.00 0.00 0.00 3.95
2917 3097 6.259346 ACTTATACTACTACTCCCTCCGTT 57.741 41.667 0.00 0.00 0.00 4.44
2918 3098 5.903198 ACTTATACTACTACTCCCTCCGT 57.097 43.478 0.00 0.00 0.00 4.69
2919 3099 7.094848 GCTTAACTTATACTACTACTCCCTCCG 60.095 44.444 0.00 0.00 0.00 4.63
2920 3100 7.723172 TGCTTAACTTATACTACTACTCCCTCC 59.277 40.741 0.00 0.00 0.00 4.30
2921 3101 8.688747 TGCTTAACTTATACTACTACTCCCTC 57.311 38.462 0.00 0.00 0.00 4.30
2922 3102 9.657728 ATTGCTTAACTTATACTACTACTCCCT 57.342 33.333 0.00 0.00 0.00 4.20
2923 3103 9.911138 GATTGCTTAACTTATACTACTACTCCC 57.089 37.037 0.00 0.00 0.00 4.30
2971 3151 9.900264 GTAGTACAAAAGTTTTGCAAATTCTTG 57.100 29.630 24.86 19.06 35.49 3.02
2986 3166 3.119209 GGACGGAGGGAGTAGTACAAAAG 60.119 52.174 2.52 0.00 0.00 2.27
3009 3189 8.447833 TGTAATAAGGTCAAGACGCTTATTTTG 58.552 33.333 24.75 1.72 40.69 2.44
3010 3190 8.556213 TGTAATAAGGTCAAGACGCTTATTTT 57.444 30.769 24.75 14.90 40.69 1.82
3016 3196 5.148651 AGTTGTAATAAGGTCAAGACGCT 57.851 39.130 0.00 0.00 0.00 5.07
3017 3197 5.857822 AAGTTGTAATAAGGTCAAGACGC 57.142 39.130 0.00 0.00 0.00 5.19
3018 3198 7.186021 ACAAAGTTGTAATAAGGTCAAGACG 57.814 36.000 0.00 0.00 40.16 4.18
3022 3202 8.143193 TCGAGTACAAAGTTGTAATAAGGTCAA 58.857 33.333 5.49 0.00 44.46 3.18
3023 3203 7.660112 TCGAGTACAAAGTTGTAATAAGGTCA 58.340 34.615 5.49 0.00 44.46 4.02
3024 3204 7.811713 ACTCGAGTACAAAGTTGTAATAAGGTC 59.188 37.037 18.46 0.00 44.46 3.85
3025 3205 7.664758 ACTCGAGTACAAAGTTGTAATAAGGT 58.335 34.615 18.46 2.43 44.46 3.50
3026 3206 8.530269 AACTCGAGTACAAAGTTGTAATAAGG 57.470 34.615 20.39 1.92 44.46 2.69
3057 3237 8.557029 CCGTCTCAAAATAAGTGTCTTAACTTT 58.443 33.333 0.00 0.00 40.77 2.66
3058 3238 7.929785 TCCGTCTCAAAATAAGTGTCTTAACTT 59.070 33.333 0.00 0.00 42.89 2.66
3059 3239 7.439381 TCCGTCTCAAAATAAGTGTCTTAACT 58.561 34.615 0.00 0.00 0.00 2.24
3060 3240 7.647907 TCCGTCTCAAAATAAGTGTCTTAAC 57.352 36.000 0.00 0.00 0.00 2.01
3063 3243 9.751542 CTATATCCGTCTCAAAATAAGTGTCTT 57.248 33.333 0.00 0.00 0.00 3.01
3064 3244 8.915036 ACTATATCCGTCTCAAAATAAGTGTCT 58.085 33.333 0.00 0.00 0.00 3.41
3079 3259 9.286946 CGTCCTTAATGAAATACTATATCCGTC 57.713 37.037 0.00 0.00 0.00 4.79
3080 3260 7.758528 GCGTCCTTAATGAAATACTATATCCGT 59.241 37.037 0.00 0.00 0.00 4.69
3081 3261 7.222224 GGCGTCCTTAATGAAATACTATATCCG 59.778 40.741 0.00 0.00 0.00 4.18
3082 3262 8.038944 TGGCGTCCTTAATGAAATACTATATCC 58.961 37.037 0.00 0.00 0.00 2.59
3083 3263 8.997621 TGGCGTCCTTAATGAAATACTATATC 57.002 34.615 0.00 0.00 0.00 1.63
3084 3264 9.959721 ATTGGCGTCCTTAATGAAATACTATAT 57.040 29.630 0.00 0.00 0.00 0.86
3085 3265 9.431887 GATTGGCGTCCTTAATGAAATACTATA 57.568 33.333 0.00 0.00 0.00 1.31
3086 3266 7.390718 GGATTGGCGTCCTTAATGAAATACTAT 59.609 37.037 1.81 0.00 35.32 2.12
3087 3267 6.708949 GGATTGGCGTCCTTAATGAAATACTA 59.291 38.462 1.81 0.00 35.32 1.82
3088 3268 5.531287 GGATTGGCGTCCTTAATGAAATACT 59.469 40.000 1.81 0.00 35.32 2.12
3089 3269 5.531287 AGGATTGGCGTCCTTAATGAAATAC 59.469 40.000 5.50 0.00 46.45 1.89
3090 3270 5.690865 AGGATTGGCGTCCTTAATGAAATA 58.309 37.500 5.50 0.00 46.45 1.40
3091 3271 4.536765 AGGATTGGCGTCCTTAATGAAAT 58.463 39.130 5.50 0.00 46.45 2.17
3105 3285 3.850173 TGATTACCCCCTATAGGATTGGC 59.150 47.826 21.07 5.59 38.24 4.52
3114 3294 9.805204 ATTCATTATCTAGTGATTACCCCCTAT 57.195 33.333 0.00 0.00 34.32 2.57
3155 3335 7.370383 AGCAAGTAGTGTACAAATTTGGATTG 58.630 34.615 21.74 13.96 0.00 2.67
3230 3410 9.051259 AGGTGTGCCACATAATTATATAGATCT 57.949 33.333 0.00 0.00 35.86 2.75
3231 3411 9.102757 CAGGTGTGCCACATAATTATATAGATC 57.897 37.037 0.00 0.00 35.86 2.75
3232 3412 8.825774 TCAGGTGTGCCACATAATTATATAGAT 58.174 33.333 0.00 0.00 35.86 1.98
3233 3413 8.094548 GTCAGGTGTGCCACATAATTATATAGA 58.905 37.037 0.00 0.00 35.86 1.98
3234 3414 7.877612 TGTCAGGTGTGCCACATAATTATATAG 59.122 37.037 0.00 0.00 35.86 1.31
3235 3415 7.740805 TGTCAGGTGTGCCACATAATTATATA 58.259 34.615 0.00 0.00 35.86 0.86
3236 3416 6.600388 TGTCAGGTGTGCCACATAATTATAT 58.400 36.000 0.00 0.00 35.86 0.86
3237 3417 5.995446 TGTCAGGTGTGCCACATAATTATA 58.005 37.500 0.00 0.00 35.86 0.98
3238 3418 4.854173 TGTCAGGTGTGCCACATAATTAT 58.146 39.130 0.00 0.00 35.86 1.28
3239 3419 4.260985 CTGTCAGGTGTGCCACATAATTA 58.739 43.478 0.00 0.00 35.86 1.40
3240 3420 3.084039 CTGTCAGGTGTGCCACATAATT 58.916 45.455 0.00 0.00 35.86 1.40
3241 3421 2.715046 CTGTCAGGTGTGCCACATAAT 58.285 47.619 0.00 0.00 35.86 1.28
3242 3422 1.881925 GCTGTCAGGTGTGCCACATAA 60.882 52.381 0.00 0.00 35.86 1.90
3243 3423 0.321564 GCTGTCAGGTGTGCCACATA 60.322 55.000 0.00 0.00 35.86 2.29
3244 3424 1.601759 GCTGTCAGGTGTGCCACAT 60.602 57.895 0.00 0.00 35.86 3.21
3245 3425 2.203195 GCTGTCAGGTGTGCCACA 60.203 61.111 1.14 0.00 35.86 4.17
3246 3426 1.963338 GAGCTGTCAGGTGTGCCAC 60.963 63.158 9.79 0.00 37.19 5.01
3247 3427 2.142761 AGAGCTGTCAGGTGTGCCA 61.143 57.895 9.79 0.00 37.19 4.92
3248 3428 1.670406 CAGAGCTGTCAGGTGTGCC 60.670 63.158 15.31 0.00 30.35 5.01
3249 3429 3.963222 CAGAGCTGTCAGGTGTGC 58.037 61.111 15.31 0.00 30.35 4.57
3250 3430 0.321387 ATGCAGAGCTGTCAGGTGTG 60.321 55.000 21.47 21.47 39.62 3.82
3251 3431 1.206610 CTATGCAGAGCTGTCAGGTGT 59.793 52.381 9.79 1.83 0.00 4.16
3252 3432 1.937278 CTATGCAGAGCTGTCAGGTG 58.063 55.000 9.79 0.00 0.00 4.00
3253 3433 0.177604 GCTATGCAGAGCTGTCAGGT 59.822 55.000 25.63 3.69 39.50 4.00
3254 3434 0.177373 TGCTATGCAGAGCTGTCAGG 59.823 55.000 31.40 0.00 43.27 3.86
3255 3435 3.754766 TGCTATGCAGAGCTGTCAG 57.245 52.632 31.40 0.00 43.27 3.51
3265 3445 2.813754 GGTTTGTTCACTCTGCTATGCA 59.186 45.455 0.00 0.00 36.92 3.96
3266 3446 2.813754 TGGTTTGTTCACTCTGCTATGC 59.186 45.455 0.00 0.00 0.00 3.14
3267 3447 4.614535 GCTTGGTTTGTTCACTCTGCTATG 60.615 45.833 0.00 0.00 0.00 2.23
3268 3448 3.503748 GCTTGGTTTGTTCACTCTGCTAT 59.496 43.478 0.00 0.00 0.00 2.97
3269 3449 2.878406 GCTTGGTTTGTTCACTCTGCTA 59.122 45.455 0.00 0.00 0.00 3.49
3270 3450 1.678101 GCTTGGTTTGTTCACTCTGCT 59.322 47.619 0.00 0.00 0.00 4.24
3271 3451 1.405105 TGCTTGGTTTGTTCACTCTGC 59.595 47.619 0.00 0.00 0.00 4.26
3272 3452 3.781079 TTGCTTGGTTTGTTCACTCTG 57.219 42.857 0.00 0.00 0.00 3.35
3273 3453 4.685924 CAATTGCTTGGTTTGTTCACTCT 58.314 39.130 0.00 0.00 0.00 3.24
3274 3454 3.245990 GCAATTGCTTGGTTTGTTCACTC 59.754 43.478 23.21 0.00 38.21 3.51
3275 3455 3.197265 GCAATTGCTTGGTTTGTTCACT 58.803 40.909 23.21 0.00 38.21 3.41
3276 3456 2.935201 TGCAATTGCTTGGTTTGTTCAC 59.065 40.909 29.37 0.00 42.66 3.18
3277 3457 3.257469 TGCAATTGCTTGGTTTGTTCA 57.743 38.095 29.37 3.27 42.66 3.18


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

AutoCloner maintained by Alex Coulton.