Multiple sequence alignment - TraesCS5D01G199500

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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 TraesCS5D01G199500 chr5D 100.000 3087 0 0 1 3087 302103581 302106667 0.000000e+00 5701
1 TraesCS5D01G199500 chr5D 89.510 143 12 3 2423 2564 302161838 302161978 8.800000e-41 178
2 TraesCS5D01G199500 chr5D 86.986 146 19 0 2942 3087 302160663 302160808 6.850000e-37 165
3 TraesCS5D01G199500 chr5A 89.995 1899 103 40 599 2453 395806401 395804546 0.000000e+00 2374
4 TraesCS5D01G199500 chr5A 82.692 260 34 2 2833 3082 395804490 395804232 1.440000e-53 220
5 TraesCS5D01G199500 chr5A 88.889 171 10 6 1 163 395806744 395806575 5.220000e-48 202
6 TraesCS5D01G199500 chr5A 88.764 89 1 3 470 558 395806565 395806486 1.960000e-17 100
7 TraesCS5D01G199500 chr5B 93.410 1487 48 19 1 1460 345137122 345138585 0.000000e+00 2158
8 TraesCS5D01G199500 chr5B 93.294 850 39 11 1507 2350 345138664 345139501 0.000000e+00 1238
9 TraesCS5D01G199500 chr5B 90.395 354 30 4 2337 2688 345139552 345139903 2.170000e-126 462
10 TraesCS5D01G199500 chr5B 86.047 172 21 3 2911 3082 345140043 345140211 6.800000e-42 182
11 TraesCS5D01G199500 chr6B 82.353 119 19 2 1640 1757 38971592 38971709 5.450000e-18 102
12 TraesCS5D01G199500 chr1D 97.674 43 1 0 1820 1862 191861276 191861318 1.190000e-09 75
13 TraesCS5D01G199500 chr1B 97.674 43 1 0 1820 1862 265648393 265648435 1.190000e-09 75
14 TraesCS5D01G199500 chr1A 97.674 43 1 0 1820 1862 237746074 237746116 1.190000e-09 75


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 TraesCS5D01G199500 chr5D 302103581 302106667 3086 False 5701 5701 100.0000 1 3087 1 chr5D.!!$F1 3086
1 TraesCS5D01G199500 chr5A 395804232 395806744 2512 True 724 2374 87.5850 1 3082 4 chr5A.!!$R1 3081
2 TraesCS5D01G199500 chr5B 345137122 345140211 3089 False 1010 2158 90.7865 1 3082 4 chr5B.!!$F1 3081

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 84 0.178981 AACCACTTCTGGCAGCATGT 60.179 50.000 10.34 5.35 42.08 3.21 F
1074 1168 1.067364 CAACAACAGCCATCTTGTGCA 59.933 47.619 0.00 0.00 30.88 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1348 1447 0.179089 CCATCCTGACCTTGAGCTCG 60.179 60.0 9.64 0.0 0.0 5.03 R
2704 2932 0.034767 CTGGAGAGGATGCAGGCAAA 60.035 55.0 0.00 0.0 43.3 3.68 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
80 84 0.178981 AACCACTTCTGGCAGCATGT 60.179 50.000 10.34 5.35 42.08 3.21
152 161 3.134458 GGACATACTGTATGCAGGAAGC 58.866 50.000 23.94 7.90 46.62 3.86
268 284 2.595463 GCAGCTCAGCCAACACCA 60.595 61.111 0.00 0.00 0.00 4.17
326 342 4.289410 TGACTATGTGGATCCCCATTATGG 59.711 45.833 15.35 3.85 45.68 2.74
393 417 4.455533 GCATGACCAGTATTTCTGTTGTGA 59.544 41.667 0.00 0.00 42.19 3.58
447 471 1.671845 TGGAAACCGAAACTGAAACCG 59.328 47.619 0.00 0.00 0.00 4.44
535 559 3.416382 TTCGCCGCCACGTAAAGC 61.416 61.111 0.00 0.00 0.00 3.51
577 601 3.441572 AGAATTCCCAACGCTGATCTTTG 59.558 43.478 0.65 0.00 0.00 2.77
609 677 5.247862 TCTCATGCATGAAGAAACAAGCTA 58.752 37.500 28.39 3.42 36.18 3.32
821 894 2.483889 GGAGGGATTCAGCGAAAGGTAG 60.484 54.545 0.00 0.00 41.81 3.18
822 895 2.168728 GAGGGATTCAGCGAAAGGTAGT 59.831 50.000 0.00 0.00 41.81 2.73
823 896 3.371965 AGGGATTCAGCGAAAGGTAGTA 58.628 45.455 0.00 0.00 41.81 1.82
824 897 3.132467 AGGGATTCAGCGAAAGGTAGTAC 59.868 47.826 0.00 0.00 41.81 2.73
825 898 3.118884 GGGATTCAGCGAAAGGTAGTACA 60.119 47.826 2.06 0.00 41.81 2.90
826 899 4.113354 GGATTCAGCGAAAGGTAGTACAG 58.887 47.826 2.06 0.00 41.81 2.74
827 900 4.381718 GGATTCAGCGAAAGGTAGTACAGT 60.382 45.833 2.06 0.00 41.81 3.55
833 922 2.930040 CGAAAGGTAGTACAGTGCATGG 59.070 50.000 2.06 0.00 0.00 3.66
1031 1121 2.521708 GCCACCCAACAACTGCCT 60.522 61.111 0.00 0.00 0.00 4.75
1032 1122 2.859981 GCCACCCAACAACTGCCTG 61.860 63.158 0.00 0.00 0.00 4.85
1033 1123 2.730094 CACCCAACAACTGCCTGC 59.270 61.111 0.00 0.00 0.00 4.85
1034 1124 2.521708 ACCCAACAACTGCCTGCC 60.522 61.111 0.00 0.00 0.00 4.85
1053 1143 3.809905 GCCAAGGGCCTATATATACAGC 58.190 50.000 6.41 0.00 44.06 4.40
1056 1146 4.227300 CCAAGGGCCTATATATACAGCCAA 59.773 45.833 22.16 0.00 45.72 4.52
1057 1147 5.186198 CAAGGGCCTATATATACAGCCAAC 58.814 45.833 22.16 11.53 45.72 3.77
1058 1148 4.435137 AGGGCCTATATATACAGCCAACA 58.565 43.478 22.16 0.00 45.72 3.33
1062 1152 5.643777 GGCCTATATATACAGCCAACAACAG 59.356 44.000 18.32 0.00 43.32 3.16
1073 1167 1.603678 CCAACAACAGCCATCTTGTGC 60.604 52.381 0.00 0.00 30.88 4.57
1074 1168 1.067364 CAACAACAGCCATCTTGTGCA 59.933 47.619 0.00 0.00 30.88 4.57
1097 1191 3.685139 TCAAGTCTCCAACCATCTCAC 57.315 47.619 0.00 0.00 0.00 3.51
1114 1209 1.482593 TCACCTCTAGCTAGCTTTGGC 59.517 52.381 24.88 0.00 39.06 4.52
1131 1226 1.571460 GCGAAGTTGTGCTGTCAGG 59.429 57.895 1.14 0.00 0.00 3.86
1174 1269 3.161067 TCAGGAAGAGAACAGAGTCTGG 58.839 50.000 23.79 6.57 35.51 3.86
1179 1274 1.889829 AGAGAACAGAGTCTGGTTCGG 59.110 52.381 23.79 0.00 35.51 4.30
1209 1308 4.764050 TGGGTGTTTTCTTGACTCTGTA 57.236 40.909 0.00 0.00 0.00 2.74
1215 1314 6.366630 GTGTTTTCTTGACTCTGTATCTTGC 58.633 40.000 0.00 0.00 0.00 4.01
1282 1381 1.402984 GGCACTCTGGACTACTTGTCG 60.403 57.143 0.00 0.00 46.24 4.35
1348 1447 2.828933 GAAGCAGTTCCAGACGGTC 58.171 57.895 0.00 0.00 0.00 4.79
1494 1642 8.937634 ATGATGTCCTTTCAAAAGAATTATGC 57.062 30.769 4.06 0.00 38.28 3.14
1495 1643 7.894708 TGATGTCCTTTCAAAAGAATTATGCA 58.105 30.769 4.06 0.00 38.28 3.96
1496 1644 8.533657 TGATGTCCTTTCAAAAGAATTATGCAT 58.466 29.630 3.79 3.79 38.28 3.96
1497 1645 8.712285 ATGTCCTTTCAAAAGAATTATGCATG 57.288 30.769 10.16 0.00 38.28 4.06
1498 1646 7.098477 TGTCCTTTCAAAAGAATTATGCATGG 58.902 34.615 10.16 0.00 38.28 3.66
1499 1647 6.036408 GTCCTTTCAAAAGAATTATGCATGGC 59.964 38.462 10.16 0.00 38.28 4.40
1500 1648 5.295045 CCTTTCAAAAGAATTATGCATGGCC 59.705 40.000 10.16 0.00 38.28 5.36
1531 1679 2.163211 GCTGGAAAACTGAGAGGCATTC 59.837 50.000 0.00 0.00 0.00 2.67
1636 1790 3.555324 TGGTGAAGCGGGTGCAGA 61.555 61.111 0.00 0.00 46.23 4.26
1638 1792 2.280797 GTGAAGCGGGTGCAGACA 60.281 61.111 0.00 0.00 46.23 3.41
1883 2040 0.318441 CCTCCGTGAAGCAAGAGACA 59.682 55.000 0.00 0.00 0.00 3.41
1894 2051 1.393726 CAAGAGACATCGATCGAGCG 58.606 55.000 23.84 18.51 0.00 5.03
1942 2099 3.059884 GACATGTATGTATGTGGCTCCG 58.940 50.000 0.00 0.00 41.15 4.63
1985 2142 8.343366 TGCGTGTGTTGTTTAGATTGTAAATTA 58.657 29.630 0.00 0.00 0.00 1.40
1986 2143 8.837059 GCGTGTGTTGTTTAGATTGTAAATTAG 58.163 33.333 0.00 0.00 0.00 1.73
1987 2144 9.872757 CGTGTGTTGTTTAGATTGTAAATTAGT 57.127 29.630 0.00 0.00 0.00 2.24
2019 2179 7.309867 GGAGAGAAAAGAGCGTATATATGGGAA 60.310 40.741 4.14 0.00 0.00 3.97
2076 2236 7.988737 CATGTGTGCTGGAATCTTAATCTTTA 58.011 34.615 0.00 0.00 0.00 1.85
2109 2269 7.566760 TTGCAGTGTTAGATCTTTCTTTTCA 57.433 32.000 0.00 0.00 33.17 2.69
2110 2270 7.194607 TGCAGTGTTAGATCTTTCTTTTCAG 57.805 36.000 0.00 0.00 33.17 3.02
2121 2281 2.099141 TCTTTTCAGGGATCGCACAG 57.901 50.000 12.83 1.74 0.00 3.66
2148 2308 7.214467 AGATTGTTGATTTTGAACACGGTAT 57.786 32.000 0.00 0.00 33.06 2.73
2174 2334 0.173481 AGACGCTCACATACACGCAT 59.827 50.000 0.00 0.00 0.00 4.73
2224 2384 6.775708 TGTAACCTAGCAGAACTTTAACCAT 58.224 36.000 0.00 0.00 0.00 3.55
2324 2486 2.024414 ACTAAAGGATGGATTTGCGCC 58.976 47.619 4.18 0.00 0.00 6.53
2340 2567 3.068560 TGCGCCGAAACTAAACATAACT 58.931 40.909 4.18 0.00 0.00 2.24
2343 2570 3.365820 CGCCGAAACTAAACATAACTCGT 59.634 43.478 0.00 0.00 0.00 4.18
2346 2573 6.464311 GCCGAAACTAAACATAACTCGTAAG 58.536 40.000 0.00 0.00 0.00 2.34
2434 2661 1.745115 TCGCGGGATTTTGAGCAGG 60.745 57.895 6.13 0.00 0.00 4.85
2480 2707 6.934083 TCCCTTTATTGAAAGAATTTTGGTGC 59.066 34.615 0.00 0.00 44.23 5.01
2502 2729 4.640201 GCCTACAATAGCTTTTGATCCACA 59.360 41.667 21.69 1.41 0.00 4.17
2503 2730 5.125417 GCCTACAATAGCTTTTGATCCACAA 59.875 40.000 21.69 0.00 36.65 3.33
2589 2816 3.579151 AGTGAAGAAGTGGTACTCCTTCC 59.421 47.826 16.42 7.46 37.60 3.46
2592 2819 1.203149 AGAAGTGGTACTCCTTCCGGT 60.203 52.381 16.42 2.30 37.60 5.28
2609 2836 2.747446 CCGGTCTTGAAGGGTATGTTTG 59.253 50.000 0.00 0.00 0.00 2.93
2617 2844 4.658063 TGAAGGGTATGTTTGGTTACCTG 58.342 43.478 2.07 0.00 38.34 4.00
2622 2849 3.130340 GGTATGTTTGGTTACCTGCATGG 59.870 47.826 2.07 0.00 42.93 3.66
2636 2864 2.739913 CTGCATGGATTTTGGCACTTTG 59.260 45.455 0.00 0.00 32.06 2.77
2654 2882 1.146041 GCATATGTGGCCCGACTCA 59.854 57.895 0.00 0.00 0.00 3.41
2656 2884 0.250038 CATATGTGGCCCGACTCAGG 60.250 60.000 0.00 0.00 0.00 3.86
2657 2885 0.691078 ATATGTGGCCCGACTCAGGT 60.691 55.000 0.00 0.00 0.00 4.00
2660 2888 1.982938 GTGGCCCGACTCAGGTAGT 60.983 63.158 0.00 0.00 42.80 2.73
2674 2902 5.201713 TCAGGTAGTCTGAGTGAAAACAG 57.798 43.478 0.00 0.00 46.71 3.16
2675 2903 4.893524 TCAGGTAGTCTGAGTGAAAACAGA 59.106 41.667 0.00 0.00 46.71 3.41
2676 2904 5.540337 TCAGGTAGTCTGAGTGAAAACAGAT 59.460 40.000 0.00 0.00 46.71 2.90
2679 2907 7.872993 CAGGTAGTCTGAGTGAAAACAGATAAA 59.127 37.037 0.00 0.00 46.18 1.40
2708 2936 8.458843 ACCATGTTCTATACATAGTTTGTTTGC 58.541 33.333 0.00 0.00 45.71 3.68
2709 2937 7.915397 CCATGTTCTATACATAGTTTGTTTGCC 59.085 37.037 0.00 0.00 45.71 4.52
2710 2938 8.677300 CATGTTCTATACATAGTTTGTTTGCCT 58.323 33.333 0.00 0.00 45.71 4.75
2711 2939 8.039603 TGTTCTATACATAGTTTGTTTGCCTG 57.960 34.615 0.00 0.00 39.87 4.85
2712 2940 6.677781 TCTATACATAGTTTGTTTGCCTGC 57.322 37.500 0.00 0.00 39.87 4.85
2713 2941 6.176896 TCTATACATAGTTTGTTTGCCTGCA 58.823 36.000 0.00 0.00 39.87 4.41
2714 2942 5.920193 ATACATAGTTTGTTTGCCTGCAT 57.080 34.783 0.00 0.00 39.87 3.96
2715 2943 4.178545 ACATAGTTTGTTTGCCTGCATC 57.821 40.909 0.00 0.00 33.74 3.91
2716 2944 3.056607 ACATAGTTTGTTTGCCTGCATCC 60.057 43.478 0.00 0.00 33.74 3.51
2717 2945 1.708341 AGTTTGTTTGCCTGCATCCT 58.292 45.000 0.00 0.00 0.00 3.24
2718 2946 1.615392 AGTTTGTTTGCCTGCATCCTC 59.385 47.619 0.00 0.00 0.00 3.71
2719 2947 1.615392 GTTTGTTTGCCTGCATCCTCT 59.385 47.619 0.00 0.00 0.00 3.69
2720 2948 1.538047 TTGTTTGCCTGCATCCTCTC 58.462 50.000 0.00 0.00 0.00 3.20
2721 2949 0.322816 TGTTTGCCTGCATCCTCTCC 60.323 55.000 0.00 0.00 0.00 3.71
2722 2950 0.322816 GTTTGCCTGCATCCTCTCCA 60.323 55.000 0.00 0.00 0.00 3.86
2723 2951 0.034767 TTTGCCTGCATCCTCTCCAG 60.035 55.000 0.00 0.00 0.00 3.86
2724 2952 2.203181 GCCTGCATCCTCTCCAGC 60.203 66.667 0.00 0.00 0.00 4.85
2725 2953 2.509916 CCTGCATCCTCTCCAGCC 59.490 66.667 0.00 0.00 0.00 4.85
2726 2954 2.071262 CCTGCATCCTCTCCAGCCT 61.071 63.158 0.00 0.00 0.00 4.58
2727 2955 0.762082 CCTGCATCCTCTCCAGCCTA 60.762 60.000 0.00 0.00 0.00 3.93
2728 2956 1.126488 CTGCATCCTCTCCAGCCTAA 58.874 55.000 0.00 0.00 0.00 2.69
2743 2971 1.202076 GCCTAATTGAGCAGAACGCAC 60.202 52.381 0.00 0.00 46.13 5.34
2744 2972 1.398390 CCTAATTGAGCAGAACGCACC 59.602 52.381 0.00 0.00 46.13 5.01
2764 2992 1.411977 CCATGGTGTTTGGTTGCAAGA 59.588 47.619 2.57 0.00 0.00 3.02
2787 3015 6.036517 AGACTGTTCTAAGATAATGCAAAGCG 59.963 38.462 0.00 0.00 0.00 4.68
2790 3018 7.333423 ACTGTTCTAAGATAATGCAAAGCGTTA 59.667 33.333 6.17 6.17 42.92 3.18
2794 3022 9.542462 TTCTAAGATAATGCAAAGCGTTACTAT 57.458 29.630 5.86 0.00 41.81 2.12
2798 3026 7.639945 AGATAATGCAAAGCGTTACTATTTCC 58.360 34.615 5.86 0.00 41.81 3.13
2799 3027 4.632538 ATGCAAAGCGTTACTATTTCCC 57.367 40.909 0.00 0.00 0.00 3.97
2800 3028 2.750712 TGCAAAGCGTTACTATTTCCCC 59.249 45.455 0.00 0.00 0.00 4.81
2801 3029 2.098607 GCAAAGCGTTACTATTTCCCCC 59.901 50.000 0.00 0.00 0.00 5.40
2802 3030 2.320745 AAGCGTTACTATTTCCCCCG 57.679 50.000 0.00 0.00 0.00 5.73
2803 3031 0.179065 AGCGTTACTATTTCCCCCGC 60.179 55.000 0.00 0.00 39.91 6.13
2804 3032 0.462403 GCGTTACTATTTCCCCCGCA 60.462 55.000 0.00 0.00 39.45 5.69
2805 3033 2.013058 GCGTTACTATTTCCCCCGCAA 61.013 52.381 0.00 0.00 39.45 4.85
2806 3034 2.358015 CGTTACTATTTCCCCCGCAAA 58.642 47.619 0.00 0.00 0.00 3.68
2807 3035 2.748532 CGTTACTATTTCCCCCGCAAAA 59.251 45.455 0.00 0.00 0.00 2.44
2808 3036 3.190953 CGTTACTATTTCCCCCGCAAAAA 59.809 43.478 0.00 0.00 0.00 1.94
2826 3054 3.912496 AAAAGCATTGCTATTTCCCCC 57.088 42.857 12.39 0.00 38.25 5.40
2827 3055 1.402787 AAGCATTGCTATTTCCCCCG 58.597 50.000 12.39 0.00 38.25 5.73
2828 3056 1.109323 AGCATTGCTATTTCCCCCGC 61.109 55.000 10.00 0.00 36.99 6.13
2829 3057 1.391157 GCATTGCTATTTCCCCCGCA 61.391 55.000 0.16 0.00 0.00 5.69
2830 3058 1.110442 CATTGCTATTTCCCCCGCAA 58.890 50.000 0.00 0.00 45.16 4.85
2831 3059 1.480137 CATTGCTATTTCCCCCGCAAA 59.520 47.619 0.00 0.00 44.39 3.68
2832 3060 1.633774 TTGCTATTTCCCCCGCAAAA 58.366 45.000 0.00 0.00 39.19 2.44
2833 3061 1.633774 TGCTATTTCCCCCGCAAAAA 58.366 45.000 0.00 0.00 0.00 1.94
2857 3085 4.768448 AGCATTGCTATTTGGCTATATGCA 59.232 37.500 10.00 0.00 39.62 3.96
2858 3086 5.244402 AGCATTGCTATTTGGCTATATGCAA 59.756 36.000 10.00 10.55 39.62 4.08
2859 3087 5.575606 GCATTGCTATTTGGCTATATGCAAG 59.424 40.000 0.16 0.00 45.15 4.01
2860 3088 6.570957 GCATTGCTATTTGGCTATATGCAAGA 60.571 38.462 0.16 0.00 45.15 3.02
2892 3120 7.707104 GTTTGATAACCTCATTATTGGAGTGG 58.293 38.462 0.00 0.00 33.37 4.00
2897 3125 3.813443 CCTCATTATTGGAGTGGTGAGG 58.187 50.000 4.98 4.98 44.54 3.86
2901 3129 6.409695 CCTCATTATTGGAGTGGTGAGGTTAT 60.410 42.308 10.30 0.00 44.75 1.89
2902 3130 6.591935 TCATTATTGGAGTGGTGAGGTTATC 58.408 40.000 0.00 0.00 0.00 1.75
2913 3141 3.338249 GTGAGGTTATCAGCACACACAT 58.662 45.455 2.37 0.00 40.53 3.21
2933 3177 7.062722 CACACATAGAGACACAACATAGACAAG 59.937 40.741 0.00 0.00 0.00 3.16
2934 3178 6.035435 CACATAGAGACACAACATAGACAAGC 59.965 42.308 0.00 0.00 0.00 4.01
2960 3214 6.803154 AGCATAAACCAGAGTCTTAAACAC 57.197 37.500 0.00 0.00 0.00 3.32
2962 3216 6.942576 AGCATAAACCAGAGTCTTAAACACAT 59.057 34.615 0.00 0.00 0.00 3.21
2964 3218 8.391106 GCATAAACCAGAGTCTTAAACACATAG 58.609 37.037 0.00 0.00 0.00 2.23
2965 3219 8.883731 CATAAACCAGAGTCTTAAACACATAGG 58.116 37.037 0.00 0.00 0.00 2.57
2973 3227 6.281405 AGTCTTAAACACATAGGGATAAGCG 58.719 40.000 0.00 0.00 0.00 4.68
2974 3228 6.097839 AGTCTTAAACACATAGGGATAAGCGA 59.902 38.462 0.00 0.00 0.00 4.93
2979 3233 9.616156 TTAAACACATAGGGATAAGCGATTAAA 57.384 29.630 0.00 0.00 0.00 1.52
2981 3235 7.907214 ACACATAGGGATAAGCGATTAAATC 57.093 36.000 0.00 0.00 0.00 2.17
3025 3279 7.959175 AGTCTTACACTACTAAACATCCAACA 58.041 34.615 0.00 0.00 31.37 3.33
3036 3290 8.514330 ACTAAACATCCAACACAAAAGTCTTA 57.486 30.769 0.00 0.00 0.00 2.10
3039 3293 8.474006 AAACATCCAACACAAAAGTCTTAAAC 57.526 30.769 0.00 0.00 0.00 2.01
3046 3300 4.035017 CACAAAAGTCTTAAACTGGTGCG 58.965 43.478 0.00 0.00 38.58 5.34
3048 3302 2.632987 AAGTCTTAAACTGGTGCGGT 57.367 45.000 0.00 0.00 38.58 5.68
3055 3309 2.561478 AAACTGGTGCGGTGATAACT 57.439 45.000 0.00 0.00 0.00 2.24
3063 3317 4.196971 GGTGCGGTGATAACTTCCTAAAT 58.803 43.478 0.00 0.00 0.00 1.40
3072 3326 7.121315 GGTGATAACTTCCTAAATATCCATGGC 59.879 40.741 6.96 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 156 1.065126 ACCAGCCTCTATGTTGCTTCC 60.065 52.381 0.00 0.00 31.77 3.46
152 161 2.237143 TCCTTCACCAGCCTCTATGTTG 59.763 50.000 0.00 0.00 0.00 3.33
256 272 4.498346 CCATGTGGTGTTGGCTGA 57.502 55.556 0.00 0.00 0.00 4.26
263 279 2.282674 CCAGCTGCCATGTGGTGT 60.283 61.111 8.66 0.00 37.57 4.16
289 305 5.780282 CCACATAGTCATCCTAGGACCAATA 59.220 44.000 15.42 7.52 35.89 1.90
326 342 2.914289 CAGGGAGGGAGGTGCATC 59.086 66.667 0.00 0.00 0.00 3.91
393 417 1.106944 CAGCCTGGACGTGGGTTTTT 61.107 55.000 0.00 0.00 32.37 1.94
535 559 9.334693 GAATTCTACTTAAACATTTGTCAGCAG 57.665 33.333 0.00 0.00 0.00 4.24
577 601 9.395707 GTTTCTTCATGCATGAGATGATTTATC 57.604 33.333 27.25 9.55 38.19 1.75
609 677 0.890542 TCTTCTTGCGTGCATGGCTT 60.891 50.000 8.27 0.00 0.00 4.35
661 729 1.005867 TGGAAAGGGCACGTACGTC 60.006 57.895 19.94 13.15 0.00 4.34
813 886 4.184629 CTCCATGCACTGTACTACCTTTC 58.815 47.826 0.00 0.00 0.00 2.62
821 894 2.893637 CTGTACCTCCATGCACTGTAC 58.106 52.381 0.00 0.00 33.96 2.90
822 895 1.207089 GCTGTACCTCCATGCACTGTA 59.793 52.381 0.00 0.00 0.00 2.74
823 896 0.036010 GCTGTACCTCCATGCACTGT 60.036 55.000 0.00 0.00 0.00 3.55
824 897 1.086067 CGCTGTACCTCCATGCACTG 61.086 60.000 0.00 0.00 0.00 3.66
825 898 1.219124 CGCTGTACCTCCATGCACT 59.781 57.895 0.00 0.00 0.00 4.40
826 899 0.807667 CTCGCTGTACCTCCATGCAC 60.808 60.000 0.00 0.00 0.00 4.57
827 900 1.517361 CTCGCTGTACCTCCATGCA 59.483 57.895 0.00 0.00 0.00 3.96
833 922 2.180159 TTTGCCCCTCGCTGTACCTC 62.180 60.000 0.00 0.00 38.78 3.85
852 941 2.092699 GCCAGAAGCTTCCCAAGATACT 60.093 50.000 22.81 0.00 38.99 2.12
979 1069 4.321082 GCGGTACTCCACCTAGCTAATAAG 60.321 50.000 0.00 0.00 46.19 1.73
980 1070 3.571401 GCGGTACTCCACCTAGCTAATAA 59.429 47.826 0.00 0.00 46.19 1.40
981 1071 3.152341 GCGGTACTCCACCTAGCTAATA 58.848 50.000 0.00 0.00 46.19 0.98
1033 1123 3.780294 TGGCTGTATATATAGGCCCTTGG 59.220 47.826 24.22 0.00 41.84 3.61
1034 1124 5.186198 GTTGGCTGTATATATAGGCCCTTG 58.814 45.833 24.22 0.00 41.84 3.61
1050 1140 0.963962 AAGATGGCTGTTGTTGGCTG 59.036 50.000 0.00 0.00 0.00 4.85
1053 1143 1.603678 GCACAAGATGGCTGTTGTTGG 60.604 52.381 0.00 0.00 36.79 3.77
1056 1146 0.670162 GTGCACAAGATGGCTGTTGT 59.330 50.000 13.17 0.00 39.29 3.32
1057 1147 0.669619 TGTGCACAAGATGGCTGTTG 59.330 50.000 19.28 0.00 0.00 3.33
1058 1148 1.542915 GATGTGCACAAGATGGCTGTT 59.457 47.619 25.72 2.19 0.00 3.16
1062 1152 1.542915 ACTTGATGTGCACAAGATGGC 59.457 47.619 25.72 9.61 44.92 4.40
1073 1167 3.937706 GAGATGGTTGGAGACTTGATGTG 59.062 47.826 0.00 0.00 0.00 3.21
1074 1168 3.584406 TGAGATGGTTGGAGACTTGATGT 59.416 43.478 0.00 0.00 0.00 3.06
1097 1191 0.747255 TCGCCAAAGCTAGCTAGAGG 59.253 55.000 25.15 19.96 36.60 3.69
1114 1209 1.845809 GCCCTGACAGCACAACTTCG 61.846 60.000 0.00 0.00 0.00 3.79
1131 1226 1.227556 AGTTGGTCACACAGTCGCC 60.228 57.895 0.00 0.00 0.00 5.54
1179 1274 1.802337 GAAAACACCCAAGGACCGGC 61.802 60.000 0.00 0.00 0.00 6.13
1209 1308 1.067565 TCTCGACGAAAGCAGCAAGAT 60.068 47.619 0.00 0.00 0.00 2.40
1215 1314 0.241213 TGTCCTCTCGACGAAAGCAG 59.759 55.000 0.00 0.00 45.23 4.24
1348 1447 0.179089 CCATCCTGACCTTGAGCTCG 60.179 60.000 9.64 0.00 0.00 5.03
1473 1576 7.098477 CCATGCATAATTCTTTTGAAAGGACA 58.902 34.615 0.00 0.00 42.31 4.02
1494 1642 2.027929 TCCAGCATTTTTCTTGGCCATG 60.028 45.455 6.09 9.88 0.00 3.66
1495 1643 2.259012 TCCAGCATTTTTCTTGGCCAT 58.741 42.857 6.09 0.00 0.00 4.40
1496 1644 1.714541 TCCAGCATTTTTCTTGGCCA 58.285 45.000 0.00 0.00 0.00 5.36
1497 1645 2.837532 TTCCAGCATTTTTCTTGGCC 57.162 45.000 0.00 0.00 0.00 5.36
1498 1646 4.024641 CAGTTTTCCAGCATTTTTCTTGGC 60.025 41.667 0.00 0.00 0.00 4.52
1499 1647 5.358922 TCAGTTTTCCAGCATTTTTCTTGG 58.641 37.500 0.00 0.00 0.00 3.61
1500 1648 6.275335 TCTCAGTTTTCCAGCATTTTTCTTG 58.725 36.000 0.00 0.00 0.00 3.02
1531 1679 2.610232 GCACCCCTGCAAAATACAACAG 60.610 50.000 0.00 0.00 43.62 3.16
1636 1790 2.434774 GGCCTTCTTCCCGGTTGT 59.565 61.111 0.00 0.00 0.00 3.32
1638 1792 2.926242 TCGGCCTTCTTCCCGGTT 60.926 61.111 0.00 0.00 44.45 4.44
1704 1858 1.404315 GCCTTCTTGTCGTAGGTCTGG 60.404 57.143 0.00 0.00 33.05 3.86
1809 1966 1.300971 CGCTGAACATGGTGGTGAGG 61.301 60.000 0.00 0.00 0.00 3.86
1883 2040 3.243274 GACCTCGCGCTCGATCGAT 62.243 63.158 19.78 0.00 44.56 3.59
1894 2051 0.798776 CCAAGAACACATGACCTCGC 59.201 55.000 0.00 0.00 0.00 5.03
1942 2099 1.303309 GCATGCCATACACTCTGTCC 58.697 55.000 6.36 0.00 0.00 4.02
1985 2142 5.612351 ACGCTCTTTTCTCTCCTTTTTACT 58.388 37.500 0.00 0.00 0.00 2.24
1986 2143 5.926214 ACGCTCTTTTCTCTCCTTTTTAC 57.074 39.130 0.00 0.00 0.00 2.01
2019 2179 8.293699 ACAGAAACCTGAAAAACAAAGACTAT 57.706 30.769 0.00 0.00 35.67 2.12
2076 2236 6.344500 AGATCTAACACTGCAAAAGATCGAT 58.656 36.000 0.00 0.00 44.65 3.59
2090 2250 7.201565 CGATCCCTGAAAAGAAAGATCTAACAC 60.202 40.741 0.00 0.00 33.77 3.32
2109 2269 2.501723 ACAATCTAACTGTGCGATCCCT 59.498 45.455 0.00 0.00 0.00 4.20
2110 2270 2.906354 ACAATCTAACTGTGCGATCCC 58.094 47.619 0.00 0.00 0.00 3.85
2121 2281 6.915843 ACCGTGTTCAAAATCAACAATCTAAC 59.084 34.615 0.00 0.00 35.53 2.34
2148 2308 3.004862 TGTATGTGAGCGTCTTCGACTA 58.995 45.455 0.00 0.00 39.71 2.59
2224 2384 9.515020 GAAAATTATGATCTGGTAAAATTGCGA 57.485 29.630 0.00 0.00 0.00 5.10
2324 2486 7.274442 AGCTTACGAGTTATGTTTAGTTTCG 57.726 36.000 0.00 0.00 0.00 3.46
2340 2567 5.382616 TCATAGTCATAGGGAAGCTTACGA 58.617 41.667 1.68 0.00 0.00 3.43
2343 2570 6.787458 TCCAATCATAGTCATAGGGAAGCTTA 59.213 38.462 0.00 0.00 0.00 3.09
2346 2573 5.012561 ACTCCAATCATAGTCATAGGGAAGC 59.987 44.000 0.00 0.00 0.00 3.86
2434 2661 7.557724 AGGGAGTATAGAAGTAAGAAAAGCAC 58.442 38.462 0.00 0.00 0.00 4.40
2453 2680 8.150296 CACCAAAATTCTTTCAATAAAGGGAGT 58.850 33.333 0.00 0.00 42.09 3.85
2475 2702 4.027674 TCAAAAGCTATTGTAGGCACCA 57.972 40.909 0.00 0.00 0.00 4.17
2480 2707 6.757897 TTGTGGATCAAAAGCTATTGTAGG 57.242 37.500 0.00 0.00 32.64 3.18
2502 2729 8.031277 GGAAGTTTCTGATATGACATTTGCTTT 58.969 33.333 0.00 0.00 0.00 3.51
2503 2730 7.177216 TGGAAGTTTCTGATATGACATTTGCTT 59.823 33.333 0.00 0.00 0.00 3.91
2558 2785 5.729974 ACCACTTCTTCACTTACGAAAAC 57.270 39.130 0.00 0.00 0.00 2.43
2564 2791 5.725325 AGGAGTACCACTTCTTCACTTAC 57.275 43.478 0.00 0.00 26.59 2.34
2589 2816 2.747446 CCAAACATACCCTTCAAGACCG 59.253 50.000 0.00 0.00 0.00 4.79
2592 2819 5.073965 AGGTAACCAAACATACCCTTCAAGA 59.926 40.000 0.00 0.00 42.11 3.02
2603 2830 3.168035 TCCATGCAGGTAACCAAACAT 57.832 42.857 0.00 0.00 39.02 2.71
2609 2836 2.418609 GCCAAAATCCATGCAGGTAACC 60.419 50.000 0.00 0.00 39.02 2.85
2617 2844 1.465777 GCAAAGTGCCAAAATCCATGC 59.534 47.619 0.00 0.00 37.42 4.06
2622 2849 4.330620 CCACATATGCAAAGTGCCAAAATC 59.669 41.667 1.58 0.00 44.23 2.17
2636 2864 0.882042 CTGAGTCGGGCCACATATGC 60.882 60.000 4.39 0.00 0.00 3.14
2654 2882 7.540474 TTATCTGTTTTCACTCAGACTACCT 57.460 36.000 0.00 0.00 42.30 3.08
2688 2916 6.657117 TGCAGGCAAACAAACTATGTATAGAA 59.343 34.615 5.93 0.00 42.99 2.10
2689 2917 6.176896 TGCAGGCAAACAAACTATGTATAGA 58.823 36.000 5.93 0.00 42.99 1.98
2690 2918 6.435430 TGCAGGCAAACAAACTATGTATAG 57.565 37.500 0.00 0.00 42.99 1.31
2691 2919 6.039270 GGATGCAGGCAAACAAACTATGTATA 59.961 38.462 0.00 0.00 42.99 1.47
2692 2920 5.163519 GGATGCAGGCAAACAAACTATGTAT 60.164 40.000 0.00 0.00 42.99 2.29
2693 2921 4.157656 GGATGCAGGCAAACAAACTATGTA 59.842 41.667 0.00 0.00 42.99 2.29
2694 2922 3.056607 GGATGCAGGCAAACAAACTATGT 60.057 43.478 0.00 0.00 46.82 2.29
2695 2923 3.194116 AGGATGCAGGCAAACAAACTATG 59.806 43.478 0.00 0.00 0.00 2.23
2696 2924 3.434309 AGGATGCAGGCAAACAAACTAT 58.566 40.909 0.00 0.00 0.00 2.12
2697 2925 2.819608 GAGGATGCAGGCAAACAAACTA 59.180 45.455 0.00 0.00 0.00 2.24
2698 2926 1.615392 GAGGATGCAGGCAAACAAACT 59.385 47.619 0.00 0.00 0.00 2.66
2699 2927 1.615392 AGAGGATGCAGGCAAACAAAC 59.385 47.619 0.00 0.00 0.00 2.93
2700 2928 1.888512 GAGAGGATGCAGGCAAACAAA 59.111 47.619 0.00 0.00 0.00 2.83
2701 2929 1.538047 GAGAGGATGCAGGCAAACAA 58.462 50.000 0.00 0.00 0.00 2.83
2702 2930 0.322816 GGAGAGGATGCAGGCAAACA 60.323 55.000 0.00 0.00 0.00 2.83
2703 2931 0.322816 TGGAGAGGATGCAGGCAAAC 60.323 55.000 0.00 0.00 0.00 2.93
2704 2932 0.034767 CTGGAGAGGATGCAGGCAAA 60.035 55.000 0.00 0.00 43.30 3.68
2705 2933 1.605992 CTGGAGAGGATGCAGGCAA 59.394 57.895 0.00 0.00 43.30 4.52
2706 2934 3.040206 GCTGGAGAGGATGCAGGCA 62.040 63.158 0.00 0.00 46.85 4.75
2707 2935 2.203181 GCTGGAGAGGATGCAGGC 60.203 66.667 0.00 0.00 46.85 4.85
2708 2936 0.762082 TAGGCTGGAGAGGATGCAGG 60.762 60.000 0.00 0.00 46.85 4.85
2710 2938 1.811778 ATTAGGCTGGAGAGGATGCA 58.188 50.000 0.00 0.00 0.00 3.96
2711 2939 2.105477 TCAATTAGGCTGGAGAGGATGC 59.895 50.000 0.00 0.00 0.00 3.91
2712 2940 3.806507 GCTCAATTAGGCTGGAGAGGATG 60.807 52.174 0.00 0.00 0.00 3.51
2713 2941 2.371510 GCTCAATTAGGCTGGAGAGGAT 59.628 50.000 0.00 0.00 0.00 3.24
2714 2942 1.765314 GCTCAATTAGGCTGGAGAGGA 59.235 52.381 0.00 0.00 0.00 3.71
2715 2943 1.487976 TGCTCAATTAGGCTGGAGAGG 59.512 52.381 0.00 0.00 0.00 3.69
2716 2944 2.433604 TCTGCTCAATTAGGCTGGAGAG 59.566 50.000 0.00 0.34 0.00 3.20
2717 2945 2.470990 TCTGCTCAATTAGGCTGGAGA 58.529 47.619 0.00 0.00 0.00 3.71
2718 2946 2.941720 GTTCTGCTCAATTAGGCTGGAG 59.058 50.000 0.00 0.00 0.00 3.86
2719 2947 2.677902 CGTTCTGCTCAATTAGGCTGGA 60.678 50.000 0.00 0.00 0.00 3.86
2720 2948 1.667724 CGTTCTGCTCAATTAGGCTGG 59.332 52.381 0.00 0.00 0.00 4.85
2721 2949 1.063174 GCGTTCTGCTCAATTAGGCTG 59.937 52.381 0.00 3.71 41.73 4.85
2722 2950 1.339055 TGCGTTCTGCTCAATTAGGCT 60.339 47.619 0.00 0.00 46.63 4.58
2723 2951 1.086696 TGCGTTCTGCTCAATTAGGC 58.913 50.000 0.00 0.00 46.63 3.93
2724 2952 1.398390 GGTGCGTTCTGCTCAATTAGG 59.602 52.381 0.00 0.00 46.63 2.69
2725 2953 1.398390 GGGTGCGTTCTGCTCAATTAG 59.602 52.381 0.00 0.00 46.63 1.73
2726 2954 1.271108 TGGGTGCGTTCTGCTCAATTA 60.271 47.619 0.00 0.00 46.63 1.40
2727 2955 0.537143 TGGGTGCGTTCTGCTCAATT 60.537 50.000 0.00 0.00 46.63 2.32
2728 2956 0.322816 ATGGGTGCGTTCTGCTCAAT 60.323 50.000 0.00 0.00 46.63 2.57
2743 2971 0.467384 TTGCAACCAAACACCATGGG 59.533 50.000 18.09 7.72 42.48 4.00
2744 2972 1.411977 TCTTGCAACCAAACACCATGG 59.588 47.619 11.19 11.19 43.84 3.66
2764 2992 5.643777 ACGCTTTGCATTATCTTAGAACAGT 59.356 36.000 0.00 0.00 0.00 3.55
2787 3015 4.787260 TTTTTGCGGGGGAAATAGTAAC 57.213 40.909 0.00 0.00 0.00 2.50
2805 3033 3.369366 CGGGGGAAATAGCAATGCTTTTT 60.369 43.478 20.44 20.44 41.09 1.94
2806 3034 2.168313 CGGGGGAAATAGCAATGCTTTT 59.832 45.455 14.85 9.38 40.44 2.27
2807 3035 1.756538 CGGGGGAAATAGCAATGCTTT 59.243 47.619 14.85 1.72 40.44 3.51
2808 3036 1.402787 CGGGGGAAATAGCAATGCTT 58.597 50.000 14.85 0.00 40.44 3.91
2809 3037 1.109323 GCGGGGGAAATAGCAATGCT 61.109 55.000 13.92 13.92 43.41 3.79
2810 3038 1.363807 GCGGGGGAAATAGCAATGC 59.636 57.895 0.00 0.00 0.00 3.56
2811 3039 1.110442 TTGCGGGGGAAATAGCAATG 58.890 50.000 0.00 0.00 43.55 2.82
2812 3040 1.859302 TTTGCGGGGGAAATAGCAAT 58.141 45.000 2.52 0.00 46.92 3.56
2813 3041 1.633774 TTTTGCGGGGGAAATAGCAA 58.366 45.000 0.00 0.00 46.22 3.91
2814 3042 1.633774 TTTTTGCGGGGGAAATAGCA 58.366 45.000 0.00 0.00 37.89 3.49
2830 3058 7.172019 GCATATAGCCAAATAGCAATGCTTTTT 59.828 33.333 14.85 15.54 39.58 1.94
2831 3059 6.647895 GCATATAGCCAAATAGCAATGCTTTT 59.352 34.615 14.85 9.38 40.03 2.27
2832 3060 6.161381 GCATATAGCCAAATAGCAATGCTTT 58.839 36.000 14.85 1.72 40.03 3.51
2833 3061 5.244402 TGCATATAGCCAAATAGCAATGCTT 59.756 36.000 14.85 0.00 44.83 3.91
2837 3065 6.491062 TGTCTTGCATATAGCCAAATAGCAAT 59.509 34.615 0.00 0.00 44.83 3.56
2841 3069 7.303261 CACATGTCTTGCATATAGCCAAATAG 58.697 38.462 0.00 0.00 44.83 1.73
2849 3077 6.682423 TCAAACCACATGTCTTGCATATAG 57.318 37.500 0.00 0.00 35.74 1.31
2852 3080 6.851609 GTTATCAAACCACATGTCTTGCATA 58.148 36.000 0.00 0.00 35.74 3.14
2881 3109 5.629133 GCTGATAACCTCACCACTCCAATAA 60.629 44.000 0.00 0.00 0.00 1.40
2892 3120 2.766313 TGTGTGTGCTGATAACCTCAC 58.234 47.619 0.00 0.00 0.00 3.51
2897 3125 5.289675 GTGTCTCTATGTGTGTGCTGATAAC 59.710 44.000 0.00 0.00 0.00 1.89
2901 3129 2.627699 TGTGTCTCTATGTGTGTGCTGA 59.372 45.455 0.00 0.00 0.00 4.26
2902 3130 3.030668 TGTGTCTCTATGTGTGTGCTG 57.969 47.619 0.00 0.00 0.00 4.41
2913 3141 4.217767 ACGCTTGTCTATGTTGTGTCTCTA 59.782 41.667 0.00 0.00 0.00 2.43
2933 3177 3.166489 AGACTCTGGTTTATGCTACGC 57.834 47.619 0.00 0.00 0.00 4.42
2934 3178 6.588756 TGTTTAAGACTCTGGTTTATGCTACG 59.411 38.462 0.00 0.00 0.00 3.51
2973 3227 7.572759 TGTCACAACTGTTTCTCGATTTAATC 58.427 34.615 0.00 0.00 0.00 1.75
2974 3228 7.490962 TGTCACAACTGTTTCTCGATTTAAT 57.509 32.000 0.00 0.00 0.00 1.40
2979 3233 4.876107 ACTTTGTCACAACTGTTTCTCGAT 59.124 37.500 0.00 0.00 0.00 3.59
2981 3235 4.330074 AGACTTTGTCACAACTGTTTCTCG 59.670 41.667 0.00 0.00 34.60 4.04
2984 3238 6.741358 GTGTAAGACTTTGTCACAACTGTTTC 59.259 38.462 0.00 0.00 34.60 2.78
3025 3279 3.066203 CCGCACCAGTTTAAGACTTTTGT 59.934 43.478 0.00 0.00 36.10 2.83
3036 3290 2.561478 AGTTATCACCGCACCAGTTT 57.439 45.000 0.00 0.00 0.00 2.66
3039 3293 1.066143 AGGAAGTTATCACCGCACCAG 60.066 52.381 0.00 0.00 0.00 4.00
3046 3300 7.121315 GCCATGGATATTTAGGAAGTTATCACC 59.879 40.741 18.40 0.00 0.00 4.02
3048 3302 7.754624 TGCCATGGATATTTAGGAAGTTATCA 58.245 34.615 18.40 0.00 0.00 2.15
3055 3309 6.100404 GCATTTGCCATGGATATTTAGGAA 57.900 37.500 18.40 0.00 34.31 3.36


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

AutoCloner maintained by Alex Coulton.