Multiple sequence alignment - TraesCS6A01G121600

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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 TraesCS6A01G121600 chr6A 100.000 3281 0 0 1 3281 93820625 93817345 0.000000e+00 6059
1 TraesCS6A01G121600 chr6D 91.809 2820 164 46 1 2772 78273246 78270446 0.000000e+00 3866
2 TraesCS6A01G121600 chr6D 95.720 257 11 0 3001 3257 78269989 78269733 6.550000e-112 414
3 TraesCS6A01G121600 chr6D 94.488 127 6 1 2863 2988 78270380 78270254 9.290000e-46 195
4 TraesCS6A01G121600 chr6B 91.523 2666 133 35 1 2619 151136047 151133428 0.000000e+00 3585
5 TraesCS6A01G121600 chr7A 79.809 941 166 19 1000 1925 625739663 625738732 0.000000e+00 664


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 TraesCS6A01G121600 chr6A 93817345 93820625 3280 True 6059.000000 6059 100.000000 1 3281 1 chr6A.!!$R1 3280
1 TraesCS6A01G121600 chr6D 78269733 78273246 3513 True 1491.666667 3866 94.005667 1 3257 3 chr6D.!!$R1 3256
2 TraesCS6A01G121600 chr6B 151133428 151136047 2619 True 3585.000000 3585 91.523000 1 2619 1 chr6B.!!$R1 2618
3 TraesCS6A01G121600 chr7A 625738732 625739663 931 True 664.000000 664 79.809000 1000 1925 1 chr7A.!!$R1 925

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
43 44 0.463204 TGTGTGGTTTTCGTACGGGA 59.537 50.000 16.52 1.41 0.00 5.14 F
891 909 1.065926 TGTGGTGATGGAGATGCAGAC 60.066 52.381 0.00 0.00 0.00 3.51 F
1482 1500 1.332997 CAGCAGAAGCATCCGAATTCC 59.667 52.381 0.00 0.00 45.49 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1374 1392 1.302511 CTGGTTAAGGTGCTGCCGT 60.303 57.895 0.00 0.0 43.7 5.68 R
2121 2162 0.030638 GAAATGTGGCGTGCACTTGT 59.969 50.000 16.19 0.0 0.0 3.16 R
2404 2460 0.034863 TGAACAATAACGGGGGAGGC 60.035 55.000 0.00 0.0 0.0 4.70 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
35 36 2.051345 CGCCGCTGTGTGGTTTTC 60.051 61.111 0.00 0.00 35.34 2.29
43 44 0.463204 TGTGTGGTTTTCGTACGGGA 59.537 50.000 16.52 1.41 0.00 5.14
48 50 3.631227 TGTGGTTTTCGTACGGGATTTTT 59.369 39.130 16.52 0.00 0.00 1.94
61 63 1.552254 GGATTTTTCCCCTCCCAGCAA 60.552 52.381 0.00 0.00 0.00 3.91
65 67 1.643310 TTTCCCCTCCCAGCAATTTG 58.357 50.000 0.00 0.00 0.00 2.32
150 157 2.813100 TCGTTCGGCGAGTTTAACC 58.187 52.632 10.46 0.00 45.68 2.85
165 172 5.775686 AGTTTAACCGAACTAATTTTGGGC 58.224 37.500 0.00 0.00 42.75 5.36
182 189 5.994416 TTGGGCTTTAGGGATCTTCTTAT 57.006 39.130 0.00 0.00 0.00 1.73
183 190 7.460214 TTTGGGCTTTAGGGATCTTCTTATA 57.540 36.000 0.00 0.00 0.00 0.98
260 268 4.214971 AGCTGCCGCATAGATTTTGATTAG 59.785 41.667 2.05 0.00 39.10 1.73
271 279 9.844790 CATAGATTTTGATTAGTTTCTTGTGCA 57.155 29.630 0.00 0.00 0.00 4.57
347 357 3.905968 TGATTCATCAGGCCATGTGATT 58.094 40.909 5.01 1.88 32.06 2.57
479 492 3.436704 TGCGGTCAATCTCTTTGAATGTC 59.563 43.478 0.00 0.00 45.71 3.06
503 516 3.103742 GGCATTTCAGGGGGAATGTTTA 58.896 45.455 0.00 0.00 34.91 2.01
504 517 3.132824 GGCATTTCAGGGGGAATGTTTAG 59.867 47.826 0.00 0.00 34.91 1.85
505 518 3.132824 GCATTTCAGGGGGAATGTTTAGG 59.867 47.826 0.00 0.00 34.91 2.69
571 584 7.761409 TCTCTTGCACATTTGAATTATACACC 58.239 34.615 0.00 0.00 0.00 4.16
581 594 2.729028 ATTATACACCTGGTGGCCAC 57.271 50.000 28.57 28.57 37.94 5.01
891 909 1.065926 TGTGGTGATGGAGATGCAGAC 60.066 52.381 0.00 0.00 0.00 3.51
992 1010 6.759497 AGATACATTTGGTAGGCAAAGTTC 57.241 37.500 0.00 0.00 34.92 3.01
993 1011 6.245408 AGATACATTTGGTAGGCAAAGTTCA 58.755 36.000 0.00 0.00 34.92 3.18
994 1012 6.891908 AGATACATTTGGTAGGCAAAGTTCAT 59.108 34.615 0.00 0.00 34.92 2.57
1071 1089 3.442625 TCGACCTCGACATACAACTTGAT 59.557 43.478 0.00 0.00 44.22 2.57
1110 1128 2.301870 TGTTACTTGCCCGATCTGTCTT 59.698 45.455 0.00 0.00 0.00 3.01
1119 1137 2.205074 CCGATCTGTCTTGATTTCCCG 58.795 52.381 0.00 0.00 0.00 5.14
1299 1317 3.002042 GTGACAGCATCCATTTCATCTCG 59.998 47.826 0.00 0.00 0.00 4.04
1374 1392 4.819761 GCTGTCATCGGCGAGGCA 62.820 66.667 17.76 16.32 36.18 4.75
1482 1500 1.332997 CAGCAGAAGCATCCGAATTCC 59.667 52.381 0.00 0.00 45.49 3.01
1769 1790 1.552792 GAGAAGTGGTGGAAGGAGGAG 59.447 57.143 0.00 0.00 0.00 3.69
1992 2020 1.865788 GCCGCTTTCTGTCATTGGCA 61.866 55.000 0.00 0.00 40.66 4.92
2002 2030 1.818060 TGTCATTGGCATGTGGCTAAC 59.182 47.619 8.09 0.00 46.32 2.34
2012 2042 3.066760 GCATGTGGCTAACAGAATTACCC 59.933 47.826 0.00 0.00 43.64 3.69
2018 2048 3.454812 GGCTAACAGAATTACCCCTCTGA 59.545 47.826 6.10 0.00 41.38 3.27
2019 2049 4.443598 GGCTAACAGAATTACCCCTCTGAG 60.444 50.000 6.10 0.00 41.38 3.35
2020 2050 4.162509 GCTAACAGAATTACCCCTCTGAGT 59.837 45.833 3.66 0.00 41.38 3.41
2022 2052 5.941555 AACAGAATTACCCCTCTGAGTAG 57.058 43.478 3.66 0.00 41.38 2.57
2023 2053 4.949121 ACAGAATTACCCCTCTGAGTAGT 58.051 43.478 3.66 3.21 41.38 2.73
2024 2054 6.088541 ACAGAATTACCCCTCTGAGTAGTA 57.911 41.667 3.66 2.25 41.38 1.82
2027 2065 7.724951 ACAGAATTACCCCTCTGAGTAGTATAC 59.275 40.741 3.66 0.00 41.38 1.47
2072 2110 2.748209 AAGGTGCCACTTTAACCACT 57.252 45.000 0.00 0.00 36.37 4.00
2073 2111 3.868619 AAGGTGCCACTTTAACCACTA 57.131 42.857 0.00 0.00 36.37 2.74
2074 2112 3.418684 AGGTGCCACTTTAACCACTAG 57.581 47.619 0.00 0.00 36.37 2.57
2115 2156 9.185192 CTGAACAATGTCTTTATCCTTTGAAAC 57.815 33.333 0.00 0.00 0.00 2.78
2121 2162 6.061441 TGTCTTTATCCTTTGAAACTCAGCA 58.939 36.000 0.00 0.00 0.00 4.41
2123 2164 6.017109 GTCTTTATCCTTTGAAACTCAGCACA 60.017 38.462 0.00 0.00 0.00 4.57
2148 2189 2.665519 GCACGCCACATTTCTAACTGTG 60.666 50.000 6.29 6.29 41.89 3.66
2217 2259 0.598562 TCACTTCGGCAGTCTCTGAC 59.401 55.000 0.66 0.00 35.89 3.51
2296 2351 1.302366 CTAGGATCGCAATGCAGCAA 58.698 50.000 5.91 0.00 0.00 3.91
2323 2378 2.026449 AGGAAGTTCAGAAGCATCCCAG 60.026 50.000 5.01 0.00 0.00 4.45
2326 2381 2.191400 AGTTCAGAAGCATCCCAGCTA 58.809 47.619 0.00 0.00 45.89 3.32
2351 2407 2.095461 GCCTGTTTCATTCCTTCTCCC 58.905 52.381 0.00 0.00 0.00 4.30
2404 2460 1.000171 TGCATAGACGATAGCAGCAGG 60.000 52.381 0.00 0.00 42.67 4.85
2405 2461 1.707632 CATAGACGATAGCAGCAGGC 58.292 55.000 0.00 0.00 45.30 4.85
2406 2462 0.605589 ATAGACGATAGCAGCAGGCC 59.394 55.000 0.00 0.00 46.50 5.19
2407 2463 0.468214 TAGACGATAGCAGCAGGCCT 60.468 55.000 0.00 0.00 46.50 5.19
2410 2466 2.429494 GATAGCAGCAGGCCTCCC 59.571 66.667 0.00 0.00 46.50 4.30
2472 2536 9.609346 TCTTCATGTAAATACTTAGCCTTTACC 57.391 33.333 11.92 0.66 35.47 2.85
2485 2555 5.437191 AGCCTTTACCTTATAGCAGTGTT 57.563 39.130 0.00 0.00 0.00 3.32
2486 2556 5.186198 AGCCTTTACCTTATAGCAGTGTTG 58.814 41.667 0.00 0.00 0.00 3.33
2487 2557 5.045869 AGCCTTTACCTTATAGCAGTGTTGA 60.046 40.000 0.00 0.00 0.00 3.18
2512 2582 1.301874 TTTCCGTCCGCGAAACCAT 60.302 52.632 8.23 0.00 41.33 3.55
2528 2598 6.345723 GCGAAACCATTGTATGTGAAAAACAG 60.346 38.462 0.00 0.00 43.64 3.16
2569 2639 0.458716 TCCGTGCGCGATAATTGTCA 60.459 50.000 23.45 0.00 41.33 3.58
2570 2640 0.581529 CCGTGCGCGATAATTGTCAT 59.418 50.000 23.45 0.00 41.33 3.06
2598 2668 4.708909 AGGCTTTGGAATGGATTTCTCTTC 59.291 41.667 0.00 0.00 34.56 2.87
2621 2691 4.444306 CCCTGTAGAAAGAAGGTTGTGTGA 60.444 45.833 0.00 0.00 0.00 3.58
2622 2692 4.511826 CCTGTAGAAAGAAGGTTGTGTGAC 59.488 45.833 0.00 0.00 0.00 3.67
2626 2698 2.717639 AAGAAGGTTGTGTGACTGCT 57.282 45.000 0.00 0.00 0.00 4.24
2631 2703 0.751643 GGTTGTGTGACTGCTGGGTT 60.752 55.000 0.00 0.00 0.00 4.11
2636 2708 1.360192 GTGACTGCTGGGTTTGTGC 59.640 57.895 0.00 0.00 0.00 4.57
2643 2715 2.124529 TGGGTTTGTGCGCTGTGA 60.125 55.556 9.73 0.00 0.00 3.58
2644 2716 1.723608 CTGGGTTTGTGCGCTGTGAA 61.724 55.000 9.73 0.00 0.00 3.18
2645 2717 1.299089 GGGTTTGTGCGCTGTGAAC 60.299 57.895 9.73 8.37 0.00 3.18
2647 2719 0.100503 GGTTTGTGCGCTGTGAACTT 59.899 50.000 9.73 0.00 0.00 2.66
2659 2740 4.498009 CGCTGTGAACTTTCCTTCATTGTT 60.498 41.667 0.00 0.00 32.78 2.83
2664 2745 6.320926 TGTGAACTTTCCTTCATTGTTCATCA 59.679 34.615 9.53 7.40 45.33 3.07
2673 2754 3.489355 TCATTGTTCATCAGCAACAGGT 58.511 40.909 0.00 0.00 35.22 4.00
2677 2758 4.350368 TGTTCATCAGCAACAGGTCTTA 57.650 40.909 0.00 0.00 30.16 2.10
2683 2764 2.027192 TCAGCAACAGGTCTTACCATCC 60.027 50.000 0.00 0.00 41.95 3.51
2684 2765 1.985159 AGCAACAGGTCTTACCATCCA 59.015 47.619 0.00 0.00 41.95 3.41
2685 2766 2.578021 AGCAACAGGTCTTACCATCCAT 59.422 45.455 0.00 0.00 41.95 3.41
2686 2767 3.010584 AGCAACAGGTCTTACCATCCATT 59.989 43.478 0.00 0.00 41.95 3.16
2731 2815 4.783764 AACTTTTGCCACCTTATAGCAC 57.216 40.909 0.00 0.00 35.96 4.40
2732 2816 3.089284 ACTTTTGCCACCTTATAGCACC 58.911 45.455 0.00 0.00 35.96 5.01
2734 2818 0.616371 TTGCCACCTTATAGCACCGT 59.384 50.000 0.00 0.00 35.96 4.83
2737 2821 0.249322 CCACCTTATAGCACCGTCGG 60.249 60.000 10.48 10.48 0.00 4.79
2768 2852 3.998672 TCCGCGGAACCACCTGTC 61.999 66.667 28.99 0.00 36.31 3.51
2772 2856 1.227853 GCGGAACCACCTGTCTGTT 60.228 57.895 0.00 0.00 36.31 3.16
2773 2857 1.228657 GCGGAACCACCTGTCTGTTC 61.229 60.000 0.00 0.00 38.08 3.18
2774 2858 0.393077 CGGAACCACCTGTCTGTTCT 59.607 55.000 0.00 0.00 38.68 3.01
2775 2859 1.202651 CGGAACCACCTGTCTGTTCTT 60.203 52.381 0.00 0.00 38.68 2.52
2776 2860 2.495084 GGAACCACCTGTCTGTTCTTC 58.505 52.381 0.00 0.00 38.68 2.87
2777 2861 2.135933 GAACCACCTGTCTGTTCTTCG 58.864 52.381 0.00 0.00 36.36 3.79
2778 2862 1.410004 ACCACCTGTCTGTTCTTCGA 58.590 50.000 0.00 0.00 0.00 3.71
2783 2867 4.495844 CCACCTGTCTGTTCTTCGAAAAAC 60.496 45.833 7.42 7.42 0.00 2.43
2785 2869 4.094442 ACCTGTCTGTTCTTCGAAAAACAC 59.906 41.667 12.91 5.59 32.28 3.32
2786 2870 4.495844 CCTGTCTGTTCTTCGAAAAACACC 60.496 45.833 12.91 7.48 32.28 4.16
2787 2871 3.062909 TGTCTGTTCTTCGAAAAACACCG 59.937 43.478 12.91 5.24 32.28 4.94
2788 2872 2.031191 TCTGTTCTTCGAAAAACACCGC 59.969 45.455 12.91 0.00 32.28 5.68
2789 2873 1.064357 TGTTCTTCGAAAAACACCGCC 59.936 47.619 12.91 0.00 30.73 6.13
2790 2874 0.305313 TTCTTCGAAAAACACCGCCG 59.695 50.000 0.00 0.00 0.00 6.46
2793 2877 4.003011 CGAAAAACACCGCCGCGA 62.003 61.111 15.93 0.00 0.00 5.87
2794 2878 2.328639 GAAAAACACCGCCGCGAA 59.671 55.556 15.93 0.00 0.00 4.70
2795 2879 1.724581 GAAAAACACCGCCGCGAAG 60.725 57.895 15.93 8.64 0.00 3.79
2796 2880 2.108344 GAAAAACACCGCCGCGAAGA 62.108 55.000 15.93 0.00 0.00 2.87
2797 2881 1.512156 AAAAACACCGCCGCGAAGAT 61.512 50.000 15.93 0.00 0.00 2.40
2798 2882 1.908066 AAAACACCGCCGCGAAGATC 61.908 55.000 15.93 0.00 0.00 2.75
2799 2883 2.781595 AAACACCGCCGCGAAGATCT 62.782 55.000 15.93 0.00 0.00 2.75
2800 2884 2.509336 CACCGCCGCGAAGATCTT 60.509 61.111 15.93 7.95 0.00 2.40
2801 2885 2.202756 ACCGCCGCGAAGATCTTC 60.203 61.111 23.20 23.20 36.29 2.87
2809 2893 4.072913 GAAGATCTTCGTGCGCGA 57.927 55.556 20.10 20.10 46.36 5.87
2817 2901 4.710695 TCGTGCGCGACAATCGGT 62.711 61.111 20.10 0.00 42.81 4.69
2818 2902 4.483683 CGTGCGCGACAATCGGTG 62.484 66.667 16.08 0.00 40.84 4.94
2819 2903 3.411351 GTGCGCGACAATCGGTGT 61.411 61.111 12.10 0.00 45.74 4.16
2820 2904 3.410516 TGCGCGACAATCGGTGTG 61.411 61.111 12.10 0.00 41.96 3.82
2821 2905 4.147322 GCGCGACAATCGGTGTGG 62.147 66.667 12.10 0.00 41.96 4.17
2822 2906 2.431771 CGCGACAATCGGTGTGGA 60.432 61.111 0.00 0.00 41.96 4.02
2823 2907 2.024868 CGCGACAATCGGTGTGGAA 61.025 57.895 0.00 0.00 41.96 3.53
2824 2908 1.561717 CGCGACAATCGGTGTGGAAA 61.562 55.000 0.00 0.00 41.96 3.13
2825 2909 0.802494 GCGACAATCGGTGTGGAAAT 59.198 50.000 6.40 0.00 41.96 2.17
2826 2910 1.465689 GCGACAATCGGTGTGGAAATG 60.466 52.381 6.40 0.00 41.96 2.32
2827 2911 1.804151 CGACAATCGGTGTGGAAATGT 59.196 47.619 0.00 0.00 41.96 2.71
2828 2912 2.159707 CGACAATCGGTGTGGAAATGTC 60.160 50.000 0.00 0.00 41.96 3.06
2829 2913 2.159382 ACAATCGGTGTGGAAATGTCC 58.841 47.619 0.00 0.00 45.21 4.02
2830 2914 1.472480 CAATCGGTGTGGAAATGTCCC 59.528 52.381 0.00 0.00 44.23 4.46
2831 2915 0.392461 ATCGGTGTGGAAATGTCCCG 60.392 55.000 0.00 0.00 44.23 5.14
2832 2916 1.302192 CGGTGTGGAAATGTCCCGT 60.302 57.895 0.00 0.00 44.23 5.28
2833 2917 1.573829 CGGTGTGGAAATGTCCCGTG 61.574 60.000 0.00 0.00 44.23 4.94
2834 2918 1.241315 GGTGTGGAAATGTCCCGTGG 61.241 60.000 0.00 0.00 44.23 4.94
2884 2981 6.398095 ACTTTTCTGTGAAAAGGAAGGTTTG 58.602 36.000 26.29 8.60 40.54 2.93
2890 2987 2.763448 TGAAAAGGAAGGTTTGTGTGGG 59.237 45.455 0.00 0.00 0.00 4.61
2891 2988 2.543037 AAAGGAAGGTTTGTGTGGGT 57.457 45.000 0.00 0.00 0.00 4.51
2914 3011 2.555547 GGTTGTGTGCTGTGCTCCC 61.556 63.158 0.00 0.00 0.00 4.30
2922 3019 2.433446 CTGTGCTCCCCTTGTGCT 59.567 61.111 0.00 0.00 34.56 4.40
2934 3031 1.741327 CTTGTGCTGCTGGGCTTGTT 61.741 55.000 0.00 0.00 0.00 2.83
2988 3085 4.455533 GTCTGAATGAATGCCACTTGTGTA 59.544 41.667 0.00 0.00 0.00 2.90
2990 3087 3.188254 TGAATGAATGCCACTTGTGTACG 59.812 43.478 0.00 0.00 0.00 3.67
2991 3088 2.248280 TGAATGCCACTTGTGTACGT 57.752 45.000 0.00 0.00 0.00 3.57
2992 3089 3.388345 TGAATGCCACTTGTGTACGTA 57.612 42.857 0.00 0.00 0.00 3.57
2995 3092 2.143008 TGCCACTTGTGTACGTACTG 57.857 50.000 25.12 14.75 0.00 2.74
2996 3093 1.409790 TGCCACTTGTGTACGTACTGT 59.590 47.619 25.12 15.42 0.00 3.55
2997 3094 2.622470 TGCCACTTGTGTACGTACTGTA 59.378 45.455 25.12 9.71 0.00 2.74
2998 3095 3.256383 TGCCACTTGTGTACGTACTGTAT 59.744 43.478 25.12 5.86 35.02 2.29
2999 3096 4.458642 TGCCACTTGTGTACGTACTGTATA 59.541 41.667 25.12 2.87 35.02 1.47
3000 3097 5.125900 TGCCACTTGTGTACGTACTGTATAT 59.874 40.000 25.12 5.36 35.02 0.86
3001 3098 5.684626 GCCACTTGTGTACGTACTGTATATC 59.315 44.000 25.12 6.29 35.02 1.63
3002 3099 6.459298 GCCACTTGTGTACGTACTGTATATCT 60.459 42.308 25.12 0.00 35.02 1.98
3003 3100 7.254898 GCCACTTGTGTACGTACTGTATATCTA 60.255 40.741 25.12 0.00 35.02 1.98
3004 3101 8.781196 CCACTTGTGTACGTACTGTATATCTAT 58.219 37.037 25.12 0.00 35.02 1.98
3005 3102 9.808808 CACTTGTGTACGTACTGTATATCTATC 57.191 37.037 25.12 0.00 35.02 2.08
3006 3103 9.775854 ACTTGTGTACGTACTGTATATCTATCT 57.224 33.333 25.12 0.00 35.02 1.98
3095 3444 2.943653 GTCAACCGGTTTCCTGCG 59.056 61.111 19.55 5.30 0.00 5.18
3125 3474 1.602377 GTTGACTTGGACTTCCGTTGG 59.398 52.381 0.00 0.00 39.43 3.77
3152 3501 1.501741 CCAACGGGTTGAAGATGCG 59.498 57.895 12.89 0.00 42.93 4.73
3158 3507 0.243636 GGGTTGAAGATGCGTTTGGG 59.756 55.000 0.00 0.00 0.00 4.12
3172 3521 3.638484 CGTTTGGGATCCTGTTTGTTTC 58.362 45.455 12.58 0.00 0.00 2.78
3242 3591 1.522355 CACGGCTTCATCATCGGCT 60.522 57.895 0.00 0.00 0.00 5.52
3257 3606 2.590092 GCTATGGCCACGGAACCT 59.410 61.111 8.16 0.00 0.00 3.50
3258 3607 1.077716 GCTATGGCCACGGAACCTT 60.078 57.895 8.16 0.00 0.00 3.50
3259 3608 0.179468 GCTATGGCCACGGAACCTTA 59.821 55.000 8.16 0.00 0.00 2.69
3260 3609 1.810412 GCTATGGCCACGGAACCTTAG 60.810 57.143 8.16 4.21 36.97 2.18
3261 3610 0.834612 TATGGCCACGGAACCTTAGG 59.165 55.000 8.16 0.00 0.00 2.69
3262 3611 1.205460 ATGGCCACGGAACCTTAGGT 61.205 55.000 8.16 0.00 37.65 3.08
3264 3613 0.251033 GGCCACGGAACCTTAGGTTT 60.251 55.000 18.52 0.00 46.95 3.27
3265 3614 1.003464 GGCCACGGAACCTTAGGTTTA 59.997 52.381 18.52 0.00 46.95 2.01
3266 3615 2.353323 GCCACGGAACCTTAGGTTTAG 58.647 52.381 18.52 16.38 46.95 1.85
3267 3616 2.027837 GCCACGGAACCTTAGGTTTAGA 60.028 50.000 18.52 0.00 46.95 2.10
3268 3617 3.370209 GCCACGGAACCTTAGGTTTAGAT 60.370 47.826 18.52 1.94 46.95 1.98
3269 3618 4.141869 GCCACGGAACCTTAGGTTTAGATA 60.142 45.833 18.52 0.00 46.95 1.98
3270 3619 5.598769 CCACGGAACCTTAGGTTTAGATAG 58.401 45.833 18.52 8.58 46.95 2.08
3271 3620 5.128335 CCACGGAACCTTAGGTTTAGATAGT 59.872 44.000 18.52 9.15 46.95 2.12
3272 3621 6.322201 CCACGGAACCTTAGGTTTAGATAGTA 59.678 42.308 18.52 0.00 46.95 1.82
3273 3622 7.147846 CCACGGAACCTTAGGTTTAGATAGTAA 60.148 40.741 18.52 0.00 46.95 2.24
3274 3623 8.419442 CACGGAACCTTAGGTTTAGATAGTAAT 58.581 37.037 18.52 0.00 46.95 1.89
3275 3624 9.646522 ACGGAACCTTAGGTTTAGATAGTAATA 57.353 33.333 18.52 0.00 46.95 0.98
3276 3625 9.905171 CGGAACCTTAGGTTTAGATAGTAATAC 57.095 37.037 18.52 0.30 46.95 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.825308 GGGAAAAATCCCGTACGAAAAC 58.175 45.455 18.76 0.00 40.59 2.43
43 44 2.647846 ATTGCTGGGAGGGGAAAAAT 57.352 45.000 0.00 0.00 0.00 1.82
48 50 1.377690 TACAAATTGCTGGGAGGGGA 58.622 50.000 0.00 0.00 0.00 4.81
61 63 4.852609 GGCTACACGACGAAATACAAAT 57.147 40.909 0.00 0.00 0.00 2.32
107 109 2.497273 CCACAAGGGGGCAAATAAGAAG 59.503 50.000 0.00 0.00 0.00 2.85
113 115 4.213630 CACCACAAGGGGGCAAAT 57.786 55.556 0.00 0.00 42.91 2.32
150 157 4.703093 TCCCTAAAGCCCAAAATTAGTTCG 59.297 41.667 0.00 0.00 0.00 3.95
182 189 6.314400 ACACGCACAAAGAAAAAGAGTAACTA 59.686 34.615 0.00 0.00 0.00 2.24
183 190 5.123344 ACACGCACAAAGAAAAAGAGTAACT 59.877 36.000 0.00 0.00 0.00 2.24
199 206 0.108774 TAACCCATCCAACACGCACA 59.891 50.000 0.00 0.00 0.00 4.57
239 247 5.679734 ACTAATCAAAATCTATGCGGCAG 57.320 39.130 9.25 0.00 0.00 4.85
338 348 9.837525 TTTTTCTTTTTCACAAAAATCACATGG 57.162 25.926 0.00 0.00 39.43 3.66
427 440 4.442375 TTCAGCGGAAGACAAAAACAAA 57.558 36.364 0.00 0.00 0.00 2.83
479 492 1.483415 CATTCCCCCTGAAATGCCAAG 59.517 52.381 0.00 0.00 36.33 3.61
503 516 4.682778 TTGTGTGCTACAAAGTCTACCT 57.317 40.909 4.91 0.00 45.86 3.08
571 584 1.818674 GGAATTTACTGTGGCCACCAG 59.181 52.381 32.62 28.05 32.34 4.00
680 698 6.880942 TGACAAGATCACATCATTTGTCAA 57.119 33.333 17.29 6.12 36.00 3.18
697 715 2.636830 CCCAGCCTAGTTCATGACAAG 58.363 52.381 0.00 0.00 0.00 3.16
698 716 1.281867 CCCCAGCCTAGTTCATGACAA 59.718 52.381 0.00 0.00 0.00 3.18
736 754 3.012518 CCCTTGACCAAGTAATGAGCAG 58.987 50.000 8.72 0.00 36.72 4.24
874 892 1.761784 AGAGTCTGCATCTCCATCACC 59.238 52.381 13.19 0.00 32.93 4.02
891 909 5.747197 CCATAAGCAATAAAAGCAGCAAGAG 59.253 40.000 0.00 0.00 0.00 2.85
992 1010 2.133281 TCCTGAACCCATGCTGAATG 57.867 50.000 0.00 0.00 35.89 2.67
993 1011 2.905415 TTCCTGAACCCATGCTGAAT 57.095 45.000 0.00 0.00 0.00 2.57
994 1012 2.673775 TTTCCTGAACCCATGCTGAA 57.326 45.000 0.00 0.00 0.00 3.02
1071 1089 4.360951 AACATCCTCCGTCCAACTTTTA 57.639 40.909 0.00 0.00 0.00 1.52
1110 1128 2.950673 GCGTTGTGCGGGAAATCA 59.049 55.556 0.00 0.00 41.69 2.57
1119 1137 3.649986 AGCAAGACCGCGTTGTGC 61.650 61.111 4.92 9.28 41.47 4.57
1299 1317 2.612604 GGGTGGTTGTTTGTGTTTGAC 58.387 47.619 0.00 0.00 0.00 3.18
1374 1392 1.302511 CTGGTTAAGGTGCTGCCGT 60.303 57.895 0.00 0.00 43.70 5.68
1425 1443 3.428045 GCTCATGGAAGTTGCCAACATAC 60.428 47.826 10.69 0.00 42.16 2.39
1769 1790 3.050275 GACCAGACCTGTTGCCGC 61.050 66.667 0.00 0.00 0.00 6.53
1992 2020 3.527665 AGGGGTAATTCTGTTAGCCACAT 59.472 43.478 15.43 1.65 42.63 3.21
2002 2030 7.177041 GGTATACTACTCAGAGGGGTAATTCTG 59.823 44.444 1.53 0.00 41.67 3.02
2072 2110 8.902806 CATTGTTCAGGGCAATAAAATCTACTA 58.097 33.333 0.00 0.00 35.09 1.82
2073 2111 7.397192 ACATTGTTCAGGGCAATAAAATCTACT 59.603 33.333 0.00 0.00 35.09 2.57
2074 2112 7.547227 ACATTGTTCAGGGCAATAAAATCTAC 58.453 34.615 0.00 0.00 35.09 2.59
2087 2128 6.434028 TCAAAGGATAAAGACATTGTTCAGGG 59.566 38.462 0.00 0.00 0.00 4.45
2115 2156 2.250485 GCGTGCACTTGTGCTGAG 59.750 61.111 23.53 15.96 35.49 3.35
2121 2162 0.030638 GAAATGTGGCGTGCACTTGT 59.969 50.000 16.19 0.00 0.00 3.16
2123 2164 1.890876 TAGAAATGTGGCGTGCACTT 58.109 45.000 16.19 0.00 0.00 3.16
2165 2206 8.705594 AGCAGCTAGGATTTGTTATAGTTTCTA 58.294 33.333 0.00 0.00 0.00 2.10
2230 2272 2.025037 TGGGATCCCTGGATTGACAAAG 60.025 50.000 31.05 0.00 34.60 2.77
2271 2326 0.530650 CATTGCGATCCTAGGCGTGT 60.531 55.000 2.96 0.00 0.00 4.49
2296 2351 4.090761 TGCTTCTGAACTTCCTGATTGT 57.909 40.909 0.00 0.00 0.00 2.71
2323 2378 1.130561 GAATGAAACAGGCGGTGTAGC 59.869 52.381 0.00 0.00 39.03 3.58
2326 2381 0.110486 AGGAATGAAACAGGCGGTGT 59.890 50.000 0.00 0.00 43.24 4.16
2404 2460 0.034863 TGAACAATAACGGGGGAGGC 60.035 55.000 0.00 0.00 0.00 4.70
2405 2461 1.003812 TGTGAACAATAACGGGGGAGG 59.996 52.381 0.00 0.00 0.00 4.30
2406 2462 2.356135 CTGTGAACAATAACGGGGGAG 58.644 52.381 0.00 0.00 0.00 4.30
2407 2463 1.003812 CCTGTGAACAATAACGGGGGA 59.996 52.381 0.00 0.00 38.90 4.81
2410 2466 3.000727 GAGACCTGTGAACAATAACGGG 58.999 50.000 0.00 0.00 46.56 5.28
2472 2536 4.938080 ACCGAGATCAACACTGCTATAAG 58.062 43.478 0.00 0.00 0.00 1.73
2512 2582 2.287909 GGCGGCTGTTTTTCACATACAA 60.288 45.455 0.00 0.00 33.76 2.41
2569 2639 6.899631 AGAAATCCATTCCAAAGCCTTTCTAT 59.100 34.615 0.00 0.00 38.94 1.98
2570 2640 6.256053 AGAAATCCATTCCAAAGCCTTTCTA 58.744 36.000 0.00 0.00 38.94 2.10
2598 2668 3.815401 CACACAACCTTCTTTCTACAGGG 59.185 47.826 0.00 0.00 31.19 4.45
2621 2691 3.595758 GCGCACAAACCCAGCAGT 61.596 61.111 0.30 0.00 0.00 4.40
2622 2692 3.289834 AGCGCACAAACCCAGCAG 61.290 61.111 11.47 0.00 0.00 4.24
2626 2698 1.750780 TTCACAGCGCACAAACCCA 60.751 52.632 11.47 0.00 0.00 4.51
2631 2703 0.380378 GGAAAGTTCACAGCGCACAA 59.620 50.000 11.47 0.00 0.00 3.33
2636 2708 3.003689 ACAATGAAGGAAAGTTCACAGCG 59.996 43.478 0.00 0.00 39.25 5.18
2643 2715 5.302568 TGCTGATGAACAATGAAGGAAAGTT 59.697 36.000 0.00 0.00 0.00 2.66
2644 2716 4.828939 TGCTGATGAACAATGAAGGAAAGT 59.171 37.500 0.00 0.00 0.00 2.66
2645 2717 5.381174 TGCTGATGAACAATGAAGGAAAG 57.619 39.130 0.00 0.00 0.00 2.62
2647 2719 4.583907 TGTTGCTGATGAACAATGAAGGAA 59.416 37.500 0.00 0.00 30.35 3.36
2659 2740 2.637382 TGGTAAGACCTGTTGCTGATGA 59.363 45.455 0.00 0.00 39.58 2.92
2664 2745 1.985159 TGGATGGTAAGACCTGTTGCT 59.015 47.619 0.00 0.00 39.58 3.91
2673 2754 5.779241 AGAACCTGAAATGGATGGTAAGA 57.221 39.130 0.00 0.00 31.82 2.10
2677 2758 4.387026 TGAAGAACCTGAAATGGATGGT 57.613 40.909 0.00 0.00 0.00 3.55
2708 2792 5.359860 GGTGCTATAAGGTGGCAAAAGTTAT 59.640 40.000 0.00 0.00 46.49 1.89
2709 2793 4.703093 GGTGCTATAAGGTGGCAAAAGTTA 59.297 41.667 0.00 0.00 46.49 2.24
2711 2795 3.089284 GGTGCTATAAGGTGGCAAAAGT 58.911 45.455 0.00 0.00 46.49 2.66
2715 2799 0.616371 ACGGTGCTATAAGGTGGCAA 59.384 50.000 0.00 0.00 46.49 4.52
2716 2800 0.177141 GACGGTGCTATAAGGTGGCA 59.823 55.000 0.00 0.00 42.55 4.92
2719 2803 0.249322 CCCGACGGTGCTATAAGGTG 60.249 60.000 13.94 0.00 0.00 4.00
2720 2804 0.685458 ACCCGACGGTGCTATAAGGT 60.685 55.000 13.94 0.00 42.48 3.50
2732 2816 4.471726 CGGAACCGAGACCCGACG 62.472 72.222 7.53 0.00 45.58 5.12
2734 2818 4.666253 ACCGGAACCGAGACCCGA 62.666 66.667 9.46 0.00 45.58 5.14
2762 2846 4.094442 GTGTTTTTCGAAGAACAGACAGGT 59.906 41.667 28.53 0.00 45.90 4.00
2768 2852 2.372350 GCGGTGTTTTTCGAAGAACAG 58.628 47.619 28.53 20.43 45.90 3.16
2772 2856 1.935925 CGGCGGTGTTTTTCGAAGA 59.064 52.632 0.00 0.00 0.00 2.87
2773 2857 1.724581 GCGGCGGTGTTTTTCGAAG 60.725 57.895 9.78 0.00 0.00 3.79
2774 2858 2.328639 GCGGCGGTGTTTTTCGAA 59.671 55.556 9.78 0.00 0.00 3.71
2775 2859 4.003011 CGCGGCGGTGTTTTTCGA 62.003 61.111 15.84 0.00 0.00 3.71
2776 2860 3.509296 TTCGCGGCGGTGTTTTTCG 62.509 57.895 23.46 0.20 0.00 3.46
2777 2861 1.724581 CTTCGCGGCGGTGTTTTTC 60.725 57.895 23.46 0.00 0.00 2.29
2778 2862 1.512156 ATCTTCGCGGCGGTGTTTTT 61.512 50.000 23.46 0.00 0.00 1.94
2783 2867 2.509336 AAGATCTTCGCGGCGGTG 60.509 61.111 23.46 15.11 0.00 4.94
2801 2885 4.483683 CACCGATTGTCGCGCACG 62.484 66.667 8.75 3.96 38.82 5.34
2802 2886 3.411351 ACACCGATTGTCGCGCAC 61.411 61.111 8.75 5.56 38.82 5.34
2803 2887 3.410516 CACACCGATTGTCGCGCA 61.411 61.111 8.75 0.00 38.82 6.09
2804 2888 4.147322 CCACACCGATTGTCGCGC 62.147 66.667 0.00 0.00 38.82 6.86
2805 2889 1.561717 TTTCCACACCGATTGTCGCG 61.562 55.000 0.00 0.00 38.82 5.87
2806 2890 0.802494 ATTTCCACACCGATTGTCGC 59.198 50.000 0.00 0.00 38.82 5.19
2807 2891 1.804151 ACATTTCCACACCGATTGTCG 59.196 47.619 0.00 0.00 35.67 4.35
2808 2892 2.161609 GGACATTTCCACACCGATTGTC 59.838 50.000 0.00 0.00 42.30 3.18
2809 2893 2.159382 GGACATTTCCACACCGATTGT 58.841 47.619 0.00 0.00 42.30 2.71
2810 2894 1.472480 GGGACATTTCCACACCGATTG 59.528 52.381 0.00 0.00 44.98 2.67
2811 2895 1.834188 GGGACATTTCCACACCGATT 58.166 50.000 0.00 0.00 44.98 3.34
2812 2896 0.392461 CGGGACATTTCCACACCGAT 60.392 55.000 0.00 0.00 44.98 4.18
2813 2897 1.004320 CGGGACATTTCCACACCGA 60.004 57.895 0.00 0.00 44.98 4.69
2814 2898 1.302192 ACGGGACATTTCCACACCG 60.302 57.895 0.00 0.00 44.98 4.94
2815 2899 1.241315 CCACGGGACATTTCCACACC 61.241 60.000 0.00 0.00 44.98 4.16
2816 2900 0.536460 ACCACGGGACATTTCCACAC 60.536 55.000 0.00 0.00 44.98 3.82
2817 2901 1.057471 TACCACGGGACATTTCCACA 58.943 50.000 0.00 0.00 44.98 4.17
2818 2902 2.188062 TTACCACGGGACATTTCCAC 57.812 50.000 0.00 0.00 44.98 4.02
2819 2903 3.085533 CAATTACCACGGGACATTTCCA 58.914 45.455 0.00 0.00 44.98 3.53
2820 2904 3.086282 ACAATTACCACGGGACATTTCC 58.914 45.455 0.00 0.00 41.95 3.13
2821 2905 4.776795 AACAATTACCACGGGACATTTC 57.223 40.909 0.00 0.00 0.00 2.17
2822 2906 5.946972 TCATAACAATTACCACGGGACATTT 59.053 36.000 0.00 0.00 0.00 2.32
2823 2907 5.502079 TCATAACAATTACCACGGGACATT 58.498 37.500 0.00 0.00 0.00 2.71
2824 2908 5.105567 TCATAACAATTACCACGGGACAT 57.894 39.130 0.00 0.00 0.00 3.06
2825 2909 4.554960 TCATAACAATTACCACGGGACA 57.445 40.909 0.00 0.00 0.00 4.02
2826 2910 5.883503 TTTCATAACAATTACCACGGGAC 57.116 39.130 0.00 0.00 0.00 4.46
2827 2911 6.896021 TTTTTCATAACAATTACCACGGGA 57.104 33.333 0.00 0.00 0.00 5.14
2855 2939 5.835113 TCCTTTTCACAGAAAAGTTGGAG 57.165 39.130 23.11 12.43 35.94 3.86
2860 2944 6.014584 ACAAACCTTCCTTTTCACAGAAAAGT 60.015 34.615 23.11 8.94 35.94 2.66
2861 2945 6.311200 CACAAACCTTCCTTTTCACAGAAAAG 59.689 38.462 19.96 19.96 37.08 2.27
2862 2946 6.162777 CACAAACCTTCCTTTTCACAGAAAA 58.837 36.000 5.00 5.00 0.00 2.29
2863 2947 5.245075 ACACAAACCTTCCTTTTCACAGAAA 59.755 36.000 0.00 0.00 0.00 2.52
2864 2948 4.770010 ACACAAACCTTCCTTTTCACAGAA 59.230 37.500 0.00 0.00 0.00 3.02
2884 2981 0.892063 ACACAACCAAACACCCACAC 59.108 50.000 0.00 0.00 0.00 3.82
2890 2987 1.627879 CACAGCACACAACCAAACAC 58.372 50.000 0.00 0.00 0.00 3.32
2891 2988 0.108898 GCACAGCACACAACCAAACA 60.109 50.000 0.00 0.00 0.00 2.83
2914 3011 2.599578 AAGCCCAGCAGCACAAGG 60.600 61.111 0.00 0.00 34.23 3.61
2988 3085 6.091034 CGCAGTCAGATAGATATACAGTACGT 59.909 42.308 0.00 0.00 0.00 3.57
2990 3087 7.598189 TCGCAGTCAGATAGATATACAGTAC 57.402 40.000 0.00 0.00 0.00 2.73
2991 3088 8.794335 AATCGCAGTCAGATAGATATACAGTA 57.206 34.615 0.00 0.00 0.00 2.74
2992 3089 7.695480 AATCGCAGTCAGATAGATATACAGT 57.305 36.000 0.00 0.00 0.00 3.55
2995 3092 6.021074 CGCAAATCGCAGTCAGATAGATATAC 60.021 42.308 0.00 0.00 42.60 1.47
2996 3093 6.030228 CGCAAATCGCAGTCAGATAGATATA 58.970 40.000 0.00 0.00 42.60 0.86
2997 3094 4.861462 CGCAAATCGCAGTCAGATAGATAT 59.139 41.667 0.00 0.00 42.60 1.63
2998 3095 4.229876 CGCAAATCGCAGTCAGATAGATA 58.770 43.478 0.00 0.00 42.60 1.98
2999 3096 3.055591 CGCAAATCGCAGTCAGATAGAT 58.944 45.455 0.00 0.00 42.60 1.98
3000 3097 2.159240 ACGCAAATCGCAGTCAGATAGA 60.159 45.455 0.00 0.00 42.60 1.98
3001 3098 2.034254 CACGCAAATCGCAGTCAGATAG 60.034 50.000 0.00 0.00 42.60 2.08
3002 3099 1.926510 CACGCAAATCGCAGTCAGATA 59.073 47.619 0.00 0.00 42.60 1.98
3003 3100 0.723414 CACGCAAATCGCAGTCAGAT 59.277 50.000 0.00 0.00 42.60 2.90
3004 3101 1.900585 GCACGCAAATCGCAGTCAGA 61.901 55.000 0.00 0.00 42.60 3.27
3005 3102 1.510623 GCACGCAAATCGCAGTCAG 60.511 57.895 0.00 0.00 42.60 3.51
3006 3103 2.555782 GCACGCAAATCGCAGTCA 59.444 55.556 0.00 0.00 42.60 3.41
3038 3387 2.029666 GGATCAGGACGGGCATCG 59.970 66.667 0.00 0.00 45.88 3.84
3086 3435 1.644786 CCCGGAATCACGCAGGAAAC 61.645 60.000 0.73 0.00 0.00 2.78
3090 3439 2.046314 AACCCGGAATCACGCAGG 60.046 61.111 0.73 0.00 0.00 4.85
3095 3444 1.165270 CCAAGTCAACCCGGAATCAC 58.835 55.000 0.73 0.00 0.00 3.06
3152 3501 3.638484 CGAAACAAACAGGATCCCAAAC 58.362 45.455 8.55 0.00 0.00 2.93
3158 3507 0.517316 AGCGCGAAACAAACAGGATC 59.483 50.000 12.10 0.00 0.00 3.36
3172 3521 2.094258 TGCATCTTCTAAAGAAAGCGCG 59.906 45.455 0.00 0.00 42.21 6.86
3242 3591 0.834612 CCTAAGGTTCCGTGGCCATA 59.165 55.000 9.72 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.