Multiple sequence alignment - TraesCS1A01G126200

Loading Multiple Alignment...

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 TraesCS1A01G126200 chr1A 100.000 3051 0 0 1 3051 151350543 151353593 0.000000e+00 5635.0
1 TraesCS1A01G126200 chr1A 90.164 244 23 1 531 773 49290521 49290278 1.770000e-82 316.0
2 TraesCS1A01G126200 chr1B 95.696 1301 41 7 879 2173 198759072 198760363 0.000000e+00 2078.0
3 TraesCS1A01G126200 chr1B 88.745 231 24 2 531 759 138737049 138736819 6.440000e-72 281.0
4 TraesCS1A01G126200 chr1B 100.000 39 0 0 843 881 198759050 198759088 4.220000e-09 73.1
5 TraesCS1A01G126200 chr1B 100.000 28 0 0 801 828 198754585 198754612 5.000000e-03 52.8
6 TraesCS1A01G126200 chr1D 93.884 1357 46 16 785 2129 139905990 139904659 0.000000e+00 2012.0
7 TraesCS1A01G126200 chr1D 91.228 114 9 1 288 400 65844417 65844530 1.460000e-33 154.0
8 TraesCS1A01G126200 chr3A 94.956 793 36 4 1 790 706192976 706192185 0.000000e+00 1240.0
9 TraesCS1A01G126200 chr3A 89.510 143 15 0 637 779 673464414 673464272 6.720000e-42 182.0
10 TraesCS1A01G126200 chr6A 92.190 781 55 6 1 779 293106634 293107410 0.000000e+00 1099.0
11 TraesCS1A01G126200 chr3B 89.178 730 70 5 2174 2901 413839783 413839061 0.000000e+00 902.0
12 TraesCS1A01G126200 chr3B 83.960 505 56 14 285 785 260379110 260378627 7.710000e-126 460.0
13 TraesCS1A01G126200 chr7A 89.408 642 62 3 2261 2901 48013994 48013358 0.000000e+00 804.0
14 TraesCS1A01G126200 chr7D 85.852 311 39 4 288 594 63780474 63780165 2.930000e-85 326.0
15 TraesCS1A01G126200 chr5D 89.344 244 23 3 532 773 477177073 477177315 1.370000e-78 303.0
16 TraesCS1A01G126200 chr2D 88.934 244 26 1 531 773 55926930 55926687 1.780000e-77 300.0
17 TraesCS1A01G126200 chr2D 88.525 244 27 1 531 773 391397414 391397657 8.270000e-76 294.0
18 TraesCS1A01G126200 chr6D 87.665 227 24 2 531 753 315628379 315628605 8.390000e-66 261.0
19 TraesCS1A01G126200 chr6D 100.000 28 0 0 281 308 86608981 86608954 5.000000e-03 52.8
20 TraesCS1A01G126200 chr4A 93.289 149 10 0 2903 3051 727057827 727057679 1.420000e-53 220.0
21 TraesCS1A01G126200 chr4A 97.059 34 1 0 355 388 127225301 127225334 1.180000e-04 58.4
22 TraesCS1A01G126200 chr4A 90.698 43 4 0 2798 2840 705171741 705171699 1.180000e-04 58.4
23 TraesCS1A01G126200 chr6B 91.150 113 10 0 288 400 708792511 708792399 1.460000e-33 154.0
24 TraesCS1A01G126200 chrUn 78.605 215 35 8 191 400 97311716 97311924 6.860000e-27 132.0
25 TraesCS1A01G126200 chrUn 77.778 216 37 6 191 400 97211619 97211829 4.130000e-24 122.0
26 TraesCS1A01G126200 chr3D 85.915 71 10 0 281 351 466837715 466837785 3.260000e-10 76.8
27 TraesCS1A01G126200 chr2A 97.059 34 1 0 355 388 736539656 736539689 1.180000e-04 58.4


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 TraesCS1A01G126200 chr1A 151350543 151353593 3050 False 5635.00 5635 100.000 1 3051 1 chr1A.!!$F1 3050
1 TraesCS1A01G126200 chr1B 198759050 198760363 1313 False 1075.55 2078 97.848 843 2173 2 chr1B.!!$F2 1330
2 TraesCS1A01G126200 chr1D 139904659 139905990 1331 True 2012.00 2012 93.884 785 2129 1 chr1D.!!$R1 1344
3 TraesCS1A01G126200 chr3A 706192185 706192976 791 True 1240.00 1240 94.956 1 790 1 chr3A.!!$R2 789
4 TraesCS1A01G126200 chr6A 293106634 293107410 776 False 1099.00 1099 92.190 1 779 1 chr6A.!!$F1 778
5 TraesCS1A01G126200 chr3B 413839061 413839783 722 True 902.00 902 89.178 2174 2901 1 chr3B.!!$R2 727
6 TraesCS1A01G126200 chr7A 48013358 48013994 636 True 804.00 804 89.408 2261 2901 1 chr7A.!!$R1 640

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
792 797 0.249955 TACCCCCGCTTTAAGTTCCG 59.75 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2681 2704 0.036388 CCTTTCTGCTTCACCGGCTA 60.036 55.0 0.0 0.0 0.0 3.93 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
27 28 0.744057 CACGGCACCACTGATGCATA 60.744 55.000 0.00 0.00 45.27 3.14
34 35 3.681034 GCACCACTGATGCATACTCTCTT 60.681 47.826 0.00 0.00 42.88 2.85
121 122 2.356553 CGAACCGGCGAGAACCAA 60.357 61.111 9.30 0.00 0.00 3.67
415 417 1.953559 TCTGTCACAGCACCTTTGTC 58.046 50.000 0.00 0.00 0.00 3.18
461 464 1.677576 CTGCAACATCACCACAGTTGT 59.322 47.619 0.00 0.00 43.31 3.32
528 531 2.614057 CTCCGCACAAAGTCTCTGTTTT 59.386 45.455 0.00 0.00 0.00 2.43
564 567 3.715495 TGTTGCAATTTTTGACGCTCAT 58.285 36.364 0.59 0.00 0.00 2.90
568 571 3.243334 TGCAATTTTTGACGCTCATGTGA 60.243 39.130 0.00 0.00 0.00 3.58
570 573 4.786507 CAATTTTTGACGCTCATGTGAGA 58.213 39.130 13.94 0.00 44.74 3.27
595 600 1.114722 TAACGACGTGGGAGGTGGTT 61.115 55.000 0.00 0.00 38.23 3.67
629 634 4.303993 AACCAACGGCCGCGTAGT 62.304 61.111 28.58 15.31 0.00 2.73
724 729 4.063967 AGCGCGTCCATCCAACGA 62.064 61.111 8.43 0.00 42.62 3.85
774 779 2.747460 ACTGGCCGACGCGTAGTA 60.747 61.111 13.97 0.00 33.05 1.82
780 785 4.241999 CGACGCGTAGTACCCCCG 62.242 72.222 13.97 4.75 0.00 5.73
781 786 4.559229 GACGCGTAGTACCCCCGC 62.559 72.222 13.97 10.38 43.74 6.13
791 796 1.280133 AGTACCCCCGCTTTAAGTTCC 59.720 52.381 0.00 0.00 0.00 3.62
792 797 0.249955 TACCCCCGCTTTAAGTTCCG 59.750 55.000 0.00 0.00 0.00 4.30
797 802 0.589223 CCGCTTTAAGTTCCGTGCAA 59.411 50.000 0.00 0.00 0.00 4.08
799 804 2.351350 CCGCTTTAAGTTCCGTGCAAAT 60.351 45.455 0.00 0.00 0.00 2.32
810 815 4.844998 TCCGTGCAAATCAAGATTTCAA 57.155 36.364 5.11 0.00 38.84 2.69
814 819 4.386350 CGTGCAAATCAAGATTTCAATGCA 59.614 37.500 13.11 13.11 38.84 3.96
828 833 3.972133 TCAATGCAGACATCCAAATCCT 58.028 40.909 0.00 0.00 34.62 3.24
830 835 5.128205 TCAATGCAGACATCCAAATCCTAG 58.872 41.667 0.00 0.00 34.62 3.02
831 836 5.104402 TCAATGCAGACATCCAAATCCTAGA 60.104 40.000 0.00 0.00 34.62 2.43
832 837 4.412796 TGCAGACATCCAAATCCTAGAG 57.587 45.455 0.00 0.00 0.00 2.43
881 890 4.807304 CGAGGTAAACGCATAGTACCAAAT 59.193 41.667 2.20 0.00 34.61 2.32
891 900 6.481954 GCATAGTACCAAATGCATAGTACC 57.518 41.667 21.75 9.95 46.19 3.34
892 901 5.995282 GCATAGTACCAAATGCATAGTACCA 59.005 40.000 21.75 14.21 46.19 3.25
893 902 6.485313 GCATAGTACCAAATGCATAGTACCAA 59.515 38.462 21.75 14.98 46.19 3.67
894 903 7.012894 GCATAGTACCAAATGCATAGTACCAAA 59.987 37.037 21.75 13.31 46.19 3.28
895 904 9.066892 CATAGTACCAAATGCATAGTACCAAAT 57.933 33.333 21.75 14.41 36.56 2.32
896 905 7.333528 AGTACCAAATGCATAGTACCAAATG 57.666 36.000 21.75 0.00 36.56 2.32
897 906 5.009854 ACCAAATGCATAGTACCAAATGC 57.990 39.130 15.12 15.12 46.92 3.56
920 929 5.449304 CGTTCCAACCTATTCTTGTCAAAC 58.551 41.667 0.00 0.00 0.00 2.93
996 1005 3.282745 TTCGCTCGCTCCACACTCC 62.283 63.158 0.00 0.00 0.00 3.85
1090 1099 3.490759 CTCACGCACCGGACATGC 61.491 66.667 9.46 7.03 39.81 4.06
1215 1224 2.046892 TCCTGCTTTGCGCTCTCC 60.047 61.111 9.73 0.00 40.11 3.71
1808 1823 3.450115 GGAGGCGCAGTAGGACGT 61.450 66.667 10.83 0.00 0.00 4.34
1809 1824 2.117156 GGAGGCGCAGTAGGACGTA 61.117 63.158 10.83 0.00 0.00 3.57
1810 1825 1.355916 GAGGCGCAGTAGGACGTAG 59.644 63.158 10.83 0.00 0.00 3.51
1896 1914 5.298276 CACTAGCTCTAGCATATAGGTAGGC 59.702 48.000 15.22 11.70 44.96 3.93
1924 1942 2.547826 GTCGTGAGTAGTATTTGGGGC 58.452 52.381 0.00 0.00 0.00 5.80
1998 2016 5.862924 ACTGTTGTAGCATTGTGTATGAC 57.137 39.130 0.00 0.00 36.26 3.06
2066 2086 6.974048 TCACTCAGATGTCACATTTTGTTTTG 59.026 34.615 0.00 0.00 0.00 2.44
2072 2093 8.084073 CAGATGTCACATTTTGTTTTGTAGGAT 58.916 33.333 0.00 0.00 0.00 3.24
2222 2245 6.871044 TTGATTTCTCATCTCGTTAAGTCG 57.129 37.500 0.00 0.00 0.00 4.18
2228 2251 3.538591 TCATCTCGTTAAGTCGCCTCTA 58.461 45.455 0.00 0.00 0.00 2.43
2275 2298 2.571757 CGCACCGCTTACCTCTCA 59.428 61.111 0.00 0.00 0.00 3.27
2304 2327 1.902508 TCTTCTCGGGTGAAGCAATCT 59.097 47.619 5.79 0.00 42.15 2.40
2313 2336 2.012673 GTGAAGCAATCTCATCCGCTT 58.987 47.619 0.00 0.00 46.90 4.68
2440 2463 0.388907 GCCAACGCTTCATGTTGCAT 60.389 50.000 11.73 0.00 44.12 3.96
2458 2481 2.033141 GGACTCTGCAAGCTGCCA 59.967 61.111 0.00 0.00 44.23 4.92
2466 2489 2.679092 CAAGCTGCCAGATGGGGA 59.321 61.111 0.00 0.00 37.04 4.81
2530 2553 2.823147 GCAGCTGGCATCTCGCTT 60.823 61.111 17.12 0.00 43.97 4.68
2532 2555 1.449070 CAGCTGGCATCTCGCTTCA 60.449 57.895 5.57 0.00 41.91 3.02
2533 2556 1.449246 AGCTGGCATCTCGCTTCAC 60.449 57.895 0.00 0.00 41.91 3.18
2534 2557 1.449246 GCTGGCATCTCGCTTCACT 60.449 57.895 0.00 0.00 41.91 3.41
2536 2559 1.703438 CTGGCATCTCGCTTCACTGC 61.703 60.000 0.00 0.00 41.91 4.40
2537 2560 1.742880 GGCATCTCGCTTCACTGCA 60.743 57.895 0.00 0.00 41.91 4.41
2541 2564 0.820226 ATCTCGCTTCACTGCAGCTA 59.180 50.000 15.27 0.00 34.88 3.32
2667 2690 0.810031 GTCACCGGTATTGCGATGCT 60.810 55.000 6.87 0.00 0.00 3.79
2677 2700 4.221422 GCGATGCTGGCGGGACTA 62.221 66.667 0.00 0.00 0.00 2.59
2681 2704 1.961180 GATGCTGGCGGGACTACAGT 61.961 60.000 0.00 0.00 33.38 3.55
2819 2843 2.161486 CGGAGCTACAGTGAAGCGC 61.161 63.158 0.00 0.00 44.87 5.92
2842 2866 1.878775 GGAGTTGCAATGAAGCGCT 59.121 52.632 2.64 2.64 37.31 5.92
2843 2867 0.455633 GGAGTTGCAATGAAGCGCTG 60.456 55.000 12.58 0.00 37.31 5.18
2844 2868 0.455633 GAGTTGCAATGAAGCGCTGG 60.456 55.000 12.58 0.00 37.31 4.85
2845 2869 1.444895 GTTGCAATGAAGCGCTGGG 60.445 57.895 12.58 0.00 37.31 4.45
2846 2870 2.638354 TTGCAATGAAGCGCTGGGG 61.638 57.895 12.58 0.00 37.31 4.96
2847 2871 2.751436 GCAATGAAGCGCTGGGGA 60.751 61.111 12.58 0.00 0.00 4.81
2888 2912 0.026803 GTCGCGGCAATGAAGCTAAG 59.973 55.000 5.47 0.00 34.17 2.18
2890 2914 1.369091 CGCGGCAATGAAGCTAAGGT 61.369 55.000 0.00 0.00 34.17 3.50
2901 2926 2.946947 GCTAAGGTGGAGCTGCAAA 58.053 52.632 10.44 0.00 36.96 3.68
2902 2927 1.467920 GCTAAGGTGGAGCTGCAAAT 58.532 50.000 10.44 1.34 36.96 2.32
2903 2928 1.821136 GCTAAGGTGGAGCTGCAAATT 59.179 47.619 10.44 10.41 36.96 1.82
2904 2929 2.232208 GCTAAGGTGGAGCTGCAAATTT 59.768 45.455 10.44 7.40 36.96 1.82
2905 2930 3.306294 GCTAAGGTGGAGCTGCAAATTTT 60.306 43.478 10.44 4.82 36.96 1.82
2906 2931 3.843893 AAGGTGGAGCTGCAAATTTTT 57.156 38.095 10.44 0.00 0.00 1.94
2923 2948 2.922740 TTTTGAGGGCTAACGACAGT 57.077 45.000 0.00 0.00 0.00 3.55
2924 2949 2.163818 TTTGAGGGCTAACGACAGTG 57.836 50.000 0.00 0.00 0.00 3.66
2925 2950 0.320374 TTGAGGGCTAACGACAGTGG 59.680 55.000 0.00 0.00 0.00 4.00
2926 2951 1.218316 GAGGGCTAACGACAGTGGG 59.782 63.158 0.00 0.00 0.00 4.61
2927 2952 1.229082 AGGGCTAACGACAGTGGGA 60.229 57.895 0.00 0.00 0.00 4.37
2928 2953 0.834687 AGGGCTAACGACAGTGGGAA 60.835 55.000 0.00 0.00 0.00 3.97
2929 2954 0.035739 GGGCTAACGACAGTGGGAAA 59.964 55.000 0.00 0.00 0.00 3.13
2930 2955 1.439679 GGCTAACGACAGTGGGAAAG 58.560 55.000 0.00 0.00 0.00 2.62
2931 2956 1.439679 GCTAACGACAGTGGGAAAGG 58.560 55.000 0.00 0.00 0.00 3.11
2932 2957 1.439679 CTAACGACAGTGGGAAAGGC 58.560 55.000 0.00 0.00 0.00 4.35
2933 2958 1.002087 CTAACGACAGTGGGAAAGGCT 59.998 52.381 0.00 0.00 0.00 4.58
2934 2959 0.250338 AACGACAGTGGGAAAGGCTC 60.250 55.000 0.00 0.00 0.00 4.70
2935 2960 1.376037 CGACAGTGGGAAAGGCTCC 60.376 63.158 0.00 0.00 44.54 4.70
2943 2968 2.887790 GGAAAGGCTCCCATTGACC 58.112 57.895 0.00 0.00 38.44 4.02
2944 2969 0.332972 GGAAAGGCTCCCATTGACCT 59.667 55.000 0.00 0.00 38.44 3.85
2945 2970 1.272704 GGAAAGGCTCCCATTGACCTT 60.273 52.381 0.00 0.00 44.37 3.50
2946 2971 1.821136 GAAAGGCTCCCATTGACCTTG 59.179 52.381 0.00 0.00 41.65 3.61
2947 2972 0.779997 AAGGCTCCCATTGACCTTGT 59.220 50.000 0.00 0.00 40.97 3.16
2948 2973 0.779997 AGGCTCCCATTGACCTTGTT 59.220 50.000 0.00 0.00 0.00 2.83
2949 2974 1.147817 AGGCTCCCATTGACCTTGTTT 59.852 47.619 0.00 0.00 0.00 2.83
2950 2975 2.378547 AGGCTCCCATTGACCTTGTTTA 59.621 45.455 0.00 0.00 0.00 2.01
2951 2976 3.011708 AGGCTCCCATTGACCTTGTTTAT 59.988 43.478 0.00 0.00 0.00 1.40
2952 2977 3.381590 GGCTCCCATTGACCTTGTTTATC 59.618 47.826 0.00 0.00 0.00 1.75
2953 2978 4.273318 GCTCCCATTGACCTTGTTTATCT 58.727 43.478 0.00 0.00 0.00 1.98
2954 2979 4.706962 GCTCCCATTGACCTTGTTTATCTT 59.293 41.667 0.00 0.00 0.00 2.40
2955 2980 5.185828 GCTCCCATTGACCTTGTTTATCTTT 59.814 40.000 0.00 0.00 0.00 2.52
2956 2981 6.295292 GCTCCCATTGACCTTGTTTATCTTTT 60.295 38.462 0.00 0.00 0.00 2.27
2957 2982 7.610580 TCCCATTGACCTTGTTTATCTTTTT 57.389 32.000 0.00 0.00 0.00 1.94
2987 3012 8.902540 AATAAATGTCAAGAGTCAACTGTACA 57.097 30.769 0.00 0.00 0.00 2.90
2988 3013 8.902540 ATAAATGTCAAGAGTCAACTGTACAA 57.097 30.769 0.00 0.00 0.00 2.41
2989 3014 7.624360 AAATGTCAAGAGTCAACTGTACAAA 57.376 32.000 0.00 0.00 0.00 2.83
2990 3015 7.624360 AATGTCAAGAGTCAACTGTACAAAA 57.376 32.000 0.00 0.00 0.00 2.44
2991 3016 7.807977 ATGTCAAGAGTCAACTGTACAAAAT 57.192 32.000 0.00 0.00 0.00 1.82
2992 3017 8.902540 ATGTCAAGAGTCAACTGTACAAAATA 57.097 30.769 0.00 0.00 0.00 1.40
2993 3018 8.902540 TGTCAAGAGTCAACTGTACAAAATAT 57.097 30.769 0.00 0.00 0.00 1.28
2994 3019 9.337396 TGTCAAGAGTCAACTGTACAAAATATT 57.663 29.630 0.00 0.00 0.00 1.28
3018 3043 7.834881 TTACATATGAGGGTGTTAGAGTAGG 57.165 40.000 10.38 0.00 0.00 3.18
3019 3044 6.027025 ACATATGAGGGTGTTAGAGTAGGA 57.973 41.667 10.38 0.00 0.00 2.94
3020 3045 6.071984 ACATATGAGGGTGTTAGAGTAGGAG 58.928 44.000 10.38 0.00 0.00 3.69
3021 3046 4.883021 ATGAGGGTGTTAGAGTAGGAGA 57.117 45.455 0.00 0.00 0.00 3.71
3022 3047 4.237976 TGAGGGTGTTAGAGTAGGAGAG 57.762 50.000 0.00 0.00 0.00 3.20
3023 3048 3.850774 TGAGGGTGTTAGAGTAGGAGAGA 59.149 47.826 0.00 0.00 0.00 3.10
3024 3049 4.080243 TGAGGGTGTTAGAGTAGGAGAGAG 60.080 50.000 0.00 0.00 0.00 3.20
3025 3050 3.853784 AGGGTGTTAGAGTAGGAGAGAGT 59.146 47.826 0.00 0.00 0.00 3.24
3026 3051 3.949113 GGGTGTTAGAGTAGGAGAGAGTG 59.051 52.174 0.00 0.00 0.00 3.51
3027 3052 3.949113 GGTGTTAGAGTAGGAGAGAGTGG 59.051 52.174 0.00 0.00 0.00 4.00
3028 3053 3.949113 GTGTTAGAGTAGGAGAGAGTGGG 59.051 52.174 0.00 0.00 0.00 4.61
3029 3054 3.850774 TGTTAGAGTAGGAGAGAGTGGGA 59.149 47.826 0.00 0.00 0.00 4.37
3030 3055 4.479056 TGTTAGAGTAGGAGAGAGTGGGAT 59.521 45.833 0.00 0.00 0.00 3.85
3031 3056 3.593442 AGAGTAGGAGAGAGTGGGATG 57.407 52.381 0.00 0.00 0.00 3.51
3032 3057 3.127250 AGAGTAGGAGAGAGTGGGATGA 58.873 50.000 0.00 0.00 0.00 2.92
3033 3058 3.726859 AGAGTAGGAGAGAGTGGGATGAT 59.273 47.826 0.00 0.00 0.00 2.45
3034 3059 3.826157 GAGTAGGAGAGAGTGGGATGATG 59.174 52.174 0.00 0.00 0.00 3.07
3035 3060 2.100128 AGGAGAGAGTGGGATGATGG 57.900 55.000 0.00 0.00 0.00 3.51
3036 3061 1.055040 GGAGAGAGTGGGATGATGGG 58.945 60.000 0.00 0.00 0.00 4.00
3037 3062 1.413662 GGAGAGAGTGGGATGATGGGA 60.414 57.143 0.00 0.00 0.00 4.37
3038 3063 1.969923 GAGAGAGTGGGATGATGGGAG 59.030 57.143 0.00 0.00 0.00 4.30
3039 3064 1.055040 GAGAGTGGGATGATGGGAGG 58.945 60.000 0.00 0.00 0.00 4.30
3040 3065 0.644380 AGAGTGGGATGATGGGAGGA 59.356 55.000 0.00 0.00 0.00 3.71
3041 3066 0.761802 GAGTGGGATGATGGGAGGAC 59.238 60.000 0.00 0.00 0.00 3.85
3042 3067 0.344790 AGTGGGATGATGGGAGGACT 59.655 55.000 0.00 0.00 0.00 3.85
3043 3068 1.580658 AGTGGGATGATGGGAGGACTA 59.419 52.381 0.00 0.00 0.00 2.59
3044 3069 2.022035 AGTGGGATGATGGGAGGACTAA 60.022 50.000 0.00 0.00 0.00 2.24
3045 3070 2.104963 GTGGGATGATGGGAGGACTAAC 59.895 54.545 0.00 0.00 0.00 2.34
3046 3071 2.293519 TGGGATGATGGGAGGACTAACA 60.294 50.000 0.00 0.00 0.00 2.41
3047 3072 2.104963 GGGATGATGGGAGGACTAACAC 59.895 54.545 0.00 0.00 0.00 3.32
3048 3073 3.041946 GGATGATGGGAGGACTAACACT 58.958 50.000 0.00 0.00 0.00 3.55
3049 3074 4.223953 GGATGATGGGAGGACTAACACTA 58.776 47.826 0.00 0.00 0.00 2.74
3050 3075 4.282195 GGATGATGGGAGGACTAACACTAG 59.718 50.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 2.125269 GCGTCCCACTTACCGCAT 60.125 61.111 0.00 0.00 45.12 4.73
221 222 0.253160 AGGAAGGTAGGTGATGCCCA 60.253 55.000 0.00 0.00 38.26 5.36
227 228 1.561643 CAGCTGAGGAAGGTAGGTGA 58.438 55.000 8.42 0.00 41.17 4.02
351 353 3.172824 GTTGCGGAAACTTTTTCAACGA 58.827 40.909 0.00 0.00 35.75 3.85
461 464 7.763528 ACAATGATGTTGTTGCAGAAAACTTTA 59.236 29.630 8.95 2.16 35.91 1.85
564 567 3.119955 CCACGTCGTTAGATCTTCTCACA 60.120 47.826 0.00 0.00 0.00 3.58
568 571 2.683867 CTCCCACGTCGTTAGATCTTCT 59.316 50.000 0.00 0.00 0.00 2.85
570 573 1.749634 CCTCCCACGTCGTTAGATCTT 59.250 52.381 0.00 0.00 0.00 2.40
595 600 1.278127 GGTTGAAGTTCGGGGAGATCA 59.722 52.381 0.00 0.00 0.00 2.92
629 634 5.517411 CGGTGTTATAGAAACAAGATGCGTA 59.483 40.000 0.00 0.00 31.20 4.42
634 639 5.488341 AGTGCGGTGTTATAGAAACAAGAT 58.512 37.500 0.00 0.00 31.20 2.40
635 640 4.890088 AGTGCGGTGTTATAGAAACAAGA 58.110 39.130 0.00 0.00 31.20 3.02
774 779 1.002990 CGGAACTTAAAGCGGGGGT 60.003 57.895 0.00 0.00 0.00 4.95
780 785 3.896122 TGATTTGCACGGAACTTAAAGC 58.104 40.909 0.00 0.00 0.00 3.51
781 786 5.757886 TCTTGATTTGCACGGAACTTAAAG 58.242 37.500 0.00 0.00 0.00 1.85
782 787 5.759506 TCTTGATTTGCACGGAACTTAAA 57.240 34.783 0.00 0.00 0.00 1.52
791 796 4.386350 TGCATTGAAATCTTGATTTGCACG 59.614 37.500 12.62 6.57 0.00 5.34
792 797 5.636121 TCTGCATTGAAATCTTGATTTGCAC 59.364 36.000 12.62 0.95 0.00 4.57
797 802 6.153851 TGGATGTCTGCATTGAAATCTTGATT 59.846 34.615 6.19 0.00 35.07 2.57
799 804 5.011586 TGGATGTCTGCATTGAAATCTTGA 58.988 37.500 6.19 0.00 35.07 3.02
810 815 4.411540 ACTCTAGGATTTGGATGTCTGCAT 59.588 41.667 0.00 0.00 38.18 3.96
814 819 8.043710 CAGTTTTACTCTAGGATTTGGATGTCT 58.956 37.037 0.00 0.00 0.00 3.41
828 833 6.452242 TCTTCGTGAATGCAGTTTTACTCTA 58.548 36.000 0.00 0.00 0.00 2.43
830 835 5.591643 TCTTCGTGAATGCAGTTTTACTC 57.408 39.130 0.00 0.00 0.00 2.59
831 836 6.373779 CAATCTTCGTGAATGCAGTTTTACT 58.626 36.000 0.00 0.00 0.00 2.24
832 837 5.569059 CCAATCTTCGTGAATGCAGTTTTAC 59.431 40.000 0.00 0.00 0.00 2.01
881 890 2.680841 GGAACGCATTTGGTACTATGCA 59.319 45.455 20.16 0.00 43.52 3.96
884 893 3.692593 GGTTGGAACGCATTTGGTACTAT 59.307 43.478 0.00 0.00 0.00 2.12
886 895 1.883926 GGTTGGAACGCATTTGGTACT 59.116 47.619 0.00 0.00 0.00 2.73
887 896 1.883926 AGGTTGGAACGCATTTGGTAC 59.116 47.619 0.00 0.00 0.00 3.34
888 897 2.279935 AGGTTGGAACGCATTTGGTA 57.720 45.000 0.00 0.00 0.00 3.25
889 898 2.279935 TAGGTTGGAACGCATTTGGT 57.720 45.000 0.00 0.00 0.00 3.67
890 899 3.443681 AGAATAGGTTGGAACGCATTTGG 59.556 43.478 0.00 0.00 0.00 3.28
891 900 4.701956 AGAATAGGTTGGAACGCATTTG 57.298 40.909 0.00 0.00 0.00 2.32
892 901 4.522789 ACAAGAATAGGTTGGAACGCATTT 59.477 37.500 0.00 0.00 0.00 2.32
893 902 4.079253 ACAAGAATAGGTTGGAACGCATT 58.921 39.130 0.00 0.00 0.00 3.56
894 903 3.686016 ACAAGAATAGGTTGGAACGCAT 58.314 40.909 0.00 0.00 0.00 4.73
895 904 3.071479 GACAAGAATAGGTTGGAACGCA 58.929 45.455 0.00 0.00 0.00 5.24
896 905 3.071479 TGACAAGAATAGGTTGGAACGC 58.929 45.455 0.00 0.00 0.00 4.84
897 906 5.449304 GTTTGACAAGAATAGGTTGGAACG 58.551 41.667 0.00 0.00 0.00 3.95
898 907 5.449304 CGTTTGACAAGAATAGGTTGGAAC 58.551 41.667 0.00 0.00 0.00 3.62
899 908 4.023536 GCGTTTGACAAGAATAGGTTGGAA 60.024 41.667 0.00 0.00 0.00 3.53
900 909 3.500680 GCGTTTGACAAGAATAGGTTGGA 59.499 43.478 0.00 0.00 0.00 3.53
996 1005 1.285641 GTTGGTTGCATGGTGTCGG 59.714 57.895 0.00 0.00 0.00 4.79
1136 1145 4.738998 CCTCGGTGGCCATGGCAA 62.739 66.667 36.56 25.95 44.11 4.52
1479 1488 1.000060 TCCTTCCGGTACACAAACTCG 60.000 52.381 0.00 0.00 0.00 4.18
1694 1706 3.458163 CCTTCCCGGCGCACTCTA 61.458 66.667 10.83 0.00 0.00 2.43
1767 1779 2.045242 CTCTCCCCGTCGTCCAGA 60.045 66.667 0.00 0.00 0.00 3.86
1839 1854 6.074356 GCGCGCATAATAAGGAAATGAAAAAT 60.074 34.615 29.10 0.00 0.00 1.82
1855 1873 3.317036 GCTACGACGCGCGCATAA 61.317 61.111 32.58 12.72 46.04 1.90
1896 1914 6.402118 CCAAATACTACTCACGACCACAAATG 60.402 42.308 0.00 0.00 0.00 2.32
1924 1942 4.149617 CGAATACTACTCGCGATAACCAG 58.850 47.826 10.36 5.15 0.00 4.00
1971 1989 8.664798 TCATACACAATGCTACAACAGTTATTC 58.335 33.333 0.00 0.00 35.38 1.75
2066 2086 0.597637 AGCGCGCACACATATCCTAC 60.598 55.000 35.10 0.00 0.00 3.18
2072 2093 1.145759 GCTCTAAGCGCGCACACATA 61.146 55.000 35.10 16.00 0.00 2.29
2156 2179 9.512588 CTTTTCCATTATCTATTGGAGCAGTAT 57.487 33.333 0.00 0.00 42.73 2.12
2157 2180 8.494433 ACTTTTCCATTATCTATTGGAGCAGTA 58.506 33.333 10.00 0.00 42.73 2.74
2159 2182 7.718753 AGACTTTTCCATTATCTATTGGAGCAG 59.281 37.037 0.00 0.00 42.73 4.24
2199 2222 5.288712 GCGACTTAACGAGATGAGAAATCAA 59.711 40.000 0.00 0.00 35.09 2.57
2222 2245 2.820037 GTGGCGCAAGGTAGAGGC 60.820 66.667 10.83 0.00 38.28 4.70
2275 2298 3.709587 TCACCCGAGAAGATAAGGAAGT 58.290 45.455 0.00 0.00 0.00 3.01
2304 2327 0.807275 CGAGCATGTGAAGCGGATGA 60.807 55.000 0.00 0.00 37.01 2.92
2313 2336 0.465705 GAAGGGGATCGAGCATGTGA 59.534 55.000 1.84 0.00 0.00 3.58
2404 2427 1.604593 GCAATCAGTGGTGGCTGGT 60.605 57.895 0.00 0.00 37.12 4.00
2450 2473 3.004951 CTCCCCATCTGGCAGCTT 58.995 61.111 10.34 0.00 0.00 3.74
2529 2552 2.047274 GCCGGTAGCTGCAGTGAA 60.047 61.111 16.64 0.00 38.99 3.18
2530 2553 4.082523 GGCCGGTAGCTGCAGTGA 62.083 66.667 16.64 0.00 43.05 3.41
2598 2621 0.388659 GCAAGGTGGATGTTGCAACA 59.611 50.000 32.78 32.78 46.83 3.33
2605 2628 1.601419 GCATGCAGCAAGGTGGATGT 61.601 55.000 26.57 0.00 45.41 3.06
2647 2670 0.810031 GCATCGCAATACCGGTGACT 60.810 55.000 19.93 0.00 41.67 3.41
2667 2690 2.056223 GGCTACTGTAGTCCCGCCA 61.056 63.158 15.71 0.00 36.57 5.69
2677 2700 1.185618 TCTGCTTCACCGGCTACTGT 61.186 55.000 0.00 0.00 0.00 3.55
2681 2704 0.036388 CCTTTCTGCTTCACCGGCTA 60.036 55.000 0.00 0.00 0.00 3.93
2715 2738 1.815003 CCCACGCGATGCTTCATCA 60.815 57.895 15.93 0.00 40.54 3.07
2741 2764 1.808799 CGCGCTTCACTGCATCTCT 60.809 57.895 5.56 0.00 0.00 3.10
2819 2843 2.257286 CTTCATTGCAACTCCGGCGG 62.257 60.000 22.51 22.51 0.00 6.13
2854 2878 2.763881 GACGACGAGCTTCAACGC 59.236 61.111 0.00 0.00 0.00 4.84
2903 2928 2.875933 CACTGTCGTTAGCCCTCAAAAA 59.124 45.455 0.00 0.00 0.00 1.94
2904 2929 2.489971 CACTGTCGTTAGCCCTCAAAA 58.510 47.619 0.00 0.00 0.00 2.44
2905 2930 1.270625 CCACTGTCGTTAGCCCTCAAA 60.271 52.381 0.00 0.00 0.00 2.69
2906 2931 0.320374 CCACTGTCGTTAGCCCTCAA 59.680 55.000 0.00 0.00 0.00 3.02
2907 2932 1.541310 CCCACTGTCGTTAGCCCTCA 61.541 60.000 0.00 0.00 0.00 3.86
2908 2933 1.218316 CCCACTGTCGTTAGCCCTC 59.782 63.158 0.00 0.00 0.00 4.30
2909 2934 0.834687 TTCCCACTGTCGTTAGCCCT 60.835 55.000 0.00 0.00 0.00 5.19
2910 2935 0.035739 TTTCCCACTGTCGTTAGCCC 59.964 55.000 0.00 0.00 0.00 5.19
2911 2936 1.439679 CTTTCCCACTGTCGTTAGCC 58.560 55.000 0.00 0.00 0.00 3.93
2912 2937 1.439679 CCTTTCCCACTGTCGTTAGC 58.560 55.000 0.00 0.00 0.00 3.09
2913 2938 1.002087 AGCCTTTCCCACTGTCGTTAG 59.998 52.381 0.00 0.00 0.00 2.34
2914 2939 1.001633 GAGCCTTTCCCACTGTCGTTA 59.998 52.381 0.00 0.00 0.00 3.18
2915 2940 0.250338 GAGCCTTTCCCACTGTCGTT 60.250 55.000 0.00 0.00 0.00 3.85
2916 2941 1.371558 GAGCCTTTCCCACTGTCGT 59.628 57.895 0.00 0.00 0.00 4.34
2917 2942 1.376037 GGAGCCTTTCCCACTGTCG 60.376 63.158 0.00 0.00 40.37 4.35
2918 2943 4.724262 GGAGCCTTTCCCACTGTC 57.276 61.111 0.00 0.00 40.37 3.51
2925 2950 0.332972 AGGTCAATGGGAGCCTTTCC 59.667 55.000 0.00 0.00 45.21 3.13
2926 2951 1.821136 CAAGGTCAATGGGAGCCTTTC 59.179 52.381 0.00 0.00 45.21 2.62
2927 2952 1.147817 ACAAGGTCAATGGGAGCCTTT 59.852 47.619 0.00 0.00 45.21 3.11
2928 2953 0.779997 ACAAGGTCAATGGGAGCCTT 59.220 50.000 0.00 0.00 45.21 4.35
2929 2954 0.779997 AACAAGGTCAATGGGAGCCT 59.220 50.000 0.00 0.00 45.21 4.58
2930 2955 1.632589 AAACAAGGTCAATGGGAGCC 58.367 50.000 0.00 0.00 45.21 4.70
2931 2956 4.273318 AGATAAACAAGGTCAATGGGAGC 58.727 43.478 0.00 0.00 44.43 4.70
2932 2957 6.840780 AAAGATAAACAAGGTCAATGGGAG 57.159 37.500 0.00 0.00 0.00 4.30
2933 2958 7.610580 AAAAAGATAAACAAGGTCAATGGGA 57.389 32.000 0.00 0.00 0.00 4.37
2961 2986 9.990360 TGTACAGTTGACTCTTGACATTTATTA 57.010 29.630 0.00 0.00 0.00 0.98
2962 2987 8.902540 TGTACAGTTGACTCTTGACATTTATT 57.097 30.769 0.00 0.00 0.00 1.40
2963 2988 8.902540 TTGTACAGTTGACTCTTGACATTTAT 57.097 30.769 0.00 0.00 0.00 1.40
2964 2989 8.725405 TTTGTACAGTTGACTCTTGACATTTA 57.275 30.769 0.00 0.00 0.00 1.40
2965 2990 7.624360 TTTGTACAGTTGACTCTTGACATTT 57.376 32.000 0.00 0.00 0.00 2.32
2966 2991 7.624360 TTTTGTACAGTTGACTCTTGACATT 57.376 32.000 0.00 0.00 0.00 2.71
2967 2992 7.807977 ATTTTGTACAGTTGACTCTTGACAT 57.192 32.000 0.00 0.00 0.00 3.06
2968 2993 8.902540 ATATTTTGTACAGTTGACTCTTGACA 57.097 30.769 0.00 0.00 0.00 3.58
2992 3017 8.871125 CCTACTCTAACACCCTCATATGTAAAT 58.129 37.037 1.90 0.00 0.00 1.40
2993 3018 8.063153 TCCTACTCTAACACCCTCATATGTAAA 58.937 37.037 1.90 0.00 0.00 2.01
2994 3019 7.589081 TCCTACTCTAACACCCTCATATGTAA 58.411 38.462 1.90 0.00 0.00 2.41
2995 3020 7.073343 TCTCCTACTCTAACACCCTCATATGTA 59.927 40.741 1.90 0.00 0.00 2.29
2996 3021 6.027025 TCCTACTCTAACACCCTCATATGT 57.973 41.667 1.90 0.00 0.00 2.29
2997 3022 6.307776 TCTCCTACTCTAACACCCTCATATG 58.692 44.000 0.00 0.00 0.00 1.78
2998 3023 6.333168 TCTCTCCTACTCTAACACCCTCATAT 59.667 42.308 0.00 0.00 0.00 1.78
2999 3024 5.670818 TCTCTCCTACTCTAACACCCTCATA 59.329 44.000 0.00 0.00 0.00 2.15
3000 3025 4.479056 TCTCTCCTACTCTAACACCCTCAT 59.521 45.833 0.00 0.00 0.00 2.90
3001 3026 3.850774 TCTCTCCTACTCTAACACCCTCA 59.149 47.826 0.00 0.00 0.00 3.86
3002 3027 4.080186 ACTCTCTCCTACTCTAACACCCTC 60.080 50.000 0.00 0.00 0.00 4.30
3003 3028 3.853784 ACTCTCTCCTACTCTAACACCCT 59.146 47.826 0.00 0.00 0.00 4.34
3004 3029 3.949113 CACTCTCTCCTACTCTAACACCC 59.051 52.174 0.00 0.00 0.00 4.61
3005 3030 3.949113 CCACTCTCTCCTACTCTAACACC 59.051 52.174 0.00 0.00 0.00 4.16
3006 3031 3.949113 CCCACTCTCTCCTACTCTAACAC 59.051 52.174 0.00 0.00 0.00 3.32
3007 3032 3.850774 TCCCACTCTCTCCTACTCTAACA 59.149 47.826 0.00 0.00 0.00 2.41
3008 3033 4.506937 TCCCACTCTCTCCTACTCTAAC 57.493 50.000 0.00 0.00 0.00 2.34
3009 3034 4.727332 TCATCCCACTCTCTCCTACTCTAA 59.273 45.833 0.00 0.00 0.00 2.10
3010 3035 4.308128 TCATCCCACTCTCTCCTACTCTA 58.692 47.826 0.00 0.00 0.00 2.43
3011 3036 3.127250 TCATCCCACTCTCTCCTACTCT 58.873 50.000 0.00 0.00 0.00 3.24
3012 3037 3.586470 TCATCCCACTCTCTCCTACTC 57.414 52.381 0.00 0.00 0.00 2.59
3013 3038 3.437784 CCATCATCCCACTCTCTCCTACT 60.438 52.174 0.00 0.00 0.00 2.57
3014 3039 2.896685 CCATCATCCCACTCTCTCCTAC 59.103 54.545 0.00 0.00 0.00 3.18
3015 3040 2.158249 CCCATCATCCCACTCTCTCCTA 60.158 54.545 0.00 0.00 0.00 2.94
3016 3041 1.414245 CCCATCATCCCACTCTCTCCT 60.414 57.143 0.00 0.00 0.00 3.69
3017 3042 1.055040 CCCATCATCCCACTCTCTCC 58.945 60.000 0.00 0.00 0.00 3.71
3018 3043 1.969923 CTCCCATCATCCCACTCTCTC 59.030 57.143 0.00 0.00 0.00 3.20
3019 3044 1.414245 CCTCCCATCATCCCACTCTCT 60.414 57.143 0.00 0.00 0.00 3.10
3020 3045 1.055040 CCTCCCATCATCCCACTCTC 58.945 60.000 0.00 0.00 0.00 3.20
3021 3046 0.644380 TCCTCCCATCATCCCACTCT 59.356 55.000 0.00 0.00 0.00 3.24
3022 3047 0.761802 GTCCTCCCATCATCCCACTC 59.238 60.000 0.00 0.00 0.00 3.51
3023 3048 0.344790 AGTCCTCCCATCATCCCACT 59.655 55.000 0.00 0.00 0.00 4.00
3024 3049 2.103153 TAGTCCTCCCATCATCCCAC 57.897 55.000 0.00 0.00 0.00 4.61
3025 3050 2.293519 TGTTAGTCCTCCCATCATCCCA 60.294 50.000 0.00 0.00 0.00 4.37
3026 3051 2.104963 GTGTTAGTCCTCCCATCATCCC 59.895 54.545 0.00 0.00 0.00 3.85
3027 3052 3.041946 AGTGTTAGTCCTCCCATCATCC 58.958 50.000 0.00 0.00 0.00 3.51
3028 3053 5.461032 CTAGTGTTAGTCCTCCCATCATC 57.539 47.826 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.