Multiple sequence alignment - TraesCS2D01G358700

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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 TraesCS2D01G358700 chr2D 100.000 3656 0 0 1 3656 460763841 460760186 0.000000e+00 6752.0
1 TraesCS2D01G358700 chr2D 95.619 776 29 3 1 774 2488910 2489682 0.000000e+00 1240.0
2 TraesCS2D01G358700 chr2D 95.103 776 33 3 1 774 187968215 187967443 0.000000e+00 1218.0
3 TraesCS2D01G358700 chr2A 95.321 2180 65 21 766 2916 603564114 603561943 0.000000e+00 3426.0
4 TraesCS2D01G358700 chr2A 88.128 657 41 22 3019 3653 603561945 603561304 0.000000e+00 747.0
5 TraesCS2D01G358700 chr2B 94.899 1686 55 15 1549 3224 542265408 542263744 0.000000e+00 2608.0
6 TraesCS2D01G358700 chr2B 94.710 775 38 3 1 773 247938708 247937935 0.000000e+00 1201.0
7 TraesCS2D01G358700 chr2B 94.452 775 38 3 1 774 662578758 662577988 0.000000e+00 1188.0
8 TraesCS2D01G358700 chr2B 89.055 402 11 18 766 1135 542265802 542265402 5.530000e-128 468.0
9 TraesCS2D01G358700 chr2B 93.985 133 6 1 1331 1463 411513842 411513712 2.230000e-47 200.0
10 TraesCS2D01G358700 chr2B 90.541 148 12 2 1535 1682 411513723 411513578 1.040000e-45 195.0
11 TraesCS2D01G358700 chr2B 93.277 119 7 1 1766 1884 411513581 411513464 1.350000e-39 174.0
12 TraesCS2D01G358700 chr2B 95.918 49 2 0 1389 1437 743350814 743350862 3.030000e-11 80.5
13 TraesCS2D01G358700 chr7D 94.757 782 35 6 1 779 408032393 408031615 0.000000e+00 1212.0
14 TraesCS2D01G358700 chr5D 94.968 775 33 3 1 774 91635271 91634502 0.000000e+00 1210.0
15 TraesCS2D01G358700 chr1D 94.839 775 36 2 1 774 234834442 234833671 0.000000e+00 1206.0
16 TraesCS2D01G358700 chr4B 93.943 776 45 2 1 774 613203860 613204635 0.000000e+00 1171.0
17 TraesCS2D01G358700 chr4B 95.918 49 2 0 1389 1437 535055081 535055033 3.030000e-11 80.5
18 TraesCS2D01G358700 chr1A 90.090 777 68 9 1 774 574363562 574362792 0.000000e+00 1000.0
19 TraesCS2D01G358700 chr3B 97.436 78 2 0 2859 2936 513659049 513659126 2.290000e-27 134.0
20 TraesCS2D01G358700 chr3B 93.878 49 3 0 1389 1437 808332833 808332881 1.410000e-09 75.0
21 TraesCS2D01G358700 chr5A 93.878 49 3 0 1389 1437 17421309 17421357 1.410000e-09 75.0
22 TraesCS2D01G358700 chr7B 100.000 38 0 0 1389 1426 701340487 701340524 1.820000e-08 71.3


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 TraesCS2D01G358700 chr2D 460760186 460763841 3655 True 6752.0 6752 100.0000 1 3656 1 chr2D.!!$R2 3655
1 TraesCS2D01G358700 chr2D 2488910 2489682 772 False 1240.0 1240 95.6190 1 774 1 chr2D.!!$F1 773
2 TraesCS2D01G358700 chr2D 187967443 187968215 772 True 1218.0 1218 95.1030 1 774 1 chr2D.!!$R1 773
3 TraesCS2D01G358700 chr2A 603561304 603564114 2810 True 2086.5 3426 91.7245 766 3653 2 chr2A.!!$R1 2887
4 TraesCS2D01G358700 chr2B 542263744 542265802 2058 True 1538.0 2608 91.9770 766 3224 2 chr2B.!!$R4 2458
5 TraesCS2D01G358700 chr2B 247937935 247938708 773 True 1201.0 1201 94.7100 1 773 1 chr2B.!!$R1 772
6 TraesCS2D01G358700 chr2B 662577988 662578758 770 True 1188.0 1188 94.4520 1 774 1 chr2B.!!$R2 773
7 TraesCS2D01G358700 chr7D 408031615 408032393 778 True 1212.0 1212 94.7570 1 779 1 chr7D.!!$R1 778
8 TraesCS2D01G358700 chr5D 91634502 91635271 769 True 1210.0 1210 94.9680 1 774 1 chr5D.!!$R1 773
9 TraesCS2D01G358700 chr1D 234833671 234834442 771 True 1206.0 1206 94.8390 1 774 1 chr1D.!!$R1 773
10 TraesCS2D01G358700 chr4B 613203860 613204635 775 False 1171.0 1171 93.9430 1 774 1 chr4B.!!$F1 773
11 TraesCS2D01G358700 chr1A 574362792 574363562 770 True 1000.0 1000 90.0900 1 774 1 chr1A.!!$R1 773

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
626 630 0.100503 GCCCCGCATGTCATAAACAC 59.899 55.000 0.0 0.0 41.75 3.32 F
1617 1656 1.004440 GACCTTCGTGCTGGAGCTT 60.004 57.895 0.0 0.0 42.66 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1721 1760 0.383590 CTCGAGCAGGATCATGTCGT 59.616 55.0 22.23 5.74 32.49 4.34 R
3172 3337 0.169451 CGCATGTTGCTGAATGCTGA 59.831 50.0 13.58 0.00 45.62 4.26 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
322 325 2.684927 CGATGGCCTTGGAGGAAATTCT 60.685 50.000 3.32 0.00 37.67 2.40
626 630 0.100503 GCCCCGCATGTCATAAACAC 59.899 55.000 0.00 0.00 41.75 3.32
679 684 5.813080 AAGTGGTAGTTTTCAGTCACAAC 57.187 39.130 0.00 0.00 0.00 3.32
745 751 1.071228 GTTCTGTGGGACGGTAACCTT 59.929 52.381 3.42 0.00 0.00 3.50
752 758 4.285517 TGTGGGACGGTAACCTTTAATGTA 59.714 41.667 3.42 0.00 0.00 2.29
955 966 2.434336 CCTTGATCTGTCCATAACCGGA 59.566 50.000 9.46 0.00 0.00 5.14
1173 1212 2.355837 GAGACACTGACGCGCCAA 60.356 61.111 5.73 0.00 0.00 4.52
1224 1263 4.969196 CAGTCACCGGCGCACAGT 62.969 66.667 10.83 0.00 0.00 3.55
1341 1380 3.324108 TACCGGGTGCCCAAGTCC 61.324 66.667 10.66 0.00 35.37 3.85
1497 1536 2.181021 GACGTCACCGCCTACCTG 59.819 66.667 11.55 0.00 37.70 4.00
1617 1656 1.004440 GACCTTCGTGCTGGAGCTT 60.004 57.895 0.00 0.00 42.66 3.74
1721 1760 3.813143 CATGCACGCCATCCGCAA 61.813 61.111 0.00 0.00 39.48 4.85
2473 2512 1.380112 GACAGCTACCTCTCCGGGT 60.380 63.158 0.00 0.00 42.86 5.28
2679 2723 4.219999 GCTCGAGCTCCAGCCTCC 62.220 72.222 29.88 0.00 43.38 4.30
2680 2724 2.757508 CTCGAGCTCCAGCCTCCA 60.758 66.667 8.47 0.00 43.38 3.86
2681 2725 2.757508 TCGAGCTCCAGCCTCCAG 60.758 66.667 8.47 0.00 43.38 3.86
2711 2755 5.279456 GCAGGTGGATTTTGGATTACAGTTT 60.279 40.000 0.00 0.00 0.00 2.66
2718 2767 8.087750 TGGATTTTGGATTACAGTTTGACATTC 58.912 33.333 0.00 0.00 0.00 2.67
2822 2878 8.800370 TTTGAGTTGCATCCTGTTAATATACA 57.200 30.769 0.00 0.00 0.00 2.29
2841 2897 2.431057 ACATACTCGATTCTGGTGGGAC 59.569 50.000 0.00 0.00 0.00 4.46
2848 2904 2.434336 CGATTCTGGTGGGACAAGGATA 59.566 50.000 0.00 0.00 44.16 2.59
2852 2908 4.946160 TCTGGTGGGACAAGGATATTTT 57.054 40.909 0.00 0.00 44.16 1.82
2857 2913 3.513515 GTGGGACAAGGATATTTTTGGCA 59.486 43.478 7.90 0.00 44.16 4.92
2858 2914 4.020662 GTGGGACAAGGATATTTTTGGCAA 60.021 41.667 0.00 0.00 44.16 4.52
2859 2915 4.594920 TGGGACAAGGATATTTTTGGCAAA 59.405 37.500 8.93 8.93 33.91 3.68
2916 3079 1.616994 GGGACATCTTGAGGGGTTTGG 60.617 57.143 0.00 0.00 0.00 3.28
2917 3080 1.354368 GGACATCTTGAGGGGTTTGGA 59.646 52.381 0.00 0.00 0.00 3.53
2918 3081 2.437413 GACATCTTGAGGGGTTTGGAC 58.563 52.381 0.00 0.00 0.00 4.02
2919 3082 1.271379 ACATCTTGAGGGGTTTGGACG 60.271 52.381 0.00 0.00 0.00 4.79
2920 3083 0.322546 ATCTTGAGGGGTTTGGACGC 60.323 55.000 0.00 0.00 37.95 5.19
2921 3084 1.073199 CTTGAGGGGTTTGGACGCT 59.927 57.895 0.00 0.00 38.65 5.07
2922 3085 0.955919 CTTGAGGGGTTTGGACGCTC 60.956 60.000 0.00 0.00 45.11 5.03
2923 3086 1.415672 TTGAGGGGTTTGGACGCTCT 61.416 55.000 10.19 0.00 45.12 4.09
2924 3087 1.079057 GAGGGGTTTGGACGCTCTC 60.079 63.158 0.00 0.00 42.58 3.20
2925 3088 1.827399 GAGGGGTTTGGACGCTCTCA 61.827 60.000 0.00 0.00 42.58 3.27
2926 3089 1.201429 AGGGGTTTGGACGCTCTCAT 61.201 55.000 0.00 0.00 38.65 2.90
2927 3090 1.026718 GGGGTTTGGACGCTCTCATG 61.027 60.000 0.00 0.00 38.65 3.07
2928 3091 1.026718 GGGTTTGGACGCTCTCATGG 61.027 60.000 0.00 0.00 35.94 3.66
2929 3092 0.321653 GGTTTGGACGCTCTCATGGT 60.322 55.000 0.00 0.00 0.00 3.55
2930 3093 1.079503 GTTTGGACGCTCTCATGGTC 58.920 55.000 0.00 0.00 0.00 4.02
2931 3094 0.389817 TTTGGACGCTCTCATGGTCG 60.390 55.000 0.00 0.00 0.00 4.79
2932 3095 1.532604 TTGGACGCTCTCATGGTCGT 61.533 55.000 0.00 0.00 37.92 4.34
2933 3096 1.517257 GGACGCTCTCATGGTCGTG 60.517 63.158 7.07 0.00 35.12 4.35
2934 3097 1.517257 GACGCTCTCATGGTCGTGG 60.517 63.158 7.07 0.00 35.12 4.94
2935 3098 1.934220 GACGCTCTCATGGTCGTGGA 61.934 60.000 7.07 0.00 35.12 4.02
2936 3099 1.226802 CGCTCTCATGGTCGTGGAG 60.227 63.158 0.00 0.00 0.00 3.86
2937 3100 1.657751 CGCTCTCATGGTCGTGGAGA 61.658 60.000 0.00 0.00 36.35 3.71
2938 3101 0.532573 GCTCTCATGGTCGTGGAGAA 59.467 55.000 0.00 0.00 37.24 2.87
2939 3102 1.137872 GCTCTCATGGTCGTGGAGAAT 59.862 52.381 0.00 0.00 37.24 2.40
2940 3103 2.419297 GCTCTCATGGTCGTGGAGAATT 60.419 50.000 0.00 0.00 37.24 2.17
2941 3104 3.193263 CTCTCATGGTCGTGGAGAATTG 58.807 50.000 0.00 0.00 37.24 2.32
2942 3105 2.567169 TCTCATGGTCGTGGAGAATTGT 59.433 45.455 0.00 0.00 34.91 2.71
2943 3106 3.007940 TCTCATGGTCGTGGAGAATTGTT 59.992 43.478 0.00 0.00 34.91 2.83
2944 3107 3.334691 TCATGGTCGTGGAGAATTGTTC 58.665 45.455 0.00 0.00 0.00 3.18
2945 3108 2.920724 TGGTCGTGGAGAATTGTTCA 57.079 45.000 0.00 0.00 0.00 3.18
2946 3109 3.201353 TGGTCGTGGAGAATTGTTCAA 57.799 42.857 0.00 0.00 0.00 2.69
2947 3110 3.750371 TGGTCGTGGAGAATTGTTCAAT 58.250 40.909 0.00 0.00 0.00 2.57
2948 3111 4.141287 TGGTCGTGGAGAATTGTTCAATT 58.859 39.130 10.04 10.04 0.00 2.32
2949 3112 4.023279 TGGTCGTGGAGAATTGTTCAATTG 60.023 41.667 14.29 0.00 0.00 2.32
2950 3113 4.215399 GGTCGTGGAGAATTGTTCAATTGA 59.785 41.667 14.29 3.38 0.00 2.57
2951 3114 5.385617 GTCGTGGAGAATTGTTCAATTGAG 58.614 41.667 14.29 0.00 0.00 3.02
2952 3115 4.083324 TCGTGGAGAATTGTTCAATTGAGC 60.083 41.667 14.76 14.76 0.00 4.26
2953 3116 4.320421 CGTGGAGAATTGTTCAATTGAGCA 60.320 41.667 19.66 19.66 33.42 4.26
2954 3117 5.620654 CGTGGAGAATTGTTCAATTGAGCAT 60.621 40.000 23.33 11.42 35.26 3.79
2955 3118 6.161381 GTGGAGAATTGTTCAATTGAGCATT 58.839 36.000 23.33 17.49 35.26 3.56
2956 3119 6.647895 GTGGAGAATTGTTCAATTGAGCATTT 59.352 34.615 23.33 23.56 35.26 2.32
2957 3120 6.647481 TGGAGAATTGTTCAATTGAGCATTTG 59.353 34.615 26.70 0.00 35.26 2.32
2958 3121 6.401796 GGAGAATTGTTCAATTGAGCATTTGC 60.402 38.462 26.70 19.91 35.26 3.68
2959 3122 5.992829 AGAATTGTTCAATTGAGCATTTGCA 59.007 32.000 26.70 14.14 45.16 4.08
2960 3123 6.653320 AGAATTGTTCAATTGAGCATTTGCAT 59.347 30.769 26.70 15.46 45.16 3.96
2961 3124 5.849357 TTGTTCAATTGAGCATTTGCATC 57.151 34.783 23.33 0.82 45.16 3.91
2962 3125 5.142061 TGTTCAATTGAGCATTTGCATCT 57.858 34.783 19.66 0.00 45.16 2.90
2963 3126 4.926832 TGTTCAATTGAGCATTTGCATCTG 59.073 37.500 19.66 0.00 45.16 2.90
2964 3127 3.517602 TCAATTGAGCATTTGCATCTGC 58.482 40.909 3.38 11.90 45.16 4.26
2965 3128 8.893837 TGTTCAATTGAGCATTTGCATCTGCA 62.894 38.462 19.66 0.00 45.16 4.41
2979 3142 4.990257 GCATCTGCACATTTTATGACTGT 58.010 39.130 0.00 0.00 41.59 3.55
2980 3143 6.122850 GCATCTGCACATTTTATGACTGTA 57.877 37.500 0.00 0.00 41.59 2.74
2981 3144 5.967674 GCATCTGCACATTTTATGACTGTAC 59.032 40.000 0.00 0.00 41.59 2.90
2982 3145 6.403527 GCATCTGCACATTTTATGACTGTACA 60.404 38.462 0.00 0.00 41.59 2.90
2983 3146 6.480524 TCTGCACATTTTATGACTGTACAC 57.519 37.500 0.00 0.00 0.00 2.90
2984 3147 5.994668 TCTGCACATTTTATGACTGTACACA 59.005 36.000 0.00 0.00 0.00 3.72
2985 3148 6.654582 TCTGCACATTTTATGACTGTACACAT 59.345 34.615 4.56 4.56 0.00 3.21
2986 3149 7.174772 TCTGCACATTTTATGACTGTACACATT 59.825 33.333 4.47 0.00 0.00 2.71
2987 3150 7.656412 TGCACATTTTATGACTGTACACATTT 58.344 30.769 4.47 0.00 0.00 2.32
2988 3151 8.140628 TGCACATTTTATGACTGTACACATTTT 58.859 29.630 4.47 0.00 0.00 1.82
2989 3152 9.619316 GCACATTTTATGACTGTACACATTTTA 57.381 29.630 4.47 0.00 0.00 1.52
2998 3161 8.942669 TGACTGTACACATTTTAATTTTAGCG 57.057 30.769 0.00 0.00 0.00 4.26
2999 3162 8.775527 TGACTGTACACATTTTAATTTTAGCGA 58.224 29.630 0.00 0.00 0.00 4.93
3000 3163 8.944212 ACTGTACACATTTTAATTTTAGCGAC 57.056 30.769 0.00 0.00 0.00 5.19
3001 3164 8.019094 ACTGTACACATTTTAATTTTAGCGACC 58.981 33.333 0.00 0.00 0.00 4.79
3002 3165 7.872881 TGTACACATTTTAATTTTAGCGACCA 58.127 30.769 0.00 0.00 0.00 4.02
3003 3166 8.018520 TGTACACATTTTAATTTTAGCGACCAG 58.981 33.333 0.00 0.00 0.00 4.00
3004 3167 6.386654 ACACATTTTAATTTTAGCGACCAGG 58.613 36.000 0.00 0.00 0.00 4.45
3005 3168 5.804979 CACATTTTAATTTTAGCGACCAGGG 59.195 40.000 0.00 0.00 0.00 4.45
3006 3169 5.712917 ACATTTTAATTTTAGCGACCAGGGA 59.287 36.000 0.00 0.00 0.00 4.20
3007 3170 5.890424 TTTTAATTTTAGCGACCAGGGAG 57.110 39.130 0.00 0.00 0.00 4.30
3008 3171 4.829872 TTAATTTTAGCGACCAGGGAGA 57.170 40.909 0.00 0.00 0.00 3.71
3009 3172 3.713826 AATTTTAGCGACCAGGGAGAA 57.286 42.857 0.00 0.00 0.00 2.87
3010 3173 3.933861 ATTTTAGCGACCAGGGAGAAT 57.066 42.857 0.00 0.00 0.00 2.40
3011 3174 3.713826 TTTTAGCGACCAGGGAGAATT 57.286 42.857 0.00 0.00 0.00 2.17
3012 3175 2.691409 TTAGCGACCAGGGAGAATTG 57.309 50.000 0.00 0.00 0.00 2.32
3013 3176 1.568504 TAGCGACCAGGGAGAATTGT 58.431 50.000 0.00 0.00 0.00 2.71
3014 3177 0.693049 AGCGACCAGGGAGAATTGTT 59.307 50.000 0.00 0.00 0.00 2.83
3015 3178 1.087501 GCGACCAGGGAGAATTGTTC 58.912 55.000 0.00 0.00 0.00 3.18
3016 3179 1.610624 GCGACCAGGGAGAATTGTTCA 60.611 52.381 0.00 0.00 0.00 3.18
3017 3180 2.350522 CGACCAGGGAGAATTGTTCAG 58.649 52.381 0.00 0.00 0.00 3.02
3018 3181 2.289694 CGACCAGGGAGAATTGTTCAGT 60.290 50.000 0.00 0.00 0.00 3.41
3019 3182 3.756117 GACCAGGGAGAATTGTTCAGTT 58.244 45.455 0.00 0.00 0.00 3.16
3020 3183 3.490348 ACCAGGGAGAATTGTTCAGTTG 58.510 45.455 0.00 0.00 0.00 3.16
3053 3216 5.505173 AGGTCAAATGTCAGTCTTGTTTG 57.495 39.130 0.00 0.00 0.00 2.93
3137 3302 2.029380 CACGTCTCAGTTACATGTGGGA 60.029 50.000 9.11 0.00 0.00 4.37
3141 3306 4.804139 CGTCTCAGTTACATGTGGGAATAC 59.196 45.833 9.11 0.00 0.00 1.89
3246 3411 8.346300 TGAAGAGAAGATAACGACACTATGATC 58.654 37.037 0.00 0.00 0.00 2.92
3251 3416 7.390996 AGAAGATAACGACACTATGATCCGTAT 59.609 37.037 0.00 0.00 32.81 3.06
3270 3440 5.470437 CCGTATGATGCTTCTACTCTAGTCA 59.530 44.000 0.88 0.00 0.00 3.41
3334 3504 2.283145 AGGCTTTCATTCACACAGCT 57.717 45.000 0.00 0.00 0.00 4.24
3386 3556 7.603784 CCCTTTTTCCTTTTGATACCAATTCAG 59.396 37.037 0.00 0.00 31.46 3.02
3426 3596 2.431057 TCGATGCTCTCCCCTAAGAAAC 59.569 50.000 0.00 0.00 0.00 2.78
3427 3597 2.483889 CGATGCTCTCCCCTAAGAAACC 60.484 54.545 0.00 0.00 0.00 3.27
3511 3684 4.645535 TCAGAGCATAAAGGGCATCATAC 58.354 43.478 0.00 0.00 0.00 2.39
3512 3685 3.755378 CAGAGCATAAAGGGCATCATACC 59.245 47.826 0.00 0.00 0.00 2.73
3513 3686 3.395607 AGAGCATAAAGGGCATCATACCA 59.604 43.478 0.00 0.00 0.00 3.25
3525 3700 5.047802 GGGCATCATACCATTATCAACTTGG 60.048 44.000 0.00 0.00 36.56 3.61
3528 3703 6.675026 CATCATACCATTATCAACTTGGCAG 58.325 40.000 0.00 0.00 33.66 4.85
3532 3707 3.245229 ACCATTATCAACTTGGCAGTGGA 60.245 43.478 10.21 0.00 37.38 4.02
3560 3735 3.963676 TGCAAATGTTGTGCACTCC 57.036 47.368 19.41 8.86 46.76 3.85
3561 3736 1.109609 TGCAAATGTTGTGCACTCCA 58.890 45.000 19.41 14.49 46.76 3.86
3562 3737 1.067364 TGCAAATGTTGTGCACTCCAG 59.933 47.619 19.41 4.34 46.76 3.86
3563 3738 1.603678 GCAAATGTTGTGCACTCCAGG 60.604 52.381 19.41 9.13 41.80 4.45
3564 3739 0.675633 AAATGTTGTGCACTCCAGGC 59.324 50.000 19.41 2.50 0.00 4.85
3567 3742 1.360192 GTTGTGCACTCCAGGCAAC 59.640 57.895 19.41 8.34 43.91 4.17
3568 3743 1.827789 TTGTGCACTCCAGGCAACC 60.828 57.895 19.41 0.00 43.91 3.77
3569 3744 2.985847 GTGCACTCCAGGCAACCC 60.986 66.667 10.32 0.00 43.91 4.11
3570 3745 3.177884 TGCACTCCAGGCAACCCT 61.178 61.111 0.00 0.00 44.25 4.34
3578 3753 3.404773 AGGCAACCCTGGAGTAGC 58.595 61.111 0.00 0.00 40.94 3.58
3582 3766 1.553690 GCAACCCTGGAGTAGCCTGA 61.554 60.000 0.00 0.00 37.79 3.86
3586 3770 1.207791 CCCTGGAGTAGCCTGACAAT 58.792 55.000 0.00 0.00 37.79 2.71
3594 3778 7.241042 TGGAGTAGCCTGACAATAATATACC 57.759 40.000 0.00 0.00 37.63 2.73
3605 3789 8.445275 TGACAATAATATACCGTTTTCTGCAT 57.555 30.769 0.00 0.00 0.00 3.96
3612 3796 2.306847 ACCGTTTTCTGCATTCACCTT 58.693 42.857 0.00 0.00 0.00 3.50
3613 3797 3.482436 ACCGTTTTCTGCATTCACCTTA 58.518 40.909 0.00 0.00 0.00 2.69
3629 3813 5.509498 TCACCTTATATCAGGCAAAAAGCT 58.491 37.500 2.65 0.00 44.79 3.74
3640 3824 3.259123 AGGCAAAAAGCTAAATGTCAGGG 59.741 43.478 0.00 0.00 44.79 4.45
3649 3833 4.400567 AGCTAAATGTCAGGGCAATCTTTC 59.599 41.667 0.00 0.00 0.00 2.62
3650 3834 4.400567 GCTAAATGTCAGGGCAATCTTTCT 59.599 41.667 0.00 0.00 0.00 2.52
3654 3838 4.589216 TGTCAGGGCAATCTTTCTTTTG 57.411 40.909 0.00 0.00 0.00 2.44
3655 3839 3.960102 TGTCAGGGCAATCTTTCTTTTGT 59.040 39.130 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
304 307 1.428912 ACAGAATTTCCTCCAAGGCCA 59.571 47.619 5.01 0.00 34.61 5.36
378 381 2.119484 CTGGCGTTGGTTGGGGACTA 62.119 60.000 0.00 0.00 0.00 2.59
532 536 6.005289 CGTTACGTTGACTGTTATTACAAGC 58.995 40.000 0.00 0.00 32.92 4.01
626 630 4.390909 AGGCCAGTTTAGACGATTTAAACG 59.609 41.667 5.01 8.12 42.80 3.60
774 781 1.948145 CTGCCGAGTACTCCTTCGTAT 59.052 52.381 17.23 0.00 0.00 3.06
830 837 2.060326 TGCTTGTCGTGCTGTACTAC 57.940 50.000 0.00 0.00 0.00 2.73
955 966 2.888447 GCTGCTGGGTCTCACTGGT 61.888 63.158 0.00 0.00 0.00 4.00
1207 1246 4.969196 ACTGTGCGCCGGTGACTG 62.969 66.667 21.76 18.53 0.00 3.51
1208 1247 4.664677 GACTGTGCGCCGGTGACT 62.665 66.667 21.76 0.00 30.89 3.41
1422 1461 1.078918 CTTGTGGCGCTCCATCTCA 60.079 57.895 7.64 0.00 45.62 3.27
1721 1760 0.383590 CTCGAGCAGGATCATGTCGT 59.616 55.000 22.23 5.74 32.49 4.34
2473 2512 1.448497 GGTTCACCTGGTCCGACAA 59.552 57.895 0.00 0.00 0.00 3.18
2697 2741 9.883142 AAAAAGAATGTCAAACTGTAATCCAAA 57.117 25.926 0.00 0.00 0.00 3.28
2726 2775 4.619973 TCAAAACTGTAATGCAAGCCAAG 58.380 39.130 0.00 0.00 0.00 3.61
2739 2790 6.707161 CCAACCAATCAATCAATCAAAACTGT 59.293 34.615 0.00 0.00 0.00 3.55
2795 2851 7.944729 ATATTAACAGGATGCAACTCAAAGT 57.055 32.000 0.00 0.00 42.53 2.66
2822 2878 2.747177 TGTCCCACCAGAATCGAGTAT 58.253 47.619 0.00 0.00 0.00 2.12
2916 3079 1.517257 CCACGACCATGAGAGCGTC 60.517 63.158 0.00 0.00 34.37 5.19
2917 3080 1.938657 CTCCACGACCATGAGAGCGT 61.939 60.000 0.00 0.00 37.48 5.07
2918 3081 1.226802 CTCCACGACCATGAGAGCG 60.227 63.158 0.00 0.00 0.00 5.03
2919 3082 0.532573 TTCTCCACGACCATGAGAGC 59.467 55.000 0.00 0.00 36.57 4.09
2920 3083 3.193263 CAATTCTCCACGACCATGAGAG 58.807 50.000 0.00 0.00 36.57 3.20
2921 3084 2.567169 ACAATTCTCCACGACCATGAGA 59.433 45.455 0.00 0.00 33.50 3.27
2922 3085 2.977914 ACAATTCTCCACGACCATGAG 58.022 47.619 0.00 0.00 0.00 2.90
2923 3086 3.244387 TGAACAATTCTCCACGACCATGA 60.244 43.478 0.00 0.00 0.00 3.07
2924 3087 3.073678 TGAACAATTCTCCACGACCATG 58.926 45.455 0.00 0.00 0.00 3.66
2925 3088 3.417069 TGAACAATTCTCCACGACCAT 57.583 42.857 0.00 0.00 0.00 3.55
2926 3089 2.920724 TGAACAATTCTCCACGACCA 57.079 45.000 0.00 0.00 0.00 4.02
2927 3090 4.215399 TCAATTGAACAATTCTCCACGACC 59.785 41.667 5.45 0.00 38.84 4.79
2928 3091 5.356882 TCAATTGAACAATTCTCCACGAC 57.643 39.130 5.45 0.00 38.84 4.34
2929 3092 4.083324 GCTCAATTGAACAATTCTCCACGA 60.083 41.667 9.88 3.60 38.84 4.35
2930 3093 4.161333 GCTCAATTGAACAATTCTCCACG 58.839 43.478 9.88 0.00 38.84 4.94
2931 3094 5.125100 TGCTCAATTGAACAATTCTCCAC 57.875 39.130 9.07 0.95 38.84 4.02
2932 3095 5.988310 ATGCTCAATTGAACAATTCTCCA 57.012 34.783 15.08 7.45 38.84 3.86
2933 3096 6.401796 GCAAATGCTCAATTGAACAATTCTCC 60.402 38.462 15.08 1.87 37.20 3.71
2934 3097 6.146510 TGCAAATGCTCAATTGAACAATTCTC 59.853 34.615 15.08 8.09 39.21 2.87
2935 3098 5.992829 TGCAAATGCTCAATTGAACAATTCT 59.007 32.000 15.08 0.00 39.21 2.40
2936 3099 6.230849 TGCAAATGCTCAATTGAACAATTC 57.769 33.333 15.08 8.29 39.21 2.17
2937 3100 6.653320 AGATGCAAATGCTCAATTGAACAATT 59.347 30.769 15.08 10.53 40.57 2.32
2938 3101 6.092122 CAGATGCAAATGCTCAATTGAACAAT 59.908 34.615 15.08 4.64 42.66 2.71
2939 3102 5.407084 CAGATGCAAATGCTCAATTGAACAA 59.593 36.000 15.08 0.00 42.66 2.83
2940 3103 4.926832 CAGATGCAAATGCTCAATTGAACA 59.073 37.500 13.61 13.61 42.66 3.18
2941 3104 4.201685 GCAGATGCAAATGCTCAATTGAAC 60.202 41.667 16.81 5.69 42.66 3.18
2942 3105 3.930229 GCAGATGCAAATGCTCAATTGAA 59.070 39.130 16.81 0.00 42.66 2.69
2943 3106 3.517602 GCAGATGCAAATGCTCAATTGA 58.482 40.909 16.81 8.12 42.66 2.57
2944 3107 3.925688 GCAGATGCAAATGCTCAATTG 57.074 42.857 16.81 0.00 42.66 2.32
2957 3120 4.990257 ACAGTCATAAAATGTGCAGATGC 58.010 39.130 0.00 0.00 42.50 3.91
2958 3121 6.963242 GTGTACAGTCATAAAATGTGCAGATG 59.037 38.462 0.00 0.00 39.65 2.90
2959 3122 6.654582 TGTGTACAGTCATAAAATGTGCAGAT 59.345 34.615 0.00 0.00 39.65 2.90
2960 3123 5.994668 TGTGTACAGTCATAAAATGTGCAGA 59.005 36.000 0.00 0.00 39.65 4.26
2961 3124 6.239908 TGTGTACAGTCATAAAATGTGCAG 57.760 37.500 0.00 0.00 39.65 4.41
2962 3125 6.816134 ATGTGTACAGTCATAAAATGTGCA 57.184 33.333 0.00 0.00 37.24 4.57
2963 3126 8.519492 AAAATGTGTACAGTCATAAAATGTGC 57.481 30.769 0.00 0.00 0.00 4.57
2972 3135 9.554724 CGCTAAAATTAAAATGTGTACAGTCAT 57.445 29.630 0.00 0.00 0.00 3.06
2973 3136 8.775527 TCGCTAAAATTAAAATGTGTACAGTCA 58.224 29.630 0.00 0.00 0.00 3.41
2974 3137 9.047871 GTCGCTAAAATTAAAATGTGTACAGTC 57.952 33.333 0.00 0.00 0.00 3.51
2975 3138 8.019094 GGTCGCTAAAATTAAAATGTGTACAGT 58.981 33.333 0.00 0.00 0.00 3.55
2976 3139 8.018520 TGGTCGCTAAAATTAAAATGTGTACAG 58.981 33.333 0.00 0.00 0.00 2.74
2977 3140 7.872881 TGGTCGCTAAAATTAAAATGTGTACA 58.127 30.769 0.00 0.00 0.00 2.90
2978 3141 7.483691 CCTGGTCGCTAAAATTAAAATGTGTAC 59.516 37.037 0.00 0.00 0.00 2.90
2979 3142 7.362229 CCCTGGTCGCTAAAATTAAAATGTGTA 60.362 37.037 0.00 0.00 0.00 2.90
2980 3143 6.386654 CCTGGTCGCTAAAATTAAAATGTGT 58.613 36.000 0.00 0.00 0.00 3.72
2981 3144 5.804979 CCCTGGTCGCTAAAATTAAAATGTG 59.195 40.000 0.00 0.00 0.00 3.21
2982 3145 5.712917 TCCCTGGTCGCTAAAATTAAAATGT 59.287 36.000 0.00 0.00 0.00 2.71
2983 3146 6.094881 TCTCCCTGGTCGCTAAAATTAAAATG 59.905 38.462 0.00 0.00 0.00 2.32
2984 3147 6.184789 TCTCCCTGGTCGCTAAAATTAAAAT 58.815 36.000 0.00 0.00 0.00 1.82
2985 3148 5.562635 TCTCCCTGGTCGCTAAAATTAAAA 58.437 37.500 0.00 0.00 0.00 1.52
2986 3149 5.168647 TCTCCCTGGTCGCTAAAATTAAA 57.831 39.130 0.00 0.00 0.00 1.52
2987 3150 4.829872 TCTCCCTGGTCGCTAAAATTAA 57.170 40.909 0.00 0.00 0.00 1.40
2988 3151 4.829872 TTCTCCCTGGTCGCTAAAATTA 57.170 40.909 0.00 0.00 0.00 1.40
2989 3152 3.713826 TTCTCCCTGGTCGCTAAAATT 57.286 42.857 0.00 0.00 0.00 1.82
2990 3153 3.933861 ATTCTCCCTGGTCGCTAAAAT 57.066 42.857 0.00 0.00 0.00 1.82
2991 3154 3.244770 ACAATTCTCCCTGGTCGCTAAAA 60.245 43.478 0.00 0.00 0.00 1.52
2992 3155 2.304761 ACAATTCTCCCTGGTCGCTAAA 59.695 45.455 0.00 0.00 0.00 1.85
2993 3156 1.906574 ACAATTCTCCCTGGTCGCTAA 59.093 47.619 0.00 0.00 0.00 3.09
2994 3157 1.568504 ACAATTCTCCCTGGTCGCTA 58.431 50.000 0.00 0.00 0.00 4.26
2995 3158 0.693049 AACAATTCTCCCTGGTCGCT 59.307 50.000 0.00 0.00 0.00 4.93
2996 3159 1.087501 GAACAATTCTCCCTGGTCGC 58.912 55.000 0.00 0.00 0.00 5.19
2997 3160 2.289694 ACTGAACAATTCTCCCTGGTCG 60.290 50.000 0.00 0.00 31.56 4.79
2998 3161 3.425162 ACTGAACAATTCTCCCTGGTC 57.575 47.619 0.00 0.00 0.00 4.02
2999 3162 3.138283 TCAACTGAACAATTCTCCCTGGT 59.862 43.478 0.00 0.00 0.00 4.00
3000 3163 3.754965 TCAACTGAACAATTCTCCCTGG 58.245 45.455 0.00 0.00 0.00 4.45
3001 3164 3.190118 GCTCAACTGAACAATTCTCCCTG 59.810 47.826 0.00 0.00 0.00 4.45
3002 3165 3.181440 TGCTCAACTGAACAATTCTCCCT 60.181 43.478 0.00 0.00 0.00 4.20
3003 3166 3.149196 TGCTCAACTGAACAATTCTCCC 58.851 45.455 0.00 0.00 0.00 4.30
3004 3167 5.382618 AATGCTCAACTGAACAATTCTCC 57.617 39.130 0.00 0.00 0.00 3.71
3005 3168 5.118203 GCAAATGCTCAACTGAACAATTCTC 59.882 40.000 0.00 0.00 38.21 2.87
3006 3169 4.986659 GCAAATGCTCAACTGAACAATTCT 59.013 37.500 0.00 0.00 38.21 2.40
3007 3170 4.746115 TGCAAATGCTCAACTGAACAATTC 59.254 37.500 6.97 0.00 42.66 2.17
3008 3171 4.695396 TGCAAATGCTCAACTGAACAATT 58.305 34.783 6.97 0.00 42.66 2.32
3009 3172 4.325028 TGCAAATGCTCAACTGAACAAT 57.675 36.364 6.97 0.00 42.66 2.71
3010 3173 3.797451 TGCAAATGCTCAACTGAACAA 57.203 38.095 6.97 0.00 42.66 2.83
3011 3174 3.491276 CCTTGCAAATGCTCAACTGAACA 60.491 43.478 0.00 0.00 42.66 3.18
3012 3175 3.054878 CCTTGCAAATGCTCAACTGAAC 58.945 45.455 0.00 0.00 42.66 3.18
3013 3176 2.694628 ACCTTGCAAATGCTCAACTGAA 59.305 40.909 0.00 0.00 42.66 3.02
3014 3177 2.294233 GACCTTGCAAATGCTCAACTGA 59.706 45.455 0.00 0.00 42.66 3.41
3015 3178 2.034939 TGACCTTGCAAATGCTCAACTG 59.965 45.455 0.00 0.00 42.66 3.16
3016 3179 2.309613 TGACCTTGCAAATGCTCAACT 58.690 42.857 0.00 0.00 42.66 3.16
3017 3180 2.798976 TGACCTTGCAAATGCTCAAC 57.201 45.000 0.00 0.00 42.66 3.18
3018 3181 3.815856 TTTGACCTTGCAAATGCTCAA 57.184 38.095 0.00 5.45 42.66 3.02
3041 3204 3.777106 ATCAGCCTCAAACAAGACTGA 57.223 42.857 0.00 0.00 38.42 3.41
3053 3216 4.396478 GTGGAAAACCTTAGAATCAGCCTC 59.604 45.833 0.00 0.00 0.00 4.70
3098 3263 2.287009 CGTGGAAGGACAGAAAACTTGC 60.287 50.000 0.00 0.00 33.80 4.01
3141 3306 9.239002 CTACGTCCAGATAAGAAAAGAGTTATG 57.761 37.037 0.00 0.00 0.00 1.90
3163 3328 3.969899 TGCTGAATGCTGATCTACTACG 58.030 45.455 0.00 0.00 43.37 3.51
3168 3333 3.314357 GCATGTTGCTGAATGCTGATCTA 59.686 43.478 9.80 0.00 44.64 1.98
3169 3334 2.099263 GCATGTTGCTGAATGCTGATCT 59.901 45.455 9.80 0.00 44.64 2.75
3170 3335 2.460918 GCATGTTGCTGAATGCTGATC 58.539 47.619 9.80 0.00 44.64 2.92
3172 3337 0.169451 CGCATGTTGCTGAATGCTGA 59.831 50.000 13.58 0.00 45.62 4.26
3173 3338 1.410737 GCGCATGTTGCTGAATGCTG 61.411 55.000 0.30 9.48 45.62 4.41
3174 3339 1.153901 GCGCATGTTGCTGAATGCT 60.154 52.632 0.30 0.00 45.62 3.79
3175 3340 2.502123 CGCGCATGTTGCTGAATGC 61.502 57.895 8.75 7.68 42.25 3.56
3176 3341 1.870458 CCGCGCATGTTGCTGAATG 60.870 57.895 8.75 0.00 42.25 2.67
3177 3342 1.378882 ATCCGCGCATGTTGCTGAAT 61.379 50.000 8.75 0.00 42.25 2.57
3178 3343 2.039974 ATCCGCGCATGTTGCTGAA 61.040 52.632 8.75 0.00 42.25 3.02
3179 3344 2.436469 ATCCGCGCATGTTGCTGA 60.436 55.556 8.75 8.98 42.25 4.26
3180 3345 2.277692 CATCCGCGCATGTTGCTG 60.278 61.111 8.75 4.29 42.25 4.41
3181 3346 4.183686 GCATCCGCGCATGTTGCT 62.184 61.111 12.36 0.00 42.25 3.91
3246 3411 5.470437 TGACTAGAGTAGAAGCATCATACGG 59.530 44.000 0.00 0.00 0.00 4.02
3251 3416 5.534278 CCTGATGACTAGAGTAGAAGCATCA 59.466 44.000 0.00 0.00 38.57 3.07
3334 3504 0.179020 CTGGGCGCTTCCATTCCATA 60.179 55.000 7.64 0.00 36.05 2.74
3362 3532 9.546428 AACTGAATTGGTATCAAAAGGAAAAAG 57.454 29.630 0.00 0.00 36.36 2.27
3386 3556 1.736681 GATGCTGCTCACTGGAAGAAC 59.263 52.381 0.00 0.00 37.43 3.01
3452 3625 1.494628 GCATATGCGTCGATGCTGG 59.505 57.895 28.53 16.27 44.15 4.85
3511 3684 3.129287 GTCCACTGCCAAGTTGATAATGG 59.871 47.826 3.87 7.10 32.98 3.16
3512 3685 3.129287 GGTCCACTGCCAAGTTGATAATG 59.871 47.826 3.87 0.00 32.98 1.90
3513 3686 3.356290 GGTCCACTGCCAAGTTGATAAT 58.644 45.455 3.87 0.00 32.98 1.28
3525 3700 1.959085 CACATGTTGGGTCCACTGC 59.041 57.895 0.00 0.00 0.00 4.40
3528 3703 0.749649 TTTGCACATGTTGGGTCCAC 59.250 50.000 0.00 0.00 0.00 4.02
3560 3735 1.078143 GCTACTCCAGGGTTGCCTG 60.078 63.158 0.00 0.00 37.54 4.85
3561 3736 3.404773 GCTACTCCAGGGTTGCCT 58.595 61.111 0.00 0.00 33.26 4.75
3562 3737 2.272471 GGCTACTCCAGGGTTGCC 59.728 66.667 7.38 7.38 46.61 4.52
3563 3738 1.078143 CAGGCTACTCCAGGGTTGC 60.078 63.158 0.00 0.00 37.26 4.17
3564 3739 0.250513 GTCAGGCTACTCCAGGGTTG 59.749 60.000 0.00 0.00 37.29 3.77
3567 3742 1.207791 ATTGTCAGGCTACTCCAGGG 58.792 55.000 0.00 0.00 37.29 4.45
3568 3743 4.696479 ATTATTGTCAGGCTACTCCAGG 57.304 45.455 0.00 0.00 37.29 4.45
3569 3744 7.324178 GGTATATTATTGTCAGGCTACTCCAG 58.676 42.308 0.00 0.00 37.29 3.86
3570 3745 6.071560 CGGTATATTATTGTCAGGCTACTCCA 60.072 42.308 0.00 0.00 37.29 3.86
3571 3746 6.071503 ACGGTATATTATTGTCAGGCTACTCC 60.072 42.308 0.00 0.00 0.00 3.85
3573 3748 6.912951 ACGGTATATTATTGTCAGGCTACT 57.087 37.500 0.00 0.00 0.00 2.57
3575 3750 8.426489 AGAAAACGGTATATTATTGTCAGGCTA 58.574 33.333 0.00 0.00 0.00 3.93
3577 3752 7.352739 CAGAAAACGGTATATTATTGTCAGGC 58.647 38.462 0.00 0.00 0.00 4.85
3578 3753 7.011950 TGCAGAAAACGGTATATTATTGTCAGG 59.988 37.037 0.00 0.00 0.00 3.86
3582 3766 8.898761 TGAATGCAGAAAACGGTATATTATTGT 58.101 29.630 0.00 0.00 0.00 2.71
3586 3770 7.051623 AGGTGAATGCAGAAAACGGTATATTA 58.948 34.615 0.00 0.00 0.00 0.98
3594 3778 7.015226 TGATATAAGGTGAATGCAGAAAACG 57.985 36.000 0.00 0.00 0.00 3.60
3605 3789 5.951747 AGCTTTTTGCCTGATATAAGGTGAA 59.048 36.000 8.02 0.62 44.23 3.18
3612 3796 8.518430 TGACATTTAGCTTTTTGCCTGATATA 57.482 30.769 0.00 0.00 44.23 0.86
3613 3797 7.408756 TGACATTTAGCTTTTTGCCTGATAT 57.591 32.000 0.00 0.00 44.23 1.63
3629 3813 6.916360 AAAGAAAGATTGCCCTGACATTTA 57.084 33.333 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.