Multiple sequence alignment - TraesCS4B01G132000

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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 TraesCS4B01G132000 chr4B 100.000 3920 0 0 1 3920 172376955 172380874 0.000000e+00 7239.0
1 TraesCS4B01G132000 chr4B 75.870 460 91 15 2041 2481 171142245 171141787 2.370000e-52 217.0
2 TraesCS4B01G132000 chr4B 87.209 86 6 5 2996 3077 32425882 32425798 4.170000e-15 93.5
3 TraesCS4B01G132000 chr4B 87.500 72 6 2 2977 3045 339894755 339894684 3.250000e-11 80.5
4 TraesCS4B01G132000 chr4B 84.932 73 10 1 2994 3066 142519128 142519199 5.430000e-09 73.1
5 TraesCS4B01G132000 chr4B 95.238 42 2 0 864 905 500870406 500870365 2.530000e-07 67.6
6 TraesCS4B01G132000 chr4B 79.570 93 17 2 814 905 630482063 630482154 9.090000e-07 65.8
7 TraesCS4B01G132000 chr4A 94.992 2975 94 20 1 2957 465548772 465545835 0.000000e+00 4617.0
8 TraesCS4B01G132000 chr4A 93.782 386 21 3 3036 3418 465545769 465545384 9.440000e-161 577.0
9 TraesCS4B01G132000 chr4A 97.015 335 9 1 3587 3920 465545047 465544713 2.640000e-156 562.0
10 TraesCS4B01G132000 chr4A 75.427 468 88 18 2041 2481 465891101 465890634 6.640000e-48 202.0
11 TraesCS4B01G132000 chr4A 94.792 96 4 1 3417 3512 465545351 465545257 8.780000e-32 148.0
12 TraesCS4B01G132000 chr4A 95.238 42 2 0 864 905 61617601 61617560 2.530000e-07 67.6
13 TraesCS4B01G132000 chr4D 95.589 2675 85 14 298 2964 111584813 111587462 0.000000e+00 4255.0
14 TraesCS4B01G132000 chr4D 94.882 508 21 4 3417 3920 111587903 111588409 0.000000e+00 789.0
15 TraesCS4B01G132000 chr4D 73.558 2254 441 103 486 2626 111053257 111055468 0.000000e+00 717.0
16 TraesCS4B01G132000 chr4D 91.214 387 24 5 3038 3418 111587488 111587870 5.810000e-143 518.0
17 TraesCS4B01G132000 chr4D 88.672 256 14 6 1 256 111584573 111584813 8.230000e-77 298.0
18 TraesCS4B01G132000 chr4D 95.238 42 2 0 864 905 404112985 404112944 2.530000e-07 67.6
19 TraesCS4B01G132000 chr5D 81.579 152 13 6 1 138 467760052 467759902 1.150000e-20 111.0
20 TraesCS4B01G132000 chr5D 86.842 76 4 5 2977 3047 546015942 546015868 3.250000e-11 80.5
21 TraesCS4B01G132000 chr3A 90.244 82 8 0 3046 3127 95018428 95018347 1.490000e-19 108.0
22 TraesCS4B01G132000 chr3A 91.525 59 5 0 3079 3137 427779557 427779499 9.030000e-12 82.4
23 TraesCS4B01G132000 chr2A 92.424 66 4 1 2977 3042 762890646 762890710 4.170000e-15 93.5
24 TraesCS4B01G132000 chr2A 88.889 63 5 2 3076 3137 150913988 150914049 4.200000e-10 76.8
25 TraesCS4B01G132000 chr2A 89.831 59 6 0 3079 3137 733413994 733413936 4.200000e-10 76.8
26 TraesCS4B01G132000 chr2A 100.000 33 0 0 2581 2613 608047285 608047317 1.180000e-05 62.1
27 TraesCS4B01G132000 chr5A 87.342 79 6 4 2994 3070 569715224 569715148 1.940000e-13 87.9
28 TraesCS4B01G132000 chr1B 93.333 60 2 2 2994 3053 400753361 400753304 1.940000e-13 87.9
29 TraesCS4B01G132000 chr1D 88.000 75 5 3 2994 3067 469018639 469018710 6.980000e-13 86.1
30 TraesCS4B01G132000 chr5B 87.013 77 6 3 2970 3043 533269738 533269663 2.510000e-12 84.2
31 TraesCS4B01G132000 chr3B 97.872 47 1 0 3079 3125 126578553 126578599 9.030000e-12 82.4
32 TraesCS4B01G132000 chr3B 84.270 89 8 6 2994 3078 178387615 178387529 9.030000e-12 82.4
33 TraesCS4B01G132000 chr3B 92.593 54 4 0 3081 3134 125576560 125576613 1.170000e-10 78.7
34 TraesCS4B01G132000 chrUn 92.593 54 4 0 3081 3134 478962443 478962496 1.170000e-10 78.7
35 TraesCS4B01G132000 chr7D 95.833 48 2 0 2566 2613 458726718 458726765 1.170000e-10 78.7
36 TraesCS4B01G132000 chr7B 95.833 48 2 0 2566 2613 480694804 480694851 1.170000e-10 78.7
37 TraesCS4B01G132000 chr7A 93.750 48 3 0 2566 2613 541383460 541383413 5.430000e-09 73.1
38 TraesCS4B01G132000 chr2B 84.211 76 8 4 2994 3069 25022370 25022299 1.950000e-08 71.3
39 TraesCS4B01G132000 chr2B 100.000 33 0 0 2581 2613 546614954 546614986 1.180000e-05 62.1
40 TraesCS4B01G132000 chr6B 87.302 63 3 4 3011 3070 689088738 689088678 2.530000e-07 67.6


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 TraesCS4B01G132000 chr4B 172376955 172380874 3919 False 7239 7239 100.00000 1 3920 1 chr4B.!!$F2 3919
1 TraesCS4B01G132000 chr4A 465544713 465548772 4059 True 1476 4617 95.14525 1 3920 4 chr4A.!!$R3 3919
2 TraesCS4B01G132000 chr4D 111584573 111588409 3836 False 1465 4255 92.58925 1 3920 4 chr4D.!!$F2 3919
3 TraesCS4B01G132000 chr4D 111053257 111055468 2211 False 717 717 73.55800 486 2626 1 chr4D.!!$F1 2140

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
258 272 0.714994 TTGATTACGTTACGTGCCGC 59.285 50.0 21.22 7.68 41.39 6.53 F
314 328 1.059942 GCCAAACAATTCTTTCCGCG 58.940 50.0 0.00 0.00 0.00 6.46 F
1126 1156 0.685785 TGAGGCAGAGCTCGATTCCT 60.686 55.0 8.37 12.84 0.00 3.36 F
2541 2658 0.039035 GAACAAGGGGGTACATGGCA 59.961 55.0 0.00 0.00 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1107 1137 0.685785 AGGAATCGAGCTCTGCCTCA 60.686 55.0 12.85 0.0 0.00 3.86 R
1327 1357 0.737715 GAAGGCGTGTAGAGGCACAG 60.738 60.0 6.89 0.0 39.19 3.66 R
2626 2743 0.328258 ACCCAATCCGAAACCCTCTG 59.672 55.0 0.00 0.0 0.00 3.35 R
3663 3988 0.979709 CATGCCTGGAGGAGGACAGA 60.980 60.0 0.00 0.0 46.33 3.41 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
83 84 1.673400 CGTGTGATCCAACACCAACAA 59.327 47.619 9.94 0.00 46.29 2.83
87 88 1.944024 TGATCCAACACCAACAACGTC 59.056 47.619 0.00 0.00 0.00 4.34
116 117 7.435192 GTGTTTTTCTTACTGTATTTGCTTGCT 59.565 33.333 0.00 0.00 0.00 3.91
161 172 2.353323 GTCCCATTACCGGAACAAGTC 58.647 52.381 9.46 0.00 0.00 3.01
170 181 1.574702 CGGAACAAGTCGGGCCTTTC 61.575 60.000 0.84 0.00 0.00 2.62
183 194 0.973496 GCCTTTCTCCTCCTCGTCCT 60.973 60.000 0.00 0.00 0.00 3.85
184 195 1.685491 GCCTTTCTCCTCCTCGTCCTA 60.685 57.143 0.00 0.00 0.00 2.94
185 196 2.303175 CCTTTCTCCTCCTCGTCCTAG 58.697 57.143 0.00 0.00 0.00 3.02
194 205 1.445716 CCTCGTCCTAGTACTGCCCG 61.446 65.000 5.39 2.80 0.00 6.13
258 272 0.714994 TTGATTACGTTACGTGCCGC 59.285 50.000 21.22 7.68 41.39 6.53
259 273 1.077645 TGATTACGTTACGTGCCGCC 61.078 55.000 21.22 5.76 41.39 6.13
260 274 2.069743 GATTACGTTACGTGCCGCCG 62.070 60.000 21.22 0.00 41.39 6.46
264 278 2.810458 GTTACGTGCCGCCGCTAA 60.810 61.111 0.00 0.00 35.36 3.09
265 279 2.810458 TTACGTGCCGCCGCTAAC 60.810 61.111 0.00 0.00 35.36 2.34
266 280 3.285523 TTACGTGCCGCCGCTAACT 62.286 57.895 0.00 0.00 35.36 2.24
267 281 2.768503 TTACGTGCCGCCGCTAACTT 62.769 55.000 0.00 0.00 35.36 2.66
314 328 1.059942 GCCAAACAATTCTTTCCGCG 58.940 50.000 0.00 0.00 0.00 6.46
325 339 3.758973 TTTCCGCGGTGACAGCCAA 62.759 57.895 27.15 6.25 0.00 4.52
326 340 3.758973 TTCCGCGGTGACAGCCAAA 62.759 57.895 27.15 5.40 0.00 3.28
1107 1137 3.375299 GCAAGATCTACAATTTCAGCCGT 59.625 43.478 0.00 0.00 0.00 5.68
1126 1156 0.685785 TGAGGCAGAGCTCGATTCCT 60.686 55.000 8.37 12.84 0.00 3.36
1131 1161 1.830408 AGAGCTCGATTCCTCGGGG 60.830 63.158 8.37 0.00 45.80 5.73
1149 1179 1.811860 GCATTTCTTGGCCAGCGAT 59.188 52.632 5.11 0.00 0.00 4.58
1293 1323 1.299976 GATGGCGTTCTCCAACCCT 59.700 57.895 0.00 0.00 39.96 4.34
1831 1879 2.594592 GCAACCAGGGCAAGTCGT 60.595 61.111 0.00 0.00 0.00 4.34
2038 2098 2.429930 CCACCAGGAAGTTCCGCA 59.570 61.111 16.31 0.00 42.75 5.69
2217 2286 1.685224 GATGTGGGGGTTCTGCTCA 59.315 57.895 0.00 0.00 0.00 4.26
2541 2658 0.039035 GAACAAGGGGGTACATGGCA 59.961 55.000 0.00 0.00 0.00 4.92
2626 2743 1.004745 TCCTGGAACTGATGAAAGGGC 59.995 52.381 0.00 0.00 0.00 5.19
2637 2754 0.250727 TGAAAGGGCAGAGGGTTTCG 60.251 55.000 0.00 0.00 32.58 3.46
2703 2820 1.135083 ACCGTGGTGAAGATGATCGTC 60.135 52.381 6.84 6.84 0.00 4.20
2760 2877 1.002134 CCTGGTGGATGAACGGCTT 60.002 57.895 0.00 0.00 34.57 4.35
2878 2995 1.756430 AGTGCAGACGCTCATCTCTA 58.244 50.000 0.00 0.00 39.64 2.43
2957 3074 4.760878 ACATGTGTTAGTGTGTGTGTGTA 58.239 39.130 0.00 0.00 0.00 2.90
2960 3077 6.422701 ACATGTGTTAGTGTGTGTGTGTATAC 59.577 38.462 0.00 0.00 0.00 1.47
2961 3078 5.903810 TGTGTTAGTGTGTGTGTGTATACA 58.096 37.500 0.08 0.08 0.00 2.29
2962 3079 5.980715 TGTGTTAGTGTGTGTGTGTATACAG 59.019 40.000 5.62 0.00 37.52 2.74
2963 3080 4.986034 TGTTAGTGTGTGTGTGTATACAGC 59.014 41.667 5.62 3.16 37.52 4.40
2965 3082 3.914312 AGTGTGTGTGTGTATACAGCTC 58.086 45.455 5.62 4.41 37.52 4.09
2966 3083 3.320826 AGTGTGTGTGTGTATACAGCTCA 59.679 43.478 5.62 6.88 37.52 4.26
2967 3084 4.021104 AGTGTGTGTGTGTATACAGCTCAT 60.021 41.667 5.62 0.00 37.52 2.90
2968 3085 4.327357 GTGTGTGTGTGTATACAGCTCATC 59.673 45.833 5.62 7.07 37.52 2.92
2969 3086 4.220602 TGTGTGTGTGTATACAGCTCATCT 59.779 41.667 5.62 0.00 37.52 2.90
2970 3087 4.800993 GTGTGTGTGTATACAGCTCATCTC 59.199 45.833 5.62 0.00 37.52 2.75
2971 3088 4.706962 TGTGTGTGTATACAGCTCATCTCT 59.293 41.667 5.62 0.00 37.52 3.10
2972 3089 5.039984 GTGTGTGTATACAGCTCATCTCTG 58.960 45.833 5.62 0.00 37.52 3.35
2973 3090 4.047822 GTGTGTATACAGCTCATCTCTGC 58.952 47.826 5.62 0.00 37.52 4.26
2974 3091 3.701040 TGTGTATACAGCTCATCTCTGCA 59.299 43.478 5.62 0.00 35.04 4.41
2976 3093 4.037327 GTGTATACAGCTCATCTCTGCAGA 59.963 45.833 17.19 17.19 35.04 4.26
2977 3094 3.731652 ATACAGCTCATCTCTGCAGAC 57.268 47.619 13.74 1.43 35.04 3.51
2978 3095 0.173029 ACAGCTCATCTCTGCAGACG 59.827 55.000 13.74 9.51 35.04 4.18
2980 3097 0.682532 AGCTCATCTCTGCAGACGGA 60.683 55.000 13.74 10.44 0.00 4.69
2981 3098 0.388659 GCTCATCTCTGCAGACGGAT 59.611 55.000 13.74 12.48 0.00 4.18
2982 3099 1.868930 GCTCATCTCTGCAGACGGATG 60.869 57.143 27.93 27.93 37.49 3.51
2983 3100 1.408340 CTCATCTCTGCAGACGGATGT 59.592 52.381 30.26 8.83 37.44 3.06
2984 3101 2.620585 CTCATCTCTGCAGACGGATGTA 59.379 50.000 30.26 21.18 37.44 2.29
2985 3102 3.225940 TCATCTCTGCAGACGGATGTAT 58.774 45.455 30.26 7.97 37.44 2.29
2986 3103 3.254411 TCATCTCTGCAGACGGATGTATC 59.746 47.826 30.26 0.00 37.44 2.24
2987 3104 2.654863 TCTCTGCAGACGGATGTATCA 58.345 47.619 13.74 0.00 0.00 2.15
2988 3105 3.023832 TCTCTGCAGACGGATGTATCAA 58.976 45.455 13.74 0.00 0.00 2.57
2990 3107 1.863454 CTGCAGACGGATGTATCAAGC 59.137 52.381 8.42 0.00 0.00 4.01
2991 3108 1.221414 GCAGACGGATGTATCAAGCC 58.779 55.000 0.00 0.00 0.00 4.35
2992 3109 1.473257 GCAGACGGATGTATCAAGCCA 60.473 52.381 0.00 0.00 0.00 4.75
2993 3110 2.205074 CAGACGGATGTATCAAGCCAC 58.795 52.381 0.00 0.00 0.00 5.01
2994 3111 1.202417 AGACGGATGTATCAAGCCACG 60.202 52.381 0.00 0.00 0.00 4.94
2995 3112 0.535335 ACGGATGTATCAAGCCACGT 59.465 50.000 0.00 0.00 0.00 4.49
2996 3113 1.752498 ACGGATGTATCAAGCCACGTA 59.248 47.619 0.00 0.00 0.00 3.57
2997 3114 2.364324 ACGGATGTATCAAGCCACGTAT 59.636 45.455 0.00 0.00 0.00 3.06
2998 3115 2.987149 CGGATGTATCAAGCCACGTATC 59.013 50.000 0.00 0.00 0.00 2.24
2999 3116 3.305403 CGGATGTATCAAGCCACGTATCT 60.305 47.826 0.00 0.00 0.00 1.98
3000 3117 4.082949 CGGATGTATCAAGCCACGTATCTA 60.083 45.833 0.00 0.00 0.00 1.98
3001 3118 5.403246 GGATGTATCAAGCCACGTATCTAG 58.597 45.833 0.00 0.00 0.00 2.43
3002 3119 5.183331 GGATGTATCAAGCCACGTATCTAGA 59.817 44.000 0.00 0.00 0.00 2.43
3003 3120 5.434352 TGTATCAAGCCACGTATCTAGAC 57.566 43.478 0.00 0.00 0.00 2.59
3004 3121 4.885325 TGTATCAAGCCACGTATCTAGACA 59.115 41.667 0.00 0.00 0.00 3.41
3005 3122 5.358725 TGTATCAAGCCACGTATCTAGACAA 59.641 40.000 0.00 0.00 0.00 3.18
3006 3123 4.371855 TCAAGCCACGTATCTAGACAAG 57.628 45.455 0.00 0.00 0.00 3.16
3007 3124 3.762288 TCAAGCCACGTATCTAGACAAGT 59.238 43.478 0.00 0.00 0.00 3.16
3008 3125 4.219944 TCAAGCCACGTATCTAGACAAGTT 59.780 41.667 0.00 0.00 0.00 2.66
3009 3126 4.803098 AGCCACGTATCTAGACAAGTTT 57.197 40.909 0.00 0.00 0.00 2.66
3011 3128 6.276832 AGCCACGTATCTAGACAAGTTTAA 57.723 37.500 0.00 0.00 0.00 1.52
3012 3129 6.331061 AGCCACGTATCTAGACAAGTTTAAG 58.669 40.000 0.00 0.00 0.00 1.85
3014 3131 6.253083 GCCACGTATCTAGACAAGTTTAAGAC 59.747 42.308 0.00 0.00 0.00 3.01
3016 3133 7.811236 CCACGTATCTAGACAAGTTTAAGACAA 59.189 37.037 0.00 0.00 0.00 3.18
3017 3134 8.851416 CACGTATCTAGACAAGTTTAAGACAAG 58.149 37.037 0.00 0.00 0.00 3.16
3019 3136 9.622004 CGTATCTAGACAAGTTTAAGACAAGAA 57.378 33.333 0.00 0.00 0.00 2.52
3026 3143 8.197439 AGACAAGTTTAAGACAAGAATTTTGGG 58.803 33.333 5.68 0.00 0.00 4.12
3028 3145 7.979537 ACAAGTTTAAGACAAGAATTTTGGGAC 59.020 33.333 5.68 0.00 0.00 4.46
3029 3146 6.735130 AGTTTAAGACAAGAATTTTGGGACG 58.265 36.000 5.68 0.00 0.00 4.79
3030 3147 5.699097 TTAAGACAAGAATTTTGGGACGG 57.301 39.130 0.00 0.00 0.00 4.79
3031 3148 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3032 3149 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3034 3151 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3035 3152 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
3036 3153 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
3037 3154 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
3038 3155 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3039 3156 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
3040 3157 2.852714 TTTGGGACGGAGGGAGTATA 57.147 50.000 0.00 0.00 0.00 1.47
3041 3158 3.339713 TTTGGGACGGAGGGAGTATAT 57.660 47.619 0.00 0.00 0.00 0.86
3042 3159 3.339713 TTGGGACGGAGGGAGTATATT 57.660 47.619 0.00 0.00 0.00 1.28
3043 3160 4.474303 TTGGGACGGAGGGAGTATATTA 57.526 45.455 0.00 0.00 0.00 0.98
3044 3161 4.687262 TGGGACGGAGGGAGTATATTAT 57.313 45.455 0.00 0.00 0.00 1.28
3045 3162 5.019657 TGGGACGGAGGGAGTATATTATT 57.980 43.478 0.00 0.00 0.00 1.40
3073 3190 4.513442 CCTCCGATCCAAAATAAGTGTCA 58.487 43.478 0.00 0.00 0.00 3.58
3076 3193 5.309638 TCCGATCCAAAATAAGTGTCACAA 58.690 37.500 5.62 0.00 0.00 3.33
3077 3194 5.180492 TCCGATCCAAAATAAGTGTCACAAC 59.820 40.000 5.62 0.00 0.00 3.32
3099 3216 4.947388 ACTCAACCTTAGTTCAAAACTGCA 59.053 37.500 2.65 0.00 42.84 4.41
3162 3279 7.601886 CCCACAAATTATGTCTTTGTTAATGCA 59.398 33.333 0.00 0.00 42.58 3.96
3278 3396 5.073554 TGGTATCATAGCTGATTTGGGACAT 59.926 40.000 0.00 0.00 42.23 3.06
3333 3454 0.034670 AGTCCTGCTGCATTTCCTCC 60.035 55.000 1.31 0.00 0.00 4.30
3334 3455 1.034292 GTCCTGCTGCATTTCCTCCC 61.034 60.000 1.31 0.00 0.00 4.30
3351 3472 2.493278 CTCCCGTTGCCAGATGAAAAAT 59.507 45.455 0.00 0.00 0.00 1.82
3391 3513 8.523658 TGTCATACATAGAACACCTATATCAGC 58.476 37.037 0.00 0.00 35.96 4.26
3396 3518 2.036475 AGAACACCTATATCAGCTGGCG 59.964 50.000 15.13 0.00 0.00 5.69
3594 3918 5.643348 TGCACAAGGATACAACTATGTTCAG 59.357 40.000 0.00 0.00 41.05 3.02
3621 3946 5.647658 TCAAACTGAAGCTTCTTCAACTGAA 59.352 36.000 26.09 2.72 0.00 3.02
3663 3988 2.676748 TCCATTGTTGGCCTGTTCTTT 58.323 42.857 3.32 0.00 43.29 2.52
3728 4053 2.742053 TCGCTTGCAGGTAGTTGAAATC 59.258 45.455 0.00 0.00 0.00 2.17
3845 4170 3.270433 ACATGGACATCCTCCTCCAAATT 59.730 43.478 0.00 0.00 40.05 1.82
3897 4222 4.632153 ACACTAGTTCAAGAAGCACGATT 58.368 39.130 0.00 0.00 0.00 3.34
3900 4225 2.069273 AGTTCAAGAAGCACGATTCCG 58.931 47.619 0.00 0.00 42.50 4.30
3912 4237 2.554806 CGATTCCGTAGCTGTACACA 57.445 50.000 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 7.781548 ATACAGTAAGAAAAACACTTGACGT 57.218 32.000 0.00 0.00 0.00 4.34
87 88 8.856490 AGCAAATACAGTAAGAAAAACACTTG 57.144 30.769 0.00 0.00 0.00 3.16
156 167 0.391793 GAGGAGAAAGGCCCGACTTG 60.392 60.000 0.00 0.00 0.00 3.16
161 172 2.904131 GAGGAGGAGAAAGGCCCG 59.096 66.667 0.00 0.00 0.00 6.13
170 181 2.841215 CAGTACTAGGACGAGGAGGAG 58.159 57.143 0.00 0.00 0.00 3.69
206 217 3.624410 GGTCGCCGGAGTTTGTAATATTT 59.376 43.478 5.05 0.00 0.00 1.40
207 218 3.200483 GGTCGCCGGAGTTTGTAATATT 58.800 45.455 5.05 0.00 0.00 1.28
208 219 2.800629 CGGTCGCCGGAGTTTGTAATAT 60.801 50.000 5.05 0.00 44.15 1.28
209 220 1.469595 CGGTCGCCGGAGTTTGTAATA 60.470 52.381 5.05 0.00 44.15 0.98
210 221 0.738412 CGGTCGCCGGAGTTTGTAAT 60.738 55.000 5.05 0.00 44.15 1.89
258 272 5.051153 GGAAAAGGATAGAGAAGTTAGCGG 58.949 45.833 0.00 0.00 0.00 5.52
259 273 5.051153 GGGAAAAGGATAGAGAAGTTAGCG 58.949 45.833 0.00 0.00 0.00 4.26
260 274 5.051153 CGGGAAAAGGATAGAGAAGTTAGC 58.949 45.833 0.00 0.00 0.00 3.09
261 275 6.466885 TCGGGAAAAGGATAGAGAAGTTAG 57.533 41.667 0.00 0.00 0.00 2.34
262 276 6.041751 GGATCGGGAAAAGGATAGAGAAGTTA 59.958 42.308 0.00 0.00 0.00 2.24
263 277 5.163290 GGATCGGGAAAAGGATAGAGAAGTT 60.163 44.000 0.00 0.00 0.00 2.66
264 278 4.345547 GGATCGGGAAAAGGATAGAGAAGT 59.654 45.833 0.00 0.00 0.00 3.01
265 279 4.559704 CGGATCGGGAAAAGGATAGAGAAG 60.560 50.000 0.00 0.00 0.00 2.85
266 280 3.321111 CGGATCGGGAAAAGGATAGAGAA 59.679 47.826 0.00 0.00 0.00 2.87
267 281 2.891580 CGGATCGGGAAAAGGATAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
314 328 0.606401 TAGCTGCTTTGGCTGTCACC 60.606 55.000 7.79 0.00 40.52 4.02
325 339 1.819288 TCGTTAGTGCTCTAGCTGCTT 59.181 47.619 7.79 0.00 42.66 3.91
326 340 1.464734 TCGTTAGTGCTCTAGCTGCT 58.535 50.000 7.57 7.57 42.66 4.24
424 439 4.631247 AAGCAGAGCACAGCCGCA 62.631 61.111 0.00 0.00 0.00 5.69
1107 1137 0.685785 AGGAATCGAGCTCTGCCTCA 60.686 55.000 12.85 0.00 0.00 3.86
1113 1143 1.830408 CCCCGAGGAATCGAGCTCT 60.830 63.158 12.85 0.00 33.47 4.09
1126 1156 2.362375 GGCCAAGAAATGCCCCGA 60.362 61.111 0.00 0.00 41.97 5.14
1131 1161 1.024271 TATCGCTGGCCAAGAAATGC 58.976 50.000 7.01 4.30 0.00 3.56
1293 1323 2.046411 ACGCCGTGGATGATGCAA 60.046 55.556 0.00 0.00 0.00 4.08
1327 1357 0.737715 GAAGGCGTGTAGAGGCACAG 60.738 60.000 6.89 0.00 39.19 3.66
1450 1480 2.251642 GCGCCACGAACTTCACCTT 61.252 57.895 0.00 0.00 0.00 3.50
1482 1518 1.125093 TGAGGTCGAAGCCCCAGAAA 61.125 55.000 0.00 0.00 0.00 2.52
1831 1879 7.893124 AGAATCCGTAGAAGTAGAACCATAA 57.107 36.000 0.00 0.00 0.00 1.90
2506 2602 2.344981 TTCCTCGGATCCGCGACAA 61.345 57.895 29.62 15.77 39.59 3.18
2626 2743 0.328258 ACCCAATCCGAAACCCTCTG 59.672 55.000 0.00 0.00 0.00 3.35
2637 2754 1.076044 CCCATCCACCACCCAATCC 60.076 63.158 0.00 0.00 0.00 3.01
2760 2877 2.223456 CGCATGGTTAAATTCGCCATCA 60.223 45.455 0.00 0.00 40.68 3.07
2775 2892 4.318263 GCAAATATTTTAGCTTGCGCATGG 60.318 41.667 22.96 14.79 39.10 3.66
2878 2995 6.781507 TCATTATCTCTGGACTCATCATCTGT 59.218 38.462 0.00 0.00 0.00 3.41
2957 3074 2.034432 CGTCTGCAGAGATGAGCTGTAT 59.966 50.000 18.89 0.00 37.41 2.29
2960 3077 0.528033 CCGTCTGCAGAGATGAGCTG 60.528 60.000 18.89 0.00 37.41 4.24
2961 3078 0.682532 TCCGTCTGCAGAGATGAGCT 60.683 55.000 18.89 0.00 37.41 4.09
2962 3079 0.388659 ATCCGTCTGCAGAGATGAGC 59.611 55.000 18.89 2.83 37.41 4.26
2963 3080 1.408340 ACATCCGTCTGCAGAGATGAG 59.592 52.381 34.98 21.72 38.72 2.90
2965 3082 3.005155 TGATACATCCGTCTGCAGAGATG 59.995 47.826 30.23 30.23 41.50 2.90
2966 3083 3.225940 TGATACATCCGTCTGCAGAGAT 58.774 45.455 18.89 14.58 0.00 2.75
2967 3084 2.654863 TGATACATCCGTCTGCAGAGA 58.345 47.619 18.89 12.69 0.00 3.10
2968 3085 3.379240 CTTGATACATCCGTCTGCAGAG 58.621 50.000 18.89 11.25 0.00 3.35
2969 3086 2.481969 GCTTGATACATCCGTCTGCAGA 60.482 50.000 13.74 13.74 0.00 4.26
2970 3087 1.863454 GCTTGATACATCCGTCTGCAG 59.137 52.381 7.63 7.63 0.00 4.41
2971 3088 1.473257 GGCTTGATACATCCGTCTGCA 60.473 52.381 0.00 0.00 0.00 4.41
2972 3089 1.221414 GGCTTGATACATCCGTCTGC 58.779 55.000 0.00 0.00 0.00 4.26
2973 3090 2.205074 GTGGCTTGATACATCCGTCTG 58.795 52.381 0.00 0.00 0.00 3.51
2974 3091 1.202417 CGTGGCTTGATACATCCGTCT 60.202 52.381 0.00 0.00 0.00 4.18
2976 3093 0.535335 ACGTGGCTTGATACATCCGT 59.465 50.000 0.00 0.00 0.00 4.69
2977 3094 2.502213 TACGTGGCTTGATACATCCG 57.498 50.000 0.00 0.00 0.00 4.18
2978 3095 4.258702 AGATACGTGGCTTGATACATCC 57.741 45.455 0.00 0.00 0.00 3.51
2980 3097 5.535030 TGTCTAGATACGTGGCTTGATACAT 59.465 40.000 0.00 0.00 0.00 2.29
2981 3098 4.885325 TGTCTAGATACGTGGCTTGATACA 59.115 41.667 0.00 0.00 0.00 2.29
2982 3099 5.434352 TGTCTAGATACGTGGCTTGATAC 57.566 43.478 0.00 0.00 0.00 2.24
2983 3100 5.593095 ACTTGTCTAGATACGTGGCTTGATA 59.407 40.000 0.00 0.00 0.00 2.15
2984 3101 4.402793 ACTTGTCTAGATACGTGGCTTGAT 59.597 41.667 0.00 0.00 0.00 2.57
2985 3102 3.762288 ACTTGTCTAGATACGTGGCTTGA 59.238 43.478 0.00 0.00 0.00 3.02
2986 3103 4.111375 ACTTGTCTAGATACGTGGCTTG 57.889 45.455 0.00 0.00 0.00 4.01
2987 3104 4.803098 AACTTGTCTAGATACGTGGCTT 57.197 40.909 0.00 0.00 0.00 4.35
2988 3105 4.803098 AAACTTGTCTAGATACGTGGCT 57.197 40.909 0.00 0.00 0.00 4.75
2990 3107 7.310664 TGTCTTAAACTTGTCTAGATACGTGG 58.689 38.462 0.00 0.00 0.00 4.94
2991 3108 8.738199 TTGTCTTAAACTTGTCTAGATACGTG 57.262 34.615 0.00 0.00 0.00 4.49
2992 3109 8.790718 TCTTGTCTTAAACTTGTCTAGATACGT 58.209 33.333 0.00 0.00 0.00 3.57
2993 3110 9.622004 TTCTTGTCTTAAACTTGTCTAGATACG 57.378 33.333 0.00 0.00 0.00 3.06
3000 3117 8.197439 CCCAAAATTCTTGTCTTAAACTTGTCT 58.803 33.333 0.00 0.00 0.00 3.41
3001 3118 8.194769 TCCCAAAATTCTTGTCTTAAACTTGTC 58.805 33.333 0.00 0.00 0.00 3.18
3002 3119 7.979537 GTCCCAAAATTCTTGTCTTAAACTTGT 59.020 33.333 0.00 0.00 0.00 3.16
3003 3120 7.167468 CGTCCCAAAATTCTTGTCTTAAACTTG 59.833 37.037 0.00 0.00 0.00 3.16
3004 3121 7.200455 CGTCCCAAAATTCTTGTCTTAAACTT 58.800 34.615 0.00 0.00 0.00 2.66
3005 3122 6.238925 CCGTCCCAAAATTCTTGTCTTAAACT 60.239 38.462 0.00 0.00 0.00 2.66
3006 3123 5.918576 CCGTCCCAAAATTCTTGTCTTAAAC 59.081 40.000 0.00 0.00 0.00 2.01
3007 3124 5.828859 TCCGTCCCAAAATTCTTGTCTTAAA 59.171 36.000 0.00 0.00 0.00 1.52
3008 3125 5.378332 TCCGTCCCAAAATTCTTGTCTTAA 58.622 37.500 0.00 0.00 0.00 1.85
3009 3126 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3011 3128 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3012 3129 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3014 3131 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3016 3133 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3017 3134 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3019 3136 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3020 3137 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
3022 3139 3.339713 AATATACTCCCTCCGTCCCAA 57.660 47.619 0.00 0.00 0.00 4.12
3023 3140 4.687262 ATAATATACTCCCTCCGTCCCA 57.313 45.455 0.00 0.00 0.00 4.37
3024 3141 6.666980 AGTAAATAATATACTCCCTCCGTCCC 59.333 42.308 0.00 0.00 0.00 4.46
3025 3142 7.715266 AGTAAATAATATACTCCCTCCGTCC 57.285 40.000 0.00 0.00 0.00 4.79
3034 3151 8.631797 GGATCGGAGGGAGTAAATAATATACTC 58.368 40.741 5.37 5.37 45.50 2.59
3035 3152 8.120538 TGGATCGGAGGGAGTAAATAATATACT 58.879 37.037 0.00 0.00 36.34 2.12
3036 3153 8.302515 TGGATCGGAGGGAGTAAATAATATAC 57.697 38.462 0.00 0.00 0.00 1.47
3037 3154 8.904648 TTGGATCGGAGGGAGTAAATAATATA 57.095 34.615 0.00 0.00 0.00 0.86
3038 3155 7.808279 TTGGATCGGAGGGAGTAAATAATAT 57.192 36.000 0.00 0.00 0.00 1.28
3039 3156 7.621006 TTTGGATCGGAGGGAGTAAATAATA 57.379 36.000 0.00 0.00 0.00 0.98
3040 3157 6.509523 TTTGGATCGGAGGGAGTAAATAAT 57.490 37.500 0.00 0.00 0.00 1.28
3041 3158 5.961398 TTTGGATCGGAGGGAGTAAATAA 57.039 39.130 0.00 0.00 0.00 1.40
3042 3159 5.961398 TTTTGGATCGGAGGGAGTAAATA 57.039 39.130 0.00 0.00 0.00 1.40
3043 3160 4.855298 TTTTGGATCGGAGGGAGTAAAT 57.145 40.909 0.00 0.00 0.00 1.40
3044 3161 4.855298 ATTTTGGATCGGAGGGAGTAAA 57.145 40.909 0.00 0.00 0.00 2.01
3045 3162 5.427481 ACTTATTTTGGATCGGAGGGAGTAA 59.573 40.000 0.00 0.00 0.00 2.24
3073 3190 6.625081 GCAGTTTTGAACTAAGGTTGAGTTGT 60.625 38.462 0.00 0.00 40.46 3.32
3076 3193 4.947388 TGCAGTTTTGAACTAAGGTTGAGT 59.053 37.500 0.00 0.00 40.46 3.41
3077 3194 5.499139 TGCAGTTTTGAACTAAGGTTGAG 57.501 39.130 0.00 0.00 40.46 3.02
3099 3216 3.135895 CCCTCCGGTCCATAATAAGTGTT 59.864 47.826 0.00 0.00 0.00 3.32
3164 3281 9.817809 CAGGTAAACTTCTACATTTCTGCTATA 57.182 33.333 0.00 0.00 0.00 1.31
3167 3284 6.534634 ACAGGTAAACTTCTACATTTCTGCT 58.465 36.000 0.00 0.00 0.00 4.24
3176 3293 5.701290 ACATCTGCAACAGGTAAACTTCTAC 59.299 40.000 0.00 0.00 31.51 2.59
3278 3396 6.358974 TGATCCAGTTGACAATCTAAGTGA 57.641 37.500 0.00 0.00 30.60 3.41
3334 3455 5.221880 TCAAAGATTTTTCATCTGGCAACG 58.778 37.500 0.00 0.00 42.51 4.10
3396 3518 4.672587 TGGTATCATCTGGTAACTGCTC 57.327 45.455 0.00 0.00 35.12 4.26
3557 3836 6.702449 ATCCTTGTGCATAGGTATTCCATA 57.298 37.500 15.17 0.00 35.89 2.74
3594 3918 4.900635 TGAAGAAGCTTCAGTTTGAACC 57.099 40.909 27.57 3.64 32.21 3.62
3621 3946 5.397334 GGAATCAATAGTTGAGAGCCTCCTT 60.397 44.000 0.00 0.00 43.98 3.36
3663 3988 0.979709 CATGCCTGGAGGAGGACAGA 60.980 60.000 0.00 0.00 46.33 3.41
3728 4053 1.517257 GATGTCAGACTGGACGGCG 60.517 63.158 4.80 4.80 40.72 6.46
3845 4170 7.548196 ACAAGAATTCTCGACTTTGTTGTTA 57.452 32.000 8.78 0.00 34.38 2.41
3897 4222 2.094390 GGTTGATGTGTACAGCTACGGA 60.094 50.000 0.00 0.00 38.51 4.69


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

AutoCloner maintained by Alex Coulton.