Multiple sequence alignment - TraesCS3D01G180200

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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 TraesCS3D01G180200 chr3D 100.000 3858 0 0 1 3858 162179384 162175527 0.000000e+00 7125.0
1 TraesCS3D01G180200 chr3D 100.000 72 0 0 3072 3143 162176258 162176187 2.420000e-27 134.0
2 TraesCS3D01G180200 chr3D 100.000 72 0 0 3127 3198 162176313 162176242 2.420000e-27 134.0
3 TraesCS3D01G180200 chr3B 94.726 2863 106 14 249 3088 239249684 239246844 0.000000e+00 4409.0
4 TraesCS3D01G180200 chr3B 92.794 680 39 6 3182 3858 239246860 239246188 0.000000e+00 976.0
5 TraesCS3D01G180200 chr3B 87.444 223 22 4 1299 1515 605028648 605028870 6.400000e-63 252.0
6 TraesCS3D01G180200 chr3B 97.143 105 3 0 50 154 239249853 239249749 1.100000e-40 178.0
7 TraesCS3D01G180200 chr3B 98.305 59 1 0 1 59 239250533 239250475 1.900000e-18 104.0
8 TraesCS3D01G180200 chr3B 95.000 40 2 0 203 242 239249746 239249707 3.220000e-06 63.9
9 TraesCS3D01G180200 chr3A 94.400 2250 87 11 856 3088 192818469 192816242 0.000000e+00 3421.0
10 TraesCS3D01G180200 chr3A 90.762 682 47 7 3182 3858 192816258 192815588 0.000000e+00 896.0
11 TraesCS3D01G180200 chr3A 92.687 547 20 6 330 863 192823400 192822861 0.000000e+00 771.0
12 TraesCS3D01G180200 chr3A 92.050 239 17 1 8 246 192825067 192824831 6.180000e-88 335.0
13 TraesCS3D01G180200 chr3A 92.771 166 10 1 81 246 192824796 192824633 4.980000e-59 239.0
14 TraesCS3D01G180200 chr4D 92.553 282 21 0 1265 1546 450197935 450198216 4.640000e-109 405.0
15 TraesCS3D01G180200 chr4D 76.866 670 112 29 3222 3858 421933555 421932896 4.770000e-89 339.0
16 TraesCS3D01G180200 chr2B 90.592 287 26 1 1253 1539 380511072 380510787 2.810000e-101 379.0
17 TraesCS3D01G180200 chr2B 91.020 245 19 2 1583 1825 380510789 380510546 1.030000e-85 327.0
18 TraesCS3D01G180200 chr2B 78.275 313 62 6 2197 2506 95760732 95761041 3.040000e-46 196.0
19 TraesCS3D01G180200 chr7B 78.194 587 97 23 3294 3858 6750683 6750106 2.850000e-91 346.0
20 TraesCS3D01G180200 chr1A 76.350 685 111 34 3208 3843 508148004 508148686 1.730000e-83 320.0
21 TraesCS3D01G180200 chr2A 78.914 313 60 6 2197 2506 61467959 61468268 1.400000e-49 207.0
22 TraesCS3D01G180200 chr5D 82.684 231 36 4 1312 1541 561620189 561620416 6.540000e-48 202.0
23 TraesCS3D01G180200 chr2D 77.316 313 65 6 2197 2506 60945685 60945994 3.060000e-41 180.0


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 TraesCS3D01G180200 chr3D 162175527 162179384 3857 True 2464.333333 7125 100.000000 1 3858 3 chr3D.!!$R1 3857
1 TraesCS3D01G180200 chr3B 239246188 239250533 4345 True 1146.180000 4409 95.593600 1 3858 5 chr3B.!!$R1 3857
2 TraesCS3D01G180200 chr3A 192815588 192818469 2881 True 2158.500000 3421 92.581000 856 3858 2 chr3A.!!$R1 3002
3 TraesCS3D01G180200 chr3A 192822861 192825067 2206 True 448.333333 771 92.502667 8 863 3 chr3A.!!$R2 855
4 TraesCS3D01G180200 chr4D 421932896 421933555 659 True 339.000000 339 76.866000 3222 3858 1 chr4D.!!$R1 636
5 TraesCS3D01G180200 chr2B 380510546 380511072 526 True 353.000000 379 90.806000 1253 1825 2 chr2B.!!$R1 572
6 TraesCS3D01G180200 chr7B 6750106 6750683 577 True 346.000000 346 78.194000 3294 3858 1 chr7B.!!$R1 564
7 TraesCS3D01G180200 chr1A 508148004 508148686 682 False 320.000000 320 76.350000 3208 3843 1 chr1A.!!$F1 635

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
922 2972 1.065782 TGCGCCAAGGCAGATTACTTA 60.066 47.619 12.19 0.0 42.06 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2890 4970 0.60864 GGAATACATCGATCCCGGCT 59.391 55.0 0.0 0.0 36.24 5.52 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
169 999 1.940613 GCGGTACATGGTTGAGGAATC 59.059 52.381 0.00 0.00 0.00 2.52
199 1029 3.611025 TTGGGGGTCAAATTTCAGACT 57.389 42.857 8.17 0.00 35.18 3.24
211 1041 8.782144 GTCAAATTTCAGACTGAAGAAATCTCT 58.218 33.333 17.06 0.00 42.02 3.10
246 1076 1.264295 AGTACTCCTTCCGTCCCAAC 58.736 55.000 0.00 0.00 0.00 3.77
247 1077 5.762610 GAAGTACTCCTTCCGTCCCAACG 62.763 56.522 0.00 0.00 43.25 4.10
300 2334 7.367285 GTGTGTTGCTAATTGAACCATCTTAA 58.633 34.615 0.00 0.00 0.00 1.85
516 2556 2.969238 CCGGTGCGCTCATGATCC 60.969 66.667 9.73 0.00 0.00 3.36
611 2656 4.052229 CGGGACACGTTCTCGGCT 62.052 66.667 10.83 0.00 45.31 5.52
612 2657 2.432628 GGGACACGTTCTCGGCTG 60.433 66.667 0.00 0.00 41.85 4.85
613 2658 3.112709 GGACACGTTCTCGGCTGC 61.113 66.667 0.00 0.00 41.85 5.25
614 2659 2.049063 GACACGTTCTCGGCTGCT 60.049 61.111 0.00 0.00 41.85 4.24
616 2661 1.891060 GACACGTTCTCGGCTGCTTG 61.891 60.000 0.00 0.00 41.85 4.01
618 2663 2.740055 CGTTCTCGGCTGCTTGCT 60.740 61.111 0.00 0.00 42.39 3.91
619 2664 2.734673 CGTTCTCGGCTGCTTGCTC 61.735 63.158 0.00 0.00 42.39 4.26
768 2818 6.619801 ATGCACCGGAAGATAATTTACTTC 57.380 37.500 9.46 12.74 40.91 3.01
769 2819 5.492895 TGCACCGGAAGATAATTTACTTCA 58.507 37.500 9.46 3.45 42.67 3.02
849 2899 3.019564 AGTTGATAAAGACCTGCATGCC 58.980 45.455 16.68 0.00 0.00 4.40
878 2928 1.781025 TTGCGCACCTTTCTTCCACG 61.781 55.000 11.12 0.00 0.00 4.94
922 2972 1.065782 TGCGCCAAGGCAGATTACTTA 60.066 47.619 12.19 0.00 42.06 2.24
988 3042 1.958579 CCAATGGTCATGCCCATACAG 59.041 52.381 9.05 2.44 44.55 2.74
1512 3587 2.266055 GGGAGTCTTCGCAGTGGG 59.734 66.667 0.00 0.00 36.36 4.61
1629 3704 3.488978 CGTCGCGTCGAGGAGTCT 61.489 66.667 20.81 0.00 43.12 3.24
2067 4144 4.116328 TTCTCGAGCGGCTGGACG 62.116 66.667 7.50 5.04 0.00 4.79
2095 4172 2.178892 GAGCGCCACCGTTGGTAAAC 62.179 60.000 2.29 0.00 45.98 2.01
2177 4254 3.277211 ATGCTGCTGCTTTGCGTGG 62.277 57.895 17.00 0.00 40.48 4.94
2298 4375 4.082523 CCGCTCGGCCTTCTTCCA 62.083 66.667 0.00 0.00 0.00 3.53
2306 4383 2.742372 CCTTCTTCCACGTGGCCG 60.742 66.667 30.25 21.38 40.83 6.13
2356 4433 1.038130 ACTCGCTCCGGCAGTTCTAT 61.038 55.000 0.00 0.00 38.60 1.98
2359 4436 1.300233 GCTCCGGCAGTTCTATCGG 60.300 63.158 0.00 0.00 43.42 4.18
2611 4688 0.040646 TCATGGAGTCGTACCTGGGT 59.959 55.000 0.00 0.00 0.00 4.51
2803 4880 2.885644 CGGTTCATCGACGGCCTG 60.886 66.667 0.00 0.00 0.00 4.85
2869 4946 5.929697 TCAAGAAATGACACACTAGCAAG 57.070 39.130 0.00 0.00 31.50 4.01
2890 4970 3.531397 AGTGGTCAATTTGGGGATGGATA 59.469 43.478 0.00 0.00 0.00 2.59
2896 4976 1.715019 TTTGGGGATGGATAGCCGGG 61.715 60.000 2.18 0.00 36.79 5.73
2914 4994 3.451178 CCGGGATCGATGTATTCCCTTAT 59.549 47.826 17.00 0.00 45.90 1.73
2918 4998 7.368833 CGGGATCGATGTATTCCCTTATATAC 58.631 42.308 17.00 0.00 45.90 1.47
2919 4999 7.230913 CGGGATCGATGTATTCCCTTATATACT 59.769 40.741 17.00 0.00 45.90 2.12
2920 5000 8.578151 GGGATCGATGTATTCCCTTATATACTC 58.422 40.741 12.92 0.00 44.86 2.59
2921 5001 8.291032 GGATCGATGTATTCCCTTATATACTCG 58.709 40.741 0.54 0.00 33.83 4.18
2922 5002 8.749026 ATCGATGTATTCCCTTATATACTCGT 57.251 34.615 0.00 0.00 34.00 4.18
2924 5004 7.609146 TCGATGTATTCCCTTATATACTCGTGT 59.391 37.037 0.00 0.00 34.00 4.49
2929 5009 9.798994 GTATTCCCTTATATACTCGTGTATTGG 57.201 37.037 14.73 11.59 39.77 3.16
2930 5010 8.660295 ATTCCCTTATATACTCGTGTATTGGA 57.340 34.615 14.73 10.46 39.77 3.53
2931 5011 8.481492 TTCCCTTATATACTCGTGTATTGGAA 57.519 34.615 14.73 14.51 39.77 3.53
2932 5012 8.118976 TCCCTTATATACTCGTGTATTGGAAG 57.881 38.462 14.73 13.95 39.77 3.46
2933 5013 7.177921 TCCCTTATATACTCGTGTATTGGAAGG 59.822 40.741 22.56 22.56 39.77 3.46
2934 5014 7.039223 CCCTTATATACTCGTGTATTGGAAGGT 60.039 40.741 24.71 6.37 38.17 3.50
2935 5015 9.017509 CCTTATATACTCGTGTATTGGAAGGTA 57.982 37.037 21.92 6.09 39.77 3.08
2936 5016 9.837525 CTTATATACTCGTGTATTGGAAGGTAC 57.162 37.037 14.73 0.00 39.77 3.34
2937 5017 7.828508 ATATACTCGTGTATTGGAAGGTACA 57.171 36.000 14.73 0.00 39.77 2.90
2938 5018 4.451629 ACTCGTGTATTGGAAGGTACAG 57.548 45.455 0.00 0.00 31.95 2.74
2953 5033 9.103582 TGGAAGGTACAGTAAAATTTAGTAGGA 57.896 33.333 0.00 0.00 0.00 2.94
2956 5036 8.959705 AGGTACAGTAAAATTTAGTAGGATGC 57.040 34.615 0.00 0.00 0.00 3.91
2972 5052 3.577848 AGGATGCTTACAAATGTTTGCCA 59.422 39.130 5.44 0.00 41.79 4.92
2973 5053 3.679502 GGATGCTTACAAATGTTTGCCAC 59.320 43.478 5.44 0.00 41.79 5.01
2977 5057 3.666797 GCTTACAAATGTTTGCCACGTAC 59.333 43.478 5.44 0.00 41.79 3.67
3064 5147 6.056884 TGTTTAGATCTTAACAACAACGGGT 58.943 36.000 21.63 0.00 31.75 5.28
3066 5149 4.345859 AGATCTTAACAACAACGGGTCA 57.654 40.909 0.00 0.00 0.00 4.02
3071 5154 2.045561 AACAACAACGGGTCACATGA 57.954 45.000 0.00 0.00 0.00 3.07
3072 5155 2.045561 ACAACAACGGGTCACATGAA 57.954 45.000 0.00 0.00 0.00 2.57
3073 5156 2.582052 ACAACAACGGGTCACATGAAT 58.418 42.857 0.00 0.00 0.00 2.57
3074 5157 2.955660 ACAACAACGGGTCACATGAATT 59.044 40.909 0.00 0.00 0.00 2.17
3075 5158 3.243367 ACAACAACGGGTCACATGAATTG 60.243 43.478 0.00 0.00 0.00 2.32
3076 5159 2.582052 ACAACGGGTCACATGAATTGT 58.418 42.857 0.00 0.00 39.91 2.71
3077 5160 3.745799 ACAACGGGTCACATGAATTGTA 58.254 40.909 0.00 0.00 36.57 2.41
3078 5161 3.500680 ACAACGGGTCACATGAATTGTAC 59.499 43.478 0.00 0.00 36.57 2.90
3079 5162 3.695830 ACGGGTCACATGAATTGTACT 57.304 42.857 0.00 0.00 36.57 2.73
3080 5163 3.596214 ACGGGTCACATGAATTGTACTC 58.404 45.455 0.00 0.00 36.57 2.59
3081 5164 2.603110 CGGGTCACATGAATTGTACTCG 59.397 50.000 0.00 0.00 36.57 4.18
3082 5165 3.596214 GGGTCACATGAATTGTACTCGT 58.404 45.455 0.00 0.00 36.57 4.18
3083 5166 3.370978 GGGTCACATGAATTGTACTCGTG 59.629 47.826 0.00 0.00 36.57 4.35
3084 5167 4.242475 GGTCACATGAATTGTACTCGTGA 58.758 43.478 0.00 0.00 36.57 4.35
3085 5168 4.870426 GGTCACATGAATTGTACTCGTGAT 59.130 41.667 0.00 0.00 36.57 3.06
3086 5169 5.351465 GGTCACATGAATTGTACTCGTGATT 59.649 40.000 0.00 0.00 36.57 2.57
3087 5170 6.128282 GGTCACATGAATTGTACTCGTGATTT 60.128 38.462 0.00 0.00 36.57 2.17
3088 5171 7.298122 GTCACATGAATTGTACTCGTGATTTT 58.702 34.615 0.00 0.00 36.57 1.82
3089 5172 7.478667 GTCACATGAATTGTACTCGTGATTTTC 59.521 37.037 0.00 0.00 36.57 2.29
3090 5173 7.387673 TCACATGAATTGTACTCGTGATTTTCT 59.612 33.333 0.00 0.00 36.57 2.52
3091 5174 8.655970 CACATGAATTGTACTCGTGATTTTCTA 58.344 33.333 0.00 0.00 36.57 2.10
3092 5175 9.383519 ACATGAATTGTACTCGTGATTTTCTAT 57.616 29.630 0.00 0.00 36.57 1.98
3100 5183 9.872757 TGTACTCGTGATTTTCTATTTTTGAAC 57.127 29.630 0.00 0.00 0.00 3.18
3101 5184 9.872757 GTACTCGTGATTTTCTATTTTTGAACA 57.127 29.630 0.00 0.00 0.00 3.18
3102 5185 8.782533 ACTCGTGATTTTCTATTTTTGAACAC 57.217 30.769 0.00 0.00 0.00 3.32
3103 5186 7.586300 ACTCGTGATTTTCTATTTTTGAACACG 59.414 33.333 0.00 0.00 40.00 4.49
3104 5187 6.853872 TCGTGATTTTCTATTTTTGAACACGG 59.146 34.615 0.62 0.00 39.56 4.94
3105 5188 6.853872 CGTGATTTTCTATTTTTGAACACGGA 59.146 34.615 0.00 0.00 37.57 4.69
3106 5189 7.377397 CGTGATTTTCTATTTTTGAACACGGAA 59.623 33.333 0.00 0.00 37.57 4.30
3107 5190 8.476925 GTGATTTTCTATTTTTGAACACGGAAC 58.523 33.333 0.00 0.00 0.00 3.62
3108 5191 8.191446 TGATTTTCTATTTTTGAACACGGAACA 58.809 29.630 0.00 0.00 0.00 3.18
3109 5192 8.934507 ATTTTCTATTTTTGAACACGGAACAA 57.065 26.923 0.00 0.00 0.00 2.83
3110 5193 8.758633 TTTTCTATTTTTGAACACGGAACAAA 57.241 26.923 0.00 0.00 0.00 2.83
3111 5194 8.758633 TTTCTATTTTTGAACACGGAACAAAA 57.241 26.923 0.00 0.00 40.23 2.44
3112 5195 7.979115 TCTATTTTTGAACACGGAACAAAAG 57.021 32.000 0.00 0.00 41.92 2.27
3113 5196 4.912528 TTTTTGAACACGGAACAAAAGC 57.087 36.364 0.00 0.00 41.92 3.51
3114 5197 3.577649 TTTGAACACGGAACAAAAGCA 57.422 38.095 0.00 0.00 31.94 3.91
3115 5198 3.577649 TTGAACACGGAACAAAAGCAA 57.422 38.095 0.00 0.00 0.00 3.91
3116 5199 3.143807 TGAACACGGAACAAAAGCAAG 57.856 42.857 0.00 0.00 0.00 4.01
3117 5200 1.852280 GAACACGGAACAAAAGCAAGC 59.148 47.619 0.00 0.00 0.00 4.01
3118 5201 0.248458 ACACGGAACAAAAGCAAGCG 60.248 50.000 0.00 0.00 0.00 4.68
3119 5202 1.299089 ACGGAACAAAAGCAAGCGC 60.299 52.632 0.00 0.00 38.99 5.92
3131 5214 2.549633 GCAAGCGCTCATACAATTGT 57.450 45.000 12.06 16.68 34.30 2.71
3132 5215 3.673746 GCAAGCGCTCATACAATTGTA 57.326 42.857 20.14 20.14 34.30 2.41
3133 5216 3.354397 GCAAGCGCTCATACAATTGTAC 58.646 45.455 20.26 7.11 31.83 2.90
3134 5217 3.063997 GCAAGCGCTCATACAATTGTACT 59.936 43.478 20.26 9.12 31.83 2.73
3135 5218 4.783450 GCAAGCGCTCATACAATTGTACTC 60.783 45.833 20.26 8.82 31.83 2.59
3136 5219 3.116300 AGCGCTCATACAATTGTACTCG 58.884 45.455 20.26 19.03 32.72 4.18
3137 5220 2.858344 GCGCTCATACAATTGTACTCGT 59.142 45.455 20.26 1.97 32.72 4.18
3138 5221 3.301835 GCGCTCATACAATTGTACTCGTG 60.302 47.826 20.26 14.29 32.72 4.35
3139 5222 4.102649 CGCTCATACAATTGTACTCGTGA 58.897 43.478 20.26 17.40 32.72 4.35
3140 5223 4.740205 CGCTCATACAATTGTACTCGTGAT 59.260 41.667 20.26 1.13 32.72 3.06
3141 5224 5.232202 CGCTCATACAATTGTACTCGTGATT 59.768 40.000 20.26 0.00 32.72 2.57
3142 5225 6.237835 CGCTCATACAATTGTACTCGTGATTT 60.238 38.462 20.26 0.00 32.72 2.17
3143 5226 7.464358 GCTCATACAATTGTACTCGTGATTTT 58.536 34.615 20.26 0.00 32.72 1.82
3144 5227 7.636359 GCTCATACAATTGTACTCGTGATTTTC 59.364 37.037 20.26 6.65 32.72 2.29
3145 5228 8.771920 TCATACAATTGTACTCGTGATTTTCT 57.228 30.769 20.26 0.00 32.72 2.52
3146 5229 9.863845 TCATACAATTGTACTCGTGATTTTCTA 57.136 29.630 20.26 0.00 32.72 2.10
3155 5238 9.872757 TGTACTCGTGATTTTCTATTTTTGAAC 57.127 29.630 0.00 0.00 0.00 3.18
3156 5239 9.872757 GTACTCGTGATTTTCTATTTTTGAACA 57.127 29.630 0.00 0.00 0.00 3.18
3157 5240 8.782533 ACTCGTGATTTTCTATTTTTGAACAC 57.217 30.769 0.00 0.00 0.00 3.32
3158 5241 7.586300 ACTCGTGATTTTCTATTTTTGAACACG 59.414 33.333 0.00 0.00 40.00 4.49
3159 5242 6.853872 TCGTGATTTTCTATTTTTGAACACGG 59.146 34.615 0.62 0.00 39.56 4.94
3160 5243 6.853872 CGTGATTTTCTATTTTTGAACACGGA 59.146 34.615 0.00 0.00 37.57 4.69
3161 5244 7.377397 CGTGATTTTCTATTTTTGAACACGGAA 59.623 33.333 0.00 0.00 37.57 4.30
3162 5245 8.476925 GTGATTTTCTATTTTTGAACACGGAAC 58.523 33.333 0.00 0.00 0.00 3.62
3163 5246 8.191446 TGATTTTCTATTTTTGAACACGGAACA 58.809 29.630 0.00 0.00 0.00 3.18
3164 5247 8.934507 ATTTTCTATTTTTGAACACGGAACAA 57.065 26.923 0.00 0.00 0.00 2.83
3165 5248 8.758633 TTTTCTATTTTTGAACACGGAACAAA 57.241 26.923 0.00 0.00 0.00 2.83
3166 5249 8.758633 TTTCTATTTTTGAACACGGAACAAAA 57.241 26.923 0.00 0.00 40.23 2.44
3167 5250 7.979115 TCTATTTTTGAACACGGAACAAAAG 57.021 32.000 0.00 0.00 41.92 2.27
3168 5251 4.912528 TTTTTGAACACGGAACAAAAGC 57.087 36.364 0.00 0.00 41.92 3.51
3169 5252 3.577649 TTTGAACACGGAACAAAAGCA 57.422 38.095 0.00 0.00 31.94 3.91
3170 5253 3.577649 TTGAACACGGAACAAAAGCAA 57.422 38.095 0.00 0.00 0.00 3.91
3171 5254 3.143807 TGAACACGGAACAAAAGCAAG 57.856 42.857 0.00 0.00 0.00 4.01
3172 5255 1.852280 GAACACGGAACAAAAGCAAGC 59.148 47.619 0.00 0.00 0.00 4.01
3173 5256 0.248458 ACACGGAACAAAAGCAAGCG 60.248 50.000 0.00 0.00 0.00 4.68
3174 5257 1.299089 ACGGAACAAAAGCAAGCGC 60.299 52.632 0.00 0.00 38.99 5.92
3230 5313 2.363306 AAACATGACTGCACCAAGGA 57.637 45.000 0.00 0.00 0.00 3.36
3234 5317 2.025605 ACATGACTGCACCAAGGATCAT 60.026 45.455 0.00 0.00 0.00 2.45
3322 5419 3.076621 TCTTTGCGGATGATATGATGGC 58.923 45.455 0.00 0.00 0.00 4.40
3461 5577 1.460504 ACGACTATGCACGAAGAGGA 58.539 50.000 1.06 0.00 0.00 3.71
3462 5578 1.402259 ACGACTATGCACGAAGAGGAG 59.598 52.381 1.06 0.00 0.00 3.69
3463 5579 1.268794 CGACTATGCACGAAGAGGAGG 60.269 57.143 0.00 0.00 0.00 4.30
3508 5631 5.763204 GTGGTACCTCAAAAGACATCTTTCA 59.237 40.000 14.36 0.00 44.69 2.69
3591 5714 7.862274 ATCATAACAGGATGGATGAAGTAGA 57.138 36.000 0.00 0.00 43.02 2.59
3596 5719 4.648762 ACAGGATGGATGAAGTAGAGTCAG 59.351 45.833 0.00 0.00 43.62 3.51
3732 5863 3.735591 TGTCCAAAGTTAGGTGTAGCAC 58.264 45.455 0.00 0.00 0.00 4.40
3818 5957 7.876068 TGATAAAGTTGGGGTATCATCGATTAC 59.124 37.037 0.00 0.00 31.01 1.89
3827 5966 5.164954 GGTATCATCGATTACAGAGAAGGC 58.835 45.833 8.99 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
181 1011 3.154827 TCAGTCTGAAATTTGACCCCC 57.845 47.619 0.00 0.00 34.02 5.40
182 1012 4.398319 TCTTCAGTCTGAAATTTGACCCC 58.602 43.478 15.97 0.00 35.73 4.95
183 1013 6.391227 TTTCTTCAGTCTGAAATTTGACCC 57.609 37.500 15.97 0.00 35.73 4.46
184 1014 7.880105 AGATTTCTTCAGTCTGAAATTTGACC 58.120 34.615 15.97 3.60 41.30 4.02
246 1076 3.268023 AGCAAAATTCTACTCCCTCCG 57.732 47.619 0.00 0.00 0.00 4.63
247 1077 5.360649 ACTAGCAAAATTCTACTCCCTCC 57.639 43.478 0.00 0.00 0.00 4.30
364 2398 1.134220 TCTTCAACGAGGGTGTTTGCT 60.134 47.619 0.00 0.00 0.00 3.91
516 2556 2.034879 ACAGCGAATTGGGCAGTCG 61.035 57.895 0.00 0.00 37.82 4.18
573 2613 2.504032 GGGACGATTCGGGCATGA 59.496 61.111 11.29 0.00 0.00 3.07
609 2654 3.036783 CTTGGAGCGAGCAAGCAGC 62.037 63.158 6.21 4.71 46.19 5.25
610 2655 0.390340 TACTTGGAGCGAGCAAGCAG 60.390 55.000 6.21 0.00 40.15 4.24
611 2656 0.250234 ATACTTGGAGCGAGCAAGCA 59.750 50.000 6.21 0.00 40.15 3.91
612 2657 0.933796 GATACTTGGAGCGAGCAAGC 59.066 55.000 0.00 0.00 37.41 4.01
613 2658 1.202302 TCGATACTTGGAGCGAGCAAG 60.202 52.381 0.00 0.00 0.00 4.01
614 2659 0.815095 TCGATACTTGGAGCGAGCAA 59.185 50.000 0.00 0.00 0.00 3.91
616 2661 0.595310 GGTCGATACTTGGAGCGAGC 60.595 60.000 6.93 6.93 42.66 5.03
619 2664 4.303853 CGGTCGATACTTGGAGCG 57.696 61.111 0.00 0.00 43.30 5.03
768 2818 3.635331 GAATGATTGGTCCGATTGCATG 58.365 45.455 0.00 0.00 0.00 4.06
769 2819 2.291465 CGAATGATTGGTCCGATTGCAT 59.709 45.455 0.00 0.00 0.00 3.96
849 2899 3.631145 AAGGTGCGCAAATATAGCATG 57.369 42.857 14.00 0.00 43.17 4.06
863 2913 1.305201 TTGTCGTGGAAGAAAGGTGC 58.695 50.000 0.00 0.00 0.00 5.01
878 2928 3.200165 AGGGAGGCAAGGTATAGTTTGTC 59.800 47.826 0.00 0.00 0.00 3.18
922 2972 2.076863 GCATTGCTGACGAAGGTAAGT 58.923 47.619 0.16 0.00 0.00 2.24
1038 3104 1.510480 GAAGCGCCAACAGAAGCAGT 61.510 55.000 2.29 0.00 0.00 4.40
1161 3227 2.029470 AGAAGAGGAGACGTTGAAGCAG 60.029 50.000 0.00 0.00 0.00 4.24
2095 4172 3.970610 CGAGACAGAATTTGCACTTTGTG 59.029 43.478 0.00 0.00 36.51 3.33
2306 4383 4.083862 GTCCTGGTGCCCCTCGAC 62.084 72.222 0.00 0.00 0.00 4.20
2713 4790 4.404098 CACTTTACCCGCCCGGCT 62.404 66.667 8.05 0.00 33.26 5.52
2725 4802 2.855014 TGGTACCCCGGCCACTTT 60.855 61.111 10.07 0.00 0.00 2.66
2869 4946 2.230130 TCCATCCCCAAATTGACCAC 57.770 50.000 0.00 0.00 0.00 4.16
2890 4970 0.608640 GGAATACATCGATCCCGGCT 59.391 55.000 0.00 0.00 36.24 5.52
2896 4976 8.838365 ACGAGTATATAAGGGAATACATCGATC 58.162 37.037 0.00 0.00 35.37 3.69
2914 4994 6.830324 ACTGTACCTTCCAATACACGAGTATA 59.170 38.462 5.92 0.00 40.00 1.47
2918 4998 4.451629 ACTGTACCTTCCAATACACGAG 57.548 45.455 0.00 0.00 0.00 4.18
2919 4999 5.981088 TTACTGTACCTTCCAATACACGA 57.019 39.130 0.00 0.00 0.00 4.35
2920 5000 7.605410 ATTTTACTGTACCTTCCAATACACG 57.395 36.000 0.00 0.00 0.00 4.49
2926 5006 9.729281 CCTACTAAATTTTACTGTACCTTCCAA 57.271 33.333 0.00 0.00 0.00 3.53
2927 5007 9.103582 TCCTACTAAATTTTACTGTACCTTCCA 57.896 33.333 0.00 0.00 0.00 3.53
2930 5010 9.392259 GCATCCTACTAAATTTTACTGTACCTT 57.608 33.333 0.00 0.00 0.00 3.50
2931 5011 8.769359 AGCATCCTACTAAATTTTACTGTACCT 58.231 33.333 0.00 0.00 0.00 3.08
2932 5012 8.959705 AGCATCCTACTAAATTTTACTGTACC 57.040 34.615 0.00 0.00 0.00 3.34
2935 5015 9.953565 TGTAAGCATCCTACTAAATTTTACTGT 57.046 29.630 0.00 0.00 0.00 3.55
2953 5033 3.243704 ACGTGGCAAACATTTGTAAGCAT 60.244 39.130 6.24 0.00 40.24 3.79
2956 5036 3.903644 CGTACGTGGCAAACATTTGTAAG 59.096 43.478 7.22 1.92 40.24 2.34
2972 5052 2.855963 CGTCCATTCTAATTGCGTACGT 59.144 45.455 17.90 0.00 0.00 3.57
2973 5053 2.855963 ACGTCCATTCTAATTGCGTACG 59.144 45.455 11.84 11.84 0.00 3.67
3061 5141 3.370978 CACGAGTACAATTCATGTGACCC 59.629 47.826 0.00 0.00 43.77 4.46
3064 5147 7.387673 AGAAAATCACGAGTACAATTCATGTGA 59.612 33.333 0.00 0.00 43.77 3.58
3066 5149 7.672983 AGAAAATCACGAGTACAATTCATGT 57.327 32.000 0.00 0.00 46.36 3.21
3074 5157 9.872757 GTTCAAAAATAGAAAATCACGAGTACA 57.127 29.630 0.00 0.00 0.00 2.90
3075 5158 9.872757 TGTTCAAAAATAGAAAATCACGAGTAC 57.127 29.630 0.00 0.00 0.00 2.73
3076 5159 9.872757 GTGTTCAAAAATAGAAAATCACGAGTA 57.127 29.630 0.00 0.00 0.00 2.59
3077 5160 7.586300 CGTGTTCAAAAATAGAAAATCACGAGT 59.414 33.333 0.00 0.00 41.48 4.18
3078 5161 7.059488 CCGTGTTCAAAAATAGAAAATCACGAG 59.941 37.037 14.77 5.84 41.48 4.18
3079 5162 6.853872 CCGTGTTCAAAAATAGAAAATCACGA 59.146 34.615 14.77 0.00 41.48 4.35
3080 5163 6.853872 TCCGTGTTCAAAAATAGAAAATCACG 59.146 34.615 0.00 0.00 40.06 4.35
3081 5164 8.476925 GTTCCGTGTTCAAAAATAGAAAATCAC 58.523 33.333 0.00 0.00 0.00 3.06
3082 5165 8.191446 TGTTCCGTGTTCAAAAATAGAAAATCA 58.809 29.630 0.00 0.00 0.00 2.57
3083 5166 8.568732 TGTTCCGTGTTCAAAAATAGAAAATC 57.431 30.769 0.00 0.00 0.00 2.17
3084 5167 8.934507 TTGTTCCGTGTTCAAAAATAGAAAAT 57.065 26.923 0.00 0.00 0.00 1.82
3085 5168 8.758633 TTTGTTCCGTGTTCAAAAATAGAAAA 57.241 26.923 0.00 0.00 0.00 2.29
3086 5169 8.758633 TTTTGTTCCGTGTTCAAAAATAGAAA 57.241 26.923 0.00 0.00 37.86 2.52
3087 5170 7.009723 GCTTTTGTTCCGTGTTCAAAAATAGAA 59.990 33.333 0.00 0.00 39.44 2.10
3088 5171 6.474102 GCTTTTGTTCCGTGTTCAAAAATAGA 59.526 34.615 0.00 0.00 39.44 1.98
3089 5172 6.254589 TGCTTTTGTTCCGTGTTCAAAAATAG 59.745 34.615 0.00 0.00 39.44 1.73
3090 5173 6.100004 TGCTTTTGTTCCGTGTTCAAAAATA 58.900 32.000 0.00 0.00 39.44 1.40
3091 5174 4.932200 TGCTTTTGTTCCGTGTTCAAAAAT 59.068 33.333 0.00 0.00 39.44 1.82
3092 5175 4.307432 TGCTTTTGTTCCGTGTTCAAAAA 58.693 34.783 0.00 0.00 39.44 1.94
3093 5176 3.914312 TGCTTTTGTTCCGTGTTCAAAA 58.086 36.364 0.00 0.00 38.27 2.44
3094 5177 3.577649 TGCTTTTGTTCCGTGTTCAAA 57.422 38.095 0.00 0.00 0.00 2.69
3095 5178 3.506810 CTTGCTTTTGTTCCGTGTTCAA 58.493 40.909 0.00 0.00 0.00 2.69
3096 5179 2.733858 GCTTGCTTTTGTTCCGTGTTCA 60.734 45.455 0.00 0.00 0.00 3.18
3097 5180 1.852280 GCTTGCTTTTGTTCCGTGTTC 59.148 47.619 0.00 0.00 0.00 3.18
3098 5181 1.797348 CGCTTGCTTTTGTTCCGTGTT 60.797 47.619 0.00 0.00 0.00 3.32
3099 5182 0.248458 CGCTTGCTTTTGTTCCGTGT 60.248 50.000 0.00 0.00 0.00 4.49
3100 5183 1.539776 GCGCTTGCTTTTGTTCCGTG 61.540 55.000 0.00 0.00 35.07 4.94
3101 5184 1.299089 GCGCTTGCTTTTGTTCCGT 60.299 52.632 0.00 0.00 35.07 4.69
3102 5185 3.526029 GCGCTTGCTTTTGTTCCG 58.474 55.556 0.00 0.00 35.07 4.30
3107 5190 9.226221 GTACAATTGTATGAGCGCTTGCTTTTG 62.226 40.741 20.72 12.42 40.06 2.44
3108 5191 7.327712 GTACAATTGTATGAGCGCTTGCTTTT 61.328 38.462 20.72 0.00 40.06 2.27
3109 5192 5.899837 GTACAATTGTATGAGCGCTTGCTTT 60.900 40.000 20.72 0.00 40.06 3.51
3110 5193 4.437390 GTACAATTGTATGAGCGCTTGCTT 60.437 41.667 20.72 0.00 40.06 3.91
3111 5194 3.063997 GTACAATTGTATGAGCGCTTGCT 59.936 43.478 20.72 1.38 41.59 3.91
3112 5195 2.549633 ACAATTGTATGAGCGCTTGC 57.450 45.000 13.26 0.00 39.58 4.01
3113 5196 4.548916 CGAGTACAATTGTATGAGCGCTTG 60.549 45.833 20.72 11.80 32.54 4.01
3114 5197 3.551890 CGAGTACAATTGTATGAGCGCTT 59.448 43.478 20.72 0.00 32.54 4.68
3115 5198 3.116300 CGAGTACAATTGTATGAGCGCT 58.884 45.455 20.72 11.27 32.54 5.92
3116 5199 2.858344 ACGAGTACAATTGTATGAGCGC 59.142 45.455 20.72 0.00 32.54 5.92
3117 5200 4.102649 TCACGAGTACAATTGTATGAGCG 58.897 43.478 20.72 20.61 32.54 5.03
3118 5201 6.589830 AATCACGAGTACAATTGTATGAGC 57.410 37.500 20.72 8.50 32.54 4.26
3119 5202 8.873830 AGAAAATCACGAGTACAATTGTATGAG 58.126 33.333 20.72 15.89 32.54 2.90
3120 5203 8.771920 AGAAAATCACGAGTACAATTGTATGA 57.228 30.769 20.72 18.91 32.54 2.15
3129 5212 9.872757 GTTCAAAAATAGAAAATCACGAGTACA 57.127 29.630 0.00 0.00 0.00 2.90
3130 5213 9.872757 TGTTCAAAAATAGAAAATCACGAGTAC 57.127 29.630 0.00 0.00 0.00 2.73
3131 5214 9.872757 GTGTTCAAAAATAGAAAATCACGAGTA 57.127 29.630 0.00 0.00 0.00 2.59
3132 5215 7.586300 CGTGTTCAAAAATAGAAAATCACGAGT 59.414 33.333 0.00 0.00 41.48 4.18
3133 5216 7.059488 CCGTGTTCAAAAATAGAAAATCACGAG 59.941 37.037 14.77 5.84 41.48 4.18
3134 5217 6.853872 CCGTGTTCAAAAATAGAAAATCACGA 59.146 34.615 14.77 0.00 41.48 4.35
3135 5218 6.853872 TCCGTGTTCAAAAATAGAAAATCACG 59.146 34.615 0.00 0.00 40.06 4.35
3136 5219 8.476925 GTTCCGTGTTCAAAAATAGAAAATCAC 58.523 33.333 0.00 0.00 0.00 3.06
3137 5220 8.191446 TGTTCCGTGTTCAAAAATAGAAAATCA 58.809 29.630 0.00 0.00 0.00 2.57
3138 5221 8.568732 TGTTCCGTGTTCAAAAATAGAAAATC 57.431 30.769 0.00 0.00 0.00 2.17
3139 5222 8.934507 TTGTTCCGTGTTCAAAAATAGAAAAT 57.065 26.923 0.00 0.00 0.00 1.82
3140 5223 8.758633 TTTGTTCCGTGTTCAAAAATAGAAAA 57.241 26.923 0.00 0.00 0.00 2.29
3141 5224 8.758633 TTTTGTTCCGTGTTCAAAAATAGAAA 57.241 26.923 0.00 0.00 37.86 2.52
3142 5225 7.009723 GCTTTTGTTCCGTGTTCAAAAATAGAA 59.990 33.333 0.00 0.00 39.44 2.10
3143 5226 6.474102 GCTTTTGTTCCGTGTTCAAAAATAGA 59.526 34.615 0.00 0.00 39.44 1.98
3144 5227 6.254589 TGCTTTTGTTCCGTGTTCAAAAATAG 59.745 34.615 0.00 0.00 39.44 1.73
3145 5228 6.100004 TGCTTTTGTTCCGTGTTCAAAAATA 58.900 32.000 0.00 0.00 39.44 1.40
3146 5229 4.932200 TGCTTTTGTTCCGTGTTCAAAAAT 59.068 33.333 0.00 0.00 39.44 1.82
3147 5230 4.307432 TGCTTTTGTTCCGTGTTCAAAAA 58.693 34.783 0.00 0.00 39.44 1.94
3148 5231 3.914312 TGCTTTTGTTCCGTGTTCAAAA 58.086 36.364 0.00 0.00 38.27 2.44
3149 5232 3.577649 TGCTTTTGTTCCGTGTTCAAA 57.422 38.095 0.00 0.00 0.00 2.69
3150 5233 3.506810 CTTGCTTTTGTTCCGTGTTCAA 58.493 40.909 0.00 0.00 0.00 2.69
3151 5234 2.733858 GCTTGCTTTTGTTCCGTGTTCA 60.734 45.455 0.00 0.00 0.00 3.18
3152 5235 1.852280 GCTTGCTTTTGTTCCGTGTTC 59.148 47.619 0.00 0.00 0.00 3.18
3153 5236 1.797348 CGCTTGCTTTTGTTCCGTGTT 60.797 47.619 0.00 0.00 0.00 3.32
3154 5237 0.248458 CGCTTGCTTTTGTTCCGTGT 60.248 50.000 0.00 0.00 0.00 4.49
3155 5238 1.539776 GCGCTTGCTTTTGTTCCGTG 61.540 55.000 0.00 0.00 35.07 4.94
3156 5239 1.299089 GCGCTTGCTTTTGTTCCGT 60.299 52.632 0.00 0.00 35.07 4.69
3157 5240 3.526029 GCGCTTGCTTTTGTTCCG 58.474 55.556 0.00 0.00 35.07 4.30
3162 5245 9.226221 GTACAATTGTATGAGCGCTTGCTTTTG 62.226 40.741 20.72 12.42 40.06 2.44
3163 5246 7.327712 GTACAATTGTATGAGCGCTTGCTTTT 61.328 38.462 20.72 0.00 40.06 2.27
3164 5247 5.899837 GTACAATTGTATGAGCGCTTGCTTT 60.900 40.000 20.72 0.00 40.06 3.51
3165 5248 4.437390 GTACAATTGTATGAGCGCTTGCTT 60.437 41.667 20.72 0.00 40.06 3.91
3166 5249 3.063997 GTACAATTGTATGAGCGCTTGCT 59.936 43.478 20.72 1.38 41.59 3.91
3167 5250 2.549633 ACAATTGTATGAGCGCTTGC 57.450 45.000 13.26 0.00 39.58 4.01
3168 5251 4.548916 CGAGTACAATTGTATGAGCGCTTG 60.549 45.833 20.72 11.80 32.54 4.01
3169 5252 3.551890 CGAGTACAATTGTATGAGCGCTT 59.448 43.478 20.72 0.00 32.54 4.68
3170 5253 3.116300 CGAGTACAATTGTATGAGCGCT 58.884 45.455 20.72 11.27 32.54 5.92
3171 5254 2.858344 ACGAGTACAATTGTATGAGCGC 59.142 45.455 20.72 0.00 32.54 5.92
3172 5255 4.102649 TCACGAGTACAATTGTATGAGCG 58.897 43.478 20.72 20.61 32.54 5.03
3173 5256 6.589830 AATCACGAGTACAATTGTATGAGC 57.410 37.500 20.72 8.50 32.54 4.26
3174 5257 7.963981 ACAAATCACGAGTACAATTGTATGAG 58.036 34.615 20.72 15.89 32.54 2.90
3175 5258 7.899178 ACAAATCACGAGTACAATTGTATGA 57.101 32.000 20.72 18.91 32.54 2.15
3176 5259 8.948853 AAACAAATCACGAGTACAATTGTATG 57.051 30.769 20.72 14.62 32.54 2.39
3177 5260 9.393249 CAAAACAAATCACGAGTACAATTGTAT 57.607 29.630 20.72 10.28 32.54 2.29
3178 5261 8.613482 TCAAAACAAATCACGAGTACAATTGTA 58.387 29.630 14.35 14.35 0.00 2.41
3179 5262 7.431084 GTCAAAACAAATCACGAGTACAATTGT 59.569 33.333 16.68 16.68 0.00 2.71
3180 5263 7.430793 TGTCAAAACAAATCACGAGTACAATTG 59.569 33.333 3.24 3.24 30.70 2.32
3230 5313 8.146412 GCAAAAATATAAGGGCTCAAAGATGAT 58.854 33.333 0.00 0.00 34.37 2.45
3234 5317 7.100458 GAGCAAAAATATAAGGGCTCAAAGA 57.900 36.000 0.00 0.00 45.23 2.52
3250 5333 0.679640 ATCCATCGCCGGAGCAAAAA 60.680 50.000 5.05 0.00 38.83 1.94
3251 5334 1.077787 ATCCATCGCCGGAGCAAAA 60.078 52.632 5.05 0.00 38.83 2.44
3420 5518 6.322969 TCGTACTGAAACCATACCTCATGTAT 59.677 38.462 0.00 0.00 40.91 2.29
3461 5577 0.911769 TCCATCAACGGCAATCTCCT 59.088 50.000 0.00 0.00 0.00 3.69
3462 5578 1.017387 GTCCATCAACGGCAATCTCC 58.983 55.000 0.00 0.00 0.00 3.71
3463 5579 1.737838 TGTCCATCAACGGCAATCTC 58.262 50.000 0.00 0.00 0.00 2.75
3508 5631 8.680903 CCTTCTACAACATTGAGCTCAAATATT 58.319 33.333 31.55 21.71 39.55 1.28
3591 5714 4.504858 CATAGGACGTTAAAAGCCTGACT 58.495 43.478 1.65 0.00 32.04 3.41
3596 5719 2.030091 GTCGCATAGGACGTTAAAAGCC 59.970 50.000 0.00 0.00 0.00 4.35
3649 5775 4.038361 CACAGATCGAATCGTTGTCCTAG 58.962 47.826 1.52 0.00 0.00 3.02
3732 5863 7.876582 ACATATCCATCTCAACATACACATCTG 59.123 37.037 0.00 0.00 0.00 2.90
3818 5957 2.354259 GATGTTGGACAGCCTTCTCTG 58.646 52.381 0.00 0.00 39.86 3.35
3827 5966 0.608130 TCCCAGACGATGTTGGACAG 59.392 55.000 0.00 0.00 36.55 3.51


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

AutoCloner maintained by Alex Coulton.