Multiple sequence alignment - TraesCS5A01G125900

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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 TraesCS5A01G125900 chr5A 100.000 6978 0 0 1 6978 277331260 277338237 0.000000e+00 12887.0
1 TraesCS5A01G125900 chr5A 84.914 232 27 7 5402 5630 503680738 503680512 1.960000e-55 228.0
2 TraesCS5A01G125900 chr5A 84.052 232 29 7 5402 5630 358638536 358638762 4.240000e-52 217.0
3 TraesCS5A01G125900 chr5A 79.429 175 18 3 5222 5379 259071857 259072030 2.660000e-19 108.0
4 TraesCS5A01G125900 chr5D 94.387 5879 177 36 1128 6910 213319874 213325695 0.000000e+00 8887.0
5 TraesCS5A01G125900 chr5B 96.622 3997 91 12 2347 6328 227639971 227643938 0.000000e+00 6593.0
6 TraesCS5A01G125900 chr5B 99.645 1127 4 0 1 1127 669223054 669224180 0.000000e+00 2060.0
7 TraesCS5A01G125900 chr5B 92.605 1244 46 18 1128 2351 227638687 227639904 0.000000e+00 1746.0
8 TraesCS5A01G125900 chr5B 89.840 374 19 9 6325 6681 227644194 227644565 4.930000e-126 462.0
9 TraesCS5A01G125900 chr5B 88.889 234 21 3 6678 6910 227645323 227645552 4.120000e-72 283.0
10 TraesCS5A01G125900 chrUn 100.000 393 0 0 283 675 479547896 479548288 0.000000e+00 726.0
11 TraesCS5A01G125900 chr6D 85.512 283 26 10 238 511 361420099 361420375 1.480000e-71 281.0
12 TraesCS5A01G125900 chr6D 85.512 283 25 12 238 511 460381672 460381397 1.480000e-71 281.0
13 TraesCS5A01G125900 chr6D 92.899 169 11 1 956 1124 417749894 417750061 1.940000e-60 244.0
14 TraesCS5A01G125900 chr6D 79.755 163 23 6 5224 5376 2939728 2939566 7.400000e-20 110.0
15 TraesCS5A01G125900 chr4D 85.512 283 26 10 238 511 445096569 445096845 1.480000e-71 281.0
16 TraesCS5A01G125900 chr3D 85.512 283 26 10 238 511 419990036 419990312 1.480000e-71 281.0
17 TraesCS5A01G125900 chr3D 85.159 283 27 8 238 511 61845196 61844920 6.890000e-70 276.0
18 TraesCS5A01G125900 chr3D 84.337 166 16 4 5224 5379 301774496 301774661 3.370000e-33 154.0
19 TraesCS5A01G125900 chr7D 85.461 282 26 11 238 511 36414973 36414699 5.330000e-71 279.0
20 TraesCS5A01G125900 chr7D 84.649 228 30 5 5405 5630 466189305 466189529 9.110000e-54 222.0
21 TraesCS5A01G125900 chr7D 82.955 176 10 8 5224 5379 167107668 167107843 2.620000e-29 141.0
22 TraesCS5A01G125900 chr1D 85.159 283 27 10 238 511 110014456 110014732 6.890000e-70 276.0
23 TraesCS5A01G125900 chr2A 85.281 231 28 5 5402 5630 164565913 164566139 4.210000e-57 233.0
24 TraesCS5A01G125900 chr2A 84.848 231 28 6 5402 5630 180337167 180336942 7.040000e-55 226.0
25 TraesCS5A01G125900 chr7A 85.022 227 29 4 5406 5630 332399147 332399370 7.040000e-55 226.0
26 TraesCS5A01G125900 chr7A 83.700 227 32 4 5406 5630 332415300 332415523 7.090000e-50 209.0
27 TraesCS5A01G125900 chr1B 83.682 239 32 6 5394 5627 558082684 558082448 1.180000e-52 219.0
28 TraesCS5A01G125900 chr1B 91.489 94 8 0 5286 5379 372868141 372868048 5.680000e-26 130.0
29 TraesCS5A01G125900 chr3A 84.337 166 16 4 5224 5379 440027215 440027050 3.370000e-33 154.0
30 TraesCS5A01G125900 chr3A 78.977 176 17 7 5224 5379 655234756 655234581 1.240000e-17 102.0
31 TraesCS5A01G125900 chr2B 83.735 166 17 4 5224 5379 644335515 644335680 1.570000e-31 148.0
32 TraesCS5A01G125900 chr1A 82.184 174 19 7 5221 5383 268804647 268804819 9.440000e-29 139.0
33 TraesCS5A01G125900 chr2D 82.979 94 13 2 5286 5379 641368245 641368335 1.610000e-11 82.4


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 TraesCS5A01G125900 chr5A 277331260 277338237 6977 False 12887 12887 100.000 1 6978 1 chr5A.!!$F2 6977
1 TraesCS5A01G125900 chr5D 213319874 213325695 5821 False 8887 8887 94.387 1128 6910 1 chr5D.!!$F1 5782
2 TraesCS5A01G125900 chr5B 227638687 227645552 6865 False 2271 6593 91.989 1128 6910 4 chr5B.!!$F2 5782
3 TraesCS5A01G125900 chr5B 669223054 669224180 1126 False 2060 2060 99.645 1 1127 1 chr5B.!!$F1 1126

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
710 711 2.682856 TGTGTCTCAACTCAAACTTGCC 59.317 45.455 0.0 0.0 0.00 4.52 F
1327 1337 1.174783 ACCAGTACACCGCTAGTCAG 58.825 55.000 0.0 0.0 0.00 3.51 F
2041 2096 0.323451 GGTGGAGGGGAATGGTTGTC 60.323 60.000 0.0 0.0 0.00 3.18 F
2060 2115 0.523072 CTTTGGATGTGTTGGAGGCG 59.477 55.000 0.0 0.0 0.00 5.52 F
2780 2918 1.740025 CCTTGGCCGATTCTCTTGAAC 59.260 52.381 0.0 0.0 34.71 3.18 F
4034 4180 2.463047 AACCAAAAGTAAGTGGCCCA 57.537 45.000 0.0 0.0 38.58 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2096 0.523072 CGCCTCCAACACATCCAAAG 59.477 55.000 0.00 0.00 0.00 2.77 R
3188 3331 0.106894 GGATTGCCCGGAGAACCTAG 59.893 60.000 0.73 0.00 0.00 3.02 R
3189 3332 0.619255 TGGATTGCCCGGAGAACCTA 60.619 55.000 0.73 0.00 37.93 3.08 R
4030 4176 0.702316 TTTAGGGAGGAAAGGTGGGC 59.298 55.000 0.00 0.00 0.00 5.36 R
4154 4300 5.824624 TGGCAAAGACTTGATATCATCTTCC 59.175 40.000 17.78 15.92 34.14 3.46 R
6032 6205 2.039216 TGATAACCCGGAGCAAGAAACA 59.961 45.455 0.73 0.00 0.00 2.83 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
281 282 4.720649 GGAAATAGTTTTTCCTCTGCCC 57.279 45.455 15.57 0.00 43.45 5.36
675 676 8.718656 TCATTTTTCTTCTAATTTTCCCCCAAA 58.281 29.630 0.00 0.00 0.00 3.28
710 711 2.682856 TGTGTCTCAACTCAAACTTGCC 59.317 45.455 0.00 0.00 0.00 4.52
1231 1232 1.454847 TTTTCCCTGCTGCCACGTT 60.455 52.632 0.00 0.00 0.00 3.99
1291 1296 3.364267 CCACATGACGTGTCAAGAATGTG 60.364 47.826 19.93 19.93 44.78 3.21
1299 1304 4.142773 ACGTGTCAAGAATGTGTTCGTTTT 60.143 37.500 0.00 0.00 39.38 2.43
1327 1337 1.174783 ACCAGTACACCGCTAGTCAG 58.825 55.000 0.00 0.00 0.00 3.51
1352 1362 1.996191 GTTCGATGCTCACACTTCTCC 59.004 52.381 0.00 0.00 0.00 3.71
1643 1689 4.664677 CGGCCCGATCCATCCGTC 62.665 72.222 0.00 0.00 37.33 4.79
1644 1690 4.664677 GGCCCGATCCATCCGTCG 62.665 72.222 0.00 0.00 37.58 5.12
1921 1976 1.683790 CGCTTCTTAGGACGCAACCG 61.684 60.000 4.23 0.00 36.66 4.44
2041 2096 0.323451 GGTGGAGGGGAATGGTTGTC 60.323 60.000 0.00 0.00 0.00 3.18
2052 2107 3.573967 GGAATGGTTGTCTTTGGATGTGT 59.426 43.478 0.00 0.00 0.00 3.72
2060 2115 0.523072 CTTTGGATGTGTTGGAGGCG 59.477 55.000 0.00 0.00 0.00 5.52
2112 2167 2.721231 GCGCAGTCCAACAAAGCA 59.279 55.556 0.30 0.00 0.00 3.91
2180 2235 8.649973 GATGGAATCTGAACGAACTAAATACT 57.350 34.615 0.00 0.00 41.17 2.12
2181 2236 9.745880 GATGGAATCTGAACGAACTAAATACTA 57.254 33.333 0.00 0.00 41.17 1.82
2213 2268 2.882761 GGTACGATTTTATGGGAAGGCC 59.117 50.000 0.00 0.00 0.00 5.19
2289 2344 6.303839 TCCTACAAAGCATATAATGTTCCCC 58.696 40.000 0.00 0.00 0.00 4.81
2314 2369 2.605366 GCTCTCAATTGGCGACTTACTC 59.395 50.000 5.42 0.00 0.00 2.59
2424 2549 7.884877 ACATTCTCCACAACTCTCATAATTGAA 59.115 33.333 0.00 0.00 0.00 2.69
2429 2554 5.181811 CCACAACTCTCATAATTGAAGTGCA 59.818 40.000 0.00 0.00 0.00 4.57
2742 2880 5.897377 ATTTTGTTCCAGAACCCTATTCG 57.103 39.130 8.01 0.00 40.46 3.34
2780 2918 1.740025 CCTTGGCCGATTCTCTTGAAC 59.260 52.381 0.00 0.00 34.71 3.18
3003 3141 3.848377 TGATGAGCCCTGGATATGCTAAT 59.152 43.478 0.00 0.00 34.99 1.73
3029 3167 3.821033 GCAAACAGTCCAATTCCTACACT 59.179 43.478 0.00 0.00 0.00 3.55
3188 3331 8.276325 CCAAGTCGCTCATGTTAATACTATTTC 58.724 37.037 0.00 0.00 0.00 2.17
3189 3332 9.035607 CAAGTCGCTCATGTTAATACTATTTCT 57.964 33.333 0.00 0.00 0.00 2.52
3258 3402 4.357097 TGATAGCTCCCTAGGTTAGATGGA 59.643 45.833 8.29 0.00 34.60 3.41
3262 3406 5.401470 TAGCTCCCTAGGTTAGATGGAACAT 60.401 44.000 8.29 0.00 37.68 2.71
4008 4154 5.385509 AGTTAAGAGAGCTCACTGAAGAC 57.614 43.478 17.77 11.44 0.00 3.01
4030 4176 7.645402 AGACGAAAATAACCAAAAGTAAGTGG 58.355 34.615 0.00 0.00 41.00 4.00
4034 4180 2.463047 AACCAAAAGTAAGTGGCCCA 57.537 45.000 0.00 0.00 38.58 5.36
4192 4338 2.584835 TTGCCATGCTTTCAGGTACT 57.415 45.000 0.00 0.00 43.88 2.73
4568 4714 6.642131 CAGAATCTAGAGCTCTAACTTGATGC 59.358 42.308 23.37 19.19 31.51 3.91
4892 5039 5.093849 TGGCCACAACCTATTCTAACTAC 57.906 43.478 0.00 0.00 0.00 2.73
4912 5059 3.468770 ACAGTAATACGTGTTTGCACCA 58.531 40.909 1.91 0.00 42.39 4.17
5051 5198 7.458397 TCTACCACCTGTTCTTTGATAATTGT 58.542 34.615 0.00 0.00 0.00 2.71
5405 5569 0.179134 CACGCCAGTGCTAGACTACC 60.179 60.000 0.00 0.00 41.94 3.18
5422 5586 7.437713 AGACTACCCATCATCACTTGAATTA 57.562 36.000 0.00 0.00 38.03 1.40
5444 5608 3.889520 AGACTCATTTCCCGACCTTAC 57.110 47.619 0.00 0.00 0.00 2.34
5457 5621 4.082245 CCCGACCTTACTTTGAATGCAAAT 60.082 41.667 0.00 0.00 42.66 2.32
5484 5648 7.067251 GCTATATACTGTACCCACTGGATACTC 59.933 44.444 1.02 0.00 33.60 2.59
5485 5649 3.468071 ACTGTACCCACTGGATACTCA 57.532 47.619 1.02 0.00 34.81 3.41
5486 5650 3.995636 ACTGTACCCACTGGATACTCAT 58.004 45.455 1.02 0.00 34.81 2.90
5487 5651 4.362677 ACTGTACCCACTGGATACTCATT 58.637 43.478 1.02 0.00 34.81 2.57
5488 5652 4.162320 ACTGTACCCACTGGATACTCATTG 59.838 45.833 1.02 0.00 34.81 2.82
5489 5653 3.454447 TGTACCCACTGGATACTCATTGG 59.546 47.826 1.02 0.00 37.26 3.16
5490 5654 2.645838 CCCACTGGATACTCATTGGG 57.354 55.000 5.99 5.99 46.45 4.12
5491 5655 1.846439 CCCACTGGATACTCATTGGGT 59.154 52.381 10.84 0.00 46.46 4.51
5492 5656 3.045634 CCCACTGGATACTCATTGGGTA 58.954 50.000 10.84 0.00 46.46 3.69
5493 5657 3.652869 CCCACTGGATACTCATTGGGTAT 59.347 47.826 8.97 8.97 46.46 2.73
5494 5658 4.844085 CCCACTGGATACTCATTGGGTATA 59.156 45.833 9.18 0.00 46.46 1.47
5495 5659 5.046304 CCCACTGGATACTCATTGGGTATAG 60.046 48.000 9.18 6.99 46.46 1.31
5822 5995 8.134202 TGCTGTAGTATAGCATACCATGTTAT 57.866 34.615 16.76 1.90 45.52 1.89
6032 6205 8.840321 CATTCATATACGTGGGAAGAATTCTTT 58.160 33.333 21.33 7.52 46.56 2.52
6043 6216 5.923114 GGGAAGAATTCTTTGTTTCTTGCTC 59.077 40.000 21.33 4.67 46.56 4.26
6060 6233 0.182537 CTCCGGGTTATCAATGGCCA 59.817 55.000 8.56 8.56 0.00 5.36
6088 6261 1.137825 GAACAGAGACCCGAGAGCG 59.862 63.158 0.00 0.00 37.24 5.03
6091 6264 0.681564 ACAGAGACCCGAGAGCGAAT 60.682 55.000 0.00 0.00 40.82 3.34
6256 6429 3.127548 AGCTTGTATGCTGCATGTTGTAC 59.872 43.478 24.59 14.52 42.33 2.90
6260 6433 2.495155 ATGCTGCATGTTGTACCTCA 57.505 45.000 15.44 0.00 0.00 3.86
6294 6467 6.153000 AGGACTGTAGTAGAAACATGTACAGG 59.847 42.308 20.94 5.87 43.21 4.00
6353 6783 7.036220 GCACTGAAAACATAGACTAGAAGCTA 58.964 38.462 0.00 0.00 0.00 3.32
6553 6985 6.029346 TCTTTTGAAAATGGCTCTCATTCC 57.971 37.500 0.00 0.00 44.68 3.01
6554 6986 4.806640 TTTGAAAATGGCTCTCATTCCC 57.193 40.909 0.00 0.00 44.68 3.97
6555 6987 3.744940 TGAAAATGGCTCTCATTCCCT 57.255 42.857 0.00 0.00 44.68 4.20
6567 7004 2.307098 CTCATTCCCTTCTTCTGTGGGT 59.693 50.000 0.00 0.00 41.58 4.51
6579 7016 3.420482 GTGGGTGATGGGGAGGGG 61.420 72.222 0.00 0.00 0.00 4.79
6602 7039 3.375443 TAGCCGCTGGTAGCCCTCT 62.375 63.158 2.16 0.00 38.18 3.69
6603 7040 4.537433 GCCGCTGGTAGCCCTCTG 62.537 72.222 0.00 0.00 38.18 3.35
6606 7043 2.904131 GCTGGTAGCCCTCTGTCC 59.096 66.667 0.00 0.00 34.48 4.02
6607 7044 2.736826 GCTGGTAGCCCTCTGTCCC 61.737 68.421 0.00 0.00 34.48 4.46
6659 7107 1.354368 TGCCTCCTAAGGTTCCTTTGG 59.646 52.381 20.48 20.48 45.34 3.28
6675 7123 4.066139 GGCAATGGCTCCTGGGGT 62.066 66.667 0.00 0.00 40.87 4.95
6685 7894 0.763223 CTCCTGGGGTATTAGGCGGT 60.763 60.000 0.00 0.00 34.00 5.68
6690 7899 1.629181 GGGGTATTAGGCGGTGTGGT 61.629 60.000 0.00 0.00 0.00 4.16
6748 7958 1.269831 GCGGTAGATTGAGGCTCGATT 60.270 52.381 18.18 10.70 0.00 3.34
6792 8002 3.897122 GGTGGTTGGGGCAGTCCA 61.897 66.667 0.00 0.00 37.22 4.02
6805 8015 2.217038 AGTCCATGGCCTCGTGTGT 61.217 57.895 6.96 0.00 0.00 3.72
6817 8027 2.394708 CTCGTGTGTCATGAAGTCGTT 58.605 47.619 0.00 0.00 0.00 3.85
6825 8035 3.206150 GTCATGAAGTCGTTGGGCATAT 58.794 45.455 0.00 0.00 0.00 1.78
6834 8044 4.345257 AGTCGTTGGGCATATACAGATCTT 59.655 41.667 0.00 0.00 0.00 2.40
6841 8051 5.126222 TGGGCATATACAGATCTTCGATCTC 59.874 44.000 3.50 0.00 0.00 2.75
6844 8054 5.163703 GCATATACAGATCTTCGATCTCGGT 60.164 44.000 3.50 3.44 40.29 4.69
6847 8057 4.074627 ACAGATCTTCGATCTCGGTCTA 57.925 45.455 3.50 0.00 40.29 2.59
6854 8064 3.487120 TCGATCTCGGTCTATTCTCCA 57.513 47.619 0.00 0.00 40.29 3.86
6910 8120 2.233186 GGAGCGGAAGGTTGTTAGTACT 59.767 50.000 0.00 0.00 45.11 2.73
6911 8121 3.445096 GGAGCGGAAGGTTGTTAGTACTA 59.555 47.826 0.00 0.00 45.11 1.82
6912 8122 4.439837 GGAGCGGAAGGTTGTTAGTACTAG 60.440 50.000 2.23 0.00 45.11 2.57
6913 8123 4.338879 AGCGGAAGGTTGTTAGTACTAGA 58.661 43.478 2.23 0.00 40.01 2.43
6914 8124 4.768968 AGCGGAAGGTTGTTAGTACTAGAA 59.231 41.667 2.23 0.00 40.01 2.10
6915 8125 4.861462 GCGGAAGGTTGTTAGTACTAGAAC 59.139 45.833 14.35 14.35 0.00 3.01
6916 8126 5.405797 CGGAAGGTTGTTAGTACTAGAACC 58.594 45.833 25.16 25.16 37.01 3.62
6917 8127 5.405797 GGAAGGTTGTTAGTACTAGAACCG 58.594 45.833 25.63 0.00 40.89 4.44
6918 8128 5.183904 GGAAGGTTGTTAGTACTAGAACCGA 59.816 44.000 25.63 8.17 40.89 4.69
6919 8129 5.893897 AGGTTGTTAGTACTAGAACCGAG 57.106 43.478 25.63 0.00 40.89 4.63
6920 8130 4.157472 AGGTTGTTAGTACTAGAACCGAGC 59.843 45.833 25.63 15.65 40.89 5.03
6921 8131 4.419280 GTTGTTAGTACTAGAACCGAGCC 58.581 47.826 12.67 0.00 0.00 4.70
6922 8132 3.019564 TGTTAGTACTAGAACCGAGCCC 58.980 50.000 2.23 0.00 0.00 5.19
6923 8133 1.959042 TAGTACTAGAACCGAGCCCG 58.041 55.000 0.00 0.00 0.00 6.13
6924 8134 1.065436 GTACTAGAACCGAGCCCGC 59.935 63.158 0.00 0.00 0.00 6.13
6925 8135 1.378911 TACTAGAACCGAGCCCGCA 60.379 57.895 0.00 0.00 0.00 5.69
6926 8136 1.660560 TACTAGAACCGAGCCCGCAC 61.661 60.000 0.00 0.00 0.00 5.34
6927 8137 4.124351 TAGAACCGAGCCCGCACG 62.124 66.667 0.00 0.00 0.00 5.34
6933 8143 4.873129 CGAGCCCGCACGCATAGT 62.873 66.667 0.00 0.00 0.00 2.12
6934 8144 2.511600 GAGCCCGCACGCATAGTT 60.512 61.111 0.00 0.00 0.00 2.24
6935 8145 2.046314 AGCCCGCACGCATAGTTT 60.046 55.556 0.00 0.00 0.00 2.66
6936 8146 0.808453 GAGCCCGCACGCATAGTTTA 60.808 55.000 0.00 0.00 0.00 2.01
6937 8147 1.087771 AGCCCGCACGCATAGTTTAC 61.088 55.000 0.00 0.00 0.00 2.01
6938 8148 2.011453 CCCGCACGCATAGTTTACC 58.989 57.895 0.00 0.00 0.00 2.85
6939 8149 0.461339 CCCGCACGCATAGTTTACCT 60.461 55.000 0.00 0.00 0.00 3.08
6940 8150 1.202440 CCCGCACGCATAGTTTACCTA 60.202 52.381 0.00 0.00 0.00 3.08
6941 8151 2.124903 CCGCACGCATAGTTTACCTAG 58.875 52.381 0.00 0.00 0.00 3.02
6942 8152 2.124903 CGCACGCATAGTTTACCTAGG 58.875 52.381 7.41 7.41 0.00 3.02
6943 8153 2.480759 CGCACGCATAGTTTACCTAGGT 60.481 50.000 20.57 20.57 30.07 3.08
6944 8154 3.528532 GCACGCATAGTTTACCTAGGTT 58.471 45.455 22.11 4.10 30.07 3.50
6945 8155 3.937079 GCACGCATAGTTTACCTAGGTTT 59.063 43.478 22.11 6.45 30.07 3.27
6946 8156 5.111293 GCACGCATAGTTTACCTAGGTTTA 58.889 41.667 22.11 5.99 30.07 2.01
6947 8157 5.581874 GCACGCATAGTTTACCTAGGTTTAA 59.418 40.000 22.11 12.23 30.07 1.52
6948 8158 6.238022 GCACGCATAGTTTACCTAGGTTTAAG 60.238 42.308 22.11 6.53 30.07 1.85
6949 8159 5.814188 ACGCATAGTTTACCTAGGTTTAAGC 59.186 40.000 22.11 11.40 30.07 3.09
6950 8160 5.235831 CGCATAGTTTACCTAGGTTTAAGCC 59.764 44.000 22.11 0.00 30.07 4.35
6951 8161 6.354938 GCATAGTTTACCTAGGTTTAAGCCT 58.645 40.000 22.11 15.78 42.43 4.58
6952 8162 6.827251 GCATAGTTTACCTAGGTTTAAGCCTT 59.173 38.462 22.11 1.10 39.94 4.35
6953 8163 7.012138 GCATAGTTTACCTAGGTTTAAGCCTTC 59.988 40.741 22.11 3.22 39.94 3.46
6954 8164 5.485620 AGTTTACCTAGGTTTAAGCCTTCG 58.514 41.667 22.11 9.19 39.94 3.79
6955 8165 5.246883 AGTTTACCTAGGTTTAAGCCTTCGA 59.753 40.000 22.11 0.00 39.94 3.71
6956 8166 5.945144 TTACCTAGGTTTAAGCCTTCGAT 57.055 39.130 22.11 3.15 39.94 3.59
6957 8167 4.138487 ACCTAGGTTTAAGCCTTCGATG 57.862 45.455 16.71 3.89 39.94 3.84
6958 8168 3.773119 ACCTAGGTTTAAGCCTTCGATGA 59.227 43.478 16.71 0.00 39.94 2.92
6959 8169 4.141914 ACCTAGGTTTAAGCCTTCGATGAG 60.142 45.833 16.71 6.40 39.94 2.90
6960 8170 3.268023 AGGTTTAAGCCTTCGATGAGG 57.732 47.619 4.80 0.00 39.93 3.86
6961 8171 2.838202 AGGTTTAAGCCTTCGATGAGGA 59.162 45.455 4.80 0.00 39.25 3.71
6962 8172 2.937149 GGTTTAAGCCTTCGATGAGGAC 59.063 50.000 7.36 0.00 39.25 3.85
6963 8173 3.369576 GGTTTAAGCCTTCGATGAGGACT 60.370 47.826 7.36 1.40 39.25 3.85
6964 8174 4.142004 GGTTTAAGCCTTCGATGAGGACTA 60.142 45.833 7.36 0.00 39.25 2.59
6965 8175 5.416947 GTTTAAGCCTTCGATGAGGACTAA 58.583 41.667 7.36 1.21 39.25 2.24
6966 8176 5.871396 TTAAGCCTTCGATGAGGACTAAT 57.129 39.130 7.36 0.00 39.25 1.73
6967 8177 6.971726 TTAAGCCTTCGATGAGGACTAATA 57.028 37.500 7.36 0.00 39.25 0.98
6968 8178 4.857509 AGCCTTCGATGAGGACTAATAC 57.142 45.455 7.36 0.00 39.25 1.89
6969 8179 3.574826 AGCCTTCGATGAGGACTAATACC 59.425 47.826 7.36 0.00 39.25 2.73
6970 8180 3.306156 GCCTTCGATGAGGACTAATACCC 60.306 52.174 7.36 0.00 39.25 3.69
6971 8181 4.153411 CCTTCGATGAGGACTAATACCCT 58.847 47.826 0.00 0.00 39.25 4.34
6972 8182 5.322754 CCTTCGATGAGGACTAATACCCTA 58.677 45.833 0.00 0.00 39.25 3.53
6973 8183 5.183522 CCTTCGATGAGGACTAATACCCTAC 59.816 48.000 0.00 0.00 39.25 3.18
6974 8184 5.314718 TCGATGAGGACTAATACCCTACA 57.685 43.478 0.00 0.00 31.84 2.74
6975 8185 5.888901 TCGATGAGGACTAATACCCTACAT 58.111 41.667 0.00 0.00 31.84 2.29
6976 8186 5.944599 TCGATGAGGACTAATACCCTACATC 59.055 44.000 0.00 0.00 35.79 3.06
6977 8187 5.710567 CGATGAGGACTAATACCCTACATCA 59.289 44.000 0.00 0.00 37.18 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
281 282 6.346279 GCAAACAATTGTGATGATGAACACAG 60.346 38.462 22.25 0.00 45.50 3.66
710 711 4.007659 AGCAACTCGGGGTGTTATTTTAG 58.992 43.478 0.36 0.00 0.00 1.85
1111 1112 0.739813 ATTTGGACGCGACTAGCCAC 60.740 55.000 15.93 0.00 44.76 5.01
1291 1296 3.624410 ACTGGTACAACAGGAAAACGAAC 59.376 43.478 0.00 0.00 42.75 3.95
1327 1337 2.408050 AGTGTGAGCATCGAACAAGAC 58.592 47.619 0.00 0.00 38.61 3.01
1352 1362 0.600057 GCCTTTGGCTTCTTCACTGG 59.400 55.000 0.73 0.00 46.69 4.00
1989 2044 4.253685 CGTTCCCAAATCTACAGTGACAT 58.746 43.478 0.00 0.00 0.00 3.06
2041 2096 0.523072 CGCCTCCAACACATCCAAAG 59.477 55.000 0.00 0.00 0.00 2.77
2052 2107 1.614996 TTCAGCAATTTCGCCTCCAA 58.385 45.000 0.00 0.00 0.00 3.53
2060 2115 5.163963 CGGGTAGCAAAAATTCAGCAATTTC 60.164 40.000 0.00 0.00 40.68 2.17
2127 2182 5.652518 ACACTCTTCTAGAAATAGCGGAAC 58.347 41.667 6.63 0.00 0.00 3.62
2213 2268 9.014297 AGGTAGAAATCAAGTTAAGAAACATGG 57.986 33.333 0.00 0.00 38.12 3.66
2289 2344 2.102438 TCGCCAATTGAGAGCAGCG 61.102 57.895 15.50 15.50 44.61 5.18
2333 2388 8.651389 ACAATCTAATAGCTTGAGCCACTATAA 58.349 33.333 10.41 0.00 43.38 0.98
2424 2549 6.701340 TGAAACTCATAACATAGTCTGCACT 58.299 36.000 0.00 0.00 36.55 4.40
2724 2862 1.906574 AGCGAATAGGGTTCTGGAACA 59.093 47.619 14.25 0.00 42.85 3.18
2742 2880 0.109532 GGGGGAAGAGAGCCATAAGC 59.890 60.000 0.00 0.00 44.25 3.09
2780 2918 2.221055 GGCGTCGATAAAGCATGTAAGG 59.779 50.000 0.00 0.00 33.55 2.69
3003 3141 1.340889 GGAATTGGACTGTTTGCTGCA 59.659 47.619 0.00 0.00 0.00 4.41
3188 3331 0.106894 GGATTGCCCGGAGAACCTAG 59.893 60.000 0.73 0.00 0.00 3.02
3189 3332 0.619255 TGGATTGCCCGGAGAACCTA 60.619 55.000 0.73 0.00 37.93 3.08
3262 3406 9.323985 CCAGAAAAACAATAGTCCAAAATTGAA 57.676 29.630 2.30 0.00 36.73 2.69
3329 3474 5.722021 AACCCTAAATGGACAACATCAAC 57.278 39.130 0.00 0.00 39.40 3.18
3552 3698 6.259346 AGCTTCTTTTCTATCAGCCCTATT 57.741 37.500 0.00 0.00 0.00 1.73
3968 4114 2.146342 ACTTGTCTCGCATTTCACTGG 58.854 47.619 0.00 0.00 0.00 4.00
4008 4154 5.631929 GGCCACTTACTTTTGGTTATTTTCG 59.368 40.000 0.00 0.00 35.09 3.46
4030 4176 0.702316 TTTAGGGAGGAAAGGTGGGC 59.298 55.000 0.00 0.00 0.00 5.36
4034 4180 6.971932 AATACTCTTTTAGGGAGGAAAGGT 57.028 37.500 0.00 0.00 34.45 3.50
4154 4300 5.824624 TGGCAAAGACTTGATATCATCTTCC 59.175 40.000 17.78 15.92 34.14 3.46
4912 5059 5.625150 AGGAAGTAGTGAAGTTGAGCATTT 58.375 37.500 0.00 0.00 0.00 2.32
5063 5210 6.801539 ATCTCGCAGTTTATCAGTTTTTCA 57.198 33.333 0.00 0.00 0.00 2.69
5064 5211 7.298122 TGAATCTCGCAGTTTATCAGTTTTTC 58.702 34.615 0.00 0.00 0.00 2.29
5116 5263 8.706322 ATTTGGGTATTCCTAATATTGGTCAC 57.294 34.615 0.00 0.00 38.80 3.67
5314 5477 7.554118 CCATGCTCTACCCATATATTTTACAGG 59.446 40.741 0.00 0.00 0.00 4.00
5405 5569 9.722184 ATGAGTCTATAATTCAAGTGATGATGG 57.278 33.333 0.00 0.00 38.03 3.51
5422 5586 5.209659 AGTAAGGTCGGGAAATGAGTCTAT 58.790 41.667 0.00 0.00 0.00 1.98
5435 5599 4.497473 TTTGCATTCAAAGTAAGGTCGG 57.503 40.909 0.00 0.00 37.28 4.79
5457 5621 5.069518 TCCAGTGGGTACAGTATATAGCA 57.930 43.478 9.92 0.00 34.93 3.49
5489 5653 7.392953 GCCTATAACTATCGGGTATCCTATACC 59.607 44.444 7.45 7.45 36.88 2.73
5490 5654 7.941238 TGCCTATAACTATCGGGTATCCTATAC 59.059 40.741 0.00 0.00 0.00 1.47
5491 5655 8.049165 TGCCTATAACTATCGGGTATCCTATA 57.951 38.462 0.00 0.00 0.00 1.31
5492 5656 6.919158 TGCCTATAACTATCGGGTATCCTAT 58.081 40.000 0.00 0.00 0.00 2.57
5493 5657 6.331577 TGCCTATAACTATCGGGTATCCTA 57.668 41.667 0.00 0.00 0.00 2.94
5494 5658 5.202746 TGCCTATAACTATCGGGTATCCT 57.797 43.478 0.00 0.00 0.00 3.24
5495 5659 5.221461 CCATGCCTATAACTATCGGGTATCC 60.221 48.000 0.00 0.00 0.00 2.59
5822 5995 3.074390 AGGAGTCCAATGGTTTCACATCA 59.926 43.478 12.86 0.00 0.00 3.07
6032 6205 2.039216 TGATAACCCGGAGCAAGAAACA 59.961 45.455 0.73 0.00 0.00 2.83
6043 6216 1.613437 GATTGGCCATTGATAACCCGG 59.387 52.381 6.09 0.00 0.00 5.73
6060 6233 4.020218 TCGGGTCTCTGTTCTGAATTGATT 60.020 41.667 0.00 0.00 0.00 2.57
6256 6429 5.794894 ACTACAGTCCTAATGTTGTTGAGG 58.205 41.667 0.00 0.00 33.76 3.86
6260 6433 8.426489 TGTTTCTACTACAGTCCTAATGTTGTT 58.574 33.333 0.52 0.00 37.68 2.83
6294 6467 3.426568 GTCACGGAGCTTGCTGCC 61.427 66.667 8.47 5.08 44.23 4.85
6353 6783 3.129638 ACGGTTTGTGTTACAACTGCATT 59.870 39.130 0.00 0.00 37.90 3.56
6547 6979 2.040278 CACCCACAGAAGAAGGGAATGA 59.960 50.000 3.32 0.00 45.80 2.57
6548 6980 2.040278 TCACCCACAGAAGAAGGGAATG 59.960 50.000 3.32 0.00 45.80 2.67
6549 6981 2.348472 TCACCCACAGAAGAAGGGAAT 58.652 47.619 3.32 0.00 45.80 3.01
6550 6982 1.814429 TCACCCACAGAAGAAGGGAA 58.186 50.000 3.32 0.00 45.80 3.97
6551 6983 1.630369 CATCACCCACAGAAGAAGGGA 59.370 52.381 3.32 0.00 45.80 4.20
6553 6985 1.340405 CCCATCACCCACAGAAGAAGG 60.340 57.143 0.00 0.00 0.00 3.46
6554 6986 1.340405 CCCCATCACCCACAGAAGAAG 60.340 57.143 0.00 0.00 0.00 2.85
6555 6987 0.698238 CCCCATCACCCACAGAAGAA 59.302 55.000 0.00 0.00 0.00 2.52
6579 7016 3.130227 CTACCAGCGGCTAGGGTC 58.870 66.667 14.59 0.00 36.14 4.46
6602 7039 4.020617 CGGCAGCAAGGAGGGACA 62.021 66.667 0.00 0.00 0.00 4.02
6603 7040 4.785453 CCGGCAGCAAGGAGGGAC 62.785 72.222 0.00 0.00 0.00 4.46
6647 7095 0.686789 GCCATTGCCAAAGGAACCTT 59.313 50.000 2.23 0.00 37.98 3.50
6659 7107 0.106015 AATACCCCAGGAGCCATTGC 60.106 55.000 0.00 0.00 37.95 3.56
6675 7123 0.102844 GCGTACCACACCGCCTAATA 59.897 55.000 0.00 0.00 43.96 0.98
6748 7958 4.240103 CGCCATCCGCCAGATCCA 62.240 66.667 0.00 0.00 30.59 3.41
6792 8002 0.324614 TTCATGACACACGAGGCCAT 59.675 50.000 5.01 0.00 0.00 4.40
6805 8015 3.558931 ATATGCCCAACGACTTCATGA 57.441 42.857 0.00 0.00 0.00 3.07
6817 8027 5.019470 AGATCGAAGATCTGTATATGCCCA 58.981 41.667 11.31 0.00 45.12 5.36
6825 8035 4.074627 AGACCGAGATCGAAGATCTGTA 57.925 45.455 16.25 0.00 45.12 2.74
6834 8044 3.487120 TGGAGAATAGACCGAGATCGA 57.513 47.619 3.31 0.00 43.02 3.59
6841 8051 4.238761 TCGCTATTTGGAGAATAGACCG 57.761 45.455 9.36 5.21 33.22 4.79
6844 8054 4.503296 GGGCTTCGCTATTTGGAGAATAGA 60.503 45.833 9.36 0.00 33.22 1.98
6847 8057 2.576615 GGGCTTCGCTATTTGGAGAAT 58.423 47.619 0.00 0.00 0.00 2.40
6854 8064 1.453928 GGCAGGGGCTTCGCTATTT 60.454 57.895 0.00 0.00 40.87 1.40
6879 8089 3.876589 TTCCGCTCCGTCAGTTGGC 62.877 63.158 0.00 0.00 0.00 4.52
6910 8120 4.124351 CGTGCGGGCTCGGTTCTA 62.124 66.667 8.71 0.00 36.79 2.10
6916 8126 4.873129 ACTATGCGTGCGGGCTCG 62.873 66.667 0.00 0.00 39.81 5.03
6917 8127 0.808453 TAAACTATGCGTGCGGGCTC 60.808 55.000 0.36 0.00 0.00 4.70
6918 8128 1.087771 GTAAACTATGCGTGCGGGCT 61.088 55.000 0.36 0.00 0.00 5.19
6919 8129 1.350665 GTAAACTATGCGTGCGGGC 59.649 57.895 0.00 0.00 0.00 6.13
6920 8130 0.461339 AGGTAAACTATGCGTGCGGG 60.461 55.000 0.00 0.00 0.00 6.13
6921 8131 2.124903 CTAGGTAAACTATGCGTGCGG 58.875 52.381 0.00 0.00 0.00 5.69
6922 8132 2.124903 CCTAGGTAAACTATGCGTGCG 58.875 52.381 0.00 0.00 0.00 5.34
6923 8133 3.175109 ACCTAGGTAAACTATGCGTGC 57.825 47.619 14.41 0.00 0.00 5.34
6924 8134 6.238022 GCTTAAACCTAGGTAAACTATGCGTG 60.238 42.308 16.67 0.20 0.00 5.34
6925 8135 5.814188 GCTTAAACCTAGGTAAACTATGCGT 59.186 40.000 16.67 0.00 0.00 5.24
6926 8136 5.235831 GGCTTAAACCTAGGTAAACTATGCG 59.764 44.000 16.67 1.56 0.00 4.73
6927 8137 6.354938 AGGCTTAAACCTAGGTAAACTATGC 58.645 40.000 16.67 15.95 38.67 3.14
6928 8138 7.224167 CGAAGGCTTAAACCTAGGTAAACTATG 59.776 40.741 16.67 8.02 39.93 2.23
6929 8139 7.124750 TCGAAGGCTTAAACCTAGGTAAACTAT 59.875 37.037 16.67 0.00 39.93 2.12
6930 8140 6.437162 TCGAAGGCTTAAACCTAGGTAAACTA 59.563 38.462 16.67 1.84 39.93 2.24
6931 8141 5.246883 TCGAAGGCTTAAACCTAGGTAAACT 59.753 40.000 16.67 5.27 39.93 2.66
6932 8142 5.482006 TCGAAGGCTTAAACCTAGGTAAAC 58.518 41.667 16.67 1.81 39.93 2.01
6933 8143 5.743636 TCGAAGGCTTAAACCTAGGTAAA 57.256 39.130 16.67 11.89 39.93 2.01
6934 8144 5.422970 TCATCGAAGGCTTAAACCTAGGTAA 59.577 40.000 16.67 5.84 39.93 2.85
6935 8145 4.957954 TCATCGAAGGCTTAAACCTAGGTA 59.042 41.667 16.67 0.00 39.93 3.08
6936 8146 3.773119 TCATCGAAGGCTTAAACCTAGGT 59.227 43.478 9.21 9.21 39.93 3.08
6937 8147 4.372656 CTCATCGAAGGCTTAAACCTAGG 58.627 47.826 7.41 7.41 39.93 3.02
6938 8148 4.099573 TCCTCATCGAAGGCTTAAACCTAG 59.900 45.833 0.00 0.00 39.93 3.02
6939 8149 4.028131 TCCTCATCGAAGGCTTAAACCTA 58.972 43.478 0.00 0.00 39.93 3.08
6940 8150 2.838202 TCCTCATCGAAGGCTTAAACCT 59.162 45.455 0.00 0.00 43.91 3.50
6941 8151 2.937149 GTCCTCATCGAAGGCTTAAACC 59.063 50.000 0.00 0.00 36.29 3.27
6942 8152 3.863041 AGTCCTCATCGAAGGCTTAAAC 58.137 45.455 0.00 0.00 36.29 2.01
6943 8153 5.670792 TTAGTCCTCATCGAAGGCTTAAA 57.329 39.130 0.00 0.00 36.29 1.52
6944 8154 5.871396 ATTAGTCCTCATCGAAGGCTTAA 57.129 39.130 0.00 1.12 36.29 1.85
6945 8155 5.243283 GGTATTAGTCCTCATCGAAGGCTTA 59.757 44.000 0.00 0.00 36.29 3.09
6946 8156 4.039366 GGTATTAGTCCTCATCGAAGGCTT 59.961 45.833 0.00 0.00 36.29 4.35
6947 8157 3.574826 GGTATTAGTCCTCATCGAAGGCT 59.425 47.826 0.00 2.54 36.29 4.58
6948 8158 3.306156 GGGTATTAGTCCTCATCGAAGGC 60.306 52.174 0.00 0.00 36.29 4.35
6949 8159 4.153411 AGGGTATTAGTCCTCATCGAAGG 58.847 47.826 0.00 0.00 37.81 3.46
6950 8160 5.768662 TGTAGGGTATTAGTCCTCATCGAAG 59.231 44.000 0.00 0.00 34.75 3.79
6951 8161 5.698104 TGTAGGGTATTAGTCCTCATCGAA 58.302 41.667 0.00 0.00 34.75 3.71
6952 8162 5.314718 TGTAGGGTATTAGTCCTCATCGA 57.685 43.478 0.00 0.00 34.75 3.59
6953 8163 5.710567 TGATGTAGGGTATTAGTCCTCATCG 59.289 44.000 0.00 0.00 38.73 3.84


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

AutoCloner maintained by Alex Coulton.