Multiple sequence alignment - TraesCS7D01G280000

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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 TraesCS7D01G280000 chr7D 100.000 2237 0 0 1 2237 271935838 271938074 0.000000e+00 4132.0
1 TraesCS7D01G280000 chr7D 94.059 101 6 0 2137 2237 57104485 57104585 1.070000e-33 154.0
2 TraesCS7D01G280000 chr7D 94.059 101 6 0 2137 2237 271951629 271951729 1.070000e-33 154.0
3 TraesCS7D01G280000 chr7A 93.587 1341 46 18 537 1856 304328391 304329712 0.000000e+00 1964.0
4 TraesCS7D01G280000 chr7A 96.296 135 5 0 1851 1985 304330814 304330948 2.890000e-54 222.0
5 TraesCS7D01G280000 chr7A 93.651 126 4 3 2016 2140 304331014 304331136 3.790000e-43 185.0
6 TraesCS7D01G280000 chr7A 95.833 96 4 0 2142 2237 69753180 69753085 2.970000e-34 156.0
7 TraesCS7D01G280000 chr7A 86.923 130 14 3 533 661 304327719 304327846 2.320000e-30 143.0
8 TraesCS7D01G280000 chr7A 94.937 79 4 0 4 82 304328187 304328265 8.390000e-25 124.0
9 TraesCS7D01G280000 chr7B 90.486 1419 58 25 718 2093 266564872 266563488 0.000000e+00 1801.0
10 TraesCS7D01G280000 chr7B 88.550 131 6 5 537 666 266565002 266564880 1.380000e-32 150.0
11 TraesCS7D01G280000 chr7B 76.206 311 46 10 1828 2112 266561739 266561431 3.000000e-29 139.0
12 TraesCS7D01G280000 chr3D 94.059 101 6 0 2137 2237 461529566 461529666 1.070000e-33 154.0
13 TraesCS7D01G280000 chr3D 91.509 106 9 0 2132 2237 566352302 566352197 1.790000e-31 147.0
14 TraesCS7D01G280000 chr3D 82.895 76 9 4 24 97 600818656 600818583 5.160000e-07 65.8
15 TraesCS7D01G280000 chr1D 94.059 101 6 0 2137 2237 467893135 467893035 1.070000e-33 154.0
16 TraesCS7D01G280000 chr1D 93.137 102 5 2 2137 2237 256082334 256082234 4.980000e-32 148.0
17 TraesCS7D01G280000 chr1D 93.137 102 6 1 2137 2237 477246244 477246143 4.980000e-32 148.0
18 TraesCS7D01G280000 chr2D 94.000 100 5 1 2138 2237 644088063 644087965 1.380000e-32 150.0


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 TraesCS7D01G280000 chr7D 271935838 271938074 2236 False 4132.000000 4132 100.000000 1 2237 1 chr7D.!!$F2 2236
1 TraesCS7D01G280000 chr7A 304327719 304331136 3417 False 527.600000 1964 93.078800 4 2140 5 chr7A.!!$F1 2136
2 TraesCS7D01G280000 chr7B 266561431 266565002 3571 True 696.666667 1801 85.080667 537 2112 3 chr7B.!!$R1 1575

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
731 1246 0.324943 AAGACAGACGGTGGAATGGG 59.675 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 5941 0.321919 TAAGAGCCAAGCTGCACCTG 60.322 55.0 1.02 0.0 39.88 4.0 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
113 579 6.442952 TCTGTGAATAAAATGTGAAAACGGG 58.557 36.000 0.00 0.00 0.00 5.28
114 580 5.533482 TGTGAATAAAATGTGAAAACGGGG 58.467 37.500 0.00 0.00 0.00 5.73
117 583 6.871492 GTGAATAAAATGTGAAAACGGGGATT 59.129 34.615 0.00 0.00 0.00 3.01
118 584 7.386573 GTGAATAAAATGTGAAAACGGGGATTT 59.613 33.333 0.00 0.00 0.00 2.17
119 585 7.934120 TGAATAAAATGTGAAAACGGGGATTTT 59.066 29.630 0.00 0.00 34.46 1.82
120 586 8.684386 AATAAAATGTGAAAACGGGGATTTTT 57.316 26.923 0.00 0.00 31.90 1.94
147 662 5.595885 TCGAAATTCCTGAACATTTTTGCA 58.404 33.333 0.00 0.00 0.00 4.08
148 663 6.045318 TCGAAATTCCTGAACATTTTTGCAA 58.955 32.000 0.00 0.00 0.00 4.08
149 664 6.536582 TCGAAATTCCTGAACATTTTTGCAAA 59.463 30.769 8.05 8.05 0.00 3.68
150 665 7.065085 TCGAAATTCCTGAACATTTTTGCAAAA 59.935 29.630 20.46 20.46 0.00 2.44
151 666 7.856894 CGAAATTCCTGAACATTTTTGCAAAAT 59.143 29.630 24.39 10.35 0.00 1.82
153 668 9.518906 AAATTCCTGAACATTTTTGCAAAATTC 57.481 25.926 24.39 22.77 0.00 2.17
154 669 6.284475 TCCTGAACATTTTTGCAAAATTCG 57.716 33.333 24.39 17.20 29.45 3.34
155 670 6.045318 TCCTGAACATTTTTGCAAAATTCGA 58.955 32.000 24.39 14.92 29.45 3.71
157 672 6.847289 CCTGAACATTTTTGCAAAATTCGAAG 59.153 34.615 24.39 17.09 29.45 3.79
158 673 7.254387 CCTGAACATTTTTGCAAAATTCGAAGA 60.254 33.333 24.39 8.92 29.45 2.87
159 674 8.140677 TGAACATTTTTGCAAAATTCGAAGAT 57.859 26.923 24.39 10.82 35.04 2.40
160 675 8.610896 TGAACATTTTTGCAAAATTCGAAGATT 58.389 25.926 24.39 10.77 35.04 2.40
161 676 9.437045 GAACATTTTTGCAAAATTCGAAGATTT 57.563 25.926 24.39 10.20 35.04 2.17
162 677 9.786105 AACATTTTTGCAAAATTCGAAGATTTT 57.214 22.222 24.39 10.03 41.12 1.82
163 678 9.786105 ACATTTTTGCAAAATTCGAAGATTTTT 57.214 22.222 24.39 3.03 46.63 1.94
210 725 9.883142 TTGGAAAACATAAACATTTCTGAAAGT 57.117 25.926 8.95 4.54 33.76 2.66
211 726 9.883142 TGGAAAACATAAACATTTCTGAAAGTT 57.117 25.926 8.95 9.73 33.76 2.66
325 840 6.088719 TGAACAAAATTTTGAAACACGAGC 57.911 33.333 32.20 13.03 40.55 5.03
326 841 5.635280 TGAACAAAATTTTGAAACACGAGCA 59.365 32.000 32.20 14.89 40.55 4.26
327 842 6.312426 TGAACAAAATTTTGAAACACGAGCAT 59.688 30.769 32.20 7.11 40.55 3.79
328 843 6.660887 ACAAAATTTTGAAACACGAGCATT 57.339 29.167 32.20 6.92 40.55 3.56
329 844 7.071014 ACAAAATTTTGAAACACGAGCATTT 57.929 28.000 32.20 6.51 40.55 2.32
330 845 7.525759 ACAAAATTTTGAAACACGAGCATTTT 58.474 26.923 32.20 5.91 40.55 1.82
331 846 8.020244 ACAAAATTTTGAAACACGAGCATTTTT 58.980 25.926 32.20 5.56 40.55 1.94
332 847 7.951706 AAATTTTGAAACACGAGCATTTTTG 57.048 28.000 0.00 0.00 0.00 2.44
333 848 6.900568 ATTTTGAAACACGAGCATTTTTGA 57.099 29.167 0.00 0.00 0.00 2.69
334 849 6.712241 TTTTGAAACACGAGCATTTTTGAA 57.288 29.167 0.00 0.00 0.00 2.69
335 850 6.712241 TTTGAAACACGAGCATTTTTGAAA 57.288 29.167 0.00 0.00 0.00 2.69
336 851 6.900568 TTGAAACACGAGCATTTTTGAAAT 57.099 29.167 0.00 0.00 0.00 2.17
337 852 6.900568 TGAAACACGAGCATTTTTGAAATT 57.099 29.167 0.00 0.00 0.00 1.82
338 853 6.932051 TGAAACACGAGCATTTTTGAAATTC 58.068 32.000 0.00 0.00 0.00 2.17
339 854 6.533012 TGAAACACGAGCATTTTTGAAATTCA 59.467 30.769 0.00 0.00 0.00 2.57
340 855 6.900568 AACACGAGCATTTTTGAAATTCAA 57.099 29.167 4.03 4.03 34.03 2.69
341 856 6.900568 ACACGAGCATTTTTGAAATTCAAA 57.099 29.167 16.28 16.28 43.84 2.69
452 967 9.807921 ATTAGGAAGAAAATAACAAGGAACAGA 57.192 29.630 0.00 0.00 0.00 3.41
453 968 9.635404 TTAGGAAGAAAATAACAAGGAACAGAA 57.365 29.630 0.00 0.00 0.00 3.02
454 969 8.533569 AGGAAGAAAATAACAAGGAACAGAAA 57.466 30.769 0.00 0.00 0.00 2.52
455 970 8.977412 AGGAAGAAAATAACAAGGAACAGAAAA 58.023 29.630 0.00 0.00 0.00 2.29
456 971 9.764363 GGAAGAAAATAACAAGGAACAGAAAAT 57.236 29.630 0.00 0.00 0.00 1.82
488 1003 9.868277 TTCTAAAAGCAGAGAAAAACAAAATGA 57.132 25.926 0.00 0.00 0.00 2.57
489 1004 9.868277 TCTAAAAGCAGAGAAAAACAAAATGAA 57.132 25.926 0.00 0.00 0.00 2.57
511 1026 5.637006 AAAAACCAAAAAGCCAGAAAACC 57.363 34.783 0.00 0.00 0.00 3.27
512 1027 3.990959 AACCAAAAAGCCAGAAAACCA 57.009 38.095 0.00 0.00 0.00 3.67
513 1028 3.541996 ACCAAAAAGCCAGAAAACCAG 57.458 42.857 0.00 0.00 0.00 4.00
514 1029 2.837591 ACCAAAAAGCCAGAAAACCAGT 59.162 40.909 0.00 0.00 0.00 4.00
515 1030 4.027437 ACCAAAAAGCCAGAAAACCAGTA 58.973 39.130 0.00 0.00 0.00 2.74
516 1031 4.468153 ACCAAAAAGCCAGAAAACCAGTAA 59.532 37.500 0.00 0.00 0.00 2.24
517 1032 5.046231 ACCAAAAAGCCAGAAAACCAGTAAA 60.046 36.000 0.00 0.00 0.00 2.01
518 1033 5.877564 CCAAAAAGCCAGAAAACCAGTAAAA 59.122 36.000 0.00 0.00 0.00 1.52
519 1034 6.372937 CCAAAAAGCCAGAAAACCAGTAAAAA 59.627 34.615 0.00 0.00 0.00 1.94
520 1035 6.978343 AAAAGCCAGAAAACCAGTAAAAAC 57.022 33.333 0.00 0.00 0.00 2.43
521 1036 4.665833 AGCCAGAAAACCAGTAAAAACC 57.334 40.909 0.00 0.00 0.00 3.27
522 1037 3.386726 AGCCAGAAAACCAGTAAAAACCC 59.613 43.478 0.00 0.00 0.00 4.11
523 1038 3.133183 GCCAGAAAACCAGTAAAAACCCA 59.867 43.478 0.00 0.00 0.00 4.51
524 1039 4.739436 GCCAGAAAACCAGTAAAAACCCAG 60.739 45.833 0.00 0.00 0.00 4.45
525 1040 4.404394 CCAGAAAACCAGTAAAAACCCAGT 59.596 41.667 0.00 0.00 0.00 4.00
526 1041 5.595133 CCAGAAAACCAGTAAAAACCCAGTA 59.405 40.000 0.00 0.00 0.00 2.74
527 1042 6.097129 CCAGAAAACCAGTAAAAACCCAGTAA 59.903 38.462 0.00 0.00 0.00 2.24
528 1043 7.363968 CCAGAAAACCAGTAAAAACCCAGTAAA 60.364 37.037 0.00 0.00 0.00 2.01
529 1044 8.035984 CAGAAAACCAGTAAAAACCCAGTAAAA 58.964 33.333 0.00 0.00 0.00 1.52
530 1045 8.595421 AGAAAACCAGTAAAAACCCAGTAAAAA 58.405 29.630 0.00 0.00 0.00 1.94
555 1070 2.038837 GGTTGTGAAGTAGGCGGCC 61.039 63.158 12.11 12.11 0.00 6.13
560 1075 4.452733 GAAGTAGGCGGCCGTGCT 62.453 66.667 28.70 14.18 34.52 4.40
633 1148 1.095228 ATTCGGCCGTTTCGCATGAT 61.095 50.000 27.15 3.73 0.00 2.45
637 1152 2.408835 CCGTTTCGCATGATGGCC 59.591 61.111 0.00 0.00 0.00 5.36
684 1199 4.554919 CGACGTATGGTCCATAAGAGACAG 60.555 50.000 25.95 10.44 42.99 3.51
731 1246 0.324943 AAGACAGACGGTGGAATGGG 59.675 55.000 0.00 0.00 0.00 4.00
804 1319 4.344865 AGACGGGCGGTTGGCATT 62.345 61.111 0.00 0.00 46.16 3.56
878 1393 4.572389 GCCCGTCCTAGAATTGCATATATG 59.428 45.833 8.45 8.45 0.00 1.78
908 1439 0.460284 AGCACGAATAGCCGGAACTG 60.460 55.000 5.05 0.00 0.00 3.16
1134 1665 3.817655 GTGCAGCGCATGATGGCA 61.818 61.111 11.47 6.47 41.91 4.92
1264 1795 1.827399 ATTTCACCTCAGCCGTCCGT 61.827 55.000 0.00 0.00 0.00 4.69
1367 1898 3.407967 CCTGAGGCCGGCCCTAAA 61.408 66.667 41.72 23.07 46.60 1.85
1383 1914 6.035975 CGGCCCTAAATTTGTTTGATCAATTC 59.964 38.462 9.40 6.59 0.00 2.17
1480 2011 8.980481 AGTTTCCTGTGATTCTTTTCTTTCTA 57.020 30.769 0.00 0.00 0.00 2.10
1561 2093 5.726980 TGTGTACGGGTGATTAAGTAACT 57.273 39.130 0.00 0.00 0.00 2.24
1578 2110 3.420839 AACTTGTGCACTTGTGCTTAC 57.579 42.857 23.53 15.80 35.49 2.34
1580 2112 2.355756 ACTTGTGCACTTGTGCTTACAG 59.644 45.455 23.53 16.30 35.49 2.74
1646 2178 3.225104 CCAATTGGTACCTCCCATGATG 58.775 50.000 16.90 1.33 33.60 3.07
1681 2220 6.952773 TTTCCCAATAAGATTAATCGGGTG 57.047 37.500 19.17 12.24 33.70 4.61
1753 2297 3.268103 ATCAGGTTGGCCGGTGGAC 62.268 63.158 1.90 0.00 40.50 4.02
1926 3611 4.249638 TCCTGAATCATTACCCCCTTTG 57.750 45.455 0.00 0.00 0.00 2.77
1966 3651 1.156645 AATTCTCTGCTCGATGCGCC 61.157 55.000 4.18 0.00 46.63 6.53
1985 3670 1.471119 CACCTGCCTGCAAAGATGAT 58.529 50.000 0.00 0.00 0.00 2.45
2029 5765 6.017605 AGCTTGCCTCAATAGATAAATCAACG 60.018 38.462 0.00 0.00 0.00 4.10
2052 5790 3.199071 ACCTTTGTAGAACTCCACACACA 59.801 43.478 0.00 0.00 0.00 3.72
2053 5791 3.560068 CCTTTGTAGAACTCCACACACAC 59.440 47.826 0.00 0.00 0.00 3.82
2086 5824 3.742882 CACACCACACATAGTCAAGACAG 59.257 47.826 2.72 0.00 0.00 3.51
2140 5880 2.295269 TGATTAATCAGGGGTGGGGA 57.705 50.000 14.23 0.00 32.11 4.81
2141 5881 2.800656 TGATTAATCAGGGGTGGGGAT 58.199 47.619 14.23 0.00 32.11 3.85
2142 5882 2.446666 TGATTAATCAGGGGTGGGGATG 59.553 50.000 14.23 0.00 32.11 3.51
2143 5883 1.994399 TTAATCAGGGGTGGGGATGT 58.006 50.000 0.00 0.00 0.00 3.06
2144 5884 1.994399 TAATCAGGGGTGGGGATGTT 58.006 50.000 0.00 0.00 0.00 2.71
2145 5885 1.994399 AATCAGGGGTGGGGATGTTA 58.006 50.000 0.00 0.00 0.00 2.41
2146 5886 1.222567 ATCAGGGGTGGGGATGTTAC 58.777 55.000 0.00 0.00 0.00 2.50
2147 5887 0.178858 TCAGGGGTGGGGATGTTACA 60.179 55.000 0.00 0.00 0.00 2.41
2148 5888 0.701731 CAGGGGTGGGGATGTTACAA 59.298 55.000 0.00 0.00 0.00 2.41
2149 5889 1.287739 CAGGGGTGGGGATGTTACAAT 59.712 52.381 0.00 0.00 0.00 2.71
2150 5890 2.512056 CAGGGGTGGGGATGTTACAATA 59.488 50.000 0.00 0.00 0.00 1.90
2151 5891 2.512476 AGGGGTGGGGATGTTACAATAC 59.488 50.000 0.00 0.00 0.00 1.89
2152 5892 2.242708 GGGGTGGGGATGTTACAATACA 59.757 50.000 0.00 0.00 0.00 2.29
2153 5893 3.309265 GGGGTGGGGATGTTACAATACAA 60.309 47.826 0.00 0.00 0.00 2.41
2154 5894 3.697542 GGGTGGGGATGTTACAATACAAC 59.302 47.826 0.00 0.00 0.00 3.32
2155 5895 4.569015 GGGTGGGGATGTTACAATACAACT 60.569 45.833 0.00 0.00 0.00 3.16
2156 5896 5.014202 GGTGGGGATGTTACAATACAACTT 58.986 41.667 0.00 0.00 0.00 2.66
2157 5897 5.105917 GGTGGGGATGTTACAATACAACTTG 60.106 44.000 0.00 0.00 0.00 3.16
2158 5898 5.475564 GTGGGGATGTTACAATACAACTTGT 59.524 40.000 0.00 0.00 41.95 3.16
2159 5899 6.655848 GTGGGGATGTTACAATACAACTTGTA 59.344 38.462 4.08 4.08 39.88 2.41
2160 5900 7.175293 GTGGGGATGTTACAATACAACTTGTAA 59.825 37.037 5.73 5.54 44.93 2.41
2176 5916 9.047947 ACAACTTGTAATAGGATTAAGACTCCT 57.952 33.333 1.82 1.82 45.22 3.69
2179 5919 9.939424 ACTTGTAATAGGATTAAGACTCCTACT 57.061 33.333 5.62 0.00 45.72 2.57
2181 5921 8.618702 TGTAATAGGATTAAGACTCCTACTCG 57.381 38.462 5.62 0.00 45.72 4.18
2182 5922 8.435187 TGTAATAGGATTAAGACTCCTACTCGA 58.565 37.037 5.62 0.00 45.72 4.04
2183 5923 9.282569 GTAATAGGATTAAGACTCCTACTCGAA 57.717 37.037 5.62 0.00 45.72 3.71
2184 5924 8.943594 AATAGGATTAAGACTCCTACTCGAAT 57.056 34.615 5.62 0.00 45.72 3.34
2185 5925 8.943594 ATAGGATTAAGACTCCTACTCGAATT 57.056 34.615 5.62 0.00 45.72 2.17
2186 5926 7.663043 AGGATTAAGACTCCTACTCGAATTT 57.337 36.000 0.00 0.00 41.42 1.82
2187 5927 8.080363 AGGATTAAGACTCCTACTCGAATTTT 57.920 34.615 0.00 0.00 41.42 1.82
2188 5928 9.198475 AGGATTAAGACTCCTACTCGAATTTTA 57.802 33.333 0.00 0.00 41.42 1.52
2189 5929 9.813446 GGATTAAGACTCCTACTCGAATTTTAA 57.187 33.333 0.00 0.00 0.00 1.52
2194 5934 9.819267 AAGACTCCTACTCGAATTTTAATAAGG 57.181 33.333 0.00 0.00 0.00 2.69
2195 5935 7.927092 AGACTCCTACTCGAATTTTAATAAGGC 59.073 37.037 0.00 0.00 0.00 4.35
2196 5936 7.793036 ACTCCTACTCGAATTTTAATAAGGCT 58.207 34.615 0.00 0.00 0.00 4.58
2197 5937 8.921205 ACTCCTACTCGAATTTTAATAAGGCTA 58.079 33.333 0.00 0.00 0.00 3.93
2198 5938 9.413048 CTCCTACTCGAATTTTAATAAGGCTAG 57.587 37.037 0.00 0.00 0.00 3.42
2199 5939 8.365647 TCCTACTCGAATTTTAATAAGGCTAGG 58.634 37.037 0.00 0.00 0.00 3.02
2200 5940 6.862711 ACTCGAATTTTAATAAGGCTAGGC 57.137 37.500 8.55 8.55 0.00 3.93
2211 5951 4.106925 GCTAGGCCAGGTGCAGCT 62.107 66.667 13.85 13.85 43.89 4.24
2212 5952 2.673523 CTAGGCCAGGTGCAGCTT 59.326 61.111 17.45 4.14 43.89 3.74
2213 5953 1.748122 CTAGGCCAGGTGCAGCTTG 60.748 63.158 17.45 14.64 43.89 4.01
2214 5954 3.272364 TAGGCCAGGTGCAGCTTGG 62.272 63.158 17.45 20.60 46.12 3.61
2217 5957 3.060615 CCAGGTGCAGCTTGGCTC 61.061 66.667 17.45 0.00 37.53 4.70
2218 5958 2.033757 CAGGTGCAGCTTGGCTCT 59.966 61.111 17.45 0.00 36.40 4.09
2219 5959 1.602888 CAGGTGCAGCTTGGCTCTT 60.603 57.895 17.45 0.00 36.40 2.85
2220 5960 0.321919 CAGGTGCAGCTTGGCTCTTA 60.322 55.000 17.45 0.00 36.40 2.10
2221 5961 0.622665 AGGTGCAGCTTGGCTCTTAT 59.377 50.000 13.85 0.00 36.40 1.73
2222 5962 1.839994 AGGTGCAGCTTGGCTCTTATA 59.160 47.619 13.85 0.00 36.40 0.98
2223 5963 2.441001 AGGTGCAGCTTGGCTCTTATAT 59.559 45.455 13.85 0.00 36.40 0.86
2224 5964 3.648067 AGGTGCAGCTTGGCTCTTATATA 59.352 43.478 13.85 0.00 36.40 0.86
2225 5965 4.288105 AGGTGCAGCTTGGCTCTTATATAT 59.712 41.667 13.85 0.00 36.40 0.86
2226 5966 5.485353 AGGTGCAGCTTGGCTCTTATATATA 59.515 40.000 13.85 0.00 36.40 0.86
2227 5967 5.582665 GGTGCAGCTTGGCTCTTATATATAC 59.417 44.000 9.07 0.00 36.40 1.47
2228 5968 6.402222 GTGCAGCTTGGCTCTTATATATACT 58.598 40.000 0.00 0.00 36.40 2.12
2229 5969 6.876257 GTGCAGCTTGGCTCTTATATATACTT 59.124 38.462 0.00 0.00 36.40 2.24
2230 5970 7.064016 GTGCAGCTTGGCTCTTATATATACTTC 59.936 40.741 0.00 0.00 36.40 3.01
2231 5971 7.038729 TGCAGCTTGGCTCTTATATATACTTCT 60.039 37.037 0.00 0.00 36.40 2.85
2232 5972 7.821846 GCAGCTTGGCTCTTATATATACTTCTT 59.178 37.037 0.00 0.00 36.40 2.52
2233 5973 9.149225 CAGCTTGGCTCTTATATATACTTCTTG 57.851 37.037 0.00 0.00 36.40 3.02
2234 5974 8.875168 AGCTTGGCTCTTATATATACTTCTTGT 58.125 33.333 0.00 0.00 30.62 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 552 8.977505 CCGTTTTCACATTTTATTCACAGATTT 58.022 29.630 0.00 0.00 0.00 2.17
87 553 7.598493 CCCGTTTTCACATTTTATTCACAGATT 59.402 33.333 0.00 0.00 0.00 2.40
88 554 7.090173 CCCGTTTTCACATTTTATTCACAGAT 58.910 34.615 0.00 0.00 0.00 2.90
89 555 6.442952 CCCGTTTTCACATTTTATTCACAGA 58.557 36.000 0.00 0.00 0.00 3.41
90 556 5.633182 CCCCGTTTTCACATTTTATTCACAG 59.367 40.000 0.00 0.00 0.00 3.66
92 558 5.774630 TCCCCGTTTTCACATTTTATTCAC 58.225 37.500 0.00 0.00 0.00 3.18
93 559 6.597832 ATCCCCGTTTTCACATTTTATTCA 57.402 33.333 0.00 0.00 0.00 2.57
94 560 7.899178 AAATCCCCGTTTTCACATTTTATTC 57.101 32.000 0.00 0.00 0.00 1.75
95 561 8.684386 AAAAATCCCCGTTTTCACATTTTATT 57.316 26.923 0.00 0.00 31.29 1.40
120 586 7.907563 GCAAAAATGTTCAGGAATTTCGAAAAA 59.092 29.630 15.66 0.15 0.00 1.94
121 587 7.065085 TGCAAAAATGTTCAGGAATTTCGAAAA 59.935 29.630 15.66 0.00 0.00 2.29
123 589 6.045318 TGCAAAAATGTTCAGGAATTTCGAA 58.955 32.000 0.00 0.00 0.00 3.71
125 591 5.903764 TGCAAAAATGTTCAGGAATTTCG 57.096 34.783 0.00 0.00 0.00 3.46
126 592 9.518906 AATTTTGCAAAAATGTTCAGGAATTTC 57.481 25.926 27.10 0.00 0.00 2.17
132 647 6.284475 TCGAATTTTGCAAAAATGTTCAGG 57.716 33.333 27.10 14.37 0.00 3.86
133 648 7.620215 TCTTCGAATTTTGCAAAAATGTTCAG 58.380 30.769 27.10 18.46 0.00 3.02
184 699 9.883142 ACTTTCAGAAATGTTTATGTTTTCCAA 57.117 25.926 0.00 0.00 31.69 3.53
185 700 9.883142 AACTTTCAGAAATGTTTATGTTTTCCA 57.117 25.926 0.00 0.00 30.84 3.53
299 814 8.324567 GCTCGTGTTTCAAAATTTTGTTCATAA 58.675 29.630 25.98 12.88 39.18 1.90
300 815 7.489435 TGCTCGTGTTTCAAAATTTTGTTCATA 59.511 29.630 25.98 7.82 39.18 2.15
301 816 6.312426 TGCTCGTGTTTCAAAATTTTGTTCAT 59.688 30.769 25.98 0.00 39.18 2.57
302 817 5.635280 TGCTCGTGTTTCAAAATTTTGTTCA 59.365 32.000 25.98 19.96 39.18 3.18
303 818 6.088719 TGCTCGTGTTTCAAAATTTTGTTC 57.911 33.333 25.98 18.15 39.18 3.18
304 819 6.660887 ATGCTCGTGTTTCAAAATTTTGTT 57.339 29.167 25.98 0.00 39.18 2.83
305 820 6.660887 AATGCTCGTGTTTCAAAATTTTGT 57.339 29.167 25.98 4.02 39.18 2.83
306 821 7.951706 AAAATGCTCGTGTTTCAAAATTTTG 57.048 28.000 22.40 22.40 39.48 2.44
307 822 8.233190 TCAAAAATGCTCGTGTTTCAAAATTTT 58.767 25.926 0.00 0.00 0.00 1.82
308 823 7.746929 TCAAAAATGCTCGTGTTTCAAAATTT 58.253 26.923 0.00 0.00 0.00 1.82
309 824 7.301068 TCAAAAATGCTCGTGTTTCAAAATT 57.699 28.000 0.00 0.00 0.00 1.82
310 825 6.900568 TCAAAAATGCTCGTGTTTCAAAAT 57.099 29.167 0.00 0.00 0.00 1.82
311 826 6.712241 TTCAAAAATGCTCGTGTTTCAAAA 57.288 29.167 0.00 0.00 0.00 2.44
312 827 6.712241 TTTCAAAAATGCTCGTGTTTCAAA 57.288 29.167 0.00 0.00 0.00 2.69
313 828 6.900568 ATTTCAAAAATGCTCGTGTTTCAA 57.099 29.167 0.00 0.00 0.00 2.69
314 829 6.533012 TGAATTTCAAAAATGCTCGTGTTTCA 59.467 30.769 0.00 0.00 0.00 2.69
315 830 6.932051 TGAATTTCAAAAATGCTCGTGTTTC 58.068 32.000 0.00 0.00 0.00 2.78
316 831 6.900568 TGAATTTCAAAAATGCTCGTGTTT 57.099 29.167 0.00 0.00 0.00 2.83
317 832 6.900568 TTGAATTTCAAAAATGCTCGTGTT 57.099 29.167 9.36 0.00 32.71 3.32
318 833 6.900568 TTTGAATTTCAAAAATGCTCGTGT 57.099 29.167 19.57 0.00 42.72 4.49
426 941 9.807921 TCTGTTCCTTGTTATTTTCTTCCTAAT 57.192 29.630 0.00 0.00 0.00 1.73
427 942 9.635404 TTCTGTTCCTTGTTATTTTCTTCCTAA 57.365 29.630 0.00 0.00 0.00 2.69
428 943 9.635404 TTTCTGTTCCTTGTTATTTTCTTCCTA 57.365 29.630 0.00 0.00 0.00 2.94
429 944 8.533569 TTTCTGTTCCTTGTTATTTTCTTCCT 57.466 30.769 0.00 0.00 0.00 3.36
430 945 9.764363 ATTTTCTGTTCCTTGTTATTTTCTTCC 57.236 29.630 0.00 0.00 0.00 3.46
462 977 9.868277 TCATTTTGTTTTTCTCTGCTTTTAGAA 57.132 25.926 0.00 0.00 0.00 2.10
463 978 9.868277 TTCATTTTGTTTTTCTCTGCTTTTAGA 57.132 25.926 0.00 0.00 0.00 2.10
489 1004 5.073428 TGGTTTTCTGGCTTTTTGGTTTTT 58.927 33.333 0.00 0.00 0.00 1.94
490 1005 4.657013 TGGTTTTCTGGCTTTTTGGTTTT 58.343 34.783 0.00 0.00 0.00 2.43
491 1006 4.260985 CTGGTTTTCTGGCTTTTTGGTTT 58.739 39.130 0.00 0.00 0.00 3.27
492 1007 3.263170 ACTGGTTTTCTGGCTTTTTGGTT 59.737 39.130 0.00 0.00 0.00 3.67
493 1008 2.837591 ACTGGTTTTCTGGCTTTTTGGT 59.162 40.909 0.00 0.00 0.00 3.67
494 1009 3.541996 ACTGGTTTTCTGGCTTTTTGG 57.458 42.857 0.00 0.00 0.00 3.28
495 1010 6.976636 TTTTACTGGTTTTCTGGCTTTTTG 57.023 33.333 0.00 0.00 0.00 2.44
496 1011 6.373216 GGTTTTTACTGGTTTTCTGGCTTTTT 59.627 34.615 0.00 0.00 0.00 1.94
497 1012 5.878116 GGTTTTTACTGGTTTTCTGGCTTTT 59.122 36.000 0.00 0.00 0.00 2.27
498 1013 5.424757 GGTTTTTACTGGTTTTCTGGCTTT 58.575 37.500 0.00 0.00 0.00 3.51
499 1014 4.141801 GGGTTTTTACTGGTTTTCTGGCTT 60.142 41.667 0.00 0.00 0.00 4.35
500 1015 3.386726 GGGTTTTTACTGGTTTTCTGGCT 59.613 43.478 0.00 0.00 0.00 4.75
501 1016 3.133183 TGGGTTTTTACTGGTTTTCTGGC 59.867 43.478 0.00 0.00 0.00 4.85
502 1017 4.404394 ACTGGGTTTTTACTGGTTTTCTGG 59.596 41.667 0.00 0.00 0.00 3.86
503 1018 5.592104 ACTGGGTTTTTACTGGTTTTCTG 57.408 39.130 0.00 0.00 0.00 3.02
504 1019 7.721409 TTTACTGGGTTTTTACTGGTTTTCT 57.279 32.000 0.00 0.00 0.00 2.52
505 1020 8.774890 TTTTTACTGGGTTTTTACTGGTTTTC 57.225 30.769 0.00 0.00 0.00 2.29
527 1042 2.375146 ACTTCACAACCTCGGCTTTTT 58.625 42.857 0.00 0.00 0.00 1.94
528 1043 2.052782 ACTTCACAACCTCGGCTTTT 57.947 45.000 0.00 0.00 0.00 2.27
529 1044 2.550208 CCTACTTCACAACCTCGGCTTT 60.550 50.000 0.00 0.00 0.00 3.51
530 1045 1.002087 CCTACTTCACAACCTCGGCTT 59.998 52.381 0.00 0.00 0.00 4.35
531 1046 0.608640 CCTACTTCACAACCTCGGCT 59.391 55.000 0.00 0.00 0.00 5.52
532 1047 1.019805 GCCTACTTCACAACCTCGGC 61.020 60.000 0.00 0.00 0.00 5.54
533 1048 0.736325 CGCCTACTTCACAACCTCGG 60.736 60.000 0.00 0.00 0.00 4.63
534 1049 0.736325 CCGCCTACTTCACAACCTCG 60.736 60.000 0.00 0.00 0.00 4.63
535 1050 1.019805 GCCGCCTACTTCACAACCTC 61.020 60.000 0.00 0.00 0.00 3.85
555 1070 0.392998 AGAGGCCCATTTGTAGCACG 60.393 55.000 0.00 0.00 0.00 5.34
560 1075 5.249780 TCAAAACTAGAGGCCCATTTGTA 57.750 39.130 0.00 0.00 0.00 2.41
596 1111 5.296531 GCCGAATGAATTTATGGCCAATTTT 59.703 36.000 10.96 0.62 36.51 1.82
617 1132 2.023181 CATCATGCGAAACGGCCG 59.977 61.111 26.86 26.86 0.00 6.13
633 1148 1.750332 CGCCCAGAATAAGAATGGCCA 60.750 52.381 8.56 8.56 35.46 5.36
637 1152 5.006746 GTCAACTACGCCCAGAATAAGAATG 59.993 44.000 0.00 0.00 0.00 2.67
684 1199 2.249844 TTTTGAGAGGTTCCACCGTC 57.750 50.000 0.00 0.00 44.90 4.79
707 1222 2.249844 TCCACCGTCTGTCTTTTTCC 57.750 50.000 0.00 0.00 0.00 3.13
731 1246 0.041576 GAACCGTTCGCTTCAACCAC 60.042 55.000 0.00 0.00 0.00 4.16
804 1319 1.507630 GCCATTGTTGCATGCGAGA 59.492 52.632 14.09 7.00 0.00 4.04
878 1393 2.135664 ATTCGTGCTCGCACCTATAC 57.864 50.000 15.65 0.00 43.49 1.47
908 1439 1.337821 CTCGCGTGTCTTGGTTAGTC 58.662 55.000 5.77 0.00 0.00 2.59
980 1511 1.125633 TATCGGCCCCTTGTAGTTCC 58.874 55.000 0.00 0.00 0.00 3.62
1264 1795 0.399091 AGATGGATCGGCTCCTGGAA 60.399 55.000 0.00 0.00 45.21 3.53
1367 1898 9.768662 AGTAGCAAAAGAATTGATCAAACAAAT 57.231 25.926 13.09 0.00 33.44 2.32
1480 2011 3.184541 CCGACGATCGACAAAAAGGTAT 58.815 45.455 24.34 0.00 43.74 2.73
1578 2110 5.463286 TGCAATGCTTCAACTGATTAACTG 58.537 37.500 6.82 0.00 0.00 3.16
1580 2112 6.094719 TCATGCAATGCTTCAACTGATTAAC 58.905 36.000 6.82 0.00 46.21 2.01
1632 2164 5.808366 TGATACTTCATCATGGGAGGTAC 57.192 43.478 10.77 7.35 38.79 3.34
1665 2197 6.688073 ATCACCTCACCCGATTAATCTTAT 57.312 37.500 13.45 0.00 0.00 1.73
1681 2220 2.100631 CGCACCGTGGAATCACCTC 61.101 63.158 0.00 0.00 40.65 3.85
1815 2359 2.758423 GACTTCCACCAAACAACCTGTT 59.242 45.455 0.00 0.00 43.41 3.16
1817 2395 1.333619 CGACTTCCACCAAACAACCTG 59.666 52.381 0.00 0.00 0.00 4.00
1926 3611 3.609853 TGCATGAATCCTACCAAGTGTC 58.390 45.455 0.00 0.00 0.00 3.67
1966 3651 1.134367 CATCATCTTTGCAGGCAGGTG 59.866 52.381 0.00 0.00 0.00 4.00
2003 3696 7.467811 CGTTGATTTATCTATTGAGGCAAGCTT 60.468 37.037 0.00 0.00 0.00 3.74
2004 3697 6.017605 CGTTGATTTATCTATTGAGGCAAGCT 60.018 38.462 0.00 0.00 0.00 3.74
2005 3698 6.017934 TCGTTGATTTATCTATTGAGGCAAGC 60.018 38.462 0.00 0.00 0.00 4.01
2006 3699 7.348201 GTCGTTGATTTATCTATTGAGGCAAG 58.652 38.462 0.00 0.00 0.00 4.01
2007 3700 6.260050 GGTCGTTGATTTATCTATTGAGGCAA 59.740 38.462 0.00 0.00 0.00 4.52
2008 3701 5.758296 GGTCGTTGATTTATCTATTGAGGCA 59.242 40.000 0.00 0.00 0.00 4.75
2012 3705 8.786826 ACAAAGGTCGTTGATTTATCTATTGA 57.213 30.769 3.83 0.00 32.59 2.57
2029 5765 3.808174 GTGTGTGGAGTTCTACAAAGGTC 59.192 47.826 0.00 0.00 39.06 3.85
2052 5790 3.644265 TGTGTGGTGTGGTATCTAGTTGT 59.356 43.478 0.00 0.00 0.00 3.32
2053 5791 4.265904 TGTGTGGTGTGGTATCTAGTTG 57.734 45.455 0.00 0.00 0.00 3.16
2135 5875 5.636123 ACAAGTTGTATTGTAACATCCCCA 58.364 37.500 6.75 0.00 41.53 4.96
2136 5876 7.690952 TTACAAGTTGTATTGTAACATCCCC 57.309 36.000 16.26 0.00 45.85 4.81
2150 5890 9.047947 AGGAGTCTTAATCCTATTACAAGTTGT 57.952 33.333 14.05 14.05 45.58 3.32
2161 5901 8.763984 AAATTCGAGTAGGAGTCTTAATCCTA 57.236 34.615 4.39 0.00 45.58 2.94
2163 5903 9.813446 TTAAAATTCGAGTAGGAGTCTTAATCC 57.187 33.333 4.39 0.00 37.07 3.01
2168 5908 9.819267 CCTTATTAAAATTCGAGTAGGAGTCTT 57.181 33.333 0.00 0.00 0.00 3.01
2169 5909 7.927092 GCCTTATTAAAATTCGAGTAGGAGTCT 59.073 37.037 0.00 0.00 0.00 3.24
2170 5910 7.927092 AGCCTTATTAAAATTCGAGTAGGAGTC 59.073 37.037 0.00 0.00 0.00 3.36
2171 5911 7.793036 AGCCTTATTAAAATTCGAGTAGGAGT 58.207 34.615 0.00 0.00 0.00 3.85
2172 5912 9.413048 CTAGCCTTATTAAAATTCGAGTAGGAG 57.587 37.037 0.00 0.00 0.00 3.69
2173 5913 8.365647 CCTAGCCTTATTAAAATTCGAGTAGGA 58.634 37.037 0.00 0.00 0.00 2.94
2174 5914 7.117956 GCCTAGCCTTATTAAAATTCGAGTAGG 59.882 40.741 0.00 0.00 0.00 3.18
2175 5915 7.117956 GGCCTAGCCTTATTAAAATTCGAGTAG 59.882 40.741 0.00 0.00 46.69 2.57
2176 5916 6.932960 GGCCTAGCCTTATTAAAATTCGAGTA 59.067 38.462 0.00 0.00 46.69 2.59
2177 5917 5.763698 GGCCTAGCCTTATTAAAATTCGAGT 59.236 40.000 0.00 0.00 46.69 4.18
2178 5918 6.242508 GGCCTAGCCTTATTAAAATTCGAG 57.757 41.667 0.00 0.00 46.69 4.04
2194 5934 3.635268 AAGCTGCACCTGGCCTAGC 62.635 63.158 3.32 3.08 43.89 3.42
2195 5935 1.748122 CAAGCTGCACCTGGCCTAG 60.748 63.158 3.32 0.00 43.89 3.02
2196 5936 2.352422 CAAGCTGCACCTGGCCTA 59.648 61.111 3.32 0.00 43.89 3.93
2197 5937 4.673375 CCAAGCTGCACCTGGCCT 62.673 66.667 3.32 0.00 43.89 5.19
2200 5940 3.060615 GAGCCAAGCTGCACCTGG 61.061 66.667 1.02 6.74 39.88 4.45
2201 5941 0.321919 TAAGAGCCAAGCTGCACCTG 60.322 55.000 1.02 0.00 39.88 4.00
2202 5942 0.622665 ATAAGAGCCAAGCTGCACCT 59.377 50.000 1.02 0.00 39.88 4.00
2203 5943 2.332063 TATAAGAGCCAAGCTGCACC 57.668 50.000 1.02 0.00 39.88 5.01
2204 5944 6.402222 AGTATATATAAGAGCCAAGCTGCAC 58.598 40.000 1.02 0.00 39.88 4.57
2205 5945 6.611613 AGTATATATAAGAGCCAAGCTGCA 57.388 37.500 1.02 0.00 39.88 4.41
2206 5946 7.327214 AGAAGTATATATAAGAGCCAAGCTGC 58.673 38.462 0.00 0.00 39.88 5.25
2207 5947 9.149225 CAAGAAGTATATATAAGAGCCAAGCTG 57.851 37.037 0.00 0.00 39.88 4.24
2208 5948 8.875168 ACAAGAAGTATATATAAGAGCCAAGCT 58.125 33.333 0.00 0.00 43.88 3.74


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

AutoCloner maintained by Alex Coulton.