Multiple sequence alignment - TraesCS3D01G179900

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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 TraesCS3D01G179900 chr3D 100.000 2435 0 0 1 2435 161821257 161818823 0.000000e+00 4497.0
1 TraesCS3D01G179900 chr3D 94.454 577 31 1 206 781 608409123 608409699 0.000000e+00 887.0
2 TraesCS3D01G179900 chr3D 94.194 155 8 1 1 155 162782774 162782927 4.050000e-58 235.0
3 TraesCS3D01G179900 chr3D 90.099 101 4 4 114 210 93566827 93566925 2.540000e-25 126.0
4 TraesCS3D01G179900 chr3D 89.423 104 5 4 112 210 350742800 350742902 2.540000e-25 126.0
5 TraesCS3D01G179900 chr6B 91.267 2233 104 30 209 2435 171555160 171557307 0.000000e+00 2959.0
6 TraesCS3D01G179900 chr6B 92.500 160 10 2 1 159 585019048 585018890 6.770000e-56 228.0
7 TraesCS3D01G179900 chr6B 72.340 423 113 4 2012 2432 380495281 380494861 1.960000e-26 130.0
8 TraesCS3D01G179900 chr6B 71.362 426 101 15 1825 2240 628979467 628979881 9.270000e-15 91.6
9 TraesCS3D01G179900 chr6B 71.158 423 107 11 1825 2240 628982211 628982625 9.270000e-15 91.6
10 TraesCS3D01G179900 chr4D 92.669 1596 85 16 866 2435 58434995 58436584 0.000000e+00 2272.0
11 TraesCS3D01G179900 chr4D 93.708 1494 78 9 895 2384 58461710 58463191 0.000000e+00 2224.0
12 TraesCS3D01G179900 chr4D 90.196 714 57 8 192 892 58461066 58461779 0.000000e+00 918.0
13 TraesCS3D01G179900 chr4D 91.441 666 53 3 192 856 58434399 58435061 0.000000e+00 911.0
14 TraesCS3D01G179900 chr4D 90.099 101 4 4 114 210 362424725 362424627 2.540000e-25 126.0
15 TraesCS3D01G179900 chr4D 95.833 48 2 0 2388 2435 58463330 58463377 7.220000e-11 78.7
16 TraesCS3D01G179900 chr7D 93.112 1539 69 13 902 2435 500907448 500908954 0.000000e+00 2220.0
17 TraesCS3D01G179900 chr7D 92.025 652 48 3 206 857 500906868 500907515 0.000000e+00 913.0
18 TraesCS3D01G179900 chr7D 94.839 155 7 1 1 155 320416724 320416877 8.700000e-60 241.0
19 TraesCS3D01G179900 chr7D 94.194 155 8 1 1 155 517080020 517079867 4.050000e-58 235.0
20 TraesCS3D01G179900 chr1A 91.520 1592 107 14 206 1786 1641138 1642712 0.000000e+00 2167.0
21 TraesCS3D01G179900 chr1A 96.563 611 21 0 1825 2435 1642723 1643333 0.000000e+00 1013.0
22 TraesCS3D01G179900 chr1A 91.875 160 11 2 1 159 413036366 413036208 3.150000e-54 222.0
23 TraesCS3D01G179900 chr1B 94.384 1389 75 3 1050 2435 449809465 449810853 0.000000e+00 2130.0
24 TraesCS3D01G179900 chr1B 88.385 749 82 3 206 954 449782681 449783424 0.000000e+00 896.0
25 TraesCS3D01G179900 chr2B 95.105 1144 41 3 1289 2432 747123275 747124403 0.000000e+00 1788.0
26 TraesCS3D01G179900 chrUn 90.549 1312 96 14 206 1506 233797278 233795984 0.000000e+00 1711.0
27 TraesCS3D01G179900 chrUn 76.687 163 17 17 1262 1422 233796125 233795982 1.210000e-08 71.3
28 TraesCS3D01G179900 chr7B 93.686 586 23 1 1003 1588 97681889 97681318 0.000000e+00 865.0
29 TraesCS3D01G179900 chr7B 94.270 541 21 1 212 752 97682433 97681903 0.000000e+00 819.0
30 TraesCS3D01G179900 chr3A 88.426 216 19 5 490 699 490623533 490623748 3.110000e-64 255.0
31 TraesCS3D01G179900 chr2D 97.241 145 4 0 1 145 115223723 115223867 1.870000e-61 246.0
32 TraesCS3D01G179900 chr2D 97.222 144 4 0 1 144 143263298 143263441 6.730000e-61 244.0
33 TraesCS3D01G179900 chr2A 96.575 146 4 1 1 146 418686092 418686236 8.700000e-60 241.0
34 TraesCS3D01G179900 chr2A 91.875 160 11 2 1 159 221910872 221910714 3.150000e-54 222.0
35 TraesCS3D01G179900 chr6A 93.548 155 9 1 1 155 330464728 330464575 1.880000e-56 230.0
36 TraesCS3D01G179900 chr6A 89.524 105 4 5 110 210 88392679 88392780 2.540000e-25 126.0
37 TraesCS3D01G179900 chr3B 92.500 160 10 2 1 159 466086728 466086886 6.770000e-56 228.0
38 TraesCS3D01G179900 chr3B 87.611 113 8 4 102 210 120331909 120332019 2.540000e-25 126.0
39 TraesCS3D01G179900 chr1D 92.903 155 10 1 1 155 174519457 174519304 8.760000e-55 224.0
40 TraesCS3D01G179900 chr5A 71.619 599 148 17 1845 2432 353720028 353720615 7.020000e-31 145.0
41 TraesCS3D01G179900 chr5A 100.000 69 0 0 144 212 474999981 474999913 7.070000e-26 128.0
42 TraesCS3D01G179900 chr7A 87.500 112 7 5 105 210 580920690 580920800 3.290000e-24 122.0


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 TraesCS3D01G179900 chr3D 161818823 161821257 2434 True 4497.000000 4497 100.000000 1 2435 1 chr3D.!!$R1 2434
1 TraesCS3D01G179900 chr3D 608409123 608409699 576 False 887.000000 887 94.454000 206 781 1 chr3D.!!$F4 575
2 TraesCS3D01G179900 chr6B 171555160 171557307 2147 False 2959.000000 2959 91.267000 209 2435 1 chr6B.!!$F1 2226
3 TraesCS3D01G179900 chr4D 58434399 58436584 2185 False 1591.500000 2272 92.055000 192 2435 2 chr4D.!!$F1 2243
4 TraesCS3D01G179900 chr4D 58461066 58463377 2311 False 1073.566667 2224 93.245667 192 2435 3 chr4D.!!$F2 2243
5 TraesCS3D01G179900 chr7D 500906868 500908954 2086 False 1566.500000 2220 92.568500 206 2435 2 chr7D.!!$F2 2229
6 TraesCS3D01G179900 chr1A 1641138 1643333 2195 False 1590.000000 2167 94.041500 206 2435 2 chr1A.!!$F1 2229
7 TraesCS3D01G179900 chr1B 449809465 449810853 1388 False 2130.000000 2130 94.384000 1050 2435 1 chr1B.!!$F2 1385
8 TraesCS3D01G179900 chr1B 449782681 449783424 743 False 896.000000 896 88.385000 206 954 1 chr1B.!!$F1 748
9 TraesCS3D01G179900 chr2B 747123275 747124403 1128 False 1788.000000 1788 95.105000 1289 2432 1 chr2B.!!$F1 1143
10 TraesCS3D01G179900 chrUn 233795982 233797278 1296 True 891.150000 1711 83.618000 206 1506 2 chrUn.!!$R1 1300
11 TraesCS3D01G179900 chr7B 97681318 97682433 1115 True 842.000000 865 93.978000 212 1588 2 chr7B.!!$R1 1376

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
22 23 0.037303 CCTCTGCTTCCCTCTGCAAA 59.963 55.0 0.0 0.0 38.81 3.68 F
24 25 0.037303 TCTGCTTCCCTCTGCAAAGG 59.963 55.0 0.0 0.0 38.81 3.11 F
444 446 0.171231 GCCCGCTCAGCCTTTTTAAG 59.829 55.0 0.0 0.0 0.00 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1001 1129 0.105194 TCCAGTGAGTCCCAACCTCA 60.105 55.0 0.00 0.00 36.63 3.86 R
1077 1205 0.893270 CATGAACGGAAGGTTGGCCA 60.893 55.0 0.00 0.00 39.50 5.36 R
2386 2662 0.108041 ATAACCGCGGTCCGAAACAT 60.108 50.0 34.29 16.21 40.02 2.71 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
18 19 3.547567 CAACCTCTGCTTCCCTCTG 57.452 57.895 0.00 0.00 0.00 3.35
19 20 0.676151 CAACCTCTGCTTCCCTCTGC 60.676 60.000 0.00 0.00 0.00 4.26
20 21 1.130054 AACCTCTGCTTCCCTCTGCA 61.130 55.000 0.00 0.00 37.63 4.41
21 22 1.130054 ACCTCTGCTTCCCTCTGCAA 61.130 55.000 0.00 0.00 38.81 4.08
22 23 0.037303 CCTCTGCTTCCCTCTGCAAA 59.963 55.000 0.00 0.00 38.81 3.68
23 24 1.451067 CTCTGCTTCCCTCTGCAAAG 58.549 55.000 0.00 0.00 38.81 2.77
24 25 0.037303 TCTGCTTCCCTCTGCAAAGG 59.963 55.000 0.00 0.00 38.81 3.11
33 34 3.515602 CCTCTGCAAAGGGCCTATATT 57.484 47.619 6.41 0.00 43.89 1.28
34 35 3.837355 CCTCTGCAAAGGGCCTATATTT 58.163 45.455 6.41 0.00 43.89 1.40
35 36 4.218312 CCTCTGCAAAGGGCCTATATTTT 58.782 43.478 6.41 0.00 43.89 1.82
36 37 5.385198 CCTCTGCAAAGGGCCTATATTTTA 58.615 41.667 6.41 0.00 43.89 1.52
37 38 5.241728 CCTCTGCAAAGGGCCTATATTTTAC 59.758 44.000 6.41 0.00 43.89 2.01
38 39 6.013554 TCTGCAAAGGGCCTATATTTTACT 57.986 37.500 6.41 0.00 43.89 2.24
39 40 6.431722 TCTGCAAAGGGCCTATATTTTACTT 58.568 36.000 6.41 0.00 43.89 2.24
40 41 6.895204 TCTGCAAAGGGCCTATATTTTACTTT 59.105 34.615 6.41 0.00 43.89 2.66
41 42 7.398904 TCTGCAAAGGGCCTATATTTTACTTTT 59.601 33.333 6.41 0.00 43.89 2.27
42 43 7.552459 TGCAAAGGGCCTATATTTTACTTTTC 58.448 34.615 6.41 0.00 43.89 2.29
43 44 7.179338 TGCAAAGGGCCTATATTTTACTTTTCA 59.821 33.333 6.41 0.00 43.89 2.69
44 45 7.706607 GCAAAGGGCCTATATTTTACTTTTCAG 59.293 37.037 6.41 0.00 36.11 3.02
45 46 8.749354 CAAAGGGCCTATATTTTACTTTTCAGT 58.251 33.333 6.41 0.00 36.99 3.41
46 47 9.984590 AAAGGGCCTATATTTTACTTTTCAGTA 57.015 29.630 6.41 0.00 34.06 2.74
80 81 7.992754 ATGCAAAGAGTCAAAGTTATTCTCT 57.007 32.000 0.00 0.00 37.12 3.10
81 82 7.426929 TGCAAAGAGTCAAAGTTATTCTCTC 57.573 36.000 0.00 0.00 34.91 3.20
82 83 7.220030 TGCAAAGAGTCAAAGTTATTCTCTCT 58.780 34.615 0.00 0.00 34.91 3.10
83 84 8.367911 TGCAAAGAGTCAAAGTTATTCTCTCTA 58.632 33.333 0.00 0.00 34.91 2.43
84 85 9.377312 GCAAAGAGTCAAAGTTATTCTCTCTAT 57.623 33.333 0.00 0.00 34.91 1.98
88 89 8.700973 AGAGTCAAAGTTATTCTCTCTATTCCC 58.299 37.037 0.00 0.00 30.98 3.97
89 90 8.616799 AGTCAAAGTTATTCTCTCTATTCCCT 57.383 34.615 0.00 0.00 0.00 4.20
90 91 9.052365 AGTCAAAGTTATTCTCTCTATTCCCTT 57.948 33.333 0.00 0.00 0.00 3.95
91 92 9.674068 GTCAAAGTTATTCTCTCTATTCCCTTT 57.326 33.333 0.00 0.00 0.00 3.11
101 102 9.508642 TTCTCTCTATTCCCTTTTCTTTTTCTC 57.491 33.333 0.00 0.00 0.00 2.87
102 103 8.885346 TCTCTCTATTCCCTTTTCTTTTTCTCT 58.115 33.333 0.00 0.00 0.00 3.10
103 104 9.513906 CTCTCTATTCCCTTTTCTTTTTCTCTT 57.486 33.333 0.00 0.00 0.00 2.85
104 105 9.868160 TCTCTATTCCCTTTTCTTTTTCTCTTT 57.132 29.630 0.00 0.00 0.00 2.52
107 108 9.481340 CTATTCCCTTTTCTTTTTCTCTTTTGG 57.519 33.333 0.00 0.00 0.00 3.28
108 109 5.670485 TCCCTTTTCTTTTTCTCTTTTGGC 58.330 37.500 0.00 0.00 0.00 4.52
109 110 5.188751 TCCCTTTTCTTTTTCTCTTTTGGCA 59.811 36.000 0.00 0.00 0.00 4.92
110 111 5.879777 CCCTTTTCTTTTTCTCTTTTGGCAA 59.120 36.000 0.00 0.00 0.00 4.52
111 112 6.037500 CCCTTTTCTTTTTCTCTTTTGGCAAG 59.962 38.462 0.00 0.00 0.00 4.01
112 113 6.421377 TTTTCTTTTTCTCTTTTGGCAAGC 57.579 33.333 0.00 0.00 0.00 4.01
113 114 4.734398 TCTTTTTCTCTTTTGGCAAGCA 57.266 36.364 0.00 0.00 0.00 3.91
114 115 5.280654 TCTTTTTCTCTTTTGGCAAGCAT 57.719 34.783 0.00 0.00 0.00 3.79
115 116 5.291971 TCTTTTTCTCTTTTGGCAAGCATC 58.708 37.500 0.00 0.00 0.00 3.91
116 117 4.669206 TTTTCTCTTTTGGCAAGCATCA 57.331 36.364 0.00 0.00 0.00 3.07
117 118 4.877378 TTTCTCTTTTGGCAAGCATCAT 57.123 36.364 0.00 0.00 0.00 2.45
118 119 3.861276 TCTCTTTTGGCAAGCATCATG 57.139 42.857 0.00 0.00 0.00 3.07
119 120 3.159472 TCTCTTTTGGCAAGCATCATGT 58.841 40.909 0.00 0.00 0.00 3.21
120 121 3.057104 TCTCTTTTGGCAAGCATCATGTG 60.057 43.478 0.00 0.00 0.00 3.21
121 122 2.028839 TCTTTTGGCAAGCATCATGTGG 60.029 45.455 0.00 0.00 0.00 4.17
122 123 1.340088 TTTGGCAAGCATCATGTGGT 58.660 45.000 0.00 0.00 41.11 4.16
123 124 0.604073 TTGGCAAGCATCATGTGGTG 59.396 50.000 0.00 0.00 38.84 4.17
124 125 0.251253 TGGCAAGCATCATGTGGTGA 60.251 50.000 0.00 0.00 42.06 4.02
125 126 0.454600 GGCAAGCATCATGTGGTGAG 59.545 55.000 0.00 0.00 40.92 3.51
126 127 0.454600 GCAAGCATCATGTGGTGAGG 59.545 55.000 0.00 0.00 40.92 3.86
127 128 1.951895 GCAAGCATCATGTGGTGAGGA 60.952 52.381 0.00 0.00 41.02 3.71
128 129 2.439409 CAAGCATCATGTGGTGAGGAA 58.561 47.619 0.00 0.00 41.02 3.36
129 130 2.821378 CAAGCATCATGTGGTGAGGAAA 59.179 45.455 0.00 0.00 41.02 3.13
130 131 2.719739 AGCATCATGTGGTGAGGAAAG 58.280 47.619 0.00 0.00 41.02 2.62
131 132 2.306805 AGCATCATGTGGTGAGGAAAGA 59.693 45.455 0.00 0.00 41.02 2.52
132 133 3.053842 AGCATCATGTGGTGAGGAAAGAT 60.054 43.478 0.00 0.00 41.02 2.40
133 134 3.314635 GCATCATGTGGTGAGGAAAGATC 59.685 47.826 0.00 0.00 41.02 2.75
134 135 4.778579 CATCATGTGGTGAGGAAAGATCT 58.221 43.478 0.00 0.00 41.02 2.75
135 136 5.685861 GCATCATGTGGTGAGGAAAGATCTA 60.686 44.000 0.00 0.00 41.02 1.98
136 137 5.604758 TCATGTGGTGAGGAAAGATCTAG 57.395 43.478 0.00 0.00 31.80 2.43
137 138 4.406972 TCATGTGGTGAGGAAAGATCTAGG 59.593 45.833 0.00 0.00 31.80 3.02
138 139 2.501723 TGTGGTGAGGAAAGATCTAGGC 59.498 50.000 0.00 0.00 0.00 3.93
139 140 2.501723 GTGGTGAGGAAAGATCTAGGCA 59.498 50.000 0.00 0.00 0.00 4.75
140 141 2.501723 TGGTGAGGAAAGATCTAGGCAC 59.498 50.000 0.00 0.81 0.00 5.01
141 142 2.501723 GGTGAGGAAAGATCTAGGCACA 59.498 50.000 0.00 0.00 0.00 4.57
142 143 3.135530 GGTGAGGAAAGATCTAGGCACAT 59.864 47.826 0.00 0.00 0.00 3.21
143 144 4.345257 GGTGAGGAAAGATCTAGGCACATA 59.655 45.833 0.00 0.00 0.00 2.29
144 145 5.012561 GGTGAGGAAAGATCTAGGCACATAT 59.987 44.000 0.00 0.00 0.00 1.78
145 146 6.211584 GGTGAGGAAAGATCTAGGCACATATA 59.788 42.308 0.00 0.00 0.00 0.86
146 147 7.256332 GGTGAGGAAAGATCTAGGCACATATAA 60.256 40.741 0.00 0.00 0.00 0.98
147 148 8.317679 GTGAGGAAAGATCTAGGCACATATAAT 58.682 37.037 0.00 0.00 0.00 1.28
148 149 9.547279 TGAGGAAAGATCTAGGCACATATAATA 57.453 33.333 0.00 0.00 0.00 0.98
235 236 4.196193 CCTCCATTCCGTTTTATAGTGCA 58.804 43.478 0.00 0.00 0.00 4.57
247 248 8.280497 CCGTTTTATAGTGCATATAGTTTCCAC 58.720 37.037 0.00 0.00 0.00 4.02
311 312 7.394077 GTCTAATATACCCCTCCACTAACTCTC 59.606 44.444 0.00 0.00 0.00 3.20
338 340 1.307355 CCATGTGCGCATCACCTCAA 61.307 55.000 15.91 0.00 45.03 3.02
441 443 3.365265 CGCCCGCTCAGCCTTTTT 61.365 61.111 0.00 0.00 0.00 1.94
444 446 0.171231 GCCCGCTCAGCCTTTTTAAG 59.829 55.000 0.00 0.00 0.00 1.85
448 450 3.565516 CCGCTCAGCCTTTTTAAGTTTC 58.434 45.455 0.00 0.00 0.00 2.78
606 608 2.108168 AGACTATAGCGGTCTTGCCAA 58.892 47.619 0.00 0.00 40.65 4.52
719 721 4.395231 TCTTCTTGCTGATCATTTGCTCAG 59.605 41.667 6.98 6.98 40.27 3.35
744 746 7.555914 AGCACCTTGGTTTGTTGATTTATTTTT 59.444 29.630 0.00 0.00 0.00 1.94
794 838 3.251509 TGAAGCTGAGCCTGGCCA 61.252 61.111 16.57 4.71 0.00 5.36
799 843 2.924640 CTGAGCCTGGCCATGGAT 59.075 61.111 18.40 16.62 0.00 3.41
803 889 4.881440 GCCTGGCCATGGATGCGA 62.881 66.667 18.40 0.00 0.00 5.10
804 890 2.124193 CCTGGCCATGGATGCGAA 60.124 61.111 18.40 0.00 0.00 4.70
805 891 2.191513 CCTGGCCATGGATGCGAAG 61.192 63.158 18.40 2.43 0.00 3.79
806 892 2.124193 TGGCCATGGATGCGAAGG 60.124 61.111 18.40 0.00 0.00 3.46
807 893 3.599704 GGCCATGGATGCGAAGGC 61.600 66.667 18.40 5.94 44.48 4.35
808 894 3.957535 GCCATGGATGCGAAGGCG 61.958 66.667 18.40 0.00 44.10 5.52
857 943 3.509137 GAGACGCCGGTTGTGGACA 62.509 63.158 1.90 0.00 0.00 4.02
859 945 3.802418 GACGCCGGTTGTGGACACT 62.802 63.158 1.90 0.00 0.00 3.55
907 1029 4.148825 GATGTGGAGACGCCGGCT 62.149 66.667 26.68 11.91 41.24 5.52
922 1044 4.735132 GCTGTGGACGCGTAGGCA 62.735 66.667 13.97 10.40 39.92 4.75
924 1046 3.282745 CTGTGGACGCGTAGGCACT 62.283 63.158 13.97 0.00 46.37 4.40
927 1049 4.065281 GGACGCGTAGGCACTGGT 62.065 66.667 13.97 0.00 41.52 4.00
961 1083 3.986006 GTGGACGCGGAGACACCA 61.986 66.667 12.47 7.17 38.90 4.17
962 1084 3.680786 TGGACGCGGAGACACCAG 61.681 66.667 12.47 0.00 38.90 4.00
1103 1231 3.880047 ACCTTCCGTTCATGTCGATAA 57.120 42.857 12.77 7.29 0.00 1.75
1185 1325 5.471556 TTGGCATTGACTTGAATGTTGAT 57.528 34.783 0.00 0.00 35.98 2.57
1193 1333 6.505044 TGACTTGAATGTTGATCTTGATGG 57.495 37.500 0.00 0.00 0.00 3.51
1237 1377 5.568685 TGAAAATGTTGAAGGAAACGACA 57.431 34.783 0.00 0.00 36.32 4.35
1238 1378 5.336744 TGAAAATGTTGAAGGAAACGACAC 58.663 37.500 0.00 0.00 34.98 3.67
1303 1443 3.004002 ATGCATACATGTGTGCTATGCAC 59.996 43.478 36.88 15.57 46.05 4.57
1360 1500 3.132111 TGCGTACTGCTTCATGGATTCTA 59.868 43.478 10.27 0.00 46.63 2.10
1378 1518 6.598457 GGATTCTAGATCATGCATGCTTGTAT 59.402 38.462 27.12 20.10 0.00 2.29
1451 1591 6.014584 TGCTTATAGTGGTCATGTATACTGGG 60.015 42.308 4.17 0.00 0.00 4.45
1506 1647 2.559668 ACTGGTTCCTGCATGATTGTTG 59.440 45.455 0.00 0.00 0.00 3.33
1550 1691 1.202290 CCATGACGCCACTTATTTGCC 60.202 52.381 0.00 0.00 0.00 4.52
1619 1760 5.924825 GCAAAATCTATTTGCCATGATCCTC 59.075 40.000 13.45 0.00 46.51 3.71
1688 1829 3.629855 TCGCTGAAGAAACAAACATTCCA 59.370 39.130 0.00 0.00 0.00 3.53
1692 1833 5.754890 GCTGAAGAAACAAACATTCCATTGT 59.245 36.000 0.00 0.00 41.31 2.71
1746 1887 1.304381 GCTGGTGGATTGCAGGGAA 60.304 57.895 0.00 0.00 0.00 3.97
1747 1888 1.598701 GCTGGTGGATTGCAGGGAAC 61.599 60.000 0.00 0.00 0.00 3.62
1842 1983 9.838339 TTGATCTAAGAAAAAGAACAAGTCTCT 57.162 29.630 0.00 0.00 34.56 3.10
1949 2090 5.186215 TGCCATCAAATCAACATTGACAGAT 59.814 36.000 0.00 0.00 40.49 2.90
1958 2099 9.550406 AAATCAACATTGACAGATGAAAACAAT 57.450 25.926 0.00 0.00 40.49 2.71
1985 2126 5.508489 GGCTAGGGTTAAGTTTTGTTTGTCC 60.508 44.000 0.00 0.00 0.00 4.02
2034 2175 2.933906 CAGCCAACATTTGATGGAATGC 59.066 45.455 10.71 0.00 40.03 3.56
2077 2218 2.826128 AGAAGTGGTTCTATCGCACTCA 59.174 45.455 0.00 0.00 41.54 3.41
2318 2459 0.397187 TTACTAAGGTGTTGCCGGCA 59.603 50.000 29.03 29.03 43.70 5.69
2389 2665 3.624777 CCATTAAGGAGAAGTGGCATGT 58.375 45.455 0.00 0.00 41.22 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.676151 GCAGAGGGAAGCAGAGGTTG 60.676 60.000 0.00 0.00 0.00 3.77
2 3 1.130054 TTGCAGAGGGAAGCAGAGGT 61.130 55.000 0.00 0.00 42.39 3.85
3 4 0.037303 TTTGCAGAGGGAAGCAGAGG 59.963 55.000 0.00 0.00 42.39 3.69
4 5 1.451067 CTTTGCAGAGGGAAGCAGAG 58.549 55.000 0.00 0.00 42.39 3.35
6 7 2.564471 CCTTTGCAGAGGGAAGCAG 58.436 57.895 15.60 0.00 42.39 4.24
7 8 4.828409 CCTTTGCAGAGGGAAGCA 57.172 55.556 15.60 0.00 39.32 3.91
13 14 3.515602 AATATAGGCCCTTTGCAGAGG 57.484 47.619 16.42 16.42 43.89 3.69
14 15 6.064717 AGTAAAATATAGGCCCTTTGCAGAG 58.935 40.000 0.00 0.00 43.89 3.35
15 16 6.013554 AGTAAAATATAGGCCCTTTGCAGA 57.986 37.500 0.00 0.00 43.89 4.26
16 17 6.715347 AAGTAAAATATAGGCCCTTTGCAG 57.285 37.500 0.00 0.00 43.89 4.41
17 18 7.179338 TGAAAAGTAAAATATAGGCCCTTTGCA 59.821 33.333 0.00 0.00 43.89 4.08
18 19 7.552459 TGAAAAGTAAAATATAGGCCCTTTGC 58.448 34.615 0.00 0.00 40.16 3.68
19 20 8.749354 ACTGAAAAGTAAAATATAGGCCCTTTG 58.251 33.333 0.00 0.00 0.00 2.77
20 21 8.895141 ACTGAAAAGTAAAATATAGGCCCTTT 57.105 30.769 0.00 0.00 0.00 3.11
54 55 9.507329 AGAGAATAACTTTGACTCTTTGCATAA 57.493 29.630 0.00 0.00 34.85 1.90
55 56 9.155975 GAGAGAATAACTTTGACTCTTTGCATA 57.844 33.333 0.00 0.00 37.93 3.14
56 57 7.882271 AGAGAGAATAACTTTGACTCTTTGCAT 59.118 33.333 0.00 0.00 37.93 3.96
57 58 7.220030 AGAGAGAATAACTTTGACTCTTTGCA 58.780 34.615 0.00 0.00 37.93 4.08
58 59 7.665561 AGAGAGAATAACTTTGACTCTTTGC 57.334 36.000 0.00 0.00 37.93 3.68
62 63 8.700973 GGGAATAGAGAGAATAACTTTGACTCT 58.299 37.037 0.00 0.00 40.05 3.24
63 64 8.700973 AGGGAATAGAGAGAATAACTTTGACTC 58.299 37.037 0.00 0.00 0.00 3.36
64 65 8.616799 AGGGAATAGAGAGAATAACTTTGACT 57.383 34.615 0.00 0.00 0.00 3.41
65 66 9.674068 AAAGGGAATAGAGAGAATAACTTTGAC 57.326 33.333 0.00 0.00 0.00 3.18
75 76 9.508642 GAGAAAAAGAAAAGGGAATAGAGAGAA 57.491 33.333 0.00 0.00 0.00 2.87
76 77 8.885346 AGAGAAAAAGAAAAGGGAATAGAGAGA 58.115 33.333 0.00 0.00 0.00 3.10
77 78 9.513906 AAGAGAAAAAGAAAAGGGAATAGAGAG 57.486 33.333 0.00 0.00 0.00 3.20
78 79 9.868160 AAAGAGAAAAAGAAAAGGGAATAGAGA 57.132 29.630 0.00 0.00 0.00 3.10
81 82 9.481340 CCAAAAGAGAAAAAGAAAAGGGAATAG 57.519 33.333 0.00 0.00 0.00 1.73
82 83 7.931407 GCCAAAAGAGAAAAAGAAAAGGGAATA 59.069 33.333 0.00 0.00 0.00 1.75
83 84 6.767902 GCCAAAAGAGAAAAAGAAAAGGGAAT 59.232 34.615 0.00 0.00 0.00 3.01
84 85 6.112734 GCCAAAAGAGAAAAAGAAAAGGGAA 58.887 36.000 0.00 0.00 0.00 3.97
85 86 5.188751 TGCCAAAAGAGAAAAAGAAAAGGGA 59.811 36.000 0.00 0.00 0.00 4.20
86 87 5.427378 TGCCAAAAGAGAAAAAGAAAAGGG 58.573 37.500 0.00 0.00 0.00 3.95
87 88 6.457392 GCTTGCCAAAAGAGAAAAAGAAAAGG 60.457 38.462 0.00 0.00 0.00 3.11
88 89 6.092533 TGCTTGCCAAAAGAGAAAAAGAAAAG 59.907 34.615 0.00 0.00 0.00 2.27
89 90 5.936956 TGCTTGCCAAAAGAGAAAAAGAAAA 59.063 32.000 0.00 0.00 0.00 2.29
90 91 5.486526 TGCTTGCCAAAAGAGAAAAAGAAA 58.513 33.333 0.00 0.00 0.00 2.52
91 92 5.083533 TGCTTGCCAAAAGAGAAAAAGAA 57.916 34.783 0.00 0.00 0.00 2.52
92 93 4.734398 TGCTTGCCAAAAGAGAAAAAGA 57.266 36.364 0.00 0.00 0.00 2.52
93 94 5.051816 TGATGCTTGCCAAAAGAGAAAAAG 58.948 37.500 0.00 0.00 0.00 2.27
94 95 5.021033 TGATGCTTGCCAAAAGAGAAAAA 57.979 34.783 0.00 0.00 0.00 1.94
95 96 4.669206 TGATGCTTGCCAAAAGAGAAAA 57.331 36.364 0.00 0.00 0.00 2.29
96 97 4.039488 ACATGATGCTTGCCAAAAGAGAAA 59.961 37.500 0.00 0.00 0.00 2.52
97 98 3.575256 ACATGATGCTTGCCAAAAGAGAA 59.425 39.130 0.00 0.00 0.00 2.87
98 99 3.057104 CACATGATGCTTGCCAAAAGAGA 60.057 43.478 0.00 0.00 0.00 3.10
99 100 3.250744 CACATGATGCTTGCCAAAAGAG 58.749 45.455 0.00 0.00 0.00 2.85
100 101 2.028839 CCACATGATGCTTGCCAAAAGA 60.029 45.455 0.00 0.00 0.00 2.52
101 102 2.289195 ACCACATGATGCTTGCCAAAAG 60.289 45.455 0.00 0.00 0.00 2.27
102 103 1.693062 ACCACATGATGCTTGCCAAAA 59.307 42.857 0.00 0.00 0.00 2.44
103 104 1.001068 CACCACATGATGCTTGCCAAA 59.999 47.619 0.00 0.00 0.00 3.28
104 105 0.604073 CACCACATGATGCTTGCCAA 59.396 50.000 0.00 0.00 0.00 4.52
105 106 0.251253 TCACCACATGATGCTTGCCA 60.251 50.000 0.00 0.00 29.99 4.92
106 107 0.454600 CTCACCACATGATGCTTGCC 59.545 55.000 0.00 0.00 36.48 4.52
107 108 0.454600 CCTCACCACATGATGCTTGC 59.545 55.000 0.00 0.00 36.48 4.01
108 109 2.118313 TCCTCACCACATGATGCTTG 57.882 50.000 0.00 0.00 36.48 4.01
109 110 2.885135 TTCCTCACCACATGATGCTT 57.115 45.000 0.00 0.00 36.48 3.91
110 111 2.306805 TCTTTCCTCACCACATGATGCT 59.693 45.455 0.00 0.00 36.48 3.79
111 112 2.715046 TCTTTCCTCACCACATGATGC 58.285 47.619 0.00 0.00 36.48 3.91
112 113 4.778579 AGATCTTTCCTCACCACATGATG 58.221 43.478 0.00 0.00 36.48 3.07
113 114 5.071519 CCTAGATCTTTCCTCACCACATGAT 59.928 44.000 0.00 0.00 36.48 2.45
114 115 4.406972 CCTAGATCTTTCCTCACCACATGA 59.593 45.833 0.00 0.00 35.45 3.07
115 116 4.701765 CCTAGATCTTTCCTCACCACATG 58.298 47.826 0.00 0.00 0.00 3.21
116 117 3.135530 GCCTAGATCTTTCCTCACCACAT 59.864 47.826 0.00 0.00 0.00 3.21
117 118 2.501723 GCCTAGATCTTTCCTCACCACA 59.498 50.000 0.00 0.00 0.00 4.17
118 119 2.501723 TGCCTAGATCTTTCCTCACCAC 59.498 50.000 0.00 0.00 0.00 4.16
119 120 2.501723 GTGCCTAGATCTTTCCTCACCA 59.498 50.000 0.00 0.00 0.00 4.17
120 121 2.501723 TGTGCCTAGATCTTTCCTCACC 59.498 50.000 0.00 0.00 0.00 4.02
121 122 3.895232 TGTGCCTAGATCTTTCCTCAC 57.105 47.619 0.00 3.68 0.00 3.51
122 123 7.855784 TTATATGTGCCTAGATCTTTCCTCA 57.144 36.000 0.00 0.00 0.00 3.86
188 189 9.944376 GGGAGTACAATTCTAGCATGAATAATA 57.056 33.333 0.00 0.00 35.82 0.98
189 190 8.664079 AGGGAGTACAATTCTAGCATGAATAAT 58.336 33.333 0.00 0.72 35.82 1.28
190 191 8.034313 AGGGAGTACAATTCTAGCATGAATAA 57.966 34.615 0.00 0.00 35.82 1.40
191 192 7.256332 GGAGGGAGTACAATTCTAGCATGAATA 60.256 40.741 0.00 0.00 35.82 1.75
192 193 6.465035 GGAGGGAGTACAATTCTAGCATGAAT 60.465 42.308 0.00 0.00 38.19 2.57
193 194 5.163301 GGAGGGAGTACAATTCTAGCATGAA 60.163 44.000 0.00 0.00 0.00 2.57
194 195 4.345257 GGAGGGAGTACAATTCTAGCATGA 59.655 45.833 0.00 0.00 0.00 3.07
195 196 4.101585 TGGAGGGAGTACAATTCTAGCATG 59.898 45.833 0.00 0.00 0.00 4.06
196 197 4.298626 TGGAGGGAGTACAATTCTAGCAT 58.701 43.478 0.00 0.00 0.00 3.79
202 203 3.118371 ACGGAATGGAGGGAGTACAATTC 60.118 47.826 0.00 0.00 0.00 2.17
204 205 2.478292 ACGGAATGGAGGGAGTACAAT 58.522 47.619 0.00 0.00 0.00 2.71
207 208 3.345508 AAAACGGAATGGAGGGAGTAC 57.654 47.619 0.00 0.00 0.00 2.73
235 236 4.103469 TGGTATTGCCGGTGGAAACTATAT 59.897 41.667 1.90 0.00 41.21 0.86
247 248 1.942657 CTCACTCATTGGTATTGCCGG 59.057 52.381 0.00 0.00 41.21 6.13
357 359 3.657727 ACTTTCCCTCCAATTTCTCTCCA 59.342 43.478 0.00 0.00 0.00 3.86
441 443 6.231211 GTCCTGGAGAGTTGATTGAAACTTA 58.769 40.000 0.00 0.00 40.48 2.24
444 446 3.433615 CGTCCTGGAGAGTTGATTGAAAC 59.566 47.826 0.00 0.00 0.00 2.78
448 450 1.406069 CCCGTCCTGGAGAGTTGATTG 60.406 57.143 0.00 0.00 42.00 2.67
592 594 0.673644 GCTCTTTGGCAAGACCGCTA 60.674 55.000 0.00 0.00 43.94 4.26
606 608 4.385825 CTCCAGATCGTAGTCTAGCTCTT 58.614 47.826 0.00 0.00 0.00 2.85
719 721 6.859420 AAATAAATCAACAAACCAAGGTGC 57.141 33.333 0.00 0.00 0.00 5.01
849 935 1.302192 GGCGCCTAAGTGTCCACAA 60.302 57.895 22.15 0.00 0.00 3.33
850 936 2.345991 GGCGCCTAAGTGTCCACA 59.654 61.111 22.15 0.00 0.00 4.17
881 967 0.320374 GTCTCCACATCCACGGTCAA 59.680 55.000 0.00 0.00 0.00 3.18
882 968 1.873270 CGTCTCCACATCCACGGTCA 61.873 60.000 0.00 0.00 0.00 4.02
884 970 2.970639 CGTCTCCACATCCACGGT 59.029 61.111 0.00 0.00 0.00 4.83
907 1029 3.299977 AGTGCCTACGCGTCCACA 61.300 61.111 27.76 18.16 38.08 4.17
953 1075 1.448540 CATCCACGGCTGGTGTCTC 60.449 63.158 0.00 0.00 45.52 3.36
954 1076 2.665000 CATCCACGGCTGGTGTCT 59.335 61.111 0.00 0.00 45.52 3.41
955 1077 3.127533 GCATCCACGGCTGGTGTC 61.128 66.667 0.00 0.00 45.52 3.67
964 1086 3.576356 GCCATGTCCGCATCCACG 61.576 66.667 0.00 0.00 31.99 4.94
965 1087 3.211963 GGCCATGTCCGCATCCAC 61.212 66.667 0.00 0.00 31.99 4.02
966 1088 4.854924 CGGCCATGTCCGCATCCA 62.855 66.667 0.56 0.00 43.18 3.41
993 1121 0.739813 GTCCCAACCTCATTCGTCCG 60.740 60.000 0.00 0.00 0.00 4.79
994 1122 0.613777 AGTCCCAACCTCATTCGTCC 59.386 55.000 0.00 0.00 0.00 4.79
995 1123 1.275291 TGAGTCCCAACCTCATTCGTC 59.725 52.381 0.00 0.00 34.12 4.20
996 1124 1.002087 GTGAGTCCCAACCTCATTCGT 59.998 52.381 0.00 0.00 40.79 3.85
997 1125 1.276421 AGTGAGTCCCAACCTCATTCG 59.724 52.381 0.00 0.00 40.79 3.34
998 1126 2.616510 CCAGTGAGTCCCAACCTCATTC 60.617 54.545 0.00 0.00 40.79 2.67
999 1127 1.352352 CCAGTGAGTCCCAACCTCATT 59.648 52.381 0.00 0.00 40.79 2.57
1000 1128 0.987294 CCAGTGAGTCCCAACCTCAT 59.013 55.000 0.00 0.00 40.79 2.90
1001 1129 0.105194 TCCAGTGAGTCCCAACCTCA 60.105 55.000 0.00 0.00 36.63 3.86
1077 1205 0.893270 CATGAACGGAAGGTTGGCCA 60.893 55.000 0.00 0.00 39.50 5.36
1103 1231 3.433343 TCCATGTTCAAGTCAATGCCAT 58.567 40.909 0.00 0.00 0.00 4.40
1185 1325 1.511305 GGCGTCGACTCCATCAAGA 59.489 57.895 19.57 0.00 0.00 3.02
1193 1333 2.267681 ATCAACTCCGGCGTCGACTC 62.268 60.000 12.93 5.30 39.00 3.36
1303 1443 2.492019 CAAGCATGCATGATCCACAG 57.508 50.000 30.64 8.67 0.00 3.66
1360 1500 4.212716 ACCAATACAAGCATGCATGATCT 58.787 39.130 30.64 15.59 0.00 2.75
1451 1591 1.741706 AGCAGTACAAGCATGCATGAC 59.258 47.619 30.64 20.09 42.45 3.06
1550 1691 5.924825 CCTTCTCTTTTTCTTGCCTTCATTG 59.075 40.000 0.00 0.00 0.00 2.82
1617 1758 1.896465 ACCCAAAGAAGACCTCTCGAG 59.104 52.381 5.93 5.93 31.02 4.04
1619 1760 3.955650 TTACCCAAAGAAGACCTCTCG 57.044 47.619 0.00 0.00 31.02 4.04
1670 1811 6.871844 TCACAATGGAATGTTTGTTTCTTCA 58.128 32.000 0.00 0.00 33.93 3.02
1688 1829 6.540189 GCCATCTCAGTTGTATAGTTCACAAT 59.460 38.462 0.00 0.00 38.13 2.71
1692 1833 5.395657 CCAGCCATCTCAGTTGTATAGTTCA 60.396 44.000 0.00 0.00 0.00 3.18
1746 1887 1.072965 CTTGGTCCTCTTGCTCAAGGT 59.927 52.381 9.48 0.00 38.88 3.50
1747 1888 1.349026 TCTTGGTCCTCTTGCTCAAGG 59.651 52.381 9.48 0.00 38.88 3.61
1842 1983 8.886719 CATGTTCAACTCATTAGCAAGATCTTA 58.113 33.333 7.86 0.00 0.00 2.10
1949 2090 4.668138 AACCCTAGCCCTATTGTTTTCA 57.332 40.909 0.00 0.00 0.00 2.69
1958 2099 5.587760 AACAAAACTTAACCCTAGCCCTA 57.412 39.130 0.00 0.00 0.00 3.53
1985 2126 3.181493 GGATGCTTAGTGGCTGAAACATG 60.181 47.826 0.00 0.00 0.00 3.21
2034 2175 4.432712 TCATCTATGTGGATGACGTTGTG 58.567 43.478 5.11 0.00 44.65 3.33
2318 2459 3.857157 TGGCTAACTTTCCTTGTCACT 57.143 42.857 0.00 0.00 0.00 3.41
2386 2662 0.108041 ATAACCGCGGTCCGAAACAT 60.108 50.000 34.29 16.21 40.02 2.71
2389 2665 1.153588 GGATAACCGCGGTCCGAAA 60.154 57.895 34.29 15.23 40.02 3.46


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

AutoCloner maintained by Alex Coulton.