Multiple sequence alignment - TraesCS6B01G034900

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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 TraesCS6B01G034900 chr6B 100.000 2445 0 0 1 2445 20877069 20874625 0.000000e+00 4516
1 TraesCS6B01G034900 chr6B 90.905 2276 162 31 184 2442 207192973 207195220 0.000000e+00 3014
2 TraesCS6B01G034900 chr2B 91.854 2271 165 12 185 2442 398369476 398371739 0.000000e+00 3151
3 TraesCS6B01G034900 chr2B 89.320 206 20 2 1 204 64756621 64756826 8.670000e-65 257
4 TraesCS6B01G034900 chr1D 90.581 2272 163 29 185 2442 75674609 75676843 0.000000e+00 2963
5 TraesCS6B01G034900 chr1D 92.432 185 13 1 1 184 6641295 6641111 1.860000e-66 263
6 TraesCS6B01G034900 chr7D 90.430 2278 176 25 185 2442 601144616 601146871 0.000000e+00 2961
7 TraesCS6B01G034900 chr7D 87.604 2275 239 31 185 2442 140036675 140038923 0.000000e+00 2599
8 TraesCS6B01G034900 chr7D 92.391 184 13 1 2 184 554961834 554962017 6.710000e-66 261
9 TraesCS6B01G034900 chr5D 90.316 2282 179 24 181 2443 498582014 498584272 0.000000e+00 2952
10 TraesCS6B01G034900 chr5D 89.925 2273 190 23 185 2442 47938359 47940607 0.000000e+00 2892
11 TraesCS6B01G034900 chr5D 88.933 2033 181 28 435 2442 512179912 512177899 0.000000e+00 2468
12 TraesCS6B01G034900 chr6D 90.196 2295 161 36 190 2442 40065309 40067581 0.000000e+00 2933
13 TraesCS6B01G034900 chr2D 90.229 2272 183 25 185 2442 563161847 563164093 0.000000e+00 2929
14 TraesCS6B01G034900 chr2D 92.135 1920 125 19 543 2442 650190368 650188455 0.000000e+00 2686
15 TraesCS6B01G034900 chr2D 88.063 2287 223 35 180 2443 91294842 91292583 0.000000e+00 2665
16 TraesCS6B01G034900 chr3D 89.361 2284 191 25 184 2442 592737908 592735652 0.000000e+00 2824
17 TraesCS6B01G034900 chr3D 89.528 2034 174 29 435 2442 609351828 609349808 0.000000e+00 2540
18 TraesCS6B01G034900 chr3D 89.293 2036 172 29 435 2443 42773022 42775038 0.000000e+00 2510
19 TraesCS6B01G034900 chr3D 93.514 185 11 1 1 184 58551398 58551214 8.610000e-70 274
20 TraesCS6B01G034900 chr3A 87.582 2287 227 33 185 2442 718947748 718950006 0.000000e+00 2597
21 TraesCS6B01G034900 chr3A 92.473 186 11 3 1 184 616974250 616974066 1.860000e-66 263
22 TraesCS6B01G034900 chr7B 87.298 2291 228 32 185 2442 113827035 113829295 0.000000e+00 2560
23 TraesCS6B01G034900 chr7B 89.646 1951 159 30 518 2445 725095457 725093527 0.000000e+00 2444
24 TraesCS6B01G034900 chr7B 92.973 185 12 1 1 184 143239177 143239361 4.010000e-68 268
25 TraesCS6B01G034900 chr7B 92.350 183 13 1 3 184 587972711 587972529 2.410000e-65 259
26 TraesCS6B01G034900 chrUn 89.217 2031 175 29 436 2442 114914017 114912007 0.000000e+00 2497
27 TraesCS6B01G034900 chrUn 86.945 2275 205 43 185 2442 7463228 7461029 0.000000e+00 2471
28 TraesCS6B01G034900 chrUn 86.152 2087 190 53 435 2442 82253295 82251229 0.000000e+00 2161
29 TraesCS6B01G034900 chrUn 88.173 1691 150 20 798 2442 12672427 12674113 0.000000e+00 1969
30 TraesCS6B01G034900 chrUn 90.342 1346 101 13 1111 2442 189428449 189429779 0.000000e+00 1738
31 TraesCS6B01G034900 chrUn 92.481 133 8 2 2312 2442 321635952 321636084 3.210000e-44 189
32 TraesCS6B01G034900 chrUn 92.481 133 8 2 2312 2442 371702767 371702635 3.210000e-44 189
33 TraesCS6B01G034900 chr4D 90.114 1922 148 23 544 2445 24426873 24424974 0.000000e+00 2459
34 TraesCS6B01G034900 chr4A 89.673 1956 164 25 515 2445 673810348 673812290 0.000000e+00 2459
35 TraesCS6B01G034900 chr4A 87.712 1945 176 31 544 2445 647699406 647697482 0.000000e+00 2209
36 TraesCS6B01G034900 chr6A 87.003 2039 183 44 462 2442 617858955 617856941 0.000000e+00 2222
37 TraesCS6B01G034900 chr3B 87.028 1272 136 11 185 1453 809385043 809386288 0.000000e+00 1408
38 TraesCS6B01G034900 chr3B 92.432 185 13 1 1 184 452605791 452605607 1.860000e-66 263
39 TraesCS6B01G034900 chr1A 89.458 332 28 1 2118 2442 555467603 555467272 1.750000e-111 412
40 TraesCS6B01G034900 chr4B 82.558 344 57 3 336 678 217770864 217771205 1.420000e-77 300
41 TraesCS6B01G034900 chr7A 92.432 185 13 1 1 184 597570464 597570280 1.860000e-66 263


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 TraesCS6B01G034900 chr6B 20874625 20877069 2444 True 4516 4516 100.000 1 2445 1 chr6B.!!$R1 2444
1 TraesCS6B01G034900 chr6B 207192973 207195220 2247 False 3014 3014 90.905 184 2442 1 chr6B.!!$F1 2258
2 TraesCS6B01G034900 chr2B 398369476 398371739 2263 False 3151 3151 91.854 185 2442 1 chr2B.!!$F2 2257
3 TraesCS6B01G034900 chr1D 75674609 75676843 2234 False 2963 2963 90.581 185 2442 1 chr1D.!!$F1 2257
4 TraesCS6B01G034900 chr7D 601144616 601146871 2255 False 2961 2961 90.430 185 2442 1 chr7D.!!$F3 2257
5 TraesCS6B01G034900 chr7D 140036675 140038923 2248 False 2599 2599 87.604 185 2442 1 chr7D.!!$F1 2257
6 TraesCS6B01G034900 chr5D 498582014 498584272 2258 False 2952 2952 90.316 181 2443 1 chr5D.!!$F2 2262
7 TraesCS6B01G034900 chr5D 47938359 47940607 2248 False 2892 2892 89.925 185 2442 1 chr5D.!!$F1 2257
8 TraesCS6B01G034900 chr5D 512177899 512179912 2013 True 2468 2468 88.933 435 2442 1 chr5D.!!$R1 2007
9 TraesCS6B01G034900 chr6D 40065309 40067581 2272 False 2933 2933 90.196 190 2442 1 chr6D.!!$F1 2252
10 TraesCS6B01G034900 chr2D 563161847 563164093 2246 False 2929 2929 90.229 185 2442 1 chr2D.!!$F1 2257
11 TraesCS6B01G034900 chr2D 650188455 650190368 1913 True 2686 2686 92.135 543 2442 1 chr2D.!!$R2 1899
12 TraesCS6B01G034900 chr2D 91292583 91294842 2259 True 2665 2665 88.063 180 2443 1 chr2D.!!$R1 2263
13 TraesCS6B01G034900 chr3D 592735652 592737908 2256 True 2824 2824 89.361 184 2442 1 chr3D.!!$R2 2258
14 TraesCS6B01G034900 chr3D 609349808 609351828 2020 True 2540 2540 89.528 435 2442 1 chr3D.!!$R3 2007
15 TraesCS6B01G034900 chr3D 42773022 42775038 2016 False 2510 2510 89.293 435 2443 1 chr3D.!!$F1 2008
16 TraesCS6B01G034900 chr3A 718947748 718950006 2258 False 2597 2597 87.582 185 2442 1 chr3A.!!$F1 2257
17 TraesCS6B01G034900 chr7B 113827035 113829295 2260 False 2560 2560 87.298 185 2442 1 chr7B.!!$F1 2257
18 TraesCS6B01G034900 chr7B 725093527 725095457 1930 True 2444 2444 89.646 518 2445 1 chr7B.!!$R2 1927
19 TraesCS6B01G034900 chrUn 114912007 114914017 2010 True 2497 2497 89.217 436 2442 1 chrUn.!!$R3 2006
20 TraesCS6B01G034900 chrUn 7461029 7463228 2199 True 2471 2471 86.945 185 2442 1 chrUn.!!$R1 2257
21 TraesCS6B01G034900 chrUn 82251229 82253295 2066 True 2161 2161 86.152 435 2442 1 chrUn.!!$R2 2007
22 TraesCS6B01G034900 chrUn 12672427 12674113 1686 False 1969 1969 88.173 798 2442 1 chrUn.!!$F1 1644
23 TraesCS6B01G034900 chrUn 189428449 189429779 1330 False 1738 1738 90.342 1111 2442 1 chrUn.!!$F2 1331
24 TraesCS6B01G034900 chr4D 24424974 24426873 1899 True 2459 2459 90.114 544 2445 1 chr4D.!!$R1 1901
25 TraesCS6B01G034900 chr4A 673810348 673812290 1942 False 2459 2459 89.673 515 2445 1 chr4A.!!$F1 1930
26 TraesCS6B01G034900 chr4A 647697482 647699406 1924 True 2209 2209 87.712 544 2445 1 chr4A.!!$R1 1901
27 TraesCS6B01G034900 chr6A 617856941 617858955 2014 True 2222 2222 87.003 462 2442 1 chr6A.!!$R1 1980
28 TraesCS6B01G034900 chr3B 809385043 809386288 1245 False 1408 1408 87.028 185 1453 1 chr3B.!!$F1 1268

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
39 40 0.037232 AGACGAGGCCCGAAGAAAAG 60.037 55.0 18.74 0.0 41.76 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 1933 0.474184 ACCAGACTCAAACAGGTGGG 59.526 55.0 0.0 0.0 35.47 4.61 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
30 31 2.493501 GGTAACGAGACGAGGCCC 59.506 66.667 0.00 0.00 0.00 5.80
31 32 2.101770 GTAACGAGACGAGGCCCG 59.898 66.667 11.48 11.48 45.44 6.13
32 33 2.046023 TAACGAGACGAGGCCCGA 60.046 61.111 18.74 0.00 41.76 5.14
33 34 1.675310 TAACGAGACGAGGCCCGAA 60.675 57.895 18.74 0.00 41.76 4.30
34 35 1.651240 TAACGAGACGAGGCCCGAAG 61.651 60.000 18.74 9.62 41.76 3.79
35 36 3.132139 CGAGACGAGGCCCGAAGA 61.132 66.667 18.74 0.00 41.76 2.87
36 37 2.697761 CGAGACGAGGCCCGAAGAA 61.698 63.158 18.74 0.00 41.76 2.52
37 38 1.590147 GAGACGAGGCCCGAAGAAA 59.410 57.895 18.74 0.00 41.76 2.52
38 39 0.037605 GAGACGAGGCCCGAAGAAAA 60.038 55.000 18.74 0.00 41.76 2.29
39 40 0.037232 AGACGAGGCCCGAAGAAAAG 60.037 55.000 18.74 0.00 41.76 2.27
40 41 1.003718 ACGAGGCCCGAAGAAAAGG 60.004 57.895 18.74 0.00 41.76 3.11
41 42 1.003718 CGAGGCCCGAAGAAAAGGT 60.004 57.895 0.00 0.00 41.76 3.50
42 43 0.605589 CGAGGCCCGAAGAAAAGGTT 60.606 55.000 0.00 0.00 41.76 3.50
43 44 0.881796 GAGGCCCGAAGAAAAGGTTG 59.118 55.000 0.00 0.00 0.00 3.77
44 45 1.179174 AGGCCCGAAGAAAAGGTTGC 61.179 55.000 0.00 0.00 0.00 4.17
45 46 1.081442 GCCCGAAGAAAAGGTTGCG 60.081 57.895 0.00 0.00 0.00 4.85
46 47 1.081442 CCCGAAGAAAAGGTTGCGC 60.081 57.895 0.00 0.00 0.00 6.09
47 48 1.081442 CCGAAGAAAAGGTTGCGCC 60.081 57.895 4.18 0.00 37.58 6.53
48 49 1.081442 CGAAGAAAAGGTTGCGCCC 60.081 57.895 4.18 0.00 38.26 6.13
49 50 1.791103 CGAAGAAAAGGTTGCGCCCA 61.791 55.000 4.18 0.00 38.26 5.36
50 51 0.039165 GAAGAAAAGGTTGCGCCCAG 60.039 55.000 4.18 0.00 38.26 4.45
51 52 0.467290 AAGAAAAGGTTGCGCCCAGA 60.467 50.000 4.18 0.00 38.26 3.86
52 53 0.251341 AGAAAAGGTTGCGCCCAGAT 60.251 50.000 4.18 0.00 38.26 2.90
53 54 0.109132 GAAAAGGTTGCGCCCAGATG 60.109 55.000 4.18 0.00 38.26 2.90
54 55 0.539438 AAAAGGTTGCGCCCAGATGA 60.539 50.000 4.18 0.00 38.26 2.92
55 56 0.539438 AAAGGTTGCGCCCAGATGAA 60.539 50.000 4.18 0.00 38.26 2.57
56 57 0.539438 AAGGTTGCGCCCAGATGAAA 60.539 50.000 4.18 0.00 38.26 2.69
57 58 0.962356 AGGTTGCGCCCAGATGAAAG 60.962 55.000 4.18 0.00 38.26 2.62
58 59 1.508088 GTTGCGCCCAGATGAAAGG 59.492 57.895 4.18 0.00 0.00 3.11
59 60 1.074775 TTGCGCCCAGATGAAAGGT 59.925 52.632 4.18 0.00 0.00 3.50
60 61 0.539438 TTGCGCCCAGATGAAAGGTT 60.539 50.000 4.18 0.00 0.00 3.50
61 62 0.960364 TGCGCCCAGATGAAAGGTTC 60.960 55.000 4.18 0.00 0.00 3.62
62 63 0.960364 GCGCCCAGATGAAAGGTTCA 60.960 55.000 0.00 0.00 45.01 3.18
73 74 3.753815 TGAAAGGTTCATGATCACAGCA 58.246 40.909 0.00 0.00 34.08 4.41
74 75 4.143543 TGAAAGGTTCATGATCACAGCAA 58.856 39.130 0.00 0.00 34.08 3.91
75 76 4.768448 TGAAAGGTTCATGATCACAGCAAT 59.232 37.500 0.00 0.00 34.08 3.56
76 77 4.978083 AAGGTTCATGATCACAGCAATC 57.022 40.909 0.00 0.00 0.00 2.67
77 78 2.941064 AGGTTCATGATCACAGCAATCG 59.059 45.455 0.00 0.00 0.00 3.34
78 79 2.540361 GGTTCATGATCACAGCAATCGC 60.540 50.000 0.00 0.00 38.99 4.58
79 80 0.932399 TCATGATCACAGCAATCGCG 59.068 50.000 0.00 0.00 45.49 5.87
80 81 0.041576 CATGATCACAGCAATCGCGG 60.042 55.000 6.13 0.00 45.49 6.46
81 82 0.179076 ATGATCACAGCAATCGCGGA 60.179 50.000 6.13 0.00 45.49 5.54
82 83 1.083806 TGATCACAGCAATCGCGGAC 61.084 55.000 6.13 0.00 45.49 4.79
83 84 2.082437 GATCACAGCAATCGCGGACG 62.082 60.000 6.13 0.00 45.49 4.79
95 96 4.444838 CGGACGATGGCCAACCGA 62.445 66.667 29.72 0.00 45.31 4.69
96 97 2.511600 GGACGATGGCCAACCGAG 60.512 66.667 29.72 14.35 39.70 4.63
97 98 2.264794 GACGATGGCCAACCGAGT 59.735 61.111 29.72 17.08 39.70 4.18
98 99 2.047274 ACGATGGCCAACCGAGTG 60.047 61.111 29.72 10.04 39.70 3.51
99 100 2.264480 CGATGGCCAACCGAGTGA 59.736 61.111 21.87 0.00 39.70 3.41
100 101 1.375396 CGATGGCCAACCGAGTGAA 60.375 57.895 21.87 0.00 39.70 3.18
101 102 1.635663 CGATGGCCAACCGAGTGAAC 61.636 60.000 21.87 0.00 39.70 3.18
102 103 1.303317 ATGGCCAACCGAGTGAACC 60.303 57.895 10.96 0.00 39.70 3.62
103 104 2.671963 GGCCAACCGAGTGAACCC 60.672 66.667 0.00 0.00 0.00 4.11
104 105 3.047877 GCCAACCGAGTGAACCCG 61.048 66.667 0.00 0.00 0.00 5.28
111 112 4.754667 GAGTGAACCCGGCGGACC 62.755 72.222 30.79 16.07 0.00 4.46
113 114 4.629523 GTGAACCCGGCGGACCAA 62.630 66.667 30.79 7.44 34.57 3.67
114 115 4.323477 TGAACCCGGCGGACCAAG 62.323 66.667 30.79 13.10 34.57 3.61
118 119 4.856801 CCCGGCGGACCAAGGATG 62.857 72.222 30.79 2.47 34.57 3.51
120 121 4.776322 CGGCGGACCAAGGATGCA 62.776 66.667 0.00 0.00 34.57 3.96
121 122 2.124151 GGCGGACCAAGGATGCAT 60.124 61.111 0.00 0.00 35.26 3.96
122 123 1.754234 GGCGGACCAAGGATGCATT 60.754 57.895 0.00 0.00 35.26 3.56
123 124 1.322538 GGCGGACCAAGGATGCATTT 61.323 55.000 0.00 0.00 35.26 2.32
124 125 0.532115 GCGGACCAAGGATGCATTTT 59.468 50.000 0.00 0.00 0.00 1.82
125 126 1.469767 GCGGACCAAGGATGCATTTTC 60.470 52.381 0.00 0.00 0.00 2.29
126 127 2.094675 CGGACCAAGGATGCATTTTCT 58.905 47.619 0.00 0.00 0.00 2.52
127 128 2.159338 CGGACCAAGGATGCATTTTCTG 60.159 50.000 0.00 0.00 0.00 3.02
145 146 1.725641 TGCTCAGTGCGGAACTATTG 58.274 50.000 0.00 0.00 46.63 1.90
146 147 1.001974 TGCTCAGTGCGGAACTATTGT 59.998 47.619 0.00 0.00 46.63 2.71
147 148 2.076863 GCTCAGTGCGGAACTATTGTT 58.923 47.619 0.00 0.00 36.83 2.83
148 149 3.259064 GCTCAGTGCGGAACTATTGTTA 58.741 45.455 0.00 0.00 36.83 2.41
149 150 3.307242 GCTCAGTGCGGAACTATTGTTAG 59.693 47.826 0.00 0.00 36.83 2.34
150 151 3.857052 TCAGTGCGGAACTATTGTTAGG 58.143 45.455 0.00 0.00 36.83 2.69
151 152 2.936498 CAGTGCGGAACTATTGTTAGGG 59.064 50.000 0.00 0.00 36.83 3.53
152 153 2.835764 AGTGCGGAACTATTGTTAGGGA 59.164 45.455 0.00 0.00 37.36 4.20
153 154 2.934553 GTGCGGAACTATTGTTAGGGAC 59.065 50.000 0.00 0.00 36.39 4.46
154 155 2.568062 TGCGGAACTATTGTTAGGGACA 59.432 45.455 0.00 0.00 36.39 4.02
155 156 3.195661 GCGGAACTATTGTTAGGGACAG 58.804 50.000 0.00 0.00 39.94 3.51
156 157 3.195661 CGGAACTATTGTTAGGGACAGC 58.804 50.000 0.00 0.00 39.94 4.40
157 158 3.369052 CGGAACTATTGTTAGGGACAGCA 60.369 47.826 0.00 0.00 39.94 4.41
158 159 4.683400 CGGAACTATTGTTAGGGACAGCAT 60.683 45.833 0.00 0.00 39.94 3.79
159 160 4.816925 GGAACTATTGTTAGGGACAGCATC 59.183 45.833 0.00 0.00 39.94 3.91
160 161 4.781934 AACTATTGTTAGGGACAGCATCC 58.218 43.478 0.00 0.00 39.94 3.51
167 168 4.766970 GGACAGCATCCCGATCAG 57.233 61.111 0.00 0.00 42.46 2.90
168 169 1.596477 GGACAGCATCCCGATCAGC 60.596 63.158 0.00 0.00 42.46 4.26
169 170 1.144716 GACAGCATCCCGATCAGCA 59.855 57.895 0.00 0.00 0.00 4.41
170 171 0.250209 GACAGCATCCCGATCAGCAT 60.250 55.000 0.00 0.00 0.00 3.79
171 172 0.250209 ACAGCATCCCGATCAGCATC 60.250 55.000 0.00 0.00 0.00 3.91
172 173 0.954449 CAGCATCCCGATCAGCATCC 60.954 60.000 0.00 0.00 0.00 3.51
173 174 1.071987 GCATCCCGATCAGCATCCA 59.928 57.895 0.00 0.00 0.00 3.41
174 175 1.233285 GCATCCCGATCAGCATCCAC 61.233 60.000 0.00 0.00 0.00 4.02
175 176 0.947660 CATCCCGATCAGCATCCACG 60.948 60.000 0.00 0.00 0.00 4.94
176 177 1.402896 ATCCCGATCAGCATCCACGT 61.403 55.000 0.00 0.00 0.00 4.49
177 178 0.753848 TCCCGATCAGCATCCACGTA 60.754 55.000 0.00 0.00 0.00 3.57
178 179 0.318441 CCCGATCAGCATCCACGTAT 59.682 55.000 0.00 0.00 0.00 3.06
179 180 1.422388 CCGATCAGCATCCACGTATG 58.578 55.000 0.00 0.00 0.00 2.39
284 285 2.998480 TTCCAACGGCTAGGCGGA 60.998 61.111 37.39 24.36 33.14 5.54
342 367 0.534203 ATCGGTTCGTGCCACAAACT 60.534 50.000 0.00 0.00 0.00 2.66
429 468 0.916086 ATGCCATGAACCGGGACTAA 59.084 50.000 6.32 0.00 0.00 2.24
581 691 0.894141 ATTGCTCGAGCTCACACTCT 59.106 50.000 35.27 10.26 42.66 3.24
705 818 8.370940 AGCTCTTGCAATGCTCTATAAGTATAA 58.629 33.333 17.79 0.00 42.74 0.98
749 893 8.751215 TTGGGAGGAATTATATGTGGTAGTAT 57.249 34.615 0.00 0.00 0.00 2.12
819 965 5.874897 TGTAGGTGTGGTTTACTTAGTGT 57.125 39.130 0.00 0.00 0.00 3.55
911 1069 8.447053 GTGAGCCTCTTGTTCTTATCTTTTTAG 58.553 37.037 0.00 0.00 0.00 1.85
1016 1180 3.627577 AGTGTCATGGTTTTGATATCCGC 59.372 43.478 0.00 0.00 0.00 5.54
1102 1274 6.531594 TGTTGCATTTCGTGTTTATGACAAAA 59.468 30.769 0.00 0.00 40.65 2.44
1184 1358 2.108168 CCAACCCTATTGTCGAGAGGA 58.892 52.381 1.94 0.00 39.18 3.71
1325 1511 3.855950 GGAGAAAATGCGCTTGAAGATTG 59.144 43.478 9.73 0.00 0.00 2.67
1335 1521 5.182950 TGCGCTTGAAGATTGGAAAGATTAA 59.817 36.000 9.73 0.00 0.00 1.40
1525 1743 3.006112 TGGTCTTTTTGGTGCTGTGTA 57.994 42.857 0.00 0.00 0.00 2.90
1546 1765 2.936919 ATGAAGATGAGCCGGCAATA 57.063 45.000 31.54 14.91 0.00 1.90
1587 1806 4.860022 CTCTCCCCAGTTCATTAATGGTT 58.140 43.478 15.36 0.00 31.85 3.67
1628 1848 3.353836 GAGGCAAACAAGCGGCGA 61.354 61.111 12.98 0.00 34.64 5.54
1655 1876 3.643199 TTATGCCTTGTCCATGTGCTA 57.357 42.857 0.00 0.00 0.00 3.49
1656 1877 2.512692 ATGCCTTGTCCATGTGCTAA 57.487 45.000 0.00 0.00 0.00 3.09
1701 1933 3.994392 TCTAAGTCAAGAACCATTCACGC 59.006 43.478 0.00 0.00 0.00 5.34
1780 2013 6.745857 AGAAAGAGGGGTTATGATGGAAAAT 58.254 36.000 0.00 0.00 0.00 1.82
1829 2062 1.079073 CCTGGCAATGGGTTCCCTT 59.921 57.895 9.43 0.00 0.00 3.95
1932 2237 0.605589 GATGATCTAGGTCGGGCCAG 59.394 60.000 4.39 0.00 40.61 4.85
1935 2240 0.755698 GATCTAGGTCGGGCCAGTGA 60.756 60.000 4.39 0.00 40.61 3.41
2000 2311 1.303309 GCAGCGCATGTTAGAGGATT 58.697 50.000 11.47 0.00 0.00 3.01
2141 2458 9.412460 TGATAATGTTAAAGAAGATGCTTCCAT 57.588 29.630 3.71 0.00 0.00 3.41
2190 2508 3.279434 ACGAAGCAAAGAAGGTTGTCTT 58.721 40.909 0.00 0.00 39.60 3.01
2229 2547 4.282068 GTGTAGAAAATACATGCATGCCG 58.718 43.478 26.53 9.08 0.00 5.69
2252 2570 1.068250 GACTGCATCCTCTACCGCC 59.932 63.158 0.00 0.00 0.00 6.13
2355 2673 4.821589 CGAGCGCCCCAGGAAGAC 62.822 72.222 2.29 0.00 0.00 3.01
2379 2704 0.251297 CCTGCCAAGGTGATGTTCCA 60.251 55.000 0.00 0.00 38.96 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.788308 TCGTTACCGAAGTTTTGCTCG 59.212 47.619 0.00 0.00 40.86 5.03
3 4 2.409371 CGTCTCGTTACCGAAGTTTTGC 60.409 50.000 0.00 0.00 43.69 3.68
5 6 3.303406 CTCGTCTCGTTACCGAAGTTTT 58.697 45.455 0.00 0.00 43.69 2.43
6 7 2.351157 CCTCGTCTCGTTACCGAAGTTT 60.351 50.000 0.00 0.00 43.69 2.66
7 8 1.198637 CCTCGTCTCGTTACCGAAGTT 59.801 52.381 0.00 0.00 43.69 2.66
8 9 0.801251 CCTCGTCTCGTTACCGAAGT 59.199 55.000 0.00 0.00 43.69 3.01
9 10 0.522915 GCCTCGTCTCGTTACCGAAG 60.523 60.000 0.00 0.00 43.69 3.79
10 11 1.503542 GCCTCGTCTCGTTACCGAA 59.496 57.895 0.00 0.00 43.69 4.30
11 12 2.401766 GGCCTCGTCTCGTTACCGA 61.402 63.158 0.00 0.00 41.73 4.69
12 13 2.101770 GGCCTCGTCTCGTTACCG 59.898 66.667 0.00 0.00 0.00 4.02
13 14 2.493501 GGGCCTCGTCTCGTTACC 59.506 66.667 0.84 0.00 0.00 2.85
14 15 1.926511 TTCGGGCCTCGTCTCGTTAC 61.927 60.000 0.84 0.00 40.32 2.50
15 16 1.651240 CTTCGGGCCTCGTCTCGTTA 61.651 60.000 0.84 0.00 40.32 3.18
16 17 2.987547 TTCGGGCCTCGTCTCGTT 60.988 61.111 0.84 0.00 40.32 3.85
17 18 3.441290 CTTCGGGCCTCGTCTCGT 61.441 66.667 0.84 0.00 40.32 4.18
18 19 2.209064 TTTCTTCGGGCCTCGTCTCG 62.209 60.000 0.84 0.00 40.32 4.04
19 20 0.037605 TTTTCTTCGGGCCTCGTCTC 60.038 55.000 0.84 0.00 40.32 3.36
20 21 0.037232 CTTTTCTTCGGGCCTCGTCT 60.037 55.000 0.84 0.00 40.32 4.18
21 22 1.019805 CCTTTTCTTCGGGCCTCGTC 61.020 60.000 0.84 0.00 40.32 4.20
22 23 1.003718 CCTTTTCTTCGGGCCTCGT 60.004 57.895 0.84 0.00 40.32 4.18
23 24 0.605589 AACCTTTTCTTCGGGCCTCG 60.606 55.000 0.84 4.76 40.90 4.63
24 25 0.881796 CAACCTTTTCTTCGGGCCTC 59.118 55.000 0.84 0.00 0.00 4.70
25 26 1.179174 GCAACCTTTTCTTCGGGCCT 61.179 55.000 0.84 0.00 0.00 5.19
26 27 1.289066 GCAACCTTTTCTTCGGGCC 59.711 57.895 0.00 0.00 0.00 5.80
27 28 1.081442 CGCAACCTTTTCTTCGGGC 60.081 57.895 0.00 0.00 0.00 6.13
28 29 1.081442 GCGCAACCTTTTCTTCGGG 60.081 57.895 0.30 0.00 0.00 5.14
29 30 1.081442 GGCGCAACCTTTTCTTCGG 60.081 57.895 10.83 0.00 34.51 4.30
30 31 1.081442 GGGCGCAACCTTTTCTTCG 60.081 57.895 10.83 0.00 39.10 3.79
31 32 0.039165 CTGGGCGCAACCTTTTCTTC 60.039 55.000 10.83 0.00 39.10 2.87
32 33 0.467290 TCTGGGCGCAACCTTTTCTT 60.467 50.000 10.83 0.00 39.10 2.52
33 34 0.251341 ATCTGGGCGCAACCTTTTCT 60.251 50.000 10.83 0.00 39.10 2.52
34 35 0.109132 CATCTGGGCGCAACCTTTTC 60.109 55.000 10.83 0.00 39.10 2.29
35 36 0.539438 TCATCTGGGCGCAACCTTTT 60.539 50.000 10.83 0.00 39.10 2.27
36 37 0.539438 TTCATCTGGGCGCAACCTTT 60.539 50.000 10.83 0.00 39.10 3.11
37 38 0.539438 TTTCATCTGGGCGCAACCTT 60.539 50.000 10.83 0.00 39.10 3.50
38 39 0.962356 CTTTCATCTGGGCGCAACCT 60.962 55.000 10.83 0.00 39.10 3.50
39 40 1.508088 CTTTCATCTGGGCGCAACC 59.492 57.895 10.83 1.84 37.93 3.77
40 41 1.244019 ACCTTTCATCTGGGCGCAAC 61.244 55.000 10.83 1.07 0.00 4.17
41 42 0.539438 AACCTTTCATCTGGGCGCAA 60.539 50.000 10.83 0.00 0.00 4.85
42 43 0.960364 GAACCTTTCATCTGGGCGCA 60.960 55.000 10.83 2.47 0.00 6.09
43 44 0.960364 TGAACCTTTCATCTGGGCGC 60.960 55.000 0.00 0.00 34.08 6.53
44 45 3.248043 TGAACCTTTCATCTGGGCG 57.752 52.632 0.00 0.00 34.08 6.13
52 53 3.753815 TGCTGTGATCATGAACCTTTCA 58.246 40.909 0.00 0.00 45.01 2.69
53 54 4.771590 TTGCTGTGATCATGAACCTTTC 57.228 40.909 0.00 0.00 0.00 2.62
54 55 4.142534 CGATTGCTGTGATCATGAACCTTT 60.143 41.667 0.00 0.00 0.00 3.11
55 56 3.376234 CGATTGCTGTGATCATGAACCTT 59.624 43.478 0.00 0.00 0.00 3.50
56 57 2.941064 CGATTGCTGTGATCATGAACCT 59.059 45.455 0.00 0.00 0.00 3.50
57 58 2.540361 GCGATTGCTGTGATCATGAACC 60.540 50.000 0.00 0.00 38.39 3.62
58 59 2.713011 GCGATTGCTGTGATCATGAAC 58.287 47.619 0.00 0.00 38.39 3.18
59 60 1.328374 CGCGATTGCTGTGATCATGAA 59.672 47.619 0.00 0.00 39.65 2.57
60 61 0.932399 CGCGATTGCTGTGATCATGA 59.068 50.000 0.00 0.00 39.65 3.07
61 62 0.041576 CCGCGATTGCTGTGATCATG 60.042 55.000 8.23 0.00 39.65 3.07
62 63 0.179076 TCCGCGATTGCTGTGATCAT 60.179 50.000 8.23 0.00 39.65 2.45
63 64 1.083806 GTCCGCGATTGCTGTGATCA 61.084 55.000 8.23 0.00 39.65 2.92
64 65 1.638467 GTCCGCGATTGCTGTGATC 59.362 57.895 8.23 0.00 39.65 2.92
65 66 2.167219 CGTCCGCGATTGCTGTGAT 61.167 57.895 8.23 0.00 41.33 3.06
66 67 2.809174 CGTCCGCGATTGCTGTGA 60.809 61.111 8.23 0.00 41.33 3.58
67 68 2.809174 TCGTCCGCGATTGCTGTG 60.809 61.111 8.23 0.00 42.81 3.66
78 79 4.444838 TCGGTTGGCCATCGTCCG 62.445 66.667 23.73 23.73 42.12 4.79
79 80 2.511600 CTCGGTTGGCCATCGTCC 60.512 66.667 22.69 14.93 34.09 4.79
80 81 2.100631 CACTCGGTTGGCCATCGTC 61.101 63.158 22.69 8.55 34.09 4.20
81 82 2.047274 CACTCGGTTGGCCATCGT 60.047 61.111 22.69 7.71 34.09 3.73
82 83 1.375396 TTCACTCGGTTGGCCATCG 60.375 57.895 19.20 19.20 34.09 3.84
83 84 1.305930 GGTTCACTCGGTTGGCCATC 61.306 60.000 6.09 5.53 34.09 3.51
84 85 1.303317 GGTTCACTCGGTTGGCCAT 60.303 57.895 6.09 0.00 34.09 4.40
85 86 2.112297 GGTTCACTCGGTTGGCCA 59.888 61.111 0.00 0.00 34.09 5.36
86 87 2.671963 GGGTTCACTCGGTTGGCC 60.672 66.667 0.00 0.00 0.00 5.36
87 88 3.047877 CGGGTTCACTCGGTTGGC 61.048 66.667 0.00 0.00 0.00 4.52
88 89 2.358247 CCGGGTTCACTCGGTTGG 60.358 66.667 10.31 0.00 41.23 3.77
94 95 4.754667 GGTCCGCCGGGTTCACTC 62.755 72.222 1.90 0.00 33.83 3.51
96 97 4.629523 TTGGTCCGCCGGGTTCAC 62.630 66.667 1.90 0.00 37.67 3.18
97 98 4.323477 CTTGGTCCGCCGGGTTCA 62.323 66.667 1.90 0.00 37.67 3.18
101 102 4.856801 CATCCTTGGTCCGCCGGG 62.857 72.222 1.90 0.00 37.67 5.73
103 104 4.776322 TGCATCCTTGGTCCGCCG 62.776 66.667 0.00 0.00 37.67 6.46
104 105 1.322538 AAATGCATCCTTGGTCCGCC 61.323 55.000 0.00 0.00 0.00 6.13
105 106 0.532115 AAAATGCATCCTTGGTCCGC 59.468 50.000 0.00 0.00 0.00 5.54
106 107 2.094675 AGAAAATGCATCCTTGGTCCG 58.905 47.619 0.00 0.00 0.00 4.79
107 108 3.515330 CAGAAAATGCATCCTTGGTCC 57.485 47.619 0.00 0.00 0.00 4.46
119 120 1.159285 TCCGCACTGAGCAGAAAATG 58.841 50.000 4.21 0.00 46.13 2.32
120 121 1.537202 GTTCCGCACTGAGCAGAAAAT 59.463 47.619 4.21 0.00 41.06 1.82
121 122 0.944386 GTTCCGCACTGAGCAGAAAA 59.056 50.000 4.21 0.00 41.06 2.29
122 123 0.106708 AGTTCCGCACTGAGCAGAAA 59.893 50.000 4.21 0.00 41.06 2.52
123 124 0.966179 TAGTTCCGCACTGAGCAGAA 59.034 50.000 4.21 0.00 46.13 3.02
124 125 1.186200 ATAGTTCCGCACTGAGCAGA 58.814 50.000 4.21 0.00 46.13 4.26
125 126 1.662629 CAATAGTTCCGCACTGAGCAG 59.337 52.381 0.00 0.00 46.13 4.24
126 127 1.001974 ACAATAGTTCCGCACTGAGCA 59.998 47.619 0.00 0.00 46.13 4.26
127 128 1.726853 ACAATAGTTCCGCACTGAGC 58.273 50.000 0.00 0.00 35.97 4.26
128 129 3.865745 CCTAACAATAGTTCCGCACTGAG 59.134 47.826 0.00 0.00 39.15 3.35
129 130 3.369052 CCCTAACAATAGTTCCGCACTGA 60.369 47.826 0.00 0.00 39.15 3.41
130 131 2.936498 CCCTAACAATAGTTCCGCACTG 59.064 50.000 0.00 0.00 39.15 3.66
131 132 2.835764 TCCCTAACAATAGTTCCGCACT 59.164 45.455 0.00 0.00 39.15 4.40
132 133 2.934553 GTCCCTAACAATAGTTCCGCAC 59.065 50.000 0.00 0.00 39.15 5.34
133 134 2.568062 TGTCCCTAACAATAGTTCCGCA 59.432 45.455 0.00 0.00 39.15 5.69
134 135 3.195661 CTGTCCCTAACAATAGTTCCGC 58.804 50.000 0.00 0.00 39.15 5.54
135 136 3.195661 GCTGTCCCTAACAATAGTTCCG 58.804 50.000 0.00 0.00 39.15 4.30
136 137 4.216411 TGCTGTCCCTAACAATAGTTCC 57.784 45.455 0.00 0.00 39.15 3.62
137 138 4.816925 GGATGCTGTCCCTAACAATAGTTC 59.183 45.833 0.00 0.00 41.50 3.01
138 139 4.781934 GGATGCTGTCCCTAACAATAGTT 58.218 43.478 0.00 0.00 41.50 2.24
139 140 4.423625 GGATGCTGTCCCTAACAATAGT 57.576 45.455 0.00 0.00 41.50 2.12
151 152 0.250209 ATGCTGATCGGGATGCTGTC 60.250 55.000 7.88 0.00 0.00 3.51
152 153 0.250209 GATGCTGATCGGGATGCTGT 60.250 55.000 13.96 0.00 0.00 4.40
153 154 0.954449 GGATGCTGATCGGGATGCTG 60.954 60.000 18.44 0.00 0.00 4.41
154 155 1.374190 GGATGCTGATCGGGATGCT 59.626 57.895 18.44 0.00 0.00 3.79
155 156 1.071987 TGGATGCTGATCGGGATGC 59.928 57.895 18.81 18.81 0.00 3.91
156 157 0.947660 CGTGGATGCTGATCGGGATG 60.948 60.000 13.96 0.00 0.00 3.51
157 158 1.368950 CGTGGATGCTGATCGGGAT 59.631 57.895 8.48 8.48 0.00 3.85
158 159 0.753848 TACGTGGATGCTGATCGGGA 60.754 55.000 3.14 0.00 0.00 5.14
159 160 0.318441 ATACGTGGATGCTGATCGGG 59.682 55.000 3.14 0.00 0.00 5.14
160 161 1.422388 CATACGTGGATGCTGATCGG 58.578 55.000 0.00 0.00 0.00 4.18
171 172 2.691409 ACTGGTGATTCCATACGTGG 57.309 50.000 0.00 0.00 46.12 4.94
172 173 4.649088 TCTACTGGTGATTCCATACGTG 57.351 45.455 0.00 0.00 46.12 4.49
173 174 5.670792 TTTCTACTGGTGATTCCATACGT 57.329 39.130 0.00 0.00 46.12 3.57
174 175 6.037172 CCTTTTTCTACTGGTGATTCCATACG 59.963 42.308 0.00 0.00 46.12 3.06
175 176 6.318900 CCCTTTTTCTACTGGTGATTCCATAC 59.681 42.308 0.00 0.00 46.12 2.39
176 177 6.423182 CCCTTTTTCTACTGGTGATTCCATA 58.577 40.000 0.00 0.00 46.12 2.74
177 178 5.264395 CCCTTTTTCTACTGGTGATTCCAT 58.736 41.667 0.00 0.00 46.12 3.41
178 179 4.662278 CCCTTTTTCTACTGGTGATTCCA 58.338 43.478 0.00 0.00 45.01 3.53
179 180 3.444034 GCCCTTTTTCTACTGGTGATTCC 59.556 47.826 0.00 0.00 0.00 3.01
180 181 3.444034 GGCCCTTTTTCTACTGGTGATTC 59.556 47.826 0.00 0.00 0.00 2.52
181 182 3.076032 AGGCCCTTTTTCTACTGGTGATT 59.924 43.478 0.00 0.00 0.00 2.57
182 183 2.649816 AGGCCCTTTTTCTACTGGTGAT 59.350 45.455 0.00 0.00 0.00 3.06
187 188 5.253330 TCACATTAGGCCCTTTTTCTACTG 58.747 41.667 0.00 0.00 0.00 2.74
284 285 2.467880 ACCAGGACTAATGACCATCGT 58.532 47.619 0.00 0.00 0.00 3.73
342 367 1.626825 GCCACCACCTCTTTAGTACCA 59.373 52.381 0.00 0.00 0.00 3.25
386 425 1.183549 CGGTACTAGAGGTGCTGGTT 58.816 55.000 0.00 0.00 39.29 3.67
429 468 1.065418 CCGGGACTAAAGGTGCATCTT 60.065 52.381 6.34 6.34 38.05 2.40
603 713 1.203288 TGGATGGGGTGCCTTCAAATT 60.203 47.619 0.00 0.00 0.00 1.82
705 818 7.084268 TCCCAAAATAAAACCCACAAATCAT 57.916 32.000 0.00 0.00 0.00 2.45
819 965 2.444421 GTTAGGACAGAGACGGGAAGA 58.556 52.381 0.00 0.00 0.00 2.87
1069 1237 6.747659 AACACGAAATGCAACAAATAGTTC 57.252 33.333 0.00 0.00 38.74 3.01
1102 1274 6.191657 TCTATGTCAACTTGATGGGCATAT 57.808 37.500 0.00 0.00 0.00 1.78
1225 1399 3.092301 CTCCCCCTCAATCCTTTTCAAC 58.908 50.000 0.00 0.00 0.00 3.18
1234 1408 2.412591 TCCATCTTCTCCCCCTCAATC 58.587 52.381 0.00 0.00 0.00 2.67
1335 1521 5.065218 GCCTCACTATCGATGACACATTTTT 59.935 40.000 8.54 0.00 0.00 1.94
1341 1527 3.119291 CAAGCCTCACTATCGATGACAC 58.881 50.000 8.54 0.00 0.00 3.67
1525 1743 1.838112 TTGCCGGCTCATCTTCATTT 58.162 45.000 29.70 0.00 0.00 2.32
1546 1765 5.047164 GGAGAGCATCAGTCATCATACATCT 60.047 44.000 0.00 0.00 37.82 2.90
1587 1806 2.351641 CCGCAAGCAGAAAAGTATGCAA 60.352 45.455 0.00 0.00 44.71 4.08
1628 1848 4.531732 ACATGGACAAGGCATAAAACCATT 59.468 37.500 0.00 0.00 34.96 3.16
1701 1933 0.474184 ACCAGACTCAAACAGGTGGG 59.526 55.000 0.00 0.00 35.47 4.61
1780 2013 4.698780 TCGTCGTCCTCTTCTTCTTCATTA 59.301 41.667 0.00 0.00 0.00 1.90
1829 2062 5.369833 CCCCATTGTTGTACCATCGTATTA 58.630 41.667 0.00 0.00 0.00 0.98
1932 2237 4.164294 GCAGTTTCTCTTTGCATCATCAC 58.836 43.478 0.00 0.00 37.75 3.06
1935 2240 2.415090 GCGCAGTTTCTCTTTGCATCAT 60.415 45.455 0.30 0.00 37.69 2.45
2000 2311 7.364200 CAATTCGGGTACAACAATTTCTTGTA 58.636 34.615 0.00 2.56 44.83 2.41
2141 2458 4.191544 CTCTCGGGCAATTCATTGTTCTA 58.808 43.478 1.59 0.00 39.88 2.10
2144 2461 2.795329 ACTCTCGGGCAATTCATTGTT 58.205 42.857 1.59 0.00 39.88 2.83
2197 2515 7.173390 GCATGTATTTTCTACACCTCTAATCCC 59.827 40.741 0.00 0.00 0.00 3.85
2215 2533 4.023792 CAGTCATTACGGCATGCATGTATT 60.024 41.667 26.79 14.13 0.00 1.89
2229 2547 3.643763 CGGTAGAGGATGCAGTCATTAC 58.356 50.000 0.00 0.00 31.96 1.89
2252 2570 4.651994 GCGTTCAAATCCTTGTACTCATG 58.348 43.478 0.00 0.00 32.31 3.07
2355 2673 1.019673 CATCACCTTGGCAGGAATCG 58.980 55.000 9.53 0.00 44.19 3.34


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

AutoCloner maintained by Alex Coulton.