Multiple sequence alignment - TraesCS2B01G238700

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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 TraesCS2B01G238700 chr2B 100.000 2372 0 0 1 2372 239998555 239996184 0.000000e+00 4381.0
1 TraesCS2B01G238700 chr2B 91.033 513 18 3 1600 2085 216856122 216855611 0.000000e+00 667.0
2 TraesCS2B01G238700 chr2B 92.715 151 9 2 1 150 697788287 697788138 1.430000e-52 217.0
3 TraesCS2B01G238700 chr2B 95.000 40 2 0 134 173 239998362 239998323 1.970000e-06 63.9
4 TraesCS2B01G238700 chr2B 92.308 39 2 1 135 173 29008820 29008783 1.000000e-03 54.7
5 TraesCS2B01G238700 chr2B 92.308 39 2 1 135 173 48242227 48242190 1.000000e-03 54.7
6 TraesCS2B01G238700 chr7B 92.363 1519 85 14 844 2333 712762057 712760541 0.000000e+00 2134.0
7 TraesCS2B01G238700 chr7B 94.663 787 37 5 232 1017 613885844 613886626 0.000000e+00 1216.0
8 TraesCS2B01G238700 chr7B 94.536 787 38 5 232 1017 613909571 613910353 0.000000e+00 1210.0
9 TraesCS2B01G238700 chr7B 94.000 150 8 1 1 150 186147964 186147816 2.370000e-55 226.0
10 TraesCS2B01G238700 chr7B 88.235 51 4 2 134 184 613378883 613378835 2.550000e-05 60.2
11 TraesCS2B01G238700 chr3B 93.284 1206 75 4 232 1433 233223245 233224448 0.000000e+00 1773.0
12 TraesCS2B01G238700 chr3B 96.146 934 35 1 1438 2371 233224478 233225410 0.000000e+00 1524.0
13 TraesCS2B01G238700 chr3B 95.824 934 39 0 1438 2371 272588050 272587117 0.000000e+00 1509.0
14 TraesCS2B01G238700 chr3B 96.022 553 21 1 232 784 272589223 272588672 0.000000e+00 898.0
15 TraesCS2B01G238700 chr3B 90.317 599 48 6 844 1433 272588677 272588080 0.000000e+00 776.0
16 TraesCS2B01G238700 chr3B 93.333 150 9 1 1 150 818603116 818602968 1.100000e-53 220.0
17 TraesCS2B01G238700 chr3B 93.333 150 9 1 1 150 818647369 818647221 1.100000e-53 220.0
18 TraesCS2B01G238700 chr5B 95.508 935 42 0 1438 2372 619683807 619682873 0.000000e+00 1495.0
19 TraesCS2B01G238700 chr5B 95.307 554 26 0 232 785 619684981 619684428 0.000000e+00 880.0
20 TraesCS2B01G238700 chr5B 93.333 150 9 1 1 150 37738892 37738744 1.100000e-53 220.0
21 TraesCS2B01G238700 chr5B 97.619 42 1 0 196 237 676288288 676288247 3.270000e-09 73.1
22 TraesCS2B01G238700 chr6B 93.215 958 40 8 1438 2371 664805964 664806920 0.000000e+00 1386.0
23 TraesCS2B01G238700 chr6B 93.924 790 46 2 232 1020 673196107 673195319 0.000000e+00 1192.0
24 TraesCS2B01G238700 chr6B 90.754 411 35 3 1024 1433 664805526 664805934 1.600000e-151 545.0
25 TraesCS2B01G238700 chr6B 97.945 146 3 0 1 146 464406318 464406463 1.090000e-63 254.0
26 TraesCS2B01G238700 chr6B 97.674 43 1 0 195 237 652695584 652695626 9.090000e-10 75.0
27 TraesCS2B01G238700 chr6B 88.000 50 2 2 146 193 7161550 7161597 3.290000e-04 56.5
28 TraesCS2B01G238700 chr3A 90.093 1080 76 7 851 1900 54532994 54531916 0.000000e+00 1373.0
29 TraesCS2B01G238700 chr3A 96.057 558 21 1 232 789 54533548 54532992 0.000000e+00 907.0
30 TraesCS2B01G238700 chr6A 90.028 1083 74 15 851 1900 567627369 567628450 0.000000e+00 1371.0
31 TraesCS2B01G238700 chr6A 96.057 558 22 0 232 789 567626814 567627371 0.000000e+00 909.0
32 TraesCS2B01G238700 chr6A 89.447 597 55 7 844 1433 580784042 580784637 0.000000e+00 747.0
33 TraesCS2B01G238700 chr6A 95.032 463 23 0 1438 1900 580784667 580785129 0.000000e+00 728.0
34 TraesCS2B01G238700 chr6A 90.972 288 25 1 2084 2371 197516 197230 1.030000e-103 387.0
35 TraesCS2B01G238700 chr1B 94.289 788 43 2 234 1020 512227958 512227172 0.000000e+00 1205.0
36 TraesCS2B01G238700 chr1B 83.777 376 41 12 1024 1390 646172443 646172079 2.920000e-89 339.0
37 TraesCS2B01G238700 chr7D 97.391 345 9 0 2028 2372 613748545 613748889 2.630000e-164 588.0
38 TraesCS2B01G238700 chr7D 96.512 344 12 0 2028 2371 26668442 26668099 9.510000e-159 569.0
39 TraesCS2B01G238700 chr7D 96.512 344 12 0 2028 2371 543342047 543341704 9.510000e-159 569.0
40 TraesCS2B01G238700 chr7D 97.561 41 1 0 196 236 26672189 26672149 1.180000e-08 71.3
41 TraesCS2B01G238700 chr3D 97.093 344 10 0 2028 2371 501321931 501321588 4.390000e-162 580.0
42 TraesCS2B01G238700 chr3D 97.093 344 10 0 2028 2371 583552387 583552044 4.390000e-162 580.0
43 TraesCS2B01G238700 chr3D 96.512 344 12 0 2028 2371 580207993 580208336 9.510000e-159 569.0
44 TraesCS2B01G238700 chr3D 96.221 344 13 0 2028 2371 98584254 98583911 4.430000e-157 564.0
45 TraesCS2B01G238700 chr3D 95.502 289 12 1 2084 2371 597392483 597392771 5.970000e-126 460.0
46 TraesCS2B01G238700 chr3D 97.561 41 1 0 196 236 501325964 501325924 1.180000e-08 71.3
47 TraesCS2B01G238700 chr2D 96.802 344 11 0 2028 2371 117556335 117555992 2.040000e-160 575.0
48 TraesCS2B01G238700 chr2D 86.986 292 27 8 1785 2066 159689414 159689124 3.800000e-83 318.0
49 TraesCS2B01G238700 chr2D 96.296 54 2 0 1686 1739 159689557 159689504 3.250000e-14 89.8
50 TraesCS2B01G238700 chr2D 97.561 41 1 0 196 236 20828590 20828550 1.180000e-08 71.3
51 TraesCS2B01G238700 chr4D 96.512 344 11 1 2028 2371 448037494 448037152 3.420000e-158 568.0
52 TraesCS2B01G238700 chr4D 94.767 344 18 0 2029 2372 359526267 359525924 9.650000e-149 536.0
53 TraesCS2B01G238700 chr4D 93.403 288 18 1 2084 2371 435099714 435099428 2.180000e-115 425.0
54 TraesCS2B01G238700 chr4D 97.561 41 1 0 196 236 4183446 4183486 1.180000e-08 71.3
55 TraesCS2B01G238700 chr4D 88.000 50 3 2 135 184 4183446 4183492 3.290000e-04 56.5
56 TraesCS2B01G238700 chr5D 95.640 344 15 0 2028 2371 551209877 551210220 9.580000e-154 553.0
57 TraesCS2B01G238700 chr5D 92.369 249 19 0 2084 2332 19020289 19020041 2.900000e-94 355.0
58 TraesCS2B01G238700 chr5D 90.698 86 8 0 2267 2352 475523257 475523342 5.360000e-22 115.0
59 TraesCS2B01G238700 chr5D 97.561 41 1 0 196 236 433036134 433036174 1.180000e-08 71.3
60 TraesCS2B01G238700 chr6D 94.810 289 14 1 2084 2371 67660288 67660576 1.290000e-122 449.0
61 TraesCS2B01G238700 chr6D 94.000 150 8 1 1 150 10822923 10822775 2.370000e-55 226.0
62 TraesCS2B01G238700 chr6D 93.333 150 9 1 1 150 409262328 409262476 1.100000e-53 220.0
63 TraesCS2B01G238700 chrUn 92.647 272 18 2 689 960 378347301 378347570 7.950000e-105 390.0
64 TraesCS2B01G238700 chr1D 88.552 297 23 4 1140 1431 467928396 467928106 1.350000e-92 350.0
65 TraesCS2B01G238700 chr1D 94.444 198 10 1 2174 2371 54470470 54470666 1.070000e-78 303.0
66 TraesCS2B01G238700 chr1D 97.810 137 3 0 2084 2220 54470345 54470481 1.100000e-58 237.0
67 TraesCS2B01G238700 chr1D 88.889 54 2 2 1443 1496 467928065 467928016 1.970000e-06 63.9
68 TraesCS2B01G238700 chr2A 86.007 293 28 5 1785 2066 170934811 170934521 3.830000e-78 302.0
69 TraesCS2B01G238700 chr2A 93.151 73 5 0 1686 1758 170934968 170934896 8.960000e-20 108.0
70 TraesCS2B01G238700 chr4A 94.000 150 8 1 1 150 660155920 660155772 2.370000e-55 226.0
71 TraesCS2B01G238700 chr4A 92.308 39 2 1 135 173 409225147 409225184 1.000000e-03 54.7
72 TraesCS2B01G238700 chr4B 93.333 150 9 1 1 150 154979703 154979555 1.100000e-53 220.0
73 TraesCS2B01G238700 chr4B 97.619 42 0 1 196 236 153304852 153304893 1.180000e-08 71.3
74 TraesCS2B01G238700 chr4B 97.561 41 1 0 196 236 218598060 218598020 1.180000e-08 71.3
75 TraesCS2B01G238700 chr4B 89.796 49 3 2 135 183 153304852 153304898 7.080000e-06 62.1
76 TraesCS2B01G238700 chr7A 92.308 39 2 1 135 173 682822941 682822904 1.000000e-03 54.7


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 TraesCS2B01G238700 chr2B 239996184 239998555 2371 True 2222.45 4381 97.500000 1 2372 2 chr2B.!!$R5 2371
1 TraesCS2B01G238700 chr2B 216855611 216856122 511 True 667.00 667 91.033000 1600 2085 1 chr2B.!!$R3 485
2 TraesCS2B01G238700 chr7B 712760541 712762057 1516 True 2134.00 2134 92.363000 844 2333 1 chr7B.!!$R3 1489
3 TraesCS2B01G238700 chr7B 613885844 613886626 782 False 1216.00 1216 94.663000 232 1017 1 chr7B.!!$F1 785
4 TraesCS2B01G238700 chr7B 613909571 613910353 782 False 1210.00 1210 94.536000 232 1017 1 chr7B.!!$F2 785
5 TraesCS2B01G238700 chr3B 233223245 233225410 2165 False 1648.50 1773 94.715000 232 2371 2 chr3B.!!$F1 2139
6 TraesCS2B01G238700 chr3B 272587117 272589223 2106 True 1061.00 1509 94.054333 232 2371 3 chr3B.!!$R3 2139
7 TraesCS2B01G238700 chr5B 619682873 619684981 2108 True 1187.50 1495 95.407500 232 2372 2 chr5B.!!$R3 2140
8 TraesCS2B01G238700 chr6B 673195319 673196107 788 True 1192.00 1192 93.924000 232 1020 1 chr6B.!!$R1 788
9 TraesCS2B01G238700 chr6B 664805526 664806920 1394 False 965.50 1386 91.984500 1024 2371 2 chr6B.!!$F4 1347
10 TraesCS2B01G238700 chr3A 54531916 54533548 1632 True 1140.00 1373 93.075000 232 1900 2 chr3A.!!$R1 1668
11 TraesCS2B01G238700 chr6A 567626814 567628450 1636 False 1140.00 1371 93.042500 232 1900 2 chr6A.!!$F1 1668
12 TraesCS2B01G238700 chr6A 580784042 580785129 1087 False 737.50 747 92.239500 844 1900 2 chr6A.!!$F2 1056
13 TraesCS2B01G238700 chr1B 512227172 512227958 786 True 1205.00 1205 94.289000 234 1020 1 chr1B.!!$R1 786
14 TraesCS2B01G238700 chr7D 26668099 26672189 4090 True 320.15 569 97.036500 196 2371 2 chr7D.!!$R2 2175
15 TraesCS2B01G238700 chr3D 501321588 501325964 4376 True 325.65 580 97.327000 196 2371 2 chr3D.!!$R3 2175

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
815 2598 0.039618 CCACACCCCCAAGCACTATT 59.96 55.0 0.0 0.0 0.0 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2308 5322 0.248843 CTCCTCCTCACACCTGAAGC 59.751 60.0 0.0 0.0 0.0 3.86 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
26 27 9.923786 CATTTGGTCAATTGTGCATTAAATATG 57.076 29.630 5.13 0.00 0.00 1.78
27 28 8.489990 TTTGGTCAATTGTGCATTAAATATGG 57.510 30.769 5.13 0.00 0.00 2.74
28 29 6.047870 TGGTCAATTGTGCATTAAATATGGC 58.952 36.000 5.13 0.00 0.00 4.40
29 30 5.466393 GGTCAATTGTGCATTAAATATGGCC 59.534 40.000 5.13 0.00 0.00 5.36
30 31 6.282930 GTCAATTGTGCATTAAATATGGCCT 58.717 36.000 3.32 0.00 0.00 5.19
31 32 7.432869 GTCAATTGTGCATTAAATATGGCCTA 58.567 34.615 3.32 0.00 0.00 3.93
32 33 7.596248 GTCAATTGTGCATTAAATATGGCCTAG 59.404 37.037 3.32 0.00 0.00 3.02
33 34 7.287466 TCAATTGTGCATTAAATATGGCCTAGT 59.713 33.333 3.32 0.00 0.00 2.57
34 35 8.575589 CAATTGTGCATTAAATATGGCCTAGTA 58.424 33.333 3.32 0.00 0.00 1.82
35 36 8.884124 ATTGTGCATTAAATATGGCCTAGTAT 57.116 30.769 3.32 0.00 0.00 2.12
36 37 8.704849 TTGTGCATTAAATATGGCCTAGTATT 57.295 30.769 3.32 3.55 0.00 1.89
37 38 8.704849 TGTGCATTAAATATGGCCTAGTATTT 57.295 30.769 18.61 18.61 35.39 1.40
38 39 9.142014 TGTGCATTAAATATGGCCTAGTATTTT 57.858 29.630 19.34 8.46 33.75 1.82
64 65 7.650890 AGAAAAATGATTTGGTCCAATTTTGC 58.349 30.769 14.67 12.16 0.00 3.68
65 66 6.956202 AAAATGATTTGGTCCAATTTTGCA 57.044 29.167 4.80 0.42 0.00 4.08
66 67 6.956202 AAATGATTTGGTCCAATTTTGCAA 57.044 29.167 4.80 0.00 0.00 4.08
67 68 7.527568 AAATGATTTGGTCCAATTTTGCAAT 57.472 28.000 4.80 0.00 0.00 3.56
68 69 8.632906 AAATGATTTGGTCCAATTTTGCAATA 57.367 26.923 4.80 0.00 0.00 1.90
69 70 8.632906 AATGATTTGGTCCAATTTTGCAATAA 57.367 26.923 4.80 0.00 0.00 1.40
70 71 8.810990 ATGATTTGGTCCAATTTTGCAATAAT 57.189 26.923 4.80 0.39 0.00 1.28
71 72 8.632906 TGATTTGGTCCAATTTTGCAATAATT 57.367 26.923 4.80 6.85 0.00 1.40
72 73 9.730705 TGATTTGGTCCAATTTTGCAATAATTA 57.269 25.926 4.80 0.00 0.00 1.40
77 78 8.954350 TGGTCCAATTTTGCAATAATTATTTGG 58.046 29.630 8.01 11.21 0.00 3.28
78 79 8.955388 GGTCCAATTTTGCAATAATTATTTGGT 58.045 29.630 16.78 0.00 0.00 3.67
84 85 9.830975 ATTTTGCAATAATTATTTGGTAGGTCC 57.169 29.630 8.01 0.00 0.00 4.46
85 86 8.602472 TTTGCAATAATTATTTGGTAGGTCCT 57.398 30.769 8.01 0.00 37.07 3.85
86 87 8.602472 TTGCAATAATTATTTGGTAGGTCCTT 57.398 30.769 8.01 0.00 37.07 3.36
87 88 8.232913 TGCAATAATTATTTGGTAGGTCCTTC 57.767 34.615 8.01 0.00 37.07 3.46
88 89 7.836685 TGCAATAATTATTTGGTAGGTCCTTCA 59.163 33.333 8.01 0.00 37.07 3.02
89 90 8.135529 GCAATAATTATTTGGTAGGTCCTTCAC 58.864 37.037 8.01 0.00 37.07 3.18
90 91 9.184523 CAATAATTATTTGGTAGGTCCTTCACA 57.815 33.333 8.01 0.00 37.07 3.58
91 92 9.762381 AATAATTATTTGGTAGGTCCTTCACAA 57.238 29.630 4.81 0.00 37.07 3.33
92 93 9.762381 ATAATTATTTGGTAGGTCCTTCACAAA 57.238 29.630 14.08 14.08 37.07 2.83
93 94 8.485578 AATTATTTGGTAGGTCCTTCACAAAA 57.514 30.769 15.11 7.75 37.07 2.44
94 95 7.899648 TTATTTGGTAGGTCCTTCACAAAAA 57.100 32.000 15.11 6.80 37.07 1.94
128 129 4.696455 AGGCACTCAAAAACTGGAAAATG 58.304 39.130 0.00 0.00 0.00 2.32
129 130 3.809279 GGCACTCAAAAACTGGAAAATGG 59.191 43.478 0.00 0.00 0.00 3.16
130 131 3.248363 GCACTCAAAAACTGGAAAATGGC 59.752 43.478 0.00 0.00 0.00 4.40
131 132 4.696455 CACTCAAAAACTGGAAAATGGCT 58.304 39.130 0.00 0.00 0.00 4.75
132 133 4.746611 CACTCAAAAACTGGAAAATGGCTC 59.253 41.667 0.00 0.00 0.00 4.70
133 134 4.651045 ACTCAAAAACTGGAAAATGGCTCT 59.349 37.500 0.00 0.00 0.00 4.09
134 135 5.129320 ACTCAAAAACTGGAAAATGGCTCTT 59.871 36.000 0.00 0.00 0.00 2.85
135 136 5.988287 TCAAAAACTGGAAAATGGCTCTTT 58.012 33.333 0.00 0.00 0.00 2.52
136 137 6.413892 TCAAAAACTGGAAAATGGCTCTTTT 58.586 32.000 0.00 0.00 0.00 2.27
137 138 6.315891 TCAAAAACTGGAAAATGGCTCTTTTG 59.684 34.615 3.62 0.00 34.25 2.44
138 139 5.357742 AAACTGGAAAATGGCTCTTTTGT 57.642 34.783 3.62 0.00 0.00 2.83
139 140 4.326504 ACTGGAAAATGGCTCTTTTGTG 57.673 40.909 3.62 0.00 0.00 3.33
140 141 3.062042 CTGGAAAATGGCTCTTTTGTGC 58.938 45.455 3.62 0.00 38.13 4.57
141 142 2.433604 TGGAAAATGGCTCTTTTGTGCA 59.566 40.909 3.62 0.00 40.38 4.57
142 143 3.118482 TGGAAAATGGCTCTTTTGTGCAA 60.118 39.130 0.00 0.00 40.38 4.08
143 144 4.067192 GGAAAATGGCTCTTTTGTGCAAT 58.933 39.130 0.00 0.00 40.38 3.56
144 145 4.083696 GGAAAATGGCTCTTTTGTGCAATG 60.084 41.667 0.00 0.00 40.38 2.82
145 146 4.339872 AAATGGCTCTTTTGTGCAATGA 57.660 36.364 0.00 0.00 40.38 2.57
146 147 4.546829 AATGGCTCTTTTGTGCAATGAT 57.453 36.364 0.00 0.00 40.38 2.45
147 148 4.546829 ATGGCTCTTTTGTGCAATGATT 57.453 36.364 0.00 0.00 40.38 2.57
148 149 5.664294 ATGGCTCTTTTGTGCAATGATTA 57.336 34.783 0.00 0.00 40.38 1.75
149 150 5.664294 TGGCTCTTTTGTGCAATGATTAT 57.336 34.783 0.00 0.00 40.38 1.28
150 151 6.040209 TGGCTCTTTTGTGCAATGATTATT 57.960 33.333 0.00 0.00 40.38 1.40
151 152 6.465948 TGGCTCTTTTGTGCAATGATTATTT 58.534 32.000 0.00 0.00 40.38 1.40
152 153 6.369340 TGGCTCTTTTGTGCAATGATTATTTG 59.631 34.615 0.00 0.00 40.38 2.32
153 154 6.183360 GGCTCTTTTGTGCAATGATTATTTGG 60.183 38.462 0.00 0.00 40.38 3.28
154 155 6.369615 GCTCTTTTGTGCAATGATTATTTGGT 59.630 34.615 0.00 0.00 38.65 3.67
155 156 7.545265 GCTCTTTTGTGCAATGATTATTTGGTA 59.455 33.333 0.00 0.00 38.65 3.25
156 157 8.984891 TCTTTTGTGCAATGATTATTTGGTAG 57.015 30.769 0.00 0.00 0.00 3.18
157 158 8.034215 TCTTTTGTGCAATGATTATTTGGTAGG 58.966 33.333 0.00 0.00 0.00 3.18
158 159 6.849085 TTGTGCAATGATTATTTGGTAGGT 57.151 33.333 0.00 0.00 0.00 3.08
159 160 6.449635 TGTGCAATGATTATTTGGTAGGTC 57.550 37.500 0.00 0.00 0.00 3.85
160 161 5.359576 TGTGCAATGATTATTTGGTAGGTCC 59.640 40.000 0.00 0.00 0.00 4.46
161 162 5.594317 GTGCAATGATTATTTGGTAGGTCCT 59.406 40.000 0.00 0.00 37.07 3.85
162 163 6.096846 GTGCAATGATTATTTGGTAGGTCCTT 59.903 38.462 0.00 0.00 37.07 3.36
163 164 6.321181 TGCAATGATTATTTGGTAGGTCCTTC 59.679 38.462 0.00 0.00 37.07 3.46
164 165 6.321181 GCAATGATTATTTGGTAGGTCCTTCA 59.679 38.462 0.00 0.00 37.07 3.02
165 166 7.682021 GCAATGATTATTTGGTAGGTCCTTCAC 60.682 40.741 0.00 0.00 37.07 3.18
166 167 6.381498 TGATTATTTGGTAGGTCCTTCACA 57.619 37.500 0.00 0.00 37.07 3.58
167 168 6.785076 TGATTATTTGGTAGGTCCTTCACAA 58.215 36.000 0.00 0.00 37.07 3.33
168 169 7.235079 TGATTATTTGGTAGGTCCTTCACAAA 58.765 34.615 14.08 14.08 37.07 2.83
169 170 7.726291 TGATTATTTGGTAGGTCCTTCACAAAA 59.274 33.333 15.11 7.75 37.07 2.44
170 171 7.899648 TTATTTGGTAGGTCCTTCACAAAAA 57.100 32.000 15.11 6.80 37.07 1.94
188 189 1.501169 AAATGGCTCTTTTTGCACGC 58.499 45.000 0.00 0.00 0.00 5.34
189 190 0.664166 AATGGCTCTTTTTGCACGCG 60.664 50.000 3.53 3.53 0.00 6.01
190 191 1.514678 ATGGCTCTTTTTGCACGCGA 61.515 50.000 15.93 0.00 0.00 5.87
191 192 1.008995 GGCTCTTTTTGCACGCGAA 60.009 52.632 15.93 0.00 0.00 4.70
192 193 0.593773 GGCTCTTTTTGCACGCGAAA 60.594 50.000 15.93 0.00 0.00 3.46
193 194 1.408422 GCTCTTTTTGCACGCGAAAT 58.592 45.000 15.93 0.00 0.00 2.17
194 195 1.786579 GCTCTTTTTGCACGCGAAATT 59.213 42.857 15.93 0.00 0.00 1.82
418 1101 1.224315 CCAATGGACAGATCGGGCA 59.776 57.895 0.00 0.00 0.00 5.36
422 1269 2.037620 ATGGACAGATCGGGCAGCTC 62.038 60.000 0.00 0.00 0.00 4.09
805 2588 1.228459 GAGTTCAACCCACACCCCC 60.228 63.158 0.00 0.00 0.00 5.40
807 2590 1.075896 GTTCAACCCACACCCCCAA 60.076 57.895 0.00 0.00 0.00 4.12
808 2591 1.112916 GTTCAACCCACACCCCCAAG 61.113 60.000 0.00 0.00 0.00 3.61
809 2592 2.917227 CAACCCACACCCCCAAGC 60.917 66.667 0.00 0.00 0.00 4.01
810 2593 3.434179 AACCCACACCCCCAAGCA 61.434 61.111 0.00 0.00 0.00 3.91
811 2594 3.749284 AACCCACACCCCCAAGCAC 62.749 63.158 0.00 0.00 0.00 4.40
812 2595 3.902112 CCCACACCCCCAAGCACT 61.902 66.667 0.00 0.00 0.00 4.40
813 2596 2.534396 CCCACACCCCCAAGCACTA 61.534 63.158 0.00 0.00 0.00 2.74
815 2598 0.039618 CCACACCCCCAAGCACTATT 59.960 55.000 0.00 0.00 0.00 1.73
816 2599 1.176527 CACACCCCCAAGCACTATTG 58.823 55.000 0.00 0.00 0.00 1.90
826 2609 3.086733 GCACTATTGCTCCACCCTC 57.913 57.895 0.00 0.00 46.17 4.30
827 2610 0.543749 GCACTATTGCTCCACCCTCT 59.456 55.000 0.00 0.00 46.17 3.69
830 2613 0.761802 CTATTGCTCCACCCTCTCCC 59.238 60.000 0.00 0.00 0.00 4.30
831 2614 1.048724 TATTGCTCCACCCTCTCCCG 61.049 60.000 0.00 0.00 0.00 5.14
926 2893 0.188587 TCCCTACCCAGATCGAGCAT 59.811 55.000 2.38 0.00 0.00 3.79
947 2914 1.847968 CCACCTCCCCCTCACACTT 60.848 63.158 0.00 0.00 0.00 3.16
970 2946 0.991920 TCCACTGACCCTTTCATCCC 59.008 55.000 0.00 0.00 32.17 3.85
1035 3210 1.959848 CCATCTGATCTCGCGCCTA 59.040 57.895 0.00 0.00 0.00 3.93
1131 3308 1.263484 GATCGAATCGCTCTACACCGA 59.737 52.381 0.00 0.00 37.91 4.69
1147 3324 4.562082 ACACCGAGTTTCGTGATTGATTA 58.438 39.130 0.00 0.00 38.40 1.75
1159 3336 8.909708 TTCGTGATTGATTAATTGATTGGTTC 57.090 30.769 0.00 0.00 0.00 3.62
1163 3340 9.781834 GTGATTGATTAATTGATTGGTTCGTTA 57.218 29.630 0.00 0.00 0.00 3.18
1172 3349 1.600023 TTGGTTCGTTAGTTGGCTGG 58.400 50.000 0.00 0.00 0.00 4.85
1245 3423 2.501128 CTGGACATGGACGGCGAT 59.499 61.111 16.62 0.00 0.00 4.58
1279 3457 4.659172 CCGACTTTGCCTGCCCCA 62.659 66.667 0.00 0.00 0.00 4.96
1400 3584 2.103941 CTCCTCCTCCTACTTGGATTGC 59.896 54.545 0.00 0.00 45.16 3.56
1402 3586 2.507471 CCTCCTCCTACTTGGATTGCTT 59.493 50.000 0.00 0.00 45.16 3.91
1575 4505 1.118838 GCTCTAGTGAGGTCTGGCAT 58.881 55.000 0.00 0.00 40.53 4.40
1622 4552 2.663119 GCAAACTTGGATCAATTGCGTC 59.337 45.455 0.00 1.38 32.39 5.19
1773 4727 9.788960 CAGCCTACTAAAACCAAATTATTCTTC 57.211 33.333 0.00 0.00 0.00 2.87
1847 4801 2.701423 TGCAATAGGGTATCAACGCCTA 59.299 45.455 0.00 0.00 39.30 3.93
1977 4958 5.924825 AGATGCTCAAGAAATGCTTTGTTTC 59.075 36.000 0.00 0.00 33.60 2.78
2054 5068 5.988310 TCTGGACTCGAATGTAAAACCTA 57.012 39.130 0.00 0.00 0.00 3.08
2087 5101 0.531657 GCCATTGCCATGCACTACAA 59.468 50.000 0.00 0.00 38.71 2.41
2148 5162 6.155221 TGCATGTAGAATTCTGGTCTCTTACT 59.845 38.462 18.47 0.00 0.00 2.24
2308 5322 1.531149 CTGACCAACCTGCGTGTTTAG 59.469 52.381 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.923786 CATATTTAATGCACAATTGACCAAATG 57.076 29.630 13.59 0.00 0.00 2.32
1 2 9.111613 CCATATTTAATGCACAATTGACCAAAT 57.888 29.630 13.59 10.36 0.00 2.32
2 3 7.065563 GCCATATTTAATGCACAATTGACCAAA 59.934 33.333 13.59 4.03 0.00 3.28
3 4 6.538021 GCCATATTTAATGCACAATTGACCAA 59.462 34.615 13.59 0.00 0.00 3.67
4 5 6.047870 GCCATATTTAATGCACAATTGACCA 58.952 36.000 13.59 8.76 0.00 4.02
5 6 5.466393 GGCCATATTTAATGCACAATTGACC 59.534 40.000 13.59 2.79 0.00 4.02
6 7 6.282930 AGGCCATATTTAATGCACAATTGAC 58.717 36.000 13.59 4.32 0.00 3.18
7 8 6.482898 AGGCCATATTTAATGCACAATTGA 57.517 33.333 13.59 0.00 0.00 2.57
8 9 7.436118 ACTAGGCCATATTTAATGCACAATTG 58.564 34.615 5.01 3.24 0.00 2.32
9 10 7.601705 ACTAGGCCATATTTAATGCACAATT 57.398 32.000 5.01 0.00 0.00 2.32
10 11 8.884124 ATACTAGGCCATATTTAATGCACAAT 57.116 30.769 5.01 0.00 0.00 2.71
11 12 8.704849 AATACTAGGCCATATTTAATGCACAA 57.295 30.769 5.01 0.00 0.00 3.33
12 13 8.704849 AAATACTAGGCCATATTTAATGCACA 57.295 30.769 5.01 0.00 30.87 4.57
38 39 8.782144 GCAAAATTGGACCAAATCATTTTTCTA 58.218 29.630 11.82 0.00 29.57 2.10
39 40 7.284944 TGCAAAATTGGACCAAATCATTTTTCT 59.715 29.630 11.82 0.00 29.57 2.52
40 41 7.424001 TGCAAAATTGGACCAAATCATTTTTC 58.576 30.769 11.82 8.45 29.57 2.29
41 42 7.344095 TGCAAAATTGGACCAAATCATTTTT 57.656 28.000 11.82 10.03 31.08 1.94
42 43 6.956202 TGCAAAATTGGACCAAATCATTTT 57.044 29.167 11.82 10.40 0.00 1.82
43 44 6.956202 TTGCAAAATTGGACCAAATCATTT 57.044 29.167 11.82 4.33 0.00 2.32
44 45 8.632906 TTATTGCAAAATTGGACCAAATCATT 57.367 26.923 11.82 0.00 0.00 2.57
45 46 8.810990 ATTATTGCAAAATTGGACCAAATCAT 57.189 26.923 11.82 0.00 0.00 2.45
46 47 8.632906 AATTATTGCAAAATTGGACCAAATCA 57.367 26.923 11.82 2.39 0.00 2.57
51 52 8.954350 CCAAATAATTATTGCAAAATTGGACCA 58.046 29.630 20.39 0.00 0.00 4.02
52 53 8.955388 ACCAAATAATTATTGCAAAATTGGACC 58.045 29.630 21.51 0.00 0.00 4.46
58 59 9.830975 GGACCTACCAAATAATTATTGCAAAAT 57.169 29.630 11.42 2.09 38.79 1.82
59 60 9.041354 AGGACCTACCAAATAATTATTGCAAAA 57.959 29.630 11.42 0.00 42.04 2.44
60 61 8.602472 AGGACCTACCAAATAATTATTGCAAA 57.398 30.769 11.42 0.00 42.04 3.68
61 62 8.602472 AAGGACCTACCAAATAATTATTGCAA 57.398 30.769 11.42 0.00 42.04 4.08
62 63 7.836685 TGAAGGACCTACCAAATAATTATTGCA 59.163 33.333 11.42 0.00 42.04 4.08
63 64 8.135529 GTGAAGGACCTACCAAATAATTATTGC 58.864 37.037 11.42 0.00 42.04 3.56
64 65 9.184523 TGTGAAGGACCTACCAAATAATTATTG 57.815 33.333 11.42 3.08 42.04 1.90
65 66 9.762381 TTGTGAAGGACCTACCAAATAATTATT 57.238 29.630 4.81 4.81 42.04 1.40
66 67 9.762381 TTTGTGAAGGACCTACCAAATAATTAT 57.238 29.630 0.00 0.00 42.04 1.28
67 68 9.589461 TTTTGTGAAGGACCTACCAAATAATTA 57.411 29.630 11.70 0.00 42.04 1.40
68 69 8.485578 TTTTGTGAAGGACCTACCAAATAATT 57.514 30.769 11.70 0.00 42.04 1.40
69 70 8.485578 TTTTTGTGAAGGACCTACCAAATAAT 57.514 30.769 11.70 0.00 42.04 1.28
70 71 7.899648 TTTTTGTGAAGGACCTACCAAATAA 57.100 32.000 11.70 8.02 42.04 1.40
103 104 3.011566 TCCAGTTTTTGAGTGCCTCAA 57.988 42.857 12.03 12.03 46.93 3.02
104 105 2.727123 TCCAGTTTTTGAGTGCCTCA 57.273 45.000 1.25 1.25 38.87 3.86
105 106 4.385358 TTTTCCAGTTTTTGAGTGCCTC 57.615 40.909 0.00 0.00 0.00 4.70
106 107 4.443315 CCATTTTCCAGTTTTTGAGTGCCT 60.443 41.667 0.00 0.00 0.00 4.75
107 108 3.809279 CCATTTTCCAGTTTTTGAGTGCC 59.191 43.478 0.00 0.00 0.00 5.01
108 109 3.248363 GCCATTTTCCAGTTTTTGAGTGC 59.752 43.478 0.00 0.00 0.00 4.40
109 110 4.696455 AGCCATTTTCCAGTTTTTGAGTG 58.304 39.130 0.00 0.00 0.00 3.51
110 111 4.651045 AGAGCCATTTTCCAGTTTTTGAGT 59.349 37.500 0.00 0.00 0.00 3.41
111 112 5.205759 AGAGCCATTTTCCAGTTTTTGAG 57.794 39.130 0.00 0.00 0.00 3.02
112 113 5.612725 AAGAGCCATTTTCCAGTTTTTGA 57.387 34.783 0.00 0.00 0.00 2.69
113 114 6.093909 ACAAAAGAGCCATTTTCCAGTTTTTG 59.906 34.615 0.00 0.00 38.35 2.44
114 115 6.093909 CACAAAAGAGCCATTTTCCAGTTTTT 59.906 34.615 0.00 0.00 30.01 1.94
115 116 5.585844 CACAAAAGAGCCATTTTCCAGTTTT 59.414 36.000 0.00 0.00 30.01 2.43
116 117 5.118286 CACAAAAGAGCCATTTTCCAGTTT 58.882 37.500 0.00 0.00 30.01 2.66
117 118 4.696455 CACAAAAGAGCCATTTTCCAGTT 58.304 39.130 0.00 0.00 30.01 3.16
118 119 3.493176 GCACAAAAGAGCCATTTTCCAGT 60.493 43.478 0.00 0.00 30.01 4.00
119 120 3.062042 GCACAAAAGAGCCATTTTCCAG 58.938 45.455 0.00 0.00 30.01 3.86
120 121 2.433604 TGCACAAAAGAGCCATTTTCCA 59.566 40.909 0.00 0.00 30.01 3.53
121 122 3.110447 TGCACAAAAGAGCCATTTTCC 57.890 42.857 0.00 0.00 30.01 3.13
122 123 4.751098 TCATTGCACAAAAGAGCCATTTTC 59.249 37.500 0.00 0.00 30.01 2.29
123 124 4.706035 TCATTGCACAAAAGAGCCATTTT 58.294 34.783 0.00 0.00 32.65 1.82
124 125 4.339872 TCATTGCACAAAAGAGCCATTT 57.660 36.364 0.00 0.00 0.00 2.32
125 126 4.546829 ATCATTGCACAAAAGAGCCATT 57.453 36.364 0.00 0.00 0.00 3.16
126 127 4.546829 AATCATTGCACAAAAGAGCCAT 57.453 36.364 0.00 0.00 0.00 4.40
127 128 5.664294 ATAATCATTGCACAAAAGAGCCA 57.336 34.783 0.00 0.00 0.00 4.75
128 129 6.183360 CCAAATAATCATTGCACAAAAGAGCC 60.183 38.462 0.00 0.00 0.00 4.70
129 130 6.369615 ACCAAATAATCATTGCACAAAAGAGC 59.630 34.615 0.00 0.00 0.00 4.09
130 131 7.894376 ACCAAATAATCATTGCACAAAAGAG 57.106 32.000 0.00 0.00 0.00 2.85
131 132 8.034215 CCTACCAAATAATCATTGCACAAAAGA 58.966 33.333 0.00 0.00 0.00 2.52
132 133 7.818930 ACCTACCAAATAATCATTGCACAAAAG 59.181 33.333 0.00 0.00 0.00 2.27
133 134 7.675062 ACCTACCAAATAATCATTGCACAAAA 58.325 30.769 0.00 0.00 0.00 2.44
134 135 7.238486 ACCTACCAAATAATCATTGCACAAA 57.762 32.000 0.00 0.00 0.00 2.83
135 136 6.127479 GGACCTACCAAATAATCATTGCACAA 60.127 38.462 0.00 0.00 38.79 3.33
136 137 5.359576 GGACCTACCAAATAATCATTGCACA 59.640 40.000 0.00 0.00 38.79 4.57
137 138 5.594317 AGGACCTACCAAATAATCATTGCAC 59.406 40.000 0.00 0.00 42.04 4.57
138 139 5.765510 AGGACCTACCAAATAATCATTGCA 58.234 37.500 0.00 0.00 42.04 4.08
139 140 6.321181 TGAAGGACCTACCAAATAATCATTGC 59.679 38.462 0.00 0.00 42.04 3.56
140 141 7.339212 TGTGAAGGACCTACCAAATAATCATTG 59.661 37.037 0.00 0.00 42.04 2.82
141 142 7.410174 TGTGAAGGACCTACCAAATAATCATT 58.590 34.615 0.00 0.00 42.04 2.57
142 143 6.969043 TGTGAAGGACCTACCAAATAATCAT 58.031 36.000 0.00 0.00 42.04 2.45
143 144 6.381498 TGTGAAGGACCTACCAAATAATCA 57.619 37.500 0.00 0.00 42.04 2.57
144 145 7.696992 TTTGTGAAGGACCTACCAAATAATC 57.303 36.000 0.00 0.00 42.04 1.75
145 146 8.485578 TTTTTGTGAAGGACCTACCAAATAAT 57.514 30.769 11.70 0.00 42.04 1.28
146 147 7.899648 TTTTTGTGAAGGACCTACCAAATAA 57.100 32.000 11.70 8.02 42.04 1.40
167 168 2.287644 GCGTGCAAAAAGAGCCATTTTT 59.712 40.909 0.00 3.94 41.78 1.94
168 169 1.866601 GCGTGCAAAAAGAGCCATTTT 59.133 42.857 0.00 0.00 33.86 1.82
169 170 1.501169 GCGTGCAAAAAGAGCCATTT 58.499 45.000 0.00 0.00 0.00 2.32
170 171 0.664166 CGCGTGCAAAAAGAGCCATT 60.664 50.000 0.00 0.00 0.00 3.16
171 172 1.081242 CGCGTGCAAAAAGAGCCAT 60.081 52.632 0.00 0.00 0.00 4.40
172 173 1.719725 TTCGCGTGCAAAAAGAGCCA 61.720 50.000 5.77 0.00 0.00 4.75
173 174 0.593773 TTTCGCGTGCAAAAAGAGCC 60.594 50.000 5.77 0.00 0.00 4.70
174 175 1.408422 ATTTCGCGTGCAAAAAGAGC 58.592 45.000 5.77 0.00 0.00 4.09
175 176 4.436365 AAAATTTCGCGTGCAAAAAGAG 57.564 36.364 5.77 0.00 0.00 2.85
176 177 4.849111 AAAAATTTCGCGTGCAAAAAGA 57.151 31.818 5.77 0.00 0.00 2.52
194 195 9.660180 GGACCTACCAAATAATTATTGCAAAAA 57.340 29.630 11.42 0.00 38.79 1.94
785 2568 1.534697 GGGTGTGGGTTGAACTCCA 59.465 57.895 0.00 0.00 33.72 3.86
793 2576 3.434179 TGCTTGGGGGTGTGGGTT 61.434 61.111 0.00 0.00 0.00 4.11
809 2592 1.139853 GGAGAGGGTGGAGCAATAGTG 59.860 57.143 0.00 0.00 0.00 2.74
810 2593 1.501582 GGAGAGGGTGGAGCAATAGT 58.498 55.000 0.00 0.00 0.00 2.12
811 2594 0.761802 GGGAGAGGGTGGAGCAATAG 59.238 60.000 0.00 0.00 0.00 1.73
812 2595 1.048724 CGGGAGAGGGTGGAGCAATA 61.049 60.000 0.00 0.00 0.00 1.90
813 2596 2.370445 CGGGAGAGGGTGGAGCAAT 61.370 63.158 0.00 0.00 0.00 3.56
832 2615 4.530857 GTCGAGGTGGGATGGGCG 62.531 72.222 0.00 0.00 0.00 6.13
833 2616 4.530857 CGTCGAGGTGGGATGGGC 62.531 72.222 0.00 0.00 0.00 5.36
836 2619 2.052690 AGTCCGTCGAGGTGGGATG 61.053 63.158 4.18 0.00 41.99 3.51
837 2620 2.052690 CAGTCCGTCGAGGTGGGAT 61.053 63.158 4.18 0.00 41.99 3.85
838 2621 2.675423 CAGTCCGTCGAGGTGGGA 60.675 66.667 4.18 0.00 41.99 4.37
841 2624 3.343788 GAGGCAGTCCGTCGAGGTG 62.344 68.421 4.18 0.00 41.99 4.00
842 2625 3.063084 GAGGCAGTCCGTCGAGGT 61.063 66.667 4.18 0.00 41.99 3.85
843 2626 3.062466 TGAGGCAGTCCGTCGAGG 61.062 66.667 0.00 0.00 42.97 4.63
845 2628 3.371063 GGTGAGGCAGTCCGTCGA 61.371 66.667 0.00 0.00 37.47 4.20
926 2893 2.450243 GTGAGGGGGAGGTGGAGA 59.550 66.667 0.00 0.00 0.00 3.71
947 2914 1.741028 TGAAAGGGTCAGTGGATGGA 58.259 50.000 0.00 0.00 0.00 3.41
970 2946 2.202623 CTCGCTCCTTCGTTCCCG 60.203 66.667 0.00 0.00 0.00 5.14
1071 3246 4.468689 GGGAGGGTACTGGCGTGC 62.469 72.222 0.00 0.00 0.00 5.34
1095 3272 3.982475 TCGATCCAATTGATCCGAAGAG 58.018 45.455 7.12 0.00 46.06 2.85
1100 3277 2.159787 GCGATTCGATCCAATTGATCCG 60.160 50.000 10.88 6.97 46.06 4.18
1106 3283 4.051922 GTGTAGAGCGATTCGATCCAATT 58.948 43.478 19.70 4.99 43.62 2.32
1131 3308 8.522830 ACCAATCAATTAATCAATCACGAAACT 58.477 29.630 0.00 0.00 0.00 2.66
1147 3324 4.522789 AGCCAACTAACGAACCAATCAATT 59.477 37.500 0.00 0.00 0.00 2.32
1159 3336 3.004315 ACAAATCAACCAGCCAACTAACG 59.996 43.478 0.00 0.00 0.00 3.18
1163 3340 1.608590 CGACAAATCAACCAGCCAACT 59.391 47.619 0.00 0.00 0.00 3.16
1172 3349 4.035017 CACACAAGAACCGACAAATCAAC 58.965 43.478 0.00 0.00 0.00 3.18
1215 3393 2.124768 TCCAGCTCATCCACCCCA 59.875 61.111 0.00 0.00 0.00 4.96
1219 3397 0.543277 TCCATGTCCAGCTCATCCAC 59.457 55.000 0.00 0.00 0.00 4.02
1279 3457 0.892358 TCGTGGTCCTCGTAGCAGTT 60.892 55.000 12.76 0.00 0.00 3.16
1400 3584 5.533154 ACGTACTCCATGGATCTCTAGAAAG 59.467 44.000 16.63 1.50 0.00 2.62
1402 3586 5.050126 ACGTACTCCATGGATCTCTAGAA 57.950 43.478 16.63 0.00 0.00 2.10
1433 3617 0.725686 CTGAACAAGAGCGCTCCATG 59.274 55.000 32.94 30.75 0.00 3.66
1575 4505 5.593909 CCCCTTGTGCACATCTAAAATCATA 59.406 40.000 22.39 0.00 0.00 2.15
1622 4552 3.133721 ACTTAGACATGCCCAAGCTCTAG 59.866 47.826 0.00 0.00 40.80 2.43
1666 4596 4.816385 GGATCATAAGGAACGATTCTTGCA 59.184 41.667 0.00 0.00 0.00 4.08
1756 4710 9.710900 GGACATTGAGAAGAATAATTTGGTTTT 57.289 29.630 0.00 0.00 0.00 2.43
2054 5068 3.019564 GCAATGGCAGTTAGGATCAAGT 58.980 45.455 0.00 0.00 40.72 3.16
2308 5322 0.248843 CTCCTCCTCACACCTGAAGC 59.751 60.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.