Multiple sequence alignment - TraesCS3D01G109000

Loading Multiple Alignment...

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 TraesCS3D01G109000 chr3D 100.000 4691 0 0 1 4691 62066808 62071498 0.000000e+00 8663
1 TraesCS3D01G109000 chr3A 94.482 3842 117 40 408 4210 71146026 71149811 0.000000e+00 5832
2 TraesCS3D01G109000 chr3A 88.415 492 29 14 4213 4680 71149846 71150333 6.810000e-158 568
3 TraesCS3D01G109000 chr3A 89.175 194 21 0 3 196 71145138 71145331 4.690000e-60 243
4 TraesCS3D01G109000 chr3A 89.062 128 7 6 263 386 71145717 71145841 8.130000e-33 152
5 TraesCS3D01G109000 chr3B 95.620 3242 117 17 400 3626 100965076 100968307 0.000000e+00 5177
6 TraesCS3D01G109000 chr3B 91.548 840 26 16 3615 4415 100968455 100969288 0.000000e+00 1116
7 TraesCS3D01G109000 chr3B 91.053 190 15 1 4493 4680 100969290 100969479 6.020000e-64 255
8 TraesCS3D01G109000 chr2A 89.168 757 60 10 1933 2681 610179279 610178537 0.000000e+00 924
9 TraesCS3D01G109000 chr6B 86.842 760 71 10 1930 2679 661997942 661998682 0.000000e+00 822
10 TraesCS3D01G109000 chr6B 81.867 739 86 27 2690 3403 578650450 578651165 3.150000e-161 579
11 TraesCS3D01G109000 chr7B 83.178 214 34 2 3398 3610 492495887 492496099 1.330000e-45 195
12 TraesCS3D01G109000 chr7D 82.710 214 35 2 3398 3610 468937308 468937520 6.200000e-44 189
13 TraesCS3D01G109000 chr7A 81.991 211 36 2 3401 3610 531730459 531730250 1.340000e-40 178


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 TraesCS3D01G109000 chr3D 62066808 62071498 4690 False 8663.000000 8663 100.000000 1 4691 1 chr3D.!!$F1 4690
1 TraesCS3D01G109000 chr3A 71145138 71150333 5195 False 1698.750000 5832 90.283500 3 4680 4 chr3A.!!$F1 4677
2 TraesCS3D01G109000 chr3B 100965076 100969479 4403 False 2182.666667 5177 92.740333 400 4680 3 chr3B.!!$F1 4280
3 TraesCS3D01G109000 chr2A 610178537 610179279 742 True 924.000000 924 89.168000 1933 2681 1 chr2A.!!$R1 748
4 TraesCS3D01G109000 chr6B 661997942 661998682 740 False 822.000000 822 86.842000 1930 2679 1 chr6B.!!$F2 749
5 TraesCS3D01G109000 chr6B 578650450 578651165 715 False 579.000000 579 81.867000 2690 3403 1 chr6B.!!$F1 713

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
231 232 0.179092 CCCTCCCGATGGTACGAAAC 60.179 60.000 0.00 0.00 35.09 2.78 F
234 235 0.247185 TCCCGATGGTACGAAACACC 59.753 55.000 0.00 0.00 36.54 4.16 F
246 247 0.310854 GAAACACCACCGGAGCAAAG 59.689 55.000 9.46 0.00 0.00 2.77 F
474 959 0.319083 TACACACCTGTGGGTAAGCG 59.681 55.000 9.86 0.00 46.96 4.68 F
1316 1810 0.333312 TGTTTGGTCTGTTGGGTGGT 59.667 50.000 0.00 0.00 0.00 4.16 F
1504 2003 1.063469 CGTAGCCGGGCTTGTTATTTG 59.937 52.381 29.02 4.60 40.44 2.32 F
2366 2877 1.483004 GGTGCCTAAAGGAGTCCTCTC 59.517 57.143 13.43 0.13 39.76 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1318 1812 0.037447 AAGAACAAGCTCCTCTGCCC 59.963 55.000 0.00 0.00 0.00 5.36 R
1436 1935 0.612744 CAATTTGCGGTTTCCCCCAT 59.387 50.000 0.00 0.00 0.00 4.00 R
1437 1936 0.760945 ACAATTTGCGGTTTCCCCCA 60.761 50.000 0.00 0.00 0.00 4.96 R
1487 1986 1.544246 GAACAAATAACAAGCCCGGCT 59.456 47.619 5.94 5.94 42.56 5.52 R
2932 3450 0.251519 AAGCTGCAAGGGGGAGAAAG 60.252 55.000 1.02 0.00 37.05 2.62 R
3187 3732 2.736192 GAGCTTCTTCAGTGCTTCAGTC 59.264 50.000 0.00 0.00 37.16 3.51 R
4126 4845 0.240945 CAACGAACCAGCCACCAATC 59.759 55.000 0.00 0.00 0.00 2.67 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
29 30 1.268589 CCAGAACTCATCGACGCGTAT 60.269 52.381 13.97 0.00 0.00 3.06
34 35 0.865639 CTCATCGACGCGTATGCACA 60.866 55.000 13.97 0.00 42.97 4.57
54 55 2.046217 GAGAAACCCCACCTCGCC 60.046 66.667 0.00 0.00 0.00 5.54
55 56 2.852075 AGAAACCCCACCTCGCCA 60.852 61.111 0.00 0.00 0.00 5.69
65 66 2.231380 ACCTCGCCACCCCAAGAAT 61.231 57.895 0.00 0.00 0.00 2.40
78 79 6.070656 CACCCCAAGAATACCACATGAATAT 58.929 40.000 0.00 0.00 0.00 1.28
96 97 0.684479 ATGTGCTGGAGCTCCGTCTA 60.684 55.000 27.43 13.01 42.66 2.59
105 106 1.108132 AGCTCCGTCTATTCCGTCCC 61.108 60.000 0.00 0.00 0.00 4.46
150 151 0.690192 TGCCCAAAAGACCATCTCGA 59.310 50.000 0.00 0.00 0.00 4.04
155 156 1.649171 CAAAAGACCATCTCGACGACG 59.351 52.381 0.00 0.00 41.26 5.12
170 171 2.740714 GACGAAGCGCCACCATCAC 61.741 63.158 2.29 0.00 0.00 3.06
172 173 3.499737 GAAGCGCCACCATCACCG 61.500 66.667 2.29 0.00 0.00 4.94
179 180 2.880879 CACCATCACCGAGCGTCG 60.881 66.667 0.00 0.00 40.07 5.12
183 184 4.194720 ATCACCGAGCGTCGCCTC 62.195 66.667 14.86 9.89 38.82 4.70
198 199 2.664081 CCTCTGTGAGGGCCACTCC 61.664 68.421 6.18 9.57 45.43 3.85
199 200 1.915266 CTCTGTGAGGGCCACTCCA 60.915 63.158 6.18 12.64 46.01 3.86
200 201 1.229625 TCTGTGAGGGCCACTCCAT 60.230 57.895 6.18 0.00 46.01 3.41
201 202 1.222936 CTGTGAGGGCCACTCCATC 59.777 63.158 6.18 8.95 46.01 3.51
202 203 2.262774 CTGTGAGGGCCACTCCATCC 62.263 65.000 6.18 5.16 44.77 3.51
203 204 1.997874 GTGAGGGCCACTCCATCCT 60.998 63.158 6.18 0.00 44.77 3.24
204 205 1.690633 TGAGGGCCACTCCATCCTC 60.691 63.158 6.18 6.61 44.77 3.71
205 206 2.765807 AGGGCCACTCCATCCTCG 60.766 66.667 6.18 0.00 36.21 4.63
206 207 4.554036 GGGCCACTCCATCCTCGC 62.554 72.222 4.39 0.00 36.21 5.03
207 208 4.899239 GGCCACTCCATCCTCGCG 62.899 72.222 0.00 0.00 34.01 5.87
209 210 4.899239 CCACTCCATCCTCGCGCC 62.899 72.222 0.00 0.00 0.00 6.53
210 211 4.147449 CACTCCATCCTCGCGCCA 62.147 66.667 0.00 0.00 0.00 5.69
211 212 3.842923 ACTCCATCCTCGCGCCAG 61.843 66.667 0.00 0.00 0.00 4.85
225 226 2.445845 CCAGCCCTCCCGATGGTA 60.446 66.667 0.00 0.00 0.00 3.25
226 227 2.808206 CCAGCCCTCCCGATGGTAC 61.808 68.421 0.00 0.00 0.00 3.34
227 228 2.838225 AGCCCTCCCGATGGTACG 60.838 66.667 0.00 0.00 0.00 3.67
228 229 2.836360 GCCCTCCCGATGGTACGA 60.836 66.667 0.00 0.00 35.09 3.43
229 230 2.428925 GCCCTCCCGATGGTACGAA 61.429 63.158 0.00 0.00 35.09 3.85
230 231 1.963464 GCCCTCCCGATGGTACGAAA 61.963 60.000 0.00 0.00 35.09 3.46
231 232 0.179092 CCCTCCCGATGGTACGAAAC 60.179 60.000 0.00 0.00 35.09 2.78
232 233 0.533491 CCTCCCGATGGTACGAAACA 59.467 55.000 0.00 0.00 35.09 2.83
233 234 1.636988 CTCCCGATGGTACGAAACAC 58.363 55.000 0.00 0.00 35.09 3.32
234 235 0.247185 TCCCGATGGTACGAAACACC 59.753 55.000 0.00 0.00 36.54 4.16
238 239 2.582713 CGATGGTACGAAACACCACCG 61.583 57.143 0.00 0.00 46.14 4.94
239 240 1.069427 TGGTACGAAACACCACCGG 59.931 57.895 0.00 0.00 41.17 5.28
240 241 1.367102 GGTACGAAACACCACCGGA 59.633 57.895 9.46 0.00 36.01 5.14
241 242 0.668401 GGTACGAAACACCACCGGAG 60.668 60.000 9.46 0.00 36.01 4.63
242 243 1.005867 TACGAAACACCACCGGAGC 60.006 57.895 9.46 0.00 0.00 4.70
243 244 1.746322 TACGAAACACCACCGGAGCA 61.746 55.000 9.46 0.00 0.00 4.26
244 245 1.890041 CGAAACACCACCGGAGCAA 60.890 57.895 9.46 0.00 0.00 3.91
245 246 1.440938 CGAAACACCACCGGAGCAAA 61.441 55.000 9.46 0.00 0.00 3.68
246 247 0.310854 GAAACACCACCGGAGCAAAG 59.689 55.000 9.46 0.00 0.00 2.77
247 248 1.106944 AAACACCACCGGAGCAAAGG 61.107 55.000 9.46 2.12 0.00 3.11
248 249 3.365265 CACCACCGGAGCAAAGGC 61.365 66.667 9.46 0.00 41.61 4.35
249 250 3.884774 ACCACCGGAGCAAAGGCA 61.885 61.111 9.46 0.00 44.61 4.75
250 251 2.597217 CCACCGGAGCAAAGGCAA 60.597 61.111 9.46 0.00 44.61 4.52
251 252 2.199652 CCACCGGAGCAAAGGCAAA 61.200 57.895 9.46 0.00 44.61 3.68
252 253 1.286880 CACCGGAGCAAAGGCAAAG 59.713 57.895 9.46 0.00 44.61 2.77
253 254 2.259511 CCGGAGCAAAGGCAAAGC 59.740 61.111 0.00 0.00 44.61 3.51
254 255 2.563798 CCGGAGCAAAGGCAAAGCA 61.564 57.895 0.00 0.00 44.61 3.91
255 256 1.080974 CGGAGCAAAGGCAAAGCAG 60.081 57.895 0.00 0.00 44.61 4.24
256 257 1.291272 GGAGCAAAGGCAAAGCAGG 59.709 57.895 0.00 0.00 44.61 4.85
257 258 1.291272 GAGCAAAGGCAAAGCAGGG 59.709 57.895 0.00 0.00 44.61 4.45
258 259 2.163601 GAGCAAAGGCAAAGCAGGGG 62.164 60.000 0.00 0.00 44.61 4.79
259 260 2.209315 GCAAAGGCAAAGCAGGGGA 61.209 57.895 0.00 0.00 40.72 4.81
260 261 1.969862 CAAAGGCAAAGCAGGGGAG 59.030 57.895 0.00 0.00 0.00 4.30
261 262 0.540365 CAAAGGCAAAGCAGGGGAGA 60.540 55.000 0.00 0.00 0.00 3.71
262 263 0.411058 AAAGGCAAAGCAGGGGAGAT 59.589 50.000 0.00 0.00 0.00 2.75
263 264 1.298953 AAGGCAAAGCAGGGGAGATA 58.701 50.000 0.00 0.00 0.00 1.98
264 265 1.298953 AGGCAAAGCAGGGGAGATAA 58.701 50.000 0.00 0.00 0.00 1.75
265 266 1.640670 AGGCAAAGCAGGGGAGATAAA 59.359 47.619 0.00 0.00 0.00 1.40
266 267 2.245806 AGGCAAAGCAGGGGAGATAAAT 59.754 45.455 0.00 0.00 0.00 1.40
267 268 2.363359 GGCAAAGCAGGGGAGATAAATG 59.637 50.000 0.00 0.00 0.00 2.32
268 269 2.363359 GCAAAGCAGGGGAGATAAATGG 59.637 50.000 0.00 0.00 0.00 3.16
269 270 3.902218 CAAAGCAGGGGAGATAAATGGA 58.098 45.455 0.00 0.00 0.00 3.41
312 630 0.745468 GTCGTGGAGGTGGGTAGATC 59.255 60.000 0.00 0.00 0.00 2.75
322 640 2.504519 GGTAGATCGGCCACCACC 59.495 66.667 2.24 0.00 32.32 4.61
323 641 2.504519 GTAGATCGGCCACCACCC 59.495 66.667 2.24 0.00 0.00 4.61
330 651 2.866726 CGGCCACCACCCTTTTTGG 61.867 63.158 2.24 0.00 40.32 3.28
382 703 5.610982 ACCCTTCATAGCTCCATAACCATTA 59.389 40.000 0.00 0.00 0.00 1.90
386 707 8.105829 CCTTCATAGCTCCATAACCATTAGATT 58.894 37.037 0.00 0.00 0.00 2.40
387 708 8.853077 TTCATAGCTCCATAACCATTAGATTG 57.147 34.615 0.00 0.00 0.00 2.67
390 724 8.725148 CATAGCTCCATAACCATTAGATTGTTC 58.275 37.037 0.00 0.00 0.00 3.18
464 949 6.455647 TGAACTCTCAAATAGTACACACCTG 58.544 40.000 0.00 0.00 0.00 4.00
474 959 0.319083 TACACACCTGTGGGTAAGCG 59.681 55.000 9.86 0.00 46.96 4.68
518 1003 3.894759 CTCCATGAACCACAATCTCCAT 58.105 45.455 0.00 0.00 0.00 3.41
526 1011 3.942829 ACCACAATCTCCATACACACTG 58.057 45.455 0.00 0.00 0.00 3.66
539 1025 3.439857 ACACACTGGATTGTATGGCTT 57.560 42.857 0.00 0.00 0.00 4.35
544 1030 6.767902 ACACACTGGATTGTATGGCTTATAAG 59.232 38.462 8.20 8.20 0.00 1.73
549 1035 8.903820 ACTGGATTGTATGGCTTATAAGTTTTC 58.096 33.333 13.91 3.07 0.00 2.29
550 1036 9.125026 CTGGATTGTATGGCTTATAAGTTTTCT 57.875 33.333 13.91 0.00 0.00 2.52
702 1188 3.577848 CCATGGAGTGAAAATTCCCAACA 59.422 43.478 5.56 0.00 32.29 3.33
798 1285 2.669777 AAAACGCTAGGGCCACACGT 62.670 55.000 6.18 9.31 38.88 4.49
809 1296 1.007336 GCCACACGTAGTTCAGACGG 61.007 60.000 0.00 0.00 41.61 4.79
1310 1804 4.493547 TGCTCTTTTTGTTTGGTCTGTTG 58.506 39.130 0.00 0.00 0.00 3.33
1313 1807 3.835395 TCTTTTTGTTTGGTCTGTTGGGT 59.165 39.130 0.00 0.00 0.00 4.51
1314 1808 3.601443 TTTTGTTTGGTCTGTTGGGTG 57.399 42.857 0.00 0.00 0.00 4.61
1316 1810 0.333312 TGTTTGGTCTGTTGGGTGGT 59.667 50.000 0.00 0.00 0.00 4.16
1318 1812 1.136110 GTTTGGTCTGTTGGGTGGTTG 59.864 52.381 0.00 0.00 0.00 3.77
1395 1894 5.106157 CCCACCTGTTCTTAATTAGTTGCAG 60.106 44.000 0.00 0.00 0.00 4.41
1400 1899 7.094205 ACCTGTTCTTAATTAGTTGCAGATTGG 60.094 37.037 9.35 0.00 0.00 3.16
1412 1911 1.547223 GCAGATTGGGGATGCTATGCT 60.547 52.381 0.00 0.00 0.00 3.79
1418 1917 5.728253 AGATTGGGGATGCTATGCTAGATTA 59.272 40.000 0.00 0.00 0.00 1.75
1419 1918 4.826274 TGGGGATGCTATGCTAGATTAC 57.174 45.455 0.00 0.00 0.00 1.89
1434 1933 3.855668 AGATTACTAGCATGCTCCCTCT 58.144 45.455 26.57 16.51 0.00 3.69
1436 1935 5.398236 AGATTACTAGCATGCTCCCTCTAA 58.602 41.667 26.57 13.19 0.00 2.10
1437 1936 6.022315 AGATTACTAGCATGCTCCCTCTAAT 58.978 40.000 26.57 16.98 0.00 1.73
1487 1986 5.959618 TTAGAGATATTAGCTGCTGCGTA 57.040 39.130 13.43 2.76 45.42 4.42
1504 2003 1.063469 CGTAGCCGGGCTTGTTATTTG 59.937 52.381 29.02 4.60 40.44 2.32
1516 2015 5.239525 GGCTTGTTATTTGTTCTGTCAGACT 59.760 40.000 0.78 0.00 0.00 3.24
1585 2084 2.682352 GGAGCAAGAAGAAATCAGGCTC 59.318 50.000 0.00 0.00 46.95 4.70
1605 2106 7.121168 CAGGCTCAGAATTTGGTACTATTTCAA 59.879 37.037 0.00 0.00 0.00 2.69
1730 2232 3.004419 GTGGCTGTTTTACCAAGGAAGAC 59.996 47.826 0.00 0.00 37.79 3.01
1793 2295 5.048782 TGGAATAGCTTGTTTACAGCTGTTG 60.049 40.000 27.06 9.61 39.46 3.33
1856 2358 2.271800 CTGTGAGAACAAGATACGGCC 58.728 52.381 0.00 0.00 0.00 6.13
1994 2497 4.212214 GCTATAACAAGGTAGCTCATGTGC 59.788 45.833 11.79 11.79 33.15 4.57
2145 2648 7.657354 TCATCATCTGTTCCTCCATATTTTACG 59.343 37.037 0.00 0.00 0.00 3.18
2204 2715 3.632643 TGTCTTTCATGGCATCTGCTA 57.367 42.857 0.00 0.00 41.70 3.49
2366 2877 1.483004 GGTGCCTAAAGGAGTCCTCTC 59.517 57.143 13.43 0.13 39.76 3.20
2495 3009 6.272822 AGTCCTTTAAAGCTTGCTATTTGG 57.727 37.500 9.86 0.00 0.00 3.28
2512 3026 8.150945 TGCTATTTGGTTTTGGCTAACAATTTA 58.849 29.630 5.64 0.00 39.21 1.40
2932 3450 4.691216 CCAGGCTTGTAGAAGTGTAAGTTC 59.309 45.833 1.12 0.00 46.65 3.01
2942 3460 4.325119 GAAGTGTAAGTTCTTTCTCCCCC 58.675 47.826 0.00 0.00 42.97 5.40
3187 3732 5.303845 TCCATCTATCAGGAGACATGACTTG 59.696 44.000 0.00 0.00 0.00 3.16
3327 3872 3.432252 GTCGAGGTACCACACATTTCAAG 59.568 47.826 15.94 0.00 0.00 3.02
4020 4739 1.048601 TCCTGTCTGTTGTGGAGTCC 58.951 55.000 0.73 0.73 0.00 3.85
4118 4837 5.762825 ATTGCTGTATGTGTCATGGATTC 57.237 39.130 0.00 0.00 0.00 2.52
4126 4845 1.860950 GTGTCATGGATTCGGTGATCG 59.139 52.381 0.00 0.00 40.90 3.69
4135 4854 1.153449 TCGGTGATCGATTGGTGGC 60.153 57.895 0.00 0.00 43.74 5.01
4200 4919 2.802816 CTCTGGTTCCTTGTCACTTTCG 59.197 50.000 0.00 0.00 0.00 3.46
4210 4929 1.270094 TGTCACTTTCGGCTGTACCAG 60.270 52.381 0.00 0.00 39.03 4.00
4254 5018 2.039974 TGTGCACGCCATTGCCTAG 61.040 57.895 13.13 0.00 42.25 3.02
4257 5021 2.793946 CACGCCATTGCCTAGCAC 59.206 61.111 0.00 0.00 38.71 4.40
4269 5033 1.293924 CCTAGCACAAATGGAGCTCG 58.706 55.000 7.83 0.00 39.68 5.03
4288 5057 1.507630 GCCGCAGCATCAACATTGA 59.492 52.632 0.00 0.00 42.14 2.57
4298 5067 2.049077 TCAACATTGAACGCATGCAC 57.951 45.000 19.57 8.95 33.55 4.57
4299 5068 1.062258 CAACATTGAACGCATGCACC 58.938 50.000 19.57 6.26 0.00 5.01
4300 5069 0.672889 AACATTGAACGCATGCACCA 59.327 45.000 19.57 9.00 0.00 4.17
4304 5073 0.250510 TTGAACGCATGCACCAGGTA 60.251 50.000 19.57 0.00 0.00 3.08
4305 5074 0.250510 TGAACGCATGCACCAGGTAA 60.251 50.000 19.57 0.00 0.00 2.85
4306 5075 0.168128 GAACGCATGCACCAGGTAAC 59.832 55.000 19.57 1.82 0.00 2.50
4337 5124 1.663695 AGACCAACAAACACCGTCAG 58.336 50.000 0.00 0.00 0.00 3.51
4338 5125 0.661020 GACCAACAAACACCGTCAGG 59.339 55.000 0.00 0.00 45.13 3.86
4442 5229 3.119291 GGAAGACTACGATGCTGTGATG 58.881 50.000 0.00 0.00 0.00 3.07
4473 5262 5.121454 GGTGTGTGCATGAAAAACAGAAAAA 59.879 36.000 0.00 0.00 0.00 1.94
4571 5362 3.507622 TGAGAAGATCTCTTGCTTCACGA 59.492 43.478 8.68 0.00 43.73 4.35
4635 5429 3.917329 TTCTTGTCACTGGTAGAGTCG 57.083 47.619 0.00 0.00 29.75 4.18
4680 5474 2.097825 GCTTCTCCATTGACCAGCATT 58.902 47.619 0.00 0.00 0.00 3.56
4681 5475 2.159282 GCTTCTCCATTGACCAGCATTG 60.159 50.000 0.00 0.00 0.00 2.82
4682 5476 2.885135 TCTCCATTGACCAGCATTGT 57.115 45.000 0.00 0.00 0.00 2.71
4683 5477 2.715046 TCTCCATTGACCAGCATTGTC 58.285 47.619 0.00 0.00 0.00 3.18
4684 5478 2.040145 TCTCCATTGACCAGCATTGTCA 59.960 45.455 0.00 0.00 40.80 3.58
4685 5479 3.021695 CTCCATTGACCAGCATTGTCAT 58.978 45.455 4.17 0.00 41.99 3.06
4686 5480 3.433343 TCCATTGACCAGCATTGTCATT 58.567 40.909 4.17 0.00 41.99 2.57
4687 5481 4.598022 TCCATTGACCAGCATTGTCATTA 58.402 39.130 4.17 0.00 41.99 1.90
4688 5482 5.202765 TCCATTGACCAGCATTGTCATTAT 58.797 37.500 4.17 0.00 41.99 1.28
4689 5483 5.068067 TCCATTGACCAGCATTGTCATTATG 59.932 40.000 4.17 6.09 41.99 1.90
4690 5484 5.163488 CCATTGACCAGCATTGTCATTATGT 60.163 40.000 4.17 0.00 41.99 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.926200 GTCGATGAGTTCTGGTGACATG 59.074 50.000 0.00 0.00 41.51 3.21
3 4 2.416027 CGTCGATGAGTTCTGGTGACAT 60.416 50.000 0.00 0.00 41.51 3.06
5 6 1.618861 CGTCGATGAGTTCTGGTGAC 58.381 55.000 0.00 0.00 0.00 3.67
6 7 0.109272 GCGTCGATGAGTTCTGGTGA 60.109 55.000 9.31 0.00 0.00 4.02
7 8 1.406219 CGCGTCGATGAGTTCTGGTG 61.406 60.000 9.31 0.00 0.00 4.17
8 9 1.154016 CGCGTCGATGAGTTCTGGT 60.154 57.895 9.31 0.00 0.00 4.00
20 21 2.018137 CGTTGTGCATACGCGTCG 59.982 61.111 18.63 10.08 42.97 5.12
29 30 1.098712 GTGGGGTTTCTCGTTGTGCA 61.099 55.000 0.00 0.00 0.00 4.57
34 35 1.370064 CGAGGTGGGGTTTCTCGTT 59.630 57.895 0.00 0.00 43.51 3.85
54 55 3.364460 TCATGTGGTATTCTTGGGGTG 57.636 47.619 0.00 0.00 0.00 4.61
55 56 4.608170 ATTCATGTGGTATTCTTGGGGT 57.392 40.909 0.00 0.00 0.00 4.95
78 79 0.684479 ATAGACGGAGCTCCAGCACA 60.684 55.000 31.67 13.02 45.16 4.57
82 83 0.312416 CGGAATAGACGGAGCTCCAG 59.688 60.000 31.67 24.69 35.14 3.86
105 106 0.713883 CACCTCGAATTCGTCCAACG 59.286 55.000 25.93 11.19 44.19 4.10
144 145 2.277373 GCGCTTCGTCGTCGAGAT 60.277 61.111 0.00 0.00 46.81 2.75
150 151 4.373116 ATGGTGGCGCTTCGTCGT 62.373 61.111 7.64 0.00 32.50 4.34
155 156 3.499737 CGGTGATGGTGGCGCTTC 61.500 66.667 7.64 0.00 0.00 3.86
172 173 2.202544 CTCACAGAGGCGACGCTC 60.203 66.667 20.77 14.63 39.02 5.03
208 209 2.445845 TACCATCGGGAGGGCTGG 60.446 66.667 0.00 0.00 35.25 4.85
209 210 2.822399 GTACCATCGGGAGGGCTG 59.178 66.667 0.00 0.00 35.25 4.85
210 211 2.838225 CGTACCATCGGGAGGGCT 60.838 66.667 0.00 0.00 35.25 5.19
211 212 1.963464 TTTCGTACCATCGGGAGGGC 61.963 60.000 0.00 0.00 35.25 5.19
212 213 0.179092 GTTTCGTACCATCGGGAGGG 60.179 60.000 0.00 0.00 38.43 4.30
213 214 0.533491 TGTTTCGTACCATCGGGAGG 59.467 55.000 0.00 0.00 38.05 4.30
214 215 1.636988 GTGTTTCGTACCATCGGGAG 58.363 55.000 0.00 0.00 38.05 4.30
215 216 0.247185 GGTGTTTCGTACCATCGGGA 59.753 55.000 0.00 0.00 38.12 5.14
216 217 0.037139 TGGTGTTTCGTACCATCGGG 60.037 55.000 0.00 0.00 43.00 5.14
217 218 3.518381 TGGTGTTTCGTACCATCGG 57.482 52.632 0.00 0.00 43.00 4.18
221 222 1.069427 CCGGTGGTGTTTCGTACCA 59.931 57.895 0.00 0.00 45.52 3.25
222 223 0.668401 CTCCGGTGGTGTTTCGTACC 60.668 60.000 0.00 0.00 38.71 3.34
223 224 1.287041 GCTCCGGTGGTGTTTCGTAC 61.287 60.000 0.00 0.00 0.00 3.67
224 225 1.005867 GCTCCGGTGGTGTTTCGTA 60.006 57.895 0.00 0.00 0.00 3.43
225 226 2.280592 GCTCCGGTGGTGTTTCGT 60.281 61.111 0.00 0.00 0.00 3.85
226 227 1.440938 TTTGCTCCGGTGGTGTTTCG 61.441 55.000 0.00 0.00 0.00 3.46
227 228 0.310854 CTTTGCTCCGGTGGTGTTTC 59.689 55.000 0.00 0.00 0.00 2.78
228 229 1.106944 CCTTTGCTCCGGTGGTGTTT 61.107 55.000 0.00 0.00 0.00 2.83
229 230 1.528309 CCTTTGCTCCGGTGGTGTT 60.528 57.895 0.00 0.00 0.00 3.32
230 231 2.113139 CCTTTGCTCCGGTGGTGT 59.887 61.111 0.00 0.00 0.00 4.16
231 232 3.365265 GCCTTTGCTCCGGTGGTG 61.365 66.667 0.00 0.00 33.53 4.17
232 233 2.920076 TTTGCCTTTGCTCCGGTGGT 62.920 55.000 0.00 0.00 38.71 4.16
233 234 2.146073 CTTTGCCTTTGCTCCGGTGG 62.146 60.000 0.00 0.00 38.71 4.61
234 235 1.286880 CTTTGCCTTTGCTCCGGTG 59.713 57.895 0.00 0.00 38.71 4.94
235 236 2.564721 GCTTTGCCTTTGCTCCGGT 61.565 57.895 0.00 0.00 38.71 5.28
236 237 2.259511 GCTTTGCCTTTGCTCCGG 59.740 61.111 0.00 0.00 38.71 5.14
237 238 1.080974 CTGCTTTGCCTTTGCTCCG 60.081 57.895 0.00 0.00 38.71 4.63
238 239 1.291272 CCTGCTTTGCCTTTGCTCC 59.709 57.895 0.00 0.00 38.71 4.70
239 240 1.291272 CCCTGCTTTGCCTTTGCTC 59.709 57.895 0.00 0.00 38.71 4.26
240 241 2.212110 CCCCTGCTTTGCCTTTGCT 61.212 57.895 0.00 0.00 38.71 3.91
241 242 2.163601 CTCCCCTGCTTTGCCTTTGC 62.164 60.000 0.00 0.00 38.26 3.68
242 243 0.540365 TCTCCCCTGCTTTGCCTTTG 60.540 55.000 0.00 0.00 0.00 2.77
243 244 0.411058 ATCTCCCCTGCTTTGCCTTT 59.589 50.000 0.00 0.00 0.00 3.11
244 245 1.298953 TATCTCCCCTGCTTTGCCTT 58.701 50.000 0.00 0.00 0.00 4.35
245 246 1.298953 TTATCTCCCCTGCTTTGCCT 58.701 50.000 0.00 0.00 0.00 4.75
246 247 2.143876 TTTATCTCCCCTGCTTTGCC 57.856 50.000 0.00 0.00 0.00 4.52
247 248 2.363359 CCATTTATCTCCCCTGCTTTGC 59.637 50.000 0.00 0.00 0.00 3.68
248 249 3.902218 TCCATTTATCTCCCCTGCTTTG 58.098 45.455 0.00 0.00 0.00 2.77
249 250 4.540715 CTTCCATTTATCTCCCCTGCTTT 58.459 43.478 0.00 0.00 0.00 3.51
250 251 3.117360 CCTTCCATTTATCTCCCCTGCTT 60.117 47.826 0.00 0.00 0.00 3.91
251 252 2.444766 CCTTCCATTTATCTCCCCTGCT 59.555 50.000 0.00 0.00 0.00 4.24
252 253 2.443255 TCCTTCCATTTATCTCCCCTGC 59.557 50.000 0.00 0.00 0.00 4.85
253 254 3.976654 TCTCCTTCCATTTATCTCCCCTG 59.023 47.826 0.00 0.00 0.00 4.45
254 255 4.238669 CTCTCCTTCCATTTATCTCCCCT 58.761 47.826 0.00 0.00 0.00 4.79
255 256 3.329225 CCTCTCCTTCCATTTATCTCCCC 59.671 52.174 0.00 0.00 0.00 4.81
256 257 3.329225 CCCTCTCCTTCCATTTATCTCCC 59.671 52.174 0.00 0.00 0.00 4.30
257 258 3.329225 CCCCTCTCCTTCCATTTATCTCC 59.671 52.174 0.00 0.00 0.00 3.71
258 259 3.329225 CCCCCTCTCCTTCCATTTATCTC 59.671 52.174 0.00 0.00 0.00 2.75
259 260 3.331120 CCCCCTCTCCTTCCATTTATCT 58.669 50.000 0.00 0.00 0.00 1.98
260 261 3.797559 CCCCCTCTCCTTCCATTTATC 57.202 52.381 0.00 0.00 0.00 1.75
281 599 0.676466 TCCACGACATTGACCATGGC 60.676 55.000 13.04 5.35 37.59 4.40
283 601 1.339055 ACCTCCACGACATTGACCATG 60.339 52.381 0.00 0.00 39.07 3.66
284 602 0.984230 ACCTCCACGACATTGACCAT 59.016 50.000 0.00 0.00 0.00 3.55
285 603 0.034756 CACCTCCACGACATTGACCA 59.965 55.000 0.00 0.00 0.00 4.02
312 630 2.733945 CAAAAAGGGTGGTGGCCG 59.266 61.111 0.00 0.00 0.00 6.13
322 640 1.243902 TCGCTACCAAGCCAAAAAGG 58.756 50.000 0.00 0.00 46.68 3.11
323 641 3.689649 ACTATCGCTACCAAGCCAAAAAG 59.310 43.478 0.00 0.00 46.68 2.27
330 651 2.229302 CTCCCTACTATCGCTACCAAGC 59.771 54.545 0.00 0.00 45.86 4.01
439 923 7.099764 CAGGTGTGTACTATTTGAGAGTTCAT 58.900 38.462 0.00 0.00 32.27 2.57
464 949 0.180406 ATGGATGGACGCTTACCCAC 59.820 55.000 0.00 0.00 34.92 4.61
474 959 5.591877 AGCTTTTCATAACTCATGGATGGAC 59.408 40.000 0.00 0.00 35.16 4.02
518 1003 4.568072 AAGCCATACAATCCAGTGTGTA 57.432 40.909 0.00 0.00 34.84 2.90
555 1041 8.161699 TCTTTTAGTTTGGAAATTCGCTTAGT 57.838 30.769 0.00 0.00 0.00 2.24
556 1042 8.902735 GTTCTTTTAGTTTGGAAATTCGCTTAG 58.097 33.333 0.00 0.00 0.00 2.18
557 1043 8.407064 TGTTCTTTTAGTTTGGAAATTCGCTTA 58.593 29.630 0.00 0.00 0.00 3.09
558 1044 7.262048 TGTTCTTTTAGTTTGGAAATTCGCTT 58.738 30.769 0.00 0.00 0.00 4.68
559 1045 6.801575 TGTTCTTTTAGTTTGGAAATTCGCT 58.198 32.000 0.00 0.00 0.00 4.93
560 1046 7.458038 TTGTTCTTTTAGTTTGGAAATTCGC 57.542 32.000 0.00 0.00 0.00 4.70
561 1047 7.435192 AGCTTGTTCTTTTAGTTTGGAAATTCG 59.565 33.333 0.00 0.00 0.00 3.34
562 1048 8.648557 AGCTTGTTCTTTTAGTTTGGAAATTC 57.351 30.769 0.00 0.00 0.00 2.17
564 1050 7.011389 GCAAGCTTGTTCTTTTAGTTTGGAAAT 59.989 33.333 26.55 0.00 32.74 2.17
565 1051 6.312672 GCAAGCTTGTTCTTTTAGTTTGGAAA 59.687 34.615 26.55 0.00 32.74 3.13
798 1285 1.305549 GGGTCCCCCGTCTGAACTA 60.306 63.158 0.00 0.00 32.13 2.24
1310 1804 3.256960 TCCTCTGCCCAACCACCC 61.257 66.667 0.00 0.00 0.00 4.61
1313 1807 2.156098 AAGCTCCTCTGCCCAACCA 61.156 57.895 0.00 0.00 0.00 3.67
1314 1808 1.676967 CAAGCTCCTCTGCCCAACC 60.677 63.158 0.00 0.00 0.00 3.77
1316 1810 0.250901 GAACAAGCTCCTCTGCCCAA 60.251 55.000 0.00 0.00 0.00 4.12
1318 1812 0.037447 AAGAACAAGCTCCTCTGCCC 59.963 55.000 0.00 0.00 0.00 5.36
1395 1894 3.988976 TCTAGCATAGCATCCCCAATC 57.011 47.619 0.00 0.00 38.99 2.67
1412 1911 5.004361 AGAGGGAGCATGCTAGTAATCTA 57.996 43.478 22.74 0.00 0.00 1.98
1418 1917 2.636893 CCATTAGAGGGAGCATGCTAGT 59.363 50.000 22.74 8.03 0.00 2.57
1419 1918 3.331478 CCATTAGAGGGAGCATGCTAG 57.669 52.381 22.74 2.22 0.00 3.42
1434 1933 2.234908 CAATTTGCGGTTTCCCCCATTA 59.765 45.455 0.00 0.00 0.00 1.90
1436 1935 0.612744 CAATTTGCGGTTTCCCCCAT 59.387 50.000 0.00 0.00 0.00 4.00
1437 1936 0.760945 ACAATTTGCGGTTTCCCCCA 60.761 50.000 0.00 0.00 0.00 4.96
1442 1941 9.233232 CTAATCCTTAATACAATTTGCGGTTTC 57.767 33.333 0.00 0.00 0.00 2.78
1487 1986 1.544246 GAACAAATAACAAGCCCGGCT 59.456 47.619 5.94 5.94 42.56 5.52
1605 2106 6.270064 GGCCGTTGCAACTATACATTTAAAT 58.730 36.000 26.09 0.00 40.13 1.40
1730 2232 3.868757 TGACCAGAGTCCAGAAATACG 57.131 47.619 0.00 0.00 42.81 3.06
1793 2295 3.243704 TGGCACAAGGACACAAATTTAGC 60.244 43.478 0.00 0.00 31.92 3.09
1994 2497 6.173339 ACATGTCTACCAAACAGGAATACAG 58.827 40.000 0.00 0.00 41.22 2.74
2113 2616 4.100653 TGGAGGAACAGATGATGATGACTC 59.899 45.833 0.00 0.00 0.00 3.36
2145 2648 5.337169 GGAGGTAATAGGAGCAGATGATCAC 60.337 48.000 0.00 0.00 30.87 3.06
2204 2715 1.912043 AGCTGCTCCCAACTGTAAGAT 59.088 47.619 0.00 0.00 37.43 2.40
2366 2877 4.380841 AGAGCAATGCCACAATAACATG 57.619 40.909 0.00 0.00 0.00 3.21
2512 3026 6.831868 ACTTTGCCTGGGATAACGTATAAAAT 59.168 34.615 0.00 0.00 0.00 1.82
2520 3034 2.936498 CTGTACTTTGCCTGGGATAACG 59.064 50.000 0.00 0.00 0.00 3.18
2932 3450 0.251519 AAGCTGCAAGGGGGAGAAAG 60.252 55.000 1.02 0.00 37.05 2.62
2942 3460 7.118971 ACATTCTAGAAACTAGAAAGCTGCAAG 59.881 37.037 20.10 9.11 37.15 4.01
2982 3506 3.744660 ACCTCAGTCAGATGTTGAAACC 58.255 45.455 0.00 0.00 37.61 3.27
3187 3732 2.736192 GAGCTTCTTCAGTGCTTCAGTC 59.264 50.000 0.00 0.00 37.16 3.51
3327 3872 6.149973 TGGTTCTCAAGTGATCACATGAATTC 59.850 38.462 28.07 20.61 38.37 2.17
4118 4837 1.153369 AGCCACCAATCGATCACCG 60.153 57.895 0.00 0.00 40.25 4.94
4126 4845 0.240945 CAACGAACCAGCCACCAATC 59.759 55.000 0.00 0.00 0.00 2.67
4135 4854 0.746563 ACCCACACACAACGAACCAG 60.747 55.000 0.00 0.00 0.00 4.00
4210 4929 1.641123 GCTTTGCATGTGCCCAATGC 61.641 55.000 2.07 8.07 41.18 3.56
4254 5018 2.486966 GCCGAGCTCCATTTGTGC 59.513 61.111 8.47 0.00 0.00 4.57
4257 5021 3.880846 GCGGCCGAGCTCCATTTG 61.881 66.667 33.48 0.00 0.00 2.32
4269 5033 1.517694 CAATGTTGATGCTGCGGCC 60.518 57.895 16.57 0.02 37.74 6.13
4288 5057 0.250727 AGTTACCTGGTGCATGCGTT 60.251 50.000 14.09 0.00 0.00 4.84
4298 5067 3.578716 TCTTCTCTGACCAAGTTACCTGG 59.421 47.826 0.00 0.00 0.00 4.45
4299 5068 4.561105 GTCTTCTCTGACCAAGTTACCTG 58.439 47.826 0.00 0.00 0.00 4.00
4300 5069 4.875561 GTCTTCTCTGACCAAGTTACCT 57.124 45.455 0.00 0.00 0.00 3.08
4310 5079 3.312697 GGTGTTTGTTGGTCTTCTCTGAC 59.687 47.826 0.00 0.00 36.31 3.51
4311 5080 3.541632 GGTGTTTGTTGGTCTTCTCTGA 58.458 45.455 0.00 0.00 0.00 3.27
4371 5158 8.459635 TGCCTAGTACTATTAGATTATGCTTCG 58.540 37.037 2.33 0.00 0.00 3.79
4407 5194 5.064962 CGTAGTCTTCCTACAGGTGTCTTAG 59.935 48.000 0.00 0.00 45.40 2.18
4442 5229 0.035317 TCATGCACACACCAGAGACC 59.965 55.000 0.00 0.00 0.00 3.85
4512 5303 2.546795 GGATGGCTTGATCTTCGTCGAT 60.547 50.000 0.00 0.00 0.00 3.59
4513 5304 1.202417 GGATGGCTTGATCTTCGTCGA 60.202 52.381 0.00 0.00 0.00 4.20
4540 5331 7.267128 AGCAAGAGATCTTCTCATTAACTCTG 58.733 38.462 0.00 0.00 45.73 3.35
4587 5378 6.204495 GCTTGAAATACCAATTGGCAAAGAAA 59.796 34.615 24.79 11.45 39.32 2.52
4590 5384 4.392754 GGCTTGAAATACCAATTGGCAAAG 59.607 41.667 24.79 17.52 39.32 2.77
4591 5385 4.041444 AGGCTTGAAATACCAATTGGCAAA 59.959 37.500 24.79 10.71 39.32 3.68
4592 5386 3.582208 AGGCTTGAAATACCAATTGGCAA 59.418 39.130 24.79 17.45 39.32 4.52


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

AutoCloner maintained by Alex Coulton.