Multiple sequence alignment - TraesCS6D01G124300

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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 TraesCS6D01G124300 chr6D 100.000 5304 0 0 1 5304 89005377 89010680 0.000000e+00 9795.0
1 TraesCS6D01G124300 chr6B 90.179 5254 326 98 2 5171 169319718 169324865 0.000000e+00 6669.0
2 TraesCS6D01G124300 chr6B 87.056 1097 90 17 4099 5171 169395923 169396991 0.000000e+00 1192.0
3 TraesCS6D01G124300 chr6B 95.522 134 6 0 5171 5304 75672409 75672276 1.160000e-51 215.0
4 TraesCS6D01G124300 chr6A 94.486 3736 157 14 1452 5171 107116729 107120431 0.000000e+00 5712.0
5 TraesCS6D01G124300 chr6A 88.980 735 50 18 655 1377 107115982 107116697 0.000000e+00 880.0
6 TraesCS6D01G124300 chr6A 85.495 455 23 17 1 448 107115227 107115645 8.160000e-118 435.0
7 TraesCS6D01G124300 chr6A 82.906 351 17 14 314 633 107115652 107115990 5.230000e-70 276.0
8 TraesCS6D01G124300 chr4D 94.853 136 7 0 5169 5304 298844844 298844709 4.160000e-51 213.0
9 TraesCS6D01G124300 chr4D 94.776 134 7 0 5171 5304 156646120 156645987 5.380000e-50 209.0
10 TraesCS6D01G124300 chr4B 94.815 135 7 0 5170 5304 290724428 290724294 1.500000e-50 211.0
11 TraesCS6D01G124300 chr1A 94.815 135 7 0 5170 5304 208287924 208288058 1.500000e-50 211.0
12 TraesCS6D01G124300 chr1A 89.873 158 13 3 5150 5304 441023998 441023841 3.240000e-47 200.0
13 TraesCS6D01G124300 chr7A 93.056 144 9 1 5162 5304 556161080 556161223 5.380000e-50 209.0
14 TraesCS6D01G124300 chr5B 91.892 148 12 0 5157 5304 656245371 656245518 1.940000e-49 207.0
15 TraesCS6D01G124300 chr1D 91.216 148 13 0 5157 5304 75148306 75148453 9.010000e-48 202.0
16 TraesCS6D01G124300 chr2A 91.228 57 4 1 4720 4775 706284774 706284718 5.700000e-10 76.8
17 TraesCS6D01G124300 chr2B 89.474 57 5 1 4720 4775 678568385 678568329 2.650000e-08 71.3


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 TraesCS6D01G124300 chr6D 89005377 89010680 5303 False 9795.00 9795 100.00000 1 5304 1 chr6D.!!$F1 5303
1 TraesCS6D01G124300 chr6B 169319718 169324865 5147 False 6669.00 6669 90.17900 2 5171 1 chr6B.!!$F1 5169
2 TraesCS6D01G124300 chr6B 169395923 169396991 1068 False 1192.00 1192 87.05600 4099 5171 1 chr6B.!!$F2 1072
3 TraesCS6D01G124300 chr6A 107115227 107120431 5204 False 1825.75 5712 87.96675 1 5171 4 chr6A.!!$F1 5170

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
134 141 0.037232 CCGTGACCCTCTCTTTGTCC 60.037 60.000 0.00 0.0 0.00 4.02 F
1109 1308 0.037326 GTCTTGTCTGGATGGACGCA 60.037 55.000 0.00 0.0 38.91 5.24 F
1637 1842 0.249447 TATGATGAACTGCCGAGCCG 60.249 55.000 0.00 0.0 0.00 5.52 F
2151 2356 0.466372 TCGGTGAGCCTCGAGATGAT 60.466 55.000 15.71 0.0 0.00 2.45 F
2206 2411 0.482446 TGGTGAGGCAATGTCCCTTT 59.518 50.000 0.00 0.0 31.41 3.11 F
2207 2412 1.177401 GGTGAGGCAATGTCCCTTTC 58.823 55.000 0.00 0.0 31.41 2.62 F
3994 4199 1.082756 GCTGGCACGTTTCGTTGAG 60.083 57.895 0.00 0.0 38.32 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1146 1348 0.475906 GATCCCCATCCAGAACCAGG 59.524 60.000 0.00 0.00 0.00 4.45 R
1914 2119 0.536460 TGTTCGGAAAGTTGGGAGGC 60.536 55.000 0.00 0.00 0.00 4.70 R
2635 2840 1.517242 CACCCACTTCAGCTTCAGAC 58.483 55.000 0.00 0.00 0.00 3.51 R
3700 3905 1.186917 CCATGGCCAACCTTGCTTCA 61.187 55.000 10.96 0.00 39.30 3.02 R
3994 4199 2.034104 TGGTCTCATTCTCTGCATGC 57.966 50.000 11.82 11.82 0.00 4.06 R
4048 4253 3.067601 ACCGGATTGTTTTCTTCACCAAC 59.932 43.478 9.46 0.00 0.00 3.77 R
5175 5420 1.876156 TGCATTGCACGTACACATTGA 59.124 42.857 7.38 0.00 31.71 2.57 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
108 115 3.492482 GGAGAAAGTGATAGCTCAGCTCC 60.492 52.174 0.00 0.00 40.44 4.70
130 137 3.069778 GGCCGTGACCCTCTCTTT 58.930 61.111 0.00 0.00 0.00 2.52
131 138 1.376037 GGCCGTGACCCTCTCTTTG 60.376 63.158 0.00 0.00 0.00 2.77
132 139 1.371558 GCCGTGACCCTCTCTTTGT 59.628 57.895 0.00 0.00 0.00 2.83
133 140 0.670854 GCCGTGACCCTCTCTTTGTC 60.671 60.000 0.00 0.00 0.00 3.18
134 141 0.037232 CCGTGACCCTCTCTTTGTCC 60.037 60.000 0.00 0.00 0.00 4.02
135 142 0.388649 CGTGACCCTCTCTTTGTCCG 60.389 60.000 0.00 0.00 0.00 4.79
136 143 0.680061 GTGACCCTCTCTTTGTCCGT 59.320 55.000 0.00 0.00 0.00 4.69
139 146 1.296715 CCCTCTCTTTGTCCGTGGG 59.703 63.158 0.00 0.00 0.00 4.61
142 149 2.111999 CTCTCTTTGTCCGTGGGCCA 62.112 60.000 0.00 0.00 0.00 5.36
165 172 4.237207 GGGTACGGCAGCCCTAGC 62.237 72.222 5.63 8.51 41.63 3.42
174 181 4.499116 AGCCCTAGCCCGTCCCAT 62.499 66.667 0.00 0.00 41.25 4.00
176 183 3.616721 CCCTAGCCCGTCCCATCG 61.617 72.222 0.00 0.00 0.00 3.84
177 184 2.520982 CCTAGCCCGTCCCATCGA 60.521 66.667 0.00 0.00 0.00 3.59
178 185 2.728817 CTAGCCCGTCCCATCGAC 59.271 66.667 0.00 0.00 38.21 4.20
179 186 1.828660 CTAGCCCGTCCCATCGACT 60.829 63.158 0.00 0.00 39.56 4.18
180 187 1.380785 TAGCCCGTCCCATCGACTT 60.381 57.895 0.00 0.00 39.56 3.01
181 188 1.672854 TAGCCCGTCCCATCGACTTG 61.673 60.000 0.00 0.00 39.56 3.16
183 190 1.153628 CCCGTCCCATCGACTTGAC 60.154 63.158 0.00 0.00 39.56 3.18
184 191 1.589630 CCGTCCCATCGACTTGACA 59.410 57.895 9.76 0.00 39.56 3.58
190 197 1.026718 CCATCGACTTGACAAGGGCC 61.027 60.000 19.16 0.00 0.00 5.80
212 222 0.322975 CTTGGAGTCCAGTGGGTCAG 59.677 60.000 12.67 0.84 33.81 3.51
402 412 7.569957 CGCAGTAACTAAACTATTTTTCACCGT 60.570 37.037 0.00 0.00 0.00 4.83
416 426 3.047877 CCGTTTGGTCTCCCGTGC 61.048 66.667 0.00 0.00 0.00 5.34
430 595 3.050275 GTGCCAGCAAGGGTCGAC 61.050 66.667 7.13 7.13 38.09 4.20
533 701 0.521735 GAAATGCTCCGCCTTTCGTT 59.478 50.000 1.88 0.00 34.65 3.85
534 702 0.521735 AAATGCTCCGCCTTTCGTTC 59.478 50.000 0.00 0.00 36.19 3.95
535 703 1.635663 AATGCTCCGCCTTTCGTTCG 61.636 55.000 0.00 0.00 36.19 3.95
536 704 2.737376 GCTCCGCCTTTCGTTCGT 60.737 61.111 0.00 0.00 36.19 3.85
723 902 4.042809 TCCTTCCAATTCCAAGCAGTAAGA 59.957 41.667 0.00 0.00 0.00 2.10
728 907 8.415950 TTCCAATTCCAAGCAGTAAGAAAATA 57.584 30.769 0.00 0.00 0.00 1.40
747 926 0.620556 AGGCATCCATCCACGTCTTT 59.379 50.000 0.00 0.00 0.00 2.52
915 1102 2.359975 CCCAACGGCCCAGAAGAC 60.360 66.667 0.00 0.00 0.00 3.01
917 1104 1.002134 CCAACGGCCCAGAAGACAT 60.002 57.895 0.00 0.00 0.00 3.06
919 1106 1.026718 CAACGGCCCAGAAGACATCC 61.027 60.000 0.00 0.00 0.00 3.51
923 1110 0.842635 GGCCCAGAAGACATCCATCT 59.157 55.000 0.00 0.00 0.00 2.90
930 1129 1.139853 GAAGACATCCATCTTCCGCCT 59.860 52.381 4.49 0.00 46.04 5.52
948 1147 1.074951 TCTCCACTGAGGCGAGACA 59.925 57.895 0.00 0.00 39.23 3.41
950 1149 2.126307 CCACTGAGGCGAGACACG 60.126 66.667 0.00 0.00 45.66 4.49
1005 1204 2.439156 GAGGTGGCAGCCATGACC 60.439 66.667 19.75 14.79 35.28 4.02
1006 1205 3.259314 AGGTGGCAGCCATGACCA 61.259 61.111 19.75 0.00 35.28 4.02
1109 1308 0.037326 GTCTTGTCTGGATGGACGCA 60.037 55.000 0.00 0.00 38.91 5.24
1133 1335 3.440127 CTCCCTCTTCTTCTTCCTCTGT 58.560 50.000 0.00 0.00 0.00 3.41
1142 1344 2.011122 TCTTCCTCTGTTCCTCCGTT 57.989 50.000 0.00 0.00 0.00 4.44
1146 1348 1.346722 TCCTCTGTTCCTCCGTTTTCC 59.653 52.381 0.00 0.00 0.00 3.13
1174 1376 2.036475 CTGGATGGGGATCTCGTAAGTG 59.964 54.545 0.00 0.00 39.48 3.16
1186 1388 6.238786 GGATCTCGTAAGTGCTCTCATTCTTA 60.239 42.308 0.00 0.00 39.48 2.10
1278 1481 6.049955 TGATTACGAGTCCCTTTCATCTTT 57.950 37.500 0.00 0.00 0.00 2.52
1456 1661 5.132897 TGACAAAATATGGTCAGTTTGCC 57.867 39.130 0.00 0.00 39.00 4.52
1461 1666 6.437162 ACAAAATATGGTCAGTTTGCCTACAT 59.563 34.615 0.00 0.00 34.94 2.29
1478 1683 7.853299 TGCCTACATGTAATCCTTACTGTTTA 58.147 34.615 7.06 0.00 37.06 2.01
1581 1786 5.957842 TTTGCTTACAAGACATAGTTGGG 57.042 39.130 0.00 0.00 37.04 4.12
1605 1810 3.697166 GGAGGAAATTTTAGGCACTGGA 58.303 45.455 0.00 0.00 41.52 3.86
1637 1842 0.249447 TATGATGAACTGCCGAGCCG 60.249 55.000 0.00 0.00 0.00 5.52
1648 1853 0.949105 GCCGAGCCGTTCTTCAAAGA 60.949 55.000 0.00 0.00 0.00 2.52
1653 1858 2.734079 GAGCCGTTCTTCAAAGAGTGAG 59.266 50.000 0.00 0.00 37.61 3.51
1790 1995 3.445008 TCAACTATCTTGAGGACCAGCT 58.555 45.455 0.00 0.00 0.00 4.24
1798 2003 1.131638 TGAGGACCAGCTGTTCTTGT 58.868 50.000 13.81 2.16 30.74 3.16
1807 2012 3.489738 CCAGCTGTTCTTGTTTGGTTCAG 60.490 47.826 13.81 0.00 0.00 3.02
1856 2061 4.441079 GGCTGATCAAATGGTTGAAGATGG 60.441 45.833 0.00 0.00 46.66 3.51
1863 2068 4.664688 AATGGTTGAAGATGGTCCTTCT 57.335 40.909 1.33 1.33 42.20 2.85
1898 2103 6.619329 AGCTAAGTTTCCTCTTTCTCTGAT 57.381 37.500 0.00 0.00 0.00 2.90
1925 2130 1.074889 ACCATTTACGCCTCCCAACTT 59.925 47.619 0.00 0.00 0.00 2.66
1981 2186 3.821033 AGATAAACCTGCAAAGAAGCGTT 59.179 39.130 0.00 0.00 37.31 4.84
2049 2254 8.099364 ACTACATAAAATTGGTCTTGACTGTG 57.901 34.615 0.61 0.00 0.00 3.66
2088 2293 3.423571 CTTCTCGTTCATTGCTGCATTC 58.576 45.455 1.84 0.00 0.00 2.67
2151 2356 0.466372 TCGGTGAGCCTCGAGATGAT 60.466 55.000 15.71 0.00 0.00 2.45
2174 2379 3.325293 TCCTCTTCTTCACATGCAGTC 57.675 47.619 0.00 0.00 0.00 3.51
2178 2383 0.955428 TTCTTCACATGCAGTCGGCC 60.955 55.000 0.00 0.00 43.89 6.13
2184 2389 2.112928 ATGCAGTCGGCCAACACA 59.887 55.556 2.24 0.00 43.89 3.72
2199 2404 4.828409 ACACCTGGTGAGGCAATG 57.172 55.556 32.30 4.42 44.33 2.82
2206 2411 0.482446 TGGTGAGGCAATGTCCCTTT 59.518 50.000 0.00 0.00 31.41 3.11
2207 2412 1.177401 GGTGAGGCAATGTCCCTTTC 58.823 55.000 0.00 0.00 31.41 2.62
2212 2417 1.707427 AGGCAATGTCCCTTTCTGTCT 59.293 47.619 0.00 0.00 0.00 3.41
2220 2425 4.942944 TGTCCCTTTCTGTCTACCTATGA 58.057 43.478 0.00 0.00 0.00 2.15
2224 2429 4.040952 CCCTTTCTGTCTACCTATGATGGG 59.959 50.000 0.00 0.00 0.00 4.00
2272 2477 9.695155 ATCATATATCATCAATTTCATGCAGGA 57.305 29.630 0.00 0.00 0.00 3.86
2389 2594 4.864704 TCCATGCTGTTTTAAAACCTCC 57.135 40.909 24.55 14.53 38.11 4.30
2391 2596 4.280677 TCCATGCTGTTTTAAAACCTCCAG 59.719 41.667 24.55 17.06 38.11 3.86
2459 2664 3.438087 CACAAGTGATGCTCCTAAACCAG 59.562 47.826 0.00 0.00 0.00 4.00
2510 2715 2.363795 CACCACCGCCTCCTCCTA 60.364 66.667 0.00 0.00 0.00 2.94
2635 2840 2.169789 CGAGCAGGCCAGTGAATCG 61.170 63.158 5.01 5.60 0.00 3.34
2796 3001 8.028938 ACAAGTTATTAATCCATTTGTCTGCAC 58.971 33.333 0.00 0.00 0.00 4.57
3025 3230 3.870419 GAGGACATTCAAGATGCTCTCAC 59.130 47.826 0.00 0.00 0.00 3.51
3037 3242 1.821753 TGCTCTCACTGAAGGTAGCTC 59.178 52.381 0.00 0.00 0.00 4.09
3043 3248 2.488545 TCACTGAAGGTAGCTCTTCGTC 59.511 50.000 9.81 1.53 44.38 4.20
3052 3257 4.098196 AGGTAGCTCTTCGTCCATAAGAAC 59.902 45.833 0.00 0.00 32.77 3.01
3053 3258 4.142227 GGTAGCTCTTCGTCCATAAGAACA 60.142 45.833 0.00 0.00 32.77 3.18
3061 3266 9.529325 CTCTTCGTCCATAAGAACATATTGTTA 57.471 33.333 0.00 0.00 41.28 2.41
3109 3314 6.604396 TCATATGTGGAAAAGATGCATGTTCT 59.396 34.615 9.83 0.00 0.00 3.01
3194 3399 5.644636 ACTTCCTAGACTACTTCTTGAGACG 59.355 44.000 0.00 0.00 35.55 4.18
3236 3441 2.909006 TGATGAGGAGGAGCTGAAACTT 59.091 45.455 0.00 0.00 0.00 2.66
3417 3622 3.935828 GGAGGTAAGCTAAGTGAAAGCAG 59.064 47.826 0.00 0.00 42.62 4.24
3425 3630 4.274459 AGCTAAGTGAAAGCAGTTGACTTG 59.726 41.667 12.95 6.48 42.62 3.16
3460 3665 4.338118 TGAAAAGCACTCCAACCTTTACTG 59.662 41.667 0.00 0.00 0.00 2.74
3465 3670 5.140454 AGCACTCCAACCTTTACTGAAATT 58.860 37.500 0.00 0.00 0.00 1.82
3502 3707 2.270986 GGCTGCTTGTGGGGAACTG 61.271 63.158 0.00 0.00 0.00 3.16
3511 3716 2.359975 GGGGAACTGAAGCACCGG 60.360 66.667 0.00 0.00 0.00 5.28
3523 3728 3.957383 GCACCGGCTTTTTCTGAAA 57.043 47.368 0.00 0.00 36.96 2.69
3604 3809 4.764679 TGCTAACGCATTCAAACTTGAT 57.235 36.364 0.00 0.00 42.25 2.57
3892 4097 4.142403 GCTTTATCTGCCAGTGTATTGCAA 60.142 41.667 0.00 0.00 34.06 4.08
3991 4196 2.586635 TCGCTGGCACGTTTCGTT 60.587 55.556 8.80 0.00 38.32 3.85
3994 4199 1.082756 GCTGGCACGTTTCGTTGAG 60.083 57.895 0.00 0.00 38.32 3.02
4048 4253 7.257003 TGAAAGAAGAGAAGAGATTGAGATCG 58.743 38.462 0.00 0.00 37.37 3.69
4099 4304 5.066893 CCATGGAAACGATGTGAAAGATGAT 59.933 40.000 5.56 0.00 0.00 2.45
4225 4430 1.228429 TGGCAGTTGTAACCCAGCC 60.228 57.895 13.34 13.34 40.28 4.85
4291 4496 6.382282 TGGATGATCATTTAGATAGCTCGGAT 59.618 38.462 10.14 0.00 37.00 4.18
4387 4592 4.737054 CAAATACCCATTTGCAGAGACAC 58.263 43.478 0.00 0.00 43.30 3.67
4490 4701 6.360618 TGCCACATACACATGGTTATATCAA 58.639 36.000 0.00 0.00 38.34 2.57
4565 4777 2.916716 CGTTCTTGCAAAATGGGATTCG 59.083 45.455 0.00 0.00 0.00 3.34
4635 4848 7.303261 AGGCACGTAAAAGCTTCTTTTATTAC 58.697 34.615 12.96 2.88 0.00 1.89
4838 5069 6.606796 ACCTGCATGTAAATATTTGTGATGGA 59.393 34.615 11.05 9.58 0.00 3.41
4934 5166 4.442375 TTTTTGCTCAAACTTCCACGAA 57.558 36.364 0.00 0.00 0.00 3.85
5039 5274 3.810941 TCACACGGTTTTACTGTTCATCC 59.189 43.478 0.00 0.00 35.04 3.51
5157 5402 5.989477 TCTCTACATGGGTTTAGATTGGTG 58.011 41.667 0.00 0.00 0.00 4.17
5158 5403 5.487488 TCTCTACATGGGTTTAGATTGGTGT 59.513 40.000 0.00 0.00 0.00 4.16
5171 5416 8.539674 GTTTAGATTGGTGTTGTTTGAATTCAC 58.460 33.333 7.89 0.00 0.00 3.18
5172 5417 6.469782 AGATTGGTGTTGTTTGAATTCACT 57.530 33.333 7.89 0.00 0.00 3.41
5173 5418 7.581213 AGATTGGTGTTGTTTGAATTCACTA 57.419 32.000 7.89 0.00 0.00 2.74
5174 5419 7.651808 AGATTGGTGTTGTTTGAATTCACTAG 58.348 34.615 7.89 0.00 0.00 2.57
5175 5420 6.767524 TTGGTGTTGTTTGAATTCACTAGT 57.232 33.333 7.89 0.00 0.00 2.57
5176 5421 6.371809 TGGTGTTGTTTGAATTCACTAGTC 57.628 37.500 7.89 0.26 0.00 2.59
5177 5422 5.883115 TGGTGTTGTTTGAATTCACTAGTCA 59.117 36.000 7.89 2.93 0.00 3.41
5178 5423 6.375736 TGGTGTTGTTTGAATTCACTAGTCAA 59.624 34.615 7.89 6.73 38.93 3.18
5179 5424 7.068103 TGGTGTTGTTTGAATTCACTAGTCAAT 59.932 33.333 7.89 0.00 40.21 2.57
5180 5425 7.379529 GGTGTTGTTTGAATTCACTAGTCAATG 59.620 37.037 7.89 0.00 40.21 2.82
5181 5426 7.915397 GTGTTGTTTGAATTCACTAGTCAATGT 59.085 33.333 7.89 0.00 40.21 2.71
5182 5427 7.914871 TGTTGTTTGAATTCACTAGTCAATGTG 59.085 33.333 7.89 0.00 40.21 3.21
5183 5428 7.566760 TGTTTGAATTCACTAGTCAATGTGT 57.433 32.000 7.89 0.00 40.21 3.72
5184 5429 8.669946 TGTTTGAATTCACTAGTCAATGTGTA 57.330 30.769 7.89 0.00 40.21 2.90
5185 5430 8.556194 TGTTTGAATTCACTAGTCAATGTGTAC 58.444 33.333 7.89 0.00 40.21 2.90
5186 5431 6.944557 TGAATTCACTAGTCAATGTGTACG 57.055 37.500 3.38 0.00 35.82 3.67
5187 5432 6.452242 TGAATTCACTAGTCAATGTGTACGT 58.548 36.000 3.38 0.00 35.82 3.57
5188 5433 6.364976 TGAATTCACTAGTCAATGTGTACGTG 59.635 38.462 3.38 0.00 35.82 4.49
5189 5434 3.571571 TCACTAGTCAATGTGTACGTGC 58.428 45.455 0.00 0.00 35.82 5.34
5190 5435 3.004944 TCACTAGTCAATGTGTACGTGCA 59.995 43.478 0.82 0.82 35.82 4.57
5191 5436 3.738791 CACTAGTCAATGTGTACGTGCAA 59.261 43.478 8.25 0.00 0.00 4.08
5192 5437 4.388773 CACTAGTCAATGTGTACGTGCAAT 59.611 41.667 8.25 1.77 0.00 3.56
5193 5438 3.811722 AGTCAATGTGTACGTGCAATG 57.188 42.857 8.25 8.35 0.00 2.82
5194 5439 2.095768 AGTCAATGTGTACGTGCAATGC 60.096 45.455 8.25 0.00 0.00 3.56
5195 5440 1.876156 TCAATGTGTACGTGCAATGCA 59.124 42.857 8.25 2.72 35.60 3.96
5209 5454 5.573296 TGCAATGCACGTTAATTTGAAAG 57.427 34.783 2.72 0.00 31.71 2.62
5210 5455 5.046529 TGCAATGCACGTTAATTTGAAAGT 58.953 33.333 2.72 0.00 31.71 2.66
5211 5456 6.209361 TGCAATGCACGTTAATTTGAAAGTA 58.791 32.000 2.72 0.00 31.71 2.24
5212 5457 6.865726 TGCAATGCACGTTAATTTGAAAGTAT 59.134 30.769 2.72 0.00 31.71 2.12
5213 5458 8.023706 TGCAATGCACGTTAATTTGAAAGTATA 58.976 29.630 2.72 0.00 31.71 1.47
5214 5459 9.019764 GCAATGCACGTTAATTTGAAAGTATAT 57.980 29.630 0.00 0.00 0.00 0.86
5227 5472 9.740239 ATTTGAAAGTATATTAAGTGCATGCAG 57.260 29.630 23.41 0.00 0.00 4.41
5228 5473 8.504812 TTGAAAGTATATTAAGTGCATGCAGA 57.495 30.769 23.41 6.71 0.00 4.26
5229 5474 8.681486 TGAAAGTATATTAAGTGCATGCAGAT 57.319 30.769 23.41 15.47 0.00 2.90
5230 5475 9.777297 TGAAAGTATATTAAGTGCATGCAGATA 57.223 29.630 23.41 14.35 0.00 1.98
5240 5485 9.830975 TTAAGTGCATGCAGATATTAAGTAAGA 57.169 29.630 23.41 0.00 0.00 2.10
5241 5486 8.915057 AAGTGCATGCAGATATTAAGTAAGAT 57.085 30.769 23.41 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 91 3.102972 AGCTGAGCTATCACTTTCTCCA 58.897 45.455 4.49 0.00 36.99 3.86
127 134 2.672996 CCTGGCCCACGGACAAAG 60.673 66.667 0.00 0.00 41.95 2.77
169 176 0.613260 CCCTTGTCAAGTCGATGGGA 59.387 55.000 11.61 0.00 35.00 4.37
171 178 1.026718 GGCCCTTGTCAAGTCGATGG 61.027 60.000 11.61 6.20 0.00 3.51
172 179 0.036010 AGGCCCTTGTCAAGTCGATG 60.036 55.000 11.61 0.00 0.00 3.84
174 181 0.034896 GAAGGCCCTTGTCAAGTCGA 59.965 55.000 0.00 0.00 0.00 4.20
176 183 1.882623 CAAGAAGGCCCTTGTCAAGTC 59.117 52.381 0.00 2.33 38.87 3.01
177 184 1.479389 CCAAGAAGGCCCTTGTCAAGT 60.479 52.381 17.38 0.00 41.34 3.16
178 185 1.202927 TCCAAGAAGGCCCTTGTCAAG 60.203 52.381 17.38 5.53 41.34 3.02
179 186 0.850100 TCCAAGAAGGCCCTTGTCAA 59.150 50.000 17.38 3.73 41.34 3.18
180 187 0.401738 CTCCAAGAAGGCCCTTGTCA 59.598 55.000 17.38 5.95 41.34 3.58
181 188 0.402121 ACTCCAAGAAGGCCCTTGTC 59.598 55.000 17.38 3.57 41.34 3.18
183 190 0.322906 GGACTCCAAGAAGGCCCTTG 60.323 60.000 0.00 13.27 38.67 3.61
184 191 0.772124 TGGACTCCAAGAAGGCCCTT 60.772 55.000 0.00 0.00 44.69 3.95
190 197 1.002544 GACCCACTGGACTCCAAGAAG 59.997 57.143 0.00 0.00 30.80 2.85
234 244 3.368571 GTCGTTCCCGGGAGACGT 61.369 66.667 35.61 0.00 42.24 4.34
412 422 4.680237 TCGACCCTTGCTGGCACG 62.680 66.667 0.00 0.00 35.43 5.34
416 426 2.266055 GAGGTCGACCCTTGCTGG 59.734 66.667 30.82 0.00 46.51 4.85
430 595 1.604185 GGATTCAGATTCCGCTCGAGG 60.604 57.143 15.58 4.19 0.00 4.63
533 701 8.703743 AGAAGAGAAACTACTCCTATAGTACGA 58.296 37.037 0.00 0.00 39.80 3.43
534 702 8.891671 AGAAGAGAAACTACTCCTATAGTACG 57.108 38.462 0.00 0.00 39.80 3.67
535 703 9.276590 GGAGAAGAGAAACTACTCCTATAGTAC 57.723 40.741 0.00 0.00 42.41 2.73
652 827 2.202810 GGAAGAAGAGCCGAGCCG 60.203 66.667 0.00 0.00 0.00 5.52
653 828 1.153469 CAGGAAGAAGAGCCGAGCC 60.153 63.158 0.00 0.00 0.00 4.70
654 829 1.813337 GCAGGAAGAAGAGCCGAGC 60.813 63.158 0.00 0.00 0.00 5.03
655 830 0.179113 GAGCAGGAAGAAGAGCCGAG 60.179 60.000 0.00 0.00 0.00 4.63
656 831 0.613292 AGAGCAGGAAGAAGAGCCGA 60.613 55.000 0.00 0.00 0.00 5.54
723 902 3.117888 AGACGTGGATGGATGCCTATTTT 60.118 43.478 0.00 0.00 0.00 1.82
728 907 0.620556 AAAGACGTGGATGGATGCCT 59.379 50.000 0.00 0.00 0.00 4.75
747 926 2.617308 TGGCGTTCGTTGTTTTTATGGA 59.383 40.909 0.00 0.00 0.00 3.41
816 998 2.827190 TCGGTCGGCTCGCACTAT 60.827 61.111 0.00 0.00 0.00 2.12
911 1098 1.139853 GAGGCGGAAGATGGATGTCTT 59.860 52.381 0.00 0.00 40.99 3.01
913 1100 0.755686 AGAGGCGGAAGATGGATGTC 59.244 55.000 0.00 0.00 0.00 3.06
915 1102 0.034616 GGAGAGGCGGAAGATGGATG 59.965 60.000 0.00 0.00 0.00 3.51
917 1104 1.001631 TGGAGAGGCGGAAGATGGA 59.998 57.895 0.00 0.00 0.00 3.41
919 1106 0.179089 CAGTGGAGAGGCGGAAGATG 60.179 60.000 0.00 0.00 0.00 2.90
923 1110 3.700109 CTCAGTGGAGAGGCGGAA 58.300 61.111 0.00 0.00 44.26 4.30
930 1129 1.074951 TGTCTCGCCTCAGTGGAGA 59.925 57.895 0.00 0.00 44.26 3.71
948 1147 0.395312 AACCCACCATCTTTCGACGT 59.605 50.000 0.00 0.00 0.00 4.34
950 1149 2.030274 CCAAAACCCACCATCTTTCGAC 60.030 50.000 0.00 0.00 0.00 4.20
1005 1204 1.225704 GAGCAACCCCATCCTCCTG 59.774 63.158 0.00 0.00 0.00 3.86
1006 1205 2.370445 CGAGCAACCCCATCCTCCT 61.370 63.158 0.00 0.00 0.00 3.69
1109 1308 1.080329 AGGAAGAAGAAGAGGGAGGCT 59.920 52.381 0.00 0.00 0.00 4.58
1133 1335 0.848053 AACCAGGGAAAACGGAGGAA 59.152 50.000 0.00 0.00 0.00 3.36
1142 1344 0.704076 CCCATCCAGAACCAGGGAAA 59.296 55.000 0.00 0.00 42.25 3.13
1146 1348 0.475906 GATCCCCATCCAGAACCAGG 59.524 60.000 0.00 0.00 0.00 4.45
1174 1376 6.183360 CCGTCCCTATCTATAAGAATGAGAGC 60.183 46.154 0.00 0.00 0.00 4.09
1186 1388 8.554870 TGTACTATTACATCCGTCCCTATCTAT 58.445 37.037 0.00 0.00 32.98 1.98
1248 1451 6.544564 TGAAAGGGACTCGTAATCAAAAGTTT 59.455 34.615 0.00 0.00 38.49 2.66
1258 1461 6.531021 AGAAAAAGATGAAAGGGACTCGTAA 58.469 36.000 0.00 0.00 38.49 3.18
1288 1491 5.488341 TGAGTAAACAACAGAGGCCTATTC 58.512 41.667 4.42 0.00 0.00 1.75
1290 1493 5.431765 CATGAGTAAACAACAGAGGCCTAT 58.568 41.667 4.42 0.00 0.00 2.57
1346 1549 3.054875 AGAAACAGCCTGTGATGCTCATA 60.055 43.478 0.00 0.00 36.81 2.15
1435 1640 5.391312 AGGCAAACTGACCATATTTTGTC 57.609 39.130 0.00 0.00 34.46 3.18
1439 1644 5.951747 ACATGTAGGCAAACTGACCATATTT 59.048 36.000 0.00 0.00 0.00 1.40
1446 1651 5.186198 AGGATTACATGTAGGCAAACTGAC 58.814 41.667 5.56 0.00 0.00 3.51
1581 1786 1.134367 GTGCCTAAAATTTCCTCCGCC 59.866 52.381 0.00 0.00 0.00 6.13
1605 1810 4.997395 AGTTCATCATAAGCAAACGTCTGT 59.003 37.500 0.00 0.00 0.00 3.41
1637 1842 5.341407 CTTCAGCTCACTCTTTGAAGAAC 57.659 43.478 7.16 0.00 45.82 3.01
1648 1853 0.894141 AGCATCGTCTTCAGCTCACT 59.106 50.000 0.00 0.00 30.05 3.41
1653 1858 1.645034 TAAGCAGCATCGTCTTCAGC 58.355 50.000 0.00 0.00 0.00 4.26
1790 1995 5.253330 AGAAGTCTGAACCAAACAAGAACA 58.747 37.500 0.00 0.00 0.00 3.18
1798 2003 6.433847 TCTTGGATAGAAGTCTGAACCAAA 57.566 37.500 0.00 0.00 35.33 3.28
1850 2055 1.834263 CTCCGGAAGAAGGACCATCTT 59.166 52.381 11.73 11.73 39.76 2.40
1856 2061 0.974383 TTCACCTCCGGAAGAAGGAC 59.026 55.000 14.09 0.00 33.58 3.85
1863 2068 1.640917 ACTTAGCTTCACCTCCGGAA 58.359 50.000 5.23 0.00 0.00 4.30
1879 2084 5.802821 GCTCCATCAGAGAAAGAGGAAACTT 60.803 44.000 0.00 0.00 46.50 2.66
1880 2085 4.323409 GCTCCATCAGAGAAAGAGGAAACT 60.323 45.833 0.00 0.00 46.50 2.66
1914 2119 0.536460 TGTTCGGAAAGTTGGGAGGC 60.536 55.000 0.00 0.00 0.00 4.70
1925 2130 1.007038 CGAGGTTCGGTGTTCGGAA 60.007 57.895 0.00 0.00 39.77 4.30
1950 2155 2.490509 TGCAGGTTTATCTTCGAGACGA 59.509 45.455 0.00 0.00 0.00 4.20
1952 2157 4.929808 TCTTTGCAGGTTTATCTTCGAGAC 59.070 41.667 0.00 0.00 0.00 3.36
2088 2293 3.942829 TCCACAGCAGTAGAAAATCAGG 58.057 45.455 0.00 0.00 0.00 3.86
2151 2356 3.262660 ACTGCATGTGAAGAAGAGGATGA 59.737 43.478 0.00 0.00 0.00 2.92
2174 2379 3.286751 CACCAGGTGTGTTGGCCG 61.287 66.667 11.99 0.00 40.26 6.13
2178 2383 0.751277 TTGCCTCACCAGGTGTGTTG 60.751 55.000 19.65 6.52 45.61 3.33
2184 2389 1.380302 GGACATTGCCTCACCAGGT 59.620 57.895 0.00 0.00 42.74 4.00
2199 2404 5.221541 CCATCATAGGTAGACAGAAAGGGAC 60.222 48.000 0.00 0.00 0.00 4.46
2206 2411 4.620723 ACAACCCATCATAGGTAGACAGA 58.379 43.478 0.00 0.00 36.27 3.41
2207 2412 5.129485 AGAACAACCCATCATAGGTAGACAG 59.871 44.000 0.00 0.00 36.27 3.51
2212 2417 4.538490 ACCAAGAACAACCCATCATAGGTA 59.462 41.667 0.00 0.00 36.27 3.08
2220 2425 1.063266 ACCACACCAAGAACAACCCAT 60.063 47.619 0.00 0.00 0.00 4.00
2224 2429 8.500753 TGATATAATACCACACCAAGAACAAC 57.499 34.615 0.00 0.00 0.00 3.32
2254 2459 4.201657 ACGATCCTGCATGAAATTGATGA 58.798 39.130 0.00 0.00 0.00 2.92
2389 2594 1.432514 CGGGAGTTGACACATCACTG 58.567 55.000 0.00 0.00 33.38 3.66
2391 2596 1.626654 CGCGGGAGTTGACACATCAC 61.627 60.000 0.00 0.00 33.38 3.06
2635 2840 1.517242 CACCCACTTCAGCTTCAGAC 58.483 55.000 0.00 0.00 0.00 3.51
3025 3230 1.819288 TGGACGAAGAGCTACCTTCAG 59.181 52.381 13.78 9.48 41.89 3.02
3052 3257 9.454585 CAAGCTACATGACCAATTAACAATATG 57.545 33.333 0.00 0.00 0.00 1.78
3053 3258 8.137437 GCAAGCTACATGACCAATTAACAATAT 58.863 33.333 0.00 0.00 0.00 1.28
3061 3266 6.377996 TGAATAAGCAAGCTACATGACCAATT 59.622 34.615 0.00 0.00 0.00 2.32
3109 3314 4.219070 AGAATGCTGCTTTTATCTGTGCAA 59.781 37.500 0.00 0.00 34.90 4.08
3122 3327 3.015327 GGAAATGTCAGAGAATGCTGCT 58.985 45.455 0.00 0.00 35.86 4.24
3194 3399 8.464404 TCATCATTTGGTTTCATTCTCAAGATC 58.536 33.333 0.00 0.00 0.00 2.75
3236 3441 2.170012 AGTCCCCATCGTAAAGCCTA 57.830 50.000 0.00 0.00 0.00 3.93
3405 3610 4.941263 ACACAAGTCAACTGCTTTCACTTA 59.059 37.500 0.00 0.00 0.00 2.24
3425 3630 7.816640 TGGAGTGCTTTTCAGATTTAATACAC 58.183 34.615 0.00 0.00 0.00 2.90
3460 3665 7.755373 GCCTGACACCAAAAAGATAGTAATTTC 59.245 37.037 0.00 0.00 0.00 2.17
3465 3670 5.245531 CAGCCTGACACCAAAAAGATAGTA 58.754 41.667 0.00 0.00 0.00 1.82
3511 3716 4.914504 GCTTCTAGCAGTTTCAGAAAAAGC 59.085 41.667 11.21 11.21 41.89 3.51
3523 3728 6.203723 CAGTTTTAAGAACAGCTTCTAGCAGT 59.796 38.462 1.09 0.00 45.56 4.40
3541 3746 6.267070 GTCATTCAAACGGTTTCCAGTTTTA 58.733 36.000 2.51 0.00 38.37 1.52
3700 3905 1.186917 CCATGGCCAACCTTGCTTCA 61.187 55.000 10.96 0.00 39.30 3.02
3874 4079 3.012518 GAGTTGCAATACACTGGCAGAT 58.987 45.455 23.66 11.38 38.97 2.90
3991 4196 2.419713 GGTCTCATTCTCTGCATGCTCA 60.420 50.000 20.33 3.99 0.00 4.26
3994 4199 2.034104 TGGTCTCATTCTCTGCATGC 57.966 50.000 11.82 11.82 0.00 4.06
4039 4244 5.530915 TGTTTTCTTCACCAACGATCTCAAT 59.469 36.000 0.00 0.00 0.00 2.57
4048 4253 3.067601 ACCGGATTGTTTTCTTCACCAAC 59.932 43.478 9.46 0.00 0.00 3.77
4099 4304 5.324409 ACAATGACAAAGAGGCTAAATCCA 58.676 37.500 0.00 0.00 0.00 3.41
4225 4430 2.173569 CTCCTGGGGATTTAACTGGGAG 59.826 54.545 0.00 0.00 34.17 4.30
4387 4592 8.607441 ATGTGGCATTTGTATGTATACAGTAG 57.393 34.615 11.91 0.00 43.44 2.57
4424 4634 4.116961 GCCTCTGCAAACATGTACGTATA 58.883 43.478 0.00 0.00 37.47 1.47
4428 4638 1.155889 TGCCTCTGCAAACATGTACG 58.844 50.000 0.00 0.00 46.66 3.67
4565 4777 9.143631 CTGATCAGGAAATTGTGAATTAAAACC 57.856 33.333 15.38 0.00 0.00 3.27
4641 4854 9.494271 GGAAATTTAAAGAGAAGCTTGGAATTT 57.506 29.630 2.10 5.81 40.63 1.82
4642 4855 8.650490 TGGAAATTTAAAGAGAAGCTTGGAATT 58.350 29.630 2.10 0.00 36.80 2.17
4643 4856 8.193953 TGGAAATTTAAAGAGAAGCTTGGAAT 57.806 30.769 2.10 0.00 36.80 3.01
4644 4857 7.595819 TGGAAATTTAAAGAGAAGCTTGGAA 57.404 32.000 2.10 0.00 36.80 3.53
4645 4858 7.595819 TTGGAAATTTAAAGAGAAGCTTGGA 57.404 32.000 2.10 0.00 36.80 3.53
4646 4859 8.551205 GTTTTGGAAATTTAAAGAGAAGCTTGG 58.449 33.333 2.10 0.00 36.80 3.61
4647 4860 8.551205 GGTTTTGGAAATTTAAAGAGAAGCTTG 58.449 33.333 2.10 0.00 36.80 4.01
4648 4861 8.264347 TGGTTTTGGAAATTTAAAGAGAAGCTT 58.736 29.630 0.00 0.00 38.88 3.74
4649 4862 7.710907 GTGGTTTTGGAAATTTAAAGAGAAGCT 59.289 33.333 0.00 0.00 0.00 3.74
4650 4863 7.306574 CGTGGTTTTGGAAATTTAAAGAGAAGC 60.307 37.037 0.00 0.00 0.00 3.86
4651 4864 7.918562 TCGTGGTTTTGGAAATTTAAAGAGAAG 59.081 33.333 0.00 0.00 0.00 2.85
4652 4865 7.773149 TCGTGGTTTTGGAAATTTAAAGAGAA 58.227 30.769 0.00 0.00 0.00 2.87
4653 4866 7.336161 TCGTGGTTTTGGAAATTTAAAGAGA 57.664 32.000 0.00 0.00 0.00 3.10
4654 4867 6.143919 GCTCGTGGTTTTGGAAATTTAAAGAG 59.856 38.462 0.00 0.00 0.00 2.85
4655 4868 5.980715 GCTCGTGGTTTTGGAAATTTAAAGA 59.019 36.000 0.00 0.00 0.00 2.52
4656 4869 5.751028 TGCTCGTGGTTTTGGAAATTTAAAG 59.249 36.000 0.00 0.00 0.00 1.85
4657 4870 5.661458 TGCTCGTGGTTTTGGAAATTTAAA 58.339 33.333 0.00 0.00 0.00 1.52
4658 4871 5.067936 TCTGCTCGTGGTTTTGGAAATTTAA 59.932 36.000 0.00 0.00 0.00 1.52
4717 4930 0.750249 TCGAGCTCACAAACTCCACA 59.250 50.000 15.40 0.00 0.00 4.17
4788 5018 1.888512 ACACATTGATGTCTGTTGCCC 59.111 47.619 0.00 0.00 39.39 5.36
4838 5069 9.829507 TTAATCCAAACTTTCACAAATGTCATT 57.170 25.926 0.00 0.00 0.00 2.57
4870 5101 3.666274 TCCTTTTTGGAGCGTCGATTTA 58.334 40.909 0.00 0.00 40.56 1.40
4917 5149 2.548057 GACATTCGTGGAAGTTTGAGCA 59.452 45.455 0.00 0.00 0.00 4.26
5009 5244 9.240159 GAACAGTAAAACCGTGTGAAATAAAAT 57.760 29.630 0.00 0.00 0.00 1.82
5157 5402 7.915397 ACACATTGACTAGTGAATTCAAACAAC 59.085 33.333 10.35 3.26 39.03 3.32
5158 5403 7.995289 ACACATTGACTAGTGAATTCAAACAA 58.005 30.769 10.35 11.88 39.03 2.83
5171 5416 4.724885 GCATTGCACGTACACATTGACTAG 60.725 45.833 3.15 0.00 0.00 2.57
5172 5417 3.124466 GCATTGCACGTACACATTGACTA 59.876 43.478 3.15 0.00 0.00 2.59
5173 5418 2.095768 GCATTGCACGTACACATTGACT 60.096 45.455 3.15 0.00 0.00 3.41
5174 5419 2.241722 GCATTGCACGTACACATTGAC 58.758 47.619 3.15 1.49 0.00 3.18
5175 5420 1.876156 TGCATTGCACGTACACATTGA 59.124 42.857 7.38 0.00 31.71 2.57
5176 5421 2.328655 TGCATTGCACGTACACATTG 57.671 45.000 7.38 0.00 31.71 2.82
5187 5432 5.046529 ACTTTCAAATTAACGTGCATTGCA 58.953 33.333 7.38 7.38 35.60 4.08
5188 5433 5.574815 ACTTTCAAATTAACGTGCATTGC 57.425 34.783 0.46 0.46 0.00 3.56
5201 5446 9.740239 CTGCATGCACTTAATATACTTTCAAAT 57.260 29.630 18.46 0.00 0.00 2.32
5202 5447 8.955388 TCTGCATGCACTTAATATACTTTCAAA 58.045 29.630 18.46 0.00 0.00 2.69
5203 5448 8.504812 TCTGCATGCACTTAATATACTTTCAA 57.495 30.769 18.46 0.00 0.00 2.69
5204 5449 8.681486 ATCTGCATGCACTTAATATACTTTCA 57.319 30.769 18.46 0.00 0.00 2.69
5214 5459 9.830975 TCTTACTTAATATCTGCATGCACTTAA 57.169 29.630 18.46 15.72 0.00 1.85
5216 5461 8.915057 ATCTTACTTAATATCTGCATGCACTT 57.085 30.769 18.46 9.62 0.00 3.16


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

AutoCloner maintained by Alex Coulton.