Multiple sequence alignment - TraesCS5B01G222900

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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 TraesCS5B01G222900 chr5B 100.000 2222 0 0 1 2222 397839137 397836916 0.000000e+00 4104.0
1 TraesCS5B01G222900 chr5A 89.885 1473 95 28 1 1456 439557235 439555800 0.000000e+00 1845.0
2 TraesCS5B01G222900 chr5A 81.653 714 40 23 1464 2149 439555486 439554836 1.970000e-140 508.0
3 TraesCS5B01G222900 chr5D 87.811 1288 97 25 410 1680 338666210 338664966 0.000000e+00 1454.0
4 TraesCS5B01G222900 chr5D 88.372 215 13 5 1 204 338666676 338666463 4.740000e-62 248.0
5 TraesCS5B01G222900 chr5D 93.103 58 4 0 1740 1797 338664942 338664885 3.930000e-13 86.1
6 TraesCS5B01G222900 chr6A 79.268 164 34 0 1060 1223 587563970 587564133 5.010000e-22 115.0
7 TraesCS5B01G222900 chr6B 78.788 165 35 0 1060 1224 663800525 663800689 6.490000e-21 111.0
8 TraesCS5B01G222900 chr6D 82.500 120 21 0 1060 1179 438460921 438461040 3.020000e-19 106.0
9 TraesCS5B01G222900 chr7A 78.667 150 17 8 850 994 10888702 10888841 3.930000e-13 86.1


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 TraesCS5B01G222900 chr5B 397836916 397839137 2221 True 4104.000000 4104 100.000 1 2222 1 chr5B.!!$R1 2221
1 TraesCS5B01G222900 chr5A 439554836 439557235 2399 True 1176.500000 1845 85.769 1 2149 2 chr5A.!!$R1 2148
2 TraesCS5B01G222900 chr5D 338664885 338666676 1791 True 596.033333 1454 89.762 1 1797 3 chr5D.!!$R1 1796

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
942 1083 0.475906 AGCTGTTGGTCTTCTTGCCT 59.524 50.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 2679 0.254462 TGCGGCAATGTCCCTCAATA 59.746 50.0 0.0 0.0 0.0 1.9 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
141 152 3.317993 GCAGTCTGCCCTCTTTACAAAAA 59.682 43.478 14.27 0.00 37.42 1.94
166 185 5.343249 GTTGTCTATGCAAATCATGGAACC 58.657 41.667 0.00 0.00 43.06 3.62
202 221 5.306678 TGTTTCCCTTGATTTTACTTGCCAT 59.693 36.000 0.00 0.00 0.00 4.40
204 223 7.015682 TGTTTCCCTTGATTTTACTTGCCATTA 59.984 33.333 0.00 0.00 0.00 1.90
206 225 6.930731 TCCCTTGATTTTACTTGCCATTAAC 58.069 36.000 0.00 0.00 0.00 2.01
207 226 6.723977 TCCCTTGATTTTACTTGCCATTAACT 59.276 34.615 0.00 0.00 0.00 2.24
209 228 7.378181 CCTTGATTTTACTTGCCATTAACTGT 58.622 34.615 0.00 0.00 0.00 3.55
211 230 9.559958 CTTGATTTTACTTGCCATTAACTGTAG 57.440 33.333 0.00 0.00 0.00 2.74
212 231 7.535139 TGATTTTACTTGCCATTAACTGTAGC 58.465 34.615 0.00 0.00 0.00 3.58
213 232 7.393234 TGATTTTACTTGCCATTAACTGTAGCT 59.607 33.333 0.00 0.00 0.00 3.32
215 234 4.559862 ACTTGCCATTAACTGTAGCTCT 57.440 40.909 0.00 0.00 0.00 4.09
216 235 4.256920 ACTTGCCATTAACTGTAGCTCTG 58.743 43.478 0.00 0.00 0.00 3.35
217 236 3.981071 TGCCATTAACTGTAGCTCTGT 57.019 42.857 0.00 0.00 0.00 3.41
219 238 5.414789 TGCCATTAACTGTAGCTCTGTAA 57.585 39.130 0.00 0.00 0.00 2.41
242 261 4.891756 AGCTCCATTTGGGTTGATCATAAG 59.108 41.667 0.00 0.00 38.11 1.73
268 287 5.465724 AGTTTGTTACCTCAACATCTCGAAC 59.534 40.000 0.00 0.00 46.38 3.95
294 313 5.489249 TGTTGACAACACTGTTAAGGTACA 58.511 37.500 17.02 0.00 36.25 2.90
295 314 6.116806 TGTTGACAACACTGTTAAGGTACAT 58.883 36.000 17.02 0.00 36.25 2.29
296 315 7.273712 TGTTGACAACACTGTTAAGGTACATA 58.726 34.615 17.02 0.00 36.25 2.29
297 316 7.225145 TGTTGACAACACTGTTAAGGTACATAC 59.775 37.037 17.02 0.00 36.25 2.39
301 320 7.086376 ACAACACTGTTAAGGTACATACTACG 58.914 38.462 0.00 0.00 28.57 3.51
397 451 3.960755 TGTTGTTCTTCTGAGACTCCTGA 59.039 43.478 0.00 0.00 0.00 3.86
425 563 2.604914 CACAAGGAGCTAGTATGTTGCG 59.395 50.000 0.00 0.00 0.00 4.85
510 650 5.790593 ACACTACTTAGCTTTCGAATTGGA 58.209 37.500 0.00 0.00 0.00 3.53
590 730 7.224297 ACTGATACTTTGTTGCCTTCTAAGAA 58.776 34.615 0.00 0.00 0.00 2.52
595 735 1.418637 TGTTGCCTTCTAAGAACCGGT 59.581 47.619 0.00 0.00 0.00 5.28
600 740 4.510571 TGCCTTCTAAGAACCGGTTAATC 58.489 43.478 22.33 8.46 0.00 1.75
684 824 2.941064 CAGATTCCGTGATGCTGTTGAT 59.059 45.455 0.00 0.00 0.00 2.57
698 838 7.339976 TGATGCTGTTGATTTCCATTATCTGAA 59.660 33.333 0.00 0.00 0.00 3.02
699 839 7.649533 TGCTGTTGATTTCCATTATCTGAAT 57.350 32.000 0.00 0.00 0.00 2.57
728 868 7.334421 ACTGTTTACACTGAACATGATCATACC 59.666 37.037 8.15 1.24 36.51 2.73
799 939 8.300286 TGTTCTGAACATGTTGAAACAAGTAAA 58.700 29.630 17.58 0.00 39.62 2.01
838 978 9.643693 AATGAATTATGTGTAGGCTTTTCAAAG 57.356 29.630 0.00 0.00 39.03 2.77
845 985 1.332195 AGGCTTTTCAAAGTCCAGGC 58.668 50.000 12.43 2.87 41.45 4.85
861 1001 2.286772 CCAGGCAACGAAAACTGTGTAC 60.287 50.000 0.00 0.00 46.39 2.90
898 1039 2.814336 CAGGTTCAGTGTTCTAAAGCCC 59.186 50.000 0.00 0.00 0.00 5.19
904 1045 1.073923 AGTGTTCTAAAGCCCCTGTGG 59.926 52.381 0.00 0.00 37.09 4.17
937 1078 2.037772 ACAATCGAGCTGTTGGTCTTCT 59.962 45.455 0.00 0.00 38.45 2.85
942 1083 0.475906 AGCTGTTGGTCTTCTTGCCT 59.524 50.000 0.00 0.00 0.00 4.75
958 1099 3.143807 TGCCTCGTTTTGTTTTGACAG 57.856 42.857 0.00 0.00 0.00 3.51
998 1139 7.172703 GGTACCATTACGATTTATTTCAGAGGG 59.827 40.741 7.15 0.00 0.00 4.30
1241 1383 3.188667 TGATACGTTCATAGCGGCTCTAG 59.811 47.826 5.39 0.00 0.00 2.43
1251 1393 1.671901 GCGGCTCTAGACTTGCTCCT 61.672 60.000 2.84 0.00 0.00 3.69
1261 1406 0.109342 ACTTGCTCCTGTGGTTCTGG 59.891 55.000 0.00 0.00 36.63 3.86
1277 1422 1.338655 TCTGGACGACGAACAATGTCA 59.661 47.619 0.00 0.00 36.11 3.58
1289 1434 6.483687 ACGAACAATGTCAGTTAACAGTTTC 58.516 36.000 8.61 0.00 31.50 2.78
1293 1438 7.807977 ACAATGTCAGTTAACAGTTTCATCT 57.192 32.000 8.61 0.00 31.50 2.90
1315 1460 1.976474 GGCATTCCAGTTTGCGGGA 60.976 57.895 0.00 0.00 39.78 5.14
1325 1470 0.966179 GTTTGCGGGAAGGGATGTTT 59.034 50.000 0.00 0.00 0.00 2.83
1345 1491 5.147767 GTTTTCCCCCTAATAGGCATTCAT 58.852 41.667 0.00 0.00 32.73 2.57
1363 1510 7.443259 CATTCATGCCACAGATAATGTATGA 57.557 36.000 0.00 0.00 41.41 2.15
1408 1557 2.380064 TGGCTTCTCCAAATGGTGTT 57.620 45.000 0.00 0.00 43.21 3.32
1412 1561 4.837860 TGGCTTCTCCAAATGGTGTTATTT 59.162 37.500 0.00 0.00 43.21 1.40
1569 2034 2.118404 CACCACACGGTTTGCTGGT 61.118 57.895 0.00 0.00 46.31 4.00
1609 2084 0.384309 GCTCGTATCGTGTGGATGGA 59.616 55.000 0.00 0.00 36.55 3.41
1610 2085 1.864435 GCTCGTATCGTGTGGATGGAC 60.864 57.143 0.00 0.00 36.55 4.02
1611 2086 0.379316 TCGTATCGTGTGGATGGACG 59.621 55.000 0.00 0.00 38.08 4.79
1612 2087 1.206745 CGTATCGTGTGGATGGACGC 61.207 60.000 0.00 0.00 36.55 5.19
1613 2088 0.179121 GTATCGTGTGGATGGACGCA 60.179 55.000 0.00 0.00 36.55 5.24
1614 2089 0.102300 TATCGTGTGGATGGACGCAG 59.898 55.000 0.00 0.00 36.55 5.18
1615 2090 3.490759 CGTGTGGATGGACGCAGC 61.491 66.667 0.00 0.00 0.00 5.25
1616 2091 2.046892 GTGTGGATGGACGCAGCT 60.047 61.111 0.00 0.00 0.00 4.24
1617 2092 2.046988 TGTGGATGGACGCAGCTG 60.047 61.111 10.11 10.11 0.00 4.24
1618 2093 2.821366 GTGGATGGACGCAGCTGG 60.821 66.667 17.12 8.27 0.00 4.85
1706 2188 5.911280 TGAACTTTGAGTAGACGAGTTTACG 59.089 40.000 0.00 0.00 39.31 3.18
1797 2292 1.227556 GCACGGGTATGCCAGTAGG 60.228 63.158 5.14 0.00 41.23 3.18
1798 2293 1.968050 GCACGGGTATGCCAGTAGGT 61.968 60.000 5.14 0.00 41.23 3.08
1799 2294 0.179084 CACGGGTATGCCAGTAGGTG 60.179 60.000 5.14 0.00 41.23 4.00
1800 2295 0.324923 ACGGGTATGCCAGTAGGTGA 60.325 55.000 3.33 0.00 41.37 4.02
1801 2296 1.048601 CGGGTATGCCAGTAGGTGAT 58.951 55.000 1.04 0.00 37.19 3.06
1802 2297 1.270305 CGGGTATGCCAGTAGGTGATG 60.270 57.143 1.04 0.00 37.19 3.07
1803 2298 1.768870 GGGTATGCCAGTAGGTGATGT 59.231 52.381 1.04 0.00 37.19 3.06
1804 2299 2.224305 GGGTATGCCAGTAGGTGATGTC 60.224 54.545 1.04 0.00 37.19 3.06
1805 2300 2.434336 GGTATGCCAGTAGGTGATGTCA 59.566 50.000 0.00 0.00 37.19 3.58
1806 2301 2.996249 ATGCCAGTAGGTGATGTCAG 57.004 50.000 0.00 0.00 37.19 3.51
1807 2302 1.937191 TGCCAGTAGGTGATGTCAGA 58.063 50.000 0.00 0.00 37.19 3.27
1808 2303 2.256306 TGCCAGTAGGTGATGTCAGAA 58.744 47.619 0.00 0.00 37.19 3.02
1809 2304 2.637382 TGCCAGTAGGTGATGTCAGAAA 59.363 45.455 0.00 0.00 37.19 2.52
1810 2305 3.072330 TGCCAGTAGGTGATGTCAGAAAA 59.928 43.478 0.00 0.00 37.19 2.29
1811 2306 4.072131 GCCAGTAGGTGATGTCAGAAAAA 58.928 43.478 0.00 0.00 37.19 1.94
1842 2337 2.746279 TTCCCAAAAGAGTTGCAGGA 57.254 45.000 0.00 0.00 0.00 3.86
1844 2339 3.025322 TCCCAAAAGAGTTGCAGGAAA 57.975 42.857 0.00 0.00 0.00 3.13
1845 2340 2.958355 TCCCAAAAGAGTTGCAGGAAAG 59.042 45.455 0.00 0.00 0.00 2.62
1848 2343 4.141959 CCCAAAAGAGTTGCAGGAAAGAAA 60.142 41.667 0.00 0.00 0.00 2.52
1872 2367 0.678950 AATTGCGAACCAACTTGGGG 59.321 50.000 12.62 2.54 43.37 4.96
1888 2383 1.272092 TGGGGCCTCTTTGATTCACAG 60.272 52.381 3.07 0.00 0.00 3.66
1889 2384 1.004745 GGGGCCTCTTTGATTCACAGA 59.995 52.381 0.84 2.70 0.00 3.41
1890 2385 2.555227 GGGGCCTCTTTGATTCACAGAA 60.555 50.000 0.84 0.00 0.00 3.02
1946 2441 9.889128 TCAGTTCATAATCAAATCATGACAGTA 57.111 29.630 0.00 0.00 41.93 2.74
1963 2458 9.980780 CATGACAGTATAAGTATAGAGATCACG 57.019 37.037 0.00 0.00 0.00 4.35
2005 2503 8.691661 ACAACCAAATATATGGACCATCTAAC 57.308 34.615 11.17 0.00 43.54 2.34
2008 2506 7.159372 ACCAAATATATGGACCATCTAACGAC 58.841 38.462 11.17 0.00 43.54 4.34
2011 2509 7.406031 AATATATGGACCATCTAACGACGAT 57.594 36.000 11.17 0.00 0.00 3.73
2023 2521 1.710013 ACGACGATTACAAGCACTGG 58.290 50.000 0.00 0.00 0.00 4.00
2026 2524 2.415491 CGACGATTACAAGCACTGGAGA 60.415 50.000 0.00 0.00 0.00 3.71
2030 2528 2.751166 TTACAAGCACTGGAGAGAGC 57.249 50.000 0.00 0.00 36.14 4.09
2036 2534 1.599606 GCACTGGAGAGAGCCGAAGA 61.600 60.000 0.00 0.00 30.07 2.87
2037 2535 0.891373 CACTGGAGAGAGCCGAAGAA 59.109 55.000 0.00 0.00 0.00 2.52
2045 2543 4.314440 AGCCGAAGAAGCGCCACA 62.314 61.111 2.29 0.00 34.64 4.17
2066 2564 2.350057 TCATCGTCCTCCCTCACTAG 57.650 55.000 0.00 0.00 0.00 2.57
2069 2567 0.107116 TCGTCCTCCCTCACTAGAGC 60.107 60.000 0.00 0.00 40.68 4.09
2071 2569 1.141254 CGTCCTCCCTCACTAGAGCTA 59.859 57.143 0.00 0.00 40.68 3.32
2088 2586 5.675538 AGAGCTAGGCAAACTTTATGGTAG 58.324 41.667 0.00 0.00 0.00 3.18
2096 2595 5.163824 GGCAAACTTTATGGTAGTAACGGTC 60.164 44.000 0.00 0.00 0.00 4.79
2105 2604 1.812571 GTAGTAACGGTCGGGAAGTCA 59.187 52.381 0.00 0.00 0.00 3.41
2122 2621 3.525537 AGTCATCGTGCGAAAATCTCAT 58.474 40.909 0.00 0.00 0.00 2.90
2131 2630 2.545946 GCGAAAATCTCATAGGACCAGC 59.454 50.000 0.00 0.00 0.00 4.85
2134 2633 1.418334 AATCTCATAGGACCAGCGCT 58.582 50.000 2.64 2.64 0.00 5.92
2137 2636 2.093537 CTCATAGGACCAGCGCTCCC 62.094 65.000 7.13 9.67 0.00 4.30
2140 2639 3.949885 TAGGACCAGCGCTCCCGAA 62.950 63.158 7.13 0.43 36.29 4.30
2141 2640 4.162690 GGACCAGCGCTCCCGAAT 62.163 66.667 7.13 0.00 36.29 3.34
2149 2648 1.891060 GCGCTCCCGAATAGCAATCG 61.891 60.000 0.00 0.00 40.08 3.34
2150 2649 0.597637 CGCTCCCGAATAGCAATCGT 60.598 55.000 5.33 0.00 40.08 3.73
2151 2650 1.140816 GCTCCCGAATAGCAATCGTC 58.859 55.000 5.33 0.00 39.83 4.20
2152 2651 1.409412 CTCCCGAATAGCAATCGTCG 58.591 55.000 5.33 0.00 38.60 5.12
2153 2652 1.001706 CTCCCGAATAGCAATCGTCGA 60.002 52.381 0.00 0.00 38.60 4.20
2154 2653 1.001706 TCCCGAATAGCAATCGTCGAG 60.002 52.381 0.00 0.00 38.60 4.04
2155 2654 1.409412 CCGAATAGCAATCGTCGAGG 58.591 55.000 0.00 0.00 38.60 4.63
2156 2655 1.001706 CCGAATAGCAATCGTCGAGGA 60.002 52.381 10.66 10.66 38.60 3.71
2157 2656 2.351835 CCGAATAGCAATCGTCGAGGAT 60.352 50.000 14.64 14.64 38.60 3.24
2158 2657 2.911723 CGAATAGCAATCGTCGAGGATC 59.088 50.000 20.03 9.50 35.54 3.36
2159 2658 3.609409 CGAATAGCAATCGTCGAGGATCA 60.609 47.826 20.03 7.43 35.54 2.92
2160 2659 4.299155 GAATAGCAATCGTCGAGGATCAA 58.701 43.478 20.03 7.42 33.17 2.57
2161 2660 2.672961 AGCAATCGTCGAGGATCAAA 57.327 45.000 20.03 0.00 33.17 2.69
2162 2661 2.271800 AGCAATCGTCGAGGATCAAAC 58.728 47.619 20.03 10.35 33.17 2.93
2163 2662 2.093973 AGCAATCGTCGAGGATCAAACT 60.094 45.455 20.03 12.18 33.17 2.66
2164 2663 2.673368 GCAATCGTCGAGGATCAAACTT 59.327 45.455 20.03 2.52 33.17 2.66
2165 2664 3.484229 GCAATCGTCGAGGATCAAACTTG 60.484 47.826 20.03 14.85 33.17 3.16
2166 2665 2.363788 TCGTCGAGGATCAAACTTGG 57.636 50.000 3.17 0.00 33.17 3.61
2167 2666 1.890489 TCGTCGAGGATCAAACTTGGA 59.110 47.619 3.17 0.00 33.17 3.53
2168 2667 2.297880 TCGTCGAGGATCAAACTTGGAA 59.702 45.455 3.17 0.00 33.17 3.53
2169 2668 2.668457 CGTCGAGGATCAAACTTGGAAG 59.332 50.000 0.00 0.00 33.17 3.46
2170 2669 3.614150 CGTCGAGGATCAAACTTGGAAGA 60.614 47.826 0.00 0.00 33.17 2.87
2171 2670 3.680458 GTCGAGGATCAAACTTGGAAGAC 59.320 47.826 0.00 0.00 33.17 3.01
2172 2671 3.323691 TCGAGGATCAAACTTGGAAGACA 59.676 43.478 0.00 0.00 33.17 3.41
2173 2672 4.020218 TCGAGGATCAAACTTGGAAGACAT 60.020 41.667 0.00 0.00 33.17 3.06
2174 2673 4.697352 CGAGGATCAAACTTGGAAGACATT 59.303 41.667 0.00 0.00 33.17 2.71
2175 2674 5.874810 CGAGGATCAAACTTGGAAGACATTA 59.125 40.000 0.00 0.00 33.17 1.90
2176 2675 6.183360 CGAGGATCAAACTTGGAAGACATTAC 60.183 42.308 0.00 0.00 33.17 1.89
2177 2676 6.784031 AGGATCAAACTTGGAAGACATTACT 58.216 36.000 0.00 0.00 0.00 2.24
2178 2677 6.881602 AGGATCAAACTTGGAAGACATTACTC 59.118 38.462 0.00 0.00 0.00 2.59
2179 2678 6.094186 GGATCAAACTTGGAAGACATTACTCC 59.906 42.308 0.00 0.00 0.00 3.85
2180 2679 6.187727 TCAAACTTGGAAGACATTACTCCT 57.812 37.500 0.00 0.00 0.00 3.69
2181 2680 7.311092 TCAAACTTGGAAGACATTACTCCTA 57.689 36.000 0.00 0.00 0.00 2.94
2182 2681 7.918076 TCAAACTTGGAAGACATTACTCCTAT 58.082 34.615 0.00 0.00 0.00 2.57
2183 2682 8.383175 TCAAACTTGGAAGACATTACTCCTATT 58.617 33.333 0.00 0.00 0.00 1.73
2184 2683 8.454106 CAAACTTGGAAGACATTACTCCTATTG 58.546 37.037 0.00 0.00 0.00 1.90
2185 2684 7.496346 ACTTGGAAGACATTACTCCTATTGA 57.504 36.000 0.00 0.00 0.00 2.57
2187 2686 6.485830 TGGAAGACATTACTCCTATTGAGG 57.514 41.667 0.00 0.00 46.01 3.86
2188 2687 5.366768 TGGAAGACATTACTCCTATTGAGGG 59.633 44.000 0.00 0.00 46.01 4.30
2189 2688 5.602978 GGAAGACATTACTCCTATTGAGGGA 59.397 44.000 0.00 0.00 46.01 4.20
2190 2689 6.463190 GGAAGACATTACTCCTATTGAGGGAC 60.463 46.154 0.00 0.00 46.01 4.46
2191 2690 5.529289 AGACATTACTCCTATTGAGGGACA 58.471 41.667 0.00 0.00 46.01 4.02
2192 2691 6.146760 AGACATTACTCCTATTGAGGGACAT 58.853 40.000 0.00 0.00 46.01 3.06
2193 2692 6.617371 AGACATTACTCCTATTGAGGGACATT 59.383 38.462 0.00 0.00 46.01 2.71
2194 2693 6.595682 ACATTACTCCTATTGAGGGACATTG 58.404 40.000 0.00 0.00 46.01 2.82
2195 2694 3.567478 ACTCCTATTGAGGGACATTGC 57.433 47.619 0.00 0.00 46.01 3.56
2196 2695 2.173569 ACTCCTATTGAGGGACATTGCC 59.826 50.000 0.00 0.00 46.01 4.52
2197 2696 1.140852 TCCTATTGAGGGACATTGCCG 59.859 52.381 0.00 0.00 43.94 5.69
2198 2697 0.947244 CTATTGAGGGACATTGCCGC 59.053 55.000 0.00 0.00 30.73 6.53
2199 2698 0.254462 TATTGAGGGACATTGCCGCA 59.746 50.000 0.00 0.00 35.65 5.69
2200 2699 1.228398 TTGAGGGACATTGCCGCAA 60.228 52.632 8.55 8.55 44.34 4.85
2201 2700 1.523154 TTGAGGGACATTGCCGCAAC 61.523 55.000 8.25 0.00 42.04 4.17
2202 2701 2.676471 AGGGACATTGCCGCAACC 60.676 61.111 8.25 5.30 30.73 3.77
2203 2702 2.988684 GGGACATTGCCGCAACCA 60.989 61.111 8.25 0.00 0.00 3.67
2204 2703 2.258286 GGACATTGCCGCAACCAC 59.742 61.111 8.25 2.54 0.00 4.16
2205 2704 2.560119 GGACATTGCCGCAACCACA 61.560 57.895 8.25 0.00 0.00 4.17
2206 2705 1.371635 GACATTGCCGCAACCACAC 60.372 57.895 8.25 0.00 0.00 3.82
2207 2706 2.069465 GACATTGCCGCAACCACACA 62.069 55.000 8.25 0.00 0.00 3.72
2208 2707 1.289694 CATTGCCGCAACCACACAT 59.710 52.632 8.25 0.00 0.00 3.21
2209 2708 0.733566 CATTGCCGCAACCACACATC 60.734 55.000 8.25 0.00 0.00 3.06
2210 2709 1.876497 ATTGCCGCAACCACACATCC 61.876 55.000 8.25 0.00 0.00 3.51
2211 2710 2.672996 GCCGCAACCACACATCCT 60.673 61.111 0.00 0.00 0.00 3.24
2212 2711 2.268076 GCCGCAACCACACATCCTT 61.268 57.895 0.00 0.00 0.00 3.36
2213 2712 0.958382 GCCGCAACCACACATCCTTA 60.958 55.000 0.00 0.00 0.00 2.69
2214 2713 1.529226 CCGCAACCACACATCCTTAA 58.471 50.000 0.00 0.00 0.00 1.85
2215 2714 1.199097 CCGCAACCACACATCCTTAAC 59.801 52.381 0.00 0.00 0.00 2.01
2216 2715 1.199097 CGCAACCACACATCCTTAACC 59.801 52.381 0.00 0.00 0.00 2.85
2217 2716 2.235016 GCAACCACACATCCTTAACCA 58.765 47.619 0.00 0.00 0.00 3.67
2218 2717 2.625790 GCAACCACACATCCTTAACCAA 59.374 45.455 0.00 0.00 0.00 3.67
2219 2718 3.305335 GCAACCACACATCCTTAACCAAG 60.305 47.826 0.00 0.00 0.00 3.61
2220 2719 4.141287 CAACCACACATCCTTAACCAAGA 58.859 43.478 0.00 0.00 33.20 3.02
2221 2720 3.751518 ACCACACATCCTTAACCAAGAC 58.248 45.455 0.00 0.00 33.20 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 116 4.040461 GGGCAGACTGCTATATTAAGACCA 59.960 45.833 25.92 0.00 44.28 4.02
123 133 4.178956 ACCTTTTTGTAAAGAGGGCAGA 57.821 40.909 15.73 0.00 42.81 4.26
125 135 4.027437 ACAACCTTTTTGTAAAGAGGGCA 58.973 39.130 15.73 0.00 42.81 5.36
141 152 4.858850 TCCATGATTTGCATAGACAACCT 58.141 39.130 0.00 0.00 34.82 3.50
166 185 3.160679 AGGGAAACAACAGATCCTTGG 57.839 47.619 5.87 0.00 33.61 3.61
211 230 2.619074 ACCCAAATGGAGCTTACAGAGC 60.619 50.000 0.00 0.00 44.51 4.09
212 231 3.356529 ACCCAAATGGAGCTTACAGAG 57.643 47.619 0.00 0.00 37.39 3.35
213 232 3.073798 TCAACCCAAATGGAGCTTACAGA 59.926 43.478 0.00 0.00 37.39 3.41
215 234 3.517296 TCAACCCAAATGGAGCTTACA 57.483 42.857 0.00 0.00 37.39 2.41
216 235 4.016444 TGATCAACCCAAATGGAGCTTAC 58.984 43.478 0.00 0.00 37.39 2.34
217 236 4.314522 TGATCAACCCAAATGGAGCTTA 57.685 40.909 0.00 0.00 37.39 3.09
219 238 2.905415 TGATCAACCCAAATGGAGCT 57.095 45.000 0.00 0.00 37.39 4.09
288 307 6.475596 AAATTGGCTACGTAGTATGTACCT 57.524 37.500 22.98 0.00 44.56 3.08
291 310 8.822855 CAATCAAAATTGGCTACGTAGTATGTA 58.177 33.333 22.98 2.29 39.61 2.29
292 311 7.693952 CAATCAAAATTGGCTACGTAGTATGT 58.306 34.615 22.98 7.70 39.61 2.29
397 451 5.072329 ACATACTAGCTCCTTGTGGCAATAT 59.928 40.000 0.00 0.00 0.00 1.28
469 607 7.312899 AGTAGTGTATGCCAGCAAAATTTTAC 58.687 34.615 2.44 0.00 0.00 2.01
477 617 3.197766 AGCTAAGTAGTGTATGCCAGCAA 59.802 43.478 0.00 0.00 0.00 3.91
590 730 5.908341 ACAACACAATTTTGATTAACCGGT 58.092 33.333 0.00 0.00 0.00 5.28
624 764 4.768968 TGAACCCTGAACCTAGTAGTGTAC 59.231 45.833 0.00 0.00 0.00 2.90
728 868 2.851195 ACCACCTGCTAGTGAACTTTG 58.149 47.619 8.09 0.00 40.34 2.77
799 939 5.827797 ACATAATTCATTTACGTGCTGGGAT 59.172 36.000 0.00 0.00 0.00 3.85
838 978 1.021968 ACAGTTTTCGTTGCCTGGAC 58.978 50.000 0.00 0.00 0.00 4.02
845 985 3.463944 AGAGGGTACACAGTTTTCGTTG 58.536 45.455 0.00 0.00 0.00 4.10
861 1001 6.127026 ACTGAACCTGCTAGTATTTTAGAGGG 60.127 42.308 0.00 0.00 0.00 4.30
898 1039 1.073763 TGTTCAGGGATGAACCACAGG 59.926 52.381 16.20 0.00 45.41 4.00
904 1045 2.352960 GCTCGATTGTTCAGGGATGAAC 59.647 50.000 12.95 12.95 46.00 3.18
922 1063 0.877743 GGCAAGAAGACCAACAGCTC 59.122 55.000 0.00 0.00 0.00 4.09
937 1078 3.057174 ACTGTCAAAACAAAACGAGGCAA 60.057 39.130 0.00 0.00 34.24 4.52
942 1083 4.912766 GTGTCAACTGTCAAAACAAAACGA 59.087 37.500 0.00 0.00 34.24 3.85
958 1099 3.120321 TGGTACCACATCAGTGTCAAC 57.880 47.619 11.60 0.00 44.39 3.18
998 1139 0.257039 AGATGCACTGTTCCCCATCC 59.743 55.000 0.00 0.00 35.78 3.51
1020 1161 1.682740 CAGTTGGGGTAACGGTTGTT 58.317 50.000 3.07 0.00 44.15 2.83
1029 1170 3.586470 TTTTCTTCTGCAGTTGGGGTA 57.414 42.857 14.67 0.00 0.00 3.69
1241 1383 1.517242 CAGAACCACAGGAGCAAGTC 58.483 55.000 0.00 0.00 0.00 3.01
1251 1393 0.249155 GTTCGTCGTCCAGAACCACA 60.249 55.000 0.00 0.00 40.42 4.17
1261 1406 4.207635 TGTTAACTGACATTGTTCGTCGTC 59.792 41.667 7.22 0.00 36.11 4.20
1277 1422 4.202461 TGCCCAGAGATGAAACTGTTAACT 60.202 41.667 7.22 0.00 32.93 2.24
1325 1470 4.387026 CATGAATGCCTATTAGGGGGAA 57.613 45.455 11.72 0.00 35.37 3.97
1345 1491 8.530311 ACAAAATTTCATACATTATCTGTGGCA 58.470 29.630 0.00 0.00 38.92 4.92
1376 1523 2.548480 GAGAAGCCAAACACAGTACCAC 59.452 50.000 0.00 0.00 0.00 4.16
1412 1561 6.607198 AGGAAGAAACAAGAATGTCTCCAAAA 59.393 34.615 0.00 0.00 39.40 2.44
1569 2034 3.070748 CACATATTCCACAACACCGTGA 58.929 45.455 5.28 0.00 39.34 4.35
1706 2188 4.059459 CAACGGTCTGCGTCGCAC 62.059 66.667 17.58 7.62 33.79 5.34
1715 2197 1.952635 GTTCGCGAACCAACGGTCT 60.953 57.895 35.88 0.00 33.12 3.85
1717 2199 3.332409 CGTTCGCGAACCAACGGT 61.332 61.111 38.04 0.00 44.71 4.83
1855 2350 2.494530 GCCCCAAGTTGGTTCGCAA 61.495 57.895 20.54 0.00 35.17 4.85
1939 2434 9.425577 CTCGTGATCTCTATACTTATACTGTCA 57.574 37.037 0.00 0.00 0.00 3.58
1948 2443 9.562408 TTGTTATCTCTCGTGATCTCTATACTT 57.438 33.333 0.00 0.00 0.00 2.24
1949 2444 9.562408 TTTGTTATCTCTCGTGATCTCTATACT 57.438 33.333 0.00 0.00 0.00 2.12
1992 2490 4.340097 TGTAATCGTCGTTAGATGGTCCAT 59.660 41.667 3.26 3.26 34.23 3.41
2005 2503 1.920574 CTCCAGTGCTTGTAATCGTCG 59.079 52.381 0.00 0.00 0.00 5.12
2008 2506 3.443037 CTCTCTCCAGTGCTTGTAATCG 58.557 50.000 0.00 0.00 0.00 3.34
2011 2509 1.276421 GGCTCTCTCCAGTGCTTGTAA 59.724 52.381 0.00 0.00 38.87 2.41
2023 2521 1.876263 GCGCTTCTTCGGCTCTCTC 60.876 63.158 0.00 0.00 0.00 3.20
2030 2528 1.298157 TGATTGTGGCGCTTCTTCGG 61.298 55.000 7.64 0.00 0.00 4.30
2036 2534 1.369091 GGACGATGATTGTGGCGCTT 61.369 55.000 7.64 0.00 0.00 4.68
2037 2535 1.815421 GGACGATGATTGTGGCGCT 60.815 57.895 7.64 0.00 0.00 5.92
2045 2543 2.166907 AGTGAGGGAGGACGATGATT 57.833 50.000 0.00 0.00 0.00 2.57
2066 2564 5.429130 ACTACCATAAAGTTTGCCTAGCTC 58.571 41.667 0.00 0.00 0.00 4.09
2069 2567 6.257193 CCGTTACTACCATAAAGTTTGCCTAG 59.743 42.308 0.00 0.00 0.00 3.02
2071 2569 4.939439 CCGTTACTACCATAAAGTTTGCCT 59.061 41.667 0.00 0.00 0.00 4.75
2088 2586 1.796617 CGATGACTTCCCGACCGTTAC 60.797 57.143 0.00 0.00 0.00 2.50
2096 2595 1.011968 TTTCGCACGATGACTTCCCG 61.012 55.000 0.00 0.00 0.00 5.14
2105 2604 4.051922 GTCCTATGAGATTTTCGCACGAT 58.948 43.478 0.00 0.00 0.00 3.73
2131 2630 0.597637 ACGATTGCTATTCGGGAGCG 60.598 55.000 0.00 0.00 43.19 5.03
2134 2633 1.001706 CTCGACGATTGCTATTCGGGA 60.002 52.381 0.00 0.00 40.83 5.14
2137 2636 2.401017 TCCTCGACGATTGCTATTCG 57.599 50.000 0.00 2.68 42.20 3.34
2140 2639 4.051922 GTTTGATCCTCGACGATTGCTAT 58.948 43.478 0.00 0.00 0.00 2.97
2141 2640 3.130516 AGTTTGATCCTCGACGATTGCTA 59.869 43.478 0.00 0.00 0.00 3.49
2149 2648 3.680458 GTCTTCCAAGTTTGATCCTCGAC 59.320 47.826 0.00 0.00 0.00 4.20
2150 2649 3.323691 TGTCTTCCAAGTTTGATCCTCGA 59.676 43.478 0.00 0.00 0.00 4.04
2151 2650 3.664107 TGTCTTCCAAGTTTGATCCTCG 58.336 45.455 0.00 0.00 0.00 4.63
2152 2651 6.881602 AGTAATGTCTTCCAAGTTTGATCCTC 59.118 38.462 0.00 0.00 0.00 3.71
2153 2652 6.784031 AGTAATGTCTTCCAAGTTTGATCCT 58.216 36.000 0.00 0.00 0.00 3.24
2154 2653 6.094186 GGAGTAATGTCTTCCAAGTTTGATCC 59.906 42.308 0.00 0.00 0.00 3.36
2155 2654 6.881602 AGGAGTAATGTCTTCCAAGTTTGATC 59.118 38.462 0.00 0.00 0.00 2.92
2156 2655 6.784031 AGGAGTAATGTCTTCCAAGTTTGAT 58.216 36.000 0.00 0.00 0.00 2.57
2157 2656 6.187727 AGGAGTAATGTCTTCCAAGTTTGA 57.812 37.500 0.00 0.00 0.00 2.69
2158 2657 8.454106 CAATAGGAGTAATGTCTTCCAAGTTTG 58.546 37.037 0.00 0.00 0.00 2.93
2159 2658 8.383175 TCAATAGGAGTAATGTCTTCCAAGTTT 58.617 33.333 0.00 0.00 0.00 2.66
2160 2659 7.918076 TCAATAGGAGTAATGTCTTCCAAGTT 58.082 34.615 0.00 0.00 0.00 2.66
2161 2660 7.496346 TCAATAGGAGTAATGTCTTCCAAGT 57.504 36.000 0.00 0.00 0.00 3.16
2178 2677 1.597742 CGGCAATGTCCCTCAATAGG 58.402 55.000 0.00 0.00 43.25 2.57
2179 2678 0.947244 GCGGCAATGTCCCTCAATAG 59.053 55.000 0.00 0.00 0.00 1.73
2180 2679 0.254462 TGCGGCAATGTCCCTCAATA 59.746 50.000 0.00 0.00 0.00 1.90
2181 2680 0.611618 TTGCGGCAATGTCCCTCAAT 60.612 50.000 12.11 0.00 0.00 2.57
2182 2681 1.228398 TTGCGGCAATGTCCCTCAA 60.228 52.632 12.11 0.00 0.00 3.02
2183 2682 1.971167 GTTGCGGCAATGTCCCTCA 60.971 57.895 19.53 0.00 0.00 3.86
2184 2683 2.700773 GGTTGCGGCAATGTCCCTC 61.701 63.158 19.53 3.67 0.00 4.30
2185 2684 2.676471 GGTTGCGGCAATGTCCCT 60.676 61.111 19.53 0.00 0.00 4.20
2186 2685 2.988684 TGGTTGCGGCAATGTCCC 60.989 61.111 19.53 15.17 0.00 4.46
2187 2686 2.258286 GTGGTTGCGGCAATGTCC 59.742 61.111 19.53 15.53 0.00 4.02
2188 2687 1.371635 GTGTGGTTGCGGCAATGTC 60.372 57.895 19.53 11.91 0.00 3.06
2189 2688 1.462731 ATGTGTGGTTGCGGCAATGT 61.463 50.000 19.53 0.00 0.00 2.71
2190 2689 0.733566 GATGTGTGGTTGCGGCAATG 60.734 55.000 19.53 0.00 0.00 2.82
2191 2690 1.586028 GATGTGTGGTTGCGGCAAT 59.414 52.632 19.53 0.00 0.00 3.56
2192 2691 2.560119 GGATGTGTGGTTGCGGCAA 61.560 57.895 12.11 12.11 0.00 4.52
2193 2692 2.974692 AAGGATGTGTGGTTGCGGCA 62.975 55.000 0.00 0.00 0.00 5.69
2194 2693 0.958382 TAAGGATGTGTGGTTGCGGC 60.958 55.000 0.00 0.00 0.00 6.53
2195 2694 1.199097 GTTAAGGATGTGTGGTTGCGG 59.801 52.381 0.00 0.00 0.00 5.69
2196 2695 1.199097 GGTTAAGGATGTGTGGTTGCG 59.801 52.381 0.00 0.00 0.00 4.85
2197 2696 2.235016 TGGTTAAGGATGTGTGGTTGC 58.765 47.619 0.00 0.00 0.00 4.17
2198 2697 4.023193 GTCTTGGTTAAGGATGTGTGGTTG 60.023 45.833 0.00 0.00 34.59 3.77
2199 2698 4.142038 GTCTTGGTTAAGGATGTGTGGTT 58.858 43.478 0.00 0.00 34.59 3.67
2200 2699 3.751518 GTCTTGGTTAAGGATGTGTGGT 58.248 45.455 0.00 0.00 34.59 4.16


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

AutoCloner maintained by Alex Coulton.