Multiple sequence alignment - TraesCS4A01G342300

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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 TraesCS4A01G342300 chr4A 100.000 2978 0 0 1 2978 622182104 622179127 0.000000e+00 5500.0
1 TraesCS4A01G342300 chr4A 89.091 110 11 1 6 114 622197830 622197721 5.180000e-28 135.0
2 TraesCS4A01G342300 chr5B 88.821 1145 71 25 1870 2978 689905733 689904610 0.000000e+00 1352.0
3 TraesCS4A01G342300 chr5B 80.583 1133 123 49 521 1590 689907735 689906637 0.000000e+00 784.0
4 TraesCS4A01G342300 chr5B 84.211 247 16 12 1598 1841 689906290 689906064 5.000000e-53 219.0
5 TraesCS4A01G342300 chr5D 85.188 1411 88 47 262 1590 546818537 546819908 0.000000e+00 1336.0
6 TraesCS4A01G342300 chr5D 89.593 1057 76 20 1916 2948 546820792 546821838 0.000000e+00 1312.0
7 TraesCS4A01G342300 chr5D 92.021 188 11 3 3 190 546818023 546818206 8.190000e-66 261.0
8 TraesCS4A01G342300 chr6D 95.122 41 2 0 2533 2573 142149701 142149661 6.890000e-07 65.8


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 TraesCS4A01G342300 chr4A 622179127 622182104 2977 True 5500.000000 5500 100.000000 1 2978 1 chr4A.!!$R1 2977
1 TraesCS4A01G342300 chr5B 689904610 689907735 3125 True 785.000000 1352 84.538333 521 2978 3 chr5B.!!$R1 2457
2 TraesCS4A01G342300 chr5D 546818023 546821838 3815 False 969.666667 1336 88.934000 3 2948 3 chr5D.!!$F1 2945

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
338 600 0.111061 TGACATGGCACCTTGAAGCT 59.889 50.0 0.00 0.0 0.00 3.74 F
1168 1521 0.522626 TGCAATGCAATCCACTGTCG 59.477 50.0 5.01 0.0 34.76 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1555 1943 0.389948 GTGAAGAAGTCGGCGGTGAT 60.390 55.0 7.21 0.0 0.0 3.06 R
2654 3747 0.798776 CGGCCACTCACTGAATTGTC 59.201 55.0 2.24 0.0 0.0 3.18 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
69 70 2.194326 GGCTGGATCTCCCTTGGC 59.806 66.667 0.00 0.00 35.38 4.52
117 118 2.223745 TGGGCCTTCGTGTTTTCTTAC 58.776 47.619 4.53 0.00 0.00 2.34
134 135 0.896940 TACGGAAGAACGAGCCTGGT 60.897 55.000 0.00 0.00 37.61 4.00
138 139 1.535896 GGAAGAACGAGCCTGGTTTTC 59.464 52.381 0.00 0.84 0.00 2.29
164 165 7.775053 TTTTTAGATTGAGCCTTGGTGTTAT 57.225 32.000 0.00 0.00 0.00 1.89
165 166 8.871629 TTTTTAGATTGAGCCTTGGTGTTATA 57.128 30.769 0.00 0.00 0.00 0.98
166 167 9.474313 TTTTTAGATTGAGCCTTGGTGTTATAT 57.526 29.630 0.00 0.00 0.00 0.86
167 168 9.474313 TTTTAGATTGAGCCTTGGTGTTATATT 57.526 29.630 0.00 0.00 0.00 1.28
185 186 8.432013 TGTTATATTGAGCTGACCTGATAATGT 58.568 33.333 0.00 0.00 0.00 2.71
213 248 8.339714 TGTTGTACCTCTAAAAATGAAACGAAG 58.660 33.333 0.00 0.00 0.00 3.79
216 251 9.932207 TGTACCTCTAAAAATGAAACGAAGATA 57.068 29.630 0.00 0.00 0.00 1.98
234 269 4.138290 AGATATATCTATGAGCCCGTCCG 58.862 47.826 13.76 0.00 34.85 4.79
235 270 2.217510 ATATCTATGAGCCCGTCCGT 57.782 50.000 0.00 0.00 0.00 4.69
236 271 1.244816 TATCTATGAGCCCGTCCGTG 58.755 55.000 0.00 0.00 0.00 4.94
260 296 4.163078 AGTCCATGTGGTTTCTCCTAGATG 59.837 45.833 0.00 0.00 37.07 2.90
261 297 4.162320 GTCCATGTGGTTTCTCCTAGATGA 59.838 45.833 0.00 0.00 37.07 2.92
262 298 4.782691 TCCATGTGGTTTCTCCTAGATGAA 59.217 41.667 0.00 0.00 37.07 2.57
264 300 5.491070 CATGTGGTTTCTCCTAGATGAACA 58.509 41.667 0.00 0.00 37.07 3.18
265 301 5.762179 TGTGGTTTCTCCTAGATGAACAT 57.238 39.130 0.00 0.00 37.07 2.71
338 600 0.111061 TGACATGGCACCTTGAAGCT 59.889 50.000 0.00 0.00 0.00 3.74
355 620 4.578928 TGAAGCTTTCTTCTTTTAACCGCT 59.421 37.500 0.00 0.00 46.81 5.52
358 623 4.762251 AGCTTTCTTCTTTTAACCGCTGAT 59.238 37.500 0.00 0.00 0.00 2.90
369 634 9.567848 TCTTTTAACCGCTGATCAATATTTTTC 57.432 29.630 0.00 0.00 0.00 2.29
379 644 7.524367 GCTGATCAATATTTTTCCCGGATCATT 60.524 37.037 0.73 0.00 38.96 2.57
391 656 6.693315 TCCCGGATCATTAAATTTGACTTC 57.307 37.500 0.73 0.00 0.00 3.01
439 704 7.531280 AAATCGACTTCTCACTATGTGAATG 57.469 36.000 2.00 0.00 42.26 2.67
509 794 4.158949 TGATGATGAGCATTGGAGGTTTTG 59.841 41.667 0.00 0.00 37.34 2.44
514 799 5.096443 TGAGCATTGGAGGTTTTGTTTTT 57.904 34.783 0.00 0.00 0.00 1.94
543 828 5.815581 TGGTGAATTTAGAATGTGGCTAGT 58.184 37.500 0.00 0.00 0.00 2.57
544 829 5.880332 TGGTGAATTTAGAATGTGGCTAGTC 59.120 40.000 0.00 0.00 0.00 2.59
545 830 5.880332 GGTGAATTTAGAATGTGGCTAGTCA 59.120 40.000 0.00 0.00 0.00 3.41
564 849 2.788230 ATCAGGTCTGCCCTTCCCCA 62.788 60.000 0.00 0.00 42.73 4.96
623 908 3.569277 TGGTTGTCACTGTTTCATGGATG 59.431 43.478 0.00 0.00 0.00 3.51
659 951 3.306917 TCATGATTTTGGCTGCAGTTG 57.693 42.857 16.64 0.00 0.00 3.16
684 976 8.458052 TGTTTCTATTTGTGATGATAAACGCAT 58.542 29.630 0.00 0.00 0.00 4.73
685 977 9.929722 GTTTCTATTTGTGATGATAAACGCATA 57.070 29.630 0.00 0.00 0.00 3.14
686 978 9.929722 TTTCTATTTGTGATGATAAACGCATAC 57.070 29.630 0.00 0.00 0.00 2.39
706 1001 2.288030 ACTGGTACGTCTGAGGTTTTCG 60.288 50.000 8.42 0.00 0.00 3.46
720 1015 4.127907 AGGTTTTCGTTCTGAAGAGGAAC 58.872 43.478 0.00 0.00 37.99 3.62
773 1068 9.093970 GCTCTCTTTTACTCTTTCTTTATCTCC 57.906 37.037 0.00 0.00 0.00 3.71
884 1185 2.858839 CGTATGCAGTGACGTACTTGA 58.141 47.619 9.70 0.00 37.60 3.02
890 1197 2.029649 GCAGTGACGTACTTGAGGGTAA 60.030 50.000 0.00 0.00 37.60 2.85
895 1202 1.888512 ACGTACTTGAGGGTAAAGCGA 59.111 47.619 0.00 0.00 0.00 4.93
925 1232 4.650754 ATACGGTGTATGTCTGGAGTTC 57.349 45.455 0.00 0.00 0.00 3.01
930 1237 4.389077 CGGTGTATGTCTGGAGTTCTTTTC 59.611 45.833 0.00 0.00 0.00 2.29
963 1290 7.916977 TGTACACCTGTTATTATTACTGTAGCG 59.083 37.037 0.00 0.00 0.00 4.26
980 1307 5.464168 TGTAGCGAGTTTCAGTTAAGGTAC 58.536 41.667 0.00 0.00 0.00 3.34
981 1308 4.595762 AGCGAGTTTCAGTTAAGGTACA 57.404 40.909 0.00 0.00 0.00 2.90
982 1309 5.148651 AGCGAGTTTCAGTTAAGGTACAT 57.851 39.130 0.00 0.00 0.00 2.29
983 1310 6.276832 AGCGAGTTTCAGTTAAGGTACATA 57.723 37.500 0.00 0.00 0.00 2.29
984 1311 6.331061 AGCGAGTTTCAGTTAAGGTACATAG 58.669 40.000 0.00 0.00 0.00 2.23
985 1312 5.519206 GCGAGTTTCAGTTAAGGTACATAGG 59.481 44.000 0.00 0.00 0.00 2.57
986 1313 6.628185 CGAGTTTCAGTTAAGGTACATAGGT 58.372 40.000 0.00 0.00 0.00 3.08
987 1314 7.095270 CGAGTTTCAGTTAAGGTACATAGGTT 58.905 38.462 0.00 0.00 0.00 3.50
988 1315 8.246180 CGAGTTTCAGTTAAGGTACATAGGTTA 58.754 37.037 0.00 0.00 0.00 2.85
989 1316 9.583765 GAGTTTCAGTTAAGGTACATAGGTTAG 57.416 37.037 0.00 0.00 0.00 2.34
990 1317 8.537858 AGTTTCAGTTAAGGTACATAGGTTAGG 58.462 37.037 0.00 0.00 0.00 2.69
991 1318 8.316946 GTTTCAGTTAAGGTACATAGGTTAGGT 58.683 37.037 0.00 0.00 0.00 3.08
992 1319 9.545928 TTTCAGTTAAGGTACATAGGTTAGGTA 57.454 33.333 0.00 0.00 0.00 3.08
993 1320 8.525290 TCAGTTAAGGTACATAGGTTAGGTAC 57.475 38.462 0.00 3.23 43.16 3.34
994 1321 8.115384 TCAGTTAAGGTACATAGGTTAGGTACA 58.885 37.037 11.61 0.00 45.02 2.90
995 1322 8.752187 CAGTTAAGGTACATAGGTTAGGTACAA 58.248 37.037 11.61 0.00 45.02 2.41
996 1323 8.975295 AGTTAAGGTACATAGGTTAGGTACAAG 58.025 37.037 11.61 0.00 45.02 3.16
997 1324 8.971073 GTTAAGGTACATAGGTTAGGTACAAGA 58.029 37.037 11.61 0.00 45.02 3.02
998 1325 7.415592 AAGGTACATAGGTTAGGTACAAGAC 57.584 40.000 11.61 0.00 45.02 3.01
1129 1471 1.260538 CCAGTCCTCAGGTGCTGCTA 61.261 60.000 11.14 0.00 0.00 3.49
1168 1521 0.522626 TGCAATGCAATCCACTGTCG 59.477 50.000 5.01 0.00 34.76 4.35
1176 1529 3.244078 TGCAATCCACTGTCGGTATATCC 60.244 47.826 0.00 0.00 0.00 2.59
1198 1556 8.764524 ATCCGTTATTAGACTGATGAAATAGC 57.235 34.615 0.00 0.00 0.00 2.97
1204 1562 1.202568 CTGATGAAATAGCGGCGCG 59.797 57.895 27.59 0.00 0.00 6.86
1207 1565 1.762222 GATGAAATAGCGGCGCGTGT 61.762 55.000 27.59 14.76 0.00 4.49
1358 1721 4.132441 CTGCGGCGGGGTACGTTA 62.132 66.667 9.78 0.00 46.52 3.18
1383 1747 1.929038 GCACACGCTCTACTCGTTCAA 60.929 52.381 0.00 0.00 38.19 2.69
1384 1748 2.596452 CACACGCTCTACTCGTTCAAT 58.404 47.619 0.00 0.00 38.19 2.57
1386 1750 2.987149 ACACGCTCTACTCGTTCAATTG 59.013 45.455 0.00 0.00 38.19 2.32
1387 1751 2.987149 CACGCTCTACTCGTTCAATTGT 59.013 45.455 5.13 0.00 38.19 2.71
1389 1753 4.619760 CACGCTCTACTCGTTCAATTGTAA 59.380 41.667 5.13 0.00 38.19 2.41
1390 1754 4.857588 ACGCTCTACTCGTTCAATTGTAAG 59.142 41.667 5.13 0.00 36.72 2.34
1391 1755 5.093457 CGCTCTACTCGTTCAATTGTAAGA 58.907 41.667 5.13 2.92 0.00 2.10
1392 1756 5.228220 CGCTCTACTCGTTCAATTGTAAGAG 59.772 44.000 20.72 20.72 0.00 2.85
1393 1757 6.323266 GCTCTACTCGTTCAATTGTAAGAGA 58.677 40.000 26.34 13.74 0.00 3.10
1395 1759 7.626664 GCTCTACTCGTTCAATTGTAAGAGAGA 60.627 40.741 26.34 21.69 0.00 3.10
1396 1760 8.282455 TCTACTCGTTCAATTGTAAGAGAGAT 57.718 34.615 26.34 12.46 0.00 2.75
1397 1761 9.392259 TCTACTCGTTCAATTGTAAGAGAGATA 57.608 33.333 26.34 12.82 0.00 1.98
1409 1791 8.718102 TTGTAAGAGAGATAATAACTGGCAAC 57.282 34.615 0.00 0.00 0.00 4.17
1423 1805 2.174107 CAACCTCATGCACGCACG 59.826 61.111 0.00 0.00 0.00 5.34
1424 1806 3.726517 AACCTCATGCACGCACGC 61.727 61.111 0.00 0.00 0.00 5.34
1514 1902 2.180769 CGACGCCGTCATCCAGAA 59.819 61.111 18.40 0.00 32.09 3.02
1521 1909 1.599047 CGTCATCCAGAAGGCCAGT 59.401 57.895 5.01 0.00 33.74 4.00
1530 1918 3.240134 GAAGGCCAGTCAGCGGTCA 62.240 63.158 5.01 0.00 0.00 4.02
1533 1921 2.887568 GCCAGTCAGCGGTCATCG 60.888 66.667 0.00 0.00 42.76 3.84
1534 1922 2.573869 CCAGTCAGCGGTCATCGT 59.426 61.111 0.00 0.00 41.72 3.73
1540 1928 4.831307 AGCGGTCATCGTCGTCGC 62.831 66.667 0.00 0.00 45.72 5.19
1559 1947 2.100631 CCGACGTGGCCTTCATCAC 61.101 63.158 3.32 0.00 0.00 3.06
1640 2379 1.888512 GCATTTCAGCCTCAAGACCAA 59.111 47.619 0.00 0.00 0.00 3.67
1697 2436 2.634815 AAGCATCACATCCCTGCTAG 57.365 50.000 0.00 0.00 45.10 3.42
1698 2437 1.504912 AGCATCACATCCCTGCTAGT 58.495 50.000 0.00 0.00 44.08 2.57
1699 2438 2.682594 AGCATCACATCCCTGCTAGTA 58.317 47.619 0.00 0.00 44.08 1.82
1700 2439 2.366916 AGCATCACATCCCTGCTAGTAC 59.633 50.000 0.00 0.00 44.08 2.73
1701 2440 2.103094 GCATCACATCCCTGCTAGTACA 59.897 50.000 0.00 0.00 33.15 2.90
1702 2441 3.244353 GCATCACATCCCTGCTAGTACAT 60.244 47.826 0.00 0.00 33.15 2.29
1703 2442 4.744867 GCATCACATCCCTGCTAGTACATT 60.745 45.833 0.00 0.00 33.15 2.71
1707 2446 5.880332 TCACATCCCTGCTAGTACATTTTTC 59.120 40.000 0.00 0.00 0.00 2.29
1709 2448 5.044846 ACATCCCTGCTAGTACATTTTTCCT 60.045 40.000 0.00 0.00 0.00 3.36
1711 2450 5.985911 TCCCTGCTAGTACATTTTTCCTAC 58.014 41.667 0.00 0.00 0.00 3.18
1714 2453 7.069578 TCCCTGCTAGTACATTTTTCCTACTAG 59.930 40.741 0.00 6.70 41.28 2.57
1732 2471 9.429109 TCCTACTAGTAATACAATCCATCACAA 57.571 33.333 3.76 0.00 0.00 3.33
1763 2504 6.095160 AGAGACAGAAATGCCAATTCTTCATC 59.905 38.462 0.00 0.00 34.99 2.92
1780 2521 5.302823 TCTTCATCTCACTGTCTCTTGTCAA 59.697 40.000 0.00 0.00 0.00 3.18
1781 2522 5.735285 TCATCTCACTGTCTCTTGTCAAT 57.265 39.130 0.00 0.00 0.00 2.57
1782 2523 5.718146 TCATCTCACTGTCTCTTGTCAATC 58.282 41.667 0.00 0.00 0.00 2.67
1783 2524 5.244626 TCATCTCACTGTCTCTTGTCAATCA 59.755 40.000 0.00 0.00 0.00 2.57
1784 2525 5.735285 TCTCACTGTCTCTTGTCAATCAT 57.265 39.130 0.00 0.00 0.00 2.45
1785 2526 5.718146 TCTCACTGTCTCTTGTCAATCATC 58.282 41.667 0.00 0.00 0.00 2.92
1786 2527 5.479724 TCTCACTGTCTCTTGTCAATCATCT 59.520 40.000 0.00 0.00 0.00 2.90
1787 2528 6.660949 TCTCACTGTCTCTTGTCAATCATCTA 59.339 38.462 0.00 0.00 0.00 1.98
1788 2529 7.341512 TCTCACTGTCTCTTGTCAATCATCTAT 59.658 37.037 0.00 0.00 0.00 1.98
1789 2530 7.263496 TCACTGTCTCTTGTCAATCATCTATG 58.737 38.462 0.00 0.00 0.00 2.23
1790 2531 6.018913 CACTGTCTCTTGTCAATCATCTATGC 60.019 42.308 0.00 0.00 0.00 3.14
1791 2532 5.981174 TGTCTCTTGTCAATCATCTATGCA 58.019 37.500 0.00 0.00 0.00 3.96
1817 2558 0.246635 GCTACGAGGAGGTGCTCAAA 59.753 55.000 0.00 0.00 31.08 2.69
1842 2583 3.370953 CCTGGGTTTCTTCATCGAATCCT 60.371 47.826 0.00 0.00 34.60 3.24
1845 2586 3.628032 GGGTTTCTTCATCGAATCCTTCC 59.372 47.826 0.00 0.00 34.60 3.46
1846 2587 4.518249 GGTTTCTTCATCGAATCCTTCCT 58.482 43.478 0.00 0.00 32.50 3.36
1848 2589 6.292150 GGTTTCTTCATCGAATCCTTCCTAT 58.708 40.000 0.00 0.00 32.50 2.57
1849 2590 6.768381 GGTTTCTTCATCGAATCCTTCCTATT 59.232 38.462 0.00 0.00 32.50 1.73
1850 2591 7.931948 GGTTTCTTCATCGAATCCTTCCTATTA 59.068 37.037 0.00 0.00 32.50 0.98
1851 2592 9.495572 GTTTCTTCATCGAATCCTTCCTATTAT 57.504 33.333 0.00 0.00 0.00 1.28
1926 2989 7.421530 AAATAGTATATCGATGCACACAACC 57.578 36.000 8.54 0.00 0.00 3.77
1931 2994 1.234821 TCGATGCACACAACCCTTTC 58.765 50.000 0.00 0.00 0.00 2.62
1996 3059 9.416794 CATGTTAGTGGCACATTTTAAACAATA 57.583 29.630 21.41 0.00 44.52 1.90
2022 3085 6.371825 TGTGTGTGTGTGTGTGTTTATTTCTA 59.628 34.615 0.00 0.00 0.00 2.10
2025 3088 7.912773 TGTGTGTGTGTGTGTTTATTTCTATTG 59.087 33.333 0.00 0.00 0.00 1.90
2027 3090 8.341903 TGTGTGTGTGTGTTTATTTCTATTGAG 58.658 33.333 0.00 0.00 0.00 3.02
2028 3091 7.323656 GTGTGTGTGTGTTTATTTCTATTGAGC 59.676 37.037 0.00 0.00 0.00 4.26
2030 3093 7.535258 GTGTGTGTGTTTATTTCTATTGAGCAG 59.465 37.037 0.00 0.00 0.00 4.24
2062 3125 0.647410 GATCGTGAATCGTGTGGCTG 59.353 55.000 0.00 0.00 40.80 4.85
2064 3127 0.246360 TCGTGAATCGTGTGGCTGAT 59.754 50.000 0.00 0.00 40.80 2.90
2073 3136 1.811965 CGTGTGGCTGATTCATGGAAA 59.188 47.619 0.00 0.00 0.00 3.13
2076 3139 4.427312 GTGTGGCTGATTCATGGAAATTC 58.573 43.478 0.00 0.00 0.00 2.17
2104 3167 4.065088 TGGTCTCACACATTGCTAGTTTC 58.935 43.478 0.00 0.00 0.00 2.78
2143 3208 8.586273 CAAATATCCGAGTAATGTTTTTGCAAG 58.414 33.333 0.00 0.00 0.00 4.01
2144 3209 5.705609 ATCCGAGTAATGTTTTTGCAAGT 57.294 34.783 0.00 0.00 0.00 3.16
2146 3211 6.621316 TCCGAGTAATGTTTTTGCAAGTTA 57.379 33.333 0.00 0.00 0.00 2.24
2147 3212 6.432107 TCCGAGTAATGTTTTTGCAAGTTAC 58.568 36.000 0.00 6.05 0.00 2.50
2148 3213 6.261381 TCCGAGTAATGTTTTTGCAAGTTACT 59.739 34.615 16.23 16.23 35.69 2.24
2149 3214 6.359617 CCGAGTAATGTTTTTGCAAGTTACTG 59.640 38.462 18.96 13.81 33.82 2.74
2150 3215 6.910433 CGAGTAATGTTTTTGCAAGTTACTGT 59.090 34.615 18.96 7.74 33.82 3.55
2206 3285 1.787155 GGCTACTCGCACATGTAATCG 59.213 52.381 0.00 2.87 41.67 3.34
2209 3288 1.145759 ACTCGCACATGTAATCGGCG 61.146 55.000 18.37 18.37 44.45 6.46
2257 3336 0.661020 ACCAAGTCAAAAAGCCGTCG 59.339 50.000 0.00 0.00 0.00 5.12
2269 3348 2.528041 AGCCGTCGAAAGTTTCTCTT 57.472 45.000 13.56 0.00 38.10 2.85
2293 3372 1.967066 AGCCTCTGGGATGAATACTCG 59.033 52.381 0.00 0.00 33.58 4.18
2397 3477 9.410556 GCAAAAATTATAAGCTGAAGAGAACAA 57.589 29.630 0.00 0.00 0.00 2.83
2428 3508 2.421952 GCTTGACAGCATGGGATTAGGA 60.422 50.000 0.00 0.00 46.49 2.94
2528 3616 7.703058 AGGCTTTAGTGTGCAAATAAGTTAT 57.297 32.000 0.00 0.00 0.00 1.89
2531 3622 8.244113 GGCTTTAGTGTGCAAATAAGTTATTCT 58.756 33.333 8.56 3.59 0.00 2.40
2573 3664 6.054295 AGGCTCATCTTAGAAATCACATCAC 58.946 40.000 0.00 0.00 0.00 3.06
2591 3682 5.184479 ACATCACCTTCAATCATTGGTTGAG 59.816 40.000 11.92 5.14 37.89 3.02
2646 3738 8.932434 TTAATGTAGGATTGCTATATTTGCCA 57.068 30.769 11.37 0.00 0.00 4.92
2654 3747 5.534207 TTGCTATATTTGCCAATCCCAAG 57.466 39.130 0.00 0.00 0.00 3.61
2688 3781 1.579429 GCCGTGGAACCATGAACAC 59.421 57.895 13.85 0.00 35.09 3.32
2689 3782 1.862602 GCCGTGGAACCATGAACACC 61.863 60.000 13.85 0.00 35.09 4.16
2690 3783 1.573829 CCGTGGAACCATGAACACCG 61.574 60.000 13.85 3.20 35.09 4.94
2722 3815 6.316890 AGGCAAAACTACTACAACTTCGAAAA 59.683 34.615 0.00 0.00 0.00 2.29
2725 3818 7.058016 GCAAAACTACTACAACTTCGAAAATCG 59.942 37.037 0.00 0.00 42.10 3.34
2730 3823 5.416947 ACTACAACTTCGAAAATCGGCTAT 58.583 37.500 0.00 0.00 40.88 2.97
2737 3830 9.370126 CAACTTCGAAAATCGGCTATATTTTAG 57.630 33.333 0.00 0.00 40.88 1.85
2813 3911 9.483489 TTCATAGTATTGTGGTACCTCTTCTAA 57.517 33.333 14.36 0.09 0.00 2.10
2883 3981 3.317150 GTGTGCCTGCAAAATAAGAACC 58.683 45.455 0.00 0.00 0.00 3.62
2889 3987 3.553922 CCTGCAAAATAAGAACCGCCAAA 60.554 43.478 0.00 0.00 0.00 3.28
2894 3992 7.721402 TGCAAAATAAGAACCGCCAAATATAT 58.279 30.769 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.507944 CCAAGGGAGATCCAGCCG 59.492 66.667 0.47 0.00 38.24 5.52
69 70 0.882474 TTCCGTTAATTTGGGCCACG 59.118 50.000 5.23 5.15 0.00 4.94
117 118 0.602905 AAACCAGGCTCGTTCTTCCG 60.603 55.000 0.00 0.00 0.00 4.30
164 165 6.051074 CACACATTATCAGGTCAGCTCAATA 58.949 40.000 0.00 0.00 0.00 1.90
165 166 4.880120 CACACATTATCAGGTCAGCTCAAT 59.120 41.667 0.00 0.00 0.00 2.57
166 167 4.256110 CACACATTATCAGGTCAGCTCAA 58.744 43.478 0.00 0.00 0.00 3.02
167 168 3.261643 ACACACATTATCAGGTCAGCTCA 59.738 43.478 0.00 0.00 0.00 4.26
185 186 7.280428 TCGTTTCATTTTTAGAGGTACAACACA 59.720 33.333 0.00 0.00 0.00 3.72
213 248 3.884091 ACGGACGGGCTCATAGATATATC 59.116 47.826 4.42 4.42 0.00 1.63
216 251 1.819288 CACGGACGGGCTCATAGATAT 59.181 52.381 0.00 0.00 0.00 1.63
234 269 2.039084 AGGAGAAACCACATGGACTCAC 59.961 50.000 4.53 0.00 42.04 3.51
235 270 2.338809 AGGAGAAACCACATGGACTCA 58.661 47.619 4.53 0.00 42.04 3.41
236 271 3.769844 TCTAGGAGAAACCACATGGACTC 59.230 47.826 4.53 9.79 42.04 3.36
338 600 6.627395 TTGATCAGCGGTTAAAAGAAGAAA 57.373 33.333 0.00 0.00 0.00 2.52
355 620 7.838079 AATGATCCGGGAAAAATATTGATCA 57.162 32.000 0.00 12.24 40.72 2.92
369 634 6.699575 AGAAGTCAAATTTAATGATCCGGG 57.300 37.500 0.00 0.00 0.00 5.73
413 678 7.582435 TTCACATAGTGAGAAGTCGATTTTC 57.418 36.000 0.00 0.00 43.69 2.29
414 679 7.413438 GCATTCACATAGTGAGAAGTCGATTTT 60.413 37.037 0.00 0.00 43.69 1.82
415 680 6.036517 GCATTCACATAGTGAGAAGTCGATTT 59.963 38.462 0.00 0.00 43.69 2.17
416 681 5.521735 GCATTCACATAGTGAGAAGTCGATT 59.478 40.000 0.00 0.00 43.69 3.34
427 692 2.535534 CGAACTGCGCATTCACATAGTG 60.536 50.000 23.12 8.41 34.45 2.74
439 704 0.727398 AGAAATAAGCCGAACTGCGC 59.273 50.000 0.00 0.00 39.11 6.09
485 770 3.210232 ACCTCCAATGCTCATCATCAG 57.790 47.619 0.00 0.00 33.40 2.90
509 794 9.701355 CATTCTAAATTCACCAACAACAAAAAC 57.299 29.630 0.00 0.00 0.00 2.43
514 799 6.511416 CCACATTCTAAATTCACCAACAACA 58.489 36.000 0.00 0.00 0.00 3.33
564 849 1.597027 CCAGGTTTTCGTCCGTGCT 60.597 57.895 0.00 0.00 0.00 4.40
623 908 9.710979 CAAAATCATGATCCATAAATTTTGTGC 57.289 29.630 9.06 0.00 38.92 4.57
659 951 8.841444 ATGCGTTTATCATCACAAATAGAAAC 57.159 30.769 0.00 0.00 0.00 2.78
680 972 1.268589 CCTCAGACGTACCAGTATGCG 60.269 57.143 0.00 0.00 33.74 4.73
684 976 3.058016 CGAAAACCTCAGACGTACCAGTA 60.058 47.826 0.00 0.00 0.00 2.74
685 977 2.288030 CGAAAACCTCAGACGTACCAGT 60.288 50.000 0.00 0.00 0.00 4.00
686 978 2.288030 ACGAAAACCTCAGACGTACCAG 60.288 50.000 0.00 0.00 35.49 4.00
706 1001 3.070748 GCCTCTTGTTCCTCTTCAGAAC 58.929 50.000 0.00 0.00 43.20 3.01
741 1036 3.859411 AGAGTAAAAGAGAGCGACTGG 57.141 47.619 0.00 0.00 0.00 4.00
797 1096 4.582701 TCAGACAATTTGCCACGAATTT 57.417 36.364 0.00 0.00 0.00 1.82
851 1152 4.072131 ACTGCATACGTGTTTGATTTCCT 58.928 39.130 0.00 0.00 0.00 3.36
858 1159 2.211449 CGTCACTGCATACGTGTTTG 57.789 50.000 0.00 0.00 34.48 2.93
878 1179 2.895404 ACTGTCGCTTTACCCTCAAGTA 59.105 45.455 0.00 0.00 0.00 2.24
881 1182 4.546829 AATACTGTCGCTTTACCCTCAA 57.453 40.909 0.00 0.00 0.00 3.02
884 1185 6.211515 CGTATAAATACTGTCGCTTTACCCT 58.788 40.000 0.00 0.00 0.00 4.34
890 1197 5.002464 ACACCGTATAAATACTGTCGCTT 57.998 39.130 0.00 0.00 29.90 4.68
895 1202 7.286087 TCCAGACATACACCGTATAAATACTGT 59.714 37.037 0.00 0.71 32.06 3.55
925 1232 4.451900 ACAGGTGTACAGACCTTGAAAAG 58.548 43.478 2.29 0.00 44.53 2.27
930 1237 9.095065 GTAATAATAACAGGTGTACAGACCTTG 57.905 37.037 2.29 0.00 44.53 3.61
963 1290 9.583765 CTAACCTATGTACCTTAACTGAAACTC 57.416 37.037 0.00 0.00 0.00 3.01
980 1307 5.527582 GCCATTGTCTTGTACCTAACCTATG 59.472 44.000 0.00 0.00 0.00 2.23
981 1308 5.681639 GCCATTGTCTTGTACCTAACCTAT 58.318 41.667 0.00 0.00 0.00 2.57
982 1309 4.382254 CGCCATTGTCTTGTACCTAACCTA 60.382 45.833 0.00 0.00 0.00 3.08
983 1310 3.618997 CGCCATTGTCTTGTACCTAACCT 60.619 47.826 0.00 0.00 0.00 3.50
984 1311 2.676342 CGCCATTGTCTTGTACCTAACC 59.324 50.000 0.00 0.00 0.00 2.85
985 1312 3.332034 ACGCCATTGTCTTGTACCTAAC 58.668 45.455 0.00 0.00 0.00 2.34
986 1313 3.592059 GACGCCATTGTCTTGTACCTAA 58.408 45.455 0.00 0.00 35.95 2.69
987 1314 2.416296 CGACGCCATTGTCTTGTACCTA 60.416 50.000 0.00 0.00 36.71 3.08
988 1315 1.671850 CGACGCCATTGTCTTGTACCT 60.672 52.381 0.00 0.00 36.71 3.08
989 1316 0.719465 CGACGCCATTGTCTTGTACC 59.281 55.000 0.00 0.00 36.71 3.34
990 1317 1.389106 GTCGACGCCATTGTCTTGTAC 59.611 52.381 0.00 0.00 36.71 2.90
991 1318 1.705256 GTCGACGCCATTGTCTTGTA 58.295 50.000 0.00 0.00 36.71 2.41
992 1319 1.282248 CGTCGACGCCATTGTCTTGT 61.282 55.000 26.59 0.00 36.71 3.16
993 1320 1.416049 CGTCGACGCCATTGTCTTG 59.584 57.895 26.59 0.00 36.71 3.02
994 1321 1.736645 CCGTCGACGCCATTGTCTT 60.737 57.895 31.73 0.00 36.71 3.01
995 1322 2.126071 CCGTCGACGCCATTGTCT 60.126 61.111 31.73 0.00 36.71 3.41
996 1323 3.849953 GCCGTCGACGCCATTGTC 61.850 66.667 31.73 10.43 38.18 3.18
1044 1371 4.671590 TCGAGGACCTGCCCGACA 62.672 66.667 0.00 0.00 35.40 4.35
1129 1471 4.363990 CCGAGTGAGCGTGCCAGT 62.364 66.667 0.00 0.00 0.00 4.00
1155 1508 3.326747 GGATATACCGACAGTGGATTGC 58.673 50.000 0.00 0.00 0.00 3.56
1176 1529 6.400091 GCCGCTATTTCATCAGTCTAATAACG 60.400 42.308 0.00 0.00 0.00 3.18
1198 1556 4.724697 CTCTGCAAACACGCGCCG 62.725 66.667 5.73 0.00 33.35 6.46
1204 1562 0.890996 CTCCACCCCTCTGCAAACAC 60.891 60.000 0.00 0.00 0.00 3.32
1207 1565 3.170362 CCTCCACCCCTCTGCAAA 58.830 61.111 0.00 0.00 0.00 3.68
1277 1640 2.355837 GCACCAGCTTGACGACGA 60.356 61.111 0.00 0.00 37.91 4.20
1341 1704 4.132441 TAACGTACCCCGCCGCAG 62.132 66.667 0.00 0.00 41.42 5.18
1383 1747 9.331282 GTTGCCAGTTATTATCTCTCTTACAAT 57.669 33.333 0.00 0.00 0.00 2.71
1384 1748 7.769044 GGTTGCCAGTTATTATCTCTCTTACAA 59.231 37.037 0.00 0.00 0.00 2.41
1386 1750 7.501844 AGGTTGCCAGTTATTATCTCTCTTAC 58.498 38.462 0.00 0.00 0.00 2.34
1387 1751 7.344612 TGAGGTTGCCAGTTATTATCTCTCTTA 59.655 37.037 0.00 0.00 0.00 2.10
1389 1753 5.663106 TGAGGTTGCCAGTTATTATCTCTCT 59.337 40.000 0.00 0.00 0.00 3.10
1390 1754 5.918608 TGAGGTTGCCAGTTATTATCTCTC 58.081 41.667 0.00 0.00 0.00 3.20
1391 1755 5.957771 TGAGGTTGCCAGTTATTATCTCT 57.042 39.130 0.00 0.00 0.00 3.10
1392 1756 5.049129 GCATGAGGTTGCCAGTTATTATCTC 60.049 44.000 0.00 0.00 36.60 2.75
1393 1757 4.823989 GCATGAGGTTGCCAGTTATTATCT 59.176 41.667 0.00 0.00 36.60 1.98
1395 1759 4.339247 GTGCATGAGGTTGCCAGTTATTAT 59.661 41.667 0.00 0.00 42.06 1.28
1396 1760 3.694072 GTGCATGAGGTTGCCAGTTATTA 59.306 43.478 0.00 0.00 42.06 0.98
1397 1761 2.493278 GTGCATGAGGTTGCCAGTTATT 59.507 45.455 0.00 0.00 42.06 1.40
1398 1762 2.094675 GTGCATGAGGTTGCCAGTTAT 58.905 47.619 0.00 0.00 42.06 1.89
1399 1763 1.533625 GTGCATGAGGTTGCCAGTTA 58.466 50.000 0.00 0.00 42.06 2.24
1400 1764 1.518056 CGTGCATGAGGTTGCCAGTT 61.518 55.000 0.00 0.00 42.06 3.16
1431 1813 2.279517 GCGTCGTATCCCTGCAGG 60.280 66.667 26.87 26.87 0.00 4.85
1514 1902 3.005539 ATGACCGCTGACTGGCCT 61.006 61.111 3.32 0.00 0.00 5.19
1521 1909 2.483745 GACGACGATGACCGCTGA 59.516 61.111 0.00 0.00 43.32 4.26
1540 1928 2.511600 GATGAAGGCCACGTCGGG 60.512 66.667 5.01 0.00 34.06 5.14
1541 1929 2.100631 GTGATGAAGGCCACGTCGG 61.101 63.158 5.01 0.00 38.11 4.79
1542 1930 2.100631 GGTGATGAAGGCCACGTCG 61.101 63.158 5.01 0.00 34.30 5.12
1555 1943 0.389948 GTGAAGAAGTCGGCGGTGAT 60.390 55.000 7.21 0.00 0.00 3.06
1559 1947 1.738099 CAGGTGAAGAAGTCGGCGG 60.738 63.158 7.21 0.00 0.00 6.13
1590 1978 3.817709 TGATCATTACAGTGCCGATCA 57.182 42.857 9.19 9.19 39.99 2.92
1591 1979 3.120408 GCATGATCATTACAGTGCCGATC 60.120 47.826 5.16 0.00 34.40 3.69
1592 1980 2.810274 GCATGATCATTACAGTGCCGAT 59.190 45.455 5.16 0.00 0.00 4.18
1593 1981 2.212652 GCATGATCATTACAGTGCCGA 58.787 47.619 5.16 0.00 0.00 5.54
1594 1982 1.941975 TGCATGATCATTACAGTGCCG 59.058 47.619 5.16 0.00 0.00 5.69
1595 1983 3.305131 CCATGCATGATCATTACAGTGCC 60.305 47.826 28.31 0.00 0.00 5.01
1596 1984 3.566742 TCCATGCATGATCATTACAGTGC 59.433 43.478 28.31 7.64 0.00 4.40
1714 2453 8.892723 TCTCAACATTGTGATGGATTGTATTAC 58.107 33.333 0.00 0.00 37.60 1.89
1720 2459 5.413523 TGTCTCTCAACATTGTGATGGATTG 59.586 40.000 0.00 0.00 37.60 2.67
1732 2471 4.025040 TGGCATTTCTGTCTCTCAACAT 57.975 40.909 0.00 0.00 0.00 2.71
1763 2504 5.722263 AGATGATTGACAAGAGACAGTGAG 58.278 41.667 0.00 0.00 0.00 3.51
1789 2530 1.671261 CCTCCTCGTAGCTGCATATGC 60.671 57.143 21.09 21.09 42.50 3.14
1790 2531 1.615883 ACCTCCTCGTAGCTGCATATG 59.384 52.381 1.02 0.00 0.00 1.78
1791 2532 1.615883 CACCTCCTCGTAGCTGCATAT 59.384 52.381 1.02 0.00 0.00 1.78
1853 2594 9.656040 CACTGTAACCTCTCGTAGATATACTAT 57.344 37.037 0.00 0.00 33.89 2.12
1854 2595 8.093307 CCACTGTAACCTCTCGTAGATATACTA 58.907 40.741 0.00 0.00 33.89 1.82
1856 2597 6.933521 TCCACTGTAACCTCTCGTAGATATAC 59.066 42.308 0.00 0.00 33.89 1.47
1857 2598 7.015974 TCTCCACTGTAACCTCTCGTAGATATA 59.984 40.741 0.00 0.00 33.89 0.86
1858 2599 5.938279 TCCACTGTAACCTCTCGTAGATAT 58.062 41.667 0.00 0.00 33.89 1.63
1860 2601 4.080469 TCTCCACTGTAACCTCTCGTAGAT 60.080 45.833 0.00 0.00 33.89 1.98
1861 2602 3.262660 TCTCCACTGTAACCTCTCGTAGA 59.737 47.826 0.00 0.00 0.00 2.59
1862 2603 3.607741 TCTCCACTGTAACCTCTCGTAG 58.392 50.000 0.00 0.00 0.00 3.51
1863 2604 3.607741 CTCTCCACTGTAACCTCTCGTA 58.392 50.000 0.00 0.00 0.00 3.43
1864 2605 2.438411 CTCTCCACTGTAACCTCTCGT 58.562 52.381 0.00 0.00 0.00 4.18
1905 2968 4.587262 AGGGTTGTGTGCATCGATATACTA 59.413 41.667 0.00 0.00 0.00 1.82
1906 2969 3.388024 AGGGTTGTGTGCATCGATATACT 59.612 43.478 0.00 0.00 0.00 2.12
1907 2970 3.728845 AGGGTTGTGTGCATCGATATAC 58.271 45.455 0.00 0.57 0.00 1.47
1908 2971 4.415881 AAGGGTTGTGTGCATCGATATA 57.584 40.909 0.00 0.00 0.00 0.86
1996 3059 5.574891 AATAAACACACACACACACACAT 57.425 34.783 0.00 0.00 0.00 3.21
2022 3085 5.735285 TCGATGAAGGATATCTGCTCAAT 57.265 39.130 2.05 0.00 0.00 2.57
2025 3088 4.142491 ACGATCGATGAAGGATATCTGCTC 60.142 45.833 24.34 0.00 0.00 4.26
2027 3090 3.856521 CACGATCGATGAAGGATATCTGC 59.143 47.826 24.34 0.00 0.00 4.26
2028 3091 5.302357 TCACGATCGATGAAGGATATCTG 57.698 43.478 24.34 4.58 0.00 2.90
2030 3093 6.804534 GATTCACGATCGATGAAGGATATC 57.195 41.667 24.34 15.77 39.36 1.63
2054 3117 4.159135 AGAATTTCCATGAATCAGCCACAC 59.841 41.667 0.00 0.00 0.00 3.82
2062 3125 7.779073 AGACCAATTCAGAATTTCCATGAATC 58.221 34.615 5.58 4.17 41.56 2.52
2064 3127 6.720748 TGAGACCAATTCAGAATTTCCATGAA 59.279 34.615 5.58 4.21 37.36 2.57
2073 3136 5.336213 GCAATGTGTGAGACCAATTCAGAAT 60.336 40.000 0.00 0.00 0.00 2.40
2076 3139 3.504906 AGCAATGTGTGAGACCAATTCAG 59.495 43.478 0.00 0.00 0.00 3.02
2104 3167 3.627577 CGGATATTTGTTTCCCTGACCAG 59.372 47.826 0.00 0.00 0.00 4.00
2143 3208 4.808895 TCTGTGTGATGTGTGAACAGTAAC 59.191 41.667 0.00 0.00 39.39 2.50
2144 3209 5.017294 TCTGTGTGATGTGTGAACAGTAA 57.983 39.130 0.00 0.00 39.39 2.24
2146 3211 3.541996 TCTGTGTGATGTGTGAACAGT 57.458 42.857 0.00 0.00 39.39 3.55
2147 3212 4.400036 CATCTGTGTGATGTGTGAACAG 57.600 45.455 0.00 0.00 45.55 3.16
2209 3288 2.939103 AGAAGACAGCGCCAATAATGAC 59.061 45.455 2.29 0.00 0.00 3.06
2222 3301 4.962155 ACTTGGTTACTTCCAGAAGACAG 58.038 43.478 14.19 1.00 40.79 3.51
2257 3336 5.278218 CCAGAGGCTCAAAAGAGAAACTTTC 60.278 44.000 18.26 0.00 46.55 2.62
2269 3348 3.782523 AGTATTCATCCCAGAGGCTCAAA 59.217 43.478 18.26 0.00 0.00 2.69
2293 3372 2.413239 CGAGTTGTGGCACATGATTGTC 60.413 50.000 22.73 10.56 44.52 3.18
2408 3488 3.209410 GTCCTAATCCCATGCTGTCAAG 58.791 50.000 0.00 0.00 0.00 3.02
2409 3489 2.092429 GGTCCTAATCCCATGCTGTCAA 60.092 50.000 0.00 0.00 0.00 3.18
2528 3616 5.628433 GCCTAATAAACCGGAAAGGAGAGAA 60.628 44.000 9.46 0.00 45.00 2.87
2531 3622 3.778629 AGCCTAATAAACCGGAAAGGAGA 59.221 43.478 9.46 0.00 45.00 3.71
2573 3664 4.520111 TGTGACTCAACCAATGATTGAAGG 59.480 41.667 6.76 0.00 37.44 3.46
2591 3682 8.245701 TGTTAAATTTTGGTTTTCAGTGTGAC 57.754 30.769 0.00 0.00 0.00 3.67
2623 3715 7.838079 TTGGCAAATATAGCAATCCTACATT 57.162 32.000 0.00 0.00 0.00 2.71
2646 3738 4.763793 CACTCACTGAATTGTCTTGGGATT 59.236 41.667 0.00 0.00 0.00 3.01
2654 3747 0.798776 CGGCCACTCACTGAATTGTC 59.201 55.000 2.24 0.00 0.00 3.18
2688 3781 2.000447 GTAGTTTTGCCTGTCTAGCGG 59.000 52.381 0.00 0.00 0.00 5.52
2689 3782 2.960819 AGTAGTTTTGCCTGTCTAGCG 58.039 47.619 0.00 0.00 0.00 4.26
2690 3783 4.817517 TGTAGTAGTTTTGCCTGTCTAGC 58.182 43.478 0.00 0.00 0.00 3.42
2722 3815 8.108551 AGTAGAACGACTAAAATATAGCCGAT 57.891 34.615 0.00 0.00 32.49 4.18
2725 3818 9.182933 CAGAAGTAGAACGACTAAAATATAGCC 57.817 37.037 0.00 0.00 32.49 3.93
2730 3823 7.372714 TGCACAGAAGTAGAACGACTAAAATA 58.627 34.615 0.00 0.00 32.49 1.40
2737 3830 5.061064 CAGTTATGCACAGAAGTAGAACGAC 59.939 44.000 0.00 0.00 0.00 4.34
2785 3883 8.822805 AGAAGAGGTACCACAATACTATGAAAA 58.177 33.333 15.94 0.00 0.00 2.29
2813 3911 3.701542 TGAGGATGCGTCACTTAGAAGAT 59.298 43.478 8.47 0.00 0.00 2.40
2883 3981 6.969366 TGGAGTGATCAAAATATATTTGGCG 58.031 36.000 11.42 4.23 0.00 5.69
2894 3992 6.462552 TGAACATTGTTGGAGTGATCAAAA 57.537 33.333 6.80 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.