Multiple sequence alignment - TraesCS1B01G365400

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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 TraesCS1B01G365400 chr1B 100.000 2669 0 0 1 2669 596306986 596309654 0.000000e+00 4929
1 TraesCS1B01G365400 chr1B 88.306 744 61 12 1945 2666 133046463 133047202 0.000000e+00 869
2 TraesCS1B01G365400 chr1D 90.937 1291 55 15 544 1821 439506264 439507505 0.000000e+00 1679
3 TraesCS1B01G365400 chr1D 85.714 532 31 17 38 527 439505691 439506219 1.100000e-143 520
4 TraesCS1B01G365400 chr1A 89.580 1190 51 30 713 1875 539316993 539315850 0.000000e+00 1443
5 TraesCS1B01G365400 chr1A 87.683 682 35 21 1 640 539317784 539317110 0.000000e+00 749
6 TraesCS1B01G365400 chr4B 88.187 728 62 6 1942 2669 604041734 604041031 0.000000e+00 846
7 TraesCS1B01G365400 chr4B 83.806 741 85 15 1945 2667 642919606 642918883 0.000000e+00 671
8 TraesCS1B01G365400 chr4B 92.523 214 13 2 2456 2669 642916394 642916184 1.200000e-78 303
9 TraesCS1B01G365400 chr7B 87.399 746 67 9 1945 2669 719539769 719539030 0.000000e+00 832
10 TraesCS1B01G365400 chr7B 84.972 539 46 22 2162 2668 642988109 642987574 5.090000e-142 514
11 TraesCS1B01G365400 chr7B 82.883 555 44 28 2162 2668 643001404 643000853 4.050000e-123 451
12 TraesCS1B01G365400 chr7B 82.794 494 61 10 1945 2416 211799159 211799650 1.140000e-113 420
13 TraesCS1B01G365400 chr7B 91.506 259 21 1 2410 2668 643014062 643013805 3.270000e-94 355
14 TraesCS1B01G365400 chr7B 91.031 223 17 3 2448 2669 642970679 642970459 5.590000e-77 298
15 TraesCS1B01G365400 chr7B 91.031 223 17 3 2448 2669 642986107 642985887 5.590000e-77 298
16 TraesCS1B01G365400 chr6B 87.032 748 66 19 1944 2669 164617368 164618106 0.000000e+00 815
17 TraesCS1B01G365400 chr2B 87.193 570 44 12 1945 2492 786869375 786869937 2.920000e-174 621
18 TraesCS1B01G365400 chr2B 84.514 381 47 8 2054 2434 708047172 708046804 1.510000e-97 366
19 TraesCS1B01G365400 chr4D 83.806 494 56 10 1945 2416 98911058 98910567 5.240000e-122 448
20 TraesCS1B01G365400 chr2D 83.130 492 77 6 1945 2434 531492138 531491651 6.780000e-121 444
21 TraesCS1B01G365400 chr2A 85.284 299 31 5 2136 2434 174386527 174386242 2.010000e-76 296


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 TraesCS1B01G365400 chr1B 596306986 596309654 2668 False 4929.0 4929 100.0000 1 2669 1 chr1B.!!$F2 2668
1 TraesCS1B01G365400 chr1B 133046463 133047202 739 False 869.0 869 88.3060 1945 2666 1 chr1B.!!$F1 721
2 TraesCS1B01G365400 chr1D 439505691 439507505 1814 False 1099.5 1679 88.3255 38 1821 2 chr1D.!!$F1 1783
3 TraesCS1B01G365400 chr1A 539315850 539317784 1934 True 1096.0 1443 88.6315 1 1875 2 chr1A.!!$R1 1874
4 TraesCS1B01G365400 chr4B 604041031 604041734 703 True 846.0 846 88.1870 1942 2669 1 chr4B.!!$R1 727
5 TraesCS1B01G365400 chr4B 642916184 642919606 3422 True 487.0 671 88.1645 1945 2669 2 chr4B.!!$R2 724
6 TraesCS1B01G365400 chr7B 719539030 719539769 739 True 832.0 832 87.3990 1945 2669 1 chr7B.!!$R4 724
7 TraesCS1B01G365400 chr7B 643000853 643001404 551 True 451.0 451 82.8830 2162 2668 1 chr7B.!!$R2 506
8 TraesCS1B01G365400 chr7B 642985887 642988109 2222 True 406.0 514 88.0015 2162 2669 2 chr7B.!!$R5 507
9 TraesCS1B01G365400 chr6B 164617368 164618106 738 False 815.0 815 87.0320 1944 2669 1 chr6B.!!$F1 725
10 TraesCS1B01G365400 chr2B 786869375 786869937 562 False 621.0 621 87.1930 1945 2492 1 chr2B.!!$F1 547

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
612 711 0.465705 GCTAGCTCCACATGCAGGTA 59.534 55.0 2.51 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 2142 0.110486 GTGGGAAGGACAGCCTGAAA 59.89 55.0 0.0 0.0 46.28 2.69 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 1.184970 TCTGAGGTCCACATGCGACA 61.185 55.000 13.78 0.00 31.55 4.35
37 38 3.114616 ACATGCGACAGTGCGAGC 61.115 61.111 10.49 4.87 37.81 5.03
38 39 3.113979 CATGCGACAGTGCGAGCA 61.114 61.111 9.65 9.65 44.13 4.26
39 40 3.114616 ATGCGACAGTGCGAGCAC 61.115 61.111 19.45 19.45 46.50 4.40
73 82 2.031157 CACTGAGGCGAAACGGAAAAAT 60.031 45.455 0.00 0.00 0.00 1.82
80 89 6.017275 TGAGGCGAAACGGAAAAATAAGTTTA 60.017 34.615 0.00 0.00 37.00 2.01
166 175 2.597903 GGGGATCAGGAGGCCAAC 59.402 66.667 5.01 0.00 0.00 3.77
301 313 3.650950 AGCCACGCTCCCCAATGT 61.651 61.111 0.00 0.00 30.62 2.71
304 316 1.746615 CCACGCTCCCCAATGTCAG 60.747 63.158 0.00 0.00 0.00 3.51
326 338 7.605691 GTCAGGATCAATTAATCTACCCATCTG 59.394 40.741 0.00 0.00 0.00 2.90
350 362 8.313944 TGCTCATCTATTTTAACAGGGTAGTA 57.686 34.615 0.00 0.00 0.00 1.82
351 363 8.421784 TGCTCATCTATTTTAACAGGGTAGTAG 58.578 37.037 0.00 0.00 0.00 2.57
352 364 8.422566 GCTCATCTATTTTAACAGGGTAGTAGT 58.577 37.037 0.00 0.00 0.00 2.73
382 422 9.317827 ACTTAATAGGACCACAGTAACTAAAGA 57.682 33.333 0.00 0.00 0.00 2.52
400 440 0.672342 GAATGGCATCATGTGGGAGC 59.328 55.000 0.00 0.00 33.18 4.70
451 491 4.563337 GGTCAAACCCTGTCAAAGTAAC 57.437 45.455 0.00 0.00 30.04 2.50
462 518 5.392811 CCTGTCAAAGTAACCGTCCTACTAG 60.393 48.000 0.00 0.00 0.00 2.57
509 565 4.135153 CGAGGGACAGAGCACGGG 62.135 72.222 0.00 0.00 0.00 5.28
527 583 4.000988 ACGGGTGATGAACTACATTTGTC 58.999 43.478 0.00 0.00 39.56 3.18
547 642 1.069022 CGGCACAATTCAACTGACTGG 60.069 52.381 0.00 0.00 0.00 4.00
557 652 4.271696 TCAACTGACTGGTATCCAACAG 57.728 45.455 15.42 15.42 40.80 3.16
612 711 0.465705 GCTAGCTCCACATGCAGGTA 59.534 55.000 2.51 0.00 0.00 3.08
676 850 1.975407 GTGCTTCCATGCCTGCAGT 60.975 57.895 13.81 0.00 36.03 4.40
703 877 5.179045 CAGTTCACTGCTCTTCATTTGTT 57.821 39.130 0.00 0.00 37.15 2.83
704 878 5.585390 CAGTTCACTGCTCTTCATTTGTTT 58.415 37.500 0.00 0.00 37.15 2.83
705 879 5.457799 CAGTTCACTGCTCTTCATTTGTTTG 59.542 40.000 0.00 0.00 37.15 2.93
706 880 5.126061 AGTTCACTGCTCTTCATTTGTTTGT 59.874 36.000 0.00 0.00 0.00 2.83
707 881 5.581126 TCACTGCTCTTCATTTGTTTGTT 57.419 34.783 0.00 0.00 0.00 2.83
708 882 5.964758 TCACTGCTCTTCATTTGTTTGTTT 58.035 33.333 0.00 0.00 0.00 2.83
709 883 7.094508 TCACTGCTCTTCATTTGTTTGTTTA 57.905 32.000 0.00 0.00 0.00 2.01
710 884 7.542890 TCACTGCTCTTCATTTGTTTGTTTAA 58.457 30.769 0.00 0.00 0.00 1.52
727 901 2.514205 TAATTAGAACCCTACGGCGC 57.486 50.000 6.90 0.00 0.00 6.53
840 1014 4.887071 AGCAACTGGTCAAACATAAGACAA 59.113 37.500 0.00 0.00 36.50 3.18
850 1024 3.460857 ACATAAGACAAGATCGAGCCC 57.539 47.619 0.00 0.00 0.00 5.19
851 1025 3.034635 ACATAAGACAAGATCGAGCCCT 58.965 45.455 0.00 0.00 0.00 5.19
852 1026 4.215908 ACATAAGACAAGATCGAGCCCTA 58.784 43.478 0.00 0.00 0.00 3.53
853 1027 4.279671 ACATAAGACAAGATCGAGCCCTAG 59.720 45.833 0.00 0.00 0.00 3.02
854 1028 1.698506 AGACAAGATCGAGCCCTAGG 58.301 55.000 0.06 0.06 0.00 3.02
947 1126 1.597027 CCACCGTCGTCCAGCTTTT 60.597 57.895 0.00 0.00 0.00 2.27
948 1127 1.566018 CCACCGTCGTCCAGCTTTTC 61.566 60.000 0.00 0.00 0.00 2.29
1009 1191 1.002430 GCTCAGTGAGAATGGTGTCCA 59.998 52.381 24.55 0.00 38.19 4.02
1071 1253 0.325203 GCTCCCTCCTCCTCTGTTCT 60.325 60.000 0.00 0.00 0.00 3.01
1094 1276 2.818274 GTCCATGGACGAACCGGC 60.818 66.667 28.52 3.94 42.61 6.13
1124 1306 4.427661 GCACGTCGCTCCAGCTCT 62.428 66.667 0.00 0.00 39.32 4.09
1125 1307 2.505777 CACGTCGCTCCAGCTCTG 60.506 66.667 0.00 0.00 39.32 3.35
1126 1308 2.986413 ACGTCGCTCCAGCTCTGT 60.986 61.111 0.00 0.00 39.32 3.41
1127 1309 2.202544 CGTCGCTCCAGCTCTGTC 60.203 66.667 0.00 0.00 39.32 3.51
1128 1310 2.202544 GTCGCTCCAGCTCTGTCG 60.203 66.667 0.00 0.00 39.32 4.35
1129 1311 4.121669 TCGCTCCAGCTCTGTCGC 62.122 66.667 0.00 0.00 39.32 5.19
1131 1313 3.768922 GCTCCAGCTCTGTCGCCT 61.769 66.667 0.00 0.00 38.21 5.52
1132 1314 2.977178 CTCCAGCTCTGTCGCCTT 59.023 61.111 0.00 0.00 0.00 4.35
1133 1315 1.153667 CTCCAGCTCTGTCGCCTTC 60.154 63.158 0.00 0.00 0.00 3.46
1134 1316 2.507992 CCAGCTCTGTCGCCTTCG 60.508 66.667 0.00 0.00 0.00 3.79
1135 1317 2.259818 CAGCTCTGTCGCCTTCGT 59.740 61.111 0.00 0.00 36.96 3.85
1136 1318 1.803519 CAGCTCTGTCGCCTTCGTC 60.804 63.158 0.00 0.00 36.96 4.20
1137 1319 2.507324 GCTCTGTCGCCTTCGTCC 60.507 66.667 0.00 0.00 36.96 4.79
1138 1320 2.995872 GCTCTGTCGCCTTCGTCCT 61.996 63.158 0.00 0.00 36.96 3.85
1139 1321 1.654954 GCTCTGTCGCCTTCGTCCTA 61.655 60.000 0.00 0.00 36.96 2.94
1140 1322 0.099082 CTCTGTCGCCTTCGTCCTAC 59.901 60.000 0.00 0.00 36.96 3.18
1141 1323 1.139095 CTGTCGCCTTCGTCCTACC 59.861 63.158 0.00 0.00 36.96 3.18
1142 1324 2.280823 CTGTCGCCTTCGTCCTACCC 62.281 65.000 0.00 0.00 36.96 3.69
1143 1325 2.757099 TCGCCTTCGTCCTACCCC 60.757 66.667 0.00 0.00 36.96 4.95
1144 1326 3.846430 CGCCTTCGTCCTACCCCC 61.846 72.222 0.00 0.00 0.00 5.40
1273 1461 1.380112 GCCAGTACGTCCTCCTCCT 60.380 63.158 0.00 0.00 0.00 3.69
1274 1462 1.385756 GCCAGTACGTCCTCCTCCTC 61.386 65.000 0.00 0.00 0.00 3.71
1389 1584 3.372554 GAGCGGGTACAGGGTGCTC 62.373 68.421 0.00 1.90 44.37 4.26
1664 1864 2.436646 CAAGTGCCCGGCCTACTG 60.437 66.667 7.03 0.00 0.00 2.74
1688 1888 1.338107 TGATTGAGGAGTGTGGACGT 58.662 50.000 0.00 0.00 0.00 4.34
1710 1910 2.512515 GCCCGCACCAGATGAGAC 60.513 66.667 0.00 0.00 0.00 3.36
1825 2040 5.297527 AGGTTTGGGTCGTTTTAGTTTGTAG 59.702 40.000 0.00 0.00 0.00 2.74
1830 2045 4.815846 GGGTCGTTTTAGTTTGTAGTCCAA 59.184 41.667 0.00 0.00 0.00 3.53
1834 2049 5.459762 TCGTTTTAGTTTGTAGTCCAACGAG 59.540 40.000 0.00 0.00 39.69 4.18
1835 2050 5.459762 CGTTTTAGTTTGTAGTCCAACGAGA 59.540 40.000 0.00 0.00 38.38 4.04
1855 2070 4.130118 AGAGTACTTGCTGTGGTTTGAAG 58.870 43.478 0.00 0.00 0.00 3.02
1863 2078 3.128589 TGCTGTGGTTTGAAGTTGAAGTC 59.871 43.478 0.00 0.00 0.00 3.01
1871 2086 5.395642 GTTTGAAGTTGAAGTCGTTTCCAA 58.604 37.500 0.00 0.00 34.77 3.53
1875 2090 5.182380 TGAAGTTGAAGTCGTTTCCAAGTTT 59.818 36.000 0.00 0.00 34.77 2.66
1876 2091 5.231265 AGTTGAAGTCGTTTCCAAGTTTC 57.769 39.130 1.15 0.00 34.77 2.78
1877 2092 4.941873 AGTTGAAGTCGTTTCCAAGTTTCT 59.058 37.500 1.15 0.00 34.77 2.52
1878 2093 5.414765 AGTTGAAGTCGTTTCCAAGTTTCTT 59.585 36.000 1.15 0.00 34.77 2.52
1879 2094 5.890424 TGAAGTCGTTTCCAAGTTTCTTT 57.110 34.783 1.15 0.00 34.77 2.52
1880 2095 6.988622 TGAAGTCGTTTCCAAGTTTCTTTA 57.011 33.333 1.15 0.00 34.77 1.85
1881 2096 7.562454 TGAAGTCGTTTCCAAGTTTCTTTAT 57.438 32.000 1.15 0.00 34.77 1.40
1882 2097 7.636326 TGAAGTCGTTTCCAAGTTTCTTTATC 58.364 34.615 1.15 0.00 34.77 1.75
1883 2098 6.224420 AGTCGTTTCCAAGTTTCTTTATCG 57.776 37.500 0.00 0.00 0.00 2.92
1884 2099 5.756833 AGTCGTTTCCAAGTTTCTTTATCGT 59.243 36.000 0.00 0.00 0.00 3.73
1885 2100 6.259387 AGTCGTTTCCAAGTTTCTTTATCGTT 59.741 34.615 0.00 0.00 0.00 3.85
1886 2101 6.356190 GTCGTTTCCAAGTTTCTTTATCGTTG 59.644 38.462 0.00 0.00 0.00 4.10
1887 2102 6.258287 TCGTTTCCAAGTTTCTTTATCGTTGA 59.742 34.615 0.00 0.00 0.00 3.18
1888 2103 6.908284 CGTTTCCAAGTTTCTTTATCGTTGAA 59.092 34.615 0.00 0.00 0.00 2.69
1889 2104 7.429920 CGTTTCCAAGTTTCTTTATCGTTGAAA 59.570 33.333 0.00 0.00 0.00 2.69
1890 2105 8.743099 GTTTCCAAGTTTCTTTATCGTTGAAAG 58.257 33.333 0.00 0.00 35.60 2.62
1891 2106 6.966021 TCCAAGTTTCTTTATCGTTGAAAGG 58.034 36.000 6.61 0.00 35.11 3.11
1892 2107 6.768861 TCCAAGTTTCTTTATCGTTGAAAGGA 59.231 34.615 6.61 0.00 35.11 3.36
1893 2108 7.283580 TCCAAGTTTCTTTATCGTTGAAAGGAA 59.716 33.333 6.61 2.71 35.11 3.36
1894 2109 8.082242 CCAAGTTTCTTTATCGTTGAAAGGAAT 58.918 33.333 4.33 0.00 34.63 3.01
1895 2110 9.118236 CAAGTTTCTTTATCGTTGAAAGGAATC 57.882 33.333 4.33 0.00 34.63 2.52
1896 2111 7.519002 AGTTTCTTTATCGTTGAAAGGAATCG 58.481 34.615 4.33 0.00 34.63 3.34
1897 2112 7.172703 AGTTTCTTTATCGTTGAAAGGAATCGT 59.827 33.333 4.33 0.00 34.63 3.73
1898 2113 7.429636 TTCTTTATCGTTGAAAGGAATCGTT 57.570 32.000 6.61 0.00 35.11 3.85
1899 2114 7.429636 TCTTTATCGTTGAAAGGAATCGTTT 57.570 32.000 0.10 0.10 35.11 3.60
1900 2115 7.515643 TCTTTATCGTTGAAAGGAATCGTTTC 58.484 34.615 18.28 18.28 38.30 2.78
1913 2128 3.980136 CGTTTCCACGTTGTTGTGT 57.020 47.368 0.00 0.00 41.84 3.72
1914 2129 1.529802 CGTTTCCACGTTGTTGTGTG 58.470 50.000 0.00 0.00 41.84 3.82
1915 2130 1.135916 CGTTTCCACGTTGTTGTGTGT 60.136 47.619 0.00 0.00 41.84 3.72
1916 2131 2.093941 CGTTTCCACGTTGTTGTGTGTA 59.906 45.455 0.00 0.00 41.84 2.90
1917 2132 3.424565 CGTTTCCACGTTGTTGTGTGTAA 60.425 43.478 0.00 0.00 41.84 2.41
1918 2133 4.092816 GTTTCCACGTTGTTGTGTGTAAG 58.907 43.478 0.00 0.00 38.20 2.34
1919 2134 2.975266 TCCACGTTGTTGTGTGTAAGT 58.025 42.857 0.00 0.00 38.20 2.24
1920 2135 3.336468 TCCACGTTGTTGTGTGTAAGTT 58.664 40.909 0.00 0.00 38.20 2.66
1921 2136 3.752222 TCCACGTTGTTGTGTGTAAGTTT 59.248 39.130 0.00 0.00 38.20 2.66
1922 2137 3.849145 CCACGTTGTTGTGTGTAAGTTTG 59.151 43.478 0.00 0.00 38.20 2.93
1923 2138 3.299542 CACGTTGTTGTGTGTAAGTTTGC 59.700 43.478 0.00 0.00 35.12 3.68
1924 2139 2.849473 CGTTGTTGTGTGTAAGTTTGCC 59.151 45.455 0.00 0.00 0.00 4.52
1925 2140 3.183754 GTTGTTGTGTGTAAGTTTGCCC 58.816 45.455 0.00 0.00 0.00 5.36
1926 2141 2.729194 TGTTGTGTGTAAGTTTGCCCT 58.271 42.857 0.00 0.00 0.00 5.19
1927 2142 3.093057 TGTTGTGTGTAAGTTTGCCCTT 58.907 40.909 0.00 0.00 0.00 3.95
1928 2143 3.511934 TGTTGTGTGTAAGTTTGCCCTTT 59.488 39.130 0.00 0.00 0.00 3.11
1929 2144 4.021016 TGTTGTGTGTAAGTTTGCCCTTTT 60.021 37.500 0.00 0.00 0.00 2.27
1930 2145 4.379339 TGTGTGTAAGTTTGCCCTTTTC 57.621 40.909 0.00 0.00 0.00 2.29
1931 2146 3.764434 TGTGTGTAAGTTTGCCCTTTTCA 59.236 39.130 0.00 0.00 0.00 2.69
1932 2147 4.142271 TGTGTGTAAGTTTGCCCTTTTCAG 60.142 41.667 0.00 0.00 0.00 3.02
1933 2148 3.383185 TGTGTAAGTTTGCCCTTTTCAGG 59.617 43.478 0.00 0.00 40.45 3.86
1947 2162 1.779061 TTCAGGCTGTCCTTCCCACC 61.779 60.000 15.27 0.00 41.93 4.61
1961 2176 2.424793 TCCCACCAGTAGAAAAAGGGT 58.575 47.619 0.00 0.00 36.24 4.34
2040 2255 1.180456 TGTCGGTTCCAACGGCTAGA 61.180 55.000 0.00 0.00 36.79 2.43
2044 2259 1.291272 GTTCCAACGGCTAGACGGT 59.709 57.895 24.42 14.72 38.39 4.83
2060 2275 3.383825 AGACGGTCGGCTTTCATTAGTAT 59.616 43.478 1.89 0.00 0.00 2.12
2070 2285 4.802039 GCTTTCATTAGTATCGGTTCGTGA 59.198 41.667 0.00 0.00 0.00 4.35
2105 2320 3.700577 GTTCGTGCCATGAACCATG 57.299 52.632 17.21 0.00 37.98 3.66
2106 2321 1.164411 GTTCGTGCCATGAACCATGA 58.836 50.000 17.21 0.00 43.81 3.07
2116 2331 4.943705 GCCATGAACCATGAACTAAAGAGA 59.056 41.667 8.38 0.00 43.81 3.10
2126 2341 3.582647 TGAACTAAAGAGATGGTGGCAGA 59.417 43.478 0.00 0.00 0.00 4.26
2145 2360 4.254709 TTGTGTCAGGCTGCGGCT 62.255 61.111 18.85 8.21 39.66 5.52
2170 2385 4.828939 CACCATGACCTATAGTACCGGTTA 59.171 45.833 15.04 0.00 0.00 2.85
2194 2409 2.929592 GCCACAAACCGGTACTAGAGTG 60.930 54.545 8.00 10.50 0.00 3.51
2319 2534 5.645497 ACTTGGTCTTCATTGAACTCTATGC 59.355 40.000 0.00 0.00 0.00 3.14
2320 2535 5.164620 TGGTCTTCATTGAACTCTATGCA 57.835 39.130 0.00 0.00 0.00 3.96
2323 2538 7.512130 TGGTCTTCATTGAACTCTATGCATAT 58.488 34.615 6.92 0.00 0.00 1.78
2344 2589 5.912149 ATGATCTATGGCCTCTTAAACCA 57.088 39.130 3.32 0.00 37.99 3.67
2471 3059 1.340889 TGGCAAAAACTGGATGCACTC 59.659 47.619 0.00 0.00 41.80 3.51
2492 3080 4.426416 TCCGTGTATAAACTGGACAATCG 58.574 43.478 3.39 0.00 0.00 3.34
2528 3117 6.745116 TCAGAGTTTCAGACGAAAACTCATA 58.255 36.000 24.92 15.66 42.66 2.15
2534 3123 9.436957 AGTTTCAGACGAAAACTCATATGTTAT 57.563 29.630 1.90 0.00 42.66 1.89
2545 3136 9.686683 AAAACTCATATGTTATAGAGGCACTTT 57.313 29.630 1.90 0.00 41.55 2.66
2587 3517 2.427095 ACAACTCCAGACTTTTTGTGCC 59.573 45.455 0.00 0.00 0.00 5.01
2634 5585 6.072728 CCACGTCATCAACTTTCAATCCTTTA 60.073 38.462 0.00 0.00 0.00 1.85
2637 5588 7.174946 ACGTCATCAACTTTCAATCCTTTATGT 59.825 33.333 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 67 6.144854 AGTAAACTTATTTTTCCGTTTCGCC 58.855 36.000 0.00 0.00 32.46 5.54
166 175 4.729856 GCGGCCAAGGCAAGCAAG 62.730 66.667 20.67 4.38 42.67 4.01
301 313 7.683578 CAGATGGGTAGATTAATTGATCCTGA 58.316 38.462 6.60 0.00 0.00 3.86
304 316 6.479884 AGCAGATGGGTAGATTAATTGATCC 58.520 40.000 6.60 0.00 0.00 3.36
326 338 8.422566 ACTACTACCCTGTTAAAATAGATGAGC 58.577 37.037 0.00 0.00 0.00 4.26
356 368 9.317827 TCTTTAGTTACTGTGGTCCTATTAAGT 57.682 33.333 0.00 0.00 0.00 2.24
381 421 0.672342 GCTCCCACATGATGCCATTC 59.328 55.000 0.00 0.00 0.00 2.67
382 422 0.032912 TGCTCCCACATGATGCCATT 60.033 50.000 0.00 0.00 0.00 3.16
400 440 7.308229 CCCTTTTACTGAACTGAATCTTGACTG 60.308 40.741 0.00 0.00 0.00 3.51
451 491 0.813184 TGAAACGGCTAGTAGGACGG 59.187 55.000 0.00 0.00 42.77 4.79
462 518 2.095415 AGCTTAAATCGGTTGAAACGGC 60.095 45.455 1.61 0.00 0.00 5.68
509 565 3.435327 TGCCGACAAATGTAGTTCATCAC 59.565 43.478 0.00 0.00 35.48 3.06
527 583 1.069022 CCAGTCAGTTGAATTGTGCCG 60.069 52.381 0.00 0.00 0.00 5.69
547 642 0.392461 TCTTGGCGCCTGTTGGATAC 60.392 55.000 29.70 0.00 34.57 2.24
612 711 4.891756 CCAGAATCCTGCCATGTTTTCTAT 59.108 41.667 0.00 0.00 39.07 1.98
727 901 4.057224 TGTTGCCAACACTAGCGG 57.943 55.556 6.08 0.00 36.25 5.52
794 968 6.754209 GCTTCGTGATCAAATAAGAGAAGAGA 59.246 38.462 14.12 0.00 36.82 3.10
795 969 6.533012 TGCTTCGTGATCAAATAAGAGAAGAG 59.467 38.462 14.12 0.44 36.82 2.85
796 970 6.398095 TGCTTCGTGATCAAATAAGAGAAGA 58.602 36.000 14.12 0.00 36.82 2.87
797 971 6.653273 TGCTTCGTGATCAAATAAGAGAAG 57.347 37.500 14.12 12.42 37.49 2.85
798 972 6.650807 AGTTGCTTCGTGATCAAATAAGAGAA 59.349 34.615 14.12 5.83 0.00 2.87
850 1024 1.470051 GCTAGCTAGCTAGGGCCTAG 58.530 60.000 39.60 32.12 45.62 3.02
851 1025 3.674029 GCTAGCTAGCTAGGGCCTA 57.326 57.895 39.60 13.73 45.62 3.93
852 1026 4.531351 GCTAGCTAGCTAGGGCCT 57.469 61.111 39.60 12.58 45.62 5.19
872 1048 1.118356 GCAGGGAGAGGTCCATCGAT 61.118 60.000 0.00 0.00 46.07 3.59
998 1180 2.715046 TGAAGCTGATGGACACCATTC 58.285 47.619 4.74 0.34 45.26 2.67
1009 1191 3.748027 GCTCCATGGATCTTGAAGCTGAT 60.748 47.826 16.63 0.00 0.00 2.90
1044 1226 2.955246 AGGAGGGAGCCCAGGAGA 60.955 66.667 8.53 0.00 38.92 3.71
1089 1271 4.323477 TTGTAAGCAGCGGCCGGT 62.323 61.111 26.97 26.97 42.56 5.28
1123 1305 1.139095 GGTAGGACGAAGGCGACAG 59.861 63.158 0.00 0.00 41.64 3.51
1124 1306 2.345760 GGGTAGGACGAAGGCGACA 61.346 63.158 0.00 0.00 41.64 4.35
1125 1307 2.493501 GGGTAGGACGAAGGCGAC 59.506 66.667 0.00 0.00 41.64 5.19
1126 1308 2.757099 GGGGTAGGACGAAGGCGA 60.757 66.667 0.00 0.00 41.64 5.54
1127 1309 3.846430 GGGGGTAGGACGAAGGCG 61.846 72.222 0.00 0.00 44.79 5.52
1273 1461 2.091278 AGAGGTAGAATGGGATGTCGGA 60.091 50.000 0.00 0.00 0.00 4.55
1274 1462 2.297597 GAGAGGTAGAATGGGATGTCGG 59.702 54.545 0.00 0.00 0.00 4.79
1372 1567 3.391382 GAGCACCCTGTACCCGCT 61.391 66.667 0.00 0.00 35.14 5.52
1389 1584 2.476051 GCCGTGCTCGTCATGTTG 59.524 61.111 7.47 0.00 35.01 3.33
1426 1621 0.892755 TCGTACACCATCACCAGGAC 59.107 55.000 0.00 0.00 0.00 3.85
1664 1864 2.093288 TCCACACTCCTCAATCATCAGC 60.093 50.000 0.00 0.00 0.00 4.26
1669 1869 1.338107 ACGTCCACACTCCTCAATCA 58.662 50.000 0.00 0.00 0.00 2.57
1672 1872 1.338973 GTGTACGTCCACACTCCTCAA 59.661 52.381 13.20 0.00 44.41 3.02
1688 1888 3.387091 ATCTGGTGCGGGCGTGTA 61.387 61.111 0.00 0.00 0.00 2.90
1702 1902 0.687354 AACACTTGCCCGTCTCATCT 59.313 50.000 0.00 0.00 0.00 2.90
1710 1910 2.518349 ACCCACAACACTTGCCCG 60.518 61.111 0.00 0.00 0.00 6.13
1825 2040 2.288273 ACAGCAAGTACTCTCGTTGGAC 60.288 50.000 0.00 0.00 0.00 4.02
1830 2045 1.329256 ACCACAGCAAGTACTCTCGT 58.671 50.000 0.00 0.00 0.00 4.18
1834 2049 3.877508 ACTTCAAACCACAGCAAGTACTC 59.122 43.478 0.00 0.00 0.00 2.59
1835 2050 3.886123 ACTTCAAACCACAGCAAGTACT 58.114 40.909 0.00 0.00 0.00 2.73
1843 2058 3.374058 ACGACTTCAACTTCAAACCACAG 59.626 43.478 0.00 0.00 0.00 3.66
1855 2070 5.231265 AGAAACTTGGAAACGACTTCAAC 57.769 39.130 0.00 0.00 35.55 3.18
1863 2078 6.423862 TCAACGATAAAGAAACTTGGAAACG 58.576 36.000 0.00 0.00 0.00 3.60
1871 2086 7.172703 ACGATTCCTTTCAACGATAAAGAAACT 59.827 33.333 9.42 0.00 36.27 2.66
1875 2090 7.429636 AAACGATTCCTTTCAACGATAAAGA 57.570 32.000 9.42 0.00 36.27 2.52
1876 2091 7.706454 GAAACGATTCCTTTCAACGATAAAG 57.294 36.000 0.00 0.00 34.40 1.85
1891 2106 3.033185 CACAACAACGTGGAAACGATTC 58.967 45.455 5.12 0.00 36.85 2.52
1892 2107 2.420722 ACACAACAACGTGGAAACGATT 59.579 40.909 5.12 0.00 41.38 3.34
1893 2108 2.011222 ACACAACAACGTGGAAACGAT 58.989 42.857 5.12 0.00 41.38 3.73
1894 2109 1.128878 CACACAACAACGTGGAAACGA 59.871 47.619 5.12 0.00 41.38 3.85
1895 2110 1.135916 ACACACAACAACGTGGAAACG 60.136 47.619 0.00 0.00 41.38 3.60
1896 2111 2.622546 ACACACAACAACGTGGAAAC 57.377 45.000 0.00 0.00 41.38 2.78
1897 2112 3.752222 ACTTACACACAACAACGTGGAAA 59.248 39.130 0.00 0.00 41.38 3.13
1898 2113 3.336468 ACTTACACACAACAACGTGGAA 58.664 40.909 0.00 0.00 41.38 3.53
1899 2114 2.975266 ACTTACACACAACAACGTGGA 58.025 42.857 0.00 0.00 41.38 4.02
1900 2115 3.750639 AACTTACACACAACAACGTGG 57.249 42.857 0.00 0.00 41.38 4.94
1901 2116 3.299542 GCAAACTTACACACAACAACGTG 59.700 43.478 0.00 0.00 42.81 4.49
1902 2117 3.494232 GCAAACTTACACACAACAACGT 58.506 40.909 0.00 0.00 0.00 3.99
1903 2118 2.849473 GGCAAACTTACACACAACAACG 59.151 45.455 0.00 0.00 0.00 4.10
1904 2119 3.119280 AGGGCAAACTTACACACAACAAC 60.119 43.478 0.00 0.00 0.00 3.32
1905 2120 3.093057 AGGGCAAACTTACACACAACAA 58.907 40.909 0.00 0.00 0.00 2.83
1906 2121 2.729194 AGGGCAAACTTACACACAACA 58.271 42.857 0.00 0.00 0.00 3.33
1907 2122 3.793797 AAGGGCAAACTTACACACAAC 57.206 42.857 0.00 0.00 0.00 3.32
1908 2123 4.220821 TGAAAAGGGCAAACTTACACACAA 59.779 37.500 0.00 0.00 0.00 3.33
1909 2124 3.764434 TGAAAAGGGCAAACTTACACACA 59.236 39.130 0.00 0.00 0.00 3.72
1910 2125 4.359706 CTGAAAAGGGCAAACTTACACAC 58.640 43.478 0.00 0.00 0.00 3.82
1911 2126 3.383185 CCTGAAAAGGGCAAACTTACACA 59.617 43.478 0.00 0.00 0.00 3.72
1912 2127 3.977427 CCTGAAAAGGGCAAACTTACAC 58.023 45.455 0.00 0.00 0.00 2.90
1922 2137 0.540597 AAGGACAGCCTGAAAAGGGC 60.541 55.000 0.00 0.00 46.28 5.19
1923 2138 1.539157 GAAGGACAGCCTGAAAAGGG 58.461 55.000 0.00 0.00 46.28 3.95
1924 2139 1.539157 GGAAGGACAGCCTGAAAAGG 58.461 55.000 0.00 0.00 46.28 3.11
1925 2140 1.202927 TGGGAAGGACAGCCTGAAAAG 60.203 52.381 0.00 0.00 46.28 2.27
1926 2141 0.850100 TGGGAAGGACAGCCTGAAAA 59.150 50.000 0.00 0.00 46.28 2.29
1927 2142 0.110486 GTGGGAAGGACAGCCTGAAA 59.890 55.000 0.00 0.00 46.28 2.69
1928 2143 1.761174 GTGGGAAGGACAGCCTGAA 59.239 57.895 0.00 0.00 46.28 3.02
1929 2144 2.224159 GGTGGGAAGGACAGCCTGA 61.224 63.158 0.00 0.00 46.28 3.86
1930 2145 2.352805 GGTGGGAAGGACAGCCTG 59.647 66.667 0.00 0.00 46.28 4.85
1932 2147 1.198759 TACTGGTGGGAAGGACAGCC 61.199 60.000 0.00 0.00 35.58 4.85
1933 2148 0.250513 CTACTGGTGGGAAGGACAGC 59.749 60.000 0.00 0.00 34.40 4.40
1934 2149 1.938585 TCTACTGGTGGGAAGGACAG 58.061 55.000 0.00 0.00 37.01 3.51
1935 2150 2.409064 TTCTACTGGTGGGAAGGACA 57.591 50.000 0.00 0.00 0.00 4.02
1936 2151 3.782656 TTTTCTACTGGTGGGAAGGAC 57.217 47.619 0.00 0.00 0.00 3.85
1937 2152 3.073946 CCTTTTTCTACTGGTGGGAAGGA 59.926 47.826 0.00 0.00 35.55 3.36
1938 2153 3.421844 CCTTTTTCTACTGGTGGGAAGG 58.578 50.000 0.00 0.00 0.00 3.46
1939 2154 3.181433 ACCCTTTTTCTACTGGTGGGAAG 60.181 47.826 0.00 0.00 37.06 3.46
1940 2155 2.787035 ACCCTTTTTCTACTGGTGGGAA 59.213 45.455 0.00 0.00 37.06 3.97
1947 2162 7.979444 TGAACATAAGACCCTTTTTCTACTG 57.021 36.000 0.00 0.00 0.00 2.74
1961 2176 7.016268 ACTGGGACTAAAGAGTTGAACATAAGA 59.984 37.037 0.00 0.00 35.45 2.10
2040 2255 3.714391 GATACTAATGAAAGCCGACCGT 58.286 45.455 0.00 0.00 0.00 4.83
2044 2259 4.365723 GAACCGATACTAATGAAAGCCGA 58.634 43.478 0.00 0.00 0.00 5.54
2084 2299 3.960237 GTTCATGGCACGAACCGA 58.040 55.556 15.10 0.00 37.40 4.69
2104 2319 3.582647 TCTGCCACCATCTCTTTAGTTCA 59.417 43.478 0.00 0.00 0.00 3.18
2105 2320 3.935828 GTCTGCCACCATCTCTTTAGTTC 59.064 47.826 0.00 0.00 0.00 3.01
2106 2321 3.584848 AGTCTGCCACCATCTCTTTAGTT 59.415 43.478 0.00 0.00 0.00 2.24
2116 2331 0.473755 TGACACAAGTCTGCCACCAT 59.526 50.000 0.00 0.00 45.20 3.55
2126 2341 2.281070 CCGCAGCCTGACACAAGT 60.281 61.111 0.00 0.00 0.00 3.16
2145 2360 3.493334 CGGTACTATAGGTCATGGTGGA 58.507 50.000 4.43 0.00 29.93 4.02
2170 2385 2.303600 TCTAGTACCGGTTTGTGGCATT 59.696 45.455 15.04 0.00 0.00 3.56
2194 2409 6.208644 TGCTGCAGAAAGAATGAACTAAAAC 58.791 36.000 20.43 0.00 0.00 2.43
2319 2534 7.397221 TGGTTTAAGAGGCCATAGATCATATG 58.603 38.462 5.01 0.00 0.00 1.78
2320 2535 7.238514 ACTGGTTTAAGAGGCCATAGATCATAT 59.761 37.037 5.01 0.00 0.00 1.78
2323 2538 4.721776 ACTGGTTTAAGAGGCCATAGATCA 59.278 41.667 5.01 0.00 0.00 2.92
2344 2589 8.324306 TCTGAATTGTCAATAGGAATCTTCACT 58.676 33.333 0.00 0.00 31.88 3.41
2440 2703 1.189227 GTTTTTGCCAAAACGCGCTAG 59.811 47.619 5.73 0.00 41.80 3.42
2471 3059 3.000925 GCGATTGTCCAGTTTATACACGG 59.999 47.826 0.00 0.00 0.00 4.94
2478 3066 3.655486 TCGAAAGCGATTGTCCAGTTTA 58.345 40.909 0.00 0.00 42.51 2.01
2492 3080 5.864474 TCTGAAACTCTGATACTTCGAAAGC 59.136 40.000 0.00 0.00 0.00 3.51
2508 3096 7.730364 AACATATGAGTTTTCGTCTGAAACT 57.270 32.000 10.38 2.20 43.54 2.66
2587 3517 5.105797 TGGCTTTGAATGGTGCATACTAAAG 60.106 40.000 0.00 0.00 0.00 1.85
2634 5585 9.932207 TGCATGAAAAATAGAAAATGAAGACAT 57.068 25.926 0.00 0.00 38.50 3.06


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

AutoCloner maintained by Alex Coulton.