Multiple sequence alignment - TraesCS2B01G457200

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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 TraesCS2B01G457200 chr2B 100.000 4139 0 0 1 4139 651924266 651928404 0.000000e+00 7644
1 TraesCS2B01G457200 chr2B 94.340 689 38 1 3451 4139 785751002 785750315 0.000000e+00 1055
2 TraesCS2B01G457200 chr2B 93.353 677 38 5 3463 4139 2755817 2756486 0.000000e+00 994
3 TraesCS2B01G457200 chr2B 95.663 392 15 1 3452 3843 165403534 165403145 2.720000e-176 628
4 TraesCS2B01G457200 chr2B 97.394 307 7 1 3833 4139 165390100 165389795 4.740000e-144 521
5 TraesCS2B01G457200 chr2A 94.198 1310 66 7 2159 3463 688238244 688236940 0.000000e+00 1989
6 TraesCS2B01G457200 chr2A 86.828 1154 83 29 516 1623 688240668 688239538 0.000000e+00 1225
7 TraesCS2B01G457200 chr2A 90.323 465 26 4 1700 2162 688239354 688238907 3.560000e-165 592
8 TraesCS2B01G457200 chr2A 84.783 460 40 17 4 444 688241294 688240846 6.350000e-118 435
9 TraesCS2B01G457200 chr2A 89.630 135 12 2 1564 1698 688239557 688239425 1.980000e-38 171
10 TraesCS2B01G457200 chr2D 94.082 1318 57 12 2159 3463 545035000 545036309 0.000000e+00 1982
11 TraesCS2B01G457200 chr2D 88.776 1078 52 34 568 1617 545033108 545034144 0.000000e+00 1256
12 TraesCS2B01G457200 chr2D 93.952 463 23 2 1700 2162 545034311 545034768 0.000000e+00 695
13 TraesCS2B01G457200 chr2D 87.071 495 30 15 1 486 545032521 545032990 2.830000e-146 529
14 TraesCS2B01G457200 chr2D 88.889 90 7 3 1564 1652 545034131 545034218 1.570000e-19 108
15 TraesCS2B01G457200 chr1B 96.807 689 21 1 3451 4139 496502774 496503461 0.000000e+00 1149
16 TraesCS2B01G457200 chr7B 96.667 690 22 1 3450 4139 472503892 472504580 0.000000e+00 1146
17 TraesCS2B01G457200 chr7B 91.872 689 55 1 3451 4139 585890301 585890988 0.000000e+00 961
18 TraesCS2B01G457200 chr6B 94.920 689 34 1 3451 4139 672487734 672488421 0.000000e+00 1077
19 TraesCS2B01G457200 chr4A 91.715 688 51 5 3453 4139 176529972 176530654 0.000000e+00 950
20 TraesCS2B01G457200 chr3B 90.393 687 64 2 3453 4139 697459378 697458694 0.000000e+00 902


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 TraesCS2B01G457200 chr2B 651924266 651928404 4138 False 7644.0 7644 100.0000 1 4139 1 chr2B.!!$F2 4138
1 TraesCS2B01G457200 chr2B 785750315 785751002 687 True 1055.0 1055 94.3400 3451 4139 1 chr2B.!!$R3 688
2 TraesCS2B01G457200 chr2B 2755817 2756486 669 False 994.0 994 93.3530 3463 4139 1 chr2B.!!$F1 676
3 TraesCS2B01G457200 chr2A 688236940 688241294 4354 True 882.4 1989 89.1524 4 3463 5 chr2A.!!$R1 3459
4 TraesCS2B01G457200 chr2D 545032521 545036309 3788 False 914.0 1982 90.5540 1 3463 5 chr2D.!!$F1 3462
5 TraesCS2B01G457200 chr1B 496502774 496503461 687 False 1149.0 1149 96.8070 3451 4139 1 chr1B.!!$F1 688
6 TraesCS2B01G457200 chr7B 472503892 472504580 688 False 1146.0 1146 96.6670 3450 4139 1 chr7B.!!$F1 689
7 TraesCS2B01G457200 chr7B 585890301 585890988 687 False 961.0 961 91.8720 3451 4139 1 chr7B.!!$F2 688
8 TraesCS2B01G457200 chr6B 672487734 672488421 687 False 1077.0 1077 94.9200 3451 4139 1 chr6B.!!$F1 688
9 TraesCS2B01G457200 chr4A 176529972 176530654 682 False 950.0 950 91.7150 3453 4139 1 chr4A.!!$F1 686
10 TraesCS2B01G457200 chr3B 697458694 697459378 684 True 902.0 902 90.3930 3453 4139 1 chr3B.!!$R1 686

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
50 51 0.031721 GCAAGCAGTTGAAAGCAGCT 59.968 50.0 0.0 0.0 35.46 4.24 F
600 750 0.034059 GTGGGTCAGTGAGTGAGTGG 59.966 60.0 0.0 0.0 35.13 4.00 F
1736 2061 0.329261 TCAGCCTAATGCAGTTGCCT 59.671 50.0 0.0 0.0 44.83 4.75 F
1737 2062 0.454600 CAGCCTAATGCAGTTGCCTG 59.545 55.0 0.0 0.0 44.83 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1315 1524 0.105709 TGGAGACACCAGACCAGACA 60.106 55.000 0.00 0.0 44.64 3.41 R
2166 3159 0.039618 CCATCCATATTTCCCCCGGG 59.960 60.000 15.80 15.8 0.00 5.73 R
3084 4084 0.911769 TGGTCATGAGCGAATCCCTT 59.088 50.000 19.36 0.0 0.00 3.95 R
3386 4391 1.620819 AGACGACTGATGCCTGAAAGT 59.379 47.619 0.00 0.0 0.00 2.66 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
21 22 1.275291 GGTCTTCGGGAAGTGATGACA 59.725 52.381 8.19 0.00 40.42 3.58
22 23 2.338500 GTCTTCGGGAAGTGATGACAC 58.662 52.381 8.19 0.00 46.24 3.67
41 42 1.816835 ACCATCATCAGCAAGCAGTTG 59.183 47.619 0.00 0.00 36.67 3.16
50 51 0.031721 GCAAGCAGTTGAAAGCAGCT 59.968 50.000 0.00 0.00 35.46 4.24
65 66 1.229082 AGCTGACTGTTCCGGGGTA 60.229 57.895 0.00 0.00 0.00 3.69
67 68 1.542187 GCTGACTGTTCCGGGGTAGT 61.542 60.000 0.00 3.02 0.00 2.73
68 69 1.843368 CTGACTGTTCCGGGGTAGTA 58.157 55.000 0.00 0.00 0.00 1.82
69 70 1.749634 CTGACTGTTCCGGGGTAGTAG 59.250 57.143 0.00 0.00 0.00 2.57
70 71 1.109609 GACTGTTCCGGGGTAGTAGG 58.890 60.000 0.00 0.00 0.00 3.18
71 72 0.706433 ACTGTTCCGGGGTAGTAGGA 59.294 55.000 0.00 0.00 0.00 2.94
72 73 1.077663 ACTGTTCCGGGGTAGTAGGAA 59.922 52.381 0.00 0.00 41.28 3.36
74 75 3.305181 TTCCGGGGTAGTAGGAACC 57.695 57.895 0.00 0.00 38.94 3.62
87 89 0.178961 AGGAACCAACCAGGAAAGCC 60.179 55.000 0.00 0.00 41.22 4.35
145 147 0.961857 GAACCGGGCCGTGGTAAAAT 60.962 55.000 26.32 3.23 39.29 1.82
185 194 6.603599 GCATAGAGGTGAAAATTAAGAAGGGT 59.396 38.462 0.00 0.00 0.00 4.34
315 329 4.920112 CGTGACCACCACCGGCAA 62.920 66.667 0.00 0.00 42.76 4.52
368 390 1.645710 AAGGGTACAGTGGAGGAGTG 58.354 55.000 0.00 0.00 0.00 3.51
445 471 9.793259 TCTTCTCACCTTGAATAAAGTTTACAT 57.207 29.630 0.00 0.00 33.66 2.29
474 559 9.662947 CTTCTCACTCATGCAAATATATATGGA 57.337 33.333 0.00 0.00 0.00 3.41
476 561 9.440773 TCTCACTCATGCAAATATATATGGAAC 57.559 33.333 0.00 0.00 0.00 3.62
515 661 8.226448 TGAAATATATTTTTGCTTGTTTTGGCG 58.774 29.630 11.92 0.00 0.00 5.69
553 703 6.402981 ACAGTAAAAGGGTGGGAATATCTT 57.597 37.500 0.00 0.00 0.00 2.40
555 705 7.246027 ACAGTAAAAGGGTGGGAATATCTTTT 58.754 34.615 0.00 0.00 39.80 2.27
596 746 1.758440 GCCAGTGGGTCAGTGAGTGA 61.758 60.000 12.15 0.00 36.99 3.41
599 749 1.043816 AGTGGGTCAGTGAGTGAGTG 58.956 55.000 0.00 0.00 35.13 3.51
600 750 0.034059 GTGGGTCAGTGAGTGAGTGG 59.966 60.000 0.00 0.00 35.13 4.00
601 751 1.121407 TGGGTCAGTGAGTGAGTGGG 61.121 60.000 0.00 0.00 35.13 4.61
642 796 1.342074 CAGGTCCAGTCCAGTCAAGA 58.658 55.000 0.00 0.00 0.00 3.02
654 808 3.451178 TCCAGTCAAGACCAGCCTAATAC 59.549 47.826 0.00 0.00 0.00 1.89
667 823 3.632145 AGCCTAATACAAAAATCAGCCCG 59.368 43.478 0.00 0.00 0.00 6.13
691 847 5.123661 GGTAAAACGATGATTAAAACCGGGA 59.876 40.000 6.32 0.00 0.00 5.14
693 849 5.708877 AAACGATGATTAAAACCGGGAAA 57.291 34.783 6.32 0.00 0.00 3.13
694 850 4.690184 ACGATGATTAAAACCGGGAAAC 57.310 40.909 6.32 0.00 0.00 2.78
751 922 3.800863 GTCGTCTCCGCGCAGAGA 61.801 66.667 19.24 19.24 40.62 3.10
752 923 3.500642 TCGTCTCCGCGCAGAGAG 61.501 66.667 23.29 17.04 43.47 3.20
753 924 3.500642 CGTCTCCGCGCAGAGAGA 61.501 66.667 23.29 19.03 43.47 3.10
754 925 2.407210 GTCTCCGCGCAGAGAGAG 59.593 66.667 23.29 12.12 43.47 3.20
755 926 2.109739 GTCTCCGCGCAGAGAGAGA 61.110 63.158 23.29 14.16 43.47 3.10
756 927 1.817520 TCTCCGCGCAGAGAGAGAG 60.818 63.158 19.24 6.80 37.98 3.20
757 928 2.826287 TCCGCGCAGAGAGAGAGG 60.826 66.667 8.75 0.00 38.31 3.69
758 929 3.898509 CCGCGCAGAGAGAGAGGG 61.899 72.222 8.75 0.00 33.48 4.30
836 1007 3.822192 CATCCACCGGCGAGACGA 61.822 66.667 9.30 0.00 35.47 4.20
837 1008 3.518998 ATCCACCGGCGAGACGAG 61.519 66.667 9.30 0.00 35.47 4.18
838 1009 3.989838 ATCCACCGGCGAGACGAGA 62.990 63.158 9.30 0.00 35.47 4.04
839 1010 4.180946 CCACCGGCGAGACGAGAG 62.181 72.222 9.30 0.00 35.47 3.20
840 1011 4.838486 CACCGGCGAGACGAGAGC 62.838 72.222 9.30 0.00 35.47 4.09
843 1014 4.583254 CGGCGAGACGAGAGCGAG 62.583 72.222 0.00 0.00 41.64 5.03
844 1015 3.196394 GGCGAGACGAGAGCGAGA 61.196 66.667 0.00 0.00 41.64 4.04
845 1016 2.751913 GGCGAGACGAGAGCGAGAA 61.752 63.158 0.00 0.00 41.64 2.87
846 1017 1.297304 GCGAGACGAGAGCGAGAAG 60.297 63.158 0.00 0.00 41.64 2.85
847 1018 1.697772 GCGAGACGAGAGCGAGAAGA 61.698 60.000 0.00 0.00 41.64 2.87
848 1019 0.722282 CGAGACGAGAGCGAGAAGAA 59.278 55.000 0.00 0.00 41.64 2.52
849 1020 1.128878 CGAGACGAGAGCGAGAAGAAA 59.871 52.381 0.00 0.00 41.64 2.52
850 1021 2.412977 CGAGACGAGAGCGAGAAGAAAA 60.413 50.000 0.00 0.00 41.64 2.29
851 1022 2.912345 GAGACGAGAGCGAGAAGAAAAC 59.088 50.000 0.00 0.00 41.64 2.43
852 1023 1.644780 GACGAGAGCGAGAAGAAAACG 59.355 52.381 0.00 0.00 41.64 3.60
948 1124 3.130160 CAGGCCAGAAAGCGAGCC 61.130 66.667 5.01 0.00 46.13 4.70
1146 1355 2.604686 AAGACGCTCTGGGAGGCA 60.605 61.111 0.00 0.00 0.00 4.75
1241 1450 4.790140 CGTCAACAGATACAAGGTACGTAC 59.210 45.833 17.56 17.56 0.00 3.67
1242 1451 5.098211 GTCAACAGATACAAGGTACGTACC 58.902 45.833 33.16 33.16 46.82 3.34
1255 1464 3.629398 GGTACGTACCTGTGTGCTATACT 59.371 47.826 32.93 0.00 43.10 2.12
1258 1467 3.377485 ACGTACCTGTGTGCTATACTCTG 59.623 47.826 0.00 0.00 0.00 3.35
1267 1476 1.005630 CTATACTCTGCCTGCCGCC 60.006 63.158 0.00 0.00 36.24 6.13
1268 1477 1.748329 CTATACTCTGCCTGCCGCCA 61.748 60.000 0.00 0.00 36.24 5.69
1269 1478 1.121407 TATACTCTGCCTGCCGCCAT 61.121 55.000 0.00 0.00 36.24 4.40
1280 1489 3.451894 CCGCCATTCCCTTGCACC 61.452 66.667 0.00 0.00 0.00 5.01
1281 1490 2.361610 CGCCATTCCCTTGCACCT 60.362 61.111 0.00 0.00 0.00 4.00
1284 1493 1.318158 GCCATTCCCTTGCACCTCTG 61.318 60.000 0.00 0.00 0.00 3.35
1286 1495 1.000396 ATTCCCTTGCACCTCTGCC 60.000 57.895 0.00 0.00 43.51 4.85
1287 1496 1.504275 ATTCCCTTGCACCTCTGCCT 61.504 55.000 0.00 0.00 43.51 4.75
1289 1498 2.045536 CCTTGCACCTCTGCCTCC 60.046 66.667 0.00 0.00 43.51 4.30
1292 1501 1.229496 TTGCACCTCTGCCTCCCTA 60.229 57.895 0.00 0.00 43.51 3.53
1293 1502 0.840288 TTGCACCTCTGCCTCCCTAA 60.840 55.000 0.00 0.00 43.51 2.69
1307 1516 5.014123 TGCCTCCCTAATAATGGAGTAATGG 59.986 44.000 4.96 0.00 45.56 3.16
1309 1518 6.467339 GCCTCCCTAATAATGGAGTAATGGTT 60.467 42.308 4.96 0.00 45.56 3.67
1310 1519 7.256908 GCCTCCCTAATAATGGAGTAATGGTTA 60.257 40.741 4.96 0.00 45.56 2.85
1311 1520 8.836735 CCTCCCTAATAATGGAGTAATGGTTAT 58.163 37.037 4.96 0.00 45.56 1.89
1314 1523 9.614792 CCCTAATAATGGAGTAATGGTTATAGC 57.385 37.037 0.00 0.00 0.00 2.97
1318 1527 9.726438 AATAATGGAGTAATGGTTATAGCTGTC 57.274 33.333 0.00 0.00 0.00 3.51
1320 1529 6.161855 TGGAGTAATGGTTATAGCTGTCTG 57.838 41.667 0.00 0.00 0.00 3.51
1474 1686 2.105649 GGCCCCTTTCTATCTCAAGAGG 59.894 54.545 0.00 0.00 0.00 3.69
1495 1713 3.732048 TCCTTTTGGGATTGGTAGGAC 57.268 47.619 0.00 0.00 39.58 3.85
1532 1750 6.907212 CCTTTGCTGCTTATAAATGACTAACG 59.093 38.462 0.00 0.00 0.00 3.18
1550 1768 2.514803 ACGTTTCAATCAAAGGGAGGG 58.485 47.619 0.00 0.00 34.67 4.30
1558 1776 1.885049 TCAAAGGGAGGGATCTCTGG 58.115 55.000 0.00 0.00 39.86 3.86
1640 1896 3.288092 CCCTAGGCAACCTAAAATGACC 58.712 50.000 2.05 0.00 35.49 4.02
1650 1906 6.091169 GCAACCTAAAATGACCAATGAATGTG 59.909 38.462 0.00 0.00 0.00 3.21
1661 1917 6.100404 ACCAATGAATGTGTAGCATTGTTT 57.900 33.333 0.00 0.00 46.90 2.83
1666 1922 6.141560 TGAATGTGTAGCATTGTTTGACAA 57.858 33.333 0.00 0.00 46.90 3.18
1669 1925 5.168526 TGTGTAGCATTGTTTGACAAGTC 57.831 39.130 0.00 0.00 41.94 3.01
1698 1954 7.010923 GTGTTGAATTGCACACCTTTAATTTCA 59.989 33.333 5.70 0.00 35.81 2.69
1719 2044 5.309638 TCACGGAGTTTAAAATCCATGTCA 58.690 37.500 28.64 10.92 43.06 3.58
1734 2059 1.167851 TGTCAGCCTAATGCAGTTGC 58.832 50.000 0.00 0.00 44.83 4.17
1735 2060 0.453390 GTCAGCCTAATGCAGTTGCC 59.547 55.000 0.00 0.00 44.83 4.52
1736 2061 0.329261 TCAGCCTAATGCAGTTGCCT 59.671 50.000 0.00 0.00 44.83 4.75
1737 2062 0.454600 CAGCCTAATGCAGTTGCCTG 59.545 55.000 0.00 0.00 44.83 4.85
1801 2126 8.402683 TCTTCTTCTTATAGATATGCCCTAGGT 58.597 37.037 8.29 0.00 0.00 3.08
1834 2160 6.115448 AGGCTTTTCTGAGTATAGTTGTGT 57.885 37.500 0.00 0.00 0.00 3.72
1899 2225 6.768029 TTAGCATTTCACTTTGTTCATTGC 57.232 33.333 0.00 0.00 0.00 3.56
1936 2262 4.142609 AGCTAATCCAACATGACACGAT 57.857 40.909 0.00 0.00 0.00 3.73
1976 2302 5.449553 AGGATAACCCAAGGAATCATCAAC 58.550 41.667 0.00 0.00 37.41 3.18
1984 2310 6.098695 ACCCAAGGAATCATCAACAATAATGG 59.901 38.462 0.00 0.00 0.00 3.16
2009 2335 2.568546 TGCTCCTGATAGAAAGGGGA 57.431 50.000 0.00 0.00 37.50 4.81
2010 2336 2.845659 TGCTCCTGATAGAAAGGGGAA 58.154 47.619 0.00 0.00 37.50 3.97
2043 2369 5.604231 AGCTCAGGTGAATATGGTCAGATTA 59.396 40.000 0.00 0.00 0.00 1.75
2052 2378 9.035607 GTGAATATGGTCAGATTAGTAAGTGTG 57.964 37.037 0.00 0.00 0.00 3.82
2074 2400 1.149923 AGGAAAAGCCAGGGTGGAATT 59.850 47.619 0.00 0.00 40.96 2.17
2133 2460 1.200020 GAATGGAGGCCACGAGTTTTG 59.800 52.381 5.01 0.00 35.80 2.44
2171 3164 3.076079 ACTATTTTTGTACACCCCGGG 57.924 47.619 15.80 15.80 0.00 5.73
2192 3185 3.903090 GGGGAAATATGGATGGCATTTCA 59.097 43.478 0.00 4.09 39.40 2.69
2321 3321 7.174253 TGTTAGGTTTAGAATGACGCTGATTTT 59.826 33.333 0.00 0.00 0.00 1.82
2330 3330 2.428890 TGACGCTGATTTTGGGTTTGTT 59.571 40.909 0.00 0.00 0.00 2.83
2333 3333 3.194062 CGCTGATTTTGGGTTTGTTTGT 58.806 40.909 0.00 0.00 0.00 2.83
2354 3354 4.221703 TGTGTGTTGGAACCAATTTCAAGT 59.778 37.500 9.53 0.00 38.28 3.16
2370 3370 9.934190 CAATTTCAAGTTTTCAGGTAAAAATGG 57.066 29.630 0.00 0.00 38.76 3.16
2377 3377 7.216494 AGTTTTCAGGTAAAAATGGTCCATTG 58.784 34.615 18.02 4.56 38.76 2.82
2412 3412 3.907894 TGTGTCGCCTAATTTGTTTCC 57.092 42.857 0.00 0.00 0.00 3.13
2454 3454 2.986728 ACATTCCACTACACCCCTCTTT 59.013 45.455 0.00 0.00 0.00 2.52
2550 3550 6.775594 AGTTTATGGGGCAATAACTCTTTC 57.224 37.500 0.00 0.00 0.00 2.62
2589 3589 7.093596 GGGAAAGAAACATCTGATCCAGAAAAT 60.094 37.037 0.43 0.00 44.04 1.82
2748 3748 2.837947 TCTGGGGAGTCTGATGACAAT 58.162 47.619 0.00 0.00 45.20 2.71
2785 3785 1.554617 TCAGCGATGATGAGAAACCCA 59.445 47.619 0.00 0.00 0.00 4.51
2809 3809 2.733945 GCAAAAAGCGGAAGGCCA 59.266 55.556 5.01 0.00 45.17 5.36
3042 4042 1.339610 GAGCAGTCATGGATAGAGCGT 59.660 52.381 0.00 0.00 0.00 5.07
3063 4063 1.478510 GAGGAACAGCGAAGGATGAGA 59.521 52.381 0.00 0.00 32.75 3.27
3199 4199 8.511604 ACTAGACATCATTTTTCTTACCATGG 57.488 34.615 11.19 11.19 0.00 3.66
3224 4224 8.398665 GGTTCATCGATTCTTTTTAGCTATTGT 58.601 33.333 0.00 0.00 0.00 2.71
3246 4246 3.430042 ACATGCTGTTGTCCAGAAGAT 57.570 42.857 0.00 0.00 44.49 2.40
3258 4258 4.397103 TGTCCAGAAGATGATGTTTGATGC 59.603 41.667 0.00 0.00 0.00 3.91
3286 4286 9.899226 GCTTATTAACTTTATAGGGCTCATTTG 57.101 33.333 0.00 0.00 0.00 2.32
3429 4434 4.692228 TGCGTGAATATCATGTGCTCTAA 58.308 39.130 0.00 0.00 35.86 2.10
3543 4548 5.109210 CAGGACCCAACAGAAAAAGAAAAC 58.891 41.667 0.00 0.00 0.00 2.43
3613 4619 0.321298 AAACGTGATCGGGTCCTTGG 60.321 55.000 0.00 0.00 41.85 3.61
3640 4646 3.382832 CCCGGACTGAACCTCGCT 61.383 66.667 0.73 0.00 0.00 4.93
3645 4651 3.575351 GACTGAACCTCGCTGCCGT 62.575 63.158 0.00 0.00 35.54 5.68
3692 4698 3.407424 AATCGCCATAGAAGCATAGCA 57.593 42.857 0.00 0.00 0.00 3.49
4115 5121 1.153549 GGAGCTCGAGAACGGCATT 60.154 57.895 18.75 0.00 40.21 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.338500 GTGTCATCACTTCCCGAAGAC 58.662 52.381 11.35 0.00 40.79 3.01
21 22 1.816835 CAACTGCTTGCTGATGATGGT 59.183 47.619 6.50 0.00 0.00 3.55
22 23 2.089201 TCAACTGCTTGCTGATGATGG 58.911 47.619 7.99 0.00 0.00 3.51
41 42 0.514691 CGGAACAGTCAGCTGCTTTC 59.485 55.000 9.47 13.98 46.30 2.62
50 51 1.617804 CCTACTACCCCGGAACAGTCA 60.618 57.143 0.73 0.00 0.00 3.41
65 66 2.224793 GCTTTCCTGGTTGGTTCCTACT 60.225 50.000 0.00 0.00 37.07 2.57
67 68 1.074889 GGCTTTCCTGGTTGGTTCCTA 59.925 52.381 0.00 0.00 37.07 2.94
68 69 0.178961 GGCTTTCCTGGTTGGTTCCT 60.179 55.000 0.00 0.00 37.07 3.36
69 70 1.185618 GGGCTTTCCTGGTTGGTTCC 61.186 60.000 0.00 0.00 37.07 3.62
70 71 0.178961 AGGGCTTTCCTGGTTGGTTC 60.179 55.000 0.00 0.00 46.07 3.62
71 72 1.938327 AGGGCTTTCCTGGTTGGTT 59.062 52.632 0.00 0.00 46.07 3.67
72 73 3.688032 AGGGCTTTCCTGGTTGGT 58.312 55.556 0.00 0.00 46.07 3.67
87 89 6.318900 GGTCACCAGAAAATTATTGTAGGAGG 59.681 42.308 0.00 0.00 0.00 4.30
145 147 4.284490 CCTCTATGCTATGCCTACCAAGAA 59.716 45.833 0.00 0.00 0.00 2.52
267 281 1.153269 TTCTGCTGCCACGTGAACA 60.153 52.632 19.30 13.93 0.00 3.18
368 390 6.033341 CGAATAGAATAGATCTGCTGCTACC 58.967 44.000 5.18 0.00 39.30 3.18
447 473 9.662947 CCATATATATTTGCATGAGTGAGAAGA 57.337 33.333 0.00 0.00 0.00 2.87
448 474 9.662947 TCCATATATATTTGCATGAGTGAGAAG 57.337 33.333 0.00 0.00 0.00 2.85
450 476 9.440773 GTTCCATATATATTTGCATGAGTGAGA 57.559 33.333 0.00 0.00 0.00 3.27
451 477 9.223099 TGTTCCATATATATTTGCATGAGTGAG 57.777 33.333 0.00 0.00 0.00 3.51
452 478 9.571816 TTGTTCCATATATATTTGCATGAGTGA 57.428 29.630 0.00 0.00 0.00 3.41
488 573 9.328721 GCCAAAACAAGCAAAAATATATTTCAC 57.671 29.630 11.08 4.45 0.00 3.18
490 575 7.691877 CCGCCAAAACAAGCAAAAATATATTTC 59.308 33.333 11.08 0.00 0.00 2.17
492 577 6.876257 TCCGCCAAAACAAGCAAAAATATATT 59.124 30.769 0.00 0.00 0.00 1.28
493 578 6.402222 TCCGCCAAAACAAGCAAAAATATAT 58.598 32.000 0.00 0.00 0.00 0.86
494 579 5.784177 TCCGCCAAAACAAGCAAAAATATA 58.216 33.333 0.00 0.00 0.00 0.86
495 580 4.636249 TCCGCCAAAACAAGCAAAAATAT 58.364 34.783 0.00 0.00 0.00 1.28
504 650 5.801947 CAGATTATTCTTCCGCCAAAACAAG 59.198 40.000 0.00 0.00 0.00 3.16
511 657 4.161565 ACTGTACAGATTATTCTTCCGCCA 59.838 41.667 29.30 0.00 0.00 5.69
515 661 9.110502 CCCTTTTACTGTACAGATTATTCTTCC 57.889 37.037 29.30 0.00 0.00 3.46
553 703 2.703007 CCCATCCCCAAGAACAAACAAA 59.297 45.455 0.00 0.00 0.00 2.83
555 705 1.501170 TCCCATCCCCAAGAACAAACA 59.499 47.619 0.00 0.00 0.00 2.83
642 796 4.402474 GGCTGATTTTTGTATTAGGCTGGT 59.598 41.667 0.00 0.00 34.92 4.00
654 808 2.983803 CGTTTTACCGGGCTGATTTTTG 59.016 45.455 6.32 0.00 0.00 2.44
667 823 5.123661 TCCCGGTTTTAATCATCGTTTTACC 59.876 40.000 0.00 0.00 0.00 2.85
691 847 1.443872 CTAGCTGTCGTCCGCGTTT 60.444 57.895 4.92 0.00 39.49 3.60
693 849 3.054503 ACTAGCTGTCGTCCGCGT 61.055 61.111 4.92 0.00 39.49 6.01
694 850 2.577112 CACTAGCTGTCGTCCGCG 60.577 66.667 0.00 0.00 39.92 6.46
751 922 1.680651 CACACGCCTCTCCCTCTCT 60.681 63.158 0.00 0.00 0.00 3.10
752 923 1.251527 TTCACACGCCTCTCCCTCTC 61.252 60.000 0.00 0.00 0.00 3.20
753 924 0.616111 ATTCACACGCCTCTCCCTCT 60.616 55.000 0.00 0.00 0.00 3.69
754 925 0.460987 CATTCACACGCCTCTCCCTC 60.461 60.000 0.00 0.00 0.00 4.30
755 926 1.599047 CATTCACACGCCTCTCCCT 59.401 57.895 0.00 0.00 0.00 4.20
756 927 1.450312 CCATTCACACGCCTCTCCC 60.450 63.158 0.00 0.00 0.00 4.30
757 928 1.450312 CCCATTCACACGCCTCTCC 60.450 63.158 0.00 0.00 0.00 3.71
758 929 2.109126 GCCCATTCACACGCCTCTC 61.109 63.158 0.00 0.00 0.00 3.20
834 1005 1.965083 TCGTTTTCTTCTCGCTCTCG 58.035 50.000 0.00 0.00 0.00 4.04
835 1006 3.420672 CGTTTCGTTTTCTTCTCGCTCTC 60.421 47.826 0.00 0.00 0.00 3.20
836 1007 2.471743 CGTTTCGTTTTCTTCTCGCTCT 59.528 45.455 0.00 0.00 0.00 4.09
837 1008 2.470257 TCGTTTCGTTTTCTTCTCGCTC 59.530 45.455 0.00 0.00 0.00 5.03
838 1009 2.466846 TCGTTTCGTTTTCTTCTCGCT 58.533 42.857 0.00 0.00 0.00 4.93
839 1010 2.916735 TCGTTTCGTTTTCTTCTCGC 57.083 45.000 0.00 0.00 0.00 5.03
840 1011 4.142532 GCTTTTCGTTTCGTTTTCTTCTCG 59.857 41.667 0.00 0.00 0.00 4.04
843 1014 3.177061 CCGCTTTTCGTTTCGTTTTCTTC 59.823 43.478 0.00 0.00 36.19 2.87
844 1015 3.103007 CCGCTTTTCGTTTCGTTTTCTT 58.897 40.909 0.00 0.00 36.19 2.52
845 1016 2.540157 CCCGCTTTTCGTTTCGTTTTCT 60.540 45.455 0.00 0.00 36.19 2.52
846 1017 1.776897 CCCGCTTTTCGTTTCGTTTTC 59.223 47.619 0.00 0.00 36.19 2.29
847 1018 1.534385 CCCCGCTTTTCGTTTCGTTTT 60.534 47.619 0.00 0.00 36.19 2.43
848 1019 0.029700 CCCCGCTTTTCGTTTCGTTT 59.970 50.000 0.00 0.00 36.19 3.60
849 1020 1.650363 CCCCGCTTTTCGTTTCGTT 59.350 52.632 0.00 0.00 36.19 3.85
850 1021 2.900167 GCCCCGCTTTTCGTTTCGT 61.900 57.895 0.00 0.00 36.19 3.85
851 1022 2.127003 GCCCCGCTTTTCGTTTCG 60.127 61.111 0.00 0.00 36.19 3.46
852 1023 2.127003 CGCCCCGCTTTTCGTTTC 60.127 61.111 0.00 0.00 36.19 2.78
1014 1220 3.083997 CTGAACCCTCCTCCCCCG 61.084 72.222 0.00 0.00 0.00 5.73
1241 1450 1.759445 AGGCAGAGTATAGCACACAGG 59.241 52.381 0.00 0.00 0.00 4.00
1242 1451 2.819115 CAGGCAGAGTATAGCACACAG 58.181 52.381 0.00 0.00 0.00 3.66
1243 1452 1.134699 GCAGGCAGAGTATAGCACACA 60.135 52.381 0.00 0.00 0.00 3.72
1244 1453 1.576356 GCAGGCAGAGTATAGCACAC 58.424 55.000 0.00 0.00 0.00 3.82
1245 1454 0.465705 GGCAGGCAGAGTATAGCACA 59.534 55.000 0.00 0.00 0.00 4.57
1246 1455 0.598680 CGGCAGGCAGAGTATAGCAC 60.599 60.000 0.00 0.00 0.00 4.40
1247 1456 1.742146 CGGCAGGCAGAGTATAGCA 59.258 57.895 0.00 0.00 0.00 3.49
1248 1457 1.666234 GCGGCAGGCAGAGTATAGC 60.666 63.158 0.00 0.00 42.87 2.97
1249 1458 1.005630 GGCGGCAGGCAGAGTATAG 60.006 63.158 3.07 0.00 46.16 1.31
1250 1459 3.138625 GGCGGCAGGCAGAGTATA 58.861 61.111 3.07 0.00 46.16 1.47
1280 1489 4.550076 CTCCATTATTAGGGAGGCAGAG 57.450 50.000 4.50 0.00 46.28 3.35
1292 1501 9.726438 GACAGCTATAACCATTACTCCATTATT 57.274 33.333 0.00 0.00 0.00 1.40
1293 1502 9.105844 AGACAGCTATAACCATTACTCCATTAT 57.894 33.333 0.00 0.00 0.00 1.28
1307 1516 3.195825 ACACCAGACCAGACAGCTATAAC 59.804 47.826 0.00 0.00 0.00 1.89
1309 1518 3.024547 GACACCAGACCAGACAGCTATA 58.975 50.000 0.00 0.00 0.00 1.31
1310 1519 1.827969 GACACCAGACCAGACAGCTAT 59.172 52.381 0.00 0.00 0.00 2.97
1311 1520 1.203063 AGACACCAGACCAGACAGCTA 60.203 52.381 0.00 0.00 0.00 3.32
1312 1521 0.470833 AGACACCAGACCAGACAGCT 60.471 55.000 0.00 0.00 0.00 4.24
1314 1523 0.605589 GGAGACACCAGACCAGACAG 59.394 60.000 0.00 0.00 38.79 3.51
1315 1524 0.105709 TGGAGACACCAGACCAGACA 60.106 55.000 0.00 0.00 44.64 3.41
1452 1664 1.762957 TCTTGAGATAGAAAGGGGCCG 59.237 52.381 0.00 0.00 0.00 6.13
1457 1669 5.948742 AAGGACCTCTTGAGATAGAAAGG 57.051 43.478 0.00 0.00 33.76 3.11
1505 1723 5.509498 AGTCATTTATAAGCAGCAAAGGGA 58.491 37.500 0.00 0.00 0.00 4.20
1506 1724 5.841957 AGTCATTTATAAGCAGCAAAGGG 57.158 39.130 0.00 0.00 0.00 3.95
1507 1725 6.907212 CGTTAGTCATTTATAAGCAGCAAAGG 59.093 38.462 0.00 0.00 0.00 3.11
1508 1726 7.464358 ACGTTAGTCATTTATAAGCAGCAAAG 58.536 34.615 0.00 0.00 0.00 2.77
1509 1727 7.372451 ACGTTAGTCATTTATAAGCAGCAAA 57.628 32.000 0.00 0.00 0.00 3.68
1532 1750 4.604156 AGATCCCTCCCTTTGATTGAAAC 58.396 43.478 0.00 0.00 0.00 2.78
1550 1768 5.983540 ACTAATTCAACAGGACCAGAGATC 58.016 41.667 0.00 0.00 0.00 2.75
1558 1776 7.393515 AGGGATAAACAACTAATTCAACAGGAC 59.606 37.037 0.00 0.00 0.00 3.85
1632 1888 6.343716 TGCTACACATTCATTGGTCATTTT 57.656 33.333 0.00 0.00 0.00 1.82
1640 1896 6.641723 TGTCAAACAATGCTACACATTCATTG 59.358 34.615 11.29 11.29 46.28 2.82
1650 1906 5.626543 CACATGACTTGTCAAACAATGCTAC 59.373 40.000 7.57 0.00 37.48 3.58
1661 1917 4.097589 TGCAATTCAACACATGACTTGTCA 59.902 37.500 0.00 5.89 45.55 3.58
1698 1954 4.156008 GCTGACATGGATTTTAAACTCCGT 59.844 41.667 17.09 14.80 34.05 4.69
1734 2059 6.449635 TTGTAATTTAGCATTACAGCCAGG 57.550 37.500 7.81 0.00 42.98 4.45
1735 2060 6.498304 CCTTGTAATTTAGCATTACAGCCAG 58.502 40.000 7.81 4.37 42.98 4.85
1736 2061 5.163561 GCCTTGTAATTTAGCATTACAGCCA 60.164 40.000 7.81 0.00 42.98 4.75
1737 2062 5.163561 TGCCTTGTAATTTAGCATTACAGCC 60.164 40.000 12.88 6.32 42.98 4.85
1801 2126 1.349026 CAGAAAAGCCTCACTCCCAGA 59.651 52.381 0.00 0.00 0.00 3.86
1834 2160 6.811253 ACACTTTTTCGCATACCAATTAGA 57.189 33.333 0.00 0.00 0.00 2.10
1899 2225 6.605594 TGGATTAGCTTTACCCCAAAATACAG 59.394 38.462 0.00 0.00 0.00 2.74
1936 2262 2.742348 TCCTAGCCTCATACGGAACAA 58.258 47.619 0.00 0.00 0.00 2.83
1976 2302 9.676861 TCTATCAGGAGCAATTATCCATTATTG 57.323 33.333 10.63 0.00 39.47 1.90
1984 2310 5.942826 CCCCTTTCTATCAGGAGCAATTATC 59.057 44.000 0.00 0.00 32.41 1.75
2009 2335 3.213206 TCACCTGAGCTGACATGTTTT 57.787 42.857 0.00 0.00 0.00 2.43
2010 2336 2.936919 TCACCTGAGCTGACATGTTT 57.063 45.000 0.00 0.00 0.00 2.83
2043 2369 4.137543 CTGGCTTTTCCTTCACACTTACT 58.862 43.478 0.00 0.00 35.26 2.24
2052 2378 0.112412 TCCACCCTGGCTTTTCCTTC 59.888 55.000 0.00 0.00 37.47 3.46
2074 2400 6.379988 ACTGAAGTTTCCCTTAAAGCAAAGAA 59.620 34.615 0.00 0.00 32.03 2.52
2122 2449 5.229921 TCTTTTTCTGACAAAACTCGTGG 57.770 39.130 0.00 0.00 0.00 4.94
2123 2450 7.406553 TGTATCTTTTTCTGACAAAACTCGTG 58.593 34.615 0.00 0.00 0.00 4.35
2124 2451 7.280205 ACTGTATCTTTTTCTGACAAAACTCGT 59.720 33.333 0.00 0.00 0.00 4.18
2126 2453 9.865484 GTACTGTATCTTTTTCTGACAAAACTC 57.135 33.333 0.00 0.00 0.00 3.01
2166 3159 0.039618 CCATCCATATTTCCCCCGGG 59.960 60.000 15.80 15.80 0.00 5.73
2171 3164 4.834496 TCTGAAATGCCATCCATATTTCCC 59.166 41.667 0.00 0.00 39.09 3.97
2177 3170 4.458256 ACCATCTGAAATGCCATCCATA 57.542 40.909 0.00 0.00 32.67 2.74
2321 3321 2.248248 TCCAACACACAAACAAACCCA 58.752 42.857 0.00 0.00 0.00 4.51
2330 3330 4.808414 TGAAATTGGTTCCAACACACAA 57.192 36.364 6.41 0.00 35.12 3.33
2333 3333 5.413309 AACTTGAAATTGGTTCCAACACA 57.587 34.783 6.41 5.07 35.12 3.72
2354 3354 6.465035 CCCAATGGACCATTTTTACCTGAAAA 60.465 38.462 17.42 0.00 35.16 2.29
2370 3370 3.644966 TGTAGGAACATCCCAATGGAC 57.355 47.619 0.00 0.00 45.58 4.02
2377 3377 2.936498 CGACACATTGTAGGAACATCCC 59.064 50.000 0.00 0.00 37.19 3.85
2454 3454 8.050778 ACTTATAATCGCAAAGATGACCAAAA 57.949 30.769 0.00 0.00 40.02 2.44
2460 3460 7.148255 ACAGCAAACTTATAATCGCAAAGATGA 60.148 33.333 0.00 0.00 40.02 2.92
2463 3463 6.072728 ACACAGCAAACTTATAATCGCAAAGA 60.073 34.615 0.00 0.00 0.00 2.52
2470 3470 7.028962 TGCAATCACACAGCAAACTTATAATC 58.971 34.615 0.00 0.00 34.97 1.75
2514 3514 4.956075 CCCCATAAACTAAGCAATGAAGGT 59.044 41.667 0.00 0.00 0.00 3.50
2515 3515 4.202151 GCCCCATAAACTAAGCAATGAAGG 60.202 45.833 0.00 0.00 0.00 3.46
2516 3516 4.402155 TGCCCCATAAACTAAGCAATGAAG 59.598 41.667 0.00 0.00 0.00 3.02
2524 3524 7.881775 AAGAGTTATTGCCCCATAAACTAAG 57.118 36.000 0.00 0.00 0.00 2.18
2589 3589 2.696526 AGAAGGGACACTGTCTACCA 57.303 50.000 9.08 0.00 32.47 3.25
2748 3748 2.677836 GCTGACTTCAACGCCATATTCA 59.322 45.455 0.00 0.00 0.00 2.57
2785 3785 3.429410 GCCTTCCGCTTTTTGCTTATCAT 60.429 43.478 0.00 0.00 40.11 2.45
2808 3808 2.301346 GATGGTTGCCCCTTATCACTG 58.699 52.381 0.00 0.00 0.00 3.66
2809 3809 1.134098 CGATGGTTGCCCCTTATCACT 60.134 52.381 0.00 0.00 0.00 3.41
3042 4042 1.205655 CTCATCCTTCGCTGTTCCTCA 59.794 52.381 0.00 0.00 0.00 3.86
3084 4084 0.911769 TGGTCATGAGCGAATCCCTT 59.088 50.000 19.36 0.00 0.00 3.95
3246 4246 7.395190 AGTTAATAAGCTGCATCAAACATCA 57.605 32.000 1.02 0.00 0.00 3.07
3258 4258 8.854614 ATGAGCCCTATAAAGTTAATAAGCTG 57.145 34.615 0.00 0.00 0.00 4.24
3286 4286 6.644248 AATATAACCCCGGTAAAGAATTGC 57.356 37.500 0.00 0.00 0.00 3.56
3386 4391 1.620819 AGACGACTGATGCCTGAAAGT 59.379 47.619 0.00 0.00 0.00 2.66
3429 4434 4.895668 AGGAACAATGCCATGAAAATGT 57.104 36.364 0.00 0.00 0.00 2.71
3570 4575 1.650528 CTCTCAGTTTGGGGTCCTCT 58.349 55.000 0.00 0.00 0.00 3.69
3645 4651 2.738480 CAAGTGGTTCGTCCCCGA 59.262 61.111 0.00 0.00 42.41 5.14
3706 4712 2.639065 AGTTTCAACTGCAACTCGGAA 58.361 42.857 0.00 0.00 37.98 4.30
3836 4842 4.444022 GCTTATCAGCAGAGGATTCCTTGA 60.444 45.833 6.68 6.97 46.49 3.02
3875 4881 2.652590 AGATGCAGAAATCTGAAGCCC 58.347 47.619 14.43 0.00 46.59 5.19


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

AutoCloner maintained by Alex Coulton.