Multiple sequence alignment - TraesCS4B01G252000

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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 TraesCS4B01G252000 chr4B 100.000 3727 0 0 1 3727 518078258 518081984 0.000000e+00 6883.0
1 TraesCS4B01G252000 chr4A 89.133 1914 142 36 135 1990 43289858 43287953 0.000000e+00 2322.0
2 TraesCS4B01G252000 chr4A 92.288 778 48 4 1989 2766 43287924 43287159 0.000000e+00 1094.0
3 TraesCS4B01G252000 chr4A 77.923 992 117 42 2754 3689 43287123 43286178 3.300000e-145 525.0
4 TraesCS4B01G252000 chr4D 88.708 1966 132 33 97 1990 420919002 420920949 0.000000e+00 2318.0
5 TraesCS4B01G252000 chr4D 91.805 781 49 5 1989 2766 420920978 420921746 0.000000e+00 1074.0
6 TraesCS4B01G252000 chr4D 87.531 810 59 21 2917 3718 420922186 420922961 0.000000e+00 898.0
7 TraesCS4B01G252000 chr4D 91.597 119 8 1 2764 2882 420921786 420921902 2.980000e-36 163.0
8 TraesCS4B01G252000 chr2D 91.736 121 10 0 404 524 574646060 574645940 6.400000e-38 169.0
9 TraesCS4B01G252000 chr1B 89.256 121 13 0 404 524 77722707 77722827 6.450000e-33 152.0
10 TraesCS4B01G252000 chr6B 74.857 175 27 11 2988 3149 455402467 455402637 3.110000e-06 63.9


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 TraesCS4B01G252000 chr4B 518078258 518081984 3726 False 6883.000000 6883 100.00000 1 3727 1 chr4B.!!$F1 3726
1 TraesCS4B01G252000 chr4A 43286178 43289858 3680 True 1313.666667 2322 86.44800 135 3689 3 chr4A.!!$R1 3554
2 TraesCS4B01G252000 chr4D 420919002 420922961 3959 False 1113.250000 2318 89.91025 97 3718 4 chr4D.!!$F1 3621

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
579 633 0.167908 CGCGCAAAGGTAAATCTGCA 59.832 50.0 8.75 0.0 34.39 4.41 F
1949 2037 0.038744 AGTCTGACAATGGCAAGGGG 59.961 55.0 10.88 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 2081 0.03601 CTCCCTCGGCAATTCACTGT 60.036 55.0 0.0 0.0 0.0 3.55 R
2952 3373 0.38539 AAAGTCAAACAGGCCTTGCG 59.615 50.0 0.0 0.0 0.0 4.85 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
35 36 9.952030 TGTCAGTATGTAAAATATGAAGGAACA 57.048 29.630 0.00 0.00 37.40 3.18
37 38 9.093970 TCAGTATGTAAAATATGAAGGAACACG 57.906 33.333 0.00 0.00 37.40 4.49
38 39 8.879759 CAGTATGTAAAATATGAAGGAACACGT 58.120 33.333 0.00 0.00 0.00 4.49
39 40 8.879759 AGTATGTAAAATATGAAGGAACACGTG 58.120 33.333 15.48 15.48 0.00 4.49
40 41 5.933790 TGTAAAATATGAAGGAACACGTGC 58.066 37.500 17.22 0.00 0.00 5.34
41 42 5.470437 TGTAAAATATGAAGGAACACGTGCA 59.530 36.000 17.22 4.42 0.00 4.57
42 43 4.685169 AAATATGAAGGAACACGTGCAG 57.315 40.909 17.22 0.00 0.00 4.41
43 44 2.093306 TATGAAGGAACACGTGCAGG 57.907 50.000 17.22 4.53 0.00 4.85
44 45 0.396435 ATGAAGGAACACGTGCAGGA 59.604 50.000 17.22 0.00 0.00 3.86
45 46 0.531974 TGAAGGAACACGTGCAGGAC 60.532 55.000 17.22 3.93 0.00 3.85
55 56 2.106750 CGTGCAGGACGTGATAGTAG 57.893 55.000 6.25 0.00 43.50 2.57
56 57 1.669265 CGTGCAGGACGTGATAGTAGA 59.331 52.381 6.25 0.00 43.50 2.59
57 58 2.290916 CGTGCAGGACGTGATAGTAGAT 59.709 50.000 6.25 0.00 43.50 1.98
58 59 3.243101 CGTGCAGGACGTGATAGTAGATT 60.243 47.826 6.25 0.00 43.50 2.40
59 60 4.291783 GTGCAGGACGTGATAGTAGATTC 58.708 47.826 0.00 0.00 0.00 2.52
60 61 4.036971 GTGCAGGACGTGATAGTAGATTCT 59.963 45.833 0.00 0.00 0.00 2.40
61 62 4.276183 TGCAGGACGTGATAGTAGATTCTC 59.724 45.833 0.00 0.00 0.00 2.87
62 63 4.517453 GCAGGACGTGATAGTAGATTCTCT 59.483 45.833 0.00 0.00 0.00 3.10
63 64 5.701750 GCAGGACGTGATAGTAGATTCTCTA 59.298 44.000 0.00 0.00 0.00 2.43
64 65 6.205076 GCAGGACGTGATAGTAGATTCTCTAA 59.795 42.308 0.00 0.00 29.58 2.10
65 66 7.255173 GCAGGACGTGATAGTAGATTCTCTAAA 60.255 40.741 0.00 0.00 29.58 1.85
66 67 8.622157 CAGGACGTGATAGTAGATTCTCTAAAA 58.378 37.037 0.00 0.00 29.58 1.52
67 68 8.623030 AGGACGTGATAGTAGATTCTCTAAAAC 58.377 37.037 0.00 0.00 29.58 2.43
68 69 7.861872 GGACGTGATAGTAGATTCTCTAAAACC 59.138 40.741 0.00 0.00 29.58 3.27
69 70 7.714703 ACGTGATAGTAGATTCTCTAAAACCC 58.285 38.462 0.00 0.00 29.58 4.11
70 71 6.856938 CGTGATAGTAGATTCTCTAAAACCCG 59.143 42.308 0.00 0.00 29.58 5.28
71 72 7.146648 GTGATAGTAGATTCTCTAAAACCCGG 58.853 42.308 0.00 0.00 29.58 5.73
72 73 6.267014 TGATAGTAGATTCTCTAAAACCCGGG 59.733 42.308 22.25 22.25 29.58 5.73
73 74 4.617593 AGTAGATTCTCTAAAACCCGGGA 58.382 43.478 32.02 2.56 29.58 5.14
74 75 4.650131 AGTAGATTCTCTAAAACCCGGGAG 59.350 45.833 32.02 14.97 29.58 4.30
75 76 3.451890 AGATTCTCTAAAACCCGGGAGT 58.548 45.455 32.02 12.31 0.00 3.85
76 77 4.617593 AGATTCTCTAAAACCCGGGAGTA 58.382 43.478 32.02 14.71 0.00 2.59
77 78 5.217400 AGATTCTCTAAAACCCGGGAGTAT 58.783 41.667 32.02 12.21 0.00 2.12
78 79 6.379579 AGATTCTCTAAAACCCGGGAGTATA 58.620 40.000 32.02 13.35 0.00 1.47
79 80 6.842807 AGATTCTCTAAAACCCGGGAGTATAA 59.157 38.462 32.02 10.91 0.00 0.98
80 81 7.513091 AGATTCTCTAAAACCCGGGAGTATAAT 59.487 37.037 32.02 15.20 0.00 1.28
81 82 6.415206 TCTCTAAAACCCGGGAGTATAATG 57.585 41.667 32.02 10.78 0.00 1.90
82 83 5.901276 TCTCTAAAACCCGGGAGTATAATGT 59.099 40.000 32.02 0.00 0.00 2.71
83 84 6.384886 TCTCTAAAACCCGGGAGTATAATGTT 59.615 38.462 32.02 6.57 0.00 2.71
84 85 6.585416 TCTAAAACCCGGGAGTATAATGTTC 58.415 40.000 32.02 0.00 0.00 3.18
85 86 4.847990 AAACCCGGGAGTATAATGTTCA 57.152 40.909 32.02 0.00 0.00 3.18
86 87 4.847990 AACCCGGGAGTATAATGTTCAA 57.152 40.909 32.02 0.00 0.00 2.69
87 88 4.847990 ACCCGGGAGTATAATGTTCAAA 57.152 40.909 32.02 0.00 0.00 2.69
88 89 5.182169 ACCCGGGAGTATAATGTTCAAAA 57.818 39.130 32.02 0.00 0.00 2.44
89 90 5.572252 ACCCGGGAGTATAATGTTCAAAAA 58.428 37.500 32.02 0.00 0.00 1.94
109 110 6.474140 AAAAAGAAACAAACCGGGAGTATT 57.526 33.333 6.32 0.00 0.00 1.89
179 180 1.676014 GGATAAACCAGCTGAGCACGT 60.676 52.381 17.39 0.04 38.79 4.49
180 181 1.661112 GATAAACCAGCTGAGCACGTC 59.339 52.381 17.39 2.28 0.00 4.34
181 182 0.679505 TAAACCAGCTGAGCACGTCT 59.320 50.000 17.39 0.00 0.00 4.18
182 183 0.601311 AAACCAGCTGAGCACGTCTC 60.601 55.000 17.39 7.74 42.23 3.36
183 184 2.505777 CCAGCTGAGCACGTCTCG 60.506 66.667 17.39 0.00 44.86 4.04
184 185 2.563427 CAGCTGAGCACGTCTCGA 59.437 61.111 8.42 0.00 44.86 4.04
185 186 1.138459 CAGCTGAGCACGTCTCGAT 59.862 57.895 8.42 2.81 44.86 3.59
228 240 4.021925 GCGGAGAAGTGGTGGCCT 62.022 66.667 3.32 0.00 0.00 5.19
375 403 3.657038 TAGCGCCCCTCGTTCCTCT 62.657 63.158 2.29 0.00 41.07 3.69
385 413 3.437049 CCCTCGTTCCTCTGTTCATTTTC 59.563 47.826 0.00 0.00 0.00 2.29
426 477 2.365370 CTGCTCCTCCTCTGGCCT 60.365 66.667 3.32 0.00 0.00 5.19
442 493 2.588877 CTATGGTGAAGCGCCCGG 60.589 66.667 2.29 0.00 32.22 5.73
491 542 2.337749 ATCGTGCTCCCGTGATCGAC 62.338 60.000 0.00 0.00 39.71 4.20
510 561 0.179111 CGGAGTCGCCTGATTTGCTA 60.179 55.000 0.00 0.00 0.00 3.49
527 578 3.617284 TGCTACTCAAGGTACGATCTCA 58.383 45.455 0.00 0.00 0.00 3.27
529 580 4.276183 TGCTACTCAAGGTACGATCTCATC 59.724 45.833 0.00 0.00 0.00 2.92
532 583 5.923733 ACTCAAGGTACGATCTCATCTTT 57.076 39.130 0.00 0.00 0.00 2.52
537 588 9.967346 CTCAAGGTACGATCTCATCTTTATTTA 57.033 33.333 0.00 0.00 0.00 1.40
571 625 1.579698 TGTTGTTACGCGCAAAGGTA 58.420 45.000 5.73 0.00 0.00 3.08
579 633 0.167908 CGCGCAAAGGTAAATCTGCA 59.832 50.000 8.75 0.00 34.39 4.41
626 689 7.716998 TCCCATTTCAGACTGCTTATAGATTTC 59.283 37.037 0.00 0.00 0.00 2.17
646 709 3.162666 TCTGTATGTTCCTCGAACTGGT 58.837 45.455 6.13 0.00 42.39 4.00
647 710 4.338012 TCTGTATGTTCCTCGAACTGGTA 58.662 43.478 6.13 0.00 42.39 3.25
648 711 4.157289 TCTGTATGTTCCTCGAACTGGTAC 59.843 45.833 6.13 7.04 42.39 3.34
649 712 3.827876 TGTATGTTCCTCGAACTGGTACA 59.172 43.478 4.49 4.49 42.39 2.90
650 713 2.806608 TGTTCCTCGAACTGGTACAC 57.193 50.000 6.13 0.00 42.39 2.90
726 789 6.357367 AGATGTGTAACCAACTGAACTTCTT 58.643 36.000 0.00 0.00 34.36 2.52
763 826 1.336755 GTTGTTGGCAAACTGACGGAT 59.663 47.619 0.00 0.00 37.19 4.18
854 918 6.982160 TTACCAGTAACCTGTAAGAGTTGA 57.018 37.500 0.00 0.00 36.95 3.18
860 924 7.331193 CCAGTAACCTGTAAGAGTTGATGTTAC 59.669 40.741 0.00 0.00 37.98 2.50
867 931 7.876068 CCTGTAAGAGTTGATGTTACCTTGTTA 59.124 37.037 0.00 0.00 36.94 2.41
903 967 9.017509 AGGTATATGGCATCATTTTAATCAGTG 57.982 33.333 1.65 0.00 34.96 3.66
910 974 9.407380 TGGCATCATTTTAATCAGTGTATTACT 57.593 29.630 0.00 0.00 41.36 2.24
938 1002 2.404265 TGCATGCTTCTTGTTCAACG 57.596 45.000 20.33 0.00 0.00 4.10
940 1004 1.335324 GCATGCTTCTTGTTCAACGCT 60.335 47.619 11.37 0.00 0.00 5.07
946 1010 1.662517 TCTTGTTCAACGCTTGCAGA 58.337 45.000 0.00 0.00 0.00 4.26
994 1058 0.466543 ACAAGGCAACCAGTCGTACA 59.533 50.000 0.00 0.00 37.17 2.90
1107 1175 0.038892 GCCCTGACAGAAACGTACGA 60.039 55.000 24.41 0.00 0.00 3.43
1129 1197 4.180723 AGGGTACTCAATTCCCCAACTTA 58.819 43.478 0.00 0.00 41.95 2.24
1132 1200 5.104067 GGGTACTCAATTCCCCAACTTAGAT 60.104 44.000 0.00 0.00 37.09 1.98
1133 1201 6.100714 GGGTACTCAATTCCCCAACTTAGATA 59.899 42.308 0.00 0.00 37.09 1.98
1135 1203 8.218488 GGTACTCAATTCCCCAACTTAGATAAT 58.782 37.037 0.00 0.00 0.00 1.28
1138 1209 8.506083 ACTCAATTCCCCAACTTAGATAATCAT 58.494 33.333 0.00 0.00 0.00 2.45
1144 1215 8.331931 TCCCCAACTTAGATAATCATAACTGT 57.668 34.615 0.00 0.00 0.00 3.55
1203 1291 2.060383 CAGGGGCAGGAGATCGACA 61.060 63.158 0.00 0.00 0.00 4.35
1208 1296 0.952280 GGCAGGAGATCGACATCGTA 59.048 55.000 0.54 0.00 40.80 3.43
1330 1418 1.735386 CTCTCGGAGAAGTACGACCA 58.265 55.000 9.32 0.00 34.09 4.02
1521 1609 0.970937 GGTGGAGTCCATGGAGACGA 60.971 60.000 16.81 6.70 41.83 4.20
1523 1611 0.331616 TGGAGTCCATGGAGACGAGA 59.668 55.000 16.81 0.00 41.83 4.04
1655 1743 2.249139 GTGTACTTCCAGGAGGTCACT 58.751 52.381 7.67 0.00 35.89 3.41
1686 1774 1.345741 TCAGCTCTGACAAGAACCTGG 59.654 52.381 0.00 0.00 34.73 4.45
1689 1777 1.338579 GCTCTGACAAGAACCTGGAGG 60.339 57.143 0.00 0.00 42.17 4.30
1691 1779 0.671781 CTGACAAGAACCTGGAGGCG 60.672 60.000 0.00 0.00 39.32 5.52
1730 1818 3.504204 GATGGAGGGCATGGAGGGC 62.504 68.421 0.00 0.00 0.00 5.19
1778 1866 1.735920 GTGTCTGCGGTCTGAGCTG 60.736 63.158 5.23 0.28 35.28 4.24
1784 1872 1.742880 GCGGTCTGAGCTGATGCAA 60.743 57.895 5.23 0.00 42.74 4.08
1785 1873 1.094073 GCGGTCTGAGCTGATGCAAT 61.094 55.000 5.23 0.00 42.74 3.56
1802 1890 3.568007 TGCAATTCAAGGAGCTTTACGTT 59.432 39.130 0.00 0.00 0.00 3.99
1805 1893 5.562890 GCAATTCAAGGAGCTTTACGTTTCT 60.563 40.000 0.00 0.00 0.00 2.52
1806 1894 6.438763 CAATTCAAGGAGCTTTACGTTTCTT 58.561 36.000 0.00 0.00 0.00 2.52
1807 1895 5.668558 TTCAAGGAGCTTTACGTTTCTTC 57.331 39.130 0.00 0.00 0.00 2.87
1811 1899 2.411069 GGAGCTTTACGTTTCTTCGTCC 59.589 50.000 0.00 0.00 43.12 4.79
1906 1994 0.179119 GGTCGGTCCAGTAATGACGG 60.179 60.000 0.00 0.00 35.19 4.79
1927 2015 3.842602 CGTCGACGTCAATGCTGT 58.157 55.556 29.08 0.00 34.11 4.40
1928 2016 2.141781 CGTCGACGTCAATGCTGTT 58.858 52.632 29.08 0.00 34.11 3.16
1949 2037 0.038744 AGTCTGACAATGGCAAGGGG 59.961 55.000 10.88 0.00 0.00 4.79
1990 2081 3.599730 AGTCGCTGATCTTGTCAATGA 57.400 42.857 0.00 0.00 36.14 2.57
1992 2083 2.995939 GTCGCTGATCTTGTCAATGACA 59.004 45.455 12.63 12.63 41.09 3.58
2017 2138 2.680352 GCCGAGGGAGGACTGTCA 60.680 66.667 10.38 0.00 0.00 3.58
2032 2153 6.064060 AGGACTGTCAAAACATTCAATCTGA 58.936 36.000 10.38 0.00 36.93 3.27
2037 2158 6.680810 TGTCAAAACATTCAATCTGATGACC 58.319 36.000 0.00 0.00 0.00 4.02
2048 2169 6.772605 TCAATCTGATGACCGGAATATCAAT 58.227 36.000 9.46 8.37 33.10 2.57
2073 2194 0.667487 AACGTCTGCTGATGTCGTGG 60.667 55.000 17.58 0.00 41.19 4.94
2102 2223 2.421619 GCAGGACAGAAAAGGAGAGTG 58.578 52.381 0.00 0.00 0.00 3.51
2153 2274 3.452755 TTCAAGAGCGTGAACTCTGAA 57.547 42.857 0.00 0.00 46.38 3.02
2164 2285 4.211164 CGTGAACTCTGAATGTTGCAAGTA 59.789 41.667 0.00 0.00 0.00 2.24
2170 2291 3.758023 TCTGAATGTTGCAAGTACATGGG 59.242 43.478 0.00 0.00 36.41 4.00
2203 2324 0.036010 ATGTCCGAAAGTCTGGCAGG 60.036 55.000 15.73 0.00 0.00 4.85
2232 2353 0.457035 CTCAGAGTCAGAGCCAGAGC 59.543 60.000 0.00 0.00 40.32 4.09
2233 2354 0.969917 TCAGAGTCAGAGCCAGAGCC 60.970 60.000 0.00 0.00 41.25 4.70
2234 2355 0.971959 CAGAGTCAGAGCCAGAGCCT 60.972 60.000 0.00 0.00 41.25 4.58
2235 2356 0.971959 AGAGTCAGAGCCAGAGCCTG 60.972 60.000 0.00 0.00 41.25 4.85
2236 2357 0.969917 GAGTCAGAGCCAGAGCCTGA 60.970 60.000 4.00 0.00 41.25 3.86
2237 2358 0.325484 AGTCAGAGCCAGAGCCTGAT 60.325 55.000 8.70 0.00 43.54 2.90
2238 2359 0.179078 GTCAGAGCCAGAGCCTGATG 60.179 60.000 8.70 0.00 43.54 3.07
2239 2360 1.524165 CAGAGCCAGAGCCTGATGC 60.524 63.158 4.00 0.77 41.25 3.91
2240 2361 2.203181 GAGCCAGAGCCTGATGCC 60.203 66.667 4.00 0.00 42.71 4.40
2241 2362 2.691623 AGCCAGAGCCTGATGCCT 60.692 61.111 4.00 0.00 42.71 4.75
2279 2400 0.179134 CCGAGATCGTGGAGGTGAAC 60.179 60.000 1.09 0.00 37.74 3.18
2282 2406 4.682482 CGAGATCGTGGAGGTGAACTCG 62.682 59.091 7.35 7.35 46.13 4.18
2576 2700 3.692406 GTGGAGGACGGTCGCCTT 61.692 66.667 16.38 0.00 35.44 4.35
2591 2715 2.711922 CCTTAGGCGCGTGGAGAGT 61.712 63.158 13.84 0.00 0.00 3.24
2747 2871 2.551912 CGCGCCAGGGTTTTGAACT 61.552 57.895 0.00 0.00 0.00 3.01
2762 2886 1.209128 GAACTGTGTCAGGTGTCACG 58.791 55.000 0.00 1.85 36.99 4.35
2775 2947 3.994392 AGGTGTCACGAATGTAATGTCAC 59.006 43.478 0.00 0.00 33.42 3.67
2780 2952 2.741517 CACGAATGTAATGTCACCTGCA 59.258 45.455 0.00 0.00 0.00 4.41
2854 3026 2.730069 TGCAACTCAAACTCAAATGCG 58.270 42.857 0.00 0.00 35.18 4.73
2865 3037 2.094545 ACTCAAATGCGGCCAAAGAATC 60.095 45.455 2.24 0.00 0.00 2.52
2889 3083 5.354234 CCACTTTTGCTACATCTCCGTTTAT 59.646 40.000 0.00 0.00 0.00 1.40
2911 3105 3.187637 TGTCGATTTCCTTTTGTTAGGCG 59.812 43.478 0.00 0.00 35.15 5.52
2915 3336 5.292589 TCGATTTCCTTTTGTTAGGCGATAC 59.707 40.000 0.00 0.00 35.15 2.24
2945 3366 8.483758 GTTGGTTTCTAAGATACTCCATCCTTA 58.516 37.037 0.00 0.00 33.75 2.69
2954 3375 6.514063 AGATACTCCATCCTTAGTAAAACGC 58.486 40.000 0.00 0.00 33.75 4.84
3001 3422 6.801377 TGTATTTGAATTTGATGCACGACTTC 59.199 34.615 0.00 0.00 0.00 3.01
3018 3439 5.347907 ACGACTTCGACCATTTATCAAACTC 59.652 40.000 5.47 0.00 43.02 3.01
3020 3441 6.454318 CGACTTCGACCATTTATCAAACTCTG 60.454 42.308 0.00 0.00 43.02 3.35
3021 3442 6.231211 ACTTCGACCATTTATCAAACTCTGT 58.769 36.000 0.00 0.00 0.00 3.41
3022 3443 6.369065 ACTTCGACCATTTATCAAACTCTGTC 59.631 38.462 0.00 0.00 0.00 3.51
3030 3454 9.865321 CCATTTATCAAACTCTGTCAATTGAAT 57.135 29.630 10.35 0.00 35.62 2.57
3115 3542 8.999431 ACACTAATTTTGTGGACATACAGTAAG 58.001 33.333 14.06 0.00 39.52 2.34
3143 3570 4.154195 AGTCATAGTCAAAATTGTGCGACC 59.846 41.667 0.00 0.00 0.00 4.79
3144 3571 4.068599 TCATAGTCAAAATTGTGCGACCA 58.931 39.130 0.00 0.00 0.00 4.02
3218 3656 6.069673 TGGAGGGAGTAGATTTTTGATAAGCA 60.070 38.462 0.00 0.00 0.00 3.91
3271 3710 1.401905 CCAGGCCTATTCTTCGCAAAC 59.598 52.381 3.98 0.00 0.00 2.93
3282 3721 7.323656 CCTATTCTTCGCAAACACTTTAAACTG 59.676 37.037 0.00 0.00 0.00 3.16
3377 3822 2.154462 GTAGCTGTTGCCAGAATGTGT 58.846 47.619 0.00 0.00 41.50 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.952030 TGTTCCTTCATATTTTACATACTGACA 57.048 29.630 0.00 0.00 0.00 3.58
11 12 9.093970 CGTGTTCCTTCATATTTTACATACTGA 57.906 33.333 0.00 0.00 0.00 3.41
12 13 8.879759 ACGTGTTCCTTCATATTTTACATACTG 58.120 33.333 0.00 0.00 0.00 2.74
13 14 8.879759 CACGTGTTCCTTCATATTTTACATACT 58.120 33.333 7.58 0.00 0.00 2.12
14 15 7.638683 GCACGTGTTCCTTCATATTTTACATAC 59.361 37.037 18.38 0.00 0.00 2.39
15 16 7.334671 TGCACGTGTTCCTTCATATTTTACATA 59.665 33.333 18.38 0.00 0.00 2.29
16 17 6.150307 TGCACGTGTTCCTTCATATTTTACAT 59.850 34.615 18.38 0.00 0.00 2.29
17 18 5.470437 TGCACGTGTTCCTTCATATTTTACA 59.530 36.000 18.38 0.00 0.00 2.41
18 19 5.933790 TGCACGTGTTCCTTCATATTTTAC 58.066 37.500 18.38 0.00 0.00 2.01
19 20 5.123186 CCTGCACGTGTTCCTTCATATTTTA 59.877 40.000 18.38 0.00 0.00 1.52
20 21 4.082787 CCTGCACGTGTTCCTTCATATTTT 60.083 41.667 18.38 0.00 0.00 1.82
21 22 3.440173 CCTGCACGTGTTCCTTCATATTT 59.560 43.478 18.38 0.00 0.00 1.40
22 23 3.009723 CCTGCACGTGTTCCTTCATATT 58.990 45.455 18.38 0.00 0.00 1.28
23 24 2.236146 TCCTGCACGTGTTCCTTCATAT 59.764 45.455 18.38 0.00 0.00 1.78
24 25 1.621317 TCCTGCACGTGTTCCTTCATA 59.379 47.619 18.38 0.00 0.00 2.15
25 26 0.396435 TCCTGCACGTGTTCCTTCAT 59.604 50.000 18.38 0.00 0.00 2.57
26 27 0.531974 GTCCTGCACGTGTTCCTTCA 60.532 55.000 18.38 4.22 0.00 3.02
27 28 1.557443 CGTCCTGCACGTGTTCCTTC 61.557 60.000 18.38 0.00 44.07 3.46
28 29 1.594293 CGTCCTGCACGTGTTCCTT 60.594 57.895 18.38 0.00 44.07 3.36
29 30 2.029073 CGTCCTGCACGTGTTCCT 59.971 61.111 18.38 0.00 44.07 3.36
37 38 3.992260 ATCTACTATCACGTCCTGCAC 57.008 47.619 0.00 0.00 0.00 4.57
38 39 4.207955 AGAATCTACTATCACGTCCTGCA 58.792 43.478 0.00 0.00 0.00 4.41
39 40 4.789784 GAGAATCTACTATCACGTCCTGC 58.210 47.826 0.00 0.00 0.00 4.85
55 56 3.908643 ACTCCCGGGTTTTAGAGAATC 57.091 47.619 22.86 0.00 0.00 2.52
56 57 7.072076 ACATTATACTCCCGGGTTTTAGAGAAT 59.928 37.037 22.86 9.57 0.00 2.40
57 58 6.384886 ACATTATACTCCCGGGTTTTAGAGAA 59.615 38.462 22.86 7.73 0.00 2.87
58 59 5.901276 ACATTATACTCCCGGGTTTTAGAGA 59.099 40.000 22.86 4.61 0.00 3.10
59 60 6.170846 ACATTATACTCCCGGGTTTTAGAG 57.829 41.667 22.86 12.11 0.00 2.43
60 61 6.156602 TGAACATTATACTCCCGGGTTTTAGA 59.843 38.462 22.86 4.65 0.00 2.10
61 62 6.350906 TGAACATTATACTCCCGGGTTTTAG 58.649 40.000 22.86 13.37 0.00 1.85
62 63 6.310764 TGAACATTATACTCCCGGGTTTTA 57.689 37.500 22.86 10.65 0.00 1.52
63 64 5.182169 TGAACATTATACTCCCGGGTTTT 57.818 39.130 22.86 8.51 0.00 2.43
64 65 4.847990 TGAACATTATACTCCCGGGTTT 57.152 40.909 22.86 11.35 0.00 3.27
65 66 4.847990 TTGAACATTATACTCCCGGGTT 57.152 40.909 22.86 11.76 0.00 4.11
66 67 4.847990 TTTGAACATTATACTCCCGGGT 57.152 40.909 22.86 4.16 0.00 5.28
86 87 6.127281 ACAATACTCCCGGTTTGTTTCTTTTT 60.127 34.615 0.00 0.00 30.79 1.94
87 88 5.361571 ACAATACTCCCGGTTTGTTTCTTTT 59.638 36.000 0.00 0.00 30.79 2.27
88 89 4.891168 ACAATACTCCCGGTTTGTTTCTTT 59.109 37.500 0.00 0.00 30.79 2.52
89 90 4.466827 ACAATACTCCCGGTTTGTTTCTT 58.533 39.130 0.00 0.00 30.79 2.52
90 91 4.070009 GACAATACTCCCGGTTTGTTTCT 58.930 43.478 0.00 0.00 33.11 2.52
91 92 3.120442 CGACAATACTCCCGGTTTGTTTC 60.120 47.826 0.00 0.00 33.11 2.78
92 93 2.809696 CGACAATACTCCCGGTTTGTTT 59.190 45.455 0.00 0.00 33.11 2.83
93 94 2.224354 ACGACAATACTCCCGGTTTGTT 60.224 45.455 0.00 0.00 33.11 2.83
94 95 1.345415 ACGACAATACTCCCGGTTTGT 59.655 47.619 0.00 2.14 34.46 2.83
95 96 2.088950 ACGACAATACTCCCGGTTTG 57.911 50.000 0.00 0.00 0.00 2.93
96 97 2.415893 CGTACGACAATACTCCCGGTTT 60.416 50.000 10.44 0.00 0.00 3.27
97 98 1.133025 CGTACGACAATACTCCCGGTT 59.867 52.381 10.44 0.00 0.00 4.44
98 99 0.734889 CGTACGACAATACTCCCGGT 59.265 55.000 10.44 0.00 0.00 5.28
99 100 0.593263 GCGTACGACAATACTCCCGG 60.593 60.000 21.65 0.00 0.00 5.73
100 101 0.099259 TGCGTACGACAATACTCCCG 59.901 55.000 21.65 0.00 0.00 5.14
101 102 1.133790 AGTGCGTACGACAATACTCCC 59.866 52.381 21.65 3.14 0.00 4.30
179 180 0.750546 CACCACCCCTACGATCGAGA 60.751 60.000 24.34 8.25 0.00 4.04
180 181 1.734137 CACCACCCCTACGATCGAG 59.266 63.158 24.34 14.23 0.00 4.04
181 182 1.755395 CCACCACCCCTACGATCGA 60.755 63.158 24.34 4.52 0.00 3.59
182 183 2.812499 CCACCACCCCTACGATCG 59.188 66.667 14.88 14.88 0.00 3.69
183 184 2.504519 GCCACCACCCCTACGATC 59.495 66.667 0.00 0.00 0.00 3.69
184 185 3.087906 GGCCACCACCCCTACGAT 61.088 66.667 0.00 0.00 0.00 3.73
185 186 4.326227 AGGCCACCACCCCTACGA 62.326 66.667 5.01 0.00 0.00 3.43
262 283 1.062148 GGAAACTATCGCTTTGGTCGC 59.938 52.381 0.00 0.00 0.00 5.19
275 296 2.353858 TCGCAACCCGAGGAAACTA 58.646 52.632 0.00 0.00 44.43 2.24
375 403 1.806542 GAGCAGCGAGGAAAATGAACA 59.193 47.619 0.00 0.00 0.00 3.18
385 413 2.105466 GCCAAAGAGAGCAGCGAGG 61.105 63.158 0.00 0.00 0.00 4.63
426 477 4.849310 GCCGGGCGCTTCACCATA 62.849 66.667 7.64 0.00 0.00 2.74
491 542 0.179111 TAGCAAATCAGGCGACTCCG 60.179 55.000 0.00 0.00 40.21 4.63
492 543 1.134670 AGTAGCAAATCAGGCGACTCC 60.135 52.381 0.00 0.00 42.38 3.85
496 547 2.621338 CTTGAGTAGCAAATCAGGCGA 58.379 47.619 0.00 0.00 35.74 5.54
502 553 5.593010 AGATCGTACCTTGAGTAGCAAATC 58.407 41.667 0.00 0.00 35.74 2.17
505 556 4.014406 TGAGATCGTACCTTGAGTAGCAA 58.986 43.478 0.00 0.00 34.73 3.91
510 561 5.923733 AAAGATGAGATCGTACCTTGAGT 57.076 39.130 0.00 0.00 0.00 3.41
529 580 9.840427 AACAAATGTGGAGATCGTTAAATAAAG 57.160 29.630 0.00 0.00 0.00 1.85
532 583 8.330466 ACAACAAATGTGGAGATCGTTAAATA 57.670 30.769 0.00 0.00 41.93 1.40
537 588 5.333798 CGTAACAACAAATGTGGAGATCGTT 60.334 40.000 0.00 0.00 42.99 3.85
601 655 7.718753 AGAAATCTATAAGCAGTCTGAAATGGG 59.281 37.037 3.32 0.00 0.00 4.00
626 689 3.594603 ACCAGTTCGAGGAACATACAG 57.405 47.619 10.74 0.00 44.11 2.74
630 693 2.631062 TGTGTACCAGTTCGAGGAACAT 59.369 45.455 10.74 0.00 44.11 2.71
681 744 6.053632 TCTCTGAATACTTCAAGCCATCAA 57.946 37.500 0.00 0.00 39.58 2.57
703 766 6.260050 TCAAGAAGTTCAGTTGGTTACACATC 59.740 38.462 5.50 0.00 0.00 3.06
704 767 6.038271 GTCAAGAAGTTCAGTTGGTTACACAT 59.962 38.462 5.50 0.00 0.00 3.21
705 768 5.353123 GTCAAGAAGTTCAGTTGGTTACACA 59.647 40.000 5.50 0.00 0.00 3.72
752 815 6.037610 GCATCTTCAGATTTATCCGTCAGTTT 59.962 38.462 0.00 0.00 31.21 2.66
763 826 7.229306 ACAACTGTCAAAGCATCTTCAGATTTA 59.771 33.333 0.00 0.00 31.21 1.40
903 967 6.287107 AGCATGCATCAAACGTAGTAATAC 57.713 37.500 21.98 0.00 45.00 1.89
910 974 3.501828 ACAAGAAGCATGCATCAAACGTA 59.498 39.130 23.62 0.00 0.00 3.57
911 975 2.294233 ACAAGAAGCATGCATCAAACGT 59.706 40.909 23.62 12.02 0.00 3.99
912 976 2.937591 ACAAGAAGCATGCATCAAACG 58.062 42.857 23.62 11.44 0.00 3.60
913 977 4.300803 TGAACAAGAAGCATGCATCAAAC 58.699 39.130 23.62 10.94 0.00 2.93
914 978 4.587584 TGAACAAGAAGCATGCATCAAA 57.412 36.364 23.62 1.15 0.00 2.69
919 983 1.600164 GCGTTGAACAAGAAGCATGCA 60.600 47.619 21.98 0.00 0.00 3.96
938 1002 3.193691 TCCTAGTGTAGTCTTCTGCAAGC 59.806 47.826 0.00 0.00 37.97 4.01
940 1004 4.218635 CAGTCCTAGTGTAGTCTTCTGCAA 59.781 45.833 0.00 0.00 37.97 4.08
946 1010 5.244189 TCAGTCAGTCCTAGTGTAGTCTT 57.756 43.478 0.00 0.00 0.00 3.01
994 1058 2.700371 TGTCAATCTCGGCCATCTGTAT 59.300 45.455 2.24 0.00 0.00 2.29
1107 1175 2.644151 AGTTGGGGAATTGAGTACCCT 58.356 47.619 0.00 0.00 43.72 4.34
1133 1201 7.934120 GCAGGAACTAGGAATACAGTTATGATT 59.066 37.037 0.00 0.00 36.02 2.57
1135 1203 6.611642 AGCAGGAACTAGGAATACAGTTATGA 59.388 38.462 0.00 0.00 36.02 2.15
1138 1209 5.955959 TGAGCAGGAACTAGGAATACAGTTA 59.044 40.000 0.00 0.00 36.02 2.24
1144 1215 5.453339 CGGATTTGAGCAGGAACTAGGAATA 60.453 44.000 0.00 0.00 36.02 1.75
1147 1218 2.168521 CGGATTTGAGCAGGAACTAGGA 59.831 50.000 0.00 0.00 36.02 2.94
1148 1219 2.093447 ACGGATTTGAGCAGGAACTAGG 60.093 50.000 0.00 0.00 36.02 3.02
1203 1291 0.107654 GCCAGCTCCTTGGTTACGAT 60.108 55.000 0.00 0.00 40.49 3.73
1208 1296 2.032681 GTCGCCAGCTCCTTGGTT 59.967 61.111 0.00 0.00 40.49 3.67
1521 1609 2.835431 CCGCTCCAGGATCCGTCT 60.835 66.667 5.98 0.00 0.00 4.18
1523 1611 4.458829 TCCCGCTCCAGGATCCGT 62.459 66.667 5.98 0.00 0.00 4.69
1686 1774 1.680522 TTCTGCCTCCTGATCGCCTC 61.681 60.000 0.00 0.00 0.00 4.70
1689 1777 1.227497 CCTTCTGCCTCCTGATCGC 60.227 63.158 0.00 0.00 0.00 4.58
1691 1779 0.758123 CCTCCTTCTGCCTCCTGATC 59.242 60.000 0.00 0.00 0.00 2.92
1730 1818 3.184683 GTCTTCGCCAGCAGCTCG 61.185 66.667 0.00 0.00 40.39 5.03
1778 1866 4.142600 ACGTAAAGCTCCTTGAATTGCATC 60.143 41.667 0.00 0.00 0.00 3.91
1784 1872 5.107065 CGAAGAAACGTAAAGCTCCTTGAAT 60.107 40.000 0.00 0.00 0.00 2.57
1785 1873 4.210537 CGAAGAAACGTAAAGCTCCTTGAA 59.789 41.667 0.00 0.00 0.00 2.69
1818 1906 2.267642 CGAGGCCCGAACCATGAA 59.732 61.111 0.00 0.00 41.76 2.57
1927 2015 3.420893 CCCTTGCCATTGTCAGACTTAA 58.579 45.455 1.31 0.00 0.00 1.85
1928 2016 2.290896 CCCCTTGCCATTGTCAGACTTA 60.291 50.000 1.31 0.00 0.00 2.24
1949 2037 0.390472 CTCCTCGTGGTTCTTGGCTC 60.390 60.000 2.99 0.00 34.23 4.70
1990 2081 0.036010 CTCCCTCGGCAATTCACTGT 60.036 55.000 0.00 0.00 0.00 3.55
1992 2083 0.909610 TCCTCCCTCGGCAATTCACT 60.910 55.000 0.00 0.00 0.00 3.41
2017 2138 5.009631 TCCGGTCATCAGATTGAATGTTTT 58.990 37.500 0.00 0.00 0.00 2.43
2032 2153 4.206375 TGCAACATTGATATTCCGGTCAT 58.794 39.130 0.00 0.00 0.00 3.06
2037 2158 4.014847 ACGTTGCAACATTGATATTCCG 57.985 40.909 28.01 12.56 0.00 4.30
2073 2194 2.550830 TTCTGTCCTGCCTGAACTTC 57.449 50.000 0.00 0.00 0.00 3.01
2153 2274 0.810648 CGCCCATGTACTTGCAACAT 59.189 50.000 0.00 0.00 38.08 2.71
2187 2308 0.762418 TTTCCTGCCAGACTTTCGGA 59.238 50.000 0.00 0.00 0.00 4.55
2189 2310 2.072298 CTCTTTCCTGCCAGACTTTCG 58.928 52.381 0.00 0.00 0.00 3.46
2194 2315 0.392327 GCCTCTCTTTCCTGCCAGAC 60.392 60.000 0.00 0.00 0.00 3.51
2195 2316 0.546267 AGCCTCTCTTTCCTGCCAGA 60.546 55.000 0.00 0.00 0.00 3.86
2203 2324 3.088532 TCTGACTCTGAGCCTCTCTTTC 58.911 50.000 4.19 0.00 0.00 2.62
2234 2355 4.100084 CCGGCACCTGAGGCATCA 62.100 66.667 0.00 0.00 0.00 3.07
2240 2361 4.379243 ACGAAGCCGGCACCTGAG 62.379 66.667 31.54 15.48 40.78 3.35
2241 2362 4.373116 GACGAAGCCGGCACCTGA 62.373 66.667 31.54 0.00 44.91 3.86
2279 2400 1.807573 GCCGTCAGCCTCTTTCGAG 60.808 63.158 0.00 0.00 37.01 4.04
2282 2406 2.095252 GTCGCCGTCAGCCTCTTTC 61.095 63.158 0.00 0.00 38.78 2.62
2294 2418 4.764336 TACAACTCGCCGTCGCCG 62.764 66.667 0.00 0.00 35.26 6.46
2387 2511 0.244994 TCAGCTTCTCGTCCTTGAGC 59.755 55.000 0.00 0.00 35.90 4.26
2504 2628 1.832167 GATCTCCTCCCGCAGCTCT 60.832 63.158 0.00 0.00 0.00 4.09
2576 2700 2.117156 GGTACTCTCCACGCGCCTA 61.117 63.158 5.73 0.00 0.00 3.93
2747 2871 1.138069 ACATTCGTGACACCTGACACA 59.862 47.619 0.00 0.00 39.92 3.72
2762 2886 4.156556 ACACATGCAGGTGACATTACATTC 59.843 41.667 35.67 0.00 41.32 2.67
2775 2947 1.135972 GCAAGTACGAACACATGCAGG 60.136 52.381 0.00 0.00 34.20 4.85
2780 2952 3.190535 GGGAATTGCAAGTACGAACACAT 59.809 43.478 4.94 0.00 0.00 3.21
2819 2991 7.897575 TTGAGTTGCAAGTTTAAACAACATT 57.102 28.000 20.06 3.10 43.74 2.71
2854 3026 2.416747 GCAAAAGTGGATTCTTTGGCC 58.583 47.619 0.00 0.00 44.18 5.36
2865 3037 2.699954 ACGGAGATGTAGCAAAAGTGG 58.300 47.619 0.00 0.00 0.00 4.00
2889 3083 3.187637 CGCCTAACAAAAGGAAATCGACA 59.812 43.478 0.00 0.00 39.15 4.35
2915 3336 9.535878 GATGGAGTATCTTAGAAACCAACTTAG 57.464 37.037 0.00 0.00 33.73 2.18
2936 3357 4.258543 CCTTGCGTTTTACTAAGGATGGA 58.741 43.478 0.00 0.00 41.71 3.41
2937 3358 3.181500 GCCTTGCGTTTTACTAAGGATGG 60.181 47.826 6.08 0.00 41.71 3.51
2945 3366 1.687563 AACAGGCCTTGCGTTTTACT 58.312 45.000 0.00 0.00 0.00 2.24
2952 3373 0.385390 AAAGTCAAACAGGCCTTGCG 59.615 50.000 0.00 0.00 0.00 4.85
2954 3375 1.136695 TGCAAAGTCAAACAGGCCTTG 59.863 47.619 0.00 0.00 0.00 3.61
3001 3422 6.480524 TTGACAGAGTTTGATAAATGGTCG 57.519 37.500 0.00 0.00 0.00 4.79
3115 3542 6.086765 CGCACAATTTTGACTATGACTTTCAC 59.913 38.462 0.00 0.00 0.00 3.18
3218 3656 5.866335 TCCATTCGTAAAAATAGCACGTT 57.134 34.783 0.00 0.00 37.02 3.99
3271 3710 7.865707 ACTAGTTCAATGCTCAGTTTAAAGTG 58.134 34.615 15.66 15.66 0.00 3.16
3559 4015 8.073768 AGTTCACCATGTAGTAAAAATTGTTCG 58.926 33.333 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.