Multiple sequence alignment - TraesCS3A01G154800

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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 TraesCS3A01G154800 chr3A 100.000 2755 0 0 1 2755 146561266 146564020 0.000000e+00 5088.0
1 TraesCS3A01G154800 chr3A 96.175 732 26 2 1 731 705259170 705258440 0.000000e+00 1195.0
2 TraesCS3A01G154800 chr2A 97.954 733 13 2 1 731 775767173 775766441 0.000000e+00 1269.0
3 TraesCS3A01G154800 chr2A 96.585 732 23 2 1 731 496561590 496560860 0.000000e+00 1212.0
4 TraesCS3A01G154800 chr4A 97.131 732 19 2 1 731 620868140 620867410 0.000000e+00 1234.0
5 TraesCS3A01G154800 chr7B 96.594 734 20 2 1 733 562174350 562173621 0.000000e+00 1212.0
6 TraesCS3A01G154800 chr7B 76.842 285 37 14 174 441 139528892 139529164 1.720000e-27 134.0
7 TraesCS3A01G154800 chr3D 87.500 1096 67 37 829 1893 132906539 132907595 0.000000e+00 1201.0
8 TraesCS3A01G154800 chr3D 97.143 105 2 1 741 844 132905512 132905616 2.820000e-40 176.0
9 TraesCS3A01G154800 chr2B 95.907 733 25 2 1 732 759455438 759456166 0.000000e+00 1182.0
10 TraesCS3A01G154800 chr3B 86.933 926 81 23 982 1899 189387708 189388601 0.000000e+00 1003.0
11 TraesCS3A01G154800 chr3B 86.569 685 60 13 2082 2743 189389481 189390156 0.000000e+00 726.0
12 TraesCS3A01G154800 chr3B 100.000 34 0 0 886 919 189387625 189387658 2.290000e-06 63.9
13 TraesCS3A01G154800 chr5B 96.703 455 14 1 280 733 430666747 430667201 0.000000e+00 756.0
14 TraesCS3A01G154800 chr5B 96.528 288 6 1 1 288 430665237 430665520 8.930000e-130 473.0
15 TraesCS3A01G154800 chr7A 78.906 256 39 11 174 424 176280010 176280255 2.840000e-35 159.0
16 TraesCS3A01G154800 chr5D 78.626 262 41 9 180 436 365087557 365087306 2.840000e-35 159.0
17 TraesCS3A01G154800 chr1B 79.032 124 17 9 2623 2742 36279934 36280052 2.940000e-10 76.8


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 TraesCS3A01G154800 chr3A 146561266 146564020 2754 False 5088.000000 5088 100.000000 1 2755 1 chr3A.!!$F1 2754
1 TraesCS3A01G154800 chr3A 705258440 705259170 730 True 1195.000000 1195 96.175000 1 731 1 chr3A.!!$R1 730
2 TraesCS3A01G154800 chr2A 775766441 775767173 732 True 1269.000000 1269 97.954000 1 731 1 chr2A.!!$R2 730
3 TraesCS3A01G154800 chr2A 496560860 496561590 730 True 1212.000000 1212 96.585000 1 731 1 chr2A.!!$R1 730
4 TraesCS3A01G154800 chr4A 620867410 620868140 730 True 1234.000000 1234 97.131000 1 731 1 chr4A.!!$R1 730
5 TraesCS3A01G154800 chr7B 562173621 562174350 729 True 1212.000000 1212 96.594000 1 733 1 chr7B.!!$R1 732
6 TraesCS3A01G154800 chr3D 132905512 132907595 2083 False 688.500000 1201 92.321500 741 1893 2 chr3D.!!$F1 1152
7 TraesCS3A01G154800 chr2B 759455438 759456166 728 False 1182.000000 1182 95.907000 1 732 1 chr2B.!!$F1 731
8 TraesCS3A01G154800 chr3B 189387625 189390156 2531 False 597.633333 1003 91.167333 886 2743 3 chr3B.!!$F1 1857
9 TraesCS3A01G154800 chr5B 430665237 430667201 1964 False 614.500000 756 96.615500 1 733 2 chr5B.!!$F1 732

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
980 3177 0.239613 GCAACACACACACACACACA 59.76 50.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 4918 0.3199 AGGTGCAACTGCGTAGTGAG 60.32 55.0 1.66 4.4 45.83 3.51 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
57 58 4.457496 CATGGCGCAGGTCTCGGT 62.457 66.667 10.83 0.00 0.00 4.69
211 213 3.844211 ACCTTTGTAGAGAGTTGGCCATA 59.156 43.478 6.09 0.00 0.00 2.74
725 1964 7.040201 TCCGTAGCAGTATAGGTACCATAAAAG 60.040 40.741 15.94 0.70 38.83 2.27
733 1972 8.643324 AGTATAGGTACCATAAAAGAGCTCTTG 58.357 37.037 29.09 18.04 36.12 3.02
734 1973 5.763876 AGGTACCATAAAAGAGCTCTTGT 57.236 39.130 29.09 25.72 36.12 3.16
735 1974 6.128138 AGGTACCATAAAAGAGCTCTTGTT 57.872 37.500 29.09 23.67 36.12 2.83
736 1975 6.543735 AGGTACCATAAAAGAGCTCTTGTTT 58.456 36.000 29.09 21.63 36.12 2.83
737 1976 6.431234 AGGTACCATAAAAGAGCTCTTGTTTG 59.569 38.462 29.09 25.69 36.12 2.93
738 1977 6.430000 GGTACCATAAAAGAGCTCTTGTTTGA 59.570 38.462 28.74 12.99 36.12 2.69
739 1978 6.566197 ACCATAAAAGAGCTCTTGTTTGAG 57.434 37.500 28.74 22.14 36.12 3.02
870 3048 6.093633 GTCACTGTCATGGGGTTAATTAAGTC 59.906 42.308 0.00 0.00 0.00 3.01
871 3049 5.064707 CACTGTCATGGGGTTAATTAAGTCG 59.935 44.000 0.00 0.00 0.00 4.18
872 3050 5.046159 ACTGTCATGGGGTTAATTAAGTCGA 60.046 40.000 0.00 0.00 0.00 4.20
873 3051 5.424757 TGTCATGGGGTTAATTAAGTCGAG 58.575 41.667 0.00 0.00 0.00 4.04
874 3052 4.272748 GTCATGGGGTTAATTAAGTCGAGC 59.727 45.833 0.00 0.00 0.00 5.03
875 3053 4.163458 TCATGGGGTTAATTAAGTCGAGCT 59.837 41.667 0.00 0.00 0.00 4.09
876 3054 3.869065 TGGGGTTAATTAAGTCGAGCTG 58.131 45.455 0.00 0.00 0.00 4.24
877 3055 3.516300 TGGGGTTAATTAAGTCGAGCTGA 59.484 43.478 0.00 0.00 0.00 4.26
878 3056 4.163458 TGGGGTTAATTAAGTCGAGCTGAT 59.837 41.667 0.00 0.00 0.00 2.90
879 3057 4.750598 GGGGTTAATTAAGTCGAGCTGATC 59.249 45.833 0.00 0.00 0.00 2.92
880 3058 5.453480 GGGGTTAATTAAGTCGAGCTGATCT 60.453 44.000 0.00 0.00 0.00 2.75
881 3059 6.049790 GGGTTAATTAAGTCGAGCTGATCTT 58.950 40.000 0.00 0.00 0.00 2.40
882 3060 7.208080 GGGTTAATTAAGTCGAGCTGATCTTA 58.792 38.462 0.00 0.00 0.00 2.10
919 3104 3.118371 GGGTACAACAAGGCTATAGCTGT 60.118 47.826 23.53 20.14 41.70 4.40
920 3105 3.871594 GGTACAACAAGGCTATAGCTGTG 59.128 47.826 23.53 21.50 41.70 3.66
921 3106 2.991250 ACAACAAGGCTATAGCTGTGG 58.009 47.619 23.53 19.46 41.70 4.17
923 3108 3.201290 CAACAAGGCTATAGCTGTGGAG 58.799 50.000 23.53 13.71 41.70 3.86
924 3109 1.765314 ACAAGGCTATAGCTGTGGAGG 59.235 52.381 23.53 9.44 41.70 4.30
925 3110 2.042464 CAAGGCTATAGCTGTGGAGGA 58.958 52.381 23.53 0.00 41.70 3.71
927 3112 0.320050 GGCTATAGCTGTGGAGGAGC 59.680 60.000 23.53 0.00 41.70 4.70
928 3113 1.043816 GCTATAGCTGTGGAGGAGCA 58.956 55.000 17.75 0.00 39.05 4.26
974 3171 1.499502 CACACGCAACACACACACA 59.500 52.632 0.00 0.00 0.00 3.72
975 3172 0.792729 CACACGCAACACACACACAC 60.793 55.000 0.00 0.00 0.00 3.82
976 3173 1.231296 ACACGCAACACACACACACA 61.231 50.000 0.00 0.00 0.00 3.72
977 3174 0.792729 CACGCAACACACACACACAC 60.793 55.000 0.00 0.00 0.00 3.82
978 3175 1.231296 ACGCAACACACACACACACA 61.231 50.000 0.00 0.00 0.00 3.72
979 3176 0.792729 CGCAACACACACACACACAC 60.793 55.000 0.00 0.00 0.00 3.82
980 3177 0.239613 GCAACACACACACACACACA 59.760 50.000 0.00 0.00 0.00 3.72
981 3178 1.962412 CAACACACACACACACACAC 58.038 50.000 0.00 0.00 0.00 3.82
982 3179 1.265365 CAACACACACACACACACACA 59.735 47.619 0.00 0.00 0.00 3.72
983 3180 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
984 3181 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
985 3182 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
986 3183 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
987 3184 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
988 3185 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
989 3186 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
990 3187 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
991 3188 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
992 3189 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
993 3190 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
994 3191 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
995 3192 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
996 3193 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
997 3194 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
998 3195 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
999 3196 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1010 3207 1.300620 ACACACACATGGACGACGG 60.301 57.895 0.00 0.00 0.00 4.79
1272 3494 2.035442 GTTCTCCCACTCAAGCGCC 61.035 63.158 2.29 0.00 0.00 6.53
1333 3562 0.041312 CTTTGTCTGTTCCCGCGTTG 60.041 55.000 4.92 0.00 0.00 4.10
1352 3581 2.358003 GCTTGCGTGCAGGACTCT 60.358 61.111 11.29 0.00 0.00 3.24
1540 3786 1.407618 TGATGATTGATGGCAAGCTGC 59.592 47.619 0.00 0.00 40.90 5.25
1575 3821 3.316283 GAGCAAATTGAAACATGGCGAA 58.684 40.909 0.00 0.00 0.00 4.70
1576 3822 3.928375 GAGCAAATTGAAACATGGCGAAT 59.072 39.130 0.00 0.00 0.00 3.34
1577 3823 3.928375 AGCAAATTGAAACATGGCGAATC 59.072 39.130 0.00 0.00 0.00 2.52
1578 3824 3.241741 GCAAATTGAAACATGGCGAATCG 60.242 43.478 0.00 0.00 0.00 3.34
1601 3847 0.321122 GTGTGCAGGAGGAGGTTCAG 60.321 60.000 0.00 0.00 0.00 3.02
1637 3883 2.438614 GGCCGGAAAGGGAAGCTC 60.439 66.667 5.05 0.00 41.48 4.09
1748 3994 3.817647 AGAGCAACAAAAGTAGGAGCAAG 59.182 43.478 0.00 0.00 0.00 4.01
1810 4061 3.686726 AGATTTGAGCATCTCCGTTCAAC 59.313 43.478 0.00 0.00 36.08 3.18
1812 4063 2.768253 TGAGCATCTCCGTTCAACAT 57.232 45.000 0.00 0.00 34.92 2.71
1815 4066 4.769688 TGAGCATCTCCGTTCAACATAAT 58.230 39.130 0.00 0.00 34.92 1.28
1816 4067 5.912892 TGAGCATCTCCGTTCAACATAATA 58.087 37.500 0.00 0.00 34.92 0.98
1849 4100 9.860898 AAGAAAATCCATTTTACTAATGCTCAC 57.139 29.630 0.00 0.00 39.86 3.51
1883 4134 6.219473 TGCTTCTTTGAAGTCTAGTTCAGAG 58.781 40.000 10.40 10.40 39.11 3.35
1895 4146 7.220030 AGTCTAGTTCAGAGAAGAAAATGCAA 58.780 34.615 0.00 0.00 32.51 4.08
1899 4150 6.501781 AGTTCAGAGAAGAAAATGCAACTTG 58.498 36.000 0.00 0.00 0.00 3.16
1911 4892 2.977054 GCAACTTGCACTTTTCAACG 57.023 45.000 8.97 0.00 44.26 4.10
1913 4894 2.733858 GCAACTTGCACTTTTCAACGGA 60.734 45.455 8.97 0.00 44.26 4.69
1928 4909 1.878953 ACGGAGTGAAAAAGCGTCAT 58.121 45.000 0.00 0.00 42.51 3.06
1937 4918 7.061752 AGTGAAAAAGCGTCATATACACTTC 57.938 36.000 0.00 0.00 33.29 3.01
1970 4954 1.961277 CACCTTTCGGCAGCGACTT 60.961 57.895 0.00 0.00 0.00 3.01
1978 4962 0.860618 CGGCAGCGACTTAGACGTAC 60.861 60.000 5.97 0.00 0.00 3.67
1982 4966 2.538535 GCAGCGACTTAGACGTACTACC 60.539 54.545 5.97 0.00 0.00 3.18
1986 4970 3.001127 GCGACTTAGACGTACTACCTCTG 59.999 52.174 5.97 0.00 0.00 3.35
1987 4971 4.180057 CGACTTAGACGTACTACCTCTGT 58.820 47.826 0.00 0.00 0.00 3.41
1993 4977 7.663493 ACTTAGACGTACTACCTCTGTTAACTT 59.337 37.037 7.22 0.00 0.00 2.66
2007 4991 9.788960 CCTCTGTTAACTTTTTATAAGGCATTC 57.211 33.333 7.22 0.00 0.00 2.67
2027 5011 8.159344 GCATTCTTAGAGTTTAATATGCCAGT 57.841 34.615 2.42 0.00 33.00 4.00
2028 5012 8.072567 GCATTCTTAGAGTTTAATATGCCAGTG 58.927 37.037 2.42 0.00 33.00 3.66
2029 5013 9.330063 CATTCTTAGAGTTTAATATGCCAGTGA 57.670 33.333 0.00 0.00 0.00 3.41
2030 5014 9.905713 ATTCTTAGAGTTTAATATGCCAGTGAA 57.094 29.630 0.00 0.00 0.00 3.18
2031 5015 9.733556 TTCTTAGAGTTTAATATGCCAGTGAAA 57.266 29.630 0.00 0.00 0.00 2.69
2032 5016 9.733556 TCTTAGAGTTTAATATGCCAGTGAAAA 57.266 29.630 0.00 0.00 0.00 2.29
2036 5020 9.023962 AGAGTTTAATATGCCAGTGAAAATTCA 57.976 29.630 0.00 0.00 34.20 2.57
2037 5021 9.638239 GAGTTTAATATGCCAGTGAAAATTCAA 57.362 29.630 0.00 0.00 39.21 2.69
2038 5022 9.995003 AGTTTAATATGCCAGTGAAAATTCAAA 57.005 25.926 0.00 0.00 39.21 2.69
2098 5082 7.973048 AGTATTGAGTTTGGGAGATAGTACA 57.027 36.000 0.00 0.00 0.00 2.90
2099 5083 8.012957 AGTATTGAGTTTGGGAGATAGTACAG 57.987 38.462 0.00 0.00 0.00 2.74
2164 5148 7.403312 TGTCAATTGTGGGAAAATATACTGG 57.597 36.000 5.13 0.00 0.00 4.00
2165 5149 6.127479 TGTCAATTGTGGGAAAATATACTGGC 60.127 38.462 5.13 0.00 0.00 4.85
2194 5178 5.536538 CCACTCCTTAGATGCTACTGTGATA 59.463 44.000 0.00 0.00 0.00 2.15
2195 5179 6.210385 CCACTCCTTAGATGCTACTGTGATAT 59.790 42.308 0.00 0.00 0.00 1.63
2197 5181 8.458052 CACTCCTTAGATGCTACTGTGATATAG 58.542 40.741 0.00 0.00 0.00 1.31
2218 5202 2.654749 GGCACCAAGGCTGTTAAATC 57.345 50.000 0.00 0.00 40.24 2.17
2223 5207 3.820467 CACCAAGGCTGTTAAATCTGTGA 59.180 43.478 0.00 0.00 0.00 3.58
2241 5225 4.071423 TGTGATCCAACGAACAACATCAT 58.929 39.130 0.00 0.00 0.00 2.45
2243 5227 3.370672 TGATCCAACGAACAACATCATCG 59.629 43.478 0.00 0.00 42.05 3.84
2246 5230 2.159707 CCAACGAACAACATCATCGGAC 60.160 50.000 0.00 0.00 40.71 4.79
2252 5236 2.972625 ACAACATCATCGGACGTGAAT 58.027 42.857 0.00 0.00 0.00 2.57
2266 5250 5.629020 CGGACGTGAATCAAAACATCATTTT 59.371 36.000 0.00 0.00 0.00 1.82
2279 5263 9.695526 CAAAACATCATTTTAGGAATGTTGAGA 57.304 29.630 13.68 0.00 33.70 3.27
2281 5265 7.636150 ACATCATTTTAGGAATGTTGAGAGG 57.364 36.000 13.68 0.00 33.70 3.69
2282 5266 7.177878 ACATCATTTTAGGAATGTTGAGAGGT 58.822 34.615 13.68 0.00 33.70 3.85
2283 5267 7.671398 ACATCATTTTAGGAATGTTGAGAGGTT 59.329 33.333 13.68 0.00 33.70 3.50
2284 5268 8.526147 CATCATTTTAGGAATGTTGAGAGGTTT 58.474 33.333 4.58 0.00 32.07 3.27
2285 5269 8.477419 TCATTTTAGGAATGTTGAGAGGTTTT 57.523 30.769 0.00 0.00 0.00 2.43
2288 5272 9.807921 ATTTTAGGAATGTTGAGAGGTTTTCTA 57.192 29.630 0.00 0.00 35.87 2.10
2305 5289 1.953686 TCTACAAAACTTGCACTGGCC 59.046 47.619 0.00 0.00 40.13 5.36
2330 5314 0.943673 CGGCCATTTGATGCACGATA 59.056 50.000 2.24 0.00 32.21 2.92
2336 5320 3.732219 CCATTTGATGCACGATACAATGC 59.268 43.478 0.00 0.00 42.40 3.56
2344 5328 2.030946 GCACGATACAATGCTCCAGAAC 59.969 50.000 0.00 0.00 38.84 3.01
2349 5333 1.750399 CAATGCTCCAGAACCCCGG 60.750 63.158 0.00 0.00 0.00 5.73
2350 5334 2.231380 AATGCTCCAGAACCCCGGT 61.231 57.895 0.00 0.00 0.00 5.28
2369 5370 3.305131 CGGTAGCATCTAAAGGTGCGATA 60.305 47.826 9.47 0.00 45.69 2.92
2401 5402 5.746307 ATGCACTATGTCAACTATTGCTG 57.254 39.130 0.00 0.00 0.00 4.41
2442 5443 1.956297 TTTACGGTGTTGTGTGAGGG 58.044 50.000 0.00 0.00 0.00 4.30
2456 5457 4.819630 TGTGTGAGGGTCATGTTCTTTTAC 59.180 41.667 0.00 0.00 0.00 2.01
2469 5470 4.518970 TGTTCTTTTACTGTTGATGGGAGC 59.481 41.667 0.00 0.00 0.00 4.70
2475 5476 2.440409 ACTGTTGATGGGAGCATTGTC 58.560 47.619 0.00 0.00 0.00 3.18
2486 5487 4.527427 TGGGAGCATTGTCAAATTCATTGA 59.473 37.500 0.00 0.00 45.71 2.57
2546 5550 7.552458 AAATGTTAGTGCAAAAGGGAAAAAG 57.448 32.000 0.00 0.00 0.00 2.27
2547 5551 5.017294 TGTTAGTGCAAAAGGGAAAAAGG 57.983 39.130 0.00 0.00 0.00 3.11
2576 5583 4.499183 AGAGACTGCTCGGTTTATTGAAG 58.501 43.478 0.00 0.00 45.98 3.02
2577 5584 3.600388 AGACTGCTCGGTTTATTGAAGG 58.400 45.455 0.00 0.00 0.00 3.46
2580 5587 4.394729 ACTGCTCGGTTTATTGAAGGAAA 58.605 39.130 0.00 0.00 0.00 3.13
2581 5588 4.825085 ACTGCTCGGTTTATTGAAGGAAAA 59.175 37.500 0.00 0.00 0.00 2.29
2583 5590 4.022676 TGCTCGGTTTATTGAAGGAAAACC 60.023 41.667 6.20 6.20 45.64 3.27
2596 5603 6.112058 TGAAGGAAAACCAAATGAAAACCTG 58.888 36.000 0.00 0.00 0.00 4.00
2609 5616 3.190535 TGAAAACCTGAATAAAGGCGAGC 59.809 43.478 0.00 0.00 41.46 5.03
2621 5628 1.003718 GGCGAGCCACACCTAGTTT 60.004 57.895 9.58 0.00 35.81 2.66
2626 5633 2.230508 CGAGCCACACCTAGTTTGACTA 59.769 50.000 0.00 0.00 0.00 2.59
2641 5648 7.299246 AGTTTGACTAGGTCTAAAGCACTAA 57.701 36.000 0.00 0.00 30.38 2.24
2675 5682 3.965780 CTGAAAGGCCAAACACCAC 57.034 52.632 5.01 0.00 0.00 4.16
2689 5696 2.126071 CCACAGGACACGTAGCCG 60.126 66.667 0.00 0.00 40.83 5.52
2704 5711 2.789917 CCGGGTACTCGAGTGTCG 59.210 66.667 28.12 24.20 42.10 4.35
2731 5738 1.163420 CGCTACCAAAGTGCACACCA 61.163 55.000 21.04 0.00 0.00 4.17
2743 5750 1.219646 GCACACCAAAACCATTGCTG 58.780 50.000 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
211 213 6.372381 GCTTAAAACCTGAATTTGCATTGGAT 59.628 34.615 0.00 0.00 0.00 3.41
309 1546 7.610865 AGTGATGTCAAAAACTTTCTTCCAAA 58.389 30.769 0.00 0.00 0.00 3.28
681 1919 7.097834 GCTACGGAAAAAGGAGCAGTATATAT 58.902 38.462 0.00 0.00 33.26 0.86
725 1964 2.037772 TCCACTCCTCAAACAAGAGCTC 59.962 50.000 5.27 5.27 34.26 4.09
733 1972 2.569404 AGGTGATCTCCACTCCTCAAAC 59.431 50.000 15.93 0.00 45.03 2.93
734 1973 2.834549 GAGGTGATCTCCACTCCTCAAA 59.165 50.000 15.93 0.00 45.03 2.69
735 1974 2.461695 GAGGTGATCTCCACTCCTCAA 58.538 52.381 15.93 0.00 45.03 3.02
736 1975 2.151502 GAGGTGATCTCCACTCCTCA 57.848 55.000 15.93 0.00 45.03 3.86
772 2011 2.982744 GCCCAACGCAGCTTCCTTC 61.983 63.158 0.00 0.00 37.47 3.46
798 2037 6.072508 GCATATTCTGAAACTCAAGTCAACCA 60.073 38.462 0.00 0.00 0.00 3.67
870 3048 4.090138 AGCACGATATAAGATCAGCTCG 57.910 45.455 0.00 0.00 0.00 5.03
871 3049 4.157656 AGGAGCACGATATAAGATCAGCTC 59.842 45.833 14.95 14.95 41.28 4.09
872 3050 4.085733 AGGAGCACGATATAAGATCAGCT 58.914 43.478 0.00 0.00 33.60 4.24
873 3051 4.448537 AGGAGCACGATATAAGATCAGC 57.551 45.455 0.00 0.00 0.00 4.26
874 3052 5.564768 CGTAGGAGCACGATATAAGATCAG 58.435 45.833 0.00 0.00 44.69 2.90
875 3053 5.547181 CGTAGGAGCACGATATAAGATCA 57.453 43.478 0.00 0.00 44.69 2.92
919 3104 2.172483 GACGCTTCCTTGCTCCTCCA 62.172 60.000 0.00 0.00 0.00 3.86
920 3105 1.448717 GACGCTTCCTTGCTCCTCC 60.449 63.158 0.00 0.00 0.00 4.30
921 3106 1.448717 GGACGCTTCCTTGCTCCTC 60.449 63.158 1.07 0.00 39.13 3.71
923 3108 1.301677 CTTGGACGCTTCCTTGCTCC 61.302 60.000 11.01 0.00 43.31 4.70
924 3109 1.301677 CCTTGGACGCTTCCTTGCTC 61.302 60.000 11.01 0.00 43.31 4.26
925 3110 1.302832 CCTTGGACGCTTCCTTGCT 60.303 57.895 11.01 0.00 43.31 3.91
927 3112 0.250295 TGACCTTGGACGCTTCCTTG 60.250 55.000 11.01 3.20 43.31 3.61
928 3113 0.250338 GTGACCTTGGACGCTTCCTT 60.250 55.000 11.01 0.00 43.31 3.36
946 3140 1.133982 TGTTGCGTGTGCTTGATTTGT 59.866 42.857 0.00 0.00 43.34 2.83
974 3171 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
975 3172 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
976 3173 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
977 3174 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
978 3175 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
979 3176 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
980 3177 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
981 3178 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
982 3179 1.468127 CATGTGTGTGTGTGTGTGTGT 59.532 47.619 0.00 0.00 0.00 3.72
983 3180 1.202166 CCATGTGTGTGTGTGTGTGTG 60.202 52.381 0.00 0.00 0.00 3.82
984 3181 1.093972 CCATGTGTGTGTGTGTGTGT 58.906 50.000 0.00 0.00 0.00 3.72
985 3182 1.063912 GTCCATGTGTGTGTGTGTGTG 59.936 52.381 0.00 0.00 0.00 3.82
986 3183 1.378531 GTCCATGTGTGTGTGTGTGT 58.621 50.000 0.00 0.00 0.00 3.72
987 3184 0.304401 CGTCCATGTGTGTGTGTGTG 59.696 55.000 0.00 0.00 0.00 3.82
988 3185 0.176910 TCGTCCATGTGTGTGTGTGT 59.823 50.000 0.00 0.00 0.00 3.72
989 3186 0.581529 GTCGTCCATGTGTGTGTGTG 59.418 55.000 0.00 0.00 0.00 3.82
990 3187 0.874175 CGTCGTCCATGTGTGTGTGT 60.874 55.000 0.00 0.00 0.00 3.72
991 3188 1.556591 CCGTCGTCCATGTGTGTGTG 61.557 60.000 0.00 0.00 0.00 3.82
992 3189 1.300620 CCGTCGTCCATGTGTGTGT 60.301 57.895 0.00 0.00 0.00 3.72
993 3190 2.027073 CCCGTCGTCCATGTGTGTG 61.027 63.158 0.00 0.00 0.00 3.82
994 3191 2.342279 CCCGTCGTCCATGTGTGT 59.658 61.111 0.00 0.00 0.00 3.72
995 3192 2.434185 CCCCGTCGTCCATGTGTG 60.434 66.667 0.00 0.00 0.00 3.82
996 3193 4.388499 GCCCCGTCGTCCATGTGT 62.388 66.667 0.00 0.00 0.00 3.72
1237 3434 0.106719 AACCCAATATGTGCGAGGGG 60.107 55.000 0.00 0.00 43.96 4.79
1261 3458 3.730761 GGCACAGGCGCTTGAGTG 61.731 66.667 27.58 19.74 42.47 3.51
1338 3567 2.340078 GTCAGAGTCCTGCACGCA 59.660 61.111 0.00 0.00 40.20 5.24
1390 3619 3.027170 GCCGAGCACATGTTGTCCG 62.027 63.158 0.00 0.00 0.00 4.79
1512 3741 6.350194 GCTTGCCATCAATCATCATCATGTAT 60.350 38.462 0.00 0.00 0.00 2.29
1514 3743 4.262036 GCTTGCCATCAATCATCATCATGT 60.262 41.667 0.00 0.00 0.00 3.21
1515 3744 4.021981 AGCTTGCCATCAATCATCATCATG 60.022 41.667 0.00 0.00 0.00 3.07
1517 3746 3.317993 CAGCTTGCCATCAATCATCATCA 59.682 43.478 0.00 0.00 0.00 3.07
1518 3764 3.857383 GCAGCTTGCCATCAATCATCATC 60.857 47.826 0.00 0.00 37.42 2.92
1575 3821 1.037579 TCCTCCTGCACACGATCGAT 61.038 55.000 24.34 6.46 0.00 3.59
1576 3822 1.657751 CTCCTCCTGCACACGATCGA 61.658 60.000 24.34 0.00 0.00 3.59
1577 3823 1.226802 CTCCTCCTGCACACGATCG 60.227 63.158 14.88 14.88 0.00 3.69
1578 3824 1.142748 CCTCCTCCTGCACACGATC 59.857 63.158 0.00 0.00 0.00 3.69
1724 3970 3.815401 TGCTCCTACTTTTGTTGCTCTTC 59.185 43.478 0.00 0.00 0.00 2.87
1748 3994 5.140177 CGACATTTTAACTTGTGTCAGAGC 58.860 41.667 5.37 0.00 40.65 4.09
1824 4075 8.184192 CGTGAGCATTAGTAAAATGGATTTTCT 58.816 33.333 0.60 2.56 40.24 2.52
1847 4098 0.792640 AAGAAGCAATCACTCGCGTG 59.207 50.000 5.77 6.24 42.59 5.34
1848 4099 1.195448 CAAAGAAGCAATCACTCGCGT 59.805 47.619 5.77 0.00 0.00 6.01
1849 4100 1.460743 TCAAAGAAGCAATCACTCGCG 59.539 47.619 0.00 0.00 0.00 5.87
1860 4111 6.451393 TCTCTGAACTAGACTTCAAAGAAGC 58.549 40.000 6.67 0.89 26.59 3.86
1861 4112 8.519492 CTTCTCTGAACTAGACTTCAAAGAAG 57.481 38.462 17.85 17.85 43.72 2.85
1895 4146 2.097466 CACTCCGTTGAAAAGTGCAAGT 59.903 45.455 0.00 0.00 34.55 3.16
1899 4150 3.414549 TTTCACTCCGTTGAAAAGTGC 57.585 42.857 2.54 0.00 41.48 4.40
1904 4155 2.420722 ACGCTTTTTCACTCCGTTGAAA 59.579 40.909 1.17 1.17 42.47 2.69
1905 4156 2.011222 ACGCTTTTTCACTCCGTTGAA 58.989 42.857 0.00 0.00 33.55 2.69
1906 4157 1.595794 GACGCTTTTTCACTCCGTTGA 59.404 47.619 0.00 0.00 31.65 3.18
1911 4892 5.796813 GTGTATATGACGCTTTTTCACTCC 58.203 41.667 0.00 0.00 35.54 3.85
1928 4909 5.637809 CAACTGCGTAGTGAGAAGTGTATA 58.362 41.667 7.01 0.00 37.19 1.47
1937 4918 0.319900 AGGTGCAACTGCGTAGTGAG 60.320 55.000 1.66 4.40 45.83 3.51
1970 4954 7.986085 AAAGTTAACAGAGGTAGTACGTCTA 57.014 36.000 21.76 7.38 40.92 2.59
1978 4962 9.444600 TGCCTTATAAAAAGTTAACAGAGGTAG 57.555 33.333 8.61 0.00 0.00 3.18
2002 4986 8.072567 CACTGGCATATTAAACTCTAAGAATGC 58.927 37.037 0.00 0.00 0.00 3.56
2068 5052 9.968870 CTATCTCCCAAACTCAATACTACTAAC 57.031 37.037 0.00 0.00 0.00 2.34
2069 5053 9.710818 ACTATCTCCCAAACTCAATACTACTAA 57.289 33.333 0.00 0.00 0.00 2.24
2072 5056 8.910944 TGTACTATCTCCCAAACTCAATACTAC 58.089 37.037 0.00 0.00 0.00 2.73
2073 5057 9.132923 CTGTACTATCTCCCAAACTCAATACTA 57.867 37.037 0.00 0.00 0.00 1.82
2074 5058 7.839705 TCTGTACTATCTCCCAAACTCAATACT 59.160 37.037 0.00 0.00 0.00 2.12
2075 5059 8.008513 TCTGTACTATCTCCCAAACTCAATAC 57.991 38.462 0.00 0.00 0.00 1.89
2076 5060 8.603898 TTCTGTACTATCTCCCAAACTCAATA 57.396 34.615 0.00 0.00 0.00 1.90
2077 5061 7.496346 TTCTGTACTATCTCCCAAACTCAAT 57.504 36.000 0.00 0.00 0.00 2.57
2078 5062 6.928348 TTCTGTACTATCTCCCAAACTCAA 57.072 37.500 0.00 0.00 0.00 3.02
2079 5063 6.928348 TTTCTGTACTATCTCCCAAACTCA 57.072 37.500 0.00 0.00 0.00 3.41
2106 5090 6.205658 GGGTATATCCAAGTCTTGAGAAATGC 59.794 42.308 14.42 5.67 38.11 3.56
2147 5131 2.092646 AGCGCCAGTATATTTTCCCACA 60.093 45.455 2.29 0.00 0.00 4.17
2148 5132 2.572290 AGCGCCAGTATATTTTCCCAC 58.428 47.619 2.29 0.00 0.00 4.61
2164 5148 1.870167 GCATCTAAGGAGTGGTAGCGC 60.870 57.143 0.00 0.00 0.00 5.92
2165 5149 1.683917 AGCATCTAAGGAGTGGTAGCG 59.316 52.381 0.00 0.00 0.00 4.26
2194 5178 1.509548 AACAGCCTTGGTGCCCCTAT 61.510 55.000 0.00 0.00 34.04 2.57
2195 5179 0.842905 TAACAGCCTTGGTGCCCCTA 60.843 55.000 0.00 0.00 34.04 3.53
2197 5181 0.830023 TTTAACAGCCTTGGTGCCCC 60.830 55.000 0.00 0.00 34.04 5.80
2210 5194 5.760743 TGTTCGTTGGATCACAGATTTAACA 59.239 36.000 0.00 0.00 0.00 2.41
2213 5197 5.760743 TGTTGTTCGTTGGATCACAGATTTA 59.239 36.000 0.00 0.00 0.00 1.40
2215 5199 4.133820 TGTTGTTCGTTGGATCACAGATT 58.866 39.130 0.00 0.00 0.00 2.40
2218 5202 3.498018 TGATGTTGTTCGTTGGATCACAG 59.502 43.478 0.00 0.00 0.00 3.66
2223 5207 2.677836 CCGATGATGTTGTTCGTTGGAT 59.322 45.455 0.00 0.00 38.12 3.41
2241 5225 3.394719 TGATGTTTTGATTCACGTCCGA 58.605 40.909 0.00 0.00 0.00 4.55
2243 5227 7.273381 CCTAAAATGATGTTTTGATTCACGTCC 59.727 37.037 0.00 0.00 0.00 4.79
2246 5230 8.741101 TTCCTAAAATGATGTTTTGATTCACG 57.259 30.769 0.00 0.00 0.00 4.35
2252 5236 9.695526 CTCAACATTCCTAAAATGATGTTTTGA 57.304 29.630 4.86 3.59 33.73 2.69
2266 5250 7.311092 TGTAGAAAACCTCTCAACATTCCTA 57.689 36.000 0.00 0.00 35.41 2.94
2279 5263 8.779758 GCCAGTGCAAGTTTTGTAGAAAACCT 62.780 42.308 21.00 8.77 43.33 3.50
2281 5265 4.267690 GCCAGTGCAAGTTTTGTAGAAAAC 59.732 41.667 17.98 17.98 43.02 2.43
2282 5266 4.429108 GCCAGTGCAAGTTTTGTAGAAAA 58.571 39.130 0.00 0.00 37.47 2.29
2283 5267 3.181480 GGCCAGTGCAAGTTTTGTAGAAA 60.181 43.478 0.00 0.00 40.13 2.52
2284 5268 2.360801 GGCCAGTGCAAGTTTTGTAGAA 59.639 45.455 0.00 0.00 40.13 2.10
2285 5269 1.953686 GGCCAGTGCAAGTTTTGTAGA 59.046 47.619 0.00 0.00 40.13 2.59
2288 5272 0.901124 TTGGCCAGTGCAAGTTTTGT 59.099 45.000 5.11 0.00 40.13 2.83
2305 5289 1.155424 GCATCAAATGGCCGGCATTG 61.155 55.000 30.85 27.08 0.00 2.82
2313 5297 3.419264 TTGTATCGTGCATCAAATGGC 57.581 42.857 0.00 0.00 0.00 4.40
2319 5303 2.212652 GGAGCATTGTATCGTGCATCA 58.787 47.619 0.00 0.00 43.63 3.07
2330 5314 1.002134 CGGGGTTCTGGAGCATTGT 60.002 57.895 0.00 0.00 0.00 2.71
2336 5320 1.338136 ATGCTACCGGGGTTCTGGAG 61.338 60.000 6.32 0.00 42.08 3.86
2344 5328 1.129058 ACCTTTAGATGCTACCGGGG 58.871 55.000 6.32 0.00 0.00 5.73
2349 5333 3.675698 GCTATCGCACCTTTAGATGCTAC 59.324 47.826 0.00 0.00 39.79 3.58
2350 5334 3.320826 TGCTATCGCACCTTTAGATGCTA 59.679 43.478 0.00 0.00 42.25 3.49
2369 5370 3.070590 TGACATAGTGCATATCAGCTGCT 59.929 43.478 9.47 0.82 40.34 4.24
2373 5374 7.516481 CAATAGTTGACATAGTGCATATCAGC 58.484 38.462 0.00 0.00 0.00 4.26
2377 5378 6.429078 CCAGCAATAGTTGACATAGTGCATAT 59.571 38.462 10.21 0.00 44.42 1.78
2381 5382 4.191544 TCCAGCAATAGTTGACATAGTGC 58.808 43.478 1.23 1.23 42.83 4.40
2425 5426 0.390124 GACCCTCACACAACACCGTA 59.610 55.000 0.00 0.00 0.00 4.02
2428 5429 1.238439 CATGACCCTCACACAACACC 58.762 55.000 0.00 0.00 0.00 4.16
2432 5433 3.576078 AAGAACATGACCCTCACACAA 57.424 42.857 0.00 0.00 0.00 3.33
2442 5443 6.206634 TCCCATCAACAGTAAAAGAACATGAC 59.793 38.462 0.00 0.00 0.00 3.06
2456 5457 2.439409 TGACAATGCTCCCATCAACAG 58.561 47.619 0.00 0.00 0.00 3.16
2576 5583 8.669946 TTATTCAGGTTTTCATTTGGTTTTCC 57.330 30.769 0.00 0.00 41.14 3.13
2580 5587 6.710295 GCCTTTATTCAGGTTTTCATTTGGTT 59.290 34.615 0.00 0.00 36.15 3.67
2581 5588 6.230472 GCCTTTATTCAGGTTTTCATTTGGT 58.770 36.000 0.00 0.00 36.15 3.67
2583 5590 6.155827 TCGCCTTTATTCAGGTTTTCATTTG 58.844 36.000 0.00 0.00 36.15 2.32
2584 5591 6.339587 TCGCCTTTATTCAGGTTTTCATTT 57.660 33.333 0.00 0.00 36.15 2.32
2596 5603 0.733150 GGTGTGGCTCGCCTTTATTC 59.267 55.000 11.72 0.00 42.91 1.75
2641 5648 4.321230 CCTTTCAGGCGTCTTGCTATTTTT 60.321 41.667 0.00 0.00 45.43 1.94
2657 5664 1.067516 CTGTGGTGTTTGGCCTTTCAG 59.932 52.381 3.32 0.00 0.00 3.02
2667 5674 1.808891 GCTACGTGTCCTGTGGTGTTT 60.809 52.381 0.00 0.00 0.00 2.83
2675 5682 2.048023 TACCCGGCTACGTGTCCTG 61.048 63.158 0.00 0.00 38.78 3.86
2689 5696 1.130186 GAAGACGACACTCGAGTACCC 59.870 57.143 19.57 9.20 43.74 3.69
2704 5711 0.669625 ACTTTGGTAGCGGCGAAGAC 60.670 55.000 12.98 4.15 0.00 3.01
2731 5738 3.444029 AGATTAGGCCAGCAATGGTTTT 58.556 40.909 5.01 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.