Multiple sequence alignment - TraesCS3B01G103400

Loading Multiple Alignment...

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 TraesCS3B01G103400 chr3B 100.000 7687 0 0 1 7687 70104417 70096731 0.000000e+00 14196.0
1 TraesCS3B01G103400 chr3B 97.492 4386 105 5 2618 6999 687765594 687761210 0.000000e+00 7485.0
2 TraesCS3B01G103400 chr3B 93.051 4821 316 16 2001 6816 672727207 672722401 0.000000e+00 7029.0
3 TraesCS3B01G103400 chr3B 95.906 2711 102 5 1 2707 754333008 754335713 0.000000e+00 4383.0
4 TraesCS3B01G103400 chr3B 96.424 2629 84 6 1 2623 687777283 687774659 0.000000e+00 4325.0
5 TraesCS3B01G103400 chr3B 90.722 97 5 4 6905 6998 783156123 783156218 8.100000e-25 126.0
6 TraesCS3B01G103400 chr2B 97.097 6992 186 13 1 6983 10998190 11005173 0.000000e+00 11771.0
7 TraesCS3B01G103400 chr2B 92.658 6851 469 16 7 6847 699080355 699087181 0.000000e+00 9834.0
8 TraesCS3B01G103400 chr2B 84.615 156 15 4 6846 7000 208222679 208222532 6.220000e-31 147.0
9 TraesCS3B01G103400 chr5B 96.635 7014 214 17 1 7005 409461158 409468158 0.000000e+00 11625.0
10 TraesCS3B01G103400 chr5B 92.616 6460 447 22 398 6847 75715091 75708652 0.000000e+00 9260.0
11 TraesCS3B01G103400 chr5B 89.871 6990 646 41 39 6998 506517783 506524740 0.000000e+00 8929.0
12 TraesCS3B01G103400 chr5B 92.525 3933 276 17 7 3929 566062068 566058144 0.000000e+00 5618.0
13 TraesCS3B01G103400 chr5B 92.450 3033 187 14 3977 6998 566058134 566055133 0.000000e+00 4294.0
14 TraesCS3B01G103400 chr5B 85.526 152 13 4 6846 6997 75708591 75708449 4.810000e-32 150.0
15 TraesCS3B01G103400 chr7B 89.574 6973 667 41 58 6998 376422115 376429059 0.000000e+00 8794.0
16 TraesCS3B01G103400 chr7B 93.256 519 24 2 6332 6847 702456103 702456613 0.000000e+00 754.0
17 TraesCS3B01G103400 chr7B 92.391 92 6 1 6911 7002 689897606 689897516 6.260000e-26 130.0
18 TraesCS3B01G103400 chr7B 82.353 153 19 4 6846 6998 706063025 706063169 8.100000e-25 126.0
19 TraesCS3B01G103400 chrUn 90.578 4065 357 14 2793 6853 246199599 246203641 0.000000e+00 5361.0
20 TraesCS3B01G103400 chr3A 79.279 555 55 33 7134 7678 56738447 56737943 4.450000e-87 333.0
21 TraesCS3B01G103400 chr3D 83.333 378 29 10 6999 7367 44975205 44974853 1.240000e-82 318.0
22 TraesCS3B01G103400 chr6A 83.784 74 8 4 7167 7239 30838671 30838601 4.980000e-07 67.6


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 TraesCS3B01G103400 chr3B 70096731 70104417 7686 True 14196 14196 100.0000 1 7687 1 chr3B.!!$R1 7686
1 TraesCS3B01G103400 chr3B 687761210 687765594 4384 True 7485 7485 97.4920 2618 6999 1 chr3B.!!$R3 4381
2 TraesCS3B01G103400 chr3B 672722401 672727207 4806 True 7029 7029 93.0510 2001 6816 1 chr3B.!!$R2 4815
3 TraesCS3B01G103400 chr3B 754333008 754335713 2705 False 4383 4383 95.9060 1 2707 1 chr3B.!!$F1 2706
4 TraesCS3B01G103400 chr3B 687774659 687777283 2624 True 4325 4325 96.4240 1 2623 1 chr3B.!!$R4 2622
5 TraesCS3B01G103400 chr2B 10998190 11005173 6983 False 11771 11771 97.0970 1 6983 1 chr2B.!!$F1 6982
6 TraesCS3B01G103400 chr2B 699080355 699087181 6826 False 9834 9834 92.6580 7 6847 1 chr2B.!!$F2 6840
7 TraesCS3B01G103400 chr5B 409461158 409468158 7000 False 11625 11625 96.6350 1 7005 1 chr5B.!!$F1 7004
8 TraesCS3B01G103400 chr5B 506517783 506524740 6957 False 8929 8929 89.8710 39 6998 1 chr5B.!!$F2 6959
9 TraesCS3B01G103400 chr5B 566055133 566062068 6935 True 4956 5618 92.4875 7 6998 2 chr5B.!!$R2 6991
10 TraesCS3B01G103400 chr5B 75708449 75715091 6642 True 4705 9260 89.0710 398 6997 2 chr5B.!!$R1 6599
11 TraesCS3B01G103400 chr7B 376422115 376429059 6944 False 8794 8794 89.5740 58 6998 1 chr7B.!!$F1 6940
12 TraesCS3B01G103400 chr7B 702456103 702456613 510 False 754 754 93.2560 6332 6847 1 chr7B.!!$F2 515
13 TraesCS3B01G103400 chrUn 246199599 246203641 4042 False 5361 5361 90.5780 2793 6853 1 chrUn.!!$F1 4060
14 TraesCS3B01G103400 chr3A 56737943 56738447 504 True 333 333 79.2790 7134 7678 1 chr3A.!!$R1 544

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
352 353 0.324738 TGGTGGAGGCCTAGTGAGAG 60.325 60.000 4.42 0.0 0.00 3.20 F
658 670 0.469917 GGGAATCGCTCTGGGAATGA 59.530 55.000 0.00 0.0 0.00 2.57 F
1669 1693 0.109723 GGGTGTTTGTGAGGTGGCTA 59.890 55.000 0.00 0.0 0.00 3.93 F
2981 3015 1.774894 TTGGGGTTGGAGTCCTTCGG 61.775 60.000 11.33 0.0 0.00 4.30 F
3410 3449 0.903942 TGGTTACGGTGTATGGGGAC 59.096 55.000 0.00 0.0 0.00 4.46 F
3781 3822 1.217916 TGGACACAGGGGAAACTCAA 58.782 50.000 0.00 0.0 0.00 3.02 F
5033 5076 2.624364 TGTTTGACATTGCTGCTGATGT 59.376 40.909 17.70 17.7 39.09 3.06 F
6366 6415 0.320771 TCTTCTCTTGCTCGGTTGCC 60.321 55.000 0.00 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1534 1557 0.918983 TTGATCATCACCCCTGTCCC 59.081 55.000 0.00 0.0 0.00 4.46 R
1818 1842 1.194781 TCTCCACCACCTTCTCAGCC 61.195 60.000 0.00 0.0 0.00 4.85 R
3410 3449 1.160137 CTTTTCCCTCCTTCTGTGCG 58.840 55.000 0.00 0.0 0.00 5.34 R
4015 4056 2.099098 CGCATTTAAACCCATGACCTCC 59.901 50.000 0.00 0.0 0.00 4.30 R
5332 5375 1.891933 TCAGATACAGGCATCCCCAA 58.108 50.000 0.00 0.0 35.39 4.12 R
5369 5412 4.908601 TCAGTTACACAATCCCACTGAT 57.091 40.909 0.00 0.0 39.12 2.90 R
6481 6530 3.602104 CTGAAATCCCCACCAGCAT 57.398 52.632 0.00 0.0 0.00 3.79 R
7566 7698 0.035343 ATGAGAGACCGGAGACACGA 60.035 55.000 9.46 0.0 35.47 4.35 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
110 111 7.420800 GGATAGATGCAGAAATTGTTCGAATT 58.579 34.615 0.00 0.00 38.90 2.17
153 154 7.361438 TGTTCATCCCATAATCCCTGTATTTT 58.639 34.615 0.00 0.00 0.00 1.82
209 210 2.032620 CAGAGTACCCCTATTGCGAGT 58.967 52.381 0.00 0.00 0.00 4.18
312 313 7.040686 GCTCAGTTGGAAAGGATTTAAACACTA 60.041 37.037 0.00 0.00 39.27 2.74
352 353 0.324738 TGGTGGAGGCCTAGTGAGAG 60.325 60.000 4.42 0.00 0.00 3.20
555 565 2.093500 GGGAATGGCAATTTTGGAGGAC 60.093 50.000 0.00 0.00 0.00 3.85
563 573 4.381932 GGCAATTTTGGAGGACGATTCAAT 60.382 41.667 0.00 0.00 0.00 2.57
564 574 4.563976 GCAATTTTGGAGGACGATTCAATG 59.436 41.667 0.00 0.00 0.00 2.82
574 584 6.083098 AGGACGATTCAATGATACTGAGAG 57.917 41.667 0.00 0.00 0.00 3.20
583 593 3.931241 TGATACTGAGAGGATGGGGAT 57.069 47.619 0.00 0.00 0.00 3.85
658 670 0.469917 GGGAATCGCTCTGGGAATGA 59.530 55.000 0.00 0.00 0.00 2.57
666 678 2.158842 CGCTCTGGGAATGAGAAGGATT 60.159 50.000 0.00 0.00 33.68 3.01
716 728 1.000270 AGCTGAGAGGAGCGAGGAA 60.000 57.895 0.00 0.00 44.24 3.36
767 785 3.494749 GGAAAGATGCAGGAGGAGAGATG 60.495 52.174 0.00 0.00 0.00 2.90
814 832 4.280929 GGAAGGTGCTGTAATGGAAAAAGT 59.719 41.667 0.00 0.00 0.00 2.66
821 839 4.762251 GCTGTAATGGAAAAAGTGAGGAGT 59.238 41.667 0.00 0.00 0.00 3.85
864 882 1.034356 TCAGCAGCAGCAACAATTGT 58.966 45.000 4.92 4.92 45.49 2.71
881 899 5.065988 ACAATTGTTGTTGACTTCGCTACTT 59.934 36.000 4.92 0.00 42.22 2.24
946 964 2.042842 TGGAAGGAATGGCTGGAAATCA 59.957 45.455 0.00 0.00 0.00 2.57
953 971 4.080975 GGAATGGCTGGAAATCAAATTGGA 60.081 41.667 0.00 0.00 0.00 3.53
977 995 4.660168 ACATGCTTGGAAGAGAAAGTCAT 58.340 39.130 4.44 0.00 0.00 3.06
1017 1035 2.553904 CCTGATGGGCAACAGAGAGTTT 60.554 50.000 0.00 0.00 38.74 2.66
1076 1095 2.445525 AGAAGCAAGGGGGTAAAAGTGA 59.554 45.455 0.00 0.00 0.00 3.41
1311 1331 3.652869 TGGGAATTCTTCTGGTTCAGAGT 59.347 43.478 5.23 0.00 41.75 3.24
1395 1418 5.879223 AGGAAGCATTAATGAGACTGAACTG 59.121 40.000 19.73 0.00 0.00 3.16
1411 1434 3.582647 TGAACTGGTGAAAGCTATGGAGA 59.417 43.478 0.00 0.00 33.76 3.71
1628 1652 0.178990 GTCAGGTTGGCCAAAGTCCT 60.179 55.000 22.47 19.96 37.19 3.85
1669 1693 0.109723 GGGTGTTTGTGAGGTGGCTA 59.890 55.000 0.00 0.00 0.00 3.93
1818 1842 4.599041 TCATGTTTAGAATTGGGGTGGAG 58.401 43.478 0.00 0.00 0.00 3.86
1875 1899 6.729428 AGATGAGAAGAGGAAAAATGATGGT 58.271 36.000 0.00 0.00 0.00 3.55
1877 1901 8.331740 AGATGAGAAGAGGAAAAATGATGGTAA 58.668 33.333 0.00 0.00 0.00 2.85
2009 2038 7.512992 AGTGAGGAGGTTGATATAAGAATTGG 58.487 38.462 0.00 0.00 0.00 3.16
2029 2058 3.072915 TGGAGGAATGAAAGCTCAAGTGA 59.927 43.478 0.00 0.00 34.49 3.41
2332 2361 9.650539 TTGAAGATTATGAGAAAGAGACTCAAG 57.349 33.333 5.02 0.00 45.44 3.02
2481 2510 3.774216 AGAGGGAGGAGAAAGATGTTGAG 59.226 47.826 0.00 0.00 0.00 3.02
2779 2812 6.012508 GGGGGATGTGAAGAGGATGATAAATA 60.013 42.308 0.00 0.00 0.00 1.40
2981 3015 1.774894 TTGGGGTTGGAGTCCTTCGG 61.775 60.000 11.33 0.00 0.00 4.30
3144 3183 9.732130 ACAAGAAAAGATATATTAGGGAGATGC 57.268 33.333 0.00 0.00 0.00 3.91
3398 3437 3.848272 ATGCACTGGAATTTGGTTACG 57.152 42.857 0.00 0.00 0.00 3.18
3410 3449 0.903942 TGGTTACGGTGTATGGGGAC 59.096 55.000 0.00 0.00 0.00 4.46
3781 3822 1.217916 TGGACACAGGGGAAACTCAA 58.782 50.000 0.00 0.00 0.00 3.02
3881 3922 6.150332 TGGAATGAGAGATACTTTGGGGATA 58.850 40.000 0.00 0.00 0.00 2.59
3882 3923 6.043243 TGGAATGAGAGATACTTTGGGGATAC 59.957 42.308 0.00 0.00 0.00 2.24
3891 3932 8.344939 AGATACTTTGGGGATACTTTGGATAA 57.655 34.615 0.00 0.00 0.00 1.75
3979 4020 8.925700 GCTTGGTACAGAAAAATAAAAATGGAG 58.074 33.333 0.00 0.00 42.39 3.86
4015 4056 6.867816 AGCTTGATGATTTAGATAAGAGAGCG 59.132 38.462 0.00 0.00 0.00 5.03
4109 4150 5.371526 TGATACAAGAGGAGATGAAATGGC 58.628 41.667 0.00 0.00 0.00 4.40
4264 4305 7.348274 GGGGATGAGAGGTTGATGGAATATATA 59.652 40.741 0.00 0.00 0.00 0.86
4575 4617 6.969993 TGGCATAATTACCTTAATCCCAAC 57.030 37.500 0.00 0.00 0.00 3.77
4918 4961 5.512942 TTGGGTGATGGAAACTATGAGAA 57.487 39.130 0.00 0.00 0.00 2.87
5033 5076 2.624364 TGTTTGACATTGCTGCTGATGT 59.376 40.909 17.70 17.70 39.09 3.06
5124 5167 6.246163 GGGGAAGGGGATTAATATGTTACAG 58.754 44.000 0.00 0.00 0.00 2.74
5568 5612 0.962356 GATCCAGGTTGGTGTGGCAG 60.962 60.000 0.00 0.00 39.03 4.85
5586 5630 3.564644 GGCAGGATGATGAGAATGTCAAG 59.435 47.826 0.00 0.00 39.69 3.02
6366 6415 0.320771 TCTTCTCTTGCTCGGTTGCC 60.321 55.000 0.00 0.00 0.00 4.52
6439 6488 5.981315 CCGTCTAGTGTGAAAGACTGTTTTA 59.019 40.000 0.00 0.00 42.32 1.52
6524 6573 4.880696 CCTGCTTTGGTCAATTTGGAAAAA 59.119 37.500 0.00 0.00 0.00 1.94
6598 6647 1.350684 TCAAGCTAATGTGCAGGTGGA 59.649 47.619 0.00 0.00 34.99 4.02
6913 7030 2.032290 CGGTTGGACCTCTTCGTTTTTC 60.032 50.000 0.00 0.00 35.66 2.29
6914 7031 2.946990 GGTTGGACCTCTTCGTTTTTCA 59.053 45.455 0.00 0.00 34.73 2.69
7034 7157 9.650539 TTCAAAAGTTGTGAATGATTTTTCAGA 57.349 25.926 4.25 0.00 36.34 3.27
7035 7158 9.820725 TCAAAAGTTGTGAATGATTTTTCAGAT 57.179 25.926 0.00 0.00 36.34 2.90
7039 7162 9.603921 AAGTTGTGAATGATTTTTCAGATTTGT 57.396 25.926 0.00 0.00 36.34 2.83
7040 7163 9.037737 AGTTGTGAATGATTTTTCAGATTTGTG 57.962 29.630 0.00 0.00 36.34 3.33
7041 7164 9.033481 GTTGTGAATGATTTTTCAGATTTGTGA 57.967 29.630 0.00 0.00 36.34 3.58
7042 7165 9.597170 TTGTGAATGATTTTTCAGATTTGTGAA 57.403 25.926 0.00 0.00 36.34 3.18
7043 7166 9.767228 TGTGAATGATTTTTCAGATTTGTGAAT 57.233 25.926 0.00 0.00 36.34 2.57
7045 7168 9.767228 TGAATGATTTTTCAGATTTGTGAATGT 57.233 25.926 0.00 0.00 36.34 2.71
7063 7186 8.663911 TGTGAATGTTTTTCAAAATCAAGAACC 58.336 29.630 0.00 0.00 0.00 3.62
7064 7187 8.663911 GTGAATGTTTTTCAAAATCAAGAACCA 58.336 29.630 0.00 0.00 0.00 3.67
7065 7188 9.393512 TGAATGTTTTTCAAAATCAAGAACCAT 57.606 25.926 0.00 0.00 0.00 3.55
7066 7189 9.654417 GAATGTTTTTCAAAATCAAGAACCATG 57.346 29.630 0.00 0.00 0.00 3.66
7067 7190 8.961294 ATGTTTTTCAAAATCAAGAACCATGA 57.039 26.923 0.00 0.00 0.00 3.07
7068 7191 8.783833 TGTTTTTCAAAATCAAGAACCATGAA 57.216 26.923 0.00 0.00 0.00 2.57
7069 7192 9.393512 TGTTTTTCAAAATCAAGAACCATGAAT 57.606 25.926 0.00 0.00 0.00 2.57
7072 7195 7.872163 TTCAAAATCAAGAACCATGAATTCG 57.128 32.000 0.04 0.00 0.00 3.34
7073 7196 6.980593 TCAAAATCAAGAACCATGAATTCGT 58.019 32.000 0.04 0.00 0.00 3.85
7074 7197 6.862608 TCAAAATCAAGAACCATGAATTCGTG 59.137 34.615 19.02 19.02 37.03 4.35
7075 7198 6.573664 AAATCAAGAACCATGAATTCGTGA 57.426 33.333 25.99 21.36 44.77 4.35
7076 7199 6.573664 AATCAAGAACCATGAATTCGTGAA 57.426 33.333 25.99 12.32 44.18 3.18
7077 7200 5.356882 TCAAGAACCATGAATTCGTGAAC 57.643 39.130 25.99 16.43 40.22 3.18
7078 7201 5.063204 TCAAGAACCATGAATTCGTGAACT 58.937 37.500 25.99 18.03 40.22 3.01
7079 7202 5.530915 TCAAGAACCATGAATTCGTGAACTT 59.469 36.000 25.99 21.60 40.22 2.66
7080 7203 5.362556 AGAACCATGAATTCGTGAACTTG 57.637 39.130 25.99 12.90 34.90 3.16
7081 7204 4.821805 AGAACCATGAATTCGTGAACTTGT 59.178 37.500 25.99 13.49 34.90 3.16
7082 7205 5.299279 AGAACCATGAATTCGTGAACTTGTT 59.701 36.000 25.99 19.88 34.90 2.83
7083 7206 5.514274 ACCATGAATTCGTGAACTTGTTT 57.486 34.783 25.99 0.60 34.90 2.83
7084 7207 5.901552 ACCATGAATTCGTGAACTTGTTTT 58.098 33.333 25.99 0.00 34.90 2.43
7085 7208 7.033530 ACCATGAATTCGTGAACTTGTTTTA 57.966 32.000 25.99 0.00 34.90 1.52
7086 7209 7.484975 ACCATGAATTCGTGAACTTGTTTTAA 58.515 30.769 25.99 0.00 34.90 1.52
7087 7210 7.976734 ACCATGAATTCGTGAACTTGTTTTAAA 59.023 29.630 25.99 0.00 34.90 1.52
7088 7211 8.977505 CCATGAATTCGTGAACTTGTTTTAAAT 58.022 29.630 25.99 0.00 34.90 1.40
7117 7240 9.786105 ATTTCATTTGTTTTTGCCTAGTTTTTG 57.214 25.926 0.00 0.00 0.00 2.44
7118 7241 7.313951 TCATTTGTTTTTGCCTAGTTTTTGG 57.686 32.000 0.00 0.00 0.00 3.28
7125 7248 2.997485 GCCTAGTTTTTGGCTGACTG 57.003 50.000 0.00 0.00 45.26 3.51
7126 7249 2.504367 GCCTAGTTTTTGGCTGACTGA 58.496 47.619 0.00 0.00 45.26 3.41
7127 7250 3.084786 GCCTAGTTTTTGGCTGACTGAT 58.915 45.455 0.00 0.00 45.26 2.90
7128 7251 3.507622 GCCTAGTTTTTGGCTGACTGATT 59.492 43.478 0.00 0.00 45.26 2.57
7129 7252 4.021981 GCCTAGTTTTTGGCTGACTGATTT 60.022 41.667 0.00 0.00 45.26 2.17
7130 7253 5.509670 GCCTAGTTTTTGGCTGACTGATTTT 60.510 40.000 0.00 0.00 45.26 1.82
7131 7254 6.515832 CCTAGTTTTTGGCTGACTGATTTTT 58.484 36.000 0.00 0.00 0.00 1.94
7190 7313 7.978414 TGAAAAATGTTCAGTGTGCATTTAGAA 59.022 29.630 19.72 10.77 40.58 2.10
7200 7323 8.412456 TCAGTGTGCATTTAGAAAAATCTTCAA 58.588 29.630 0.00 0.00 32.87 2.69
7302 7426 7.742556 TGTGTATCTGAAAATGTGTTCATCA 57.257 32.000 0.00 0.00 36.92 3.07
7303 7427 8.339344 TGTGTATCTGAAAATGTGTTCATCAT 57.661 30.769 0.00 0.00 36.92 2.45
7304 7428 9.447157 TGTGTATCTGAAAATGTGTTCATCATA 57.553 29.630 0.00 0.00 36.92 2.15
7361 7488 4.475944 AGTTTGTATTGAAAGATGCGCAC 58.524 39.130 14.90 7.11 0.00 5.34
7368 7495 6.484977 TGTATTGAAAGATGCGCACCATATAA 59.515 34.615 14.90 5.21 33.29 0.98
7372 7499 7.686438 TGAAAGATGCGCACCATATAATAAT 57.314 32.000 14.90 0.00 33.29 1.28
7496 7628 9.670719 CAAACTTGGAAGAGAATAGAAAAAGTC 57.329 33.333 0.00 0.00 0.00 3.01
7500 7632 9.890352 CTTGGAAGAGAATAGAAAAAGTCAAAG 57.110 33.333 0.00 0.00 0.00 2.77
7533 7665 8.865590 AAAAAGTAAGCACAAATCGTACATTT 57.134 26.923 0.00 0.00 0.00 2.32
7534 7666 8.865590 AAAAGTAAGCACAAATCGTACATTTT 57.134 26.923 0.00 0.00 0.00 1.82
7535 7667 8.865590 AAAGTAAGCACAAATCGTACATTTTT 57.134 26.923 0.00 0.00 0.00 1.94
7561 7693 3.250040 GGGGTCACAAATCGTACATATGC 59.750 47.826 1.58 0.00 0.00 3.14
7565 7697 3.489416 TCACAAATCGTACATATGCTCGC 59.511 43.478 1.58 0.00 0.00 5.03
7566 7698 3.490896 CACAAATCGTACATATGCTCGCT 59.509 43.478 1.58 0.00 0.00 4.93
7567 7699 3.736252 ACAAATCGTACATATGCTCGCTC 59.264 43.478 1.58 0.00 0.00 5.03
7568 7700 2.248828 ATCGTACATATGCTCGCTCG 57.751 50.000 1.58 0.00 0.00 5.03
7569 7701 0.942252 TCGTACATATGCTCGCTCGT 59.058 50.000 1.58 0.00 0.00 4.18
7570 7702 1.045477 CGTACATATGCTCGCTCGTG 58.955 55.000 1.58 0.00 0.00 4.35
7571 7703 1.597199 CGTACATATGCTCGCTCGTGT 60.597 52.381 1.58 0.00 0.00 4.49
7572 7704 2.044860 GTACATATGCTCGCTCGTGTC 58.955 52.381 1.58 0.00 0.00 3.67
7573 7705 0.741326 ACATATGCTCGCTCGTGTCT 59.259 50.000 1.58 0.00 0.00 3.41
7574 7706 1.268794 ACATATGCTCGCTCGTGTCTC 60.269 52.381 1.58 0.00 0.00 3.36
7575 7707 0.312416 ATATGCTCGCTCGTGTCTCC 59.688 55.000 0.00 0.00 0.00 3.71
7576 7708 2.048312 TATGCTCGCTCGTGTCTCCG 62.048 60.000 0.00 0.00 0.00 4.63
7577 7709 4.838486 GCTCGCTCGTGTCTCCGG 62.838 72.222 0.00 0.00 0.00 5.14
7578 7710 3.432588 CTCGCTCGTGTCTCCGGT 61.433 66.667 0.00 0.00 0.00 5.28
7579 7711 3.384014 CTCGCTCGTGTCTCCGGTC 62.384 68.421 0.00 0.00 0.00 4.79
7580 7712 3.432588 CGCTCGTGTCTCCGGTCT 61.433 66.667 0.00 0.00 0.00 3.85
7597 7729 2.203112 TCTCATGCCCGCAGATGC 60.203 61.111 0.00 0.00 37.78 3.91
7630 7768 1.972872 ATGCCCATGTAGCAGCTAAC 58.027 50.000 2.87 0.00 44.90 2.34
7631 7769 0.461870 TGCCCATGTAGCAGCTAACG 60.462 55.000 2.87 0.00 34.69 3.18
7636 7774 0.866061 ATGTAGCAGCTAACGACGCG 60.866 55.000 3.53 3.53 0.00 6.01
7641 7779 2.086426 CAGCTAACGACGCGAGCAA 61.086 57.895 15.93 0.00 38.73 3.91
7652 7792 3.036084 CGAGCAACCTGACGCGTT 61.036 61.111 15.53 0.00 0.00 4.84
7672 7812 1.602237 CCCGCTACAAGTGACCCAT 59.398 57.895 0.00 0.00 0.00 4.00
7675 7815 2.548067 CCCGCTACAAGTGACCCATATC 60.548 54.545 0.00 0.00 0.00 1.63
7678 7818 3.990469 CGCTACAAGTGACCCATATCATC 59.010 47.826 0.00 0.00 0.00 2.92
7679 7819 4.262207 CGCTACAAGTGACCCATATCATCT 60.262 45.833 0.00 0.00 0.00 2.90
7680 7820 5.233988 GCTACAAGTGACCCATATCATCTC 58.766 45.833 0.00 0.00 0.00 2.75
7681 7821 4.696479 ACAAGTGACCCATATCATCTCC 57.304 45.455 0.00 0.00 0.00 3.71
7682 7822 3.392616 ACAAGTGACCCATATCATCTCCC 59.607 47.826 0.00 0.00 0.00 4.30
7683 7823 3.350992 AGTGACCCATATCATCTCCCA 57.649 47.619 0.00 0.00 0.00 4.37
7684 7824 3.668821 AGTGACCCATATCATCTCCCAA 58.331 45.455 0.00 0.00 0.00 4.12
7685 7825 3.392616 AGTGACCCATATCATCTCCCAAC 59.607 47.826 0.00 0.00 0.00 3.77
7686 7826 3.392616 GTGACCCATATCATCTCCCAACT 59.607 47.826 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 4.079787 CCCAAAATCTACATCCTCTTCCCA 60.080 45.833 0.00 0.00 0.00 4.37
209 210 1.203001 CCCCCTTTCACACCTAAGCAA 60.203 52.381 0.00 0.00 0.00 3.91
264 265 2.735151 CCCAAAAAGTATCAGGGGTCC 58.265 52.381 0.00 0.00 35.83 4.46
312 313 1.852157 TCAGGCCCACCTCCACATT 60.852 57.895 0.00 0.00 46.34 2.71
494 504 0.474614 GAGCCCCAAATCCTCTACCC 59.525 60.000 0.00 0.00 0.00 3.69
555 565 5.868258 CCATCCTCTCAGTATCATTGAATCG 59.132 44.000 0.00 0.00 0.00 3.34
563 573 3.931241 ATCCCCATCCTCTCAGTATCA 57.069 47.619 0.00 0.00 0.00 2.15
564 574 4.653341 CCATATCCCCATCCTCTCAGTATC 59.347 50.000 0.00 0.00 0.00 2.24
574 584 2.243221 CCTCCATTCCATATCCCCATCC 59.757 54.545 0.00 0.00 0.00 3.51
583 593 2.373169 GCATGTCTCCCTCCATTCCATA 59.627 50.000 0.00 0.00 0.00 2.74
658 670 3.543665 GCATCTCTGCTCAAATCCTTCT 58.456 45.455 0.00 0.00 45.32 2.85
716 728 3.244181 CCTTAGCTTGCCACACCAAATTT 60.244 43.478 0.00 0.00 0.00 1.82
814 832 4.223953 AGAAGTCTGGTTGTTACTCCTCA 58.776 43.478 0.00 0.00 0.00 3.86
821 839 2.703536 TGCCTGAGAAGTCTGGTTGTTA 59.296 45.455 0.94 0.00 42.51 2.41
864 882 4.689071 TGAGAAAGTAGCGAAGTCAACAA 58.311 39.130 0.00 0.00 0.00 2.83
881 899 0.473694 TCCCCTGAACCAGCTGAGAA 60.474 55.000 17.39 0.00 0.00 2.87
946 964 5.305128 TCTCTTCCAAGCATGTTTCCAATTT 59.695 36.000 0.00 0.00 0.00 1.82
953 971 4.889409 TGACTTTCTCTTCCAAGCATGTTT 59.111 37.500 0.00 0.00 0.00 2.83
977 995 2.197465 GGGGCTCCCTCTTCTTTTCTA 58.803 52.381 4.74 0.00 41.34 2.10
1017 1035 0.325933 CCTGCTCCACCATCTTGTCA 59.674 55.000 0.00 0.00 0.00 3.58
1076 1095 2.091720 TCTTCATACCCATGCTGCCAAT 60.092 45.455 0.00 0.00 31.73 3.16
1177 1197 1.426251 ATCAAGCAGTGTCCCACCCA 61.426 55.000 0.00 0.00 34.49 4.51
1395 1418 5.904362 ACATTTTCTCCATAGCTTTCACC 57.096 39.130 0.00 0.00 0.00 4.02
1411 1434 1.693606 CCAGCCCCAGTCAAACATTTT 59.306 47.619 0.00 0.00 0.00 1.82
1534 1557 0.918983 TTGATCATCACCCCTGTCCC 59.081 55.000 0.00 0.00 0.00 4.46
1615 1639 3.806949 ACAATCTAGGACTTTGGCCAA 57.193 42.857 16.05 16.05 0.00 4.52
1818 1842 1.194781 TCTCCACCACCTTCTCAGCC 61.195 60.000 0.00 0.00 0.00 4.85
1897 1926 6.226787 TCTTCCTGTTGTCAATCTCTTCTTC 58.773 40.000 0.00 0.00 0.00 2.87
1898 1927 6.179906 TCTTCCTGTTGTCAATCTCTTCTT 57.820 37.500 0.00 0.00 0.00 2.52
1899 1928 5.279910 CCTCTTCCTGTTGTCAATCTCTTCT 60.280 44.000 0.00 0.00 0.00 2.85
2009 2038 5.471456 TCTTTCACTTGAGCTTTCATTCCTC 59.529 40.000 0.00 0.00 0.00 3.71
2029 2058 2.028748 GCCACTGCATCATGGTTTCTTT 60.029 45.455 12.07 0.00 38.34 2.52
2253 2282 3.554752 CCTCTCTATTAGCAGCCTCTTGC 60.555 52.174 0.00 0.00 44.41 4.01
2332 2361 6.816140 CCAGACTCAGTATCTTCCTTTTTCTC 59.184 42.308 0.00 0.00 0.00 2.87
2481 2510 6.492007 TTGTTTCTCATGCTTCTCTTGATC 57.508 37.500 0.00 0.00 0.00 2.92
2981 3015 9.549078 TTAGACTTCTTTTCTTTCTTCCTTCTC 57.451 33.333 0.00 0.00 0.00 2.87
3144 3183 9.995003 AATAAAGTCTAGCTTCTGATCCATAAG 57.005 33.333 0.00 0.00 36.17 1.73
3398 3437 1.449601 CTGTGCGTCCCCATACACC 60.450 63.158 0.00 0.00 31.98 4.16
3410 3449 1.160137 CTTTTCCCTCCTTCTGTGCG 58.840 55.000 0.00 0.00 0.00 5.34
3551 3591 2.094545 GGCATTGAACATGAAGGACCAC 60.095 50.000 0.00 0.00 0.00 4.16
3881 3922 5.484998 ACCTTGATTGCCATTTATCCAAAGT 59.515 36.000 0.00 0.00 0.00 2.66
3882 3923 5.981174 ACCTTGATTGCCATTTATCCAAAG 58.019 37.500 0.00 0.00 0.00 2.77
3891 3932 3.173953 TCCTCAACCTTGATTGCCATT 57.826 42.857 0.00 0.00 36.46 3.16
4015 4056 2.099098 CGCATTTAAACCCATGACCTCC 59.901 50.000 0.00 0.00 0.00 4.30
4575 4617 9.844790 TCTGAATTTGTTTAGCATCATTAGTTG 57.155 29.630 0.00 0.00 0.00 3.16
4918 4961 3.336694 ACTTTAATCCCAACATGTCCCCT 59.663 43.478 0.00 0.00 0.00 4.79
5033 5076 6.467677 GCATTACTCATTATGAAGGCTAGGA 58.532 40.000 0.00 0.00 0.00 2.94
5124 5167 9.610705 ATCAAGAATATGGTATCATCAGCATAC 57.389 33.333 0.00 0.00 40.59 2.39
5332 5375 1.891933 TCAGATACAGGCATCCCCAA 58.108 50.000 0.00 0.00 35.39 4.12
5369 5412 4.908601 TCAGTTACACAATCCCACTGAT 57.091 40.909 0.00 0.00 39.12 2.90
5373 5416 8.519526 TCAATTTTATCAGTTACACAATCCCAC 58.480 33.333 0.00 0.00 0.00 4.61
5568 5612 7.500227 TGGTATTTCTTGACATTCTCATCATCC 59.500 37.037 0.00 0.00 0.00 3.51
5586 5630 9.396022 TCTTTCCAATTCACTAGATGGTATTTC 57.604 33.333 0.00 0.00 34.50 2.17
6366 6415 7.979444 TCTAACCAAACTCCATAACAAAGAG 57.021 36.000 0.00 0.00 0.00 2.85
6439 6488 9.807921 TTTGTTAAATTTCCTAATCCAGTCTCT 57.192 29.630 0.00 0.00 0.00 3.10
6481 6530 3.602104 CTGAAATCCCCACCAGCAT 57.398 52.632 0.00 0.00 0.00 3.79
7008 7131 9.650539 TCTGAAAAATCATTCACAACTTTTGAA 57.349 25.926 0.00 0.00 37.38 2.69
7009 7132 9.820725 ATCTGAAAAATCATTCACAACTTTTGA 57.179 25.926 0.00 0.00 35.55 2.69
7013 7136 9.603921 ACAAATCTGAAAAATCATTCACAACTT 57.396 25.926 0.00 0.00 35.55 2.66
7014 7137 9.037737 CACAAATCTGAAAAATCATTCACAACT 57.962 29.630 0.00 0.00 35.55 3.16
7015 7138 9.033481 TCACAAATCTGAAAAATCATTCACAAC 57.967 29.630 0.00 0.00 35.55 3.32
7016 7139 9.597170 TTCACAAATCTGAAAAATCATTCACAA 57.403 25.926 0.00 0.00 35.55 3.33
7017 7140 9.767228 ATTCACAAATCTGAAAAATCATTCACA 57.233 25.926 0.00 0.00 35.55 3.58
7019 7142 9.767228 ACATTCACAAATCTGAAAAATCATTCA 57.233 25.926 0.00 0.00 37.70 2.57
7037 7160 8.663911 GGTTCTTGATTTTGAAAAACATTCACA 58.336 29.630 1.44 0.00 0.00 3.58
7038 7161 8.663911 TGGTTCTTGATTTTGAAAAACATTCAC 58.336 29.630 1.44 0.00 0.00 3.18
7039 7162 8.783833 TGGTTCTTGATTTTGAAAAACATTCA 57.216 26.923 1.44 0.00 0.00 2.57
7040 7163 9.654417 CATGGTTCTTGATTTTGAAAAACATTC 57.346 29.630 1.44 0.00 0.00 2.67
7041 7164 9.393512 TCATGGTTCTTGATTTTGAAAAACATT 57.606 25.926 1.44 0.00 0.00 2.71
7042 7165 8.961294 TCATGGTTCTTGATTTTGAAAAACAT 57.039 26.923 1.44 0.00 0.00 2.71
7043 7166 8.783833 TTCATGGTTCTTGATTTTGAAAAACA 57.216 26.923 0.00 0.00 0.00 2.83
7046 7169 8.763356 CGAATTCATGGTTCTTGATTTTGAAAA 58.237 29.630 6.22 0.00 0.00 2.29
7047 7170 7.925483 ACGAATTCATGGTTCTTGATTTTGAAA 59.075 29.630 6.22 0.00 0.00 2.69
7048 7171 7.381948 CACGAATTCATGGTTCTTGATTTTGAA 59.618 33.333 6.22 0.00 29.28 2.69
7049 7172 6.862608 CACGAATTCATGGTTCTTGATTTTGA 59.137 34.615 6.22 0.00 29.28 2.69
7050 7173 6.862608 TCACGAATTCATGGTTCTTGATTTTG 59.137 34.615 6.22 0.00 31.47 2.44
7051 7174 6.980593 TCACGAATTCATGGTTCTTGATTTT 58.019 32.000 6.22 0.00 31.47 1.82
7052 7175 6.573664 TCACGAATTCATGGTTCTTGATTT 57.426 33.333 6.22 0.00 31.47 2.17
7053 7176 6.207417 AGTTCACGAATTCATGGTTCTTGATT 59.793 34.615 16.02 9.11 34.94 2.57
7054 7177 5.707298 AGTTCACGAATTCATGGTTCTTGAT 59.293 36.000 16.02 5.68 34.94 2.57
7055 7178 5.063204 AGTTCACGAATTCATGGTTCTTGA 58.937 37.500 6.22 13.19 33.66 3.02
7056 7179 5.362556 AGTTCACGAATTCATGGTTCTTG 57.637 39.130 6.22 10.11 0.00 3.02
7057 7180 5.299279 ACAAGTTCACGAATTCATGGTTCTT 59.701 36.000 6.22 4.05 0.00 2.52
7058 7181 4.821805 ACAAGTTCACGAATTCATGGTTCT 59.178 37.500 6.22 0.00 0.00 3.01
7059 7182 5.108385 ACAAGTTCACGAATTCATGGTTC 57.892 39.130 6.22 0.00 0.00 3.62
7060 7183 5.514274 AACAAGTTCACGAATTCATGGTT 57.486 34.783 6.22 0.00 0.00 3.67
7061 7184 5.514274 AAACAAGTTCACGAATTCATGGT 57.486 34.783 6.22 0.00 0.00 3.55
7062 7185 7.922505 TTAAAACAAGTTCACGAATTCATGG 57.077 32.000 6.22 0.00 0.00 3.66
7091 7214 9.786105 CAAAAACTAGGCAAAAACAAATGAAAT 57.214 25.926 0.00 0.00 0.00 2.17
7092 7215 8.239998 CCAAAAACTAGGCAAAAACAAATGAAA 58.760 29.630 0.00 0.00 0.00 2.69
7093 7216 7.756558 CCAAAAACTAGGCAAAAACAAATGAA 58.243 30.769 0.00 0.00 0.00 2.57
7094 7217 7.313951 CCAAAAACTAGGCAAAAACAAATGA 57.686 32.000 0.00 0.00 0.00 2.57
7107 7230 5.712152 AAATCAGTCAGCCAAAAACTAGG 57.288 39.130 0.00 0.00 0.00 3.02
7472 7604 8.980481 TGACTTTTTCTATTCTCTTCCAAGTT 57.020 30.769 0.00 0.00 0.00 2.66
7533 7665 5.374921 TGTACGATTTGTGACCCCTAAAAA 58.625 37.500 0.00 0.00 0.00 1.94
7534 7666 4.970711 TGTACGATTTGTGACCCCTAAAA 58.029 39.130 0.00 0.00 0.00 1.52
7535 7667 4.620589 TGTACGATTTGTGACCCCTAAA 57.379 40.909 0.00 0.00 0.00 1.85
7542 7674 4.606232 GCGAGCATATGTACGATTTGTGAC 60.606 45.833 21.11 4.03 0.00 3.67
7543 7675 3.489416 GCGAGCATATGTACGATTTGTGA 59.511 43.478 21.11 0.00 0.00 3.58
7561 7693 3.384014 GACCGGAGACACGAGCGAG 62.384 68.421 9.46 0.00 35.47 5.03
7565 7697 0.673956 TGAGAGACCGGAGACACGAG 60.674 60.000 9.46 0.00 35.47 4.18
7566 7698 0.035343 ATGAGAGACCGGAGACACGA 60.035 55.000 9.46 0.00 35.47 4.35
7567 7699 0.099613 CATGAGAGACCGGAGACACG 59.900 60.000 9.46 0.00 0.00 4.49
7568 7700 0.179124 GCATGAGAGACCGGAGACAC 60.179 60.000 9.46 0.00 0.00 3.67
7569 7701 1.323271 GGCATGAGAGACCGGAGACA 61.323 60.000 9.46 0.83 0.00 3.41
7570 7702 1.439644 GGCATGAGAGACCGGAGAC 59.560 63.158 9.46 0.00 0.00 3.36
7571 7703 1.758514 GGGCATGAGAGACCGGAGA 60.759 63.158 9.46 0.00 0.00 3.71
7572 7704 2.818132 GGGCATGAGAGACCGGAG 59.182 66.667 9.46 0.00 0.00 4.63
7573 7705 3.147595 CGGGCATGAGAGACCGGA 61.148 66.667 9.46 0.00 42.48 5.14
7574 7706 4.899239 GCGGGCATGAGAGACCGG 62.899 72.222 10.55 0.00 46.04 5.28
7576 7708 2.037620 ATCTGCGGGCATGAGAGACC 62.038 60.000 0.00 0.00 0.00 3.85
7577 7709 0.879400 CATCTGCGGGCATGAGAGAC 60.879 60.000 0.00 0.00 0.00 3.36
7578 7710 1.444672 CATCTGCGGGCATGAGAGA 59.555 57.895 0.00 0.00 0.00 3.10
7579 7711 2.252346 GCATCTGCGGGCATGAGAG 61.252 63.158 0.00 0.00 0.00 3.20
7580 7712 2.203112 GCATCTGCGGGCATGAGA 60.203 61.111 0.00 0.00 0.00 3.27
7612 7750 0.461870 CGTTAGCTGCTACATGGGCA 60.462 55.000 9.27 13.50 38.10 5.36
7630 7768 3.470567 GTCAGGTTGCTCGCGTCG 61.471 66.667 5.77 0.00 0.00 5.12
7631 7769 3.470567 CGTCAGGTTGCTCGCGTC 61.471 66.667 5.77 0.00 0.00 5.19
7636 7774 2.551270 CAACGCGTCAGGTTGCTC 59.449 61.111 14.44 0.00 38.41 4.26
7652 7792 2.345991 GGTCACTTGTAGCGGGCA 59.654 61.111 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.