Multiple sequence alignment - TraesCS2D01G233500

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 TraesCS2D01G233500 chr2D 100.000 7245 0 0 1 7245 208543552 208536308 0.000000e+00 13380.0
1 TraesCS2D01G233500 chr2D 89.286 56 6 0 4683 4738 208538815 208538870 3.630000e-08 71.3
2 TraesCS2D01G233500 chr2D 97.059 34 1 0 4080 4113 208539443 208539410 2.820000e-04 58.4
3 TraesCS2D01G233500 chr2D 97.059 34 1 0 4110 4143 208539473 208539440 2.820000e-04 58.4
4 TraesCS2D01G233500 chr2B 95.326 3145 83 23 4110 7245 262901824 262898735 0.000000e+00 4935.0
5 TraesCS2D01G233500 chr2B 96.303 1190 26 7 1942 3116 262905279 262904093 0.000000e+00 1938.0
6 TraesCS2D01G233500 chr2B 95.938 640 25 1 1235 1873 262906075 262905436 0.000000e+00 1037.0
7 TraesCS2D01G233500 chr2B 87.219 712 24 13 166 835 262907388 262906702 0.000000e+00 749.0
8 TraesCS2D01G233500 chr2B 98.701 385 5 0 3730 4114 262902174 262901790 0.000000e+00 684.0
9 TraesCS2D01G233500 chr2B 95.782 403 11 4 3114 3515 262903936 262903539 0.000000e+00 645.0
10 TraesCS2D01G233500 chr2B 97.368 266 4 1 933 1198 262906338 262906076 3.990000e-122 449.0
11 TraesCS2D01G233500 chr2B 97.357 227 3 2 3508 3733 262902490 262902266 4.100000e-102 383.0
12 TraesCS2D01G233500 chr2B 96.667 150 3 1 1 148 262907520 262907371 1.560000e-61 248.0
13 TraesCS2D01G233500 chr2B 90.566 106 5 4 3308 3410 594837480 594837583 1.270000e-27 135.0
14 TraesCS2D01G233500 chr2B 87.692 65 6 2 4675 4737 225254374 225254310 2.800000e-09 75.0
15 TraesCS2D01G233500 chr2B 95.556 45 2 0 4684 4728 225254310 225254354 1.010000e-08 73.1
16 TraesCS2D01G233500 chr2A 92.594 2741 102 40 166 2856 261185149 261182460 0.000000e+00 3843.0
17 TraesCS2D01G233500 chr2A 95.508 1625 38 6 4902 6525 261173540 261171950 0.000000e+00 2564.0
18 TraesCS2D01G233500 chr2A 95.254 611 21 6 4110 4715 261174333 261173726 0.000000e+00 961.0
19 TraesCS2D01G233500 chr2A 85.874 715 39 36 3408 4114 261174959 261174299 0.000000e+00 704.0
20 TraesCS2D01G233500 chr2A 94.277 332 18 1 6543 6874 261171965 261171635 2.330000e-139 507.0
21 TraesCS2D01G233500 chr2A 89.137 313 29 5 6934 7245 261171153 261170845 1.140000e-102 385.0
22 TraesCS2D01G233500 chr2A 91.697 277 14 6 2844 3115 261175601 261175329 6.860000e-100 375.0
23 TraesCS2D01G233500 chr2A 93.069 202 13 1 3114 3315 261175168 261174968 1.980000e-75 294.0
24 TraesCS2D01G233500 chr2A 97.973 148 3 0 1 148 261185279 261185132 2.590000e-64 257.0
25 TraesCS2D01G233500 chr2A 95.798 119 4 1 4709 4826 261173702 261173584 2.670000e-44 191.0
26 TraesCS2D01G233500 chr2A 94.624 93 3 1 3318 3410 65084811 65084901 7.580000e-30 143.0
27 TraesCS2D01G233500 chr3B 96.667 90 3 0 3323 3412 62394194 62394283 4.530000e-32 150.0
28 TraesCS2D01G233500 chr4D 95.604 91 2 1 3322 3412 64347360 64347448 2.110000e-30 145.0
29 TraesCS2D01G233500 chr6B 94.624 93 3 1 3322 3414 13827611 13827521 7.580000e-30 143.0
30 TraesCS2D01G233500 chr5D 91.509 106 5 3 3310 3413 452219496 452219393 7.580000e-30 143.0
31 TraesCS2D01G233500 chr7A 95.455 88 2 2 3322 3409 181833209 181833294 9.800000e-29 139.0
32 TraesCS2D01G233500 chr4B 92.784 97 4 3 3313 3409 447451701 447451794 3.530000e-28 137.0
33 TraesCS2D01G233500 chr1A 92.982 57 4 0 4684 4740 85844087 85844031 4.660000e-12 84.2
34 TraesCS2D01G233500 chr1A 94.444 54 3 0 4684 4737 85844034 85844087 4.660000e-12 84.2
35 TraesCS2D01G233500 chr1B 89.474 57 4 1 4684 4738 630926400 630926456 3.630000e-08 71.3


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 TraesCS2D01G233500 chr2D 208536308 208543552 7244 True 13380.000000 13380 100.00000 1 7245 1 chr2D.!!$R1 7244
1 TraesCS2D01G233500 chr2B 262898735 262907520 8785 True 1229.777778 4935 95.62900 1 7245 9 chr2B.!!$R2 7244
2 TraesCS2D01G233500 chr2A 261182460 261185279 2819 True 2050.000000 3843 95.28350 1 2856 2 chr2A.!!$R2 2855
3 TraesCS2D01G233500 chr2A 261170845 261175601 4756 True 747.625000 2564 92.57675 2844 7245 8 chr2A.!!$R1 4401

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
844 893 0.032615 TCCCCTCTCTCTCTCCTTGC 60.033 60.000 0.0 0.0 0.00 4.01 F
1691 2004 0.107456 CATATCAAGGGCACTCGGCT 59.893 55.000 0.0 0.0 44.01 5.52 F
1932 2356 1.556911 ACCATGAATCGAGGTTCTGCT 59.443 47.619 0.0 0.0 29.58 4.24 F
3719 5403 1.037493 GTTGGGTTTGTCCTTGGTCC 58.963 55.000 0.0 0.0 36.25 4.46 F
4332 6111 1.419720 GGCCTTGGATAGACTCCCCC 61.420 65.000 0.0 0.0 44.23 5.40 F
5748 7566 1.152030 TTGGGCTGGACCACTCTCT 60.152 57.895 0.0 0.0 41.03 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2653 3096 1.080974 GCCACAACTGTGCAGCATC 60.081 57.895 0.00 0.0 44.34 3.91 R
2654 3097 2.567497 GGCCACAACTGTGCAGCAT 61.567 57.895 0.00 0.0 44.34 3.79 R
3833 5612 1.103803 TGCTAGCCCAGTAGACTTCG 58.896 55.000 13.29 0.0 0.00 3.79 R
4648 6429 0.033366 GGTTTTTGGTCGCAGCCATT 59.967 50.000 0.00 0.0 38.48 3.16 R
5771 7589 1.812571 ACACGCCAAGATTTAAGCAGG 59.187 47.619 0.00 0.0 0.00 4.85 R
6928 8841 0.107897 ATGATGGCTACCGCAAACGA 60.108 50.000 0.00 0.0 43.93 3.85 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
148 151 8.719648 CGTCGTGGAGTAATAAGTCTCTTATAT 58.280 37.037 3.01 0.00 0.00 0.86
295 298 0.958876 TAAGCGTCGGACAGAGCAGA 60.959 55.000 9.10 0.00 0.00 4.26
296 299 2.202544 GCGTCGGACAGAGCAGAG 60.203 66.667 9.10 0.00 0.00 3.35
297 300 2.202544 CGTCGGACAGAGCAGAGC 60.203 66.667 9.10 0.00 0.00 4.09
298 301 2.965783 GTCGGACAGAGCAGAGCA 59.034 61.111 2.62 0.00 0.00 4.26
299 302 1.153862 GTCGGACAGAGCAGAGCAG 60.154 63.158 2.62 0.00 0.00 4.24
306 309 0.738063 CAGAGCAGAGCAGTGCAGAG 60.738 60.000 19.20 7.11 46.60 3.35
347 350 6.107343 GGGAGACAGACAAGACTTTATAACC 58.893 44.000 0.00 0.00 0.00 2.85
397 401 2.831685 AAAACCGAGAAAAATGCCCC 57.168 45.000 0.00 0.00 0.00 5.80
455 474 2.416432 GGGTCGGAGTCGGAAGGAG 61.416 68.421 1.41 0.00 36.95 3.69
804 853 2.527624 TGTGGCTCTGTGCTCCCT 60.528 61.111 1.44 0.00 42.39 4.20
825 874 1.802636 CGCAACGGCTCATTCCAAT 59.197 52.632 0.00 0.00 38.10 3.16
826 875 0.248215 CGCAACGGCTCATTCCAATC 60.248 55.000 0.00 0.00 38.10 2.67
828 877 0.740737 CAACGGCTCATTCCAATCCC 59.259 55.000 0.00 0.00 0.00 3.85
833 882 1.202867 GGCTCATTCCAATCCCCTCTC 60.203 57.143 0.00 0.00 0.00 3.20
834 883 1.773653 GCTCATTCCAATCCCCTCTCT 59.226 52.381 0.00 0.00 0.00 3.10
835 884 2.224499 GCTCATTCCAATCCCCTCTCTC 60.224 54.545 0.00 0.00 0.00 3.20
836 885 3.316501 CTCATTCCAATCCCCTCTCTCT 58.683 50.000 0.00 0.00 0.00 3.10
837 886 3.312890 TCATTCCAATCCCCTCTCTCTC 58.687 50.000 0.00 0.00 0.00 3.20
838 887 3.051496 TCATTCCAATCCCCTCTCTCTCT 60.051 47.826 0.00 0.00 0.00 3.10
839 888 2.765689 TCCAATCCCCTCTCTCTCTC 57.234 55.000 0.00 0.00 0.00 3.20
840 889 1.219213 TCCAATCCCCTCTCTCTCTCC 59.781 57.143 0.00 0.00 0.00 3.71
841 890 1.220236 CCAATCCCCTCTCTCTCTCCT 59.780 57.143 0.00 0.00 0.00 3.69
842 891 2.360209 CCAATCCCCTCTCTCTCTCCTT 60.360 54.545 0.00 0.00 0.00 3.36
843 892 2.699846 CAATCCCCTCTCTCTCTCCTTG 59.300 54.545 0.00 0.00 0.00 3.61
844 893 0.032615 TCCCCTCTCTCTCTCCTTGC 60.033 60.000 0.00 0.00 0.00 4.01
881 930 0.519519 CATAGCAAAACGGAACCGCA 59.480 50.000 13.32 0.00 44.19 5.69
900 949 0.531532 AATCGCAGGATCGCAGGAAG 60.532 55.000 0.00 0.00 30.81 3.46
1081 1394 3.721706 CCTCCACCTCCAGGCACC 61.722 72.222 0.00 0.00 39.32 5.01
1290 1603 3.844090 GACAGGGAGGCCGAGCTC 61.844 72.222 2.73 2.73 0.00 4.09
1464 1777 3.148279 GAGATCGAGGCCGTGGGT 61.148 66.667 0.00 0.00 37.05 4.51
1691 2004 0.107456 CATATCAAGGGCACTCGGCT 59.893 55.000 0.00 0.00 44.01 5.52
1821 2134 2.202623 GTCTCTCGGTTCGCGCAT 60.203 61.111 8.75 0.00 0.00 4.73
1842 2155 2.808906 AAGGCAGGATCCAGGTAAAC 57.191 50.000 15.82 0.00 0.00 2.01
1854 2167 6.014840 GGATCCAGGTAAACTCGTATTCCATA 60.015 42.308 6.95 0.00 0.00 2.74
1921 2345 9.472361 CAAAAATATCTCCATCAACCATGAATC 57.528 33.333 0.00 0.00 39.49 2.52
1924 2348 4.063998 TCTCCATCAACCATGAATCGAG 57.936 45.455 0.00 0.00 39.49 4.04
1925 2349 3.136763 CTCCATCAACCATGAATCGAGG 58.863 50.000 0.00 0.00 39.49 4.63
1927 2351 3.054434 TCCATCAACCATGAATCGAGGTT 60.054 43.478 0.00 0.40 46.03 3.50
1928 2352 3.313526 CCATCAACCATGAATCGAGGTTC 59.686 47.826 3.20 0.00 43.43 3.62
1929 2353 3.981071 TCAACCATGAATCGAGGTTCT 57.019 42.857 3.20 0.00 43.43 3.01
1930 2354 3.599343 TCAACCATGAATCGAGGTTCTG 58.401 45.455 3.20 0.00 43.43 3.02
1931 2355 2.029838 ACCATGAATCGAGGTTCTGC 57.970 50.000 0.00 0.00 29.58 4.26
1932 2356 1.556911 ACCATGAATCGAGGTTCTGCT 59.443 47.619 0.00 0.00 29.58 4.24
1933 2357 2.026822 ACCATGAATCGAGGTTCTGCTT 60.027 45.455 0.00 0.00 29.58 3.91
1934 2358 3.012518 CCATGAATCGAGGTTCTGCTTT 58.987 45.455 0.00 0.00 0.00 3.51
1936 2360 4.818546 CCATGAATCGAGGTTCTGCTTTAT 59.181 41.667 0.00 0.00 0.00 1.40
1940 2371 8.651588 CATGAATCGAGGTTCTGCTTTATATAC 58.348 37.037 0.00 0.00 0.00 1.47
2150 2581 3.127030 GCTCAACCAAAAATAGACGGGAG 59.873 47.826 0.00 0.00 0.00 4.30
2486 2929 3.693807 ACGTTCAGTACAGTAGGATGGA 58.306 45.455 0.00 0.00 0.00 3.41
2574 3017 6.183360 GCACCCCTCAAAAGAAAAAGAAAAAG 60.183 38.462 0.00 0.00 0.00 2.27
2586 3029 6.591448 AGAAAAAGAAAAAGAGTTGTGGCTTG 59.409 34.615 0.00 0.00 0.00 4.01
2653 3096 5.163622 GGTTTGTATCATGTGGAGATTGTGG 60.164 44.000 0.00 0.00 0.00 4.17
2654 3097 5.434182 TTGTATCATGTGGAGATTGTGGA 57.566 39.130 0.00 0.00 0.00 4.02
3004 3462 5.772825 AGCTGTTCTTGTTTGCAGAAATA 57.227 34.783 0.00 0.00 0.00 1.40
3014 3472 4.220163 TGTTTGCAGAAATATGGTGCATGA 59.780 37.500 0.00 0.00 46.18 3.07
3307 3930 2.035961 GAGGCATCGAGGTATTAGCACA 59.964 50.000 0.00 0.00 0.00 4.57
3308 3931 2.434336 AGGCATCGAGGTATTAGCACAA 59.566 45.455 0.00 0.00 0.00 3.33
3351 3974 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
3425 4048 4.503991 GGGAGTACATAAGATGGCTTGAGG 60.504 50.000 0.00 0.00 35.56 3.86
3527 5210 7.201696 GGTCTTTTCTTAGAATGTCACAACACA 60.202 37.037 0.00 0.00 38.48 3.72
3560 5243 4.301628 TGTAGTATGCTCTTGATGATGCG 58.698 43.478 0.00 0.00 0.00 4.73
3658 5341 5.050644 TGCAAATGAATGTAGTCTGCAAG 57.949 39.130 0.00 0.00 35.53 4.01
3719 5403 1.037493 GTTGGGTTTGTCCTTGGTCC 58.963 55.000 0.00 0.00 36.25 4.46
3833 5612 2.771089 TGATAGAAATCCATCTGCGGC 58.229 47.619 0.00 0.00 0.00 6.53
3970 5749 3.248495 TGGTAAACTCGTGTGTTCACA 57.752 42.857 1.23 1.23 44.02 3.58
4114 5893 4.278975 ACTCCTTCATCAAGAGGTGAAC 57.721 45.455 0.00 0.00 40.50 3.18
4115 5894 3.906846 ACTCCTTCATCAAGAGGTGAACT 59.093 43.478 0.00 0.00 40.50 3.01
4116 5895 4.020662 ACTCCTTCATCAAGAGGTGAACTC 60.021 45.833 0.00 0.00 46.98 3.01
4127 5906 3.403968 GAGGTGAACTCCAAGAAACTCC 58.596 50.000 0.00 0.00 40.49 3.85
4128 5907 3.049344 AGGTGAACTCCAAGAAACTCCT 58.951 45.455 0.00 0.00 0.00 3.69
4129 5908 3.459969 AGGTGAACTCCAAGAAACTCCTT 59.540 43.478 0.00 0.00 0.00 3.36
4130 5909 3.815962 GGTGAACTCCAAGAAACTCCTTC 59.184 47.826 0.00 0.00 0.00 3.46
4131 5910 4.451900 GTGAACTCCAAGAAACTCCTTCA 58.548 43.478 0.00 0.00 36.40 3.02
4132 5911 5.066593 GTGAACTCCAAGAAACTCCTTCAT 58.933 41.667 0.00 0.00 36.40 2.57
4133 5912 5.180304 GTGAACTCCAAGAAACTCCTTCATC 59.820 44.000 0.00 0.00 36.40 2.92
4134 5913 4.982241 ACTCCAAGAAACTCCTTCATCA 57.018 40.909 0.00 0.00 36.40 3.07
4135 5914 5.310409 ACTCCAAGAAACTCCTTCATCAA 57.690 39.130 0.00 0.00 36.40 2.57
4136 5915 5.312079 ACTCCAAGAAACTCCTTCATCAAG 58.688 41.667 0.00 0.00 36.40 3.02
4137 5916 5.072329 ACTCCAAGAAACTCCTTCATCAAGA 59.928 40.000 0.00 0.00 36.40 3.02
4138 5917 5.555017 TCCAAGAAACTCCTTCATCAAGAG 58.445 41.667 0.00 0.00 36.40 2.85
4139 5918 4.699257 CCAAGAAACTCCTTCATCAAGAGG 59.301 45.833 0.00 0.00 36.40 3.69
4140 5919 5.513788 CCAAGAAACTCCTTCATCAAGAGGA 60.514 44.000 0.00 0.00 36.40 3.71
4332 6111 1.419720 GGCCTTGGATAGACTCCCCC 61.420 65.000 0.00 0.00 44.23 5.40
4498 6277 2.693069 CACTTAGGTTCACTCCAGCAG 58.307 52.381 0.00 0.00 0.00 4.24
4648 6429 4.023878 GGCGTAAAATACAACACCACAAGA 60.024 41.667 0.00 0.00 0.00 3.02
4674 6455 3.452474 CTGCGACCAAAAACCAAATCAA 58.548 40.909 0.00 0.00 0.00 2.57
4675 6456 3.861840 TGCGACCAAAAACCAAATCAAA 58.138 36.364 0.00 0.00 0.00 2.69
4731 6548 3.490249 CGTCTTACATTATGGGACGCAGA 60.490 47.826 18.12 0.00 41.99 4.26
4916 6734 5.220739 GCAATCAGAGTCAATAATGAGCGTT 60.221 40.000 0.00 0.00 35.88 4.84
4938 6756 7.597369 GCGTTCCCTATTTTTATTTTGTCAACT 59.403 33.333 0.00 0.00 0.00 3.16
5336 7154 1.276622 TGGAGGTCAGGGTAAGAAGC 58.723 55.000 0.00 0.00 0.00 3.86
5710 7528 3.991121 GTCACTCTGGTCTTCTAAGCAAC 59.009 47.826 0.00 0.00 0.00 4.17
5748 7566 1.152030 TTGGGCTGGACCACTCTCT 60.152 57.895 0.00 0.00 41.03 3.10
5771 7589 7.094631 TCTTGGCATTATATATACGTGTGACC 58.905 38.462 0.00 0.00 0.00 4.02
5930 7748 6.594788 TTTCTTAAGCCTGATGCAATCTTT 57.405 33.333 0.00 0.00 45.81 2.52
6051 7894 8.629158 GGTAATAATGATTTGCAGGAACACATA 58.371 33.333 0.00 0.00 0.00 2.29
6052 7895 9.450807 GTAATAATGATTTGCAGGAACACATAC 57.549 33.333 0.00 0.00 0.00 2.39
6053 7896 5.981088 AATGATTTGCAGGAACACATACA 57.019 34.783 0.00 0.00 0.00 2.29
6054 7897 6.534475 AATGATTTGCAGGAACACATACAT 57.466 33.333 0.00 0.00 0.00 2.29
6055 7898 5.981088 TGATTTGCAGGAACACATACATT 57.019 34.783 0.00 0.00 0.00 2.71
6056 7899 7.643569 ATGATTTGCAGGAACACATACATTA 57.356 32.000 0.00 0.00 0.00 1.90
6057 7900 7.643569 TGATTTGCAGGAACACATACATTAT 57.356 32.000 0.00 0.00 0.00 1.28
6058 7901 7.482474 TGATTTGCAGGAACACATACATTATG 58.518 34.615 0.00 0.00 41.88 1.90
6073 7916 9.944376 ACATACATTATGTACTTTTGACTCACT 57.056 29.630 7.26 0.00 46.90 3.41
6415 8258 1.133982 TGTTTTGTGCAACTGCGACAT 59.866 42.857 0.00 0.00 45.83 3.06
6473 8316 5.796424 ATGCTGGTCTTGTTTCTTTTGAT 57.204 34.783 0.00 0.00 0.00 2.57
6518 8362 7.148557 ACGTACCATTTTTGGTTTTGTTCTTTG 60.149 33.333 2.53 0.00 42.99 2.77
6522 8366 7.334171 ACCATTTTTGGTTTTGTTCTTTGAGAG 59.666 33.333 0.00 0.00 39.57 3.20
6537 8381 0.440371 GAGAGAACGCAAAAGCCTCG 59.560 55.000 0.00 0.00 0.00 4.63
6546 8390 0.798776 CAAAAGCCTCGCGTCTTGAT 59.201 50.000 5.77 0.00 0.00 2.57
6622 8472 1.136252 CACAACGCACTCGATTTGGAG 60.136 52.381 0.00 0.00 39.97 3.86
6625 8475 2.163818 ACGCACTCGATTTGGAGAAA 57.836 45.000 0.00 0.00 37.49 2.52
6626 8476 2.699954 ACGCACTCGATTTGGAGAAAT 58.300 42.857 0.00 0.00 37.49 2.17
6627 8477 3.857052 ACGCACTCGATTTGGAGAAATA 58.143 40.909 0.00 0.00 37.49 1.40
6628 8478 4.442706 ACGCACTCGATTTGGAGAAATAT 58.557 39.130 0.00 0.00 37.49 1.28
6629 8479 5.597806 ACGCACTCGATTTGGAGAAATATA 58.402 37.500 0.00 0.00 37.49 0.86
6630 8480 5.692204 ACGCACTCGATTTGGAGAAATATAG 59.308 40.000 0.00 0.00 37.49 1.31
6908 8821 2.031919 CAGCAAGTGCCCGTACCA 59.968 61.111 0.00 0.00 43.38 3.25
6928 8841 4.072131 CCACTTGCAACACCTAGTGTATT 58.928 43.478 11.85 0.00 46.79 1.89
6949 9221 1.378531 GTTTGCGGTAGCCATCATCA 58.621 50.000 0.00 0.00 44.33 3.07
6980 9252 1.617018 ATAGCAGGAGCCAGCGTTCA 61.617 55.000 0.00 0.00 43.56 3.18
7022 9294 2.204059 AGGCAGCCCCTCAGAGTT 60.204 61.111 8.22 0.00 41.21 3.01
7136 9423 3.193267 ACAGTTCTCTAAGCTCAGCAGAG 59.807 47.826 7.56 7.56 44.96 3.35
7177 9464 0.942252 AAAAACTGGTCGAACTCGGC 59.058 50.000 0.33 0.00 44.28 5.54
7178 9465 1.219522 AAAACTGGTCGAACTCGGCG 61.220 55.000 0.33 0.00 46.26 6.46
7192 9479 2.624364 ACTCGGCGGGTTTTTGTAAAAT 59.376 40.909 6.58 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
295 298 1.003597 CTGCCTTCTCTGCACTGCT 60.004 57.895 1.98 0.00 34.46 4.24
296 299 2.688794 GCTGCCTTCTCTGCACTGC 61.689 63.158 0.00 0.00 34.46 4.40
297 300 1.003597 AGCTGCCTTCTCTGCACTG 60.004 57.895 0.00 0.00 34.46 3.66
298 301 1.296068 GAGCTGCCTTCTCTGCACT 59.704 57.895 0.00 0.00 34.46 4.40
299 302 2.099431 CGAGCTGCCTTCTCTGCAC 61.099 63.158 0.00 0.00 34.46 4.57
306 309 2.684843 CCAACTGCGAGCTGCCTTC 61.685 63.158 0.00 0.00 45.60 3.46
376 379 3.641906 TGGGGCATTTTTCTCGGTTTTAA 59.358 39.130 0.00 0.00 0.00 1.52
377 380 3.231818 TGGGGCATTTTTCTCGGTTTTA 58.768 40.909 0.00 0.00 0.00 1.52
378 381 2.043227 TGGGGCATTTTTCTCGGTTTT 58.957 42.857 0.00 0.00 0.00 2.43
379 382 1.710816 TGGGGCATTTTTCTCGGTTT 58.289 45.000 0.00 0.00 0.00 3.27
397 401 1.160137 CCGACTTCAGCTCCCTTTTG 58.840 55.000 0.00 0.00 0.00 2.44
507 531 2.348591 GCTACACGTTGCTTTCTCACAC 60.349 50.000 0.00 0.00 0.00 3.82
578 602 4.477975 CGAGTCGTCGTCCCTGCC 62.478 72.222 3.82 0.00 41.57 4.85
761 790 2.190578 CAGAATGGCGGGGGAGAC 59.809 66.667 0.00 0.00 0.00 3.36
825 874 0.032615 GCAAGGAGAGAGAGAGGGGA 60.033 60.000 0.00 0.00 0.00 4.81
826 875 1.391157 CGCAAGGAGAGAGAGAGGGG 61.391 65.000 0.00 0.00 0.00 4.79
828 877 1.437160 GCGCAAGGAGAGAGAGAGG 59.563 63.158 0.30 0.00 38.28 3.69
833 882 3.452786 TCCGGCGCAAGGAGAGAG 61.453 66.667 18.23 0.00 33.19 3.20
881 930 0.531532 CTTCCTGCGATCCTGCGATT 60.532 55.000 0.00 0.00 37.81 3.34
900 949 0.459411 GAGGAAGAGAAGCTCCACGC 60.459 60.000 0.00 0.00 39.57 5.34
1081 1394 1.827315 TTGACGTTGAAGAAGCGCCG 61.827 55.000 2.29 0.00 0.00 6.46
1587 1900 2.871427 GAGCTCGTTATTGGCGGCG 61.871 63.158 0.51 0.51 33.25 6.46
1740 2053 2.125512 GCCATCCGAGCGACAAGT 60.126 61.111 0.00 0.00 0.00 3.16
1817 2130 1.233019 CTGGATCCTGCCTTTATGCG 58.767 55.000 14.23 0.00 0.00 4.73
1821 2134 3.850173 AGTTTACCTGGATCCTGCCTTTA 59.150 43.478 14.23 0.00 0.00 1.85
1887 2201 9.455847 GTTGATGGAGATATTTTTGTCTAATGC 57.544 33.333 0.00 0.00 0.00 3.56
1888 2202 9.956720 GGTTGATGGAGATATTTTTGTCTAATG 57.043 33.333 0.00 0.00 0.00 1.90
1890 2204 9.699410 ATGGTTGATGGAGATATTTTTGTCTAA 57.301 29.630 0.00 0.00 0.00 2.10
1893 2207 7.999679 TCATGGTTGATGGAGATATTTTTGTC 58.000 34.615 0.00 0.00 32.26 3.18
1900 2228 6.364568 TCGATTCATGGTTGATGGAGATAT 57.635 37.500 0.00 0.00 32.26 1.63
1921 2345 7.946655 TCAATGTATATAAAGCAGAACCTCG 57.053 36.000 0.00 0.00 0.00 4.63
1932 2356 8.925700 GCGTCACTGATCATCAATGTATATAAA 58.074 33.333 0.00 0.00 0.00 1.40
1933 2357 8.087750 TGCGTCACTGATCATCAATGTATATAA 58.912 33.333 0.00 0.00 0.00 0.98
1934 2358 7.601856 TGCGTCACTGATCATCAATGTATATA 58.398 34.615 0.00 0.00 0.00 0.86
1936 2360 5.841810 TGCGTCACTGATCATCAATGTATA 58.158 37.500 0.00 0.00 0.00 1.47
1940 2371 4.547406 AATGCGTCACTGATCATCAATG 57.453 40.909 0.00 0.00 0.00 2.82
2150 2581 3.004419 GGGCTGTCAAGTTTTTAGACCAC 59.996 47.826 0.00 0.00 36.54 4.16
2486 2929 2.254546 TCAGTCTGCCATTGAAACGT 57.745 45.000 0.00 0.00 0.00 3.99
2574 3017 4.507710 TCAGATATGACAAGCCACAACTC 58.492 43.478 0.00 0.00 0.00 3.01
2586 3029 6.812656 GTGACATCTCATCCATCAGATATGAC 59.187 42.308 0.00 0.00 32.37 3.06
2653 3096 1.080974 GCCACAACTGTGCAGCATC 60.081 57.895 0.00 0.00 44.34 3.91
2654 3097 2.567497 GGCCACAACTGTGCAGCAT 61.567 57.895 0.00 0.00 44.34 3.79
3004 3462 7.557724 TGTTAATCAATGAATTCATGCACCAT 58.442 30.769 21.39 8.84 36.56 3.55
3316 3939 4.870636 TCTTTACGGAGGGAGTACCAATA 58.129 43.478 0.00 0.00 43.89 1.90
3317 3940 3.716431 TCTTTACGGAGGGAGTACCAAT 58.284 45.455 0.00 0.00 43.89 3.16
3320 3943 4.750021 ATTTCTTTACGGAGGGAGTACC 57.250 45.455 0.00 0.00 40.67 3.34
3321 3944 8.854117 TCTTATATTTCTTTACGGAGGGAGTAC 58.146 37.037 0.00 0.00 0.00 2.73
3425 4048 7.686438 AATCCTTTTTATCCACCAAAATTGC 57.314 32.000 0.00 0.00 0.00 3.56
3833 5612 1.103803 TGCTAGCCCAGTAGACTTCG 58.896 55.000 13.29 0.00 0.00 3.79
3970 5749 7.864882 GCTTGAAGCTTTAGAACTTTCTTGATT 59.135 33.333 10.44 0.00 38.45 2.57
4114 5893 5.555017 TCTTGATGAAGGAGTTTCTTGGAG 58.445 41.667 0.00 0.00 36.71 3.86
4115 5894 5.513788 CCTCTTGATGAAGGAGTTTCTTGGA 60.514 44.000 0.00 0.00 36.71 3.53
4116 5895 4.699257 CCTCTTGATGAAGGAGTTTCTTGG 59.301 45.833 0.00 0.00 36.71 3.61
4117 5896 5.555017 TCCTCTTGATGAAGGAGTTTCTTG 58.445 41.667 0.00 0.00 36.71 3.02
4118 5897 5.545723 TCTCCTCTTGATGAAGGAGTTTCTT 59.454 40.000 15.94 0.00 45.89 2.52
4119 5898 5.046663 GTCTCCTCTTGATGAAGGAGTTTCT 60.047 44.000 15.94 0.00 45.89 2.52
4120 5899 5.175127 GTCTCCTCTTGATGAAGGAGTTTC 58.825 45.833 15.94 6.74 45.89 2.78
4121 5900 4.594920 TGTCTCCTCTTGATGAAGGAGTTT 59.405 41.667 15.94 0.00 45.89 2.66
4122 5901 4.163427 TGTCTCCTCTTGATGAAGGAGTT 58.837 43.478 15.94 0.00 45.89 3.01
4123 5902 3.784178 TGTCTCCTCTTGATGAAGGAGT 58.216 45.455 15.94 0.00 45.89 3.85
4124 5903 5.356291 AATGTCTCCTCTTGATGAAGGAG 57.644 43.478 11.40 11.40 46.82 3.69
4125 5904 5.768980 AAATGTCTCCTCTTGATGAAGGA 57.231 39.130 0.00 0.00 0.00 3.36
4126 5905 6.036517 CGTAAAATGTCTCCTCTTGATGAAGG 59.963 42.308 0.00 0.00 0.00 3.46
4127 5906 6.813649 TCGTAAAATGTCTCCTCTTGATGAAG 59.186 38.462 0.00 0.00 0.00 3.02
4128 5907 6.697395 TCGTAAAATGTCTCCTCTTGATGAA 58.303 36.000 0.00 0.00 0.00 2.57
4129 5908 6.152831 TCTCGTAAAATGTCTCCTCTTGATGA 59.847 38.462 0.00 0.00 0.00 2.92
4130 5909 6.333416 TCTCGTAAAATGTCTCCTCTTGATG 58.667 40.000 0.00 0.00 0.00 3.07
4131 5910 6.531503 TCTCGTAAAATGTCTCCTCTTGAT 57.468 37.500 0.00 0.00 0.00 2.57
4132 5911 5.977489 TCTCGTAAAATGTCTCCTCTTGA 57.023 39.130 0.00 0.00 0.00 3.02
4133 5912 6.390721 TCTTCTCGTAAAATGTCTCCTCTTG 58.609 40.000 0.00 0.00 0.00 3.02
4134 5913 6.591750 TCTTCTCGTAAAATGTCTCCTCTT 57.408 37.500 0.00 0.00 0.00 2.85
4135 5914 6.434652 TCTTCTTCTCGTAAAATGTCTCCTCT 59.565 38.462 0.00 0.00 0.00 3.69
4136 5915 6.528774 GTCTTCTTCTCGTAAAATGTCTCCTC 59.471 42.308 0.00 0.00 0.00 3.71
4137 5916 6.015350 TGTCTTCTTCTCGTAAAATGTCTCCT 60.015 38.462 0.00 0.00 0.00 3.69
4138 5917 6.157211 TGTCTTCTTCTCGTAAAATGTCTCC 58.843 40.000 0.00 0.00 0.00 3.71
4139 5918 7.359347 GGTTGTCTTCTTCTCGTAAAATGTCTC 60.359 40.741 0.00 0.00 0.00 3.36
4140 5919 6.424207 GGTTGTCTTCTTCTCGTAAAATGTCT 59.576 38.462 0.00 0.00 0.00 3.41
4141 5920 6.202188 TGGTTGTCTTCTTCTCGTAAAATGTC 59.798 38.462 0.00 0.00 0.00 3.06
4142 5921 6.053005 TGGTTGTCTTCTTCTCGTAAAATGT 58.947 36.000 0.00 0.00 0.00 2.71
4143 5922 6.539649 TGGTTGTCTTCTTCTCGTAAAATG 57.460 37.500 0.00 0.00 0.00 2.32
4144 5923 7.282450 ACTTTGGTTGTCTTCTTCTCGTAAAAT 59.718 33.333 0.00 0.00 0.00 1.82
4145 5924 6.596497 ACTTTGGTTGTCTTCTTCTCGTAAAA 59.404 34.615 0.00 0.00 0.00 1.52
4332 6111 6.819397 ATATGCAATGATCTCCATGAGTTG 57.181 37.500 0.00 0.00 35.24 3.16
4648 6429 0.033366 GGTTTTTGGTCGCAGCCATT 59.967 50.000 0.00 0.00 38.48 3.16
4728 6545 9.712305 TTTATTTGTCTTTCCTTCTACTCTCTG 57.288 33.333 0.00 0.00 0.00 3.35
4731 6548 9.495572 CAGTTTATTTGTCTTTCCTTCTACTCT 57.504 33.333 0.00 0.00 0.00 3.24
4869 6687 2.519302 GCAAGGGGGCATATGCGT 60.519 61.111 21.04 3.27 43.26 5.24
4900 6718 3.914426 AGGGAACGCTCATTATTGACT 57.086 42.857 0.00 0.00 0.00 3.41
4916 6734 9.137459 TCACAGTTGACAAAATAAAAATAGGGA 57.863 29.630 0.00 0.00 0.00 4.20
4938 6756 6.015603 TGCATGGAAGAAACAAATATGTCACA 60.016 34.615 0.00 0.00 39.40 3.58
5336 7154 2.300433 TGATGAATCTGGGCCATTTCG 58.700 47.619 6.72 0.00 0.00 3.46
5710 7528 7.284034 AGCCCAAGAAGAACAGAATATATTGTG 59.716 37.037 18.42 18.42 37.12 3.33
5748 7566 6.014070 AGGGTCACACGTATATATAATGCCAA 60.014 38.462 0.00 0.00 0.00 4.52
5771 7589 1.812571 ACACGCCAAGATTTAAGCAGG 59.187 47.619 0.00 0.00 0.00 4.85
5930 7748 1.962807 CTTGGCATCAACCCTGTTCAA 59.037 47.619 0.00 0.00 0.00 2.69
5952 7771 4.935352 TTTTTGCTGTTATGTCAGGCTT 57.065 36.364 0.00 0.00 36.12 4.35
6054 7897 9.841295 AGGTTAAAGTGAGTCAAAAGTACATAA 57.159 29.630 0.00 0.00 0.00 1.90
6055 7898 9.841295 AAGGTTAAAGTGAGTCAAAAGTACATA 57.159 29.630 0.00 0.00 0.00 2.29
6056 7899 8.621286 CAAGGTTAAAGTGAGTCAAAAGTACAT 58.379 33.333 0.00 0.00 0.00 2.29
6057 7900 7.825270 TCAAGGTTAAAGTGAGTCAAAAGTACA 59.175 33.333 0.00 0.00 0.00 2.90
6058 7901 8.205131 TCAAGGTTAAAGTGAGTCAAAAGTAC 57.795 34.615 0.00 0.00 0.00 2.73
6059 7902 8.795842 TTCAAGGTTAAAGTGAGTCAAAAGTA 57.204 30.769 0.00 0.00 0.00 2.24
6060 7903 7.696992 TTCAAGGTTAAAGTGAGTCAAAAGT 57.303 32.000 0.00 0.00 0.00 2.66
6061 7904 9.023967 CAATTCAAGGTTAAAGTGAGTCAAAAG 57.976 33.333 0.00 0.00 0.00 2.27
6062 7905 8.527810 ACAATTCAAGGTTAAAGTGAGTCAAAA 58.472 29.630 0.00 0.00 0.00 2.44
6063 7906 8.062065 ACAATTCAAGGTTAAAGTGAGTCAAA 57.938 30.769 0.00 0.00 0.00 2.69
6064 7907 7.639113 ACAATTCAAGGTTAAAGTGAGTCAA 57.361 32.000 0.00 0.00 0.00 3.18
6065 7908 7.122055 ACAACAATTCAAGGTTAAAGTGAGTCA 59.878 33.333 0.00 0.00 0.00 3.41
6066 7909 7.432252 CACAACAATTCAAGGTTAAAGTGAGTC 59.568 37.037 0.00 0.00 0.00 3.36
6067 7910 7.093945 ACACAACAATTCAAGGTTAAAGTGAGT 60.094 33.333 0.00 0.00 0.00 3.41
6068 7911 7.220683 CACACAACAATTCAAGGTTAAAGTGAG 59.779 37.037 0.00 0.00 30.47 3.51
6069 7912 7.032580 CACACAACAATTCAAGGTTAAAGTGA 58.967 34.615 0.00 0.00 30.47 3.41
6070 7913 6.255453 CCACACAACAATTCAAGGTTAAAGTG 59.745 38.462 0.00 0.00 0.00 3.16
6071 7914 6.153680 TCCACACAACAATTCAAGGTTAAAGT 59.846 34.615 0.00 0.00 0.00 2.66
6072 7915 6.568869 TCCACACAACAATTCAAGGTTAAAG 58.431 36.000 0.00 0.00 0.00 1.85
6073 7916 6.153680 ACTCCACACAACAATTCAAGGTTAAA 59.846 34.615 0.00 0.00 0.00 1.52
6074 7917 5.654650 ACTCCACACAACAATTCAAGGTTAA 59.345 36.000 0.00 0.00 0.00 2.01
6415 8258 3.826524 TGTTTGCTTCCCAGTCAATACA 58.173 40.909 0.00 0.00 0.00 2.29
6473 8316 4.630111 ACGTACATAAACCGAAACAGGAA 58.370 39.130 0.00 0.00 34.73 3.36
6537 8381 5.403246 TCTTCTTCTACAGAATCAAGACGC 58.597 41.667 8.45 0.00 40.95 5.19
6541 8385 5.976458 AGCCTCTTCTTCTACAGAATCAAG 58.024 41.667 0.00 0.00 40.95 3.02
6546 8390 4.219507 CACTGAGCCTCTTCTTCTACAGAA 59.780 45.833 0.00 0.00 39.39 3.02
6622 8472 6.207614 GGATGAAGAAGTTGGGCCTATATTTC 59.792 42.308 4.53 1.03 0.00 2.17
6625 8475 4.916424 AGGATGAAGAAGTTGGGCCTATAT 59.084 41.667 4.53 0.00 0.00 0.86
6626 8476 4.307259 AGGATGAAGAAGTTGGGCCTATA 58.693 43.478 4.53 0.00 0.00 1.31
6627 8477 3.126453 AGGATGAAGAAGTTGGGCCTAT 58.874 45.455 4.53 0.00 0.00 2.57
6628 8478 2.562296 AGGATGAAGAAGTTGGGCCTA 58.438 47.619 4.53 0.00 0.00 3.93
6629 8479 1.376649 AGGATGAAGAAGTTGGGCCT 58.623 50.000 4.53 0.00 0.00 5.19
6630 8480 2.222227 AAGGATGAAGAAGTTGGGCC 57.778 50.000 0.00 0.00 0.00 5.80
6685 8535 4.760047 GCGGTGATGAGCCCGTGT 62.760 66.667 0.00 0.00 45.91 4.49
6783 8633 3.306088 GCTGTCACACACTACTACATGGT 60.306 47.826 0.00 0.00 0.00 3.55
6801 8651 1.975407 GCATTGCTGGGAGTGCTGT 60.975 57.895 0.16 0.00 34.85 4.40
6874 8787 2.125106 GCAAGCTGGAGTACGGGG 60.125 66.667 0.00 0.00 0.00 5.73
6903 8816 2.806244 CACTAGGTGTTGCAAGTGGTAC 59.194 50.000 0.00 0.00 36.53 3.34
6908 8821 3.994392 CGAATACACTAGGTGTTGCAAGT 59.006 43.478 0.00 0.00 45.08 3.16
6928 8841 0.107897 ATGATGGCTACCGCAAACGA 60.108 50.000 0.00 0.00 43.93 3.85
6980 9252 3.587797 TGCTACTGCGCTACTAAAACT 57.412 42.857 9.73 0.00 43.34 2.66
7022 9294 3.243401 CCATGACCGTCACTAATCATCGA 60.243 47.826 2.57 0.00 29.25 3.59
7091 9378 4.238669 TGGGATCCCTGGTTTCAATTTTT 58.761 39.130 31.05 0.00 36.94 1.94
7092 9379 3.868062 TGGGATCCCTGGTTTCAATTTT 58.132 40.909 31.05 0.00 36.94 1.82
7093 9380 3.558608 TGGGATCCCTGGTTTCAATTT 57.441 42.857 31.05 0.00 36.94 1.82
7094 9381 3.173151 GTTGGGATCCCTGGTTTCAATT 58.827 45.455 31.05 0.00 36.94 2.32
7095 9382 2.111613 TGTTGGGATCCCTGGTTTCAAT 59.888 45.455 31.05 0.00 36.94 2.57
7096 9383 1.501170 TGTTGGGATCCCTGGTTTCAA 59.499 47.619 31.05 12.71 36.94 2.69
7097 9384 1.075374 CTGTTGGGATCCCTGGTTTCA 59.925 52.381 31.05 17.78 36.94 2.69
7098 9385 1.075536 ACTGTTGGGATCCCTGGTTTC 59.924 52.381 31.05 14.55 36.94 2.78
7099 9386 1.158007 ACTGTTGGGATCCCTGGTTT 58.842 50.000 31.05 10.46 36.94 3.27
7136 9423 3.476295 TCTGTTCGATTGCTTGAATGC 57.524 42.857 0.00 0.00 0.00 3.56
7162 9449 4.052229 CCGCCGAGTTCGACCAGT 62.052 66.667 2.59 0.00 43.02 4.00
7166 9453 1.501337 AAAAACCCGCCGAGTTCGAC 61.501 55.000 2.59 0.00 43.02 4.20
7167 9454 1.227615 AAAAACCCGCCGAGTTCGA 60.228 52.632 2.59 0.00 43.02 3.71
7168 9455 1.082366 CAAAAACCCGCCGAGTTCG 60.082 57.895 0.00 0.00 39.44 3.95
7169 9456 1.228533 TACAAAAACCCGCCGAGTTC 58.771 50.000 0.00 0.00 0.00 3.01
7171 9458 1.677942 TTTACAAAAACCCGCCGAGT 58.322 45.000 0.00 0.00 0.00 4.18
7173 9460 2.030096 GGATTTTACAAAAACCCGCCGA 60.030 45.455 3.08 0.00 35.50 5.54
7174 9461 2.330286 GGATTTTACAAAAACCCGCCG 58.670 47.619 3.08 0.00 35.50 6.46
7176 9463 3.285816 TCGGATTTTACAAAAACCCGC 57.714 42.857 12.15 0.00 42.54 6.13
7177 9464 5.049398 TCATCGGATTTTACAAAAACCCG 57.951 39.130 10.98 10.98 43.34 5.28
7178 9465 5.636121 GGTTCATCGGATTTTACAAAAACCC 59.364 40.000 7.82 4.42 37.50 4.11


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

AutoCloner maintained by Alex Coulton.