Multiple sequence alignment - TraesCS6D01G179100

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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 TraesCS6D01G179100 chr6D 100.000 6163 0 0 1 6163 191647533 191653695 0.000000e+00 11382.0
1 TraesCS6D01G179100 chr6D 91.473 258 21 1 5907 6163 191662830 191663087 2.730000e-93 353.0
2 TraesCS6D01G179100 chr6D 89.734 263 23 4 5904 6163 162709127 162708866 3.560000e-87 333.0
3 TraesCS6D01G179100 chr6D 97.727 88 2 0 3883 3970 47662503 47662590 1.070000e-32 152.0
4 TraesCS6D01G179100 chr6B 95.275 2730 77 12 1 2719 361578053 361580741 0.000000e+00 4279.0
5 TraesCS6D01G179100 chr6B 97.339 1954 40 8 3965 5906 361582582 361584535 0.000000e+00 3310.0
6 TraesCS6D01G179100 chr6B 97.517 1168 18 4 2718 3884 361581427 361582584 0.000000e+00 1986.0
7 TraesCS6D01G179100 chr6B 95.349 86 4 0 3882 3967 618335033 618334948 3.000000e-28 137.0
8 TraesCS6D01G179100 chr6B 100.000 28 0 0 2555 2582 361580682 361580655 1.100000e-02 52.8
9 TraesCS6D01G179100 chr6A 97.686 2204 37 7 528 2719 301093932 301091731 0.000000e+00 3775.0
10 TraesCS6D01G179100 chr6A 95.110 2229 66 23 3965 6163 301090307 301088092 0.000000e+00 3472.0
11 TraesCS6D01G179100 chr6A 96.936 1175 16 7 2718 3884 301091467 301090305 0.000000e+00 1953.0
12 TraesCS6D01G179100 chr6A 91.828 465 34 1 73 537 301095593 301095133 0.000000e+00 645.0
13 TraesCS6D01G179100 chr6A 100.000 29 0 0 2554 2582 301091791 301091819 3.000000e-03 54.7
14 TraesCS6D01G179100 chr3D 92.453 265 18 2 5901 6163 236801310 236801574 1.620000e-100 377.0
15 TraesCS6D01G179100 chr3D 91.120 259 20 3 5907 6163 271383894 271384151 1.270000e-91 348.0
16 TraesCS6D01G179100 chr1D 90.698 258 22 2 5907 6163 237089397 237089653 5.920000e-90 342.0
17 TraesCS6D01G179100 chr1D 93.750 96 5 1 3883 3977 355171575 355171670 6.440000e-30 143.0
18 TraesCS6D01G179100 chr1A 90.698 258 21 3 5907 6162 204109484 204109740 2.130000e-89 340.0
19 TraesCS6D01G179100 chr1A 90.698 258 21 3 5907 6162 204130697 204130953 2.130000e-89 340.0
20 TraesCS6D01G179100 chr1A 85.321 109 5 4 1386 1483 28705640 28705748 1.090000e-17 102.0
21 TraesCS6D01G179100 chr1A 96.296 54 2 0 1412 1465 342432364 342432311 8.510000e-14 89.8
22 TraesCS6D01G179100 chr5D 90.310 258 24 1 5907 6163 101902420 101902163 2.750000e-88 337.0
23 TraesCS6D01G179100 chr5D 100.000 86 0 0 3882 3967 215254144 215254059 6.390000e-35 159.0
24 TraesCS6D01G179100 chr5D 94.253 87 5 0 3883 3969 216627852 216627766 3.880000e-27 134.0
25 TraesCS6D01G179100 chr5D 85.849 106 12 2 1382 1484 465001219 465001324 6.530000e-20 110.0
26 TraesCS6D01G179100 chr7D 96.471 85 3 0 3883 3967 226690346 226690430 2.320000e-29 141.0
27 TraesCS6D01G179100 chr7D 91.667 96 8 0 3876 3971 169823462 169823367 3.880000e-27 134.0
28 TraesCS6D01G179100 chr7D 94.186 86 5 0 3882 3967 51998768 51998853 1.390000e-26 132.0
29 TraesCS6D01G179100 chr7D 80.282 142 27 1 263 404 40113477 40113337 8.450000e-19 106.0
30 TraesCS6D01G179100 chr7D 83.529 85 11 3 1398 1480 575772280 575772363 6.620000e-10 76.8
31 TraesCS6D01G179100 chr2A 89.381 113 8 4 5726 5834 759847495 759847607 8.330000e-29 139.0
32 TraesCS6D01G179100 chr2A 86.400 125 7 10 5715 5832 740120210 740120331 1.800000e-25 128.0
33 TraesCS6D01G179100 chr2A 85.600 125 8 10 5715 5832 740080371 740080492 8.390000e-24 122.0
34 TraesCS6D01G179100 chr2A 85.600 125 8 10 5715 5832 740144401 740144522 8.390000e-24 122.0
35 TraesCS6D01G179100 chr2D 89.286 112 9 2 5726 5834 197870831 197870942 3.000000e-28 137.0
36 TraesCS6D01G179100 chr4D 89.720 107 8 3 5727 5830 105123850 105123956 3.880000e-27 134.0
37 TraesCS6D01G179100 chr3B 88.496 113 10 3 3864 3974 417370243 417370132 3.880000e-27 134.0
38 TraesCS6D01G179100 chr4B 86.508 126 10 6 5715 5834 235376191 235376067 1.390000e-26 132.0
39 TraesCS6D01G179100 chr2B 89.000 100 7 3 1388 1483 683014778 683014679 3.020000e-23 121.0
40 TraesCS6D01G179100 chr4A 83.810 105 10 6 1387 1484 628941872 628941976 6.580000e-15 93.5
41 TraesCS6D01G179100 chr5A 83.333 108 7 3 1387 1483 82866706 82866599 8.510000e-14 89.8
42 TraesCS6D01G179100 chr7B 83.529 85 11 3 1398 1480 637913995 637914078 6.620000e-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 TraesCS6D01G179100 chr6D 191647533 191653695 6162 False 11382.000000 11382 100.000000 1 6163 1 chr6D.!!$F2 6162
1 TraesCS6D01G179100 chr6B 361578053 361584535 6482 False 3191.666667 4279 96.710333 1 5906 3 chr6B.!!$F1 5905
2 TraesCS6D01G179100 chr6A 301088092 301095593 7501 True 2461.250000 3775 95.390000 73 6163 4 chr6A.!!$R1 6090

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
109 111 0.893727 GGGCATTGGGTTGTTCTCGT 60.894 55.0 0.0 0.0 0.00 4.18 F
1066 2280 0.396139 TCTCCGCCCCGTGTTACTAT 60.396 55.0 0.0 0.0 0.00 2.12 F
2656 3881 0.044092 TACAGCATCCTCCCCTTCCA 59.956 55.0 0.0 0.0 0.00 3.53 F
3897 5823 0.042131 ATGGTACTCCCTCCGTTCCA 59.958 55.0 0.0 0.0 36.47 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1215 2435 1.207593 CCTGCGTTTTGAGCTTCCG 59.792 57.895 0.0 0.0 35.28 4.30 R
2974 4892 2.838736 ACAGAACCAACAGCAGTACAG 58.161 47.619 0.0 0.0 0.00 2.74 R
3946 5872 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.000 0.0 0.0 0.00 1.90 R
5887 7852 0.613012 AATGCTGCTCCCCAGGTTTC 60.613 55.000 0.0 0.0 42.03 2.78 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
43 44 5.233225 CAGACATCACAACACACACTATCT 58.767 41.667 0.00 0.00 0.00 1.98
57 58 4.707448 CACACTATCTGACTAGAGTTGGGT 59.293 45.833 0.00 0.00 36.14 4.51
60 61 7.068839 CACACTATCTGACTAGAGTTGGGTAAT 59.931 40.741 0.00 0.00 36.14 1.89
87 89 1.398390 GTGTGCTCGGCCTTTATGAAG 59.602 52.381 0.00 0.00 0.00 3.02
109 111 0.893727 GGGCATTGGGTTGTTCTCGT 60.894 55.000 0.00 0.00 0.00 4.18
138 140 6.565435 CGAGACCGTGTCGTTTGTAGATATAT 60.565 42.308 9.81 0.00 37.67 0.86
302 304 6.588204 TCACTTAACTTCCTGCTTTCTGTTA 58.412 36.000 0.00 0.00 0.00 2.41
445 447 3.514645 GCTCATAGCAAAACATGGGTTG 58.485 45.455 0.00 1.76 41.89 3.77
446 448 3.056607 GCTCATAGCAAAACATGGGTTGT 60.057 43.478 11.05 3.16 41.89 3.32
539 541 8.581578 TGAACTTGTTTTTAGAGTTTCTTTGGT 58.418 29.630 0.00 0.00 34.02 3.67
541 543 7.320399 ACTTGTTTTTAGAGTTTCTTTGGTGG 58.680 34.615 0.00 0.00 0.00 4.61
1066 2280 0.396139 TCTCCGCCCCGTGTTACTAT 60.396 55.000 0.00 0.00 0.00 2.12
1088 2302 1.538047 TTTCTGCATCTCTGTTGGCC 58.462 50.000 0.00 0.00 0.00 5.36
1122 2336 5.653769 CCTTGATTTGGATTGGAGAAGCTTA 59.346 40.000 0.00 0.00 0.00 3.09
1250 2470 3.308866 CGCAGGGATAGGAAAAACTTACG 59.691 47.826 0.00 0.00 0.00 3.18
1328 2548 2.361757 TGTTGTTTGGATGTCAAGCAGG 59.638 45.455 0.00 0.00 45.02 4.85
1617 2837 4.092675 ACGGCACAAAAACAAAATGAACAG 59.907 37.500 0.00 0.00 0.00 3.16
1627 2847 4.710324 ACAAAATGAACAGTTCCCGTAGA 58.290 39.130 10.93 0.00 0.00 2.59
1628 2848 5.313712 ACAAAATGAACAGTTCCCGTAGAT 58.686 37.500 10.93 0.00 0.00 1.98
1693 2913 3.067601 CGGGGCCTTGGAAATTTACATAC 59.932 47.826 3.35 0.00 0.00 2.39
1764 2984 3.788333 TTAGCAGAATGATTGCCTTGC 57.212 42.857 0.00 0.00 42.48 4.01
1773 2993 2.372264 TGATTGCCTTGCTGAAGATCC 58.628 47.619 0.00 0.00 0.00 3.36
2412 3636 6.262496 GGTCAGTTAGCTTCTTGGTAGTTTTT 59.738 38.462 0.00 0.00 0.00 1.94
2537 3761 6.459710 GGGAAACATAGGTAACATGCTTTAGC 60.460 42.308 0.00 0.00 40.02 3.09
2600 3824 7.828508 TCCGAATTCTTAGGTAGCTGTATTA 57.171 36.000 4.27 0.00 0.00 0.98
2654 3879 2.224646 GGAATACAGCATCCTCCCCTTC 60.225 54.545 0.00 0.00 32.75 3.46
2656 3881 0.044092 TACAGCATCCTCCCCTTCCA 59.956 55.000 0.00 0.00 0.00 3.53
2657 3882 0.625683 ACAGCATCCTCCCCTTCCAT 60.626 55.000 0.00 0.00 0.00 3.41
2767 4684 4.275689 TCACACACCTTTCATGCTTACTTG 59.724 41.667 0.00 0.00 0.00 3.16
2974 4892 6.283694 TCTGTTTGCATCTATGACTACCATC 58.716 40.000 0.00 0.00 36.71 3.51
3202 5128 7.600065 ACTTTCATCATTTCCTGTGAATCTTG 58.400 34.615 0.00 0.00 31.39 3.02
3254 5180 4.870123 AATGCCTGCTGACAAACAAATA 57.130 36.364 0.00 0.00 0.00 1.40
3506 5432 9.991906 TTAGTTACTCATGTTTGCTAGTTAGTT 57.008 29.630 0.00 0.00 0.00 2.24
3508 5434 9.640963 AGTTACTCATGTTTGCTAGTTAGTTAG 57.359 33.333 0.00 0.00 0.00 2.34
3509 5435 9.420551 GTTACTCATGTTTGCTAGTTAGTTAGT 57.579 33.333 0.00 0.00 0.00 2.24
3510 5436 9.991906 TTACTCATGTTTGCTAGTTAGTTAGTT 57.008 29.630 0.00 0.00 0.00 2.24
3563 5489 5.239525 AGTGGTGACTTGTTTATTCTTCAGC 59.760 40.000 0.00 0.00 33.20 4.26
3885 5811 3.895704 ACCAACTGGGAAAATGGTACT 57.104 42.857 0.00 0.00 44.11 2.73
3886 5812 3.763057 ACCAACTGGGAAAATGGTACTC 58.237 45.455 0.00 0.00 44.11 2.59
3887 5813 3.089284 CCAACTGGGAAAATGGTACTCC 58.911 50.000 0.00 0.00 40.01 3.85
3891 5817 2.730934 GGGAAAATGGTACTCCCTCC 57.269 55.000 9.40 2.37 44.81 4.30
3892 5818 1.134189 GGGAAAATGGTACTCCCTCCG 60.134 57.143 9.40 0.00 44.81 4.63
3893 5819 1.558294 GGAAAATGGTACTCCCTCCGT 59.442 52.381 0.00 0.00 0.00 4.69
3894 5820 2.026542 GGAAAATGGTACTCCCTCCGTT 60.027 50.000 0.00 0.00 34.83 4.44
3895 5821 3.268330 GAAAATGGTACTCCCTCCGTTC 58.732 50.000 0.00 0.00 32.55 3.95
3896 5822 1.201424 AATGGTACTCCCTCCGTTCC 58.799 55.000 0.00 0.00 0.00 3.62
3897 5823 0.042131 ATGGTACTCCCTCCGTTCCA 59.958 55.000 0.00 0.00 36.47 3.53
3898 5824 0.042131 TGGTACTCCCTCCGTTCCAT 59.958 55.000 0.00 0.00 28.53 3.41
3899 5825 1.288633 TGGTACTCCCTCCGTTCCATA 59.711 52.381 0.00 0.00 28.53 2.74
3900 5826 2.292389 TGGTACTCCCTCCGTTCCATAA 60.292 50.000 0.00 0.00 28.53 1.90
3901 5827 2.970640 GGTACTCCCTCCGTTCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
3902 5828 4.154942 GGTACTCCCTCCGTTCCATAATA 58.845 47.826 0.00 0.00 0.00 0.98
3903 5829 4.776308 GGTACTCCCTCCGTTCCATAATAT 59.224 45.833 0.00 0.00 0.00 1.28
3904 5830 5.954150 GGTACTCCCTCCGTTCCATAATATA 59.046 44.000 0.00 0.00 0.00 0.86
3905 5831 6.438425 GGTACTCCCTCCGTTCCATAATATAA 59.562 42.308 0.00 0.00 0.00 0.98
3906 5832 6.607004 ACTCCCTCCGTTCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
3907 5833 6.320518 ACTCCCTCCGTTCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
3908 5834 6.437793 ACTCCCTCCGTTCCATAATATAAGAG 59.562 42.308 0.00 0.00 0.00 2.85
3909 5835 5.187186 TCCCTCCGTTCCATAATATAAGAGC 59.813 44.000 0.00 0.00 0.00 4.09
3910 5836 5.103000 CCTCCGTTCCATAATATAAGAGCG 58.897 45.833 3.06 3.06 33.46 5.03
3911 5837 5.336531 CCTCCGTTCCATAATATAAGAGCGT 60.337 44.000 7.53 0.00 32.01 5.07
3912 5838 6.092955 TCCGTTCCATAATATAAGAGCGTT 57.907 37.500 7.53 0.00 32.01 4.84
3913 5839 6.518493 TCCGTTCCATAATATAAGAGCGTTT 58.482 36.000 7.53 0.00 32.01 3.60
3914 5840 6.643770 TCCGTTCCATAATATAAGAGCGTTTC 59.356 38.462 7.53 0.00 32.01 2.78
3915 5841 6.645415 CCGTTCCATAATATAAGAGCGTTTCT 59.355 38.462 7.53 0.00 37.93 2.52
3916 5842 7.359264 CCGTTCCATAATATAAGAGCGTTTCTG 60.359 40.741 7.53 0.00 35.91 3.02
3917 5843 7.381408 CGTTCCATAATATAAGAGCGTTTCTGA 59.619 37.037 0.00 0.00 35.91 3.27
3918 5844 8.488764 GTTCCATAATATAAGAGCGTTTCTGAC 58.511 37.037 0.00 0.00 35.91 3.51
3919 5845 7.722363 TCCATAATATAAGAGCGTTTCTGACA 58.278 34.615 0.00 0.00 35.91 3.58
3920 5846 7.652105 TCCATAATATAAGAGCGTTTCTGACAC 59.348 37.037 0.00 0.00 35.91 3.67
3921 5847 7.653713 CCATAATATAAGAGCGTTTCTGACACT 59.346 37.037 0.00 0.00 35.91 3.55
3922 5848 9.678941 CATAATATAAGAGCGTTTCTGACACTA 57.321 33.333 0.00 0.00 35.91 2.74
3923 5849 9.900710 ATAATATAAGAGCGTTTCTGACACTAG 57.099 33.333 0.00 0.00 35.91 2.57
3924 5850 2.355717 AGAGCGTTTCTGACACTAGC 57.644 50.000 0.00 0.00 33.93 3.42
3925 5851 0.985549 GAGCGTTTCTGACACTAGCG 59.014 55.000 0.00 0.00 0.00 4.26
3926 5852 0.314302 AGCGTTTCTGACACTAGCGT 59.686 50.000 0.00 0.00 0.00 5.07
3927 5853 1.538512 AGCGTTTCTGACACTAGCGTA 59.461 47.619 0.00 0.00 0.00 4.42
3928 5854 1.912110 GCGTTTCTGACACTAGCGTAG 59.088 52.381 0.00 0.00 0.00 3.51
3929 5855 2.667724 GCGTTTCTGACACTAGCGTAGT 60.668 50.000 0.00 0.00 40.28 2.73
3944 5870 3.854286 CGTAGTGTCAAAAACGCTCTT 57.146 42.857 0.00 0.00 45.69 2.85
3945 5871 4.959631 CGTAGTGTCAAAAACGCTCTTA 57.040 40.909 0.00 0.00 45.69 2.10
3946 5872 5.511088 CGTAGTGTCAAAAACGCTCTTAT 57.489 39.130 0.00 0.00 45.69 1.73
3947 5873 6.621737 CGTAGTGTCAAAAACGCTCTTATA 57.378 37.500 0.00 0.00 45.69 0.98
3948 5874 7.218145 CGTAGTGTCAAAAACGCTCTTATAT 57.782 36.000 0.00 0.00 45.69 0.86
3949 5875 7.672738 CGTAGTGTCAAAAACGCTCTTATATT 58.327 34.615 0.00 0.00 45.69 1.28
3950 5876 7.630987 CGTAGTGTCAAAAACGCTCTTATATTG 59.369 37.037 0.00 0.00 45.69 1.90
3951 5877 7.435068 AGTGTCAAAAACGCTCTTATATTGT 57.565 32.000 0.00 0.00 45.69 2.71
3952 5878 7.298122 AGTGTCAAAAACGCTCTTATATTGTG 58.702 34.615 0.00 0.00 45.69 3.33
3953 5879 6.523201 GTGTCAAAAACGCTCTTATATTGTGG 59.477 38.462 0.00 0.00 35.42 4.17
3954 5880 6.027749 GTCAAAAACGCTCTTATATTGTGGG 58.972 40.000 0.00 0.00 0.00 4.61
3955 5881 5.941058 TCAAAAACGCTCTTATATTGTGGGA 59.059 36.000 0.00 0.00 0.00 4.37
3956 5882 5.813080 AAAACGCTCTTATATTGTGGGAC 57.187 39.130 0.00 0.00 0.00 4.46
3957 5883 3.093717 ACGCTCTTATATTGTGGGACG 57.906 47.619 0.00 0.00 0.00 4.79
3958 5884 2.223971 ACGCTCTTATATTGTGGGACGG 60.224 50.000 0.00 0.00 0.00 4.79
3959 5885 2.035449 CGCTCTTATATTGTGGGACGGA 59.965 50.000 0.00 0.00 0.00 4.69
3960 5886 3.654414 GCTCTTATATTGTGGGACGGAG 58.346 50.000 0.00 0.00 0.00 4.63
3961 5887 3.555168 GCTCTTATATTGTGGGACGGAGG 60.555 52.174 0.00 0.00 0.00 4.30
3962 5888 2.969950 TCTTATATTGTGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
3963 5889 2.779429 TATATTGTGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3964 5890 1.424638 ATATTGTGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3965 5891 0.042131 TATTGTGGGACGGAGGGAGT 59.958 55.000 0.00 0.00 0.00 3.85
3966 5892 0.042131 ATTGTGGGACGGAGGGAGTA 59.958 55.000 0.00 0.00 0.00 2.59
4145 6071 9.569167 TTACTTCATGTTATCAGTTAGAAGTCG 57.431 33.333 8.03 0.00 42.07 4.18
4381 6307 6.397272 TGTTGCATTTAATTCTTCCCATCAC 58.603 36.000 0.00 0.00 0.00 3.06
4751 6677 4.526970 GGGGAGAAAGTGCAGATTTCATA 58.473 43.478 20.68 0.00 38.79 2.15
5129 7055 7.584987 ACTTTGATAACTTGTTGATCTTTCCG 58.415 34.615 0.00 0.00 0.00 4.30
5418 7344 9.629878 CTCCCTTCGACCTATAATATAGTGTAT 57.370 37.037 6.55 0.00 0.00 2.29
5481 7407 8.088365 AGTAGTTTTTGCAAAAGTGAAGTTTCT 58.912 29.630 22.78 10.97 0.00 2.52
5599 7530 9.609346 ACTAATGGTACTGATTTGGTATTGTAC 57.391 33.333 0.00 0.00 0.00 2.90
5629 7560 6.535150 TGACATTCTATAAACTTGCTCGAAGG 59.465 38.462 0.00 0.00 35.78 3.46
5659 7590 9.346725 CAAACTTTGACTTGAAGGATATTTAGC 57.653 33.333 0.00 0.00 0.00 3.09
5851 7812 2.632377 CCGTGCCAGTGATTCTTATGT 58.368 47.619 0.00 0.00 0.00 2.29
5910 7875 2.046023 TGGGGAGCAGCATTGTCG 60.046 61.111 0.00 0.00 0.00 4.35
5913 7878 2.401766 GGGAGCAGCATTGTCGTGG 61.402 63.158 0.00 0.00 0.00 4.94
5915 7880 2.360350 AGCAGCATTGTCGTGGGG 60.360 61.111 0.00 0.00 0.00 4.96
5965 7930 3.801068 TTGTGGTTCGGCAAGGGGG 62.801 63.158 0.00 0.00 0.00 5.40
5997 7962 0.784778 CACAAAGAGCGGAGAACGTC 59.215 55.000 0.00 0.00 46.52 4.34
6031 7997 4.165779 CAGAATCACACGGGCAATTTTAC 58.834 43.478 0.00 0.00 0.00 2.01
6040 8006 2.252714 GGGCAATTTTACCCAGGTTCA 58.747 47.619 0.00 0.00 46.22 3.18
6043 8009 2.353704 GCAATTTTACCCAGGTTCAGGC 60.354 50.000 0.00 0.00 0.00 4.85
6044 8010 3.165071 CAATTTTACCCAGGTTCAGGCT 58.835 45.455 0.00 0.00 0.00 4.58
6069 8035 1.470458 CGAGGCGTAAAACCCTACTCC 60.470 57.143 0.00 0.00 0.00 3.85
6083 8049 2.025887 CCTACTCCTGCTTTGGTGGATT 60.026 50.000 0.00 0.00 0.00 3.01
6084 8050 1.915141 ACTCCTGCTTTGGTGGATTG 58.085 50.000 0.00 0.00 0.00 2.67
6085 8051 1.425066 ACTCCTGCTTTGGTGGATTGA 59.575 47.619 0.00 0.00 0.00 2.57
6086 8052 2.042162 ACTCCTGCTTTGGTGGATTGAT 59.958 45.455 0.00 0.00 0.00 2.57
6087 8053 3.266772 ACTCCTGCTTTGGTGGATTGATA 59.733 43.478 0.00 0.00 0.00 2.15
6088 8054 3.881688 CTCCTGCTTTGGTGGATTGATAG 59.118 47.826 0.00 0.00 0.00 2.08
6089 8055 3.266772 TCCTGCTTTGGTGGATTGATAGT 59.733 43.478 0.00 0.00 0.00 2.12
6090 8056 3.379372 CCTGCTTTGGTGGATTGATAGTG 59.621 47.826 0.00 0.00 0.00 2.74
6091 8057 3.355378 TGCTTTGGTGGATTGATAGTGG 58.645 45.455 0.00 0.00 0.00 4.00
6092 8058 3.010027 TGCTTTGGTGGATTGATAGTGGA 59.990 43.478 0.00 0.00 0.00 4.02
6093 8059 4.210331 GCTTTGGTGGATTGATAGTGGAT 58.790 43.478 0.00 0.00 0.00 3.41
6101 8067 3.885297 GGATTGATAGTGGATTGTGGTGG 59.115 47.826 0.00 0.00 0.00 4.61
6134 8100 0.549169 TAGCCTGGTAGGGTTGCCTT 60.549 55.000 4.75 0.00 45.25 4.35
6135 8101 1.378646 GCCTGGTAGGGTTGCCTTC 60.379 63.158 0.00 0.00 35.37 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.517901 CCCACATTACCCAACTCTAGTCA 59.482 47.826 0.00 0.00 0.00 3.41
57 58 1.298340 CGAGCACACCCCCACATTA 59.702 57.895 0.00 0.00 0.00 1.90
87 89 3.295304 GAACAACCCAATGCCCGGC 62.295 63.158 1.04 1.04 0.00 6.13
292 294 2.746362 AGCAGCATGTCTAACAGAAAGC 59.254 45.455 0.00 0.00 39.31 3.51
368 370 5.644977 TTCGATGACATGAGACTACAACT 57.355 39.130 0.00 0.00 0.00 3.16
1066 2280 2.751259 GCCAACAGAGATGCAGAAATCA 59.249 45.455 0.00 0.00 0.00 2.57
1088 2302 4.156455 TCCAAATCAAGGCTAGCTAAGG 57.844 45.455 15.72 5.99 0.00 2.69
1122 2336 1.385631 ATCTGATCTGCCCCCAGCT 60.386 57.895 0.00 0.00 44.23 4.24
1215 2435 1.207593 CCTGCGTTTTGAGCTTCCG 59.792 57.895 0.00 0.00 35.28 4.30
1250 2470 8.258007 TGTAGGAATTCCGGATACATGATATTC 58.742 37.037 18.82 8.86 42.08 1.75
1617 2837 7.406031 TGAAGGATATGATATCTACGGGAAC 57.594 40.000 11.85 0.00 0.00 3.62
1693 2913 6.418057 AGAATAAGTAGAGAAGCATCCTGG 57.582 41.667 0.00 0.00 0.00 4.45
1764 2984 4.159135 CCAATTGTTTCCCAGGATCTTCAG 59.841 45.833 4.43 0.00 0.00 3.02
1773 2993 3.118445 ACACCAAACCAATTGTTTCCCAG 60.118 43.478 4.43 0.00 45.35 4.45
2297 3518 9.708092 AGCGAAAAATAGAACTTCTACTTACTT 57.292 29.630 0.33 0.00 30.79 2.24
2314 3535 5.146010 TGGATTAAGCCAAAGCGAAAAAT 57.854 34.783 10.72 0.00 46.67 1.82
2537 3761 5.005012 CCTTTCATAATGAACTTGCATTGCG 59.995 40.000 3.84 0.00 38.80 4.85
2600 3824 9.494271 GTGACAAACATATATGTAGATGGTCAT 57.506 33.333 21.21 7.63 40.80 3.06
2767 4684 7.382898 TGGCTGTTTTATCTGTTTTATTTCCC 58.617 34.615 0.00 0.00 0.00 3.97
2974 4892 2.838736 ACAGAACCAACAGCAGTACAG 58.161 47.619 0.00 0.00 0.00 2.74
3202 5128 7.394641 AGGAAAATAAAGTTCAGAAGGACATCC 59.605 37.037 0.00 0.00 0.00 3.51
3504 5430 2.409975 TCGCAGCTTGTGGTAACTAAC 58.590 47.619 0.00 0.00 37.61 2.34
3505 5431 2.823924 TCGCAGCTTGTGGTAACTAA 57.176 45.000 0.00 0.00 37.61 2.24
3506 5432 2.496070 AGATCGCAGCTTGTGGTAACTA 59.504 45.455 0.00 0.00 37.61 2.24
3507 5433 1.276421 AGATCGCAGCTTGTGGTAACT 59.724 47.619 0.00 0.00 37.61 2.24
3508 5434 1.726853 AGATCGCAGCTTGTGGTAAC 58.273 50.000 0.00 0.00 0.00 2.50
3509 5435 3.132111 TGATAGATCGCAGCTTGTGGTAA 59.868 43.478 0.00 0.00 0.00 2.85
3510 5436 2.693074 TGATAGATCGCAGCTTGTGGTA 59.307 45.455 0.00 0.00 0.00 3.25
3511 5437 1.482182 TGATAGATCGCAGCTTGTGGT 59.518 47.619 0.00 0.00 0.00 4.16
3563 5489 3.276857 AGGCTAACAGACAATGATGCTG 58.723 45.455 0.00 0.00 37.00 4.41
3884 5810 6.628398 GCTCTTATATTATGGAACGGAGGGAG 60.628 46.154 0.00 0.00 0.00 4.30
3885 5811 5.187186 GCTCTTATATTATGGAACGGAGGGA 59.813 44.000 0.00 0.00 0.00 4.20
3886 5812 5.420409 GCTCTTATATTATGGAACGGAGGG 58.580 45.833 0.00 0.00 0.00 4.30
3887 5813 5.103000 CGCTCTTATATTATGGAACGGAGG 58.897 45.833 0.00 0.00 0.00 4.30
3888 5814 5.710984 ACGCTCTTATATTATGGAACGGAG 58.289 41.667 0.00 0.00 0.00 4.63
3889 5815 5.717078 ACGCTCTTATATTATGGAACGGA 57.283 39.130 0.00 0.00 0.00 4.69
3890 5816 6.645415 AGAAACGCTCTTATATTATGGAACGG 59.355 38.462 0.00 0.00 0.00 4.44
3891 5817 7.381408 TCAGAAACGCTCTTATATTATGGAACG 59.619 37.037 0.00 0.00 29.07 3.95
3892 5818 8.488764 GTCAGAAACGCTCTTATATTATGGAAC 58.511 37.037 0.00 0.00 29.07 3.62
3893 5819 8.201464 TGTCAGAAACGCTCTTATATTATGGAA 58.799 33.333 0.00 0.00 29.07 3.53
3894 5820 7.652105 GTGTCAGAAACGCTCTTATATTATGGA 59.348 37.037 0.00 0.00 35.42 3.41
3895 5821 7.653713 AGTGTCAGAAACGCTCTTATATTATGG 59.346 37.037 0.00 0.00 45.69 2.74
3896 5822 8.581057 AGTGTCAGAAACGCTCTTATATTATG 57.419 34.615 0.00 0.00 45.69 1.90
3897 5823 9.900710 CTAGTGTCAGAAACGCTCTTATATTAT 57.099 33.333 0.00 0.00 45.69 1.28
3898 5824 7.861372 GCTAGTGTCAGAAACGCTCTTATATTA 59.139 37.037 0.00 0.00 45.69 0.98
3899 5825 6.697892 GCTAGTGTCAGAAACGCTCTTATATT 59.302 38.462 0.00 0.00 45.69 1.28
3900 5826 6.210078 GCTAGTGTCAGAAACGCTCTTATAT 58.790 40.000 0.00 0.00 45.69 0.86
3901 5827 5.579718 GCTAGTGTCAGAAACGCTCTTATA 58.420 41.667 0.00 0.00 45.69 0.98
3902 5828 4.425520 GCTAGTGTCAGAAACGCTCTTAT 58.574 43.478 0.00 0.00 45.69 1.73
3903 5829 3.669824 CGCTAGTGTCAGAAACGCTCTTA 60.670 47.826 0.00 0.00 45.69 2.10
3904 5830 2.678324 GCTAGTGTCAGAAACGCTCTT 58.322 47.619 0.00 0.00 45.69 2.85
3905 5831 1.401670 CGCTAGTGTCAGAAACGCTCT 60.402 52.381 0.00 0.00 45.69 4.09
3906 5832 0.985549 CGCTAGTGTCAGAAACGCTC 59.014 55.000 0.00 0.00 45.69 5.03
3908 5834 1.912110 CTACGCTAGTGTCAGAAACGC 59.088 52.381 13.25 0.00 38.74 4.84
3909 5835 3.198863 ACTACGCTAGTGTCAGAAACG 57.801 47.619 13.25 0.00 37.69 3.60
3924 5850 3.854286 AAGAGCGTTTTTGACACTACG 57.146 42.857 0.00 0.00 37.09 3.51
3925 5851 8.440833 ACAATATAAGAGCGTTTTTGACACTAC 58.559 33.333 0.00 0.00 0.00 2.73
3926 5852 8.440059 CACAATATAAGAGCGTTTTTGACACTA 58.560 33.333 0.00 0.00 0.00 2.74
3927 5853 7.298122 CACAATATAAGAGCGTTTTTGACACT 58.702 34.615 0.00 0.00 0.00 3.55
3928 5854 6.523201 CCACAATATAAGAGCGTTTTTGACAC 59.477 38.462 0.00 0.00 0.00 3.67
3929 5855 6.348950 CCCACAATATAAGAGCGTTTTTGACA 60.349 38.462 0.00 0.00 0.00 3.58
3930 5856 6.027749 CCCACAATATAAGAGCGTTTTTGAC 58.972 40.000 0.00 0.00 0.00 3.18
3931 5857 5.941058 TCCCACAATATAAGAGCGTTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
3932 5858 6.027749 GTCCCACAATATAAGAGCGTTTTTG 58.972 40.000 0.00 0.00 0.00 2.44
3933 5859 5.163794 CGTCCCACAATATAAGAGCGTTTTT 60.164 40.000 0.00 0.00 0.00 1.94
3934 5860 4.331717 CGTCCCACAATATAAGAGCGTTTT 59.668 41.667 0.00 0.00 0.00 2.43
3935 5861 3.869246 CGTCCCACAATATAAGAGCGTTT 59.131 43.478 0.00 0.00 0.00 3.60
3936 5862 3.454375 CGTCCCACAATATAAGAGCGTT 58.546 45.455 0.00 0.00 0.00 4.84
3937 5863 2.223971 CCGTCCCACAATATAAGAGCGT 60.224 50.000 0.00 0.00 0.00 5.07
3938 5864 2.035449 TCCGTCCCACAATATAAGAGCG 59.965 50.000 0.00 0.00 0.00 5.03
3939 5865 3.555168 CCTCCGTCCCACAATATAAGAGC 60.555 52.174 0.00 0.00 0.00 4.09
3940 5866 3.006967 CCCTCCGTCCCACAATATAAGAG 59.993 52.174 0.00 0.00 0.00 2.85
3941 5867 2.969950 CCCTCCGTCCCACAATATAAGA 59.030 50.000 0.00 0.00 0.00 2.10
3942 5868 2.969950 TCCCTCCGTCCCACAATATAAG 59.030 50.000 0.00 0.00 0.00 1.73
3943 5869 2.969950 CTCCCTCCGTCCCACAATATAA 59.030 50.000 0.00 0.00 0.00 0.98
3944 5870 2.090943 ACTCCCTCCGTCCCACAATATA 60.091 50.000 0.00 0.00 0.00 0.86
3945 5871 1.344087 ACTCCCTCCGTCCCACAATAT 60.344 52.381 0.00 0.00 0.00 1.28
3946 5872 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.000 0.00 0.00 0.00 1.90
3947 5873 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71
3948 5874 0.042131 ATACTCCCTCCGTCCCACAA 59.958 55.000 0.00 0.00 0.00 3.33
3949 5875 0.042131 AATACTCCCTCCGTCCCACA 59.958 55.000 0.00 0.00 0.00 4.17
3950 5876 2.077687 TAATACTCCCTCCGTCCCAC 57.922 55.000 0.00 0.00 0.00 4.61
3951 5877 2.605257 CATAATACTCCCTCCGTCCCA 58.395 52.381 0.00 0.00 0.00 4.37
3952 5878 1.275573 GCATAATACTCCCTCCGTCCC 59.724 57.143 0.00 0.00 0.00 4.46
3953 5879 1.968493 TGCATAATACTCCCTCCGTCC 59.032 52.381 0.00 0.00 0.00 4.79
3954 5880 3.555168 CCTTGCATAATACTCCCTCCGTC 60.555 52.174 0.00 0.00 0.00 4.79
3955 5881 2.368875 CCTTGCATAATACTCCCTCCGT 59.631 50.000 0.00 0.00 0.00 4.69
3956 5882 2.632996 TCCTTGCATAATACTCCCTCCG 59.367 50.000 0.00 0.00 0.00 4.63
3957 5883 4.706842 TTCCTTGCATAATACTCCCTCC 57.293 45.455 0.00 0.00 0.00 4.30
3958 5884 7.285401 TGAAAATTCCTTGCATAATACTCCCTC 59.715 37.037 0.00 0.00 0.00 4.30
3959 5885 7.125391 TGAAAATTCCTTGCATAATACTCCCT 58.875 34.615 0.00 0.00 0.00 4.20
3960 5886 7.068716 ACTGAAAATTCCTTGCATAATACTCCC 59.931 37.037 0.00 0.00 0.00 4.30
3961 5887 8.000780 ACTGAAAATTCCTTGCATAATACTCC 57.999 34.615 0.00 0.00 0.00 3.85
3962 5888 8.677300 TGACTGAAAATTCCTTGCATAATACTC 58.323 33.333 0.00 0.00 0.00 2.59
3963 5889 8.579850 TGACTGAAAATTCCTTGCATAATACT 57.420 30.769 0.00 0.00 0.00 2.12
3964 5890 9.455847 GATGACTGAAAATTCCTTGCATAATAC 57.544 33.333 0.00 0.00 0.00 1.89
3965 5891 8.344831 CGATGACTGAAAATTCCTTGCATAATA 58.655 33.333 0.00 0.00 0.00 0.98
3966 5892 7.067372 TCGATGACTGAAAATTCCTTGCATAAT 59.933 33.333 0.00 0.00 0.00 1.28
4145 6071 3.883489 GCCCATTGATACTCAAACCTACC 59.117 47.826 0.00 0.00 40.12 3.18
4381 6307 8.936070 TTGAAGAAATGCATCCTGAATTATTG 57.064 30.769 0.00 0.00 0.00 1.90
5157 7083 8.250332 GTCATTGCCACTTTCCTCATTTTATAA 58.750 33.333 0.00 0.00 0.00 0.98
5176 7102 5.537188 TGAGGTTGTAATTTTGGTCATTGC 58.463 37.500 0.00 0.00 0.00 3.56
5418 7344 6.103997 GGGACGAACAGAGTATCAAACAATA 58.896 40.000 0.00 0.00 37.82 1.90
5434 7360 3.916761 TGTACACTGTTATGGGACGAAC 58.083 45.455 0.00 0.00 0.00 3.95
5599 7530 7.637519 CGAGCAAGTTTATAGAATGTCAACATG 59.362 37.037 0.00 0.00 36.56 3.21
5659 7590 1.981254 ACCGAATTGCGCAAATCAAG 58.019 45.000 31.33 24.74 39.11 3.02
5818 7779 1.181786 GGCACGGGAATCCATTTTGA 58.818 50.000 0.09 0.00 0.00 2.69
5851 7812 7.517614 TGTTTTGTCTTAATGTGCAGGATAA 57.482 32.000 0.00 0.00 0.00 1.75
5887 7852 0.613012 AATGCTGCTCCCCAGGTTTC 60.613 55.000 0.00 0.00 42.03 2.78
5910 7875 1.304134 GGTGACCATGGTTCCCCAC 60.304 63.158 20.85 20.85 45.65 4.61
5913 7878 1.133792 CCATAGGTGACCATGGTTCCC 60.134 57.143 26.23 23.66 37.51 3.97
5915 7880 1.133792 CCCCATAGGTGACCATGGTTC 60.134 57.143 20.85 15.03 40.17 3.62
5965 7930 3.499048 CTCTTTGTGCAATGTGCTCATC 58.501 45.455 1.01 0.00 44.81 2.92
5997 7962 3.411703 GATTCTGTCGTGCTGCGCG 62.412 63.158 27.90 27.90 41.07 6.86
6053 8019 1.066358 AGCAGGAGTAGGGTTTTACGC 60.066 52.381 0.00 0.00 0.00 4.42
6054 8020 3.329929 AAGCAGGAGTAGGGTTTTACG 57.670 47.619 0.00 0.00 0.00 3.18
6069 8035 3.379372 CCACTATCAATCCACCAAAGCAG 59.621 47.826 0.00 0.00 0.00 4.24
6083 8049 4.331968 GTTTCCACCACAATCCACTATCA 58.668 43.478 0.00 0.00 0.00 2.15
6084 8050 3.374058 CGTTTCCACCACAATCCACTATC 59.626 47.826 0.00 0.00 0.00 2.08
6085 8051 3.343617 CGTTTCCACCACAATCCACTAT 58.656 45.455 0.00 0.00 0.00 2.12
6086 8052 2.773487 CGTTTCCACCACAATCCACTA 58.227 47.619 0.00 0.00 0.00 2.74
6087 8053 1.604604 CGTTTCCACCACAATCCACT 58.395 50.000 0.00 0.00 0.00 4.00
6088 8054 0.039527 GCGTTTCCACCACAATCCAC 60.040 55.000 0.00 0.00 0.00 4.02
6089 8055 0.466372 TGCGTTTCCACCACAATCCA 60.466 50.000 0.00 0.00 0.00 3.41
6090 8056 0.671251 TTGCGTTTCCACCACAATCC 59.329 50.000 0.00 0.00 0.00 3.01
6091 8057 1.766069 GTTGCGTTTCCACCACAATC 58.234 50.000 0.00 0.00 0.00 2.67
6092 8058 0.030101 CGTTGCGTTTCCACCACAAT 59.970 50.000 0.00 0.00 0.00 2.71
6093 8059 1.429825 CGTTGCGTTTCCACCACAA 59.570 52.632 0.00 0.00 0.00 3.33
6101 8067 1.014564 AGGCTAGAGCGTTGCGTTTC 61.015 55.000 0.00 0.00 43.26 2.78


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

AutoCloner maintained by Alex Coulton.