Multiple sequence alignment - TraesCS5D01G306000

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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 TraesCS5D01G306000 chr5D 100.000 4213 0 0 1 4213 402200709 402204921 0.000000e+00 7781.0
1 TraesCS5D01G306000 chr5D 99.454 183 1 0 1 183 276444521 276444339 2.430000e-87 333.0
2 TraesCS5D01G306000 chr5D 74.947 471 76 27 180 633 327994917 327995362 1.200000e-40 178.0
3 TraesCS5D01G306000 chr5D 84.211 114 15 1 182 295 205981878 205981768 1.600000e-19 108.0
4 TraesCS5D01G306000 chr5D 86.813 91 9 1 179 269 422949748 422949661 9.640000e-17 99.0
5 TraesCS5D01G306000 chr5B 95.299 2680 68 27 886 3524 481140943 481143605 0.000000e+00 4198.0
6 TraesCS5D01G306000 chr5B 92.507 694 46 2 3525 4213 481143872 481144564 0.000000e+00 989.0
7 TraesCS5D01G306000 chr5B 95.041 121 6 0 785 905 481140806 481140926 1.550000e-44 191.0
8 TraesCS5D01G306000 chr5B 89.130 92 7 1 180 271 510700195 510700107 1.240000e-20 111.0
9 TraesCS5D01G306000 chr5B 77.632 152 31 3 483 632 500535059 500534909 5.800000e-14 89.8
10 TraesCS5D01G306000 chr5A 96.700 1788 54 2 1738 3525 507966490 507968272 0.000000e+00 2970.0
11 TraesCS5D01G306000 chr5A 93.901 869 31 9 886 1740 507965527 507966387 0.000000e+00 1291.0
12 TraesCS5D01G306000 chr5A 93.525 695 38 3 3525 4213 507968371 507969064 0.000000e+00 1027.0
13 TraesCS5D01G306000 chr5A 86.594 731 59 13 179 905 507964815 507965510 0.000000e+00 771.0
14 TraesCS5D01G306000 chr5A 91.705 434 35 1 3780 4213 170841400 170840968 6.030000e-168 601.0
15 TraesCS5D01G306000 chr2B 81.228 863 141 17 2363 3212 435156422 435157276 0.000000e+00 676.0
16 TraesCS5D01G306000 chr2D 81.112 863 142 16 2363 3212 366498268 366499122 0.000000e+00 671.0
17 TraesCS5D01G306000 chr2D 91.705 434 36 0 3780 4213 284549626 284550059 1.680000e-168 603.0
18 TraesCS5D01G306000 chr2D 98.919 185 2 0 1 185 226509782 226509598 8.730000e-87 331.0
19 TraesCS5D01G306000 chr2D 96.447 197 6 1 1 196 323582010 323581814 1.460000e-84 324.0
20 TraesCS5D01G306000 chr2D 96.875 32 1 0 3718 3749 32188045 32188076 2.000000e-03 54.7
21 TraesCS5D01G306000 chr2A 80.997 863 143 16 2363 3212 495958007 495958861 0.000000e+00 665.0
22 TraesCS5D01G306000 chr7B 93.088 434 30 0 3780 4213 366049750 366050183 1.650000e-178 636.0
23 TraesCS5D01G306000 chr4B 92.220 437 31 2 3780 4213 22842282 22841846 2.150000e-172 616.0
24 TraesCS5D01G306000 chr4B 82.014 417 62 10 179 588 652766713 652767123 4.030000e-90 342.0
25 TraesCS5D01G306000 chr4B 91.304 46 4 0 3718 3763 448310991 448310946 3.520000e-06 63.9
26 TraesCS5D01G306000 chr6A 91.935 434 35 0 3780 4213 58016548 58016115 3.600000e-170 608.0
27 TraesCS5D01G306000 chr4A 91.935 434 32 1 3780 4213 590229693 590230123 4.660000e-169 604.0
28 TraesCS5D01G306000 chr4A 100.000 28 0 0 3717 3744 32056967 32056994 8.000000e-03 52.8
29 TraesCS5D01G306000 chr3D 91.705 434 36 0 3780 4213 329443871 329443438 1.680000e-168 603.0
30 TraesCS5D01G306000 chr3D 100.000 180 0 0 1 180 277867540 277867361 2.430000e-87 333.0
31 TraesCS5D01G306000 chr3D 96.891 193 4 2 1 191 423881440 423881248 5.250000e-84 322.0
32 TraesCS5D01G306000 chr3D 77.407 270 49 8 179 445 18406939 18407199 2.620000e-32 150.0
33 TraesCS5D01G306000 chr7D 98.907 183 2 0 1 183 486387184 486387002 1.130000e-85 327.0
34 TraesCS5D01G306000 chr7D 98.895 181 2 0 1 181 570799724 570799904 1.460000e-84 324.0
35 TraesCS5D01G306000 chr7D 96.410 195 4 2 1 194 496591902 496592094 6.800000e-83 318.0
36 TraesCS5D01G306000 chr7D 95.238 42 2 0 3721 3762 577775981 577775940 2.720000e-07 67.6
37 TraesCS5D01G306000 chr7D 100.000 28 0 0 3717 3744 380628637 380628664 8.000000e-03 52.8
38 TraesCS5D01G306000 chr4D 98.913 184 1 1 1 183 231375789 231375972 1.130000e-85 327.0
39 TraesCS5D01G306000 chr3B 77.172 495 92 11 180 660 377687507 377687020 6.940000e-68 268.0
40 TraesCS5D01G306000 chr1D 75.972 566 104 21 187 726 15312026 15311467 3.230000e-66 263.0


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 TraesCS5D01G306000 chr5D 402200709 402204921 4212 False 7781.000000 7781 100.000000 1 4213 1 chr5D.!!$F2 4212
1 TraesCS5D01G306000 chr5B 481140806 481144564 3758 False 1792.666667 4198 94.282333 785 4213 3 chr5B.!!$F1 3428
2 TraesCS5D01G306000 chr5A 507964815 507969064 4249 False 1514.750000 2970 92.680000 179 4213 4 chr5A.!!$F1 4034
3 TraesCS5D01G306000 chr2B 435156422 435157276 854 False 676.000000 676 81.228000 2363 3212 1 chr2B.!!$F1 849
4 TraesCS5D01G306000 chr2D 366498268 366499122 854 False 671.000000 671 81.112000 2363 3212 1 chr2D.!!$F3 849
5 TraesCS5D01G306000 chr2A 495958007 495958861 854 False 665.000000 665 80.997000 2363 3212 1 chr2A.!!$F1 849
6 TraesCS5D01G306000 chr1D 15311467 15312026 559 True 263.000000 263 75.972000 187 726 1 chr1D.!!$R1 539

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
553 578 0.034896 GAGTGTTGTGTCCCCGACAT 59.965 55.0 0.00 0.00 44.63 3.06 F
850 880 0.807667 CCCGCTCCAGAATTCTGTCG 60.808 60.0 29.03 25.88 42.27 4.35 F
2515 2709 0.037975 CACCACAGAAAATGCAGGCC 60.038 55.0 0.00 0.00 32.05 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2479 2673 0.530288 GTGGCGCAAATGGTGGTATT 59.470 50.000 10.83 0.0 0.00 1.89 R
2695 2922 1.153667 GAAGCTCGAGCACCTCTGG 60.154 63.158 36.87 0.0 45.16 3.86 R
3859 4387 0.616395 TAATCGACCTCCCAGGCACA 60.616 55.000 0.00 0.0 39.63 4.57 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
24 25 6.688578 TCTTTGATTAACGAGCTAGTCAAGT 58.311 36.000 0.00 0.00 31.56 3.16
25 26 7.823665 TCTTTGATTAACGAGCTAGTCAAGTA 58.176 34.615 0.00 0.00 31.56 2.24
26 27 7.968956 TCTTTGATTAACGAGCTAGTCAAGTAG 59.031 37.037 0.00 0.00 31.56 2.57
27 28 6.997239 TGATTAACGAGCTAGTCAAGTAGA 57.003 37.500 0.00 0.00 0.00 2.59
28 29 7.017498 TGATTAACGAGCTAGTCAAGTAGAG 57.983 40.000 0.00 0.00 0.00 2.43
29 30 5.814764 TTAACGAGCTAGTCAAGTAGAGG 57.185 43.478 0.00 0.00 0.00 3.69
30 31 2.018515 ACGAGCTAGTCAAGTAGAGGC 58.981 52.381 0.00 0.00 0.00 4.70
31 32 2.017782 CGAGCTAGTCAAGTAGAGGCA 58.982 52.381 0.00 0.00 0.00 4.75
32 33 2.621055 CGAGCTAGTCAAGTAGAGGCAT 59.379 50.000 0.00 0.00 0.00 4.40
33 34 3.815962 CGAGCTAGTCAAGTAGAGGCATA 59.184 47.826 0.00 0.00 0.00 3.14
34 35 4.319911 CGAGCTAGTCAAGTAGAGGCATAC 60.320 50.000 0.00 0.00 0.00 2.39
35 36 4.798882 AGCTAGTCAAGTAGAGGCATACT 58.201 43.478 0.00 0.00 37.61 2.12
36 37 5.942961 AGCTAGTCAAGTAGAGGCATACTA 58.057 41.667 3.23 0.00 34.90 1.82
37 38 6.001460 AGCTAGTCAAGTAGAGGCATACTAG 58.999 44.000 0.00 0.00 38.50 2.57
38 39 5.766174 GCTAGTCAAGTAGAGGCATACTAGT 59.234 44.000 0.00 0.00 38.02 2.57
39 40 6.293735 GCTAGTCAAGTAGAGGCATACTAGTG 60.294 46.154 5.39 0.00 38.02 2.74
40 41 5.756918 AGTCAAGTAGAGGCATACTAGTGA 58.243 41.667 5.39 2.59 34.90 3.41
41 42 5.591067 AGTCAAGTAGAGGCATACTAGTGAC 59.409 44.000 17.97 17.97 40.57 3.67
42 43 5.357314 GTCAAGTAGAGGCATACTAGTGACA 59.643 44.000 19.41 0.00 40.28 3.58
43 44 5.357314 TCAAGTAGAGGCATACTAGTGACAC 59.643 44.000 5.39 0.00 34.90 3.67
44 45 5.118729 AGTAGAGGCATACTAGTGACACT 57.881 43.478 13.68 13.68 34.21 3.55
45 46 5.127491 AGTAGAGGCATACTAGTGACACTC 58.873 45.833 12.39 8.31 34.21 3.51
46 47 4.243793 AGAGGCATACTAGTGACACTCT 57.756 45.455 12.39 10.40 0.00 3.24
47 48 3.951037 AGAGGCATACTAGTGACACTCTG 59.049 47.826 12.39 9.04 33.23 3.35
48 49 3.697045 GAGGCATACTAGTGACACTCTGT 59.303 47.826 12.39 14.35 0.00 3.41
49 50 4.090090 AGGCATACTAGTGACACTCTGTT 58.910 43.478 12.39 0.00 0.00 3.16
50 51 4.528596 AGGCATACTAGTGACACTCTGTTT 59.471 41.667 12.39 5.23 0.00 2.83
51 52 4.627467 GGCATACTAGTGACACTCTGTTTG 59.373 45.833 12.39 16.63 0.00 2.93
52 53 5.230942 GCATACTAGTGACACTCTGTTTGT 58.769 41.667 12.39 5.61 0.00 2.83
53 54 5.346281 GCATACTAGTGACACTCTGTTTGTC 59.654 44.000 12.39 9.81 43.22 3.18
54 55 6.682746 CATACTAGTGACACTCTGTTTGTCT 58.317 40.000 12.39 0.00 43.30 3.41
55 56 7.575155 GCATACTAGTGACACTCTGTTTGTCTA 60.575 40.741 12.39 0.00 43.30 2.59
56 57 6.902771 ACTAGTGACACTCTGTTTGTCTAT 57.097 37.500 12.39 0.00 43.30 1.98
57 58 7.997773 ACTAGTGACACTCTGTTTGTCTATA 57.002 36.000 12.39 0.00 43.30 1.31
58 59 8.582657 ACTAGTGACACTCTGTTTGTCTATAT 57.417 34.615 12.39 0.00 43.30 0.86
59 60 9.682465 ACTAGTGACACTCTGTTTGTCTATATA 57.318 33.333 12.39 0.00 43.30 0.86
63 64 9.803315 GTGACACTCTGTTTGTCTATATATTCA 57.197 33.333 0.00 0.00 43.30 2.57
64 65 9.803315 TGACACTCTGTTTGTCTATATATTCAC 57.197 33.333 11.01 0.00 43.30 3.18
65 66 9.803315 GACACTCTGTTTGTCTATATATTCACA 57.197 33.333 0.00 0.00 40.30 3.58
66 67 9.587772 ACACTCTGTTTGTCTATATATTCACAC 57.412 33.333 0.00 0.00 0.00 3.82
67 68 9.586435 CACTCTGTTTGTCTATATATTCACACA 57.414 33.333 0.00 0.00 0.00 3.72
83 84 6.429791 TTCACACATGTATTATGTTTCCGG 57.570 37.500 0.00 0.00 0.00 5.14
84 85 5.492895 TCACACATGTATTATGTTTCCGGT 58.507 37.500 0.00 0.00 0.00 5.28
85 86 5.941058 TCACACATGTATTATGTTTCCGGTT 59.059 36.000 0.00 0.00 0.00 4.44
86 87 7.104290 TCACACATGTATTATGTTTCCGGTTA 58.896 34.615 0.00 0.00 0.00 2.85
87 88 7.606839 TCACACATGTATTATGTTTCCGGTTAA 59.393 33.333 0.00 0.00 0.00 2.01
88 89 8.402472 CACACATGTATTATGTTTCCGGTTAAT 58.598 33.333 0.00 1.95 0.00 1.40
89 90 9.616156 ACACATGTATTATGTTTCCGGTTAATA 57.384 29.630 0.00 0.00 0.00 0.98
90 91 9.872757 CACATGTATTATGTTTCCGGTTAATAC 57.127 33.333 0.00 12.47 37.73 1.89
91 92 9.616156 ACATGTATTATGTTTCCGGTTAATACA 57.384 29.630 22.83 22.83 44.85 2.29
99 100 7.311364 TGTTTCCGGTTAATACAATTCTAGC 57.689 36.000 0.00 0.00 0.00 3.42
100 101 6.879993 TGTTTCCGGTTAATACAATTCTAGCA 59.120 34.615 0.00 0.00 0.00 3.49
101 102 7.554835 TGTTTCCGGTTAATACAATTCTAGCAT 59.445 33.333 0.00 0.00 0.00 3.79
102 103 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
103 104 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
104 105 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
105 106 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.00 38.19 2.57
106 107 9.214957 CCGGTTAATACAATTCTAGCATGAATA 57.785 33.333 0.00 0.00 35.82 1.75
163 164 9.907229 ATAATACTTTATTATTGCCTCTAGGGC 57.093 33.333 13.60 13.60 44.30 5.19
175 176 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
176 177 4.904241 CCTCTAGGGCATATTTCCTTCAG 58.096 47.826 0.00 0.00 34.75 3.02
177 178 4.349342 CCTCTAGGGCATATTTCCTTCAGT 59.651 45.833 0.00 0.00 34.75 3.41
183 184 2.614057 GCATATTTCCTTCAGTGGGTCG 59.386 50.000 0.00 0.00 0.00 4.79
206 207 1.273838 ACAACCCTAGCATGAGGAGGA 60.274 52.381 0.00 0.00 39.15 3.71
212 213 2.298610 CTAGCATGAGGAGGACGTACA 58.701 52.381 0.00 0.00 0.00 2.90
214 215 2.111384 AGCATGAGGAGGACGTACATT 58.889 47.619 0.00 0.00 0.00 2.71
219 220 1.471684 GAGGAGGACGTACATTGTCGT 59.528 52.381 0.00 12.06 43.00 4.34
221 222 1.990563 GGAGGACGTACATTGTCGTTG 59.009 52.381 0.00 0.00 40.39 4.10
222 223 1.389106 GAGGACGTACATTGTCGTTGC 59.611 52.381 0.00 4.72 40.39 4.17
223 224 0.441145 GGACGTACATTGTCGTTGCC 59.559 55.000 13.02 8.69 40.39 4.52
338 352 1.902508 TCTTCTTCGCCTGAATGGTCT 59.097 47.619 0.00 0.00 38.35 3.85
376 390 1.263484 GCCGATTCTATGTCGAGTCGA 59.737 52.381 12.09 12.09 43.21 4.20
379 393 2.222213 CGATTCTATGTCGAGTCGAGCT 59.778 50.000 17.12 8.73 43.21 4.09
382 396 5.390040 CGATTCTATGTCGAGTCGAGCTATT 60.390 44.000 17.12 1.83 43.21 1.73
389 403 0.102481 GAGTCGAGCTATTTCCGCCA 59.898 55.000 0.00 0.00 0.00 5.69
423 440 1.137513 CGCGGTTTCTTCTTCTTCGT 58.862 50.000 0.00 0.00 0.00 3.85
424 441 1.525619 CGCGGTTTCTTCTTCTTCGTT 59.474 47.619 0.00 0.00 0.00 3.85
474 495 2.663196 CGGTTTCTTCGGGGCTCT 59.337 61.111 0.00 0.00 0.00 4.09
491 515 4.037413 TGGCCATGGAGGGAGGGA 62.037 66.667 18.40 0.00 38.09 4.20
526 551 4.407365 GGAGGGTTTTTGGAATGAGAGAA 58.593 43.478 0.00 0.00 0.00 2.87
553 578 0.034896 GAGTGTTGTGTCCCCGACAT 59.965 55.000 0.00 0.00 44.63 3.06
565 590 4.758251 CGACATGCGGGGCAGTGA 62.758 66.667 0.00 0.00 43.65 3.41
610 635 2.745884 CGGGCGCTGTCCATTTCA 60.746 61.111 7.64 0.00 0.00 2.69
645 670 3.056607 CCCAAATTTGAGTCGGAAATGCT 60.057 43.478 19.86 0.00 0.00 3.79
648 673 5.221880 CAAATTTGAGTCGGAAATGCTTCA 58.778 37.500 13.08 0.00 32.75 3.02
653 678 1.003839 TCGGAAATGCTTCAGCGGT 60.004 52.632 0.00 0.00 45.83 5.68
667 692 1.138036 GCGGTGGATAAAAACGGGC 59.862 57.895 0.00 0.00 0.00 6.13
668 693 1.587933 GCGGTGGATAAAAACGGGCA 61.588 55.000 0.00 0.00 0.00 5.36
684 710 2.288763 CGGGCATTTGGCTGTTTACTTT 60.289 45.455 4.85 0.00 44.01 2.66
685 711 3.325870 GGGCATTTGGCTGTTTACTTTC 58.674 45.455 4.01 0.00 44.01 2.62
705 733 1.500512 GCGCGTTGGGCCGATATTTA 61.501 55.000 8.43 0.00 38.94 1.40
736 764 1.135315 CTCAAGCGACCATTTGGCG 59.865 57.895 0.00 3.03 39.32 5.69
737 765 1.577328 CTCAAGCGACCATTTGGCGT 61.577 55.000 12.62 1.36 39.32 5.68
752 780 2.789208 TGGCGTAACTCGTATTTCTCG 58.211 47.619 0.00 0.00 42.13 4.04
753 781 2.419673 TGGCGTAACTCGTATTTCTCGA 59.580 45.455 0.00 0.00 42.13 4.04
754 782 3.119884 TGGCGTAACTCGTATTTCTCGAA 60.120 43.478 0.00 0.00 42.13 3.71
755 783 3.853671 GGCGTAACTCGTATTTCTCGAAA 59.146 43.478 0.00 0.00 42.13 3.46
756 784 4.027864 GGCGTAACTCGTATTTCTCGAAAG 60.028 45.833 0.00 0.00 42.13 2.62
828 858 2.162681 GTTCCTTGACCCAGTCCATTG 58.837 52.381 0.00 0.00 0.00 2.82
850 880 0.807667 CCCGCTCCAGAATTCTGTCG 60.808 60.000 29.03 25.88 42.27 4.35
896 926 2.612604 GTTTCGCTCTCTTCTTCCTCC 58.387 52.381 0.00 0.00 0.00 4.30
905 935 1.289530 TCTTCTTCCTCCTCCCTCTCC 59.710 57.143 0.00 0.00 0.00 3.71
906 936 1.007721 CTTCTTCCTCCTCCCTCTCCA 59.992 57.143 0.00 0.00 0.00 3.86
945 1015 1.977293 GCTCCCGCATCTTCTTCCCT 61.977 60.000 0.00 0.00 35.78 4.20
947 1017 1.821332 CCCGCATCTTCTTCCCTGC 60.821 63.158 0.00 0.00 0.00 4.85
948 1018 1.821332 CCGCATCTTCTTCCCTGCC 60.821 63.158 0.00 0.00 0.00 4.85
949 1019 1.821332 CGCATCTTCTTCCCTGCCC 60.821 63.158 0.00 0.00 0.00 5.36
950 1020 1.454663 GCATCTTCTTCCCTGCCCC 60.455 63.158 0.00 0.00 0.00 5.80
1243 1313 8.395633 GTGCGAATAGTTAGTTAAATTGTGGAT 58.604 33.333 0.00 0.00 0.00 3.41
1356 1436 8.822805 TGATAGTGTAATTAGTTTGGGACTCTT 58.177 33.333 0.00 0.00 39.86 2.85
1380 1460 4.584325 TGAATTTCCTTCTTGTCAAGTGGG 59.416 41.667 19.59 17.59 34.75 4.61
1483 1564 5.221742 TGGTGGCATCGTGGTATGATTATAA 60.222 40.000 0.00 0.00 0.00 0.98
1484 1565 5.880332 GGTGGCATCGTGGTATGATTATAAT 59.120 40.000 0.00 0.00 0.00 1.28
1518 1599 2.804986 TGCACATGTCCCATGTATGT 57.195 45.000 9.35 0.00 35.56 2.29
1620 1708 7.134163 CGATGCATCATGTCTAAATGCTTTAA 58.866 34.615 25.70 0.00 44.75 1.52
1647 1735 3.184382 TGGACTTCCCTCATGTACTCA 57.816 47.619 0.00 0.00 35.38 3.41
1722 1811 8.422566 ACCTCATTAGTTACTTATTAGCCTGTC 58.577 37.037 0.00 0.00 0.00 3.51
1731 1820 2.622064 ATTAGCCTGTCCGGTTCATC 57.378 50.000 0.00 0.00 34.25 2.92
2272 2466 1.303074 CACTGCCACAGCTGGTCAT 60.303 57.895 19.93 0.00 41.92 3.06
2324 2518 2.240279 CCGGTATACTAGGCTTCAGCT 58.760 52.381 2.25 0.00 41.70 4.24
2479 2673 4.534500 TGCTTGAAAGAGGGGTCTATTACA 59.466 41.667 0.00 0.00 0.00 2.41
2515 2709 0.037975 CACCACAGAAAATGCAGGCC 60.038 55.000 0.00 0.00 32.05 5.19
2623 2817 6.423001 GTGGGTATTACGCAAGGTAAGAATAG 59.577 42.308 14.38 0.00 43.96 1.73
2652 2846 4.452455 CCCAGAAACGATACATATCTTGCC 59.548 45.833 0.00 0.00 0.00 4.52
2813 3040 1.469940 CGCTCCGTCTTCTGCTTATGT 60.470 52.381 0.00 0.00 0.00 2.29
2912 3139 3.490759 ATCGTGCTGCCTTTCGCG 61.491 61.111 0.00 0.00 42.08 5.87
3350 3577 6.836007 TGTGTTATATCCTCTGATGTCACTCT 59.164 38.462 0.00 0.00 32.18 3.24
3470 3727 7.806690 TCTTGTGAACCTAAGAATCAAATTCG 58.193 34.615 0.00 0.00 43.92 3.34
3545 4068 2.683968 TCTGAAGGTTCACATACGTGC 58.316 47.619 0.00 0.00 43.28 5.34
3564 4087 4.554526 CGTGCTGCACTCAAGATGTTTTAA 60.555 41.667 28.04 0.00 31.34 1.52
3650 4178 6.357367 ACTTGTATGGTTCACATTCCTATCC 58.643 40.000 0.00 0.00 41.03 2.59
3877 4405 1.488705 TTGTGCCTGGGAGGTCGATT 61.489 55.000 0.00 0.00 37.80 3.34
3896 4424 7.065803 GGTCGATTATGGAAGTCATTTTCTTGA 59.934 37.037 0.00 0.00 37.30 3.02
3943 4472 3.204158 TGGAGAAAAAGGCCCTGCATATA 59.796 43.478 0.00 0.00 0.00 0.86
3971 4500 2.024176 TGACTTGGAGAAGGCCTACA 57.976 50.000 5.16 0.00 36.19 2.74
4055 4584 6.699575 ACATTACCCTCATTAAGAACATGC 57.300 37.500 0.00 0.00 0.00 4.06
4064 4593 9.234827 CCCTCATTAAGAACATGCATGATAATA 57.765 33.333 32.75 16.30 0.00 0.98
4092 4621 3.312421 ACAAGTGTTCGAACAAGTGATGG 59.688 43.478 32.89 21.26 41.21 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.688578 ACTTGACTAGCTCGTTAATCAAAGA 58.311 36.000 0.00 0.00 0.00 2.52
1 2 6.952935 ACTTGACTAGCTCGTTAATCAAAG 57.047 37.500 0.00 0.00 0.00 2.77
2 3 7.823665 TCTACTTGACTAGCTCGTTAATCAAA 58.176 34.615 0.00 0.00 0.00 2.69
3 4 7.387119 TCTACTTGACTAGCTCGTTAATCAA 57.613 36.000 0.00 0.00 0.00 2.57
4 5 6.038382 CCTCTACTTGACTAGCTCGTTAATCA 59.962 42.308 0.00 0.00 0.00 2.57
5 6 6.432107 CCTCTACTTGACTAGCTCGTTAATC 58.568 44.000 0.00 0.00 0.00 1.75
6 7 5.221087 GCCTCTACTTGACTAGCTCGTTAAT 60.221 44.000 0.00 0.00 0.00 1.40
7 8 4.096081 GCCTCTACTTGACTAGCTCGTTAA 59.904 45.833 0.00 0.00 0.00 2.01
8 9 3.626670 GCCTCTACTTGACTAGCTCGTTA 59.373 47.826 0.00 0.00 0.00 3.18
9 10 2.424246 GCCTCTACTTGACTAGCTCGTT 59.576 50.000 0.00 0.00 0.00 3.85
10 11 2.018515 GCCTCTACTTGACTAGCTCGT 58.981 52.381 0.00 0.00 0.00 4.18
11 12 2.017782 TGCCTCTACTTGACTAGCTCG 58.982 52.381 0.00 0.00 0.00 5.03
12 13 4.825085 AGTATGCCTCTACTTGACTAGCTC 59.175 45.833 0.00 0.00 0.00 4.09
13 14 4.798882 AGTATGCCTCTACTTGACTAGCT 58.201 43.478 0.00 0.00 0.00 3.32
14 15 5.766174 ACTAGTATGCCTCTACTTGACTAGC 59.234 44.000 0.00 0.00 38.86 3.42
15 16 6.993308 TCACTAGTATGCCTCTACTTGACTAG 59.007 42.308 0.00 0.00 40.35 2.57
16 17 6.766944 GTCACTAGTATGCCTCTACTTGACTA 59.233 42.308 0.00 0.00 36.95 2.59
17 18 5.591067 GTCACTAGTATGCCTCTACTTGACT 59.409 44.000 0.00 0.00 36.95 3.41
18 19 5.357314 TGTCACTAGTATGCCTCTACTTGAC 59.643 44.000 0.00 11.98 38.64 3.18
19 20 5.357314 GTGTCACTAGTATGCCTCTACTTGA 59.643 44.000 0.00 0.18 33.96 3.02
20 21 5.358442 AGTGTCACTAGTATGCCTCTACTTG 59.642 44.000 2.87 0.00 33.96 3.16
21 22 5.511363 AGTGTCACTAGTATGCCTCTACTT 58.489 41.667 2.87 0.00 33.96 2.24
22 23 5.104277 AGAGTGTCACTAGTATGCCTCTACT 60.104 44.000 5.21 0.00 36.04 2.57
23 24 5.008217 CAGAGTGTCACTAGTATGCCTCTAC 59.992 48.000 5.21 0.00 0.00 2.59
24 25 5.126779 CAGAGTGTCACTAGTATGCCTCTA 58.873 45.833 5.21 0.00 0.00 2.43
25 26 3.951037 CAGAGTGTCACTAGTATGCCTCT 59.049 47.826 5.21 1.89 0.00 3.69
26 27 3.697045 ACAGAGTGTCACTAGTATGCCTC 59.303 47.826 5.21 0.00 0.00 4.70
27 28 3.702792 ACAGAGTGTCACTAGTATGCCT 58.297 45.455 5.21 0.00 0.00 4.75
28 29 4.457834 AACAGAGTGTCACTAGTATGCC 57.542 45.455 5.21 0.00 0.00 4.40
29 30 5.230942 ACAAACAGAGTGTCACTAGTATGC 58.769 41.667 5.21 0.00 0.00 3.14
30 31 6.682746 AGACAAACAGAGTGTCACTAGTATG 58.317 40.000 5.21 5.56 46.44 2.39
31 32 6.902771 AGACAAACAGAGTGTCACTAGTAT 57.097 37.500 5.21 0.00 46.44 2.12
32 33 7.997773 ATAGACAAACAGAGTGTCACTAGTA 57.002 36.000 5.21 0.00 46.44 1.82
33 34 6.902771 ATAGACAAACAGAGTGTCACTAGT 57.097 37.500 5.21 5.11 46.44 2.57
37 38 9.803315 TGAATATATAGACAAACAGAGTGTCAC 57.197 33.333 7.26 0.00 46.44 3.67
38 39 9.803315 GTGAATATATAGACAAACAGAGTGTCA 57.197 33.333 7.26 0.00 46.44 3.58
39 40 9.803315 TGTGAATATATAGACAAACAGAGTGTC 57.197 33.333 0.00 0.00 44.75 3.67
40 41 9.587772 GTGTGAATATATAGACAAACAGAGTGT 57.412 33.333 7.14 0.00 0.00 3.55
41 42 9.586435 TGTGTGAATATATAGACAAACAGAGTG 57.414 33.333 9.49 0.00 0.00 3.51
57 58 8.783093 CCGGAAACATAATACATGTGTGAATAT 58.217 33.333 9.11 0.00 31.80 1.28
58 59 7.771361 ACCGGAAACATAATACATGTGTGAATA 59.229 33.333 9.46 0.00 31.80 1.75
59 60 6.601613 ACCGGAAACATAATACATGTGTGAAT 59.398 34.615 9.46 0.00 31.80 2.57
60 61 5.941058 ACCGGAAACATAATACATGTGTGAA 59.059 36.000 9.46 0.00 31.80 3.18
61 62 5.492895 ACCGGAAACATAATACATGTGTGA 58.507 37.500 9.46 0.00 31.80 3.58
62 63 5.811399 ACCGGAAACATAATACATGTGTG 57.189 39.130 9.46 4.81 31.80 3.82
63 64 7.925043 TTAACCGGAAACATAATACATGTGT 57.075 32.000 9.46 0.00 31.80 3.72
64 65 9.872757 GTATTAACCGGAAACATAATACATGTG 57.127 33.333 9.46 0.00 39.40 3.21
65 66 9.616156 TGTATTAACCGGAAACATAATACATGT 57.384 29.630 22.31 2.69 42.13 3.21
73 74 9.048446 GCTAGAATTGTATTAACCGGAAACATA 57.952 33.333 9.46 0.00 0.00 2.29
74 75 7.554835 TGCTAGAATTGTATTAACCGGAAACAT 59.445 33.333 9.46 0.00 0.00 2.71
75 76 6.879993 TGCTAGAATTGTATTAACCGGAAACA 59.120 34.615 9.46 1.34 0.00 2.83
76 77 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
77 78 7.771361 TCATGCTAGAATTGTATTAACCGGAAA 59.229 33.333 9.46 1.61 0.00 3.13
78 79 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
79 80 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
80 81 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
154 155 4.349342 ACTGAAGGAAATATGCCCTAGAGG 59.651 45.833 0.00 0.00 39.47 3.69
155 156 5.303971 CACTGAAGGAAATATGCCCTAGAG 58.696 45.833 0.00 0.46 31.36 2.43
156 157 4.103153 CCACTGAAGGAAATATGCCCTAGA 59.897 45.833 0.00 0.00 31.36 2.43
157 158 4.392940 CCACTGAAGGAAATATGCCCTAG 58.607 47.826 0.00 0.00 31.36 3.02
158 159 3.138283 CCCACTGAAGGAAATATGCCCTA 59.862 47.826 0.00 0.00 31.36 3.53
159 160 2.091665 CCCACTGAAGGAAATATGCCCT 60.092 50.000 0.00 0.00 0.00 5.19
160 161 2.310538 CCCACTGAAGGAAATATGCCC 58.689 52.381 0.00 0.00 0.00 5.36
161 162 2.952310 GACCCACTGAAGGAAATATGCC 59.048 50.000 0.00 0.00 0.00 4.40
162 163 2.614057 CGACCCACTGAAGGAAATATGC 59.386 50.000 0.00 0.00 0.00 3.14
163 164 3.206150 CCGACCCACTGAAGGAAATATG 58.794 50.000 0.00 0.00 0.00 1.78
164 165 2.421529 GCCGACCCACTGAAGGAAATAT 60.422 50.000 0.00 0.00 0.00 1.28
165 166 1.065709 GCCGACCCACTGAAGGAAATA 60.066 52.381 0.00 0.00 0.00 1.40
166 167 0.322546 GCCGACCCACTGAAGGAAAT 60.323 55.000 0.00 0.00 0.00 2.17
167 168 1.072505 GCCGACCCACTGAAGGAAA 59.927 57.895 0.00 0.00 0.00 3.13
168 169 2.144078 TGCCGACCCACTGAAGGAA 61.144 57.895 0.00 0.00 0.00 3.36
169 170 2.525629 TGCCGACCCACTGAAGGA 60.526 61.111 0.00 0.00 0.00 3.36
170 171 2.358737 GTGCCGACCCACTGAAGG 60.359 66.667 0.00 0.00 33.02 3.46
171 172 1.227823 TTGTGCCGACCCACTGAAG 60.228 57.895 0.00 0.00 36.68 3.02
172 173 1.525077 GTTGTGCCGACCCACTGAA 60.525 57.895 0.00 0.00 36.68 3.02
173 174 2.110213 GTTGTGCCGACCCACTGA 59.890 61.111 0.00 0.00 36.68 3.41
174 175 2.978010 GGTTGTGCCGACCCACTG 60.978 66.667 1.15 0.00 36.68 3.66
183 184 0.749454 CCTCATGCTAGGGTTGTGCC 60.749 60.000 0.00 0.00 32.55 5.01
376 390 1.815421 CACGCTGGCGGAAATAGCT 60.815 57.895 18.99 0.00 44.69 3.32
379 393 1.813753 GCTCACGCTGGCGGAAATA 60.814 57.895 18.99 0.00 44.69 1.40
400 414 0.391597 AGAAGAAGAAACCGCGGTCA 59.608 50.000 34.29 0.00 0.00 4.02
474 495 3.594747 TTCCCTCCCTCCATGGCCA 62.595 63.158 8.56 8.56 0.00 5.36
501 525 0.894835 CATTCCAAAAACCCTCCCGG 59.105 55.000 0.00 0.00 37.81 5.73
526 551 3.636764 GGGGACACAACACTCTCATTTTT 59.363 43.478 0.00 0.00 0.00 1.94
533 558 1.046472 TGTCGGGGACACAACACTCT 61.046 55.000 0.00 0.00 37.67 3.24
537 562 1.599518 GCATGTCGGGGACACAACA 60.600 57.895 0.00 0.00 45.65 3.33
553 578 4.329545 GTCCTTCACTGCCCCGCA 62.330 66.667 0.00 0.00 36.92 5.69
565 590 4.250305 ACGCACGCCCTTGTCCTT 62.250 61.111 0.00 0.00 0.00 3.36
594 619 1.212751 GTTGAAATGGACAGCGCCC 59.787 57.895 2.29 0.00 0.00 6.13
645 670 1.807742 CCGTTTTTATCCACCGCTGAA 59.192 47.619 0.00 0.00 0.00 3.02
648 673 1.310216 GCCCGTTTTTATCCACCGCT 61.310 55.000 0.00 0.00 0.00 5.52
653 678 2.354203 GCCAAATGCCCGTTTTTATCCA 60.354 45.455 0.00 0.00 0.00 3.41
667 692 2.656422 CGCGAAAGTAAACAGCCAAATG 59.344 45.455 0.00 0.00 0.00 2.32
668 693 2.920647 GCGCGAAAGTAAACAGCCAAAT 60.921 45.455 12.10 0.00 0.00 2.32
698 726 8.488764 GCTTGAGACTAAACGGACATAAATATC 58.511 37.037 0.00 0.00 0.00 1.63
699 727 7.169308 CGCTTGAGACTAAACGGACATAAATAT 59.831 37.037 0.00 0.00 0.00 1.28
700 728 6.474427 CGCTTGAGACTAAACGGACATAAATA 59.526 38.462 0.00 0.00 0.00 1.40
705 733 2.230508 TCGCTTGAGACTAAACGGACAT 59.769 45.455 0.00 0.00 0.00 3.06
736 764 9.513554 CTTTTTCTTTCGAGAAATACGAGTTAC 57.486 33.333 2.77 0.00 40.72 2.50
737 765 9.467258 TCTTTTTCTTTCGAGAAATACGAGTTA 57.533 29.630 2.77 0.00 40.72 2.24
771 799 0.671163 CCGCAACTACGTTAGGCCAA 60.671 55.000 5.01 0.00 0.00 4.52
772 800 1.079681 CCGCAACTACGTTAGGCCA 60.080 57.895 5.01 0.00 0.00 5.36
828 858 2.517166 GAATTCTGGAGCGGGGGC 60.517 66.667 0.00 0.00 0.00 5.80
850 880 2.222707 GGTTTGTTTTGTTGCTTGCGAC 60.223 45.455 6.06 6.06 0.00 5.19
1243 1313 2.875296 CCAACTGGGGAACTGAATGAA 58.125 47.619 0.00 0.00 0.00 2.57
1356 1436 5.068987 CCCACTTGACAAGAAGGAAATTCAA 59.931 40.000 21.95 0.00 40.67 2.69
1380 1460 2.743538 TGCAGGCAGACACGCATC 60.744 61.111 0.00 0.00 0.00 3.91
1540 1628 5.987019 TTATTGGCCAACTACCTATCCTT 57.013 39.130 23.27 2.23 0.00 3.36
1620 1708 4.939255 ACATGAGGGAAGTCCATTTTCAT 58.061 39.130 0.00 0.77 38.24 2.57
1647 1735 2.754946 ATGGTGTACCGACGAAATGT 57.245 45.000 0.00 0.00 39.43 2.71
1722 1811 6.073058 CCAATCATGTAACTATGATGAACCGG 60.073 42.308 0.00 0.00 44.74 5.28
1731 1820 6.927936 CAGAGGAGACCAATCATGTAACTATG 59.072 42.308 0.00 0.00 0.00 2.23
2297 2491 3.464111 GCCTAGTATACCGGCTCAAAA 57.536 47.619 20.81 0.00 40.62 2.44
2324 2518 8.849168 CCACATATAACTTCAGAATAAATGGCA 58.151 33.333 0.00 0.00 0.00 4.92
2479 2673 0.530288 GTGGCGCAAATGGTGGTATT 59.470 50.000 10.83 0.00 0.00 1.89
2515 2709 4.202305 GGAGTATCAGGAGGAATCAAGTGG 60.202 50.000 0.00 0.00 36.25 4.00
2623 2817 1.829222 TGTATCGTTTCTGGGAGGGAC 59.171 52.381 0.00 0.00 0.00 4.46
2695 2922 1.153667 GAAGCTCGAGCACCTCTGG 60.154 63.158 36.87 0.00 45.16 3.86
3275 3502 2.558795 TCGGACTTCTCAGAGAAAGGTG 59.441 50.000 14.01 5.11 33.19 4.00
3470 3727 2.159028 AGCCTCCTGACTAGCGAAAATC 60.159 50.000 0.00 0.00 0.00 2.17
3564 4087 5.936372 ACAGCAATGCGTCATCATAATCTAT 59.064 36.000 0.00 0.00 0.00 1.98
3859 4387 0.616395 TAATCGACCTCCCAGGCACA 60.616 55.000 0.00 0.00 39.63 4.57
3877 4405 8.038351 TGTCGTATCAAGAAAATGACTTCCATA 58.962 33.333 8.61 0.00 34.45 2.74
3896 4424 5.417894 TGTATCTCTCCACAAGTTGTCGTAT 59.582 40.000 5.27 0.00 0.00 3.06
3943 4472 4.392940 CCTTCTCCAAGTCAATGAACACT 58.607 43.478 0.00 0.00 0.00 3.55
3971 4500 4.330944 TGACATTCCGCGGTATCTTATT 57.669 40.909 27.15 2.04 0.00 1.40
4055 4584 8.603181 TCGAACACTTGTCACAATATTATCATG 58.397 33.333 0.00 0.00 0.00 3.07
4064 4593 4.394920 ACTTGTTCGAACACTTGTCACAAT 59.605 37.500 29.74 0.12 38.92 2.71
4092 4621 0.716108 CGGAAAGTCATCAGTGTCGC 59.284 55.000 0.00 0.00 0.00 5.19
4108 4637 3.531538 GTGCAGTCCTATTTTGATCGGA 58.468 45.455 0.00 0.00 0.00 4.55


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

AutoCloner maintained by Alex Coulton.