Multiple sequence alignment - TraesCS2D01G536600

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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 TraesCS2D01G536600 chr2D 100.000 3340 0 0 1 3340 618902556 618905895 0.000000e+00 6168.0
1 TraesCS2D01G536600 chr2D 83.274 562 76 8 1881 2426 586357438 586357997 4.970000e-138 501.0
2 TraesCS2D01G536600 chr2D 84.082 245 35 4 2435 2679 586358054 586358294 2.000000e-57 233.0
3 TraesCS2D01G536600 chr2D 86.869 198 21 4 2440 2633 618879003 618879199 2.020000e-52 217.0
4 TraesCS2D01G536600 chr2D 94.898 98 5 0 3243 3340 60774850 60774753 1.600000e-33 154.0
5 TraesCS2D01G536600 chr2D 97.778 45 0 1 833 877 578878832 578878875 3.570000e-10 76.8
6 TraesCS2D01G536600 chr2B 91.966 1394 91 10 1881 3256 756311817 756310427 0.000000e+00 1934.0
7 TraesCS2D01G536600 chr2B 91.894 1394 92 10 1881 3256 756326652 756325262 0.000000e+00 1929.0
8 TraesCS2D01G536600 chr2B 91.816 1393 94 9 1881 3256 756340953 756339564 0.000000e+00 1923.0
9 TraesCS2D01G536600 chr2B 83.837 563 72 9 1881 2426 708209013 708208453 4.940000e-143 518.0
10 TraesCS2D01G536600 chr2B 87.293 181 19 4 2440 2618 756176741 756176919 1.570000e-48 204.0
11 TraesCS2D01G536600 chr1B 96.128 1033 29 9 1 1029 22741691 22740666 0.000000e+00 1676.0
12 TraesCS2D01G536600 chr1B 96.288 862 28 2 1023 1881 22740634 22739774 0.000000e+00 1411.0
13 TraesCS2D01G536600 chr1B 95.604 91 4 0 3250 3340 565996684 565996594 2.690000e-31 147.0
14 TraesCS2D01G536600 chr1B 94.681 94 5 0 3247 3340 639103118 639103025 2.690000e-31 147.0
15 TraesCS2D01G536600 chr3A 91.176 884 64 8 147 1029 281226294 281225424 0.000000e+00 1188.0
16 TraesCS2D01G536600 chr3A 89.273 867 72 14 1023 1880 281225392 281224538 0.000000e+00 1066.0
17 TraesCS2D01G536600 chr3A 94.079 152 8 1 1 151 281228188 281228037 2.590000e-56 230.0
18 TraesCS2D01G536600 chr1A 86.735 490 32 17 1078 1553 584474979 584474509 6.390000e-142 514.0
19 TraesCS2D01G536600 chr1A 88.789 223 18 3 1661 1881 584474090 584473873 1.980000e-67 267.0
20 TraesCS2D01G536600 chr1A 88.462 130 5 4 1551 1670 584474447 584474318 7.470000e-32 148.0
21 TraesCS2D01G536600 chr1A 86.885 61 6 2 1836 1895 590712215 590712156 2.150000e-07 67.6
22 TraesCS2D01G536600 chr1A 89.796 49 4 1 1835 1882 71787348 71787300 1.000000e-05 62.1
23 TraesCS2D01G536600 chr2A 83.392 566 72 9 1881 2426 721589423 721588860 3.850000e-139 505.0
24 TraesCS2D01G536600 chr2A 85.654 237 32 2 2435 2670 721588804 721588569 7.160000e-62 248.0
25 TraesCS2D01G536600 chr2A 84.211 247 31 6 2435 2679 749866720 749866960 2.000000e-57 233.0
26 TraesCS2D01G536600 chr2A 93.750 48 3 0 830 877 42865697 42865744 4.620000e-09 73.1
27 TraesCS2D01G536600 chr2A 93.750 48 3 0 830 877 42945175 42945222 4.620000e-09 73.1
28 TraesCS2D01G536600 chr2A 93.750 48 3 0 830 877 42988409 42988456 4.620000e-09 73.1
29 TraesCS2D01G536600 chr2A 93.750 48 3 0 830 877 43032403 43032450 4.620000e-09 73.1
30 TraesCS2D01G536600 chr6B 87.645 259 28 3 1278 1533 657254638 657254381 7.010000e-77 298.0
31 TraesCS2D01G536600 chr4A 81.132 318 41 11 475 788 624125245 624124943 1.550000e-58 237.0
32 TraesCS2D01G536600 chr7A 96.774 93 3 0 3248 3340 36511297 36511389 4.460000e-34 156.0
33 TraesCS2D01G536600 chr7A 94.681 94 5 0 3247 3340 571691981 571692074 2.690000e-31 147.0
34 TraesCS2D01G536600 chr5D 96.667 90 3 0 3251 3340 468359063 468358974 2.080000e-32 150.0
35 TraesCS2D01G536600 chr5D 95.745 47 2 0 831 877 443263897 443263851 3.570000e-10 76.8
36 TraesCS2D01G536600 chr5B 93.878 98 6 0 3243 3340 562963086 562963183 7.470000e-32 148.0
37 TraesCS2D01G536600 chr1D 94.505 91 5 0 3250 3340 99831668 99831758 1.250000e-29 141.0
38 TraesCS2D01G536600 chr7D 92.708 96 7 0 3245 3340 595599982 595599887 4.490000e-29 139.0
39 TraesCS2D01G536600 chr7B 82.022 89 14 2 1785 1872 10242660 10242573 1.290000e-09 75.0
40 TraesCS2D01G536600 chr4D 95.556 45 2 0 833 877 133626257 133626301 4.620000e-09 73.1
41 TraesCS2D01G536600 chr4D 95.556 45 2 0 1837 1881 496937555 496937511 4.620000e-09 73.1
42 TraesCS2D01G536600 chr6D 93.333 45 3 0 1837 1881 97712155 97712111 2.150000e-07 67.6
43 TraesCS2D01G536600 chr3D 100.000 29 0 0 1850 1878 607577642 607577670 2.000000e-03 54.7


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 TraesCS2D01G536600 chr2D 618902556 618905895 3339 False 6168.000000 6168 100.000000 1 3340 1 chr2D.!!$F3 3339
1 TraesCS2D01G536600 chr2D 586357438 586358294 856 False 367.000000 501 83.678000 1881 2679 2 chr2D.!!$F4 798
2 TraesCS2D01G536600 chr2B 756310427 756311817 1390 True 1934.000000 1934 91.966000 1881 3256 1 chr2B.!!$R2 1375
3 TraesCS2D01G536600 chr2B 756325262 756326652 1390 True 1929.000000 1929 91.894000 1881 3256 1 chr2B.!!$R3 1375
4 TraesCS2D01G536600 chr2B 756339564 756340953 1389 True 1923.000000 1923 91.816000 1881 3256 1 chr2B.!!$R4 1375
5 TraesCS2D01G536600 chr2B 708208453 708209013 560 True 518.000000 518 83.837000 1881 2426 1 chr2B.!!$R1 545
6 TraesCS2D01G536600 chr1B 22739774 22741691 1917 True 1543.500000 1676 96.208000 1 1881 2 chr1B.!!$R3 1880
7 TraesCS2D01G536600 chr3A 281224538 281228188 3650 True 828.000000 1188 91.509333 1 1880 3 chr3A.!!$R1 1879
8 TraesCS2D01G536600 chr1A 584473873 584474979 1106 True 309.666667 514 87.995333 1078 1881 3 chr1A.!!$R3 803
9 TraesCS2D01G536600 chr2A 721588569 721589423 854 True 376.500000 505 84.523000 1881 2670 2 chr2A.!!$R1 789

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
462 2212 0.822944 CAACTGTGCCACCCATGACA 60.823 55.0 0.00 0.00 0.00 3.58 F
1020 2773 0.108804 TGACAGGAATTCCGTCTCGC 60.109 55.0 31.19 17.65 42.08 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 4307 0.321122 GTGCCCAACTCAGTGAGGAG 60.321 60.0 23.79 14.83 40.79 3.69 R
2660 4851 0.451783 CTAGTGGCGCCCATTTTCAC 59.548 55.0 26.77 13.80 35.28 3.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.220206 CTCTAGGCTGGGTGCACTG 59.780 63.158 17.98 8.62 45.15 3.66
186 1935 7.364522 TCTGTATTCTTGAGAAATCGGTTTG 57.635 36.000 0.00 0.00 37.61 2.93
241 1990 4.082571 CCAGGAGGACAAAGTTTAATGCAG 60.083 45.833 0.00 0.00 36.89 4.41
328 2078 2.290960 GGTAGGTTGCCCTCAGTTTGAT 60.291 50.000 0.00 0.00 41.45 2.57
462 2212 0.822944 CAACTGTGCCACCCATGACA 60.823 55.000 0.00 0.00 0.00 3.58
472 2223 4.350520 TGCCACCCATGACATATCATTCTA 59.649 41.667 0.00 0.00 43.40 2.10
506 2257 4.503296 CGGGACTATGAATTGGAACTAGGG 60.503 50.000 0.00 0.00 0.00 3.53
516 2267 7.935405 TGAATTGGAACTAGGGGTTAGTATTT 58.065 34.615 0.00 0.00 41.80 1.40
577 2328 8.746922 TGATGCAAATCAACTATTTCTTCAAC 57.253 30.769 0.00 0.00 35.54 3.18
662 2413 7.109501 ACTGTAGGCATGTCATATTTGTTGTA 58.890 34.615 0.00 0.00 0.00 2.41
663 2414 7.280876 ACTGTAGGCATGTCATATTTGTTGTAG 59.719 37.037 0.00 0.00 0.00 2.74
698 2449 1.690893 TCCTGCAGCAGATACTCCATC 59.309 52.381 24.90 0.00 32.44 3.51
699 2450 1.604947 CCTGCAGCAGATACTCCATCG 60.605 57.143 24.90 0.00 38.81 3.84
958 2711 2.925724 TGTGTGTCTCCAATCGGTTTT 58.074 42.857 0.00 0.00 0.00 2.43
961 2714 3.066203 GTGTGTCTCCAATCGGTTTTGTT 59.934 43.478 0.00 0.00 0.00 2.83
1002 2755 3.951563 TTTTCAGGGGGAGGTGATATG 57.048 47.619 0.00 0.00 0.00 1.78
1018 2771 4.985409 GTGATATGACAGGAATTCCGTCTC 59.015 45.833 31.19 24.94 42.08 3.36
1019 2772 2.586258 ATGACAGGAATTCCGTCTCG 57.414 50.000 31.19 18.52 42.08 4.04
1020 2773 0.108804 TGACAGGAATTCCGTCTCGC 60.109 55.000 31.19 17.65 42.08 5.03
1021 2774 0.173708 GACAGGAATTCCGTCTCGCT 59.826 55.000 27.68 7.94 42.08 4.93
1054 2843 4.041567 TGGAAGAAGGTTTCAGTGAGCATA 59.958 41.667 0.00 0.00 0.00 3.14
1220 3012 6.824305 AGTGTAAGTTTGCTAGATTTGCAT 57.176 33.333 0.00 0.00 40.34 3.96
1314 3106 3.358111 TTCAGTTCTTTGTGGTGTCCA 57.642 42.857 0.00 0.00 0.00 4.02
1378 3179 1.003464 TGCCAGTGTGTATGTGATGCT 59.997 47.619 0.00 0.00 0.00 3.79
1466 3267 6.012858 TCCTGAATTAGAATACACAACACCCT 60.013 38.462 0.00 0.00 0.00 4.34
1542 3350 5.049405 AGTGGTTTCTTTGCGATTAGAACAG 60.049 40.000 0.00 0.00 30.53 3.16
1606 3488 4.823989 CAGGATGATGGGGTCAATTAAGAC 59.176 45.833 0.00 0.00 40.97 3.01
1674 3793 1.954362 GACGGCTCAGTCTGGCTCAT 61.954 60.000 11.55 0.88 38.09 2.90
1836 3957 1.202806 CCCCATGCTATTGGACGATGT 60.203 52.381 0.00 0.00 39.25 3.06
1951 4072 0.517316 GTGGAAGTGATGTCAACGCC 59.483 55.000 0.00 0.00 0.00 5.68
1994 4115 2.530701 CTCCTCTACTATTGCCGGGAT 58.469 52.381 2.18 0.00 0.00 3.85
2000 4121 1.051812 ACTATTGCCGGGATGGAGAG 58.948 55.000 2.18 0.00 42.00 3.20
2120 4255 3.261897 ACCCACAACTCTTCCTATCTGTG 59.738 47.826 0.00 0.00 35.14 3.66
2159 4295 4.381292 CCATTTGGAAATGCAGGAGAAGAC 60.381 45.833 6.58 0.00 43.38 3.01
2186 4325 2.061220 CTCCTCACTGAGTTGGGCA 58.939 57.895 5.32 0.00 0.00 5.36
2282 4421 5.066505 GGATCTAAAACCTGCCAACATACTG 59.933 44.000 0.00 0.00 0.00 2.74
2316 4457 2.937149 GGTTCCAAAGATAGCGGACTTC 59.063 50.000 0.00 0.00 0.00 3.01
2352 4493 5.447010 GCTGTTTATTGATGAGCAGACAGAC 60.447 44.000 8.86 0.18 28.32 3.51
2385 4526 3.331150 ACAGACGCGGTATGATTGAAAA 58.669 40.909 12.47 0.00 0.00 2.29
2386 4527 3.124636 ACAGACGCGGTATGATTGAAAAC 59.875 43.478 12.47 0.00 0.00 2.43
2484 4673 1.476007 GCAGGGGATATGTCGCTCCT 61.476 60.000 6.48 0.00 37.45 3.69
2490 4679 2.229302 GGGATATGTCGCTCCTGAGTAC 59.771 54.545 0.00 0.00 34.67 2.73
2518 4707 2.436115 GGGCCCTGACGTACAAGC 60.436 66.667 17.04 0.00 0.00 4.01
2556 4746 1.470632 GGAGTCGTCTTGCTGGAGATG 60.471 57.143 0.00 0.00 34.63 2.90
2557 4747 1.203523 GAGTCGTCTTGCTGGAGATGT 59.796 52.381 5.03 0.00 34.86 3.06
2648 4839 0.397187 CCTCCCTGATGCATCCTCTG 59.603 60.000 23.67 10.93 0.00 3.35
2657 4848 3.265221 TGATGCATCCTCTGGTTTCTTCT 59.735 43.478 23.67 0.00 0.00 2.85
2660 4851 3.269178 GCATCCTCTGGTTTCTTCTCAG 58.731 50.000 0.00 0.00 0.00 3.35
2670 4861 4.584325 TGGTTTCTTCTCAGTGAAAATGGG 59.416 41.667 0.00 0.00 34.52 4.00
2671 4862 4.550422 GTTTCTTCTCAGTGAAAATGGGC 58.450 43.478 0.00 0.00 28.34 5.36
2730 4921 2.094026 GCCTGGGAATTGTGGAATCAAC 60.094 50.000 0.00 0.00 0.00 3.18
2754 4945 4.645809 GCGGGGAGCTTCTTGATT 57.354 55.556 0.00 0.00 44.04 2.57
2828 5019 1.661463 TCCAGATTGGCCTTCTCTGT 58.339 50.000 20.89 0.00 37.47 3.41
2887 5078 3.369546 AGTTGTGGCAATGCTAAACAC 57.630 42.857 4.82 5.27 0.00 3.32
2897 5088 2.340210 TGCTAAACACCAGCTCACAA 57.660 45.000 0.00 0.00 39.83 3.33
2927 5118 2.038659 CCACTGAAACCCACACCAAAT 58.961 47.619 0.00 0.00 0.00 2.32
2931 5122 1.883275 TGAAACCCACACCAAATAGCG 59.117 47.619 0.00 0.00 0.00 4.26
2977 5168 3.046280 CGAGCCGGACCTTCTTAAC 57.954 57.895 5.05 0.00 0.00 2.01
2994 5185 2.989422 AACGTGGCTATTTTGCTCAC 57.011 45.000 0.00 0.00 33.75 3.51
2996 5187 0.521242 CGTGGCTATTTTGCTCACGC 60.521 55.000 13.82 0.00 43.98 5.34
3000 5191 0.657840 GCTATTTTGCTCACGCGGAT 59.342 50.000 12.47 0.00 39.65 4.18
3014 5205 3.771160 GGATGTGACCCCGCGAGT 61.771 66.667 8.23 4.06 0.00 4.18
3032 5223 1.911269 TCCAGGCACGGAAGCTACA 60.911 57.895 0.00 0.00 29.93 2.74
3048 5239 2.596452 CTACAGTGTAGTGCTTCGGTG 58.404 52.381 20.29 0.00 0.00 4.94
3062 5259 0.040646 TCGGTGTATCAGGGTGAGGT 59.959 55.000 0.00 0.00 0.00 3.85
3082 5279 0.403271 AGTGGCAGTGCAAGAGGAAT 59.597 50.000 18.61 0.00 0.00 3.01
3083 5280 1.630369 AGTGGCAGTGCAAGAGGAATA 59.370 47.619 18.61 0.00 0.00 1.75
3085 5282 2.421424 GTGGCAGTGCAAGAGGAATAAG 59.579 50.000 18.61 0.00 0.00 1.73
3086 5283 1.403323 GGCAGTGCAAGAGGAATAAGC 59.597 52.381 18.61 0.00 0.00 3.09
3088 5285 2.943199 GCAGTGCAAGAGGAATAAGCCT 60.943 50.000 11.09 0.00 42.17 4.58
3095 5294 5.415701 TGCAAGAGGAATAAGCCTAAACTTG 59.584 40.000 0.00 0.00 39.00 3.16
3105 5304 2.010544 GCCTAAACTTGCTACCGGTCC 61.011 57.143 12.40 3.85 0.00 4.46
3128 5327 2.514592 CGGGACTTGCGGCATGAT 60.515 61.111 21.01 6.74 0.00 2.45
3142 5341 5.873712 TGCGGCATGATTTTGATGTTTATTT 59.126 32.000 0.00 0.00 0.00 1.40
3179 5378 2.070783 GATGTCGCCGTTGTTTTCCTA 58.929 47.619 0.00 0.00 0.00 2.94
3184 5383 2.028839 TCGCCGTTGTTTTCCTATCTGA 60.029 45.455 0.00 0.00 0.00 3.27
3190 5389 5.572896 CCGTTGTTTTCCTATCTGAATTTGC 59.427 40.000 0.00 0.00 0.00 3.68
3191 5390 6.381801 CGTTGTTTTCCTATCTGAATTTGCT 58.618 36.000 0.00 0.00 0.00 3.91
3192 5391 6.306356 CGTTGTTTTCCTATCTGAATTTGCTG 59.694 38.462 0.00 0.00 0.00 4.41
3193 5392 6.271488 TGTTTTCCTATCTGAATTTGCTGG 57.729 37.500 0.00 0.00 0.00 4.85
3194 5393 6.009589 TGTTTTCCTATCTGAATTTGCTGGA 58.990 36.000 0.00 0.00 0.00 3.86
3195 5394 6.493115 TGTTTTCCTATCTGAATTTGCTGGAA 59.507 34.615 0.00 0.00 0.00 3.53
3196 5395 6.515272 TTTCCTATCTGAATTTGCTGGAAC 57.485 37.500 0.00 0.00 32.87 3.62
3198 5397 5.819991 TCCTATCTGAATTTGCTGGAACTT 58.180 37.500 0.00 0.00 0.00 2.66
3199 5398 5.649395 TCCTATCTGAATTTGCTGGAACTTG 59.351 40.000 0.00 0.00 0.00 3.16
3200 5399 3.648339 TCTGAATTTGCTGGAACTTGC 57.352 42.857 0.00 0.00 0.00 4.01
3201 5400 3.225104 TCTGAATTTGCTGGAACTTGCT 58.775 40.909 0.00 0.00 0.00 3.91
3203 5402 2.064014 GAATTTGCTGGAACTTGCTGC 58.936 47.619 5.36 5.36 33.54 5.25
3204 5403 0.038892 ATTTGCTGGAACTTGCTGCG 60.039 50.000 7.48 0.00 35.55 5.18
3205 5404 2.074230 TTTGCTGGAACTTGCTGCGG 62.074 55.000 7.48 0.00 35.55 5.69
3206 5405 4.410743 GCTGGAACTTGCTGCGGC 62.411 66.667 11.65 11.65 39.26 6.53
3234 5435 0.036732 TGGAACTTACTGCCAGCCTG 59.963 55.000 0.00 0.00 0.00 4.85
3239 5440 0.038166 CTTACTGCCAGCCTGGGAAA 59.962 55.000 13.78 0.61 37.44 3.13
3250 5451 3.056607 CAGCCTGGGAAATCGATGTTTTT 60.057 43.478 0.00 0.00 0.00 1.94
3279 5480 8.447787 TTTGAAAAATCGAGCAAATTACTAGC 57.552 30.769 0.00 0.00 0.00 3.42
3280 5481 7.377766 TGAAAAATCGAGCAAATTACTAGCT 57.622 32.000 0.00 0.00 42.17 3.32
3281 5482 7.816640 TGAAAAATCGAGCAAATTACTAGCTT 58.183 30.769 0.00 0.00 39.02 3.74
3282 5483 7.750458 TGAAAAATCGAGCAAATTACTAGCTTG 59.250 33.333 0.00 0.00 39.02 4.01
3286 5487 6.589830 TCGAGCAAATTACTAGCTTGATTC 57.410 37.500 1.04 0.00 42.30 2.52
3287 5488 6.106003 TCGAGCAAATTACTAGCTTGATTCA 58.894 36.000 1.04 0.00 42.30 2.57
3288 5489 6.256539 TCGAGCAAATTACTAGCTTGATTCAG 59.743 38.462 1.04 0.00 42.30 3.02
3289 5490 6.256539 CGAGCAAATTACTAGCTTGATTCAGA 59.743 38.462 1.04 0.00 41.30 3.27
3290 5491 7.042187 CGAGCAAATTACTAGCTTGATTCAGAT 60.042 37.037 1.04 0.00 41.30 2.90
3291 5492 8.517062 AGCAAATTACTAGCTTGATTCAGATT 57.483 30.769 1.04 0.00 34.37 2.40
3292 5493 8.964772 AGCAAATTACTAGCTTGATTCAGATTT 58.035 29.630 1.04 0.00 34.37 2.17
3296 5497 9.618890 AATTACTAGCTTGATTCAGATTTAGCA 57.381 29.630 1.04 0.00 0.00 3.49
3297 5498 8.654230 TTACTAGCTTGATTCAGATTTAGCAG 57.346 34.615 1.04 7.30 0.00 4.24
3298 5499 6.882656 ACTAGCTTGATTCAGATTTAGCAGA 58.117 36.000 1.04 0.00 0.00 4.26
3299 5500 7.334090 ACTAGCTTGATTCAGATTTAGCAGAA 58.666 34.615 1.04 0.00 0.00 3.02
3300 5501 7.826252 ACTAGCTTGATTCAGATTTAGCAGAAA 59.174 33.333 1.04 0.00 0.00 2.52
3301 5502 7.086230 AGCTTGATTCAGATTTAGCAGAAAG 57.914 36.000 9.34 0.00 0.00 2.62
3302 5503 5.742926 GCTTGATTCAGATTTAGCAGAAAGC 59.257 40.000 3.05 0.00 46.19 3.51
3311 5512 3.972227 GCAGAAAGCAGCGGAAGA 58.028 55.556 0.00 0.00 44.79 2.87
3312 5513 2.247790 GCAGAAAGCAGCGGAAGAA 58.752 52.632 0.00 0.00 44.79 2.52
3313 5514 0.110010 GCAGAAAGCAGCGGAAGAAC 60.110 55.000 0.00 0.00 44.79 3.01
3314 5515 1.229428 CAGAAAGCAGCGGAAGAACA 58.771 50.000 0.00 0.00 0.00 3.18
3315 5516 1.603802 CAGAAAGCAGCGGAAGAACAA 59.396 47.619 0.00 0.00 0.00 2.83
3316 5517 1.604278 AGAAAGCAGCGGAAGAACAAC 59.396 47.619 0.00 0.00 0.00 3.32
3317 5518 1.333619 GAAAGCAGCGGAAGAACAACA 59.666 47.619 0.00 0.00 0.00 3.33
3318 5519 1.609208 AAGCAGCGGAAGAACAACAT 58.391 45.000 0.00 0.00 0.00 2.71
3319 5520 0.877071 AGCAGCGGAAGAACAACATG 59.123 50.000 0.00 0.00 0.00 3.21
3320 5521 0.109597 GCAGCGGAAGAACAACATGG 60.110 55.000 0.00 0.00 0.00 3.66
3321 5522 1.238439 CAGCGGAAGAACAACATGGT 58.762 50.000 0.00 0.00 0.00 3.55
3322 5523 1.069022 CAGCGGAAGAACAACATGGTG 60.069 52.381 9.83 9.83 0.00 4.17
3323 5524 1.202758 AGCGGAAGAACAACATGGTGA 60.203 47.619 19.90 0.00 0.00 4.02
3324 5525 1.606668 GCGGAAGAACAACATGGTGAA 59.393 47.619 19.90 0.00 0.00 3.18
3325 5526 2.350772 GCGGAAGAACAACATGGTGAAG 60.351 50.000 19.90 1.42 0.00 3.02
3326 5527 3.138304 CGGAAGAACAACATGGTGAAGA 58.862 45.455 19.90 0.00 0.00 2.87
3327 5528 3.753272 CGGAAGAACAACATGGTGAAGAT 59.247 43.478 19.90 0.17 0.00 2.40
3328 5529 4.142816 CGGAAGAACAACATGGTGAAGATC 60.143 45.833 19.90 9.98 0.00 2.75
3329 5530 4.156739 GGAAGAACAACATGGTGAAGATCC 59.843 45.833 19.90 15.09 0.00 3.36
3330 5531 3.338249 AGAACAACATGGTGAAGATCCG 58.662 45.455 19.90 0.00 0.00 4.18
3331 5532 3.007940 AGAACAACATGGTGAAGATCCGA 59.992 43.478 19.90 0.00 0.00 4.55
3332 5533 3.417069 ACAACATGGTGAAGATCCGAA 57.583 42.857 19.90 0.00 0.00 4.30
3333 5534 3.338249 ACAACATGGTGAAGATCCGAAG 58.662 45.455 19.90 0.00 0.00 3.79
3334 5535 3.007940 ACAACATGGTGAAGATCCGAAGA 59.992 43.478 19.90 0.00 0.00 2.87
3335 5536 4.194640 CAACATGGTGAAGATCCGAAGAT 58.805 43.478 4.15 0.00 34.57 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.428187 CGGTTGGGTGGTGCACTA 59.572 61.111 17.98 8.10 34.40 2.74
57 58 0.321653 ACTTGTGAATCGACTGCCCC 60.322 55.000 0.00 0.00 0.00 5.80
186 1935 4.985538 TGATCTTGCCATACCTAATTCCC 58.014 43.478 0.00 0.00 0.00 3.97
241 1990 2.115291 GCACCCGCAAAGGATCTCC 61.115 63.158 0.00 0.00 45.00 3.71
328 2078 9.964354 TCAATCAGATTTTAGAAATTGAGGAGA 57.036 29.630 0.00 0.00 31.50 3.71
462 2212 8.621286 GTCCCGTTTCACAAAATAGAATGATAT 58.379 33.333 0.00 0.00 0.00 1.63
472 2223 6.834168 ATTCATAGTCCCGTTTCACAAAAT 57.166 33.333 0.00 0.00 0.00 1.82
577 2328 1.299541 ATTACAGCGAGGAATTGCCG 58.700 50.000 0.00 0.00 43.43 5.69
698 2449 2.809696 TGACATGCCTATGATCAATGCG 59.190 45.455 0.00 0.00 37.73 4.73
699 2450 6.317893 TGATATGACATGCCTATGATCAATGC 59.682 38.462 0.00 3.38 37.73 3.56
958 2711 5.292765 TGCAACAAGTTCTTGTTTCAAACA 58.707 33.333 22.90 15.00 42.69 2.83
961 2714 7.172190 TGAAAATGCAACAAGTTCTTGTTTCAA 59.828 29.630 24.94 15.81 42.69 2.69
975 2728 1.631405 CTCCCCCTGAAAATGCAACA 58.369 50.000 0.00 0.00 0.00 3.33
1002 2755 0.173708 AGCGAGACGGAATTCCTGTC 59.826 55.000 27.70 27.70 38.73 3.51
1018 2771 0.394192 TCTTCCAGGGATGCATAGCG 59.606 55.000 0.00 0.00 0.00 4.26
1019 2772 2.502295 CTTCTTCCAGGGATGCATAGC 58.498 52.381 0.00 0.00 0.00 2.97
1020 2773 2.441001 ACCTTCTTCCAGGGATGCATAG 59.559 50.000 0.00 0.00 38.42 2.23
1021 2774 2.492025 ACCTTCTTCCAGGGATGCATA 58.508 47.619 0.00 0.00 38.42 3.14
1054 2843 0.110486 AACACTCCGGTGCTTGGATT 59.890 50.000 0.00 0.00 46.57 3.01
1220 3012 1.398041 CTGCTCCGCAAATCGAATTCA 59.602 47.619 6.22 0.00 38.41 2.57
1314 3106 1.271054 ACTTCTTGCTTGCGTCAGGAT 60.271 47.619 0.00 0.00 0.00 3.24
1378 3179 5.220970 GGAACTCAAGTTGACAATCGGAAAA 60.221 40.000 0.08 0.00 38.56 2.29
1466 3267 7.252612 TCCTCCAAACAGATTCTACATTACA 57.747 36.000 0.00 0.00 0.00 2.41
1542 3350 2.489938 TGACCATTGGCCTAACAGTC 57.510 50.000 3.32 6.00 0.00 3.51
1606 3488 5.289193 CCAACCATGAATTTAATGCAACTCG 59.711 40.000 0.00 0.00 0.00 4.18
1802 3923 0.994247 ATGGGGATCTGTGCTGTCAA 59.006 50.000 0.00 0.00 0.00 3.18
1836 3957 4.458397 GGCTCAGATGATCCTGAAATCAA 58.542 43.478 3.67 0.00 42.05 2.57
1951 4072 1.843368 AGCAAGATTGACATGGGTGG 58.157 50.000 0.00 0.00 0.00 4.61
1994 4115 4.048600 AGACTAGTATCCACTCCTCTCCA 58.951 47.826 0.00 0.00 36.14 3.86
2000 4121 4.751098 CACTCGTAGACTAGTATCCACTCC 59.249 50.000 0.00 0.00 36.14 3.85
2108 4243 3.274288 GAGGCCAAACACAGATAGGAAG 58.726 50.000 5.01 0.00 0.00 3.46
2120 4255 0.827507 ATGGGTGTGTGAGGCCAAAC 60.828 55.000 5.01 2.59 0.00 2.93
2168 4307 0.321122 GTGCCCAACTCAGTGAGGAG 60.321 60.000 23.79 14.83 40.79 3.69
2186 4325 4.634443 CCTCGAATTATTTCCCGTCTTTGT 59.366 41.667 0.00 0.00 0.00 2.83
2282 4421 1.301479 GGAACCCACGTCACTGACC 60.301 63.158 3.50 0.00 0.00 4.02
2352 4493 2.451132 CGCGTCTGTACTAATGTCAGG 58.549 52.381 0.00 0.00 0.00 3.86
2385 4526 5.640147 TGAAAACATTAGATGGGTTGGAGT 58.360 37.500 0.00 0.00 33.60 3.85
2386 4527 6.780457 ATGAAAACATTAGATGGGTTGGAG 57.220 37.500 0.00 0.00 33.60 3.86
2456 4645 4.761739 CGACATATCCCCTGCATTTAACAT 59.238 41.667 0.00 0.00 0.00 2.71
2484 4673 1.694693 GCCCCTTCCCCTATGTACTCA 60.695 57.143 0.00 0.00 0.00 3.41
2518 4707 5.298197 ACTCCGAAGCTATATACATCACG 57.702 43.478 0.00 0.00 0.00 4.35
2556 4746 2.687935 TGTTCTCCTTTTGCCACTGAAC 59.312 45.455 0.00 0.00 34.66 3.18
2557 4747 3.011566 TGTTCTCCTTTTGCCACTGAA 57.988 42.857 0.00 0.00 0.00 3.02
2648 4839 4.559502 GCCCATTTTCACTGAGAAGAAACC 60.560 45.833 4.80 0.00 37.57 3.27
2657 4848 1.228398 TGGCGCCCATTTTCACTGA 60.228 52.632 26.77 0.00 0.00 3.41
2660 4851 0.451783 CTAGTGGCGCCCATTTTCAC 59.548 55.000 26.77 13.80 35.28 3.18
2708 4899 0.740737 GATTCCACAATTCCCAGGCG 59.259 55.000 0.00 0.00 0.00 5.52
2754 4945 3.810188 TTCACCACCCACCGCCAA 61.810 61.111 0.00 0.00 0.00 4.52
2849 5040 3.248043 TTCAGACATTGAAGGCCCG 57.752 52.632 0.00 0.00 40.82 6.13
2887 5078 1.002868 CTGGGGAGTTGTGAGCTGG 60.003 63.158 0.00 0.00 0.00 4.85
2897 5088 1.774217 TTTCAGTGGCCTGGGGAGT 60.774 57.895 3.32 0.00 39.31 3.85
2976 5167 0.796312 CGTGAGCAAAATAGCCACGT 59.204 50.000 16.23 0.00 45.42 4.49
2977 5168 3.586039 CGTGAGCAAAATAGCCACG 57.414 52.632 12.71 12.71 45.32 4.94
3009 5200 4.373116 TTCCGTGCCTGGACTCGC 62.373 66.667 0.00 0.00 37.89 5.03
3014 5205 1.888436 CTGTAGCTTCCGTGCCTGGA 61.888 60.000 0.00 0.00 35.83 3.86
3022 5213 1.202582 AGCACTACACTGTAGCTTCCG 59.797 52.381 15.05 2.08 29.98 4.30
3032 5223 2.823747 TGATACACCGAAGCACTACACT 59.176 45.455 0.00 0.00 0.00 3.55
3048 5239 1.413077 GCCACTACCTCACCCTGATAC 59.587 57.143 0.00 0.00 0.00 2.24
3062 5259 1.055849 TTCCTCTTGCACTGCCACTA 58.944 50.000 0.00 0.00 0.00 2.74
3082 5279 2.568509 ACCGGTAGCAAGTTTAGGCTTA 59.431 45.455 4.49 0.00 41.41 3.09
3083 5280 1.350019 ACCGGTAGCAAGTTTAGGCTT 59.650 47.619 4.49 0.00 41.41 4.35
3085 5282 1.366679 GACCGGTAGCAAGTTTAGGC 58.633 55.000 7.34 0.00 0.00 3.93
3086 5283 1.738030 CGGACCGGTAGCAAGTTTAGG 60.738 57.143 7.34 0.00 0.00 2.69
3088 5285 0.247185 CCGGACCGGTAGCAAGTTTA 59.753 55.000 25.54 0.00 42.73 2.01
3111 5310 1.656818 AAATCATGCCGCAAGTCCCG 61.657 55.000 0.00 0.00 0.00 5.14
3114 5313 2.634982 TCAAAATCATGCCGCAAGTC 57.365 45.000 0.00 0.00 0.00 3.01
3158 5357 0.109919 GGAAAACAACGGCGACATCC 60.110 55.000 16.62 8.47 0.00 3.51
3162 5361 2.093783 CAGATAGGAAAACAACGGCGAC 59.906 50.000 16.62 0.00 0.00 5.19
3168 5367 6.587608 CCAGCAAATTCAGATAGGAAAACAAC 59.412 38.462 0.00 0.00 0.00 3.32
3179 5378 3.830755 AGCAAGTTCCAGCAAATTCAGAT 59.169 39.130 0.00 0.00 0.00 2.90
3184 5383 1.603678 CGCAGCAAGTTCCAGCAAATT 60.604 47.619 0.00 0.00 0.00 1.82
3199 5398 1.444895 CCAACAATCTTGCCGCAGC 60.445 57.895 0.00 0.00 40.48 5.25
3200 5399 0.597568 TTCCAACAATCTTGCCGCAG 59.402 50.000 0.00 0.00 0.00 5.18
3201 5400 0.313672 GTTCCAACAATCTTGCCGCA 59.686 50.000 0.00 0.00 0.00 5.69
3203 5402 3.502211 AGTAAGTTCCAACAATCTTGCCG 59.498 43.478 0.00 0.00 0.00 5.69
3204 5403 4.798574 CAGTAAGTTCCAACAATCTTGCC 58.201 43.478 0.00 0.00 0.00 4.52
3205 5404 4.229876 GCAGTAAGTTCCAACAATCTTGC 58.770 43.478 0.00 0.00 0.00 4.01
3206 5405 4.278170 TGGCAGTAAGTTCCAACAATCTTG 59.722 41.667 0.00 0.00 0.00 3.02
3208 5407 4.074970 CTGGCAGTAAGTTCCAACAATCT 58.925 43.478 6.28 0.00 0.00 2.40
3253 5454 8.911662 GCTAGTAATTTGCTCGATTTTTCAAAA 58.088 29.630 0.00 0.00 32.97 2.44
3256 5457 7.377766 AGCTAGTAATTTGCTCGATTTTTCA 57.622 32.000 0.00 0.00 32.13 2.69
3257 5458 7.962918 TCAAGCTAGTAATTTGCTCGATTTTTC 59.037 33.333 0.00 0.00 36.86 2.29
3258 5459 7.816640 TCAAGCTAGTAATTTGCTCGATTTTT 58.183 30.769 0.00 0.00 36.86 1.94
3259 5460 7.377766 TCAAGCTAGTAATTTGCTCGATTTT 57.622 32.000 0.00 0.00 36.86 1.82
3260 5461 6.985188 TCAAGCTAGTAATTTGCTCGATTT 57.015 33.333 0.00 0.00 36.86 2.17
3261 5462 7.280876 TGAATCAAGCTAGTAATTTGCTCGATT 59.719 33.333 0.00 0.00 41.73 3.34
3262 5463 6.763135 TGAATCAAGCTAGTAATTTGCTCGAT 59.237 34.615 0.00 0.00 36.86 3.59
3263 5464 6.106003 TGAATCAAGCTAGTAATTTGCTCGA 58.894 36.000 0.00 0.00 36.86 4.04
3264 5465 6.256539 TCTGAATCAAGCTAGTAATTTGCTCG 59.743 38.462 0.00 0.00 36.86 5.03
3265 5466 7.545362 TCTGAATCAAGCTAGTAATTTGCTC 57.455 36.000 0.00 0.00 36.86 4.26
3266 5467 8.517062 AATCTGAATCAAGCTAGTAATTTGCT 57.483 30.769 0.00 0.00 39.64 3.91
3270 5471 9.618890 TGCTAAATCTGAATCAAGCTAGTAATT 57.381 29.630 5.60 0.00 0.00 1.40
3271 5472 9.270640 CTGCTAAATCTGAATCAAGCTAGTAAT 57.729 33.333 5.60 0.00 0.00 1.89
3272 5473 8.478066 TCTGCTAAATCTGAATCAAGCTAGTAA 58.522 33.333 5.60 0.00 0.00 2.24
3273 5474 8.011844 TCTGCTAAATCTGAATCAAGCTAGTA 57.988 34.615 5.60 0.00 0.00 1.82
3274 5475 6.882656 TCTGCTAAATCTGAATCAAGCTAGT 58.117 36.000 5.60 0.00 0.00 2.57
3275 5476 7.783090 TTCTGCTAAATCTGAATCAAGCTAG 57.217 36.000 5.60 2.59 0.00 3.42
3276 5477 7.201679 GCTTTCTGCTAAATCTGAATCAAGCTA 60.202 37.037 5.60 0.00 38.95 3.32
3277 5478 6.404513 GCTTTCTGCTAAATCTGAATCAAGCT 60.405 38.462 5.60 0.00 38.95 3.74
3278 5479 5.742926 GCTTTCTGCTAAATCTGAATCAAGC 59.257 40.000 0.00 0.00 38.95 4.01
3279 5480 6.849502 TGCTTTCTGCTAAATCTGAATCAAG 58.150 36.000 0.00 0.00 43.37 3.02
3280 5481 6.624423 GCTGCTTTCTGCTAAATCTGAATCAA 60.624 38.462 0.00 0.00 43.37 2.57
3281 5482 5.163683 GCTGCTTTCTGCTAAATCTGAATCA 60.164 40.000 0.00 0.00 43.37 2.57
3282 5483 5.272397 GCTGCTTTCTGCTAAATCTGAATC 58.728 41.667 0.00 0.00 43.37 2.52
3283 5484 4.201891 CGCTGCTTTCTGCTAAATCTGAAT 60.202 41.667 0.00 0.00 43.37 2.57
3284 5485 3.125829 CGCTGCTTTCTGCTAAATCTGAA 59.874 43.478 0.00 0.00 43.37 3.02
3285 5486 2.674852 CGCTGCTTTCTGCTAAATCTGA 59.325 45.455 0.00 0.00 43.37 3.27
3286 5487 2.223203 CCGCTGCTTTCTGCTAAATCTG 60.223 50.000 0.00 0.00 43.37 2.90
3287 5488 2.012673 CCGCTGCTTTCTGCTAAATCT 58.987 47.619 0.00 0.00 43.37 2.40
3288 5489 2.009774 TCCGCTGCTTTCTGCTAAATC 58.990 47.619 0.00 0.00 43.37 2.17
3289 5490 2.113860 TCCGCTGCTTTCTGCTAAAT 57.886 45.000 0.00 0.00 43.37 1.40
3290 5491 1.806542 CTTCCGCTGCTTTCTGCTAAA 59.193 47.619 0.00 0.00 43.37 1.85
3291 5492 1.001974 TCTTCCGCTGCTTTCTGCTAA 59.998 47.619 0.00 0.00 43.37 3.09
3292 5493 0.608130 TCTTCCGCTGCTTTCTGCTA 59.392 50.000 0.00 0.00 43.37 3.49
3293 5494 0.250467 TTCTTCCGCTGCTTTCTGCT 60.250 50.000 0.00 0.00 43.37 4.24
3294 5495 0.110010 GTTCTTCCGCTGCTTTCTGC 60.110 55.000 0.00 0.00 43.25 4.26
3295 5496 1.229428 TGTTCTTCCGCTGCTTTCTG 58.771 50.000 0.00 0.00 0.00 3.02
3296 5497 1.604278 GTTGTTCTTCCGCTGCTTTCT 59.396 47.619 0.00 0.00 0.00 2.52
3297 5498 1.333619 TGTTGTTCTTCCGCTGCTTTC 59.666 47.619 0.00 0.00 0.00 2.62
3298 5499 1.388547 TGTTGTTCTTCCGCTGCTTT 58.611 45.000 0.00 0.00 0.00 3.51
3299 5500 1.267806 CATGTTGTTCTTCCGCTGCTT 59.732 47.619 0.00 0.00 0.00 3.91
3300 5501 0.877071 CATGTTGTTCTTCCGCTGCT 59.123 50.000 0.00 0.00 0.00 4.24
3301 5502 0.109597 CCATGTTGTTCTTCCGCTGC 60.110 55.000 0.00 0.00 0.00 5.25
3302 5503 1.069022 CACCATGTTGTTCTTCCGCTG 60.069 52.381 0.00 0.00 0.00 5.18
3303 5504 1.202758 TCACCATGTTGTTCTTCCGCT 60.203 47.619 0.00 0.00 0.00 5.52
3304 5505 1.234821 TCACCATGTTGTTCTTCCGC 58.765 50.000 0.00 0.00 0.00 5.54
3305 5506 3.138304 TCTTCACCATGTTGTTCTTCCG 58.862 45.455 0.00 0.00 0.00 4.30
3306 5507 4.156739 GGATCTTCACCATGTTGTTCTTCC 59.843 45.833 0.00 0.00 0.00 3.46
3307 5508 4.142816 CGGATCTTCACCATGTTGTTCTTC 60.143 45.833 0.00 0.00 0.00 2.87
3308 5509 3.753272 CGGATCTTCACCATGTTGTTCTT 59.247 43.478 0.00 0.00 0.00 2.52
3309 5510 3.007940 TCGGATCTTCACCATGTTGTTCT 59.992 43.478 0.00 0.00 0.00 3.01
3310 5511 3.334691 TCGGATCTTCACCATGTTGTTC 58.665 45.455 0.00 0.00 0.00 3.18
3311 5512 3.417069 TCGGATCTTCACCATGTTGTT 57.583 42.857 0.00 0.00 0.00 2.83
3312 5513 3.007940 TCTTCGGATCTTCACCATGTTGT 59.992 43.478 0.00 0.00 0.00 3.32
3313 5514 3.599343 TCTTCGGATCTTCACCATGTTG 58.401 45.455 0.00 0.00 0.00 3.33
3314 5515 3.981071 TCTTCGGATCTTCACCATGTT 57.019 42.857 0.00 0.00 0.00 2.71
3315 5516 4.065321 GATCTTCGGATCTTCACCATGT 57.935 45.455 0.00 0.00 45.34 3.21


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

AutoCloner maintained by Alex Coulton.