Multiple sequence alignment - TraesCS4D01G211900

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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 TraesCS4D01G211900 chr4D 100.000 4837 0 0 1 4837 364548706 364543870 0.000000e+00 8933.0
1 TraesCS4D01G211900 chr4D 98.182 165 3 0 4265 4429 281177251 281177087 6.130000e-74 289.0
2 TraesCS4D01G211900 chr4D 95.977 174 6 1 4255 4428 16666771 16666599 1.020000e-71 281.0
3 TraesCS4D01G211900 chr4B 92.019 2794 95 38 1 2716 449649412 449646669 0.000000e+00 3807.0
4 TraesCS4D01G211900 chr4B 90.781 1421 38 30 2772 4138 449646583 449645202 0.000000e+00 1812.0
5 TraesCS4D01G211900 chr4B 95.276 381 5 5 4457 4837 449645034 449644667 4.170000e-165 592.0
6 TraesCS4D01G211900 chr4B 90.798 163 15 0 4104 4266 449645198 449645036 8.150000e-53 219.0
7 TraesCS4D01G211900 chr4B 90.000 50 5 0 4435 4484 427496673 427496722 1.120000e-06 65.8
8 TraesCS4D01G211900 chr4A 89.201 1889 73 30 469 2318 100666236 100668032 0.000000e+00 2237.0
9 TraesCS4D01G211900 chr4A 89.139 1777 71 37 2439 4138 100668069 100669800 0.000000e+00 2100.0
10 TraesCS4D01G211900 chr4A 94.550 367 12 7 4471 4837 100671585 100671943 1.180000e-155 560.0
11 TraesCS4D01G211900 chr4A 86.269 386 15 5 35 418 100665870 100666219 7.590000e-103 385.0
12 TraesCS4D01G211900 chr4A 94.286 35 1 1 4458 4491 692728181 692728147 9.000000e-03 52.8
13 TraesCS4D01G211900 chr3D 100.000 167 0 0 4265 4431 488387660 488387494 4.700000e-80 309.0
14 TraesCS4D01G211900 chr3D 97.661 171 4 0 4258 4428 495237646 495237816 1.320000e-75 294.0
15 TraesCS4D01G211900 chr7D 97.688 173 4 0 4257 4429 285787 285959 1.020000e-76 298.0
16 TraesCS4D01G211900 chrUn 98.193 166 3 0 4265 4430 90921968 90922133 1.700000e-74 291.0
17 TraesCS4D01G211900 chrUn 97.143 35 0 1 4458 4491 326972463 326972497 1.880000e-04 58.4
18 TraesCS4D01G211900 chrUn 97.143 35 0 1 4458 4491 326975489 326975523 1.880000e-04 58.4
19 TraesCS4D01G211900 chrUn 97.143 35 0 1 4458 4491 345995471 345995505 1.880000e-04 58.4
20 TraesCS4D01G211900 chr2D 97.633 169 4 0 4265 4433 18206976 18207144 1.700000e-74 291.0
21 TraesCS4D01G211900 chr2D 98.193 166 3 0 4265 4430 330215064 330215229 1.700000e-74 291.0
22 TraesCS4D01G211900 chr2D 94.286 35 0 1 4457 4489 23306031 23305997 9.000000e-03 52.8
23 TraesCS4D01G211900 chr3A 95.480 177 7 1 4257 4432 41183449 41183273 1.020000e-71 281.0
24 TraesCS4D01G211900 chr5B 76.106 226 41 12 4210 4431 362131006 362131222 6.620000e-19 106.0
25 TraesCS4D01G211900 chr7B 100.000 31 0 0 4461 4491 518910658 518910628 1.880000e-04 58.4


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 TraesCS4D01G211900 chr4D 364543870 364548706 4836 True 8933.0 8933 100.00000 1 4837 1 chr4D.!!$R3 4836
1 TraesCS4D01G211900 chr4B 449644667 449649412 4745 True 1607.5 3807 92.21850 1 4837 4 chr4B.!!$R1 4836
2 TraesCS4D01G211900 chr4A 100665870 100671943 6073 False 1320.5 2237 89.78975 35 4837 4 chr4A.!!$F1 4802

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
269 273 0.328258 ACCGTTAGGGATTGCTTGCT 59.672 50.0 0.00 0.0 43.47 3.91 F
957 978 0.692476 ACACTTGGCCATACAGAGCA 59.308 50.0 6.09 0.0 0.00 4.26 F
2339 2403 0.429736 CGCTTCGTACGCATATTCGG 59.570 55.0 11.24 0.0 0.00 4.30 F
3070 3277 0.327924 TCACGGCTGATGATTTGGGT 59.672 50.0 0.00 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 2056 0.734889 ATTGCGTTCAGTAGCATGCC 59.265 50.0 15.66 0.00 43.42 4.40 R
2496 2585 0.528901 GGGCGATGCATGTACGTACA 60.529 55.0 29.15 29.15 40.98 2.90 R
3345 3552 0.322277 ACTTGATCTGCAGCAGGTGG 60.322 55.0 22.62 10.04 31.51 4.61 R
4676 6435 0.389817 TGGTCCTTGTGCGATTCTCG 60.390 55.0 0.00 0.00 43.89 4.04 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
75 76 4.083862 GAAAGGGACTCGGGCGCT 62.084 66.667 7.64 0.00 38.49 5.92
263 267 3.689649 CCAGAAGAAACCGTTAGGGATTG 59.310 47.826 0.00 0.00 43.47 2.67
264 268 3.127030 CAGAAGAAACCGTTAGGGATTGC 59.873 47.826 0.00 0.00 43.47 3.56
265 269 3.009143 AGAAGAAACCGTTAGGGATTGCT 59.991 43.478 0.00 0.00 43.47 3.91
266 270 3.434940 AGAAACCGTTAGGGATTGCTT 57.565 42.857 0.00 0.00 43.47 3.91
267 271 3.081804 AGAAACCGTTAGGGATTGCTTG 58.918 45.455 0.00 0.00 43.47 4.01
268 272 1.173913 AACCGTTAGGGATTGCTTGC 58.826 50.000 0.00 0.00 43.47 4.01
269 273 0.328258 ACCGTTAGGGATTGCTTGCT 59.672 50.000 0.00 0.00 43.47 3.91
270 274 1.017387 CCGTTAGGGATTGCTTGCTC 58.983 55.000 0.00 0.00 38.47 4.26
326 330 3.165058 TGAACGATGTGATGGTAGCTC 57.835 47.619 0.00 0.00 0.00 4.09
537 542 4.633175 TGTAGTTGGCGAGTAAAACATGA 58.367 39.130 0.00 0.00 0.00 3.07
955 976 2.086869 CCAACACTTGGCCATACAGAG 58.913 52.381 6.09 2.21 45.17 3.35
956 977 1.470098 CAACACTTGGCCATACAGAGC 59.530 52.381 6.09 0.00 0.00 4.09
957 978 0.692476 ACACTTGGCCATACAGAGCA 59.308 50.000 6.09 0.00 0.00 4.26
958 979 1.339438 ACACTTGGCCATACAGAGCAG 60.339 52.381 6.09 0.00 0.00 4.24
962 983 0.979709 TGGCCATACAGAGCAGAGCT 60.980 55.000 0.00 0.00 43.88 4.09
1002 1023 4.783621 GCATCCACGGAGCCAGCA 62.784 66.667 0.00 0.00 0.00 4.41
1403 1427 1.645034 CCATTGTACGTCCAGCTCTG 58.355 55.000 0.00 0.00 0.00 3.35
1409 1433 1.632948 TACGTCCAGCTCTGACGACG 61.633 60.000 31.23 21.90 44.75 5.12
1567 1592 2.743928 GGAGTGGGCGCTGAACAG 60.744 66.667 7.64 0.00 0.00 3.16
2147 2208 0.815734 TAGACAGCTTACGCCTGGAC 59.184 55.000 0.00 0.00 36.60 4.02
2148 2209 0.900647 AGACAGCTTACGCCTGGACT 60.901 55.000 0.00 0.00 36.60 3.85
2149 2210 0.737715 GACAGCTTACGCCTGGACTG 60.738 60.000 0.00 0.00 36.60 3.51
2284 2345 4.696877 TGCTAACATGGACATGAACTTCTG 59.303 41.667 18.38 3.50 41.20 3.02
2333 2397 2.158959 GCTGACGCTTCGTACGCAT 61.159 57.895 11.24 0.00 41.37 4.73
2339 2403 0.429736 CGCTTCGTACGCATATTCGG 59.570 55.000 11.24 0.00 0.00 4.30
2372 2436 0.753262 ACGAGCAGGCAGGGTAATAG 59.247 55.000 0.00 0.00 0.00 1.73
2374 2438 1.961394 CGAGCAGGCAGGGTAATAGTA 59.039 52.381 0.00 0.00 0.00 1.82
2375 2439 2.288273 CGAGCAGGCAGGGTAATAGTAC 60.288 54.545 0.00 0.00 0.00 2.73
2385 2468 2.686119 GGTAATAGTACCTGGGGCAGA 58.314 52.381 12.14 0.00 45.72 4.26
2489 2572 2.461695 AGAGGGACGTTGATCATCACT 58.538 47.619 0.00 0.00 0.00 3.41
2495 2584 4.097437 GGGACGTTGATCATCACTACAGTA 59.903 45.833 0.00 0.00 0.00 2.74
2496 2585 5.221263 GGGACGTTGATCATCACTACAGTAT 60.221 44.000 0.00 0.00 0.00 2.12
2576 2683 2.557317 GGATGTTAATTTCCCGAGCGA 58.443 47.619 0.00 0.00 0.00 4.93
2581 2688 2.566057 TAATTTCCCGAGCGAGCGCA 62.566 55.000 17.68 0.00 44.88 6.09
2657 2774 1.893137 TGTCGGGGATAAGATCGGATG 59.107 52.381 0.00 0.00 0.00 3.51
2704 2821 2.353605 GGTACGTTACGTGGATTTGGGA 60.354 50.000 21.22 0.00 41.39 4.37
2749 2923 0.575390 CGCGGAAGGTAATTAGTGCG 59.425 55.000 0.00 0.00 38.28 5.34
2958 3144 2.741985 CGCACCAACCTGATCGCA 60.742 61.111 0.00 0.00 0.00 5.10
2960 3146 1.965930 GCACCAACCTGATCGCACA 60.966 57.895 0.00 0.00 0.00 4.57
3002 3188 2.537560 CGCGTGCTCCAATCCATCC 61.538 63.158 0.00 0.00 0.00 3.51
3051 3243 1.697982 ACCCTCTACTTTTCGCACCTT 59.302 47.619 0.00 0.00 0.00 3.50
3070 3277 0.327924 TCACGGCTGATGATTTGGGT 59.672 50.000 0.00 0.00 0.00 4.51
3190 3397 4.794439 CGGTGTGCATCGGCGAGA 62.794 66.667 17.22 0.00 45.35 4.04
3371 3578 3.567797 GCAGATCAAGTCCGGCGC 61.568 66.667 0.00 0.00 0.00 6.53
3372 3579 2.892425 CAGATCAAGTCCGGCGCC 60.892 66.667 19.07 19.07 0.00 6.53
3373 3580 4.514577 AGATCAAGTCCGGCGCCG 62.515 66.667 41.00 41.00 39.44 6.46
3635 3857 2.042259 CCAAGGAATCGCAGCAGCA 61.042 57.895 0.82 0.00 42.27 4.41
3636 3858 1.428219 CAAGGAATCGCAGCAGCAG 59.572 57.895 0.82 0.00 42.27 4.24
3637 3859 2.404995 AAGGAATCGCAGCAGCAGC 61.405 57.895 0.82 0.00 42.27 5.25
3638 3860 3.129502 GGAATCGCAGCAGCAGCA 61.130 61.111 10.77 0.00 45.49 4.41
3639 3861 2.403987 GAATCGCAGCAGCAGCAG 59.596 61.111 10.77 0.00 45.49 4.24
3753 3984 0.464870 TCAACCTGGACGAAACGGAA 59.535 50.000 0.00 0.00 0.00 4.30
3859 4096 3.224884 TGACACTCGTCGCAAATATGA 57.775 42.857 0.00 0.00 45.80 2.15
3860 4097 3.580731 TGACACTCGTCGCAAATATGAA 58.419 40.909 0.00 0.00 45.80 2.57
3861 4098 3.991121 TGACACTCGTCGCAAATATGAAA 59.009 39.130 0.00 0.00 45.80 2.69
3862 4099 4.629634 TGACACTCGTCGCAAATATGAAAT 59.370 37.500 0.00 0.00 45.80 2.17
3863 4100 5.808030 TGACACTCGTCGCAAATATGAAATA 59.192 36.000 0.00 0.00 45.80 1.40
3864 4101 6.478673 TGACACTCGTCGCAAATATGAAATAT 59.521 34.615 0.00 0.00 45.80 1.28
3896 4133 5.475719 TCTGTAAATACGTTTCAGGTGAGG 58.524 41.667 0.00 0.00 0.00 3.86
3898 4135 2.109425 AATACGTTTCAGGTGAGGCC 57.891 50.000 0.00 0.00 37.58 5.19
3960 4212 2.211250 TTGGGAGTGAGCTACGTACT 57.789 50.000 0.00 0.00 0.00 2.73
4039 4291 2.437343 GCTCAACGAAGCTCCGTCG 61.437 63.158 0.00 0.46 42.54 5.12
4048 4300 2.858344 CGAAGCTCCGTCGATGTAAATT 59.142 45.455 3.52 0.00 41.02 1.82
4065 4317 6.924111 TGTAAATTTGAAAGAATCTCCCAGC 58.076 36.000 0.00 0.00 0.00 4.85
4072 4324 1.582389 AGAATCTCCCAGCTCTGCTT 58.418 50.000 0.00 0.00 36.40 3.91
4144 4435 3.674997 AGAAAATGTATGACGCCACAGT 58.325 40.909 0.00 0.00 0.00 3.55
4165 4456 2.959484 CGGCTTCCTGGGAGCAGAA 61.959 63.158 27.65 0.00 0.00 3.02
4166 4457 1.377856 GGCTTCCTGGGAGCAGAAC 60.378 63.158 27.65 7.25 0.00 3.01
4168 4459 1.674057 CTTCCTGGGAGCAGAACGT 59.326 57.895 0.00 0.00 0.00 3.99
4170 4461 0.895530 TTCCTGGGAGCAGAACGTAG 59.104 55.000 0.00 0.00 0.00 3.51
4189 4480 1.066143 AGTAGGAAGTGTGGGCAATCG 60.066 52.381 0.00 0.00 0.00 3.34
4201 4492 2.798689 CAATCGAGCGGACCGAGA 59.201 61.111 20.50 13.68 39.55 4.04
4205 4496 0.875728 ATCGAGCGGACCGAGATAAG 59.124 55.000 20.50 1.93 39.55 1.73
4207 4498 0.875728 CGAGCGGACCGAGATAAGAT 59.124 55.000 20.50 0.00 0.00 2.40
4218 4509 3.247173 CCGAGATAAGATGAAACTGCAGC 59.753 47.826 15.27 0.00 0.00 5.25
4270 4561 9.283768 GTACTACCTCTCTAACTAAATACTCCC 57.716 40.741 0.00 0.00 0.00 4.30
4272 4563 8.219868 ACTACCTCTCTAACTAAATACTCCCTC 58.780 40.741 0.00 0.00 0.00 4.30
4273 4564 6.375418 ACCTCTCTAACTAAATACTCCCTCC 58.625 44.000 0.00 0.00 0.00 4.30
4275 4566 6.011122 TCTCTAACTAAATACTCCCTCCGT 57.989 41.667 0.00 0.00 0.00 4.69
4276 4567 6.430007 TCTCTAACTAAATACTCCCTCCGTT 58.570 40.000 0.00 0.00 0.00 4.44
4277 4568 6.545298 TCTCTAACTAAATACTCCCTCCGTTC 59.455 42.308 0.00 0.00 0.00 3.95
4278 4569 4.750021 AACTAAATACTCCCTCCGTTCC 57.250 45.455 0.00 0.00 0.00 3.62
4280 4571 5.134725 ACTAAATACTCCCTCCGTTCCTA 57.865 43.478 0.00 0.00 0.00 2.94
4281 4572 5.522641 ACTAAATACTCCCTCCGTTCCTAA 58.477 41.667 0.00 0.00 0.00 2.69
4282 4573 5.960202 ACTAAATACTCCCTCCGTTCCTAAA 59.040 40.000 0.00 0.00 0.00 1.85
4283 4574 5.970501 AAATACTCCCTCCGTTCCTAAAT 57.029 39.130 0.00 0.00 0.00 1.40
4284 4575 7.786464 ACTAAATACTCCCTCCGTTCCTAAATA 59.214 37.037 0.00 0.00 0.00 1.40
4287 4578 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4288 4579 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4290 4581 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
4291 4582 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
4292 4583 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
4293 4584 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
4294 4585 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
4295 4586 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
4296 4587 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
4297 4588 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
4313 4604 9.559732 TGTCTTTCTAGAAGTTTCAAATGATGA 57.440 29.630 5.12 0.00 31.46 2.92
4314 4605 9.818796 GTCTTTCTAGAAGTTTCAAATGATGAC 57.181 33.333 5.12 0.00 32.53 3.06
4315 4606 9.784531 TCTTTCTAGAAGTTTCAAATGATGACT 57.215 29.630 5.12 0.00 37.92 3.41
4318 4609 9.996554 TTCTAGAAGTTTCAAATGATGACTACA 57.003 29.630 0.00 0.00 37.92 2.74
4322 4613 8.873830 AGAAGTTTCAAATGATGACTACATACG 58.126 33.333 0.00 0.00 37.92 3.06
4323 4614 7.539712 AGTTTCAAATGATGACTACATACGG 57.460 36.000 0.00 0.00 37.92 4.02
4324 4615 7.327975 AGTTTCAAATGATGACTACATACGGA 58.672 34.615 0.00 0.00 37.92 4.69
4326 4617 7.534085 TTCAAATGATGACTACATACGGAAC 57.466 36.000 0.00 0.00 37.92 3.62
4329 4620 7.604545 TCAAATGATGACTACATACGGAACAAA 59.395 33.333 0.00 0.00 36.82 2.83
4331 4622 8.506168 AATGATGACTACATACGGAACAAAAT 57.494 30.769 0.00 0.00 36.82 1.82
4334 4625 6.961359 TGACTACATACGGAACAAAATGAG 57.039 37.500 0.00 0.00 0.00 2.90
4335 4626 6.460781 TGACTACATACGGAACAAAATGAGT 58.539 36.000 0.00 0.00 0.00 3.41
4336 4627 6.367695 TGACTACATACGGAACAAAATGAGTG 59.632 38.462 0.00 0.00 0.00 3.51
4337 4628 6.460781 ACTACATACGGAACAAAATGAGTGA 58.539 36.000 0.00 0.00 0.00 3.41
4340 4631 6.842163 ACATACGGAACAAAATGAGTGAATC 58.158 36.000 0.00 0.00 0.00 2.52
4343 4634 6.481954 ACGGAACAAAATGAGTGAATCTAC 57.518 37.500 0.00 0.00 0.00 2.59
4344 4635 5.995282 ACGGAACAAAATGAGTGAATCTACA 59.005 36.000 0.00 0.00 0.00 2.74
4346 4637 7.174946 ACGGAACAAAATGAGTGAATCTACATT 59.825 33.333 0.00 0.00 34.99 2.71
4347 4638 7.693951 CGGAACAAAATGAGTGAATCTACATTC 59.306 37.037 0.00 0.00 39.24 2.67
4348 4639 8.734386 GGAACAAAATGAGTGAATCTACATTCT 58.266 33.333 0.00 0.00 39.49 2.40
4378 4669 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
4379 4670 7.153217 TGTCTATATACATCCGTATGTGGTG 57.847 40.000 3.56 0.00 45.99 4.17
4380 4671 6.943718 TGTCTATATACATCCGTATGTGGTGA 59.056 38.462 3.56 0.00 45.99 4.02
4381 4672 7.094506 TGTCTATATACATCCGTATGTGGTGAC 60.095 40.741 3.56 5.93 45.99 3.67
4382 4673 3.746045 ATACATCCGTATGTGGTGACC 57.254 47.619 3.56 0.00 45.99 4.02
4383 4674 1.271856 ACATCCGTATGTGGTGACCA 58.728 50.000 0.00 0.00 44.79 4.02
4385 4676 2.238646 ACATCCGTATGTGGTGACCATT 59.761 45.455 7.94 0.86 44.79 3.16
4386 4677 3.278574 CATCCGTATGTGGTGACCATTT 58.721 45.455 7.94 0.45 35.28 2.32
4387 4678 2.705730 TCCGTATGTGGTGACCATTTG 58.294 47.619 7.94 0.00 35.28 2.32
4388 4679 2.303311 TCCGTATGTGGTGACCATTTGA 59.697 45.455 7.94 0.00 35.28 2.69
4389 4680 3.078097 CCGTATGTGGTGACCATTTGAA 58.922 45.455 7.94 0.00 35.28 2.69
4391 4682 4.157656 CCGTATGTGGTGACCATTTGAAAT 59.842 41.667 7.94 0.00 35.28 2.17
4392 4683 5.331902 CGTATGTGGTGACCATTTGAAATC 58.668 41.667 7.94 0.00 35.28 2.17
4395 4686 4.728772 TGTGGTGACCATTTGAAATCTCT 58.271 39.130 7.94 0.00 35.28 3.10
4396 4687 5.875224 TGTGGTGACCATTTGAAATCTCTA 58.125 37.500 7.94 0.00 35.28 2.43
4397 4688 5.939883 TGTGGTGACCATTTGAAATCTCTAG 59.060 40.000 7.94 0.00 35.28 2.43
4399 4690 6.655003 GTGGTGACCATTTGAAATCTCTAGAA 59.345 38.462 7.94 0.00 35.28 2.10
4401 4692 7.391554 TGGTGACCATTTGAAATCTCTAGAAAG 59.608 37.037 0.00 0.00 0.00 2.62
4402 4693 7.607991 GGTGACCATTTGAAATCTCTAGAAAGA 59.392 37.037 0.00 0.00 0.00 2.52
4403 4694 8.447053 GTGACCATTTGAAATCTCTAGAAAGAC 58.553 37.037 0.00 0.00 0.00 3.01
4404 4695 8.156820 TGACCATTTGAAATCTCTAGAAAGACA 58.843 33.333 0.00 0.00 0.00 3.41
4405 4696 8.924511 ACCATTTGAAATCTCTAGAAAGACAA 57.075 30.769 0.00 0.00 0.00 3.18
4406 4697 9.354673 ACCATTTGAAATCTCTAGAAAGACAAA 57.645 29.630 0.00 4.41 0.00 2.83
4420 4711 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
4421 4712 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
4422 4713 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
4423 4714 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
4425 4716 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
4426 4717 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
4427 4718 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
4428 4719 6.667558 AATATTTAGGAACGGAGGGAGTAG 57.332 41.667 0.00 0.00 0.00 2.57
4431 4722 2.433662 AGGAACGGAGGGAGTAGTAC 57.566 55.000 0.00 0.00 0.00 2.73
4432 4723 1.637553 AGGAACGGAGGGAGTAGTACA 59.362 52.381 2.52 0.00 0.00 2.90
4433 4724 2.042162 AGGAACGGAGGGAGTAGTACAA 59.958 50.000 2.52 0.00 0.00 2.41
4434 4725 2.827921 GGAACGGAGGGAGTAGTACAAA 59.172 50.000 2.52 0.00 0.00 2.83
4676 6435 2.426024 AGATTCATCACTTGCCATGTGC 59.574 45.455 5.88 0.00 41.77 4.57
4783 6542 6.650239 TTAATTATCGCGACAAGCTTGTTA 57.350 33.333 31.58 17.40 45.59 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
241 245 3.629142 ATCCCTAACGGTTTCTTCTGG 57.371 47.619 0.00 0.00 0.00 3.86
263 267 2.744307 AAGCAAGCAAGCGAGCAAGC 62.744 55.000 12.73 8.64 40.15 4.01
264 268 1.002250 CAAGCAAGCAAGCGAGCAAG 61.002 55.000 12.73 0.00 40.15 4.01
265 269 1.008194 CAAGCAAGCAAGCGAGCAA 60.008 52.632 12.73 0.00 40.15 3.91
266 270 2.188829 ACAAGCAAGCAAGCGAGCA 61.189 52.632 12.73 0.00 40.15 4.26
267 271 1.728426 CACAAGCAAGCAAGCGAGC 60.728 57.895 4.06 4.06 40.15 5.03
268 272 0.385223 GACACAAGCAAGCAAGCGAG 60.385 55.000 0.00 0.00 40.15 5.03
269 273 1.094650 TGACACAAGCAAGCAAGCGA 61.095 50.000 0.00 0.00 40.15 4.93
270 274 0.039798 ATGACACAAGCAAGCAAGCG 60.040 50.000 0.00 0.00 40.15 4.68
378 382 2.442212 TCGACATGGAAACTTGCGTA 57.558 45.000 0.00 0.00 39.00 4.42
421 425 0.666577 GAACCGTCACCGAGGAAGTG 60.667 60.000 0.00 0.00 35.63 3.16
436 440 4.035675 CAGAAACAGACTGAACTTGGAACC 59.964 45.833 10.08 0.00 37.54 3.62
515 520 4.633175 TCATGTTTTACTCGCCAACTACA 58.367 39.130 0.00 0.00 0.00 2.74
537 542 4.103785 TGGCCTAATACGACCTACTAGTCT 59.896 45.833 3.32 0.00 34.46 3.24
973 994 3.341043 GGATGCGATGCGATGCGT 61.341 61.111 0.00 0.00 0.00 5.24
1403 1427 2.223377 AGAAAACCAATCTTGCGTCGTC 59.777 45.455 0.00 0.00 0.00 4.20
1567 1592 1.464429 CGCGTACATGCTCGTCACTC 61.464 60.000 0.00 0.00 0.00 3.51
1948 1994 3.511595 TACGCGTGCGGGGAGTAG 61.512 66.667 24.59 0.00 44.69 2.57
1976 2024 3.304794 CGCATAGTGGCTAGTAAGAGTCC 60.305 52.174 0.00 0.00 0.00 3.85
2008 2056 0.734889 ATTGCGTTCAGTAGCATGCC 59.265 50.000 15.66 0.00 43.42 4.40
2111 2172 5.346822 GCTGTCTACTTGGCAATGATTTTTG 59.653 40.000 0.00 0.00 0.00 2.44
2112 2173 5.244626 AGCTGTCTACTTGGCAATGATTTTT 59.755 36.000 0.00 0.00 0.00 1.94
2147 2208 1.745653 TCAGACTCGTATCACCAGCAG 59.254 52.381 0.00 0.00 0.00 4.24
2148 2209 1.472878 GTCAGACTCGTATCACCAGCA 59.527 52.381 0.00 0.00 0.00 4.41
2149 2210 1.532090 CGTCAGACTCGTATCACCAGC 60.532 57.143 0.00 0.00 0.00 4.85
2372 2436 1.683365 TACGGTCTGCCCCAGGTAC 60.683 63.158 0.00 0.00 31.51 3.34
2374 2438 3.001406 GTACGGTCTGCCCCAGGT 61.001 66.667 0.00 0.00 31.51 4.00
2375 2439 4.143333 CGTACGGTCTGCCCCAGG 62.143 72.222 7.57 0.00 31.51 4.45
2399 2482 4.854173 TGTAGCCATGATAATGGTGTTGT 58.146 39.130 11.02 0.00 43.53 3.32
2415 2498 3.639538 CACCGACATACATACTGTAGCC 58.360 50.000 0.00 0.00 36.14 3.93
2424 2507 3.261951 GCGCGCACCGACATACAT 61.262 61.111 29.10 0.00 40.02 2.29
2489 2572 5.445845 CGATGCATGTACGTACATACTGTA 58.554 41.667 34.24 25.26 44.57 2.74
2496 2585 0.528901 GGGCGATGCATGTACGTACA 60.529 55.000 29.15 29.15 40.98 2.90
2499 2588 2.203015 GGGGCGATGCATGTACGT 60.203 61.111 2.46 0.00 0.00 3.57
2541 2648 1.008206 ACATCCCTTCTCCTCTGCTCT 59.992 52.381 0.00 0.00 0.00 4.09
2542 2649 1.494960 ACATCCCTTCTCCTCTGCTC 58.505 55.000 0.00 0.00 0.00 4.26
2543 2650 1.963985 AACATCCCTTCTCCTCTGCT 58.036 50.000 0.00 0.00 0.00 4.24
2544 2651 3.914426 TTAACATCCCTTCTCCTCTGC 57.086 47.619 0.00 0.00 0.00 4.26
2545 2652 5.825151 GGAAATTAACATCCCTTCTCCTCTG 59.175 44.000 0.00 0.00 0.00 3.35
2581 2688 1.055551 TAATTATGTCCCCGGCCCGT 61.056 55.000 0.85 0.00 0.00 5.28
2704 2821 2.484417 GCAATGATGATGAGTCCTCCGT 60.484 50.000 0.00 0.00 0.00 4.69
2749 2923 2.511600 CCCTCCGTCGTCATTGCC 60.512 66.667 0.00 0.00 0.00 4.52
2967 3153 1.150567 GCGGCGAGACTAGACGAGTA 61.151 60.000 15.61 0.00 44.04 2.59
2971 3157 3.862402 ACGCGGCGAGACTAGACG 61.862 66.667 30.94 6.44 44.15 4.18
3002 3188 3.992260 TGGTCAAATTAACAACGGGTG 57.008 42.857 0.00 0.00 0.00 4.61
3051 3243 0.327924 ACCCAAATCATCAGCCGTGA 59.672 50.000 0.00 0.00 37.02 4.35
3070 3277 2.626266 ACGTCACTACTCATGTGTCCAA 59.374 45.455 3.19 0.00 36.83 3.53
3190 3397 3.893763 CTCGCCGTCGATGCTCCT 61.894 66.667 0.00 0.00 44.56 3.69
3345 3552 0.322277 ACTTGATCTGCAGCAGGTGG 60.322 55.000 22.62 10.04 31.51 4.61
3376 3583 4.821589 CCAGAAGACGGAGCCGCC 62.822 72.222 9.14 0.00 44.19 6.13
3640 3862 4.838486 GACGACGGCGAGCTCCTG 62.838 72.222 22.49 8.72 41.64 3.86
3863 4100 9.647797 TGAAACGTATTTACAGATGTTGTAGAT 57.352 29.630 0.00 0.00 42.92 1.98
3864 4101 9.135843 CTGAAACGTATTTACAGATGTTGTAGA 57.864 33.333 0.00 0.00 42.92 2.59
3914 4151 3.621558 GCTTAGGCTTTATCCACACCTT 58.378 45.455 0.00 0.00 35.22 3.50
3960 4212 4.275810 AGCCCGAATTACTCACTACTACA 58.724 43.478 0.00 0.00 0.00 2.74
4039 4291 7.704047 GCTGGGAGATTCTTTCAAATTTACATC 59.296 37.037 0.00 0.00 0.00 3.06
4048 4300 3.871463 GCAGAGCTGGGAGATTCTTTCAA 60.871 47.826 0.00 0.00 0.00 2.69
4065 4317 6.108687 TGTCTATTATGTGACCAAAGCAGAG 58.891 40.000 0.00 0.00 32.67 3.35
4072 4324 9.733556 ACAAGTTAATGTCTATTATGTGACCAA 57.266 29.630 0.00 0.00 32.67 3.67
4120 4411 3.190327 TGTGGCGTCATACATTTTCTTGG 59.810 43.478 0.00 0.00 0.00 3.61
4121 4412 4.083324 ACTGTGGCGTCATACATTTTCTTG 60.083 41.667 0.00 0.00 0.00 3.02
4144 4435 3.706373 GCTCCCAGGAAGCCGTCA 61.706 66.667 0.00 0.00 0.00 4.35
4165 4456 0.893447 GCCCACACTTCCTACTACGT 59.107 55.000 0.00 0.00 0.00 3.57
4166 4457 0.892755 TGCCCACACTTCCTACTACG 59.107 55.000 0.00 0.00 0.00 3.51
4168 4459 2.167693 CGATTGCCCACACTTCCTACTA 59.832 50.000 0.00 0.00 0.00 1.82
4170 4461 1.066430 TCGATTGCCCACACTTCCTAC 60.066 52.381 0.00 0.00 0.00 3.18
4189 4480 1.880675 TCATCTTATCTCGGTCCGCTC 59.119 52.381 6.34 0.00 0.00 5.03
4201 4492 4.002982 TGTTCGCTGCAGTTTCATCTTAT 58.997 39.130 16.64 0.00 0.00 1.73
4205 4496 2.286950 TGTTGTTCGCTGCAGTTTCATC 60.287 45.455 16.64 9.33 0.00 2.92
4207 4498 1.090728 TGTTGTTCGCTGCAGTTTCA 58.909 45.000 16.64 7.21 0.00 2.69
4218 4509 7.408132 TTCTTATTCAGAGAAGTGTTGTTCG 57.592 36.000 0.00 0.00 31.12 3.95
4266 4557 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
4267 4558 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
4268 4559 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
4270 4561 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
4272 4563 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
4287 4578 9.559732 TCATCATTTGAAACTTCTAGAAAGACA 57.440 29.630 6.63 2.44 0.00 3.41
4288 4579 9.818796 GTCATCATTTGAAACTTCTAGAAAGAC 57.181 33.333 6.63 0.00 35.70 3.01
4292 4583 9.996554 TGTAGTCATCATTTGAAACTTCTAGAA 57.003 29.630 4.81 4.81 35.70 2.10
4296 4587 8.873830 CGTATGTAGTCATCATTTGAAACTTCT 58.126 33.333 4.83 0.00 35.70 2.85
4297 4588 8.116753 CCGTATGTAGTCATCATTTGAAACTTC 58.883 37.037 4.83 2.03 35.70 3.01
4300 4591 7.534085 TCCGTATGTAGTCATCATTTGAAAC 57.466 36.000 0.00 0.00 35.70 2.78
4301 4592 7.604545 TGTTCCGTATGTAGTCATCATTTGAAA 59.395 33.333 0.00 0.00 35.70 2.69
4304 4595 6.902224 TGTTCCGTATGTAGTCATCATTTG 57.098 37.500 0.00 0.00 35.70 2.32
4305 4596 7.915293 TTTGTTCCGTATGTAGTCATCATTT 57.085 32.000 0.00 0.00 35.70 2.32
4307 4598 7.768582 TCATTTTGTTCCGTATGTAGTCATCAT 59.231 33.333 0.00 0.00 35.70 2.45
4308 4599 7.100409 TCATTTTGTTCCGTATGTAGTCATCA 58.900 34.615 0.00 0.00 35.70 3.07
4309 4600 7.277981 ACTCATTTTGTTCCGTATGTAGTCATC 59.722 37.037 0.00 0.00 35.70 2.92
4312 4603 6.588756 TCACTCATTTTGTTCCGTATGTAGTC 59.411 38.462 0.00 0.00 0.00 2.59
4313 4604 6.460781 TCACTCATTTTGTTCCGTATGTAGT 58.539 36.000 0.00 0.00 0.00 2.73
4314 4605 6.961359 TCACTCATTTTGTTCCGTATGTAG 57.039 37.500 0.00 0.00 0.00 2.74
4315 4606 7.822334 AGATTCACTCATTTTGTTCCGTATGTA 59.178 33.333 0.00 0.00 0.00 2.29
4317 4608 7.076842 AGATTCACTCATTTTGTTCCGTATG 57.923 36.000 0.00 0.00 0.00 2.39
4318 4609 7.822334 TGTAGATTCACTCATTTTGTTCCGTAT 59.178 33.333 0.00 0.00 0.00 3.06
4320 4611 5.995282 TGTAGATTCACTCATTTTGTTCCGT 59.005 36.000 0.00 0.00 0.00 4.69
4321 4612 6.480524 TGTAGATTCACTCATTTTGTTCCG 57.519 37.500 0.00 0.00 0.00 4.30
4322 4613 8.734386 AGAATGTAGATTCACTCATTTTGTTCC 58.266 33.333 14.46 0.00 40.59 3.62
4352 4643 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
4357 4648 6.376299 GGTCACCACATACGGATGTATATAGA 59.624 42.308 14.23 4.80 44.82 1.98
4358 4649 6.152154 TGGTCACCACATACGGATGTATATAG 59.848 42.308 14.23 0.00 44.82 1.31
4361 4652 4.216708 TGGTCACCACATACGGATGTATA 58.783 43.478 14.23 0.00 44.82 1.47
4362 4653 3.035363 TGGTCACCACATACGGATGTAT 58.965 45.455 14.23 1.38 44.82 2.29
4363 4654 2.458620 TGGTCACCACATACGGATGTA 58.541 47.619 14.23 0.00 44.82 2.29
4365 4656 2.620251 ATGGTCACCACATACGGATG 57.380 50.000 5.94 5.94 35.80 3.51
4367 4658 2.303311 TCAAATGGTCACCACATACGGA 59.697 45.455 0.00 0.00 35.80 4.69
4368 4659 2.705730 TCAAATGGTCACCACATACGG 58.294 47.619 0.00 0.00 35.80 4.02
4369 4660 4.757799 TTTCAAATGGTCACCACATACG 57.242 40.909 0.00 0.00 35.80 3.06
4370 4661 6.375455 AGAGATTTCAAATGGTCACCACATAC 59.625 38.462 0.00 0.00 35.80 2.39
4371 4662 6.484288 AGAGATTTCAAATGGTCACCACATA 58.516 36.000 0.00 0.00 35.80 2.29
4372 4663 5.327732 AGAGATTTCAAATGGTCACCACAT 58.672 37.500 0.00 0.00 35.80 3.21
4373 4664 4.728772 AGAGATTTCAAATGGTCACCACA 58.271 39.130 0.00 0.00 35.80 4.17
4374 4665 6.173339 TCTAGAGATTTCAAATGGTCACCAC 58.827 40.000 0.00 0.00 35.80 4.16
4375 4666 6.373005 TCTAGAGATTTCAAATGGTCACCA 57.627 37.500 0.00 0.00 38.19 4.17
4376 4667 7.607991 TCTTTCTAGAGATTTCAAATGGTCACC 59.392 37.037 0.00 0.00 0.00 4.02
4377 4668 8.447053 GTCTTTCTAGAGATTTCAAATGGTCAC 58.553 37.037 0.00 0.00 0.00 3.67
4378 4669 8.156820 TGTCTTTCTAGAGATTTCAAATGGTCA 58.843 33.333 0.00 0.00 0.00 4.02
4379 4670 8.553459 TGTCTTTCTAGAGATTTCAAATGGTC 57.447 34.615 0.00 0.00 0.00 4.02
4380 4671 8.924511 TTGTCTTTCTAGAGATTTCAAATGGT 57.075 30.769 0.00 0.00 0.00 3.55
4395 4686 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
4396 4687 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
4397 4688 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
4399 4690 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
4401 4692 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
4402 4693 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
4403 4694 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4404 4695 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4405 4696 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
4406 4697 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
4408 4699 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
4409 4700 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
4412 4703 1.637553 TGTACTACTCCCTCCGTTCCT 59.362 52.381 0.00 0.00 0.00 3.36
4413 4704 2.134789 TGTACTACTCCCTCCGTTCC 57.865 55.000 0.00 0.00 0.00 3.62
4415 4706 4.351127 AGATTTGTACTACTCCCTCCGTT 58.649 43.478 0.00 0.00 0.00 4.44
4416 4707 3.978610 AGATTTGTACTACTCCCTCCGT 58.021 45.455 0.00 0.00 0.00 4.69
4417 4708 6.461110 TTAAGATTTGTACTACTCCCTCCG 57.539 41.667 0.00 0.00 0.00 4.63
4418 4709 9.682465 AAATTTAAGATTTGTACTACTCCCTCC 57.318 33.333 0.00 0.00 0.00 4.30
4503 6262 2.612212 CAATCCCATGCAGTAACGGTAC 59.388 50.000 1.22 1.22 0.00 3.34
4539 6298 3.560882 CCCCTTTCATGTGCTCTCTTCTT 60.561 47.826 0.00 0.00 0.00 2.52
4676 6435 0.389817 TGGTCCTTGTGCGATTCTCG 60.390 55.000 0.00 0.00 43.89 4.04
4760 6519 5.539582 AACAAGCTTGTCGCGATAATTAA 57.460 34.783 31.20 5.76 45.59 1.40
4761 6520 5.276678 GCTAACAAGCTTGTCGCGATAATTA 60.277 40.000 31.20 15.56 45.59 1.40
4762 6521 4.494199 GCTAACAAGCTTGTCGCGATAATT 60.494 41.667 31.20 15.26 45.59 1.40
4763 6522 3.001330 GCTAACAAGCTTGTCGCGATAAT 59.999 43.478 31.20 15.96 45.59 1.28
4783 6542 2.907917 CGTAGGGCGAGCCTAGCT 60.908 66.667 14.33 5.40 44.77 3.32


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

AutoCloner maintained by Alex Coulton.