Multiple sequence alignment - TraesCS6D01G139100

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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 TraesCS6D01G139100 chr6D 100.000 4579 0 0 1 4579 108243590 108239012 0.000000e+00 8456.0
1 TraesCS6D01G139100 chr6A 92.332 3182 135 46 2 3132 133376442 133373319 0.000000e+00 4423.0
2 TraesCS6D01G139100 chr6A 92.113 1065 56 13 3140 4199 133373264 133372223 0.000000e+00 1476.0
3 TraesCS6D01G139100 chr6B 93.619 2523 90 30 603 3093 195533707 195531224 0.000000e+00 3701.0
4 TraesCS6D01G139100 chr6B 92.593 1080 60 13 3132 4202 195530379 195529311 0.000000e+00 1533.0
5 TraesCS6D01G139100 chr6B 86.418 589 64 10 1 588 195534697 195534124 8.360000e-177 630.0
6 TraesCS6D01G139100 chr6B 88.550 131 9 6 4355 4483 195529100 195528974 2.210000e-33 154.0
7 TraesCS6D01G139100 chr6B 92.553 94 7 0 4264 4357 195529222 195529129 7.990000e-28 135.0
8 TraesCS6D01G139100 chr6B 88.542 96 11 0 4484 4579 708830957 708830862 2.890000e-22 117.0
9 TraesCS6D01G139100 chr6B 86.869 99 11 2 4480 4578 703457390 703457294 4.840000e-20 110.0
10 TraesCS6D01G139100 chr6B 98.000 50 1 0 3083 3132 195530475 195530426 2.270000e-13 87.9
11 TraesCS6D01G139100 chr5B 78.676 272 49 8 323 588 152549793 152549525 6.090000e-39 172.0
12 TraesCS6D01G139100 chr5A 78.319 226 41 6 323 542 221281101 221280878 6.180000e-29 139.0
13 TraesCS6D01G139100 chr5A 80.282 142 25 3 324 463 68610920 68611060 2.250000e-18 104.0
14 TraesCS6D01G139100 chr2D 78.818 203 35 7 347 543 69962602 69962402 3.720000e-26 130.0
15 TraesCS6D01G139100 chr1D 90.722 97 8 1 4483 4579 405921 406016 1.340000e-25 128.0
16 TraesCS6D01G139100 chr4A 90.426 94 9 0 4483 4576 559153269 559153362 1.730000e-24 124.0
17 TraesCS6D01G139100 chr3A 88.660 97 11 0 4483 4579 568537136 568537232 8.050000e-23 119.0
18 TraesCS6D01G139100 chr7A 88.889 90 10 0 4483 4572 18537984 18537895 1.350000e-20 111.0
19 TraesCS6D01G139100 chr5D 87.129 101 9 4 4480 4579 246308913 246308816 1.350000e-20 111.0
20 TraesCS6D01G139100 chr5D 83.529 85 11 2 378 462 98299668 98299587 4.910000e-10 76.8
21 TraesCS6D01G139100 chr4B 88.298 94 8 3 4482 4574 264996653 264996562 4.840000e-20 110.0
22 TraesCS6D01G139100 chr4B 86.598 97 11 2 4484 4579 596644916 596644821 6.270000e-19 106.0


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 TraesCS6D01G139100 chr6D 108239012 108243590 4578 True 8456.00 8456 100.0000 1 4579 1 chr6D.!!$R1 4578
1 TraesCS6D01G139100 chr6A 133372223 133376442 4219 True 2949.50 4423 92.2225 2 4199 2 chr6A.!!$R1 4197
2 TraesCS6D01G139100 chr6B 195528974 195534697 5723 True 1040.15 3701 91.9555 1 4483 6 chr6B.!!$R3 4482

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
478 486 0.313672 GCACGCAATTGGGAGACAAA 59.686 50.0 27.32 0.0 43.46 2.83 F
1035 1464 0.253394 CCCTTTCCCTCTCCTCCCTT 60.253 60.0 0.00 0.0 0.00 3.95 F
1287 1716 0.838608 TGTTCCACCACCGGTTTAGT 59.161 50.0 2.97 0.0 31.02 2.24 F
2649 3105 0.908910 TGTGGACGCACTGGGATTAT 59.091 50.0 0.00 0.0 0.00 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2291 2747 1.140852 ACTTGCTGCTGACACCTAACA 59.859 47.619 0.00 0.0 0.00 2.41 R
2926 3383 0.727970 CTGATGCTGACTTGCTGAGC 59.272 55.000 0.00 0.0 0.00 4.26 R
3043 3500 0.529992 AATCCCGCGCTTGCTACTAC 60.530 55.000 5.56 0.0 36.08 2.73 R
4232 5513 0.091344 GAGTCGTGCGTGTCAATTCG 59.909 55.000 0.00 0.0 0.00 3.34 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
30 31 6.294955 CCTGTTGATCATGGAGATTATCTCGA 60.295 42.308 15.09 12.27 44.28 4.04
255 262 6.966021 TGAAAAAGTAATACACCTTGCACTC 58.034 36.000 0.00 0.00 0.00 3.51
279 286 0.321653 ATGGAAAGTGCTGACGGGTC 60.322 55.000 0.00 0.00 0.00 4.46
361 369 5.898972 AGGTGTATATTTTTGGCATGGTGAT 59.101 36.000 0.00 0.00 0.00 3.06
367 375 2.307496 TTTGGCATGGTGATCAAGGT 57.693 45.000 0.00 0.00 0.00 3.50
413 421 9.903682 ATGATGAAATTATCCTTCGCTAATTTG 57.096 29.630 4.41 0.00 37.55 2.32
417 425 8.735315 TGAAATTATCCTTCGCTAATTTGTTGA 58.265 29.630 4.41 0.00 37.55 3.18
422 430 7.865706 ATCCTTCGCTAATTTGTTGATTAGT 57.134 32.000 6.53 0.00 40.26 2.24
446 454 4.762251 GGCAAGTAAATCTATTAGGCCAGG 59.238 45.833 5.01 0.00 38.71 4.45
478 486 0.313672 GCACGCAATTGGGAGACAAA 59.686 50.000 27.32 0.00 43.46 2.83
488 496 6.808704 GCAATTGGGAGACAAATACTTTCTTC 59.191 38.462 7.72 0.00 43.46 2.87
508 517 6.958767 TCTTCCTTTTTACAAGGAGGGATAG 58.041 40.000 8.99 0.59 46.21 2.08
527 536 2.147436 GATGCAATCGGGAGAGAGAC 57.853 55.000 0.00 0.00 45.48 3.36
533 542 3.516615 CAATCGGGAGAGAGACACTTTC 58.483 50.000 0.00 0.00 45.48 2.62
589 598 6.963322 AGGAATTAGAGAAATGCACCTTAGT 58.037 36.000 0.00 0.00 0.00 2.24
698 1110 3.572255 TGGCTTTGGGTACATCTTCAAAC 59.428 43.478 0.00 0.00 0.00 2.93
720 1132 1.981256 AAGTTCGCCATGGAGTGTTT 58.019 45.000 18.40 5.64 0.00 2.83
920 1349 1.514678 CCACAACCATCACCACCACG 61.515 60.000 0.00 0.00 0.00 4.94
924 1353 1.701031 AACCATCACCACCACGACCA 61.701 55.000 0.00 0.00 0.00 4.02
1035 1464 0.253394 CCCTTTCCCTCTCCTCCCTT 60.253 60.000 0.00 0.00 0.00 3.95
1270 1699 3.563224 TGAGTGCTGCCTGCCTGT 61.563 61.111 0.00 0.00 42.00 4.00
1287 1716 0.838608 TGTTCCACCACCGGTTTAGT 59.161 50.000 2.97 0.00 31.02 2.24
1289 1718 2.300433 GTTCCACCACCGGTTTAGTTT 58.700 47.619 2.97 0.00 31.02 2.66
1290 1719 2.259266 TCCACCACCGGTTTAGTTTC 57.741 50.000 2.97 0.00 31.02 2.78
1291 1720 1.770061 TCCACCACCGGTTTAGTTTCT 59.230 47.619 2.97 0.00 31.02 2.52
1292 1721 1.877443 CCACCACCGGTTTAGTTTCTG 59.123 52.381 2.97 0.00 31.02 3.02
1645 2078 4.451435 CCCGTTAGACTCTTCTTTTGTTCC 59.549 45.833 0.00 0.00 32.75 3.62
2016 2458 9.401058 CCATTGATATAACTTTCTTTCACCTCT 57.599 33.333 0.00 0.00 0.00 3.69
2034 2486 6.372659 TCACCTCTTTAGACTGCATTTTGATC 59.627 38.462 0.00 0.00 0.00 2.92
2036 2488 5.649395 CCTCTTTAGACTGCATTTTGATCCA 59.351 40.000 0.00 0.00 0.00 3.41
2249 2705 9.054922 CCATCAAAGAAAACAAAACCAATGTAT 57.945 29.630 0.00 0.00 0.00 2.29
2291 2747 7.931015 TTGGATGTTTACATATAGTCCTCCT 57.069 36.000 0.00 0.00 36.57 3.69
2463 2919 9.562408 TGTCCTTGTACTTTTGATATGTTGTAA 57.438 29.630 0.00 0.00 0.00 2.41
2649 3105 0.908910 TGTGGACGCACTGGGATTAT 59.091 50.000 0.00 0.00 0.00 1.28
2715 3171 4.735283 GCTGCTAAAGAGAGTGGCTACTAC 60.735 50.000 1.28 0.43 37.25 2.73
2751 3207 5.827797 GCAGACCATGGAACAGGAATTATTA 59.172 40.000 21.47 0.00 46.40 0.98
2813 3270 7.960738 TCTTTCTTGACTAACAGTTTGTTTTCG 59.039 33.333 1.72 0.00 41.45 3.46
2818 3275 7.225523 TGACTAACAGTTTGTTTTCGTCTAC 57.774 36.000 1.72 0.00 41.45 2.59
2855 3312 5.293079 GGTTGAGATGATACTTCAAGCACTC 59.707 44.000 9.86 0.00 38.29 3.51
2888 3345 6.793505 AAGGGTAAGTTCCTACTGATACAG 57.206 41.667 0.00 0.00 34.01 2.74
2893 3350 4.332683 AGTTCCTACTGATACAGTCCCA 57.667 45.455 7.68 0.00 41.21 4.37
2926 3383 9.386010 ACATGGATGTTTGGATAATTTGATTTG 57.614 29.630 0.00 0.00 37.90 2.32
3043 3500 2.975489 AGTTATAGGGGAGGCATGACTG 59.025 50.000 5.31 0.00 0.00 3.51
3057 3514 0.456142 TGACTGTAGTAGCAAGCGCG 60.456 55.000 0.00 0.00 45.49 6.86
3119 4335 1.130054 ACATGCACTGGGAGGAGTGT 61.130 55.000 0.00 0.00 44.53 3.55
3137 4400 6.720288 AGGAGTGTGTGTAAAGATGTAGTAGT 59.280 38.462 0.00 0.00 0.00 2.73
3145 4408 8.030692 TGTGTAAAGATGTAGTAGTGCGTTAAT 58.969 33.333 0.00 0.00 0.00 1.40
3233 4496 5.507315 CGGCAGGTTTGTATTCTTGTTTTCT 60.507 40.000 0.00 0.00 0.00 2.52
3348 4612 9.825109 ACATTTCTAGGAAACTTTCTAGATAGC 57.175 33.333 9.83 0.00 40.83 2.97
3453 4719 4.840716 ATATCTCCCATCTTGCAGGATC 57.159 45.455 8.60 0.00 0.00 3.36
3468 4734 4.349048 TGCAGGATCCAAATACTAGCTCAT 59.651 41.667 15.82 0.00 0.00 2.90
3581 4847 6.042143 GGTTGCATCAAGAAGAAAGTGAAAA 58.958 36.000 0.00 0.00 0.00 2.29
3599 4865 7.546358 AGTGAAAACAAGTGATCAAATGACAA 58.454 30.769 14.17 0.00 0.00 3.18
3600 4866 8.034215 AGTGAAAACAAGTGATCAAATGACAAA 58.966 29.630 14.17 0.00 0.00 2.83
3601 4867 8.819974 GTGAAAACAAGTGATCAAATGACAAAT 58.180 29.630 14.17 0.00 0.00 2.32
3610 4881 4.827304 TCAAATGACAAATTCACGAGCA 57.173 36.364 0.00 0.00 36.92 4.26
3661 4932 1.730902 CAGCGCCGGATCTGTATCG 60.731 63.158 5.05 0.00 32.44 2.92
3669 4940 2.858344 CCGGATCTGTATCGTGTTTCAC 59.142 50.000 0.00 0.00 32.44 3.18
3678 4949 0.534203 TCGTGTTTCACTTCAGGGCC 60.534 55.000 0.00 0.00 31.34 5.80
3679 4950 0.535102 CGTGTTTCACTTCAGGGCCT 60.535 55.000 0.00 0.00 31.34 5.19
3680 4951 1.692411 GTGTTTCACTTCAGGGCCTT 58.308 50.000 1.32 0.00 0.00 4.35
3681 4952 2.031870 GTGTTTCACTTCAGGGCCTTT 58.968 47.619 1.32 0.00 0.00 3.11
3750 5021 3.064958 CAGATCAGCCAGTTGTATTGCAG 59.935 47.826 0.00 0.00 0.00 4.41
3754 5025 0.097674 GCCAGTTGTATTGCAGAGCG 59.902 55.000 0.00 0.00 0.00 5.03
3780 5051 0.966179 TTCACTTGTAGCTCGCCTGA 59.034 50.000 0.00 0.00 0.00 3.86
3835 5114 6.377146 GCCCCTTTCTGATGTAAAATCAGTTA 59.623 38.462 13.49 3.08 44.30 2.24
3836 5115 7.093945 GCCCCTTTCTGATGTAAAATCAGTTAA 60.094 37.037 13.49 9.19 44.30 2.01
3837 5116 8.244113 CCCCTTTCTGATGTAAAATCAGTTAAC 58.756 37.037 13.49 0.00 44.30 2.01
3838 5117 9.014297 CCCTTTCTGATGTAAAATCAGTTAACT 57.986 33.333 13.49 1.12 44.30 2.24
3840 5119 9.746711 CTTTCTGATGTAAAATCAGTTAACTCG 57.253 33.333 4.77 2.02 44.30 4.18
3841 5120 8.827177 TTCTGATGTAAAATCAGTTAACTCGT 57.173 30.769 4.77 0.00 44.30 4.18
3842 5121 8.827177 TCTGATGTAAAATCAGTTAACTCGTT 57.173 30.769 4.77 0.57 44.30 3.85
3856 5135 3.746045 ACTCGTTGACACCAATACAGT 57.254 42.857 0.00 0.00 34.39 3.55
3871 5150 7.277981 CACCAATACAGTGTACTCCTGTTAATC 59.722 40.741 19.30 0.00 42.83 1.75
3896 5175 1.062002 CCCATCGTTTCGATCGTTTGG 59.938 52.381 15.94 12.88 45.19 3.28
3902 5181 6.452642 ATCGTTTCGATCGTTTGGTAACGC 62.453 45.833 15.94 0.00 43.45 4.84
3919 5198 3.913548 ACGCTATCTCTGCTGTCATAG 57.086 47.619 7.00 7.00 0.00 2.23
3950 5230 4.229876 GCTGTGCTTTTGGTATCAACTTC 58.770 43.478 0.00 0.00 31.78 3.01
3963 5243 3.878086 TCAACTTCATTGCTTCGTCAC 57.122 42.857 0.00 0.00 38.29 3.67
3991 5271 3.364442 CGGAGCATTGTTTGGGCA 58.636 55.556 0.00 0.00 0.00 5.36
4004 5284 3.217626 GTTTGGGCATGCTAGCTAGAAT 58.782 45.455 25.15 17.22 34.17 2.40
4017 5297 6.126940 TGCTAGCTAGAATTTTCAGTGGATCT 60.127 38.462 25.15 0.00 0.00 2.75
4023 5303 7.984617 GCTAGAATTTTCAGTGGATCTAGAGTT 59.015 37.037 10.57 0.00 38.97 3.01
4068 5348 7.931407 GGAATCATGTTTAGGGTTTCTTTGTTT 59.069 33.333 0.00 0.00 0.00 2.83
4071 5351 7.038659 TCATGTTTAGGGTTTCTTTGTTTGTG 58.961 34.615 0.00 0.00 0.00 3.33
4072 5352 5.172205 TGTTTAGGGTTTCTTTGTTTGTGC 58.828 37.500 0.00 0.00 0.00 4.57
4073 5353 5.172205 GTTTAGGGTTTCTTTGTTTGTGCA 58.828 37.500 0.00 0.00 0.00 4.57
4199 5480 9.308000 TCCTACAAATCAAACCATCTTACAAAT 57.692 29.630 0.00 0.00 0.00 2.32
4212 5493 8.482128 ACCATCTTACAAATTTCTTTTGAACCA 58.518 29.630 5.17 0.00 46.36 3.67
4213 5494 9.323985 CCATCTTACAAATTTCTTTTGAACCAA 57.676 29.630 5.17 0.00 46.36 3.67
4216 5497 9.712305 TCTTACAAATTTCTTTTGAACCAAACA 57.288 25.926 5.17 0.00 46.36 2.83
4219 5500 7.815641 ACAAATTTCTTTTGAACCAAACAAGG 58.184 30.769 5.17 0.00 46.36 3.61
4221 5502 8.510505 CAAATTTCTTTTGAACCAAACAAGGAA 58.489 29.630 0.00 0.00 46.36 3.36
4222 5503 8.806429 AATTTCTTTTGAACCAAACAAGGAAT 57.194 26.923 0.00 0.00 38.30 3.01
4223 5504 9.898152 AATTTCTTTTGAACCAAACAAGGAATA 57.102 25.926 0.00 0.00 38.30 1.75
4225 5506 8.940768 TTCTTTTGAACCAAACAAGGAATAAG 57.059 30.769 0.00 0.00 32.79 1.73
4226 5507 8.073467 TCTTTTGAACCAAACAAGGAATAAGT 57.927 30.769 0.00 0.00 32.79 2.24
4227 5508 9.191479 TCTTTTGAACCAAACAAGGAATAAGTA 57.809 29.630 0.00 0.00 32.79 2.24
4228 5509 9.463443 CTTTTGAACCAAACAAGGAATAAGTAG 57.537 33.333 0.00 0.00 32.79 2.57
4229 5510 6.569179 TGAACCAAACAAGGAATAAGTAGC 57.431 37.500 0.00 0.00 0.00 3.58
4230 5511 6.065374 TGAACCAAACAAGGAATAAGTAGCA 58.935 36.000 0.00 0.00 0.00 3.49
4231 5512 6.206634 TGAACCAAACAAGGAATAAGTAGCAG 59.793 38.462 0.00 0.00 0.00 4.24
4232 5513 4.459337 ACCAAACAAGGAATAAGTAGCAGC 59.541 41.667 0.00 0.00 0.00 5.25
4233 5514 4.437390 CCAAACAAGGAATAAGTAGCAGCG 60.437 45.833 0.00 0.00 0.00 5.18
4235 5516 4.202245 ACAAGGAATAAGTAGCAGCGAA 57.798 40.909 0.00 0.00 0.00 4.70
4236 5517 4.770795 ACAAGGAATAAGTAGCAGCGAAT 58.229 39.130 0.00 0.00 0.00 3.34
4238 5519 5.065218 ACAAGGAATAAGTAGCAGCGAATTG 59.935 40.000 0.00 0.00 0.00 2.32
4239 5520 5.023533 AGGAATAAGTAGCAGCGAATTGA 57.976 39.130 0.00 0.00 0.00 2.57
4240 5521 4.811557 AGGAATAAGTAGCAGCGAATTGAC 59.188 41.667 0.00 0.00 0.00 3.18
4242 5523 5.470845 AATAAGTAGCAGCGAATTGACAC 57.529 39.130 0.00 0.00 0.00 3.67
4243 5524 1.350193 AGTAGCAGCGAATTGACACG 58.650 50.000 0.00 0.00 0.00 4.49
4249 5530 4.698496 CGAATTGACACGCACGAC 57.302 55.556 0.00 0.00 0.00 4.34
4268 5576 6.510799 GCACGACTCAGATCAAATCAATAAGG 60.511 42.308 0.00 0.00 0.00 2.69
4275 5583 6.263842 TCAGATCAAATCAATAAGGTGATGGC 59.736 38.462 0.00 0.00 38.28 4.40
4291 5599 1.016627 TGGCGATTATCACAGCTTGC 58.983 50.000 0.00 0.00 0.00 4.01
4294 5602 2.603892 GGCGATTATCACAGCTTGCATG 60.604 50.000 0.00 0.00 0.00 4.06
4351 5659 4.159557 TCTTGGGGAAAGGGAAATCAAAG 58.840 43.478 0.00 0.00 36.46 2.77
4357 5665 4.322273 GGGAAAGGGAAATCAAAGCTGAAG 60.322 45.833 0.00 0.00 34.49 3.02
4359 5667 2.812658 AGGGAAATCAAAGCTGAAGGG 58.187 47.619 0.00 0.00 34.49 3.95
4360 5668 1.205655 GGGAAATCAAAGCTGAAGGGC 59.794 52.381 0.00 0.00 34.49 5.19
4412 5750 5.394224 TCATCATGATGCACACAACAAAT 57.606 34.783 27.68 0.00 38.65 2.32
4425 5763 6.474427 GCACACAACAAATCCATAGATGATTG 59.526 38.462 0.00 0.00 31.29 2.67
4426 5764 7.541162 CACACAACAAATCCATAGATGATTGT 58.459 34.615 0.00 0.00 34.99 2.71
4429 5767 9.426837 CACAACAAATCCATAGATGATTGTTTT 57.573 29.630 13.56 8.53 37.08 2.43
4430 5768 9.643693 ACAACAAATCCATAGATGATTGTTTTC 57.356 29.630 13.56 0.00 37.08 2.29
4452 5790 9.712305 TTTTCTTCTTATAACTCTTCCAGACAG 57.288 33.333 0.00 0.00 0.00 3.51
4453 5791 8.651589 TTCTTCTTATAACTCTTCCAGACAGA 57.348 34.615 0.00 0.00 0.00 3.41
4460 5798 3.686016 ACTCTTCCAGACAGAGTCTCTC 58.314 50.000 0.00 0.00 46.79 3.20
4462 5800 4.202567 ACTCTTCCAGACAGAGTCTCTCTT 60.203 45.833 0.00 0.00 46.79 2.85
4465 5803 1.824230 CCAGACAGAGTCTCTCTTGGG 59.176 57.143 0.00 0.00 41.37 4.12
4466 5804 2.524306 CAGACAGAGTCTCTCTTGGGT 58.476 52.381 0.00 0.00 41.37 4.51
4467 5805 2.491693 CAGACAGAGTCTCTCTTGGGTC 59.508 54.545 0.00 4.38 41.37 4.46
4468 5806 2.109128 AGACAGAGTCTCTCTTGGGTCA 59.891 50.000 15.79 0.00 38.71 4.02
4469 5807 2.230266 GACAGAGTCTCTCTTGGGTCAC 59.770 54.545 0.00 0.00 38.99 3.67
4474 5813 1.822371 GTCTCTCTTGGGTCACTCTCC 59.178 57.143 0.00 0.00 0.00 3.71
4483 5822 1.187087 GGTCACTCTCCGTGGAAGAT 58.813 55.000 5.48 0.00 43.94 2.40
4484 5823 2.376109 GGTCACTCTCCGTGGAAGATA 58.624 52.381 5.48 0.00 43.94 1.98
4485 5824 2.099427 GGTCACTCTCCGTGGAAGATAC 59.901 54.545 5.48 3.71 43.94 2.24
4486 5825 3.018149 GTCACTCTCCGTGGAAGATACT 58.982 50.000 5.48 0.00 43.94 2.12
4487 5826 3.065648 GTCACTCTCCGTGGAAGATACTC 59.934 52.174 5.48 0.00 43.94 2.59
4488 5827 2.359531 CACTCTCCGTGGAAGATACTCC 59.640 54.545 5.48 0.00 40.02 3.85
4489 5828 1.957877 CTCTCCGTGGAAGATACTCCC 59.042 57.143 0.00 0.00 34.22 4.30
4490 5829 1.569548 TCTCCGTGGAAGATACTCCCT 59.430 52.381 0.00 0.00 34.22 4.20
4491 5830 2.024273 TCTCCGTGGAAGATACTCCCTT 60.024 50.000 0.00 0.00 34.22 3.95
4492 5831 2.362717 CTCCGTGGAAGATACTCCCTTC 59.637 54.545 0.00 0.00 39.32 3.46
4493 5832 2.024273 TCCGTGGAAGATACTCCCTTCT 60.024 50.000 0.00 0.00 39.80 2.85
4494 5833 2.766828 CCGTGGAAGATACTCCCTTCTT 59.233 50.000 0.00 0.00 39.80 2.52
4495 5834 3.197983 CCGTGGAAGATACTCCCTTCTTT 59.802 47.826 0.00 0.00 39.80 2.52
4496 5835 4.434520 CGTGGAAGATACTCCCTTCTTTC 58.565 47.826 0.00 0.00 39.80 2.62
4497 5836 4.680975 CGTGGAAGATACTCCCTTCTTTCC 60.681 50.000 0.00 0.00 39.80 3.13
4498 5837 4.471747 GTGGAAGATACTCCCTTCTTTCCT 59.528 45.833 0.00 0.00 39.80 3.36
4499 5838 5.045505 GTGGAAGATACTCCCTTCTTTCCTT 60.046 44.000 0.00 0.00 39.80 3.36
4500 5839 5.551977 TGGAAGATACTCCCTTCTTTCCTTT 59.448 40.000 0.00 0.00 39.80 3.11
4501 5840 6.733807 TGGAAGATACTCCCTTCTTTCCTTTA 59.266 38.462 0.00 0.00 39.80 1.85
4502 5841 7.406151 TGGAAGATACTCCCTTCTTTCCTTTAT 59.594 37.037 0.00 0.00 39.80 1.40
4503 5842 8.935741 GGAAGATACTCCCTTCTTTCCTTTATA 58.064 37.037 0.00 0.00 39.80 0.98
4510 5849 9.907229 ACTCCCTTCTTTCCTTTATATAAAGTG 57.093 33.333 26.18 19.46 40.73 3.16
4511 5850 9.907229 CTCCCTTCTTTCCTTTATATAAAGTGT 57.093 33.333 26.18 0.00 40.73 3.55
4547 5886 8.422973 TGATAATATTTCAAAATGCAAGGTGC 57.577 30.769 0.00 0.00 45.29 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.488792 CAGATCGAGATAATCTCCATGATCAAC 59.511 40.741 0.00 0.00 40.34 3.18
13 14 6.006449 TGACAGATCGAGATAATCTCCATGA 58.994 40.000 0.00 0.00 40.34 3.07
14 15 6.150809 TCTGACAGATCGAGATAATCTCCATG 59.849 42.308 0.00 0.00 40.34 3.66
255 262 2.416547 CCGTCAGCACTTTCCATTACAG 59.583 50.000 0.00 0.00 0.00 2.74
279 286 2.671888 GCGAGTGGCATAGATCATCATG 59.328 50.000 0.00 0.00 42.87 3.07
320 328 3.016736 CACCTTCCATAAACGAATGGCT 58.983 45.455 10.17 0.00 45.21 4.75
328 336 8.254508 TGCCAAAAATATACACCTTCCATAAAC 58.745 33.333 0.00 0.00 0.00 2.01
404 412 4.980590 TGCCACTAATCAACAAATTAGCG 58.019 39.130 4.06 0.00 41.12 4.26
417 425 7.665974 GGCCTAATAGATTTACTTGCCACTAAT 59.334 37.037 0.00 0.00 36.40 1.73
422 430 5.376625 CTGGCCTAATAGATTTACTTGCCA 58.623 41.667 3.32 0.00 43.55 4.92
446 454 1.442769 TGCGTGCATCTCTTCCTTTC 58.557 50.000 0.00 0.00 0.00 2.62
478 486 7.670140 CCCTCCTTGTAAAAAGGAAGAAAGTAT 59.330 37.037 8.13 0.00 45.10 2.12
488 496 5.532779 GCATCTATCCCTCCTTGTAAAAAGG 59.467 44.000 0.00 0.00 38.78 3.11
508 517 1.410517 TGTCTCTCTCCCGATTGCATC 59.589 52.381 0.00 0.00 0.00 3.91
557 566 7.699812 GTGCATTTCTCTAATTCCTCACAATTC 59.300 37.037 0.00 0.00 0.00 2.17
678 1090 4.846779 TGTTTGAAGATGTACCCAAAGC 57.153 40.909 0.00 0.00 0.00 3.51
698 1110 1.608590 ACACTCCATGGCGAACTTTTG 59.391 47.619 9.17 0.00 0.00 2.44
747 1170 1.365368 CCAATCGCGTGTGCATGGTA 61.365 55.000 5.77 0.00 42.97 3.25
910 1339 3.552384 GGGTGGTCGTGGTGGTGA 61.552 66.667 0.00 0.00 0.00 4.02
920 1349 4.815108 GGGAATGCCGGGGTGGTC 62.815 72.222 2.18 0.00 41.21 4.02
1270 1699 2.173143 AGAAACTAAACCGGTGGTGGAA 59.827 45.455 8.52 0.00 35.34 3.53
1292 1721 2.099062 CCGACGATGCAAGCAAGC 59.901 61.111 0.00 0.00 0.00 4.01
1645 2078 8.638685 ATCTCAAAGTTGAAAGACACAAAATG 57.361 30.769 0.00 0.00 36.64 2.32
2042 2494 8.347004 TGCTCATTATGAAGTTTCACCAATTA 57.653 30.769 0.00 0.00 40.49 1.40
2080 2532 4.168675 AGCCCATATTTCATTCTCTTCCCA 59.831 41.667 0.00 0.00 0.00 4.37
2249 2705 3.963374 TCCAATGTTGTCCAAATGTCCAA 59.037 39.130 0.00 0.00 0.00 3.53
2250 2706 3.570540 TCCAATGTTGTCCAAATGTCCA 58.429 40.909 0.00 0.00 0.00 4.02
2251 2707 4.021192 ACATCCAATGTTGTCCAAATGTCC 60.021 41.667 0.00 0.00 41.63 4.02
2252 2708 5.138125 ACATCCAATGTTGTCCAAATGTC 57.862 39.130 0.00 0.00 41.63 3.06
2291 2747 1.140852 ACTTGCTGCTGACACCTAACA 59.859 47.619 0.00 0.00 0.00 2.41
2374 2830 6.388435 AGGATATCACTCGTTACCTTGTAC 57.612 41.667 4.83 0.00 0.00 2.90
2375 2831 6.238566 CGAAGGATATCACTCGTTACCTTGTA 60.239 42.308 14.39 0.00 36.58 2.41
2376 2832 5.450137 CGAAGGATATCACTCGTTACCTTGT 60.450 44.000 14.39 0.00 36.58 3.16
2377 2833 4.976731 CGAAGGATATCACTCGTTACCTTG 59.023 45.833 14.39 0.00 36.58 3.61
2463 2919 8.345724 AGAACAGCATGAGATAAGTGAATTTT 57.654 30.769 0.00 0.00 39.69 1.82
2633 3089 1.940613 GTTGATAATCCCAGTGCGTCC 59.059 52.381 0.00 0.00 0.00 4.79
2802 3259 7.704789 AATAGAACGTAGACGAAAACAAACT 57.295 32.000 9.41 0.00 43.02 2.66
2813 3270 8.976986 TCTCAACCTAAAAATAGAACGTAGAC 57.023 34.615 0.00 0.00 0.00 2.59
2855 3312 5.173664 AGGAACTTACCCTTTTCGTATTCG 58.826 41.667 0.00 0.00 27.25 3.34
2874 3331 4.466370 CACTTGGGACTGTATCAGTAGGAA 59.534 45.833 2.29 0.00 45.44 3.36
2893 3350 4.380843 TCCAAACATCCATGTACCACTT 57.619 40.909 0.00 0.00 40.80 3.16
2926 3383 0.727970 CTGATGCTGACTTGCTGAGC 59.272 55.000 0.00 0.00 0.00 4.26
3013 3470 5.778750 TGCCTCCCCTATAACTATACTGAAC 59.221 44.000 0.00 0.00 0.00 3.18
3043 3500 0.529992 AATCCCGCGCTTGCTACTAC 60.530 55.000 5.56 0.00 36.08 2.73
3075 3533 4.043435 AGGTAGGCTGAGAACCAAAAGATT 59.957 41.667 6.93 0.00 35.64 2.40
3119 4335 5.381174 ACGCACTACTACATCTTTACACA 57.619 39.130 0.00 0.00 0.00 3.72
3137 4400 5.637006 AACAATAGAAAGGCATTAACGCA 57.363 34.783 0.00 0.00 0.00 5.24
3145 4408 8.420222 TGAGAAATCAAAAACAATAGAAAGGCA 58.580 29.630 0.00 0.00 0.00 4.75
3233 4496 1.767088 CAGCAGAATCTGATGGGAGGA 59.233 52.381 19.73 0.00 43.16 3.71
3331 4595 6.407202 TCTGGTTGCTATCTAGAAAGTTTCC 58.593 40.000 12.05 0.00 0.00 3.13
3345 4609 4.398988 CAGGCATTAATGTTCTGGTTGCTA 59.601 41.667 22.26 0.00 32.07 3.49
3346 4610 3.194116 CAGGCATTAATGTTCTGGTTGCT 59.806 43.478 22.26 0.02 32.07 3.91
3347 4611 3.193267 TCAGGCATTAATGTTCTGGTTGC 59.807 43.478 25.97 10.70 34.45 4.17
3348 4612 4.676196 GCTCAGGCATTAATGTTCTGGTTG 60.676 45.833 25.97 20.23 38.54 3.77
3453 4719 5.591877 AGCTTTTCCATGAGCTAGTATTTGG 59.408 40.000 4.90 0.00 46.78 3.28
3566 4832 8.055279 TGATCACTTGTTTTCACTTTCTTCTT 57.945 30.769 0.00 0.00 0.00 2.52
3581 4847 6.638063 CGTGAATTTGTCATTTGATCACTTGT 59.362 34.615 0.00 0.00 38.90 3.16
3634 4905 0.107897 ATCCGGCGCTGACAATTGTA 60.108 50.000 20.25 0.00 0.00 2.41
3661 4932 1.692411 AAGGCCCTGAAGTGAAACAC 58.308 50.000 0.00 0.00 41.43 3.32
3669 4940 2.937519 GGGATAAGAAAGGCCCTGAAG 58.062 52.381 0.00 0.00 37.59 3.02
3678 4949 4.631813 CGGTTTGTCTCAGGGATAAGAAAG 59.368 45.833 0.00 0.00 0.00 2.62
3679 4950 4.564821 CCGGTTTGTCTCAGGGATAAGAAA 60.565 45.833 0.00 0.00 0.00 2.52
3680 4951 3.055385 CCGGTTTGTCTCAGGGATAAGAA 60.055 47.826 0.00 0.00 0.00 2.52
3681 4952 2.500098 CCGGTTTGTCTCAGGGATAAGA 59.500 50.000 0.00 0.00 0.00 2.10
3750 5021 1.594331 ACAAGTGAAAAGACCCGCTC 58.406 50.000 0.00 0.00 0.00 5.03
3754 5025 2.737252 CGAGCTACAAGTGAAAAGACCC 59.263 50.000 0.00 0.00 0.00 4.46
3780 5051 2.283388 CTTGGTGCTGGGCATGGT 60.283 61.111 0.00 0.00 41.91 3.55
3835 5114 3.807622 CACTGTATTGGTGTCAACGAGTT 59.192 43.478 0.00 0.00 35.48 3.01
3836 5115 3.181469 ACACTGTATTGGTGTCAACGAGT 60.181 43.478 0.00 0.00 43.35 4.18
3837 5116 3.390135 ACACTGTATTGGTGTCAACGAG 58.610 45.455 0.00 0.00 43.35 4.18
3838 5117 3.462483 ACACTGTATTGGTGTCAACGA 57.538 42.857 0.00 0.00 43.35 3.85
3839 5118 4.304110 AGTACACTGTATTGGTGTCAACG 58.696 43.478 2.70 0.00 45.23 4.10
3840 5119 4.689345 GGAGTACACTGTATTGGTGTCAAC 59.311 45.833 2.70 0.00 45.23 3.18
3841 5120 4.591498 AGGAGTACACTGTATTGGTGTCAA 59.409 41.667 2.70 0.00 45.23 3.18
3842 5121 4.021456 CAGGAGTACACTGTATTGGTGTCA 60.021 45.833 8.87 0.00 45.23 3.58
3856 5135 2.429610 GGCCTCGATTAACAGGAGTACA 59.570 50.000 0.00 0.00 30.32 2.90
3871 5150 1.215655 GATCGAAACGATGGGCCTCG 61.216 60.000 19.32 19.32 47.00 4.63
3896 5175 3.422417 TGACAGCAGAGATAGCGTTAC 57.578 47.619 0.00 0.00 37.01 2.50
3908 5187 4.093556 CAGCATGCATATCTATGACAGCAG 59.906 45.833 21.98 0.00 35.75 4.24
3950 5230 1.225475 GCGACGTGACGAAGCAATG 60.225 57.895 13.70 0.00 34.54 2.82
3975 5255 0.741927 GCATGCCCAAACAATGCTCC 60.742 55.000 6.36 0.00 35.55 4.70
3986 5266 3.582998 AAATTCTAGCTAGCATGCCCA 57.417 42.857 18.83 1.07 0.00 5.36
3989 5269 5.505324 CCACTGAAAATTCTAGCTAGCATGC 60.505 44.000 18.83 10.51 0.00 4.06
3991 5271 5.994250 TCCACTGAAAATTCTAGCTAGCAT 58.006 37.500 18.83 8.07 0.00 3.79
4004 5284 9.284968 CCTTTTTAACTCTAGATCCACTGAAAA 57.715 33.333 0.00 0.00 0.00 2.29
4017 5297 8.265055 CCCAGATATGTCACCTTTTTAACTCTA 58.735 37.037 0.00 0.00 0.00 2.43
4023 5303 7.638444 TGATTCCCAGATATGTCACCTTTTTA 58.362 34.615 0.00 0.00 0.00 1.52
4029 5309 4.978099 ACATGATTCCCAGATATGTCACC 58.022 43.478 0.00 0.00 0.00 4.02
4038 5318 4.946160 AACCCTAAACATGATTCCCAGA 57.054 40.909 0.00 0.00 0.00 3.86
4040 5320 5.269554 AGAAACCCTAAACATGATTCCCA 57.730 39.130 0.00 0.00 0.00 4.37
4068 5348 2.555325 CAGGATCAAAGAGCTTTGCACA 59.445 45.455 16.12 2.40 46.92 4.57
4071 5351 4.637534 TCATACAGGATCAAAGAGCTTTGC 59.362 41.667 16.12 5.36 46.92 3.68
4073 5353 6.059787 AGTCATACAGGATCAAAGAGCTTT 57.940 37.500 0.00 0.00 0.00 3.51
4082 5363 8.193953 TCATATGCTTTAGTCATACAGGATCA 57.806 34.615 0.00 0.00 30.16 2.92
4112 5393 2.412870 TCAAACGCACTTCGATGACAT 58.587 42.857 5.16 0.00 41.67 3.06
4119 5400 1.447938 GTTGCAATCAAACGCACTTCG 59.552 47.619 0.59 0.00 45.38 3.79
4199 5480 9.377312 CTTATTCCTTGTTTGGTTCAAAAGAAA 57.623 29.630 0.00 0.00 35.03 2.52
4202 5483 9.463443 CTACTTATTCCTTGTTTGGTTCAAAAG 57.537 33.333 0.00 0.00 35.03 2.27
4203 5484 7.923878 GCTACTTATTCCTTGTTTGGTTCAAAA 59.076 33.333 0.00 0.00 35.03 2.44
4204 5485 7.068839 TGCTACTTATTCCTTGTTTGGTTCAAA 59.931 33.333 0.00 0.00 0.00 2.69
4207 5488 6.569179 TGCTACTTATTCCTTGTTTGGTTC 57.431 37.500 0.00 0.00 0.00 3.62
4208 5489 5.048013 GCTGCTACTTATTCCTTGTTTGGTT 60.048 40.000 0.00 0.00 0.00 3.67
4209 5490 4.459337 GCTGCTACTTATTCCTTGTTTGGT 59.541 41.667 0.00 0.00 0.00 3.67
4210 5491 4.437390 CGCTGCTACTTATTCCTTGTTTGG 60.437 45.833 0.00 0.00 0.00 3.28
4212 5493 4.575885 TCGCTGCTACTTATTCCTTGTTT 58.424 39.130 0.00 0.00 0.00 2.83
4213 5494 4.202245 TCGCTGCTACTTATTCCTTGTT 57.798 40.909 0.00 0.00 0.00 2.83
4214 5495 3.887621 TCGCTGCTACTTATTCCTTGT 57.112 42.857 0.00 0.00 0.00 3.16
4215 5496 5.294306 TCAATTCGCTGCTACTTATTCCTTG 59.706 40.000 0.00 0.00 0.00 3.61
4216 5497 5.294552 GTCAATTCGCTGCTACTTATTCCTT 59.705 40.000 0.00 0.00 0.00 3.36
4217 5498 4.811557 GTCAATTCGCTGCTACTTATTCCT 59.188 41.667 0.00 0.00 0.00 3.36
4218 5499 4.570772 TGTCAATTCGCTGCTACTTATTCC 59.429 41.667 0.00 0.00 0.00 3.01
4219 5500 5.493735 GTGTCAATTCGCTGCTACTTATTC 58.506 41.667 0.00 0.00 0.00 1.75
4221 5502 3.551890 CGTGTCAATTCGCTGCTACTTAT 59.448 43.478 0.00 0.00 0.00 1.73
4222 5503 2.921121 CGTGTCAATTCGCTGCTACTTA 59.079 45.455 0.00 0.00 0.00 2.24
4223 5504 1.726791 CGTGTCAATTCGCTGCTACTT 59.273 47.619 0.00 0.00 0.00 2.24
4225 5506 3.858040 CGTGTCAATTCGCTGCTAC 57.142 52.632 0.00 0.00 0.00 3.58
4232 5513 0.091344 GAGTCGTGCGTGTCAATTCG 59.909 55.000 0.00 0.00 0.00 3.34
4233 5514 1.125021 CTGAGTCGTGCGTGTCAATTC 59.875 52.381 0.00 0.00 0.00 2.17
4235 5516 0.313987 TCTGAGTCGTGCGTGTCAAT 59.686 50.000 0.00 0.00 0.00 2.57
4236 5517 0.313987 ATCTGAGTCGTGCGTGTCAA 59.686 50.000 0.00 0.00 0.00 3.18
4238 5519 0.109735 TGATCTGAGTCGTGCGTGTC 60.110 55.000 0.00 0.00 0.00 3.67
4239 5520 0.313987 TTGATCTGAGTCGTGCGTGT 59.686 50.000 0.00 0.00 0.00 4.49
4240 5521 1.418373 TTTGATCTGAGTCGTGCGTG 58.582 50.000 0.00 0.00 0.00 5.34
4242 5523 2.262211 TGATTTGATCTGAGTCGTGCG 58.738 47.619 0.00 0.00 0.00 5.34
4243 5524 4.871993 ATTGATTTGATCTGAGTCGTGC 57.128 40.909 0.00 0.00 0.00 5.34
4244 5525 6.536582 ACCTTATTGATTTGATCTGAGTCGTG 59.463 38.462 0.00 0.00 0.00 4.35
4247 5528 8.557864 CATCACCTTATTGATTTGATCTGAGTC 58.442 37.037 0.00 0.00 33.74 3.36
4248 5529 7.501559 CCATCACCTTATTGATTTGATCTGAGT 59.498 37.037 0.00 0.00 33.74 3.41
4249 5530 7.521748 GCCATCACCTTATTGATTTGATCTGAG 60.522 40.741 0.00 0.00 33.74 3.35
4275 5583 3.558829 ACTCATGCAAGCTGTGATAATCG 59.441 43.478 0.00 0.00 0.00 3.34
4287 5595 2.602211 GTCGACTCATCACTCATGCAAG 59.398 50.000 8.70 0.00 31.70 4.01
4291 5599 1.401905 TCCGTCGACTCATCACTCATG 59.598 52.381 14.70 0.00 0.00 3.07
4294 5602 1.862008 GCATCCGTCGACTCATCACTC 60.862 57.143 14.70 0.00 0.00 3.51
4327 5635 3.778265 TGATTTCCCTTTCCCCAAGAAG 58.222 45.455 0.00 0.00 35.40 2.85
4351 5659 3.155093 CAACACATATTGCCCTTCAGC 57.845 47.619 0.00 0.00 0.00 4.26
4360 5668 3.866910 GCCAGGAATTGCAACACATATTG 59.133 43.478 0.00 0.00 0.00 1.90
4446 5784 2.491693 GACCCAAGAGAGACTCTGTCTG 59.508 54.545 10.44 7.18 43.53 3.51
4452 5790 2.752903 GAGAGTGACCCAAGAGAGACTC 59.247 54.545 0.00 0.00 0.00 3.36
4453 5791 2.556559 GGAGAGTGACCCAAGAGAGACT 60.557 54.545 0.00 0.00 0.00 3.24
4465 5803 5.987495 GGAGTATCTTCCACGGAGAGTGAC 61.987 54.167 0.00 0.00 44.52 3.67
4466 5804 3.936031 GGAGTATCTTCCACGGAGAGTGA 60.936 52.174 0.00 0.00 44.52 3.41
4467 5805 2.359531 GGAGTATCTTCCACGGAGAGTG 59.640 54.545 0.00 0.00 42.60 3.51
4468 5806 2.657143 GGAGTATCTTCCACGGAGAGT 58.343 52.381 0.00 0.00 37.20 3.24
4469 5807 1.957877 GGGAGTATCTTCCACGGAGAG 59.042 57.143 0.00 0.00 39.09 3.20
4474 5813 4.434520 GAAAGAAGGGAGTATCTTCCACG 58.565 47.826 0.00 0.00 40.94 4.94
4484 5823 9.907229 CACTTTATATAAAGGAAAGAAGGGAGT 57.093 33.333 29.82 9.96 45.23 3.85
4485 5824 9.907229 ACACTTTATATAAAGGAAAGAAGGGAG 57.093 33.333 29.82 9.43 45.23 4.30
4521 5860 8.881743 GCACCTTGCATTTTGAAATATTATCAA 58.118 29.630 8.21 8.21 44.26 2.57
4522 5861 8.422973 GCACCTTGCATTTTGAAATATTATCA 57.577 30.769 0.00 0.00 44.26 2.15


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

AutoCloner maintained by Alex Coulton.