Multiple sequence alignment - TraesCS6D01G246100

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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 TraesCS6D01G246100 chr6D 100.000 4267 0 0 1 4267 348088196 348092462 0.000000e+00 7880
1 TraesCS6D01G246100 chr6A 97.032 3470 84 8 3 3468 495448412 495444958 0.000000e+00 5819
2 TraesCS6D01G246100 chr6A 93.357 572 25 6 3473 4034 495443603 495443035 0.000000e+00 833
3 TraesCS6D01G246100 chr6B 95.460 3480 102 20 3 3468 531738080 531734643 0.000000e+00 5500
4 TraesCS6D01G246100 chr6B 91.787 414 21 7 3471 3877 531734575 531734168 8.010000e-157 564


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 TraesCS6D01G246100 chr6D 348088196 348092462 4266 False 7880 7880 100.0000 1 4267 1 chr6D.!!$F1 4266
1 TraesCS6D01G246100 chr6A 495443035 495448412 5377 True 3326 5819 95.1945 3 4034 2 chr6A.!!$R1 4031
2 TraesCS6D01G246100 chr6B 531734168 531738080 3912 True 3032 5500 93.6235 3 3877 2 chr6B.!!$R1 3874

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
68 69 1.421268 TGCCTTCAGTCCTTCACATGT 59.579 47.619 0.0 0.0 0.0 3.21 F
1737 1742 1.745489 CGGGAGGCAGTTTGGTAGC 60.745 63.158 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 2004 1.667236 TCATACTGAAATGGCGCCAG 58.333 50.0 35.36 22.7 0.00 4.85 R
3427 3444 0.104855 ACAGCGAGTGTGCAAGAAGA 59.895 50.0 0.00 0.0 38.28 2.87 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
68 69 1.421268 TGCCTTCAGTCCTTCACATGT 59.579 47.619 0.00 0.00 0.00 3.21
151 152 2.027625 GCACCCCAACTCGTTCTCG 61.028 63.158 0.00 0.00 38.55 4.04
595 600 2.431454 GGTCTTGAGGAAGCAAAGAGG 58.569 52.381 0.00 0.00 0.00 3.69
880 885 5.068198 ACTGTGTCATTTGTTCATCAGCTTT 59.932 36.000 0.00 0.00 0.00 3.51
960 965 4.020485 TGAGGCTCCTTGGTTACTAACTTC 60.020 45.833 12.86 0.00 0.00 3.01
1094 1099 3.907474 TCCCTGGACTCTATTTGTGACAA 59.093 43.478 0.00 0.00 0.00 3.18
1329 1334 3.721035 TCATATCATCAGCCAACAGTCG 58.279 45.455 0.00 0.00 0.00 4.18
1672 1677 3.057386 CAGTGATGATGAGAGAGATCGGG 60.057 52.174 0.00 0.00 0.00 5.14
1737 1742 1.745489 CGGGAGGCAGTTTGGTAGC 60.745 63.158 0.00 0.00 0.00 3.58
1952 1957 9.221775 GATAAATCACTTAAACGGCAACTAATG 57.778 33.333 0.00 0.00 0.00 1.90
1999 2004 8.516234 TCGCTATCTTCTATTAGTTTCCAGATC 58.484 37.037 0.00 0.00 0.00 2.75
2072 2077 2.026262 ACCACTACCACTGGCATTTAGG 60.026 50.000 0.00 0.00 31.13 2.69
2097 2102 6.530120 AGGTCAAAACAAACCTGAACTTTTT 58.470 32.000 0.00 0.00 44.26 1.94
2098 2103 6.649141 AGGTCAAAACAAACCTGAACTTTTTC 59.351 34.615 0.00 0.00 44.26 2.29
2099 2104 6.425417 GGTCAAAACAAACCTGAACTTTTTCA 59.575 34.615 0.00 0.00 39.55 2.69
2144 2149 4.504097 CACCAGCAAGCTTTTACAAAGTTC 59.496 41.667 0.00 0.00 0.00 3.01
2150 2155 5.009710 GCAAGCTTTTACAAAGTTCCCTAGT 59.990 40.000 0.00 0.00 0.00 2.57
2250 2257 3.698040 GGTGAATACTGGAGTTCTCGGTA 59.302 47.826 0.00 6.70 0.00 4.02
2383 2390 7.672983 TTAGGATCTGTCACTTTTTGCTTAG 57.327 36.000 0.00 0.00 0.00 2.18
2619 2627 9.161629 TGTATTTCTCGTGAATGTGATGTTATT 57.838 29.630 0.02 0.00 31.56 1.40
2826 2834 1.998315 CAGCAAGTGAAGGACGATCAG 59.002 52.381 0.00 0.00 0.00 2.90
2886 2894 2.447047 ACAAAGGAGGTCCAAGGAATGT 59.553 45.455 0.00 0.00 38.89 2.71
3068 3076 6.925211 TGTTCAACACAAAGGTAACAATCAA 58.075 32.000 0.00 0.00 31.99 2.57
3073 3081 8.877779 TCAACACAAAGGTAACAATCAAATTTG 58.122 29.630 12.15 12.15 41.41 2.32
3117 3125 1.405661 CCTCTTCCCCGTTTCTACTGC 60.406 57.143 0.00 0.00 0.00 4.40
3155 3163 4.256110 TGTACCATTCTGCTTGACATCTG 58.744 43.478 0.00 0.00 0.00 2.90
3194 3202 3.844741 GAGGGCTCCTCGGTCTAC 58.155 66.667 5.60 0.00 41.08 2.59
3322 3338 5.695851 CAGAATGGTCCATTATGTTAGCC 57.304 43.478 25.08 8.80 38.00 3.93
3468 3485 7.387122 GCTGTAATGATCTGATGCTTCTGATTA 59.613 37.037 18.81 16.10 39.73 1.75
3469 3486 8.599055 TGTAATGATCTGATGCTTCTGATTAC 57.401 34.615 18.81 17.40 39.73 1.89
3471 3488 5.520376 TGATCTGATGCTTCTGATTACGA 57.480 39.130 18.81 5.77 39.73 3.43
3513 4880 3.006112 TGTCTTGGGTTGCAACACTTA 57.994 42.857 30.67 18.18 32.22 2.24
3521 4888 4.142271 TGGGTTGCAACACTTACTTCAAAG 60.142 41.667 30.67 0.00 32.22 2.77
3527 4894 4.735338 GCAACACTTACTTCAAAGTTGAGC 59.265 41.667 0.00 1.43 37.61 4.26
3560 4927 3.525199 AGATGGGACTGGTGCTTTAGATT 59.475 43.478 0.00 0.00 0.00 2.40
3579 4949 0.984230 TCTTACCACCTTGAGCCCAG 59.016 55.000 0.00 0.00 0.00 4.45
3719 5094 2.984989 AGGAGGGGGTGGTATTAGTT 57.015 50.000 0.00 0.00 0.00 2.24
3752 5127 3.733344 GATTCGGGCTGCCTGCGTA 62.733 63.158 22.83 10.66 44.05 4.42
3805 5180 3.553095 GAGAAACTGGGGCGGCAGT 62.553 63.158 12.47 3.25 0.00 4.40
3806 5181 3.365265 GAAACTGGGGCGGCAGTG 61.365 66.667 12.47 1.72 0.00 3.66
3807 5182 4.974721 AAACTGGGGCGGCAGTGG 62.975 66.667 12.47 0.00 0.00 4.00
3830 5205 1.250840 GGGGTGGTTGAGCATGGTTC 61.251 60.000 0.00 0.00 0.00 3.62
3831 5206 1.250840 GGGTGGTTGAGCATGGTTCC 61.251 60.000 0.00 3.43 0.00 3.62
3832 5207 0.539438 GGTGGTTGAGCATGGTTCCA 60.539 55.000 0.00 6.11 0.00 3.53
3877 5255 1.209261 CTTCAGGAGAGGAAGAAGGCC 59.791 57.143 0.00 0.00 43.46 5.19
3898 5276 4.264253 CCTATGGTTTCACATGAGCTTGA 58.736 43.478 0.00 0.00 32.39 3.02
4034 5414 0.672401 CGGAGCCCGCAGAGTAAAAA 60.672 55.000 0.56 0.00 41.17 1.94
4055 5435 2.815384 AAAAACAGACCAACCCGGG 58.185 52.632 22.25 22.25 40.22 5.73
4061 5441 2.582978 GACCAACCCGGGCTAGAC 59.417 66.667 24.08 5.60 41.26 2.59
4062 5442 3.007323 ACCAACCCGGGCTAGACC 61.007 66.667 24.08 3.74 40.22 3.85
4063 5443 3.006728 CCAACCCGGGCTAGACCA 61.007 66.667 24.08 0.00 42.05 4.02
4064 5444 2.598787 CCAACCCGGGCTAGACCAA 61.599 63.158 24.08 0.00 42.05 3.67
4065 5445 1.376812 CAACCCGGGCTAGACCAAC 60.377 63.158 24.08 0.00 42.05 3.77
4066 5446 1.538135 AACCCGGGCTAGACCAACT 60.538 57.895 24.08 0.00 42.05 3.16
4067 5447 1.838073 AACCCGGGCTAGACCAACTG 61.838 60.000 24.08 1.46 42.05 3.16
4068 5448 2.584608 CCGGGCTAGACCAACTGG 59.415 66.667 16.92 3.22 42.05 4.00
4069 5449 1.987855 CCGGGCTAGACCAACTGGA 60.988 63.158 16.92 0.00 42.05 3.86
4070 5450 1.517832 CGGGCTAGACCAACTGGAG 59.482 63.158 16.92 0.00 42.05 3.86
4071 5451 1.222113 GGGCTAGACCAACTGGAGC 59.778 63.158 10.77 0.97 42.05 4.70
4072 5452 1.222113 GGCTAGACCAACTGGAGCC 59.778 63.158 10.32 10.32 42.91 4.70
4073 5453 1.222113 GCTAGACCAACTGGAGCCC 59.778 63.158 1.86 0.00 38.94 5.19
4074 5454 1.553690 GCTAGACCAACTGGAGCCCA 61.554 60.000 1.86 0.00 38.94 5.36
4075 5455 0.984230 CTAGACCAACTGGAGCCCAA 59.016 55.000 1.86 0.00 38.94 4.12
4076 5456 0.984230 TAGACCAACTGGAGCCCAAG 59.016 55.000 1.86 0.00 38.94 3.61
4077 5457 1.062488 AGACCAACTGGAGCCCAAGT 61.062 55.000 1.86 0.00 38.94 3.16
4078 5458 0.178990 GACCAACTGGAGCCCAAGTT 60.179 55.000 1.86 0.00 38.94 2.66
4079 5459 0.468029 ACCAACTGGAGCCCAAGTTG 60.468 55.000 8.49 8.49 39.72 3.16
4080 5460 1.662044 CAACTGGAGCCCAAGTTGC 59.338 57.895 2.14 0.00 36.59 4.17
4081 5461 1.531602 AACTGGAGCCCAAGTTGCC 60.532 57.895 0.00 0.00 30.80 4.52
4082 5462 2.011617 AACTGGAGCCCAAGTTGCCT 62.012 55.000 0.00 0.00 30.80 4.75
4083 5463 1.228675 CTGGAGCCCAAGTTGCCTT 60.229 57.895 0.00 0.00 30.80 4.35
4084 5464 1.228552 TGGAGCCCAAGTTGCCTTC 60.229 57.895 0.00 0.00 0.00 3.46
4085 5465 1.979155 GGAGCCCAAGTTGCCTTCC 60.979 63.158 0.00 0.00 0.00 3.46
4086 5466 1.228552 GAGCCCAAGTTGCCTTCCA 60.229 57.895 0.00 0.00 0.00 3.53
4087 5467 1.527433 GAGCCCAAGTTGCCTTCCAC 61.527 60.000 0.00 0.00 0.00 4.02
4088 5468 2.574018 GCCCAAGTTGCCTTCCACC 61.574 63.158 0.00 0.00 0.00 4.61
4089 5469 1.153756 CCCAAGTTGCCTTCCACCT 59.846 57.895 0.00 0.00 0.00 4.00
4090 5470 0.469892 CCCAAGTTGCCTTCCACCTT 60.470 55.000 0.00 0.00 0.00 3.50
4091 5471 1.203001 CCCAAGTTGCCTTCCACCTTA 60.203 52.381 0.00 0.00 0.00 2.69
4092 5472 1.886542 CCAAGTTGCCTTCCACCTTAC 59.113 52.381 0.00 0.00 0.00 2.34
4093 5473 1.535462 CAAGTTGCCTTCCACCTTACG 59.465 52.381 0.00 0.00 0.00 3.18
4094 5474 0.036306 AGTTGCCTTCCACCTTACGG 59.964 55.000 0.00 0.00 0.00 4.02
4096 5476 1.002315 GTTGCCTTCCACCTTACGGTA 59.998 52.381 0.00 0.00 43.24 4.02
4097 5477 1.575419 TGCCTTCCACCTTACGGTAT 58.425 50.000 0.00 0.00 43.24 2.73
4098 5478 1.910671 TGCCTTCCACCTTACGGTATT 59.089 47.619 0.00 0.00 43.24 1.89
4099 5479 2.306512 TGCCTTCCACCTTACGGTATTT 59.693 45.455 0.00 0.00 43.24 1.40
4100 5480 3.244981 TGCCTTCCACCTTACGGTATTTT 60.245 43.478 0.00 0.00 43.24 1.82
4101 5481 4.019501 TGCCTTCCACCTTACGGTATTTTA 60.020 41.667 0.00 0.00 43.24 1.52
4102 5482 4.943093 GCCTTCCACCTTACGGTATTTTAA 59.057 41.667 0.00 0.00 43.24 1.52
4103 5483 5.065602 GCCTTCCACCTTACGGTATTTTAAG 59.934 44.000 0.00 0.00 43.24 1.85
4104 5484 5.587443 CCTTCCACCTTACGGTATTTTAAGG 59.413 44.000 5.32 5.32 46.86 2.69
4105 5485 4.516323 TCCACCTTACGGTATTTTAAGGC 58.484 43.478 6.56 0.00 45.84 4.35
4106 5486 4.225717 TCCACCTTACGGTATTTTAAGGCT 59.774 41.667 6.56 0.00 45.84 4.58
4107 5487 4.573607 CCACCTTACGGTATTTTAAGGCTC 59.426 45.833 6.56 0.00 45.84 4.70
4108 5488 4.269363 CACCTTACGGTATTTTAAGGCTCG 59.731 45.833 6.56 0.00 45.84 5.03
4109 5489 4.081476 ACCTTACGGTATTTTAAGGCTCGT 60.081 41.667 6.56 0.00 45.84 4.18
4110 5490 4.872124 CCTTACGGTATTTTAAGGCTCGTT 59.128 41.667 0.00 0.00 38.37 3.85
4111 5491 5.220529 CCTTACGGTATTTTAAGGCTCGTTG 60.221 44.000 0.00 0.00 38.37 4.10
4112 5492 3.929094 ACGGTATTTTAAGGCTCGTTGA 58.071 40.909 0.00 0.00 0.00 3.18
4113 5493 4.510571 ACGGTATTTTAAGGCTCGTTGAT 58.489 39.130 0.00 0.00 0.00 2.57
4114 5494 5.663456 ACGGTATTTTAAGGCTCGTTGATA 58.337 37.500 0.00 0.00 0.00 2.15
4115 5495 6.285990 ACGGTATTTTAAGGCTCGTTGATAT 58.714 36.000 0.00 0.00 0.00 1.63
4116 5496 6.764560 ACGGTATTTTAAGGCTCGTTGATATT 59.235 34.615 0.00 0.00 0.00 1.28
4117 5497 7.281549 ACGGTATTTTAAGGCTCGTTGATATTT 59.718 33.333 0.00 0.00 0.00 1.40
4118 5498 8.126700 CGGTATTTTAAGGCTCGTTGATATTTT 58.873 33.333 0.00 0.00 0.00 1.82
4156 5536 7.578169 AAAGTCGTGTAACAATTACTAGAGC 57.422 36.000 0.00 0.00 35.74 4.09
4157 5537 6.263516 AGTCGTGTAACAATTACTAGAGCA 57.736 37.500 0.00 0.00 35.74 4.26
4158 5538 6.864342 AGTCGTGTAACAATTACTAGAGCAT 58.136 36.000 0.00 0.00 35.74 3.79
4159 5539 7.321153 AGTCGTGTAACAATTACTAGAGCATT 58.679 34.615 0.00 0.00 35.74 3.56
4160 5540 7.817962 AGTCGTGTAACAATTACTAGAGCATTT 59.182 33.333 0.00 0.00 35.74 2.32
4161 5541 9.079833 GTCGTGTAACAATTACTAGAGCATTTA 57.920 33.333 0.00 0.00 35.74 1.40
4162 5542 9.297586 TCGTGTAACAATTACTAGAGCATTTAG 57.702 33.333 0.00 0.00 35.74 1.85
4163 5543 9.297586 CGTGTAACAATTACTAGAGCATTTAGA 57.702 33.333 0.00 0.00 35.74 2.10
4178 5558 9.416794 AGAGCATTTAGAGACATTATAATCACG 57.583 33.333 0.00 0.00 0.00 4.35
4179 5559 8.023050 AGCATTTAGAGACATTATAATCACGC 57.977 34.615 0.00 0.00 0.00 5.34
4180 5560 7.657354 AGCATTTAGAGACATTATAATCACGCA 59.343 33.333 0.00 0.00 0.00 5.24
4181 5561 7.742089 GCATTTAGAGACATTATAATCACGCAC 59.258 37.037 0.00 0.00 0.00 5.34
4182 5562 8.982685 CATTTAGAGACATTATAATCACGCACT 58.017 33.333 0.00 0.00 0.00 4.40
4186 5566 8.749841 AGAGACATTATAATCACGCACTATTC 57.250 34.615 0.00 0.00 0.00 1.75
4187 5567 7.539022 AGAGACATTATAATCACGCACTATTCG 59.461 37.037 0.00 0.00 0.00 3.34
4188 5568 7.368059 AGACATTATAATCACGCACTATTCGA 58.632 34.615 0.00 0.00 0.00 3.71
4189 5569 7.539022 AGACATTATAATCACGCACTATTCGAG 59.461 37.037 0.00 0.00 0.00 4.04
4190 5570 6.089551 ACATTATAATCACGCACTATTCGAGC 59.910 38.462 0.00 0.00 0.00 5.03
4191 5571 1.571919 AATCACGCACTATTCGAGCC 58.428 50.000 0.00 0.00 0.00 4.70
4192 5572 0.249489 ATCACGCACTATTCGAGCCC 60.249 55.000 0.00 0.00 0.00 5.19
4193 5573 1.141881 CACGCACTATTCGAGCCCT 59.858 57.895 0.00 0.00 0.00 5.19
4194 5574 0.872021 CACGCACTATTCGAGCCCTC 60.872 60.000 0.00 0.00 0.00 4.30
4195 5575 1.038130 ACGCACTATTCGAGCCCTCT 61.038 55.000 0.00 0.00 0.00 3.69
4196 5576 0.318275 CGCACTATTCGAGCCCTCTC 60.318 60.000 0.00 0.00 35.99 3.20
4197 5577 0.747255 GCACTATTCGAGCCCTCTCA 59.253 55.000 0.00 0.00 39.30 3.27
4198 5578 1.269517 GCACTATTCGAGCCCTCTCAG 60.270 57.143 0.00 0.00 39.30 3.35
4199 5579 1.339610 CACTATTCGAGCCCTCTCAGG 59.660 57.143 0.00 0.00 39.30 3.86
4207 5587 2.045536 CCCTCTCAGGCCACTTGC 60.046 66.667 5.01 0.00 40.16 4.01
4208 5588 2.435586 CCTCTCAGGCCACTTGCG 60.436 66.667 5.01 0.00 42.61 4.85
4209 5589 2.345244 CTCTCAGGCCACTTGCGT 59.655 61.111 5.01 0.00 42.61 5.24
4210 5590 1.302033 CTCTCAGGCCACTTGCGTT 60.302 57.895 5.01 0.00 42.61 4.84
4211 5591 0.886490 CTCTCAGGCCACTTGCGTTT 60.886 55.000 5.01 0.00 42.61 3.60
4212 5592 1.165907 TCTCAGGCCACTTGCGTTTG 61.166 55.000 5.01 0.00 42.61 2.93
4213 5593 2.355009 CAGGCCACTTGCGTTTGC 60.355 61.111 5.01 0.00 42.61 3.68
4223 5603 2.744709 GCGTTTGCGGCCCTTAGA 60.745 61.111 0.00 0.00 38.78 2.10
4224 5604 2.112815 GCGTTTGCGGCCCTTAGAT 61.113 57.895 0.00 0.00 38.78 1.98
4225 5605 0.812412 GCGTTTGCGGCCCTTAGATA 60.812 55.000 0.00 0.00 38.78 1.98
4226 5606 1.878953 CGTTTGCGGCCCTTAGATAT 58.121 50.000 0.00 0.00 0.00 1.63
4227 5607 1.798813 CGTTTGCGGCCCTTAGATATC 59.201 52.381 0.00 0.00 0.00 1.63
4228 5608 2.548067 CGTTTGCGGCCCTTAGATATCT 60.548 50.000 10.73 10.73 0.00 1.98
4229 5609 2.808543 GTTTGCGGCCCTTAGATATCTG 59.191 50.000 15.79 0.00 0.00 2.90
4230 5610 2.009681 TGCGGCCCTTAGATATCTGA 57.990 50.000 15.79 6.24 0.00 3.27
4231 5611 2.325484 TGCGGCCCTTAGATATCTGAA 58.675 47.619 15.79 5.21 0.00 3.02
4232 5612 2.703536 TGCGGCCCTTAGATATCTGAAA 59.296 45.455 15.79 1.65 0.00 2.69
4233 5613 3.135712 TGCGGCCCTTAGATATCTGAAAA 59.864 43.478 15.79 0.91 0.00 2.29
4234 5614 4.202461 TGCGGCCCTTAGATATCTGAAAAT 60.202 41.667 15.79 0.00 0.00 1.82
4235 5615 4.154918 GCGGCCCTTAGATATCTGAAAATG 59.845 45.833 15.79 0.00 0.00 2.32
4236 5616 5.551233 CGGCCCTTAGATATCTGAAAATGA 58.449 41.667 15.79 0.00 0.00 2.57
4237 5617 5.641209 CGGCCCTTAGATATCTGAAAATGAG 59.359 44.000 15.79 2.33 0.00 2.90
4238 5618 5.414144 GGCCCTTAGATATCTGAAAATGAGC 59.586 44.000 15.79 7.08 0.00 4.26
4239 5619 6.000219 GCCCTTAGATATCTGAAAATGAGCA 59.000 40.000 15.79 0.00 0.00 4.26
4240 5620 6.658391 GCCCTTAGATATCTGAAAATGAGCAT 59.342 38.462 15.79 0.00 0.00 3.79
4241 5621 7.176340 GCCCTTAGATATCTGAAAATGAGCATT 59.824 37.037 15.79 0.00 0.00 3.56
4242 5622 9.075678 CCCTTAGATATCTGAAAATGAGCATTT 57.924 33.333 15.79 2.74 42.35 2.32
4246 5626 8.167605 AGATATCTGAAAATGAGCATTTCTGG 57.832 34.615 3.89 3.30 39.88 3.86
4247 5627 7.778853 AGATATCTGAAAATGAGCATTTCTGGT 59.221 33.333 3.89 6.25 39.88 4.00
4256 5636 3.751621 GAGCATTTCTGGTCGTTGAATG 58.248 45.455 0.00 0.00 39.85 2.67
4257 5637 3.411446 AGCATTTCTGGTCGTTGAATGA 58.589 40.909 0.00 0.00 0.00 2.57
4258 5638 3.189287 AGCATTTCTGGTCGTTGAATGAC 59.811 43.478 8.99 8.99 33.46 3.06
4265 5645 2.107950 GTCGTTGAATGACCATCCCA 57.892 50.000 6.26 0.00 0.00 4.37
4266 5646 1.737793 GTCGTTGAATGACCATCCCAC 59.262 52.381 6.26 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.645059 TTCATGTAGAACTTATGAGCATATAGC 57.355 33.333 0.00 0.00 46.19 2.97
68 69 6.486657 AGAACTAGCAAGCAAAATGTAACTGA 59.513 34.615 0.00 0.00 0.00 3.41
311 315 2.899975 TGATCCCATTTTTCAAGGGCA 58.100 42.857 0.00 0.00 42.52 5.36
312 316 5.612725 TTATGATCCCATTTTTCAAGGGC 57.387 39.130 0.00 0.00 42.52 5.19
313 317 7.128234 ACATTATGATCCCATTTTTCAAGGG 57.872 36.000 0.00 0.00 44.22 3.95
392 397 4.234530 AGTGCAAGAAATCAGAAGTTGC 57.765 40.909 0.00 0.00 43.09 4.17
595 600 1.337260 ACACTGGACGAGACATGAAGC 60.337 52.381 0.00 0.00 0.00 3.86
880 885 4.453480 AAGGAACCAAATGGAAGAGACA 57.547 40.909 6.42 0.00 38.94 3.41
960 965 7.965107 GCCTTCACTCAATATCTAAAACAACAG 59.035 37.037 0.00 0.00 0.00 3.16
998 1003 2.725221 ACCTCCCTCAGCAATCATTC 57.275 50.000 0.00 0.00 0.00 2.67
1094 1099 6.059787 AGTTTCCTTGCTCAATCTCTGTAT 57.940 37.500 0.00 0.00 0.00 2.29
1329 1334 8.461222 TCATAGTCATCCATTTGTTGTTCAATC 58.539 33.333 0.00 0.00 35.84 2.67
1586 1591 6.962182 TCCTTGAATAGGTGAGATTGATTGT 58.038 36.000 0.00 0.00 45.03 2.71
1587 1592 7.937942 AGATCCTTGAATAGGTGAGATTGATTG 59.062 37.037 0.00 0.00 45.03 2.67
1672 1677 1.817911 GCTCCTACTACCCCCATCGC 61.818 65.000 0.00 0.00 0.00 4.58
1904 1909 6.431198 TCTGTAACTGTGAGAACCAAAAAC 57.569 37.500 0.00 0.00 0.00 2.43
1999 2004 1.667236 TCATACTGAAATGGCGCCAG 58.333 50.000 35.36 22.70 0.00 4.85
2072 2077 4.983671 AGTTCAGGTTTGTTTTGACCTC 57.016 40.909 0.00 0.00 44.28 3.85
2144 2149 2.904434 AGGTGGACTGTTGTAACTAGGG 59.096 50.000 0.00 0.00 0.00 3.53
2150 2155 9.880157 GAACTTATATTAGGTGGACTGTTGTAA 57.120 33.333 0.00 0.00 0.00 2.41
2250 2257 7.660112 TGCACATCAATTTGTCAACTAAATCT 58.340 30.769 0.00 0.00 0.00 2.40
2383 2390 4.742438 TCACAACTGTTTTATCTTCGGC 57.258 40.909 0.00 0.00 0.00 5.54
2640 2648 5.005094 ACTATAGAGGCTCGGTCATTCTAC 58.995 45.833 9.22 0.00 0.00 2.59
2826 2834 2.011046 GCTCCATTCAGCTGACTGTCC 61.011 57.143 26.67 14.02 44.77 4.02
2886 2894 3.541996 ACTATGCGGACATCAACATGA 57.458 42.857 0.00 0.00 37.74 3.07
3068 3076 8.389603 CAATGTGTTGCTTTGAGTAAACAAATT 58.610 29.630 0.00 0.00 38.73 1.82
3073 3081 4.209080 GCCAATGTGTTGCTTTGAGTAAAC 59.791 41.667 0.00 0.00 35.10 2.01
3117 3125 3.755905 TGGTACAACCATGTGTGCTAATG 59.244 43.478 4.89 0.00 44.79 1.90
3155 3163 3.806521 CAGATATCTGCACAGTAGGCAAC 59.193 47.826 19.47 0.00 41.39 4.17
3251 3259 5.631512 GTGGCTAAGCTAACTGAAGATATCG 59.368 44.000 0.00 0.00 0.00 2.92
3302 3310 4.729868 AGGGCTAACATAATGGACCATTC 58.270 43.478 23.11 7.09 35.54 2.67
3322 3338 3.689649 GCTCACACTTTGGTAATGGTAGG 59.310 47.826 0.00 0.00 0.00 3.18
3427 3444 0.104855 ACAGCGAGTGTGCAAGAAGA 59.895 50.000 0.00 0.00 38.28 2.87
3428 3445 1.783284 TACAGCGAGTGTGCAAGAAG 58.217 50.000 0.00 0.00 40.69 2.85
3429 3446 2.232756 TTACAGCGAGTGTGCAAGAA 57.767 45.000 0.00 0.00 40.69 2.52
3468 3485 6.269315 TGTGCAAGTTAATTTGTGAATTCGT 58.731 32.000 11.77 0.00 36.82 3.85
3469 3486 6.746104 TGTGCAAGTTAATTTGTGAATTCG 57.254 33.333 11.77 0.00 36.82 3.34
3471 3488 7.927629 AGACATGTGCAAGTTAATTTGTGAATT 59.072 29.630 1.15 0.00 38.88 2.17
3513 4880 3.132824 CCTTTTGGGCTCAACTTTGAAGT 59.867 43.478 0.00 0.00 37.02 3.01
3560 4927 0.984230 CTGGGCTCAAGGTGGTAAGA 59.016 55.000 0.00 0.00 0.00 2.10
3719 5094 3.527533 CCGAATCAATCCGACTGGTAAA 58.472 45.455 0.00 0.00 36.30 2.01
3752 5127 1.153628 GCCGATCTTGCTGGTACGT 60.154 57.895 0.00 0.00 0.00 3.57
3805 5180 3.182263 CTCAACCACCCCACCCCA 61.182 66.667 0.00 0.00 0.00 4.96
3806 5181 4.678743 GCTCAACCACCCCACCCC 62.679 72.222 0.00 0.00 0.00 4.95
3807 5182 3.224007 ATGCTCAACCACCCCACCC 62.224 63.158 0.00 0.00 0.00 4.61
3808 5183 1.978617 CATGCTCAACCACCCCACC 60.979 63.158 0.00 0.00 0.00 4.61
3831 5206 0.177604 GTCCTGGCAGATCCTGACTG 59.822 60.000 17.94 0.76 40.76 3.51
3832 5207 0.042431 AGTCCTGGCAGATCCTGACT 59.958 55.000 17.94 16.13 40.76 3.41
3877 5255 5.181009 TCTCAAGCTCATGTGAAACCATAG 58.819 41.667 0.00 0.00 34.36 2.23
3898 5276 3.194968 ACGTTCTCACCGGACATTAATCT 59.805 43.478 9.46 0.00 0.00 2.40
4037 5417 1.396607 GCCCGGGTTGGTCTGTTTTT 61.397 55.000 24.63 0.00 35.15 1.94
4038 5418 1.830847 GCCCGGGTTGGTCTGTTTT 60.831 57.895 24.63 0.00 35.15 2.43
4039 5419 1.420532 TAGCCCGGGTTGGTCTGTTT 61.421 55.000 24.63 0.00 35.15 2.83
4040 5420 1.838073 CTAGCCCGGGTTGGTCTGTT 61.838 60.000 24.63 0.00 35.15 3.16
4041 5421 2.203877 TAGCCCGGGTTGGTCTGT 60.204 61.111 24.63 0.00 35.15 3.41
4042 5422 1.987855 TCTAGCCCGGGTTGGTCTG 60.988 63.158 24.63 6.09 35.15 3.51
4043 5423 1.988406 GTCTAGCCCGGGTTGGTCT 60.988 63.158 24.63 12.87 35.15 3.85
4044 5424 2.582978 GTCTAGCCCGGGTTGGTC 59.417 66.667 24.63 12.71 35.15 4.02
4045 5425 3.007323 GGTCTAGCCCGGGTTGGT 61.007 66.667 24.63 7.21 35.15 3.67
4046 5426 2.598787 TTGGTCTAGCCCGGGTTGG 61.599 63.158 24.63 19.66 36.04 3.77
4047 5427 1.376812 GTTGGTCTAGCCCGGGTTG 60.377 63.158 24.63 12.73 36.04 3.77
4048 5428 1.538135 AGTTGGTCTAGCCCGGGTT 60.538 57.895 24.63 20.60 36.04 4.11
4049 5429 2.122056 AGTTGGTCTAGCCCGGGT 59.878 61.111 24.63 11.76 36.04 5.28
4050 5430 2.584608 CAGTTGGTCTAGCCCGGG 59.415 66.667 19.09 19.09 36.04 5.73
4051 5431 1.961180 CTCCAGTTGGTCTAGCCCGG 61.961 65.000 0.00 0.00 36.04 5.73
4052 5432 1.517832 CTCCAGTTGGTCTAGCCCG 59.482 63.158 0.00 0.00 36.04 6.13
4053 5433 1.222113 GCTCCAGTTGGTCTAGCCC 59.778 63.158 0.00 0.00 36.04 5.19
4054 5434 1.222113 GGCTCCAGTTGGTCTAGCC 59.778 63.158 12.09 12.09 42.91 3.93
4055 5435 1.222113 GGGCTCCAGTTGGTCTAGC 59.778 63.158 0.00 0.16 36.34 3.42
4056 5436 0.984230 TTGGGCTCCAGTTGGTCTAG 59.016 55.000 0.00 0.00 33.81 2.43
4057 5437 0.984230 CTTGGGCTCCAGTTGGTCTA 59.016 55.000 0.00 0.00 33.81 2.59
4058 5438 1.062488 ACTTGGGCTCCAGTTGGTCT 61.062 55.000 0.00 0.00 33.81 3.85
4059 5439 0.178990 AACTTGGGCTCCAGTTGGTC 60.179 55.000 1.50 0.00 33.81 4.02
4060 5440 0.468029 CAACTTGGGCTCCAGTTGGT 60.468 55.000 20.29 4.64 38.13 3.67
4061 5441 1.809567 GCAACTTGGGCTCCAGTTGG 61.810 60.000 26.80 12.42 40.03 3.77
4062 5442 1.662044 GCAACTTGGGCTCCAGTTG 59.338 57.895 22.97 22.97 41.24 3.16
4063 5443 1.531602 GGCAACTTGGGCTCCAGTT 60.532 57.895 0.00 0.00 33.81 3.16
4064 5444 2.116125 GGCAACTTGGGCTCCAGT 59.884 61.111 0.00 0.00 33.81 4.00
4088 5468 5.577945 TCAACGAGCCTTAAAATACCGTAAG 59.422 40.000 0.00 0.00 0.00 2.34
4089 5469 5.477510 TCAACGAGCCTTAAAATACCGTAA 58.522 37.500 0.00 0.00 0.00 3.18
4090 5470 5.070770 TCAACGAGCCTTAAAATACCGTA 57.929 39.130 0.00 0.00 0.00 4.02
4091 5471 3.929094 TCAACGAGCCTTAAAATACCGT 58.071 40.909 0.00 0.00 0.00 4.83
4092 5472 6.780706 ATATCAACGAGCCTTAAAATACCG 57.219 37.500 0.00 0.00 0.00 4.02
4130 5510 9.132521 GCTCTAGTAATTGTTACACGACTTTTA 57.867 33.333 0.00 0.00 38.60 1.52
4131 5511 7.654520 TGCTCTAGTAATTGTTACACGACTTTT 59.345 33.333 0.00 0.00 38.60 2.27
4132 5512 7.149973 TGCTCTAGTAATTGTTACACGACTTT 58.850 34.615 0.00 0.00 38.60 2.66
4133 5513 6.684686 TGCTCTAGTAATTGTTACACGACTT 58.315 36.000 0.00 0.00 38.60 3.01
4134 5514 6.263516 TGCTCTAGTAATTGTTACACGACT 57.736 37.500 0.00 0.00 38.60 4.18
4135 5515 7.521509 AATGCTCTAGTAATTGTTACACGAC 57.478 36.000 0.00 0.00 38.60 4.34
4136 5516 9.297586 CTAAATGCTCTAGTAATTGTTACACGA 57.702 33.333 0.00 0.00 38.60 4.35
4137 5517 9.297586 TCTAAATGCTCTAGTAATTGTTACACG 57.702 33.333 3.05 0.00 38.60 4.49
4152 5532 9.416794 CGTGATTATAATGTCTCTAAATGCTCT 57.583 33.333 1.78 0.00 0.00 4.09
4153 5533 8.165428 GCGTGATTATAATGTCTCTAAATGCTC 58.835 37.037 1.78 0.00 0.00 4.26
4154 5534 7.657354 TGCGTGATTATAATGTCTCTAAATGCT 59.343 33.333 1.78 0.00 0.00 3.79
4155 5535 7.742089 GTGCGTGATTATAATGTCTCTAAATGC 59.258 37.037 1.78 0.00 0.00 3.56
4156 5536 8.982685 AGTGCGTGATTATAATGTCTCTAAATG 58.017 33.333 1.78 0.00 0.00 2.32
4160 5540 9.841880 GAATAGTGCGTGATTATAATGTCTCTA 57.158 33.333 1.78 1.24 0.00 2.43
4161 5541 7.539022 CGAATAGTGCGTGATTATAATGTCTCT 59.461 37.037 1.78 0.00 0.00 3.10
4162 5542 7.537649 TCGAATAGTGCGTGATTATAATGTCTC 59.462 37.037 1.78 0.00 0.00 3.36
4163 5543 7.368059 TCGAATAGTGCGTGATTATAATGTCT 58.632 34.615 1.78 0.00 0.00 3.41
4164 5544 7.562640 TCGAATAGTGCGTGATTATAATGTC 57.437 36.000 1.78 0.00 0.00 3.06
4165 5545 6.089551 GCTCGAATAGTGCGTGATTATAATGT 59.910 38.462 1.78 0.00 0.00 2.71
4166 5546 6.454318 GGCTCGAATAGTGCGTGATTATAATG 60.454 42.308 1.78 0.00 40.04 1.90
4167 5547 5.577164 GGCTCGAATAGTGCGTGATTATAAT 59.423 40.000 0.00 0.00 40.04 1.28
4168 5548 4.921515 GGCTCGAATAGTGCGTGATTATAA 59.078 41.667 0.00 0.00 40.04 0.98
4169 5549 4.482386 GGCTCGAATAGTGCGTGATTATA 58.518 43.478 0.00 0.00 40.04 0.98
4170 5550 3.318017 GGCTCGAATAGTGCGTGATTAT 58.682 45.455 0.00 0.00 40.04 1.28
4171 5551 2.545113 GGGCTCGAATAGTGCGTGATTA 60.545 50.000 0.00 0.00 40.04 1.75
4172 5552 1.571919 GGCTCGAATAGTGCGTGATT 58.428 50.000 0.00 0.00 40.04 2.57
4173 5553 0.249489 GGGCTCGAATAGTGCGTGAT 60.249 55.000 0.00 0.00 40.04 3.06
4174 5554 1.141019 GGGCTCGAATAGTGCGTGA 59.859 57.895 0.00 0.00 40.04 4.35
4175 5555 0.872021 GAGGGCTCGAATAGTGCGTG 60.872 60.000 0.00 0.00 40.04 5.34
4176 5556 1.038130 AGAGGGCTCGAATAGTGCGT 61.038 55.000 0.00 0.00 40.04 5.24
4177 5557 0.318275 GAGAGGGCTCGAATAGTGCG 60.318 60.000 0.00 0.00 40.04 5.34
4178 5558 0.747255 TGAGAGGGCTCGAATAGTGC 59.253 55.000 0.00 0.00 44.33 4.40
4179 5559 1.339610 CCTGAGAGGGCTCGAATAGTG 59.660 57.143 0.00 0.00 44.33 2.74
4180 5560 1.698506 CCTGAGAGGGCTCGAATAGT 58.301 55.000 0.00 0.00 44.33 2.12
4190 5570 2.045536 GCAAGTGGCCTGAGAGGG 60.046 66.667 3.32 0.00 35.37 4.30
4191 5571 2.435586 CGCAAGTGGCCTGAGAGG 60.436 66.667 3.32 0.00 40.31 3.69
4204 5584 2.594882 TAAGGGCCGCAAACGCAA 60.595 55.556 0.00 0.00 38.22 4.85
4205 5585 2.813226 ATCTAAGGGCCGCAAACGCA 62.813 55.000 0.00 0.00 38.22 5.24
4206 5586 0.812412 TATCTAAGGGCCGCAAACGC 60.812 55.000 0.00 0.00 38.22 4.84
4207 5587 1.798813 GATATCTAAGGGCCGCAAACG 59.201 52.381 0.00 0.00 39.67 3.60
4208 5588 2.808543 CAGATATCTAAGGGCCGCAAAC 59.191 50.000 4.54 0.00 0.00 2.93
4209 5589 2.703536 TCAGATATCTAAGGGCCGCAAA 59.296 45.455 4.54 0.00 0.00 3.68
4210 5590 2.325484 TCAGATATCTAAGGGCCGCAA 58.675 47.619 4.54 0.00 0.00 4.85
4211 5591 2.009681 TCAGATATCTAAGGGCCGCA 57.990 50.000 4.54 0.00 0.00 5.69
4212 5592 3.402628 TTTCAGATATCTAAGGGCCGC 57.597 47.619 4.54 0.00 0.00 6.53
4213 5593 5.551233 TCATTTTCAGATATCTAAGGGCCG 58.449 41.667 4.54 0.00 0.00 6.13
4214 5594 5.414144 GCTCATTTTCAGATATCTAAGGGCC 59.586 44.000 4.54 0.00 0.00 5.80
4215 5595 6.000219 TGCTCATTTTCAGATATCTAAGGGC 59.000 40.000 4.54 0.00 0.00 5.19
4216 5596 8.632906 AATGCTCATTTTCAGATATCTAAGGG 57.367 34.615 4.54 0.00 0.00 3.95
4220 5600 9.281371 CCAGAAATGCTCATTTTCAGATATCTA 57.719 33.333 4.54 0.00 40.77 1.98
4221 5601 7.778853 ACCAGAAATGCTCATTTTCAGATATCT 59.221 33.333 8.98 0.00 40.77 1.98
4222 5602 7.938715 ACCAGAAATGCTCATTTTCAGATATC 58.061 34.615 8.98 0.00 40.77 1.63
4223 5603 7.255035 CGACCAGAAATGCTCATTTTCAGATAT 60.255 37.037 8.98 0.00 40.77 1.63
4224 5604 6.037500 CGACCAGAAATGCTCATTTTCAGATA 59.962 38.462 8.98 0.00 40.77 1.98
4225 5605 5.163683 CGACCAGAAATGCTCATTTTCAGAT 60.164 40.000 8.98 0.00 40.77 2.90
4226 5606 4.154737 CGACCAGAAATGCTCATTTTCAGA 59.845 41.667 8.98 0.00 40.77 3.27
4227 5607 4.083110 ACGACCAGAAATGCTCATTTTCAG 60.083 41.667 8.98 4.33 40.77 3.02
4228 5608 3.820467 ACGACCAGAAATGCTCATTTTCA 59.180 39.130 8.98 0.00 40.77 2.69
4229 5609 4.425577 ACGACCAGAAATGCTCATTTTC 57.574 40.909 8.98 2.93 40.77 2.29
4230 5610 4.278170 TCAACGACCAGAAATGCTCATTTT 59.722 37.500 8.98 0.00 40.77 1.82
4231 5611 3.820467 TCAACGACCAGAAATGCTCATTT 59.180 39.130 7.49 7.49 43.14 2.32
4232 5612 3.411446 TCAACGACCAGAAATGCTCATT 58.589 40.909 0.00 0.00 0.00 2.57
4233 5613 3.057969 TCAACGACCAGAAATGCTCAT 57.942 42.857 0.00 0.00 0.00 2.90
4234 5614 2.542020 TCAACGACCAGAAATGCTCA 57.458 45.000 0.00 0.00 0.00 4.26
4235 5615 3.436704 TCATTCAACGACCAGAAATGCTC 59.563 43.478 0.00 0.00 0.00 4.26
4236 5616 3.189287 GTCATTCAACGACCAGAAATGCT 59.811 43.478 0.00 0.00 0.00 3.79
4237 5617 3.492313 GTCATTCAACGACCAGAAATGC 58.508 45.455 0.00 0.00 0.00 3.56
4246 5626 1.737793 GTGGGATGGTCATTCAACGAC 59.262 52.381 0.00 0.00 0.00 4.34
4247 5627 2.107950 GTGGGATGGTCATTCAACGA 57.892 50.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.