Multiple sequence alignment - TraesCS7B01G208500

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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 TraesCS7B01G208500 chr7B 100.000 4717 0 0 1 4717 381479284 381474568 0.000000e+00 8711.0
1 TraesCS7B01G208500 chr7D 93.260 4451 182 40 1 4394 386650212 386645823 0.000000e+00 6449.0
2 TraesCS7B01G208500 chr7A 94.088 3620 123 24 454 4045 435972759 435969203 0.000000e+00 5415.0
3 TraesCS7B01G208500 chr7A 92.837 363 23 3 4032 4393 435960845 435960485 1.500000e-144 523.0
4 TraesCS7B01G208500 chr7A 84.292 452 39 18 1 427 435975432 435974988 3.400000e-111 412.0
5 TraesCS7B01G208500 chr7A 89.844 256 26 0 4462 4717 435960477 435960222 3.520000e-86 329.0
6 TraesCS7B01G208500 chr5B 96.970 33 1 0 4406 4438 13103084 13103052 6.590000e-04 56.5
7 TraesCS7B01G208500 chr2A 100.000 28 0 0 931 958 365082957 365082984 9.000000e-03 52.8


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 TraesCS7B01G208500 chr7B 381474568 381479284 4716 True 8711.0 8711 100.0000 1 4717 1 chr7B.!!$R1 4716
1 TraesCS7B01G208500 chr7D 386645823 386650212 4389 True 6449.0 6449 93.2600 1 4394 1 chr7D.!!$R1 4393
2 TraesCS7B01G208500 chr7A 435969203 435975432 6229 True 2913.5 5415 89.1900 1 4045 2 chr7A.!!$R2 4044
3 TraesCS7B01G208500 chr7A 435960222 435960845 623 True 426.0 523 91.3405 4032 4717 2 chr7A.!!$R1 685

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
90 92 0.109086 CGTGGACTCTGCACCTACAG 60.109 60.0 0.00 0.0 35.09 2.74 F
649 2876 0.248289 GAGGTGCACGGGCTTACTAA 59.752 55.0 12.74 0.0 41.91 2.24 F
1912 4165 0.107993 GCCTCTGCATGTGCTACTGA 60.108 55.0 6.55 0.0 42.66 3.41 F
3123 5385 0.881118 GGCGGTTGAGCATTTCTTCA 59.119 50.0 0.00 0.0 39.27 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 4116 1.282382 TCGGGGTAGAAGGGGAAAAG 58.718 55.0 0.0 0.0 0.00 2.27 R
2401 4658 0.321653 CCTGGTGGTGTAGTTCTGGC 60.322 60.0 0.0 0.0 0.00 4.85 R
3203 5465 1.322442 GAACAGAATAGCCCCATGCC 58.678 55.0 0.0 0.0 42.71 4.40 R
4401 6668 0.398522 TGGGACGGAGGCAGTATCAT 60.399 55.0 0.0 0.0 0.00 2.45 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
62 64 2.043652 GCTGGATGGGTGCATGGT 60.044 61.111 0.00 0.00 0.00 3.55
73 75 1.605202 GGTGCATGGTCAAATTTGCGT 60.605 47.619 13.54 0.00 37.92 5.24
79 81 1.606668 TGGTCAAATTTGCGTGGACTC 59.393 47.619 13.54 1.95 0.00 3.36
80 82 1.880027 GGTCAAATTTGCGTGGACTCT 59.120 47.619 13.54 0.00 0.00 3.24
83 85 1.001487 CAAATTTGCGTGGACTCTGCA 60.001 47.619 5.01 0.00 36.72 4.41
90 92 0.109086 CGTGGACTCTGCACCTACAG 60.109 60.000 0.00 0.00 35.09 2.74
93 95 1.544825 GGACTCTGCACCTACAGCCA 61.545 60.000 0.00 0.00 37.59 4.75
138 141 0.957888 TTCCGCGTCCATTTGCATCA 60.958 50.000 4.92 0.00 0.00 3.07
146 149 2.098934 GTCCATTTGCATCATGGCGTTA 59.901 45.455 17.23 1.70 41.10 3.18
173 176 2.357154 GGCCTCAATACCCAACATCACT 60.357 50.000 0.00 0.00 0.00 3.41
180 183 5.013704 TCAATACCCAACATCACTAGTGGTT 59.986 40.000 22.48 15.97 0.00 3.67
211 214 0.606401 ACGTTGCCTCATTGTCCCTG 60.606 55.000 0.00 0.00 0.00 4.45
212 215 0.321564 CGTTGCCTCATTGTCCCTGA 60.322 55.000 0.00 0.00 0.00 3.86
213 216 1.168714 GTTGCCTCATTGTCCCTGAC 58.831 55.000 0.00 0.00 0.00 3.51
258 261 2.649129 GCCCCGCAGCAAGGATTTT 61.649 57.895 1.68 0.00 0.00 1.82
259 262 1.216178 CCCCGCAGCAAGGATTTTG 59.784 57.895 0.00 0.00 0.00 2.44
280 297 2.423892 GAGAGCTACCATGTCGTTCTCA 59.576 50.000 12.07 0.00 36.29 3.27
297 314 2.752903 TCTCATCGACCGACAATCTTGA 59.247 45.455 0.00 0.00 0.00 3.02
298 315 3.192633 TCTCATCGACCGACAATCTTGAA 59.807 43.478 0.00 0.00 0.00 2.69
310 327 3.317711 ACAATCTTGAATCGCAACAACCA 59.682 39.130 0.00 0.00 31.96 3.67
312 329 2.293170 TCTTGAATCGCAACAACCACA 58.707 42.857 0.00 0.00 31.96 4.17
321 338 2.535331 GCAACAACCACAAAATGACGT 58.465 42.857 0.00 0.00 0.00 4.34
341 358 0.955428 GCACATCTTTGCGGTCTCCA 60.955 55.000 0.00 0.00 31.51 3.86
348 365 1.676006 CTTTGCGGTCTCCACAACTTT 59.324 47.619 0.00 0.00 0.00 2.66
353 370 2.288886 GCGGTCTCCACAACTTTAGAGT 60.289 50.000 0.00 0.00 37.87 3.24
415 440 2.689034 AGTAGGGCCTGCCACCTC 60.689 66.667 18.53 0.00 38.30 3.85
508 2735 1.002502 CCGACCAGGGAGGAAAACC 60.003 63.158 0.00 0.00 41.22 3.27
513 2740 0.897621 CCAGGGAGGAAAACCATTGC 59.102 55.000 0.00 0.00 41.22 3.56
517 2744 1.531739 GGAGGAAAACCATTGCGGCA 61.532 55.000 0.00 0.00 39.03 5.69
528 2755 2.159128 CCATTGCGGCATGTTGGATTAA 60.159 45.455 17.43 0.00 0.00 1.40
576 2803 0.990374 ATTGAGGAGCAGGCAAGTCT 59.010 50.000 0.00 0.00 0.00 3.24
582 2809 0.251354 GAGCAGGCAAGTCTCATCCA 59.749 55.000 0.00 0.00 0.00 3.41
583 2810 0.694771 AGCAGGCAAGTCTCATCCAA 59.305 50.000 0.00 0.00 0.00 3.53
594 2821 4.686972 AGTCTCATCCAACATGTATGTCG 58.313 43.478 0.00 0.00 40.80 4.35
605 2832 3.930229 ACATGTATGTCGCGTTGTAATGT 59.070 39.130 5.77 8.03 35.87 2.71
620 2847 5.410355 TGTAATGTACGGGCTTCTTACTT 57.590 39.130 0.00 0.00 0.00 2.24
621 2848 5.797051 TGTAATGTACGGGCTTCTTACTTT 58.203 37.500 0.00 0.00 0.00 2.66
622 2849 6.232692 TGTAATGTACGGGCTTCTTACTTTT 58.767 36.000 0.00 0.00 0.00 2.27
623 2850 6.711645 TGTAATGTACGGGCTTCTTACTTTTT 59.288 34.615 0.00 0.00 0.00 1.94
641 2868 2.619362 TTTTTACGAGGTGCACGGG 58.381 52.632 11.45 4.78 34.93 5.28
642 2869 1.508808 TTTTTACGAGGTGCACGGGC 61.509 55.000 11.45 0.34 41.68 6.13
643 2870 2.386064 TTTTACGAGGTGCACGGGCT 62.386 55.000 12.74 1.70 41.91 5.19
644 2871 2.386064 TTTACGAGGTGCACGGGCTT 62.386 55.000 12.74 0.00 41.91 4.35
645 2872 1.534336 TTACGAGGTGCACGGGCTTA 61.534 55.000 12.74 0.00 41.91 3.09
646 2873 2.216750 TACGAGGTGCACGGGCTTAC 62.217 60.000 12.74 0.00 41.91 2.34
647 2874 2.663196 GAGGTGCACGGGCTTACT 59.337 61.111 12.74 6.05 41.91 2.24
648 2875 1.895238 GAGGTGCACGGGCTTACTA 59.105 57.895 12.74 0.00 41.91 1.82
649 2876 0.248289 GAGGTGCACGGGCTTACTAA 59.752 55.000 12.74 0.00 41.91 2.24
653 2880 3.054948 AGGTGCACGGGCTTACTAATTAA 60.055 43.478 12.74 0.00 41.91 1.40
659 2886 5.448225 GCACGGGCTTACTAATTAAAGGAAC 60.448 44.000 0.00 0.00 36.96 3.62
720 2948 2.009774 CGATTCGCCAGTCCAAAGAAT 58.990 47.619 0.00 0.00 34.64 2.40
722 2950 3.621268 CGATTCGCCAGTCCAAAGAATTA 59.379 43.478 0.00 0.00 32.42 1.40
723 2951 4.273480 CGATTCGCCAGTCCAAAGAATTAT 59.727 41.667 0.00 0.00 32.42 1.28
731 2960 3.119495 AGTCCAAAGAATTATTGCGTGCC 60.119 43.478 0.00 0.00 0.00 5.01
741 2970 7.362662 AGAATTATTGCGTGCCAAATATAGTG 58.637 34.615 0.00 0.00 36.92 2.74
793 3023 4.159135 TCCTGTCCTTTATCTACACCGTTC 59.841 45.833 0.00 0.00 0.00 3.95
908 3138 4.466370 ACTGATTCGAACTGGATTCCACTA 59.534 41.667 0.00 0.00 33.26 2.74
934 3164 2.596338 CGGCGGTTTGGGTTCCTT 60.596 61.111 0.00 0.00 0.00 3.36
935 3165 2.197605 CGGCGGTTTGGGTTCCTTT 61.198 57.895 0.00 0.00 0.00 3.11
936 3166 1.663739 GGCGGTTTGGGTTCCTTTC 59.336 57.895 0.00 0.00 0.00 2.62
987 3217 4.394712 CTTTCCCACCTCGCGGCT 62.395 66.667 6.13 0.00 0.00 5.52
1608 3856 1.478510 CTCTCCAAGTACGACTGGCAT 59.521 52.381 6.77 0.00 0.00 4.40
1670 3918 3.114616 CGTCTGGCACGGCTTCAG 61.115 66.667 0.00 0.00 45.46 3.02
1852 4105 1.136329 AGGATTCCACCAGGTGCACT 61.136 55.000 17.98 4.16 35.89 4.40
1878 4131 2.506231 CCTCTCCTTTTCCCCTTCTACC 59.494 54.545 0.00 0.00 0.00 3.18
1889 4142 3.043418 CCCCTTCTACCCCGAATTTCTA 58.957 50.000 0.00 0.00 0.00 2.10
1912 4165 0.107993 GCCTCTGCATGTGCTACTGA 60.108 55.000 6.55 0.00 42.66 3.41
1978 4231 4.655963 ACTGTGTGTTTCTATTGGATGCT 58.344 39.130 0.00 0.00 0.00 3.79
1979 4232 5.804639 ACTGTGTGTTTCTATTGGATGCTA 58.195 37.500 0.00 0.00 0.00 3.49
1980 4233 5.877012 ACTGTGTGTTTCTATTGGATGCTAG 59.123 40.000 0.00 0.00 0.00 3.42
2154 4407 5.210715 GTTGCTGTTCAGTCTTTCTTGATG 58.789 41.667 1.78 0.00 0.00 3.07
2221 4478 9.190317 GTCAAACTTTGAATAATAGAGGGGAAT 57.810 33.333 5.76 0.00 42.15 3.01
2337 4594 6.069381 AGGTCAAAAGCTTATCCTCTACCATT 60.069 38.462 0.00 0.00 0.00 3.16
2352 4609 2.119495 ACCATTCCCTCAAGATACGCT 58.881 47.619 0.00 0.00 0.00 5.07
2435 4692 0.991920 CCAGGGTGATGGTTACTGGT 59.008 55.000 0.00 0.00 42.83 4.00
2786 5043 2.783510 AGGACCAATGTTATGTAGGGGG 59.216 50.000 0.00 0.00 0.00 5.40
2847 5104 2.642311 TGCACCCAATGAAACCTAGAGA 59.358 45.455 0.00 0.00 0.00 3.10
2865 5122 3.255149 AGAGAATGGCTGCTGTTTTTCAG 59.745 43.478 0.00 0.00 46.12 3.02
2871 5128 4.183101 TGGCTGCTGTTTTTCAGAAAAAG 58.817 39.130 19.46 11.21 46.27 2.27
2915 5177 3.149196 ACATGAAACTAGCCTGTGGTTG 58.851 45.455 0.00 0.00 28.60 3.77
2924 5186 2.851195 AGCCTGTGGTTGTACTTGAAG 58.149 47.619 0.00 0.00 0.00 3.02
3032 5294 4.471025 TCTGGATTTCTAAGAGCACATCCA 59.529 41.667 0.00 0.00 38.27 3.41
3066 5328 3.646162 AGTGTCACTTCACCACCTTGATA 59.354 43.478 0.00 0.00 38.91 2.15
3119 5381 1.701704 CAAAGGCGGTTGAGCATTTC 58.298 50.000 0.00 0.00 46.26 2.17
3123 5385 0.881118 GGCGGTTGAGCATTTCTTCA 59.119 50.000 0.00 0.00 39.27 3.02
3203 5465 5.233225 TCAAGATCACTTACTGCTTCAGTG 58.767 41.667 9.52 0.00 45.01 3.66
3730 5992 7.468922 TGCATTCGTAGTGATTCTTGAATAG 57.531 36.000 0.00 0.00 32.59 1.73
3731 5993 6.018751 TGCATTCGTAGTGATTCTTGAATAGC 60.019 38.462 0.00 0.00 32.59 2.97
3736 5998 7.264947 TCGTAGTGATTCTTGAATAGCATTGA 58.735 34.615 0.00 0.00 0.00 2.57
3742 6004 9.661187 GTGATTCTTGAATAGCATTGAATACTG 57.339 33.333 0.00 0.00 33.31 2.74
3766 6028 8.484214 TGATCTGGAGTAGATAATTTACAGCT 57.516 34.615 0.00 0.00 46.12 4.24
3841 6107 5.514136 CCACTTCATTTTGGGTCTGTAGGTA 60.514 44.000 0.00 0.00 0.00 3.08
4017 6283 8.366401 AGATCTCCAACTGAACACATATGATAG 58.634 37.037 10.38 1.42 0.00 2.08
4076 6342 6.551601 TCTGTTGTAATTCTCCTCTATCTCCC 59.448 42.308 0.00 0.00 0.00 4.30
4093 6359 3.014110 TCTCCCCCTGTAAATCTTCTCCT 59.986 47.826 0.00 0.00 0.00 3.69
4157 6423 5.042387 AGCCCCATCCTATCAATATAAGCT 58.958 41.667 0.00 0.00 0.00 3.74
4159 6425 5.605534 CCCCATCCTATCAATATAAGCTCG 58.394 45.833 0.00 0.00 0.00 5.03
4163 6429 4.733850 TCCTATCAATATAAGCTCGTGCG 58.266 43.478 3.48 0.00 45.42 5.34
4215 6481 5.086058 CGCTTCACACAATTTACATGGTAC 58.914 41.667 0.00 0.00 0.00 3.34
4236 6502 4.015084 ACAGAGAGCCATTCTTTTCCATG 58.985 43.478 0.00 0.00 35.87 3.66
4255 6522 4.091945 CCATGTCATTAGTGTCACAAGTCG 59.908 45.833 5.62 0.00 0.00 4.18
4264 6531 0.304705 GTCACAAGTCGCAACCTGTG 59.695 55.000 0.00 0.00 45.38 3.66
4303 6570 7.812191 CCCAACAATCGATGTATTTCAGAAAAA 59.188 33.333 0.00 0.00 42.99 1.94
4394 6661 2.092375 GGGCAGCTAGGGTTCTTGTATT 60.092 50.000 0.00 0.00 0.00 1.89
4395 6662 3.135895 GGGCAGCTAGGGTTCTTGTATTA 59.864 47.826 0.00 0.00 0.00 0.98
4396 6663 4.381411 GGCAGCTAGGGTTCTTGTATTAG 58.619 47.826 0.00 0.00 0.00 1.73
4397 6664 3.810386 GCAGCTAGGGTTCTTGTATTAGC 59.190 47.826 0.00 0.00 35.06 3.09
4398 6665 4.683400 GCAGCTAGGGTTCTTGTATTAGCA 60.683 45.833 4.40 0.00 36.78 3.49
4399 6666 5.428253 CAGCTAGGGTTCTTGTATTAGCAA 58.572 41.667 4.40 0.00 36.78 3.91
4400 6667 6.058183 CAGCTAGGGTTCTTGTATTAGCAAT 58.942 40.000 4.40 0.00 36.78 3.56
4401 6668 7.217200 CAGCTAGGGTTCTTGTATTAGCAATA 58.783 38.462 4.40 0.00 36.78 1.90
4402 6669 7.880195 CAGCTAGGGTTCTTGTATTAGCAATAT 59.120 37.037 4.40 0.00 36.78 1.28
4403 6670 7.880195 AGCTAGGGTTCTTGTATTAGCAATATG 59.120 37.037 4.40 0.00 36.78 1.78
4404 6671 7.878127 GCTAGGGTTCTTGTATTAGCAATATGA 59.122 37.037 0.00 0.00 34.98 2.15
4405 6672 9.950496 CTAGGGTTCTTGTATTAGCAATATGAT 57.050 33.333 0.00 0.00 0.00 2.45
4407 6674 9.726438 AGGGTTCTTGTATTAGCAATATGATAC 57.274 33.333 0.00 0.00 0.00 2.24
4408 6675 9.726438 GGGTTCTTGTATTAGCAATATGATACT 57.274 33.333 0.00 0.00 0.00 2.12
4411 6678 8.777865 TCTTGTATTAGCAATATGATACTGCC 57.222 34.615 1.87 0.00 36.73 4.85
4412 6679 8.597167 TCTTGTATTAGCAATATGATACTGCCT 58.403 33.333 1.87 0.00 36.73 4.75
4413 6680 8.777865 TTGTATTAGCAATATGATACTGCCTC 57.222 34.615 1.87 0.00 36.73 4.70
4414 6681 7.331026 TGTATTAGCAATATGATACTGCCTCC 58.669 38.462 1.87 0.00 36.73 4.30
4415 6682 3.325293 AGCAATATGATACTGCCTCCG 57.675 47.619 1.87 0.00 36.73 4.63
4416 6683 2.634940 AGCAATATGATACTGCCTCCGT 59.365 45.455 1.87 0.00 36.73 4.69
4417 6684 2.996621 GCAATATGATACTGCCTCCGTC 59.003 50.000 0.00 0.00 0.00 4.79
4418 6685 3.589988 CAATATGATACTGCCTCCGTCC 58.410 50.000 0.00 0.00 0.00 4.79
4419 6686 1.629043 TATGATACTGCCTCCGTCCC 58.371 55.000 0.00 0.00 0.00 4.46
4420 6687 0.398522 ATGATACTGCCTCCGTCCCA 60.399 55.000 0.00 0.00 0.00 4.37
4421 6688 0.398522 TGATACTGCCTCCGTCCCAT 60.399 55.000 0.00 0.00 0.00 4.00
4422 6689 1.133294 TGATACTGCCTCCGTCCCATA 60.133 52.381 0.00 0.00 0.00 2.74
4423 6690 1.968493 GATACTGCCTCCGTCCCATAA 59.032 52.381 0.00 0.00 0.00 1.90
4424 6691 2.097110 TACTGCCTCCGTCCCATAAT 57.903 50.000 0.00 0.00 0.00 1.28
4425 6692 2.097110 ACTGCCTCCGTCCCATAATA 57.903 50.000 0.00 0.00 0.00 0.98
4426 6693 2.621070 ACTGCCTCCGTCCCATAATAT 58.379 47.619 0.00 0.00 0.00 1.28
4427 6694 3.786553 ACTGCCTCCGTCCCATAATATA 58.213 45.455 0.00 0.00 0.00 0.86
4428 6695 4.164981 ACTGCCTCCGTCCCATAATATAA 58.835 43.478 0.00 0.00 0.00 0.98
4429 6696 4.595781 ACTGCCTCCGTCCCATAATATAAA 59.404 41.667 0.00 0.00 0.00 1.40
4430 6697 5.072600 ACTGCCTCCGTCCCATAATATAAAA 59.927 40.000 0.00 0.00 0.00 1.52
4431 6698 5.310451 TGCCTCCGTCCCATAATATAAAAC 58.690 41.667 0.00 0.00 0.00 2.43
4432 6699 5.163184 TGCCTCCGTCCCATAATATAAAACA 60.163 40.000 0.00 0.00 0.00 2.83
4433 6700 5.944007 GCCTCCGTCCCATAATATAAAACAT 59.056 40.000 0.00 0.00 0.00 2.71
4434 6701 6.433093 GCCTCCGTCCCATAATATAAAACATT 59.567 38.462 0.00 0.00 0.00 2.71
4435 6702 7.608761 GCCTCCGTCCCATAATATAAAACATTA 59.391 37.037 0.00 0.00 0.00 1.90
4436 6703 9.681062 CCTCCGTCCCATAATATAAAACATTAT 57.319 33.333 0.00 0.00 0.00 1.28
4550 6817 1.504647 TATACTCCAGCGAGCGACGG 61.505 60.000 0.00 0.00 40.03 4.79
4560 6827 4.635925 AGCGACGGCGATCAATAG 57.364 55.556 18.90 0.00 46.35 1.73
4576 6843 8.533153 GCGATCAATAGAAAGTAAACACTAGAC 58.467 37.037 0.00 0.00 0.00 2.59
4602 6869 3.296854 ACAGGTGACAACTACAGAGACA 58.703 45.455 0.00 0.00 0.00 3.41
4617 6884 3.180584 CAGAGACAAAGAAACTGACGACG 59.819 47.826 0.00 0.00 0.00 5.12
4620 6887 3.550678 AGACAAAGAAACTGACGACGTTC 59.449 43.478 0.13 0.00 0.00 3.95
4624 6891 0.158928 GAAACTGACGACGTTCAGCG 59.841 55.000 15.56 5.06 46.09 5.18
4625 6892 1.818221 AAACTGACGACGTTCAGCGC 61.818 55.000 15.56 0.00 46.09 5.92
4635 6902 1.125847 CGTTCAGCGCGCCAAATAAC 61.126 55.000 30.33 21.77 0.00 1.89
4660 6927 2.357517 CACTCCCTTTCGCGTGCT 60.358 61.111 5.77 0.00 0.00 4.40
4685 6952 2.225019 CCAGATGCTCATAAACGATGCC 59.775 50.000 0.00 0.00 35.29 4.40
4703 6970 0.179056 CCGTATCGGCAGATTTGGGT 60.179 55.000 4.22 0.00 41.17 4.51
4705 6972 2.484065 CCGTATCGGCAGATTTGGGTTA 60.484 50.000 4.22 0.00 41.17 2.85
4708 6975 3.864789 ATCGGCAGATTTGGGTTATCT 57.135 42.857 0.00 0.00 32.03 1.98
4710 6977 2.238646 TCGGCAGATTTGGGTTATCTGT 59.761 45.455 12.78 0.00 46.84 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 49 0.113972 TTTGACCATGCACCCATCCA 59.886 50.000 0.00 0.00 0.00 3.41
50 52 2.616001 GCAAATTTGACCATGCACCCAT 60.616 45.455 22.31 0.00 38.63 4.00
62 64 1.266718 GCAGAGTCCACGCAAATTTGA 59.733 47.619 22.31 0.00 0.00 2.69
73 75 1.544825 GGCTGTAGGTGCAGAGTCCA 61.545 60.000 0.00 0.00 38.70 4.02
79 81 1.675641 GGGTTGGCTGTAGGTGCAG 60.676 63.158 0.00 0.00 39.37 4.41
80 82 2.000825 TTGGGTTGGCTGTAGGTGCA 62.001 55.000 0.00 0.00 0.00 4.57
83 85 0.536460 CGTTTGGGTTGGCTGTAGGT 60.536 55.000 0.00 0.00 0.00 3.08
90 92 2.924880 GCTTTATGTCGTTTGGGTTGGC 60.925 50.000 0.00 0.00 0.00 4.52
93 95 2.496111 TCGCTTTATGTCGTTTGGGTT 58.504 42.857 0.00 0.00 0.00 4.11
125 128 0.457035 ACGCCATGATGCAAATGGAC 59.543 50.000 27.57 19.27 46.44 4.02
138 141 0.107654 GAGGCCAACTCTAACGCCAT 60.108 55.000 5.01 0.00 44.18 4.40
146 149 1.668826 TGGGTATTGAGGCCAACTCT 58.331 50.000 5.01 0.00 46.72 3.24
180 183 1.302993 GCAACGTTCCTAGGGGCAA 60.303 57.895 9.46 0.00 0.00 4.52
211 214 1.153997 GCCGTCAGAGGACTTCGTC 60.154 63.158 0.00 0.00 42.05 4.20
212 215 1.587933 GAGCCGTCAGAGGACTTCGT 61.588 60.000 0.00 0.00 42.05 3.85
213 216 1.137825 GAGCCGTCAGAGGACTTCG 59.862 63.158 0.00 0.00 42.05 3.79
247 250 3.009473 TGGTAGCTCTCAAAATCCTTGCT 59.991 43.478 0.00 0.00 0.00 3.91
258 261 2.423892 GAGAACGACATGGTAGCTCTCA 59.576 50.000 0.00 0.00 33.08 3.27
259 262 2.423892 TGAGAACGACATGGTAGCTCTC 59.576 50.000 0.00 4.45 33.32 3.20
280 297 3.116300 CGATTCAAGATTGTCGGTCGAT 58.884 45.455 0.00 0.00 0.00 3.59
288 305 3.317711 TGGTTGTTGCGATTCAAGATTGT 59.682 39.130 0.00 0.00 34.91 2.71
297 314 3.801594 GTCATTTTGTGGTTGTTGCGATT 59.198 39.130 0.00 0.00 0.00 3.34
298 315 3.380142 GTCATTTTGTGGTTGTTGCGAT 58.620 40.909 0.00 0.00 0.00 4.58
310 327 3.988379 AAGATGTGCACGTCATTTTGT 57.012 38.095 34.33 14.88 34.41 2.83
312 329 3.052036 GCAAAGATGTGCACGTCATTTT 58.948 40.909 34.33 24.98 44.29 1.82
321 338 0.955428 GGAGACCGCAAAGATGTGCA 60.955 55.000 0.00 0.00 45.19 4.57
341 358 3.050619 CGACGCAGAACTCTAAAGTTGT 58.949 45.455 0.00 0.00 45.80 3.32
348 365 1.310933 GGGGTCGACGCAGAACTCTA 61.311 60.000 30.51 0.00 0.00 2.43
508 2735 2.867287 TAATCCAACATGCCGCAATG 57.133 45.000 0.00 0.00 0.00 2.82
513 2740 4.268405 GCTCATTTTTAATCCAACATGCCG 59.732 41.667 0.00 0.00 0.00 5.69
517 2744 5.650543 GACCGCTCATTTTTAATCCAACAT 58.349 37.500 0.00 0.00 0.00 2.71
528 2755 1.078426 CTCCCCGACCGCTCATTTT 60.078 57.895 0.00 0.00 0.00 1.82
576 2803 2.200899 CGCGACATACATGTTGGATGA 58.799 47.619 12.91 0.00 41.23 2.92
582 2809 4.390603 ACATTACAACGCGACATACATGTT 59.609 37.500 15.93 0.00 41.95 2.71
583 2810 3.930229 ACATTACAACGCGACATACATGT 59.070 39.130 15.93 10.76 45.16 3.21
594 2821 1.061566 GAAGCCCGTACATTACAACGC 59.938 52.381 0.00 0.00 37.78 4.84
623 2850 1.508808 GCCCGTGCACCTCGTAAAAA 61.509 55.000 12.15 0.00 37.47 1.94
624 2851 1.962306 GCCCGTGCACCTCGTAAAA 60.962 57.895 12.15 0.00 37.47 1.52
625 2852 2.357760 GCCCGTGCACCTCGTAAA 60.358 61.111 12.15 0.00 37.47 2.01
626 2853 1.534336 TAAGCCCGTGCACCTCGTAA 61.534 55.000 12.15 0.00 41.13 3.18
627 2854 1.978080 TAAGCCCGTGCACCTCGTA 60.978 57.895 12.15 0.42 41.13 3.43
628 2855 3.307906 TAAGCCCGTGCACCTCGT 61.308 61.111 12.15 1.41 41.13 4.18
629 2856 1.940883 TAGTAAGCCCGTGCACCTCG 61.941 60.000 12.15 0.00 41.13 4.63
630 2857 0.248289 TTAGTAAGCCCGTGCACCTC 59.752 55.000 12.15 0.01 41.13 3.85
631 2858 0.909623 ATTAGTAAGCCCGTGCACCT 59.090 50.000 12.15 2.86 41.13 4.00
632 2859 1.746470 AATTAGTAAGCCCGTGCACC 58.254 50.000 12.15 0.00 41.13 5.01
633 2860 4.201881 CCTTTAATTAGTAAGCCCGTGCAC 60.202 45.833 6.82 6.82 41.13 4.57
634 2861 3.942748 CCTTTAATTAGTAAGCCCGTGCA 59.057 43.478 0.00 0.00 41.13 4.57
635 2862 4.193865 TCCTTTAATTAGTAAGCCCGTGC 58.806 43.478 0.00 0.00 37.95 5.34
636 2863 5.878669 AGTTCCTTTAATTAGTAAGCCCGTG 59.121 40.000 0.00 0.00 0.00 4.94
637 2864 6.058553 AGTTCCTTTAATTAGTAAGCCCGT 57.941 37.500 0.00 0.00 0.00 5.28
638 2865 6.997239 AAGTTCCTTTAATTAGTAAGCCCG 57.003 37.500 0.00 0.00 0.00 6.13
717 2945 7.138736 ACACTATATTTGGCACGCAATAATTC 58.861 34.615 0.00 0.00 0.00 2.17
720 2948 7.555306 TTACACTATATTTGGCACGCAATAA 57.445 32.000 0.00 0.00 0.00 1.40
722 2950 6.443934 TTTACACTATATTTGGCACGCAAT 57.556 33.333 0.00 0.00 0.00 3.56
723 2951 5.881777 TTTACACTATATTTGGCACGCAA 57.118 34.783 0.00 0.00 0.00 4.85
793 3023 8.498054 TTTGACAGCCAGAGAGAAAATATTAG 57.502 34.615 0.00 0.00 0.00 1.73
804 3034 2.170397 TCACTGTTTTGACAGCCAGAGA 59.830 45.455 6.47 1.32 41.19 3.10
908 3138 4.887190 AAACCGCCGTGCCCAACT 62.887 61.111 0.00 0.00 0.00 3.16
934 3164 2.878406 CAGCAACCGGAAAGAAGAAGAA 59.122 45.455 9.46 0.00 0.00 2.52
935 3165 2.494059 CAGCAACCGGAAAGAAGAAGA 58.506 47.619 9.46 0.00 0.00 2.87
936 3166 1.068954 GCAGCAACCGGAAAGAAGAAG 60.069 52.381 9.46 0.00 0.00 2.85
1134 3364 2.372688 GTGGGGAGGATGAGGGGA 59.627 66.667 0.00 0.00 0.00 4.81
1372 3620 3.782443 GTGGAGGTTCGCCGGGAT 61.782 66.667 2.18 0.00 43.66 3.85
1536 3784 4.492160 TCGTCATCGGCGAGCACC 62.492 66.667 17.22 2.07 37.69 5.01
1608 3856 2.731571 GCCGAGGTACCATGGCTCA 61.732 63.158 30.16 0.00 44.16 4.26
1852 4105 2.351276 GGAAAAGGAGAGGCGGCA 59.649 61.111 13.08 0.00 0.00 5.69
1863 4116 1.282382 TCGGGGTAGAAGGGGAAAAG 58.718 55.000 0.00 0.00 0.00 2.27
1878 4131 3.243201 GCAGAGGCAAATAGAAATTCGGG 60.243 47.826 0.00 0.00 40.72 5.14
1933 4186 2.749280 TTTCGCAGCAATCTCTCTCA 57.251 45.000 0.00 0.00 0.00 3.27
1936 4189 3.373439 AGTTGATTTCGCAGCAATCTCTC 59.627 43.478 6.93 0.00 32.63 3.20
1979 4232 8.778059 TCAATTTCCCCATAACTATGAACTACT 58.222 33.333 0.00 0.00 35.75 2.57
1980 4233 8.974060 TCAATTTCCCCATAACTATGAACTAC 57.026 34.615 0.00 0.00 35.75 2.73
2117 4370 4.558226 ACAGCAACATGACAATCCTAGA 57.442 40.909 0.00 0.00 0.00 2.43
2154 4407 4.517285 TCTCAACAACAATCCTAGGATGC 58.483 43.478 25.20 0.00 34.70 3.91
2221 4478 5.825593 ACCTTTCAGTCTCTCACCAATAA 57.174 39.130 0.00 0.00 0.00 1.40
2337 4594 1.480954 GGTTCAGCGTATCTTGAGGGA 59.519 52.381 0.00 0.00 0.00 4.20
2352 4609 1.588674 GATTGGTGTCGTGTGGTTCA 58.411 50.000 0.00 0.00 0.00 3.18
2401 4658 0.321653 CCTGGTGGTGTAGTTCTGGC 60.322 60.000 0.00 0.00 0.00 4.85
2435 4692 3.165875 ACTAGGAGAGTGCAGCAGTTAA 58.834 45.455 3.65 0.00 36.87 2.01
2568 4825 2.128771 ATGCCACAATGGTCACCTAC 57.871 50.000 0.00 0.00 40.46 3.18
2573 4830 1.632920 TCCAGTATGCCACAATGGTCA 59.367 47.619 0.00 0.00 40.46 4.02
2653 4910 5.583969 AACGTTTATTTCGGCAAAATTGG 57.416 34.783 0.00 0.00 38.53 3.16
2811 5068 7.395772 TCATTGGGTGCAAAATACAGATAAAGA 59.604 33.333 0.00 0.00 0.00 2.52
2847 5104 4.405116 TTTCTGAAAAACAGCAGCCATT 57.595 36.364 0.00 0.00 45.38 3.16
2915 5177 3.680789 GTGTGTGCACAACTTCAAGTAC 58.319 45.455 23.59 5.41 43.77 2.73
3032 5294 4.141711 TGAAGTGACACTAAAGGAGCAAGT 60.142 41.667 8.91 0.00 0.00 3.16
3066 5328 5.289510 ACCAGGGTAAAGAGGATAGACATT 58.710 41.667 0.00 0.00 0.00 2.71
3153 5415 4.970003 GTCATAGCACACTGTTTGTTGAAC 59.030 41.667 0.00 0.00 35.67 3.18
3203 5465 1.322442 GAACAGAATAGCCCCATGCC 58.678 55.000 0.00 0.00 42.71 4.40
3284 5546 1.338200 ACATTGCGACCTCTTCTCCAC 60.338 52.381 0.00 0.00 0.00 4.02
3437 5699 5.124645 TGAATCAAGTTTGGCAAGCATTTT 58.875 33.333 16.52 4.37 0.00 1.82
3730 5992 6.753180 TCTACTCCAGATCAGTATTCAATGC 58.247 40.000 0.00 0.00 0.00 3.56
3742 6004 9.202273 CAAGCTGTAAATTATCTACTCCAGATC 57.798 37.037 0.00 0.00 43.27 2.75
3807 6073 3.576078 AAATGAAGTGGGACAGTGTGA 57.424 42.857 0.00 0.00 43.84 3.58
3964 6230 1.148273 TCCTTGACGTGCAGCCTTT 59.852 52.632 0.00 0.00 0.00 3.11
4017 6283 9.101655 CCTCTAACTACTCTCTAACAACTACTC 57.898 40.741 0.00 0.00 0.00 2.59
4030 6296 9.536510 AACAGAGAATAAACCTCTAACTACTCT 57.463 33.333 0.00 0.00 38.84 3.24
4076 6342 5.428184 AACTGAGGAGAAGATTTACAGGG 57.572 43.478 0.00 0.00 0.00 4.45
4215 6481 4.015084 ACATGGAAAAGAATGGCTCTCTG 58.985 43.478 0.00 0.00 31.02 3.35
4236 6502 3.057019 TGCGACTTGTGACACTAATGAC 58.943 45.455 7.20 0.00 0.00 3.06
4264 6531 1.828979 TGTTGGGGGAATTTCGTAGC 58.171 50.000 0.00 0.00 0.00 3.58
4373 6640 0.909623 TACAAGAACCCTAGCTGCCC 59.090 55.000 0.00 0.00 0.00 5.36
4394 6661 3.832490 ACGGAGGCAGTATCATATTGCTA 59.168 43.478 11.59 0.00 40.73 3.49
4395 6662 2.634940 ACGGAGGCAGTATCATATTGCT 59.365 45.455 11.59 0.00 40.73 3.91
4396 6663 2.996621 GACGGAGGCAGTATCATATTGC 59.003 50.000 3.54 3.54 40.27 3.56
4397 6664 3.589988 GGACGGAGGCAGTATCATATTG 58.410 50.000 0.00 0.00 0.00 1.90
4398 6665 2.567615 GGGACGGAGGCAGTATCATATT 59.432 50.000 0.00 0.00 0.00 1.28
4399 6666 2.180276 GGGACGGAGGCAGTATCATAT 58.820 52.381 0.00 0.00 0.00 1.78
4400 6667 1.133294 TGGGACGGAGGCAGTATCATA 60.133 52.381 0.00 0.00 0.00 2.15
4401 6668 0.398522 TGGGACGGAGGCAGTATCAT 60.399 55.000 0.00 0.00 0.00 2.45
4402 6669 0.398522 ATGGGACGGAGGCAGTATCA 60.399 55.000 0.00 0.00 0.00 2.15
4403 6670 1.629043 TATGGGACGGAGGCAGTATC 58.371 55.000 0.00 0.00 0.00 2.24
4404 6671 2.097110 TTATGGGACGGAGGCAGTAT 57.903 50.000 0.00 0.00 0.00 2.12
4405 6672 2.097110 ATTATGGGACGGAGGCAGTA 57.903 50.000 0.00 0.00 0.00 2.74
4406 6673 2.097110 TATTATGGGACGGAGGCAGT 57.903 50.000 0.00 0.00 0.00 4.40
4407 6674 4.819105 TTATATTATGGGACGGAGGCAG 57.181 45.455 0.00 0.00 0.00 4.85
4408 6675 5.163184 TGTTTTATATTATGGGACGGAGGCA 60.163 40.000 0.00 0.00 0.00 4.75
4409 6676 5.310451 TGTTTTATATTATGGGACGGAGGC 58.690 41.667 0.00 0.00 0.00 4.70
4410 6677 7.996098 AATGTTTTATATTATGGGACGGAGG 57.004 36.000 0.00 0.00 0.00 4.30
4471 6738 7.789831 ACTCCCTCAGTCCAATAATATAAGACA 59.210 37.037 5.69 0.00 0.00 3.41
4472 6739 8.196378 ACTCCCTCAGTCCAATAATATAAGAC 57.804 38.462 0.00 0.00 0.00 3.01
4484 6751 2.786445 AGCTATCTACTCCCTCAGTCCA 59.214 50.000 0.00 0.00 36.43 4.02
4507 6774 2.413837 CGAAGCCTATAACCCGAATGG 58.586 52.381 0.00 0.00 41.37 3.16
4550 6817 8.533153 GTCTAGTGTTTACTTTCTATTGATCGC 58.467 37.037 0.00 0.00 38.36 4.58
4558 6825 9.309516 CTGTTGTTGTCTAGTGTTTACTTTCTA 57.690 33.333 0.00 0.00 38.36 2.10
4560 6827 7.065443 ACCTGTTGTTGTCTAGTGTTTACTTTC 59.935 37.037 0.00 0.00 38.36 2.62
4576 6843 4.188462 TCTGTAGTTGTCACCTGTTGTTG 58.812 43.478 0.00 0.00 0.00 3.33
4602 6869 2.284417 GCTGAACGTCGTCAGTTTCTTT 59.716 45.455 16.51 0.00 45.75 2.52
4617 6884 1.125847 CGTTATTTGGCGCGCTGAAC 61.126 55.000 32.29 23.18 0.00 3.18
4620 6887 2.277247 CCGTTATTTGGCGCGCTG 60.277 61.111 32.29 10.20 0.00 5.18
4635 6902 1.971695 GAAAGGGAGTGGTTGGCCG 60.972 63.158 0.00 0.00 37.67 6.13
4660 6927 2.499693 TCGTTTATGAGCATCTGGTGGA 59.500 45.455 0.00 0.00 34.92 4.02
4685 6952 1.663695 AACCCAAATCTGCCGATACG 58.336 50.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.