Multiple sequence alignment - TraesCS1D01G076100

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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 TraesCS1D01G076100 chr1D 100.000 4505 0 0 1 4505 58512122 58516626 0.000000e+00 8320.0
1 TraesCS1D01G076100 chr1D 81.731 104 13 6 3638 3736 409501710 409501608 1.040000e-11 82.4
2 TraesCS1D01G076100 chr1A 95.728 3418 136 6 818 4233 57204643 57208052 0.000000e+00 5494.0
3 TraesCS1D01G076100 chr1A 93.407 182 6 3 4230 4411 57208084 57208259 9.610000e-67 265.0
4 TraesCS1D01G076100 chr1B 93.774 2827 154 14 851 3667 94012824 94010010 0.000000e+00 4226.0
5 TraesCS1D01G076100 chr6D 91.932 818 60 4 1 813 445651384 445652200 0.000000e+00 1140.0
6 TraesCS1D01G076100 chr3A 90.998 822 64 7 1 813 670554138 670553318 0.000000e+00 1099.0
7 TraesCS1D01G076100 chr5D 90.552 815 71 5 1 813 305778595 305779405 0.000000e+00 1074.0
8 TraesCS1D01G076100 chr5D 72.862 269 65 6 3816 4079 360126150 360125885 8.030000e-13 86.1
9 TraesCS1D01G076100 chr7D 90.453 817 71 5 2 814 552303921 552304734 0.000000e+00 1070.0
10 TraesCS1D01G076100 chr7D 89.976 818 73 7 1 813 135438470 135439283 0.000000e+00 1048.0
11 TraesCS1D01G076100 chr7D 89.866 819 74 6 1 813 532629029 532629844 0.000000e+00 1044.0
12 TraesCS1D01G076100 chr5B 89.878 820 73 7 1 813 697492411 697491595 0.000000e+00 1046.0
13 TraesCS1D01G076100 chr4A 89.756 820 72 7 1 813 727414500 727415314 0.000000e+00 1038.0
14 TraesCS1D01G076100 chr2B 89.693 815 77 5 1 813 96627442 96626633 0.000000e+00 1033.0
15 TraesCS1D01G076100 chr4B 85.185 81 12 0 3787 3867 169811057 169811137 2.890000e-12 84.2
16 TraesCS1D01G076100 chr5A 81.915 94 12 4 3842 3931 461014245 461014153 1.740000e-09 75.0
17 TraesCS1D01G076100 chr5A 81.818 77 13 1 3633 3709 436375713 436375638 3.760000e-06 63.9
18 TraesCS1D01G076100 chr3B 91.071 56 3 2 3656 3709 3069026 3068971 1.740000e-09 75.0
19 TraesCS1D01G076100 chr3D 83.133 83 11 3 3638 3718 430380208 430380127 6.250000e-09 73.1


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 TraesCS1D01G076100 chr1D 58512122 58516626 4504 False 8320.0 8320 100.0000 1 4505 1 chr1D.!!$F1 4504
1 TraesCS1D01G076100 chr1A 57204643 57208259 3616 False 2879.5 5494 94.5675 818 4411 2 chr1A.!!$F1 3593
2 TraesCS1D01G076100 chr1B 94010010 94012824 2814 True 4226.0 4226 93.7740 851 3667 1 chr1B.!!$R1 2816
3 TraesCS1D01G076100 chr6D 445651384 445652200 816 False 1140.0 1140 91.9320 1 813 1 chr6D.!!$F1 812
4 TraesCS1D01G076100 chr3A 670553318 670554138 820 True 1099.0 1099 90.9980 1 813 1 chr3A.!!$R1 812
5 TraesCS1D01G076100 chr5D 305778595 305779405 810 False 1074.0 1074 90.5520 1 813 1 chr5D.!!$F1 812
6 TraesCS1D01G076100 chr7D 552303921 552304734 813 False 1070.0 1070 90.4530 2 814 1 chr7D.!!$F3 812
7 TraesCS1D01G076100 chr7D 135438470 135439283 813 False 1048.0 1048 89.9760 1 813 1 chr7D.!!$F1 812
8 TraesCS1D01G076100 chr7D 532629029 532629844 815 False 1044.0 1044 89.8660 1 813 1 chr7D.!!$F2 812
9 TraesCS1D01G076100 chr5B 697491595 697492411 816 True 1046.0 1046 89.8780 1 813 1 chr5B.!!$R1 812
10 TraesCS1D01G076100 chr4A 727414500 727415314 814 False 1038.0 1038 89.7560 1 813 1 chr4A.!!$F1 812
11 TraesCS1D01G076100 chr2B 96626633 96627442 809 True 1033.0 1033 89.6930 1 813 1 chr2B.!!$R1 812

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
815 829 0.108424 GCTGTTGGAGATGCTCTCGT 60.108 55.0 6.97 0.0 44.28 4.18 F
1044 1067 0.319040 ATCGTCGCCAATCCATCTCG 60.319 55.0 0.00 0.0 0.00 4.04 F
2733 2759 0.907486 CACAGCTCTCCCATCTCCAA 59.093 55.0 0.00 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2733 2759 0.034380 TGGCAGCTAGGTCGAGTAGT 60.034 55.000 0.00 0.0 0.00 2.73 R
2886 2912 1.135139 CAGTTCACATCGATCCGGTCT 59.865 52.381 0.00 0.0 0.00 3.85 R
4419 4483 0.032130 GGATAATCTGCGAGCACCGA 59.968 55.000 2.63 0.0 41.76 4.69 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
32 33 1.078356 CCTCCTCCGACGTCTGAGA 60.078 63.158 31.24 18.82 30.03 3.27
33 34 0.464735 CCTCCTCCGACGTCTGAGAT 60.465 60.000 31.24 0.00 30.03 2.75
35 36 1.746220 CTCCTCCGACGTCTGAGATTT 59.254 52.381 31.24 0.00 30.03 2.17
41 42 1.429463 GACGTCTGAGATTTGGCGTT 58.571 50.000 8.70 0.00 32.56 4.84
131 132 2.981977 TTCCGCGTTCGCTTGTCCTT 62.982 55.000 14.92 0.00 0.00 3.36
173 174 0.758685 CTCCTCTTCGCCCTCTCCAT 60.759 60.000 0.00 0.00 0.00 3.41
186 187 0.633378 TCTCCATCCTCCTCTCAGCA 59.367 55.000 0.00 0.00 0.00 4.41
323 324 0.395311 TCCTCGTCGGTGATAAGCCT 60.395 55.000 0.00 0.00 0.00 4.58
389 390 1.234821 GCGAAGTTCATGTCCCAACA 58.765 50.000 3.32 0.00 40.38 3.33
464 466 1.906824 TGTCGAAGGTTCCGAGGCT 60.907 57.895 0.00 0.00 36.66 4.58
505 507 2.023318 CGAATCTCGGCGGAGTAGT 58.977 57.895 19.51 7.18 41.26 2.73
608 610 1.376553 GCGGCAAGGAGAGAAAGCT 60.377 57.895 0.00 0.00 0.00 3.74
750 759 3.764049 GAGCGCGCGAAAACGTCT 61.764 61.111 37.18 19.51 34.88 4.18
752 761 4.054455 GCGCGCGAAAACGTCTCA 62.054 61.111 37.18 0.00 34.88 3.27
814 828 0.809241 GGCTGTTGGAGATGCTCTCG 60.809 60.000 6.97 0.00 44.28 4.04
815 829 0.108424 GCTGTTGGAGATGCTCTCGT 60.108 55.000 6.97 0.00 44.28 4.18
816 830 1.638133 CTGTTGGAGATGCTCTCGTG 58.362 55.000 6.97 0.00 44.28 4.35
819 833 2.164422 TGTTGGAGATGCTCTCGTGTAG 59.836 50.000 6.97 0.00 44.28 2.74
832 846 1.402968 TCGTGTAGATGACCTAACCGC 59.597 52.381 0.00 0.00 0.00 5.68
839 853 1.400494 GATGACCTAACCGCGCAAAAT 59.600 47.619 8.75 0.00 0.00 1.82
973 996 1.086696 CAACGACCAGCCCACATTAG 58.913 55.000 0.00 0.00 0.00 1.73
990 1013 7.147846 CCCACATTAGATAGCTCAACCATTTTT 60.148 37.037 0.00 0.00 0.00 1.94
1044 1067 0.319040 ATCGTCGCCAATCCATCTCG 60.319 55.000 0.00 0.00 0.00 4.04
1062 1085 1.658673 GACGATACGCGGGGAGAAT 59.341 57.895 12.47 0.00 46.49 2.40
1112 1135 2.270986 CCCCAGACAAACTGCAGCC 61.271 63.158 15.27 0.00 44.52 4.85
1255 1281 3.127099 TGGAAGTCCACTCTGACGT 57.873 52.632 0.00 0.00 42.01 4.34
1842 1868 1.829222 TCGGGTGTTATTCCTCCTGAC 59.171 52.381 0.00 0.00 31.39 3.51
1890 1916 3.728845 TCTGTTCTTCCTGCACTACAAC 58.271 45.455 0.00 0.00 0.00 3.32
2220 2246 4.495349 CCTGCAACTATTTCATCGCTCAAG 60.495 45.833 0.00 0.00 0.00 3.02
2279 2305 1.824230 TGGTACAATCCCAAGCATTGC 59.176 47.619 0.00 0.00 39.89 3.56
2455 2481 8.428063 AGGATCTATTGTTCCTAGATTTGTCAG 58.572 37.037 5.12 0.00 39.81 3.51
2505 2531 2.438021 AGCTGGGTCCGCTAATTTATCA 59.562 45.455 4.94 0.00 35.63 2.15
2705 2731 3.262405 TCGTTTAGTGGTAGCATTCCCTT 59.738 43.478 0.00 0.00 0.00 3.95
2733 2759 0.907486 CACAGCTCTCCCATCTCCAA 59.093 55.000 0.00 0.00 0.00 3.53
2761 2787 2.164422 GACCTAGCTGCCAACCAATTTC 59.836 50.000 0.00 0.00 0.00 2.17
2850 2876 4.836825 ACATGACTTCACTAATCCACCAG 58.163 43.478 0.00 0.00 0.00 4.00
2854 2880 4.072131 GACTTCACTAATCCACCAGCAAA 58.928 43.478 0.00 0.00 0.00 3.68
2872 2898 7.137426 CCAGCAAATTTTACATCTAGATGCTC 58.863 38.462 28.86 10.01 42.39 4.26
2873 2899 7.201758 CCAGCAAATTTTACATCTAGATGCTCA 60.202 37.037 28.86 14.04 42.39 4.26
2915 2941 4.115401 TCGATGTGAACTGGAAGATGAG 57.885 45.455 0.00 0.00 37.43 2.90
2930 2956 3.652055 AGATGAGGAGCTACACATTCCT 58.348 45.455 10.45 1.19 43.86 3.36
2977 3003 3.878086 TCGATTTATCAGGCAATTCGC 57.122 42.857 0.00 0.00 41.28 4.70
3014 3040 1.195115 ACCGAGCTAGCAAATCTCCA 58.805 50.000 18.83 0.00 0.00 3.86
3171 3197 2.745515 AACTGCCGTCTCTTAGTTCC 57.254 50.000 0.00 0.00 0.00 3.62
3311 3337 0.889186 TGCTCCAAAGGTTCTTCGGC 60.889 55.000 0.00 0.00 0.00 5.54
3363 3389 7.458409 TGAAACCGTGTATTTCTACTACTCT 57.542 36.000 0.00 0.00 37.05 3.24
3453 3479 6.708949 GGAGGACTTATGTTTTCTGTTGTGTA 59.291 38.462 0.00 0.00 0.00 2.90
3460 3486 3.496884 TGTTTTCTGTTGTGTAGATCGCC 59.503 43.478 0.00 0.00 0.00 5.54
3461 3487 3.678056 TTTCTGTTGTGTAGATCGCCT 57.322 42.857 0.00 0.00 0.00 5.52
3462 3488 2.654749 TCTGTTGTGTAGATCGCCTG 57.345 50.000 0.00 0.00 0.00 4.85
3679 3706 3.182887 TGGCCCCTTCATATTTTGTGT 57.817 42.857 0.00 0.00 0.00 3.72
3706 3733 7.972832 AATTTTGACCGTAGATTGACTAACA 57.027 32.000 0.00 0.00 32.49 2.41
3802 3830 1.076923 ACGTCTAGGTCGGAGCCAT 60.077 57.895 3.13 0.00 0.00 4.40
3822 3850 1.810151 TGGTGCAATCGCTTTAAGTCC 59.190 47.619 0.00 0.00 39.64 3.85
3849 3877 5.661759 AGGGAGTAAGACCGTTCTTATTCAT 59.338 40.000 21.20 10.42 46.01 2.57
3855 3883 4.290942 AGACCGTTCTTATTCATCCCTCT 58.709 43.478 0.00 0.00 0.00 3.69
3860 3888 6.555360 ACCGTTCTTATTCATCCCTCTCTATT 59.445 38.462 0.00 0.00 0.00 1.73
3918 3946 1.705873 CGGAAGGGGTACATAGCTCT 58.294 55.000 0.00 0.00 35.74 4.09
4056 4085 1.822581 CGTCTCGTCGCATGAATGTA 58.177 50.000 0.00 0.00 0.00 2.29
4065 4094 3.187227 GTCGCATGAATGTAGCCCTTATG 59.813 47.826 0.00 0.00 0.00 1.90
4137 4166 3.006003 GCAGCTGGTCTAGGGTAAGTATC 59.994 52.174 17.12 0.00 0.00 2.24
4140 4169 4.079096 AGCTGGTCTAGGGTAAGTATCTGT 60.079 45.833 0.00 0.00 0.00 3.41
4179 4208 3.249189 TGAGCGCAGGGAAGGGTT 61.249 61.111 11.47 0.00 0.00 4.11
4239 4303 3.084039 TGCACTAGAATTTCTGGCTTGG 58.916 45.455 9.22 0.00 0.00 3.61
4306 4370 1.032794 TCGCTATGTGCTCGAATCCT 58.967 50.000 0.00 0.00 40.11 3.24
4307 4371 1.001268 TCGCTATGTGCTCGAATCCTC 60.001 52.381 0.00 0.00 40.11 3.71
4308 4372 1.269257 CGCTATGTGCTCGAATCCTCA 60.269 52.381 0.00 0.00 40.11 3.86
4309 4373 2.799562 CGCTATGTGCTCGAATCCTCAA 60.800 50.000 0.00 0.00 40.11 3.02
4312 4376 1.372582 TGTGCTCGAATCCTCAATGC 58.627 50.000 0.00 0.00 0.00 3.56
4313 4377 0.659957 GTGCTCGAATCCTCAATGCC 59.340 55.000 0.00 0.00 0.00 4.40
4314 4378 0.252761 TGCTCGAATCCTCAATGCCA 59.747 50.000 0.00 0.00 0.00 4.92
4315 4379 1.134007 TGCTCGAATCCTCAATGCCAT 60.134 47.619 0.00 0.00 0.00 4.40
4316 4380 1.952296 GCTCGAATCCTCAATGCCATT 59.048 47.619 0.00 0.00 0.00 3.16
4317 4381 3.141398 GCTCGAATCCTCAATGCCATTA 58.859 45.455 0.00 0.00 0.00 1.90
4381 4445 1.001503 GGACATTTGGGCCCATGGA 59.998 57.895 29.23 15.75 0.00 3.41
4414 4478 4.974721 CAACTTGTGGGCCGCCCT 62.975 66.667 28.97 5.57 45.70 5.19
4415 4479 4.660938 AACTTGTGGGCCGCCCTC 62.661 66.667 28.97 25.15 45.70 4.30
4433 4497 4.498520 CCGTCGGTGCTCGCAGAT 62.499 66.667 2.08 0.00 39.05 2.90
4434 4498 2.507102 CGTCGGTGCTCGCAGATT 60.507 61.111 0.00 0.00 39.05 2.40
4435 4499 1.226575 CGTCGGTGCTCGCAGATTA 60.227 57.895 0.00 0.00 39.05 1.75
4436 4500 0.595053 CGTCGGTGCTCGCAGATTAT 60.595 55.000 0.00 0.00 39.05 1.28
4437 4501 1.132588 GTCGGTGCTCGCAGATTATC 58.867 55.000 0.00 0.00 39.05 1.75
4438 4502 0.032130 TCGGTGCTCGCAGATTATCC 59.968 55.000 0.00 0.00 39.05 2.59
4439 4503 0.249447 CGGTGCTCGCAGATTATCCA 60.249 55.000 0.00 0.00 33.89 3.41
4440 4504 1.506493 GGTGCTCGCAGATTATCCAG 58.494 55.000 0.00 0.00 33.89 3.86
4441 4505 1.069204 GGTGCTCGCAGATTATCCAGA 59.931 52.381 0.00 0.00 33.89 3.86
4442 4506 2.131183 GTGCTCGCAGATTATCCAGAC 58.869 52.381 0.00 0.00 33.89 3.51
4443 4507 1.756538 TGCTCGCAGATTATCCAGACA 59.243 47.619 0.00 0.00 33.89 3.41
4444 4508 2.131183 GCTCGCAGATTATCCAGACAC 58.869 52.381 0.00 0.00 33.89 3.67
4445 4509 2.748605 CTCGCAGATTATCCAGACACC 58.251 52.381 0.00 0.00 33.89 4.16
4446 4510 2.363680 CTCGCAGATTATCCAGACACCT 59.636 50.000 0.00 0.00 33.89 4.00
4447 4511 2.766263 TCGCAGATTATCCAGACACCTT 59.234 45.455 0.00 0.00 0.00 3.50
4448 4512 2.868583 CGCAGATTATCCAGACACCTTG 59.131 50.000 0.00 0.00 0.00 3.61
4449 4513 3.679917 CGCAGATTATCCAGACACCTTGT 60.680 47.826 0.00 0.00 0.00 3.16
4457 4521 4.456806 GACACCTTGTCTTGGCGT 57.543 55.556 0.00 0.00 43.73 5.68
4458 4522 2.702847 GACACCTTGTCTTGGCGTT 58.297 52.632 0.00 0.00 43.73 4.84
4459 4523 1.021968 GACACCTTGTCTTGGCGTTT 58.978 50.000 0.00 0.00 43.73 3.60
4460 4524 0.738389 ACACCTTGTCTTGGCGTTTG 59.262 50.000 0.00 0.00 0.00 2.93
4461 4525 1.021202 CACCTTGTCTTGGCGTTTGA 58.979 50.000 0.00 0.00 0.00 2.69
4462 4526 1.021968 ACCTTGTCTTGGCGTTTGAC 58.978 50.000 0.00 0.00 0.00 3.18
4463 4527 0.310854 CCTTGTCTTGGCGTTTGACC 59.689 55.000 0.00 0.00 0.00 4.02
4464 4528 0.310854 CTTGTCTTGGCGTTTGACCC 59.689 55.000 0.00 0.00 0.00 4.46
4465 4529 1.104577 TTGTCTTGGCGTTTGACCCC 61.105 55.000 0.00 0.00 0.00 4.95
4466 4530 2.114411 TCTTGGCGTTTGACCCCC 59.886 61.111 0.00 0.00 0.00 5.40
4467 4531 2.115266 CTTGGCGTTTGACCCCCT 59.885 61.111 0.00 0.00 0.00 4.79
4468 4532 1.971695 CTTGGCGTTTGACCCCCTC 60.972 63.158 0.00 0.00 0.00 4.30
4469 4533 3.501040 TTGGCGTTTGACCCCCTCC 62.501 63.158 0.00 0.00 0.00 4.30
4472 4536 3.633116 CGTTTGACCCCCTCCGGT 61.633 66.667 0.00 0.00 39.49 5.28
4473 4537 2.285024 CGTTTGACCCCCTCCGGTA 61.285 63.158 0.00 0.00 35.79 4.02
4474 4538 1.619807 CGTTTGACCCCCTCCGGTAT 61.620 60.000 0.00 0.00 35.79 2.73
4475 4539 0.179702 GTTTGACCCCCTCCGGTATC 59.820 60.000 0.00 0.00 35.79 2.24
4476 4540 0.043637 TTTGACCCCCTCCGGTATCT 59.956 55.000 0.00 0.00 35.79 1.98
4477 4541 0.043637 TTGACCCCCTCCGGTATCTT 59.956 55.000 0.00 0.00 35.79 2.40
4478 4542 0.398098 TGACCCCCTCCGGTATCTTC 60.398 60.000 0.00 0.00 35.79 2.87
4479 4543 0.105607 GACCCCCTCCGGTATCTTCT 60.106 60.000 0.00 0.00 35.79 2.85
4480 4544 0.105607 ACCCCCTCCGGTATCTTCTC 60.106 60.000 0.00 0.00 33.04 2.87
4481 4545 1.179814 CCCCCTCCGGTATCTTCTCG 61.180 65.000 0.00 0.00 0.00 4.04
4482 4546 1.179814 CCCCTCCGGTATCTTCTCGG 61.180 65.000 0.00 0.00 44.59 4.63
4483 4547 0.467659 CCCTCCGGTATCTTCTCGGT 60.468 60.000 0.00 0.00 43.75 4.69
4484 4548 1.400737 CCTCCGGTATCTTCTCGGTT 58.599 55.000 0.00 0.00 43.75 4.44
4485 4549 1.067212 CCTCCGGTATCTTCTCGGTTG 59.933 57.143 0.00 0.00 43.75 3.77
4486 4550 1.067212 CTCCGGTATCTTCTCGGTTGG 59.933 57.143 0.00 0.00 43.75 3.77
4487 4551 0.529992 CCGGTATCTTCTCGGTTGGC 60.530 60.000 0.00 0.00 39.04 4.52
4488 4552 0.460311 CGGTATCTTCTCGGTTGGCT 59.540 55.000 0.00 0.00 0.00 4.75
4489 4553 1.536284 CGGTATCTTCTCGGTTGGCTC 60.536 57.143 0.00 0.00 0.00 4.70
4490 4554 1.536284 GGTATCTTCTCGGTTGGCTCG 60.536 57.143 0.00 0.00 0.00 5.03
4491 4555 0.744874 TATCTTCTCGGTTGGCTCGG 59.255 55.000 0.00 0.00 0.00 4.63
4492 4556 2.579684 ATCTTCTCGGTTGGCTCGGC 62.580 60.000 0.00 0.00 0.00 5.54
4493 4557 3.589654 CTTCTCGGTTGGCTCGGCA 62.590 63.158 0.00 0.00 0.00 5.69
4494 4558 2.859273 CTTCTCGGTTGGCTCGGCAT 62.859 60.000 0.00 0.00 0.00 4.40
4495 4559 1.609635 TTCTCGGTTGGCTCGGCATA 61.610 55.000 0.00 0.00 0.00 3.14
4496 4560 1.883084 CTCGGTTGGCTCGGCATAC 60.883 63.158 0.00 0.00 0.00 2.39
4497 4561 2.895372 CGGTTGGCTCGGCATACC 60.895 66.667 11.82 11.82 32.65 2.73
4498 4562 2.270850 GGTTGGCTCGGCATACCA 59.729 61.111 14.93 0.00 34.92 3.25
4499 4563 2.112815 GGTTGGCTCGGCATACCAC 61.113 63.158 14.93 3.30 34.92 4.16
4500 4564 2.125310 TTGGCTCGGCATACCACG 60.125 61.111 0.00 0.00 34.57 4.94
4501 4565 4.830765 TGGCTCGGCATACCACGC 62.831 66.667 0.00 0.00 34.57 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.524414 GCGGTTCCTTAACGCCAAAT 59.476 50.000 0.00 0.00 36.39 2.32
33 34 0.535553 AGCGGTTCCTTAACGCCAAA 60.536 50.000 3.30 0.00 36.46 3.28
35 36 1.375013 GAGCGGTTCCTTAACGCCA 60.375 57.895 3.30 0.00 36.46 5.69
41 42 2.180017 GCGACGAGCGGTTCCTTA 59.820 61.111 0.00 0.00 41.29 2.69
173 174 2.301296 CAGTTCTTTGCTGAGAGGAGGA 59.699 50.000 0.00 0.00 36.12 3.71
186 187 6.718454 ACATCATCAATGAGGAACAGTTCTTT 59.282 34.615 13.13 2.14 40.76 2.52
323 324 3.894547 GAGTTGGCGCCTTTCCCGA 62.895 63.158 29.70 1.01 0.00 5.14
442 444 2.431942 CGGAACCTTCGACACCGG 60.432 66.667 0.00 0.00 39.92 5.28
588 590 1.003355 CTTTCTCTCCTTGCCGCCA 60.003 57.895 0.00 0.00 0.00 5.69
595 597 3.103742 CCCTCTACAGCTTTCTCTCCTT 58.896 50.000 0.00 0.00 0.00 3.36
608 610 1.490910 TCTCTCATCGCTCCCTCTACA 59.509 52.381 0.00 0.00 0.00 2.74
642 644 1.535015 GGCGCGCCTATAAAATTGCAA 60.535 47.619 41.71 0.00 0.00 4.08
714 723 4.265056 AGCGGTGGCGGGAAACTT 62.265 61.111 0.00 0.00 46.35 2.66
750 759 1.160946 TGGCTTTTTAGCACGCGTGA 61.161 50.000 41.19 20.36 36.33 4.35
752 761 1.164041 ACTGGCTTTTTAGCACGCGT 61.164 50.000 5.58 5.58 36.33 6.01
814 828 1.836383 CGCGGTTAGGTCATCTACAC 58.164 55.000 0.00 0.00 0.00 2.90
815 829 0.101759 GCGCGGTTAGGTCATCTACA 59.898 55.000 8.83 0.00 0.00 2.74
816 830 0.101759 TGCGCGGTTAGGTCATCTAC 59.898 55.000 8.83 0.00 0.00 2.59
819 833 0.800012 TTTTGCGCGGTTAGGTCATC 59.200 50.000 8.83 0.00 0.00 2.92
839 853 2.048222 CGAGGAGGCGCAAACTCA 60.048 61.111 10.83 0.00 36.70 3.41
914 928 3.621715 AGTCCGAACTTGTTGAAGTGTTC 59.378 43.478 0.00 0.00 41.87 3.18
915 929 3.606687 AGTCCGAACTTGTTGAAGTGTT 58.393 40.909 0.00 0.00 41.87 3.32
916 930 3.261981 AGTCCGAACTTGTTGAAGTGT 57.738 42.857 0.00 0.00 41.87 3.55
973 996 5.351465 TCTGACGAAAAATGGTTGAGCTATC 59.649 40.000 0.00 0.00 0.00 2.08
1044 1067 0.663568 CATTCTCCCCGCGTATCGTC 60.664 60.000 4.92 0.00 36.19 4.20
1062 1085 1.198094 TCGAGGGGTGATTTGCTCCA 61.198 55.000 0.00 0.00 31.65 3.86
1112 1135 0.109153 TCTGGATTCCATGGCATCCG 59.891 55.000 30.65 25.31 41.90 4.18
1253 1279 2.464189 CGTTTGCGTCGGAGAACG 59.536 61.111 15.27 15.27 39.69 3.95
1255 1281 3.039588 GGCGTTTGCGTCGGAGAA 61.040 61.111 0.00 0.00 44.10 2.87
1275 1301 1.358402 CCATGACGAGAGCGGAGAG 59.642 63.158 0.00 0.00 43.17 3.20
1307 1333 3.524648 GACCAAGAACCGCACGGGA 62.525 63.158 14.51 0.00 39.97 5.14
1574 1600 2.202676 GGAGGACAAGAGCTCGCG 60.203 66.667 8.37 0.00 0.00 5.87
1683 1709 1.076533 CCAACTCCGTCGGAATCGTG 61.077 60.000 16.23 10.27 37.69 4.35
1842 1868 0.177604 CAGGCCAGCTAGTGAAGAGG 59.822 60.000 5.01 0.00 0.00 3.69
2011 2037 2.041620 TCCTCCCCAAATCCAGAAACTG 59.958 50.000 0.00 0.00 0.00 3.16
2220 2246 5.047660 ACTGAAGTCAAGACTGTACAGATCC 60.048 44.000 29.30 16.35 41.58 3.36
2279 2305 4.094590 CAGCTGAGAGCAATTTCTTACTGG 59.905 45.833 8.42 0.00 45.56 4.00
2455 2481 0.610785 TTCCCGGAGAAACCATTGCC 60.611 55.000 0.73 0.00 38.90 4.52
2505 2531 4.435425 CCAAATGCAATGATTCCAACGAT 58.565 39.130 4.54 0.00 0.00 3.73
2608 2634 3.749665 TGGAATTTGGCTGGAAAAGTG 57.250 42.857 0.00 0.00 0.00 3.16
2640 2666 4.171234 TCCTCAGGAAAGGAAGACTTGAT 58.829 43.478 0.00 0.00 42.56 2.57
2705 2731 0.250038 GGAGAGCTGTGACAGTTGCA 60.250 55.000 14.82 0.00 33.43 4.08
2733 2759 0.034380 TGGCAGCTAGGTCGAGTAGT 60.034 55.000 0.00 0.00 0.00 2.73
2850 2876 7.923888 TCTGAGCATCTAGATGTAAAATTTGC 58.076 34.615 28.92 15.97 40.80 3.68
2872 2898 5.050769 CGATCCGGTCTACAAAATTCATCTG 60.051 44.000 0.00 0.00 0.00 2.90
2873 2899 5.050490 CGATCCGGTCTACAAAATTCATCT 58.950 41.667 0.00 0.00 0.00 2.90
2886 2912 1.135139 CAGTTCACATCGATCCGGTCT 59.865 52.381 0.00 0.00 0.00 3.85
2915 2941 2.365941 GTCCCTAGGAATGTGTAGCTCC 59.634 54.545 11.48 0.00 31.38 4.70
2930 2956 4.955811 ATCATAAGTGCAATCGTCCCTA 57.044 40.909 0.00 0.00 0.00 3.53
3171 3197 9.874205 GAGAGATTATTATTGGAGAGATTGAGG 57.126 37.037 0.00 0.00 0.00 3.86
3225 3251 0.544697 AAGGGTCGTCCAGTGTTTGT 59.455 50.000 0.04 0.00 38.24 2.83
3311 3337 1.069513 TGTCCCGTGTTTCCACAGTAG 59.930 52.381 0.00 0.00 41.93 2.57
3326 3352 1.602377 CGGTTTCAAGTTCTGTGTCCC 59.398 52.381 0.00 0.00 0.00 4.46
3453 3479 3.494048 CCTTATCTTGAAGCAGGCGATCT 60.494 47.826 0.00 0.00 0.00 2.75
3460 3486 8.950210 TCTTTTCATAACCTTATCTTGAAGCAG 58.050 33.333 0.00 0.00 0.00 4.24
3461 3487 8.730680 GTCTTTTCATAACCTTATCTTGAAGCA 58.269 33.333 0.00 0.00 0.00 3.91
3462 3488 7.905493 CGTCTTTTCATAACCTTATCTTGAAGC 59.095 37.037 0.00 0.00 0.00 3.86
3679 3706 8.500773 GTTAGTCAATCTACGGTCAAAATTTGA 58.499 33.333 4.03 4.03 37.33 2.69
3781 3808 1.748122 GCTCCGACCTAGACGTGGA 60.748 63.158 0.00 0.00 0.00 4.02
3782 3809 2.772691 GGCTCCGACCTAGACGTGG 61.773 68.421 0.00 0.00 0.00 4.94
3802 3830 1.810151 GGACTTAAAGCGATTGCACCA 59.190 47.619 7.90 0.00 46.23 4.17
3822 3850 3.679824 AGAACGGTCTTACTCCCTTTG 57.320 47.619 0.00 0.00 0.00 2.77
3849 3877 5.483174 TGGGAAGACTAAATAGAGAGGGA 57.517 43.478 0.00 0.00 0.00 4.20
3888 3916 2.632537 ACCCCTTCCGGCAAGATATAT 58.367 47.619 13.28 0.00 33.29 0.86
3918 3946 7.645058 AAAATGAGAGAGGTCTTTGTCAAAA 57.355 32.000 0.00 0.00 30.97 2.44
3975 4004 0.180171 CGGCCCACATGACCATAAGA 59.820 55.000 0.00 0.00 0.00 2.10
3977 4006 0.843309 ATCGGCCCACATGACCATAA 59.157 50.000 0.00 0.00 0.00 1.90
4041 4070 0.529773 GGGCTACATTCATGCGACGA 60.530 55.000 0.00 0.00 0.00 4.20
4056 4085 4.444022 CAGACACATCTAAGCATAAGGGCT 60.444 45.833 0.00 0.00 38.46 5.19
4065 4094 5.895928 TGTATCTGTCAGACACATCTAAGC 58.104 41.667 9.94 0.00 33.23 3.09
4137 4166 0.608640 AAGAAGGTGTCGCCCTACAG 59.391 55.000 0.00 0.00 38.26 2.74
4140 4169 1.192146 AGCAAGAAGGTGTCGCCCTA 61.192 55.000 0.00 0.00 38.26 3.53
4172 4201 8.837788 ATGAATTTTCAGAATCAAAACCCTTC 57.162 30.769 0.00 0.00 41.08 3.46
4179 4208 6.995364 TGCTGGATGAATTTTCAGAATCAAA 58.005 32.000 0.00 0.00 41.08 2.69
4306 4370 2.752354 CCGTGGAAACTAATGGCATTGA 59.248 45.455 22.57 6.15 0.00 2.57
4307 4371 2.735126 GCCGTGGAAACTAATGGCATTG 60.735 50.000 22.57 14.18 42.03 2.82
4308 4372 1.476488 GCCGTGGAAACTAATGGCATT 59.524 47.619 18.01 18.01 42.03 3.56
4309 4373 1.102978 GCCGTGGAAACTAATGGCAT 58.897 50.000 0.00 0.00 42.03 4.40
4312 4376 1.427819 GCGCCGTGGAAACTAATGG 59.572 57.895 0.00 0.00 0.00 3.16
4313 4377 1.427819 GGCGCCGTGGAAACTAATG 59.572 57.895 12.58 0.00 0.00 1.90
4314 4378 1.747745 GGGCGCCGTGGAAACTAAT 60.748 57.895 22.54 0.00 0.00 1.73
4315 4379 2.358984 GGGCGCCGTGGAAACTAA 60.359 61.111 22.54 0.00 0.00 2.24
4316 4380 2.677765 TTTGGGCGCCGTGGAAACTA 62.678 55.000 22.54 0.00 0.00 2.24
4317 4381 4.572571 TTGGGCGCCGTGGAAACT 62.573 61.111 22.54 0.00 0.00 2.66
4361 4425 1.682005 CATGGGCCCAAATGTCCGT 60.682 57.895 32.58 6.47 0.00 4.69
4416 4480 2.607668 TAATCTGCGAGCACCGACGG 62.608 60.000 13.61 13.61 41.76 4.79
4417 4481 0.595053 ATAATCTGCGAGCACCGACG 60.595 55.000 2.63 0.00 41.76 5.12
4418 4482 1.132588 GATAATCTGCGAGCACCGAC 58.867 55.000 2.63 0.00 41.76 4.79
4419 4483 0.032130 GGATAATCTGCGAGCACCGA 59.968 55.000 2.63 0.00 41.76 4.69
4420 4484 0.249447 TGGATAATCTGCGAGCACCG 60.249 55.000 0.00 0.00 42.21 4.94
4421 4485 1.069204 TCTGGATAATCTGCGAGCACC 59.931 52.381 0.00 0.00 0.00 5.01
4422 4486 2.131183 GTCTGGATAATCTGCGAGCAC 58.869 52.381 0.00 0.00 0.00 4.40
4423 4487 1.756538 TGTCTGGATAATCTGCGAGCA 59.243 47.619 0.00 0.00 0.00 4.26
4424 4488 2.131183 GTGTCTGGATAATCTGCGAGC 58.869 52.381 0.00 0.00 0.00 5.03
4425 4489 2.363680 AGGTGTCTGGATAATCTGCGAG 59.636 50.000 0.00 0.00 0.00 5.03
4426 4490 2.388735 AGGTGTCTGGATAATCTGCGA 58.611 47.619 0.00 0.00 0.00 5.10
4427 4491 2.868583 CAAGGTGTCTGGATAATCTGCG 59.131 50.000 0.00 0.00 0.00 5.18
4428 4492 3.873952 GACAAGGTGTCTGGATAATCTGC 59.126 47.826 1.09 0.00 43.73 4.26
4440 4504 4.456806 ACGCCAAGACAAGGTGTC 57.543 55.556 0.00 0.00 46.34 3.67
4442 4506 1.021202 TCAAACGCCAAGACAAGGTG 58.979 50.000 0.00 0.00 42.31 4.00
4443 4507 1.021968 GTCAAACGCCAAGACAAGGT 58.978 50.000 0.00 0.00 32.68 3.50
4444 4508 0.310854 GGTCAAACGCCAAGACAAGG 59.689 55.000 0.00 0.00 34.04 3.61
4445 4509 0.310854 GGGTCAAACGCCAAGACAAG 59.689 55.000 0.00 0.00 34.04 3.16
4446 4510 2.410466 GGGTCAAACGCCAAGACAA 58.590 52.632 0.00 0.00 34.04 3.18
4447 4511 4.150994 GGGTCAAACGCCAAGACA 57.849 55.556 0.00 0.00 34.04 3.41
4466 4530 1.067212 CCAACCGAGAAGATACCGGAG 59.933 57.143 9.46 0.00 45.58 4.63
4467 4531 1.108776 CCAACCGAGAAGATACCGGA 58.891 55.000 9.46 0.00 45.58 5.14
4469 4533 0.460311 AGCCAACCGAGAAGATACCG 59.540 55.000 0.00 0.00 0.00 4.02
4470 4534 1.536284 CGAGCCAACCGAGAAGATACC 60.536 57.143 0.00 0.00 0.00 2.73
4471 4535 1.536284 CCGAGCCAACCGAGAAGATAC 60.536 57.143 0.00 0.00 0.00 2.24
4472 4536 0.744874 CCGAGCCAACCGAGAAGATA 59.255 55.000 0.00 0.00 0.00 1.98
4473 4537 1.517832 CCGAGCCAACCGAGAAGAT 59.482 57.895 0.00 0.00 0.00 2.40
4474 4538 2.970639 CCGAGCCAACCGAGAAGA 59.029 61.111 0.00 0.00 0.00 2.87
4475 4539 2.815647 GCCGAGCCAACCGAGAAG 60.816 66.667 0.00 0.00 0.00 2.85
4476 4540 1.609635 TATGCCGAGCCAACCGAGAA 61.610 55.000 0.00 0.00 0.00 2.87
4477 4541 2.055633 TATGCCGAGCCAACCGAGA 61.056 57.895 0.00 0.00 0.00 4.04
4478 4542 1.883084 GTATGCCGAGCCAACCGAG 60.883 63.158 0.00 0.00 0.00 4.63
4479 4543 2.185867 GTATGCCGAGCCAACCGA 59.814 61.111 0.00 0.00 0.00 4.69
4480 4544 2.895372 GGTATGCCGAGCCAACCG 60.895 66.667 0.00 0.00 0.00 4.44
4481 4545 2.112815 GTGGTATGCCGAGCCAACC 61.113 63.158 0.00 8.73 37.67 3.77
4482 4546 2.461110 CGTGGTATGCCGAGCCAAC 61.461 63.158 0.00 0.00 37.67 3.77
4483 4547 2.125310 CGTGGTATGCCGAGCCAA 60.125 61.111 0.00 0.00 37.67 4.52
4484 4548 4.830765 GCGTGGTATGCCGAGCCA 62.831 66.667 7.88 0.00 37.67 4.75


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

AutoCloner maintained by Alex Coulton.