Multiple sequence alignment - TraesCS3B01G374400

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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 TraesCS3B01G374400 chr3B 100.000 3717 0 0 690 4406 587565687 587569403 0.000000e+00 6865.0
1 TraesCS3B01G374400 chr3B 100.000 346 0 0 1 346 587564998 587565343 1.340000e-179 640.0
2 TraesCS3B01G374400 chr3A 96.729 1804 54 4 690 2491 589392796 589394596 0.000000e+00 3000.0
3 TraesCS3B01G374400 chr3A 87.005 1716 106 54 2716 4374 589394933 589396588 0.000000e+00 1825.0
4 TraesCS3B01G374400 chr3A 93.966 348 13 4 1 346 589392434 589392775 1.820000e-143 520.0
5 TraesCS3B01G374400 chr3A 92.488 213 11 2 2511 2718 589394668 589394880 2.580000e-77 300.0
6 TraesCS3B01G374400 chr3D 97.588 1617 38 1 693 2308 447989258 447990874 0.000000e+00 2769.0
7 TraesCS3B01G374400 chr3D 88.139 1703 86 49 2717 4374 447991531 447993162 0.000000e+00 1919.0
8 TraesCS3B01G374400 chr3D 93.476 935 56 2 930 1859 206467204 206466270 0.000000e+00 1384.0
9 TraesCS3B01G374400 chr3D 93.678 348 11 4 1 346 447988895 447989233 1.090000e-140 510.0
10 TraesCS3B01G374400 chr3D 93.458 214 8 3 2511 2718 447991264 447991477 3.310000e-81 313.0
11 TraesCS3B01G374400 chr1A 89.173 859 80 5 930 1787 193040815 193041661 0.000000e+00 1059.0
12 TraesCS3B01G374400 chr1A 77.283 1325 265 27 993 2299 496046317 496045011 0.000000e+00 747.0
13 TraesCS3B01G374400 chr1A 81.726 591 100 7 2790 3376 496044270 496043684 1.840000e-133 486.0
14 TraesCS3B01G374400 chr1D 78.145 1240 239 22 1076 2299 399190925 399189702 0.000000e+00 760.0
15 TraesCS3B01G374400 chr1D 82.712 590 96 5 2790 3376 399188907 399188321 1.820000e-143 520.0
16 TraesCS3B01G374400 chr1D 79.891 184 32 5 1511 1692 399044424 399044244 3.580000e-26 130.0
17 TraesCS3B01G374400 chr1B 81.895 591 99 7 2790 3376 535384850 535384264 3.960000e-135 492.0
18 TraesCS3B01G374400 chr1B 79.196 572 111 8 2790 3357 535143911 535143344 1.490000e-104 390.0
19 TraesCS3B01G374400 chr2D 77.713 341 71 3 3018 3357 56106718 56107054 2.080000e-48 204.0
20 TraesCS3B01G374400 chr2A 77.551 343 68 5 3018 3357 57549151 57549487 9.670000e-47 198.0
21 TraesCS3B01G374400 chr2B 78.716 296 60 1 3062 3357 88841215 88841507 1.250000e-45 195.0
22 TraesCS3B01G374400 chr5D 90.000 50 3 2 3066 3114 432041665 432041617 3.680000e-06 63.9
23 TraesCS3B01G374400 chr5B 97.297 37 1 0 3066 3102 523908273 523908309 3.680000e-06 63.9


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 TraesCS3B01G374400 chr3B 587564998 587569403 4405 False 3752.50 6865 100.00000 1 4406 2 chr3B.!!$F1 4405
1 TraesCS3B01G374400 chr3A 589392434 589396588 4154 False 1411.25 3000 92.54700 1 4374 4 chr3A.!!$F1 4373
2 TraesCS3B01G374400 chr3D 206466270 206467204 934 True 1384.00 1384 93.47600 930 1859 1 chr3D.!!$R1 929
3 TraesCS3B01G374400 chr3D 447988895 447993162 4267 False 1377.75 2769 93.21575 1 4374 4 chr3D.!!$F1 4373
4 TraesCS3B01G374400 chr1A 193040815 193041661 846 False 1059.00 1059 89.17300 930 1787 1 chr1A.!!$F1 857
5 TraesCS3B01G374400 chr1A 496043684 496046317 2633 True 616.50 747 79.50450 993 3376 2 chr1A.!!$R1 2383
6 TraesCS3B01G374400 chr1D 399188321 399190925 2604 True 640.00 760 80.42850 1076 3376 2 chr1D.!!$R2 2300
7 TraesCS3B01G374400 chr1B 535384264 535384850 586 True 492.00 492 81.89500 2790 3376 1 chr1B.!!$R2 586
8 TraesCS3B01G374400 chr1B 535143344 535143911 567 True 390.00 390 79.19600 2790 3357 1 chr1B.!!$R1 567

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
45 46 4.642429 ACGGAAGAGTTCTTAAATGCTGT 58.358 39.13 0.0 0.0 36.11 4.40 F
1569 1589 1.177401 GTCTCCCCAAATTGAGGCAC 58.823 55.00 0.0 0.0 33.44 5.01 F
1714 1735 0.250513 GCCTTCTCCTTCACCGACAT 59.749 55.00 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 1735 2.128290 CTGGGCACTGATGGTGGTGA 62.128 60.0 0.00 0.0 45.44 4.02 R
3057 3743 0.826672 AGACGTCCGACTTCTGGGTT 60.827 55.0 13.01 0.0 0.00 4.11 R
3666 4373 0.248458 CAGGACAACACAAACACCGC 60.248 55.0 0.00 0.0 0.00 5.68 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
27 28 6.774170 TGATAGCTAAGATAGGTACAAACGGA 59.226 38.462 0.00 0.00 41.07 4.69
45 46 4.642429 ACGGAAGAGTTCTTAAATGCTGT 58.358 39.130 0.00 0.00 36.11 4.40
70 71 6.213397 TCCCAGAACTCTCAAGAACATTATCA 59.787 38.462 0.00 0.00 0.00 2.15
264 265 5.581126 ATGCAACCCATACACTGTTAATG 57.419 39.130 0.00 0.00 30.69 1.90
267 268 5.182950 TGCAACCCATACACTGTTAATGAAG 59.817 40.000 0.00 0.00 0.00 3.02
268 269 5.414454 GCAACCCATACACTGTTAATGAAGA 59.586 40.000 1.66 0.00 0.00 2.87
269 270 6.403636 GCAACCCATACACTGTTAATGAAGAG 60.404 42.308 1.66 0.00 32.20 2.85
270 271 6.620877 ACCCATACACTGTTAATGAAGAGA 57.379 37.500 0.00 0.00 30.50 3.10
272 273 6.879458 ACCCATACACTGTTAATGAAGAGAAC 59.121 38.462 0.00 0.00 30.50 3.01
273 274 6.878923 CCCATACACTGTTAATGAAGAGAACA 59.121 38.462 0.00 0.00 30.50 3.18
714 717 6.234177 GGAATCCACTATTAGTCCTTCCATG 58.766 44.000 16.52 0.00 31.98 3.66
727 730 5.105063 GTCCTTCCATGCTTCTATTTTTGC 58.895 41.667 0.00 0.00 0.00 3.68
739 742 8.959548 TGCTTCTATTTTTGCATATCTCTTGAA 58.040 29.630 0.00 0.00 0.00 2.69
862 866 5.174037 TGGGACCTTCCTTTTACATGTAG 57.826 43.478 5.56 0.00 36.57 2.74
1569 1589 1.177401 GTCTCCCCAAATTGAGGCAC 58.823 55.000 0.00 0.00 33.44 5.01
1714 1735 0.250513 GCCTTCTCCTTCACCGACAT 59.749 55.000 0.00 0.00 0.00 3.06
1773 1794 1.004745 TGGAAAAGGATCAGGACAGGC 59.995 52.381 0.00 0.00 0.00 4.85
1818 1839 2.025887 AGGAGGGGTATTGTTGCTTCTG 60.026 50.000 0.00 0.00 0.00 3.02
1971 1995 4.041444 AGTGTTCAGGAAGCAGAGAGAAAT 59.959 41.667 0.00 0.00 0.00 2.17
1998 2022 2.479275 GGTTTTCTTCGAGGGTTCTTCG 59.521 50.000 0.00 0.00 0.00 3.79
2133 2157 3.848975 AGAGATTGAAGGAGATGGTGGTT 59.151 43.478 0.00 0.00 0.00 3.67
2260 2284 4.298626 ACTGGTGTATGACTATGTCCCAT 58.701 43.478 0.00 0.00 0.00 4.00
2304 2328 6.403866 TTGCATGGTATGTTCTTTGTTTCT 57.596 33.333 0.00 0.00 0.00 2.52
2311 2335 7.284074 TGGTATGTTCTTTGTTTCTCCTGTTA 58.716 34.615 0.00 0.00 0.00 2.41
2353 2396 7.117092 GCCTATTAGTGCTTATGAACTTCTAGC 59.883 40.741 0.00 0.00 33.29 3.42
2400 2443 1.382522 GCATTGAAGCGAGGATTGGA 58.617 50.000 0.00 0.00 0.00 3.53
2407 2450 4.647611 TGAAGCGAGGATTGGAAACTTAA 58.352 39.130 0.00 0.00 0.00 1.85
2412 2455 5.181433 AGCGAGGATTGGAAACTTAAAACTC 59.819 40.000 0.00 0.00 0.00 3.01
2429 2472 4.682778 AACTCAACTGTTGGCACTAGTA 57.317 40.909 19.55 0.00 0.00 1.82
2434 2477 1.276421 ACTGTTGGCACTAGTAGGCTG 59.724 52.381 15.99 0.00 0.00 4.85
2459 2502 6.275335 CAAGCATATCCAAAACATAGTTGGG 58.725 40.000 3.49 0.00 44.82 4.12
2463 2506 8.004215 AGCATATCCAAAACATAGTTGGGATTA 58.996 33.333 16.50 7.78 44.82 1.75
2481 2524 9.832445 TTGGGATTAATACTGTAGATTCACTTC 57.168 33.333 0.00 0.00 0.00 3.01
2483 2526 8.358148 GGGATTAATACTGTAGATTCACTTCGA 58.642 37.037 0.00 0.00 0.00 3.71
2495 2538 2.658285 TCACTTCGAAAGTCACGTAGC 58.342 47.619 0.00 0.00 40.46 3.58
2498 2551 2.287188 ACTTCGAAAGTCACGTAGCGAA 60.287 45.455 0.00 0.00 37.02 4.70
2500 2553 2.512885 TCGAAAGTCACGTAGCGAATC 58.487 47.619 0.00 0.00 0.00 2.52
2668 2887 2.158769 ACTGCAGTCAGATTGTGGAACA 60.159 45.455 15.25 0.00 44.32 3.18
2680 2899 2.862541 TGTGGAACATCCTCCTGTTTG 58.137 47.619 0.00 0.00 45.67 2.93
2686 2905 4.080299 GGAACATCCTCCTGTTTGTCCTAT 60.080 45.833 0.00 0.00 39.40 2.57
2699 2918 7.228706 CCTGTTTGTCCTATTTAGTGTTCACTT 59.771 37.037 10.74 0.00 0.00 3.16
2718 2937 4.024556 CACTTTAGCACTGAACTCAACTGG 60.025 45.833 0.00 0.00 0.00 4.00
2719 2938 2.169832 TAGCACTGAACTCAACTGGC 57.830 50.000 0.00 0.00 0.00 4.85
2720 2939 0.471617 AGCACTGAACTCAACTGGCT 59.528 50.000 0.00 0.00 0.00 4.75
2721 2940 0.590195 GCACTGAACTCAACTGGCTG 59.410 55.000 0.00 0.00 0.00 4.85
2722 2941 1.811558 GCACTGAACTCAACTGGCTGA 60.812 52.381 0.00 0.00 0.00 4.26
2723 2942 2.775890 CACTGAACTCAACTGGCTGAT 58.224 47.619 0.00 0.00 0.00 2.90
2724 2943 3.866066 GCACTGAACTCAACTGGCTGATA 60.866 47.826 0.00 0.00 0.00 2.15
2728 3316 5.046014 ACTGAACTCAACTGGCTGATAAGAT 60.046 40.000 0.00 0.00 0.00 2.40
2910 3596 1.103398 GCGGGAAGTTCATCCATGGG 61.103 60.000 13.02 0.00 41.55 4.00
2949 3635 3.392616 ACATCCTTCTGTCACAGAACCTT 59.607 43.478 16.67 1.06 44.27 3.50
2964 3650 2.259818 CTTGACGGCTGCGTCTCT 59.740 61.111 19.62 0.00 39.41 3.10
3000 3686 1.196766 AGCTCATGACCACTCTGCCA 61.197 55.000 0.00 0.00 0.00 4.92
3057 3743 1.420138 GTCCTGGAGACCAAGAAACCA 59.580 52.381 0.00 0.00 39.84 3.67
3243 3929 2.035626 CTCCGGCACCCCAACATT 59.964 61.111 0.00 0.00 0.00 2.71
3258 3944 2.932614 CAACATTGAGGACGAGATGGTC 59.067 50.000 0.00 0.00 36.18 4.02
3333 4019 2.443958 AGATGGACGAGGTGATCAGA 57.556 50.000 0.00 0.00 0.00 3.27
3427 4116 3.399181 AGGGCGCGGGAGATGAAA 61.399 61.111 8.83 0.00 0.00 2.69
3428 4117 2.437716 GGGCGCGGGAGATGAAAA 60.438 61.111 8.83 0.00 0.00 2.29
3429 4118 2.472909 GGGCGCGGGAGATGAAAAG 61.473 63.158 8.83 0.00 0.00 2.27
3430 4119 2.472909 GGCGCGGGAGATGAAAAGG 61.473 63.158 8.83 0.00 0.00 3.11
3431 4120 2.472909 GCGCGGGAGATGAAAAGGG 61.473 63.158 8.83 0.00 0.00 3.95
3432 4121 2.472909 CGCGGGAGATGAAAAGGGC 61.473 63.158 0.00 0.00 0.00 5.19
3433 4122 1.378514 GCGGGAGATGAAAAGGGCA 60.379 57.895 0.00 0.00 0.00 5.36
3434 4123 0.753111 GCGGGAGATGAAAAGGGCAT 60.753 55.000 0.00 0.00 0.00 4.40
3532 4231 1.732259 CGAAAGTTGATAGCCGCTTGT 59.268 47.619 0.00 0.00 0.00 3.16
3544 4243 2.228822 AGCCGCTTGTTTGGTTGATTAG 59.771 45.455 0.00 0.00 0.00 1.73
3545 4244 2.030274 GCCGCTTGTTTGGTTGATTAGT 60.030 45.455 0.00 0.00 0.00 2.24
3550 4249 4.795962 GCTTGTTTGGTTGATTAGTGTGGG 60.796 45.833 0.00 0.00 0.00 4.61
3554 4253 2.058705 TGGTTGATTAGTGTGGGGTGA 58.941 47.619 0.00 0.00 0.00 4.02
3557 4256 1.285280 TGATTAGTGTGGGGTGAGGG 58.715 55.000 0.00 0.00 0.00 4.30
3569 4268 1.630878 GGGTGAGGGTTCTGTTGATCT 59.369 52.381 0.00 0.00 0.00 2.75
3576 4275 5.013495 TGAGGGTTCTGTTGATCTCTGATTT 59.987 40.000 0.00 0.00 0.00 2.17
3578 4277 7.020827 AGGGTTCTGTTGATCTCTGATTTTA 57.979 36.000 0.00 0.00 0.00 1.52
3580 4279 8.112183 AGGGTTCTGTTGATCTCTGATTTTATT 58.888 33.333 0.00 0.00 0.00 1.40
3581 4280 8.401709 GGGTTCTGTTGATCTCTGATTTTATTC 58.598 37.037 0.00 0.00 0.00 1.75
3582 4281 9.171877 GGTTCTGTTGATCTCTGATTTTATTCT 57.828 33.333 0.00 0.00 0.00 2.40
3651 4358 7.697946 AGTCTACTGATCTGGATATCTGATGA 58.302 38.462 13.65 7.15 34.74 2.92
3655 4362 5.837438 ACTGATCTGGATATCTGATGACACA 59.163 40.000 13.65 7.08 34.74 3.72
3669 4376 3.168271 CACAGATGGTGTTCGCGG 58.832 61.111 6.13 0.00 42.75 6.46
3670 4377 1.667830 CACAGATGGTGTTCGCGGT 60.668 57.895 6.13 0.00 42.75 5.68
3671 4378 1.667830 ACAGATGGTGTTCGCGGTG 60.668 57.895 6.13 0.00 34.94 4.94
3672 4379 1.667830 CAGATGGTGTTCGCGGTGT 60.668 57.895 6.13 0.00 0.00 4.16
3673 4380 1.070786 AGATGGTGTTCGCGGTGTT 59.929 52.632 6.13 0.00 0.00 3.32
3681 4388 0.179184 GTTCGCGGTGTTTGTGTTGT 60.179 50.000 6.13 0.00 0.00 3.32
3688 4395 2.031191 CGGTGTTTGTGTTGTCCTGTAC 59.969 50.000 0.00 0.00 0.00 2.90
3728 4437 8.648557 TTCTCCAGAGTGTGATTAATTTATCG 57.351 34.615 0.38 0.00 0.00 2.92
3729 4438 8.007405 TCTCCAGAGTGTGATTAATTTATCGA 57.993 34.615 0.38 0.00 0.00 3.59
3730 4439 8.138074 TCTCCAGAGTGTGATTAATTTATCGAG 58.862 37.037 0.00 0.00 0.00 4.04
3735 4444 9.823647 AGAGTGTGATTAATTTATCGAGTTGAT 57.176 29.630 0.00 0.00 41.30 2.57
3767 4481 4.339247 CCTGTTTGTCACCTGTCAGATTTT 59.661 41.667 0.00 0.00 0.00 1.82
3779 4502 6.833933 ACCTGTCAGATTTTTAGTTTGGAAGT 59.166 34.615 0.00 0.00 0.00 3.01
3791 4514 3.049912 GTTTGGAAGTTTTGATCCGTGC 58.950 45.455 0.00 0.00 0.00 5.34
3847 4577 4.353437 GACGTCGACGGCCTTGGT 62.353 66.667 37.89 18.30 42.67 3.67
3849 4579 4.351938 CGTCGACGGCCTTGGTGA 62.352 66.667 29.70 0.00 35.37 4.02
3850 4580 2.737376 GTCGACGGCCTTGGTGAC 60.737 66.667 0.00 0.00 0.00 3.67
3851 4581 2.915659 TCGACGGCCTTGGTGACT 60.916 61.111 0.00 0.00 0.00 3.41
3852 4582 2.432628 CGACGGCCTTGGTGACTC 60.433 66.667 0.00 0.00 0.00 3.36
3894 4624 4.456806 GTGGACACGCTCTGGTTT 57.543 55.556 0.00 0.00 0.00 3.27
3895 4625 2.702847 GTGGACACGCTCTGGTTTT 58.297 52.632 0.00 0.00 0.00 2.43
3896 4626 0.586802 GTGGACACGCTCTGGTTTTC 59.413 55.000 0.00 0.00 0.00 2.29
3897 4627 0.534203 TGGACACGCTCTGGTTTTCC 60.534 55.000 0.00 0.00 41.14 3.13
3898 4628 1.566018 GGACACGCTCTGGTTTTCCG 61.566 60.000 0.00 0.00 44.36 4.30
3899 4629 2.171489 GACACGCTCTGGTTTTCCGC 62.171 60.000 0.00 0.00 44.36 5.54
3900 4630 2.668550 ACGCTCTGGTTTTCCGCC 60.669 61.111 0.00 0.00 44.36 6.13
3901 4631 3.788766 CGCTCTGGTTTTCCGCCG 61.789 66.667 0.00 0.00 44.36 6.46
3902 4632 2.668550 GCTCTGGTTTTCCGCCGT 60.669 61.111 0.00 0.00 44.36 5.68
3903 4633 2.966309 GCTCTGGTTTTCCGCCGTG 61.966 63.158 0.00 0.00 44.36 4.94
3904 4634 2.281208 TCTGGTTTTCCGCCGTGG 60.281 61.111 0.00 0.00 44.36 4.94
3953 4683 4.495939 CCTCCGTCGTCGTCGTCG 62.496 72.222 13.54 13.54 44.85 5.12
3978 4711 2.659610 GCGCCTCTTCCAGTCTGT 59.340 61.111 0.00 0.00 0.00 3.41
3987 4720 0.753867 TTCCAGTCTGTAACACGCCA 59.246 50.000 0.00 0.00 0.00 5.69
4117 4854 1.792757 AATGCCAGCCACTCTTGGGA 61.793 55.000 0.00 0.00 44.15 4.37
4126 4863 1.305046 ACTCTTGGGATCGGTCGGT 60.305 57.895 0.00 0.00 0.00 4.69
4179 4917 1.805871 CGGCAATCAAGGCTCTCTCTC 60.806 57.143 0.00 0.00 0.00 3.20
4265 5016 4.070552 GGACTCCGCTCCGCTGTT 62.071 66.667 0.00 0.00 0.00 3.16
4333 5089 1.426598 ACATGGGGGATGATGATGGAC 59.573 52.381 0.00 0.00 35.80 4.02
4337 5097 1.352352 GGGGGATGATGATGGACGATT 59.648 52.381 0.00 0.00 0.00 3.34
4354 5114 4.794648 TGCCTTCATTCGCCGGGG 62.795 66.667 13.31 13.31 0.00 5.73
4381 5142 4.619227 CCTGTTGGCGGTGTCGGT 62.619 66.667 0.00 0.00 36.79 4.69
4382 5143 2.590575 CTGTTGGCGGTGTCGGTT 60.591 61.111 0.00 0.00 36.79 4.44
4383 5144 2.892334 CTGTTGGCGGTGTCGGTTG 61.892 63.158 0.00 0.00 36.79 3.77
4384 5145 4.322385 GTTGGCGGTGTCGGTTGC 62.322 66.667 0.00 0.00 36.79 4.17
4389 5150 4.007940 CGGTGTCGGTTGCGGTTG 62.008 66.667 0.00 0.00 0.00 3.77
4390 5151 3.656045 GGTGTCGGTTGCGGTTGG 61.656 66.667 0.00 0.00 0.00 3.77
4391 5152 3.656045 GTGTCGGTTGCGGTTGGG 61.656 66.667 0.00 0.00 0.00 4.12
4392 5153 3.862991 TGTCGGTTGCGGTTGGGA 61.863 61.111 0.00 0.00 0.00 4.37
4393 5154 2.359478 GTCGGTTGCGGTTGGGAT 60.359 61.111 0.00 0.00 0.00 3.85
4394 5155 2.046700 TCGGTTGCGGTTGGGATC 60.047 61.111 0.00 0.00 0.00 3.36
4395 5156 3.496131 CGGTTGCGGTTGGGATCG 61.496 66.667 0.00 0.00 0.00 3.69
4401 5162 3.486263 CGGTTGGGATCGCTGAAC 58.514 61.111 11.46 7.76 0.00 3.18
4402 5163 1.375396 CGGTTGGGATCGCTGAACA 60.375 57.895 11.46 0.00 0.00 3.18
4403 5164 1.361668 CGGTTGGGATCGCTGAACAG 61.362 60.000 11.46 5.21 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.396478 GGGACAGCATTTAAGAACTCTTCC 59.604 45.833 0.00 0.00 37.40 3.46
27 28 4.985538 TGGGACAGCATTTAAGAACTCTT 58.014 39.130 0.00 0.00 39.85 2.85
45 46 4.982241 AATGTTCTTGAGAGTTCTGGGA 57.018 40.909 0.00 0.00 0.00 4.37
70 71 5.304614 AGCAATAGTATACCTCGTCCAACAT 59.695 40.000 0.00 0.00 0.00 2.71
254 255 8.562892 ACTGAAATGTTCTCTTCATTAACAGTG 58.437 33.333 19.25 0.00 42.88 3.66
264 265 8.770438 AAGTGAGATACTGAAATGTTCTCTTC 57.230 34.615 0.00 0.00 40.26 2.87
691 694 5.703130 GCATGGAAGGACTAATAGTGGATTC 59.297 44.000 0.00 0.00 0.00 2.52
714 717 9.230932 GTTCAAGAGATATGCAAAAATAGAAGC 57.769 33.333 0.00 0.00 0.00 3.86
739 742 8.814038 AACTGCCTGAGAATTAGAAAATATGT 57.186 30.769 0.00 0.00 0.00 2.29
862 866 8.774586 ACAAAACATCGAGGCAATAATAGATAC 58.225 33.333 0.00 0.00 0.00 2.24
1569 1589 6.017400 AGGTTGTTGTTGCTCATATTCAAG 57.983 37.500 0.00 0.00 0.00 3.02
1714 1735 2.128290 CTGGGCACTGATGGTGGTGA 62.128 60.000 0.00 0.00 45.44 4.02
1971 1995 4.426736 ACCCTCGAAGAAAACCAGTTTA 57.573 40.909 0.00 0.00 34.09 2.01
1998 2022 6.183360 GCAAATCCTCCAGGTCAAAGTTATAC 60.183 42.308 0.00 0.00 36.34 1.47
2133 2157 3.728845 CTGTTCGAAGTCTTTCTTCCCA 58.271 45.455 0.00 0.00 46.97 4.37
2236 2260 5.274015 TGGGACATAGTCATACACCAGTAA 58.726 41.667 0.00 0.00 33.68 2.24
2260 2284 1.297689 CAGCAGCAAGGCTACCAGA 59.702 57.895 0.00 0.00 43.68 3.86
2304 2328 7.771183 GGCAACTGATTTCAAATATAACAGGA 58.229 34.615 0.00 0.00 0.00 3.86
2353 2396 6.316390 AGAAACATTTTGAATAGGCTAGACCG 59.684 38.462 0.00 0.00 46.52 4.79
2400 2443 5.867174 GTGCCAACAGTTGAGTTTTAAGTTT 59.133 36.000 15.36 0.00 0.00 2.66
2407 2450 3.886123 ACTAGTGCCAACAGTTGAGTTT 58.114 40.909 15.36 0.75 0.00 2.66
2412 2455 2.076863 GCCTACTAGTGCCAACAGTTG 58.923 52.381 5.39 6.28 0.00 3.16
2429 2472 2.148446 TTTGGATATGCTTGCAGCCT 57.852 45.000 0.87 0.00 41.51 4.58
2434 2477 5.750067 CCAACTATGTTTTGGATATGCTTGC 59.250 40.000 0.00 0.00 45.69 4.01
2442 2485 9.936329 AGTATTAATCCCAACTATGTTTTGGAT 57.064 29.630 2.58 2.63 45.69 3.41
2463 2506 8.304596 TGACTTTCGAAGTGAATCTACAGTATT 58.695 33.333 0.00 0.00 43.03 1.89
2472 2515 4.201504 GCTACGTGACTTTCGAAGTGAATC 60.202 45.833 0.00 0.00 43.03 2.52
2474 2517 3.047796 GCTACGTGACTTTCGAAGTGAA 58.952 45.455 0.00 0.00 43.03 3.18
2475 2518 2.658285 GCTACGTGACTTTCGAAGTGA 58.342 47.619 0.00 0.00 43.03 3.41
2481 2524 1.249491 CGATTCGCTACGTGACTTTCG 59.751 52.381 0.00 0.00 0.00 3.46
2495 2538 4.806247 AGAGAAAAGATAACAGGCGATTCG 59.194 41.667 0.62 0.62 0.00 3.34
2498 2551 8.738645 ATTTTAGAGAAAAGATAACAGGCGAT 57.261 30.769 0.00 0.00 37.94 4.58
2500 2553 9.278734 GAAATTTTAGAGAAAAGATAACAGGCG 57.721 33.333 0.00 0.00 37.94 5.52
2540 2751 4.341487 TGGAGGATTCGTCTTAAGAGTGA 58.659 43.478 5.12 4.31 0.00 3.41
2541 2752 4.720649 TGGAGGATTCGTCTTAAGAGTG 57.279 45.455 5.12 1.70 0.00 3.51
2542 2753 5.941555 ATTGGAGGATTCGTCTTAAGAGT 57.058 39.130 5.12 0.00 0.00 3.24
2668 2887 6.215636 ACACTAAATAGGACAAACAGGAGGAT 59.784 38.462 0.00 0.00 0.00 3.24
2680 2899 7.603024 AGTGCTAAAGTGAACACTAAATAGGAC 59.397 37.037 22.79 22.79 41.41 3.85
2699 2918 2.104792 AGCCAGTTGAGTTCAGTGCTAA 59.895 45.455 0.00 0.00 0.00 3.09
2718 2937 5.182760 CCATGGGCTCTAAAATCTTATCAGC 59.817 44.000 2.85 0.00 0.00 4.26
2719 2938 6.206243 CACCATGGGCTCTAAAATCTTATCAG 59.794 42.308 18.09 0.00 0.00 2.90
2720 2939 6.064060 CACCATGGGCTCTAAAATCTTATCA 58.936 40.000 18.09 0.00 0.00 2.15
2721 2940 6.064717 ACACCATGGGCTCTAAAATCTTATC 58.935 40.000 18.09 0.00 0.00 1.75
2722 2941 6.018433 ACACCATGGGCTCTAAAATCTTAT 57.982 37.500 18.09 0.00 0.00 1.73
2723 2942 5.191722 AGACACCATGGGCTCTAAAATCTTA 59.808 40.000 18.09 0.00 0.00 2.10
2724 2943 4.018050 AGACACCATGGGCTCTAAAATCTT 60.018 41.667 18.09 0.00 0.00 2.40
2728 3316 2.375174 ACAGACACCATGGGCTCTAAAA 59.625 45.455 18.09 0.00 0.00 1.52
2910 3596 3.062234 GGATGTTCGACGATTTGAGGTTC 59.938 47.826 0.00 0.00 0.00 3.62
3054 3740 1.752833 GTCCGACTTCTGGGTTGGT 59.247 57.895 0.00 0.00 40.65 3.67
3057 3743 0.826672 AGACGTCCGACTTCTGGGTT 60.827 55.000 13.01 0.00 0.00 4.11
3138 3824 3.726631 CTCGACAGAGTCCTCGCGC 62.727 68.421 0.00 0.00 39.60 6.86
3300 3986 3.077556 ATCTTCGGCCGCTGGTCT 61.078 61.111 23.51 0.00 0.00 3.85
3410 4099 2.876368 CTTTTCATCTCCCGCGCCCT 62.876 60.000 0.00 0.00 0.00 5.19
3411 4100 2.437716 TTTTCATCTCCCGCGCCC 60.438 61.111 0.00 0.00 0.00 6.13
3414 4103 2.472909 GCCCTTTTCATCTCCCGCG 61.473 63.158 0.00 0.00 0.00 6.46
3416 4105 1.767759 AATGCCCTTTTCATCTCCCG 58.232 50.000 0.00 0.00 0.00 5.14
3418 4107 3.259123 ACACAAATGCCCTTTTCATCTCC 59.741 43.478 0.00 0.00 0.00 3.71
3419 4108 4.525912 ACACAAATGCCCTTTTCATCTC 57.474 40.909 0.00 0.00 0.00 2.75
3421 4110 5.120674 GCTAAACACAAATGCCCTTTTCATC 59.879 40.000 0.00 0.00 0.00 2.92
3423 4112 4.141846 TGCTAAACACAAATGCCCTTTTCA 60.142 37.500 0.00 0.00 0.00 2.69
3424 4113 4.376146 TGCTAAACACAAATGCCCTTTTC 58.624 39.130 0.00 0.00 0.00 2.29
3425 4114 4.414337 TGCTAAACACAAATGCCCTTTT 57.586 36.364 0.00 0.00 0.00 2.27
3427 4116 3.865684 GCATGCTAAACACAAATGCCCTT 60.866 43.478 11.37 0.00 38.12 3.95
3428 4117 2.354003 GCATGCTAAACACAAATGCCCT 60.354 45.455 11.37 0.00 38.12 5.19
3429 4118 2.001872 GCATGCTAAACACAAATGCCC 58.998 47.619 11.37 0.00 38.12 5.36
3430 4119 2.669434 CTGCATGCTAAACACAAATGCC 59.331 45.455 20.33 0.00 42.31 4.40
3431 4120 3.577667 TCTGCATGCTAAACACAAATGC 58.422 40.909 20.33 0.00 43.08 3.56
3432 4121 4.171005 CCTCTGCATGCTAAACACAAATG 58.829 43.478 20.33 0.00 0.00 2.32
3433 4122 3.828451 ACCTCTGCATGCTAAACACAAAT 59.172 39.130 20.33 0.00 0.00 2.32
3434 4123 3.221771 ACCTCTGCATGCTAAACACAAA 58.778 40.909 20.33 0.00 0.00 2.83
3532 4231 3.117474 TCACCCCACACTAATCAACCAAA 60.117 43.478 0.00 0.00 0.00 3.28
3544 4243 1.073199 CAGAACCCTCACCCCACAC 59.927 63.158 0.00 0.00 0.00 3.82
3545 4244 0.991355 AACAGAACCCTCACCCCACA 60.991 55.000 0.00 0.00 0.00 4.17
3550 4249 2.569404 AGAGATCAACAGAACCCTCACC 59.431 50.000 0.00 0.00 0.00 4.02
3554 4253 5.511386 AAATCAGAGATCAACAGAACCCT 57.489 39.130 0.00 0.00 0.00 4.34
3583 4282 7.413109 GCACAGAAAAATTACCCGAAACAAAAA 60.413 33.333 0.00 0.00 0.00 1.94
3584 4283 6.036191 GCACAGAAAAATTACCCGAAACAAAA 59.964 34.615 0.00 0.00 0.00 2.44
3585 4284 5.520649 GCACAGAAAAATTACCCGAAACAAA 59.479 36.000 0.00 0.00 0.00 2.83
3628 4335 7.392953 GTGTCATCAGATATCCAGATCAGTAGA 59.607 40.741 0.00 0.00 0.00 2.59
3655 4362 0.534203 AAACACCGCGAACACCATCT 60.534 50.000 8.23 0.00 0.00 2.90
3665 4372 1.298041 GGACAACACAAACACCGCG 60.298 57.895 0.00 0.00 0.00 6.46
3666 4373 0.248458 CAGGACAACACAAACACCGC 60.248 55.000 0.00 0.00 0.00 5.68
3667 4374 1.091537 ACAGGACAACACAAACACCG 58.908 50.000 0.00 0.00 0.00 4.94
3668 4375 3.275999 AGTACAGGACAACACAAACACC 58.724 45.455 0.00 0.00 0.00 4.16
3669 4376 4.957759 AAGTACAGGACAACACAAACAC 57.042 40.909 0.00 0.00 0.00 3.32
3670 4377 4.156922 CCAAAGTACAGGACAACACAAACA 59.843 41.667 0.00 0.00 0.00 2.83
3671 4378 4.668289 CCAAAGTACAGGACAACACAAAC 58.332 43.478 0.00 0.00 0.00 2.93
3672 4379 3.129638 GCCAAAGTACAGGACAACACAAA 59.870 43.478 0.00 0.00 0.00 2.83
3673 4380 2.685897 GCCAAAGTACAGGACAACACAA 59.314 45.455 0.00 0.00 0.00 3.33
3681 4388 2.584835 AAGCATGCCAAAGTACAGGA 57.415 45.000 15.66 0.00 0.00 3.86
3706 4415 7.782049 ACTCGATAAATTAATCACACTCTGGA 58.218 34.615 0.00 0.00 0.00 3.86
3767 4481 5.506649 GCACGGATCAAAACTTCCAAACTAA 60.507 40.000 0.00 0.00 0.00 2.24
3779 4502 4.096558 GCGGCGCACGGATCAAAA 62.097 61.111 29.21 0.00 44.51 2.44
3881 4611 2.251642 GCGGAAAACCAGAGCGTGT 61.252 57.895 0.00 0.00 0.00 4.49
3882 4612 2.556287 GCGGAAAACCAGAGCGTG 59.444 61.111 0.00 0.00 0.00 5.34
3883 4613 2.668550 GGCGGAAAACCAGAGCGT 60.669 61.111 0.00 0.00 0.00 5.07
3884 4614 3.788766 CGGCGGAAAACCAGAGCG 61.789 66.667 0.00 0.00 0.00 5.03
3885 4615 2.668550 ACGGCGGAAAACCAGAGC 60.669 61.111 13.24 0.00 0.00 4.09
3886 4616 2.325082 CCACGGCGGAAAACCAGAG 61.325 63.158 13.24 0.00 36.56 3.35
3887 4617 2.281208 CCACGGCGGAAAACCAGA 60.281 61.111 13.24 0.00 36.56 3.86
3888 4618 2.281208 TCCACGGCGGAAAACCAG 60.281 61.111 13.24 0.00 42.52 4.00
3901 4631 2.433318 GCTCCAGAGCGTGTCCAC 60.433 66.667 3.49 0.00 45.29 4.02
3978 4711 2.437002 GCCCCGATTGGCGTGTTA 60.437 61.111 0.00 0.00 42.54 2.41
3987 4720 3.782443 GTGTCCTCCGCCCCGATT 61.782 66.667 0.00 0.00 0.00 3.34
4009 4742 0.533032 GAGGAACGGGGACTGAAGAG 59.467 60.000 0.00 0.00 38.67 2.85
4117 4854 4.783621 TCCGTCCGACCGACCGAT 62.784 66.667 0.00 0.00 38.36 4.18
4337 5097 4.794648 CCCCGGCGAATGAAGGCA 62.795 66.667 9.30 0.00 0.00 4.75
4374 5135 3.656045 CCCAACCGCAACCGACAC 61.656 66.667 0.00 0.00 36.29 3.67
4375 5136 3.185299 ATCCCAACCGCAACCGACA 62.185 57.895 0.00 0.00 36.29 4.35
4376 5137 2.359478 ATCCCAACCGCAACCGAC 60.359 61.111 0.00 0.00 36.29 4.79
4377 5138 2.046700 GATCCCAACCGCAACCGA 60.047 61.111 0.00 0.00 36.29 4.69
4378 5139 3.496131 CGATCCCAACCGCAACCG 61.496 66.667 0.00 0.00 0.00 4.44
4384 5145 1.361668 CTGTTCAGCGATCCCAACCG 61.362 60.000 0.00 0.00 0.00 4.44
4385 5146 1.648467 GCTGTTCAGCGATCCCAACC 61.648 60.000 9.04 0.00 0.00 3.77
4386 5147 0.674895 AGCTGTTCAGCGATCCCAAC 60.675 55.000 17.28 0.00 40.27 3.77
4387 5148 1.679311 AGCTGTTCAGCGATCCCAA 59.321 52.632 17.28 0.00 40.27 4.12
4388 5149 3.392228 AGCTGTTCAGCGATCCCA 58.608 55.556 17.28 0.00 40.27 4.37


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

AutoCloner maintained by Alex Coulton.