Multiple sequence alignment - TraesCS6A01G266900

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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 TraesCS6A01G266900 chr6A 100.000 5756 0 0 993 6748 492701927 492707682 0.000000e+00 10630.0
1 TraesCS6A01G266900 chr6A 100.000 880 0 0 1 880 492700935 492701814 0.000000e+00 1626.0
2 TraesCS6A01G266900 chr6A 97.701 174 4 0 3671 3844 492704518 492704691 3.960000e-77 300.0
3 TraesCS6A01G266900 chr6A 97.701 174 4 0 3584 3757 492704605 492704778 3.960000e-77 300.0
4 TraesCS6A01G266900 chr6A 97.701 87 2 0 3758 3844 492704518 492704604 4.220000e-32 150.0
5 TraesCS6A01G266900 chr6A 97.701 87 2 0 3584 3670 492704692 492704778 4.220000e-32 150.0
6 TraesCS6A01G266900 chr6A 82.500 80 10 3 6308 6384 417623151 417623073 4.370000e-07 67.6
7 TraesCS6A01G266900 chr6D 95.865 2781 58 17 996 3757 351117281 351114539 0.000000e+00 4446.0
8 TraesCS6A01G266900 chr6D 97.567 2589 50 12 3671 6252 351114712 351112130 0.000000e+00 4420.0
9 TraesCS6A01G266900 chr6D 96.296 378 11 2 6372 6748 351111642 351111267 9.610000e-173 617.0
10 TraesCS6A01G266900 chr6D 81.378 537 67 18 1 515 351118300 351117775 2.270000e-109 407.0
11 TraesCS6A01G266900 chr6D 94.271 192 10 1 687 878 351117508 351117318 6.620000e-75 292.0
12 TraesCS6A01G266900 chr6D 98.851 87 1 0 3584 3670 351114625 351114539 9.060000e-34 156.0
13 TraesCS6A01G266900 chr6D 97.701 87 2 0 3758 3844 351114712 351114626 4.220000e-32 150.0
14 TraesCS6A01G266900 chr6B 97.052 2137 52 6 3758 5886 528620129 528622262 0.000000e+00 3587.0
15 TraesCS6A01G266900 chr6B 93.878 1813 61 15 1553 3341 528617699 528619485 0.000000e+00 2687.0
16 TraesCS6A01G266900 chr6B 96.089 537 19 2 1033 1567 528617042 528617578 0.000000e+00 874.0
17 TraesCS6A01G266900 chr6B 89.535 516 52 2 1 515 528615760 528616274 0.000000e+00 652.0
18 TraesCS6A01G266900 chr6B 92.973 370 13 5 5884 6251 528622365 528622723 1.670000e-145 527.0
19 TraesCS6A01G266900 chr6B 97.909 287 6 0 3384 3670 528619929 528620215 1.310000e-136 497.0
20 TraesCS6A01G266900 chr6B 92.197 346 20 4 6405 6748 528622809 528623149 3.660000e-132 483.0
21 TraesCS6A01G266900 chr6B 84.533 375 41 13 513 878 528616309 528616675 8.320000e-94 355.0
22 TraesCS6A01G266900 chr6B 97.701 87 2 0 3671 3757 528620129 528620215 4.220000e-32 150.0
23 TraesCS6A01G266900 chr3B 88.889 72 8 0 6313 6384 43181583 43181512 9.320000e-14 89.8
24 TraesCS6A01G266900 chr3B 90.000 60 6 0 6331 6390 128758776 128758835 2.020000e-10 78.7
25 TraesCS6A01G266900 chr3B 88.710 62 7 0 6331 6392 252934605 252934666 7.260000e-10 76.8
26 TraesCS6A01G266900 chr3B 82.759 87 9 6 6296 6379 72722883 72722966 9.390000e-09 73.1
27 TraesCS6A01G266900 chr7D 88.060 67 6 2 6331 6396 514348222 514348287 2.020000e-10 78.7
28 TraesCS6A01G266900 chr4D 86.301 73 8 1 6315 6387 424579674 424579604 2.020000e-10 78.7
29 TraesCS6A01G266900 chr2B 91.228 57 5 0 6331 6387 493852708 493852652 2.020000e-10 78.7
30 TraesCS6A01G266900 chr4A 83.117 77 11 2 6331 6405 595812054 595811978 1.210000e-07 69.4
31 TraesCS6A01G266900 chr1D 92.500 40 2 1 6279 6317 442376675 442376636 1.000000e-03 56.5


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 TraesCS6A01G266900 chr6A 492700935 492707682 6747 False 2192.666667 10630 98.467333 1 6748 6 chr6A.!!$F1 6747
1 TraesCS6A01G266900 chr6D 351111267 351118300 7033 True 1498.285714 4446 94.561286 1 6748 7 chr6D.!!$R1 6747
2 TraesCS6A01G266900 chr6B 528615760 528623149 7389 False 1090.222222 3587 93.540778 1 6748 9 chr6B.!!$F1 6747

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
368 389 0.323633 CCATGACCACCAAGATGGCA 60.324 55.000 0.00 0.00 44.33 4.92 F
842 981 1.065031 CAAGCACGCACAAATACGCC 61.065 55.000 0.00 0.00 0.00 5.68 F
1851 2355 1.202245 GGCACACACACACACGAAAAT 60.202 47.619 0.00 0.00 0.00 1.82 F
2928 3437 0.322816 ACGCTGCTCATTTCCCATGT 60.323 50.000 0.00 0.00 0.00 3.21 F
3350 3880 0.546122 TGTTGTCTGAGCACTTGGGT 59.454 50.000 0.00 0.00 0.00 4.51 F
3756 4687 0.179009 ACTGCTGTTGTGCATCCACT 60.179 50.000 0.00 0.00 42.48 4.00 F
3759 4690 0.804989 GCTGTTGTGCATCCACTACC 59.195 55.000 0.00 0.00 43.87 3.18 F
5597 6539 1.587054 CAAGACCGACGGCTTCTCT 59.413 57.895 15.39 6.34 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2316 2823 1.905843 ACTCTGGCGTCTCAGCTGT 60.906 57.895 14.67 0.00 37.29 4.40 R
2385 2892 5.769662 CAGTCTCATAGTCTCCTGCTCTATT 59.230 44.000 0.00 0.00 0.00 1.73 R
3740 4671 0.804989 GGTAGTGGATGCACAACAGC 59.195 55.000 20.21 9.72 0.00 4.40 R
3741 4672 2.183478 TGGTAGTGGATGCACAACAG 57.817 50.000 20.21 0.00 0.00 3.16 R
5210 6150 0.675083 TCAAATGCTGCAGTTGGGTG 59.325 50.000 33.59 16.23 39.46 4.61 R
5597 6539 1.552337 AGCTTCGCAATCTCTCTTCCA 59.448 47.619 0.00 0.00 0.00 3.53 R
5609 6551 2.510012 CTCGCCATCAGCTTCGCA 60.510 61.111 0.00 0.00 40.39 5.10 R
6634 8070 1.101635 CCTGGATGCCGTCTCGACTA 61.102 60.000 0.00 0.00 0.00 2.59 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
66 69 2.036428 TAGAGAGCCCGATCGGACGA 62.036 60.000 35.42 13.47 37.50 4.20
241 261 3.196039 CCAGCCAATGAAATGATGAACCA 59.804 43.478 0.00 0.00 0.00 3.67
253 273 2.835156 TGATGAACCATTGGTCCGACTA 59.165 45.455 9.22 0.00 33.12 2.59
261 282 4.261801 CCATTGGTCCGACTAGTGAAAAT 58.738 43.478 0.00 0.00 0.00 1.82
263 284 3.604875 TGGTCCGACTAGTGAAAATCC 57.395 47.619 0.00 0.00 0.00 3.01
279 300 2.425143 ATCCAAGCCGACAACATCAT 57.575 45.000 0.00 0.00 0.00 2.45
280 301 2.198827 TCCAAGCCGACAACATCATT 57.801 45.000 0.00 0.00 0.00 2.57
285 306 4.487948 CAAGCCGACAACATCATTGATTT 58.512 39.130 0.00 0.00 0.00 2.17
298 319 4.661222 TCATTGATTTAGCCACAGGTTCA 58.339 39.130 0.00 0.00 0.00 3.18
301 322 4.901197 TGATTTAGCCACAGGTTCAGTA 57.099 40.909 0.00 0.00 0.00 2.74
325 346 5.975693 TTAAAACTATGAAACCAGGGCAG 57.024 39.130 0.00 0.00 0.00 4.85
338 359 4.814294 GGCAGCACCGACGGTAGG 62.814 72.222 21.25 12.97 32.11 3.18
368 389 0.323633 CCATGACCACCAAGATGGCA 60.324 55.000 0.00 0.00 44.33 4.92
373 394 3.136123 CACCAAGATGGCAGGCCG 61.136 66.667 5.74 0.00 42.67 6.13
374 395 3.650950 ACCAAGATGGCAGGCCGT 61.651 61.111 4.34 4.34 42.67 5.68
383 404 3.138798 GCAGGCCGTCGTCCTCTA 61.139 66.667 0.00 0.00 0.00 2.43
386 407 1.303888 AGGCCGTCGTCCTCTAACA 60.304 57.895 0.00 0.00 0.00 2.41
529 590 3.138468 ACCAAGGGAAGTAGCTTTTGACT 59.862 43.478 0.00 0.00 0.00 3.41
575 636 8.050930 TGTCTAGGGTCTTCTTTGTTAGTTTTT 58.949 33.333 0.00 0.00 0.00 1.94
580 641 6.041637 GGGTCTTCTTTGTTAGTTTTTGGGAT 59.958 38.462 0.00 0.00 0.00 3.85
595 656 6.367374 TTTTGGGATCCCTTTGTTATTTCC 57.633 37.500 31.05 0.39 36.94 3.13
621 682 2.635915 CCTGTAGGGTCCTGTGTGTAAA 59.364 50.000 0.00 0.00 0.00 2.01
635 771 6.208599 CCTGTGTGTAAAATGTTCCCTACAAT 59.791 38.462 0.00 0.00 40.89 2.71
646 782 1.349688 TCCCTACAATTCAGCAACGGT 59.650 47.619 0.00 0.00 0.00 4.83
667 806 6.128227 ACGGTTGCGCAGTTAAAATATAAAGA 60.128 34.615 11.31 0.00 0.00 2.52
668 807 6.410914 CGGTTGCGCAGTTAAAATATAAAGAG 59.589 38.462 11.31 0.00 0.00 2.85
669 808 7.469260 GGTTGCGCAGTTAAAATATAAAGAGA 58.531 34.615 11.31 0.00 0.00 3.10
670 809 7.640240 GGTTGCGCAGTTAAAATATAAAGAGAG 59.360 37.037 11.31 0.00 0.00 3.20
671 810 8.388103 GTTGCGCAGTTAAAATATAAAGAGAGA 58.612 33.333 11.31 0.00 0.00 3.10
672 811 8.487313 TGCGCAGTTAAAATATAAAGAGAGAA 57.513 30.769 5.66 0.00 0.00 2.87
673 812 8.604035 TGCGCAGTTAAAATATAAAGAGAGAAG 58.396 33.333 5.66 0.00 0.00 2.85
674 813 8.604890 GCGCAGTTAAAATATAAAGAGAGAAGT 58.395 33.333 0.30 0.00 0.00 3.01
731 870 2.420022 CCGTCTTCCGCATCAAGAAAAT 59.580 45.455 0.00 0.00 31.60 1.82
732 871 3.485877 CCGTCTTCCGCATCAAGAAAATC 60.486 47.826 0.00 0.00 31.60 2.17
740 879 3.181517 CGCATCAAGAAAATCGAGAAGCA 60.182 43.478 0.00 0.00 0.00 3.91
747 886 3.748568 AGAAAATCGAGAAGCACCTTCAC 59.251 43.478 7.62 0.77 42.37 3.18
756 895 3.945285 AGAAGCACCTTCACGAAGAAAAA 59.055 39.130 8.38 0.00 42.37 1.94
815 954 3.011635 GCAAGCCGAGCTGGAGAGA 62.012 63.158 0.00 0.00 39.62 3.10
842 981 1.065031 CAAGCACGCACAAATACGCC 61.065 55.000 0.00 0.00 0.00 5.68
878 1017 4.925576 CTCGATCGAACCGGCGGG 62.926 72.222 31.78 13.02 40.11 6.13
1302 1653 4.208047 CGCGAATTCGAAAAGAGAGATGAT 59.792 41.667 31.01 0.00 43.02 2.45
1364 1717 3.126000 GGCTCAGTTATGTCTGTGCTTTC 59.874 47.826 18.25 5.91 46.98 2.62
1496 1849 1.268999 GCAGATCGAGCTCGTGAGATT 60.269 52.381 33.33 13.79 40.84 2.40
1539 1892 5.666969 TTGTTCTTACTTCGTTGGTCATG 57.333 39.130 0.00 0.00 0.00 3.07
1629 2117 4.129380 TCAGGCATTTCAATATCACGAGG 58.871 43.478 0.00 0.00 0.00 4.63
1816 2312 2.765699 GGGGATGCCACACACAATAATT 59.234 45.455 5.30 0.00 0.00 1.40
1851 2355 1.202245 GGCACACACACACACGAAAAT 60.202 47.619 0.00 0.00 0.00 1.82
1852 2356 2.032302 GGCACACACACACACGAAAATA 59.968 45.455 0.00 0.00 0.00 1.40
2001 2506 8.814038 AATCAAGTTCTACTGCATCCTATTTT 57.186 30.769 0.00 0.00 0.00 1.82
2010 2515 9.725019 TCTACTGCATCCTATTTTATTACATGG 57.275 33.333 0.00 0.00 0.00 3.66
2113 2620 2.621055 TGTGTGTTTATGTGGAGTTGCC 59.379 45.455 0.00 0.00 37.10 4.52
2166 2673 8.855279 CGTGTAGAGTATGAAGAGAAGAAAAAG 58.145 37.037 0.00 0.00 0.00 2.27
2316 2823 8.671921 CAAGAAGAATCTGCAATTAAGCTAGAA 58.328 33.333 0.00 0.00 35.59 2.10
2385 2892 1.416401 ACAGAGAAGGAAAAGGCACGA 59.584 47.619 0.00 0.00 0.00 4.35
2789 3298 9.162764 TCAGTGCAATTAGTAAGGAGTTAATTC 57.837 33.333 0.00 0.00 0.00 2.17
2853 3362 4.195416 CCTTCTCTTATTCCCTCAAGTGC 58.805 47.826 0.00 0.00 0.00 4.40
2928 3437 0.322816 ACGCTGCTCATTTCCCATGT 60.323 50.000 0.00 0.00 0.00 3.21
3046 3568 7.328737 AGTGGAGTTAGAAGTGCGTATAATTT 58.671 34.615 0.00 0.00 0.00 1.82
3048 3570 8.448615 GTGGAGTTAGAAGTGCGTATAATTTTT 58.551 33.333 0.00 0.00 0.00 1.94
3210 3732 9.100554 CAACATATGTTTGGCAATAATGTTGAT 57.899 29.630 29.67 12.51 46.18 2.57
3346 3876 4.265073 AGTCTTTTGTTGTCTGAGCACTT 58.735 39.130 0.00 0.00 0.00 3.16
3350 3880 0.546122 TGTTGTCTGAGCACTTGGGT 59.454 50.000 0.00 0.00 0.00 4.51
3365 3895 2.048127 GGTCTGCACGGACTGGAC 60.048 66.667 9.37 0.00 36.55 4.02
3704 4635 4.946478 AGGTATGCTCCAAGTGTATCTC 57.054 45.455 0.00 0.00 0.00 2.75
3728 4659 9.379791 CTCGACCTTGTAAACTAAGGAATTAAT 57.620 33.333 10.50 0.00 46.08 1.40
3729 4660 9.729281 TCGACCTTGTAAACTAAGGAATTAATT 57.271 29.630 10.50 0.00 46.08 1.40
3730 4661 9.769093 CGACCTTGTAAACTAAGGAATTAATTG 57.231 33.333 5.17 0.00 46.08 2.32
3731 4662 9.569167 GACCTTGTAAACTAAGGAATTAATTGC 57.431 33.333 11.44 11.44 46.08 3.56
3732 4663 9.309224 ACCTTGTAAACTAAGGAATTAATTGCT 57.691 29.630 15.75 15.75 46.08 3.91
3740 4671 9.696917 AACTAAGGAATTAATTGCTTGAAACTG 57.303 29.630 32.97 20.95 45.95 3.16
3741 4672 7.814587 ACTAAGGAATTAATTGCTTGAAACTGC 59.185 33.333 32.97 6.02 45.95 4.40
3742 4673 6.350629 AGGAATTAATTGCTTGAAACTGCT 57.649 33.333 15.75 0.00 34.65 4.24
3743 4674 6.161381 AGGAATTAATTGCTTGAAACTGCTG 58.839 36.000 15.75 0.00 34.65 4.41
3744 4675 5.928264 GGAATTAATTGCTTGAAACTGCTGT 59.072 36.000 12.05 0.00 0.00 4.40
3745 4676 6.424812 GGAATTAATTGCTTGAAACTGCTGTT 59.575 34.615 12.05 2.72 38.16 3.16
3746 4677 6.774354 ATTAATTGCTTGAAACTGCTGTTG 57.226 33.333 9.95 0.00 36.39 3.33
3747 4678 3.806625 ATTGCTTGAAACTGCTGTTGT 57.193 38.095 9.95 0.72 36.39 3.32
3748 4679 2.565210 TGCTTGAAACTGCTGTTGTG 57.435 45.000 9.95 2.51 36.39 3.33
3749 4680 1.203065 GCTTGAAACTGCTGTTGTGC 58.797 50.000 9.95 8.26 36.39 4.57
3750 4681 1.469595 GCTTGAAACTGCTGTTGTGCA 60.470 47.619 9.95 6.33 41.05 4.57
3751 4682 2.800629 GCTTGAAACTGCTGTTGTGCAT 60.801 45.455 9.95 0.00 42.48 3.96
3752 4683 2.780065 TGAAACTGCTGTTGTGCATC 57.220 45.000 9.95 4.16 42.48 3.91
3753 4684 1.337703 TGAAACTGCTGTTGTGCATCC 59.662 47.619 9.95 0.00 42.48 3.51
3754 4685 1.337703 GAAACTGCTGTTGTGCATCCA 59.662 47.619 9.95 0.00 42.48 3.41
3755 4686 0.670162 AACTGCTGTTGTGCATCCAC 59.330 50.000 8.32 0.00 42.48 4.02
3756 4687 0.179009 ACTGCTGTTGTGCATCCACT 60.179 50.000 0.00 0.00 42.48 4.00
3757 4688 1.072173 ACTGCTGTTGTGCATCCACTA 59.928 47.619 0.00 0.00 42.48 2.74
3758 4689 1.466167 CTGCTGTTGTGCATCCACTAC 59.534 52.381 0.00 0.00 44.46 2.73
3759 4690 0.804989 GCTGTTGTGCATCCACTACC 59.195 55.000 0.00 0.00 43.87 3.18
3760 4691 1.881925 GCTGTTGTGCATCCACTACCA 60.882 52.381 0.00 0.00 43.87 3.25
3761 4692 2.715046 CTGTTGTGCATCCACTACCAT 58.285 47.619 0.00 0.00 43.87 3.55
3762 4693 3.872696 CTGTTGTGCATCCACTACCATA 58.127 45.455 0.00 0.00 43.87 2.74
3763 4694 4.260985 CTGTTGTGCATCCACTACCATAA 58.739 43.478 0.00 0.00 43.87 1.90
3764 4695 4.657013 TGTTGTGCATCCACTACCATAAA 58.343 39.130 0.00 0.00 43.87 1.40
3765 4696 5.260424 TGTTGTGCATCCACTACCATAAAT 58.740 37.500 0.00 0.00 43.87 1.40
3766 4697 5.714333 TGTTGTGCATCCACTACCATAAATT 59.286 36.000 0.00 0.00 43.87 1.82
3767 4698 5.833406 TGTGCATCCACTACCATAAATTG 57.167 39.130 0.00 0.00 42.54 2.32
3768 4699 5.504853 TGTGCATCCACTACCATAAATTGA 58.495 37.500 0.00 0.00 42.54 2.57
3769 4700 5.948758 TGTGCATCCACTACCATAAATTGAA 59.051 36.000 0.00 0.00 42.54 2.69
3770 4701 6.435591 TGTGCATCCACTACCATAAATTGAAA 59.564 34.615 0.00 0.00 42.54 2.69
3771 4702 6.974622 GTGCATCCACTACCATAAATTGAAAG 59.025 38.462 0.00 0.00 38.93 2.62
3772 4703 6.096705 TGCATCCACTACCATAAATTGAAAGG 59.903 38.462 0.00 0.00 0.00 3.11
3773 4704 6.096846 GCATCCACTACCATAAATTGAAAGGT 59.903 38.462 0.00 0.00 36.40 3.50
3774 4705 7.284489 GCATCCACTACCATAAATTGAAAGGTA 59.716 37.037 0.00 0.00 33.91 3.08
3775 4706 9.354673 CATCCACTACCATAAATTGAAAGGTAT 57.645 33.333 0.00 0.00 34.59 2.73
3776 4707 8.746052 TCCACTACCATAAATTGAAAGGTATG 57.254 34.615 0.00 0.00 34.59 2.39
3777 4708 7.284489 TCCACTACCATAAATTGAAAGGTATGC 59.716 37.037 0.00 0.00 34.59 3.14
3778 4709 7.285401 CCACTACCATAAATTGAAAGGTATGCT 59.715 37.037 0.00 0.00 34.59 3.79
3779 4710 8.345565 CACTACCATAAATTGAAAGGTATGCTC 58.654 37.037 0.00 0.00 34.59 4.26
3780 4711 6.715347 ACCATAAATTGAAAGGTATGCTCC 57.285 37.500 0.00 0.00 0.00 4.70
3781 4712 6.194235 ACCATAAATTGAAAGGTATGCTCCA 58.806 36.000 0.00 0.00 0.00 3.86
3782 4713 6.667414 ACCATAAATTGAAAGGTATGCTCCAA 59.333 34.615 0.00 0.00 0.00 3.53
3783 4714 7.147846 ACCATAAATTGAAAGGTATGCTCCAAG 60.148 37.037 0.00 0.00 0.00 3.61
3784 4715 7.147846 CCATAAATTGAAAGGTATGCTCCAAGT 60.148 37.037 0.00 0.00 0.00 3.16
3785 4716 5.649782 AATTGAAAGGTATGCTCCAAGTG 57.350 39.130 0.00 0.00 0.00 3.16
3786 4717 3.788227 TGAAAGGTATGCTCCAAGTGT 57.212 42.857 0.00 0.00 0.00 3.55
3787 4718 4.901197 TGAAAGGTATGCTCCAAGTGTA 57.099 40.909 0.00 0.00 0.00 2.90
3788 4719 5.435686 TGAAAGGTATGCTCCAAGTGTAT 57.564 39.130 0.00 0.00 0.00 2.29
3789 4720 5.428253 TGAAAGGTATGCTCCAAGTGTATC 58.572 41.667 0.00 0.00 0.00 2.24
3790 4721 5.189736 TGAAAGGTATGCTCCAAGTGTATCT 59.810 40.000 0.00 0.00 0.00 1.98
3791 4722 5.700402 AAGGTATGCTCCAAGTGTATCTT 57.300 39.130 0.00 0.00 36.75 2.40
3806 4737 8.876275 AAGTGTATCTTGACGTTGTAAACTAA 57.124 30.769 0.00 0.00 38.77 2.24
3807 4738 8.516811 AGTGTATCTTGACGTTGTAAACTAAG 57.483 34.615 0.00 0.00 46.99 2.18
3808 4739 7.597743 AGTGTATCTTGACGTTGTAAACTAAGG 59.402 37.037 0.00 0.00 46.99 2.69
3809 4740 7.596248 GTGTATCTTGACGTTGTAAACTAAGGA 59.404 37.037 0.00 0.00 46.99 3.36
3810 4741 8.143193 TGTATCTTGACGTTGTAAACTAAGGAA 58.857 33.333 0.00 0.00 46.99 3.36
3811 4742 9.148104 GTATCTTGACGTTGTAAACTAAGGAAT 57.852 33.333 0.00 0.00 46.99 3.01
3812 4743 8.617290 ATCTTGACGTTGTAAACTAAGGAATT 57.383 30.769 0.00 0.00 46.99 2.17
3813 4744 9.715121 ATCTTGACGTTGTAAACTAAGGAATTA 57.285 29.630 0.00 0.00 46.99 1.40
3814 4745 9.545105 TCTTGACGTTGTAAACTAAGGAATTAA 57.455 29.630 0.00 0.00 46.99 1.40
3828 4759 7.814587 ACTAAGGAATTAATTGCTTGAAACTGC 59.185 33.333 32.97 6.02 45.95 4.40
3839 4770 3.450578 CTTGAAACTGCTGTTGTGCATT 58.549 40.909 9.95 0.00 42.48 3.56
4234 5167 6.034898 GGTGAAGACTGTTTTGTGTCAAAATG 59.965 38.462 10.15 9.06 35.81 2.32
4476 5409 2.108168 CGAGGGAAGTATCCTTGGTCA 58.892 52.381 0.00 0.00 45.77 4.02
4566 5499 2.962421 TGGGAAAGGTTTTGGTGATGTC 59.038 45.455 0.00 0.00 0.00 3.06
4572 5505 5.458041 AAGGTTTTGGTGATGTCATTCTG 57.542 39.130 0.00 0.00 0.00 3.02
5037 5976 8.114290 GTGATTTTGCAGCATTTGATATTTCAG 58.886 33.333 0.00 0.00 32.27 3.02
5097 6036 3.622455 GCAGTAGAAGGGGTAGCAATGTT 60.622 47.826 0.00 0.00 0.00 2.71
5210 6150 7.375053 TCTTGTTGGTAATATGTTTTGCCTTC 58.625 34.615 0.00 0.00 33.04 3.46
5405 6347 3.021695 TGACCGTATCGATGAGGTTCTT 58.978 45.455 22.10 5.19 37.07 2.52
5597 6539 1.587054 CAAGACCGACGGCTTCTCT 59.413 57.895 15.39 6.34 0.00 3.10
5849 6792 7.305820 CGCTGATTCTTTTTGCTTTGCTATATG 60.306 37.037 0.00 0.00 0.00 1.78
5888 6936 6.547510 GGAATTTTGGAGGCTTACATGTATCT 59.452 38.462 6.36 5.10 0.00 1.98
5955 7003 6.417191 TTTCTGTTCTATTTGTCCGCATAC 57.583 37.500 0.00 0.00 0.00 2.39
5984 7032 5.005094 CCTTTGGTGGCATGATTTGATTTT 58.995 37.500 0.00 0.00 0.00 1.82
6185 7235 4.152625 GCGATGCACACAGCCGAC 62.153 66.667 0.00 0.00 44.83 4.79
6200 7250 4.176752 GACCCGCACCATCTCCCC 62.177 72.222 0.00 0.00 0.00 4.81
6201 7251 4.741239 ACCCGCACCATCTCCCCT 62.741 66.667 0.00 0.00 0.00 4.79
6203 7253 3.866582 CCGCACCATCTCCCCTCC 61.867 72.222 0.00 0.00 0.00 4.30
6261 7380 5.950758 TTTTATGCAGCGGAGAACTAAAA 57.049 34.783 0.00 0.00 0.00 1.52
6274 7393 6.342111 GGAGAACTAAAATACTCCCTCTGTG 58.658 44.000 0.00 0.00 41.89 3.66
6379 7812 8.535690 ACGCTCTTATATTAATTTACAGAGGC 57.464 34.615 16.85 12.16 0.00 4.70
6496 7929 4.443394 GCAAGTGCAGATTTCTTTTCACTG 59.557 41.667 0.00 0.00 41.59 3.66
6620 8056 2.569853 ACGGTGGTGATGGAAGATACAA 59.430 45.455 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.001460 CCTGGAAATTTTGTGTACAGACCTA 58.999 40.000 0.00 0.00 0.00 3.08
19 20 6.391227 AGAACCTGGAAATTTTGTGTACAG 57.609 37.500 0.00 0.00 0.00 2.74
116 136 1.339631 TGTTGAATTACCCGCCTCCTG 60.340 52.381 0.00 0.00 0.00 3.86
234 254 2.838202 ACTAGTCGGACCAATGGTTCAT 59.162 45.455 11.85 0.00 35.25 2.57
241 261 4.019681 TGGATTTTCACTAGTCGGACCAAT 60.020 41.667 4.14 0.00 0.00 3.16
253 273 2.270352 TGTCGGCTTGGATTTTCACT 57.730 45.000 0.00 0.00 0.00 3.41
261 282 1.811965 CAATGATGTTGTCGGCTTGGA 59.188 47.619 0.00 0.00 0.00 3.53
263 284 3.770263 ATCAATGATGTTGTCGGCTTG 57.230 42.857 0.00 0.00 0.00 4.01
279 300 4.098914 ACTGAACCTGTGGCTAAATCAA 57.901 40.909 0.00 0.00 0.00 2.57
280 301 3.788227 ACTGAACCTGTGGCTAAATCA 57.212 42.857 0.00 0.00 0.00 2.57
285 306 7.228590 AGTTTTAAATACTGAACCTGTGGCTA 58.771 34.615 0.00 0.00 0.00 3.93
298 319 7.672239 TGCCCTGGTTTCATAGTTTTAAATACT 59.328 33.333 0.00 7.76 0.00 2.12
301 322 6.574269 GCTGCCCTGGTTTCATAGTTTTAAAT 60.574 38.462 0.00 0.00 0.00 1.40
325 346 2.030958 CCAAACCTACCGTCGGTGC 61.031 63.158 27.20 0.00 36.19 5.01
356 377 3.136123 CGGCCTGCCATCTTGGTG 61.136 66.667 9.17 0.00 40.46 4.17
368 389 0.896940 TTGTTAGAGGACGACGGCCT 60.897 55.000 25.81 25.81 38.81 5.19
373 394 1.617357 ACCAGGTTGTTAGAGGACGAC 59.383 52.381 0.00 0.00 33.92 4.34
374 395 1.616865 CACCAGGTTGTTAGAGGACGA 59.383 52.381 0.00 0.00 0.00 4.20
383 404 1.331214 CAAGGATGCACCAGGTTGTT 58.669 50.000 7.86 0.00 42.04 2.83
386 407 1.077265 CCCAAGGATGCACCAGGTT 59.923 57.895 7.86 0.00 42.04 3.50
529 590 3.242478 ACAGAAAATGAAAACGCGTTCGA 60.242 39.130 26.77 12.39 39.41 3.71
575 636 4.045334 ACAGGAAATAACAAAGGGATCCCA 59.955 41.667 32.69 11.39 38.92 4.37
580 641 5.076873 CAGGAACAGGAAATAACAAAGGGA 58.923 41.667 0.00 0.00 0.00 4.20
595 656 1.276421 CACAGGACCCTACAGGAACAG 59.724 57.143 0.00 0.00 39.89 3.16
621 682 4.082787 CGTTGCTGAATTGTAGGGAACATT 60.083 41.667 0.00 0.00 38.10 2.71
646 782 8.487313 TCTCTCTTTATATTTTAACTGCGCAA 57.513 30.769 13.05 0.00 0.00 4.85
680 819 6.052360 GCCTCGGATATTTCTCTCTCTTTTT 58.948 40.000 0.00 0.00 0.00 1.94
681 820 5.606505 GCCTCGGATATTTCTCTCTCTTTT 58.393 41.667 0.00 0.00 0.00 2.27
682 821 4.261825 CGCCTCGGATATTTCTCTCTCTTT 60.262 45.833 0.00 0.00 0.00 2.52
683 822 3.254657 CGCCTCGGATATTTCTCTCTCTT 59.745 47.826 0.00 0.00 0.00 2.85
684 823 2.817258 CGCCTCGGATATTTCTCTCTCT 59.183 50.000 0.00 0.00 0.00 3.10
685 824 2.814919 TCGCCTCGGATATTTCTCTCTC 59.185 50.000 0.00 0.00 0.00 3.20
686 825 2.865079 TCGCCTCGGATATTTCTCTCT 58.135 47.619 0.00 0.00 0.00 3.10
687 826 3.570559 CTTCGCCTCGGATATTTCTCTC 58.429 50.000 0.00 0.00 0.00 3.20
740 879 5.163550 CCTTTTCCTTTTTCTTCGTGAAGGT 60.164 40.000 9.58 0.00 39.67 3.50
747 886 6.031471 TCGTTTTCCTTTTCCTTTTTCTTCG 58.969 36.000 0.00 0.00 0.00 3.79
756 895 3.815962 GCTCTTCTCGTTTTCCTTTTCCT 59.184 43.478 0.00 0.00 0.00 3.36
842 981 3.605749 AACGTGGTGGGAGATGCGG 62.606 63.158 0.00 0.00 0.00 5.69
992 1131 4.433877 CGGCGGCCATGGTTTTGG 62.434 66.667 20.71 0.00 39.94 3.28
1302 1653 3.820467 CACCTACCTTTTTGACATCAGCA 59.180 43.478 0.00 0.00 0.00 4.41
1473 1826 3.815396 ACGAGCTCGATCTGCGCA 61.815 61.111 40.58 10.98 43.02 6.09
1496 1849 6.046593 ACAAACAACGAGATGACAGAAAGTA 58.953 36.000 0.00 0.00 0.00 2.24
1539 1892 3.848272 TGCCAATTCGTTCAAAGGATC 57.152 42.857 0.00 0.00 0.00 3.36
1629 2117 7.088905 AGTACTAGCAGTAATGTACACAACAC 58.911 38.462 0.00 0.00 42.09 3.32
1757 2253 6.548321 AGTACACCATTGGACCTGAATTTAA 58.452 36.000 10.37 0.00 37.25 1.52
1758 2254 6.012858 AGAGTACACCATTGGACCTGAATTTA 60.013 38.462 10.37 0.00 37.25 1.40
1762 2258 3.248024 AGAGTACACCATTGGACCTGAA 58.752 45.455 10.37 0.00 37.25 3.02
1816 2312 4.301505 GCCACTGAAAGATCGGCA 57.698 55.556 0.00 0.00 43.42 5.69
1839 2335 7.851822 AATAGCAGTTTTATTTTCGTGTGTG 57.148 32.000 0.00 0.00 0.00 3.82
1955 2460 3.334583 TCAGTCAAGCAGTTGGTATCC 57.665 47.619 0.00 0.00 34.09 2.59
2010 2515 5.105797 TGGGCATGATCTGAAACATTTACAC 60.106 40.000 0.00 0.00 0.00 2.90
2113 2620 4.543692 CTCTCCTGCAAATGTGACAAAAG 58.456 43.478 0.00 0.00 0.00 2.27
2316 2823 1.905843 ACTCTGGCGTCTCAGCTGT 60.906 57.895 14.67 0.00 37.29 4.40
2385 2892 5.769662 CAGTCTCATAGTCTCCTGCTCTATT 59.230 44.000 0.00 0.00 0.00 1.73
2755 3264 9.290988 TCCTTACTAATTGCACTGAAACATAAA 57.709 29.630 0.00 0.00 0.00 1.40
2756 3265 8.856153 TCCTTACTAATTGCACTGAAACATAA 57.144 30.769 0.00 0.00 0.00 1.90
2789 3298 5.869344 TCGTCTAAAAACATGTGATCTCTGG 59.131 40.000 0.00 0.00 0.00 3.86
2853 3362 6.201615 TGTGAGCTTAGAGATTAATTCATGCG 59.798 38.462 0.00 0.00 0.00 4.73
3234 3756 2.747989 TCAACTAGTCTGCTACCAGTCG 59.252 50.000 0.00 0.00 40.09 4.18
3346 3876 3.625897 CCAGTCCGTGCAGACCCA 61.626 66.667 2.65 0.00 37.49 4.51
3350 3880 2.203640 AGGTCCAGTCCGTGCAGA 60.204 61.111 0.00 0.00 0.00 4.26
3365 3895 3.118992 TGCAGCACTATTAGACACTCAGG 60.119 47.826 0.00 0.00 0.00 3.86
3704 4635 9.769093 CAATTAATTCCTTAGTTTACAAGGTCG 57.231 33.333 0.00 0.00 42.73 4.79
3728 4659 2.878580 CACAACAGCAGTTTCAAGCAA 58.121 42.857 0.00 0.00 35.28 3.91
3729 4660 1.469595 GCACAACAGCAGTTTCAAGCA 60.470 47.619 0.00 0.00 35.28 3.91
3730 4661 1.203065 GCACAACAGCAGTTTCAAGC 58.797 50.000 0.00 0.00 35.28 4.01
3731 4662 2.565210 TGCACAACAGCAGTTTCAAG 57.435 45.000 0.00 0.00 40.11 3.02
3740 4671 0.804989 GGTAGTGGATGCACAACAGC 59.195 55.000 20.21 9.72 0.00 4.40
3741 4672 2.183478 TGGTAGTGGATGCACAACAG 57.817 50.000 20.21 0.00 0.00 3.16
3742 4673 2.877097 ATGGTAGTGGATGCACAACA 57.123 45.000 20.21 14.05 0.00 3.33
3743 4674 5.835113 ATTTATGGTAGTGGATGCACAAC 57.165 39.130 20.21 8.80 0.00 3.32
3744 4675 5.948758 TCAATTTATGGTAGTGGATGCACAA 59.051 36.000 20.21 3.32 0.00 3.33
3745 4676 5.504853 TCAATTTATGGTAGTGGATGCACA 58.495 37.500 20.21 2.78 0.00 4.57
3746 4677 6.449635 TTCAATTTATGGTAGTGGATGCAC 57.550 37.500 9.70 9.70 0.00 4.57
3747 4678 6.096705 CCTTTCAATTTATGGTAGTGGATGCA 59.903 38.462 0.00 0.00 0.00 3.96
3748 4679 6.096846 ACCTTTCAATTTATGGTAGTGGATGC 59.903 38.462 0.00 0.00 0.00 3.91
3749 4680 7.645058 ACCTTTCAATTTATGGTAGTGGATG 57.355 36.000 0.00 0.00 0.00 3.51
3750 4681 9.354673 CATACCTTTCAATTTATGGTAGTGGAT 57.645 33.333 0.00 0.00 36.81 3.41
3751 4682 7.284489 GCATACCTTTCAATTTATGGTAGTGGA 59.716 37.037 0.00 0.00 36.81 4.02
3752 4683 7.285401 AGCATACCTTTCAATTTATGGTAGTGG 59.715 37.037 0.00 0.00 36.81 4.00
3753 4684 8.225603 AGCATACCTTTCAATTTATGGTAGTG 57.774 34.615 0.00 0.00 36.81 2.74
3754 4685 7.502561 GGAGCATACCTTTCAATTTATGGTAGT 59.497 37.037 0.00 0.00 36.81 2.73
3755 4686 7.502226 TGGAGCATACCTTTCAATTTATGGTAG 59.498 37.037 0.00 0.00 36.81 3.18
3756 4687 7.350382 TGGAGCATACCTTTCAATTTATGGTA 58.650 34.615 0.00 0.00 33.82 3.25
3757 4688 6.194235 TGGAGCATACCTTTCAATTTATGGT 58.806 36.000 0.00 0.00 35.81 3.55
3758 4689 6.713762 TGGAGCATACCTTTCAATTTATGG 57.286 37.500 0.00 0.00 0.00 2.74
3759 4690 7.703621 CACTTGGAGCATACCTTTCAATTTATG 59.296 37.037 0.00 0.00 0.00 1.90
3760 4691 7.397192 ACACTTGGAGCATACCTTTCAATTTAT 59.603 33.333 0.00 0.00 0.00 1.40
3761 4692 6.719370 ACACTTGGAGCATACCTTTCAATTTA 59.281 34.615 0.00 0.00 0.00 1.40
3762 4693 5.539955 ACACTTGGAGCATACCTTTCAATTT 59.460 36.000 0.00 0.00 0.00 1.82
3763 4694 5.079643 ACACTTGGAGCATACCTTTCAATT 58.920 37.500 0.00 0.00 0.00 2.32
3764 4695 4.666512 ACACTTGGAGCATACCTTTCAAT 58.333 39.130 0.00 0.00 0.00 2.57
3765 4696 4.098914 ACACTTGGAGCATACCTTTCAA 57.901 40.909 0.00 0.00 0.00 2.69
3766 4697 3.788227 ACACTTGGAGCATACCTTTCA 57.212 42.857 0.00 0.00 0.00 2.69
3767 4698 5.675538 AGATACACTTGGAGCATACCTTTC 58.324 41.667 0.00 0.00 0.00 2.62
3768 4699 5.700402 AGATACACTTGGAGCATACCTTT 57.300 39.130 0.00 0.00 0.00 3.11
3769 4700 5.700402 AAGATACACTTGGAGCATACCTT 57.300 39.130 0.00 0.00 37.45 3.50
3778 4709 7.899401 AGTTTACAACGTCAAGATACACTTGGA 60.899 37.037 9.22 0.00 44.64 3.53
3779 4710 6.202188 AGTTTACAACGTCAAGATACACTTGG 59.798 38.462 9.22 0.00 44.64 3.61
3780 4711 7.173863 AGTTTACAACGTCAAGATACACTTG 57.826 36.000 0.00 0.00 45.21 3.16
3781 4712 8.876275 TTAGTTTACAACGTCAAGATACACTT 57.124 30.769 0.00 0.00 36.43 3.16
3782 4713 7.597743 CCTTAGTTTACAACGTCAAGATACACT 59.402 37.037 0.00 0.00 36.23 3.55
3783 4714 7.596248 TCCTTAGTTTACAACGTCAAGATACAC 59.404 37.037 0.00 0.00 36.23 2.90
3784 4715 7.660112 TCCTTAGTTTACAACGTCAAGATACA 58.340 34.615 0.00 0.00 36.23 2.29
3785 4716 8.524870 TTCCTTAGTTTACAACGTCAAGATAC 57.475 34.615 0.00 0.00 36.23 2.24
3786 4717 9.715121 AATTCCTTAGTTTACAACGTCAAGATA 57.285 29.630 0.00 0.00 36.23 1.98
3787 4718 8.617290 AATTCCTTAGTTTACAACGTCAAGAT 57.383 30.769 0.00 0.00 36.23 2.40
3788 4719 9.545105 TTAATTCCTTAGTTTACAACGTCAAGA 57.455 29.630 0.00 0.00 36.23 3.02
3792 4723 9.058424 GCAATTAATTCCTTAGTTTACAACGTC 57.942 33.333 0.00 0.00 36.23 4.34
3793 4724 8.789762 AGCAATTAATTCCTTAGTTTACAACGT 58.210 29.630 0.00 0.00 36.23 3.99
3794 4725 9.620660 AAGCAATTAATTCCTTAGTTTACAACG 57.379 29.630 2.39 0.00 36.23 4.10
3801 4732 9.696917 CAGTTTCAAGCAATTAATTCCTTAGTT 57.303 29.630 4.04 0.00 0.00 2.24
3802 4733 7.814587 GCAGTTTCAAGCAATTAATTCCTTAGT 59.185 33.333 4.04 0.00 0.00 2.24
3803 4734 8.031277 AGCAGTTTCAAGCAATTAATTCCTTAG 58.969 33.333 4.04 0.70 0.00 2.18
3804 4735 7.814107 CAGCAGTTTCAAGCAATTAATTCCTTA 59.186 33.333 4.04 0.00 0.00 2.69
3805 4736 6.647895 CAGCAGTTTCAAGCAATTAATTCCTT 59.352 34.615 0.00 0.00 0.00 3.36
3806 4737 6.161381 CAGCAGTTTCAAGCAATTAATTCCT 58.839 36.000 0.00 0.00 0.00 3.36
3807 4738 5.928264 ACAGCAGTTTCAAGCAATTAATTCC 59.072 36.000 0.00 0.00 0.00 3.01
3808 4739 7.042523 ACAACAGCAGTTTCAAGCAATTAATTC 60.043 33.333 0.00 0.00 35.28 2.17
3809 4740 6.762661 ACAACAGCAGTTTCAAGCAATTAATT 59.237 30.769 0.00 0.00 35.28 1.40
3810 4741 6.201425 CACAACAGCAGTTTCAAGCAATTAAT 59.799 34.615 0.00 0.00 35.28 1.40
3811 4742 5.519566 CACAACAGCAGTTTCAAGCAATTAA 59.480 36.000 0.00 0.00 35.28 1.40
3812 4743 5.042593 CACAACAGCAGTTTCAAGCAATTA 58.957 37.500 0.00 0.00 35.28 1.40
3813 4744 3.866910 CACAACAGCAGTTTCAAGCAATT 59.133 39.130 0.00 0.00 35.28 2.32
3814 4745 3.450578 CACAACAGCAGTTTCAAGCAAT 58.549 40.909 0.00 0.00 35.28 3.56
4234 5167 8.261522 AGGATAAGAAGGTCAAGAACTATGTTC 58.738 37.037 2.54 2.54 0.00 3.18
5210 6150 0.675083 TCAAATGCTGCAGTTGGGTG 59.325 50.000 33.59 16.23 39.46 4.61
5355 6297 2.358737 GTCAAGGTCACCAGGCCG 60.359 66.667 0.00 0.00 0.00 6.13
5405 6347 3.099171 CCAGGCAGGGGGAATTCA 58.901 61.111 7.93 0.00 0.00 2.57
5597 6539 1.552337 AGCTTCGCAATCTCTCTTCCA 59.448 47.619 0.00 0.00 0.00 3.53
5609 6551 2.510012 CTCGCCATCAGCTTCGCA 60.510 61.111 0.00 0.00 40.39 5.10
5762 6704 3.325135 ACTCTCTCCCGAACTGAACATTT 59.675 43.478 0.00 0.00 0.00 2.32
5849 6792 3.628646 ATTCCGCCCAGGTGTCAGC 62.629 63.158 0.00 0.00 41.99 4.26
5888 6936 3.398406 AGTGCATCATGTTCACGTTGTA 58.602 40.909 0.00 0.00 35.97 2.41
6122 7170 4.649218 TCCCTTCACAAAAGAAAAAGGAGG 59.351 41.667 1.10 0.00 39.05 4.30
6185 7235 3.866582 GAGGGGAGATGGTGCGGG 61.867 72.222 0.00 0.00 0.00 6.13
6191 7241 3.459598 TGATGTTTAAGGAGGGGAGATGG 59.540 47.826 0.00 0.00 0.00 3.51
6200 7250 9.956720 CTAAAATGCCTTATGATGTTTAAGGAG 57.043 33.333 12.50 0.00 45.76 3.69
6201 7251 9.474313 ACTAAAATGCCTTATGATGTTTAAGGA 57.526 29.630 12.50 0.56 45.76 3.36
6356 7789 9.495572 ACTGCCTCTGTAAATTAATATAAGAGC 57.504 33.333 9.98 7.62 0.00 4.09
6389 7822 6.270927 ACTGCTGCTATGATCCTTCCTTATAA 59.729 38.462 0.00 0.00 0.00 0.98
6603 8039 5.569355 ACATTGTTGTATCTTCCATCACCA 58.431 37.500 0.00 0.00 33.16 4.17
6620 8056 6.073167 CCGTCTCGACTATATCTGTACATTGT 60.073 42.308 0.00 0.00 0.00 2.71
6634 8070 1.101635 CCTGGATGCCGTCTCGACTA 61.102 60.000 0.00 0.00 0.00 2.59
6674 8110 3.106407 GTGCGACGTGCCTGAGAC 61.106 66.667 0.00 0.00 45.60 3.36


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

AutoCloner maintained by Alex Coulton.