Multiple sequence alignment - TraesCS3D01G234200

Loading Multiple Alignment...

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 TraesCS3D01G234200 chr3D 100.000 9852 0 0 1 9852 323148098 323157949 0.000000e+00 18194
1 TraesCS3D01G234200 chr3D 95.229 7190 270 31 2674 9852 395858070 395865197 0.000000e+00 11310
2 TraesCS3D01G234200 chr3D 92.155 3977 273 29 1 3956 364949331 364945373 0.000000e+00 5579
3 TraesCS3D01G234200 chr2D 95.312 7188 265 32 2674 9852 412327584 412334708 0.000000e+00 11341
4 TraesCS3D01G234200 chr2D 92.218 5937 348 40 3955 9852 273053379 273059240 0.000000e+00 8299
5 TraesCS3D01G234200 chr2D 95.656 3821 145 14 6038 9852 259244211 259240406 0.000000e+00 6117
6 TraesCS3D01G234200 chr2D 94.662 2679 133 6 1 2671 412324992 412327668 0.000000e+00 4146
7 TraesCS3D01G234200 chr4D 94.292 7341 300 31 1 7321 144585660 144578419 0.000000e+00 11125
8 TraesCS3D01G234200 chr5D 95.714 5903 203 20 3955 9852 190783507 190777650 0.000000e+00 9454
9 TraesCS3D01G234200 chr5D 91.889 4007 260 40 1 3956 419883791 419887783 0.000000e+00 5539
10 TraesCS3D01G234200 chr5D 92.569 3203 196 30 1 3173 211807141 211803951 0.000000e+00 4558
11 TraesCS3D01G234200 chr5D 92.348 2640 163 14 3955 6590 419887493 419890097 0.000000e+00 3720
12 TraesCS3D01G234200 chr5D 92.648 1945 109 23 2041 3956 378825562 378823623 0.000000e+00 2769
13 TraesCS3D01G234200 chr7A 94.083 5374 264 32 1 5348 265351905 265357250 0.000000e+00 8113
14 TraesCS3D01G234200 chr7A 94.220 4481 203 24 5378 9852 265357248 265361678 0.000000e+00 6789
15 TraesCS3D01G234200 chr7A 93.373 4346 231 30 5520 9852 458659525 458655224 0.000000e+00 6377
16 TraesCS3D01G234200 chr1D 95.498 4065 131 20 5800 9852 371719382 371723406 0.000000e+00 6445
17 TraesCS3D01G234200 chr1D 91.716 3863 265 38 1 3836 151356607 151360441 0.000000e+00 5310
18 TraesCS3D01G234200 chr1D 95.124 2892 122 12 2173 5049 371714919 371717806 0.000000e+00 4542
19 TraesCS3D01G234200 chr2A 93.087 4354 229 40 5514 9852 160671516 160667220 0.000000e+00 6307
20 TraesCS3D01G234200 chr2A 92.591 3644 239 16 338 3956 378106399 378110036 0.000000e+00 5204
21 TraesCS3D01G234200 chr7D 95.860 3599 138 10 6261 9852 291611850 291615444 0.000000e+00 5810
22 TraesCS3D01G234200 chr7D 93.978 1943 88 20 2037 3956 291607672 291609608 0.000000e+00 2913
23 TraesCS3D01G234200 chr5A 92.961 4006 237 22 5514 9511 154815318 154811350 0.000000e+00 5794
24 TraesCS3D01G234200 chr5A 95.105 286 12 2 9568 9852 154811358 154811074 5.430000e-122 449
25 TraesCS3D01G234200 chr6D 92.225 3987 249 33 1 3956 165555175 165559131 0.000000e+00 5589
26 TraesCS3D01G234200 chr6D 92.005 2639 161 19 3955 6590 186935204 186932613 0.000000e+00 3659
27 TraesCS3D01G234200 chr1B 93.128 3638 211 16 6153 9781 425399209 425402816 0.000000e+00 5297
28 TraesCS3D01G234200 chr1B 90.484 3636 260 59 6261 9852 163067078 163063485 0.000000e+00 4719
29 TraesCS3D01G234200 chr4B 92.427 3605 226 27 6261 9852 425954220 425950650 0.000000e+00 5101


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 TraesCS3D01G234200 chr3D 323148098 323157949 9851 False 18194.0 18194 100.0000 1 9852 1 chr3D.!!$F1 9851
1 TraesCS3D01G234200 chr3D 395858070 395865197 7127 False 11310.0 11310 95.2290 2674 9852 1 chr3D.!!$F2 7178
2 TraesCS3D01G234200 chr3D 364945373 364949331 3958 True 5579.0 5579 92.1550 1 3956 1 chr3D.!!$R1 3955
3 TraesCS3D01G234200 chr2D 273053379 273059240 5861 False 8299.0 8299 92.2180 3955 9852 1 chr2D.!!$F1 5897
4 TraesCS3D01G234200 chr2D 412324992 412334708 9716 False 7743.5 11341 94.9870 1 9852 2 chr2D.!!$F2 9851
5 TraesCS3D01G234200 chr2D 259240406 259244211 3805 True 6117.0 6117 95.6560 6038 9852 1 chr2D.!!$R1 3814
6 TraesCS3D01G234200 chr4D 144578419 144585660 7241 True 11125.0 11125 94.2920 1 7321 1 chr4D.!!$R1 7320
7 TraesCS3D01G234200 chr5D 190777650 190783507 5857 True 9454.0 9454 95.7140 3955 9852 1 chr5D.!!$R1 5897
8 TraesCS3D01G234200 chr5D 419883791 419890097 6306 False 4629.5 5539 92.1185 1 6590 2 chr5D.!!$F1 6589
9 TraesCS3D01G234200 chr5D 211803951 211807141 3190 True 4558.0 4558 92.5690 1 3173 1 chr5D.!!$R2 3172
10 TraesCS3D01G234200 chr5D 378823623 378825562 1939 True 2769.0 2769 92.6480 2041 3956 1 chr5D.!!$R3 1915
11 TraesCS3D01G234200 chr7A 265351905 265361678 9773 False 7451.0 8113 94.1515 1 9852 2 chr7A.!!$F1 9851
12 TraesCS3D01G234200 chr7A 458655224 458659525 4301 True 6377.0 6377 93.3730 5520 9852 1 chr7A.!!$R1 4332
13 TraesCS3D01G234200 chr1D 371714919 371723406 8487 False 5493.5 6445 95.3110 2173 9852 2 chr1D.!!$F2 7679
14 TraesCS3D01G234200 chr1D 151356607 151360441 3834 False 5310.0 5310 91.7160 1 3836 1 chr1D.!!$F1 3835
15 TraesCS3D01G234200 chr2A 160667220 160671516 4296 True 6307.0 6307 93.0870 5514 9852 1 chr2A.!!$R1 4338
16 TraesCS3D01G234200 chr2A 378106399 378110036 3637 False 5204.0 5204 92.5910 338 3956 1 chr2A.!!$F1 3618
17 TraesCS3D01G234200 chr7D 291607672 291615444 7772 False 4361.5 5810 94.9190 2037 9852 2 chr7D.!!$F1 7815
18 TraesCS3D01G234200 chr5A 154811074 154815318 4244 True 3121.5 5794 94.0330 5514 9852 2 chr5A.!!$R1 4338
19 TraesCS3D01G234200 chr6D 165555175 165559131 3956 False 5589.0 5589 92.2250 1 3956 1 chr6D.!!$F1 3955
20 TraesCS3D01G234200 chr6D 186932613 186935204 2591 True 3659.0 3659 92.0050 3955 6590 1 chr6D.!!$R1 2635
21 TraesCS3D01G234200 chr1B 425399209 425402816 3607 False 5297.0 5297 93.1280 6153 9781 1 chr1B.!!$F1 3628
22 TraesCS3D01G234200 chr1B 163063485 163067078 3593 True 4719.0 4719 90.4840 6261 9852 1 chr1B.!!$R1 3591
23 TraesCS3D01G234200 chr4B 425950650 425954220 3570 True 5101.0 5101 92.4270 6261 9852 1 chr4B.!!$R1 3591

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
18 19 1.377994 CTGAGTTTGAGGCTGCCCT 59.622 57.895 16.57 4.34 46.74 5.19 F
669 674 1.452108 GCTATGGGACCACACAGGC 60.452 63.158 0.00 0.00 43.14 4.85 F
1521 1560 0.806868 CAGATGCCAGCGTCAACAAT 59.193 50.000 13.99 0.00 34.59 2.71 F
2663 2731 0.532573 ACAAGACGGATCAGTGCGAT 59.467 50.000 2.27 0.00 42.26 4.58 F
3016 3115 0.473694 TCTCTCTCCCAAGCCCACAA 60.474 55.000 0.00 0.00 0.00 3.33 F
3322 3421 0.618680 ACCTAGATGGCAGCAGTCCA 60.619 55.000 5.19 0.00 40.22 4.02 F
4734 5133 0.750911 ACTTCTACGACCGCCCCTAG 60.751 60.000 0.00 0.00 0.00 3.02 F
5772 7040 0.597637 CCGTGTATAAGCGCTCAGGG 60.598 60.000 12.06 15.75 0.00 4.45 F
5921 7189 0.846693 AGCTATCTGGGCCGGAAAAT 59.153 50.000 21.02 5.57 0.00 1.82 F
7528 8828 0.805322 CTGGAGATCGTCTGCACAGC 60.805 60.000 5.39 0.00 39.98 4.40 F
8459 14789 0.603975 GCGCCTCAAAGACTTCCTGT 60.604 55.000 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 1551 1.044725 GCAGCGTTTGATTGTTGACG 58.955 50.000 0.00 0.0 38.45 4.35 R
1942 1983 1.359848 CTCATTGTGTACCGAGGCAC 58.640 55.000 0.00 0.0 36.26 5.01 R
2688 2757 0.396435 ATCCCACTTGCACGTCTCAA 59.604 50.000 0.00 0.0 0.00 3.02 R
4620 5019 0.380733 CGTACGCATCTACTCCTGCA 59.619 55.000 0.52 0.0 38.30 4.41 R
4763 5162 2.067365 AGGAAAACGAAGGCAGGTTT 57.933 45.000 0.00 0.0 37.94 3.27 R
5118 6381 5.336744 TCAACTTTTGAAGCGTTGTTAAGG 58.663 37.500 8.00 0.0 39.14 2.69 R
6590 7873 0.031043 TCGTTCGTTGACGTGTGGAT 59.969 50.000 0.00 0.0 43.23 3.41 R
6707 7994 0.471022 TGGTGTGAGTGGCCTGACTA 60.471 55.000 3.32 0.0 0.00 2.59 R
7622 13913 0.681887 TGGGAGGTTCATCGTCGCTA 60.682 55.000 0.00 0.0 41.98 4.26 R
8665 14996 1.377725 GTGGTCTGCCCTGTCCATG 60.378 63.158 0.00 0.0 32.45 3.66 R
9427 15781 4.067972 TGTTCAAGTGTACCAGAACTCC 57.932 45.455 14.26 0.0 40.62 3.85 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
17 18 3.993535 CTGAGTTTGAGGCTGCCC 58.006 61.111 16.57 7.66 0.00 5.36
18 19 1.377994 CTGAGTTTGAGGCTGCCCT 59.622 57.895 16.57 4.34 46.74 5.19
124 125 7.285401 TCAGCCTACTTCAAAGAAATTTTCTGT 59.715 33.333 12.27 4.17 40.59 3.41
421 426 2.088423 TGCAGAAGGAACAAAACACGT 58.912 42.857 0.00 0.00 0.00 4.49
552 557 2.224793 GGAAGAGCCCACAAAGTACCTT 60.225 50.000 0.00 0.00 0.00 3.50
669 674 1.452108 GCTATGGGACCACACAGGC 60.452 63.158 0.00 0.00 43.14 4.85
853 865 7.451255 CAGAGAAATACATCCTCAGGAGATACT 59.549 40.741 0.00 0.00 34.05 2.12
930 942 3.381272 CGTCAAACAAGGCATCCCAATAT 59.619 43.478 0.00 0.00 0.00 1.28
1013 1025 3.667087 GCAAATGGCGAGGTCACA 58.333 55.556 0.00 0.00 0.00 3.58
1077 1090 4.365514 TTCTGCTGAAAATGGAGGTGTA 57.634 40.909 3.21 0.00 0.00 2.90
1265 1278 3.848301 ATGGTGCTGCAGGCGAACA 62.848 57.895 17.12 0.71 45.43 3.18
1277 1290 2.030893 CAGGCGAACAACATGACAACAT 60.031 45.455 0.00 0.00 37.19 2.71
1462 1501 1.507630 GCATGCGGATTCTGCAACA 59.492 52.632 23.20 1.22 46.87 3.33
1521 1560 0.806868 CAGATGCCAGCGTCAACAAT 59.193 50.000 13.99 0.00 34.59 2.71
1537 1576 1.675483 ACAATCAAACGCTGCACAAGA 59.325 42.857 0.00 0.00 0.00 3.02
1539 1578 3.114809 CAATCAAACGCTGCACAAGAAA 58.885 40.909 0.00 0.00 0.00 2.52
1549 1588 2.036217 CTGCACAAGAAAATTGGAGCCA 59.964 45.455 0.00 0.00 0.00 4.75
1567 1606 3.332485 AGCCACCCAAGTTTCTACCAATA 59.668 43.478 0.00 0.00 0.00 1.90
1728 1768 7.821359 TCAAATGAAGACGATGAAGAAGAAGAT 59.179 33.333 0.00 0.00 0.00 2.40
1942 1983 9.220767 ACTGAAAAATAAGCTTGTAGTCTTAGG 57.779 33.333 9.86 0.00 0.00 2.69
2186 2228 0.601558 TGTCGACCAGTAACTCAGCC 59.398 55.000 14.12 0.00 0.00 4.85
2364 2412 6.483640 AGTTCAGAAAGACCATCAGTACAAAC 59.516 38.462 0.00 0.00 0.00 2.93
2581 2649 5.453866 AGTACCACAGTAGAGGAGTACAT 57.546 43.478 0.00 0.00 34.03 2.29
2663 2731 0.532573 ACAAGACGGATCAGTGCGAT 59.467 50.000 2.27 0.00 42.26 4.58
2688 2757 0.632835 AATGCCATCATCACCACCCT 59.367 50.000 0.00 0.00 31.27 4.34
2897 2996 3.338250 GCCTCCCACACATCCCCA 61.338 66.667 0.00 0.00 0.00 4.96
2935 3034 2.200955 ACCCCTTTCTCTTCCATCTCC 58.799 52.381 0.00 0.00 0.00 3.71
2965 3064 2.683572 GGAACCACCATTGCCCCC 60.684 66.667 0.00 0.00 38.79 5.40
2979 3078 1.575447 GCCCCCTTCCATCTCCACTT 61.575 60.000 0.00 0.00 0.00 3.16
3016 3115 0.473694 TCTCTCTCCCAAGCCCACAA 60.474 55.000 0.00 0.00 0.00 3.33
3264 3363 1.504647 CGGCTAGCGTCGTAGGATCA 61.505 60.000 9.00 0.00 32.61 2.92
3267 3366 1.135632 GCTAGCGTCGTAGGATCATCC 60.136 57.143 0.00 0.00 36.58 3.51
3303 3402 4.525487 ACTACACCAACGAAGATGAACCTA 59.475 41.667 0.00 0.00 29.10 3.08
3322 3421 0.618680 ACCTAGATGGCAGCAGTCCA 60.619 55.000 5.19 0.00 40.22 4.02
3371 3470 4.075854 TACCACATCGCAGCGGCA 62.076 61.111 16.42 0.00 41.24 5.69
3422 3522 4.440839 CCCTGTTTGGCTTATCTGTTTC 57.559 45.455 0.00 0.00 0.00 2.78
3461 3561 9.480053 TCCTGAAAATTTCATCAGATTTGTTTC 57.520 29.630 17.71 0.00 44.64 2.78
3497 3597 7.329499 TGTACTAGTGTGGTTTGTGAAAAGTA 58.671 34.615 5.39 0.00 0.00 2.24
3585 3685 6.417930 GGATTACTATTTGGAAAATCTTGCGC 59.582 38.462 0.00 0.00 0.00 6.09
3650 3753 9.383519 ACTTGATCCAATAGTGTAGTTTATGTG 57.616 33.333 0.00 0.00 0.00 3.21
3809 3913 9.617523 AAAGTAAACTAAACTAGTACCAAAGCA 57.382 29.630 0.00 0.00 38.26 3.91
3810 3914 8.828688 AGTAAACTAAACTAGTACCAAAGCAG 57.171 34.615 0.00 0.00 38.26 4.24
3811 3915 8.645110 AGTAAACTAAACTAGTACCAAAGCAGA 58.355 33.333 0.00 0.00 38.26 4.26
3812 3916 9.264719 GTAAACTAAACTAGTACCAAAGCAGAA 57.735 33.333 0.00 0.00 38.26 3.02
3813 3917 7.725818 AACTAAACTAGTACCAAAGCAGAAC 57.274 36.000 0.00 0.00 38.26 3.01
3814 3918 6.823497 ACTAAACTAGTACCAAAGCAGAACA 58.177 36.000 0.00 0.00 37.23 3.18
3815 3919 7.450903 ACTAAACTAGTACCAAAGCAGAACAT 58.549 34.615 0.00 0.00 37.23 2.71
3816 3920 8.591072 ACTAAACTAGTACCAAAGCAGAACATA 58.409 33.333 0.00 0.00 37.23 2.29
3817 3921 7.668525 AAACTAGTACCAAAGCAGAACATAC 57.331 36.000 0.00 0.00 0.00 2.39
3818 3922 6.354794 ACTAGTACCAAAGCAGAACATACA 57.645 37.500 0.00 0.00 0.00 2.29
3819 3923 6.765403 ACTAGTACCAAAGCAGAACATACAA 58.235 36.000 0.00 0.00 0.00 2.41
3820 3924 5.941948 AGTACCAAAGCAGAACATACAAC 57.058 39.130 0.00 0.00 0.00 3.32
3821 3925 5.373222 AGTACCAAAGCAGAACATACAACA 58.627 37.500 0.00 0.00 0.00 3.33
3822 3926 6.003950 AGTACCAAAGCAGAACATACAACAT 58.996 36.000 0.00 0.00 0.00 2.71
3823 3927 5.789643 ACCAAAGCAGAACATACAACATT 57.210 34.783 0.00 0.00 0.00 2.71
3824 3928 5.531634 ACCAAAGCAGAACATACAACATTG 58.468 37.500 0.00 0.00 0.00 2.82
3825 3929 5.301551 ACCAAAGCAGAACATACAACATTGA 59.698 36.000 0.00 0.00 0.00 2.57
3826 3930 5.630680 CCAAAGCAGAACATACAACATTGAC 59.369 40.000 0.00 0.00 0.00 3.18
3827 3931 6.441274 CAAAGCAGAACATACAACATTGACT 58.559 36.000 0.00 0.00 0.00 3.41
3828 3932 5.618056 AGCAGAACATACAACATTGACTG 57.382 39.130 0.00 0.00 0.00 3.51
3829 3933 5.308014 AGCAGAACATACAACATTGACTGA 58.692 37.500 0.00 0.00 0.00 3.41
3830 3934 5.764686 AGCAGAACATACAACATTGACTGAA 59.235 36.000 0.00 0.00 0.00 3.02
3831 3935 6.262944 AGCAGAACATACAACATTGACTGAAA 59.737 34.615 0.00 0.00 0.00 2.69
3832 3936 6.360681 GCAGAACATACAACATTGACTGAAAC 59.639 38.462 0.00 0.00 0.00 2.78
3833 3937 7.642669 CAGAACATACAACATTGACTGAAACT 58.357 34.615 0.00 0.00 0.00 2.66
3834 3938 8.773645 CAGAACATACAACATTGACTGAAACTA 58.226 33.333 0.00 0.00 0.00 2.24
3835 3939 9.507329 AGAACATACAACATTGACTGAAACTAT 57.493 29.630 0.00 0.00 0.00 2.12
3836 3940 9.546909 GAACATACAACATTGACTGAAACTATG 57.453 33.333 0.00 0.00 0.00 2.23
3837 3941 8.621532 ACATACAACATTGACTGAAACTATGT 57.378 30.769 0.00 0.00 35.89 2.29
3838 3942 9.719355 ACATACAACATTGACTGAAACTATGTA 57.281 29.630 0.00 0.00 34.06 2.29
3845 3949 9.561069 ACATTGACTGAAACTATGTATAATCCC 57.439 33.333 0.00 0.00 33.60 3.85
3846 3950 9.559732 CATTGACTGAAACTATGTATAATCCCA 57.440 33.333 0.00 0.00 0.00 4.37
3848 3952 9.967451 TTGACTGAAACTATGTATAATCCCAAA 57.033 29.630 0.00 0.00 0.00 3.28
3849 3953 9.967451 TGACTGAAACTATGTATAATCCCAAAA 57.033 29.630 0.00 0.00 0.00 2.44
3903 4007 9.661563 TTCAGAACTTTGTTTACTAGTTTCTGA 57.338 29.630 20.60 20.60 36.04 3.27
3904 4008 9.661563 TCAGAACTTTGTTTACTAGTTTCTGAA 57.338 29.630 21.56 11.09 35.56 3.02
3905 4009 9.922305 CAGAACTTTGTTTACTAGTTTCTGAAG 57.078 33.333 18.52 12.46 33.65 3.02
3906 4010 9.668497 AGAACTTTGTTTACTAGTTTCTGAAGT 57.332 29.630 0.00 4.40 32.58 3.01
3909 4013 9.880157 ACTTTGTTTACTAGTTTCTGAAGTACA 57.120 29.630 0.00 0.00 0.00 2.90
3916 4020 9.871238 TTACTAGTTTCTGAAGTACATTCATCC 57.129 33.333 0.00 0.00 46.71 3.51
3917 4021 7.907389 ACTAGTTTCTGAAGTACATTCATCCA 58.093 34.615 0.00 0.00 46.71 3.41
3918 4022 8.543774 ACTAGTTTCTGAAGTACATTCATCCAT 58.456 33.333 0.00 0.00 46.71 3.41
3919 4023 9.388506 CTAGTTTCTGAAGTACATTCATCCATT 57.611 33.333 0.00 0.00 46.71 3.16
3921 4025 9.739276 AGTTTCTGAAGTACATTCATCCATTAA 57.261 29.630 0.00 0.00 46.71 1.40
3975 4079 8.853077 ATTCATGTTTCTGAACTTGATGTAGA 57.147 30.769 8.17 0.00 44.46 2.59
3999 4103 9.007901 AGAGAAGTATTTTCTGAATTTGGTCTG 57.992 33.333 0.00 0.00 0.00 3.51
4011 4115 8.236586 TCTGAATTTGGTCTGATGTTATTTTCG 58.763 33.333 0.00 0.00 0.00 3.46
4056 4161 3.314913 TGTGAAGCACTGGTTATGTGTTG 59.685 43.478 0.00 0.00 37.70 3.33
4060 4165 2.158682 AGCACTGGTTATGTGTTGTCCA 60.159 45.455 0.00 0.00 37.70 4.02
4064 4169 5.221880 CACTGGTTATGTGTTGTCCAATTG 58.778 41.667 0.00 0.00 0.00 2.32
4457 4856 3.402110 ACAAGTTCATCGACATTCAGCA 58.598 40.909 0.00 0.00 0.00 4.41
4511 4910 2.365617 ACGACTCCTTGACTGATGTTGT 59.634 45.455 0.00 0.00 0.00 3.32
4620 5019 2.101582 GCCAGACAACCTCATCGAGTAT 59.898 50.000 0.00 0.00 0.00 2.12
4671 5070 7.374272 ACAAGTCATGGATCATAATCGACTAG 58.626 38.462 0.00 0.00 32.34 2.57
4734 5133 0.750911 ACTTCTACGACCGCCCCTAG 60.751 60.000 0.00 0.00 0.00 3.02
4747 5146 1.518367 CCCCTAGTGCCCCTTTATGA 58.482 55.000 0.00 0.00 0.00 2.15
4763 5162 8.159447 CCCCTTTATGAGATGAAGATACATCAA 58.841 37.037 0.00 0.00 46.11 2.57
5062 6325 5.355910 ACAACGTTGTTCCATGTCTAGTTTT 59.644 36.000 27.70 0.00 38.47 2.43
5118 6381 6.833342 AAACAATCAGCACAATTTGAGTTC 57.167 33.333 2.79 0.00 0.00 3.01
5180 6443 8.539770 AGTACTTCATGTAGTGTTCTCATTTG 57.460 34.615 14.64 0.00 33.81 2.32
5253 6516 3.822735 AGCATCAGCACACACTTATGTTT 59.177 39.130 0.00 0.00 45.49 2.83
5276 6539 7.692460 TTGTCACTTGCAGATTAAGAATGAT 57.308 32.000 0.00 0.00 0.00 2.45
5410 6674 7.727181 ACTATGAATGGACTATCAGTACAACC 58.273 38.462 0.00 0.00 43.35 3.77
5544 6809 7.209471 ACACTTACACAAAACTGACAAGAAA 57.791 32.000 0.00 0.00 0.00 2.52
5560 6825 9.573133 CTGACAAGAAACAGAACAAAAAGTATT 57.427 29.630 0.00 0.00 36.38 1.89
5737 7003 4.351054 CCAGGGCCCACAGGTCAC 62.351 72.222 27.56 0.00 40.78 3.67
5772 7040 0.597637 CCGTGTATAAGCGCTCAGGG 60.598 60.000 12.06 15.75 0.00 4.45
5921 7189 0.846693 AGCTATCTGGGCCGGAAAAT 59.153 50.000 21.02 5.57 0.00 1.82
6032 7302 9.974980 ACAAGAAAAAGTGTTTTAGTTCTTGAA 57.025 25.926 23.49 0.00 44.48 2.69
6037 7307 9.974980 AAAAAGTGTTTTAGTTCTTGAAACTGA 57.025 25.926 0.81 0.00 36.51 3.41
6038 7308 9.974980 AAAAGTGTTTTAGTTCTTGAAACTGAA 57.025 25.926 0.81 0.00 36.51 3.02
6039 7309 9.974980 AAAGTGTTTTAGTTCTTGAAACTGAAA 57.025 25.926 4.38 4.38 36.51 2.69
6040 7310 9.974980 AAGTGTTTTAGTTCTTGAAACTGAAAA 57.025 25.926 8.77 5.75 37.44 2.29
6102 7373 6.995511 TCGCAGGCAATAACTTTAAATACT 57.004 33.333 0.00 0.00 0.00 2.12
6150 7423 3.681594 GCTCTCCACCACGGATGATAAAA 60.682 47.826 0.00 0.00 45.19 1.52
6151 7424 4.122776 CTCTCCACCACGGATGATAAAAG 58.877 47.826 0.00 0.00 45.19 2.27
6647 7931 3.668142 AATCCCCCAACCCACCCG 61.668 66.667 0.00 0.00 0.00 5.28
6728 8016 2.281761 CAGGCCACTCACACCACC 60.282 66.667 5.01 0.00 0.00 4.61
6900 8190 0.890996 CAACAACTCCCAGGGCACTC 60.891 60.000 0.00 0.00 0.00 3.51
6993 8290 3.664107 ACATCACAAAGCATACGTCACT 58.336 40.909 0.00 0.00 0.00 3.41
7111 8409 5.359860 ACAGTAAAAACCCTTTGACTTGGAG 59.640 40.000 0.00 0.00 34.43 3.86
7165 8463 1.597854 CTGAGCGGTTGCCACAAGA 60.598 57.895 0.00 0.00 44.31 3.02
7403 8703 3.909662 GCCAAGCGTCATCATGGT 58.090 55.556 0.00 0.00 35.34 3.55
7415 8715 1.402896 ATCATGGTGAGCCGTCGGAT 61.403 55.000 17.49 9.33 37.67 4.18
7421 8721 1.022735 GTGAGCCGTCGGATAAGAGA 58.977 55.000 17.49 0.00 0.00 3.10
7526 8826 1.216444 GCTGGAGATCGTCTGCACA 59.784 57.895 12.60 0.00 39.98 4.57
7528 8828 0.805322 CTGGAGATCGTCTGCACAGC 60.805 60.000 5.39 0.00 39.98 4.40
7688 13980 4.809070 AGGAACTCTGCTTGGTGC 57.191 55.556 0.00 0.00 43.25 5.01
7701 13993 3.434319 GGTGCACCACATCGCAGG 61.434 66.667 31.23 0.00 39.20 4.85
7753 14045 9.639601 CTGTTCATTCATCTGTTGTACTAGTAA 57.360 33.333 3.61 0.00 0.00 2.24
8053 14371 3.117491 AGGTCCATATCTTGATGCACG 57.883 47.619 0.00 0.00 0.00 5.34
8218 14540 7.894708 TGATTCTTGAATTTGGTGAAGCATTA 58.105 30.769 0.00 0.00 29.84 1.90
8387 14715 7.873739 ACCAAAAAGCAGAAGAATTAAATCG 57.126 32.000 0.00 0.00 0.00 3.34
8459 14789 0.603975 GCGCCTCAAAGACTTCCTGT 60.604 55.000 0.00 0.00 0.00 4.00
8665 14996 1.160137 ACAGCGGCATGAAGAAGAAC 58.840 50.000 1.45 0.00 0.00 3.01
9722 16158 1.167851 AGCATCAACCCACATTGACG 58.832 50.000 0.00 0.00 41.29 4.35
9757 16193 9.139174 ACTAGTTTCAAACAACACAAGAAAATG 57.861 29.630 2.41 0.00 30.52 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 8.660373 GTTGTACTTATCCATGAGTCTTTTCAG 58.340 37.037 0.00 0.00 0.00 3.02
18 19 7.606456 GGTTGTACTTATCCATGAGTCTTTTCA 59.394 37.037 0.00 0.00 0.00 2.69
124 125 2.314246 TGTGTGGATGTCATTTTGGCA 58.686 42.857 0.00 0.00 35.91 4.92
361 364 7.174253 TGACCAAATTATTAGTTTTCTCGCAGT 59.826 33.333 0.00 0.00 0.00 4.40
421 426 4.394729 GTGTCAAACCCATAGAAGGTCAA 58.605 43.478 0.00 0.00 36.27 3.18
552 557 1.153147 TGGGTTGTTGTAGCGCACA 60.153 52.632 11.47 9.55 34.51 4.57
853 865 1.673009 GGATGTTCGGGCGTTTGGA 60.673 57.895 0.00 0.00 0.00 3.53
1013 1025 2.104111 TCAAGTTTGTCCATGACGACCT 59.896 45.455 0.00 0.00 34.95 3.85
1077 1090 3.271250 AATGGCTTCATTGTCCGCT 57.729 47.368 0.00 0.00 39.43 5.52
1277 1290 1.960040 CTGCTGCCGGTAGGATGTCA 61.960 60.000 21.82 9.02 41.02 3.58
1462 1501 3.737047 CGGTAGTTATGGTTGCTCACGAT 60.737 47.826 0.00 0.00 0.00 3.73
1512 1551 1.044725 GCAGCGTTTGATTGTTGACG 58.955 50.000 0.00 0.00 38.45 4.35
1521 1560 2.929531 TTTTCTTGTGCAGCGTTTGA 57.070 40.000 0.00 0.00 0.00 2.69
1537 1576 2.101640 ACTTGGGTGGCTCCAATTTT 57.898 45.000 8.03 0.00 44.79 1.82
1539 1578 1.970640 GAAACTTGGGTGGCTCCAATT 59.029 47.619 8.03 2.92 44.79 2.32
1549 1588 5.546499 TGTCTCTATTGGTAGAAACTTGGGT 59.454 40.000 0.00 0.00 36.54 4.51
1567 1606 2.100916 AGCTGTTACGTGTGTTGTCTCT 59.899 45.455 0.00 0.00 0.00 3.10
1728 1768 3.100658 TGGTCGTCATTCTCGTCAAAA 57.899 42.857 0.00 0.00 0.00 2.44
1942 1983 1.359848 CTCATTGTGTACCGAGGCAC 58.640 55.000 0.00 0.00 36.26 5.01
2038 2079 5.624900 CGGGCACAAATCACAAATTATATCG 59.375 40.000 0.00 0.00 0.00 2.92
2364 2412 7.275341 TCGCATTTTGCTTGAGGTAATTATTTG 59.725 33.333 0.00 0.00 42.25 2.32
2483 2547 8.932945 TGTGTGATGCTAATGTTTTTAAAACA 57.067 26.923 22.90 22.90 34.31 2.83
2581 2649 1.843851 GGGTTGGTGATGATGGAGGTA 59.156 52.381 0.00 0.00 0.00 3.08
2663 2731 4.887071 GGTGGTGATGATGGCATTTTACTA 59.113 41.667 0.00 0.00 34.11 1.82
2688 2757 0.396435 ATCCCACTTGCACGTCTCAA 59.604 50.000 0.00 0.00 0.00 3.02
2897 2996 1.396996 GGTATTTTGCAGTGCGTCGAT 59.603 47.619 11.20 4.61 0.00 3.59
2965 3064 3.407424 TGTGTGAAGTGGAGATGGAAG 57.593 47.619 0.00 0.00 0.00 3.46
2979 3078 5.710099 AGAGAGAAGTTTTTGGTTTGTGTGA 59.290 36.000 0.00 0.00 0.00 3.58
3049 3148 2.182496 CCATGATGACGCTTGGCAA 58.818 52.632 0.00 0.00 0.00 4.52
3050 3149 3.908189 CCATGATGACGCTTGGCA 58.092 55.556 0.00 0.00 0.00 4.92
3173 3272 2.711922 GGTGCGGACGATCTCCAGT 61.712 63.158 0.00 0.00 39.39 4.00
3241 3340 1.515519 CTACGACGCTAGCCGCAAA 60.516 57.895 9.66 0.00 41.76 3.68
3264 3363 2.443260 TAGTGCACACCAACGCGGAT 62.443 55.000 21.04 0.00 38.63 4.18
3267 3366 2.241190 TGTAGTGCACACCAACGCG 61.241 57.895 21.04 3.53 30.04 6.01
3289 3388 4.585162 CCATCTAGGTAGGTTCATCTTCGT 59.415 45.833 0.00 0.00 0.00 3.85
3303 3402 0.618680 TGGACTGCTGCCATCTAGGT 60.619 55.000 0.00 0.00 40.61 3.08
3322 3421 3.030308 CGTCGACGCACAACTGCT 61.030 61.111 26.59 0.00 41.77 4.24
3454 3554 6.195600 AGTACATCTAGTTGGGGAAACAAA 57.804 37.500 5.80 0.00 41.61 2.83
3650 3753 9.214953 CAGAAACATCTTTTTAATACATCGAGC 57.785 33.333 0.00 0.00 0.00 5.03
3798 3902 5.373222 TGTTGTATGTTCTGCTTTGGTACT 58.627 37.500 0.00 0.00 0.00 2.73
3799 3903 5.682943 TGTTGTATGTTCTGCTTTGGTAC 57.317 39.130 0.00 0.00 0.00 3.34
3800 3904 6.488344 TCAATGTTGTATGTTCTGCTTTGGTA 59.512 34.615 0.00 0.00 0.00 3.25
3801 3905 5.301551 TCAATGTTGTATGTTCTGCTTTGGT 59.698 36.000 0.00 0.00 0.00 3.67
3802 3906 5.630680 GTCAATGTTGTATGTTCTGCTTTGG 59.369 40.000 0.00 0.00 0.00 3.28
3803 3907 6.361481 CAGTCAATGTTGTATGTTCTGCTTTG 59.639 38.462 0.00 0.00 0.00 2.77
3804 3908 6.262944 TCAGTCAATGTTGTATGTTCTGCTTT 59.737 34.615 0.00 0.00 0.00 3.51
3805 3909 5.764686 TCAGTCAATGTTGTATGTTCTGCTT 59.235 36.000 0.00 0.00 0.00 3.91
3806 3910 5.308014 TCAGTCAATGTTGTATGTTCTGCT 58.692 37.500 0.00 0.00 0.00 4.24
3807 3911 5.611796 TCAGTCAATGTTGTATGTTCTGC 57.388 39.130 0.00 0.00 0.00 4.26
3808 3912 7.642669 AGTTTCAGTCAATGTTGTATGTTCTG 58.357 34.615 0.00 0.00 0.00 3.02
3809 3913 7.807977 AGTTTCAGTCAATGTTGTATGTTCT 57.192 32.000 0.00 0.00 0.00 3.01
3810 3914 9.546909 CATAGTTTCAGTCAATGTTGTATGTTC 57.453 33.333 0.00 0.00 0.00 3.18
3811 3915 9.066892 ACATAGTTTCAGTCAATGTTGTATGTT 57.933 29.630 0.00 0.00 0.00 2.71
3812 3916 8.621532 ACATAGTTTCAGTCAATGTTGTATGT 57.378 30.769 0.00 0.00 0.00 2.29
3819 3923 9.561069 GGGATTATACATAGTTTCAGTCAATGT 57.439 33.333 0.00 0.00 35.16 2.71
3820 3924 9.559732 TGGGATTATACATAGTTTCAGTCAATG 57.440 33.333 0.00 0.00 0.00 2.82
3822 3926 9.967451 TTTGGGATTATACATAGTTTCAGTCAA 57.033 29.630 0.00 0.00 0.00 3.18
3823 3927 9.967451 TTTTGGGATTATACATAGTTTCAGTCA 57.033 29.630 0.00 0.00 0.00 3.41
3877 3981 9.661563 TCAGAAACTAGTAAACAAAGTTCTGAA 57.338 29.630 21.56 11.09 36.11 3.02
3878 3982 9.661563 TTCAGAAACTAGTAAACAAAGTTCTGA 57.338 29.630 20.60 20.60 36.61 3.27
3879 3983 9.922305 CTTCAGAAACTAGTAAACAAAGTTCTG 57.078 33.333 17.72 17.72 32.42 3.02
3880 3984 9.668497 ACTTCAGAAACTAGTAAACAAAGTTCT 57.332 29.630 0.00 0.00 32.42 3.01
3883 3987 9.880157 TGTACTTCAGAAACTAGTAAACAAAGT 57.120 29.630 13.87 13.87 0.00 2.66
3890 3994 9.871238 GGATGAATGTACTTCAGAAACTAGTAA 57.129 33.333 0.00 0.00 46.71 2.24
3891 3995 9.031537 TGGATGAATGTACTTCAGAAACTAGTA 57.968 33.333 0.00 0.00 46.71 1.82
3892 3996 7.907389 TGGATGAATGTACTTCAGAAACTAGT 58.093 34.615 11.60 0.00 46.71 2.57
3893 3997 8.954950 ATGGATGAATGTACTTCAGAAACTAG 57.045 34.615 11.60 0.00 46.71 2.57
3895 3999 9.739276 TTAATGGATGAATGTACTTCAGAAACT 57.261 29.630 11.60 0.00 46.71 2.66
3946 4050 7.177921 ACATCAAGTTCAGAAACATGAATCCAT 59.822 33.333 0.00 0.00 43.86 3.41
3947 4051 6.491062 ACATCAAGTTCAGAAACATGAATCCA 59.509 34.615 0.00 0.00 43.86 3.41
3948 4052 6.917533 ACATCAAGTTCAGAAACATGAATCC 58.082 36.000 0.00 0.00 43.86 3.01
3949 4053 8.939929 TCTACATCAAGTTCAGAAACATGAATC 58.060 33.333 0.00 0.00 43.86 2.52
3950 4054 8.853077 TCTACATCAAGTTCAGAAACATGAAT 57.147 30.769 0.00 0.00 43.86 2.57
3951 4055 8.150296 TCTCTACATCAAGTTCAGAAACATGAA 58.850 33.333 0.00 0.00 43.86 2.57
3952 4056 7.670364 TCTCTACATCAAGTTCAGAAACATGA 58.330 34.615 0.00 0.00 44.51 3.07
3953 4057 7.895975 TCTCTACATCAAGTTCAGAAACATG 57.104 36.000 0.00 0.00 37.88 3.21
3975 4079 8.924511 TCAGACCAAATTCAGAAAATACTTCT 57.075 30.769 0.00 0.00 0.00 2.85
3995 4099 8.722342 TTTTGCTTACGAAAATAACATCAGAC 57.278 30.769 0.00 0.00 0.00 3.51
4029 4134 4.644685 ACATAACCAGTGCTTCACAAAGTT 59.355 37.500 0.00 2.99 36.74 2.66
4034 4139 3.207265 ACACATAACCAGTGCTTCACA 57.793 42.857 0.00 0.00 40.59 3.58
4511 4910 2.731571 GGGTGGATGACGCTGGCTA 61.732 63.158 0.00 0.00 34.65 3.93
4620 5019 0.380733 CGTACGCATCTACTCCTGCA 59.619 55.000 0.52 0.00 38.30 4.41
4671 5070 5.106038 TGCAAATTCTGAACCATCTGTGATC 60.106 40.000 0.00 0.00 0.00 2.92
4734 5133 4.156455 TCTTCATCTCATAAAGGGGCAC 57.844 45.455 0.00 0.00 0.00 5.01
4747 5146 5.591877 GGCAGGTTTTGATGTATCTTCATCT 59.408 40.000 7.92 0.00 43.03 2.90
4763 5162 2.067365 AGGAAAACGAAGGCAGGTTT 57.933 45.000 0.00 0.00 37.94 3.27
5118 6381 5.336744 TCAACTTTTGAAGCGTTGTTAAGG 58.663 37.500 8.00 0.00 39.14 2.69
5179 6442 9.443323 TTGTTAATTTTCTAGCAGCTACATACA 57.557 29.630 0.00 0.00 0.00 2.29
5180 6443 9.922305 CTTGTTAATTTTCTAGCAGCTACATAC 57.078 33.333 0.00 0.00 0.00 2.39
5216 6479 7.228507 TGTGCTGATGCTTCTTAACTTTTTCTA 59.771 33.333 0.88 0.00 40.48 2.10
5253 6516 8.043113 ACTATCATTCTTAATCTGCAAGTGACA 58.957 33.333 0.00 0.00 33.76 3.58
5276 6539 6.643388 TGTCCGATCAAGTGTACTAGTACTA 58.357 40.000 28.56 15.40 37.00 1.82
5410 6674 4.634184 ATGGTACTTGCGTGTAGACTAG 57.366 45.455 0.00 0.00 0.00 2.57
5544 6809 8.747538 ACTTGGACTAATACTTTTTGTTCTGT 57.252 30.769 0.00 0.00 0.00 3.41
5560 6825 3.830755 GACTCCACCAGTAACTTGGACTA 59.169 47.826 0.00 0.00 40.87 2.59
5737 7003 4.605967 GGCGCTCGCTCTCTCTCG 62.606 72.222 7.64 0.00 41.60 4.04
5772 7040 4.158025 TGGTCGAACTCCTCTGAATACTTC 59.842 45.833 0.33 0.00 0.00 3.01
5893 7161 2.050895 CAGATAGCTCGTCCGCGG 60.051 66.667 22.12 22.12 38.89 6.46
6133 7406 5.393027 CCTTTTCTTTTATCATCCGTGGTGG 60.393 44.000 0.00 0.00 40.09 4.61
6590 7873 0.031043 TCGTTCGTTGACGTGTGGAT 59.969 50.000 0.00 0.00 43.23 3.41
6598 7881 0.982673 CGACCAGATCGTTCGTTGAC 59.017 55.000 5.73 0.00 46.25 3.18
6659 7946 9.936759 TGTCATATGTATGTTTGAACTGAGTTA 57.063 29.630 0.00 0.00 35.26 2.24
6707 7994 0.471022 TGGTGTGAGTGGCCTGACTA 60.471 55.000 3.32 0.00 0.00 2.59
6728 8016 3.241784 CGGTTTTGAAATTTGGTGTCACG 59.758 43.478 0.00 0.00 0.00 4.35
7111 8409 1.979155 GGCCTGGAAGAAGCAACCC 60.979 63.158 0.00 0.00 34.07 4.11
7165 8463 2.430367 GGTCCCCGTTTGCAGTCT 59.570 61.111 0.00 0.00 0.00 3.24
7403 8703 1.676529 CTTCTCTTATCCGACGGCTCA 59.323 52.381 9.66 0.00 0.00 4.26
7415 8715 2.244695 TGGACGAGGTTGCTTCTCTTA 58.755 47.619 0.00 0.00 0.00 2.10
7421 8721 1.202758 TGAACATGGACGAGGTTGCTT 60.203 47.619 0.00 0.00 0.00 3.91
7507 8807 1.253593 TGTGCAGACGATCTCCAGCT 61.254 55.000 0.00 0.00 0.00 4.24
7526 8826 2.032681 GCCTTGTCTGGTTCGGCT 59.967 61.111 0.00 0.00 37.76 5.52
7528 8828 2.742372 CGGCCTTGTCTGGTTCGG 60.742 66.667 0.00 0.00 0.00 4.30
7571 13862 3.638592 ATACAAGCCGCCGCCCTTT 62.639 57.895 0.00 0.00 34.57 3.11
7622 13913 0.681887 TGGGAGGTTCATCGTCGCTA 60.682 55.000 0.00 0.00 41.98 4.26
7688 13980 2.821366 GGCTCCTGCGATGTGGTG 60.821 66.667 0.00 0.00 40.82 4.17
8218 14540 2.568956 TGCTATCTTCAGTGCTTCACCT 59.431 45.455 0.00 0.00 34.49 4.00
8459 14789 7.458397 ACAAATGTGTACAATTTCTCCTCCTA 58.542 34.615 0.00 0.00 35.72 2.94
8665 14996 1.377725 GTGGTCTGCCCTGTCCATG 60.378 63.158 0.00 0.00 32.45 3.66
9019 15365 3.625764 AGCTAGCAAACTTGTTGAACGAA 59.374 39.130 18.83 0.00 0.00 3.85
9427 15781 4.067972 TGTTCAAGTGTACCAGAACTCC 57.932 45.455 14.26 0.00 40.62 3.85
9490 15855 4.963276 TTTATGGAATGCGAACTGAAGG 57.037 40.909 0.00 0.00 0.00 3.46
9722 16158 4.127171 TGTTTGAAACTAGTGCCTCACTC 58.873 43.478 9.69 0.00 41.21 3.51
9757 16193 9.282247 CAATTGTGCTAGTACTTTGATCATTTC 57.718 33.333 12.42 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.