Multiple sequence alignment - TraesCS3A01G253500

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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 TraesCS3A01G253500 chr3A 100.000 3751 0 0 1 3751 474813155 474809405 0.000000e+00 6927.0
1 TraesCS3A01G253500 chr3A 86.189 391 54 0 1812 2202 33000434 33000824 1.250000e-114 424.0
2 TraesCS3A01G253500 chr3A 85.556 90 10 3 1292 1381 120296205 120296291 1.430000e-14 91.6
3 TraesCS3A01G253500 chr3B 92.741 2714 158 20 1 2694 456982932 456980238 0.000000e+00 3884.0
4 TraesCS3A01G253500 chr3B 83.717 651 97 8 2783 3428 825271732 825271086 1.150000e-169 606.0
5 TraesCS3A01G253500 chr3B 85.749 407 58 0 1820 2226 41857694 41858100 7.440000e-117 431.0
6 TraesCS3A01G253500 chr3B 87.379 206 26 0 1181 1386 41857071 41857276 1.740000e-58 237.0
7 TraesCS3A01G253500 chr3B 95.506 89 4 0 3497 3585 456980091 456980003 3.910000e-30 143.0
8 TraesCS3A01G253500 chr3B 96.721 61 2 0 2714 2774 456980164 456980104 6.630000e-18 102.0
9 TraesCS3A01G253500 chr3B 98.214 56 1 0 3617 3672 456979463 456979408 8.570000e-17 99.0
10 TraesCS3A01G253500 chr3D 94.553 2313 99 19 386 2688 355796827 355794532 0.000000e+00 3548.0
11 TraesCS3A01G253500 chr3D 87.330 884 89 14 2714 3589 355793229 355792361 0.000000e+00 990.0
12 TraesCS3A01G253500 chr3D 93.386 378 24 1 1 377 355797445 355797068 3.270000e-155 558.0
13 TraesCS3A01G253500 chr3D 86.957 391 51 0 1812 2202 23744723 23745113 1.240000e-119 440.0
14 TraesCS3A01G253500 chr3D 83.232 328 40 9 1064 1386 23743991 23744308 1.700000e-73 287.0
15 TraesCS3A01G253500 chr3D 81.818 319 43 10 1073 1386 23746315 23746623 1.730000e-63 254.0
16 TraesCS3A01G253500 chr3D 77.143 455 75 18 336 774 388310171 388309730 1.740000e-58 237.0
17 TraesCS3A01G253500 chr3D 93.333 90 3 2 3583 3672 355792319 355792233 3.040000e-26 130.0
18 TraesCS3A01G253500 chr2B 83.703 1534 190 33 1039 2544 144078575 144077074 0.000000e+00 1393.0
19 TraesCS3A01G253500 chr2B 84.987 786 84 22 1445 2226 144034724 144035479 0.000000e+00 767.0
20 TraesCS3A01G253500 chr5A 98.293 703 12 0 2066 2768 627486372 627485670 0.000000e+00 1232.0
21 TraesCS3A01G253500 chr2D 83.284 1017 129 21 1039 2042 92891476 92892464 0.000000e+00 898.0
22 TraesCS3A01G253500 chr2D 84.713 785 91 20 1445 2226 92832185 92832943 0.000000e+00 758.0
23 TraesCS3A01G253500 chr2D 83.232 656 94 11 2782 3429 53791717 53792364 4.170000e-164 588.0
24 TraesCS3A01G253500 chr2D 90.617 405 38 0 1821 2225 92889411 92889815 4.260000e-149 538.0
25 TraesCS3A01G253500 chr2D 87.838 222 24 1 2320 2541 92912162 92912380 1.340000e-64 257.0
26 TraesCS3A01G253500 chr2D 87.963 216 26 0 1169 1384 92831856 92832071 4.810000e-64 255.0
27 TraesCS3A01G253500 chr2D 80.242 248 43 4 185 430 29756222 29756465 8.280000e-42 182.0
28 TraesCS3A01G253500 chr2D 84.106 151 20 3 2390 2539 92737693 92737840 3.910000e-30 143.0
29 TraesCS3A01G253500 chr7B 84.959 605 86 5 2782 3383 217303936 217303334 3.200000e-170 608.0
30 TraesCS3A01G253500 chrUn 83.333 654 98 10 2781 3428 8241764 8241116 8.970000e-166 593.0
31 TraesCS3A01G253500 chrUn 83.333 654 97 11 2781 3428 399760466 399759819 8.970000e-166 593.0
32 TraesCS3A01G253500 chrUn 81.176 255 40 6 185 438 452972429 452972676 8.220000e-47 198.0
33 TraesCS3A01G253500 chrUn 81.176 255 40 6 185 438 453010754 453011001 8.220000e-47 198.0
34 TraesCS3A01G253500 chr4A 83.207 661 95 13 2780 3433 21229120 21229771 3.230000e-165 592.0
35 TraesCS3A01G253500 chr4B 83.308 653 96 12 2782 3428 16081857 16082502 1.160000e-164 590.0
36 TraesCS3A01G253500 chr5B 83.257 651 97 9 2779 3424 680927230 680927873 4.170000e-164 588.0
37 TraesCS3A01G253500 chr5B 78.014 564 97 16 185 733 135999881 136000432 2.790000e-86 329.0
38 TraesCS3A01G253500 chr7D 81.250 208 26 6 196 395 99967087 99966885 5.020000e-34 156.0
39 TraesCS3A01G253500 chr7D 78.788 165 23 9 196 355 609885033 609884876 2.380000e-17 100.0
40 TraesCS3A01G253500 chr7D 78.788 165 23 9 196 355 609902231 609902074 2.380000e-17 100.0
41 TraesCS3A01G253500 chr7A 81.548 168 19 6 195 354 102373505 102373342 1.090000e-25 128.0


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 TraesCS3A01G253500 chr3A 474809405 474813155 3750 True 6927.0 6927 100.000000 1 3751 1 chr3A.!!$R1 3750
1 TraesCS3A01G253500 chr3B 456979408 456982932 3524 True 1057.0 3884 95.795500 1 3672 4 chr3B.!!$R2 3671
2 TraesCS3A01G253500 chr3B 825271086 825271732 646 True 606.0 606 83.717000 2783 3428 1 chr3B.!!$R1 645
3 TraesCS3A01G253500 chr3B 41857071 41858100 1029 False 334.0 431 86.564000 1181 2226 2 chr3B.!!$F1 1045
4 TraesCS3A01G253500 chr3D 355792233 355797445 5212 True 1306.5 3548 92.150500 1 3672 4 chr3D.!!$R2 3671
5 TraesCS3A01G253500 chr3D 23743991 23746623 2632 False 327.0 440 84.002333 1064 2202 3 chr3D.!!$F1 1138
6 TraesCS3A01G253500 chr2B 144077074 144078575 1501 True 1393.0 1393 83.703000 1039 2544 1 chr2B.!!$R1 1505
7 TraesCS3A01G253500 chr2B 144034724 144035479 755 False 767.0 767 84.987000 1445 2226 1 chr2B.!!$F1 781
8 TraesCS3A01G253500 chr5A 627485670 627486372 702 True 1232.0 1232 98.293000 2066 2768 1 chr5A.!!$R1 702
9 TraesCS3A01G253500 chr2D 92889411 92892464 3053 False 718.0 898 86.950500 1039 2225 2 chr2D.!!$F6 1186
10 TraesCS3A01G253500 chr2D 53791717 53792364 647 False 588.0 588 83.232000 2782 3429 1 chr2D.!!$F2 647
11 TraesCS3A01G253500 chr2D 92831856 92832943 1087 False 506.5 758 86.338000 1169 2226 2 chr2D.!!$F5 1057
12 TraesCS3A01G253500 chr7B 217303334 217303936 602 True 608.0 608 84.959000 2782 3383 1 chr7B.!!$R1 601
13 TraesCS3A01G253500 chrUn 8241116 8241764 648 True 593.0 593 83.333000 2781 3428 1 chrUn.!!$R1 647
14 TraesCS3A01G253500 chrUn 399759819 399760466 647 True 593.0 593 83.333000 2781 3428 1 chrUn.!!$R2 647
15 TraesCS3A01G253500 chr4A 21229120 21229771 651 False 592.0 592 83.207000 2780 3433 1 chr4A.!!$F1 653
16 TraesCS3A01G253500 chr4B 16081857 16082502 645 False 590.0 590 83.308000 2782 3428 1 chr4B.!!$F1 646
17 TraesCS3A01G253500 chr5B 680927230 680927873 643 False 588.0 588 83.257000 2779 3424 1 chr5B.!!$F2 645
18 TraesCS3A01G253500 chr5B 135999881 136000432 551 False 329.0 329 78.014000 185 733 1 chr5B.!!$F1 548

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
817 1065 0.741326 GTCACTCGATGCAGAGGCTA 59.259 55.0 7.77 0.0 42.31 3.93 F
1786 2898 0.179225 CAAACGCGCTGACCATACAC 60.179 55.0 5.73 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 3107 0.464373 CATACATGGTCTTGGCGCCT 60.464 55.0 29.70 6.08 0.0 5.52 R
3724 7317 0.247460 CAGAGCAAGACCGGATCACA 59.753 55.0 9.46 0.00 0.0 3.58 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
85 86 2.270923 CGAACAAGATGCCTTCGATCA 58.729 47.619 0.00 0.00 39.29 2.92
93 94 1.971481 TGCCTTCGATCAATCCCATG 58.029 50.000 0.00 0.00 0.00 3.66
118 119 4.260985 TGGATCGCATTGTACAAGTCAAT 58.739 39.130 14.65 5.37 36.16 2.57
173 174 8.303156 CCAATTTAATTATTCACACACCACTCA 58.697 33.333 0.00 0.00 0.00 3.41
296 302 5.980116 AGTCGATTCAACATCTATTCCTTCG 59.020 40.000 0.00 0.00 0.00 3.79
366 372 1.546589 AATCTACCACCGCCCACGAA 61.547 55.000 0.00 0.00 43.93 3.85
422 661 2.224281 TGCATCCGAAGTTGAAGTGTCT 60.224 45.455 0.00 0.00 0.00 3.41
430 669 4.915667 CGAAGTTGAAGTGTCTGATTCGTA 59.084 41.667 0.00 0.00 35.00 3.43
547 790 4.257267 CATTAGCTGGATCCATACGTGA 57.743 45.455 16.63 0.00 0.00 4.35
558 801 6.097129 TGGATCCATACGTGATTGTTACTACA 59.903 38.462 11.44 0.00 0.00 2.74
580 827 2.498941 GGATGAGGATCGGGCGTCA 61.499 63.158 0.00 3.93 38.61 4.35
589 837 2.288825 GGATCGGGCGTCATCTTTGATA 60.289 50.000 0.00 0.00 33.56 2.15
599 847 4.371786 GTCATCTTTGATACAGCCGATGA 58.628 43.478 0.00 0.00 36.04 2.92
600 848 4.811024 GTCATCTTTGATACAGCCGATGAA 59.189 41.667 0.00 0.00 38.96 2.57
814 1062 4.391539 CGTCACTCGATGCAGAGG 57.608 61.111 7.77 0.00 42.31 3.69
815 1063 1.875813 CGTCACTCGATGCAGAGGC 60.876 63.158 7.77 0.00 42.31 4.70
816 1064 1.515020 GTCACTCGATGCAGAGGCT 59.485 57.895 7.77 0.00 42.31 4.58
817 1065 0.741326 GTCACTCGATGCAGAGGCTA 59.259 55.000 7.77 0.00 42.31 3.93
818 1066 1.135139 GTCACTCGATGCAGAGGCTAA 59.865 52.381 7.77 0.00 42.31 3.09
943 1196 6.092807 GGACGATTTCAAAATGTTAGAGCTCT 59.907 38.462 22.17 22.17 0.00 4.09
959 1212 5.527951 AGAGCTCTCATCGTGATGAAATAC 58.472 41.667 11.45 4.43 46.10 1.89
1137 2168 2.357881 CGCCTCTGCAGCTTGTCA 60.358 61.111 9.47 0.00 37.32 3.58
1277 2308 4.045104 GCAACTACATCATCCACTACTCG 58.955 47.826 0.00 0.00 0.00 4.18
1534 2641 0.472471 GGAGGAATTCCGGTATGGCA 59.528 55.000 18.82 0.00 42.08 4.92
1723 2830 7.486647 AGGTAACGTGTACCACATAAATAGAG 58.513 38.462 21.28 0.00 46.39 2.43
1786 2898 0.179225 CAAACGCGCTGACCATACAC 60.179 55.000 5.73 0.00 0.00 2.90
1843 2961 2.465813 CAGAGAGGAAGGAGGTGATGT 58.534 52.381 0.00 0.00 0.00 3.06
2518 3658 1.819632 GCCGTCCATCATGTCCACC 60.820 63.158 0.00 0.00 0.00 4.61
2519 3659 1.601703 CCGTCCATCATGTCCACCA 59.398 57.895 0.00 0.00 0.00 4.17
2520 3660 0.744414 CCGTCCATCATGTCCACCAC 60.744 60.000 0.00 0.00 0.00 4.16
2859 5353 2.571216 CCACCTCGTCTCCGTTGGT 61.571 63.158 0.00 0.00 40.52 3.67
2862 5356 2.273179 CCTCGTCTCCGTTGGTCCA 61.273 63.158 0.00 0.00 35.01 4.02
2864 5358 0.032952 CTCGTCTCCGTTGGTCCAAA 59.967 55.000 5.69 0.00 35.01 3.28
2923 5417 1.183549 GAGGGCTCCGTTTCTAGTCA 58.816 55.000 0.00 0.00 0.00 3.41
2928 5422 3.374367 GGGCTCCGTTTCTAGTCATTTTC 59.626 47.826 0.00 0.00 0.00 2.29
2931 5425 5.873164 GGCTCCGTTTCTAGTCATTTTCTTA 59.127 40.000 0.00 0.00 0.00 2.10
2953 5448 9.999660 TCTTAAGTTTTGTTAGGGTTTTTGTTT 57.000 25.926 1.63 0.00 0.00 2.83
2965 5460 4.503910 GGTTTTTGTTTTGCTCAGGAAGT 58.496 39.130 0.00 0.00 0.00 3.01
2967 5462 5.167845 GTTTTTGTTTTGCTCAGGAAGTCA 58.832 37.500 0.00 0.00 0.00 3.41
2983 5478 4.379243 CAAGACGGCGGTGGCTCT 62.379 66.667 13.24 0.58 39.81 4.09
2988 5483 4.803426 CGGCGGTGGCTCTCTGTC 62.803 72.222 0.00 0.00 39.81 3.51
2989 5484 3.695606 GGCGGTGGCTCTCTGTCA 61.696 66.667 0.00 0.00 39.81 3.58
3006 5501 5.419542 TCTGTCAATGGAATAAAGGTCTCG 58.580 41.667 0.00 0.00 0.00 4.04
3130 5632 3.358707 TGTCGTCTACGTTCATGTGTT 57.641 42.857 0.00 0.00 40.80 3.32
3139 5641 6.964934 GTCTACGTTCATGTGTTTTCTGTTTT 59.035 34.615 0.00 0.00 0.00 2.43
3143 5645 6.811170 ACGTTCATGTGTTTTCTGTTTTGATT 59.189 30.769 0.00 0.00 0.00 2.57
3196 5698 0.605050 TTGCTGTTATGGTGCGCTGA 60.605 50.000 9.73 0.00 0.00 4.26
3205 5707 2.689553 TGGTGCGCTGATTCTATGAA 57.310 45.000 9.73 0.00 0.00 2.57
3226 5728 0.601558 TCTTAGCACGGCGACTTTCT 59.398 50.000 16.62 5.16 0.00 2.52
3231 5733 0.388134 GCACGGCGACTTTCTGACTA 60.388 55.000 16.62 0.00 0.00 2.59
3236 5738 3.884091 ACGGCGACTTTCTGACTATCTAT 59.116 43.478 16.62 0.00 0.00 1.98
3258 5760 1.588674 CAACAAGTTGTGCCCGACTA 58.411 50.000 9.79 0.00 34.00 2.59
3259 5761 2.151202 CAACAAGTTGTGCCCGACTAT 58.849 47.619 9.79 0.00 34.00 2.12
3262 5764 2.027192 ACAAGTTGTGCCCGACTATGAT 60.027 45.455 7.96 0.00 34.00 2.45
3320 5822 3.916172 CGCTTTAGTGCTTGTAGTCGTTA 59.084 43.478 0.00 0.00 0.00 3.18
3340 5842 5.688500 CGTTACTAGGTGGTCTATGGGTCTA 60.689 48.000 0.00 0.00 0.00 2.59
3383 5885 5.471116 TCTGATGTTCATTATACTGCCATGC 59.529 40.000 0.00 0.00 0.00 4.06
3384 5886 4.520111 TGATGTTCATTATACTGCCATGCC 59.480 41.667 0.00 0.00 0.00 4.40
3385 5887 3.221771 TGTTCATTATACTGCCATGCCC 58.778 45.455 0.00 0.00 0.00 5.36
3388 5890 4.116782 TCATTATACTGCCATGCCCAAT 57.883 40.909 0.00 0.00 0.00 3.16
3389 5891 3.827876 TCATTATACTGCCATGCCCAATG 59.172 43.478 0.00 0.00 35.89 2.82
3390 5892 3.591695 TTATACTGCCATGCCCAATGA 57.408 42.857 0.00 0.00 38.72 2.57
3395 5897 1.483004 CTGCCATGCCCAATGATTGAA 59.517 47.619 6.76 0.00 38.72 2.69
3398 6248 2.367567 GCCATGCCCAATGATTGAAGAT 59.632 45.455 6.76 0.00 38.72 2.40
3399 6249 3.802329 GCCATGCCCAATGATTGAAGATG 60.802 47.826 6.76 5.24 38.72 2.90
3450 6300 2.548057 ACAACCTGATGTACACGCTTTG 59.452 45.455 0.00 1.19 0.00 2.77
3672 7265 6.886459 AGAATACAACCATCATAAGCAACACT 59.114 34.615 0.00 0.00 0.00 3.55
3673 7266 4.771590 ACAACCATCATAAGCAACACTG 57.228 40.909 0.00 0.00 0.00 3.66
3674 7267 4.397420 ACAACCATCATAAGCAACACTGA 58.603 39.130 0.00 0.00 0.00 3.41
3675 7268 4.456911 ACAACCATCATAAGCAACACTGAG 59.543 41.667 0.00 0.00 0.00 3.35
3676 7269 3.012518 ACCATCATAAGCAACACTGAGC 58.987 45.455 0.00 0.00 0.00 4.26
3677 7270 2.031314 CCATCATAAGCAACACTGAGCG 59.969 50.000 0.00 0.00 35.48 5.03
3678 7271 1.725641 TCATAAGCAACACTGAGCGG 58.274 50.000 0.00 0.00 35.48 5.52
3679 7272 0.729116 CATAAGCAACACTGAGCGGG 59.271 55.000 0.00 0.00 35.48 6.13
3680 7273 1.026718 ATAAGCAACACTGAGCGGGC 61.027 55.000 0.00 0.00 35.48 6.13
3683 7276 3.414700 CAACACTGAGCGGGCGAC 61.415 66.667 0.00 0.00 0.00 5.19
3695 7288 2.980233 GGCGACCTTGCTTGCTGT 60.980 61.111 0.00 0.00 34.52 4.40
3696 7289 1.671054 GGCGACCTTGCTTGCTGTA 60.671 57.895 0.00 0.00 34.52 2.74
3697 7290 1.234615 GGCGACCTTGCTTGCTGTAA 61.235 55.000 0.00 0.00 34.52 2.41
3698 7291 0.804989 GCGACCTTGCTTGCTGTAAT 59.195 50.000 0.00 0.00 0.00 1.89
3699 7292 2.006888 GCGACCTTGCTTGCTGTAATA 58.993 47.619 0.00 0.00 0.00 0.98
3700 7293 2.614057 GCGACCTTGCTTGCTGTAATAT 59.386 45.455 0.00 0.00 0.00 1.28
3701 7294 3.807622 GCGACCTTGCTTGCTGTAATATA 59.192 43.478 0.00 0.00 0.00 0.86
3702 7295 4.272504 GCGACCTTGCTTGCTGTAATATAA 59.727 41.667 0.00 0.00 0.00 0.98
3703 7296 5.049405 GCGACCTTGCTTGCTGTAATATAAT 60.049 40.000 0.00 0.00 0.00 1.28
3704 7297 6.593978 CGACCTTGCTTGCTGTAATATAATC 58.406 40.000 0.00 0.00 0.00 1.75
3705 7298 6.202762 CGACCTTGCTTGCTGTAATATAATCA 59.797 38.462 0.00 0.00 0.00 2.57
3706 7299 7.095060 CGACCTTGCTTGCTGTAATATAATCAT 60.095 37.037 0.00 0.00 0.00 2.45
3707 7300 8.469309 ACCTTGCTTGCTGTAATATAATCATT 57.531 30.769 0.00 0.00 0.00 2.57
3708 7301 8.355169 ACCTTGCTTGCTGTAATATAATCATTG 58.645 33.333 0.00 0.00 0.00 2.82
3709 7302 8.570488 CCTTGCTTGCTGTAATATAATCATTGA 58.430 33.333 0.00 0.00 0.00 2.57
3712 7305 9.511272 TGCTTGCTGTAATATAATCATTGATCT 57.489 29.630 0.00 0.00 0.00 2.75
3726 7319 6.899393 TCATTGATCTTACAGCCTTTTTGT 57.101 33.333 0.00 0.00 0.00 2.83
3727 7320 6.680810 TCATTGATCTTACAGCCTTTTTGTG 58.319 36.000 0.00 0.00 0.00 3.33
3728 7321 6.489700 TCATTGATCTTACAGCCTTTTTGTGA 59.510 34.615 0.00 0.00 0.00 3.58
3729 7322 6.899393 TTGATCTTACAGCCTTTTTGTGAT 57.101 33.333 0.00 0.00 0.00 3.06
3730 7323 6.500684 TGATCTTACAGCCTTTTTGTGATC 57.499 37.500 0.00 0.00 32.68 2.92
3731 7324 5.415701 TGATCTTACAGCCTTTTTGTGATCC 59.584 40.000 0.00 0.00 31.79 3.36
3732 7325 3.751175 TCTTACAGCCTTTTTGTGATCCG 59.249 43.478 0.00 0.00 0.00 4.18
3733 7326 1.247567 ACAGCCTTTTTGTGATCCGG 58.752 50.000 0.00 0.00 0.00 5.14
3734 7327 1.247567 CAGCCTTTTTGTGATCCGGT 58.752 50.000 0.00 0.00 0.00 5.28
3735 7328 1.200020 CAGCCTTTTTGTGATCCGGTC 59.800 52.381 0.00 0.00 0.00 4.79
3736 7329 1.073923 AGCCTTTTTGTGATCCGGTCT 59.926 47.619 0.00 0.00 0.00 3.85
3737 7330 1.886542 GCCTTTTTGTGATCCGGTCTT 59.113 47.619 0.00 0.00 0.00 3.01
3738 7331 2.351738 GCCTTTTTGTGATCCGGTCTTG 60.352 50.000 0.00 0.00 0.00 3.02
3739 7332 2.351738 CCTTTTTGTGATCCGGTCTTGC 60.352 50.000 0.00 0.00 0.00 4.01
3740 7333 2.270352 TTTTGTGATCCGGTCTTGCT 57.730 45.000 0.00 0.00 0.00 3.91
3741 7334 1.808411 TTTGTGATCCGGTCTTGCTC 58.192 50.000 0.00 0.00 0.00 4.26
3742 7335 0.976641 TTGTGATCCGGTCTTGCTCT 59.023 50.000 0.00 0.00 0.00 4.09
3743 7336 0.247460 TGTGATCCGGTCTTGCTCTG 59.753 55.000 0.00 0.00 0.00 3.35
3744 7337 0.247736 GTGATCCGGTCTTGCTCTGT 59.752 55.000 0.00 0.00 0.00 3.41
3745 7338 0.976641 TGATCCGGTCTTGCTCTGTT 59.023 50.000 0.00 0.00 0.00 3.16
3746 7339 1.338105 TGATCCGGTCTTGCTCTGTTG 60.338 52.381 0.00 0.00 0.00 3.33
3747 7340 0.976641 ATCCGGTCTTGCTCTGTTGA 59.023 50.000 0.00 0.00 0.00 3.18
3748 7341 0.976641 TCCGGTCTTGCTCTGTTGAT 59.023 50.000 0.00 0.00 0.00 2.57
3749 7342 1.066858 TCCGGTCTTGCTCTGTTGATC 60.067 52.381 0.00 0.00 0.00 2.92
3750 7343 1.338105 CCGGTCTTGCTCTGTTGATCA 60.338 52.381 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 2.355756 ACTTGTACAATGCGATCCATGC 59.644 45.455 9.13 0.00 33.49 4.06
173 174 8.686334 ACCTTGCGATCAAAATCATTAATTAGT 58.314 29.630 0.00 0.00 31.76 2.24
251 257 5.564550 ACTCCTCATCACTACAAAAGCAAT 58.435 37.500 0.00 0.00 0.00 3.56
296 302 0.606401 TAGCTTGGCAAGTGGACAGC 60.606 55.000 26.71 12.73 34.57 4.40
334 340 6.649557 GCGGTGGTAGATTAAAAGCTATATGT 59.350 38.462 0.00 0.00 0.00 2.29
422 661 4.269183 AGTGCAAATTCCCATACGAATCA 58.731 39.130 0.00 0.00 31.14 2.57
430 669 5.990996 CACAAAGTAAAGTGCAAATTCCCAT 59.009 36.000 0.00 0.00 0.00 4.00
508 751 6.044871 AGCTAATGGCCTTGAAGATAACCTAT 59.955 38.462 3.32 0.00 43.05 2.57
509 752 5.369699 AGCTAATGGCCTTGAAGATAACCTA 59.630 40.000 3.32 0.00 43.05 3.08
547 790 6.620877 TCCTCATCCTTGTGTAGTAACAAT 57.379 37.500 0.00 0.00 39.25 2.71
558 801 1.832912 GCCCGATCCTCATCCTTGT 59.167 57.895 0.00 0.00 0.00 3.16
580 827 5.674525 TCTTTCATCGGCTGTATCAAAGAT 58.325 37.500 0.00 0.00 0.00 2.40
589 837 1.740380 CGACCATCTTTCATCGGCTGT 60.740 52.381 0.00 0.00 0.00 4.40
599 847 6.373216 TGAATAAATTCCGAACGACCATCTTT 59.627 34.615 0.00 0.00 35.97 2.52
600 848 5.878116 TGAATAAATTCCGAACGACCATCTT 59.122 36.000 0.00 0.00 35.97 2.40
700 948 4.016444 TGCTGCTCCAAAGGTAAATTAGG 58.984 43.478 0.00 0.00 0.00 2.69
716 964 0.253894 TATCACACATGGCTGCTGCT 59.746 50.000 15.64 0.00 39.59 4.24
943 1196 4.273235 GCCACATGTATTTCATCACGATGA 59.727 41.667 5.62 5.62 45.30 2.92
959 1212 1.468520 CCAACTTCCGTTAGCCACATG 59.531 52.381 0.00 0.00 0.00 3.21
1084 2112 2.686416 GCCATTGTGGTGGATGTGGATA 60.686 50.000 0.00 0.00 42.02 2.59
1334 2365 4.818863 TCGGACCATCGGCCGGTA 62.819 66.667 27.83 7.28 40.72 4.02
1530 2637 0.531532 CAACCGCAAAATTGGTGCCA 60.532 50.000 8.40 0.00 38.82 4.92
1534 2641 1.300542 CCGCAACCGCAAAATTGGT 60.301 52.632 0.00 0.00 41.20 3.67
1723 2830 3.429881 GCACTTAATTGCTCTGGTTTTGC 59.570 43.478 10.33 0.00 39.59 3.68
1786 2898 5.221145 GCGGTGATGATATGGTAGGAGATAG 60.221 48.000 0.00 0.00 0.00 2.08
1843 2961 2.568612 CAGGAACAGCGAGCTCGA 59.431 61.111 38.74 0.00 43.02 4.04
1989 3107 0.464373 CATACATGGTCTTGGCGCCT 60.464 55.000 29.70 6.08 0.00 5.52
2518 3658 2.256158 CAGCCGTGGTTGCATGTG 59.744 61.111 0.00 0.00 0.00 3.21
2556 3696 8.326713 GCACTATCTGAATATAGATCATTTGCG 58.673 37.037 0.00 0.00 38.35 4.85
2859 5353 2.166346 TGTCCCCATGGCCTTTGGA 61.166 57.895 22.57 13.23 36.26 3.53
2862 5356 1.863155 ATCGTGTCCCCATGGCCTTT 61.863 55.000 6.09 0.00 0.00 3.11
2864 5358 2.692368 ATCGTGTCCCCATGGCCT 60.692 61.111 6.09 0.00 0.00 5.19
2877 5371 1.528824 CCTTGCCAGGATCCATCGT 59.471 57.895 15.82 0.00 44.19 3.73
2880 5374 2.605299 GCCCTTGCCAGGATCCAT 59.395 61.111 15.82 0.00 44.19 3.41
2931 5425 7.229707 AGCAAAACAAAAACCCTAACAAAACTT 59.770 29.630 0.00 0.00 0.00 2.66
2948 5443 4.096382 GTCTTGACTTCCTGAGCAAAACAA 59.904 41.667 0.00 0.00 0.00 2.83
2953 5448 1.270305 CCGTCTTGACTTCCTGAGCAA 60.270 52.381 0.00 0.00 0.00 3.91
2965 5460 4.373116 GAGCCACCGCCGTCTTGA 62.373 66.667 0.00 0.00 34.57 3.02
2967 5462 4.070552 GAGAGCCACCGCCGTCTT 62.071 66.667 0.00 0.00 34.57 3.01
2983 5478 5.419542 CGAGACCTTTATTCCATTGACAGA 58.580 41.667 0.00 0.00 0.00 3.41
2987 5482 3.541632 GGCGAGACCTTTATTCCATTGA 58.458 45.455 0.00 0.00 34.51 2.57
2988 5483 2.287915 CGGCGAGACCTTTATTCCATTG 59.712 50.000 0.00 0.00 35.61 2.82
2989 5484 2.561569 CGGCGAGACCTTTATTCCATT 58.438 47.619 0.00 0.00 35.61 3.16
3006 5501 1.079336 AAAACGAGGACTAGGCGGC 60.079 57.895 0.00 0.00 0.00 6.53
3171 5673 1.074072 ACCATAACAGCAACCGCCA 59.926 52.632 0.00 0.00 39.83 5.69
3196 5698 4.372656 GCCGTGCTAAGACTTCATAGAAT 58.627 43.478 0.00 0.00 0.00 2.40
3205 5707 0.317479 AAAGTCGCCGTGCTAAGACT 59.683 50.000 0.00 0.00 44.81 3.24
3226 5728 7.333423 GGCACAACTTGTTGTAATAGATAGTCA 59.667 37.037 17.26 0.00 33.17 3.41
3231 5733 4.394920 CGGGCACAACTTGTTGTAATAGAT 59.605 41.667 17.26 0.00 33.17 1.98
3236 5738 1.671845 GTCGGGCACAACTTGTTGTAA 59.328 47.619 17.26 1.17 33.17 2.41
3258 5760 0.327259 CATCGCCCCTCCATCATCAT 59.673 55.000 0.00 0.00 0.00 2.45
3259 5761 0.763986 TCATCGCCCCTCCATCATCA 60.764 55.000 0.00 0.00 0.00 3.07
3262 5764 2.796193 CGTCATCGCCCCTCCATCA 61.796 63.158 0.00 0.00 0.00 3.07
3303 5805 5.122869 CACCTAGTAACGACTACAAGCACTA 59.877 44.000 0.00 0.00 37.10 2.74
3320 5822 4.052922 TCTAGACCCATAGACCACCTAGT 58.947 47.826 0.00 0.00 0.00 2.57
3383 5885 6.296803 TCTGATCTCATCTTCAATCATTGGG 58.703 40.000 0.00 0.00 0.00 4.12
3384 5886 7.499563 ACTTCTGATCTCATCTTCAATCATTGG 59.500 37.037 0.00 0.00 0.00 3.16
3385 5887 8.439993 ACTTCTGATCTCATCTTCAATCATTG 57.560 34.615 0.00 0.00 0.00 2.82
3388 5890 8.859236 AAAACTTCTGATCTCATCTTCAATCA 57.141 30.769 0.00 0.00 0.00 2.57
3389 5891 8.397148 GGAAAACTTCTGATCTCATCTTCAATC 58.603 37.037 0.00 0.00 0.00 2.67
3390 5892 7.338957 GGGAAAACTTCTGATCTCATCTTCAAT 59.661 37.037 0.00 0.00 0.00 2.57
3395 5897 5.768980 TGGGAAAACTTCTGATCTCATCT 57.231 39.130 0.00 0.00 0.00 2.90
3424 6274 5.726397 AGCGTGTACATCAGGTTGTATTTA 58.274 37.500 0.00 0.00 34.76 1.40
3428 6278 3.671008 AAGCGTGTACATCAGGTTGTA 57.329 42.857 0.00 0.00 34.79 2.41
3430 6280 2.548057 ACAAAGCGTGTACATCAGGTTG 59.452 45.455 0.00 3.51 39.29 3.77
3450 6300 8.448615 CAAGGCCAATTACTAGTAGTTTACAAC 58.551 37.037 8.40 0.00 0.00 3.32
3677 7270 3.741476 CAGCAAGCAAGGTCGCCC 61.741 66.667 0.00 0.00 0.00 6.13
3678 7271 1.234615 TTACAGCAAGCAAGGTCGCC 61.235 55.000 0.00 0.00 0.00 5.54
3679 7272 0.804989 ATTACAGCAAGCAAGGTCGC 59.195 50.000 0.00 0.00 0.00 5.19
3680 7273 5.984233 TTATATTACAGCAAGCAAGGTCG 57.016 39.130 0.00 0.00 0.00 4.79
3681 7274 7.496529 TGATTATATTACAGCAAGCAAGGTC 57.503 36.000 0.00 0.00 0.00 3.85
3682 7275 8.355169 CAATGATTATATTACAGCAAGCAAGGT 58.645 33.333 0.00 0.00 0.00 3.50
3683 7276 8.570488 TCAATGATTATATTACAGCAAGCAAGG 58.430 33.333 0.00 0.00 0.00 3.61
3686 7279 9.511272 AGATCAATGATTATATTACAGCAAGCA 57.489 29.630 0.00 0.00 0.00 3.91
3700 7293 9.023962 ACAAAAAGGCTGTAAGATCAATGATTA 57.976 29.630 0.00 0.00 34.07 1.75
3701 7294 7.816031 CACAAAAAGGCTGTAAGATCAATGATT 59.184 33.333 0.00 0.00 34.07 2.57
3702 7295 7.177216 TCACAAAAAGGCTGTAAGATCAATGAT 59.823 33.333 0.00 0.00 34.07 2.45
3703 7296 6.489700 TCACAAAAAGGCTGTAAGATCAATGA 59.510 34.615 0.00 0.00 34.07 2.57
3704 7297 6.680810 TCACAAAAAGGCTGTAAGATCAATG 58.319 36.000 0.00 0.00 34.07 2.82
3705 7298 6.899393 TCACAAAAAGGCTGTAAGATCAAT 57.101 33.333 0.00 0.00 34.07 2.57
3706 7299 6.071952 GGATCACAAAAAGGCTGTAAGATCAA 60.072 38.462 13.30 0.00 34.07 2.57
3707 7300 5.415701 GGATCACAAAAAGGCTGTAAGATCA 59.584 40.000 13.30 0.00 34.07 2.92
3708 7301 5.447818 CGGATCACAAAAAGGCTGTAAGATC 60.448 44.000 0.00 0.00 34.07 2.75
3709 7302 4.396166 CGGATCACAAAAAGGCTGTAAGAT 59.604 41.667 0.00 0.00 34.07 2.40
3710 7303 3.751175 CGGATCACAAAAAGGCTGTAAGA 59.249 43.478 0.00 0.00 34.07 2.10
3711 7304 3.119849 CCGGATCACAAAAAGGCTGTAAG 60.120 47.826 0.00 0.00 0.00 2.34
3712 7305 2.817258 CCGGATCACAAAAAGGCTGTAA 59.183 45.455 0.00 0.00 0.00 2.41
3713 7306 2.224670 ACCGGATCACAAAAAGGCTGTA 60.225 45.455 9.46 0.00 0.00 2.74
3714 7307 1.247567 CCGGATCACAAAAAGGCTGT 58.752 50.000 0.00 0.00 0.00 4.40
3715 7308 1.200020 GACCGGATCACAAAAAGGCTG 59.800 52.381 9.46 0.00 0.00 4.85
3716 7309 1.073923 AGACCGGATCACAAAAAGGCT 59.926 47.619 9.46 0.00 0.00 4.58
3717 7310 1.534729 AGACCGGATCACAAAAAGGC 58.465 50.000 9.46 0.00 0.00 4.35
3718 7311 2.351738 GCAAGACCGGATCACAAAAAGG 60.352 50.000 9.46 0.00 0.00 3.11
3719 7312 2.554032 AGCAAGACCGGATCACAAAAAG 59.446 45.455 9.46 0.00 0.00 2.27
3720 7313 2.552315 GAGCAAGACCGGATCACAAAAA 59.448 45.455 9.46 0.00 0.00 1.94
3721 7314 2.151202 GAGCAAGACCGGATCACAAAA 58.849 47.619 9.46 0.00 0.00 2.44
3722 7315 1.347707 AGAGCAAGACCGGATCACAAA 59.652 47.619 9.46 0.00 0.00 2.83
3723 7316 0.976641 AGAGCAAGACCGGATCACAA 59.023 50.000 9.46 0.00 0.00 3.33
3724 7317 0.247460 CAGAGCAAGACCGGATCACA 59.753 55.000 9.46 0.00 0.00 3.58
3725 7318 0.247736 ACAGAGCAAGACCGGATCAC 59.752 55.000 9.46 0.00 0.00 3.06
3726 7319 0.976641 AACAGAGCAAGACCGGATCA 59.023 50.000 9.46 0.00 0.00 2.92
3727 7320 1.066858 TCAACAGAGCAAGACCGGATC 60.067 52.381 9.46 1.42 0.00 3.36
3728 7321 0.976641 TCAACAGAGCAAGACCGGAT 59.023 50.000 9.46 0.00 0.00 4.18
3729 7322 0.976641 ATCAACAGAGCAAGACCGGA 59.023 50.000 9.46 0.00 0.00 5.14
3730 7323 1.338105 TGATCAACAGAGCAAGACCGG 60.338 52.381 0.00 0.00 0.00 5.28
3731 7324 2.084610 TGATCAACAGAGCAAGACCG 57.915 50.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.