Multiple sequence alignment - TraesCS3D01G354400

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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 TraesCS3D01G354400 chr3D 100.000 4064 0 0 1 4064 465029033 465024970 0.000000e+00 7505.0
1 TraesCS3D01G354400 chr3D 81.430 1217 182 32 1878 3060 464808961 464807755 0.000000e+00 955.0
2 TraesCS3D01G354400 chr3B 92.174 3514 137 54 85 3498 618444014 618440539 0.000000e+00 4839.0
3 TraesCS3D01G354400 chr3B 82.877 987 160 9 1878 2861 618155767 618154787 0.000000e+00 878.0
4 TraesCS3D01G354400 chr3B 84.006 644 53 26 3462 4064 618440539 618439905 1.270000e-159 573.0
5 TraesCS3D01G354400 chr3B 79.104 134 28 0 1656 1789 618156440 618156307 4.330000e-15 93.5
6 TraesCS3D01G354400 chr3A 95.242 2375 78 18 1133 3477 608348119 608345750 0.000000e+00 3727.0
7 TraesCS3D01G354400 chr3A 85.324 1172 104 33 3 1129 608349301 608348153 0.000000e+00 1149.0
8 TraesCS3D01G354400 chr3A 81.209 1208 190 31 1878 3060 608195759 608194564 0.000000e+00 939.0
9 TraesCS3D01G354400 chr3A 91.358 162 11 3 3615 3776 608345373 608345215 6.840000e-53 219.0
10 TraesCS3D01G354400 chr7D 78.796 1429 260 34 1658 3065 149181675 149183081 0.000000e+00 920.0
11 TraesCS3D01G354400 chr7D 79.466 1198 226 16 1881 3064 149085145 149083954 0.000000e+00 832.0
12 TraesCS3D01G354400 chr7D 84.794 388 57 2 1181 1567 149181290 149181676 4.930000e-104 388.0
13 TraesCS3D01G354400 chr7D 89.189 74 7 1 3594 3667 133233793 133233721 1.560000e-14 91.6
14 TraesCS3D01G354400 chr7B 81.624 985 171 9 1882 2861 111943059 111944038 0.000000e+00 808.0
15 TraesCS3D01G354400 chr2B 76.434 1447 286 40 1658 3070 232290926 232289501 0.000000e+00 732.0
16 TraesCS3D01G354400 chr2B 85.942 377 49 4 1181 1555 232291311 232290937 2.280000e-107 399.0
17 TraesCS3D01G354400 chr2B 85.445 371 50 4 1181 1549 232261523 232261891 2.290000e-102 383.0
18 TraesCS3D01G354400 chr4D 74.608 1213 248 37 1880 3064 360451970 360453150 2.840000e-131 479.0
19 TraesCS3D01G354400 chr4D 83.784 74 10 2 3592 3665 499588264 499588193 7.290000e-08 69.4
20 TraesCS3D01G354400 chr5B 84.872 390 55 4 1181 1568 679311152 679311539 1.370000e-104 390.0
21 TraesCS3D01G354400 chr5B 88.636 132 15 0 1658 1789 679311537 679311668 1.170000e-35 161.0
22 TraesCS3D01G354400 chr2D 85.676 370 51 2 1181 1549 165485351 165484983 4.930000e-104 388.0
23 TraesCS3D01G354400 chr5D 84.576 389 56 4 1182 1568 538255194 538255580 2.290000e-102 383.0
24 TraesCS3D01G354400 chr7A 84.040 401 55 7 1160 1556 150021865 150022260 1.070000e-100 377.0
25 TraesCS3D01G354400 chr7A 86.076 79 11 0 3588 3666 262855452 262855530 7.240000e-13 86.1
26 TraesCS3D01G354400 chr7A 88.571 70 7 1 3598 3667 131842471 131842403 2.600000e-12 84.2
27 TraesCS3D01G354400 chr4A 82.278 79 10 4 3485 3560 605559008 605558931 9.430000e-07 65.8
28 TraesCS3D01G354400 chr4A 80.723 83 12 4 3501 3580 186475862 186475781 1.220000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G354400 chr3D 465024970 465029033 4063 True 7505.000000 7505 100.000000 1 4064 1 chr3D.!!$R2 4063
1 TraesCS3D01G354400 chr3D 464807755 464808961 1206 True 955.000000 955 81.430000 1878 3060 1 chr3D.!!$R1 1182
2 TraesCS3D01G354400 chr3B 618439905 618444014 4109 True 2706.000000 4839 88.090000 85 4064 2 chr3B.!!$R2 3979
3 TraesCS3D01G354400 chr3B 618154787 618156440 1653 True 485.750000 878 80.990500 1656 2861 2 chr3B.!!$R1 1205
4 TraesCS3D01G354400 chr3A 608345215 608349301 4086 True 1698.333333 3727 90.641333 3 3776 3 chr3A.!!$R2 3773
5 TraesCS3D01G354400 chr3A 608194564 608195759 1195 True 939.000000 939 81.209000 1878 3060 1 chr3A.!!$R1 1182
6 TraesCS3D01G354400 chr7D 149083954 149085145 1191 True 832.000000 832 79.466000 1881 3064 1 chr7D.!!$R2 1183
7 TraesCS3D01G354400 chr7D 149181290 149183081 1791 False 654.000000 920 81.795000 1181 3065 2 chr7D.!!$F1 1884
8 TraesCS3D01G354400 chr7B 111943059 111944038 979 False 808.000000 808 81.624000 1882 2861 1 chr7B.!!$F1 979
9 TraesCS3D01G354400 chr2B 232289501 232291311 1810 True 565.500000 732 81.188000 1181 3070 2 chr2B.!!$R1 1889
10 TraesCS3D01G354400 chr4D 360451970 360453150 1180 False 479.000000 479 74.608000 1880 3064 1 chr4D.!!$F1 1184
11 TraesCS3D01G354400 chr5B 679311152 679311668 516 False 275.500000 390 86.754000 1181 1789 2 chr5B.!!$F1 608

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
365 368 0.032952 ACCGCACTTCATACACGTGT 59.967 50.0 26.52 26.52 0.00 4.49 F
912 964 0.042731 ACCTCTAGGGCAAGCACCTA 59.957 55.0 0.20 8.39 39.54 3.08 F
1594 1693 0.682852 TTCGTCCTACAAGGTGGTGG 59.317 55.0 0.00 0.00 36.53 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1639 1743 1.343506 CCTGAGCACGTACGTAAACC 58.656 55.0 22.34 10.99 0.0 3.27 R
2449 3027 1.137513 CGAAGGAGACGTTGTTCACC 58.862 55.0 0.00 0.00 0.0 4.02 R
3481 4161 0.030369 CCCGGACGGAAGAAGTATCG 59.970 60.0 13.13 0.00 37.5 2.92 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
23 24 6.632171 CAAAAGTGTTTCAGAGACAAAACC 57.368 37.500 0.00 0.00 35.07 3.27
101 102 3.557264 GGGGAATGATCAACCCGATACTC 60.557 52.174 25.15 13.02 44.09 2.59
112 113 3.305720 ACCCGATACTCTGGCAGAATAA 58.694 45.455 19.29 7.10 0.00 1.40
165 166 4.309950 CTATGGCGGCCCGGGTAC 62.310 72.222 24.63 15.00 0.00 3.34
223 225 0.615261 GACGGACTCCTTCCCCTCTT 60.615 60.000 0.00 0.00 42.27 2.85
233 235 5.104318 ACTCCTTCCCCTCTTCAAATATCAC 60.104 44.000 0.00 0.00 0.00 3.06
234 236 4.788075 TCCTTCCCCTCTTCAAATATCACA 59.212 41.667 0.00 0.00 0.00 3.58
246 248 7.337689 TCTTCAAATATCACACCATTCCTCAAG 59.662 37.037 0.00 0.00 0.00 3.02
365 368 0.032952 ACCGCACTTCATACACGTGT 59.967 50.000 26.52 26.52 0.00 4.49
368 371 1.386748 CGCACTTCATACACGTGTCTG 59.613 52.381 27.16 25.21 0.00 3.51
376 379 4.271661 TCATACACGTGTCTGGGTACATA 58.728 43.478 27.16 3.31 0.00 2.29
466 474 1.837439 ACTGTTGGCGATAGGGAATCA 59.163 47.619 3.37 0.00 33.87 2.57
469 477 2.437651 TGTTGGCGATAGGGAATCATCA 59.562 45.455 0.00 0.00 33.87 3.07
516 524 3.347216 ACTAATGGTCCACATTCTGTGC 58.653 45.455 0.00 0.00 46.67 4.57
518 526 2.592102 ATGGTCCACATTCTGTGCTT 57.408 45.000 0.00 0.00 46.51 3.91
520 528 1.421268 TGGTCCACATTCTGTGCTTCT 59.579 47.619 1.71 0.00 46.51 2.85
521 529 2.079925 GGTCCACATTCTGTGCTTCTC 58.920 52.381 1.71 0.00 46.51 2.87
522 530 2.079925 GTCCACATTCTGTGCTTCTCC 58.920 52.381 1.71 0.00 46.51 3.71
523 531 1.980765 TCCACATTCTGTGCTTCTCCT 59.019 47.619 1.71 0.00 46.51 3.69
524 532 3.055819 GTCCACATTCTGTGCTTCTCCTA 60.056 47.826 1.71 0.00 46.51 2.94
525 533 3.055819 TCCACATTCTGTGCTTCTCCTAC 60.056 47.826 1.71 0.00 46.51 3.18
526 534 3.055530 CCACATTCTGTGCTTCTCCTACT 60.056 47.826 1.71 0.00 46.51 2.57
527 535 4.160439 CCACATTCTGTGCTTCTCCTACTA 59.840 45.833 1.71 0.00 46.51 1.82
528 536 5.105752 CACATTCTGTGCTTCTCCTACTAC 58.894 45.833 0.00 0.00 41.89 2.73
529 537 5.020132 ACATTCTGTGCTTCTCCTACTACT 58.980 41.667 0.00 0.00 0.00 2.57
530 538 6.095580 CACATTCTGTGCTTCTCCTACTACTA 59.904 42.308 0.00 0.00 41.89 1.82
531 539 6.320164 ACATTCTGTGCTTCTCCTACTACTAG 59.680 42.308 0.00 0.00 0.00 2.57
532 540 5.438698 TCTGTGCTTCTCCTACTACTAGT 57.561 43.478 0.00 0.00 0.00 2.57
533 541 6.556974 TCTGTGCTTCTCCTACTACTAGTA 57.443 41.667 1.89 1.89 0.00 1.82
540 548 7.105588 GCTTCTCCTACTACTAGTATACTCCC 58.894 46.154 9.12 0.00 29.08 4.30
542 550 7.552050 TCTCCTACTACTAGTATACTCCCAC 57.448 44.000 9.12 0.00 29.08 4.61
543 551 7.078396 TCTCCTACTACTAGTATACTCCCACA 58.922 42.308 9.12 0.00 29.08 4.17
544 552 7.016072 TCTCCTACTACTAGTATACTCCCACAC 59.984 44.444 9.12 0.00 29.08 3.82
545 553 6.848631 TCCTACTACTAGTATACTCCCACACT 59.151 42.308 9.12 0.00 29.08 3.55
577 585 8.265055 TCTTGATAATTAAGACCGGACATTCTT 58.735 33.333 9.46 9.62 36.10 2.52
645 662 1.064946 GAGCCCGATCAGAGTGACG 59.935 63.158 0.00 0.00 0.00 4.35
912 964 0.042731 ACCTCTAGGGCAAGCACCTA 59.957 55.000 0.20 8.39 39.54 3.08
962 1018 0.694771 ATTTGGCTGTCCAGAGCTCA 59.305 50.000 17.77 0.00 44.53 4.26
1009 1067 2.237751 CGTAGAGAAATGGCGGCCG 61.238 63.158 24.05 24.05 0.00 6.13
1046 1104 2.357517 GGTGGTGCTGTCCGTCAG 60.358 66.667 1.25 1.25 46.12 3.51
1092 1150 5.464030 AGTACCAGTTCGATGTAAGTTGT 57.536 39.130 0.00 0.00 0.00 3.32
1106 1171 5.398169 TGTAAGTTGTTCAGTTTGTTGCAG 58.602 37.500 0.00 0.00 0.00 4.41
1110 1175 6.019779 AGTTGTTCAGTTTGTTGCAGTTAA 57.980 33.333 0.00 0.00 0.00 2.01
1115 1180 4.654015 TCAGTTTGTTGCAGTTAACGTTC 58.346 39.130 2.82 0.00 33.28 3.95
1130 1195 3.338818 ACGTTCTTCAGTTGTTGCATG 57.661 42.857 0.00 0.00 0.00 4.06
1131 1196 2.046313 CGTTCTTCAGTTGTTGCATGC 58.954 47.619 11.82 11.82 0.00 4.06
1146 1241 0.722469 CATGCTTGACGACGTTGTGC 60.722 55.000 14.59 11.43 0.00 4.57
1156 1251 0.802494 GACGTTGTGCTTGGTATGGG 59.198 55.000 0.00 0.00 0.00 4.00
1158 1253 1.348366 ACGTTGTGCTTGGTATGGGTA 59.652 47.619 0.00 0.00 0.00 3.69
1594 1693 0.682852 TTCGTCCTACAAGGTGGTGG 59.317 55.000 0.00 0.00 36.53 4.61
1596 1695 1.002502 GTCCTACAAGGTGGTGGCC 60.003 63.158 0.00 0.00 36.53 5.36
1610 1709 1.376683 TGGCCGGTGATAAGTGTGC 60.377 57.895 1.90 0.00 0.00 4.57
1626 1730 1.874466 TGCGCGCATGCATGAATTG 60.874 52.632 33.09 16.17 40.62 2.32
1820 1926 1.795286 GCTTCATCTACCTACATGCGC 59.205 52.381 0.00 0.00 0.00 6.09
2791 3369 2.914097 AACCTCGTCGACCCCGTT 60.914 61.111 10.58 6.48 37.05 4.44
2877 3506 2.100252 CAGGTTGGAATCCATGCATCAC 59.900 50.000 1.39 0.00 31.53 3.06
3065 3742 3.118038 TCCGATCTTCCCAAATGTTAGGG 60.118 47.826 0.00 0.00 46.90 3.53
3100 3777 3.955471 TCTCCAATTTCCACAGGACATC 58.045 45.455 0.00 0.00 0.00 3.06
3119 3796 1.008538 CGTCCGCTTTTGCTTGCTT 60.009 52.632 0.00 0.00 44.80 3.91
3148 3825 1.940758 GTGCGTGCACAACTGCTTG 60.941 57.895 19.45 0.00 44.57 4.01
3211 3890 5.276240 GCTTTCTTAGCTGTGTTCTCTTC 57.724 43.478 0.00 0.00 46.77 2.87
3291 3971 5.392487 GCAAGAGGCTTAGGACTTTCATTTC 60.392 44.000 0.00 0.00 40.25 2.17
3337 4017 2.713967 TAACGTACGGGAGCTGGGC 61.714 63.158 21.06 0.00 0.00 5.36
3481 4161 4.183101 CACAAATTCCATGGCCATTGTAC 58.817 43.478 17.92 0.00 30.48 2.90
3507 4327 3.515104 ACTTCTTCCGTCCGGGTTTATTA 59.485 43.478 0.00 0.00 37.00 0.98
3508 4328 3.806625 TCTTCCGTCCGGGTTTATTAG 57.193 47.619 0.00 0.00 37.00 1.73
3512 4332 2.689983 TCCGTCCGGGTTTATTAGTCTC 59.310 50.000 0.00 0.00 37.00 3.36
3514 4334 3.243334 CCGTCCGGGTTTATTAGTCTCTC 60.243 52.174 0.00 0.00 0.00 3.20
3515 4335 3.547613 CGTCCGGGTTTATTAGTCTCTCG 60.548 52.174 0.00 0.00 0.00 4.04
3516 4336 3.379688 GTCCGGGTTTATTAGTCTCTCGT 59.620 47.826 0.00 0.00 0.00 4.18
3517 4337 4.576463 GTCCGGGTTTATTAGTCTCTCGTA 59.424 45.833 0.00 0.00 0.00 3.43
3522 4342 7.493645 CCGGGTTTATTAGTCTCTCGTATTTTT 59.506 37.037 0.00 0.00 0.00 1.94
3590 4410 9.502145 TTTATCTATTAAAAATTGCACTGCGAG 57.498 29.630 0.00 0.00 0.00 5.03
3653 4578 7.553881 TGCTAGTTAAATCTATGGTCAAAGC 57.446 36.000 0.00 0.00 0.00 3.51
3739 4664 0.975040 AAGGGCCAAGCAACACAACA 60.975 50.000 6.18 0.00 0.00 3.33
3751 4676 3.857010 GCAACACAACAGATACTTTGGGC 60.857 47.826 0.00 0.00 28.35 5.36
3758 4683 3.718723 ACAGATACTTTGGGCTCTCTCT 58.281 45.455 0.00 0.00 0.00 3.10
3759 4684 3.704061 ACAGATACTTTGGGCTCTCTCTC 59.296 47.826 0.00 0.00 0.00 3.20
3760 4685 3.069443 CAGATACTTTGGGCTCTCTCTCC 59.931 52.174 0.00 0.00 0.00 3.71
3761 4686 1.475403 TACTTTGGGCTCTCTCTCCG 58.525 55.000 0.00 0.00 0.00 4.63
3778 4713 1.003812 TCCGGGGTGAAAACCTATGTG 59.996 52.381 0.00 0.00 0.00 3.21
3793 4728 1.610554 ATGTGGCTCAAGCAATGGCC 61.611 55.000 0.00 0.00 44.36 5.36
3794 4729 2.117858 TGGCTCAAGCAATGGCCA 59.882 55.556 8.56 8.56 46.55 5.36
3809 4744 0.673985 GGCCAAGGAGGTGTTGTTTC 59.326 55.000 0.00 0.00 40.61 2.78
3810 4745 1.398692 GCCAAGGAGGTGTTGTTTCA 58.601 50.000 0.00 0.00 40.61 2.69
3811 4746 1.963515 GCCAAGGAGGTGTTGTTTCAT 59.036 47.619 0.00 0.00 40.61 2.57
3812 4747 3.153919 GCCAAGGAGGTGTTGTTTCATA 58.846 45.455 0.00 0.00 40.61 2.15
3818 4753 7.264947 CAAGGAGGTGTTGTTTCATAGTTTTT 58.735 34.615 0.00 0.00 0.00 1.94
3822 4757 8.573035 GGAGGTGTTGTTTCATAGTTTTTGATA 58.427 33.333 0.00 0.00 0.00 2.15
3828 4763 9.394477 GTTGTTTCATAGTTTTTGATACTCACC 57.606 33.333 0.00 0.00 0.00 4.02
3837 4772 6.601613 AGTTTTTGATACTCACCTGTTTGTCA 59.398 34.615 0.00 0.00 0.00 3.58
3853 4789 6.822442 TGTTTGTCAGAGGTGTATGTCTTTA 58.178 36.000 0.00 0.00 0.00 1.85
3855 4791 5.661056 TGTCAGAGGTGTATGTCTTTAGG 57.339 43.478 0.00 0.00 0.00 2.69
3856 4792 5.084519 TGTCAGAGGTGTATGTCTTTAGGT 58.915 41.667 0.00 0.00 0.00 3.08
3858 4794 4.466370 TCAGAGGTGTATGTCTTTAGGTGG 59.534 45.833 0.00 0.00 0.00 4.61
3859 4795 3.197983 AGAGGTGTATGTCTTTAGGTGGC 59.802 47.826 0.00 0.00 0.00 5.01
3860 4796 2.910319 AGGTGTATGTCTTTAGGTGGCA 59.090 45.455 0.00 0.00 0.00 4.92
3864 4800 4.700213 GTGTATGTCTTTAGGTGGCATTGT 59.300 41.667 0.00 0.00 0.00 2.71
3886 4822 4.616802 GTGCCACGTTATGATTTTGTCTTG 59.383 41.667 0.00 0.00 0.00 3.02
3897 4833 5.579047 TGATTTTGTCTTGGGGTGACATAT 58.421 37.500 0.00 0.00 42.95 1.78
3899 4835 4.927267 TTTGTCTTGGGGTGACATATCT 57.073 40.909 0.00 0.00 42.95 1.98
3912 4848 6.543831 GGGTGACATATCTAATGAGTTTTGCT 59.456 38.462 0.00 0.00 0.00 3.91
3913 4849 7.067494 GGGTGACATATCTAATGAGTTTTGCTT 59.933 37.037 0.00 0.00 0.00 3.91
3932 4868 2.936928 GGTGTAAAACCCCGACCTG 58.063 57.895 0.00 0.00 44.02 4.00
3933 4869 0.607217 GGTGTAAAACCCCGACCTGG 60.607 60.000 0.00 0.00 44.02 4.45
3938 4874 1.647334 AAAACCCCGACCTGGAACCA 61.647 55.000 0.00 0.00 42.00 3.67
3958 4908 0.250338 GTCACCTTCTTGGAGGCGTT 60.250 55.000 0.00 0.00 40.65 4.84
3978 4928 5.347342 CGTTGTCTTGAGATTCTAGCATCT 58.653 41.667 4.42 4.42 36.12 2.90
3979 4929 6.499172 CGTTGTCTTGAGATTCTAGCATCTA 58.501 40.000 4.77 0.00 33.36 1.98
3980 4930 7.144661 CGTTGTCTTGAGATTCTAGCATCTAT 58.855 38.462 4.77 0.00 33.36 1.98
3981 4931 8.293157 CGTTGTCTTGAGATTCTAGCATCTATA 58.707 37.037 4.77 0.00 33.36 1.31
3982 4932 9.624697 GTTGTCTTGAGATTCTAGCATCTATAG 57.375 37.037 4.77 6.00 33.36 1.31
3984 4934 9.008965 TGTCTTGAGATTCTAGCATCTATAGTC 57.991 37.037 4.77 4.74 33.36 2.59
3985 4935 9.231297 GTCTTGAGATTCTAGCATCTATAGTCT 57.769 37.037 4.77 0.00 33.36 3.24
3986 4936 9.448438 TCTTGAGATTCTAGCATCTATAGTCTC 57.552 37.037 4.77 2.42 33.36 3.36
3987 4937 8.574251 TTGAGATTCTAGCATCTATAGTCTCC 57.426 38.462 4.77 0.00 33.36 3.71
3988 4938 7.694093 TGAGATTCTAGCATCTATAGTCTCCA 58.306 38.462 4.77 0.00 33.36 3.86
3989 4939 8.335484 TGAGATTCTAGCATCTATAGTCTCCAT 58.665 37.037 4.77 0.00 33.36 3.41
3990 4940 8.752005 AGATTCTAGCATCTATAGTCTCCATC 57.248 38.462 2.76 0.62 31.25 3.51
3992 4942 6.650622 TCTAGCATCTATAGTCTCCATCCT 57.349 41.667 0.00 0.00 0.00 3.24
3993 4943 6.422333 TCTAGCATCTATAGTCTCCATCCTG 58.578 44.000 0.00 0.00 0.00 3.86
3994 4944 4.352009 AGCATCTATAGTCTCCATCCTGG 58.648 47.826 0.00 0.00 39.43 4.45
3995 4945 4.045207 AGCATCTATAGTCTCCATCCTGGA 59.955 45.833 0.00 0.00 45.98 3.86
4020 4975 4.039124 GGAAGTTTTTGAGATGGCTTTGGA 59.961 41.667 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.155827 TGGTTTTGTCTCTGAAACACTTTTG 58.844 36.000 0.00 0.00 37.46 2.44
3 4 5.975693 TTGGTTTTGTCTCTGAAACACTT 57.024 34.783 0.00 0.00 37.46 3.16
4 5 5.975693 TTTGGTTTTGTCTCTGAAACACT 57.024 34.783 0.00 0.00 37.46 3.55
5 6 6.089417 CACTTTTGGTTTTGTCTCTGAAACAC 59.911 38.462 0.00 0.00 37.46 3.32
6 7 6.155827 CACTTTTGGTTTTGTCTCTGAAACA 58.844 36.000 0.00 0.00 37.46 2.83
7 8 6.156519 ACACTTTTGGTTTTGTCTCTGAAAC 58.843 36.000 0.00 0.00 35.54 2.78
58 59 9.736819 TTCCCCCATGATTATAATTAGGTTTTT 57.263 29.630 0.00 0.00 0.00 1.94
63 64 9.359653 GATCATTCCCCCATGATTATAATTAGG 57.640 37.037 0.00 0.00 42.85 2.69
70 71 5.336102 GGTTGATCATTCCCCCATGATTAT 58.664 41.667 0.00 0.00 42.85 1.28
75 76 1.708341 GGGTTGATCATTCCCCCATG 58.292 55.000 19.85 0.00 33.94 3.66
76 77 0.185901 CGGGTTGATCATTCCCCCAT 59.814 55.000 22.74 0.00 38.09 4.00
78 79 0.478507 ATCGGGTTGATCATTCCCCC 59.521 55.000 22.74 16.31 38.09 5.40
112 113 3.030415 CCAACGGTAAAGGCAAGGT 57.970 52.632 0.00 0.00 0.00 3.50
161 162 4.047142 GGAGAATTATTGGTCGTCGTACC 58.953 47.826 6.85 6.85 40.19 3.34
165 166 4.430007 TCTTGGAGAATTATTGGTCGTCG 58.570 43.478 0.00 0.00 0.00 5.12
168 169 9.503427 GTTAATTTCTTGGAGAATTATTGGTCG 57.497 33.333 0.00 0.00 33.67 4.79
211 212 4.788075 TGTGATATTTGAAGAGGGGAAGGA 59.212 41.667 0.00 0.00 0.00 3.36
223 225 6.375174 CACTTGAGGAATGGTGTGATATTTGA 59.625 38.462 0.00 0.00 0.00 2.69
233 235 1.171308 CTGGCACTTGAGGAATGGTG 58.829 55.000 0.00 0.00 0.00 4.17
234 236 0.038744 CCTGGCACTTGAGGAATGGT 59.961 55.000 0.00 0.00 0.00 3.55
246 248 2.736400 GCACATCAAATAAGCCTGGCAC 60.736 50.000 22.65 0.00 0.00 5.01
365 368 6.460781 CCATTTTACGCTATATGTACCCAGA 58.539 40.000 0.00 0.00 0.00 3.86
368 371 5.243207 AGCCATTTTACGCTATATGTACCC 58.757 41.667 0.00 0.00 32.26 3.69
466 474 9.399797 TCATACATCTTGACTTAATTGCTTGAT 57.600 29.630 0.00 0.00 0.00 2.57
516 524 8.096414 GTGGGAGTATACTAGTAGTAGGAGAAG 58.904 44.444 15.08 0.00 33.66 2.85
518 526 7.016072 GTGTGGGAGTATACTAGTAGTAGGAGA 59.984 44.444 15.08 0.00 33.66 3.71
520 528 6.848631 AGTGTGGGAGTATACTAGTAGTAGGA 59.151 42.308 15.08 0.22 33.66 2.94
521 529 7.077050 AGTGTGGGAGTATACTAGTAGTAGG 57.923 44.000 15.08 0.00 33.66 3.18
522 530 8.869109 AGTAGTGTGGGAGTATACTAGTAGTAG 58.131 40.741 15.08 2.87 33.66 2.57
523 531 8.789767 AGTAGTGTGGGAGTATACTAGTAGTA 57.210 38.462 12.38 12.38 34.82 1.82
524 532 7.688918 AGTAGTGTGGGAGTATACTAGTAGT 57.311 40.000 5.09 8.14 29.51 2.73
527 535 8.947305 AGATTAGTAGTGTGGGAGTATACTAGT 58.053 37.037 5.09 0.00 33.96 2.57
528 536 9.796180 AAGATTAGTAGTGTGGGAGTATACTAG 57.204 37.037 5.09 0.00 32.26 2.57
529 537 9.570468 CAAGATTAGTAGTGTGGGAGTATACTA 57.430 37.037 5.09 0.00 0.00 1.82
530 538 8.280084 TCAAGATTAGTAGTGTGGGAGTATACT 58.720 37.037 4.68 4.68 0.00 2.12
531 539 8.461249 TCAAGATTAGTAGTGTGGGAGTATAC 57.539 38.462 0.00 0.00 0.00 1.47
533 541 9.656323 TTATCAAGATTAGTAGTGTGGGAGTAT 57.344 33.333 0.00 0.00 0.00 2.12
577 585 5.182380 CCTTTCCAAGGCTTAATTAACACGA 59.818 40.000 0.00 0.00 42.78 4.35
645 662 1.294459 GTCTGGTTACCCGTCACCC 59.706 63.158 0.00 0.00 31.24 4.61
951 1003 1.206849 CTTCTTCCCTGAGCTCTGGAC 59.793 57.143 34.33 1.48 37.15 4.02
962 1018 0.692756 GCTAGCTCCCCTTCTTCCCT 60.693 60.000 7.70 0.00 0.00 4.20
1092 1150 4.688511 ACGTTAACTGCAACAAACTGAA 57.311 36.364 3.71 0.00 0.00 3.02
1106 1171 4.654015 TGCAACAACTGAAGAACGTTAAC 58.346 39.130 0.00 0.00 0.00 2.01
1110 1175 2.541588 GCATGCAACAACTGAAGAACGT 60.542 45.455 14.21 0.00 0.00 3.99
1115 1180 3.047796 GTCAAGCATGCAACAACTGAAG 58.952 45.455 21.98 0.00 0.00 3.02
1130 1195 0.654472 CAAGCACAACGTCGTCAAGC 60.654 55.000 0.00 2.95 0.00 4.01
1131 1196 0.042188 CCAAGCACAACGTCGTCAAG 60.042 55.000 0.00 0.00 0.00 3.02
1146 1241 2.957680 TGCATGCATTACCCATACCAAG 59.042 45.455 18.46 0.00 0.00 3.61
1156 1251 1.064621 CGCCACCTGCATGCATTAC 59.935 57.895 22.97 8.45 41.33 1.89
1158 1253 2.361483 TCGCCACCTGCATGCATT 60.361 55.556 22.97 8.63 41.33 3.56
1594 1693 3.089784 CGCACACTTATCACCGGC 58.910 61.111 0.00 0.00 0.00 6.13
1596 1695 2.695055 CGCGCACACTTATCACCG 59.305 61.111 8.75 0.00 0.00 4.94
1626 1730 5.616785 CGTACGTAAACCAACAAACTTAAGC 59.383 40.000 7.22 0.00 0.00 3.09
1636 1740 2.126467 TGAGCACGTACGTAAACCAAC 58.874 47.619 22.34 8.91 0.00 3.77
1639 1743 1.343506 CCTGAGCACGTACGTAAACC 58.656 55.000 22.34 10.99 0.00 3.27
1820 1926 3.665323 GCTTGCTTGATCAGTAACACACG 60.665 47.826 0.00 0.00 0.00 4.49
1868 1974 4.450122 GTCTGCATGGCACGCACG 62.450 66.667 3.16 1.05 35.08 5.34
2449 3027 1.137513 CGAAGGAGACGTTGTTCACC 58.862 55.000 0.00 0.00 0.00 4.02
3065 3742 2.949451 TGGAGAAGACGCAATCTCTC 57.051 50.000 10.56 2.96 41.45 3.20
3100 3777 2.406452 AAGCAAGCAAAAGCGGACGG 62.406 55.000 0.00 0.00 35.48 4.79
3148 3825 2.717190 CACGCGCGACACACAAAC 60.717 61.111 39.36 0.00 0.00 2.93
3205 3884 5.760253 GGACTTGACATGAAAGTTGAAGAGA 59.240 40.000 16.15 0.00 37.98 3.10
3211 3890 3.809832 ACGAGGACTTGACATGAAAGTTG 59.190 43.478 16.15 10.88 37.98 3.16
3291 3971 0.872021 GGCGACTAATCAGCAGTCCG 60.872 60.000 0.00 0.00 39.43 4.79
3337 4017 0.111832 AGAGGCACATGGGCATATGG 59.888 55.000 23.88 0.00 46.44 2.74
3481 4161 0.030369 CCCGGACGGAAGAAGTATCG 59.970 60.000 13.13 0.00 37.50 2.92
3580 4400 0.036105 ATCATTGGACTCGCAGTGCA 60.036 50.000 16.83 6.44 44.95 4.57
3581 4401 1.939974 TATCATTGGACTCGCAGTGC 58.060 50.000 4.58 4.58 37.06 4.40
3653 4578 8.115490 AGTTCTTCCTTGTATTTTGGATCAAG 57.885 34.615 0.00 0.00 37.57 3.02
3685 4610 3.233507 TGTACCTACTTCCTCCGTTGTT 58.766 45.455 0.00 0.00 0.00 2.83
3687 4612 4.430908 GAATGTACCTACTTCCTCCGTTG 58.569 47.826 0.00 0.00 0.00 4.10
3688 4613 3.450096 GGAATGTACCTACTTCCTCCGTT 59.550 47.826 0.00 0.00 36.36 4.44
3739 4664 3.304829 GGAGAGAGAGCCCAAAGTATCT 58.695 50.000 0.00 0.00 0.00 1.98
3751 4676 1.066787 GTTTTCACCCCGGAGAGAGAG 60.067 57.143 0.73 0.00 0.00 3.20
3758 4683 1.003812 CACATAGGTTTTCACCCCGGA 59.996 52.381 0.73 0.00 45.63 5.14
3759 4684 1.459450 CACATAGGTTTTCACCCCGG 58.541 55.000 0.00 0.00 45.63 5.73
3760 4685 1.459450 CCACATAGGTTTTCACCCCG 58.541 55.000 0.00 0.00 45.63 5.73
3761 4686 1.182667 GCCACATAGGTTTTCACCCC 58.817 55.000 0.00 0.00 45.63 4.95
3778 4713 1.217244 CTTGGCCATTGCTTGAGCC 59.783 57.895 6.09 10.54 40.28 4.70
3793 4728 6.391227 AAACTATGAAACAACACCTCCTTG 57.609 37.500 0.00 0.00 0.00 3.61
3794 4729 7.123547 TCAAAAACTATGAAACAACACCTCCTT 59.876 33.333 0.00 0.00 0.00 3.36
3812 4747 7.201732 CTGACAAACAGGTGAGTATCAAAAACT 60.202 37.037 0.00 0.00 41.94 2.66
3818 4753 4.021104 CCTCTGACAAACAGGTGAGTATCA 60.021 45.833 0.00 0.00 44.74 2.15
3822 4757 2.119495 ACCTCTGACAAACAGGTGAGT 58.881 47.619 0.00 0.00 45.76 3.41
3828 4763 4.887748 AGACATACACCTCTGACAAACAG 58.112 43.478 0.00 0.00 46.97 3.16
3837 4772 3.197983 GCCACCTAAAGACATACACCTCT 59.802 47.826 0.00 0.00 0.00 3.69
3858 4794 2.849880 ATCATAACGTGGCACAATGC 57.150 45.000 19.09 0.00 44.16 3.56
3859 4795 4.922692 ACAAAATCATAACGTGGCACAATG 59.077 37.500 19.09 16.61 44.16 2.82
3860 4796 5.048083 AGACAAAATCATAACGTGGCACAAT 60.048 36.000 19.09 7.93 44.16 2.71
3864 4800 4.320861 CCAAGACAAAATCATAACGTGGCA 60.321 41.667 0.00 0.00 0.00 4.92
3886 4822 6.238759 GCAAAACTCATTAGATATGTCACCCC 60.239 42.308 0.00 0.00 0.00 4.95
3897 4833 7.575414 TTTACACCAAGCAAAACTCATTAGA 57.425 32.000 0.00 0.00 0.00 2.10
3899 4835 6.981559 GGTTTTACACCAAGCAAAACTCATTA 59.018 34.615 8.53 0.00 46.42 1.90
3925 4861 1.004918 GTGACTGGTTCCAGGTCGG 60.005 63.158 20.88 0.00 38.30 4.79
3926 4862 1.004918 GGTGACTGGTTCCAGGTCG 60.005 63.158 20.88 0.00 38.30 4.79
3928 4864 0.765510 GAAGGTGACTGGTTCCAGGT 59.234 55.000 20.88 8.35 42.68 4.00
3929 4865 1.059913 AGAAGGTGACTGGTTCCAGG 58.940 55.000 20.88 5.51 42.68 4.45
3930 4866 2.498167 CAAGAAGGTGACTGGTTCCAG 58.502 52.381 16.25 16.25 42.68 3.86
3931 4867 1.142870 CCAAGAAGGTGACTGGTTCCA 59.857 52.381 0.00 0.00 42.68 3.53
3932 4868 1.420138 TCCAAGAAGGTGACTGGTTCC 59.580 52.381 0.00 0.00 42.68 3.62
3933 4869 2.551071 CCTCCAAGAAGGTGACTGGTTC 60.551 54.545 0.00 0.00 42.68 3.62
3958 4908 8.932434 ACTATAGATGCTAGAATCTCAAGACA 57.068 34.615 17.06 0.00 37.98 3.41
3987 4937 5.072741 TCTCAAAAACTTCCTTCCAGGATG 58.927 41.667 0.00 4.51 45.34 3.51
3988 4938 5.324832 TCTCAAAAACTTCCTTCCAGGAT 57.675 39.130 0.00 0.00 45.34 3.24
3989 4939 4.788925 TCTCAAAAACTTCCTTCCAGGA 57.211 40.909 0.00 0.00 44.10 3.86
3990 4940 4.219288 CCATCTCAAAAACTTCCTTCCAGG 59.781 45.833 0.00 0.00 36.46 4.45
3992 4942 3.573967 GCCATCTCAAAAACTTCCTTCCA 59.426 43.478 0.00 0.00 0.00 3.53
3993 4943 3.829026 AGCCATCTCAAAAACTTCCTTCC 59.171 43.478 0.00 0.00 0.00 3.46
3994 4944 5.459536 AAGCCATCTCAAAAACTTCCTTC 57.540 39.130 0.00 0.00 0.00 3.46
3995 4945 5.453762 CCAAAGCCATCTCAAAAACTTCCTT 60.454 40.000 0.00 0.00 0.00 3.36
3996 4946 4.039609 CCAAAGCCATCTCAAAAACTTCCT 59.960 41.667 0.00 0.00 0.00 3.36
3997 4947 4.039124 TCCAAAGCCATCTCAAAAACTTCC 59.961 41.667 0.00 0.00 0.00 3.46
3999 4949 4.405358 TGTCCAAAGCCATCTCAAAAACTT 59.595 37.500 0.00 0.00 0.00 2.66
4000 4950 3.960102 TGTCCAAAGCCATCTCAAAAACT 59.040 39.130 0.00 0.00 0.00 2.66
4001 4951 4.320608 TGTCCAAAGCCATCTCAAAAAC 57.679 40.909 0.00 0.00 0.00 2.43
4002 4952 5.299148 CATTGTCCAAAGCCATCTCAAAAA 58.701 37.500 0.00 0.00 0.00 1.94
4003 4953 4.262549 CCATTGTCCAAAGCCATCTCAAAA 60.263 41.667 0.00 0.00 0.00 2.44
4004 4954 3.258872 CCATTGTCCAAAGCCATCTCAAA 59.741 43.478 0.00 0.00 0.00 2.69
4005 4955 2.827322 CCATTGTCCAAAGCCATCTCAA 59.173 45.455 0.00 0.00 0.00 3.02
4006 4956 2.449464 CCATTGTCCAAAGCCATCTCA 58.551 47.619 0.00 0.00 0.00 3.27
4007 4957 1.135721 GCCATTGTCCAAAGCCATCTC 59.864 52.381 0.00 0.00 0.00 2.75
4020 4975 3.256960 ACCCTCCACGGCCATTGT 61.257 61.111 2.24 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.