Multiple sequence alignment - TraesCS3D01G517200

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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 TraesCS3D01G517200 chr3D 100.000 2818 0 0 1 2818 600583821 600586638 0.000000e+00 5204.0
1 TraesCS3D01G517200 chr3D 82.571 809 82 28 747 1533 600607534 600608305 0.000000e+00 658.0
2 TraesCS3D01G517200 chr3D 82.042 813 82 30 747 1533 600594108 600594882 3.960000e-178 634.0
3 TraesCS3D01G517200 chr3D 82.132 666 92 22 881 1533 600563185 600563836 1.910000e-151 545.0
4 TraesCS3D01G517200 chr3D 84.516 155 20 3 1950 2102 572312976 572313128 1.750000e-32 150.0
5 TraesCS3D01G517200 chr3D 81.818 165 26 3 1939 2102 572321442 572321603 4.900000e-28 135.0
6 TraesCS3D01G517200 chr3D 86.250 80 10 1 2718 2796 561754921 561755000 5.000000e-13 86.1
7 TraesCS3D01G517200 chr3D 79.130 115 17 6 2682 2792 25578388 25578277 3.890000e-09 73.1
8 TraesCS3D01G517200 chr3A 93.501 1785 100 6 750 2522 730267770 730265990 0.000000e+00 2639.0
9 TraesCS3D01G517200 chr3A 82.434 797 85 31 757 1533 730178666 730177905 0.000000e+00 645.0
10 TraesCS3D01G517200 chr3A 81.605 810 85 30 750 1533 730208968 730208197 1.860000e-171 612.0
11 TraesCS3D01G517200 chr3A 82.380 664 90 18 881 1533 730280167 730279520 1.140000e-153 553.0
12 TraesCS3D01G517200 chr3A 86.207 493 33 14 275 735 730268245 730267756 4.190000e-138 501.0
13 TraesCS3D01G517200 chr3A 89.716 282 22 3 1 275 730268565 730268284 1.240000e-93 353.0
14 TraesCS3D01G517200 chr3A 90.547 201 17 2 2612 2810 730265775 730265575 5.990000e-67 265.0
15 TraesCS3D01G517200 chr3B 88.567 1277 116 15 747 2005 807855648 807856912 0.000000e+00 1522.0
16 TraesCS3D01G517200 chr3B 82.302 808 80 32 747 1533 807930063 807930828 2.370000e-180 641.0
17 TraesCS3D01G517200 chr3B 81.459 809 89 31 747 1533 807881624 807882393 8.630000e-170 606.0
18 TraesCS3D01G517200 chr3B 80.385 831 99 41 747 1533 807812580 807813390 8.760000e-160 573.0
19 TraesCS3D01G517200 chr3B 84.036 332 31 7 747 1073 807852942 807853256 1.640000e-77 300.0
20 TraesCS3D01G517200 chr3B 88.525 122 12 2 1950 2069 761567674 761567553 2.260000e-31 147.0
21 TraesCS3D01G517200 chr3B 83.929 112 9 4 622 733 807812493 807812595 6.420000e-17 99.0
22 TraesCS3D01G517200 chr3B 88.889 63 7 0 2718 2780 749144433 749144495 8.370000e-11 78.7
23 TraesCS3D01G517200 chr3B 100.000 31 0 0 705 735 807855635 807855665 1.090000e-04 58.4
24 TraesCS3D01G517200 chr1D 76.600 547 68 28 1843 2362 306629229 306629742 2.170000e-61 246.0
25 TraesCS3D01G517200 chr1D 83.871 155 18 6 1954 2106 488104717 488104866 1.050000e-29 141.0
26 TraesCS3D01G517200 chr6B 81.333 225 31 7 2601 2818 713732523 713732743 3.730000e-39 172.0
27 TraesCS3D01G517200 chr2B 84.211 171 18 9 1947 2110 781263234 781263066 1.050000e-34 158.0
28 TraesCS3D01G517200 chr7A 88.525 122 14 0 1966 2087 155213657 155213536 6.290000e-32 148.0
29 TraesCS3D01G517200 chr5A 82.468 154 21 5 1947 2097 566454705 566454555 2.280000e-26 130.0
30 TraesCS3D01G517200 chr1B 84.848 99 13 2 2721 2818 469551524 469551427 6.420000e-17 99.0


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 TraesCS3D01G517200 chr3D 600583821 600586638 2817 False 5204.0 5204 100.000000 1 2818 1 chr3D.!!$F5 2817
1 TraesCS3D01G517200 chr3D 600607534 600608305 771 False 658.0 658 82.571000 747 1533 1 chr3D.!!$F7 786
2 TraesCS3D01G517200 chr3D 600594108 600594882 774 False 634.0 634 82.042000 747 1533 1 chr3D.!!$F6 786
3 TraesCS3D01G517200 chr3D 600563185 600563836 651 False 545.0 545 82.132000 881 1533 1 chr3D.!!$F4 652
4 TraesCS3D01G517200 chr3A 730265575 730268565 2990 True 939.5 2639 89.992750 1 2810 4 chr3A.!!$R4 2809
5 TraesCS3D01G517200 chr3A 730177905 730178666 761 True 645.0 645 82.434000 757 1533 1 chr3A.!!$R1 776
6 TraesCS3D01G517200 chr3A 730208197 730208968 771 True 612.0 612 81.605000 750 1533 1 chr3A.!!$R2 783
7 TraesCS3D01G517200 chr3A 730279520 730280167 647 True 553.0 553 82.380000 881 1533 1 chr3A.!!$R3 652
8 TraesCS3D01G517200 chr3B 807930063 807930828 765 False 641.0 641 82.302000 747 1533 1 chr3B.!!$F3 786
9 TraesCS3D01G517200 chr3B 807852942 807856912 3970 False 626.8 1522 90.867667 705 2005 3 chr3B.!!$F5 1300
10 TraesCS3D01G517200 chr3B 807881624 807882393 769 False 606.0 606 81.459000 747 1533 1 chr3B.!!$F2 786
11 TraesCS3D01G517200 chr3B 807812493 807813390 897 False 336.0 573 82.157000 622 1533 2 chr3B.!!$F4 911
12 TraesCS3D01G517200 chr1D 306629229 306629742 513 False 246.0 246 76.600000 1843 2362 1 chr1D.!!$F1 519

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
171 172 0.106918 TTTGAAGGAAGGGCGTGTGT 60.107 50.0 0.0 0.0 0.0 3.72 F
1081 3912 0.246635 ACGTGCTCTTAGAATGGCGT 59.753 50.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1726 4645 0.036875 ACTCGGGGGCTCTCAAAAAG 59.963 55.0 0.0 0.0 0.0 2.27 R
1990 4932 0.955428 TCTTCGCCACATCAACCTGC 60.955 55.0 0.0 0.0 0.0 4.85 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
25 26 1.135228 CGATCACCCATACACGTGACA 60.135 52.381 25.01 9.98 41.56 3.58
29 30 0.892755 ACCCATACACGTGACACGAT 59.107 50.000 33.12 21.84 46.05 3.73
31 32 1.188558 CCATACACGTGACACGATCG 58.811 55.000 33.12 21.61 46.05 3.69
34 35 0.169451 TACACGTGACACGATCGCAT 59.831 50.000 33.12 7.88 46.05 4.73
47 48 4.312231 CGCATTACATGGCCGCCG 62.312 66.667 4.58 0.00 0.00 6.46
90 91 3.472263 CAGGCGTGCTGTTTTAACC 57.528 52.632 0.00 0.00 0.00 2.85
95 96 1.135774 GCGTGCTGTTTTAACCCTAGC 60.136 52.381 0.00 0.00 35.06 3.42
114 115 0.390860 CAGCTAGGGCGTGCTATCTT 59.609 55.000 0.00 0.00 44.37 2.40
133 134 4.606210 TCTTATTTTTAGGGGAAGGGCAC 58.394 43.478 0.00 0.00 0.00 5.01
147 148 5.279960 GGGAAGGGCACATTGTTTATTTTCT 60.280 40.000 0.00 0.00 0.00 2.52
148 149 5.639082 GGAAGGGCACATTGTTTATTTTCTG 59.361 40.000 0.00 0.00 0.00 3.02
155 156 8.063630 GGCACATTGTTTATTTTCTGTTCTTTG 58.936 33.333 0.00 0.00 0.00 2.77
171 172 0.106918 TTTGAAGGAAGGGCGTGTGT 60.107 50.000 0.00 0.00 0.00 3.72
186 187 4.035208 GGCGTGTGTTCTTTTAGGATATGG 59.965 45.833 0.00 0.00 0.00 2.74
188 189 4.876107 CGTGTGTTCTTTTAGGATATGGCT 59.124 41.667 0.00 0.00 0.00 4.75
190 191 6.018994 CGTGTGTTCTTTTAGGATATGGCTAC 60.019 42.308 0.00 0.00 0.00 3.58
191 192 6.260271 GTGTGTTCTTTTAGGATATGGCTACC 59.740 42.308 0.00 0.00 0.00 3.18
192 193 6.157994 TGTGTTCTTTTAGGATATGGCTACCT 59.842 38.462 0.00 0.00 37.76 3.08
193 194 7.346175 TGTGTTCTTTTAGGATATGGCTACCTA 59.654 37.037 0.00 0.00 35.52 3.08
194 195 8.208903 GTGTTCTTTTAGGATATGGCTACCTAA 58.791 37.037 0.00 0.00 42.24 2.69
225 233 3.659786 CACGTACTGTTTCCTTGGATCA 58.340 45.455 0.00 0.00 0.00 2.92
259 267 2.911484 AGGCAAAAGTCTGATCGATCC 58.089 47.619 22.31 7.46 0.00 3.36
284 331 8.956426 CCTAACTTCTTTTTAGGAATGTATGCA 58.044 33.333 2.47 0.00 46.05 3.96
355 402 8.943002 ACGTTTTCTCCACTAAAGTTATAATGG 58.057 33.333 0.00 0.00 0.00 3.16
356 403 7.908601 CGTTTTCTCCACTAAAGTTATAATGGC 59.091 37.037 0.00 0.00 0.00 4.40
359 406 7.859325 TCTCCACTAAAGTTATAATGGCAAC 57.141 36.000 0.00 0.00 0.00 4.17
360 407 6.826741 TCTCCACTAAAGTTATAATGGCAACC 59.173 38.462 0.00 0.00 0.00 3.77
366 413 1.066454 GTTATAATGGCAACCGTGGGC 59.934 52.381 0.00 0.00 0.00 5.36
432 480 8.477984 AAGTATACTAAAAATTAACGGTCGCA 57.522 30.769 5.65 0.00 0.00 5.10
433 481 8.652810 AGTATACTAAAAATTAACGGTCGCAT 57.347 30.769 2.75 0.00 0.00 4.73
593 646 9.923143 TTAATAAGAATCAAGTGACGAGAAAGA 57.077 29.630 0.00 0.00 0.00 2.52
615 668 5.050091 AGAGAGTTACAGCAACACATTTTCG 60.050 40.000 0.00 0.00 39.81 3.46
616 669 4.814234 AGAGTTACAGCAACACATTTTCGA 59.186 37.500 0.00 0.00 39.81 3.71
617 670 5.295787 AGAGTTACAGCAACACATTTTCGAA 59.704 36.000 0.00 0.00 39.81 3.71
729 808 4.649674 ACCCTTTCCCAAAAGAGAGAAAAC 59.350 41.667 0.00 0.00 43.90 2.43
730 809 4.649218 CCCTTTCCCAAAAGAGAGAAAACA 59.351 41.667 0.00 0.00 43.90 2.83
731 810 5.128663 CCCTTTCCCAAAAGAGAGAAAACAA 59.871 40.000 0.00 0.00 43.90 2.83
732 811 6.042777 CCTTTCCCAAAAGAGAGAAAACAAC 58.957 40.000 0.00 0.00 43.90 3.32
733 812 6.127338 CCTTTCCCAAAAGAGAGAAAACAACT 60.127 38.462 0.00 0.00 43.90 3.16
734 813 6.850752 TTCCCAAAAGAGAGAAAACAACTT 57.149 33.333 0.00 0.00 0.00 2.66
735 814 6.451064 TCCCAAAAGAGAGAAAACAACTTC 57.549 37.500 0.00 0.00 0.00 3.01
736 815 6.187682 TCCCAAAAGAGAGAAAACAACTTCT 58.812 36.000 0.00 0.00 38.39 2.85
737 816 6.663523 TCCCAAAAGAGAGAAAACAACTTCTT 59.336 34.615 0.00 0.00 35.76 2.52
738 817 7.178451 TCCCAAAAGAGAGAAAACAACTTCTTT 59.822 33.333 0.00 0.00 35.76 2.52
739 818 7.819415 CCCAAAAGAGAGAAAACAACTTCTTTT 59.181 33.333 4.66 4.66 35.76 2.27
740 819 9.208022 CCAAAAGAGAGAAAACAACTTCTTTTT 57.792 29.630 7.15 0.00 35.76 1.94
743 822 9.631452 AAAGAGAGAAAACAACTTCTTTTTCTG 57.369 29.630 12.73 0.00 46.98 3.02
744 823 8.567285 AGAGAGAAAACAACTTCTTTTTCTGA 57.433 30.769 12.73 0.00 46.98 3.27
745 824 8.672815 AGAGAGAAAACAACTTCTTTTTCTGAG 58.327 33.333 12.73 0.00 46.98 3.35
748 827 8.972262 AGAAAACAACTTCTTTTTCTGAGAAC 57.028 30.769 8.20 0.00 45.86 3.01
857 936 4.151258 ACGATGCTGAAAATGTTCACAG 57.849 40.909 0.00 0.00 38.88 3.66
922 1012 5.718130 TGGAATCATCTTTGCTCTCCAATTT 59.282 36.000 0.00 0.00 32.49 1.82
1081 3912 0.246635 ACGTGCTCTTAGAATGGCGT 59.753 50.000 0.00 0.00 0.00 5.68
1202 4042 3.376078 CAAGCACGGCCTTGGCAT 61.376 61.111 11.75 0.00 38.78 4.40
1203 4055 2.045708 CAAGCACGGCCTTGGCATA 61.046 57.895 11.75 0.00 38.78 3.14
1260 4133 1.157870 CCAACACCACTGACGTCCAC 61.158 60.000 14.12 0.00 0.00 4.02
1270 4143 1.733399 GACGTCCACTGCTTCGACC 60.733 63.158 3.51 0.00 0.00 4.79
1347 4232 2.344203 CCACGGGCTCTTCGACTCT 61.344 63.158 0.00 0.00 0.00 3.24
1620 4529 3.838903 AGTTATAATAGCCGGCTAGCCTT 59.161 43.478 37.16 28.67 31.45 4.35
1694 4603 2.466846 GGTAACGTCATGACATACCCG 58.533 52.381 30.26 18.50 37.41 5.28
1726 4645 7.320443 TGATTTGAATGACCACTGCTATTAC 57.680 36.000 0.00 0.00 0.00 1.89
1741 4660 3.632604 GCTATTACTTTTTGAGAGCCCCC 59.367 47.826 0.00 0.00 0.00 5.40
1757 4676 2.638363 GCCCCCGAGTAATCTTTCCTAT 59.362 50.000 0.00 0.00 0.00 2.57
1762 4681 7.310858 GCCCCCGAGTAATCTTTCCTATTTATA 60.311 40.741 0.00 0.00 0.00 0.98
1864 4783 4.378459 GGAGTAAAGTGCTCAAAACCATCG 60.378 45.833 0.00 0.00 34.83 3.84
2089 5031 0.032217 CTCTGGGCTCCTCTCTCCTT 60.032 60.000 0.00 0.00 0.00 3.36
2094 5036 1.062810 GGGCTCCTCTCTCCTTTCCTA 60.063 57.143 0.00 0.00 0.00 2.94
2114 5056 1.341581 ACTCTTCTCCCCTCTCCTTCG 60.342 57.143 0.00 0.00 0.00 3.79
2150 5092 1.300697 GCGACCGTGGAAGAACAGT 60.301 57.895 0.00 0.00 0.00 3.55
2333 5281 2.189521 CCGTGCCCATACCCACTC 59.810 66.667 0.00 0.00 0.00 3.51
2336 5284 3.087253 TGCCCATACCCACTCCGG 61.087 66.667 0.00 0.00 0.00 5.14
2337 5285 4.564110 GCCCATACCCACTCCGGC 62.564 72.222 0.00 0.00 0.00 6.13
2385 5333 4.660938 GCCCCTGCAAACTCCGGT 62.661 66.667 0.00 0.00 37.47 5.28
2484 5432 1.135689 GTTCAATGTGGTAGGCTTGCG 60.136 52.381 0.00 0.00 0.00 4.85
2516 5464 4.120331 GTGCCATGACGCCTTGCC 62.120 66.667 0.00 0.00 0.00 4.52
2518 5466 3.818787 GCCATGACGCCTTGCCTG 61.819 66.667 0.00 0.00 0.00 4.85
2522 5470 3.925630 ATGACGCCTTGCCTGGTGG 62.926 63.158 9.87 0.00 41.59 4.61
2523 5471 4.329545 GACGCCTTGCCTGGTGGA 62.330 66.667 9.87 0.00 41.59 4.02
2524 5472 3.628646 GACGCCTTGCCTGGTGGAT 62.629 63.158 9.87 0.00 41.59 3.41
2525 5473 2.825836 CGCCTTGCCTGGTGGATC 60.826 66.667 0.00 0.00 34.20 3.36
2526 5474 2.440980 GCCTTGCCTGGTGGATCC 60.441 66.667 4.20 4.20 34.57 3.36
2527 5475 2.124570 CCTTGCCTGGTGGATCCG 60.125 66.667 7.39 0.00 39.52 4.18
2528 5476 2.124570 CTTGCCTGGTGGATCCGG 60.125 66.667 7.39 2.89 42.06 5.14
2529 5477 2.933287 TTGCCTGGTGGATCCGGT 60.933 61.111 7.39 0.00 40.86 5.28
2530 5478 3.266686 TTGCCTGGTGGATCCGGTG 62.267 63.158 7.39 0.00 40.86 4.94
2531 5479 4.489771 GCCTGGTGGATCCGGTGG 62.490 72.222 7.39 7.82 40.86 4.61
2532 5480 4.489771 CCTGGTGGATCCGGTGGC 62.490 72.222 7.39 0.00 40.86 5.01
2533 5481 4.489771 CTGGTGGATCCGGTGGCC 62.490 72.222 7.39 0.00 39.52 5.36
2544 5492 3.087906 GGTGGCCGGTACCTGGAT 61.088 66.667 22.13 0.00 35.30 3.41
2545 5493 2.504519 GTGGCCGGTACCTGGATC 59.495 66.667 22.13 14.62 0.00 3.36
2546 5494 2.766651 TGGCCGGTACCTGGATCC 60.767 66.667 22.13 4.20 0.00 3.36
2547 5495 3.925090 GGCCGGTACCTGGATCCG 61.925 72.222 22.13 20.62 43.30 4.18
2550 5498 4.280494 CGGTACCTGGATCCGGCG 62.280 72.222 15.84 9.42 40.49 6.46
2551 5499 4.603946 GGTACCTGGATCCGGCGC 62.604 72.222 15.84 0.00 0.00 6.53
2552 5500 3.537874 GTACCTGGATCCGGCGCT 61.538 66.667 15.84 2.07 0.00 5.92
2553 5501 3.536917 TACCTGGATCCGGCGCTG 61.537 66.667 15.84 9.96 0.00 5.18
2573 5521 4.208686 GCCGGTGGGAGCTCGTAG 62.209 72.222 7.83 0.00 34.06 3.51
2574 5522 3.528370 CCGGTGGGAGCTCGTAGG 61.528 72.222 7.83 2.87 34.06 3.18
2575 5523 3.528370 CGGTGGGAGCTCGTAGGG 61.528 72.222 7.83 0.00 0.00 3.53
2576 5524 3.851128 GGTGGGAGCTCGTAGGGC 61.851 72.222 7.83 0.00 0.00 5.19
2577 5525 3.075005 GTGGGAGCTCGTAGGGCA 61.075 66.667 7.83 0.00 0.00 5.36
2578 5526 2.759973 TGGGAGCTCGTAGGGCAG 60.760 66.667 7.83 0.00 0.00 4.85
2579 5527 4.228567 GGGAGCTCGTAGGGCAGC 62.229 72.222 7.83 0.00 35.73 5.25
2580 5528 4.228567 GGAGCTCGTAGGGCAGCC 62.229 72.222 7.83 1.26 36.17 4.85
2581 5529 4.228567 GAGCTCGTAGGGCAGCCC 62.229 72.222 24.90 24.90 45.90 5.19
2597 5545 4.742201 CCCGCCGTGTCAGGTGAG 62.742 72.222 0.00 0.00 44.18 3.51
2598 5546 4.742201 CCGCCGTGTCAGGTGAGG 62.742 72.222 0.00 0.00 44.18 3.86
2599 5547 3.991051 CGCCGTGTCAGGTGAGGT 61.991 66.667 0.00 0.00 44.18 3.85
2600 5548 2.357517 GCCGTGTCAGGTGAGGTG 60.358 66.667 0.00 0.00 0.00 4.00
2601 5549 2.343758 CCGTGTCAGGTGAGGTGG 59.656 66.667 0.00 0.00 0.00 4.61
2602 5550 2.357517 CGTGTCAGGTGAGGTGGC 60.358 66.667 0.00 0.00 0.00 5.01
2603 5551 2.032681 GTGTCAGGTGAGGTGGCC 59.967 66.667 0.00 0.00 0.00 5.36
2604 5552 3.625897 TGTCAGGTGAGGTGGCCG 61.626 66.667 0.00 0.00 0.00 6.13
2605 5553 4.394712 GTCAGGTGAGGTGGCCGG 62.395 72.222 0.00 0.00 0.00 6.13
2606 5554 4.631740 TCAGGTGAGGTGGCCGGA 62.632 66.667 5.05 0.00 0.00 5.14
2607 5555 4.087892 CAGGTGAGGTGGCCGGAG 62.088 72.222 5.05 0.00 0.00 4.63
2633 5706 3.474570 GGGAGCGGAGATGGCTGT 61.475 66.667 0.00 0.00 41.72 4.40
2680 5753 4.155733 CGGCATGGTGCGGGAGTA 62.156 66.667 0.00 0.00 46.21 2.59
2694 5767 1.553704 GGGAGTAGCCGGAGAAAGAAA 59.446 52.381 5.05 0.00 37.63 2.52
2714 5787 6.769512 AGAAAAAGAAAAGGGGGAAATAAGC 58.230 36.000 0.00 0.00 0.00 3.09
2750 5823 4.416738 GGCCCTGTCCACCTCAGC 62.417 72.222 0.00 0.00 0.00 4.26
2779 5854 7.506114 TCAACACATTGACTAGGACTAGTTTT 58.494 34.615 12.84 0.00 45.63 2.43
2780 5855 7.656137 TCAACACATTGACTAGGACTAGTTTTC 59.344 37.037 12.84 2.29 45.63 2.29
2789 5864 3.474920 AGGACTAGTTTTCCCCCATCAT 58.525 45.455 0.00 0.00 33.01 2.45
2791 5866 3.435169 GGACTAGTTTTCCCCCATCATCC 60.435 52.174 0.00 0.00 0.00 3.51
2796 5871 0.546122 TTTCCCCCATCATCCTGACG 59.454 55.000 0.00 0.00 0.00 4.35
2803 5878 1.097547 CATCATCCTGACGGTTGGGC 61.098 60.000 0.00 0.00 32.04 5.36
2804 5879 2.270874 ATCATCCTGACGGTTGGGCC 62.271 60.000 0.00 0.00 32.04 5.80
2813 5888 4.678743 GGTTGGGCCCCACTGGTC 62.679 72.222 24.44 5.12 38.35 4.02
2814 5889 3.897122 GTTGGGCCCCACTGGTCA 61.897 66.667 22.27 0.00 42.20 4.02
2815 5890 3.579302 TTGGGCCCCACTGGTCAG 61.579 66.667 22.27 0.00 42.20 3.51
2816 5891 4.918360 TGGGCCCCACTGGTCAGT 62.918 66.667 22.27 0.00 42.20 3.41
2817 5892 3.580319 GGGCCCCACTGGTCAGTT 61.580 66.667 12.23 0.00 42.20 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.221466 CGGCCATGTAATGCGATCGT 61.221 55.000 17.81 0.00 44.97 3.73
29 30 2.899838 GGCGGCCATGTAATGCGA 60.900 61.111 15.62 0.00 44.97 5.10
31 32 3.964875 CCGGCGGCCATGTAATGC 61.965 66.667 20.71 0.00 44.97 3.56
47 48 3.058160 ATGCACTTGCGACAGGCC 61.058 61.111 0.00 0.00 45.83 5.19
53 54 2.771435 CATCTCCATGCACTTGCGA 58.229 52.632 0.00 0.00 45.83 5.10
95 96 0.390860 AAGATAGCACGCCCTAGCTG 59.609 55.000 0.00 0.00 41.97 4.24
104 105 6.204882 CCTTCCCCTAAAAATAAGATAGCACG 59.795 42.308 0.00 0.00 0.00 5.34
114 115 4.618378 ATGTGCCCTTCCCCTAAAAATA 57.382 40.909 0.00 0.00 0.00 1.40
147 148 1.133915 ACGCCCTTCCTTCAAAGAACA 60.134 47.619 0.00 0.00 0.00 3.18
148 149 1.266989 CACGCCCTTCCTTCAAAGAAC 59.733 52.381 0.00 0.00 0.00 3.01
155 156 0.250338 AGAACACACGCCCTTCCTTC 60.250 55.000 0.00 0.00 0.00 3.46
171 172 7.792736 TCCTTAGGTAGCCATATCCTAAAAGAA 59.207 37.037 0.00 0.00 41.38 2.52
186 187 1.139256 GTGCTTCCCTCCTTAGGTAGC 59.861 57.143 0.00 1.86 43.73 3.58
188 189 1.272872 ACGTGCTTCCCTCCTTAGGTA 60.273 52.381 0.00 0.00 41.89 3.08
190 191 1.136500 GTACGTGCTTCCCTCCTTAGG 59.864 57.143 0.00 0.00 43.25 2.69
191 192 2.100989 AGTACGTGCTTCCCTCCTTAG 58.899 52.381 0.00 0.00 0.00 2.18
192 193 1.822990 CAGTACGTGCTTCCCTCCTTA 59.177 52.381 2.37 0.00 0.00 2.69
193 194 0.608640 CAGTACGTGCTTCCCTCCTT 59.391 55.000 2.37 0.00 0.00 3.36
194 195 0.542232 ACAGTACGTGCTTCCCTCCT 60.542 55.000 2.37 0.00 0.00 3.69
201 209 2.158871 TCCAAGGAAACAGTACGTGCTT 60.159 45.455 2.37 0.00 0.00 3.91
202 210 1.414919 TCCAAGGAAACAGTACGTGCT 59.585 47.619 0.00 0.00 0.00 4.40
295 342 2.326428 GTGGGGCCTACTAGATTGCTA 58.674 52.381 13.48 0.00 0.00 3.49
297 344 0.108774 GGTGGGGCCTACTAGATTGC 59.891 60.000 20.11 0.00 0.00 3.56
321 368 6.539649 TTAGTGGAGAAAACGTTTCATGAG 57.460 37.500 15.01 0.00 0.00 2.90
355 402 0.033366 AGAAAATTGCCCACGGTTGC 59.967 50.000 0.00 0.00 0.00 4.17
356 403 2.524569 AAGAAAATTGCCCACGGTTG 57.475 45.000 0.00 0.00 0.00 3.77
359 406 3.934457 AAGTAAGAAAATTGCCCACGG 57.066 42.857 0.00 0.00 0.00 4.94
360 407 7.812669 AGATTTAAAGTAAGAAAATTGCCCACG 59.187 33.333 0.00 0.00 0.00 4.94
577 630 4.920640 AACTCTCTTTCTCGTCACTTGA 57.079 40.909 0.00 0.00 0.00 3.02
580 633 4.320641 GCTGTAACTCTCTTTCTCGTCACT 60.321 45.833 0.00 0.00 0.00 3.41
593 646 4.814234 TCGAAAATGTGTTGCTGTAACTCT 59.186 37.500 9.94 0.00 40.05 3.24
615 668 1.666888 CCGCTGCTTTCAACACCATTC 60.667 52.381 0.00 0.00 0.00 2.67
616 669 0.314935 CCGCTGCTTTCAACACCATT 59.685 50.000 0.00 0.00 0.00 3.16
617 670 0.537143 TCCGCTGCTTTCAACACCAT 60.537 50.000 0.00 0.00 0.00 3.55
729 808 6.477033 TCTCTCGTTCTCAGAAAAAGAAGTTG 59.523 38.462 0.00 0.00 33.57 3.16
730 809 6.574350 TCTCTCGTTCTCAGAAAAAGAAGTT 58.426 36.000 0.00 0.00 33.57 2.66
731 810 6.150396 TCTCTCGTTCTCAGAAAAAGAAGT 57.850 37.500 0.00 0.00 33.57 3.01
732 811 7.470289 TTTCTCTCGTTCTCAGAAAAAGAAG 57.530 36.000 0.00 0.00 34.04 2.85
733 812 7.333423 TGTTTTCTCTCGTTCTCAGAAAAAGAA 59.667 33.333 7.47 0.00 44.03 2.52
734 813 6.816640 TGTTTTCTCTCGTTCTCAGAAAAAGA 59.183 34.615 7.47 0.00 44.03 2.52
735 814 7.005062 TGTTTTCTCTCGTTCTCAGAAAAAG 57.995 36.000 7.47 0.00 44.03 2.27
736 815 6.978343 TGTTTTCTCTCGTTCTCAGAAAAA 57.022 33.333 7.47 0.00 44.03 1.94
737 816 6.594159 AGTTGTTTTCTCTCGTTCTCAGAAAA 59.406 34.615 0.00 2.65 41.61 2.29
738 817 6.106673 AGTTGTTTTCTCTCGTTCTCAGAAA 58.893 36.000 0.00 0.00 34.94 2.52
739 818 5.661458 AGTTGTTTTCTCTCGTTCTCAGAA 58.339 37.500 0.00 0.00 0.00 3.02
740 819 5.263968 AGTTGTTTTCTCTCGTTCTCAGA 57.736 39.130 0.00 0.00 0.00 3.27
741 820 5.520288 TCAAGTTGTTTTCTCTCGTTCTCAG 59.480 40.000 2.11 0.00 0.00 3.35
742 821 5.416083 TCAAGTTGTTTTCTCTCGTTCTCA 58.584 37.500 2.11 0.00 0.00 3.27
743 822 5.968387 TCAAGTTGTTTTCTCTCGTTCTC 57.032 39.130 2.11 0.00 0.00 2.87
744 823 6.049149 TGATCAAGTTGTTTTCTCTCGTTCT 58.951 36.000 2.11 0.00 0.00 3.01
745 824 6.201044 TCTGATCAAGTTGTTTTCTCTCGTTC 59.799 38.462 2.11 0.00 0.00 3.95
748 827 6.367149 TCATCTGATCAAGTTGTTTTCTCTCG 59.633 38.462 2.11 0.00 0.00 4.04
857 936 7.333528 TGAAATCAATATTTGGGACTGTAGC 57.666 36.000 0.00 0.00 35.41 3.58
922 1012 3.817787 CGACGGACGGTGGAGATA 58.182 61.111 0.00 0.00 38.46 1.98
1081 3912 1.940883 CTGCCGCCGTTGTAGTAGGA 61.941 60.000 0.00 0.00 0.00 2.94
1682 4591 5.134202 TCAACTATAGCGGGTATGTCATG 57.866 43.478 9.85 4.43 0.00 3.07
1687 4596 7.387673 TCATTCAAATCAACTATAGCGGGTATG 59.612 37.037 9.85 3.19 0.00 2.39
1694 4603 7.412853 CAGTGGTCATTCAAATCAACTATAGC 58.587 38.462 0.00 0.00 0.00 2.97
1726 4645 0.036875 ACTCGGGGGCTCTCAAAAAG 59.963 55.000 0.00 0.00 0.00 2.27
1757 4676 7.831753 TCGCCACCAATTTCAATCTTTATAAA 58.168 30.769 0.00 0.00 0.00 1.40
1762 4681 3.573967 ACTCGCCACCAATTTCAATCTTT 59.426 39.130 0.00 0.00 0.00 2.52
1780 4699 6.712241 ATGTTAGACTCAAATGTGAACTCG 57.288 37.500 0.00 0.00 31.88 4.18
1821 4740 3.009723 CCACATGTGGGAATCACTGTAC 58.990 50.000 33.56 0.00 46.81 2.90
1849 4768 4.616802 CACAAATACGATGGTTTTGAGCAC 59.383 41.667 16.35 0.00 35.03 4.40
1864 4783 5.927281 TGGAGTACCCTAGACACAAATAC 57.073 43.478 0.00 0.00 35.38 1.89
1902 4822 9.575783 GTAGTGGTCTTTTGTGATTTTTGTTAA 57.424 29.630 0.00 0.00 0.00 2.01
1903 4823 8.962679 AGTAGTGGTCTTTTGTGATTTTTGTTA 58.037 29.630 0.00 0.00 0.00 2.41
1904 4824 7.836842 AGTAGTGGTCTTTTGTGATTTTTGTT 58.163 30.769 0.00 0.00 0.00 2.83
1905 4825 7.404671 AGTAGTGGTCTTTTGTGATTTTTGT 57.595 32.000 0.00 0.00 0.00 2.83
1961 4902 2.260869 CCCACCCGTCAGTTTGCTG 61.261 63.158 0.00 0.00 43.87 4.41
1986 4928 1.588824 CGCCACATCAACCTGCACAT 61.589 55.000 0.00 0.00 0.00 3.21
1990 4932 0.955428 TCTTCGCCACATCAACCTGC 60.955 55.000 0.00 0.00 0.00 4.85
2034 4976 4.250170 ACCCCCGTCCACCTCAGT 62.250 66.667 0.00 0.00 0.00 3.41
2089 5031 2.245287 GGAGAGGGGAGAAGAGTAGGAA 59.755 54.545 0.00 0.00 0.00 3.36
2094 5036 1.341581 CGAAGGAGAGGGGAGAAGAGT 60.342 57.143 0.00 0.00 0.00 3.24
2114 5056 2.266055 CGCTCCTGTGGGAAGGAC 59.734 66.667 0.00 0.00 41.60 3.85
2319 5267 3.087253 CCGGAGTGGGTATGGGCA 61.087 66.667 0.00 0.00 0.00 5.36
2424 5372 2.614446 CGCTTTGAGCTGCAGCACT 61.614 57.895 38.24 21.10 45.16 4.40
2431 5379 1.296432 CGAATCGCGCTTTGAGCTG 60.296 57.895 5.56 0.00 39.60 4.24
2453 5401 3.118454 ATTGAACTCGGCGGTGCG 61.118 61.111 7.21 0.00 0.00 5.34
2456 5404 1.671054 CCACATTGAACTCGGCGGT 60.671 57.895 7.21 0.19 0.00 5.68
2468 5416 2.046285 GCCGCAAGCCTACCACATT 61.046 57.895 0.00 0.00 34.35 2.71
2506 5454 3.628646 ATCCACCAGGCAAGGCGTC 62.629 63.158 0.00 0.00 33.74 5.19
2516 5464 4.489771 GGCCACCGGATCCACCAG 62.490 72.222 9.46 0.00 38.90 4.00
2527 5475 3.087906 ATCCAGGTACCGGCCACC 61.088 66.667 16.39 16.39 36.22 4.61
2528 5476 2.504519 GATCCAGGTACCGGCCAC 59.495 66.667 15.48 0.00 0.00 5.01
2529 5477 2.766651 GGATCCAGGTACCGGCCA 60.767 66.667 6.95 1.77 0.00 5.36
2530 5478 3.925090 CGGATCCAGGTACCGGCC 61.925 72.222 13.41 11.64 42.48 6.13
2533 5481 4.280494 CGCCGGATCCAGGTACCG 62.280 72.222 13.41 16.37 45.24 4.02
2534 5482 4.603946 GCGCCGGATCCAGGTACC 62.604 72.222 13.41 2.73 0.00 3.34
2535 5483 3.537874 AGCGCCGGATCCAGGTAC 61.538 66.667 13.41 10.03 0.00 3.34
2536 5484 3.536917 CAGCGCCGGATCCAGGTA 61.537 66.667 13.41 0.00 0.00 3.08
2556 5504 4.208686 CTACGAGCTCCCACCGGC 62.209 72.222 8.47 0.00 0.00 6.13
2557 5505 3.528370 CCTACGAGCTCCCACCGG 61.528 72.222 8.47 0.00 0.00 5.28
2558 5506 3.528370 CCCTACGAGCTCCCACCG 61.528 72.222 8.47 0.00 0.00 4.94
2559 5507 3.851128 GCCCTACGAGCTCCCACC 61.851 72.222 8.47 0.00 0.00 4.61
2560 5508 3.075005 TGCCCTACGAGCTCCCAC 61.075 66.667 8.47 0.00 0.00 4.61
2561 5509 2.759973 CTGCCCTACGAGCTCCCA 60.760 66.667 8.47 0.00 0.00 4.37
2562 5510 4.228567 GCTGCCCTACGAGCTCCC 62.229 72.222 8.47 0.00 32.12 4.30
2563 5511 4.228567 GGCTGCCCTACGAGCTCC 62.229 72.222 7.66 0.00 35.42 4.70
2564 5512 4.228567 GGGCTGCCCTACGAGCTC 62.229 72.222 30.42 2.73 41.34 4.09
2580 5528 4.742201 CTCACCTGACACGGCGGG 62.742 72.222 8.04 8.04 40.29 6.13
2581 5529 4.742201 CCTCACCTGACACGGCGG 62.742 72.222 13.24 2.35 0.00 6.13
2582 5530 3.991051 ACCTCACCTGACACGGCG 61.991 66.667 4.80 4.80 0.00 6.46
2583 5531 2.357517 CACCTCACCTGACACGGC 60.358 66.667 0.00 0.00 0.00 5.68
2584 5532 2.343758 CCACCTCACCTGACACGG 59.656 66.667 0.00 0.00 0.00 4.94
2585 5533 2.357517 GCCACCTCACCTGACACG 60.358 66.667 0.00 0.00 0.00 4.49
2586 5534 2.032681 GGCCACCTCACCTGACAC 59.967 66.667 0.00 0.00 0.00 3.67
2587 5535 3.625897 CGGCCACCTCACCTGACA 61.626 66.667 2.24 0.00 0.00 3.58
2588 5536 4.394712 CCGGCCACCTCACCTGAC 62.395 72.222 2.24 0.00 0.00 3.51
2589 5537 4.631740 TCCGGCCACCTCACCTGA 62.632 66.667 2.24 0.00 0.00 3.86
2590 5538 4.087892 CTCCGGCCACCTCACCTG 62.088 72.222 2.24 0.00 0.00 4.00
2651 5724 1.667830 CATGCCGACCGTCACAACT 60.668 57.895 0.00 0.00 0.00 3.16
2665 5738 2.897350 GCTACTCCCGCACCATGC 60.897 66.667 0.00 0.00 40.69 4.06
2680 5753 4.038042 CCTTTTCTTTTTCTTTCTCCGGCT 59.962 41.667 0.00 0.00 0.00 5.52
2694 5767 4.498493 TGGCTTATTTCCCCCTTTTCTTT 58.502 39.130 0.00 0.00 0.00 2.52
2714 5787 1.676635 CCACCTGTCAGCCACATGG 60.677 63.158 0.00 0.00 33.23 3.66
2796 5871 4.678743 GACCAGTGGGGCCCAACC 62.679 72.222 30.70 16.93 42.05 3.77


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

AutoCloner maintained by Alex Coulton.