Multiple sequence alignment - TraesCS6D01G198900

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 TraesCS6D01G198900 chr6D 100.000 4831 0 0 1 4831 277023782 277018952 0.000000e+00 8922.0
1 TraesCS6D01G198900 chr6D 98.507 67 1 0 2583 2649 277021092 277021026 8.490000e-23 119.0
2 TraesCS6D01G198900 chr6D 98.507 67 1 0 2691 2757 277021200 277021134 8.490000e-23 119.0
3 TraesCS6D01G198900 chr6B 94.190 2599 77 21 2 2566 438917377 438914819 0.000000e+00 3895.0
4 TraesCS6D01G198900 chr6B 94.993 2197 84 9 2652 4831 438914816 438912629 0.000000e+00 3424.0
5 TraesCS6D01G198900 chr6A 93.486 2579 96 25 41 2566 398637533 398640092 0.000000e+00 3766.0
6 TraesCS6D01G198900 chr6A 93.283 2114 84 20 2652 4750 398640095 398642165 0.000000e+00 3064.0
7 TraesCS6D01G198900 chr6A 77.632 152 28 5 2129 2277 7401202 7401054 2.400000e-13 87.9
8 TraesCS6D01G198900 chr5B 84.524 168 24 2 2130 2296 10544677 10544511 1.080000e-36 165.0
9 TraesCS6D01G198900 chr5B 80.925 173 29 3 2128 2297 60893973 60894144 3.030000e-27 134.0
10 TraesCS6D01G198900 chr2A 80.233 172 32 2 2130 2300 765170440 765170270 1.410000e-25 128.0
11 TraesCS6D01G198900 chr5D 79.532 171 31 3 2130 2297 57395071 57394902 8.490000e-23 119.0
12 TraesCS6D01G198900 chr3A 80.247 162 27 5 2130 2288 671322187 671322346 3.050000e-22 117.0
13 TraesCS6D01G198900 chr3A 88.889 63 4 3 337 399 563835737 563835678 1.860000e-09 75.0
14 TraesCS6D01G198900 chr2B 74.899 247 52 7 2130 2372 69179434 69179194 2.380000e-18 104.0
15 TraesCS6D01G198900 chr3D 88.889 63 4 3 337 399 424887587 424887646 1.860000e-09 75.0
16 TraesCS6D01G198900 chr3B 88.889 63 4 3 337 399 554986633 554986692 1.860000e-09 75.0


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 TraesCS6D01G198900 chr6D 277018952 277023782 4830 True 3053.333333 8922 99.004667 1 4831 3 chr6D.!!$R1 4830
1 TraesCS6D01G198900 chr6B 438912629 438917377 4748 True 3659.500000 3895 94.591500 2 4831 2 chr6B.!!$R1 4829
2 TraesCS6D01G198900 chr6A 398637533 398642165 4632 False 3415.000000 3766 93.384500 41 4750 2 chr6A.!!$F1 4709

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
640 655 0.304705 CTTTCTGAACACGCGTTGCT 59.695 50.0 10.22 0.0 34.75 3.91 F
1733 1770 0.310543 GCATTTCGCCAGTTCACACA 59.689 50.0 0.00 0.0 32.94 3.72 F
2620 2700 0.030235 TCGACGTGTGTCTTGTCCTG 59.970 55.0 0.00 0.0 43.21 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2309 2389 0.721718 CGAGATCCAACTTTGACCGC 59.278 55.0 0.00 0.0 0.00 5.68 R
3069 3149 0.112995 GGCTATGGGATGGCAATGGA 59.887 55.0 0.00 0.0 38.67 3.41 R
4456 4550 0.240945 CTAGGTGCGCCCAGTTTTTG 59.759 55.0 14.07 0.0 34.66 2.44 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
121 122 1.303643 CTCCTCGCCTTTTGCCCTT 60.304 57.895 0.00 0.00 36.24 3.95
247 248 2.203788 AACTCCCCAGCGTCTCCA 60.204 61.111 0.00 0.00 0.00 3.86
294 295 3.062466 CCTCTCGCGTCCTGACCA 61.062 66.667 5.77 0.00 0.00 4.02
315 316 4.039852 CCAAGGCTCTAAATCTCTCCTACC 59.960 50.000 0.00 0.00 0.00 3.18
316 317 4.825199 AGGCTCTAAATCTCTCCTACCT 57.175 45.455 0.00 0.00 0.00 3.08
318 319 3.830178 GGCTCTAAATCTCTCCTACCTCC 59.170 52.174 0.00 0.00 0.00 4.30
319 320 3.504520 GCTCTAAATCTCTCCTACCTCCG 59.495 52.174 0.00 0.00 0.00 4.63
320 321 4.747316 GCTCTAAATCTCTCCTACCTCCGA 60.747 50.000 0.00 0.00 0.00 4.55
355 367 2.202008 GCCGTTCGCGTTCTTTCG 60.202 61.111 5.77 3.37 39.32 3.46
367 379 2.125673 CTTTCGCCGTCGGGACAT 60.126 61.111 14.38 0.00 36.13 3.06
379 391 3.195698 GGACATCGCGTTCCTGCC 61.196 66.667 5.77 0.00 0.00 4.85
426 438 3.784178 TGGCCATAGGGTTTTGATTGAA 58.216 40.909 0.00 0.00 36.17 2.69
442 454 0.740868 TGAAGTATGCACGAGGCTGC 60.741 55.000 0.00 0.00 45.15 5.25
451 463 2.027314 CGAGGCTGCTCTCATCCG 59.973 66.667 15.25 2.26 33.82 4.18
454 466 4.925861 GGCTGCTCTCATCCGGCC 62.926 72.222 0.00 0.00 45.37 6.13
640 655 0.304705 CTTTCTGAACACGCGTTGCT 59.695 50.000 10.22 0.00 34.75 3.91
654 669 1.643810 CGTTGCTTATTTTCACAGCGC 59.356 47.619 0.00 0.00 36.24 5.92
655 670 2.660490 GTTGCTTATTTTCACAGCGCA 58.340 42.857 11.47 0.00 36.24 6.09
708 723 2.159170 TGGGTTTGCCTTTTCGAAACAG 60.159 45.455 10.79 10.94 32.30 3.16
715 730 2.286536 GCCTTTTCGAAACAGCGTGTTA 60.287 45.455 10.79 0.00 40.14 2.41
724 739 4.090786 CGAAACAGCGTGTTATGATGTGTA 59.909 41.667 4.24 0.00 40.14 2.90
725 740 5.388994 CGAAACAGCGTGTTATGATGTGTAA 60.389 40.000 4.24 0.00 40.14 2.41
726 741 5.933187 AACAGCGTGTTATGATGTGTAAA 57.067 34.783 2.19 0.00 39.09 2.01
727 742 6.494893 AACAGCGTGTTATGATGTGTAAAT 57.505 33.333 2.19 0.00 39.09 1.40
728 743 6.106877 ACAGCGTGTTATGATGTGTAAATC 57.893 37.500 0.00 0.00 31.80 2.17
729 744 5.064707 ACAGCGTGTTATGATGTGTAAATCC 59.935 40.000 0.00 0.00 31.80 3.01
730 745 5.294306 CAGCGTGTTATGATGTGTAAATCCT 59.706 40.000 0.00 0.00 0.00 3.24
731 746 5.294306 AGCGTGTTATGATGTGTAAATCCTG 59.706 40.000 0.00 0.00 0.00 3.86
732 747 5.064707 GCGTGTTATGATGTGTAAATCCTGT 59.935 40.000 0.00 0.00 0.00 4.00
733 748 6.477742 CGTGTTATGATGTGTAAATCCTGTG 58.522 40.000 0.00 0.00 0.00 3.66
734 749 6.258160 GTGTTATGATGTGTAAATCCTGTGC 58.742 40.000 0.00 0.00 0.00 4.57
754 780 2.855180 CAAGCTGCAATTTCTACACCG 58.145 47.619 1.02 0.00 0.00 4.94
819 845 4.961438 ATCTTGGTTGCCTTCACAAAAT 57.039 36.364 0.00 0.00 0.00 1.82
841 867 9.936759 AAAATAATGTGGTCCGATGTTAAAAAT 57.063 25.926 0.00 0.00 0.00 1.82
897 923 2.492881 CAGCACAATAGCATTGGGAACA 59.507 45.455 13.24 0.00 36.85 3.18
1123 1160 0.941542 TGTTGTAAGCGTGTTCCTGC 59.058 50.000 0.00 0.00 0.00 4.85
1324 1361 5.126707 CAGCCAAGAAGCCATTAAGAAGAAT 59.873 40.000 0.00 0.00 0.00 2.40
1733 1770 0.310543 GCATTTCGCCAGTTCACACA 59.689 50.000 0.00 0.00 32.94 3.72
1852 1893 3.382865 TCTCAGTATGCCTTACTCAGCTG 59.617 47.826 7.63 7.63 39.19 4.24
1913 1954 7.557719 ACTTGCTATGCCTTTTACTATGACATT 59.442 33.333 0.00 0.00 0.00 2.71
1946 1987 8.986477 AAACAGAAATTACATGATTACTTGGC 57.014 30.769 0.00 0.00 0.00 4.52
2001 2069 1.277842 TCCTTTCACGCCTCTTGCATA 59.722 47.619 0.00 0.00 41.33 3.14
2183 2251 8.441608 CACACACATTTCAAAAATCAACTTTGA 58.558 29.630 0.00 0.00 40.21 2.69
2184 2252 8.442384 ACACACATTTCAAAAATCAACTTTGAC 58.558 29.630 0.00 0.00 41.32 3.18
2185 2253 8.441608 CACACATTTCAAAAATCAACTTTGACA 58.558 29.630 0.00 0.00 41.32 3.58
2186 2254 8.997323 ACACATTTCAAAAATCAACTTTGACAA 58.003 25.926 0.00 0.00 41.32 3.18
2187 2255 9.823098 CACATTTCAAAAATCAACTTTGACAAA 57.177 25.926 0.00 0.00 41.32 2.83
2249 2329 9.550406 AAAGTTATGCCATTGGATTCATATTTG 57.450 29.630 6.95 0.00 0.00 2.32
2325 2405 3.575965 ATTTGCGGTCAAAGTTGGATC 57.424 42.857 4.46 0.00 44.47 3.36
2354 2434 2.679450 CATGGGCGCATTATTCAATGG 58.321 47.619 14.46 0.00 41.64 3.16
2375 2455 6.001449 TGGAATGGAGGGAATAAGTACTTG 57.999 41.667 18.56 0.00 0.00 3.16
2433 2513 0.835971 TACTCCCCTTGCAGCACTCA 60.836 55.000 0.00 0.00 0.00 3.41
2580 2660 9.302345 GTTTATGTATATGGATGTGGATACTCG 57.698 37.037 0.00 0.00 37.61 4.18
2581 2661 8.589701 TTATGTATATGGATGTGGATACTCGT 57.410 34.615 0.00 0.00 37.61 4.18
2582 2662 9.689501 TTATGTATATGGATGTGGATACTCGTA 57.310 33.333 0.00 0.00 37.61 3.43
2583 2663 8.768501 ATGTATATGGATGTGGATACTCGTAT 57.231 34.615 0.00 0.00 37.61 3.06
2584 2664 8.589701 TGTATATGGATGTGGATACTCGTATT 57.410 34.615 0.00 0.00 37.61 1.89
2585 2665 9.689501 TGTATATGGATGTGGATACTCGTATTA 57.310 33.333 0.00 0.00 37.61 0.98
2587 2667 8.824756 ATATGGATGTGGATACTCGTATTAGT 57.175 34.615 0.00 0.00 37.61 2.24
2588 2668 6.971726 TGGATGTGGATACTCGTATTAGTT 57.028 37.500 0.00 0.00 37.61 2.24
2589 2669 7.356089 TGGATGTGGATACTCGTATTAGTTT 57.644 36.000 0.00 0.00 37.61 2.66
2590 2670 7.431249 TGGATGTGGATACTCGTATTAGTTTC 58.569 38.462 0.00 0.00 37.61 2.78
2591 2671 6.867293 GGATGTGGATACTCGTATTAGTTTCC 59.133 42.308 6.56 6.56 43.82 3.13
2596 2676 8.701908 TGGATACTCGTATTAGTTTCCACTAT 57.298 34.615 10.82 0.00 46.33 2.12
2597 2677 9.797642 TGGATACTCGTATTAGTTTCCACTATA 57.202 33.333 10.82 0.00 46.33 1.31
2601 2681 8.517062 ACTCGTATTAGTTTCCACTATACTGT 57.483 34.615 0.00 0.00 35.32 3.55
2602 2682 8.619546 ACTCGTATTAGTTTCCACTATACTGTC 58.380 37.037 0.00 0.00 35.32 3.51
2603 2683 7.633621 TCGTATTAGTTTCCACTATACTGTCG 58.366 38.462 0.00 0.00 35.32 4.35
2604 2684 7.495606 TCGTATTAGTTTCCACTATACTGTCGA 59.504 37.037 0.00 0.00 35.32 4.20
2605 2685 7.585573 CGTATTAGTTTCCACTATACTGTCGAC 59.414 40.741 9.11 9.11 35.32 4.20
2606 2686 4.352600 AGTTTCCACTATACTGTCGACG 57.647 45.455 11.62 8.41 0.00 5.12
2607 2687 3.755378 AGTTTCCACTATACTGTCGACGT 59.245 43.478 11.62 13.86 0.00 4.34
2608 2688 3.752412 TTCCACTATACTGTCGACGTG 57.248 47.619 18.82 14.95 0.00 4.49
2609 2689 2.703416 TCCACTATACTGTCGACGTGT 58.297 47.619 18.82 17.56 0.00 4.49
2610 2690 2.417586 TCCACTATACTGTCGACGTGTG 59.582 50.000 19.77 17.44 0.00 3.82
2611 2691 2.161012 CCACTATACTGTCGACGTGTGT 59.839 50.000 19.77 16.47 0.00 3.72
2612 2692 3.414464 CACTATACTGTCGACGTGTGTC 58.586 50.000 19.77 0.00 41.91 3.67
2613 2693 3.124806 CACTATACTGTCGACGTGTGTCT 59.875 47.826 19.77 8.43 43.21 3.41
2614 2694 3.750130 ACTATACTGTCGACGTGTGTCTT 59.250 43.478 19.77 8.10 43.21 3.01
2615 2695 2.394545 TACTGTCGACGTGTGTCTTG 57.605 50.000 19.77 2.31 43.21 3.02
2616 2696 0.454600 ACTGTCGACGTGTGTCTTGT 59.545 50.000 11.62 0.00 43.21 3.16
2617 2697 1.121240 CTGTCGACGTGTGTCTTGTC 58.879 55.000 11.62 0.00 43.21 3.18
2618 2698 0.248743 TGTCGACGTGTGTCTTGTCC 60.249 55.000 11.62 0.00 43.21 4.02
2619 2699 0.030369 GTCGACGTGTGTCTTGTCCT 59.970 55.000 0.00 0.00 43.21 3.85
2620 2700 0.030235 TCGACGTGTGTCTTGTCCTG 59.970 55.000 0.00 0.00 43.21 3.86
2621 2701 0.248907 CGACGTGTGTCTTGTCCTGT 60.249 55.000 0.00 0.00 43.21 4.00
2622 2702 1.801395 CGACGTGTGTCTTGTCCTGTT 60.801 52.381 0.00 0.00 43.21 3.16
2623 2703 2.277084 GACGTGTGTCTTGTCCTGTTT 58.723 47.619 0.00 0.00 42.08 2.83
2624 2704 2.277084 ACGTGTGTCTTGTCCTGTTTC 58.723 47.619 0.00 0.00 0.00 2.78
2625 2705 2.276201 CGTGTGTCTTGTCCTGTTTCA 58.724 47.619 0.00 0.00 0.00 2.69
2626 2706 2.285220 CGTGTGTCTTGTCCTGTTTCAG 59.715 50.000 0.00 0.00 0.00 3.02
2627 2707 3.270877 GTGTGTCTTGTCCTGTTTCAGT 58.729 45.455 0.00 0.00 0.00 3.41
2628 2708 3.689649 GTGTGTCTTGTCCTGTTTCAGTT 59.310 43.478 0.00 0.00 0.00 3.16
2629 2709 4.156008 GTGTGTCTTGTCCTGTTTCAGTTT 59.844 41.667 0.00 0.00 0.00 2.66
2630 2710 5.353123 GTGTGTCTTGTCCTGTTTCAGTTTA 59.647 40.000 0.00 0.00 0.00 2.01
2631 2711 6.038271 GTGTGTCTTGTCCTGTTTCAGTTTAT 59.962 38.462 0.00 0.00 0.00 1.40
2632 2712 6.601613 TGTGTCTTGTCCTGTTTCAGTTTATT 59.398 34.615 0.00 0.00 0.00 1.40
2633 2713 7.122055 TGTGTCTTGTCCTGTTTCAGTTTATTT 59.878 33.333 0.00 0.00 0.00 1.40
2634 2714 8.617809 GTGTCTTGTCCTGTTTCAGTTTATTTA 58.382 33.333 0.00 0.00 0.00 1.40
2635 2715 8.617809 TGTCTTGTCCTGTTTCAGTTTATTTAC 58.382 33.333 0.00 0.00 0.00 2.01
2636 2716 8.837389 GTCTTGTCCTGTTTCAGTTTATTTACT 58.163 33.333 0.00 0.00 0.00 2.24
2637 2717 9.403583 TCTTGTCCTGTTTCAGTTTATTTACTT 57.596 29.630 0.00 0.00 0.00 2.24
2639 2719 9.796120 TTGTCCTGTTTCAGTTTATTTACTTTG 57.204 29.630 0.00 0.00 0.00 2.77
2640 2720 9.179909 TGTCCTGTTTCAGTTTATTTACTTTGA 57.820 29.630 0.00 0.00 0.00 2.69
2649 2729 9.974980 TCAGTTTATTTACTTTGAATTTGTCCC 57.025 29.630 0.00 0.00 0.00 4.46
2650 2730 8.911662 CAGTTTATTTACTTTGAATTTGTCCCG 58.088 33.333 0.00 0.00 0.00 5.14
2665 2745 3.408634 TGTCCCGGAATCTTCAACTTTC 58.591 45.455 0.73 0.00 0.00 2.62
2676 2756 8.184848 GGAATCTTCAACTTTCCTAATTGCTAC 58.815 37.037 0.00 0.00 36.73 3.58
2715 2795 3.503363 TGTTTCCACTATACTGTCGACGT 59.497 43.478 11.62 13.86 0.00 4.34
2764 2844 5.138125 ACTTTGAATTTGTCCGCAATGAT 57.862 34.783 0.00 0.00 34.18 2.45
2775 2855 6.499234 TGTCCGCAATGATTTATATGGATG 57.501 37.500 0.00 0.00 0.00 3.51
2778 2858 5.415389 TCCGCAATGATTTATATGGATGTGG 59.585 40.000 0.00 0.00 38.28 4.17
2800 2880 8.476447 TGTGGATACTCGTATTAAACAATGGTA 58.524 33.333 0.00 0.00 37.61 3.25
2838 2918 9.809096 TTCTTGCATCTGTTTTGTGTAAATAAA 57.191 25.926 0.00 0.00 0.00 1.40
2868 2948 4.097892 GCATGTATAAACTGTTGGAAGGGG 59.902 45.833 0.00 0.00 0.00 4.79
2896 2976 0.510359 CAGAGAGGAAATATGCGCGC 59.490 55.000 27.26 27.26 0.00 6.86
3002 3082 1.544246 GCTAAAAATGGGCGTTGGACT 59.456 47.619 0.00 0.00 0.00 3.85
3036 3116 2.134287 GCCTCCCATAGCCACTCGA 61.134 63.158 0.00 0.00 0.00 4.04
3080 3160 1.392589 ACGACCATTCCATTGCCATC 58.607 50.000 0.00 0.00 0.00 3.51
3283 3374 6.493458 AGGCTAACATAAACCAACAGTCATTT 59.507 34.615 0.00 0.00 0.00 2.32
3354 3445 4.827692 TGTTGTCGGTCTTTACATGCTAT 58.172 39.130 0.00 0.00 0.00 2.97
3418 3509 5.374142 CAACATTTGTTGTTTCTGTTCCG 57.626 39.130 13.95 0.00 46.51 4.30
3603 3694 6.344500 CACATTCATAGGCTCACTCTAGTTT 58.656 40.000 0.00 0.00 0.00 2.66
3630 3721 1.790043 CGTGTCACTCAACGCATTACA 59.210 47.619 0.65 0.00 0.00 2.41
3659 3750 7.485595 GCAATCTGCAATTTTGTTTCAGTTTTT 59.514 29.630 0.00 0.00 44.26 1.94
3741 3832 5.824624 TCTTTTGATGAAGTTGAGCTTGACT 59.175 36.000 0.00 0.00 37.59 3.41
3745 3836 2.216046 TGAAGTTGAGCTTGACTGCTG 58.784 47.619 9.16 0.00 44.17 4.41
3799 3890 2.869801 AGCTGAGAGACGAGATAAGTCG 59.130 50.000 0.00 0.00 45.76 4.18
3906 3998 0.761187 AACACTGCTTGCTCAGGAGA 59.239 50.000 11.14 0.00 43.79 3.71
3952 4044 4.018484 AGATGCTGCTGTTCTTTTCTCT 57.982 40.909 0.00 0.00 0.00 3.10
3979 4071 4.979335 TGTTGTGATGGATGAACCTAACA 58.021 39.130 0.00 0.00 39.86 2.41
3994 4086 5.192327 ACCTAACATACTATCGGGTTTCG 57.808 43.478 0.00 0.00 40.90 3.46
4139 4231 0.881118 TTTTCAGCTTGGTCATCGGC 59.119 50.000 0.00 0.00 0.00 5.54
4262 4354 4.837896 TGCTAAGTGGATAGATGAGTCG 57.162 45.455 0.00 0.00 0.00 4.18
4377 4470 4.389576 GTGGAGCTTTGCCGTGCG 62.390 66.667 0.00 0.00 0.00 5.34
4493 4588 8.024285 CGCACCTAGTCCTTTCTCTATATTTAG 58.976 40.741 0.00 0.00 0.00 1.85
4585 4680 9.719279 CAACAATTTAAACAATTGAAATGCACT 57.281 25.926 13.59 0.00 39.36 4.40
4588 4683 5.573296 TTAAACAATTGAAATGCACTGCG 57.427 34.783 13.59 0.00 0.00 5.18
4614 4709 7.923878 GTCCAACAATTCAGCTAAAAACCTAAA 59.076 33.333 0.00 0.00 0.00 1.85
4750 4845 1.538047 CCACCATCAAACTCCACCAG 58.462 55.000 0.00 0.00 0.00 4.00
4792 4893 2.421314 CACCACCACGAGCACTCA 59.579 61.111 0.00 0.00 0.00 3.41
4800 4901 4.069232 CGAGCACTCAGGGCCGAA 62.069 66.667 0.00 0.00 0.00 4.30
4803 4904 4.329545 GCACTCAGGGCCGAACCA 62.330 66.667 0.00 0.00 42.05 3.67
4817 4918 2.414029 CCGAACCACGATTTTGTCATGG 60.414 50.000 0.00 0.00 45.64 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.420687 GGTTTTCATTTGTTGTGGCCCA 60.421 45.455 0.00 0.00 0.00 5.36
82 83 2.089936 CGCAACGGTCGGATTTCGA 61.090 57.895 5.61 0.00 46.77 3.71
267 268 2.042843 GCGAGAGGAAGAGGGGGA 60.043 66.667 0.00 0.00 0.00 4.81
294 295 5.144832 GAGGTAGGAGAGATTTAGAGCCTT 58.855 45.833 0.00 0.00 0.00 4.35
315 316 4.838486 GCGTGAGAGGCGTCGGAG 62.838 72.222 0.00 0.00 0.00 4.63
367 379 4.415332 GAGACGGCAGGAACGCGA 62.415 66.667 15.93 0.00 34.00 5.87
426 438 1.142748 GAGCAGCCTCGTGCATACT 59.857 57.895 0.00 0.00 46.60 2.12
442 454 1.688735 TCAGTAATGGCCGGATGAGAG 59.311 52.381 5.05 0.00 0.00 3.20
451 463 1.202818 GGTGGGATCTCAGTAATGGCC 60.203 57.143 0.00 0.00 0.00 5.36
454 466 2.224066 GGTCGGTGGGATCTCAGTAATG 60.224 54.545 0.00 0.00 0.00 1.90
708 723 5.064707 ACAGGATTTACACATCATAACACGC 59.935 40.000 0.00 0.00 0.00 5.34
715 730 4.142315 GCTTGCACAGGATTTACACATCAT 60.142 41.667 0.00 0.00 0.00 2.45
733 748 2.599659 GGTGTAGAAATTGCAGCTTGC 58.400 47.619 0.00 1.70 45.29 4.01
734 749 2.855180 CGGTGTAGAAATTGCAGCTTG 58.145 47.619 0.00 0.00 37.70 4.01
754 780 3.648545 AGGACTTCCCTATCCTATTGTGC 59.351 47.826 0.00 0.00 45.48 4.57
897 923 2.475111 CGACAGAAGCAATACACAACGT 59.525 45.455 0.00 0.00 0.00 3.99
1072 1098 6.884832 TCCATACCATGAATTAGTTTCGAGT 58.115 36.000 0.00 0.00 37.13 4.18
1123 1160 3.060615 GCCCTCTTGCCTGCACAG 61.061 66.667 0.00 0.00 0.00 3.66
1324 1361 3.834813 AGATTGTAGTCTTGCTCAGTGGA 59.165 43.478 0.00 0.00 0.00 4.02
1815 1856 8.150945 GGCATACTGAGATAAACATTCTTCCTA 58.849 37.037 0.00 0.00 0.00 2.94
1821 1862 8.894768 AGTAAGGCATACTGAGATAAACATTC 57.105 34.615 0.91 0.00 43.33 2.67
1852 1893 4.946784 AGTGCATTCGGTTATGAAAGAC 57.053 40.909 0.00 0.00 0.00 3.01
2001 2069 6.380079 AAAAGGACATGATACAGTTCCTCT 57.620 37.500 0.00 0.00 0.00 3.69
2050 2118 2.056577 GAACAAGCTTGCAGCAATCAC 58.943 47.619 26.27 1.44 45.56 3.06
2309 2389 0.721718 CGAGATCCAACTTTGACCGC 59.278 55.000 0.00 0.00 0.00 5.68
2325 2405 1.996786 ATGCGCCCATGCTTTTCGAG 61.997 55.000 4.18 0.00 35.36 4.04
2343 2423 9.317827 CTTATTCCCTCCATTCCATTGAATAAT 57.682 33.333 0.00 0.00 39.20 1.28
2354 2434 5.823045 CCACAAGTACTTATTCCCTCCATTC 59.177 44.000 8.04 0.00 0.00 2.67
2375 2455 4.771590 TGAATTCAGAAGCAACATCCAC 57.228 40.909 3.38 0.00 0.00 4.02
2433 2513 9.216117 CCACAAGTTTAACTATAGCTAGTTGTT 57.784 33.333 11.42 11.56 45.61 2.83
2566 2646 6.867293 GGAAACTAATACGAGTATCCACATCC 59.133 42.308 0.00 0.38 0.00 3.51
2567 2647 7.381678 GTGGAAACTAATACGAGTATCCACATC 59.618 40.741 18.88 7.62 42.25 3.06
2568 2648 7.069578 AGTGGAAACTAATACGAGTATCCACAT 59.930 37.037 22.74 12.03 44.32 3.21
2569 2649 6.379133 AGTGGAAACTAATACGAGTATCCACA 59.621 38.462 22.74 5.85 44.32 4.17
2570 2650 6.803642 AGTGGAAACTAATACGAGTATCCAC 58.196 40.000 17.25 17.25 42.80 4.02
2571 2651 8.701908 ATAGTGGAAACTAATACGAGTATCCA 57.298 34.615 0.00 0.00 0.00 3.41
2575 2655 9.618890 ACAGTATAGTGGAAACTAATACGAGTA 57.381 33.333 12.20 0.00 0.00 2.59
2576 2656 8.517062 ACAGTATAGTGGAAACTAATACGAGT 57.483 34.615 12.20 0.00 0.00 4.18
2577 2657 7.797587 CGACAGTATAGTGGAAACTAATACGAG 59.202 40.741 12.20 0.00 0.00 4.18
2578 2658 7.495606 TCGACAGTATAGTGGAAACTAATACGA 59.504 37.037 12.20 0.00 0.00 3.43
2579 2659 7.585573 GTCGACAGTATAGTGGAAACTAATACG 59.414 40.741 11.55 0.00 0.00 3.06
2580 2660 7.585573 CGTCGACAGTATAGTGGAAACTAATAC 59.414 40.741 17.16 0.00 0.00 1.89
2581 2661 7.280876 ACGTCGACAGTATAGTGGAAACTAATA 59.719 37.037 17.16 0.00 0.00 0.98
2582 2662 6.094603 ACGTCGACAGTATAGTGGAAACTAAT 59.905 38.462 17.16 0.00 0.00 1.73
2583 2663 5.412594 ACGTCGACAGTATAGTGGAAACTAA 59.587 40.000 17.16 0.00 0.00 2.24
2584 2664 4.937620 ACGTCGACAGTATAGTGGAAACTA 59.062 41.667 17.16 0.00 0.00 2.24
2585 2665 3.755378 ACGTCGACAGTATAGTGGAAACT 59.245 43.478 17.16 0.00 0.00 2.66
2586 2666 3.850273 CACGTCGACAGTATAGTGGAAAC 59.150 47.826 17.16 5.67 0.00 2.78
2587 2667 3.503363 ACACGTCGACAGTATAGTGGAAA 59.497 43.478 17.16 0.00 34.28 3.13
2588 2668 3.076621 ACACGTCGACAGTATAGTGGAA 58.923 45.455 17.16 0.00 34.28 3.53
2589 2669 2.417586 CACACGTCGACAGTATAGTGGA 59.582 50.000 17.16 0.00 34.28 4.02
2590 2670 2.161012 ACACACGTCGACAGTATAGTGG 59.839 50.000 17.16 10.20 34.28 4.00
2591 2671 3.414464 GACACACGTCGACAGTATAGTG 58.586 50.000 17.16 15.77 35.89 2.74
2592 2672 3.736530 GACACACGTCGACAGTATAGT 57.263 47.619 17.16 12.28 31.07 2.12
2603 2683 1.935933 AACAGGACAAGACACACGTC 58.064 50.000 0.00 0.00 42.95 4.34
2604 2684 2.277084 GAAACAGGACAAGACACACGT 58.723 47.619 0.00 0.00 0.00 4.49
2605 2685 2.276201 TGAAACAGGACAAGACACACG 58.724 47.619 0.00 0.00 0.00 4.49
2606 2686 3.270877 ACTGAAACAGGACAAGACACAC 58.729 45.455 0.00 0.00 35.51 3.82
2607 2687 3.627395 ACTGAAACAGGACAAGACACA 57.373 42.857 0.00 0.00 35.51 3.72
2608 2688 4.965119 AAACTGAAACAGGACAAGACAC 57.035 40.909 0.00 0.00 35.51 3.67
2609 2689 7.639113 AAATAAACTGAAACAGGACAAGACA 57.361 32.000 0.00 0.00 35.51 3.41
2610 2690 8.837389 AGTAAATAAACTGAAACAGGACAAGAC 58.163 33.333 0.00 0.00 35.51 3.01
2611 2691 8.974060 AGTAAATAAACTGAAACAGGACAAGA 57.026 30.769 0.00 0.00 35.51 3.02
2613 2693 9.796120 CAAAGTAAATAAACTGAAACAGGACAA 57.204 29.630 0.00 0.00 35.51 3.18
2614 2694 9.179909 TCAAAGTAAATAAACTGAAACAGGACA 57.820 29.630 0.00 0.00 35.51 4.02
2623 2703 9.974980 GGGACAAATTCAAAGTAAATAAACTGA 57.025 29.630 0.00 0.00 0.00 3.41
2624 2704 8.911662 CGGGACAAATTCAAAGTAAATAAACTG 58.088 33.333 0.00 0.00 0.00 3.16
2625 2705 8.085909 CCGGGACAAATTCAAAGTAAATAAACT 58.914 33.333 0.00 0.00 0.00 2.66
2626 2706 8.083462 TCCGGGACAAATTCAAAGTAAATAAAC 58.917 33.333 0.00 0.00 0.00 2.01
2627 2707 8.179509 TCCGGGACAAATTCAAAGTAAATAAA 57.820 30.769 0.00 0.00 0.00 1.40
2628 2708 7.762588 TCCGGGACAAATTCAAAGTAAATAA 57.237 32.000 0.00 0.00 0.00 1.40
2629 2709 7.762588 TTCCGGGACAAATTCAAAGTAAATA 57.237 32.000 0.00 0.00 0.00 1.40
2630 2710 6.658188 TTCCGGGACAAATTCAAAGTAAAT 57.342 33.333 0.00 0.00 0.00 1.40
2631 2711 6.492087 AGATTCCGGGACAAATTCAAAGTAAA 59.508 34.615 0.00 0.00 0.00 2.01
2632 2712 6.007703 AGATTCCGGGACAAATTCAAAGTAA 58.992 36.000 0.00 0.00 0.00 2.24
2633 2713 5.566469 AGATTCCGGGACAAATTCAAAGTA 58.434 37.500 0.00 0.00 0.00 2.24
2634 2714 4.407365 AGATTCCGGGACAAATTCAAAGT 58.593 39.130 0.00 0.00 0.00 2.66
2635 2715 5.048083 TGAAGATTCCGGGACAAATTCAAAG 60.048 40.000 0.00 0.00 0.00 2.77
2636 2716 4.830046 TGAAGATTCCGGGACAAATTCAAA 59.170 37.500 0.00 0.00 0.00 2.69
2637 2717 4.402829 TGAAGATTCCGGGACAAATTCAA 58.597 39.130 0.00 0.00 0.00 2.69
2638 2718 4.027674 TGAAGATTCCGGGACAAATTCA 57.972 40.909 0.00 2.73 0.00 2.57
2639 2719 4.459337 AGTTGAAGATTCCGGGACAAATTC 59.541 41.667 0.00 0.00 0.00 2.17
2640 2720 4.407365 AGTTGAAGATTCCGGGACAAATT 58.593 39.130 0.00 0.00 0.00 1.82
2641 2721 4.034285 AGTTGAAGATTCCGGGACAAAT 57.966 40.909 0.00 0.00 0.00 2.32
2642 2722 3.502123 AGTTGAAGATTCCGGGACAAA 57.498 42.857 0.00 0.00 0.00 2.83
2643 2723 3.502123 AAGTTGAAGATTCCGGGACAA 57.498 42.857 0.00 0.00 0.00 3.18
2644 2724 3.408634 GAAAGTTGAAGATTCCGGGACA 58.591 45.455 0.00 0.00 0.00 4.02
2645 2725 2.747989 GGAAAGTTGAAGATTCCGGGAC 59.252 50.000 0.00 0.00 33.86 4.46
2646 2726 2.642807 AGGAAAGTTGAAGATTCCGGGA 59.357 45.455 0.00 0.00 45.78 5.14
2647 2727 3.073274 AGGAAAGTTGAAGATTCCGGG 57.927 47.619 0.00 0.00 45.78 5.73
2648 2728 6.555315 CAATTAGGAAAGTTGAAGATTCCGG 58.445 40.000 0.00 0.00 45.78 5.14
2649 2729 6.030228 GCAATTAGGAAAGTTGAAGATTCCG 58.970 40.000 3.97 0.00 45.78 4.30
2650 2730 7.163001 AGCAATTAGGAAAGTTGAAGATTCC 57.837 36.000 1.69 1.69 42.38 3.01
2715 2795 3.627395 ACTGAAACAGGACAAGACACA 57.373 42.857 0.00 0.00 35.51 3.72
2753 2833 6.317088 CACATCCATATAAATCATTGCGGAC 58.683 40.000 0.00 0.00 0.00 4.79
2754 2834 5.415389 CCACATCCATATAAATCATTGCGGA 59.585 40.000 0.00 0.00 0.00 5.54
2775 2855 7.781548 ACCATTGTTTAATACGAGTATCCAC 57.218 36.000 0.00 0.00 0.00 4.02
2838 2918 5.105797 CCAACAGTTTATACATGCCATGTGT 60.106 40.000 20.36 16.01 44.60 3.72
2868 2948 3.810310 ATTTCCTCTCTGTCCGATCAC 57.190 47.619 0.00 0.00 0.00 3.06
2896 2976 2.609459 ACTGCACAAAACTTGTCTCTCG 59.391 45.455 0.00 0.00 43.23 4.04
3002 3082 2.562125 GGCATGGCCGTTAAACTCA 58.438 52.632 8.35 0.00 39.62 3.41
3036 3116 1.485066 CGGCTATGTAGGGTTGAAGGT 59.515 52.381 0.00 0.00 0.00 3.50
3069 3149 0.112995 GGCTATGGGATGGCAATGGA 59.887 55.000 0.00 0.00 38.67 3.41
3080 3160 1.561542 AGAAGGACAAGTGGCTATGGG 59.438 52.381 0.00 0.00 0.00 4.00
3205 3296 3.140895 AGCTGAATAAGGGGCCATGTAAT 59.859 43.478 4.39 0.00 0.00 1.89
3283 3374 4.813161 CGGGAACATACTAGACGACTAAGA 59.187 45.833 0.00 0.00 0.00 2.10
3354 3445 7.814107 GCAAATGACAAACAAGGATATCTTCAA 59.186 33.333 2.05 0.00 32.41 2.69
3418 3509 8.352201 TGGTATCAACATAATGCATTAAAGAGC 58.648 33.333 22.37 12.93 0.00 4.09
3468 3559 1.236616 CGGTGCAACTGCCTGAATCA 61.237 55.000 0.00 0.00 41.18 2.57
3603 3694 2.029486 GCGTTGAGTGACACGTTAAACA 59.971 45.455 0.00 0.00 0.00 2.83
3630 3721 5.064558 TGAAACAAAATTGCAGATTGCCAT 58.935 33.333 7.78 0.00 44.23 4.40
3659 3750 2.827652 TGCACACGAGTTACATGTGAA 58.172 42.857 9.11 5.16 45.34 3.18
3741 3832 0.911045 TCCTCCAGGAATGAGCAGCA 60.911 55.000 0.00 0.00 42.18 4.41
3799 3890 1.771255 ACTCCAGGCTCCATGGATAAC 59.229 52.381 16.63 8.61 45.64 1.89
3906 3998 6.868622 AGCATTCTAATTCTACAGTCGACTT 58.131 36.000 17.26 10.23 0.00 3.01
3952 4044 3.325870 GTTCATCCATCACAACAGACGA 58.674 45.455 0.00 0.00 0.00 4.20
3979 4071 3.788937 CAACACCGAAACCCGATAGTAT 58.211 45.455 0.00 0.00 41.76 2.12
3994 4086 1.656441 CTGCTTCCACTGCAACACC 59.344 57.895 0.00 0.00 40.13 4.16
4049 4141 4.430007 GACCATTTACGCATCACTGACTA 58.570 43.478 0.00 0.00 0.00 2.59
4061 4153 3.421826 GCGATCTTATGCGACCATTTACG 60.422 47.826 0.00 0.00 32.85 3.18
4139 4231 7.769272 TTCAATTTTGGCAAAAGACAGTTAG 57.231 32.000 27.21 12.67 33.22 2.34
4262 4354 4.590850 AAAGATTGAAGTGACTTTGCCC 57.409 40.909 0.00 0.00 32.49 5.36
4377 4470 4.116238 GGTTAGAGATGCTCTTAGTGCAC 58.884 47.826 9.40 9.40 43.59 4.57
4456 4550 0.240945 CTAGGTGCGCCCAGTTTTTG 59.759 55.000 14.07 0.00 34.66 2.44
4493 4588 6.458342 CCGTCAGAAAATTGTTATTAGGGAGC 60.458 42.308 0.00 0.00 0.00 4.70
4585 4680 2.177394 TAGCTGAATTGTTGGACGCA 57.823 45.000 0.00 0.00 0.00 5.24
4588 4683 5.842907 AGGTTTTTAGCTGAATTGTTGGAC 58.157 37.500 0.00 0.00 0.00 4.02
4614 4709 8.608185 AAATTATTGGATTGGGTGAACTATGT 57.392 30.769 0.00 0.00 0.00 2.29
4649 4744 7.120579 TGGCTTTTCGATGAACTATGTTTATGT 59.879 33.333 0.00 0.00 0.00 2.29
4657 4752 3.950397 TGGTGGCTTTTCGATGAACTAT 58.050 40.909 0.00 0.00 0.00 2.12
4750 4845 2.871022 GTGACCATGAGAGTGCATGATC 59.129 50.000 0.00 0.00 46.64 2.92
4792 4893 1.074248 AAAATCGTGGTTCGGCCCT 59.926 52.632 0.00 0.00 40.32 5.19
4803 4904 3.007940 TGGAGAGACCATGACAAAATCGT 59.992 43.478 0.00 0.00 44.64 3.73


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

AutoCloner maintained by Alex Coulton.