Multiple sequence alignment - TraesCS4D01G226100

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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 TraesCS4D01G226100 chr4D 100.000 3620 0 0 1 3620 385509885 385513504 0.000000e+00 6685
1 TraesCS4D01G226100 chr4D 76.981 265 48 10 1573 1832 147080011 147080267 4.870000e-29 139
2 TraesCS4D01G226100 chr4B 93.519 2901 92 26 6 2847 472132295 472135158 0.000000e+00 4228
3 TraesCS4D01G226100 chr4B 91.523 696 42 12 2866 3553 472135301 472135987 0.000000e+00 942
4 TraesCS4D01G226100 chr4A 95.917 1984 58 11 704 2674 66909418 66911391 0.000000e+00 3193
5 TraesCS4D01G226100 chr4A 89.977 868 55 18 2714 3553 66911388 66912251 0.000000e+00 1092
6 TraesCS4D01G226100 chr4A 87.448 717 17 24 1 675 66908736 66909421 0.000000e+00 758
7 TraesCS4D01G226100 chr4A 76.226 265 50 10 1573 1832 379465163 379465419 1.060000e-25 128
8 TraesCS4D01G226100 chr1A 77.731 1190 199 55 1364 2523 573242696 573243849 0.000000e+00 669
9 TraesCS4D01G226100 chr1D 78.537 1039 171 44 1508 2523 477189448 477190457 1.420000e-178 636
10 TraesCS4D01G226100 chr1D 76.548 1066 210 37 1481 2529 474375501 474376543 6.830000e-152 547
11 TraesCS4D01G226100 chr1B 76.851 1067 205 38 1481 2529 659724086 659725128 6.790000e-157 564
12 TraesCS4D01G226100 chr7A 75.725 1207 241 41 1342 2525 545934574 545935751 3.160000e-155 558
13 TraesCS4D01G226100 chr7A 74.810 659 137 23 1864 2512 167904018 167903379 1.660000e-68 270
14 TraesCS4D01G226100 chr7B 75.247 1216 254 40 1342 2537 470836764 470835576 5.320000e-148 534
15 TraesCS4D01G226100 chr7B 73.349 848 182 37 1679 2507 130746848 130746026 1.280000e-69 274
16 TraesCS4D01G226100 chr7D 75.104 1205 252 39 1342 2525 451187598 451186421 1.490000e-143 520
17 TraesCS4D01G226100 chr6D 73.944 852 183 31 1669 2505 383227681 383226854 1.260000e-79 307
18 TraesCS4D01G226100 chr6D 76.981 265 48 10 1573 1832 36222562 36222818 4.870000e-29 139
19 TraesCS4D01G226100 chr6B 77.358 265 47 10 1573 1832 75915784 75916040 1.050000e-30 145
20 TraesCS4D01G226100 chr6A 76.981 265 48 11 1573 1832 40217847 40218103 4.870000e-29 139


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 TraesCS4D01G226100 chr4D 385509885 385513504 3619 False 6685 6685 100.000 1 3620 1 chr4D.!!$F2 3619
1 TraesCS4D01G226100 chr4B 472132295 472135987 3692 False 2585 4228 92.521 6 3553 2 chr4B.!!$F1 3547
2 TraesCS4D01G226100 chr4A 66908736 66912251 3515 False 1681 3193 91.114 1 3553 3 chr4A.!!$F2 3552
3 TraesCS4D01G226100 chr1A 573242696 573243849 1153 False 669 669 77.731 1364 2523 1 chr1A.!!$F1 1159
4 TraesCS4D01G226100 chr1D 477189448 477190457 1009 False 636 636 78.537 1508 2523 1 chr1D.!!$F2 1015
5 TraesCS4D01G226100 chr1D 474375501 474376543 1042 False 547 547 76.548 1481 2529 1 chr1D.!!$F1 1048
6 TraesCS4D01G226100 chr1B 659724086 659725128 1042 False 564 564 76.851 1481 2529 1 chr1B.!!$F1 1048
7 TraesCS4D01G226100 chr7A 545934574 545935751 1177 False 558 558 75.725 1342 2525 1 chr7A.!!$F1 1183
8 TraesCS4D01G226100 chr7A 167903379 167904018 639 True 270 270 74.810 1864 2512 1 chr7A.!!$R1 648
9 TraesCS4D01G226100 chr7B 470835576 470836764 1188 True 534 534 75.247 1342 2537 1 chr7B.!!$R2 1195
10 TraesCS4D01G226100 chr7B 130746026 130746848 822 True 274 274 73.349 1679 2507 1 chr7B.!!$R1 828
11 TraesCS4D01G226100 chr7D 451186421 451187598 1177 True 520 520 75.104 1342 2525 1 chr7D.!!$R1 1183
12 TraesCS4D01G226100 chr6D 383226854 383227681 827 True 307 307 73.944 1669 2505 1 chr6D.!!$R1 836

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
423 444 0.179012 CTACCCGTCTCTCTCCTCCC 60.179 65.0 0.0 0.0 0.0 4.3 F
427 448 0.179029 CCGTCTCTCTCCTCCCTCTC 60.179 65.0 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1793 0.394192 GGATGATCATGGACGCCAGA 59.606 55.000 14.30 3.52 36.75 3.86 R
2674 2837 1.083015 GCGCGTGTGTTTACTGTGG 60.083 57.895 8.43 0.00 0.00 4.17 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
72 73 4.731612 CCTGTCACGCAGCTCGCT 62.732 66.667 5.63 0.00 43.71 4.93
87 88 4.049393 GCTCAACCAACACGAGCT 57.951 55.556 3.46 0.00 46.86 4.09
416 437 2.093021 ACCTGTCTACTACCCGTCTCTC 60.093 54.545 0.00 0.00 0.00 3.20
417 438 2.171027 CCTGTCTACTACCCGTCTCTCT 59.829 54.545 0.00 0.00 0.00 3.10
418 439 3.460103 CTGTCTACTACCCGTCTCTCTC 58.540 54.545 0.00 0.00 0.00 3.20
419 440 2.170187 TGTCTACTACCCGTCTCTCTCC 59.830 54.545 0.00 0.00 0.00 3.71
420 441 2.435437 GTCTACTACCCGTCTCTCTCCT 59.565 54.545 0.00 0.00 0.00 3.69
421 442 2.699846 TCTACTACCCGTCTCTCTCCTC 59.300 54.545 0.00 0.00 0.00 3.71
422 443 0.547553 ACTACCCGTCTCTCTCCTCC 59.452 60.000 0.00 0.00 0.00 4.30
423 444 0.179012 CTACCCGTCTCTCTCCTCCC 60.179 65.000 0.00 0.00 0.00 4.30
424 445 0.623911 TACCCGTCTCTCTCCTCCCT 60.624 60.000 0.00 0.00 0.00 4.20
425 446 1.152839 CCCGTCTCTCTCCTCCCTC 60.153 68.421 0.00 0.00 0.00 4.30
426 447 1.641552 CCCGTCTCTCTCCTCCCTCT 61.642 65.000 0.00 0.00 0.00 3.69
427 448 0.179029 CCGTCTCTCTCCTCCCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
428 449 0.837272 CGTCTCTCTCCTCCCTCTCT 59.163 60.000 0.00 0.00 0.00 3.10
539 583 8.110860 ACAGTAACACTTTTGGATTAGAATGG 57.889 34.615 0.00 0.00 0.00 3.16
559 605 0.590732 CGTGGTCGATACGTACAGCC 60.591 60.000 14.60 0.00 39.71 4.85
570 637 3.376078 TACAGCCCCGTCGTCACC 61.376 66.667 0.00 0.00 0.00 4.02
587 660 3.514309 GTCACCTGGAGTTGTACTGGTAT 59.486 47.826 0.00 0.00 37.19 2.73
588 661 4.708421 GTCACCTGGAGTTGTACTGGTATA 59.292 45.833 0.00 0.00 37.19 1.47
589 662 4.708421 TCACCTGGAGTTGTACTGGTATAC 59.292 45.833 0.00 0.00 37.19 1.47
656 729 3.702048 GTGCAGGTACAGGCCGGA 61.702 66.667 10.86 0.00 0.00 5.14
679 756 0.729116 TAGTCGTGGCACGTAGTAGC 59.271 55.000 35.65 20.15 41.61 3.58
876 953 4.657824 CCGTCGCCGTCTGGTTGT 62.658 66.667 0.00 0.00 37.67 3.32
877 954 2.256158 CGTCGCCGTCTGGTTGTA 59.744 61.111 0.00 0.00 37.67 2.41
986 1063 3.939581 CGACTACGCACGTACGTC 58.060 61.111 18.56 12.42 44.43 4.34
989 1066 2.941013 CTACGCACGTACGTCCGC 60.941 66.667 29.99 23.54 44.43 5.54
1178 1261 2.544277 CCGTCAACCTCAAGTACGTCAA 60.544 50.000 0.00 0.00 31.87 3.18
1360 1443 4.008330 CCTCACCGTCTACTACTTCAAGA 58.992 47.826 0.00 0.00 0.00 3.02
1473 1556 2.174334 CACCGGGTGCTTCAATCAG 58.826 57.895 15.29 0.00 0.00 2.90
1677 1760 1.299089 CGACGTGCGCATCCTCATA 60.299 57.895 15.91 0.00 0.00 2.15
1710 1793 3.569049 CTTCAACCCGACGCCGTCT 62.569 63.158 16.07 0.00 0.00 4.18
2674 2837 7.281100 ACGAAGATTACATGATTCTTTTCTCCC 59.719 37.037 0.00 0.00 29.75 4.30
2675 2838 7.254932 CGAAGATTACATGATTCTTTTCTCCCC 60.255 40.741 0.00 0.00 29.75 4.81
2676 2839 6.973642 AGATTACATGATTCTTTTCTCCCCA 58.026 36.000 0.00 0.00 0.00 4.96
2677 2840 6.830838 AGATTACATGATTCTTTTCTCCCCAC 59.169 38.462 0.00 0.00 0.00 4.61
2678 2841 4.387026 ACATGATTCTTTTCTCCCCACA 57.613 40.909 0.00 0.00 0.00 4.17
2679 2842 4.338879 ACATGATTCTTTTCTCCCCACAG 58.661 43.478 0.00 0.00 0.00 3.66
2680 2843 4.202609 ACATGATTCTTTTCTCCCCACAGT 60.203 41.667 0.00 0.00 0.00 3.55
2681 2844 5.014123 ACATGATTCTTTTCTCCCCACAGTA 59.986 40.000 0.00 0.00 0.00 2.74
2682 2845 5.576563 TGATTCTTTTCTCCCCACAGTAA 57.423 39.130 0.00 0.00 0.00 2.24
2683 2846 5.947663 TGATTCTTTTCTCCCCACAGTAAA 58.052 37.500 0.00 0.00 0.00 2.01
2684 2847 5.768164 TGATTCTTTTCTCCCCACAGTAAAC 59.232 40.000 0.00 0.00 0.00 2.01
2685 2848 4.781775 TCTTTTCTCCCCACAGTAAACA 57.218 40.909 0.00 0.00 0.00 2.83
2686 2849 4.457466 TCTTTTCTCCCCACAGTAAACAC 58.543 43.478 0.00 0.00 0.00 3.32
2687 2850 3.935818 TTTCTCCCCACAGTAAACACA 57.064 42.857 0.00 0.00 0.00 3.72
2688 2851 2.922740 TCTCCCCACAGTAAACACAC 57.077 50.000 0.00 0.00 0.00 3.82
2689 2852 1.069513 TCTCCCCACAGTAAACACACG 59.930 52.381 0.00 0.00 0.00 4.49
2690 2853 0.533308 TCCCCACAGTAAACACACGC 60.533 55.000 0.00 0.00 0.00 5.34
2691 2854 1.567537 CCCACAGTAAACACACGCG 59.432 57.895 3.53 3.53 0.00 6.01
2692 2855 1.083015 CCACAGTAAACACACGCGC 60.083 57.895 5.73 0.00 0.00 6.86
2693 2856 1.436446 CACAGTAAACACACGCGCG 60.436 57.895 30.96 30.96 0.00 6.86
2694 2857 2.170036 CAGTAAACACACGCGCGG 59.830 61.111 35.22 24.36 0.00 6.46
2695 2858 2.279650 AGTAAACACACGCGCGGT 60.280 55.556 35.22 25.06 0.00 5.68
2705 2868 4.215742 CGCGCGGTGGGGAGATTA 62.216 66.667 24.84 0.00 0.00 1.75
2706 2869 2.426023 GCGCGGTGGGGAGATTAT 59.574 61.111 8.83 0.00 0.00 1.28
2707 2870 1.669440 GCGCGGTGGGGAGATTATA 59.331 57.895 8.83 0.00 0.00 0.98
2708 2871 0.249398 GCGCGGTGGGGAGATTATAT 59.751 55.000 8.83 0.00 0.00 0.86
2709 2872 1.479323 GCGCGGTGGGGAGATTATATA 59.521 52.381 8.83 0.00 0.00 0.86
2710 2873 2.737679 GCGCGGTGGGGAGATTATATAC 60.738 54.545 8.83 0.00 0.00 1.47
2711 2874 2.758979 CGCGGTGGGGAGATTATATACT 59.241 50.000 0.00 0.00 0.00 2.12
2712 2875 3.428999 CGCGGTGGGGAGATTATATACTG 60.429 52.174 0.00 0.00 0.00 2.74
2713 2876 3.679083 GCGGTGGGGAGATTATATACTGC 60.679 52.174 0.00 0.00 32.66 4.40
2714 2877 3.769844 CGGTGGGGAGATTATATACTGCT 59.230 47.826 0.00 0.00 0.00 4.24
2715 2878 4.954202 CGGTGGGGAGATTATATACTGCTA 59.046 45.833 0.00 0.00 0.00 3.49
2716 2879 5.163540 CGGTGGGGAGATTATATACTGCTAC 60.164 48.000 0.00 0.00 0.00 3.58
2764 2927 0.977395 AGGTGGCTGTACTTCAGGTC 59.023 55.000 0.00 0.00 43.78 3.85
2840 3014 7.325338 ACAATATATACGACGAGGTTTCATTCG 59.675 37.037 0.00 0.00 42.26 3.34
2859 3137 8.471361 TCATTCGAGCTTATGATTGTATGATC 57.529 34.615 0.00 0.00 29.07 2.92
2862 3140 6.986250 TCGAGCTTATGATTGTATGATCTGT 58.014 36.000 0.00 0.00 0.00 3.41
2865 3143 7.148672 CGAGCTTATGATTGTATGATCTGTTCC 60.149 40.741 0.00 0.00 0.00 3.62
2866 3144 7.743749 AGCTTATGATTGTATGATCTGTTCCT 58.256 34.615 0.00 0.00 0.00 3.36
2936 3233 0.669318 GGATTGTGTTCGCGGTCTCA 60.669 55.000 6.13 4.18 0.00 3.27
2957 3254 0.817634 CACGTGAGCCTCCCAAAACA 60.818 55.000 10.90 0.00 0.00 2.83
2959 3256 0.523072 CGTGAGCCTCCCAAAACATG 59.477 55.000 0.00 0.00 0.00 3.21
2960 3257 1.620822 GTGAGCCTCCCAAAACATGT 58.379 50.000 0.00 0.00 0.00 3.21
2965 3262 1.335872 GCCTCCCAAAACATGTTGTCG 60.336 52.381 12.82 0.00 0.00 4.35
2968 3265 0.030101 CCCAAAACATGTTGTCGCGT 59.970 50.000 12.82 0.00 0.00 6.01
3043 3340 1.005340 CCTTGATCTGAACGAGCTGC 58.995 55.000 0.00 0.00 0.00 5.25
3112 3413 2.287308 GCTCATTGGTGTAACGTGCAAA 60.287 45.455 0.00 0.00 38.12 3.68
3117 3423 3.182341 TGGTGTAACGTGCAAAGTAGT 57.818 42.857 0.00 0.00 38.12 2.73
3182 3489 0.114560 TTTGGCCCCCGTGGAAAATA 59.885 50.000 0.00 0.00 35.39 1.40
3183 3490 0.323908 TTGGCCCCCGTGGAAAATAG 60.324 55.000 0.00 0.00 35.39 1.73
3184 3491 1.305287 GGCCCCCGTGGAAAATAGT 59.695 57.895 0.00 0.00 35.39 2.12
3385 3694 1.710249 TCGAAAACTCGAAAGCGTACG 59.290 47.619 11.84 11.84 39.34 3.67
3418 3727 5.309323 TGCTCTGATTTACGGGAATTTTG 57.691 39.130 0.00 0.00 0.00 2.44
3422 3731 6.645003 GCTCTGATTTACGGGAATTTTGTTTT 59.355 34.615 0.00 0.00 0.00 2.43
3423 3732 7.810759 GCTCTGATTTACGGGAATTTTGTTTTA 59.189 33.333 0.00 0.00 0.00 1.52
3453 3762 9.248291 TCTTTTGTCAAAAACTTGCAATCTATC 57.752 29.630 11.73 0.00 31.94 2.08
3469 3778 7.661027 TGCAATCTATCCATCAAATATCACGAA 59.339 33.333 0.00 0.00 0.00 3.85
3549 3859 2.611971 CGGGTACAAGCACTAGAGCAAA 60.612 50.000 14.80 0.00 36.85 3.68
3553 3863 2.498167 ACAAGCACTAGAGCAAACCAG 58.502 47.619 14.80 0.39 36.85 4.00
3554 3864 2.104792 ACAAGCACTAGAGCAAACCAGA 59.895 45.455 14.80 0.00 36.85 3.86
3555 3865 2.464157 AGCACTAGAGCAAACCAGAC 57.536 50.000 14.80 0.00 36.85 3.51
3556 3866 1.002544 AGCACTAGAGCAAACCAGACC 59.997 52.381 14.80 0.00 36.85 3.85
3557 3867 1.270839 GCACTAGAGCAAACCAGACCA 60.271 52.381 7.33 0.00 0.00 4.02
3558 3868 2.616510 GCACTAGAGCAAACCAGACCAT 60.617 50.000 7.33 0.00 0.00 3.55
3559 3869 3.265791 CACTAGAGCAAACCAGACCATC 58.734 50.000 0.00 0.00 0.00 3.51
3560 3870 3.055530 CACTAGAGCAAACCAGACCATCT 60.056 47.826 0.00 0.00 0.00 2.90
3561 3871 4.160439 CACTAGAGCAAACCAGACCATCTA 59.840 45.833 0.00 0.00 0.00 1.98
3562 3872 3.902881 AGAGCAAACCAGACCATCTAG 57.097 47.619 0.00 0.00 0.00 2.43
3563 3873 2.093235 AGAGCAAACCAGACCATCTAGC 60.093 50.000 0.00 0.00 0.00 3.42
3564 3874 1.630369 AGCAAACCAGACCATCTAGCA 59.370 47.619 0.00 0.00 0.00 3.49
3565 3875 2.040278 AGCAAACCAGACCATCTAGCAA 59.960 45.455 0.00 0.00 0.00 3.91
3566 3876 2.162408 GCAAACCAGACCATCTAGCAAC 59.838 50.000 0.00 0.00 0.00 4.17
3567 3877 2.386661 AACCAGACCATCTAGCAACG 57.613 50.000 0.00 0.00 0.00 4.10
3568 3878 1.557099 ACCAGACCATCTAGCAACGA 58.443 50.000 0.00 0.00 0.00 3.85
3569 3879 1.478510 ACCAGACCATCTAGCAACGAG 59.521 52.381 0.00 0.00 0.00 4.18
3570 3880 1.565305 CAGACCATCTAGCAACGAGC 58.435 55.000 0.00 0.00 46.19 5.03
3584 3894 3.366629 GAGCATATCGGAGCCGGA 58.633 61.111 5.05 0.00 40.25 5.14
3585 3895 1.214062 GAGCATATCGGAGCCGGAG 59.786 63.158 5.05 0.00 40.25 4.63
3586 3896 2.433318 GCATATCGGAGCCGGAGC 60.433 66.667 5.05 4.78 40.25 4.70
3587 3897 3.051210 CATATCGGAGCCGGAGCA 58.949 61.111 5.05 0.00 43.56 4.26
3588 3898 1.367471 CATATCGGAGCCGGAGCAA 59.633 57.895 5.05 0.00 43.56 3.91
3589 3899 0.668706 CATATCGGAGCCGGAGCAAG 60.669 60.000 5.05 0.00 43.56 4.01
3590 3900 2.441822 ATATCGGAGCCGGAGCAAGC 62.442 60.000 5.05 0.00 43.56 4.01
3593 3903 4.722700 GGAGCCGGAGCAAGCCAA 62.723 66.667 5.05 0.00 43.56 4.52
3594 3904 2.672996 GAGCCGGAGCAAGCCAAA 60.673 61.111 5.05 0.00 43.56 3.28
3595 3905 2.982744 GAGCCGGAGCAAGCCAAAC 61.983 63.158 5.05 0.00 43.56 2.93
3596 3906 3.294493 GCCGGAGCAAGCCAAACA 61.294 61.111 5.05 0.00 39.53 2.83
3597 3907 2.644992 CCGGAGCAAGCCAAACAC 59.355 61.111 0.00 0.00 0.00 3.32
3598 3908 2.644992 CGGAGCAAGCCAAACACC 59.355 61.111 0.00 0.00 0.00 4.16
3599 3909 2.192861 CGGAGCAAGCCAAACACCA 61.193 57.895 0.00 0.00 0.00 4.17
3600 3910 1.526575 CGGAGCAAGCCAAACACCAT 61.527 55.000 0.00 0.00 0.00 3.55
3601 3911 1.544724 GGAGCAAGCCAAACACCATA 58.455 50.000 0.00 0.00 0.00 2.74
3602 3912 1.892474 GGAGCAAGCCAAACACCATAA 59.108 47.619 0.00 0.00 0.00 1.90
3603 3913 2.497273 GGAGCAAGCCAAACACCATAAT 59.503 45.455 0.00 0.00 0.00 1.28
3604 3914 3.699038 GGAGCAAGCCAAACACCATAATA 59.301 43.478 0.00 0.00 0.00 0.98
3605 3915 4.159506 GGAGCAAGCCAAACACCATAATAA 59.840 41.667 0.00 0.00 0.00 1.40
3606 3916 5.329035 AGCAAGCCAAACACCATAATAAG 57.671 39.130 0.00 0.00 0.00 1.73
3607 3917 4.772100 AGCAAGCCAAACACCATAATAAGT 59.228 37.500 0.00 0.00 0.00 2.24
3608 3918 5.949354 AGCAAGCCAAACACCATAATAAGTA 59.051 36.000 0.00 0.00 0.00 2.24
3609 3919 6.435904 AGCAAGCCAAACACCATAATAAGTAA 59.564 34.615 0.00 0.00 0.00 2.24
3610 3920 7.039363 AGCAAGCCAAACACCATAATAAGTAAA 60.039 33.333 0.00 0.00 0.00 2.01
3611 3921 7.600752 GCAAGCCAAACACCATAATAAGTAAAA 59.399 33.333 0.00 0.00 0.00 1.52
3612 3922 9.651913 CAAGCCAAACACCATAATAAGTAAAAT 57.348 29.630 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 2.325583 AAGAAGCTCGTGTTGGTTGA 57.674 45.000 0.00 0.00 0.00 3.18
87 88 1.573829 ATGCGCCGCGAAGAAAAGAA 61.574 50.000 18.91 0.00 0.00 2.52
240 242 2.490217 CTCGAGCGATCCAACGGT 59.510 61.111 0.00 0.00 46.35 4.83
295 304 2.854777 CGACGCGTACAGTACTACTAGT 59.145 50.000 13.97 0.00 0.00 2.57
296 305 2.854777 ACGACGCGTACAGTACTACTAG 59.145 50.000 13.97 0.00 38.73 2.57
297 306 2.852413 GACGACGCGTACAGTACTACTA 59.148 50.000 13.97 0.00 41.37 1.82
416 437 3.450817 GGAGAAAGAAAGAGAGGGAGGAG 59.549 52.174 0.00 0.00 0.00 3.69
417 438 3.445987 GGAGAAAGAAAGAGAGGGAGGA 58.554 50.000 0.00 0.00 0.00 3.71
418 439 2.167487 CGGAGAAAGAAAGAGAGGGAGG 59.833 54.545 0.00 0.00 0.00 4.30
419 440 2.167487 CCGGAGAAAGAAAGAGAGGGAG 59.833 54.545 0.00 0.00 0.00 4.30
420 441 2.180276 CCGGAGAAAGAAAGAGAGGGA 58.820 52.381 0.00 0.00 0.00 4.20
421 442 1.903183 ACCGGAGAAAGAAAGAGAGGG 59.097 52.381 9.46 0.00 0.00 4.30
422 443 3.591023 GAACCGGAGAAAGAAAGAGAGG 58.409 50.000 9.46 0.00 0.00 3.69
423 444 3.246619 CGAACCGGAGAAAGAAAGAGAG 58.753 50.000 9.46 0.00 0.00 3.20
424 445 2.609737 GCGAACCGGAGAAAGAAAGAGA 60.610 50.000 9.46 0.00 0.00 3.10
425 446 1.727335 GCGAACCGGAGAAAGAAAGAG 59.273 52.381 9.46 0.00 0.00 2.85
426 447 1.343465 AGCGAACCGGAGAAAGAAAGA 59.657 47.619 9.46 0.00 0.00 2.52
427 448 1.797025 AGCGAACCGGAGAAAGAAAG 58.203 50.000 9.46 0.00 0.00 2.62
428 449 2.249844 AAGCGAACCGGAGAAAGAAA 57.750 45.000 9.46 0.00 0.00 2.52
463 484 1.671901 GAGGAGAAGAGGCGTCAGGG 61.672 65.000 9.41 0.00 0.00 4.45
538 582 0.590732 CTGTACGTATCGACCACGCC 60.591 60.000 18.37 11.35 43.10 5.68
539 583 1.198608 GCTGTACGTATCGACCACGC 61.199 60.000 18.37 6.67 43.10 5.34
559 605 2.571216 AACTCCAGGTGACGACGGG 61.571 63.158 0.00 0.00 0.00 5.28
587 660 8.903062 ACTACCCGTACCCAAACTTGGTAGTA 62.903 46.154 14.87 3.85 44.88 1.82
656 729 0.520404 CTACGTGCCACGACTACAGT 59.480 55.000 25.94 1.36 46.05 3.55
679 756 3.541632 ACGGAAACCCAGCATAATACTG 58.458 45.455 0.00 0.00 34.82 2.74
748 825 0.878961 GCCGACCCGTATTCCACATC 60.879 60.000 0.00 0.00 0.00 3.06
751 828 2.202974 GGCCGACCCGTATTCCAC 60.203 66.667 0.00 0.00 0.00 4.02
791 868 2.752903 CAAACTTATAGGCGCCCAAACT 59.247 45.455 26.15 6.59 0.00 2.66
866 943 2.731721 TGCGCGTACAACCAGACG 60.732 61.111 8.43 0.00 41.97 4.18
876 953 2.613595 CGGTATATATAGGGTGCGCGTA 59.386 50.000 8.43 0.00 0.00 4.42
877 954 1.402968 CGGTATATATAGGGTGCGCGT 59.597 52.381 8.43 0.00 0.00 6.01
986 1063 2.152297 CTCCATGGATCTCGAGGCGG 62.152 65.000 16.63 4.63 0.00 6.13
989 1066 1.612950 CAGACTCCATGGATCTCGAGG 59.387 57.143 16.63 3.93 0.00 4.63
1677 1760 0.761187 TGAAGAGGCTGCAGTTGACT 59.239 50.000 16.64 8.75 0.00 3.41
1710 1793 0.394192 GGATGATCATGGACGCCAGA 59.606 55.000 14.30 3.52 36.75 3.86
2674 2837 1.083015 GCGCGTGTGTTTACTGTGG 60.083 57.895 8.43 0.00 0.00 4.17
2675 2838 1.436446 CGCGCGTGTGTTTACTGTG 60.436 57.895 24.19 0.00 0.00 3.66
2676 2839 2.591311 CCGCGCGTGTGTTTACTGT 61.591 57.895 29.95 0.00 0.00 3.55
2677 2840 2.170036 CCGCGCGTGTGTTTACTG 59.830 61.111 29.95 4.86 0.00 2.74
2678 2841 2.279650 ACCGCGCGTGTGTTTACT 60.280 55.556 29.95 0.00 0.00 2.24
2679 2842 2.127906 CACCGCGCGTGTGTTTAC 60.128 61.111 30.53 0.00 37.73 2.01
2680 2843 3.339464 CCACCGCGCGTGTGTTTA 61.339 61.111 33.50 0.00 41.26 2.01
2688 2851 2.149803 TATAATCTCCCCACCGCGCG 62.150 60.000 25.67 25.67 0.00 6.86
2689 2852 0.249398 ATATAATCTCCCCACCGCGC 59.751 55.000 0.00 0.00 0.00 6.86
2690 2853 2.758979 AGTATATAATCTCCCCACCGCG 59.241 50.000 0.00 0.00 0.00 6.46
2691 2854 3.679083 GCAGTATATAATCTCCCCACCGC 60.679 52.174 0.00 0.00 0.00 5.68
2692 2855 3.769844 AGCAGTATATAATCTCCCCACCG 59.230 47.826 0.00 0.00 0.00 4.94
2693 2856 5.958987 AGTAGCAGTATATAATCTCCCCACC 59.041 44.000 0.00 0.00 0.00 4.61
2694 2857 8.770010 ATAGTAGCAGTATATAATCTCCCCAC 57.230 38.462 0.00 0.00 0.00 4.61
2695 2858 9.863650 GTATAGTAGCAGTATATAATCTCCCCA 57.136 37.037 0.00 0.00 0.00 4.96
2707 2870 9.838339 AATGCAGAAAAAGTATAGTAGCAGTAT 57.162 29.630 0.00 0.00 32.59 2.12
2708 2871 9.667107 AAATGCAGAAAAAGTATAGTAGCAGTA 57.333 29.630 0.00 0.00 32.59 2.74
2709 2872 8.567285 AAATGCAGAAAAAGTATAGTAGCAGT 57.433 30.769 0.00 0.00 32.59 4.40
2710 2873 7.848051 CGAAATGCAGAAAAAGTATAGTAGCAG 59.152 37.037 0.00 0.00 32.59 4.24
2711 2874 7.333423 ACGAAATGCAGAAAAAGTATAGTAGCA 59.667 33.333 0.00 0.00 0.00 3.49
2712 2875 7.685594 ACGAAATGCAGAAAAAGTATAGTAGC 58.314 34.615 0.00 0.00 0.00 3.58
2715 2878 8.021396 GGAAACGAAATGCAGAAAAAGTATAGT 58.979 33.333 0.00 0.00 0.00 2.12
2716 2879 7.484959 GGGAAACGAAATGCAGAAAAAGTATAG 59.515 37.037 0.00 0.00 0.00 1.31
2764 2927 1.606224 GCTGAAAACAATGGCACTGGG 60.606 52.381 0.00 0.00 0.00 4.45
2840 3014 7.877097 AGGAACAGATCATACAATCATAAGCTC 59.123 37.037 0.00 0.00 0.00 4.09
2859 3137 3.314635 GCAGCAATCTAATCCAGGAACAG 59.685 47.826 0.00 0.00 0.00 3.16
2862 3140 3.434167 GGAGCAGCAATCTAATCCAGGAA 60.434 47.826 0.00 0.00 0.00 3.36
2865 3143 2.141517 CGGAGCAGCAATCTAATCCAG 58.858 52.381 0.00 0.00 0.00 3.86
2866 3144 1.202687 CCGGAGCAGCAATCTAATCCA 60.203 52.381 0.00 0.00 0.00 3.41
2936 3233 0.400213 TTTTGGGAGGCTCACGTGAT 59.600 50.000 20.40 3.85 0.00 3.06
2949 3246 0.030101 ACGCGACAACATGTTTTGGG 59.970 50.000 15.93 13.99 0.00 4.12
2957 3254 2.476619 CAGAAGAGAAACGCGACAACAT 59.523 45.455 15.93 0.00 0.00 2.71
2959 3256 1.192534 CCAGAAGAGAAACGCGACAAC 59.807 52.381 15.93 0.65 0.00 3.32
2960 3257 1.202486 ACCAGAAGAGAAACGCGACAA 60.202 47.619 15.93 0.00 0.00 3.18
2965 3262 1.627550 GCCGACCAGAAGAGAAACGC 61.628 60.000 0.00 0.00 0.00 4.84
2968 3265 2.352421 CGTTAGCCGACCAGAAGAGAAA 60.352 50.000 0.00 0.00 39.56 2.52
2993 3290 1.675641 CGAGGGCCAAGGAAACCAG 60.676 63.158 6.18 0.00 0.00 4.00
3069 3366 1.895798 TGCATGTCGAGACTCTTCCTT 59.104 47.619 4.78 0.00 0.00 3.36
3112 3413 8.972458 AGTATCGCTCATCATCATATACTACT 57.028 34.615 0.00 0.00 29.35 2.57
3117 3423 6.381133 ACCCAAGTATCGCTCATCATCATATA 59.619 38.462 0.00 0.00 0.00 0.86
3182 3489 0.469917 CATGCCCCGAACTGGATACT 59.530 55.000 0.00 0.00 42.00 2.12
3183 3490 1.166531 GCATGCCCCGAACTGGATAC 61.167 60.000 6.36 0.00 42.00 2.24
3184 3491 1.148273 GCATGCCCCGAACTGGATA 59.852 57.895 6.36 0.00 42.00 2.59
3385 3694 1.490574 ATCAGAGCAGGAGTACACCC 58.509 55.000 5.63 0.81 0.00 4.61
3397 3706 5.310720 ACAAAATTCCCGTAAATCAGAGC 57.689 39.130 0.00 0.00 0.00 4.09
3423 3732 9.558648 GATTGCAAGTTTTTGACAAAAGAAATT 57.441 25.926 12.84 3.31 35.51 1.82
3425 3734 8.321650 AGATTGCAAGTTTTTGACAAAAGAAA 57.678 26.923 12.84 3.92 35.51 2.52
3426 3735 7.903995 AGATTGCAAGTTTTTGACAAAAGAA 57.096 28.000 12.84 0.00 35.51 2.52
3427 3736 9.248291 GATAGATTGCAAGTTTTTGACAAAAGA 57.752 29.630 12.84 3.12 35.51 2.52
3428 3737 8.490355 GGATAGATTGCAAGTTTTTGACAAAAG 58.510 33.333 12.84 3.78 35.51 2.27
3441 3750 7.961283 CGTGATATTTGATGGATAGATTGCAAG 59.039 37.037 4.94 0.00 0.00 4.01
3448 3757 7.154656 CACCTTCGTGATATTTGATGGATAGA 58.845 38.462 10.00 0.00 43.14 1.98
3453 3762 3.627123 TGCACCTTCGTGATATTTGATGG 59.373 43.478 0.00 0.00 43.14 3.51
3501 3810 5.746245 GCTAGGTGATCTACAATATCGATGC 59.254 44.000 8.54 0.00 0.00 3.91
3506 3815 5.864474 CCGTTGCTAGGTGATCTACAATATC 59.136 44.000 0.00 0.00 0.00 1.63
3517 3827 1.274167 CTTGTACCCGTTGCTAGGTGA 59.726 52.381 0.00 0.00 36.88 4.02
3549 3859 1.478510 CTCGTTGCTAGATGGTCTGGT 59.521 52.381 0.00 0.00 0.00 4.00
3553 3863 2.231215 ATGCTCGTTGCTAGATGGTC 57.769 50.000 0.00 0.00 43.37 4.02
3554 3864 3.612717 CGATATGCTCGTTGCTAGATGGT 60.613 47.826 0.00 0.00 42.56 3.55
3555 3865 2.919859 CGATATGCTCGTTGCTAGATGG 59.080 50.000 0.00 0.00 42.56 3.51
3556 3866 2.919859 CCGATATGCTCGTTGCTAGATG 59.080 50.000 0.00 0.00 46.18 2.90
3557 3867 2.820197 TCCGATATGCTCGTTGCTAGAT 59.180 45.455 0.00 0.00 46.18 1.98
3558 3868 2.226674 CTCCGATATGCTCGTTGCTAGA 59.773 50.000 0.00 0.00 46.18 2.43
3559 3869 2.590073 CTCCGATATGCTCGTTGCTAG 58.410 52.381 5.00 0.00 46.18 3.42
3560 3870 1.335964 GCTCCGATATGCTCGTTGCTA 60.336 52.381 5.00 0.00 46.18 3.49
3561 3871 0.598680 GCTCCGATATGCTCGTTGCT 60.599 55.000 5.00 0.00 46.18 3.91
3562 3872 1.560860 GGCTCCGATATGCTCGTTGC 61.561 60.000 0.00 0.00 46.18 4.17
3563 3873 1.278172 CGGCTCCGATATGCTCGTTG 61.278 60.000 1.35 0.00 46.18 4.10
3564 3874 1.007271 CGGCTCCGATATGCTCGTT 60.007 57.895 1.35 0.00 46.18 3.85
3565 3875 2.645567 CGGCTCCGATATGCTCGT 59.354 61.111 1.35 0.00 46.18 4.18
3567 3877 1.214062 CTCCGGCTCCGATATGCTC 59.786 63.158 10.28 0.00 42.83 4.26
3568 3878 2.936912 GCTCCGGCTCCGATATGCT 61.937 63.158 10.28 0.00 42.83 3.79
3569 3879 2.433318 GCTCCGGCTCCGATATGC 60.433 66.667 10.28 4.71 42.83 3.14
3570 3880 0.668706 CTTGCTCCGGCTCCGATATG 60.669 60.000 10.28 0.00 42.83 1.78
3571 3881 1.668294 CTTGCTCCGGCTCCGATAT 59.332 57.895 10.28 0.00 42.83 1.63
3572 3882 3.129300 CTTGCTCCGGCTCCGATA 58.871 61.111 10.28 0.00 42.83 2.92
3573 3883 4.537433 GCTTGCTCCGGCTCCGAT 62.537 66.667 10.28 0.00 42.83 4.18
3576 3886 4.722700 TTGGCTTGCTCCGGCTCC 62.723 66.667 0.00 0.00 39.59 4.70
3577 3887 2.672996 TTTGGCTTGCTCCGGCTC 60.673 61.111 0.00 0.00 39.59 4.70
3578 3888 2.985847 GTTTGGCTTGCTCCGGCT 60.986 61.111 0.00 0.00 39.59 5.52
3579 3889 3.294493 TGTTTGGCTTGCTCCGGC 61.294 61.111 0.00 0.00 39.26 6.13
3580 3890 2.644992 GTGTTTGGCTTGCTCCGG 59.355 61.111 0.00 0.00 0.00 5.14
3581 3891 1.526575 ATGGTGTTTGGCTTGCTCCG 61.527 55.000 0.00 0.00 0.00 4.63
3582 3892 1.544724 TATGGTGTTTGGCTTGCTCC 58.455 50.000 0.00 0.00 0.00 4.70
3583 3893 3.874392 ATTATGGTGTTTGGCTTGCTC 57.126 42.857 0.00 0.00 0.00 4.26
3584 3894 4.772100 ACTTATTATGGTGTTTGGCTTGCT 59.228 37.500 0.00 0.00 0.00 3.91
3585 3895 5.072040 ACTTATTATGGTGTTTGGCTTGC 57.928 39.130 0.00 0.00 0.00 4.01
3586 3896 9.651913 ATTTTACTTATTATGGTGTTTGGCTTG 57.348 29.630 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.