Multiple sequence alignment - TraesCS6A01G374600

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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 TraesCS6A01G374600 chr6A 100.000 4599 0 0 1 4599 597339222 597343820 0.000000e+00 8493
1 TraesCS6A01G374600 chr6D 90.524 4717 182 110 1 4569 451558403 451553804 0.000000e+00 5989
2 TraesCS6A01G374600 chr6D 91.859 651 18 14 3509 4148 341539955 341539329 0.000000e+00 876
3 TraesCS6A01G374600 chr6B 88.512 4744 185 132 1 4542 685965417 685970002 0.000000e+00 5409
4 TraesCS6A01G374600 chr1D 92.049 654 18 14 3506 4148 409370585 409371215 0.000000e+00 889
5 TraesCS6A01G374600 chrUn 92.166 651 16 13 3509 4148 101283095 101282469 0.000000e+00 887
6 TraesCS6A01G374600 chrUn 91.859 651 16 16 3509 4148 21738571 21737947 0.000000e+00 874
7 TraesCS6A01G374600 chr2D 91.871 652 17 15 3509 4148 520923525 520922898 0.000000e+00 878
8 TraesCS6A01G374600 chr5D 91.590 654 21 14 3506 4148 81017934 81018564 0.000000e+00 872
9 TraesCS6A01G374600 chr4D 91.705 651 18 15 3509 4148 2712940 2712315 0.000000e+00 870
10 TraesCS6A01G374600 chr1B 89.303 617 37 13 3889 4494 233895752 233896350 0.000000e+00 747
11 TraesCS6A01G374600 chr2B 88.009 467 34 9 4039 4494 328869306 328868851 2.440000e-147 532


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 TraesCS6A01G374600 chr6A 597339222 597343820 4598 False 8493 8493 100.000 1 4599 1 chr6A.!!$F1 4598
1 TraesCS6A01G374600 chr6D 451553804 451558403 4599 True 5989 5989 90.524 1 4569 1 chr6D.!!$R2 4568
2 TraesCS6A01G374600 chr6D 341539329 341539955 626 True 876 876 91.859 3509 4148 1 chr6D.!!$R1 639
3 TraesCS6A01G374600 chr6B 685965417 685970002 4585 False 5409 5409 88.512 1 4542 1 chr6B.!!$F1 4541
4 TraesCS6A01G374600 chr1D 409370585 409371215 630 False 889 889 92.049 3506 4148 1 chr1D.!!$F1 642
5 TraesCS6A01G374600 chrUn 101282469 101283095 626 True 887 887 92.166 3509 4148 1 chrUn.!!$R2 639
6 TraesCS6A01G374600 chrUn 21737947 21738571 624 True 874 874 91.859 3509 4148 1 chrUn.!!$R1 639
7 TraesCS6A01G374600 chr2D 520922898 520923525 627 True 878 878 91.871 3509 4148 1 chr2D.!!$R1 639
8 TraesCS6A01G374600 chr5D 81017934 81018564 630 False 872 872 91.590 3506 4148 1 chr5D.!!$F1 642
9 TraesCS6A01G374600 chr4D 2712315 2712940 625 True 870 870 91.705 3509 4148 1 chr4D.!!$R1 639
10 TraesCS6A01G374600 chr1B 233895752 233896350 598 False 747 747 89.303 3889 4494 1 chr1B.!!$F1 605

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
792 861 0.037232 AGATAAGCCCGATTAGCGCC 60.037 55.0 2.29 0.0 39.11 6.53 F
1446 1567 0.931662 CCGTTCGTTCAGTTCGTCGT 60.932 55.0 0.00 0.0 0.00 4.34 F
2642 2849 0.748367 CATCGTCCTCCTCGGAGTCA 60.748 60.0 11.76 0.0 44.20 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2624 2831 0.183971 ATGACTCCGAGGAGGACGAT 59.816 55.0 21.79 1.64 45.98 3.73 R
2989 3208 1.089112 CTTGTCGATCTGGCAATGCA 58.911 50.0 7.79 0.00 0.00 3.96 R
4499 4831 0.321387 TGTAGAGGCGACGACTGACT 60.321 55.0 8.65 1.68 0.00 3.41 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
27 28 3.305709 CTCTGGAAGGAAACACGCA 57.694 52.632 0.00 0.00 0.00 5.24
28 29 0.868406 CTCTGGAAGGAAACACGCAC 59.132 55.000 0.00 0.00 0.00 5.34
29 30 0.179234 TCTGGAAGGAAACACGCACA 59.821 50.000 0.00 0.00 0.00 4.57
30 31 0.588252 CTGGAAGGAAACACGCACAG 59.412 55.000 0.00 0.00 0.00 3.66
31 32 1.282875 GGAAGGAAACACGCACAGC 59.717 57.895 0.00 0.00 0.00 4.40
32 33 1.444119 GGAAGGAAACACGCACAGCA 61.444 55.000 0.00 0.00 0.00 4.41
33 34 0.593128 GAAGGAAACACGCACAGCAT 59.407 50.000 0.00 0.00 0.00 3.79
34 35 0.593128 AAGGAAACACGCACAGCATC 59.407 50.000 0.00 0.00 0.00 3.91
35 36 1.210155 GGAAACACGCACAGCATCC 59.790 57.895 0.00 0.00 0.00 3.51
36 37 1.514678 GGAAACACGCACAGCATCCA 61.515 55.000 0.00 0.00 0.00 3.41
74 76 7.552458 AAAAAGAGCAAATTCAAATTCGGTT 57.448 28.000 0.00 0.00 0.00 4.44
76 78 7.552458 AAAGAGCAAATTCAAATTCGGTTTT 57.448 28.000 0.00 0.00 0.00 2.43
77 79 6.769608 AGAGCAAATTCAAATTCGGTTTTC 57.230 33.333 0.00 0.00 0.00 2.29
78 80 5.402270 AGAGCAAATTCAAATTCGGTTTTCG 59.598 36.000 0.00 0.00 40.90 3.46
443 473 2.433970 CCAAACATGAAACAACCACCCT 59.566 45.455 0.00 0.00 0.00 4.34
444 474 3.118445 CCAAACATGAAACAACCACCCTT 60.118 43.478 0.00 0.00 0.00 3.95
445 475 3.817709 AACATGAAACAACCACCCTTG 57.182 42.857 0.00 0.00 0.00 3.61
446 476 3.025322 ACATGAAACAACCACCCTTGA 57.975 42.857 0.00 0.00 0.00 3.02
520 578 5.820423 AGAAAAAGAAAAATGGAAAACCCGG 59.180 36.000 0.00 0.00 37.93 5.73
635 699 2.357952 GCCGTCACTTTGAAAAAGGAGT 59.642 45.455 4.86 0.00 0.00 3.85
643 707 4.335594 ACTTTGAAAAAGGAGTCTGGTTCG 59.664 41.667 4.86 0.00 0.00 3.95
655 719 0.319555 CTGGTTCGGTTCGCAGAAGA 60.320 55.000 0.00 0.00 45.90 2.87
656 720 0.320374 TGGTTCGGTTCGCAGAAGAT 59.680 50.000 0.00 0.00 45.90 2.40
667 731 7.040617 TCGGTTCGCAGAAGATATATATATCCC 60.041 40.741 23.44 17.21 45.90 3.85
678 742 1.035932 ATATATCCCTCGGCCGGACG 61.036 60.000 27.95 27.95 30.39 4.79
679 743 4.973023 TATATATCCCTCGGCCGGACGG 62.973 59.091 33.03 20.79 38.57 4.79
706 770 9.984190 ACCCGTTTGTTTATTTACAAATATGTT 57.016 25.926 5.36 0.00 46.29 2.71
728 792 3.690422 TGCTTGTTTGTTTTACAGCTCG 58.310 40.909 0.00 0.00 0.00 5.03
741 808 4.992294 GCTCGGAGGAGATCGCGC 62.992 72.222 0.00 0.00 43.27 6.86
791 860 2.649331 TAGATAAGCCCGATTAGCGC 57.351 50.000 0.00 0.00 39.11 5.92
792 861 0.037232 AGATAAGCCCGATTAGCGCC 60.037 55.000 2.29 0.00 39.11 6.53
793 862 0.037232 GATAAGCCCGATTAGCGCCT 60.037 55.000 2.29 0.00 39.11 5.52
794 863 0.037232 ATAAGCCCGATTAGCGCCTC 60.037 55.000 2.29 0.00 39.11 4.70
797 866 2.862223 GCCCGATTAGCGCCTCTCT 61.862 63.158 2.29 0.00 39.11 3.10
816 885 2.430244 GTCCGCTTGCGAGACGAA 60.430 61.111 16.99 0.00 0.00 3.85
818 887 1.733041 TCCGCTTGCGAGACGAAAG 60.733 57.895 16.99 7.42 44.56 2.62
902 978 2.120909 GGTGCCATGTATTGCCGCT 61.121 57.895 0.00 0.00 0.00 5.52
1054 1135 1.474879 GAAGACGGGAAGAGAGTCAGG 59.525 57.143 0.00 0.00 37.36 3.86
1418 1520 1.876799 CACATTGGCACGGTGAGTAAA 59.123 47.619 13.29 0.14 34.52 2.01
1419 1521 2.292016 CACATTGGCACGGTGAGTAAAA 59.708 45.455 13.29 0.00 34.52 1.52
1420 1522 2.952978 ACATTGGCACGGTGAGTAAAAA 59.047 40.909 13.29 0.00 0.00 1.94
1446 1567 0.931662 CCGTTCGTTCAGTTCGTCGT 60.932 55.000 0.00 0.00 0.00 4.34
1453 1574 4.695231 CAGTTCGTCGTCGGCGGT 62.695 66.667 20.32 1.34 38.89 5.68
1538 1659 2.802816 CGATTTTAAGGAGGAGCGGATG 59.197 50.000 0.00 0.00 0.00 3.51
1567 1688 3.729965 CTGCCTGCCTGACCTAGCG 62.730 68.421 0.00 0.00 0.00 4.26
1718 1851 4.973360 CGGCGCACCACCAAAACG 62.973 66.667 10.83 0.00 34.57 3.60
1771 1911 2.272146 CACATGGAAGGGGACGGG 59.728 66.667 0.00 0.00 0.00 5.28
1772 1912 2.124085 ACATGGAAGGGGACGGGA 59.876 61.111 0.00 0.00 0.00 5.14
1773 1913 2.298661 ACATGGAAGGGGACGGGAC 61.299 63.158 0.00 0.00 0.00 4.46
1830 1971 4.377760 AGGAGCGGGAGGGAACGA 62.378 66.667 0.00 0.00 0.00 3.85
1833 1974 3.660732 GAGCGGGAGGGAACGAACC 62.661 68.421 0.00 0.00 0.00 3.62
1840 1981 2.577593 GGGAACGAACCCTCCTCG 59.422 66.667 12.83 0.00 45.90 4.63
1842 1983 2.281295 GGAACGAACCCTCCTCGGT 61.281 63.158 0.00 0.00 39.39 4.69
1843 1984 1.080025 GAACGAACCCTCCTCGGTG 60.080 63.158 0.00 0.00 36.08 4.94
1844 1985 2.502692 GAACGAACCCTCCTCGGTGG 62.503 65.000 0.00 0.00 36.08 4.61
1949 2117 1.878953 CCGTGACCAAAGTTACTGCT 58.121 50.000 0.00 0.00 30.49 4.24
1950 2118 1.531149 CCGTGACCAAAGTTACTGCTG 59.469 52.381 0.00 0.00 30.49 4.41
1958 2127 4.202441 CCAAAGTTACTGCTGCTCCATAT 58.798 43.478 0.00 0.00 0.00 1.78
1990 2163 1.869824 TTTACTGGTGGGGATGGGGC 61.870 60.000 0.00 0.00 0.00 5.80
2024 2197 3.076916 GTTACGTACCGGGGGCCT 61.077 66.667 6.32 0.00 0.00 5.19
2170 2343 1.067821 CCCCTTTACGCAACAGCAAAA 59.932 47.619 0.00 0.00 0.00 2.44
2183 2356 5.540911 CAACAGCAAAATAAACCCATCACT 58.459 37.500 0.00 0.00 0.00 3.41
2236 2431 7.958125 GCGTTTGCTTTACTGATTGAACAGTG 61.958 42.308 10.91 0.00 43.33 3.66
2246 2441 4.503910 TGATTGAACAGTGGTCTATTCGG 58.496 43.478 10.10 0.00 30.50 4.30
2247 2442 3.328382 TTGAACAGTGGTCTATTCGGG 57.672 47.619 10.10 0.00 30.50 5.14
2249 2444 2.635915 TGAACAGTGGTCTATTCGGGTT 59.364 45.455 10.10 0.00 30.50 4.11
2276 2479 1.625616 AAAGTAGTCGCGTCGATTGG 58.374 50.000 5.77 0.00 38.42 3.16
2300 2503 1.344438 CTGCAGTGAACTGGGAGTGTA 59.656 52.381 5.25 0.00 43.94 2.90
2301 2504 1.977854 TGCAGTGAACTGGGAGTGTAT 59.022 47.619 12.20 0.00 43.94 2.29
2560 2767 3.419759 GGACGGCGCGAACAATGT 61.420 61.111 12.10 0.00 0.00 2.71
2642 2849 0.748367 CATCGTCCTCCTCGGAGTCA 60.748 60.000 11.76 0.00 44.20 3.41
2989 3208 3.077519 GCGAGGTGCGGAGGTGTAT 62.078 63.158 0.00 0.00 41.29 2.29
3059 3278 2.280119 AAGACGCTCTGCAACGCA 60.280 55.556 7.54 0.00 36.92 5.24
3140 3359 2.359850 TTCGTGCCAGCCATCCAC 60.360 61.111 0.00 0.00 0.00 4.02
3185 3404 0.392193 AGATGCGCCAGAAGGTTGAG 60.392 55.000 4.18 0.00 37.19 3.02
3243 3462 1.742768 GATTGATCGAGCTCCCCGT 59.257 57.895 8.47 0.00 0.00 5.28
3275 3504 3.677648 CCGGACGGTTGGTCTCGT 61.678 66.667 0.00 0.00 45.35 4.18
3279 3508 4.169271 ACGGTTGGTCTCGTCTCA 57.831 55.556 0.00 0.00 34.20 3.27
3344 3573 2.195389 GCATGCTTGCTTCCATCCA 58.805 52.632 16.80 0.00 45.77 3.41
3345 3574 0.750850 GCATGCTTGCTTCCATCCAT 59.249 50.000 16.80 0.00 45.77 3.41
3346 3575 1.538204 GCATGCTTGCTTCCATCCATG 60.538 52.381 16.80 0.00 45.77 3.66
3425 3677 0.798776 CGGTTTCAGTCAGCATCCAC 59.201 55.000 0.00 0.00 0.00 4.02
3503 3760 5.241064 GGGTTTACTCCACCTCTTTTTCTTC 59.759 44.000 0.00 0.00 34.36 2.87
3584 3842 2.023015 TGAGGAGGGCAGGAGAAATAGA 60.023 50.000 0.00 0.00 0.00 1.98
3585 3843 3.247162 GAGGAGGGCAGGAGAAATAGAT 58.753 50.000 0.00 0.00 0.00 1.98
3586 3844 2.978278 AGGAGGGCAGGAGAAATAGATG 59.022 50.000 0.00 0.00 0.00 2.90
3587 3845 2.039613 GGAGGGCAGGAGAAATAGATGG 59.960 54.545 0.00 0.00 0.00 3.51
3704 3972 1.042003 CAGAGGCAGAGGCAGCTAGA 61.042 60.000 0.00 0.00 43.71 2.43
3783 4061 6.861065 TTGTTGGTTTGCTAAGTTAGAGAG 57.139 37.500 14.27 0.00 0.00 3.20
3834 4114 1.212195 GGTTGAAGTAGGGGGATCACC 59.788 57.143 5.01 5.01 39.11 4.02
3835 4115 1.913419 GTTGAAGTAGGGGGATCACCA 59.087 52.381 17.85 0.00 42.91 4.17
3836 4116 2.307686 GTTGAAGTAGGGGGATCACCAA 59.692 50.000 17.85 0.00 42.91 3.67
3837 4117 2.858644 TGAAGTAGGGGGATCACCAAT 58.141 47.619 17.85 6.23 42.91 3.16
3932 4212 9.847224 CTATGTTTAGGGATTTATAAGTGGTGT 57.153 33.333 0.00 0.00 0.00 4.16
3933 4213 8.747538 ATGTTTAGGGATTTATAAGTGGTGTC 57.252 34.615 0.00 0.00 0.00 3.67
3968 4248 9.927668 TTGTGTTTTATACTAGTAGTGTTACCC 57.072 33.333 13.29 0.00 0.00 3.69
4059 4343 3.305539 GCAAGTTGTGATCATCCAAGCAA 60.306 43.478 0.00 0.00 0.00 3.91
4094 4378 1.280457 TGAGCTCTTCTTCTTCCCCC 58.720 55.000 16.19 0.00 0.00 5.40
4148 4477 4.336993 AGCACTGCTACTGATAGTGACTAC 59.663 45.833 0.21 0.00 43.35 2.73
4149 4478 4.336993 GCACTGCTACTGATAGTGACTACT 59.663 45.833 7.71 0.00 43.35 2.57
4150 4479 5.527951 GCACTGCTACTGATAGTGACTACTA 59.472 44.000 7.71 0.00 43.35 1.82
4151 4480 6.512091 GCACTGCTACTGATAGTGACTACTAC 60.512 46.154 7.71 0.00 43.35 2.73
4152 4481 6.764085 CACTGCTACTGATAGTGACTACTACT 59.236 42.308 0.00 0.00 43.35 2.57
4153 4482 6.987992 ACTGCTACTGATAGTGACTACTACTC 59.012 42.308 0.00 0.00 41.92 2.59
4154 4483 6.289834 TGCTACTGATAGTGACTACTACTCC 58.710 44.000 0.00 0.00 41.92 3.85
4155 4484 6.099990 TGCTACTGATAGTGACTACTACTCCT 59.900 42.308 0.00 0.00 41.92 3.69
4156 4485 7.289549 TGCTACTGATAGTGACTACTACTCCTA 59.710 40.741 0.00 0.00 41.92 2.94
4302 4634 1.765314 GGTCCTGGAGCACACTCATAT 59.235 52.381 20.44 0.00 45.42 1.78
4303 4635 2.965831 GGTCCTGGAGCACACTCATATA 59.034 50.000 20.44 0.00 45.42 0.86
4304 4636 3.580458 GGTCCTGGAGCACACTCATATAT 59.420 47.826 20.44 0.00 45.42 0.86
4305 4637 4.562347 GGTCCTGGAGCACACTCATATATG 60.562 50.000 20.44 6.36 45.42 1.78
4306 4638 3.580022 TCCTGGAGCACACTCATATATGG 59.420 47.826 12.78 6.31 45.42 2.74
4307 4639 3.580022 CCTGGAGCACACTCATATATGGA 59.420 47.826 12.78 0.00 45.42 3.41
4336 4668 7.615365 TGGCCTGTCCATCCATATAATAAATTC 59.385 37.037 3.32 0.00 40.72 2.17
4375 4707 0.850883 ATTCCCATGTCCACCCCAGT 60.851 55.000 0.00 0.00 0.00 4.00
4408 4740 5.360714 TGCTCAATTGGATTGGATTACCTTC 59.639 40.000 5.42 0.00 40.61 3.46
4462 4794 3.692257 AGAGAGTGGGTCACATCTTTG 57.308 47.619 0.78 0.00 36.74 2.77
4465 4797 1.537202 GAGTGGGTCACATCTTTGCAC 59.463 52.381 0.00 0.00 36.74 4.57
4476 4808 2.380064 TCTTTGCACCCACAAATCCT 57.620 45.000 0.00 0.00 38.76 3.24
4494 4826 7.836183 ACAAATCCTAGCCATGTTAAGAGATTT 59.164 33.333 0.00 0.00 33.05 2.17
4495 4827 8.689972 CAAATCCTAGCCATGTTAAGAGATTTT 58.310 33.333 0.00 0.00 31.06 1.82
4497 4829 6.049149 TCCTAGCCATGTTAAGAGATTTTCG 58.951 40.000 0.00 0.00 0.00 3.46
4499 4831 4.009675 AGCCATGTTAAGAGATTTTCGCA 58.990 39.130 0.00 0.00 0.00 5.10
4500 4832 4.095483 AGCCATGTTAAGAGATTTTCGCAG 59.905 41.667 0.00 0.00 0.00 5.18
4501 4833 4.142600 GCCATGTTAAGAGATTTTCGCAGT 60.143 41.667 0.00 0.00 0.00 4.40
4535 4867 4.578871 TCTACATGGTCCAATCAACACAG 58.421 43.478 0.00 0.00 0.00 3.66
4547 4879 5.916883 CCAATCAACACAGTTTCATCTCAAC 59.083 40.000 0.00 0.00 0.00 3.18
4560 4892 7.229306 AGTTTCATCTCAACTGCTACATTTTCA 59.771 33.333 0.00 0.00 33.04 2.69
4565 4897 6.705302 TCTCAACTGCTACATTTTCATCTCT 58.295 36.000 0.00 0.00 0.00 3.10
4569 4901 8.886719 TCAACTGCTACATTTTCATCTCTATTG 58.113 33.333 0.00 0.00 0.00 1.90
4570 4902 7.256756 ACTGCTACATTTTCATCTCTATTGC 57.743 36.000 0.00 0.00 0.00 3.56
4571 4903 7.052873 ACTGCTACATTTTCATCTCTATTGCT 58.947 34.615 0.00 0.00 0.00 3.91
4572 4904 7.555554 ACTGCTACATTTTCATCTCTATTGCTT 59.444 33.333 0.00 0.00 0.00 3.91
4573 4905 7.700505 TGCTACATTTTCATCTCTATTGCTTG 58.299 34.615 0.00 0.00 0.00 4.01
4574 4906 7.337689 TGCTACATTTTCATCTCTATTGCTTGT 59.662 33.333 0.00 0.00 0.00 3.16
4575 4907 7.642978 GCTACATTTTCATCTCTATTGCTTGTG 59.357 37.037 0.00 0.00 0.00 3.33
4576 4908 6.860080 ACATTTTCATCTCTATTGCTTGTGG 58.140 36.000 0.00 0.00 0.00 4.17
4577 4909 5.902613 TTTTCATCTCTATTGCTTGTGGG 57.097 39.130 0.00 0.00 0.00 4.61
4578 4910 3.565764 TCATCTCTATTGCTTGTGGGG 57.434 47.619 0.00 0.00 0.00 4.96
4579 4911 2.173356 TCATCTCTATTGCTTGTGGGGG 59.827 50.000 0.00 0.00 0.00 5.40
4580 4912 1.965414 TCTCTATTGCTTGTGGGGGA 58.035 50.000 0.00 0.00 0.00 4.81
4581 4913 2.274542 TCTCTATTGCTTGTGGGGGAA 58.725 47.619 0.00 0.00 0.00 3.97
4582 4914 2.026262 TCTCTATTGCTTGTGGGGGAAC 60.026 50.000 0.00 0.00 0.00 3.62
4597 4929 3.382048 GGGAACCGGACTCATGTATAC 57.618 52.381 9.46 0.00 40.86 1.47
4598 4930 2.696707 GGGAACCGGACTCATGTATACA 59.303 50.000 9.46 8.27 40.86 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.458669 CCTTGGATTGGATGCTGTGC 59.541 55.000 0.00 0.00 0.00 4.57
26 27 1.108776 CCCTTGGATTGGATGCTGTG 58.891 55.000 0.00 0.00 0.00 3.66
27 28 0.706433 ACCCTTGGATTGGATGCTGT 59.294 50.000 0.00 0.00 0.00 4.40
28 29 2.734755 TACCCTTGGATTGGATGCTG 57.265 50.000 0.00 0.00 0.00 4.41
29 30 3.756082 TTTACCCTTGGATTGGATGCT 57.244 42.857 0.00 0.00 0.00 3.79
30 31 4.817318 TTTTTACCCTTGGATTGGATGC 57.183 40.909 0.00 0.00 0.00 3.91
54 56 5.402270 CGAAAACCGAATTTGAATTTGCTCT 59.598 36.000 0.00 0.00 41.76 4.09
55 57 5.401079 TCGAAAACCGAATTTGAATTTGCTC 59.599 36.000 0.00 0.00 45.43 4.26
56 58 5.285651 TCGAAAACCGAATTTGAATTTGCT 58.714 33.333 0.00 0.00 45.43 3.91
233 241 0.320596 TATAATTAACGCCCCGCCCG 60.321 55.000 0.00 0.00 0.00 6.13
635 699 0.319555 CTTCTGCGAACCGAACCAGA 60.320 55.000 0.00 0.00 32.90 3.86
643 707 8.184304 AGGGATATATATATCTTCTGCGAACC 57.816 38.462 25.12 16.77 39.24 3.62
655 719 4.342359 GTCCGGCCGAGGGATATATATAT 58.658 47.826 30.73 4.86 35.67 0.86
656 720 3.759581 GTCCGGCCGAGGGATATATATA 58.240 50.000 30.73 0.00 35.67 0.86
706 770 4.101942 CGAGCTGTAAAACAAACAAGCAA 58.898 39.130 0.00 0.00 0.00 3.91
707 771 3.488384 CCGAGCTGTAAAACAAACAAGCA 60.488 43.478 0.00 0.00 0.00 3.91
708 772 3.042887 CCGAGCTGTAAAACAAACAAGC 58.957 45.455 0.00 0.00 0.00 4.01
709 773 4.527564 CTCCGAGCTGTAAAACAAACAAG 58.472 43.478 0.00 0.00 0.00 3.16
728 792 2.334653 CAGAGCGCGATCTCCTCC 59.665 66.667 26.20 0.00 33.66 4.30
741 808 6.065374 TCTCTAACCTCTAATGCTACCAGAG 58.935 44.000 0.00 0.00 36.40 3.35
758 825 9.781633 TCGGGCTTATCTATATCTATCTCTAAC 57.218 37.037 0.00 0.00 0.00 2.34
791 860 2.202676 GCAAGCGGACGAGAGAGG 60.203 66.667 0.00 0.00 0.00 3.69
792 861 2.578178 CGCAAGCGGACGAGAGAG 60.578 66.667 6.55 0.00 35.56 3.20
793 862 3.053896 TCGCAAGCGGACGAGAGA 61.054 61.111 14.98 0.00 40.25 3.10
844 914 8.614346 GCGGATTTACATACACACCTAAAATTA 58.386 33.333 0.00 0.00 0.00 1.40
845 915 7.415877 GGCGGATTTACATACACACCTAAAATT 60.416 37.037 0.00 0.00 0.00 1.82
846 916 6.038936 GGCGGATTTACATACACACCTAAAAT 59.961 38.462 0.00 0.00 0.00 1.82
847 917 5.354792 GGCGGATTTACATACACACCTAAAA 59.645 40.000 0.00 0.00 0.00 1.52
848 918 4.877251 GGCGGATTTACATACACACCTAAA 59.123 41.667 0.00 0.00 0.00 1.85
849 919 4.162698 AGGCGGATTTACATACACACCTAA 59.837 41.667 0.00 0.00 0.00 2.69
850 920 3.707611 AGGCGGATTTACATACACACCTA 59.292 43.478 0.00 0.00 0.00 3.08
851 921 2.504175 AGGCGGATTTACATACACACCT 59.496 45.455 0.00 0.00 0.00 4.00
861 931 6.033966 CCAAATTAAGACAAGGCGGATTTAC 58.966 40.000 0.00 0.00 0.00 2.01
862 932 5.712917 ACCAAATTAAGACAAGGCGGATTTA 59.287 36.000 0.00 0.00 0.00 1.40
865 935 3.443681 CACCAAATTAAGACAAGGCGGAT 59.556 43.478 0.00 0.00 0.00 4.18
866 936 2.817258 CACCAAATTAAGACAAGGCGGA 59.183 45.455 0.00 0.00 0.00 5.54
868 938 2.595386 GCACCAAATTAAGACAAGGCG 58.405 47.619 0.00 0.00 0.00 5.52
902 978 1.077501 GCATCCAGGGTAAGCAGCA 60.078 57.895 0.00 0.00 0.00 4.41
913 994 1.069703 CACGCATTAATCGGCATCCAG 60.070 52.381 10.58 0.00 0.00 3.86
1046 1127 0.787084 TCTCCTCAACCCCTGACTCT 59.213 55.000 0.00 0.00 0.00 3.24
1047 1128 1.872773 ATCTCCTCAACCCCTGACTC 58.127 55.000 0.00 0.00 0.00 3.36
1054 1135 2.242196 TCAATCCCAATCTCCTCAACCC 59.758 50.000 0.00 0.00 0.00 4.11
1418 1520 4.642445 ACTGAACGAACGGGAAAATTTT 57.358 36.364 2.28 2.28 0.00 1.82
1419 1521 4.603985 GAACTGAACGAACGGGAAAATTT 58.396 39.130 0.00 0.00 0.00 1.82
1420 1522 3.303526 CGAACTGAACGAACGGGAAAATT 60.304 43.478 0.00 0.00 0.00 1.82
1421 1523 2.222445 CGAACTGAACGAACGGGAAAAT 59.778 45.455 0.00 0.00 0.00 1.82
1426 1528 1.602877 CGACGAACTGAACGAACGGG 61.603 60.000 0.00 0.00 33.89 5.28
1480 1601 2.835895 AACCACCCAACCAACCGC 60.836 61.111 0.00 0.00 0.00 5.68
1631 1752 3.049080 GCAGGCAGGGGTAAGGGAG 62.049 68.421 0.00 0.00 0.00 4.30
1634 1755 3.017581 AGGCAGGCAGGGGTAAGG 61.018 66.667 0.00 0.00 0.00 2.69
1830 1971 4.974438 TGGCCACCGAGGAGGGTT 62.974 66.667 0.00 0.00 46.96 4.11
1894 2061 2.113243 GACACCTCCACCTCCACCAC 62.113 65.000 0.00 0.00 0.00 4.16
1895 2062 1.841556 GACACCTCCACCTCCACCA 60.842 63.158 0.00 0.00 0.00 4.17
1896 2063 2.943978 CGACACCTCCACCTCCACC 61.944 68.421 0.00 0.00 0.00 4.61
1958 2127 7.785506 TCCCCACCAGTAAAAGAAAAGAAAATA 59.214 33.333 0.00 0.00 0.00 1.40
2024 2197 4.320057 GCTAGCTAACTACCGAAAGCGATA 60.320 45.833 7.70 0.00 39.94 2.92
2265 2468 3.257561 CAGCCTCCAATCGACGCG 61.258 66.667 3.53 3.53 0.00 6.01
2276 2479 1.673665 CCCAGTTCACTGCAGCCTC 60.674 63.158 15.27 2.02 42.47 4.70
2300 2503 4.019174 GGAATCCCATGTCAGAAACACAT 58.981 43.478 0.00 0.00 41.75 3.21
2301 2504 3.074390 AGGAATCCCATGTCAGAAACACA 59.926 43.478 0.00 0.00 41.75 3.72
2560 2767 4.083271 TGTTGTTGTTCATGTTCACGTTGA 60.083 37.500 0.00 0.00 0.00 3.18
2615 2822 2.278013 GAGGACGATGCCGACGAC 60.278 66.667 0.00 0.00 39.50 4.34
2618 2825 2.413765 GAGGAGGACGATGCCGAC 59.586 66.667 0.00 0.00 39.50 4.79
2624 2831 0.183971 ATGACTCCGAGGAGGACGAT 59.816 55.000 21.79 1.64 45.98 3.73
2987 3206 2.618442 TGTCGATCTGGCAATGCATA 57.382 45.000 7.79 0.00 0.00 3.14
2989 3208 1.089112 CTTGTCGATCTGGCAATGCA 58.911 50.000 7.79 0.00 0.00 3.96
3140 3359 1.421646 ACCTTCTTGTGGGAGTTGGAG 59.578 52.381 0.00 0.00 0.00 3.86
3229 3448 4.593864 GGCACGGGGAGCTCGATC 62.594 72.222 7.83 0.00 0.00 3.69
3267 3492 1.381327 GGGGGATGAGACGAGACCA 60.381 63.158 0.00 0.00 0.00 4.02
3275 3504 9.607333 CATATATAATAGCTAAGGGGGATGAGA 57.393 37.037 0.00 0.00 0.00 3.27
3276 3505 9.386122 ACATATATAATAGCTAAGGGGGATGAG 57.614 37.037 0.00 0.00 0.00 2.90
3341 3570 3.378427 CGATGACTGACTGACTACATGGA 59.622 47.826 0.00 0.00 0.00 3.41
3343 3572 4.346970 GACGATGACTGACTGACTACATG 58.653 47.826 0.00 0.00 0.00 3.21
3344 3573 3.064134 CGACGATGACTGACTGACTACAT 59.936 47.826 0.00 0.00 0.00 2.29
3345 3574 2.415512 CGACGATGACTGACTGACTACA 59.584 50.000 0.00 0.00 0.00 2.74
3346 3575 2.415857 ACGACGATGACTGACTGACTAC 59.584 50.000 0.00 0.00 0.00 2.73
3425 3677 4.873810 TGCCCGGCGATTGATGGG 62.874 66.667 9.30 0.00 44.88 4.00
3584 3842 4.411212 TGACTCTGTGATTGATCCATCCAT 59.589 41.667 4.43 0.00 0.00 3.41
3585 3843 3.776417 TGACTCTGTGATTGATCCATCCA 59.224 43.478 4.43 2.08 0.00 3.41
3586 3844 4.141756 ACTGACTCTGTGATTGATCCATCC 60.142 45.833 4.43 0.00 0.00 3.51
3587 3845 4.809958 CACTGACTCTGTGATTGATCCATC 59.190 45.833 9.86 0.00 35.76 3.51
3673 3938 3.128188 CCTCTGCTGCTGCTGCTG 61.128 66.667 27.67 26.32 40.48 4.41
3676 3941 3.128188 CTGCCTCTGCTGCTGCTG 61.128 66.667 17.00 15.94 40.48 4.41
3704 3972 5.299279 CACACCAACTTTCCTAATTGACTGT 59.701 40.000 0.00 0.00 0.00 3.55
3783 4061 5.526111 TGGCTACTACTTGACACAAAGTTTC 59.474 40.000 0.00 0.00 40.77 2.78
3837 4117 9.276590 CCAATATAAACTGCTGACTATGATTGA 57.723 33.333 0.00 0.00 0.00 2.57
3930 4210 8.958119 AGTATAAAACACAAGAAAGACAGACA 57.042 30.769 0.00 0.00 0.00 3.41
4059 4343 8.722422 AGAAGAGCTCAAGGATTATAATTCCTT 58.278 33.333 17.77 16.95 43.95 3.36
4148 4477 9.988815 AGCATTTATAATTGTCACTAGGAGTAG 57.011 33.333 8.68 0.00 0.00 2.57
4153 4482 9.831737 GCATTAGCATTTATAATTGTCACTAGG 57.168 33.333 8.68 0.00 41.58 3.02
4154 4483 9.533983 CGCATTAGCATTTATAATTGTCACTAG 57.466 33.333 8.68 0.00 42.27 2.57
4155 4484 8.015087 GCGCATTAGCATTTATAATTGTCACTA 58.985 33.333 0.30 1.09 42.27 2.74
4156 4485 6.857964 GCGCATTAGCATTTATAATTGTCACT 59.142 34.615 0.30 1.84 42.27 3.41
4302 4634 3.019816 TGGACAGGCCACATCCATA 57.980 52.632 16.46 0.00 43.33 2.74
4303 4635 3.839589 TGGACAGGCCACATCCAT 58.160 55.556 16.46 0.00 43.33 3.41
4336 4668 5.465390 GGAATGTTCATTGCCATCAATCATG 59.535 40.000 2.63 0.00 40.74 3.07
4375 4707 3.438216 TCCAATTGAGCATCTGTCCAA 57.562 42.857 7.12 0.00 34.92 3.53
4408 4740 1.366679 CACTAGCAGAGCACATGGTG 58.633 55.000 0.00 0.00 36.51 4.17
4462 4794 0.323360 TGGCTAGGATTTGTGGGTGC 60.323 55.000 0.00 0.00 0.00 5.01
4465 4797 2.442236 ACATGGCTAGGATTTGTGGG 57.558 50.000 0.00 0.00 0.00 4.61
4476 4808 5.182487 TGCGAAAATCTCTTAACATGGCTA 58.818 37.500 0.00 0.00 0.00 3.93
4494 4826 2.428569 GCGACGACTGACTGCGAA 60.429 61.111 0.00 0.00 0.00 4.70
4495 4827 4.400109 GGCGACGACTGACTGCGA 62.400 66.667 0.00 0.00 0.00 5.10
4497 4829 1.645704 TAGAGGCGACGACTGACTGC 61.646 60.000 8.65 0.00 0.00 4.40
4499 4831 0.321387 TGTAGAGGCGACGACTGACT 60.321 55.000 8.65 1.68 0.00 3.41
4500 4832 0.733729 ATGTAGAGGCGACGACTGAC 59.266 55.000 8.65 6.68 0.00 3.51
4501 4833 0.733150 CATGTAGAGGCGACGACTGA 59.267 55.000 8.65 0.00 0.00 3.41
4535 4867 7.362662 TGAAAATGTAGCAGTTGAGATGAAAC 58.637 34.615 0.00 0.00 0.00 2.78
4547 4879 7.493743 AGCAATAGAGATGAAAATGTAGCAG 57.506 36.000 0.00 0.00 0.00 4.24
4555 4887 4.706476 CCCCACAAGCAATAGAGATGAAAA 59.294 41.667 0.00 0.00 0.00 2.29
4560 4892 2.492025 TCCCCCACAAGCAATAGAGAT 58.508 47.619 0.00 0.00 0.00 2.75
4565 4897 0.322997 CGGTTCCCCCACAAGCAATA 60.323 55.000 0.00 0.00 0.00 1.90
4569 4901 3.961414 TCCGGTTCCCCCACAAGC 61.961 66.667 0.00 0.00 0.00 4.01
4570 4902 2.033602 GTCCGGTTCCCCCACAAG 59.966 66.667 0.00 0.00 0.00 3.16
4571 4903 2.448931 AGTCCGGTTCCCCCACAA 60.449 61.111 0.00 0.00 0.00 3.33
4572 4904 2.926242 GAGTCCGGTTCCCCCACA 60.926 66.667 0.00 0.00 0.00 4.17
4573 4905 2.298661 ATGAGTCCGGTTCCCCCAC 61.299 63.158 0.00 0.00 0.00 4.61
4574 4906 2.124085 ATGAGTCCGGTTCCCCCA 59.876 61.111 0.00 0.00 0.00 4.96
4575 4907 0.979187 TACATGAGTCCGGTTCCCCC 60.979 60.000 0.00 0.00 0.00 5.40
4576 4908 1.129058 ATACATGAGTCCGGTTCCCC 58.871 55.000 0.00 0.00 0.00 4.81
4577 4909 2.696707 TGTATACATGAGTCCGGTTCCC 59.303 50.000 0.08 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.