Multiple sequence alignment - TraesCS3A01G220000

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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 TraesCS3A01G220000 chr3A 100.000 6206 0 0 1 6206 405695081 405688876 0.000000e+00 11461.0
1 TraesCS3A01G220000 chr3A 86.400 250 30 3 584 832 185171776 185171530 2.850000e-68 270.0
2 TraesCS3A01G220000 chr3A 91.765 170 9 4 3412 3579 675873020 675873186 1.350000e-56 231.0
3 TraesCS3A01G220000 chr3A 90.968 155 13 1 3425 3578 267044918 267045072 2.270000e-49 207.0
4 TraesCS3A01G220000 chr3B 94.715 1892 74 9 869 2735 399976010 399974120 0.000000e+00 2916.0
5 TraesCS3A01G220000 chr3B 95.550 1573 47 9 2983 4550 399973708 399972154 0.000000e+00 2495.0
6 TraesCS3A01G220000 chr3B 94.618 929 29 7 4968 5882 399971218 399970297 0.000000e+00 1419.0
7 TraesCS3A01G220000 chr3B 96.742 399 7 5 4536 4931 399971609 399971214 0.000000e+00 660.0
8 TraesCS3A01G220000 chr3B 96.407 334 11 1 5873 6206 399968481 399968149 3.270000e-152 549.0
9 TraesCS3A01G220000 chr3B 95.238 252 10 1 2734 2985 399974038 399973789 1.250000e-106 398.0
10 TraesCS3A01G220000 chr3B 86.454 251 32 2 584 832 766016965 766016715 2.200000e-69 274.0
11 TraesCS3A01G220000 chr3D 94.051 1866 82 12 889 2735 320427189 320429044 0.000000e+00 2804.0
12 TraesCS3A01G220000 chr3D 93.997 1366 66 8 2734 4096 320429138 320430490 0.000000e+00 2054.0
13 TraesCS3A01G220000 chr3D 95.386 1127 40 8 4594 5713 320430486 320431607 0.000000e+00 1783.0
14 TraesCS3A01G220000 chr3D 96.898 548 13 4 1 547 590400031 590399487 0.000000e+00 915.0
15 TraesCS3A01G220000 chr3D 92.578 512 15 9 5703 6206 320431997 320432493 0.000000e+00 713.0
16 TraesCS3A01G220000 chr3D 85.714 546 47 16 4325 4840 54835193 54835737 1.180000e-151 547.0
17 TraesCS3A01G220000 chr3D 88.824 170 15 3 3412 3579 540569252 540569085 8.150000e-49 206.0
18 TraesCS3A01G220000 chr5D 96.533 548 17 2 1 547 478458404 478458950 0.000000e+00 905.0
19 TraesCS3A01G220000 chr5D 96.533 548 16 3 1 547 318819321 318818776 0.000000e+00 904.0
20 TraesCS3A01G220000 chr5D 82.669 727 84 16 4154 4840 196352823 196352099 1.910000e-169 606.0
21 TraesCS3A01G220000 chr5D 82.079 731 88 17 4151 4840 191261244 191261972 8.960000e-163 584.0
22 TraesCS3A01G220000 chr5D 94.012 167 9 1 3412 3577 399614685 399614519 1.030000e-62 252.0
23 TraesCS3A01G220000 chr6D 96.168 548 19 2 1 547 107937961 107938507 0.000000e+00 894.0
24 TraesCS3A01G220000 chr6D 96.168 548 19 2 1 547 457743000 457742454 0.000000e+00 894.0
25 TraesCS3A01G220000 chr6D 88.095 252 28 2 584 833 107938491 107938742 1.310000e-76 298.0
26 TraesCS3A01G220000 chr2D 96.168 548 19 2 1 547 573908934 573908388 0.000000e+00 894.0
27 TraesCS3A01G220000 chr2D 95.993 549 20 2 1 547 538955623 538955075 0.000000e+00 891.0
28 TraesCS3A01G220000 chr2D 87.149 249 29 3 584 830 249985930 249986177 4.740000e-71 279.0
29 TraesCS3A01G220000 chr2D 86.853 251 29 2 584 833 95504746 95504993 1.700000e-70 278.0
30 TraesCS3A01G220000 chr2D 86.400 250 30 2 584 832 35246836 35246590 2.850000e-68 270.0
31 TraesCS3A01G220000 chr2D 100.000 28 0 0 2316 2343 433022485 433022458 1.100000e-02 52.8
32 TraesCS3A01G220000 chr1D 96.168 548 19 2 1 547 59533347 59533893 0.000000e+00 894.0
33 TraesCS3A01G220000 chr4D 95.985 548 20 2 1 547 487285060 487284514 0.000000e+00 889.0
34 TraesCS3A01G220000 chr4D 88.306 248 27 2 584 830 487284530 487284284 4.700000e-76 296.0
35 TraesCS3A01G220000 chr4D 81.303 353 56 7 4157 4505 205903352 205903006 1.700000e-70 278.0
36 TraesCS3A01G220000 chr2A 81.456 728 95 16 4151 4840 475794880 475795605 1.510000e-155 560.0
37 TraesCS3A01G220000 chr2A 87.097 248 28 2 584 830 160730572 160730816 1.700000e-70 278.0
38 TraesCS3A01G220000 chr4B 85.091 550 53 14 4320 4840 34782025 34781476 9.160000e-148 534.0
39 TraesCS3A01G220000 chr4B 90.937 331 30 0 4505 4835 299745025 299745355 4.410000e-121 446.0
40 TraesCS3A01G220000 chr4B 86.170 188 25 1 4320 4506 299744810 299744997 1.050000e-47 202.0
41 TraesCS3A01G220000 chr4B 90.164 61 5 1 2316 2375 640002232 640002172 1.850000e-10 78.7
42 TraesCS3A01G220000 chr4B 91.304 46 1 3 2331 2376 144758339 144758297 6.720000e-05 60.2
43 TraesCS3A01G220000 chr5B 91.940 335 27 0 4505 4839 323891468 323891134 2.620000e-128 470.0
44 TraesCS3A01G220000 chr5B 93.413 167 10 1 3412 3577 479726998 479726832 4.800000e-61 246.0
45 TraesCS3A01G220000 chr5B 92.063 63 3 1 2313 2375 564187853 564187913 3.080000e-13 87.9
46 TraesCS3A01G220000 chr1A 91.343 335 29 0 4505 4839 208681998 208682332 5.670000e-125 459.0
47 TraesCS3A01G220000 chr1A 87.698 252 30 1 584 834 99251218 99250967 6.080000e-75 292.0
48 TraesCS3A01G220000 chr1A 89.024 164 17 1 3412 3574 520812189 520812352 1.050000e-47 202.0
49 TraesCS3A01G220000 chr1A 82.741 197 30 4 3797 3992 472166204 472166011 8.270000e-39 172.0
50 TraesCS3A01G220000 chr1A 91.304 69 2 2 2308 2376 399227853 399227917 2.380000e-14 91.6
51 TraesCS3A01G220000 chr6B 81.586 353 54 7 4154 4502 719428888 719429233 1.320000e-71 281.0
52 TraesCS3A01G220000 chr6A 90.854 164 13 1 3411 3574 47466951 47466790 1.050000e-52 219.0
53 TraesCS3A01G220000 chr7A 88.406 138 15 1 3731 3867 731229643 731229780 1.380000e-36 165.0
54 TraesCS3A01G220000 chr1B 96.610 59 1 1 2319 2376 338014832 338014774 5.120000e-16 97.1
55 TraesCS3A01G220000 chr1B 93.103 58 2 2 2316 2372 98724129 98724185 3.990000e-12 84.2
56 TraesCS3A01G220000 chr7D 87.324 71 9 0 3827 3897 634717303 634717233 1.430000e-11 82.4
57 TraesCS3A01G220000 chr4A 89.286 56 1 4 2320 2375 474726341 474726391 1.440000e-06 65.8


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 TraesCS3A01G220000 chr3A 405688876 405695081 6205 True 11461.000000 11461 100.0000 1 6206 1 chr3A.!!$R2 6205
1 TraesCS3A01G220000 chr3B 399968149 399976010 7861 True 1406.166667 2916 95.5450 869 6206 6 chr3B.!!$R2 5337
2 TraesCS3A01G220000 chr3D 320427189 320432493 5304 False 1838.500000 2804 94.0030 889 6206 4 chr3D.!!$F2 5317
3 TraesCS3A01G220000 chr3D 590399487 590400031 544 True 915.000000 915 96.8980 1 547 1 chr3D.!!$R2 546
4 TraesCS3A01G220000 chr3D 54835193 54835737 544 False 547.000000 547 85.7140 4325 4840 1 chr3D.!!$F1 515
5 TraesCS3A01G220000 chr5D 478458404 478458950 546 False 905.000000 905 96.5330 1 547 1 chr5D.!!$F2 546
6 TraesCS3A01G220000 chr5D 318818776 318819321 545 True 904.000000 904 96.5330 1 547 1 chr5D.!!$R2 546
7 TraesCS3A01G220000 chr5D 196352099 196352823 724 True 606.000000 606 82.6690 4154 4840 1 chr5D.!!$R1 686
8 TraesCS3A01G220000 chr5D 191261244 191261972 728 False 584.000000 584 82.0790 4151 4840 1 chr5D.!!$F1 689
9 TraesCS3A01G220000 chr6D 457742454 457743000 546 True 894.000000 894 96.1680 1 547 1 chr6D.!!$R1 546
10 TraesCS3A01G220000 chr6D 107937961 107938742 781 False 596.000000 894 92.1315 1 833 2 chr6D.!!$F1 832
11 TraesCS3A01G220000 chr2D 573908388 573908934 546 True 894.000000 894 96.1680 1 547 1 chr2D.!!$R4 546
12 TraesCS3A01G220000 chr2D 538955075 538955623 548 True 891.000000 891 95.9930 1 547 1 chr2D.!!$R3 546
13 TraesCS3A01G220000 chr1D 59533347 59533893 546 False 894.000000 894 96.1680 1 547 1 chr1D.!!$F1 546
14 TraesCS3A01G220000 chr4D 487284284 487285060 776 True 592.500000 889 92.1455 1 830 2 chr4D.!!$R2 829
15 TraesCS3A01G220000 chr2A 475794880 475795605 725 False 560.000000 560 81.4560 4151 4840 1 chr2A.!!$F2 689
16 TraesCS3A01G220000 chr4B 34781476 34782025 549 True 534.000000 534 85.0910 4320 4840 1 chr4B.!!$R1 520
17 TraesCS3A01G220000 chr4B 299744810 299745355 545 False 324.000000 446 88.5535 4320 4835 2 chr4B.!!$F1 515

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
98 100 0.398098 ATACCCAACCCGTCGGAGAT 60.398 55.000 14.39 0.0 40.67 2.75 F
1036 1048 1.065854 CATTCTCCGGCAGTCTCCTTT 60.066 52.381 0.00 0.0 0.00 3.11 F
1457 1469 2.136196 TTTTGGTGCCGATTGCGTCC 62.136 55.000 0.00 0.0 45.60 4.79 F
3106 3329 1.332889 ACAGGCGAGCATCCTCATCA 61.333 55.000 0.00 0.0 38.00 3.07 F
3908 4135 0.530431 ACCGGTTGTTACGTGTGGAC 60.530 55.000 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 1815 1.621814 GCCCAGACGGTATAATAGGCA 59.378 52.381 0.0 0.0 39.01 4.75 R
2456 2498 1.993370 GAGGGACGAATCAACTTCACG 59.007 52.381 0.0 0.0 33.10 4.35 R
3282 3505 0.610232 AGTCTTGCAGCCCAATGACC 60.610 55.000 0.0 0.0 34.73 4.02 R
4130 4357 0.172578 CATCAGCCACCTGTGCAATG 59.827 55.000 0.0 0.0 40.09 2.82 R
5861 7104 0.322816 TTCCTCTGCCATCTTGGTGC 60.323 55.000 0.0 0.0 40.46 5.01 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
38 39 4.895668 ACGACAAAGGGTACTATTTGGA 57.104 40.909 20.12 0.00 38.57 3.53
98 100 0.398098 ATACCCAACCCGTCGGAGAT 60.398 55.000 14.39 0.00 40.67 2.75
318 320 4.756642 ACGATCAATGCTTTCAGTTTCAGA 59.243 37.500 0.00 0.00 0.00 3.27
384 386 4.883585 AGCAGTTCACTCAGTTTCATGAAA 59.116 37.500 16.91 16.91 33.09 2.69
443 445 6.682423 AATGATTTCGTTGAGCATATGTGA 57.318 33.333 4.29 0.00 0.00 3.58
581 585 8.834749 ACTATGAAGACAGTAGAAAAAGTTCC 57.165 34.615 0.00 0.00 33.92 3.62
582 586 8.652290 ACTATGAAGACAGTAGAAAAAGTTCCT 58.348 33.333 0.00 0.00 33.92 3.36
585 589 8.658499 TGAAGACAGTAGAAAAAGTTCCTAAC 57.342 34.615 0.00 0.00 33.92 2.34
586 590 8.483758 TGAAGACAGTAGAAAAAGTTCCTAACT 58.516 33.333 0.00 0.00 45.46 2.24
587 591 9.978044 GAAGACAGTAGAAAAAGTTCCTAACTA 57.022 33.333 0.00 0.00 41.91 2.24
675 680 8.789825 AATGCAAATCAATGTAAAATTAGGCA 57.210 26.923 0.00 0.00 31.63 4.75
703 708 1.411246 GGCCACGTCTGTACATATGGA 59.589 52.381 15.37 0.00 0.00 3.41
715 720 1.066454 ACATATGGATCGACGCGTTGA 59.934 47.619 30.13 30.13 0.00 3.18
740 745 2.349817 CGCTGCCGATCCATATGAAAAC 60.350 50.000 3.65 0.00 36.29 2.43
741 746 2.618241 GCTGCCGATCCATATGAAAACA 59.382 45.455 3.65 0.00 0.00 2.83
742 747 3.304257 GCTGCCGATCCATATGAAAACAG 60.304 47.826 3.65 5.34 0.00 3.16
744 749 3.214328 GCCGATCCATATGAAAACAGGT 58.786 45.455 3.65 0.00 0.00 4.00
750 756 3.262151 TCCATATGAAAACAGGTCGGACA 59.738 43.478 10.76 0.00 0.00 4.02
785 791 1.135333 GACCCAAACGGACAAAAAGCA 59.865 47.619 0.00 0.00 34.64 3.91
786 792 1.550976 ACCCAAACGGACAAAAAGCAA 59.449 42.857 0.00 0.00 34.64 3.91
788 794 3.202097 CCCAAACGGACAAAAAGCAAAT 58.798 40.909 0.00 0.00 0.00 2.32
792 798 5.491973 CAAACGGACAAAAAGCAAATGAAG 58.508 37.500 0.00 0.00 0.00 3.02
796 802 4.359706 GGACAAAAAGCAAATGAAGTCGT 58.640 39.130 0.00 0.00 0.00 4.34
798 804 4.992688 ACAAAAAGCAAATGAAGTCGTCA 58.007 34.783 0.00 0.00 41.67 4.35
807 813 2.519377 TGAAGTCGTCATCCGTTTGT 57.481 45.000 0.00 0.00 37.94 2.83
808 814 3.646611 TGAAGTCGTCATCCGTTTGTA 57.353 42.857 0.00 0.00 37.94 2.41
813 819 1.473677 TCGTCATCCGTTTGTATCGGT 59.526 47.619 4.36 0.00 46.86 4.69
821 827 1.081094 GTTTGTATCGGTCCGTTGGG 58.919 55.000 11.88 0.00 0.00 4.12
833 839 2.093341 GTCCGTTGGGGTTGCTCTAATA 60.093 50.000 0.00 0.00 37.00 0.98
834 840 2.572556 TCCGTTGGGGTTGCTCTAATAA 59.427 45.455 0.00 0.00 37.00 1.40
835 841 2.943033 CCGTTGGGGTTGCTCTAATAAG 59.057 50.000 0.00 0.00 0.00 1.73
836 842 3.370103 CCGTTGGGGTTGCTCTAATAAGA 60.370 47.826 0.00 0.00 0.00 2.10
837 843 7.367741 TCCGTTGGGGTTGCTCTAATAAGAG 62.368 48.000 0.00 0.00 43.73 2.85
853 859 9.806448 TCTAATAAGAGCAGTAGAGATTGATCT 57.194 33.333 0.00 0.00 39.49 2.75
856 862 8.710749 ATAAGAGCAGTAGAGATTGATCTTCT 57.289 34.615 8.09 0.00 42.40 2.85
857 863 6.639632 AGAGCAGTAGAGATTGATCTTCTC 57.360 41.667 14.75 14.75 34.71 2.87
858 864 5.239306 AGAGCAGTAGAGATTGATCTTCTCG 59.761 44.000 15.91 7.23 43.55 4.04
859 865 3.980775 GCAGTAGAGATTGATCTTCTCGC 59.019 47.826 15.91 13.65 43.55 5.03
860 866 4.498850 GCAGTAGAGATTGATCTTCTCGCA 60.499 45.833 15.91 8.86 43.55 5.10
861 867 5.214417 CAGTAGAGATTGATCTTCTCGCAG 58.786 45.833 15.91 9.43 43.55 5.18
862 868 3.731652 AGAGATTGATCTTCTCGCAGG 57.268 47.619 15.91 0.00 43.55 4.85
863 869 3.030291 AGAGATTGATCTTCTCGCAGGT 58.970 45.455 15.91 1.81 43.55 4.00
864 870 3.450457 AGAGATTGATCTTCTCGCAGGTT 59.550 43.478 15.91 1.28 43.55 3.50
865 871 4.646945 AGAGATTGATCTTCTCGCAGGTTA 59.353 41.667 15.91 0.00 43.55 2.85
866 872 4.942852 AGATTGATCTTCTCGCAGGTTAG 58.057 43.478 0.00 0.00 31.97 2.34
867 873 4.646945 AGATTGATCTTCTCGCAGGTTAGA 59.353 41.667 0.00 0.00 31.97 2.10
871 877 5.352284 TGATCTTCTCGCAGGTTAGATTTC 58.648 41.667 0.00 0.00 0.00 2.17
886 892 3.131396 AGATTTCCGTTGTGAGTCACAC 58.869 45.455 25.43 18.03 44.47 3.82
1036 1048 1.065854 CATTCTCCGGCAGTCTCCTTT 60.066 52.381 0.00 0.00 0.00 3.11
1070 1082 4.579384 AACACCACAGCCCCCGTG 62.579 66.667 0.00 0.00 0.00 4.94
1448 1460 2.912025 ACCCTGCTTTTGGTGCCG 60.912 61.111 0.00 0.00 32.36 5.69
1457 1469 2.136196 TTTTGGTGCCGATTGCGTCC 62.136 55.000 0.00 0.00 45.60 4.79
1603 1615 6.037500 GCATTTTCTCTGCCTTTTCTTTGTTT 59.962 34.615 0.00 0.00 33.44 2.83
1662 1674 5.448360 GGAACTAGAATCAAGTGCAATGCTC 60.448 44.000 6.82 2.32 0.00 4.26
1801 1815 8.950007 TCTTGGTTAAGGGAATTAGTCAAAAT 57.050 30.769 0.00 0.00 34.59 1.82
2081 2115 6.100004 AGGTAAGATAACAGTCAACATCACG 58.900 40.000 0.00 0.00 0.00 4.35
2199 2234 7.094248 TGCGTAGTACTCATACAGTTCCTAAAA 60.094 37.037 0.00 0.00 36.43 1.52
2207 2242 8.643324 ACTCATACAGTTCCTAAAAGCTATAGG 58.357 37.037 16.09 16.09 41.14 2.57
2247 2282 8.854237 ATATTTACTAATTGGGGGCTCTTTTT 57.146 30.769 0.00 0.00 0.00 1.94
2382 2417 7.359264 CGTCTTACATTTTGAGACAGTACAAGG 60.359 40.741 0.00 0.00 39.74 3.61
2456 2498 9.309274 GCTACTTGCACATGATACATGGTACAC 62.309 44.444 14.70 2.22 41.70 2.90
2597 2641 6.156519 TGTCATGATATTGTGCGTACCTATC 58.843 40.000 0.00 13.07 0.00 2.08
2818 2958 5.366186 GGACAGGATCTATGATGGATGCTAT 59.634 44.000 12.10 1.44 39.28 2.97
2854 2994 5.710513 CCACCCATTGATTGTGGTATATG 57.289 43.478 10.19 0.00 43.62 1.78
2872 3012 7.238723 TGGTATATGCTGGAATAATGTAAGGGA 59.761 37.037 0.00 0.00 0.00 4.20
3106 3329 1.332889 ACAGGCGAGCATCCTCATCA 61.333 55.000 0.00 0.00 38.00 3.07
3678 3902 9.515020 ACAAATTCTGTAAATTGTTGTACTGTG 57.485 29.630 0.00 0.00 35.63 3.66
3782 4006 5.237779 ACCGTGGTAATTCAAAACTACAGTG 59.762 40.000 0.00 0.00 0.00 3.66
3791 4015 6.767524 TTCAAAACTACAGTGTTCCAATGT 57.232 33.333 0.00 2.76 44.74 2.71
3883 4110 2.823154 GGCTGGTGCTGTTTTACCATAA 59.177 45.455 0.00 0.00 45.28 1.90
3908 4135 0.530431 ACCGGTTGTTACGTGTGGAC 60.530 55.000 0.00 0.00 0.00 4.02
3967 4194 1.474077 ACGACCGGACTAATTAGCGTT 59.526 47.619 9.46 0.00 0.00 4.84
4035 4262 1.678627 CGTCTGCACCTAGATGCTAGT 59.321 52.381 11.24 0.00 46.28 2.57
4040 4267 5.242838 GTCTGCACCTAGATGCTAGTATCTT 59.757 44.000 25.66 8.02 46.28 2.40
4126 4353 4.721776 TCACCTAATCTAGCACCTGGATTT 59.278 41.667 0.00 0.00 38.24 2.17
4127 4354 4.818546 CACCTAATCTAGCACCTGGATTTG 59.181 45.833 0.00 7.26 38.24 2.32
4128 4355 3.817647 CCTAATCTAGCACCTGGATTTGC 59.182 47.826 0.00 0.00 38.24 3.68
4129 4356 1.959042 ATCTAGCACCTGGATTTGCG 58.041 50.000 0.00 0.00 43.87 4.85
4130 4357 0.744414 TCTAGCACCTGGATTTGCGC 60.744 55.000 0.00 0.00 43.87 6.09
4132 4359 0.394216 TAGCACCTGGATTTGCGCAT 60.394 50.000 12.75 0.00 43.87 4.73
4133 4360 1.216178 GCACCTGGATTTGCGCATT 59.784 52.632 12.75 0.75 0.00 3.56
4134 4361 1.079875 GCACCTGGATTTGCGCATTG 61.080 55.000 12.75 0.00 0.00 2.82
4135 4362 1.079875 CACCTGGATTTGCGCATTGC 61.080 55.000 12.75 8.30 46.70 3.56
4173 4400 2.271944 AGGCTTCAACTAACACACCC 57.728 50.000 0.00 0.00 0.00 4.61
4211 4438 0.244450 ATGAACACGCCATTGCAAGG 59.756 50.000 4.94 4.26 37.32 3.61
4219 4446 3.085533 ACGCCATTGCAAGGTATGTTAA 58.914 40.909 10.60 0.00 37.32 2.01
4227 4454 5.794687 TGCAAGGTATGTTAATCTTCACG 57.205 39.130 0.00 0.00 0.00 4.35
4359 4596 0.673644 ACATCTTAGCAGGCGCGTTT 60.674 50.000 8.43 0.00 45.49 3.60
4371 4608 3.477090 CAGGCGCGTTTTATTGTAAATCG 59.523 43.478 8.43 7.98 0.00 3.34
4519 4786 5.183228 GGGAGACCGAATTGAGATGTAAAA 58.817 41.667 0.00 0.00 43.64 1.52
4759 5586 9.166173 CACTCATGATATTTTCTGGAAGTGTAA 57.834 33.333 0.00 0.00 33.76 2.41
4919 5749 7.954248 GCATCATAATCGACAATAGCTAACTTG 59.046 37.037 0.00 1.05 0.00 3.16
4954 5784 4.753233 CTTGCCTAGGATATCTGATTCCG 58.247 47.826 14.75 0.00 37.10 4.30
5014 5844 4.968812 TTGCATCTTGATGTACCACATG 57.031 40.909 11.61 0.00 39.27 3.21
5246 6076 4.524714 TGTTGTCTTGGAACAGTGGAAAAA 59.475 37.500 0.00 0.00 42.39 1.94
5291 6123 4.530946 AGAGGGAACTGGAAATTCTCGTAA 59.469 41.667 0.00 0.00 44.43 3.18
5330 6162 2.436417 TGTTATGCACAGAGAAAGGGC 58.564 47.619 0.00 0.00 0.00 5.19
5360 6192 1.529309 GAGACCATGAAGCCTCCCC 59.471 63.158 0.00 0.00 0.00 4.81
5458 6293 2.827921 GAGTTCATTGGAATTGGCCTGT 59.172 45.455 3.32 0.00 35.05 4.00
5484 6319 5.394224 TTGTCATCTCGTGTTGTATGGTA 57.606 39.130 0.00 0.00 0.00 3.25
5492 6327 2.572290 GTGTTGTATGGTATGGGGAGC 58.428 52.381 0.00 0.00 0.00 4.70
5654 6489 1.742761 TTCTGCTGCAGTTATGGCTC 58.257 50.000 27.24 0.00 32.61 4.70
5777 7015 1.300620 AAAGCGCGTGCAGTCAGTA 60.301 52.632 24.79 0.00 46.23 2.74
5839 7082 4.550255 CGCGCTACTTAAAAATAGACTGGC 60.550 45.833 5.56 0.00 0.00 4.85
5861 7104 4.213482 GCGGGCATTTAGGAAATACTGTAG 59.787 45.833 0.00 0.00 0.00 2.74
5862 7105 4.213482 CGGGCATTTAGGAAATACTGTAGC 59.787 45.833 0.00 0.00 0.00 3.58
5915 8989 4.637977 TGCCTACGAAAATACAATGATGCA 59.362 37.500 0.00 0.00 0.00 3.96
5933 9007 6.100668 TGATGCACATTGTTCCATGTAAATG 58.899 36.000 0.00 0.00 36.35 2.32
5966 9040 6.879458 GGACTTTTAGCAAATAGTCAAGAGGA 59.121 38.462 9.77 0.00 38.96 3.71
6080 9154 7.760131 AATAGCAATCAAATCCAAACGATTG 57.240 32.000 0.00 0.00 44.82 2.67
6093 9167 7.876896 TCCAAACGATTGTAAAATTTTAGGC 57.123 32.000 10.92 1.67 34.60 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 5.827756 TCCACTGAGGATATATACCGTCAT 58.172 41.667 0.00 0.00 43.07 3.06
98 100 6.739331 TCTTGGGCAAATCTTTTCCTTTTA 57.261 33.333 0.00 0.00 0.00 1.52
291 293 6.149308 TGAAACTGAAAGCATTGATCGTACAT 59.851 34.615 0.00 0.00 37.60 2.29
303 305 4.406648 TCTCACTCTGAAACTGAAAGCA 57.593 40.909 0.00 0.00 37.60 3.91
318 320 2.775890 CTCAGGCACAACATTCTCACT 58.224 47.619 0.00 0.00 0.00 3.41
384 386 2.228822 GAGTTTCCCAATCACGCATGTT 59.771 45.455 0.00 0.00 0.00 2.71
428 430 4.330894 ACATGAGTTCACATATGCTCAACG 59.669 41.667 12.80 10.25 40.71 4.10
443 445 4.406456 TCTATTGGTTGCCAACATGAGTT 58.594 39.130 10.18 0.00 46.95 3.01
555 559 9.274206 GGAACTTTTTCTACTGTCTTCATAGTT 57.726 33.333 0.00 0.00 31.71 2.24
556 560 8.652290 AGGAACTTTTTCTACTGTCTTCATAGT 58.348 33.333 0.00 0.00 27.25 2.12
559 563 9.274206 GTTAGGAACTTTTTCTACTGTCTTCAT 57.726 33.333 0.00 0.00 41.75 2.57
560 564 8.483758 AGTTAGGAACTTTTTCTACTGTCTTCA 58.516 33.333 0.00 0.00 39.04 3.02
561 565 8.890124 AGTTAGGAACTTTTTCTACTGTCTTC 57.110 34.615 0.00 0.00 39.04 2.87
578 582 9.715121 CGCCCAAATAAATAGTATAGTTAGGAA 57.285 33.333 0.00 0.00 34.37 3.36
579 583 8.316214 CCGCCCAAATAAATAGTATAGTTAGGA 58.684 37.037 0.00 0.00 34.37 2.94
580 584 7.065443 GCCGCCCAAATAAATAGTATAGTTAGG 59.935 40.741 0.00 0.00 34.37 2.69
581 585 7.822822 AGCCGCCCAAATAAATAGTATAGTTAG 59.177 37.037 0.00 0.00 34.37 2.34
582 586 7.682628 AGCCGCCCAAATAAATAGTATAGTTA 58.317 34.615 0.00 0.00 35.44 2.24
583 587 6.540083 AGCCGCCCAAATAAATAGTATAGTT 58.460 36.000 0.00 0.00 31.73 2.24
584 588 6.123045 AGCCGCCCAAATAAATAGTATAGT 57.877 37.500 0.00 0.00 0.00 2.12
585 589 8.448615 GTTTAGCCGCCCAAATAAATAGTATAG 58.551 37.037 0.00 0.00 0.00 1.31
586 590 8.158789 AGTTTAGCCGCCCAAATAAATAGTATA 58.841 33.333 0.00 0.00 0.00 1.47
587 591 7.002276 AGTTTAGCCGCCCAAATAAATAGTAT 58.998 34.615 0.00 0.00 0.00 2.12
588 592 6.358991 AGTTTAGCCGCCCAAATAAATAGTA 58.641 36.000 0.00 0.00 0.00 1.82
589 593 5.198207 AGTTTAGCCGCCCAAATAAATAGT 58.802 37.500 0.00 0.00 0.00 2.12
590 594 5.767816 AGTTTAGCCGCCCAAATAAATAG 57.232 39.130 0.00 0.00 0.00 1.73
591 595 7.826918 AATAGTTTAGCCGCCCAAATAAATA 57.173 32.000 0.00 0.00 0.00 1.40
592 596 6.724893 AATAGTTTAGCCGCCCAAATAAAT 57.275 33.333 0.00 0.00 0.00 1.40
593 597 6.532988 AAATAGTTTAGCCGCCCAAATAAA 57.467 33.333 0.00 0.00 0.00 1.40
594 598 6.334202 CAAAATAGTTTAGCCGCCCAAATAA 58.666 36.000 0.00 0.00 0.00 1.40
595 599 5.680151 GCAAAATAGTTTAGCCGCCCAAATA 60.680 40.000 0.00 0.00 0.00 1.40
596 600 4.754322 CAAAATAGTTTAGCCGCCCAAAT 58.246 39.130 0.00 0.00 0.00 2.32
597 601 3.615351 GCAAAATAGTTTAGCCGCCCAAA 60.615 43.478 0.00 0.00 0.00 3.28
598 602 2.094442 GCAAAATAGTTTAGCCGCCCAA 60.094 45.455 0.00 0.00 0.00 4.12
599 603 1.474879 GCAAAATAGTTTAGCCGCCCA 59.525 47.619 0.00 0.00 0.00 5.36
649 654 9.881649 TGCCTAATTTTACATTGATTTGCATTA 57.118 25.926 0.00 0.00 0.00 1.90
690 695 2.095919 CGCGTCGATCCATATGTACAGA 60.096 50.000 0.33 0.00 0.00 3.41
694 699 2.291190 TCAACGCGTCGATCCATATGTA 59.709 45.455 14.44 0.00 0.00 2.29
728 733 3.262151 TGTCCGACCTGTTTTCATATGGA 59.738 43.478 2.13 0.00 0.00 3.41
755 761 1.152756 GTTTGGGTCAGCCACCTGT 60.153 57.895 0.00 0.00 45.95 4.00
757 763 2.113139 CGTTTGGGTCAGCCACCT 59.887 61.111 0.00 0.00 45.95 4.00
760 766 2.112297 GTCCGTTTGGGTCAGCCA 59.888 61.111 0.00 0.00 37.00 4.75
764 770 1.135333 GCTTTTTGTCCGTTTGGGTCA 59.865 47.619 0.00 0.00 37.00 4.02
785 791 3.813166 ACAAACGGATGACGACTTCATTT 59.187 39.130 0.00 0.00 45.67 2.32
786 792 3.399330 ACAAACGGATGACGACTTCATT 58.601 40.909 0.00 0.00 45.67 2.57
807 813 1.597989 CAACCCCAACGGACCGATA 59.402 57.895 23.38 0.00 34.64 2.92
808 814 2.349755 CAACCCCAACGGACCGAT 59.650 61.111 23.38 5.64 34.64 4.18
813 819 0.988832 ATTAGAGCAACCCCAACGGA 59.011 50.000 0.00 0.00 34.64 4.69
833 839 6.238731 CGAGAAGATCAATCTCTACTGCTCTT 60.239 42.308 20.03 0.00 40.93 2.85
834 840 5.239306 CGAGAAGATCAATCTCTACTGCTCT 59.761 44.000 20.03 0.00 40.93 4.09
835 841 5.451908 CGAGAAGATCAATCTCTACTGCTC 58.548 45.833 20.03 0.00 40.93 4.26
836 842 4.261572 GCGAGAAGATCAATCTCTACTGCT 60.262 45.833 20.03 0.00 40.93 4.24
837 843 3.980775 GCGAGAAGATCAATCTCTACTGC 59.019 47.826 20.03 14.37 40.93 4.40
838 844 5.180367 TGCGAGAAGATCAATCTCTACTG 57.820 43.478 20.03 10.11 40.93 2.74
839 845 4.278170 CCTGCGAGAAGATCAATCTCTACT 59.722 45.833 20.03 0.00 40.93 2.57
840 846 4.037446 ACCTGCGAGAAGATCAATCTCTAC 59.963 45.833 20.03 14.56 40.93 2.59
841 847 4.211125 ACCTGCGAGAAGATCAATCTCTA 58.789 43.478 20.03 11.69 40.93 2.43
842 848 3.030291 ACCTGCGAGAAGATCAATCTCT 58.970 45.455 20.03 6.65 40.93 3.10
843 849 3.451141 ACCTGCGAGAAGATCAATCTC 57.549 47.619 15.14 15.14 39.94 2.75
844 850 3.902881 AACCTGCGAGAAGATCAATCT 57.097 42.857 0.00 0.00 39.22 2.40
845 851 4.938080 TCTAACCTGCGAGAAGATCAATC 58.062 43.478 0.00 0.00 0.00 2.67
846 852 5.543507 ATCTAACCTGCGAGAAGATCAAT 57.456 39.130 0.00 0.00 0.00 2.57
847 853 5.344743 AATCTAACCTGCGAGAAGATCAA 57.655 39.130 0.00 0.00 0.00 2.57
848 854 5.344743 AAATCTAACCTGCGAGAAGATCA 57.655 39.130 0.00 0.00 0.00 2.92
849 855 4.747605 GGAAATCTAACCTGCGAGAAGATC 59.252 45.833 0.00 0.00 0.00 2.75
850 856 4.698575 GGAAATCTAACCTGCGAGAAGAT 58.301 43.478 0.00 0.00 0.00 2.40
851 857 3.428999 CGGAAATCTAACCTGCGAGAAGA 60.429 47.826 0.00 0.00 0.00 2.87
852 858 2.860735 CGGAAATCTAACCTGCGAGAAG 59.139 50.000 0.00 0.00 0.00 2.85
853 859 2.232941 ACGGAAATCTAACCTGCGAGAA 59.767 45.455 0.00 0.00 0.00 2.87
854 860 1.822990 ACGGAAATCTAACCTGCGAGA 59.177 47.619 0.00 0.00 0.00 4.04
855 861 2.295253 ACGGAAATCTAACCTGCGAG 57.705 50.000 0.00 0.00 0.00 5.03
856 862 2.289195 ACAACGGAAATCTAACCTGCGA 60.289 45.455 0.00 0.00 0.00 5.10
857 863 2.073816 ACAACGGAAATCTAACCTGCG 58.926 47.619 0.00 0.00 0.00 5.18
858 864 3.071479 TCACAACGGAAATCTAACCTGC 58.929 45.455 0.00 0.00 0.00 4.85
859 865 4.315803 ACTCACAACGGAAATCTAACCTG 58.684 43.478 0.00 0.00 0.00 4.00
860 866 4.039973 TGACTCACAACGGAAATCTAACCT 59.960 41.667 0.00 0.00 0.00 3.50
861 867 4.151867 GTGACTCACAACGGAAATCTAACC 59.848 45.833 4.17 0.00 34.08 2.85
862 868 4.748102 TGTGACTCACAACGGAAATCTAAC 59.252 41.667 9.54 0.00 41.69 2.34
863 869 4.748102 GTGTGACTCACAACGGAAATCTAA 59.252 41.667 13.57 0.00 46.28 2.10
864 870 4.304110 GTGTGACTCACAACGGAAATCTA 58.696 43.478 13.57 0.00 46.28 1.98
865 871 3.131396 GTGTGACTCACAACGGAAATCT 58.869 45.455 13.57 0.00 46.28 2.40
866 872 3.521524 GTGTGACTCACAACGGAAATC 57.478 47.619 13.57 0.00 46.28 2.17
886 892 1.336440 CTCCTACCAGATCTGCGAGTG 59.664 57.143 17.76 5.80 0.00 3.51
891 897 2.035321 GCACTACTCCTACCAGATCTGC 59.965 54.545 17.76 0.00 0.00 4.26
1200 1212 4.344865 TCCTCCGCCCCTTGTTGC 62.345 66.667 0.00 0.00 0.00 4.17
1457 1469 2.417516 CCTGGTATCGACCCTGCG 59.582 66.667 4.72 0.00 46.32 5.18
1505 1517 1.987855 CCTCGGGACACCCAGCTTA 60.988 63.158 7.62 0.00 45.83 3.09
1603 1615 6.934645 ACGGTCAAGTTTGAAGATTTCATAGA 59.065 34.615 0.00 0.00 39.84 1.98
1637 1649 4.397417 GCATTGCACTTGATTCTAGTTCCT 59.603 41.667 3.15 0.00 0.00 3.36
1801 1815 1.621814 GCCCAGACGGTATAATAGGCA 59.378 52.381 0.00 0.00 39.01 4.75
1959 1992 2.237643 TGCTAGTACACGTGGTGGTAA 58.762 47.619 21.57 0.00 37.94 2.85
2081 2115 6.428159 CCTGTATATCCACATAAGGTGCTTTC 59.572 42.308 0.00 0.00 46.50 2.62
2218 2253 6.274672 AGAGCCCCCAATTAGTAAATATAGCA 59.725 38.462 0.00 0.00 0.00 3.49
2247 2282 3.011369 TCCTCTAGAGAAGTGGTGGCTTA 59.989 47.826 21.76 0.00 39.48 3.09
2253 2288 9.716556 TCTAATAAATTCCTCTAGAGAAGTGGT 57.283 33.333 21.76 4.42 39.48 4.16
2431 2473 6.018751 GTGTACCATGTATCATGTGCAAGTAG 60.019 42.308 8.57 0.00 0.00 2.57
2456 2498 1.993370 GAGGGACGAATCAACTTCACG 59.007 52.381 0.00 0.00 33.10 4.35
2458 2500 2.363788 CGAGGGACGAATCAACTTCA 57.636 50.000 0.00 0.00 45.77 3.02
2583 2627 4.260139 TCAACTTGATAGGTACGCACAA 57.740 40.909 0.00 0.00 0.00 3.33
2597 2641 6.563422 TCTTTTTGACAGATGGTTCAACTTG 58.437 36.000 0.00 0.00 0.00 3.16
2751 2891 7.230712 GGAAATTTCACCCTCTTTTCAGAAGTA 59.769 37.037 19.49 0.00 0.00 2.24
2752 2892 6.040955 GGAAATTTCACCCTCTTTTCAGAAGT 59.959 38.462 19.49 0.00 0.00 3.01
2795 2935 4.822685 AGCATCCATCATAGATCCTGTC 57.177 45.455 0.00 0.00 0.00 3.51
2854 2994 6.930731 TGTTTTTCCCTTACATTATTCCAGC 58.069 36.000 0.00 0.00 0.00 4.85
2872 3012 7.825270 AGTTTCGGGGAAGTTTTATTTGTTTTT 59.175 29.630 0.00 0.00 0.00 1.94
2906 3046 3.643199 TGGAATGGCTATGCTACACAA 57.357 42.857 0.00 0.00 0.00 3.33
3087 3310 1.332889 TGATGAGGATGCTCGCCTGT 61.333 55.000 9.88 0.00 35.44 4.00
3106 3329 7.275341 CACGGCACATGTATTATGTTCAAAATT 59.725 33.333 0.00 0.00 0.00 1.82
3282 3505 0.610232 AGTCTTGCAGCCCAATGACC 60.610 55.000 0.00 0.00 34.73 4.02
3427 3650 3.748645 ATGGAGAGAGACTACCACTGT 57.251 47.619 0.00 0.00 35.19 3.55
3701 3925 1.595311 TCAGCCCCATGTAACTGGAT 58.405 50.000 6.34 0.00 38.69 3.41
3712 3936 2.072487 GCCCTAGTCATCAGCCCCA 61.072 63.158 0.00 0.00 0.00 4.96
3782 4006 1.080569 CTTGCCCGCACATTGGAAC 60.081 57.895 0.00 0.00 0.00 3.62
3791 4015 0.906066 TGTAGTATTCCTTGCCCGCA 59.094 50.000 0.00 0.00 0.00 5.69
3883 4110 2.944349 ACACGTAACAACCGGTCAAAAT 59.056 40.909 8.04 0.00 0.00 1.82
3908 4135 2.069273 CTGAGTTAGGTTCAGTTGCCG 58.931 52.381 0.00 0.00 37.79 5.69
4035 4262 5.643777 GTGAAAACTCAGGCTGCTAAAGATA 59.356 40.000 10.34 0.00 0.00 1.98
4040 4267 3.492102 AGTGAAAACTCAGGCTGCTAA 57.508 42.857 10.34 0.00 0.00 3.09
4128 4355 3.367743 AGCCACCTGTGCAATGCG 61.368 61.111 0.00 0.00 0.00 4.73
4129 4356 1.601419 ATCAGCCACCTGTGCAATGC 61.601 55.000 0.00 0.00 40.09 3.56
4130 4357 0.172578 CATCAGCCACCTGTGCAATG 59.827 55.000 0.00 0.00 40.09 2.82
4132 4359 0.467844 AACATCAGCCACCTGTGCAA 60.468 50.000 0.00 0.00 40.09 4.08
4133 4360 0.467844 AAACATCAGCCACCTGTGCA 60.468 50.000 0.00 0.00 40.09 4.57
4134 4361 1.533625 TAAACATCAGCCACCTGTGC 58.466 50.000 0.00 0.00 40.09 4.57
4135 4362 2.489329 CCTTAAACATCAGCCACCTGTG 59.511 50.000 0.00 0.00 40.09 3.66
4136 4363 2.795329 CCTTAAACATCAGCCACCTGT 58.205 47.619 0.00 0.00 40.09 4.00
4173 4400 9.229784 GTGTTCATTTGAAGCAGAATACATATG 57.770 33.333 0.00 0.00 33.86 1.78
4309 4538 9.851686 ATCACATATCAGGCATAAAGTTTTAGA 57.148 29.630 0.00 0.00 0.00 2.10
4892 5722 6.309009 AGTTAGCTATTGTCGATTATGATGCG 59.691 38.462 0.00 0.00 0.00 4.73
4919 5749 1.224870 GGCAAGCCCTCTAACTCCC 59.775 63.158 0.00 0.00 0.00 4.30
4954 5784 6.174049 AGTAACTCCACTGAATTAAAGCCTC 58.826 40.000 0.00 0.00 0.00 4.70
5014 5844 7.133133 TCTAAAAGGGGGAGTATAACATGTC 57.867 40.000 0.00 0.00 0.00 3.06
5062 5892 6.588756 GTGATCTCACCACTACAAATAACGAA 59.411 38.462 0.00 0.00 40.85 3.85
5261 6091 3.787001 CAGTTCCCTCTCCCGGCC 61.787 72.222 0.00 0.00 0.00 6.13
5317 6149 3.445096 CCTATTTTGGCCCTTTCTCTGTG 59.555 47.826 0.00 0.00 0.00 3.66
5330 6162 2.513738 TCATGGTCTCCCCCTATTTTGG 59.486 50.000 0.00 0.00 0.00 3.28
5360 6192 3.701604 GACGGGCAGCAGGACTACG 62.702 68.421 0.00 0.00 0.00 3.51
5458 6293 5.810074 CCATACAACACGAGATGACAATGTA 59.190 40.000 0.00 0.00 0.00 2.29
5484 6319 1.064166 CAACATCCTCAAGCTCCCCAT 60.064 52.381 0.00 0.00 0.00 4.00
5492 6327 1.742761 ATGCGGTCAACATCCTCAAG 58.257 50.000 0.00 0.00 0.00 3.02
5654 6489 1.528309 ACAAAGGCAAGACCACCCG 60.528 57.895 0.00 0.00 43.14 5.28
5777 7015 1.374190 CAGCACACCTTCAGCTCCT 59.626 57.895 0.00 0.00 36.26 3.69
5839 7082 4.213482 GCTACAGTATTTCCTAAATGCCCG 59.787 45.833 0.00 0.00 34.50 6.13
5861 7104 0.322816 TTCCTCTGCCATCTTGGTGC 60.323 55.000 0.00 0.00 40.46 5.01
5862 7105 1.004044 ACTTCCTCTGCCATCTTGGTG 59.996 52.381 0.00 0.00 40.46 4.17
5933 9007 4.911514 TTTGCTAAAAGTCCACAAGTCC 57.088 40.909 0.00 0.00 0.00 3.85
5966 9040 5.417580 ACCATTGTATTTTCGTAGGCATTGT 59.582 36.000 0.00 0.00 0.00 2.71
6076 9150 9.435688 AGTTTGATGGCCTAAAATTTTACAATC 57.564 29.630 3.32 7.54 0.00 2.67
6093 9167 9.003658 AGTAGAACAGTCAATTAAGTTTGATGG 57.996 33.333 0.00 0.00 37.88 3.51


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

AutoCloner maintained by Alex Coulton.