Multiple sequence alignment - TraesCS5D01G322200

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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 TraesCS5D01G322200 chr5D 100.000 3558 0 0 1 3558 414015467 414011910 0.000000e+00 6571.0
1 TraesCS5D01G322200 chr5D 100.000 529 0 0 3827 4355 414011641 414011113 0.000000e+00 977.0
2 TraesCS5D01G322200 chr5A 95.324 2823 104 11 741 3537 526526155 526523335 0.000000e+00 4457.0
3 TraesCS5D01G322200 chr6B 90.749 2335 208 5 1032 3362 643185778 643188108 0.000000e+00 3109.0
4 TraesCS5D01G322200 chr6B 81.798 2280 365 41 1101 3355 642894249 642891995 0.000000e+00 1866.0
5 TraesCS5D01G322200 chr6B 81.714 2275 374 34 1111 3363 642909207 642906953 0.000000e+00 1858.0
6 TraesCS5D01G322200 chr6B 80.627 2266 397 37 1111 3355 643639426 643641670 0.000000e+00 1714.0
7 TraesCS5D01G322200 chr6A 82.503 2269 349 39 1111 3355 571700794 571698550 0.000000e+00 1947.0
8 TraesCS5D01G322200 chr6A 81.424 2261 362 39 1111 3355 571791503 571789285 0.000000e+00 1796.0
9 TraesCS5D01G322200 chr6A 81.250 2272 380 36 1102 3347 17956202 17958453 0.000000e+00 1794.0
10 TraesCS5D01G322200 chr6A 80.610 2264 401 30 1111 3355 572336170 572338414 0.000000e+00 1714.0
11 TraesCS5D01G322200 chr6D 81.818 2266 370 33 1111 3355 427072386 427070142 0.000000e+00 1864.0
12 TraesCS5D01G322200 chr6D 89.019 1448 148 8 1918 3362 427266873 427268312 0.000000e+00 1783.0
13 TraesCS5D01G322200 chr6D 80.467 2268 394 38 1111 3355 427713124 427710883 0.000000e+00 1688.0
14 TraesCS5D01G322200 chr1D 96.264 696 26 0 1 696 7758856 7758161 0.000000e+00 1142.0
15 TraesCS5D01G322200 chr4D 95.402 696 26 3 1 696 349001917 349001228 0.000000e+00 1103.0
16 TraesCS5D01G322200 chr4D 77.427 412 69 16 3898 4286 468477846 468478256 1.580000e-54 224.0
17 TraesCS5D01G322200 chr3D 93.966 696 40 2 1 696 30696804 30697497 0.000000e+00 1051.0
18 TraesCS5D01G322200 chr2D 93.966 696 39 2 1 696 528420340 528421032 0.000000e+00 1050.0
19 TraesCS5D01G322200 chr2D 92.529 696 41 3 1 696 206634432 206635116 0.000000e+00 987.0
20 TraesCS5D01G322200 chr2D 81.006 358 41 11 3902 4238 285350437 285350086 4.320000e-65 259.0
21 TraesCS5D01G322200 chr4B 93.678 696 42 2 1 696 483516807 483516114 0.000000e+00 1040.0
22 TraesCS5D01G322200 chr4B 78.502 414 62 20 3898 4286 587012976 587013387 3.360000e-61 246.0
23 TraesCS5D01G322200 chr7B 93.391 696 44 2 1 696 58246349 58245656 0.000000e+00 1029.0
24 TraesCS5D01G322200 chr2B 93.247 696 46 1 1 696 757927267 757927961 0.000000e+00 1024.0
25 TraesCS5D01G322200 chr2B 80.201 399 53 13 3902 4282 321693053 321693443 4.290000e-70 276.0
26 TraesCS5D01G322200 chr2B 89.730 185 18 1 510 693 757926934 757926750 7.280000e-58 235.0
27 TraesCS5D01G322200 chr3A 92.143 700 47 8 1 696 555679910 555679215 0.000000e+00 981.0
28 TraesCS5D01G322200 chr3A 90.141 71 6 1 4002 4071 602900430 602900360 1.670000e-14 91.6
29 TraesCS5D01G322200 chr5B 88.302 530 28 20 3827 4347 499073012 499072508 4.820000e-169 604.0
30 TraesCS5D01G322200 chr5B 98.198 111 2 0 3448 3558 499073178 499073068 1.240000e-45 195.0
31 TraesCS5D01G322200 chr2A 81.390 403 50 12 3902 4285 356718881 356718485 5.470000e-79 305.0
32 TraesCS5D01G322200 chr7A 83.108 148 21 4 4096 4239 37730924 37731071 9.830000e-27 132.0
33 TraesCS5D01G322200 chr7D 79.144 187 32 7 4103 4283 392623701 392623516 5.910000e-24 122.0
34 TraesCS5D01G322200 chr1B 74.286 350 61 21 3957 4285 553136895 553136554 2.130000e-23 121.0


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 TraesCS5D01G322200 chr5D 414011113 414015467 4354 True 3774.0 6571 100.000 1 4355 2 chr5D.!!$R1 4354
1 TraesCS5D01G322200 chr5A 526523335 526526155 2820 True 4457.0 4457 95.324 741 3537 1 chr5A.!!$R1 2796
2 TraesCS5D01G322200 chr6B 643185778 643188108 2330 False 3109.0 3109 90.749 1032 3362 1 chr6B.!!$F1 2330
3 TraesCS5D01G322200 chr6B 642891995 642894249 2254 True 1866.0 1866 81.798 1101 3355 1 chr6B.!!$R1 2254
4 TraesCS5D01G322200 chr6B 642906953 642909207 2254 True 1858.0 1858 81.714 1111 3363 1 chr6B.!!$R2 2252
5 TraesCS5D01G322200 chr6B 643639426 643641670 2244 False 1714.0 1714 80.627 1111 3355 1 chr6B.!!$F2 2244
6 TraesCS5D01G322200 chr6A 571698550 571700794 2244 True 1947.0 1947 82.503 1111 3355 1 chr6A.!!$R1 2244
7 TraesCS5D01G322200 chr6A 571789285 571791503 2218 True 1796.0 1796 81.424 1111 3355 1 chr6A.!!$R2 2244
8 TraesCS5D01G322200 chr6A 17956202 17958453 2251 False 1794.0 1794 81.250 1102 3347 1 chr6A.!!$F1 2245
9 TraesCS5D01G322200 chr6A 572336170 572338414 2244 False 1714.0 1714 80.610 1111 3355 1 chr6A.!!$F2 2244
10 TraesCS5D01G322200 chr6D 427070142 427072386 2244 True 1864.0 1864 81.818 1111 3355 1 chr6D.!!$R1 2244
11 TraesCS5D01G322200 chr6D 427266873 427268312 1439 False 1783.0 1783 89.019 1918 3362 1 chr6D.!!$F1 1444
12 TraesCS5D01G322200 chr6D 427710883 427713124 2241 True 1688.0 1688 80.467 1111 3355 1 chr6D.!!$R2 2244
13 TraesCS5D01G322200 chr1D 7758161 7758856 695 True 1142.0 1142 96.264 1 696 1 chr1D.!!$R1 695
14 TraesCS5D01G322200 chr4D 349001228 349001917 689 True 1103.0 1103 95.402 1 696 1 chr4D.!!$R1 695
15 TraesCS5D01G322200 chr3D 30696804 30697497 693 False 1051.0 1051 93.966 1 696 1 chr3D.!!$F1 695
16 TraesCS5D01G322200 chr2D 528420340 528421032 692 False 1050.0 1050 93.966 1 696 1 chr2D.!!$F2 695
17 TraesCS5D01G322200 chr2D 206634432 206635116 684 False 987.0 987 92.529 1 696 1 chr2D.!!$F1 695
18 TraesCS5D01G322200 chr4B 483516114 483516807 693 True 1040.0 1040 93.678 1 696 1 chr4B.!!$R1 695
19 TraesCS5D01G322200 chr7B 58245656 58246349 693 True 1029.0 1029 93.391 1 696 1 chr7B.!!$R1 695
20 TraesCS5D01G322200 chr2B 757927267 757927961 694 False 1024.0 1024 93.247 1 696 1 chr2B.!!$F2 695
21 TraesCS5D01G322200 chr3A 555679215 555679910 695 True 981.0 981 92.143 1 696 1 chr3A.!!$R1 695
22 TraesCS5D01G322200 chr5B 499072508 499073178 670 True 399.5 604 93.250 3448 4347 2 chr5B.!!$R1 899

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
735 749 0.107654 GGGAGAGGTTGGTTGGATCG 60.108 60.0 0.0 0.0 0.0 3.69 F
740 754 0.250727 AGGTTGGTTGGATCGTGTGG 60.251 55.0 0.0 0.0 0.0 4.17 F
741 755 0.536460 GGTTGGTTGGATCGTGTGGT 60.536 55.0 0.0 0.0 0.0 4.16 F
743 757 0.601576 TTGGTTGGATCGTGTGGTCG 60.602 55.0 0.0 0.0 0.0 4.79 F
746 760 1.012486 GTTGGATCGTGTGGTCGGAC 61.012 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2451 2502 2.126228 TGGAACACGATCGTCGCC 60.126 61.111 19.84 19.1 45.12 5.54 R
2643 2697 3.118408 ACATGATGTTATACTGCACCCGT 60.118 43.478 0.00 0.0 0.00 5.28 R
2949 3003 2.758327 ACGGCCATCTGCTCGGTA 60.758 61.111 2.24 0.0 40.92 4.02 R
3092 3152 3.036084 CGTTGCTGCCGACGTTCT 61.036 61.111 14.85 0.0 42.56 3.01 R
3409 3473 3.675225 CGATCTACATATTGAAGGGCACG 59.325 47.826 0.00 0.0 0.00 5.34 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
283 285 3.077556 GAGGAAGCAGGGAGGCGA 61.078 66.667 0.00 0.00 39.27 5.54
624 638 2.185004 ACGCTAGACATGGTGCTTTT 57.815 45.000 0.00 0.00 0.00 2.27
625 639 2.076863 ACGCTAGACATGGTGCTTTTC 58.923 47.619 0.00 0.00 0.00 2.29
626 640 2.076100 CGCTAGACATGGTGCTTTTCA 58.924 47.619 0.00 0.00 0.00 2.69
655 669 7.215085 AGAAACTGTATCCTAGTGTTTTTCGT 58.785 34.615 0.00 0.00 32.01 3.85
668 682 4.276678 GTGTTTTTCGTAAACCTAGCCCTT 59.723 41.667 11.45 0.00 0.00 3.95
698 712 9.754382 ATGATGATTTTATGCAATTTACTCCAC 57.246 29.630 0.00 0.00 0.00 4.02
699 713 7.914871 TGATGATTTTATGCAATTTACTCCACG 59.085 33.333 0.00 0.00 0.00 4.94
700 714 7.384439 TGATTTTATGCAATTTACTCCACGA 57.616 32.000 0.00 0.00 0.00 4.35
701 715 7.471721 TGATTTTATGCAATTTACTCCACGAG 58.528 34.615 0.00 0.00 35.52 4.18
702 716 7.335673 TGATTTTATGCAATTTACTCCACGAGA 59.664 33.333 0.00 0.00 33.32 4.04
704 718 3.953712 TGCAATTTACTCCACGAGAGA 57.046 42.857 12.99 0.00 46.50 3.10
705 719 3.849911 TGCAATTTACTCCACGAGAGAG 58.150 45.455 12.99 6.85 46.50 3.20
706 720 2.605366 GCAATTTACTCCACGAGAGAGC 59.395 50.000 12.99 4.80 46.50 4.09
707 721 2.853731 ATTTACTCCACGAGAGAGCG 57.146 50.000 12.99 0.00 46.50 5.03
708 722 1.817357 TTTACTCCACGAGAGAGCGA 58.183 50.000 12.99 0.00 46.50 4.93
709 723 1.370609 TTACTCCACGAGAGAGCGAG 58.629 55.000 12.99 0.00 46.50 5.03
710 724 0.249676 TACTCCACGAGAGAGCGAGT 59.750 55.000 12.99 4.50 46.50 4.18
711 725 1.302383 ACTCCACGAGAGAGCGAGTG 61.302 60.000 12.99 0.00 46.50 3.51
712 726 2.487428 CCACGAGAGAGCGAGTGG 59.513 66.667 0.00 0.00 46.52 4.00
713 727 2.202544 CACGAGAGAGCGAGTGGC 60.203 66.667 0.00 0.00 44.05 5.01
722 736 4.803426 GCGAGTGGCGTGGGAGAG 62.803 72.222 0.00 0.00 43.41 3.20
723 737 4.135153 CGAGTGGCGTGGGAGAGG 62.135 72.222 0.00 0.00 34.64 3.69
724 738 2.997897 GAGTGGCGTGGGAGAGGT 60.998 66.667 0.00 0.00 0.00 3.85
725 739 2.526873 AGTGGCGTGGGAGAGGTT 60.527 61.111 0.00 0.00 0.00 3.50
726 740 2.358737 GTGGCGTGGGAGAGGTTG 60.359 66.667 0.00 0.00 0.00 3.77
727 741 3.636231 TGGCGTGGGAGAGGTTGG 61.636 66.667 0.00 0.00 0.00 3.77
728 742 3.637273 GGCGTGGGAGAGGTTGGT 61.637 66.667 0.00 0.00 0.00 3.67
729 743 2.430367 GCGTGGGAGAGGTTGGTT 59.570 61.111 0.00 0.00 0.00 3.67
730 744 1.966451 GCGTGGGAGAGGTTGGTTG 60.966 63.158 0.00 0.00 0.00 3.77
731 745 1.302511 CGTGGGAGAGGTTGGTTGG 60.303 63.158 0.00 0.00 0.00 3.77
732 746 1.764571 CGTGGGAGAGGTTGGTTGGA 61.765 60.000 0.00 0.00 0.00 3.53
733 747 0.698818 GTGGGAGAGGTTGGTTGGAT 59.301 55.000 0.00 0.00 0.00 3.41
734 748 0.991920 TGGGAGAGGTTGGTTGGATC 59.008 55.000 0.00 0.00 0.00 3.36
735 749 0.107654 GGGAGAGGTTGGTTGGATCG 60.108 60.000 0.00 0.00 0.00 3.69
736 750 0.613777 GGAGAGGTTGGTTGGATCGT 59.386 55.000 0.00 0.00 0.00 3.73
737 751 1.676014 GGAGAGGTTGGTTGGATCGTG 60.676 57.143 0.00 0.00 0.00 4.35
738 752 1.002087 GAGAGGTTGGTTGGATCGTGT 59.998 52.381 0.00 0.00 0.00 4.49
739 753 1.156736 GAGGTTGGTTGGATCGTGTG 58.843 55.000 0.00 0.00 0.00 3.82
740 754 0.250727 AGGTTGGTTGGATCGTGTGG 60.251 55.000 0.00 0.00 0.00 4.17
741 755 0.536460 GGTTGGTTGGATCGTGTGGT 60.536 55.000 0.00 0.00 0.00 4.16
742 756 0.872388 GTTGGTTGGATCGTGTGGTC 59.128 55.000 0.00 0.00 0.00 4.02
743 757 0.601576 TTGGTTGGATCGTGTGGTCG 60.602 55.000 0.00 0.00 0.00 4.79
744 758 1.740296 GGTTGGATCGTGTGGTCGG 60.740 63.158 0.00 0.00 0.00 4.79
745 759 1.290955 GTTGGATCGTGTGGTCGGA 59.709 57.895 0.00 0.00 0.00 4.55
746 760 1.012486 GTTGGATCGTGTGGTCGGAC 61.012 60.000 0.00 0.00 0.00 4.79
768 782 2.963854 CAGCAGCGTCCGCCATAG 60.964 66.667 8.23 0.00 43.17 2.23
785 799 3.314913 CCATAGAAATACGCACATGGCAA 59.685 43.478 0.00 0.00 45.17 4.52
798 812 2.505407 ACATGGCAACTCTAGTGGCATA 59.495 45.455 17.14 0.53 46.64 3.14
829 850 9.970395 TGGTACTAATTTGGAATACATACTACG 57.030 33.333 0.00 0.00 0.00 3.51
836 857 3.638160 TGGAATACATACTACGGTCCACC 59.362 47.826 0.00 0.00 0.00 4.61
875 896 2.639286 GGCAGCCACGTGAAACAG 59.361 61.111 19.30 4.19 35.74 3.16
893 914 1.458445 CAGGATAACATGCGAGCGATG 59.542 52.381 0.00 6.14 0.00 3.84
952 985 3.868985 ACCCGTTGGCCAGTTCGT 61.869 61.111 19.89 8.54 33.59 3.85
953 986 3.047877 CCCGTTGGCCAGTTCGTC 61.048 66.667 19.89 4.04 0.00 4.20
977 1010 1.870055 TTATAGCGCCCCCGATCGAC 61.870 60.000 18.66 1.89 36.29 4.20
997 1030 1.663074 GAGGGCTGCATCGATCGAC 60.663 63.158 22.06 9.52 0.00 4.20
1022 1055 4.530857 GCTGACCATACCGCCGCT 62.531 66.667 0.00 0.00 0.00 5.52
1104 1140 3.519930 GAGGGGCTCGAGACGGAC 61.520 72.222 18.75 7.43 0.00 4.79
1227 1263 2.494918 GTCCCCGTGGAGATGTCG 59.505 66.667 0.00 0.00 42.85 4.35
1944 1995 1.045407 TCTACAAAGACACCACCGCT 58.955 50.000 0.00 0.00 0.00 5.52
2451 2502 1.922135 GCACACAAGCATACCCCGTG 61.922 60.000 0.00 0.00 0.00 4.94
2643 2697 2.791927 CTCGACGGCGACATGAGA 59.208 61.111 10.67 0.00 42.51 3.27
3147 3207 3.976701 AAAGATCACCAGCCCCGCG 62.977 63.158 0.00 0.00 0.00 6.46
3362 3422 1.000938 TGCGGAGATGTGATCGATCAG 60.001 52.381 27.95 15.22 37.51 2.90
3409 3473 2.612221 CCGAGACCCAAACTAGAACCAC 60.612 54.545 0.00 0.00 0.00 4.16
3410 3474 2.685100 GAGACCCAAACTAGAACCACG 58.315 52.381 0.00 0.00 0.00 4.94
3413 3477 0.872388 CCCAAACTAGAACCACGTGC 59.128 55.000 10.91 0.00 0.00 5.34
3424 3488 1.750193 ACCACGTGCCCTTCAATATG 58.250 50.000 10.91 0.00 0.00 1.78
3425 3489 1.004277 ACCACGTGCCCTTCAATATGT 59.996 47.619 10.91 0.00 0.00 2.29
3438 3502 7.766278 GCCCTTCAATATGTAGATCGACATAAT 59.234 37.037 26.05 18.28 43.66 1.28
3851 3916 7.715265 ATCTGATTATTTGGCACTACTTACG 57.285 36.000 0.00 0.00 0.00 3.18
3852 3917 6.636705 TCTGATTATTTGGCACTACTTACGT 58.363 36.000 0.00 0.00 0.00 3.57
3853 3918 7.101054 TCTGATTATTTGGCACTACTTACGTT 58.899 34.615 0.00 0.00 0.00 3.99
3854 3919 7.064134 TCTGATTATTTGGCACTACTTACGTTG 59.936 37.037 0.00 0.00 0.00 4.10
3914 3981 5.793026 TTTTGCAAAGGACACAACAATTC 57.207 34.783 12.41 0.00 0.00 2.17
3921 3988 0.521735 GACACAACAATTCGGCTCCC 59.478 55.000 0.00 0.00 0.00 4.30
4009 4080 3.624326 TTTTGCCACAGAAGATGTTCG 57.376 42.857 0.00 0.00 41.41 3.95
4012 4083 1.344438 TGCCACAGAAGATGTTCGAGT 59.656 47.619 0.00 0.00 41.41 4.18
4020 4091 4.091075 CAGAAGATGTTCGAGTGTGTGATG 59.909 45.833 0.00 0.00 37.79 3.07
4035 4106 4.202336 TGTGTGATGTCCATGCCAAATTTT 60.202 37.500 0.00 0.00 0.00 1.82
4046 4117 3.942829 TGCCAAATTTTGTGGTGTTTGA 58.057 36.364 8.26 0.00 38.50 2.69
4047 4118 4.521146 TGCCAAATTTTGTGGTGTTTGAT 58.479 34.783 8.26 0.00 38.50 2.57
4049 4120 6.294473 TGCCAAATTTTGTGGTGTTTGATAT 58.706 32.000 8.26 0.00 38.50 1.63
4050 4121 6.426328 TGCCAAATTTTGTGGTGTTTGATATC 59.574 34.615 8.26 0.00 38.50 1.63
4051 4122 6.650390 GCCAAATTTTGTGGTGTTTGATATCT 59.350 34.615 8.26 0.00 38.50 1.98
4052 4123 7.816995 GCCAAATTTTGTGGTGTTTGATATCTA 59.183 33.333 8.26 0.00 38.50 1.98
4053 4124 9.703892 CCAAATTTTGTGGTGTTTGATATCTAA 57.296 29.630 8.26 0.00 34.38 2.10
4058 4129 7.843490 TTGTGGTGTTTGATATCTAAGTAGC 57.157 36.000 3.98 5.53 0.00 3.58
4059 4130 7.182817 TGTGGTGTTTGATATCTAAGTAGCT 57.817 36.000 3.98 0.00 0.00 3.32
4060 4131 7.265673 TGTGGTGTTTGATATCTAAGTAGCTC 58.734 38.462 3.98 6.40 0.00 4.09
4061 4132 7.124298 TGTGGTGTTTGATATCTAAGTAGCTCT 59.876 37.037 3.98 0.00 0.00 4.09
4062 4133 7.982354 GTGGTGTTTGATATCTAAGTAGCTCTT 59.018 37.037 3.98 0.00 39.89 2.85
4063 4134 8.198109 TGGTGTTTGATATCTAAGTAGCTCTTC 58.802 37.037 3.98 0.00 37.56 2.87
4064 4135 7.380065 GGTGTTTGATATCTAAGTAGCTCTTCG 59.620 40.741 3.98 0.00 37.56 3.79
4065 4136 6.918569 TGTTTGATATCTAAGTAGCTCTTCGC 59.081 38.462 3.98 0.00 37.56 4.70
4101 4172 4.272748 GGTCTGCGAGAAAGTTTACTGTTT 59.727 41.667 0.00 0.00 0.00 2.83
4105 4176 4.034742 TGCGAGAAAGTTTACTGTTTGGAC 59.965 41.667 0.00 0.00 0.00 4.02
4107 4178 4.318546 CGAGAAAGTTTACTGTTTGGACCG 60.319 45.833 0.00 0.00 0.00 4.79
4171 4242 3.447742 GATGAAATTTTGCCCGGACATC 58.552 45.455 0.73 0.00 0.00 3.06
4174 4245 1.626686 AATTTTGCCCGGACATCACA 58.373 45.000 0.73 0.00 0.00 3.58
4190 4261 2.929641 TCACACATTTGAGTGGCTTCA 58.070 42.857 8.02 0.00 43.72 3.02
4284 4357 6.465144 GCTCGAGCTCATAAATGAATATTCG 58.535 40.000 29.88 0.00 36.18 3.34
4288 4361 8.826710 TCGAGCTCATAAATGAATATTCGTTTT 58.173 29.630 30.77 23.06 42.12 2.43
4292 4365 7.434897 GCTCATAAATGAATATTCGTTTTGCCA 59.565 33.333 30.77 18.57 42.12 4.92
4325 4398 3.956199 TGATCTTTGATGATTTGCCCTCC 59.044 43.478 0.00 0.00 0.00 4.30
4347 4420 1.963515 GCAAGTGGGACCTTGTGAAAT 59.036 47.619 0.00 0.00 43.03 2.17
4348 4421 2.029918 GCAAGTGGGACCTTGTGAAATC 60.030 50.000 0.00 0.00 43.03 2.17
4349 4422 3.490348 CAAGTGGGACCTTGTGAAATCT 58.510 45.455 0.00 0.00 37.61 2.40
4350 4423 3.425162 AGTGGGACCTTGTGAAATCTC 57.575 47.619 0.00 0.00 0.00 2.75
4351 4424 2.711009 AGTGGGACCTTGTGAAATCTCA 59.289 45.455 0.00 0.00 0.00 3.27
4352 4425 3.138283 AGTGGGACCTTGTGAAATCTCAA 59.862 43.478 0.00 0.00 31.88 3.02
4353 4426 3.888930 GTGGGACCTTGTGAAATCTCAAA 59.111 43.478 0.00 0.00 31.88 2.69
4354 4427 4.340950 GTGGGACCTTGTGAAATCTCAAAA 59.659 41.667 0.00 0.00 31.88 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
411 413 3.089874 CGCAATCCCCTCCCCAGA 61.090 66.667 0.00 0.00 0.00 3.86
547 552 3.308866 GCCGCGTTAAGTGAGTTTATGAT 59.691 43.478 4.92 0.00 0.00 2.45
655 669 9.487442 AAATCATCATTTTAAGGGCTAGGTTTA 57.513 29.630 0.00 0.00 0.00 2.01
696 710 2.202544 GCCACTCGCTCTCTCGTG 60.203 66.667 0.00 0.00 0.00 4.35
697 711 3.805307 CGCCACTCGCTCTCTCGT 61.805 66.667 0.00 0.00 34.21 4.18
698 712 3.805307 ACGCCACTCGCTCTCTCG 61.805 66.667 0.00 0.00 43.23 4.04
699 713 2.202544 CACGCCACTCGCTCTCTC 60.203 66.667 0.00 0.00 43.23 3.20
700 714 3.753434 CCACGCCACTCGCTCTCT 61.753 66.667 0.00 0.00 43.23 3.10
701 715 4.803426 CCCACGCCACTCGCTCTC 62.803 72.222 0.00 0.00 43.23 3.20
703 717 4.803426 CTCCCACGCCACTCGCTC 62.803 72.222 0.00 0.00 43.23 5.03
705 719 4.803426 CTCTCCCACGCCACTCGC 62.803 72.222 0.00 0.00 43.23 5.03
706 720 4.135153 CCTCTCCCACGCCACTCG 62.135 72.222 0.00 0.00 45.38 4.18
707 721 2.584391 AACCTCTCCCACGCCACTC 61.584 63.158 0.00 0.00 0.00 3.51
708 722 2.526873 AACCTCTCCCACGCCACT 60.527 61.111 0.00 0.00 0.00 4.00
709 723 2.358737 CAACCTCTCCCACGCCAC 60.359 66.667 0.00 0.00 0.00 5.01
710 724 3.636231 CCAACCTCTCCCACGCCA 61.636 66.667 0.00 0.00 0.00 5.69
711 725 3.192103 AACCAACCTCTCCCACGCC 62.192 63.158 0.00 0.00 0.00 5.68
712 726 1.966451 CAACCAACCTCTCCCACGC 60.966 63.158 0.00 0.00 0.00 5.34
713 727 1.302511 CCAACCAACCTCTCCCACG 60.303 63.158 0.00 0.00 0.00 4.94
714 728 0.698818 ATCCAACCAACCTCTCCCAC 59.301 55.000 0.00 0.00 0.00 4.61
715 729 0.991920 GATCCAACCAACCTCTCCCA 59.008 55.000 0.00 0.00 0.00 4.37
716 730 0.107654 CGATCCAACCAACCTCTCCC 60.108 60.000 0.00 0.00 0.00 4.30
717 731 0.613777 ACGATCCAACCAACCTCTCC 59.386 55.000 0.00 0.00 0.00 3.71
718 732 1.002087 ACACGATCCAACCAACCTCTC 59.998 52.381 0.00 0.00 0.00 3.20
719 733 1.056660 ACACGATCCAACCAACCTCT 58.943 50.000 0.00 0.00 0.00 3.69
720 734 1.156736 CACACGATCCAACCAACCTC 58.843 55.000 0.00 0.00 0.00 3.85
721 735 0.250727 CCACACGATCCAACCAACCT 60.251 55.000 0.00 0.00 0.00 3.50
722 736 0.536460 ACCACACGATCCAACCAACC 60.536 55.000 0.00 0.00 0.00 3.77
723 737 0.872388 GACCACACGATCCAACCAAC 59.128 55.000 0.00 0.00 0.00 3.77
724 738 0.601576 CGACCACACGATCCAACCAA 60.602 55.000 0.00 0.00 35.09 3.67
725 739 1.005512 CGACCACACGATCCAACCA 60.006 57.895 0.00 0.00 35.09 3.67
726 740 1.740296 CCGACCACACGATCCAACC 60.740 63.158 0.00 0.00 35.09 3.77
727 741 1.012486 GTCCGACCACACGATCCAAC 61.012 60.000 0.00 0.00 35.09 3.77
728 742 1.290955 GTCCGACCACACGATCCAA 59.709 57.895 0.00 0.00 35.09 3.53
729 743 2.967397 GTCCGACCACACGATCCA 59.033 61.111 0.00 0.00 35.09 3.41
730 744 2.202570 CGTCCGACCACACGATCC 60.203 66.667 0.00 0.00 38.32 3.36
731 745 1.513586 GTCGTCCGACCACACGATC 60.514 63.158 8.60 0.00 46.13 3.69
732 746 2.564975 GTCGTCCGACCACACGAT 59.435 61.111 8.60 0.00 46.13 3.73
733 747 4.016629 CGTCGTCCGACCACACGA 62.017 66.667 13.66 0.00 42.61 4.35
735 749 4.634133 TGCGTCGTCCGACCACAC 62.634 66.667 13.66 2.76 41.76 3.82
736 750 4.337060 CTGCGTCGTCCGACCACA 62.337 66.667 13.66 11.11 41.76 4.17
768 782 2.420022 AGAGTTGCCATGTGCGTATTTC 59.580 45.455 0.00 0.00 45.60 2.17
785 799 4.252570 ACCAGTACTATGCCACTAGAGT 57.747 45.455 0.00 0.00 0.00 3.24
829 850 0.969894 CTCCAGATATCCGGTGGACC 59.030 60.000 6.64 0.00 35.36 4.46
836 857 1.187087 GGCCCTACTCCAGATATCCG 58.813 60.000 0.00 0.00 0.00 4.18
837 858 2.327325 TGGCCCTACTCCAGATATCC 57.673 55.000 0.00 0.00 0.00 2.59
875 896 1.457303 GTCATCGCTCGCATGTTATCC 59.543 52.381 0.00 0.00 0.00 2.59
977 1010 2.356793 GATCGATGCAGCCCTCGG 60.357 66.667 0.54 0.00 35.64 4.63
997 1030 0.109342 GGTATGGTCAGCTCCATGGG 59.891 60.000 13.02 3.69 46.27 4.00
1104 1140 1.134401 ACAATGTAGGAGGACATGCCG 60.134 52.381 0.00 0.00 39.99 5.69
1650 1695 2.338984 GACACCGTCTCGCCAACT 59.661 61.111 0.00 0.00 0.00 3.16
2193 2244 2.409975 CCGACTTCGCAGGTTTTAGAA 58.590 47.619 0.00 0.00 38.18 2.10
2451 2502 2.126228 TGGAACACGATCGTCGCC 60.126 61.111 19.84 19.10 45.12 5.54
2643 2697 3.118408 ACATGATGTTATACTGCACCCGT 60.118 43.478 0.00 0.00 0.00 5.28
2949 3003 2.758327 ACGGCCATCTGCTCGGTA 60.758 61.111 2.24 0.00 40.92 4.02
3092 3152 3.036084 CGTTGCTGCCGACGTTCT 61.036 61.111 14.85 0.00 42.56 3.01
3409 3473 3.675225 CGATCTACATATTGAAGGGCACG 59.325 47.826 0.00 0.00 0.00 5.34
3410 3474 4.686554 GTCGATCTACATATTGAAGGGCAC 59.313 45.833 0.00 0.00 0.00 5.01
3850 3915 3.308530 GGCAAATTCTCAAAGTCCAACG 58.691 45.455 0.00 0.00 0.00 4.10
3851 3916 3.321968 AGGGCAAATTCTCAAAGTCCAAC 59.678 43.478 0.00 0.00 0.00 3.77
3852 3917 3.575805 AGGGCAAATTCTCAAAGTCCAA 58.424 40.909 0.00 0.00 0.00 3.53
3853 3918 3.243359 AGGGCAAATTCTCAAAGTCCA 57.757 42.857 0.00 0.00 0.00 4.02
3854 3919 3.056536 GGAAGGGCAAATTCTCAAAGTCC 60.057 47.826 0.00 0.00 0.00 3.85
3900 3967 1.523758 GAGCCGAATTGTTGTGTCCT 58.476 50.000 0.00 0.00 0.00 3.85
3982 4053 5.048224 ACATCTTCTGTGGCAAAAAGATCAG 60.048 40.000 14.06 5.29 36.56 2.90
3983 4054 4.828939 ACATCTTCTGTGGCAAAAAGATCA 59.171 37.500 14.06 0.00 36.56 2.92
3984 4055 5.382618 ACATCTTCTGTGGCAAAAAGATC 57.617 39.130 14.06 0.00 36.56 2.75
3986 4057 4.261155 CGAACATCTTCTGTGGCAAAAAGA 60.261 41.667 9.14 9.14 38.39 2.52
3987 4058 3.976942 CGAACATCTTCTGTGGCAAAAAG 59.023 43.478 0.00 0.00 38.39 2.27
3997 4068 3.642705 TCACACACTCGAACATCTTCTG 58.357 45.455 0.00 0.00 0.00 3.02
3998 4069 4.240888 CATCACACACTCGAACATCTTCT 58.759 43.478 0.00 0.00 0.00 2.85
4009 4080 1.089920 GGCATGGACATCACACACTC 58.910 55.000 0.00 0.00 0.00 3.51
4012 4083 1.992538 TTTGGCATGGACATCACACA 58.007 45.000 0.00 0.00 0.00 3.72
4020 4091 2.807392 CACCACAAAATTTGGCATGGAC 59.193 45.455 17.29 0.00 37.69 4.02
4035 4106 7.124298 AGAGCTACTTAGATATCAAACACCACA 59.876 37.037 5.32 0.00 0.00 4.17
4082 4153 4.034742 GTCCAAACAGTAAACTTTCTCGCA 59.965 41.667 0.00 0.00 0.00 5.10
4133 4204 2.159379 TCATCGTGTTCGGACATCTGAG 60.159 50.000 0.00 0.00 38.23 3.35
4171 4242 3.928727 ATGAAGCCACTCAAATGTGTG 57.071 42.857 8.29 8.29 38.75 3.82
4174 4245 3.308438 GCAATGAAGCCACTCAAATGT 57.692 42.857 0.00 0.00 0.00 2.71
4284 4357 6.223120 AGATCAAAATAAGGTGTGGCAAAAC 58.777 36.000 0.00 0.00 0.00 2.43
4288 4361 5.538053 TCAAAGATCAAAATAAGGTGTGGCA 59.462 36.000 0.00 0.00 0.00 4.92
4319 4392 3.650950 TCCCACTTGCAGGAGGGC 61.651 66.667 24.10 0.00 41.22 5.19


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

AutoCloner maintained by Alex Coulton.