Multiple sequence alignment - TraesCS2D01G494300

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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 TraesCS2D01G494300 chr2D 100.000 2855 0 0 1 2855 591436746 591439600 0.000000e+00 5273.0
1 TraesCS2D01G494300 chr2D 87.325 1286 88 41 777 2010 591388357 591389619 0.000000e+00 1402.0
2 TraesCS2D01G494300 chr2D 92.997 871 38 11 935 1792 591548070 591548930 0.000000e+00 1249.0
3 TraesCS2D01G494300 chr2D 88.422 786 84 5 1 782 582691902 582692684 0.000000e+00 941.0
4 TraesCS2D01G494300 chr2D 88.010 784 88 5 1 782 52021669 52022448 0.000000e+00 922.0
5 TraesCS2D01G494300 chr2D 82.763 731 77 33 784 1480 591300576 591301291 8.750000e-170 606.0
6 TraesCS2D01G494300 chr2D 89.100 211 17 5 1796 2006 591553378 591553582 1.010000e-64 257.0
7 TraesCS2D01G494300 chr2D 94.565 92 5 0 784 875 591547862 591547953 2.970000e-30 143.0
8 TraesCS2D01G494300 chr2D 86.429 140 8 5 1731 1869 591603951 591604080 2.970000e-30 143.0
9 TraesCS2D01G494300 chr2D 90.698 86 6 1 784 867 591320110 591320195 2.320000e-21 113.0
10 TraesCS2D01G494300 chr2D 100.000 34 0 0 905 938 591548023 591548056 2.370000e-06 63.9
11 TraesCS2D01G494300 chr5D 97.882 850 17 1 2007 2855 445715876 445715027 0.000000e+00 1469.0
12 TraesCS2D01G494300 chr7D 97.872 846 16 2 2010 2855 549776951 549777794 0.000000e+00 1461.0
13 TraesCS2D01G494300 chr7D 89.172 785 77 8 1 782 392625408 392626187 0.000000e+00 972.0
14 TraesCS2D01G494300 chr7D 86.962 790 88 6 1 787 523399397 523400174 0.000000e+00 874.0
15 TraesCS2D01G494300 chr7D 84.962 266 40 0 2060 2325 637860321 637860056 1.300000e-68 270.0
16 TraesCS2D01G494300 chr4D 97.653 852 18 2 2004 2855 509085710 509084861 0.000000e+00 1461.0
17 TraesCS2D01G494300 chr4D 89.258 782 82 2 1 781 21168703 21169483 0.000000e+00 977.0
18 TraesCS2D01G494300 chr1D 97.052 848 24 1 2008 2855 350261346 350262192 0.000000e+00 1426.0
19 TraesCS2D01G494300 chr1A 93.728 845 49 2 2010 2854 486706305 486705465 0.000000e+00 1264.0
20 TraesCS2D01G494300 chr2B 93.286 849 54 3 2008 2854 168537803 168536956 0.000000e+00 1249.0
21 TraesCS2D01G494300 chr2B 82.367 1259 128 49 787 1976 717097761 717098994 0.000000e+00 1009.0
22 TraesCS2D01G494300 chr2B 85.478 785 107 6 1 780 708301119 708301901 0.000000e+00 811.0
23 TraesCS2D01G494300 chr2B 82.615 742 76 26 790 1483 717043156 717043892 8.750000e-170 606.0
24 TraesCS2D01G494300 chr2B 83.237 173 19 4 1731 1903 717328955 717329117 1.770000e-32 150.0
25 TraesCS2D01G494300 chr2A 88.469 980 67 19 1038 2010 726273240 726274180 0.000000e+00 1142.0
26 TraesCS2D01G494300 chr2A 83.292 1221 89 64 784 1953 726295607 726296763 0.000000e+00 1018.0
27 TraesCS2D01G494300 chr2A 84.615 1053 99 29 957 1988 726223881 726224891 0.000000e+00 989.0
28 TraesCS2D01G494300 chr2A 94.565 92 5 0 784 875 726223726 726223817 2.970000e-30 143.0
29 TraesCS2D01G494300 chr2A 77.419 279 29 16 784 1029 726272737 726273014 4.960000e-28 135.0
30 TraesCS2D01G494300 chrUn 87.484 783 89 4 1 782 67915271 67916045 0.000000e+00 894.0
31 TraesCS2D01G494300 chrUn 89.888 445 32 10 1040 1483 317867669 317868101 6.910000e-156 560.0
32 TraesCS2D01G494300 chrUn 91.398 93 7 1 784 875 317867313 317867405 2.990000e-25 126.0
33 TraesCS2D01G494300 chr7B 86.521 779 94 6 1 775 580998946 580999717 0.000000e+00 846.0
34 TraesCS2D01G494300 chr3D 90.880 625 54 2 1 625 579357381 579358002 0.000000e+00 835.0
35 TraesCS2D01G494300 chr3D 84.117 787 100 12 1 782 578355178 578355944 0.000000e+00 737.0
36 TraesCS2D01G494300 chr6B 82.984 811 100 18 1 782 594672778 594673579 0.000000e+00 699.0


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 TraesCS2D01G494300 chr2D 591436746 591439600 2854 False 5273.0 5273 100.000 1 2855 1 chr2D.!!$F6 2854
1 TraesCS2D01G494300 chr2D 591388357 591389619 1262 False 1402.0 1402 87.325 777 2010 1 chr2D.!!$F5 1233
2 TraesCS2D01G494300 chr2D 582691902 582692684 782 False 941.0 941 88.422 1 782 1 chr2D.!!$F2 781
3 TraesCS2D01G494300 chr2D 52021669 52022448 779 False 922.0 922 88.010 1 782 1 chr2D.!!$F1 781
4 TraesCS2D01G494300 chr2D 591300576 591301291 715 False 606.0 606 82.763 784 1480 1 chr2D.!!$F3 696
5 TraesCS2D01G494300 chr2D 591547862 591548930 1068 False 485.3 1249 95.854 784 1792 3 chr2D.!!$F9 1008
6 TraesCS2D01G494300 chr5D 445715027 445715876 849 True 1469.0 1469 97.882 2007 2855 1 chr5D.!!$R1 848
7 TraesCS2D01G494300 chr7D 549776951 549777794 843 False 1461.0 1461 97.872 2010 2855 1 chr7D.!!$F3 845
8 TraesCS2D01G494300 chr7D 392625408 392626187 779 False 972.0 972 89.172 1 782 1 chr7D.!!$F1 781
9 TraesCS2D01G494300 chr7D 523399397 523400174 777 False 874.0 874 86.962 1 787 1 chr7D.!!$F2 786
10 TraesCS2D01G494300 chr4D 509084861 509085710 849 True 1461.0 1461 97.653 2004 2855 1 chr4D.!!$R1 851
11 TraesCS2D01G494300 chr4D 21168703 21169483 780 False 977.0 977 89.258 1 781 1 chr4D.!!$F1 780
12 TraesCS2D01G494300 chr1D 350261346 350262192 846 False 1426.0 1426 97.052 2008 2855 1 chr1D.!!$F1 847
13 TraesCS2D01G494300 chr1A 486705465 486706305 840 True 1264.0 1264 93.728 2010 2854 1 chr1A.!!$R1 844
14 TraesCS2D01G494300 chr2B 168536956 168537803 847 True 1249.0 1249 93.286 2008 2854 1 chr2B.!!$R1 846
15 TraesCS2D01G494300 chr2B 717097761 717098994 1233 False 1009.0 1009 82.367 787 1976 1 chr2B.!!$F3 1189
16 TraesCS2D01G494300 chr2B 708301119 708301901 782 False 811.0 811 85.478 1 780 1 chr2B.!!$F1 779
17 TraesCS2D01G494300 chr2B 717043156 717043892 736 False 606.0 606 82.615 790 1483 1 chr2B.!!$F2 693
18 TraesCS2D01G494300 chr2A 726295607 726296763 1156 False 1018.0 1018 83.292 784 1953 1 chr2A.!!$F1 1169
19 TraesCS2D01G494300 chr2A 726272737 726274180 1443 False 638.5 1142 82.944 784 2010 2 chr2A.!!$F3 1226
20 TraesCS2D01G494300 chr2A 726223726 726224891 1165 False 566.0 989 89.590 784 1988 2 chr2A.!!$F2 1204
21 TraesCS2D01G494300 chrUn 67915271 67916045 774 False 894.0 894 87.484 1 782 1 chrUn.!!$F1 781
22 TraesCS2D01G494300 chrUn 317867313 317868101 788 False 343.0 560 90.643 784 1483 2 chrUn.!!$F2 699
23 TraesCS2D01G494300 chr7B 580998946 580999717 771 False 846.0 846 86.521 1 775 1 chr7B.!!$F1 774
24 TraesCS2D01G494300 chr3D 579357381 579358002 621 False 835.0 835 90.880 1 625 1 chr3D.!!$F2 624
25 TraesCS2D01G494300 chr3D 578355178 578355944 766 False 737.0 737 84.117 1 782 1 chr3D.!!$F1 781
26 TraesCS2D01G494300 chr6B 594672778 594673579 801 False 699.0 699 82.984 1 782 1 chr6B.!!$F1 781

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
731 776 0.0293 CCGCGCTGACCCATATTTTG 59.971 55.0 5.56 0.0 0.0 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 2502 1.143073 AGTGGTTTCTGGGTGTTCCTC 59.857 52.381 0.0 0.0 36.2 3.71 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
64 65 2.499205 GACGGTCCATCATCGCCA 59.501 61.111 0.00 0.00 0.00 5.69
65 66 1.069765 GACGGTCCATCATCGCCAT 59.930 57.895 0.00 0.00 0.00 4.40
88 89 2.033801 TCTTTCGGTTCTCGTCTTCGTT 59.966 45.455 0.00 0.00 40.32 3.85
148 149 3.926527 CGATAGTTTGCAAGCAGTGTCTA 59.073 43.478 16.04 0.00 0.00 2.59
236 238 2.834574 ACGTGAACAAAAATCGCACA 57.165 40.000 0.00 0.00 0.00 4.57
264 267 2.332063 ACCAACTATGCATAGCGCTT 57.668 45.000 29.60 16.16 43.06 4.68
295 298 0.951558 CAAGCAAACACTAACCGGCT 59.048 50.000 0.00 0.00 0.00 5.52
397 430 2.731374 CTCTTCTCGCCGGATCCC 59.269 66.667 5.05 0.00 0.00 3.85
425 466 2.519302 GGGGCGGTGCAGCATATT 60.519 61.111 17.33 0.00 39.27 1.28
625 670 1.190323 CGAGGCGAAAATCTGCGTATC 59.810 52.381 0.00 0.00 0.00 2.24
653 698 2.656055 GGCCAAGATTTTGCCGCA 59.344 55.556 0.00 0.00 32.79 5.69
658 703 1.532794 AAGATTTTGCCGCACCCCA 60.533 52.632 0.00 0.00 0.00 4.96
672 717 4.327627 CCGCACCCCATAAAAATTTTTACG 59.672 41.667 22.35 15.86 35.65 3.18
673 718 4.327627 CGCACCCCATAAAAATTTTTACGG 59.672 41.667 22.94 22.94 36.14 4.02
674 719 5.480205 GCACCCCATAAAAATTTTTACGGA 58.520 37.500 28.69 10.94 38.00 4.69
675 720 5.349270 GCACCCCATAAAAATTTTTACGGAC 59.651 40.000 28.69 18.41 38.00 4.79
676 721 5.870433 CACCCCATAAAAATTTTTACGGACC 59.130 40.000 28.69 0.00 38.00 4.46
677 722 5.103687 CCCCATAAAAATTTTTACGGACCG 58.896 41.667 28.69 13.61 38.00 4.79
678 723 5.103687 CCCATAAAAATTTTTACGGACCGG 58.896 41.667 28.69 18.73 38.00 5.28
679 724 4.563580 CCATAAAAATTTTTACGGACCGGC 59.436 41.667 24.76 0.00 38.00 6.13
680 725 2.728690 AAAATTTTTACGGACCGGCC 57.271 45.000 20.00 2.44 0.00 6.13
690 735 4.025401 GACCGGCCGTGTTTGCAG 62.025 66.667 26.12 8.44 0.00 4.41
696 741 3.343972 CCGTGTTTGCAGGGTCTG 58.656 61.111 0.00 0.00 43.57 3.51
697 742 1.525995 CCGTGTTTGCAGGGTCTGT 60.526 57.895 0.00 0.00 43.57 3.41
698 743 1.101049 CCGTGTTTGCAGGGTCTGTT 61.101 55.000 0.00 0.00 43.57 3.16
699 744 0.307760 CGTGTTTGCAGGGTCTGTTC 59.692 55.000 0.00 0.00 33.43 3.18
700 745 0.307760 GTGTTTGCAGGGTCTGTTCG 59.692 55.000 0.00 0.00 33.43 3.95
701 746 0.817634 TGTTTGCAGGGTCTGTTCGG 60.818 55.000 0.00 0.00 33.43 4.30
702 747 1.228124 TTTGCAGGGTCTGTTCGGG 60.228 57.895 0.00 0.00 33.43 5.14
703 748 1.990160 TTTGCAGGGTCTGTTCGGGT 61.990 55.000 0.00 0.00 33.43 5.28
704 749 2.358737 GCAGGGTCTGTTCGGGTG 60.359 66.667 0.00 0.00 33.43 4.61
705 750 2.347490 CAGGGTCTGTTCGGGTGG 59.653 66.667 0.00 0.00 0.00 4.61
706 751 2.203182 AGGGTCTGTTCGGGTGGA 59.797 61.111 0.00 0.00 0.00 4.02
707 752 1.460689 AGGGTCTGTTCGGGTGGAA 60.461 57.895 0.00 0.00 0.00 3.53
708 753 0.840722 AGGGTCTGTTCGGGTGGAAT 60.841 55.000 0.00 0.00 36.92 3.01
709 754 0.037734 GGGTCTGTTCGGGTGGAATT 59.962 55.000 0.00 0.00 36.92 2.17
710 755 1.546998 GGGTCTGTTCGGGTGGAATTT 60.547 52.381 0.00 0.00 36.92 1.82
711 756 2.235891 GGTCTGTTCGGGTGGAATTTT 58.764 47.619 0.00 0.00 36.92 1.82
712 757 2.228103 GGTCTGTTCGGGTGGAATTTTC 59.772 50.000 0.00 0.00 36.92 2.29
721 766 4.765611 GGAATTTTCCGCGCTGAC 57.234 55.556 5.56 0.00 37.65 3.51
722 767 1.136774 GGAATTTTCCGCGCTGACC 59.863 57.895 5.56 0.00 37.65 4.02
723 768 1.136774 GAATTTTCCGCGCTGACCC 59.863 57.895 5.56 0.00 0.00 4.46
724 769 1.582610 GAATTTTCCGCGCTGACCCA 61.583 55.000 5.56 0.00 0.00 4.51
725 770 0.965363 AATTTTCCGCGCTGACCCAT 60.965 50.000 5.56 0.00 0.00 4.00
726 771 0.107410 ATTTTCCGCGCTGACCCATA 60.107 50.000 5.56 0.00 0.00 2.74
727 772 0.107410 TTTTCCGCGCTGACCCATAT 60.107 50.000 5.56 0.00 0.00 1.78
728 773 0.107410 TTTCCGCGCTGACCCATATT 60.107 50.000 5.56 0.00 0.00 1.28
729 774 0.107410 TTCCGCGCTGACCCATATTT 60.107 50.000 5.56 0.00 0.00 1.40
730 775 0.107410 TCCGCGCTGACCCATATTTT 60.107 50.000 5.56 0.00 0.00 1.82
731 776 0.029300 CCGCGCTGACCCATATTTTG 59.971 55.000 5.56 0.00 0.00 2.44
732 777 1.013596 CGCGCTGACCCATATTTTGA 58.986 50.000 5.56 0.00 0.00 2.69
733 778 1.268032 CGCGCTGACCCATATTTTGAC 60.268 52.381 5.56 0.00 0.00 3.18
734 779 1.268032 GCGCTGACCCATATTTTGACG 60.268 52.381 0.00 0.00 0.00 4.35
735 780 1.330521 CGCTGACCCATATTTTGACGG 59.669 52.381 0.00 0.00 0.00 4.79
736 781 2.365582 GCTGACCCATATTTTGACGGT 58.634 47.619 0.00 0.00 0.00 4.83
737 782 2.752903 GCTGACCCATATTTTGACGGTT 59.247 45.455 0.00 0.00 0.00 4.44
738 783 3.942748 GCTGACCCATATTTTGACGGTTA 59.057 43.478 0.00 0.00 0.00 2.85
739 784 4.578928 GCTGACCCATATTTTGACGGTTAT 59.421 41.667 0.00 0.00 0.00 1.89
740 785 5.067283 GCTGACCCATATTTTGACGGTTATT 59.933 40.000 0.00 0.00 0.00 1.40
741 786 6.405397 GCTGACCCATATTTTGACGGTTATTT 60.405 38.462 0.00 0.00 0.00 1.40
742 787 7.469537 TGACCCATATTTTGACGGTTATTTT 57.530 32.000 0.00 0.00 0.00 1.82
743 788 8.577048 TGACCCATATTTTGACGGTTATTTTA 57.423 30.769 0.00 0.00 0.00 1.52
744 789 9.191479 TGACCCATATTTTGACGGTTATTTTAT 57.809 29.630 0.00 0.00 0.00 1.40
745 790 9.458374 GACCCATATTTTGACGGTTATTTTATG 57.542 33.333 0.00 0.00 0.00 1.90
746 791 8.417884 ACCCATATTTTGACGGTTATTTTATGG 58.582 33.333 10.78 10.78 35.44 2.74
747 792 7.870445 CCCATATTTTGACGGTTATTTTATGGG 59.130 37.037 17.48 17.48 44.22 4.00
748 793 7.383843 CCATATTTTGACGGTTATTTTATGGGC 59.616 37.037 10.24 0.00 33.19 5.36
749 794 4.722361 TTTGACGGTTATTTTATGGGCC 57.278 40.909 0.00 0.00 0.00 5.80
750 795 3.367646 TGACGGTTATTTTATGGGCCA 57.632 42.857 9.61 9.61 0.00 5.36
751 796 3.283751 TGACGGTTATTTTATGGGCCAG 58.716 45.455 13.78 0.00 0.00 4.85
752 797 2.621526 GACGGTTATTTTATGGGCCAGG 59.378 50.000 13.78 0.00 0.00 4.45
753 798 1.960689 CGGTTATTTTATGGGCCAGGG 59.039 52.381 13.78 0.00 0.00 4.45
754 799 1.691976 GGTTATTTTATGGGCCAGGGC 59.308 52.381 13.78 3.77 41.06 5.19
755 800 2.677914 GTTATTTTATGGGCCAGGGCT 58.322 47.619 13.78 0.00 41.60 5.19
756 801 3.038280 GTTATTTTATGGGCCAGGGCTT 58.962 45.455 13.78 3.56 41.60 4.35
757 802 2.268796 ATTTTATGGGCCAGGGCTTT 57.731 45.000 13.78 3.18 41.60 3.51
758 803 2.037385 TTTTATGGGCCAGGGCTTTT 57.963 45.000 13.78 0.00 41.60 2.27
759 804 2.037385 TTTATGGGCCAGGGCTTTTT 57.963 45.000 13.78 0.00 41.60 1.94
760 805 2.930109 TTATGGGCCAGGGCTTTTTA 57.070 45.000 13.78 0.00 41.60 1.52
761 806 2.153034 TATGGGCCAGGGCTTTTTAC 57.847 50.000 13.78 0.00 41.60 2.01
762 807 0.970427 ATGGGCCAGGGCTTTTTACG 60.970 55.000 13.78 0.00 41.60 3.18
763 808 2.348104 GGGCCAGGGCTTTTTACGG 61.348 63.158 13.81 0.00 41.60 4.02
764 809 2.348104 GGCCAGGGCTTTTTACGGG 61.348 63.158 10.60 0.00 41.60 5.28
765 810 1.605451 GCCAGGGCTTTTTACGGGT 60.605 57.895 2.30 0.00 38.26 5.28
766 811 1.183030 GCCAGGGCTTTTTACGGGTT 61.183 55.000 2.30 0.00 38.26 4.11
767 812 1.334160 CCAGGGCTTTTTACGGGTTT 58.666 50.000 0.00 0.00 0.00 3.27
768 813 1.000394 CCAGGGCTTTTTACGGGTTTG 60.000 52.381 0.00 0.00 0.00 2.93
769 814 0.677288 AGGGCTTTTTACGGGTTTGC 59.323 50.000 0.00 0.00 0.00 3.68
770 815 0.677288 GGGCTTTTTACGGGTTTGCT 59.323 50.000 0.00 0.00 0.00 3.91
771 816 1.887854 GGGCTTTTTACGGGTTTGCTA 59.112 47.619 0.00 0.00 0.00 3.49
772 817 2.094906 GGGCTTTTTACGGGTTTGCTAG 60.095 50.000 0.00 0.00 0.00 3.42
773 818 2.815503 GGCTTTTTACGGGTTTGCTAGA 59.184 45.455 0.00 0.00 0.00 2.43
774 819 3.119955 GGCTTTTTACGGGTTTGCTAGAG 60.120 47.826 0.00 0.00 0.00 2.43
775 820 3.501062 GCTTTTTACGGGTTTGCTAGAGT 59.499 43.478 0.00 0.00 0.00 3.24
776 821 4.023450 GCTTTTTACGGGTTTGCTAGAGTT 60.023 41.667 0.00 0.00 0.00 3.01
777 822 5.427036 TTTTTACGGGTTTGCTAGAGTTG 57.573 39.130 0.00 0.00 0.00 3.16
778 823 2.088950 TACGGGTTTGCTAGAGTTGC 57.911 50.000 0.00 0.00 0.00 4.17
779 824 0.396811 ACGGGTTTGCTAGAGTTGCT 59.603 50.000 0.00 0.00 0.00 3.91
780 825 1.079503 CGGGTTTGCTAGAGTTGCTC 58.920 55.000 0.00 0.00 0.00 4.26
781 826 1.338200 CGGGTTTGCTAGAGTTGCTCT 60.338 52.381 4.02 4.02 43.83 4.09
782 827 2.079925 GGGTTTGCTAGAGTTGCTCTG 58.920 52.381 8.75 1.26 41.37 3.35
1015 1190 2.747460 CACCACCCACATCCTGCG 60.747 66.667 0.00 0.00 0.00 5.18
1086 1489 1.405272 AACCAACGACTCCTCCGGTT 61.405 55.000 0.00 0.00 31.97 4.44
1294 1706 2.048222 CGGCGTTCCTTGAGCTGA 60.048 61.111 0.00 0.00 39.46 4.26
1538 1959 4.760047 GCGACGGAGCACACCCAT 62.760 66.667 0.00 0.00 37.05 4.00
1539 1960 2.509336 CGACGGAGCACACCCATC 60.509 66.667 0.00 0.00 0.00 3.51
1540 1961 2.662596 GACGGAGCACACCCATCA 59.337 61.111 0.00 0.00 0.00 3.07
1653 2104 2.031616 TGCTCCTCTGCACTGCAC 59.968 61.111 0.00 0.00 38.12 4.57
1654 2105 3.117171 GCTCCTCTGCACTGCACG 61.117 66.667 0.00 0.00 33.79 5.34
1696 2154 2.584236 CGTACTGGAGCTGGGTAGTAT 58.416 52.381 0.00 0.00 0.00 2.12
1698 2156 3.501445 CGTACTGGAGCTGGGTAGTATAC 59.499 52.174 0.00 0.00 42.04 1.47
1715 2173 7.396339 GGTAGTATACTATGTGATGGTGATGGA 59.604 40.741 15.53 0.00 42.51 3.41
1716 2174 7.233389 AGTATACTATGTGATGGTGATGGAC 57.767 40.000 2.75 0.00 0.00 4.02
2102 2589 7.054751 GCTACTAAGGGTATCTGGACATTTTT 58.945 38.462 0.00 0.00 0.00 1.94
2146 2633 1.611006 CTTCTCGCCATAGCAGCTAGA 59.389 52.381 8.43 0.00 39.83 2.43
2446 2933 2.217038 GCCCAGGTGGTCTCTGACA 61.217 63.158 0.00 0.00 33.68 3.58
2688 3176 2.579201 CCGCTGGTCTTCGTCCAT 59.421 61.111 0.00 0.00 34.26 3.41
2727 3215 4.424711 GGGGTGGGCATTCTCGCA 62.425 66.667 0.00 0.00 0.00 5.10
2788 3276 7.503566 TCCAAATATCTCATCAGAAATTGGACC 59.496 37.037 6.92 0.00 40.39 4.46
2834 3322 5.447683 CCGTCAACATGGACACAATTATCTG 60.448 44.000 0.00 0.00 37.66 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 1.797046 CCGAAAGAGATGGCGATGATG 59.203 52.381 0.00 0.00 0.00 3.07
58 59 1.482593 AGAACCGAAAGAGATGGCGAT 59.517 47.619 0.00 0.00 0.00 4.58
64 65 3.426426 CGAAGACGAGAACCGAAAGAGAT 60.426 47.826 0.00 0.00 42.66 2.75
65 66 2.095869 CGAAGACGAGAACCGAAAGAGA 60.096 50.000 0.00 0.00 42.66 3.10
88 89 1.293498 GCTCTTGCCGTGAAGGAGA 59.707 57.895 0.00 0.00 45.00 3.71
148 149 0.599558 TTCGGACGACTCGGATGTTT 59.400 50.000 2.98 0.00 0.00 2.83
236 238 1.094785 GCATAGTTGGTTGATGCGGT 58.905 50.000 0.00 0.00 36.89 5.68
264 267 0.248565 TTTGCTTGTGCTTTGTGCCA 59.751 45.000 0.00 0.00 42.00 4.92
320 349 4.715130 AGCCACCCCTAGTCGCCA 62.715 66.667 0.00 0.00 32.13 5.69
421 462 0.926293 CCACCCTCCACCACCAATAT 59.074 55.000 0.00 0.00 0.00 1.28
640 685 0.904394 ATGGGGTGCGGCAAAATCTT 60.904 50.000 3.23 0.00 0.00 2.40
658 703 4.746729 GGCCGGTCCGTAAAAATTTTTAT 58.253 39.130 22.66 3.75 35.35 1.40
673 718 4.025401 CTGCAAACACGGCCGGTC 62.025 66.667 31.76 12.76 0.00 4.79
677 722 3.670377 GACCCTGCAAACACGGCC 61.670 66.667 0.00 0.00 0.00 6.13
678 723 2.594592 AGACCCTGCAAACACGGC 60.595 61.111 0.00 0.00 0.00 5.68
679 724 1.101049 AACAGACCCTGCAAACACGG 61.101 55.000 0.00 0.00 34.37 4.94
680 725 0.307760 GAACAGACCCTGCAAACACG 59.692 55.000 0.00 0.00 34.37 4.49
681 726 0.307760 CGAACAGACCCTGCAAACAC 59.692 55.000 0.00 0.00 34.37 3.32
682 727 0.817634 CCGAACAGACCCTGCAAACA 60.818 55.000 0.00 0.00 34.37 2.83
683 728 1.515521 CCCGAACAGACCCTGCAAAC 61.516 60.000 0.00 0.00 34.37 2.93
684 729 1.228124 CCCGAACAGACCCTGCAAA 60.228 57.895 0.00 0.00 34.37 3.68
685 730 2.429930 CCCGAACAGACCCTGCAA 59.570 61.111 0.00 0.00 34.37 4.08
686 731 2.847234 ACCCGAACAGACCCTGCA 60.847 61.111 0.00 0.00 34.37 4.41
687 732 2.358737 CACCCGAACAGACCCTGC 60.359 66.667 0.00 0.00 34.37 4.85
688 733 1.764571 TTCCACCCGAACAGACCCTG 61.765 60.000 0.00 0.00 37.52 4.45
689 734 0.840722 ATTCCACCCGAACAGACCCT 60.841 55.000 0.00 0.00 31.79 4.34
690 735 0.037734 AATTCCACCCGAACAGACCC 59.962 55.000 0.00 0.00 31.79 4.46
691 736 1.905637 AAATTCCACCCGAACAGACC 58.094 50.000 0.00 0.00 31.79 3.85
692 737 2.228103 GGAAAATTCCACCCGAACAGAC 59.772 50.000 7.32 0.00 46.76 3.51
693 738 2.510613 GGAAAATTCCACCCGAACAGA 58.489 47.619 7.32 0.00 46.76 3.41
704 749 1.136774 GGTCAGCGCGGAAAATTCC 59.863 57.895 12.98 4.99 44.05 3.01
705 750 1.136774 GGGTCAGCGCGGAAAATTC 59.863 57.895 12.98 0.00 0.00 2.17
706 751 0.965363 ATGGGTCAGCGCGGAAAATT 60.965 50.000 12.98 0.00 0.00 1.82
707 752 0.107410 TATGGGTCAGCGCGGAAAAT 60.107 50.000 12.98 8.79 0.00 1.82
708 753 0.107410 ATATGGGTCAGCGCGGAAAA 60.107 50.000 12.98 0.80 0.00 2.29
709 754 0.107410 AATATGGGTCAGCGCGGAAA 60.107 50.000 12.98 1.20 0.00 3.13
710 755 0.107410 AAATATGGGTCAGCGCGGAA 60.107 50.000 12.98 0.00 0.00 4.30
711 756 0.107410 AAAATATGGGTCAGCGCGGA 60.107 50.000 8.83 6.01 0.00 5.54
712 757 0.029300 CAAAATATGGGTCAGCGCGG 59.971 55.000 8.83 0.00 0.00 6.46
713 758 1.013596 TCAAAATATGGGTCAGCGCG 58.986 50.000 0.00 0.00 0.00 6.86
714 759 1.268032 CGTCAAAATATGGGTCAGCGC 60.268 52.381 0.00 0.00 0.00 5.92
715 760 1.330521 CCGTCAAAATATGGGTCAGCG 59.669 52.381 0.00 0.00 0.00 5.18
716 761 2.365582 ACCGTCAAAATATGGGTCAGC 58.634 47.619 0.00 0.00 0.00 4.26
717 762 6.693315 AATAACCGTCAAAATATGGGTCAG 57.307 37.500 0.00 0.00 0.00 3.51
718 763 7.469537 AAAATAACCGTCAAAATATGGGTCA 57.530 32.000 0.00 0.00 0.00 4.02
719 764 9.458374 CATAAAATAACCGTCAAAATATGGGTC 57.542 33.333 0.00 0.00 0.00 4.46
720 765 8.417884 CCATAAAATAACCGTCAAAATATGGGT 58.582 33.333 0.00 0.00 35.65 4.51
721 766 7.870445 CCCATAAAATAACCGTCAAAATATGGG 59.130 37.037 11.43 11.43 46.41 4.00
722 767 7.383843 GCCCATAAAATAACCGTCAAAATATGG 59.616 37.037 0.00 0.00 37.86 2.74
723 768 7.383843 GGCCCATAAAATAACCGTCAAAATATG 59.616 37.037 0.00 0.00 0.00 1.78
724 769 7.070074 TGGCCCATAAAATAACCGTCAAAATAT 59.930 33.333 0.00 0.00 0.00 1.28
725 770 6.380274 TGGCCCATAAAATAACCGTCAAAATA 59.620 34.615 0.00 0.00 0.00 1.40
726 771 5.187967 TGGCCCATAAAATAACCGTCAAAAT 59.812 36.000 0.00 0.00 0.00 1.82
727 772 4.527038 TGGCCCATAAAATAACCGTCAAAA 59.473 37.500 0.00 0.00 0.00 2.44
728 773 4.087182 TGGCCCATAAAATAACCGTCAAA 58.913 39.130 0.00 0.00 0.00 2.69
729 774 3.697045 CTGGCCCATAAAATAACCGTCAA 59.303 43.478 0.00 0.00 0.00 3.18
730 775 3.283751 CTGGCCCATAAAATAACCGTCA 58.716 45.455 0.00 0.00 0.00 4.35
731 776 2.621526 CCTGGCCCATAAAATAACCGTC 59.378 50.000 0.00 0.00 0.00 4.79
732 777 2.661718 CCTGGCCCATAAAATAACCGT 58.338 47.619 0.00 0.00 0.00 4.83
733 778 1.960689 CCCTGGCCCATAAAATAACCG 59.039 52.381 0.00 0.00 0.00 4.44
734 779 1.691976 GCCCTGGCCCATAAAATAACC 59.308 52.381 0.00 0.00 34.56 2.85
735 780 2.677914 AGCCCTGGCCCATAAAATAAC 58.322 47.619 4.13 0.00 43.17 1.89
736 781 3.413105 AAGCCCTGGCCCATAAAATAA 57.587 42.857 4.13 0.00 43.17 1.40
737 782 3.413105 AAAGCCCTGGCCCATAAAATA 57.587 42.857 4.13 0.00 43.17 1.40
738 783 2.268796 AAAGCCCTGGCCCATAAAAT 57.731 45.000 4.13 0.00 43.17 1.82
739 784 2.037385 AAAAGCCCTGGCCCATAAAA 57.963 45.000 4.13 0.00 43.17 1.52
740 785 2.037385 AAAAAGCCCTGGCCCATAAA 57.963 45.000 4.13 0.00 43.17 1.40
741 786 2.462723 GTAAAAAGCCCTGGCCCATAA 58.537 47.619 4.13 0.00 43.17 1.90
742 787 1.683629 CGTAAAAAGCCCTGGCCCATA 60.684 52.381 4.13 0.00 43.17 2.74
743 788 0.970427 CGTAAAAAGCCCTGGCCCAT 60.970 55.000 4.13 0.00 43.17 4.00
744 789 1.605165 CGTAAAAAGCCCTGGCCCA 60.605 57.895 4.13 0.00 43.17 5.36
745 790 2.348104 CCGTAAAAAGCCCTGGCCC 61.348 63.158 4.13 0.00 43.17 5.80
746 791 2.348104 CCCGTAAAAAGCCCTGGCC 61.348 63.158 4.13 0.00 43.17 5.36
747 792 1.183030 AACCCGTAAAAAGCCCTGGC 61.183 55.000 0.00 0.00 42.33 4.85
748 793 1.000394 CAAACCCGTAAAAAGCCCTGG 60.000 52.381 0.00 0.00 0.00 4.45
749 794 1.604438 GCAAACCCGTAAAAAGCCCTG 60.604 52.381 0.00 0.00 0.00 4.45
750 795 0.677288 GCAAACCCGTAAAAAGCCCT 59.323 50.000 0.00 0.00 0.00 5.19
751 796 0.677288 AGCAAACCCGTAAAAAGCCC 59.323 50.000 0.00 0.00 0.00 5.19
752 797 2.815503 TCTAGCAAACCCGTAAAAAGCC 59.184 45.455 0.00 0.00 0.00 4.35
753 798 3.501062 ACTCTAGCAAACCCGTAAAAAGC 59.499 43.478 0.00 0.00 0.00 3.51
754 799 5.449304 CAACTCTAGCAAACCCGTAAAAAG 58.551 41.667 0.00 0.00 0.00 2.27
755 800 4.261280 GCAACTCTAGCAAACCCGTAAAAA 60.261 41.667 0.00 0.00 0.00 1.94
756 801 3.251487 GCAACTCTAGCAAACCCGTAAAA 59.749 43.478 0.00 0.00 0.00 1.52
757 802 2.809696 GCAACTCTAGCAAACCCGTAAA 59.190 45.455 0.00 0.00 0.00 2.01
758 803 2.038033 AGCAACTCTAGCAAACCCGTAA 59.962 45.455 0.00 0.00 0.00 3.18
759 804 1.621814 AGCAACTCTAGCAAACCCGTA 59.378 47.619 0.00 0.00 0.00 4.02
760 805 0.396811 AGCAACTCTAGCAAACCCGT 59.603 50.000 0.00 0.00 0.00 5.28
761 806 1.079503 GAGCAACTCTAGCAAACCCG 58.920 55.000 0.00 0.00 0.00 5.28
762 807 2.079925 CAGAGCAACTCTAGCAAACCC 58.920 52.381 0.00 0.00 38.99 4.11
763 808 2.079925 CCAGAGCAACTCTAGCAAACC 58.920 52.381 0.00 0.00 38.99 3.27
764 809 2.999355 CTCCAGAGCAACTCTAGCAAAC 59.001 50.000 0.00 0.00 38.99 2.93
765 810 2.899900 TCTCCAGAGCAACTCTAGCAAA 59.100 45.455 0.00 0.00 38.99 3.68
766 811 2.529632 TCTCCAGAGCAACTCTAGCAA 58.470 47.619 0.00 0.00 38.99 3.91
767 812 2.222227 TCTCCAGAGCAACTCTAGCA 57.778 50.000 0.00 0.00 38.99 3.49
768 813 3.888930 AGTATCTCCAGAGCAACTCTAGC 59.111 47.826 0.00 0.00 38.99 3.42
769 814 5.129634 TCAGTATCTCCAGAGCAACTCTAG 58.870 45.833 0.00 0.00 38.99 2.43
770 815 5.117406 TCAGTATCTCCAGAGCAACTCTA 57.883 43.478 0.00 0.00 38.99 2.43
771 816 3.974719 TCAGTATCTCCAGAGCAACTCT 58.025 45.455 0.00 0.00 42.11 3.24
772 817 4.099266 ACATCAGTATCTCCAGAGCAACTC 59.901 45.833 0.00 0.00 0.00 3.01
773 818 4.029520 ACATCAGTATCTCCAGAGCAACT 58.970 43.478 0.00 0.00 0.00 3.16
774 819 4.367450 GACATCAGTATCTCCAGAGCAAC 58.633 47.826 0.00 0.00 0.00 4.17
775 820 3.067320 CGACATCAGTATCTCCAGAGCAA 59.933 47.826 0.00 0.00 0.00 3.91
776 821 2.620585 CGACATCAGTATCTCCAGAGCA 59.379 50.000 0.00 0.00 0.00 4.26
777 822 2.621055 ACGACATCAGTATCTCCAGAGC 59.379 50.000 0.00 0.00 0.00 4.09
778 823 3.549827 GCACGACATCAGTATCTCCAGAG 60.550 52.174 0.00 0.00 0.00 3.35
779 824 2.359214 GCACGACATCAGTATCTCCAGA 59.641 50.000 0.00 0.00 0.00 3.86
780 825 2.544694 GGCACGACATCAGTATCTCCAG 60.545 54.545 0.00 0.00 0.00 3.86
781 826 1.409064 GGCACGACATCAGTATCTCCA 59.591 52.381 0.00 0.00 0.00 3.86
782 827 1.683917 AGGCACGACATCAGTATCTCC 59.316 52.381 0.00 0.00 0.00 3.71
1565 1998 2.357517 CCGTGCCTGTCACCAGTC 60.358 66.667 0.00 0.00 42.69 3.51
1587 2026 3.740397 CTGTGCGTACCCGTCCGA 61.740 66.667 0.00 0.00 36.15 4.55
1652 2103 3.527427 TCTGATCGCCGGCATCGT 61.527 61.111 28.98 8.57 33.95 3.73
1653 2104 3.032609 GTCTGATCGCCGGCATCG 61.033 66.667 28.98 20.72 0.00 3.84
1654 2105 2.106938 TGTCTGATCGCCGGCATC 59.893 61.111 28.98 25.74 0.00 3.91
1667 2118 3.324099 CTCCAGTACGCGCGTGTCT 62.324 63.158 42.78 34.10 0.00 3.41
1696 2154 5.208121 TCAGTCCATCACCATCACATAGTA 58.792 41.667 0.00 0.00 0.00 1.82
1698 2156 4.677673 TCAGTCCATCACCATCACATAG 57.322 45.455 0.00 0.00 0.00 2.23
1715 2173 9.476928 AATCAGTTACTAACTAGTACCATCAGT 57.523 33.333 0.00 0.00 40.46 3.41
1716 2174 9.737427 CAATCAGTTACTAACTAGTACCATCAG 57.263 37.037 0.00 0.00 40.46 2.90
1842 2322 8.807667 ACAACAAGAACAATCAATCAATCTTC 57.192 30.769 0.00 0.00 0.00 2.87
2015 2502 1.143073 AGTGGTTTCTGGGTGTTCCTC 59.857 52.381 0.00 0.00 36.20 3.71
2102 2589 4.895297 ACAAGGAAATTTCAGCCTCTTTGA 59.105 37.500 19.49 0.00 31.44 2.69
2146 2633 2.224079 CAGCAACAAACTAGCACACGAT 59.776 45.455 0.00 0.00 0.00 3.73
2727 3215 1.301479 GAACCGGAAGACAACGCCT 60.301 57.895 9.46 0.00 0.00 5.52
2788 3276 2.098293 GGCTACAATTGGCCAGTCG 58.902 57.895 17.82 0.00 46.84 4.18
2807 3295 0.464554 TGTGTCCATGTTGACGGCAA 60.465 50.000 0.00 0.00 38.11 4.52


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

AutoCloner maintained by Alex Coulton.