Multiple sequence alignment - TraesCS1A01G227400

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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 TraesCS1A01G227400 chr1A 100.000 3558 0 0 1 3558 398130552 398134109 0.000000e+00 6571.0
1 TraesCS1A01G227400 chr1D 93.824 2105 103 13 801 2902 317178697 317180777 0.000000e+00 3142.0
2 TraesCS1A01G227400 chr1D 84.858 667 61 15 2905 3558 317180814 317181453 1.390000e-178 636.0
3 TraesCS1A01G227400 chr1D 78.907 659 131 8 1 655 75886541 75887195 1.170000e-119 440.0
4 TraesCS1A01G227400 chr1D 73.643 258 61 5 2197 2453 317389011 317388760 3.780000e-15 93.5
5 TraesCS1A01G227400 chr1D 81.250 112 14 6 2229 2335 403337980 403337871 2.280000e-12 84.2
6 TraesCS1A01G227400 chr1B 94.244 1772 97 5 1133 2902 429275441 429277209 0.000000e+00 2702.0
7 TraesCS1A01G227400 chr1B 88.530 558 42 10 2901 3437 429277242 429277798 0.000000e+00 656.0
8 TraesCS1A01G227400 chr1B 86.927 436 26 10 718 1137 429269841 429270261 9.000000e-126 460.0
9 TraesCS1A01G227400 chr1B 86.572 283 30 3 3284 3558 429279076 429279358 4.460000e-79 305.0
10 TraesCS1A01G227400 chr1B 78.095 105 18 4 2229 2329 542761383 542761280 1.070000e-05 62.1
11 TraesCS1A01G227400 chr3D 88.280 657 72 5 1 655 64112660 64112007 0.000000e+00 782.0
12 TraesCS1A01G227400 chr3D 87.976 657 74 5 1 655 564488758 564489411 0.000000e+00 771.0
13 TraesCS1A01G227400 chr6B 87.823 657 77 3 1 655 712988445 712989100 0.000000e+00 767.0
14 TraesCS1A01G227400 chr2D 87.823 657 77 3 1 655 595412229 595412884 0.000000e+00 767.0
15 TraesCS1A01G227400 chr3B 87.082 658 80 5 1 655 700346025 700345370 0.000000e+00 739.0
16 TraesCS1A01G227400 chr3B 89.087 504 52 3 154 655 806109468 806108966 1.080000e-174 623.0
17 TraesCS1A01G227400 chr5B 79.876 646 125 5 13 655 401140411 401139768 5.380000e-128 468.0
18 TraesCS1A01G227400 chr5B 78.582 663 129 12 1 655 402728286 402728943 3.280000e-115 425.0
19 TraesCS1A01G227400 chr5D 75.566 221 52 2 2232 2451 441122881 441122662 1.350000e-19 108.0
20 TraesCS1A01G227400 chr5D 74.615 260 57 9 2195 2451 440917381 440917634 4.860000e-19 106.0
21 TraesCS1A01G227400 chr5D 76.705 176 37 4 2276 2451 441111576 441111405 1.050000e-15 95.3
22 TraesCS1A01G227400 chr5D 72.986 211 52 4 2223 2432 440902026 440902232 6.370000e-08 69.4


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 TraesCS1A01G227400 chr1A 398130552 398134109 3557 False 6571 6571 100.000 1 3558 1 chr1A.!!$F1 3557
1 TraesCS1A01G227400 chr1D 317178697 317181453 2756 False 1889 3142 89.341 801 3558 2 chr1D.!!$F2 2757
2 TraesCS1A01G227400 chr1D 75886541 75887195 654 False 440 440 78.907 1 655 1 chr1D.!!$F1 654
3 TraesCS1A01G227400 chr1B 429275441 429279358 3917 False 1221 2702 89.782 1133 3558 3 chr1B.!!$F2 2425
4 TraesCS1A01G227400 chr3D 64112007 64112660 653 True 782 782 88.280 1 655 1 chr3D.!!$R1 654
5 TraesCS1A01G227400 chr3D 564488758 564489411 653 False 771 771 87.976 1 655 1 chr3D.!!$F1 654
6 TraesCS1A01G227400 chr6B 712988445 712989100 655 False 767 767 87.823 1 655 1 chr6B.!!$F1 654
7 TraesCS1A01G227400 chr2D 595412229 595412884 655 False 767 767 87.823 1 655 1 chr2D.!!$F1 654
8 TraesCS1A01G227400 chr3B 700345370 700346025 655 True 739 739 87.082 1 655 1 chr3B.!!$R1 654
9 TraesCS1A01G227400 chr3B 806108966 806109468 502 True 623 623 89.087 154 655 1 chr3B.!!$R2 501
10 TraesCS1A01G227400 chr5B 401139768 401140411 643 True 468 468 79.876 13 655 1 chr5B.!!$R1 642
11 TraesCS1A01G227400 chr5B 402728286 402728943 657 False 425 425 78.582 1 655 1 chr5B.!!$F1 654

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
652 659 0.171231 GCTGAAAAAGACCGATGCCC 59.829 55.0 0.00 0.00 0.0 5.36 F
2031 2041 0.109086 AGAAGCTCGTCATCACGGTG 60.109 55.0 0.56 0.56 46.7 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 2057 0.032952 CCGGCGCTATAAGCTACCAA 59.967 55.0 7.64 0.0 39.60 3.67 R
3110 3157 0.523519 GTTAGCAAAGCTCACCTGGC 59.476 55.0 0.00 0.0 40.44 4.85 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
30 31 1.070758 CAGTAGTCATTCCATCCCCGG 59.929 57.143 0.00 0.00 0.00 5.73
32 33 1.415672 TAGTCATTCCATCCCCGGCC 61.416 60.000 0.00 0.00 0.00 6.13
35 36 3.501911 ATTCCATCCCCGGCCCTG 61.502 66.667 0.00 0.00 0.00 4.45
50 51 2.270205 CTGCGGATCAAGCCCTGT 59.730 61.111 9.48 0.00 0.00 4.00
74 75 1.746615 CACTTCCCTGCCGGTGATG 60.747 63.158 1.90 0.30 32.12 3.07
125 126 2.123428 GCATCCCGCCTGCAGAAAT 61.123 57.895 17.39 0.00 39.46 2.17
134 135 1.406903 CCTGCAGAAATTCCCCATCC 58.593 55.000 17.39 0.00 0.00 3.51
176 177 1.299850 ACGCGCGCATAAGCTATCA 60.300 52.632 32.58 0.00 39.10 2.15
197 198 1.406887 GGCTTCTCCATTAGTCGCCAA 60.407 52.381 0.00 0.00 39.69 4.52
215 216 2.754552 CCAAGCCTGTTTTGCTAGCATA 59.245 45.455 20.13 11.56 38.34 3.14
236 239 9.321562 AGCATAGCATCATTAAATTTTTCCAAG 57.678 29.630 0.00 0.00 0.00 3.61
373 377 6.921307 CCGTAACTTTTTGACATAAGCCTTTT 59.079 34.615 0.00 0.00 0.00 2.27
388 393 3.195396 AGCCTTTTGTGAGCTTGAAACAA 59.805 39.130 0.00 0.00 31.27 2.83
396 401 4.214119 TGTGAGCTTGAAACAACTCATAGC 59.786 41.667 14.41 0.00 40.95 2.97
427 432 1.203100 AGGGCTTGAATCACAGCCTTT 60.203 47.619 24.67 15.96 40.25 3.11
478 483 5.607939 TCAACTTCTCACAGTAACCTTGA 57.392 39.130 0.00 0.00 0.00 3.02
487 492 2.986728 ACAGTAACCTTGAACCCTGGAT 59.013 45.455 0.00 0.00 0.00 3.41
493 498 1.467920 CTTGAACCCTGGATCTTGCC 58.532 55.000 0.00 0.00 0.00 4.52
508 513 3.480470 TCTTGCCTGCTCCTTAATATGC 58.520 45.455 0.00 0.00 0.00 3.14
532 537 4.222114 CAAAGCTGTTTTCCGTGATCTTC 58.778 43.478 0.00 0.00 0.00 2.87
564 571 0.690762 GGCAACCCAGGTACTTCTCA 59.309 55.000 0.00 0.00 34.60 3.27
579 586 6.071840 GGTACTTCTCAGTCAAAGCTTCTCTA 60.072 42.308 0.00 0.00 34.06 2.43
580 587 6.412362 ACTTCTCAGTCAAAGCTTCTCTAA 57.588 37.500 0.00 0.00 0.00 2.10
606 613 9.777008 AAGATTTGTAAAATATTCCTTACCCCA 57.223 29.630 7.32 0.00 0.00 4.96
607 614 9.777008 AGATTTGTAAAATATTCCTTACCCCAA 57.223 29.630 7.32 0.92 0.00 4.12
650 657 3.702478 GGCTGAAAAAGACCGATGC 57.298 52.632 0.00 0.00 0.00 3.91
652 659 0.171231 GCTGAAAAAGACCGATGCCC 59.829 55.000 0.00 0.00 0.00 5.36
654 661 2.162681 CTGAAAAAGACCGATGCCCTT 58.837 47.619 0.00 0.00 0.00 3.95
655 662 2.159382 TGAAAAAGACCGATGCCCTTC 58.841 47.619 0.00 0.00 0.00 3.46
656 663 2.224769 TGAAAAAGACCGATGCCCTTCT 60.225 45.455 0.00 0.00 0.00 2.85
657 664 2.115343 AAAAGACCGATGCCCTTCTC 57.885 50.000 0.00 0.00 0.00 2.87
658 665 1.280457 AAAGACCGATGCCCTTCTCT 58.720 50.000 0.00 0.00 0.00 3.10
659 666 0.827368 AAGACCGATGCCCTTCTCTC 59.173 55.000 0.00 0.00 0.00 3.20
660 667 0.324738 AGACCGATGCCCTTCTCTCA 60.325 55.000 0.00 0.00 0.00 3.27
661 668 0.755686 GACCGATGCCCTTCTCTCAT 59.244 55.000 0.00 0.00 0.00 2.90
662 669 0.755686 ACCGATGCCCTTCTCTCATC 59.244 55.000 0.00 0.00 34.74 2.92
663 670 1.047002 CCGATGCCCTTCTCTCATCT 58.953 55.000 0.00 0.00 35.64 2.90
664 671 2.242926 CCGATGCCCTTCTCTCATCTA 58.757 52.381 0.00 0.00 35.64 1.98
665 672 2.630098 CCGATGCCCTTCTCTCATCTAA 59.370 50.000 0.00 0.00 35.64 2.10
666 673 3.070159 CCGATGCCCTTCTCTCATCTAAA 59.930 47.826 0.00 0.00 35.64 1.85
667 674 4.443457 CCGATGCCCTTCTCTCATCTAAAA 60.443 45.833 0.00 0.00 35.64 1.52
668 675 5.118990 CGATGCCCTTCTCTCATCTAAAAA 58.881 41.667 0.00 0.00 35.64 1.94
708 715 5.766150 TTTTGAGACAACACACCCTTATG 57.234 39.130 0.00 0.00 0.00 1.90
709 716 4.431416 TTGAGACAACACACCCTTATGT 57.569 40.909 0.00 0.00 0.00 2.29
710 717 4.002906 TGAGACAACACACCCTTATGTC 57.997 45.455 0.00 0.00 40.45 3.06
711 718 3.244422 TGAGACAACACACCCTTATGTCC 60.244 47.826 0.00 0.00 40.92 4.02
712 719 2.073816 GACAACACACCCTTATGTCCG 58.926 52.381 0.00 0.00 35.51 4.79
713 720 1.271163 ACAACACACCCTTATGTCCGG 60.271 52.381 0.00 0.00 0.00 5.14
714 721 0.322187 AACACACCCTTATGTCCGGC 60.322 55.000 0.00 0.00 0.00 6.13
715 722 1.451387 CACACCCTTATGTCCGGCC 60.451 63.158 0.00 0.00 0.00 6.13
716 723 1.921346 ACACCCTTATGTCCGGCCA 60.921 57.895 2.24 0.00 0.00 5.36
717 724 1.451387 CACCCTTATGTCCGGCCAC 60.451 63.158 2.24 0.00 0.00 5.01
718 725 2.203015 CCCTTATGTCCGGCCACG 60.203 66.667 2.24 0.00 40.55 4.94
730 737 4.123545 GCCACGGCCCACCCTATT 62.124 66.667 0.00 0.00 34.56 1.73
731 738 2.124320 CCACGGCCCACCCTATTG 60.124 66.667 0.00 0.00 0.00 1.90
732 739 2.674754 CACGGCCCACCCTATTGT 59.325 61.111 0.00 0.00 0.00 2.71
733 740 1.451387 CACGGCCCACCCTATTGTC 60.451 63.158 0.00 0.00 0.00 3.18
734 741 2.203015 CGGCCCACCCTATTGTCG 60.203 66.667 0.00 0.00 0.00 4.35
735 742 2.516225 GGCCCACCCTATTGTCGC 60.516 66.667 0.00 0.00 0.00 5.19
736 743 2.590092 GCCCACCCTATTGTCGCT 59.410 61.111 0.00 0.00 0.00 4.93
737 744 1.819632 GCCCACCCTATTGTCGCTG 60.820 63.158 0.00 0.00 0.00 5.18
738 745 1.819632 CCCACCCTATTGTCGCTGC 60.820 63.158 0.00 0.00 0.00 5.25
739 746 1.078497 CCACCCTATTGTCGCTGCA 60.078 57.895 0.00 0.00 0.00 4.41
740 747 0.464373 CCACCCTATTGTCGCTGCAT 60.464 55.000 0.00 0.00 0.00 3.96
741 748 1.382522 CACCCTATTGTCGCTGCATT 58.617 50.000 0.00 0.00 0.00 3.56
742 749 1.331756 CACCCTATTGTCGCTGCATTC 59.668 52.381 0.00 0.00 0.00 2.67
743 750 1.065491 ACCCTATTGTCGCTGCATTCA 60.065 47.619 0.00 0.00 0.00 2.57
744 751 1.331756 CCCTATTGTCGCTGCATTCAC 59.668 52.381 0.00 0.00 0.00 3.18
745 752 2.283298 CCTATTGTCGCTGCATTCACT 58.717 47.619 0.00 0.00 0.00 3.41
746 753 2.679837 CCTATTGTCGCTGCATTCACTT 59.320 45.455 0.00 0.00 0.00 3.16
747 754 3.871006 CCTATTGTCGCTGCATTCACTTA 59.129 43.478 0.00 0.00 0.00 2.24
748 755 3.747099 ATTGTCGCTGCATTCACTTAC 57.253 42.857 0.00 0.00 0.00 2.34
749 756 2.162319 TGTCGCTGCATTCACTTACA 57.838 45.000 0.00 0.00 0.00 2.41
750 757 2.488952 TGTCGCTGCATTCACTTACAA 58.511 42.857 0.00 0.00 0.00 2.41
751 758 3.073678 TGTCGCTGCATTCACTTACAAT 58.926 40.909 0.00 0.00 0.00 2.71
752 759 3.125146 TGTCGCTGCATTCACTTACAATC 59.875 43.478 0.00 0.00 0.00 2.67
753 760 3.372206 GTCGCTGCATTCACTTACAATCT 59.628 43.478 0.00 0.00 0.00 2.40
754 761 3.371898 TCGCTGCATTCACTTACAATCTG 59.628 43.478 0.00 0.00 0.00 2.90
755 762 3.486375 CGCTGCATTCACTTACAATCTGG 60.486 47.826 0.00 0.00 0.00 3.86
756 763 3.181493 GCTGCATTCACTTACAATCTGGG 60.181 47.826 0.00 0.00 0.00 4.45
757 764 2.754552 TGCATTCACTTACAATCTGGGC 59.245 45.455 0.00 0.00 0.00 5.36
758 765 2.099756 GCATTCACTTACAATCTGGGCC 59.900 50.000 0.00 0.00 0.00 5.80
759 766 3.624777 CATTCACTTACAATCTGGGCCT 58.375 45.455 4.53 0.00 0.00 5.19
760 767 2.787473 TCACTTACAATCTGGGCCTG 57.213 50.000 4.53 4.06 0.00 4.85
761 768 2.265367 TCACTTACAATCTGGGCCTGA 58.735 47.619 15.94 15.94 0.00 3.86
762 769 2.642311 TCACTTACAATCTGGGCCTGAA 59.358 45.455 17.53 0.00 0.00 3.02
763 770 3.266772 TCACTTACAATCTGGGCCTGAAT 59.733 43.478 17.53 6.15 0.00 2.57
764 771 3.629398 CACTTACAATCTGGGCCTGAATC 59.371 47.826 17.53 0.00 0.00 2.52
765 772 3.217626 CTTACAATCTGGGCCTGAATCC 58.782 50.000 17.53 0.00 0.00 3.01
766 773 1.302907 ACAATCTGGGCCTGAATCCT 58.697 50.000 17.53 0.00 0.00 3.24
767 774 1.642762 ACAATCTGGGCCTGAATCCTT 59.357 47.619 17.53 4.23 0.00 3.36
768 775 2.305009 CAATCTGGGCCTGAATCCTTC 58.695 52.381 17.53 0.00 0.00 3.46
769 776 1.904440 ATCTGGGCCTGAATCCTTCT 58.096 50.000 17.53 0.00 0.00 2.85
770 777 1.673767 TCTGGGCCTGAATCCTTCTT 58.326 50.000 11.07 0.00 0.00 2.52
771 778 2.845659 TCTGGGCCTGAATCCTTCTTA 58.154 47.619 11.07 0.00 0.00 2.10
772 779 3.397527 TCTGGGCCTGAATCCTTCTTAT 58.602 45.455 11.07 0.00 0.00 1.73
773 780 3.392616 TCTGGGCCTGAATCCTTCTTATC 59.607 47.826 11.07 0.00 0.00 1.75
774 781 3.122480 TGGGCCTGAATCCTTCTTATCA 58.878 45.455 4.53 0.00 0.00 2.15
775 782 3.137176 TGGGCCTGAATCCTTCTTATCAG 59.863 47.826 4.53 0.00 39.16 2.90
776 783 3.137360 GGGCCTGAATCCTTCTTATCAGT 59.863 47.826 0.84 0.00 38.06 3.41
777 784 4.348168 GGGCCTGAATCCTTCTTATCAGTA 59.652 45.833 0.84 0.00 38.06 2.74
778 785 5.163195 GGGCCTGAATCCTTCTTATCAGTAA 60.163 44.000 0.84 0.00 38.06 2.24
779 786 5.994668 GGCCTGAATCCTTCTTATCAGTAAG 59.005 44.000 0.00 0.00 38.06 2.34
780 787 5.468409 GCCTGAATCCTTCTTATCAGTAAGC 59.532 44.000 0.00 0.00 38.06 3.09
781 788 5.994668 CCTGAATCCTTCTTATCAGTAAGCC 59.005 44.000 0.00 0.00 38.06 4.35
782 789 6.408548 CCTGAATCCTTCTTATCAGTAAGCCA 60.409 42.308 0.00 0.00 38.06 4.75
783 790 6.586344 TGAATCCTTCTTATCAGTAAGCCAG 58.414 40.000 0.00 0.00 37.75 4.85
784 791 6.384015 TGAATCCTTCTTATCAGTAAGCCAGA 59.616 38.462 0.00 0.00 37.75 3.86
785 792 5.860941 TCCTTCTTATCAGTAAGCCAGAG 57.139 43.478 0.00 0.00 37.75 3.35
786 793 4.100189 TCCTTCTTATCAGTAAGCCAGAGC 59.900 45.833 0.00 0.00 37.75 4.09
787 794 4.376146 CTTCTTATCAGTAAGCCAGAGCC 58.624 47.826 0.00 0.00 41.25 4.70
788 795 3.647636 TCTTATCAGTAAGCCAGAGCCT 58.352 45.455 0.00 0.00 41.25 4.58
789 796 4.033709 TCTTATCAGTAAGCCAGAGCCTT 58.966 43.478 0.00 0.00 41.25 4.35
790 797 4.471386 TCTTATCAGTAAGCCAGAGCCTTT 59.529 41.667 0.00 0.00 41.25 3.11
791 798 2.479566 TCAGTAAGCCAGAGCCTTTG 57.520 50.000 0.00 0.00 41.25 2.77
792 799 1.699634 TCAGTAAGCCAGAGCCTTTGT 59.300 47.619 0.00 0.00 41.25 2.83
793 800 2.079925 CAGTAAGCCAGAGCCTTTGTC 58.920 52.381 0.00 0.00 41.25 3.18
794 801 1.981495 AGTAAGCCAGAGCCTTTGTCT 59.019 47.619 0.00 0.00 41.25 3.41
795 802 3.055819 CAGTAAGCCAGAGCCTTTGTCTA 60.056 47.826 0.00 0.00 41.25 2.59
796 803 3.583086 AGTAAGCCAGAGCCTTTGTCTAA 59.417 43.478 0.00 0.00 41.25 2.10
797 804 3.508845 AAGCCAGAGCCTTTGTCTAAA 57.491 42.857 0.00 0.00 41.25 1.85
798 805 3.508845 AGCCAGAGCCTTTGTCTAAAA 57.491 42.857 0.00 0.00 41.25 1.52
799 806 3.416156 AGCCAGAGCCTTTGTCTAAAAG 58.584 45.455 0.00 0.00 41.25 2.27
800 807 3.073062 AGCCAGAGCCTTTGTCTAAAAGA 59.927 43.478 0.00 0.00 41.25 2.52
801 808 3.821033 GCCAGAGCCTTTGTCTAAAAGAA 59.179 43.478 0.00 0.00 0.00 2.52
802 809 4.460731 GCCAGAGCCTTTGTCTAAAAGAAT 59.539 41.667 0.00 0.00 0.00 2.40
834 841 2.674380 GGAGTTGTGGCCCAGCAG 60.674 66.667 0.00 0.00 0.00 4.24
903 912 1.048601 AACCCACTCGCAGAAAGAGA 58.951 50.000 0.00 0.00 38.97 3.10
911 920 2.999355 CTCGCAGAAAGAGAGGGAAAAG 59.001 50.000 0.00 0.00 40.11 2.27
912 921 2.079925 CGCAGAAAGAGAGGGAAAAGG 58.920 52.381 0.00 0.00 0.00 3.11
914 923 2.224892 GCAGAAAGAGAGGGAAAAGGGT 60.225 50.000 0.00 0.00 0.00 4.34
915 924 3.416156 CAGAAAGAGAGGGAAAAGGGTG 58.584 50.000 0.00 0.00 0.00 4.61
916 925 3.073062 CAGAAAGAGAGGGAAAAGGGTGA 59.927 47.826 0.00 0.00 0.00 4.02
964 974 4.102113 CCCCCAAAACTCCAGCAG 57.898 61.111 0.00 0.00 0.00 4.24
965 975 2.278330 CCCCCAAAACTCCAGCAGC 61.278 63.158 0.00 0.00 0.00 5.25
966 976 2.629656 CCCCAAAACTCCAGCAGCG 61.630 63.158 0.00 0.00 0.00 5.18
967 977 1.600636 CCCAAAACTCCAGCAGCGA 60.601 57.895 0.00 0.00 0.00 4.93
968 978 1.576421 CCAAAACTCCAGCAGCGAC 59.424 57.895 0.00 0.00 0.00 5.19
969 979 1.205064 CAAAACTCCAGCAGCGACG 59.795 57.895 0.00 0.00 0.00 5.12
1087 1097 1.144936 CCCGACAGCATTCTCTCCC 59.855 63.158 0.00 0.00 0.00 4.30
1107 1117 4.176752 GTCATCACCCGCCTCCCC 62.177 72.222 0.00 0.00 0.00 4.81
1108 1118 4.731853 TCATCACCCGCCTCCCCA 62.732 66.667 0.00 0.00 0.00 4.96
1109 1119 4.489771 CATCACCCGCCTCCCCAC 62.490 72.222 0.00 0.00 0.00 4.61
1451 1461 4.778143 CTGCCGTTTCCCCGAGGG 62.778 72.222 0.00 0.00 46.11 4.30
1470 1480 4.157120 ATTTCCCCGACCCTCGCG 62.157 66.667 0.00 0.00 38.82 5.87
1620 1630 1.297967 CATCGACTCGCCGACTCTG 60.298 63.158 0.00 0.00 41.70 3.35
1719 1729 8.929827 TGATTGCATTTGATAATTTCGACATT 57.070 26.923 1.90 1.90 0.00 2.71
1759 1769 1.610522 GACTGCAGATGGTGTGCTTTT 59.389 47.619 23.35 0.00 41.78 2.27
1826 1836 3.618997 CGGGTAACTACTGCCTTCATTGT 60.619 47.826 0.00 0.00 0.00 2.71
1831 1841 6.092259 GGTAACTACTGCCTTCATTGTAACAG 59.908 42.308 0.00 0.00 0.00 3.16
1839 1849 6.000840 TGCCTTCATTGTAACAGTCACATTA 58.999 36.000 0.00 0.00 0.00 1.90
1850 1860 8.154203 TGTAACAGTCACATTAATTTCTCAGGA 58.846 33.333 0.00 0.00 0.00 3.86
1921 1931 0.392336 TGGTGGAAACTTGGCAATGC 59.608 50.000 0.00 0.00 0.00 3.56
2031 2041 0.109086 AGAAGCTCGTCATCACGGTG 60.109 55.000 0.56 0.56 46.70 4.94
2033 2043 0.532573 AAGCTCGTCATCACGGTGAT 59.467 50.000 17.62 17.62 46.70 3.06
2040 2050 2.600420 CGTCATCACGGTGATTCTCTTG 59.400 50.000 20.52 10.47 42.73 3.02
2043 2053 4.505922 GTCATCACGGTGATTCTCTTGATC 59.494 45.833 20.52 7.25 34.28 2.92
2047 2057 5.551233 TCACGGTGATTCTCTTGATCTTTT 58.449 37.500 6.76 0.00 0.00 2.27
2048 2058 5.997746 TCACGGTGATTCTCTTGATCTTTTT 59.002 36.000 6.76 0.00 0.00 1.94
2057 2067 9.167311 GATTCTCTTGATCTTTTTGGTAGCTTA 57.833 33.333 0.00 0.00 0.00 3.09
2088 2098 6.202954 CCGGATAAACTCCATTCAGTTCATAC 59.797 42.308 0.00 0.00 45.24 2.39
2091 2101 7.280205 GGATAAACTCCATTCAGTTCATACGTT 59.720 37.037 0.00 0.00 44.26 3.99
2099 2109 6.128822 CCATTCAGTTCATACGTTATCCATCG 60.129 42.308 0.00 0.00 0.00 3.84
2100 2110 4.866921 TCAGTTCATACGTTATCCATCGG 58.133 43.478 0.00 0.00 0.00 4.18
2251 2261 4.263018 TGAATGTCTTGACCTCAGTCTG 57.737 45.455 0.00 0.00 43.91 3.51
2464 2474 4.222124 TGAGTTTGGAGAAGCTTATCCC 57.778 45.455 31.90 19.34 37.77 3.85
2542 2552 0.796927 GTACCTCTTGCGGAGTTTGC 59.203 55.000 5.91 0.00 40.30 3.68
2561 2571 2.221169 GCGGGCATACTGATTGATGAA 58.779 47.619 0.00 0.00 0.00 2.57
2579 2589 4.280436 TGAAATCACCCTTCACGTGTAT 57.720 40.909 16.51 0.00 32.86 2.29
2601 2611 8.015087 TGTATTTCGAACTTTTTCTGTATGCAG 58.985 33.333 4.14 4.14 43.87 4.41
2694 2705 7.451566 ACAACCTCATCAGGCTACTTTAATTTT 59.548 33.333 0.00 0.00 45.05 1.82
2797 2808 2.507484 TGAATGTGGTTCTGCTTCAGG 58.493 47.619 0.00 0.00 37.72 3.86
2798 2809 1.815003 GAATGTGGTTCTGCTTCAGGG 59.185 52.381 0.00 0.00 33.89 4.45
2888 2899 8.034804 GGATAATATGGTTTGCTGAAACAGTTT 58.965 33.333 0.00 0.00 42.95 2.66
2902 2913 1.134175 ACAGTTTGGGCTGTTTGTTCG 59.866 47.619 0.00 0.00 46.45 3.95
2903 2914 0.744281 AGTTTGGGCTGTTTGTTCGG 59.256 50.000 0.00 0.00 0.00 4.30
2915 2961 3.886505 TGTTTGTTCGGGCTTTTATCAGT 59.113 39.130 0.00 0.00 0.00 3.41
2920 2966 4.464951 TGTTCGGGCTTTTATCAGTAGAGA 59.535 41.667 0.00 0.00 0.00 3.10
2932 2978 5.869753 ATCAGTAGAGATGTGTGCAAAAC 57.130 39.130 0.00 0.00 0.00 2.43
2935 2981 4.684242 CAGTAGAGATGTGTGCAAAACGTA 59.316 41.667 0.00 0.00 0.00 3.57
2955 3001 6.582206 CGTAAAACACGTTTCATCATTCAG 57.418 37.500 0.00 0.00 45.82 3.02
3094 3141 6.868622 ACTTCCATAGTAGAGATGTTGTCAC 58.131 40.000 0.00 0.00 34.56 3.67
3110 3157 5.723672 TTGTCACTCAACCTTAGGAGTAG 57.276 43.478 4.77 1.06 42.22 2.57
3177 3224 5.067153 TGCAATCCAAATATTCGTAAGGGTG 59.933 40.000 0.00 0.00 38.47 4.61
3180 3227 4.787551 TCCAAATATTCGTAAGGGTGCAT 58.212 39.130 0.00 0.00 38.47 3.96
3238 3285 4.414852 CGTGAGCCATTGGATTTGTTAAG 58.585 43.478 6.95 0.00 0.00 1.85
3239 3286 4.176271 GTGAGCCATTGGATTTGTTAAGC 58.824 43.478 6.95 0.00 0.00 3.09
3240 3287 3.831333 TGAGCCATTGGATTTGTTAAGCA 59.169 39.130 6.95 0.00 0.00 3.91
3241 3288 4.282957 TGAGCCATTGGATTTGTTAAGCAA 59.717 37.500 6.95 0.00 34.87 3.91
3261 3319 1.632409 ACTCTGATGTGGTGAAGGCAT 59.368 47.619 0.00 0.00 0.00 4.40
3264 3322 0.251253 TGATGTGGTGAAGGCATGCA 60.251 50.000 21.36 0.00 0.00 3.96
3304 4829 6.250819 CAATCGTTGAATAACATCAGACACC 58.749 40.000 0.00 0.00 36.58 4.16
3305 4830 5.147330 TCGTTGAATAACATCAGACACCT 57.853 39.130 0.00 0.00 36.58 4.00
3306 4831 5.547465 TCGTTGAATAACATCAGACACCTT 58.453 37.500 0.00 0.00 36.58 3.50
3307 4832 5.995282 TCGTTGAATAACATCAGACACCTTT 59.005 36.000 0.00 0.00 36.58 3.11
3308 4833 6.485313 TCGTTGAATAACATCAGACACCTTTT 59.515 34.615 0.00 0.00 36.58 2.27
3309 4834 7.012894 TCGTTGAATAACATCAGACACCTTTTT 59.987 33.333 0.00 0.00 36.58 1.94
3378 4906 8.755696 ATAACATGTGCAATTACGACAATTTT 57.244 26.923 0.00 0.00 0.00 1.82
3414 4942 2.162208 CGAGTATTTTGCAGCACACCAT 59.838 45.455 0.00 0.00 0.00 3.55
3443 4973 6.816134 TTGCAACACAATGTCTGTATGTAT 57.184 33.333 0.00 0.00 36.10 2.29
3452 4982 8.071967 CACAATGTCTGTATGTATGCAATAAGG 58.928 37.037 0.00 0.00 36.10 2.69
3457 4987 9.407380 TGTCTGTATGTATGCAATAAGGAAATT 57.593 29.630 0.00 0.00 0.00 1.82
3461 4991 9.800433 TGTATGTATGCAATAAGGAAATTTGTG 57.200 29.630 0.00 0.00 0.00 3.33
3469 4999 2.138596 AGGAAATTTGTGTGCTTGCG 57.861 45.000 0.00 0.00 0.00 4.85
3536 5066 2.693797 ATCTCGCAGCAACAAAGTTG 57.306 45.000 5.56 5.56 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.424638 CCGGGGATGGAATGACTACT 58.575 55.000 0.00 0.00 0.00 2.57
35 36 1.401905 CTTAAACAGGGCTTGATCCGC 59.598 52.381 2.65 0.00 0.00 5.54
44 45 0.888619 GGGAAGTGCTTAAACAGGGC 59.111 55.000 0.00 0.00 0.00 5.19
50 51 0.608035 CCGGCAGGGAAGTGCTTAAA 60.608 55.000 0.00 0.00 43.45 1.52
152 153 2.860628 CTTATGCGCGCGTGTCCTC 61.861 63.158 34.70 14.02 0.00 3.71
176 177 0.466124 GGCGACTAATGGAGAAGCCT 59.534 55.000 0.00 0.00 43.27 4.58
188 189 1.234821 CAAAACAGGCTTGGCGACTA 58.765 50.000 0.00 0.00 0.00 2.59
215 216 7.329226 CGTGACTTGGAAAAATTTAATGATGCT 59.671 33.333 0.00 0.00 0.00 3.79
224 225 5.989168 GGGATTTCGTGACTTGGAAAAATTT 59.011 36.000 0.00 0.00 35.93 1.82
227 228 3.954904 TGGGATTTCGTGACTTGGAAAAA 59.045 39.130 0.00 0.00 35.93 1.94
236 239 0.744771 GAGGCCTGGGATTTCGTGAC 60.745 60.000 12.00 0.00 0.00 3.67
373 377 4.214119 GCTATGAGTTGTTTCAAGCTCACA 59.786 41.667 12.80 5.55 40.24 3.58
388 393 2.171840 CTACCGGCCTATGCTATGAGT 58.828 52.381 0.00 0.00 37.74 3.41
427 432 1.406887 GCGGCAAGGATGGTTCTTCTA 60.407 52.381 0.00 0.00 0.00 2.10
478 483 1.000396 GCAGGCAAGATCCAGGGTT 60.000 57.895 0.00 0.00 0.00 4.11
487 492 3.117926 TGCATATTAAGGAGCAGGCAAGA 60.118 43.478 0.00 0.00 32.48 3.02
493 498 4.337555 AGCTTTGTGCATATTAAGGAGCAG 59.662 41.667 0.00 0.00 45.94 4.24
508 513 2.842208 TCACGGAAAACAGCTTTGTG 57.158 45.000 0.00 0.00 0.00 3.33
564 571 9.561069 TTACAAATCTTTAGAGAAGCTTTGACT 57.439 29.630 17.05 3.38 34.93 3.41
580 587 9.777008 TGGGGTAAGGAATATTTTACAAATCTT 57.223 29.630 10.67 0.00 32.68 2.40
685 692 5.654650 ACATAAGGGTGTGTTGTCTCAAAAA 59.345 36.000 0.00 0.00 0.00 1.94
686 693 5.197451 ACATAAGGGTGTGTTGTCTCAAAA 58.803 37.500 0.00 0.00 0.00 2.44
687 694 4.787551 ACATAAGGGTGTGTTGTCTCAAA 58.212 39.130 0.00 0.00 0.00 2.69
688 695 4.385825 GACATAAGGGTGTGTTGTCTCAA 58.614 43.478 0.00 0.00 35.09 3.02
689 696 3.244422 GGACATAAGGGTGTGTTGTCTCA 60.244 47.826 0.00 0.00 37.45 3.27
690 697 3.335579 GGACATAAGGGTGTGTTGTCTC 58.664 50.000 0.00 0.00 37.45 3.36
691 698 2.289444 CGGACATAAGGGTGTGTTGTCT 60.289 50.000 0.00 0.00 37.45 3.41
692 699 2.073816 CGGACATAAGGGTGTGTTGTC 58.926 52.381 0.00 0.00 36.76 3.18
693 700 1.271163 CCGGACATAAGGGTGTGTTGT 60.271 52.381 0.00 0.00 31.16 3.32
694 701 1.448985 CCGGACATAAGGGTGTGTTG 58.551 55.000 0.00 0.00 31.16 3.33
695 702 0.322187 GCCGGACATAAGGGTGTGTT 60.322 55.000 5.05 0.00 31.16 3.32
696 703 1.298667 GCCGGACATAAGGGTGTGT 59.701 57.895 5.05 0.00 31.16 3.72
697 704 1.451387 GGCCGGACATAAGGGTGTG 60.451 63.158 5.05 0.00 31.16 3.82
698 705 1.921346 TGGCCGGACATAAGGGTGT 60.921 57.895 5.41 0.00 34.39 4.16
699 706 1.451387 GTGGCCGGACATAAGGGTG 60.451 63.158 16.47 0.00 0.00 4.61
700 707 2.995547 GTGGCCGGACATAAGGGT 59.004 61.111 16.47 0.00 0.00 4.34
701 708 2.203015 CGTGGCCGGACATAAGGG 60.203 66.667 16.47 0.00 0.00 3.95
713 720 4.123545 AATAGGGTGGGCCGTGGC 62.124 66.667 1.16 1.16 41.06 5.01
714 721 2.124320 CAATAGGGTGGGCCGTGG 60.124 66.667 0.00 0.00 34.32 4.94
715 722 1.451387 GACAATAGGGTGGGCCGTG 60.451 63.158 0.00 0.00 34.32 4.94
716 723 2.995547 GACAATAGGGTGGGCCGT 59.004 61.111 0.00 0.00 36.71 5.68
717 724 2.203015 CGACAATAGGGTGGGCCG 60.203 66.667 0.00 0.00 34.97 6.13
718 725 2.516225 GCGACAATAGGGTGGGCC 60.516 66.667 0.00 0.00 0.00 5.80
719 726 1.819632 CAGCGACAATAGGGTGGGC 60.820 63.158 0.00 0.00 0.00 5.36
720 727 1.819632 GCAGCGACAATAGGGTGGG 60.820 63.158 0.00 0.00 32.53 4.61
721 728 0.464373 ATGCAGCGACAATAGGGTGG 60.464 55.000 0.00 0.00 32.53 4.61
722 729 1.331756 GAATGCAGCGACAATAGGGTG 59.668 52.381 0.00 0.00 34.90 4.61
723 730 1.065491 TGAATGCAGCGACAATAGGGT 60.065 47.619 0.00 0.00 0.00 4.34
724 731 1.331756 GTGAATGCAGCGACAATAGGG 59.668 52.381 0.00 0.00 0.00 3.53
725 732 2.283298 AGTGAATGCAGCGACAATAGG 58.717 47.619 0.00 0.00 0.00 2.57
726 733 4.329801 TGTAAGTGAATGCAGCGACAATAG 59.670 41.667 0.00 0.00 0.00 1.73
727 734 4.249661 TGTAAGTGAATGCAGCGACAATA 58.750 39.130 0.00 0.00 0.00 1.90
728 735 3.073678 TGTAAGTGAATGCAGCGACAAT 58.926 40.909 0.00 0.00 0.00 2.71
729 736 2.488952 TGTAAGTGAATGCAGCGACAA 58.511 42.857 0.00 0.00 0.00 3.18
730 737 2.162319 TGTAAGTGAATGCAGCGACA 57.838 45.000 0.00 0.00 0.00 4.35
731 738 3.372206 AGATTGTAAGTGAATGCAGCGAC 59.628 43.478 0.00 0.00 0.00 5.19
732 739 3.371898 CAGATTGTAAGTGAATGCAGCGA 59.628 43.478 0.00 0.00 0.00 4.93
733 740 3.486375 CCAGATTGTAAGTGAATGCAGCG 60.486 47.826 0.00 0.00 0.00 5.18
734 741 3.181493 CCCAGATTGTAAGTGAATGCAGC 60.181 47.826 0.00 0.00 0.00 5.25
735 742 3.181493 GCCCAGATTGTAAGTGAATGCAG 60.181 47.826 0.00 0.00 0.00 4.41
736 743 2.754552 GCCCAGATTGTAAGTGAATGCA 59.245 45.455 0.00 0.00 0.00 3.96
737 744 2.099756 GGCCCAGATTGTAAGTGAATGC 59.900 50.000 0.00 0.00 0.00 3.56
738 745 3.379372 CAGGCCCAGATTGTAAGTGAATG 59.621 47.826 0.00 0.00 0.00 2.67
739 746 3.266772 TCAGGCCCAGATTGTAAGTGAAT 59.733 43.478 0.00 0.00 0.00 2.57
740 747 2.642311 TCAGGCCCAGATTGTAAGTGAA 59.358 45.455 0.00 0.00 0.00 3.18
741 748 2.265367 TCAGGCCCAGATTGTAAGTGA 58.735 47.619 0.00 0.00 0.00 3.41
742 749 2.787473 TCAGGCCCAGATTGTAAGTG 57.213 50.000 0.00 0.00 0.00 3.16
743 750 3.372025 GGATTCAGGCCCAGATTGTAAGT 60.372 47.826 0.00 0.00 0.00 2.24
744 751 3.117738 AGGATTCAGGCCCAGATTGTAAG 60.118 47.826 0.00 0.00 0.00 2.34
745 752 2.852449 AGGATTCAGGCCCAGATTGTAA 59.148 45.455 0.00 0.00 0.00 2.41
746 753 2.492025 AGGATTCAGGCCCAGATTGTA 58.508 47.619 0.00 0.00 0.00 2.41
747 754 1.302907 AGGATTCAGGCCCAGATTGT 58.697 50.000 0.00 0.00 0.00 2.71
748 755 2.305009 GAAGGATTCAGGCCCAGATTG 58.695 52.381 0.00 0.00 46.62 2.67
749 756 2.744352 GAAGGATTCAGGCCCAGATT 57.256 50.000 0.00 0.00 46.62 2.40
760 767 8.429008 GCTCTGGCTTACTGATAAGAAGGATTC 61.429 44.444 0.00 0.00 40.38 2.52
761 768 6.687647 GCTCTGGCTTACTGATAAGAAGGATT 60.688 42.308 0.00 0.00 40.38 3.01
762 769 5.221621 GCTCTGGCTTACTGATAAGAAGGAT 60.222 44.000 0.00 0.00 40.38 3.24
763 770 4.100189 GCTCTGGCTTACTGATAAGAAGGA 59.900 45.833 0.00 0.00 40.38 3.36
764 771 4.376146 GCTCTGGCTTACTGATAAGAAGG 58.624 47.826 0.00 0.00 40.38 3.46
765 772 4.100808 AGGCTCTGGCTTACTGATAAGAAG 59.899 45.833 0.00 0.00 40.38 2.85
766 773 4.033709 AGGCTCTGGCTTACTGATAAGAA 58.966 43.478 0.00 0.00 40.38 2.52
767 774 3.647636 AGGCTCTGGCTTACTGATAAGA 58.352 45.455 0.00 0.00 40.38 2.10
768 775 4.414337 AAGGCTCTGGCTTACTGATAAG 57.586 45.455 4.55 0.00 46.45 1.73
778 785 3.073062 TCTTTTAGACAAAGGCTCTGGCT 59.927 43.478 0.00 0.00 41.24 4.75
779 786 3.412386 TCTTTTAGACAAAGGCTCTGGC 58.588 45.455 0.00 0.00 37.82 4.85
780 787 5.707298 TGATTCTTTTAGACAAAGGCTCTGG 59.293 40.000 0.00 0.00 0.00 3.86
781 788 6.808008 TGATTCTTTTAGACAAAGGCTCTG 57.192 37.500 0.00 0.00 0.00 3.35
782 789 8.302438 CAATTGATTCTTTTAGACAAAGGCTCT 58.698 33.333 0.00 0.00 0.00 4.09
783 790 7.543520 CCAATTGATTCTTTTAGACAAAGGCTC 59.456 37.037 7.12 0.00 0.00 4.70
784 791 7.233348 TCCAATTGATTCTTTTAGACAAAGGCT 59.767 33.333 7.12 0.00 0.00 4.58
785 792 7.378181 TCCAATTGATTCTTTTAGACAAAGGC 58.622 34.615 7.12 0.00 0.00 4.35
786 793 8.031277 CCTCCAATTGATTCTTTTAGACAAAGG 58.969 37.037 7.12 0.00 0.00 3.11
787 794 7.543520 GCCTCCAATTGATTCTTTTAGACAAAG 59.456 37.037 7.12 0.00 0.00 2.77
788 795 7.378181 GCCTCCAATTGATTCTTTTAGACAAA 58.622 34.615 7.12 0.00 0.00 2.83
789 796 6.071391 GGCCTCCAATTGATTCTTTTAGACAA 60.071 38.462 7.12 0.00 0.00 3.18
790 797 5.418840 GGCCTCCAATTGATTCTTTTAGACA 59.581 40.000 7.12 0.00 0.00 3.41
791 798 5.654209 AGGCCTCCAATTGATTCTTTTAGAC 59.346 40.000 7.12 0.00 0.00 2.59
792 799 5.831103 AGGCCTCCAATTGATTCTTTTAGA 58.169 37.500 7.12 0.00 0.00 2.10
793 800 6.335777 CAAGGCCTCCAATTGATTCTTTTAG 58.664 40.000 5.23 0.00 0.00 1.85
794 801 5.187576 CCAAGGCCTCCAATTGATTCTTTTA 59.812 40.000 5.23 0.00 0.00 1.52
795 802 4.019950 CCAAGGCCTCCAATTGATTCTTTT 60.020 41.667 5.23 0.00 0.00 2.27
796 803 3.516700 CCAAGGCCTCCAATTGATTCTTT 59.483 43.478 5.23 0.00 0.00 2.52
797 804 3.102204 CCAAGGCCTCCAATTGATTCTT 58.898 45.455 5.23 0.86 0.00 2.52
798 805 2.312741 TCCAAGGCCTCCAATTGATTCT 59.687 45.455 5.23 0.00 0.00 2.40
799 806 2.692041 CTCCAAGGCCTCCAATTGATTC 59.308 50.000 5.23 0.00 0.00 2.52
800 807 2.043526 ACTCCAAGGCCTCCAATTGATT 59.956 45.455 5.23 0.00 0.00 2.57
801 808 1.642762 ACTCCAAGGCCTCCAATTGAT 59.357 47.619 5.23 0.00 0.00 2.57
802 809 1.075601 ACTCCAAGGCCTCCAATTGA 58.924 50.000 5.23 0.00 0.00 2.57
862 869 1.415659 CCGGAGAATGAGAATCTGGCT 59.584 52.381 0.00 0.00 32.91 4.75
863 870 1.414181 TCCGGAGAATGAGAATCTGGC 59.586 52.381 0.00 0.00 39.04 4.85
865 872 3.873952 GGTTTCCGGAGAATGAGAATCTG 59.126 47.826 3.34 0.00 34.92 2.90
866 873 3.118223 GGGTTTCCGGAGAATGAGAATCT 60.118 47.826 3.34 0.00 34.92 2.40
867 874 3.206964 GGGTTTCCGGAGAATGAGAATC 58.793 50.000 3.34 0.00 0.00 2.52
868 875 2.576191 TGGGTTTCCGGAGAATGAGAAT 59.424 45.455 3.34 0.00 35.24 2.40
869 876 1.982226 TGGGTTTCCGGAGAATGAGAA 59.018 47.619 3.34 0.00 35.24 2.87
870 877 1.278127 GTGGGTTTCCGGAGAATGAGA 59.722 52.381 3.34 0.00 35.24 3.27
871 878 1.279271 AGTGGGTTTCCGGAGAATGAG 59.721 52.381 3.34 0.00 35.24 2.90
872 879 1.278127 GAGTGGGTTTCCGGAGAATGA 59.722 52.381 3.34 0.00 35.24 2.57
903 912 1.641192 GGAATCCTCACCCTTTTCCCT 59.359 52.381 0.00 0.00 31.60 4.20
904 913 1.641192 AGGAATCCTCACCCTTTTCCC 59.359 52.381 0.00 0.00 37.20 3.97
951 961 1.205064 CGTCGCTGCTGGAGTTTTG 59.795 57.895 0.00 0.00 0.00 2.44
955 965 4.057428 GTCCGTCGCTGCTGGAGT 62.057 66.667 5.53 0.00 31.04 3.85
956 966 4.803426 GGTCCGTCGCTGCTGGAG 62.803 72.222 5.53 0.00 31.04 3.86
959 969 4.803426 GAGGGTCCGTCGCTGCTG 62.803 72.222 0.00 0.00 39.46 4.41
1055 1065 4.247380 CGGGGAGGAGGCTGATGC 62.247 72.222 0.00 0.00 38.76 3.91
1077 1087 2.158842 GGTGATGACCTGGGAGAGAATG 60.159 54.545 0.00 0.00 39.47 2.67
1365 1375 1.517257 CGGCAGCAGAAGGTCGTAG 60.517 63.158 0.00 0.00 0.00 3.51
1451 1461 2.513897 CGAGGGTCGGGGAAATGC 60.514 66.667 0.00 0.00 36.00 3.56
1596 1606 2.202756 GGCGAGTCGATGACCACC 60.203 66.667 18.61 1.56 32.18 4.61
1620 1630 1.427020 GACAATGCCGAAGCTCTGC 59.573 57.895 0.00 0.00 40.80 4.26
1719 1729 0.395724 TAGGCGCTCTGATCACCTGA 60.396 55.000 7.64 0.00 31.79 3.86
1759 1769 1.765904 TGTAGTCTTGTGGCTGTCCAA 59.234 47.619 0.00 0.00 45.53 3.53
1794 1804 3.105283 AGTAGTTACCCGAGAAGCCATT 58.895 45.455 0.00 0.00 0.00 3.16
1826 1836 9.567776 TTTCCTGAGAAATTAATGTGACTGTTA 57.432 29.630 0.00 0.00 37.07 2.41
2031 2041 7.622893 AGCTACCAAAAAGATCAAGAGAATC 57.377 36.000 0.00 0.00 0.00 2.52
2040 2050 5.334182 GGCGCTATAAGCTACCAAAAAGATC 60.334 44.000 7.64 0.00 39.60 2.75
2043 2053 3.303132 CGGCGCTATAAGCTACCAAAAAG 60.303 47.826 7.64 0.00 39.60 2.27
2047 2057 0.032952 CCGGCGCTATAAGCTACCAA 59.967 55.000 7.64 0.00 39.60 3.67
2048 2058 0.824595 TCCGGCGCTATAAGCTACCA 60.825 55.000 7.64 0.00 39.60 3.25
2057 2067 3.908737 GGAGTTTATCCGGCGCTAT 57.091 52.632 7.64 0.00 38.67 2.97
2066 2076 7.772332 ACGTATGAACTGAATGGAGTTTATC 57.228 36.000 0.00 0.00 36.27 1.75
2088 2098 0.750850 ACCTGGACCGATGGATAACG 59.249 55.000 0.00 0.00 0.00 3.18
2091 2101 3.605726 TTCTACCTGGACCGATGGATA 57.394 47.619 0.00 0.00 0.00 2.59
2099 2109 2.468915 AGGCTAGTTTCTACCTGGACC 58.531 52.381 0.00 0.00 0.00 4.46
2100 2110 4.554960 AAAGGCTAGTTTCTACCTGGAC 57.445 45.455 0.00 0.00 31.32 4.02
2251 2261 4.009370 ACCCTTCAGCACTACTTCTTTC 57.991 45.455 0.00 0.00 0.00 2.62
2464 2474 3.176708 GCTGCATGCAAATGTAGTGAAG 58.823 45.455 22.88 6.32 42.31 3.02
2542 2552 4.516321 TGATTTCATCAATCAGTATGCCCG 59.484 41.667 0.00 0.00 45.45 6.13
2561 2571 3.682858 CGAAATACACGTGAAGGGTGATT 59.317 43.478 25.01 6.73 36.91 2.57
2565 2575 3.062042 GTTCGAAATACACGTGAAGGGT 58.938 45.455 25.01 0.85 41.15 4.34
2694 2705 6.545666 CAGTTCATAACCAAGGGTATATTGCA 59.454 38.462 0.00 0.00 33.12 4.08
2818 2829 5.010012 ACTGCTGGTTTCTTCAGGTAAAATG 59.990 40.000 0.00 0.00 33.16 2.32
2819 2830 5.140454 ACTGCTGGTTTCTTCAGGTAAAAT 58.860 37.500 0.00 0.00 33.16 1.82
2858 2869 3.814842 TCAGCAAACCATATTATCCAGCG 59.185 43.478 0.00 0.00 0.00 5.18
2888 2899 2.909965 GCCCGAACAAACAGCCCA 60.910 61.111 0.00 0.00 0.00 5.36
2902 2913 5.525378 CACACATCTCTACTGATAAAAGCCC 59.475 44.000 0.00 0.00 0.00 5.19
2903 2914 5.007136 GCACACATCTCTACTGATAAAAGCC 59.993 44.000 0.00 0.00 0.00 4.35
2915 2961 6.037281 TGTTTTACGTTTTGCACACATCTCTA 59.963 34.615 0.00 0.00 0.00 2.43
2935 2981 4.202101 TGCCTGAATGATGAAACGTGTTTT 60.202 37.500 0.00 0.00 32.11 2.43
2993 3039 4.153655 CGACCTGGCATCAATCATATTCTG 59.846 45.833 0.00 0.00 0.00 3.02
3063 3110 8.546083 ACATCTCTACTATGGAAGTCTTTCAT 57.454 34.615 11.24 11.24 39.80 2.57
3094 3141 2.432510 CCTGGCTACTCCTAAGGTTGAG 59.567 54.545 0.00 0.00 35.26 3.02
3101 3148 1.007238 AGCTCACCTGGCTACTCCTAA 59.993 52.381 0.00 0.00 38.36 2.69
3110 3157 0.523519 GTTAGCAAAGCTCACCTGGC 59.476 55.000 0.00 0.00 40.44 4.85
3202 3249 2.525055 GCTCACGCAGTTCAACAAAAA 58.475 42.857 0.00 0.00 41.61 1.94
3231 3278 4.275689 CACCACATCAGAGTTGCTTAACAA 59.724 41.667 0.00 0.00 35.33 2.83
3233 3280 4.065088 TCACCACATCAGAGTTGCTTAAC 58.935 43.478 0.00 0.00 0.00 2.01
3234 3281 4.350368 TCACCACATCAGAGTTGCTTAA 57.650 40.909 0.00 0.00 0.00 1.85
3235 3282 4.318332 CTTCACCACATCAGAGTTGCTTA 58.682 43.478 0.00 0.00 0.00 3.09
3236 3283 2.936919 TCACCACATCAGAGTTGCTT 57.063 45.000 0.00 0.00 0.00 3.91
3238 3285 1.808945 CCTTCACCACATCAGAGTTGC 59.191 52.381 0.00 0.00 0.00 4.17
3239 3286 1.808945 GCCTTCACCACATCAGAGTTG 59.191 52.381 0.00 0.00 0.00 3.16
3240 3287 1.421268 TGCCTTCACCACATCAGAGTT 59.579 47.619 0.00 0.00 0.00 3.01
3241 3288 1.059098 TGCCTTCACCACATCAGAGT 58.941 50.000 0.00 0.00 0.00 3.24
3261 3319 1.887242 GTGAGCTGAACCACGTGCA 60.887 57.895 10.91 1.67 0.00 4.57
3264 3322 3.226242 TGGTGAGCTGAACCACGT 58.774 55.556 12.84 0.00 42.82 4.49
3308 4833 7.094933 GGAAATAGAAGAGTCTAACCGCAAAAA 60.095 37.037 0.00 0.00 39.81 1.94
3309 4834 6.370718 GGAAATAGAAGAGTCTAACCGCAAAA 59.629 38.462 0.00 0.00 39.81 2.44
3310 4835 5.873164 GGAAATAGAAGAGTCTAACCGCAAA 59.127 40.000 0.00 0.00 39.81 3.68
3311 4836 5.046878 TGGAAATAGAAGAGTCTAACCGCAA 60.047 40.000 0.00 0.00 39.81 4.85
3312 4837 4.464951 TGGAAATAGAAGAGTCTAACCGCA 59.535 41.667 0.00 0.00 39.81 5.69
3313 4838 4.804665 GTGGAAATAGAAGAGTCTAACCGC 59.195 45.833 0.00 0.00 39.81 5.68
3314 4839 6.210287 AGTGGAAATAGAAGAGTCTAACCG 57.790 41.667 0.00 0.00 39.81 4.44
3383 4911 8.761497 GTGCTGCAAAATACTCGATTTATACTA 58.239 33.333 2.77 0.00 36.71 1.82
3389 4917 4.475944 GTGTGCTGCAAAATACTCGATTT 58.524 39.130 2.77 0.00 39.56 2.17
3392 4920 1.804151 GGTGTGCTGCAAAATACTCGA 59.196 47.619 2.77 0.00 0.00 4.04
3414 4942 9.786105 CATACAGACATTGTGTTGCAATAATTA 57.214 29.630 0.59 0.00 45.33 1.40
3438 4968 7.278424 GCACACAAATTTCCTTATTGCATACAT 59.722 33.333 0.00 0.00 0.00 2.29
3439 4969 6.589523 GCACACAAATTTCCTTATTGCATACA 59.410 34.615 0.00 0.00 0.00 2.29
3443 4973 5.212532 AGCACACAAATTTCCTTATTGCA 57.787 34.783 0.00 0.00 0.00 4.08
3452 4982 2.216263 GTGTCGCAAGCACACAAATTTC 59.784 45.455 16.99 0.00 43.28 2.17
3461 4991 2.638719 TGCATGTGTCGCAAGCAC 59.361 55.556 12.00 0.00 45.41 4.40
3469 4999 3.244976 GCACAGGTTATTTGCATGTGTC 58.755 45.455 14.04 5.12 46.38 3.67
3518 5048 0.662619 CCAACTTTGTTGCTGCGAGA 59.337 50.000 5.04 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.