Multiple sequence alignment - TraesCS5D01G050200

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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 TraesCS5D01G050200 chr5D 100.000 2369 0 0 1 2369 47795042 47792674 0.000000e+00 4375
1 TraesCS5D01G050200 chr5D 97.031 640 18 1 1731 2369 411240402 411239763 0.000000e+00 1075
2 TraesCS5D01G050200 chr4D 97.063 647 16 3 1726 2369 484882288 484881642 0.000000e+00 1086
3 TraesCS5D01G050200 chr4D 97.027 639 17 2 1732 2369 422306028 422306665 0.000000e+00 1074
4 TraesCS5D01G050200 chr4D 97.027 639 18 1 1732 2369 437936096 437935458 0.000000e+00 1074
5 TraesCS5D01G050200 chr1D 97.188 640 16 2 1732 2369 464174243 464174882 0.000000e+00 1081
6 TraesCS5D01G050200 chr1D 97.179 638 17 1 1732 2368 7735427 7736064 0.000000e+00 1077
7 TraesCS5D01G050200 chr7D 97.183 639 16 2 1732 2369 606786687 606786050 0.000000e+00 1079
8 TraesCS5D01G050200 chr2D 97.045 643 15 4 1729 2369 619806057 619805417 0.000000e+00 1079
9 TraesCS5D01G050200 chr6D 96.605 648 21 1 1723 2369 7177898 7178545 0.000000e+00 1074
10 TraesCS5D01G050200 chr5B 90.347 808 45 16 880 1659 50507804 50507002 0.000000e+00 1029
11 TraesCS5D01G050200 chr5B 90.222 675 45 10 1 665 625131866 625131203 0.000000e+00 861
12 TraesCS5D01G050200 chr5B 92.466 292 13 2 1449 1731 50506416 50506125 2.190000e-110 409
13 TraesCS5D01G050200 chr2B 92.308 663 35 9 1 659 22009257 22009907 0.000000e+00 928
14 TraesCS5D01G050200 chr2B 91.642 670 40 6 1 665 73314678 73314020 0.000000e+00 913
15 TraesCS5D01G050200 chr2B 91.480 669 41 7 1 664 772634157 772634814 0.000000e+00 905
16 TraesCS5D01G050200 chr3B 91.642 670 43 4 1 666 4767314 4767974 0.000000e+00 915
17 TraesCS5D01G050200 chr3B 91.483 634 42 5 28 658 252667518 252666894 0.000000e+00 861
18 TraesCS5D01G050200 chr3B 88.567 691 53 16 1 670 809823723 809823038 0.000000e+00 815
19 TraesCS5D01G050200 chr3B 88.839 672 51 14 1 652 52622894 52623561 0.000000e+00 804
20 TraesCS5D01G050200 chr3B 89.362 658 43 18 1 641 811177582 811178229 0.000000e+00 802
21 TraesCS5D01G050200 chr3B 88.496 678 54 14 1 658 53034221 53033548 0.000000e+00 798
22 TraesCS5D01G050200 chr7B 91.420 676 40 9 1 669 178412429 178411765 0.000000e+00 911
23 TraesCS5D01G050200 chr3D 90.620 661 50 5 1 658 549765179 549764528 0.000000e+00 867
24 TraesCS5D01G050200 chr6B 90.135 669 45 10 1 659 233687478 233686821 0.000000e+00 850
25 TraesCS5D01G050200 chr6B 88.754 658 45 18 1 641 183402326 183401681 0.000000e+00 778
26 TraesCS5D01G050200 chr1B 89.583 672 46 14 1 652 203657898 203658565 0.000000e+00 832
27 TraesCS5D01G050200 chr3A 89.286 672 48 16 1 652 730661617 730662284 0.000000e+00 821
28 TraesCS5D01G050200 chr3A 88.702 655 44 20 1 634 628902852 628902207 0.000000e+00 773
29 TraesCS5D01G050200 chr4A 91.429 560 42 4 1 556 715942206 715941649 0.000000e+00 763
30 TraesCS5D01G050200 chr5A 90.541 74 7 0 1040 1113 37974422 37974349 5.390000e-17 99


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 TraesCS5D01G050200 chr5D 47792674 47795042 2368 True 4375 4375 100.0000 1 2369 1 chr5D.!!$R1 2368
1 TraesCS5D01G050200 chr5D 411239763 411240402 639 True 1075 1075 97.0310 1731 2369 1 chr5D.!!$R2 638
2 TraesCS5D01G050200 chr4D 484881642 484882288 646 True 1086 1086 97.0630 1726 2369 1 chr4D.!!$R2 643
3 TraesCS5D01G050200 chr4D 422306028 422306665 637 False 1074 1074 97.0270 1732 2369 1 chr4D.!!$F1 637
4 TraesCS5D01G050200 chr4D 437935458 437936096 638 True 1074 1074 97.0270 1732 2369 1 chr4D.!!$R1 637
5 TraesCS5D01G050200 chr1D 464174243 464174882 639 False 1081 1081 97.1880 1732 2369 1 chr1D.!!$F2 637
6 TraesCS5D01G050200 chr1D 7735427 7736064 637 False 1077 1077 97.1790 1732 2368 1 chr1D.!!$F1 636
7 TraesCS5D01G050200 chr7D 606786050 606786687 637 True 1079 1079 97.1830 1732 2369 1 chr7D.!!$R1 637
8 TraesCS5D01G050200 chr2D 619805417 619806057 640 True 1079 1079 97.0450 1729 2369 1 chr2D.!!$R1 640
9 TraesCS5D01G050200 chr6D 7177898 7178545 647 False 1074 1074 96.6050 1723 2369 1 chr6D.!!$F1 646
10 TraesCS5D01G050200 chr5B 625131203 625131866 663 True 861 861 90.2220 1 665 1 chr5B.!!$R1 664
11 TraesCS5D01G050200 chr5B 50506125 50507804 1679 True 719 1029 91.4065 880 1731 2 chr5B.!!$R2 851
12 TraesCS5D01G050200 chr2B 22009257 22009907 650 False 928 928 92.3080 1 659 1 chr2B.!!$F1 658
13 TraesCS5D01G050200 chr2B 73314020 73314678 658 True 913 913 91.6420 1 665 1 chr2B.!!$R1 664
14 TraesCS5D01G050200 chr2B 772634157 772634814 657 False 905 905 91.4800 1 664 1 chr2B.!!$F2 663
15 TraesCS5D01G050200 chr3B 4767314 4767974 660 False 915 915 91.6420 1 666 1 chr3B.!!$F1 665
16 TraesCS5D01G050200 chr3B 252666894 252667518 624 True 861 861 91.4830 28 658 1 chr3B.!!$R2 630
17 TraesCS5D01G050200 chr3B 809823038 809823723 685 True 815 815 88.5670 1 670 1 chr3B.!!$R3 669
18 TraesCS5D01G050200 chr3B 52622894 52623561 667 False 804 804 88.8390 1 652 1 chr3B.!!$F2 651
19 TraesCS5D01G050200 chr3B 811177582 811178229 647 False 802 802 89.3620 1 641 1 chr3B.!!$F3 640
20 TraesCS5D01G050200 chr3B 53033548 53034221 673 True 798 798 88.4960 1 658 1 chr3B.!!$R1 657
21 TraesCS5D01G050200 chr7B 178411765 178412429 664 True 911 911 91.4200 1 669 1 chr7B.!!$R1 668
22 TraesCS5D01G050200 chr3D 549764528 549765179 651 True 867 867 90.6200 1 658 1 chr3D.!!$R1 657
23 TraesCS5D01G050200 chr6B 233686821 233687478 657 True 850 850 90.1350 1 659 1 chr6B.!!$R2 658
24 TraesCS5D01G050200 chr6B 183401681 183402326 645 True 778 778 88.7540 1 641 1 chr6B.!!$R1 640
25 TraesCS5D01G050200 chr1B 203657898 203658565 667 False 832 832 89.5830 1 652 1 chr1B.!!$F1 651
26 TraesCS5D01G050200 chr3A 730661617 730662284 667 False 821 821 89.2860 1 652 1 chr3A.!!$F1 651
27 TraesCS5D01G050200 chr3A 628902207 628902852 645 True 773 773 88.7020 1 634 1 chr3A.!!$R1 633
28 TraesCS5D01G050200 chr4A 715941649 715942206 557 True 763 763 91.4290 1 556 1 chr4A.!!$R1 555

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
931 968 0.037975 GTACGGGCCTTCTTCGAACA 60.038 55.0 0.84 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 2623 0.461135 GGTATTACGAGGGCCGAACA 59.539 55.0 0.0 0.0 41.76 3.18 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
104 105 2.601666 TCCACGTCTGCAGCTCCT 60.602 61.111 9.47 0.00 0.00 3.69
158 164 1.640428 GCTTCATCATCCACGACGAA 58.360 50.000 0.00 0.00 0.00 3.85
164 170 0.386113 TCATCCACGACGAACACACA 59.614 50.000 0.00 0.00 0.00 3.72
188 194 1.549170 GACCACGACTACCTCAACCAT 59.451 52.381 0.00 0.00 0.00 3.55
231 244 4.500887 GCTACCTCGACATTAATGGCTACA 60.501 45.833 19.04 2.34 32.20 2.74
275 290 0.249322 CTCCAGTCAACAACGTCCGT 60.249 55.000 0.00 0.00 0.00 4.69
336 353 3.374318 GGGAGGGAATAGAGGAGAAGACA 60.374 52.174 0.00 0.00 0.00 3.41
397 415 1.688735 CCGACCTATCAGCCATCAGAA 59.311 52.381 0.00 0.00 0.00 3.02
421 439 1.937899 CAGTTGATGATGATGCAGCGA 59.062 47.619 0.00 0.00 0.00 4.93
627 660 2.752354 CCAATGCACGGGTTAGATCAAA 59.248 45.455 0.00 0.00 0.00 2.69
666 703 9.330063 TCAGCAATCCTATACTTTTTCACATAG 57.670 33.333 0.00 0.00 0.00 2.23
683 720 8.437360 TTCACATAGATAAGTAAGCAATGTGG 57.563 34.615 11.38 0.00 41.76 4.17
684 721 6.992123 TCACATAGATAAGTAAGCAATGTGGG 59.008 38.462 11.38 0.00 41.76 4.61
685 722 6.205464 CACATAGATAAGTAAGCAATGTGGGG 59.795 42.308 0.00 0.00 39.19 4.96
686 723 6.101150 ACATAGATAAGTAAGCAATGTGGGGA 59.899 38.462 0.00 0.00 0.00 4.81
687 724 4.781934 AGATAAGTAAGCAATGTGGGGAC 58.218 43.478 0.00 0.00 0.00 4.46
688 725 4.475016 AGATAAGTAAGCAATGTGGGGACT 59.525 41.667 0.00 0.00 0.00 3.85
689 726 2.496899 AGTAAGCAATGTGGGGACTG 57.503 50.000 0.00 0.00 0.00 3.51
690 727 1.004745 AGTAAGCAATGTGGGGACTGG 59.995 52.381 0.00 0.00 0.00 4.00
691 728 1.072266 TAAGCAATGTGGGGACTGGT 58.928 50.000 0.00 0.00 0.00 4.00
692 729 0.188342 AAGCAATGTGGGGACTGGTT 59.812 50.000 0.00 0.00 0.00 3.67
693 730 0.540365 AGCAATGTGGGGACTGGTTG 60.540 55.000 0.00 0.00 0.00 3.77
694 731 0.539438 GCAATGTGGGGACTGGTTGA 60.539 55.000 0.00 0.00 0.00 3.18
695 732 1.247567 CAATGTGGGGACTGGTTGAC 58.752 55.000 0.00 0.00 0.00 3.18
696 733 1.149101 AATGTGGGGACTGGTTGACT 58.851 50.000 0.00 0.00 0.00 3.41
697 734 0.401738 ATGTGGGGACTGGTTGACTG 59.598 55.000 0.00 0.00 0.00 3.51
698 735 0.692756 TGTGGGGACTGGTTGACTGA 60.693 55.000 0.00 0.00 0.00 3.41
699 736 0.250338 GTGGGGACTGGTTGACTGAC 60.250 60.000 0.00 0.00 0.00 3.51
700 737 1.375326 GGGGACTGGTTGACTGACC 59.625 63.158 0.00 0.00 40.23 4.02
701 738 1.004918 GGGACTGGTTGACTGACCG 60.005 63.158 0.00 0.00 42.83 4.79
703 740 1.469335 GGACTGGTTGACTGACCGGA 61.469 60.000 9.46 0.00 46.98 5.14
704 741 0.038159 GACTGGTTGACTGACCGGAG 60.038 60.000 9.46 0.00 46.98 4.63
705 742 0.469331 ACTGGTTGACTGACCGGAGA 60.469 55.000 9.46 0.00 46.98 3.71
706 743 0.679505 CTGGTTGACTGACCGGAGAA 59.320 55.000 9.46 0.00 46.98 2.87
707 744 1.070134 CTGGTTGACTGACCGGAGAAA 59.930 52.381 9.46 0.00 46.98 2.52
708 745 1.487142 TGGTTGACTGACCGGAGAAAA 59.513 47.619 9.46 0.00 42.83 2.29
709 746 2.092861 TGGTTGACTGACCGGAGAAAAA 60.093 45.455 9.46 0.00 42.83 1.94
710 747 3.146847 GGTTGACTGACCGGAGAAAAAT 58.853 45.455 9.46 0.00 0.00 1.82
711 748 3.058224 GGTTGACTGACCGGAGAAAAATG 60.058 47.826 9.46 0.00 0.00 2.32
712 749 2.778299 TGACTGACCGGAGAAAAATGG 58.222 47.619 9.46 0.00 0.00 3.16
713 750 2.370519 TGACTGACCGGAGAAAAATGGA 59.629 45.455 9.46 0.00 0.00 3.41
714 751 3.003480 GACTGACCGGAGAAAAATGGAG 58.997 50.000 9.46 0.00 0.00 3.86
715 752 2.637872 ACTGACCGGAGAAAAATGGAGA 59.362 45.455 9.46 0.00 0.00 3.71
716 753 3.072476 ACTGACCGGAGAAAAATGGAGAA 59.928 43.478 9.46 0.00 0.00 2.87
717 754 3.674997 TGACCGGAGAAAAATGGAGAAG 58.325 45.455 9.46 0.00 0.00 2.85
718 755 3.010420 GACCGGAGAAAAATGGAGAAGG 58.990 50.000 9.46 0.00 0.00 3.46
719 756 2.290960 ACCGGAGAAAAATGGAGAAGGG 60.291 50.000 9.46 0.00 0.00 3.95
720 757 2.026262 CCGGAGAAAAATGGAGAAGGGA 60.026 50.000 0.00 0.00 0.00 4.20
721 758 3.561313 CCGGAGAAAAATGGAGAAGGGAA 60.561 47.826 0.00 0.00 0.00 3.97
722 759 4.273318 CGGAGAAAAATGGAGAAGGGAAT 58.727 43.478 0.00 0.00 0.00 3.01
723 760 4.336713 CGGAGAAAAATGGAGAAGGGAATC 59.663 45.833 0.00 0.00 0.00 2.52
724 761 5.514169 GGAGAAAAATGGAGAAGGGAATCT 58.486 41.667 0.00 0.00 0.00 2.40
725 762 5.954752 GGAGAAAAATGGAGAAGGGAATCTT 59.045 40.000 0.00 0.00 38.65 2.40
726 763 6.127507 GGAGAAAAATGGAGAAGGGAATCTTG 60.128 42.308 0.00 0.00 35.50 3.02
727 764 6.318112 AGAAAAATGGAGAAGGGAATCTTGT 58.682 36.000 0.00 0.00 35.50 3.16
728 765 6.435591 AGAAAAATGGAGAAGGGAATCTTGTC 59.564 38.462 0.00 0.00 42.91 3.18
729 766 5.527026 AAATGGAGAAGGGAATCTTGTCT 57.473 39.130 0.00 0.00 43.12 3.41
730 767 5.527026 AATGGAGAAGGGAATCTTGTCTT 57.473 39.130 0.00 0.00 43.12 3.01
731 768 4.292186 TGGAGAAGGGAATCTTGTCTTG 57.708 45.455 0.00 0.00 43.12 3.02
732 769 3.013219 GGAGAAGGGAATCTTGTCTTGC 58.987 50.000 0.00 0.00 43.12 4.01
733 770 3.308046 GGAGAAGGGAATCTTGTCTTGCT 60.308 47.826 0.00 0.00 43.12 3.91
734 771 3.683802 AGAAGGGAATCTTGTCTTGCTG 58.316 45.455 0.00 0.00 35.50 4.41
735 772 1.831580 AGGGAATCTTGTCTTGCTGC 58.168 50.000 0.00 0.00 0.00 5.25
736 773 0.449388 GGGAATCTTGTCTTGCTGCG 59.551 55.000 0.00 0.00 0.00 5.18
737 774 0.179179 GGAATCTTGTCTTGCTGCGC 60.179 55.000 0.00 0.00 0.00 6.09
738 775 0.519999 GAATCTTGTCTTGCTGCGCG 60.520 55.000 0.00 0.00 0.00 6.86
739 776 1.915614 AATCTTGTCTTGCTGCGCGG 61.916 55.000 13.18 13.18 0.00 6.46
740 777 4.748679 CTTGTCTTGCTGCGCGGC 62.749 66.667 34.00 34.00 0.00 6.53
752 789 2.486504 CGCGGCCGTAGTGACTTA 59.513 61.111 28.70 0.00 0.00 2.24
753 790 1.065273 CGCGGCCGTAGTGACTTAT 59.935 57.895 28.70 0.00 0.00 1.73
754 791 0.933509 CGCGGCCGTAGTGACTTATC 60.934 60.000 28.70 3.74 0.00 1.75
755 792 0.384669 GCGGCCGTAGTGACTTATCT 59.615 55.000 28.70 0.00 0.00 1.98
756 793 1.202382 GCGGCCGTAGTGACTTATCTT 60.202 52.381 28.70 0.00 0.00 2.40
757 794 2.728922 CGGCCGTAGTGACTTATCTTC 58.271 52.381 19.50 0.00 0.00 2.87
758 795 2.728922 GGCCGTAGTGACTTATCTTCG 58.271 52.381 0.00 0.00 0.00 3.79
759 796 2.543238 GGCCGTAGTGACTTATCTTCGG 60.543 54.545 0.00 6.01 43.76 4.30
760 797 2.098770 GCCGTAGTGACTTATCTTCGGT 59.901 50.000 10.68 0.00 43.18 4.69
761 798 3.791455 GCCGTAGTGACTTATCTTCGGTC 60.791 52.174 10.68 0.00 43.18 4.79
762 799 3.545624 CCGTAGTGACTTATCTTCGGTCG 60.546 52.174 0.00 0.00 38.91 4.79
763 800 3.063180 CGTAGTGACTTATCTTCGGTCGT 59.937 47.826 0.00 0.00 33.21 4.34
764 801 3.761311 AGTGACTTATCTTCGGTCGTC 57.239 47.619 0.00 0.00 33.21 4.20
765 802 2.095532 AGTGACTTATCTTCGGTCGTCG 59.904 50.000 0.00 0.00 40.90 5.12
766 803 1.202110 TGACTTATCTTCGGTCGTCGC 60.202 52.381 0.00 0.00 39.05 5.19
767 804 1.063764 GACTTATCTTCGGTCGTCGCT 59.936 52.381 0.00 0.00 39.05 4.93
768 805 1.202154 ACTTATCTTCGGTCGTCGCTG 60.202 52.381 0.00 0.00 39.05 5.18
769 806 0.524816 TTATCTTCGGTCGTCGCTGC 60.525 55.000 0.00 0.00 39.05 5.25
770 807 2.642249 TATCTTCGGTCGTCGCTGCG 62.642 60.000 17.25 17.25 39.05 5.18
787 824 2.809601 GTGCGTTGGCTCGTCGAT 60.810 61.111 0.00 0.00 40.82 3.59
788 825 2.048597 TGCGTTGGCTCGTCGATT 60.049 55.556 0.00 0.00 40.82 3.34
789 826 2.379634 TGCGTTGGCTCGTCGATTG 61.380 57.895 0.00 0.00 40.82 2.67
790 827 2.092291 GCGTTGGCTCGTCGATTGA 61.092 57.895 0.00 0.00 35.83 2.57
791 828 1.421410 GCGTTGGCTCGTCGATTGAT 61.421 55.000 0.00 0.00 35.83 2.57
792 829 0.572590 CGTTGGCTCGTCGATTGATC 59.427 55.000 0.00 0.00 0.00 2.92
807 844 5.760193 GATTGATCGACTGCATATGTCTC 57.240 43.478 4.29 0.00 32.70 3.36
808 845 4.926140 TTGATCGACTGCATATGTCTCT 57.074 40.909 4.29 0.00 32.70 3.10
809 846 4.926140 TGATCGACTGCATATGTCTCTT 57.074 40.909 4.29 0.00 32.70 2.85
810 847 5.268118 TGATCGACTGCATATGTCTCTTT 57.732 39.130 4.29 0.00 32.70 2.52
811 848 5.284864 TGATCGACTGCATATGTCTCTTTC 58.715 41.667 4.29 0.00 32.70 2.62
812 849 3.695816 TCGACTGCATATGTCTCTTTCG 58.304 45.455 4.29 5.05 32.70 3.46
813 850 3.128764 TCGACTGCATATGTCTCTTTCGT 59.871 43.478 4.29 0.00 32.70 3.85
814 851 3.483922 CGACTGCATATGTCTCTTTCGTC 59.516 47.826 4.29 0.07 32.70 4.20
815 852 3.439293 ACTGCATATGTCTCTTTCGTCG 58.561 45.455 4.29 0.00 0.00 5.12
816 853 2.791560 CTGCATATGTCTCTTTCGTCGG 59.208 50.000 4.29 0.00 0.00 4.79
817 854 2.165641 TGCATATGTCTCTTTCGTCGGT 59.834 45.455 4.29 0.00 0.00 4.69
818 855 2.789893 GCATATGTCTCTTTCGTCGGTC 59.210 50.000 4.29 0.00 0.00 4.79
819 856 2.819422 TATGTCTCTTTCGTCGGTCG 57.181 50.000 0.00 0.00 41.41 4.79
820 857 0.879765 ATGTCTCTTTCGTCGGTCGT 59.120 50.000 0.00 0.00 40.80 4.34
821 858 0.236711 TGTCTCTTTCGTCGGTCGTC 59.763 55.000 0.00 0.00 40.80 4.20
822 859 0.788645 GTCTCTTTCGTCGGTCGTCG 60.789 60.000 3.88 3.88 40.80 5.12
823 860 1.206072 CTCTTTCGTCGGTCGTCGT 59.794 57.895 9.38 0.00 40.80 4.34
824 861 1.058590 CTCTTTCGTCGGTCGTCGTG 61.059 60.000 9.38 3.20 40.80 4.35
825 862 1.369689 CTTTCGTCGGTCGTCGTGT 60.370 57.895 9.38 0.00 40.80 4.49
826 863 0.110688 CTTTCGTCGGTCGTCGTGTA 60.111 55.000 9.38 0.00 40.80 2.90
827 864 0.384230 TTTCGTCGGTCGTCGTGTAC 60.384 55.000 9.38 0.00 40.80 2.90
836 873 2.431942 GTCGTGTACGGCCACCAG 60.432 66.667 2.24 0.00 38.15 4.00
837 874 2.913578 TCGTGTACGGCCACCAGT 60.914 61.111 2.24 0.00 40.29 4.00
838 875 2.431942 CGTGTACGGCCACCAGTC 60.432 66.667 2.24 0.00 35.37 3.51
839 876 2.738480 GTGTACGGCCACCAGTCA 59.262 61.111 2.24 0.00 0.00 3.41
840 877 1.666872 GTGTACGGCCACCAGTCAC 60.667 63.158 2.24 0.00 0.00 3.67
841 878 2.431942 GTACGGCCACCAGTCACG 60.432 66.667 2.24 0.00 0.00 4.35
842 879 4.367023 TACGGCCACCAGTCACGC 62.367 66.667 2.24 0.00 0.00 5.34
851 888 4.680237 CAGTCACGCGGGCCTTGA 62.680 66.667 12.47 0.61 0.00 3.02
852 889 4.681978 AGTCACGCGGGCCTTGAC 62.682 66.667 16.44 16.44 40.04 3.18
853 890 4.681978 GTCACGCGGGCCTTGACT 62.682 66.667 12.47 0.00 37.31 3.41
854 891 2.992689 TCACGCGGGCCTTGACTA 60.993 61.111 12.47 0.00 0.00 2.59
855 892 2.047655 CACGCGGGCCTTGACTAA 60.048 61.111 12.47 0.00 0.00 2.24
856 893 2.047560 ACGCGGGCCTTGACTAAC 60.048 61.111 12.47 0.00 0.00 2.34
857 894 2.818274 CGCGGGCCTTGACTAACC 60.818 66.667 0.84 0.00 0.00 2.85
858 895 2.818274 GCGGGCCTTGACTAACCG 60.818 66.667 0.84 0.00 46.78 4.44
859 896 2.818274 CGGGCCTTGACTAACCGC 60.818 66.667 0.84 0.00 37.93 5.68
860 897 2.349755 GGGCCTTGACTAACCGCA 59.650 61.111 0.84 0.00 0.00 5.69
861 898 1.745489 GGGCCTTGACTAACCGCAG 60.745 63.158 0.84 0.00 0.00 5.18
862 899 1.295423 GGCCTTGACTAACCGCAGA 59.705 57.895 0.00 0.00 0.00 4.26
863 900 0.321298 GGCCTTGACTAACCGCAGAA 60.321 55.000 0.00 0.00 0.00 3.02
864 901 1.519408 GCCTTGACTAACCGCAGAAA 58.481 50.000 0.00 0.00 0.00 2.52
865 902 2.084546 GCCTTGACTAACCGCAGAAAT 58.915 47.619 0.00 0.00 0.00 2.17
866 903 2.488153 GCCTTGACTAACCGCAGAAATT 59.512 45.455 0.00 0.00 0.00 1.82
867 904 3.057526 GCCTTGACTAACCGCAGAAATTT 60.058 43.478 0.00 0.00 0.00 1.82
868 905 4.475944 CCTTGACTAACCGCAGAAATTTG 58.524 43.478 0.00 0.00 0.00 2.32
869 906 4.475944 CTTGACTAACCGCAGAAATTTGG 58.524 43.478 0.00 0.00 0.00 3.28
870 907 3.482436 TGACTAACCGCAGAAATTTGGT 58.518 40.909 0.00 0.00 35.90 3.67
871 908 3.252215 TGACTAACCGCAGAAATTTGGTG 59.748 43.478 0.00 0.00 34.26 4.17
872 909 2.556622 ACTAACCGCAGAAATTTGGTGG 59.443 45.455 14.45 14.45 38.16 4.61
873 910 1.408969 AACCGCAGAAATTTGGTGGT 58.591 45.000 15.49 15.49 46.73 4.16
874 911 2.279935 ACCGCAGAAATTTGGTGGTA 57.720 45.000 18.35 0.00 43.20 3.25
875 912 2.802719 ACCGCAGAAATTTGGTGGTAT 58.197 42.857 18.35 1.22 43.20 2.73
876 913 2.752903 ACCGCAGAAATTTGGTGGTATC 59.247 45.455 18.35 0.00 43.20 2.24
877 914 3.016736 CCGCAGAAATTTGGTGGTATCT 58.983 45.455 0.00 0.00 0.00 1.98
878 915 3.065371 CCGCAGAAATTTGGTGGTATCTC 59.935 47.826 0.00 0.00 0.00 2.75
882 919 5.295540 GCAGAAATTTGGTGGTATCTCTCTC 59.704 44.000 0.00 0.00 0.00 3.20
890 927 3.135994 GTGGTATCTCTCTCTCTCGACC 58.864 54.545 0.00 0.00 0.00 4.79
891 928 2.772515 TGGTATCTCTCTCTCTCGACCA 59.227 50.000 0.00 0.00 33.41 4.02
895 932 0.724549 CTCTCTCTCTCGACCACACG 59.275 60.000 0.00 0.00 0.00 4.49
896 933 0.673956 TCTCTCTCTCGACCACACGG 60.674 60.000 0.00 0.00 38.77 4.94
905 942 1.211190 GACCACACGGACGGTCTAC 59.789 63.158 8.23 0.00 46.83 2.59
911 948 2.919229 CACACGGACGGTCTACAAATAC 59.081 50.000 8.23 0.00 0.00 1.89
913 950 1.812571 ACGGACGGTCTACAAATACGT 59.187 47.619 8.23 3.69 40.85 3.57
919 956 2.463876 GGTCTACAAATACGTACGGGC 58.536 52.381 21.06 0.00 0.00 6.13
927 964 0.383231 ATACGTACGGGCCTTCTTCG 59.617 55.000 21.06 0.00 0.00 3.79
929 966 1.213537 CGTACGGGCCTTCTTCGAA 59.786 57.895 7.57 0.00 0.00 3.71
931 968 0.037975 GTACGGGCCTTCTTCGAACA 60.038 55.000 0.84 0.00 0.00 3.18
932 969 0.245539 TACGGGCCTTCTTCGAACAG 59.754 55.000 0.84 0.00 0.00 3.16
942 979 2.071540 TCTTCGAACAGCAAGCATCAG 58.928 47.619 0.00 0.00 0.00 2.90
960 997 0.743688 AGAGCAGGATAGCAGACGTG 59.256 55.000 0.00 0.00 36.85 4.49
972 1017 1.502231 CAGACGTGCACAACTAGCTT 58.498 50.000 18.64 0.00 0.00 3.74
978 1023 2.410262 CGTGCACAACTAGCTTTCGAAG 60.410 50.000 18.64 0.00 0.00 3.79
992 1037 1.733041 CGAAGCCTCGCTCGAAACA 60.733 57.895 0.00 0.00 38.25 2.83
998 1043 1.284982 CCTCGCTCGAAACACACCAG 61.285 60.000 0.00 0.00 0.00 4.00
999 1044 1.891060 CTCGCTCGAAACACACCAGC 61.891 60.000 0.00 0.00 0.00 4.85
1000 1045 2.243957 CGCTCGAAACACACCAGCA 61.244 57.895 0.00 0.00 0.00 4.41
1014 1065 3.640407 AGCATGGCGTCCCACAGT 61.640 61.111 0.00 0.00 45.77 3.55
1064 1115 1.322865 CATATCGCTCTCTTCGTCGC 58.677 55.000 0.00 0.00 0.00 5.19
1066 1117 1.093496 TATCGCTCTCTTCGTCGCCA 61.093 55.000 0.00 0.00 0.00 5.69
1335 1392 1.074072 TGGGTGCCGCACAGTTTAT 59.926 52.632 24.43 0.00 35.86 1.40
1343 1400 2.680841 GCCGCACAGTTTATGGATGTAA 59.319 45.455 0.00 0.00 0.00 2.41
1380 1437 0.602905 AGCCCTAATTACATCCGCGC 60.603 55.000 0.00 0.00 0.00 6.86
1385 1442 0.249114 TAATTACATCCGCGCGCAGA 60.249 50.000 32.61 26.87 0.00 4.26
1408 1468 1.064906 CCATCTCCCAGACACAATGCT 60.065 52.381 0.00 0.00 0.00 3.79
1479 1539 1.619332 TCACGCACCACCTTATGTACA 59.381 47.619 0.00 0.00 0.00 2.90
1549 2410 3.421919 TCTGGATTGTTGCATGTCTGA 57.578 42.857 0.00 0.00 0.00 3.27
1564 2425 5.630680 GCATGTCTGAAATTTCGTGTGAATT 59.369 36.000 13.34 0.00 33.20 2.17
1582 2443 6.482641 TGTGAATTCATGGTCAATTTTTGTGG 59.517 34.615 12.12 0.00 0.00 4.17
1588 2449 3.546724 TGGTCAATTTTTGTGGAGACGA 58.453 40.909 0.00 0.00 0.00 4.20
1594 2455 7.908601 GGTCAATTTTTGTGGAGACGATATTAC 59.091 37.037 0.00 0.00 0.00 1.89
1613 2474 5.998454 TTACGTTTGGTTCGGAATTTACA 57.002 34.783 0.00 0.00 0.00 2.41
1622 2483 8.597662 TTGGTTCGGAATTTACAGCTATATAC 57.402 34.615 0.00 0.00 0.00 1.47
1634 2495 6.624352 ACAGCTATATACCAATGCACAAAG 57.376 37.500 0.00 0.00 0.00 2.77
1744 2614 6.116126 GGTCATTGCTCCACTAGTAGAAAAT 58.884 40.000 3.59 0.00 0.00 1.82
1753 2623 7.208064 TCCACTAGTAGAAAATAGGGCATTT 57.792 36.000 3.59 0.00 38.54 2.32
2000 2870 2.504274 TTGGTCCTCGTTGCGGTCT 61.504 57.895 0.00 0.00 0.00 3.85
2059 2929 0.533531 CGGTTTATAAGCCCGTCCCC 60.534 60.000 12.28 0.00 37.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 194 1.070601 CCGATCATGGTGATGTAGCCA 59.929 52.381 0.00 0.00 37.20 4.75
231 244 1.482182 TGCCGATGAGTTGCTGTAGAT 59.518 47.619 0.00 0.00 0.00 1.98
336 353 2.234296 CCCTTCTGGTGCCTTCCCT 61.234 63.158 0.00 0.00 0.00 4.20
383 401 2.093500 ACTGCGTTTCTGATGGCTGATA 60.093 45.455 8.28 0.00 0.00 2.15
397 415 2.086094 TGCATCATCATCAACTGCGTT 58.914 42.857 0.00 0.00 35.63 4.84
413 431 0.038251 TGTCGTCTTCTTCGCTGCAT 60.038 50.000 0.00 0.00 0.00 3.96
421 439 1.295792 TGCGCTTTTGTCGTCTTCTT 58.704 45.000 9.73 0.00 0.00 2.52
611 644 3.003897 TGTTGTTTTGATCTAACCCGTGC 59.996 43.478 8.25 0.00 0.00 5.34
666 703 4.576463 CAGTCCCCACATTGCTTACTTATC 59.424 45.833 0.00 0.00 0.00 1.75
670 707 1.004745 CCAGTCCCCACATTGCTTACT 59.995 52.381 0.00 0.00 0.00 2.24
671 708 1.271926 ACCAGTCCCCACATTGCTTAC 60.272 52.381 0.00 0.00 0.00 2.34
672 709 1.072266 ACCAGTCCCCACATTGCTTA 58.928 50.000 0.00 0.00 0.00 3.09
673 710 0.188342 AACCAGTCCCCACATTGCTT 59.812 50.000 0.00 0.00 0.00 3.91
674 711 0.540365 CAACCAGTCCCCACATTGCT 60.540 55.000 0.00 0.00 0.00 3.91
675 712 0.539438 TCAACCAGTCCCCACATTGC 60.539 55.000 0.00 0.00 0.00 3.56
676 713 1.202927 AGTCAACCAGTCCCCACATTG 60.203 52.381 0.00 0.00 0.00 2.82
677 714 1.149101 AGTCAACCAGTCCCCACATT 58.851 50.000 0.00 0.00 0.00 2.71
678 715 0.401738 CAGTCAACCAGTCCCCACAT 59.598 55.000 0.00 0.00 0.00 3.21
679 716 0.692756 TCAGTCAACCAGTCCCCACA 60.693 55.000 0.00 0.00 0.00 4.17
680 717 0.250338 GTCAGTCAACCAGTCCCCAC 60.250 60.000 0.00 0.00 0.00 4.61
681 718 1.415672 GGTCAGTCAACCAGTCCCCA 61.416 60.000 0.00 0.00 39.27 4.96
682 719 1.375326 GGTCAGTCAACCAGTCCCC 59.625 63.158 0.00 0.00 39.27 4.81
683 720 1.004918 CGGTCAGTCAACCAGTCCC 60.005 63.158 0.00 0.00 39.43 4.46
684 721 1.004918 CCGGTCAGTCAACCAGTCC 60.005 63.158 0.00 0.00 39.43 3.85
685 722 0.038159 CTCCGGTCAGTCAACCAGTC 60.038 60.000 0.00 0.00 39.43 3.51
686 723 0.469331 TCTCCGGTCAGTCAACCAGT 60.469 55.000 0.00 0.00 39.43 4.00
687 724 0.679505 TTCTCCGGTCAGTCAACCAG 59.320 55.000 0.00 0.00 39.43 4.00
688 725 1.124780 TTTCTCCGGTCAGTCAACCA 58.875 50.000 0.00 0.00 39.43 3.67
689 726 2.249844 TTTTCTCCGGTCAGTCAACC 57.750 50.000 0.00 0.00 35.86 3.77
690 727 3.058224 CCATTTTTCTCCGGTCAGTCAAC 60.058 47.826 0.00 0.00 0.00 3.18
691 728 3.146066 CCATTTTTCTCCGGTCAGTCAA 58.854 45.455 0.00 0.00 0.00 3.18
692 729 2.370519 TCCATTTTTCTCCGGTCAGTCA 59.629 45.455 0.00 0.00 0.00 3.41
693 730 3.003480 CTCCATTTTTCTCCGGTCAGTC 58.997 50.000 0.00 0.00 0.00 3.51
694 731 2.637872 TCTCCATTTTTCTCCGGTCAGT 59.362 45.455 0.00 0.00 0.00 3.41
695 732 3.334583 TCTCCATTTTTCTCCGGTCAG 57.665 47.619 0.00 0.00 0.00 3.51
696 733 3.559171 CCTTCTCCATTTTTCTCCGGTCA 60.559 47.826 0.00 0.00 0.00 4.02
697 734 3.010420 CCTTCTCCATTTTTCTCCGGTC 58.990 50.000 0.00 0.00 0.00 4.79
698 735 2.290960 CCCTTCTCCATTTTTCTCCGGT 60.291 50.000 0.00 0.00 0.00 5.28
699 736 2.026262 TCCCTTCTCCATTTTTCTCCGG 60.026 50.000 0.00 0.00 0.00 5.14
700 737 3.350219 TCCCTTCTCCATTTTTCTCCG 57.650 47.619 0.00 0.00 0.00 4.63
701 738 5.514169 AGATTCCCTTCTCCATTTTTCTCC 58.486 41.667 0.00 0.00 0.00 3.71
702 739 6.435591 ACAAGATTCCCTTCTCCATTTTTCTC 59.564 38.462 0.00 0.00 31.42 2.87
703 740 6.318112 ACAAGATTCCCTTCTCCATTTTTCT 58.682 36.000 0.00 0.00 31.42 2.52
704 741 6.435591 AGACAAGATTCCCTTCTCCATTTTTC 59.564 38.462 0.00 0.00 31.42 2.29
705 742 6.318112 AGACAAGATTCCCTTCTCCATTTTT 58.682 36.000 0.00 0.00 31.42 1.94
706 743 5.896963 AGACAAGATTCCCTTCTCCATTTT 58.103 37.500 0.00 0.00 31.42 1.82
707 744 5.527026 AGACAAGATTCCCTTCTCCATTT 57.473 39.130 0.00 0.00 31.42 2.32
708 745 5.259632 CAAGACAAGATTCCCTTCTCCATT 58.740 41.667 0.00 0.00 31.42 3.16
709 746 4.853007 CAAGACAAGATTCCCTTCTCCAT 58.147 43.478 0.00 0.00 31.42 3.41
710 747 3.560025 GCAAGACAAGATTCCCTTCTCCA 60.560 47.826 0.00 0.00 31.42 3.86
711 748 3.013219 GCAAGACAAGATTCCCTTCTCC 58.987 50.000 0.00 0.00 31.42 3.71
712 749 3.688673 CAGCAAGACAAGATTCCCTTCTC 59.311 47.826 0.00 0.00 31.42 2.87
713 750 3.683802 CAGCAAGACAAGATTCCCTTCT 58.316 45.455 0.00 0.00 31.42 2.85
714 751 2.163211 GCAGCAAGACAAGATTCCCTTC 59.837 50.000 0.00 0.00 31.42 3.46
715 752 2.165998 GCAGCAAGACAAGATTCCCTT 58.834 47.619 0.00 0.00 34.91 3.95
716 753 1.831580 GCAGCAAGACAAGATTCCCT 58.168 50.000 0.00 0.00 0.00 4.20
717 754 0.449388 CGCAGCAAGACAAGATTCCC 59.551 55.000 0.00 0.00 0.00 3.97
718 755 3.984292 CGCAGCAAGACAAGATTCC 57.016 52.632 0.00 0.00 0.00 3.01
734 771 2.948840 ATAAGTCACTACGGCCGCGC 62.949 60.000 28.58 9.09 0.00 6.86
735 772 0.933509 GATAAGTCACTACGGCCGCG 60.934 60.000 28.58 19.74 0.00 6.46
736 773 0.384669 AGATAAGTCACTACGGCCGC 59.615 55.000 28.58 7.73 0.00 6.53
737 774 2.728922 GAAGATAAGTCACTACGGCCG 58.271 52.381 26.86 26.86 0.00 6.13
738 775 2.543238 CCGAAGATAAGTCACTACGGCC 60.543 54.545 0.00 0.00 33.24 6.13
739 776 2.098770 ACCGAAGATAAGTCACTACGGC 59.901 50.000 0.00 0.00 42.29 5.68
740 777 3.545624 CGACCGAAGATAAGTCACTACGG 60.546 52.174 0.00 0.00 43.79 4.02
741 778 3.063180 ACGACCGAAGATAAGTCACTACG 59.937 47.826 0.00 0.00 0.00 3.51
742 779 4.586334 GACGACCGAAGATAAGTCACTAC 58.414 47.826 0.00 0.00 0.00 2.73
743 780 3.308053 CGACGACCGAAGATAAGTCACTA 59.692 47.826 0.00 0.00 41.76 2.74
744 781 2.095532 CGACGACCGAAGATAAGTCACT 59.904 50.000 0.00 0.00 41.76 3.41
745 782 2.438583 CGACGACCGAAGATAAGTCAC 58.561 52.381 0.00 0.00 41.76 3.67
746 783 1.202110 GCGACGACCGAAGATAAGTCA 60.202 52.381 0.00 0.00 41.76 3.41
747 784 1.063764 AGCGACGACCGAAGATAAGTC 59.936 52.381 0.00 0.00 41.76 3.01
748 785 1.093159 AGCGACGACCGAAGATAAGT 58.907 50.000 0.00 0.00 41.76 2.24
749 786 1.467875 CAGCGACGACCGAAGATAAG 58.532 55.000 0.00 0.00 41.76 1.73
750 787 0.524816 GCAGCGACGACCGAAGATAA 60.525 55.000 0.00 0.00 41.76 1.75
751 788 1.063649 GCAGCGACGACCGAAGATA 59.936 57.895 0.00 0.00 41.76 1.98
752 789 2.202623 GCAGCGACGACCGAAGAT 60.203 61.111 0.00 0.00 41.76 2.40
753 790 4.753877 CGCAGCGACGACCGAAGA 62.754 66.667 9.98 0.00 41.76 2.87
770 807 2.380410 AATCGACGAGCCAACGCAC 61.380 57.895 3.01 0.00 37.52 5.34
771 808 2.048597 AATCGACGAGCCAACGCA 60.049 55.556 3.01 0.00 37.52 5.24
772 809 1.421410 ATCAATCGACGAGCCAACGC 61.421 55.000 3.01 0.00 36.70 4.84
773 810 0.572590 GATCAATCGACGAGCCAACG 59.427 55.000 3.01 0.00 39.31 4.10
785 822 5.468592 AGAGACATATGCAGTCGATCAATC 58.531 41.667 1.58 0.00 40.84 2.67
786 823 5.465532 AGAGACATATGCAGTCGATCAAT 57.534 39.130 1.58 0.00 40.84 2.57
787 824 4.926140 AGAGACATATGCAGTCGATCAA 57.074 40.909 1.58 0.00 40.84 2.57
788 825 4.926140 AAGAGACATATGCAGTCGATCA 57.074 40.909 1.58 0.00 40.84 2.92
789 826 4.381270 CGAAAGAGACATATGCAGTCGATC 59.619 45.833 1.58 1.25 40.84 3.69
790 827 4.202060 ACGAAAGAGACATATGCAGTCGAT 60.202 41.667 1.58 0.00 40.84 3.59
791 828 3.128764 ACGAAAGAGACATATGCAGTCGA 59.871 43.478 1.58 0.00 40.84 4.20
792 829 3.439293 ACGAAAGAGACATATGCAGTCG 58.561 45.455 1.58 6.47 40.84 4.18
793 830 3.483922 CGACGAAAGAGACATATGCAGTC 59.516 47.826 1.58 0.00 36.26 3.51
794 831 3.439293 CGACGAAAGAGACATATGCAGT 58.561 45.455 1.58 0.00 0.00 4.40
795 832 2.791560 CCGACGAAAGAGACATATGCAG 59.208 50.000 1.58 0.00 0.00 4.41
796 833 2.165641 ACCGACGAAAGAGACATATGCA 59.834 45.455 1.58 0.00 0.00 3.96
797 834 2.789893 GACCGACGAAAGAGACATATGC 59.210 50.000 1.58 0.00 0.00 3.14
798 835 3.036633 CGACCGACGAAAGAGACATATG 58.963 50.000 0.00 0.00 45.77 1.78
799 836 2.681848 ACGACCGACGAAAGAGACATAT 59.318 45.455 0.00 0.00 45.77 1.78
800 837 2.079158 ACGACCGACGAAAGAGACATA 58.921 47.619 0.00 0.00 45.77 2.29
801 838 0.879765 ACGACCGACGAAAGAGACAT 59.120 50.000 0.00 0.00 45.77 3.06
802 839 0.236711 GACGACCGACGAAAGAGACA 59.763 55.000 0.00 0.00 45.77 3.41
803 840 0.788645 CGACGACCGACGAAAGAGAC 60.789 60.000 8.40 0.00 45.77 3.36
804 841 1.224069 ACGACGACCGACGAAAGAGA 61.224 55.000 19.17 0.00 45.77 3.10
805 842 1.058590 CACGACGACCGACGAAAGAG 61.059 60.000 19.17 2.42 45.77 2.85
806 843 1.082561 CACGACGACCGACGAAAGA 60.083 57.895 19.17 0.00 45.77 2.52
807 844 0.110688 TACACGACGACCGACGAAAG 60.111 55.000 19.17 11.29 45.77 2.62
808 845 0.384230 GTACACGACGACCGACGAAA 60.384 55.000 19.17 3.34 45.77 3.46
809 846 1.204062 GTACACGACGACCGACGAA 59.796 57.895 19.17 3.65 45.77 3.85
810 847 2.853210 GTACACGACGACCGACGA 59.147 61.111 19.17 0.00 45.77 4.20
819 856 2.431942 CTGGTGGCCGTACACGAC 60.432 66.667 2.76 0.00 42.23 4.34
820 857 2.913578 ACTGGTGGCCGTACACGA 60.914 61.111 2.76 0.00 42.23 4.35
821 858 2.431942 GACTGGTGGCCGTACACG 60.432 66.667 0.00 0.00 42.23 4.49
822 859 1.666872 GTGACTGGTGGCCGTACAC 60.667 63.158 0.00 0.00 40.60 2.90
823 860 2.738480 GTGACTGGTGGCCGTACA 59.262 61.111 0.00 0.00 0.00 2.90
824 861 2.431942 CGTGACTGGTGGCCGTAC 60.432 66.667 0.00 0.00 0.00 3.67
825 862 4.367023 GCGTGACTGGTGGCCGTA 62.367 66.667 0.00 0.00 0.00 4.02
834 871 4.680237 TCAAGGCCCGCGTGACTG 62.680 66.667 0.00 0.00 0.00 3.51
835 872 4.681978 GTCAAGGCCCGCGTGACT 62.682 66.667 16.79 5.22 0.00 3.41
836 873 2.775032 TTAGTCAAGGCCCGCGTGAC 62.775 60.000 16.44 16.44 0.00 3.67
837 874 2.575893 TTAGTCAAGGCCCGCGTGA 61.576 57.895 4.92 0.00 0.00 4.35
838 875 2.047655 TTAGTCAAGGCCCGCGTG 60.048 61.111 4.92 0.00 0.00 5.34
839 876 2.047560 GTTAGTCAAGGCCCGCGT 60.048 61.111 4.92 0.00 0.00 6.01
840 877 2.818274 GGTTAGTCAAGGCCCGCG 60.818 66.667 0.00 0.00 0.00 6.46
841 878 2.818274 CGGTTAGTCAAGGCCCGC 60.818 66.667 0.00 0.00 0.00 6.13
842 879 2.818274 GCGGTTAGTCAAGGCCCG 60.818 66.667 0.00 0.00 41.50 6.13
843 880 1.745489 CTGCGGTTAGTCAAGGCCC 60.745 63.158 0.00 0.00 0.00 5.80
844 881 0.321298 TTCTGCGGTTAGTCAAGGCC 60.321 55.000 0.00 0.00 0.00 5.19
845 882 1.519408 TTTCTGCGGTTAGTCAAGGC 58.481 50.000 0.00 0.00 0.00 4.35
846 883 4.475944 CAAATTTCTGCGGTTAGTCAAGG 58.524 43.478 0.00 0.00 0.00 3.61
847 884 4.023193 ACCAAATTTCTGCGGTTAGTCAAG 60.023 41.667 0.00 0.00 0.00 3.02
848 885 3.886505 ACCAAATTTCTGCGGTTAGTCAA 59.113 39.130 0.00 0.00 0.00 3.18
849 886 3.252215 CACCAAATTTCTGCGGTTAGTCA 59.748 43.478 0.00 0.00 0.00 3.41
850 887 3.365969 CCACCAAATTTCTGCGGTTAGTC 60.366 47.826 0.00 0.00 0.00 2.59
851 888 2.556622 CCACCAAATTTCTGCGGTTAGT 59.443 45.455 0.00 0.00 0.00 2.24
852 889 2.556622 ACCACCAAATTTCTGCGGTTAG 59.443 45.455 0.00 0.00 0.00 2.34
853 890 2.588620 ACCACCAAATTTCTGCGGTTA 58.411 42.857 0.00 0.00 0.00 2.85
854 891 1.408969 ACCACCAAATTTCTGCGGTT 58.591 45.000 0.00 0.00 0.00 4.44
855 892 2.279935 TACCACCAAATTTCTGCGGT 57.720 45.000 0.00 0.00 0.00 5.68
856 893 3.016736 AGATACCACCAAATTTCTGCGG 58.983 45.455 0.00 0.00 0.00 5.69
857 894 3.941483 AGAGATACCACCAAATTTCTGCG 59.059 43.478 0.00 0.00 0.00 5.18
858 895 5.189180 AGAGAGATACCACCAAATTTCTGC 58.811 41.667 0.00 0.00 0.00 4.26
859 896 6.648192 AGAGAGAGATACCACCAAATTTCTG 58.352 40.000 0.00 0.00 0.00 3.02
860 897 6.671779 AGAGAGAGAGATACCACCAAATTTCT 59.328 38.462 0.00 0.00 0.00 2.52
861 898 6.883744 AGAGAGAGAGATACCACCAAATTTC 58.116 40.000 0.00 0.00 0.00 2.17
862 899 6.406400 CGAGAGAGAGAGATACCACCAAATTT 60.406 42.308 0.00 0.00 0.00 1.82
863 900 5.068460 CGAGAGAGAGAGATACCACCAAATT 59.932 44.000 0.00 0.00 0.00 1.82
864 901 4.582656 CGAGAGAGAGAGATACCACCAAAT 59.417 45.833 0.00 0.00 0.00 2.32
865 902 3.948473 CGAGAGAGAGAGATACCACCAAA 59.052 47.826 0.00 0.00 0.00 3.28
866 903 3.200165 TCGAGAGAGAGAGATACCACCAA 59.800 47.826 0.00 0.00 34.84 3.67
867 904 2.772515 TCGAGAGAGAGAGATACCACCA 59.227 50.000 0.00 0.00 34.84 4.17
868 905 3.135994 GTCGAGAGAGAGAGATACCACC 58.864 54.545 0.00 0.00 43.49 4.61
869 906 3.135994 GGTCGAGAGAGAGAGATACCAC 58.864 54.545 0.00 0.00 43.49 4.16
870 907 2.772515 TGGTCGAGAGAGAGAGATACCA 59.227 50.000 0.00 0.00 43.49 3.25
871 908 3.135994 GTGGTCGAGAGAGAGAGATACC 58.864 54.545 0.00 0.00 43.49 2.73
872 909 3.558418 GTGTGGTCGAGAGAGAGAGATAC 59.442 52.174 0.00 0.00 43.49 2.24
873 910 3.738590 CGTGTGGTCGAGAGAGAGAGATA 60.739 52.174 0.00 0.00 43.49 1.98
874 911 2.639065 GTGTGGTCGAGAGAGAGAGAT 58.361 52.381 0.00 0.00 43.49 2.75
875 912 1.673329 CGTGTGGTCGAGAGAGAGAGA 60.673 57.143 0.00 0.00 43.49 3.10
876 913 0.724549 CGTGTGGTCGAGAGAGAGAG 59.275 60.000 0.00 0.00 43.49 3.20
877 914 0.673956 CCGTGTGGTCGAGAGAGAGA 60.674 60.000 0.00 0.00 43.49 3.10
878 915 0.673956 TCCGTGTGGTCGAGAGAGAG 60.674 60.000 0.00 0.00 43.49 3.20
890 927 2.074547 ATTTGTAGACCGTCCGTGTG 57.925 50.000 0.00 0.00 0.00 3.82
891 928 2.414559 CGTATTTGTAGACCGTCCGTGT 60.415 50.000 0.00 0.00 0.00 4.49
895 932 3.354397 CGTACGTATTTGTAGACCGTCC 58.646 50.000 7.22 0.00 33.32 4.79
896 933 3.354397 CCGTACGTATTTGTAGACCGTC 58.646 50.000 15.21 0.00 33.32 4.79
900 937 2.099756 AGGCCCGTACGTATTTGTAGAC 59.900 50.000 15.21 0.00 0.00 2.59
905 942 2.304751 AGAAGGCCCGTACGTATTTG 57.695 50.000 15.21 0.00 0.00 2.32
911 948 1.074872 GTTCGAAGAAGGCCCGTACG 61.075 60.000 8.69 8.69 45.90 3.67
913 950 0.245539 CTGTTCGAAGAAGGCCCGTA 59.754 55.000 0.00 0.00 45.90 4.02
919 956 1.229428 TGCTTGCTGTTCGAAGAAGG 58.771 50.000 0.00 0.00 45.90 3.46
927 964 1.130749 CTGCTCTGATGCTTGCTGTTC 59.869 52.381 0.00 0.00 0.00 3.18
929 966 0.677098 CCTGCTCTGATGCTTGCTGT 60.677 55.000 0.00 0.00 0.00 4.40
931 968 0.547075 ATCCTGCTCTGATGCTTGCT 59.453 50.000 0.00 0.00 0.00 3.91
932 969 2.144730 CTATCCTGCTCTGATGCTTGC 58.855 52.381 0.00 0.00 0.00 4.01
942 979 0.873743 GCACGTCTGCTATCCTGCTC 60.874 60.000 0.00 0.00 40.63 4.26
978 1023 2.668280 GGTGTGTTTCGAGCGAGGC 61.668 63.158 0.00 0.00 0.00 4.70
998 1043 3.434319 CACTGTGGGACGCCATGC 61.434 66.667 0.00 0.00 38.60 4.06
999 1044 3.434319 GCACTGTGGGACGCCATG 61.434 66.667 10.21 0.00 38.60 3.66
1000 1045 3.640407 AGCACTGTGGGACGCCAT 61.640 61.111 10.21 0.00 38.60 4.40
1047 1098 1.093496 TGGCGACGAAGAGAGCGATA 61.093 55.000 0.00 0.00 0.00 2.92
1064 1115 4.889856 TGATGACCGCGGCGATGG 62.890 66.667 28.58 14.71 0.00 3.51
1066 1117 2.356313 GATGATGACCGCGGCGAT 60.356 61.111 28.58 17.95 0.00 4.58
1075 1126 1.929836 GACGGAGCTGTTGATGATGAC 59.070 52.381 0.00 0.00 0.00 3.06
1126 1180 1.972223 CCGACGACTGACCTGAGGT 60.972 63.158 2.41 2.41 39.44 3.85
1291 1348 1.839747 TGTAGGGTTGACCGGCACT 60.840 57.895 0.00 0.00 46.96 4.40
1335 1392 1.376166 CGCCGGTGGTTTACATCCA 60.376 57.895 7.26 0.00 0.00 3.41
1357 1414 1.072331 CGGATGTAATTAGGGCTGGCT 59.928 52.381 0.00 0.00 0.00 4.75
1380 1437 3.083349 TGGGAGATGGGGTCTGCG 61.083 66.667 0.00 0.00 45.47 5.18
1385 1442 0.475632 TTGTGTCTGGGAGATGGGGT 60.476 55.000 0.00 0.00 0.00 4.95
1408 1468 4.402474 ACATATATCGATGGATCCTCGCAA 59.598 41.667 21.64 14.88 36.11 4.85
1536 2397 4.202000 ACACGAAATTTCAGACATGCAACA 60.202 37.500 17.99 0.00 0.00 3.33
1549 2410 6.083098 TGACCATGAATTCACACGAAATTT 57.917 33.333 11.07 0.00 34.01 1.82
1564 2425 4.023279 CGTCTCCACAAAAATTGACCATGA 60.023 41.667 0.00 0.00 0.00 3.07
1582 2443 4.205792 CCGAACCAAACGTAATATCGTCTC 59.794 45.833 0.00 0.00 43.38 3.36
1588 2449 8.266392 TGTAAATTCCGAACCAAACGTAATAT 57.734 30.769 0.00 0.00 0.00 1.28
1594 2455 3.058501 AGCTGTAAATTCCGAACCAAACG 60.059 43.478 0.00 0.00 0.00 3.60
1613 2474 8.746052 TTTACTTTGTGCATTGGTATATAGCT 57.254 30.769 12.87 0.00 0.00 3.32
1644 2506 4.773674 TGAATGAGGATGCCTTCATTTTGT 59.226 37.500 3.70 0.00 34.26 2.83
1744 2614 4.329831 GGCCGAACAAATGCCCTA 57.670 55.556 0.00 0.00 39.30 3.53
1753 2623 0.461135 GGTATTACGAGGGCCGAACA 59.539 55.000 0.00 0.00 41.76 3.18
1938 2808 2.290071 ACAAACCGGGACTAATGGTCAG 60.290 50.000 6.32 0.00 46.16 3.51
2000 2870 1.816863 GCGAGGTGGGACTGAACTCA 61.817 60.000 0.00 0.00 0.00 3.41
2059 2929 0.676151 GGAGCTCAACAAGGCAGAGG 60.676 60.000 17.19 0.00 0.00 3.69
2226 3097 7.624360 ACACACAAAAAGTCTGTAAAGATCA 57.376 32.000 0.00 0.00 26.70 2.92
2340 3213 7.839680 AACTCATCTGTTACAAAGGGATTTT 57.160 32.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.