Multiple sequence alignment - TraesCS3B01G407300

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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 TraesCS3B01G407300 chr3B 100.000 2815 0 0 1 2815 642817951 642820765 0.000000e+00 5199
1 TraesCS3B01G407300 chr3B 79.046 587 101 13 15 588 523278871 523279448 1.580000e-102 383
2 TraesCS3B01G407300 chr3B 76.480 642 97 31 6 604 664917056 664917686 1.640000e-77 300
3 TraesCS3B01G407300 chr3A 90.537 2050 128 32 781 2815 624532700 624534698 0.000000e+00 2651
4 TraesCS3B01G407300 chr3A 81.407 597 92 9 1 588 201496000 201496586 1.180000e-128 470
5 TraesCS3B01G407300 chr3D 90.331 1903 120 28 779 2674 481526562 481528407 0.000000e+00 2436
6 TraesCS3B01G407300 chr4A 84.473 541 63 13 4 536 524177513 524176986 5.380000e-142 514
7 TraesCS3B01G407300 chr4A 79.779 633 87 23 1 606 100663350 100663968 3.350000e-114 422
8 TraesCS3B01G407300 chr7D 81.569 548 77 15 4 536 617207190 617206652 5.570000e-117 431
9 TraesCS3B01G407300 chr7A 79.355 620 100 21 2 609 706365146 706364543 7.260000e-111 411
10 TraesCS3B01G407300 chr2A 79.475 609 101 17 1 601 13109735 13109143 7.260000e-111 411
11 TraesCS3B01G407300 chr2B 78.519 540 88 19 1 526 16786596 16787121 2.090000e-86 329
12 TraesCS3B01G407300 chr1A 80.285 421 57 15 1 396 297877065 297876646 7.630000e-76 294
13 TraesCS3B01G407300 chr5D 75.469 640 111 30 3 609 424942834 424942208 1.290000e-68 270
14 TraesCS3B01G407300 chr5D 82.927 287 26 9 1 265 514152068 514152353 1.300000e-58 237
15 TraesCS3B01G407300 chr5D 87.879 132 14 1 1 132 521097250 521097121 1.350000e-33 154
16 TraesCS3B01G407300 chr5A 77.525 396 65 12 62 442 17631769 17631383 1.700000e-52 217


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 TraesCS3B01G407300 chr3B 642817951 642820765 2814 False 5199 5199 100.000 1 2815 1 chr3B.!!$F2 2814
1 TraesCS3B01G407300 chr3B 523278871 523279448 577 False 383 383 79.046 15 588 1 chr3B.!!$F1 573
2 TraesCS3B01G407300 chr3B 664917056 664917686 630 False 300 300 76.480 6 604 1 chr3B.!!$F3 598
3 TraesCS3B01G407300 chr3A 624532700 624534698 1998 False 2651 2651 90.537 781 2815 1 chr3A.!!$F2 2034
4 TraesCS3B01G407300 chr3A 201496000 201496586 586 False 470 470 81.407 1 588 1 chr3A.!!$F1 587
5 TraesCS3B01G407300 chr3D 481526562 481528407 1845 False 2436 2436 90.331 779 2674 1 chr3D.!!$F1 1895
6 TraesCS3B01G407300 chr4A 524176986 524177513 527 True 514 514 84.473 4 536 1 chr4A.!!$R1 532
7 TraesCS3B01G407300 chr4A 100663350 100663968 618 False 422 422 79.779 1 606 1 chr4A.!!$F1 605
8 TraesCS3B01G407300 chr7D 617206652 617207190 538 True 431 431 81.569 4 536 1 chr7D.!!$R1 532
9 TraesCS3B01G407300 chr7A 706364543 706365146 603 True 411 411 79.355 2 609 1 chr7A.!!$R1 607
10 TraesCS3B01G407300 chr2A 13109143 13109735 592 True 411 411 79.475 1 601 1 chr2A.!!$R1 600
11 TraesCS3B01G407300 chr2B 16786596 16787121 525 False 329 329 78.519 1 526 1 chr2B.!!$F1 525
12 TraesCS3B01G407300 chr5D 424942208 424942834 626 True 270 270 75.469 3 609 1 chr5D.!!$R1 606

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
719 790 0.029567 GACCGGATAGTGACTGAGCG 59.97 60.0 9.46 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 2361 1.133407 TCAAAACTGTGTTTGCCCGTC 59.867 47.619 9.23 0.0 38.2 4.79 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
144 190 4.758251 CCCGCTGTCACGCCATGA 62.758 66.667 0.00 0.00 33.79 3.07
204 250 1.763770 CACCAGAGAAGGGGTTGCT 59.236 57.895 0.00 0.00 34.45 3.91
207 253 1.743252 CAGAGAAGGGGTTGCTCGC 60.743 63.158 0.00 0.00 33.98 5.03
320 370 2.161410 CGGACGCAATGGATTTTTGAGA 59.839 45.455 0.00 0.00 0.00 3.27
396 448 2.568956 CCAGACAACCATCTCCTCTTCA 59.431 50.000 0.00 0.00 0.00 3.02
397 449 3.369261 CCAGACAACCATCTCCTCTTCAG 60.369 52.174 0.00 0.00 0.00 3.02
398 450 2.235898 AGACAACCATCTCCTCTTCAGC 59.764 50.000 0.00 0.00 0.00 4.26
399 451 2.235898 GACAACCATCTCCTCTTCAGCT 59.764 50.000 0.00 0.00 0.00 4.24
400 452 2.235898 ACAACCATCTCCTCTTCAGCTC 59.764 50.000 0.00 0.00 0.00 4.09
401 453 2.500910 CAACCATCTCCTCTTCAGCTCT 59.499 50.000 0.00 0.00 0.00 4.09
402 454 2.831565 ACCATCTCCTCTTCAGCTCTT 58.168 47.619 0.00 0.00 0.00 2.85
403 455 2.765699 ACCATCTCCTCTTCAGCTCTTC 59.234 50.000 0.00 0.00 0.00 2.87
473 525 0.250858 CAGATCCATTGCCCGCCATA 60.251 55.000 0.00 0.00 0.00 2.74
513 565 2.671963 GGGGACGAGTTTGGGTGC 60.672 66.667 0.00 0.00 0.00 5.01
519 571 2.747686 GAGTTTGGGTGCCGGAGA 59.252 61.111 5.05 0.00 0.00 3.71
536 605 2.243810 GAGAGGAGTGAGTGAAGTGGT 58.756 52.381 0.00 0.00 0.00 4.16
539 608 4.421131 AGAGGAGTGAGTGAAGTGGTTAT 58.579 43.478 0.00 0.00 0.00 1.89
544 613 4.642429 AGTGAGTGAAGTGGTTATGGTTC 58.358 43.478 0.00 0.00 0.00 3.62
567 637 2.903357 GGCGAGCAGATGGGAAGA 59.097 61.111 0.00 0.00 0.00 2.87
574 644 4.390297 GCGAGCAGATGGGAAGAAATATAC 59.610 45.833 0.00 0.00 0.00 1.47
588 659 2.062971 ATATACGTGAGGTCGGTGGT 57.937 50.000 0.00 0.00 34.94 4.16
593 664 1.317431 CGTGAGGTCGGTGGTCCATA 61.317 60.000 0.00 0.00 0.00 2.74
609 680 1.762460 ATAGTGGGCCAGGTCCGAG 60.762 63.158 6.40 0.00 0.00 4.63
619 690 4.424566 GGTCCGAGCGCAACCGTA 62.425 66.667 11.47 0.00 36.67 4.02
620 691 2.202703 GTCCGAGCGCAACCGTAT 60.203 61.111 11.47 0.00 36.67 3.06
621 692 1.808390 GTCCGAGCGCAACCGTATT 60.808 57.895 11.47 0.00 36.67 1.89
622 693 1.079681 TCCGAGCGCAACCGTATTT 60.080 52.632 11.47 0.00 36.67 1.40
623 694 1.060308 CCGAGCGCAACCGTATTTG 59.940 57.895 11.47 0.00 36.67 2.32
624 695 1.060308 CGAGCGCAACCGTATTTGG 59.940 57.895 11.47 0.00 36.67 3.28
625 696 1.427819 GAGCGCAACCGTATTTGGG 59.572 57.895 11.47 0.00 41.23 4.12
627 698 3.585856 CGCAACCGTATTTGGGCT 58.414 55.556 0.00 0.00 33.26 5.19
628 699 1.136565 CGCAACCGTATTTGGGCTG 59.863 57.895 0.00 0.00 33.26 4.85
629 700 1.302383 CGCAACCGTATTTGGGCTGA 61.302 55.000 0.00 0.00 33.26 4.26
630 701 0.885196 GCAACCGTATTTGGGCTGAA 59.115 50.000 0.00 0.00 0.00 3.02
631 702 1.476488 GCAACCGTATTTGGGCTGAAT 59.524 47.619 0.00 0.00 0.00 2.57
632 703 2.685897 GCAACCGTATTTGGGCTGAATA 59.314 45.455 0.00 0.00 0.00 1.75
633 704 3.317993 GCAACCGTATTTGGGCTGAATAT 59.682 43.478 0.00 0.00 0.00 1.28
634 705 4.792704 GCAACCGTATTTGGGCTGAATATG 60.793 45.833 5.96 5.96 0.00 1.78
635 706 4.431416 ACCGTATTTGGGCTGAATATGA 57.569 40.909 11.55 0.00 30.89 2.15
636 707 4.389374 ACCGTATTTGGGCTGAATATGAG 58.611 43.478 11.55 6.76 30.89 2.90
637 708 3.753272 CCGTATTTGGGCTGAATATGAGG 59.247 47.826 11.55 6.33 30.89 3.86
638 709 4.504864 CCGTATTTGGGCTGAATATGAGGA 60.505 45.833 11.55 0.00 30.89 3.71
639 710 4.692625 CGTATTTGGGCTGAATATGAGGAG 59.307 45.833 6.72 0.00 30.89 3.69
640 711 4.803329 ATTTGGGCTGAATATGAGGAGT 57.197 40.909 0.00 0.00 0.00 3.85
641 712 3.565764 TTGGGCTGAATATGAGGAGTG 57.434 47.619 0.00 0.00 0.00 3.51
642 713 1.141657 TGGGCTGAATATGAGGAGTGC 59.858 52.381 0.00 0.00 0.00 4.40
643 714 1.544314 GGGCTGAATATGAGGAGTGCC 60.544 57.143 0.00 0.00 38.49 5.01
644 715 1.506493 GCTGAATATGAGGAGTGCCG 58.494 55.000 0.00 0.00 39.96 5.69
645 716 1.069204 GCTGAATATGAGGAGTGCCGA 59.931 52.381 0.00 0.00 39.96 5.54
646 717 2.289320 GCTGAATATGAGGAGTGCCGAT 60.289 50.000 0.00 0.00 39.96 4.18
647 718 3.583806 CTGAATATGAGGAGTGCCGATC 58.416 50.000 0.00 0.00 39.96 3.69
648 719 2.965147 TGAATATGAGGAGTGCCGATCA 59.035 45.455 0.00 0.00 39.96 2.92
649 720 3.387699 TGAATATGAGGAGTGCCGATCAA 59.612 43.478 0.00 0.00 39.96 2.57
650 721 4.040829 TGAATATGAGGAGTGCCGATCAAT 59.959 41.667 0.00 0.00 39.96 2.57
651 722 2.540265 ATGAGGAGTGCCGATCAATC 57.460 50.000 0.00 0.00 38.94 2.67
655 726 2.892305 GAGTGCCGATCAATCCGAG 58.108 57.895 0.00 0.00 33.94 4.63
656 727 1.218230 GAGTGCCGATCAATCCGAGC 61.218 60.000 0.00 0.00 33.94 5.03
664 735 1.594862 GATCAATCCGAGCGTTTGAGG 59.405 52.381 10.00 0.00 33.26 3.86
665 736 1.019278 TCAATCCGAGCGTTTGAGGC 61.019 55.000 0.00 0.00 0.00 4.70
666 737 1.745489 AATCCGAGCGTTTGAGGCC 60.745 57.895 0.00 0.00 0.00 5.19
667 738 3.682292 ATCCGAGCGTTTGAGGCCC 62.682 63.158 0.00 0.00 0.00 5.80
668 739 4.697756 CCGAGCGTTTGAGGCCCA 62.698 66.667 0.00 0.00 0.00 5.36
669 740 3.423154 CGAGCGTTTGAGGCCCAC 61.423 66.667 0.00 0.00 0.00 4.61
670 741 2.032681 GAGCGTTTGAGGCCCACT 59.967 61.111 0.00 0.00 0.00 4.00
671 742 1.600916 GAGCGTTTGAGGCCCACTT 60.601 57.895 0.00 0.00 0.00 3.16
672 743 0.321298 GAGCGTTTGAGGCCCACTTA 60.321 55.000 0.00 0.00 0.00 2.24
673 744 0.109723 AGCGTTTGAGGCCCACTTAA 59.890 50.000 0.00 0.00 0.00 1.85
674 745 0.521735 GCGTTTGAGGCCCACTTAAG 59.478 55.000 0.00 0.00 0.00 1.85
675 746 1.880646 GCGTTTGAGGCCCACTTAAGA 60.881 52.381 10.09 0.00 0.00 2.10
676 747 1.804748 CGTTTGAGGCCCACTTAAGAC 59.195 52.381 10.09 0.00 0.00 3.01
677 748 1.804748 GTTTGAGGCCCACTTAAGACG 59.195 52.381 10.09 0.00 0.00 4.18
678 749 1.053424 TTGAGGCCCACTTAAGACGT 58.947 50.000 10.09 0.00 0.00 4.34
679 750 1.053424 TGAGGCCCACTTAAGACGTT 58.947 50.000 10.09 0.00 0.00 3.99
680 751 1.418637 TGAGGCCCACTTAAGACGTTT 59.581 47.619 10.09 0.00 0.00 3.60
681 752 1.804748 GAGGCCCACTTAAGACGTTTG 59.195 52.381 10.09 0.00 0.00 2.93
682 753 1.142262 AGGCCCACTTAAGACGTTTGT 59.858 47.619 10.09 0.00 0.00 2.83
683 754 1.534163 GGCCCACTTAAGACGTTTGTC 59.466 52.381 10.09 0.00 45.86 3.18
694 765 3.768468 GACGTTTGTCTGGGTCAAAAA 57.232 42.857 0.00 0.00 42.08 1.94
695 766 4.301637 GACGTTTGTCTGGGTCAAAAAT 57.698 40.909 0.00 0.00 42.08 1.82
696 767 4.678622 GACGTTTGTCTGGGTCAAAAATT 58.321 39.130 0.00 0.00 42.08 1.82
697 768 5.079689 ACGTTTGTCTGGGTCAAAAATTT 57.920 34.783 0.00 0.00 36.71 1.82
698 769 4.867608 ACGTTTGTCTGGGTCAAAAATTTG 59.132 37.500 0.00 0.00 36.71 2.32
699 770 4.867608 CGTTTGTCTGGGTCAAAAATTTGT 59.132 37.500 5.84 0.00 39.18 2.83
700 771 5.220378 CGTTTGTCTGGGTCAAAAATTTGTG 60.220 40.000 1.55 1.55 39.18 3.33
701 772 5.667539 TTGTCTGGGTCAAAAATTTGTGA 57.332 34.783 6.98 6.98 39.18 3.58
702 773 5.004922 TGTCTGGGTCAAAAATTTGTGAC 57.995 39.130 26.93 26.93 42.83 3.67
710 781 6.009115 GTCAAAAATTTGTGACCGGATAGT 57.991 37.500 25.26 0.00 38.57 2.12
711 782 5.856455 GTCAAAAATTTGTGACCGGATAGTG 59.144 40.000 25.26 0.00 38.57 2.74
712 783 5.765677 TCAAAAATTTGTGACCGGATAGTGA 59.234 36.000 9.46 0.00 39.18 3.41
713 784 5.622770 AAAATTTGTGACCGGATAGTGAC 57.377 39.130 9.46 0.00 0.00 3.67
714 785 4.553330 AATTTGTGACCGGATAGTGACT 57.447 40.909 9.46 0.00 0.00 3.41
715 786 3.313012 TTTGTGACCGGATAGTGACTG 57.687 47.619 9.46 0.00 0.00 3.51
716 787 2.209690 TGTGACCGGATAGTGACTGA 57.790 50.000 9.46 0.00 0.00 3.41
717 788 2.092323 TGTGACCGGATAGTGACTGAG 58.908 52.381 9.46 0.00 0.00 3.35
718 789 1.103803 TGACCGGATAGTGACTGAGC 58.896 55.000 9.46 0.00 0.00 4.26
719 790 0.029567 GACCGGATAGTGACTGAGCG 59.970 60.000 9.46 0.00 0.00 5.03
720 791 1.360551 CCGGATAGTGACTGAGCGG 59.639 63.158 0.00 0.00 0.00 5.52
721 792 1.384989 CCGGATAGTGACTGAGCGGT 61.385 60.000 0.00 0.00 0.00 5.68
722 793 0.029567 CGGATAGTGACTGAGCGGTC 59.970 60.000 7.89 7.89 36.81 4.79
723 794 0.386113 GGATAGTGACTGAGCGGTCC 59.614 60.000 12.85 0.00 35.54 4.46
724 795 0.029567 GATAGTGACTGAGCGGTCCG 59.970 60.000 12.85 6.99 35.54 4.79
725 796 0.680280 ATAGTGACTGAGCGGTCCGT 60.680 55.000 13.94 11.61 35.54 4.69
726 797 1.303799 TAGTGACTGAGCGGTCCGTC 61.304 60.000 26.15 26.15 37.42 4.79
727 798 3.371063 TGACTGAGCGGTCCGTCC 61.371 66.667 28.53 15.62 36.38 4.79
728 799 3.371063 GACTGAGCGGTCCGTCCA 61.371 66.667 23.56 10.07 32.28 4.02
729 800 3.343788 GACTGAGCGGTCCGTCCAG 62.344 68.421 23.56 24.01 32.28 3.86
730 801 3.374402 CTGAGCGGTCCGTCCAGT 61.374 66.667 20.02 0.71 35.57 4.00
731 802 3.343788 CTGAGCGGTCCGTCCAGTC 62.344 68.421 20.02 8.91 35.57 3.51
732 803 3.371063 GAGCGGTCCGTCCAGTCA 61.371 66.667 13.94 0.00 35.57 3.41
733 804 2.680352 AGCGGTCCGTCCAGTCAT 60.680 61.111 13.94 0.00 35.57 3.06
734 805 1.379443 AGCGGTCCGTCCAGTCATA 60.379 57.895 13.94 0.00 35.57 2.15
735 806 1.226888 GCGGTCCGTCCAGTCATAC 60.227 63.158 13.94 0.00 35.57 2.39
736 807 1.940883 GCGGTCCGTCCAGTCATACA 61.941 60.000 13.94 0.00 35.57 2.29
737 808 0.528924 CGGTCCGTCCAGTCATACAA 59.471 55.000 2.08 0.00 35.57 2.41
738 809 1.469251 CGGTCCGTCCAGTCATACAAG 60.469 57.143 2.08 0.00 35.57 3.16
739 810 1.822990 GGTCCGTCCAGTCATACAAGA 59.177 52.381 0.00 0.00 35.97 3.02
740 811 2.416972 GGTCCGTCCAGTCATACAAGAC 60.417 54.545 0.00 0.00 38.81 3.01
741 812 1.471287 TCCGTCCAGTCATACAAGACG 59.529 52.381 12.26 12.26 43.24 4.18
742 813 1.909376 CGTCCAGTCATACAAGACGG 58.091 55.000 11.68 0.00 43.24 4.79
745 816 2.762535 CCAGTCATACAAGACGGGTT 57.237 50.000 5.31 0.00 45.23 4.11
746 817 3.053831 CCAGTCATACAAGACGGGTTT 57.946 47.619 5.31 0.00 45.23 3.27
747 818 2.742053 CCAGTCATACAAGACGGGTTTG 59.258 50.000 5.31 0.00 45.23 2.93
748 819 3.556213 CCAGTCATACAAGACGGGTTTGA 60.556 47.826 5.31 0.00 45.23 2.69
749 820 3.679980 CAGTCATACAAGACGGGTTTGAG 59.320 47.826 3.33 0.00 43.24 3.02
750 821 3.000727 GTCATACAAGACGGGTTTGAGG 58.999 50.000 3.33 0.00 29.03 3.86
751 822 1.737793 CATACAAGACGGGTTTGAGGC 59.262 52.381 3.33 0.00 0.00 4.70
752 823 0.320073 TACAAGACGGGTTTGAGGCG 60.320 55.000 3.33 0.00 0.00 5.52
753 824 1.597027 CAAGACGGGTTTGAGGCGT 60.597 57.895 0.00 0.00 0.00 5.68
754 825 1.301479 AAGACGGGTTTGAGGCGTC 60.301 57.895 0.00 0.00 0.00 5.19
755 826 3.110178 GACGGGTTTGAGGCGTCG 61.110 66.667 1.39 0.00 0.00 5.12
756 827 4.675029 ACGGGTTTGAGGCGTCGG 62.675 66.667 1.39 0.00 0.00 4.79
766 837 4.891566 GGCGTCGGGCTATAGATG 57.108 61.111 3.21 0.00 42.94 2.90
767 838 1.446272 GGCGTCGGGCTATAGATGC 60.446 63.158 3.21 0.00 45.73 3.91
768 839 1.587054 GCGTCGGGCTATAGATGCT 59.413 57.895 3.21 0.00 43.78 3.79
769 840 0.456995 GCGTCGGGCTATAGATGCTC 60.457 60.000 3.21 0.00 43.78 4.26
774 845 1.551452 GGGCTATAGATGCTCGGACT 58.449 55.000 3.21 0.00 0.00 3.85
775 846 1.474879 GGGCTATAGATGCTCGGACTC 59.525 57.143 3.21 0.00 0.00 3.36
776 847 2.442413 GGCTATAGATGCTCGGACTCT 58.558 52.381 3.21 0.00 0.00 3.24
777 848 2.163412 GGCTATAGATGCTCGGACTCTG 59.837 54.545 3.21 0.00 0.00 3.35
818 889 2.001361 ATACGCGGTCGCTAGTTGCT 62.001 55.000 12.47 0.00 40.11 3.91
826 897 2.520979 GTCGCTAGTTGCTACACTGAG 58.479 52.381 0.13 0.00 37.32 3.35
830 901 2.612972 GCTAGTTGCTACACTGAGCCAA 60.613 50.000 0.13 0.00 42.11 4.52
843 914 3.244044 ACTGAGCCAAGAGACAAGAAGAC 60.244 47.826 0.00 0.00 0.00 3.01
946 1018 0.394625 TTAACCGGCCCTGGTATTGC 60.395 55.000 0.00 0.00 42.89 3.56
947 1019 1.563577 TAACCGGCCCTGGTATTGCA 61.564 55.000 0.00 0.00 42.89 4.08
964 1036 1.270518 TGCACTCTCTCAAGCCTGAAC 60.271 52.381 0.00 0.00 0.00 3.18
978 1050 0.622665 CTGAACCTCCATCCTGCCTT 59.377 55.000 0.00 0.00 0.00 4.35
981 1057 0.846427 AACCTCCATCCTGCCTTCCA 60.846 55.000 0.00 0.00 0.00 3.53
1152 1228 1.625818 GAGAAGCTCCCCAGTTTCAGA 59.374 52.381 0.00 0.00 41.23 3.27
1155 1231 1.743252 GCTCCCCAGTTTCAGAGCG 60.743 63.158 0.00 0.00 42.02 5.03
1301 1377 3.067833 GGTTGCTCTTTCAGGTCAGTAC 58.932 50.000 0.00 0.00 0.00 2.73
1302 1378 3.494398 GGTTGCTCTTTCAGGTCAGTACA 60.494 47.826 0.00 0.00 0.00 2.90
1303 1379 3.667497 TGCTCTTTCAGGTCAGTACAG 57.333 47.619 0.00 0.00 0.00 2.74
1304 1380 2.965831 TGCTCTTTCAGGTCAGTACAGT 59.034 45.455 0.00 0.00 0.00 3.55
1305 1381 4.149598 TGCTCTTTCAGGTCAGTACAGTA 58.850 43.478 0.00 0.00 0.00 2.74
1306 1382 4.022242 TGCTCTTTCAGGTCAGTACAGTAC 60.022 45.833 2.05 2.05 0.00 2.73
1316 1392 5.952947 AGGTCAGTACAGTACTAAGCATTCT 59.047 40.000 13.12 2.39 37.23 2.40
1339 1415 2.205074 GAGCCGTGTTGGAGTATGATG 58.795 52.381 0.00 0.00 42.00 3.07
1341 1417 1.933853 GCCGTGTTGGAGTATGATGTC 59.066 52.381 0.00 0.00 42.00 3.06
1342 1418 2.418746 GCCGTGTTGGAGTATGATGTCT 60.419 50.000 0.00 0.00 42.00 3.41
1343 1419 3.190079 CCGTGTTGGAGTATGATGTCTG 58.810 50.000 0.00 0.00 42.00 3.51
1344 1420 2.604914 CGTGTTGGAGTATGATGTCTGC 59.395 50.000 0.00 0.00 0.00 4.26
1345 1421 3.677148 CGTGTTGGAGTATGATGTCTGCT 60.677 47.826 0.00 0.00 0.00 4.24
1346 1422 3.868077 GTGTTGGAGTATGATGTCTGCTC 59.132 47.826 0.00 0.00 0.00 4.26
1348 1424 4.223700 TGTTGGAGTATGATGTCTGCTCTT 59.776 41.667 0.00 0.00 0.00 2.85
1349 1425 4.662468 TGGAGTATGATGTCTGCTCTTC 57.338 45.455 0.00 0.00 0.00 2.87
1351 1427 4.340666 TGGAGTATGATGTCTGCTCTTCTC 59.659 45.833 0.00 0.00 0.00 2.87
1352 1428 4.584325 GGAGTATGATGTCTGCTCTTCTCT 59.416 45.833 0.00 0.00 0.00 3.10
1353 1429 5.278463 GGAGTATGATGTCTGCTCTTCTCTC 60.278 48.000 0.00 0.00 0.00 3.20
1354 1430 5.448654 AGTATGATGTCTGCTCTTCTCTCT 58.551 41.667 0.00 0.00 0.00 3.10
1355 1431 4.924305 ATGATGTCTGCTCTTCTCTCTC 57.076 45.455 0.00 0.00 0.00 3.20
1356 1432 3.966979 TGATGTCTGCTCTTCTCTCTCT 58.033 45.455 0.00 0.00 0.00 3.10
1357 1433 3.947196 TGATGTCTGCTCTTCTCTCTCTC 59.053 47.826 0.00 0.00 0.00 3.20
1392 1500 6.480763 TCAGCTTAGAATTCAATACACCCAA 58.519 36.000 8.44 0.00 0.00 4.12
1393 1501 7.118723 TCAGCTTAGAATTCAATACACCCAAT 58.881 34.615 8.44 0.00 0.00 3.16
1408 1520 6.331369 ACACCCAATTAGAACTGATGTTTG 57.669 37.500 0.00 0.00 36.39 2.93
1425 1537 4.950050 TGTTTGTGTTGAACCTGTTTGTT 58.050 34.783 0.00 0.00 0.00 2.83
1502 1614 0.988832 AAGGTATGGCAACCCGAGAA 59.011 50.000 13.08 0.00 40.71 2.87
1511 1623 1.350193 CAACCCGAGAACTGACGATG 58.650 55.000 0.00 0.00 0.00 3.84
1518 1630 2.408704 CGAGAACTGACGATGTGGTTTC 59.591 50.000 0.00 0.00 0.00 2.78
1520 1632 3.804036 AGAACTGACGATGTGGTTTCAA 58.196 40.909 0.00 0.00 0.00 2.69
1521 1633 4.196193 AGAACTGACGATGTGGTTTCAAA 58.804 39.130 0.00 0.00 0.00 2.69
1522 1634 3.963383 ACTGACGATGTGGTTTCAAAC 57.037 42.857 0.00 0.00 0.00 2.93
1523 1635 3.541632 ACTGACGATGTGGTTTCAAACT 58.458 40.909 0.00 0.00 0.00 2.66
1524 1636 3.945285 ACTGACGATGTGGTTTCAAACTT 59.055 39.130 0.00 0.00 0.00 2.66
1525 1637 4.398044 ACTGACGATGTGGTTTCAAACTTT 59.602 37.500 0.00 0.00 0.00 2.66
1526 1638 4.915704 TGACGATGTGGTTTCAAACTTTC 58.084 39.130 0.00 0.00 0.00 2.62
1527 1639 4.396478 TGACGATGTGGTTTCAAACTTTCA 59.604 37.500 0.00 0.00 0.00 2.69
1528 1640 5.106118 TGACGATGTGGTTTCAAACTTTCAA 60.106 36.000 0.00 0.00 0.00 2.69
1529 1641 5.901552 ACGATGTGGTTTCAAACTTTCAAT 58.098 33.333 0.00 0.00 0.00 2.57
1530 1642 6.337356 ACGATGTGGTTTCAAACTTTCAATT 58.663 32.000 0.00 0.00 0.00 2.32
1559 1671 7.393216 ACTTCAGATTTCTTCAGCTGATACTT 58.607 34.615 19.04 1.64 37.25 2.24
1563 1675 7.332926 TCAGATTTCTTCAGCTGATACTTCAAC 59.667 37.037 19.04 5.81 32.85 3.18
1619 1731 1.777272 GGGATCAGGCTAGGGTTCATT 59.223 52.381 0.00 0.00 0.00 2.57
1665 1777 1.819229 CTGGCCTACATCGACTGCT 59.181 57.895 3.32 0.00 0.00 4.24
1807 1919 1.739466 GAAGTCCATTCAGATTGCGCA 59.261 47.619 5.66 5.66 37.88 6.09
1832 1944 1.881973 TGACAAGCCTGTTCAGATTGC 59.118 47.619 13.52 5.11 35.30 3.56
1836 1948 1.154150 GCCTGTTCAGATTGCGCAC 60.154 57.895 11.12 0.00 0.00 5.34
1838 1950 0.806868 CCTGTTCAGATTGCGCACAT 59.193 50.000 11.12 7.25 0.00 3.21
1851 1963 1.002468 GCGCACATTTGACAAGTCTGT 60.002 47.619 0.30 0.00 38.98 3.41
1866 1978 6.265577 ACAAGTCTGTTAAATTGTGCAAGTC 58.734 36.000 0.00 0.00 34.71 3.01
1899 2011 1.022735 GGAACATGATGCAGCAGGAG 58.977 55.000 24.79 11.81 0.00 3.69
1901 2013 2.089980 GAACATGATGCAGCAGGAGTT 58.910 47.619 24.79 20.06 0.00 3.01
1921 2033 7.389053 AGGAGTTTCATTCTCTGTTGATACAAC 59.611 37.037 7.55 7.55 32.92 3.32
1935 2047 8.786826 TGTTGATACAACTTTGTAATCCCTAG 57.213 34.615 14.19 0.00 45.74 3.02
1941 2057 9.802039 ATACAACTTTGTAATCCCTAGTTTTCA 57.198 29.630 5.94 0.00 45.74 2.69
1972 2088 5.942236 TCCTTTCATGTTCTCTTCCAAGATG 59.058 40.000 0.00 0.00 33.93 2.90
2074 2195 7.444487 GGACTTCAACAGTTAGACTAATTGGTT 59.556 37.037 18.66 11.21 35.01 3.67
2079 2200 9.349713 TCAACAGTTAGACTAATTGGTTGAAAT 57.650 29.630 23.01 4.06 30.68 2.17
2118 2239 2.614983 ACACGCACACGGTAAAGAAAAT 59.385 40.909 0.00 0.00 46.04 1.82
2240 2361 3.189287 GCCAACCACTATCTCAAACACAG 59.811 47.826 0.00 0.00 0.00 3.66
2258 2379 1.134175 CAGACGGGCAAACACAGTTTT 59.866 47.619 0.00 0.00 0.00 2.43
2339 2460 7.043788 GCAATATCTTTAGCTAACTTTGCTTGC 60.044 37.037 20.01 18.31 41.46 4.01
2360 2481 2.289010 CCCTTTGGCAAACTCATGGAAC 60.289 50.000 8.93 0.00 0.00 3.62
2411 2532 1.014044 GGAATCGTGCAAGCTCGTCA 61.014 55.000 14.90 0.00 34.95 4.35
2417 2538 1.267235 CGTGCAAGCTCGTCATTCATC 60.267 52.381 8.21 0.00 0.00 2.92
2443 2564 4.575645 ACTAACTATGTGCTCGTACCTCTC 59.424 45.833 0.00 0.00 0.00 3.20
2493 2614 6.509317 ACTGCATTTATTCACAACAAAACG 57.491 33.333 0.00 0.00 0.00 3.60
2510 2631 2.981400 ACGCCGGTCAAACAAATTAG 57.019 45.000 1.90 0.00 0.00 1.73
2512 2633 3.401182 ACGCCGGTCAAACAAATTAGTA 58.599 40.909 1.90 0.00 0.00 1.82
2541 2664 0.248661 TTCTGCTCGCTCGACATAGC 60.249 55.000 2.03 2.03 39.21 2.97
2552 2675 4.084849 CGCTCGACATAGCTCCTTAAAATG 60.085 45.833 0.00 0.00 40.49 2.32
2601 2724 2.030185 CGACTCGGAAAACTTCTCAGGA 60.030 50.000 0.00 0.00 0.00 3.86
2687 2810 9.614792 GTACATAATAAACTTCTCAGGGTTCAT 57.385 33.333 0.00 0.00 0.00 2.57
2746 2870 2.636403 ACACTACAAGGACCTTACACCC 59.364 50.000 6.38 0.00 0.00 4.61
2757 2881 1.476833 CCTTACACCCTGTGTTGTGCT 60.477 52.381 5.06 0.00 45.08 4.40
2769 2893 6.344500 CCTGTGTTGTGCTAAGAGATTAGAT 58.656 40.000 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 0.534412 CGGAGTCACATTCTCTGGCT 59.466 55.000 0.00 0.00 35.41 4.75
126 127 4.758251 CATGGCGTGACAGCGGGA 62.758 66.667 0.00 0.00 38.18 5.14
166 212 1.825191 GCCGATGCCATGGACACAT 60.825 57.895 18.40 9.72 37.99 3.21
191 237 2.436824 GGCGAGCAACCCCTTCTC 60.437 66.667 0.00 0.00 0.00 2.87
192 238 4.035102 GGGCGAGCAACCCCTTCT 62.035 66.667 0.00 0.00 42.01 2.85
207 253 4.430765 CCGAACGAGGTGGACGGG 62.431 72.222 0.00 0.00 39.92 5.28
211 257 2.577059 GCATCCGAACGAGGTGGA 59.423 61.111 0.00 0.00 35.96 4.02
320 370 2.262915 CAGCGCTCGGACTCCTTT 59.737 61.111 7.13 0.00 0.00 3.11
350 400 2.035155 TCCGCCACTCTCGAGGAA 59.965 61.111 13.56 0.00 0.00 3.36
356 406 1.739562 CTTGCACTCCGCCACTCTC 60.740 63.158 0.00 0.00 41.33 3.20
377 429 2.235898 GCTGAAGAGGAGATGGTTGTCT 59.764 50.000 0.00 0.00 0.00 3.41
473 525 3.374402 CGTCCGGCAGTCTCTGGT 61.374 66.667 0.00 0.00 34.12 4.00
513 565 0.814457 CTTCACTCACTCCTCTCCGG 59.186 60.000 0.00 0.00 0.00 5.14
519 571 3.261897 CCATAACCACTTCACTCACTCCT 59.738 47.826 0.00 0.00 0.00 3.69
536 605 2.184836 CGCCGGACCGAACCATAA 59.815 61.111 17.49 0.00 0.00 1.90
567 637 2.762327 ACCACCGACCTCACGTATATTT 59.238 45.455 0.00 0.00 0.00 1.40
574 644 1.317431 TATGGACCACCGACCTCACG 61.317 60.000 0.00 0.00 39.42 4.35
588 659 1.692749 GGACCTGGCCCACTATGGA 60.693 63.158 0.00 0.00 40.96 3.41
609 680 2.202557 GCCCAAATACGGTTGCGC 60.203 61.111 0.00 0.00 0.00 6.09
610 681 1.136565 CAGCCCAAATACGGTTGCG 59.863 57.895 0.00 0.00 0.00 4.85
611 682 0.885196 TTCAGCCCAAATACGGTTGC 59.115 50.000 0.00 0.00 32.06 4.17
612 683 4.578516 TCATATTCAGCCCAAATACGGTTG 59.421 41.667 0.00 0.00 33.20 3.77
613 684 4.787551 TCATATTCAGCCCAAATACGGTT 58.212 39.130 0.00 0.00 0.00 4.44
614 685 4.389374 CTCATATTCAGCCCAAATACGGT 58.611 43.478 0.00 0.00 0.00 4.83
615 686 3.753272 CCTCATATTCAGCCCAAATACGG 59.247 47.826 0.00 0.00 0.00 4.02
616 687 4.641396 TCCTCATATTCAGCCCAAATACG 58.359 43.478 0.00 0.00 0.00 3.06
617 688 5.471456 CACTCCTCATATTCAGCCCAAATAC 59.529 44.000 0.00 0.00 0.00 1.89
618 689 5.624159 CACTCCTCATATTCAGCCCAAATA 58.376 41.667 0.00 0.00 0.00 1.40
619 690 4.467769 CACTCCTCATATTCAGCCCAAAT 58.532 43.478 0.00 0.00 0.00 2.32
620 691 3.889815 CACTCCTCATATTCAGCCCAAA 58.110 45.455 0.00 0.00 0.00 3.28
621 692 2.421952 GCACTCCTCATATTCAGCCCAA 60.422 50.000 0.00 0.00 0.00 4.12
622 693 1.141657 GCACTCCTCATATTCAGCCCA 59.858 52.381 0.00 0.00 0.00 5.36
623 694 1.544314 GGCACTCCTCATATTCAGCCC 60.544 57.143 0.00 0.00 34.94 5.19
624 695 1.875576 CGGCACTCCTCATATTCAGCC 60.876 57.143 0.00 0.00 37.54 4.85
625 696 1.069204 TCGGCACTCCTCATATTCAGC 59.931 52.381 0.00 0.00 0.00 4.26
626 697 3.006217 TGATCGGCACTCCTCATATTCAG 59.994 47.826 0.00 0.00 0.00 3.02
627 698 2.965147 TGATCGGCACTCCTCATATTCA 59.035 45.455 0.00 0.00 0.00 2.57
628 699 3.667497 TGATCGGCACTCCTCATATTC 57.333 47.619 0.00 0.00 0.00 1.75
629 700 4.564406 GGATTGATCGGCACTCCTCATATT 60.564 45.833 7.86 0.00 41.72 1.28
630 701 3.055530 GGATTGATCGGCACTCCTCATAT 60.056 47.826 7.86 0.00 41.72 1.78
631 702 2.300152 GGATTGATCGGCACTCCTCATA 59.700 50.000 7.86 0.00 41.72 2.15
632 703 1.071385 GGATTGATCGGCACTCCTCAT 59.929 52.381 7.86 0.00 41.72 2.90
633 704 0.465705 GGATTGATCGGCACTCCTCA 59.534 55.000 7.86 0.00 41.72 3.86
634 705 0.598680 CGGATTGATCGGCACTCCTC 60.599 60.000 11.63 0.00 42.53 3.71
635 706 1.043116 TCGGATTGATCGGCACTCCT 61.043 55.000 11.63 0.00 42.53 3.69
636 707 0.598680 CTCGGATTGATCGGCACTCC 60.599 60.000 5.80 5.80 41.59 3.85
637 708 1.218230 GCTCGGATTGATCGGCACTC 61.218 60.000 0.00 0.00 0.00 3.51
638 709 1.227380 GCTCGGATTGATCGGCACT 60.227 57.895 0.00 0.00 0.00 4.40
639 710 2.589492 CGCTCGGATTGATCGGCAC 61.589 63.158 0.00 0.00 32.74 5.01
640 711 2.279451 CGCTCGGATTGATCGGCA 60.279 61.111 0.00 0.00 32.74 5.69
641 712 1.429148 AAACGCTCGGATTGATCGGC 61.429 55.000 0.00 0.00 40.41 5.54
642 713 0.301687 CAAACGCTCGGATTGATCGG 59.698 55.000 4.73 0.00 40.41 4.18
643 714 1.256376 CTCAAACGCTCGGATTGATCG 59.744 52.381 11.26 0.00 41.79 3.69
644 715 1.594862 CCTCAAACGCTCGGATTGATC 59.405 52.381 11.26 0.00 33.03 2.92
645 716 1.656652 CCTCAAACGCTCGGATTGAT 58.343 50.000 11.26 0.00 33.03 2.57
646 717 1.019278 GCCTCAAACGCTCGGATTGA 61.019 55.000 10.65 10.65 0.00 2.57
647 718 1.425428 GCCTCAAACGCTCGGATTG 59.575 57.895 0.00 0.00 0.00 2.67
648 719 1.745489 GGCCTCAAACGCTCGGATT 60.745 57.895 0.00 0.00 0.00 3.01
649 720 2.125106 GGCCTCAAACGCTCGGAT 60.125 61.111 0.00 0.00 0.00 4.18
650 721 4.388499 GGGCCTCAAACGCTCGGA 62.388 66.667 0.84 0.00 0.00 4.55
651 722 4.697756 TGGGCCTCAAACGCTCGG 62.698 66.667 4.53 0.00 0.00 4.63
652 723 3.423154 GTGGGCCTCAAACGCTCG 61.423 66.667 4.53 0.00 0.00 5.03
653 724 0.321298 TAAGTGGGCCTCAAACGCTC 60.321 55.000 4.53 0.00 0.00 5.03
654 725 0.109723 TTAAGTGGGCCTCAAACGCT 59.890 50.000 4.53 0.00 0.00 5.07
655 726 0.521735 CTTAAGTGGGCCTCAAACGC 59.478 55.000 4.53 0.00 0.00 4.84
656 727 1.804748 GTCTTAAGTGGGCCTCAAACG 59.195 52.381 4.53 0.00 0.00 3.60
657 728 1.804748 CGTCTTAAGTGGGCCTCAAAC 59.195 52.381 4.53 0.00 0.00 2.93
658 729 1.418637 ACGTCTTAAGTGGGCCTCAAA 59.581 47.619 4.53 0.00 0.00 2.69
659 730 1.053424 ACGTCTTAAGTGGGCCTCAA 58.947 50.000 4.53 0.00 0.00 3.02
660 731 1.053424 AACGTCTTAAGTGGGCCTCA 58.947 50.000 4.53 0.00 0.00 3.86
661 732 1.804748 CAAACGTCTTAAGTGGGCCTC 59.195 52.381 4.53 0.00 0.00 4.70
662 733 1.142262 ACAAACGTCTTAAGTGGGCCT 59.858 47.619 4.53 0.00 0.00 5.19
663 734 1.534163 GACAAACGTCTTAAGTGGGCC 59.466 52.381 1.63 0.00 0.00 5.80
664 735 2.223377 CAGACAAACGTCTTAAGTGGGC 59.777 50.000 1.63 0.00 41.96 5.36
665 736 2.806244 CCAGACAAACGTCTTAAGTGGG 59.194 50.000 1.63 0.00 41.96 4.61
666 737 2.806244 CCCAGACAAACGTCTTAAGTGG 59.194 50.000 1.63 0.00 41.96 4.00
667 738 3.463944 ACCCAGACAAACGTCTTAAGTG 58.536 45.455 1.63 0.00 41.96 3.16
668 739 3.133362 TGACCCAGACAAACGTCTTAAGT 59.867 43.478 1.63 0.00 41.96 2.24
669 740 3.724374 TGACCCAGACAAACGTCTTAAG 58.276 45.455 0.00 0.00 41.96 1.85
670 741 3.823281 TGACCCAGACAAACGTCTTAA 57.177 42.857 0.00 0.00 41.96 1.85
671 742 3.823281 TTGACCCAGACAAACGTCTTA 57.177 42.857 0.00 0.00 41.96 2.10
672 743 2.702592 TTGACCCAGACAAACGTCTT 57.297 45.000 0.00 0.00 41.96 3.01
673 744 2.702592 TTTGACCCAGACAAACGTCT 57.297 45.000 0.00 0.00 44.80 4.18
674 745 3.768468 TTTTTGACCCAGACAAACGTC 57.232 42.857 0.00 0.00 37.05 4.34
675 746 4.729227 AATTTTTGACCCAGACAAACGT 57.271 36.364 0.00 0.00 37.05 3.99
676 747 4.867608 ACAAATTTTTGACCCAGACAAACG 59.132 37.500 9.88 0.00 40.55 3.60
677 748 5.872070 TCACAAATTTTTGACCCAGACAAAC 59.128 36.000 9.88 0.00 40.55 2.93
678 749 5.872070 GTCACAAATTTTTGACCCAGACAAA 59.128 36.000 21.66 0.00 40.55 2.83
679 750 5.415221 GTCACAAATTTTTGACCCAGACAA 58.585 37.500 21.66 0.00 40.55 3.18
680 751 5.004922 GTCACAAATTTTTGACCCAGACA 57.995 39.130 21.66 0.00 40.55 3.41
687 758 5.856455 CACTATCCGGTCACAAATTTTTGAC 59.144 40.000 23.37 23.37 40.55 3.18
688 759 5.765677 TCACTATCCGGTCACAAATTTTTGA 59.234 36.000 9.88 2.88 40.55 2.69
689 760 5.856455 GTCACTATCCGGTCACAAATTTTTG 59.144 40.000 0.00 0.00 43.62 2.44
690 761 5.768164 AGTCACTATCCGGTCACAAATTTTT 59.232 36.000 0.00 0.00 0.00 1.94
691 762 5.181245 CAGTCACTATCCGGTCACAAATTTT 59.819 40.000 0.00 0.00 0.00 1.82
692 763 4.695455 CAGTCACTATCCGGTCACAAATTT 59.305 41.667 0.00 0.00 0.00 1.82
693 764 4.020573 TCAGTCACTATCCGGTCACAAATT 60.021 41.667 0.00 0.00 0.00 1.82
694 765 3.513912 TCAGTCACTATCCGGTCACAAAT 59.486 43.478 0.00 0.00 0.00 2.32
695 766 2.894765 TCAGTCACTATCCGGTCACAAA 59.105 45.455 0.00 0.00 0.00 2.83
696 767 2.492088 CTCAGTCACTATCCGGTCACAA 59.508 50.000 0.00 0.00 0.00 3.33
697 768 2.092323 CTCAGTCACTATCCGGTCACA 58.908 52.381 0.00 0.00 0.00 3.58
698 769 1.202313 GCTCAGTCACTATCCGGTCAC 60.202 57.143 0.00 0.00 0.00 3.67
699 770 1.103803 GCTCAGTCACTATCCGGTCA 58.896 55.000 0.00 0.00 0.00 4.02
700 771 0.029567 CGCTCAGTCACTATCCGGTC 59.970 60.000 0.00 0.00 0.00 4.79
701 772 1.384989 CCGCTCAGTCACTATCCGGT 61.385 60.000 0.00 0.00 0.00 5.28
702 773 1.360551 CCGCTCAGTCACTATCCGG 59.639 63.158 0.00 0.00 0.00 5.14
703 774 0.029567 GACCGCTCAGTCACTATCCG 59.970 60.000 0.00 0.00 36.73 4.18
704 775 0.386113 GGACCGCTCAGTCACTATCC 59.614 60.000 0.00 0.00 38.59 2.59
705 776 0.029567 CGGACCGCTCAGTCACTATC 59.970 60.000 0.00 0.00 38.59 2.08
706 777 0.680280 ACGGACCGCTCAGTCACTAT 60.680 55.000 15.39 0.00 38.59 2.12
707 778 1.303074 ACGGACCGCTCAGTCACTA 60.303 57.895 15.39 0.00 38.59 2.74
708 779 2.597805 ACGGACCGCTCAGTCACT 60.598 61.111 15.39 0.00 38.59 3.41
709 780 2.126424 GACGGACCGCTCAGTCAC 60.126 66.667 15.39 0.00 40.34 3.67
710 781 3.371063 GGACGGACCGCTCAGTCA 61.371 66.667 15.39 0.00 41.87 3.41
711 782 3.343788 CTGGACGGACCGCTCAGTC 62.344 68.421 21.83 10.10 42.61 3.51
712 783 3.374402 CTGGACGGACCGCTCAGT 61.374 66.667 21.83 1.61 42.61 3.41
713 784 3.343788 GACTGGACGGACCGCTCAG 62.344 68.421 25.90 25.90 42.61 3.35
714 785 3.371063 GACTGGACGGACCGCTCA 61.371 66.667 15.39 11.59 42.61 4.26
715 786 1.381928 TATGACTGGACGGACCGCTC 61.382 60.000 15.39 10.69 42.61 5.03
716 787 1.379443 TATGACTGGACGGACCGCT 60.379 57.895 15.39 0.48 42.61 5.52
717 788 1.226888 GTATGACTGGACGGACCGC 60.227 63.158 15.39 6.79 42.61 5.68
718 789 0.528924 TTGTATGACTGGACGGACCG 59.471 55.000 13.61 13.61 42.61 4.79
719 790 1.822990 TCTTGTATGACTGGACGGACC 59.177 52.381 0.00 0.00 39.54 4.46
720 791 2.731341 CGTCTTGTATGACTGGACGGAC 60.731 54.545 13.12 0.00 43.69 4.79
721 792 1.471287 CGTCTTGTATGACTGGACGGA 59.529 52.381 13.12 0.00 43.69 4.69
722 793 1.909376 CGTCTTGTATGACTGGACGG 58.091 55.000 13.12 0.00 43.69 4.79
723 794 1.469251 CCCGTCTTGTATGACTGGACG 60.469 57.143 13.64 13.64 45.92 4.79
724 795 1.549170 ACCCGTCTTGTATGACTGGAC 59.451 52.381 12.93 0.00 41.78 4.02
725 796 1.933021 ACCCGTCTTGTATGACTGGA 58.067 50.000 12.93 0.00 41.78 3.86
726 797 2.742053 CAAACCCGTCTTGTATGACTGG 59.258 50.000 6.76 6.76 43.82 4.00
727 798 3.659786 TCAAACCCGTCTTGTATGACTG 58.340 45.455 0.00 0.00 35.00 3.51
728 799 3.306780 CCTCAAACCCGTCTTGTATGACT 60.307 47.826 0.00 0.00 35.00 3.41
729 800 3.000727 CCTCAAACCCGTCTTGTATGAC 58.999 50.000 0.00 0.00 0.00 3.06
730 801 2.614481 GCCTCAAACCCGTCTTGTATGA 60.614 50.000 0.00 0.00 0.00 2.15
731 802 1.737793 GCCTCAAACCCGTCTTGTATG 59.262 52.381 0.00 0.00 0.00 2.39
732 803 1.674817 CGCCTCAAACCCGTCTTGTAT 60.675 52.381 0.00 0.00 0.00 2.29
733 804 0.320073 CGCCTCAAACCCGTCTTGTA 60.320 55.000 0.00 0.00 0.00 2.41
734 805 1.597027 CGCCTCAAACCCGTCTTGT 60.597 57.895 0.00 0.00 0.00 3.16
735 806 1.566018 GACGCCTCAAACCCGTCTTG 61.566 60.000 5.29 0.00 45.56 3.02
736 807 1.301479 GACGCCTCAAACCCGTCTT 60.301 57.895 5.29 0.00 45.56 3.01
737 808 2.342648 GACGCCTCAAACCCGTCT 59.657 61.111 5.29 0.00 45.56 4.18
738 809 3.110178 CGACGCCTCAAACCCGTC 61.110 66.667 2.63 2.63 45.56 4.79
739 810 4.675029 CCGACGCCTCAAACCCGT 62.675 66.667 0.00 0.00 37.99 5.28
742 813 2.588856 ATAGCCCGACGCCTCAAACC 62.589 60.000 0.00 0.00 38.78 3.27
743 814 0.103572 TATAGCCCGACGCCTCAAAC 59.896 55.000 0.00 0.00 38.78 2.93
744 815 0.387929 CTATAGCCCGACGCCTCAAA 59.612 55.000 0.00 0.00 38.78 2.69
745 816 0.466739 TCTATAGCCCGACGCCTCAA 60.467 55.000 0.00 0.00 38.78 3.02
746 817 0.251209 ATCTATAGCCCGACGCCTCA 60.251 55.000 0.00 0.00 38.78 3.86
747 818 0.171455 CATCTATAGCCCGACGCCTC 59.829 60.000 0.00 0.00 38.78 4.70
748 819 1.878656 GCATCTATAGCCCGACGCCT 61.879 60.000 0.00 0.00 38.78 5.52
749 820 1.446272 GCATCTATAGCCCGACGCC 60.446 63.158 0.00 0.00 38.78 5.68
750 821 0.456995 GAGCATCTATAGCCCGACGC 60.457 60.000 0.00 0.00 37.98 5.19
751 822 0.179187 CGAGCATCTATAGCCCGACG 60.179 60.000 0.00 0.00 35.05 5.12
752 823 0.171455 CCGAGCATCTATAGCCCGAC 59.829 60.000 0.00 0.00 35.05 4.79
753 824 0.037734 TCCGAGCATCTATAGCCCGA 59.962 55.000 0.00 0.00 35.05 5.14
754 825 0.171455 GTCCGAGCATCTATAGCCCG 59.829 60.000 0.00 0.00 32.74 6.13
755 826 1.474879 GAGTCCGAGCATCTATAGCCC 59.525 57.143 0.00 0.00 0.00 5.19
756 827 2.163412 CAGAGTCCGAGCATCTATAGCC 59.837 54.545 0.00 0.00 0.00 3.93
757 828 2.817258 ACAGAGTCCGAGCATCTATAGC 59.183 50.000 0.00 0.00 0.00 2.97
758 829 6.112734 AGATACAGAGTCCGAGCATCTATAG 58.887 44.000 0.00 0.00 0.00 1.31
759 830 6.056090 AGATACAGAGTCCGAGCATCTATA 57.944 41.667 0.00 0.00 0.00 1.31
760 831 4.917385 AGATACAGAGTCCGAGCATCTAT 58.083 43.478 0.00 0.00 0.00 1.98
761 832 4.359434 AGATACAGAGTCCGAGCATCTA 57.641 45.455 0.00 0.00 0.00 1.98
762 833 3.222173 AGATACAGAGTCCGAGCATCT 57.778 47.619 0.00 0.00 0.00 2.90
763 834 5.440234 TTAAGATACAGAGTCCGAGCATC 57.560 43.478 0.00 0.00 0.00 3.91
764 835 7.526142 TTATTAAGATACAGAGTCCGAGCAT 57.474 36.000 0.00 0.00 0.00 3.79
765 836 6.954487 TTATTAAGATACAGAGTCCGAGCA 57.046 37.500 0.00 0.00 0.00 4.26
766 837 8.819643 AATTTATTAAGATACAGAGTCCGAGC 57.180 34.615 0.00 0.00 0.00 5.03
818 889 3.230976 TCTTGTCTCTTGGCTCAGTGTA 58.769 45.455 0.00 0.00 0.00 2.90
826 897 0.793250 GCGTCTTCTTGTCTCTTGGC 59.207 55.000 0.00 0.00 0.00 4.52
830 901 1.878656 CGGGGCGTCTTCTTGTCTCT 61.879 60.000 0.00 0.00 0.00 3.10
843 914 2.491022 TTTTTGGTTGGTCGGGGCG 61.491 57.895 0.00 0.00 0.00 6.13
863 934 1.038130 AGCTGGTACCGCCTAGACAG 61.038 60.000 20.36 6.24 38.35 3.51
869 941 2.663196 GACAAGCTGGTACCGCCT 59.337 61.111 20.36 10.89 38.35 5.52
875 947 4.922206 AGAAATGAATGGACAAGCTGGTA 58.078 39.130 0.00 0.00 0.00 3.25
946 1018 1.622811 AGGTTCAGGCTTGAGAGAGTG 59.377 52.381 0.00 0.00 34.15 3.51
947 1019 1.899142 GAGGTTCAGGCTTGAGAGAGT 59.101 52.381 0.00 0.00 34.15 3.24
964 1036 1.225704 GTGGAAGGCAGGATGGAGG 59.774 63.158 0.00 0.00 35.86 4.30
978 1050 3.053245 TGTTCTTTTCTTTCTGGGGTGGA 60.053 43.478 0.00 0.00 0.00 4.02
981 1057 3.897505 CCATGTTCTTTTCTTTCTGGGGT 59.102 43.478 0.00 0.00 0.00 4.95
1079 1155 3.455469 GGCCATGGCTGCTGGAAC 61.455 66.667 34.70 13.03 41.60 3.62
1152 1228 2.915659 TTCACGGACACCCTCGCT 60.916 61.111 0.00 0.00 0.00 4.93
1155 1231 2.047179 GGCTTCACGGACACCCTC 60.047 66.667 0.00 0.00 0.00 4.30
1301 1377 4.033358 CGGCTCAAAGAATGCTTAGTACTG 59.967 45.833 5.39 0.00 32.98 2.74
1302 1378 4.184629 CGGCTCAAAGAATGCTTAGTACT 58.815 43.478 0.00 0.00 32.98 2.73
1303 1379 3.933332 ACGGCTCAAAGAATGCTTAGTAC 59.067 43.478 0.00 0.00 32.98 2.73
1304 1380 3.932710 CACGGCTCAAAGAATGCTTAGTA 59.067 43.478 0.00 0.00 32.98 1.82
1305 1381 2.744202 CACGGCTCAAAGAATGCTTAGT 59.256 45.455 0.00 0.00 32.98 2.24
1306 1382 2.744202 ACACGGCTCAAAGAATGCTTAG 59.256 45.455 0.00 0.00 32.98 2.18
1316 1392 2.037902 TCATACTCCAACACGGCTCAAA 59.962 45.455 0.00 0.00 33.14 2.69
1339 1415 3.873952 GAGAGAGAGAGAGAAGAGCAGAC 59.126 52.174 0.00 0.00 0.00 3.51
1341 1417 4.125703 GAGAGAGAGAGAGAGAAGAGCAG 58.874 52.174 0.00 0.00 0.00 4.24
1342 1418 3.776969 AGAGAGAGAGAGAGAGAAGAGCA 59.223 47.826 0.00 0.00 0.00 4.26
1343 1419 4.100808 AGAGAGAGAGAGAGAGAGAAGAGC 59.899 50.000 0.00 0.00 0.00 4.09
1344 1420 5.598005 AGAGAGAGAGAGAGAGAGAGAAGAG 59.402 48.000 0.00 0.00 0.00 2.85
1345 1421 5.523588 AGAGAGAGAGAGAGAGAGAGAAGA 58.476 45.833 0.00 0.00 0.00 2.87
1346 1422 5.362143 TGAGAGAGAGAGAGAGAGAGAGAAG 59.638 48.000 0.00 0.00 0.00 2.85
1348 1424 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
1349 1425 4.501229 GCTGAGAGAGAGAGAGAGAGAGAG 60.501 54.167 0.00 0.00 0.00 3.20
1351 1427 3.387374 AGCTGAGAGAGAGAGAGAGAGAG 59.613 52.174 0.00 0.00 0.00 3.20
1352 1428 3.378512 AGCTGAGAGAGAGAGAGAGAGA 58.621 50.000 0.00 0.00 0.00 3.10
1353 1429 3.834489 AGCTGAGAGAGAGAGAGAGAG 57.166 52.381 0.00 0.00 0.00 3.20
1354 1430 4.962362 TCTAAGCTGAGAGAGAGAGAGAGA 59.038 45.833 0.00 0.00 0.00 3.10
1355 1431 5.282055 TCTAAGCTGAGAGAGAGAGAGAG 57.718 47.826 0.00 0.00 0.00 3.20
1356 1432 5.692115 TTCTAAGCTGAGAGAGAGAGAGA 57.308 43.478 0.00 0.00 0.00 3.10
1357 1433 6.543465 TGAATTCTAAGCTGAGAGAGAGAGAG 59.457 42.308 7.05 0.00 0.00 3.20
1392 1500 7.285401 AGGTTCAACACAAACATCAGTTCTAAT 59.715 33.333 0.00 0.00 36.84 1.73
1393 1501 6.601613 AGGTTCAACACAAACATCAGTTCTAA 59.398 34.615 0.00 0.00 36.84 2.10
1408 1520 2.670905 GCCAAACAAACAGGTTCAACAC 59.329 45.455 0.00 0.00 0.00 3.32
1425 1537 2.351924 GACTGTTCCCCCACTGCCAA 62.352 60.000 0.00 0.00 0.00 4.52
1493 1605 0.966920 ACATCGTCAGTTCTCGGGTT 59.033 50.000 0.00 0.00 0.00 4.11
1502 1614 3.541632 AGTTTGAAACCACATCGTCAGT 58.458 40.909 4.14 0.00 0.00 3.41
1511 1623 8.871686 AGTATCAATTGAAAGTTTGAAACCAC 57.128 30.769 13.09 0.00 35.63 4.16
1525 1637 8.671921 GCTGAAGAAATCTGAAGTATCAATTGA 58.328 33.333 11.26 11.26 34.49 2.57
1526 1638 8.675504 AGCTGAAGAAATCTGAAGTATCAATTG 58.324 33.333 0.00 0.00 34.49 2.32
1527 1639 8.675504 CAGCTGAAGAAATCTGAAGTATCAATT 58.324 33.333 8.42 0.00 34.49 2.32
1528 1640 8.045507 TCAGCTGAAGAAATCTGAAGTATCAAT 58.954 33.333 15.67 0.00 34.49 2.57
1529 1641 7.389232 TCAGCTGAAGAAATCTGAAGTATCAA 58.611 34.615 15.67 0.00 34.49 2.57
1530 1642 6.939622 TCAGCTGAAGAAATCTGAAGTATCA 58.060 36.000 15.67 0.00 33.17 2.15
1559 1671 3.181477 CCTGTTTGCACATGGAAAGTTGA 60.181 43.478 0.00 0.00 36.05 3.18
1563 1675 2.546373 CCACCTGTTTGCACATGGAAAG 60.546 50.000 0.00 0.00 35.71 2.62
1665 1777 3.998672 GGTCGCCGGAGACACCAA 61.999 66.667 34.59 0.00 42.62 3.67
1807 1919 3.620488 TCTGAACAGGCTTGTCAAACTT 58.380 40.909 0.32 0.00 36.23 2.66
1832 1944 3.338818 AACAGACTTGTCAAATGTGCG 57.661 42.857 3.49 0.00 36.23 5.34
1836 1948 7.222417 TGCACAATTTAACAGACTTGTCAAATG 59.778 33.333 3.49 0.00 34.71 2.32
1838 1950 6.625362 TGCACAATTTAACAGACTTGTCAAA 58.375 32.000 3.49 0.00 36.23 2.69
1866 1978 2.260844 TGTTCCTTCTTCACTGGCAG 57.739 50.000 14.16 14.16 0.00 4.85
1869 1981 3.128242 GCATCATGTTCCTTCTTCACTGG 59.872 47.826 0.00 0.00 0.00 4.00
1899 2011 9.173939 CAAAGTTGTATCAACAGAGAATGAAAC 57.826 33.333 13.74 0.00 36.83 2.78
1901 2013 8.450578 ACAAAGTTGTATCAACAGAGAATGAA 57.549 30.769 13.74 0.00 40.16 2.57
1921 2033 8.178313 ACCTTTGAAAACTAGGGATTACAAAG 57.822 34.615 0.00 0.00 41.03 2.77
2074 2195 8.609176 GTGTGTACTCTGTAACTCAAAATTTCA 58.391 33.333 0.00 0.00 0.00 2.69
2079 2200 4.505191 GCGTGTGTACTCTGTAACTCAAAA 59.495 41.667 0.00 0.00 0.00 2.44
2118 2239 8.839343 CAATGCTCCAGTTGTTATATTGACATA 58.161 33.333 0.00 0.00 0.00 2.29
2240 2361 1.133407 TCAAAACTGTGTTTGCCCGTC 59.867 47.619 9.23 0.00 38.20 4.79
2258 2379 3.006940 GGCGTGTTCCAGTTCATAATCA 58.993 45.455 0.00 0.00 0.00 2.57
2339 2460 1.631405 TCCATGAGTTTGCCAAAGGG 58.369 50.000 0.00 0.00 37.18 3.95
2360 2481 2.283298 ACAGCTGATATTGGACTTGCG 58.717 47.619 23.35 0.00 0.00 4.85
2411 2532 5.750547 CGAGCACATAGTTAGTGTGATGAAT 59.249 40.000 10.17 0.00 45.22 2.57
2443 2564 3.211288 CCAGTGAGGAGGCTACGG 58.789 66.667 0.00 0.00 41.22 4.02
2493 2614 6.307077 GTGAATTACTAATTTGTTTGACCGGC 59.693 38.462 0.00 0.00 0.00 6.13
2510 2631 4.974591 AGCGAGCAGAAATTGTGAATTAC 58.025 39.130 0.00 0.00 0.00 1.89
2512 2633 3.425359 CGAGCGAGCAGAAATTGTGAATT 60.425 43.478 0.00 0.00 0.00 2.17
2541 2664 9.892130 AGTGAGGTAAGTATTCATTTTAAGGAG 57.108 33.333 0.00 0.00 0.00 3.69
2666 2789 8.383175 AGTTCATGAACCCTGAGAAGTTTATTA 58.617 33.333 30.34 0.00 42.06 0.98
2708 2832 6.363065 TGTAGTGTCGATCCTATTCCTACTT 58.637 40.000 0.00 0.00 0.00 2.24
2713 2837 4.583489 TCCTTGTAGTGTCGATCCTATTCC 59.417 45.833 0.00 0.00 0.00 3.01
2746 2870 9.539825 AATATCTAATCTCTTAGCACAACACAG 57.460 33.333 0.00 0.00 35.32 3.66
2786 2910 6.112734 GGGCCTACCAATTTAAAAATTCCAG 58.887 40.000 0.84 0.00 36.52 3.86


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

AutoCloner maintained by Alex Coulton.