Multiple sequence alignment - TraesCS7D01G375100

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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 TraesCS7D01G375100 chr7D 100.000 4026 0 0 1 4026 485514407 485518432 0.000 7435.0
1 TraesCS7D01G375100 chr7D 98.462 585 8 1 1 584 230482966 230482382 0.000 1029.0
2 TraesCS7D01G375100 chr7D 98.291 585 9 1 1 584 347645079 347645663 0.000 1024.0
3 TraesCS7D01G375100 chr7B 94.226 3204 125 31 860 4026 513239957 513243137 0.000 4837.0
4 TraesCS7D01G375100 chr7A 90.754 3169 162 51 929 4026 553746444 553749552 0.000 4108.0
5 TraesCS7D01G375100 chr4D 97.819 596 10 3 1 593 506565065 506564470 0.000 1026.0
6 TraesCS7D01G375100 chr6D 98.291 585 9 1 1 584 233643299 233643883 0.000 1024.0
7 TraesCS7D01G375100 chr3D 98.291 585 9 1 1 584 44814158 44814742 0.000 1024.0
8 TraesCS7D01G375100 chr3D 97.963 589 10 2 1 588 400826921 400827508 0.000 1020.0
9 TraesCS7D01G375100 chr1D 98.291 585 9 1 1 584 205326585 205326001 0.000 1024.0
10 TraesCS7D01G375100 chr5D 97.804 592 11 2 1 590 479287207 479286616 0.000 1020.0
11 TraesCS7D01G375100 chr2D 97.651 596 10 4 1 594 255504266 255503673 0.000 1020.0
12 TraesCS7D01G375100 chr3A 100.000 29 0 0 654 682 477146766 477146738 0.002 54.7


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 TraesCS7D01G375100 chr7D 485514407 485518432 4025 False 7435 7435 100.000 1 4026 1 chr7D.!!$F2 4025
1 TraesCS7D01G375100 chr7D 230482382 230482966 584 True 1029 1029 98.462 1 584 1 chr7D.!!$R1 583
2 TraesCS7D01G375100 chr7D 347645079 347645663 584 False 1024 1024 98.291 1 584 1 chr7D.!!$F1 583
3 TraesCS7D01G375100 chr7B 513239957 513243137 3180 False 4837 4837 94.226 860 4026 1 chr7B.!!$F1 3166
4 TraesCS7D01G375100 chr7A 553746444 553749552 3108 False 4108 4108 90.754 929 4026 1 chr7A.!!$F1 3097
5 TraesCS7D01G375100 chr4D 506564470 506565065 595 True 1026 1026 97.819 1 593 1 chr4D.!!$R1 592
6 TraesCS7D01G375100 chr6D 233643299 233643883 584 False 1024 1024 98.291 1 584 1 chr6D.!!$F1 583
7 TraesCS7D01G375100 chr3D 44814158 44814742 584 False 1024 1024 98.291 1 584 1 chr3D.!!$F1 583
8 TraesCS7D01G375100 chr3D 400826921 400827508 587 False 1020 1020 97.963 1 588 1 chr3D.!!$F2 587
9 TraesCS7D01G375100 chr1D 205326001 205326585 584 True 1024 1024 98.291 1 584 1 chr1D.!!$R1 583
10 TraesCS7D01G375100 chr5D 479286616 479287207 591 True 1020 1020 97.804 1 590 1 chr5D.!!$R1 589
11 TraesCS7D01G375100 chr2D 255503673 255504266 593 True 1020 1020 97.651 1 594 1 chr2D.!!$R1 593

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
702 704 0.039035 AACCTTAAATGCCCGAGCCA 59.961 50.0 0.00 0.0 38.69 4.75 F
923 925 0.098200 GCGTCCATCTTAAAACCGCC 59.902 55.0 0.00 0.0 34.06 6.13 F
926 928 0.393267 TCCATCTTAAAACCGCCGGG 60.393 55.0 8.57 0.0 40.11 5.73 F
2406 2506 0.235665 GTCATGTGCAGGTGTTCGTG 59.764 55.0 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 1977 0.111089 CAGCACGCGTGAAAGTTCTC 60.111 55.0 41.19 21.02 0.0 2.87 R
2387 2487 0.235665 CACGAACACCTGCACATGAC 59.764 55.0 0.00 0.00 0.0 3.06 R
2583 2683 0.747852 GCCCGGAGTAGAAGAGGAAG 59.252 60.0 0.73 0.00 0.0 3.46 R
3400 3505 0.458543 CGTGTAAGATGTCAGCGGCT 60.459 55.0 0.00 0.00 0.0 5.52 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
328 330 2.456119 CCGGATTCACACGCTGCTC 61.456 63.158 0.00 0.00 0.00 4.26
555 557 3.301794 TGAGGTGTTACCGGCTAGATA 57.698 47.619 0.00 0.00 44.90 1.98
588 590 0.325671 ATCGGGGTCCTGACACATCT 60.326 55.000 1.44 0.00 36.16 2.90
589 591 0.333652 TCGGGGTCCTGACACATCTA 59.666 55.000 1.44 0.00 36.16 1.98
590 592 0.460311 CGGGGTCCTGACACATCTAC 59.540 60.000 1.44 0.00 36.16 2.59
592 594 1.906574 GGGGTCCTGACACATCTACAA 59.093 52.381 1.44 0.00 36.16 2.41
593 595 2.354805 GGGGTCCTGACACATCTACAAC 60.355 54.545 1.44 0.00 36.16 3.32
595 597 3.244422 GGGTCCTGACACATCTACAACAA 60.244 47.826 0.00 0.00 34.14 2.83
596 598 3.997021 GGTCCTGACACATCTACAACAAG 59.003 47.826 0.00 0.00 0.00 3.16
597 599 4.262463 GGTCCTGACACATCTACAACAAGA 60.262 45.833 0.00 0.00 0.00 3.02
598 600 4.686554 GTCCTGACACATCTACAACAAGAC 59.313 45.833 0.00 0.00 0.00 3.01
599 601 4.343814 TCCTGACACATCTACAACAAGACA 59.656 41.667 0.00 0.00 0.00 3.41
600 602 5.012046 TCCTGACACATCTACAACAAGACAT 59.988 40.000 0.00 0.00 0.00 3.06
601 603 5.702670 CCTGACACATCTACAACAAGACATT 59.297 40.000 0.00 0.00 0.00 2.71
602 604 6.205464 CCTGACACATCTACAACAAGACATTT 59.795 38.462 0.00 0.00 0.00 2.32
603 605 7.189693 TGACACATCTACAACAAGACATTTC 57.810 36.000 0.00 0.00 0.00 2.17
604 606 6.765512 TGACACATCTACAACAAGACATTTCA 59.234 34.615 0.00 0.00 0.00 2.69
605 607 7.281999 TGACACATCTACAACAAGACATTTCAA 59.718 33.333 0.00 0.00 0.00 2.69
606 608 7.995289 ACACATCTACAACAAGACATTTCAAA 58.005 30.769 0.00 0.00 0.00 2.69
607 609 7.915397 ACACATCTACAACAAGACATTTCAAAC 59.085 33.333 0.00 0.00 0.00 2.93
608 610 7.379529 CACATCTACAACAAGACATTTCAAACC 59.620 37.037 0.00 0.00 0.00 3.27
609 611 6.385649 TCTACAACAAGACATTTCAAACCC 57.614 37.500 0.00 0.00 0.00 4.11
610 612 4.400529 ACAACAAGACATTTCAAACCCC 57.599 40.909 0.00 0.00 0.00 4.95
611 613 3.133901 ACAACAAGACATTTCAAACCCCC 59.866 43.478 0.00 0.00 0.00 5.40
612 614 3.328535 ACAAGACATTTCAAACCCCCT 57.671 42.857 0.00 0.00 0.00 4.79
613 615 3.230976 ACAAGACATTTCAAACCCCCTC 58.769 45.455 0.00 0.00 0.00 4.30
614 616 3.230134 CAAGACATTTCAAACCCCCTCA 58.770 45.455 0.00 0.00 0.00 3.86
615 617 3.611025 AGACATTTCAAACCCCCTCAA 57.389 42.857 0.00 0.00 0.00 3.02
616 618 3.922375 AGACATTTCAAACCCCCTCAAA 58.078 40.909 0.00 0.00 0.00 2.69
617 619 3.641436 AGACATTTCAAACCCCCTCAAAC 59.359 43.478 0.00 0.00 0.00 2.93
618 620 2.364002 ACATTTCAAACCCCCTCAAACG 59.636 45.455 0.00 0.00 0.00 3.60
619 621 2.146920 TTTCAAACCCCCTCAAACGT 57.853 45.000 0.00 0.00 0.00 3.99
620 622 1.682740 TTCAAACCCCCTCAAACGTC 58.317 50.000 0.00 0.00 0.00 4.34
621 623 0.179012 TCAAACCCCCTCAAACGTCC 60.179 55.000 0.00 0.00 0.00 4.79
622 624 1.228033 AAACCCCCTCAAACGTCCG 60.228 57.895 0.00 0.00 0.00 4.79
623 625 1.698067 AAACCCCCTCAAACGTCCGA 61.698 55.000 0.00 0.00 0.00 4.55
624 626 2.108278 AACCCCCTCAAACGTCCGAG 62.108 60.000 7.11 7.11 0.00 4.63
625 627 2.434359 CCCCTCAAACGTCCGAGC 60.434 66.667 8.34 0.00 0.00 5.03
626 628 2.809601 CCCTCAAACGTCCGAGCG 60.810 66.667 8.34 0.00 37.94 5.03
627 629 2.809601 CCTCAAACGTCCGAGCGG 60.810 66.667 1.74 1.74 35.98 5.52
628 630 2.809601 CTCAAACGTCCGAGCGGG 60.810 66.667 9.29 0.00 35.98 6.13
650 652 3.455152 CCAGTCACTGGTCGGTCA 58.545 61.111 16.65 0.00 45.82 4.02
651 653 1.745890 CCAGTCACTGGTCGGTCAA 59.254 57.895 16.65 0.00 45.82 3.18
652 654 0.319900 CCAGTCACTGGTCGGTCAAG 60.320 60.000 16.65 0.00 45.82 3.02
653 655 0.673985 CAGTCACTGGTCGGTCAAGA 59.326 55.000 0.00 0.00 0.00 3.02
654 656 1.068588 CAGTCACTGGTCGGTCAAGAA 59.931 52.381 0.00 0.00 0.00 2.52
655 657 1.760613 AGTCACTGGTCGGTCAAGAAA 59.239 47.619 0.00 0.00 0.00 2.52
656 658 2.368875 AGTCACTGGTCGGTCAAGAAAT 59.631 45.455 0.00 0.00 0.00 2.17
657 659 3.139077 GTCACTGGTCGGTCAAGAAATT 58.861 45.455 0.00 0.00 0.00 1.82
658 660 3.564225 GTCACTGGTCGGTCAAGAAATTT 59.436 43.478 0.00 0.00 0.00 1.82
659 661 3.813166 TCACTGGTCGGTCAAGAAATTTC 59.187 43.478 10.33 10.33 0.00 2.17
660 662 2.806244 ACTGGTCGGTCAAGAAATTTCG 59.194 45.455 12.42 0.59 0.00 3.46
661 663 3.064207 CTGGTCGGTCAAGAAATTTCGA 58.936 45.455 12.42 3.08 0.00 3.71
662 664 2.803956 TGGTCGGTCAAGAAATTTCGAC 59.196 45.455 15.58 15.58 43.95 4.20
663 665 3.450893 GTCGGTCAAGAAATTTCGACC 57.549 47.619 24.50 24.50 43.73 4.79
664 666 2.159037 GTCGGTCAAGAAATTTCGACCC 59.841 50.000 26.53 18.03 44.20 4.46
665 667 2.147958 CGGTCAAGAAATTTCGACCCA 58.852 47.619 26.53 6.87 44.20 4.51
666 668 2.159627 CGGTCAAGAAATTTCGACCCAG 59.840 50.000 26.53 16.55 44.20 4.45
667 669 2.095212 GGTCAAGAAATTTCGACCCAGC 60.095 50.000 24.18 11.01 41.77 4.85
668 670 2.095212 GTCAAGAAATTTCGACCCAGCC 60.095 50.000 12.42 0.00 0.00 4.85
669 671 1.135689 CAAGAAATTTCGACCCAGCCG 60.136 52.381 12.42 0.00 0.00 5.52
670 672 0.676782 AGAAATTTCGACCCAGCCGG 60.677 55.000 12.42 0.00 37.81 6.13
671 673 0.675522 GAAATTTCGACCCAGCCGGA 60.676 55.000 5.05 0.00 34.64 5.14
672 674 0.958876 AAATTTCGACCCAGCCGGAC 60.959 55.000 5.05 0.00 34.64 4.79
680 682 4.697756 CCAGCCGGACGCCTCAAA 62.698 66.667 5.05 0.00 38.78 2.69
681 683 3.423154 CAGCCGGACGCCTCAAAC 61.423 66.667 5.05 0.00 38.78 2.93
682 684 3.936203 AGCCGGACGCCTCAAACA 61.936 61.111 5.05 0.00 38.78 2.83
683 685 2.975799 GCCGGACGCCTCAAACAA 60.976 61.111 5.05 0.00 0.00 2.83
684 686 2.548295 GCCGGACGCCTCAAACAAA 61.548 57.895 5.05 0.00 0.00 2.83
685 687 1.281656 CCGGACGCCTCAAACAAAC 59.718 57.895 0.00 0.00 0.00 2.93
686 688 1.281656 CGGACGCCTCAAACAAACC 59.718 57.895 0.00 0.00 0.00 3.27
687 689 1.164041 CGGACGCCTCAAACAAACCT 61.164 55.000 0.00 0.00 0.00 3.50
688 690 1.029681 GGACGCCTCAAACAAACCTT 58.970 50.000 0.00 0.00 0.00 3.50
689 691 2.223745 GGACGCCTCAAACAAACCTTA 58.776 47.619 0.00 0.00 0.00 2.69
690 692 2.619646 GGACGCCTCAAACAAACCTTAA 59.380 45.455 0.00 0.00 0.00 1.85
691 693 3.067040 GGACGCCTCAAACAAACCTTAAA 59.933 43.478 0.00 0.00 0.00 1.52
692 694 4.261867 GGACGCCTCAAACAAACCTTAAAT 60.262 41.667 0.00 0.00 0.00 1.40
693 695 4.616953 ACGCCTCAAACAAACCTTAAATG 58.383 39.130 0.00 0.00 0.00 2.32
694 696 3.428534 CGCCTCAAACAAACCTTAAATGC 59.571 43.478 0.00 0.00 0.00 3.56
695 697 3.745975 GCCTCAAACAAACCTTAAATGCC 59.254 43.478 0.00 0.00 0.00 4.40
696 698 4.314961 CCTCAAACAAACCTTAAATGCCC 58.685 43.478 0.00 0.00 0.00 5.36
697 699 3.983741 TCAAACAAACCTTAAATGCCCG 58.016 40.909 0.00 0.00 0.00 6.13
698 700 3.637229 TCAAACAAACCTTAAATGCCCGA 59.363 39.130 0.00 0.00 0.00 5.14
699 701 3.934457 AACAAACCTTAAATGCCCGAG 57.066 42.857 0.00 0.00 0.00 4.63
700 702 1.544246 ACAAACCTTAAATGCCCGAGC 59.456 47.619 0.00 0.00 40.48 5.03
701 703 1.135112 CAAACCTTAAATGCCCGAGCC 60.135 52.381 0.00 0.00 38.69 4.70
702 704 0.039035 AACCTTAAATGCCCGAGCCA 59.961 50.000 0.00 0.00 38.69 4.75
703 705 0.258774 ACCTTAAATGCCCGAGCCAT 59.741 50.000 0.00 0.00 38.69 4.40
704 706 1.493022 ACCTTAAATGCCCGAGCCATA 59.507 47.619 0.00 0.00 38.69 2.74
705 707 2.092103 ACCTTAAATGCCCGAGCCATAA 60.092 45.455 0.00 0.00 38.69 1.90
706 708 2.293399 CCTTAAATGCCCGAGCCATAAC 59.707 50.000 0.00 0.00 38.69 1.89
707 709 1.975660 TAAATGCCCGAGCCATAACC 58.024 50.000 0.00 0.00 38.69 2.85
708 710 0.755327 AAATGCCCGAGCCATAACCC 60.755 55.000 0.00 0.00 38.69 4.11
709 711 1.645402 AATGCCCGAGCCATAACCCT 61.645 55.000 0.00 0.00 38.69 4.34
710 712 2.203209 GCCCGAGCCATAACCCTG 60.203 66.667 0.00 0.00 0.00 4.45
711 713 2.510906 CCCGAGCCATAACCCTGG 59.489 66.667 0.00 0.00 39.45 4.45
712 714 2.510906 CCGAGCCATAACCCTGGG 59.489 66.667 12.28 12.28 36.75 4.45
716 718 2.828549 GCCATAACCCTGGGCGTG 60.829 66.667 14.08 9.09 38.04 5.34
717 719 2.674754 CCATAACCCTGGGCGTGT 59.325 61.111 14.08 0.00 32.28 4.49
718 720 1.001393 CCATAACCCTGGGCGTGTT 60.001 57.895 14.08 1.62 32.28 3.32
719 721 1.029947 CCATAACCCTGGGCGTGTTC 61.030 60.000 14.08 0.00 32.28 3.18
720 722 1.078708 ATAACCCTGGGCGTGTTCG 60.079 57.895 14.08 0.00 40.37 3.95
730 732 2.128274 CGTGTTCGCGGACGTTTG 60.128 61.111 13.91 0.00 41.18 2.93
731 733 2.424640 GTGTTCGCGGACGTTTGC 60.425 61.111 13.91 3.13 41.18 3.68
754 756 1.386533 AGCGGATTTGCTCAATCTGG 58.613 50.000 15.70 7.71 45.43 3.86
755 757 1.098050 GCGGATTTGCTCAATCTGGT 58.902 50.000 15.70 0.00 45.43 4.00
756 758 1.474077 GCGGATTTGCTCAATCTGGTT 59.526 47.619 15.70 0.00 45.43 3.67
757 759 2.733227 GCGGATTTGCTCAATCTGGTTG 60.733 50.000 15.70 0.00 45.43 3.77
758 760 2.489329 CGGATTTGCTCAATCTGGTTGT 59.511 45.455 0.00 0.00 42.63 3.32
759 761 3.689161 CGGATTTGCTCAATCTGGTTGTA 59.311 43.478 0.00 0.00 42.63 2.41
760 762 4.201851 CGGATTTGCTCAATCTGGTTGTAG 60.202 45.833 0.00 0.00 42.63 2.74
761 763 4.943705 GGATTTGCTCAATCTGGTTGTAGA 59.056 41.667 0.00 0.00 41.22 2.59
762 764 5.591877 GGATTTGCTCAATCTGGTTGTAGAT 59.408 40.000 0.00 0.00 41.22 1.98
763 765 5.885230 TTTGCTCAATCTGGTTGTAGATG 57.115 39.130 0.00 0.00 37.48 2.90
764 766 3.273434 TGCTCAATCTGGTTGTAGATGC 58.727 45.455 0.00 0.67 37.48 3.91
765 767 3.054875 TGCTCAATCTGGTTGTAGATGCT 60.055 43.478 0.00 0.00 37.48 3.79
766 768 3.559242 GCTCAATCTGGTTGTAGATGCTC 59.441 47.826 0.00 0.00 37.48 4.26
767 769 4.682859 GCTCAATCTGGTTGTAGATGCTCT 60.683 45.833 0.00 0.00 37.48 4.09
768 770 5.016051 TCAATCTGGTTGTAGATGCTCTC 57.984 43.478 0.00 0.00 37.48 3.20
769 771 4.467438 TCAATCTGGTTGTAGATGCTCTCA 59.533 41.667 0.00 0.00 37.48 3.27
770 772 4.669206 ATCTGGTTGTAGATGCTCTCAG 57.331 45.455 0.00 0.00 36.12 3.35
771 773 3.701664 TCTGGTTGTAGATGCTCTCAGA 58.298 45.455 0.00 0.00 0.00 3.27
772 774 3.698539 TCTGGTTGTAGATGCTCTCAGAG 59.301 47.826 0.00 0.00 0.00 3.35
773 775 2.762887 TGGTTGTAGATGCTCTCAGAGG 59.237 50.000 3.18 0.00 0.00 3.69
774 776 2.763448 GGTTGTAGATGCTCTCAGAGGT 59.237 50.000 3.18 0.00 0.00 3.85
775 777 3.181480 GGTTGTAGATGCTCTCAGAGGTC 60.181 52.174 3.18 0.00 0.00 3.85
776 778 3.660970 TGTAGATGCTCTCAGAGGTCT 57.339 47.619 3.18 0.00 0.00 3.85
777 779 3.286353 TGTAGATGCTCTCAGAGGTCTG 58.714 50.000 3.18 0.10 45.08 3.51
790 792 4.869215 CAGAGGTCTGATGCTGTAGTATG 58.131 47.826 0.22 0.00 46.59 2.39
791 793 3.320541 AGAGGTCTGATGCTGTAGTATGC 59.679 47.826 0.00 0.00 0.00 3.14
792 794 3.033909 AGGTCTGATGCTGTAGTATGCA 58.966 45.455 0.00 0.00 43.67 3.96
802 804 4.406648 CTGTAGTATGCAGGATCAACCA 57.593 45.455 0.00 0.00 45.67 3.67
803 805 4.122776 CTGTAGTATGCAGGATCAACCAC 58.877 47.826 0.00 0.00 45.67 4.16
804 806 2.717639 AGTATGCAGGATCAACCACC 57.282 50.000 0.00 0.00 42.04 4.61
805 807 1.915489 AGTATGCAGGATCAACCACCA 59.085 47.619 0.00 0.00 42.04 4.17
806 808 2.092753 AGTATGCAGGATCAACCACCAG 60.093 50.000 0.00 0.00 42.04 4.00
807 809 0.994247 ATGCAGGATCAACCACCAGA 59.006 50.000 0.00 0.00 42.04 3.86
808 810 0.994247 TGCAGGATCAACCACCAGAT 59.006 50.000 0.00 0.00 42.04 2.90
809 811 1.355381 TGCAGGATCAACCACCAGATT 59.645 47.619 0.00 0.00 42.04 2.40
810 812 2.225091 TGCAGGATCAACCACCAGATTT 60.225 45.455 0.00 0.00 42.04 2.17
811 813 2.827921 GCAGGATCAACCACCAGATTTT 59.172 45.455 0.00 0.00 42.04 1.82
812 814 3.367703 GCAGGATCAACCACCAGATTTTG 60.368 47.826 0.00 0.00 42.04 2.44
813 815 3.828451 CAGGATCAACCACCAGATTTTGT 59.172 43.478 0.00 0.00 42.04 2.83
814 816 4.281688 CAGGATCAACCACCAGATTTTGTT 59.718 41.667 0.00 0.00 42.04 2.83
815 817 5.476599 CAGGATCAACCACCAGATTTTGTTA 59.523 40.000 0.00 0.00 42.04 2.41
816 818 6.015519 CAGGATCAACCACCAGATTTTGTTAA 60.016 38.462 0.00 0.00 42.04 2.01
817 819 6.553100 AGGATCAACCACCAGATTTTGTTAAA 59.447 34.615 0.00 0.00 42.04 1.52
818 820 6.868339 GGATCAACCACCAGATTTTGTTAAAG 59.132 38.462 0.00 0.00 38.79 1.85
819 821 6.783708 TCAACCACCAGATTTTGTTAAAGT 57.216 33.333 0.00 0.00 0.00 2.66
820 822 6.801575 TCAACCACCAGATTTTGTTAAAGTC 58.198 36.000 0.00 0.00 0.00 3.01
821 823 6.605594 TCAACCACCAGATTTTGTTAAAGTCT 59.394 34.615 0.00 0.00 37.88 3.24
837 839 9.069078 TGTTAAAGTCTGATAAAGTCGTATTCG 57.931 33.333 0.00 0.00 38.55 3.34
838 840 6.570690 AAAGTCTGATAAAGTCGTATTCGC 57.429 37.500 0.00 0.00 36.96 4.70
839 841 5.502153 AGTCTGATAAAGTCGTATTCGCT 57.498 39.130 0.00 0.00 36.96 4.93
840 842 5.892568 AGTCTGATAAAGTCGTATTCGCTT 58.107 37.500 0.00 0.00 35.95 4.68
841 843 6.331061 AGTCTGATAAAGTCGTATTCGCTTT 58.669 36.000 14.62 14.62 41.78 3.51
842 844 7.478322 AGTCTGATAAAGTCGTATTCGCTTTA 58.522 34.615 16.88 16.88 42.78 1.85
843 845 7.972277 AGTCTGATAAAGTCGTATTCGCTTTAA 59.028 33.333 17.79 8.12 42.39 1.52
844 846 8.589629 GTCTGATAAAGTCGTATTCGCTTTAAA 58.410 33.333 17.79 11.98 42.39 1.52
845 847 9.142515 TCTGATAAAGTCGTATTCGCTTTAAAA 57.857 29.630 17.79 11.77 42.39 1.52
846 848 9.916397 CTGATAAAGTCGTATTCGCTTTAAAAT 57.084 29.630 17.79 8.85 42.39 1.82
847 849 9.697250 TGATAAAGTCGTATTCGCTTTAAAATG 57.303 29.630 17.79 0.00 42.39 2.32
848 850 6.848470 AAAGTCGTATTCGCTTTAAAATGC 57.152 33.333 10.63 0.00 39.51 3.56
849 851 5.539582 AGTCGTATTCGCTTTAAAATGCA 57.460 34.783 0.00 0.00 36.96 3.96
850 852 5.933790 AGTCGTATTCGCTTTAAAATGCAA 58.066 33.333 0.00 0.00 36.96 4.08
851 853 6.021596 AGTCGTATTCGCTTTAAAATGCAAG 58.978 36.000 0.00 0.00 36.96 4.01
852 854 6.019152 GTCGTATTCGCTTTAAAATGCAAGA 58.981 36.000 0.00 0.00 36.96 3.02
853 855 6.687105 GTCGTATTCGCTTTAAAATGCAAGAT 59.313 34.615 0.00 0.00 36.96 2.40
854 856 6.686679 TCGTATTCGCTTTAAAATGCAAGATG 59.313 34.615 0.00 0.00 36.96 2.90
855 857 6.686679 CGTATTCGCTTTAAAATGCAAGATGA 59.313 34.615 0.00 0.00 0.00 2.92
856 858 7.218014 CGTATTCGCTTTAAAATGCAAGATGAA 59.782 33.333 0.00 0.00 0.00 2.57
857 859 9.023967 GTATTCGCTTTAAAATGCAAGATGAAT 57.976 29.630 0.00 0.00 34.11 2.57
865 867 5.565592 AAATGCAAGATGAATAAGTCGCA 57.434 34.783 0.00 0.00 0.00 5.10
869 871 5.953183 TGCAAGATGAATAAGTCGCATTTT 58.047 33.333 0.00 0.00 0.00 1.82
918 920 2.702592 ATCCGGCGTCCATCTTAAAA 57.297 45.000 6.01 0.00 0.00 1.52
920 922 0.730840 CCGGCGTCCATCTTAAAACC 59.269 55.000 6.01 0.00 0.00 3.27
921 923 0.372334 CGGCGTCCATCTTAAAACCG 59.628 55.000 0.00 0.00 0.00 4.44
923 925 0.098200 GCGTCCATCTTAAAACCGCC 59.902 55.000 0.00 0.00 34.06 6.13
926 928 0.393267 TCCATCTTAAAACCGCCGGG 60.393 55.000 8.57 0.00 40.11 5.73
927 929 0.393267 CCATCTTAAAACCGCCGGGA 60.393 55.000 8.57 0.00 36.97 5.14
946 951 0.679960 AGCATTAAACACCCGCCTCC 60.680 55.000 0.00 0.00 0.00 4.30
1055 1063 1.665679 CACCAATCCAATCGGACGAAG 59.334 52.381 0.00 0.00 46.79 3.79
1453 1485 1.274126 TGGAGTACACCATCCCCATGA 60.274 52.381 8.07 0.00 34.77 3.07
1576 1608 1.817941 AACACGGTGAGCGCACTTT 60.818 52.632 20.23 4.64 44.52 2.66
1581 1613 1.598130 GGTGAGCGCACTTTCCTGT 60.598 57.895 20.23 0.00 44.52 4.00
1583 1615 0.601311 GTGAGCGCACTTTCCTGTCT 60.601 55.000 13.84 0.00 41.84 3.41
1676 1714 4.911514 TTACCTTTCACTTTTGACCTGC 57.088 40.909 0.00 0.00 0.00 4.85
1697 1741 4.210331 GCCAATGTTACCCTCTCATTGAT 58.790 43.478 15.57 0.00 46.20 2.57
1715 1759 0.958822 ATCAAACGTGAAGGCAACCC 59.041 50.000 0.00 0.00 37.30 4.11
1792 1836 4.379290 GGAAACTAGACACTAGACGACACC 60.379 50.000 11.94 4.18 0.00 4.16
1842 1886 2.159099 TGTCTTCTCGTGCAGAGTTTGT 60.159 45.455 11.37 0.00 46.86 2.83
1855 1899 6.198966 GTGCAGAGTTTGTTTACCTTTTCATG 59.801 38.462 0.00 0.00 0.00 3.07
1865 1912 9.810545 TTGTTTACCTTTTCATGTTTTTCTAGG 57.189 29.630 0.00 0.00 0.00 3.02
1876 1923 7.432869 TCATGTTTTTCTAGGTGGAATTTGTG 58.567 34.615 0.00 0.00 0.00 3.33
1888 1935 5.451798 GGTGGAATTTGTGTCACATTTGTCT 60.452 40.000 6.48 0.00 32.29 3.41
1926 1992 2.218953 TCTTGAGAACTTTCACGCGT 57.781 45.000 5.58 5.58 0.00 6.01
1972 2038 4.381718 CCCAGTTTGAGCACTACTAGTACC 60.382 50.000 0.00 0.00 0.00 3.34
1974 2040 3.768215 AGTTTGAGCACTACTAGTACCCC 59.232 47.826 0.00 0.00 0.00 4.95
1976 2042 1.642238 TGAGCACTACTAGTACCCCCA 59.358 52.381 0.00 0.00 0.00 4.96
1993 2061 8.002459 AGTACCCCCATATTTACAATTGGTTAG 58.998 37.037 10.83 0.00 0.00 2.34
2093 2161 5.919755 TGGTACTGTGACAACAAGTGAATA 58.080 37.500 0.00 0.00 35.37 1.75
2124 2197 2.914289 GCTCCTGGTGATGAGGGG 59.086 66.667 0.00 0.00 33.68 4.79
2145 2218 3.206964 GAGCAAAAGTAGCTGGTATCCC 58.793 50.000 0.00 0.00 43.58 3.85
2146 2219 2.576191 AGCAAAAGTAGCTGGTATCCCA 59.424 45.455 0.00 0.00 41.61 4.37
2387 2487 1.726248 TGAATGTGACGTGCGATCTTG 59.274 47.619 0.00 0.00 0.00 3.02
2406 2506 0.235665 GTCATGTGCAGGTGTTCGTG 59.764 55.000 0.00 0.00 0.00 4.35
2553 2653 2.436824 GAGTTCTTGGGCTCCGGC 60.437 66.667 0.00 0.00 37.82 6.13
2583 2683 4.373771 GTGGGGAACGTGTCCTTC 57.626 61.111 13.94 8.98 46.92 3.46
2595 2695 3.506844 ACGTGTCCTTCTTCCTCTTCTAC 59.493 47.826 0.00 0.00 0.00 2.59
2598 2698 4.158949 GTGTCCTTCTTCCTCTTCTACTCC 59.841 50.000 0.00 0.00 0.00 3.85
2679 2779 2.257371 GCGGTGCTCTACGACACA 59.743 61.111 0.00 0.00 38.57 3.72
2686 2786 1.954382 TGCTCTACGACACACTCAACT 59.046 47.619 0.00 0.00 0.00 3.16
2778 2878 1.402984 GGTCTCGTCTTCGACATGCTT 60.403 52.381 0.00 0.00 41.35 3.91
2881 2981 3.181450 ACAGAAGCTTACATCATAGGCCC 60.181 47.826 0.00 0.00 0.00 5.80
3073 3178 1.302033 ACAGGAACCAAGCTGCGAG 60.302 57.895 0.00 0.00 0.00 5.03
3085 3190 3.832237 CTGCGAGGTGGCAAGTGGT 62.832 63.158 0.00 0.00 43.39 4.16
3238 3343 5.414454 TGCCAAAGTATACAACAGGTGAATC 59.586 40.000 5.50 0.00 0.00 2.52
3240 3345 5.642063 CCAAAGTATACAACAGGTGAATCGT 59.358 40.000 5.50 0.00 0.00 3.73
3306 3411 1.526575 CTTGCGCCATGGAACTGGTT 61.527 55.000 18.40 0.00 38.63 3.67
3391 3496 4.270245 TCATCACAGCAACACACATCTA 57.730 40.909 0.00 0.00 0.00 1.98
3393 3498 5.247862 TCATCACAGCAACACACATCTATT 58.752 37.500 0.00 0.00 0.00 1.73
3420 3525 0.457853 GCCGCTGACATCTTACACGA 60.458 55.000 0.00 0.00 0.00 4.35
3445 3550 3.135225 CCGTTATTTATGGTCGCCATCA 58.865 45.455 13.58 2.21 40.74 3.07
3508 3613 0.697658 TGACCTCCACAATCATGGCA 59.302 50.000 0.00 0.00 39.85 4.92
3573 3678 3.063510 CTTGATGAGCTCCTGGTTCAA 57.936 47.619 12.15 11.16 38.58 2.69
3595 3700 1.807755 GCCTGCTGCTCGATGTAATGA 60.808 52.381 0.00 0.00 36.87 2.57
3673 3778 2.159653 CGAAGCTTTTGATGAACCCTCG 60.160 50.000 0.00 0.00 0.00 4.63
3697 3802 1.747206 CGACAGAAATGGGGGATGGAC 60.747 57.143 0.00 0.00 0.00 4.02
3698 3803 1.284785 GACAGAAATGGGGGATGGACA 59.715 52.381 0.00 0.00 0.00 4.02
3994 4100 7.099266 TGGTACAATGAAAATCTTAGGCATG 57.901 36.000 0.00 0.00 31.92 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.646526 CACATACCAAGCATTTCAATCATACAG 59.353 37.037 0.00 0.00 0.00 2.74
458 460 0.658897 GGACCGTTTGCGTCTTTTGA 59.341 50.000 0.00 0.00 36.15 2.69
555 557 1.210478 CCCCGATTCCAAGTCACATCT 59.790 52.381 0.00 0.00 0.00 2.90
588 590 4.342665 GGGGGTTTGAAATGTCTTGTTGTA 59.657 41.667 0.00 0.00 0.00 2.41
589 591 3.133901 GGGGGTTTGAAATGTCTTGTTGT 59.866 43.478 0.00 0.00 0.00 3.32
590 592 3.387699 AGGGGGTTTGAAATGTCTTGTTG 59.612 43.478 0.00 0.00 0.00 3.33
592 594 3.230976 GAGGGGGTTTGAAATGTCTTGT 58.769 45.455 0.00 0.00 0.00 3.16
593 595 3.230134 TGAGGGGGTTTGAAATGTCTTG 58.770 45.455 0.00 0.00 0.00 3.02
595 597 3.611025 TTGAGGGGGTTTGAAATGTCT 57.389 42.857 0.00 0.00 0.00 3.41
596 598 3.552068 CGTTTGAGGGGGTTTGAAATGTC 60.552 47.826 0.00 0.00 0.00 3.06
597 599 2.364002 CGTTTGAGGGGGTTTGAAATGT 59.636 45.455 0.00 0.00 0.00 2.71
598 600 2.364002 ACGTTTGAGGGGGTTTGAAATG 59.636 45.455 0.00 0.00 0.00 2.32
599 601 2.626266 GACGTTTGAGGGGGTTTGAAAT 59.374 45.455 0.00 0.00 0.00 2.17
600 602 2.025898 GACGTTTGAGGGGGTTTGAAA 58.974 47.619 0.00 0.00 0.00 2.69
601 603 1.682740 GACGTTTGAGGGGGTTTGAA 58.317 50.000 0.00 0.00 0.00 2.69
602 604 0.179012 GGACGTTTGAGGGGGTTTGA 60.179 55.000 0.00 0.00 0.00 2.69
603 605 1.512156 CGGACGTTTGAGGGGGTTTG 61.512 60.000 0.00 0.00 0.00 2.93
604 606 1.228033 CGGACGTTTGAGGGGGTTT 60.228 57.895 0.00 0.00 0.00 3.27
605 607 2.108278 CTCGGACGTTTGAGGGGGTT 62.108 60.000 9.45 0.00 0.00 4.11
606 608 2.524887 TCGGACGTTTGAGGGGGT 60.525 61.111 0.00 0.00 0.00 4.95
607 609 2.264794 CTCGGACGTTTGAGGGGG 59.735 66.667 9.45 0.00 0.00 5.40
608 610 2.434359 GCTCGGACGTTTGAGGGG 60.434 66.667 16.66 0.00 32.78 4.79
609 611 2.809601 CGCTCGGACGTTTGAGGG 60.810 66.667 16.64 16.64 38.55 4.30
610 612 2.809601 CCGCTCGGACGTTTGAGG 60.810 66.667 16.66 8.84 37.50 3.86
611 613 2.809601 CCCGCTCGGACGTTTGAG 60.810 66.667 10.28 12.22 37.50 3.02
634 636 0.673985 TCTTGACCGACCAGTGACTG 59.326 55.000 5.42 5.42 0.00 3.51
635 637 1.410004 TTCTTGACCGACCAGTGACT 58.590 50.000 0.00 0.00 0.00 3.41
636 638 2.234300 TTTCTTGACCGACCAGTGAC 57.766 50.000 0.00 0.00 0.00 3.67
637 639 3.485463 AATTTCTTGACCGACCAGTGA 57.515 42.857 0.00 0.00 0.00 3.41
638 640 3.363970 CGAAATTTCTTGACCGACCAGTG 60.364 47.826 15.92 0.00 0.00 3.66
639 641 2.806244 CGAAATTTCTTGACCGACCAGT 59.194 45.455 15.92 0.00 0.00 4.00
640 642 3.064207 TCGAAATTTCTTGACCGACCAG 58.936 45.455 15.92 0.00 0.00 4.00
641 643 2.803956 GTCGAAATTTCTTGACCGACCA 59.196 45.455 15.92 0.00 40.03 4.02
642 644 3.450893 GTCGAAATTTCTTGACCGACC 57.549 47.619 15.92 0.60 40.03 4.79
643 645 3.450893 GGTCGAAATTTCTTGACCGAC 57.549 47.619 21.91 18.83 41.26 4.79
647 649 2.095212 GGCTGGGTCGAAATTTCTTGAC 60.095 50.000 15.92 15.07 0.00 3.18
648 650 2.159382 GGCTGGGTCGAAATTTCTTGA 58.841 47.619 15.92 4.32 0.00 3.02
649 651 1.135689 CGGCTGGGTCGAAATTTCTTG 60.136 52.381 15.92 1.92 29.41 3.02
650 652 1.165270 CGGCTGGGTCGAAATTTCTT 58.835 50.000 15.92 0.00 29.41 2.52
651 653 0.676782 CCGGCTGGGTCGAAATTTCT 60.677 55.000 15.92 0.00 29.41 2.52
652 654 0.675522 TCCGGCTGGGTCGAAATTTC 60.676 55.000 12.87 8.20 37.00 2.17
653 655 0.958876 GTCCGGCTGGGTCGAAATTT 60.959 55.000 12.87 0.00 37.00 1.82
654 656 1.376812 GTCCGGCTGGGTCGAAATT 60.377 57.895 12.87 0.00 37.00 1.82
655 657 2.267961 GTCCGGCTGGGTCGAAAT 59.732 61.111 12.87 0.00 37.00 2.17
666 668 2.548295 TTTGTTTGAGGCGTCCGGC 61.548 57.895 4.96 4.96 42.51 6.13
667 669 1.281656 GTTTGTTTGAGGCGTCCGG 59.718 57.895 3.56 0.00 0.00 5.14
668 670 1.164041 AGGTTTGTTTGAGGCGTCCG 61.164 55.000 3.56 0.00 0.00 4.79
669 671 1.029681 AAGGTTTGTTTGAGGCGTCC 58.970 50.000 3.56 0.00 0.00 4.79
670 672 3.974871 TTAAGGTTTGTTTGAGGCGTC 57.025 42.857 0.00 0.00 0.00 5.19
671 673 4.616953 CATTTAAGGTTTGTTTGAGGCGT 58.383 39.130 0.00 0.00 0.00 5.68
672 674 3.428534 GCATTTAAGGTTTGTTTGAGGCG 59.571 43.478 0.00 0.00 0.00 5.52
673 675 3.745975 GGCATTTAAGGTTTGTTTGAGGC 59.254 43.478 0.00 0.00 0.00 4.70
674 676 4.314961 GGGCATTTAAGGTTTGTTTGAGG 58.685 43.478 0.00 0.00 0.00 3.86
675 677 3.987220 CGGGCATTTAAGGTTTGTTTGAG 59.013 43.478 0.00 0.00 0.00 3.02
676 678 3.637229 TCGGGCATTTAAGGTTTGTTTGA 59.363 39.130 0.00 0.00 0.00 2.69
677 679 3.983741 TCGGGCATTTAAGGTTTGTTTG 58.016 40.909 0.00 0.00 0.00 2.93
678 680 3.554129 GCTCGGGCATTTAAGGTTTGTTT 60.554 43.478 0.00 0.00 38.54 2.83
679 681 2.029380 GCTCGGGCATTTAAGGTTTGTT 60.029 45.455 0.00 0.00 38.54 2.83
680 682 1.544246 GCTCGGGCATTTAAGGTTTGT 59.456 47.619 0.00 0.00 38.54 2.83
681 683 1.135112 GGCTCGGGCATTTAAGGTTTG 60.135 52.381 10.74 0.00 40.87 2.93
682 684 1.182667 GGCTCGGGCATTTAAGGTTT 58.817 50.000 10.74 0.00 40.87 3.27
683 685 0.039035 TGGCTCGGGCATTTAAGGTT 59.961 50.000 10.74 0.00 40.87 3.50
684 686 0.258774 ATGGCTCGGGCATTTAAGGT 59.741 50.000 10.74 0.00 46.61 3.50
685 687 2.270352 TATGGCTCGGGCATTTAAGG 57.730 50.000 10.74 0.00 46.61 2.69
686 688 2.293399 GGTTATGGCTCGGGCATTTAAG 59.707 50.000 10.74 0.00 46.61 1.85
687 689 2.303175 GGTTATGGCTCGGGCATTTAA 58.697 47.619 10.74 0.00 46.61 1.52
688 690 1.477923 GGGTTATGGCTCGGGCATTTA 60.478 52.381 10.74 0.00 46.61 1.40
689 691 0.755327 GGGTTATGGCTCGGGCATTT 60.755 55.000 10.74 0.00 46.61 2.32
690 692 1.152756 GGGTTATGGCTCGGGCATT 60.153 57.895 10.74 0.00 46.61 3.56
692 694 2.690881 AGGGTTATGGCTCGGGCA 60.691 61.111 10.74 6.05 43.52 5.36
693 695 2.203209 CAGGGTTATGGCTCGGGC 60.203 66.667 0.00 0.00 37.82 6.13
694 696 2.510906 CCAGGGTTATGGCTCGGG 59.489 66.667 0.00 0.00 32.48 5.14
695 697 2.510906 CCCAGGGTTATGGCTCGG 59.489 66.667 0.00 0.00 39.17 4.63
696 698 2.203209 GCCCAGGGTTATGGCTCG 60.203 66.667 7.55 0.00 42.01 5.03
697 699 2.203209 CGCCCAGGGTTATGGCTC 60.203 66.667 7.55 0.00 43.12 4.70
698 700 3.015145 ACGCCCAGGGTTATGGCT 61.015 61.111 7.55 0.00 43.12 4.75
699 701 2.828549 CACGCCCAGGGTTATGGC 60.829 66.667 7.55 0.00 39.17 4.40
700 702 1.001393 AACACGCCCAGGGTTATGG 60.001 57.895 7.55 0.00 46.30 2.74
701 703 4.734652 AACACGCCCAGGGTTATG 57.265 55.556 7.55 5.79 46.30 1.90
713 715 2.128274 CAAACGTCCGCGAACACG 60.128 61.111 19.30 19.30 42.00 4.49
714 716 2.424640 GCAAACGTCCGCGAACAC 60.425 61.111 8.23 0.00 42.00 3.32
724 726 3.894547 AATCCGCTCCCGCAAACGT 62.895 57.895 0.00 0.00 37.70 3.99
725 727 2.686816 AAATCCGCTCCCGCAAACG 61.687 57.895 0.00 0.00 39.67 3.60
726 728 1.154035 CAAATCCGCTCCCGCAAAC 60.154 57.895 0.00 0.00 35.30 2.93
727 729 2.988688 GCAAATCCGCTCCCGCAAA 61.989 57.895 0.00 0.00 35.30 3.68
728 730 3.439540 GCAAATCCGCTCCCGCAA 61.440 61.111 0.00 0.00 35.30 4.85
729 731 4.408821 AGCAAATCCGCTCCCGCA 62.409 61.111 0.00 0.00 37.91 5.69
735 737 1.340405 ACCAGATTGAGCAAATCCGCT 60.340 47.619 8.16 0.00 45.10 5.52
736 738 1.098050 ACCAGATTGAGCAAATCCGC 58.902 50.000 8.16 0.00 45.10 5.54
737 739 2.489329 ACAACCAGATTGAGCAAATCCG 59.511 45.455 8.16 0.00 45.10 4.18
738 740 4.943705 TCTACAACCAGATTGAGCAAATCC 59.056 41.667 8.16 0.00 45.10 3.01
739 741 6.493116 CATCTACAACCAGATTGAGCAAATC 58.507 40.000 4.42 4.42 44.44 2.17
740 742 5.163581 GCATCTACAACCAGATTGAGCAAAT 60.164 40.000 0.00 0.00 41.23 2.32
741 743 4.156556 GCATCTACAACCAGATTGAGCAAA 59.843 41.667 0.00 0.00 41.23 3.68
742 744 3.691118 GCATCTACAACCAGATTGAGCAA 59.309 43.478 0.00 0.00 41.23 3.91
743 745 3.054875 AGCATCTACAACCAGATTGAGCA 60.055 43.478 0.00 0.00 41.23 4.26
744 746 3.539604 AGCATCTACAACCAGATTGAGC 58.460 45.455 0.00 0.00 41.23 4.26
768 770 4.795635 GCATACTACAGCATCAGACCTCTG 60.796 50.000 0.00 0.00 45.08 3.35
769 771 3.320541 GCATACTACAGCATCAGACCTCT 59.679 47.826 0.00 0.00 0.00 3.69
770 772 3.068732 TGCATACTACAGCATCAGACCTC 59.931 47.826 0.00 0.00 35.51 3.85
771 773 3.033909 TGCATACTACAGCATCAGACCT 58.966 45.455 0.00 0.00 35.51 3.85
772 774 3.388308 CTGCATACTACAGCATCAGACC 58.612 50.000 0.00 0.00 40.42 3.85
773 775 3.068732 TCCTGCATACTACAGCATCAGAC 59.931 47.826 0.00 0.00 40.42 3.51
774 776 3.299503 TCCTGCATACTACAGCATCAGA 58.700 45.455 0.00 0.00 40.42 3.27
775 777 3.740631 TCCTGCATACTACAGCATCAG 57.259 47.619 0.00 0.00 40.42 2.90
776 778 3.642848 TGATCCTGCATACTACAGCATCA 59.357 43.478 0.00 0.00 39.45 3.07
777 779 4.263018 TGATCCTGCATACTACAGCATC 57.737 45.455 0.00 0.00 40.42 3.91
778 780 4.384056 GTTGATCCTGCATACTACAGCAT 58.616 43.478 0.00 0.00 40.42 3.79
779 781 3.432186 GGTTGATCCTGCATACTACAGCA 60.432 47.826 0.00 0.00 39.25 4.41
780 782 3.134458 GGTTGATCCTGCATACTACAGC 58.866 50.000 0.00 0.00 33.65 4.40
781 783 4.122776 GTGGTTGATCCTGCATACTACAG 58.877 47.826 0.00 0.00 37.07 2.74
782 784 3.118408 GGTGGTTGATCCTGCATACTACA 60.118 47.826 0.00 0.00 37.07 2.74
783 785 3.118408 TGGTGGTTGATCCTGCATACTAC 60.118 47.826 0.00 0.00 37.07 2.73
784 786 3.111484 TGGTGGTTGATCCTGCATACTA 58.889 45.455 0.00 0.00 37.07 1.82
785 787 1.915489 TGGTGGTTGATCCTGCATACT 59.085 47.619 0.00 0.00 37.07 2.12
786 788 2.092968 TCTGGTGGTTGATCCTGCATAC 60.093 50.000 0.00 0.00 37.07 2.39
787 789 2.195727 TCTGGTGGTTGATCCTGCATA 58.804 47.619 0.00 0.00 37.07 3.14
788 790 0.994247 TCTGGTGGTTGATCCTGCAT 59.006 50.000 0.00 0.00 37.07 3.96
789 791 0.994247 ATCTGGTGGTTGATCCTGCA 59.006 50.000 0.00 0.00 37.07 4.41
790 792 2.134789 AATCTGGTGGTTGATCCTGC 57.865 50.000 0.00 0.00 37.07 4.85
791 793 3.828451 ACAAAATCTGGTGGTTGATCCTG 59.172 43.478 0.00 0.00 37.07 3.86
792 794 4.118168 ACAAAATCTGGTGGTTGATCCT 57.882 40.909 0.00 0.00 37.07 3.24
793 795 4.871933 AACAAAATCTGGTGGTTGATCC 57.128 40.909 0.00 0.00 0.00 3.36
794 796 7.433680 ACTTTAACAAAATCTGGTGGTTGATC 58.566 34.615 0.00 0.00 0.00 2.92
795 797 7.287696 AGACTTTAACAAAATCTGGTGGTTGAT 59.712 33.333 0.00 0.00 0.00 2.57
796 798 6.605594 AGACTTTAACAAAATCTGGTGGTTGA 59.394 34.615 0.00 0.00 0.00 3.18
797 799 6.697019 CAGACTTTAACAAAATCTGGTGGTTG 59.303 38.462 2.91 0.00 34.43 3.77
798 800 6.605594 TCAGACTTTAACAAAATCTGGTGGTT 59.394 34.615 9.46 0.00 37.87 3.67
799 801 6.126409 TCAGACTTTAACAAAATCTGGTGGT 58.874 36.000 9.46 0.00 37.87 4.16
800 802 6.633500 TCAGACTTTAACAAAATCTGGTGG 57.367 37.500 9.46 0.00 37.87 4.61
811 813 9.069078 CGAATACGACTTTATCAGACTTTAACA 57.931 33.333 0.00 0.00 42.66 2.41
812 814 8.049014 GCGAATACGACTTTATCAGACTTTAAC 58.951 37.037 0.00 0.00 42.66 2.01
813 815 7.972277 AGCGAATACGACTTTATCAGACTTTAA 59.028 33.333 0.00 0.00 42.66 1.52
814 816 7.478322 AGCGAATACGACTTTATCAGACTTTA 58.522 34.615 0.00 0.00 42.66 1.85
815 817 6.331061 AGCGAATACGACTTTATCAGACTTT 58.669 36.000 0.00 0.00 42.66 2.66
816 818 5.892568 AGCGAATACGACTTTATCAGACTT 58.107 37.500 0.00 0.00 42.66 3.01
817 819 5.502153 AGCGAATACGACTTTATCAGACT 57.498 39.130 0.00 0.00 42.66 3.24
818 820 6.570690 AAAGCGAATACGACTTTATCAGAC 57.429 37.500 0.00 0.00 40.71 3.51
819 821 8.692110 TTTAAAGCGAATACGACTTTATCAGA 57.308 30.769 0.69 0.00 41.86 3.27
820 822 9.916397 ATTTTAAAGCGAATACGACTTTATCAG 57.084 29.630 0.69 0.00 41.86 2.90
821 823 9.697250 CATTTTAAAGCGAATACGACTTTATCA 57.303 29.630 0.69 0.00 41.86 2.15
822 824 8.670668 GCATTTTAAAGCGAATACGACTTTATC 58.329 33.333 0.69 0.00 41.86 1.75
823 825 8.178964 TGCATTTTAAAGCGAATACGACTTTAT 58.821 29.630 0.69 0.00 41.86 1.40
824 826 7.519843 TGCATTTTAAAGCGAATACGACTTTA 58.480 30.769 0.00 0.00 41.68 1.85
825 827 6.375377 TGCATTTTAAAGCGAATACGACTTT 58.625 32.000 0.00 0.00 42.85 2.66
826 828 5.933790 TGCATTTTAAAGCGAATACGACTT 58.066 33.333 0.00 0.00 42.66 3.01
827 829 5.539582 TGCATTTTAAAGCGAATACGACT 57.460 34.783 0.00 0.00 42.66 4.18
828 830 6.019152 TCTTGCATTTTAAAGCGAATACGAC 58.981 36.000 0.00 0.00 42.66 4.34
829 831 6.171932 TCTTGCATTTTAAAGCGAATACGA 57.828 33.333 0.00 0.00 42.66 3.43
830 832 6.686679 TCATCTTGCATTTTAAAGCGAATACG 59.313 34.615 0.00 0.00 42.93 3.06
831 833 7.969387 TCATCTTGCATTTTAAAGCGAATAC 57.031 32.000 0.00 0.00 0.00 1.89
833 835 9.585099 TTATTCATCTTGCATTTTAAAGCGAAT 57.415 25.926 0.00 0.00 33.55 3.34
834 836 8.978564 TTATTCATCTTGCATTTTAAAGCGAA 57.021 26.923 0.00 0.00 0.00 4.70
835 837 8.243426 ACTTATTCATCTTGCATTTTAAAGCGA 58.757 29.630 0.00 0.00 0.00 4.93
836 838 8.398491 ACTTATTCATCTTGCATTTTAAAGCG 57.602 30.769 0.00 0.00 0.00 4.68
837 839 8.526681 CGACTTATTCATCTTGCATTTTAAAGC 58.473 33.333 0.00 0.00 0.00 3.51
838 840 8.526681 GCGACTTATTCATCTTGCATTTTAAAG 58.473 33.333 0.00 0.00 0.00 1.85
839 841 8.026026 TGCGACTTATTCATCTTGCATTTTAAA 58.974 29.630 0.00 0.00 0.00 1.52
840 842 7.534282 TGCGACTTATTCATCTTGCATTTTAA 58.466 30.769 0.00 0.00 0.00 1.52
841 843 7.082700 TGCGACTTATTCATCTTGCATTTTA 57.917 32.000 0.00 0.00 0.00 1.52
842 844 5.953183 TGCGACTTATTCATCTTGCATTTT 58.047 33.333 0.00 0.00 0.00 1.82
843 845 5.565592 TGCGACTTATTCATCTTGCATTT 57.434 34.783 0.00 0.00 0.00 2.32
844 846 5.762825 ATGCGACTTATTCATCTTGCATT 57.237 34.783 0.00 0.00 38.56 3.56
845 847 5.762825 AATGCGACTTATTCATCTTGCAT 57.237 34.783 0.00 0.00 43.06 3.96
846 848 5.565592 AAATGCGACTTATTCATCTTGCA 57.434 34.783 0.00 0.00 35.35 4.08
847 849 6.875926 AAAAATGCGACTTATTCATCTTGC 57.124 33.333 0.00 0.00 0.00 4.01
869 871 8.531146 CCATTTCTCCTCTTTTAGGCAAATAAA 58.469 33.333 0.00 0.00 46.10 1.40
872 874 6.256053 TCCATTTCTCCTCTTTTAGGCAAAT 58.744 36.000 0.00 0.00 46.10 2.32
876 878 5.104259 TCTCCATTTCTCCTCTTTTAGGC 57.896 43.478 0.00 0.00 46.10 3.93
904 906 0.098200 GGCGGTTTTAAGATGGACGC 59.902 55.000 0.00 0.00 44.20 5.19
918 920 1.747745 GTTTAATGCTCCCGGCGGT 60.748 57.895 26.32 7.53 45.43 5.68
920 922 1.427819 GTGTTTAATGCTCCCGGCG 59.572 57.895 0.00 0.00 45.43 6.46
921 923 1.663379 GGGTGTTTAATGCTCCCGGC 61.663 60.000 0.00 0.00 42.22 6.13
926 928 0.733150 GAGGCGGGTGTTTAATGCTC 59.267 55.000 0.00 0.00 0.00 4.26
927 929 0.679960 GGAGGCGGGTGTTTAATGCT 60.680 55.000 0.00 0.00 0.00 3.79
1055 1063 4.262463 GGTGGTGGGAATTTTCTCTTTTCC 60.262 45.833 0.00 0.00 38.54 3.13
1576 1608 1.063942 TCGGATCTAGGCAAGACAGGA 60.064 52.381 0.00 0.00 36.93 3.86
1581 1613 1.248486 CCGATCGGATCTAGGCAAGA 58.752 55.000 30.62 0.00 39.02 3.02
1583 1615 1.666011 GCCGATCGGATCTAGGCAA 59.334 57.895 37.64 0.00 46.48 4.52
1676 1714 5.439721 TGATCAATGAGAGGGTAACATTGG 58.560 41.667 15.62 2.46 45.87 3.16
1697 1741 1.440938 CGGGTTGCCTTCACGTTTGA 61.441 55.000 0.00 0.00 0.00 2.69
1715 1759 3.635734 CTGCTCAACCGAAAGCGCG 62.636 63.158 0.00 0.00 41.51 6.86
1792 1836 5.911280 GTCATGTGAAAGTTGTGAGATGTTG 59.089 40.000 0.00 0.00 0.00 3.33
1842 1886 8.417884 CCACCTAGAAAAACATGAAAAGGTAAA 58.582 33.333 0.00 0.00 34.40 2.01
1855 1899 6.695713 GTGACACAAATTCCACCTAGAAAAAC 59.304 38.462 0.00 0.00 0.00 2.43
1865 1912 5.591099 AGACAAATGTGACACAAATTCCAC 58.409 37.500 13.23 1.94 0.00 4.02
1876 1923 4.130118 AGACACAGGAAGACAAATGTGAC 58.870 43.478 10.84 5.04 44.56 3.67
1911 1977 0.111089 CAGCACGCGTGAAAGTTCTC 60.111 55.000 41.19 21.02 0.00 2.87
1993 2061 3.277481 CCAGCGACGCGTATTAAATTTC 58.723 45.455 13.97 0.00 0.00 2.17
2066 2134 3.181465 ACTTGTTGTCACAGTACCAGAGG 60.181 47.826 0.00 0.00 33.22 3.69
2093 2161 2.489329 CCAGGAGCGACAATTCACAAAT 59.511 45.455 0.00 0.00 0.00 2.32
2145 2218 5.107760 CCATTCGTCAGTTTCTTGCATTTTG 60.108 40.000 0.00 0.00 0.00 2.44
2146 2219 4.984161 CCATTCGTCAGTTTCTTGCATTTT 59.016 37.500 0.00 0.00 0.00 1.82
2202 2282 4.284550 GGGTGAGCCAAGCCACCA 62.285 66.667 21.07 1.12 45.16 4.17
2314 2414 2.362375 GGCAATTGGAGCGGGGAA 60.362 61.111 7.72 0.00 0.00 3.97
2387 2487 0.235665 CACGAACACCTGCACATGAC 59.764 55.000 0.00 0.00 0.00 3.06
2583 2683 0.747852 GCCCGGAGTAGAAGAGGAAG 59.252 60.000 0.73 0.00 0.00 3.46
2679 2779 0.940126 CGAACTGCAGCAAGTTGAGT 59.060 50.000 15.27 0.00 40.48 3.41
2686 2786 2.253758 GCCTGACGAACTGCAGCAA 61.254 57.895 15.27 0.00 0.00 3.91
2881 2981 2.093921 TGCAATTCCACAGCCATTGATG 60.094 45.455 0.00 0.00 30.66 3.07
2891 2991 1.608055 CAGTCCACTGCAATTCCACA 58.392 50.000 0.00 0.00 37.15 4.17
2969 3069 6.892658 TGTTGCAACTTACATAGGACAAAT 57.107 33.333 28.61 0.00 0.00 2.32
3073 3178 1.812571 CATCTGTTACCACTTGCCACC 59.187 52.381 0.00 0.00 0.00 4.61
3085 3190 4.365514 TCTTGACCTTTGCCATCTGTTA 57.634 40.909 0.00 0.00 0.00 2.41
3174 3279 6.718522 ATGTCCTCTAAGCTAGGAGTAAAC 57.281 41.667 3.83 5.51 43.81 2.01
3306 3411 1.686355 CTGCTGTTGTTTGTGGGGTA 58.314 50.000 0.00 0.00 0.00 3.69
3393 3498 3.848301 ATGTCAGCGGCTTGGCACA 62.848 57.895 0.00 1.32 35.17 4.57
3400 3505 0.458543 CGTGTAAGATGTCAGCGGCT 60.459 55.000 0.00 0.00 0.00 5.52
3420 3525 2.679336 GGCGACCATAAATAACGGTGTT 59.321 45.455 0.00 0.00 31.63 3.32
3508 3613 1.686325 CCGACCAAGACCCCGATGAT 61.686 60.000 0.00 0.00 0.00 2.45
3562 3667 2.328099 GCAGGCGTTGAACCAGGAG 61.328 63.158 0.00 0.00 0.00 3.69
3595 3700 2.507471 CCCTTTCCACCAAGAGCTCTAT 59.493 50.000 18.59 4.56 0.00 1.98
3673 3778 2.106683 CCCCCATTTCTGTCGACGC 61.107 63.158 11.62 0.00 0.00 5.19
3697 3802 6.072286 GGACTATGCAGATTATGGACCATTTG 60.072 42.308 13.40 7.79 28.84 2.32
3698 3803 6.006449 GGACTATGCAGATTATGGACCATTT 58.994 40.000 13.40 0.29 28.84 2.32
3773 3878 6.114767 TGCTCATCAAGACATTATTGCACTA 58.885 36.000 0.00 0.00 0.00 2.74
3780 3885 5.292834 CACTCGTTGCTCATCAAGACATTAT 59.707 40.000 0.00 0.00 34.91 1.28
3928 4033 7.812648 TGTTTCGAAGACCCAATAGTAATTTG 58.187 34.615 0.00 0.00 34.32 2.32
3994 4100 2.094182 TCTCAGCGTGTTGGAAGGTATC 60.094 50.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.