Multiple sequence alignment - TraesCS2D01G233400

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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 TraesCS2D01G233400 chr2D 100.000 3306 0 0 1 3306 207905527 207908832 0.000000e+00 6106
1 TraesCS2D01G233400 chr2B 94.631 2440 94 9 888 3306 262806520 262808943 0.000000e+00 3746
2 TraesCS2D01G233400 chr2B 87.160 1067 124 7 2245 3303 262638589 262639650 0.000000e+00 1199
3 TraesCS2D01G233400 chr2B 89.076 595 36 17 2 578 262805943 262806526 0.000000e+00 712
4 TraesCS2D01G233400 chr2B 88.636 308 29 4 578 881 131178184 131178489 1.450000e-98 370
5 TraesCS2D01G233400 chr2B 87.382 317 34 4 569 881 24865906 24866220 3.140000e-95 359
6 TraesCS2D01G233400 chr2B 86.047 215 25 4 3084 3297 656006140 656005930 3.320000e-55 226
7 TraesCS2D01G233400 chr2B 83.019 212 29 6 88 298 131622641 131622846 5.630000e-43 185
8 TraesCS2D01G233400 chr2B 91.667 132 9 1 2112 2243 262638047 262638176 7.290000e-42 182
9 TraesCS2D01G233400 chr2A 93.348 1338 65 12 1424 2750 260548483 260549807 0.000000e+00 1956
10 TraesCS2D01G233400 chr2A 90.240 584 40 14 2 578 260547401 260547974 0.000000e+00 747
11 TraesCS2D01G233400 chr2A 93.050 518 21 1 884 1386 260547964 260548481 0.000000e+00 743
12 TraesCS2D01G233400 chr2A 92.593 324 23 1 2981 3303 260555910 260556233 6.460000e-127 464
13 TraesCS2D01G233400 chr2A 90.228 307 25 3 579 882 729554942 729555246 2.390000e-106 396
14 TraesCS2D01G233400 chr4D 89.803 304 26 3 581 881 226385249 226384948 5.180000e-103 385
15 TraesCS2D01G233400 chr4D 88.779 303 30 2 581 881 226455341 226455041 5.210000e-98 368
16 TraesCS2D01G233400 chr5D 89.439 303 27 3 579 879 375170919 375170620 8.660000e-101 377
17 TraesCS2D01G233400 chr3D 88.925 307 27 5 579 881 488121200 488120897 4.030000e-99 372
18 TraesCS2D01G233400 chr7B 88.599 307 29 4 579 881 85134881 85135185 5.210000e-98 368
19 TraesCS2D01G233400 chr7D 86.997 323 34 6 579 897 82851436 82851118 1.130000e-94 357
20 TraesCS2D01G233400 chr5B 84.946 279 33 8 29 303 631635049 631634776 1.170000e-69 274
21 TraesCS2D01G233400 chr4A 89.820 167 15 2 24 189 734070732 734070897 2.580000e-51 213
22 TraesCS2D01G233400 chr3B 85.149 202 26 4 2 200 228804164 228803964 1.560000e-48 204
23 TraesCS2D01G233400 chr3B 78.188 298 51 11 3 292 508470065 508470356 9.430000e-41 178
24 TraesCS2D01G233400 chr6B 80.972 247 31 16 5 246 279193998 279193763 7.290000e-42 182
25 TraesCS2D01G233400 chr6B 80.631 222 37 6 2 219 623716640 623716421 2.040000e-37 167


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 TraesCS2D01G233400 chr2D 207905527 207908832 3305 False 6106.000000 6106 100.000000 1 3306 1 chr2D.!!$F1 3305
1 TraesCS2D01G233400 chr2B 262805943 262808943 3000 False 2229.000000 3746 91.853500 2 3306 2 chr2B.!!$F5 3304
2 TraesCS2D01G233400 chr2B 262638047 262639650 1603 False 690.500000 1199 89.413500 2112 3303 2 chr2B.!!$F4 1191
3 TraesCS2D01G233400 chr2A 260547401 260549807 2406 False 1148.666667 1956 92.212667 2 2750 3 chr2A.!!$F3 2748

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
790 812 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.0 4.96 0.0 31.08 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2537 2991 0.386985 GTCTCGTCTCGTCGCCTTTT 60.387 55.0 0.0 0.0 0.0 2.27 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
406 425 5.459536 AAAGCCTAAAGAAAAGCAGGAAG 57.540 39.130 0.00 0.00 0.00 3.46
407 426 4.373156 AGCCTAAAGAAAAGCAGGAAGA 57.627 40.909 0.00 0.00 0.00 2.87
447 467 1.587043 CGAGTCGCAAGGTCCTCTCA 61.587 60.000 0.00 0.00 38.47 3.27
519 539 4.261572 CGATGCCCTCACAAAAGAAAAAGA 60.262 41.667 0.00 0.00 0.00 2.52
569 591 0.535102 CGCTGTCAACCCAACCTCTT 60.535 55.000 0.00 0.00 0.00 2.85
570 592 0.954452 GCTGTCAACCCAACCTCTTG 59.046 55.000 0.00 0.00 0.00 3.02
571 593 1.750682 GCTGTCAACCCAACCTCTTGT 60.751 52.381 0.00 0.00 0.00 3.16
572 594 1.949525 CTGTCAACCCAACCTCTTGTG 59.050 52.381 0.00 0.00 0.00 3.33
573 595 1.562008 TGTCAACCCAACCTCTTGTGA 59.438 47.619 0.00 0.00 0.00 3.58
574 596 1.947456 GTCAACCCAACCTCTTGTGAC 59.053 52.381 0.00 0.00 0.00 3.67
575 597 1.562008 TCAACCCAACCTCTTGTGACA 59.438 47.619 0.00 0.00 0.00 3.58
576 598 1.949525 CAACCCAACCTCTTGTGACAG 59.050 52.381 0.00 0.00 0.00 3.51
577 599 0.179018 ACCCAACCTCTTGTGACAGC 60.179 55.000 0.00 0.00 0.00 4.40
578 600 1.230635 CCCAACCTCTTGTGACAGCG 61.231 60.000 0.00 0.00 0.00 5.18
579 601 1.571460 CAACCTCTTGTGACAGCGC 59.429 57.895 0.00 0.00 0.00 5.92
580 602 1.956170 AACCTCTTGTGACAGCGCG 60.956 57.895 0.00 0.00 0.00 6.86
581 603 2.049156 CCTCTTGTGACAGCGCGA 60.049 61.111 12.10 0.00 0.00 5.87
582 604 1.664649 CCTCTTGTGACAGCGCGAA 60.665 57.895 12.10 0.00 0.00 4.70
583 605 1.488957 CTCTTGTGACAGCGCGAAC 59.511 57.895 12.10 0.00 0.00 3.95
584 606 1.891060 CTCTTGTGACAGCGCGAACC 61.891 60.000 12.10 0.00 0.00 3.62
585 607 2.202946 TTGTGACAGCGCGAACCA 60.203 55.556 12.10 0.00 0.00 3.67
586 608 1.771073 CTTGTGACAGCGCGAACCAA 61.771 55.000 12.10 2.00 0.00 3.67
587 609 2.042520 TTGTGACAGCGCGAACCAAC 62.043 55.000 12.10 2.02 0.00 3.77
588 610 2.970324 TGACAGCGCGAACCAACC 60.970 61.111 12.10 0.00 0.00 3.77
589 611 2.665185 GACAGCGCGAACCAACCT 60.665 61.111 12.10 0.00 0.00 3.50
590 612 2.954753 GACAGCGCGAACCAACCTG 61.955 63.158 12.10 8.35 0.00 4.00
591 613 2.972505 CAGCGCGAACCAACCTGT 60.973 61.111 12.10 0.00 0.00 4.00
592 614 2.972505 AGCGCGAACCAACCTGTG 60.973 61.111 12.10 0.00 0.00 3.66
607 629 4.086706 ACCTGTGGTTGAAAGGTTAGAG 57.913 45.455 0.00 0.00 41.65 2.43
608 630 3.181443 ACCTGTGGTTGAAAGGTTAGAGG 60.181 47.826 0.00 0.00 41.65 3.69
609 631 3.412386 CTGTGGTTGAAAGGTTAGAGGG 58.588 50.000 0.00 0.00 0.00 4.30
610 632 3.050089 TGTGGTTGAAAGGTTAGAGGGA 58.950 45.455 0.00 0.00 0.00 4.20
611 633 3.181448 TGTGGTTGAAAGGTTAGAGGGAC 60.181 47.826 0.00 0.00 0.00 4.46
613 635 3.072476 TGGTTGAAAGGTTAGAGGGACTG 59.928 47.826 0.00 0.00 41.55 3.51
614 636 3.072622 GGTTGAAAGGTTAGAGGGACTGT 59.927 47.826 0.00 0.00 41.55 3.55
615 637 4.065789 GTTGAAAGGTTAGAGGGACTGTG 58.934 47.826 0.00 0.00 41.55 3.66
616 638 2.637872 TGAAAGGTTAGAGGGACTGTGG 59.362 50.000 0.00 0.00 41.55 4.17
617 639 2.417719 AAGGTTAGAGGGACTGTGGT 57.582 50.000 0.00 0.00 41.55 4.16
618 640 3.555117 AAGGTTAGAGGGACTGTGGTA 57.445 47.619 0.00 0.00 41.55 3.25
619 641 3.778622 AGGTTAGAGGGACTGTGGTAT 57.221 47.619 0.00 0.00 41.55 2.73
620 642 3.644335 AGGTTAGAGGGACTGTGGTATC 58.356 50.000 0.00 0.00 41.55 2.24
621 643 2.699321 GGTTAGAGGGACTGTGGTATCC 59.301 54.545 0.00 0.00 41.55 2.59
626 648 1.527370 GGACTGTGGTATCCCCAGC 59.473 63.158 0.00 0.00 46.45 4.85
627 649 1.527370 GACTGTGGTATCCCCAGCC 59.473 63.158 0.00 0.00 46.45 4.85
628 650 1.984288 GACTGTGGTATCCCCAGCCC 61.984 65.000 0.00 0.00 46.45 5.19
629 651 2.000701 CTGTGGTATCCCCAGCCCA 61.001 63.158 0.00 0.00 46.45 5.36
630 652 1.308657 TGTGGTATCCCCAGCCCAT 60.309 57.895 0.00 0.00 46.45 4.00
631 653 1.352622 TGTGGTATCCCCAGCCCATC 61.353 60.000 0.00 0.00 46.45 3.51
632 654 1.005423 TGGTATCCCCAGCCCATCA 59.995 57.895 0.00 0.00 38.72 3.07
633 655 1.061905 TGGTATCCCCAGCCCATCAG 61.062 60.000 0.00 0.00 38.72 2.90
634 656 1.763770 GTATCCCCAGCCCATCAGG 59.236 63.158 0.00 0.00 39.47 3.86
644 666 4.344237 CCATCAGGGTTCAAGGCC 57.656 61.111 0.00 0.00 0.00 5.19
645 667 1.693640 CCATCAGGGTTCAAGGCCT 59.306 57.895 0.00 0.00 0.00 5.19
646 668 0.918983 CCATCAGGGTTCAAGGCCTA 59.081 55.000 5.16 0.00 0.00 3.93
647 669 1.133976 CCATCAGGGTTCAAGGCCTAG 60.134 57.143 5.16 0.00 0.00 3.02
648 670 1.561542 CATCAGGGTTCAAGGCCTAGT 59.438 52.381 5.16 0.00 0.00 2.57
649 671 0.984230 TCAGGGTTCAAGGCCTAGTG 59.016 55.000 5.16 0.47 0.00 2.74
650 672 0.678048 CAGGGTTCAAGGCCTAGTGC 60.678 60.000 5.16 0.00 40.16 4.40
651 673 0.842467 AGGGTTCAAGGCCTAGTGCT 60.842 55.000 5.16 0.00 40.92 4.40
652 674 0.393132 GGGTTCAAGGCCTAGTGCTC 60.393 60.000 5.16 0.00 40.92 4.26
653 675 0.741221 GGTTCAAGGCCTAGTGCTCG 60.741 60.000 5.16 0.00 40.92 5.03
654 676 1.079127 TTCAAGGCCTAGTGCTCGC 60.079 57.895 5.16 0.00 40.92 5.03
655 677 1.826340 TTCAAGGCCTAGTGCTCGCA 61.826 55.000 5.16 0.00 40.92 5.10
656 678 1.153289 CAAGGCCTAGTGCTCGCAT 60.153 57.895 5.16 0.00 40.92 4.73
657 679 0.745845 CAAGGCCTAGTGCTCGCATT 60.746 55.000 5.16 0.00 40.92 3.56
658 680 0.830648 AAGGCCTAGTGCTCGCATTA 59.169 50.000 5.16 0.00 40.92 1.90
659 681 1.051812 AGGCCTAGTGCTCGCATTAT 58.948 50.000 1.29 0.00 40.92 1.28
660 682 1.417890 AGGCCTAGTGCTCGCATTATT 59.582 47.619 1.29 0.00 40.92 1.40
661 683 1.801178 GGCCTAGTGCTCGCATTATTC 59.199 52.381 0.00 0.00 40.92 1.75
662 684 2.548920 GGCCTAGTGCTCGCATTATTCT 60.549 50.000 0.00 0.00 40.92 2.40
663 685 3.134458 GCCTAGTGCTCGCATTATTCTT 58.866 45.455 0.00 0.00 36.87 2.52
664 686 3.059325 GCCTAGTGCTCGCATTATTCTTG 60.059 47.826 0.00 0.00 36.87 3.02
665 687 4.371786 CCTAGTGCTCGCATTATTCTTGA 58.628 43.478 0.00 0.00 0.00 3.02
666 688 4.811024 CCTAGTGCTCGCATTATTCTTGAA 59.189 41.667 0.00 0.00 0.00 2.69
667 689 5.468072 CCTAGTGCTCGCATTATTCTTGAAT 59.532 40.000 0.00 1.35 0.00 2.57
668 690 5.824904 AGTGCTCGCATTATTCTTGAATT 57.175 34.783 0.95 0.00 0.00 2.17
669 691 6.199937 AGTGCTCGCATTATTCTTGAATTT 57.800 33.333 0.95 0.00 0.00 1.82
670 692 7.320443 AGTGCTCGCATTATTCTTGAATTTA 57.680 32.000 0.95 0.00 0.00 1.40
671 693 7.934457 AGTGCTCGCATTATTCTTGAATTTAT 58.066 30.769 0.95 0.00 0.00 1.40
672 694 8.408601 AGTGCTCGCATTATTCTTGAATTTATT 58.591 29.630 0.95 0.00 0.00 1.40
673 695 9.023967 GTGCTCGCATTATTCTTGAATTTATTT 57.976 29.630 0.95 0.00 0.00 1.40
674 696 9.236691 TGCTCGCATTATTCTTGAATTTATTTC 57.763 29.630 0.95 0.00 34.72 2.17
675 697 9.236691 GCTCGCATTATTCTTGAATTTATTTCA 57.763 29.630 0.95 0.00 42.62 2.69
677 699 9.734620 TCGCATTATTCTTGAATTTATTTCAGG 57.265 29.630 0.95 0.00 44.90 3.86
678 700 9.734620 CGCATTATTCTTGAATTTATTTCAGGA 57.265 29.630 0.95 0.00 45.60 3.86
684 706 9.807649 ATTCTTGAATTTATTTCAGGATTTCCG 57.192 29.630 3.25 0.00 46.25 4.30
685 707 7.771183 TCTTGAATTTATTTCAGGATTTCCGG 58.229 34.615 0.00 0.00 43.30 5.14
686 708 5.901552 TGAATTTATTTCAGGATTTCCGGC 58.098 37.500 0.00 0.00 39.44 6.13
687 709 5.420421 TGAATTTATTTCAGGATTTCCGGCA 59.580 36.000 0.00 0.00 39.44 5.69
688 710 5.930837 ATTTATTTCAGGATTTCCGGCAA 57.069 34.783 0.00 0.00 42.08 4.52
689 711 5.930837 TTTATTTCAGGATTTCCGGCAAT 57.069 34.783 0.00 0.00 42.08 3.56
690 712 3.806625 ATTTCAGGATTTCCGGCAATG 57.193 42.857 3.34 0.00 42.08 2.82
691 713 2.214376 TTCAGGATTTCCGGCAATGT 57.786 45.000 3.34 0.00 42.08 2.71
692 714 1.462616 TCAGGATTTCCGGCAATGTG 58.537 50.000 3.34 1.77 42.08 3.21
693 715 0.179129 CAGGATTTCCGGCAATGTGC 60.179 55.000 3.34 0.00 44.08 4.57
694 716 0.323725 AGGATTTCCGGCAATGTGCT 60.324 50.000 3.34 0.00 44.28 4.40
695 717 0.532115 GGATTTCCGGCAATGTGCTT 59.468 50.000 3.34 0.00 44.28 3.91
696 718 1.066929 GGATTTCCGGCAATGTGCTTT 60.067 47.619 3.34 0.00 44.28 3.51
697 719 2.262211 GATTTCCGGCAATGTGCTTTC 58.738 47.619 3.34 0.00 44.28 2.62
698 720 1.035923 TTTCCGGCAATGTGCTTTCA 58.964 45.000 0.00 0.00 44.28 2.69
699 721 1.035923 TTCCGGCAATGTGCTTTCAA 58.964 45.000 0.00 0.00 44.28 2.69
700 722 1.255882 TCCGGCAATGTGCTTTCAAT 58.744 45.000 0.00 0.00 44.28 2.57
701 723 1.067706 TCCGGCAATGTGCTTTCAATG 60.068 47.619 0.00 0.00 44.28 2.82
702 724 1.352114 CGGCAATGTGCTTTCAATGG 58.648 50.000 0.00 0.00 44.28 3.16
703 725 1.729284 GGCAATGTGCTTTCAATGGG 58.271 50.000 0.00 0.00 44.28 4.00
704 726 1.275856 GGCAATGTGCTTTCAATGGGA 59.724 47.619 0.00 0.00 44.28 4.37
705 727 2.613691 GCAATGTGCTTTCAATGGGAG 58.386 47.619 0.00 0.00 40.96 4.30
706 728 2.675889 GCAATGTGCTTTCAATGGGAGG 60.676 50.000 0.00 0.00 40.96 4.30
707 729 2.827322 CAATGTGCTTTCAATGGGAGGA 59.173 45.455 0.00 0.00 0.00 3.71
708 730 2.205022 TGTGCTTTCAATGGGAGGAG 57.795 50.000 0.00 0.00 0.00 3.69
709 731 1.704628 TGTGCTTTCAATGGGAGGAGA 59.295 47.619 0.00 0.00 0.00 3.71
710 732 2.087646 GTGCTTTCAATGGGAGGAGAC 58.912 52.381 0.00 0.00 0.00 3.36
711 733 1.339055 TGCTTTCAATGGGAGGAGACG 60.339 52.381 0.00 0.00 0.00 4.18
712 734 1.339151 GCTTTCAATGGGAGGAGACGT 60.339 52.381 0.00 0.00 0.00 4.34
713 735 2.876079 GCTTTCAATGGGAGGAGACGTT 60.876 50.000 0.00 0.00 0.00 3.99
714 736 2.762535 TTCAATGGGAGGAGACGTTC 57.237 50.000 0.00 0.00 0.00 3.95
735 757 2.046988 TCGACGACGAGGCACCTA 60.047 61.111 5.75 0.00 43.81 3.08
736 758 2.099831 CGACGACGAGGCACCTAC 59.900 66.667 0.00 0.00 42.66 3.18
737 759 2.099831 GACGACGAGGCACCTACG 59.900 66.667 0.00 8.24 0.00 3.51
738 760 3.392595 GACGACGAGGCACCTACGG 62.393 68.421 0.00 0.00 0.00 4.02
739 761 3.437795 CGACGAGGCACCTACGGT 61.438 66.667 11.43 1.54 35.62 4.83
740 762 2.108514 CGACGAGGCACCTACGGTA 61.109 63.158 11.43 0.00 32.11 4.02
741 763 1.647545 CGACGAGGCACCTACGGTAA 61.648 60.000 11.43 0.00 32.11 2.85
742 764 0.179153 GACGAGGCACCTACGGTAAC 60.179 60.000 11.43 0.00 32.11 2.50
743 765 0.610232 ACGAGGCACCTACGGTAACT 60.610 55.000 11.43 0.00 32.11 2.24
744 766 0.179145 CGAGGCACCTACGGTAACTG 60.179 60.000 0.00 0.00 32.11 3.16
745 767 0.893447 GAGGCACCTACGGTAACTGT 59.107 55.000 0.00 0.00 32.11 3.55
746 768 2.094675 GAGGCACCTACGGTAACTGTA 58.905 52.381 0.00 0.00 32.11 2.74
747 769 2.493278 GAGGCACCTACGGTAACTGTAA 59.507 50.000 0.00 0.00 32.11 2.41
748 770 2.899256 AGGCACCTACGGTAACTGTAAA 59.101 45.455 0.00 0.00 32.11 2.01
749 771 3.516700 AGGCACCTACGGTAACTGTAAAT 59.483 43.478 0.00 0.00 32.11 1.40
750 772 4.019950 AGGCACCTACGGTAACTGTAAATT 60.020 41.667 0.00 0.00 32.11 1.82
751 773 4.696877 GGCACCTACGGTAACTGTAAATTT 59.303 41.667 0.00 0.00 32.11 1.82
752 774 5.163824 GGCACCTACGGTAACTGTAAATTTC 60.164 44.000 0.00 0.00 32.11 2.17
753 775 5.409214 GCACCTACGGTAACTGTAAATTTCA 59.591 40.000 0.00 0.00 32.11 2.69
754 776 6.073112 GCACCTACGGTAACTGTAAATTTCAA 60.073 38.462 0.00 0.00 32.11 2.69
755 777 7.515643 CACCTACGGTAACTGTAAATTTCAAG 58.484 38.462 0.00 0.00 32.11 3.02
756 778 7.385752 CACCTACGGTAACTGTAAATTTCAAGA 59.614 37.037 0.00 0.00 32.11 3.02
757 779 8.098912 ACCTACGGTAACTGTAAATTTCAAGAT 58.901 33.333 0.00 0.00 32.11 2.40
758 780 9.590451 CCTACGGTAACTGTAAATTTCAAGATA 57.410 33.333 0.00 0.00 0.00 1.98
761 783 9.275398 ACGGTAACTGTAAATTTCAAGATAACA 57.725 29.630 0.00 0.00 0.00 2.41
765 787 8.986477 AACTGTAAATTTCAAGATAACATGCC 57.014 30.769 0.00 0.00 0.00 4.40
766 788 7.250569 ACTGTAAATTTCAAGATAACATGCCG 58.749 34.615 0.00 0.00 0.00 5.69
767 789 6.559810 TGTAAATTTCAAGATAACATGCCGG 58.440 36.000 0.00 0.00 0.00 6.13
768 790 3.715628 ATTTCAAGATAACATGCCGGC 57.284 42.857 22.73 22.73 0.00 6.13
769 791 2.418368 TTCAAGATAACATGCCGGCT 57.582 45.000 29.70 9.99 0.00 5.52
770 792 1.953559 TCAAGATAACATGCCGGCTC 58.046 50.000 29.70 15.82 0.00 4.70
771 793 1.209261 TCAAGATAACATGCCGGCTCA 59.791 47.619 29.70 8.87 0.00 4.26
772 794 1.600957 CAAGATAACATGCCGGCTCAG 59.399 52.381 29.70 19.20 0.00 3.35
773 795 0.833287 AGATAACATGCCGGCTCAGT 59.167 50.000 29.70 19.90 0.00 3.41
774 796 1.202580 AGATAACATGCCGGCTCAGTC 60.203 52.381 29.70 17.11 0.00 3.51
775 797 0.833287 ATAACATGCCGGCTCAGTCT 59.167 50.000 29.70 14.84 0.00 3.24
776 798 0.175760 TAACATGCCGGCTCAGTCTC 59.824 55.000 29.70 0.00 0.00 3.36
777 799 1.548357 AACATGCCGGCTCAGTCTCT 61.548 55.000 29.70 5.70 0.00 3.10
778 800 1.227205 CATGCCGGCTCAGTCTCTC 60.227 63.158 29.70 0.00 0.00 3.20
779 801 2.780094 ATGCCGGCTCAGTCTCTCG 61.780 63.158 29.70 0.00 0.00 4.04
780 802 4.200283 GCCGGCTCAGTCTCTCGG 62.200 72.222 22.15 0.00 43.13 4.63
781 803 2.438614 CCGGCTCAGTCTCTCGGA 60.439 66.667 0.00 0.00 42.94 4.55
782 804 2.477176 CCGGCTCAGTCTCTCGGAG 61.477 68.421 0.00 0.00 42.94 4.63
783 805 2.477176 CGGCTCAGTCTCTCGGAGG 61.477 68.421 4.96 0.00 38.48 4.30
784 806 1.379309 GGCTCAGTCTCTCGGAGGT 60.379 63.158 4.96 0.00 38.48 3.85
785 807 1.662438 GGCTCAGTCTCTCGGAGGTG 61.662 65.000 4.96 0.00 38.48 4.00
786 808 1.806568 CTCAGTCTCTCGGAGGTGC 59.193 63.158 4.96 0.00 35.32 5.01
787 809 0.679640 CTCAGTCTCTCGGAGGTGCT 60.680 60.000 4.96 0.00 35.32 4.40
788 810 0.678366 TCAGTCTCTCGGAGGTGCTC 60.678 60.000 4.96 0.00 0.00 4.26
789 811 0.962855 CAGTCTCTCGGAGGTGCTCA 60.963 60.000 4.96 0.00 31.08 4.26
790 812 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.000 4.96 0.00 31.08 2.90
791 813 1.213182 AGTCTCTCGGAGGTGCTCATA 59.787 52.381 4.96 0.00 31.08 2.15
792 814 2.025155 GTCTCTCGGAGGTGCTCATAA 58.975 52.381 4.96 0.00 31.08 1.90
793 815 2.625790 GTCTCTCGGAGGTGCTCATAAT 59.374 50.000 4.96 0.00 31.08 1.28
794 816 2.625314 TCTCTCGGAGGTGCTCATAATG 59.375 50.000 4.96 0.00 31.08 1.90
795 817 1.688735 TCTCGGAGGTGCTCATAATGG 59.311 52.381 4.96 0.00 31.08 3.16
796 818 1.414181 CTCGGAGGTGCTCATAATGGT 59.586 52.381 0.00 0.00 31.08 3.55
797 819 2.628178 CTCGGAGGTGCTCATAATGGTA 59.372 50.000 0.00 0.00 31.08 3.25
798 820 2.628178 TCGGAGGTGCTCATAATGGTAG 59.372 50.000 0.00 0.00 31.08 3.18
799 821 2.289072 CGGAGGTGCTCATAATGGTAGG 60.289 54.545 0.00 0.00 31.08 3.18
800 822 2.039084 GGAGGTGCTCATAATGGTAGGG 59.961 54.545 0.00 0.00 31.08 3.53
801 823 2.706190 GAGGTGCTCATAATGGTAGGGT 59.294 50.000 0.00 0.00 0.00 4.34
802 824 2.439507 AGGTGCTCATAATGGTAGGGTG 59.560 50.000 0.00 0.00 0.00 4.61
803 825 2.172717 GGTGCTCATAATGGTAGGGTGT 59.827 50.000 0.00 0.00 0.00 4.16
804 826 3.206150 GTGCTCATAATGGTAGGGTGTG 58.794 50.000 0.00 0.00 0.00 3.82
805 827 2.222027 GCTCATAATGGTAGGGTGTGC 58.778 52.381 0.00 0.00 0.00 4.57
806 828 2.421388 GCTCATAATGGTAGGGTGTGCA 60.421 50.000 0.00 0.00 31.69 4.57
807 829 3.748668 GCTCATAATGGTAGGGTGTGCAT 60.749 47.826 0.00 0.00 31.69 3.96
808 830 3.817084 CTCATAATGGTAGGGTGTGCATG 59.183 47.826 0.00 0.00 0.00 4.06
809 831 3.201930 TCATAATGGTAGGGTGTGCATGT 59.798 43.478 0.00 0.00 0.00 3.21
810 832 2.128771 AATGGTAGGGTGTGCATGTC 57.871 50.000 0.00 0.00 0.00 3.06
811 833 1.289160 ATGGTAGGGTGTGCATGTCT 58.711 50.000 0.00 0.00 0.00 3.41
812 834 0.324614 TGGTAGGGTGTGCATGTCTG 59.675 55.000 0.00 0.00 0.00 3.51
824 846 1.863454 GCATGTCTGCGTTCATAGAGG 59.137 52.381 0.00 0.00 38.92 3.69
825 847 2.739932 GCATGTCTGCGTTCATAGAGGT 60.740 50.000 0.00 0.00 38.92 3.85
826 848 2.654749 TGTCTGCGTTCATAGAGGTG 57.345 50.000 0.00 0.00 0.00 4.00
827 849 2.167662 TGTCTGCGTTCATAGAGGTGA 58.832 47.619 0.00 0.00 0.00 4.02
828 850 2.164422 TGTCTGCGTTCATAGAGGTGAG 59.836 50.000 0.00 0.00 0.00 3.51
829 851 1.135139 TCTGCGTTCATAGAGGTGAGC 59.865 52.381 0.00 0.00 0.00 4.26
833 855 3.627732 CGTTCATAGAGGTGAGCGTAT 57.372 47.619 5.22 0.00 44.41 3.06
834 856 3.300857 CGTTCATAGAGGTGAGCGTATG 58.699 50.000 5.22 1.99 44.41 2.39
835 857 3.053455 GTTCATAGAGGTGAGCGTATGC 58.947 50.000 0.00 0.00 43.24 3.14
851 873 5.650966 CGTATGCGCGTATATATATGAGC 57.349 43.478 25.34 25.34 42.83 4.26
854 876 4.632538 TGCGCGTATATATATGAGCACT 57.367 40.909 28.83 0.00 45.63 4.40
855 877 4.993905 TGCGCGTATATATATGAGCACTT 58.006 39.130 28.83 0.00 45.63 3.16
856 878 4.798387 TGCGCGTATATATATGAGCACTTG 59.202 41.667 28.83 10.59 45.63 3.16
857 879 4.317418 GCGCGTATATATATGAGCACTTGC 60.317 45.833 26.46 13.70 42.32 4.01
876 898 3.536158 GCGTCTGCACTGATGTTAAAA 57.464 42.857 0.00 0.00 42.15 1.52
877 899 3.884169 GCGTCTGCACTGATGTTAAAAA 58.116 40.909 0.00 0.00 42.15 1.94
976 998 1.589993 CTACGACTGCCATCCGCTG 60.590 63.158 0.00 0.00 41.91 5.18
1086 1109 2.106332 GAGGTACCATGGCGACCG 59.894 66.667 24.09 0.00 38.35 4.79
1181 1204 1.215382 CCTCGACATCGACAAGCCA 59.785 57.895 0.00 0.00 44.22 4.75
1244 1267 4.790962 TACTCTCCCGCGCGGTCT 62.791 66.667 43.12 23.78 0.00 3.85
1382 1423 1.573108 CCTCTAGGGCTGTTTCCAGA 58.427 55.000 0.00 0.00 41.50 3.86
1421 1462 2.107953 GAGATGGAGCTGGCCGAC 59.892 66.667 0.00 0.00 0.00 4.79
1594 1635 1.001760 TCTACCTCCCAGGGCTCAC 59.998 63.158 0.00 0.00 40.58 3.51
1595 1636 1.306141 CTACCTCCCAGGGCTCACA 60.306 63.158 0.00 0.00 40.58 3.58
1614 1655 3.435186 GGAGGAACAAGCTGCCGC 61.435 66.667 0.00 0.00 0.00 6.53
1702 1743 2.640302 GCGTCCAGCCTGAGTCAGA 61.640 63.158 22.09 0.00 40.81 3.27
1719 1760 1.586564 GAGTCGGACGATCCAAGCG 60.587 63.158 1.89 0.00 35.91 4.68
1783 1824 2.504920 TCGAGTGCCGATTCTCCAT 58.495 52.632 0.00 0.00 43.23 3.41
2000 2041 4.717629 TCTGCGAAGGTGGCGACG 62.718 66.667 0.00 0.00 0.00 5.12
2159 2201 0.693049 ACGCTTGATCTGGTTTCCCT 59.307 50.000 0.00 0.00 0.00 4.20
2198 2240 4.694339 ACTCGCAGTTTCTTGTAAGTTCT 58.306 39.130 0.00 0.00 0.00 3.01
2199 2241 5.839621 ACTCGCAGTTTCTTGTAAGTTCTA 58.160 37.500 0.00 0.00 0.00 2.10
2287 2740 9.767684 CGCAATGTTTTCATATTACTACTTCAA 57.232 29.630 0.00 0.00 39.94 2.69
2324 2777 3.884895 TCGATTTATGCATGGTCCAAGT 58.115 40.909 10.16 0.00 0.00 3.16
2390 2843 6.886459 TCCCACTTCATTTTCTTCCAGAATAG 59.114 38.462 0.00 0.00 33.67 1.73
2537 2991 1.072331 GAAGCCTGAACTCCAACCAGA 59.928 52.381 0.00 0.00 0.00 3.86
2668 3134 2.618053 CCACCTTAAGCACCTAACGAG 58.382 52.381 0.00 0.00 0.00 4.18
2809 3275 1.070914 TCAAGCACGTCACCCAACATA 59.929 47.619 0.00 0.00 0.00 2.29
2826 3292 5.067674 CCAACATATCGAAATCCAACACCAT 59.932 40.000 0.00 0.00 0.00 3.55
2941 3407 2.514824 GATGCTCGTTGAGGGGCC 60.515 66.667 0.00 0.00 0.00 5.80
2995 3463 4.357947 GACTCGCAGGTGTCGCCA 62.358 66.667 4.97 0.00 40.61 5.69
3012 3480 2.033141 ACTGCCAGCACGAGCAAT 59.967 55.556 7.77 0.00 45.49 3.56
3032 3500 1.354368 TCCGAGCAGGGATTTTTCCTT 59.646 47.619 0.00 0.00 41.52 3.36
3042 3510 4.835056 AGGGATTTTTCCTTAGCATATGGC 59.165 41.667 4.56 0.00 45.30 4.40
3126 3594 6.968131 ATATGTGTACAAGTTGTGCTACAG 57.032 37.500 22.27 0.00 33.97 2.74
3195 3663 7.131451 TGTGTAACCCGGGCCTATTATATATA 58.869 38.462 24.08 0.00 34.36 0.86
3242 3710 8.312669 AGACTAGACATAAGTTGAAGGCTAAT 57.687 34.615 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
268 276 9.636879 TTGATCATGTGTACAAAAATTGTATGG 57.363 29.630 0.00 0.00 46.73 2.74
365 384 8.887036 AGGCTTTAATTTTGTTTTTCGATTCT 57.113 26.923 0.00 0.00 0.00 2.40
378 397 8.428852 TCCTGCTTTTCTTTAGGCTTTAATTTT 58.571 29.630 0.00 0.00 0.00 1.82
439 459 0.455295 CTCGCGTCACTTGAGAGGAC 60.455 60.000 5.77 0.00 30.70 3.85
447 467 3.607310 CGCTTCTATATCTCGCGTCACTT 60.607 47.826 5.77 0.00 39.07 3.16
569 591 2.202946 TTGGTTCGCGCTGTCACA 60.203 55.556 5.56 0.00 0.00 3.58
570 592 2.248431 GTTGGTTCGCGCTGTCAC 59.752 61.111 5.56 0.00 0.00 3.67
571 593 2.970324 GGTTGGTTCGCGCTGTCA 60.970 61.111 5.56 0.00 0.00 3.58
572 594 2.665185 AGGTTGGTTCGCGCTGTC 60.665 61.111 5.56 0.00 0.00 3.51
573 595 2.972505 CAGGTTGGTTCGCGCTGT 60.973 61.111 5.56 0.00 0.00 4.40
574 596 2.972505 ACAGGTTGGTTCGCGCTG 60.973 61.111 5.56 3.32 0.00 5.18
575 597 2.972505 CACAGGTTGGTTCGCGCT 60.973 61.111 5.56 0.00 0.00 5.92
576 598 4.025401 CCACAGGTTGGTTCGCGC 62.025 66.667 0.00 0.00 41.10 6.86
586 608 3.181443 CCTCTAACCTTTCAACCACAGGT 60.181 47.826 0.00 0.00 43.17 4.00
587 609 3.412386 CCTCTAACCTTTCAACCACAGG 58.588 50.000 0.00 0.00 0.00 4.00
588 610 3.072476 TCCCTCTAACCTTTCAACCACAG 59.928 47.826 0.00 0.00 0.00 3.66
589 611 3.050089 TCCCTCTAACCTTTCAACCACA 58.950 45.455 0.00 0.00 0.00 4.17
590 612 3.072622 AGTCCCTCTAACCTTTCAACCAC 59.927 47.826 0.00 0.00 0.00 4.16
591 613 3.072476 CAGTCCCTCTAACCTTTCAACCA 59.928 47.826 0.00 0.00 0.00 3.67
592 614 3.072622 ACAGTCCCTCTAACCTTTCAACC 59.927 47.826 0.00 0.00 0.00 3.77
593 615 4.065789 CACAGTCCCTCTAACCTTTCAAC 58.934 47.826 0.00 0.00 0.00 3.18
594 616 3.072476 CCACAGTCCCTCTAACCTTTCAA 59.928 47.826 0.00 0.00 0.00 2.69
595 617 2.637872 CCACAGTCCCTCTAACCTTTCA 59.362 50.000 0.00 0.00 0.00 2.69
596 618 2.638363 ACCACAGTCCCTCTAACCTTTC 59.362 50.000 0.00 0.00 0.00 2.62
597 619 2.702748 ACCACAGTCCCTCTAACCTTT 58.297 47.619 0.00 0.00 0.00 3.11
598 620 2.417719 ACCACAGTCCCTCTAACCTT 57.582 50.000 0.00 0.00 0.00 3.50
599 621 3.630311 GGATACCACAGTCCCTCTAACCT 60.630 52.174 0.00 0.00 0.00 3.50
600 622 2.699321 GGATACCACAGTCCCTCTAACC 59.301 54.545 0.00 0.00 0.00 2.85
616 638 1.763770 CCTGATGGGCTGGGGATAC 59.236 63.158 0.00 0.00 32.31 2.24
617 639 4.337474 CCTGATGGGCTGGGGATA 57.663 61.111 0.00 0.00 32.31 2.59
627 649 0.918983 TAGGCCTTGAACCCTGATGG 59.081 55.000 12.58 0.00 41.37 3.51
628 650 1.561542 ACTAGGCCTTGAACCCTGATG 59.438 52.381 21.63 0.00 32.65 3.07
629 651 1.561542 CACTAGGCCTTGAACCCTGAT 59.438 52.381 21.63 0.00 32.65 2.90
630 652 0.984230 CACTAGGCCTTGAACCCTGA 59.016 55.000 21.63 0.00 32.65 3.86
631 653 0.678048 GCACTAGGCCTTGAACCCTG 60.678 60.000 21.63 9.14 36.11 4.45
632 654 0.842467 AGCACTAGGCCTTGAACCCT 60.842 55.000 21.63 7.84 46.50 4.34
633 655 0.393132 GAGCACTAGGCCTTGAACCC 60.393 60.000 21.63 5.74 46.50 4.11
634 656 0.741221 CGAGCACTAGGCCTTGAACC 60.741 60.000 21.63 8.11 46.50 3.62
635 657 1.362406 GCGAGCACTAGGCCTTGAAC 61.362 60.000 21.63 11.64 46.50 3.18
636 658 1.079127 GCGAGCACTAGGCCTTGAA 60.079 57.895 21.63 0.00 46.50 2.69
637 659 1.617018 ATGCGAGCACTAGGCCTTGA 61.617 55.000 21.63 0.00 46.50 3.02
638 660 0.745845 AATGCGAGCACTAGGCCTTG 60.746 55.000 12.58 12.86 46.50 3.61
639 661 0.830648 TAATGCGAGCACTAGGCCTT 59.169 50.000 12.58 0.00 46.50 4.35
640 662 1.051812 ATAATGCGAGCACTAGGCCT 58.948 50.000 11.78 11.78 46.50 5.19
641 663 1.801178 GAATAATGCGAGCACTAGGCC 59.199 52.381 0.00 0.00 46.50 5.19
642 664 2.760374 AGAATAATGCGAGCACTAGGC 58.240 47.619 0.00 0.00 45.30 3.93
643 665 4.371786 TCAAGAATAATGCGAGCACTAGG 58.628 43.478 0.00 0.00 0.00 3.02
644 666 5.973651 TTCAAGAATAATGCGAGCACTAG 57.026 39.130 0.00 0.00 0.00 2.57
645 667 6.925610 AATTCAAGAATAATGCGAGCACTA 57.074 33.333 0.00 0.00 0.00 2.74
646 668 5.824904 AATTCAAGAATAATGCGAGCACT 57.175 34.783 0.00 0.00 0.00 4.40
647 669 8.566008 AATAAATTCAAGAATAATGCGAGCAC 57.434 30.769 0.00 0.00 0.00 4.40
648 670 9.236691 GAAATAAATTCAAGAATAATGCGAGCA 57.763 29.630 0.00 0.00 37.99 4.26
649 671 9.236691 TGAAATAAATTCAAGAATAATGCGAGC 57.763 29.630 0.00 0.00 44.94 5.03
663 685 5.420421 TGCCGGAAATCCTGAAATAAATTCA 59.580 36.000 5.05 0.00 45.71 2.57
664 686 5.901552 TGCCGGAAATCCTGAAATAAATTC 58.098 37.500 5.05 0.00 38.60 2.17
665 687 5.930837 TGCCGGAAATCCTGAAATAAATT 57.069 34.783 5.05 0.00 0.00 1.82
666 688 5.930837 TTGCCGGAAATCCTGAAATAAAT 57.069 34.783 5.05 0.00 0.00 1.40
667 689 5.186797 ACATTGCCGGAAATCCTGAAATAAA 59.813 36.000 4.04 0.00 0.00 1.40
668 690 4.709397 ACATTGCCGGAAATCCTGAAATAA 59.291 37.500 4.04 0.00 0.00 1.40
669 691 4.097741 CACATTGCCGGAAATCCTGAAATA 59.902 41.667 4.04 0.00 0.00 1.40
670 692 3.099141 ACATTGCCGGAAATCCTGAAAT 58.901 40.909 4.04 0.00 0.00 2.17
671 693 2.230992 CACATTGCCGGAAATCCTGAAA 59.769 45.455 4.04 0.00 0.00 2.69
672 694 1.818060 CACATTGCCGGAAATCCTGAA 59.182 47.619 4.04 0.00 0.00 3.02
673 695 1.462616 CACATTGCCGGAAATCCTGA 58.537 50.000 4.04 0.00 0.00 3.86
674 696 0.179129 GCACATTGCCGGAAATCCTG 60.179 55.000 4.04 4.82 37.42 3.86
675 697 0.323725 AGCACATTGCCGGAAATCCT 60.324 50.000 4.04 0.00 46.52 3.24
676 698 0.532115 AAGCACATTGCCGGAAATCC 59.468 50.000 4.04 0.00 46.52 3.01
677 699 2.262211 GAAAGCACATTGCCGGAAATC 58.738 47.619 4.04 0.00 46.52 2.17
678 700 1.617850 TGAAAGCACATTGCCGGAAAT 59.382 42.857 5.05 2.38 46.52 2.17
679 701 1.035923 TGAAAGCACATTGCCGGAAA 58.964 45.000 5.05 0.00 46.52 3.13
680 702 1.035923 TTGAAAGCACATTGCCGGAA 58.964 45.000 5.05 0.00 46.52 4.30
681 703 1.067706 CATTGAAAGCACATTGCCGGA 60.068 47.619 5.05 0.00 46.52 5.14
682 704 1.352114 CATTGAAAGCACATTGCCGG 58.648 50.000 0.00 0.00 46.52 6.13
683 705 1.352114 CCATTGAAAGCACATTGCCG 58.648 50.000 0.00 0.00 46.52 5.69
684 706 1.275856 TCCCATTGAAAGCACATTGCC 59.724 47.619 0.00 0.00 46.52 4.52
685 707 2.613691 CTCCCATTGAAAGCACATTGC 58.386 47.619 0.00 0.00 45.46 3.56
686 708 2.827322 TCCTCCCATTGAAAGCACATTG 59.173 45.455 0.00 0.00 0.00 2.82
687 709 3.094572 CTCCTCCCATTGAAAGCACATT 58.905 45.455 0.00 0.00 0.00 2.71
688 710 2.309755 TCTCCTCCCATTGAAAGCACAT 59.690 45.455 0.00 0.00 0.00 3.21
689 711 1.704628 TCTCCTCCCATTGAAAGCACA 59.295 47.619 0.00 0.00 0.00 4.57
690 712 2.087646 GTCTCCTCCCATTGAAAGCAC 58.912 52.381 0.00 0.00 0.00 4.40
691 713 1.339055 CGTCTCCTCCCATTGAAAGCA 60.339 52.381 0.00 0.00 0.00 3.91
692 714 1.339151 ACGTCTCCTCCCATTGAAAGC 60.339 52.381 0.00 0.00 0.00 3.51
693 715 2.770164 ACGTCTCCTCCCATTGAAAG 57.230 50.000 0.00 0.00 0.00 2.62
694 716 2.290071 GGAACGTCTCCTCCCATTGAAA 60.290 50.000 8.87 0.00 41.61 2.69
695 717 1.278127 GGAACGTCTCCTCCCATTGAA 59.722 52.381 8.87 0.00 41.61 2.69
696 718 0.902531 GGAACGTCTCCTCCCATTGA 59.097 55.000 8.87 0.00 41.61 2.57
697 719 3.460648 GGAACGTCTCCTCCCATTG 57.539 57.895 8.87 0.00 41.61 2.82
717 739 2.393768 TAGGTGCCTCGTCGTCGAC 61.394 63.158 15.51 15.51 41.35 4.20
718 740 2.046988 TAGGTGCCTCGTCGTCGA 60.047 61.111 4.42 4.42 44.12 4.20
719 741 2.099831 GTAGGTGCCTCGTCGTCG 59.900 66.667 0.00 0.00 38.55 5.12
720 742 2.099831 CGTAGGTGCCTCGTCGTC 59.900 66.667 0.00 0.00 0.00 4.20
735 757 9.275398 TGTTATCTTGAAATTTACAGTTACCGT 57.725 29.630 0.00 0.00 0.00 4.83
740 762 7.754924 CGGCATGTTATCTTGAAATTTACAGTT 59.245 33.333 0.00 0.00 0.00 3.16
741 763 7.250569 CGGCATGTTATCTTGAAATTTACAGT 58.749 34.615 0.00 0.00 0.00 3.55
742 764 6.692681 CCGGCATGTTATCTTGAAATTTACAG 59.307 38.462 0.00 0.00 0.00 2.74
743 765 6.559810 CCGGCATGTTATCTTGAAATTTACA 58.440 36.000 0.00 0.00 0.00 2.41
744 766 5.458779 GCCGGCATGTTATCTTGAAATTTAC 59.541 40.000 24.80 0.00 0.00 2.01
745 767 5.359576 AGCCGGCATGTTATCTTGAAATTTA 59.640 36.000 31.54 0.00 0.00 1.40
746 768 4.160252 AGCCGGCATGTTATCTTGAAATTT 59.840 37.500 31.54 0.00 0.00 1.82
747 769 3.701040 AGCCGGCATGTTATCTTGAAATT 59.299 39.130 31.54 0.00 0.00 1.82
748 770 3.290710 AGCCGGCATGTTATCTTGAAAT 58.709 40.909 31.54 0.00 0.00 2.17
749 771 2.682856 GAGCCGGCATGTTATCTTGAAA 59.317 45.455 31.54 0.00 0.00 2.69
750 772 2.288666 GAGCCGGCATGTTATCTTGAA 58.711 47.619 31.54 0.00 0.00 2.69
751 773 1.209261 TGAGCCGGCATGTTATCTTGA 59.791 47.619 31.54 0.00 0.00 3.02
752 774 1.600957 CTGAGCCGGCATGTTATCTTG 59.399 52.381 31.54 9.45 0.00 3.02
753 775 1.210478 ACTGAGCCGGCATGTTATCTT 59.790 47.619 31.54 3.33 0.00 2.40
754 776 0.833287 ACTGAGCCGGCATGTTATCT 59.167 50.000 31.54 4.27 0.00 1.98
755 777 1.202580 AGACTGAGCCGGCATGTTATC 60.203 52.381 31.54 16.99 0.00 1.75
756 778 0.833287 AGACTGAGCCGGCATGTTAT 59.167 50.000 31.54 6.18 0.00 1.89
757 779 0.175760 GAGACTGAGCCGGCATGTTA 59.824 55.000 31.54 8.60 0.00 2.41
758 780 1.078848 GAGACTGAGCCGGCATGTT 60.079 57.895 31.54 7.63 0.00 2.71
759 781 1.954362 GAGAGACTGAGCCGGCATGT 61.954 60.000 31.54 23.16 0.00 3.21
760 782 1.227205 GAGAGACTGAGCCGGCATG 60.227 63.158 31.54 19.90 0.00 4.06
761 783 2.780094 CGAGAGACTGAGCCGGCAT 61.780 63.158 31.54 14.28 0.00 4.40
762 784 3.443925 CGAGAGACTGAGCCGGCA 61.444 66.667 31.54 7.98 0.00 5.69
763 785 4.200283 CCGAGAGACTGAGCCGGC 62.200 72.222 21.89 21.89 33.47 6.13
764 786 2.438614 TCCGAGAGACTGAGCCGG 60.439 66.667 0.00 0.00 41.36 6.13
765 787 2.477176 CCTCCGAGAGACTGAGCCG 61.477 68.421 0.00 0.00 0.00 5.52
766 788 1.379309 ACCTCCGAGAGACTGAGCC 60.379 63.158 0.00 0.00 0.00 4.70
767 789 1.806568 CACCTCCGAGAGACTGAGC 59.193 63.158 0.00 0.00 0.00 4.26
768 790 0.679640 AGCACCTCCGAGAGACTGAG 60.680 60.000 0.00 0.00 0.00 3.35
769 791 0.678366 GAGCACCTCCGAGAGACTGA 60.678 60.000 0.00 0.00 0.00 3.41
770 792 0.962855 TGAGCACCTCCGAGAGACTG 60.963 60.000 0.00 0.22 0.00 3.51
771 793 0.033601 ATGAGCACCTCCGAGAGACT 60.034 55.000 0.00 0.00 0.00 3.24
772 794 1.681538 TATGAGCACCTCCGAGAGAC 58.318 55.000 0.00 0.00 0.00 3.36
773 795 2.437085 TTATGAGCACCTCCGAGAGA 57.563 50.000 0.00 0.00 0.00 3.10
774 796 2.288702 CCATTATGAGCACCTCCGAGAG 60.289 54.545 0.00 0.00 0.00 3.20
775 797 1.688735 CCATTATGAGCACCTCCGAGA 59.311 52.381 0.00 0.00 0.00 4.04
776 798 1.414181 ACCATTATGAGCACCTCCGAG 59.586 52.381 0.00 0.00 0.00 4.63
777 799 1.496060 ACCATTATGAGCACCTCCGA 58.504 50.000 0.00 0.00 0.00 4.55
778 800 2.289072 CCTACCATTATGAGCACCTCCG 60.289 54.545 0.00 0.00 0.00 4.63
779 801 2.039084 CCCTACCATTATGAGCACCTCC 59.961 54.545 0.00 0.00 0.00 4.30
780 802 2.706190 ACCCTACCATTATGAGCACCTC 59.294 50.000 0.00 0.00 0.00 3.85
781 803 2.439507 CACCCTACCATTATGAGCACCT 59.560 50.000 0.00 0.00 0.00 4.00
782 804 2.172717 ACACCCTACCATTATGAGCACC 59.827 50.000 0.00 0.00 0.00 5.01
783 805 3.206150 CACACCCTACCATTATGAGCAC 58.794 50.000 0.00 0.00 0.00 4.40
784 806 2.421388 GCACACCCTACCATTATGAGCA 60.421 50.000 0.00 0.00 0.00 4.26
785 807 2.222027 GCACACCCTACCATTATGAGC 58.778 52.381 0.00 0.00 0.00 4.26
786 808 3.558931 TGCACACCCTACCATTATGAG 57.441 47.619 0.00 0.00 0.00 2.90
787 809 3.201930 ACATGCACACCCTACCATTATGA 59.798 43.478 0.00 0.00 0.00 2.15
788 810 3.554934 ACATGCACACCCTACCATTATG 58.445 45.455 0.00 0.00 0.00 1.90
789 811 3.459598 AGACATGCACACCCTACCATTAT 59.540 43.478 0.00 0.00 0.00 1.28
790 812 2.843730 AGACATGCACACCCTACCATTA 59.156 45.455 0.00 0.00 0.00 1.90
791 813 1.635487 AGACATGCACACCCTACCATT 59.365 47.619 0.00 0.00 0.00 3.16
792 814 1.065199 CAGACATGCACACCCTACCAT 60.065 52.381 0.00 0.00 0.00 3.55
793 815 0.324614 CAGACATGCACACCCTACCA 59.675 55.000 0.00 0.00 0.00 3.25
794 816 3.159298 CAGACATGCACACCCTACC 57.841 57.895 0.00 0.00 0.00 3.18
805 827 2.862536 CACCTCTATGAACGCAGACATG 59.137 50.000 0.00 0.00 32.21 3.21
806 828 2.760650 TCACCTCTATGAACGCAGACAT 59.239 45.455 0.00 0.00 33.83 3.06
807 829 2.164422 CTCACCTCTATGAACGCAGACA 59.836 50.000 0.00 0.00 0.00 3.41
808 830 2.803451 CTCACCTCTATGAACGCAGAC 58.197 52.381 0.00 0.00 0.00 3.51
809 831 1.135139 GCTCACCTCTATGAACGCAGA 59.865 52.381 0.00 0.00 0.00 4.26
810 832 1.565305 GCTCACCTCTATGAACGCAG 58.435 55.000 0.00 0.00 0.00 5.18
811 833 0.179137 CGCTCACCTCTATGAACGCA 60.179 55.000 0.00 0.00 32.08 5.24
812 834 0.179134 ACGCTCACCTCTATGAACGC 60.179 55.000 0.00 0.00 40.91 4.84
813 835 3.300857 CATACGCTCACCTCTATGAACG 58.699 50.000 0.00 0.00 42.48 3.95
814 836 3.053455 GCATACGCTCACCTCTATGAAC 58.947 50.000 0.00 0.00 34.30 3.18
815 837 2.287608 CGCATACGCTCACCTCTATGAA 60.288 50.000 0.00 0.00 35.30 2.57
816 838 1.266989 CGCATACGCTCACCTCTATGA 59.733 52.381 0.00 0.00 35.30 2.15
817 839 1.691127 CGCATACGCTCACCTCTATG 58.309 55.000 0.00 0.00 35.30 2.23
829 851 5.058128 GTGCTCATATATATACGCGCATACG 59.942 44.000 5.73 0.00 44.07 3.06
830 852 6.143496 AGTGCTCATATATATACGCGCATAC 58.857 40.000 21.37 10.88 0.00 2.39
831 853 6.313744 AGTGCTCATATATATACGCGCATA 57.686 37.500 21.37 2.88 0.00 3.14
832 854 5.188327 AGTGCTCATATATATACGCGCAT 57.812 39.130 21.37 0.00 0.00 4.73
833 855 4.632538 AGTGCTCATATATATACGCGCA 57.367 40.909 21.37 11.36 0.00 6.09
834 856 4.317418 GCAAGTGCTCATATATATACGCGC 60.317 45.833 5.73 15.73 38.21 6.86
835 857 4.086075 CGCAAGTGCTCATATATATACGCG 60.086 45.833 3.53 3.53 39.32 6.01
836 858 5.302855 CGCAAGTGCTCATATATATACGC 57.697 43.478 1.21 2.12 39.32 4.42
856 878 3.536158 TTTTAACATCAGTGCAGACGC 57.464 42.857 0.00 0.00 39.24 5.19
876 898 3.792124 GCTTTGCTGTCACTAGCGTTTTT 60.792 43.478 0.00 0.00 46.61 1.94
877 899 2.287009 GCTTTGCTGTCACTAGCGTTTT 60.287 45.455 0.00 0.00 46.61 2.43
878 900 1.264288 GCTTTGCTGTCACTAGCGTTT 59.736 47.619 0.00 0.00 46.61 3.60
879 901 0.868406 GCTTTGCTGTCACTAGCGTT 59.132 50.000 0.00 0.00 46.61 4.84
880 902 0.951040 GGCTTTGCTGTCACTAGCGT 60.951 55.000 0.00 0.00 46.61 5.07
881 903 0.950555 TGGCTTTGCTGTCACTAGCG 60.951 55.000 0.00 0.00 46.61 4.26
882 904 0.801251 CTGGCTTTGCTGTCACTAGC 59.199 55.000 0.00 0.00 43.95 3.42
883 905 0.801251 GCTGGCTTTGCTGTCACTAG 59.199 55.000 0.00 0.00 0.00 2.57
884 906 0.606401 GGCTGGCTTTGCTGTCACTA 60.606 55.000 0.00 0.00 0.00 2.74
885 907 1.900498 GGCTGGCTTTGCTGTCACT 60.900 57.895 0.00 0.00 0.00 3.41
925 947 0.385849 CACGACAGCACGTACCGTAA 60.386 55.000 0.00 0.00 44.76 3.18
926 948 1.207339 CACGACAGCACGTACCGTA 59.793 57.895 0.00 0.00 44.76 4.02
976 998 4.320608 TTTGAGTTTGAACCAATGGAGC 57.679 40.909 6.16 0.00 0.00 4.70
1095 1118 0.599204 TCCGGTTCTTCTTGCGACAC 60.599 55.000 0.00 0.00 0.00 3.67
1109 1132 1.908483 GATCTGCCTTTCCTCCGGT 59.092 57.895 0.00 0.00 0.00 5.28
1181 1204 4.741239 ACGGAGGGGATGGGCAGT 62.741 66.667 0.00 0.00 0.00 4.40
1421 1462 0.982673 GGATGACGTCGAACTCGTTG 59.017 55.000 11.62 0.00 41.64 4.10
1594 1635 1.580845 CGGCAGCTTGTTCCTCCTTG 61.581 60.000 0.00 0.00 0.00 3.61
1595 1636 1.302832 CGGCAGCTTGTTCCTCCTT 60.303 57.895 0.00 0.00 0.00 3.36
1684 1725 2.125753 CTGACTCAGGCTGGACGC 60.126 66.667 15.73 2.76 38.13 5.19
1702 1743 2.341101 ACGCTTGGATCGTCCGACT 61.341 57.895 0.00 0.00 40.17 4.18
2110 2151 4.789075 AACGCGATGGTCGGTCGG 62.789 66.667 15.93 0.00 40.84 4.79
2159 2201 6.096423 ACTGCGAGTACATTTCTACCAGATTA 59.904 38.462 0.00 0.00 0.00 1.75
2287 2740 9.132521 GCATAAATCGAAATGCAAAAGCTATAT 57.867 29.630 19.83 0.00 46.19 0.86
2324 2777 9.352784 CTACATCTGCAAATTTTCGGATTAAAA 57.647 29.630 9.15 0.00 33.15 1.52
2537 2991 0.386985 GTCTCGTCTCGTCGCCTTTT 60.387 55.000 0.00 0.00 0.00 2.27
2600 3057 1.987306 TGGAGCCGTAGCCATGTGA 60.987 57.895 0.00 0.00 41.25 3.58
2601 3058 1.815421 GTGGAGCCGTAGCCATGTG 60.815 63.158 0.00 0.00 41.25 3.21
2602 3059 1.836999 TTGTGGAGCCGTAGCCATGT 61.837 55.000 0.00 0.00 41.25 3.21
2766 3232 2.161211 GTGGATTGCTTCAGTGCTTCTC 59.839 50.000 0.00 0.00 0.00 2.87
2809 3275 3.364460 TCCATGGTGTTGGATTTCGAT 57.636 42.857 12.58 0.00 40.90 3.59
2826 3292 1.191489 TTGGATGCTCTCGGTGTCCA 61.191 55.000 0.00 0.00 37.20 4.02
2883 3349 3.000819 TCCAGATTGGACGGCGGT 61.001 61.111 13.24 0.00 42.67 5.68
2995 3463 2.033141 ATTGCTCGTGCTGGCAGT 59.967 55.556 17.16 0.00 39.68 4.40
3005 3473 2.374830 ATCCCTGCTCGGATTGCTCG 62.375 60.000 0.00 0.00 39.80 5.03
3012 3480 0.991920 AGGAAAAATCCCTGCTCGGA 59.008 50.000 0.00 0.00 36.02 4.55
3028 3496 0.321671 GCTCGGCCATATGCTAAGGA 59.678 55.000 2.24 0.00 40.92 3.36
3032 3500 1.339055 GGATTGCTCGGCCATATGCTA 60.339 52.381 2.24 0.00 40.92 3.49
3042 3510 1.039233 ATGGCTTTGGGATTGCTCGG 61.039 55.000 0.00 0.00 0.00 4.63
3126 3594 3.064820 CCACCGCTAATTACATGTCCAAC 59.935 47.826 0.00 0.00 0.00 3.77
3242 3710 5.163301 GGCTGTCCCTTTTGTGATCTCTATA 60.163 44.000 0.00 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.