Multiple sequence alignment - TraesCS3D01G459900

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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 TraesCS3D01G459900 chr3D 100.000 2944 0 0 1 2944 565036530 565039473 0.000000e+00 5437.0
1 TraesCS3D01G459900 chr3D 95.315 619 9 8 2345 2944 252170717 252171334 0.000000e+00 965.0
2 TraesCS3D01G459900 chr3D 94.198 586 25 5 1 577 61776058 61775473 0.000000e+00 885.0
3 TraesCS3D01G459900 chr3D 94.533 567 25 5 22 583 61792699 61792134 0.000000e+00 870.0
4 TraesCS3D01G459900 chr3D 97.193 285 6 1 2258 2540 274613821 274613537 5.710000e-132 481.0
5 TraesCS3D01G459900 chr3A 89.925 1340 85 27 794 2090 699520966 699522298 0.000000e+00 1681.0
6 TraesCS3D01G459900 chr3A 94.056 286 15 1 2258 2541 249822062 249821777 1.620000e-117 433.0
7 TraesCS3D01G459900 chr3A 95.312 64 3 0 2148 2211 699522382 699522445 5.190000e-18 102.0
8 TraesCS3D01G459900 chr3B 88.088 1276 67 24 841 2045 753174605 753173344 0.000000e+00 1435.0
9 TraesCS3D01G459900 chr3B 100.000 38 0 0 2221 2258 424131075 424131038 1.460000e-08 71.3
10 TraesCS3D01G459900 chr2D 95.319 705 15 5 2258 2944 196631750 196631046 0.000000e+00 1103.0
11 TraesCS3D01G459900 chr2D 94.460 704 15 7 2259 2944 312262664 312263361 0.000000e+00 1062.0
12 TraesCS3D01G459900 chr2D 95.570 632 10 6 2258 2871 321162083 321162714 0.000000e+00 996.0
13 TraesCS3D01G459900 chr2D 93.042 618 24 9 2345 2944 130401450 130400834 0.000000e+00 885.0
14 TraesCS3D01G459900 chr2D 97.544 285 5 2 2257 2539 14505706 14505422 1.230000e-133 486.0
15 TraesCS3D01G459900 chr4D 95.035 705 17 3 2258 2944 482082881 482083585 0.000000e+00 1092.0
16 TraesCS3D01G459900 chr4D 97.561 615 13 2 2259 2871 137403972 137403358 0.000000e+00 1051.0
17 TraesCS3D01G459900 chr4D 94.549 587 23 2 1 578 434344609 434345195 0.000000e+00 898.0
18 TraesCS3D01G459900 chr4D 93.367 588 32 5 1 582 83122589 83123175 0.000000e+00 863.0
19 TraesCS3D01G459900 chr4D 94.276 297 14 2 2259 2553 99639762 99640057 4.470000e-123 451.0
20 TraesCS3D01G459900 chr4D 94.257 296 13 3 2250 2541 220315620 220315325 1.610000e-122 449.0
21 TraesCS3D01G459900 chr4D 91.437 327 25 2 2256 2580 284677777 284678102 2.080000e-121 446.0
22 TraesCS3D01G459900 chr4D 78.947 190 29 8 1326 1508 112197199 112197014 5.150000e-23 119.0
23 TraesCS3D01G459900 chr5D 93.099 710 26 4 2258 2944 29412274 29412983 0.000000e+00 1018.0
24 TraesCS3D01G459900 chr5D 93.707 588 26 7 1 579 237255908 237256493 0.000000e+00 870.0
25 TraesCS3D01G459900 chr5D 98.592 142 2 0 2803 2944 555974563 555974704 4.870000e-63 252.0
26 TraesCS3D01G459900 chr1D 94.669 619 14 7 2345 2944 2631684 2631066 0.000000e+00 942.0
27 TraesCS3D01G459900 chr1D 93.739 591 23 9 1 582 348731947 348732532 0.000000e+00 874.0
28 TraesCS3D01G459900 chr1D 86.872 617 57 17 2258 2871 491321154 491321749 0.000000e+00 669.0
29 TraesCS3D01G459900 chr1D 95.105 286 12 1 2259 2542 417393605 417393890 1.610000e-122 449.0
30 TraesCS3D01G459900 chrUn 94.359 585 27 5 1 582 20386528 20387109 0.000000e+00 893.0
31 TraesCS3D01G459900 chr6D 94.876 566 23 5 22 582 362792637 362793201 0.000000e+00 880.0
32 TraesCS3D01G459900 chr6D 90.931 419 19 2 2526 2944 179539956 179540355 2.000000e-151 545.0
33 TraesCS3D01G459900 chr6D 97.203 286 6 2 2259 2542 460039666 460039951 1.590000e-132 483.0
34 TraesCS3D01G459900 chr7D 93.718 589 25 5 1 577 543721302 543721890 0.000000e+00 872.0
35 TraesCS3D01G459900 chr7D 86.449 583 53 18 2293 2871 81549769 81550329 1.500000e-172 616.0
36 TraesCS3D01G459900 chr5A 87.329 584 58 13 1 580 362801086 362800515 0.000000e+00 654.0
37 TraesCS3D01G459900 chr4B 88.506 87 10 0 1422 1508 658966977 658967063 4.010000e-19 106.0
38 TraesCS3D01G459900 chr4B 100.000 38 0 0 2221 2258 274044754 274044791 1.460000e-08 71.3
39 TraesCS3D01G459900 chr4B 100.000 36 0 0 2220 2255 12887864 12887899 1.890000e-07 67.6
40 TraesCS3D01G459900 chr5B 100.000 37 0 0 2219 2255 387760390 387760426 5.260000e-08 69.4
41 TraesCS3D01G459900 chr5B 97.436 39 1 0 2220 2258 555192776 555192738 1.890000e-07 67.6
42 TraesCS3D01G459900 chr7B 100.000 36 0 0 2220 2255 673660629 673660664 1.890000e-07 67.6
43 TraesCS3D01G459900 chr6B 100.000 36 0 0 2220 2255 522632743 522632778 1.890000e-07 67.6
44 TraesCS3D01G459900 chr6B 97.436 39 1 0 2220 2258 690305326 690305288 1.890000e-07 67.6
45 TraesCS3D01G459900 chr1B 100.000 36 0 0 2220 2255 612208064 612208099 1.890000e-07 67.6


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 TraesCS3D01G459900 chr3D 565036530 565039473 2943 False 5437.0 5437 100.0000 1 2944 1 chr3D.!!$F2 2943
1 TraesCS3D01G459900 chr3D 252170717 252171334 617 False 965.0 965 95.3150 2345 2944 1 chr3D.!!$F1 599
2 TraesCS3D01G459900 chr3D 61775473 61776058 585 True 885.0 885 94.1980 1 577 1 chr3D.!!$R1 576
3 TraesCS3D01G459900 chr3D 61792134 61792699 565 True 870.0 870 94.5330 22 583 1 chr3D.!!$R2 561
4 TraesCS3D01G459900 chr3A 699520966 699522445 1479 False 891.5 1681 92.6185 794 2211 2 chr3A.!!$F1 1417
5 TraesCS3D01G459900 chr3B 753173344 753174605 1261 True 1435.0 1435 88.0880 841 2045 1 chr3B.!!$R2 1204
6 TraesCS3D01G459900 chr2D 196631046 196631750 704 True 1103.0 1103 95.3190 2258 2944 1 chr2D.!!$R3 686
7 TraesCS3D01G459900 chr2D 312262664 312263361 697 False 1062.0 1062 94.4600 2259 2944 1 chr2D.!!$F1 685
8 TraesCS3D01G459900 chr2D 321162083 321162714 631 False 996.0 996 95.5700 2258 2871 1 chr2D.!!$F2 613
9 TraesCS3D01G459900 chr2D 130400834 130401450 616 True 885.0 885 93.0420 2345 2944 1 chr2D.!!$R2 599
10 TraesCS3D01G459900 chr4D 482082881 482083585 704 False 1092.0 1092 95.0350 2258 2944 1 chr4D.!!$F5 686
11 TraesCS3D01G459900 chr4D 137403358 137403972 614 True 1051.0 1051 97.5610 2259 2871 1 chr4D.!!$R2 612
12 TraesCS3D01G459900 chr4D 434344609 434345195 586 False 898.0 898 94.5490 1 578 1 chr4D.!!$F4 577
13 TraesCS3D01G459900 chr4D 83122589 83123175 586 False 863.0 863 93.3670 1 582 1 chr4D.!!$F1 581
14 TraesCS3D01G459900 chr5D 29412274 29412983 709 False 1018.0 1018 93.0990 2258 2944 1 chr5D.!!$F1 686
15 TraesCS3D01G459900 chr5D 237255908 237256493 585 False 870.0 870 93.7070 1 579 1 chr5D.!!$F2 578
16 TraesCS3D01G459900 chr1D 2631066 2631684 618 True 942.0 942 94.6690 2345 2944 1 chr1D.!!$R1 599
17 TraesCS3D01G459900 chr1D 348731947 348732532 585 False 874.0 874 93.7390 1 582 1 chr1D.!!$F1 581
18 TraesCS3D01G459900 chr1D 491321154 491321749 595 False 669.0 669 86.8720 2258 2871 1 chr1D.!!$F3 613
19 TraesCS3D01G459900 chrUn 20386528 20387109 581 False 893.0 893 94.3590 1 582 1 chrUn.!!$F1 581
20 TraesCS3D01G459900 chr6D 362792637 362793201 564 False 880.0 880 94.8760 22 582 1 chr6D.!!$F2 560
21 TraesCS3D01G459900 chr7D 543721302 543721890 588 False 872.0 872 93.7180 1 577 1 chr7D.!!$F2 576
22 TraesCS3D01G459900 chr7D 81549769 81550329 560 False 616.0 616 86.4490 2293 2871 1 chr7D.!!$F1 578
23 TraesCS3D01G459900 chr5A 362800515 362801086 571 True 654.0 654 87.3290 1 580 1 chr5A.!!$R1 579

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
791 814 0.107831 TTATATGGGCCAGGCACGAC 59.892 55.0 15.19 0.34 32.76 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2419 2570 0.040067 GCAGACGACAAAGGCTTTGG 60.04 55.0 35.57 24.21 44.81 3.28 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
151 167 5.026790 CCCCTCCTCCACTCCTTTATATAG 58.973 50.000 0.00 0.00 0.00 1.31
235 256 2.126882 CCTCCACCATAATCCACCTCA 58.873 52.381 0.00 0.00 0.00 3.86
246 267 7.000472 CCATAATCCACCTCAGTCATATTGTT 59.000 38.462 0.00 0.00 0.00 2.83
354 375 0.526211 CTGGATCGTGAGTTCGTGGA 59.474 55.000 0.00 0.00 0.00 4.02
378 399 3.767230 CCGAGCTGAACGTGTGCG 61.767 66.667 0.00 0.00 44.93 5.34
591 614 3.268013 CCAACACGTGGTTCAAAGATC 57.732 47.619 21.57 0.00 43.20 2.75
592 615 2.878406 CCAACACGTGGTTCAAAGATCT 59.122 45.455 21.57 0.00 43.20 2.75
593 616 3.315191 CCAACACGTGGTTCAAAGATCTT 59.685 43.478 21.57 0.88 43.20 2.40
594 617 4.282068 CAACACGTGGTTCAAAGATCTTG 58.718 43.478 21.57 6.61 37.72 3.02
595 618 3.804036 ACACGTGGTTCAAAGATCTTGA 58.196 40.909 21.57 6.14 0.00 3.02
596 619 4.389374 ACACGTGGTTCAAAGATCTTGAT 58.611 39.130 21.57 0.00 0.00 2.57
597 620 4.214119 ACACGTGGTTCAAAGATCTTGATG 59.786 41.667 21.57 4.70 0.00 3.07
598 621 4.214119 CACGTGGTTCAAAGATCTTGATGT 59.786 41.667 9.17 0.00 0.00 3.06
599 622 5.408299 CACGTGGTTCAAAGATCTTGATGTA 59.592 40.000 9.17 0.00 0.00 2.29
600 623 5.995282 ACGTGGTTCAAAGATCTTGATGTAA 59.005 36.000 9.17 0.00 0.00 2.41
601 624 6.655003 ACGTGGTTCAAAGATCTTGATGTAAT 59.345 34.615 9.17 0.00 0.00 1.89
602 625 7.174946 ACGTGGTTCAAAGATCTTGATGTAATT 59.825 33.333 9.17 0.00 0.00 1.40
603 626 8.023128 CGTGGTTCAAAGATCTTGATGTAATTT 58.977 33.333 9.17 0.00 0.00 1.82
604 627 9.696917 GTGGTTCAAAGATCTTGATGTAATTTT 57.303 29.630 9.17 0.00 0.00 1.82
637 660 7.283625 TGTTTCAGGTGCTTTGTATAATTGT 57.716 32.000 0.00 0.00 0.00 2.71
638 661 8.397575 TGTTTCAGGTGCTTTGTATAATTGTA 57.602 30.769 0.00 0.00 0.00 2.41
639 662 9.019656 TGTTTCAGGTGCTTTGTATAATTGTAT 57.980 29.630 0.00 0.00 0.00 2.29
640 663 9.855021 GTTTCAGGTGCTTTGTATAATTGTATT 57.145 29.630 0.00 0.00 0.00 1.89
642 665 9.853555 TTCAGGTGCTTTGTATAATTGTATTTG 57.146 29.630 0.00 0.00 0.00 2.32
643 666 9.019656 TCAGGTGCTTTGTATAATTGTATTTGT 57.980 29.630 0.00 0.00 0.00 2.83
644 667 9.075519 CAGGTGCTTTGTATAATTGTATTTGTG 57.924 33.333 0.00 0.00 0.00 3.33
645 668 8.250332 AGGTGCTTTGTATAATTGTATTTGTGG 58.750 33.333 0.00 0.00 0.00 4.17
646 669 8.032451 GGTGCTTTGTATAATTGTATTTGTGGT 58.968 33.333 0.00 0.00 0.00 4.16
696 719 8.678593 AAAAAGGTTCTTGGTTTTAAACACAA 57.321 26.923 10.14 10.00 0.00 3.33
697 720 8.678593 AAAAGGTTCTTGGTTTTAAACACAAA 57.321 26.923 10.14 0.74 0.00 2.83
698 721 8.678593 AAAGGTTCTTGGTTTTAAACACAAAA 57.321 26.923 10.14 6.44 0.00 2.44
699 722 8.678593 AAGGTTCTTGGTTTTAAACACAAAAA 57.321 26.923 10.14 2.70 0.00 1.94
700 723 8.317891 AGGTTCTTGGTTTTAAACACAAAAAG 57.682 30.769 10.14 5.45 0.00 2.27
701 724 7.389330 AGGTTCTTGGTTTTAAACACAAAAAGG 59.611 33.333 10.14 1.44 0.00 3.11
702 725 7.388224 GGTTCTTGGTTTTAAACACAAAAAGGA 59.612 33.333 10.14 3.40 0.00 3.36
703 726 8.775527 GTTCTTGGTTTTAAACACAAAAAGGAA 58.224 29.630 10.14 8.13 0.00 3.36
704 727 8.904099 TCTTGGTTTTAAACACAAAAAGGAAA 57.096 26.923 10.14 0.00 0.00 3.13
705 728 9.338622 TCTTGGTTTTAAACACAAAAAGGAAAA 57.661 25.926 10.14 0.00 0.00 2.29
706 729 9.388346 CTTGGTTTTAAACACAAAAAGGAAAAC 57.612 29.630 10.14 0.00 35.55 2.43
707 730 8.446599 TGGTTTTAAACACAAAAAGGAAAACA 57.553 26.923 10.14 0.00 37.15 2.83
708 731 8.899771 TGGTTTTAAACACAAAAAGGAAAACAA 58.100 25.926 10.14 0.00 37.15 2.83
709 732 9.731819 GGTTTTAAACACAAAAAGGAAAACAAA 57.268 25.926 10.14 0.00 37.15 2.83
732 755 5.488645 AAAACACACCGATTTTTCGTACT 57.511 34.783 0.00 0.00 0.00 2.73
733 756 6.601741 AAAACACACCGATTTTTCGTACTA 57.398 33.333 0.00 0.00 0.00 1.82
734 757 5.580911 AACACACCGATTTTTCGTACTAC 57.419 39.130 0.00 0.00 0.00 2.73
735 758 3.670055 ACACACCGATTTTTCGTACTACG 59.330 43.478 1.93 1.93 44.19 3.51
736 759 3.059834 CACACCGATTTTTCGTACTACGG 59.940 47.826 8.71 0.00 42.81 4.02
737 760 2.599973 CACCGATTTTTCGTACTACGGG 59.400 50.000 8.71 3.02 42.81 5.28
738 761 2.231235 ACCGATTTTTCGTACTACGGGT 59.769 45.455 8.71 3.61 42.81 5.28
739 762 3.253230 CCGATTTTTCGTACTACGGGTT 58.747 45.455 8.71 0.00 42.81 4.11
740 763 4.082463 ACCGATTTTTCGTACTACGGGTTA 60.082 41.667 8.71 0.00 42.81 2.85
741 764 5.043248 CCGATTTTTCGTACTACGGGTTAT 58.957 41.667 8.71 0.00 42.81 1.89
742 765 6.183360 ACCGATTTTTCGTACTACGGGTTATA 60.183 38.462 8.71 0.00 42.81 0.98
743 766 6.142320 CCGATTTTTCGTACTACGGGTTATAC 59.858 42.308 8.71 0.00 42.81 1.47
744 767 6.142320 CGATTTTTCGTACTACGGGTTATACC 59.858 42.308 8.71 0.00 42.81 2.73
745 768 6.524101 TTTTTCGTACTACGGGTTATACCT 57.476 37.500 8.71 0.00 42.81 3.08
746 769 6.524101 TTTTCGTACTACGGGTTATACCTT 57.476 37.500 8.71 0.00 42.81 3.50
747 770 5.499139 TTCGTACTACGGGTTATACCTTG 57.501 43.478 8.71 0.00 42.81 3.61
748 771 3.315191 TCGTACTACGGGTTATACCTTGC 59.685 47.826 8.71 0.00 42.81 4.01
749 772 3.550842 CGTACTACGGGTTATACCTTGCC 60.551 52.174 0.26 0.00 38.64 4.52
750 773 2.469952 ACTACGGGTTATACCTTGCCA 58.530 47.619 0.00 0.00 38.64 4.92
751 774 2.839425 ACTACGGGTTATACCTTGCCAA 59.161 45.455 0.00 0.00 38.64 4.52
752 775 2.883122 ACGGGTTATACCTTGCCAAA 57.117 45.000 0.00 0.00 38.64 3.28
753 776 3.375647 ACGGGTTATACCTTGCCAAAT 57.624 42.857 0.00 0.00 38.64 2.32
754 777 3.020984 ACGGGTTATACCTTGCCAAATG 58.979 45.455 0.00 0.00 38.64 2.32
755 778 2.360801 CGGGTTATACCTTGCCAAATGG 59.639 50.000 0.00 0.00 38.64 3.16
756 779 2.698274 GGGTTATACCTTGCCAAATGGG 59.302 50.000 0.90 0.00 38.64 4.00
774 797 4.726304 CCGGCCCGGCAAGGTTTA 62.726 66.667 10.42 0.00 41.17 2.01
775 798 2.439519 CGGCCCGGCAAGGTTTAT 60.440 61.111 12.58 0.00 38.74 1.40
776 799 1.153127 CGGCCCGGCAAGGTTTATA 60.153 57.895 12.58 0.00 38.74 0.98
777 800 0.536460 CGGCCCGGCAAGGTTTATAT 60.536 55.000 12.58 0.00 38.74 0.86
778 801 0.958822 GGCCCGGCAAGGTTTATATG 59.041 55.000 12.58 0.00 38.74 1.78
779 802 0.958822 GCCCGGCAAGGTTTATATGG 59.041 55.000 3.91 0.00 38.74 2.74
780 803 1.616159 CCCGGCAAGGTTTATATGGG 58.384 55.000 0.00 0.00 38.74 4.00
781 804 0.958822 CCGGCAAGGTTTATATGGGC 59.041 55.000 0.00 0.00 34.51 5.36
782 805 0.958822 CGGCAAGGTTTATATGGGCC 59.041 55.000 0.00 0.00 36.62 5.80
783 806 1.752436 CGGCAAGGTTTATATGGGCCA 60.752 52.381 9.61 9.61 39.87 5.36
784 807 1.963515 GGCAAGGTTTATATGGGCCAG 59.036 52.381 13.78 0.00 39.66 4.85
785 808 1.963515 GCAAGGTTTATATGGGCCAGG 59.036 52.381 13.78 0.00 0.00 4.45
786 809 1.963515 CAAGGTTTATATGGGCCAGGC 59.036 52.381 13.78 1.26 0.00 4.85
787 810 1.231018 AGGTTTATATGGGCCAGGCA 58.769 50.000 15.19 0.00 0.00 4.75
788 811 1.133482 AGGTTTATATGGGCCAGGCAC 60.133 52.381 15.19 11.31 0.00 5.01
789 812 0.951558 GTTTATATGGGCCAGGCACG 59.048 55.000 15.19 0.00 32.76 5.34
790 813 0.840617 TTTATATGGGCCAGGCACGA 59.159 50.000 15.19 1.25 32.76 4.35
791 814 0.107831 TTATATGGGCCAGGCACGAC 59.892 55.000 15.19 0.34 32.76 4.34
792 815 1.051556 TATATGGGCCAGGCACGACA 61.052 55.000 15.19 6.80 32.76 4.35
806 829 4.700213 AGGCACGACAATTATAAACTTGCT 59.300 37.500 0.00 0.00 0.00 3.91
884 907 2.485122 GATTCGGCCAGGTTTGCG 59.515 61.111 2.24 0.00 0.00 4.85
916 941 2.158841 GTCTCTGTCTCTCACGAGTCAC 59.841 54.545 0.00 0.00 38.45 3.67
964 993 3.161557 GGCACTCCCCTGTTCAGT 58.838 61.111 0.00 0.00 0.00 3.41
1037 1066 3.992260 ATCTGGTAAAGATCGTCTCCG 57.008 47.619 0.00 0.00 42.27 4.63
1040 1069 1.404391 TGGTAAAGATCGTCTCCGCTC 59.596 52.381 0.00 0.00 0.00 5.03
1048 1077 0.098905 TCGTCTCCGCTCTTTCATCG 59.901 55.000 0.00 0.00 0.00 3.84
1051 1080 0.532573 TCTCCGCTCTTTCATCGCTT 59.467 50.000 0.00 0.00 0.00 4.68
1079 1108 2.160205 CGGGATTATCTCTCGGCTACA 58.840 52.381 0.00 0.00 44.47 2.74
1175 1204 4.779733 ACGACCCCCTCATCGCCT 62.780 66.667 0.00 0.00 42.12 5.52
1176 1205 3.917760 CGACCCCCTCATCGCCTC 61.918 72.222 0.00 0.00 0.00 4.70
1573 1614 2.185608 GCTGAGGAGGAAGACGCC 59.814 66.667 0.00 0.00 39.70 5.68
1598 1639 1.869767 ACGAAGAAAAGTCTGCAGCAG 59.130 47.619 17.10 17.10 33.05 4.24
1616 1657 0.663568 AGCTGAAGAACGTTCGTCCG 60.664 55.000 31.93 27.89 35.27 4.79
1641 1682 6.216569 GTGAGTGAGTGAACTGAACTAATGA 58.783 40.000 0.00 0.00 0.00 2.57
1648 1689 7.276438 TGAGTGAACTGAACTAATGATTCATCG 59.724 37.037 0.00 0.00 35.57 3.84
1690 1759 8.847444 AATGATTTTAGTCTGATTCGAAATGC 57.153 30.769 0.00 0.00 0.00 3.56
1708 1778 7.705325 TCGAAATGCCTCTTCTTTACTGTATAC 59.295 37.037 0.00 0.00 0.00 1.47
1710 1780 8.723942 AAATGCCTCTTCTTTACTGTATACTG 57.276 34.615 8.11 8.11 0.00 2.74
1712 1782 7.949690 TGCCTCTTCTTTACTGTATACTGTA 57.050 36.000 16.18 16.18 0.00 2.74
1767 1837 5.127356 GGTAGTGTACCTCTAGCAAAGATGT 59.873 44.000 14.96 3.28 45.52 3.06
1797 1867 9.855021 TTTTCTTTATAAGTCTGCCTTTTATGC 57.145 29.630 0.00 0.00 34.46 3.14
1829 1906 3.634397 TTTTATCAGCCTCTCCAGTGG 57.366 47.619 1.40 1.40 0.00 4.00
1856 1933 2.071540 GCTTTACCCCTGTTACACGTC 58.928 52.381 0.00 0.00 0.00 4.34
1987 2097 9.419297 CACAACTACAGTACTTGTGTGTATAAT 57.581 33.333 18.25 0.00 41.10 1.28
1988 2098 9.991906 ACAACTACAGTACTTGTGTGTATAATT 57.008 29.630 0.00 0.00 41.10 1.40
2011 2121 1.271102 ACACAACACACAACACCCAAC 59.729 47.619 0.00 0.00 0.00 3.77
2012 2122 1.270826 CACAACACACAACACCCAACA 59.729 47.619 0.00 0.00 0.00 3.33
2018 2128 0.455410 CACAACACCCAACACCAGTG 59.545 55.000 0.00 0.00 37.53 3.66
2046 2156 6.422776 AGCAAAATCACCGTCTATAAGTTG 57.577 37.500 0.00 0.00 0.00 3.16
2051 2161 5.796350 ATCACCGTCTATAAGTTGTTTGC 57.204 39.130 0.00 0.00 0.00 3.68
2059 2169 6.730619 CGTCTATAAGTTGTTTGCGTTACTTG 59.269 38.462 0.00 0.00 33.28 3.16
2062 2172 8.702438 TCTATAAGTTGTTTGCGTTACTTGTAC 58.298 33.333 0.00 0.00 33.28 2.90
2065 2175 4.871557 AGTTGTTTGCGTTACTTGTACAGA 59.128 37.500 0.00 0.00 0.00 3.41
2069 2179 5.005971 TGTTTGCGTTACTTGTACAGACTTC 59.994 40.000 0.00 0.00 0.00 3.01
2073 2183 5.221130 GCGTTACTTGTACAGACTTCTCTT 58.779 41.667 0.00 0.00 0.00 2.85
2090 2200 9.356433 GACTTCTCTTCTTGTAGGTTTACATAC 57.644 37.037 0.00 0.00 39.43 2.39
2102 2253 9.781633 TGTAGGTTTACATACTATCTCTCTCTC 57.218 37.037 6.30 0.00 34.91 3.20
2109 2260 7.817418 ACATACTATCTCTCTCTCTGTTTCC 57.183 40.000 0.00 0.00 0.00 3.13
2121 2272 1.343465 TCTGTTTCCTCTTCCCACGAC 59.657 52.381 0.00 0.00 0.00 4.34
2122 2273 0.032952 TGTTTCCTCTTCCCACGACG 59.967 55.000 0.00 0.00 0.00 5.12
2123 2274 0.033090 GTTTCCTCTTCCCACGACGT 59.967 55.000 0.00 0.00 0.00 4.34
2125 2276 0.824595 TTCCTCTTCCCACGACGTCA 60.825 55.000 17.16 0.00 0.00 4.35
2126 2277 1.080705 CCTCTTCCCACGACGTCAC 60.081 63.158 17.16 0.00 0.00 3.67
2128 2279 1.162698 CTCTTCCCACGACGTCACTA 58.837 55.000 17.16 0.00 0.00 2.74
2129 2280 1.538512 CTCTTCCCACGACGTCACTAA 59.461 52.381 17.16 1.30 0.00 2.24
2131 2282 2.361757 TCTTCCCACGACGTCACTAAAA 59.638 45.455 17.16 3.12 0.00 1.52
2132 2283 3.006110 TCTTCCCACGACGTCACTAAAAT 59.994 43.478 17.16 0.00 0.00 1.82
2133 2284 3.389925 TCCCACGACGTCACTAAAATT 57.610 42.857 17.16 0.00 0.00 1.82
2134 2285 3.319755 TCCCACGACGTCACTAAAATTC 58.680 45.455 17.16 0.00 0.00 2.17
2135 2286 2.414138 CCCACGACGTCACTAAAATTCC 59.586 50.000 17.16 0.00 0.00 3.01
2136 2287 2.091588 CCACGACGTCACTAAAATTCCG 59.908 50.000 17.16 0.00 0.00 4.30
2137 2288 2.727798 CACGACGTCACTAAAATTCCGT 59.272 45.455 17.16 0.06 0.00 4.69
2138 2289 3.182972 CACGACGTCACTAAAATTCCGTT 59.817 43.478 17.16 0.00 0.00 4.44
2139 2290 3.182972 ACGACGTCACTAAAATTCCGTTG 59.817 43.478 17.16 0.00 36.16 4.10
2140 2291 3.182972 CGACGTCACTAAAATTCCGTTGT 59.817 43.478 17.16 0.00 0.00 3.32
2141 2292 4.382457 CGACGTCACTAAAATTCCGTTGTA 59.618 41.667 17.16 0.00 0.00 2.41
2142 2293 5.442390 CGACGTCACTAAAATTCCGTTGTAG 60.442 44.000 17.16 0.00 34.35 2.74
2143 2294 4.151157 ACGTCACTAAAATTCCGTTGTAGC 59.849 41.667 0.00 0.00 31.77 3.58
2144 2295 4.150980 CGTCACTAAAATTCCGTTGTAGCA 59.849 41.667 0.00 0.00 31.77 3.49
2145 2296 5.618561 GTCACTAAAATTCCGTTGTAGCAG 58.381 41.667 0.00 0.00 31.77 4.24
2146 2297 4.693566 TCACTAAAATTCCGTTGTAGCAGG 59.306 41.667 0.00 0.00 31.77 4.85
2155 2306 0.881796 GTTGTAGCAGGCAACCCTTC 59.118 55.000 6.75 0.00 40.33 3.46
2165 2316 1.680249 GGCAACCCTTCCAGATGACTC 60.680 57.143 0.00 0.00 0.00 3.36
2182 2333 6.661377 AGATGACTCACTAGACACTGTTGTAT 59.339 38.462 0.00 0.00 35.47 2.29
2211 2362 0.897621 GGTGGGGCTCCTTTGATTTG 59.102 55.000 3.07 0.00 0.00 2.32
2212 2363 0.897621 GTGGGGCTCCTTTGATTTGG 59.102 55.000 3.07 0.00 0.00 3.28
2213 2364 0.486879 TGGGGCTCCTTTGATTTGGT 59.513 50.000 3.07 0.00 0.00 3.67
2214 2365 0.897621 GGGGCTCCTTTGATTTGGTG 59.102 55.000 0.00 0.00 0.00 4.17
2215 2366 1.632589 GGGCTCCTTTGATTTGGTGT 58.367 50.000 0.00 0.00 0.00 4.16
2216 2367 1.970640 GGGCTCCTTTGATTTGGTGTT 59.029 47.619 0.00 0.00 0.00 3.32
2217 2368 2.289010 GGGCTCCTTTGATTTGGTGTTG 60.289 50.000 0.00 0.00 0.00 3.33
2218 2369 2.407090 GCTCCTTTGATTTGGTGTTGC 58.593 47.619 0.00 0.00 0.00 4.17
2219 2370 2.664916 CTCCTTTGATTTGGTGTTGCG 58.335 47.619 0.00 0.00 0.00 4.85
2220 2371 1.139163 CCTTTGATTTGGTGTTGCGC 58.861 50.000 0.00 0.00 0.00 6.09
2221 2372 1.537776 CCTTTGATTTGGTGTTGCGCA 60.538 47.619 5.66 5.66 0.00 6.09
2222 2373 2.200067 CTTTGATTTGGTGTTGCGCAA 58.800 42.857 21.02 21.02 0.00 4.85
2223 2374 2.522836 TTGATTTGGTGTTGCGCAAT 57.477 40.000 27.79 8.17 0.00 3.56
2224 2375 2.522836 TGATTTGGTGTTGCGCAATT 57.477 40.000 27.79 5.39 0.00 2.32
2225 2376 2.402305 TGATTTGGTGTTGCGCAATTC 58.598 42.857 27.79 20.61 0.00 2.17
2226 2377 1.726248 GATTTGGTGTTGCGCAATTCC 59.274 47.619 27.79 27.82 0.00 3.01
2227 2378 0.461548 TTTGGTGTTGCGCAATTCCA 59.538 45.000 31.06 31.06 0.00 3.53
2228 2379 0.678395 TTGGTGTTGCGCAATTCCAT 59.322 45.000 33.25 0.00 0.00 3.41
2229 2380 1.539157 TGGTGTTGCGCAATTCCATA 58.461 45.000 31.06 18.15 0.00 2.74
2230 2381 1.472082 TGGTGTTGCGCAATTCCATAG 59.528 47.619 31.06 0.00 0.00 2.23
2231 2382 1.472480 GGTGTTGCGCAATTCCATAGT 59.528 47.619 27.79 0.00 0.00 2.12
2232 2383 2.094752 GGTGTTGCGCAATTCCATAGTT 60.095 45.455 27.79 0.00 0.00 2.24
2233 2384 3.574614 GTGTTGCGCAATTCCATAGTTT 58.425 40.909 27.79 0.00 0.00 2.66
2234 2385 3.364621 GTGTTGCGCAATTCCATAGTTTG 59.635 43.478 27.79 0.00 0.00 2.93
2235 2386 2.276472 TGCGCAATTCCATAGTTTGC 57.724 45.000 8.16 0.00 41.73 3.68
2236 2387 1.135141 TGCGCAATTCCATAGTTTGCC 60.135 47.619 8.16 0.00 42.05 4.52
2237 2388 1.135141 GCGCAATTCCATAGTTTGCCA 60.135 47.619 0.30 0.00 42.05 4.92
2238 2389 2.481795 GCGCAATTCCATAGTTTGCCAT 60.482 45.455 0.30 0.00 42.05 4.40
2239 2390 3.374745 CGCAATTCCATAGTTTGCCATC 58.625 45.455 0.00 0.00 42.05 3.51
2240 2391 3.721035 GCAATTCCATAGTTTGCCATCC 58.279 45.455 0.00 0.00 39.80 3.51
2241 2392 3.132646 GCAATTCCATAGTTTGCCATCCA 59.867 43.478 0.00 0.00 39.80 3.41
2242 2393 4.382901 GCAATTCCATAGTTTGCCATCCAA 60.383 41.667 0.00 0.00 39.80 3.53
2243 2394 5.732633 CAATTCCATAGTTTGCCATCCAAA 58.267 37.500 0.00 0.00 40.97 3.28
2254 2405 2.905085 TGCCATCCAAACATGATTTGGT 59.095 40.909 25.70 16.74 46.75 3.67
2255 2406 3.264104 GCCATCCAAACATGATTTGGTG 58.736 45.455 25.70 22.59 46.75 4.17
2256 2407 3.306919 GCCATCCAAACATGATTTGGTGT 60.307 43.478 25.70 18.14 46.75 4.16
2708 2877 0.322277 CAGGAAGCACAGCTGGATGT 60.322 55.000 19.93 0.00 39.62 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 112 3.399181 CCTAGGCGCACCCCAAGA 61.399 66.667 10.83 0.00 36.11 3.02
235 256 5.817816 GCCTAAGCACTACAACAATATGACT 59.182 40.000 0.00 0.00 39.53 3.41
313 334 2.334023 AGAGTGTCAGGGAAGAGCTTT 58.666 47.619 0.00 0.00 0.00 3.51
378 399 2.475466 TACGACACCTCCGCGATCC 61.475 63.158 8.23 0.00 0.00 3.36
611 634 9.019656 ACAATTATACAAAGCACCTGAAACATA 57.980 29.630 0.00 0.00 0.00 2.29
612 635 7.895759 ACAATTATACAAAGCACCTGAAACAT 58.104 30.769 0.00 0.00 0.00 2.71
613 636 7.283625 ACAATTATACAAAGCACCTGAAACA 57.716 32.000 0.00 0.00 0.00 2.83
614 637 9.855021 AATACAATTATACAAAGCACCTGAAAC 57.145 29.630 0.00 0.00 0.00 2.78
616 639 9.853555 CAAATACAATTATACAAAGCACCTGAA 57.146 29.630 0.00 0.00 0.00 3.02
617 640 9.019656 ACAAATACAATTATACAAAGCACCTGA 57.980 29.630 0.00 0.00 0.00 3.86
618 641 9.075519 CACAAATACAATTATACAAAGCACCTG 57.924 33.333 0.00 0.00 0.00 4.00
619 642 8.250332 CCACAAATACAATTATACAAAGCACCT 58.750 33.333 0.00 0.00 0.00 4.00
620 643 8.032451 ACCACAAATACAATTATACAAAGCACC 58.968 33.333 0.00 0.00 0.00 5.01
621 644 8.980143 ACCACAAATACAATTATACAAAGCAC 57.020 30.769 0.00 0.00 0.00 4.40
671 694 8.678593 TTGTGTTTAAAACCAAGAACCTTTTT 57.321 26.923 0.00 0.00 0.00 1.94
672 695 8.678593 TTTGTGTTTAAAACCAAGAACCTTTT 57.321 26.923 0.00 0.00 0.00 2.27
673 696 8.678593 TTTTGTGTTTAAAACCAAGAACCTTT 57.321 26.923 0.00 0.00 0.00 3.11
674 697 8.678593 TTTTTGTGTTTAAAACCAAGAACCTT 57.321 26.923 0.00 0.00 29.89 3.50
675 698 7.389330 CCTTTTTGTGTTTAAAACCAAGAACCT 59.611 33.333 0.00 0.00 29.89 3.50
676 699 7.388224 TCCTTTTTGTGTTTAAAACCAAGAACC 59.612 33.333 0.00 0.00 29.89 3.62
677 700 8.312896 TCCTTTTTGTGTTTAAAACCAAGAAC 57.687 30.769 0.00 0.00 29.89 3.01
678 701 8.904099 TTCCTTTTTGTGTTTAAAACCAAGAA 57.096 26.923 0.00 0.00 29.89 2.52
679 702 8.904099 TTTCCTTTTTGTGTTTAAAACCAAGA 57.096 26.923 0.00 0.00 29.89 3.02
680 703 9.388346 GTTTTCCTTTTTGTGTTTAAAACCAAG 57.612 29.630 0.00 0.00 32.11 3.61
681 704 8.899771 TGTTTTCCTTTTTGTGTTTAAAACCAA 58.100 25.926 0.00 0.00 35.52 3.67
682 705 8.446599 TGTTTTCCTTTTTGTGTTTAAAACCA 57.553 26.923 0.00 0.00 35.52 3.67
683 706 9.731819 TTTGTTTTCCTTTTTGTGTTTAAAACC 57.268 25.926 0.00 0.00 35.52 3.27
709 732 5.882553 AGTACGAAAAATCGGTGTGTTTTT 58.117 33.333 3.12 0.00 39.47 1.94
710 733 5.488645 AGTACGAAAAATCGGTGTGTTTT 57.511 34.783 3.12 0.00 37.45 2.43
711 734 5.332506 CGTAGTACGAAAAATCGGTGTGTTT 60.333 40.000 17.85 0.00 46.05 2.83
712 735 4.148696 CGTAGTACGAAAAATCGGTGTGTT 59.851 41.667 17.85 0.00 46.05 3.32
713 736 3.670055 CGTAGTACGAAAAATCGGTGTGT 59.330 43.478 17.85 0.00 46.05 3.72
714 737 3.059834 CCGTAGTACGAAAAATCGGTGTG 59.940 47.826 23.95 0.00 46.05 3.82
715 738 3.244976 CCGTAGTACGAAAAATCGGTGT 58.755 45.455 23.95 0.00 46.05 4.16
716 739 2.599973 CCCGTAGTACGAAAAATCGGTG 59.400 50.000 23.95 3.00 46.05 4.94
717 740 2.231235 ACCCGTAGTACGAAAAATCGGT 59.769 45.455 23.95 16.45 46.05 4.69
718 741 2.879826 ACCCGTAGTACGAAAAATCGG 58.120 47.619 23.95 15.82 46.05 4.18
719 742 6.142320 GGTATAACCCGTAGTACGAAAAATCG 59.858 42.308 23.95 5.15 46.05 3.34
720 743 7.203218 AGGTATAACCCGTAGTACGAAAAATC 58.797 38.462 23.95 8.30 42.28 2.17
721 744 7.112452 AGGTATAACCCGTAGTACGAAAAAT 57.888 36.000 23.95 13.37 42.28 1.82
722 745 6.524101 AGGTATAACCCGTAGTACGAAAAA 57.476 37.500 23.95 7.19 42.28 1.94
723 746 6.329496 CAAGGTATAACCCGTAGTACGAAAA 58.671 40.000 23.95 6.84 42.28 2.29
724 747 5.678616 GCAAGGTATAACCCGTAGTACGAAA 60.679 44.000 23.95 6.50 42.28 3.46
725 748 4.202010 GCAAGGTATAACCCGTAGTACGAA 60.202 45.833 23.95 6.84 42.28 3.85
726 749 3.315191 GCAAGGTATAACCCGTAGTACGA 59.685 47.826 23.95 4.19 42.28 3.43
727 750 3.550842 GGCAAGGTATAACCCGTAGTACG 60.551 52.174 15.86 15.86 39.75 3.67
728 751 3.384467 TGGCAAGGTATAACCCGTAGTAC 59.616 47.826 0.00 0.00 39.75 2.73
729 752 3.641046 TGGCAAGGTATAACCCGTAGTA 58.359 45.455 0.00 0.00 39.75 1.82
730 753 2.469952 TGGCAAGGTATAACCCGTAGT 58.530 47.619 0.00 0.00 39.75 2.73
731 754 3.547054 TTGGCAAGGTATAACCCGTAG 57.453 47.619 0.00 0.00 39.75 3.51
732 755 3.996921 TTTGGCAAGGTATAACCCGTA 57.003 42.857 0.00 0.00 39.75 4.02
733 756 2.883122 TTTGGCAAGGTATAACCCGT 57.117 45.000 0.00 0.00 39.75 5.28
734 757 2.360801 CCATTTGGCAAGGTATAACCCG 59.639 50.000 0.00 0.00 39.75 5.28
735 758 2.698274 CCCATTTGGCAAGGTATAACCC 59.302 50.000 0.00 0.00 39.75 4.11
758 781 0.536460 ATATAAACCTTGCCGGGCCG 60.536 55.000 21.46 21.46 36.97 6.13
759 782 0.958822 CATATAAACCTTGCCGGGCC 59.041 55.000 17.97 0.00 36.97 5.80
760 783 0.958822 CCATATAAACCTTGCCGGGC 59.041 55.000 13.32 13.32 36.97 6.13
761 784 1.616159 CCCATATAAACCTTGCCGGG 58.384 55.000 2.18 0.00 36.97 5.73
762 785 0.958822 GCCCATATAAACCTTGCCGG 59.041 55.000 0.00 0.00 39.35 6.13
763 786 0.958822 GGCCCATATAAACCTTGCCG 59.041 55.000 0.00 0.00 0.00 5.69
764 787 1.963515 CTGGCCCATATAAACCTTGCC 59.036 52.381 0.00 0.00 37.90 4.52
765 788 1.963515 CCTGGCCCATATAAACCTTGC 59.036 52.381 0.00 0.00 0.00 4.01
766 789 1.963515 GCCTGGCCCATATAAACCTTG 59.036 52.381 7.66 0.00 0.00 3.61
767 790 1.573376 TGCCTGGCCCATATAAACCTT 59.427 47.619 17.53 0.00 0.00 3.50
768 791 1.133482 GTGCCTGGCCCATATAAACCT 60.133 52.381 17.53 0.00 0.00 3.50
769 792 1.328279 GTGCCTGGCCCATATAAACC 58.672 55.000 17.53 0.00 0.00 3.27
770 793 0.951558 CGTGCCTGGCCCATATAAAC 59.048 55.000 17.53 3.74 0.00 2.01
771 794 0.840617 TCGTGCCTGGCCCATATAAA 59.159 50.000 17.53 0.00 0.00 1.40
772 795 0.107831 GTCGTGCCTGGCCCATATAA 59.892 55.000 17.53 0.00 0.00 0.98
773 796 1.051556 TGTCGTGCCTGGCCCATATA 61.052 55.000 17.53 0.00 0.00 0.86
774 797 1.920734 TTGTCGTGCCTGGCCCATAT 61.921 55.000 17.53 0.00 0.00 1.78
775 798 1.920734 ATTGTCGTGCCTGGCCCATA 61.921 55.000 17.53 0.00 0.00 2.74
776 799 2.786512 AATTGTCGTGCCTGGCCCAT 62.787 55.000 17.53 0.00 0.00 4.00
777 800 2.130821 TAATTGTCGTGCCTGGCCCA 62.131 55.000 17.53 4.78 0.00 5.36
778 801 0.751643 ATAATTGTCGTGCCTGGCCC 60.752 55.000 17.53 2.94 0.00 5.80
779 802 1.961793 TATAATTGTCGTGCCTGGCC 58.038 50.000 17.53 6.66 0.00 5.36
780 803 3.377172 AGTTTATAATTGTCGTGCCTGGC 59.623 43.478 12.87 12.87 0.00 4.85
781 804 5.331902 CAAGTTTATAATTGTCGTGCCTGG 58.668 41.667 0.00 0.00 0.00 4.45
782 805 4.793216 GCAAGTTTATAATTGTCGTGCCTG 59.207 41.667 1.80 0.00 0.00 4.85
783 806 4.700213 AGCAAGTTTATAATTGTCGTGCCT 59.300 37.500 11.37 0.00 35.01 4.75
784 807 4.793216 CAGCAAGTTTATAATTGTCGTGCC 59.207 41.667 11.37 0.00 35.01 5.01
785 808 4.793216 CCAGCAAGTTTATAATTGTCGTGC 59.207 41.667 1.80 0.00 34.76 5.34
786 809 5.331902 CCCAGCAAGTTTATAATTGTCGTG 58.668 41.667 1.80 0.00 0.00 4.35
787 810 4.142469 GCCCAGCAAGTTTATAATTGTCGT 60.142 41.667 1.80 0.00 0.00 4.34
788 811 4.351192 GCCCAGCAAGTTTATAATTGTCG 58.649 43.478 1.80 0.00 0.00 4.35
789 812 4.159506 TGGCCCAGCAAGTTTATAATTGTC 59.840 41.667 0.00 0.00 0.00 3.18
790 813 4.093011 TGGCCCAGCAAGTTTATAATTGT 58.907 39.130 0.00 0.00 0.00 2.71
791 814 4.441913 CCTGGCCCAGCAAGTTTATAATTG 60.442 45.833 4.81 0.00 0.00 2.32
792 815 3.706086 CCTGGCCCAGCAAGTTTATAATT 59.294 43.478 4.81 0.00 0.00 1.40
884 907 1.596895 GACAGAGACAGGGACCCGTC 61.597 65.000 21.14 21.14 0.00 4.79
916 941 1.067582 GGGGATGAACTCTACGCCG 59.932 63.158 0.00 0.00 0.00 6.46
951 980 1.835494 TCGACTACTGAACAGGGGAG 58.165 55.000 6.76 3.58 0.00 4.30
1037 1066 4.148000 CGAGAGATAAAGCGATGAAAGAGC 59.852 45.833 0.00 0.00 0.00 4.09
1040 1069 3.738282 CCCGAGAGATAAAGCGATGAAAG 59.262 47.826 0.00 0.00 0.00 2.62
1042 1071 2.956333 TCCCGAGAGATAAAGCGATGAA 59.044 45.455 0.00 0.00 0.00 2.57
1048 1077 6.524101 AGAGATAATCCCGAGAGATAAAGC 57.476 41.667 0.00 0.00 0.00 3.51
1051 1080 5.186942 CCGAGAGATAATCCCGAGAGATAA 58.813 45.833 0.00 0.00 0.00 1.75
1079 1108 4.778213 TCTCCATGGAGAAATCGGAATT 57.222 40.909 37.09 0.00 46.89 2.17
1206 1235 3.067742 CCGTATGAAGTCCTGGTTACGAT 59.932 47.826 0.00 0.00 35.65 3.73
1207 1236 2.424601 CCGTATGAAGTCCTGGTTACGA 59.575 50.000 0.00 0.00 35.65 3.43
1303 1344 0.322456 CCGCCATGGAGTTCTTGGAA 60.322 55.000 18.40 0.00 41.70 3.53
1558 1599 3.760035 GCGGCGTCTTCCTCCTCA 61.760 66.667 9.37 0.00 0.00 3.86
1573 1614 1.136502 GCAGACTTTTCTTCGTCAGCG 60.137 52.381 0.00 0.00 33.96 5.18
1594 1635 0.249489 ACGAACGTTCTTCAGCTGCT 60.249 50.000 24.80 0.00 0.00 4.24
1598 1639 1.615107 CCGGACGAACGTTCTTCAGC 61.615 60.000 29.05 15.91 0.00 4.26
1616 1657 3.460857 AGTTCAGTTCACTCACTCACC 57.539 47.619 0.00 0.00 0.00 4.02
1648 1689 6.992063 AATCATTACCATCATCGCTAATCC 57.008 37.500 0.00 0.00 0.00 3.01
1708 1778 8.999431 AGCGGGTAAACAAATATTCATATACAG 58.001 33.333 0.00 0.00 0.00 2.74
1710 1780 9.216117 AGAGCGGGTAAACAAATATTCATATAC 57.784 33.333 0.00 0.00 0.00 1.47
1712 1782 8.691661 AAGAGCGGGTAAACAAATATTCATAT 57.308 30.769 0.00 0.00 0.00 1.78
1797 1867 3.691609 GGCTGATAAAAAGGTCTGACAGG 59.308 47.826 10.38 0.00 0.00 4.00
1829 1906 1.812507 CAGGGGTAAAGCGCGGTAC 60.813 63.158 12.91 7.01 0.00 3.34
1987 2097 2.488545 GGGTGTTGTGTGTTGTGTGTAA 59.511 45.455 0.00 0.00 0.00 2.41
1988 2098 2.085320 GGGTGTTGTGTGTTGTGTGTA 58.915 47.619 0.00 0.00 0.00 2.90
1989 2099 0.885196 GGGTGTTGTGTGTTGTGTGT 59.115 50.000 0.00 0.00 0.00 3.72
1990 2100 0.884514 TGGGTGTTGTGTGTTGTGTG 59.115 50.000 0.00 0.00 0.00 3.82
1992 2102 1.270826 TGTTGGGTGTTGTGTGTTGTG 59.729 47.619 0.00 0.00 0.00 3.33
2001 2111 1.318886 TGCACTGGTGTTGGGTGTTG 61.319 55.000 2.64 0.00 33.96 3.33
2018 2128 3.764885 AGACGGTGATTTTGCTATTGC 57.235 42.857 0.00 0.00 40.20 3.56
2046 2156 5.233689 AGAAGTCTGTACAAGTAACGCAAAC 59.766 40.000 0.00 0.00 0.00 2.93
2051 2161 6.670233 AGAAGAGAAGTCTGTACAAGTAACG 58.330 40.000 0.00 0.00 31.37 3.18
2059 2169 6.578163 ACCTACAAGAAGAGAAGTCTGTAC 57.422 41.667 0.00 0.00 31.37 2.90
2062 2172 7.434492 TGTAAACCTACAAGAAGAGAAGTCTG 58.566 38.462 0.00 0.00 35.03 3.51
2065 2175 9.091220 AGTATGTAAACCTACAAGAAGAGAAGT 57.909 33.333 0.00 0.00 41.36 3.01
2090 2200 6.263168 GGAAGAGGAAACAGAGAGAGAGATAG 59.737 46.154 0.00 0.00 0.00 2.08
2094 2245 3.447229 GGGAAGAGGAAACAGAGAGAGAG 59.553 52.174 0.00 0.00 0.00 3.20
2102 2253 1.797025 GTCGTGGGAAGAGGAAACAG 58.203 55.000 0.00 0.00 0.00 3.16
2108 2259 1.080705 GTGACGTCGTGGGAAGAGG 60.081 63.158 11.62 0.00 0.00 3.69
2109 2260 1.162698 TAGTGACGTCGTGGGAAGAG 58.837 55.000 11.62 0.00 0.00 2.85
2121 2272 4.150980 TGCTACAACGGAATTTTAGTGACG 59.849 41.667 0.00 0.00 0.00 4.35
2122 2273 5.390567 CCTGCTACAACGGAATTTTAGTGAC 60.391 44.000 0.00 0.00 0.00 3.67
2123 2274 4.693566 CCTGCTACAACGGAATTTTAGTGA 59.306 41.667 0.00 0.00 0.00 3.41
2125 2276 3.439129 GCCTGCTACAACGGAATTTTAGT 59.561 43.478 0.00 0.00 0.00 2.24
2126 2277 3.438781 TGCCTGCTACAACGGAATTTTAG 59.561 43.478 0.00 0.00 0.00 1.85
2128 2279 2.235016 TGCCTGCTACAACGGAATTTT 58.765 42.857 0.00 0.00 0.00 1.82
2129 2280 1.904287 TGCCTGCTACAACGGAATTT 58.096 45.000 0.00 0.00 0.00 1.82
2131 2282 1.165270 GTTGCCTGCTACAACGGAAT 58.835 50.000 0.00 0.00 38.18 3.01
2132 2283 0.887387 GGTTGCCTGCTACAACGGAA 60.887 55.000 6.10 0.00 46.65 4.30
2133 2284 1.302192 GGTTGCCTGCTACAACGGA 60.302 57.895 6.10 0.00 46.65 4.69
2134 2285 2.332654 GGGTTGCCTGCTACAACGG 61.333 63.158 6.10 0.00 46.65 4.44
2135 2286 0.889186 AAGGGTTGCCTGCTACAACG 60.889 55.000 6.10 0.00 46.65 4.10
2136 2287 0.881796 GAAGGGTTGCCTGCTACAAC 59.118 55.000 6.10 8.09 45.30 3.32
2137 2288 0.251165 GGAAGGGTTGCCTGCTACAA 60.251 55.000 6.10 0.00 0.00 2.41
2138 2289 1.378762 GGAAGGGTTGCCTGCTACA 59.621 57.895 6.10 0.00 0.00 2.74
2139 2290 0.678048 CTGGAAGGGTTGCCTGCTAC 60.678 60.000 0.00 0.00 0.00 3.58
2140 2291 0.840288 TCTGGAAGGGTTGCCTGCTA 60.840 55.000 0.00 0.00 0.00 3.49
2141 2292 1.504275 ATCTGGAAGGGTTGCCTGCT 61.504 55.000 0.00 0.00 0.00 4.24
2142 2293 1.000396 ATCTGGAAGGGTTGCCTGC 60.000 57.895 0.00 0.00 0.00 4.85
2143 2294 0.329261 TCATCTGGAAGGGTTGCCTG 59.671 55.000 0.00 0.00 0.00 4.85
2144 2295 0.329596 GTCATCTGGAAGGGTTGCCT 59.670 55.000 0.00 0.00 0.00 4.75
2145 2296 0.329596 AGTCATCTGGAAGGGTTGCC 59.670 55.000 0.00 0.00 0.00 4.52
2146 2297 1.003580 TGAGTCATCTGGAAGGGTTGC 59.996 52.381 0.00 0.00 0.00 4.17
2155 2306 3.761218 ACAGTGTCTAGTGAGTCATCTGG 59.239 47.826 0.00 0.00 31.19 3.86
2165 2316 5.050490 GGGCATATACAACAGTGTCTAGTG 58.950 45.833 0.00 0.00 39.30 2.74
2211 2362 1.472480 ACTATGGAATTGCGCAACACC 59.528 47.619 27.64 28.46 0.00 4.16
2212 2363 2.919666 ACTATGGAATTGCGCAACAC 57.080 45.000 27.64 21.03 0.00 3.32
2213 2364 3.573598 CAAACTATGGAATTGCGCAACA 58.426 40.909 27.64 19.62 0.00 3.33
2214 2365 2.345341 GCAAACTATGGAATTGCGCAAC 59.655 45.455 27.64 13.99 39.89 4.17
2215 2366 2.605030 GCAAACTATGGAATTGCGCAA 58.395 42.857 27.24 27.24 39.89 4.85
2216 2367 2.276472 GCAAACTATGGAATTGCGCA 57.724 45.000 5.66 5.66 39.89 6.09
2219 2370 3.132646 TGGATGGCAAACTATGGAATTGC 59.867 43.478 13.13 13.13 46.60 3.56
2220 2371 5.341872 TTGGATGGCAAACTATGGAATTG 57.658 39.130 0.00 0.00 0.00 2.32
2221 2372 5.248020 TGTTTGGATGGCAAACTATGGAATT 59.752 36.000 1.28 0.00 41.58 2.17
2222 2373 4.776837 TGTTTGGATGGCAAACTATGGAAT 59.223 37.500 1.28 0.00 41.58 3.01
2223 2374 4.155709 TGTTTGGATGGCAAACTATGGAA 58.844 39.130 1.28 0.00 41.58 3.53
2224 2375 3.772387 TGTTTGGATGGCAAACTATGGA 58.228 40.909 1.28 0.00 41.58 3.41
2225 2376 4.160065 TCATGTTTGGATGGCAAACTATGG 59.840 41.667 1.28 0.00 41.58 2.74
2226 2377 5.327616 TCATGTTTGGATGGCAAACTATG 57.672 39.130 1.28 4.75 41.58 2.23
2227 2378 6.549433 AATCATGTTTGGATGGCAAACTAT 57.451 33.333 1.28 0.00 41.58 2.12
2228 2379 5.999205 AATCATGTTTGGATGGCAAACTA 57.001 34.783 1.28 0.00 41.58 2.24
2229 2380 4.895668 AATCATGTTTGGATGGCAAACT 57.104 36.364 1.28 0.00 41.58 2.66
2230 2381 5.285798 CAAATCATGTTTGGATGGCAAAC 57.714 39.130 0.00 0.00 41.45 2.93
2240 2391 6.502652 TGTAGTGAACACCAAATCATGTTTG 58.497 36.000 11.52 11.52 39.13 2.93
2241 2392 6.239008 CCTGTAGTGAACACCAAATCATGTTT 60.239 38.462 1.11 0.00 39.13 2.83
2242 2393 5.241506 CCTGTAGTGAACACCAAATCATGTT 59.758 40.000 1.11 0.00 41.70 2.71
2243 2394 4.761739 CCTGTAGTGAACACCAAATCATGT 59.238 41.667 1.11 0.00 33.45 3.21
2244 2395 5.003160 TCCTGTAGTGAACACCAAATCATG 58.997 41.667 1.11 0.00 33.45 3.07
2245 2396 5.241403 TCCTGTAGTGAACACCAAATCAT 57.759 39.130 1.11 0.00 33.45 2.45
2246 2397 4.698201 TCCTGTAGTGAACACCAAATCA 57.302 40.909 1.11 0.00 33.45 2.57
2247 2398 5.705441 TGATTCCTGTAGTGAACACCAAATC 59.295 40.000 1.11 2.83 33.45 2.17
2248 2399 5.630121 TGATTCCTGTAGTGAACACCAAAT 58.370 37.500 1.11 0.00 33.45 2.32
2249 2400 5.042463 TGATTCCTGTAGTGAACACCAAA 57.958 39.130 1.11 0.00 33.45 3.28
2250 2401 4.641396 CTGATTCCTGTAGTGAACACCAA 58.359 43.478 1.11 0.00 33.45 3.67
2251 2402 3.557054 GCTGATTCCTGTAGTGAACACCA 60.557 47.826 1.11 0.00 33.45 4.17
2252 2403 3.003480 GCTGATTCCTGTAGTGAACACC 58.997 50.000 1.11 0.00 33.45 4.16
2253 2404 3.931578 AGCTGATTCCTGTAGTGAACAC 58.068 45.455 0.00 0.00 33.45 3.32
2254 2405 5.939764 ATAGCTGATTCCTGTAGTGAACA 57.060 39.130 0.00 0.00 36.42 3.18
2255 2406 7.467623 CAAAATAGCTGATTCCTGTAGTGAAC 58.532 38.462 0.00 0.00 0.00 3.18
2256 2407 6.094048 GCAAAATAGCTGATTCCTGTAGTGAA 59.906 38.462 0.00 0.00 0.00 3.18
2301 2452 1.022451 GTCCGCCGTTCATGCCTTTA 61.022 55.000 0.00 0.00 0.00 1.85
2419 2570 0.040067 GCAGACGACAAAGGCTTTGG 60.040 55.000 35.57 24.21 44.81 3.28
2708 2877 1.300620 CGGCAAAGAGGACACGTGA 60.301 57.895 25.01 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.