Multiple sequence alignment - TraesCS2A01G439500

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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 TraesCS2A01G439500 chr2A 100.000 2940 0 0 1 2940 690741922 690744861 0.000000e+00 5430.0
1 TraesCS2A01G439500 chr2A 100.000 675 0 0 3219 3893 690745140 690745814 0.000000e+00 1247.0
2 TraesCS2A01G439500 chr2B 94.237 2065 91 13 620 2671 653750195 653752244 0.000000e+00 3129.0
3 TraesCS2A01G439500 chr2B 91.564 652 48 4 1 650 653749546 653750192 0.000000e+00 893.0
4 TraesCS2A01G439500 chr2B 88.865 458 39 4 3436 3893 653760938 653761383 1.580000e-153 553.0
5 TraesCS2A01G439500 chr2B 80.987 547 102 2 3272 3816 653807503 653808049 2.150000e-117 433.0
6 TraesCS2A01G439500 chr2B 92.478 226 16 1 3226 3450 653752459 653752684 4.850000e-84 322.0
7 TraesCS2A01G439500 chr2B 98.333 120 2 0 2820 2939 653752237 653752356 1.100000e-50 211.0
8 TraesCS2A01G439500 chr2D 91.803 2135 114 28 557 2656 547271974 547274082 0.000000e+00 2916.0
9 TraesCS2A01G439500 chr2D 87.630 671 64 11 3226 3893 547274308 547274962 0.000000e+00 761.0
10 TraesCS2A01G439500 chr6A 93.631 157 6 1 2665 2817 448657852 448658008 8.410000e-57 231.0
11 TraesCS2A01G439500 chr7B 93.960 149 5 2 2672 2816 728117133 728117281 5.060000e-54 222.0
12 TraesCS2A01G439500 chr4A 93.197 147 6 1 2672 2814 617043671 617043817 3.050000e-51 213.0
13 TraesCS2A01G439500 chr5A 91.304 69 6 0 11 79 219710277 219710345 1.150000e-15 95.3
14 TraesCS2A01G439500 chr5B 96.078 51 2 0 22 72 13706958 13707008 2.490000e-12 84.2
15 TraesCS2A01G439500 chr7D 89.474 57 6 0 11 67 99187089 99187145 5.400000e-09 73.1
16 TraesCS2A01G439500 chr7A 89.474 57 6 0 8 64 194059932 194059988 5.400000e-09 73.1
17 TraesCS2A01G439500 chr3D 86.667 60 6 1 15 74 101552164 101552107 9.030000e-07 65.8
18 TraesCS2A01G439500 chr1A 95.122 41 2 0 15 55 495180336 495180296 9.030000e-07 65.8


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 TraesCS2A01G439500 chr2A 690741922 690745814 3892 False 3338.50 5430 100.0000 1 3893 2 chr2A.!!$F1 3892
1 TraesCS2A01G439500 chr2B 653749546 653752684 3138 False 1138.75 3129 94.1530 1 3450 4 chr2B.!!$F3 3449
2 TraesCS2A01G439500 chr2B 653807503 653808049 546 False 433.00 433 80.9870 3272 3816 1 chr2B.!!$F2 544
3 TraesCS2A01G439500 chr2D 547271974 547274962 2988 False 1838.50 2916 89.7165 557 3893 2 chr2D.!!$F1 3336

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
419 421 0.033796 ACCCTGACATTGGCCATCAG 60.034 55.0 22.82 22.82 39.7 2.90 F
595 597 0.250124 ACACGCCGATGGTCTTTCAA 60.250 50.0 0.00 0.00 0.0 2.69 F
2085 2130 0.039074 ACACTCCGCTCTTTCTCACG 60.039 55.0 0.00 0.00 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 1623 0.719465 GGTACGCGTTCACCATGAAG 59.281 55.0 23.14 0.0 37.0 3.02 R
2421 2466 0.107081 TACTTGGGTCAACGGTGGTG 59.893 55.0 0.00 0.0 0.0 4.17 R
3453 3535 0.108138 CAGCGACGAAAGGGAAGGAT 60.108 55.0 0.00 0.0 0.0 3.24 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
117 119 1.234821 GATCGACACCACAAAAGCCA 58.765 50.000 0.00 0.00 0.00 4.75
127 129 3.270027 CCACAAAAGCCATAGTCATCGA 58.730 45.455 0.00 0.00 0.00 3.59
135 137 7.624360 AAAGCCATAGTCATCGACATTAAAA 57.376 32.000 0.00 0.00 34.60 1.52
215 217 2.287977 AAACCTAACTTCAGCACCCC 57.712 50.000 0.00 0.00 0.00 4.95
222 224 3.003173 TTCAGCACCCCGAGGAGG 61.003 66.667 0.00 0.00 40.63 4.30
237 239 1.923850 AGGAGGTAGCAGGACTCTACA 59.076 52.381 0.00 0.00 38.45 2.74
262 264 3.199880 AGGTCTGCTTAATCCATTCCG 57.800 47.619 0.00 0.00 0.00 4.30
286 288 4.065088 TGAACGAACTTGAAGGAGGATTG 58.935 43.478 0.00 0.00 0.00 2.67
294 296 2.907892 TGAAGGAGGATTGGAGTCTGT 58.092 47.619 0.00 0.00 0.00 3.41
315 317 6.918569 TCTGTAAGACTGACTCGAAGAAAAAG 59.081 38.462 0.00 0.00 38.67 2.27
328 330 2.590821 AGAAAAAGTGCTGCCATCTGT 58.409 42.857 0.00 0.00 0.00 3.41
329 331 2.555757 AGAAAAAGTGCTGCCATCTGTC 59.444 45.455 0.00 0.00 0.00 3.51
337 339 1.032794 CTGCCATCTGTCCTAGCGTA 58.967 55.000 0.00 0.00 0.00 4.42
342 344 2.490115 CCATCTGTCCTAGCGTAGATCC 59.510 54.545 0.00 0.00 0.00 3.36
400 402 1.699054 CCGAGGCATCAGGATTCCCA 61.699 60.000 0.00 0.00 33.88 4.37
404 406 1.649271 GGCATCAGGATTCCCACCCT 61.649 60.000 0.00 0.00 33.88 4.34
409 411 3.443095 AGGATTCCCACCCTGACAT 57.557 52.632 0.00 0.00 33.88 3.06
414 416 2.362889 CCCACCCTGACATTGGCC 60.363 66.667 0.00 0.00 0.00 5.36
415 417 2.440147 CCACCCTGACATTGGCCA 59.560 61.111 0.00 0.00 0.00 5.36
419 421 0.033796 ACCCTGACATTGGCCATCAG 60.034 55.000 22.82 22.82 39.70 2.90
443 445 1.406887 GGCAAGTAGAAGGGATGCGAA 60.407 52.381 0.00 0.00 37.88 4.70
448 450 4.696479 AGTAGAAGGGATGCGAATTCAT 57.304 40.909 6.22 0.00 0.00 2.57
449 451 5.808366 AGTAGAAGGGATGCGAATTCATA 57.192 39.130 6.22 0.00 0.00 2.15
458 460 1.140816 GCGAATTCATAGGCTCGGTC 58.859 55.000 6.22 0.00 0.00 4.79
461 463 0.597637 AATTCATAGGCTCGGTCGCG 60.598 55.000 0.00 0.00 0.00 5.87
462 464 1.452953 ATTCATAGGCTCGGTCGCGA 61.453 55.000 3.71 3.71 0.00 5.87
484 486 2.301738 CCGAGGGGAGGAAGGCTTT 61.302 63.158 0.00 0.00 34.06 3.51
502 504 3.667960 GCTTTCCATAGTCACTTTGTGCG 60.668 47.826 0.00 0.00 32.98 5.34
516 518 2.097110 TGTGCGAGGGGAAGGTATAT 57.903 50.000 0.00 0.00 0.00 0.86
519 521 1.975680 TGCGAGGGGAAGGTATATTCC 59.024 52.381 0.00 0.00 46.82 3.01
531 533 6.073003 GGAAGGTATATTCCGCAAATGAAGAG 60.073 42.308 0.00 0.00 39.47 2.85
570 572 0.536006 GCTGTGGGATAGGACCATGC 60.536 60.000 0.00 0.00 40.70 4.06
594 596 0.669318 GACACGCCGATGGTCTTTCA 60.669 55.000 0.00 0.00 0.00 2.69
595 597 0.250124 ACACGCCGATGGTCTTTCAA 60.250 50.000 0.00 0.00 0.00 2.69
596 598 0.871722 CACGCCGATGGTCTTTCAAA 59.128 50.000 0.00 0.00 0.00 2.69
597 599 1.265635 CACGCCGATGGTCTTTCAAAA 59.734 47.619 0.00 0.00 0.00 2.44
601 603 4.142687 ACGCCGATGGTCTTTCAAAAATAG 60.143 41.667 0.00 0.00 0.00 1.73
632 634 6.112058 GCTTTCTAGTCATTCTCTCCATTGT 58.888 40.000 0.00 0.00 0.00 2.71
633 635 6.036953 GCTTTCTAGTCATTCTCTCCATTGTG 59.963 42.308 0.00 0.00 0.00 3.33
656 692 2.203139 CACGGTTGCTGTGTGGGA 60.203 61.111 0.27 0.00 36.14 4.37
663 699 2.229792 GTTGCTGTGTGGGAATCTTCA 58.770 47.619 0.00 0.00 0.00 3.02
664 700 2.821969 GTTGCTGTGTGGGAATCTTCAT 59.178 45.455 0.00 0.00 0.00 2.57
665 701 2.715046 TGCTGTGTGGGAATCTTCATC 58.285 47.619 0.00 0.00 0.00 2.92
666 702 2.306805 TGCTGTGTGGGAATCTTCATCT 59.693 45.455 0.00 0.00 0.00 2.90
667 703 2.941720 GCTGTGTGGGAATCTTCATCTC 59.058 50.000 0.00 0.00 0.00 2.75
668 704 3.539604 CTGTGTGGGAATCTTCATCTCC 58.460 50.000 0.00 0.00 0.00 3.71
676 712 3.071602 GGAATCTTCATCTCCCATCGGAA 59.928 47.826 0.00 0.00 37.86 4.30
688 724 1.358877 CATCGGAATTGTCAGCGTCA 58.641 50.000 0.00 0.00 0.00 4.35
691 727 2.422597 TCGGAATTGTCAGCGTCAATT 58.577 42.857 13.49 13.49 44.67 2.32
701 737 4.422506 CGTCAATTCGCAGTGTGC 57.577 55.556 0.00 0.00 40.69 4.57
747 783 2.881513 TGCATCGCAAGGTAGAACAAAA 59.118 40.909 0.00 0.00 34.76 2.44
750 786 5.163764 TGCATCGCAAGGTAGAACAAAATAG 60.164 40.000 0.00 0.00 34.76 1.73
751 787 5.064707 GCATCGCAAGGTAGAACAAAATAGA 59.935 40.000 0.00 0.00 38.47 1.98
752 788 6.709643 CATCGCAAGGTAGAACAAAATAGAG 58.290 40.000 0.00 0.00 38.47 2.43
753 789 6.032956 TCGCAAGGTAGAACAAAATAGAGA 57.967 37.500 0.00 0.00 38.47 3.10
808 844 6.323203 TCAGAGCCAAAGAAAAGAATCTTG 57.677 37.500 0.00 0.00 39.54 3.02
831 868 1.454201 GGTTAGCAACCCTCTCAAGC 58.546 55.000 6.76 0.00 46.12 4.01
861 898 9.449719 ACTCCAGAAATAAGTAAATAACCACAG 57.550 33.333 0.00 0.00 0.00 3.66
942 983 2.785357 AGGATCTCTCCCCGATTTCT 57.215 50.000 0.00 0.00 43.21 2.52
1479 1524 3.827898 CACTCCCTCGGCGTCCTC 61.828 72.222 6.85 0.00 0.00 3.71
1752 1797 4.101448 ATGGAGCGGCTCGGCTTT 62.101 61.111 22.63 3.74 44.93 3.51
2019 2064 4.323843 CCGATCTACGACGCCGGG 62.324 72.222 2.18 0.00 45.77 5.73
2080 2125 2.608268 GGTTCTACACTCCGCTCTTTC 58.392 52.381 0.00 0.00 0.00 2.62
2085 2130 0.039074 ACACTCCGCTCTTTCTCACG 60.039 55.000 0.00 0.00 0.00 4.35
2110 2155 2.773487 TGTTAACTAGCCACATTGCGT 58.227 42.857 7.22 0.00 36.02 5.24
2453 2498 4.283722 TGACCCAAGTAAGACTTCTTCCTC 59.716 45.833 0.00 0.00 36.03 3.71
2470 2540 3.018149 TCCTCCTCTTCTTCTTCTACGC 58.982 50.000 0.00 0.00 0.00 4.42
2507 2583 7.178274 AGCTGGATCGATCTTGTCTCTAATTAT 59.822 37.037 23.96 0.00 0.00 1.28
2508 2584 7.816995 GCTGGATCGATCTTGTCTCTAATTATT 59.183 37.037 23.96 0.00 0.00 1.40
2619 2698 3.761218 TGACTTGTCATTGTGTTTGGTGT 59.239 39.130 0.00 0.00 0.00 4.16
2620 2699 4.142491 TGACTTGTCATTGTGTTTGGTGTC 60.142 41.667 0.00 0.00 0.00 3.67
2623 2702 2.687425 TGTCATTGTGTTTGGTGTCCAG 59.313 45.455 0.00 0.00 33.81 3.86
2633 2712 1.896220 TGGTGTCCAGCATGTTTCTC 58.104 50.000 0.00 0.00 33.39 2.87
2646 2725 5.817616 CATGTTTCTCATGCAACTTTGTC 57.182 39.130 0.00 0.00 45.69 3.18
2656 2735 7.013178 TCTCATGCAACTTTGTCTGTCAAATTA 59.987 33.333 0.00 0.00 43.78 1.40
2657 2736 7.140705 TCATGCAACTTTGTCTGTCAAATTAG 58.859 34.615 0.00 0.00 43.78 1.73
2658 2737 6.691754 TGCAACTTTGTCTGTCAAATTAGA 57.308 33.333 0.77 0.00 43.78 2.10
2659 2738 7.094508 TGCAACTTTGTCTGTCAAATTAGAA 57.905 32.000 0.77 0.00 43.78 2.10
2660 2739 7.195646 TGCAACTTTGTCTGTCAAATTAGAAG 58.804 34.615 0.77 0.00 43.78 2.85
2661 2740 7.066887 TGCAACTTTGTCTGTCAAATTAGAAGA 59.933 33.333 0.77 0.00 43.78 2.87
2662 2741 7.377131 GCAACTTTGTCTGTCAAATTAGAAGAC 59.623 37.037 0.77 0.00 43.78 3.01
2663 2742 7.178712 ACTTTGTCTGTCAAATTAGAAGACG 57.821 36.000 0.77 0.00 43.78 4.18
2664 2743 6.984474 ACTTTGTCTGTCAAATTAGAAGACGA 59.016 34.615 0.77 0.00 43.78 4.20
2666 2745 7.780008 TTGTCTGTCAAATTAGAAGACGAAA 57.220 32.000 0.00 0.00 40.10 3.46
2667 2746 7.408132 TGTCTGTCAAATTAGAAGACGAAAG 57.592 36.000 0.00 0.00 40.10 2.62
2668 2747 7.207383 TGTCTGTCAAATTAGAAGACGAAAGA 58.793 34.615 0.00 0.00 40.10 2.52
2669 2748 7.709182 TGTCTGTCAAATTAGAAGACGAAAGAA 59.291 33.333 0.00 0.00 40.10 2.52
2670 2749 8.548721 GTCTGTCAAATTAGAAGACGAAAGAAA 58.451 33.333 0.00 0.00 35.09 2.52
2671 2750 8.548721 TCTGTCAAATTAGAAGACGAAAGAAAC 58.451 33.333 0.00 0.00 35.09 2.78
2672 2751 7.342194 TGTCAAATTAGAAGACGAAAGAAACG 58.658 34.615 0.00 0.00 35.09 3.60
2673 2752 7.223193 TGTCAAATTAGAAGACGAAAGAAACGA 59.777 33.333 0.00 0.00 35.09 3.85
2674 2753 8.060090 GTCAAATTAGAAGACGAAAGAAACGAA 58.940 33.333 0.00 0.00 34.70 3.85
2675 2754 8.605746 TCAAATTAGAAGACGAAAGAAACGAAA 58.394 29.630 0.00 0.00 34.70 3.46
2676 2755 8.670668 CAAATTAGAAGACGAAAGAAACGAAAC 58.329 33.333 0.00 0.00 34.70 2.78
2677 2756 7.710766 ATTAGAAGACGAAAGAAACGAAACT 57.289 32.000 0.00 0.00 34.70 2.66
2678 2757 5.391060 AGAAGACGAAAGAAACGAAACTG 57.609 39.130 0.00 0.00 34.70 3.16
2679 2758 3.587403 AGACGAAAGAAACGAAACTGC 57.413 42.857 0.00 0.00 34.70 4.40
2680 2759 3.195661 AGACGAAAGAAACGAAACTGCT 58.804 40.909 0.00 0.00 34.70 4.24
2681 2760 3.245519 AGACGAAAGAAACGAAACTGCTC 59.754 43.478 0.00 0.00 34.70 4.26
2682 2761 3.195661 ACGAAAGAAACGAAACTGCTCT 58.804 40.909 0.00 0.00 34.70 4.09
2683 2762 4.365723 ACGAAAGAAACGAAACTGCTCTA 58.634 39.130 0.00 0.00 34.70 2.43
2684 2763 4.989168 ACGAAAGAAACGAAACTGCTCTAT 59.011 37.500 0.00 0.00 34.70 1.98
2685 2764 5.107453 ACGAAAGAAACGAAACTGCTCTATG 60.107 40.000 0.00 0.00 34.70 2.23
2686 2765 5.118664 CGAAAGAAACGAAACTGCTCTATGA 59.881 40.000 0.00 0.00 0.00 2.15
2687 2766 5.847670 AAGAAACGAAACTGCTCTATGAC 57.152 39.130 0.00 0.00 0.00 3.06
2688 2767 4.883083 AGAAACGAAACTGCTCTATGACA 58.117 39.130 0.00 0.00 0.00 3.58
2689 2768 5.297547 AGAAACGAAACTGCTCTATGACAA 58.702 37.500 0.00 0.00 0.00 3.18
2690 2769 5.758296 AGAAACGAAACTGCTCTATGACAAA 59.242 36.000 0.00 0.00 0.00 2.83
2691 2770 6.260050 AGAAACGAAACTGCTCTATGACAAAA 59.740 34.615 0.00 0.00 0.00 2.44
2692 2771 5.344207 ACGAAACTGCTCTATGACAAAAC 57.656 39.130 0.00 0.00 0.00 2.43
2693 2772 4.814234 ACGAAACTGCTCTATGACAAAACA 59.186 37.500 0.00 0.00 0.00 2.83
2694 2773 5.470098 ACGAAACTGCTCTATGACAAAACAT 59.530 36.000 0.00 0.00 0.00 2.71
2695 2774 5.791974 CGAAACTGCTCTATGACAAAACATG 59.208 40.000 0.00 0.00 0.00 3.21
2696 2775 5.633830 AACTGCTCTATGACAAAACATGG 57.366 39.130 0.00 0.00 0.00 3.66
2697 2776 4.910195 ACTGCTCTATGACAAAACATGGA 58.090 39.130 0.00 0.00 36.59 3.41
2698 2777 4.697352 ACTGCTCTATGACAAAACATGGAC 59.303 41.667 0.00 0.00 34.86 4.02
2699 2778 4.650734 TGCTCTATGACAAAACATGGACA 58.349 39.130 0.00 0.00 34.86 4.02
2700 2779 5.069318 TGCTCTATGACAAAACATGGACAA 58.931 37.500 0.00 0.00 34.86 3.18
2701 2780 5.711506 TGCTCTATGACAAAACATGGACAAT 59.288 36.000 0.00 0.00 34.86 2.71
2702 2781 6.032094 GCTCTATGACAAAACATGGACAATG 58.968 40.000 0.00 0.00 42.48 2.82
2711 2790 1.807139 CATGGACAATGTGTGGACGA 58.193 50.000 0.00 0.00 0.00 4.20
2712 2791 1.464608 CATGGACAATGTGTGGACGAC 59.535 52.381 0.00 0.00 0.00 4.34
2713 2792 0.466124 TGGACAATGTGTGGACGACA 59.534 50.000 0.00 0.00 0.00 4.35
2714 2793 1.134371 TGGACAATGTGTGGACGACAA 60.134 47.619 0.00 0.00 35.91 3.18
2715 2794 1.263217 GGACAATGTGTGGACGACAAC 59.737 52.381 0.00 0.00 35.91 3.32
2716 2795 1.937223 GACAATGTGTGGACGACAACA 59.063 47.619 0.00 0.00 35.91 3.33
2717 2796 2.353269 GACAATGTGTGGACGACAACAA 59.647 45.455 0.00 0.00 35.91 2.83
2718 2797 2.750166 ACAATGTGTGGACGACAACAAA 59.250 40.909 0.00 0.00 35.91 2.83
2719 2798 3.380004 ACAATGTGTGGACGACAACAAAT 59.620 39.130 0.00 0.00 35.91 2.32
2720 2799 3.896648 ATGTGTGGACGACAACAAATC 57.103 42.857 0.00 0.00 35.91 2.17
2721 2800 1.944024 TGTGTGGACGACAACAAATCC 59.056 47.619 0.00 0.00 35.91 3.01
2722 2801 1.944024 GTGTGGACGACAACAAATCCA 59.056 47.619 0.00 0.00 38.94 3.41
2723 2802 2.356382 GTGTGGACGACAACAAATCCAA 59.644 45.455 0.00 0.00 42.79 3.53
2724 2803 2.356382 TGTGGACGACAACAAATCCAAC 59.644 45.455 0.00 0.00 42.79 3.77
2725 2804 2.616842 GTGGACGACAACAAATCCAACT 59.383 45.455 0.00 0.00 42.79 3.16
2726 2805 2.616376 TGGACGACAACAAATCCAACTG 59.384 45.455 0.00 0.00 38.30 3.16
2727 2806 2.604614 GGACGACAACAAATCCAACTGC 60.605 50.000 0.00 0.00 0.00 4.40
2728 2807 1.336755 ACGACAACAAATCCAACTGCC 59.663 47.619 0.00 0.00 0.00 4.85
2729 2808 1.662876 CGACAACAAATCCAACTGCCG 60.663 52.381 0.00 0.00 0.00 5.69
2730 2809 1.336755 GACAACAAATCCAACTGCCGT 59.663 47.619 0.00 0.00 0.00 5.68
2731 2810 1.754226 ACAACAAATCCAACTGCCGTT 59.246 42.857 0.00 0.00 0.00 4.44
2738 2817 4.980903 CAACTGCCGTTGCACCGC 62.981 66.667 8.12 0.00 44.23 5.68
2747 2826 4.972733 TTGCACCGCTGTGGGCAT 62.973 61.111 19.31 0.00 44.64 4.40
2751 2830 4.746309 ACCGCTGTGGGCATGCAT 62.746 61.111 21.36 0.00 44.64 3.96
2752 2831 4.201679 CCGCTGTGGGCATGCATG 62.202 66.667 22.70 22.70 41.91 4.06
2753 2832 3.445687 CGCTGTGGGCATGCATGT 61.446 61.111 26.79 0.00 41.91 3.21
2754 2833 2.183300 GCTGTGGGCATGCATGTG 59.817 61.111 26.79 5.68 41.35 3.21
2755 2834 2.642254 GCTGTGGGCATGCATGTGT 61.642 57.895 26.79 0.00 41.35 3.72
2756 2835 1.214325 CTGTGGGCATGCATGTGTG 59.786 57.895 26.79 4.46 0.00 3.82
2765 2844 3.136123 GCATGTGTGCGGCCAGAT 61.136 61.111 2.24 0.00 42.28 2.90
2766 2845 2.703798 GCATGTGTGCGGCCAGATT 61.704 57.895 2.24 0.00 42.28 2.40
2767 2846 1.375853 GCATGTGTGCGGCCAGATTA 61.376 55.000 2.24 0.00 42.28 1.75
2768 2847 1.311859 CATGTGTGCGGCCAGATTAT 58.688 50.000 2.24 0.00 0.00 1.28
2769 2848 1.265095 CATGTGTGCGGCCAGATTATC 59.735 52.381 2.24 0.00 0.00 1.75
2770 2849 0.251634 TGTGTGCGGCCAGATTATCA 59.748 50.000 2.24 0.00 0.00 2.15
2771 2850 0.657840 GTGTGCGGCCAGATTATCAC 59.342 55.000 2.24 0.00 0.00 3.06
2772 2851 0.541392 TGTGCGGCCAGATTATCACT 59.459 50.000 2.24 0.00 0.00 3.41
2773 2852 0.940126 GTGCGGCCAGATTATCACTG 59.060 55.000 2.24 0.00 35.43 3.66
2774 2853 0.541392 TGCGGCCAGATTATCACTGT 59.459 50.000 2.24 0.00 34.04 3.55
2775 2854 1.221414 GCGGCCAGATTATCACTGTC 58.779 55.000 2.24 0.00 34.04 3.51
2776 2855 1.491670 CGGCCAGATTATCACTGTCG 58.508 55.000 2.24 0.00 34.04 4.35
2777 2856 1.202417 CGGCCAGATTATCACTGTCGT 60.202 52.381 2.24 0.00 34.04 4.34
2778 2857 2.738643 CGGCCAGATTATCACTGTCGTT 60.739 50.000 2.24 0.00 34.04 3.85
2779 2858 2.866762 GGCCAGATTATCACTGTCGTTC 59.133 50.000 0.00 0.00 34.04 3.95
2780 2859 3.521560 GCCAGATTATCACTGTCGTTCA 58.478 45.455 0.00 0.00 34.04 3.18
2781 2860 4.122776 GCCAGATTATCACTGTCGTTCAT 58.877 43.478 0.00 0.00 34.04 2.57
2782 2861 4.025396 GCCAGATTATCACTGTCGTTCATG 60.025 45.833 0.00 0.00 34.04 3.07
2783 2862 5.351458 CCAGATTATCACTGTCGTTCATGA 58.649 41.667 0.00 0.00 34.04 3.07
2784 2863 5.461407 CCAGATTATCACTGTCGTTCATGAG 59.539 44.000 0.00 0.00 34.04 2.90
2785 2864 6.038985 CAGATTATCACTGTCGTTCATGAGT 58.961 40.000 0.00 0.00 0.00 3.41
2786 2865 6.533012 CAGATTATCACTGTCGTTCATGAGTT 59.467 38.462 0.00 0.00 0.00 3.01
2787 2866 6.533012 AGATTATCACTGTCGTTCATGAGTTG 59.467 38.462 0.00 0.00 0.00 3.16
2788 2867 3.452755 TCACTGTCGTTCATGAGTTGT 57.547 42.857 0.00 0.00 0.00 3.32
2789 2868 3.381045 TCACTGTCGTTCATGAGTTGTC 58.619 45.455 0.00 0.00 0.00 3.18
2790 2869 3.068165 TCACTGTCGTTCATGAGTTGTCT 59.932 43.478 0.00 0.00 0.00 3.41
2791 2870 3.183172 CACTGTCGTTCATGAGTTGTCTG 59.817 47.826 0.00 0.00 0.00 3.51
2792 2871 3.068165 ACTGTCGTTCATGAGTTGTCTGA 59.932 43.478 0.00 0.00 0.00 3.27
2793 2872 4.240888 CTGTCGTTCATGAGTTGTCTGAT 58.759 43.478 0.00 0.00 0.00 2.90
2794 2873 4.631131 TGTCGTTCATGAGTTGTCTGATT 58.369 39.130 0.00 0.00 0.00 2.57
2795 2874 5.056480 TGTCGTTCATGAGTTGTCTGATTT 58.944 37.500 0.00 0.00 0.00 2.17
2796 2875 5.527214 TGTCGTTCATGAGTTGTCTGATTTT 59.473 36.000 0.00 0.00 0.00 1.82
2797 2876 5.848036 GTCGTTCATGAGTTGTCTGATTTTG 59.152 40.000 0.00 0.00 0.00 2.44
2798 2877 5.527214 TCGTTCATGAGTTGTCTGATTTTGT 59.473 36.000 0.00 0.00 0.00 2.83
2799 2878 5.848036 CGTTCATGAGTTGTCTGATTTTGTC 59.152 40.000 0.00 0.00 0.00 3.18
2800 2879 5.596268 TCATGAGTTGTCTGATTTTGTCG 57.404 39.130 0.00 0.00 0.00 4.35
2801 2880 5.056480 TCATGAGTTGTCTGATTTTGTCGT 58.944 37.500 0.00 0.00 0.00 4.34
2802 2881 5.177511 TCATGAGTTGTCTGATTTTGTCGTC 59.822 40.000 0.00 0.00 0.00 4.20
2803 2882 3.807622 TGAGTTGTCTGATTTTGTCGTCC 59.192 43.478 0.00 0.00 0.00 4.79
2804 2883 2.800544 AGTTGTCTGATTTTGTCGTCCG 59.199 45.455 0.00 0.00 0.00 4.79
2805 2884 2.519377 TGTCTGATTTTGTCGTCCGT 57.481 45.000 0.00 0.00 0.00 4.69
2806 2885 3.646611 TGTCTGATTTTGTCGTCCGTA 57.353 42.857 0.00 0.00 0.00 4.02
2807 2886 4.182693 TGTCTGATTTTGTCGTCCGTAT 57.817 40.909 0.00 0.00 0.00 3.06
2808 2887 5.313520 TGTCTGATTTTGTCGTCCGTATA 57.686 39.130 0.00 0.00 0.00 1.47
2809 2888 5.337554 TGTCTGATTTTGTCGTCCGTATAG 58.662 41.667 0.00 0.00 0.00 1.31
2810 2889 4.206609 GTCTGATTTTGTCGTCCGTATAGC 59.793 45.833 0.00 0.00 0.00 2.97
2811 2890 4.109766 CTGATTTTGTCGTCCGTATAGCA 58.890 43.478 0.00 0.00 0.00 3.49
2812 2891 4.496360 TGATTTTGTCGTCCGTATAGCAA 58.504 39.130 0.00 0.00 0.00 3.91
2813 2892 5.113383 TGATTTTGTCGTCCGTATAGCAAT 58.887 37.500 0.00 0.00 0.00 3.56
2814 2893 4.850859 TTTTGTCGTCCGTATAGCAATG 57.149 40.909 0.00 0.00 0.00 2.82
2815 2894 3.513680 TTGTCGTCCGTATAGCAATGT 57.486 42.857 0.00 0.00 0.00 2.71
2816 2895 3.513680 TGTCGTCCGTATAGCAATGTT 57.486 42.857 0.00 0.00 0.00 2.71
2817 2896 3.183754 TGTCGTCCGTATAGCAATGTTG 58.816 45.455 0.00 0.00 0.00 3.33
2818 2897 3.184541 GTCGTCCGTATAGCAATGTTGT 58.815 45.455 0.00 0.00 0.00 3.32
2863 2942 7.096551 ACCTTAAATTGTTGCATGGTTACATC 58.903 34.615 0.00 0.00 34.35 3.06
2939 3018 5.637810 TGCGAGTTTGACCTATTTGAGTTAG 59.362 40.000 0.00 0.00 0.00 2.34
3287 3367 7.158099 ACACTTTGTCCCTCAAAATTATAGC 57.842 36.000 0.00 0.00 44.08 2.97
3293 3373 9.487790 TTTGTCCCTCAAAATTATAGCTTTTTG 57.512 29.630 12.99 12.99 42.18 2.44
3301 3381 9.487790 TCAAAATTATAGCTTTTTGTCCCAAAG 57.512 29.630 16.86 0.00 41.40 2.77
3385 3466 2.683933 GCCCCTCTCGACCTCCAA 60.684 66.667 0.00 0.00 0.00 3.53
3389 3470 1.977544 CCTCTCGACCTCCAACCGT 60.978 63.158 0.00 0.00 0.00 4.83
3453 3535 2.121735 TCCCACATCCCCACCACA 60.122 61.111 0.00 0.00 0.00 4.17
3454 3536 1.543642 TCCCACATCCCCACCACAT 60.544 57.895 0.00 0.00 0.00 3.21
3460 3542 0.106519 CATCCCCACCACATCCTTCC 60.107 60.000 0.00 0.00 0.00 3.46
3484 3566 2.125552 TCGCTGGCACCAGAATCG 60.126 61.111 20.92 13.91 46.30 3.34
3629 3711 2.100989 GTCTACGAGACTGGAATGGGT 58.899 52.381 7.50 0.00 41.88 4.51
3640 3722 2.040278 CTGGAATGGGTCTTCTTCACCA 59.960 50.000 0.00 0.00 35.35 4.17
3646 3728 1.420138 GGGTCTTCTTCACCACCTTCA 59.580 52.381 0.00 0.00 35.35 3.02
3652 3734 6.295688 GGTCTTCTTCACCACCTTCATTACTA 60.296 42.308 0.00 0.00 33.63 1.82
3659 3741 3.264450 ACCACCTTCATTACTAAGCTGCT 59.736 43.478 0.00 0.00 0.00 4.24
3711 3793 5.884322 TCTCTATCATGGCCTATGCATTTT 58.116 37.500 3.54 0.00 40.13 1.82
3723 3805 2.582728 TGCATTTTGGCGAATCATCC 57.417 45.000 0.00 0.00 36.28 3.51
3750 3832 1.067565 AGCAGCTTCTTCGTCGAATCA 60.068 47.619 8.36 0.00 0.00 2.57
3762 3844 2.083774 GTCGAATCAGCCCACAAATCA 58.916 47.619 0.00 0.00 0.00 2.57
3769 3851 2.040947 TCAGCCCACAAATCATACACCA 59.959 45.455 0.00 0.00 0.00 4.17
3809 3891 3.831333 TGAAATCTGGCAAGGCATAACAA 59.169 39.130 0.00 0.00 0.00 2.83
3834 3916 2.101917 CCCCCTCTATGCTTGCAATTTG 59.898 50.000 0.00 0.00 0.00 2.32
3840 3922 6.294176 CCCTCTATGCTTGCAATTTGGTATAC 60.294 42.308 0.00 0.00 0.00 1.47
3855 3937 2.993899 GGTATACGATTCCCATTGCTCG 59.006 50.000 0.00 0.00 37.17 5.03
3856 3938 2.169832 ATACGATTCCCATTGCTCGG 57.830 50.000 0.00 0.00 35.52 4.63
3857 3939 0.105964 TACGATTCCCATTGCTCGGG 59.894 55.000 0.00 0.00 46.03 5.14
3870 3952 0.389426 GCTCGGGACATTACACACGT 60.389 55.000 0.00 0.00 0.00 4.49
3872 3954 2.793933 CTCGGGACATTACACACGTAG 58.206 52.381 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 3.146066 TGACTATGGCTTTTGTGGTGTC 58.854 45.455 0.00 0.00 0.00 3.67
117 119 8.786826 TTCAAGGTTTTAATGTCGATGACTAT 57.213 30.769 0.00 0.00 33.15 2.12
171 173 0.796870 TGTGCATACGCGAAGACGAG 60.797 55.000 15.93 0.00 42.97 4.18
215 217 0.106918 AGAGTCCTGCTACCTCCTCG 60.107 60.000 0.00 0.00 0.00 4.63
222 224 1.747709 TCGGTGTAGAGTCCTGCTAC 58.252 55.000 0.00 0.00 38.90 3.58
237 239 1.906574 TGGATTAAGCAGACCTTCGGT 59.093 47.619 0.00 0.00 39.44 4.69
249 251 5.523916 AGTTCGTTCATCGGAATGGATTAAG 59.476 40.000 0.00 0.00 39.90 1.85
257 259 3.684788 CCTTCAAGTTCGTTCATCGGAAT 59.315 43.478 0.00 0.00 40.32 3.01
259 261 2.297880 TCCTTCAAGTTCGTTCATCGGA 59.702 45.455 0.00 0.00 40.32 4.55
262 264 3.926616 TCCTCCTTCAAGTTCGTTCATC 58.073 45.455 0.00 0.00 0.00 2.92
294 296 5.462398 GCACTTTTTCTTCGAGTCAGTCTTA 59.538 40.000 0.00 0.00 0.00 2.10
306 308 3.005155 ACAGATGGCAGCACTTTTTCTTC 59.995 43.478 5.19 0.00 0.00 2.87
315 317 0.813210 GCTAGGACAGATGGCAGCAC 60.813 60.000 5.19 0.00 0.00 4.40
328 330 0.108019 TCGCAGGATCTACGCTAGGA 59.892 55.000 0.00 0.00 0.00 2.94
329 331 0.519519 CTCGCAGGATCTACGCTAGG 59.480 60.000 0.00 0.00 0.00 3.02
342 344 3.604875 TTAGGGTTTTAGTCCTCGCAG 57.395 47.619 0.00 0.00 34.75 5.18
400 402 0.033796 CTGATGGCCAATGTCAGGGT 60.034 55.000 22.26 0.00 36.57 4.34
404 406 0.745486 CGCTCTGATGGCCAATGTCA 60.745 55.000 10.96 8.71 0.00 3.58
414 416 2.200067 CTTCTACTTGCCGCTCTGATG 58.800 52.381 0.00 0.00 0.00 3.07
415 417 1.137872 CCTTCTACTTGCCGCTCTGAT 59.862 52.381 0.00 0.00 0.00 2.90
419 421 0.466124 ATCCCTTCTACTTGCCGCTC 59.534 55.000 0.00 0.00 0.00 5.03
429 431 4.563580 GCCTATGAATTCGCATCCCTTCTA 60.564 45.833 0.04 0.00 0.00 2.10
443 445 1.007271 CGCGACCGAGCCTATGAAT 60.007 57.895 0.00 0.00 36.29 2.57
448 450 2.437180 TCTTCGCGACCGAGCCTA 60.437 61.111 9.15 0.00 45.35 3.93
449 451 4.117661 GTCTTCGCGACCGAGCCT 62.118 66.667 9.15 0.00 45.35 4.58
458 460 4.194720 CTCCCCTCGGTCTTCGCG 62.195 72.222 0.00 0.00 39.05 5.87
461 463 1.331399 CCTTCCTCCCCTCGGTCTTC 61.331 65.000 0.00 0.00 0.00 2.87
462 464 1.306226 CCTTCCTCCCCTCGGTCTT 60.306 63.158 0.00 0.00 0.00 3.01
467 469 1.222113 GAAAGCCTTCCTCCCCTCG 59.778 63.158 0.00 0.00 0.00 4.63
484 486 2.353704 CCTCGCACAAAGTGACTATGGA 60.354 50.000 0.58 0.00 35.23 3.41
502 504 1.975680 TGCGGAATATACCTTCCCCTC 59.024 52.381 0.43 0.00 41.46 4.30
516 518 5.703978 TGAATTTCTCTTCATTTGCGGAA 57.296 34.783 0.00 0.00 30.34 4.30
519 521 6.638063 TGAAGTTGAATTTCTCTTCATTTGCG 59.362 34.615 21.61 0.00 40.46 4.85
531 533 6.087291 CACAGCTCGAAATGAAGTTGAATTTC 59.913 38.462 3.69 9.25 38.74 2.17
570 572 1.626654 GACCATCGGCGTGTCAGTTG 61.627 60.000 6.85 0.00 0.00 3.16
601 603 7.651704 GGAGAGAATGACTAGAAAGCAAGATAC 59.348 40.741 0.00 0.00 0.00 2.24
618 620 4.514441 GTGCCTATCACAATGGAGAGAATG 59.486 45.833 0.00 0.00 44.98 2.67
656 692 4.989875 ATTCCGATGGGAGATGAAGATT 57.010 40.909 0.00 0.00 44.98 2.40
663 699 2.486191 GCTGACAATTCCGATGGGAGAT 60.486 50.000 0.00 0.00 44.98 2.75
664 700 1.134401 GCTGACAATTCCGATGGGAGA 60.134 52.381 0.00 0.00 44.98 3.71
665 701 1.303309 GCTGACAATTCCGATGGGAG 58.697 55.000 0.00 0.00 44.98 4.30
666 702 0.461870 CGCTGACAATTCCGATGGGA 60.462 55.000 0.00 0.00 41.83 4.37
667 703 0.744414 ACGCTGACAATTCCGATGGG 60.744 55.000 0.00 0.00 0.00 4.00
668 704 0.652592 GACGCTGACAATTCCGATGG 59.347 55.000 0.00 0.00 0.00 3.51
672 708 2.900122 AATTGACGCTGACAATTCCG 57.100 45.000 10.96 0.00 41.98 4.30
701 737 2.222027 AGCTTTGTCCCTTTCTTGACG 58.778 47.619 0.00 0.00 34.18 4.35
747 783 5.045286 ACATGTTCTTTCCTTGGCTCTCTAT 60.045 40.000 0.00 0.00 0.00 1.98
750 786 3.416156 ACATGTTCTTTCCTTGGCTCTC 58.584 45.455 0.00 0.00 0.00 3.20
751 787 3.515602 ACATGTTCTTTCCTTGGCTCT 57.484 42.857 0.00 0.00 0.00 4.09
752 788 3.569701 TGAACATGTTCTTTCCTTGGCTC 59.430 43.478 32.57 8.94 40.14 4.70
753 789 3.565307 TGAACATGTTCTTTCCTTGGCT 58.435 40.909 32.57 0.00 40.14 4.75
861 898 3.132563 AGCACTGAGGAGTGATTTGCAC 61.133 50.000 6.38 0.00 46.88 4.57
880 917 2.924290 GCAGTGTGCAGTTACTAGTAGC 59.076 50.000 8.59 8.59 44.26 3.58
942 983 3.611766 GCAGTAGTCGAGTGATGTGTGAA 60.612 47.826 2.10 0.00 0.00 3.18
1442 1487 3.082579 GCGGCGGAGACCTTGATCT 62.083 63.158 9.78 0.00 0.00 2.75
1578 1623 0.719465 GGTACGCGTTCACCATGAAG 59.281 55.000 23.14 0.00 37.00 3.02
2080 2125 3.187700 GGCTAGTTAACATCACCGTGAG 58.812 50.000 8.61 2.35 0.00 3.51
2085 2130 4.438744 GCAATGTGGCTAGTTAACATCACC 60.439 45.833 8.61 4.34 33.48 4.02
2137 2182 2.344500 CGCCGGTGTTACCTTGGA 59.656 61.111 6.91 0.00 35.66 3.53
2421 2466 0.107081 TACTTGGGTCAACGGTGGTG 59.893 55.000 0.00 0.00 0.00 4.17
2427 2472 3.991367 AGAAGTCTTACTTGGGTCAACG 58.009 45.455 0.00 0.00 38.80 4.10
2453 2498 3.056465 ACTTGGCGTAGAAGAAGAAGAGG 60.056 47.826 0.00 0.00 0.00 3.69
2470 2540 3.797039 TCGATCCAGCTGAAATACTTGG 58.203 45.455 17.39 0.00 0.00 3.61
2507 2583 1.814394 ACAGAGTATGTCGCCGTGTAA 59.186 47.619 0.00 0.00 37.75 2.41
2508 2584 1.456296 ACAGAGTATGTCGCCGTGTA 58.544 50.000 0.00 0.00 37.75 2.90
2509 2585 0.601558 AACAGAGTATGTCGCCGTGT 59.398 50.000 0.00 0.00 43.00 4.49
2597 2675 3.761218 ACACCAAACACAATGACAAGTCA 59.239 39.130 5.24 5.24 44.59 3.41
2646 2725 7.527516 CGTTTCTTTCGTCTTCTAATTTGACAG 59.472 37.037 0.00 0.00 0.00 3.51
2656 2735 4.260253 GCAGTTTCGTTTCTTTCGTCTTCT 60.260 41.667 0.00 0.00 0.00 2.85
2657 2736 3.960621 GCAGTTTCGTTTCTTTCGTCTTC 59.039 43.478 0.00 0.00 0.00 2.87
2658 2737 3.621715 AGCAGTTTCGTTTCTTTCGTCTT 59.378 39.130 0.00 0.00 0.00 3.01
2659 2738 3.195661 AGCAGTTTCGTTTCTTTCGTCT 58.804 40.909 0.00 0.00 0.00 4.18
2660 2739 3.245519 AGAGCAGTTTCGTTTCTTTCGTC 59.754 43.478 0.00 0.00 0.00 4.20
2661 2740 3.195661 AGAGCAGTTTCGTTTCTTTCGT 58.804 40.909 0.00 0.00 0.00 3.85
2662 2741 3.861569 AGAGCAGTTTCGTTTCTTTCG 57.138 42.857 0.00 0.00 0.00 3.46
2663 2742 6.073765 TGTCATAGAGCAGTTTCGTTTCTTTC 60.074 38.462 0.00 0.00 0.00 2.62
2664 2743 5.758296 TGTCATAGAGCAGTTTCGTTTCTTT 59.242 36.000 0.00 0.00 0.00 2.52
2666 2745 4.883083 TGTCATAGAGCAGTTTCGTTTCT 58.117 39.130 0.00 0.00 0.00 2.52
2667 2746 5.591643 TTGTCATAGAGCAGTTTCGTTTC 57.408 39.130 0.00 0.00 0.00 2.78
2668 2747 6.183360 TGTTTTGTCATAGAGCAGTTTCGTTT 60.183 34.615 0.00 0.00 0.00 3.60
2669 2748 5.295787 TGTTTTGTCATAGAGCAGTTTCGTT 59.704 36.000 0.00 0.00 0.00 3.85
2670 2749 4.814234 TGTTTTGTCATAGAGCAGTTTCGT 59.186 37.500 0.00 0.00 0.00 3.85
2671 2750 5.342806 TGTTTTGTCATAGAGCAGTTTCG 57.657 39.130 0.00 0.00 0.00 3.46
2672 2751 6.072508 TCCATGTTTTGTCATAGAGCAGTTTC 60.073 38.462 0.00 0.00 0.00 2.78
2673 2752 5.769662 TCCATGTTTTGTCATAGAGCAGTTT 59.230 36.000 0.00 0.00 0.00 2.66
2674 2753 5.182001 GTCCATGTTTTGTCATAGAGCAGTT 59.818 40.000 0.00 0.00 0.00 3.16
2675 2754 4.697352 GTCCATGTTTTGTCATAGAGCAGT 59.303 41.667 0.00 0.00 0.00 4.40
2676 2755 4.696877 TGTCCATGTTTTGTCATAGAGCAG 59.303 41.667 0.00 0.00 0.00 4.24
2677 2756 4.650734 TGTCCATGTTTTGTCATAGAGCA 58.349 39.130 0.00 0.00 0.00 4.26
2678 2757 5.627499 TTGTCCATGTTTTGTCATAGAGC 57.373 39.130 0.00 0.00 0.00 4.09
2679 2758 7.025365 CACATTGTCCATGTTTTGTCATAGAG 58.975 38.462 0.00 0.00 44.40 2.43
2680 2759 6.489700 ACACATTGTCCATGTTTTGTCATAGA 59.510 34.615 0.00 0.00 44.40 1.98
2681 2760 6.583427 CACACATTGTCCATGTTTTGTCATAG 59.417 38.462 0.00 0.00 44.40 2.23
2682 2761 6.445475 CACACATTGTCCATGTTTTGTCATA 58.555 36.000 0.00 0.00 44.40 2.15
2683 2762 5.291178 CACACATTGTCCATGTTTTGTCAT 58.709 37.500 0.00 0.00 44.40 3.06
2684 2763 4.441217 CCACACATTGTCCATGTTTTGTCA 60.441 41.667 0.00 0.00 44.40 3.58
2685 2764 4.050553 CCACACATTGTCCATGTTTTGTC 58.949 43.478 0.00 0.00 44.40 3.18
2686 2765 3.703556 TCCACACATTGTCCATGTTTTGT 59.296 39.130 0.00 0.00 44.40 2.83
2687 2766 4.050553 GTCCACACATTGTCCATGTTTTG 58.949 43.478 0.00 0.00 44.40 2.44
2688 2767 3.243367 CGTCCACACATTGTCCATGTTTT 60.243 43.478 0.00 0.00 44.40 2.43
2689 2768 2.293122 CGTCCACACATTGTCCATGTTT 59.707 45.455 0.00 0.00 44.40 2.83
2690 2769 1.879380 CGTCCACACATTGTCCATGTT 59.121 47.619 0.00 0.00 44.40 2.71
2692 2771 1.464608 GTCGTCCACACATTGTCCATG 59.535 52.381 0.00 0.00 39.07 3.66
2693 2772 1.071542 TGTCGTCCACACATTGTCCAT 59.928 47.619 0.00 0.00 0.00 3.41
2694 2773 0.466124 TGTCGTCCACACATTGTCCA 59.534 50.000 0.00 0.00 0.00 4.02
2695 2774 1.263217 GTTGTCGTCCACACATTGTCC 59.737 52.381 0.00 0.00 33.41 4.02
2696 2775 1.937223 TGTTGTCGTCCACACATTGTC 59.063 47.619 0.00 0.00 33.41 3.18
2697 2776 2.031258 TGTTGTCGTCCACACATTGT 57.969 45.000 0.00 0.00 33.41 2.71
2698 2777 3.412981 TTTGTTGTCGTCCACACATTG 57.587 42.857 0.00 0.00 33.41 2.82
2699 2778 3.004315 GGATTTGTTGTCGTCCACACATT 59.996 43.478 0.00 0.00 33.41 2.71
2700 2779 2.552315 GGATTTGTTGTCGTCCACACAT 59.448 45.455 0.00 0.00 33.41 3.21
2701 2780 1.944024 GGATTTGTTGTCGTCCACACA 59.056 47.619 0.00 0.00 33.41 3.72
2702 2781 1.944024 TGGATTTGTTGTCGTCCACAC 59.056 47.619 0.00 0.00 35.91 3.82
2703 2782 2.333688 TGGATTTGTTGTCGTCCACA 57.666 45.000 0.00 0.00 35.91 4.17
2704 2783 2.616842 AGTTGGATTTGTTGTCGTCCAC 59.383 45.455 0.00 0.00 40.27 4.02
2705 2784 2.616376 CAGTTGGATTTGTTGTCGTCCA 59.384 45.455 0.00 0.00 38.90 4.02
2706 2785 2.604614 GCAGTTGGATTTGTTGTCGTCC 60.605 50.000 0.00 0.00 0.00 4.79
2707 2786 2.604614 GGCAGTTGGATTTGTTGTCGTC 60.605 50.000 0.00 0.00 0.00 4.20
2708 2787 1.336755 GGCAGTTGGATTTGTTGTCGT 59.663 47.619 0.00 0.00 0.00 4.34
2709 2788 1.662876 CGGCAGTTGGATTTGTTGTCG 60.663 52.381 0.00 0.00 0.00 4.35
2710 2789 1.336755 ACGGCAGTTGGATTTGTTGTC 59.663 47.619 0.00 0.00 0.00 3.18
2711 2790 1.398692 ACGGCAGTTGGATTTGTTGT 58.601 45.000 0.00 0.00 0.00 3.32
2712 2791 2.507339 AACGGCAGTTGGATTTGTTG 57.493 45.000 0.00 0.00 39.48 3.33
2737 2816 2.183300 CACATGCATGCCCACAGC 59.817 61.111 26.53 0.00 44.14 4.40
2738 2817 1.214325 CACACATGCATGCCCACAG 59.786 57.895 26.53 11.63 0.00 3.66
2739 2818 3.367725 CACACATGCATGCCCACA 58.632 55.556 26.53 0.00 0.00 4.17
2749 2828 1.265095 GATAATCTGGCCGCACACATG 59.735 52.381 0.00 0.00 0.00 3.21
2750 2829 1.134128 TGATAATCTGGCCGCACACAT 60.134 47.619 0.00 0.00 0.00 3.21
2751 2830 0.251634 TGATAATCTGGCCGCACACA 59.748 50.000 0.00 0.00 0.00 3.72
2752 2831 0.657840 GTGATAATCTGGCCGCACAC 59.342 55.000 0.00 0.00 0.00 3.82
2753 2832 0.541392 AGTGATAATCTGGCCGCACA 59.459 50.000 0.00 0.00 0.00 4.57
2754 2833 0.940126 CAGTGATAATCTGGCCGCAC 59.060 55.000 0.00 0.00 0.00 5.34
2755 2834 0.541392 ACAGTGATAATCTGGCCGCA 59.459 50.000 0.00 0.00 37.25 5.69
2756 2835 1.221414 GACAGTGATAATCTGGCCGC 58.779 55.000 0.00 0.00 35.13 6.53
2757 2836 1.202417 ACGACAGTGATAATCTGGCCG 60.202 52.381 0.00 0.00 37.64 6.13
2758 2837 2.604046 ACGACAGTGATAATCTGGCC 57.396 50.000 0.00 0.00 37.64 5.36
2759 2838 3.521560 TGAACGACAGTGATAATCTGGC 58.478 45.455 0.00 0.00 37.56 4.85
2760 2839 5.351458 TCATGAACGACAGTGATAATCTGG 58.649 41.667 0.00 0.00 37.25 3.86
2761 2840 6.038985 ACTCATGAACGACAGTGATAATCTG 58.961 40.000 0.00 0.00 38.68 2.90
2762 2841 6.214191 ACTCATGAACGACAGTGATAATCT 57.786 37.500 0.00 0.00 0.00 2.40
2763 2842 6.311445 ACAACTCATGAACGACAGTGATAATC 59.689 38.462 0.00 0.00 0.00 1.75
2764 2843 6.166279 ACAACTCATGAACGACAGTGATAAT 58.834 36.000 0.00 0.00 0.00 1.28
2765 2844 5.538118 ACAACTCATGAACGACAGTGATAA 58.462 37.500 0.00 0.00 0.00 1.75
2766 2845 5.048013 AGACAACTCATGAACGACAGTGATA 60.048 40.000 0.00 0.00 0.00 2.15
2767 2846 3.990469 GACAACTCATGAACGACAGTGAT 59.010 43.478 0.00 0.00 0.00 3.06
2768 2847 3.068165 AGACAACTCATGAACGACAGTGA 59.932 43.478 0.00 0.00 0.00 3.41
2769 2848 3.183172 CAGACAACTCATGAACGACAGTG 59.817 47.826 0.00 0.00 0.00 3.66
2770 2849 3.068165 TCAGACAACTCATGAACGACAGT 59.932 43.478 0.00 0.00 0.00 3.55
2771 2850 3.642705 TCAGACAACTCATGAACGACAG 58.357 45.455 0.00 0.00 0.00 3.51
2772 2851 3.726291 TCAGACAACTCATGAACGACA 57.274 42.857 0.00 0.00 0.00 4.35
2773 2852 5.597813 AAATCAGACAACTCATGAACGAC 57.402 39.130 0.00 0.00 0.00 4.34
2774 2853 5.527214 ACAAAATCAGACAACTCATGAACGA 59.473 36.000 0.00 0.00 0.00 3.85
2775 2854 5.751680 ACAAAATCAGACAACTCATGAACG 58.248 37.500 0.00 0.00 0.00 3.95
2776 2855 5.848036 CGACAAAATCAGACAACTCATGAAC 59.152 40.000 0.00 0.00 0.00 3.18
2777 2856 5.527214 ACGACAAAATCAGACAACTCATGAA 59.473 36.000 0.00 0.00 0.00 2.57
2778 2857 5.056480 ACGACAAAATCAGACAACTCATGA 58.944 37.500 0.00 0.00 0.00 3.07
2779 2858 5.348418 ACGACAAAATCAGACAACTCATG 57.652 39.130 0.00 0.00 0.00 3.07
2780 2859 4.452455 GGACGACAAAATCAGACAACTCAT 59.548 41.667 0.00 0.00 0.00 2.90
2781 2860 3.807622 GGACGACAAAATCAGACAACTCA 59.192 43.478 0.00 0.00 0.00 3.41
2782 2861 3.120991 CGGACGACAAAATCAGACAACTC 60.121 47.826 0.00 0.00 0.00 3.01
2783 2862 2.800544 CGGACGACAAAATCAGACAACT 59.199 45.455 0.00 0.00 0.00 3.16
2784 2863 2.542595 ACGGACGACAAAATCAGACAAC 59.457 45.455 0.00 0.00 0.00 3.32
2785 2864 2.828877 ACGGACGACAAAATCAGACAA 58.171 42.857 0.00 0.00 0.00 3.18
2786 2865 2.519377 ACGGACGACAAAATCAGACA 57.481 45.000 0.00 0.00 0.00 3.41
2787 2866 4.206609 GCTATACGGACGACAAAATCAGAC 59.793 45.833 0.00 0.00 0.00 3.51
2788 2867 4.142337 TGCTATACGGACGACAAAATCAGA 60.142 41.667 0.00 0.00 0.00 3.27
2789 2868 4.109766 TGCTATACGGACGACAAAATCAG 58.890 43.478 0.00 0.00 0.00 2.90
2790 2869 4.112716 TGCTATACGGACGACAAAATCA 57.887 40.909 0.00 0.00 0.00 2.57
2791 2870 5.006358 ACATTGCTATACGGACGACAAAATC 59.994 40.000 0.00 0.00 0.00 2.17
2792 2871 4.873827 ACATTGCTATACGGACGACAAAAT 59.126 37.500 0.00 0.00 0.00 1.82
2793 2872 4.247258 ACATTGCTATACGGACGACAAAA 58.753 39.130 0.00 0.00 0.00 2.44
2794 2873 3.852286 ACATTGCTATACGGACGACAAA 58.148 40.909 0.00 0.00 0.00 2.83
2795 2874 3.513680 ACATTGCTATACGGACGACAA 57.486 42.857 0.00 0.00 0.00 3.18
2796 2875 3.183754 CAACATTGCTATACGGACGACA 58.816 45.455 0.00 0.00 0.00 4.35
2797 2876 3.000078 CACAACATTGCTATACGGACGAC 60.000 47.826 0.00 0.00 0.00 4.34
2798 2877 3.119424 TCACAACATTGCTATACGGACGA 60.119 43.478 0.00 0.00 0.00 4.20
2799 2878 3.183754 TCACAACATTGCTATACGGACG 58.816 45.455 0.00 0.00 0.00 4.79
2800 2879 5.106869 TGTTTCACAACATTGCTATACGGAC 60.107 40.000 0.00 0.00 38.03 4.79
2801 2880 4.998033 TGTTTCACAACATTGCTATACGGA 59.002 37.500 0.00 0.00 38.03 4.69
2802 2881 5.289917 TGTTTCACAACATTGCTATACGG 57.710 39.130 0.00 0.00 38.03 4.02
2803 2882 7.616103 TTTTGTTTCACAACATTGCTATACG 57.384 32.000 0.00 0.00 42.66 3.06
2804 2883 8.977505 ACATTTTGTTTCACAACATTGCTATAC 58.022 29.630 0.00 0.00 42.66 1.47
2805 2884 9.539825 AACATTTTGTTTCACAACATTGCTATA 57.460 25.926 0.00 0.00 42.66 1.31
2806 2885 8.436046 AACATTTTGTTTCACAACATTGCTAT 57.564 26.923 0.00 0.00 42.66 2.97
2807 2886 7.840342 AACATTTTGTTTCACAACATTGCTA 57.160 28.000 0.00 0.00 42.66 3.49
2808 2887 6.740411 AACATTTTGTTTCACAACATTGCT 57.260 29.167 0.00 0.00 42.66 3.91
2838 2917 6.412362 TGTAACCATGCAACAATTTAAGGT 57.588 33.333 0.00 0.00 0.00 3.50
3218 3297 0.471022 AATCCCCAAACCACCACCAC 60.471 55.000 0.00 0.00 0.00 4.16
3219 3298 1.158904 TAATCCCCAAACCACCACCA 58.841 50.000 0.00 0.00 0.00 4.17
3220 3299 1.897133 GTTAATCCCCAAACCACCACC 59.103 52.381 0.00 0.00 0.00 4.61
3221 3300 1.897133 GGTTAATCCCCAAACCACCAC 59.103 52.381 0.00 0.00 43.84 4.16
3222 3301 2.312424 GGTTAATCCCCAAACCACCA 57.688 50.000 0.00 0.00 43.84 4.17
3247 3326 4.946478 AAGTGTCTGAGGGATATGCTAC 57.054 45.455 0.00 0.00 0.00 3.58
3301 3381 1.826385 AACAAGCTACATGGTGCCTC 58.174 50.000 8.29 0.00 0.00 4.70
3389 3470 2.751436 GATGGCTCTTTGGCGGCA 60.751 61.111 7.97 7.97 45.14 5.69
3443 3525 1.928567 GGGAAGGATGTGGTGGGGA 60.929 63.158 0.00 0.00 0.00 4.81
3453 3535 0.108138 CAGCGACGAAAGGGAAGGAT 60.108 55.000 0.00 0.00 0.00 3.24
3454 3536 1.292223 CAGCGACGAAAGGGAAGGA 59.708 57.895 0.00 0.00 0.00 3.36
3460 3542 3.423154 GGTGCCAGCGACGAAAGG 61.423 66.667 0.00 0.00 0.00 3.11
3617 3699 3.339141 GTGAAGAAGACCCATTCCAGTC 58.661 50.000 0.00 0.00 0.00 3.51
3619 3701 2.040278 TGGTGAAGAAGACCCATTCCAG 59.960 50.000 0.00 0.00 31.84 3.86
3629 3711 5.825593 AGTAATGAAGGTGGTGAAGAAGA 57.174 39.130 0.00 0.00 0.00 2.87
3640 3722 3.786635 CGAGCAGCTTAGTAATGAAGGT 58.213 45.455 0.00 0.00 35.05 3.50
3659 3741 0.249447 CGAGCATACAGGAATGGCGA 60.249 55.000 0.00 0.00 0.00 5.54
3711 3793 0.537653 TACAACGGGATGATTCGCCA 59.462 50.000 0.00 0.00 0.00 5.69
3723 3805 0.716108 CGAAGAAGCTGCTACAACGG 59.284 55.000 0.90 0.00 0.00 4.44
3750 3832 2.446435 GTGGTGTATGATTTGTGGGCT 58.554 47.619 0.00 0.00 0.00 5.19
3786 3868 3.831333 TGTTATGCCTTGCCAGATTTCAA 59.169 39.130 0.00 0.00 0.00 2.69
3787 3869 3.429492 TGTTATGCCTTGCCAGATTTCA 58.571 40.909 0.00 0.00 0.00 2.69
3809 3891 1.077005 TGCAAGCATAGAGGGGGTTTT 59.923 47.619 0.00 0.00 0.00 2.43
3834 3916 2.993899 CGAGCAATGGGAATCGTATACC 59.006 50.000 0.00 0.00 0.00 2.73
3855 3937 4.445452 TTCTCTACGTGTGTAATGTCCC 57.555 45.455 0.00 0.00 0.00 4.46
3856 3938 5.706916 TCTTTCTCTACGTGTGTAATGTCC 58.293 41.667 0.00 0.00 0.00 4.02
3857 3939 6.609533 TCTCTTTCTCTACGTGTGTAATGTC 58.390 40.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.