Multiple sequence alignment - TraesCS5A01G189000

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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 TraesCS5A01G189000 chr5A 100.000 6185 0 0 1 6185 391522309 391516125 0.000000e+00 11422.0
1 TraesCS5A01G189000 chr5A 90.370 405 35 1 768 1172 391526773 391526373 4.250000e-146 529.0
2 TraesCS5A01G189000 chr5D 94.203 2829 114 23 1 2788 306197220 306200039 0.000000e+00 4270.0
3 TraesCS5A01G189000 chr5D 95.267 1648 44 8 3816 5432 306200944 306202588 0.000000e+00 2580.0
4 TraesCS5A01G189000 chr5D 94.444 720 32 5 2889 3603 306200098 306200814 0.000000e+00 1101.0
5 TraesCS5A01G189000 chr5D 93.333 330 10 3 5471 5799 306202586 306202904 1.560000e-130 477.0
6 TraesCS5A01G189000 chr5D 95.402 87 4 0 2786 2872 470760633 470760719 8.360000e-29 139.0
7 TraesCS5A01G189000 chr5D 90.099 101 9 1 2781 2881 216627762 216627861 5.030000e-26 130.0
8 TraesCS5A01G189000 chr5D 98.361 61 1 0 3758 3818 306200805 306200865 2.360000e-19 108.0
9 TraesCS5A01G189000 chr5D 94.203 69 4 0 6117 6185 306203796 306203864 8.480000e-19 106.0
10 TraesCS5A01G189000 chr5D 92.857 70 5 0 3687 3756 541589751 541589820 1.100000e-17 102.0
11 TraesCS5A01G189000 chr5B 94.065 2797 132 16 1 2788 351480573 351483344 0.000000e+00 4215.0
12 TraesCS5A01G189000 chr5B 95.525 1475 51 7 2889 4360 351483403 351484865 0.000000e+00 2344.0
13 TraesCS5A01G189000 chr5B 96.048 1164 32 4 4361 5515 351484894 351486052 0.000000e+00 1882.0
14 TraesCS5A01G189000 chr5B 89.320 103 10 1 2777 2878 406061628 406061526 1.810000e-25 128.0
15 TraesCS5A01G189000 chr1D 90.370 135 13 0 3625 3759 127221827 127221693 1.770000e-40 178.0
16 TraesCS5A01G189000 chr1D 97.561 82 2 0 2787 2868 232558458 232558539 2.320000e-29 141.0
17 TraesCS5A01G189000 chr1D 91.304 46 4 0 4352 4397 340658136 340658181 5.180000e-06 63.9
18 TraesCS5A01G189000 chr1A 90.226 133 13 0 3627 3759 201861434 201861302 2.290000e-39 174.0
19 TraesCS5A01G189000 chr1A 93.407 91 6 0 2787 2877 439847104 439847014 1.080000e-27 135.0
20 TraesCS5A01G189000 chr1A 97.368 38 1 0 4357 4394 164468753 164468790 1.440000e-06 65.8
21 TraesCS5A01G189000 chr7D 94.565 92 4 1 2787 2878 246397228 246397138 2.320000e-29 141.0
22 TraesCS5A01G189000 chr7D 89.041 73 8 0 3690 3762 632329380 632329308 2.370000e-14 91.6
23 TraesCS5A01G189000 chr7D 94.872 39 2 0 4363 4401 177117127 177117089 1.860000e-05 62.1
24 TraesCS5A01G189000 chr3B 90.196 102 10 0 2777 2878 661222544 661222645 3.890000e-27 134.0
25 TraesCS5A01G189000 chr3B 88.732 71 8 0 3686 3756 754149007 754149077 3.070000e-13 87.9
26 TraesCS5A01G189000 chr7A 91.667 96 6 2 2774 2868 556767962 556768056 1.400000e-26 132.0
27 TraesCS5A01G189000 chr4A 93.182 88 6 0 2784 2871 17382971 17382884 5.030000e-26 130.0
28 TraesCS5A01G189000 chr3A 82.000 150 18 3 3620 3760 722209288 722209437 1.090000e-22 119.0
29 TraesCS5A01G189000 chr3A 85.849 106 14 1 3620 3724 722208876 722208981 1.820000e-20 111.0
30 TraesCS5A01G189000 chr2D 92.857 70 5 0 3687 3756 535728584 535728653 1.100000e-17 102.0
31 TraesCS5A01G189000 chr6D 97.368 38 1 0 4363 4400 395533124 395533087 1.440000e-06 65.8
32 TraesCS5A01G189000 chr6B 92.857 42 1 2 4365 4404 42775656 42775615 6.700000e-05 60.2
33 TraesCS5A01G189000 chr7B 94.595 37 1 1 4363 4398 83912830 83912866 8.660000e-04 56.5
34 TraesCS5A01G189000 chr4B 94.595 37 1 1 4366 4401 609499467 609499431 8.660000e-04 56.5


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 TraesCS5A01G189000 chr5A 391516125 391522309 6184 True 11422.000000 11422 100.000000 1 6185 1 chr5A.!!$R1 6184
1 TraesCS5A01G189000 chr5D 306197220 306203864 6644 False 1440.333333 4270 94.968500 1 6185 6 chr5D.!!$F4 6184
2 TraesCS5A01G189000 chr5B 351480573 351486052 5479 False 2813.666667 4215 95.212667 1 5515 3 chr5B.!!$F1 5514

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
522 550 0.034089 AGTGGCCACTTCCATTAGCC 60.034 55.0 33.2 2.59 44.13 3.93 F
740 768 0.038310 TCTGAGGAGCCGAGACAAGA 59.962 55.0 0.0 0.00 0.00 3.02 F
1806 1847 0.976641 TGGTCTCCTGCGTCAAGAAT 59.023 50.0 0.0 0.00 0.00 2.40 F
3008 3094 0.032952 TAATCGGCATCGGTGTAGCC 59.967 55.0 0.0 0.00 44.89 3.93 F
3255 3341 0.757935 CAAGCCTATGCCCTGCCATT 60.758 55.0 0.0 0.00 38.69 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 1955 0.610174 GCTCCATCACCACAGACTCA 59.390 55.000 0.00 0.00 0.00 3.41 R
2022 2063 1.760086 CTGCTCCTCCATCTCCCGT 60.760 63.158 0.00 0.00 0.00 5.28 R
3707 3798 1.081094 TAGCGATTCGTGACGAGTCA 58.919 50.000 25.94 7.92 41.49 3.41 R
4845 5055 1.303888 CCTGCTGCCTGTTGGATGT 60.304 57.895 0.00 0.00 34.57 3.06 R
5281 5498 4.073293 TCCTCAGTTCCTGTTCAACTTC 57.927 45.455 0.00 0.00 31.40 3.01 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
33 34 1.074889 ACGGTAGCAACCTCCCAAAAT 59.925 47.619 0.00 0.00 44.35 1.82
71 72 4.156477 AGTCTAGCACCTCTTCAAGTCTT 58.844 43.478 0.00 0.00 0.00 3.01
103 104 2.161012 TGTTCGCGTAGATTTCTCTCGT 59.839 45.455 5.77 0.00 32.66 4.18
108 109 4.510711 TCGCGTAGATTTCTCTCGTCTTAT 59.489 41.667 5.77 0.00 32.66 1.73
114 116 7.166142 CGTAGATTTCTCTCGTCTTATGGTTTC 59.834 40.741 0.00 0.00 32.66 2.78
115 117 7.176589 AGATTTCTCTCGTCTTATGGTTTCT 57.823 36.000 0.00 0.00 0.00 2.52
116 118 7.262048 AGATTTCTCTCGTCTTATGGTTTCTC 58.738 38.462 0.00 0.00 0.00 2.87
117 119 4.985538 TCTCTCGTCTTATGGTTTCTCC 57.014 45.455 0.00 0.00 0.00 3.71
125 127 1.507140 TATGGTTTCTCCGCCTCCAT 58.493 50.000 0.00 0.00 41.10 3.41
142 144 6.385033 GCCTCCATTATTGTGCATTCTATTC 58.615 40.000 0.00 0.00 0.00 1.75
147 149 7.039574 TCCATTATTGTGCATTCTATTCCATGG 60.040 37.037 4.97 4.97 0.00 3.66
171 196 8.271458 TGGCTATCCAACTAATATGTTCTGAAA 58.729 33.333 0.00 0.00 39.99 2.69
335 360 2.490509 TGAGGAGAATAACGACGCTTCA 59.509 45.455 0.00 0.00 0.00 3.02
339 364 2.853003 GAGAATAACGACGCTTCACCTC 59.147 50.000 0.00 0.00 0.00 3.85
376 402 3.960755 GCCTTTGCCTTATATTCTTGGGT 59.039 43.478 0.00 0.00 0.00 4.51
395 421 3.378427 GGGTGGCAAGTAAGATCAATGAC 59.622 47.826 0.00 0.00 0.00 3.06
417 444 3.128349 GTGTGGCGGTATGGTATAACTG 58.872 50.000 0.00 0.00 0.00 3.16
419 446 3.451540 TGTGGCGGTATGGTATAACTGAA 59.548 43.478 0.00 0.00 0.00 3.02
480 508 6.016443 AGCTTTGAGAGAAGGTGATGAAAAAG 60.016 38.462 0.00 0.00 36.13 2.27
494 522 7.228706 GGTGATGAAAAAGGACAAGTTAGAAGA 59.771 37.037 0.00 0.00 0.00 2.87
522 550 0.034089 AGTGGCCACTTCCATTAGCC 60.034 55.000 33.20 2.59 44.13 3.93
557 585 8.792633 ACCATTCATCTTATTTTCTTGAACGAA 58.207 29.630 0.00 0.00 0.00 3.85
588 616 9.692325 AAAGACATTTAAGATCTTTGATAGGCT 57.308 29.630 14.36 5.30 40.35 4.58
596 624 4.349048 AGATCTTTGATAGGCTATGGTGCA 59.651 41.667 12.68 0.28 34.04 4.57
658 686 7.095024 CGATAAGGTTAAGATCGTCATCAAC 57.905 40.000 0.00 0.00 38.10 3.18
659 687 6.695713 CGATAAGGTTAAGATCGTCATCAACA 59.304 38.462 0.00 0.00 38.10 3.33
660 688 7.096436 CGATAAGGTTAAGATCGTCATCAACAG 60.096 40.741 0.00 0.00 38.10 3.16
662 690 6.525578 AGGTTAAGATCGTCATCAACAGTA 57.474 37.500 0.00 0.00 0.00 2.74
663 691 6.931838 AGGTTAAGATCGTCATCAACAGTAA 58.068 36.000 0.00 0.00 0.00 2.24
664 692 7.556844 AGGTTAAGATCGTCATCAACAGTAAT 58.443 34.615 0.00 0.00 0.00 1.89
665 693 7.492669 AGGTTAAGATCGTCATCAACAGTAATG 59.507 37.037 0.00 0.00 0.00 1.90
666 694 7.277981 GGTTAAGATCGTCATCAACAGTAATGT 59.722 37.037 0.00 0.00 0.00 2.71
667 695 6.893958 AAGATCGTCATCAACAGTAATGTC 57.106 37.500 0.00 0.00 0.00 3.06
669 697 6.398095 AGATCGTCATCAACAGTAATGTCAA 58.602 36.000 0.00 0.00 0.00 3.18
670 698 7.044181 AGATCGTCATCAACAGTAATGTCAAT 58.956 34.615 0.00 0.00 0.00 2.57
673 701 8.541133 TCGTCATCAACAGTAATGTCAATAAA 57.459 30.769 0.00 0.00 0.00 1.40
706 734 9.190858 GAGACTATAACACATGAGATGATTGAC 57.809 37.037 0.00 0.00 0.00 3.18
728 756 7.679783 TGACAAGACAAATTTAGATCTGAGGA 58.320 34.615 5.18 0.00 0.00 3.71
740 768 0.038310 TCTGAGGAGCCGAGACAAGA 59.962 55.000 0.00 0.00 0.00 3.02
751 779 2.224066 CCGAGACAAGAAAGTCAGTGGT 60.224 50.000 0.00 0.00 40.98 4.16
797 833 3.550437 ACATTGTATCAGGCCTCTCAC 57.450 47.619 0.00 0.42 0.00 3.51
801 837 2.470990 TGTATCAGGCCTCTCACACAT 58.529 47.619 0.00 0.00 0.00 3.21
839 875 6.436890 CCCTAAAAACCCATAGATAACCCAA 58.563 40.000 0.00 0.00 0.00 4.12
840 876 6.322969 CCCTAAAAACCCATAGATAACCCAAC 59.677 42.308 0.00 0.00 0.00 3.77
841 877 6.322969 CCTAAAAACCCATAGATAACCCAACC 59.677 42.308 0.00 0.00 0.00 3.77
842 878 4.957606 AAACCCATAGATAACCCAACCA 57.042 40.909 0.00 0.00 0.00 3.67
1551 1592 1.138883 CAACGATCTCCGCCTCGAA 59.861 57.895 0.00 0.00 43.32 3.71
1599 1640 1.067582 CGATAAGTCGCCCCACTCC 59.932 63.158 0.00 0.00 41.49 3.85
1623 1664 3.057547 CTCCACCGCCGAGAGTGAG 62.058 68.421 0.00 0.00 36.01 3.51
1782 1823 2.323580 GCACACTGAGAGCACTGCC 61.324 63.158 0.00 0.00 33.66 4.85
1806 1847 0.976641 TGGTCTCCTGCGTCAAGAAT 59.023 50.000 0.00 0.00 0.00 2.40
1914 1955 2.158900 GGTGTCCACCGATGATCTCATT 60.159 50.000 0.00 0.00 42.29 2.57
2022 2063 3.064207 GCGTGACCTCATTAAACAGACA 58.936 45.455 0.00 0.00 0.00 3.41
2142 2183 3.728474 CTGCGGATGGAGCATGAC 58.272 61.111 0.00 0.00 44.26 3.06
2433 2474 0.255318 CCAAGCTGCAGGAGGAGATT 59.745 55.000 17.12 0.00 42.81 2.40
2666 2708 7.253422 GTTTAGATCATTTGTAGCTGCATTGT 58.747 34.615 4.98 0.00 0.00 2.71
2736 2778 3.274281 TGATCCTGATGGGCTATGGTA 57.726 47.619 0.00 0.00 34.39 3.25
2786 2831 9.528489 TGGTAAAAGCCTAATTTGATAAGAAGT 57.472 29.630 0.00 0.00 0.00 3.01
2791 2836 8.966069 AAGCCTAATTTGATAAGAAGTACTCC 57.034 34.615 0.00 0.00 0.00 3.85
2792 2837 7.510407 AGCCTAATTTGATAAGAAGTACTCCC 58.490 38.462 0.00 0.00 0.00 4.30
2793 2838 7.348537 AGCCTAATTTGATAAGAAGTACTCCCT 59.651 37.037 0.00 0.00 0.00 4.20
2794 2839 7.658167 GCCTAATTTGATAAGAAGTACTCCCTC 59.342 40.741 0.00 0.00 0.00 4.30
2795 2840 8.929487 CCTAATTTGATAAGAAGTACTCCCTCT 58.071 37.037 0.00 0.00 0.00 3.69
2796 2841 9.757227 CTAATTTGATAAGAAGTACTCCCTCTG 57.243 37.037 0.00 0.00 0.00 3.35
2797 2842 7.741554 ATTTGATAAGAAGTACTCCCTCTGT 57.258 36.000 0.00 0.00 0.00 3.41
2798 2843 6.777213 TTGATAAGAAGTACTCCCTCTGTC 57.223 41.667 0.00 0.00 0.00 3.51
2799 2844 5.202004 TGATAAGAAGTACTCCCTCTGTCC 58.798 45.833 0.00 0.00 0.00 4.02
2800 2845 2.535836 AGAAGTACTCCCTCTGTCCC 57.464 55.000 0.00 0.00 0.00 4.46
2801 2846 1.717077 AGAAGTACTCCCTCTGTCCCA 59.283 52.381 0.00 0.00 0.00 4.37
2802 2847 2.111972 AGAAGTACTCCCTCTGTCCCAA 59.888 50.000 0.00 0.00 0.00 4.12
2803 2848 2.715763 AGTACTCCCTCTGTCCCAAA 57.284 50.000 0.00 0.00 0.00 3.28
2804 2849 2.986050 AGTACTCCCTCTGTCCCAAAA 58.014 47.619 0.00 0.00 0.00 2.44
2805 2850 3.532102 AGTACTCCCTCTGTCCCAAAAT 58.468 45.455 0.00 0.00 0.00 1.82
2806 2851 4.695606 AGTACTCCCTCTGTCCCAAAATA 58.304 43.478 0.00 0.00 0.00 1.40
2807 2852 5.289510 AGTACTCCCTCTGTCCCAAAATAT 58.710 41.667 0.00 0.00 0.00 1.28
2808 2853 6.449956 AGTACTCCCTCTGTCCCAAAATATA 58.550 40.000 0.00 0.00 0.00 0.86
2809 2854 6.906901 AGTACTCCCTCTGTCCCAAAATATAA 59.093 38.462 0.00 0.00 0.00 0.98
2810 2855 6.253946 ACTCCCTCTGTCCCAAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
2811 2856 5.970640 ACTCCCTCTGTCCCAAAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
2812 2857 6.100424 ACTCCCTCTGTCCCAAAATATAAGAG 59.900 42.308 0.00 0.00 0.00 2.85
2813 2858 5.066593 CCCTCTGTCCCAAAATATAAGAGC 58.933 45.833 0.00 0.00 0.00 4.09
2814 2859 4.752101 CCTCTGTCCCAAAATATAAGAGCG 59.248 45.833 0.00 0.00 0.00 5.03
2815 2860 4.127171 TCTGTCCCAAAATATAAGAGCGC 58.873 43.478 0.00 0.00 0.00 5.92
2816 2861 4.130118 CTGTCCCAAAATATAAGAGCGCT 58.870 43.478 11.27 11.27 0.00 5.92
2817 2862 4.523083 TGTCCCAAAATATAAGAGCGCTT 58.477 39.130 13.26 8.09 38.15 4.68
2818 2863 4.947388 TGTCCCAAAATATAAGAGCGCTTT 59.053 37.500 13.26 1.42 35.56 3.51
2819 2864 5.417580 TGTCCCAAAATATAAGAGCGCTTTT 59.582 36.000 17.98 17.98 35.56 2.27
2820 2865 5.743872 GTCCCAAAATATAAGAGCGCTTTTG 59.256 40.000 22.35 19.60 36.84 2.44
2821 2866 5.650266 TCCCAAAATATAAGAGCGCTTTTGA 59.350 36.000 22.35 11.00 38.46 2.69
2822 2867 5.743872 CCCAAAATATAAGAGCGCTTTTGAC 59.256 40.000 22.35 4.04 38.46 3.18
2823 2868 6.321717 CCAAAATATAAGAGCGCTTTTGACA 58.678 36.000 22.35 8.10 38.46 3.58
2824 2869 6.251376 CCAAAATATAAGAGCGCTTTTGACAC 59.749 38.462 22.35 2.46 38.46 3.67
2825 2870 6.743575 AAATATAAGAGCGCTTTTGACACT 57.256 33.333 22.35 5.03 35.56 3.55
2826 2871 7.843490 AAATATAAGAGCGCTTTTGACACTA 57.157 32.000 22.35 2.21 35.56 2.74
2827 2872 6.830114 ATATAAGAGCGCTTTTGACACTAC 57.170 37.500 22.35 0.08 35.56 2.73
2828 2873 2.526304 AGAGCGCTTTTGACACTACA 57.474 45.000 13.26 0.00 0.00 2.74
2829 2874 2.135933 AGAGCGCTTTTGACACTACAC 58.864 47.619 13.26 0.00 0.00 2.90
2830 2875 2.135933 GAGCGCTTTTGACACTACACT 58.864 47.619 13.26 0.00 0.00 3.55
2831 2876 3.005472 AGAGCGCTTTTGACACTACACTA 59.995 43.478 13.26 0.00 0.00 2.74
2832 2877 3.318017 AGCGCTTTTGACACTACACTAG 58.682 45.455 2.64 0.00 0.00 2.57
2833 2878 3.057734 GCGCTTTTGACACTACACTAGT 58.942 45.455 0.00 0.00 40.28 2.57
2862 2907 6.391227 AAATGCTCTTATATTTTGGGACGG 57.609 37.500 0.00 0.00 0.00 4.79
2863 2908 4.764050 TGCTCTTATATTTTGGGACGGA 57.236 40.909 0.00 0.00 0.00 4.69
2864 2909 4.703897 TGCTCTTATATTTTGGGACGGAG 58.296 43.478 0.00 0.00 0.00 4.63
2865 2910 4.065789 GCTCTTATATTTTGGGACGGAGG 58.934 47.826 0.00 0.00 0.00 4.30
2866 2911 4.642429 CTCTTATATTTTGGGACGGAGGG 58.358 47.826 0.00 0.00 0.00 4.30
2867 2912 4.300345 TCTTATATTTTGGGACGGAGGGA 58.700 43.478 0.00 0.00 0.00 4.20
2868 2913 4.722781 TCTTATATTTTGGGACGGAGGGAA 59.277 41.667 0.00 0.00 0.00 3.97
2886 2931 9.238368 CGGAGGGAATAAAATATTTAGGCATAA 57.762 33.333 0.01 0.00 0.00 1.90
2990 3076 1.765074 GGGACCCTGCCACTTGTTA 59.235 57.895 2.09 0.00 0.00 2.41
2999 3085 2.475200 GCCACTTGTTAATCGGCATC 57.525 50.000 0.00 0.00 42.50 3.91
3008 3094 0.032952 TAATCGGCATCGGTGTAGCC 59.967 55.000 0.00 0.00 44.89 3.93
3163 3249 6.106877 TGCTTTACTAATGATTCGTCTTGC 57.893 37.500 0.00 0.00 0.00 4.01
3255 3341 0.757935 CAAGCCTATGCCCTGCCATT 60.758 55.000 0.00 0.00 38.69 3.16
3318 3405 3.494398 CGCTGGCCTGGTTATACTATGTT 60.494 47.826 12.06 0.00 0.00 2.71
3621 3712 1.400494 ACCACTGTTTTTGAGTCACGC 59.600 47.619 0.00 0.00 0.00 5.34
3654 3745 2.360350 CGCACTGCCAGGGTTGAT 60.360 61.111 0.00 0.00 0.00 2.57
3675 3766 1.001633 TCAAACCCCTCAACTAGTCGC 59.998 52.381 0.00 0.00 0.00 5.19
3707 3798 4.702131 GTGATTAGTCAATTGGTCAGGCTT 59.298 41.667 5.42 0.00 35.80 4.35
4032 4211 3.768757 TGCTAATTGCCTGTTAATGCCTT 59.231 39.130 0.00 0.00 42.00 4.35
4036 4217 3.940209 TTGCCTGTTAATGCCTTTCAG 57.060 42.857 0.00 0.00 0.00 3.02
4037 4218 3.153369 TGCCTGTTAATGCCTTTCAGA 57.847 42.857 7.69 0.00 0.00 3.27
4038 4219 3.495331 TGCCTGTTAATGCCTTTCAGAA 58.505 40.909 7.69 0.00 0.00 3.02
4039 4220 3.255642 TGCCTGTTAATGCCTTTCAGAAC 59.744 43.478 7.69 0.00 0.00 3.01
4115 4297 7.330946 AGTTGTTAAGTTTTCTTTCAAAGTGGC 59.669 33.333 0.00 0.00 40.91 5.01
4574 4784 1.771255 AGAGAAGACACAAAGGCCACT 59.229 47.619 5.01 0.00 0.00 4.00
4997 5207 2.476320 GCATGAGGAGAAAGGCGCC 61.476 63.158 21.89 21.89 36.60 6.53
5078 5288 1.451504 CAACTGAGGCACCTGGTGA 59.548 57.895 30.23 8.39 35.23 4.02
5081 5291 1.748122 CTGAGGCACCTGGTGATGC 60.748 63.158 30.23 14.89 41.29 3.91
5262 5479 1.903860 TCGGGGTATATGGGTACATGC 59.096 52.381 0.00 0.00 37.97 4.06
5295 5512 2.432874 TGGTCGAGAAGTTGAACAGGAA 59.567 45.455 0.00 0.00 29.58 3.36
5297 5514 3.492829 GGTCGAGAAGTTGAACAGGAACT 60.493 47.826 0.00 0.00 43.88 3.01
5338 5557 9.994432 GATATGAGTCAATTGAACTTAAACTGG 57.006 33.333 10.35 0.00 0.00 4.00
5344 5565 6.691388 GTCAATTGAACTTAAACTGGTGTGTC 59.309 38.462 10.35 0.00 0.00 3.67
5345 5566 6.601613 TCAATTGAACTTAAACTGGTGTGTCT 59.398 34.615 5.45 0.00 0.00 3.41
5398 5619 0.599558 TGCTTGATGTTCTTGCTGGC 59.400 50.000 0.00 0.00 0.00 4.85
5460 5682 5.281037 CCCTGAGGAAATAGGTTTTGGTAGT 60.281 44.000 0.00 0.00 33.47 2.73
5487 5709 4.821589 GGCCTCTCCTTGCCGTCG 62.822 72.222 0.00 0.00 38.00 5.12
5496 5718 1.079819 CTTGCCGTCGATGGTGACT 60.080 57.895 24.33 0.00 36.71 3.41
5524 5746 4.083484 AGCAGGTATTCTTGTTTTACGCAC 60.083 41.667 0.00 0.00 0.00 5.34
5656 5879 2.266055 GGGAGTGGCGAGAACTGG 59.734 66.667 0.00 0.00 0.00 4.00
5665 5888 1.882989 GCGAGAACTGGCTCCACTCT 61.883 60.000 1.80 0.99 0.00 3.24
5666 5889 0.108898 CGAGAACTGGCTCCACTCTG 60.109 60.000 0.00 0.00 0.00 3.35
5667 5890 0.390998 GAGAACTGGCTCCACTCTGC 60.391 60.000 1.60 0.00 0.00 4.26
5668 5891 0.835543 AGAACTGGCTCCACTCTGCT 60.836 55.000 0.00 0.00 0.00 4.24
5669 5892 0.673022 GAACTGGCTCCACTCTGCTG 60.673 60.000 0.00 0.00 0.00 4.41
5670 5893 2.121992 AACTGGCTCCACTCTGCTGG 62.122 60.000 0.00 0.00 0.00 4.85
5671 5894 2.527624 TGGCTCCACTCTGCTGGT 60.528 61.111 0.00 0.00 32.50 4.00
5672 5895 2.121992 CTGGCTCCACTCTGCTGGTT 62.122 60.000 0.00 0.00 32.50 3.67
5673 5896 1.673665 GGCTCCACTCTGCTGGTTG 60.674 63.158 0.00 0.00 32.50 3.77
5674 5897 1.372683 GCTCCACTCTGCTGGTTGA 59.627 57.895 0.00 0.00 32.50 3.18
5705 5928 8.339247 TGTAAACACTACCTAGGGATTACTACT 58.661 37.037 14.81 0.00 42.21 2.57
5746 5969 0.464036 TTGGCTCTTCGCGATGGTAT 59.536 50.000 20.35 0.00 40.44 2.73
5780 6003 2.257207 CTCCGGGGCTATGGAAAGATA 58.743 52.381 0.00 0.00 32.89 1.98
5807 6058 2.223203 GCAGACTGATTGCCTTGATTCG 60.223 50.000 6.65 0.00 35.54 3.34
5815 6066 4.393062 TGATTGCCTTGATTCGAGAAGTTC 59.607 41.667 2.22 0.00 0.00 3.01
5817 6068 3.738982 TGCCTTGATTCGAGAAGTTCAA 58.261 40.909 5.50 2.98 0.00 2.69
5832 6083 3.733337 AGTTCAATGGCGCCTATCTTAG 58.267 45.455 29.70 10.42 0.00 2.18
5840 6091 3.388024 TGGCGCCTATCTTAGATGAAACT 59.612 43.478 29.70 0.00 0.00 2.66
5862 6113 6.687604 ACTGGGGATCGTTTATTTCTTTTTG 58.312 36.000 0.00 0.00 0.00 2.44
5894 6158 3.872240 GCTGATACTGTTGCCCACCTTTA 60.872 47.826 0.00 0.00 0.00 1.85
5909 6173 3.742369 CACCTTTATGCCAAACAAGCAAG 59.258 43.478 0.00 0.00 44.83 4.01
5910 6174 2.738314 CCTTTATGCCAAACAAGCAAGC 59.262 45.455 0.00 0.00 44.83 4.01
5912 6176 2.437200 TATGCCAAACAAGCAAGCAC 57.563 45.000 0.00 0.00 44.83 4.40
5916 6180 1.563111 CCAAACAAGCAAGCACACTG 58.437 50.000 0.00 0.00 0.00 3.66
5928 6192 0.322975 GCACACTGGAGGTCACAGAT 59.677 55.000 0.00 0.00 39.24 2.90
5929 6193 1.271054 GCACACTGGAGGTCACAGATT 60.271 52.381 0.00 0.00 39.24 2.40
5930 6194 2.811873 GCACACTGGAGGTCACAGATTT 60.812 50.000 0.00 0.00 39.24 2.17
5931 6195 2.810274 CACACTGGAGGTCACAGATTTG 59.190 50.000 0.00 0.00 39.24 2.32
5932 6196 1.808945 CACTGGAGGTCACAGATTTGC 59.191 52.381 0.00 0.00 39.24 3.68
5933 6197 1.081892 CTGGAGGTCACAGATTTGCG 58.918 55.000 0.00 0.00 38.20 4.85
5934 6198 0.321564 TGGAGGTCACAGATTTGCGG 60.322 55.000 0.00 0.00 0.00 5.69
5935 6199 1.026718 GGAGGTCACAGATTTGCGGG 61.027 60.000 0.00 0.00 0.00 6.13
5936 6200 0.036388 GAGGTCACAGATTTGCGGGA 60.036 55.000 0.00 0.00 0.00 5.14
5938 6202 0.734889 GGTCACAGATTTGCGGGATG 59.265 55.000 0.00 0.00 0.00 3.51
5939 6203 1.678728 GGTCACAGATTTGCGGGATGA 60.679 52.381 0.00 0.00 0.00 2.92
5940 6204 2.083774 GTCACAGATTTGCGGGATGAA 58.916 47.619 0.00 0.00 0.00 2.57
5941 6205 2.083774 TCACAGATTTGCGGGATGAAC 58.916 47.619 0.00 0.00 0.00 3.18
5942 6206 2.086869 CACAGATTTGCGGGATGAACT 58.913 47.619 0.00 0.00 0.00 3.01
5943 6207 2.489329 CACAGATTTGCGGGATGAACTT 59.511 45.455 0.00 0.00 0.00 2.66
5944 6208 3.057315 CACAGATTTGCGGGATGAACTTT 60.057 43.478 0.00 0.00 0.00 2.66
5945 6209 4.155826 CACAGATTTGCGGGATGAACTTTA 59.844 41.667 0.00 0.00 0.00 1.85
5946 6210 4.156008 ACAGATTTGCGGGATGAACTTTAC 59.844 41.667 0.00 0.00 0.00 2.01
5947 6211 3.374058 AGATTTGCGGGATGAACTTTACG 59.626 43.478 0.00 0.00 0.00 3.18
5948 6212 0.800012 TTGCGGGATGAACTTTACGC 59.200 50.000 0.00 0.00 46.34 4.42
5949 6213 1.022451 TGCGGGATGAACTTTACGCC 61.022 55.000 0.00 0.00 45.67 5.68
5950 6214 0.743345 GCGGGATGAACTTTACGCCT 60.743 55.000 0.00 0.00 41.02 5.52
5951 6215 1.472026 GCGGGATGAACTTTACGCCTA 60.472 52.381 0.00 0.00 41.02 3.93
5965 6229 1.084289 CGCCTACTTGTAACTTGCCC 58.916 55.000 0.00 0.00 0.00 5.36
5980 6244 0.400381 TGCCCCCTAGCAGATGATGA 60.400 55.000 0.00 0.00 38.00 2.92
5981 6245 0.990374 GCCCCCTAGCAGATGATGAT 59.010 55.000 0.00 0.00 0.00 2.45
5993 6257 0.552848 ATGATGATGGGGCGGTTTCT 59.447 50.000 0.00 0.00 0.00 2.52
6004 6268 3.006003 GGGGCGGTTTCTGTTGAATAAAA 59.994 43.478 0.00 0.00 31.56 1.52
6007 6271 6.391537 GGGCGGTTTCTGTTGAATAAAAATA 58.608 36.000 0.00 0.00 31.56 1.40
6010 6274 7.973944 GGCGGTTTCTGTTGAATAAAAATATCT 59.026 33.333 0.00 0.00 31.56 1.98
6035 6299 1.667722 CCCCCAAAAGCAAGTGAGC 59.332 57.895 0.00 0.00 0.00 4.26
6037 6301 1.114722 CCCCAAAAGCAAGTGAGCCA 61.115 55.000 0.00 0.00 34.23 4.75
6038 6302 0.752054 CCCAAAAGCAAGTGAGCCAA 59.248 50.000 0.00 0.00 34.23 4.52
6039 6303 1.538849 CCCAAAAGCAAGTGAGCCAAC 60.539 52.381 0.00 0.00 34.23 3.77
6040 6304 1.136695 CCAAAAGCAAGTGAGCCAACA 59.863 47.619 0.00 0.00 34.23 3.33
6041 6305 2.418471 CCAAAAGCAAGTGAGCCAACAA 60.418 45.455 0.00 0.00 34.23 2.83
6042 6306 3.260740 CAAAAGCAAGTGAGCCAACAAA 58.739 40.909 0.00 0.00 34.23 2.83
6043 6307 3.825143 AAAGCAAGTGAGCCAACAAAT 57.175 38.095 0.00 0.00 34.23 2.32
6044 6308 2.806608 AGCAAGTGAGCCAACAAATG 57.193 45.000 0.00 0.00 34.23 2.32
6045 6309 2.034124 AGCAAGTGAGCCAACAAATGT 58.966 42.857 0.00 0.00 34.23 2.71
6046 6310 2.431782 AGCAAGTGAGCCAACAAATGTT 59.568 40.909 0.00 0.00 39.12 2.71
6047 6311 2.796593 GCAAGTGAGCCAACAAATGTTC 59.203 45.455 0.00 0.00 35.83 3.18
6048 6312 3.044986 CAAGTGAGCCAACAAATGTTCG 58.955 45.455 0.00 0.00 35.83 3.95
6049 6313 1.001378 AGTGAGCCAACAAATGTTCGC 60.001 47.619 7.66 7.66 41.44 4.70
6050 6314 1.028130 TGAGCCAACAAATGTTCGCA 58.972 45.000 16.27 3.62 43.13 5.10
6062 6326 2.659244 TTCGCAACGTGTCCGGTC 60.659 61.111 0.00 0.00 38.78 4.79
6069 6333 4.986587 CGTGTCCGGTCGCGTTCA 62.987 66.667 23.54 1.27 36.71 3.18
6071 6335 4.986587 TGTCCGGTCGCGTTCACG 62.987 66.667 5.77 6.76 43.27 4.35
6094 6358 1.474332 AACGCCCGGTCACCTCTTAA 61.474 55.000 0.00 0.00 0.00 1.85
6115 6379 4.998671 AATTTCACACATCACAACCACA 57.001 36.364 0.00 0.00 0.00 4.17
6152 6974 3.980646 TTTACACATCACAAGCACACC 57.019 42.857 0.00 0.00 0.00 4.16
6163 6985 4.218200 TCACAAGCACACCCATAATTTGAG 59.782 41.667 0.00 0.00 0.00 3.02
6164 6986 3.511146 ACAAGCACACCCATAATTTGAGG 59.489 43.478 0.00 0.00 0.00 3.86
6176 6998 8.267183 ACCCATAATTTGAGGATTTCCATTTTC 58.733 33.333 0.00 0.00 38.89 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 5.535030 TGCTAGACTACTCAGTTGTTGAAGA 59.465 40.000 0.00 0.00 34.21 2.87
71 72 1.647346 ACGCGAACAACTTTGTCTCA 58.353 45.000 15.93 0.00 41.31 3.27
103 104 1.485066 GGAGGCGGAGAAACCATAAGA 59.515 52.381 0.00 0.00 38.90 2.10
108 109 1.281419 TAATGGAGGCGGAGAAACCA 58.719 50.000 0.00 0.00 38.90 3.67
114 116 0.947244 GCACAATAATGGAGGCGGAG 59.053 55.000 0.00 0.00 0.00 4.63
115 117 0.254462 TGCACAATAATGGAGGCGGA 59.746 50.000 0.00 0.00 0.00 5.54
116 118 1.321474 ATGCACAATAATGGAGGCGG 58.679 50.000 0.00 0.00 0.00 6.13
117 119 2.620115 AGAATGCACAATAATGGAGGCG 59.380 45.455 0.00 0.00 0.00 5.52
125 127 5.834742 AGCCATGGAATAGAATGCACAATAA 59.165 36.000 18.40 0.00 0.00 1.40
142 144 7.120285 CAGAACATATTAGTTGGATAGCCATGG 59.880 40.741 7.63 7.63 45.46 3.66
171 196 9.423061 GTTATAAGGACAAAATGAAAGCACATT 57.577 29.630 0.00 0.00 41.43 2.71
287 312 4.562082 TCTTTTGGAGGTATACGTGTGTG 58.438 43.478 2.13 0.00 0.00 3.82
348 373 4.820173 AGAATATAAGGCAAAGGCGGTAAC 59.180 41.667 0.00 0.00 42.47 2.50
376 402 3.684305 CACGTCATTGATCTTACTTGCCA 59.316 43.478 0.00 0.00 0.00 4.92
395 421 2.129607 GTTATACCATACCGCCACACG 58.870 52.381 0.00 0.00 43.15 4.49
458 486 6.263168 GTCCTTTTTCATCACCTTCTCTCAAA 59.737 38.462 0.00 0.00 0.00 2.69
494 522 4.929479 TGGAAGTGGCCACTAATGTATTT 58.071 39.130 37.89 20.39 41.58 1.40
562 590 9.692325 AGCCTATCAAAGATCTTAAATGTCTTT 57.308 29.630 8.75 0.00 41.48 2.52
578 606 4.854173 TCTTTGCACCATAGCCTATCAAA 58.146 39.130 0.00 0.00 0.00 2.69
588 616 7.392953 TCAATTAGTTGTCATCTTTGCACCATA 59.607 33.333 0.00 0.00 36.69 2.74
673 701 9.911788 ATCTCATGTGTTATAGTCTCCATTTTT 57.088 29.630 0.00 0.00 0.00 1.94
706 734 6.038050 GGCTCCTCAGATCTAAATTTGTCTTG 59.962 42.308 0.00 0.00 0.00 3.02
728 756 1.689273 ACTGACTTTCTTGTCTCGGCT 59.311 47.619 0.00 0.00 37.79 5.52
758 786 4.462508 TGTTCACCATTGTGCTCAAAAA 57.537 36.364 5.15 0.00 42.46 1.94
785 821 1.576577 ATCATGTGTGAGAGGCCTGA 58.423 50.000 12.00 0.00 37.87 3.86
1173 1214 2.096030 CACGGAGAGACGTCGTCG 59.904 66.667 19.11 14.34 46.75 5.12
1806 1847 3.009192 GCCGGACCGTGACCATGTA 62.009 63.158 13.94 0.00 0.00 2.29
1914 1955 0.610174 GCTCCATCACCACAGACTCA 59.390 55.000 0.00 0.00 0.00 3.41
2022 2063 1.760086 CTGCTCCTCCATCTCCCGT 60.760 63.158 0.00 0.00 0.00 5.28
2142 2183 2.202824 TTCCGCCGCTGGTTATCG 60.203 61.111 1.97 0.00 0.00 2.92
2448 2489 2.988010 TATCTGCCTGTGCGATCTTT 57.012 45.000 0.00 0.00 41.78 2.52
2666 2708 3.737047 GCATGAAGCGTAGTGGTTAGCTA 60.737 47.826 0.00 0.00 39.25 3.32
2736 2778 7.061688 CACTAGTTGTACTCCTATAAGAGGGT 58.938 42.308 3.44 0.00 46.70 4.34
2758 2800 9.528489 TTCTTATCAAATTAGGCTTTTACCACT 57.472 29.630 0.00 0.00 0.00 4.00
2786 2831 7.136885 TCTTATATTTTGGGACAGAGGGAGTA 58.863 38.462 0.00 0.00 42.39 2.59
2787 2832 5.970640 TCTTATATTTTGGGACAGAGGGAGT 59.029 40.000 0.00 0.00 42.39 3.85
2788 2833 6.500589 TCTTATATTTTGGGACAGAGGGAG 57.499 41.667 0.00 0.00 42.39 4.30
2789 2834 5.163195 GCTCTTATATTTTGGGACAGAGGGA 60.163 44.000 0.00 0.00 42.39 4.20
2790 2835 5.066593 GCTCTTATATTTTGGGACAGAGGG 58.933 45.833 0.00 0.00 42.39 4.30
2791 2836 4.752101 CGCTCTTATATTTTGGGACAGAGG 59.248 45.833 0.00 0.00 42.39 3.69
2792 2837 4.212214 GCGCTCTTATATTTTGGGACAGAG 59.788 45.833 0.00 0.00 42.39 3.35
2793 2838 4.127171 GCGCTCTTATATTTTGGGACAGA 58.873 43.478 0.00 0.00 42.39 3.41
2794 2839 4.130118 AGCGCTCTTATATTTTGGGACAG 58.870 43.478 2.64 0.00 42.39 3.51
2795 2840 4.150897 AGCGCTCTTATATTTTGGGACA 57.849 40.909 2.64 0.00 0.00 4.02
2796 2841 5.500645 AAAGCGCTCTTATATTTTGGGAC 57.499 39.130 12.06 0.00 31.02 4.46
2797 2842 5.650266 TCAAAAGCGCTCTTATATTTTGGGA 59.350 36.000 21.76 7.05 39.90 4.37
2798 2843 5.743872 GTCAAAAGCGCTCTTATATTTTGGG 59.256 40.000 21.76 4.68 39.90 4.12
2799 2844 6.251376 GTGTCAAAAGCGCTCTTATATTTTGG 59.749 38.462 21.76 5.63 39.90 3.28
2800 2845 7.023575 AGTGTCAAAAGCGCTCTTATATTTTG 58.976 34.615 12.06 16.02 40.50 2.44
2801 2846 7.145932 AGTGTCAAAAGCGCTCTTATATTTT 57.854 32.000 12.06 2.10 31.02 1.82
2802 2847 6.743575 AGTGTCAAAAGCGCTCTTATATTT 57.256 33.333 12.06 2.98 31.02 1.40
2803 2848 6.816640 TGTAGTGTCAAAAGCGCTCTTATATT 59.183 34.615 12.06 0.00 31.02 1.28
2804 2849 6.255887 GTGTAGTGTCAAAAGCGCTCTTATAT 59.744 38.462 12.06 0.00 31.02 0.86
2805 2850 5.575606 GTGTAGTGTCAAAAGCGCTCTTATA 59.424 40.000 12.06 0.00 31.02 0.98
2806 2851 4.389077 GTGTAGTGTCAAAAGCGCTCTTAT 59.611 41.667 12.06 0.00 31.02 1.73
2807 2852 3.739300 GTGTAGTGTCAAAAGCGCTCTTA 59.261 43.478 12.06 0.00 31.02 2.10
2808 2853 2.544267 GTGTAGTGTCAAAAGCGCTCTT 59.456 45.455 12.06 0.00 0.00 2.85
2809 2854 2.135933 GTGTAGTGTCAAAAGCGCTCT 58.864 47.619 12.06 3.67 0.00 4.09
2810 2855 2.135933 AGTGTAGTGTCAAAAGCGCTC 58.864 47.619 12.06 0.00 0.00 5.03
2811 2856 2.240493 AGTGTAGTGTCAAAAGCGCT 57.760 45.000 2.64 2.64 0.00 5.92
2812 2857 3.057734 ACTAGTGTAGTGTCAAAAGCGC 58.942 45.455 0.00 0.00 37.69 5.92
2837 2882 7.123547 TCCGTCCCAAAATATAAGAGCATTTTT 59.876 33.333 0.00 0.00 33.23 1.94
2838 2883 6.605594 TCCGTCCCAAAATATAAGAGCATTTT 59.394 34.615 0.00 0.00 35.30 1.82
2839 2884 6.126409 TCCGTCCCAAAATATAAGAGCATTT 58.874 36.000 0.00 0.00 0.00 2.32
2840 2885 5.690865 TCCGTCCCAAAATATAAGAGCATT 58.309 37.500 0.00 0.00 0.00 3.56
2841 2886 5.304686 TCCGTCCCAAAATATAAGAGCAT 57.695 39.130 0.00 0.00 0.00 3.79
2842 2887 4.444306 CCTCCGTCCCAAAATATAAGAGCA 60.444 45.833 0.00 0.00 0.00 4.26
2843 2888 4.065789 CCTCCGTCCCAAAATATAAGAGC 58.934 47.826 0.00 0.00 0.00 4.09
2844 2889 4.347000 TCCCTCCGTCCCAAAATATAAGAG 59.653 45.833 0.00 0.00 0.00 2.85
2845 2890 4.300345 TCCCTCCGTCCCAAAATATAAGA 58.700 43.478 0.00 0.00 0.00 2.10
2846 2891 4.699925 TCCCTCCGTCCCAAAATATAAG 57.300 45.455 0.00 0.00 0.00 1.73
2847 2892 5.656549 ATTCCCTCCGTCCCAAAATATAA 57.343 39.130 0.00 0.00 0.00 0.98
2848 2893 6.766997 TTATTCCCTCCGTCCCAAAATATA 57.233 37.500 0.00 0.00 0.00 0.86
2849 2894 5.656549 TTATTCCCTCCGTCCCAAAATAT 57.343 39.130 0.00 0.00 0.00 1.28
2850 2895 5.453866 TTTATTCCCTCCGTCCCAAAATA 57.546 39.130 0.00 0.00 0.00 1.40
2851 2896 4.325084 TTTATTCCCTCCGTCCCAAAAT 57.675 40.909 0.00 0.00 0.00 1.82
2852 2897 3.810721 TTTATTCCCTCCGTCCCAAAA 57.189 42.857 0.00 0.00 0.00 2.44
2853 2898 3.810721 TTTTATTCCCTCCGTCCCAAA 57.189 42.857 0.00 0.00 0.00 3.28
2854 2899 5.656549 ATATTTTATTCCCTCCGTCCCAA 57.343 39.130 0.00 0.00 0.00 4.12
2855 2900 5.656549 AATATTTTATTCCCTCCGTCCCA 57.343 39.130 0.00 0.00 0.00 4.37
2856 2901 6.657966 CCTAAATATTTTATTCCCTCCGTCCC 59.342 42.308 5.91 0.00 0.00 4.46
2857 2902 6.150641 GCCTAAATATTTTATTCCCTCCGTCC 59.849 42.308 5.91 0.00 0.00 4.79
2858 2903 6.713450 TGCCTAAATATTTTATTCCCTCCGTC 59.287 38.462 5.91 0.00 0.00 4.79
2859 2904 6.607019 TGCCTAAATATTTTATTCCCTCCGT 58.393 36.000 5.91 0.00 0.00 4.69
2860 2905 7.703058 ATGCCTAAATATTTTATTCCCTCCG 57.297 36.000 5.91 0.00 0.00 4.63
2886 2931 4.574674 TTAAGCCTGACCATCTTGTGAT 57.425 40.909 0.00 0.00 0.00 3.06
2887 2932 4.574674 ATTAAGCCTGACCATCTTGTGA 57.425 40.909 0.00 0.00 0.00 3.58
2990 3076 1.227556 GGCTACACCGATGCCGATT 60.228 57.895 0.00 0.00 37.11 3.34
2999 3085 2.545526 GTGATGAATGATGGCTACACCG 59.454 50.000 0.00 0.00 43.94 4.94
3008 3094 9.681692 TTTTAACAAGAACAGTGATGAATGATG 57.318 29.630 0.00 0.00 0.00 3.07
3035 3121 2.954989 TGGTAGCTGCATGACACAAAAA 59.045 40.909 3.61 0.00 0.00 1.94
3036 3122 2.553602 CTGGTAGCTGCATGACACAAAA 59.446 45.455 3.61 0.00 0.00 2.44
3318 3405 1.367346 TGGTTACCTGGCAATCTGGA 58.633 50.000 2.07 0.00 37.82 3.86
3654 3745 2.549349 GCGACTAGTTGAGGGGTTTGAA 60.549 50.000 14.70 0.00 0.00 2.69
3685 3776 4.574674 AGCCTGACCAATTGACTAATCA 57.425 40.909 7.12 2.05 0.00 2.57
3686 3777 4.943705 TCAAGCCTGACCAATTGACTAATC 59.056 41.667 7.12 0.00 0.00 1.75
3687 3778 4.702131 GTCAAGCCTGACCAATTGACTAAT 59.298 41.667 7.12 0.00 45.41 1.73
3688 3779 4.072131 GTCAAGCCTGACCAATTGACTAA 58.928 43.478 7.12 0.00 45.41 2.24
3689 3780 3.674997 GTCAAGCCTGACCAATTGACTA 58.325 45.455 7.12 0.00 45.41 2.59
3690 3781 2.508526 GTCAAGCCTGACCAATTGACT 58.491 47.619 7.12 0.00 45.41 3.41
3691 3782 2.997485 GTCAAGCCTGACCAATTGAC 57.003 50.000 7.12 0.00 45.41 3.18
3707 3798 1.081094 TAGCGATTCGTGACGAGTCA 58.919 50.000 25.94 7.92 41.49 3.41
3752 3843 8.576442 CATAACCTCTGAGTTAAAAACATGGTT 58.424 33.333 3.66 0.00 35.90 3.67
3824 3996 2.048503 CAGCAAAGCAGCCAAGGC 60.049 61.111 2.02 2.02 42.33 4.35
4032 4211 6.072230 TGGTGCGATCAATATTTTGTTCTGAA 60.072 34.615 0.00 0.00 34.32 3.02
4036 4217 5.640732 ACTGGTGCGATCAATATTTTGTTC 58.359 37.500 0.00 0.00 34.32 3.18
4037 4218 5.643379 ACTGGTGCGATCAATATTTTGTT 57.357 34.783 0.00 0.00 34.32 2.83
4038 4219 5.643379 AACTGGTGCGATCAATATTTTGT 57.357 34.783 0.00 0.00 34.32 2.83
4039 4220 6.857964 GGATAACTGGTGCGATCAATATTTTG 59.142 38.462 0.00 0.00 0.00 2.44
4112 4294 1.737199 ACCCTGTTTAGTACCTGCCA 58.263 50.000 0.00 0.00 0.00 4.92
4115 4297 9.847224 ATATCAAATAACCCTGTTTAGTACCTG 57.153 33.333 0.00 0.00 0.00 4.00
4197 4379 6.784031 AGGAAGAAGGTTTGTGATAACTGAT 58.216 36.000 0.00 0.00 0.00 2.90
4574 4784 1.405105 GCAAGTGCCAAGTTGTCTTCA 59.595 47.619 1.45 0.00 38.73 3.02
4824 5034 2.429930 CGGTGCCTTCTGGTTGGA 59.570 61.111 0.00 0.00 35.27 3.53
4845 5055 1.303888 CCTGCTGCCTGTTGGATGT 60.304 57.895 0.00 0.00 34.57 3.06
5281 5498 4.073293 TCCTCAGTTCCTGTTCAACTTC 57.927 45.455 0.00 0.00 31.40 3.01
5295 5512 0.178831 ATCCCCAAGGGTTCCTCAGT 60.179 55.000 4.11 0.00 44.74 3.41
5297 5514 2.135189 CATATCCCCAAGGGTTCCTCA 58.865 52.381 4.11 0.00 44.74 3.86
5312 5530 9.994432 CCAGTTTAAGTTCAATTGACTCATATC 57.006 33.333 7.89 0.00 0.00 1.63
5323 5542 5.885912 ACAGACACACCAGTTTAAGTTCAAT 59.114 36.000 0.00 0.00 0.00 2.57
5338 5557 6.647067 AGCAATAAACTAGAGAACAGACACAC 59.353 38.462 0.00 0.00 0.00 3.82
5398 5619 0.963355 TCTCGCCCAAAATTTCCCCG 60.963 55.000 0.00 0.00 0.00 5.73
5487 5709 3.059352 ACCTGCTTTACAGTCACCATC 57.941 47.619 0.00 0.00 45.68 3.51
5496 5718 7.577979 CGTAAAACAAGAATACCTGCTTTACA 58.422 34.615 8.14 0.00 30.88 2.41
5529 5751 3.397317 CAGGCAAAACGCAAGCGC 61.397 61.111 15.09 0.00 45.17 5.92
5563 5786 2.111384 GTAGCCTTCATCTGGAGGACA 58.889 52.381 8.81 0.00 0.00 4.02
5568 5791 6.327365 TGATCTTTATGTAGCCTTCATCTGGA 59.673 38.462 0.00 0.00 0.00 3.86
5656 5879 0.035630 ATCAACCAGCAGAGTGGAGC 60.036 55.000 0.00 0.00 40.44 4.70
5665 5888 3.067461 GTGTTTACACCAATCAACCAGCA 59.933 43.478 1.52 0.00 40.85 4.41
5666 5889 3.638484 GTGTTTACACCAATCAACCAGC 58.362 45.455 1.52 0.00 40.85 4.85
5705 5928 5.505181 AAGCTTCAGAAATAAGAGGGTCA 57.495 39.130 0.00 0.00 0.00 4.02
5746 5969 1.548269 CCCGGAGCTTGGCAAAAATAA 59.452 47.619 0.73 0.00 0.00 1.40
5780 6003 4.951715 TCAAGGCAATCAGTCTGCATAATT 59.048 37.500 0.00 0.00 41.78 1.40
5807 6058 2.024176 TAGGCGCCATTGAACTTCTC 57.976 50.000 31.54 0.00 0.00 2.87
5815 6066 3.930336 TCATCTAAGATAGGCGCCATTG 58.070 45.455 31.54 13.26 0.00 2.82
5817 6068 4.040952 AGTTTCATCTAAGATAGGCGCCAT 59.959 41.667 31.54 19.95 0.00 4.40
5832 6083 6.318900 AGAAATAAACGATCCCCAGTTTCATC 59.681 38.462 0.00 0.11 40.54 2.92
5840 6091 6.041069 ACACAAAAAGAAATAAACGATCCCCA 59.959 34.615 0.00 0.00 0.00 4.96
5894 6158 0.464870 TGTGCTTGCTTGTTTGGCAT 59.535 45.000 0.00 0.00 39.54 4.40
5909 6173 0.322975 ATCTGTGACCTCCAGTGTGC 59.677 55.000 0.00 0.00 0.00 4.57
5910 6174 2.810274 CAAATCTGTGACCTCCAGTGTG 59.190 50.000 0.00 0.00 0.00 3.82
5912 6176 1.808945 GCAAATCTGTGACCTCCAGTG 59.191 52.381 0.00 0.00 0.00 3.66
5916 6180 1.026718 CCCGCAAATCTGTGACCTCC 61.027 60.000 0.00 0.00 34.83 4.30
5928 6192 1.198178 GCGTAAAGTTCATCCCGCAAA 59.802 47.619 0.00 0.00 40.72 3.68
5929 6193 0.800012 GCGTAAAGTTCATCCCGCAA 59.200 50.000 0.00 0.00 40.72 4.85
5930 6194 1.022451 GGCGTAAAGTTCATCCCGCA 61.022 55.000 0.00 0.00 42.63 5.69
5931 6195 0.743345 AGGCGTAAAGTTCATCCCGC 60.743 55.000 0.00 0.00 40.33 6.13
5932 6196 2.159142 AGTAGGCGTAAAGTTCATCCCG 60.159 50.000 0.00 0.00 0.00 5.14
5933 6197 3.538634 AGTAGGCGTAAAGTTCATCCC 57.461 47.619 0.00 0.00 0.00 3.85
5934 6198 4.251268 ACAAGTAGGCGTAAAGTTCATCC 58.749 43.478 0.00 0.00 0.00 3.51
5935 6199 6.589139 AGTTACAAGTAGGCGTAAAGTTCATC 59.411 38.462 0.00 0.00 29.82 2.92
5936 6200 6.461640 AGTTACAAGTAGGCGTAAAGTTCAT 58.538 36.000 0.00 0.00 29.82 2.57
5938 6202 6.587651 CAAGTTACAAGTAGGCGTAAAGTTC 58.412 40.000 0.00 0.00 29.82 3.01
5939 6203 5.049886 GCAAGTTACAAGTAGGCGTAAAGTT 60.050 40.000 0.00 0.00 29.82 2.66
5940 6204 4.450080 GCAAGTTACAAGTAGGCGTAAAGT 59.550 41.667 0.00 0.00 29.82 2.66
5941 6205 4.142966 GGCAAGTTACAAGTAGGCGTAAAG 60.143 45.833 0.00 0.00 29.82 1.85
5942 6206 3.747529 GGCAAGTTACAAGTAGGCGTAAA 59.252 43.478 0.00 0.00 29.82 2.01
5943 6207 3.328505 GGCAAGTTACAAGTAGGCGTAA 58.671 45.455 0.00 0.00 0.00 3.18
5944 6208 2.354003 GGGCAAGTTACAAGTAGGCGTA 60.354 50.000 0.00 0.00 0.00 4.42
5945 6209 1.609841 GGGCAAGTTACAAGTAGGCGT 60.610 52.381 0.00 0.00 0.00 5.68
5946 6210 1.084289 GGGCAAGTTACAAGTAGGCG 58.916 55.000 0.00 0.00 0.00 5.52
5947 6211 1.460504 GGGGCAAGTTACAAGTAGGC 58.539 55.000 0.00 0.00 0.00 3.93
5948 6212 1.633945 AGGGGGCAAGTTACAAGTAGG 59.366 52.381 0.00 0.00 0.00 3.18
5949 6213 3.681874 GCTAGGGGGCAAGTTACAAGTAG 60.682 52.174 0.00 0.00 0.00 2.57
5950 6214 2.237893 GCTAGGGGGCAAGTTACAAGTA 59.762 50.000 0.00 0.00 0.00 2.24
5951 6215 1.004394 GCTAGGGGGCAAGTTACAAGT 59.996 52.381 0.00 0.00 0.00 3.16
5965 6229 1.281287 CCCCATCATCATCTGCTAGGG 59.719 57.143 0.00 0.00 32.69 3.53
5980 6244 0.178975 TTCAACAGAAACCGCCCCAT 60.179 50.000 0.00 0.00 0.00 4.00
5981 6245 0.178975 ATTCAACAGAAACCGCCCCA 60.179 50.000 0.00 0.00 0.00 4.96
6019 6283 0.752054 TTGGCTCACTTGCTTTTGGG 59.248 50.000 0.00 0.00 0.00 4.12
6021 6285 2.582728 TGTTGGCTCACTTGCTTTTG 57.417 45.000 0.00 0.00 0.00 2.44
6025 6289 2.034124 ACATTTGTTGGCTCACTTGCT 58.966 42.857 0.00 0.00 0.00 3.91
6035 6299 1.516453 CACGTTGCGAACATTTGTTGG 59.484 47.619 0.00 0.74 38.56 3.77
6037 6301 2.446282 GACACGTTGCGAACATTTGTT 58.554 42.857 0.00 0.00 41.64 2.83
6038 6302 1.268335 GGACACGTTGCGAACATTTGT 60.268 47.619 0.00 0.00 0.00 2.83
6039 6303 1.394697 GGACACGTTGCGAACATTTG 58.605 50.000 0.00 0.00 0.00 2.32
6040 6304 0.041663 CGGACACGTTGCGAACATTT 60.042 50.000 5.92 0.00 42.80 2.32
6041 6305 1.567537 CGGACACGTTGCGAACATT 59.432 52.632 5.92 0.00 42.80 2.71
6042 6306 2.314647 CCGGACACGTTGCGAACAT 61.315 57.895 0.00 0.00 42.80 2.71
6043 6307 2.962786 CCGGACACGTTGCGAACA 60.963 61.111 0.00 0.00 42.80 3.18
6044 6308 2.935446 GACCGGACACGTTGCGAAC 61.935 63.158 9.46 3.88 42.80 3.95
6045 6309 2.659244 GACCGGACACGTTGCGAA 60.659 61.111 9.46 0.00 42.80 4.70
6046 6310 4.986587 CGACCGGACACGTTGCGA 62.987 66.667 9.46 0.00 42.80 5.10
6050 6314 4.573950 AACGCGACCGGACACGTT 62.574 61.111 23.31 23.31 43.32 3.99
6083 6347 7.078228 GTGATGTGTGAAATTTAAGAGGTGAC 58.922 38.462 0.00 0.00 0.00 3.67
6094 6358 4.402155 AGTGTGGTTGTGATGTGTGAAATT 59.598 37.500 0.00 0.00 0.00 1.82
6115 6379 9.614792 GATGTGTAAAATATAAGGGAAGTGAGT 57.385 33.333 0.00 0.00 0.00 3.41
6152 6974 9.841295 ATGAAAATGGAAATCCTCAAATTATGG 57.159 29.630 0.44 0.00 36.82 2.74


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

AutoCloner maintained by Alex Coulton.