Multiple sequence alignment - TraesCS3A01G349900

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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 TraesCS3A01G349900 chr3A 100.000 5492 0 0 1 5492 598559068 598564559 0.000000e+00 10142.0
1 TraesCS3A01G349900 chr3A 93.289 149 6 4 2736 2884 111763010 111763154 3.330000e-52 217.0
2 TraesCS3A01G349900 chr3D 90.945 2772 161 34 1 2756 455875017 455877714 0.000000e+00 3646.0
3 TraesCS3A01G349900 chr3D 94.776 1474 47 12 4041 5492 455879058 455880523 0.000000e+00 2268.0
4 TraesCS3A01G349900 chr3D 91.938 769 30 3 2883 3621 455877716 455878482 0.000000e+00 1048.0
5 TraesCS3A01G349900 chr3D 94.118 391 22 1 3623 4013 455878522 455878911 1.320000e-165 593.0
6 TraesCS3A01G349900 chr3D 100.000 128 0 0 2757 2884 67064784 67064911 2.560000e-58 237.0
7 TraesCS3A01G349900 chr3B 89.256 2811 179 51 1 2756 602359594 602362336 0.000000e+00 3404.0
8 TraesCS3A01G349900 chr3B 91.101 1562 58 30 3953 5483 602363430 602364941 0.000000e+00 2039.0
9 TraesCS3A01G349900 chr3B 92.578 768 25 5 2883 3621 602362338 602363102 0.000000e+00 1074.0
10 TraesCS3A01G349900 chr3B 93.511 262 9 3 3620 3874 602363148 602363408 3.100000e-102 383.0
11 TraesCS3A01G349900 chr3B 95.833 144 4 2 2746 2888 797464011 797463869 1.190000e-56 231.0
12 TraesCS3A01G349900 chrUn 98.507 134 2 0 2751 2884 322720543 322720410 2.560000e-58 237.0
13 TraesCS3A01G349900 chr7B 98.507 134 2 0 2752 2885 505938660 505938527 2.560000e-58 237.0
14 TraesCS3A01G349900 chr7B 96.454 141 4 1 2748 2888 141907227 141907366 1.190000e-56 231.0
15 TraesCS3A01G349900 chr1D 99.237 131 1 0 2757 2887 368493812 368493682 2.560000e-58 237.0
16 TraesCS3A01G349900 chr1B 96.454 141 3 2 2748 2887 482450482 482450621 1.190000e-56 231.0
17 TraesCS3A01G349900 chr4A 95.172 145 5 2 2741 2884 682683438 682683581 1.540000e-55 228.0
18 TraesCS3A01G349900 chr2B 95.172 145 3 2 2744 2887 547962625 547962484 5.540000e-55 226.0
19 TraesCS3A01G349900 chr2B 95.745 141 4 2 2746 2884 790694949 790695089 5.540000e-55 226.0
20 TraesCS3A01G349900 chr2B 96.947 131 3 1 2758 2888 210262827 210262698 9.260000e-53 219.0
21 TraesCS3A01G349900 chr6B 94.000 150 6 3 2758 2906 40715985 40715838 1.990000e-54 224.0
22 TraesCS3A01G349900 chr6B 94.483 145 7 1 2740 2884 18270489 18270632 7.160000e-54 222.0
23 TraesCS3A01G349900 chr5A 94.483 145 7 1 2741 2884 279670566 279670422 7.160000e-54 222.0
24 TraesCS3A01G349900 chr2A 94.483 145 7 1 2741 2884 708949027 708949171 7.160000e-54 222.0
25 TraesCS3A01G349900 chr4B 100.000 31 0 0 257 287 646120915 646120945 2.140000e-04 58.4


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 TraesCS3A01G349900 chr3A 598559068 598564559 5491 False 10142.00 10142 100.00000 1 5492 1 chr3A.!!$F2 5491
1 TraesCS3A01G349900 chr3D 455875017 455880523 5506 False 1888.75 3646 92.94425 1 5492 4 chr3D.!!$F2 5491
2 TraesCS3A01G349900 chr3B 602359594 602364941 5347 False 1725.00 3404 91.61150 1 5483 4 chr3B.!!$F1 5482

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
536 553 0.260230 ATGAGAGAGAAGCGAGGGGA 59.740 55.000 0.00 0.0 0.00 4.81 F
1145 1169 0.035056 AGGGATGCTGCTGTGTTACC 60.035 55.000 0.00 0.0 0.00 2.85 F
1618 1651 0.177141 ATGTCCATAACCACGTCCGG 59.823 55.000 0.00 0.0 0.00 5.14 F
1732 1765 0.461961 AGCACGGTTCTCCATAGCTC 59.538 55.000 0.00 0.0 32.07 4.09 F
1864 1920 1.269051 GGCCAAAACTCTTGAACACGG 60.269 52.381 0.00 0.0 0.00 4.94 F
2776 2846 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.0 44.66 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 1914 0.179936 TTTCCCCGTGTAACCGTGTT 59.820 50.0 0.00 0.00 0.00 3.32 R
2757 2827 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.0 13.64 0.00 46.06 2.59 R
2758 2828 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.0 13.64 0.00 46.06 3.85 R
2760 2830 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 R
3575 3704 0.393077 ACCTTCCTCCGTGTGACTTG 59.607 55.0 0.00 0.00 0.00 3.16 R
4620 4932 0.393077 AACTCACGTGTCTGAAGGGG 59.607 55.0 16.51 0.00 0.00 4.79 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
109 110 1.880340 GAAGTCGAGCATCCAGGCG 60.880 63.158 0.00 0.00 39.27 5.52
238 239 4.400961 AGGTTCTGCAGCGCCTCC 62.401 66.667 19.09 11.89 0.00 4.30
489 490 1.607612 GAGGCGAATTTGGGAGGGA 59.392 57.895 0.00 0.00 0.00 4.20
490 491 0.464554 GAGGCGAATTTGGGAGGGAG 60.465 60.000 0.00 0.00 0.00 4.30
502 503 3.758133 GAGGGAGGGGATGAGCGGA 62.758 68.421 0.00 0.00 0.00 5.54
528 545 1.407258 GACCGTGGGATGAGAGAGAAG 59.593 57.143 0.00 0.00 0.00 2.85
536 553 0.260230 ATGAGAGAGAAGCGAGGGGA 59.740 55.000 0.00 0.00 0.00 4.81
542 559 3.157949 GAAGCGAGGGGAGGGAGG 61.158 72.222 0.00 0.00 0.00 4.30
775 797 3.929610 AGCGCTAGAGAACACAGATTTTC 59.070 43.478 8.99 0.00 0.00 2.29
990 1014 2.990735 CGTTCGCATCTCGTGAGC 59.009 61.111 0.00 0.00 39.67 4.26
1141 1165 2.267006 CGAGGGATGCTGCTGTGT 59.733 61.111 0.00 0.00 0.00 3.72
1143 1167 0.108186 CGAGGGATGCTGCTGTGTTA 60.108 55.000 0.00 0.00 0.00 2.41
1145 1169 0.035056 AGGGATGCTGCTGTGTTACC 60.035 55.000 0.00 0.00 0.00 2.85
1189 1213 4.115199 CGGCCAAGGGGGAGAAGG 62.115 72.222 2.24 0.00 40.01 3.46
1573 1606 1.490490 TGGAAGGGGATGATACTGTGC 59.510 52.381 0.00 0.00 0.00 4.57
1618 1651 0.177141 ATGTCCATAACCACGTCCGG 59.823 55.000 0.00 0.00 0.00 5.14
1641 1674 1.872773 TTTTGGGTATTGGATGGGGC 58.127 50.000 0.00 0.00 0.00 5.80
1665 1698 1.668237 GGAAGAGGAATCTGCGCTTTC 59.332 52.381 9.73 9.28 0.00 2.62
1681 1714 1.283029 CTTTCCTCCCATTCAGCAGGA 59.717 52.381 0.00 0.00 32.94 3.86
1703 1736 3.819337 AGCTGCATGTCTATTTGCCTATG 59.181 43.478 1.02 0.00 38.08 2.23
1727 1760 3.735237 CTATGTAGCACGGTTCTCCAT 57.265 47.619 0.00 0.00 0.00 3.41
1728 1761 4.848562 CTATGTAGCACGGTTCTCCATA 57.151 45.455 0.00 0.00 0.00 2.74
1729 1762 3.735237 ATGTAGCACGGTTCTCCATAG 57.265 47.619 0.00 0.00 0.00 2.23
1730 1763 1.136305 TGTAGCACGGTTCTCCATAGC 59.864 52.381 0.00 0.00 0.00 2.97
1731 1764 1.409427 GTAGCACGGTTCTCCATAGCT 59.591 52.381 0.00 0.00 38.01 3.32
1732 1765 0.461961 AGCACGGTTCTCCATAGCTC 59.538 55.000 0.00 0.00 32.07 4.09
1762 1795 7.201600 GCTAATGGAATGAGAGAGACAGAAAAC 60.202 40.741 0.00 0.00 0.00 2.43
1857 1913 1.354368 TCCCCTAGGCCAAAACTCTTG 59.646 52.381 5.01 0.00 0.00 3.02
1858 1914 1.354368 CCCCTAGGCCAAAACTCTTGA 59.646 52.381 5.01 0.00 0.00 3.02
1862 1918 3.253432 CCTAGGCCAAAACTCTTGAACAC 59.747 47.826 5.01 0.00 0.00 3.32
1863 1919 1.676006 AGGCCAAAACTCTTGAACACG 59.324 47.619 5.01 0.00 0.00 4.49
1864 1920 1.269051 GGCCAAAACTCTTGAACACGG 60.269 52.381 0.00 0.00 0.00 4.94
1865 1921 1.404035 GCCAAAACTCTTGAACACGGT 59.596 47.619 0.00 0.00 0.00 4.83
1866 1922 2.159296 GCCAAAACTCTTGAACACGGTT 60.159 45.455 0.00 0.00 0.00 4.44
1894 1950 3.256631 GGGAAATCAGCTGCAGAGAAAAA 59.743 43.478 20.43 0.00 0.00 1.94
2025 2084 3.905784 AGCATCAAGTAACTTTGCTTGC 58.094 40.909 13.26 4.91 46.27 4.01
2056 2115 6.041523 AGCCTGTCTATTAGAAGATTCACTCC 59.958 42.308 0.00 0.00 0.00 3.85
2067 2126 6.640518 AGAAGATTCACTCCGCAACTTATTA 58.359 36.000 0.00 0.00 0.00 0.98
2079 2138 4.201724 CGCAACTTATTAGACAGTTCCTGC 60.202 45.833 0.00 0.00 34.37 4.85
2086 2145 3.935993 GACAGTTCCTGCTGGCTTA 57.064 52.632 4.42 0.00 41.18 3.09
2121 2180 4.464244 TGCTGGGCATCTCTATCACTATAC 59.536 45.833 0.00 0.00 31.71 1.47
2122 2181 4.464244 GCTGGGCATCTCTATCACTATACA 59.536 45.833 0.00 0.00 0.00 2.29
2132 2191 7.535738 TCTCTATCACTATACAAGGGAATGGA 58.464 38.462 0.00 0.00 42.28 3.41
2145 2204 6.071165 ACAAGGGAATGGATCTTCACAATTTC 60.071 38.462 0.33 0.00 30.62 2.17
2166 2225 8.644318 ATTTCGAACGCTAGACATTTACTTAT 57.356 30.769 0.00 0.00 0.00 1.73
2235 2302 4.919774 TTCTCCCCACAGCTTTTACATA 57.080 40.909 0.00 0.00 0.00 2.29
2241 2308 5.184864 TCCCCACAGCTTTTACATACATTTG 59.815 40.000 0.00 0.00 0.00 2.32
2242 2309 4.864247 CCCACAGCTTTTACATACATTTGC 59.136 41.667 0.00 0.00 0.00 3.68
2249 2316 6.430925 AGCTTTTACATACATTTGCTCAGACA 59.569 34.615 0.00 0.00 0.00 3.41
2268 2335 4.273480 AGACACGTTTGGTTTCAGATTGAG 59.727 41.667 0.00 0.00 0.00 3.02
2298 2365 5.602628 ACAGTTACTGAAGGTGAGAAAGAC 58.397 41.667 20.07 0.00 35.18 3.01
2424 2491 3.437049 CCTTTCTTCGGGAAGTTCATGAC 59.563 47.826 5.01 0.00 39.38 3.06
2488 2555 5.274015 TGTCTGATGTACCTGGTATGGTAA 58.726 41.667 10.23 0.00 43.36 2.85
2509 2576 9.109393 TGGTAACAGCTCAATATGTTTCTAATC 57.891 33.333 0.00 0.00 46.17 1.75
2518 2585 7.771183 TCAATATGTTTCTAATCACCCTTTGC 58.229 34.615 0.00 0.00 0.00 3.68
2519 2586 7.615365 TCAATATGTTTCTAATCACCCTTTGCT 59.385 33.333 0.00 0.00 0.00 3.91
2520 2587 8.902806 CAATATGTTTCTAATCACCCTTTGCTA 58.097 33.333 0.00 0.00 0.00 3.49
2547 2614 7.270579 GCACAAAGTCGTCAATTATTACTTTCC 59.729 37.037 0.00 0.00 38.08 3.13
2559 2626 9.541143 CAATTATTACTTTCCCACTTTGTTGTT 57.459 29.630 0.00 0.00 0.00 2.83
2564 2631 3.374042 TTCCCACTTTGTTGTTCTCCA 57.626 42.857 0.00 0.00 0.00 3.86
2650 2720 7.786178 TTTTGGATAAATCTATGTCACCTCG 57.214 36.000 0.00 0.00 0.00 4.63
2664 2734 3.313526 GTCACCTCGCATATGCTTCATTT 59.686 43.478 24.56 2.18 39.32 2.32
2681 2751 7.958567 TGCTTCATTTACCGTACTTTTTAATCG 59.041 33.333 0.00 0.00 0.00 3.34
2685 2755 9.368674 TCATTTACCGTACTTTTTAATCGATGA 57.631 29.630 0.00 0.00 0.00 2.92
2701 2771 5.144692 TCGATGAATTTTGGGCAAATCAA 57.855 34.783 0.00 0.00 33.60 2.57
2761 2831 3.961477 TGTGTGCACAAACATGTACTC 57.039 42.857 23.59 5.41 38.56 2.59
2762 2832 2.616376 TGTGTGCACAAACATGTACTCC 59.384 45.455 23.59 4.84 38.56 3.85
2763 2833 2.031157 GTGTGCACAAACATGTACTCCC 60.031 50.000 23.59 0.00 36.29 4.30
2764 2834 2.158682 TGTGCACAAACATGTACTCCCT 60.159 45.455 19.28 0.00 36.29 4.20
2765 2835 2.484264 GTGCACAAACATGTACTCCCTC 59.516 50.000 13.17 0.00 32.93 4.30
2766 2836 2.084546 GCACAAACATGTACTCCCTCC 58.915 52.381 0.00 0.00 0.00 4.30
2767 2837 2.346803 CACAAACATGTACTCCCTCCG 58.653 52.381 0.00 0.00 0.00 4.63
2768 2838 1.975680 ACAAACATGTACTCCCTCCGT 59.024 47.619 0.00 0.00 0.00 4.69
2769 2839 2.028385 ACAAACATGTACTCCCTCCGTC 60.028 50.000 0.00 0.00 0.00 4.79
2770 2840 1.192428 AACATGTACTCCCTCCGTCC 58.808 55.000 0.00 0.00 0.00 4.79
2771 2841 1.035932 ACATGTACTCCCTCCGTCCG 61.036 60.000 0.00 0.00 0.00 4.79
2772 2842 1.455217 ATGTACTCCCTCCGTCCGG 60.455 63.158 0.00 0.00 0.00 5.14
2773 2843 1.929860 ATGTACTCCCTCCGTCCGGA 61.930 60.000 0.00 0.00 42.90 5.14
2774 2844 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2775 2845 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2776 2846 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2777 2847 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2778 2848 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2779 2849 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2780 2850 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2781 2851 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2782 2852 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2783 2853 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2784 2854 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2785 2855 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
2786 2856 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
2787 2857 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
2788 2858 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
2789 2859 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
2790 2860 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
2791 2861 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
2792 2862 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
2793 2863 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
2794 2864 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
2795 2865 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
2803 2873 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
2804 2874 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
2805 2875 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
2806 2876 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
2807 2877 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
2808 2878 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
2811 2881 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
2817 2887 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
2825 2895 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
2847 2917 9.886132 TTAGTTCTAGATACATCCCTTTTTGTC 57.114 33.333 0.00 0.00 0.00 3.18
2848 2918 7.339482 AGTTCTAGATACATCCCTTTTTGTCC 58.661 38.462 0.00 0.00 0.00 4.02
2849 2919 6.884472 TCTAGATACATCCCTTTTTGTCCA 57.116 37.500 0.00 0.00 0.00 4.02
2850 2920 7.451731 TCTAGATACATCCCTTTTTGTCCAT 57.548 36.000 0.00 0.00 0.00 3.41
2851 2921 7.872138 TCTAGATACATCCCTTTTTGTCCATT 58.128 34.615 0.00 0.00 0.00 3.16
2852 2922 8.336235 TCTAGATACATCCCTTTTTGTCCATTT 58.664 33.333 0.00 0.00 0.00 2.32
2853 2923 7.797121 AGATACATCCCTTTTTGTCCATTTT 57.203 32.000 0.00 0.00 0.00 1.82
2854 2924 7.614494 AGATACATCCCTTTTTGTCCATTTTG 58.386 34.615 0.00 0.00 0.00 2.44
2855 2925 5.885449 ACATCCCTTTTTGTCCATTTTGA 57.115 34.783 0.00 0.00 0.00 2.69
2856 2926 6.438186 ACATCCCTTTTTGTCCATTTTGAT 57.562 33.333 0.00 0.00 0.00 2.57
2857 2927 6.232692 ACATCCCTTTTTGTCCATTTTGATG 58.767 36.000 0.00 0.00 33.80 3.07
2858 2928 6.043012 ACATCCCTTTTTGTCCATTTTGATGA 59.957 34.615 0.00 0.00 32.39 2.92
2859 2929 5.852827 TCCCTTTTTGTCCATTTTGATGAC 58.147 37.500 0.00 0.00 0.00 3.06
2860 2930 5.365025 TCCCTTTTTGTCCATTTTGATGACA 59.635 36.000 0.00 0.00 0.00 3.58
2861 2931 6.054295 CCCTTTTTGTCCATTTTGATGACAA 58.946 36.000 0.00 0.00 34.47 3.18
2862 2932 6.203338 CCCTTTTTGTCCATTTTGATGACAAG 59.797 38.462 0.00 0.00 37.13 3.16
2863 2933 6.762661 CCTTTTTGTCCATTTTGATGACAAGT 59.237 34.615 0.00 0.00 37.13 3.16
2864 2934 7.925483 CCTTTTTGTCCATTTTGATGACAAGTA 59.075 33.333 0.00 0.00 37.13 2.24
2865 2935 9.480053 CTTTTTGTCCATTTTGATGACAAGTAT 57.520 29.630 0.00 0.00 37.13 2.12
2866 2936 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
2867 2937 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
2868 2938 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
2869 2939 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
2870 2940 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
2871 2941 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
2872 2942 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
2873 2943 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
2874 2944 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2875 2945 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2876 2946 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2877 2947 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2878 2948 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2879 2949 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2880 2950 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2881 2951 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2904 2974 8.299570 GGAGTAATACCCATTTGATTATTGCTG 58.700 37.037 0.00 0.00 30.05 4.41
2948 3018 0.394192 CAGGCATATCAGAGGGCGAA 59.606 55.000 0.00 0.00 39.85 4.70
3111 3181 9.007901 TGATTGAGGTTTTTGTTGTTGATTTTT 57.992 25.926 0.00 0.00 0.00 1.94
3145 3215 4.352595 TCCCTACTCTTGTTGAATTTGGGA 59.647 41.667 0.00 0.00 37.65 4.37
3150 3220 7.447238 CCTACTCTTGTTGAATTTGGGACTTAA 59.553 37.037 0.00 0.00 0.00 1.85
3153 3223 7.038154 TCTTGTTGAATTTGGGACTTAACAG 57.962 36.000 0.00 0.00 0.00 3.16
3163 3233 3.195661 GGGACTTAACAGCTGGTATTCG 58.804 50.000 19.93 9.91 0.00 3.34
3197 3267 6.358991 TCAGGCAAATGAGATATTGTCATCA 58.641 36.000 2.82 0.00 33.34 3.07
3327 3397 6.757897 TTTCAAATAAGGCATTCAGATCGT 57.242 33.333 0.00 0.00 0.00 3.73
3381 3510 5.150715 AGCTGTGTATCATTCTCTCCCATA 58.849 41.667 0.00 0.00 0.00 2.74
3423 3552 1.380246 TGCCCTTGCATGGTCATCC 60.380 57.895 16.81 1.74 44.23 3.51
3473 3602 2.754946 TCGTGAAGGATGTACAACCC 57.245 50.000 17.87 13.17 0.00 4.11
3536 3665 1.496060 TGCTGGTATGGTCTACTGGG 58.504 55.000 0.00 0.00 0.00 4.45
3575 3704 2.415893 CGTCAAGTCATTGCCATTTCCC 60.416 50.000 0.00 0.00 36.30 3.97
3644 3820 4.084265 CCTGTTGGCTCATGTGCA 57.916 55.556 20.43 5.13 34.04 4.57
3646 3822 0.675083 CCTGTTGGCTCATGTGCAAA 59.325 50.000 20.43 13.42 34.04 3.68
3647 3823 1.274167 CCTGTTGGCTCATGTGCAAAT 59.726 47.619 20.43 0.00 34.04 2.32
3648 3824 2.602878 CTGTTGGCTCATGTGCAAATC 58.397 47.619 20.43 11.01 34.04 2.17
3732 3914 5.014123 TGTTCCTTCTGTCCCAGATGTATTT 59.986 40.000 0.00 0.00 40.39 1.40
3736 3918 5.396772 CCTTCTGTCCCAGATGTATTTGCTA 60.397 44.000 0.00 0.00 40.39 3.49
3859 4041 7.935338 ATGAAAGCATTTTGTCAAGTTACTG 57.065 32.000 0.00 0.00 39.27 2.74
3902 4084 6.642540 GCTTTTGTATTGTTTCCTCTTTCCTG 59.357 38.462 0.00 0.00 0.00 3.86
3906 4088 6.003950 TGTATTGTTTCCTCTTTCCTGAAGG 58.996 40.000 0.00 0.00 35.98 3.46
3935 4117 5.256474 AGAACTGGGTGGAATAGAAACATG 58.744 41.667 0.00 0.00 0.00 3.21
3986 4168 2.424601 ACATCCCATCAAATTGCAGACG 59.575 45.455 0.00 0.00 0.00 4.18
4009 4191 0.975887 GGGTTGTTGGGCATGACATT 59.024 50.000 0.00 0.00 0.00 2.71
4035 4240 1.456296 TCTCTTTGCGATGCTGCATT 58.544 45.000 17.36 0.09 45.78 3.56
4036 4241 1.399440 TCTCTTTGCGATGCTGCATTC 59.601 47.619 17.36 12.06 45.78 2.67
4037 4242 1.400846 CTCTTTGCGATGCTGCATTCT 59.599 47.619 17.36 0.00 45.78 2.40
4039 4244 2.352651 TCTTTGCGATGCTGCATTCTAC 59.647 45.455 17.36 7.30 45.78 2.59
4267 4568 0.961753 CAAGGTTGGTTGCTCTTCCC 59.038 55.000 0.00 0.00 0.00 3.97
4309 4610 1.003233 TCACTAGACGCTCAGGAGTCA 59.997 52.381 0.00 0.00 43.18 3.41
4322 4623 1.140816 GGAGTCAAACTGAGCGTGTC 58.859 55.000 0.00 0.00 0.00 3.67
4327 4632 3.309954 AGTCAAACTGAGCGTGTCTTTTC 59.690 43.478 0.00 0.00 0.00 2.29
4359 4664 2.039084 GGACTCGAAGGGCATATCCATT 59.961 50.000 0.00 0.00 42.38 3.16
4502 4807 5.979656 AGCCGTATCTAGGGTATCTATCT 57.020 43.478 0.00 0.00 37.77 1.98
4503 4808 5.686753 AGCCGTATCTAGGGTATCTATCTG 58.313 45.833 0.00 0.00 37.77 2.90
4504 4809 5.429109 AGCCGTATCTAGGGTATCTATCTGA 59.571 44.000 0.00 0.00 37.77 3.27
4505 4810 5.761234 GCCGTATCTAGGGTATCTATCTGAG 59.239 48.000 0.00 0.00 33.89 3.35
4506 4811 6.633127 GCCGTATCTAGGGTATCTATCTGAGT 60.633 46.154 0.00 0.00 33.89 3.41
4507 4812 7.418827 GCCGTATCTAGGGTATCTATCTGAGTA 60.419 44.444 0.00 0.00 33.89 2.59
4508 4813 8.653191 CCGTATCTAGGGTATCTATCTGAGTAT 58.347 40.741 0.00 0.00 0.00 2.12
4524 4829 5.608860 TCTGAGTATCTGTAGATCTCTGGGA 59.391 44.000 0.00 0.00 36.05 4.37
4570 4875 6.453092 ACAATATATAGGCCACGAACACTAC 58.547 40.000 5.01 0.00 0.00 2.73
4580 4885 5.447279 GGCCACGAACACTACAAGAAATATG 60.447 44.000 0.00 0.00 0.00 1.78
4586 4891 7.093640 ACGAACACTACAAGAAATATGGGTCTA 60.094 37.037 0.00 0.00 0.00 2.59
4616 4928 0.911525 TTTCCCCTCCTGCTCCTCTG 60.912 60.000 0.00 0.00 0.00 3.35
4618 4930 1.221909 TCCCCTCCTGCTCCTCTGTA 61.222 60.000 0.00 0.00 0.00 2.74
4620 4932 1.337118 CCCTCCTGCTCCTCTGTATC 58.663 60.000 0.00 0.00 0.00 2.24
4621 4933 1.337118 CCTCCTGCTCCTCTGTATCC 58.663 60.000 0.00 0.00 0.00 2.59
4624 4936 0.105246 CCTGCTCCTCTGTATCCCCT 60.105 60.000 0.00 0.00 0.00 4.79
4629 4952 2.691241 GCTCCTCTGTATCCCCTTCAGA 60.691 54.545 0.00 0.00 36.85 3.27
4653 4976 3.068024 ACGTGAGTTCCAAATGCACAATT 59.932 39.130 0.00 0.00 46.40 2.32
4657 4981 6.193761 GTGAGTTCCAAATGCACAATTTTTG 58.806 36.000 0.00 0.00 36.28 2.44
4718 5042 5.527214 TGATCTTCAAGTTACTTGGTGTGTG 59.473 40.000 22.82 8.73 41.33 3.82
4757 5081 3.002246 TGCAACTGTAGTTTCTTTGCTCG 59.998 43.478 6.22 0.00 42.48 5.03
4840 5164 7.671495 AAATGCAAAACCAAGATAATGGAAC 57.329 32.000 0.00 0.00 43.54 3.62
4890 5214 6.819649 CCATCAAATGAAACAATGCCATAGTT 59.180 34.615 0.00 0.00 0.00 2.24
4891 5215 7.201574 CCATCAAATGAAACAATGCCATAGTTG 60.202 37.037 0.00 0.00 0.00 3.16
4922 5246 8.617290 TTCTTTAGAGGTTACATTTCCAGTTC 57.383 34.615 0.00 0.00 0.00 3.01
4933 5257 6.687081 ACATTTCCAGTTCGTTGTTTTCTA 57.313 33.333 0.00 0.00 0.00 2.10
4945 5269 6.655062 TCGTTGTTTTCTACTTGCAATAGTG 58.345 36.000 0.00 0.00 0.00 2.74
4951 5275 7.499563 TGTTTTCTACTTGCAATAGTGTACCAA 59.500 33.333 0.00 0.00 0.00 3.67
4957 5281 6.503524 ACTTGCAATAGTGTACCAAGTTTTG 58.496 36.000 0.00 0.00 42.26 2.44
5004 5328 6.824553 ACTTCTATTTCATCATCTGCTAGCA 58.175 36.000 18.22 18.22 0.00 3.49
5092 5416 7.173390 GCTTTTGAGAGTAACTTATGTTGGAGT 59.827 37.037 4.33 0.00 37.59 3.85
5315 5639 0.036164 TCATCCCACAACAACCCTCG 59.964 55.000 0.00 0.00 0.00 4.63
5397 5721 9.498176 GGACTAAACAGAACCATTCTAGTAAAA 57.502 33.333 0.00 0.00 38.11 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.701780 CGTCGACCTCCAGTCCCTG 61.702 68.421 10.58 0.00 43.08 4.45
489 490 4.888325 CCCCTCCGCTCATCCCCT 62.888 72.222 0.00 0.00 0.00 4.79
490 491 4.880426 TCCCCTCCGCTCATCCCC 62.880 72.222 0.00 0.00 0.00 4.81
502 503 2.365635 CATCCCACGGTCTCCCCT 60.366 66.667 0.00 0.00 0.00 4.79
536 553 0.401395 TGTCAACAACTCCCCTCCCT 60.401 55.000 0.00 0.00 0.00 4.20
542 559 1.002544 CTCTCCCTGTCAACAACTCCC 59.997 57.143 0.00 0.00 0.00 4.30
544 561 1.609320 GCCTCTCCCTGTCAACAACTC 60.609 57.143 0.00 0.00 0.00 3.01
775 797 5.852282 AAAACCGATAAATGGAAGGATGG 57.148 39.130 0.00 0.00 0.00 3.51
1126 1150 0.035056 GGTAACACAGCAGCATCCCT 60.035 55.000 0.00 0.00 0.00 4.20
1395 1419 1.110518 CGAGGAGGAAGTAGGAGCCC 61.111 65.000 0.00 0.00 0.00 5.19
1618 1651 3.450817 CCCCATCCAATACCCAAAAAGAC 59.549 47.826 0.00 0.00 0.00 3.01
1641 1674 1.399791 GCGCAGATTCCTCTTCCTTTG 59.600 52.381 0.30 0.00 0.00 2.77
1665 1698 1.153005 GCTCCTGCTGAATGGGAGG 60.153 63.158 9.78 0.00 44.76 4.30
1681 1714 2.431954 AGGCAAATAGACATGCAGCT 57.568 45.000 0.00 0.00 44.32 4.24
1706 1739 1.136305 TGGAGAACCGTGCTACATAGC 59.864 52.381 3.84 3.84 43.54 2.97
1713 1746 0.461961 GAGCTATGGAGAACCGTGCT 59.538 55.000 0.00 0.00 39.94 4.40
1716 1749 2.297597 GCATAGAGCTATGGAGAACCGT 59.702 50.000 16.76 0.00 42.32 4.83
1717 1750 2.953020 GCATAGAGCTATGGAGAACCG 58.047 52.381 16.76 0.00 42.32 4.44
1729 1762 6.035368 TCTCTCATTCCATTAGCATAGAGC 57.965 41.667 0.00 0.00 46.19 4.09
1730 1763 7.039853 TGTCTCTCTCATTCCATTAGCATAGAG 60.040 40.741 0.00 0.00 0.00 2.43
1731 1764 6.779539 TGTCTCTCTCATTCCATTAGCATAGA 59.220 38.462 0.00 0.00 0.00 1.98
1732 1765 6.990798 TGTCTCTCTCATTCCATTAGCATAG 58.009 40.000 0.00 0.00 0.00 2.23
1762 1795 0.321122 GAGTGGGAGCTGGTGACAAG 60.321 60.000 0.00 0.00 42.06 3.16
1814 1868 7.442666 GGGAAATGAATTCTAAGCTAGTACTGG 59.557 40.741 5.39 3.15 38.18 4.00
1857 1913 0.249826 TTCCCCGTGTAACCGTGTTC 60.250 55.000 0.00 0.00 0.00 3.18
1858 1914 0.179936 TTTCCCCGTGTAACCGTGTT 59.820 50.000 0.00 0.00 0.00 3.32
1862 1918 1.365699 CTGATTTCCCCGTGTAACCG 58.634 55.000 0.00 0.00 0.00 4.44
1863 1919 1.092348 GCTGATTTCCCCGTGTAACC 58.908 55.000 0.00 0.00 0.00 2.85
1864 1920 1.737793 CAGCTGATTTCCCCGTGTAAC 59.262 52.381 8.42 0.00 0.00 2.50
1865 1921 1.948611 GCAGCTGATTTCCCCGTGTAA 60.949 52.381 20.43 0.00 0.00 2.41
1866 1922 0.392461 GCAGCTGATTTCCCCGTGTA 60.392 55.000 20.43 0.00 0.00 2.90
2025 2084 5.136828 TCTTCTAATAGACAGGCTCCTGAG 58.863 45.833 21.75 8.10 46.30 3.35
2033 2092 6.442952 CGGAGTGAATCTTCTAATAGACAGG 58.557 44.000 0.00 0.00 0.00 4.00
2041 2100 4.537135 AGTTGCGGAGTGAATCTTCTAA 57.463 40.909 0.00 0.00 0.00 2.10
2099 2158 4.464244 TGTATAGTGATAGAGATGCCCAGC 59.536 45.833 0.00 0.00 0.00 4.85
2103 2162 5.717178 TCCCTTGTATAGTGATAGAGATGCC 59.283 44.000 0.00 0.00 0.00 4.40
2121 2180 5.927281 AATTGTGAAGATCCATTCCCTTG 57.073 39.130 0.00 0.00 0.00 3.61
2122 2181 5.126061 CGAAATTGTGAAGATCCATTCCCTT 59.874 40.000 0.00 0.00 0.00 3.95
2132 2191 5.062308 GTCTAGCGTTCGAAATTGTGAAGAT 59.938 40.000 0.00 0.00 0.00 2.40
2145 2204 6.142480 CCTCATAAGTAAATGTCTAGCGTTCG 59.858 42.308 0.00 0.00 0.00 3.95
2166 2225 3.029483 TGCAATATGCCAAATCCCTCA 57.971 42.857 0.00 0.00 44.23 3.86
2196 2255 4.391830 GGAGAAATGCTCATGTTGTTCGTA 59.608 41.667 0.00 0.00 45.81 3.43
2198 2257 3.426695 GGGAGAAATGCTCATGTTGTTCG 60.427 47.826 0.00 0.00 45.81 3.95
2235 2302 2.033299 CCAAACGTGTCTGAGCAAATGT 59.967 45.455 0.00 0.00 0.00 2.71
2241 2308 1.668751 TGAAACCAAACGTGTCTGAGC 59.331 47.619 0.00 0.00 28.99 4.26
2242 2309 3.194861 TCTGAAACCAAACGTGTCTGAG 58.805 45.455 0.00 0.00 33.10 3.35
2249 2316 3.945285 ACACTCAATCTGAAACCAAACGT 59.055 39.130 0.00 0.00 0.00 3.99
2268 2335 4.051922 CACCTTCAGTAACTGTCTCACAC 58.948 47.826 0.00 0.00 32.61 3.82
2298 2365 1.247567 ATTTCCACGGCTTCAAGGTG 58.752 50.000 0.00 0.00 0.00 4.00
2424 2491 1.591059 CCTGCGGATCTCTTGAGCG 60.591 63.158 0.00 0.00 0.00 5.03
2488 2555 6.543831 GGGTGATTAGAAACATATTGAGCTGT 59.456 38.462 0.00 0.00 0.00 4.40
2502 2569 4.261801 GTGCTAGCAAAGGGTGATTAGAA 58.738 43.478 21.29 0.00 0.00 2.10
2509 2576 2.712057 CTTTGTGCTAGCAAAGGGTG 57.288 50.000 21.29 4.20 46.81 4.61
2518 2585 8.186178 AGTAATAATTGACGACTTTGTGCTAG 57.814 34.615 0.00 0.00 0.00 3.42
2519 2586 8.542497 AAGTAATAATTGACGACTTTGTGCTA 57.458 30.769 0.00 0.00 0.00 3.49
2520 2587 7.435068 AAGTAATAATTGACGACTTTGTGCT 57.565 32.000 0.00 0.00 0.00 4.40
2547 2614 8.055279 ACATTATATGGAGAACAACAAAGTGG 57.945 34.615 0.00 0.00 33.60 4.00
2650 2720 5.924475 AGTACGGTAAATGAAGCATATGC 57.076 39.130 20.36 20.36 42.49 3.14
2677 2747 5.732633 TGATTTGCCCAAAATTCATCGATT 58.267 33.333 0.00 0.00 38.64 3.34
2678 2748 5.341872 TGATTTGCCCAAAATTCATCGAT 57.658 34.783 0.00 0.00 38.64 3.59
2727 2797 5.244755 TGTGCACACAAGCTATATTCTGAA 58.755 37.500 17.42 0.00 38.56 3.02
2756 2826 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
2757 2827 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2758 2828 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2759 2829 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2760 2830 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2761 2831 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2762 2832 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2763 2833 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
2764 2834 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
2765 2835 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
2766 2836 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
2767 2837 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
2768 2838 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
2769 2839 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
2770 2840 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
2777 2847 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
2778 2848 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
2779 2849 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
2780 2850 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
2781 2851 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
2782 2852 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
2785 2855 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
2791 2861 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
2799 2869 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
2821 2891 9.886132 GACAAAAAGGGATGTATCTAGAACTAA 57.114 33.333 0.00 0.00 0.00 2.24
2822 2892 8.483758 GGACAAAAAGGGATGTATCTAGAACTA 58.516 37.037 0.00 0.00 0.00 2.24
2823 2893 7.037586 TGGACAAAAAGGGATGTATCTAGAACT 60.038 37.037 0.00 0.00 0.00 3.01
2824 2894 7.110155 TGGACAAAAAGGGATGTATCTAGAAC 58.890 38.462 0.00 0.00 0.00 3.01
2825 2895 7.265599 TGGACAAAAAGGGATGTATCTAGAA 57.734 36.000 0.00 0.00 0.00 2.10
2826 2896 6.884472 TGGACAAAAAGGGATGTATCTAGA 57.116 37.500 0.00 0.00 0.00 2.43
2827 2897 8.525290 AAATGGACAAAAAGGGATGTATCTAG 57.475 34.615 0.00 0.00 0.00 2.43
2828 2898 8.748412 CAAAATGGACAAAAAGGGATGTATCTA 58.252 33.333 0.00 0.00 0.00 1.98
2829 2899 7.454380 TCAAAATGGACAAAAAGGGATGTATCT 59.546 33.333 0.00 0.00 0.00 1.98
2830 2900 7.610865 TCAAAATGGACAAAAAGGGATGTATC 58.389 34.615 0.00 0.00 0.00 2.24
2831 2901 7.552050 TCAAAATGGACAAAAAGGGATGTAT 57.448 32.000 0.00 0.00 0.00 2.29
2832 2902 6.985653 TCAAAATGGACAAAAAGGGATGTA 57.014 33.333 0.00 0.00 0.00 2.29
2833 2903 5.885449 TCAAAATGGACAAAAAGGGATGT 57.115 34.783 0.00 0.00 0.00 3.06
2834 2904 6.369615 GTCATCAAAATGGACAAAAAGGGATG 59.630 38.462 0.00 0.00 33.42 3.51
2835 2905 6.043012 TGTCATCAAAATGGACAAAAAGGGAT 59.957 34.615 0.00 0.00 33.42 3.85
2836 2906 5.365025 TGTCATCAAAATGGACAAAAAGGGA 59.635 36.000 0.00 0.00 33.42 4.20
2837 2907 5.609423 TGTCATCAAAATGGACAAAAAGGG 58.391 37.500 0.00 0.00 33.42 3.95
2838 2908 6.762661 ACTTGTCATCAAAATGGACAAAAAGG 59.237 34.615 7.70 0.11 34.98 3.11
2839 2909 7.775397 ACTTGTCATCAAAATGGACAAAAAG 57.225 32.000 7.70 0.11 34.98 2.27
2840 2910 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
2841 2911 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
2842 2912 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
2843 2913 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
2844 2914 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
2845 2915 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
2846 2916 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
2847 2917 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
2848 2918 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
2849 2919 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2850 2920 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2851 2921 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2852 2922 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2853 2923 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2854 2924 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2855 2925 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2856 2926 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2857 2927 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2858 2928 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2859 2929 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2860 2930 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2861 2931 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2862 2932 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2863 2933 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2864 2934 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2865 2935 1.631405 TTACTCCCTCCGTCCGAAAA 58.369 50.000 0.00 0.00 0.00 2.29
2866 2936 1.856629 ATTACTCCCTCCGTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
2867 2937 2.301346 GTATTACTCCCTCCGTCCGAA 58.699 52.381 0.00 0.00 0.00 4.30
2868 2938 1.477558 GGTATTACTCCCTCCGTCCGA 60.478 57.143 0.00 0.00 0.00 4.55
2869 2939 0.957362 GGTATTACTCCCTCCGTCCG 59.043 60.000 0.00 0.00 0.00 4.79
2870 2940 1.336131 GGGTATTACTCCCTCCGTCC 58.664 60.000 0.00 0.00 41.58 4.79
2871 2941 2.077687 TGGGTATTACTCCCTCCGTC 57.922 55.000 2.65 0.00 44.84 4.79
2872 2942 2.789323 ATGGGTATTACTCCCTCCGT 57.211 50.000 2.65 0.00 44.84 4.69
2873 2943 3.389983 TCAAATGGGTATTACTCCCTCCG 59.610 47.826 2.65 0.00 44.84 4.63
2874 2944 5.584551 ATCAAATGGGTATTACTCCCTCC 57.415 43.478 2.65 0.00 44.84 4.30
2875 2945 9.014297 CAATAATCAAATGGGTATTACTCCCTC 57.986 37.037 2.65 0.00 44.84 4.30
2876 2946 7.451566 GCAATAATCAAATGGGTATTACTCCCT 59.548 37.037 2.65 0.00 44.84 4.20
2877 2947 7.451566 AGCAATAATCAAATGGGTATTACTCCC 59.548 37.037 0.00 0.00 44.81 4.30
2878 2948 8.299570 CAGCAATAATCAAATGGGTATTACTCC 58.700 37.037 0.00 0.00 0.00 3.85
2879 2949 9.066892 TCAGCAATAATCAAATGGGTATTACTC 57.933 33.333 0.00 0.00 0.00 2.59
2880 2950 8.995027 TCAGCAATAATCAAATGGGTATTACT 57.005 30.769 0.00 0.00 0.00 2.24
2881 2951 9.630098 CATCAGCAATAATCAAATGGGTATTAC 57.370 33.333 0.00 0.00 0.00 1.89
2900 2970 5.361571 ACAAAATAGCATTGATCCATCAGCA 59.638 36.000 4.22 0.00 38.19 4.41
2904 2974 9.585099 TGTTTAACAAAATAGCATTGATCCATC 57.415 29.630 0.00 0.00 0.00 3.51
2948 3018 1.508088 GTGCAATAGCCTGCGCTTT 59.492 52.632 9.73 0.00 45.55 3.51
3031 3101 5.230942 AGTAACGTTCTTTCACATCTCTGG 58.769 41.667 2.82 0.00 0.00 3.86
3111 3181 7.716123 TCAACAAGAGTAGGGAACGAATAAAAA 59.284 33.333 0.00 0.00 0.00 1.94
3113 3183 6.761312 TCAACAAGAGTAGGGAACGAATAAA 58.239 36.000 0.00 0.00 0.00 1.40
3114 3184 6.349243 TCAACAAGAGTAGGGAACGAATAA 57.651 37.500 0.00 0.00 0.00 1.40
3115 3185 5.988310 TCAACAAGAGTAGGGAACGAATA 57.012 39.130 0.00 0.00 0.00 1.75
3119 3189 5.334879 CCAAATTCAACAAGAGTAGGGAACG 60.335 44.000 0.00 0.00 0.00 3.95
3121 3191 5.076873 CCCAAATTCAACAAGAGTAGGGAA 58.923 41.667 0.00 0.00 34.98 3.97
3145 3215 2.236395 AGCCGAATACCAGCTGTTAAGT 59.764 45.455 13.81 5.75 34.99 2.24
3150 3220 1.003118 TGAAAGCCGAATACCAGCTGT 59.997 47.619 13.81 3.45 36.84 4.40
3153 3223 3.128589 TGAAATGAAAGCCGAATACCAGC 59.871 43.478 0.00 0.00 0.00 4.85
3197 3267 0.811616 GCCTGAGGCGAACATCGAAT 60.812 55.000 8.16 0.00 43.74 3.34
3225 3295 9.716531 ATTACTGACCTTAACTAGTTGGTTTAC 57.283 33.333 18.56 6.83 32.30 2.01
3327 3397 8.593679 CAACTACCAACTATGTATATCATGGGA 58.406 37.037 0.00 0.00 38.98 4.37
3473 3602 5.356751 TCCATTGTCCAGGATTAATTTGTCG 59.643 40.000 0.00 0.00 0.00 4.35
3536 3665 1.812571 ACGAATGATGAAGCACCAACC 59.187 47.619 0.00 0.00 0.00 3.77
3575 3704 0.393077 ACCTTCCTCCGTGTGACTTG 59.607 55.000 0.00 0.00 0.00 3.16
3646 3822 9.860393 ACATAACCTATTAAGAATCCTAGGGAT 57.140 33.333 9.46 0.00 45.46 3.85
3658 3840 8.612619 CCTGCAAACAGTACATAACCTATTAAG 58.387 37.037 0.00 0.00 42.81 1.85
3732 3914 2.093890 CCACAGCAATCACCAATAGCA 58.906 47.619 0.00 0.00 0.00 3.49
3736 3918 2.762327 GGAATCCACAGCAATCACCAAT 59.238 45.455 0.00 0.00 0.00 3.16
3803 3985 6.922247 ACTGCATCAAGATAGTTCATGAAG 57.078 37.500 8.80 0.00 33.64 3.02
3821 4003 7.395190 AATGCTTTCATACTATTGAACTGCA 57.605 32.000 12.93 12.93 43.28 4.41
3883 4065 5.416013 CCCTTCAGGAAAGAGGAAACAATAC 59.584 44.000 0.00 0.00 37.12 1.89
3884 4066 5.570320 CCCTTCAGGAAAGAGGAAACAATA 58.430 41.667 0.00 0.00 37.12 1.90
3902 4084 2.369394 CACCCAGTTCTATTGCCCTTC 58.631 52.381 0.00 0.00 0.00 3.46
3906 4088 2.507407 TTCCACCCAGTTCTATTGCC 57.493 50.000 0.00 0.00 0.00 4.52
3935 4117 9.382275 ACCATCTGTTCAATTTTATTTTATGCC 57.618 29.630 0.00 0.00 0.00 4.40
3980 4162 1.008538 CAACAACCCAAGCGTCTGC 60.009 57.895 0.00 0.00 43.24 4.26
3986 4168 1.004679 CATGCCCAACAACCCAAGC 60.005 57.895 0.00 0.00 0.00 4.01
4009 4191 4.794329 GCAGCATCGCAAAGAGATAGTCTA 60.794 45.833 0.00 0.00 32.65 2.59
4035 4240 4.993705 AGTGGGGAACAAAATCAGTAGA 57.006 40.909 0.00 0.00 0.00 2.59
4036 4241 4.827284 ACAAGTGGGGAACAAAATCAGTAG 59.173 41.667 0.00 0.00 0.00 2.57
4037 4242 4.798882 ACAAGTGGGGAACAAAATCAGTA 58.201 39.130 0.00 0.00 0.00 2.74
4039 4244 4.827284 AGTACAAGTGGGGAACAAAATCAG 59.173 41.667 0.00 0.00 0.00 2.90
4263 4564 4.648762 TGCAAAGATTCACAAAGAAGGGAA 59.351 37.500 0.00 0.00 40.15 3.97
4267 4568 6.267817 TGAACTGCAAAGATTCACAAAGAAG 58.732 36.000 0.00 0.00 40.15 2.85
4309 4610 1.947456 GGGAAAAGACACGCTCAGTTT 59.053 47.619 0.00 0.00 0.00 2.66
4322 4623 3.198872 GAGTCCTGCGAATAGGGAAAAG 58.801 50.000 0.00 0.00 38.42 2.27
4327 4632 0.744874 TTCGAGTCCTGCGAATAGGG 59.255 55.000 0.00 0.00 42.17 3.53
4502 4807 5.913946 TCCCAGAGATCTACAGATACTCA 57.086 43.478 0.00 0.60 34.31 3.41
4570 4875 9.790344 AAAGATGATCTAGACCCATATTTCTTG 57.210 33.333 17.16 0.00 29.09 3.02
4616 4928 1.822990 TCACGTGTCTGAAGGGGATAC 59.177 52.381 16.51 0.00 0.00 2.24
4618 4930 0.898320 CTCACGTGTCTGAAGGGGAT 59.102 55.000 16.51 0.00 0.00 3.85
4620 4932 0.393077 AACTCACGTGTCTGAAGGGG 59.607 55.000 16.51 0.00 0.00 4.79
4621 4933 1.605712 GGAACTCACGTGTCTGAAGGG 60.606 57.143 16.51 0.00 0.00 3.95
4624 4936 2.971660 TTGGAACTCACGTGTCTGAA 57.028 45.000 16.51 1.11 0.00 3.02
4629 4952 1.333619 GTGCATTTGGAACTCACGTGT 59.666 47.619 16.51 0.00 0.00 4.49
4718 5042 6.037172 ACAGTTGCATAAGTATTCAATCGTCC 59.963 38.462 0.00 0.00 0.00 4.79
4757 5081 1.069358 GGAGACCGATCACTCATTCCC 59.931 57.143 11.70 0.00 35.17 3.97
4840 5164 7.595502 GGTTCGTGTAGTCTTCCTGATATTATG 59.404 40.741 0.00 0.00 0.00 1.90
4851 5175 5.637810 TCATTTGATGGTTCGTGTAGTCTTC 59.362 40.000 0.00 0.00 0.00 2.87
4890 5214 5.633655 TGTAACCTCTAAAGAAACACCCA 57.366 39.130 0.00 0.00 0.00 4.51
4891 5215 7.309012 GGAAATGTAACCTCTAAAGAAACACCC 60.309 40.741 0.00 0.00 0.00 4.61
4922 5246 6.427150 ACACTATTGCAAGTAGAAAACAACG 58.573 36.000 17.40 0.00 0.00 4.10
4933 5257 6.320164 TCAAAACTTGGTACACTATTGCAAGT 59.680 34.615 4.94 0.00 39.29 3.16
4951 5275 4.965814 TCTCATGAGAGCAAGTCAAAACT 58.034 39.130 21.67 0.00 41.81 2.66
4957 5281 6.204495 AGTTCTTTTTCTCATGAGAGCAAGTC 59.796 38.462 28.37 23.94 41.81 3.01
5092 5416 9.578576 AAGCCTGATCTTTTATGCTCATTTATA 57.421 29.630 0.00 0.00 0.00 0.98
5397 5721 6.899089 ACAATGTTCTTTCCCTTTCCATTTT 58.101 32.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.