Multiple sequence alignment - TraesCS3D01G243700

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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 TraesCS3D01G243700 chr3D 100.000 2996 0 0 1 2996 338944505 338947500 0.000000e+00 5533.0
1 TraesCS3D01G243700 chr3D 90.327 703 43 7 1 678 571896684 571895982 0.000000e+00 898.0
2 TraesCS3D01G243700 chr3B 95.267 1310 48 8 734 2035 437509704 437511007 0.000000e+00 2063.0
3 TraesCS3D01G243700 chr3B 92.070 681 23 10 1 658 670158299 670158971 0.000000e+00 929.0
4 TraesCS3D01G243700 chr3B 90.332 693 49 9 1 675 721032682 721031990 0.000000e+00 893.0
5 TraesCS3D01G243700 chr3B 88.429 700 56 14 1 675 688290201 688289502 0.000000e+00 821.0
6 TraesCS3D01G243700 chr3B 89.494 514 30 5 2397 2898 437512679 437513180 1.960000e-176 628.0
7 TraesCS3D01G243700 chr3B 86.328 256 18 5 2563 2813 437513110 437513353 2.290000e-66 263.0
8 TraesCS3D01G243700 chr3B 93.642 173 6 1 2063 2235 437512519 437512686 1.380000e-63 254.0
9 TraesCS3D01G243700 chr3B 89.535 86 1 1 2911 2996 437512915 437512992 5.280000e-18 102.0
10 TraesCS3D01G243700 chr3B 97.917 48 1 0 2949 2996 437513191 437513238 1.910000e-12 84.2
11 TraesCS3D01G243700 chr3A 91.875 1477 49 20 706 2155 465822187 465820755 0.000000e+00 1997.0
12 TraesCS3D01G243700 chrUn 96.110 694 11 3 1 679 89948932 89949624 0.000000e+00 1118.0
13 TraesCS3D01G243700 chr2D 96.450 676 22 2 1 675 632659583 632660257 0.000000e+00 1114.0
14 TraesCS3D01G243700 chr2D 96.557 668 15 3 1 660 547943366 547942699 0.000000e+00 1099.0
15 TraesCS3D01G243700 chr2D 91.667 168 7 4 2234 2394 586594861 586595028 3.000000e-55 226.0
16 TraesCS3D01G243700 chr7D 96.064 686 19 3 1 679 22989584 22990268 0.000000e+00 1110.0
17 TraesCS3D01G243700 chr7D 90.533 169 9 5 2235 2396 526381891 526382059 1.810000e-52 217.0
18 TraesCS3D01G243700 chr7D 85.185 162 3 5 2235 2396 568399865 568400005 2.410000e-31 147.0
19 TraesCS3D01G243700 chr6A 94.583 683 27 4 1 675 610648805 610649485 0.000000e+00 1048.0
20 TraesCS3D01G243700 chr6A 96.741 491 15 1 1 490 608519689 608519199 0.000000e+00 817.0
21 TraesCS3D01G243700 chr4B 91.702 699 26 12 1 675 150987833 150987143 0.000000e+00 941.0
22 TraesCS3D01G243700 chr2B 91.716 676 33 6 3 675 760250712 760250057 0.000000e+00 917.0
23 TraesCS3D01G243700 chr1D 91.667 168 7 4 2236 2396 439594301 439594134 3.000000e-55 226.0
24 TraesCS3D01G243700 chr6D 93.233 133 9 0 2272 2404 450009724 450009856 2.360000e-46 196.0
25 TraesCS3D01G243700 chr6D 96.875 32 1 0 2232 2263 166763723 166763754 2.000000e-03 54.7
26 TraesCS3D01G243700 chr5A 77.011 174 25 12 2235 2397 622229723 622229554 5.320000e-13 86.1
27 TraesCS3D01G243700 chr5A 97.500 40 1 0 1486 1525 47584997 47584958 5.360000e-08 69.4
28 TraesCS3D01G243700 chr5D 80.909 110 16 4 1417 1525 59215437 59215332 6.880000e-12 82.4
29 TraesCS3D01G243700 chr1B 74.771 218 36 13 1345 1554 606494061 606494267 2.480000e-11 80.5
30 TraesCS3D01G243700 chr5B 75.862 174 27 11 2234 2396 467139699 467139530 1.150000e-09 75.0
31 TraesCS3D01G243700 chr5B 97.500 40 1 0 1486 1525 72082947 72082986 5.360000e-08 69.4
32 TraesCS3D01G243700 chr5B 87.037 54 1 3 2236 2283 373527375 373527322 4.170000e-04 56.5
33 TraesCS3D01G243700 chr5B 76.923 117 14 9 2235 2341 561695776 561695889 2.000000e-03 54.7
34 TraesCS3D01G243700 chr6B 75.460 163 27 9 2236 2396 380549915 380549764 1.930000e-07 67.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G243700 chr3D 338944505 338947500 2995 False 5533.0 5533 100.0000 1 2996 1 chr3D.!!$F1 2995
1 TraesCS3D01G243700 chr3D 571895982 571896684 702 True 898.0 898 90.3270 1 678 1 chr3D.!!$R1 677
2 TraesCS3D01G243700 chr3B 670158299 670158971 672 False 929.0 929 92.0700 1 658 1 chr3B.!!$F1 657
3 TraesCS3D01G243700 chr3B 721031990 721032682 692 True 893.0 893 90.3320 1 675 1 chr3B.!!$R2 674
4 TraesCS3D01G243700 chr3B 688289502 688290201 699 True 821.0 821 88.4290 1 675 1 chr3B.!!$R1 674
5 TraesCS3D01G243700 chr3B 437509704 437513353 3649 False 565.7 2063 92.0305 734 2996 6 chr3B.!!$F2 2262
6 TraesCS3D01G243700 chr3A 465820755 465822187 1432 True 1997.0 1997 91.8750 706 2155 1 chr3A.!!$R1 1449
7 TraesCS3D01G243700 chrUn 89948932 89949624 692 False 1118.0 1118 96.1100 1 679 1 chrUn.!!$F1 678
8 TraesCS3D01G243700 chr2D 632659583 632660257 674 False 1114.0 1114 96.4500 1 675 1 chr2D.!!$F2 674
9 TraesCS3D01G243700 chr2D 547942699 547943366 667 True 1099.0 1099 96.5570 1 660 1 chr2D.!!$R1 659
10 TraesCS3D01G243700 chr7D 22989584 22990268 684 False 1110.0 1110 96.0640 1 679 1 chr7D.!!$F1 678
11 TraesCS3D01G243700 chr6A 610648805 610649485 680 False 1048.0 1048 94.5830 1 675 1 chr6A.!!$F1 674
12 TraesCS3D01G243700 chr4B 150987143 150987833 690 True 941.0 941 91.7020 1 675 1 chr4B.!!$R1 674
13 TraesCS3D01G243700 chr2B 760250057 760250712 655 True 917.0 917 91.7160 3 675 1 chr2B.!!$R1 672

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
896 958 0.033796 ACATGGGAAGTGCATGGGAG 60.034 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2390 3944 0.034059 ACTTCACTTCGGCTCAGTGG 59.966 55.0 11.66 1.82 41.83 4.0 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
368 389 0.764890 ATAGGGCTGCCATTTAGCGA 59.235 50.000 22.05 0.00 42.03 4.93
441 494 1.985116 GAACGAGAGGGTCTGGCCT 60.985 63.158 3.32 0.00 37.43 5.19
556 610 1.061711 CGAAGGAGCAGAATTCTTGCG 59.938 52.381 4.86 0.00 0.00 4.85
557 611 0.807496 AAGGAGCAGAATTCTTGCGC 59.193 50.000 18.33 18.33 0.00 6.09
636 692 1.892474 GCACAAGGCCAAGTTTCCATA 59.108 47.619 5.01 0.00 36.11 2.74
643 699 4.086457 AGGCCAAGTTTCCATATTTTCGT 58.914 39.130 5.01 0.00 0.00 3.85
661 717 5.676532 TTCGTTGAATGTACGGTTTTCAT 57.323 34.783 0.00 0.00 39.38 2.57
675 731 7.113658 ACGGTTTTCATCAGATATGTACTCT 57.886 36.000 0.00 0.00 0.00 3.24
678 734 9.133627 CGGTTTTCATCAGATATGTACTCTATG 57.866 37.037 0.00 0.00 0.00 2.23
684 740 9.579932 TCATCAGATATGTACTCTATGACAAGT 57.420 33.333 0.00 0.00 0.00 3.16
685 741 9.623350 CATCAGATATGTACTCTATGACAAGTG 57.377 37.037 0.00 0.00 0.00 3.16
686 742 8.980481 TCAGATATGTACTCTATGACAAGTGA 57.020 34.615 0.00 0.00 0.00 3.41
687 743 8.841300 TCAGATATGTACTCTATGACAAGTGAC 58.159 37.037 0.00 0.00 0.00 3.67
688 744 8.624776 CAGATATGTACTCTATGACAAGTGACA 58.375 37.037 0.00 0.00 0.00 3.58
689 745 9.190317 AGATATGTACTCTATGACAAGTGACAA 57.810 33.333 0.00 0.00 0.00 3.18
690 746 9.803315 GATATGTACTCTATGACAAGTGACAAA 57.197 33.333 0.00 0.00 0.00 2.83
691 747 7.891183 ATGTACTCTATGACAAGTGACAAAC 57.109 36.000 0.00 0.00 0.00 2.93
692 748 6.811954 TGTACTCTATGACAAGTGACAAACA 58.188 36.000 0.00 0.00 0.00 2.83
693 749 7.441836 TGTACTCTATGACAAGTGACAAACAT 58.558 34.615 0.00 0.00 0.00 2.71
694 750 7.931407 TGTACTCTATGACAAGTGACAAACATT 59.069 33.333 0.00 0.00 0.00 2.71
695 751 7.426929 ACTCTATGACAAGTGACAAACATTC 57.573 36.000 0.00 0.00 0.00 2.67
696 752 6.992123 ACTCTATGACAAGTGACAAACATTCA 59.008 34.615 0.00 0.00 0.00 2.57
697 753 7.498900 ACTCTATGACAAGTGACAAACATTCAA 59.501 33.333 0.00 0.00 0.00 2.69
698 754 7.639039 TCTATGACAAGTGACAAACATTCAAC 58.361 34.615 0.00 0.00 0.00 3.18
699 755 5.635417 TGACAAGTGACAAACATTCAACA 57.365 34.783 0.00 0.00 0.00 3.33
700 756 6.206395 TGACAAGTGACAAACATTCAACAT 57.794 33.333 0.00 0.00 0.00 2.71
701 757 6.035217 TGACAAGTGACAAACATTCAACATG 58.965 36.000 0.00 0.00 0.00 3.21
702 758 5.350633 ACAAGTGACAAACATTCAACATGG 58.649 37.500 0.00 0.00 0.00 3.66
703 759 5.126869 ACAAGTGACAAACATTCAACATGGA 59.873 36.000 0.00 0.00 0.00 3.41
704 760 5.443185 AGTGACAAACATTCAACATGGAG 57.557 39.130 0.00 0.00 0.00 3.86
705 761 5.132502 AGTGACAAACATTCAACATGGAGA 58.867 37.500 0.00 0.00 0.00 3.71
706 762 5.240183 AGTGACAAACATTCAACATGGAGAG 59.760 40.000 0.00 0.00 0.00 3.20
707 763 5.009010 GTGACAAACATTCAACATGGAGAGT 59.991 40.000 0.00 0.00 0.00 3.24
708 764 5.593909 TGACAAACATTCAACATGGAGAGTT 59.406 36.000 0.00 0.00 0.00 3.01
709 765 6.076981 ACAAACATTCAACATGGAGAGTTC 57.923 37.500 0.00 0.00 0.00 3.01
712 768 5.954296 ACATTCAACATGGAGAGTTCTTG 57.046 39.130 0.00 0.00 0.00 3.02
790 851 2.921754 CGATTACGCGTTCTTTCCTTCT 59.078 45.455 20.78 0.00 0.00 2.85
866 928 4.985538 TCCAAACTTGCCTCTTCAATACT 58.014 39.130 0.00 0.00 0.00 2.12
867 929 6.121776 TCCAAACTTGCCTCTTCAATACTA 57.878 37.500 0.00 0.00 0.00 1.82
868 930 5.938125 TCCAAACTTGCCTCTTCAATACTAC 59.062 40.000 0.00 0.00 0.00 2.73
896 958 0.033796 ACATGGGAAGTGCATGGGAG 60.034 55.000 0.00 0.00 0.00 4.30
1006 1075 2.721167 CCTCCGTTCTCGATGGCCA 61.721 63.158 8.56 8.56 39.71 5.36
1073 1142 2.835431 CTGCGGGGTCGAGGAGAT 60.835 66.667 0.00 0.00 39.00 2.75
1077 1146 3.551407 GGGGTCGAGGAGATGCCC 61.551 72.222 0.00 0.00 37.37 5.36
1079 1148 2.501610 GGTCGAGGAGATGCCCAC 59.498 66.667 0.00 0.00 37.37 4.61
1554 1623 1.523095 GTCAAGATATGCGACTTCGGC 59.477 52.381 0.02 0.00 40.23 5.54
1807 1876 1.229082 TGGCCGTCCTACAACTCCT 60.229 57.895 0.00 0.00 0.00 3.69
1939 2008 3.691744 CTCCTCTCCTGCGACGCAC 62.692 68.421 20.50 0.00 33.79 5.34
1952 2021 2.432456 CGCACGCAAGAGGCTGTA 60.432 61.111 0.00 0.00 41.67 2.74
1953 2022 1.811266 CGCACGCAAGAGGCTGTAT 60.811 57.895 0.00 0.00 41.67 2.29
1958 2027 2.182842 GCAAGAGGCTGTATGCGGG 61.183 63.158 0.00 0.00 44.05 6.13
1962 2031 1.220749 GAGGCTGTATGCGGGTGAA 59.779 57.895 0.00 0.00 44.05 3.18
2003 2072 3.371965 TCACCACCAACTAGATAGGACC 58.628 50.000 0.00 0.00 0.00 4.46
2018 2087 1.301479 GACCACGCTCCGGAAACTT 60.301 57.895 5.23 0.00 0.00 2.66
2035 2104 3.764885 ACTTTGATTTGATAGCGTGCC 57.235 42.857 0.00 0.00 0.00 5.01
2036 2105 2.095853 ACTTTGATTTGATAGCGTGCCG 59.904 45.455 0.00 0.00 0.00 5.69
2039 2108 1.286501 GATTTGATAGCGTGCCGACA 58.713 50.000 0.00 0.00 0.00 4.35
2058 2127 2.347452 ACAAACGTTCTTGTGTCGACAG 59.653 45.455 20.73 7.81 38.12 3.51
2126 3680 1.201629 GGAATTGTCGACGTTCGTTCG 60.202 52.381 20.39 5.30 41.35 3.95
2129 3683 2.050985 GTCGACGTTCGTTCGGGT 60.051 61.111 0.00 0.00 41.35 5.28
2158 3712 4.569943 ACTTGTGCTCGTTACTTCATCAT 58.430 39.130 0.00 0.00 0.00 2.45
2159 3713 5.720202 ACTTGTGCTCGTTACTTCATCATA 58.280 37.500 0.00 0.00 0.00 2.15
2160 3714 5.577164 ACTTGTGCTCGTTACTTCATCATAC 59.423 40.000 0.00 0.00 0.00 2.39
2161 3715 5.324784 TGTGCTCGTTACTTCATCATACT 57.675 39.130 0.00 0.00 0.00 2.12
2162 3716 5.102313 TGTGCTCGTTACTTCATCATACTG 58.898 41.667 0.00 0.00 0.00 2.74
2197 3751 2.961768 CGGCCATGTGTTTGGGTC 59.038 61.111 2.24 0.00 37.24 4.46
2207 3761 0.753479 TGTTTGGGTCGTGGCACATT 60.753 50.000 19.09 0.00 44.52 2.71
2235 3789 1.448985 TTGTATCCACAAGCCGAAGC 58.551 50.000 0.00 0.00 39.75 3.86
2236 3790 0.323302 TGTATCCACAAGCCGAAGCA 59.677 50.000 0.00 0.00 43.56 3.91
2237 3791 1.009829 GTATCCACAAGCCGAAGCAG 58.990 55.000 0.00 0.00 43.56 4.24
2238 3792 0.744414 TATCCACAAGCCGAAGCAGC 60.744 55.000 0.00 0.00 43.56 5.25
2239 3793 4.093952 CCACAAGCCGAAGCAGCG 62.094 66.667 0.00 0.00 43.56 5.18
2291 3845 3.203161 GGCGTGAGACCATTTTTCTTC 57.797 47.619 0.00 0.00 0.00 2.87
2292 3846 2.412847 GGCGTGAGACCATTTTTCTTCG 60.413 50.000 0.00 0.00 0.00 3.79
2293 3847 2.223377 GCGTGAGACCATTTTTCTTCGT 59.777 45.455 0.00 0.00 0.00 3.85
2294 3848 3.303791 GCGTGAGACCATTTTTCTTCGTT 60.304 43.478 0.00 0.00 0.00 3.85
2295 3849 4.084223 GCGTGAGACCATTTTTCTTCGTTA 60.084 41.667 0.00 0.00 0.00 3.18
2296 3850 5.559417 GCGTGAGACCATTTTTCTTCGTTAA 60.559 40.000 0.00 0.00 0.00 2.01
2297 3851 5.844396 CGTGAGACCATTTTTCTTCGTTAAC 59.156 40.000 0.00 0.00 0.00 2.01
2298 3852 6.292703 CGTGAGACCATTTTTCTTCGTTAACT 60.293 38.462 3.71 0.00 0.00 2.24
2299 3853 6.851330 GTGAGACCATTTTTCTTCGTTAACTG 59.149 38.462 3.71 0.00 0.00 3.16
2300 3854 6.540914 TGAGACCATTTTTCTTCGTTAACTGT 59.459 34.615 3.71 0.00 0.00 3.55
2301 3855 7.711772 TGAGACCATTTTTCTTCGTTAACTGTA 59.288 33.333 3.71 0.00 0.00 2.74
2302 3856 8.084590 AGACCATTTTTCTTCGTTAACTGTAG 57.915 34.615 3.71 1.54 0.00 2.74
2303 3857 6.665465 ACCATTTTTCTTCGTTAACTGTAGC 58.335 36.000 3.71 0.00 0.00 3.58
2304 3858 5.788531 CCATTTTTCTTCGTTAACTGTAGCG 59.211 40.000 3.71 0.00 35.47 4.26
2305 3859 6.347079 CCATTTTTCTTCGTTAACTGTAGCGA 60.347 38.462 3.71 0.00 40.63 4.93
2306 3860 6.586868 TTTTTCTTCGTTAACTGTAGCGAA 57.413 33.333 3.71 11.43 46.52 4.70
2307 3861 5.565723 TTTCTTCGTTAACTGTAGCGAAC 57.434 39.130 3.71 0.00 44.70 3.95
2308 3862 4.227512 TCTTCGTTAACTGTAGCGAACA 57.772 40.909 3.71 0.00 44.70 3.18
2322 3876 4.294416 AGCGAACAGTATAGCTACAGTG 57.706 45.455 5.27 5.27 38.29 3.66
2323 3877 3.695060 AGCGAACAGTATAGCTACAGTGT 59.305 43.478 6.67 6.67 38.29 3.55
2324 3878 3.791887 GCGAACAGTATAGCTACAGTGTG 59.208 47.826 13.14 3.41 29.06 3.82
2325 3879 4.674623 GCGAACAGTATAGCTACAGTGTGT 60.675 45.833 13.14 4.19 29.06 3.72
2326 3880 5.448225 GCGAACAGTATAGCTACAGTGTGTA 60.448 44.000 13.14 0.00 29.06 2.90
2327 3881 6.726230 CGAACAGTATAGCTACAGTGTGTAT 58.274 40.000 13.14 0.00 31.66 2.29
2328 3882 7.519488 GCGAACAGTATAGCTACAGTGTGTATA 60.519 40.741 13.14 2.25 31.66 1.47
2329 3883 7.797587 CGAACAGTATAGCTACAGTGTGTATAC 59.202 40.741 13.14 13.38 31.66 1.47
2330 3884 8.515695 AACAGTATAGCTACAGTGTGTATACA 57.484 34.615 13.14 0.08 31.66 2.29
2331 3885 8.155821 ACAGTATAGCTACAGTGTGTATACAG 57.844 38.462 11.70 18.76 37.52 2.74
2332 3886 7.774157 ACAGTATAGCTACAGTGTGTATACAGT 59.226 37.037 11.70 19.15 41.09 3.55
2333 3887 8.283992 CAGTATAGCTACAGTGTGTATACAGTC 58.716 40.741 21.97 2.54 38.40 3.51
2334 3888 8.212312 AGTATAGCTACAGTGTGTATACAGTCT 58.788 37.037 21.97 4.93 38.40 3.24
2335 3889 9.486497 GTATAGCTACAGTGTGTATACAGTCTA 57.514 37.037 5.62 0.68 38.40 2.59
2336 3890 6.680874 AGCTACAGTGTGTATACAGTCTAC 57.319 41.667 5.62 3.84 38.40 2.59
2337 3891 6.178324 AGCTACAGTGTGTATACAGTCTACA 58.822 40.000 5.62 0.00 38.40 2.74
2338 3892 6.316640 AGCTACAGTGTGTATACAGTCTACAG 59.683 42.308 5.62 8.69 38.40 2.74
2339 3893 6.093771 GCTACAGTGTGTATACAGTCTACAGT 59.906 42.308 5.62 8.78 38.40 3.55
2340 3894 6.255596 ACAGTGTGTATACAGTCTACAGTG 57.744 41.667 19.24 19.24 44.27 3.66
2341 3895 5.096169 CAGTGTGTATACAGTCTACAGTGC 58.904 45.833 5.62 0.00 38.40 4.40
2342 3896 5.010933 AGTGTGTATACAGTCTACAGTGCT 58.989 41.667 5.62 0.00 35.58 4.40
2343 3897 5.477291 AGTGTGTATACAGTCTACAGTGCTT 59.523 40.000 5.62 0.00 35.58 3.91
2344 3898 5.573282 GTGTGTATACAGTCTACAGTGCTTG 59.427 44.000 5.62 0.00 37.52 4.01
2345 3899 5.475564 TGTGTATACAGTCTACAGTGCTTGA 59.524 40.000 5.62 0.00 30.07 3.02
2346 3900 6.015772 TGTGTATACAGTCTACAGTGCTTGAA 60.016 38.462 5.62 0.00 30.07 2.69
2347 3901 6.528423 GTGTATACAGTCTACAGTGCTTGAAG 59.472 42.308 5.62 0.00 30.07 3.02
2348 3902 5.984695 ATACAGTCTACAGTGCTTGAAGA 57.015 39.130 0.00 0.00 0.00 2.87
2349 3903 3.983741 ACAGTCTACAGTGCTTGAAGAC 58.016 45.455 0.00 0.00 0.00 3.01
2350 3904 3.639094 ACAGTCTACAGTGCTTGAAGACT 59.361 43.478 0.00 0.00 35.81 3.24
2351 3905 3.986572 CAGTCTACAGTGCTTGAAGACTG 59.013 47.826 17.99 17.99 44.38 3.51
2352 3906 2.734079 GTCTACAGTGCTTGAAGACTGC 59.266 50.000 18.26 5.25 42.90 4.40
2353 3907 2.072298 CTACAGTGCTTGAAGACTGCC 58.928 52.381 18.26 0.00 42.90 4.85
2354 3908 0.471617 ACAGTGCTTGAAGACTGCCT 59.528 50.000 18.26 4.41 42.90 4.75
2355 3909 0.873054 CAGTGCTTGAAGACTGCCTG 59.127 55.000 10.33 0.00 33.61 4.85
2356 3910 0.250640 AGTGCTTGAAGACTGCCTGG 60.251 55.000 0.00 0.00 0.00 4.45
2357 3911 1.073722 TGCTTGAAGACTGCCTGGG 59.926 57.895 0.00 0.00 0.00 4.45
2358 3912 1.376466 GCTTGAAGACTGCCTGGGA 59.624 57.895 0.00 0.00 0.00 4.37
2359 3913 0.957888 GCTTGAAGACTGCCTGGGAC 60.958 60.000 0.00 0.00 0.00 4.46
2360 3914 0.671781 CTTGAAGACTGCCTGGGACG 60.672 60.000 0.00 0.00 0.00 4.79
2361 3915 2.111999 TTGAAGACTGCCTGGGACGG 62.112 60.000 0.00 0.00 0.00 4.79
2362 3916 3.959991 GAAGACTGCCTGGGACGGC 62.960 68.421 0.00 0.00 45.44 5.68
2369 3923 3.775654 CCTGGGACGGCCTGAGTC 61.776 72.222 7.57 0.01 37.86 3.36
2374 3928 2.435059 GACGGCCTGAGTCCTTGC 60.435 66.667 0.00 0.00 32.78 4.01
2375 3929 3.959991 GACGGCCTGAGTCCTTGCC 62.960 68.421 0.00 4.93 40.54 4.52
2376 3930 4.785453 CGGCCTGAGTCCTTGCCC 62.785 72.222 0.00 0.00 40.87 5.36
2377 3931 4.432741 GGCCTGAGTCCTTGCCCC 62.433 72.222 0.00 0.00 37.94 5.80
2378 3932 3.650950 GCCTGAGTCCTTGCCCCA 61.651 66.667 0.00 0.00 0.00 4.96
2379 3933 2.673523 CCTGAGTCCTTGCCCCAG 59.326 66.667 0.00 0.00 0.00 4.45
2380 3934 2.045536 CTGAGTCCTTGCCCCAGC 60.046 66.667 0.00 0.00 40.48 4.85
2381 3935 3.635268 CTGAGTCCTTGCCCCAGCC 62.635 68.421 0.00 0.00 38.69 4.85
2382 3936 3.334054 GAGTCCTTGCCCCAGCCT 61.334 66.667 0.00 0.00 38.69 4.58
2383 3937 3.635268 GAGTCCTTGCCCCAGCCTG 62.635 68.421 0.00 0.00 38.69 4.85
2384 3938 4.748144 GTCCTTGCCCCAGCCTGG 62.748 72.222 2.91 2.91 38.69 4.45
2500 4054 6.146898 ACCGTAGAATCCAAATTTGTTTTCG 58.853 36.000 16.73 13.63 0.00 3.46
2524 4078 4.322080 TTGGCTATTCATCTGTAGTCCG 57.678 45.455 0.00 0.00 0.00 4.79
2560 4114 0.394352 ATTTTGCTCGAAGCCCCGAT 60.394 50.000 4.73 0.00 41.51 4.18
2626 4180 0.610174 TGAGCTCATCCACACCACTC 59.390 55.000 13.74 0.00 0.00 3.51
2628 4182 0.322975 AGCTCATCCACACCACTCAC 59.677 55.000 0.00 0.00 0.00 3.51
2725 4291 1.616187 GGGTTACCTTTTGGGAGAGCC 60.616 57.143 0.00 0.00 46.08 4.70
2735 4301 2.439156 GGAGAGCCCGCAATGCTT 60.439 61.111 2.94 0.00 39.69 3.91
2766 4332 3.713902 AGGGCGCCTCAAATGATAG 57.286 52.632 28.56 0.00 0.00 2.08
2767 4333 1.131638 AGGGCGCCTCAAATGATAGA 58.868 50.000 28.56 0.00 0.00 1.98
2772 4338 2.799412 GCGCCTCAAATGATAGAGTGAG 59.201 50.000 0.00 0.00 37.77 3.51
2780 4346 8.175925 CTCAAATGATAGAGTGAGGAGTGATA 57.824 38.462 0.00 0.00 35.01 2.15
2791 4357 4.574013 GTGAGGAGTGATATTTGCAAGAGG 59.426 45.833 0.00 0.00 0.00 3.69
2803 4369 6.909550 ATTTGCAAGAGGTAACCATTAACA 57.090 33.333 0.00 0.00 37.17 2.41
2811 4377 9.357652 CAAGAGGTAACCATTAACATGATTTTG 57.642 33.333 0.00 0.00 31.07 2.44
2827 4393 1.327303 TTTGACCAAGCGGCAAAGAT 58.673 45.000 1.45 0.00 35.05 2.40
2831 4397 0.328258 ACCAAGCGGCAAAGATACCT 59.672 50.000 1.45 0.00 34.57 3.08
2851 4417 2.599216 GCGAGGAGCTACATGAAGC 58.401 57.895 0.00 0.00 44.04 3.86
2864 4430 2.039480 ACATGAAGCTGTGTGGATGAGT 59.961 45.455 0.00 0.00 0.00 3.41
2878 4444 2.359900 GATGAGTTCATCCACACCACC 58.640 52.381 10.36 0.00 45.24 4.61
2884 4450 1.742880 CATCCACACCACCGAGCTG 60.743 63.158 0.00 0.00 0.00 4.24
2885 4451 1.913262 ATCCACACCACCGAGCTGA 60.913 57.895 0.00 0.00 0.00 4.26
2887 4453 2.357517 CACACCACCGAGCTGACC 60.358 66.667 0.00 0.00 0.00 4.02
2889 4455 2.425592 CACCACCGAGCTGACCAA 59.574 61.111 0.00 0.00 0.00 3.67
2890 4456 1.003355 CACCACCGAGCTGACCAAT 60.003 57.895 0.00 0.00 0.00 3.16
2891 4457 1.003355 ACCACCGAGCTGACCAATG 60.003 57.895 0.00 0.00 0.00 2.82
2892 4458 1.003355 CCACCGAGCTGACCAATGT 60.003 57.895 0.00 0.00 0.00 2.71
2893 4459 0.606401 CCACCGAGCTGACCAATGTT 60.606 55.000 0.00 0.00 0.00 2.71
2894 4460 1.238439 CACCGAGCTGACCAATGTTT 58.762 50.000 0.00 0.00 0.00 2.83
2895 4461 1.608590 CACCGAGCTGACCAATGTTTT 59.391 47.619 0.00 0.00 0.00 2.43
2896 4462 2.034558 CACCGAGCTGACCAATGTTTTT 59.965 45.455 0.00 0.00 0.00 1.94
2927 4493 7.479980 TGAGACAAACCAATGTAGTTCTTTTG 58.520 34.615 0.00 0.00 32.57 2.44
2947 4513 1.967779 GTGGCTTATTTGGGGTTGTGT 59.032 47.619 0.00 0.00 0.00 3.72
2948 4514 1.967066 TGGCTTATTTGGGGTTGTGTG 59.033 47.619 0.00 0.00 0.00 3.82
2949 4515 1.275010 GGCTTATTTGGGGTTGTGTGG 59.725 52.381 0.00 0.00 0.00 4.17
2950 4516 1.275010 GCTTATTTGGGGTTGTGTGGG 59.725 52.381 0.00 0.00 0.00 4.61
2951 4517 2.604139 CTTATTTGGGGTTGTGTGGGT 58.396 47.619 0.00 0.00 0.00 4.51
2952 4518 2.777459 TATTTGGGGTTGTGTGGGTT 57.223 45.000 0.00 0.00 0.00 4.11
2953 4519 1.127343 ATTTGGGGTTGTGTGGGTTG 58.873 50.000 0.00 0.00 0.00 3.77
2954 4520 0.252284 TTTGGGGTTGTGTGGGTTGT 60.252 50.000 0.00 0.00 0.00 3.32
2955 4521 0.972983 TTGGGGTTGTGTGGGTTGTG 60.973 55.000 0.00 0.00 0.00 3.33
2992 4558 5.412286 CCCAAATAAGCCACAAAAGAATTGG 59.588 40.000 0.00 0.00 34.73 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
368 389 4.081198 GTGATTCCTCTCTGGTGATTGTCT 60.081 45.833 0.00 0.00 37.07 3.41
441 494 2.022754 GCTAGGGTTAGGAGACGAGCA 61.023 57.143 0.00 0.00 0.00 4.26
556 610 6.216750 TGTACAAATTGCAAATTAAACCGC 57.783 33.333 1.71 0.00 0.00 5.68
557 611 7.330700 AGGATGTACAAATTGCAAATTAAACCG 59.669 33.333 1.71 0.00 0.00 4.44
636 692 6.496571 TGAAAACCGTACATTCAACGAAAAT 58.503 32.000 0.00 0.00 42.90 1.82
643 699 8.611757 CATATCTGATGAAAACCGTACATTCAA 58.388 33.333 0.00 0.00 36.72 2.69
661 717 8.841300 GTCACTTGTCATAGAGTACATATCTGA 58.159 37.037 0.00 0.00 0.00 3.27
675 731 7.326968 TGTTGAATGTTTGTCACTTGTCATA 57.673 32.000 0.00 0.00 0.00 2.15
678 734 5.459762 CCATGTTGAATGTTTGTCACTTGTC 59.540 40.000 0.00 0.00 0.00 3.18
679 735 5.126869 TCCATGTTGAATGTTTGTCACTTGT 59.873 36.000 0.00 0.00 0.00 3.16
680 736 5.590145 TCCATGTTGAATGTTTGTCACTTG 58.410 37.500 0.00 0.00 0.00 3.16
681 737 5.593909 TCTCCATGTTGAATGTTTGTCACTT 59.406 36.000 0.00 0.00 0.00 3.16
682 738 5.132502 TCTCCATGTTGAATGTTTGTCACT 58.867 37.500 0.00 0.00 0.00 3.41
683 739 5.009010 ACTCTCCATGTTGAATGTTTGTCAC 59.991 40.000 0.00 0.00 0.00 3.67
684 740 5.132502 ACTCTCCATGTTGAATGTTTGTCA 58.867 37.500 0.00 0.00 0.00 3.58
685 741 5.695851 ACTCTCCATGTTGAATGTTTGTC 57.304 39.130 0.00 0.00 0.00 3.18
686 742 5.829924 AGAACTCTCCATGTTGAATGTTTGT 59.170 36.000 0.00 0.00 0.00 2.83
687 743 6.323203 AGAACTCTCCATGTTGAATGTTTG 57.677 37.500 0.00 0.00 0.00 2.93
688 744 6.736794 GCAAGAACTCTCCATGTTGAATGTTT 60.737 38.462 0.00 0.00 0.00 2.83
689 745 5.278660 GCAAGAACTCTCCATGTTGAATGTT 60.279 40.000 0.00 0.00 0.00 2.71
690 746 4.217118 GCAAGAACTCTCCATGTTGAATGT 59.783 41.667 0.00 0.00 0.00 2.71
691 747 4.458295 AGCAAGAACTCTCCATGTTGAATG 59.542 41.667 0.00 0.00 0.00 2.67
692 748 4.458295 CAGCAAGAACTCTCCATGTTGAAT 59.542 41.667 0.00 0.00 0.00 2.57
693 749 3.817084 CAGCAAGAACTCTCCATGTTGAA 59.183 43.478 0.00 0.00 0.00 2.69
694 750 3.071457 TCAGCAAGAACTCTCCATGTTGA 59.929 43.478 0.00 0.00 31.23 3.18
695 751 3.405831 TCAGCAAGAACTCTCCATGTTG 58.594 45.455 0.00 0.00 0.00 3.33
696 752 3.672808 CTCAGCAAGAACTCTCCATGTT 58.327 45.455 0.00 0.00 0.00 2.71
697 753 2.614987 GCTCAGCAAGAACTCTCCATGT 60.615 50.000 0.00 0.00 0.00 3.21
698 754 2.008329 GCTCAGCAAGAACTCTCCATG 58.992 52.381 0.00 0.00 0.00 3.66
699 755 1.065564 GGCTCAGCAAGAACTCTCCAT 60.066 52.381 0.00 0.00 0.00 3.41
700 756 0.322975 GGCTCAGCAAGAACTCTCCA 59.677 55.000 0.00 0.00 0.00 3.86
701 757 0.322975 TGGCTCAGCAAGAACTCTCC 59.677 55.000 0.00 0.00 0.00 3.71
702 758 1.675415 CCTGGCTCAGCAAGAACTCTC 60.675 57.143 1.09 0.00 29.58 3.20
703 759 0.324285 CCTGGCTCAGCAAGAACTCT 59.676 55.000 1.09 0.00 29.58 3.24
704 760 0.036022 ACCTGGCTCAGCAAGAACTC 59.964 55.000 1.09 0.00 29.58 3.01
705 761 1.352083 TACCTGGCTCAGCAAGAACT 58.648 50.000 1.09 0.00 29.58 3.01
706 762 2.079925 CTTACCTGGCTCAGCAAGAAC 58.920 52.381 1.09 0.00 29.58 3.01
707 763 1.003580 CCTTACCTGGCTCAGCAAGAA 59.996 52.381 1.09 0.00 29.58 2.52
708 764 0.615331 CCTTACCTGGCTCAGCAAGA 59.385 55.000 1.09 0.00 29.58 3.02
709 765 0.393537 CCCTTACCTGGCTCAGCAAG 60.394 60.000 0.00 0.00 0.00 4.01
712 768 2.258748 GACCCCTTACCTGGCTCAGC 62.259 65.000 0.00 0.00 0.00 4.26
770 831 4.267214 GGTAGAAGGAAAGAACGCGTAATC 59.733 45.833 14.46 7.68 0.00 1.75
777 838 2.603953 GTCCGGTAGAAGGAAAGAACG 58.396 52.381 0.00 0.00 39.84 3.95
866 928 5.894964 TGCACTTCCCATGTATACTACTGTA 59.105 40.000 4.17 0.00 0.00 2.74
867 929 4.714802 TGCACTTCCCATGTATACTACTGT 59.285 41.667 4.17 0.00 0.00 3.55
868 930 5.276461 TGCACTTCCCATGTATACTACTG 57.724 43.478 4.17 0.00 0.00 2.74
896 958 2.726351 CGTGAGAGGGGAGAAGGCC 61.726 68.421 0.00 0.00 0.00 5.19
1006 1075 2.625823 CGGCTTGGGCACAAACGAT 61.626 57.895 17.68 0.00 38.52 3.73
1058 1127 4.593864 GCATCTCCTCGACCCCGC 62.594 72.222 0.00 0.00 35.37 6.13
1077 1146 2.603473 TCCTCGTGGTCCCAGGTG 60.603 66.667 2.99 3.90 33.97 4.00
1079 1148 2.283966 AGTCCTCGTGGTCCCAGG 60.284 66.667 2.99 0.00 34.23 4.45
1554 1623 4.131376 GACATGGACATGGCGAGG 57.869 61.111 15.94 0.00 42.91 4.63
1783 1852 1.255667 TTGTAGGACGGCCAGGAGAC 61.256 60.000 11.69 0.00 36.29 3.36
1962 2031 2.739996 CCATGGAAGCTCGAGGGCT 61.740 63.158 15.58 3.56 45.30 5.19
2003 2072 1.156736 ATCAAAGTTTCCGGAGCGTG 58.843 50.000 3.34 6.40 0.00 5.34
2036 2105 2.346244 TGTCGACACAAGAACGTTTGTC 59.654 45.455 15.76 17.11 39.17 3.18
2039 2108 2.601763 GTCTGTCGACACAAGAACGTTT 59.398 45.455 15.76 0.00 39.98 3.60
2054 2123 5.641209 ACAGAAATATTGCAGTCTGTCTGTC 59.359 40.000 12.87 0.00 45.88 3.51
2058 2127 5.814705 AGCTACAGAAATATTGCAGTCTGTC 59.185 40.000 19.11 9.80 45.88 3.51
2138 3692 5.576774 CAGTATGATGAAGTAACGAGCACAA 59.423 40.000 0.00 0.00 39.69 3.33
2158 3712 5.451381 CCGCACTTCCTATTGATGTACAGTA 60.451 44.000 0.33 0.00 30.69 2.74
2159 3713 4.433615 CGCACTTCCTATTGATGTACAGT 58.566 43.478 0.33 0.00 30.69 3.55
2160 3714 3.804325 CCGCACTTCCTATTGATGTACAG 59.196 47.826 0.33 0.00 30.69 2.74
2161 3715 3.792401 CCGCACTTCCTATTGATGTACA 58.208 45.455 0.00 0.00 30.69 2.90
2162 3716 2.544267 GCCGCACTTCCTATTGATGTAC 59.456 50.000 0.00 0.00 30.69 2.90
2197 3751 2.068837 AAAGCATTCAATGTGCCACG 57.931 45.000 0.00 0.00 43.50 4.94
2266 3820 3.628646 AATGGTCTCACGCCCCTGC 62.629 63.158 0.00 0.00 0.00 4.85
2267 3821 0.609131 AAAATGGTCTCACGCCCCTG 60.609 55.000 0.00 0.00 0.00 4.45
2268 3822 0.112412 AAAAATGGTCTCACGCCCCT 59.888 50.000 0.00 0.00 0.00 4.79
2269 3823 0.526211 GAAAAATGGTCTCACGCCCC 59.474 55.000 0.00 0.00 0.00 5.80
2270 3824 1.534729 AGAAAAATGGTCTCACGCCC 58.465 50.000 0.00 0.00 0.00 6.13
2271 3825 2.412847 CGAAGAAAAATGGTCTCACGCC 60.413 50.000 0.00 0.00 0.00 5.68
2272 3826 2.223377 ACGAAGAAAAATGGTCTCACGC 59.777 45.455 0.00 0.00 32.15 5.34
2273 3827 4.468095 AACGAAGAAAAATGGTCTCACG 57.532 40.909 0.00 0.00 33.84 4.35
2274 3828 6.851330 CAGTTAACGAAGAAAAATGGTCTCAC 59.149 38.462 0.00 0.00 0.00 3.51
2275 3829 6.540914 ACAGTTAACGAAGAAAAATGGTCTCA 59.459 34.615 0.00 0.00 0.00 3.27
2276 3830 6.956047 ACAGTTAACGAAGAAAAATGGTCTC 58.044 36.000 0.00 0.00 0.00 3.36
2277 3831 6.937436 ACAGTTAACGAAGAAAAATGGTCT 57.063 33.333 0.00 0.00 0.00 3.85
2278 3832 6.795593 GCTACAGTTAACGAAGAAAAATGGTC 59.204 38.462 0.00 0.00 0.00 4.02
2279 3833 6.565247 CGCTACAGTTAACGAAGAAAAATGGT 60.565 38.462 0.00 0.00 0.00 3.55
2280 3834 5.788531 CGCTACAGTTAACGAAGAAAAATGG 59.211 40.000 0.00 0.00 0.00 3.16
2281 3835 6.586751 TCGCTACAGTTAACGAAGAAAAATG 58.413 36.000 0.00 0.00 0.00 2.32
2282 3836 6.774354 TCGCTACAGTTAACGAAGAAAAAT 57.226 33.333 0.00 0.00 0.00 1.82
2283 3837 6.035866 TGTTCGCTACAGTTAACGAAGAAAAA 59.964 34.615 0.00 0.00 44.29 1.94
2284 3838 5.519566 TGTTCGCTACAGTTAACGAAGAAAA 59.480 36.000 0.00 0.00 44.29 2.29
2285 3839 5.042593 TGTTCGCTACAGTTAACGAAGAAA 58.957 37.500 0.00 0.00 44.29 2.52
2286 3840 4.609947 TGTTCGCTACAGTTAACGAAGAA 58.390 39.130 0.00 0.00 44.29 2.52
2287 3841 4.227512 TGTTCGCTACAGTTAACGAAGA 57.772 40.909 0.00 2.70 44.29 2.87
2300 3854 4.880120 ACACTGTAGCTATACTGTTCGCTA 59.120 41.667 0.00 0.00 40.80 4.26
2301 3855 3.695060 ACACTGTAGCTATACTGTTCGCT 59.305 43.478 0.00 0.00 40.80 4.93
2302 3856 3.791887 CACACTGTAGCTATACTGTTCGC 59.208 47.826 0.00 0.00 40.80 4.70
2303 3857 4.982999 ACACACTGTAGCTATACTGTTCG 58.017 43.478 0.00 0.00 40.80 3.95
2304 3858 8.618677 TGTATACACACTGTAGCTATACTGTTC 58.381 37.037 0.08 0.00 40.80 3.18
2305 3859 8.515695 TGTATACACACTGTAGCTATACTGTT 57.484 34.615 0.08 0.00 40.80 3.16
2306 3860 7.774157 ACTGTATACACACTGTAGCTATACTGT 59.226 37.037 0.08 0.79 42.76 3.55
2307 3861 8.155821 ACTGTATACACACTGTAGCTATACTG 57.844 38.462 0.08 0.16 36.14 2.74
2308 3862 8.212312 AGACTGTATACACACTGTAGCTATACT 58.788 37.037 0.08 0.00 36.14 2.12
2309 3863 8.380743 AGACTGTATACACACTGTAGCTATAC 57.619 38.462 0.08 0.00 36.14 1.47
2310 3864 9.486497 GTAGACTGTATACACACTGTAGCTATA 57.514 37.037 7.66 0.00 36.14 1.31
2311 3865 7.991460 TGTAGACTGTATACACACTGTAGCTAT 59.009 37.037 10.97 0.00 36.14 2.97
2312 3866 7.333323 TGTAGACTGTATACACACTGTAGCTA 58.667 38.462 10.97 0.00 36.14 3.32
2313 3867 6.178324 TGTAGACTGTATACACACTGTAGCT 58.822 40.000 10.97 0.00 36.14 3.32
2314 3868 6.093771 ACTGTAGACTGTATACACACTGTAGC 59.906 42.308 10.97 0.00 36.14 3.58
2315 3869 7.465173 CACTGTAGACTGTATACACACTGTAG 58.535 42.308 10.97 9.03 36.14 2.74
2316 3870 6.128090 GCACTGTAGACTGTATACACACTGTA 60.128 42.308 10.97 0.00 37.24 2.74
2317 3871 5.335740 GCACTGTAGACTGTATACACACTGT 60.336 44.000 10.97 5.47 33.80 3.55
2318 3872 5.096169 GCACTGTAGACTGTATACACACTG 58.904 45.833 10.97 8.05 0.00 3.66
2319 3873 5.010933 AGCACTGTAGACTGTATACACACT 58.989 41.667 10.97 6.85 0.00 3.55
2320 3874 5.312120 AGCACTGTAGACTGTATACACAC 57.688 43.478 10.97 4.39 0.00 3.82
2321 3875 5.475564 TCAAGCACTGTAGACTGTATACACA 59.524 40.000 10.97 0.00 0.00 3.72
2322 3876 5.950883 TCAAGCACTGTAGACTGTATACAC 58.049 41.667 10.97 2.89 0.00 2.90
2323 3877 6.433093 TCTTCAAGCACTGTAGACTGTATACA 59.567 38.462 13.94 13.94 0.00 2.29
2324 3878 6.748198 GTCTTCAAGCACTGTAGACTGTATAC 59.252 42.308 14.45 5.67 44.76 1.47
2325 3879 6.853720 GTCTTCAAGCACTGTAGACTGTATA 58.146 40.000 14.45 0.00 44.76 1.47
2326 3880 5.715070 GTCTTCAAGCACTGTAGACTGTAT 58.285 41.667 14.45 0.00 44.76 2.29
2327 3881 5.122512 GTCTTCAAGCACTGTAGACTGTA 57.877 43.478 14.45 0.00 44.76 2.74
2328 3882 3.983741 GTCTTCAAGCACTGTAGACTGT 58.016 45.455 14.45 0.00 44.76 3.55
2332 3886 2.289072 GGCAGTCTTCAAGCACTGTAGA 60.289 50.000 14.63 0.00 41.88 2.59
2333 3887 2.072298 GGCAGTCTTCAAGCACTGTAG 58.928 52.381 14.63 0.00 41.88 2.74
2334 3888 1.694150 AGGCAGTCTTCAAGCACTGTA 59.306 47.619 14.63 0.00 41.88 2.74
2335 3889 0.471617 AGGCAGTCTTCAAGCACTGT 59.528 50.000 14.63 0.00 41.88 3.55
2336 3890 0.873054 CAGGCAGTCTTCAAGCACTG 59.127 55.000 10.86 10.86 42.61 3.66
2337 3891 0.250640 CCAGGCAGTCTTCAAGCACT 60.251 55.000 0.00 0.00 0.00 4.40
2338 3892 1.239968 CCCAGGCAGTCTTCAAGCAC 61.240 60.000 0.00 0.00 0.00 4.40
2339 3893 1.073722 CCCAGGCAGTCTTCAAGCA 59.926 57.895 0.00 0.00 0.00 3.91
2340 3894 0.957888 GTCCCAGGCAGTCTTCAAGC 60.958 60.000 0.00 0.00 0.00 4.01
2341 3895 0.671781 CGTCCCAGGCAGTCTTCAAG 60.672 60.000 0.00 0.00 0.00 3.02
2342 3896 1.371183 CGTCCCAGGCAGTCTTCAA 59.629 57.895 0.00 0.00 0.00 2.69
2343 3897 2.583441 CCGTCCCAGGCAGTCTTCA 61.583 63.158 0.00 0.00 0.00 3.02
2344 3898 2.266055 CCGTCCCAGGCAGTCTTC 59.734 66.667 0.00 0.00 0.00 2.87
2352 3906 3.775654 GACTCAGGCCGTCCCAGG 61.776 72.222 0.00 0.00 35.39 4.45
2353 3907 3.775654 GGACTCAGGCCGTCCCAG 61.776 72.222 15.49 2.95 44.08 4.45
2357 3911 2.435059 GCAAGGACTCAGGCCGTC 60.435 66.667 0.00 0.00 0.00 4.79
2358 3912 4.021925 GGCAAGGACTCAGGCCGT 62.022 66.667 0.00 0.00 36.58 5.68
2360 3914 4.432741 GGGGCAAGGACTCAGGCC 62.433 72.222 0.00 0.00 46.34 5.19
2361 3915 3.635268 CTGGGGCAAGGACTCAGGC 62.635 68.421 0.00 0.00 0.00 4.85
2362 3916 2.673523 CTGGGGCAAGGACTCAGG 59.326 66.667 0.00 0.00 0.00 3.86
2363 3917 2.045536 GCTGGGGCAAGGACTCAG 60.046 66.667 0.00 0.00 38.54 3.35
2364 3918 3.650950 GGCTGGGGCAAGGACTCA 61.651 66.667 0.00 0.00 40.87 3.41
2365 3919 3.334054 AGGCTGGGGCAAGGACTC 61.334 66.667 0.00 0.00 40.87 3.36
2366 3920 3.655211 CAGGCTGGGGCAAGGACT 61.655 66.667 6.61 0.00 40.87 3.85
2367 3921 4.748144 CCAGGCTGGGGCAAGGAC 62.748 72.222 26.34 0.00 40.87 3.85
2389 3943 1.294659 CTTCACTTCGGCTCAGTGGC 61.295 60.000 11.66 0.00 41.83 5.01
2390 3944 0.034059 ACTTCACTTCGGCTCAGTGG 59.966 55.000 11.66 1.82 41.83 4.00
2391 3945 1.795286 GAACTTCACTTCGGCTCAGTG 59.205 52.381 6.60 6.60 42.74 3.66
2392 3946 1.603172 CGAACTTCACTTCGGCTCAGT 60.603 52.381 0.00 0.00 39.52 3.41
2393 3947 1.063806 CGAACTTCACTTCGGCTCAG 58.936 55.000 0.00 0.00 39.52 3.35
2394 3948 0.387929 ACGAACTTCACTTCGGCTCA 59.612 50.000 6.31 0.00 46.00 4.26
2395 3949 0.784778 CACGAACTTCACTTCGGCTC 59.215 55.000 6.31 0.00 46.00 4.70
2396 3950 0.104304 ACACGAACTTCACTTCGGCT 59.896 50.000 6.31 0.00 46.00 5.52
2397 3951 0.232303 CACACGAACTTCACTTCGGC 59.768 55.000 6.31 0.00 46.00 5.54
2398 3952 0.859232 CCACACGAACTTCACTTCGG 59.141 55.000 6.31 0.00 46.00 4.30
2399 3953 1.847818 TCCACACGAACTTCACTTCG 58.152 50.000 0.00 0.00 46.90 3.79
2400 3954 3.186613 GGAATCCACACGAACTTCACTTC 59.813 47.826 0.00 0.00 0.00 3.01
2401 3955 3.139077 GGAATCCACACGAACTTCACTT 58.861 45.455 0.00 0.00 0.00 3.16
2402 3956 2.104111 TGGAATCCACACGAACTTCACT 59.896 45.455 0.00 0.00 0.00 3.41
2403 3957 2.480419 CTGGAATCCACACGAACTTCAC 59.520 50.000 0.00 0.00 0.00 3.18
2448 4002 2.190538 CAATGAAATGGGGGAAGCCTT 58.809 47.619 0.00 0.00 0.00 4.35
2500 4054 4.816925 GGACTACAGATGAATAGCCAAACC 59.183 45.833 0.00 0.00 0.00 3.27
2560 4114 1.667830 CGGTCTCTTTGCCGCTTCA 60.668 57.895 0.00 0.00 41.53 3.02
2596 4150 2.512515 GAGCTCATCCACACGGCC 60.513 66.667 9.40 0.00 0.00 6.13
2626 4180 5.125417 CCCAAATAAGTACATTGGTCAGGTG 59.875 44.000 14.63 0.00 41.62 4.00
2628 4182 4.644685 CCCCAAATAAGTACATTGGTCAGG 59.355 45.833 14.63 8.18 41.62 3.86
2750 4316 1.869767 CACTCTATCATTTGAGGCGCC 59.130 52.381 21.89 21.89 34.84 6.53
2759 4325 7.877097 GCAAATATCACTCCTCACTCTATCATT 59.123 37.037 0.00 0.00 0.00 2.57
2766 4332 5.423015 TCTTGCAAATATCACTCCTCACTC 58.577 41.667 0.00 0.00 0.00 3.51
2767 4333 5.426504 CTCTTGCAAATATCACTCCTCACT 58.573 41.667 0.00 0.00 0.00 3.41
2772 4338 5.297029 GGTTACCTCTTGCAAATATCACTCC 59.703 44.000 0.00 0.00 0.00 3.85
2780 4346 6.909550 TGTTAATGGTTACCTCTTGCAAAT 57.090 33.333 2.07 0.00 0.00 2.32
2791 4357 9.139174 CTTGGTCAAAATCATGTTAATGGTTAC 57.861 33.333 0.00 0.00 36.03 2.50
2803 4369 1.255882 TGCCGCTTGGTCAAAATCAT 58.744 45.000 0.00 0.00 34.16 2.45
2811 4377 0.733150 GGTATCTTTGCCGCTTGGTC 59.267 55.000 0.00 0.00 34.16 4.02
2842 4408 3.261643 ACTCATCCACACAGCTTCATGTA 59.738 43.478 0.00 0.00 0.00 2.29
2843 4409 2.039480 ACTCATCCACACAGCTTCATGT 59.961 45.455 0.00 0.00 0.00 3.21
2844 4410 2.708051 ACTCATCCACACAGCTTCATG 58.292 47.619 0.00 0.00 0.00 3.07
2845 4411 3.244665 TGAACTCATCCACACAGCTTCAT 60.245 43.478 0.00 0.00 0.00 2.57
2846 4412 2.104622 TGAACTCATCCACACAGCTTCA 59.895 45.455 0.00 0.00 0.00 3.02
2847 4413 2.771089 TGAACTCATCCACACAGCTTC 58.229 47.619 0.00 0.00 0.00 3.86
2848 4414 2.936919 TGAACTCATCCACACAGCTT 57.063 45.000 0.00 0.00 0.00 3.74
2849 4415 2.983229 GATGAACTCATCCACACAGCT 58.017 47.619 8.28 0.00 45.24 4.24
2864 4430 1.003839 GCTCGGTGGTGTGGATGAA 60.004 57.895 0.00 0.00 0.00 2.57
2898 4464 8.062065 AGAACTACATTGGTTTGTCTCAAAAA 57.938 30.769 0.00 0.00 0.00 1.94
2899 4465 7.639113 AGAACTACATTGGTTTGTCTCAAAA 57.361 32.000 0.00 0.00 0.00 2.44
2900 4466 7.639113 AAGAACTACATTGGTTTGTCTCAAA 57.361 32.000 0.00 0.00 0.00 2.69
2901 4467 7.639113 AAAGAACTACATTGGTTTGTCTCAA 57.361 32.000 0.00 0.00 0.00 3.02
2902 4468 7.122055 ACAAAAGAACTACATTGGTTTGTCTCA 59.878 33.333 0.00 0.00 32.28 3.27
2903 4469 7.432252 CACAAAAGAACTACATTGGTTTGTCTC 59.568 37.037 0.00 0.00 34.13 3.36
2904 4470 7.257722 CACAAAAGAACTACATTGGTTTGTCT 58.742 34.615 0.00 0.00 34.13 3.41
2905 4471 6.475402 CCACAAAAGAACTACATTGGTTTGTC 59.525 38.462 0.00 0.00 34.13 3.18
2906 4472 6.337356 CCACAAAAGAACTACATTGGTTTGT 58.663 36.000 0.00 0.00 35.62 2.83
2907 4473 5.234116 GCCACAAAAGAACTACATTGGTTTG 59.766 40.000 0.00 0.00 31.35 2.93
2908 4474 5.128663 AGCCACAAAAGAACTACATTGGTTT 59.871 36.000 0.00 0.00 0.00 3.27
2909 4475 4.649218 AGCCACAAAAGAACTACATTGGTT 59.351 37.500 0.00 0.00 0.00 3.67
2910 4476 4.215109 AGCCACAAAAGAACTACATTGGT 58.785 39.130 0.00 0.00 0.00 3.67
2911 4477 4.853924 AGCCACAAAAGAACTACATTGG 57.146 40.909 0.00 0.00 0.00 3.16
2912 4478 8.702438 CAAATAAGCCACAAAAGAACTACATTG 58.298 33.333 0.00 0.00 0.00 2.82
2913 4479 7.872483 CCAAATAAGCCACAAAAGAACTACATT 59.128 33.333 0.00 0.00 0.00 2.71
2914 4480 7.378181 CCAAATAAGCCACAAAAGAACTACAT 58.622 34.615 0.00 0.00 0.00 2.29
2915 4481 6.239176 CCCAAATAAGCCACAAAAGAACTACA 60.239 38.462 0.00 0.00 0.00 2.74
2916 4482 6.156519 CCCAAATAAGCCACAAAAGAACTAC 58.843 40.000 0.00 0.00 0.00 2.73
2917 4483 5.245075 CCCCAAATAAGCCACAAAAGAACTA 59.755 40.000 0.00 0.00 0.00 2.24
2918 4484 4.040339 CCCCAAATAAGCCACAAAAGAACT 59.960 41.667 0.00 0.00 0.00 3.01
2919 4485 4.202315 ACCCCAAATAAGCCACAAAAGAAC 60.202 41.667 0.00 0.00 0.00 3.01
2920 4486 3.970640 ACCCCAAATAAGCCACAAAAGAA 59.029 39.130 0.00 0.00 0.00 2.52
2921 4487 3.582164 ACCCCAAATAAGCCACAAAAGA 58.418 40.909 0.00 0.00 0.00 2.52
2927 4493 1.967779 ACACAACCCCAAATAAGCCAC 59.032 47.619 0.00 0.00 0.00 5.01
2947 4513 3.070302 GGCCAACTTATTTTCACAACCCA 59.930 43.478 0.00 0.00 0.00 4.51
2948 4514 3.556213 GGGCCAACTTATTTTCACAACCC 60.556 47.826 4.39 0.00 0.00 4.11
2949 4515 3.070302 TGGGCCAACTTATTTTCACAACC 59.930 43.478 2.13 0.00 0.00 3.77
2950 4516 4.329462 TGGGCCAACTTATTTTCACAAC 57.671 40.909 2.13 0.00 0.00 3.32
2951 4517 5.359194 TTTGGGCCAACTTATTTTCACAA 57.641 34.783 20.79 0.00 0.00 3.33
2952 4518 5.559148 ATTTGGGCCAACTTATTTTCACA 57.441 34.783 20.79 0.00 0.00 3.58
2953 4519 6.092122 GCTTATTTGGGCCAACTTATTTTCAC 59.908 38.462 20.79 0.00 0.00 3.18
2954 4520 6.169800 GCTTATTTGGGCCAACTTATTTTCA 58.830 36.000 20.79 0.34 0.00 2.69
2955 4521 5.584649 GGCTTATTTGGGCCAACTTATTTTC 59.415 40.000 20.79 3.58 46.84 2.29


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

AutoCloner maintained by Alex Coulton.