Multiple sequence alignment - TraesCS2A01G114200

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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 TraesCS2A01G114200 chr2A 100.000 2303 0 0 1 2303 65397077 65394775 0.000000e+00 4253.0
1 TraesCS2A01G114200 chr2A 91.450 538 45 1 1 537 757677191 757677728 0.000000e+00 737.0
2 TraesCS2A01G114200 chr2B 89.107 1322 76 31 649 1926 99773755 99772458 0.000000e+00 1581.0
3 TraesCS2A01G114200 chr2B 92.638 163 11 1 2064 2226 99772401 99772240 1.380000e-57 233.0
4 TraesCS2A01G114200 chr2B 100.000 31 0 0 2049 2079 99772460 99772430 8.890000e-05 58.4
5 TraesCS2A01G114200 chr2D 92.155 905 38 13 649 1533 63703939 63703048 0.000000e+00 1247.0
6 TraesCS2A01G114200 chr2D 91.620 537 45 0 1 537 138786952 138786416 0.000000e+00 743.0
7 TraesCS2A01G114200 chr2D 93.385 257 11 3 2049 2299 63702543 63702287 2.160000e-100 375.0
8 TraesCS2A01G114200 chr1D 92.737 537 39 0 1 537 409990616 409991152 0.000000e+00 776.0
9 TraesCS2A01G114200 chr1D 92.737 537 36 1 1 537 378876065 378876598 0.000000e+00 773.0
10 TraesCS2A01G114200 chr5D 92.565 538 39 1 1 537 112054802 112054265 0.000000e+00 771.0
11 TraesCS2A01G114200 chr5D 92.248 129 8 2 1923 2050 448539865 448539738 5.050000e-42 182.0
12 TraesCS2A01G114200 chr3D 92.551 537 40 0 1 537 298983402 298982866 0.000000e+00 771.0
13 TraesCS2A01G114200 chr3D 93.077 130 9 0 1924 2053 5563957 5563828 8.400000e-45 191.0
14 TraesCS2A01G114200 chr3D 87.273 110 11 3 521 629 321357442 321357335 3.110000e-24 122.0
15 TraesCS2A01G114200 chr3D 80.769 130 22 3 1159 1287 553679525 553679398 5.240000e-17 99.0
16 TraesCS2A01G114200 chr4A 91.806 537 44 0 1 537 682995206 682995742 0.000000e+00 749.0
17 TraesCS2A01G114200 chr4A 91.061 537 45 1 1 537 682997567 682998100 0.000000e+00 723.0
18 TraesCS2A01G114200 chr4A 93.077 130 9 0 1924 2053 534541471 534541600 8.400000e-45 191.0
19 TraesCS2A01G114200 chr7D 91.078 538 47 1 1 537 412765885 412765348 0.000000e+00 726.0
20 TraesCS2A01G114200 chr3A 93.750 128 8 0 1923 2050 365363076 365363203 2.330000e-45 193.0
21 TraesCS2A01G114200 chr3A 91.603 131 11 0 1924 2054 198491943 198491813 5.050000e-42 182.0
22 TraesCS2A01G114200 chr3A 87.273 110 11 3 521 629 526856686 526856579 3.110000e-24 122.0
23 TraesCS2A01G114200 chr3A 81.538 130 21 3 1159 1287 690079904 690079777 1.130000e-18 104.0
24 TraesCS2A01G114200 chr6A 92.913 127 9 0 1924 2050 507147010 507146884 3.910000e-43 185.0
25 TraesCS2A01G114200 chr6B 92.248 129 10 0 1922 2050 260111552 260111424 1.410000e-42 183.0
26 TraesCS2A01G114200 chr6B 88.182 110 10 3 521 629 216586272 216586165 6.680000e-26 128.0
27 TraesCS2A01G114200 chr1A 92.188 128 10 0 1924 2051 566608995 566609122 5.050000e-42 182.0
28 TraesCS2A01G114200 chr6D 91.538 130 11 0 1923 2052 62116262 62116133 1.820000e-41 180.0
29 TraesCS2A01G114200 chr6D 87.273 110 11 3 521 629 448351680 448351787 3.110000e-24 122.0
30 TraesCS2A01G114200 chr7A 88.073 109 11 2 521 629 383183883 383183989 6.680000e-26 128.0
31 TraesCS2A01G114200 chr7A 87.387 111 9 5 521 629 385807499 385807606 3.110000e-24 122.0
32 TraesCS2A01G114200 chr5B 88.182 110 10 3 521 629 99136517 99136624 6.680000e-26 128.0
33 TraesCS2A01G114200 chr5B 88.182 110 10 3 521 629 532730454 532730347 6.680000e-26 128.0
34 TraesCS2A01G114200 chr5A 87.273 110 11 3 521 629 17522165 17522272 3.110000e-24 122.0
35 TraesCS2A01G114200 chr3B 82.090 134 18 6 1158 1287 734686482 734686351 2.420000e-20 110.0


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 TraesCS2A01G114200 chr2A 65394775 65397077 2302 True 4253.000000 4253 100.0000 1 2303 1 chr2A.!!$R1 2302
1 TraesCS2A01G114200 chr2A 757677191 757677728 537 False 737.000000 737 91.4500 1 537 1 chr2A.!!$F1 536
2 TraesCS2A01G114200 chr2B 99772240 99773755 1515 True 624.133333 1581 93.9150 649 2226 3 chr2B.!!$R1 1577
3 TraesCS2A01G114200 chr2D 63702287 63703939 1652 True 811.000000 1247 92.7700 649 2299 2 chr2D.!!$R2 1650
4 TraesCS2A01G114200 chr2D 138786416 138786952 536 True 743.000000 743 91.6200 1 537 1 chr2D.!!$R1 536
5 TraesCS2A01G114200 chr1D 409990616 409991152 536 False 776.000000 776 92.7370 1 537 1 chr1D.!!$F2 536
6 TraesCS2A01G114200 chr1D 378876065 378876598 533 False 773.000000 773 92.7370 1 537 1 chr1D.!!$F1 536
7 TraesCS2A01G114200 chr5D 112054265 112054802 537 True 771.000000 771 92.5650 1 537 1 chr5D.!!$R1 536
8 TraesCS2A01G114200 chr3D 298982866 298983402 536 True 771.000000 771 92.5510 1 537 1 chr3D.!!$R2 536
9 TraesCS2A01G114200 chr4A 682995206 682998100 2894 False 736.000000 749 91.4335 1 537 2 chr4A.!!$F2 536
10 TraesCS2A01G114200 chr7D 412765348 412765885 537 True 726.000000 726 91.0780 1 537 1 chr7D.!!$R1 536

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
545 2906 0.106708 ACGTCTGCATGACACCACTT 59.893 50.0 14.09 0.0 45.6 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1549 3949 0.096976 CGTTGAAAGCATAGCGTGGG 59.903 55.0 0.0 0.0 0.0 4.61 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
215 2575 1.154282 CTCGCGCAACGTCTCTGTA 60.154 57.895 8.75 0.00 44.19 2.74
224 2584 1.517257 CGTCTCTGTAGCTTGCCGG 60.517 63.158 0.00 0.00 0.00 6.13
227 2587 1.185618 TCTCTGTAGCTTGCCGGTGT 61.186 55.000 1.90 0.00 0.00 4.16
241 2601 1.337071 CCGGTGTCGCTCATATAGTGT 59.663 52.381 0.00 0.00 37.01 3.55
285 2645 2.434359 GCTAACTTCGGGCACGCT 60.434 61.111 1.67 0.00 40.69 5.07
362 2723 3.134458 GCGGTAGCTCATTTGATAGCTT 58.866 45.455 1.72 0.00 46.82 3.74
419 2780 4.766891 ACATGGTCATTCTTTTGTGTAGGG 59.233 41.667 0.00 0.00 0.00 3.53
422 2783 2.161609 GTCATTCTTTTGTGTAGGGCGG 59.838 50.000 0.00 0.00 0.00 6.13
426 2787 1.228306 TTTTGTGTAGGGCGGTGGG 60.228 57.895 0.00 0.00 0.00 4.61
526 2887 7.232737 TCCTTAGTAGAATCGAAGGCAATGATA 59.767 37.037 0.00 0.00 39.12 2.15
529 2890 4.060038 AGAATCGAAGGCAATGATACGT 57.940 40.909 0.00 0.00 0.00 3.57
537 2898 2.158914 AGGCAATGATACGTCTGCATGA 60.159 45.455 0.00 0.00 36.50 3.07
538 2899 2.032549 GGCAATGATACGTCTGCATGAC 60.033 50.000 0.00 6.31 42.06 3.06
539 2900 2.609002 GCAATGATACGTCTGCATGACA 59.391 45.455 14.09 0.00 45.60 3.58
540 2901 3.544834 GCAATGATACGTCTGCATGACAC 60.545 47.826 14.09 0.00 45.60 3.67
541 2902 2.293677 TGATACGTCTGCATGACACC 57.706 50.000 14.09 3.66 45.60 4.16
542 2903 1.548269 TGATACGTCTGCATGACACCA 59.452 47.619 14.09 5.52 45.60 4.17
543 2904 1.927174 GATACGTCTGCATGACACCAC 59.073 52.381 14.09 0.00 45.60 4.16
544 2905 0.966179 TACGTCTGCATGACACCACT 59.034 50.000 14.09 0.00 45.60 4.00
545 2906 0.106708 ACGTCTGCATGACACCACTT 59.893 50.000 14.09 0.00 45.60 3.16
546 2907 1.343142 ACGTCTGCATGACACCACTTA 59.657 47.619 14.09 0.00 45.60 2.24
547 2908 2.028112 ACGTCTGCATGACACCACTTAT 60.028 45.455 14.09 0.00 45.60 1.73
548 2909 3.194755 ACGTCTGCATGACACCACTTATA 59.805 43.478 14.09 0.00 45.60 0.98
549 2910 4.141937 ACGTCTGCATGACACCACTTATAT 60.142 41.667 14.09 0.00 45.60 0.86
550 2911 4.209911 CGTCTGCATGACACCACTTATATG 59.790 45.833 14.09 0.00 45.60 1.78
551 2912 5.118990 GTCTGCATGACACCACTTATATGT 58.881 41.667 0.00 0.00 44.73 2.29
552 2913 5.586243 GTCTGCATGACACCACTTATATGTT 59.414 40.000 0.00 0.00 44.73 2.71
553 2914 6.761242 GTCTGCATGACACCACTTATATGTTA 59.239 38.462 0.00 0.00 44.73 2.41
554 2915 6.761242 TCTGCATGACACCACTTATATGTTAC 59.239 38.462 0.00 0.00 0.00 2.50
555 2916 6.649155 TGCATGACACCACTTATATGTTACT 58.351 36.000 0.00 0.00 0.00 2.24
556 2917 7.787028 TGCATGACACCACTTATATGTTACTA 58.213 34.615 0.00 0.00 0.00 1.82
557 2918 7.709182 TGCATGACACCACTTATATGTTACTAC 59.291 37.037 0.00 0.00 0.00 2.73
558 2919 7.170998 GCATGACACCACTTATATGTTACTACC 59.829 40.741 0.00 0.00 0.00 3.18
559 2920 7.116075 TGACACCACTTATATGTTACTACCC 57.884 40.000 0.00 0.00 0.00 3.69
560 2921 6.668718 TGACACCACTTATATGTTACTACCCA 59.331 38.462 0.00 0.00 0.00 4.51
561 2922 6.881570 ACACCACTTATATGTTACTACCCAC 58.118 40.000 0.00 0.00 0.00 4.61
562 2923 6.670902 ACACCACTTATATGTTACTACCCACT 59.329 38.462 0.00 0.00 0.00 4.00
563 2924 7.840716 ACACCACTTATATGTTACTACCCACTA 59.159 37.037 0.00 0.00 0.00 2.74
564 2925 8.867097 CACCACTTATATGTTACTACCCACTAT 58.133 37.037 0.00 0.00 0.00 2.12
565 2926 8.867097 ACCACTTATATGTTACTACCCACTATG 58.133 37.037 0.00 0.00 0.00 2.23
566 2927 9.085645 CCACTTATATGTTACTACCCACTATGA 57.914 37.037 0.00 0.00 0.00 2.15
573 2934 8.605325 ATGTTACTACCCACTATGAAAGTAGT 57.395 34.615 6.40 6.40 44.29 2.73
574 2935 9.705103 ATGTTACTACCCACTATGAAAGTAGTA 57.295 33.333 4.64 4.64 42.59 1.82
575 2936 9.532494 TGTTACTACCCACTATGAAAGTAGTAA 57.468 33.333 14.04 14.04 46.43 2.24
596 2957 8.859236 AGTAATATAGACTAGTAACATCGGCA 57.141 34.615 0.00 0.00 0.00 5.69
597 2958 9.293404 AGTAATATAGACTAGTAACATCGGCAA 57.707 33.333 0.00 0.00 0.00 4.52
598 2959 9.557338 GTAATATAGACTAGTAACATCGGCAAG 57.443 37.037 0.00 0.00 0.00 4.01
599 2960 7.762588 ATATAGACTAGTAACATCGGCAAGT 57.237 36.000 0.00 0.00 0.00 3.16
600 2961 4.803098 AGACTAGTAACATCGGCAAGTT 57.197 40.909 0.00 0.00 0.00 2.66
601 2962 5.909621 AGACTAGTAACATCGGCAAGTTA 57.090 39.130 0.00 0.00 0.00 2.24
602 2963 5.648572 AGACTAGTAACATCGGCAAGTTAC 58.351 41.667 12.99 12.99 46.42 2.50
607 2968 3.975168 AACATCGGCAAGTTACTACCT 57.025 42.857 3.39 0.00 0.00 3.08
608 2969 3.975168 ACATCGGCAAGTTACTACCTT 57.025 42.857 3.39 0.00 0.00 3.50
609 2970 5.410355 AACATCGGCAAGTTACTACCTTA 57.590 39.130 3.39 0.00 0.00 2.69
610 2971 5.609533 ACATCGGCAAGTTACTACCTTAT 57.390 39.130 3.39 0.00 0.00 1.73
611 2972 5.357257 ACATCGGCAAGTTACTACCTTATG 58.643 41.667 11.47 11.47 0.00 1.90
612 2973 5.105064 ACATCGGCAAGTTACTACCTTATGT 60.105 40.000 12.29 12.29 0.00 2.29
613 2974 5.410355 TCGGCAAGTTACTACCTTATGTT 57.590 39.130 3.39 0.00 0.00 2.71
614 2975 6.528537 TCGGCAAGTTACTACCTTATGTTA 57.471 37.500 3.39 0.00 0.00 2.41
615 2976 6.332630 TCGGCAAGTTACTACCTTATGTTAC 58.667 40.000 3.39 0.00 0.00 2.50
616 2977 6.153340 TCGGCAAGTTACTACCTTATGTTACT 59.847 38.462 3.39 0.00 0.00 2.24
617 2978 6.474751 CGGCAAGTTACTACCTTATGTTACTC 59.525 42.308 3.39 0.00 0.00 2.59
618 2979 7.554211 GGCAAGTTACTACCTTATGTTACTCT 58.446 38.462 0.00 0.00 0.00 3.24
619 2980 8.039538 GGCAAGTTACTACCTTATGTTACTCTT 58.960 37.037 0.00 0.00 0.00 2.85
620 2981 9.085250 GCAAGTTACTACCTTATGTTACTCTTC 57.915 37.037 0.00 0.00 0.00 2.87
627 2988 8.812972 ACTACCTTATGTTACTCTTCATTGTGA 58.187 33.333 0.00 0.00 0.00 3.58
628 2989 9.307121 CTACCTTATGTTACTCTTCATTGTGAG 57.693 37.037 7.51 7.51 36.47 3.51
629 2990 7.907389 ACCTTATGTTACTCTTCATTGTGAGA 58.093 34.615 13.39 4.97 34.65 3.27
630 2991 8.543774 ACCTTATGTTACTCTTCATTGTGAGAT 58.456 33.333 13.39 3.26 34.65 2.75
631 2992 8.824781 CCTTATGTTACTCTTCATTGTGAGATG 58.175 37.037 13.39 0.00 34.65 2.90
632 2993 9.591792 CTTATGTTACTCTTCATTGTGAGATGA 57.408 33.333 13.39 0.00 34.37 2.92
633 2994 9.942850 TTATGTTACTCTTCATTGTGAGATGAA 57.057 29.630 13.39 0.97 42.18 2.57
636 2997 9.942850 TGTTACTCTTCATTGTGAGATGAATAA 57.057 29.630 13.39 0.00 43.10 1.40
642 3003 9.102757 TCTTCATTGTGAGATGAATAAACTAGC 57.897 33.333 1.25 0.00 43.10 3.42
643 3004 7.792374 TCATTGTGAGATGAATAAACTAGCC 57.208 36.000 0.00 0.00 33.31 3.93
644 3005 7.337938 TCATTGTGAGATGAATAAACTAGCCA 58.662 34.615 0.00 0.00 33.31 4.75
645 3006 7.828717 TCATTGTGAGATGAATAAACTAGCCAA 59.171 33.333 0.00 0.00 33.31 4.52
646 3007 8.627403 CATTGTGAGATGAATAAACTAGCCAAT 58.373 33.333 0.00 0.00 0.00 3.16
647 3008 8.579850 TTGTGAGATGAATAAACTAGCCAATT 57.420 30.769 0.00 0.00 0.00 2.32
695 3059 1.011968 TCTTGATTCGTGTTCCGGCG 61.012 55.000 0.00 0.00 37.11 6.46
877 3248 2.106683 CATTCCGACGAACCCTGCC 61.107 63.158 0.00 0.00 0.00 4.85
900 3277 3.000727 CTCCTACCCGTGCTGTTTAAAG 58.999 50.000 0.00 0.00 0.00 1.85
957 3334 2.359975 GCCGTCTCCCAAACCCAG 60.360 66.667 0.00 0.00 0.00 4.45
1243 3626 1.895020 CTACTACAACTGCCGCCCCA 61.895 60.000 0.00 0.00 0.00 4.96
1306 3689 2.125912 AGTGCCGCGACTGATGAC 60.126 61.111 8.23 0.00 0.00 3.06
1307 3690 2.432456 GTGCCGCGACTGATGACA 60.432 61.111 8.23 0.00 0.00 3.58
1310 3693 3.545481 CCGCGACTGATGACACGC 61.545 66.667 8.23 0.00 46.08 5.34
1312 3695 2.504026 GCGACTGATGACACGCGA 60.504 61.111 15.93 0.00 41.49 5.87
1316 3699 0.728129 GACTGATGACACGCGAACGA 60.728 55.000 15.93 0.00 43.93 3.85
1317 3700 1.002250 ACTGATGACACGCGAACGAC 61.002 55.000 15.93 1.44 43.93 4.34
1318 3701 1.674611 CTGATGACACGCGAACGACC 61.675 60.000 15.93 0.00 43.93 4.79
1319 3702 2.431942 ATGACACGCGAACGACCC 60.432 61.111 15.93 0.00 43.93 4.46
1321 3704 3.400590 GACACGCGAACGACCCAC 61.401 66.667 15.93 0.00 43.93 4.61
1339 3730 2.558313 GTTCCTGCTGCTCGTTGC 59.442 61.111 0.00 0.00 43.25 4.17
1368 3759 2.672996 CCTTGAGCCACGGGGTTG 60.673 66.667 5.12 0.00 36.17 3.77
1369 3760 2.429930 CTTGAGCCACGGGGTTGA 59.570 61.111 5.12 0.00 36.17 3.18
1370 3761 1.672356 CTTGAGCCACGGGGTTGAG 60.672 63.158 5.12 0.00 36.17 3.02
1371 3762 2.397413 CTTGAGCCACGGGGTTGAGT 62.397 60.000 5.12 0.00 36.17 3.41
1431 3823 7.010183 GTGTTGTTGTGCTTCGATGTACTATAT 59.990 37.037 17.89 0.00 0.00 0.86
1432 3824 7.010091 TGTTGTTGTGCTTCGATGTACTATATG 59.990 37.037 17.89 0.00 0.00 1.78
1433 3825 6.569780 TGTTGTGCTTCGATGTACTATATGT 58.430 36.000 17.89 0.00 0.00 2.29
1434 3826 6.475402 TGTTGTGCTTCGATGTACTATATGTG 59.525 38.462 17.89 0.00 0.00 3.21
1483 3875 0.378610 GAGCATTTAACAGAGCGGCC 59.621 55.000 0.00 0.00 0.00 6.13
1542 3942 0.461693 CCCCGTTTTATCCGCGGTTA 60.462 55.000 27.15 19.14 43.56 2.85
1549 3949 4.336932 GTTTTATCCGCGGTTACATGTTC 58.663 43.478 27.15 5.18 0.00 3.18
1550 3950 2.228138 TATCCGCGGTTACATGTTCC 57.772 50.000 27.15 6.68 0.00 3.62
1553 3953 1.641123 CCGCGGTTACATGTTCCCAC 61.641 60.000 19.50 0.00 0.00 4.61
1565 3965 1.271108 TGTTCCCACGCTATGCTTTCA 60.271 47.619 0.00 0.00 0.00 2.69
1586 3986 0.166597 CGGAGTTACAGTCGCACGTA 59.833 55.000 0.00 0.00 0.00 3.57
1597 3997 4.424430 GCACGTAACGCGGCACTG 62.424 66.667 12.47 8.87 46.52 3.66
1622 4190 7.443272 TGTCCATTGAGCTAGAACAATATGATG 59.557 37.037 12.23 4.62 35.39 3.07
1623 4191 7.443575 GTCCATTGAGCTAGAACAATATGATGT 59.556 37.037 12.23 0.00 35.39 3.06
1628 4196 9.665719 TTGAGCTAGAACAATATGATGTTACAA 57.334 29.630 0.00 0.00 43.31 2.41
1641 4209 3.830744 TGTTACAACCGCCATAGCTAT 57.169 42.857 0.00 0.00 36.60 2.97
1642 4210 4.940905 TGTTACAACCGCCATAGCTATA 57.059 40.909 5.77 0.00 36.60 1.31
1644 4212 5.294356 TGTTACAACCGCCATAGCTATAAG 58.706 41.667 5.77 2.19 36.60 1.73
1645 4213 5.069383 TGTTACAACCGCCATAGCTATAAGA 59.931 40.000 5.77 0.00 36.60 2.10
1646 4214 4.258702 ACAACCGCCATAGCTATAAGAG 57.741 45.455 5.77 2.97 36.60 2.85
1648 4216 3.170991 ACCGCCATAGCTATAAGAGGA 57.829 47.619 23.88 0.00 36.60 3.71
1649 4217 3.093057 ACCGCCATAGCTATAAGAGGAG 58.907 50.000 23.88 15.26 36.60 3.69
1650 4218 2.159170 CCGCCATAGCTATAAGAGGAGC 60.159 54.545 16.31 6.90 39.08 4.70
1651 4219 2.493675 CGCCATAGCTATAAGAGGAGCA 59.506 50.000 5.77 0.00 41.36 4.26
1652 4220 3.674682 CGCCATAGCTATAAGAGGAGCAC 60.675 52.174 5.77 0.00 41.36 4.40
1653 4221 3.259374 GCCATAGCTATAAGAGGAGCACA 59.741 47.826 5.77 0.00 41.36 4.57
1654 4222 4.081198 GCCATAGCTATAAGAGGAGCACAT 60.081 45.833 5.77 0.00 41.36 3.21
1687 4269 2.355132 CAGAGCTGCTAGCATTTTCCAG 59.645 50.000 19.72 5.64 45.56 3.86
1693 4275 2.305635 TGCTAGCATTTTCCAGTCTCCA 59.694 45.455 14.93 0.00 0.00 3.86
1712 4294 2.558359 CCATTCACCAAAACAGTCCTCC 59.442 50.000 0.00 0.00 0.00 4.30
1730 4312 2.549754 CTCCGTTTCACAGTTTCAGCAT 59.450 45.455 0.00 0.00 0.00 3.79
1739 4321 1.201647 CAGTTTCAGCATGGCCAGAAG 59.798 52.381 13.05 4.74 36.16 2.85
1773 4362 2.604914 GCATACAGAACTGATGACCACG 59.395 50.000 8.87 0.00 0.00 4.94
1775 4364 4.686972 CATACAGAACTGATGACCACGAT 58.313 43.478 8.87 0.00 0.00 3.73
1809 4398 0.035056 AAGAAATGGACGGAGGCTGG 60.035 55.000 0.00 0.00 0.00 4.85
1811 4400 2.198304 GAAATGGACGGAGGCTGGGT 62.198 60.000 0.00 0.00 0.00 4.51
1891 4480 0.888736 TGACGCCACTCCATTGTTGG 60.889 55.000 0.00 0.00 45.15 3.77
1892 4481 0.889186 GACGCCACTCCATTGTTGGT 60.889 55.000 0.00 0.00 44.06 3.67
1920 4509 3.447742 CAGGTTCCAAAACAGCAGTTTC 58.552 45.455 7.75 0.00 46.79 2.78
1921 4510 3.131046 CAGGTTCCAAAACAGCAGTTTCT 59.869 43.478 7.75 0.00 46.79 2.52
1922 4511 3.381590 AGGTTCCAAAACAGCAGTTTCTC 59.618 43.478 7.75 0.00 46.79 2.87
1923 4512 3.381590 GGTTCCAAAACAGCAGTTTCTCT 59.618 43.478 7.75 0.00 46.79 3.10
1924 4513 4.578928 GGTTCCAAAACAGCAGTTTCTCTA 59.421 41.667 7.75 0.00 46.79 2.43
1925 4514 5.505819 GGTTCCAAAACAGCAGTTTCTCTAC 60.506 44.000 7.75 4.94 46.79 2.59
1926 4515 5.036117 TCCAAAACAGCAGTTTCTCTACT 57.964 39.130 7.75 0.00 46.79 2.57
1927 4516 5.057149 TCCAAAACAGCAGTTTCTCTACTC 58.943 41.667 7.75 0.00 46.79 2.59
1928 4517 4.214332 CCAAAACAGCAGTTTCTCTACTCC 59.786 45.833 7.75 0.00 46.79 3.85
1929 4518 3.686916 AACAGCAGTTTCTCTACTCCC 57.313 47.619 0.00 0.00 33.11 4.30
1930 4519 2.896039 ACAGCAGTTTCTCTACTCCCT 58.104 47.619 0.00 0.00 0.00 4.20
1931 4520 3.243724 ACAGCAGTTTCTCTACTCCCTT 58.756 45.455 0.00 0.00 0.00 3.95
1932 4521 3.259625 ACAGCAGTTTCTCTACTCCCTTC 59.740 47.826 0.00 0.00 0.00 3.46
1933 4522 2.494073 AGCAGTTTCTCTACTCCCTTCG 59.506 50.000 0.00 0.00 0.00 3.79
1934 4523 2.231721 GCAGTTTCTCTACTCCCTTCGT 59.768 50.000 0.00 0.00 0.00 3.85
1935 4524 3.306156 GCAGTTTCTCTACTCCCTTCGTT 60.306 47.826 0.00 0.00 0.00 3.85
1936 4525 4.487019 CAGTTTCTCTACTCCCTTCGTTC 58.513 47.826 0.00 0.00 0.00 3.95
1937 4526 4.218852 CAGTTTCTCTACTCCCTTCGTTCT 59.781 45.833 0.00 0.00 0.00 3.01
1938 4527 5.415077 CAGTTTCTCTACTCCCTTCGTTCTA 59.585 44.000 0.00 0.00 0.00 2.10
1939 4528 6.008960 AGTTTCTCTACTCCCTTCGTTCTAA 58.991 40.000 0.00 0.00 0.00 2.10
1940 4529 6.492772 AGTTTCTCTACTCCCTTCGTTCTAAA 59.507 38.462 0.00 0.00 0.00 1.85
1941 4530 7.178805 AGTTTCTCTACTCCCTTCGTTCTAAAT 59.821 37.037 0.00 0.00 0.00 1.40
1942 4531 7.477945 TTCTCTACTCCCTTCGTTCTAAATT 57.522 36.000 0.00 0.00 0.00 1.82
1943 4532 8.585471 TTCTCTACTCCCTTCGTTCTAAATTA 57.415 34.615 0.00 0.00 0.00 1.40
1944 4533 7.994194 TCTCTACTCCCTTCGTTCTAAATTAC 58.006 38.462 0.00 0.00 0.00 1.89
1945 4534 7.833183 TCTCTACTCCCTTCGTTCTAAATTACT 59.167 37.037 0.00 0.00 0.00 2.24
1946 4535 8.358582 TCTACTCCCTTCGTTCTAAATTACTT 57.641 34.615 0.00 0.00 0.00 2.24
1947 4536 8.248945 TCTACTCCCTTCGTTCTAAATTACTTG 58.751 37.037 0.00 0.00 0.00 3.16
1948 4537 7.001099 ACTCCCTTCGTTCTAAATTACTTGA 57.999 36.000 0.00 0.00 0.00 3.02
1949 4538 6.872547 ACTCCCTTCGTTCTAAATTACTTGAC 59.127 38.462 0.00 0.00 0.00 3.18
1950 4539 6.168389 TCCCTTCGTTCTAAATTACTTGACC 58.832 40.000 0.00 0.00 0.00 4.02
1951 4540 5.353400 CCCTTCGTTCTAAATTACTTGACCC 59.647 44.000 0.00 0.00 0.00 4.46
1952 4541 5.935789 CCTTCGTTCTAAATTACTTGACCCA 59.064 40.000 0.00 0.00 0.00 4.51
1953 4542 6.598064 CCTTCGTTCTAAATTACTTGACCCAT 59.402 38.462 0.00 0.00 0.00 4.00
1954 4543 7.767198 CCTTCGTTCTAAATTACTTGACCCATA 59.233 37.037 0.00 0.00 0.00 2.74
1955 4544 9.326413 CTTCGTTCTAAATTACTTGACCCATAT 57.674 33.333 0.00 0.00 0.00 1.78
1956 4545 9.675464 TTCGTTCTAAATTACTTGACCCATATT 57.325 29.630 0.00 0.00 0.00 1.28
1957 4546 9.675464 TCGTTCTAAATTACTTGACCCATATTT 57.325 29.630 0.00 0.00 0.00 1.40
1968 4557 7.434492 ACTTGACCCATATTTATCTAGACACG 58.566 38.462 0.00 0.00 0.00 4.49
1969 4558 6.340962 TGACCCATATTTATCTAGACACGG 57.659 41.667 0.00 0.00 0.00 4.94
1970 4559 6.072649 TGACCCATATTTATCTAGACACGGA 58.927 40.000 0.00 0.00 0.00 4.69
1971 4560 6.724441 TGACCCATATTTATCTAGACACGGAT 59.276 38.462 0.00 0.00 0.00 4.18
1972 4561 6.936279 ACCCATATTTATCTAGACACGGATG 58.064 40.000 0.00 0.00 0.00 3.51
1973 4562 5.812642 CCCATATTTATCTAGACACGGATGC 59.187 44.000 0.00 0.00 0.00 3.91
1974 4563 6.398095 CCATATTTATCTAGACACGGATGCA 58.602 40.000 0.00 0.00 0.00 3.96
1975 4564 7.044181 CCATATTTATCTAGACACGGATGCAT 58.956 38.462 0.00 0.00 0.00 3.96
1976 4565 7.223582 CCATATTTATCTAGACACGGATGCATC 59.776 40.741 18.81 18.81 0.00 3.91
1977 4566 5.791336 TTTATCTAGACACGGATGCATCT 57.209 39.130 25.28 8.54 0.00 2.90
1978 4567 6.894339 TTTATCTAGACACGGATGCATCTA 57.106 37.500 25.28 9.27 0.00 1.98
1979 4568 6.502136 TTATCTAGACACGGATGCATCTAG 57.498 41.667 25.28 20.66 41.31 2.43
1980 4569 4.086706 TCTAGACACGGATGCATCTAGA 57.913 45.455 25.28 19.75 44.64 2.43
1981 4570 3.815962 TCTAGACACGGATGCATCTAGAC 59.184 47.826 25.28 14.97 42.92 2.59
1982 4571 2.379005 AGACACGGATGCATCTAGACA 58.621 47.619 25.28 0.00 0.00 3.41
1983 4572 2.099921 AGACACGGATGCATCTAGACAC 59.900 50.000 25.28 12.84 0.00 3.67
1984 4573 2.099921 GACACGGATGCATCTAGACACT 59.900 50.000 25.28 2.94 0.00 3.55
1985 4574 3.288092 ACACGGATGCATCTAGACACTA 58.712 45.455 25.28 0.00 0.00 2.74
1986 4575 3.699538 ACACGGATGCATCTAGACACTAA 59.300 43.478 25.28 0.00 0.00 2.24
1987 4576 4.159693 ACACGGATGCATCTAGACACTAAA 59.840 41.667 25.28 0.00 0.00 1.85
1988 4577 5.163405 ACACGGATGCATCTAGACACTAAAT 60.163 40.000 25.28 0.48 0.00 1.40
1989 4578 6.040504 ACACGGATGCATCTAGACACTAAATA 59.959 38.462 25.28 0.00 0.00 1.40
1990 4579 6.923508 CACGGATGCATCTAGACACTAAATAA 59.076 38.462 25.28 0.00 0.00 1.40
1991 4580 7.438160 CACGGATGCATCTAGACACTAAATAAA 59.562 37.037 25.28 0.00 0.00 1.40
1992 4581 8.150945 ACGGATGCATCTAGACACTAAATAAAT 58.849 33.333 25.28 0.00 0.00 1.40
1993 4582 9.639601 CGGATGCATCTAGACACTAAATAAATA 57.360 33.333 25.28 0.00 0.00 1.40
2037 4626 8.912988 AGACAAATTCAAGTCAACTAATTTGGA 58.087 29.630 22.68 1.26 46.31 3.53
2038 4627 9.528018 GACAAATTCAAGTCAACTAATTTGGAA 57.472 29.630 22.68 7.42 46.31 3.53
2041 4630 9.492973 AAATTCAAGTCAACTAATTTGGAATGG 57.507 29.630 3.85 0.00 35.69 3.16
2042 4631 7.831691 TTCAAGTCAACTAATTTGGAATGGA 57.168 32.000 0.00 0.00 35.69 3.41
2043 4632 7.452880 TCAAGTCAACTAATTTGGAATGGAG 57.547 36.000 0.00 0.00 35.69 3.86
2044 4633 6.434028 TCAAGTCAACTAATTTGGAATGGAGG 59.566 38.462 0.00 0.00 35.69 4.30
2045 4634 5.264395 AGTCAACTAATTTGGAATGGAGGG 58.736 41.667 0.00 0.00 35.69 4.30
2046 4635 5.015178 AGTCAACTAATTTGGAATGGAGGGA 59.985 40.000 0.00 0.00 35.69 4.20
2047 4636 5.358160 GTCAACTAATTTGGAATGGAGGGAG 59.642 44.000 0.00 0.00 35.69 4.30
2089 4722 1.600413 GCAAGCGTTTGACCAAAGAGG 60.600 52.381 16.78 0.00 37.88 3.69
2154 4790 3.440173 GCAATTCTGTAGTAAGCTGGCAA 59.560 43.478 0.00 0.00 0.00 4.52
2167 4803 3.368739 AAGCTGGCAATTTGCAAGATACC 60.369 43.478 26.51 10.72 43.17 2.73
2207 4843 0.036765 TGGAGACGTGTATTGGCACC 60.037 55.000 0.00 0.00 36.08 5.01
2258 4897 6.035435 CAGACGACTTATCCTCTCAAATGTTG 59.965 42.308 0.00 0.00 0.00 3.33
2269 4908 4.072131 TCTCAAATGTTGTTCAGGTAGCC 58.928 43.478 0.00 0.00 0.00 3.93
2293 4932 7.041372 GCCGTTTTATTTCAGGATATTCTGCTA 60.041 37.037 6.09 0.00 34.91 3.49
2301 4940 7.839680 TTCAGGATATTCTGCTATGTACTCA 57.160 36.000 6.09 0.00 34.91 3.41
2302 4941 8.427902 TTCAGGATATTCTGCTATGTACTCAT 57.572 34.615 6.09 0.00 35.31 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 60 1.215382 CGACCACTCCATCGCTTGA 59.785 57.895 0.00 0.00 0.00 3.02
149 2509 0.313672 TCCATGCTTGCAAACCGTTC 59.686 50.000 0.00 0.00 0.00 3.95
150 2510 0.968405 ATCCATGCTTGCAAACCGTT 59.032 45.000 0.00 0.00 0.00 4.44
161 2521 2.203070 GCCGGACGAATCCATGCT 60.203 61.111 5.05 0.00 46.67 3.79
224 2584 4.677378 GTCATCACACTATATGAGCGACAC 59.323 45.833 0.00 0.00 34.71 3.67
227 2587 4.557496 GCAGTCATCACACTATATGAGCGA 60.557 45.833 0.00 0.00 32.93 4.93
241 2601 2.432456 GTCCGCGTGCAGTCATCA 60.432 61.111 4.92 0.00 0.00 3.07
336 2696 4.989279 ATCAAATGAGCTACCGCAAATT 57.011 36.364 0.00 0.00 39.10 1.82
338 2698 3.312421 GCTATCAAATGAGCTACCGCAAA 59.688 43.478 0.00 0.00 39.10 3.68
362 2723 7.054124 AGGATCCGCAATTGAACTAAAGAATA 58.946 34.615 10.34 0.00 0.00 1.75
419 2780 1.080569 CAAAATGAGCACCCACCGC 60.081 57.895 0.00 0.00 0.00 5.68
422 2783 2.871633 CAAAACCAAAATGAGCACCCAC 59.128 45.455 0.00 0.00 0.00 4.61
426 2787 3.467374 TCCCAAAACCAAAATGAGCAC 57.533 42.857 0.00 0.00 0.00 4.40
491 2852 5.296283 TCGATTCTACTAAGGAGTGCACTAC 59.704 44.000 22.25 22.25 36.28 2.73
529 2890 5.357742 ACATATAAGTGGTGTCATGCAGA 57.642 39.130 0.00 0.00 0.00 4.26
537 2898 6.670902 AGTGGGTAGTAACATATAAGTGGTGT 59.329 38.462 0.00 0.00 0.00 4.16
538 2899 7.120923 AGTGGGTAGTAACATATAAGTGGTG 57.879 40.000 0.00 0.00 0.00 4.17
539 2900 8.867097 CATAGTGGGTAGTAACATATAAGTGGT 58.133 37.037 0.00 0.00 0.00 4.16
540 2901 9.085645 TCATAGTGGGTAGTAACATATAAGTGG 57.914 37.037 0.00 0.00 0.00 4.00
547 2908 9.705103 ACTACTTTCATAGTGGGTAGTAACATA 57.295 33.333 0.00 0.00 40.49 2.29
548 2909 8.605325 ACTACTTTCATAGTGGGTAGTAACAT 57.395 34.615 0.00 0.00 40.49 2.71
549 2910 9.532494 TTACTACTTTCATAGTGGGTAGTAACA 57.468 33.333 15.47 1.42 44.14 2.41
570 2931 9.948964 TGCCGATGTTACTAGTCTATATTACTA 57.051 33.333 0.00 0.00 0.00 1.82
571 2932 8.859236 TGCCGATGTTACTAGTCTATATTACT 57.141 34.615 0.00 0.00 0.00 2.24
572 2933 9.557338 CTTGCCGATGTTACTAGTCTATATTAC 57.443 37.037 0.00 0.00 0.00 1.89
573 2934 9.293404 ACTTGCCGATGTTACTAGTCTATATTA 57.707 33.333 0.00 0.00 0.00 0.98
574 2935 8.179509 ACTTGCCGATGTTACTAGTCTATATT 57.820 34.615 0.00 0.00 0.00 1.28
575 2936 7.762588 ACTTGCCGATGTTACTAGTCTATAT 57.237 36.000 0.00 0.00 0.00 0.86
576 2937 7.578310 AACTTGCCGATGTTACTAGTCTATA 57.422 36.000 0.00 0.00 0.00 1.31
577 2938 6.466885 AACTTGCCGATGTTACTAGTCTAT 57.533 37.500 0.00 0.00 0.00 1.98
578 2939 5.909621 AACTTGCCGATGTTACTAGTCTA 57.090 39.130 0.00 0.00 0.00 2.59
579 2940 4.803098 AACTTGCCGATGTTACTAGTCT 57.197 40.909 0.00 0.00 0.00 3.24
580 2941 5.945775 GTAACTTGCCGATGTTACTAGTC 57.054 43.478 0.00 0.00 42.82 2.59
585 2946 4.752146 AGGTAGTAACTTGCCGATGTTAC 58.248 43.478 7.64 7.64 45.03 2.50
586 2947 5.410355 AAGGTAGTAACTTGCCGATGTTA 57.590 39.130 0.00 0.00 0.00 2.41
587 2948 3.975168 AGGTAGTAACTTGCCGATGTT 57.025 42.857 0.00 0.00 0.00 2.71
588 2949 3.975168 AAGGTAGTAACTTGCCGATGT 57.025 42.857 0.00 0.00 0.00 3.06
589 2950 5.357257 ACATAAGGTAGTAACTTGCCGATG 58.643 41.667 10.86 8.52 0.00 3.84
590 2951 5.609533 ACATAAGGTAGTAACTTGCCGAT 57.390 39.130 10.86 0.00 0.00 4.18
591 2952 5.410355 AACATAAGGTAGTAACTTGCCGA 57.590 39.130 10.86 0.00 0.00 5.54
592 2953 6.335777 AGTAACATAAGGTAGTAACTTGCCG 58.664 40.000 10.86 1.61 0.00 5.69
593 2954 7.554211 AGAGTAACATAAGGTAGTAACTTGCC 58.446 38.462 10.86 0.00 0.00 4.52
594 2955 8.999220 AAGAGTAACATAAGGTAGTAACTTGC 57.001 34.615 10.86 0.00 0.00 4.01
601 2962 8.812972 TCACAATGAAGAGTAACATAAGGTAGT 58.187 33.333 0.00 0.00 0.00 2.73
602 2963 9.307121 CTCACAATGAAGAGTAACATAAGGTAG 57.693 37.037 0.00 0.00 0.00 3.18
603 2964 9.031537 TCTCACAATGAAGAGTAACATAAGGTA 57.968 33.333 7.18 0.00 33.63 3.08
604 2965 7.907389 TCTCACAATGAAGAGTAACATAAGGT 58.093 34.615 7.18 0.00 33.63 3.50
605 2966 8.824781 CATCTCACAATGAAGAGTAACATAAGG 58.175 37.037 7.18 0.00 33.63 2.69
606 2967 9.591792 TCATCTCACAATGAAGAGTAACATAAG 57.408 33.333 7.18 0.00 32.80 1.73
607 2968 9.942850 TTCATCTCACAATGAAGAGTAACATAA 57.057 29.630 7.18 0.00 39.98 1.90
610 2971 9.942850 TTATTCATCTCACAATGAAGAGTAACA 57.057 29.630 5.64 0.00 45.96 2.41
616 2977 9.102757 GCTAGTTTATTCATCTCACAATGAAGA 57.897 33.333 5.64 0.00 45.96 2.87
617 2978 8.341173 GGCTAGTTTATTCATCTCACAATGAAG 58.659 37.037 5.64 0.00 45.96 3.02
618 2979 7.828717 TGGCTAGTTTATTCATCTCACAATGAA 59.171 33.333 2.13 2.13 46.60 2.57
619 2980 7.337938 TGGCTAGTTTATTCATCTCACAATGA 58.662 34.615 0.00 0.00 33.88 2.57
620 2981 7.558161 TGGCTAGTTTATTCATCTCACAATG 57.442 36.000 0.00 0.00 0.00 2.82
621 2982 8.757982 ATTGGCTAGTTTATTCATCTCACAAT 57.242 30.769 0.00 0.00 0.00 2.71
622 2983 8.579850 AATTGGCTAGTTTATTCATCTCACAA 57.420 30.769 0.00 0.00 0.00 3.33
623 2984 9.330063 CTAATTGGCTAGTTTATTCATCTCACA 57.670 33.333 0.00 0.00 0.00 3.58
624 2985 9.547753 TCTAATTGGCTAGTTTATTCATCTCAC 57.452 33.333 0.00 0.00 0.00 3.51
625 2986 9.770097 CTCTAATTGGCTAGTTTATTCATCTCA 57.230 33.333 0.00 0.00 0.00 3.27
626 2987 9.988815 TCTCTAATTGGCTAGTTTATTCATCTC 57.011 33.333 0.00 0.00 0.00 2.75
640 3001 9.732130 GGATAGTTTATTCATCTCTAATTGGCT 57.268 33.333 0.00 0.00 0.00 4.75
641 3002 9.507329 TGGATAGTTTATTCATCTCTAATTGGC 57.493 33.333 0.00 0.00 0.00 4.52
645 3006 9.732130 GGCTTGGATAGTTTATTCATCTCTAAT 57.268 33.333 0.00 0.00 0.00 1.73
646 3007 8.713971 TGGCTTGGATAGTTTATTCATCTCTAA 58.286 33.333 0.00 0.00 0.00 2.10
647 3008 8.262601 TGGCTTGGATAGTTTATTCATCTCTA 57.737 34.615 0.00 0.00 0.00 2.43
695 3059 8.499403 AGTTTATTCATCTCTTTTACTGCCTC 57.501 34.615 0.00 0.00 0.00 4.70
877 3248 1.838073 AAACAGCACGGGTAGGAGGG 61.838 60.000 0.00 0.00 0.00 4.30
900 3277 2.122167 TTTGTGTTGTGACCGGGGC 61.122 57.895 6.32 0.00 0.00 5.80
1053 3433 4.760047 ACGATGGGTGCTGCCGAC 62.760 66.667 0.00 0.00 38.44 4.79
1054 3434 4.451150 GACGATGGGTGCTGCCGA 62.451 66.667 0.00 0.00 38.44 5.54
1316 3699 3.537206 GAGCAGCAGGAACGTGGGT 62.537 63.158 0.00 0.00 0.00 4.51
1317 3700 2.743928 GAGCAGCAGGAACGTGGG 60.744 66.667 0.00 0.00 0.00 4.61
1318 3701 3.114616 CGAGCAGCAGGAACGTGG 61.115 66.667 0.00 0.00 0.00 4.94
1319 3702 1.956170 AACGAGCAGCAGGAACGTG 60.956 57.895 0.00 0.00 37.28 4.49
1321 3704 2.856032 CAACGAGCAGCAGGAACG 59.144 61.111 0.00 0.00 0.00 3.95
1339 3730 0.514691 GCTCAAGGAAACAGCGACAG 59.485 55.000 0.00 0.00 0.00 3.51
1431 3823 5.824097 CCATCAAATCATCTCATACACCACA 59.176 40.000 0.00 0.00 0.00 4.17
1432 3824 5.824624 ACCATCAAATCATCTCATACACCAC 59.175 40.000 0.00 0.00 0.00 4.16
1433 3825 6.005066 ACCATCAAATCATCTCATACACCA 57.995 37.500 0.00 0.00 0.00 4.17
1434 3826 6.949352 AACCATCAAATCATCTCATACACC 57.051 37.500 0.00 0.00 0.00 4.16
1450 3842 7.821652 TGTTAAATGCTCGAAATTAACCATCA 58.178 30.769 14.33 0.00 37.41 3.07
1483 3875 1.655484 TGCCACATTGATACTGCTCG 58.345 50.000 0.00 0.00 0.00 5.03
1549 3949 0.096976 CGTTGAAAGCATAGCGTGGG 59.903 55.000 0.00 0.00 0.00 4.61
1550 3950 0.096976 CCGTTGAAAGCATAGCGTGG 59.903 55.000 0.00 0.00 0.00 4.94
1553 3953 1.359848 ACTCCGTTGAAAGCATAGCG 58.640 50.000 0.00 0.00 0.00 4.26
1565 3965 0.662374 CGTGCGACTGTAACTCCGTT 60.662 55.000 0.00 0.00 0.00 4.44
1586 3986 2.281484 AATGGACAGTGCCGCGTT 60.281 55.556 4.92 0.00 0.00 4.84
1591 3991 1.208052 TCTAGCTCAATGGACAGTGCC 59.792 52.381 0.00 0.00 0.00 5.01
1592 3992 2.675348 GTTCTAGCTCAATGGACAGTGC 59.325 50.000 0.00 0.00 0.00 4.40
1597 3997 7.443575 ACATCATATTGTTCTAGCTCAATGGAC 59.556 37.037 16.76 0.00 36.06 4.02
1622 4190 5.535333 TCTTATAGCTATGGCGGTTGTAAC 58.465 41.667 16.77 0.00 44.37 2.50
1623 4191 5.279306 CCTCTTATAGCTATGGCGGTTGTAA 60.279 44.000 16.77 0.00 44.37 2.41
1628 4196 3.093057 CTCCTCTTATAGCTATGGCGGT 58.907 50.000 16.77 0.00 44.37 5.68
1641 4209 2.416836 CGTTTCCGATGTGCTCCTCTTA 60.417 50.000 0.00 0.00 35.63 2.10
1642 4210 1.673033 CGTTTCCGATGTGCTCCTCTT 60.673 52.381 0.00 0.00 35.63 2.85
1644 4212 0.108804 TCGTTTCCGATGTGCTCCTC 60.109 55.000 0.00 0.00 38.40 3.71
1645 4213 0.108615 CTCGTTTCCGATGTGCTCCT 60.109 55.000 0.00 0.00 43.27 3.69
1646 4214 1.084370 CCTCGTTTCCGATGTGCTCC 61.084 60.000 0.00 0.00 43.27 4.70
1648 4216 1.741770 GCCTCGTTTCCGATGTGCT 60.742 57.895 0.00 0.00 43.27 4.40
1649 4217 1.970917 CTGCCTCGTTTCCGATGTGC 61.971 60.000 0.00 0.00 43.27 4.57
1650 4218 0.389817 TCTGCCTCGTTTCCGATGTG 60.390 55.000 0.00 0.00 43.27 3.21
1651 4219 0.108615 CTCTGCCTCGTTTCCGATGT 60.109 55.000 0.00 0.00 43.27 3.06
1652 4220 1.424493 GCTCTGCCTCGTTTCCGATG 61.424 60.000 0.00 0.00 43.27 3.84
1653 4221 1.153549 GCTCTGCCTCGTTTCCGAT 60.154 57.895 0.00 0.00 43.27 4.18
1654 4222 2.261671 GCTCTGCCTCGTTTCCGA 59.738 61.111 0.00 0.00 41.73 4.55
1687 4269 3.253432 GGACTGTTTTGGTGAATGGAGAC 59.747 47.826 0.00 0.00 0.00 3.36
1693 4275 2.158667 ACGGAGGACTGTTTTGGTGAAT 60.159 45.455 0.00 0.00 30.63 2.57
1712 4294 2.653890 CCATGCTGAAACTGTGAAACG 58.346 47.619 0.00 0.00 42.39 3.60
1730 4312 2.509548 ACAGGCATATTACTTCTGGCCA 59.490 45.455 4.71 4.71 43.72 5.36
1800 4389 2.063979 TATGACCACCCAGCCTCCG 61.064 63.158 0.00 0.00 0.00 4.63
1809 4398 1.153429 GCTCACCGGTATGACCACC 60.153 63.158 6.87 0.00 38.47 4.61
1811 4400 0.908910 AATGCTCACCGGTATGACCA 59.091 50.000 6.87 0.00 38.47 4.02
1891 4480 2.267426 GTTTTGGAACCTGCAACACAC 58.733 47.619 0.00 0.00 30.33 3.82
1892 4481 1.895798 TGTTTTGGAACCTGCAACACA 59.104 42.857 0.00 0.00 36.33 3.72
1919 4508 7.833183 AGTAATTTAGAACGAAGGGAGTAGAGA 59.167 37.037 0.00 0.00 0.00 3.10
1920 4509 7.998580 AGTAATTTAGAACGAAGGGAGTAGAG 58.001 38.462 0.00 0.00 0.00 2.43
1921 4510 7.951347 AGTAATTTAGAACGAAGGGAGTAGA 57.049 36.000 0.00 0.00 0.00 2.59
1922 4511 8.248945 TCAAGTAATTTAGAACGAAGGGAGTAG 58.751 37.037 0.00 0.00 0.00 2.57
1923 4512 8.031277 GTCAAGTAATTTAGAACGAAGGGAGTA 58.969 37.037 0.00 0.00 0.00 2.59
1924 4513 6.872547 GTCAAGTAATTTAGAACGAAGGGAGT 59.127 38.462 0.00 0.00 0.00 3.85
1925 4514 6.313164 GGTCAAGTAATTTAGAACGAAGGGAG 59.687 42.308 0.00 0.00 0.00 4.30
1926 4515 6.168389 GGTCAAGTAATTTAGAACGAAGGGA 58.832 40.000 0.00 0.00 0.00 4.20
1927 4516 5.353400 GGGTCAAGTAATTTAGAACGAAGGG 59.647 44.000 0.00 0.00 0.00 3.95
1928 4517 5.935789 TGGGTCAAGTAATTTAGAACGAAGG 59.064 40.000 0.00 0.00 0.00 3.46
1929 4518 7.611213 ATGGGTCAAGTAATTTAGAACGAAG 57.389 36.000 0.00 0.00 0.00 3.79
1930 4519 9.675464 AATATGGGTCAAGTAATTTAGAACGAA 57.325 29.630 0.00 0.00 0.00 3.85
1931 4520 9.675464 AAATATGGGTCAAGTAATTTAGAACGA 57.325 29.630 0.00 0.00 0.00 3.85
1942 4531 8.573885 CGTGTCTAGATAAATATGGGTCAAGTA 58.426 37.037 0.00 0.00 0.00 2.24
1943 4532 7.434492 CGTGTCTAGATAAATATGGGTCAAGT 58.566 38.462 0.00 0.00 0.00 3.16
1944 4533 6.868864 CCGTGTCTAGATAAATATGGGTCAAG 59.131 42.308 0.00 0.00 0.00 3.02
1945 4534 6.551975 TCCGTGTCTAGATAAATATGGGTCAA 59.448 38.462 0.00 0.00 0.00 3.18
1946 4535 6.072649 TCCGTGTCTAGATAAATATGGGTCA 58.927 40.000 0.00 0.00 0.00 4.02
1947 4536 6.585695 TCCGTGTCTAGATAAATATGGGTC 57.414 41.667 0.00 0.00 0.00 4.46
1948 4537 6.574465 GCATCCGTGTCTAGATAAATATGGGT 60.574 42.308 0.00 0.00 0.00 4.51
1949 4538 5.812642 GCATCCGTGTCTAGATAAATATGGG 59.187 44.000 0.00 0.00 0.00 4.00
1950 4539 6.398095 TGCATCCGTGTCTAGATAAATATGG 58.602 40.000 0.00 0.00 0.00 2.74
1951 4540 7.978414 AGATGCATCCGTGTCTAGATAAATATG 59.022 37.037 23.06 0.00 0.00 1.78
1952 4541 8.072321 AGATGCATCCGTGTCTAGATAAATAT 57.928 34.615 23.06 0.00 0.00 1.28
1953 4542 7.468141 AGATGCATCCGTGTCTAGATAAATA 57.532 36.000 23.06 0.00 0.00 1.40
1954 4543 6.352016 AGATGCATCCGTGTCTAGATAAAT 57.648 37.500 23.06 0.00 0.00 1.40
1955 4544 5.791336 AGATGCATCCGTGTCTAGATAAA 57.209 39.130 23.06 0.00 0.00 1.40
1956 4545 6.149640 GTCTAGATGCATCCGTGTCTAGATAA 59.850 42.308 23.06 0.00 46.25 1.75
1957 4546 5.644206 GTCTAGATGCATCCGTGTCTAGATA 59.356 44.000 23.06 4.13 46.25 1.98
1958 4547 4.457603 GTCTAGATGCATCCGTGTCTAGAT 59.542 45.833 23.06 3.09 46.25 1.98
1959 4548 3.815962 GTCTAGATGCATCCGTGTCTAGA 59.184 47.826 23.06 18.63 44.02 2.43
1960 4549 3.565902 TGTCTAGATGCATCCGTGTCTAG 59.434 47.826 23.06 16.71 40.81 2.43
1961 4550 3.315470 GTGTCTAGATGCATCCGTGTCTA 59.685 47.826 23.06 7.64 0.00 2.59
1962 4551 2.099921 GTGTCTAGATGCATCCGTGTCT 59.900 50.000 23.06 6.79 0.00 3.41
1963 4552 2.099921 AGTGTCTAGATGCATCCGTGTC 59.900 50.000 23.06 11.26 0.00 3.67
1964 4553 2.103373 AGTGTCTAGATGCATCCGTGT 58.897 47.619 23.06 7.24 0.00 4.49
1965 4554 2.879002 AGTGTCTAGATGCATCCGTG 57.121 50.000 23.06 13.10 0.00 4.94
1966 4555 5.537300 ATTTAGTGTCTAGATGCATCCGT 57.463 39.130 23.06 8.39 0.00 4.69
1967 4556 7.946655 TTTATTTAGTGTCTAGATGCATCCG 57.053 36.000 23.06 14.43 0.00 4.18
2011 4600 8.912988 TCCAAATTAGTTGACTTGAATTTGTCT 58.087 29.630 20.10 0.00 43.18 3.41
2012 4601 9.528018 TTCCAAATTAGTTGACTTGAATTTGTC 57.472 29.630 20.10 0.00 43.18 3.18
2015 4604 9.492973 CCATTCCAAATTAGTTGACTTGAATTT 57.507 29.630 0.00 0.00 39.87 1.82
2016 4605 8.869109 TCCATTCCAAATTAGTTGACTTGAATT 58.131 29.630 0.00 0.00 39.87 2.17
2017 4606 8.421249 TCCATTCCAAATTAGTTGACTTGAAT 57.579 30.769 0.00 0.00 39.87 2.57
2018 4607 7.039784 CCTCCATTCCAAATTAGTTGACTTGAA 60.040 37.037 0.00 0.00 39.87 2.69
2019 4608 6.434028 CCTCCATTCCAAATTAGTTGACTTGA 59.566 38.462 0.00 0.00 39.87 3.02
2020 4609 6.350445 CCCTCCATTCCAAATTAGTTGACTTG 60.350 42.308 0.00 0.00 39.87 3.16
2021 4610 5.716703 CCCTCCATTCCAAATTAGTTGACTT 59.283 40.000 0.00 0.00 39.87 3.01
2022 4611 5.015178 TCCCTCCATTCCAAATTAGTTGACT 59.985 40.000 0.00 0.00 39.87 3.41
2023 4612 5.261216 TCCCTCCATTCCAAATTAGTTGAC 58.739 41.667 0.00 0.00 39.87 3.18
2024 4613 5.015178 ACTCCCTCCATTCCAAATTAGTTGA 59.985 40.000 0.00 0.00 39.87 3.18
2025 4614 5.264395 ACTCCCTCCATTCCAAATTAGTTG 58.736 41.667 0.00 0.00 36.94 3.16
2026 4615 5.536497 ACTCCCTCCATTCCAAATTAGTT 57.464 39.130 0.00 0.00 0.00 2.24
2027 4616 5.491078 TGTACTCCCTCCATTCCAAATTAGT 59.509 40.000 0.00 0.00 0.00 2.24
2028 4617 6.001449 TGTACTCCCTCCATTCCAAATTAG 57.999 41.667 0.00 0.00 0.00 1.73
2029 4618 6.364701 CATGTACTCCCTCCATTCCAAATTA 58.635 40.000 0.00 0.00 0.00 1.40
2030 4619 4.946160 TGTACTCCCTCCATTCCAAATT 57.054 40.909 0.00 0.00 0.00 1.82
2031 4620 4.386761 CCATGTACTCCCTCCATTCCAAAT 60.387 45.833 0.00 0.00 0.00 2.32
2032 4621 3.053693 CCATGTACTCCCTCCATTCCAAA 60.054 47.826 0.00 0.00 0.00 3.28
2033 4622 2.509548 CCATGTACTCCCTCCATTCCAA 59.490 50.000 0.00 0.00 0.00 3.53
2034 4623 2.126882 CCATGTACTCCCTCCATTCCA 58.873 52.381 0.00 0.00 0.00 3.53
2035 4624 1.202818 GCCATGTACTCCCTCCATTCC 60.203 57.143 0.00 0.00 0.00 3.01
2036 4625 1.490490 TGCCATGTACTCCCTCCATTC 59.510 52.381 0.00 0.00 0.00 2.67
2037 4626 1.492176 CTGCCATGTACTCCCTCCATT 59.508 52.381 0.00 0.00 0.00 3.16
2038 4627 1.135094 CTGCCATGTACTCCCTCCAT 58.865 55.000 0.00 0.00 0.00 3.41
2039 4628 1.626356 GCTGCCATGTACTCCCTCCA 61.626 60.000 0.00 0.00 0.00 3.86
2040 4629 1.147153 GCTGCCATGTACTCCCTCC 59.853 63.158 0.00 0.00 0.00 4.30
2041 4630 1.147153 GGCTGCCATGTACTCCCTC 59.853 63.158 15.17 0.00 0.00 4.30
2042 4631 1.616327 TGGCTGCCATGTACTCCCT 60.616 57.895 19.30 0.00 0.00 4.20
2043 4632 1.452108 GTGGCTGCCATGTACTCCC 60.452 63.158 26.22 5.18 35.28 4.30
2044 4633 0.830648 TAGTGGCTGCCATGTACTCC 59.169 55.000 26.22 9.95 35.28 3.85
2045 4634 2.691409 TTAGTGGCTGCCATGTACTC 57.309 50.000 26.22 10.74 35.28 2.59
2046 4635 4.444876 CCTTATTAGTGGCTGCCATGTACT 60.445 45.833 26.22 18.81 35.28 2.73
2047 4636 3.815401 CCTTATTAGTGGCTGCCATGTAC 59.185 47.826 26.22 11.94 35.28 2.90
2089 4722 4.513198 TTTAGTGGTTGCCATGTTAAGC 57.487 40.909 0.00 0.00 35.28 3.09
2154 4790 3.885297 CTGATTCCCGGTATCTTGCAAAT 59.115 43.478 13.20 0.00 0.00 2.32
2167 4803 1.922570 CTACCGAACACTGATTCCCG 58.077 55.000 0.00 0.00 0.00 5.14
2258 4897 5.391629 CCTGAAATAAAACGGCTACCTGAAC 60.392 44.000 0.00 0.00 0.00 3.18
2269 4908 9.817365 CATAGCAGAATATCCTGAAATAAAACG 57.183 33.333 0.00 0.00 36.29 3.60


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

AutoCloner maintained by Alex Coulton.