Multiple sequence alignment - TraesCS5D01G342500

Loading Multiple Alignment...

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 TraesCS5D01G342500 chr5D 100.000 2552 0 0 1 2552 430544465 430547016 0.000000e+00 4713
1 TraesCS5D01G342500 chr5A 88.815 1055 52 25 779 1810 546162238 546163249 0.000000e+00 1234
2 TraesCS5D01G342500 chr5A 81.290 620 62 26 1823 2404 546163231 546163834 1.080000e-123 453
3 TraesCS5D01G342500 chr5A 82.353 544 47 25 123 644 546160783 546161299 6.520000e-116 427
4 TraesCS5D01G342500 chr5A 83.394 277 25 12 673 937 546161758 546162025 1.180000e-58 237
5 TraesCS5D01G342500 chr5A 92.121 165 7 4 779 937 546161415 546161579 7.100000e-56 228
6 TraesCS5D01G342500 chr5B 86.518 1031 67 21 823 1810 520083004 520084005 0.000000e+00 1068
7 TraesCS5D01G342500 chr5B 92.879 660 37 7 1826 2481 520083990 520084643 0.000000e+00 950
8 TraesCS5D01G342500 chr5B 80.656 579 61 29 102 646 520076758 520077319 3.950000e-108 401


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 TraesCS5D01G342500 chr5D 430544465 430547016 2551 False 4713.0 4713 100.0000 1 2552 1 chr5D.!!$F1 2551
1 TraesCS5D01G342500 chr5A 546160783 546163834 3051 False 515.8 1234 85.5946 123 2404 5 chr5A.!!$F1 2281
2 TraesCS5D01G342500 chr5B 520083004 520084643 1639 False 1009.0 1068 89.6985 823 2481 2 chr5B.!!$F2 1658
3 TraesCS5D01G342500 chr5B 520076758 520077319 561 False 401.0 401 80.6560 102 646 1 chr5B.!!$F1 544

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
705 811 0.034574 ACATGCGGCCCAAATGTAGA 60.035 50.0 10.13 0.0 32.86 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2424 3458 0.229753 CTTCGCGACGCATTACATCC 59.77 55.0 21.35 0.0 0.0 3.51 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
46 47 9.903682 TTTTTCAAATTGATGAACTTTTTGCAA 57.096 22.222 0.00 0.00 38.95 4.08
47 48 9.903682 TTTTCAAATTGATGAACTTTTTGCAAA 57.096 22.222 8.05 8.05 38.95 3.68
54 55 9.724839 ATTGATGAACTTTTTGCAAATTTTCTG 57.275 25.926 13.65 2.84 0.00 3.02
55 56 7.695820 TGATGAACTTTTTGCAAATTTTCTGG 58.304 30.769 13.65 1.53 0.00 3.86
56 57 7.551974 TGATGAACTTTTTGCAAATTTTCTGGA 59.448 29.630 13.65 1.67 0.00 3.86
57 58 7.862512 TGAACTTTTTGCAAATTTTCTGGAT 57.137 28.000 13.65 0.00 0.00 3.41
58 59 8.954950 TGAACTTTTTGCAAATTTTCTGGATA 57.045 26.923 13.65 0.00 0.00 2.59
59 60 9.558396 TGAACTTTTTGCAAATTTTCTGGATAT 57.442 25.926 13.65 0.00 0.00 1.63
138 139 8.388319 TCGATGAACTTTTATAAAATTTGGCG 57.612 30.769 15.79 14.77 0.00 5.69
159 160 6.640499 TGGCGAACTATTTTTCAACTTTGATG 59.360 34.615 0.00 0.00 37.00 3.07
239 242 6.949578 TCAATCATTTGCTTTTCGAAATCC 57.050 33.333 12.12 6.40 32.61 3.01
240 243 6.453943 TCAATCATTTGCTTTTCGAAATCCA 58.546 32.000 12.12 8.99 32.61 3.41
250 253 5.445010 GCTTTTCGAAATCCATGCACATTTC 60.445 40.000 12.12 13.86 36.18 2.17
254 257 3.243168 CGAAATCCATGCACATTTCCGAT 60.243 43.478 16.44 0.00 36.16 4.18
258 261 2.426738 TCCATGCACATTTCCGATTTCC 59.573 45.455 0.00 0.00 0.00 3.13
277 280 7.806014 CGATTTCCCTAAATTTTCGTCTTTTGA 59.194 33.333 0.00 0.00 35.41 2.69
280 283 7.996098 TCCCTAAATTTTCGTCTTTTGAGAT 57.004 32.000 0.00 0.00 0.00 2.75
282 285 8.856103 TCCCTAAATTTTCGTCTTTTGAGATTT 58.144 29.630 0.00 0.00 0.00 2.17
361 381 0.732196 GAGCGCTCGCATCTAGATGG 60.732 60.000 29.43 20.45 44.88 3.51
366 386 3.476386 CGCATCTAGATGGGCCCT 58.524 61.111 29.98 8.64 43.22 5.19
367 387 2.671145 CGCATCTAGATGGGCCCTA 58.329 57.895 29.98 10.18 43.22 3.53
370 390 3.127321 GCATCTAGATGGGCCCTAGGC 62.127 61.905 29.43 12.12 42.56 3.93
403 431 4.299586 TCTCATGGACACCAGCAATTTA 57.700 40.909 0.00 0.00 36.75 1.40
412 440 3.063452 ACACCAGCAATTTATACGCTTCG 59.937 43.478 0.00 0.00 32.48 3.79
415 443 3.242739 CCAGCAATTTATACGCTTCGCTT 60.243 43.478 0.00 0.00 32.48 4.68
416 444 4.025229 CCAGCAATTTATACGCTTCGCTTA 60.025 41.667 0.00 0.00 32.48 3.09
421 449 7.218204 AGCAATTTATACGCTTCGCTTAAAAAG 59.782 33.333 0.00 0.00 29.87 2.27
432 464 7.513041 CGCTTCGCTTAAAAAGGCAATTTATAC 60.513 37.037 0.00 0.00 0.00 1.47
435 467 5.051973 CGCTTAAAAAGGCAATTTATACGCC 60.052 40.000 0.00 0.00 46.62 5.68
451 483 8.514330 TTTATACGCCCATTTTACTGAGAAAT 57.486 30.769 0.00 0.00 0.00 2.17
466 498 4.053903 GAGAAATCACCGTGTTTTCTCG 57.946 45.455 30.86 0.00 45.38 4.04
477 516 4.271687 CGTGTTTTCTCGAAGTCCAAAAG 58.728 43.478 0.00 0.00 38.82 2.27
531 574 4.345288 CAAGAATTACACGTGCATCCATG 58.655 43.478 17.22 3.41 0.00 3.66
583 630 1.006832 CCGTGTTGCTGTAGTATGGC 58.993 55.000 0.00 0.00 0.00 4.40
602 649 3.136443 TGGCCAATCAGTTCGGATTAGAT 59.864 43.478 0.61 0.00 35.79 1.98
604 651 3.499918 GCCAATCAGTTCGGATTAGATGG 59.500 47.826 0.00 0.00 35.79 3.51
644 696 6.017852 GCTGCTACTAGGCCTTTTAATTAGTG 60.018 42.308 12.58 2.81 0.00 2.74
645 697 5.820947 TGCTACTAGGCCTTTTAATTAGTGC 59.179 40.000 12.58 12.85 0.00 4.40
646 698 5.820947 GCTACTAGGCCTTTTAATTAGTGCA 59.179 40.000 12.58 0.00 0.00 4.57
648 700 6.510879 ACTAGGCCTTTTAATTAGTGCAAC 57.489 37.500 12.58 0.00 0.00 4.17
664 716 5.689383 GTGCAACTGTATCCTTCTCAAAA 57.311 39.130 0.00 0.00 0.00 2.44
704 810 1.674359 TACATGCGGCCCAAATGTAG 58.326 50.000 13.24 0.00 36.08 2.74
705 811 0.034574 ACATGCGGCCCAAATGTAGA 60.035 50.000 10.13 0.00 32.86 2.59
706 812 0.664761 CATGCGGCCCAAATGTAGAG 59.335 55.000 0.00 0.00 0.00 2.43
707 813 1.103398 ATGCGGCCCAAATGTAGAGC 61.103 55.000 0.00 0.00 0.00 4.09
708 814 1.452108 GCGGCCCAAATGTAGAGCT 60.452 57.895 0.00 0.00 0.00 4.09
709 815 0.179056 GCGGCCCAAATGTAGAGCTA 60.179 55.000 0.00 0.00 0.00 3.32
710 816 1.583054 CGGCCCAAATGTAGAGCTAC 58.417 55.000 0.00 0.74 36.63 3.58
720 826 2.915349 TGTAGAGCTACACTAGGACGG 58.085 52.381 6.26 0.00 40.77 4.79
721 827 2.238144 TGTAGAGCTACACTAGGACGGT 59.762 50.000 6.26 0.00 40.77 4.83
722 828 1.752683 AGAGCTACACTAGGACGGTG 58.247 55.000 0.00 0.00 40.19 4.94
723 829 0.100861 GAGCTACACTAGGACGGTGC 59.899 60.000 0.00 0.00 38.14 5.01
724 830 0.323542 AGCTACACTAGGACGGTGCT 60.324 55.000 7.47 7.47 38.14 4.40
725 831 0.531200 GCTACACTAGGACGGTGCTT 59.469 55.000 7.67 0.00 38.14 3.91
726 832 1.736032 GCTACACTAGGACGGTGCTTG 60.736 57.143 7.67 8.60 38.14 4.01
727 833 0.245539 TACACTAGGACGGTGCTTGC 59.754 55.000 7.67 0.00 38.14 4.01
728 834 1.741770 CACTAGGACGGTGCTTGCC 60.742 63.158 7.67 0.00 0.00 4.52
729 835 1.913762 ACTAGGACGGTGCTTGCCT 60.914 57.895 7.67 0.00 34.56 4.75
730 836 1.153549 CTAGGACGGTGCTTGCCTC 60.154 63.158 7.67 0.00 32.04 4.70
731 837 1.608717 CTAGGACGGTGCTTGCCTCT 61.609 60.000 7.67 0.00 32.04 3.69
732 838 0.323999 TAGGACGGTGCTTGCCTCTA 60.324 55.000 7.67 0.00 32.04 2.43
733 839 1.448013 GGACGGTGCTTGCCTCTAC 60.448 63.158 0.00 0.00 0.00 2.59
734 840 1.592223 GACGGTGCTTGCCTCTACT 59.408 57.895 0.00 0.00 0.00 2.57
735 841 0.737715 GACGGTGCTTGCCTCTACTG 60.738 60.000 0.00 0.00 0.00 2.74
736 842 2.103042 CGGTGCTTGCCTCTACTGC 61.103 63.158 0.00 0.00 0.00 4.40
737 843 2.103042 GGTGCTTGCCTCTACTGCG 61.103 63.158 0.00 0.00 0.00 5.18
738 844 1.374758 GTGCTTGCCTCTACTGCGT 60.375 57.895 0.00 0.00 0.00 5.24
739 845 1.374631 TGCTTGCCTCTACTGCGTG 60.375 57.895 0.00 0.00 0.00 5.34
740 846 2.744768 GCTTGCCTCTACTGCGTGC 61.745 63.158 0.00 0.00 0.00 5.34
741 847 2.432456 TTGCCTCTACTGCGTGCG 60.432 61.111 0.00 0.00 0.00 5.34
742 848 3.220999 TTGCCTCTACTGCGTGCGT 62.221 57.895 0.00 0.00 0.00 5.24
743 849 1.868987 TTGCCTCTACTGCGTGCGTA 61.869 55.000 0.00 0.00 0.00 4.42
744 850 1.065928 GCCTCTACTGCGTGCGTAT 59.934 57.895 0.00 0.00 0.00 3.06
745 851 0.935366 GCCTCTACTGCGTGCGTATC 60.935 60.000 0.00 0.00 0.00 2.24
746 852 0.663688 CCTCTACTGCGTGCGTATCT 59.336 55.000 0.00 0.00 0.00 1.98
747 853 1.598183 CCTCTACTGCGTGCGTATCTG 60.598 57.143 0.00 0.00 0.00 2.90
748 854 0.380733 TCTACTGCGTGCGTATCTGG 59.619 55.000 0.00 0.00 0.00 3.86
749 855 0.380733 CTACTGCGTGCGTATCTGGA 59.619 55.000 0.00 0.00 0.00 3.86
750 856 0.380733 TACTGCGTGCGTATCTGGAG 59.619 55.000 0.00 0.00 0.00 3.86
751 857 1.139734 CTGCGTGCGTATCTGGAGT 59.860 57.895 0.00 0.00 0.00 3.85
752 858 1.142185 CTGCGTGCGTATCTGGAGTG 61.142 60.000 0.00 0.00 0.00 3.51
753 859 1.138883 GCGTGCGTATCTGGAGTGA 59.861 57.895 0.00 0.00 0.00 3.41
754 860 0.867753 GCGTGCGTATCTGGAGTGAG 60.868 60.000 0.00 0.00 0.00 3.51
755 861 0.248661 CGTGCGTATCTGGAGTGAGG 60.249 60.000 0.00 0.00 0.00 3.86
756 862 0.528684 GTGCGTATCTGGAGTGAGGC 60.529 60.000 0.00 0.00 0.00 4.70
757 863 0.684479 TGCGTATCTGGAGTGAGGCT 60.684 55.000 0.00 0.00 0.00 4.58
758 864 0.461961 GCGTATCTGGAGTGAGGCTT 59.538 55.000 0.00 0.00 0.00 4.35
759 865 1.537135 GCGTATCTGGAGTGAGGCTTC 60.537 57.143 0.00 0.00 0.00 3.86
760 866 1.067821 CGTATCTGGAGTGAGGCTTCC 59.932 57.143 0.00 0.00 0.00 3.46
761 867 1.414550 GTATCTGGAGTGAGGCTTCCC 59.585 57.143 1.35 0.00 0.00 3.97
762 868 0.043940 ATCTGGAGTGAGGCTTCCCT 59.956 55.000 1.35 0.00 46.74 4.20
763 869 0.710588 TCTGGAGTGAGGCTTCCCTA 59.289 55.000 1.35 0.00 43.12 3.53
764 870 1.078823 TCTGGAGTGAGGCTTCCCTAA 59.921 52.381 1.35 0.00 43.12 2.69
765 871 1.909302 CTGGAGTGAGGCTTCCCTAAA 59.091 52.381 1.35 0.00 43.12 1.85
766 872 2.305927 CTGGAGTGAGGCTTCCCTAAAA 59.694 50.000 1.35 0.00 43.12 1.52
767 873 2.919602 TGGAGTGAGGCTTCCCTAAAAT 59.080 45.455 1.35 0.00 43.12 1.82
768 874 4.108570 TGGAGTGAGGCTTCCCTAAAATA 58.891 43.478 1.35 0.00 43.12 1.40
769 875 4.538490 TGGAGTGAGGCTTCCCTAAAATAA 59.462 41.667 1.35 0.00 43.12 1.40
770 876 5.014755 TGGAGTGAGGCTTCCCTAAAATAAA 59.985 40.000 1.35 0.00 43.12 1.40
771 877 5.949952 GGAGTGAGGCTTCCCTAAAATAAAA 59.050 40.000 0.00 0.00 43.12 1.52
772 878 6.607600 GGAGTGAGGCTTCCCTAAAATAAAAT 59.392 38.462 0.00 0.00 43.12 1.82
773 879 7.778382 GGAGTGAGGCTTCCCTAAAATAAAATA 59.222 37.037 0.00 0.00 43.12 1.40
774 880 9.185680 GAGTGAGGCTTCCCTAAAATAAAATAA 57.814 33.333 0.00 0.00 43.12 1.40
775 881 9.541884 AGTGAGGCTTCCCTAAAATAAAATAAA 57.458 29.630 0.00 0.00 43.12 1.40
795 901 1.888436 AAATCTGGAGTGAGGCGCGA 61.888 55.000 12.10 0.00 0.00 5.87
796 902 2.290122 AATCTGGAGTGAGGCGCGAG 62.290 60.000 12.10 0.00 0.00 5.03
882 994 0.523072 TTGATTCCTTCAAGCGCTGC 59.477 50.000 12.58 0.00 39.44 5.25
928 1040 1.400737 CGGGGTCGTTAGGAGATTCT 58.599 55.000 0.00 0.00 0.00 2.40
975 1910 6.621931 TCCACCTCTCTCCCTCCTATATATAG 59.378 46.154 12.18 12.18 0.00 1.31
1030 1967 2.096248 CTCCTTCCAAGCTCTACTCGT 58.904 52.381 0.00 0.00 0.00 4.18
1054 1996 2.094894 CGCAAACGAAAGAGCAGATCAT 59.905 45.455 0.00 0.00 43.93 2.45
1061 2003 5.527951 ACGAAAGAGCAGATCATATCAGAC 58.472 41.667 0.00 0.00 0.00 3.51
1083 2025 1.001293 AGAGTGAGTTTGCATCTGCGA 59.999 47.619 0.00 0.00 45.83 5.10
1107 2052 1.915078 CGCCAATGGAGGGGAGAACT 61.915 60.000 2.05 0.00 43.81 3.01
1191 2138 2.659428 CTCCCCTTCCATTTCACATCC 58.341 52.381 0.00 0.00 0.00 3.51
1194 2141 1.288932 CCCTTCCATTTCACATCCCCT 59.711 52.381 0.00 0.00 0.00 4.79
1195 2142 2.659428 CCTTCCATTTCACATCCCCTC 58.341 52.381 0.00 0.00 0.00 4.30
1199 2146 3.192944 TCCATTTCACATCCCCTCTCTT 58.807 45.455 0.00 0.00 0.00 2.85
1202 2149 5.252863 TCCATTTCACATCCCCTCTCTTTTA 59.747 40.000 0.00 0.00 0.00 1.52
1203 2150 5.358160 CCATTTCACATCCCCTCTCTTTTAC 59.642 44.000 0.00 0.00 0.00 2.01
1206 2156 5.165961 TCACATCCCCTCTCTTTTACAAG 57.834 43.478 0.00 0.00 0.00 3.16
1267 2217 8.138074 CCACAGAAAAGATCTCTAATGACGATA 58.862 37.037 0.00 0.00 35.73 2.92
1268 2218 9.179552 CACAGAAAAGATCTCTAATGACGATAG 57.820 37.037 0.00 0.00 35.73 2.08
1291 2241 7.049799 AGTGTTTGTATGTTTGTTGGCTAAT 57.950 32.000 0.00 0.00 0.00 1.73
1498 2474 2.561419 TGTGTACCAAGGAGTAGACTGC 59.439 50.000 0.00 0.00 37.39 4.40
1500 2476 3.090037 TGTACCAAGGAGTAGACTGCTC 58.910 50.000 11.80 11.80 44.15 4.26
1501 2477 2.614134 ACCAAGGAGTAGACTGCTCT 57.386 50.000 18.52 4.06 44.15 4.09
1502 2478 2.175202 ACCAAGGAGTAGACTGCTCTG 58.825 52.381 18.52 10.75 44.15 3.35
1503 2479 2.175202 CCAAGGAGTAGACTGCTCTGT 58.825 52.381 18.52 5.52 44.15 3.41
1504 2480 2.165437 CCAAGGAGTAGACTGCTCTGTC 59.835 54.545 18.52 4.21 44.15 3.51
1505 2481 3.088532 CAAGGAGTAGACTGCTCTGTCT 58.911 50.000 18.52 12.79 44.15 3.41
1506 2482 4.265893 CAAGGAGTAGACTGCTCTGTCTA 58.734 47.826 18.52 11.11 44.15 2.59
1512 2488 2.722094 AGACTGCTCTGTCTACTCTGG 58.278 52.381 7.51 0.00 44.53 3.86
1513 2489 2.041081 AGACTGCTCTGTCTACTCTGGT 59.959 50.000 7.51 0.00 44.53 4.00
1514 2490 2.422127 GACTGCTCTGTCTACTCTGGTC 59.578 54.545 0.47 0.00 34.39 4.02
1519 2495 3.679361 GCTCTGTCTACTCTGGTCGTCTA 60.679 52.174 0.00 0.00 0.00 2.59
1552 2529 2.011947 GGAGGCGTACCACCAATAAAC 58.988 52.381 2.63 0.00 45.56 2.01
1553 2530 2.355412 GGAGGCGTACCACCAATAAACT 60.355 50.000 2.63 0.00 45.56 2.66
1554 2531 3.118665 GGAGGCGTACCACCAATAAACTA 60.119 47.826 2.63 0.00 45.56 2.24
1555 2532 4.506758 GAGGCGTACCACCAATAAACTAA 58.493 43.478 2.63 0.00 39.06 2.24
1556 2533 4.909001 AGGCGTACCACCAATAAACTAAA 58.091 39.130 2.63 0.00 39.06 1.85
1565 2542 8.477419 ACCACCAATAAACTAAATCCATATGG 57.523 34.615 16.25 16.25 0.00 2.74
1623 2603 1.280066 TGTCGTCGATGACATGCATG 58.720 50.000 31.55 25.09 43.62 4.06
1624 2604 1.280982 GTCGTCGATGACATGCATGT 58.719 50.000 31.82 31.82 45.16 3.21
1625 2605 1.005662 GTCGTCGATGACATGCATGTG 60.006 52.381 35.92 21.20 41.95 3.21
1626 2606 0.315625 CGTCGATGACATGCATGTGC 60.316 55.000 35.92 24.99 41.95 4.57
1645 2625 1.002033 GCATGCATGTTACTGGCTAGC 60.002 52.381 26.79 6.04 0.00 3.42
1646 2626 1.605710 CATGCATGTTACTGGCTAGCC 59.394 52.381 27.71 27.71 0.00 3.93
1659 2639 1.148759 GCTAGCCAGTACGCTTCAGC 61.149 60.000 2.29 1.84 40.39 4.26
1662 2642 0.671781 AGCCAGTACGCTTCAGCTTG 60.672 55.000 0.00 0.00 34.73 4.01
1668 2648 0.603065 TACGCTTCAGCTTGAGCAGA 59.397 50.000 16.05 0.00 45.16 4.26
1669 2649 0.036577 ACGCTTCAGCTTGAGCAGAT 60.037 50.000 16.05 1.16 45.16 2.90
1670 2650 1.085091 CGCTTCAGCTTGAGCAGATT 58.915 50.000 16.05 0.00 45.16 2.40
1671 2651 1.202043 CGCTTCAGCTTGAGCAGATTG 60.202 52.381 16.05 1.07 45.16 2.67
1673 2653 2.414293 GCTTCAGCTTGAGCAGATTGTG 60.414 50.000 12.11 0.00 45.16 3.33
1675 2655 1.348696 TCAGCTTGAGCAGATTGTGGA 59.651 47.619 5.70 0.00 45.16 4.02
1676 2656 2.156917 CAGCTTGAGCAGATTGTGGAA 58.843 47.619 5.70 0.00 45.16 3.53
1677 2657 2.095364 CAGCTTGAGCAGATTGTGGAAC 60.095 50.000 5.70 0.00 45.16 3.62
1678 2658 2.157738 GCTTGAGCAGATTGTGGAACT 58.842 47.619 0.00 0.00 41.59 3.01
1679 2659 2.095364 GCTTGAGCAGATTGTGGAACTG 60.095 50.000 0.00 0.00 41.59 3.16
1682 2662 3.603532 TGAGCAGATTGTGGAACTGATC 58.396 45.455 0.00 0.00 44.07 2.92
1702 2686 8.373981 ACTGATCGATCAATAAAGATTCTGGAT 58.626 33.333 27.09 1.82 36.18 3.41
1709 2693 9.118300 GATCAATAAAGATTCTGGATGTGAGTT 57.882 33.333 0.00 0.00 0.00 3.01
1730 2714 2.608546 TCCGTTTTGTTTCGTCGTGATT 59.391 40.909 0.00 0.00 0.00 2.57
1744 2740 5.635700 TCGTCGTGATTTGATTGTATGTTGA 59.364 36.000 0.00 0.00 0.00 3.18
1766 2762 3.515502 ACCAGATTCTTCATCGACCTTCA 59.484 43.478 0.00 0.00 36.93 3.02
1951 2948 6.347696 TGCAAATTCAAATCAGAACTTGGTT 58.652 32.000 0.00 0.00 35.81 3.67
1976 2973 0.391130 TTTGTCCTCGCTCGAATGGG 60.391 55.000 0.00 0.00 0.00 4.00
1977 2974 1.541310 TTGTCCTCGCTCGAATGGGT 61.541 55.000 0.00 0.00 0.00 4.51
1984 2981 0.721718 CGCTCGAATGGGTGTTTCTC 59.278 55.000 0.00 0.00 0.00 2.87
1986 2983 2.151202 GCTCGAATGGGTGTTTCTCAA 58.849 47.619 0.00 0.00 0.00 3.02
1993 2990 2.023673 TGGGTGTTTCTCAAGCACTTG 58.976 47.619 3.94 3.94 41.71 3.16
2021 3018 3.853831 TGAAATCGGTTAGCTCGTGTA 57.146 42.857 0.00 0.00 0.00 2.90
2052 3049 5.138800 TGTACGCGATTGATAGCTTTTTC 57.861 39.130 15.93 0.00 0.00 2.29
2085 3083 2.157474 CGATGAGCATTGTTGACGTTGA 59.843 45.455 0.00 0.00 0.00 3.18
2124 3122 1.675641 GCCTTCCGTCTTGCACCAT 60.676 57.895 0.00 0.00 0.00 3.55
2210 3210 2.766925 TTCCTTGGTGCCAGGCTGT 61.767 57.895 14.15 0.00 0.00 4.40
2234 3234 3.161450 GCCCGGCCATGAGAGGTA 61.161 66.667 2.24 0.00 0.00 3.08
2249 3251 2.494073 AGAGGTAGAAGCGGAAGAACTG 59.506 50.000 0.00 0.00 0.00 3.16
2313 3335 2.220133 CGGTTACGTCTGAGTTTGTTGG 59.780 50.000 0.00 0.00 34.81 3.77
2443 3477 0.229753 GGATGTAATGCGTCGCGAAG 59.770 55.000 18.03 18.03 33.98 3.79
2450 3484 0.801067 ATGCGTCGCGAAGTACTTCC 60.801 55.000 26.12 18.37 36.27 3.46
2454 3488 2.884207 CGCGAAGTACTTCCGCCC 60.884 66.667 29.50 17.28 36.50 6.13
2455 3489 2.577593 GCGAAGTACTTCCGCCCT 59.422 61.111 27.47 1.57 36.27 5.19
2456 3490 1.079336 GCGAAGTACTTCCGCCCTT 60.079 57.895 27.47 0.90 36.27 3.95
2457 3491 1.082679 GCGAAGTACTTCCGCCCTTC 61.083 60.000 27.47 8.47 36.27 3.46
2458 3492 0.531200 CGAAGTACTTCCGCCCTTCT 59.469 55.000 26.12 0.00 36.27 2.85
2459 3493 1.067071 CGAAGTACTTCCGCCCTTCTT 60.067 52.381 26.12 0.00 36.27 2.52
2460 3494 2.612221 CGAAGTACTTCCGCCCTTCTTT 60.612 50.000 26.12 0.00 36.27 2.52
2484 3518 2.994186 TTTCGGGGTATACTTCTGCC 57.006 50.000 2.25 0.00 0.00 4.85
2485 3519 2.170012 TTCGGGGTATACTTCTGCCT 57.830 50.000 2.25 0.00 0.00 4.75
2486 3520 1.700955 TCGGGGTATACTTCTGCCTC 58.299 55.000 2.25 0.00 0.00 4.70
2487 3521 1.063492 TCGGGGTATACTTCTGCCTCA 60.063 52.381 2.25 0.00 0.00 3.86
2488 3522 1.971357 CGGGGTATACTTCTGCCTCAT 59.029 52.381 2.25 0.00 0.00 2.90
2489 3523 2.289072 CGGGGTATACTTCTGCCTCATG 60.289 54.545 2.25 0.00 0.00 3.07
2490 3524 2.706190 GGGGTATACTTCTGCCTCATGT 59.294 50.000 2.25 0.00 0.00 3.21
2491 3525 3.901844 GGGGTATACTTCTGCCTCATGTA 59.098 47.826 2.25 0.00 0.00 2.29
2492 3526 4.532521 GGGGTATACTTCTGCCTCATGTAT 59.467 45.833 2.25 0.00 0.00 2.29
2493 3527 5.337652 GGGGTATACTTCTGCCTCATGTATC 60.338 48.000 2.25 0.00 0.00 2.24
2494 3528 5.337652 GGGTATACTTCTGCCTCATGTATCC 60.338 48.000 2.25 0.00 0.00 2.59
2495 3529 5.246203 GGTATACTTCTGCCTCATGTATCCA 59.754 44.000 2.25 0.00 0.00 3.41
2496 3530 3.550437 ACTTCTGCCTCATGTATCCAC 57.450 47.619 0.00 0.00 0.00 4.02
2497 3531 2.171448 ACTTCTGCCTCATGTATCCACC 59.829 50.000 0.00 0.00 0.00 4.61
2498 3532 0.752658 TCTGCCTCATGTATCCACCG 59.247 55.000 0.00 0.00 0.00 4.94
2499 3533 0.465705 CTGCCTCATGTATCCACCGT 59.534 55.000 0.00 0.00 0.00 4.83
2500 3534 0.177836 TGCCTCATGTATCCACCGTG 59.822 55.000 0.00 0.00 0.00 4.94
2501 3535 1.160329 GCCTCATGTATCCACCGTGC 61.160 60.000 0.00 0.00 0.00 5.34
2502 3536 0.177836 CCTCATGTATCCACCGTGCA 59.822 55.000 0.00 0.00 0.00 4.57
2503 3537 1.202687 CCTCATGTATCCACCGTGCAT 60.203 52.381 0.00 0.00 0.00 3.96
2504 3538 1.869132 CTCATGTATCCACCGTGCATG 59.131 52.381 0.00 0.00 38.49 4.06
2505 3539 0.308684 CATGTATCCACCGTGCATGC 59.691 55.000 11.82 11.82 32.03 4.06
2506 3540 0.181114 ATGTATCCACCGTGCATGCT 59.819 50.000 20.33 0.00 0.00 3.79
2507 3541 0.744057 TGTATCCACCGTGCATGCTG 60.744 55.000 20.33 11.33 0.00 4.41
2508 3542 0.744414 GTATCCACCGTGCATGCTGT 60.744 55.000 20.33 10.62 0.00 4.40
2509 3543 0.744057 TATCCACCGTGCATGCTGTG 60.744 55.000 20.33 20.86 0.00 3.66
2510 3544 2.753009 ATCCACCGTGCATGCTGTGT 62.753 55.000 20.33 9.87 0.00 3.72
2511 3545 2.253154 CACCGTGCATGCTGTGTG 59.747 61.111 20.33 17.64 0.00 3.82
2512 3546 2.110835 ACCGTGCATGCTGTGTGA 59.889 55.556 20.33 0.00 0.00 3.58
2513 3547 2.253758 ACCGTGCATGCTGTGTGAC 61.254 57.895 20.33 6.38 0.00 3.67
2514 3548 2.171701 CGTGCATGCTGTGTGACG 59.828 61.111 20.33 15.11 32.28 4.35
2515 3549 2.557805 GTGCATGCTGTGTGACGG 59.442 61.111 20.33 0.00 0.00 4.79
2516 3550 1.960763 GTGCATGCTGTGTGACGGA 60.961 57.895 20.33 0.00 0.00 4.69
2517 3551 1.003476 TGCATGCTGTGTGACGGAT 60.003 52.632 20.33 0.00 0.00 4.18
2518 3552 1.020861 TGCATGCTGTGTGACGGATC 61.021 55.000 20.33 0.00 0.00 3.36
2519 3553 2.001357 CATGCTGTGTGACGGATCG 58.999 57.895 0.00 0.00 0.00 3.69
2520 3554 1.153568 ATGCTGTGTGACGGATCGG 60.154 57.895 0.00 0.00 0.00 4.18
2521 3555 3.188786 GCTGTGTGACGGATCGGC 61.189 66.667 0.00 0.00 34.27 5.54
2522 3556 2.509336 CTGTGTGACGGATCGGCC 60.509 66.667 0.00 0.00 31.60 6.13
2523 3557 4.077184 TGTGTGACGGATCGGCCC 62.077 66.667 0.00 0.00 31.60 5.80
2531 3565 2.508928 GGATCGGCCCGATTTGGA 59.491 61.111 21.39 0.00 47.00 3.53
2532 3566 1.153046 GGATCGGCCCGATTTGGAA 60.153 57.895 21.39 0.00 47.00 3.53
2533 3567 0.537371 GGATCGGCCCGATTTGGAAT 60.537 55.000 21.39 0.00 47.00 3.01
2534 3568 0.875059 GATCGGCCCGATTTGGAATC 59.125 55.000 21.39 2.05 47.00 2.52
2535 3569 0.884704 ATCGGCCCGATTTGGAATCG 60.885 55.000 14.09 14.30 44.59 3.34
2536 3570 1.522806 CGGCCCGATTTGGAATCGA 60.523 57.895 20.86 0.00 43.59 3.59
2537 3571 1.772063 CGGCCCGATTTGGAATCGAC 61.772 60.000 20.86 13.46 43.59 4.20
2538 3572 1.444917 GGCCCGATTTGGAATCGACC 61.445 60.000 20.86 17.42 43.59 4.79
2539 3573 0.746563 GCCCGATTTGGAATCGACCA 60.747 55.000 20.86 0.00 43.59 4.02
2540 3574 1.967319 CCCGATTTGGAATCGACCAT 58.033 50.000 20.86 0.00 43.59 3.55
2541 3575 2.297701 CCCGATTTGGAATCGACCATT 58.702 47.619 20.86 0.00 43.59 3.16
2542 3576 2.290641 CCCGATTTGGAATCGACCATTC 59.709 50.000 20.86 0.00 43.59 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.903682 TTGCAAAAAGTTCATCAATTTGAAAAA 57.096 22.222 2.68 0.00 37.36 1.94
21 22 9.903682 TTTGCAAAAAGTTCATCAATTTGAAAA 57.096 22.222 10.02 0.00 36.60 2.29
28 29 9.724839 CAGAAAATTTGCAAAAAGTTCATCAAT 57.275 25.926 17.19 1.70 0.00 2.57
29 30 8.182881 CCAGAAAATTTGCAAAAAGTTCATCAA 58.817 29.630 17.19 0.00 0.00 2.57
30 31 7.551974 TCCAGAAAATTTGCAAAAAGTTCATCA 59.448 29.630 17.19 5.15 0.00 3.07
31 32 7.918643 TCCAGAAAATTTGCAAAAAGTTCATC 58.081 30.769 17.19 8.42 0.00 2.92
32 33 7.862512 TCCAGAAAATTTGCAAAAAGTTCAT 57.137 28.000 17.19 7.28 0.00 2.57
33 34 7.862512 ATCCAGAAAATTTGCAAAAAGTTCA 57.137 28.000 17.19 5.18 0.00 3.18
111 112 9.952341 GCCAAATTTTATAAAAGTTCATCGAAC 57.048 29.630 18.08 0.00 42.25 3.95
114 115 8.388319 TCGCCAAATTTTATAAAAGTTCATCG 57.612 30.769 18.08 18.74 34.39 3.84
128 129 8.432110 AGTTGAAAAATAGTTCGCCAAATTTT 57.568 26.923 0.00 0.00 34.00 1.82
218 221 6.183360 GCATGGATTTCGAAAAGCAAATGATT 60.183 34.615 15.66 0.00 0.00 2.57
221 224 4.389382 TGCATGGATTTCGAAAAGCAAATG 59.611 37.500 15.66 16.09 0.00 2.32
223 226 3.740321 GTGCATGGATTTCGAAAAGCAAA 59.260 39.130 15.66 3.37 32.03 3.68
226 229 2.945278 TGTGCATGGATTTCGAAAAGC 58.055 42.857 15.66 13.72 0.00 3.51
227 230 5.062558 GGAAATGTGCATGGATTTCGAAAAG 59.937 40.000 15.66 4.23 38.80 2.27
228 231 4.928615 GGAAATGTGCATGGATTTCGAAAA 59.071 37.500 15.66 0.00 38.80 2.29
233 236 3.781079 TCGGAAATGTGCATGGATTTC 57.219 42.857 15.38 15.38 37.69 2.17
239 242 2.428171 AGGGAAATCGGAAATGTGCATG 59.572 45.455 0.00 0.00 0.00 4.06
240 243 2.738743 AGGGAAATCGGAAATGTGCAT 58.261 42.857 0.00 0.00 0.00 3.96
250 253 5.813080 AGACGAAAATTTAGGGAAATCGG 57.187 39.130 10.05 0.00 34.01 4.18
254 257 8.228035 TCTCAAAAGACGAAAATTTAGGGAAA 57.772 30.769 0.00 0.00 0.00 3.13
350 355 0.908198 CCTAGGGCCCATCTAGATGC 59.092 60.000 27.56 15.56 37.08 3.91
376 396 2.547642 GCTGGTGTCCATGAGATAGCTC 60.548 54.545 0.00 0.00 41.67 4.09
381 408 3.377253 AATTGCTGGTGTCCATGAGAT 57.623 42.857 0.00 0.00 30.82 2.75
412 440 6.268797 GGCGTATAAATTGCCTTTTTAAGC 57.731 37.500 0.00 7.89 45.40 3.09
432 464 4.438744 GGTGATTTCTCAGTAAAATGGGCG 60.439 45.833 0.00 0.00 30.18 6.13
435 467 5.181245 ACACGGTGATTTCTCAGTAAAATGG 59.819 40.000 16.29 0.00 30.18 3.16
436 468 6.241207 ACACGGTGATTTCTCAGTAAAATG 57.759 37.500 16.29 0.00 30.18 2.32
451 483 2.466846 GACTTCGAGAAAACACGGTGA 58.533 47.619 16.29 0.00 0.00 4.02
466 498 5.422214 TCTATCCAGGACTTTTGGACTTC 57.578 43.478 0.00 0.00 46.85 3.01
477 516 0.318762 GCACCCGATCTATCCAGGAC 59.681 60.000 0.00 0.00 0.00 3.85
531 574 0.038166 TTGAGGAGGTGTTCATGCCC 59.962 55.000 0.00 0.00 0.00 5.36
566 609 2.107950 TGGCCATACTACAGCAACAC 57.892 50.000 0.00 0.00 0.00 3.32
583 630 4.708177 ACCATCTAATCCGAACTGATTGG 58.292 43.478 0.00 0.00 35.77 3.16
602 649 2.616960 CAGCATCACGTAGCTAAACCA 58.383 47.619 8.72 0.00 39.50 3.67
604 651 2.271800 AGCAGCATCACGTAGCTAAAC 58.728 47.619 8.72 3.29 39.50 2.01
667 719 9.098355 CCGCATGTATATAGTTGCACTATTTAT 57.902 33.333 14.15 5.84 38.17 1.40
669 721 6.128282 GCCGCATGTATATAGTTGCACTATTT 60.128 38.462 14.15 8.47 38.17 1.40
681 787 4.027674 ACATTTGGGCCGCATGTATATA 57.972 40.909 16.62 0.00 29.07 0.86
683 789 2.356665 ACATTTGGGCCGCATGTATA 57.643 45.000 16.62 0.00 29.07 1.47
704 810 0.100861 GCACCGTCCTAGTGTAGCTC 59.899 60.000 0.00 0.00 37.56 4.09
705 811 0.323542 AGCACCGTCCTAGTGTAGCT 60.324 55.000 0.00 0.00 37.56 3.32
706 812 0.531200 AAGCACCGTCCTAGTGTAGC 59.469 55.000 0.00 0.00 37.56 3.58
707 813 1.736032 GCAAGCACCGTCCTAGTGTAG 60.736 57.143 0.00 0.00 37.56 2.74
708 814 0.245539 GCAAGCACCGTCCTAGTGTA 59.754 55.000 0.00 0.00 37.56 2.90
709 815 1.004918 GCAAGCACCGTCCTAGTGT 60.005 57.895 0.00 0.00 37.56 3.55
710 816 1.741770 GGCAAGCACCGTCCTAGTG 60.742 63.158 0.00 0.00 38.30 2.74
711 817 1.889530 GAGGCAAGCACCGTCCTAGT 61.890 60.000 0.00 0.00 33.69 2.57
712 818 1.153549 GAGGCAAGCACCGTCCTAG 60.154 63.158 0.00 0.00 33.69 3.02
713 819 0.323999 TAGAGGCAAGCACCGTCCTA 60.324 55.000 0.00 0.00 33.69 2.94
714 820 1.609501 TAGAGGCAAGCACCGTCCT 60.610 57.895 0.00 0.00 33.69 3.85
715 821 1.448013 GTAGAGGCAAGCACCGTCC 60.448 63.158 0.00 0.00 33.69 4.79
716 822 0.737715 CAGTAGAGGCAAGCACCGTC 60.738 60.000 0.00 0.00 33.69 4.79
717 823 1.293498 CAGTAGAGGCAAGCACCGT 59.707 57.895 0.00 0.00 33.69 4.83
718 824 2.103042 GCAGTAGAGGCAAGCACCG 61.103 63.158 0.00 0.00 33.69 4.94
719 825 2.103042 CGCAGTAGAGGCAAGCACC 61.103 63.158 0.00 0.00 0.00 5.01
720 826 1.374758 ACGCAGTAGAGGCAAGCAC 60.375 57.895 0.00 0.00 41.94 4.40
721 827 1.374631 CACGCAGTAGAGGCAAGCA 60.375 57.895 0.00 0.00 41.61 3.91
722 828 2.744768 GCACGCAGTAGAGGCAAGC 61.745 63.158 0.00 0.00 41.61 4.01
723 829 2.447887 CGCACGCAGTAGAGGCAAG 61.448 63.158 0.00 0.00 41.61 4.01
724 830 1.868987 TACGCACGCAGTAGAGGCAA 61.869 55.000 0.00 0.00 41.61 4.52
725 831 1.663379 ATACGCACGCAGTAGAGGCA 61.663 55.000 0.00 0.00 41.61 4.75
726 832 0.935366 GATACGCACGCAGTAGAGGC 60.935 60.000 0.00 0.00 41.61 4.70
727 833 0.663688 AGATACGCACGCAGTAGAGG 59.336 55.000 0.00 0.00 41.61 3.69
728 834 1.598183 CCAGATACGCACGCAGTAGAG 60.598 57.143 0.00 0.00 41.61 2.43
729 835 0.380733 CCAGATACGCACGCAGTAGA 59.619 55.000 0.00 0.00 41.61 2.59
730 836 0.380733 TCCAGATACGCACGCAGTAG 59.619 55.000 0.00 0.00 41.61 2.57
731 837 0.380733 CTCCAGATACGCACGCAGTA 59.619 55.000 0.00 0.00 41.61 2.74
733 839 1.139734 ACTCCAGATACGCACGCAG 59.860 57.895 0.00 0.00 0.00 5.18
734 840 1.153842 CACTCCAGATACGCACGCA 60.154 57.895 0.00 0.00 0.00 5.24
735 841 0.867753 CTCACTCCAGATACGCACGC 60.868 60.000 0.00 0.00 0.00 5.34
736 842 0.248661 CCTCACTCCAGATACGCACG 60.249 60.000 0.00 0.00 0.00 5.34
737 843 0.528684 GCCTCACTCCAGATACGCAC 60.529 60.000 0.00 0.00 0.00 5.34
738 844 0.684479 AGCCTCACTCCAGATACGCA 60.684 55.000 0.00 0.00 0.00 5.24
739 845 0.461961 AAGCCTCACTCCAGATACGC 59.538 55.000 0.00 0.00 0.00 4.42
740 846 1.067821 GGAAGCCTCACTCCAGATACG 59.932 57.143 0.00 0.00 0.00 3.06
741 847 1.414550 GGGAAGCCTCACTCCAGATAC 59.585 57.143 0.00 0.00 0.00 2.24
742 848 1.292242 AGGGAAGCCTCACTCCAGATA 59.708 52.381 0.00 0.00 23.33 1.98
743 849 0.043940 AGGGAAGCCTCACTCCAGAT 59.956 55.000 0.00 0.00 23.33 2.90
744 850 0.710588 TAGGGAAGCCTCACTCCAGA 59.289 55.000 0.00 0.00 36.44 3.86
745 851 1.573108 TTAGGGAAGCCTCACTCCAG 58.427 55.000 0.00 0.00 36.44 3.86
746 852 2.038863 TTTAGGGAAGCCTCACTCCA 57.961 50.000 0.00 0.00 36.44 3.86
747 853 3.653835 ATTTTAGGGAAGCCTCACTCC 57.346 47.619 0.00 0.00 36.44 3.85
748 854 7.646548 ATTTTATTTTAGGGAAGCCTCACTC 57.353 36.000 0.00 0.00 36.44 3.51
749 855 9.541884 TTTATTTTATTTTAGGGAAGCCTCACT 57.458 29.630 0.00 0.00 39.30 3.41
774 880 1.168714 GCGCCTCACTCCAGATTTTT 58.831 50.000 0.00 0.00 0.00 1.94
775 881 1.021390 CGCGCCTCACTCCAGATTTT 61.021 55.000 0.00 0.00 0.00 1.82
776 882 1.448540 CGCGCCTCACTCCAGATTT 60.449 57.895 0.00 0.00 0.00 2.17
777 883 2.185350 CGCGCCTCACTCCAGATT 59.815 61.111 0.00 0.00 0.00 2.40
992 1927 6.016443 GGAAGGAGATTGATTGATGATTCACC 60.016 42.308 0.00 0.00 0.00 4.02
1054 1996 3.578282 TGCAAACTCACTCTGGTCTGATA 59.422 43.478 0.00 0.00 0.00 2.15
1061 2003 1.467734 GCAGATGCAAACTCACTCTGG 59.532 52.381 11.96 0.00 41.59 3.86
1107 2052 0.241213 CGACGAGGAAACAGAGAGCA 59.759 55.000 0.00 0.00 0.00 4.26
1168 2113 1.177401 GTGAAATGGAAGGGGAGCAC 58.823 55.000 0.00 0.00 0.00 4.40
1191 2138 7.335673 GGAGATCTTTTCTTGTAAAAGAGAGGG 59.664 40.741 15.67 0.00 45.85 4.30
1194 2141 9.495572 GAAGGAGATCTTTTCTTGTAAAAGAGA 57.504 33.333 15.67 0.00 45.85 3.10
1195 2142 9.500785 AGAAGGAGATCTTTTCTTGTAAAAGAG 57.499 33.333 15.67 0.00 45.85 2.85
1199 2146 9.067986 GGAAAGAAGGAGATCTTTTCTTGTAAA 57.932 33.333 24.91 0.00 46.77 2.01
1202 2149 6.007076 GGGAAAGAAGGAGATCTTTTCTTGT 58.993 40.000 24.91 18.27 46.77 3.16
1203 2150 6.244654 AGGGAAAGAAGGAGATCTTTTCTTG 58.755 40.000 24.91 0.00 46.77 3.02
1206 2156 7.665974 TGTAAAGGGAAAGAAGGAGATCTTTTC 59.334 37.037 0.00 4.78 46.77 2.29
1223 2173 3.907474 TGTGGAACAGAGATGTAAAGGGA 59.093 43.478 0.00 0.00 45.67 4.20
1267 2217 6.458232 TTAGCCAACAAACATACAAACACT 57.542 33.333 0.00 0.00 0.00 3.55
1268 2218 7.563270 CAATTAGCCAACAAACATACAAACAC 58.437 34.615 0.00 0.00 0.00 3.32
1498 2474 2.980568 AGACGACCAGAGTAGACAGAG 58.019 52.381 0.00 0.00 0.00 3.35
1499 2475 3.514706 ACTAGACGACCAGAGTAGACAGA 59.485 47.826 0.00 0.00 0.00 3.41
1500 2476 3.864243 ACTAGACGACCAGAGTAGACAG 58.136 50.000 0.00 0.00 0.00 3.51
1501 2477 3.977134 ACTAGACGACCAGAGTAGACA 57.023 47.619 0.00 0.00 0.00 3.41
1502 2478 6.923928 AATAACTAGACGACCAGAGTAGAC 57.076 41.667 0.00 0.00 0.00 2.59
1503 2479 6.705381 GCTAATAACTAGACGACCAGAGTAGA 59.295 42.308 0.00 0.00 0.00 2.59
1504 2480 6.707161 AGCTAATAACTAGACGACCAGAGTAG 59.293 42.308 0.00 0.00 0.00 2.57
1505 2481 6.590068 AGCTAATAACTAGACGACCAGAGTA 58.410 40.000 0.00 0.00 0.00 2.59
1506 2482 5.438833 AGCTAATAACTAGACGACCAGAGT 58.561 41.667 0.00 0.00 0.00 3.24
1507 2483 6.148150 CCTAGCTAATAACTAGACGACCAGAG 59.852 46.154 0.00 0.00 39.64 3.35
1508 2484 5.996513 CCTAGCTAATAACTAGACGACCAGA 59.003 44.000 0.00 0.00 39.64 3.86
1509 2485 5.181622 CCCTAGCTAATAACTAGACGACCAG 59.818 48.000 0.00 0.00 39.64 4.00
1510 2486 5.068636 CCCTAGCTAATAACTAGACGACCA 58.931 45.833 0.00 0.00 39.64 4.02
1511 2487 5.312079 TCCCTAGCTAATAACTAGACGACC 58.688 45.833 0.00 0.00 39.64 4.79
1512 2488 5.412286 CCTCCCTAGCTAATAACTAGACGAC 59.588 48.000 0.00 0.00 39.64 4.34
1513 2489 5.558818 CCTCCCTAGCTAATAACTAGACGA 58.441 45.833 0.00 0.00 39.64 4.20
1514 2490 4.156373 GCCTCCCTAGCTAATAACTAGACG 59.844 50.000 0.00 0.00 39.64 4.18
1519 2495 2.960163 ACGCCTCCCTAGCTAATAACT 58.040 47.619 0.00 0.00 0.00 2.24
1556 2533 9.950306 ACTATTATTCTCTAGCTCCATATGGAT 57.050 33.333 24.73 13.64 44.46 3.41
1595 2572 4.226761 TGTCATCGACGACATGCATATAC 58.773 43.478 10.77 0.00 40.94 1.47
1623 2603 0.813184 AGCCAGTAACATGCATGCAC 59.187 50.000 25.37 22.46 0.00 4.57
1624 2604 2.291365 CTAGCCAGTAACATGCATGCA 58.709 47.619 26.53 25.04 0.00 3.96
1625 2605 1.002033 GCTAGCCAGTAACATGCATGC 60.002 52.381 26.53 11.82 0.00 4.06
1626 2606 1.605710 GGCTAGCCAGTAACATGCATG 59.394 52.381 29.33 25.09 35.81 4.06
1627 2607 1.212688 TGGCTAGCCAGTAACATGCAT 59.787 47.619 32.88 0.00 41.89 3.96
1628 2608 0.617935 TGGCTAGCCAGTAACATGCA 59.382 50.000 32.88 5.59 41.89 3.96
1629 2609 3.476740 TGGCTAGCCAGTAACATGC 57.523 52.632 32.88 2.62 41.89 4.06
1639 2619 0.528684 CTGAAGCGTACTGGCTAGCC 60.529 60.000 27.71 27.71 43.93 3.93
1659 2639 3.405831 TCAGTTCCACAATCTGCTCAAG 58.594 45.455 0.00 0.00 0.00 3.02
1662 2642 2.606725 CGATCAGTTCCACAATCTGCTC 59.393 50.000 0.00 0.00 0.00 4.26
1668 2648 7.770433 TCTTTATTGATCGATCAGTTCCACAAT 59.230 33.333 25.84 16.91 38.19 2.71
1669 2649 7.102993 TCTTTATTGATCGATCAGTTCCACAA 58.897 34.615 25.84 12.66 38.19 3.33
1670 2650 6.639563 TCTTTATTGATCGATCAGTTCCACA 58.360 36.000 25.84 11.90 38.19 4.17
1671 2651 7.721286 ATCTTTATTGATCGATCAGTTCCAC 57.279 36.000 25.84 0.00 38.19 4.02
1673 2653 8.494347 CAGAATCTTTATTGATCGATCAGTTCC 58.506 37.037 25.84 11.05 38.19 3.62
1675 2655 8.206867 TCCAGAATCTTTATTGATCGATCAGTT 58.793 33.333 25.84 19.81 38.19 3.16
1676 2656 7.730084 TCCAGAATCTTTATTGATCGATCAGT 58.270 34.615 25.95 25.14 38.19 3.41
1677 2657 8.657729 CATCCAGAATCTTTATTGATCGATCAG 58.342 37.037 25.95 15.39 38.19 2.90
1678 2658 8.152898 ACATCCAGAATCTTTATTGATCGATCA 58.847 33.333 23.99 23.99 34.44 2.92
1679 2659 8.441608 CACATCCAGAATCTTTATTGATCGATC 58.558 37.037 18.72 18.72 0.00 3.69
1682 2662 7.440556 ACTCACATCCAGAATCTTTATTGATCG 59.559 37.037 0.00 0.00 0.00 3.69
1702 2686 2.743126 ACGAAACAAAACGGAACTCACA 59.257 40.909 0.00 0.00 0.00 3.58
1709 2693 1.638133 TCACGACGAAACAAAACGGA 58.362 45.000 0.00 0.00 0.00 4.69
1730 2714 7.665145 TGAAGAATCTGGTCAACATACAATCAA 59.335 33.333 0.00 0.00 0.00 2.57
1744 2740 3.515502 TGAAGGTCGATGAAGAATCTGGT 59.484 43.478 0.00 0.00 32.61 4.00
1830 2826 9.401058 AGCATCTTAATTGCAGATTAGTTAAGT 57.599 29.630 11.72 0.00 42.62 2.24
1837 2833 9.787532 GTGTTTAAGCATCTTAATTGCAGATTA 57.212 29.630 11.72 0.00 42.62 1.75
1838 2834 7.761249 GGTGTTTAAGCATCTTAATTGCAGATT 59.239 33.333 11.72 0.00 42.62 2.40
1839 2835 7.123247 AGGTGTTTAAGCATCTTAATTGCAGAT 59.877 33.333 0.00 0.00 42.62 2.90
1840 2836 6.434028 AGGTGTTTAAGCATCTTAATTGCAGA 59.566 34.615 0.00 0.00 42.62 4.26
1841 2837 6.624423 AGGTGTTTAAGCATCTTAATTGCAG 58.376 36.000 0.00 0.00 42.62 4.41
1923 2919 7.295201 CAAGTTCTGATTTGAATTTGCAATGG 58.705 34.615 0.00 0.00 37.04 3.16
1951 2948 0.667487 CGAGCGAGGACAAAGAAGCA 60.667 55.000 0.00 0.00 0.00 3.91
1976 2973 2.223572 CCACCAAGTGCTTGAGAAACAC 60.224 50.000 12.99 0.00 42.93 3.32
1977 2974 2.023673 CCACCAAGTGCTTGAGAAACA 58.976 47.619 12.99 0.00 42.93 2.83
1984 2981 1.110442 TCAAACCCACCAAGTGCTTG 58.890 50.000 5.03 5.03 40.13 4.01
1986 2983 1.859302 TTTCAAACCCACCAAGTGCT 58.141 45.000 0.00 0.00 31.34 4.40
1993 2990 2.094906 GCTAACCGATTTCAAACCCACC 60.095 50.000 0.00 0.00 0.00 4.61
2021 3018 0.321298 AATCGCGTACAAACCAGGCT 60.321 50.000 5.77 0.00 0.00 4.58
2052 3049 1.131315 TGCTCATCGTCAAGTCGAGAG 59.869 52.381 0.00 0.00 43.00 3.20
2234 3234 1.374758 CCGCAGTTCTTCCGCTTCT 60.375 57.895 0.00 0.00 0.00 2.85
2282 3302 1.064906 AGACGTAACCGATCCAGGAGA 60.065 52.381 0.00 0.00 37.88 3.71
2286 3306 1.743958 ACTCAGACGTAACCGATCCAG 59.256 52.381 0.00 0.00 37.88 3.86
2287 3307 1.830279 ACTCAGACGTAACCGATCCA 58.170 50.000 0.00 0.00 37.88 3.41
2415 3449 3.857052 ACGCATTACATCCTTTTCTCGA 58.143 40.909 0.00 0.00 0.00 4.04
2424 3458 0.229753 CTTCGCGACGCATTACATCC 59.770 55.000 21.35 0.00 0.00 3.51
2468 3502 1.410004 TGAGGCAGAAGTATACCCCG 58.590 55.000 0.00 0.00 0.00 5.73
2488 3522 3.387706 ACAGCATGCACGGTGGATACA 62.388 52.381 21.98 1.68 44.45 2.29
2489 3523 0.744414 ACAGCATGCACGGTGGATAC 60.744 55.000 21.98 9.74 42.53 2.24
2490 3524 0.744057 CACAGCATGCACGGTGGATA 60.744 55.000 21.98 0.00 42.53 2.59
2491 3525 2.042259 CACAGCATGCACGGTGGAT 61.042 57.895 21.98 9.51 42.53 3.41
2492 3526 2.669229 CACAGCATGCACGGTGGA 60.669 61.111 21.98 7.67 42.53 4.02
2493 3527 2.979676 ACACAGCATGCACGGTGG 60.980 61.111 28.76 17.16 42.53 4.61
2494 3528 2.253051 TCACACAGCATGCACGGTG 61.253 57.895 25.85 25.85 42.53 4.94
2495 3529 2.110835 TCACACAGCATGCACGGT 59.889 55.556 21.98 12.13 42.53 4.83
2496 3530 2.557805 GTCACACAGCATGCACGG 59.442 61.111 21.98 11.43 42.53 4.94
2497 3531 2.171701 CGTCACACAGCATGCACG 59.828 61.111 21.98 15.79 42.53 5.34
2498 3532 1.300971 ATCCGTCACACAGCATGCAC 61.301 55.000 21.98 7.01 42.53 4.57
2499 3533 1.003476 ATCCGTCACACAGCATGCA 60.003 52.632 21.98 0.00 42.53 3.96
2500 3534 1.717937 GATCCGTCACACAGCATGC 59.282 57.895 10.51 10.51 42.53 4.06
2501 3535 1.423721 CCGATCCGTCACACAGCATG 61.424 60.000 0.00 0.00 46.00 4.06
2502 3536 1.153568 CCGATCCGTCACACAGCAT 60.154 57.895 0.00 0.00 0.00 3.79
2503 3537 2.261361 CCGATCCGTCACACAGCA 59.739 61.111 0.00 0.00 0.00 4.41
2504 3538 3.188786 GCCGATCCGTCACACAGC 61.189 66.667 0.00 0.00 0.00 4.40
2505 3539 2.509336 GGCCGATCCGTCACACAG 60.509 66.667 0.00 0.00 0.00 3.66
2506 3540 4.077184 GGGCCGATCCGTCACACA 62.077 66.667 0.00 0.00 34.94 3.72
2509 3543 2.918230 AAATCGGGCCGATCCGTCAC 62.918 60.000 38.76 0.00 46.30 3.67
2510 3544 2.727392 AAATCGGGCCGATCCGTCA 61.727 57.895 38.76 13.20 46.30 4.35
2511 3545 2.108362 AAATCGGGCCGATCCGTC 59.892 61.111 38.76 0.00 46.30 4.79
2512 3546 2.203015 CAAATCGGGCCGATCCGT 60.203 61.111 38.76 24.70 46.30 4.69
2513 3547 2.933878 TTCCAAATCGGGCCGATCCG 62.934 60.000 38.76 30.17 46.30 4.18
2514 3548 0.537371 ATTCCAAATCGGGCCGATCC 60.537 55.000 38.76 0.00 46.30 3.36
2515 3549 0.875059 GATTCCAAATCGGGCCGATC 59.125 55.000 38.76 23.14 46.30 3.69
2517 3551 1.522806 CGATTCCAAATCGGGCCGA 60.523 57.895 33.10 33.10 41.13 5.54
2518 3552 1.522806 TCGATTCCAAATCGGGCCG 60.523 57.895 22.51 22.51 41.45 6.13
2519 3553 1.444917 GGTCGATTCCAAATCGGGCC 61.445 60.000 18.73 16.77 41.45 5.80
2520 3554 0.746563 TGGTCGATTCCAAATCGGGC 60.747 55.000 18.73 12.92 41.45 6.13
2521 3555 1.967319 ATGGTCGATTCCAAATCGGG 58.033 50.000 18.73 0.00 41.09 5.14
2522 3556 3.609103 GAATGGTCGATTCCAAATCGG 57.391 47.619 18.73 4.37 41.09 4.18


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

AutoCloner maintained by Alex Coulton.