Multiple sequence alignment - TraesCS3B01G558700

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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 TraesCS3B01G558700 chr3B 100.000 3434 0 0 1 3434 793018358 793014925 0.000000e+00 6342.0
1 TraesCS3B01G558700 chr3B 93.796 1773 92 7 789 2547 793030869 793029101 0.000000e+00 2649.0
2 TraesCS3B01G558700 chr3B 89.608 510 15 13 2608 3086 793029082 793028580 6.300000e-172 614.0
3 TraesCS3B01G558700 chr3B 93.373 332 16 1 3103 3434 793028423 793028098 1.430000e-133 486.0
4 TraesCS3B01G558700 chr3B 83.680 337 27 11 229 546 793031344 793031017 3.350000e-75 292.0
5 TraesCS3B01G558700 chr3B 91.558 154 12 1 30 182 793031579 793031426 9.660000e-51 211.0
6 TraesCS3B01G558700 chr3B 100.000 30 0 0 1 30 793060537 793060508 4.790000e-04 56.5
7 TraesCS3B01G558700 chr3D 93.309 1928 106 6 852 2760 591616072 591617995 0.000000e+00 2824.0
8 TraesCS3B01G558700 chr3D 95.157 351 13 1 3088 3434 591618402 591618752 5.010000e-153 551.0
9 TraesCS3B01G558700 chr3D 82.194 702 66 24 1754 2434 591369552 591368889 1.800000e-152 549.0
10 TraesCS3B01G558700 chr3D 93.396 212 4 4 2878 3086 591618045 591618249 4.310000e-79 305.0
11 TraesCS3B01G558700 chr3D 89.308 159 13 2 634 792 23953227 23953073 2.700000e-46 196.0
12 TraesCS3B01G558700 chr3A 93.075 1603 96 3 860 2448 721663720 721665321 0.000000e+00 2331.0
13 TraesCS3B01G558700 chr3A 80.628 191 28 7 344 527 487440396 487440208 4.620000e-29 139.0
14 TraesCS3B01G558700 chr3A 75.211 355 23 30 1503 1849 721645363 721645066 1.300000e-19 108.0
15 TraesCS3B01G558700 chr3A 95.556 45 2 0 343 387 721673803 721673847 4.750000e-09 73.1
16 TraesCS3B01G558700 chr2D 82.625 259 41 1 1770 2028 45874899 45875153 3.450000e-55 226.0
17 TraesCS3B01G558700 chr2D 84.672 137 16 5 2338 2472 45875807 45875940 7.730000e-27 132.0
18 TraesCS3B01G558700 chr2D 91.667 48 4 0 2837 2884 539450312 539450265 2.210000e-07 67.6
19 TraesCS3B01G558700 chr7B 90.323 155 13 2 637 791 437671061 437671213 5.810000e-48 202.0
20 TraesCS3B01G558700 chr7B 89.744 156 15 1 637 792 176324894 176324740 7.520000e-47 198.0
21 TraesCS3B01G558700 chr7B 89.103 156 11 4 625 780 328262941 328263090 4.520000e-44 189.0
22 TraesCS3B01G558700 chr7B 95.238 42 2 0 3327 3368 741667191 741667150 2.210000e-07 67.6
23 TraesCS3B01G558700 chr2A 80.989 263 40 5 1587 1847 62390986 62390732 2.090000e-47 200.0
24 TraesCS3B01G558700 chr2B 90.667 150 10 2 634 780 723181506 723181654 2.700000e-46 196.0
25 TraesCS3B01G558700 chr6D 87.879 165 16 2 634 794 194244169 194244005 1.260000e-44 191.0
26 TraesCS3B01G558700 chr6D 97.619 42 1 0 3328 3369 38155306 38155347 4.750000e-09 73.1
27 TraesCS3B01G558700 chr1B 90.476 147 11 1 634 780 12229496 12229639 1.260000e-44 191.0
28 TraesCS3B01G558700 chr1B 88.636 44 4 1 3024 3067 595633812 595633770 6.000000e-03 52.8
29 TraesCS3B01G558700 chr5D 88.199 161 15 4 634 792 230650832 230650990 4.520000e-44 189.0
30 TraesCS3B01G558700 chr5D 91.667 48 4 0 2837 2884 196081926 196081973 2.210000e-07 67.6
31 TraesCS3B01G558700 chr5D 87.719 57 7 0 2828 2884 520748902 520748958 2.210000e-07 67.6
32 TraesCS3B01G558700 chr4B 87.805 164 12 4 634 791 19746353 19746514 5.850000e-43 185.0
33 TraesCS3B01G558700 chr4B 93.478 46 2 1 3324 3368 580714137 580714092 2.210000e-07 67.6
34 TraesCS3B01G558700 chr1D 100.000 43 0 0 3327 3369 318382793 318382835 2.840000e-11 80.5
35 TraesCS3B01G558700 chr1D 95.556 45 0 1 3327 3369 394271114 394271158 1.710000e-08 71.3
36 TraesCS3B01G558700 chr1D 91.489 47 4 0 2838 2884 3458373 3458327 7.950000e-07 65.8
37 TraesCS3B01G558700 chr6B 92.157 51 4 0 2837 2887 663547229 663547179 4.750000e-09 73.1
38 TraesCS3B01G558700 chr5A 97.619 42 1 0 3327 3368 369634719 369634760 4.750000e-09 73.1
39 TraesCS3B01G558700 chr5A 85.965 57 8 0 2828 2884 680512543 680512599 1.030000e-05 62.1
40 TraesCS3B01G558700 chr1A 97.619 42 1 0 3327 3368 508349889 508349848 4.750000e-09 73.1
41 TraesCS3B01G558700 chr6A 92.000 50 4 0 2837 2886 182146328 182146279 1.710000e-08 71.3


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 TraesCS3B01G558700 chr3B 793014925 793018358 3433 True 6342.000000 6342 100.000 1 3434 1 chr3B.!!$R1 3433
1 TraesCS3B01G558700 chr3B 793028098 793031579 3481 True 850.400000 2649 90.403 30 3434 5 chr3B.!!$R3 3404
2 TraesCS3B01G558700 chr3D 591616072 591618752 2680 False 1226.666667 2824 93.954 852 3434 3 chr3D.!!$F1 2582
3 TraesCS3B01G558700 chr3D 591368889 591369552 663 True 549.000000 549 82.194 1754 2434 1 chr3D.!!$R2 680
4 TraesCS3B01G558700 chr3A 721663720 721665321 1601 False 2331.000000 2331 93.075 860 2448 1 chr3A.!!$F1 1588

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
202 204 1.004292 GCGCATTAATAAACGACGCCT 60.004 47.619 0.30 0.0 39.01 5.52 F
651 763 1.006758 TGATGTACTCCCTCCGTTCCT 59.993 52.381 0.00 0.0 0.00 3.36 F
1350 1483 1.947146 CGCCGAGTTCGTGTTCACA 60.947 57.895 3.87 0.0 37.74 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 1918 1.519719 GCAGAGCTCCACGGAGAAT 59.480 57.895 17.47 4.13 44.53 2.40 R
2281 2439 1.139095 GAATCCTCTCGCCGTCGTT 59.861 57.895 0.00 0.00 36.96 3.85 R
3255 3623 0.037590 TGAGGTGGGTATGTGTTGCC 59.962 55.000 0.00 0.00 0.00 4.52 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
18 19 1.212751 GAAACAAGGATGGCGTGGC 59.787 57.895 0.00 0.00 0.00 5.01
19 20 2.527547 GAAACAAGGATGGCGTGGCG 62.528 60.000 0.00 0.00 0.00 5.69
55 56 4.410400 AGTGTTAGGCCAGCCCGC 62.410 66.667 5.01 0.00 39.21 6.13
102 103 7.027874 ACCAAAGGACCTCTCACAATATTAA 57.972 36.000 0.00 0.00 0.00 1.40
123 124 4.542662 AGCAAGAAATAATGCGCACTAG 57.457 40.909 14.90 0.00 0.00 2.57
124 125 3.941483 AGCAAGAAATAATGCGCACTAGT 59.059 39.130 14.90 0.92 0.00 2.57
128 129 6.089417 GCAAGAAATAATGCGCACTAGTTTTT 59.911 34.615 14.90 11.00 0.00 1.94
162 164 5.287513 GGCGTCGTTTATTAATTGCAAATGT 59.712 36.000 1.71 0.00 0.00 2.71
184 186 8.633075 ATGTTCAAAGGAATACAAATAATGCG 57.367 30.769 0.00 0.00 35.05 4.73
185 187 6.529829 TGTTCAAAGGAATACAAATAATGCGC 59.470 34.615 0.00 0.00 35.05 6.09
186 188 6.201226 TCAAAGGAATACAAATAATGCGCA 57.799 33.333 14.96 14.96 0.00 6.09
187 189 6.804677 TCAAAGGAATACAAATAATGCGCAT 58.195 32.000 19.28 19.28 0.00 4.73
188 190 7.264221 TCAAAGGAATACAAATAATGCGCATT 58.736 30.769 35.42 35.42 34.93 3.56
191 193 9.762933 AAAGGAATACAAATAATGCGCATTAAT 57.237 25.926 38.12 30.41 36.90 1.40
197 199 9.885934 ATACAAATAATGCGCATTAATAAACGA 57.114 25.926 38.12 23.17 36.90 3.85
198 200 8.045750 ACAAATAATGCGCATTAATAAACGAC 57.954 30.769 38.12 0.00 36.90 4.34
202 204 1.004292 GCGCATTAATAAACGACGCCT 60.004 47.619 0.30 0.00 39.01 5.52
203 205 2.538132 GCGCATTAATAAACGACGCCTT 60.538 45.455 0.30 0.00 39.01 4.35
204 206 3.676540 CGCATTAATAAACGACGCCTTT 58.323 40.909 0.00 0.00 0.00 3.11
205 207 4.782822 GCGCATTAATAAACGACGCCTTTA 60.783 41.667 0.30 0.00 39.01 1.85
206 208 4.663091 CGCATTAATAAACGACGCCTTTAC 59.337 41.667 0.00 0.00 0.00 2.01
208 210 6.291743 CGCATTAATAAACGACGCCTTTACTA 60.292 38.462 0.00 0.00 0.00 1.82
209 211 7.401080 GCATTAATAAACGACGCCTTTACTAA 58.599 34.615 0.00 0.00 0.00 2.24
210 212 7.904461 GCATTAATAAACGACGCCTTTACTAAA 59.096 33.333 0.00 0.00 0.00 1.85
211 213 9.757859 CATTAATAAACGACGCCTTTACTAAAA 57.242 29.630 0.00 0.00 0.00 1.52
213 215 9.810231 TTAATAAACGACGCCTTTACTAAAAAG 57.190 29.630 0.00 0.00 0.00 2.27
241 278 6.432403 TTTCCCTTTATTTTGCTGGTGATT 57.568 33.333 0.00 0.00 0.00 2.57
275 312 8.408601 GCAAAGAAAGCCTGATTTAATGAGATA 58.591 33.333 0.00 0.00 0.00 1.98
306 343 8.164057 AGAAGAGTCCAAAACTAGGGAAATAT 57.836 34.615 0.00 0.00 38.74 1.28
314 351 8.947055 CCAAAACTAGGGAAATATCATTTTGG 57.053 34.615 9.92 9.92 44.78 3.28
324 361 8.197439 GGGAAATATCATTTTGGTTTCTAGGTG 58.803 37.037 0.00 0.00 0.00 4.00
402 454 9.382275 ACAATTAATTTGACTTTCTTTTGCACT 57.618 25.926 0.00 0.00 38.76 4.40
406 458 9.862371 TTAATTTGACTTTCTTTTGCACTTGTA 57.138 25.926 0.00 0.00 0.00 2.41
444 496 5.803020 ATAGAAAATCAGCGTTGACTTCC 57.197 39.130 17.13 0.00 35.83 3.46
447 499 2.163818 AATCAGCGTTGACTTCCGAA 57.836 45.000 3.33 0.00 35.83 4.30
448 500 2.163818 ATCAGCGTTGACTTCCGAAA 57.836 45.000 3.33 0.00 35.83 3.46
449 501 1.942677 TCAGCGTTGACTTCCGAAAA 58.057 45.000 0.00 0.00 0.00 2.29
450 502 2.281517 TCAGCGTTGACTTCCGAAAAA 58.718 42.857 0.00 0.00 0.00 1.94
498 551 5.291128 GTCAGTATCACACTATTTTGACCGG 59.709 44.000 0.00 0.00 34.98 5.28
503 556 5.873179 TCACACTATTTTGACCGGAAATC 57.127 39.130 9.46 0.00 0.00 2.17
644 756 9.710818 TTAGGGTAATATATGATGTACTCCCTC 57.289 37.037 9.60 0.00 41.27 4.30
645 757 7.133483 AGGGTAATATATGATGTACTCCCTCC 58.867 42.308 0.00 0.00 37.15 4.30
646 758 6.040616 GGGTAATATATGATGTACTCCCTCCG 59.959 46.154 0.00 0.00 0.00 4.63
647 759 6.606395 GGTAATATATGATGTACTCCCTCCGT 59.394 42.308 0.00 0.00 0.00 4.69
648 760 7.123847 GGTAATATATGATGTACTCCCTCCGTT 59.876 40.741 0.00 0.00 0.00 4.44
649 761 6.777213 ATATATGATGTACTCCCTCCGTTC 57.223 41.667 0.00 0.00 0.00 3.95
650 762 1.481871 TGATGTACTCCCTCCGTTCC 58.518 55.000 0.00 0.00 0.00 3.62
651 763 1.006758 TGATGTACTCCCTCCGTTCCT 59.993 52.381 0.00 0.00 0.00 3.36
652 764 2.242965 TGATGTACTCCCTCCGTTCCTA 59.757 50.000 0.00 0.00 0.00 2.94
653 765 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
654 766 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
655 767 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
656 768 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
657 769 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
658 770 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
659 771 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
660 772 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
661 773 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
662 774 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
663 775 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
664 776 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
665 777 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
666 778 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
667 779 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
668 780 9.341899 CTCCGTTCCTAAATATTTGTCTTTTTG 57.658 33.333 11.05 0.00 0.00 2.44
669 781 8.301002 TCCGTTCCTAAATATTTGTCTTTTTGG 58.699 33.333 11.05 3.95 0.00 3.28
670 782 8.301002 CCGTTCCTAAATATTTGTCTTTTTGGA 58.699 33.333 11.05 0.00 34.13 3.53
671 783 9.341899 CGTTCCTAAATATTTGTCTTTTTGGAG 57.658 33.333 11.05 0.00 36.25 3.86
682 794 8.436046 TTTGTCTTTTTGGAGATTTCAAATGG 57.564 30.769 0.00 0.00 34.58 3.16
683 795 7.358770 TGTCTTTTTGGAGATTTCAAATGGA 57.641 32.000 0.00 0.00 34.58 3.41
684 796 7.209475 TGTCTTTTTGGAGATTTCAAATGGAC 58.791 34.615 0.00 0.00 37.00 4.02
685 797 7.069826 TGTCTTTTTGGAGATTTCAAATGGACT 59.930 33.333 15.63 0.00 37.16 3.85
686 798 8.576442 GTCTTTTTGGAGATTTCAAATGGACTA 58.424 33.333 0.00 0.00 35.58 2.59
687 799 8.576442 TCTTTTTGGAGATTTCAAATGGACTAC 58.424 33.333 0.00 0.00 34.58 2.73
688 800 6.834168 TTTGGAGATTTCAAATGGACTACC 57.166 37.500 0.00 0.00 0.00 3.18
705 817 8.050778 TGGACTACCACATATGAATGTTTTTC 57.949 34.615 10.38 1.57 44.07 2.29
706 818 7.667635 TGGACTACCACATATGAATGTTTTTCA 59.332 33.333 10.38 0.00 44.07 2.69
707 819 8.184192 GGACTACCACATATGAATGTTTTTCAG 58.816 37.037 10.38 0.54 44.07 3.02
708 820 8.862325 ACTACCACATATGAATGTTTTTCAGA 57.138 30.769 10.38 0.00 44.07 3.27
709 821 9.466497 ACTACCACATATGAATGTTTTTCAGAT 57.534 29.630 10.38 0.00 44.07 2.90
711 823 8.991243 ACCACATATGAATGTTTTTCAGATTG 57.009 30.769 10.38 0.00 44.07 2.67
712 824 8.587608 ACCACATATGAATGTTTTTCAGATTGT 58.412 29.630 10.38 0.00 44.07 2.71
720 832 9.897744 TGAATGTTTTTCAGATTGTAGATTCAC 57.102 29.630 0.00 0.00 0.00 3.18
723 835 8.675705 TGTTTTTCAGATTGTAGATTCACTCA 57.324 30.769 0.00 0.00 0.00 3.41
724 836 9.288576 TGTTTTTCAGATTGTAGATTCACTCAT 57.711 29.630 0.00 0.00 0.00 2.90
729 841 8.853077 TCAGATTGTAGATTCACTCATTTTGT 57.147 30.769 0.00 0.00 0.00 2.83
730 842 9.288576 TCAGATTGTAGATTCACTCATTTTGTT 57.711 29.630 0.00 0.00 0.00 2.83
731 843 9.903682 CAGATTGTAGATTCACTCATTTTGTTT 57.096 29.630 0.00 0.00 0.00 2.83
733 845 8.955061 ATTGTAGATTCACTCATTTTGTTTCG 57.045 30.769 0.00 0.00 0.00 3.46
734 846 7.490962 TGTAGATTCACTCATTTTGTTTCGT 57.509 32.000 0.00 0.00 0.00 3.85
735 847 8.596271 TGTAGATTCACTCATTTTGTTTCGTA 57.404 30.769 0.00 0.00 0.00 3.43
736 848 9.214957 TGTAGATTCACTCATTTTGTTTCGTAT 57.785 29.630 0.00 0.00 0.00 3.06
737 849 9.478019 GTAGATTCACTCATTTTGTTTCGTATG 57.522 33.333 0.00 0.00 0.00 2.39
738 850 8.099364 AGATTCACTCATTTTGTTTCGTATGT 57.901 30.769 0.00 0.00 0.00 2.29
739 851 9.214957 AGATTCACTCATTTTGTTTCGTATGTA 57.785 29.630 0.00 0.00 0.00 2.29
740 852 9.478019 GATTCACTCATTTTGTTTCGTATGTAG 57.522 33.333 0.00 0.00 0.00 2.74
741 853 7.956420 TCACTCATTTTGTTTCGTATGTAGT 57.044 32.000 0.00 0.00 0.00 2.73
742 854 8.014322 TCACTCATTTTGTTTCGTATGTAGTC 57.986 34.615 0.00 0.00 0.00 2.59
743 855 7.654116 TCACTCATTTTGTTTCGTATGTAGTCA 59.346 33.333 0.00 0.00 0.00 3.41
744 856 7.740346 CACTCATTTTGTTTCGTATGTAGTCAC 59.260 37.037 0.00 0.00 0.00 3.67
745 857 7.656137 ACTCATTTTGTTTCGTATGTAGTCACT 59.344 33.333 0.00 0.00 0.00 3.41
746 858 8.373048 TCATTTTGTTTCGTATGTAGTCACTT 57.627 30.769 0.00 0.00 0.00 3.16
747 859 8.279800 TCATTTTGTTTCGTATGTAGTCACTTG 58.720 33.333 0.00 0.00 0.00 3.16
748 860 7.542534 TTTTGTTTCGTATGTAGTCACTTGT 57.457 32.000 0.00 0.00 0.00 3.16
749 861 7.542534 TTTGTTTCGTATGTAGTCACTTGTT 57.457 32.000 0.00 0.00 0.00 2.83
750 862 6.519353 TGTTTCGTATGTAGTCACTTGTTG 57.481 37.500 0.00 0.00 0.00 3.33
751 863 6.274579 TGTTTCGTATGTAGTCACTTGTTGA 58.725 36.000 0.00 0.00 0.00 3.18
752 864 6.757478 TGTTTCGTATGTAGTCACTTGTTGAA 59.243 34.615 0.00 0.00 35.39 2.69
753 865 7.278203 TGTTTCGTATGTAGTCACTTGTTGAAA 59.722 33.333 0.00 0.00 35.39 2.69
754 866 7.956420 TTCGTATGTAGTCACTTGTTGAAAT 57.044 32.000 0.00 0.00 35.39 2.17
755 867 7.576750 TCGTATGTAGTCACTTGTTGAAATC 57.423 36.000 0.00 0.00 35.39 2.17
756 868 7.375834 TCGTATGTAGTCACTTGTTGAAATCT 58.624 34.615 0.00 0.00 35.39 2.40
757 869 7.541091 TCGTATGTAGTCACTTGTTGAAATCTC 59.459 37.037 0.00 0.00 35.39 2.75
758 870 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
759 871 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
787 899 8.919777 AAGATTAATATTTAGGAACGAAGGGG 57.080 34.615 0.00 0.00 0.00 4.79
795 907 2.836667 AGGAACGAAGGGGGTATAACA 58.163 47.619 0.00 0.00 0.00 2.41
805 917 7.897565 ACGAAGGGGGTATAACAGTATATACAT 59.102 37.037 15.18 2.58 39.48 2.29
928 1049 3.983741 CCTAACGAAGGGCAATCTCTAG 58.016 50.000 0.00 0.00 42.32 2.43
929 1050 3.385111 CCTAACGAAGGGCAATCTCTAGT 59.615 47.826 0.00 0.00 42.32 2.57
1035 1168 4.529219 CTGCCCGGCGACATGCTA 62.529 66.667 9.30 0.00 45.43 3.49
1296 1429 4.821589 CTCCTTCGCCGCCTCCAC 62.822 72.222 0.00 0.00 0.00 4.02
1350 1483 1.947146 CGCCGAGTTCGTGTTCACA 60.947 57.895 3.87 0.00 37.74 3.58
2281 2439 3.019799 AGAAGATCTACGAGAAGGGCA 57.980 47.619 0.00 0.00 0.00 5.36
2282 2440 3.366396 AGAAGATCTACGAGAAGGGCAA 58.634 45.455 0.00 0.00 0.00 4.52
2318 2476 0.250295 CAGCAGGACGGTGGAAGAAA 60.250 55.000 0.00 0.00 39.55 2.52
2338 2502 1.554617 ACGATGACCATGGTGATGTCA 59.445 47.619 25.52 14.30 0.00 3.58
2373 2537 1.002868 CATGGGGATCGGAGGCATC 60.003 63.158 0.00 0.00 0.00 3.91
2382 2546 1.175347 TCGGAGGCATCGATCTGGAG 61.175 60.000 0.00 0.00 0.00 3.86
2385 2549 2.031768 GGCATCGATCTGGAGCCC 59.968 66.667 11.66 0.00 39.42 5.19
2527 2696 8.543862 AAATTGAGGAAAAGCAATGATTCTTC 57.456 30.769 0.00 0.00 35.11 2.87
2528 2697 6.653526 TTGAGGAAAAGCAATGATTCTTCA 57.346 33.333 5.19 5.19 37.39 3.02
2529 2698 6.263516 TGAGGAAAAGCAATGATTCTTCAG 57.736 37.500 5.19 0.00 35.20 3.02
2530 2699 6.005823 TGAGGAAAAGCAATGATTCTTCAGA 58.994 36.000 5.19 0.00 35.20 3.27
2531 2700 6.662234 TGAGGAAAAGCAATGATTCTTCAGAT 59.338 34.615 5.19 0.00 35.20 2.90
2532 2701 7.177921 TGAGGAAAAGCAATGATTCTTCAGATT 59.822 33.333 5.19 0.00 35.20 2.40
2533 2702 8.585471 AGGAAAAGCAATGATTCTTCAGATTA 57.415 30.769 7.85 0.00 34.73 1.75
2846 3051 5.828328 GGATTAAATCCCGTCAAATCCTCTT 59.172 40.000 5.37 0.00 43.88 2.85
2962 3167 1.838112 TGGCACATCCAGTTGATTCC 58.162 50.000 0.00 0.00 40.72 3.01
2963 3168 1.355381 TGGCACATCCAGTTGATTCCT 59.645 47.619 0.00 0.00 40.72 3.36
2964 3169 2.575735 TGGCACATCCAGTTGATTCCTA 59.424 45.455 0.00 0.00 40.72 2.94
2965 3170 3.209410 GGCACATCCAGTTGATTCCTAG 58.791 50.000 0.00 0.00 34.01 3.02
2966 3171 2.615912 GCACATCCAGTTGATTCCTAGC 59.384 50.000 0.00 0.00 0.00 3.42
3023 3228 5.843673 TCAACAAAATACTGTGCTCCAAA 57.156 34.783 0.00 0.00 0.00 3.28
3086 3294 4.994907 TCTTATTCTCGGGATCGTTGAA 57.005 40.909 0.00 0.00 37.69 2.69
3090 3454 6.479001 TCTTATTCTCGGGATCGTTGAAAATC 59.521 38.462 0.00 0.00 35.31 2.17
3180 3548 4.475016 AGGTTCTACAGGGCAGATAACATT 59.525 41.667 0.00 0.00 0.00 2.71
3225 3593 2.203209 GGAGGCCCCAACGCTATG 60.203 66.667 0.00 0.00 34.14 2.23
3276 3644 2.446435 GCAACACATACCCACCTCATT 58.554 47.619 0.00 0.00 0.00 2.57
3345 3713 3.094572 TGGTACTCCCTCCGTAAAGAAG 58.905 50.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.212751 GCCACGCCATCCTTGTTTC 59.787 57.895 0.00 0.00 0.00 2.78
1 2 2.625823 CGCCACGCCATCCTTGTTT 61.626 57.895 0.00 0.00 0.00 2.83
2 3 3.055719 CGCCACGCCATCCTTGTT 61.056 61.111 0.00 0.00 0.00 2.83
20 21 2.136196 CTCTAGATCCAGGCCGTCGC 62.136 65.000 0.00 0.00 0.00 5.19
21 22 0.820074 ACTCTAGATCCAGGCCGTCG 60.820 60.000 0.00 0.00 0.00 5.12
22 23 0.671251 CACTCTAGATCCAGGCCGTC 59.329 60.000 0.00 0.00 0.00 4.79
23 24 0.033011 ACACTCTAGATCCAGGCCGT 60.033 55.000 0.00 0.00 0.00 5.68
24 25 1.115467 AACACTCTAGATCCAGGCCG 58.885 55.000 0.00 0.00 0.00 6.13
25 26 2.630580 CCTAACACTCTAGATCCAGGCC 59.369 54.545 0.00 0.00 0.00 5.19
26 27 2.036604 GCCTAACACTCTAGATCCAGGC 59.963 54.545 12.46 12.46 40.43 4.85
27 28 2.630580 GGCCTAACACTCTAGATCCAGG 59.369 54.545 0.00 0.00 0.00 4.45
28 29 3.300388 TGGCCTAACACTCTAGATCCAG 58.700 50.000 3.32 0.00 0.00 3.86
55 56 2.145397 TACTCTGGTGCTCCACTAGG 57.855 55.000 2.64 0.00 42.06 3.02
66 67 4.031611 GGTCCTTTGGTCTATACTCTGGT 58.968 47.826 0.00 0.00 0.00 4.00
73 74 4.942944 TGTGAGAGGTCCTTTGGTCTATA 58.057 43.478 0.00 0.00 0.00 1.31
102 103 3.941483 ACTAGTGCGCATTATTTCTTGCT 59.059 39.130 15.91 3.94 36.71 3.91
162 164 6.625362 TGCGCATTATTTGTATTCCTTTGAA 58.375 32.000 5.66 0.00 34.33 2.69
182 184 1.004292 AGGCGTCGTTTATTAATGCGC 60.004 47.619 0.00 0.00 41.11 6.09
183 185 3.313274 AAGGCGTCGTTTATTAATGCG 57.687 42.857 0.00 0.69 0.00 4.73
184 186 5.803118 AGTAAAGGCGTCGTTTATTAATGC 58.197 37.500 0.00 0.00 0.00 3.56
185 187 9.757859 TTTTAGTAAAGGCGTCGTTTATTAATG 57.242 29.630 14.29 0.00 31.43 1.90
187 189 9.810231 CTTTTTAGTAAAGGCGTCGTTTATTAA 57.190 29.630 0.00 5.07 30.30 1.40
188 190 8.442384 CCTTTTTAGTAAAGGCGTCGTTTATTA 58.558 33.333 0.00 0.00 40.17 0.98
191 193 5.988561 TCCTTTTTAGTAAAGGCGTCGTTTA 59.011 36.000 10.68 0.00 44.92 2.01
192 194 4.815846 TCCTTTTTAGTAAAGGCGTCGTTT 59.184 37.500 10.68 0.00 44.92 3.60
193 195 4.379652 TCCTTTTTAGTAAAGGCGTCGTT 58.620 39.130 10.68 0.00 44.92 3.85
194 196 3.993920 TCCTTTTTAGTAAAGGCGTCGT 58.006 40.909 10.68 0.00 44.92 4.34
195 197 6.839820 ATATCCTTTTTAGTAAAGGCGTCG 57.160 37.500 10.68 0.00 44.92 5.12
196 198 8.127327 GGAAATATCCTTTTTAGTAAAGGCGTC 58.873 37.037 10.68 4.56 44.92 5.19
197 199 7.067859 GGGAAATATCCTTTTTAGTAAAGGCGT 59.932 37.037 10.68 5.65 45.77 5.68
198 200 7.284716 AGGGAAATATCCTTTTTAGTAAAGGCG 59.715 37.037 10.68 0.00 45.77 5.52
211 213 7.402941 ACCAGCAAAATAAAGGGAAATATCCTT 59.597 33.333 0.00 0.00 45.77 3.36
212 214 6.902974 ACCAGCAAAATAAAGGGAAATATCCT 59.097 34.615 0.00 0.00 45.77 3.24
213 215 6.986231 CACCAGCAAAATAAAGGGAAATATCC 59.014 38.462 0.00 0.00 45.77 2.59
214 216 7.781056 TCACCAGCAAAATAAAGGGAAATATC 58.219 34.615 0.00 0.00 0.00 1.63
215 217 7.732222 TCACCAGCAAAATAAAGGGAAATAT 57.268 32.000 0.00 0.00 0.00 1.28
216 218 7.732222 ATCACCAGCAAAATAAAGGGAAATA 57.268 32.000 0.00 0.00 0.00 1.40
217 219 6.625532 ATCACCAGCAAAATAAAGGGAAAT 57.374 33.333 0.00 0.00 0.00 2.17
218 220 6.229733 CAATCACCAGCAAAATAAAGGGAAA 58.770 36.000 0.00 0.00 0.00 3.13
219 221 5.279910 CCAATCACCAGCAAAATAAAGGGAA 60.280 40.000 0.00 0.00 0.00 3.97
220 222 4.222588 CCAATCACCAGCAAAATAAAGGGA 59.777 41.667 0.00 0.00 0.00 4.20
221 223 4.020307 ACCAATCACCAGCAAAATAAAGGG 60.020 41.667 0.00 0.00 0.00 3.95
222 224 4.931002 CACCAATCACCAGCAAAATAAAGG 59.069 41.667 0.00 0.00 0.00 3.11
223 225 5.540911 ACACCAATCACCAGCAAAATAAAG 58.459 37.500 0.00 0.00 0.00 1.85
224 226 5.543507 ACACCAATCACCAGCAAAATAAA 57.456 34.783 0.00 0.00 0.00 1.40
225 227 5.295950 CAACACCAATCACCAGCAAAATAA 58.704 37.500 0.00 0.00 0.00 1.40
227 229 3.494749 CCAACACCAATCACCAGCAAAAT 60.495 43.478 0.00 0.00 0.00 1.82
234 271 1.411977 CTTTGCCAACACCAATCACCA 59.588 47.619 0.00 0.00 0.00 4.17
275 312 3.903467 AGTTTTGGACTCTTCTTTGCCT 58.097 40.909 0.00 0.00 31.20 4.75
419 471 5.456192 AGTCAACGCTGATTTTCTATTCG 57.544 39.130 0.00 0.00 33.05 3.34
460 512 9.712305 GTGTGATACTGACCTATAATAGCAAAT 57.288 33.333 0.00 0.00 0.00 2.32
477 529 5.670792 TCCGGTCAAAATAGTGTGATACT 57.329 39.130 0.00 0.00 43.56 2.12
478 530 6.730960 TTTCCGGTCAAAATAGTGTGATAC 57.269 37.500 0.00 0.00 0.00 2.24
620 731 7.133483 GGAGGGAGTACATCATATATTACCCT 58.867 42.308 0.00 0.00 45.28 4.34
621 732 6.040616 CGGAGGGAGTACATCATATATTACCC 59.959 46.154 0.00 0.00 0.00 3.69
623 734 7.642082 ACGGAGGGAGTACATCATATATTAC 57.358 40.000 0.00 0.00 0.00 1.89
624 735 7.341256 GGAACGGAGGGAGTACATCATATATTA 59.659 40.741 0.00 0.00 0.00 0.98
635 747 6.416631 AATATTTAGGAACGGAGGGAGTAC 57.583 41.667 0.00 0.00 0.00 2.73
636 748 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
637 749 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
638 750 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
639 751 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
640 752 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
641 753 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
642 754 9.341899 CAAAAAGACAAATATTTAGGAACGGAG 57.658 33.333 0.00 0.00 0.00 4.63
643 755 8.301002 CCAAAAAGACAAATATTTAGGAACGGA 58.699 33.333 0.00 0.00 0.00 4.69
644 756 8.301002 TCCAAAAAGACAAATATTTAGGAACGG 58.699 33.333 0.00 0.00 0.00 4.44
645 757 9.341899 CTCCAAAAAGACAAATATTTAGGAACG 57.658 33.333 0.00 0.00 28.62 3.95
656 768 9.059260 CCATTTGAAATCTCCAAAAAGACAAAT 57.941 29.630 0.00 0.00 37.11 2.32
657 769 8.263640 TCCATTTGAAATCTCCAAAAAGACAAA 58.736 29.630 0.00 0.00 37.11 2.83
658 770 7.710475 GTCCATTTGAAATCTCCAAAAAGACAA 59.290 33.333 0.00 0.00 38.31 3.18
659 771 7.069826 AGTCCATTTGAAATCTCCAAAAAGACA 59.930 33.333 16.40 0.00 39.47 3.41
660 772 7.436933 AGTCCATTTGAAATCTCCAAAAAGAC 58.563 34.615 0.00 0.00 38.49 3.01
661 773 7.601705 AGTCCATTTGAAATCTCCAAAAAGA 57.398 32.000 0.00 0.00 37.11 2.52
662 774 7.814587 GGTAGTCCATTTGAAATCTCCAAAAAG 59.185 37.037 0.00 0.00 37.11 2.27
663 775 7.288852 TGGTAGTCCATTTGAAATCTCCAAAAA 59.711 33.333 0.00 0.00 39.03 1.94
664 776 6.780031 TGGTAGTCCATTTGAAATCTCCAAAA 59.220 34.615 0.00 0.00 39.03 2.44
665 777 6.208599 GTGGTAGTCCATTTGAAATCTCCAAA 59.791 38.462 0.00 0.00 46.20 3.28
666 778 5.710099 GTGGTAGTCCATTTGAAATCTCCAA 59.290 40.000 0.00 0.00 46.20 3.53
667 779 5.222027 TGTGGTAGTCCATTTGAAATCTCCA 60.222 40.000 0.00 0.00 46.20 3.86
668 780 5.253330 TGTGGTAGTCCATTTGAAATCTCC 58.747 41.667 0.00 0.00 46.20 3.71
669 781 8.562892 CATATGTGGTAGTCCATTTGAAATCTC 58.437 37.037 0.00 0.00 46.20 2.75
670 782 8.274322 TCATATGTGGTAGTCCATTTGAAATCT 58.726 33.333 1.90 0.00 46.20 2.40
671 783 8.450578 TCATATGTGGTAGTCCATTTGAAATC 57.549 34.615 1.90 0.00 46.20 2.17
672 784 8.821686 TTCATATGTGGTAGTCCATTTGAAAT 57.178 30.769 1.90 0.00 46.20 2.17
673 785 8.685427 CATTCATATGTGGTAGTCCATTTGAAA 58.315 33.333 1.90 0.00 46.20 2.69
674 786 7.833682 ACATTCATATGTGGTAGTCCATTTGAA 59.166 33.333 1.90 7.58 46.20 2.69
675 787 7.345691 ACATTCATATGTGGTAGTCCATTTGA 58.654 34.615 1.90 0.00 46.20 2.69
676 788 7.572523 ACATTCATATGTGGTAGTCCATTTG 57.427 36.000 1.90 0.00 46.20 2.32
677 789 8.593945 AAACATTCATATGTGGTAGTCCATTT 57.406 30.769 1.90 0.00 44.14 2.32
678 790 8.593945 AAAACATTCATATGTGGTAGTCCATT 57.406 30.769 1.90 0.00 44.14 3.16
679 791 8.593945 AAAAACATTCATATGTGGTAGTCCAT 57.406 30.769 1.90 0.00 44.14 3.41
680 792 7.667635 TGAAAAACATTCATATGTGGTAGTCCA 59.332 33.333 1.90 0.00 44.14 4.02
681 793 8.050778 TGAAAAACATTCATATGTGGTAGTCC 57.949 34.615 1.90 0.00 44.14 3.85
682 794 8.946085 TCTGAAAAACATTCATATGTGGTAGTC 58.054 33.333 1.90 0.00 44.14 2.59
683 795 8.862325 TCTGAAAAACATTCATATGTGGTAGT 57.138 30.769 1.90 0.00 44.14 2.73
686 798 8.587608 ACAATCTGAAAAACATTCATATGTGGT 58.412 29.630 1.90 0.00 44.14 4.16
687 799 8.991243 ACAATCTGAAAAACATTCATATGTGG 57.009 30.769 1.90 0.00 44.14 4.17
694 806 9.897744 GTGAATCTACAATCTGAAAAACATTCA 57.102 29.630 0.00 0.00 0.00 2.57
697 809 9.288576 TGAGTGAATCTACAATCTGAAAAACAT 57.711 29.630 0.00 0.00 36.14 2.71
698 810 8.675705 TGAGTGAATCTACAATCTGAAAAACA 57.324 30.769 0.00 0.00 36.14 2.83
703 815 9.288576 ACAAAATGAGTGAATCTACAATCTGAA 57.711 29.630 0.00 0.00 36.14 3.02
704 816 8.853077 ACAAAATGAGTGAATCTACAATCTGA 57.147 30.769 0.00 0.00 36.14 3.27
705 817 9.903682 AAACAAAATGAGTGAATCTACAATCTG 57.096 29.630 0.00 0.00 36.14 2.90
707 819 9.055248 CGAAACAAAATGAGTGAATCTACAATC 57.945 33.333 0.00 0.00 35.78 2.67
708 820 8.567948 ACGAAACAAAATGAGTGAATCTACAAT 58.432 29.630 0.00 0.00 0.00 2.71
709 821 7.925993 ACGAAACAAAATGAGTGAATCTACAA 58.074 30.769 0.00 0.00 0.00 2.41
710 822 7.490962 ACGAAACAAAATGAGTGAATCTACA 57.509 32.000 0.00 0.00 0.00 2.74
711 823 9.478019 CATACGAAACAAAATGAGTGAATCTAC 57.522 33.333 0.00 0.00 0.00 2.59
712 824 9.214957 ACATACGAAACAAAATGAGTGAATCTA 57.785 29.630 0.00 0.00 0.00 1.98
713 825 8.099364 ACATACGAAACAAAATGAGTGAATCT 57.901 30.769 0.00 0.00 0.00 2.40
714 826 9.478019 CTACATACGAAACAAAATGAGTGAATC 57.522 33.333 0.00 0.00 0.00 2.52
715 827 8.999431 ACTACATACGAAACAAAATGAGTGAAT 58.001 29.630 0.00 0.00 0.00 2.57
716 828 8.373048 ACTACATACGAAACAAAATGAGTGAA 57.627 30.769 0.00 0.00 0.00 3.18
717 829 7.654116 TGACTACATACGAAACAAAATGAGTGA 59.346 33.333 0.00 0.00 0.00 3.41
718 830 7.740346 GTGACTACATACGAAACAAAATGAGTG 59.260 37.037 0.00 0.00 0.00 3.51
719 831 7.656137 AGTGACTACATACGAAACAAAATGAGT 59.344 33.333 0.00 0.00 0.00 3.41
720 832 8.018677 AGTGACTACATACGAAACAAAATGAG 57.981 34.615 0.00 0.00 0.00 2.90
721 833 7.956420 AGTGACTACATACGAAACAAAATGA 57.044 32.000 0.00 0.00 0.00 2.57
722 834 8.067784 ACAAGTGACTACATACGAAACAAAATG 58.932 33.333 0.00 0.00 0.00 2.32
723 835 8.149973 ACAAGTGACTACATACGAAACAAAAT 57.850 30.769 0.00 0.00 0.00 1.82
724 836 7.542534 ACAAGTGACTACATACGAAACAAAA 57.457 32.000 0.00 0.00 0.00 2.44
725 837 7.278203 TCAACAAGTGACTACATACGAAACAAA 59.722 33.333 0.00 0.00 0.00 2.83
726 838 6.757478 TCAACAAGTGACTACATACGAAACAA 59.243 34.615 0.00 0.00 0.00 2.83
727 839 6.274579 TCAACAAGTGACTACATACGAAACA 58.725 36.000 0.00 0.00 0.00 2.83
728 840 6.758593 TCAACAAGTGACTACATACGAAAC 57.241 37.500 0.00 0.00 0.00 2.78
729 841 7.773864 TTTCAACAAGTGACTACATACGAAA 57.226 32.000 0.00 0.00 35.39 3.46
730 842 7.870954 AGATTTCAACAAGTGACTACATACGAA 59.129 33.333 0.00 0.00 35.39 3.85
731 843 7.375834 AGATTTCAACAAGTGACTACATACGA 58.624 34.615 0.00 0.00 35.39 3.43
732 844 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
733 845 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
761 873 9.350951 CCCCTTCGTTCCTAAATATTAATCTTT 57.649 33.333 4.47 4.47 0.00 2.52
762 874 7.942894 CCCCCTTCGTTCCTAAATATTAATCTT 59.057 37.037 0.00 0.00 0.00 2.40
763 875 7.073343 ACCCCCTTCGTTCCTAAATATTAATCT 59.927 37.037 0.00 0.00 0.00 2.40
764 876 7.229308 ACCCCCTTCGTTCCTAAATATTAATC 58.771 38.462 0.00 0.00 0.00 1.75
765 877 7.157947 ACCCCCTTCGTTCCTAAATATTAAT 57.842 36.000 0.00 0.00 0.00 1.40
766 878 6.579850 ACCCCCTTCGTTCCTAAATATTAA 57.420 37.500 0.00 0.00 0.00 1.40
767 879 7.876978 ATACCCCCTTCGTTCCTAAATATTA 57.123 36.000 0.00 0.00 0.00 0.98
768 880 6.775234 ATACCCCCTTCGTTCCTAAATATT 57.225 37.500 0.00 0.00 0.00 1.28
769 881 7.293062 TGTTATACCCCCTTCGTTCCTAAATAT 59.707 37.037 0.00 0.00 0.00 1.28
770 882 6.614906 TGTTATACCCCCTTCGTTCCTAAATA 59.385 38.462 0.00 0.00 0.00 1.40
771 883 5.429435 TGTTATACCCCCTTCGTTCCTAAAT 59.571 40.000 0.00 0.00 0.00 1.40
772 884 4.782156 TGTTATACCCCCTTCGTTCCTAAA 59.218 41.667 0.00 0.00 0.00 1.85
773 885 4.360889 TGTTATACCCCCTTCGTTCCTAA 58.639 43.478 0.00 0.00 0.00 2.69
774 886 3.962718 CTGTTATACCCCCTTCGTTCCTA 59.037 47.826 0.00 0.00 0.00 2.94
775 887 2.770232 CTGTTATACCCCCTTCGTTCCT 59.230 50.000 0.00 0.00 0.00 3.36
776 888 2.502947 ACTGTTATACCCCCTTCGTTCC 59.497 50.000 0.00 0.00 0.00 3.62
777 889 3.900966 ACTGTTATACCCCCTTCGTTC 57.099 47.619 0.00 0.00 0.00 3.95
778 890 7.729881 TGTATATACTGTTATACCCCCTTCGTT 59.270 37.037 13.89 0.00 35.20 3.85
779 891 7.240897 TGTATATACTGTTATACCCCCTTCGT 58.759 38.462 13.89 0.00 35.20 3.85
780 892 7.707624 TGTATATACTGTTATACCCCCTTCG 57.292 40.000 13.89 0.00 35.20 3.79
781 893 8.702819 GGATGTATATACTGTTATACCCCCTTC 58.297 40.741 13.89 0.00 35.20 3.46
782 894 8.188357 TGGATGTATATACTGTTATACCCCCTT 58.812 37.037 13.89 0.00 35.20 3.95
783 895 7.725367 TGGATGTATATACTGTTATACCCCCT 58.275 38.462 13.89 2.57 35.20 4.79
784 896 7.983166 TGGATGTATATACTGTTATACCCCC 57.017 40.000 13.89 13.17 35.20 5.40
805 917 5.261216 GGACAGGAAATTTTGGTCTATGGA 58.739 41.667 13.81 0.00 0.00 3.41
843 955 3.526899 TGTCCAAAACATCCTCCTCCTA 58.473 45.455 0.00 0.00 31.20 2.94
844 956 2.348472 TGTCCAAAACATCCTCCTCCT 58.652 47.619 0.00 0.00 31.20 3.69
846 958 3.445096 CCATTGTCCAAAACATCCTCCTC 59.555 47.826 0.00 0.00 37.82 3.71
880 1001 4.283212 TCAGGTTGGATTTTGGGTTCATTC 59.717 41.667 0.00 0.00 0.00 2.67
928 1049 3.111098 CAAGTGCCTATACGGTTACGAC 58.889 50.000 0.00 0.00 44.60 4.34
929 1050 2.480073 GCAAGTGCCTATACGGTTACGA 60.480 50.000 0.00 0.00 38.19 3.43
1035 1168 1.709994 GCGATTGGGGAGGGAGGAAT 61.710 60.000 0.00 0.00 0.00 3.01
1205 1338 1.668101 CTCCAGGTACGAGGAGCACC 61.668 65.000 16.42 0.00 45.29 5.01
1291 1424 4.227134 CTGGATCGGCCGGTGGAG 62.227 72.222 27.83 12.39 40.66 3.86
1350 1483 2.357517 CGTTTGGAGTGCGGCTCT 60.358 61.111 3.92 3.92 43.62 4.09
1634 1767 2.001361 GAAGAAGTCGATCCCGCCGA 62.001 60.000 0.00 0.00 35.37 5.54
1785 1918 1.519719 GCAGAGCTCCACGGAGAAT 59.480 57.895 17.47 4.13 44.53 2.40
1818 1963 2.762234 CGGGAGGAAGACGAGGTCG 61.762 68.421 0.00 0.00 46.33 4.79
2281 2439 1.139095 GAATCCTCTCGCCGTCGTT 59.861 57.895 0.00 0.00 36.96 3.85
2282 2440 1.994507 CTGAATCCTCTCGCCGTCGT 61.995 60.000 0.00 0.00 36.96 4.34
2318 2476 1.554617 TGACATCACCATGGTCATCGT 59.445 47.619 16.53 9.00 33.82 3.73
2338 2502 2.152016 CATGGCGATCTCATCAATGCT 58.848 47.619 0.00 0.00 0.00 3.79
2373 2537 3.531207 TCGCAGGGCTCCAGATCG 61.531 66.667 0.00 0.00 0.00 3.69
2385 2549 3.288308 AAGCTCCACCTCGTCGCAG 62.288 63.158 0.00 0.00 0.00 5.18
2435 2599 5.713792 TTCAAAAAGGTCACAACTCACAA 57.286 34.783 0.00 0.00 0.00 3.33
2436 2600 5.417266 TCATTCAAAAAGGTCACAACTCACA 59.583 36.000 0.00 0.00 0.00 3.58
2437 2601 5.890334 TCATTCAAAAAGGTCACAACTCAC 58.110 37.500 0.00 0.00 0.00 3.51
2527 2696 9.703892 CTACTCCCAGATAATGTTCTTAATCTG 57.296 37.037 4.55 4.55 36.29 2.90
2528 2697 9.440761 ACTACTCCCAGATAATGTTCTTAATCT 57.559 33.333 0.00 0.00 0.00 2.40
2531 2700 9.886132 GAAACTACTCCCAGATAATGTTCTTAA 57.114 33.333 0.00 0.00 0.00 1.85
2532 2701 9.268282 AGAAACTACTCCCAGATAATGTTCTTA 57.732 33.333 0.00 0.00 0.00 2.10
2533 2702 8.152023 AGAAACTACTCCCAGATAATGTTCTT 57.848 34.615 0.00 0.00 0.00 2.52
2709 2883 1.546773 GGGGCATACAGTTGTGGACAA 60.547 52.381 0.00 0.00 0.00 3.18
2764 2952 3.018423 ACAGAACAGAACAAGGCCTTT 57.982 42.857 17.61 1.07 0.00 3.11
2833 3021 3.878778 AGGGATTGAAGAGGATTTGACG 58.121 45.455 0.00 0.00 0.00 4.35
2834 3022 5.711976 TCAAAGGGATTGAAGAGGATTTGAC 59.288 40.000 0.00 0.00 44.94 3.18
2846 3051 3.652869 ACACCTCTTCTCAAAGGGATTGA 59.347 43.478 0.00 0.00 45.71 2.57
2873 3078 5.643379 TGTGAATCATTTAGGCCTTGTTC 57.357 39.130 12.58 10.39 0.00 3.18
2920 3125 9.379791 GCCAAAACTCTGTACATTACTACTAAT 57.620 33.333 0.00 0.00 0.00 1.73
2921 3126 8.369424 TGCCAAAACTCTGTACATTACTACTAA 58.631 33.333 0.00 0.00 0.00 2.24
2922 3127 7.816031 GTGCCAAAACTCTGTACATTACTACTA 59.184 37.037 0.00 0.00 0.00 1.82
2962 3167 5.368256 AGCAAATCTGACAAACAAGCTAG 57.632 39.130 0.00 0.00 0.00 3.42
2963 3168 7.452880 AATAGCAAATCTGACAAACAAGCTA 57.547 32.000 0.00 0.00 36.62 3.32
2964 3169 5.972107 ATAGCAAATCTGACAAACAAGCT 57.028 34.783 0.00 0.00 0.00 3.74
2965 3170 6.421801 ACAAATAGCAAATCTGACAAACAAGC 59.578 34.615 0.00 0.00 0.00 4.01
2966 3171 7.648908 TGACAAATAGCAAATCTGACAAACAAG 59.351 33.333 0.00 0.00 0.00 3.16
3086 3294 8.362639 TCTGAAAGCTGCAGAAAATTAAGATTT 58.637 29.630 20.43 0.00 39.29 2.17
3101 3465 4.432712 TGGTTTCTTTTTCTGAAAGCTGC 58.567 39.130 15.87 0.00 46.08 5.25
3158 3522 3.906720 TGTTATCTGCCCTGTAGAACC 57.093 47.619 0.00 0.00 0.00 3.62
3180 3548 3.411446 CTTGGTGTATGTGGCTTTCTGA 58.589 45.455 0.00 0.00 0.00 3.27
3255 3623 0.037590 TGAGGTGGGTATGTGTTGCC 59.962 55.000 0.00 0.00 0.00 4.52
3276 3644 7.988599 ACAACAGTATACTTGTTGGTGAACTAA 59.011 33.333 30.28 0.00 44.92 2.24


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

AutoCloner maintained by Alex Coulton.