Multiple sequence alignment - TraesCS4B01G123300

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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 TraesCS4B01G123300 chr4B 100.000 5295 0 0 1 5295 146693262 146687968 0.000000e+00 9779.0
1 TraesCS4B01G123300 chr4B 96.078 51 2 0 2719 2769 146690496 146690446 3.400000e-12 84.2
2 TraesCS4B01G123300 chr4B 96.078 51 2 0 2767 2817 146690544 146690494 3.400000e-12 84.2
3 TraesCS4B01G123300 chr4D 92.976 3303 135 23 4 3278 102410565 102407332 0.000000e+00 4724.0
4 TraesCS4B01G123300 chr4D 92.847 1454 53 20 3229 4667 102407333 102405916 0.000000e+00 2061.0
5 TraesCS4B01G123300 chr4D 86.088 611 68 10 4688 5294 440031260 440031857 4.470000e-180 641.0
6 TraesCS4B01G123300 chr4A 96.652 1643 47 3 1135 2769 472613392 472615034 0.000000e+00 2723.0
7 TraesCS4B01G123300 chr4A 93.210 1841 77 18 2767 4589 472614984 472616794 0.000000e+00 2663.0
8 TraesCS4B01G123300 chr4A 88.848 1076 67 18 1 1058 472612106 472613146 0.000000e+00 1273.0
9 TraesCS4B01G123300 chr4A 88.660 1067 77 15 1 1057 472527337 472528369 0.000000e+00 1260.0
10 TraesCS4B01G123300 chrUn 87.276 613 69 6 4686 5294 175706645 175706038 0.000000e+00 691.0
11 TraesCS4B01G123300 chr5B 87.113 613 70 6 4686 5294 670439893 670439286 0.000000e+00 686.0
12 TraesCS4B01G123300 chr5B 83.607 549 63 18 4688 5229 532323887 532324415 1.710000e-134 490.0
13 TraesCS4B01G123300 chr3D 85.940 633 61 9 4688 5294 246595198 246595828 0.000000e+00 651.0
14 TraesCS4B01G123300 chr3D 86.252 611 65 12 4688 5294 98565500 98564905 0.000000e+00 645.0
15 TraesCS4B01G123300 chr3D 79.560 318 49 12 4364 4666 120881760 120881444 4.150000e-51 213.0
16 TraesCS4B01G123300 chr3D 76.415 318 56 14 4364 4666 605094751 605094438 2.550000e-33 154.0
17 TraesCS4B01G123300 chr1D 85.597 611 70 10 4689 5294 4431966 4432563 4.500000e-175 625.0
18 TraesCS4B01G123300 chr6B 85.686 503 65 6 4688 5186 650802723 650802224 1.690000e-144 523.0
19 TraesCS4B01G123300 chr6B 85.772 246 24 3 5049 5294 659392380 659392614 3.170000e-62 250.0
20 TraesCS4B01G123300 chr6B 88.827 179 19 1 5117 5295 94142693 94142516 8.930000e-53 219.0
21 TraesCS4B01G123300 chr1B 82.680 612 82 11 4688 5294 630059791 630059199 6.080000e-144 521.0
22 TraesCS4B01G123300 chr1B 77.170 311 54 13 4365 4666 14662939 14663241 1.180000e-36 165.0
23 TraesCS4B01G123300 chr1B 77.936 281 41 14 4373 4634 629490708 629490986 7.100000e-34 156.0
24 TraesCS4B01G123300 chr1B 84.337 166 16 8 4688 4849 385767723 385767882 2.550000e-33 154.0
25 TraesCS4B01G123300 chr6A 90.449 178 16 1 5117 5294 593455825 593455649 3.190000e-57 233.0
26 TraesCS4B01G123300 chr5A 90.055 181 17 1 5114 5294 490631829 490632008 3.190000e-57 233.0
27 TraesCS4B01G123300 chr7A 88.950 181 19 1 5114 5294 718404741 718404920 6.900000e-54 222.0
28 TraesCS4B01G123300 chr7A 79.375 320 45 13 4364 4666 121399227 121398912 6.950000e-49 206.0
29 TraesCS4B01G123300 chr3B 89.266 177 18 1 5117 5293 805270068 805269893 2.480000e-53 220.0
30 TraesCS4B01G123300 chr2B 88.827 179 19 1 5117 5295 110832435 110832258 8.930000e-53 219.0
31 TraesCS4B01G123300 chr2B 79.421 311 52 9 4364 4666 473329913 473330219 5.370000e-50 209.0
32 TraesCS4B01G123300 chr5D 79.231 260 39 11 4415 4666 4224683 4224431 3.280000e-37 167.0
33 TraesCS4B01G123300 chr5D 77.259 321 50 15 4365 4667 72526749 72527064 3.280000e-37 167.0
34 TraesCS4B01G123300 chr7B 83.333 186 17 12 4688 4865 376347514 376347335 5.490000e-35 159.0
35 TraesCS4B01G123300 chr3A 76.206 311 60 12 4364 4665 382351597 382351902 9.180000e-33 152.0


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 TraesCS4B01G123300 chr4B 146687968 146693262 5294 True 3315.800000 9779 97.385333 1 5295 3 chr4B.!!$R1 5294
1 TraesCS4B01G123300 chr4D 102405916 102410565 4649 True 3392.500000 4724 92.911500 4 4667 2 chr4D.!!$R1 4663
2 TraesCS4B01G123300 chr4D 440031260 440031857 597 False 641.000000 641 86.088000 4688 5294 1 chr4D.!!$F1 606
3 TraesCS4B01G123300 chr4A 472612106 472616794 4688 False 2219.666667 2723 92.903333 1 4589 3 chr4A.!!$F2 4588
4 TraesCS4B01G123300 chr4A 472527337 472528369 1032 False 1260.000000 1260 88.660000 1 1057 1 chr4A.!!$F1 1056
5 TraesCS4B01G123300 chrUn 175706038 175706645 607 True 691.000000 691 87.276000 4686 5294 1 chrUn.!!$R1 608
6 TraesCS4B01G123300 chr5B 670439286 670439893 607 True 686.000000 686 87.113000 4686 5294 1 chr5B.!!$R1 608
7 TraesCS4B01G123300 chr5B 532323887 532324415 528 False 490.000000 490 83.607000 4688 5229 1 chr5B.!!$F1 541
8 TraesCS4B01G123300 chr3D 246595198 246595828 630 False 651.000000 651 85.940000 4688 5294 1 chr3D.!!$F1 606
9 TraesCS4B01G123300 chr3D 98564905 98565500 595 True 645.000000 645 86.252000 4688 5294 1 chr3D.!!$R1 606
10 TraesCS4B01G123300 chr1D 4431966 4432563 597 False 625.000000 625 85.597000 4689 5294 1 chr1D.!!$F1 605
11 TraesCS4B01G123300 chr1B 630059199 630059791 592 True 521.000000 521 82.680000 4688 5294 1 chr1B.!!$R1 606

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
662 703 0.032912 ACAAAAACCGTCCCACCCTT 60.033 50.000 0.00 0.0 0.00 3.95 F
664 705 0.032912 AAAAACCGTCCCACCCTTGT 60.033 50.000 0.00 0.0 0.00 3.16 F
665 706 0.032912 AAAACCGTCCCACCCTTGTT 60.033 50.000 0.00 0.0 0.00 2.83 F
744 785 0.039527 GATTTGGAGCGTTTGCCGTT 60.040 50.000 0.00 0.0 44.31 4.44 F
749 790 0.165295 GGAGCGTTTGCCGTTAACTC 59.835 55.000 3.71 0.0 44.31 3.01 F
858 901 1.060713 CGAGTAACGACACCAAGCAG 58.939 55.000 0.00 0.0 45.77 4.24 F
1557 1774 1.065928 CTACGTCATCAGGCCGGAC 59.934 63.158 8.08 0.0 0.00 4.79 F
2571 2792 1.550976 ACTGGACTGCTAGCCACTTAC 59.449 52.381 13.29 0.0 0.00 2.34 F
3712 3985 0.037326 CTACCAGAAGAACAGCGCCA 60.037 55.000 2.29 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2419 2639 0.241749 GCATGCTGCTACTGTTGCAA 59.758 50.000 16.99 0.00 40.96 4.08 R
2541 2762 3.170991 AGCAGTCCAGTACTCCTACAA 57.829 47.619 0.00 0.00 35.76 2.41 R
2557 2778 5.105716 TCAGAACTAAGTAAGTGGCTAGCAG 60.106 44.000 18.24 4.16 38.88 4.24 R
2740 2965 8.311836 TGGAATTAACTGTAGACTAAGAACTGG 58.688 37.037 0.00 0.00 0.00 4.00 R
2742 2967 9.091220 ACTGGAATTAACTGTAGACTAAGAACT 57.909 33.333 0.00 0.00 0.00 3.01 R
2764 2989 8.311836 TGGAATTAACTGTAGACTAAGAACTGG 58.688 37.037 0.00 0.00 0.00 4.00 R
3409 3682 0.961753 TCGTCACACTCTGCTGACAT 59.038 50.000 2.90 0.00 37.27 3.06 R
3798 4089 0.039472 TTTTAGGCCATGCAGCAGGA 59.961 50.000 9.10 0.00 0.00 3.86 R
4599 4890 0.178767 TGGCATGACTATGAGCGCTT 59.821 50.000 13.26 0.00 36.36 4.68 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
75 76 3.561313 GGGCTGAAACAGAAGGGATACAA 60.561 47.826 2.81 0.00 32.79 2.41
134 135 5.442391 TGGCCTTAACATATTAGGTCAACC 58.558 41.667 3.32 0.00 30.65 3.77
140 141 9.106070 CCTTAACATATTAGGTCAACCTTGTAC 57.894 37.037 7.07 0.00 46.09 2.90
240 243 5.406175 GTGTTGTACGTGAATTAGCAGGTAA 59.594 40.000 0.00 0.00 39.80 2.85
242 245 4.178540 TGTACGTGAATTAGCAGGTAAGC 58.821 43.478 0.00 0.00 39.80 3.09
249 252 2.162338 TTAGCAGGTAAGCGGTGCGT 62.162 55.000 0.00 0.00 42.26 5.24
354 357 0.320771 GCAAGAGGGCGAAAGACTCA 60.321 55.000 0.00 0.00 40.87 3.41
355 358 1.719600 CAAGAGGGCGAAAGACTCAG 58.280 55.000 0.00 0.00 40.87 3.35
356 359 0.610687 AAGAGGGCGAAAGACTCAGG 59.389 55.000 0.00 0.00 40.87 3.86
362 365 0.107945 GCGAAAGACTCAGGCATCCT 60.108 55.000 0.00 0.00 0.00 3.24
379 382 2.619931 TCCTGATCCACTCAACTCCAA 58.380 47.619 0.00 0.00 32.14 3.53
383 386 4.324099 CCTGATCCACTCAACTCCAAGATT 60.324 45.833 0.00 0.00 32.14 2.40
386 389 5.485353 TGATCCACTCAACTCCAAGATTAGT 59.515 40.000 0.00 0.00 0.00 2.24
401 409 9.621629 TCCAAGATTAGTTGTTCTTTAGTTTGA 57.378 29.630 0.00 0.00 29.85 2.69
431 439 6.093404 TCGATAACAGTTCAGATCAACAGAC 58.907 40.000 0.00 0.00 0.00 3.51
445 453 3.063452 TCAACAGACTGAAAACGAGTTGC 59.937 43.478 10.08 0.00 35.95 4.17
486 497 6.791867 ACTACAATACTTGCTAGTGGATGA 57.208 37.500 11.27 0.00 35.78 2.92
528 539 2.418983 AGACGAAACGACTGGAGTTC 57.581 50.000 0.00 0.00 30.28 3.01
546 557 2.136878 CGCTAGCCCCCTCACTGAT 61.137 63.158 9.66 0.00 0.00 2.90
558 598 4.369182 CCCTCACTGATATCACGGTTTAC 58.631 47.826 0.00 0.00 0.00 2.01
560 600 5.453339 CCCTCACTGATATCACGGTTTACAT 60.453 44.000 0.00 0.00 0.00 2.29
561 601 6.049149 CCTCACTGATATCACGGTTTACATT 58.951 40.000 0.00 0.00 0.00 2.71
562 602 7.207383 CCTCACTGATATCACGGTTTACATTA 58.793 38.462 0.00 0.00 0.00 1.90
563 603 7.709182 CCTCACTGATATCACGGTTTACATTAA 59.291 37.037 0.00 0.00 0.00 1.40
564 604 9.261180 CTCACTGATATCACGGTTTACATTAAT 57.739 33.333 0.00 0.00 0.00 1.40
565 605 9.607988 TCACTGATATCACGGTTTACATTAATT 57.392 29.630 0.00 0.00 0.00 1.40
573 613 8.851541 TCACGGTTTACATTAATTACTTTCCT 57.148 30.769 0.00 0.00 0.00 3.36
574 614 9.941325 TCACGGTTTACATTAATTACTTTCCTA 57.059 29.630 0.00 0.00 0.00 2.94
628 668 0.036765 TACTTGCCGAAATCACGCCT 60.037 50.000 0.00 0.00 0.00 5.52
656 697 0.671796 CCCTCAACAAAAACCGTCCC 59.328 55.000 0.00 0.00 0.00 4.46
657 698 1.394618 CCTCAACAAAAACCGTCCCA 58.605 50.000 0.00 0.00 0.00 4.37
662 703 0.032912 ACAAAAACCGTCCCACCCTT 60.033 50.000 0.00 0.00 0.00 3.95
663 704 0.387565 CAAAAACCGTCCCACCCTTG 59.612 55.000 0.00 0.00 0.00 3.61
664 705 0.032912 AAAAACCGTCCCACCCTTGT 60.033 50.000 0.00 0.00 0.00 3.16
665 706 0.032912 AAAACCGTCCCACCCTTGTT 60.033 50.000 0.00 0.00 0.00 2.83
706 747 1.819632 GATCGGACGGCAGCCAATT 60.820 57.895 13.30 0.00 0.00 2.32
708 749 3.864686 CGGACGGCAGCCAATTCG 61.865 66.667 13.30 5.52 0.00 3.34
738 779 1.798813 GTCACGAGATTTGGAGCGTTT 59.201 47.619 0.00 0.00 34.37 3.60
739 780 1.798223 TCACGAGATTTGGAGCGTTTG 59.202 47.619 0.00 0.00 34.37 2.93
741 782 0.179189 CGAGATTTGGAGCGTTTGCC 60.179 55.000 0.00 0.00 44.31 4.52
742 783 0.179189 GAGATTTGGAGCGTTTGCCG 60.179 55.000 0.00 0.00 44.31 5.69
744 785 0.039527 GATTTGGAGCGTTTGCCGTT 60.040 50.000 0.00 0.00 44.31 4.44
746 787 1.022735 TTTGGAGCGTTTGCCGTTAA 58.977 45.000 0.00 0.00 44.31 2.01
748 789 0.533308 TGGAGCGTTTGCCGTTAACT 60.533 50.000 3.71 0.00 44.31 2.24
749 790 0.165295 GGAGCGTTTGCCGTTAACTC 59.835 55.000 3.71 0.00 44.31 3.01
750 791 1.145803 GAGCGTTTGCCGTTAACTCT 58.854 50.000 3.71 0.00 44.31 3.24
751 792 2.331194 GAGCGTTTGCCGTTAACTCTA 58.669 47.619 3.71 0.00 44.31 2.43
752 793 2.928116 GAGCGTTTGCCGTTAACTCTAT 59.072 45.455 3.71 0.00 44.31 1.98
753 794 2.928116 AGCGTTTGCCGTTAACTCTATC 59.072 45.455 3.71 0.00 44.31 2.08
754 795 2.669434 GCGTTTGCCGTTAACTCTATCA 59.331 45.455 3.71 0.00 39.32 2.15
755 796 3.241995 GCGTTTGCCGTTAACTCTATCAG 60.242 47.826 3.71 0.00 39.32 2.90
756 797 4.171005 CGTTTGCCGTTAACTCTATCAGA 58.829 43.478 3.71 0.00 0.00 3.27
757 798 4.624024 CGTTTGCCGTTAACTCTATCAGAA 59.376 41.667 3.71 0.00 0.00 3.02
758 799 5.220228 CGTTTGCCGTTAACTCTATCAGAAG 60.220 44.000 3.71 0.00 0.00 2.85
759 800 5.654603 TTGCCGTTAACTCTATCAGAAGA 57.345 39.130 3.71 0.00 0.00 2.87
786 827 8.679288 AAAATATCAATTCGCTCACAAAAGAG 57.321 30.769 0.00 0.00 38.68 2.85
789 830 5.749596 TCAATTCGCTCACAAAAGAGAAA 57.250 34.783 0.00 0.00 38.34 2.52
790 831 5.510671 TCAATTCGCTCACAAAAGAGAAAC 58.489 37.500 0.00 0.00 38.34 2.78
792 833 4.955925 TTCGCTCACAAAAGAGAAACAA 57.044 36.364 0.00 0.00 37.87 2.83
793 834 4.536364 TCGCTCACAAAAGAGAAACAAG 57.464 40.909 0.00 0.00 37.87 3.16
833 876 2.309898 AGTAAATGTGCGCGTGAAAC 57.690 45.000 8.43 1.98 0.00 2.78
858 901 1.060713 CGAGTAACGACACCAAGCAG 58.939 55.000 0.00 0.00 45.77 4.24
899 942 1.090052 GCCCCGCATACTCACAAGAC 61.090 60.000 0.00 0.00 0.00 3.01
1023 1068 4.011023 CAACGTCTCTTTCTCCCTCTAGA 58.989 47.826 0.00 0.00 0.00 2.43
1143 1360 4.560856 GAGCGAGCGATGGCGACT 62.561 66.667 1.00 0.00 46.35 4.18
1398 1615 2.900273 CCCCACATCGTCGGACAT 59.100 61.111 9.10 0.00 0.00 3.06
1557 1774 1.065928 CTACGTCATCAGGCCGGAC 59.934 63.158 8.08 0.00 0.00 4.79
2270 2490 8.978874 AGGATCATGTTAATTGCTACATTGTA 57.021 30.769 0.00 0.00 32.88 2.41
2288 2508 8.851541 ACATTGTATTGCATTTGGAAATTTCT 57.148 26.923 17.42 0.00 0.00 2.52
2393 2613 3.698040 CCAAATGGGGATGTGAAAGAGAG 59.302 47.826 0.00 0.00 0.00 3.20
2419 2639 9.067986 GGCATTTCCTTTATTTAGCTATACAGT 57.932 33.333 0.00 0.00 0.00 3.55
2459 2679 7.117523 GCATGCTCAGTTGTTTAGATATAGAGG 59.882 40.741 11.37 0.00 0.00 3.69
2541 2762 4.785301 AGCCACTTGTATGTGCTCAATAT 58.215 39.130 0.00 0.00 36.68 1.28
2557 2778 6.183360 TGCTCAATATTGTAGGAGTACTGGAC 60.183 42.308 14.97 0.00 0.00 4.02
2570 2791 1.938585 ACTGGACTGCTAGCCACTTA 58.061 50.000 13.29 0.00 0.00 2.24
2571 2792 1.550976 ACTGGACTGCTAGCCACTTAC 59.449 52.381 13.29 0.00 0.00 2.34
2721 2946 6.820335 TGCTGTGCATCTATTGTATAGAGTT 58.180 36.000 0.00 0.00 32.09 3.01
2722 2947 6.925718 TGCTGTGCATCTATTGTATAGAGTTC 59.074 38.462 0.00 0.00 32.09 3.01
2723 2948 7.151308 GCTGTGCATCTATTGTATAGAGTTCT 58.849 38.462 0.00 0.00 32.09 3.01
2724 2949 7.655328 GCTGTGCATCTATTGTATAGAGTTCTT 59.345 37.037 0.00 0.00 32.09 2.52
2742 2967 9.310449 AGAGTTCTTAGTCTACAGTTAATTCCA 57.690 33.333 0.00 0.00 32.18 3.53
2743 2968 9.575783 GAGTTCTTAGTCTACAGTTAATTCCAG 57.424 37.037 0.00 0.00 0.00 3.86
2744 2969 9.091220 AGTTCTTAGTCTACAGTTAATTCCAGT 57.909 33.333 0.00 0.00 0.00 4.00
2745 2970 9.708092 GTTCTTAGTCTACAGTTAATTCCAGTT 57.292 33.333 0.00 0.00 0.00 3.16
2746 2971 9.924650 TTCTTAGTCTACAGTTAATTCCAGTTC 57.075 33.333 0.00 0.00 0.00 3.01
2747 2972 9.310449 TCTTAGTCTACAGTTAATTCCAGTTCT 57.690 33.333 0.00 0.00 0.00 3.01
2748 2973 9.930693 CTTAGTCTACAGTTAATTCCAGTTCTT 57.069 33.333 0.00 0.00 0.00 2.52
2751 2976 9.091220 AGTCTACAGTTAATTCCAGTTCTTAGT 57.909 33.333 0.00 0.00 0.00 2.24
2752 2977 9.356433 GTCTACAGTTAATTCCAGTTCTTAGTC 57.644 37.037 0.00 0.00 0.00 2.59
2753 2978 9.310449 TCTACAGTTAATTCCAGTTCTTAGTCT 57.690 33.333 0.00 0.00 0.00 3.24
2756 2981 8.867097 ACAGTTAATTCCAGTTCTTAGTCTACA 58.133 33.333 0.00 0.00 0.00 2.74
2757 2982 9.360093 CAGTTAATTCCAGTTCTTAGTCTACAG 57.640 37.037 0.00 0.00 0.00 2.74
2758 2983 9.091220 AGTTAATTCCAGTTCTTAGTCTACAGT 57.909 33.333 0.00 0.00 0.00 3.55
2759 2984 9.708092 GTTAATTCCAGTTCTTAGTCTACAGTT 57.292 33.333 0.00 0.00 0.00 3.16
2764 2989 9.924650 TTCCAGTTCTTAGTCTACAGTTAATTC 57.075 33.333 0.00 0.00 0.00 2.17
2765 2990 8.529476 TCCAGTTCTTAGTCTACAGTTAATTCC 58.471 37.037 0.00 0.00 0.00 3.01
2766 2991 8.311836 CCAGTTCTTAGTCTACAGTTAATTCCA 58.688 37.037 0.00 0.00 0.00 3.53
2767 2992 9.360093 CAGTTCTTAGTCTACAGTTAATTCCAG 57.640 37.037 0.00 0.00 0.00 3.86
2768 2993 9.091220 AGTTCTTAGTCTACAGTTAATTCCAGT 57.909 33.333 0.00 0.00 0.00 4.00
2935 3160 3.430042 ACCTGAGCAATGACAACTGAT 57.570 42.857 0.00 0.00 0.00 2.90
3028 3253 5.623141 CGATGACTCCTCTGTTGATGAGAAA 60.623 44.000 5.58 0.00 38.03 2.52
3074 3299 1.815003 CTACTGCAGGGAAGGCAAAAG 59.185 52.381 19.93 0.00 41.39 2.27
3093 3318 1.706443 GCAGCAGCTCCAAAAATCAC 58.294 50.000 0.00 0.00 37.91 3.06
3409 3682 7.883391 TTGTTTTTCCACCAAAGTCTGTATA 57.117 32.000 0.00 0.00 0.00 1.47
3410 3683 8.472007 TTGTTTTTCCACCAAAGTCTGTATAT 57.528 30.769 0.00 0.00 0.00 0.86
3426 3699 4.998788 TGTATATGTCAGCAGAGTGTGAC 58.001 43.478 0.00 0.00 42.93 3.67
3452 3725 7.409661 CGATTGTAACATTGTGTTGATTTCTGC 60.410 37.037 5.64 0.00 41.30 4.26
3669 3942 0.689623 AACTGGAGGTCCTCAAGCTG 59.310 55.000 21.76 10.33 35.05 4.24
3672 3945 1.194781 TGGAGGTCCTCAAGCTGGTC 61.195 60.000 20.72 1.08 35.33 4.02
3709 3982 2.166459 TCCATCTACCAGAAGAACAGCG 59.834 50.000 0.00 0.00 0.00 5.18
3711 3984 0.246635 TCTACCAGAAGAACAGCGCC 59.753 55.000 2.29 0.00 0.00 6.53
3712 3985 0.037326 CTACCAGAAGAACAGCGCCA 60.037 55.000 2.29 0.00 0.00 5.69
3798 4089 0.548682 AGTCCAGGGCATCACCTCTT 60.549 55.000 0.00 0.00 39.34 2.85
3837 4128 2.225791 CTCCGGGCATGAACGAGACA 62.226 60.000 0.00 0.00 0.00 3.41
3864 4155 3.977244 GCCAACACCTTGTGCCGG 61.977 66.667 0.00 0.00 36.98 6.13
4211 4502 5.944013 TCGCATTTTCATTATTTTGTCGGA 58.056 33.333 0.00 0.00 0.00 4.55
4248 4539 2.306847 GGGTTGTGGCAATGGTATAGG 58.693 52.381 0.00 0.00 0.00 2.57
4263 4554 8.836413 CAATGGTATAGGTCGTTTTCATATGTT 58.164 33.333 1.90 0.00 0.00 2.71
4289 4580 5.171476 TGCTCTGTGAATAAGTTAGACTGC 58.829 41.667 0.00 0.00 0.00 4.40
4294 4585 6.436218 TCTGTGAATAAGTTAGACTGCCTGTA 59.564 38.462 0.00 0.00 0.00 2.74
4309 4600 3.264706 TGCCTGTAACCTACAAATGCCTA 59.735 43.478 0.00 0.00 38.38 3.93
4337 4628 5.993748 TTTCAGTTATGAATGAAACCCCC 57.006 39.130 8.80 0.00 44.75 5.40
4340 4631 6.395780 TCAGTTATGAATGAAACCCCCTTA 57.604 37.500 0.00 0.00 30.61 2.69
4361 4652 7.309560 CCCTTAATTCCGTGGTTATGTTTTCTT 60.310 37.037 0.00 0.00 0.00 2.52
4385 4676 9.787532 CTTGTTGTTGGAATTGTATCGAATATT 57.212 29.630 0.00 0.00 0.00 1.28
4433 4724 2.163509 AGAGTCGTACTGTGTGCAGAT 58.836 47.619 1.30 0.00 45.28 2.90
4453 4744 0.319297 AGGGTACGAGTTGTGTTCGC 60.319 55.000 0.00 0.00 41.57 4.70
4493 4784 6.602406 TCTCGGACCTCTTATATAATGTAGGC 59.398 42.308 14.28 9.53 0.00 3.93
4512 4803 7.787028 TGTAGGCATAGACATACAATGTAACA 58.213 34.615 0.00 0.00 45.03 2.41
4521 4812 7.930217 AGACATACAATGTAACATATGCCAAC 58.070 34.615 1.58 0.00 45.03 3.77
4523 4814 8.236585 ACATACAATGTAACATATGCCAACAT 57.763 30.769 1.58 7.41 42.78 2.71
4534 4825 2.268762 TGCCAACATAGCACAGACAA 57.731 45.000 0.00 0.00 34.69 3.18
4538 4829 2.161012 CCAACATAGCACAGACAAGCAG 59.839 50.000 0.00 0.00 0.00 4.24
4547 4838 1.302832 AGACAAGCAGGGAAAGCCG 60.303 57.895 0.00 0.00 33.83 5.52
4549 4840 3.752339 CAAGCAGGGAAAGCCGGC 61.752 66.667 21.89 21.89 35.92 6.13
4585 4876 2.345991 GTGGCCGGTTCTGTAGCA 59.654 61.111 1.90 0.00 0.00 3.49
4593 4884 1.995484 CGGTTCTGTAGCAGTGTCATG 59.005 52.381 0.00 0.00 32.61 3.07
4599 4890 2.234661 CTGTAGCAGTGTCATGGGAAGA 59.765 50.000 0.00 0.00 0.00 2.87
4605 4896 0.674895 GTGTCATGGGAAGAAGCGCT 60.675 55.000 2.64 2.64 0.00 5.92
4615 4906 2.799412 GGAAGAAGCGCTCATAGTCATG 59.201 50.000 12.06 0.00 0.00 3.07
4618 4909 0.178767 AAGCGCTCATAGTCATGCCA 59.821 50.000 12.06 0.00 31.73 4.92
4620 4911 1.825285 GCGCTCATAGTCATGCCACG 61.825 60.000 0.00 0.00 31.73 4.94
4622 4913 0.882042 GCTCATAGTCATGCCACGGG 60.882 60.000 0.00 0.00 31.73 5.28
4623 4914 0.752658 CTCATAGTCATGCCACGGGA 59.247 55.000 0.00 0.00 31.73 5.14
4659 4950 4.753107 TGGTGAACCTCGTTAACAAATCTC 59.247 41.667 6.39 0.00 36.82 2.75
4667 4958 5.347635 CCTCGTTAACAAATCTCGATGTCAA 59.652 40.000 6.39 0.00 0.00 3.18
4668 4959 6.148270 TCGTTAACAAATCTCGATGTCAAC 57.852 37.500 6.39 0.00 0.00 3.18
4669 4960 5.007039 CGTTAACAAATCTCGATGTCAACG 58.993 41.667 10.05 10.05 42.63 4.10
4670 4961 5.388061 CGTTAACAAATCTCGATGTCAACGT 60.388 40.000 14.34 0.00 43.04 3.99
4671 4962 4.647291 AACAAATCTCGATGTCAACGTC 57.353 40.909 2.23 0.00 0.00 4.34
4677 4968 2.566997 CGATGTCAACGTCGCTAGG 58.433 57.895 11.39 0.00 46.44 3.02
4678 4969 0.179171 CGATGTCAACGTCGCTAGGT 60.179 55.000 11.39 0.00 46.44 3.08
4679 4970 1.063027 CGATGTCAACGTCGCTAGGTA 59.937 52.381 11.39 0.00 46.44 3.08
4680 4971 2.286831 CGATGTCAACGTCGCTAGGTAT 60.287 50.000 11.39 0.00 46.44 2.73
4681 4972 3.703420 GATGTCAACGTCGCTAGGTATT 58.297 45.455 0.00 0.00 0.00 1.89
4682 4973 4.553351 CGATGTCAACGTCGCTAGGTATTA 60.553 45.833 11.39 0.00 46.44 0.98
4683 4974 4.019919 TGTCAACGTCGCTAGGTATTAC 57.980 45.455 0.00 0.00 0.00 1.89
4684 4975 3.031812 GTCAACGTCGCTAGGTATTACG 58.968 50.000 0.00 0.00 39.37 3.18
4861 5166 0.174617 GCGACTCTCCCTTCTTCCTG 59.825 60.000 0.00 0.00 0.00 3.86
4867 5173 3.721706 CCCTTCTTCCTGGCGGCT 61.722 66.667 11.43 0.00 0.00 5.52
4995 5304 3.237741 GCTGCGGCCTAGGGATCT 61.238 66.667 11.72 0.00 0.00 2.75
5015 5324 4.370776 TCTTTGACCCCAGATTGGATCTA 58.629 43.478 0.00 0.00 40.96 1.98
5020 5329 1.701847 CCCCAGATTGGATCTAGGTGG 59.298 57.143 0.00 0.00 40.96 4.61
5021 5330 2.412591 CCCAGATTGGATCTAGGTGGT 58.587 52.381 0.00 0.00 40.96 4.16
5029 5340 1.001760 ATCTAGGTGGTGCTCGGGT 59.998 57.895 0.00 0.00 0.00 5.28
5060 5371 2.111043 CTTGTCAGGCGTGGTGGT 59.889 61.111 6.56 0.00 0.00 4.16
5129 5448 3.065306 CTCGGCCTGGTGGTGTTA 58.935 61.111 0.00 0.00 35.27 2.41
5166 5485 1.464997 GTGCACGAGAGTTGGATTTCC 59.535 52.381 0.00 0.00 46.40 3.13
5167 5486 0.721718 GCACGAGAGTTGGATTTCCG 59.278 55.000 0.00 0.00 46.40 4.30
5194 5513 2.095567 CAGATCTGGGTGAAAACTTGCG 60.096 50.000 15.38 0.00 0.00 4.85
5197 5516 2.096248 TCTGGGTGAAAACTTGCGTTT 58.904 42.857 0.00 0.00 44.87 3.60
5260 5580 1.351017 TCCCTTCTTGAAGGCATCGTT 59.649 47.619 20.71 0.00 38.63 3.85
5284 5604 2.224646 GGAGAAGTTCAAGGCCACTCTT 60.225 50.000 5.01 1.70 0.00 2.85
5294 5614 0.615850 GGCCACTCTTTGCTACCTCT 59.384 55.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.570550 ACTAGATGATACCTCGTGCCTTC 59.429 47.826 0.00 0.00 0.00 3.46
37 38 4.307259 TCAGCCCTACAATCTTAATCCCT 58.693 43.478 0.00 0.00 0.00 4.20
134 135 8.458052 TGTCAATAGCATGGTTATTTGTACAAG 58.542 33.333 8.56 0.00 0.00 3.16
140 141 9.888878 CTTCTATGTCAATAGCATGGTTATTTG 57.111 33.333 1.12 5.71 36.47 2.32
196 197 2.163815 ACCGTGATAACTTCGACCTCAG 59.836 50.000 0.00 0.00 0.00 3.35
198 199 2.094854 ACACCGTGATAACTTCGACCTC 60.095 50.000 5.28 0.00 0.00 3.85
233 236 1.293267 TTTACGCACCGCTTACCTGC 61.293 55.000 0.00 0.00 0.00 4.85
240 243 1.953559 ATCATGATTTACGCACCGCT 58.046 45.000 1.18 0.00 0.00 5.52
242 245 6.364976 TGAATACTATCATGATTTACGCACCG 59.635 38.462 14.65 0.00 0.00 4.94
354 357 1.211457 GTTGAGTGGATCAGGATGCCT 59.789 52.381 0.00 0.00 39.68 4.75
355 358 1.211457 AGTTGAGTGGATCAGGATGCC 59.789 52.381 0.00 0.00 39.68 4.40
356 359 2.559440 GAGTTGAGTGGATCAGGATGC 58.441 52.381 0.00 0.00 39.68 3.91
362 365 4.916041 AATCTTGGAGTTGAGTGGATCA 57.084 40.909 0.00 0.00 35.62 2.92
379 382 7.929785 TCGGTCAAACTAAAGAACAACTAATCT 59.070 33.333 0.00 0.00 0.00 2.40
383 386 7.095940 CGAATCGGTCAAACTAAAGAACAACTA 60.096 37.037 0.00 0.00 0.00 2.24
386 389 5.754406 TCGAATCGGTCAAACTAAAGAACAA 59.246 36.000 1.76 0.00 0.00 2.83
401 409 4.713824 TCTGAACTGTTATCGAATCGGT 57.286 40.909 1.76 0.00 0.00 4.69
445 453 6.687081 TGTAGTTGTTGTTTAGGTTGAAGG 57.313 37.500 0.00 0.00 0.00 3.46
486 497 3.267031 AGGTTCTAGCTAGCCAACCAAAT 59.733 43.478 31.15 17.32 40.80 2.32
528 539 0.827925 TATCAGTGAGGGGGCTAGCG 60.828 60.000 9.00 0.00 0.00 4.26
628 668 1.974265 TTTGTTGAGGGACGAATGCA 58.026 45.000 0.00 0.00 0.00 3.96
656 697 1.335872 GGCGTGATTTCAACAAGGGTG 60.336 52.381 0.00 0.00 0.00 4.61
657 698 0.958822 GGCGTGATTTCAACAAGGGT 59.041 50.000 0.00 0.00 0.00 4.34
662 703 0.317436 GCGTTGGCGTGATTTCAACA 60.317 50.000 0.00 0.00 40.31 3.33
663 704 0.317436 TGCGTTGGCGTGATTTCAAC 60.317 50.000 0.00 0.00 44.10 3.18
664 705 0.382158 TTGCGTTGGCGTGATTTCAA 59.618 45.000 0.00 0.00 44.10 2.69
665 706 0.595588 ATTGCGTTGGCGTGATTTCA 59.404 45.000 0.00 0.00 44.10 2.69
706 747 1.944709 TCTCGTGACAGAACTGAACGA 59.055 47.619 23.49 23.49 44.24 3.85
708 749 4.084328 CCAAATCTCGTGACAGAACTGAAC 60.084 45.833 8.87 5.76 0.00 3.18
738 779 5.654603 TTCTTCTGATAGAGTTAACGGCA 57.345 39.130 0.00 0.00 0.00 5.69
739 780 6.963049 TTTTCTTCTGATAGAGTTAACGGC 57.037 37.500 0.00 0.00 0.00 5.68
765 806 7.041440 TGTTTCTCTTTTGTGAGCGAATTGATA 60.041 33.333 0.00 0.00 34.29 2.15
802 843 7.123190 CGCGCACATTTACTTATTTCATTCTA 58.877 34.615 8.75 0.00 0.00 2.10
804 845 5.737290 ACGCGCACATTTACTTATTTCATTC 59.263 36.000 5.73 0.00 0.00 2.67
833 876 3.929417 TGGTGTCGTTACTCGTTTTTG 57.071 42.857 0.00 0.00 40.80 2.44
858 901 0.872021 CCGTCAATACTCGCTGCCTC 60.872 60.000 0.00 0.00 0.00 4.70
892 935 1.679139 TTTGGCAGGTGAGTCTTGTG 58.321 50.000 0.00 0.00 0.00 3.33
1023 1068 2.367947 AAGGGAGGGATTTGAGGAGT 57.632 50.000 0.00 0.00 0.00 3.85
1143 1360 2.924101 AAGACCCCCGGCGTTACA 60.924 61.111 6.01 0.00 0.00 2.41
1395 1612 2.277858 GTCGAGGTGGACCAGATGT 58.722 57.895 0.00 0.00 38.89 3.06
1800 2017 3.749064 GACGACGCTCTGGAGGCA 61.749 66.667 0.00 0.00 0.00 4.75
2270 2490 7.094549 CCAACATCAGAAATTTCCAAATGCAAT 60.095 33.333 14.61 4.38 0.00 3.56
2288 2508 5.449862 GCAATTACGCCTAATTCCAACATCA 60.450 40.000 0.00 0.00 31.25 3.07
2393 2613 9.067986 ACTGTATAGCTAAATAAAGGAAATGCC 57.932 33.333 0.00 0.00 0.00 4.40
2405 2625 7.011482 GCTACTGTTGCAACTGTATAGCTAAAT 59.989 37.037 34.20 18.68 40.80 1.40
2413 2633 2.744202 GCTGCTACTGTTGCAACTGTAT 59.256 45.455 35.00 21.38 40.80 2.29
2419 2639 0.241749 GCATGCTGCTACTGTTGCAA 59.758 50.000 16.99 0.00 40.96 4.08
2541 2762 3.170991 AGCAGTCCAGTACTCCTACAA 57.829 47.619 0.00 0.00 35.76 2.41
2557 2778 5.105716 TCAGAACTAAGTAAGTGGCTAGCAG 60.106 44.000 18.24 4.16 38.88 4.24
2721 2946 9.310449 AGAACTGGAATTAACTGTAGACTAAGA 57.690 33.333 0.00 0.00 0.00 2.10
2722 2947 9.930693 AAGAACTGGAATTAACTGTAGACTAAG 57.069 33.333 0.00 0.00 0.00 2.18
2725 2950 9.091220 ACTAAGAACTGGAATTAACTGTAGACT 57.909 33.333 0.00 0.00 0.00 3.24
2726 2951 9.356433 GACTAAGAACTGGAATTAACTGTAGAC 57.644 37.037 0.00 0.00 0.00 2.59
2727 2952 9.310449 AGACTAAGAACTGGAATTAACTGTAGA 57.690 33.333 0.00 0.00 0.00 2.59
2730 2955 8.867097 TGTAGACTAAGAACTGGAATTAACTGT 58.133 33.333 0.00 0.00 0.00 3.55
2731 2956 9.360093 CTGTAGACTAAGAACTGGAATTAACTG 57.640 37.037 0.00 0.00 0.00 3.16
2732 2957 9.091220 ACTGTAGACTAAGAACTGGAATTAACT 57.909 33.333 0.00 0.00 0.00 2.24
2733 2958 9.708092 AACTGTAGACTAAGAACTGGAATTAAC 57.292 33.333 0.00 0.00 0.00 2.01
2738 2963 9.924650 GAATTAACTGTAGACTAAGAACTGGAA 57.075 33.333 0.00 0.00 0.00 3.53
2739 2964 8.529476 GGAATTAACTGTAGACTAAGAACTGGA 58.471 37.037 0.00 0.00 0.00 3.86
2740 2965 8.311836 TGGAATTAACTGTAGACTAAGAACTGG 58.688 37.037 0.00 0.00 0.00 4.00
2741 2966 9.360093 CTGGAATTAACTGTAGACTAAGAACTG 57.640 37.037 0.00 0.00 0.00 3.16
2742 2967 9.091220 ACTGGAATTAACTGTAGACTAAGAACT 57.909 33.333 0.00 0.00 0.00 3.01
2743 2968 9.708092 AACTGGAATTAACTGTAGACTAAGAAC 57.292 33.333 0.00 0.00 0.00 3.01
2744 2969 9.924650 GAACTGGAATTAACTGTAGACTAAGAA 57.075 33.333 0.00 0.00 0.00 2.52
2745 2970 9.310449 AGAACTGGAATTAACTGTAGACTAAGA 57.690 33.333 0.00 0.00 0.00 2.10
2746 2971 9.930693 AAGAACTGGAATTAACTGTAGACTAAG 57.069 33.333 0.00 0.00 0.00 2.18
2749 2974 9.091220 ACTAAGAACTGGAATTAACTGTAGACT 57.909 33.333 0.00 0.00 0.00 3.24
2750 2975 9.356433 GACTAAGAACTGGAATTAACTGTAGAC 57.644 37.037 0.00 0.00 0.00 2.59
2751 2976 9.310449 AGACTAAGAACTGGAATTAACTGTAGA 57.690 33.333 0.00 0.00 0.00 2.59
2754 2979 8.867097 TGTAGACTAAGAACTGGAATTAACTGT 58.133 33.333 0.00 0.00 0.00 3.55
2755 2980 9.360093 CTGTAGACTAAGAACTGGAATTAACTG 57.640 37.037 0.00 0.00 0.00 3.16
2756 2981 9.091220 ACTGTAGACTAAGAACTGGAATTAACT 57.909 33.333 0.00 0.00 0.00 2.24
2757 2982 9.708092 AACTGTAGACTAAGAACTGGAATTAAC 57.292 33.333 0.00 0.00 0.00 2.01
2762 2987 9.924650 GAATTAACTGTAGACTAAGAACTGGAA 57.075 33.333 0.00 0.00 0.00 3.53
2763 2988 8.529476 GGAATTAACTGTAGACTAAGAACTGGA 58.471 37.037 0.00 0.00 0.00 3.86
2764 2989 8.311836 TGGAATTAACTGTAGACTAAGAACTGG 58.688 37.037 0.00 0.00 0.00 4.00
2765 2990 9.360093 CTGGAATTAACTGTAGACTAAGAACTG 57.640 37.037 0.00 0.00 0.00 3.16
2766 2991 9.091220 ACTGGAATTAACTGTAGACTAAGAACT 57.909 33.333 0.00 0.00 0.00 3.01
2767 2992 9.708092 AACTGGAATTAACTGTAGACTAAGAAC 57.292 33.333 0.00 0.00 0.00 3.01
2768 2993 9.924650 GAACTGGAATTAACTGTAGACTAAGAA 57.075 33.333 0.00 0.00 0.00 2.52
2935 3160 5.070446 TGCTTCCTGAAGTTACAGAAGAAGA 59.930 40.000 8.57 7.03 37.85 2.87
3028 3253 3.349022 TGTCTTCTTTCGTGGTTTTGGT 58.651 40.909 0.00 0.00 0.00 3.67
3074 3299 1.000060 TGTGATTTTTGGAGCTGCTGC 60.000 47.619 14.73 14.73 40.05 5.25
3093 3318 5.587443 TCAGTCCATTTAGCATCATGAAGTG 59.413 40.000 0.00 0.00 0.00 3.16
3240 3465 2.867456 ATAACAAAACGAAGACGGCG 57.133 45.000 4.80 4.80 44.46 6.46
3368 3641 1.406539 ACAAAAACCAGACTGCTGCAG 59.593 47.619 27.02 27.02 40.91 4.41
3409 3682 0.961753 TCGTCACACTCTGCTGACAT 59.038 50.000 2.90 0.00 37.27 3.06
3410 3683 0.961753 ATCGTCACACTCTGCTGACA 59.038 50.000 2.90 0.00 37.27 3.58
3426 3699 7.409661 GCAGAAATCAACACAATGTTACAATCG 60.410 37.037 0.00 0.00 38.77 3.34
3452 3725 3.209410 AGTTCAGAGAACTTGCTGTTGG 58.791 45.455 6.58 0.00 39.30 3.77
3669 3942 3.357079 CCAGTGGCGCTGTTGACC 61.357 66.667 25.05 0.00 43.55 4.02
3672 3945 2.401766 GGATCCAGTGGCGCTGTTG 61.402 63.158 25.05 12.08 43.55 3.33
3711 3984 1.152984 TGGTGGTTCCACTGCAGTG 60.153 57.895 35.15 35.15 41.93 3.66
3712 3985 3.330192 TGGTGGTTCCACTGCAGT 58.670 55.556 15.25 15.25 41.93 4.40
3798 4089 0.039472 TTTTAGGCCATGCAGCAGGA 59.961 50.000 9.10 0.00 0.00 3.86
3837 4128 0.106519 AGGTGTTGGCAAGCTCAACT 60.107 50.000 19.57 0.00 43.36 3.16
3864 4155 2.681848 CAGAAACCAGACATGCATCTCC 59.318 50.000 0.00 0.00 0.00 3.71
4248 4539 6.017933 CAGAGCAAGAACATATGAAAACGAC 58.982 40.000 10.38 0.00 0.00 4.34
4263 4554 7.093354 CAGTCTAACTTATTCACAGAGCAAGA 58.907 38.462 0.00 0.00 0.00 3.02
4289 4580 4.876107 CACTAGGCATTTGTAGGTTACAGG 59.124 45.833 0.00 0.00 40.24 4.00
4294 4585 4.367039 ACACACTAGGCATTTGTAGGTT 57.633 40.909 0.00 0.00 0.00 3.50
4337 4628 8.079809 ACAAGAAAACATAACCACGGAATTAAG 58.920 33.333 0.00 0.00 0.00 1.85
4340 4631 6.399639 ACAAGAAAACATAACCACGGAATT 57.600 33.333 0.00 0.00 0.00 2.17
4385 4676 9.263446 AGGTCAACTGTAATCTACCTTGTATAA 57.737 33.333 0.00 0.00 33.59 0.98
4386 4677 8.834004 AGGTCAACTGTAATCTACCTTGTATA 57.166 34.615 0.00 0.00 33.59 1.47
4387 4678 7.735326 AGGTCAACTGTAATCTACCTTGTAT 57.265 36.000 0.00 0.00 33.59 2.29
4388 4679 7.549147 AAGGTCAACTGTAATCTACCTTGTA 57.451 36.000 3.86 0.00 43.77 2.41
4389 4680 6.435292 AAGGTCAACTGTAATCTACCTTGT 57.565 37.500 3.86 0.00 43.77 3.16
4390 4681 7.837863 TCTAAGGTCAACTGTAATCTACCTTG 58.162 38.462 13.41 5.40 44.76 3.61
4391 4682 7.674772 ACTCTAAGGTCAACTGTAATCTACCTT 59.325 37.037 9.32 9.32 46.32 3.50
4392 4683 7.183460 ACTCTAAGGTCAACTGTAATCTACCT 58.817 38.462 0.00 0.00 38.98 3.08
4393 4684 7.407393 ACTCTAAGGTCAACTGTAATCTACC 57.593 40.000 0.00 0.00 0.00 3.18
4394 4685 7.148272 ACGACTCTAAGGTCAACTGTAATCTAC 60.148 40.741 0.00 0.00 36.12 2.59
4395 4686 6.883217 ACGACTCTAAGGTCAACTGTAATCTA 59.117 38.462 0.00 0.00 36.12 1.98
4396 4687 5.711036 ACGACTCTAAGGTCAACTGTAATCT 59.289 40.000 0.00 0.00 36.12 2.40
4397 4688 5.952033 ACGACTCTAAGGTCAACTGTAATC 58.048 41.667 0.00 0.00 36.12 1.75
4398 4689 5.979288 ACGACTCTAAGGTCAACTGTAAT 57.021 39.130 0.00 0.00 36.12 1.89
4399 4690 6.000219 AGTACGACTCTAAGGTCAACTGTAA 59.000 40.000 0.00 0.00 36.12 2.41
4400 4691 5.410746 CAGTACGACTCTAAGGTCAACTGTA 59.589 44.000 13.90 0.32 40.75 2.74
4401 4692 4.215827 CAGTACGACTCTAAGGTCAACTGT 59.784 45.833 13.90 1.02 40.75 3.55
4402 4693 4.215827 ACAGTACGACTCTAAGGTCAACTG 59.784 45.833 17.59 17.59 45.33 3.16
4403 4694 4.215827 CACAGTACGACTCTAAGGTCAACT 59.784 45.833 0.00 0.00 36.12 3.16
4409 4700 2.228103 TGCACACAGTACGACTCTAAGG 59.772 50.000 0.00 0.00 0.00 2.69
4433 4724 1.068333 GCGAACACAACTCGTACCCTA 60.068 52.381 0.00 0.00 38.57 3.53
4453 4744 4.341099 GTCCGAGATACAAGTGTTCTACG 58.659 47.826 0.00 0.00 0.00 3.51
4469 4760 6.377429 TGCCTACATTATATAAGAGGTCCGAG 59.623 42.308 16.52 5.19 0.00 4.63
4493 4784 9.218440 TGGCATATGTTACATTGTATGTCTATG 57.782 33.333 2.23 0.00 43.67 2.23
4501 4792 7.500559 TGCTATGTTGGCATATGTTACATTGTA 59.499 33.333 18.15 14.58 37.01 2.41
4504 4795 6.320926 TGTGCTATGTTGGCATATGTTACATT 59.679 34.615 18.15 8.32 41.86 2.71
4512 4803 4.155063 TGTCTGTGCTATGTTGGCATAT 57.845 40.909 0.00 0.00 41.86 1.78
4521 4812 1.065926 TCCCTGCTTGTCTGTGCTATG 60.066 52.381 0.00 0.00 0.00 2.23
4523 4814 1.055849 TTCCCTGCTTGTCTGTGCTA 58.944 50.000 0.00 0.00 0.00 3.49
4578 4869 2.234661 TCTTCCCATGACACTGCTACAG 59.765 50.000 0.00 0.00 37.52 2.74
4585 4876 0.674895 GCGCTTCTTCCCATGACACT 60.675 55.000 0.00 0.00 0.00 3.55
4593 4884 1.137086 TGACTATGAGCGCTTCTTCCC 59.863 52.381 13.26 0.00 0.00 3.97
4599 4890 0.178767 TGGCATGACTATGAGCGCTT 59.821 50.000 13.26 0.00 36.36 4.68
4605 4896 1.199615 TTCCCGTGGCATGACTATGA 58.800 50.000 8.63 0.00 36.36 2.15
4615 4906 1.152963 ATGGCTACATTCCCGTGGC 60.153 57.895 0.00 0.00 42.20 5.01
4618 4909 1.681780 CCAACATGGCTACATTCCCGT 60.682 52.381 0.00 0.00 34.35 5.28
4620 4911 1.750778 CACCAACATGGCTACATTCCC 59.249 52.381 0.00 0.00 42.67 3.97
4622 4913 3.119495 GGTTCACCAACATGGCTACATTC 60.119 47.826 0.00 0.00 42.67 2.67
4623 4914 2.825532 GGTTCACCAACATGGCTACATT 59.174 45.455 0.00 0.00 42.67 2.71
4659 4950 0.179171 ACCTAGCGACGTTGACATCG 60.179 55.000 7.08 4.39 41.32 3.84
4667 4958 1.599542 GACCGTAATACCTAGCGACGT 59.400 52.381 0.00 0.00 0.00 4.34
4668 4959 1.069636 GGACCGTAATACCTAGCGACG 60.070 57.143 0.00 0.00 0.00 5.12
4669 4960 1.268079 GGGACCGTAATACCTAGCGAC 59.732 57.143 0.00 0.00 0.00 5.19
4670 4961 1.609208 GGGACCGTAATACCTAGCGA 58.391 55.000 0.00 0.00 0.00 4.93
4671 4962 0.239347 CGGGACCGTAATACCTAGCG 59.761 60.000 1.86 0.00 34.35 4.26
4745 5036 4.741239 GAGGGTGGAGGAGGGCCA 62.741 72.222 6.18 0.00 36.29 5.36
4930 5239 2.608988 CAGACCCTCCACCCTGCT 60.609 66.667 0.00 0.00 0.00 4.24
4992 5301 3.790408 AGATCCAATCTGGGGTCAAAGAT 59.210 43.478 0.00 0.00 38.32 2.40
4995 5304 4.778213 CTAGATCCAATCTGGGGTCAAA 57.222 45.455 0.00 0.00 40.51 2.69
5166 5485 0.526211 TCACCCAGATCTGTTCGACG 59.474 55.000 21.11 4.80 0.00 5.12
5167 5486 2.743636 TTCACCCAGATCTGTTCGAC 57.256 50.000 21.11 0.00 0.00 4.20
5214 5534 3.622060 AAATAGCACCGCCACCGCT 62.622 57.895 0.00 0.00 39.80 5.52
5260 5580 0.843309 TGGCCTTGAACTTCTCCACA 59.157 50.000 3.32 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.