Multiple sequence alignment - TraesCS5A01G537200

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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 TraesCS5A01G537200 chr5A 100.000 2379 0 0 1 2379 693659092 693656714 0.000000e+00 4394.0
1 TraesCS5A01G537200 chr3A 97.486 875 14 7 1507 2379 649040957 649041825 0.000000e+00 1487.0
2 TraesCS5A01G537200 chr3D 91.334 877 44 15 1507 2379 567239339 567240187 0.000000e+00 1170.0
3 TraesCS5A01G537200 chr7D 91.116 878 46 17 1507 2379 184504959 184504109 0.000000e+00 1160.0
4 TraesCS5A01G537200 chr7D 86.232 276 27 10 2107 2379 536149216 536149483 2.990000e-74 289.0
5 TraesCS5A01G537200 chr2D 90.992 877 48 14 1507 2379 643667576 643668425 0.000000e+00 1153.0
6 TraesCS5A01G537200 chr2D 83.409 880 80 22 1507 2379 430011695 430010875 0.000000e+00 756.0
7 TraesCS5A01G537200 chr4B 90.753 876 52 15 1507 2379 86764715 86763866 0.000000e+00 1142.0
8 TraesCS5A01G537200 chr4B 83.979 749 87 28 6 725 659533259 659534003 0.000000e+00 688.0
9 TraesCS5A01G537200 chr4B 82.781 604 55 24 861 1426 659535391 659534799 5.910000e-136 494.0
10 TraesCS5A01G537200 chr5D 90.297 876 46 16 1507 2379 480043438 480042599 0.000000e+00 1110.0
11 TraesCS5A01G537200 chr1D 90.717 851 44 16 1535 2379 307350759 307351580 0.000000e+00 1101.0
12 TraesCS5A01G537200 chr1D 76.164 365 64 16 29 378 111519259 111518903 1.130000e-38 171.0
13 TraesCS5A01G537200 chr4D 80.841 642 60 31 868 1492 508284803 508285398 1.680000e-121 446.0
14 TraesCS5A01G537200 chr4D 85.238 420 43 16 324 730 508286667 508286254 4.730000e-112 414.0
15 TraesCS5A01G537200 chr7B 88.966 145 14 1 2237 2379 578708772 578708916 6.760000e-41 178.0
16 TraesCS5A01G537200 chr6A 80.337 178 22 9 202 377 48171710 48171544 3.210000e-24 122.0
17 TraesCS5A01G537200 chr6A 92.727 55 1 2 320 373 35303341 35303393 2.540000e-10 76.8
18 TraesCS5A01G537200 chr4A 75.661 189 32 12 195 374 688336253 688336070 5.450000e-12 82.4
19 TraesCS5A01G537200 chr7A 80.208 96 14 5 751 845 23109330 23109421 1.530000e-07 67.6


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G537200 chr5A 693656714 693659092 2378 True 4394 4394 100.000 1 2379 1 chr5A.!!$R1 2378
1 TraesCS5A01G537200 chr3A 649040957 649041825 868 False 1487 1487 97.486 1507 2379 1 chr3A.!!$F1 872
2 TraesCS5A01G537200 chr3D 567239339 567240187 848 False 1170 1170 91.334 1507 2379 1 chr3D.!!$F1 872
3 TraesCS5A01G537200 chr7D 184504109 184504959 850 True 1160 1160 91.116 1507 2379 1 chr7D.!!$R1 872
4 TraesCS5A01G537200 chr2D 643667576 643668425 849 False 1153 1153 90.992 1507 2379 1 chr2D.!!$F1 872
5 TraesCS5A01G537200 chr2D 430010875 430011695 820 True 756 756 83.409 1507 2379 1 chr2D.!!$R1 872
6 TraesCS5A01G537200 chr4B 86763866 86764715 849 True 1142 1142 90.753 1507 2379 1 chr4B.!!$R1 872
7 TraesCS5A01G537200 chr4B 659533259 659534003 744 False 688 688 83.979 6 725 1 chr4B.!!$F1 719
8 TraesCS5A01G537200 chr4B 659534799 659535391 592 True 494 494 82.781 861 1426 1 chr4B.!!$R2 565
9 TraesCS5A01G537200 chr5D 480042599 480043438 839 True 1110 1110 90.297 1507 2379 1 chr5D.!!$R1 872
10 TraesCS5A01G537200 chr1D 307350759 307351580 821 False 1101 1101 90.717 1535 2379 1 chr1D.!!$F1 844
11 TraesCS5A01G537200 chr4D 508284803 508285398 595 False 446 446 80.841 868 1492 1 chr4D.!!$F1 624

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
383 400 0.036875 AGGACACTTTGGCTACAGGC 59.963 55.0 0.00 0.0 41.50 4.85 F
421 438 0.107410 TACCACCGGAATCATGCACC 60.107 55.0 9.46 0.0 0.00 5.01 F
860 887 0.109551 CGAGTCACATCTCACACGCT 60.110 55.0 0.00 0.0 34.46 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1266 1333 0.179148 CGATGGTCGATGGTGAACGA 60.179 55.00 0.00 0.00 43.74 3.85 R
1306 1373 0.975887 TTTGGCTGAAATGGAAGGCC 59.024 50.00 0.00 0.00 42.73 5.19 R
2344 2429 3.872771 AGCTTTTTGACATGGCAAGTTTG 59.127 39.13 14.91 7.58 0.00 2.93 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
26 27 2.426522 CTCAAATGAGCTCGGGTGAAA 58.573 47.619 9.64 0.00 35.13 2.69
27 28 3.012518 CTCAAATGAGCTCGGGTGAAAT 58.987 45.455 9.64 0.00 35.13 2.17
35 36 4.394920 TGAGCTCGGGTGAAATGTAAAATC 59.605 41.667 9.64 0.00 0.00 2.17
37 38 3.442273 GCTCGGGTGAAATGTAAAATCCA 59.558 43.478 0.00 0.00 0.00 3.41
38 39 4.082463 GCTCGGGTGAAATGTAAAATCCAA 60.082 41.667 0.00 0.00 0.00 3.53
39 40 5.637006 TCGGGTGAAATGTAAAATCCAAG 57.363 39.130 0.00 0.00 0.00 3.61
41 42 5.182380 TCGGGTGAAATGTAAAATCCAAGAC 59.818 40.000 0.00 0.00 0.00 3.01
42 43 5.399013 GGGTGAAATGTAAAATCCAAGACG 58.601 41.667 0.00 0.00 0.00 4.18
43 44 5.182380 GGGTGAAATGTAAAATCCAAGACGA 59.818 40.000 0.00 0.00 0.00 4.20
52 53 8.568732 TGTAAAATCCAAGACGAATTGAAAAC 57.431 30.769 6.03 0.00 31.55 2.43
58 59 8.661352 ATCCAAGACGAATTGAAAACAAATTT 57.339 26.923 6.03 0.00 31.55 1.82
106 110 9.048446 GTCAAACACTGTTAAATGTCCTAAGTA 57.952 33.333 0.00 0.00 0.00 2.24
121 125 8.177119 TGTCCTAAGTAGTTGCAAAAATTGAT 57.823 30.769 0.00 0.00 0.00 2.57
130 134 7.481275 AGTTGCAAAAATTGATCACGAAATT 57.519 28.000 0.00 0.00 0.00 1.82
141 145 7.622893 TTGATCACGAAATTACATTCATGGA 57.377 32.000 0.00 0.00 0.00 3.41
146 152 5.959527 CACGAAATTACATTCATGGAAGTCG 59.040 40.000 14.68 14.68 42.84 4.18
180 190 5.767816 TGAAGCTCCAAAAGGTTAGTTTC 57.232 39.130 0.00 0.00 45.55 2.78
223 237 1.464734 TTTTTGCCACGACTTCCACA 58.535 45.000 0.00 0.00 0.00 4.17
234 248 3.186409 ACGACTTCCACAAATGTCATTCG 59.814 43.478 0.00 0.00 0.00 3.34
252 266 7.546316 TGTCATTCGATGATGAAATTTTGCAAT 59.454 29.630 0.00 0.00 42.04 3.56
254 268 6.557593 TTCGATGATGAAATTTTGCAATCG 57.442 33.333 0.00 15.43 0.00 3.34
257 271 7.247019 TCGATGATGAAATTTTGCAATCGTTA 58.753 30.769 18.46 0.00 0.00 3.18
262 276 9.421806 TGATGAAATTTTGCAATCGTTAGAAAT 57.578 25.926 0.00 0.00 0.00 2.17
286 301 5.412526 ACTGTCAAAGTTTATCGCGAAAA 57.587 34.783 15.24 12.42 34.57 2.29
347 363 1.893137 ACTGTTCATACCGAGCTCACA 59.107 47.619 15.40 7.55 0.00 3.58
374 391 2.064762 CGAGCTGAGAAGGACACTTTG 58.935 52.381 0.00 0.00 36.97 2.77
381 398 3.244215 TGAGAAGGACACTTTGGCTACAG 60.244 47.826 0.00 0.00 36.97 2.74
383 400 0.036875 AGGACACTTTGGCTACAGGC 59.963 55.000 0.00 0.00 41.50 4.85
389 406 0.391130 CTTTGGCTACAGGCGCTACA 60.391 55.000 7.64 0.00 44.42 2.74
396 413 1.268992 TACAGGCGCTACACCCCATT 61.269 55.000 7.64 0.00 0.00 3.16
398 415 2.270850 GGCGCTACACCCCATTGA 59.729 61.111 7.64 0.00 0.00 2.57
421 438 0.107410 TACCACCGGAATCATGCACC 60.107 55.000 9.46 0.00 0.00 5.01
427 444 2.397751 GGAATCATGCACCGACAGG 58.602 57.895 0.00 0.00 45.13 4.00
450 472 7.170320 CAGGTACGTGTTATTTATAGGCGAAAT 59.830 37.037 7.41 1.69 0.00 2.17
454 476 8.821147 ACGTGTTATTTATAGGCGAAATATCA 57.179 30.769 0.00 8.19 30.78 2.15
466 488 9.965902 ATAGGCGAAATATCAGAATCCTTAAAT 57.034 29.630 0.00 0.00 0.00 1.40
467 489 8.103948 AGGCGAAATATCAGAATCCTTAAATG 57.896 34.615 0.00 0.00 0.00 2.32
468 490 6.803807 GGCGAAATATCAGAATCCTTAAATGC 59.196 38.462 0.00 0.00 0.00 3.56
469 491 7.308830 GGCGAAATATCAGAATCCTTAAATGCT 60.309 37.037 0.00 0.00 0.00 3.79
470 492 8.721478 GCGAAATATCAGAATCCTTAAATGCTA 58.279 33.333 0.00 0.00 0.00 3.49
473 495 9.578576 AAATATCAGAATCCTTAAATGCTAGCA 57.421 29.630 21.85 21.85 0.00 3.49
474 496 6.874288 ATCAGAATCCTTAAATGCTAGCAC 57.126 37.500 22.07 2.76 0.00 4.40
475 497 4.811024 TCAGAATCCTTAAATGCTAGCACG 59.189 41.667 22.07 6.21 0.00 5.34
476 498 4.572389 CAGAATCCTTAAATGCTAGCACGT 59.428 41.667 22.07 13.43 0.00 4.49
477 499 5.753438 CAGAATCCTTAAATGCTAGCACGTA 59.247 40.000 22.07 12.32 0.00 3.57
478 500 5.753921 AGAATCCTTAAATGCTAGCACGTAC 59.246 40.000 22.07 2.39 0.00 3.67
480 502 5.080969 TCCTTAAATGCTAGCACGTACTT 57.919 39.130 22.07 7.18 0.00 2.24
481 503 4.868171 TCCTTAAATGCTAGCACGTACTTG 59.132 41.667 22.07 6.55 0.00 3.16
482 504 4.630069 CCTTAAATGCTAGCACGTACTTGT 59.370 41.667 22.07 0.00 0.00 3.16
483 505 5.808540 CCTTAAATGCTAGCACGTACTTGTA 59.191 40.000 22.07 0.00 0.00 2.41
485 507 7.650504 CCTTAAATGCTAGCACGTACTTGTATA 59.349 37.037 22.07 0.00 0.00 1.47
486 508 6.823678 AAATGCTAGCACGTACTTGTATAC 57.176 37.500 22.07 0.00 0.00 1.47
491 517 6.814644 TGCTAGCACGTACTTGTATACATTTT 59.185 34.615 14.93 0.00 0.00 1.82
506 532 4.045636 ACATTTTGCAAGTCAACTGTCC 57.954 40.909 0.00 0.00 33.73 4.02
565 591 0.768622 ACCTTTGGGTCAACCGATCA 59.231 50.000 0.00 0.00 43.38 2.92
566 592 1.165270 CCTTTGGGTCAACCGATCAC 58.835 55.000 0.00 0.00 44.64 3.06
672 699 3.845781 ATGCTGGGTAATCGTTCTGAT 57.154 42.857 0.00 0.00 39.67 2.90
676 703 3.633235 CTGGGTAATCGTTCTGATCTCG 58.367 50.000 0.00 0.00 35.84 4.04
687 714 4.861462 CGTTCTGATCTCGAATATGATGGG 59.139 45.833 0.00 0.00 0.00 4.00
689 716 4.677182 TCTGATCTCGAATATGATGGGGA 58.323 43.478 0.00 0.00 0.00 4.81
702 729 3.164268 TGATGGGGAATCAACTTGTTGG 58.836 45.455 12.75 0.00 42.49 3.77
707 734 4.141135 TGGGGAATCAACTTGTTGGAGTAA 60.141 41.667 12.75 0.00 0.00 2.24
709 736 5.070685 GGGAATCAACTTGTTGGAGTAACT 58.929 41.667 12.75 0.00 40.05 2.24
726 753 8.836959 GGAGTAACTCCGCTTTATTTAATTTG 57.163 34.615 0.00 0.00 41.08 2.32
727 754 7.913821 GGAGTAACTCCGCTTTATTTAATTTGG 59.086 37.037 0.00 0.00 41.08 3.28
728 755 8.344446 AGTAACTCCGCTTTATTTAATTTGGT 57.656 30.769 0.00 0.00 0.00 3.67
729 756 8.456471 AGTAACTCCGCTTTATTTAATTTGGTC 58.544 33.333 0.00 0.00 0.00 4.02
730 757 6.203808 ACTCCGCTTTATTTAATTTGGTCC 57.796 37.500 0.00 0.00 0.00 4.46
731 758 5.163693 ACTCCGCTTTATTTAATTTGGTCCG 60.164 40.000 0.00 0.00 0.00 4.79
732 759 4.701171 TCCGCTTTATTTAATTTGGTCCGT 59.299 37.500 0.00 0.00 0.00 4.69
733 760 5.879223 TCCGCTTTATTTAATTTGGTCCGTA 59.121 36.000 0.00 0.00 0.00 4.02
734 761 6.543100 TCCGCTTTATTTAATTTGGTCCGTAT 59.457 34.615 0.00 0.00 0.00 3.06
735 762 6.635239 CCGCTTTATTTAATTTGGTCCGTATG 59.365 38.462 0.00 0.00 0.00 2.39
736 763 7.411274 CGCTTTATTTAATTTGGTCCGTATGA 58.589 34.615 0.00 0.00 0.00 2.15
737 764 7.911205 CGCTTTATTTAATTTGGTCCGTATGAA 59.089 33.333 0.00 0.00 0.00 2.57
738 765 9.744468 GCTTTATTTAATTTGGTCCGTATGAAT 57.256 29.630 0.00 0.00 0.00 2.57
740 767 9.522804 TTTATTTAATTTGGTCCGTATGAATGC 57.477 29.630 0.00 0.00 0.00 3.56
741 768 6.516739 TTTAATTTGGTCCGTATGAATGCA 57.483 33.333 0.00 0.00 0.00 3.96
742 769 6.707440 TTAATTTGGTCCGTATGAATGCAT 57.293 33.333 0.00 0.00 38.54 3.96
743 770 7.809546 TTAATTTGGTCCGTATGAATGCATA 57.190 32.000 0.00 0.00 35.94 3.14
744 771 6.899393 AATTTGGTCCGTATGAATGCATAT 57.101 33.333 0.00 0.00 39.09 1.78
745 772 5.687770 TTTGGTCCGTATGAATGCATATG 57.312 39.130 0.00 5.97 41.57 1.78
746 773 4.615588 TGGTCCGTATGAATGCATATGA 57.384 40.909 13.80 3.54 43.59 2.15
747 774 5.164620 TGGTCCGTATGAATGCATATGAT 57.835 39.130 13.80 0.00 43.59 2.45
748 775 5.559770 TGGTCCGTATGAATGCATATGATT 58.440 37.500 13.80 3.61 43.59 2.57
749 776 5.412286 TGGTCCGTATGAATGCATATGATTG 59.588 40.000 13.80 0.00 43.59 2.67
750 777 5.412594 GGTCCGTATGAATGCATATGATTGT 59.587 40.000 13.80 0.00 43.59 2.71
751 778 6.072508 GGTCCGTATGAATGCATATGATTGTT 60.073 38.462 13.80 0.00 43.59 2.83
752 779 7.362662 GTCCGTATGAATGCATATGATTGTTT 58.637 34.615 13.80 0.00 43.59 2.83
753 780 7.862372 GTCCGTATGAATGCATATGATTGTTTT 59.138 33.333 13.80 0.00 43.59 2.43
754 781 8.412456 TCCGTATGAATGCATATGATTGTTTTT 58.588 29.630 13.80 0.00 43.59 1.94
755 782 8.481641 CCGTATGAATGCATATGATTGTTTTTG 58.518 33.333 13.80 0.00 43.59 2.44
756 783 8.481641 CGTATGAATGCATATGATTGTTTTTGG 58.518 33.333 6.97 0.00 43.59 3.28
757 784 9.531942 GTATGAATGCATATGATTGTTTTTGGA 57.468 29.630 6.97 0.00 39.09 3.53
759 786 9.621629 ATGAATGCATATGATTGTTTTTGGATT 57.378 25.926 6.97 0.00 31.57 3.01
760 787 9.451002 TGAATGCATATGATTGTTTTTGGATTT 57.549 25.926 6.97 0.00 0.00 2.17
819 846 6.683974 TCAAAATAAAGAGCTGTATGGAGC 57.316 37.500 0.00 0.00 39.46 4.70
820 847 5.590259 TCAAAATAAAGAGCTGTATGGAGCC 59.410 40.000 0.00 0.00 40.08 4.70
821 848 3.778954 ATAAAGAGCTGTATGGAGCCC 57.221 47.619 0.00 0.00 40.08 5.19
822 849 0.179000 AAAGAGCTGTATGGAGCCCG 59.821 55.000 0.00 0.00 40.08 6.13
823 850 0.687757 AAGAGCTGTATGGAGCCCGA 60.688 55.000 0.00 0.00 40.08 5.14
824 851 1.068250 GAGCTGTATGGAGCCCGAC 59.932 63.158 0.00 0.00 40.08 4.79
825 852 2.109181 GCTGTATGGAGCCCGACC 59.891 66.667 0.00 0.00 32.35 4.79
826 853 2.435693 GCTGTATGGAGCCCGACCT 61.436 63.158 0.00 0.00 32.35 3.85
827 854 1.742768 CTGTATGGAGCCCGACCTC 59.257 63.158 0.00 0.00 0.00 3.85
834 861 3.688553 GAGCCCGACCTCCATTTAG 57.311 57.895 0.00 0.00 0.00 1.85
835 862 0.533085 GAGCCCGACCTCCATTTAGC 60.533 60.000 0.00 0.00 0.00 3.09
836 863 1.223487 GCCCGACCTCCATTTAGCA 59.777 57.895 0.00 0.00 0.00 3.49
837 864 0.179018 GCCCGACCTCCATTTAGCAT 60.179 55.000 0.00 0.00 0.00 3.79
838 865 1.750682 GCCCGACCTCCATTTAGCATT 60.751 52.381 0.00 0.00 0.00 3.56
839 866 2.654863 CCCGACCTCCATTTAGCATTT 58.345 47.619 0.00 0.00 0.00 2.32
840 867 3.023832 CCCGACCTCCATTTAGCATTTT 58.976 45.455 0.00 0.00 0.00 1.82
841 868 3.066760 CCCGACCTCCATTTAGCATTTTC 59.933 47.826 0.00 0.00 0.00 2.29
842 869 3.242739 CCGACCTCCATTTAGCATTTTCG 60.243 47.826 0.00 0.00 0.00 3.46
843 870 3.621268 CGACCTCCATTTAGCATTTTCGA 59.379 43.478 0.00 0.00 0.00 3.71
844 871 4.260375 CGACCTCCATTTAGCATTTTCGAG 60.260 45.833 0.00 0.00 0.00 4.04
845 872 4.589908 ACCTCCATTTAGCATTTTCGAGT 58.410 39.130 0.00 0.00 0.00 4.18
846 873 4.636206 ACCTCCATTTAGCATTTTCGAGTC 59.364 41.667 0.00 0.00 0.00 3.36
847 874 4.635765 CCTCCATTTAGCATTTTCGAGTCA 59.364 41.667 0.00 0.00 0.00 3.41
848 875 5.447818 CCTCCATTTAGCATTTTCGAGTCAC 60.448 44.000 0.00 0.00 0.00 3.67
849 876 5.000591 TCCATTTAGCATTTTCGAGTCACA 58.999 37.500 0.00 0.00 0.00 3.58
850 877 5.647658 TCCATTTAGCATTTTCGAGTCACAT 59.352 36.000 0.00 0.00 0.00 3.21
851 878 5.967674 CCATTTAGCATTTTCGAGTCACATC 59.032 40.000 0.00 0.00 0.00 3.06
852 879 6.183360 CCATTTAGCATTTTCGAGTCACATCT 60.183 38.462 0.00 0.00 0.00 2.90
853 880 6.408858 TTTAGCATTTTCGAGTCACATCTC 57.591 37.500 0.00 0.00 0.00 2.75
854 881 3.930336 AGCATTTTCGAGTCACATCTCA 58.070 40.909 0.00 0.00 34.46 3.27
855 882 3.681897 AGCATTTTCGAGTCACATCTCAC 59.318 43.478 0.00 0.00 34.46 3.51
856 883 3.433274 GCATTTTCGAGTCACATCTCACA 59.567 43.478 0.00 0.00 34.46 3.58
857 884 4.667668 GCATTTTCGAGTCACATCTCACAC 60.668 45.833 0.00 0.00 34.46 3.82
858 885 2.331809 TTCGAGTCACATCTCACACG 57.668 50.000 0.00 0.00 34.46 4.49
859 886 0.109735 TCGAGTCACATCTCACACGC 60.110 55.000 0.00 0.00 34.46 5.34
860 887 0.109551 CGAGTCACATCTCACACGCT 60.110 55.000 0.00 0.00 34.46 5.07
861 888 1.130561 CGAGTCACATCTCACACGCTA 59.869 52.381 0.00 0.00 34.46 4.26
862 889 2.520979 GAGTCACATCTCACACGCTAC 58.479 52.381 0.00 0.00 34.88 3.58
863 890 2.162608 GAGTCACATCTCACACGCTACT 59.837 50.000 0.00 0.00 34.88 2.57
864 891 3.344515 AGTCACATCTCACACGCTACTA 58.655 45.455 0.00 0.00 0.00 1.82
865 892 3.375610 AGTCACATCTCACACGCTACTAG 59.624 47.826 0.00 0.00 0.00 2.57
889 920 2.516227 AGATCTCGTCCAGAACTCCA 57.484 50.000 0.00 0.00 33.62 3.86
896 927 6.183810 TCTCGTCCAGAACTCCATATACTA 57.816 41.667 0.00 0.00 0.00 1.82
897 928 5.996513 TCTCGTCCAGAACTCCATATACTAC 59.003 44.000 0.00 0.00 0.00 2.73
899 930 5.996513 TCGTCCAGAACTCCATATACTACTC 59.003 44.000 0.00 0.00 0.00 2.59
900 931 5.998981 CGTCCAGAACTCCATATACTACTCT 59.001 44.000 0.00 0.00 0.00 3.24
901 932 6.487331 CGTCCAGAACTCCATATACTACTCTT 59.513 42.308 0.00 0.00 0.00 2.85
902 933 7.013464 CGTCCAGAACTCCATATACTACTCTTT 59.987 40.741 0.00 0.00 0.00 2.52
903 934 8.354426 GTCCAGAACTCCATATACTACTCTTTC 58.646 40.741 0.00 0.00 0.00 2.62
904 935 8.059461 TCCAGAACTCCATATACTACTCTTTCA 58.941 37.037 0.00 0.00 0.00 2.69
905 936 8.138712 CCAGAACTCCATATACTACTCTTTCAC 58.861 40.741 0.00 0.00 0.00 3.18
929 960 3.121126 CGGCTATAAATAACCGAGCAACG 60.121 47.826 6.03 0.00 42.88 4.10
939 970 3.423154 GAGCAACGGCCAGGTTCG 61.423 66.667 2.24 3.27 42.56 3.95
961 992 1.153229 GCCCACCCACCTATTCGTC 60.153 63.158 0.00 0.00 0.00 4.20
962 993 1.525442 CCCACCCACCTATTCGTCC 59.475 63.158 0.00 0.00 0.00 4.79
1006 1037 4.419282 TCTTTCCCAAGAATCAATGGCTT 58.581 39.130 0.20 0.00 35.99 4.35
1035 1078 0.869454 CTCTGAAGATGCTCGCCGTC 60.869 60.000 0.00 0.00 0.00 4.79
1112 1155 3.250323 CGATGACTGCGCTGACGG 61.250 66.667 21.92 4.76 40.57 4.79
1159 1202 1.378531 GTGCACTGAATATTCCCGCA 58.621 50.000 10.32 14.47 0.00 5.69
1163 1206 1.331756 CACTGAATATTCCCGCACTGC 59.668 52.381 12.90 0.00 0.00 4.40
1164 1207 1.065491 ACTGAATATTCCCGCACTGCA 60.065 47.619 12.90 0.00 0.00 4.41
1165 1208 2.016318 CTGAATATTCCCGCACTGCAA 58.984 47.619 12.90 0.00 0.00 4.08
1194 1237 2.517875 GGCTGCCCCATGCTACAG 60.518 66.667 7.66 3.48 42.00 2.74
1232 1278 3.444742 CAGAAATGCTTGGATGGTTGCTA 59.555 43.478 0.00 0.00 0.00 3.49
1243 1289 0.320050 TGGTTGCTATCACGAGTGCA 59.680 50.000 0.00 0.00 0.00 4.57
1249 1295 2.752903 TGCTATCACGAGTGCAGTAGAA 59.247 45.455 8.79 0.00 0.00 2.10
1262 1329 1.067821 CAGTAGAAGGCCCTGACGATC 59.932 57.143 0.00 0.00 0.00 3.69
1275 1342 2.503158 CGATCGCGTCGTTCACCA 60.503 61.111 18.56 0.00 45.19 4.17
1276 1343 1.872234 CGATCGCGTCGTTCACCAT 60.872 57.895 18.56 0.00 45.19 3.55
1277 1344 1.798368 CGATCGCGTCGTTCACCATC 61.798 60.000 18.56 5.90 45.19 3.51
1278 1345 1.798368 GATCGCGTCGTTCACCATCG 61.798 60.000 5.77 0.00 0.00 3.84
1285 1352 0.179148 TCGTTCACCATCGACCATCG 60.179 55.000 0.00 0.00 42.10 3.84
1306 1373 4.034742 TCGTTTTCCTCTTGTTTCCTTTCG 59.965 41.667 0.00 0.00 0.00 3.46
1325 1393 0.975887 GGCCTTCCATTTCAGCCAAA 59.024 50.000 0.00 0.00 43.32 3.28
1332 1400 1.135024 CCATTTCAGCCAAACATCCCG 60.135 52.381 0.00 0.00 0.00 5.14
1359 1430 2.668945 CGTGTATGCGTGTTGATTGGTA 59.331 45.455 0.00 0.00 0.00 3.25
1363 1434 4.331443 TGTATGCGTGTTGATTGGTATGAC 59.669 41.667 0.00 0.00 0.00 3.06
1379 1450 5.105752 GGTATGACGCAAAATGGCAATAAA 58.894 37.500 0.00 0.00 0.00 1.40
1387 1458 4.328169 GCAAAATGGCAATAAAGCTCAGTC 59.672 41.667 0.00 0.00 34.17 3.51
1398 1469 2.064434 AGCTCAGTCGATCTGGATCA 57.936 50.000 12.89 0.00 43.76 2.92
1403 1474 3.879892 CTCAGTCGATCTGGATCACTGTA 59.120 47.826 24.47 17.23 43.76 2.74
1405 1476 2.952978 AGTCGATCTGGATCACTGTACC 59.047 50.000 10.62 0.00 37.69 3.34
1406 1477 1.947456 TCGATCTGGATCACTGTACCG 59.053 52.381 10.62 0.00 37.69 4.02
1407 1478 1.600663 CGATCTGGATCACTGTACCGC 60.601 57.143 10.62 0.00 37.69 5.68
1408 1479 0.385751 ATCTGGATCACTGTACCGCG 59.614 55.000 0.00 0.00 0.00 6.46
1422 1493 1.448189 CCGCGGGGTTTGTAATCGA 60.448 57.895 20.10 0.00 0.00 3.59
1426 1497 2.538132 CGCGGGGTTTGTAATCGAATTC 60.538 50.000 0.00 0.00 0.00 2.17
1427 1498 2.538132 GCGGGGTTTGTAATCGAATTCG 60.538 50.000 21.78 21.78 41.45 3.34
1428 1499 2.674357 CGGGGTTTGTAATCGAATTCGT 59.326 45.455 25.93 11.67 40.80 3.85
1429 1500 3.484557 CGGGGTTTGTAATCGAATTCGTG 60.485 47.826 25.93 0.65 40.80 4.35
1430 1501 3.437741 GGGGTTTGTAATCGAATTCGTGT 59.562 43.478 25.93 17.29 40.80 4.49
1449 1520 6.491394 TCGTGTGTTTCTTTCCTTATTGTTG 58.509 36.000 0.00 0.00 0.00 3.33
1450 1521 6.094325 TCGTGTGTTTCTTTCCTTATTGTTGT 59.906 34.615 0.00 0.00 0.00 3.32
1451 1522 6.750039 CGTGTGTTTCTTTCCTTATTGTTGTT 59.250 34.615 0.00 0.00 0.00 2.83
1466 1537 4.712122 TGTTGTTCCTTTTGTTGAGGTC 57.288 40.909 0.00 0.00 35.71 3.85
1470 1541 4.451900 TGTTCCTTTTGTTGAGGTCTCTC 58.548 43.478 0.00 0.00 40.36 3.20
1472 1543 5.126779 GTTCCTTTTGTTGAGGTCTCTCTT 58.873 41.667 0.00 0.00 40.58 2.85
1474 1545 5.126067 TCCTTTTGTTGAGGTCTCTCTTTG 58.874 41.667 0.00 0.00 40.58 2.77
1476 1547 5.358160 CCTTTTGTTGAGGTCTCTCTTTGTT 59.642 40.000 0.00 0.00 40.58 2.83
1480 1551 4.635765 TGTTGAGGTCTCTCTTTGTTTGTG 59.364 41.667 0.00 0.00 40.58 3.33
1481 1552 4.487714 TGAGGTCTCTCTTTGTTTGTGT 57.512 40.909 0.00 0.00 40.58 3.72
1482 1553 4.843728 TGAGGTCTCTCTTTGTTTGTGTT 58.156 39.130 0.00 0.00 40.58 3.32
1485 1556 7.732025 TGAGGTCTCTCTTTGTTTGTGTTATA 58.268 34.615 0.00 0.00 40.58 0.98
1495 1566 9.959749 TCTTTGTTTGTGTTATAAATCAAGGAC 57.040 29.630 0.00 0.00 0.00 3.85
1496 1567 8.789881 TTTGTTTGTGTTATAAATCAAGGACG 57.210 30.769 0.00 0.00 0.00 4.79
1497 1568 7.499321 TGTTTGTGTTATAAATCAAGGACGT 57.501 32.000 0.00 0.00 0.00 4.34
1498 1569 7.356540 TGTTTGTGTTATAAATCAAGGACGTG 58.643 34.615 0.00 0.00 0.00 4.49
1499 1570 6.489127 TTGTGTTATAAATCAAGGACGTGG 57.511 37.500 0.00 0.00 0.00 4.94
1500 1571 5.795972 TGTGTTATAAATCAAGGACGTGGA 58.204 37.500 0.00 0.00 0.00 4.02
1501 1572 6.411376 TGTGTTATAAATCAAGGACGTGGAT 58.589 36.000 0.00 0.00 0.00 3.41
1502 1573 7.557724 TGTGTTATAAATCAAGGACGTGGATA 58.442 34.615 0.00 0.00 0.00 2.59
1503 1574 8.041919 TGTGTTATAAATCAAGGACGTGGATAA 58.958 33.333 0.00 0.00 0.00 1.75
1504 1575 8.333186 GTGTTATAAATCAAGGACGTGGATAAC 58.667 37.037 0.00 0.00 0.00 1.89
1505 1576 8.262227 TGTTATAAATCAAGGACGTGGATAACT 58.738 33.333 0.00 0.00 31.56 2.24
2072 2153 5.008811 TGGCATGCCAAATTGAAAGAAAAAG 59.991 36.000 36.95 0.00 44.12 2.27
2080 2161 7.255070 GCCAAATTGAAAGAAAAAGTTGCCATA 60.255 33.333 0.00 0.00 31.76 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.414454 TCTTGGATTTTACATTTCACCCGAG 59.586 40.000 0.00 0.00 0.00 4.63
19 20 5.182380 TCGTCTTGGATTTTACATTTCACCC 59.818 40.000 0.00 0.00 0.00 4.61
21 22 8.638565 CAATTCGTCTTGGATTTTACATTTCAC 58.361 33.333 0.00 0.00 0.00 3.18
26 27 9.191995 GTTTTCAATTCGTCTTGGATTTTACAT 57.808 29.630 1.05 0.00 0.00 2.29
27 28 8.191446 TGTTTTCAATTCGTCTTGGATTTTACA 58.809 29.630 1.05 0.00 0.00 2.41
88 92 7.667043 TGCAACTACTTAGGACATTTAACAG 57.333 36.000 0.00 0.00 0.00 3.16
106 110 7.481275 AATTTCGTGATCAATTTTTGCAACT 57.519 28.000 0.00 0.00 0.00 3.16
121 125 6.183360 CGACTTCCATGAATGTAATTTCGTGA 60.183 38.462 7.74 0.00 42.63 4.35
130 134 2.027653 TGCCACGACTTCCATGAATGTA 60.028 45.455 0.00 0.00 0.00 2.29
158 164 5.197451 TGAAACTAACCTTTTGGAGCTTCA 58.803 37.500 0.00 0.00 44.07 3.02
159 165 5.767816 TGAAACTAACCTTTTGGAGCTTC 57.232 39.130 0.00 0.00 44.07 3.86
160 166 6.538945 TTTGAAACTAACCTTTTGGAGCTT 57.461 33.333 0.00 0.00 44.07 3.74
161 167 6.538945 TTTTGAAACTAACCTTTTGGAGCT 57.461 33.333 0.00 0.00 44.07 4.09
163 169 6.337356 TGCTTTTGAAACTAACCTTTTGGAG 58.663 36.000 0.00 0.00 44.07 3.86
211 225 4.466828 GAATGACATTTGTGGAAGTCGTG 58.533 43.478 1.39 0.00 33.83 4.35
213 227 3.431912 TCGAATGACATTTGTGGAAGTCG 59.568 43.478 13.94 4.96 33.83 4.18
220 234 7.980742 ATTTCATCATCGAATGACATTTGTG 57.019 32.000 13.94 11.58 43.01 3.33
222 236 9.683651 CAAAATTTCATCATCGAATGACATTTG 57.316 29.630 18.22 15.08 41.62 2.32
223 237 8.385111 GCAAAATTTCATCATCGAATGACATTT 58.615 29.630 14.29 14.29 43.08 2.32
234 248 8.619146 TCTAACGATTGCAAAATTTCATCATC 57.381 30.769 1.71 0.00 0.00 2.92
257 271 7.117236 TCGCGATAAACTTTGACAGTTATTTCT 59.883 33.333 3.71 0.00 45.77 2.52
262 276 6.528014 TTTCGCGATAAACTTTGACAGTTA 57.472 33.333 10.88 0.00 45.77 2.24
304 319 9.311916 CAGTAAAATCTGGACATTTTGAAACAA 57.688 29.630 2.15 0.00 36.75 2.83
306 321 8.871686 ACAGTAAAATCTGGACATTTTGAAAC 57.128 30.769 2.15 0.00 36.75 2.78
312 327 8.739972 GGTATGAACAGTAAAATCTGGACATTT 58.260 33.333 10.72 0.00 39.48 2.32
313 328 7.065803 CGGTATGAACAGTAAAATCTGGACATT 59.934 37.037 10.72 0.00 39.48 2.71
315 330 5.872617 CGGTATGAACAGTAAAATCTGGACA 59.127 40.000 0.00 0.00 39.48 4.02
318 334 5.006746 GCTCGGTATGAACAGTAAAATCTGG 59.993 44.000 0.00 0.00 39.48 3.86
321 337 5.810587 TGAGCTCGGTATGAACAGTAAAATC 59.189 40.000 9.64 0.00 0.00 2.17
354 370 2.064762 CAAAGTGTCCTTCTCAGCTCG 58.935 52.381 0.00 0.00 0.00 5.03
357 373 0.877743 GCCAAAGTGTCCTTCTCAGC 59.122 55.000 0.00 0.00 0.00 4.26
358 374 2.557920 AGCCAAAGTGTCCTTCTCAG 57.442 50.000 0.00 0.00 0.00 3.35
370 387 0.391130 TGTAGCGCCTGTAGCCAAAG 60.391 55.000 2.29 0.00 38.78 2.77
374 391 2.202892 GGTGTAGCGCCTGTAGCC 60.203 66.667 2.29 0.00 38.78 3.93
383 400 0.537188 AGTCTCAATGGGGTGTAGCG 59.463 55.000 0.00 0.00 0.00 4.26
389 406 1.286248 GGTGGTAGTCTCAATGGGGT 58.714 55.000 0.00 0.00 0.00 4.95
396 413 2.225382 TGATTCCGGTGGTAGTCTCA 57.775 50.000 0.00 0.00 0.00 3.27
398 415 1.139058 GCATGATTCCGGTGGTAGTCT 59.861 52.381 0.00 0.00 0.00 3.24
421 438 5.400485 GCCTATAAATAACACGTACCTGTCG 59.600 44.000 0.00 0.00 0.00 4.35
429 446 8.821147 TGATATTTCGCCTATAAATAACACGT 57.179 30.769 0.00 0.00 33.69 4.49
430 447 9.135843 TCTGATATTTCGCCTATAAATAACACG 57.864 33.333 0.00 0.00 33.69 4.49
436 453 9.965902 AAGGATTCTGATATTTCGCCTATAAAT 57.034 29.630 0.00 0.00 0.00 1.40
441 463 9.219603 CATTTAAGGATTCTGATATTTCGCCTA 57.780 33.333 0.00 0.00 0.00 3.93
450 472 6.646653 CGTGCTAGCATTTAAGGATTCTGATA 59.353 38.462 22.51 0.00 0.00 2.15
454 476 4.770795 ACGTGCTAGCATTTAAGGATTCT 58.229 39.130 22.51 0.00 0.00 2.40
463 485 6.334989 TGTATACAAGTACGTGCTAGCATTT 58.665 36.000 22.51 13.28 0.00 2.32
466 488 4.968812 TGTATACAAGTACGTGCTAGCA 57.031 40.909 14.93 14.93 0.00 3.49
467 489 6.823678 AAATGTATACAAGTACGTGCTAGC 57.176 37.500 10.14 8.10 0.00 3.42
468 490 7.117454 GCAAAATGTATACAAGTACGTGCTAG 58.883 38.462 10.14 0.00 0.00 3.42
469 491 6.590677 TGCAAAATGTATACAAGTACGTGCTA 59.409 34.615 10.14 0.00 0.00 3.49
470 492 5.410132 TGCAAAATGTATACAAGTACGTGCT 59.590 36.000 10.14 0.00 0.00 4.40
471 493 5.623335 TGCAAAATGTATACAAGTACGTGC 58.377 37.500 10.14 13.33 0.00 5.34
472 494 7.295201 ACTTGCAAAATGTATACAAGTACGTG 58.705 34.615 10.14 7.29 46.66 4.49
473 495 7.429636 ACTTGCAAAATGTATACAAGTACGT 57.570 32.000 10.14 0.00 46.66 3.57
478 500 7.862372 ACAGTTGACTTGCAAAATGTATACAAG 59.138 33.333 10.14 3.33 42.63 3.16
480 502 7.270757 ACAGTTGACTTGCAAAATGTATACA 57.729 32.000 8.27 8.27 37.09 2.29
481 503 6.801862 GGACAGTTGACTTGCAAAATGTATAC 59.198 38.462 0.00 0.00 38.24 1.47
482 504 6.348132 CGGACAGTTGACTTGCAAAATGTATA 60.348 38.462 0.00 0.00 38.24 1.47
483 505 5.562696 CGGACAGTTGACTTGCAAAATGTAT 60.563 40.000 0.00 0.00 38.24 2.29
485 507 3.489059 CGGACAGTTGACTTGCAAAATGT 60.489 43.478 0.00 0.45 39.83 2.71
486 508 3.044986 CGGACAGTTGACTTGCAAAATG 58.955 45.455 0.00 0.00 38.44 2.32
491 517 2.831685 ATACGGACAGTTGACTTGCA 57.168 45.000 0.00 0.00 0.00 4.08
568 594 2.829003 CATCTGGCTGCTGCAGGG 60.829 66.667 29.05 8.16 41.91 4.45
672 699 5.307976 AGTTGATTCCCCATCATATTCGAGA 59.692 40.000 0.00 0.00 41.82 4.04
676 703 6.966534 ACAAGTTGATTCCCCATCATATTC 57.033 37.500 10.54 0.00 41.82 1.75
687 714 6.242508 GAGTTACTCCAACAAGTTGATTCC 57.757 41.667 10.54 0.00 42.93 3.01
702 729 8.456471 ACCAAATTAAATAAAGCGGAGTTACTC 58.544 33.333 3.36 3.36 0.00 2.59
707 734 5.163693 CGGACCAAATTAAATAAAGCGGAGT 60.164 40.000 0.00 0.00 0.00 3.85
709 736 4.701171 ACGGACCAAATTAAATAAAGCGGA 59.299 37.500 0.00 0.00 0.00 5.54
718 745 6.516739 TGCATTCATACGGACCAAATTAAA 57.483 33.333 0.00 0.00 0.00 1.52
725 752 4.615588 TCATATGCATTCATACGGACCA 57.384 40.909 3.54 0.00 37.94 4.02
726 753 5.412594 ACAATCATATGCATTCATACGGACC 59.587 40.000 3.54 0.00 37.94 4.46
727 754 6.486253 ACAATCATATGCATTCATACGGAC 57.514 37.500 3.54 0.00 37.94 4.79
728 755 7.509141 AAACAATCATATGCATTCATACGGA 57.491 32.000 3.54 0.00 37.94 4.69
729 756 8.481641 CAAAAACAATCATATGCATTCATACGG 58.518 33.333 3.54 0.00 37.94 4.02
730 757 8.481641 CCAAAAACAATCATATGCATTCATACG 58.518 33.333 3.54 0.00 37.94 3.06
731 758 9.531942 TCCAAAAACAATCATATGCATTCATAC 57.468 29.630 3.54 0.00 37.94 2.39
733 760 9.621629 AATCCAAAAACAATCATATGCATTCAT 57.378 25.926 3.54 0.00 36.73 2.57
734 761 9.451002 AAATCCAAAAACAATCATATGCATTCA 57.549 25.926 3.54 0.00 0.00 2.57
793 820 8.840321 GCTCCATACAGCTCTTTATTTTGAATA 58.160 33.333 0.00 0.00 36.38 1.75
794 821 7.201857 GGCTCCATACAGCTCTTTATTTTGAAT 60.202 37.037 0.00 0.00 39.58 2.57
795 822 6.095440 GGCTCCATACAGCTCTTTATTTTGAA 59.905 38.462 0.00 0.00 39.58 2.69
796 823 5.590259 GGCTCCATACAGCTCTTTATTTTGA 59.410 40.000 0.00 0.00 39.58 2.69
797 824 5.221126 GGGCTCCATACAGCTCTTTATTTTG 60.221 44.000 0.00 0.00 36.88 2.44
798 825 4.889995 GGGCTCCATACAGCTCTTTATTTT 59.110 41.667 0.00 0.00 36.88 1.82
799 826 4.464947 GGGCTCCATACAGCTCTTTATTT 58.535 43.478 0.00 0.00 36.88 1.40
800 827 3.495100 CGGGCTCCATACAGCTCTTTATT 60.495 47.826 0.00 0.00 37.80 1.40
801 828 2.037772 CGGGCTCCATACAGCTCTTTAT 59.962 50.000 0.00 0.00 37.80 1.40
802 829 1.412710 CGGGCTCCATACAGCTCTTTA 59.587 52.381 0.00 0.00 37.80 1.85
803 830 0.179000 CGGGCTCCATACAGCTCTTT 59.821 55.000 0.00 0.00 37.80 2.52
804 831 0.687757 TCGGGCTCCATACAGCTCTT 60.688 55.000 0.00 0.00 37.80 2.85
805 832 1.075970 TCGGGCTCCATACAGCTCT 60.076 57.895 0.00 0.00 37.80 4.09
806 833 1.068250 GTCGGGCTCCATACAGCTC 59.932 63.158 0.00 0.00 39.58 4.09
807 834 2.435693 GGTCGGGCTCCATACAGCT 61.436 63.158 0.00 0.00 39.58 4.24
808 835 2.109181 GGTCGGGCTCCATACAGC 59.891 66.667 0.00 0.00 38.84 4.40
809 836 1.742768 GAGGTCGGGCTCCATACAG 59.257 63.158 0.00 0.00 0.00 2.74
810 837 1.760875 GGAGGTCGGGCTCCATACA 60.761 63.158 0.00 0.00 39.45 2.29
811 838 1.760875 TGGAGGTCGGGCTCCATAC 60.761 63.158 0.00 0.00 44.02 2.39
812 839 2.693660 TGGAGGTCGGGCTCCATA 59.306 61.111 0.00 0.00 44.02 2.74
815 842 0.106894 CTAAATGGAGGTCGGGCTCC 59.893 60.000 0.00 0.00 40.05 4.70
816 843 0.533085 GCTAAATGGAGGTCGGGCTC 60.533 60.000 0.00 0.00 0.00 4.70
817 844 1.271840 TGCTAAATGGAGGTCGGGCT 61.272 55.000 0.00 0.00 0.00 5.19
818 845 0.179018 ATGCTAAATGGAGGTCGGGC 60.179 55.000 0.00 0.00 0.00 6.13
819 846 2.348411 AATGCTAAATGGAGGTCGGG 57.652 50.000 0.00 0.00 0.00 5.14
820 847 3.242739 CGAAAATGCTAAATGGAGGTCGG 60.243 47.826 0.00 0.00 0.00 4.79
821 848 3.621268 TCGAAAATGCTAAATGGAGGTCG 59.379 43.478 0.00 0.00 0.00 4.79
822 849 4.636206 ACTCGAAAATGCTAAATGGAGGTC 59.364 41.667 0.00 0.00 0.00 3.85
823 850 4.589908 ACTCGAAAATGCTAAATGGAGGT 58.410 39.130 0.00 0.00 0.00 3.85
824 851 4.635765 TGACTCGAAAATGCTAAATGGAGG 59.364 41.667 0.00 0.00 0.00 4.30
825 852 5.122239 TGTGACTCGAAAATGCTAAATGGAG 59.878 40.000 0.00 0.00 0.00 3.86
826 853 5.000591 TGTGACTCGAAAATGCTAAATGGA 58.999 37.500 0.00 0.00 0.00 3.41
827 854 5.295431 TGTGACTCGAAAATGCTAAATGG 57.705 39.130 0.00 0.00 0.00 3.16
828 855 6.779117 AGATGTGACTCGAAAATGCTAAATG 58.221 36.000 0.00 0.00 0.00 2.32
829 856 6.595326 TGAGATGTGACTCGAAAATGCTAAAT 59.405 34.615 0.00 0.00 39.49 1.40
830 857 5.931724 TGAGATGTGACTCGAAAATGCTAAA 59.068 36.000 0.00 0.00 39.49 1.85
831 858 5.348724 GTGAGATGTGACTCGAAAATGCTAA 59.651 40.000 0.00 0.00 39.49 3.09
832 859 4.864806 GTGAGATGTGACTCGAAAATGCTA 59.135 41.667 0.00 0.00 39.49 3.49
833 860 3.681897 GTGAGATGTGACTCGAAAATGCT 59.318 43.478 0.00 0.00 39.49 3.79
834 861 3.433274 TGTGAGATGTGACTCGAAAATGC 59.567 43.478 0.00 0.00 39.49 3.56
835 862 4.433413 CGTGTGAGATGTGACTCGAAAATG 60.433 45.833 0.00 0.00 39.49 2.32
836 863 3.675225 CGTGTGAGATGTGACTCGAAAAT 59.325 43.478 0.00 0.00 39.49 1.82
837 864 3.049912 CGTGTGAGATGTGACTCGAAAA 58.950 45.455 0.00 0.00 39.49 2.29
838 865 2.661594 CGTGTGAGATGTGACTCGAAA 58.338 47.619 0.00 0.00 39.49 3.46
839 866 1.666023 GCGTGTGAGATGTGACTCGAA 60.666 52.381 8.02 0.00 39.49 3.71
840 867 0.109735 GCGTGTGAGATGTGACTCGA 60.110 55.000 8.02 0.00 39.49 4.04
841 868 0.109551 AGCGTGTGAGATGTGACTCG 60.110 55.000 0.00 0.00 39.49 4.18
842 869 2.162608 AGTAGCGTGTGAGATGTGACTC 59.837 50.000 0.00 0.00 37.42 3.36
843 870 2.163509 AGTAGCGTGTGAGATGTGACT 58.836 47.619 0.00 0.00 0.00 3.41
844 871 2.638556 AGTAGCGTGTGAGATGTGAC 57.361 50.000 0.00 0.00 0.00 3.67
845 872 3.344515 ACTAGTAGCGTGTGAGATGTGA 58.655 45.455 0.00 0.00 0.00 3.58
846 873 3.766676 ACTAGTAGCGTGTGAGATGTG 57.233 47.619 0.00 0.00 0.00 3.21
847 874 4.515361 ACTACTAGTAGCGTGTGAGATGT 58.485 43.478 26.54 3.80 36.66 3.06
848 875 5.984323 TCTACTACTAGTAGCGTGTGAGATG 59.016 44.000 26.54 3.19 45.93 2.90
849 876 6.159299 TCTACTACTAGTAGCGTGTGAGAT 57.841 41.667 26.54 9.04 45.93 2.75
850 877 5.588958 TCTACTACTAGTAGCGTGTGAGA 57.411 43.478 26.54 16.61 45.93 3.27
851 878 6.218019 AGATCTACTACTAGTAGCGTGTGAG 58.782 44.000 26.54 14.96 45.93 3.51
852 879 6.159299 AGATCTACTACTAGTAGCGTGTGA 57.841 41.667 26.54 17.54 45.93 3.58
853 880 5.117440 CGAGATCTACTACTAGTAGCGTGTG 59.883 48.000 26.54 13.62 45.93 3.82
854 881 5.221224 ACGAGATCTACTACTAGTAGCGTGT 60.221 44.000 26.54 12.74 45.93 4.49
855 882 5.221880 ACGAGATCTACTACTAGTAGCGTG 58.778 45.833 26.54 17.24 45.93 5.34
856 883 5.452078 ACGAGATCTACTACTAGTAGCGT 57.548 43.478 26.54 21.73 45.93 5.07
857 884 4.858692 GGACGAGATCTACTACTAGTAGCG 59.141 50.000 26.54 21.17 45.93 4.26
858 885 5.782047 TGGACGAGATCTACTACTAGTAGC 58.218 45.833 26.54 12.09 45.93 3.58
860 887 7.287466 AGTTCTGGACGAGATCTACTACTAGTA 59.713 40.741 1.89 1.89 30.16 1.82
861 888 6.098695 AGTTCTGGACGAGATCTACTACTAGT 59.901 42.308 0.00 0.00 30.16 2.57
862 889 6.518493 AGTTCTGGACGAGATCTACTACTAG 58.482 44.000 0.00 0.00 30.16 2.57
863 890 6.462768 GGAGTTCTGGACGAGATCTACTACTA 60.463 46.154 0.00 0.00 31.84 1.82
864 891 5.362105 AGTTCTGGACGAGATCTACTACT 57.638 43.478 0.00 0.00 30.16 2.57
865 892 4.512571 GGAGTTCTGGACGAGATCTACTAC 59.487 50.000 0.00 0.00 31.84 2.73
889 920 9.736414 TTATAGCCGAGTGAAAGAGTAGTATAT 57.264 33.333 0.00 0.00 0.00 0.86
896 927 6.985059 GGTTATTTATAGCCGAGTGAAAGAGT 59.015 38.462 0.00 0.00 0.00 3.24
897 928 7.409465 GGTTATTTATAGCCGAGTGAAAGAG 57.591 40.000 0.00 0.00 0.00 2.85
939 970 2.911221 GAATAGGTGGGTGGGCAGGC 62.911 65.000 0.00 0.00 0.00 4.85
951 982 3.627395 TGCAAATCAGGACGAATAGGT 57.373 42.857 0.00 0.00 0.00 3.08
952 983 3.065371 GGTTGCAAATCAGGACGAATAGG 59.935 47.826 0.00 0.00 0.00 2.57
953 984 3.689161 TGGTTGCAAATCAGGACGAATAG 59.311 43.478 0.00 0.00 27.25 1.73
961 992 2.426024 CAGAGGATGGTTGCAAATCAGG 59.574 50.000 0.00 0.00 42.35 3.86
962 993 2.159282 GCAGAGGATGGTTGCAAATCAG 60.159 50.000 0.00 0.00 42.35 2.90
1006 1037 2.649742 ATCTTCAGAGGGGAAGGTGA 57.350 50.000 3.37 0.00 43.52 4.02
1112 1155 2.746277 AAGCCGCCGGATTGTGTC 60.746 61.111 5.53 0.00 26.61 3.67
1156 1199 4.157817 GCAGGAATTTGCAGTGCG 57.842 55.556 11.20 0.00 43.53 5.34
1163 1206 3.806591 CAGCCAGTGCAGGAATTTG 57.193 52.632 0.00 0.00 41.13 2.32
1199 1242 1.712081 CATTTCTGCGAGCACGAGG 59.288 57.895 8.01 0.00 42.66 4.63
1200 1243 1.059994 GCATTTCTGCGAGCACGAG 59.940 57.895 8.01 2.24 42.66 4.18
1212 1258 4.098349 TGATAGCAACCATCCAAGCATTTC 59.902 41.667 0.00 0.00 0.00 2.17
1232 1278 1.134965 GCCTTCTACTGCACTCGTGAT 60.135 52.381 0.39 0.00 0.00 3.06
1243 1289 1.404843 GATCGTCAGGGCCTTCTACT 58.595 55.000 1.32 0.00 0.00 2.57
1262 1329 2.503158 TCGATGGTGAACGACGCG 60.503 61.111 3.53 3.53 33.62 6.01
1266 1333 0.179148 CGATGGTCGATGGTGAACGA 60.179 55.000 0.00 0.00 43.74 3.85
1271 1338 1.396996 GGAAAACGATGGTCGATGGTG 59.603 52.381 6.34 0.00 43.74 4.17
1272 1339 1.278127 AGGAAAACGATGGTCGATGGT 59.722 47.619 6.34 0.00 43.74 3.55
1273 1340 1.933853 GAGGAAAACGATGGTCGATGG 59.066 52.381 6.34 0.00 43.74 3.51
1274 1341 2.893637 AGAGGAAAACGATGGTCGATG 58.106 47.619 6.34 0.00 43.74 3.84
1275 1342 3.262420 CAAGAGGAAAACGATGGTCGAT 58.738 45.455 6.34 0.00 43.74 3.59
1276 1343 2.036733 ACAAGAGGAAAACGATGGTCGA 59.963 45.455 6.34 0.00 43.74 4.20
1277 1344 2.413837 ACAAGAGGAAAACGATGGTCG 58.586 47.619 0.00 0.00 46.93 4.79
1278 1345 4.320275 GGAAACAAGAGGAAAACGATGGTC 60.320 45.833 0.00 0.00 0.00 4.02
1306 1373 0.975887 TTTGGCTGAAATGGAAGGCC 59.024 50.000 0.00 0.00 42.73 5.19
1350 1421 4.742417 CCATTTTGCGTCATACCAATCAA 58.258 39.130 0.00 0.00 0.00 2.57
1359 1430 3.618150 GCTTTATTGCCATTTTGCGTCAT 59.382 39.130 0.00 0.00 0.00 3.06
1363 1434 3.252400 TGAGCTTTATTGCCATTTTGCG 58.748 40.909 0.00 0.00 0.00 4.85
1387 1458 1.600663 GCGGTACAGTGATCCAGATCG 60.601 57.143 0.00 0.00 40.63 3.69
1398 1469 1.470996 TACAAACCCCGCGGTACAGT 61.471 55.000 26.12 17.39 43.71 3.55
1405 1476 1.011333 ATTCGATTACAAACCCCGCG 58.989 50.000 0.00 0.00 0.00 6.46
1406 1477 2.538132 CGAATTCGATTACAAACCCCGC 60.538 50.000 23.29 0.00 43.02 6.13
1407 1478 2.674357 ACGAATTCGATTACAAACCCCG 59.326 45.455 33.05 3.33 43.02 5.73
1408 1479 3.437741 ACACGAATTCGATTACAAACCCC 59.562 43.478 33.05 0.00 43.02 4.95
1422 1493 7.712797 ACAATAAGGAAAGAAACACACGAATT 58.287 30.769 0.00 0.00 0.00 2.17
1426 1497 6.262601 ACAACAATAAGGAAAGAAACACACG 58.737 36.000 0.00 0.00 0.00 4.49
1427 1498 7.222031 GGAACAACAATAAGGAAAGAAACACAC 59.778 37.037 0.00 0.00 0.00 3.82
1428 1499 7.123547 AGGAACAACAATAAGGAAAGAAACACA 59.876 33.333 0.00 0.00 0.00 3.72
1429 1500 7.489160 AGGAACAACAATAAGGAAAGAAACAC 58.511 34.615 0.00 0.00 0.00 3.32
1430 1501 7.654022 AGGAACAACAATAAGGAAAGAAACA 57.346 32.000 0.00 0.00 0.00 2.83
1449 1520 4.709250 AGAGAGACCTCAACAAAAGGAAC 58.291 43.478 0.00 0.00 41.87 3.62
1450 1521 5.373812 AAGAGAGACCTCAACAAAAGGAA 57.626 39.130 0.00 0.00 41.87 3.36
1451 1522 5.126067 CAAAGAGAGACCTCAACAAAAGGA 58.874 41.667 0.00 0.00 41.87 3.36
1470 1541 8.901748 CGTCCTTGATTTATAACACAAACAAAG 58.098 33.333 5.44 0.00 0.00 2.77
1472 1543 7.858382 CACGTCCTTGATTTATAACACAAACAA 59.142 33.333 0.00 0.00 0.00 2.83
1474 1545 6.799925 CCACGTCCTTGATTTATAACACAAAC 59.200 38.462 0.00 2.41 0.00 2.93
1476 1547 6.231951 TCCACGTCCTTGATTTATAACACAA 58.768 36.000 0.00 0.00 0.00 3.33
1480 1551 8.658499 AGTTATCCACGTCCTTGATTTATAAC 57.342 34.615 0.00 0.00 0.00 1.89
1481 1552 9.754382 GTAGTTATCCACGTCCTTGATTTATAA 57.246 33.333 0.00 0.00 0.00 0.98
1482 1553 8.362639 GGTAGTTATCCACGTCCTTGATTTATA 58.637 37.037 0.00 0.00 0.00 0.98
1485 1556 5.425630 GGTAGTTATCCACGTCCTTGATTT 58.574 41.667 0.00 0.00 0.00 2.17
1492 1563 2.792542 CGTTCGGTAGTTATCCACGTCC 60.793 54.545 0.00 0.00 0.00 4.79
1493 1564 2.095853 TCGTTCGGTAGTTATCCACGTC 59.904 50.000 0.00 0.00 0.00 4.34
1494 1565 2.083774 TCGTTCGGTAGTTATCCACGT 58.916 47.619 0.00 0.00 0.00 4.49
1495 1566 2.830772 TCGTTCGGTAGTTATCCACG 57.169 50.000 0.00 0.00 0.00 4.94
1496 1567 3.861689 CCTTTCGTTCGGTAGTTATCCAC 59.138 47.826 0.00 0.00 0.00 4.02
1497 1568 3.511146 ACCTTTCGTTCGGTAGTTATCCA 59.489 43.478 0.00 0.00 0.00 3.41
1498 1569 4.115401 ACCTTTCGTTCGGTAGTTATCC 57.885 45.455 0.00 0.00 0.00 2.59
1499 1570 5.693090 GAACCTTTCGTTCGGTAGTTATC 57.307 43.478 0.00 0.00 41.51 1.75
1532 1603 2.524951 AATCGTTCGGCGGGGCTAAA 62.525 55.000 7.21 0.00 41.72 1.85
2228 2310 6.990798 TGACATGGAAAATTTATCTGCAACA 58.009 32.000 0.00 0.00 0.00 3.33
2307 2392 7.894753 TGGCAATATAGGACATTCAAATGAA 57.105 32.000 9.62 0.00 39.67 2.57
2344 2429 3.872771 AGCTTTTTGACATGGCAAGTTTG 59.127 39.130 14.91 7.58 0.00 2.93


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

AutoCloner maintained by Alex Coulton.