Multiple sequence alignment - TraesCS7D01G163600

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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 TraesCS7D01G163600 chr7D 100.000 4960 0 0 1 4960 113224701 113219742 0.000000e+00 9160.0
1 TraesCS7D01G163600 chr7D 100.000 38 0 0 355 392 113224311 113224274 2.480000e-08 71.3
2 TraesCS7D01G163600 chr7D 100.000 38 0 0 391 428 113224347 113224310 2.480000e-08 71.3
3 TraesCS7D01G163600 chr7B 92.124 4571 181 56 1 4520 72615939 72611497 0.000000e+00 6281.0
4 TraesCS7D01G163600 chr7B 100.000 38 0 0 391 428 72615566 72615529 2.480000e-08 71.3
5 TraesCS7D01G163600 chr7B 94.737 38 0 2 355 392 72615530 72615495 1.930000e-04 58.4
6 TraesCS7D01G163600 chr7A 93.688 2741 118 17 391 3117 118330451 118327752 0.000000e+00 4052.0
7 TraesCS7D01G163600 chr7A 94.844 1377 48 12 3155 4520 118327759 118326395 0.000000e+00 2128.0
8 TraesCS7D01G163600 chr7A 86.095 338 22 8 67 392 118330738 118330414 1.710000e-89 340.0
9 TraesCS7D01G163600 chr7A 96.089 179 4 3 4540 4716 118326336 118326159 6.280000e-74 289.0


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 TraesCS7D01G163600 chr7D 113219742 113224701 4959 True 3100.866667 9160 100.000000 1 4960 3 chr7D.!!$R1 4959
1 TraesCS7D01G163600 chr7B 72611497 72615939 4442 True 2136.900000 6281 95.620333 1 4520 3 chr7B.!!$R1 4519
2 TraesCS7D01G163600 chr7A 118326159 118330738 4579 True 1702.250000 4052 92.679000 67 4716 4 chr7A.!!$R1 4649

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
50 51 0.343726 AGCCCTAAGCCTACCTTCCT 59.656 55.000 0.0 0.0 45.47 3.36 F
196 232 0.956410 TACCCGGTGAATTTGGCGTG 60.956 55.000 0.0 0.0 0.00 5.34 F
1581 1624 1.134788 CCTACCACGGGCTTTACTGAG 60.135 57.143 0.0 0.0 0.00 3.35 F
2403 2447 0.940126 CATGGCTTGATACTGGCGAC 59.060 55.000 0.0 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1032 1075 1.167851 ACATTGACCTTGCATCACCG 58.832 50.000 0.00 0.0 0.00 4.94 R
1591 1634 1.270041 TGATGCTGCAACGTACTCACA 60.270 47.619 6.36 0.0 0.00 3.58 R
2672 2720 1.025812 CTGTTGGGCCACGTACAAAA 58.974 50.000 5.23 0.0 0.00 2.44 R
4256 4324 0.036010 AATGCCGACTGGAACTGAGG 60.036 55.000 0.00 0.0 37.49 3.86 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
21 22 4.679373 AGCTGTGTATGATTCCGATTCT 57.321 40.909 0.00 0.00 0.00 2.40
48 49 1.340568 CGTAGCCCTAAGCCTACCTTC 59.659 57.143 0.00 0.00 45.47 3.46
50 51 0.343726 AGCCCTAAGCCTACCTTCCT 59.656 55.000 0.00 0.00 45.47 3.36
52 53 2.022330 AGCCCTAAGCCTACCTTCCTTA 60.022 50.000 0.00 0.00 45.47 2.69
63 64 5.354513 GCCTACCTTCCTTATTCTGTTGTTC 59.645 44.000 0.00 0.00 0.00 3.18
65 66 7.168905 CCTACCTTCCTTATTCTGTTGTTCTT 58.831 38.462 0.00 0.00 0.00 2.52
71 72 6.610830 TCCTTATTCTGTTGTTCTTTCCCTT 58.389 36.000 0.00 0.00 0.00 3.95
81 82 6.603997 TGTTGTTCTTTCCCTTTTTACTGCTA 59.396 34.615 0.00 0.00 0.00 3.49
91 92 5.633182 CCCTTTTTACTGCTACGTTACGTTA 59.367 40.000 17.42 0.00 41.54 3.18
123 147 3.630312 GGGAATTTACTGATTTAGCGGCA 59.370 43.478 1.45 0.00 0.00 5.69
150 185 2.021457 AGTTATTGGCCAATGCGTACC 58.979 47.619 36.21 18.41 38.85 3.34
179 215 7.447243 AAGCGTTAGATATTTCAACGTCTAC 57.553 36.000 14.74 3.59 45.08 2.59
196 232 0.956410 TACCCGGTGAATTTGGCGTG 60.956 55.000 0.00 0.00 0.00 5.34
209 245 1.438651 TGGCGTGTAGAAACTGCATC 58.561 50.000 0.00 0.00 31.74 3.91
214 251 2.738643 CGTGTAGAAACTGCATCGGGAT 60.739 50.000 0.00 0.00 0.00 3.85
225 262 2.007360 CATCGGGATATGCAGCTCTC 57.993 55.000 0.00 0.00 0.00 3.20
332 369 3.268330 CCCTACTCTAACGCCCTTTTTC 58.732 50.000 0.00 0.00 0.00 2.29
397 434 7.110810 GGAAACTTCTATTACAAGTAGGCCTT 58.889 38.462 12.58 0.00 32.71 4.35
455 492 7.016563 TGGTGATAATACTATTGCCATCTCTGT 59.983 37.037 0.00 0.00 0.00 3.41
510 548 5.107133 CCGAACTGTACGATTTAATGGACT 58.893 41.667 0.00 0.00 0.00 3.85
533 571 6.876257 ACTGACTAGTTTGGCAATTCTAAGAG 59.124 38.462 0.00 6.05 31.66 2.85
551 590 9.646427 TTCTAAGAGAACTTTTCTAGCTGAATC 57.354 33.333 0.00 0.00 40.87 2.52
552 591 8.807118 TCTAAGAGAACTTTTCTAGCTGAATCA 58.193 33.333 0.00 0.00 40.87 2.57
555 594 8.266392 AGAGAACTTTTCTAGCTGAATCAATG 57.734 34.615 0.00 0.00 40.87 2.82
659 699 8.773033 AGAATTACTCAAATAATTGGAGCCAT 57.227 30.769 0.00 0.00 35.38 4.40
754 795 5.543507 AATCGATTCTCAGTAATCTGGCT 57.456 39.130 4.39 0.00 41.59 4.75
802 843 7.201679 CCTCACAGAAAATTATGGAAGTAGCTG 60.202 40.741 0.00 0.00 0.00 4.24
869 910 7.917505 GGATACATGGCTTTTCTATTTCAGTTG 59.082 37.037 0.00 0.00 0.00 3.16
1032 1075 9.959749 TCACTGAATAAAGTTGTTCCAAATAAC 57.040 29.630 0.00 0.00 33.27 1.89
1063 1106 7.151308 TGCAAGGTCAATGTTACCAAATAAAG 58.849 34.615 0.00 0.00 39.64 1.85
1069 1112 8.357402 GGTCAATGTTACCAAATAAAGTCACTT 58.643 33.333 0.00 0.00 36.96 3.16
1581 1624 1.134788 CCTACCACGGGCTTTACTGAG 60.135 57.143 0.00 0.00 0.00 3.35
1591 1634 3.570125 GGGCTTTACTGAGAGTTTTGCTT 59.430 43.478 0.00 0.00 0.00 3.91
2232 2276 1.266718 GCTGTTCGGAAACTTGCATCA 59.733 47.619 0.00 0.00 36.38 3.07
2354 2398 7.004086 ACATCTTCTGGGAACAAGTATCAAAA 58.996 34.615 0.00 0.00 42.06 2.44
2403 2447 0.940126 CATGGCTTGATACTGGCGAC 59.060 55.000 0.00 0.00 0.00 5.19
2669 2717 8.789825 AGATGCAATTATAGACTGATGGATTC 57.210 34.615 0.00 0.00 0.00 2.52
2672 2720 8.929260 TGCAATTATAGACTGATGGATTCATT 57.071 30.769 0.00 0.00 32.72 2.57
2843 2891 9.906660 CTAAACCAATGTACATGTTACATGTTT 57.093 29.630 31.75 19.33 38.10 2.83
2844 2892 8.586570 AAACCAATGTACATGTTACATGTTTG 57.413 30.769 31.75 27.06 38.10 2.93
2871 2919 9.643693 CATTTGCATTTCTTGTTTAGGTATCTT 57.356 29.630 0.00 0.00 0.00 2.40
2943 2991 1.077716 AGGGTTTGGCCTACGCATC 60.078 57.895 21.47 0.00 37.43 3.91
2944 2992 1.377987 GGGTTTGGCCTACGCATCA 60.378 57.895 16.85 0.00 37.43 3.07
3020 3068 2.739913 GTTGCCGTCTTGCTGTATGTAA 59.260 45.455 0.00 0.00 0.00 2.41
3126 3179 6.609533 TCTGACTACACGTCTATGAAAGTTC 58.390 40.000 0.00 0.00 43.25 3.01
3200 3253 5.071788 CCTAAATAGAAGGGCAGACCATGTA 59.928 44.000 0.00 0.00 43.89 2.29
3286 3339 4.804868 TGCAAGCCATACAAAATGATGT 57.195 36.364 0.00 0.00 37.32 3.06
3301 3354 7.537306 ACAAAATGATGTATTTGTGCGACTTAC 59.463 33.333 3.33 0.00 45.34 2.34
3311 3364 3.656559 TGTGCGACTTACTTTAGGGAAC 58.343 45.455 0.00 0.00 0.00 3.62
3314 3367 2.353109 GCGACTTACTTTAGGGAACGGT 60.353 50.000 0.00 0.00 0.00 4.83
3376 3429 6.442885 TCATCCAGGATATCATGAGTTGCTAT 59.557 38.462 18.64 0.00 0.00 2.97
3583 3636 2.177888 AGAGGTTGCTTTCTCCCCTTTT 59.822 45.455 0.00 0.00 0.00 2.27
3584 3637 2.965831 GAGGTTGCTTTCTCCCCTTTTT 59.034 45.455 0.00 0.00 0.00 1.94
3619 3672 1.136147 CGCTGCTTCTGTGGAATGC 59.864 57.895 0.00 0.00 0.00 3.56
3621 3674 1.798735 CTGCTTCTGTGGAATGCCG 59.201 57.895 0.00 0.00 36.79 5.69
3660 3715 5.048224 AGCACTTCTGTTTCATCCTGAATTG 60.048 40.000 0.00 0.00 36.11 2.32
4194 4251 2.874086 TCTGCCGTGCTTATTCATGATG 59.126 45.455 0.00 0.00 0.00 3.07
4196 4253 3.016031 TGCCGTGCTTATTCATGATGTT 58.984 40.909 0.00 0.00 0.00 2.71
4197 4254 3.065233 TGCCGTGCTTATTCATGATGTTC 59.935 43.478 0.00 0.00 0.00 3.18
4208 4275 2.836372 TCATGATGTTCTCTGGAGTGCT 59.164 45.455 0.00 0.00 0.00 4.40
4256 4324 1.339151 ACCTGAAGCGTGGGAAATCTC 60.339 52.381 0.00 0.00 0.00 2.75
4260 4328 0.984230 AAGCGTGGGAAATCTCCTCA 59.016 50.000 0.00 0.00 42.05 3.86
4267 4339 2.573462 TGGGAAATCTCCTCAGTTCCAG 59.427 50.000 3.87 0.00 41.17 3.86
4268 4340 2.573915 GGGAAATCTCCTCAGTTCCAGT 59.426 50.000 3.87 0.00 41.17 4.00
4305 4378 6.071616 GGTTATAACAAGACTGGGATTTTGCA 60.072 38.462 17.16 0.00 0.00 4.08
4391 4464 2.301346 AGTTGCCAGGAAGTTCTGTTG 58.699 47.619 2.25 0.00 33.14 3.33
4538 4629 9.007901 GTAATTTATCATGCCTAGCTTTCTCAT 57.992 33.333 0.00 0.00 0.00 2.90
4572 4688 6.987386 ACTGACATCATCTTGTATAGGCTAC 58.013 40.000 0.00 0.00 0.00 3.58
4709 4825 6.892485 TCCATCTTGTGTATTGACATCATCT 58.108 36.000 0.00 0.00 38.04 2.90
4732 4848 3.859411 TTTTGCGGGGAATGTATTGAC 57.141 42.857 0.00 0.00 0.00 3.18
4733 4849 2.498644 TTGCGGGGAATGTATTGACA 57.501 45.000 0.00 0.00 40.72 3.58
4735 4851 2.571212 TGCGGGGAATGTATTGACATC 58.429 47.619 0.00 0.00 45.93 3.06
4736 4852 2.092699 TGCGGGGAATGTATTGACATCA 60.093 45.455 0.00 0.00 45.93 3.07
4737 4853 3.149196 GCGGGGAATGTATTGACATCAT 58.851 45.455 0.00 0.00 45.93 2.45
4738 4854 3.189287 GCGGGGAATGTATTGACATCATC 59.811 47.826 0.00 0.00 45.93 2.92
4739 4855 4.645535 CGGGGAATGTATTGACATCATCT 58.354 43.478 0.00 0.00 45.93 2.90
4740 4856 5.065914 CGGGGAATGTATTGACATCATCTT 58.934 41.667 0.00 0.00 45.93 2.40
4741 4857 5.049198 CGGGGAATGTATTGACATCATCTTG 60.049 44.000 0.00 0.00 45.93 3.02
4742 4858 5.829924 GGGGAATGTATTGACATCATCTTGT 59.170 40.000 0.00 0.00 45.93 3.16
4743 4859 6.998074 GGGGAATGTATTGACATCATCTTGTA 59.002 38.462 0.00 0.00 45.93 2.41
4744 4860 7.667219 GGGGAATGTATTGACATCATCTTGTAT 59.333 37.037 0.00 0.00 45.93 2.29
4745 4861 9.725019 GGGAATGTATTGACATCATCTTGTATA 57.275 33.333 0.00 0.00 45.93 1.47
4748 4864 8.783833 ATGTATTGACATCATCTTGTATAGGC 57.216 34.615 0.00 0.00 43.01 3.93
4749 4865 7.734942 TGTATTGACATCATCTTGTATAGGCA 58.265 34.615 0.00 0.00 0.00 4.75
4750 4866 8.210265 TGTATTGACATCATCTTGTATAGGCAA 58.790 33.333 0.00 0.00 0.00 4.52
4751 4867 6.925610 TTGACATCATCTTGTATAGGCAAC 57.074 37.500 0.00 0.00 0.00 4.17
4752 4868 5.368145 TGACATCATCTTGTATAGGCAACC 58.632 41.667 0.00 0.00 37.17 3.77
4753 4869 4.380531 ACATCATCTTGTATAGGCAACCG 58.619 43.478 0.00 0.00 37.17 4.44
4754 4870 4.100963 ACATCATCTTGTATAGGCAACCGA 59.899 41.667 0.00 0.00 37.17 4.69
4755 4871 4.322080 TCATCTTGTATAGGCAACCGAG 57.678 45.455 0.00 0.00 37.17 4.63
4756 4872 3.704566 TCATCTTGTATAGGCAACCGAGT 59.295 43.478 0.00 0.00 37.17 4.18
4757 4873 3.520290 TCTTGTATAGGCAACCGAGTG 57.480 47.619 0.00 0.00 37.17 3.51
4758 4874 2.167693 TCTTGTATAGGCAACCGAGTGG 59.832 50.000 0.00 0.00 42.84 4.00
4769 4885 3.715854 CCGAGTGGTGTAGCAGTAC 57.284 57.895 0.00 0.00 0.00 2.73
4770 4886 0.885879 CCGAGTGGTGTAGCAGTACA 59.114 55.000 0.00 0.00 36.78 2.90
4771 4887 1.271379 CCGAGTGGTGTAGCAGTACAA 59.729 52.381 0.00 0.00 40.94 2.41
4772 4888 2.596452 CGAGTGGTGTAGCAGTACAAG 58.404 52.381 0.00 0.00 40.94 3.16
4773 4889 2.671351 CGAGTGGTGTAGCAGTACAAGG 60.671 54.545 0.00 0.00 40.94 3.61
4774 4890 1.002087 AGTGGTGTAGCAGTACAAGGC 59.998 52.381 0.00 0.00 40.94 4.35
4775 4891 1.052617 TGGTGTAGCAGTACAAGGCA 58.947 50.000 0.00 0.00 40.94 4.75
4776 4892 1.418264 TGGTGTAGCAGTACAAGGCAA 59.582 47.619 0.00 0.00 40.94 4.52
4777 4893 1.804748 GGTGTAGCAGTACAAGGCAAC 59.195 52.381 0.00 0.00 40.94 4.17
4778 4894 2.489971 GTGTAGCAGTACAAGGCAACA 58.510 47.619 0.00 0.00 40.94 3.33
4779 4895 3.074412 GTGTAGCAGTACAAGGCAACAT 58.926 45.455 0.00 0.00 40.94 2.71
4780 4896 3.502211 GTGTAGCAGTACAAGGCAACATT 59.498 43.478 0.00 0.00 40.94 2.71
4781 4897 4.693566 GTGTAGCAGTACAAGGCAACATTA 59.306 41.667 0.00 0.00 40.94 1.90
4782 4898 4.693566 TGTAGCAGTACAAGGCAACATTAC 59.306 41.667 0.00 0.00 36.15 1.89
4783 4899 3.750371 AGCAGTACAAGGCAACATTACA 58.250 40.909 0.00 0.00 41.41 2.41
4784 4900 3.502211 AGCAGTACAAGGCAACATTACAC 59.498 43.478 0.00 0.00 41.41 2.90
4785 4901 3.252215 GCAGTACAAGGCAACATTACACA 59.748 43.478 0.00 0.00 41.41 3.72
4786 4902 4.261405 GCAGTACAAGGCAACATTACACAA 60.261 41.667 0.00 0.00 41.41 3.33
4787 4903 5.564651 GCAGTACAAGGCAACATTACACAAT 60.565 40.000 0.00 0.00 41.41 2.71
4788 4904 6.348950 GCAGTACAAGGCAACATTACACAATA 60.349 38.462 0.00 0.00 41.41 1.90
4789 4905 7.628366 GCAGTACAAGGCAACATTACACAATAT 60.628 37.037 0.00 0.00 41.41 1.28
4790 4906 8.243426 CAGTACAAGGCAACATTACACAATATT 58.757 33.333 0.00 0.00 41.41 1.28
4791 4907 9.456147 AGTACAAGGCAACATTACACAATATTA 57.544 29.630 0.00 0.00 41.41 0.98
4793 4909 8.980143 ACAAGGCAACATTACACAATATTAAC 57.020 30.769 0.00 0.00 41.41 2.01
4794 4910 7.753132 ACAAGGCAACATTACACAATATTAACG 59.247 33.333 0.00 0.00 41.41 3.18
4795 4911 7.385778 AGGCAACATTACACAATATTAACGT 57.614 32.000 0.00 0.00 41.41 3.99
4796 4912 7.469260 AGGCAACATTACACAATATTAACGTC 58.531 34.615 0.00 0.00 41.41 4.34
4797 4913 7.335924 AGGCAACATTACACAATATTAACGTCT 59.664 33.333 0.00 0.00 41.41 4.18
4798 4914 7.966204 GGCAACATTACACAATATTAACGTCTT 59.034 33.333 0.00 0.00 0.00 3.01
4799 4915 9.337091 GCAACATTACACAATATTAACGTCTTT 57.663 29.630 0.00 0.00 0.00 2.52
4807 4923 9.872757 ACACAATATTAACGTCTTTTAACACAG 57.127 29.630 0.00 0.00 0.00 3.66
4814 4930 6.937436 AACGTCTTTTAACACAGATTTCCT 57.063 33.333 0.00 0.00 0.00 3.36
4815 4931 6.541111 ACGTCTTTTAACACAGATTTCCTC 57.459 37.500 0.00 0.00 0.00 3.71
4816 4932 6.289064 ACGTCTTTTAACACAGATTTCCTCT 58.711 36.000 0.00 0.00 33.14 3.69
4817 4933 6.766467 ACGTCTTTTAACACAGATTTCCTCTT 59.234 34.615 0.00 0.00 29.16 2.85
4818 4934 7.041984 ACGTCTTTTAACACAGATTTCCTCTTC 60.042 37.037 0.00 0.00 29.16 2.87
4819 4935 7.042051 CGTCTTTTAACACAGATTTCCTCTTCA 60.042 37.037 0.00 0.00 29.16 3.02
4820 4936 8.070769 GTCTTTTAACACAGATTTCCTCTTCAC 58.929 37.037 0.00 0.00 29.16 3.18
4821 4937 7.773224 TCTTTTAACACAGATTTCCTCTTCACA 59.227 33.333 0.00 0.00 29.16 3.58
4822 4938 7.873719 TTTAACACAGATTTCCTCTTCACAA 57.126 32.000 0.00 0.00 29.16 3.33
4823 4939 5.757850 AACACAGATTTCCTCTTCACAAC 57.242 39.130 0.00 0.00 29.16 3.32
4824 4940 4.780815 ACACAGATTTCCTCTTCACAACA 58.219 39.130 0.00 0.00 29.16 3.33
4825 4941 4.576463 ACACAGATTTCCTCTTCACAACAC 59.424 41.667 0.00 0.00 29.16 3.32
4826 4942 4.576053 CACAGATTTCCTCTTCACAACACA 59.424 41.667 0.00 0.00 29.16 3.72
4827 4943 5.066375 CACAGATTTCCTCTTCACAACACAA 59.934 40.000 0.00 0.00 29.16 3.33
4828 4944 5.066505 ACAGATTTCCTCTTCACAACACAAC 59.933 40.000 0.00 0.00 29.16 3.32
4829 4945 5.297776 CAGATTTCCTCTTCACAACACAACT 59.702 40.000 0.00 0.00 29.16 3.16
4830 4946 6.483307 CAGATTTCCTCTTCACAACACAACTA 59.517 38.462 0.00 0.00 29.16 2.24
4831 4947 7.012327 CAGATTTCCTCTTCACAACACAACTAA 59.988 37.037 0.00 0.00 29.16 2.24
4832 4948 7.556275 AGATTTCCTCTTCACAACACAACTAAA 59.444 33.333 0.00 0.00 0.00 1.85
4833 4949 7.639113 TTTCCTCTTCACAACACAACTAAAT 57.361 32.000 0.00 0.00 0.00 1.40
4834 4950 8.740123 TTTCCTCTTCACAACACAACTAAATA 57.260 30.769 0.00 0.00 0.00 1.40
4835 4951 8.918202 TTCCTCTTCACAACACAACTAAATAT 57.082 30.769 0.00 0.00 0.00 1.28
4836 4952 8.918202 TCCTCTTCACAACACAACTAAATATT 57.082 30.769 0.00 0.00 0.00 1.28
4837 4953 9.349713 TCCTCTTCACAACACAACTAAATATTT 57.650 29.630 5.89 5.89 0.00 1.40
4838 4954 9.398170 CCTCTTCACAACACAACTAAATATTTG 57.602 33.333 11.05 3.88 0.00 2.32
4839 4955 9.950680 CTCTTCACAACACAACTAAATATTTGT 57.049 29.630 11.05 4.48 36.35 2.83
4848 4964 8.880768 CACAACTAAATATTTGTGTACAGCTC 57.119 34.615 11.05 0.00 45.01 4.09
4849 4965 7.962918 CACAACTAAATATTTGTGTACAGCTCC 59.037 37.037 11.05 0.00 45.01 4.70
4850 4966 7.120726 ACAACTAAATATTTGTGTACAGCTCCC 59.879 37.037 11.05 0.00 34.61 4.30
4851 4967 5.815740 ACTAAATATTTGTGTACAGCTCCCG 59.184 40.000 11.05 0.00 0.00 5.14
4852 4968 2.018542 TATTTGTGTACAGCTCCCGC 57.981 50.000 0.00 0.00 0.00 6.13
4853 4969 0.036164 ATTTGTGTACAGCTCCCGCA 59.964 50.000 0.00 0.00 39.10 5.69
4854 4970 0.179043 TTTGTGTACAGCTCCCGCAA 60.179 50.000 0.00 0.00 39.10 4.85
4855 4971 0.179043 TTGTGTACAGCTCCCGCAAA 60.179 50.000 0.00 0.00 39.10 3.68
4856 4972 0.882927 TGTGTACAGCTCCCGCAAAC 60.883 55.000 0.00 0.00 39.10 2.93
4857 4973 0.882927 GTGTACAGCTCCCGCAAACA 60.883 55.000 0.00 0.00 39.10 2.83
4858 4974 0.179043 TGTACAGCTCCCGCAAACAA 60.179 50.000 0.00 0.00 39.10 2.83
4859 4975 1.165270 GTACAGCTCCCGCAAACAAT 58.835 50.000 0.00 0.00 39.10 2.71
4860 4976 1.539827 GTACAGCTCCCGCAAACAATT 59.460 47.619 0.00 0.00 39.10 2.32
4861 4977 1.904287 ACAGCTCCCGCAAACAATTA 58.096 45.000 0.00 0.00 39.10 1.40
4862 4978 2.446435 ACAGCTCCCGCAAACAATTAT 58.554 42.857 0.00 0.00 39.10 1.28
4863 4979 2.825532 ACAGCTCCCGCAAACAATTATT 59.174 40.909 0.00 0.00 39.10 1.40
4864 4980 3.119495 ACAGCTCCCGCAAACAATTATTC 60.119 43.478 0.00 0.00 39.10 1.75
4865 4981 3.088532 AGCTCCCGCAAACAATTATTCA 58.911 40.909 0.00 0.00 39.10 2.57
4866 4982 3.509575 AGCTCCCGCAAACAATTATTCAA 59.490 39.130 0.00 0.00 39.10 2.69
4867 4983 3.859386 GCTCCCGCAAACAATTATTCAAG 59.141 43.478 0.00 0.00 35.78 3.02
4868 4984 4.423732 CTCCCGCAAACAATTATTCAAGG 58.576 43.478 0.00 0.00 0.00 3.61
4869 4985 2.929398 CCCGCAAACAATTATTCAAGGC 59.071 45.455 0.00 0.00 0.00 4.35
4870 4986 3.368323 CCCGCAAACAATTATTCAAGGCT 60.368 43.478 0.00 0.00 0.00 4.58
4871 4987 3.613737 CCGCAAACAATTATTCAAGGCTG 59.386 43.478 0.00 0.00 0.00 4.85
4872 4988 3.613737 CGCAAACAATTATTCAAGGCTGG 59.386 43.478 0.00 0.00 0.00 4.85
4873 4989 4.617995 CGCAAACAATTATTCAAGGCTGGA 60.618 41.667 0.00 0.00 0.00 3.86
4874 4990 5.422145 GCAAACAATTATTCAAGGCTGGAT 58.578 37.500 0.00 0.00 0.00 3.41
4875 4991 5.521372 GCAAACAATTATTCAAGGCTGGATC 59.479 40.000 0.00 0.00 0.00 3.36
4876 4992 5.859205 AACAATTATTCAAGGCTGGATCC 57.141 39.130 4.20 4.20 0.00 3.36
4877 4993 4.218312 ACAATTATTCAAGGCTGGATCCC 58.782 43.478 9.90 0.00 0.00 3.85
4878 4994 2.638480 TTATTCAAGGCTGGATCCCG 57.362 50.000 9.90 3.53 0.00 5.14
4879 4995 1.801242 TATTCAAGGCTGGATCCCGA 58.199 50.000 9.90 0.00 0.00 5.14
4880 4996 1.143813 ATTCAAGGCTGGATCCCGAT 58.856 50.000 9.90 0.00 0.00 4.18
4881 4997 0.918983 TTCAAGGCTGGATCCCGATT 59.081 50.000 9.90 0.00 0.00 3.34
4882 4998 0.918983 TCAAGGCTGGATCCCGATTT 59.081 50.000 9.90 0.00 0.00 2.17
4883 4999 1.134098 TCAAGGCTGGATCCCGATTTC 60.134 52.381 9.90 0.00 0.00 2.17
4884 5000 0.918983 AAGGCTGGATCCCGATTTCA 59.081 50.000 9.90 0.00 0.00 2.69
4885 5001 1.143813 AGGCTGGATCCCGATTTCAT 58.856 50.000 9.90 0.00 0.00 2.57
4886 5002 1.496429 AGGCTGGATCCCGATTTCATT 59.504 47.619 9.90 0.00 0.00 2.57
4887 5003 2.711009 AGGCTGGATCCCGATTTCATTA 59.289 45.455 9.90 0.00 0.00 1.90
4888 5004 3.138283 AGGCTGGATCCCGATTTCATTAA 59.862 43.478 9.90 0.00 0.00 1.40
4889 5005 3.888930 GGCTGGATCCCGATTTCATTAAA 59.111 43.478 9.90 0.00 0.00 1.52
4890 5006 4.022849 GGCTGGATCCCGATTTCATTAAAG 60.023 45.833 9.90 0.00 0.00 1.85
4891 5007 4.580580 GCTGGATCCCGATTTCATTAAAGT 59.419 41.667 9.90 0.00 0.00 2.66
4892 5008 5.506317 GCTGGATCCCGATTTCATTAAAGTG 60.506 44.000 9.90 0.00 0.00 3.16
4893 5009 5.505780 TGGATCCCGATTTCATTAAAGTGT 58.494 37.500 9.90 0.00 0.00 3.55
4894 5010 6.654959 TGGATCCCGATTTCATTAAAGTGTA 58.345 36.000 9.90 0.00 0.00 2.90
4895 5011 7.113437 TGGATCCCGATTTCATTAAAGTGTAA 58.887 34.615 9.90 0.00 0.00 2.41
4896 5012 7.612244 TGGATCCCGATTTCATTAAAGTGTAAA 59.388 33.333 9.90 0.00 0.00 2.01
4897 5013 8.463607 GGATCCCGATTTCATTAAAGTGTAAAA 58.536 33.333 0.00 0.00 0.00 1.52
4898 5014 9.503427 GATCCCGATTTCATTAAAGTGTAAAAG 57.497 33.333 0.00 0.00 0.00 2.27
4899 5015 8.624367 TCCCGATTTCATTAAAGTGTAAAAGA 57.376 30.769 0.00 0.00 0.00 2.52
4900 5016 9.069082 TCCCGATTTCATTAAAGTGTAAAAGAA 57.931 29.630 0.00 0.00 0.00 2.52
4901 5017 9.124807 CCCGATTTCATTAAAGTGTAAAAGAAC 57.875 33.333 0.00 0.00 0.00 3.01
4902 5018 9.672086 CCGATTTCATTAAAGTGTAAAAGAACA 57.328 29.630 0.00 0.00 0.00 3.18
4931 5047 9.935241 AATTTATGTATATGCACAACCAAAACA 57.065 25.926 0.00 0.00 30.84 2.83
4932 5048 8.978564 TTTATGTATATGCACAACCAAAACAG 57.021 30.769 0.00 0.00 30.84 3.16
4933 5049 6.832520 ATGTATATGCACAACCAAAACAGA 57.167 33.333 0.00 0.00 30.84 3.41
4934 5050 6.641169 TGTATATGCACAACCAAAACAGAA 57.359 33.333 0.00 0.00 0.00 3.02
4935 5051 7.043961 TGTATATGCACAACCAAAACAGAAA 57.956 32.000 0.00 0.00 0.00 2.52
4936 5052 7.144661 TGTATATGCACAACCAAAACAGAAAG 58.855 34.615 0.00 0.00 0.00 2.62
4937 5053 3.244033 TGCACAACCAAAACAGAAAGG 57.756 42.857 0.00 0.00 0.00 3.11
4938 5054 2.093764 TGCACAACCAAAACAGAAAGGG 60.094 45.455 0.00 0.00 0.00 3.95
4939 5055 2.093711 GCACAACCAAAACAGAAAGGGT 60.094 45.455 0.00 0.00 0.00 4.34
4940 5056 3.131400 GCACAACCAAAACAGAAAGGGTA 59.869 43.478 0.00 0.00 0.00 3.69
4941 5057 4.382147 GCACAACCAAAACAGAAAGGGTAA 60.382 41.667 0.00 0.00 0.00 2.85
4942 5058 5.725362 CACAACCAAAACAGAAAGGGTAAA 58.275 37.500 0.00 0.00 0.00 2.01
4943 5059 6.166982 CACAACCAAAACAGAAAGGGTAAAA 58.833 36.000 0.00 0.00 0.00 1.52
4944 5060 6.651225 CACAACCAAAACAGAAAGGGTAAAAA 59.349 34.615 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 8.622948 AAAGAACAACAGAATAAGGAAGGTAG 57.377 34.615 0.00 0.00 0.00 3.18
44 45 6.071896 GGGAAAGAACAACAGAATAAGGAAGG 60.072 42.308 0.00 0.00 0.00 3.46
45 46 6.717084 AGGGAAAGAACAACAGAATAAGGAAG 59.283 38.462 0.00 0.00 0.00 3.46
48 49 6.901081 AAGGGAAAGAACAACAGAATAAGG 57.099 37.500 0.00 0.00 0.00 2.69
52 53 8.197439 CAGTAAAAAGGGAAAGAACAACAGAAT 58.803 33.333 0.00 0.00 0.00 2.40
63 64 5.684550 AACGTAGCAGTAAAAAGGGAAAG 57.315 39.130 0.00 0.00 0.00 2.62
65 66 4.685628 CGTAACGTAGCAGTAAAAAGGGAA 59.314 41.667 0.00 0.00 0.00 3.97
71 72 4.621034 GGCTAACGTAACGTAGCAGTAAAA 59.379 41.667 16.53 0.00 39.99 1.52
91 92 3.016736 CAGTAAATTCCCATGAACGGCT 58.983 45.455 0.00 0.00 32.13 5.52
96 97 6.039270 CCGCTAAATCAGTAAATTCCCATGAA 59.961 38.462 0.00 0.00 34.33 2.57
123 147 1.917872 TTGGCCAATAACTTCGCCTT 58.082 45.000 16.05 0.00 39.21 4.35
150 185 5.191059 GTTGAAATATCTAACGCTTCGCTG 58.809 41.667 0.00 0.00 0.00 5.18
179 215 0.956410 TACACGCCAAATTCACCGGG 60.956 55.000 6.32 0.00 0.00 5.73
209 245 0.665670 CACGAGAGCTGCATATCCCG 60.666 60.000 1.02 0.00 0.00 5.14
214 251 1.226688 GCGTCACGAGAGCTGCATA 60.227 57.895 0.00 0.00 0.00 3.14
316 353 2.088950 TCCGAAAAAGGGCGTTAGAG 57.911 50.000 0.00 0.00 0.00 2.43
332 369 1.038280 AGCCGGTAGGTATCTTTCCG 58.962 55.000 1.90 10.96 40.50 4.30
442 479 6.098838 TGTTACTATCAGACAGAGATGGCAAT 59.901 38.462 0.00 0.00 0.00 3.56
482 520 0.892755 AATCGTACAGTTCGGCTCCA 59.107 50.000 0.00 0.00 0.00 3.86
484 522 4.025979 CCATTAAATCGTACAGTTCGGCTC 60.026 45.833 0.00 0.00 0.00 4.70
485 523 3.869246 CCATTAAATCGTACAGTTCGGCT 59.131 43.478 0.00 0.00 0.00 5.52
486 524 3.866910 TCCATTAAATCGTACAGTTCGGC 59.133 43.478 0.00 0.00 0.00 5.54
489 527 6.812160 AGTCAGTCCATTAAATCGTACAGTTC 59.188 38.462 0.00 0.00 0.00 3.01
510 548 7.004555 TCTCTTAGAATTGCCAAACTAGTCA 57.995 36.000 0.00 0.00 0.00 3.41
533 571 6.958193 CGACATTGATTCAGCTAGAAAAGTTC 59.042 38.462 0.00 0.00 40.22 3.01
635 675 9.899226 GTATGGCTCCAATTATTTGAGTAATTC 57.101 33.333 7.68 0.00 33.24 2.17
636 676 9.646522 AGTATGGCTCCAATTATTTGAGTAATT 57.353 29.630 7.68 0.00 35.27 1.40
686 727 4.475028 TCATGCTTATCAAAAACAGCACG 58.525 39.130 0.00 0.00 44.82 5.34
719 760 7.829211 ACTGAGAATCGATTTTATTTCCAAGGA 59.171 33.333 12.81 0.00 38.61 3.36
1032 1075 1.167851 ACATTGACCTTGCATCACCG 58.832 50.000 0.00 0.00 0.00 4.94
1063 1106 5.964758 TGCATTGGGATTTAATGAAGTGAC 58.035 37.500 0.00 0.00 37.65 3.67
1069 1112 4.279982 TCTGCTGCATTGGGATTTAATGA 58.720 39.130 1.31 0.00 37.65 2.57
1308 1351 2.408565 AGGGACAGTTCTTCAGGTTCA 58.591 47.619 0.00 0.00 0.00 3.18
1497 1540 1.472480 CCCACGTAATTTTGCTCCCAG 59.528 52.381 0.00 0.00 0.00 4.45
1581 1624 4.271687 CAACGTACTCACAAGCAAAACTC 58.728 43.478 0.00 0.00 0.00 3.01
1591 1634 1.270041 TGATGCTGCAACGTACTCACA 60.270 47.619 6.36 0.00 0.00 3.58
1921 1965 9.855021 GAAGCAATGTACATTACCAAATAAAGT 57.145 29.630 20.39 0.00 0.00 2.66
2193 2237 4.046462 CAGCTGAAACAAAATCACCAGTG 58.954 43.478 8.42 0.00 0.00 3.66
2232 2276 4.666512 ACTTGTTATGGCCAGAATTCTGT 58.333 39.130 29.03 16.07 42.27 3.41
2247 2291 5.511363 TCAGGACCCTTTTTGAACTTGTTA 58.489 37.500 0.00 0.00 0.00 2.41
2374 2418 0.111061 TCAAGCCATGGAGTTGCAGT 59.889 50.000 18.40 0.00 0.00 4.40
2403 2447 3.003378 TCAGATGAGTATTACCGACTGCG 59.997 47.826 0.00 0.00 37.24 5.18
2450 2494 5.067413 TGCAAAACCATCAAATTGTGCAATT 59.933 32.000 4.48 4.48 42.35 2.32
2669 2717 2.223829 TGTTGGGCCACGTACAAAAATG 60.224 45.455 5.23 0.00 0.00 2.32
2672 2720 1.025812 CTGTTGGGCCACGTACAAAA 58.974 50.000 5.23 0.00 0.00 2.44
2844 2892 7.761249 AGATACCTAAACAAGAAATGCAAATGC 59.239 33.333 0.00 0.00 42.50 3.56
2943 2991 6.479095 AACCGATTAACAATGCCAAATTTG 57.521 33.333 11.40 11.40 0.00 2.32
2944 2992 7.503521 AAAACCGATTAACAATGCCAAATTT 57.496 28.000 0.00 0.00 0.00 1.82
2979 3027 6.268566 GCAACAACCAATTTTAAAAATGCCA 58.731 32.000 10.02 0.00 0.00 4.92
3020 3068 6.539826 CACATGACAATGATACACACCTACAT 59.460 38.462 0.00 0.00 37.24 2.29
3156 3209 5.066913 AGGAAGGAAAGGAACAAGACAAT 57.933 39.130 0.00 0.00 0.00 2.71
3286 3339 6.040209 TCCCTAAAGTAAGTCGCACAAATA 57.960 37.500 0.00 0.00 0.00 1.40
3301 3354 3.626217 GCCAGATTTACCGTTCCCTAAAG 59.374 47.826 0.00 0.00 0.00 1.85
3311 3364 1.882352 GCTATGGGGCCAGATTTACCG 60.882 57.143 4.39 0.00 0.00 4.02
3314 3367 3.598264 AGTAGCTATGGGGCCAGATTTA 58.402 45.455 4.39 0.00 0.00 1.40
3376 3429 8.523915 AATTAATGAGTCAAATATGCAGGACA 57.476 30.769 0.00 0.00 32.79 4.02
3416 3469 4.458989 TGCCAAGTACATCTTTCCATCAAC 59.541 41.667 0.00 0.00 33.63 3.18
3583 3636 6.046593 AGCAGCGTATACATAGCTTGTAAAA 58.953 36.000 3.32 3.13 43.84 1.52
3584 3637 5.597806 AGCAGCGTATACATAGCTTGTAAA 58.402 37.500 3.32 0.00 43.84 2.01
3585 3638 5.196341 AGCAGCGTATACATAGCTTGTAA 57.804 39.130 3.32 2.03 43.84 2.41
3586 3639 4.848562 AGCAGCGTATACATAGCTTGTA 57.151 40.909 3.32 10.01 44.71 2.41
3587 3640 3.735237 AGCAGCGTATACATAGCTTGT 57.265 42.857 3.32 0.00 39.48 3.16
3589 3642 4.202161 ACAGAAGCAGCGTATACATAGCTT 60.202 41.667 19.47 19.47 44.15 3.74
3619 3672 1.937223 TGCTTGTAAATATGTCGCCGG 59.063 47.619 0.00 0.00 0.00 6.13
3621 3674 4.332819 AGAAGTGCTTGTAAATATGTCGCC 59.667 41.667 0.00 0.00 0.00 5.54
3660 3715 3.243737 GGGTTCCTGGACAATGAAACAAC 60.244 47.826 0.00 0.00 0.00 3.32
3944 3999 1.540707 TGATGTTAGTACACGGCGACA 59.459 47.619 16.62 5.72 37.03 4.35
4085 4142 0.773644 TTCTCCTGCTGGCTCCTTTT 59.226 50.000 4.42 0.00 0.00 2.27
4194 4251 0.319900 TCGCAAGCACTCCAGAGAAC 60.320 55.000 0.70 0.00 37.18 3.01
4196 4253 0.895559 TCTCGCAAGCACTCCAGAGA 60.896 55.000 0.70 0.00 33.02 3.10
4197 4254 0.175302 ATCTCGCAAGCACTCCAGAG 59.825 55.000 0.00 0.00 37.18 3.35
4208 4275 2.125552 CCGCAGTCCATCTCGCAA 60.126 61.111 0.00 0.00 0.00 4.85
4256 4324 0.036010 AATGCCGACTGGAACTGAGG 60.036 55.000 0.00 0.00 37.49 3.86
4260 4328 3.540211 CAGAATGCCGACTGGAACT 57.460 52.632 0.00 0.00 37.49 3.01
4305 4378 4.336889 TGTCTCAAATTTCACCGAGTCT 57.663 40.909 3.88 0.00 0.00 3.24
4526 4617 8.409371 TCAGTACACAAGATATGAGAAAGCTAG 58.591 37.037 0.00 0.00 0.00 3.42
4538 4629 7.840931 ACAAGATGATGTCAGTACACAAGATA 58.159 34.615 0.00 0.00 38.78 1.98
4652 4768 5.247507 TCATGAATAATTGTTTGCGGGAG 57.752 39.130 0.00 0.00 0.00 4.30
4716 4832 2.571212 TGATGTCAATACATTCCCCGC 58.429 47.619 0.00 0.00 46.49 6.13
4717 4833 4.645535 AGATGATGTCAATACATTCCCCG 58.354 43.478 0.00 0.00 46.49 5.73
4718 4834 5.829924 ACAAGATGATGTCAATACATTCCCC 59.170 40.000 0.00 0.00 46.49 4.81
4719 4835 6.949352 ACAAGATGATGTCAATACATTCCC 57.051 37.500 0.00 0.00 46.49 3.97
4722 4838 9.224267 GCCTATACAAGATGATGTCAATACATT 57.776 33.333 0.00 0.00 46.49 2.71
4724 4840 7.734942 TGCCTATACAAGATGATGTCAATACA 58.265 34.615 0.00 0.00 40.69 2.29
4725 4841 8.499162 GTTGCCTATACAAGATGATGTCAATAC 58.501 37.037 0.00 0.00 34.75 1.89
4726 4842 7.661437 GGTTGCCTATACAAGATGATGTCAATA 59.339 37.037 0.00 0.00 34.75 1.90
4727 4843 6.488006 GGTTGCCTATACAAGATGATGTCAAT 59.512 38.462 0.00 0.00 34.75 2.57
4728 4844 5.822519 GGTTGCCTATACAAGATGATGTCAA 59.177 40.000 0.00 0.00 34.75 3.18
4729 4845 5.368145 GGTTGCCTATACAAGATGATGTCA 58.632 41.667 0.00 0.00 34.75 3.58
4730 4846 4.449068 CGGTTGCCTATACAAGATGATGTC 59.551 45.833 0.00 0.00 34.75 3.06
4731 4847 4.100963 TCGGTTGCCTATACAAGATGATGT 59.899 41.667 0.00 0.00 37.32 3.06
4732 4848 4.631131 TCGGTTGCCTATACAAGATGATG 58.369 43.478 0.00 0.00 0.00 3.07
4733 4849 4.345257 ACTCGGTTGCCTATACAAGATGAT 59.655 41.667 0.00 0.00 0.00 2.45
4734 4850 3.704566 ACTCGGTTGCCTATACAAGATGA 59.295 43.478 0.00 0.00 0.00 2.92
4735 4851 3.804325 CACTCGGTTGCCTATACAAGATG 59.196 47.826 0.00 0.00 0.00 2.90
4736 4852 3.181465 CCACTCGGTTGCCTATACAAGAT 60.181 47.826 0.00 0.00 0.00 2.40
4737 4853 2.167693 CCACTCGGTTGCCTATACAAGA 59.832 50.000 0.00 0.00 0.00 3.02
4738 4854 2.093658 ACCACTCGGTTGCCTATACAAG 60.094 50.000 0.00 0.00 46.31 3.16
4739 4855 1.903860 ACCACTCGGTTGCCTATACAA 59.096 47.619 0.00 0.00 46.31 2.41
4740 4856 1.206132 CACCACTCGGTTGCCTATACA 59.794 52.381 0.00 0.00 46.31 2.29
4741 4857 1.206371 ACACCACTCGGTTGCCTATAC 59.794 52.381 0.00 0.00 46.31 1.47
4742 4858 1.563924 ACACCACTCGGTTGCCTATA 58.436 50.000 0.00 0.00 46.31 1.31
4743 4859 1.480954 CTACACCACTCGGTTGCCTAT 59.519 52.381 0.00 0.00 46.31 2.57
4744 4860 0.892755 CTACACCACTCGGTTGCCTA 59.107 55.000 0.00 0.00 46.31 3.93
4745 4861 1.671742 CTACACCACTCGGTTGCCT 59.328 57.895 0.00 0.00 46.31 4.75
4746 4862 2.033194 GCTACACCACTCGGTTGCC 61.033 63.158 0.00 0.00 46.31 4.52
4747 4863 1.291877 CTGCTACACCACTCGGTTGC 61.292 60.000 0.00 0.00 46.31 4.17
4748 4864 0.033504 ACTGCTACACCACTCGGTTG 59.966 55.000 0.00 0.00 46.31 3.77
4749 4865 1.271656 GTACTGCTACACCACTCGGTT 59.728 52.381 0.00 0.00 46.31 4.44
4751 4867 0.885879 TGTACTGCTACACCACTCGG 59.114 55.000 0.00 0.00 38.77 4.63
4752 4868 2.596452 CTTGTACTGCTACACCACTCG 58.404 52.381 0.00 0.00 32.28 4.18
4753 4869 2.931320 GCCTTGTACTGCTACACCACTC 60.931 54.545 0.00 0.00 32.28 3.51
4754 4870 1.002087 GCCTTGTACTGCTACACCACT 59.998 52.381 0.00 0.00 32.28 4.00
4755 4871 1.270625 TGCCTTGTACTGCTACACCAC 60.271 52.381 0.00 0.00 32.28 4.16
4756 4872 1.052617 TGCCTTGTACTGCTACACCA 58.947 50.000 0.00 0.00 32.28 4.17
4757 4873 1.804748 GTTGCCTTGTACTGCTACACC 59.195 52.381 10.42 0.00 32.28 4.16
4758 4874 2.489971 TGTTGCCTTGTACTGCTACAC 58.510 47.619 12.74 5.24 38.09 2.90
4759 4875 2.920724 TGTTGCCTTGTACTGCTACA 57.079 45.000 12.74 12.74 40.08 2.74
4760 4876 4.693566 TGTAATGTTGCCTTGTACTGCTAC 59.306 41.667 0.00 2.69 34.49 3.58
4761 4877 4.693566 GTGTAATGTTGCCTTGTACTGCTA 59.306 41.667 0.00 0.00 0.00 3.49
4762 4878 3.502211 GTGTAATGTTGCCTTGTACTGCT 59.498 43.478 0.00 0.00 0.00 4.24
4763 4879 3.252215 TGTGTAATGTTGCCTTGTACTGC 59.748 43.478 0.00 0.00 0.00 4.40
4764 4880 5.431420 TTGTGTAATGTTGCCTTGTACTG 57.569 39.130 0.00 0.00 0.00 2.74
4765 4881 7.938140 ATATTGTGTAATGTTGCCTTGTACT 57.062 32.000 0.00 0.00 0.00 2.73
4768 4884 7.753132 CGTTAATATTGTGTAATGTTGCCTTGT 59.247 33.333 0.00 0.00 31.28 3.16
4769 4885 7.753132 ACGTTAATATTGTGTAATGTTGCCTTG 59.247 33.333 0.00 0.00 31.28 3.61
4770 4886 7.822658 ACGTTAATATTGTGTAATGTTGCCTT 58.177 30.769 0.00 0.00 31.28 4.35
4771 4887 7.335924 AGACGTTAATATTGTGTAATGTTGCCT 59.664 33.333 0.00 0.00 31.22 4.75
4772 4888 7.469260 AGACGTTAATATTGTGTAATGTTGCC 58.531 34.615 0.00 0.00 31.22 4.52
4773 4889 8.889849 AAGACGTTAATATTGTGTAATGTTGC 57.110 30.769 0.00 0.00 31.22 4.17
4781 4897 9.872757 CTGTGTTAAAAGACGTTAATATTGTGT 57.127 29.630 0.00 0.00 0.00 3.72
4788 4904 9.063615 AGGAAATCTGTGTTAAAAGACGTTAAT 57.936 29.630 0.00 0.00 0.00 1.40
4789 4905 8.441312 AGGAAATCTGTGTTAAAAGACGTTAA 57.559 30.769 0.00 0.00 0.00 2.01
4790 4906 7.929785 AGAGGAAATCTGTGTTAAAAGACGTTA 59.070 33.333 0.00 0.00 36.69 3.18
4791 4907 6.766467 AGAGGAAATCTGTGTTAAAAGACGTT 59.234 34.615 0.00 0.00 36.69 3.99
4792 4908 6.289064 AGAGGAAATCTGTGTTAAAAGACGT 58.711 36.000 0.00 0.00 36.69 4.34
4793 4909 6.787085 AGAGGAAATCTGTGTTAAAAGACG 57.213 37.500 0.00 0.00 36.69 4.18
4794 4910 8.070769 GTGAAGAGGAAATCTGTGTTAAAAGAC 58.929 37.037 0.00 0.00 38.67 3.01
4795 4911 7.773224 TGTGAAGAGGAAATCTGTGTTAAAAGA 59.227 33.333 0.00 0.00 38.67 2.52
4796 4912 7.930217 TGTGAAGAGGAAATCTGTGTTAAAAG 58.070 34.615 0.00 0.00 38.67 2.27
4797 4913 7.873719 TGTGAAGAGGAAATCTGTGTTAAAA 57.126 32.000 0.00 0.00 38.67 1.52
4798 4914 7.338196 TGTTGTGAAGAGGAAATCTGTGTTAAA 59.662 33.333 0.00 0.00 38.67 1.52
4799 4915 6.826231 TGTTGTGAAGAGGAAATCTGTGTTAA 59.174 34.615 0.00 0.00 38.67 2.01
4800 4916 6.260050 GTGTTGTGAAGAGGAAATCTGTGTTA 59.740 38.462 0.00 0.00 38.67 2.41
4801 4917 5.066505 GTGTTGTGAAGAGGAAATCTGTGTT 59.933 40.000 0.00 0.00 38.67 3.32
4802 4918 4.576463 GTGTTGTGAAGAGGAAATCTGTGT 59.424 41.667 0.00 0.00 38.67 3.72
4803 4919 4.576053 TGTGTTGTGAAGAGGAAATCTGTG 59.424 41.667 0.00 0.00 38.67 3.66
4804 4920 4.780815 TGTGTTGTGAAGAGGAAATCTGT 58.219 39.130 0.00 0.00 38.67 3.41
4805 4921 5.297776 AGTTGTGTTGTGAAGAGGAAATCTG 59.702 40.000 0.00 0.00 38.67 2.90
4806 4922 5.440610 AGTTGTGTTGTGAAGAGGAAATCT 58.559 37.500 0.00 0.00 41.27 2.40
4807 4923 5.757850 AGTTGTGTTGTGAAGAGGAAATC 57.242 39.130 0.00 0.00 0.00 2.17
4808 4924 7.639113 TTTAGTTGTGTTGTGAAGAGGAAAT 57.361 32.000 0.00 0.00 0.00 2.17
4809 4925 7.639113 ATTTAGTTGTGTTGTGAAGAGGAAA 57.361 32.000 0.00 0.00 0.00 3.13
4810 4926 8.918202 ATATTTAGTTGTGTTGTGAAGAGGAA 57.082 30.769 0.00 0.00 0.00 3.36
4811 4927 8.918202 AATATTTAGTTGTGTTGTGAAGAGGA 57.082 30.769 0.00 0.00 0.00 3.71
4812 4928 9.398170 CAAATATTTAGTTGTGTTGTGAAGAGG 57.602 33.333 0.00 0.00 0.00 3.69
4813 4929 9.950680 ACAAATATTTAGTTGTGTTGTGAAGAG 57.049 29.630 0.00 0.00 42.12 2.85
4824 4940 7.120726 GGGAGCTGTACACAAATATTTAGTTGT 59.879 37.037 0.00 7.31 44.20 3.32
4825 4941 7.472543 GGGAGCTGTACACAAATATTTAGTTG 58.527 38.462 0.00 1.70 37.30 3.16
4826 4942 6.315393 CGGGAGCTGTACACAAATATTTAGTT 59.685 38.462 0.00 0.00 0.00 2.24
4827 4943 5.815740 CGGGAGCTGTACACAAATATTTAGT 59.184 40.000 0.00 5.64 0.00 2.24
4828 4944 6.287107 CGGGAGCTGTACACAAATATTTAG 57.713 41.667 0.00 0.00 0.00 1.85
4846 4962 4.423732 CCTTGAATAATTGTTTGCGGGAG 58.576 43.478 0.00 0.00 0.00 4.30
4847 4963 3.367910 GCCTTGAATAATTGTTTGCGGGA 60.368 43.478 0.00 0.00 0.00 5.14
4848 4964 2.929398 GCCTTGAATAATTGTTTGCGGG 59.071 45.455 0.00 0.00 0.00 6.13
4849 4965 3.613737 CAGCCTTGAATAATTGTTTGCGG 59.386 43.478 0.00 0.00 0.00 5.69
4850 4966 3.613737 CCAGCCTTGAATAATTGTTTGCG 59.386 43.478 0.00 0.00 0.00 4.85
4851 4967 4.819769 TCCAGCCTTGAATAATTGTTTGC 58.180 39.130 0.00 0.00 0.00 3.68
4852 4968 6.044682 GGATCCAGCCTTGAATAATTGTTTG 58.955 40.000 6.95 0.00 0.00 2.93
4853 4969 5.129320 GGGATCCAGCCTTGAATAATTGTTT 59.871 40.000 15.23 0.00 0.00 2.83
4854 4970 4.651045 GGGATCCAGCCTTGAATAATTGTT 59.349 41.667 15.23 0.00 0.00 2.83
4855 4971 4.218312 GGGATCCAGCCTTGAATAATTGT 58.782 43.478 15.23 0.00 0.00 2.71
4856 4972 3.254166 CGGGATCCAGCCTTGAATAATTG 59.746 47.826 15.23 0.00 0.00 2.32
4857 4973 3.138283 TCGGGATCCAGCCTTGAATAATT 59.862 43.478 15.23 0.00 0.00 1.40
4858 4974 2.711009 TCGGGATCCAGCCTTGAATAAT 59.289 45.455 15.23 0.00 0.00 1.28
4859 4975 2.123589 TCGGGATCCAGCCTTGAATAA 58.876 47.619 15.23 0.00 0.00 1.40
4860 4976 1.801242 TCGGGATCCAGCCTTGAATA 58.199 50.000 15.23 0.00 0.00 1.75
4861 4977 1.143813 ATCGGGATCCAGCCTTGAAT 58.856 50.000 15.23 0.00 0.00 2.57
4862 4978 0.918983 AATCGGGATCCAGCCTTGAA 59.081 50.000 15.23 0.00 0.00 2.69
4863 4979 0.918983 AAATCGGGATCCAGCCTTGA 59.081 50.000 15.23 1.37 0.00 3.02
4864 4980 1.312815 GAAATCGGGATCCAGCCTTG 58.687 55.000 15.23 0.00 0.00 3.61
4865 4981 0.918983 TGAAATCGGGATCCAGCCTT 59.081 50.000 15.23 6.05 0.00 4.35
4866 4982 1.143813 ATGAAATCGGGATCCAGCCT 58.856 50.000 15.23 0.00 0.00 4.58
4867 4983 1.986882 AATGAAATCGGGATCCAGCC 58.013 50.000 15.23 0.00 0.00 4.85
4868 4984 4.580580 ACTTTAATGAAATCGGGATCCAGC 59.419 41.667 15.23 0.00 0.00 4.85
4869 4985 5.590259 ACACTTTAATGAAATCGGGATCCAG 59.410 40.000 15.23 10.32 0.00 3.86
4870 4986 5.505780 ACACTTTAATGAAATCGGGATCCA 58.494 37.500 15.23 0.00 0.00 3.41
4871 4987 7.562454 TTACACTTTAATGAAATCGGGATCC 57.438 36.000 1.92 1.92 0.00 3.36
4872 4988 9.503427 CTTTTACACTTTAATGAAATCGGGATC 57.497 33.333 0.00 0.00 0.00 3.36
4873 4989 9.238368 TCTTTTACACTTTAATGAAATCGGGAT 57.762 29.630 0.00 0.00 0.00 3.85
4874 4990 8.624367 TCTTTTACACTTTAATGAAATCGGGA 57.376 30.769 0.00 0.00 0.00 5.14
4875 4991 9.124807 GTTCTTTTACACTTTAATGAAATCGGG 57.875 33.333 0.00 0.00 0.00 5.14
4876 4992 9.672086 TGTTCTTTTACACTTTAATGAAATCGG 57.328 29.630 0.00 0.00 0.00 4.18
4905 5021 9.935241 TGTTTTGGTTGTGCATATACATAAATT 57.065 25.926 0.00 0.00 0.00 1.82
4906 5022 9.585099 CTGTTTTGGTTGTGCATATACATAAAT 57.415 29.630 0.00 0.00 0.00 1.40
4907 5023 8.797438 TCTGTTTTGGTTGTGCATATACATAAA 58.203 29.630 0.00 0.00 0.00 1.40
4908 5024 8.341892 TCTGTTTTGGTTGTGCATATACATAA 57.658 30.769 0.00 0.00 0.00 1.90
4909 5025 7.929941 TCTGTTTTGGTTGTGCATATACATA 57.070 32.000 0.00 0.00 0.00 2.29
4910 5026 6.832520 TCTGTTTTGGTTGTGCATATACAT 57.167 33.333 0.00 0.00 0.00 2.29
4911 5027 6.641169 TTCTGTTTTGGTTGTGCATATACA 57.359 33.333 0.00 0.00 0.00 2.29
4912 5028 6.586082 CCTTTCTGTTTTGGTTGTGCATATAC 59.414 38.462 0.00 0.00 0.00 1.47
4913 5029 6.295011 CCCTTTCTGTTTTGGTTGTGCATATA 60.295 38.462 0.00 0.00 0.00 0.86
4914 5030 5.511202 CCCTTTCTGTTTTGGTTGTGCATAT 60.511 40.000 0.00 0.00 0.00 1.78
4915 5031 4.202202 CCCTTTCTGTTTTGGTTGTGCATA 60.202 41.667 0.00 0.00 0.00 3.14
4916 5032 3.432046 CCCTTTCTGTTTTGGTTGTGCAT 60.432 43.478 0.00 0.00 0.00 3.96
4917 5033 2.093764 CCCTTTCTGTTTTGGTTGTGCA 60.094 45.455 0.00 0.00 0.00 4.57
4918 5034 2.093711 ACCCTTTCTGTTTTGGTTGTGC 60.094 45.455 0.00 0.00 0.00 4.57
4919 5035 3.885724 ACCCTTTCTGTTTTGGTTGTG 57.114 42.857 0.00 0.00 0.00 3.33
4920 5036 6.361768 TTTTACCCTTTCTGTTTTGGTTGT 57.638 33.333 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.