Multiple sequence alignment - TraesCS3A01G333900

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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 TraesCS3A01G333900 chr3A 100.000 5531 0 0 1 5531 579372071 579366541 0.000000e+00 10214
1 TraesCS3A01G333900 chr3D 96.867 4596 107 14 1 4577 439672535 439667958 0.000000e+00 7655
2 TraesCS3A01G333900 chr3D 98.400 125 1 1 4670 4793 439667959 439667835 9.330000e-53 219
3 TraesCS3A01G333900 chr3D 92.742 124 4 3 4917 5037 439667836 439667715 2.050000e-39 174
4 TraesCS3A01G333900 chr3B 96.356 3622 131 1 955 4576 576443655 576440035 0.000000e+00 5956
5 TraesCS3A01G333900 chr3B 93.608 923 38 13 9 926 576444744 576443838 0.000000e+00 1358
6 TraesCS3A01G333900 chr3B 95.906 342 12 1 4685 5026 576440023 576439684 2.250000e-153 553
7 TraesCS3A01G333900 chrUn 100.000 405 0 0 3758 4162 478229310 478228906 0.000000e+00 749
8 TraesCS3A01G333900 chr7B 99.112 338 3 0 5194 5531 66212204 66212541 4.740000e-170 608
9 TraesCS3A01G333900 chr7B 97.923 337 7 0 5195 5531 695084122 695084458 7.980000e-163 584
10 TraesCS3A01G333900 chr6B 99.110 337 3 0 5195 5531 171442687 171442351 1.700000e-169 606
11 TraesCS3A01G333900 chr6B 95.000 100 4 1 4575 4673 665514656 665514755 7.420000e-34 156
12 TraesCS3A01G333900 chr6B 90.598 117 10 1 4556 4671 529769818 529769702 2.670000e-33 154
13 TraesCS3A01G333900 chr1A 98.649 296 3 1 5195 5490 276123100 276122806 1.770000e-144 523
14 TraesCS3A01G333900 chr1B 91.057 123 8 3 4574 4694 301264481 301264602 4.430000e-36 163
15 TraesCS3A01G333900 chr1D 95.146 103 3 2 4573 4673 483907578 483907680 1.590000e-35 161
16 TraesCS3A01G333900 chr2B 92.793 111 4 4 4573 4680 743692895 743693004 2.060000e-34 158
17 TraesCS3A01G333900 chr2B 86.260 131 14 4 4551 4679 258065428 258065556 7.470000e-29 139
18 TraesCS3A01G333900 chr4B 93.333 105 6 1 4576 4679 588430419 588430315 2.670000e-33 154
19 TraesCS3A01G333900 chr4B 88.710 124 9 4 4557 4678 561643411 561643291 4.460000e-31 147
20 TraesCS3A01G333900 chr5B 88.000 125 9 6 4552 4671 13176085 13175962 5.780000e-30 143


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 TraesCS3A01G333900 chr3A 579366541 579372071 5530 True 10214.000000 10214 100.000 1 5531 1 chr3A.!!$R1 5530
1 TraesCS3A01G333900 chr3D 439667715 439672535 4820 True 2682.666667 7655 96.003 1 5037 3 chr3D.!!$R1 5036
2 TraesCS3A01G333900 chr3B 576439684 576444744 5060 True 2622.333333 5956 95.290 9 5026 3 chr3B.!!$R1 5017

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
103 106 1.138661 CTTGGGCAAGCCAAGTTTTGA 59.861 47.619 13.87 0.0 39.58 2.69 F
1511 1694 0.475632 TCCCCTTCTTCCTTCCTGCA 60.476 55.000 0.00 0.0 0.00 4.41 F
1902 2085 2.074547 TTGACGGGAGAAAGCTAACG 57.925 50.000 0.00 0.0 0.00 3.18 F
2025 2208 2.254546 TGCTTGTCTTGGACGATGTT 57.745 45.000 0.00 0.0 34.95 2.71 F
3608 3791 2.217750 TGAGGTGACACAAATTGGACG 58.782 47.619 8.08 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 1774 0.620556 ATCTGGAGCCCAATCGTGTT 59.379 50.000 0.00 0.0 30.8 3.32 R
2688 2871 0.104855 TCCCATCCTCAAATCGCTCG 59.895 55.000 0.00 0.0 0.0 5.03 R
3608 3791 0.951040 CCCAAGTCCTGTGAACTCGC 60.951 60.000 0.00 0.0 0.0 5.03 R
3756 3939 2.716969 AGGGGGTAACTTCTTCAGCTTT 59.283 45.455 0.00 0.0 0.0 3.51 R
5416 5599 0.617249 AGGGAGGAGAAGGCTGTCTG 60.617 60.000 4.31 0.0 0.0 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 75 9.965824 AAATCAAACAACAAAGTTCTGGTATAG 57.034 29.630 0.00 0.00 0.00 1.31
103 106 1.138661 CTTGGGCAAGCCAAGTTTTGA 59.861 47.619 13.87 0.00 39.58 2.69
301 320 8.938801 TTTATGTATATCCATGGCAGTCATTT 57.061 30.769 6.96 0.00 32.92 2.32
303 322 4.996758 TGTATATCCATGGCAGTCATTTCG 59.003 41.667 6.96 0.00 32.92 3.46
429 448 4.141981 TGACAACTGTGGAACGTACCTAAA 60.142 41.667 0.00 0.00 42.39 1.85
437 456 6.757237 TGTGGAACGTACCTAAACATTTAGA 58.243 36.000 12.09 0.00 40.56 2.10
450 469 8.743714 CCTAAACATTTAGAAAAAGATCCTGCT 58.256 33.333 12.09 0.00 42.05 4.24
552 571 7.331687 CCATGACACCAAATTTCTGTATTTTCC 59.668 37.037 0.00 0.00 0.00 3.13
577 596 7.916450 CCATTCTTGTGTTGCATTTTTGAAATT 59.084 29.630 0.00 0.00 0.00 1.82
605 625 5.530176 AACCAAAGAGGCCCTTAGAATTA 57.470 39.130 0.00 0.00 43.14 1.40
606 626 5.734031 ACCAAAGAGGCCCTTAGAATTAT 57.266 39.130 0.00 0.00 43.14 1.28
607 627 6.841781 ACCAAAGAGGCCCTTAGAATTATA 57.158 37.500 0.00 0.00 43.14 0.98
608 628 6.842676 ACCAAAGAGGCCCTTAGAATTATAG 58.157 40.000 0.00 0.00 43.14 1.31
719 743 5.298276 TGTGAAAGCCAAAAGTTAGGTACAG 59.702 40.000 0.00 0.00 0.00 2.74
721 745 3.502123 AGCCAAAAGTTAGGTACAGCA 57.498 42.857 0.00 0.00 0.00 4.41
907 936 5.594725 TGACTAGGCATAGTTAACCAGAGAG 59.405 44.000 13.02 0.00 42.46 3.20
1257 1440 2.158957 AGCACTTCTCGACCACTTCAAA 60.159 45.455 0.00 0.00 0.00 2.69
1511 1694 0.475632 TCCCCTTCTTCCTTCCTGCA 60.476 55.000 0.00 0.00 0.00 4.41
1591 1774 4.217334 TGGATAAAATTGCAAGAGAACGCA 59.783 37.500 4.94 0.00 36.05 5.24
1656 1839 2.997315 CCGGAGAGGCCACAGTCA 60.997 66.667 5.01 0.00 35.94 3.41
1902 2085 2.074547 TTGACGGGAGAAAGCTAACG 57.925 50.000 0.00 0.00 0.00 3.18
1965 2148 5.071653 TCCTAGCACCAACATGAATATGCTA 59.928 40.000 18.52 18.52 43.00 3.49
2025 2208 2.254546 TGCTTGTCTTGGACGATGTT 57.745 45.000 0.00 0.00 34.95 2.71
2109 2292 5.001232 GGAAGCAAGATAGTGGTTACAACA 58.999 41.667 0.00 0.00 39.25 3.33
2277 2460 4.218417 GGAAGGCAAATTGTGAAGAAGCTA 59.782 41.667 0.00 0.00 0.00 3.32
2561 2744 6.821388 TCAGGCAATCTAGAAAGAAGATACC 58.179 40.000 0.00 0.00 34.73 2.73
2581 2764 2.487934 CGGAGGATTCTGGTAATGCAG 58.512 52.381 0.00 0.00 0.00 4.41
3030 3213 7.452880 TGTCAAGCTCTATAACTTGCAAATT 57.547 32.000 0.00 0.00 42.41 1.82
3031 3214 8.560355 TGTCAAGCTCTATAACTTGCAAATTA 57.440 30.769 2.41 2.41 42.41 1.40
3377 3560 4.579869 TGCAAACTTACTCCTTCAGATCC 58.420 43.478 0.00 0.00 0.00 3.36
3378 3561 4.041567 TGCAAACTTACTCCTTCAGATCCA 59.958 41.667 0.00 0.00 0.00 3.41
3433 3616 6.877855 ACATATCGATCTCAAGGAATTGATGG 59.122 38.462 0.00 0.00 0.00 3.51
3471 3654 2.930562 AGGTTCCCGAGCTGGCTT 60.931 61.111 0.00 0.00 34.08 4.35
3504 3687 4.365514 TCTTCCTAATCTGCAAACCACA 57.634 40.909 0.00 0.00 0.00 4.17
3510 3693 5.822519 TCCTAATCTGCAAACCACACATATC 59.177 40.000 0.00 0.00 0.00 1.63
3608 3791 2.217750 TGAGGTGACACAAATTGGACG 58.782 47.619 8.08 0.00 0.00 4.79
3756 3939 2.225091 ACTTGGTCTCATCAATTGCCCA 60.225 45.455 0.00 0.00 0.00 5.36
4162 4345 5.810080 ACTTCTAGATGGCCTACAATACC 57.190 43.478 3.32 0.00 0.00 2.73
4163 4346 5.468658 ACTTCTAGATGGCCTACAATACCT 58.531 41.667 3.32 0.00 0.00 3.08
4189 4372 5.344128 CCTCGTCTCAAGCATTTTCAAATTG 59.656 40.000 0.00 0.00 0.00 2.32
4269 4452 5.305644 ACCTCACACACTTCAGTTCTTAGAT 59.694 40.000 0.00 0.00 0.00 1.98
4579 4762 9.428097 TGACATTGATACTGCAATCATATACTC 57.572 33.333 1.98 0.00 36.39 2.59
4580 4763 8.783833 ACATTGATACTGCAATCATATACTCC 57.216 34.615 1.98 0.00 36.39 3.85
4582 4765 7.559335 TTGATACTGCAATCATATACTCCCT 57.441 36.000 1.98 0.00 35.84 4.20
4583 4766 7.175347 TGATACTGCAATCATATACTCCCTC 57.825 40.000 0.00 0.00 30.92 4.30
4585 4768 3.259374 ACTGCAATCATATACTCCCTCCG 59.741 47.826 0.00 0.00 0.00 4.63
4586 4769 3.239449 TGCAATCATATACTCCCTCCGT 58.761 45.455 0.00 0.00 0.00 4.69
4587 4770 3.258372 TGCAATCATATACTCCCTCCGTC 59.742 47.826 0.00 0.00 0.00 4.79
4588 4771 3.368531 GCAATCATATACTCCCTCCGTCC 60.369 52.174 0.00 0.00 0.00 4.79
4589 4772 2.599408 TCATATACTCCCTCCGTCCC 57.401 55.000 0.00 0.00 0.00 4.46
4590 4773 1.784593 TCATATACTCCCTCCGTCCCA 59.215 52.381 0.00 0.00 0.00 4.37
4591 4774 2.178325 TCATATACTCCCTCCGTCCCAA 59.822 50.000 0.00 0.00 0.00 4.12
4592 4775 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
4593 4776 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
4594 4777 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4595 4778 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
4596 4779 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
4597 4780 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
4598 4781 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
4599 4782 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
4600 4783 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
4601 4784 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
4602 4785 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
4603 4786 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
4604 4787 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
4605 4788 3.684788 CCGTCCCAAAATAAGTGTCTCAG 59.315 47.826 0.00 0.00 0.00 3.35
4606 4789 3.125316 CGTCCCAAAATAAGTGTCTCAGC 59.875 47.826 0.00 0.00 0.00 4.26
4607 4790 4.327680 GTCCCAAAATAAGTGTCTCAGCT 58.672 43.478 0.00 0.00 0.00 4.24
4608 4791 4.762251 GTCCCAAAATAAGTGTCTCAGCTT 59.238 41.667 0.00 0.00 0.00 3.74
4609 4792 5.241728 GTCCCAAAATAAGTGTCTCAGCTTT 59.758 40.000 0.00 0.00 0.00 3.51
4610 4793 5.241506 TCCCAAAATAAGTGTCTCAGCTTTG 59.758 40.000 0.00 0.00 0.00 2.77
4611 4794 5.010012 CCCAAAATAAGTGTCTCAGCTTTGT 59.990 40.000 0.00 0.00 0.00 2.83
4612 4795 6.206634 CCCAAAATAAGTGTCTCAGCTTTGTA 59.793 38.462 0.00 0.00 0.00 2.41
4613 4796 7.078228 CCAAAATAAGTGTCTCAGCTTTGTAC 58.922 38.462 0.00 0.00 0.00 2.90
4614 4797 7.041098 CCAAAATAAGTGTCTCAGCTTTGTACT 60.041 37.037 0.00 0.00 0.00 2.73
4615 4798 8.988934 CAAAATAAGTGTCTCAGCTTTGTACTA 58.011 33.333 0.00 0.00 0.00 1.82
4616 4799 8.764524 AAATAAGTGTCTCAGCTTTGTACTAG 57.235 34.615 0.00 0.00 0.00 2.57
4617 4800 4.181309 AGTGTCTCAGCTTTGTACTAGC 57.819 45.455 11.22 11.22 38.93 3.42
4619 4802 4.282195 AGTGTCTCAGCTTTGTACTAGCTT 59.718 41.667 17.03 2.77 46.42 3.74
4620 4803 4.991687 GTGTCTCAGCTTTGTACTAGCTTT 59.008 41.667 17.03 0.00 46.42 3.51
4621 4804 6.015350 AGTGTCTCAGCTTTGTACTAGCTTTA 60.015 38.462 17.03 9.82 46.42 1.85
4622 4805 6.309251 GTGTCTCAGCTTTGTACTAGCTTTAG 59.691 42.308 17.03 16.36 46.42 1.85
4623 4806 6.015350 TGTCTCAGCTTTGTACTAGCTTTAGT 60.015 38.462 17.03 0.00 46.42 2.24
4624 4807 7.176165 TGTCTCAGCTTTGTACTAGCTTTAGTA 59.824 37.037 17.03 0.00 46.42 1.82
4625 4808 7.485595 GTCTCAGCTTTGTACTAGCTTTAGTAC 59.514 40.741 16.70 16.70 46.42 2.73
4647 4830 5.831997 ACAAAATTGTACCAAGCTTGAGAC 58.168 37.500 28.05 22.47 40.16 3.36
4648 4831 5.359576 ACAAAATTGTACCAAGCTTGAGACA 59.640 36.000 28.05 24.59 40.16 3.41
4649 4832 6.040842 ACAAAATTGTACCAAGCTTGAGACAT 59.959 34.615 28.05 13.13 40.16 3.06
4650 4833 6.655078 AAATTGTACCAAGCTTGAGACATT 57.345 33.333 28.05 20.64 0.00 2.71
4651 4834 6.655078 AATTGTACCAAGCTTGAGACATTT 57.345 33.333 28.05 24.18 0.00 2.32
4652 4835 7.759489 AATTGTACCAAGCTTGAGACATTTA 57.241 32.000 28.05 14.97 0.00 1.40
4653 4836 7.944729 ATTGTACCAAGCTTGAGACATTTAT 57.055 32.000 28.05 16.34 0.00 1.40
4654 4837 7.759489 TTGTACCAAGCTTGAGACATTTATT 57.241 32.000 28.05 2.47 0.00 1.40
4655 4838 7.759489 TGTACCAAGCTTGAGACATTTATTT 57.241 32.000 28.05 1.82 0.00 1.40
4656 4839 8.177119 TGTACCAAGCTTGAGACATTTATTTT 57.823 30.769 28.05 1.17 0.00 1.82
4657 4840 8.081633 TGTACCAAGCTTGAGACATTTATTTTG 58.918 33.333 28.05 7.94 0.00 2.44
4658 4841 6.458210 ACCAAGCTTGAGACATTTATTTTGG 58.542 36.000 28.05 8.20 37.83 3.28
4659 4842 5.870978 CCAAGCTTGAGACATTTATTTTGGG 59.129 40.000 28.05 0.30 0.00 4.12
4660 4843 5.077134 AGCTTGAGACATTTATTTTGGGC 57.923 39.130 0.00 0.00 0.00 5.36
4661 4844 3.859386 GCTTGAGACATTTATTTTGGGCG 59.141 43.478 0.00 0.00 0.00 6.13
4662 4845 4.423732 CTTGAGACATTTATTTTGGGCGG 58.576 43.478 0.00 0.00 0.00 6.13
4663 4846 3.691575 TGAGACATTTATTTTGGGCGGA 58.308 40.909 0.00 0.00 0.00 5.54
4664 4847 3.694072 TGAGACATTTATTTTGGGCGGAG 59.306 43.478 0.00 0.00 0.00 4.63
4665 4848 3.023832 AGACATTTATTTTGGGCGGAGG 58.976 45.455 0.00 0.00 0.00 4.30
4666 4849 2.100749 GACATTTATTTTGGGCGGAGGG 59.899 50.000 0.00 0.00 0.00 4.30
4667 4850 2.291930 ACATTTATTTTGGGCGGAGGGA 60.292 45.455 0.00 0.00 0.00 4.20
4668 4851 2.137810 TTTATTTTGGGCGGAGGGAG 57.862 50.000 0.00 0.00 0.00 4.30
4669 4852 0.996583 TTATTTTGGGCGGAGGGAGT 59.003 50.000 0.00 0.00 0.00 3.85
4670 4853 1.882308 TATTTTGGGCGGAGGGAGTA 58.118 50.000 0.00 0.00 0.00 2.59
4671 4854 1.222567 ATTTTGGGCGGAGGGAGTAT 58.777 50.000 0.00 0.00 0.00 2.12
4672 4855 1.882308 TTTTGGGCGGAGGGAGTATA 58.118 50.000 0.00 0.00 0.00 1.47
4673 4856 2.112279 TTTGGGCGGAGGGAGTATAT 57.888 50.000 0.00 0.00 0.00 0.86
4674 4857 3.263369 TTTGGGCGGAGGGAGTATATA 57.737 47.619 0.00 0.00 0.00 0.86
4675 4858 3.484953 TTGGGCGGAGGGAGTATATAT 57.515 47.619 0.00 0.00 0.00 0.86
4901 5084 7.811713 AGTTCTTTTGATAAATCTCTTTGCAGC 59.188 33.333 0.00 0.00 0.00 5.25
5044 5227 9.339850 ACAGATCTAATAGTGTAATCGTGTACT 57.660 33.333 0.00 0.00 0.00 2.73
5073 5256 4.864916 CACCATGAGTGTAATAGTGCAC 57.135 45.455 9.40 9.40 41.93 4.57
5086 5269 8.714179 GTGTAATAGTGCACTAAAATGTACACA 58.286 33.333 32.10 23.54 37.63 3.72
5087 5270 9.443323 TGTAATAGTGCACTAAAATGTACACAT 57.557 29.630 29.26 7.56 37.63 3.21
5088 5271 9.702726 GTAATAGTGCACTAAAATGTACACATG 57.297 33.333 29.26 0.00 37.63 3.21
5089 5272 5.046910 AGTGCACTAAAATGTACACATGC 57.953 39.130 20.16 2.91 37.63 4.06
5090 5273 4.761739 AGTGCACTAAAATGTACACATGCT 59.238 37.500 20.16 0.00 37.63 3.79
5091 5274 4.853196 GTGCACTAAAATGTACACATGCTG 59.147 41.667 10.32 0.00 35.08 4.41
5092 5275 4.759183 TGCACTAAAATGTACACATGCTGA 59.241 37.500 0.00 0.00 36.56 4.26
5093 5276 5.240403 TGCACTAAAATGTACACATGCTGAA 59.760 36.000 0.00 0.00 36.56 3.02
5094 5277 6.072008 TGCACTAAAATGTACACATGCTGAAT 60.072 34.615 0.00 0.00 36.56 2.57
5095 5278 7.120432 TGCACTAAAATGTACACATGCTGAATA 59.880 33.333 0.00 0.00 36.56 1.75
5096 5279 7.429340 GCACTAAAATGTACACATGCTGAATAC 59.571 37.037 0.00 0.00 36.56 1.89
5097 5280 8.668353 CACTAAAATGTACACATGCTGAATACT 58.332 33.333 0.00 0.00 36.56 2.12
5098 5281 8.883731 ACTAAAATGTACACATGCTGAATACTC 58.116 33.333 0.00 0.00 36.56 2.59
5099 5282 7.686438 AAAATGTACACATGCTGAATACTCA 57.314 32.000 0.00 0.00 36.56 3.41
5100 5283 6.668541 AATGTACACATGCTGAATACTCAC 57.331 37.500 0.00 0.00 36.56 3.51
5101 5284 5.146010 TGTACACATGCTGAATACTCACA 57.854 39.130 0.00 0.00 0.00 3.58
5102 5285 4.929211 TGTACACATGCTGAATACTCACAC 59.071 41.667 0.00 0.00 0.00 3.82
5103 5286 4.277515 ACACATGCTGAATACTCACACT 57.722 40.909 0.00 0.00 0.00 3.55
5104 5287 4.645535 ACACATGCTGAATACTCACACTT 58.354 39.130 0.00 0.00 0.00 3.16
5105 5288 4.453478 ACACATGCTGAATACTCACACTTG 59.547 41.667 0.00 0.00 0.00 3.16
5106 5289 4.453478 CACATGCTGAATACTCACACTTGT 59.547 41.667 0.00 0.00 0.00 3.16
5107 5290 5.639082 CACATGCTGAATACTCACACTTGTA 59.361 40.000 0.00 0.00 0.00 2.41
5108 5291 5.639506 ACATGCTGAATACTCACACTTGTAC 59.360 40.000 0.00 0.00 0.00 2.90
5109 5292 5.468540 TGCTGAATACTCACACTTGTACT 57.531 39.130 0.00 0.00 0.00 2.73
5110 5293 5.853936 TGCTGAATACTCACACTTGTACTT 58.146 37.500 0.00 0.00 0.00 2.24
5111 5294 6.988522 TGCTGAATACTCACACTTGTACTTA 58.011 36.000 0.00 0.00 0.00 2.24
5112 5295 7.611770 TGCTGAATACTCACACTTGTACTTAT 58.388 34.615 0.00 0.00 0.00 1.73
5113 5296 7.759886 TGCTGAATACTCACACTTGTACTTATC 59.240 37.037 0.00 0.00 0.00 1.75
5114 5297 7.759886 GCTGAATACTCACACTTGTACTTATCA 59.240 37.037 0.00 0.00 0.00 2.15
5115 5298 9.295214 CTGAATACTCACACTTGTACTTATCAG 57.705 37.037 0.00 0.00 0.00 2.90
5116 5299 7.759886 TGAATACTCACACTTGTACTTATCAGC 59.240 37.037 0.00 0.00 0.00 4.26
5117 5300 5.730296 ACTCACACTTGTACTTATCAGCT 57.270 39.130 0.00 0.00 0.00 4.24
5118 5301 6.835819 ACTCACACTTGTACTTATCAGCTA 57.164 37.500 0.00 0.00 0.00 3.32
5119 5302 7.411486 ACTCACACTTGTACTTATCAGCTAT 57.589 36.000 0.00 0.00 0.00 2.97
5120 5303 7.484975 ACTCACACTTGTACTTATCAGCTATC 58.515 38.462 0.00 0.00 0.00 2.08
5121 5304 7.340743 ACTCACACTTGTACTTATCAGCTATCT 59.659 37.037 0.00 0.00 0.00 1.98
5122 5305 7.484140 TCACACTTGTACTTATCAGCTATCTG 58.516 38.462 0.00 0.00 41.67 2.90
5123 5306 6.699204 CACACTTGTACTTATCAGCTATCTGG 59.301 42.308 0.00 0.00 40.69 3.86
5124 5307 6.183360 ACACTTGTACTTATCAGCTATCTGGG 60.183 42.308 0.00 0.00 40.69 4.45
5125 5308 5.900123 ACTTGTACTTATCAGCTATCTGGGT 59.100 40.000 0.00 0.00 40.69 4.51
5126 5309 6.384305 ACTTGTACTTATCAGCTATCTGGGTT 59.616 38.462 0.00 0.00 40.69 4.11
5127 5310 7.563924 ACTTGTACTTATCAGCTATCTGGGTTA 59.436 37.037 0.00 0.00 40.69 2.85
5128 5311 7.907841 TGTACTTATCAGCTATCTGGGTTAA 57.092 36.000 0.00 0.00 40.69 2.01
5129 5312 7.723324 TGTACTTATCAGCTATCTGGGTTAAC 58.277 38.462 0.00 0.00 40.69 2.01
5130 5313 7.563924 TGTACTTATCAGCTATCTGGGTTAACT 59.436 37.037 5.42 0.00 40.69 2.24
5131 5314 6.821388 ACTTATCAGCTATCTGGGTTAACTG 58.179 40.000 5.42 0.00 40.69 3.16
5132 5315 6.611642 ACTTATCAGCTATCTGGGTTAACTGA 59.388 38.462 5.42 2.58 40.69 3.41
5133 5316 5.543507 ATCAGCTATCTGGGTTAACTGAG 57.456 43.478 5.42 2.05 40.69 3.35
5134 5317 3.706594 TCAGCTATCTGGGTTAACTGAGG 59.293 47.826 5.42 1.79 40.69 3.86
5135 5318 3.452627 CAGCTATCTGGGTTAACTGAGGT 59.547 47.826 5.42 0.80 36.68 3.85
5136 5319 4.080863 CAGCTATCTGGGTTAACTGAGGTT 60.081 45.833 5.42 0.00 36.68 3.50
5137 5320 4.080863 AGCTATCTGGGTTAACTGAGGTTG 60.081 45.833 5.42 0.92 36.92 3.77
5138 5321 2.561478 TCTGGGTTAACTGAGGTTGC 57.439 50.000 5.42 0.00 36.92 4.17
5139 5322 1.771854 TCTGGGTTAACTGAGGTTGCA 59.228 47.619 5.42 0.00 36.92 4.08
5140 5323 2.375174 TCTGGGTTAACTGAGGTTGCAT 59.625 45.455 5.42 0.00 36.92 3.96
5141 5324 2.489329 CTGGGTTAACTGAGGTTGCATG 59.511 50.000 5.42 0.00 36.92 4.06
5142 5325 1.818674 GGGTTAACTGAGGTTGCATGG 59.181 52.381 5.42 0.00 36.92 3.66
5143 5326 1.818674 GGTTAACTGAGGTTGCATGGG 59.181 52.381 5.42 0.00 36.92 4.00
5144 5327 2.554344 GGTTAACTGAGGTTGCATGGGA 60.554 50.000 5.42 0.00 36.92 4.37
5145 5328 2.749621 GTTAACTGAGGTTGCATGGGAG 59.250 50.000 0.00 0.00 36.92 4.30
5146 5329 1.067295 AACTGAGGTTGCATGGGAGA 58.933 50.000 0.00 0.00 33.96 3.71
5147 5330 1.067295 ACTGAGGTTGCATGGGAGAA 58.933 50.000 0.00 0.00 0.00 2.87
5148 5331 1.637553 ACTGAGGTTGCATGGGAGAAT 59.362 47.619 0.00 0.00 0.00 2.40
5149 5332 2.042162 ACTGAGGTTGCATGGGAGAATT 59.958 45.455 0.00 0.00 0.00 2.17
5150 5333 2.686915 CTGAGGTTGCATGGGAGAATTC 59.313 50.000 0.00 0.00 0.00 2.17
5151 5334 2.309755 TGAGGTTGCATGGGAGAATTCT 59.690 45.455 7.95 7.95 0.00 2.40
5152 5335 3.523157 TGAGGTTGCATGGGAGAATTCTA 59.477 43.478 8.25 0.00 0.00 2.10
5153 5336 4.018506 TGAGGTTGCATGGGAGAATTCTAA 60.019 41.667 8.25 0.00 0.00 2.10
5154 5337 4.530875 AGGTTGCATGGGAGAATTCTAAG 58.469 43.478 8.25 0.00 0.00 2.18
5155 5338 4.018050 AGGTTGCATGGGAGAATTCTAAGT 60.018 41.667 8.25 0.00 0.00 2.24
5156 5339 5.191722 AGGTTGCATGGGAGAATTCTAAGTA 59.808 40.000 8.25 0.00 0.00 2.24
5157 5340 5.297029 GGTTGCATGGGAGAATTCTAAGTAC 59.703 44.000 8.25 0.00 0.00 2.73
5158 5341 4.693283 TGCATGGGAGAATTCTAAGTACG 58.307 43.478 8.25 0.00 0.00 3.67
5159 5342 4.058817 GCATGGGAGAATTCTAAGTACGG 58.941 47.826 8.25 0.00 0.00 4.02
5160 5343 4.443034 GCATGGGAGAATTCTAAGTACGGT 60.443 45.833 8.25 0.00 0.00 4.83
5161 5344 5.671493 CATGGGAGAATTCTAAGTACGGTT 58.329 41.667 8.25 0.00 0.00 4.44
5162 5345 5.080969 TGGGAGAATTCTAAGTACGGTTG 57.919 43.478 8.25 0.00 0.00 3.77
5163 5346 4.773674 TGGGAGAATTCTAAGTACGGTTGA 59.226 41.667 8.25 0.00 0.00 3.18
5164 5347 5.424252 TGGGAGAATTCTAAGTACGGTTGAT 59.576 40.000 8.25 0.00 0.00 2.57
5165 5348 6.608405 TGGGAGAATTCTAAGTACGGTTGATA 59.392 38.462 8.25 0.00 0.00 2.15
5166 5349 7.124599 TGGGAGAATTCTAAGTACGGTTGATAA 59.875 37.037 8.25 0.00 0.00 1.75
5167 5350 7.437565 GGGAGAATTCTAAGTACGGTTGATAAC 59.562 40.741 8.25 0.00 0.00 1.89
5184 5367 8.742554 GTTGATAACCAGTCAATTTGTAAAGG 57.257 34.615 0.00 0.00 37.84 3.11
5185 5368 8.357402 GTTGATAACCAGTCAATTTGTAAAGGT 58.643 33.333 0.00 0.00 37.84 3.50
5186 5369 8.106247 TGATAACCAGTCAATTTGTAAAGGTC 57.894 34.615 0.00 0.00 0.00 3.85
5187 5370 7.721842 TGATAACCAGTCAATTTGTAAAGGTCA 59.278 33.333 0.00 0.00 0.00 4.02
5188 5371 6.976934 AACCAGTCAATTTGTAAAGGTCAT 57.023 33.333 0.00 0.00 0.00 3.06
5189 5372 6.575162 ACCAGTCAATTTGTAAAGGTCATC 57.425 37.500 0.00 0.00 0.00 2.92
5190 5373 6.068010 ACCAGTCAATTTGTAAAGGTCATCA 58.932 36.000 0.00 0.00 0.00 3.07
5191 5374 6.207417 ACCAGTCAATTTGTAAAGGTCATCAG 59.793 38.462 0.00 0.00 0.00 2.90
5192 5375 6.088824 CAGTCAATTTGTAAAGGTCATCAGC 58.911 40.000 0.00 0.00 0.00 4.26
5193 5376 5.088739 GTCAATTTGTAAAGGTCATCAGCG 58.911 41.667 0.00 0.00 0.00 5.18
5194 5377 4.155826 TCAATTTGTAAAGGTCATCAGCGG 59.844 41.667 0.00 0.00 0.00 5.52
5195 5378 3.410631 TTTGTAAAGGTCATCAGCGGA 57.589 42.857 0.00 0.00 0.00 5.54
5196 5379 3.627395 TTGTAAAGGTCATCAGCGGAT 57.373 42.857 0.00 0.00 0.00 4.18
5221 5404 4.400961 GCTCCAGCAGGCGTTCCT 62.401 66.667 0.00 0.00 45.66 3.36
5319 5502 3.342477 GGCCTCCCCTGCCTCTTT 61.342 66.667 0.00 0.00 45.70 2.52
5320 5503 2.273776 GCCTCCCCTGCCTCTTTC 59.726 66.667 0.00 0.00 0.00 2.62
5321 5504 2.586792 CCTCCCCTGCCTCTTTCG 59.413 66.667 0.00 0.00 0.00 3.46
5322 5505 2.124942 CTCCCCTGCCTCTTTCGC 60.125 66.667 0.00 0.00 0.00 4.70
5323 5506 4.082523 TCCCCTGCCTCTTTCGCG 62.083 66.667 0.00 0.00 0.00 5.87
5324 5507 4.394712 CCCCTGCCTCTTTCGCGT 62.395 66.667 5.77 0.00 0.00 6.01
5325 5508 2.815647 CCCTGCCTCTTTCGCGTC 60.816 66.667 5.77 0.00 0.00 5.19
5326 5509 3.181967 CCTGCCTCTTTCGCGTCG 61.182 66.667 5.77 0.00 0.00 5.12
5327 5510 2.430921 CTGCCTCTTTCGCGTCGT 60.431 61.111 5.77 0.00 0.00 4.34
5328 5511 2.430244 TGCCTCTTTCGCGTCGTC 60.430 61.111 5.77 0.00 0.00 4.20
5329 5512 3.533691 GCCTCTTTCGCGTCGTCG 61.534 66.667 5.77 0.00 40.37 5.12
5330 5513 2.874780 CCTCTTTCGCGTCGTCGG 60.875 66.667 5.77 0.00 37.56 4.79
5331 5514 2.175078 CTCTTTCGCGTCGTCGGA 59.825 61.111 5.77 0.00 37.56 4.55
5332 5515 1.863880 CTCTTTCGCGTCGTCGGAG 60.864 63.158 5.77 3.15 37.56 4.63
5333 5516 3.533691 CTTTCGCGTCGTCGGAGC 61.534 66.667 5.77 0.00 37.56 4.70
5339 5522 4.099170 CGTCGTCGGAGCGGTTCT 62.099 66.667 0.00 0.00 0.00 3.01
5340 5523 2.202453 GTCGTCGGAGCGGTTCTC 60.202 66.667 0.00 0.00 41.15 2.87
5347 5530 4.475135 GAGCGGTTCTCCTGGGCC 62.475 72.222 0.00 0.00 35.77 5.80
5350 5533 4.452733 CGGTTCTCCTGGGCCGAC 62.453 72.222 12.17 0.00 46.33 4.79
5351 5534 3.003763 GGTTCTCCTGGGCCGACT 61.004 66.667 0.00 0.00 0.00 4.18
5352 5535 2.266055 GTTCTCCTGGGCCGACTG 59.734 66.667 0.00 0.00 0.00 3.51
5353 5536 3.706373 TTCTCCTGGGCCGACTGC 61.706 66.667 0.00 0.00 40.16 4.40
5376 5559 3.664869 AGGATCCTCCTTTCCCTCC 57.335 57.895 9.02 0.00 46.91 4.30
5377 5560 0.399233 AGGATCCTCCTTTCCCTCCG 60.399 60.000 9.02 0.00 46.91 4.63
5378 5561 1.448069 GATCCTCCTTTCCCTCCGC 59.552 63.158 0.00 0.00 0.00 5.54
5379 5562 2.046009 GATCCTCCTTTCCCTCCGCC 62.046 65.000 0.00 0.00 0.00 6.13
5380 5563 3.798511 CCTCCTTTCCCTCCGCCC 61.799 72.222 0.00 0.00 0.00 6.13
5381 5564 4.162690 CTCCTTTCCCTCCGCCCG 62.163 72.222 0.00 0.00 0.00 6.13
5432 5615 4.930592 GCAGACAGCCTTCTCCTC 57.069 61.111 0.00 0.00 37.23 3.71
5433 5616 1.220477 GCAGACAGCCTTCTCCTCC 59.780 63.158 0.00 0.00 37.23 4.30
5434 5617 1.904032 CAGACAGCCTTCTCCTCCC 59.096 63.158 0.00 0.00 0.00 4.30
5435 5618 0.617249 CAGACAGCCTTCTCCTCCCT 60.617 60.000 0.00 0.00 0.00 4.20
5436 5619 0.617249 AGACAGCCTTCTCCTCCCTG 60.617 60.000 0.00 0.00 0.00 4.45
5437 5620 2.250741 GACAGCCTTCTCCTCCCTGC 62.251 65.000 0.00 0.00 0.00 4.85
5438 5621 2.690510 AGCCTTCTCCTCCCTGCC 60.691 66.667 0.00 0.00 0.00 4.85
5439 5622 4.168291 GCCTTCTCCTCCCTGCCG 62.168 72.222 0.00 0.00 0.00 5.69
5440 5623 3.474570 CCTTCTCCTCCCTGCCGG 61.475 72.222 0.00 0.00 0.00 6.13
5441 5624 4.168291 CTTCTCCTCCCTGCCGGC 62.168 72.222 22.73 22.73 0.00 6.13
5476 5659 4.003788 CACGTGAGGGGTTCGGCT 62.004 66.667 10.90 0.00 0.00 5.52
5477 5660 3.692406 ACGTGAGGGGTTCGGCTC 61.692 66.667 0.00 0.00 0.00 4.70
5478 5661 4.452733 CGTGAGGGGTTCGGCTCC 62.453 72.222 0.00 0.00 38.29 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 75 2.032178 GCTTGCCCAAGATACGATTCAC 59.968 50.000 11.96 0.00 40.79 3.18
103 106 3.134574 TCAAGCCCAAGTTTACGTCAT 57.865 42.857 0.00 0.00 0.00 3.06
129 133 0.321653 CTGGAGGTGTTAGGGTGTGC 60.322 60.000 0.00 0.00 0.00 4.57
301 320 6.869913 AGTTGTAGATCCGATTTGTTTAACGA 59.130 34.615 0.00 0.00 0.00 3.85
303 322 9.968743 CTTAGTTGTAGATCCGATTTGTTTAAC 57.031 33.333 0.00 0.00 0.00 2.01
429 448 8.090831 GGAAAAGCAGGATCTTTTTCTAAATGT 58.909 33.333 16.81 0.00 43.86 2.71
437 456 5.105187 GCCATAGGAAAAGCAGGATCTTTTT 60.105 40.000 3.43 0.00 43.86 1.94
552 571 8.844441 AATTTCAAAAATGCAACACAAGAATG 57.156 26.923 0.00 0.00 0.00 2.67
577 596 1.460273 GGGCCTCTTTGGTTTGCGAA 61.460 55.000 0.84 0.00 38.35 4.70
605 625 6.942532 TGAAAAACAAGTGAGCAGTTCTAT 57.057 33.333 0.00 0.00 0.00 1.98
606 626 6.942532 ATGAAAAACAAGTGAGCAGTTCTA 57.057 33.333 0.00 0.00 0.00 2.10
607 627 5.841957 ATGAAAAACAAGTGAGCAGTTCT 57.158 34.783 0.00 0.00 0.00 3.01
608 628 6.892310 AAATGAAAAACAAGTGAGCAGTTC 57.108 33.333 0.00 0.00 0.00 3.01
719 743 1.133823 TGGATGGTGGATGGTGTATGC 60.134 52.381 0.00 0.00 0.00 3.14
721 745 1.494721 GGTGGATGGTGGATGGTGTAT 59.505 52.381 0.00 0.00 0.00 2.29
907 936 2.187351 TTGAACTTTGCAAGCGTGTC 57.813 45.000 0.00 3.47 0.00 3.67
1276 1459 1.613035 AGAGGCTCTCCAGCTTGCT 60.613 57.895 12.24 0.00 46.03 3.91
1341 1524 3.360340 GCGTCTGCCAGCTGCTTT 61.360 61.111 8.66 0.00 42.00 3.51
1591 1774 0.620556 ATCTGGAGCCCAATCGTGTT 59.379 50.000 0.00 0.00 30.80 3.32
1656 1839 4.622695 GCTGAACTATCCACAAGAGAGCTT 60.623 45.833 0.00 0.00 37.33 3.74
2025 2208 8.000709 AGCCATTTATCATAGTCTTCATTCCAA 58.999 33.333 0.00 0.00 0.00 3.53
2109 2292 1.200716 CTGCCAACATTCTCATTGCGT 59.799 47.619 0.00 0.00 0.00 5.24
2277 2460 4.645809 GCGAGAGGCAATCCCTTT 57.354 55.556 0.00 0.00 46.60 3.11
2561 2744 2.103094 TCTGCATTACCAGAATCCTCCG 59.897 50.000 0.00 0.00 38.81 4.63
2688 2871 0.104855 TCCCATCCTCAAATCGCTCG 59.895 55.000 0.00 0.00 0.00 5.03
2716 2899 3.829601 TGACGGGTCTTTATGGCATTTTT 59.170 39.130 4.78 0.00 0.00 1.94
2718 2901 3.080300 TGACGGGTCTTTATGGCATTT 57.920 42.857 4.78 0.00 0.00 2.32
3128 3311 6.796785 AATTTCCAATTCCTGGTATCCTTG 57.203 37.500 0.00 0.00 46.51 3.61
3208 3391 6.650807 TGATCCATGTTTCTTAACTCTGTGAC 59.349 38.462 0.00 0.00 35.24 3.67
3377 3560 2.802816 CCTTCCAGAACTTCGTCTTGTG 59.197 50.000 0.00 0.00 0.00 3.33
3378 3561 2.807108 GCCTTCCAGAACTTCGTCTTGT 60.807 50.000 0.00 0.00 0.00 3.16
3433 3616 1.271379 CGCCCCTGGAAAACCTTTAAC 59.729 52.381 0.00 0.00 0.00 2.01
3471 3654 6.540189 GCAGATTAGGAAGAAATGAAGTAGCA 59.460 38.462 0.00 0.00 0.00 3.49
3608 3791 0.951040 CCCAAGTCCTGTGAACTCGC 60.951 60.000 0.00 0.00 0.00 5.03
3700 3883 4.164796 AGGGAACAACTGATCAGCATCATA 59.835 41.667 22.83 0.00 38.42 2.15
3756 3939 2.716969 AGGGGGTAACTTCTTCAGCTTT 59.283 45.455 0.00 0.00 0.00 3.51
4162 4345 3.748048 TGAAAATGCTTGAGACGAGGAAG 59.252 43.478 0.00 0.00 0.00 3.46
4163 4346 3.738982 TGAAAATGCTTGAGACGAGGAA 58.261 40.909 0.00 0.00 0.00 3.36
4189 4372 3.077359 AGTCAGCAATTTGGTAGTCAGC 58.923 45.455 0.00 0.00 0.00 4.26
4577 4760 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
4579 4762 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
4580 4763 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4582 4765 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
4583 4766 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
4585 4768 4.327680 AGCTGAGACACTTATTTTGGGAC 58.672 43.478 0.00 0.00 0.00 4.46
4586 4769 4.640771 AGCTGAGACACTTATTTTGGGA 57.359 40.909 0.00 0.00 0.00 4.37
4587 4770 5.010012 ACAAAGCTGAGACACTTATTTTGGG 59.990 40.000 0.00 0.00 0.00 4.12
4588 4771 6.076981 ACAAAGCTGAGACACTTATTTTGG 57.923 37.500 0.00 0.00 0.00 3.28
4589 4772 7.865707 AGTACAAAGCTGAGACACTTATTTTG 58.134 34.615 0.00 0.00 0.00 2.44
4590 4773 9.209175 CTAGTACAAAGCTGAGACACTTATTTT 57.791 33.333 0.00 0.00 0.00 1.82
4591 4774 7.332182 GCTAGTACAAAGCTGAGACACTTATTT 59.668 37.037 11.77 0.00 37.01 1.40
4592 4775 6.814146 GCTAGTACAAAGCTGAGACACTTATT 59.186 38.462 11.77 0.00 37.01 1.40
4593 4776 6.334202 GCTAGTACAAAGCTGAGACACTTAT 58.666 40.000 11.77 0.00 37.01 1.73
4594 4777 5.710984 GCTAGTACAAAGCTGAGACACTTA 58.289 41.667 11.77 0.00 37.01 2.24
4595 4778 4.561105 GCTAGTACAAAGCTGAGACACTT 58.439 43.478 11.77 0.00 37.01 3.16
4596 4779 4.181309 GCTAGTACAAAGCTGAGACACT 57.819 45.455 11.77 0.00 37.01 3.55
4631 4814 7.759489 AAATAAATGTCTCAAGCTTGGTACA 57.241 32.000 26.37 26.37 0.00 2.90
4632 4815 7.542130 CCAAAATAAATGTCTCAAGCTTGGTAC 59.458 37.037 25.73 21.97 0.00 3.34
4633 4816 7.309744 CCCAAAATAAATGTCTCAAGCTTGGTA 60.310 37.037 25.73 11.73 0.00 3.25
4634 4817 6.458210 CCAAAATAAATGTCTCAAGCTTGGT 58.542 36.000 25.73 5.16 0.00 3.67
4635 4818 5.870978 CCCAAAATAAATGTCTCAAGCTTGG 59.129 40.000 25.73 16.25 0.00 3.61
4636 4819 5.349543 GCCCAAAATAAATGTCTCAAGCTTG 59.650 40.000 20.81 20.81 0.00 4.01
4637 4820 5.482006 GCCCAAAATAAATGTCTCAAGCTT 58.518 37.500 0.00 0.00 0.00 3.74
4638 4821 4.380867 CGCCCAAAATAAATGTCTCAAGCT 60.381 41.667 0.00 0.00 0.00 3.74
4639 4822 3.859386 CGCCCAAAATAAATGTCTCAAGC 59.141 43.478 0.00 0.00 0.00 4.01
4640 4823 4.157656 TCCGCCCAAAATAAATGTCTCAAG 59.842 41.667 0.00 0.00 0.00 3.02
4641 4824 4.082845 TCCGCCCAAAATAAATGTCTCAA 58.917 39.130 0.00 0.00 0.00 3.02
4642 4825 3.691575 TCCGCCCAAAATAAATGTCTCA 58.308 40.909 0.00 0.00 0.00 3.27
4643 4826 3.066760 CCTCCGCCCAAAATAAATGTCTC 59.933 47.826 0.00 0.00 0.00 3.36
4644 4827 3.023832 CCTCCGCCCAAAATAAATGTCT 58.976 45.455 0.00 0.00 0.00 3.41
4645 4828 2.100749 CCCTCCGCCCAAAATAAATGTC 59.899 50.000 0.00 0.00 0.00 3.06
4646 4829 2.107366 CCCTCCGCCCAAAATAAATGT 58.893 47.619 0.00 0.00 0.00 2.71
4647 4830 2.362077 CTCCCTCCGCCCAAAATAAATG 59.638 50.000 0.00 0.00 0.00 2.32
4648 4831 2.024369 ACTCCCTCCGCCCAAAATAAAT 60.024 45.455 0.00 0.00 0.00 1.40
4649 4832 1.356398 ACTCCCTCCGCCCAAAATAAA 59.644 47.619 0.00 0.00 0.00 1.40
4650 4833 0.996583 ACTCCCTCCGCCCAAAATAA 59.003 50.000 0.00 0.00 0.00 1.40
4651 4834 1.882308 TACTCCCTCCGCCCAAAATA 58.118 50.000 0.00 0.00 0.00 1.40
4652 4835 1.222567 ATACTCCCTCCGCCCAAAAT 58.777 50.000 0.00 0.00 0.00 1.82
4653 4836 1.882308 TATACTCCCTCCGCCCAAAA 58.118 50.000 0.00 0.00 0.00 2.44
4654 4837 2.112279 ATATACTCCCTCCGCCCAAA 57.888 50.000 0.00 0.00 0.00 3.28
4655 4838 3.484953 ATATATACTCCCTCCGCCCAA 57.515 47.619 0.00 0.00 0.00 4.12
4656 4839 3.484953 AATATATACTCCCTCCGCCCA 57.515 47.619 0.00 0.00 0.00 5.36
4657 4840 4.383880 GGAAAATATATACTCCCTCCGCCC 60.384 50.000 2.73 0.00 0.00 6.13
4658 4841 4.224370 TGGAAAATATATACTCCCTCCGCC 59.776 45.833 9.49 0.00 0.00 6.13
4659 4842 5.416271 TGGAAAATATATACTCCCTCCGC 57.584 43.478 9.49 0.00 0.00 5.54
4826 5009 6.710744 TGATGGTCTAGTTTGTTTCTTTCCTC 59.289 38.462 0.00 0.00 0.00 3.71
4876 5059 7.811713 AGCTGCAAAGAGATTTATCAAAAGAAC 59.188 33.333 1.02 0.00 0.00 3.01
4941 5124 6.409704 TCTAGTACACTATTACACTCGTGGT 58.590 40.000 1.77 0.00 34.19 4.16
5052 5235 4.507710 AGTGCACTATTACACTCATGGTG 58.492 43.478 20.16 11.40 43.55 4.17
5053 5236 4.826274 AGTGCACTATTACACTCATGGT 57.174 40.909 20.16 0.00 43.55 3.55
5054 5237 7.609760 TTTTAGTGCACTATTACACTCATGG 57.390 36.000 26.54 0.00 43.55 3.66
5055 5238 8.668353 ACATTTTAGTGCACTATTACACTCATG 58.332 33.333 26.54 18.74 43.55 3.07
5056 5239 8.792830 ACATTTTAGTGCACTATTACACTCAT 57.207 30.769 26.54 7.82 43.55 2.90
5057 5240 9.146984 GTACATTTTAGTGCACTATTACACTCA 57.853 33.333 26.54 6.96 43.55 3.41
5058 5241 9.146984 TGTACATTTTAGTGCACTATTACACTC 57.853 33.333 26.54 15.20 43.55 3.51
5069 5252 4.759183 TCAGCATGTGTACATTTTAGTGCA 59.241 37.500 0.00 0.00 37.40 4.57
5070 5253 5.295431 TCAGCATGTGTACATTTTAGTGC 57.705 39.130 0.00 4.12 37.40 4.40
5071 5254 8.668353 AGTATTCAGCATGTGTACATTTTAGTG 58.332 33.333 0.00 0.00 37.40 2.74
5072 5255 8.792830 AGTATTCAGCATGTGTACATTTTAGT 57.207 30.769 0.00 0.00 37.40 2.24
5073 5256 8.882736 TGAGTATTCAGCATGTGTACATTTTAG 58.117 33.333 0.00 0.00 37.40 1.85
5074 5257 8.664798 GTGAGTATTCAGCATGTGTACATTTTA 58.335 33.333 0.00 0.00 37.40 1.52
5075 5258 7.174772 TGTGAGTATTCAGCATGTGTACATTTT 59.825 33.333 0.00 0.00 37.40 1.82
5076 5259 6.654582 TGTGAGTATTCAGCATGTGTACATTT 59.345 34.615 0.00 0.00 37.40 2.32
5077 5260 6.092670 GTGTGAGTATTCAGCATGTGTACATT 59.907 38.462 0.00 0.00 37.40 2.71
5078 5261 5.582269 GTGTGAGTATTCAGCATGTGTACAT 59.418 40.000 0.00 0.00 37.40 2.29
5079 5262 4.929211 GTGTGAGTATTCAGCATGTGTACA 59.071 41.667 0.00 0.00 37.40 2.90
5080 5263 5.171476 AGTGTGAGTATTCAGCATGTGTAC 58.829 41.667 0.00 0.00 37.40 2.90
5081 5264 5.405935 AGTGTGAGTATTCAGCATGTGTA 57.594 39.130 0.00 0.00 37.40 2.90
5082 5265 4.277515 AGTGTGAGTATTCAGCATGTGT 57.722 40.909 0.00 0.00 37.40 3.72
5083 5266 4.453478 ACAAGTGTGAGTATTCAGCATGTG 59.547 41.667 0.00 0.00 37.40 3.21
5084 5267 4.645535 ACAAGTGTGAGTATTCAGCATGT 58.354 39.130 0.00 0.00 37.40 3.21
5085 5268 5.871524 AGTACAAGTGTGAGTATTCAGCATG 59.128 40.000 0.00 0.00 32.98 4.06
5086 5269 6.042638 AGTACAAGTGTGAGTATTCAGCAT 57.957 37.500 0.00 0.00 32.98 3.79
5087 5270 5.468540 AGTACAAGTGTGAGTATTCAGCA 57.531 39.130 0.00 0.00 32.98 4.41
5088 5271 7.759886 TGATAAGTACAAGTGTGAGTATTCAGC 59.240 37.037 0.00 0.00 32.98 4.26
5089 5272 9.295214 CTGATAAGTACAAGTGTGAGTATTCAG 57.705 37.037 0.00 0.00 32.98 3.02
5090 5273 7.759886 GCTGATAAGTACAAGTGTGAGTATTCA 59.240 37.037 0.00 0.00 0.00 2.57
5091 5274 7.976734 AGCTGATAAGTACAAGTGTGAGTATTC 59.023 37.037 0.00 0.00 0.00 1.75
5092 5275 7.841956 AGCTGATAAGTACAAGTGTGAGTATT 58.158 34.615 0.00 0.00 0.00 1.89
5093 5276 7.411486 AGCTGATAAGTACAAGTGTGAGTAT 57.589 36.000 0.00 0.00 0.00 2.12
5094 5277 6.835819 AGCTGATAAGTACAAGTGTGAGTA 57.164 37.500 0.00 0.00 0.00 2.59
5095 5278 5.730296 AGCTGATAAGTACAAGTGTGAGT 57.270 39.130 0.00 0.00 0.00 3.41
5096 5279 7.647318 CAGATAGCTGATAAGTACAAGTGTGAG 59.353 40.741 0.40 0.00 45.17 3.51
5097 5280 7.416777 CCAGATAGCTGATAAGTACAAGTGTGA 60.417 40.741 10.19 0.00 45.17 3.58
5098 5281 6.699204 CCAGATAGCTGATAAGTACAAGTGTG 59.301 42.308 10.19 0.00 45.17 3.82
5099 5282 6.183360 CCCAGATAGCTGATAAGTACAAGTGT 60.183 42.308 10.19 0.00 45.17 3.55
5100 5283 6.183360 ACCCAGATAGCTGATAAGTACAAGTG 60.183 42.308 10.19 0.00 45.17 3.16
5101 5284 5.900123 ACCCAGATAGCTGATAAGTACAAGT 59.100 40.000 10.19 0.00 45.17 3.16
5102 5285 6.412362 ACCCAGATAGCTGATAAGTACAAG 57.588 41.667 10.19 0.00 45.17 3.16
5103 5286 6.808321 AACCCAGATAGCTGATAAGTACAA 57.192 37.500 10.19 0.00 45.17 2.41
5104 5287 7.563924 AGTTAACCCAGATAGCTGATAAGTACA 59.436 37.037 10.19 0.00 45.17 2.90
5105 5288 7.868415 CAGTTAACCCAGATAGCTGATAAGTAC 59.132 40.741 10.19 0.68 45.17 2.73
5106 5289 7.783119 TCAGTTAACCCAGATAGCTGATAAGTA 59.217 37.037 10.19 0.00 45.17 2.24
5107 5290 6.611642 TCAGTTAACCCAGATAGCTGATAAGT 59.388 38.462 10.19 6.18 45.17 2.24
5108 5291 7.055667 TCAGTTAACCCAGATAGCTGATAAG 57.944 40.000 10.19 0.00 45.17 1.73
5109 5292 6.042093 CCTCAGTTAACCCAGATAGCTGATAA 59.958 42.308 10.19 3.38 45.17 1.75
5110 5293 5.540337 CCTCAGTTAACCCAGATAGCTGATA 59.460 44.000 10.19 0.00 45.17 2.15
5111 5294 4.346418 CCTCAGTTAACCCAGATAGCTGAT 59.654 45.833 10.19 0.00 45.17 2.90
5112 5295 3.706594 CCTCAGTTAACCCAGATAGCTGA 59.293 47.826 10.19 0.00 45.17 4.26
5113 5296 3.452627 ACCTCAGTTAACCCAGATAGCTG 59.547 47.826 0.00 0.00 41.93 4.24
5114 5297 3.725634 ACCTCAGTTAACCCAGATAGCT 58.274 45.455 0.88 0.00 0.00 3.32
5115 5298 4.192317 CAACCTCAGTTAACCCAGATAGC 58.808 47.826 0.88 0.00 33.27 2.97
5116 5299 4.192317 GCAACCTCAGTTAACCCAGATAG 58.808 47.826 0.88 0.00 33.27 2.08
5117 5300 3.585289 TGCAACCTCAGTTAACCCAGATA 59.415 43.478 0.88 0.00 33.27 1.98
5118 5301 2.375174 TGCAACCTCAGTTAACCCAGAT 59.625 45.455 0.88 0.00 33.27 2.90
5119 5302 1.771854 TGCAACCTCAGTTAACCCAGA 59.228 47.619 0.88 0.00 33.27 3.86
5120 5303 2.270352 TGCAACCTCAGTTAACCCAG 57.730 50.000 0.88 0.00 33.27 4.45
5121 5304 2.513753 CATGCAACCTCAGTTAACCCA 58.486 47.619 0.88 0.00 33.27 4.51
5122 5305 1.818674 CCATGCAACCTCAGTTAACCC 59.181 52.381 0.88 0.00 33.27 4.11
5123 5306 1.818674 CCCATGCAACCTCAGTTAACC 59.181 52.381 0.88 0.00 33.27 2.85
5124 5307 2.749621 CTCCCATGCAACCTCAGTTAAC 59.250 50.000 0.00 0.00 33.27 2.01
5125 5308 2.642311 TCTCCCATGCAACCTCAGTTAA 59.358 45.455 0.00 0.00 33.27 2.01
5126 5309 2.265367 TCTCCCATGCAACCTCAGTTA 58.735 47.619 0.00 0.00 33.27 2.24
5127 5310 1.067295 TCTCCCATGCAACCTCAGTT 58.933 50.000 0.00 0.00 36.33 3.16
5128 5311 1.067295 TTCTCCCATGCAACCTCAGT 58.933 50.000 0.00 0.00 0.00 3.41
5129 5312 2.431954 ATTCTCCCATGCAACCTCAG 57.568 50.000 0.00 0.00 0.00 3.35
5130 5313 2.309755 AGAATTCTCCCATGCAACCTCA 59.690 45.455 0.88 0.00 0.00 3.86
5131 5314 3.010200 AGAATTCTCCCATGCAACCTC 57.990 47.619 0.88 0.00 0.00 3.85
5132 5315 4.018050 ACTTAGAATTCTCCCATGCAACCT 60.018 41.667 12.24 0.00 0.00 3.50
5133 5316 4.273318 ACTTAGAATTCTCCCATGCAACC 58.727 43.478 12.24 0.00 0.00 3.77
5134 5317 5.006746 CGTACTTAGAATTCTCCCATGCAAC 59.993 44.000 12.24 0.66 0.00 4.17
5135 5318 5.116180 CGTACTTAGAATTCTCCCATGCAA 58.884 41.667 12.24 0.00 0.00 4.08
5136 5319 4.442893 CCGTACTTAGAATTCTCCCATGCA 60.443 45.833 12.24 0.00 0.00 3.96
5137 5320 4.058817 CCGTACTTAGAATTCTCCCATGC 58.941 47.826 12.24 0.00 0.00 4.06
5138 5321 5.277857 ACCGTACTTAGAATTCTCCCATG 57.722 43.478 12.24 0.00 0.00 3.66
5139 5322 5.424252 TCAACCGTACTTAGAATTCTCCCAT 59.576 40.000 12.24 0.00 0.00 4.00
5140 5323 4.773674 TCAACCGTACTTAGAATTCTCCCA 59.226 41.667 12.24 0.00 0.00 4.37
5141 5324 5.334724 TCAACCGTACTTAGAATTCTCCC 57.665 43.478 12.24 0.00 0.00 4.30
5142 5325 7.437565 GGTTATCAACCGTACTTAGAATTCTCC 59.562 40.741 12.24 0.00 42.62 3.71
5143 5326 8.350238 GGTTATCAACCGTACTTAGAATTCTC 57.650 38.462 12.24 0.00 42.62 2.87
5159 5342 8.357402 ACCTTTACAAATTGACTGGTTATCAAC 58.643 33.333 0.00 0.00 38.84 3.18
5160 5343 8.472007 ACCTTTACAAATTGACTGGTTATCAA 57.528 30.769 0.00 0.00 40.25 2.57
5161 5344 7.721842 TGACCTTTACAAATTGACTGGTTATCA 59.278 33.333 0.00 0.00 0.00 2.15
5162 5345 8.106247 TGACCTTTACAAATTGACTGGTTATC 57.894 34.615 0.00 0.00 0.00 1.75
5163 5346 8.650143 ATGACCTTTACAAATTGACTGGTTAT 57.350 30.769 0.00 2.48 0.00 1.89
5164 5347 7.721842 TGATGACCTTTACAAATTGACTGGTTA 59.278 33.333 0.00 0.22 0.00 2.85
5165 5348 6.549364 TGATGACCTTTACAAATTGACTGGTT 59.451 34.615 0.00 0.00 0.00 3.67
5166 5349 6.068010 TGATGACCTTTACAAATTGACTGGT 58.932 36.000 0.00 2.39 0.00 4.00
5167 5350 6.573664 TGATGACCTTTACAAATTGACTGG 57.426 37.500 0.00 0.00 0.00 4.00
5168 5351 6.088824 GCTGATGACCTTTACAAATTGACTG 58.911 40.000 0.00 0.00 0.00 3.51
5169 5352 5.106555 CGCTGATGACCTTTACAAATTGACT 60.107 40.000 0.00 0.00 0.00 3.41
5170 5353 5.088739 CGCTGATGACCTTTACAAATTGAC 58.911 41.667 0.00 0.00 0.00 3.18
5171 5354 4.155826 CCGCTGATGACCTTTACAAATTGA 59.844 41.667 0.00 0.00 0.00 2.57
5172 5355 4.155826 TCCGCTGATGACCTTTACAAATTG 59.844 41.667 0.00 0.00 0.00 2.32
5173 5356 4.331968 TCCGCTGATGACCTTTACAAATT 58.668 39.130 0.00 0.00 0.00 1.82
5174 5357 3.950397 TCCGCTGATGACCTTTACAAAT 58.050 40.909 0.00 0.00 0.00 2.32
5175 5358 3.410631 TCCGCTGATGACCTTTACAAA 57.589 42.857 0.00 0.00 0.00 2.83
5176 5359 3.627395 ATCCGCTGATGACCTTTACAA 57.373 42.857 0.00 0.00 0.00 2.41
5204 5387 4.400961 AGGAACGCCTGCTGGAGC 62.401 66.667 14.77 0.00 44.90 4.70
5303 5486 2.273776 GAAAGAGGCAGGGGAGGC 59.726 66.667 0.00 0.00 0.00 4.70
5304 5487 2.586792 CGAAAGAGGCAGGGGAGG 59.413 66.667 0.00 0.00 0.00 4.30
5305 5488 2.124942 GCGAAAGAGGCAGGGGAG 60.125 66.667 0.00 0.00 0.00 4.30
5306 5489 4.082523 CGCGAAAGAGGCAGGGGA 62.083 66.667 0.00 0.00 0.00 4.81
5307 5490 4.394712 ACGCGAAAGAGGCAGGGG 62.395 66.667 15.93 0.00 34.13 4.79
5308 5491 2.815647 GACGCGAAAGAGGCAGGG 60.816 66.667 15.93 0.00 39.51 4.45
5309 5492 3.181967 CGACGCGAAAGAGGCAGG 61.182 66.667 15.93 0.00 39.82 4.85
5310 5493 2.430921 ACGACGCGAAAGAGGCAG 60.431 61.111 15.93 0.00 39.82 4.85
5311 5494 2.430244 GACGACGCGAAAGAGGCA 60.430 61.111 15.93 0.00 39.82 4.75
5312 5495 3.533691 CGACGACGCGAAAGAGGC 61.534 66.667 15.93 0.00 34.57 4.70
5313 5496 2.874780 CCGACGACGCGAAAGAGG 60.875 66.667 15.93 6.71 38.29 3.69
5314 5497 1.863880 CTCCGACGACGCGAAAGAG 60.864 63.158 15.93 6.03 38.29 2.85
5315 5498 2.175078 CTCCGACGACGCGAAAGA 59.825 61.111 15.93 0.00 38.29 2.52
5316 5499 3.533691 GCTCCGACGACGCGAAAG 61.534 66.667 15.93 5.82 38.29 2.62
5322 5505 3.996744 GAGAACCGCTCCGACGACG 62.997 68.421 0.00 0.00 37.69 5.12
5323 5506 2.202453 GAGAACCGCTCCGACGAC 60.202 66.667 0.00 0.00 37.69 4.34
5330 5513 4.475135 GGCCCAGGAGAACCGCTC 62.475 72.222 0.00 0.00 43.17 5.03
5333 5516 4.452733 GTCGGCCCAGGAGAACCG 62.453 72.222 0.00 0.00 46.97 4.44
5334 5517 3.003763 AGTCGGCCCAGGAGAACC 61.004 66.667 0.00 0.00 0.00 3.62
5335 5518 2.266055 CAGTCGGCCCAGGAGAAC 59.734 66.667 0.00 0.00 0.00 3.01
5336 5519 3.706373 GCAGTCGGCCCAGGAGAA 61.706 66.667 0.00 0.00 36.11 2.87
5346 5529 4.933064 GATCCTCCGCGCAGTCGG 62.933 72.222 8.75 0.00 45.66 4.79
5347 5530 4.933064 GGATCCTCCGCGCAGTCG 62.933 72.222 8.75 0.00 39.07 4.18
5348 5531 3.492311 GAGGATCCTCCGCGCAGTC 62.492 68.421 28.84 3.23 42.75 3.51
5349 5532 3.532155 GAGGATCCTCCGCGCAGT 61.532 66.667 28.84 0.00 42.75 4.40
5360 5543 1.448069 GCGGAGGGAAAGGAGGATC 59.552 63.158 0.00 0.00 0.00 3.36
5361 5544 2.073101 GGCGGAGGGAAAGGAGGAT 61.073 63.158 0.00 0.00 0.00 3.24
5362 5545 2.687566 GGCGGAGGGAAAGGAGGA 60.688 66.667 0.00 0.00 0.00 3.71
5363 5546 3.798511 GGGCGGAGGGAAAGGAGG 61.799 72.222 0.00 0.00 0.00 4.30
5364 5547 4.162690 CGGGCGGAGGGAAAGGAG 62.163 72.222 0.00 0.00 0.00 3.69
5415 5598 1.220477 GGAGGAGAAGGCTGTCTGC 59.780 63.158 9.15 9.15 41.94 4.26
5416 5599 0.617249 AGGGAGGAGAAGGCTGTCTG 60.617 60.000 4.31 0.00 0.00 3.51
5417 5600 0.617249 CAGGGAGGAGAAGGCTGTCT 60.617 60.000 0.00 0.00 0.00 3.41
5418 5601 1.904032 CAGGGAGGAGAAGGCTGTC 59.096 63.158 0.00 0.00 0.00 3.51
5419 5602 2.297129 GCAGGGAGGAGAAGGCTGT 61.297 63.158 0.00 0.00 0.00 4.40
5420 5603 2.588989 GCAGGGAGGAGAAGGCTG 59.411 66.667 0.00 0.00 0.00 4.85
5421 5604 2.690510 GGCAGGGAGGAGAAGGCT 60.691 66.667 0.00 0.00 0.00 4.58
5422 5605 4.168291 CGGCAGGGAGGAGAAGGC 62.168 72.222 0.00 0.00 0.00 4.35
5423 5606 3.474570 CCGGCAGGGAGGAGAAGG 61.475 72.222 0.00 0.00 38.47 3.46
5424 5607 4.168291 GCCGGCAGGGAGGAGAAG 62.168 72.222 24.80 0.00 38.47 2.85
5459 5642 3.934391 GAGCCGAACCCCTCACGTG 62.934 68.421 9.94 9.94 0.00 4.49
5460 5643 3.692406 GAGCCGAACCCCTCACGT 61.692 66.667 0.00 0.00 0.00 4.49
5461 5644 4.452733 GGAGCCGAACCCCTCACG 62.453 72.222 0.00 0.00 0.00 4.35
5462 5645 3.003763 AGGAGCCGAACCCCTCAC 61.004 66.667 0.00 0.00 0.00 3.51
5463 5646 3.003173 CAGGAGCCGAACCCCTCA 61.003 66.667 0.00 0.00 0.00 3.86
5464 5647 3.787001 CCAGGAGCCGAACCCCTC 61.787 72.222 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.