Multiple sequence alignment - TraesCS4D01G303600

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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 TraesCS4D01G303600 chr4D 100.000 2743 0 0 1 2743 472157956 472160698 0.000000e+00 5066.0
1 TraesCS4D01G303600 chr4D 97.368 38 1 0 661 698 472158582 472158619 6.340000e-07 65.8
2 TraesCS4D01G303600 chr4D 97.368 38 1 0 627 664 472158616 472158653 6.340000e-07 65.8
3 TraesCS4D01G303600 chr4D 90.909 44 4 0 2437 2480 23315096 23315139 2.950000e-05 60.2
4 TraesCS4D01G303600 chr4B 94.714 1154 40 9 846 1985 594149941 594151087 0.000000e+00 1773.0
5 TraesCS4D01G303600 chr4B 89.703 437 29 7 2003 2435 594151180 594151604 6.680000e-151 544.0
6 TraesCS4D01G303600 chr4B 88.166 169 13 3 2551 2717 594151676 594151839 7.750000e-46 195.0
7 TraesCS4D01G303600 chr4B 86.555 119 14 1 700 816 594149824 594149942 2.220000e-26 130.0
8 TraesCS4D01G303600 chr4B 85.075 67 8 2 173 238 521570762 521570827 1.760000e-07 67.6
9 TraesCS4D01G303600 chr4A 92.213 1143 48 21 869 1985 679068318 679069445 0.000000e+00 1580.0
10 TraesCS4D01G303600 chr4A 87.025 316 28 6 2128 2435 679069739 679070049 7.270000e-91 344.0
11 TraesCS4D01G303600 chr4A 88.462 156 13 4 2562 2717 679070133 679070283 1.680000e-42 183.0
12 TraesCS4D01G303600 chr2D 95.536 672 27 3 1 669 342092167 342092838 0.000000e+00 1072.0
13 TraesCS4D01G303600 chr2D 91.111 45 4 0 2434 2478 45474408 45474452 8.200000e-06 62.1
14 TraesCS4D01G303600 chr3A 94.667 675 33 3 1 672 399114112 399113438 0.000000e+00 1044.0
15 TraesCS4D01G303600 chr3A 87.879 660 76 4 9 665 424467313 424466655 0.000000e+00 773.0
16 TraesCS4D01G303600 chr3A 97.368 38 1 0 661 698 399113484 399113447 6.340000e-07 65.8
17 TraesCS4D01G303600 chr7B 89.448 616 62 3 1 614 176246270 176246884 0.000000e+00 774.0
18 TraesCS4D01G303600 chr3B 87.575 668 77 5 1 665 764485475 764484811 0.000000e+00 769.0
19 TraesCS4D01G303600 chr2B 84.168 499 77 2 1 497 462900347 462899849 1.480000e-132 483.0
20 TraesCS4D01G303600 chr2A 92.857 42 3 0 2437 2478 48833185 48833226 8.200000e-06 62.1
21 TraesCS4D01G303600 chr5A 89.583 48 4 1 2436 2482 688329484 688329531 2.950000e-05 60.2


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 TraesCS4D01G303600 chr4D 472157956 472160698 2742 False 1732.533333 5066 98.245333 1 2743 3 chr4D.!!$F2 2742
1 TraesCS4D01G303600 chr4B 594149824 594151839 2015 False 660.500000 1773 89.784500 700 2717 4 chr4B.!!$F2 2017
2 TraesCS4D01G303600 chr4A 679068318 679070283 1965 False 702.333333 1580 89.233333 869 2717 3 chr4A.!!$F1 1848
3 TraesCS4D01G303600 chr2D 342092167 342092838 671 False 1072.000000 1072 95.536000 1 669 1 chr2D.!!$F2 668
4 TraesCS4D01G303600 chr3A 424466655 424467313 658 True 773.000000 773 87.879000 9 665 1 chr3A.!!$R1 656
5 TraesCS4D01G303600 chr3A 399113438 399114112 674 True 554.900000 1044 96.017500 1 698 2 chr3A.!!$R2 697
6 TraesCS4D01G303600 chr7B 176246270 176246884 614 False 774.000000 774 89.448000 1 614 1 chr7B.!!$F1 613
7 TraesCS4D01G303600 chr3B 764484811 764485475 664 True 769.000000 769 87.575000 1 665 1 chr3B.!!$R1 664

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
815 822 0.179 GGATCAACTCATGTCGGGCT 59.821 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2607 2861 0.16747 TCCTCGTAGCTTTCGTCGTG 59.833 55.0 0.0 0.0 0.0 4.35 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
112 113 2.840651 GAGTCTCCCAAATCCTCTTCCA 59.159 50.000 0.00 0.00 0.00 3.53
140 141 3.552132 TGAACAGTTTGTGGAGTGCTA 57.448 42.857 0.00 0.00 0.00 3.49
170 171 1.522668 CTCTTTGACAATCGGCCACA 58.477 50.000 2.24 0.00 0.00 4.17
223 224 3.842923 CCCGGCGCTCTGTCTGAT 61.843 66.667 7.64 0.00 0.00 2.90
286 287 8.132352 GGAATATCATATCCTGCTCCGAGAGG 62.132 50.000 0.00 3.77 42.02 3.69
336 339 1.062685 CGAGTGTATGCTCTCGCGT 59.937 57.895 19.55 0.00 46.71 6.01
337 340 0.523546 CGAGTGTATGCTCTCGCGTT 60.524 55.000 19.55 0.00 46.71 4.84
355 358 0.251742 TTGATGCCTTCCCCAACAGG 60.252 55.000 0.00 0.00 0.00 4.00
388 391 1.872773 AGTAGAAGGCCTCCTCCTTG 58.127 55.000 5.23 0.00 45.92 3.61
480 485 3.120095 CGCAATCAGATGAAACAGCTTGA 60.120 43.478 0.00 0.00 0.00 3.02
559 564 1.228124 CAAGAGACGCCAACCCCAA 60.228 57.895 0.00 0.00 0.00 4.12
615 620 0.250640 TCCGTCCGATAGCCTCCTAC 60.251 60.000 0.00 0.00 0.00 3.18
674 679 2.420628 CGCAAGCAATTGAACCTCAA 57.579 45.000 10.34 0.00 41.09 3.02
675 680 2.741612 CGCAAGCAATTGAACCTCAAA 58.258 42.857 10.34 0.00 40.12 2.69
676 681 3.122297 CGCAAGCAATTGAACCTCAAAA 58.878 40.909 10.34 0.00 40.12 2.44
677 682 3.742369 CGCAAGCAATTGAACCTCAAAAT 59.258 39.130 10.34 0.00 40.12 1.82
678 683 4.376615 CGCAAGCAATTGAACCTCAAAATG 60.377 41.667 10.34 0.00 40.12 2.32
679 684 4.751098 GCAAGCAATTGAACCTCAAAATGA 59.249 37.500 10.34 0.00 40.12 2.57
680 685 5.333568 GCAAGCAATTGAACCTCAAAATGAC 60.334 40.000 10.34 0.00 40.12 3.06
681 686 4.886579 AGCAATTGAACCTCAAAATGACC 58.113 39.130 10.34 0.00 40.12 4.02
682 687 4.344679 AGCAATTGAACCTCAAAATGACCA 59.655 37.500 10.34 0.00 40.12 4.02
683 688 5.055812 GCAATTGAACCTCAAAATGACCAA 58.944 37.500 10.34 0.00 40.12 3.67
684 689 5.178067 GCAATTGAACCTCAAAATGACCAAG 59.822 40.000 10.34 0.00 40.12 3.61
685 690 6.282930 CAATTGAACCTCAAAATGACCAAGT 58.717 36.000 0.00 0.00 40.12 3.16
686 691 5.930837 TTGAACCTCAAAATGACCAAGTT 57.069 34.783 0.00 0.00 32.71 2.66
687 692 5.261209 TGAACCTCAAAATGACCAAGTTG 57.739 39.130 0.00 0.00 0.00 3.16
688 693 4.099266 TGAACCTCAAAATGACCAAGTTGG 59.901 41.667 20.76 20.76 45.02 3.77
689 694 2.365293 ACCTCAAAATGACCAAGTTGGC 59.635 45.455 22.25 14.64 42.67 4.52
690 695 2.607771 CCTCAAAATGACCAAGTTGGCG 60.608 50.000 22.25 0.00 42.67 5.69
691 696 1.139163 CAAAATGACCAAGTTGGCGC 58.861 50.000 22.25 14.44 42.67 6.53
692 697 0.749649 AAAATGACCAAGTTGGCGCA 59.250 45.000 22.25 19.50 42.67 6.09
693 698 0.749649 AAATGACCAAGTTGGCGCAA 59.250 45.000 22.25 5.38 42.67 4.85
694 699 0.314935 AATGACCAAGTTGGCGCAAG 59.685 50.000 22.25 0.00 42.67 4.01
713 718 4.786609 GCAAGCAAACGGATAGAGCATTAC 60.787 45.833 0.00 0.00 0.00 1.89
714 719 4.137116 AGCAAACGGATAGAGCATTACA 57.863 40.909 0.00 0.00 0.00 2.41
717 722 5.237344 AGCAAACGGATAGAGCATTACATTC 59.763 40.000 0.00 0.00 0.00 2.67
722 727 6.398918 ACGGATAGAGCATTACATTCCATAC 58.601 40.000 0.00 0.00 0.00 2.39
723 728 6.014584 ACGGATAGAGCATTACATTCCATACA 60.015 38.462 0.00 0.00 0.00 2.29
727 732 9.440773 GATAGAGCATTACATTCCATACAATGA 57.559 33.333 0.25 0.00 37.24 2.57
729 734 7.512130 AGAGCATTACATTCCATACAATGAGA 58.488 34.615 0.25 0.00 37.24 3.27
732 737 6.016860 GCATTACATTCCATACAATGAGAGCA 60.017 38.462 0.25 0.00 37.24 4.26
755 760 8.970020 AGCAAAATAACATGAATATGTCCTTGA 58.030 29.630 0.00 0.00 46.54 3.02
759 766 4.508551 ACATGAATATGTCCTTGAGCCA 57.491 40.909 0.00 0.00 44.00 4.75
760 767 4.858850 ACATGAATATGTCCTTGAGCCAA 58.141 39.130 0.00 0.00 44.00 4.52
766 773 0.250295 TGTCCTTGAGCCAAACGGAG 60.250 55.000 0.00 0.00 0.00 4.63
778 785 3.001330 GCCAAACGGAGAAAGTGATATCG 59.999 47.826 0.00 0.00 0.00 2.92
814 821 0.815615 GGGATCAACTCATGTCGGGC 60.816 60.000 0.00 0.00 0.00 6.13
815 822 0.179000 GGATCAACTCATGTCGGGCT 59.821 55.000 0.00 0.00 0.00 5.19
816 823 1.407437 GGATCAACTCATGTCGGGCTT 60.407 52.381 0.00 0.00 0.00 4.35
817 824 2.359900 GATCAACTCATGTCGGGCTTT 58.640 47.619 0.00 0.00 0.00 3.51
818 825 1.808411 TCAACTCATGTCGGGCTTTC 58.192 50.000 0.00 0.00 0.00 2.62
819 826 1.071542 TCAACTCATGTCGGGCTTTCA 59.928 47.619 0.00 0.00 0.00 2.69
820 827 1.197721 CAACTCATGTCGGGCTTTCAC 59.802 52.381 0.00 0.00 0.00 3.18
821 828 0.396435 ACTCATGTCGGGCTTTCACA 59.604 50.000 0.00 0.00 0.00 3.58
822 829 1.081892 CTCATGTCGGGCTTTCACAG 58.918 55.000 0.00 0.00 0.00 3.66
823 830 0.396435 TCATGTCGGGCTTTCACAGT 59.604 50.000 0.00 0.00 0.00 3.55
824 831 0.518636 CATGTCGGGCTTTCACAGTG 59.481 55.000 0.00 0.00 0.00 3.66
825 832 0.396435 ATGTCGGGCTTTCACAGTGA 59.604 50.000 0.00 0.00 0.00 3.41
826 833 0.531974 TGTCGGGCTTTCACAGTGAC 60.532 55.000 1.52 0.00 0.00 3.67
827 834 1.070786 TCGGGCTTTCACAGTGACC 59.929 57.895 1.52 1.06 0.00 4.02
828 835 1.071471 CGGGCTTTCACAGTGACCT 59.929 57.895 1.52 0.00 0.00 3.85
829 836 0.535102 CGGGCTTTCACAGTGACCTT 60.535 55.000 1.52 0.00 0.00 3.50
830 837 0.954452 GGGCTTTCACAGTGACCTTG 59.046 55.000 1.52 0.00 0.00 3.61
831 838 1.680338 GGCTTTCACAGTGACCTTGT 58.320 50.000 1.52 0.00 0.00 3.16
832 839 2.024414 GGCTTTCACAGTGACCTTGTT 58.976 47.619 1.52 0.00 0.00 2.83
833 840 2.223572 GGCTTTCACAGTGACCTTGTTG 60.224 50.000 1.52 0.00 0.00 3.33
834 841 2.423538 GCTTTCACAGTGACCTTGTTGT 59.576 45.455 1.52 0.00 0.00 3.32
835 842 3.487544 GCTTTCACAGTGACCTTGTTGTC 60.488 47.826 1.52 0.00 35.77 3.18
836 843 2.325583 TCACAGTGACCTTGTTGTCC 57.674 50.000 0.00 0.00 34.25 4.02
837 844 1.837439 TCACAGTGACCTTGTTGTCCT 59.163 47.619 0.00 0.00 34.25 3.85
838 845 2.238646 TCACAGTGACCTTGTTGTCCTT 59.761 45.455 0.00 0.00 34.25 3.36
839 846 2.614057 CACAGTGACCTTGTTGTCCTTC 59.386 50.000 0.00 0.00 34.25 3.46
840 847 2.238646 ACAGTGACCTTGTTGTCCTTCA 59.761 45.455 0.00 0.00 34.25 3.02
841 848 3.278574 CAGTGACCTTGTTGTCCTTCAA 58.721 45.455 0.00 0.00 34.25 2.69
842 849 3.694072 CAGTGACCTTGTTGTCCTTCAAA 59.306 43.478 0.00 0.00 37.81 2.69
843 850 4.339247 CAGTGACCTTGTTGTCCTTCAAAT 59.661 41.667 0.00 0.00 37.81 2.32
844 851 4.956075 AGTGACCTTGTTGTCCTTCAAATT 59.044 37.500 0.00 0.00 37.81 1.82
907 914 3.057245 CACTAGGCAGGAAAAGGAAAAGC 60.057 47.826 0.00 0.00 0.00 3.51
933 940 5.834204 TCCTAAAGGAACCCGAAATGAAAAA 59.166 36.000 0.00 0.00 42.18 1.94
1117 1138 0.375803 AAGAACACGAACGCCAACAC 59.624 50.000 0.00 0.00 0.00 3.32
1313 1336 2.492090 CTCTCCGCCAACTCCTCG 59.508 66.667 0.00 0.00 0.00 4.63
1483 1506 4.140599 CTCCGCCTTCTCGCAGCT 62.141 66.667 0.00 0.00 0.00 4.24
1518 1541 2.704572 CCTCGAAGAAACCAGCAGAAT 58.295 47.619 0.00 0.00 34.09 2.40
1584 1610 3.108847 AGAAGAAGATCGGGAGGTTCT 57.891 47.619 0.00 0.00 0.00 3.01
1637 1663 2.142292 AAACAGGGGAAGCAGGCGAT 62.142 55.000 0.00 0.00 0.00 4.58
1742 1768 1.609555 GCCACCAACCATACGAACAAA 59.390 47.619 0.00 0.00 0.00 2.83
1743 1769 2.606065 GCCACCAACCATACGAACAAAC 60.606 50.000 0.00 0.00 0.00 2.93
1914 1946 4.430007 GAGAAGCACACGTATATGGTGAA 58.570 43.478 13.68 0.00 38.73 3.18
2019 2162 9.118300 TCTAGCTAGTTGTTACTATTGGTACTC 57.882 37.037 20.10 0.00 36.32 2.59
2035 2178 6.092955 TGGTACTCGTTACTTGTTCTGATT 57.907 37.500 0.00 0.00 0.00 2.57
2036 2179 5.924254 TGGTACTCGTTACTTGTTCTGATTG 59.076 40.000 0.00 0.00 0.00 2.67
2037 2180 6.154445 GGTACTCGTTACTTGTTCTGATTGA 58.846 40.000 0.00 0.00 0.00 2.57
2038 2181 6.089150 GGTACTCGTTACTTGTTCTGATTGAC 59.911 42.308 0.00 0.00 0.00 3.18
2039 2182 4.680110 ACTCGTTACTTGTTCTGATTGACG 59.320 41.667 0.00 0.00 0.00 4.35
2040 2183 4.862350 TCGTTACTTGTTCTGATTGACGA 58.138 39.130 0.00 0.00 35.04 4.20
2041 2184 5.466819 TCGTTACTTGTTCTGATTGACGAT 58.533 37.500 0.00 0.00 32.84 3.73
2042 2185 5.344933 TCGTTACTTGTTCTGATTGACGATG 59.655 40.000 0.00 0.00 32.84 3.84
2043 2186 5.118664 CGTTACTTGTTCTGATTGACGATGT 59.881 40.000 0.00 0.00 0.00 3.06
2053 2196 7.510549 TCTGATTGACGATGTATATGAGACA 57.489 36.000 0.00 0.00 0.00 3.41
2071 2214 5.655090 TGAGACAAAGATAACATACGGAGGA 59.345 40.000 0.00 0.00 0.00 3.71
2107 2250 4.578105 GGAGTATGCAAAATCAGGAGGAAG 59.422 45.833 0.00 0.00 0.00 3.46
2164 2391 3.121944 GTCACACAAACGCACTGATAGAG 59.878 47.826 0.00 0.00 0.00 2.43
2165 2392 3.005367 TCACACAAACGCACTGATAGAGA 59.995 43.478 0.00 0.00 0.00 3.10
2166 2393 3.366121 CACACAAACGCACTGATAGAGAG 59.634 47.826 0.00 0.00 0.00 3.20
2167 2394 3.255888 ACACAAACGCACTGATAGAGAGA 59.744 43.478 0.00 0.00 0.00 3.10
2168 2395 4.237724 CACAAACGCACTGATAGAGAGAA 58.762 43.478 0.00 0.00 0.00 2.87
2170 2397 5.349817 CACAAACGCACTGATAGAGAGAATT 59.650 40.000 0.00 0.00 0.00 2.17
2172 2399 7.063426 CACAAACGCACTGATAGAGAGAATTAA 59.937 37.037 0.00 0.00 0.00 1.40
2173 2400 7.063544 ACAAACGCACTGATAGAGAGAATTAAC 59.936 37.037 0.00 0.00 0.00 2.01
2174 2401 6.458232 ACGCACTGATAGAGAGAATTAACT 57.542 37.500 0.00 0.00 0.00 2.24
2175 2402 6.868622 ACGCACTGATAGAGAGAATTAACTT 58.131 36.000 0.00 0.00 0.00 2.66
2176 2403 6.975772 ACGCACTGATAGAGAGAATTAACTTC 59.024 38.462 0.00 0.00 0.00 3.01
2178 2405 7.704472 CGCACTGATAGAGAGAATTAACTTCTT 59.296 37.037 2.89 0.00 44.42 2.52
2201 2428 7.710044 TCTTCTTCTATAATTGCTTCTCTGCTG 59.290 37.037 0.00 0.00 0.00 4.41
2268 2495 1.812571 TCCATTTTCTCGGCTGCTTTC 59.187 47.619 0.00 0.00 0.00 2.62
2277 2504 1.812571 TCGGCTGCTTTCCATCTTTTC 59.187 47.619 0.00 0.00 0.00 2.29
2334 2564 0.970640 TCGATCCGGACTTGTTTCCA 59.029 50.000 6.12 0.00 35.04 3.53
2359 2596 4.675029 CAAAGCCCGTCGGTCCGT 62.675 66.667 11.88 0.00 0.00 4.69
2409 2646 2.126228 CGACACGTACGCCCACAT 60.126 61.111 16.72 0.00 0.00 3.21
2417 2654 1.657094 CGTACGCCCACATAACTGAAC 59.343 52.381 0.52 0.00 0.00 3.18
2420 2657 1.346395 ACGCCCACATAACTGAACAGA 59.654 47.619 8.87 0.00 0.00 3.41
2422 2659 2.778299 GCCCACATAACTGAACAGACA 58.222 47.619 8.87 0.00 0.00 3.41
2435 2672 5.184864 ACTGAACAGACACCATGAAAAACAA 59.815 36.000 8.87 0.00 0.00 2.83
2436 2673 6.127366 ACTGAACAGACACCATGAAAAACAAT 60.127 34.615 8.87 0.00 0.00 2.71
2438 2675 7.199766 TGAACAGACACCATGAAAAACAATAC 58.800 34.615 0.00 0.00 0.00 1.89
2439 2676 6.959639 ACAGACACCATGAAAAACAATACT 57.040 33.333 0.00 0.00 0.00 2.12
2440 2677 6.970484 ACAGACACCATGAAAAACAATACTC 58.030 36.000 0.00 0.00 0.00 2.59
2441 2678 6.016276 ACAGACACCATGAAAAACAATACTCC 60.016 38.462 0.00 0.00 0.00 3.85
2442 2679 5.476945 AGACACCATGAAAAACAATACTCCC 59.523 40.000 0.00 0.00 0.00 4.30
2443 2680 5.393866 ACACCATGAAAAACAATACTCCCT 58.606 37.500 0.00 0.00 0.00 4.20
2444 2681 5.838521 ACACCATGAAAAACAATACTCCCTT 59.161 36.000 0.00 0.00 0.00 3.95
2445 2682 6.015434 ACACCATGAAAAACAATACTCCCTTC 60.015 38.462 0.00 0.00 0.00 3.46
2446 2683 6.015519 CACCATGAAAAACAATACTCCCTTCA 60.016 38.462 0.00 0.00 0.00 3.02
2447 2684 6.553100 ACCATGAAAAACAATACTCCCTTCAA 59.447 34.615 0.00 0.00 0.00 2.69
2448 2685 7.235399 ACCATGAAAAACAATACTCCCTTCAAT 59.765 33.333 0.00 0.00 0.00 2.57
2449 2686 7.761249 CCATGAAAAACAATACTCCCTTCAATC 59.239 37.037 0.00 0.00 0.00 2.67
2450 2687 7.227049 TGAAAAACAATACTCCCTTCAATCC 57.773 36.000 0.00 0.00 0.00 3.01
2451 2688 6.780031 TGAAAAACAATACTCCCTTCAATCCA 59.220 34.615 0.00 0.00 0.00 3.41
2452 2689 7.454380 TGAAAAACAATACTCCCTTCAATCCAT 59.546 33.333 0.00 0.00 0.00 3.41
2453 2690 8.893563 AAAAACAATACTCCCTTCAATCCATA 57.106 30.769 0.00 0.00 0.00 2.74
2454 2691 9.492730 AAAAACAATACTCCCTTCAATCCATAT 57.507 29.630 0.00 0.00 0.00 1.78
2455 2692 9.492730 AAAACAATACTCCCTTCAATCCATATT 57.507 29.630 0.00 0.00 0.00 1.28
2460 2697 9.672673 AATACTCCCTTCAATCCATATTAATCG 57.327 33.333 0.00 0.00 0.00 3.34
2461 2698 7.079451 ACTCCCTTCAATCCATATTAATCGT 57.921 36.000 0.00 0.00 0.00 3.73
2462 2699 7.162082 ACTCCCTTCAATCCATATTAATCGTC 58.838 38.462 0.00 0.00 0.00 4.20
2463 2700 6.163476 TCCCTTCAATCCATATTAATCGTCG 58.837 40.000 0.00 0.00 0.00 5.12
2464 2701 5.932303 CCCTTCAATCCATATTAATCGTCGT 59.068 40.000 0.00 0.00 0.00 4.34
2465 2702 6.426937 CCCTTCAATCCATATTAATCGTCGTT 59.573 38.462 0.00 0.00 0.00 3.85
2466 2703 7.290842 CCTTCAATCCATATTAATCGTCGTTG 58.709 38.462 0.00 0.00 0.00 4.10
2467 2704 7.170828 CCTTCAATCCATATTAATCGTCGTTGA 59.829 37.037 0.00 0.00 0.00 3.18
2468 2705 8.601845 TTCAATCCATATTAATCGTCGTTGAT 57.398 30.769 0.00 0.00 0.00 2.57
2469 2706 8.601845 TCAATCCATATTAATCGTCGTTGATT 57.398 30.769 9.25 9.25 41.32 2.57
2470 2707 9.051679 TCAATCCATATTAATCGTCGTTGATTT 57.948 29.630 9.50 0.00 39.27 2.17
2473 2710 9.706691 ATCCATATTAATCGTCGTTGATTTAGT 57.293 29.630 9.50 1.73 39.27 2.24
2480 2717 7.647907 AATCGTCGTTGATTTAGTACAAAGT 57.352 32.000 0.00 0.00 35.03 2.66
2481 2718 7.647907 ATCGTCGTTGATTTAGTACAAAGTT 57.352 32.000 0.00 0.00 0.00 2.66
2482 2719 6.869473 TCGTCGTTGATTTAGTACAAAGTTG 58.131 36.000 0.00 0.00 0.00 3.16
2483 2720 6.476380 TCGTCGTTGATTTAGTACAAAGTTGT 59.524 34.615 1.75 1.75 44.86 3.32
2484 2721 6.568601 CGTCGTTGATTTAGTACAAAGTTGTG 59.431 38.462 6.94 0.00 42.31 3.33
2485 2722 7.404203 GTCGTTGATTTAGTACAAAGTTGTGT 58.596 34.615 6.94 0.00 42.31 3.72
2486 2723 7.906527 GTCGTTGATTTAGTACAAAGTTGTGTT 59.093 33.333 6.94 0.00 42.31 3.32
2487 2724 9.096160 TCGTTGATTTAGTACAAAGTTGTGTTA 57.904 29.630 6.94 0.00 42.31 2.41
2488 2725 9.150653 CGTTGATTTAGTACAAAGTTGTGTTAC 57.849 33.333 6.94 0.00 42.31 2.50
2491 2728 9.344772 TGATTTAGTACAAAGTTGTGTTACCAT 57.655 29.630 6.94 0.00 42.31 3.55
2495 2732 6.721321 AGTACAAAGTTGTGTTACCATTTCG 58.279 36.000 6.94 0.00 42.31 3.46
2498 2735 4.483476 AAGTTGTGTTACCATTTCGAGC 57.517 40.909 0.00 0.00 0.00 5.03
2504 2741 2.419673 TGTTACCATTTCGAGCTGCATG 59.580 45.455 1.02 0.00 0.00 4.06
2505 2742 2.401583 TACCATTTCGAGCTGCATGT 57.598 45.000 1.02 0.00 0.00 3.21
2512 2749 0.037419 TCGAGCTGCATGTAAGCACA 60.037 50.000 20.23 5.14 43.37 4.57
2513 2750 0.372679 CGAGCTGCATGTAAGCACAG 59.627 55.000 20.23 8.04 43.37 3.66
2514 2751 1.446907 GAGCTGCATGTAAGCACAGT 58.553 50.000 20.23 4.14 43.37 3.55
2523 2760 0.782384 GTAAGCACAGTGGTCGAACG 59.218 55.000 5.53 0.00 0.00 3.95
2527 2764 2.050351 ACAGTGGTCGAACGCTCG 60.050 61.111 14.96 12.27 46.87 5.03
2537 2791 3.696782 GAACGCTCGAAGTAGCTGA 57.303 52.632 0.00 0.00 40.49 4.26
2542 2796 3.639162 CTCGAAGTAGCTGAGCCTG 57.361 57.895 0.00 0.00 0.00 4.85
2543 2797 1.098869 CTCGAAGTAGCTGAGCCTGA 58.901 55.000 0.00 0.00 0.00 3.86
2545 2799 0.102120 CGAAGTAGCTGAGCCTGAGG 59.898 60.000 0.00 0.00 0.00 3.86
2555 2809 4.527583 GCCTGAGGCCGAGCTCAG 62.528 72.222 13.77 11.84 44.06 3.35
2558 2812 3.531283 TGAGGCCGAGCTCAGATC 58.469 61.111 15.40 6.41 0.00 2.75
2559 2813 1.380380 TGAGGCCGAGCTCAGATCA 60.380 57.895 15.40 9.01 0.00 2.92
2560 2814 0.972471 TGAGGCCGAGCTCAGATCAA 60.972 55.000 15.40 0.00 0.00 2.57
2585 2839 1.082117 GGTACGTGGTTCATGCTCGG 61.082 60.000 0.00 0.00 0.00 4.63
2594 2848 0.960364 TTCATGCTCGGAAACCTGCC 60.960 55.000 0.00 0.00 0.00 4.85
2595 2849 1.377725 CATGCTCGGAAACCTGCCT 60.378 57.895 0.00 0.00 0.00 4.75
2596 2850 1.377725 ATGCTCGGAAACCTGCCTG 60.378 57.895 0.00 0.00 0.00 4.85
2597 2851 3.435186 GCTCGGAAACCTGCCTGC 61.435 66.667 0.00 0.00 0.00 4.85
2619 2873 4.295119 ACGGCCACGACGAAAGCT 62.295 61.111 2.24 0.00 44.60 3.74
2682 2936 2.634940 CAAGAGAAGGTCAGAGGAACCA 59.365 50.000 0.00 0.00 0.00 3.67
2717 2971 8.958119 TGAGATTTTTAGCATTACCGAATACT 57.042 30.769 0.00 0.00 0.00 2.12
2723 2977 9.841295 TTTTTAGCATTACCGAATACTAATCCT 57.159 29.630 0.00 0.00 33.04 3.24
2724 2978 9.841295 TTTTAGCATTACCGAATACTAATCCTT 57.159 29.630 0.00 0.00 33.04 3.36
2725 2979 9.485206 TTTAGCATTACCGAATACTAATCCTTC 57.515 33.333 0.00 0.00 33.04 3.46
2726 2980 6.157211 AGCATTACCGAATACTAATCCTTCG 58.843 40.000 0.00 0.00 40.96 3.79
2727 2981 5.163982 GCATTACCGAATACTAATCCTTCGC 60.164 44.000 0.00 0.00 40.19 4.70
2728 2982 3.009301 ACCGAATACTAATCCTTCGCG 57.991 47.619 0.00 0.00 40.19 5.87
2729 2983 2.288030 ACCGAATACTAATCCTTCGCGG 60.288 50.000 6.13 0.00 40.19 6.46
2730 2984 1.719780 CGAATACTAATCCTTCGCGGC 59.280 52.381 6.13 0.00 35.85 6.53
2731 2985 2.750948 GAATACTAATCCTTCGCGGCA 58.249 47.619 6.13 0.00 0.00 5.69
2732 2986 2.440539 ATACTAATCCTTCGCGGCAG 57.559 50.000 6.13 2.24 0.00 4.85
2733 2987 0.387929 TACTAATCCTTCGCGGCAGG 59.612 55.000 16.74 16.74 0.00 4.85
2734 2988 2.203015 TAATCCTTCGCGGCAGGC 60.203 61.111 17.74 0.00 38.69 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 5.437060 GCTCTTATCACACTAATCCCCAAA 58.563 41.667 0.00 0.00 0.00 3.28
112 113 5.360714 ACTCCACAAACTGTTCATTGACAAT 59.639 36.000 0.00 0.00 0.00 2.71
140 141 4.371624 TTGTCAAAGAGGATGTCATGGT 57.628 40.909 0.00 0.00 0.00 3.55
170 171 3.486383 TCGGCATCTTCTTCCAAAAAGT 58.514 40.909 0.00 0.00 0.00 2.66
223 224 3.949754 GGAATGTGATCAAAGAGATGCCA 59.050 43.478 0.00 0.00 37.00 4.92
286 287 4.166523 TCTTGAACATCAATCGTCTCGAC 58.833 43.478 0.00 0.00 39.18 4.20
336 339 0.251742 CCTGTTGGGGAAGGCATCAA 60.252 55.000 0.00 0.00 0.00 2.57
337 340 1.383799 CCTGTTGGGGAAGGCATCA 59.616 57.895 0.00 0.00 0.00 3.07
355 358 0.606604 TCTACTTGGCGTTCCAGGAC 59.393 55.000 0.30 0.00 44.53 3.85
388 391 4.081050 GGTGACAGACCAAAGGGC 57.919 61.111 0.00 0.00 45.34 5.19
559 564 1.475751 CCACTCTCAAGCAGTTGGTGT 60.476 52.381 0.00 0.00 34.09 4.16
615 620 2.308450 TTCGATTGCGCGCAGGATTG 62.308 55.000 34.25 27.14 37.46 2.67
665 670 4.099266 CCAACTTGGTCATTTTGAGGTTCA 59.901 41.667 0.00 0.00 31.35 3.18
666 671 4.620982 CCAACTTGGTCATTTTGAGGTTC 58.379 43.478 0.00 0.00 31.35 3.62
667 672 3.181466 GCCAACTTGGTCATTTTGAGGTT 60.181 43.478 9.63 0.00 40.46 3.50
669 674 2.607771 CGCCAACTTGGTCATTTTGAGG 60.608 50.000 9.63 0.00 40.46 3.86
670 675 2.664916 CGCCAACTTGGTCATTTTGAG 58.335 47.619 9.63 0.00 40.46 3.02
671 676 1.269517 GCGCCAACTTGGTCATTTTGA 60.270 47.619 9.63 0.00 40.46 2.69
672 677 1.139163 GCGCCAACTTGGTCATTTTG 58.861 50.000 9.63 0.00 40.46 2.44
673 678 0.749649 TGCGCCAACTTGGTCATTTT 59.250 45.000 4.18 0.00 40.46 1.82
674 679 0.749649 TTGCGCCAACTTGGTCATTT 59.250 45.000 4.18 0.00 40.46 2.32
675 680 0.314935 CTTGCGCCAACTTGGTCATT 59.685 50.000 4.18 0.00 40.46 2.57
676 681 1.959085 CTTGCGCCAACTTGGTCAT 59.041 52.632 4.18 0.00 40.46 3.06
677 682 2.844451 GCTTGCGCCAACTTGGTCA 61.844 57.895 4.18 5.41 40.46 4.02
678 683 2.050077 GCTTGCGCCAACTTGGTC 60.050 61.111 4.18 2.95 40.46 4.02
679 684 1.954362 TTTGCTTGCGCCAACTTGGT 61.954 50.000 4.18 0.00 40.46 3.67
680 685 1.227205 TTTGCTTGCGCCAACTTGG 60.227 52.632 4.18 3.10 41.55 3.61
681 686 1.810221 CGTTTGCTTGCGCCAACTTG 61.810 55.000 4.18 0.00 39.05 3.16
682 687 1.588667 CGTTTGCTTGCGCCAACTT 60.589 52.632 4.18 0.00 39.05 2.66
683 688 2.026014 CGTTTGCTTGCGCCAACT 59.974 55.556 4.18 0.00 39.05 3.16
684 689 2.747507 ATCCGTTTGCTTGCGCCAAC 62.748 55.000 4.18 0.00 38.15 3.77
685 690 1.237954 TATCCGTTTGCTTGCGCCAA 61.238 50.000 4.18 0.00 34.43 4.52
686 691 1.643868 CTATCCGTTTGCTTGCGCCA 61.644 55.000 4.18 0.00 34.43 5.69
687 692 1.062525 CTATCCGTTTGCTTGCGCC 59.937 57.895 4.18 0.00 34.43 6.53
688 693 0.026803 CTCTATCCGTTTGCTTGCGC 59.973 55.000 0.00 0.00 0.00 6.09
689 694 0.026803 GCTCTATCCGTTTGCTTGCG 59.973 55.000 0.00 0.00 0.00 4.85
690 695 1.086696 TGCTCTATCCGTTTGCTTGC 58.913 50.000 0.00 0.00 0.00 4.01
691 696 4.332543 TGTAATGCTCTATCCGTTTGCTTG 59.667 41.667 0.00 0.00 0.00 4.01
692 697 4.513442 TGTAATGCTCTATCCGTTTGCTT 58.487 39.130 0.00 0.00 0.00 3.91
693 698 4.137116 TGTAATGCTCTATCCGTTTGCT 57.863 40.909 0.00 0.00 0.00 3.91
694 699 5.424121 AATGTAATGCTCTATCCGTTTGC 57.576 39.130 0.00 0.00 0.00 3.68
695 700 5.527214 TGGAATGTAATGCTCTATCCGTTTG 59.473 40.000 0.00 0.00 0.00 2.93
696 701 5.680619 TGGAATGTAATGCTCTATCCGTTT 58.319 37.500 0.00 0.00 0.00 3.60
697 702 5.290493 TGGAATGTAATGCTCTATCCGTT 57.710 39.130 0.00 0.00 0.00 4.44
698 703 4.955811 TGGAATGTAATGCTCTATCCGT 57.044 40.909 0.00 0.00 0.00 4.69
703 708 8.650490 TCTCATTGTATGGAATGTAATGCTCTA 58.350 33.333 0.00 0.00 35.25 2.43
713 718 9.241317 GTTATTTTGCTCTCATTGTATGGAATG 57.759 33.333 0.00 0.00 35.05 2.67
714 719 8.970020 TGTTATTTTGCTCTCATTGTATGGAAT 58.030 29.630 0.00 0.00 0.00 3.01
717 722 8.407832 TCATGTTATTTTGCTCTCATTGTATGG 58.592 33.333 0.00 0.00 0.00 2.74
727 732 8.757982 AGGACATATTCATGTTATTTTGCTCT 57.242 30.769 0.00 0.00 45.58 4.09
729 734 8.970020 TCAAGGACATATTCATGTTATTTTGCT 58.030 29.630 0.00 0.00 45.58 3.91
732 737 8.416329 GGCTCAAGGACATATTCATGTTATTTT 58.584 33.333 0.00 0.00 45.58 1.82
755 760 2.568623 ATCACTTTCTCCGTTTGGCT 57.431 45.000 0.00 0.00 34.14 4.75
759 766 4.113354 GAGCGATATCACTTTCTCCGTTT 58.887 43.478 3.12 0.00 0.00 3.60
760 767 3.381908 AGAGCGATATCACTTTCTCCGTT 59.618 43.478 3.12 0.00 0.00 4.44
766 773 5.438972 GCAAATGAGAGCGATATCACTTTC 58.561 41.667 0.00 4.02 0.00 2.62
778 785 0.449388 CCCTCAACGCAAATGAGAGC 59.551 55.000 10.93 0.00 45.74 4.09
814 821 3.065371 GGACAACAAGGTCACTGTGAAAG 59.935 47.826 12.81 5.40 39.59 2.62
815 822 3.013921 GGACAACAAGGTCACTGTGAAA 58.986 45.455 12.81 0.00 39.59 2.69
816 823 2.238646 AGGACAACAAGGTCACTGTGAA 59.761 45.455 12.81 0.00 39.59 3.18
817 824 1.837439 AGGACAACAAGGTCACTGTGA 59.163 47.619 6.36 6.36 39.59 3.58
818 825 2.332063 AGGACAACAAGGTCACTGTG 57.668 50.000 0.17 0.17 39.59 3.66
819 826 2.238646 TGAAGGACAACAAGGTCACTGT 59.761 45.455 0.00 0.00 39.59 3.55
820 827 2.917933 TGAAGGACAACAAGGTCACTG 58.082 47.619 0.00 0.00 39.59 3.66
821 828 3.644966 TTGAAGGACAACAAGGTCACT 57.355 42.857 0.00 0.00 39.59 3.41
822 829 4.918810 ATTTGAAGGACAACAAGGTCAC 57.081 40.909 0.00 0.00 39.59 3.67
823 830 5.200483 AGAATTTGAAGGACAACAAGGTCA 58.800 37.500 0.00 0.00 39.59 4.02
824 831 5.774498 AGAATTTGAAGGACAACAAGGTC 57.226 39.130 0.00 0.00 38.29 3.85
825 832 6.365520 AGTAGAATTTGAAGGACAACAAGGT 58.634 36.000 0.00 0.00 38.29 3.50
826 833 6.884280 AGTAGAATTTGAAGGACAACAAGG 57.116 37.500 0.00 0.00 38.29 3.61
831 838 9.547753 GCATCTATAGTAGAATTTGAAGGACAA 57.452 33.333 0.00 0.00 38.50 3.18
832 839 8.928448 AGCATCTATAGTAGAATTTGAAGGACA 58.072 33.333 0.00 0.00 38.50 4.02
841 848 9.368416 TGGAACTGTAGCATCTATAGTAGAATT 57.632 33.333 0.00 0.00 38.50 2.17
842 849 8.941995 TGGAACTGTAGCATCTATAGTAGAAT 57.058 34.615 0.00 0.00 38.50 2.40
843 850 8.630917 GTTGGAACTGTAGCATCTATAGTAGAA 58.369 37.037 0.00 0.00 38.50 2.10
844 851 7.778382 TGTTGGAACTGTAGCATCTATAGTAGA 59.222 37.037 0.00 0.00 39.50 2.59
907 914 4.523083 TCATTTCGGGTTCCTTTAGGATG 58.477 43.478 0.00 0.00 44.98 3.51
938 945 5.357089 CGCGTCAAAAGAAAAACATGAATG 58.643 37.500 0.00 0.00 0.00 2.67
939 946 4.085107 GCGCGTCAAAAGAAAAACATGAAT 60.085 37.500 8.43 0.00 0.00 2.57
940 947 3.241784 GCGCGTCAAAAGAAAAACATGAA 59.758 39.130 8.43 0.00 0.00 2.57
942 949 2.097444 GGCGCGTCAAAAGAAAAACATG 60.097 45.455 5.47 0.00 0.00 3.21
945 952 1.551145 TGGCGCGTCAAAAGAAAAAC 58.449 45.000 12.88 0.00 0.00 2.43
953 961 2.033550 ACTGTTTTATTGGCGCGTCAAA 59.966 40.909 31.51 16.60 0.00 2.69
1045 1063 4.766891 GTGGAGAGAGGAGATATGAAGAGG 59.233 50.000 0.00 0.00 0.00 3.69
1117 1138 0.383246 GTGTCGATCGATCCTCGTCG 60.383 60.000 22.50 8.65 41.35 5.12
1163 1186 2.665056 TCGATCGTAATCAGCTCGAC 57.335 50.000 15.94 0.00 36.46 4.20
1294 1317 3.378399 GAGGAGTTGGCGGAGAGGC 62.378 68.421 0.00 0.00 46.95 4.70
1313 1336 4.660938 GTCAGGGTGGTGGTGGCC 62.661 72.222 0.00 0.00 0.00 5.36
1340 1363 2.032681 GAGGTGCTGGCCGAGTTT 59.967 61.111 0.00 0.00 0.00 2.66
1445 1468 1.079057 GTTGACGAAGGAGGAGCCC 60.079 63.158 0.00 0.00 37.37 5.19
1502 1525 3.192212 CCTTGGATTCTGCTGGTTTCTTC 59.808 47.826 0.00 0.00 0.00 2.87
1518 1541 2.602676 CGCCCTCCTTTCCCTTGGA 61.603 63.158 0.00 0.00 0.00 3.53
1584 1610 3.691342 CCCGACCAGCCTCGACAA 61.691 66.667 0.00 0.00 35.58 3.18
1694 1720 2.159382 GGCCGGTCTGATCAAAAGAAA 58.841 47.619 1.90 0.00 0.00 2.52
1903 1935 9.762933 AACCATATGCAATTTTTCACCATATAC 57.237 29.630 0.00 0.00 30.36 1.47
1989 2027 9.863650 ACCAATAGTAACAACTAGCTAGATAGA 57.136 33.333 27.45 5.49 0.00 1.98
1992 2030 9.643735 AGTACCAATAGTAACAACTAGCTAGAT 57.356 33.333 27.45 13.16 31.05 1.98
1993 2031 9.118300 GAGTACCAATAGTAACAACTAGCTAGA 57.882 37.037 27.45 0.89 31.05 2.43
1994 2032 8.068977 CGAGTACCAATAGTAACAACTAGCTAG 58.931 40.741 19.44 19.44 31.05 3.42
1995 2033 7.554118 ACGAGTACCAATAGTAACAACTAGCTA 59.446 37.037 0.00 0.00 31.05 3.32
1997 2035 6.558909 ACGAGTACCAATAGTAACAACTAGC 58.441 40.000 0.00 0.00 31.05 3.42
1998 2036 9.495754 GTAACGAGTACCAATAGTAACAACTAG 57.504 37.037 0.00 0.00 31.05 2.57
1999 2037 9.231297 AGTAACGAGTACCAATAGTAACAACTA 57.769 33.333 0.00 0.00 32.58 2.24
2000 2038 8.115490 AGTAACGAGTACCAATAGTAACAACT 57.885 34.615 0.00 0.00 32.58 3.16
2001 2039 8.642020 CAAGTAACGAGTACCAATAGTAACAAC 58.358 37.037 0.00 0.00 32.58 3.32
2019 2162 5.118664 ACATCGTCAATCAGAACAAGTAACG 59.881 40.000 0.00 0.00 0.00 3.18
2035 2178 9.678941 GTTATCTTTGTCTCATATACATCGTCA 57.321 33.333 0.00 0.00 0.00 4.35
2036 2179 9.678941 TGTTATCTTTGTCTCATATACATCGTC 57.321 33.333 0.00 0.00 0.00 4.20
2041 2184 9.908152 CCGTATGTTATCTTTGTCTCATATACA 57.092 33.333 0.00 0.00 0.00 2.29
2053 2196 7.361457 TCAATCTCCTCCGTATGTTATCTTT 57.639 36.000 0.00 0.00 0.00 2.52
2060 2203 5.507482 CGTATGTTCAATCTCCTCCGTATGT 60.507 44.000 0.00 0.00 0.00 2.29
2068 2211 5.509840 GCATACTCCGTATGTTCAATCTCCT 60.510 44.000 13.64 0.00 45.23 3.69
2071 2214 5.276461 TGCATACTCCGTATGTTCAATCT 57.724 39.130 13.64 0.00 45.23 2.40
2107 2250 4.425577 ACGATGCAAACATTCCTTTCTC 57.574 40.909 0.00 0.00 36.35 2.87
2172 2399 9.598517 CAGAGAAGCAATTATAGAAGAAGAAGT 57.401 33.333 0.00 0.00 0.00 3.01
2173 2400 8.550376 GCAGAGAAGCAATTATAGAAGAAGAAG 58.450 37.037 0.00 0.00 0.00 2.85
2174 2401 8.263640 AGCAGAGAAGCAATTATAGAAGAAGAA 58.736 33.333 0.00 0.00 36.85 2.52
2175 2402 7.710044 CAGCAGAGAAGCAATTATAGAAGAAGA 59.290 37.037 0.00 0.00 36.85 2.87
2176 2403 7.518689 GCAGCAGAGAAGCAATTATAGAAGAAG 60.519 40.741 0.00 0.00 36.85 2.85
2177 2404 6.259608 GCAGCAGAGAAGCAATTATAGAAGAA 59.740 38.462 0.00 0.00 36.85 2.52
2178 2405 5.757320 GCAGCAGAGAAGCAATTATAGAAGA 59.243 40.000 0.00 0.00 36.85 2.87
2186 2413 1.271762 TGGAGCAGCAGAGAAGCAATT 60.272 47.619 0.00 0.00 36.85 2.32
2201 2428 4.570930 AGCTAAAGTAACAAGAGTGGAGC 58.429 43.478 0.00 0.00 0.00 4.70
2268 2495 0.657840 GATCACCGGCGAAAAGATGG 59.342 55.000 9.30 0.00 0.00 3.51
2277 2504 1.762222 GAAACGATGGATCACCGGCG 61.762 60.000 0.00 0.00 39.80 6.46
2405 2642 4.996758 TCATGGTGTCTGTTCAGTTATGTG 59.003 41.667 0.00 0.00 0.00 3.21
2409 2646 6.375736 TGTTTTTCATGGTGTCTGTTCAGTTA 59.624 34.615 0.00 0.00 0.00 2.24
2417 2654 6.381801 GGAGTATTGTTTTTCATGGTGTCTG 58.618 40.000 0.00 0.00 0.00 3.51
2420 2657 5.393866 AGGGAGTATTGTTTTTCATGGTGT 58.606 37.500 0.00 0.00 0.00 4.16
2422 2659 6.074648 TGAAGGGAGTATTGTTTTTCATGGT 58.925 36.000 0.00 0.00 0.00 3.55
2435 2672 8.826765 ACGATTAATATGGATTGAAGGGAGTAT 58.173 33.333 0.00 0.00 0.00 2.12
2436 2673 8.202461 ACGATTAATATGGATTGAAGGGAGTA 57.798 34.615 0.00 0.00 0.00 2.59
2438 2675 6.311445 CGACGATTAATATGGATTGAAGGGAG 59.689 42.308 0.00 0.00 0.00 4.30
2439 2676 6.163476 CGACGATTAATATGGATTGAAGGGA 58.837 40.000 0.00 0.00 0.00 4.20
2440 2677 5.932303 ACGACGATTAATATGGATTGAAGGG 59.068 40.000 0.00 0.00 0.00 3.95
2441 2678 7.170828 TCAACGACGATTAATATGGATTGAAGG 59.829 37.037 0.00 0.00 0.00 3.46
2442 2679 8.072238 TCAACGACGATTAATATGGATTGAAG 57.928 34.615 0.00 0.00 0.00 3.02
2443 2680 8.601845 ATCAACGACGATTAATATGGATTGAA 57.398 30.769 0.00 0.00 0.00 2.69
2444 2681 8.601845 AATCAACGACGATTAATATGGATTGA 57.398 30.769 0.00 0.00 33.82 2.57
2447 2684 9.706691 ACTAAATCAACGACGATTAATATGGAT 57.293 29.630 0.00 0.00 34.49 3.41
2454 2691 9.195411 ACTTTGTACTAAATCAACGACGATTAA 57.805 29.630 0.00 0.00 34.49 1.40
2455 2692 8.746922 ACTTTGTACTAAATCAACGACGATTA 57.253 30.769 0.00 0.00 34.49 1.75
2456 2693 7.647907 ACTTTGTACTAAATCAACGACGATT 57.352 32.000 0.00 0.00 37.20 3.34
2457 2694 7.170320 ACAACTTTGTACTAAATCAACGACGAT 59.830 33.333 0.00 0.00 40.16 3.73
2458 2695 6.476380 ACAACTTTGTACTAAATCAACGACGA 59.524 34.615 0.00 0.00 40.16 4.20
2459 2696 6.568601 CACAACTTTGTACTAAATCAACGACG 59.431 38.462 0.00 0.00 39.91 5.12
2460 2697 7.404203 ACACAACTTTGTACTAAATCAACGAC 58.596 34.615 0.00 0.00 39.91 4.34
2461 2698 7.542534 ACACAACTTTGTACTAAATCAACGA 57.457 32.000 0.00 0.00 39.91 3.85
2462 2699 9.150653 GTAACACAACTTTGTACTAAATCAACG 57.849 33.333 0.00 0.00 39.91 4.10
2463 2700 9.442033 GGTAACACAACTTTGTACTAAATCAAC 57.558 33.333 0.00 0.00 39.91 3.18
2464 2701 9.175312 TGGTAACACAACTTTGTACTAAATCAA 57.825 29.630 0.00 0.00 46.17 2.57
2465 2702 8.734218 TGGTAACACAACTTTGTACTAAATCA 57.266 30.769 0.00 0.00 46.17 2.57
2484 2721 2.420022 ACATGCAGCTCGAAATGGTAAC 59.580 45.455 0.00 0.00 0.00 2.50
2485 2722 2.710377 ACATGCAGCTCGAAATGGTAA 58.290 42.857 0.00 0.00 0.00 2.85
2486 2723 2.401583 ACATGCAGCTCGAAATGGTA 57.598 45.000 0.00 0.00 0.00 3.25
2487 2724 2.401583 TACATGCAGCTCGAAATGGT 57.598 45.000 0.00 0.00 0.00 3.55
2488 2725 2.540361 GCTTACATGCAGCTCGAAATGG 60.540 50.000 9.74 0.00 34.15 3.16
2491 2728 1.464608 GTGCTTACATGCAGCTCGAAA 59.535 47.619 16.35 0.00 44.20 3.46
2492 2729 1.078709 GTGCTTACATGCAGCTCGAA 58.921 50.000 16.35 0.00 44.20 3.71
2495 2732 1.129998 CACTGTGCTTACATGCAGCTC 59.870 52.381 16.35 13.60 44.20 4.09
2498 2735 1.466167 GACCACTGTGCTTACATGCAG 59.534 52.381 1.29 0.00 44.20 4.41
2504 2741 0.782384 CGTTCGACCACTGTGCTTAC 59.218 55.000 1.29 0.00 0.00 2.34
2505 2742 0.942410 GCGTTCGACCACTGTGCTTA 60.942 55.000 1.29 0.00 0.00 3.09
2527 2764 0.179086 GCCTCAGGCTCAGCTACTTC 60.179 60.000 9.09 0.00 46.69 3.01
2541 2795 0.972471 TTGATCTGAGCTCGGCCTCA 60.972 55.000 18.28 18.36 39.42 3.86
2542 2796 0.249405 CTTGATCTGAGCTCGGCCTC 60.249 60.000 18.28 16.12 0.00 4.70
2543 2797 1.684386 CCTTGATCTGAGCTCGGCCT 61.684 60.000 18.28 7.42 0.00 5.19
2545 2799 0.176680 TTCCTTGATCTGAGCTCGGC 59.823 55.000 18.28 5.44 0.00 5.54
2546 2800 1.800655 CGTTCCTTGATCTGAGCTCGG 60.801 57.143 16.98 16.98 0.00 4.63
2547 2801 1.554392 CGTTCCTTGATCTGAGCTCG 58.446 55.000 9.64 4.19 0.00 5.03
2549 2803 1.270907 ACCGTTCCTTGATCTGAGCT 58.729 50.000 0.00 0.00 0.00 4.09
2551 2805 2.163815 ACGTACCGTTCCTTGATCTGAG 59.836 50.000 0.00 0.00 36.35 3.35
2552 2806 2.094906 CACGTACCGTTCCTTGATCTGA 60.095 50.000 0.00 0.00 38.32 3.27
2553 2807 2.259618 CACGTACCGTTCCTTGATCTG 58.740 52.381 0.00 0.00 38.32 2.90
2554 2808 1.203994 CCACGTACCGTTCCTTGATCT 59.796 52.381 0.00 0.00 38.32 2.75
2555 2809 1.067354 ACCACGTACCGTTCCTTGATC 60.067 52.381 0.00 0.00 38.32 2.92
2556 2810 0.971386 ACCACGTACCGTTCCTTGAT 59.029 50.000 0.00 0.00 38.32 2.57
2557 2811 0.752054 AACCACGTACCGTTCCTTGA 59.248 50.000 0.00 0.00 38.32 3.02
2558 2812 1.142474 GAACCACGTACCGTTCCTTG 58.858 55.000 9.92 0.00 38.32 3.61
2559 2813 0.752054 TGAACCACGTACCGTTCCTT 59.248 50.000 15.66 0.00 38.32 3.36
2560 2814 0.971386 ATGAACCACGTACCGTTCCT 59.029 50.000 15.66 6.96 38.32 3.36
2575 2829 0.960364 GGCAGGTTTCCGAGCATGAA 60.960 55.000 0.00 0.00 32.62 2.57
2581 2835 2.032528 TGCAGGCAGGTTTCCGAG 59.967 61.111 0.00 0.00 0.00 4.63
2583 2837 3.365265 GGTGCAGGCAGGTTTCCG 61.365 66.667 0.00 0.00 0.00 4.30
2585 2839 2.203480 TGGGTGCAGGCAGGTTTC 60.203 61.111 0.00 0.00 0.00 2.78
2607 2861 0.167470 TCCTCGTAGCTTTCGTCGTG 59.833 55.000 0.00 0.00 0.00 4.35
2614 2868 1.337823 ACGCACATTCCTCGTAGCTTT 60.338 47.619 0.00 0.00 34.41 3.51
2619 2873 0.735978 CTGCACGCACATTCCTCGTA 60.736 55.000 0.00 0.00 34.81 3.43
2717 2971 2.203015 GCCTGCCGCGAAGGATTA 60.203 61.111 26.19 0.00 45.00 1.75


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

AutoCloner maintained by Alex Coulton.