Multiple sequence alignment - TraesCS1B01G104400

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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 TraesCS1B01G104400 chr1B 100.000 5520 0 0 1 5520 115274555 115280074 0.000000e+00 10194.0
1 TraesCS1B01G104400 chr1B 91.304 69 4 1 1 67 629931917 629931849 5.890000e-15 93.5
2 TraesCS1B01G104400 chr1D 93.567 4788 194 55 801 5520 72899947 72904688 0.000000e+00 7031.0
3 TraesCS1B01G104400 chr1D 79.470 604 51 36 60 622 72899196 72899767 1.460000e-95 361.0
4 TraesCS1B01G104400 chr1D 91.919 198 13 2 5250 5447 73051331 73051525 1.960000e-69 274.0
5 TraesCS1B01G104400 chr1D 97.143 35 0 1 734 767 307154283 307154249 2.150000e-04 58.4
6 TraesCS1B01G104400 chr1D 97.143 35 0 1 734 767 450115410 450115376 2.150000e-04 58.4
7 TraesCS1B01G104400 chr1A 92.183 2776 145 30 2779 5519 72780884 72783622 0.000000e+00 3858.0
8 TraesCS1B01G104400 chr1A 86.380 1953 108 64 790 2644 72778748 72780640 0.000000e+00 1988.0
9 TraesCS1B01G104400 chr1A 80.634 599 55 24 59 622 72778000 72778572 1.850000e-109 407.0
10 TraesCS1B01G104400 chr4A 100.000 56 0 0 1 56 707909517 707909462 2.720000e-18 104.0
11 TraesCS1B01G104400 chrUn 100.000 53 0 0 1 53 119437233 119437285 1.270000e-16 99.0
12 TraesCS1B01G104400 chrUn 100.000 53 0 0 1 53 338267954 338267902 1.270000e-16 99.0
13 TraesCS1B01G104400 chr6D 100.000 53 0 0 1 53 42428777 42428829 1.270000e-16 99.0
14 TraesCS1B01G104400 chr6D 100.000 53 0 0 1 53 42435671 42435723 1.270000e-16 99.0
15 TraesCS1B01G104400 chr6D 100.000 53 0 0 1 53 97410692 97410744 1.270000e-16 99.0
16 TraesCS1B01G104400 chr3D 96.667 60 0 2 1 59 23924779 23924721 1.270000e-16 99.0
17 TraesCS1B01G104400 chr2B 89.041 73 5 3 1 71 608765689 608765618 2.740000e-13 87.9
18 TraesCS1B01G104400 chr4B 85.714 63 7 2 731 793 568673584 568673644 1.280000e-06 65.8
19 TraesCS1B01G104400 chr2A 97.222 36 0 1 733 767 742772969 742772934 5.970000e-05 60.2
20 TraesCS1B01G104400 chr3A 97.143 35 0 1 734 767 79379854 79379888 2.150000e-04 58.4
21 TraesCS1B01G104400 chr2D 97.143 35 0 1 734 767 552066569 552066603 2.150000e-04 58.4


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 TraesCS1B01G104400 chr1B 115274555 115280074 5519 False 10194.000000 10194 100.0000 1 5520 1 chr1B.!!$F1 5519
1 TraesCS1B01G104400 chr1D 72899196 72904688 5492 False 3696.000000 7031 86.5185 60 5520 2 chr1D.!!$F2 5460
2 TraesCS1B01G104400 chr1A 72778000 72783622 5622 False 2084.333333 3858 86.3990 59 5519 3 chr1A.!!$F1 5460

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
699 834 0.036765 ATCAGGCCGACACGCTAAAA 60.037 50.000 0.0 0.00 0.00 1.52 F
712 847 0.108377 GCTAAAACCGGCCCATTTGG 60.108 55.000 0.0 1.34 37.09 3.28 F
776 911 0.727398 CGATGAAGAAAGTTCGGCCC 59.273 55.000 0.0 0.00 0.00 5.80 F
1935 2165 0.798776 CCTGTTGCTGGTCTAAAGCG 59.201 55.000 0.0 0.00 43.88 4.68 F
1958 2188 0.616679 TGTACTCACAGGTAGGGGGC 60.617 60.000 0.0 0.00 0.00 5.80 F
2878 3290 1.032014 GTGGACTTGTGGTTGTGCAT 58.968 50.000 0.0 0.00 36.93 3.96 F
4319 4764 1.551560 ACGAAGTATCTGGGACCACCA 60.552 52.381 0.0 0.00 45.23 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2181 0.045008 TGTACAATCTGGGCCCCCTA 59.955 55.0 22.27 4.47 36.94 3.53 R
1952 2182 0.627469 ATGTACAATCTGGGCCCCCT 60.627 55.0 22.27 0.00 36.94 4.79 R
1953 2183 1.145571 TATGTACAATCTGGGCCCCC 58.854 55.0 22.27 0.00 0.00 5.40 R
2861 3273 0.318955 GCATGCACAACCACAAGTCC 60.319 55.0 14.21 0.00 0.00 3.85 R
3767 4209 0.325933 TGGTGCCACTCCTCTTGATG 59.674 55.0 0.00 0.00 0.00 3.07 R
4375 4820 0.246086 CCGCCTTGGCAAAGCAATTA 59.754 50.0 19.90 0.00 31.51 1.40 R
5197 5672 0.170339 GGTTGGCGTGCAAATAGACC 59.830 55.0 0.00 0.00 0.00 3.85 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
96 97 0.179111 GTGTGCCGCTAGTAGATGCA 60.179 55.000 0.00 5.66 0.00 3.96
106 107 4.737765 CGCTAGTAGATGCAAAGAAGACTC 59.262 45.833 0.00 0.00 0.00 3.36
110 111 1.065854 AGATGCAAAGAAGACTCGGGG 60.066 52.381 0.00 0.00 0.00 5.73
111 112 0.693049 ATGCAAAGAAGACTCGGGGT 59.307 50.000 0.00 0.00 0.00 4.95
174 175 7.979537 TGTGTGTATTTAGGACATGTGATACTC 59.020 37.037 1.15 5.75 0.00 2.59
180 181 6.710597 TTAGGACATGTGATACTCAGTACC 57.289 41.667 1.15 0.00 0.00 3.34
189 190 4.028131 TGATACTCAGTACCCCGTTCATT 58.972 43.478 0.00 0.00 0.00 2.57
190 191 4.098960 TGATACTCAGTACCCCGTTCATTC 59.901 45.833 0.00 0.00 0.00 2.67
191 192 1.553704 ACTCAGTACCCCGTTCATTCC 59.446 52.381 0.00 0.00 0.00 3.01
192 193 1.553248 CTCAGTACCCCGTTCATTCCA 59.447 52.381 0.00 0.00 0.00 3.53
193 194 1.979308 TCAGTACCCCGTTCATTCCAA 59.021 47.619 0.00 0.00 0.00 3.53
194 195 2.372504 TCAGTACCCCGTTCATTCCAAA 59.627 45.455 0.00 0.00 0.00 3.28
195 196 3.150767 CAGTACCCCGTTCATTCCAAAA 58.849 45.455 0.00 0.00 0.00 2.44
196 197 3.761752 CAGTACCCCGTTCATTCCAAAAT 59.238 43.478 0.00 0.00 0.00 1.82
200 201 7.283580 CAGTACCCCGTTCATTCCAAAATATAA 59.716 37.037 0.00 0.00 0.00 0.98
201 202 6.709018 ACCCCGTTCATTCCAAAATATAAG 57.291 37.500 0.00 0.00 0.00 1.73
202 203 5.596772 ACCCCGTTCATTCCAAAATATAAGG 59.403 40.000 0.00 0.00 0.00 2.69
203 204 5.508994 CCCCGTTCATTCCAAAATATAAGGC 60.509 44.000 0.00 0.00 0.00 4.35
204 205 5.068460 CCCGTTCATTCCAAAATATAAGGCA 59.932 40.000 0.00 0.00 0.00 4.75
205 206 6.239289 CCCGTTCATTCCAAAATATAAGGCAT 60.239 38.462 0.00 0.00 0.00 4.40
206 207 7.040062 CCCGTTCATTCCAAAATATAAGGCATA 60.040 37.037 0.00 0.00 0.00 3.14
207 208 7.807907 CCGTTCATTCCAAAATATAAGGCATAC 59.192 37.037 0.00 0.00 0.00 2.39
208 209 8.567948 CGTTCATTCCAAAATATAAGGCATACT 58.432 33.333 0.00 0.00 0.00 2.12
223 224 9.726438 ATAAGGCATACTTAATATGTGGAAGTC 57.274 33.333 0.00 0.00 44.39 3.01
224 225 7.136822 AGGCATACTTAATATGTGGAAGTCA 57.863 36.000 0.00 0.00 42.52 3.41
225 226 7.749666 AGGCATACTTAATATGTGGAAGTCAT 58.250 34.615 0.00 0.00 42.52 3.06
432 441 7.516198 AGTCTGCATTATAAATGGGTTGATC 57.484 36.000 2.11 0.00 0.00 2.92
484 528 2.358247 GTCGTGTCGGGTTGGCAT 60.358 61.111 0.00 0.00 0.00 4.40
504 548 1.153429 CGTGCTACCCTTACTGGCC 60.153 63.158 0.00 0.00 0.00 5.36
506 550 1.229690 TGCTACCCTTACTGGCCCA 60.230 57.895 0.00 0.00 0.00 5.36
507 551 1.271840 TGCTACCCTTACTGGCCCAG 61.272 60.000 9.83 9.83 37.52 4.45
527 571 0.252197 GCACGGTCCCCTTCTTACAT 59.748 55.000 0.00 0.00 0.00 2.29
528 572 2.012051 GCACGGTCCCCTTCTTACATG 61.012 57.143 0.00 0.00 0.00 3.21
538 582 0.687920 TTCTTACATGGGTCGGCACA 59.312 50.000 0.00 0.00 0.00 4.57
577 621 0.892755 TGGTCCGCGTAGAATTCAGT 59.107 50.000 8.44 0.00 0.00 3.41
578 622 1.278238 GGTCCGCGTAGAATTCAGTG 58.722 55.000 8.44 5.32 0.00 3.66
581 629 0.174845 CCGCGTAGAATTCAGTGGGA 59.825 55.000 8.44 0.00 0.00 4.37
604 652 4.164988 ACTGCTTTGGACCTATATTCAGCT 59.835 41.667 0.00 0.00 0.00 4.24
609 657 6.091441 GCTTTGGACCTATATTCAGCTTATCG 59.909 42.308 0.00 0.00 0.00 2.92
610 658 6.665992 TTGGACCTATATTCAGCTTATCGT 57.334 37.500 0.00 0.00 0.00 3.73
612 660 5.538813 TGGACCTATATTCAGCTTATCGTGT 59.461 40.000 0.00 0.00 0.00 4.49
613 661 6.717997 TGGACCTATATTCAGCTTATCGTGTA 59.282 38.462 0.00 0.00 0.00 2.90
614 662 7.396339 TGGACCTATATTCAGCTTATCGTGTAT 59.604 37.037 0.00 0.00 0.00 2.29
615 663 8.900781 GGACCTATATTCAGCTTATCGTGTATA 58.099 37.037 0.00 0.00 0.00 1.47
650 785 5.861727 ACCTAATTATAAAGTGTAGGGCCG 58.138 41.667 0.00 0.00 36.44 6.13
673 808 1.580942 CACAAATGGGCCAGACACG 59.419 57.895 13.78 0.69 0.00 4.49
674 809 0.888736 CACAAATGGGCCAGACACGA 60.889 55.000 13.78 0.00 0.00 4.35
682 817 1.068250 GCCAGACACGAGGGCTATC 59.932 63.158 0.00 0.00 44.32 2.08
683 818 1.676678 GCCAGACACGAGGGCTATCA 61.677 60.000 0.00 0.00 44.32 2.15
697 832 0.384309 CTATCAGGCCGACACGCTAA 59.616 55.000 0.00 0.00 0.00 3.09
698 833 0.818938 TATCAGGCCGACACGCTAAA 59.181 50.000 0.00 0.00 0.00 1.85
699 834 0.036765 ATCAGGCCGACACGCTAAAA 60.037 50.000 0.00 0.00 0.00 1.52
700 835 0.947180 TCAGGCCGACACGCTAAAAC 60.947 55.000 0.00 0.00 0.00 2.43
701 836 1.670083 AGGCCGACACGCTAAAACC 60.670 57.895 0.00 0.00 0.00 3.27
702 837 2.472934 GCCGACACGCTAAAACCG 59.527 61.111 0.00 0.00 0.00 4.44
703 838 3.018840 GCCGACACGCTAAAACCGG 62.019 63.158 0.00 0.00 39.88 5.28
704 839 2.472934 CGACACGCTAAAACCGGC 59.527 61.111 0.00 0.00 0.00 6.13
705 840 2.865308 GACACGCTAAAACCGGCC 59.135 61.111 0.00 0.00 0.00 6.13
706 841 2.670592 ACACGCTAAAACCGGCCC 60.671 61.111 0.00 0.00 0.00 5.80
707 842 2.670251 CACGCTAAAACCGGCCCA 60.670 61.111 0.00 0.00 0.00 5.36
708 843 2.043980 CACGCTAAAACCGGCCCAT 61.044 57.895 0.00 0.00 0.00 4.00
709 844 1.303806 ACGCTAAAACCGGCCCATT 60.304 52.632 0.00 0.00 0.00 3.16
710 845 0.896479 ACGCTAAAACCGGCCCATTT 60.896 50.000 0.00 0.39 0.00 2.32
711 846 0.457681 CGCTAAAACCGGCCCATTTG 60.458 55.000 0.00 0.00 0.00 2.32
712 847 0.108377 GCTAAAACCGGCCCATTTGG 60.108 55.000 0.00 1.34 37.09 3.28
730 865 7.108847 CCATTTGGCCAGGTTTATTTTTATGA 58.891 34.615 5.11 0.00 0.00 2.15
734 869 7.309770 TGGCCAGGTTTATTTTTATGAACTT 57.690 32.000 0.00 0.00 0.00 2.66
735 870 7.158021 TGGCCAGGTTTATTTTTATGAACTTG 58.842 34.615 0.00 0.00 30.54 3.16
737 872 8.308207 GGCCAGGTTTATTTTTATGAACTTGTA 58.692 33.333 0.00 0.00 29.32 2.41
738 873 9.869757 GCCAGGTTTATTTTTATGAACTTGTAT 57.130 29.630 0.00 0.00 29.32 2.29
747 882 9.705290 ATTTTTATGAACTTGTATCCCACAAAC 57.295 29.630 0.00 0.00 46.37 2.93
748 883 8.472007 TTTTATGAACTTGTATCCCACAAACT 57.528 30.769 0.00 0.00 46.37 2.66
749 884 5.964958 ATGAACTTGTATCCCACAAACTG 57.035 39.130 0.00 0.00 46.37 3.16
750 885 4.787551 TGAACTTGTATCCCACAAACTGT 58.212 39.130 0.00 0.00 46.37 3.55
751 886 4.578516 TGAACTTGTATCCCACAAACTGTG 59.421 41.667 0.00 0.00 46.37 3.66
762 897 4.285807 CACAAACTGTGGTTTTCGATGA 57.714 40.909 0.00 0.00 44.27 2.92
763 898 4.667262 CACAAACTGTGGTTTTCGATGAA 58.333 39.130 0.00 0.00 44.27 2.57
764 899 4.734854 CACAAACTGTGGTTTTCGATGAAG 59.265 41.667 0.00 0.00 44.27 3.02
765 900 4.638421 ACAAACTGTGGTTTTCGATGAAGA 59.362 37.500 0.00 0.00 42.96 2.87
766 901 5.124776 ACAAACTGTGGTTTTCGATGAAGAA 59.875 36.000 0.00 0.00 42.96 2.52
767 902 5.828299 AACTGTGGTTTTCGATGAAGAAA 57.172 34.783 0.00 0.00 38.23 2.52
768 903 5.424121 ACTGTGGTTTTCGATGAAGAAAG 57.576 39.130 0.00 0.00 40.66 2.62
769 904 4.881850 ACTGTGGTTTTCGATGAAGAAAGT 59.118 37.500 0.00 0.00 40.66 2.66
770 905 5.357032 ACTGTGGTTTTCGATGAAGAAAGTT 59.643 36.000 0.00 0.00 40.66 2.66
771 906 5.816919 TGTGGTTTTCGATGAAGAAAGTTC 58.183 37.500 0.00 0.00 40.66 3.01
772 907 4.904154 GTGGTTTTCGATGAAGAAAGTTCG 59.096 41.667 0.00 0.00 40.66 3.95
773 908 4.024387 TGGTTTTCGATGAAGAAAGTTCGG 60.024 41.667 0.00 0.00 40.66 4.30
774 909 3.806316 TTTCGATGAAGAAAGTTCGGC 57.194 42.857 0.00 0.00 35.44 5.54
775 910 1.722011 TCGATGAAGAAAGTTCGGCC 58.278 50.000 0.00 0.00 32.67 6.13
776 911 0.727398 CGATGAAGAAAGTTCGGCCC 59.273 55.000 0.00 0.00 0.00 5.80
777 912 1.676014 CGATGAAGAAAGTTCGGCCCT 60.676 52.381 0.00 0.00 0.00 5.19
778 913 1.740025 GATGAAGAAAGTTCGGCCCTG 59.260 52.381 0.00 0.00 0.00 4.45
779 914 0.889186 TGAAGAAAGTTCGGCCCTGC 60.889 55.000 0.00 0.00 0.00 4.85
780 915 1.587043 GAAGAAAGTTCGGCCCTGCC 61.587 60.000 0.00 0.00 46.75 4.85
789 924 3.302344 GGCCCTGCCGCTCAAAAA 61.302 61.111 0.00 0.00 39.62 1.94
821 956 3.621558 CCTGCCTAAAACCTTCCCTAAG 58.378 50.000 0.00 0.00 0.00 2.18
832 968 6.375830 AACCTTCCCTAAGAAAACTCCTAG 57.624 41.667 0.00 0.00 34.37 3.02
869 1008 3.774766 AGAAAAGGGCAAAAAGGTCAACT 59.225 39.130 0.00 0.00 0.00 3.16
876 1015 2.070654 AAAAAGGTCAACTGCCGCCG 62.071 55.000 0.00 0.00 0.00 6.46
897 1036 1.949847 CTACGGGCTACTGCTGCTGT 61.950 60.000 16.37 16.37 39.59 4.40
917 1059 2.365293 GTGAACACAGGCTTTTTCCCAT 59.635 45.455 0.00 0.00 0.00 4.00
1161 1339 5.986135 CACATCCTACTAGCACTATCAAACC 59.014 44.000 0.00 0.00 0.00 3.27
1202 1390 3.104843 AGTAATCAGAGCCTCGATTGC 57.895 47.619 16.67 15.56 35.29 3.56
1205 1393 2.374830 ATCAGAGCCTCGATTGCCGG 62.375 60.000 0.00 0.00 39.14 6.13
1230 1418 1.676967 CTGCTGGTTCAGGGGCTTC 60.677 63.158 0.00 0.00 31.21 3.86
1319 1536 1.533625 GCATGCAAGAGTGTGGGTTA 58.466 50.000 14.21 0.00 0.00 2.85
1348 1565 2.098770 GGAGAATGCATGTCAGAAAGCC 59.901 50.000 0.00 0.00 0.00 4.35
1415 1638 9.142993 GTTTTGTTTTTATGATTTTTCGTCTGC 57.857 29.630 0.00 0.00 0.00 4.26
1424 1647 5.747565 TGATTTTTCGTCTGCAACACTAAG 58.252 37.500 0.00 0.00 0.00 2.18
1433 1656 5.405571 CGTCTGCAACACTAAGATGTAGTTT 59.594 40.000 0.00 0.00 34.95 2.66
1476 1702 4.612943 GAAATAGCTCTCTAGAACACGGG 58.387 47.826 0.00 0.00 0.00 5.28
1479 1705 3.083122 AGCTCTCTAGAACACGGGTTA 57.917 47.619 1.22 0.00 37.36 2.85
1548 1774 9.528018 AAATTTCACACAAAGATACGAAAATGT 57.472 25.926 0.00 0.00 0.00 2.71
1553 1779 5.079406 CACAAAGATACGAAAATGTGTCGG 58.921 41.667 0.00 0.00 42.82 4.79
1563 1789 1.299541 AATGTGTCGGCCGATTCATC 58.700 50.000 32.33 21.97 0.00 2.92
1807 2034 9.855021 AAACTTATGCACTAAAATAACCATGAC 57.145 29.630 0.00 0.00 0.00 3.06
1895 2125 5.292101 AGTGATGCGCTGTAATAGTTTTCTC 59.708 40.000 9.73 0.00 0.00 2.87
1896 2126 5.063438 GTGATGCGCTGTAATAGTTTTCTCA 59.937 40.000 9.73 0.00 0.00 3.27
1898 2128 6.983890 TGATGCGCTGTAATAGTTTTCTCATA 59.016 34.615 9.73 0.00 0.00 2.15
1935 2165 0.798776 CCTGTTGCTGGTCTAAAGCG 59.201 55.000 0.00 0.00 43.88 4.68
1958 2188 0.616679 TGTACTCACAGGTAGGGGGC 60.617 60.000 0.00 0.00 0.00 5.80
2077 2312 1.067425 CCGTTGTATGTCGTCAAGGGA 60.067 52.381 9.95 0.00 46.15 4.20
2477 2722 2.380064 TCAGGTCAGTGGGCATTTTT 57.620 45.000 0.00 0.00 0.00 1.94
2484 2729 5.543790 AGGTCAGTGGGCATTTTTATTCTTT 59.456 36.000 0.00 0.00 0.00 2.52
2646 2896 5.810525 ACTCAAGCGTATTTATGAACATGC 58.189 37.500 0.00 0.00 0.00 4.06
2690 2940 5.918426 TGCATTCTATTTTCTGCCATCAA 57.082 34.783 0.00 0.00 33.70 2.57
2695 2945 8.139989 GCATTCTATTTTCTGCCATCAAATAGT 58.860 33.333 12.23 0.00 39.76 2.12
2800 3212 3.813443 ACTATCAAGGCTCGATTTGCAT 58.187 40.909 0.00 0.00 0.00 3.96
2859 3271 5.478233 TTGTTGTACTAAGTGTGTGCTTG 57.522 39.130 0.00 0.00 0.00 4.01
2860 3272 4.509616 TGTTGTACTAAGTGTGTGCTTGT 58.490 39.130 0.00 0.00 0.00 3.16
2861 3273 4.331443 TGTTGTACTAAGTGTGTGCTTGTG 59.669 41.667 0.00 0.00 0.00 3.33
2862 3274 3.462982 TGTACTAAGTGTGTGCTTGTGG 58.537 45.455 0.00 0.00 0.00 4.17
2863 3275 3.133183 TGTACTAAGTGTGTGCTTGTGGA 59.867 43.478 0.00 0.00 0.00 4.02
2864 3276 2.561569 ACTAAGTGTGTGCTTGTGGAC 58.438 47.619 0.00 0.00 34.96 4.02
2865 3277 2.170607 ACTAAGTGTGTGCTTGTGGACT 59.829 45.455 0.00 0.00 35.45 3.85
2866 3278 2.128771 AAGTGTGTGCTTGTGGACTT 57.871 45.000 0.00 0.00 35.45 3.01
2878 3290 1.032014 GTGGACTTGTGGTTGTGCAT 58.968 50.000 0.00 0.00 36.93 3.96
2975 3406 8.305046 AGCCTTTTATTGCTTCCATGTTTATA 57.695 30.769 0.00 0.00 32.94 0.98
2986 3417 8.313292 TGCTTCCATGTTTATATTCAGCTTTTT 58.687 29.630 0.00 0.00 0.00 1.94
3035 3466 4.212425 GGGGGCTTTTCGTTGTTAAATTTG 59.788 41.667 0.00 0.00 0.00 2.32
3100 3531 2.350102 GGCCGTCAAAGGTAAAAACTCG 60.350 50.000 0.00 0.00 0.00 4.18
3256 3689 6.903883 TGACAAGTCTCTGTTCAAGTAAAC 57.096 37.500 1.53 0.00 0.00 2.01
3257 3690 6.403049 TGACAAGTCTCTGTTCAAGTAAACA 58.597 36.000 1.53 0.00 37.56 2.83
3950 4393 8.508883 TTTAAGAGACTACCAGAGAGACATAC 57.491 38.462 0.00 0.00 0.00 2.39
4034 4478 3.420839 AAGCTGTTGGTTTCTGAAACG 57.579 42.857 22.80 12.32 42.29 3.60
4065 4509 8.922676 TCAAATTTAAGCACTACTCTAAGAACG 58.077 33.333 0.00 0.00 0.00 3.95
4077 4521 5.467705 ACTCTAAGAACGTTATTGCGTCTT 58.532 37.500 17.98 9.72 45.00 3.01
4093 4537 6.268825 TGCGTCTTTTAGAGAATGAGTAGT 57.731 37.500 0.00 0.00 35.79 2.73
4122 4566 3.063997 CCGAAGTGGATAACAGCACATTC 59.936 47.826 0.00 0.00 42.00 2.67
4165 4609 4.796618 GCGTATCATTTACCCTCTGTCTCC 60.797 50.000 0.00 0.00 0.00 3.71
4225 4670 2.978824 CCCCACCTGGTACGAGTG 59.021 66.667 0.00 3.18 0.00 3.51
4258 4703 2.695666 ACTTAGAGGTGATGATGGACGG 59.304 50.000 0.00 0.00 0.00 4.79
4319 4764 1.551560 ACGAAGTATCTGGGACCACCA 60.552 52.381 0.00 0.00 45.23 4.17
4375 4820 5.335661 GGTTATTCGGAATGCAGACACTTTT 60.336 40.000 13.37 0.00 0.00 2.27
4435 4880 3.550820 TGTTGTCAACATTACCAGCAGT 58.449 40.909 14.48 0.00 36.25 4.40
4442 4887 0.461870 CATTACCAGCAGTGCGGCTA 60.462 55.000 21.05 12.30 43.68 3.93
4510 4955 6.299604 CGTGCAACTTCTTAAGATTACACTG 58.700 40.000 15.39 8.73 31.75 3.66
4511 4956 6.080406 GTGCAACTTCTTAAGATTACACTGC 58.920 40.000 5.89 10.00 0.00 4.40
4516 4961 9.593134 CAACTTCTTAAGATTACACTGCTATCT 57.407 33.333 5.89 0.00 0.00 1.98
4532 4977 3.873952 GCTATCTTAAGTTGCTGGTGAGG 59.126 47.826 1.63 0.00 0.00 3.86
4534 4979 2.334977 TCTTAAGTTGCTGGTGAGGGA 58.665 47.619 1.63 0.00 0.00 4.20
4536 4981 3.137544 TCTTAAGTTGCTGGTGAGGGAAA 59.862 43.478 1.63 0.00 0.00 3.13
4543 4988 0.322008 CTGGTGAGGGAAACTCCTGC 60.322 60.000 0.00 0.00 46.01 4.85
4546 4991 0.606673 GTGAGGGAAACTCCTGCCAC 60.607 60.000 0.00 0.00 46.01 5.01
4572 5017 8.220755 TCTGTTTTGATGTTGCTACTTAAACT 57.779 30.769 0.00 0.00 0.00 2.66
4575 5020 9.296400 TGTTTTGATGTTGCTACTTAAACTTTC 57.704 29.630 0.00 0.00 0.00 2.62
4606 5051 9.085250 CAGAGACATCAATCTTATCGGAATATG 57.915 37.037 0.00 0.00 0.00 1.78
4664 5111 4.484236 TCTGTGTTCTTTTGTGCTTTGTG 58.516 39.130 0.00 0.00 0.00 3.33
4665 5112 4.022416 TCTGTGTTCTTTTGTGCTTTGTGT 60.022 37.500 0.00 0.00 0.00 3.72
4666 5113 4.626042 TGTGTTCTTTTGTGCTTTGTGTT 58.374 34.783 0.00 0.00 0.00 3.32
4667 5114 4.447054 TGTGTTCTTTTGTGCTTTGTGTTG 59.553 37.500 0.00 0.00 0.00 3.33
4668 5115 3.993081 TGTTCTTTTGTGCTTTGTGTTGG 59.007 39.130 0.00 0.00 0.00 3.77
4669 5116 3.951775 TCTTTTGTGCTTTGTGTTGGT 57.048 38.095 0.00 0.00 0.00 3.67
4670 5117 3.583806 TCTTTTGTGCTTTGTGTTGGTG 58.416 40.909 0.00 0.00 0.00 4.17
4671 5118 1.719600 TTTGTGCTTTGTGTTGGTGC 58.280 45.000 0.00 0.00 0.00 5.01
4672 5119 0.894141 TTGTGCTTTGTGTTGGTGCT 59.106 45.000 0.00 0.00 0.00 4.40
4673 5120 0.894141 TGTGCTTTGTGTTGGTGCTT 59.106 45.000 0.00 0.00 0.00 3.91
4674 5121 1.274728 TGTGCTTTGTGTTGGTGCTTT 59.725 42.857 0.00 0.00 0.00 3.51
4675 5122 1.660104 GTGCTTTGTGTTGGTGCTTTG 59.340 47.619 0.00 0.00 0.00 2.77
4676 5123 0.652071 GCTTTGTGTTGGTGCTTTGC 59.348 50.000 0.00 0.00 0.00 3.68
4782 5243 9.070149 GCTTTATTGATGATCACTCTTGTTTTC 57.930 33.333 0.00 0.00 0.00 2.29
4840 5309 2.006772 CTAAGCCACCGTCGCATTC 58.993 57.895 0.00 0.00 0.00 2.67
4880 5349 2.125106 CGCCCTGCAGGAAGTACC 60.125 66.667 34.91 12.93 38.24 3.34
5057 5526 9.992910 TGACATGTAGTAGTAGTTAATAACACG 57.007 33.333 0.00 0.00 0.00 4.49
5069 5538 7.843490 AGTTAATAACACGCACTAATGTGAT 57.157 32.000 5.89 0.00 46.55 3.06
5089 5558 6.152492 TGTGATATCTAAATGTTTGCTGGCAA 59.848 34.615 3.98 3.72 0.00 4.52
5136 5610 2.364632 TCGGCCATGTGAATCGAATTT 58.635 42.857 2.24 0.00 0.00 1.82
5137 5611 2.752354 TCGGCCATGTGAATCGAATTTT 59.248 40.909 2.24 0.00 0.00 1.82
5138 5612 3.192422 TCGGCCATGTGAATCGAATTTTT 59.808 39.130 2.24 0.00 0.00 1.94
5139 5613 4.396478 TCGGCCATGTGAATCGAATTTTTA 59.604 37.500 2.24 0.00 0.00 1.52
5140 5614 5.067153 TCGGCCATGTGAATCGAATTTTTAT 59.933 36.000 2.24 0.00 0.00 1.40
5197 5672 4.517952 TTTTCATGTGCCCTGTTATGTG 57.482 40.909 0.00 0.00 0.00 3.21
5209 5684 4.096382 CCCTGTTATGTGGTCTATTTGCAC 59.904 45.833 0.00 0.00 0.00 4.57
5214 5689 0.878416 GTGGTCTATTTGCACGCCAA 59.122 50.000 0.00 0.00 0.00 4.52
5351 5826 0.674534 GACCGCCGATGGAGTATCTT 59.325 55.000 0.00 0.00 33.44 2.40
5384 5859 2.969806 GACTACCGCGTCCGTGTCA 61.970 63.158 4.92 0.00 31.99 3.58
5403 5878 1.069568 CACCGCTGCGAAATAAACACA 60.070 47.619 25.45 0.00 0.00 3.72
5438 5913 5.049267 TGTCAAAATGCTTACGGAAGGTAAC 60.049 40.000 10.00 0.00 36.20 2.50
5503 5979 4.693095 GTCAGCTCCCTTGTCTTTCTAAAG 59.307 45.833 0.00 0.00 37.36 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 2.019807 TGGTACCCCGAGTCTTCTTT 57.980 50.000 10.07 0.00 0.00 2.52
106 107 3.343941 TTCAAATCTCTTGGTACCCCG 57.656 47.619 10.07 0.00 0.00 5.73
144 145 5.351465 CACATGTCCTAAATACACACACTCC 59.649 44.000 0.00 0.00 0.00 3.85
145 146 6.163476 TCACATGTCCTAAATACACACACTC 58.837 40.000 0.00 0.00 0.00 3.51
155 156 7.202011 GGGTACTGAGTATCACATGTCCTAAAT 60.202 40.741 5.11 0.00 42.56 1.40
174 175 2.483014 TTGGAATGAACGGGGTACTG 57.517 50.000 0.00 0.00 0.00 2.74
180 181 5.068460 TGCCTTATATTTTGGAATGAACGGG 59.932 40.000 0.00 0.00 0.00 5.28
200 201 7.136822 TGACTTCCACATATTAAGTATGCCT 57.863 36.000 0.00 0.00 43.30 4.75
201 202 7.986085 ATGACTTCCACATATTAAGTATGCC 57.014 36.000 0.00 0.00 43.30 4.40
407 416 7.665559 GGATCAACCCATTTATAATGCAGACTA 59.334 37.037 0.00 0.00 0.00 2.59
444 453 1.189524 TGTACTTAGCGTGCCTGGGT 61.190 55.000 0.00 0.00 0.00 4.51
445 454 0.739813 GTGTACTTAGCGTGCCTGGG 60.740 60.000 0.00 0.00 0.00 4.45
484 528 1.594833 CCAGTAAGGGTAGCACGCA 59.405 57.895 0.00 0.00 32.95 5.24
492 536 3.339093 GCCTGGGCCAGTAAGGGT 61.339 66.667 30.68 0.00 38.09 4.34
520 564 0.249120 CTGTGCCGACCCATGTAAGA 59.751 55.000 0.00 0.00 0.00 2.10
543 587 2.750237 CCACCAGGCTAAACGGGC 60.750 66.667 0.00 0.00 0.00 6.13
557 601 1.278238 CTGAATTCTACGCGGACCAC 58.722 55.000 12.47 0.00 0.00 4.16
577 621 1.668826 ATAGGTCCAAAGCAGTCCCA 58.331 50.000 0.00 0.00 0.00 4.37
578 622 4.141482 TGAATATAGGTCCAAAGCAGTCCC 60.141 45.833 0.00 0.00 0.00 4.46
581 629 4.164988 AGCTGAATATAGGTCCAAAGCAGT 59.835 41.667 0.00 0.00 31.85 4.40
626 761 6.293698 CGGCCCTACACTTTATAATTAGGTT 58.706 40.000 0.00 0.00 0.00 3.50
627 762 5.221783 CCGGCCCTACACTTTATAATTAGGT 60.222 44.000 0.00 0.00 0.00 3.08
631 766 3.749632 GCCCGGCCCTACACTTTATAATT 60.750 47.826 0.00 0.00 0.00 1.40
660 795 3.402681 CCCTCGTGTCTGGCCCAT 61.403 66.667 0.00 0.00 0.00 4.00
669 804 3.221222 GCCTGATAGCCCTCGTGT 58.779 61.111 0.00 0.00 0.00 4.49
682 817 1.495951 GTTTTAGCGTGTCGGCCTG 59.504 57.895 0.00 0.00 0.00 4.85
683 818 1.670083 GGTTTTAGCGTGTCGGCCT 60.670 57.895 0.00 0.00 0.00 5.19
689 824 2.670592 GGGCCGGTTTTAGCGTGT 60.671 61.111 1.90 0.00 37.40 4.49
704 839 3.998913 AAATAAACCTGGCCAAATGGG 57.001 42.857 7.01 7.12 40.85 4.00
705 840 7.108847 TCATAAAAATAAACCTGGCCAAATGG 58.891 34.615 7.01 7.56 38.53 3.16
706 841 8.450180 GTTCATAAAAATAAACCTGGCCAAATG 58.550 33.333 7.01 0.12 0.00 2.32
707 842 8.382405 AGTTCATAAAAATAAACCTGGCCAAAT 58.618 29.630 7.01 0.00 0.00 2.32
708 843 7.740805 AGTTCATAAAAATAAACCTGGCCAAA 58.259 30.769 7.01 0.00 0.00 3.28
709 844 7.309770 AGTTCATAAAAATAAACCTGGCCAA 57.690 32.000 7.01 0.00 0.00 4.52
710 845 6.926630 AGTTCATAAAAATAAACCTGGCCA 57.073 33.333 4.71 4.71 0.00 5.36
711 846 7.158697 ACAAGTTCATAAAAATAAACCTGGCC 58.841 34.615 0.00 0.00 0.00 5.36
712 847 9.869757 ATACAAGTTCATAAAAATAAACCTGGC 57.130 29.630 0.00 0.00 0.00 4.85
741 876 4.285807 TCATCGAAAACCACAGTTTGTG 57.714 40.909 2.28 2.28 45.54 3.33
742 877 4.638421 TCTTCATCGAAAACCACAGTTTGT 59.362 37.500 0.00 0.00 45.54 2.83
743 878 5.168526 TCTTCATCGAAAACCACAGTTTG 57.831 39.130 0.00 0.00 45.54 2.93
745 880 5.357032 ACTTTCTTCATCGAAAACCACAGTT 59.643 36.000 0.00 0.00 38.03 3.16
746 881 4.881850 ACTTTCTTCATCGAAAACCACAGT 59.118 37.500 0.00 0.00 32.95 3.55
747 882 5.424121 ACTTTCTTCATCGAAAACCACAG 57.576 39.130 0.00 0.00 32.95 3.66
748 883 5.503357 CGAACTTTCTTCATCGAAAACCACA 60.503 40.000 0.00 0.00 37.48 4.17
749 884 4.904154 CGAACTTTCTTCATCGAAAACCAC 59.096 41.667 0.00 0.00 37.48 4.16
750 885 4.024387 CCGAACTTTCTTCATCGAAAACCA 60.024 41.667 0.00 0.00 37.48 3.67
751 886 4.464112 CCGAACTTTCTTCATCGAAAACC 58.536 43.478 0.00 0.00 37.48 3.27
752 887 3.906601 GCCGAACTTTCTTCATCGAAAAC 59.093 43.478 0.00 0.00 37.48 2.43
753 888 3.058501 GGCCGAACTTTCTTCATCGAAAA 60.059 43.478 0.00 0.00 37.48 2.29
754 889 2.482721 GGCCGAACTTTCTTCATCGAAA 59.517 45.455 0.00 0.00 37.48 3.46
755 890 2.073816 GGCCGAACTTTCTTCATCGAA 58.926 47.619 0.00 0.00 37.48 3.71
756 891 1.674817 GGGCCGAACTTTCTTCATCGA 60.675 52.381 0.00 0.00 37.48 3.59
757 892 0.727398 GGGCCGAACTTTCTTCATCG 59.273 55.000 0.00 0.00 35.19 3.84
758 893 1.740025 CAGGGCCGAACTTTCTTCATC 59.260 52.381 0.00 0.00 0.00 2.92
759 894 1.826385 CAGGGCCGAACTTTCTTCAT 58.174 50.000 0.00 0.00 0.00 2.57
760 895 0.889186 GCAGGGCCGAACTTTCTTCA 60.889 55.000 0.00 0.00 0.00 3.02
761 896 1.587043 GGCAGGGCCGAACTTTCTTC 61.587 60.000 0.00 0.00 39.62 2.87
762 897 1.603739 GGCAGGGCCGAACTTTCTT 60.604 57.895 0.00 0.00 39.62 2.52
763 898 2.034221 GGCAGGGCCGAACTTTCT 59.966 61.111 0.00 0.00 39.62 2.52
772 907 3.302344 TTTTTGAGCGGCAGGGCC 61.302 61.111 1.45 0.00 46.75 5.80
796 931 1.637035 GGAAGGTTTTAGGCAGGGGTA 59.363 52.381 0.00 0.00 0.00 3.69
798 933 0.324368 GGGAAGGTTTTAGGCAGGGG 60.324 60.000 0.00 0.00 0.00 4.79
821 956 6.715718 AGGAAAGGTTTTAGCTAGGAGTTTTC 59.284 38.462 0.00 3.98 0.00 2.29
876 1015 2.107141 CAGCAGTAGCCCGTAGCC 59.893 66.667 0.00 0.00 45.47 3.93
877 1016 2.586357 GCAGCAGTAGCCCGTAGC 60.586 66.667 0.00 0.00 43.56 3.58
878 1017 1.227089 CAGCAGCAGTAGCCCGTAG 60.227 63.158 0.00 0.00 43.56 3.51
879 1018 1.982395 ACAGCAGCAGTAGCCCGTA 60.982 57.895 0.00 0.00 43.56 4.02
880 1019 3.314331 ACAGCAGCAGTAGCCCGT 61.314 61.111 0.00 0.00 43.56 5.28
881 1020 2.786539 TTCACAGCAGCAGTAGCCCG 62.787 60.000 0.00 0.00 43.56 6.13
882 1021 1.003355 TTCACAGCAGCAGTAGCCC 60.003 57.895 0.00 0.00 43.56 5.19
897 1036 2.151502 TGGGAAAAAGCCTGTGTTCA 57.848 45.000 0.00 0.00 0.00 3.18
936 1078 2.981560 GCGTGGGTGTGATGCAAGG 61.982 63.158 0.00 0.00 0.00 3.61
1161 1339 2.590007 GCATAGGTGGCGCTGGAG 60.590 66.667 7.64 0.00 0.00 3.86
1205 1393 3.259425 CTGAACCAGCAGCGGCAAC 62.259 63.158 12.44 0.00 44.61 4.17
1230 1418 1.595382 CGGCCGAATTAGGAGCAGG 60.595 63.158 24.07 0.00 0.00 4.85
1256 1444 1.681793 ACTACTACTAGTGGCGCATGG 59.318 52.381 10.83 0.00 31.46 3.66
1300 1510 1.533625 TAACCCACACTCTTGCATGC 58.466 50.000 11.82 11.82 0.00 4.06
1308 1525 2.027192 TCCTGAGCATTAACCCACACTC 60.027 50.000 0.00 0.00 0.00 3.51
1319 1536 2.950309 GACATGCATTCTCCTGAGCATT 59.050 45.455 0.00 0.00 44.63 3.56
1348 1565 3.976942 CGACAAAAGAACATGCCAGAAAG 59.023 43.478 0.00 0.00 0.00 2.62
1392 1614 7.993821 TGCAGACGAAAAATCATAAAAACAA 57.006 28.000 0.00 0.00 0.00 2.83
1410 1633 6.787085 AAACTACATCTTAGTGTTGCAGAC 57.213 37.500 0.00 0.00 33.62 3.51
1424 1647 4.945543 ACCCCGAAACCATAAAACTACATC 59.054 41.667 0.00 0.00 0.00 3.06
1433 1656 3.632643 GGTAGAACCCCGAAACCATAA 57.367 47.619 0.00 0.00 30.04 1.90
1479 1705 9.732130 GGATATCCTTGTTAGCTATTTCAATCT 57.268 33.333 14.97 0.00 0.00 2.40
1548 1774 1.143838 CCAGATGAATCGGCCGACA 59.856 57.895 33.75 25.65 0.00 4.35
1553 1779 6.076981 ACATTTAAATCCAGATGAATCGGC 57.923 37.500 0.00 0.00 0.00 5.54
1842 2069 8.860088 AGTGTAGCCTCAACTGAATTAAATTTT 58.140 29.630 0.00 0.00 0.00 1.82
1864 2091 0.318441 ACAGCGCATCACTGTAGTGT 59.682 50.000 11.47 0.00 46.32 3.55
1895 2125 7.661040 ACAGGAAGAAAAACTGACCAATTATG 58.339 34.615 0.00 0.00 36.17 1.90
1896 2126 7.839680 ACAGGAAGAAAAACTGACCAATTAT 57.160 32.000 0.00 0.00 36.17 1.28
1898 2128 6.340522 CAACAGGAAGAAAAACTGACCAATT 58.659 36.000 0.00 0.00 36.17 2.32
1949 2179 0.696485 TACAATCTGGGCCCCCTACC 60.696 60.000 22.27 0.00 36.94 3.18
1950 2180 0.472898 GTACAATCTGGGCCCCCTAC 59.527 60.000 22.27 5.62 36.94 3.18
1951 2181 0.045008 TGTACAATCTGGGCCCCCTA 59.955 55.000 22.27 4.47 36.94 3.53
1952 2182 0.627469 ATGTACAATCTGGGCCCCCT 60.627 55.000 22.27 0.00 36.94 4.79
1953 2183 1.145571 TATGTACAATCTGGGCCCCC 58.854 55.000 22.27 0.00 0.00 5.40
1954 2184 2.108250 ACATATGTACAATCTGGGCCCC 59.892 50.000 22.27 0.37 0.00 5.80
1958 2188 7.630242 AGTTTTCACATATGTACAATCTGGG 57.370 36.000 8.32 0.00 0.00 4.45
2003 2238 6.805016 ATATCTGATGATAATTCCGCCTCT 57.195 37.500 0.00 0.00 38.50 3.69
2077 2312 6.655003 CACTACAAAATGAGGTCCACATACTT 59.345 38.462 1.85 0.00 0.00 2.24
2145 2380 1.555741 CGCACAAACCGCAAAATGGG 61.556 55.000 0.00 0.00 0.00 4.00
2295 2539 9.476202 CGAGGATACATTGTCATCTACATAAAA 57.524 33.333 0.00 0.00 37.10 1.52
2477 2722 4.761739 CCAAAGACAGCACCTGAAAGAATA 59.238 41.667 0.00 0.00 34.07 1.75
2484 2729 1.228245 GGCCAAAGACAGCACCTGA 60.228 57.895 0.00 0.00 35.18 3.86
2859 3271 1.032014 ATGCACAACCACAAGTCCAC 58.968 50.000 0.00 0.00 0.00 4.02
2860 3272 1.031235 CATGCACAACCACAAGTCCA 58.969 50.000 0.00 0.00 0.00 4.02
2861 3273 0.318955 GCATGCACAACCACAAGTCC 60.319 55.000 14.21 0.00 0.00 3.85
2862 3274 0.385029 TGCATGCACAACCACAAGTC 59.615 50.000 18.46 0.00 0.00 3.01
2863 3275 1.042229 ATGCATGCACAACCACAAGT 58.958 45.000 25.37 0.00 0.00 3.16
2864 3276 1.795872 CAATGCATGCACAACCACAAG 59.204 47.619 25.37 1.25 0.00 3.16
2865 3277 1.138464 ACAATGCATGCACAACCACAA 59.862 42.857 25.37 0.00 0.00 3.33
2866 3278 0.751452 ACAATGCATGCACAACCACA 59.249 45.000 25.37 0.00 0.00 4.17
2975 3406 7.889469 TCTAATTGCTCAAGAAAAAGCTGAAT 58.111 30.769 0.00 0.00 39.31 2.57
2986 3417 4.141642 TGCAGCCTATCTAATTGCTCAAGA 60.142 41.667 0.00 0.00 35.85 3.02
3035 3466 4.893424 TTCAGGCAGATAAAAATACGCC 57.107 40.909 0.00 0.00 39.90 5.68
3125 3558 9.829507 TGGAAACATAAGAAAAACAATCACATT 57.170 25.926 0.00 0.00 33.40 2.71
3256 3689 2.611751 TGACGACCATGTTTCACAACTG 59.388 45.455 0.00 0.00 33.58 3.16
3257 3690 2.912771 TGACGACCATGTTTCACAACT 58.087 42.857 0.00 0.00 33.58 3.16
3261 3694 7.867445 AATTTTTATGACGACCATGTTTCAC 57.133 32.000 0.00 0.00 36.71 3.18
3387 3828 4.925836 TGCATGGATAGTTCATGGCATAT 58.074 39.130 0.00 0.00 41.49 1.78
3767 4209 0.325933 TGGTGCCACTCCTCTTGATG 59.674 55.000 0.00 0.00 0.00 3.07
3872 4315 2.293677 TTGCACTCTACCTACATGCG 57.706 50.000 0.00 0.00 39.18 4.73
4001 4445 8.779354 AAACCAACAGCTTAACAAAATAACAA 57.221 26.923 0.00 0.00 0.00 2.83
4002 4446 8.254508 AGAAACCAACAGCTTAACAAAATAACA 58.745 29.630 0.00 0.00 0.00 2.41
4003 4447 8.539674 CAGAAACCAACAGCTTAACAAAATAAC 58.460 33.333 0.00 0.00 0.00 1.89
4004 4448 8.470805 TCAGAAACCAACAGCTTAACAAAATAA 58.529 29.630 0.00 0.00 0.00 1.40
4005 4449 8.001881 TCAGAAACCAACAGCTTAACAAAATA 57.998 30.769 0.00 0.00 0.00 1.40
4018 4462 5.955488 TGAAATTCGTTTCAGAAACCAACA 58.045 33.333 18.58 5.91 38.14 3.33
4065 4509 7.965045 ACTCATTCTCTAAAAGACGCAATAAC 58.035 34.615 0.00 0.00 32.27 1.89
4077 4521 8.045507 TCGGAAGTAGACTACTCATTCTCTAAA 58.954 37.037 15.49 0.00 38.26 1.85
4122 4566 1.738350 CAGAAGCATGAACAGCAGGAG 59.262 52.381 0.00 0.00 0.00 3.69
4225 4670 5.661458 TCACCTCTAAGTAGCATACAAAGC 58.339 41.667 0.00 0.00 46.26 3.51
4258 4703 0.725784 CCGCATTGACACTTTCACGC 60.726 55.000 0.00 0.00 32.26 5.34
4319 4764 2.516888 CCACAGGACCTCCGGTTGT 61.517 63.158 0.00 0.00 41.69 3.32
4375 4820 0.246086 CCGCCTTGGCAAAGCAATTA 59.754 50.000 19.90 0.00 31.51 1.40
4435 4880 0.947180 GAAAACTGGACGTAGCCGCA 60.947 55.000 0.00 0.00 37.70 5.69
4442 4887 4.411256 TGTAAGGAAGAAAACTGGACGT 57.589 40.909 0.00 0.00 0.00 4.34
4483 4928 6.090358 GTGTAATCTTAAGAAGTTGCACGCTA 59.910 38.462 18.23 0.00 31.57 4.26
4510 4955 3.873952 CCTCACCAGCAACTTAAGATAGC 59.126 47.826 10.09 9.69 0.00 2.97
4511 4956 4.162320 TCCCTCACCAGCAACTTAAGATAG 59.838 45.833 10.09 0.00 0.00 2.08
4516 4961 3.117663 AGTTTCCCTCACCAGCAACTTAA 60.118 43.478 0.00 0.00 0.00 1.85
4532 4977 0.398318 ACAGAGTGGCAGGAGTTTCC 59.602 55.000 0.00 0.00 36.58 3.13
4534 4979 2.689983 CAAAACAGAGTGGCAGGAGTTT 59.310 45.455 0.00 0.00 0.00 2.66
4536 4981 1.490490 TCAAAACAGAGTGGCAGGAGT 59.510 47.619 0.00 0.00 0.00 3.85
4543 4988 3.996150 AGCAACATCAAAACAGAGTGG 57.004 42.857 0.00 0.00 0.00 4.00
4546 4991 8.345565 AGTTTAAGTAGCAACATCAAAACAGAG 58.654 33.333 0.00 0.00 0.00 3.35
4572 5017 6.829229 AAGATTGATGTCTCTGCAATGAAA 57.171 33.333 0.00 0.00 32.80 2.69
4575 5020 6.347483 CCGATAAGATTGATGTCTCTGCAATG 60.347 42.308 0.00 0.00 32.80 2.82
4606 5051 4.080969 ACAGACTTGATACGAACGACTC 57.919 45.455 0.14 0.00 0.00 3.36
4664 5111 0.878416 TATGGACGCAAAGCACCAAC 59.122 50.000 8.49 0.00 37.91 3.77
4665 5112 1.832883 ATATGGACGCAAAGCACCAA 58.167 45.000 8.49 1.44 37.91 3.67
4666 5113 1.742831 GAATATGGACGCAAAGCACCA 59.257 47.619 7.21 7.21 38.48 4.17
4667 5114 2.017049 AGAATATGGACGCAAAGCACC 58.983 47.619 0.00 0.00 0.00 5.01
4668 5115 2.285834 CGAGAATATGGACGCAAAGCAC 60.286 50.000 0.00 0.00 0.00 4.40
4669 5116 1.933181 CGAGAATATGGACGCAAAGCA 59.067 47.619 0.00 0.00 0.00 3.91
4670 5117 2.201732 TCGAGAATATGGACGCAAAGC 58.798 47.619 0.00 0.00 0.00 3.51
4671 5118 6.525121 TTTATCGAGAATATGGACGCAAAG 57.475 37.500 0.00 0.00 0.00 2.77
4672 5119 7.117241 GATTTATCGAGAATATGGACGCAAA 57.883 36.000 0.00 0.00 0.00 3.68
4673 5120 6.706055 GATTTATCGAGAATATGGACGCAA 57.294 37.500 0.00 0.00 0.00 4.85
4705 5165 9.301897 CCTGGATAGCTAGTATATATGCACATA 57.698 37.037 0.00 0.00 0.00 2.29
4782 5243 9.907576 GAAGTCAAATAGTAATTTCGATGTGAG 57.092 33.333 0.00 0.00 32.87 3.51
4840 5309 2.050350 CATGCCAGGCCAGACCAAG 61.050 63.158 9.64 0.00 43.14 3.61
4863 5332 2.125106 GGTACTTCCTGCAGGGCG 60.125 66.667 32.23 23.86 35.41 6.13
4880 5349 0.091344 CAAGCGCTCGTACTGTTTCG 59.909 55.000 12.06 0.00 0.00 3.46
4909 5378 1.616921 CCATGAGGTTCCCCTGCAT 59.383 57.895 0.00 0.00 42.86 3.96
4930 5399 2.048127 GTGTCCGTCAGAGGTGCC 60.048 66.667 0.00 0.00 0.00 5.01
4984 5453 3.191371 GTGATGGATTTGTTGACCAGGTC 59.809 47.826 13.35 13.35 37.12 3.85
5040 5509 9.294030 ACATTAGTGCGTGTTATTAACTACTAC 57.706 33.333 7.99 3.28 0.00 2.73
5057 5526 9.173939 GCAAACATTTAGATATCACATTAGTGC 57.826 33.333 5.32 2.23 45.49 4.40
5069 5538 6.389091 CAACTTGCCAGCAAACATTTAGATA 58.611 36.000 6.52 0.00 35.33 1.98
5089 5558 2.566833 TTACACTCCTGCATGCAACT 57.433 45.000 22.88 0.85 0.00 3.16
5139 5613 9.558396 CTTCTCCTATCATTTTCTTAGCTTGAT 57.442 33.333 0.00 0.00 0.00 2.57
5140 5614 7.989741 CCTTCTCCTATCATTTTCTTAGCTTGA 59.010 37.037 0.00 0.00 0.00 3.02
5186 5660 4.096382 GTGCAAATAGACCACATAACAGGG 59.904 45.833 0.00 0.00 0.00 4.45
5197 5672 0.170339 GGTTGGCGTGCAAATAGACC 59.830 55.000 0.00 0.00 0.00 3.85
5209 5684 0.674581 TTGAGATGCTCTGGTTGGCG 60.675 55.000 0.00 0.00 0.00 5.69
5214 5689 4.774660 AGAATCATTGAGATGCTCTGGT 57.225 40.909 0.00 0.00 38.28 4.00
5315 5790 2.258109 GGTCTGGGTCTTCCAACTACT 58.742 52.381 0.00 0.00 46.51 2.57
5334 5809 0.389391 ACAAGATACTCCATCGGCGG 59.611 55.000 7.21 0.00 38.81 6.13
5351 5826 4.898607 GTCCCCTTGACAGCAACA 57.101 55.556 0.00 0.00 43.85 3.33
5384 5859 1.231221 TGTGTTTATTTCGCAGCGGT 58.769 45.000 16.42 4.18 0.00 5.68
5403 5878 8.698854 CGTAAGCATTTTGACATTAATGTTGTT 58.301 29.630 21.63 10.96 41.95 2.83
5463 5938 4.389992 AGCTGACGTTGTTGTTGATCTATG 59.610 41.667 0.00 0.00 0.00 2.23


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

AutoCloner maintained by Alex Coulton.