Multiple sequence alignment - TraesCS5B01G071300

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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 TraesCS5B01G071300 chr5B 100.000 5755 0 0 1 5755 82457745 82463499 0.000000e+00 10628.0
1 TraesCS5B01G071300 chr5B 92.632 95 6 1 786 879 82458441 82458535 1.010000e-27 135.0
2 TraesCS5B01G071300 chr5B 92.632 95 6 1 697 791 82458530 82458623 1.010000e-27 135.0
3 TraesCS5B01G071300 chr5A 96.321 3398 101 12 786 4165 64385581 64382190 0.000000e+00 5561.0
4 TraesCS5B01G071300 chr5A 91.605 1346 76 25 4169 5505 64382103 64380786 0.000000e+00 1825.0
5 TraesCS5B01G071300 chr5A 93.033 689 30 5 1 677 64386247 64385565 0.000000e+00 990.0
6 TraesCS5B01G071300 chr5A 88.083 193 11 5 5521 5703 64380802 64380612 9.710000e-53 219.0
7 TraesCS5B01G071300 chr5A 94.318 88 5 0 696 783 64385582 64385495 1.010000e-27 135.0
8 TraesCS5B01G071300 chr5A 89.474 57 3 3 5116 5169 64381095 64381039 1.030000e-07 69.4
9 TraesCS5B01G071300 chr5D 95.686 3199 90 17 1990 5171 71903435 71900268 0.000000e+00 5099.0
10 TraesCS5B01G071300 chr5D 95.004 1261 46 5 786 2031 71904734 71903476 0.000000e+00 1964.0
11 TraesCS5B01G071300 chr5D 93.988 682 26 3 1 677 71905389 71904718 0.000000e+00 1018.0
12 TraesCS5B01G071300 chr5D 86.297 343 30 14 3403 3741 17232531 17232202 1.970000e-94 357.0
13 TraesCS5B01G071300 chr5D 86.250 320 30 9 5293 5604 71900107 71899794 9.240000e-88 335.0
14 TraesCS5B01G071300 chr5D 85.484 186 13 6 5163 5347 71900331 71900159 1.270000e-41 182.0
15 TraesCS5B01G071300 chr5D 87.368 95 8 1 5609 5703 71899729 71899639 7.890000e-19 106.0
16 TraesCS5B01G071300 chr5D 100.000 42 0 0 1990 2031 71903476 71903435 1.720000e-10 78.7
17 TraesCS5B01G071300 chr5D 89.286 56 4 2 5293 5347 71900160 71900106 1.030000e-07 69.4
18 TraesCS5B01G071300 chr1A 85.068 884 99 23 3403 4279 157886782 157887639 0.000000e+00 870.0
19 TraesCS5B01G071300 chr1A 87.613 331 36 4 3678 4005 157886007 157886335 4.210000e-101 379.0
20 TraesCS5B01G071300 chr2B 84.729 812 95 16 3721 4528 691253229 691254015 0.000000e+00 785.0
21 TraesCS5B01G071300 chr2B 85.366 656 66 19 3403 4053 526454327 526454957 0.000000e+00 652.0
22 TraesCS5B01G071300 chr2B 90.446 314 23 7 3414 3724 691251002 691251311 1.930000e-109 407.0
23 TraesCS5B01G071300 chr1B 87.652 656 64 15 3403 4053 542695901 542696544 0.000000e+00 747.0
24 TraesCS5B01G071300 chr1D 85.075 335 36 11 3403 3735 49586 49908 4.300000e-86 329.0
25 TraesCS5B01G071300 chr1D 87.273 55 5 2 5230 5283 449233811 449233864 1.730000e-05 62.1
26 TraesCS5B01G071300 chr1D 96.970 33 0 1 5249 5281 256999905 256999874 3.000000e-03 54.7
27 TraesCS5B01G071300 chr2D 85.284 299 30 11 3446 3741 507440527 507440240 4.360000e-76 296.0
28 TraesCS5B01G071300 chr3D 87.273 55 4 2 3030 3081 591653233 591653287 6.230000e-05 60.2
29 TraesCS5B01G071300 chr3A 100.000 31 0 0 5253 5283 638761212 638761242 2.240000e-04 58.4
30 TraesCS5B01G071300 chrUn 100.000 30 0 0 5254 5283 75836608 75836579 8.060000e-04 56.5
31 TraesCS5B01G071300 chrUn 100.000 30 0 0 5254 5283 314023926 314023897 8.060000e-04 56.5
32 TraesCS5B01G071300 chrUn 100.000 30 0 0 5254 5283 314668859 314668888 8.060000e-04 56.5
33 TraesCS5B01G071300 chrUn 100.000 30 0 0 5254 5283 322507549 322507578 8.060000e-04 56.5
34 TraesCS5B01G071300 chr6D 100.000 30 0 0 5254 5283 445217082 445217111 8.060000e-04 56.5


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 TraesCS5B01G071300 chr5B 82457745 82463499 5754 False 10628.000000 10628 100.00000 1 5755 1 chr5B.!!$F1 5754
1 TraesCS5B01G071300 chr5A 64380612 64386247 5635 True 1466.566667 5561 92.13900 1 5703 6 chr5A.!!$R1 5702
2 TraesCS5B01G071300 chr5D 71899639 71905389 5750 True 1106.512500 5099 91.63325 1 5703 8 chr5D.!!$R2 5702
3 TraesCS5B01G071300 chr1A 157886007 157887639 1632 False 624.500000 870 86.34050 3403 4279 2 chr1A.!!$F1 876
4 TraesCS5B01G071300 chr2B 526454327 526454957 630 False 652.000000 652 85.36600 3403 4053 1 chr2B.!!$F1 650
5 TraesCS5B01G071300 chr2B 691251002 691254015 3013 False 596.000000 785 87.58750 3414 4528 2 chr2B.!!$F2 1114
6 TraesCS5B01G071300 chr1B 542695901 542696544 643 False 747.000000 747 87.65200 3403 4053 1 chr1B.!!$F1 650

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
813 826 0.096628 GAGTTGCTCTGCTGCATTCG 59.903 55.000 1.31 0.0 42.96 3.34 F
867 880 0.319900 CCTCGTGGGTGTTCAGACTG 60.320 60.000 0.00 0.0 0.00 3.51 F
1067 1080 0.331278 TCCCGGTTGCAGGATCAAAT 59.669 50.000 0.00 0.0 0.00 2.32 F
2227 2342 0.585357 GCACAGCATGATTAGCTCCG 59.415 55.000 0.00 0.0 41.14 4.63 F
2527 2643 0.968901 CACCACCTGCCATGCTTCAT 60.969 55.000 0.00 0.0 0.00 2.57 F
3315 3433 1.197721 GTTCTGAACATTGTCCTGCGG 59.802 52.381 15.34 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 1859 0.326264 GACTGATGTGGCTCCCTTGT 59.674 55.0 0.00 0.0 0.00 3.16 R
2863 2979 0.537188 AACACCTAGGAGTGCCATCG 59.463 55.0 17.98 0.0 41.67 3.84 R
2932 3048 1.247567 CAGCCAACCTGGACGAATTT 58.752 50.0 0.00 0.0 40.96 1.82 R
3119 3237 0.105760 TGTTGCCTTGTTGATGGGGT 60.106 50.0 0.00 0.0 0.00 4.95 R
4524 6664 0.105593 GATGATGCCGAGCTGGAAGA 59.894 55.0 0.00 0.0 42.00 2.87 R
5188 7336 0.472471 TCGGTGCCCTTGAGAACTTT 59.528 50.0 0.00 0.0 0.00 2.66 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
32 33 4.810790 TGGTCTTCTTCTTTGATCTCGTC 58.189 43.478 0.00 0.00 0.00 4.20
74 75 8.164153 CAGTTGTTCTTGATTTTCTTGTTGTTG 58.836 33.333 0.00 0.00 0.00 3.33
79 80 7.389803 TCTTGATTTTCTTGTTGTTGAGTCA 57.610 32.000 0.00 0.00 0.00 3.41
83 84 9.434420 TTGATTTTCTTGTTGTTGAGTCAAAAT 57.566 25.926 7.25 0.24 0.00 1.82
130 133 2.016165 GCTTTGCTTCGTTTGGGCG 61.016 57.895 0.00 0.00 0.00 6.13
218 226 4.608948 AGATCCAGTTGATTCCGATACC 57.391 45.455 0.00 0.00 32.41 2.73
219 227 3.967326 AGATCCAGTTGATTCCGATACCA 59.033 43.478 0.00 0.00 32.41 3.25
220 228 3.536956 TCCAGTTGATTCCGATACCAC 57.463 47.619 0.00 0.00 0.00 4.16
578 591 1.895798 CTCACTGACTGCCAAGGAGTA 59.104 52.381 0.00 0.00 0.00 2.59
595 608 8.211629 CCAAGGAGTATAAATAGCTGGTTTAGT 58.788 37.037 0.00 0.00 0.00 2.24
680 693 7.801716 TGTAACTGATACAGAGTTGCTTTTT 57.198 32.000 5.76 0.00 39.60 1.94
706 719 7.767250 TTTTGAGAGAGAGAACTGATACAGA 57.233 36.000 5.76 0.00 35.18 3.41
707 720 7.389803 TTTGAGAGAGAGAACTGATACAGAG 57.610 40.000 5.76 0.00 35.18 3.35
708 721 6.061022 TGAGAGAGAGAACTGATACAGAGT 57.939 41.667 5.76 0.00 35.18 3.24
709 722 6.480763 TGAGAGAGAGAACTGATACAGAGTT 58.519 40.000 5.76 0.00 36.33 3.01
710 723 6.374053 TGAGAGAGAGAACTGATACAGAGTTG 59.626 42.308 5.76 0.00 33.71 3.16
711 724 5.125417 AGAGAGAGAACTGATACAGAGTTGC 59.875 44.000 5.76 0.00 33.71 4.17
728 741 1.300971 TGCTCTGCTGCATTCGGTTC 61.301 55.000 1.31 0.00 38.12 3.62
739 752 3.997681 TGCATTCGGTTCGTTATTCTTCA 59.002 39.130 0.00 0.00 0.00 3.02
763 776 8.690884 TCATGTTATTTTGTTCTTGTTTCCTCA 58.309 29.630 0.00 0.00 0.00 3.86
783 796 2.940994 TGGGAATTCAGACCGAAACA 57.059 45.000 7.93 0.00 37.12 2.83
785 798 4.561500 TGGGAATTCAGACCGAAACATA 57.438 40.909 7.93 0.00 37.12 2.29
786 799 4.258543 TGGGAATTCAGACCGAAACATAC 58.741 43.478 7.93 0.00 37.12 2.39
788 801 4.332819 GGGAATTCAGACCGAAACATACTG 59.667 45.833 7.93 0.00 37.12 2.74
789 802 5.175859 GGAATTCAGACCGAAACATACTGA 58.824 41.667 7.93 0.00 37.12 3.41
791 804 6.984474 GGAATTCAGACCGAAACATACTGATA 59.016 38.462 7.93 0.00 37.12 2.15
792 805 7.042658 GGAATTCAGACCGAAACATACTGATAC 60.043 40.741 7.93 0.00 37.12 2.24
793 806 5.907866 TCAGACCGAAACATACTGATACA 57.092 39.130 0.00 0.00 33.57 2.29
794 807 5.891451 TCAGACCGAAACATACTGATACAG 58.109 41.667 0.00 0.00 37.52 2.74
795 808 5.650703 TCAGACCGAAACATACTGATACAGA 59.349 40.000 5.76 0.00 35.18 3.41
796 809 5.974158 CAGACCGAAACATACTGATACAGAG 59.026 44.000 5.76 0.00 35.18 3.35
797 810 5.652891 AGACCGAAACATACTGATACAGAGT 59.347 40.000 5.76 0.00 35.18 3.24
798 811 6.153000 AGACCGAAACATACTGATACAGAGTT 59.847 38.462 5.76 4.92 35.18 3.01
799 812 6.100004 ACCGAAACATACTGATACAGAGTTG 58.900 40.000 5.76 3.17 35.18 3.16
800 813 5.005779 CCGAAACATACTGATACAGAGTTGC 59.994 44.000 5.76 5.46 35.18 4.17
801 814 5.807520 CGAAACATACTGATACAGAGTTGCT 59.192 40.000 5.76 0.00 35.18 3.91
802 815 6.020281 CGAAACATACTGATACAGAGTTGCTC 60.020 42.308 5.76 0.00 35.18 4.26
803 816 6.537453 AACATACTGATACAGAGTTGCTCT 57.463 37.500 5.76 0.00 42.11 4.09
811 824 3.646787 AGAGTTGCTCTGCTGCATT 57.353 47.368 1.31 0.00 42.96 3.56
812 825 1.451067 AGAGTTGCTCTGCTGCATTC 58.549 50.000 1.31 0.00 42.96 2.67
813 826 0.096628 GAGTTGCTCTGCTGCATTCG 59.903 55.000 1.31 0.00 42.96 3.34
814 827 1.136147 GTTGCTCTGCTGCATTCGG 59.864 57.895 1.31 0.00 42.96 4.30
815 828 1.302752 TTGCTCTGCTGCATTCGGT 60.303 52.632 1.31 0.00 42.96 4.69
816 829 0.890542 TTGCTCTGCTGCATTCGGTT 60.891 50.000 1.31 0.00 42.96 4.44
817 830 0.890542 TGCTCTGCTGCATTCGGTTT 60.891 50.000 1.31 0.00 38.12 3.27
818 831 0.455633 GCTCTGCTGCATTCGGTTTG 60.456 55.000 1.31 0.00 0.00 2.93
819 832 0.877071 CTCTGCTGCATTCGGTTTGT 59.123 50.000 1.31 0.00 0.00 2.83
820 833 1.267806 CTCTGCTGCATTCGGTTTGTT 59.732 47.619 1.31 0.00 0.00 2.83
821 834 2.483877 CTCTGCTGCATTCGGTTTGTTA 59.516 45.455 1.31 0.00 0.00 2.41
822 835 3.081061 TCTGCTGCATTCGGTTTGTTAT 58.919 40.909 1.31 0.00 0.00 1.89
823 836 3.505680 TCTGCTGCATTCGGTTTGTTATT 59.494 39.130 1.31 0.00 0.00 1.40
824 837 3.832276 TGCTGCATTCGGTTTGTTATTC 58.168 40.909 0.00 0.00 0.00 1.75
825 838 3.505680 TGCTGCATTCGGTTTGTTATTCT 59.494 39.130 0.00 0.00 0.00 2.40
826 839 4.022416 TGCTGCATTCGGTTTGTTATTCTT 60.022 37.500 0.00 0.00 0.00 2.52
827 840 4.558860 GCTGCATTCGGTTTGTTATTCTTC 59.441 41.667 0.00 0.00 0.00 2.87
828 841 5.697473 TGCATTCGGTTTGTTATTCTTCA 57.303 34.783 0.00 0.00 0.00 3.02
829 842 6.266168 TGCATTCGGTTTGTTATTCTTCAT 57.734 33.333 0.00 0.00 0.00 2.57
830 843 6.092092 TGCATTCGGTTTGTTATTCTTCATG 58.908 36.000 0.00 0.00 0.00 3.07
831 844 6.092748 GCATTCGGTTTGTTATTCTTCATGT 58.907 36.000 0.00 0.00 0.00 3.21
832 845 6.586082 GCATTCGGTTTGTTATTCTTCATGTT 59.414 34.615 0.00 0.00 0.00 2.71
833 846 7.753132 GCATTCGGTTTGTTATTCTTCATGTTA 59.247 33.333 0.00 0.00 0.00 2.41
834 847 9.787532 CATTCGGTTTGTTATTCTTCATGTTAT 57.212 29.630 0.00 0.00 0.00 1.89
852 865 9.619316 TCATGTTATTTTGTTATTGTTTCCTCG 57.381 29.630 0.00 0.00 0.00 4.63
853 866 9.405587 CATGTTATTTTGTTATTGTTTCCTCGT 57.594 29.630 0.00 0.00 0.00 4.18
854 867 8.789881 TGTTATTTTGTTATTGTTTCCTCGTG 57.210 30.769 0.00 0.00 0.00 4.35
855 868 7.863375 TGTTATTTTGTTATTGTTTCCTCGTGG 59.137 33.333 0.00 0.00 0.00 4.94
856 869 4.839668 TTTGTTATTGTTTCCTCGTGGG 57.160 40.909 3.23 0.00 0.00 4.61
857 870 3.495434 TGTTATTGTTTCCTCGTGGGT 57.505 42.857 3.23 0.00 36.25 4.51
858 871 3.142951 TGTTATTGTTTCCTCGTGGGTG 58.857 45.455 3.23 0.00 36.25 4.61
859 872 3.143728 GTTATTGTTTCCTCGTGGGTGT 58.856 45.455 3.23 0.00 36.25 4.16
860 873 2.358322 ATTGTTTCCTCGTGGGTGTT 57.642 45.000 3.23 0.00 36.25 3.32
861 874 1.670791 TTGTTTCCTCGTGGGTGTTC 58.329 50.000 3.23 0.00 36.25 3.18
862 875 0.542333 TGTTTCCTCGTGGGTGTTCA 59.458 50.000 3.23 0.00 36.25 3.18
863 876 1.226746 GTTTCCTCGTGGGTGTTCAG 58.773 55.000 3.23 0.00 36.25 3.02
864 877 1.124780 TTTCCTCGTGGGTGTTCAGA 58.875 50.000 3.23 0.00 36.25 3.27
865 878 0.391597 TTCCTCGTGGGTGTTCAGAC 59.608 55.000 3.23 0.00 36.25 3.51
866 879 0.469331 TCCTCGTGGGTGTTCAGACT 60.469 55.000 3.23 0.00 36.25 3.24
867 880 0.319900 CCTCGTGGGTGTTCAGACTG 60.320 60.000 0.00 0.00 0.00 3.51
868 881 0.673985 CTCGTGGGTGTTCAGACTGA 59.326 55.000 0.00 0.00 0.00 3.41
869 882 1.068588 CTCGTGGGTGTTCAGACTGAA 59.931 52.381 13.99 13.99 33.32 3.02
870 883 1.483004 TCGTGGGTGTTCAGACTGAAA 59.517 47.619 19.32 7.58 38.22 2.69
871 884 1.597663 CGTGGGTGTTCAGACTGAAAC 59.402 52.381 19.32 17.32 38.22 2.78
872 885 2.639065 GTGGGTGTTCAGACTGAAACA 58.361 47.619 19.32 15.70 38.22 2.83
884 897 6.710278 TCAGACTGAAACATATGATTGGACA 58.290 36.000 10.38 0.00 0.00 4.02
885 898 7.341030 TCAGACTGAAACATATGATTGGACAT 58.659 34.615 10.38 0.00 0.00 3.06
893 906 1.477553 ATGATTGGACATGTGGTGCC 58.522 50.000 1.15 0.00 36.96 5.01
903 916 2.279918 GTGGTGCCGTTCGTCACT 60.280 61.111 6.36 0.00 33.91 3.41
907 920 1.352156 GGTGCCGTTCGTCACTGATC 61.352 60.000 6.36 0.00 33.91 2.92
928 941 1.344438 ACTTCTGTTCGATGTGGCTCA 59.656 47.619 0.00 0.00 0.00 4.26
935 948 4.707105 TGTTCGATGTGGCTCATATCATT 58.293 39.130 1.43 0.00 36.83 2.57
942 955 5.952526 TGTGGCTCATATCATTAATGCAG 57.047 39.130 10.76 2.91 0.00 4.41
1008 1021 6.616893 GCAACACAAATTAATGCATGTCACTG 60.617 38.462 0.00 0.00 37.00 3.66
1011 1024 5.346551 CACAAATTAATGCATGTCACTGTGG 59.653 40.000 17.43 0.00 0.00 4.17
1061 1074 2.429930 CTGTTCCCGGTTGCAGGA 59.570 61.111 0.00 0.00 0.00 3.86
1067 1080 0.331278 TCCCGGTTGCAGGATCAAAT 59.669 50.000 0.00 0.00 0.00 2.32
1179 1205 1.200948 GAAGGCAACCAATCTGAGCAC 59.799 52.381 0.00 0.00 37.17 4.40
1259 1285 8.047310 TCCCAGTCATTTATCCTTTCTACTTTC 58.953 37.037 0.00 0.00 0.00 2.62
1320 1347 5.182001 ACACAAGGAAGCATAGACACATTTC 59.818 40.000 0.00 0.00 0.00 2.17
1406 1433 3.375299 GGCTATTCAAGTTGCTCGTCATT 59.625 43.478 0.00 0.00 0.00 2.57
1434 1461 6.439692 TGATGTAGGATGCATATGATGAGAGT 59.560 38.462 6.97 0.00 43.13 3.24
1524 1551 8.276453 AGGCTATTGGTTAGTATTATCCAAGT 57.724 34.615 11.93 5.29 40.31 3.16
1565 1592 6.478588 CCTCTTCGTGCATTCTATTTGTTAC 58.521 40.000 0.00 0.00 0.00 2.50
1641 1668 4.158025 ACCGCCGATATGGAAATCTAGTAG 59.842 45.833 0.00 0.00 42.00 2.57
1830 1859 4.361783 TGTTCCATCAGAGAGTATCCCAA 58.638 43.478 0.00 0.00 33.66 4.12
1848 1877 0.773644 AACAAGGGAGCCACATCAGT 59.226 50.000 0.00 0.00 0.00 3.41
1898 1927 4.184629 GACTACTGGATGCTACAGTTTGG 58.815 47.826 12.40 7.41 46.38 3.28
1914 1943 9.357652 CTACAGTTTGGTGGATATTTCAATTTG 57.642 33.333 0.00 0.00 0.00 2.32
2035 2149 1.548357 CCTGCTACACTGTGAGCCCT 61.548 60.000 15.86 0.00 37.94 5.19
2038 2152 1.270839 TGCTACACTGTGAGCCCTTTC 60.271 52.381 15.86 0.00 37.94 2.62
2106 2220 7.962918 CGAACATAAATGGTGAAAGGAAAGTAG 59.037 37.037 0.00 0.00 0.00 2.57
2155 2270 4.829492 ACTTTCTATCAGCTTGCAGGTTTT 59.171 37.500 0.00 0.00 0.00 2.43
2164 2279 4.387862 CAGCTTGCAGGTTTTCATGAAATC 59.612 41.667 21.10 19.04 32.95 2.17
2227 2342 0.585357 GCACAGCATGATTAGCTCCG 59.415 55.000 0.00 0.00 41.14 4.63
2355 2471 6.430925 TGTGTGCTTCTATTCATAGCTGTTTT 59.569 34.615 0.00 0.00 35.93 2.43
2383 2499 1.977854 TGTAGGACTTGTGCTGGATGT 59.022 47.619 5.05 0.00 0.00 3.06
2527 2643 0.968901 CACCACCTGCCATGCTTCAT 60.969 55.000 0.00 0.00 0.00 2.57
2662 2778 4.022416 TGCAAGAACTTTGTGAGTGTTTGT 60.022 37.500 0.00 0.00 39.00 2.83
2738 2854 8.232913 TGAAAGTGTTGGCTAGAGTTAAATTT 57.767 30.769 0.00 0.00 0.00 1.82
3052 3170 4.326009 TGAGAAAACGCAAAAGCTTTTGTC 59.674 37.500 38.57 30.29 46.92 3.18
3308 3426 5.964958 ATCATTTCGGTTCTGAACATTGT 57.035 34.783 21.01 1.56 0.00 2.71
3315 3433 1.197721 GTTCTGAACATTGTCCTGCGG 59.802 52.381 15.34 0.00 0.00 5.69
3360 3479 5.068636 ACTCTGGCTTGATATAATGCTTGG 58.931 41.667 0.00 0.00 0.00 3.61
3371 3490 8.833231 TGATATAATGCTTGGTAGAAGCTTAC 57.167 34.615 0.00 0.00 43.38 2.34
3436 3555 9.668497 GTTCCAATTAATTCTACAACTACTCCT 57.332 33.333 0.00 0.00 0.00 3.69
3472 3591 6.314896 GTGATGTATTCCTCATATGCTTAGCC 59.685 42.308 0.29 0.00 0.00 3.93
3696 3823 7.965107 GGTTTGAATATGAAAGTAGAACAGCAG 59.035 37.037 0.00 0.00 0.00 4.24
3813 5863 5.648092 ACAATGCTTTGTATACTCCCAACTC 59.352 40.000 15.73 0.00 44.22 3.01
3931 5984 9.185192 GTTTCTAAATGCTGCCATATTATTGAC 57.815 33.333 0.00 0.00 0.00 3.18
3973 6026 5.599732 TGTGCAAATTTTACAGTCTGCAAT 58.400 33.333 0.00 0.00 41.11 3.56
4166 6219 4.837093 TTCCCCTTACTATGAACACAGG 57.163 45.455 0.00 0.00 0.00 4.00
4167 6220 3.798515 TCCCCTTACTATGAACACAGGT 58.201 45.455 0.00 0.00 0.00 4.00
4402 6542 3.377346 TTCTCATCCTATTCTCAGCGC 57.623 47.619 0.00 0.00 0.00 5.92
4502 6642 4.401022 TGTGGCTTGAGTCTGAAATCATT 58.599 39.130 0.00 0.00 0.00 2.57
4532 6672 2.260869 TGGCAACGCTTCTTCCAGC 61.261 57.895 0.00 0.00 42.51 4.85
4720 6860 1.271379 TGGCTTGAGAAGTACCCTTGC 60.271 52.381 0.00 0.00 0.00 4.01
4755 6895 4.262617 GACAGGGTCCTTTCCTTATTGAC 58.737 47.826 0.00 0.00 31.06 3.18
4782 6928 6.333416 TCATTCAGAGAAGAACATTACTCCG 58.667 40.000 0.00 0.00 0.00 4.63
5002 7150 4.804868 TTTTCACATTGCCAGCATACAT 57.195 36.364 0.00 0.00 0.00 2.29
5014 7162 3.255725 CAGCATACATGGCAAACTTTGG 58.744 45.455 0.00 0.00 0.00 3.28
5079 7227 5.588845 TGTGGGGGAAATGTTCTTATCAAT 58.411 37.500 0.00 0.00 0.00 2.57
5104 7252 4.143473 GCGCTGATCATTTTTGTTTCACTG 60.143 41.667 0.00 0.00 0.00 3.66
5115 7263 5.446143 TTTGTTTCACTGTGAACAAGTGT 57.554 34.783 21.95 0.00 35.89 3.55
5122 7270 0.523519 TGTGAACAAGTGTTTGCGCA 59.476 45.000 5.66 5.66 38.56 6.09
5164 7312 3.243941 GGCACCGACATATACCATACACA 60.244 47.826 0.00 0.00 0.00 3.72
5182 7330 2.723746 AGTGGCTTTTGCGCACTG 59.276 55.556 11.12 4.05 46.99 3.66
5188 7336 2.330231 GCTTTTGCGCACTGTTCATA 57.670 45.000 11.12 0.00 34.86 2.15
5247 7396 2.167693 GTGTCCGTTCCATCATACTCCA 59.832 50.000 0.00 0.00 0.00 3.86
5250 7399 3.069586 GTCCGTTCCATCATACTCCATCA 59.930 47.826 0.00 0.00 0.00 3.07
5274 7423 9.883142 TCAGTTTCAAATTTGAACTAAAACCAT 57.117 25.926 28.78 9.91 45.99 3.55
5283 7432 9.744468 AATTTGAACTAAAACCATGACAAGTAC 57.256 29.630 0.00 0.00 0.00 2.73
5285 7434 7.724305 TGAACTAAAACCATGACAAGTACTC 57.276 36.000 0.00 0.00 0.00 2.59
5288 7437 3.764237 AAACCATGACAAGTACTCCGT 57.236 42.857 0.00 0.00 0.00 4.69
5290 7439 4.451629 AACCATGACAAGTACTCCGTAG 57.548 45.455 0.00 0.00 0.00 3.51
5291 7440 3.428532 ACCATGACAAGTACTCCGTAGT 58.571 45.455 0.00 0.00 39.91 2.73
5292 7441 3.830755 ACCATGACAAGTACTCCGTAGTT 59.169 43.478 0.00 0.00 37.15 2.24
5293 7442 4.282703 ACCATGACAAGTACTCCGTAGTTT 59.717 41.667 0.00 0.00 37.15 2.66
5294 7443 4.625742 CCATGACAAGTACTCCGTAGTTTG 59.374 45.833 0.00 0.00 37.15 2.93
5296 7445 3.890756 TGACAAGTACTCCGTAGTTTGGA 59.109 43.478 0.00 0.00 37.15 3.53
5298 7447 4.625028 ACAAGTACTCCGTAGTTTGGAAC 58.375 43.478 0.00 0.00 37.15 3.62
5299 7448 4.343239 ACAAGTACTCCGTAGTTTGGAACT 59.657 41.667 0.00 0.00 45.40 3.01
5300 7449 4.516365 AGTACTCCGTAGTTTGGAACTG 57.484 45.455 3.70 0.00 42.84 3.16
5302 7451 4.586001 AGTACTCCGTAGTTTGGAACTGAA 59.414 41.667 3.70 0.00 42.84 3.02
5303 7452 3.991367 ACTCCGTAGTTTGGAACTGAAG 58.009 45.455 3.70 0.00 42.84 3.02
5304 7453 3.244112 ACTCCGTAGTTTGGAACTGAAGG 60.244 47.826 3.70 4.67 42.84 3.46
5305 7454 2.967201 TCCGTAGTTTGGAACTGAAGGA 59.033 45.455 3.70 6.62 42.84 3.36
5308 7457 4.392138 CCGTAGTTTGGAACTGAAGGAATC 59.608 45.833 3.70 0.00 42.84 2.52
5375 7623 8.188799 TCAACGTTCGACAAGATCTTTATATCT 58.811 33.333 4.86 0.00 37.84 1.98
5398 7646 7.749808 TCTCTTGTGTACTACTACAAATCTCG 58.250 38.462 0.00 0.00 36.47 4.04
5401 7649 8.019669 TCTTGTGTACTACTACAAATCTCGTTC 58.980 37.037 0.00 0.00 36.47 3.95
5402 7650 6.615088 TGTGTACTACTACAAATCTCGTTCC 58.385 40.000 0.00 0.00 34.53 3.62
5403 7651 6.032717 GTGTACTACTACAAATCTCGTTCCC 58.967 44.000 0.00 0.00 34.53 3.97
5420 7668 4.218417 CGTTCCCAGATCAAATGGTTCTTT 59.782 41.667 0.00 0.00 35.96 2.52
5440 7695 7.658179 TCTTTGCAGTGACTTAGAAATAGTG 57.342 36.000 0.00 0.00 0.00 2.74
5446 7701 5.578727 CAGTGACTTAGAAATAGTGGTCTGC 59.421 44.000 0.00 0.00 0.00 4.26
5449 7704 5.127194 TGACTTAGAAATAGTGGTCTGCGAT 59.873 40.000 0.00 0.00 0.00 4.58
5453 7708 8.516234 ACTTAGAAATAGTGGTCTGCGATATAG 58.484 37.037 0.00 0.00 0.00 1.31
5458 7713 9.640963 GAAATAGTGGTCTGCGATATAGTAATT 57.359 33.333 0.00 0.00 0.00 1.40
5459 7714 9.998106 AAATAGTGGTCTGCGATATAGTAATTT 57.002 29.630 0.00 0.00 0.00 1.82
5499 7754 7.855904 GTGTGTTTACTCAACGAGATGAAAAAT 59.144 33.333 0.00 0.00 38.36 1.82
5508 7763 9.793252 CTCAACGAGATGAAAAATGGAATATTT 57.207 29.630 0.00 0.00 0.00 1.40
5565 7820 7.449395 AGAAGACCAAACTGATGAATTTGATGA 59.551 33.333 0.00 0.00 37.91 2.92
5621 7946 6.570672 AATTCCATCATACATCATGCTCAC 57.429 37.500 0.00 0.00 34.35 3.51
5628 7953 0.254178 ACATCATGCTCACAGGGACC 59.746 55.000 0.00 0.00 0.00 4.46
5629 7954 0.812811 CATCATGCTCACAGGGACCG 60.813 60.000 0.00 0.00 0.00 4.79
5637 7962 1.147376 CACAGGGACCGGTTTGTGA 59.853 57.895 29.19 0.00 42.61 3.58
5638 7963 0.464735 CACAGGGACCGGTTTGTGAA 60.465 55.000 29.19 0.00 42.61 3.18
5667 7992 2.032799 ACATGTTTCAACGTCACGCATT 59.967 40.909 0.00 0.00 0.00 3.56
5673 7998 1.078709 CAACGTCACGCATTGATCCT 58.921 50.000 0.00 0.00 36.32 3.24
5703 8028 3.532155 CCTCGGAGGCTCGGAAGG 61.532 72.222 22.81 20.46 0.00 3.46
5704 8029 2.440430 CTCGGAGGCTCGGAAGGA 60.440 66.667 22.81 8.10 0.00 3.36
5705 8030 2.440430 TCGGAGGCTCGGAAGGAG 60.440 66.667 20.86 1.20 46.06 3.69
5706 8031 2.440430 CGGAGGCTCGGAAGGAGA 60.440 66.667 16.33 0.00 46.23 3.71
5707 8032 2.485795 CGGAGGCTCGGAAGGAGAG 61.486 68.421 16.33 0.00 46.23 3.20
5708 8033 2.131067 GGAGGCTCGGAAGGAGAGG 61.131 68.421 8.69 0.00 46.23 3.69
5711 8036 4.214327 GCTCGGAAGGAGAGGCGG 62.214 72.222 0.00 0.00 46.23 6.13
5712 8037 3.532155 CTCGGAAGGAGAGGCGGG 61.532 72.222 0.00 0.00 46.23 6.13
5713 8038 4.377760 TCGGAAGGAGAGGCGGGT 62.378 66.667 0.00 0.00 0.00 5.28
5714 8039 4.148825 CGGAAGGAGAGGCGGGTG 62.149 72.222 0.00 0.00 0.00 4.61
5715 8040 3.787001 GGAAGGAGAGGCGGGTGG 61.787 72.222 0.00 0.00 0.00 4.61
5716 8041 2.683933 GAAGGAGAGGCGGGTGGA 60.684 66.667 0.00 0.00 0.00 4.02
5717 8042 2.041265 AAGGAGAGGCGGGTGGAT 59.959 61.111 0.00 0.00 0.00 3.41
5718 8043 1.616628 AAGGAGAGGCGGGTGGATT 60.617 57.895 0.00 0.00 0.00 3.01
5719 8044 1.208165 AAGGAGAGGCGGGTGGATTT 61.208 55.000 0.00 0.00 0.00 2.17
5720 8045 1.208165 AGGAGAGGCGGGTGGATTTT 61.208 55.000 0.00 0.00 0.00 1.82
5721 8046 0.323451 GGAGAGGCGGGTGGATTTTT 60.323 55.000 0.00 0.00 0.00 1.94
5742 8067 5.450818 TTTTGCCTCATTCTACATAGGGT 57.549 39.130 0.00 0.00 0.00 4.34
5743 8068 5.450818 TTTGCCTCATTCTACATAGGGTT 57.549 39.130 0.00 0.00 0.00 4.11
5744 8069 5.450818 TTGCCTCATTCTACATAGGGTTT 57.549 39.130 0.00 0.00 0.00 3.27
5745 8070 4.780815 TGCCTCATTCTACATAGGGTTTG 58.219 43.478 0.00 0.00 0.00 2.93
5746 8071 4.473196 TGCCTCATTCTACATAGGGTTTGA 59.527 41.667 0.00 0.00 0.00 2.69
5747 8072 5.132648 TGCCTCATTCTACATAGGGTTTGAT 59.867 40.000 0.00 0.00 0.00 2.57
5748 8073 5.471456 GCCTCATTCTACATAGGGTTTGATG 59.529 44.000 0.00 0.00 0.00 3.07
5749 8074 6.688922 GCCTCATTCTACATAGGGTTTGATGA 60.689 42.308 0.00 0.00 0.00 2.92
5750 8075 7.456725 CCTCATTCTACATAGGGTTTGATGAT 58.543 38.462 0.00 0.00 0.00 2.45
5751 8076 7.941238 CCTCATTCTACATAGGGTTTGATGATT 59.059 37.037 0.00 0.00 0.00 2.57
5752 8077 9.347240 CTCATTCTACATAGGGTTTGATGATTT 57.653 33.333 0.00 0.00 0.00 2.17
5753 8078 9.123902 TCATTCTACATAGGGTTTGATGATTTG 57.876 33.333 0.00 0.00 0.00 2.32
5754 8079 6.942532 TCTACATAGGGTTTGATGATTTGC 57.057 37.500 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.754957 ACTGAGATCAGAGCTCGGGG 60.755 60.000 25.15 13.59 46.59 5.73
74 75 6.146673 CAGAGGGCAATTCAAAATTTTGACTC 59.853 38.462 28.78 26.60 45.99 3.36
79 80 5.466393 CGAACAGAGGGCAATTCAAAATTTT 59.534 36.000 0.00 0.00 0.00 1.82
83 84 2.955660 ACGAACAGAGGGCAATTCAAAA 59.044 40.909 0.00 0.00 0.00 2.44
86 87 2.270352 AACGAACAGAGGGCAATTCA 57.730 45.000 0.00 0.00 0.00 2.57
122 123 1.798813 CAGAGTTCTACACGCCCAAAC 59.201 52.381 0.00 0.00 0.00 2.93
130 133 5.064071 GCCAAATTCTAGCAGAGTTCTACAC 59.936 44.000 0.00 0.00 0.00 2.90
218 226 3.055602 TCAGATCATCAGAAGGTGGTGTG 60.056 47.826 0.00 0.00 38.57 3.82
219 227 3.176411 TCAGATCATCAGAAGGTGGTGT 58.824 45.455 0.00 0.00 38.57 4.16
220 228 3.900966 TCAGATCATCAGAAGGTGGTG 57.099 47.619 0.00 0.00 38.84 4.17
251 259 6.258947 GGGTAGCATGATTAGACAGAGAAAAC 59.741 42.308 0.00 0.00 0.00 2.43
578 591 6.483640 GCAGTGCTACTAAACCAGCTATTTAT 59.516 38.462 8.18 0.00 38.63 1.40
681 694 8.183104 TCTGTATCAGTTCTCTCTCTCAAAAA 57.817 34.615 0.00 0.00 32.61 1.94
682 695 7.450014 ACTCTGTATCAGTTCTCTCTCTCAAAA 59.550 37.037 0.00 0.00 32.61 2.44
683 696 6.945435 ACTCTGTATCAGTTCTCTCTCTCAAA 59.055 38.462 0.00 0.00 32.61 2.69
684 697 6.480763 ACTCTGTATCAGTTCTCTCTCTCAA 58.519 40.000 0.00 0.00 32.61 3.02
686 699 6.677920 GCAACTCTGTATCAGTTCTCTCTCTC 60.678 46.154 0.00 0.00 31.40 3.20
687 700 5.125417 GCAACTCTGTATCAGTTCTCTCTCT 59.875 44.000 0.00 0.00 31.40 3.10
688 701 5.125417 AGCAACTCTGTATCAGTTCTCTCTC 59.875 44.000 0.00 0.00 31.40 3.20
690 703 5.125417 AGAGCAACTCTGTATCAGTTCTCTC 59.875 44.000 0.00 0.00 39.62 3.20
691 704 5.016173 AGAGCAACTCTGTATCAGTTCTCT 58.984 41.667 0.00 0.00 39.62 3.10
710 723 1.427020 GAACCGAATGCAGCAGAGC 59.573 57.895 0.00 0.00 0.00 4.09
711 724 1.016130 ACGAACCGAATGCAGCAGAG 61.016 55.000 0.00 0.00 0.00 3.35
739 752 9.480053 CATGAGGAAACAAGAACAAAATAACAT 57.520 29.630 0.00 0.00 0.00 2.71
763 776 3.433306 TGTTTCGGTCTGAATTCCCAT 57.567 42.857 2.27 0.00 36.22 4.00
799 812 0.455633 CAAACCGAATGCAGCAGAGC 60.456 55.000 0.00 0.00 0.00 4.09
800 813 0.877071 ACAAACCGAATGCAGCAGAG 59.123 50.000 0.00 0.00 0.00 3.35
801 814 1.317613 AACAAACCGAATGCAGCAGA 58.682 45.000 0.00 0.00 0.00 4.26
802 815 2.987413 TAACAAACCGAATGCAGCAG 57.013 45.000 0.00 0.00 0.00 4.24
803 816 3.505680 AGAATAACAAACCGAATGCAGCA 59.494 39.130 0.00 0.00 0.00 4.41
804 817 4.096732 AGAATAACAAACCGAATGCAGC 57.903 40.909 0.00 0.00 0.00 5.25
805 818 5.698832 TGAAGAATAACAAACCGAATGCAG 58.301 37.500 0.00 0.00 0.00 4.41
806 819 5.697473 TGAAGAATAACAAACCGAATGCA 57.303 34.783 0.00 0.00 0.00 3.96
807 820 6.092748 ACATGAAGAATAACAAACCGAATGC 58.907 36.000 0.00 0.00 0.00 3.56
808 821 9.787532 ATAACATGAAGAATAACAAACCGAATG 57.212 29.630 0.00 0.00 0.00 2.67
826 839 9.619316 CGAGGAAACAATAACAAAATAACATGA 57.381 29.630 0.00 0.00 0.00 3.07
827 840 9.405587 ACGAGGAAACAATAACAAAATAACATG 57.594 29.630 0.00 0.00 0.00 3.21
828 841 9.405587 CACGAGGAAACAATAACAAAATAACAT 57.594 29.630 0.00 0.00 0.00 2.71
829 842 7.863375 CCACGAGGAAACAATAACAAAATAACA 59.137 33.333 0.00 0.00 36.89 2.41
830 843 7.327518 CCCACGAGGAAACAATAACAAAATAAC 59.672 37.037 0.00 0.00 38.24 1.89
831 844 7.014422 ACCCACGAGGAAACAATAACAAAATAA 59.986 33.333 0.00 0.00 39.89 1.40
832 845 6.490721 ACCCACGAGGAAACAATAACAAAATA 59.509 34.615 0.00 0.00 39.89 1.40
833 846 5.303333 ACCCACGAGGAAACAATAACAAAAT 59.697 36.000 0.00 0.00 39.89 1.82
834 847 4.645588 ACCCACGAGGAAACAATAACAAAA 59.354 37.500 0.00 0.00 39.89 2.44
835 848 4.036971 CACCCACGAGGAAACAATAACAAA 59.963 41.667 0.00 0.00 39.89 2.83
836 849 3.566322 CACCCACGAGGAAACAATAACAA 59.434 43.478 0.00 0.00 39.89 2.83
837 850 3.142951 CACCCACGAGGAAACAATAACA 58.857 45.455 0.00 0.00 39.89 2.41
838 851 3.143728 ACACCCACGAGGAAACAATAAC 58.856 45.455 0.00 0.00 39.89 1.89
839 852 3.495434 ACACCCACGAGGAAACAATAA 57.505 42.857 0.00 0.00 39.89 1.40
840 853 3.181453 TGAACACCCACGAGGAAACAATA 60.181 43.478 0.00 0.00 39.89 1.90
841 854 2.227194 GAACACCCACGAGGAAACAAT 58.773 47.619 0.00 0.00 39.89 2.71
842 855 1.065345 TGAACACCCACGAGGAAACAA 60.065 47.619 0.00 0.00 39.89 2.83
843 856 0.542333 TGAACACCCACGAGGAAACA 59.458 50.000 0.00 0.00 39.89 2.83
844 857 1.202604 TCTGAACACCCACGAGGAAAC 60.203 52.381 0.00 0.00 39.89 2.78
845 858 1.124780 TCTGAACACCCACGAGGAAA 58.875 50.000 0.00 0.00 39.89 3.13
846 859 0.391597 GTCTGAACACCCACGAGGAA 59.608 55.000 0.00 0.00 39.89 3.36
847 860 0.469331 AGTCTGAACACCCACGAGGA 60.469 55.000 0.00 0.00 39.89 3.71
848 861 0.319900 CAGTCTGAACACCCACGAGG 60.320 60.000 0.00 0.00 43.78 4.63
849 862 0.673985 TCAGTCTGAACACCCACGAG 59.326 55.000 0.00 0.00 0.00 4.18
850 863 1.116308 TTCAGTCTGAACACCCACGA 58.884 50.000 11.36 0.00 30.26 4.35
851 864 1.597663 GTTTCAGTCTGAACACCCACG 59.402 52.381 14.98 0.00 35.89 4.94
852 865 2.639065 TGTTTCAGTCTGAACACCCAC 58.361 47.619 14.98 10.53 35.89 4.61
853 866 3.576078 ATGTTTCAGTCTGAACACCCA 57.424 42.857 14.98 9.69 35.89 4.51
854 867 5.245531 TCATATGTTTCAGTCTGAACACCC 58.754 41.667 14.98 4.62 35.89 4.61
855 868 6.992063 ATCATATGTTTCAGTCTGAACACC 57.008 37.500 14.98 6.91 35.89 4.16
856 869 7.119699 TCCAATCATATGTTTCAGTCTGAACAC 59.880 37.037 14.98 15.23 35.89 3.32
857 870 7.119699 GTCCAATCATATGTTTCAGTCTGAACA 59.880 37.037 14.98 15.34 35.89 3.18
858 871 7.119699 TGTCCAATCATATGTTTCAGTCTGAAC 59.880 37.037 14.98 10.65 35.89 3.18
859 872 7.167535 TGTCCAATCATATGTTTCAGTCTGAA 58.832 34.615 11.36 11.36 34.03 3.02
860 873 6.710278 TGTCCAATCATATGTTTCAGTCTGA 58.290 36.000 0.00 0.00 0.00 3.27
861 874 6.990341 TGTCCAATCATATGTTTCAGTCTG 57.010 37.500 1.90 0.00 0.00 3.51
862 875 7.066645 CACATGTCCAATCATATGTTTCAGTCT 59.933 37.037 1.90 0.00 31.84 3.24
863 876 7.191551 CACATGTCCAATCATATGTTTCAGTC 58.808 38.462 1.90 0.00 31.84 3.51
864 877 6.095860 CCACATGTCCAATCATATGTTTCAGT 59.904 38.462 1.90 0.00 31.84 3.41
865 878 6.095860 ACCACATGTCCAATCATATGTTTCAG 59.904 38.462 1.90 0.00 31.84 3.02
866 879 5.951148 ACCACATGTCCAATCATATGTTTCA 59.049 36.000 1.90 0.00 31.84 2.69
867 880 6.267817 CACCACATGTCCAATCATATGTTTC 58.732 40.000 1.90 0.00 31.84 2.78
868 881 5.394443 GCACCACATGTCCAATCATATGTTT 60.394 40.000 1.90 0.00 31.84 2.83
869 882 4.098349 GCACCACATGTCCAATCATATGTT 59.902 41.667 1.90 0.00 31.84 2.71
870 883 3.633525 GCACCACATGTCCAATCATATGT 59.366 43.478 1.90 0.00 34.31 2.29
871 884 3.005050 GGCACCACATGTCCAATCATATG 59.995 47.826 0.00 0.00 0.00 1.78
872 885 3.225104 GGCACCACATGTCCAATCATAT 58.775 45.455 0.00 0.00 0.00 1.78
884 897 2.423874 TGACGAACGGCACCACAT 59.576 55.556 0.00 0.00 0.00 3.21
893 906 2.658802 CAGAAGTGATCAGTGACGAACG 59.341 50.000 3.18 0.00 0.00 3.95
907 920 1.728971 GAGCCACATCGAACAGAAGTG 59.271 52.381 0.00 0.00 45.30 3.16
942 955 5.178797 TCAGTAAGACAAGGCTAGCATTTC 58.821 41.667 18.24 15.01 0.00 2.17
1008 1021 3.134458 CAGAACTTGTTGAGACCTCCAC 58.866 50.000 0.00 0.00 0.00 4.02
1179 1205 3.995199 TGACAAGAAGCTAACTCTGGTG 58.005 45.455 0.00 0.00 0.00 4.17
1259 1285 9.424319 TGAACAAGAAAGAACTAGCTACAATAG 57.576 33.333 0.00 0.00 0.00 1.73
1406 1433 8.984855 TCTCATCATATGCATCCTACATCAATA 58.015 33.333 0.19 0.00 0.00 1.90
1434 1461 4.498177 GCACGAGCTATATCTTCACTGTCA 60.498 45.833 0.00 0.00 37.91 3.58
1524 1551 5.452496 CGAAGAGGCAAGAGGATAAGAATGA 60.452 44.000 0.00 0.00 0.00 2.57
1641 1668 8.421673 AACAACTTTTACTCAGTAACTGACTC 57.578 34.615 0.00 0.00 35.39 3.36
1830 1859 0.326264 GACTGATGTGGCTCCCTTGT 59.674 55.000 0.00 0.00 0.00 3.16
1898 1927 9.369904 ACATTGCTTACAAATTGAAATATCCAC 57.630 29.630 0.00 0.00 39.77 4.02
2035 2149 3.593442 TGAGCTTCCAAAAGGAGGAAA 57.407 42.857 0.00 0.00 44.07 3.13
2106 2220 3.108376 AGGACTGACCCTCTTTATGACC 58.892 50.000 0.00 0.00 40.05 4.02
2155 2270 2.036958 ACCATTCCGCGATTTCATGA 57.963 45.000 8.23 0.00 0.00 3.07
2164 2279 1.202371 TGTAGAGCTAACCATTCCGCG 60.202 52.381 0.00 0.00 0.00 6.46
2227 2342 5.859495 AGGAGATAGCCAATTTGCTACTAC 58.141 41.667 13.04 12.36 45.97 2.73
2355 2471 4.814234 CAGCACAAGTCCTACACAAGTAAA 59.186 41.667 0.00 0.00 0.00 2.01
2383 2499 3.364549 CCCATGACCAATTGGCTTTCTA 58.635 45.455 24.79 5.00 39.32 2.10
2707 2823 1.985473 AGCCAACACTTTCATGCTCA 58.015 45.000 0.00 0.00 0.00 4.26
2738 2854 4.379708 CCACGATTCAATGCACAGATCAAA 60.380 41.667 0.00 0.00 0.00 2.69
2863 2979 0.537188 AACACCTAGGAGTGCCATCG 59.463 55.000 17.98 0.00 41.67 3.84
2926 3042 3.138304 CAACCTGGACGAATTTGTCTGA 58.862 45.455 22.34 10.72 38.91 3.27
2932 3048 1.247567 CAGCCAACCTGGACGAATTT 58.752 50.000 0.00 0.00 40.96 1.82
3001 3117 9.902196 AGTAAAAACATTATTTAACCTTCACCG 57.098 29.630 0.00 0.00 0.00 4.94
3025 3141 3.340337 GCTTTTGCGTTTTCTCAGAGT 57.660 42.857 0.00 0.00 34.86 3.24
3052 3170 4.450419 GGTCCTTTCTATCAATGCATCGAG 59.550 45.833 0.00 0.00 0.00 4.04
3119 3237 0.105760 TGTTGCCTTGTTGATGGGGT 60.106 50.000 0.00 0.00 0.00 4.95
3315 3433 6.691508 AGTTCAAGATCCTGGCAATAAAAAC 58.308 36.000 0.00 0.00 0.00 2.43
3696 3823 4.556233 GCTCAACCAAAAGTAATGGAACC 58.444 43.478 0.00 0.00 40.56 3.62
3931 5984 6.331845 TGCACATGCCTGTAATCAAATAAAG 58.668 36.000 0.49 0.00 41.18 1.85
3973 6026 7.654923 TGCATTAAATTGTTCAGTACATGCAAA 59.345 29.630 6.61 0.00 40.42 3.68
4143 6196 4.941873 CCTGTGTTCATAGTAAGGGGAAAC 59.058 45.833 0.00 0.00 0.00 2.78
4166 6219 7.981102 AGGTCCTTAAGAACAACAATCTAAC 57.019 36.000 3.36 0.00 33.03 2.34
4167 6220 8.877195 AGTAGGTCCTTAAGAACAACAATCTAA 58.123 33.333 3.36 0.00 33.03 2.10
4249 6386 8.914011 GGATGGCAACTAAACTATAAGGAAATT 58.086 33.333 0.00 0.00 37.61 1.82
4402 6542 1.198637 CTGCAGAAAGAAAGAAGGCGG 59.801 52.381 8.42 0.00 0.00 6.13
4524 6664 0.105593 GATGATGCCGAGCTGGAAGA 59.894 55.000 0.00 0.00 42.00 2.87
4532 6672 2.057316 GAAGACGATGATGATGCCGAG 58.943 52.381 0.00 0.00 0.00 4.63
4646 6786 1.271379 CCATCCCCATATTCCACGGAC 60.271 57.143 0.00 0.00 0.00 4.79
4720 6860 2.036992 GACCCTGTCAGCCTCATATGAG 59.963 54.545 23.53 23.53 35.91 2.90
4755 6895 7.168972 GGAGTAATGTTCTTCTCTGAATGATCG 59.831 40.741 0.00 0.00 0.00 3.69
4782 6928 3.795623 ATGCAGCCATCTTCACAAATC 57.204 42.857 0.00 0.00 0.00 2.17
4914 7062 6.522625 TTCACAGACAACAGGAAAATTTGA 57.477 33.333 0.00 0.00 0.00 2.69
5002 7150 4.832266 AGATATGTTCACCAAAGTTTGCCA 59.168 37.500 10.25 2.07 0.00 4.92
5032 7180 9.088987 ACAATTTATCCAAATGTTGTACTCCTT 57.911 29.630 0.00 0.00 34.53 3.36
5079 7227 4.208873 GTGAAACAAAAATGATCAGCGCAA 59.791 37.500 11.47 0.00 36.32 4.85
5104 7252 0.913876 GTGCGCAAACACTTGTTCAC 59.086 50.000 14.00 0.00 37.25 3.18
5115 7263 5.641636 TGAGAACTTATGAATAGTGCGCAAA 59.358 36.000 14.00 3.21 29.40 3.68
5122 7270 6.116126 GTGCCCTTGAGAACTTATGAATAGT 58.884 40.000 0.00 0.00 0.00 2.12
5150 7298 6.942532 AAAGCCACTTGTGTATGGTATATG 57.057 37.500 0.00 0.00 38.34 1.78
5154 7302 3.254657 GCAAAAGCCACTTGTGTATGGTA 59.745 43.478 0.00 0.00 38.34 3.25
5158 7306 1.335872 GCGCAAAAGCCACTTGTGTAT 60.336 47.619 0.30 0.00 36.79 2.29
5164 7312 1.066257 CAGTGCGCAAAAGCCACTT 59.934 52.632 14.00 0.00 36.02 3.16
5182 7330 4.082733 GGTGCCCTTGAGAACTTTATGAAC 60.083 45.833 0.00 0.00 0.00 3.18
5188 7336 0.472471 TCGGTGCCCTTGAGAACTTT 59.528 50.000 0.00 0.00 0.00 2.66
5274 7423 3.890756 TCCAAACTACGGAGTACTTGTCA 59.109 43.478 0.00 0.00 45.11 3.58
5283 7432 3.006537 TCCTTCAGTTCCAAACTACGGAG 59.993 47.826 0.00 0.00 40.46 4.63
5285 7434 3.396260 TCCTTCAGTTCCAAACTACGG 57.604 47.619 0.00 0.00 40.46 4.02
5288 7437 5.223449 ACGATTCCTTCAGTTCCAAACTA 57.777 39.130 0.00 0.00 40.46 2.24
5290 7439 7.787725 ATATACGATTCCTTCAGTTCCAAAC 57.212 36.000 0.00 0.00 0.00 2.93
5291 7440 8.701895 ACTATATACGATTCCTTCAGTTCCAAA 58.298 33.333 0.00 0.00 0.00 3.28
5292 7441 8.141909 CACTATATACGATTCCTTCAGTTCCAA 58.858 37.037 0.00 0.00 0.00 3.53
5293 7442 7.287005 ACACTATATACGATTCCTTCAGTTCCA 59.713 37.037 0.00 0.00 0.00 3.53
5294 7443 7.659186 ACACTATATACGATTCCTTCAGTTCC 58.341 38.462 0.00 0.00 0.00 3.62
5296 7445 8.794553 CCTACACTATATACGATTCCTTCAGTT 58.205 37.037 0.00 0.00 0.00 3.16
5298 7447 8.338072 ACCTACACTATATACGATTCCTTCAG 57.662 38.462 0.00 0.00 0.00 3.02
5299 7448 8.701908 AACCTACACTATATACGATTCCTTCA 57.298 34.615 0.00 0.00 0.00 3.02
5375 7623 7.444629 ACGAGATTTGTAGTAGTACACAAGA 57.555 36.000 10.01 0.00 38.95 3.02
5383 7631 5.014858 TCTGGGAACGAGATTTGTAGTAGT 58.985 41.667 0.00 0.00 0.00 2.73
5386 7634 4.466370 TGATCTGGGAACGAGATTTGTAGT 59.534 41.667 0.00 0.00 31.30 2.73
5390 7638 5.449588 CCATTTGATCTGGGAACGAGATTTG 60.450 44.000 0.00 0.00 31.30 2.32
5391 7639 4.641989 CCATTTGATCTGGGAACGAGATTT 59.358 41.667 0.00 0.00 31.30 2.17
5398 7646 5.473039 CAAAGAACCATTTGATCTGGGAAC 58.527 41.667 4.64 0.00 41.71 3.62
5401 7649 3.258872 TGCAAAGAACCATTTGATCTGGG 59.741 43.478 4.64 0.00 41.71 4.45
5402 7650 4.021719 ACTGCAAAGAACCATTTGATCTGG 60.022 41.667 3.49 0.00 41.71 3.86
5403 7651 4.921515 CACTGCAAAGAACCATTTGATCTG 59.078 41.667 3.49 0.00 41.71 2.90
5420 7668 5.246203 AGACCACTATTTCTAAGTCACTGCA 59.754 40.000 0.00 0.00 0.00 4.41
5474 7729 6.912203 TTTTCATCTCGTTGAGTAAACACA 57.088 33.333 0.00 0.00 38.84 3.72
5520 7775 7.362487 GGTCTTCTCAATTCCCTTTTTCATCTC 60.362 40.741 0.00 0.00 0.00 2.75
5531 7786 4.398319 TCAGTTTGGTCTTCTCAATTCCC 58.602 43.478 0.00 0.00 0.00 3.97
5537 7792 6.772233 TCAAATTCATCAGTTTGGTCTTCTCA 59.228 34.615 0.00 0.00 36.30 3.27
5580 7835 9.100554 GATGGAATTTTGCATACATGATCAAAA 57.899 29.630 0.00 10.08 39.44 2.44
5621 7946 1.394618 TTTTCACAAACCGGTCCCTG 58.605 50.000 8.04 8.77 0.00 4.45
5703 8028 3.266240 AAAAATCCACCCGCCTCTC 57.734 52.632 0.00 0.00 0.00 3.20
5719 8044 5.826643 ACCCTATGTAGAATGAGGCAAAAA 58.173 37.500 0.00 0.00 0.00 1.94
5720 8045 5.450818 ACCCTATGTAGAATGAGGCAAAA 57.549 39.130 0.00 0.00 0.00 2.44
5721 8046 5.450818 AACCCTATGTAGAATGAGGCAAA 57.549 39.130 0.00 0.00 0.00 3.68
5722 8047 5.045213 TCAAACCCTATGTAGAATGAGGCAA 60.045 40.000 0.00 0.00 0.00 4.52
5723 8048 4.473196 TCAAACCCTATGTAGAATGAGGCA 59.527 41.667 0.00 0.00 0.00 4.75
5724 8049 5.036117 TCAAACCCTATGTAGAATGAGGC 57.964 43.478 0.00 0.00 0.00 4.70
5725 8050 6.830912 TCATCAAACCCTATGTAGAATGAGG 58.169 40.000 0.00 0.00 0.00 3.86
5726 8051 8.915057 AATCATCAAACCCTATGTAGAATGAG 57.085 34.615 0.00 0.00 0.00 2.90
5727 8052 9.123902 CAAATCATCAAACCCTATGTAGAATGA 57.876 33.333 0.00 0.00 0.00 2.57
5728 8053 7.864379 GCAAATCATCAAACCCTATGTAGAATG 59.136 37.037 0.00 0.00 0.00 2.67
5729 8054 7.945134 GCAAATCATCAAACCCTATGTAGAAT 58.055 34.615 0.00 0.00 0.00 2.40
5730 8055 7.333528 GCAAATCATCAAACCCTATGTAGAA 57.666 36.000 0.00 0.00 0.00 2.10
5731 8056 6.942532 GCAAATCATCAAACCCTATGTAGA 57.057 37.500 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.