Multiple sequence alignment - TraesCS2D01G519800

Loading Multiple Alignment...

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 TraesCS2D01G519800 chr2D 100.000 6358 0 0 1714 8071 609438992 609432635 0.000000e+00 11742.0
1 TraesCS2D01G519800 chr2D 100.000 1357 0 0 1 1357 609440705 609439349 0.000000e+00 2507.0
2 TraesCS2D01G519800 chr2D 94.828 754 39 0 2 755 152031222 152031975 0.000000e+00 1177.0
3 TraesCS2D01G519800 chr2D 94.437 755 41 1 2 756 252440822 252441575 0.000000e+00 1160.0
4 TraesCS2D01G519800 chr2D 90.110 91 2 5 6081 6166 272795895 272795807 2.380000e-20 111.0
5 TraesCS2D01G519800 chr2A 96.287 5844 149 29 1716 7540 742137623 742131829 0.000000e+00 9527.0
6 TraesCS2D01G519800 chr2A 95.094 530 11 5 841 1357 742138219 742137692 0.000000e+00 821.0
7 TraesCS2D01G519800 chr2A 90.947 243 8 4 7829 8071 742131487 742131259 1.690000e-81 315.0
8 TraesCS2D01G519800 chr2A 95.062 162 5 1 7910 8071 741379823 741379665 1.340000e-62 252.0
9 TraesCS2D01G519800 chr2A 90.104 192 14 1 7119 7310 741416257 741416071 2.250000e-60 244.0
10 TraesCS2D01G519800 chr2A 87.619 210 8 5 6799 7004 741417923 741417728 2.270000e-55 228.0
11 TraesCS2D01G519800 chr2A 83.854 192 22 8 7521 7712 728401985 728402167 2.990000e-39 174.0
12 TraesCS2D01G519800 chr2A 96.262 107 3 1 7803 7909 742131797 742131692 2.990000e-39 174.0
13 TraesCS2D01G519800 chr2A 90.110 91 2 5 6081 6166 726911052 726910964 2.380000e-20 111.0
14 TraesCS2D01G519800 chr2A 96.364 55 2 0 7074 7128 741417693 741417639 3.100000e-14 91.6
15 TraesCS2D01G519800 chr2B 95.534 3426 110 18 1714 5112 743733769 743730360 0.000000e+00 5439.0
16 TraesCS2D01G519800 chr2B 91.507 1307 69 13 6271 7540 743729304 743728003 0.000000e+00 1760.0
17 TraesCS2D01G519800 chr2B 94.766 1089 28 5 5146 6233 743730362 743729302 0.000000e+00 1668.0
18 TraesCS2D01G519800 chr2B 95.420 524 15 5 841 1357 743734360 743733839 0.000000e+00 826.0
19 TraesCS2D01G519800 chr2B 94.813 347 9 5 7727 8071 743728002 743727663 4.290000e-147 532.0
20 TraesCS2D01G519800 chr2B 93.089 246 17 0 991 1236 181699309 181699554 2.140000e-95 361.0
21 TraesCS2D01G519800 chr5D 94.695 754 40 0 2 755 278804180 278804933 0.000000e+00 1171.0
22 TraesCS2D01G519800 chr5D 94.695 754 40 0 2 755 412565646 412564893 0.000000e+00 1171.0
23 TraesCS2D01G519800 chr5D 85.027 187 20 6 7541 7726 354813054 354813233 4.970000e-42 183.0
24 TraesCS2D01G519800 chr5D 90.000 90 3 5 6081 6166 329122107 329122020 2.380000e-20 111.0
25 TraesCS2D01G519800 chr4D 94.920 748 38 0 2 749 273487430 273488177 0.000000e+00 1171.0
26 TraesCS2D01G519800 chr4D 94.913 747 38 0 2 748 273398636 273399382 0.000000e+00 1170.0
27 TraesCS2D01G519800 chr4D 94.570 755 39 2 2 755 8766104 8765351 0.000000e+00 1166.0
28 TraesCS2D01G519800 chr4D 94.562 754 41 0 2 755 90405927 90405174 0.000000e+00 1166.0
29 TraesCS2D01G519800 chr4D 84.492 187 20 8 7541 7726 421404950 421405128 8.320000e-40 176.0
30 TraesCS2D01G519800 chr6D 94.562 754 41 0 2 755 410726992 410727745 0.000000e+00 1166.0
31 TraesCS2D01G519800 chr1B 93.333 255 16 1 983 1236 217554382 217554636 7.650000e-100 375.0
32 TraesCS2D01G519800 chr1B 86.705 173 15 7 7541 7712 521219376 521219541 1.380000e-42 185.0
33 TraesCS2D01G519800 chr6B 87.861 173 15 5 7542 7713 583446146 583445979 1.780000e-46 198.0
34 TraesCS2D01G519800 chr6B 85.165 182 20 5 7537 7718 120226299 120226125 6.440000e-41 180.0
35 TraesCS2D01G519800 chr6B 100.000 31 0 0 799 829 244342926 244342956 3.150000e-04 58.4
36 TraesCS2D01G519800 chr6B 100.000 30 0 0 802 831 706656114 706656143 1.000000e-03 56.5
37 TraesCS2D01G519800 chr3D 87.135 171 16 5 7542 7712 87926161 87925997 1.070000e-43 189.0
38 TraesCS2D01G519800 chr3D 86.441 59 8 0 770 828 566633949 566633891 1.880000e-06 65.8
39 TraesCS2D01G519800 chr5A 87.059 170 16 5 7542 7711 414776174 414776011 3.850000e-43 187.0
40 TraesCS2D01G519800 chr7B 84.699 183 22 4 7542 7724 382332091 382331915 2.310000e-40 178.0
41 TraesCS2D01G519800 chr6A 91.111 90 2 4 6081 6166 445904343 445904256 5.120000e-22 117.0
42 TraesCS2D01G519800 chr3B 90.110 91 2 5 6081 6166 201525008 201525096 2.380000e-20 111.0
43 TraesCS2D01G519800 chrUn 89.130 92 2 4 6081 6166 23290155 23290066 3.080000e-19 108.0
44 TraesCS2D01G519800 chrUn 89.130 92 2 4 6081 6166 93411634 93411545 3.080000e-19 108.0
45 TraesCS2D01G519800 chr7D 82.278 79 13 1 758 836 117272135 117272212 5.230000e-07 67.6
46 TraesCS2D01G519800 chr1D 85.455 55 8 0 775 829 485374566 485374512 3.150000e-04 58.4
47 TraesCS2D01G519800 chr1D 100.000 29 0 0 801 829 492521739 492521711 4.000000e-03 54.7
48 TraesCS2D01G519800 chr3A 100.000 30 0 0 801 830 697127827 697127856 1.000000e-03 56.5
49 TraesCS2D01G519800 chr4B 84.906 53 8 0 777 829 44500725 44500777 4.000000e-03 54.7
50 TraesCS2D01G519800 chr4B 84.906 53 8 0 777 829 44679218 44679270 4.000000e-03 54.7


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 TraesCS2D01G519800 chr2D 609432635 609440705 8070 True 7124.50 11742 100.0000 1 8071 2 chr2D.!!$R2 8070
1 TraesCS2D01G519800 chr2D 152031222 152031975 753 False 1177.00 1177 94.8280 2 755 1 chr2D.!!$F1 753
2 TraesCS2D01G519800 chr2D 252440822 252441575 753 False 1160.00 1160 94.4370 2 756 1 chr2D.!!$F2 754
3 TraesCS2D01G519800 chr2A 742131259 742138219 6960 True 2709.25 9527 94.6475 841 8071 4 chr2A.!!$R4 7230
4 TraesCS2D01G519800 chr2B 743727663 743734360 6697 True 2045.00 5439 94.4080 841 8071 5 chr2B.!!$R1 7230
5 TraesCS2D01G519800 chr5D 278804180 278804933 753 False 1171.00 1171 94.6950 2 755 1 chr5D.!!$F1 753
6 TraesCS2D01G519800 chr5D 412564893 412565646 753 True 1171.00 1171 94.6950 2 755 1 chr5D.!!$R2 753
7 TraesCS2D01G519800 chr4D 273487430 273488177 747 False 1171.00 1171 94.9200 2 749 1 chr4D.!!$F2 747
8 TraesCS2D01G519800 chr4D 273398636 273399382 746 False 1170.00 1170 94.9130 2 748 1 chr4D.!!$F1 746
9 TraesCS2D01G519800 chr4D 8765351 8766104 753 True 1166.00 1166 94.5700 2 755 1 chr4D.!!$R1 753
10 TraesCS2D01G519800 chr4D 90405174 90405927 753 True 1166.00 1166 94.5620 2 755 1 chr4D.!!$R2 753
11 TraesCS2D01G519800 chr6D 410726992 410727745 753 False 1166.00 1166 94.5620 2 755 1 chr6D.!!$F1 753

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
833 834 0.179000 AGAGTTGCTCTTATGGGCCG 59.821 55.000 0.00 0.00 37.60 6.13 F
834 835 0.815615 GAGTTGCTCTTATGGGCCGG 60.816 60.000 0.00 0.00 0.00 6.13 F
1869 1888 1.823295 GCACTCTCCGCCATTAGGA 59.177 57.895 0.00 0.00 36.89 2.94 F
2639 2666 0.108186 TTGCCCTACTGAGCATGTCG 60.108 55.000 0.00 0.00 39.11 4.35 F
3367 3401 1.691434 AGCTATGTAAGGCTGGAGCTC 59.309 52.381 4.71 4.71 35.38 4.09 F
3626 3660 1.730446 GCACGAGCATCAAAAAGAGCC 60.730 52.381 0.00 0.00 41.58 4.70 F
4910 4957 2.110627 GCGCCATGAGGATGCTCT 59.889 61.111 15.82 0.00 36.89 4.09 F
6015 6063 0.031043 GTGTGTGCTGCATGCTCAAA 59.969 50.000 20.33 9.20 45.14 2.69 F
6751 6799 0.450983 GACAATCAGGAGCAGCTTGC 59.549 55.000 0.00 0.47 45.46 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1731 1.299976 CCTCCGAAAACAGAGGGGG 59.700 63.158 0.00 0.00 45.08 5.40 R
2482 2502 2.035632 AGCCCTAGAGATAGCACACAC 58.964 52.381 0.00 0.00 0.00 3.82 R
3247 3281 3.648545 GGAGAGCCACCACTAATATCCTT 59.351 47.826 0.00 0.00 0.00 3.36 R
4061 4095 0.595095 GCAAAGAGCCCAGTGACAAG 59.405 55.000 0.00 0.00 37.23 3.16 R
5044 5091 0.184211 ATGCATGCAGGTATGAGGCA 59.816 50.000 26.69 0.00 42.43 4.75 R
5122 5169 0.603065 AGCTCTGACGTACATGTGCA 59.397 50.000 14.55 3.90 0.00 4.57 R
6857 6905 0.325671 AATCCTCCTCCTCCGCTTCA 60.326 55.000 0.00 0.00 0.00 3.02 R
6862 6910 1.000283 CGATCAAATCCTCCTCCTCCG 60.000 57.143 0.00 0.00 0.00 4.63 R
7788 7895 1.229951 TCCAACCTCCATGGAGCCT 60.230 57.895 32.97 20.04 41.98 4.58 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 3.904717 ACCTTCGATGAGATGGACTACT 58.095 45.455 0.00 0.00 44.51 2.57
115 116 2.176798 TGTGGAAAATGGTGTTCCCTCT 59.823 45.455 0.92 0.00 43.43 3.69
120 121 3.814504 AAATGGTGTTCCCTCTGTCAT 57.185 42.857 0.00 0.00 0.00 3.06
202 203 3.393609 ACATCATATGTGGCCATCTGAGT 59.606 43.478 9.72 7.26 43.01 3.41
206 207 6.191657 TCATATGTGGCCATCTGAGTAAAT 57.808 37.500 9.72 0.00 31.41 1.40
209 210 2.308570 TGTGGCCATCTGAGTAAATGGT 59.691 45.455 9.72 0.00 43.65 3.55
216 217 6.239600 GGCCATCTGAGTAAATGGTAGTATGA 60.240 42.308 0.00 0.00 43.65 2.15
219 220 9.613428 CCATCTGAGTAAATGGTAGTATGAAAA 57.387 33.333 0.00 0.00 38.10 2.29
283 284 1.070134 TCCAAGGTCAACGAAGGAGTG 59.930 52.381 0.00 0.00 0.00 3.51
333 334 2.699954 TCTTCGCAATCTCTTCAACCC 58.300 47.619 0.00 0.00 0.00 4.11
496 497 6.463472 CCTCATTTGATACTCTGGCACTGATA 60.463 42.308 0.00 0.00 35.31 2.15
500 501 9.445878 CATTTGATACTCTGGCACTGATAATAT 57.554 33.333 0.00 0.00 35.31 1.28
578 579 2.568956 ACTCATGAGTTCCAGCTTGCTA 59.431 45.455 22.89 0.00 38.83 3.49
630 631 1.194781 AGATCACGTGCCCTGAAGGT 61.195 55.000 11.67 0.00 38.26 3.50
648 649 3.445008 AGGTCAAGGCTGTCTCTGAATA 58.555 45.455 0.00 0.00 0.00 1.75
673 674 8.774546 ATGAAGATGAAGATTCTGGTAGTAGA 57.225 34.615 0.00 0.00 0.00 2.59
733 734 5.296780 ACTGCTCGTGAAGAAATTTCAGAAA 59.703 36.000 19.99 0.00 0.00 2.52
744 745 9.956720 GAAGAAATTTCAGAAATTCTCAAGACA 57.043 29.630 19.41 0.00 40.05 3.41
755 756 4.836125 TTCTCAAGACATGGTTGCTTTC 57.164 40.909 0.00 0.00 0.00 2.62
756 757 3.819368 TCTCAAGACATGGTTGCTTTCA 58.181 40.909 0.00 0.00 0.00 2.69
757 758 3.817084 TCTCAAGACATGGTTGCTTTCAG 59.183 43.478 0.00 0.00 0.00 3.02
758 759 2.294233 TCAAGACATGGTTGCTTTCAGC 59.706 45.455 0.00 0.00 42.82 4.26
759 760 0.877071 AGACATGGTTGCTTTCAGCG 59.123 50.000 0.00 0.00 46.26 5.18
760 761 0.874390 GACATGGTTGCTTTCAGCGA 59.126 50.000 0.00 0.00 46.26 4.93
761 762 1.470098 GACATGGTTGCTTTCAGCGAT 59.530 47.619 0.00 0.00 46.26 4.58
762 763 1.888512 ACATGGTTGCTTTCAGCGATT 59.111 42.857 0.00 0.00 46.26 3.34
763 764 2.297033 ACATGGTTGCTTTCAGCGATTT 59.703 40.909 0.00 0.00 46.26 2.17
764 765 3.243839 ACATGGTTGCTTTCAGCGATTTT 60.244 39.130 0.00 0.00 46.26 1.82
765 766 2.741612 TGGTTGCTTTCAGCGATTTTG 58.258 42.857 0.00 0.00 46.26 2.44
766 767 1.456923 GGTTGCTTTCAGCGATTTTGC 59.543 47.619 0.00 0.00 46.26 3.68
767 768 2.126467 GTTGCTTTCAGCGATTTTGCA 58.874 42.857 0.00 0.00 46.26 4.08
768 769 1.769733 TGCTTTCAGCGATTTTGCAC 58.230 45.000 0.00 0.00 46.26 4.57
769 770 0.704551 GCTTTCAGCGATTTTGCACG 59.295 50.000 0.00 0.00 37.31 5.34
770 771 1.662876 GCTTTCAGCGATTTTGCACGA 60.663 47.619 0.00 0.00 37.31 4.35
771 772 2.649516 CTTTCAGCGATTTTGCACGAA 58.350 42.857 0.00 0.00 37.31 3.85
772 773 2.987413 TTCAGCGATTTTGCACGAAT 57.013 40.000 0.00 0.00 37.31 3.34
773 774 2.987413 TCAGCGATTTTGCACGAATT 57.013 40.000 0.00 0.00 37.31 2.17
774 775 2.583739 TCAGCGATTTTGCACGAATTG 58.416 42.857 0.00 2.24 37.31 2.32
775 776 2.031245 TCAGCGATTTTGCACGAATTGT 60.031 40.909 0.00 0.00 37.31 2.71
776 777 3.187432 TCAGCGATTTTGCACGAATTGTA 59.813 39.130 0.00 0.00 37.31 2.41
777 778 3.911365 CAGCGATTTTGCACGAATTGTAA 59.089 39.130 0.00 0.00 37.31 2.41
778 779 4.381270 CAGCGATTTTGCACGAATTGTAAA 59.619 37.500 0.00 0.00 37.96 2.01
779 780 4.381566 AGCGATTTTGCACGAATTGTAAAC 59.618 37.500 0.00 0.00 39.27 2.01
780 781 4.714326 GCGATTTTGCACGAATTGTAAACG 60.714 41.667 0.00 0.00 39.27 3.60
781 782 4.614417 GATTTTGCACGAATTGTAAACGC 58.386 39.130 0.00 0.00 39.27 4.84
782 783 1.664629 TTGCACGAATTGTAAACGCG 58.335 45.000 3.53 3.53 0.00 6.01
783 784 0.582482 TGCACGAATTGTAAACGCGT 59.418 45.000 5.58 5.58 39.10 6.01
784 785 1.003759 TGCACGAATTGTAAACGCGTT 60.004 42.857 20.79 20.79 36.91 4.84
785 786 2.038367 GCACGAATTGTAAACGCGTTT 58.962 42.857 36.15 36.15 36.91 3.60
786 787 2.464744 GCACGAATTGTAAACGCGTTTT 59.535 40.909 38.53 22.74 36.91 2.43
787 788 3.654551 GCACGAATTGTAAACGCGTTTTG 60.655 43.478 38.53 27.76 36.91 2.44
788 789 2.464744 ACGAATTGTAAACGCGTTTTGC 59.535 40.909 38.53 29.69 35.79 3.68
789 790 2.464380 CGAATTGTAAACGCGTTTTGCA 59.536 40.909 38.53 31.56 46.97 4.08
790 791 3.418646 CGAATTGTAAACGCGTTTTGCAG 60.419 43.478 38.53 21.35 46.97 4.41
791 792 1.828832 TTGTAAACGCGTTTTGCAGG 58.171 45.000 38.53 0.00 46.97 4.85
792 793 0.592754 TGTAAACGCGTTTTGCAGGC 60.593 50.000 38.53 21.80 46.97 4.85
793 794 1.008309 TAAACGCGTTTTGCAGGCC 60.008 52.632 38.53 0.00 46.97 5.19
794 795 2.718993 TAAACGCGTTTTGCAGGCCG 62.719 55.000 38.53 0.00 46.97 6.13
797 798 4.999939 GCGTTTTGCAGGCCGGTG 63.000 66.667 1.90 0.00 45.45 4.94
798 799 4.341502 CGTTTTGCAGGCCGGTGG 62.342 66.667 1.90 0.00 0.00 4.61
799 800 2.909965 GTTTTGCAGGCCGGTGGA 60.910 61.111 1.90 0.00 0.00 4.02
800 801 2.123683 TTTTGCAGGCCGGTGGAA 60.124 55.556 1.90 0.00 0.00 3.53
801 802 1.532794 TTTTGCAGGCCGGTGGAAT 60.533 52.632 1.90 0.00 0.00 3.01
802 803 1.814772 TTTTGCAGGCCGGTGGAATG 61.815 55.000 1.90 0.00 0.00 2.67
805 806 3.136123 CAGGCCGGTGGAATGCAG 61.136 66.667 1.90 0.00 0.00 4.41
806 807 4.431131 AGGCCGGTGGAATGCAGG 62.431 66.667 1.90 0.00 0.00 4.85
808 809 4.740822 GCCGGTGGAATGCAGGGT 62.741 66.667 1.90 0.00 0.00 4.34
809 810 2.438434 CCGGTGGAATGCAGGGTC 60.438 66.667 0.00 0.00 0.00 4.46
810 811 2.671070 CGGTGGAATGCAGGGTCT 59.329 61.111 0.00 0.00 0.00 3.85
811 812 1.746615 CGGTGGAATGCAGGGTCTG 60.747 63.158 0.00 0.00 34.12 3.51
821 822 3.450028 CAGGGTCTGCTAGAGTTGC 57.550 57.895 0.00 0.00 0.00 4.17
822 823 0.901124 CAGGGTCTGCTAGAGTTGCT 59.099 55.000 0.00 0.00 0.00 3.91
823 824 1.134848 CAGGGTCTGCTAGAGTTGCTC 60.135 57.143 0.00 0.00 0.00 4.26
824 825 1.190643 GGGTCTGCTAGAGTTGCTCT 58.809 55.000 4.02 4.02 43.83 4.09
825 826 1.552792 GGGTCTGCTAGAGTTGCTCTT 59.447 52.381 3.87 0.00 41.50 2.85
826 827 2.761208 GGGTCTGCTAGAGTTGCTCTTA 59.239 50.000 3.87 0.00 41.50 2.10
827 828 3.386402 GGGTCTGCTAGAGTTGCTCTTAT 59.614 47.826 3.87 0.00 41.50 1.73
828 829 4.367450 GGTCTGCTAGAGTTGCTCTTATG 58.633 47.826 3.87 0.00 41.50 1.90
829 830 4.367450 GTCTGCTAGAGTTGCTCTTATGG 58.633 47.826 3.87 0.00 41.50 2.74
830 831 3.386078 TCTGCTAGAGTTGCTCTTATGGG 59.614 47.826 3.87 0.00 41.50 4.00
831 832 2.158900 TGCTAGAGTTGCTCTTATGGGC 60.159 50.000 3.87 0.00 41.50 5.36
832 833 2.808567 GCTAGAGTTGCTCTTATGGGCC 60.809 54.545 3.87 0.00 41.50 5.80
833 834 0.179000 AGAGTTGCTCTTATGGGCCG 59.821 55.000 0.00 0.00 37.60 6.13
834 835 0.815615 GAGTTGCTCTTATGGGCCGG 60.816 60.000 0.00 0.00 0.00 6.13
835 836 2.124320 TTGCTCTTATGGGCCGGC 60.124 61.111 21.18 21.18 0.00 6.13
836 837 3.714487 TTGCTCTTATGGGCCGGCC 62.714 63.158 38.57 38.57 0.00 6.13
1810 1829 2.535166 CGCCGATGCCATTGTTTTATTG 59.465 45.455 0.00 0.00 0.00 1.90
1811 1830 3.520569 GCCGATGCCATTGTTTTATTGT 58.479 40.909 0.00 0.00 0.00 2.71
1812 1831 4.677584 GCCGATGCCATTGTTTTATTGTA 58.322 39.130 0.00 0.00 0.00 2.41
1813 1832 4.502645 GCCGATGCCATTGTTTTATTGTAC 59.497 41.667 0.00 0.00 0.00 2.90
1814 1833 4.732923 CCGATGCCATTGTTTTATTGTACG 59.267 41.667 0.00 0.00 0.00 3.67
1869 1888 1.823295 GCACTCTCCGCCATTAGGA 59.177 57.895 0.00 0.00 36.89 2.94
2052 2071 6.038603 TGGAATCAAGTGTTTCTTTCTCAGTG 59.961 38.462 2.94 0.00 33.63 3.66
2053 2072 6.382869 AATCAAGTGTTTCTTTCTCAGTGG 57.617 37.500 0.00 0.00 33.63 4.00
2054 2073 4.843728 TCAAGTGTTTCTTTCTCAGTGGT 58.156 39.130 0.00 0.00 33.63 4.16
2055 2074 5.984725 TCAAGTGTTTCTTTCTCAGTGGTA 58.015 37.500 0.00 0.00 33.63 3.25
2056 2075 6.049149 TCAAGTGTTTCTTTCTCAGTGGTAG 58.951 40.000 0.00 0.00 33.63 3.18
2070 2089 3.753272 CAGTGGTAGGAAGAACACAATGG 59.247 47.826 0.00 0.00 36.35 3.16
2134 2153 7.500992 TGAAGATAATGAGTTGTGGGATAGAC 58.499 38.462 0.00 0.00 0.00 2.59
2167 2186 5.180680 GCTGCATGATTACAGATAGATTGCA 59.819 40.000 0.00 0.00 35.90 4.08
2248 2267 2.038387 AGTAGCGCAAAATAGGTGGG 57.962 50.000 11.47 0.00 0.00 4.61
2466 2486 9.118236 GTTCAGTTGTTTTCTCATATAGTTTGC 57.882 33.333 0.00 0.00 0.00 3.68
2482 2502 3.620374 AGTTTGCACTATTCAGCTCATCG 59.380 43.478 0.00 0.00 0.00 3.84
2639 2666 0.108186 TTGCCCTACTGAGCATGTCG 60.108 55.000 0.00 0.00 39.11 4.35
3082 3113 5.779241 TGGAGAGAGTGGGTATTTTCATT 57.221 39.130 0.00 0.00 0.00 2.57
3084 3115 5.014123 TGGAGAGAGTGGGTATTTTCATTGT 59.986 40.000 0.00 0.00 0.00 2.71
3143 3177 3.198853 AGCTGAAAAGTAGAGGATCACCC 59.801 47.826 0.00 0.00 37.82 4.61
3261 3295 9.588096 AAGAAAAAGTTGAAGGATATTAGTGGT 57.412 29.630 0.00 0.00 0.00 4.16
3339 3373 3.689347 TGATGTATCAAAACTGCTGCCT 58.311 40.909 0.00 0.00 33.08 4.75
3367 3401 1.691434 AGCTATGTAAGGCTGGAGCTC 59.309 52.381 4.71 4.71 35.38 4.09
3445 3479 8.481314 TCTCTCAGTTCTGCACAATCTAAATAT 58.519 33.333 0.00 0.00 0.00 1.28
3531 3565 5.207110 ACCATATCAGTGCTGCTACTAAG 57.793 43.478 0.00 0.00 0.00 2.18
3550 3584 7.133891 ACTAAGTGAGTAAATGCATGTTGAC 57.866 36.000 0.00 0.00 36.27 3.18
3626 3660 1.730446 GCACGAGCATCAAAAAGAGCC 60.730 52.381 0.00 0.00 41.58 4.70
3755 3789 9.553064 GAGATAATGTAACCTTCACATTGAGAT 57.447 33.333 10.20 0.00 44.30 2.75
3999 4033 4.283467 TCATGAAATCCCCATAGTCCTACG 59.717 45.833 0.00 0.00 0.00 3.51
4776 4823 9.860650 ATAAATTAATTCACTAGCCACCATGTA 57.139 29.630 0.10 0.00 0.00 2.29
4783 4830 5.565509 TCACTAGCCACCATGTATTCAAAA 58.434 37.500 0.00 0.00 0.00 2.44
4910 4957 2.110627 GCGCCATGAGGATGCTCT 59.889 61.111 15.82 0.00 36.89 4.09
4957 5004 3.567308 TGGCACAGCTTCACCTCT 58.433 55.556 0.00 0.00 0.00 3.69
5078 5125 8.033626 ACCTGCATGCATATATATGATCGATAG 58.966 37.037 22.97 13.76 35.75 2.08
5122 5169 4.339814 TCGTTAAAGTTGCCTTTGGTGATT 59.660 37.500 0.00 0.00 41.03 2.57
5123 5170 4.444056 CGTTAAAGTTGCCTTTGGTGATTG 59.556 41.667 0.00 0.00 41.03 2.67
5190 5237 2.257371 CATTGTTGCAGCTGCGCT 59.743 55.556 32.11 12.76 45.83 5.92
5447 5494 2.704342 GATTGGGGCAATGCGATGGC 62.704 60.000 0.00 6.56 44.56 4.40
5560 5607 2.045926 ACGCCATGCAAGGTCCTC 60.046 61.111 10.15 0.00 0.00 3.71
5622 5669 2.430080 GAAAGTGCCTGCGTCGTGTG 62.430 60.000 0.00 0.00 0.00 3.82
5647 5694 6.976349 GCATTTTTAGGGGTTATTCTTTACGG 59.024 38.462 0.00 0.00 0.00 4.02
5671 5718 1.283321 AGAGGAAAAGCATGGACCTCC 59.717 52.381 0.00 0.00 45.53 4.30
5678 5725 5.299531 GGAAAAGCATGGACCTCCTTATTAC 59.700 44.000 0.00 0.00 36.82 1.89
5804 5851 6.442513 AGATAGCATTTTCAGCTGGTTAAC 57.557 37.500 15.13 0.00 43.33 2.01
5822 5869 9.463443 CTGGTTAACCTTTTTATGAGAAACAAG 57.537 33.333 24.78 4.43 36.82 3.16
6008 6056 0.887836 CTCACCAGTGTGTGCTGCAT 60.888 55.000 5.27 0.00 43.26 3.96
6015 6063 0.031043 GTGTGTGCTGCATGCTCAAA 59.969 50.000 20.33 9.20 45.14 2.69
6234 6282 5.930135 AGTTGTCTTGTGGAGAAAGTGTAT 58.070 37.500 0.00 0.00 35.79 2.29
6261 6309 5.809001 AGGAAACTTCATGCTGATACTTGA 58.191 37.500 0.00 0.00 37.44 3.02
6422 6470 4.332828 ACAAGTAGGTGTTATTTGCCTCC 58.667 43.478 0.00 0.00 33.56 4.30
6443 6491 7.016760 GCCTCCTTTTTCTTACTCCTATCCTAT 59.983 40.741 0.00 0.00 0.00 2.57
6453 6501 7.613801 TCTTACTCCTATCCTATCAAGATGCTC 59.386 40.741 0.00 0.00 0.00 4.26
6751 6799 0.450983 GACAATCAGGAGCAGCTTGC 59.549 55.000 0.00 0.47 45.46 4.01
6803 6851 0.883833 CAGAAGCTTTGCCCAACGAT 59.116 50.000 0.00 0.00 0.00 3.73
6862 6910 0.379669 CAAGACATGGGCGATGAAGC 59.620 55.000 16.77 5.25 35.80 3.86
6863 6911 1.091771 AAGACATGGGCGATGAAGCG 61.092 55.000 16.77 0.00 38.18 4.68
6864 6912 2.514592 ACATGGGCGATGAAGCGG 60.515 61.111 16.77 0.00 38.18 5.52
7046 7097 0.543883 TGAGCCTTCTGGAGTCTGCT 60.544 55.000 0.00 0.00 34.57 4.24
7119 7182 3.914426 TTCAGGTGGAAGGAGAATAGC 57.086 47.619 0.00 0.00 0.00 2.97
7135 7198 4.785453 GCCTCAGCCCGGGAGTTG 62.785 72.222 29.31 19.10 0.00 3.16
7168 7239 5.475909 GGTAGGGTTCGATCTGTACATATGA 59.524 44.000 10.38 0.00 0.00 2.15
7169 7240 6.153000 GGTAGGGTTCGATCTGTACATATGAT 59.847 42.308 10.38 0.00 0.00 2.45
7170 7241 7.338703 GGTAGGGTTCGATCTGTACATATGATA 59.661 40.741 10.38 0.00 0.00 2.15
7171 7242 7.962995 AGGGTTCGATCTGTACATATGATAT 57.037 36.000 10.38 0.00 0.00 1.63
7172 7243 7.776107 AGGGTTCGATCTGTACATATGATATG 58.224 38.462 10.38 10.75 0.00 1.78
7254 7328 4.223320 AGCAATTAATTTATGGACCGCG 57.777 40.909 0.00 0.00 0.00 6.46
7393 7469 3.274288 AGCTGCTCAATAGGTTTACTGC 58.726 45.455 0.00 0.00 0.00 4.40
7490 7597 2.428171 AGCGCATGTGCTAAAAATCCAT 59.572 40.909 31.53 4.12 45.14 3.41
7499 7606 8.723311 CATGTGCTAAAAATCCATGAATTTGTT 58.277 29.630 0.00 0.00 35.96 2.83
7540 7647 8.132604 GTGTAGCTCACATCTTAAATTACTCC 57.867 38.462 10.30 0.00 45.51 3.85
7541 7648 7.982354 GTGTAGCTCACATCTTAAATTACTCCT 59.018 37.037 10.30 0.00 45.51 3.69
7542 7649 9.197306 TGTAGCTCACATCTTAAATTACTCCTA 57.803 33.333 0.00 0.00 30.04 2.94
7543 7650 9.465985 GTAGCTCACATCTTAAATTACTCCTAC 57.534 37.037 0.00 0.00 0.00 3.18
7544 7651 8.312669 AGCTCACATCTTAAATTACTCCTACT 57.687 34.615 0.00 0.00 0.00 2.57
7545 7652 8.417884 AGCTCACATCTTAAATTACTCCTACTC 58.582 37.037 0.00 0.00 0.00 2.59
7546 7653 7.654116 GCTCACATCTTAAATTACTCCTACTCC 59.346 40.741 0.00 0.00 0.00 3.85
7547 7654 8.019656 TCACATCTTAAATTACTCCTACTCCC 57.980 38.462 0.00 0.00 0.00 4.30
7548 7655 7.844779 TCACATCTTAAATTACTCCTACTCCCT 59.155 37.037 0.00 0.00 0.00 4.20
7549 7656 8.145122 CACATCTTAAATTACTCCTACTCCCTC 58.855 40.741 0.00 0.00 0.00 4.30
7550 7657 7.290481 ACATCTTAAATTACTCCTACTCCCTCC 59.710 40.741 0.00 0.00 0.00 4.30
7551 7658 6.748969 TCTTAAATTACTCCTACTCCCTCCA 58.251 40.000 0.00 0.00 0.00 3.86
7552 7659 7.371043 TCTTAAATTACTCCTACTCCCTCCAT 58.629 38.462 0.00 0.00 0.00 3.41
7553 7660 7.849904 TCTTAAATTACTCCTACTCCCTCCATT 59.150 37.037 0.00 0.00 0.00 3.16
7554 7661 6.502074 AAATTACTCCTACTCCCTCCATTC 57.498 41.667 0.00 0.00 0.00 2.67
7555 7662 4.901785 TTACTCCTACTCCCTCCATTCT 57.098 45.455 0.00 0.00 0.00 2.40
7556 7663 3.786213 ACTCCTACTCCCTCCATTCTT 57.214 47.619 0.00 0.00 0.00 2.52
7557 7664 4.901785 ACTCCTACTCCCTCCATTCTTA 57.098 45.455 0.00 0.00 0.00 2.10
7558 7665 5.222278 ACTCCTACTCCCTCCATTCTTAA 57.778 43.478 0.00 0.00 0.00 1.85
7559 7666 5.600749 ACTCCTACTCCCTCCATTCTTAAA 58.399 41.667 0.00 0.00 0.00 1.52
7560 7667 6.213525 ACTCCTACTCCCTCCATTCTTAAAT 58.786 40.000 0.00 0.00 0.00 1.40
7561 7668 7.371043 ACTCCTACTCCCTCCATTCTTAAATA 58.629 38.462 0.00 0.00 0.00 1.40
7562 7669 8.019652 ACTCCTACTCCCTCCATTCTTAAATAT 58.980 37.037 0.00 0.00 0.00 1.28
7563 7670 9.548631 CTCCTACTCCCTCCATTCTTAAATATA 57.451 37.037 0.00 0.00 0.00 0.86
7568 7675 9.851267 ACTCCCTCCATTCTTAAATATATCTCT 57.149 33.333 0.00 0.00 0.00 3.10
7590 7697 9.057911 TCTCTTTTTAGAGATTCCAATAAGGGA 57.942 33.333 0.88 0.00 39.74 4.20
7591 7698 9.114952 CTCTTTTTAGAGATTCCAATAAGGGAC 57.885 37.037 0.00 0.00 38.13 4.46
7604 7711 9.574577 TTCCAATAAGGGACTATATATGGATGT 57.425 33.333 2.68 0.00 38.49 3.06
7647 7754 6.857964 AGTGTATTTTCACTCATTTTGCTTCG 59.142 34.615 0.00 0.00 44.07 3.79
7648 7755 6.636850 GTGTATTTTCACTCATTTTGCTTCGT 59.363 34.615 0.00 0.00 35.68 3.85
7649 7756 7.801315 GTGTATTTTCACTCATTTTGCTTCGTA 59.199 33.333 0.00 0.00 35.68 3.43
7650 7757 8.511321 TGTATTTTCACTCATTTTGCTTCGTAT 58.489 29.630 0.00 0.00 0.00 3.06
7651 7758 7.801547 ATTTTCACTCATTTTGCTTCGTATG 57.198 32.000 0.00 0.00 0.00 2.39
7652 7759 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
7653 7760 7.428282 TTTCACTCATTTTGCTTCGTATGTA 57.572 32.000 0.00 0.00 0.00 2.29
7654 7761 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
7655 7762 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
7656 7763 6.649141 TCACTCATTTTGCTTCGTATGTAGTT 59.351 34.615 0.00 0.00 0.00 2.24
7657 7764 6.955963 CACTCATTTTGCTTCGTATGTAGTTC 59.044 38.462 0.00 0.00 0.00 3.01
7658 7765 6.874134 ACTCATTTTGCTTCGTATGTAGTTCT 59.126 34.615 0.00 0.00 0.00 3.01
7659 7766 7.387948 ACTCATTTTGCTTCGTATGTAGTTCTT 59.612 33.333 0.00 0.00 0.00 2.52
7660 7767 8.094798 TCATTTTGCTTCGTATGTAGTTCTTT 57.905 30.769 0.00 0.00 0.00 2.52
7661 7768 9.210329 TCATTTTGCTTCGTATGTAGTTCTTTA 57.790 29.630 0.00 0.00 0.00 1.85
7662 7769 9.988350 CATTTTGCTTCGTATGTAGTTCTTTAT 57.012 29.630 0.00 0.00 0.00 1.40
7704 7811 8.959705 AAAGACTTATATTTAGGAACGAAGGG 57.040 34.615 0.00 0.00 0.00 3.95
7705 7812 7.909485 AGACTTATATTTAGGAACGAAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
7706 7813 7.953752 AGACTTATATTTAGGAACGAAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
7707 7814 7.564292 AGACTTATATTTAGGAACGAAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
7708 7815 8.773033 ACTTATATTTAGGAACGAAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
7709 7816 9.377238 ACTTATATTTAGGAACGAAGGGAGTAT 57.623 33.333 0.00 0.00 0.00 2.12
7713 7820 7.850935 ATTTAGGAACGAAGGGAGTATATGA 57.149 36.000 0.00 0.00 0.00 2.15
7714 7821 7.850935 TTTAGGAACGAAGGGAGTATATGAT 57.149 36.000 0.00 0.00 0.00 2.45
7715 7822 8.945195 TTTAGGAACGAAGGGAGTATATGATA 57.055 34.615 0.00 0.00 0.00 2.15
7716 7823 8.577048 TTAGGAACGAAGGGAGTATATGATAG 57.423 38.462 0.00 0.00 0.00 2.08
7717 7824 6.553857 AGGAACGAAGGGAGTATATGATAGT 58.446 40.000 0.00 0.00 0.00 2.12
7718 7825 6.434652 AGGAACGAAGGGAGTATATGATAGTG 59.565 42.308 0.00 0.00 0.00 2.74
7719 7826 6.433404 GGAACGAAGGGAGTATATGATAGTGA 59.567 42.308 0.00 0.00 0.00 3.41
7720 7827 7.039923 GGAACGAAGGGAGTATATGATAGTGAA 60.040 40.741 0.00 0.00 0.00 3.18
7721 7828 7.834881 ACGAAGGGAGTATATGATAGTGAAA 57.165 36.000 0.00 0.00 0.00 2.69
7722 7829 8.246430 ACGAAGGGAGTATATGATAGTGAAAA 57.754 34.615 0.00 0.00 0.00 2.29
7723 7830 8.871125 ACGAAGGGAGTATATGATAGTGAAAAT 58.129 33.333 0.00 0.00 0.00 1.82
7724 7831 9.712305 CGAAGGGAGTATATGATAGTGAAAATT 57.288 33.333 0.00 0.00 0.00 1.82
7762 7869 8.815912 AGCACATCCATATGTACATGTAGATTA 58.184 33.333 19.49 7.51 44.70 1.75
7897 8288 1.065551 GCAACCATGGGTAGAAATCGC 59.934 52.381 18.09 3.08 33.12 4.58
7908 8299 4.022676 GGGTAGAAATCGCCACTTTTTGAA 60.023 41.667 0.00 0.00 0.00 2.69
7909 8300 5.336451 GGGTAGAAATCGCCACTTTTTGAAT 60.336 40.000 0.00 0.00 0.00 2.57
7910 8301 6.156519 GGTAGAAATCGCCACTTTTTGAATT 58.843 36.000 0.00 0.00 0.00 2.17
7911 8302 6.645003 GGTAGAAATCGCCACTTTTTGAATTT 59.355 34.615 0.00 0.00 0.00 1.82
7912 8303 6.529463 AGAAATCGCCACTTTTTGAATTTG 57.471 33.333 0.00 0.00 0.00 2.32
7913 8304 6.279882 AGAAATCGCCACTTTTTGAATTTGA 58.720 32.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.479056 TCTTCCAGTAGGAGTAGTCCATCT 59.521 45.833 19.00 12.56 46.80 2.90
32 33 4.893524 TCGCATCTTATTCTTCCAGTAGGA 59.106 41.667 0.00 0.00 43.93 2.94
115 116 2.299013 AGCGTTCACAGAAGGTATGACA 59.701 45.455 0.00 0.00 0.00 3.58
120 121 0.679505 AGCAGCGTTCACAGAAGGTA 59.320 50.000 0.00 0.00 0.00 3.08
202 203 8.726988 GCACTCACTTTTTCATACTACCATTTA 58.273 33.333 0.00 0.00 0.00 1.40
206 207 5.865085 AGCACTCACTTTTTCATACTACCA 58.135 37.500 0.00 0.00 0.00 3.25
209 210 6.995686 TCCAAAGCACTCACTTTTTCATACTA 59.004 34.615 0.00 0.00 37.78 1.82
216 217 4.020662 TGGTTTCCAAAGCACTCACTTTTT 60.021 37.500 0.00 0.00 41.03 1.94
219 220 2.733956 TGGTTTCCAAAGCACTCACTT 58.266 42.857 0.00 0.00 41.03 3.16
283 284 1.517276 CGAGAGTCACGTTGTGTTGAC 59.483 52.381 1.42 0.00 34.79 3.18
333 334 5.673337 TTCATTGTCGAGTCTTTTGAAGG 57.327 39.130 0.00 0.00 0.00 3.46
496 497 9.530633 GACTTGTAATCTCCACGTTCTTATATT 57.469 33.333 0.00 0.00 0.00 1.28
500 501 6.015688 AGTGACTTGTAATCTCCACGTTCTTA 60.016 38.462 0.00 0.00 0.00 2.10
630 631 5.423290 TCTTCATATTCAGAGACAGCCTTGA 59.577 40.000 0.00 0.00 0.00 3.02
648 649 8.637986 GTCTACTACCAGAATCTTCATCTTCAT 58.362 37.037 0.00 0.00 0.00 2.57
673 674 3.648067 TCAGTTCTTCAGGATCACCAAGT 59.352 43.478 0.00 0.00 38.94 3.16
733 734 4.828939 TGAAAGCAACCATGTCTTGAGAAT 59.171 37.500 4.86 0.00 0.00 2.40
755 756 2.318578 ACAATTCGTGCAAAATCGCTG 58.681 42.857 0.00 0.00 0.00 5.18
756 757 2.704725 ACAATTCGTGCAAAATCGCT 57.295 40.000 0.00 0.00 0.00 4.93
757 758 4.614417 GTTTACAATTCGTGCAAAATCGC 58.386 39.130 0.00 0.00 0.00 4.58
758 759 4.714326 GCGTTTACAATTCGTGCAAAATCG 60.714 41.667 0.00 0.00 0.00 3.34
759 760 4.614417 GCGTTTACAATTCGTGCAAAATC 58.386 39.130 0.00 0.00 0.00 2.17
760 761 3.118809 CGCGTTTACAATTCGTGCAAAAT 59.881 39.130 0.00 0.00 0.00 1.82
761 762 2.464380 CGCGTTTACAATTCGTGCAAAA 59.536 40.909 0.00 0.00 0.00 2.44
762 763 2.037649 CGCGTTTACAATTCGTGCAAA 58.962 42.857 0.00 0.00 0.00 3.68
763 764 1.003759 ACGCGTTTACAATTCGTGCAA 60.004 42.857 5.58 0.00 38.40 4.08
764 765 0.582482 ACGCGTTTACAATTCGTGCA 59.418 45.000 5.58 0.00 38.40 4.57
765 766 1.665766 AACGCGTTTACAATTCGTGC 58.334 45.000 20.79 0.00 38.40 5.34
766 767 3.654551 GCAAAACGCGTTTACAATTCGTG 60.655 43.478 34.89 26.05 40.23 4.35
767 768 2.464744 GCAAAACGCGTTTACAATTCGT 59.535 40.909 34.89 15.92 34.63 3.85
768 769 2.464380 TGCAAAACGCGTTTACAATTCG 59.536 40.909 34.89 18.28 46.97 3.34
769 770 3.121496 CCTGCAAAACGCGTTTACAATTC 60.121 43.478 34.89 16.07 46.97 2.17
770 771 2.792116 CCTGCAAAACGCGTTTACAATT 59.208 40.909 34.89 18.15 46.97 2.32
771 772 2.389998 CCTGCAAAACGCGTTTACAAT 58.610 42.857 34.89 18.53 46.97 2.71
772 773 1.828832 CCTGCAAAACGCGTTTACAA 58.171 45.000 34.89 21.69 46.97 2.41
773 774 0.592754 GCCTGCAAAACGCGTTTACA 60.593 50.000 34.89 30.86 46.97 2.41
774 775 1.272784 GGCCTGCAAAACGCGTTTAC 61.273 55.000 34.89 28.39 46.97 2.01
775 776 1.008309 GGCCTGCAAAACGCGTTTA 60.008 52.632 34.89 20.06 46.97 2.01
776 777 2.279186 GGCCTGCAAAACGCGTTT 60.279 55.556 30.36 30.36 46.97 3.60
777 778 4.622456 CGGCCTGCAAAACGCGTT 62.622 61.111 20.79 20.79 46.97 4.84
780 781 4.999939 CACCGGCCTGCAAAACGC 63.000 66.667 0.00 0.00 42.89 4.84
781 782 4.341502 CCACCGGCCTGCAAAACG 62.342 66.667 0.00 0.00 0.00 3.60
782 783 1.815817 ATTCCACCGGCCTGCAAAAC 61.816 55.000 0.00 0.00 0.00 2.43
783 784 1.532794 ATTCCACCGGCCTGCAAAA 60.533 52.632 0.00 0.00 0.00 2.44
784 785 2.117206 ATTCCACCGGCCTGCAAA 59.883 55.556 0.00 0.00 0.00 3.68
785 786 2.676121 CATTCCACCGGCCTGCAA 60.676 61.111 0.00 0.00 0.00 4.08
788 789 3.136123 CTGCATTCCACCGGCCTG 61.136 66.667 0.00 0.00 0.00 4.85
789 790 4.431131 CCTGCATTCCACCGGCCT 62.431 66.667 0.00 0.00 0.00 5.19
791 792 4.740822 ACCCTGCATTCCACCGGC 62.741 66.667 0.00 0.00 0.00 6.13
792 793 2.438434 GACCCTGCATTCCACCGG 60.438 66.667 0.00 0.00 0.00 5.28
793 794 1.746615 CAGACCCTGCATTCCACCG 60.747 63.158 0.00 0.00 0.00 4.94
794 795 4.326255 CAGACCCTGCATTCCACC 57.674 61.111 0.00 0.00 0.00 4.61
803 804 0.901124 AGCAACTCTAGCAGACCCTG 59.099 55.000 0.00 0.00 34.12 4.45
804 805 1.190643 GAGCAACTCTAGCAGACCCT 58.809 55.000 0.00 0.00 0.00 4.34
805 806 1.190643 AGAGCAACTCTAGCAGACCC 58.809 55.000 0.00 0.00 39.28 4.46
806 807 4.367450 CATAAGAGCAACTCTAGCAGACC 58.633 47.826 0.00 0.00 40.28 3.85
807 808 4.367450 CCATAAGAGCAACTCTAGCAGAC 58.633 47.826 0.00 0.00 40.28 3.51
808 809 3.386078 CCCATAAGAGCAACTCTAGCAGA 59.614 47.826 0.00 0.00 40.28 4.26
809 810 3.726607 CCCATAAGAGCAACTCTAGCAG 58.273 50.000 0.00 0.00 40.28 4.24
810 811 2.158900 GCCCATAAGAGCAACTCTAGCA 60.159 50.000 0.00 0.00 40.28 3.49
811 812 2.488952 GCCCATAAGAGCAACTCTAGC 58.511 52.381 0.00 0.00 40.28 3.42
812 813 2.546795 CGGCCCATAAGAGCAACTCTAG 60.547 54.545 0.00 0.00 40.28 2.43
813 814 1.412710 CGGCCCATAAGAGCAACTCTA 59.587 52.381 0.00 0.00 40.28 2.43
814 815 0.179000 CGGCCCATAAGAGCAACTCT 59.821 55.000 0.00 0.00 43.37 3.24
815 816 0.815615 CCGGCCCATAAGAGCAACTC 60.816 60.000 0.00 0.00 0.00 3.01
816 817 1.224592 CCGGCCCATAAGAGCAACT 59.775 57.895 0.00 0.00 0.00 3.16
817 818 2.481471 GCCGGCCCATAAGAGCAAC 61.481 63.158 18.11 0.00 0.00 4.17
818 819 2.124320 GCCGGCCCATAAGAGCAA 60.124 61.111 18.11 0.00 0.00 3.91
819 820 4.189580 GGCCGGCCCATAAGAGCA 62.190 66.667 36.64 0.00 0.00 4.26
829 830 4.570874 GAGGATTCAGGGCCGGCC 62.571 72.222 38.57 38.57 0.00 6.13
830 831 3.797353 TGAGGATTCAGGGCCGGC 61.797 66.667 21.18 21.18 0.00 6.13
831 832 2.190578 GTGAGGATTCAGGGCCGG 59.809 66.667 0.00 0.00 32.98 6.13
832 833 2.202932 CGTGAGGATTCAGGGCCG 60.203 66.667 0.00 0.00 35.96 6.13
833 834 2.514824 GCGTGAGGATTCAGGGCC 60.515 66.667 0.00 0.00 39.12 5.80
835 836 2.202932 CGGCGTGAGGATTCAGGG 60.203 66.667 0.00 0.00 39.12 4.45
836 837 0.807667 CTTCGGCGTGAGGATTCAGG 60.808 60.000 6.85 0.00 41.10 3.86
837 838 0.173481 TCTTCGGCGTGAGGATTCAG 59.827 55.000 6.85 0.00 32.98 3.02
838 839 0.108804 GTCTTCGGCGTGAGGATTCA 60.109 55.000 6.85 0.00 34.90 2.57
839 840 0.806492 GGTCTTCGGCGTGAGGATTC 60.806 60.000 6.85 0.00 34.90 2.52
1713 1731 1.299976 CCTCCGAAAACAGAGGGGG 59.700 63.158 0.00 0.00 45.08 5.40
1759 1778 2.586258 TAGACTGCCAAGCGAAGATC 57.414 50.000 0.00 0.00 0.00 2.75
1810 1829 8.405531 TCCCGGCAGTTAATATAATATACGTAC 58.594 37.037 0.00 0.00 0.00 3.67
1811 1830 8.405531 GTCCCGGCAGTTAATATAATATACGTA 58.594 37.037 0.00 0.00 0.00 3.57
1812 1831 7.093814 TGTCCCGGCAGTTAATATAATATACGT 60.094 37.037 0.00 0.00 0.00 3.57
1813 1832 7.259882 TGTCCCGGCAGTTAATATAATATACG 58.740 38.462 0.00 0.00 0.00 3.06
1814 1833 9.439500 TTTGTCCCGGCAGTTAATATAATATAC 57.561 33.333 0.00 0.00 0.00 1.47
1829 1848 3.541632 GATCTTATCTTTTGTCCCGGCA 58.458 45.455 0.00 0.00 0.00 5.69
1831 1850 2.544267 GCGATCTTATCTTTTGTCCCGG 59.456 50.000 0.00 0.00 0.00 5.73
1869 1888 3.290710 ACTTGCCACAAAGAGTCAATGT 58.709 40.909 0.00 0.00 0.00 2.71
1927 1946 2.355197 TGACAATAATGTGTGCCTCCG 58.645 47.619 0.00 0.00 40.74 4.63
2032 2051 4.843728 ACCACTGAGAAAGAAACACTTGA 58.156 39.130 0.00 0.00 38.98 3.02
2052 2071 4.003648 CTGTCCATTGTGTTCTTCCTACC 58.996 47.826 0.00 0.00 0.00 3.18
2053 2072 4.642429 ACTGTCCATTGTGTTCTTCCTAC 58.358 43.478 0.00 0.00 0.00 3.18
2054 2073 4.593206 AGACTGTCCATTGTGTTCTTCCTA 59.407 41.667 3.76 0.00 0.00 2.94
2055 2074 3.392616 AGACTGTCCATTGTGTTCTTCCT 59.607 43.478 3.76 0.00 0.00 3.36
2056 2075 3.499918 CAGACTGTCCATTGTGTTCTTCC 59.500 47.826 3.76 0.00 0.00 3.46
2070 2089 7.062839 GTGAGTTTCTGAATCATACAGACTGTC 59.937 40.741 12.39 0.00 42.84 3.51
2134 2153 2.634815 AATCATGCAGCAGTAGGAGG 57.365 50.000 0.00 0.00 0.00 4.30
2167 2186 4.081862 CCATCACACTTTCAATCAAGGCAT 60.082 41.667 0.00 0.00 0.00 4.40
2235 2254 3.676291 TTTGCTTCCCACCTATTTTGC 57.324 42.857 0.00 0.00 0.00 3.68
2248 2267 4.936891 ACTGAGGAACAAACATTTGCTTC 58.063 39.130 4.25 7.44 41.79 3.86
2466 2486 3.305361 CACACACGATGAGCTGAATAGTG 59.695 47.826 14.15 14.15 36.89 2.74
2482 2502 2.035632 AGCCCTAGAGATAGCACACAC 58.964 52.381 0.00 0.00 0.00 3.82
2639 2666 8.989980 GGTCAGTCATTATACAGCTATTTAACC 58.010 37.037 0.00 0.00 0.00 2.85
3100 3134 7.392673 TCAGCTCTTCTTTCTTTCTAAATGCAT 59.607 33.333 0.00 0.00 0.00 3.96
3143 3177 7.033791 ACCACTAGTTGATTACACTATGAACG 58.966 38.462 0.08 0.00 28.63 3.95
3239 3273 6.152831 GCCACCACTAATATCCTTCAACTTTT 59.847 38.462 0.00 0.00 0.00 2.27
3243 3277 4.781934 AGCCACCACTAATATCCTTCAAC 58.218 43.478 0.00 0.00 0.00 3.18
3244 3278 4.721776 AGAGCCACCACTAATATCCTTCAA 59.278 41.667 0.00 0.00 0.00 2.69
3246 3280 4.262678 GGAGAGCCACCACTAATATCCTTC 60.263 50.000 0.00 0.00 0.00 3.46
3247 3281 3.648545 GGAGAGCCACCACTAATATCCTT 59.351 47.826 0.00 0.00 0.00 3.36
3306 3340 8.641541 AGTTTTGATACATCAGGAAACAATGTT 58.358 29.630 16.25 0.00 38.79 2.71
3367 3401 4.696479 ATATGCTACCACTCCTTCCAAG 57.304 45.455 0.00 0.00 0.00 3.61
3445 3479 7.013750 TGACAACAAACAGAATTTACCTGCATA 59.986 33.333 0.00 0.00 35.14 3.14
3497 3531 5.509840 GCACTGATATGGTACTAAGGTCAGG 60.510 48.000 17.12 10.57 36.74 3.86
3531 3565 6.024049 GCTAAGTCAACATGCATTTACTCAC 58.976 40.000 0.00 0.00 0.00 3.51
3550 3584 4.128925 TCATCTGGTACTTGCAGCTAAG 57.871 45.455 0.00 0.00 0.00 2.18
3626 3660 8.316946 TGAATATCATAGCCAGTCATCTTTAGG 58.683 37.037 0.00 0.00 0.00 2.69
3755 3789 7.432148 TGATACATAGAAGGGAAAGTAAGCA 57.568 36.000 0.00 0.00 0.00 3.91
3999 4033 3.557595 CGTTAGGCATCTGATCCTCAAAC 59.442 47.826 10.60 9.93 34.02 2.93
4061 4095 0.595095 GCAAAGAGCCCAGTGACAAG 59.405 55.000 0.00 0.00 37.23 3.16
4415 4449 4.696479 AATCCGCTCTCCATAGAACATT 57.304 40.909 0.00 0.00 0.00 2.71
4522 4556 2.052891 CAACATCGTGCACCAACAATG 58.947 47.619 12.15 9.79 0.00 2.82
4776 4823 6.839124 TGACTGCCATATTGTCTTTTGAAT 57.161 33.333 0.00 0.00 0.00 2.57
4783 4830 6.467677 GTGGTATATGACTGCCATATTGTCT 58.532 40.000 1.76 0.00 43.97 3.41
4910 4957 0.758734 CAGGACTCACCAGAACACCA 59.241 55.000 0.00 0.00 42.04 4.17
4957 5004 2.591753 GTATCTGCAGGCCAGGCA 59.408 61.111 19.46 19.46 42.05 4.75
5044 5091 0.184211 ATGCATGCAGGTATGAGGCA 59.816 50.000 26.69 0.00 42.43 4.75
5078 5125 4.486090 GATGAATCATGGATTGCATGCTC 58.514 43.478 20.33 8.93 31.89 4.26
5122 5169 0.603065 AGCTCTGACGTACATGTGCA 59.397 50.000 14.55 3.90 0.00 4.57
5123 5170 2.455032 CTAGCTCTGACGTACATGTGC 58.545 52.381 9.11 6.17 0.00 4.57
5410 5457 2.203877 TACTGGTTCCCCTGCCGT 60.204 61.111 0.00 0.00 33.14 5.68
5447 5494 1.118356 CATCCTCCCCTTCCTCCTCG 61.118 65.000 0.00 0.00 0.00 4.63
5560 5607 4.518970 AGGCAAACGCATTACCATATAAGG 59.481 41.667 0.00 0.00 0.00 2.69
5622 5669 6.976349 CCGTAAAGAATAACCCCTAAAAATGC 59.024 38.462 0.00 0.00 0.00 3.56
5647 5694 2.087646 GTCCATGCTTTTCCTCTCCAC 58.912 52.381 0.00 0.00 0.00 4.02
5671 5718 3.743396 GCATTGGCTCTCCTCGTAATAAG 59.257 47.826 0.00 0.00 36.96 1.73
5678 5725 0.531532 ATTCGCATTGGCTCTCCTCG 60.532 55.000 0.00 0.00 38.10 4.63
5804 5851 9.455847 CTTCTGTTCTTGTTTCTCATAAAAAGG 57.544 33.333 0.00 0.00 0.00 3.11
6119 6167 6.058183 CCATCTAAGATTTCGATTCCCAGTT 58.942 40.000 0.00 0.00 0.00 3.16
6261 6309 3.876341 TCGGTTACAAACAGAAACAGGT 58.124 40.909 0.00 0.00 32.68 4.00
6361 6409 9.525826 AGTTCAGGATTTGTCAAAAGATCTAAT 57.474 29.630 1.31 0.00 0.00 1.73
6409 6457 7.039993 GGAGTAAGAAAAAGGAGGCAAATAACA 60.040 37.037 0.00 0.00 0.00 2.41
6453 6501 4.900635 AAGGAAGTGTTAACAACTGCAG 57.099 40.909 13.48 13.48 0.00 4.41
6578 6626 1.550065 ATTTCATCTGCGACGAGACG 58.450 50.000 0.00 0.00 0.00 4.18
6751 6799 2.660362 GCAGCTTCTTCTTCGTTGTTCG 60.660 50.000 0.00 0.00 41.41 3.95
6803 6851 3.228243 ATTGGCCCCAGCTTCTGCA 62.228 57.895 0.00 0.00 42.74 4.41
6857 6905 0.325671 AATCCTCCTCCTCCGCTTCA 60.326 55.000 0.00 0.00 0.00 3.02
6862 6910 1.000283 CGATCAAATCCTCCTCCTCCG 60.000 57.143 0.00 0.00 0.00 4.63
6863 6911 2.298729 CTCGATCAAATCCTCCTCCTCC 59.701 54.545 0.00 0.00 0.00 4.30
6864 6912 2.298729 CCTCGATCAAATCCTCCTCCTC 59.701 54.545 0.00 0.00 0.00 3.71
6977 7025 1.267882 GCGACGTCGATGTCATAGTCA 60.268 52.381 39.74 0.00 43.02 3.41
7046 7097 1.744368 GCTAGAAGCAGCAGCAGCA 60.744 57.895 12.92 0.00 45.49 4.41
7059 7119 3.359950 TCTCTGCACATCAAGAGCTAGA 58.640 45.455 0.00 0.00 34.66 2.43
7119 7182 4.101448 CCAACTCCCGGGCTGAGG 62.101 72.222 18.49 11.75 34.06 3.86
7135 7198 3.683365 TCGAACCCTACCAAGTAAACC 57.317 47.619 0.00 0.00 0.00 3.27
7168 7239 7.998383 TCACAAAAGGTAGCACCATATTCATAT 59.002 33.333 7.86 0.00 41.95 1.78
7169 7240 7.342581 TCACAAAAGGTAGCACCATATTCATA 58.657 34.615 7.86 0.00 41.95 2.15
7170 7241 6.186957 TCACAAAAGGTAGCACCATATTCAT 58.813 36.000 7.86 0.00 41.95 2.57
7171 7242 5.565509 TCACAAAAGGTAGCACCATATTCA 58.434 37.500 7.86 0.00 41.95 2.57
7172 7243 5.449177 GCTCACAAAAGGTAGCACCATATTC 60.449 44.000 7.86 0.00 41.95 1.75
7209 7283 1.598601 GCACGACGGTAAAAGGTTTCA 59.401 47.619 0.00 0.00 0.00 2.69
7210 7284 1.069703 GGCACGACGGTAAAAGGTTTC 60.070 52.381 0.00 0.00 0.00 2.78
7254 7328 9.235537 GAAAAGGAACTCGTAATATAGTGAGAC 57.764 37.037 5.34 0.00 38.49 3.36
7304 7378 8.842358 ATAAAACCATCTACGAAGACTTTTCA 57.158 30.769 0.00 0.00 33.57 2.69
7393 7469 2.132762 GTTACAACAGAGGACGTGGTG 58.867 52.381 0.00 0.00 38.67 4.17
7542 7649 9.851267 AGAGATATATTTAAGAATGGAGGGAGT 57.149 33.333 0.00 0.00 0.00 3.85
7564 7671 9.057911 TCCCTTATTGGAATCTCTAAAAAGAGA 57.942 33.333 7.51 7.51 42.76 3.10
7565 7672 9.114952 GTCCCTTATTGGAATCTCTAAAAAGAG 57.885 37.037 0.00 0.00 35.80 2.85
7566 7673 8.836735 AGTCCCTTATTGGAATCTCTAAAAAGA 58.163 33.333 0.00 0.00 35.80 2.52
7578 7685 9.574577 ACATCCATATATAGTCCCTTATTGGAA 57.425 33.333 1.19 0.00 35.80 3.53
7623 7730 6.636850 ACGAAGCAAAATGAGTGAAAATACAC 59.363 34.615 0.00 0.00 40.60 2.90
7624 7731 6.734137 ACGAAGCAAAATGAGTGAAAATACA 58.266 32.000 0.00 0.00 0.00 2.29
7625 7732 8.788813 CATACGAAGCAAAATGAGTGAAAATAC 58.211 33.333 0.00 0.00 0.00 1.89
7626 7733 8.511321 ACATACGAAGCAAAATGAGTGAAAATA 58.489 29.630 0.00 0.00 0.00 1.40
7627 7734 7.370383 ACATACGAAGCAAAATGAGTGAAAAT 58.630 30.769 0.00 0.00 0.00 1.82
7628 7735 6.734137 ACATACGAAGCAAAATGAGTGAAAA 58.266 32.000 0.00 0.00 0.00 2.29
7629 7736 6.312399 ACATACGAAGCAAAATGAGTGAAA 57.688 33.333 0.00 0.00 0.00 2.69
7630 7737 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
7631 7738 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
7632 7739 6.408858 ACTACATACGAAGCAAAATGAGTG 57.591 37.500 0.00 0.00 0.00 3.51
7633 7740 6.874134 AGAACTACATACGAAGCAAAATGAGT 59.126 34.615 0.00 0.00 0.00 3.41
7634 7741 7.295952 AGAACTACATACGAAGCAAAATGAG 57.704 36.000 0.00 0.00 0.00 2.90
7635 7742 7.667043 AAGAACTACATACGAAGCAAAATGA 57.333 32.000 0.00 0.00 0.00 2.57
7636 7743 9.988350 ATAAAGAACTACATACGAAGCAAAATG 57.012 29.630 0.00 0.00 0.00 2.32
7678 7785 9.392259 CCCTTCGTTCCTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 0.00 2.27
7679 7786 8.765517 TCCCTTCGTTCCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
7680 7787 8.315220 TCCCTTCGTTCCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
7681 7788 7.564292 ACTCCCTTCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
7682 7789 7.724287 ACTCCCTTCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
7683 7790 7.672122 ACTCCCTTCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
7687 7794 9.543231 TCATATACTCCCTTCGTTCCTAAATAT 57.457 33.333 0.00 0.00 0.00 1.28
7688 7795 8.945195 TCATATACTCCCTTCGTTCCTAAATA 57.055 34.615 0.00 0.00 0.00 1.40
7689 7796 7.850935 TCATATACTCCCTTCGTTCCTAAAT 57.149 36.000 0.00 0.00 0.00 1.40
7690 7797 7.850935 ATCATATACTCCCTTCGTTCCTAAA 57.149 36.000 0.00 0.00 0.00 1.85
7691 7798 8.168725 ACTATCATATACTCCCTTCGTTCCTAA 58.831 37.037 0.00 0.00 0.00 2.69
7692 7799 7.610692 CACTATCATATACTCCCTTCGTTCCTA 59.389 40.741 0.00 0.00 0.00 2.94
7693 7800 6.434652 CACTATCATATACTCCCTTCGTTCCT 59.565 42.308 0.00 0.00 0.00 3.36
7694 7801 6.433404 TCACTATCATATACTCCCTTCGTTCC 59.567 42.308 0.00 0.00 0.00 3.62
7695 7802 7.450124 TCACTATCATATACTCCCTTCGTTC 57.550 40.000 0.00 0.00 0.00 3.95
7696 7803 7.834881 TTCACTATCATATACTCCCTTCGTT 57.165 36.000 0.00 0.00 0.00 3.85
7697 7804 7.834881 TTTCACTATCATATACTCCCTTCGT 57.165 36.000 0.00 0.00 0.00 3.85
7698 7805 9.712305 AATTTTCACTATCATATACTCCCTTCG 57.288 33.333 0.00 0.00 0.00 3.79
7712 7819 9.884465 GCTCCATGTATGTAAATTTTCACTATC 57.116 33.333 0.00 0.00 0.00 2.08
7713 7820 9.407380 TGCTCCATGTATGTAAATTTTCACTAT 57.593 29.630 0.00 0.00 0.00 2.12
7714 7821 8.673711 GTGCTCCATGTATGTAAATTTTCACTA 58.326 33.333 0.00 0.00 0.00 2.74
7715 7822 7.176515 TGTGCTCCATGTATGTAAATTTTCACT 59.823 33.333 0.00 0.00 0.00 3.41
7716 7823 7.312154 TGTGCTCCATGTATGTAAATTTTCAC 58.688 34.615 0.00 0.00 0.00 3.18
7717 7824 7.459795 TGTGCTCCATGTATGTAAATTTTCA 57.540 32.000 0.00 0.00 0.00 2.69
7718 7825 7.649306 GGATGTGCTCCATGTATGTAAATTTTC 59.351 37.037 0.00 0.00 44.26 2.29
7719 7826 7.491682 GGATGTGCTCCATGTATGTAAATTTT 58.508 34.615 0.00 0.00 44.26 1.82
7720 7827 7.042797 GGATGTGCTCCATGTATGTAAATTT 57.957 36.000 0.00 0.00 44.26 1.82
7721 7828 6.639632 GGATGTGCTCCATGTATGTAAATT 57.360 37.500 0.00 0.00 44.26 1.82
7788 7895 1.229951 TCCAACCTCCATGGAGCCT 60.230 57.895 32.97 20.04 41.98 4.58
7897 8288 9.748708 TCTACTGATTTCAAATTCAAAAAGTGG 57.251 29.630 9.56 7.91 0.00 4.00
7935 8326 1.614903 TGCAATGCTCCCTTGAACAAG 59.385 47.619 6.82 7.49 38.14 3.16
7992 8383 5.873179 AATTGTATTGTGTACCAACCTCG 57.127 39.130 0.00 0.00 35.44 4.63


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

AutoCloner maintained by Alex Coulton.