Multiple sequence alignment - TraesCS3A01G114500

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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 TraesCS3A01G114500 chr3A 100.000 3785 0 0 1 3785 82115060 82111276 0.000000e+00 6990.0
1 TraesCS3A01G114500 chr3A 92.792 1637 102 6 1665 3286 82240127 82238492 0.000000e+00 2355.0
2 TraesCS3A01G114500 chr3A 96.997 899 24 2 1663 2558 82347311 82346413 0.000000e+00 1507.0
3 TraesCS3A01G114500 chr3A 97.089 687 17 2 975 1659 82348611 82347926 0.000000e+00 1155.0
4 TraesCS3A01G114500 chr3A 94.729 664 31 2 2624 3286 82346270 82345610 0.000000e+00 1029.0
5 TraesCS3A01G114500 chr3A 92.672 655 32 4 1018 1659 82241244 82240593 0.000000e+00 929.0
6 TraesCS3A01G114500 chr3A 94.203 552 31 1 1 552 348643875 348644425 0.000000e+00 841.0
7 TraesCS3A01G114500 chr3A 94.033 553 30 3 1 552 66334252 66334802 0.000000e+00 835.0
8 TraesCS3A01G114500 chr3A 94.527 201 10 1 552 752 405108962 405108763 3.670000e-80 309.0
9 TraesCS3A01G114500 chr3A 94.231 52 3 0 1020 1071 82348876 82348825 3.130000e-11 80.5
10 TraesCS3A01G114500 chr3A 100.000 39 0 0 2556 2594 82346309 82346271 5.240000e-09 73.1
11 TraesCS3A01G114500 chr3D 91.041 1239 79 10 1665 2885 70706780 70705556 0.000000e+00 1644.0
12 TraesCS3A01G114500 chr3D 89.577 921 74 8 2868 3783 70705483 70704580 0.000000e+00 1149.0
13 TraesCS3A01G114500 chr3D 90.754 703 42 10 975 1659 70708739 70708042 0.000000e+00 917.0
14 TraesCS3A01G114500 chr3D 94.527 201 10 1 552 752 495656315 495656116 3.670000e-80 309.0
15 TraesCS3A01G114500 chr3D 88.333 180 20 1 750 928 608544693 608544872 8.230000e-52 215.0
16 TraesCS3A01G114500 chr4A 95.683 556 22 2 1 555 475957311 475956757 0.000000e+00 893.0
17 TraesCS3A01G114500 chr4A 94.604 556 28 2 1 555 438819421 438818867 0.000000e+00 859.0
18 TraesCS3A01G114500 chr4A 94.394 553 29 2 1 552 473230291 473230842 0.000000e+00 848.0
19 TraesCS3A01G114500 chr4A 88.690 168 18 1 758 924 313700369 313700202 1.780000e-48 204.0
20 TraesCS3A01G114500 chr7A 94.033 553 30 3 1 551 435398837 435399388 0.000000e+00 835.0
21 TraesCS3A01G114500 chr7A 94.898 196 8 1 555 750 233579315 233579122 4.750000e-79 305.0
22 TraesCS3A01G114500 chr1A 94.033 553 30 3 1 551 322673968 322674519 0.000000e+00 835.0
23 TraesCS3A01G114500 chr1A 94.033 553 29 3 1 552 388933897 388934446 0.000000e+00 835.0
24 TraesCS3A01G114500 chr1A 94.030 201 10 1 552 752 322674552 322674750 1.710000e-78 303.0
25 TraesCS3A01G114500 chr1A 87.500 176 21 1 750 924 377935282 377935107 6.410000e-48 202.0
26 TraesCS3A01G114500 chr6A 93.671 553 33 2 1 552 312569665 312570216 0.000000e+00 826.0
27 TraesCS3A01G114500 chr6A 87.293 181 22 1 750 929 602448683 602448863 4.960000e-49 206.0
28 TraesCS3A01G114500 chr5A 94.527 201 9 1 552 752 452777077 452777275 3.670000e-80 309.0
29 TraesCS3A01G114500 chr5A 91.705 217 14 4 546 760 537140466 537140680 7.950000e-77 298.0
30 TraesCS3A01G114500 chr4D 94.472 199 10 1 554 752 470809300 470809497 4.750000e-79 305.0
31 TraesCS3A01G114500 chr2A 93.301 209 11 2 552 760 86456227 86456432 4.750000e-79 305.0
32 TraesCS3A01G114500 chr2A 94.030 201 11 1 552 752 239914549 239914748 1.710000e-78 303.0
33 TraesCS3A01G114500 chr7D 89.385 179 18 1 750 927 80325262 80325084 1.370000e-54 224.0
34 TraesCS3A01G114500 chrUn 87.151 179 21 2 750 927 75232052 75231875 6.410000e-48 202.0
35 TraesCS3A01G114500 chr2D 88.095 168 19 1 758 924 523231858 523232025 8.290000e-47 198.0
36 TraesCS3A01G114500 chr2D 85.876 177 24 1 750 925 490551211 490551387 1.800000e-43 187.0
37 TraesCS3A01G114500 chr1D 88.095 168 19 1 758 924 128388426 128388593 8.290000e-47 198.0


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 TraesCS3A01G114500 chr3A 82111276 82115060 3784 True 6990.000000 6990 100.000000 1 3785 1 chr3A.!!$R1 3784
1 TraesCS3A01G114500 chr3A 82238492 82241244 2752 True 1642.000000 2355 92.732000 1018 3286 2 chr3A.!!$R3 2268
2 TraesCS3A01G114500 chr3A 348643875 348644425 550 False 841.000000 841 94.203000 1 552 1 chr3A.!!$F2 551
3 TraesCS3A01G114500 chr3A 66334252 66334802 550 False 835.000000 835 94.033000 1 552 1 chr3A.!!$F1 551
4 TraesCS3A01G114500 chr3A 82345610 82348876 3266 True 768.920000 1507 96.609200 975 3286 5 chr3A.!!$R4 2311
5 TraesCS3A01G114500 chr3D 70704580 70708739 4159 True 1236.666667 1644 90.457333 975 3783 3 chr3D.!!$R2 2808
6 TraesCS3A01G114500 chr4A 475956757 475957311 554 True 893.000000 893 95.683000 1 555 1 chr4A.!!$R3 554
7 TraesCS3A01G114500 chr4A 438818867 438819421 554 True 859.000000 859 94.604000 1 555 1 chr4A.!!$R2 554
8 TraesCS3A01G114500 chr4A 473230291 473230842 551 False 848.000000 848 94.394000 1 552 1 chr4A.!!$F1 551
9 TraesCS3A01G114500 chr7A 435398837 435399388 551 False 835.000000 835 94.033000 1 551 1 chr7A.!!$F1 550
10 TraesCS3A01G114500 chr1A 388933897 388934446 549 False 835.000000 835 94.033000 1 552 1 chr1A.!!$F1 551
11 TraesCS3A01G114500 chr1A 322673968 322674750 782 False 569.000000 835 94.031500 1 752 2 chr1A.!!$F2 751
12 TraesCS3A01G114500 chr6A 312569665 312570216 551 False 826.000000 826 93.671000 1 552 1 chr6A.!!$F1 551

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
166 170 0.033504 TCTTTCTGTCTGCGTGACCC 59.966 55.0 7.12 0.0 44.75 4.46 F
863 900 0.116342 TGGAGCAGAGAAGTGGGGTA 59.884 55.0 0.00 0.0 0.00 3.69 F
956 993 0.606604 TCACCAAGACTAGGCGTTCC 59.393 55.0 0.00 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1634 1715 0.309612 GGATCTTCTCTCTCGCGTCC 59.690 60.000 5.77 0.0 0.00 4.79 R
2250 3715 1.134580 ACATGAGTGCCTTCATCCTCG 60.135 52.381 0.00 0.0 35.67 4.63 R
2898 4582 1.136502 CGTCTTCTGCAAGTTCTTCGC 60.137 52.381 0.00 0.0 33.76 4.70 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
166 170 0.033504 TCTTTCTGTCTGCGTGACCC 59.966 55.000 7.12 0.00 44.75 4.46
241 246 2.094494 TCTGAGCGTCCAAGAGTCATTC 60.094 50.000 0.00 0.00 0.00 2.67
321 326 0.535335 GTGATTGGGCGAGGACTGTA 59.465 55.000 0.00 0.00 0.00 2.74
460 465 7.044798 GTCTTCATCAAGCTACTGGTTCTATT 58.955 38.462 0.00 0.00 0.00 1.73
464 469 8.306313 TCATCAAGCTACTGGTTCTATTCTTA 57.694 34.615 0.00 0.00 0.00 2.10
575 612 5.478679 CCATACTACCTAGCTGCTGATAGTT 59.521 44.000 20.23 3.37 30.76 2.24
578 615 5.908341 ACTACCTAGCTGCTGATAGTTTTC 58.092 41.667 13.43 0.00 30.76 2.29
586 623 4.613031 GCTGCTGATAGTTTTCGTGTTTTC 59.387 41.667 0.00 0.00 0.00 2.29
682 719 1.704641 GTTTGTCTTCAAAGCCCCCT 58.295 50.000 0.00 0.00 43.04 4.79
689 726 3.639561 GTCTTCAAAGCCCCCTTGTTTTA 59.360 43.478 0.00 0.00 0.00 1.52
701 738 6.014925 GCCCCCTTGTTTTAAAGACTTTCATA 60.015 38.462 3.07 0.00 0.00 2.15
718 755 9.326339 GACTTTCATAAAAATCGTTTACTCACC 57.674 33.333 0.00 0.00 0.00 4.02
719 756 9.063615 ACTTTCATAAAAATCGTTTACTCACCT 57.936 29.630 0.00 0.00 0.00 4.00
754 791 9.035607 AGTCGATAACTAGCACTTTCAATTATG 57.964 33.333 0.00 0.00 36.07 1.90
755 792 8.818057 GTCGATAACTAGCACTTTCAATTATGT 58.182 33.333 0.00 0.00 0.00 2.29
756 793 9.031360 TCGATAACTAGCACTTTCAATTATGTC 57.969 33.333 0.00 0.00 0.00 3.06
757 794 9.035607 CGATAACTAGCACTTTCAATTATGTCT 57.964 33.333 0.00 0.00 0.00 3.41
759 796 9.890629 ATAACTAGCACTTTCAATTATGTCTCA 57.109 29.630 0.00 0.00 0.00 3.27
760 797 7.602517 ACTAGCACTTTCAATTATGTCTCAC 57.397 36.000 0.00 0.00 0.00 3.51
761 798 7.390027 ACTAGCACTTTCAATTATGTCTCACT 58.610 34.615 0.00 0.00 0.00 3.41
762 799 6.734104 AGCACTTTCAATTATGTCTCACTC 57.266 37.500 0.00 0.00 0.00 3.51
763 800 6.233434 AGCACTTTCAATTATGTCTCACTCA 58.767 36.000 0.00 0.00 0.00 3.41
764 801 6.712095 AGCACTTTCAATTATGTCTCACTCAA 59.288 34.615 0.00 0.00 0.00 3.02
765 802 7.229306 AGCACTTTCAATTATGTCTCACTCAAA 59.771 33.333 0.00 0.00 0.00 2.69
766 803 7.862372 GCACTTTCAATTATGTCTCACTCAAAA 59.138 33.333 0.00 0.00 0.00 2.44
767 804 9.903682 CACTTTCAATTATGTCTCACTCAAAAT 57.096 29.630 0.00 0.00 0.00 1.82
778 815 8.648557 TGTCTCACTCAAAATATATTTCTCGG 57.351 34.615 11.08 5.35 0.00 4.63
779 816 7.710907 TGTCTCACTCAAAATATATTTCTCGGG 59.289 37.037 11.08 5.98 0.00 5.14
780 817 6.706270 TCTCACTCAAAATATATTTCTCGGGC 59.294 38.462 11.08 0.00 0.00 6.13
781 818 6.591935 TCACTCAAAATATATTTCTCGGGCT 58.408 36.000 11.08 0.00 0.00 5.19
782 819 6.483307 TCACTCAAAATATATTTCTCGGGCTG 59.517 38.462 11.08 4.62 0.00 4.85
783 820 6.260936 CACTCAAAATATATTTCTCGGGCTGT 59.739 38.462 11.08 1.01 0.00 4.40
784 821 6.828785 ACTCAAAATATATTTCTCGGGCTGTT 59.171 34.615 11.08 0.00 0.00 3.16
785 822 7.339466 ACTCAAAATATATTTCTCGGGCTGTTT 59.661 33.333 11.08 0.00 0.00 2.83
786 823 8.062065 TCAAAATATATTTCTCGGGCTGTTTT 57.938 30.769 11.08 0.00 0.00 2.43
787 824 7.973388 TCAAAATATATTTCTCGGGCTGTTTTG 59.027 33.333 11.08 2.76 35.37 2.44
788 825 7.639113 AAATATATTTCTCGGGCTGTTTTGA 57.361 32.000 4.81 0.00 0.00 2.69
789 826 7.823745 AATATATTTCTCGGGCTGTTTTGAT 57.176 32.000 0.00 0.00 0.00 2.57
790 827 3.855689 ATTTCTCGGGCTGTTTTGATG 57.144 42.857 0.00 0.00 0.00 3.07
791 828 2.559698 TTCTCGGGCTGTTTTGATGA 57.440 45.000 0.00 0.00 0.00 2.92
792 829 2.099141 TCTCGGGCTGTTTTGATGAG 57.901 50.000 0.00 0.00 0.00 2.90
793 830 1.089920 CTCGGGCTGTTTTGATGAGG 58.910 55.000 0.00 0.00 0.00 3.86
794 831 0.400213 TCGGGCTGTTTTGATGAGGT 59.600 50.000 0.00 0.00 0.00 3.85
795 832 0.523072 CGGGCTGTTTTGATGAGGTG 59.477 55.000 0.00 0.00 0.00 4.00
796 833 1.881925 CGGGCTGTTTTGATGAGGTGA 60.882 52.381 0.00 0.00 0.00 4.02
797 834 1.815003 GGGCTGTTTTGATGAGGTGAG 59.185 52.381 0.00 0.00 0.00 3.51
798 835 1.815003 GGCTGTTTTGATGAGGTGAGG 59.185 52.381 0.00 0.00 0.00 3.86
799 836 2.553028 GGCTGTTTTGATGAGGTGAGGA 60.553 50.000 0.00 0.00 0.00 3.71
800 837 3.149196 GCTGTTTTGATGAGGTGAGGAA 58.851 45.455 0.00 0.00 0.00 3.36
801 838 3.190118 GCTGTTTTGATGAGGTGAGGAAG 59.810 47.826 0.00 0.00 0.00 3.46
802 839 3.754965 TGTTTTGATGAGGTGAGGAAGG 58.245 45.455 0.00 0.00 0.00 3.46
803 840 3.394274 TGTTTTGATGAGGTGAGGAAGGA 59.606 43.478 0.00 0.00 0.00 3.36
804 841 4.141274 TGTTTTGATGAGGTGAGGAAGGAA 60.141 41.667 0.00 0.00 0.00 3.36
805 842 4.934797 TTTGATGAGGTGAGGAAGGAAT 57.065 40.909 0.00 0.00 0.00 3.01
806 843 3.920231 TGATGAGGTGAGGAAGGAATG 57.080 47.619 0.00 0.00 0.00 2.67
807 844 3.184628 TGATGAGGTGAGGAAGGAATGT 58.815 45.455 0.00 0.00 0.00 2.71
808 845 3.054875 TGATGAGGTGAGGAAGGAATGTG 60.055 47.826 0.00 0.00 0.00 3.21
809 846 2.619931 TGAGGTGAGGAAGGAATGTGA 58.380 47.619 0.00 0.00 0.00 3.58
810 847 3.184628 TGAGGTGAGGAAGGAATGTGAT 58.815 45.455 0.00 0.00 0.00 3.06
811 848 3.588842 TGAGGTGAGGAAGGAATGTGATT 59.411 43.478 0.00 0.00 0.00 2.57
812 849 4.782691 TGAGGTGAGGAAGGAATGTGATTA 59.217 41.667 0.00 0.00 0.00 1.75
813 850 5.104776 TGAGGTGAGGAAGGAATGTGATTAG 60.105 44.000 0.00 0.00 0.00 1.73
814 851 4.785376 AGGTGAGGAAGGAATGTGATTAGT 59.215 41.667 0.00 0.00 0.00 2.24
815 852 5.251700 AGGTGAGGAAGGAATGTGATTAGTT 59.748 40.000 0.00 0.00 0.00 2.24
816 853 5.946377 GGTGAGGAAGGAATGTGATTAGTTT 59.054 40.000 0.00 0.00 0.00 2.66
817 854 6.094186 GGTGAGGAAGGAATGTGATTAGTTTC 59.906 42.308 0.00 0.00 0.00 2.78
818 855 6.655003 GTGAGGAAGGAATGTGATTAGTTTCA 59.345 38.462 0.00 0.00 0.00 2.69
819 856 7.174946 GTGAGGAAGGAATGTGATTAGTTTCAA 59.825 37.037 0.00 0.00 0.00 2.69
820 857 7.391554 TGAGGAAGGAATGTGATTAGTTTCAAG 59.608 37.037 0.00 0.00 0.00 3.02
821 858 7.461749 AGGAAGGAATGTGATTAGTTTCAAGA 58.538 34.615 0.00 0.00 0.00 3.02
822 859 8.112183 AGGAAGGAATGTGATTAGTTTCAAGAT 58.888 33.333 0.00 0.00 0.00 2.40
823 860 9.396022 GGAAGGAATGTGATTAGTTTCAAGATA 57.604 33.333 0.00 0.00 0.00 1.98
825 862 9.965902 AAGGAATGTGATTAGTTTCAAGATACT 57.034 29.630 0.00 0.00 0.00 2.12
831 868 9.667107 TGTGATTAGTTTCAAGATACTAAAGGG 57.333 33.333 14.20 0.00 37.99 3.95
832 869 8.613482 GTGATTAGTTTCAAGATACTAAAGGGC 58.387 37.037 14.20 7.55 37.99 5.19
833 870 8.548877 TGATTAGTTTCAAGATACTAAAGGGCT 58.451 33.333 14.20 1.89 37.99 5.19
834 871 9.397280 GATTAGTTTCAAGATACTAAAGGGCTT 57.603 33.333 14.20 1.34 37.99 4.35
835 872 9.755122 ATTAGTTTCAAGATACTAAAGGGCTTT 57.245 29.630 14.20 0.00 37.99 3.51
836 873 7.689446 AGTTTCAAGATACTAAAGGGCTTTC 57.311 36.000 0.00 0.00 34.23 2.62
837 874 7.462590 AGTTTCAAGATACTAAAGGGCTTTCT 58.537 34.615 0.00 0.00 34.23 2.52
838 875 8.603304 AGTTTCAAGATACTAAAGGGCTTTCTA 58.397 33.333 0.00 0.00 34.23 2.10
839 876 9.397280 GTTTCAAGATACTAAAGGGCTTTCTAT 57.603 33.333 0.00 0.00 34.23 1.98
842 879 9.656323 TCAAGATACTAAAGGGCTTTCTATAGA 57.344 33.333 0.00 0.00 34.23 1.98
846 883 9.660180 GATACTAAAGGGCTTTCTATAGATTGG 57.340 37.037 2.58 0.00 34.23 3.16
847 884 7.691993 ACTAAAGGGCTTTCTATAGATTGGA 57.308 36.000 2.58 0.00 34.23 3.53
848 885 7.740805 ACTAAAGGGCTTTCTATAGATTGGAG 58.259 38.462 2.58 1.53 34.23 3.86
849 886 4.632327 AGGGCTTTCTATAGATTGGAGC 57.368 45.455 2.58 10.51 0.00 4.70
850 887 3.976654 AGGGCTTTCTATAGATTGGAGCA 59.023 43.478 20.24 0.00 0.00 4.26
851 888 4.041444 AGGGCTTTCTATAGATTGGAGCAG 59.959 45.833 20.24 6.11 0.00 4.24
852 889 4.040952 GGGCTTTCTATAGATTGGAGCAGA 59.959 45.833 20.24 0.00 0.00 4.26
853 890 5.237048 GGCTTTCTATAGATTGGAGCAGAG 58.763 45.833 20.24 0.85 0.00 3.35
854 891 5.011533 GGCTTTCTATAGATTGGAGCAGAGA 59.988 44.000 20.24 0.00 0.00 3.10
855 892 6.463614 GGCTTTCTATAGATTGGAGCAGAGAA 60.464 42.308 20.24 3.76 0.00 2.87
856 893 6.646240 GCTTTCTATAGATTGGAGCAGAGAAG 59.354 42.308 16.62 9.25 0.00 2.85
857 894 7.667575 TTTCTATAGATTGGAGCAGAGAAGT 57.332 36.000 2.58 0.00 0.00 3.01
858 895 6.647334 TCTATAGATTGGAGCAGAGAAGTG 57.353 41.667 0.00 0.00 0.00 3.16
859 896 4.686191 ATAGATTGGAGCAGAGAAGTGG 57.314 45.455 0.00 0.00 0.00 4.00
860 897 1.558756 AGATTGGAGCAGAGAAGTGGG 59.441 52.381 0.00 0.00 0.00 4.61
861 898 0.622665 ATTGGAGCAGAGAAGTGGGG 59.377 55.000 0.00 0.00 0.00 4.96
862 899 0.768221 TTGGAGCAGAGAAGTGGGGT 60.768 55.000 0.00 0.00 0.00 4.95
863 900 0.116342 TGGAGCAGAGAAGTGGGGTA 59.884 55.000 0.00 0.00 0.00 3.69
864 901 1.273838 TGGAGCAGAGAAGTGGGGTAT 60.274 52.381 0.00 0.00 0.00 2.73
865 902 1.840635 GGAGCAGAGAAGTGGGGTATT 59.159 52.381 0.00 0.00 0.00 1.89
866 903 2.420687 GGAGCAGAGAAGTGGGGTATTG 60.421 54.545 0.00 0.00 0.00 1.90
867 904 2.237392 GAGCAGAGAAGTGGGGTATTGT 59.763 50.000 0.00 0.00 0.00 2.71
868 905 2.644798 AGCAGAGAAGTGGGGTATTGTT 59.355 45.455 0.00 0.00 0.00 2.83
869 906 2.749621 GCAGAGAAGTGGGGTATTGTTG 59.250 50.000 0.00 0.00 0.00 3.33
870 907 2.749621 CAGAGAAGTGGGGTATTGTTGC 59.250 50.000 0.00 0.00 0.00 4.17
871 908 2.375174 AGAGAAGTGGGGTATTGTTGCA 59.625 45.455 0.00 0.00 0.00 4.08
872 909 3.153919 GAGAAGTGGGGTATTGTTGCAA 58.846 45.455 0.00 0.00 0.00 4.08
873 910 3.571590 AGAAGTGGGGTATTGTTGCAAA 58.428 40.909 0.00 0.00 0.00 3.68
874 911 3.964031 AGAAGTGGGGTATTGTTGCAAAA 59.036 39.130 0.00 0.00 0.00 2.44
875 912 4.407296 AGAAGTGGGGTATTGTTGCAAAAA 59.593 37.500 4.10 4.10 0.00 1.94
894 931 5.669164 AAAAAGCCAAACTAACCTCACAA 57.331 34.783 0.00 0.00 0.00 3.33
895 932 4.649088 AAAGCCAAACTAACCTCACAAC 57.351 40.909 0.00 0.00 0.00 3.32
896 933 2.583143 AGCCAAACTAACCTCACAACC 58.417 47.619 0.00 0.00 0.00 3.77
897 934 2.092103 AGCCAAACTAACCTCACAACCA 60.092 45.455 0.00 0.00 0.00 3.67
898 935 2.890945 GCCAAACTAACCTCACAACCAT 59.109 45.455 0.00 0.00 0.00 3.55
899 936 3.320826 GCCAAACTAACCTCACAACCATT 59.679 43.478 0.00 0.00 0.00 3.16
900 937 4.521256 GCCAAACTAACCTCACAACCATTA 59.479 41.667 0.00 0.00 0.00 1.90
901 938 5.335661 GCCAAACTAACCTCACAACCATTAG 60.336 44.000 0.00 0.00 0.00 1.73
902 939 6.001460 CCAAACTAACCTCACAACCATTAGA 58.999 40.000 0.00 0.00 0.00 2.10
903 940 6.659242 CCAAACTAACCTCACAACCATTAGAT 59.341 38.462 0.00 0.00 0.00 1.98
904 941 7.827236 CCAAACTAACCTCACAACCATTAGATA 59.173 37.037 0.00 0.00 0.00 1.98
905 942 9.396022 CAAACTAACCTCACAACCATTAGATAT 57.604 33.333 0.00 0.00 0.00 1.63
908 945 9.656323 ACTAACCTCACAACCATTAGATATAGA 57.344 33.333 0.00 0.00 0.00 1.98
911 948 8.964533 ACCTCACAACCATTAGATATAGATCT 57.035 34.615 5.03 5.03 44.90 2.75
912 949 9.030452 ACCTCACAACCATTAGATATAGATCTC 57.970 37.037 2.43 0.00 41.75 2.75
913 950 9.029368 CCTCACAACCATTAGATATAGATCTCA 57.971 37.037 2.43 0.00 41.75 3.27
932 969 9.553064 AGATCTCATGGTTAGAAATTACACATC 57.447 33.333 0.00 0.00 0.00 3.06
933 970 9.330063 GATCTCATGGTTAGAAATTACACATCA 57.670 33.333 0.00 0.00 0.00 3.07
934 971 9.857656 ATCTCATGGTTAGAAATTACACATCAT 57.142 29.630 0.00 0.00 0.00 2.45
935 972 9.330063 TCTCATGGTTAGAAATTACACATCATC 57.670 33.333 0.00 0.00 0.00 2.92
936 973 9.112725 CTCATGGTTAGAAATTACACATCATCA 57.887 33.333 0.00 0.00 0.00 3.07
937 974 9.631257 TCATGGTTAGAAATTACACATCATCAT 57.369 29.630 0.00 0.00 0.00 2.45
938 975 9.888878 CATGGTTAGAAATTACACATCATCATC 57.111 33.333 0.00 0.00 0.00 2.92
939 976 9.631257 ATGGTTAGAAATTACACATCATCATCA 57.369 29.630 0.00 0.00 0.00 3.07
940 977 8.892723 TGGTTAGAAATTACACATCATCATCAC 58.107 33.333 0.00 0.00 0.00 3.06
941 978 8.345565 GGTTAGAAATTACACATCATCATCACC 58.654 37.037 0.00 0.00 0.00 4.02
942 979 8.892723 GTTAGAAATTACACATCATCATCACCA 58.107 33.333 0.00 0.00 0.00 4.17
943 980 7.943079 AGAAATTACACATCATCATCACCAA 57.057 32.000 0.00 0.00 0.00 3.67
944 981 7.993101 AGAAATTACACATCATCATCACCAAG 58.007 34.615 0.00 0.00 0.00 3.61
945 982 7.830697 AGAAATTACACATCATCATCACCAAGA 59.169 33.333 0.00 0.00 0.00 3.02
946 983 6.932356 ATTACACATCATCATCACCAAGAC 57.068 37.500 0.00 0.00 0.00 3.01
947 984 4.564782 ACACATCATCATCACCAAGACT 57.435 40.909 0.00 0.00 0.00 3.24
948 985 5.682234 ACACATCATCATCACCAAGACTA 57.318 39.130 0.00 0.00 0.00 2.59
949 986 5.668471 ACACATCATCATCACCAAGACTAG 58.332 41.667 0.00 0.00 0.00 2.57
950 987 5.055144 CACATCATCATCACCAAGACTAGG 58.945 45.833 0.00 0.00 0.00 3.02
951 988 3.827008 TCATCATCACCAAGACTAGGC 57.173 47.619 0.00 0.00 0.00 3.93
952 989 2.101415 TCATCATCACCAAGACTAGGCG 59.899 50.000 0.00 0.00 0.00 5.52
953 990 1.557099 TCATCACCAAGACTAGGCGT 58.443 50.000 0.00 0.00 0.00 5.68
954 991 1.899814 TCATCACCAAGACTAGGCGTT 59.100 47.619 0.00 0.00 0.00 4.84
955 992 2.094182 TCATCACCAAGACTAGGCGTTC 60.094 50.000 0.00 0.00 0.00 3.95
956 993 0.606604 TCACCAAGACTAGGCGTTCC 59.393 55.000 0.00 0.00 0.00 3.62
957 994 0.736325 CACCAAGACTAGGCGTTCCG 60.736 60.000 0.00 0.00 37.47 4.30
958 995 1.153628 CCAAGACTAGGCGTTCCGG 60.154 63.158 0.00 0.00 37.47 5.14
977 1014 2.140717 GGCGTGACCGGAATAAATAGG 58.859 52.381 9.46 0.00 33.68 2.57
978 1015 2.484241 GGCGTGACCGGAATAAATAGGT 60.484 50.000 9.46 0.00 40.11 3.08
979 1016 3.200483 GCGTGACCGGAATAAATAGGTT 58.800 45.455 9.46 0.00 37.07 3.50
980 1017 3.624410 GCGTGACCGGAATAAATAGGTTT 59.376 43.478 9.46 0.00 37.07 3.27
981 1018 4.495184 GCGTGACCGGAATAAATAGGTTTG 60.495 45.833 9.46 0.00 37.07 2.93
1172 1212 2.440980 GATGCTGCCAGGTTCCCC 60.441 66.667 0.00 0.00 0.00 4.81
1298 1338 1.374758 CAAGAAGAGAGCCCGCGTT 60.375 57.895 4.92 0.00 0.00 4.84
1363 1403 4.584638 ACAGAGAGTGTCAGTATCTCCT 57.415 45.455 1.67 0.00 40.29 3.69
1659 1740 1.953686 CGAGAGAGAAGATCCCCAGAC 59.046 57.143 0.00 0.00 0.00 3.51
1660 1741 2.422803 CGAGAGAGAAGATCCCCAGACT 60.423 54.545 0.00 0.00 0.00 3.24
1661 1742 2.958355 GAGAGAGAAGATCCCCAGACTG 59.042 54.545 0.00 0.00 0.00 3.51
1762 3224 3.825014 ACTACGTAGACATGTTGTGACCT 59.175 43.478 28.74 0.00 29.96 3.85
1764 3226 3.650139 ACGTAGACATGTTGTGACCTTC 58.350 45.455 0.00 0.00 0.00 3.46
1918 3381 1.087771 CGTAATTGAGTCCCGCACCC 61.088 60.000 0.00 0.00 0.00 4.61
2068 3531 3.506067 CCCTTTCGTTGGCAAAGTATCTT 59.494 43.478 12.77 0.00 0.00 2.40
2181 3646 3.670625 TCCCTTGAGTCGTAATTTGGTG 58.329 45.455 0.00 0.00 0.00 4.17
2455 3922 4.218200 GTGGTTGATGATGGTGATTGTTGA 59.782 41.667 0.00 0.00 0.00 3.18
2483 3952 0.830023 TGTGACGTGGGAGGACATGA 60.830 55.000 0.00 0.00 0.00 3.07
2516 3985 1.136110 GTAGCAGCCTCTTCCTCTCAC 59.864 57.143 0.00 0.00 0.00 3.51
2521 3990 3.037549 CAGCCTCTTCCTCTCACCTTAT 58.962 50.000 0.00 0.00 0.00 1.73
2607 4182 6.183361 TGGTATTAGTGATAATGGAACCAGGG 60.183 42.308 0.00 0.00 0.00 4.45
2677 4252 5.052436 CCGTTATTTGCTGTAATTTGATGCG 60.052 40.000 0.00 0.00 0.00 4.73
2699 4288 4.496895 CGCTTGTTTGCTTCATATGCTAAC 59.503 41.667 0.00 1.17 42.99 2.34
2886 4568 0.329261 TGGCAATGCTAACCTCAGCT 59.671 50.000 4.82 0.00 42.30 4.24
2898 4582 4.907879 AACCTCAGCTTCACTTCTTTTG 57.092 40.909 0.00 0.00 0.00 2.44
3036 4720 1.282875 GCGCCACAGAACCTGAAAC 59.717 57.895 0.00 0.00 35.18 2.78
3108 4792 3.807622 TCCAGTTCTTCGTCAATGTTGTC 59.192 43.478 0.00 0.00 0.00 3.18
3109 4793 3.559655 CCAGTTCTTCGTCAATGTTGTCA 59.440 43.478 0.00 0.00 0.00 3.58
3125 4809 1.270907 GTCAGTCACCCATGTCCTCT 58.729 55.000 0.00 0.00 0.00 3.69
3297 4981 5.983720 CGTTTATGTCGAATCCACCTATCTT 59.016 40.000 0.00 0.00 0.00 2.40
3298 4982 6.074302 CGTTTATGTCGAATCCACCTATCTTG 60.074 42.308 0.00 0.00 0.00 3.02
3311 4995 5.242838 CCACCTATCTTGAAGTAGGAGCTAG 59.757 48.000 20.28 9.39 39.91 3.42
3336 5020 1.966451 GCAACTGGACGGTCCCAAG 60.966 63.158 23.81 17.34 35.03 3.61
3344 5028 4.410400 CGGTCCCAAGTCCAGGCC 62.410 72.222 0.00 0.00 0.00 5.19
3347 5031 3.650950 TCCCAAGTCCAGGCCTGC 61.651 66.667 28.39 14.93 0.00 4.85
3349 5033 2.360852 CCAAGTCCAGGCCTGCTG 60.361 66.667 28.39 19.10 0.00 4.41
3350 5034 2.360852 CAAGTCCAGGCCTGCTGG 60.361 66.667 28.39 15.65 43.06 4.85
3351 5035 2.856000 AAGTCCAGGCCTGCTGGT 60.856 61.111 28.39 9.33 42.35 4.00
3352 5036 1.538876 AAGTCCAGGCCTGCTGGTA 60.539 57.895 28.39 6.56 42.35 3.25
3353 5037 0.916358 AAGTCCAGGCCTGCTGGTAT 60.916 55.000 28.39 7.68 42.35 2.73
3371 5055 4.098960 TGGTATTGTACGGGAACTGATCTC 59.901 45.833 0.00 0.00 38.67 2.75
3451 5135 9.570507 GTAGTGTAAAACAAACAAACAAACAAC 57.429 29.630 0.00 0.00 0.00 3.32
3461 5145 9.915629 ACAAACAAACAAACAACTCTTGTAATA 57.084 25.926 0.00 0.00 44.59 0.98
3506 5191 5.977129 CGTGCTTAAGAAGTGTTTCCATTTT 59.023 36.000 6.67 0.00 33.64 1.82
3537 5222 8.439971 TCTGTTTATGCTCATAGATTAATGGGT 58.560 33.333 0.00 0.00 29.46 4.51
3551 5236 2.358322 ATGGGTAATTTGGTAGCCGG 57.642 50.000 0.00 0.00 43.35 6.13
3553 5238 1.634459 TGGGTAATTTGGTAGCCGGAA 59.366 47.619 5.05 0.00 43.35 4.30
3555 5240 2.019249 GGTAATTTGGTAGCCGGAACC 58.981 52.381 17.28 17.28 37.53 3.62
3556 5241 1.667212 GTAATTTGGTAGCCGGAACCG 59.333 52.381 18.45 6.25 40.08 4.44
3563 5248 3.001902 TAGCCGGAACCGAGCAGTG 62.002 63.158 21.36 5.39 42.83 3.66
3627 5312 6.832900 TGATGTTGTGGCTGGATATCAAAATA 59.167 34.615 4.83 0.00 0.00 1.40
3634 5319 5.945784 TGGCTGGATATCAAAATACTATGGC 59.054 40.000 4.83 0.00 0.00 4.40
3647 5332 9.188588 CAAAATACTATGGCATTGATGATTGTC 57.811 33.333 15.74 0.00 0.00 3.18
3663 5348 7.284944 TGATGATTGTCATGCCATGTATTGTAA 59.715 33.333 4.31 0.00 37.20 2.41
3667 5352 6.435430 TGTCATGCCATGTATTGTAAACTC 57.565 37.500 4.31 0.00 0.00 3.01
3681 5366 7.856145 ATTGTAAACTCTGAATCCATCACTC 57.144 36.000 0.00 0.00 33.47 3.51
3685 5370 4.640789 ACTCTGAATCCATCACTCGTAC 57.359 45.455 0.00 0.00 33.47 3.67
3699 5384 6.407475 TCACTCGTACATCAATTCAACATG 57.593 37.500 0.00 0.00 0.00 3.21
3700 5385 6.162777 TCACTCGTACATCAATTCAACATGA 58.837 36.000 0.00 0.00 0.00 3.07
3701 5386 6.818142 TCACTCGTACATCAATTCAACATGAT 59.182 34.615 0.00 0.00 36.74 2.45
3724 5409 8.270030 TGATGTCTAGGAATTCATGTTTCTCAT 58.730 33.333 7.93 2.06 37.22 2.90
3783 5468 0.893727 ATTGTGGGGGCTCAACGTTC 60.894 55.000 0.00 0.00 0.00 3.95
3784 5469 1.990160 TTGTGGGGGCTCAACGTTCT 61.990 55.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 170 5.175856 CAGTCCTCAAGTTAACAAGTCTTCG 59.824 44.000 8.61 0.00 0.00 3.79
241 246 2.829043 TTCGTTCACCGGCGATCCAG 62.829 60.000 9.30 0.00 36.97 3.86
330 335 4.019231 GTCTTCACCTTATTCCCCTTGAGT 60.019 45.833 0.00 0.00 0.00 3.41
460 465 9.910267 AAGTGTAAAAGTAAAGGGAAGTTAAGA 57.090 29.630 0.00 0.00 0.00 2.10
464 469 8.357290 ACAAAGTGTAAAAGTAAAGGGAAGTT 57.643 30.769 0.00 0.00 0.00 2.66
480 485 5.001237 TGACTTCACGAAGACAAAGTGTA 57.999 39.130 13.60 0.00 39.40 2.90
484 489 4.214437 GCAATGACTTCACGAAGACAAAG 58.786 43.478 13.60 10.61 43.74 2.77
575 612 4.992688 AGCAATGAAGTGAAAACACGAAA 58.007 34.783 0.00 0.00 0.00 3.46
578 615 5.510671 AGTAAGCAATGAAGTGAAAACACG 58.489 37.500 0.00 0.00 0.00 4.49
586 623 6.676456 GCCATAGTCAAGTAAGCAATGAAGTG 60.676 42.308 0.00 0.00 0.00 3.16
701 738 4.077108 GGGGAGGTGAGTAAACGATTTTT 58.923 43.478 0.00 0.00 0.00 1.94
709 746 2.658489 ACTAGAGGGGGAGGTGAGTAAA 59.342 50.000 0.00 0.00 0.00 2.01
710 747 2.244252 GACTAGAGGGGGAGGTGAGTAA 59.756 54.545 0.00 0.00 0.00 2.24
713 750 0.466555 CGACTAGAGGGGGAGGTGAG 60.467 65.000 0.00 0.00 0.00 3.51
718 755 3.512219 AGTTATCGACTAGAGGGGGAG 57.488 52.381 0.00 0.00 36.65 4.30
752 789 9.265901 CCGAGAAATATATTTTGAGTGAGACAT 57.734 33.333 11.92 0.00 0.00 3.06
753 790 7.710907 CCCGAGAAATATATTTTGAGTGAGACA 59.289 37.037 11.92 0.00 0.00 3.41
754 791 7.307455 GCCCGAGAAATATATTTTGAGTGAGAC 60.307 40.741 11.92 0.00 0.00 3.36
755 792 6.706270 GCCCGAGAAATATATTTTGAGTGAGA 59.294 38.462 11.92 0.00 0.00 3.27
756 793 6.708054 AGCCCGAGAAATATATTTTGAGTGAG 59.292 38.462 11.92 1.03 0.00 3.51
757 794 6.483307 CAGCCCGAGAAATATATTTTGAGTGA 59.517 38.462 11.92 0.00 0.00 3.41
758 795 6.260936 ACAGCCCGAGAAATATATTTTGAGTG 59.739 38.462 11.92 6.68 0.00 3.51
759 796 6.357367 ACAGCCCGAGAAATATATTTTGAGT 58.643 36.000 11.92 0.00 0.00 3.41
760 797 6.867662 ACAGCCCGAGAAATATATTTTGAG 57.132 37.500 11.92 6.49 0.00 3.02
761 798 7.639113 AAACAGCCCGAGAAATATATTTTGA 57.361 32.000 11.92 0.00 0.00 2.69
762 799 7.973388 TCAAAACAGCCCGAGAAATATATTTTG 59.027 33.333 11.92 7.10 35.60 2.44
763 800 8.062065 TCAAAACAGCCCGAGAAATATATTTT 57.938 30.769 11.92 2.96 0.00 1.82
764 801 7.639113 TCAAAACAGCCCGAGAAATATATTT 57.361 32.000 10.51 10.51 0.00 1.40
765 802 7.502226 TCATCAAAACAGCCCGAGAAATATATT 59.498 33.333 0.00 0.00 0.00 1.28
766 803 6.998074 TCATCAAAACAGCCCGAGAAATATAT 59.002 34.615 0.00 0.00 0.00 0.86
767 804 6.353323 TCATCAAAACAGCCCGAGAAATATA 58.647 36.000 0.00 0.00 0.00 0.86
768 805 5.192927 TCATCAAAACAGCCCGAGAAATAT 58.807 37.500 0.00 0.00 0.00 1.28
769 806 4.584874 TCATCAAAACAGCCCGAGAAATA 58.415 39.130 0.00 0.00 0.00 1.40
770 807 3.420893 TCATCAAAACAGCCCGAGAAAT 58.579 40.909 0.00 0.00 0.00 2.17
771 808 2.813754 CTCATCAAAACAGCCCGAGAAA 59.186 45.455 0.00 0.00 0.00 2.52
772 809 2.426522 CTCATCAAAACAGCCCGAGAA 58.573 47.619 0.00 0.00 0.00 2.87
773 810 1.339055 CCTCATCAAAACAGCCCGAGA 60.339 52.381 0.00 0.00 0.00 4.04
774 811 1.089920 CCTCATCAAAACAGCCCGAG 58.910 55.000 0.00 0.00 0.00 4.63
775 812 0.400213 ACCTCATCAAAACAGCCCGA 59.600 50.000 0.00 0.00 0.00 5.14
776 813 0.523072 CACCTCATCAAAACAGCCCG 59.477 55.000 0.00 0.00 0.00 6.13
777 814 1.815003 CTCACCTCATCAAAACAGCCC 59.185 52.381 0.00 0.00 0.00 5.19
778 815 1.815003 CCTCACCTCATCAAAACAGCC 59.185 52.381 0.00 0.00 0.00 4.85
779 816 2.783135 TCCTCACCTCATCAAAACAGC 58.217 47.619 0.00 0.00 0.00 4.40
780 817 3.755378 CCTTCCTCACCTCATCAAAACAG 59.245 47.826 0.00 0.00 0.00 3.16
781 818 3.394274 TCCTTCCTCACCTCATCAAAACA 59.606 43.478 0.00 0.00 0.00 2.83
782 819 4.021102 TCCTTCCTCACCTCATCAAAAC 57.979 45.455 0.00 0.00 0.00 2.43
783 820 4.722526 TTCCTTCCTCACCTCATCAAAA 57.277 40.909 0.00 0.00 0.00 2.44
784 821 4.043310 ACATTCCTTCCTCACCTCATCAAA 59.957 41.667 0.00 0.00 0.00 2.69
785 822 3.588842 ACATTCCTTCCTCACCTCATCAA 59.411 43.478 0.00 0.00 0.00 2.57
786 823 3.054875 CACATTCCTTCCTCACCTCATCA 60.055 47.826 0.00 0.00 0.00 3.07
787 824 3.198635 TCACATTCCTTCCTCACCTCATC 59.801 47.826 0.00 0.00 0.00 2.92
788 825 3.184628 TCACATTCCTTCCTCACCTCAT 58.815 45.455 0.00 0.00 0.00 2.90
789 826 2.619931 TCACATTCCTTCCTCACCTCA 58.380 47.619 0.00 0.00 0.00 3.86
790 827 3.922171 ATCACATTCCTTCCTCACCTC 57.078 47.619 0.00 0.00 0.00 3.85
791 828 4.785376 ACTAATCACATTCCTTCCTCACCT 59.215 41.667 0.00 0.00 0.00 4.00
792 829 5.104259 ACTAATCACATTCCTTCCTCACC 57.896 43.478 0.00 0.00 0.00 4.02
793 830 6.655003 TGAAACTAATCACATTCCTTCCTCAC 59.345 38.462 0.00 0.00 0.00 3.51
794 831 6.778821 TGAAACTAATCACATTCCTTCCTCA 58.221 36.000 0.00 0.00 0.00 3.86
795 832 7.607991 TCTTGAAACTAATCACATTCCTTCCTC 59.392 37.037 0.00 0.00 0.00 3.71
796 833 7.461749 TCTTGAAACTAATCACATTCCTTCCT 58.538 34.615 0.00 0.00 0.00 3.36
797 834 7.687941 TCTTGAAACTAATCACATTCCTTCC 57.312 36.000 0.00 0.00 0.00 3.46
799 836 9.965902 AGTATCTTGAAACTAATCACATTCCTT 57.034 29.630 0.00 0.00 0.00 3.36
805 842 9.667107 CCCTTTAGTATCTTGAAACTAATCACA 57.333 33.333 0.00 0.00 37.86 3.58
806 843 8.613482 GCCCTTTAGTATCTTGAAACTAATCAC 58.387 37.037 0.00 0.00 37.86 3.06
807 844 8.548877 AGCCCTTTAGTATCTTGAAACTAATCA 58.451 33.333 0.00 0.00 37.86 2.57
808 845 8.966069 AGCCCTTTAGTATCTTGAAACTAATC 57.034 34.615 0.00 0.00 37.86 1.75
809 846 9.755122 AAAGCCCTTTAGTATCTTGAAACTAAT 57.245 29.630 0.00 0.00 37.86 1.73
810 847 9.227777 GAAAGCCCTTTAGTATCTTGAAACTAA 57.772 33.333 0.00 0.00 36.62 2.24
811 848 8.603304 AGAAAGCCCTTTAGTATCTTGAAACTA 58.397 33.333 0.00 0.00 32.11 2.24
812 849 7.462590 AGAAAGCCCTTTAGTATCTTGAAACT 58.537 34.615 0.00 0.00 32.11 2.66
813 850 7.689446 AGAAAGCCCTTTAGTATCTTGAAAC 57.311 36.000 0.00 0.00 32.11 2.78
816 853 9.656323 TCTATAGAAAGCCCTTTAGTATCTTGA 57.344 33.333 0.00 0.00 32.11 3.02
820 857 9.660180 CCAATCTATAGAAAGCCCTTTAGTATC 57.340 37.037 6.52 0.00 32.11 2.24
821 858 9.393786 TCCAATCTATAGAAAGCCCTTTAGTAT 57.606 33.333 6.52 0.00 32.11 2.12
822 859 8.792830 TCCAATCTATAGAAAGCCCTTTAGTA 57.207 34.615 6.52 0.00 32.11 1.82
823 860 7.690549 GCTCCAATCTATAGAAAGCCCTTTAGT 60.691 40.741 6.52 0.00 32.11 2.24
824 861 6.652900 GCTCCAATCTATAGAAAGCCCTTTAG 59.347 42.308 6.52 0.00 32.11 1.85
825 862 6.101150 TGCTCCAATCTATAGAAAGCCCTTTA 59.899 38.462 19.01 5.58 32.11 1.85
826 863 5.103940 TGCTCCAATCTATAGAAAGCCCTTT 60.104 40.000 19.01 0.00 35.14 3.11
827 864 4.413520 TGCTCCAATCTATAGAAAGCCCTT 59.586 41.667 19.01 3.67 0.00 3.95
828 865 3.976654 TGCTCCAATCTATAGAAAGCCCT 59.023 43.478 19.01 0.00 0.00 5.19
829 866 4.040952 TCTGCTCCAATCTATAGAAAGCCC 59.959 45.833 19.01 5.53 0.00 5.19
830 867 5.011533 TCTCTGCTCCAATCTATAGAAAGCC 59.988 44.000 19.01 8.50 0.00 4.35
831 868 6.095432 TCTCTGCTCCAATCTATAGAAAGC 57.905 41.667 6.52 13.20 0.00 3.51
832 869 7.652909 CACTTCTCTGCTCCAATCTATAGAAAG 59.347 40.741 6.52 3.97 0.00 2.62
833 870 7.418368 CCACTTCTCTGCTCCAATCTATAGAAA 60.418 40.741 6.52 0.00 0.00 2.52
834 871 6.041409 CCACTTCTCTGCTCCAATCTATAGAA 59.959 42.308 6.52 0.00 0.00 2.10
835 872 5.538053 CCACTTCTCTGCTCCAATCTATAGA 59.462 44.000 4.57 4.57 0.00 1.98
836 873 5.279406 CCCACTTCTCTGCTCCAATCTATAG 60.279 48.000 0.00 0.00 0.00 1.31
837 874 4.590647 CCCACTTCTCTGCTCCAATCTATA 59.409 45.833 0.00 0.00 0.00 1.31
838 875 3.390639 CCCACTTCTCTGCTCCAATCTAT 59.609 47.826 0.00 0.00 0.00 1.98
839 876 2.768527 CCCACTTCTCTGCTCCAATCTA 59.231 50.000 0.00 0.00 0.00 1.98
840 877 1.558756 CCCACTTCTCTGCTCCAATCT 59.441 52.381 0.00 0.00 0.00 2.40
841 878 1.407989 CCCCACTTCTCTGCTCCAATC 60.408 57.143 0.00 0.00 0.00 2.67
842 879 0.622665 CCCCACTTCTCTGCTCCAAT 59.377 55.000 0.00 0.00 0.00 3.16
843 880 0.768221 ACCCCACTTCTCTGCTCCAA 60.768 55.000 0.00 0.00 0.00 3.53
844 881 0.116342 TACCCCACTTCTCTGCTCCA 59.884 55.000 0.00 0.00 0.00 3.86
845 882 1.501582 ATACCCCACTTCTCTGCTCC 58.498 55.000 0.00 0.00 0.00 4.70
846 883 2.237392 ACAATACCCCACTTCTCTGCTC 59.763 50.000 0.00 0.00 0.00 4.26
847 884 2.269940 ACAATACCCCACTTCTCTGCT 58.730 47.619 0.00 0.00 0.00 4.24
848 885 2.749621 CAACAATACCCCACTTCTCTGC 59.250 50.000 0.00 0.00 0.00 4.26
849 886 2.749621 GCAACAATACCCCACTTCTCTG 59.250 50.000 0.00 0.00 0.00 3.35
850 887 2.375174 TGCAACAATACCCCACTTCTCT 59.625 45.455 0.00 0.00 0.00 3.10
851 888 2.790433 TGCAACAATACCCCACTTCTC 58.210 47.619 0.00 0.00 0.00 2.87
852 889 2.969821 TGCAACAATACCCCACTTCT 57.030 45.000 0.00 0.00 0.00 2.85
853 890 4.329462 TTTTGCAACAATACCCCACTTC 57.671 40.909 0.00 0.00 0.00 3.01
854 891 4.762289 TTTTTGCAACAATACCCCACTT 57.238 36.364 0.00 0.00 0.00 3.16
872 909 5.416083 GTTGTGAGGTTAGTTTGGCTTTTT 58.584 37.500 0.00 0.00 0.00 1.94
873 910 4.142026 GGTTGTGAGGTTAGTTTGGCTTTT 60.142 41.667 0.00 0.00 0.00 2.27
874 911 3.383505 GGTTGTGAGGTTAGTTTGGCTTT 59.616 43.478 0.00 0.00 0.00 3.51
875 912 2.956333 GGTTGTGAGGTTAGTTTGGCTT 59.044 45.455 0.00 0.00 0.00 4.35
876 913 2.092103 TGGTTGTGAGGTTAGTTTGGCT 60.092 45.455 0.00 0.00 0.00 4.75
877 914 2.303175 TGGTTGTGAGGTTAGTTTGGC 58.697 47.619 0.00 0.00 0.00 4.52
878 915 6.001460 TCTAATGGTTGTGAGGTTAGTTTGG 58.999 40.000 0.00 0.00 0.00 3.28
879 916 7.687941 ATCTAATGGTTGTGAGGTTAGTTTG 57.312 36.000 0.00 0.00 0.00 2.93
882 919 9.656323 TCTATATCTAATGGTTGTGAGGTTAGT 57.344 33.333 0.00 0.00 0.00 2.24
885 922 9.386122 AGATCTATATCTAATGGTTGTGAGGTT 57.614 33.333 0.00 0.00 40.82 3.50
886 923 8.964533 AGATCTATATCTAATGGTTGTGAGGT 57.035 34.615 0.00 0.00 40.82 3.85
887 924 9.029368 TGAGATCTATATCTAATGGTTGTGAGG 57.971 37.037 0.00 0.00 42.73 3.86
906 943 9.553064 GATGTGTAATTTCTAACCATGAGATCT 57.447 33.333 0.00 0.00 0.00 2.75
907 944 9.330063 TGATGTGTAATTTCTAACCATGAGATC 57.670 33.333 0.00 0.00 0.00 2.75
908 945 9.857656 ATGATGTGTAATTTCTAACCATGAGAT 57.142 29.630 0.00 0.00 0.00 2.75
909 946 9.330063 GATGATGTGTAATTTCTAACCATGAGA 57.670 33.333 0.00 0.00 0.00 3.27
910 947 9.112725 TGATGATGTGTAATTTCTAACCATGAG 57.887 33.333 0.00 0.00 0.00 2.90
911 948 9.631257 ATGATGATGTGTAATTTCTAACCATGA 57.369 29.630 0.00 0.00 0.00 3.07
912 949 9.888878 GATGATGATGTGTAATTTCTAACCATG 57.111 33.333 0.00 0.00 0.00 3.66
913 950 9.631257 TGATGATGATGTGTAATTTCTAACCAT 57.369 29.630 0.00 0.00 0.00 3.55
914 951 8.892723 GTGATGATGATGTGTAATTTCTAACCA 58.107 33.333 0.00 0.00 0.00 3.67
915 952 8.345565 GGTGATGATGATGTGTAATTTCTAACC 58.654 37.037 0.00 0.00 0.00 2.85
916 953 8.892723 TGGTGATGATGATGTGTAATTTCTAAC 58.107 33.333 0.00 0.00 0.00 2.34
917 954 9.460019 TTGGTGATGATGATGTGTAATTTCTAA 57.540 29.630 0.00 0.00 0.00 2.10
918 955 9.112725 CTTGGTGATGATGATGTGTAATTTCTA 57.887 33.333 0.00 0.00 0.00 2.10
919 956 7.830697 TCTTGGTGATGATGATGTGTAATTTCT 59.169 33.333 0.00 0.00 0.00 2.52
920 957 7.912250 GTCTTGGTGATGATGATGTGTAATTTC 59.088 37.037 0.00 0.00 0.00 2.17
921 958 7.613022 AGTCTTGGTGATGATGATGTGTAATTT 59.387 33.333 0.00 0.00 0.00 1.82
922 959 7.114754 AGTCTTGGTGATGATGATGTGTAATT 58.885 34.615 0.00 0.00 0.00 1.40
923 960 6.656902 AGTCTTGGTGATGATGATGTGTAAT 58.343 36.000 0.00 0.00 0.00 1.89
924 961 6.053632 AGTCTTGGTGATGATGATGTGTAA 57.946 37.500 0.00 0.00 0.00 2.41
925 962 5.682234 AGTCTTGGTGATGATGATGTGTA 57.318 39.130 0.00 0.00 0.00 2.90
926 963 4.564782 AGTCTTGGTGATGATGATGTGT 57.435 40.909 0.00 0.00 0.00 3.72
927 964 5.055144 CCTAGTCTTGGTGATGATGATGTG 58.945 45.833 0.00 0.00 0.00 3.21
928 965 4.444022 GCCTAGTCTTGGTGATGATGATGT 60.444 45.833 2.16 0.00 0.00 3.06
929 966 4.063689 GCCTAGTCTTGGTGATGATGATG 58.936 47.826 2.16 0.00 0.00 3.07
930 967 3.244009 CGCCTAGTCTTGGTGATGATGAT 60.244 47.826 8.04 0.00 37.26 2.45
931 968 2.101415 CGCCTAGTCTTGGTGATGATGA 59.899 50.000 8.04 0.00 37.26 2.92
932 969 2.159043 ACGCCTAGTCTTGGTGATGATG 60.159 50.000 19.04 0.00 38.37 3.07
933 970 2.111384 ACGCCTAGTCTTGGTGATGAT 58.889 47.619 19.04 0.00 38.37 2.45
934 971 1.557099 ACGCCTAGTCTTGGTGATGA 58.443 50.000 19.04 0.00 38.37 2.92
935 972 2.271800 GAACGCCTAGTCTTGGTGATG 58.728 52.381 19.04 2.51 38.37 3.07
936 973 1.207329 GGAACGCCTAGTCTTGGTGAT 59.793 52.381 19.04 8.49 38.37 3.06
937 974 0.606604 GGAACGCCTAGTCTTGGTGA 59.393 55.000 19.04 0.00 38.37 4.02
938 975 3.139029 GGAACGCCTAGTCTTGGTG 57.861 57.895 11.75 11.75 40.62 4.17
957 994 2.140717 CCTATTTATTCCGGTCACGCC 58.859 52.381 0.00 0.00 39.22 5.68
958 995 2.830104 ACCTATTTATTCCGGTCACGC 58.170 47.619 0.00 0.00 39.22 5.34
959 996 4.871557 TCAAACCTATTTATTCCGGTCACG 59.128 41.667 0.00 0.00 40.55 4.35
960 997 6.183360 CCTTCAAACCTATTTATTCCGGTCAC 60.183 42.308 0.00 0.00 0.00 3.67
961 998 5.883673 CCTTCAAACCTATTTATTCCGGTCA 59.116 40.000 0.00 0.00 0.00 4.02
962 999 5.220989 GCCTTCAAACCTATTTATTCCGGTC 60.221 44.000 0.00 0.00 0.00 4.79
963 1000 4.643334 GCCTTCAAACCTATTTATTCCGGT 59.357 41.667 0.00 0.00 0.00 5.28
964 1001 4.037565 GGCCTTCAAACCTATTTATTCCGG 59.962 45.833 0.00 0.00 0.00 5.14
965 1002 4.037565 GGGCCTTCAAACCTATTTATTCCG 59.962 45.833 0.84 0.00 0.00 4.30
966 1003 4.959839 TGGGCCTTCAAACCTATTTATTCC 59.040 41.667 4.53 0.00 0.00 3.01
967 1004 5.656859 AGTGGGCCTTCAAACCTATTTATTC 59.343 40.000 4.53 0.00 0.00 1.75
968 1005 5.589831 AGTGGGCCTTCAAACCTATTTATT 58.410 37.500 4.53 0.00 0.00 1.40
969 1006 5.206905 AGTGGGCCTTCAAACCTATTTAT 57.793 39.130 4.53 0.00 0.00 1.40
970 1007 4.668138 AGTGGGCCTTCAAACCTATTTA 57.332 40.909 4.53 0.00 0.00 1.40
971 1008 3.542969 AGTGGGCCTTCAAACCTATTT 57.457 42.857 4.53 0.00 0.00 1.40
972 1009 3.621461 CGTAGTGGGCCTTCAAACCTATT 60.621 47.826 4.53 0.00 0.00 1.73
973 1010 2.093128 CGTAGTGGGCCTTCAAACCTAT 60.093 50.000 4.53 0.00 0.00 2.57
974 1011 1.276989 CGTAGTGGGCCTTCAAACCTA 59.723 52.381 4.53 0.00 0.00 3.08
975 1012 0.036306 CGTAGTGGGCCTTCAAACCT 59.964 55.000 4.53 0.00 0.00 3.50
976 1013 1.583495 GCGTAGTGGGCCTTCAAACC 61.583 60.000 4.53 0.00 0.00 3.27
977 1014 0.605589 AGCGTAGTGGGCCTTCAAAC 60.606 55.000 4.53 0.00 0.00 2.93
978 1015 0.605319 CAGCGTAGTGGGCCTTCAAA 60.605 55.000 4.53 0.00 0.00 2.69
979 1016 1.003839 CAGCGTAGTGGGCCTTCAA 60.004 57.895 4.53 0.00 0.00 2.69
980 1017 2.662596 CAGCGTAGTGGGCCTTCA 59.337 61.111 4.53 0.00 0.00 3.02
981 1018 1.610554 TACCAGCGTAGTGGGCCTTC 61.611 60.000 4.53 0.00 42.54 3.46
1071 1108 0.314302 ATCGATCGACCGATCCAACC 59.686 55.000 22.06 3.11 45.03 3.77
1172 1212 3.241773 CGTCGCTGTAACAGATTGTCATG 60.242 47.826 0.00 0.00 32.44 3.07
1634 1715 0.309612 GGATCTTCTCTCTCGCGTCC 59.690 60.000 5.77 0.00 0.00 4.79
1659 1740 6.789262 ACAGATTCAAACAGTCTGAAAACAG 58.211 36.000 6.91 0.00 41.38 3.16
1660 1741 6.183360 GGACAGATTCAAACAGTCTGAAAACA 60.183 38.462 6.91 0.00 41.38 2.83
1661 1742 6.183360 TGGACAGATTCAAACAGTCTGAAAAC 60.183 38.462 6.91 0.00 41.38 2.43
1762 3224 9.920946 ATCCTCCTGCAAGTAATTTATAAAGAA 57.079 29.630 3.94 0.00 0.00 2.52
1863 3326 4.476113 TCTTCATCATCAGGATCACCCTTT 59.524 41.667 0.00 0.00 44.85 3.11
1878 3341 3.436704 CGCCTTTGCTAAAGTCTTCATCA 59.563 43.478 7.53 0.00 36.77 3.07
1918 3381 5.363868 TCATAGTTATGGGTCCAGAGTCAAG 59.636 44.000 0.00 0.00 34.50 3.02
2068 3531 1.757118 CTCGGCATTTCTAGTCCCAGA 59.243 52.381 0.00 0.00 0.00 3.86
2181 3646 5.596763 TCCCATGTAGGTATAGGGATAACC 58.403 45.833 0.00 0.00 43.39 2.85
2250 3715 1.134580 ACATGAGTGCCTTCATCCTCG 60.135 52.381 0.00 0.00 35.67 4.63
2455 3922 1.445942 CCACGTCACAGACAAGGGT 59.554 57.895 0.00 0.00 32.09 4.34
2516 3985 6.428159 AGCACAACTCTTACAACTTGATAAGG 59.572 38.462 0.00 0.00 0.00 2.69
2521 3990 4.570772 GTGAGCACAACTCTTACAACTTGA 59.429 41.667 0.00 0.00 46.41 3.02
2677 4252 5.401550 TGTTAGCATATGAAGCAAACAAGC 58.598 37.500 6.97 0.00 0.00 4.01
2699 4288 6.650390 CCCCTTTTTGTTACCTTTGAATGATG 59.350 38.462 0.00 0.00 0.00 3.07
2841 4430 7.757173 AGATATATGACGGAATGAATCTTCACG 59.243 37.037 0.00 0.00 40.49 4.35
2886 4568 5.331902 CAAGTTCTTCGCAAAAGAAGTGAA 58.668 37.500 15.84 0.00 45.69 3.18
2898 4582 1.136502 CGTCTTCTGCAAGTTCTTCGC 60.137 52.381 0.00 0.00 33.76 4.70
3036 4720 1.156736 GTTCAACCAGTGGGATGTCG 58.843 55.000 15.21 0.00 38.11 4.35
3108 4792 2.692557 CTCTAGAGGACATGGGTGACTG 59.307 54.545 12.27 0.00 0.00 3.51
3109 4793 2.952702 GCTCTAGAGGACATGGGTGACT 60.953 54.545 21.23 0.00 0.00 3.41
3297 4981 2.358300 CCCCTCACTAGCTCCTACTTCA 60.358 54.545 0.00 0.00 0.00 3.02
3298 4982 2.312390 CCCCTCACTAGCTCCTACTTC 58.688 57.143 0.00 0.00 0.00 3.01
3311 4995 2.358737 CGTCCAGTTGCCCCTCAC 60.359 66.667 0.00 0.00 0.00 3.51
3344 5028 2.093658 AGTTCCCGTACAATACCAGCAG 60.094 50.000 0.00 0.00 0.00 4.24
3347 5031 3.880047 TCAGTTCCCGTACAATACCAG 57.120 47.619 0.00 0.00 0.00 4.00
3349 5033 4.501058 GGAGATCAGTTCCCGTACAATACC 60.501 50.000 0.00 0.00 0.00 2.73
3350 5034 4.098960 TGGAGATCAGTTCCCGTACAATAC 59.901 45.833 0.00 0.00 33.62 1.89
3351 5035 4.283337 TGGAGATCAGTTCCCGTACAATA 58.717 43.478 0.00 0.00 33.62 1.90
3352 5036 3.104512 TGGAGATCAGTTCCCGTACAAT 58.895 45.455 0.00 0.00 33.62 2.71
3353 5037 2.496070 CTGGAGATCAGTTCCCGTACAA 59.504 50.000 0.00 0.00 38.64 2.41
3371 5055 0.527817 GACATACTTCCGCCGTCTGG 60.528 60.000 0.00 0.00 38.77 3.86
3434 5118 8.649973 TTACAAGAGTTGTTTGTTTGTTTGTT 57.350 26.923 0.00 0.00 42.22 2.83
3435 5119 8.825667 ATTACAAGAGTTGTTTGTTTGTTTGT 57.174 26.923 0.00 0.00 42.22 2.83
3437 5121 9.083080 GCTATTACAAGAGTTGTTTGTTTGTTT 57.917 29.630 0.00 0.00 42.22 2.83
3461 5145 7.495934 AGCACGTTATTATATTCTTGTCAAGCT 59.504 33.333 7.78 0.66 0.00 3.74
3537 5222 1.554160 TCGGTTCCGGCTACCAAATTA 59.446 47.619 21.03 3.15 35.31 1.40
3539 5224 0.107848 CTCGGTTCCGGCTACCAAAT 60.108 55.000 21.03 0.00 35.31 2.32
3627 5312 5.278808 GCATGACAATCATCAATGCCATAGT 60.279 40.000 0.00 0.00 34.28 2.12
3634 5319 4.944048 ACATGGCATGACAATCATCAATG 58.056 39.130 32.74 0.00 34.28 2.82
3647 5332 6.682423 TCAGAGTTTACAATACATGGCATG 57.318 37.500 25.31 25.31 0.00 4.06
3663 5348 4.462834 TGTACGAGTGATGGATTCAGAGTT 59.537 41.667 0.00 0.00 34.17 3.01
3667 5352 4.936891 TGATGTACGAGTGATGGATTCAG 58.063 43.478 0.00 0.00 34.17 3.02
3699 5384 8.674263 ATGAGAAACATGAATTCCTAGACATC 57.326 34.615 0.00 0.00 37.87 3.06
3700 5385 8.492782 AGATGAGAAACATGAATTCCTAGACAT 58.507 33.333 0.00 5.23 39.56 3.06
3701 5386 7.855375 AGATGAGAAACATGAATTCCTAGACA 58.145 34.615 0.00 1.07 39.56 3.41
3702 5387 8.729805 AAGATGAGAAACATGAATTCCTAGAC 57.270 34.615 0.00 0.00 39.56 2.59
3703 5388 9.388506 GAAAGATGAGAAACATGAATTCCTAGA 57.611 33.333 0.00 0.00 39.56 2.43
3704 5389 9.170734 TGAAAGATGAGAAACATGAATTCCTAG 57.829 33.333 0.00 0.00 39.56 3.02
3705 5390 9.170734 CTGAAAGATGAGAAACATGAATTCCTA 57.829 33.333 0.00 0.00 39.56 2.94
3706 5391 7.122353 CCTGAAAGATGAGAAACATGAATTCCT 59.878 37.037 0.00 0.00 39.56 3.36
3707 5392 7.121759 TCCTGAAAGATGAGAAACATGAATTCC 59.878 37.037 0.00 0.00 39.56 3.01
3748 5433 5.883673 CCCCACAATAGGAAAAATAGAACGA 59.116 40.000 0.00 0.00 0.00 3.85
3764 5449 0.893727 GAACGTTGAGCCCCCACAAT 60.894 55.000 5.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.