Multiple sequence alignment - TraesCS1B01G096400

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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 TraesCS1B01G096400 chr1B 100.000 3154 0 0 1 3154 100540434 100543587 0.000000e+00 5825
1 TraesCS1B01G096400 chr1B 99.669 906 3 0 1 906 443992844 443991939 0.000000e+00 1657
2 TraesCS1B01G096400 chr1B 93.594 999 51 10 1308 2297 100631306 100632300 0.000000e+00 1478
3 TraesCS1B01G096400 chr1B 96.324 680 21 4 2477 3154 674130401 674129724 0.000000e+00 1114
4 TraesCS1B01G096400 chr1B 94.721 682 25 6 2477 3154 663677072 663677746 0.000000e+00 1050
5 TraesCS1B01G096400 chr1B 85.159 1004 125 19 1308 2295 101143250 101144245 0.000000e+00 1007
6 TraesCS1B01G096400 chr1B 88.090 848 45 15 87 906 65607095 65606276 0.000000e+00 955
7 TraesCS1B01G096400 chr1B 86.610 351 33 9 907 1255 100630947 100631285 2.970000e-100 375
8 TraesCS1B01G096400 chr1B 88.973 263 29 0 986 1248 101142964 101143226 3.030000e-85 326
9 TraesCS1B01G096400 chr1B 92.593 162 7 2 2319 2479 100645748 100645905 8.800000e-56 228
10 TraesCS1B01G096400 chr1B 82.677 254 38 3 998 1248 100422295 100422545 1.470000e-53 220
11 TraesCS1B01G096400 chr1B 94.340 106 6 0 801 906 100539878 100539773 2.520000e-36 163
12 TraesCS1B01G096400 chr1B 92.661 109 8 0 798 906 443993393 443993501 1.170000e-34 158
13 TraesCS1B01G096400 chr1B 98.571 70 0 1 23 92 65851064 65851132 4.270000e-24 122
14 TraesCS1B01G096400 chr1A 93.378 1495 92 4 988 2479 61032264 61033754 0.000000e+00 2206
15 TraesCS1B01G096400 chr1A 92.776 1495 99 5 986 2476 61284125 61285614 0.000000e+00 2154
16 TraesCS1B01G096400 chr1A 93.420 1155 64 7 1328 2479 61341453 61342598 0.000000e+00 1701
17 TraesCS1B01G096400 chr1A 85.558 1004 121 20 1308 2295 62254285 62253290 0.000000e+00 1029
18 TraesCS1B01G096400 chr1A 90.258 349 28 4 907 1255 61341078 61341420 4.800000e-123 451
19 TraesCS1B01G096400 chr1A 90.785 293 17 4 2189 2479 61158378 61158662 1.770000e-102 383
20 TraesCS1B01G096400 chr1A 88.148 270 32 0 986 1255 62254728 62254459 3.920000e-84 322
21 TraesCS1B01G096400 chr1A 78.235 340 57 12 1960 2295 62250087 62249761 5.330000e-48 202
22 TraesCS1B01G096400 chr1A 87.578 161 13 4 2321 2479 61023278 61023433 2.500000e-41 180
23 TraesCS1B01G096400 chr1A 87.578 161 13 4 2321 2479 61252495 61252650 2.500000e-41 180
24 TraesCS1B01G096400 chr1D 92.571 1548 93 14 941 2479 62935682 62937216 0.000000e+00 2202
25 TraesCS1B01G096400 chr1D 86.527 1002 111 19 1308 2295 63357323 63358314 0.000000e+00 1081
26 TraesCS1B01G096400 chr1D 84.375 160 18 6 2323 2479 62930959 62931114 1.960000e-32 150
27 TraesCS1B01G096400 chr3B 95.760 684 23 5 2475 3154 764644268 764643587 0.000000e+00 1098
28 TraesCS1B01G096400 chr3B 95.175 684 24 4 2475 3154 732331018 732331696 0.000000e+00 1072
29 TraesCS1B01G096400 chr3B 95.126 677 26 3 2477 3153 671952105 671952774 0.000000e+00 1061
30 TraesCS1B01G096400 chr2B 95.601 682 25 4 2477 3154 727295591 727294911 0.000000e+00 1088
31 TraesCS1B01G096400 chr5B 95.315 683 26 3 2476 3154 404462467 404461787 0.000000e+00 1079
32 TraesCS1B01G096400 chr5B 95.315 683 23 6 2476 3154 686033148 686033825 0.000000e+00 1075
33 TraesCS1B01G096400 chrUn 94.706 680 28 5 2477 3154 243543272 243543945 0.000000e+00 1050
34 TraesCS1B01G096400 chr7B 91.477 176 10 1 723 893 747323483 747323308 1.460000e-58 237


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 TraesCS1B01G096400 chr1B 100540434 100543587 3153 False 5825.000000 5825 100.000000 1 3154 1 chr1B.!!$F3 3153
1 TraesCS1B01G096400 chr1B 443991939 443992844 905 True 1657.000000 1657 99.669000 1 906 1 chr1B.!!$R3 905
2 TraesCS1B01G096400 chr1B 674129724 674130401 677 True 1114.000000 1114 96.324000 2477 3154 1 chr1B.!!$R4 677
3 TraesCS1B01G096400 chr1B 663677072 663677746 674 False 1050.000000 1050 94.721000 2477 3154 1 chr1B.!!$F6 677
4 TraesCS1B01G096400 chr1B 65606276 65607095 819 True 955.000000 955 88.090000 87 906 1 chr1B.!!$R1 819
5 TraesCS1B01G096400 chr1B 100630947 100632300 1353 False 926.500000 1478 90.102000 907 2297 2 chr1B.!!$F7 1390
6 TraesCS1B01G096400 chr1B 101142964 101144245 1281 False 666.500000 1007 87.066000 986 2295 2 chr1B.!!$F8 1309
7 TraesCS1B01G096400 chr1A 61032264 61033754 1490 False 2206.000000 2206 93.378000 988 2479 1 chr1A.!!$F2 1491
8 TraesCS1B01G096400 chr1A 61284125 61285614 1489 False 2154.000000 2154 92.776000 986 2476 1 chr1A.!!$F5 1490
9 TraesCS1B01G096400 chr1A 61341078 61342598 1520 False 1076.000000 1701 91.839000 907 2479 2 chr1A.!!$F6 1572
10 TraesCS1B01G096400 chr1A 62249761 62254728 4967 True 517.666667 1029 83.980333 986 2295 3 chr1A.!!$R1 1309
11 TraesCS1B01G096400 chr1D 62935682 62937216 1534 False 2202.000000 2202 92.571000 941 2479 1 chr1D.!!$F2 1538
12 TraesCS1B01G096400 chr1D 63357323 63358314 991 False 1081.000000 1081 86.527000 1308 2295 1 chr1D.!!$F3 987
13 TraesCS1B01G096400 chr3B 764643587 764644268 681 True 1098.000000 1098 95.760000 2475 3154 1 chr3B.!!$R1 679
14 TraesCS1B01G096400 chr3B 732331018 732331696 678 False 1072.000000 1072 95.175000 2475 3154 1 chr3B.!!$F2 679
15 TraesCS1B01G096400 chr3B 671952105 671952774 669 False 1061.000000 1061 95.126000 2477 3153 1 chr3B.!!$F1 676
16 TraesCS1B01G096400 chr2B 727294911 727295591 680 True 1088.000000 1088 95.601000 2477 3154 1 chr2B.!!$R1 677
17 TraesCS1B01G096400 chr5B 404461787 404462467 680 True 1079.000000 1079 95.315000 2476 3154 1 chr5B.!!$R1 678
18 TraesCS1B01G096400 chr5B 686033148 686033825 677 False 1075.000000 1075 95.315000 2476 3154 1 chr5B.!!$F1 678
19 TraesCS1B01G096400 chrUn 243543272 243543945 673 False 1050.000000 1050 94.706000 2477 3154 1 chrUn.!!$F1 677

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
815 843 0.249238 CAGTAGCGAGAGTGGATGCC 60.249 60.0 0.00 0.00 0.00 4.40 F
867 895 0.249322 CCTAGATTGGGTACGCACGG 60.249 60.0 12.81 4.79 0.00 4.94 F
898 926 0.531200 GAGACGGTCTCCACGGAATT 59.469 55.0 24.41 0.00 37.55 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 2018 0.033920 GGTCGTTAGGGTTGTCCGTT 59.966 55.0 0.00 0.00 41.52 4.44 R
1915 2068 0.184933 CTGGTTGTCAAACTCCCCCA 59.815 55.0 1.59 0.00 36.48 4.96 R
2613 4305 0.672889 TAGTTCGTGCCACGTGGTTA 59.327 50.0 33.92 21.37 43.14 2.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
576 604 4.899239 CTCTGATGCCGGCGGGTC 62.899 72.222 29.48 19.63 34.97 4.46
695 723 3.442996 CGCTGAACAGGGGAACTAG 57.557 57.895 10.36 0.00 37.68 2.57
696 724 0.895530 CGCTGAACAGGGGAACTAGA 59.104 55.000 10.36 0.00 37.68 2.43
697 725 1.482593 CGCTGAACAGGGGAACTAGAT 59.517 52.381 10.36 0.00 37.68 1.98
698 726 2.739932 CGCTGAACAGGGGAACTAGATG 60.740 54.545 10.36 0.00 37.68 2.90
699 727 2.420687 GCTGAACAGGGGAACTAGATGG 60.421 54.545 0.00 0.00 0.00 3.51
700 728 2.171448 CTGAACAGGGGAACTAGATGGG 59.829 54.545 0.00 0.00 0.00 4.00
701 729 2.225779 TGAACAGGGGAACTAGATGGGA 60.226 50.000 0.00 0.00 0.00 4.37
702 730 2.897823 ACAGGGGAACTAGATGGGAT 57.102 50.000 0.00 0.00 0.00 3.85
703 731 2.412591 ACAGGGGAACTAGATGGGATG 58.587 52.381 0.00 0.00 0.00 3.51
704 732 2.022035 ACAGGGGAACTAGATGGGATGA 60.022 50.000 0.00 0.00 0.00 2.92
705 733 3.254960 CAGGGGAACTAGATGGGATGAT 58.745 50.000 0.00 0.00 0.00 2.45
706 734 3.008813 CAGGGGAACTAGATGGGATGATG 59.991 52.174 0.00 0.00 0.00 3.07
707 735 2.982488 GGGGAACTAGATGGGATGATGT 59.018 50.000 0.00 0.00 0.00 3.06
708 736 3.395941 GGGGAACTAGATGGGATGATGTT 59.604 47.826 0.00 0.00 0.00 2.71
709 737 4.505742 GGGGAACTAGATGGGATGATGTTC 60.506 50.000 0.00 0.00 33.70 3.18
710 738 4.349342 GGGAACTAGATGGGATGATGTTCT 59.651 45.833 0.00 0.00 34.55 3.01
711 739 5.303971 GGAACTAGATGGGATGATGTTCTG 58.696 45.833 0.00 0.00 34.55 3.02
712 740 5.163258 GGAACTAGATGGGATGATGTTCTGT 60.163 44.000 0.00 0.00 34.55 3.41
713 741 5.543507 ACTAGATGGGATGATGTTCTGTC 57.456 43.478 0.00 0.00 0.00 3.51
714 742 5.215069 ACTAGATGGGATGATGTTCTGTCT 58.785 41.667 0.00 0.00 0.00 3.41
715 743 4.686191 AGATGGGATGATGTTCTGTCTC 57.314 45.455 0.00 0.00 0.00 3.36
716 744 2.967599 TGGGATGATGTTCTGTCTCG 57.032 50.000 0.00 0.00 0.00 4.04
717 745 2.179427 TGGGATGATGTTCTGTCTCGT 58.821 47.619 0.00 0.00 0.00 4.18
718 746 2.094026 TGGGATGATGTTCTGTCTCGTG 60.094 50.000 0.00 0.00 0.00 4.35
719 747 2.166459 GGGATGATGTTCTGTCTCGTGA 59.834 50.000 0.00 0.00 0.00 4.35
720 748 3.443037 GGATGATGTTCTGTCTCGTGAG 58.557 50.000 0.00 0.00 0.00 3.51
721 749 3.119316 GGATGATGTTCTGTCTCGTGAGT 60.119 47.826 0.00 0.00 0.00 3.41
722 750 3.288809 TGATGTTCTGTCTCGTGAGTG 57.711 47.619 0.00 0.00 0.00 3.51
723 751 2.884639 TGATGTTCTGTCTCGTGAGTGA 59.115 45.455 0.00 0.00 0.00 3.41
724 752 3.057946 TGATGTTCTGTCTCGTGAGTGAG 60.058 47.826 0.00 0.00 37.33 3.51
725 753 1.001268 TGTTCTGTCTCGTGAGTGAGC 60.001 52.381 0.00 0.00 35.90 4.26
726 754 0.598562 TTCTGTCTCGTGAGTGAGCC 59.401 55.000 0.00 0.00 35.90 4.70
727 755 1.154131 CTGTCTCGTGAGTGAGCCG 60.154 63.158 0.00 0.00 35.90 5.52
728 756 1.578206 CTGTCTCGTGAGTGAGCCGA 61.578 60.000 0.00 0.00 35.90 5.54
729 757 0.960861 TGTCTCGTGAGTGAGCCGAT 60.961 55.000 0.00 0.00 35.90 4.18
730 758 0.524392 GTCTCGTGAGTGAGCCGATG 60.524 60.000 0.00 0.00 35.90 3.84
731 759 0.960861 TCTCGTGAGTGAGCCGATGT 60.961 55.000 0.00 0.00 35.90 3.06
732 760 0.524392 CTCGTGAGTGAGCCGATGTC 60.524 60.000 0.00 0.00 0.00 3.06
733 761 1.869574 CGTGAGTGAGCCGATGTCG 60.870 63.158 0.00 0.00 39.44 4.35
734 762 2.161486 GTGAGTGAGCCGATGTCGC 61.161 63.158 0.00 0.00 38.18 5.19
735 763 2.181777 GAGTGAGCCGATGTCGCA 59.818 61.111 0.00 0.00 38.18 5.10
736 764 1.875813 GAGTGAGCCGATGTCGCAG 60.876 63.158 0.00 0.00 38.18 5.18
737 765 3.558411 GTGAGCCGATGTCGCAGC 61.558 66.667 0.00 0.00 38.18 5.25
745 773 4.819761 ATGTCGCAGCGTGCCGAT 62.820 61.111 15.93 0.00 41.12 4.18
758 786 3.586961 CCGATCGAGCCGAGCAGA 61.587 66.667 18.66 0.00 42.67 4.26
759 787 2.409243 CGATCGAGCCGAGCAGAA 59.591 61.111 10.26 0.00 42.67 3.02
760 788 1.656875 CGATCGAGCCGAGCAGAAG 60.657 63.158 10.26 0.00 42.67 2.85
761 789 1.948635 GATCGAGCCGAGCAGAAGC 60.949 63.158 7.77 0.00 42.09 3.86
771 799 4.090057 GCAGAAGCGCGGGTTCAC 62.090 66.667 8.83 3.37 41.76 3.18
772 800 3.777925 CAGAAGCGCGGGTTCACG 61.778 66.667 8.83 2.34 41.76 4.35
784 812 3.725459 TTCACGCGAGCCGACGTA 61.725 61.111 15.93 0.00 37.46 3.57
785 813 3.252665 TTCACGCGAGCCGACGTAA 62.253 57.895 15.93 0.00 37.46 3.18
786 814 2.730006 TTCACGCGAGCCGACGTAAA 62.730 55.000 15.93 6.46 37.46 2.01
787 815 2.503375 ACGCGAGCCGACGTAAAG 60.503 61.111 15.93 0.00 37.68 1.85
788 816 3.245315 CGCGAGCCGACGTAAAGG 61.245 66.667 0.00 0.00 40.02 3.11
789 817 2.180017 GCGAGCCGACGTAAAGGA 59.820 61.111 8.21 0.00 35.59 3.36
790 818 1.872679 GCGAGCCGACGTAAAGGAG 60.873 63.158 8.21 0.90 35.59 3.69
791 819 1.872679 CGAGCCGACGTAAAGGAGC 60.873 63.158 8.21 0.00 0.00 4.70
792 820 1.518792 GAGCCGACGTAAAGGAGCC 60.519 63.158 8.21 0.00 0.00 4.70
793 821 2.510918 GCCGACGTAAAGGAGCCC 60.511 66.667 8.21 0.00 0.00 5.19
794 822 3.015312 GCCGACGTAAAGGAGCCCT 62.015 63.158 8.21 0.00 33.87 5.19
795 823 1.153628 CCGACGTAAAGGAGCCCTG 60.154 63.158 0.00 0.00 32.13 4.45
796 824 1.810030 CGACGTAAAGGAGCCCTGC 60.810 63.158 0.00 0.00 32.13 4.85
797 825 1.295423 GACGTAAAGGAGCCCTGCA 59.705 57.895 0.00 0.00 32.13 4.41
798 826 0.741221 GACGTAAAGGAGCCCTGCAG 60.741 60.000 6.78 6.78 32.13 4.41
799 827 1.296715 CGTAAAGGAGCCCTGCAGT 59.703 57.895 13.81 0.00 32.13 4.40
800 828 0.535335 CGTAAAGGAGCCCTGCAGTA 59.465 55.000 13.81 0.00 32.13 2.74
801 829 1.471676 CGTAAAGGAGCCCTGCAGTAG 60.472 57.143 13.81 4.69 32.13 2.57
802 830 0.541863 TAAAGGAGCCCTGCAGTAGC 59.458 55.000 13.81 15.15 42.57 3.58
803 831 2.527951 AAAGGAGCCCTGCAGTAGCG 62.528 60.000 13.81 0.00 46.23 4.26
804 832 3.461773 GGAGCCCTGCAGTAGCGA 61.462 66.667 13.81 0.00 46.23 4.93
805 833 2.105930 GAGCCCTGCAGTAGCGAG 59.894 66.667 13.81 0.00 46.23 5.03
806 834 2.363018 AGCCCTGCAGTAGCGAGA 60.363 61.111 13.81 0.00 46.23 4.04
807 835 2.105930 GCCCTGCAGTAGCGAGAG 59.894 66.667 13.81 0.00 46.23 3.20
808 836 2.716017 GCCCTGCAGTAGCGAGAGT 61.716 63.158 13.81 0.00 46.23 3.24
809 837 1.140589 CCCTGCAGTAGCGAGAGTG 59.859 63.158 13.81 0.00 46.23 3.51
810 838 1.140589 CCTGCAGTAGCGAGAGTGG 59.859 63.158 13.81 0.00 46.23 4.00
811 839 1.315981 CCTGCAGTAGCGAGAGTGGA 61.316 60.000 13.81 0.00 46.23 4.02
812 840 0.743688 CTGCAGTAGCGAGAGTGGAT 59.256 55.000 5.25 0.00 46.23 3.41
813 841 0.457443 TGCAGTAGCGAGAGTGGATG 59.543 55.000 0.00 0.00 46.23 3.51
814 842 0.873743 GCAGTAGCGAGAGTGGATGC 60.874 60.000 0.00 0.00 0.00 3.91
815 843 0.249238 CAGTAGCGAGAGTGGATGCC 60.249 60.000 0.00 0.00 0.00 4.40
816 844 1.299468 GTAGCGAGAGTGGATGCCG 60.299 63.158 0.00 0.00 0.00 5.69
817 845 1.753078 TAGCGAGAGTGGATGCCGT 60.753 57.895 0.00 0.00 0.00 5.68
818 846 2.004808 TAGCGAGAGTGGATGCCGTG 62.005 60.000 0.00 0.00 0.00 4.94
819 847 2.202797 CGAGAGTGGATGCCGTGG 60.203 66.667 0.00 0.00 0.00 4.94
820 848 2.187946 GAGAGTGGATGCCGTGGG 59.812 66.667 0.00 0.00 0.00 4.61
821 849 2.284625 AGAGTGGATGCCGTGGGA 60.285 61.111 0.00 0.00 0.00 4.37
822 850 1.690219 GAGAGTGGATGCCGTGGGAT 61.690 60.000 0.00 0.00 0.00 3.85
823 851 1.524621 GAGTGGATGCCGTGGGATG 60.525 63.158 0.00 0.00 0.00 3.51
824 852 3.211963 GTGGATGCCGTGGGATGC 61.212 66.667 4.94 4.94 35.10 3.91
825 853 3.726144 TGGATGCCGTGGGATGCA 61.726 61.111 10.44 10.44 41.31 3.96
826 854 2.440065 GGATGCCGTGGGATGCAA 60.440 61.111 7.02 0.00 41.50 4.08
827 855 1.829533 GGATGCCGTGGGATGCAAT 60.830 57.895 7.02 0.00 41.50 3.56
828 856 1.656441 GATGCCGTGGGATGCAATC 59.344 57.895 0.00 0.00 44.55 2.67
829 857 2.121564 GATGCCGTGGGATGCAATCG 62.122 60.000 0.00 0.00 46.86 3.34
830 858 3.585990 GCCGTGGGATGCAATCGG 61.586 66.667 11.86 11.86 46.86 4.18
831 859 2.901840 CCGTGGGATGCAATCGGG 60.902 66.667 0.00 0.00 46.86 5.14
832 860 2.901840 CGTGGGATGCAATCGGGG 60.902 66.667 0.00 0.00 46.86 5.73
833 861 2.519302 GTGGGATGCAATCGGGGG 60.519 66.667 0.00 0.00 46.86 5.40
834 862 2.694240 TGGGATGCAATCGGGGGA 60.694 61.111 0.00 0.00 46.86 4.81
835 863 2.203351 GGGATGCAATCGGGGGAC 60.203 66.667 0.00 0.00 46.86 4.46
836 864 2.595095 GGATGCAATCGGGGGACA 59.405 61.111 0.00 0.00 46.86 4.02
837 865 1.823899 GGATGCAATCGGGGGACAC 60.824 63.158 0.00 0.00 46.86 3.67
838 866 2.124736 ATGCAATCGGGGGACACG 60.125 61.111 0.00 0.00 0.00 4.49
839 867 2.869503 GATGCAATCGGGGGACACGT 62.870 60.000 0.00 0.00 31.13 4.49
840 868 3.124921 GCAATCGGGGGACACGTG 61.125 66.667 15.48 15.48 0.00 4.49
841 869 2.435938 CAATCGGGGGACACGTGG 60.436 66.667 21.57 0.08 0.00 4.94
842 870 4.404098 AATCGGGGGACACGTGGC 62.404 66.667 21.57 18.48 0.00 5.01
847 875 4.157120 GGGGACACGTGGCGCTAT 62.157 66.667 33.92 6.07 36.11 2.97
848 876 2.585247 GGGACACGTGGCGCTATC 60.585 66.667 29.55 11.89 32.59 2.08
849 877 2.585247 GGACACGTGGCGCTATCC 60.585 66.667 21.57 12.60 0.00 2.59
850 878 2.494918 GACACGTGGCGCTATCCT 59.505 61.111 21.57 0.00 0.00 3.24
851 879 1.731433 GGACACGTGGCGCTATCCTA 61.731 60.000 21.57 0.00 0.00 2.94
852 880 0.317938 GACACGTGGCGCTATCCTAG 60.318 60.000 21.57 0.00 0.00 3.02
853 881 0.750546 ACACGTGGCGCTATCCTAGA 60.751 55.000 21.57 0.00 0.00 2.43
854 882 0.598562 CACGTGGCGCTATCCTAGAT 59.401 55.000 7.95 0.00 0.00 1.98
855 883 1.000163 CACGTGGCGCTATCCTAGATT 60.000 52.381 7.95 0.00 0.00 2.40
856 884 1.000163 ACGTGGCGCTATCCTAGATTG 60.000 52.381 7.64 0.00 0.00 2.67
857 885 1.670087 CGTGGCGCTATCCTAGATTGG 60.670 57.143 7.64 0.00 0.00 3.16
858 886 0.976641 TGGCGCTATCCTAGATTGGG 59.023 55.000 7.64 0.06 0.00 4.12
859 887 0.977395 GGCGCTATCCTAGATTGGGT 59.023 55.000 7.64 0.00 0.00 4.51
860 888 2.176889 GGCGCTATCCTAGATTGGGTA 58.823 52.381 7.64 0.00 0.00 3.69
861 889 2.094130 GGCGCTATCCTAGATTGGGTAC 60.094 54.545 7.64 0.00 0.00 3.34
862 890 2.415625 GCGCTATCCTAGATTGGGTACG 60.416 54.545 0.00 0.00 0.00 3.67
863 891 2.415625 CGCTATCCTAGATTGGGTACGC 60.416 54.545 2.35 2.35 0.00 4.42
864 892 2.561419 GCTATCCTAGATTGGGTACGCA 59.439 50.000 8.80 8.80 0.00 5.24
865 893 3.614390 GCTATCCTAGATTGGGTACGCAC 60.614 52.174 12.81 2.12 0.00 5.34
866 894 0.742505 TCCTAGATTGGGTACGCACG 59.257 55.000 12.81 0.00 0.00 5.34
867 895 0.249322 CCTAGATTGGGTACGCACGG 60.249 60.000 12.81 4.79 0.00 4.94
868 896 0.249322 CTAGATTGGGTACGCACGGG 60.249 60.000 12.81 0.00 0.00 5.28
869 897 0.683828 TAGATTGGGTACGCACGGGA 60.684 55.000 12.81 0.00 0.00 5.14
870 898 1.520787 GATTGGGTACGCACGGGAG 60.521 63.158 12.81 0.00 0.00 4.30
871 899 2.918230 GATTGGGTACGCACGGGAGG 62.918 65.000 12.81 0.00 0.00 4.30
872 900 4.682334 TGGGTACGCACGGGAGGA 62.682 66.667 8.80 0.00 0.00 3.71
873 901 3.834799 GGGTACGCACGGGAGGAG 61.835 72.222 4.83 0.00 0.00 3.69
874 902 4.509737 GGTACGCACGGGAGGAGC 62.510 72.222 0.00 0.00 0.00 4.70
875 903 4.509737 GTACGCACGGGAGGAGCC 62.510 72.222 0.00 0.00 0.00 4.70
884 912 3.151022 GGAGGAGCCCTGGAGACG 61.151 72.222 0.00 0.00 31.76 4.18
885 913 3.151022 GAGGAGCCCTGGAGACGG 61.151 72.222 0.00 0.00 31.76 4.79
886 914 3.966930 GAGGAGCCCTGGAGACGGT 62.967 68.421 0.00 0.00 31.76 4.83
887 915 3.462678 GGAGCCCTGGAGACGGTC 61.463 72.222 0.00 0.00 33.66 4.79
888 916 2.363147 GAGCCCTGGAGACGGTCT 60.363 66.667 11.09 11.09 33.66 3.85
889 917 2.363147 AGCCCTGGAGACGGTCTC 60.363 66.667 26.28 26.28 42.66 3.36
896 924 3.677527 GAGACGGTCTCCACGGAA 58.322 61.111 24.41 0.00 37.55 4.30
897 925 2.190756 GAGACGGTCTCCACGGAAT 58.809 57.895 24.41 0.00 37.55 3.01
898 926 0.531200 GAGACGGTCTCCACGGAATT 59.469 55.000 24.41 0.00 37.55 2.17
899 927 0.974383 AGACGGTCTCCACGGAATTT 59.026 50.000 4.45 0.00 35.23 1.82
900 928 1.346722 AGACGGTCTCCACGGAATTTT 59.653 47.619 4.45 0.00 35.23 1.82
901 929 2.148768 GACGGTCTCCACGGAATTTTT 58.851 47.619 0.00 0.00 35.23 1.94
930 958 4.248859 TCACAACAGCAATCTCTAGCTTC 58.751 43.478 0.00 0.00 39.50 3.86
931 959 3.373439 CACAACAGCAATCTCTAGCTTCC 59.627 47.826 0.00 0.00 39.50 3.46
932 960 3.008375 ACAACAGCAATCTCTAGCTTCCA 59.992 43.478 0.00 0.00 39.50 3.53
934 962 3.102972 ACAGCAATCTCTAGCTTCCAGA 58.897 45.455 0.00 0.00 39.50 3.86
935 963 3.118811 ACAGCAATCTCTAGCTTCCAGAC 60.119 47.826 0.00 0.00 39.50 3.51
936 964 2.433970 AGCAATCTCTAGCTTCCAGACC 59.566 50.000 0.00 0.00 38.01 3.85
937 965 2.169352 GCAATCTCTAGCTTCCAGACCA 59.831 50.000 0.00 0.00 0.00 4.02
938 966 3.791245 CAATCTCTAGCTTCCAGACCAC 58.209 50.000 0.00 0.00 0.00 4.16
939 967 1.464734 TCTCTAGCTTCCAGACCACG 58.535 55.000 0.00 0.00 0.00 4.94
984 1012 2.143122 GCAGACCACGAAACAGATCAA 58.857 47.619 0.00 0.00 0.00 2.57
1013 1041 1.077212 CAGCCATGAGGTTCCCCAG 60.077 63.158 0.00 0.00 37.19 4.45
1021 1049 1.073284 TGAGGTTCCCCAGTTTAGTGC 59.927 52.381 0.00 0.00 0.00 4.40
1326 1476 1.202065 GCCACGTGAACATGCATGTAG 60.202 52.381 31.55 23.15 40.80 2.74
1348 1499 7.828717 TGTAGCTGATCTGACCATTGATTTTTA 59.171 33.333 3.42 0.00 0.00 1.52
1354 1505 8.252417 TGATCTGACCATTGATTTTTATGTTGG 58.748 33.333 0.00 0.00 0.00 3.77
1370 1521 0.533308 TTGGTTGACACGTGTAGGGC 60.533 55.000 23.44 9.83 0.00 5.19
1657 1808 2.819595 CGTGCCATTCCCGACTGG 60.820 66.667 0.00 0.00 35.53 4.00
1769 1922 1.483595 CCCACTGCTCCTCCTTCACA 61.484 60.000 0.00 0.00 0.00 3.58
1779 1932 0.877071 CTCCTTCACACAGCGCATTT 59.123 50.000 11.47 0.00 0.00 2.32
1790 1943 3.058983 CACAGCGCATTTACAACTTCTCA 60.059 43.478 11.47 0.00 0.00 3.27
1865 2018 2.981302 CATCAGTGCCCTCCGTCA 59.019 61.111 0.00 0.00 0.00 4.35
1879 2032 3.591979 CGTCAACGGACAACCCTAA 57.408 52.632 0.00 0.00 44.54 2.69
1952 2105 6.039717 ACAACCAGTACTTCAAGAACGTACTA 59.960 38.462 16.97 0.00 41.19 1.82
2150 2303 0.307760 GCTTTGTCGTCAACCACCAG 59.692 55.000 0.00 0.00 32.93 4.00
2256 2424 8.783093 TCAGTGTATGTAATTTGACTTTCCAAG 58.217 33.333 0.00 0.00 0.00 3.61
2265 2433 6.729690 ATTTGACTTTCCAAGGTGATTTCA 57.270 33.333 0.00 0.00 0.00 2.69
2288 2456 7.644490 TCATTGTTAGTTGTTTGTGTATGTCC 58.356 34.615 0.00 0.00 0.00 4.02
2308 2590 5.478679 TGTCCAAAAGAGTTTTTCTTCCACA 59.521 36.000 0.00 0.00 45.41 4.17
2315 2598 4.094442 AGAGTTTTTCTTCCACACGTCAAC 59.906 41.667 0.00 0.00 29.61 3.18
2360 2643 1.399440 ACTAATGTGCATGCAAGCTCG 59.601 47.619 24.58 13.49 34.99 5.03
2361 2644 1.667212 CTAATGTGCATGCAAGCTCGA 59.333 47.619 24.58 5.03 34.99 4.04
2362 2645 1.100510 AATGTGCATGCAAGCTCGAT 58.899 45.000 24.58 4.92 34.99 3.59
2363 2646 0.661552 ATGTGCATGCAAGCTCGATC 59.338 50.000 24.58 7.90 34.99 3.69
2386 2670 7.380431 TCAAGGACAAACTAAAACGAAAGAA 57.620 32.000 0.00 0.00 0.00 2.52
2389 2673 9.083080 CAAGGACAAACTAAAACGAAAGAAATT 57.917 29.630 0.00 0.00 0.00 1.82
2503 2843 0.392998 CAGAACCGGGCAATAGCACT 60.393 55.000 6.32 0.00 43.86 4.40
2613 4305 1.372307 CGAACCGGTGGTAAAGGGT 59.628 57.895 8.52 0.00 33.12 4.34
2629 4321 1.594836 GGTAACCACGTGGCACGAA 60.595 57.895 42.65 20.52 46.05 3.85
2662 4354 0.909623 GCTGGAGCCCTTTAGTACCA 59.090 55.000 0.00 0.00 34.31 3.25
2801 4668 7.641020 CGATACTACACATTGTACACGTTATGA 59.359 37.037 11.34 0.00 0.00 2.15
3063 6134 3.371595 CCCTTCGGATTTATGACCTGGTT 60.372 47.826 0.00 0.00 0.00 3.67
3139 6210 1.038130 GCTTCTCCCGCACCTCTCTA 61.038 60.000 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
576 604 1.869754 CGTCCATGGGATAGTTGCTCG 60.870 57.143 13.02 0.00 32.73 5.03
693 721 4.279420 CGAGACAGAACATCATCCCATCTA 59.721 45.833 0.00 0.00 0.00 1.98
694 722 3.069300 CGAGACAGAACATCATCCCATCT 59.931 47.826 0.00 0.00 0.00 2.90
695 723 3.181471 ACGAGACAGAACATCATCCCATC 60.181 47.826 0.00 0.00 0.00 3.51
696 724 2.768527 ACGAGACAGAACATCATCCCAT 59.231 45.455 0.00 0.00 0.00 4.00
697 725 2.094026 CACGAGACAGAACATCATCCCA 60.094 50.000 0.00 0.00 0.00 4.37
698 726 2.166459 TCACGAGACAGAACATCATCCC 59.834 50.000 0.00 0.00 0.00 3.85
699 727 3.119316 ACTCACGAGACAGAACATCATCC 60.119 47.826 0.00 0.00 0.00 3.51
700 728 3.856521 CACTCACGAGACAGAACATCATC 59.143 47.826 0.00 0.00 0.00 2.92
701 729 3.507622 TCACTCACGAGACAGAACATCAT 59.492 43.478 0.00 0.00 0.00 2.45
702 730 2.884639 TCACTCACGAGACAGAACATCA 59.115 45.455 0.00 0.00 0.00 3.07
703 731 3.497118 CTCACTCACGAGACAGAACATC 58.503 50.000 0.00 0.00 34.79 3.06
704 732 2.352225 GCTCACTCACGAGACAGAACAT 60.352 50.000 0.00 0.00 34.79 2.71
705 733 1.001268 GCTCACTCACGAGACAGAACA 60.001 52.381 0.00 0.00 34.79 3.18
706 734 1.667467 GGCTCACTCACGAGACAGAAC 60.667 57.143 0.00 0.00 41.08 3.01
707 735 0.598562 GGCTCACTCACGAGACAGAA 59.401 55.000 0.00 0.00 41.08 3.02
708 736 1.578206 CGGCTCACTCACGAGACAGA 61.578 60.000 0.00 0.00 41.53 3.41
709 737 1.154131 CGGCTCACTCACGAGACAG 60.154 63.158 0.00 0.00 41.53 3.51
710 738 0.960861 ATCGGCTCACTCACGAGACA 60.961 55.000 0.00 0.00 41.53 3.41
711 739 0.524392 CATCGGCTCACTCACGAGAC 60.524 60.000 0.00 0.00 40.21 3.36
712 740 0.960861 ACATCGGCTCACTCACGAGA 60.961 55.000 0.00 0.00 40.21 4.04
713 741 0.524392 GACATCGGCTCACTCACGAG 60.524 60.000 0.00 0.00 40.21 4.18
714 742 1.506718 GACATCGGCTCACTCACGA 59.493 57.895 0.00 0.00 41.20 4.35
715 743 1.869574 CGACATCGGCTCACTCACG 60.870 63.158 0.00 0.00 35.37 4.35
716 744 2.161486 GCGACATCGGCTCACTCAC 61.161 63.158 3.08 0.00 40.23 3.51
717 745 2.181777 GCGACATCGGCTCACTCA 59.818 61.111 3.08 0.00 40.23 3.41
718 746 1.875813 CTGCGACATCGGCTCACTC 60.876 63.158 3.08 0.00 40.23 3.51
719 747 2.182791 CTGCGACATCGGCTCACT 59.817 61.111 3.08 0.00 40.23 3.41
720 748 3.558411 GCTGCGACATCGGCTCAC 61.558 66.667 3.08 0.00 40.23 3.51
741 769 2.997621 CTTCTGCTCGGCTCGATCGG 62.998 65.000 16.41 7.26 34.61 4.18
742 770 1.656875 CTTCTGCTCGGCTCGATCG 60.657 63.158 9.36 9.36 34.61 3.69
743 771 1.948635 GCTTCTGCTCGGCTCGATC 60.949 63.158 0.00 0.00 34.61 3.69
744 772 2.105930 GCTTCTGCTCGGCTCGAT 59.894 61.111 0.00 0.00 34.61 3.59
745 773 4.482684 CGCTTCTGCTCGGCTCGA 62.483 66.667 0.00 0.00 36.97 4.04
752 780 3.491652 GAACCCGCGCTTCTGCTC 61.492 66.667 5.56 0.00 36.97 4.26
753 781 4.314440 TGAACCCGCGCTTCTGCT 62.314 61.111 5.56 0.00 36.97 4.24
754 782 4.090057 GTGAACCCGCGCTTCTGC 62.090 66.667 5.56 0.00 0.00 4.26
755 783 3.777925 CGTGAACCCGCGCTTCTG 61.778 66.667 5.56 0.00 39.55 3.02
766 794 3.933900 TACGTCGGCTCGCGTGAAC 62.934 63.158 13.13 5.62 39.08 3.18
767 795 2.730006 TTTACGTCGGCTCGCGTGAA 62.730 55.000 13.13 15.81 39.08 3.18
768 796 3.252665 TTTACGTCGGCTCGCGTGA 62.253 57.895 13.13 0.00 39.08 4.35
769 797 2.774951 CTTTACGTCGGCTCGCGTG 61.775 63.158 5.77 4.44 39.08 5.34
770 798 2.503375 CTTTACGTCGGCTCGCGT 60.503 61.111 5.77 16.02 40.80 6.01
771 799 3.245315 CCTTTACGTCGGCTCGCG 61.245 66.667 0.00 0.00 34.10 5.87
772 800 1.872679 CTCCTTTACGTCGGCTCGC 60.873 63.158 0.00 0.00 0.00 5.03
773 801 1.872679 GCTCCTTTACGTCGGCTCG 60.873 63.158 0.00 0.00 0.00 5.03
774 802 1.518792 GGCTCCTTTACGTCGGCTC 60.519 63.158 0.00 0.00 0.00 4.70
775 803 2.577593 GGCTCCTTTACGTCGGCT 59.422 61.111 0.00 0.00 0.00 5.52
776 804 2.510918 GGGCTCCTTTACGTCGGC 60.511 66.667 0.00 0.00 0.00 5.54
777 805 1.153628 CAGGGCTCCTTTACGTCGG 60.154 63.158 0.00 0.00 0.00 4.79
778 806 1.810030 GCAGGGCTCCTTTACGTCG 60.810 63.158 0.00 0.00 0.00 5.12
779 807 0.741221 CTGCAGGGCTCCTTTACGTC 60.741 60.000 5.57 0.00 0.00 4.34
780 808 1.296715 CTGCAGGGCTCCTTTACGT 59.703 57.895 5.57 0.00 0.00 3.57
781 809 0.535335 TACTGCAGGGCTCCTTTACG 59.465 55.000 19.93 0.00 0.00 3.18
782 810 1.744114 GCTACTGCAGGGCTCCTTTAC 60.744 57.143 19.93 0.00 39.41 2.01
783 811 0.541863 GCTACTGCAGGGCTCCTTTA 59.458 55.000 19.93 0.00 39.41 1.85
784 812 1.301293 GCTACTGCAGGGCTCCTTT 59.699 57.895 19.93 0.00 39.41 3.11
785 813 2.993853 GCTACTGCAGGGCTCCTT 59.006 61.111 19.93 0.00 39.41 3.36
786 814 3.465403 CGCTACTGCAGGGCTCCT 61.465 66.667 24.23 5.14 39.64 3.69
787 815 3.438017 CTCGCTACTGCAGGGCTCC 62.438 68.421 24.23 7.08 39.64 4.70
788 816 2.105930 CTCGCTACTGCAGGGCTC 59.894 66.667 24.23 9.17 39.64 4.70
789 817 2.363018 TCTCGCTACTGCAGGGCT 60.363 61.111 24.23 6.48 39.64 5.19
790 818 2.105930 CTCTCGCTACTGCAGGGC 59.894 66.667 19.93 19.70 39.64 5.19
791 819 1.140589 CACTCTCGCTACTGCAGGG 59.859 63.158 19.93 11.52 39.64 4.45
792 820 1.140589 CCACTCTCGCTACTGCAGG 59.859 63.158 19.93 1.57 39.64 4.85
793 821 0.743688 ATCCACTCTCGCTACTGCAG 59.256 55.000 13.48 13.48 39.64 4.41
794 822 0.457443 CATCCACTCTCGCTACTGCA 59.543 55.000 0.00 0.00 39.64 4.41
795 823 0.873743 GCATCCACTCTCGCTACTGC 60.874 60.000 0.00 0.00 0.00 4.40
796 824 0.249238 GGCATCCACTCTCGCTACTG 60.249 60.000 0.00 0.00 0.00 2.74
797 825 1.729470 CGGCATCCACTCTCGCTACT 61.729 60.000 0.00 0.00 0.00 2.57
798 826 1.299468 CGGCATCCACTCTCGCTAC 60.299 63.158 0.00 0.00 0.00 3.58
799 827 1.753078 ACGGCATCCACTCTCGCTA 60.753 57.895 0.00 0.00 0.00 4.26
800 828 3.071206 ACGGCATCCACTCTCGCT 61.071 61.111 0.00 0.00 0.00 4.93
801 829 2.887568 CACGGCATCCACTCTCGC 60.888 66.667 0.00 0.00 0.00 5.03
802 830 2.202797 CCACGGCATCCACTCTCG 60.203 66.667 0.00 0.00 0.00 4.04
803 831 1.690219 ATCCCACGGCATCCACTCTC 61.690 60.000 0.00 0.00 0.00 3.20
804 832 1.690633 ATCCCACGGCATCCACTCT 60.691 57.895 0.00 0.00 0.00 3.24
805 833 1.524621 CATCCCACGGCATCCACTC 60.525 63.158 0.00 0.00 0.00 3.51
806 834 2.591753 CATCCCACGGCATCCACT 59.408 61.111 0.00 0.00 0.00 4.00
807 835 3.211963 GCATCCCACGGCATCCAC 61.212 66.667 0.00 0.00 0.00 4.02
808 836 2.570774 ATTGCATCCCACGGCATCCA 62.571 55.000 0.00 0.00 40.17 3.41
809 837 1.799258 GATTGCATCCCACGGCATCC 61.799 60.000 0.00 0.00 40.17 3.51
810 838 1.656441 GATTGCATCCCACGGCATC 59.344 57.895 0.00 0.00 40.17 3.91
811 839 2.188829 CGATTGCATCCCACGGCAT 61.189 57.895 0.00 0.00 40.17 4.40
812 840 2.823593 CGATTGCATCCCACGGCA 60.824 61.111 0.00 0.00 38.46 5.69
813 841 3.585990 CCGATTGCATCCCACGGC 61.586 66.667 0.00 0.00 37.32 5.68
814 842 2.901840 CCCGATTGCATCCCACGG 60.902 66.667 0.00 0.00 42.67 4.94
815 843 2.901840 CCCCGATTGCATCCCACG 60.902 66.667 0.00 0.00 0.00 4.94
816 844 2.519302 CCCCCGATTGCATCCCAC 60.519 66.667 0.00 0.00 0.00 4.61
817 845 2.694240 TCCCCCGATTGCATCCCA 60.694 61.111 0.00 0.00 0.00 4.37
818 846 2.203351 GTCCCCCGATTGCATCCC 60.203 66.667 0.00 0.00 0.00 3.85
819 847 1.823899 GTGTCCCCCGATTGCATCC 60.824 63.158 0.00 0.00 0.00 3.51
820 848 2.180204 CGTGTCCCCCGATTGCATC 61.180 63.158 0.00 0.00 0.00 3.91
821 849 2.124736 CGTGTCCCCCGATTGCAT 60.125 61.111 0.00 0.00 0.00 3.96
822 850 3.632080 ACGTGTCCCCCGATTGCA 61.632 61.111 0.00 0.00 0.00 4.08
823 851 3.124921 CACGTGTCCCCCGATTGC 61.125 66.667 7.58 0.00 0.00 3.56
824 852 2.435938 CCACGTGTCCCCCGATTG 60.436 66.667 15.65 0.00 0.00 2.67
825 853 4.404098 GCCACGTGTCCCCCGATT 62.404 66.667 15.65 0.00 0.00 3.34
830 858 4.157120 ATAGCGCCACGTGTCCCC 62.157 66.667 15.65 0.00 0.00 4.81
831 859 2.585247 GATAGCGCCACGTGTCCC 60.585 66.667 15.65 1.54 0.00 4.46
832 860 1.731433 TAGGATAGCGCCACGTGTCC 61.731 60.000 15.65 13.35 0.00 4.02
833 861 0.317938 CTAGGATAGCGCCACGTGTC 60.318 60.000 15.65 0.00 0.00 3.67
834 862 0.750546 TCTAGGATAGCGCCACGTGT 60.751 55.000 15.65 0.00 38.99 4.49
835 863 0.598562 ATCTAGGATAGCGCCACGTG 59.401 55.000 9.08 9.08 38.99 4.49
836 864 1.000163 CAATCTAGGATAGCGCCACGT 60.000 52.381 2.29 0.00 38.99 4.49
837 865 1.670087 CCAATCTAGGATAGCGCCACG 60.670 57.143 2.29 0.00 38.99 4.94
838 866 1.338200 CCCAATCTAGGATAGCGCCAC 60.338 57.143 2.29 0.00 38.99 5.01
839 867 0.976641 CCCAATCTAGGATAGCGCCA 59.023 55.000 2.29 0.00 38.99 5.69
840 868 0.977395 ACCCAATCTAGGATAGCGCC 59.023 55.000 2.29 0.00 38.99 6.53
841 869 2.415625 CGTACCCAATCTAGGATAGCGC 60.416 54.545 0.00 0.00 38.99 5.92
842 870 2.415625 GCGTACCCAATCTAGGATAGCG 60.416 54.545 0.00 0.00 38.99 4.26
843 871 2.561419 TGCGTACCCAATCTAGGATAGC 59.439 50.000 0.00 0.00 38.99 2.97
844 872 3.366070 CGTGCGTACCCAATCTAGGATAG 60.366 52.174 0.00 0.00 41.04 2.08
845 873 2.555325 CGTGCGTACCCAATCTAGGATA 59.445 50.000 0.00 0.00 0.00 2.59
846 874 1.340248 CGTGCGTACCCAATCTAGGAT 59.660 52.381 0.00 0.00 0.00 3.24
847 875 0.742505 CGTGCGTACCCAATCTAGGA 59.257 55.000 0.00 0.00 0.00 2.94
848 876 0.249322 CCGTGCGTACCCAATCTAGG 60.249 60.000 0.00 0.00 0.00 3.02
849 877 0.249322 CCCGTGCGTACCCAATCTAG 60.249 60.000 0.00 0.00 0.00 2.43
850 878 0.683828 TCCCGTGCGTACCCAATCTA 60.684 55.000 0.00 0.00 0.00 1.98
851 879 1.956629 CTCCCGTGCGTACCCAATCT 61.957 60.000 0.00 0.00 0.00 2.40
852 880 1.520787 CTCCCGTGCGTACCCAATC 60.521 63.158 0.00 0.00 0.00 2.67
853 881 2.582436 CTCCCGTGCGTACCCAAT 59.418 61.111 0.00 0.00 0.00 3.16
854 882 3.697747 CCTCCCGTGCGTACCCAA 61.698 66.667 0.00 0.00 0.00 4.12
855 883 4.682334 TCCTCCCGTGCGTACCCA 62.682 66.667 0.00 0.00 0.00 4.51
856 884 3.834799 CTCCTCCCGTGCGTACCC 61.835 72.222 0.00 0.00 0.00 3.69
857 885 4.509737 GCTCCTCCCGTGCGTACC 62.510 72.222 0.00 0.00 0.00 3.34
858 886 4.509737 GGCTCCTCCCGTGCGTAC 62.510 72.222 0.00 0.00 0.00 3.67
867 895 3.151022 CGTCTCCAGGGCTCCTCC 61.151 72.222 0.00 0.00 0.00 4.30
868 896 3.151022 CCGTCTCCAGGGCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
869 897 3.966930 GACCGTCTCCAGGGCTCCT 62.967 68.421 0.00 0.00 32.85 3.69
870 898 3.462678 GACCGTCTCCAGGGCTCC 61.463 72.222 0.00 0.00 32.85 4.70
871 899 2.363147 AGACCGTCTCCAGGGCTC 60.363 66.667 0.00 0.00 46.02 4.70
879 907 0.531200 AATTCCGTGGAGACCGTCTC 59.469 55.000 18.78 18.78 42.66 3.36
880 908 0.974383 AAATTCCGTGGAGACCGTCT 59.026 50.000 0.00 0.00 0.00 4.18
881 909 1.804601 AAAATTCCGTGGAGACCGTC 58.195 50.000 0.00 0.00 0.00 4.79
882 910 2.265589 AAAAATTCCGTGGAGACCGT 57.734 45.000 0.00 0.00 0.00 4.83
899 927 4.344679 AGATTGCTGTTGTGATGGGAAAAA 59.655 37.500 0.00 0.00 0.00 1.94
900 928 3.896888 AGATTGCTGTTGTGATGGGAAAA 59.103 39.130 0.00 0.00 0.00 2.29
901 929 3.499338 AGATTGCTGTTGTGATGGGAAA 58.501 40.909 0.00 0.00 0.00 3.13
902 930 3.084039 GAGATTGCTGTTGTGATGGGAA 58.916 45.455 0.00 0.00 0.00 3.97
903 931 2.306805 AGAGATTGCTGTTGTGATGGGA 59.693 45.455 0.00 0.00 0.00 4.37
904 932 2.719739 AGAGATTGCTGTTGTGATGGG 58.280 47.619 0.00 0.00 0.00 4.00
905 933 3.311871 GCTAGAGATTGCTGTTGTGATGG 59.688 47.826 0.00 0.00 0.00 3.51
912 940 3.517100 TCTGGAAGCTAGAGATTGCTGTT 59.483 43.478 0.00 0.00 39.71 3.16
930 958 2.744202 CTCTCCAAATTTCGTGGTCTGG 59.256 50.000 0.00 0.00 37.43 3.86
931 959 2.160417 GCTCTCCAAATTTCGTGGTCTG 59.840 50.000 0.00 0.00 37.43 3.51
932 960 2.039084 AGCTCTCCAAATTTCGTGGTCT 59.961 45.455 0.00 0.00 37.43 3.85
934 962 2.568623 AGCTCTCCAAATTTCGTGGT 57.431 45.000 0.00 0.00 37.43 4.16
935 963 3.861840 TCTAGCTCTCCAAATTTCGTGG 58.138 45.455 0.00 0.00 37.51 4.94
936 964 3.308323 GCTCTAGCTCTCCAAATTTCGTG 59.692 47.826 0.00 0.00 38.21 4.35
937 965 3.055819 TGCTCTAGCTCTCCAAATTTCGT 60.056 43.478 3.26 0.00 42.66 3.85
938 966 3.525537 TGCTCTAGCTCTCCAAATTTCG 58.474 45.455 3.26 0.00 42.66 3.46
939 967 4.095632 GGTTGCTCTAGCTCTCCAAATTTC 59.904 45.833 3.26 0.00 42.66 2.17
1013 1041 1.081442 GCCCACGCAAGCACTAAAC 60.081 57.895 0.00 0.00 45.62 2.01
1300 1329 1.159285 CATGTTCACGTGGCACTGAT 58.841 50.000 17.00 1.17 0.00 2.90
1326 1476 7.486647 ACATAAAAATCAATGGTCAGATCAGC 58.513 34.615 0.00 0.00 0.00 4.26
1348 1499 2.489971 CCTACACGTGTCAACCAACAT 58.510 47.619 27.16 0.00 0.00 2.71
1354 1505 1.566018 GCAGCCCTACACGTGTCAAC 61.566 60.000 27.16 13.33 0.00 3.18
1769 1922 3.138304 TGAGAAGTTGTAAATGCGCTGT 58.862 40.909 9.73 0.00 0.00 4.40
1779 1932 2.557056 CGACCTCACCTGAGAAGTTGTA 59.443 50.000 3.73 0.00 44.74 2.41
1790 1943 2.675772 GTCCGACCGACCTCACCT 60.676 66.667 0.00 0.00 35.23 4.00
1865 2018 0.033920 GGTCGTTAGGGTTGTCCGTT 59.966 55.000 0.00 0.00 41.52 4.44
1879 2032 4.250305 GCACCACTGTGGGGTCGT 62.250 66.667 28.55 6.00 44.72 4.34
1915 2068 0.184933 CTGGTTGTCAAACTCCCCCA 59.815 55.000 1.59 0.00 36.48 4.96
1980 2133 0.977395 GGGCTGGTGAGTAGTGTCTT 59.023 55.000 0.00 0.00 0.00 3.01
2150 2303 8.044060 TGAATGACTTTGGAATGATTGACTAC 57.956 34.615 0.00 0.00 0.00 2.73
2256 2424 7.491048 ACACAAACAACTAACAATGAAATCACC 59.509 33.333 0.00 0.00 0.00 4.02
2265 2433 7.575414 TGGACATACACAAACAACTAACAAT 57.425 32.000 0.00 0.00 0.00 2.71
2288 2456 5.399013 ACGTGTGGAAGAAAAACTCTTTTG 58.601 37.500 0.00 0.00 44.82 2.44
2315 2598 9.478019 GTCAAAACTCATAACATCATCTTTACG 57.522 33.333 0.00 0.00 0.00 3.18
2360 2643 7.636326 TCTTTCGTTTTAGTTTGTCCTTGATC 58.364 34.615 0.00 0.00 0.00 2.92
2361 2644 7.562454 TCTTTCGTTTTAGTTTGTCCTTGAT 57.438 32.000 0.00 0.00 0.00 2.57
2362 2645 6.988622 TCTTTCGTTTTAGTTTGTCCTTGA 57.011 33.333 0.00 0.00 0.00 3.02
2363 2646 8.628882 ATTTCTTTCGTTTTAGTTTGTCCTTG 57.371 30.769 0.00 0.00 0.00 3.61
2386 2670 7.485913 GCGATGTGAATTGTTTATGAGTGAATT 59.514 33.333 0.00 0.00 0.00 2.17
2389 2673 5.643348 AGCGATGTGAATTGTTTATGAGTGA 59.357 36.000 0.00 0.00 0.00 3.41
2462 2797 5.178061 TGCACTAGTGTAGTTTGGATGATG 58.822 41.667 23.44 0.00 36.76 3.07
2503 2843 3.404899 CACTAAAGGGCTTTACGAACCA 58.595 45.455 0.00 0.00 34.23 3.67
2574 4265 2.028748 GTGCTGAACCGGTACTAAAGGA 60.029 50.000 8.00 0.00 0.00 3.36
2613 4305 0.672889 TAGTTCGTGCCACGTGGTTA 59.327 50.000 33.92 21.37 43.14 2.85
2758 4625 7.818446 TGTAGTATCGTAAAATACCAGCAAACA 59.182 33.333 0.00 0.00 33.42 2.83
3063 6134 3.130340 GGAAATAGCGGGATTTTTGCTCA 59.870 43.478 0.00 0.00 40.06 4.26


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

AutoCloner maintained by Alex Coulton.