Multiple sequence alignment - TraesCS2A01G472400

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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 TraesCS2A01G472400 chr2A 100.000 4046 0 0 1 4046 714023409 714019364 0.000000e+00 7472.0
1 TraesCS2A01G472400 chr2B 92.197 1384 85 11 2677 4046 692071878 692070504 0.000000e+00 1936.0
2 TraesCS2A01G472400 chr2B 95.354 947 34 3 886 1828 692074079 692073139 0.000000e+00 1496.0
3 TraesCS2A01G472400 chr2B 85.087 865 95 22 1836 2680 692072958 692072108 0.000000e+00 852.0
4 TraesCS2A01G472400 chr6B 93.585 795 50 1 1 794 204171456 204172250 0.000000e+00 1184.0
5 TraesCS2A01G472400 chr6B 91.560 782 63 3 12 792 156405985 156406764 0.000000e+00 1075.0
6 TraesCS2A01G472400 chr5D 93.325 794 52 1 1 794 125996744 125995952 0.000000e+00 1171.0
7 TraesCS2A01G472400 chr5D 85.227 88 12 1 2019 2106 103636677 103636763 5.570000e-14 89.8
8 TraesCS2A01G472400 chr5B 92.327 782 57 3 12 792 84939044 84939823 0.000000e+00 1109.0
9 TraesCS2A01G472400 chr5B 92.190 781 57 4 12 791 255228887 255228110 0.000000e+00 1101.0
10 TraesCS2A01G472400 chr5B 91.083 785 65 5 9 790 418025338 418026120 0.000000e+00 1057.0
11 TraesCS2A01G472400 chr4A 91.614 787 58 8 9 792 624987934 624987153 0.000000e+00 1081.0
12 TraesCS2A01G472400 chrUn 91.327 784 65 3 12 794 60376947 60377728 0.000000e+00 1068.0
13 TraesCS2A01G472400 chrUn 85.124 242 33 3 1031 1272 339963321 339963559 1.120000e-60 244.0
14 TraesCS2A01G472400 chrUn 85.124 242 33 3 1031 1272 440306747 440306509 1.120000e-60 244.0
15 TraesCS2A01G472400 chrUn 84.298 242 35 3 1031 1272 306396530 306396292 2.430000e-57 233.0
16 TraesCS2A01G472400 chrUn 83.913 230 34 3 1043 1272 403564557 403564783 2.450000e-52 217.0
17 TraesCS2A01G472400 chr1B 91.421 781 60 4 12 792 592372737 592371964 0.000000e+00 1064.0
18 TraesCS2A01G472400 chr1B 85.124 242 33 3 1031 1272 689556439 689556201 1.120000e-60 244.0
19 TraesCS2A01G472400 chr1B 84.711 242 34 3 1031 1272 689505357 689505119 5.230000e-59 239.0
20 TraesCS2A01G472400 chr1B 84.711 242 34 3 1031 1272 689685140 689684902 5.230000e-59 239.0
21 TraesCS2A01G472400 chr1B 83.884 242 36 3 1031 1272 689808745 689808507 1.130000e-55 228.0
22 TraesCS2A01G472400 chr1B 86.364 88 11 1 2019 2106 525901890 525901976 1.200000e-15 95.3
23 TraesCS2A01G472400 chr1B 95.349 43 2 0 2019 2061 531122030 531122072 7.260000e-08 69.4
24 TraesCS2A01G472400 chr1D 76.329 790 139 31 1029 1792 474067862 474067095 2.950000e-101 379.0
25 TraesCS2A01G472400 chr1D 97.436 39 1 0 2019 2057 9813786 9813748 2.610000e-07 67.6
26 TraesCS2A01G472400 chr5A 86.047 86 11 1 2019 2104 94745071 94744987 1.550000e-14 91.6
27 TraesCS2A01G472400 chr5A 84.270 89 10 3 2019 2106 475530051 475530136 2.590000e-12 84.2
28 TraesCS2A01G472400 chr5A 81.319 91 16 1 2019 2109 446604123 446604034 5.610000e-09 73.1
29 TraesCS2A01G472400 chr7B 84.615 91 13 1 2019 2109 155483837 155483748 5.570000e-14 89.8
30 TraesCS2A01G472400 chr1A 97.436 39 1 0 2019 2057 11589397 11589435 2.610000e-07 67.6


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 TraesCS2A01G472400 chr2A 714019364 714023409 4045 True 7472 7472 100.000000 1 4046 1 chr2A.!!$R1 4045
1 TraesCS2A01G472400 chr2B 692070504 692074079 3575 True 1428 1936 90.879333 886 4046 3 chr2B.!!$R1 3160
2 TraesCS2A01G472400 chr6B 204171456 204172250 794 False 1184 1184 93.585000 1 794 1 chr6B.!!$F2 793
3 TraesCS2A01G472400 chr6B 156405985 156406764 779 False 1075 1075 91.560000 12 792 1 chr6B.!!$F1 780
4 TraesCS2A01G472400 chr5D 125995952 125996744 792 True 1171 1171 93.325000 1 794 1 chr5D.!!$R1 793
5 TraesCS2A01G472400 chr5B 84939044 84939823 779 False 1109 1109 92.327000 12 792 1 chr5B.!!$F1 780
6 TraesCS2A01G472400 chr5B 255228110 255228887 777 True 1101 1101 92.190000 12 791 1 chr5B.!!$R1 779
7 TraesCS2A01G472400 chr5B 418025338 418026120 782 False 1057 1057 91.083000 9 790 1 chr5B.!!$F2 781
8 TraesCS2A01G472400 chr4A 624987153 624987934 781 True 1081 1081 91.614000 9 792 1 chr4A.!!$R1 783
9 TraesCS2A01G472400 chrUn 60376947 60377728 781 False 1068 1068 91.327000 12 794 1 chrUn.!!$F1 782
10 TraesCS2A01G472400 chr1B 592371964 592372737 773 True 1064 1064 91.421000 12 792 1 chr1B.!!$R1 780
11 TraesCS2A01G472400 chr1D 474067095 474067862 767 True 379 379 76.329000 1029 1792 1 chr1D.!!$R2 763

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
271 302 0.038166 TGTCAAGGTCTTGGATGCCC 59.962 55.000 10.39 0.0 40.78 5.36 F
824 856 0.320946 TCCCGTTTTCAGTTAGCCCG 60.321 55.000 0.00 0.0 0.00 6.13 F
830 862 0.685097 TTTCAGTTAGCCCGAGTGCT 59.315 50.000 0.00 0.0 45.38 4.40 F
832 864 0.685097 TCAGTTAGCCCGAGTGCTTT 59.315 50.000 0.00 0.0 42.75 3.51 F
833 865 1.071699 TCAGTTAGCCCGAGTGCTTTT 59.928 47.619 0.00 0.0 42.75 2.27 F
1880 2107 1.073125 TGCCTTCTCCGTTGATTTGGA 59.927 47.619 0.00 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 2120 0.393808 GAGGCTATTTGTGGGCGGAA 60.394 55.000 0.00 0.0 0.0 4.30 R
2430 2683 2.050442 GCGTTTGAGTTTGCCCGG 60.050 61.111 0.00 0.0 0.0 5.73 R
2646 2899 4.098914 AGCACATTGGTTACTTCCTTCA 57.901 40.909 0.00 0.0 0.0 3.02 R
2648 2901 4.980573 TGTAGCACATTGGTTACTTCCTT 58.019 39.130 0.00 0.0 0.0 3.36 R
2765 3256 5.220472 CGTCGCAATATCTTCACACAATCTT 60.220 40.000 0.00 0.0 0.0 2.40 R
3725 4229 0.038159 CGTCCCGCCTTGGATATCTC 60.038 60.000 2.05 0.0 42.0 2.75 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
107 137 3.749064 GACTGAGCCCGTCTCGCA 61.749 66.667 0.00 0.00 44.86 5.10
109 139 3.753434 CTGAGCCCGTCTCGCACT 61.753 66.667 0.00 0.00 44.86 4.40
128 158 2.673523 GGTGCAGCAGGACAGGAT 59.326 61.111 11.86 0.00 37.91 3.24
166 197 3.003763 GGCCTCTTGGGTCTCGGT 61.004 66.667 0.00 0.00 36.61 4.69
271 302 0.038166 TGTCAAGGTCTTGGATGCCC 59.962 55.000 10.39 0.00 40.78 5.36
272 303 0.038166 GTCAAGGTCTTGGATGCCCA 59.962 55.000 10.39 0.00 40.78 5.36
341 372 0.663688 GCTTGATGCTGCCTGATGAG 59.336 55.000 0.00 0.00 38.95 2.90
349 380 2.124024 GCCTGATGAGCATGGCCA 60.124 61.111 8.56 8.56 35.83 5.36
486 517 3.118454 CGTCGCGGCCTTCATTGT 61.118 61.111 4.51 0.00 0.00 2.71
500 531 0.586319 CATTGTCCGTCGTGTTGCTT 59.414 50.000 0.00 0.00 0.00 3.91
646 677 1.742768 GGCCGAGATCTCCGATTGT 59.257 57.895 17.13 0.00 0.00 2.71
689 720 1.807139 TGCTGCGCTCAACATCTTTA 58.193 45.000 9.73 0.00 0.00 1.85
693 724 4.576053 TGCTGCGCTCAACATCTTTATATT 59.424 37.500 9.73 0.00 0.00 1.28
703 734 7.345691 TCAACATCTTTATATTCTGCCTTGGA 58.654 34.615 0.00 0.00 0.00 3.53
707 738 8.439971 ACATCTTTATATTCTGCCTTGGATGTA 58.560 33.333 0.00 0.00 38.41 2.29
721 752 3.826524 TGGATGTATGTGTTGTGTTGGT 58.173 40.909 0.00 0.00 0.00 3.67
725 756 3.348119 TGTATGTGTTGTGTTGGTGTGT 58.652 40.909 0.00 0.00 0.00 3.72
747 779 1.240256 TTGTACCGGGTTGTTGATGC 58.760 50.000 4.31 0.00 0.00 3.91
796 828 6.123871 CGAAAGTCTTTTTCGGTAAAATGC 57.876 37.500 12.72 0.00 45.17 3.56
797 829 5.683743 CGAAAGTCTTTTTCGGTAAAATGCA 59.316 36.000 12.72 0.00 45.17 3.96
798 830 6.362283 CGAAAGTCTTTTTCGGTAAAATGCAT 59.638 34.615 12.72 0.00 45.17 3.96
799 831 7.406799 AAAGTCTTTTTCGGTAAAATGCATG 57.593 32.000 0.00 0.00 35.29 4.06
800 832 6.084326 AGTCTTTTTCGGTAAAATGCATGT 57.916 33.333 0.00 0.00 35.29 3.21
801 833 7.209471 AGTCTTTTTCGGTAAAATGCATGTA 57.791 32.000 0.00 0.00 35.29 2.29
802 834 7.826690 AGTCTTTTTCGGTAAAATGCATGTAT 58.173 30.769 0.00 0.00 35.29 2.29
803 835 8.303876 AGTCTTTTTCGGTAAAATGCATGTATT 58.696 29.630 0.00 2.84 35.29 1.89
804 836 8.372521 GTCTTTTTCGGTAAAATGCATGTATTG 58.627 33.333 9.95 0.00 35.29 1.90
805 837 8.085296 TCTTTTTCGGTAAAATGCATGTATTGT 58.915 29.630 9.95 7.12 35.29 2.71
806 838 7.804614 TTTTCGGTAAAATGCATGTATTGTC 57.195 32.000 9.95 4.01 29.59 3.18
807 839 5.493133 TCGGTAAAATGCATGTATTGTCC 57.507 39.130 9.95 11.09 0.00 4.02
808 840 4.336993 TCGGTAAAATGCATGTATTGTCCC 59.663 41.667 9.95 4.06 0.00 4.46
809 841 4.606961 GGTAAAATGCATGTATTGTCCCG 58.393 43.478 9.95 0.00 0.00 5.14
810 842 4.097286 GGTAAAATGCATGTATTGTCCCGT 59.903 41.667 9.95 0.00 0.00 5.28
811 843 4.799564 AAAATGCATGTATTGTCCCGTT 57.200 36.364 9.95 0.00 0.00 4.44
812 844 4.799564 AAATGCATGTATTGTCCCGTTT 57.200 36.364 9.95 0.00 0.00 3.60
813 845 4.799564 AATGCATGTATTGTCCCGTTTT 57.200 36.364 8.34 0.00 0.00 2.43
814 846 3.840890 TGCATGTATTGTCCCGTTTTC 57.159 42.857 0.00 0.00 0.00 2.29
815 847 3.149981 TGCATGTATTGTCCCGTTTTCA 58.850 40.909 0.00 0.00 0.00 2.69
816 848 3.190327 TGCATGTATTGTCCCGTTTTCAG 59.810 43.478 0.00 0.00 0.00 3.02
817 849 3.190535 GCATGTATTGTCCCGTTTTCAGT 59.809 43.478 0.00 0.00 0.00 3.41
818 850 4.320935 GCATGTATTGTCCCGTTTTCAGTT 60.321 41.667 0.00 0.00 0.00 3.16
819 851 5.106475 GCATGTATTGTCCCGTTTTCAGTTA 60.106 40.000 0.00 0.00 0.00 2.24
820 852 6.542852 CATGTATTGTCCCGTTTTCAGTTAG 58.457 40.000 0.00 0.00 0.00 2.34
821 853 4.453136 TGTATTGTCCCGTTTTCAGTTAGC 59.547 41.667 0.00 0.00 0.00 3.09
822 854 1.886886 TGTCCCGTTTTCAGTTAGCC 58.113 50.000 0.00 0.00 0.00 3.93
823 855 1.162698 GTCCCGTTTTCAGTTAGCCC 58.837 55.000 0.00 0.00 0.00 5.19
824 856 0.320946 TCCCGTTTTCAGTTAGCCCG 60.321 55.000 0.00 0.00 0.00 6.13
825 857 0.320946 CCCGTTTTCAGTTAGCCCGA 60.321 55.000 0.00 0.00 0.00 5.14
826 858 1.076332 CCGTTTTCAGTTAGCCCGAG 58.924 55.000 0.00 0.00 0.00 4.63
827 859 1.607251 CCGTTTTCAGTTAGCCCGAGT 60.607 52.381 0.00 0.00 0.00 4.18
828 860 1.459592 CGTTTTCAGTTAGCCCGAGTG 59.540 52.381 0.00 0.00 0.00 3.51
829 861 1.197036 GTTTTCAGTTAGCCCGAGTGC 59.803 52.381 0.00 0.00 0.00 4.40
830 862 0.685097 TTTCAGTTAGCCCGAGTGCT 59.315 50.000 0.00 0.00 45.38 4.40
831 863 0.685097 TTCAGTTAGCCCGAGTGCTT 59.315 50.000 0.00 0.00 42.75 3.91
832 864 0.685097 TCAGTTAGCCCGAGTGCTTT 59.315 50.000 0.00 0.00 42.75 3.51
833 865 1.071699 TCAGTTAGCCCGAGTGCTTTT 59.928 47.619 0.00 0.00 42.75 2.27
834 866 1.880027 CAGTTAGCCCGAGTGCTTTTT 59.120 47.619 0.00 0.00 42.75 1.94
857 889 9.834628 TTTTTATTGTCAACGTCTCATATTTCC 57.165 29.630 0.00 0.00 0.00 3.13
858 890 7.548196 TTATTGTCAACGTCTCATATTTCCC 57.452 36.000 0.00 0.00 0.00 3.97
859 891 3.517602 TGTCAACGTCTCATATTTCCCG 58.482 45.455 0.00 0.00 0.00 5.14
860 892 3.193903 TGTCAACGTCTCATATTTCCCGA 59.806 43.478 0.00 0.00 0.00 5.14
861 893 3.797256 GTCAACGTCTCATATTTCCCGAG 59.203 47.826 0.00 0.00 0.00 4.63
862 894 3.446161 TCAACGTCTCATATTTCCCGAGT 59.554 43.478 0.00 0.00 0.00 4.18
863 895 3.438297 ACGTCTCATATTTCCCGAGTG 57.562 47.619 0.00 0.00 0.00 3.51
864 896 3.021695 ACGTCTCATATTTCCCGAGTGA 58.978 45.455 0.00 0.00 0.00 3.41
865 897 3.181489 ACGTCTCATATTTCCCGAGTGAC 60.181 47.826 0.00 0.00 0.00 3.67
866 898 3.718815 GTCTCATATTTCCCGAGTGACC 58.281 50.000 0.00 0.00 0.00 4.02
867 899 2.361119 TCTCATATTTCCCGAGTGACCG 59.639 50.000 0.00 0.00 0.00 4.79
868 900 2.361119 CTCATATTTCCCGAGTGACCGA 59.639 50.000 0.00 0.00 0.00 4.69
869 901 2.761767 TCATATTTCCCGAGTGACCGAA 59.238 45.455 0.00 0.00 0.00 4.30
870 902 3.196039 TCATATTTCCCGAGTGACCGAAA 59.804 43.478 0.00 0.00 0.00 3.46
871 903 2.554370 ATTTCCCGAGTGACCGAAAA 57.446 45.000 0.00 0.00 0.00 2.29
872 904 2.328819 TTTCCCGAGTGACCGAAAAA 57.671 45.000 0.00 0.00 0.00 1.94
873 905 2.554370 TTCCCGAGTGACCGAAAAAT 57.446 45.000 0.00 0.00 0.00 1.82
874 906 3.681593 TTCCCGAGTGACCGAAAAATA 57.318 42.857 0.00 0.00 0.00 1.40
875 907 3.681593 TCCCGAGTGACCGAAAAATAA 57.318 42.857 0.00 0.00 0.00 1.40
876 908 4.210724 TCCCGAGTGACCGAAAAATAAT 57.789 40.909 0.00 0.00 0.00 1.28
877 909 3.936453 TCCCGAGTGACCGAAAAATAATG 59.064 43.478 0.00 0.00 0.00 1.90
878 910 3.486875 CCCGAGTGACCGAAAAATAATGC 60.487 47.826 0.00 0.00 0.00 3.56
879 911 3.126171 CCGAGTGACCGAAAAATAATGCA 59.874 43.478 0.00 0.00 0.00 3.96
880 912 4.088648 CGAGTGACCGAAAAATAATGCAC 58.911 43.478 0.00 0.00 0.00 4.57
881 913 4.142902 CGAGTGACCGAAAAATAATGCACT 60.143 41.667 0.00 0.00 37.99 4.40
882 914 5.062934 CGAGTGACCGAAAAATAATGCACTA 59.937 40.000 0.00 0.00 35.69 2.74
883 915 6.238103 CGAGTGACCGAAAAATAATGCACTAT 60.238 38.462 0.00 0.00 35.69 2.12
884 916 7.042992 CGAGTGACCGAAAAATAATGCACTATA 60.043 37.037 0.00 0.00 35.69 1.31
907 939 2.301870 TGTACAAGCCAACTGGTAGGAG 59.698 50.000 0.00 0.00 32.75 3.69
918 950 4.354893 ACTGGTAGGAGAGTATCGTAGG 57.645 50.000 0.00 0.00 42.67 3.18
928 960 6.904654 AGGAGAGTATCGTAGGAGGAGTATAT 59.095 42.308 0.00 0.00 42.67 0.86
1020 1055 3.782244 GCAGCGCTCGTCCAACAG 61.782 66.667 7.13 0.00 0.00 3.16
1190 1225 2.971452 GACCCTTTCCGAGCTCGT 59.029 61.111 32.41 14.06 37.74 4.18
1212 1247 2.588877 GACATCGGCATCCACCCG 60.589 66.667 0.00 0.00 46.88 5.28
1233 1268 1.375326 GAAGCTCCCCAACCTTCGT 59.625 57.895 0.00 0.00 0.00 3.85
1332 1367 1.132844 CGTGTCTCGTCTCCTCGTG 59.867 63.158 0.00 0.00 34.52 4.35
1362 1415 1.307517 GTCCCCCATGGTGGTAGGA 60.308 63.158 13.52 6.85 36.17 2.94
1377 1430 2.484947 GGTAGGATTCCTTTACCCGCAG 60.485 54.545 11.25 0.00 34.61 5.18
1383 1436 4.202284 GGATTCCTTTACCCGCAGTATGTA 60.202 45.833 0.00 0.00 39.31 2.29
1482 1535 4.643387 ACGTTGTGGGAGCTGGCC 62.643 66.667 0.00 0.00 0.00 5.36
1545 1598 3.849953 GCCGACAGCCGCTTTACG 61.850 66.667 0.00 0.00 43.15 3.18
1566 1619 1.550976 GTGAAGAACCTCCTCACGGAT 59.449 52.381 0.00 0.00 39.01 4.18
1587 1640 2.528797 CGGAGCAAGCGTGTTAAGT 58.471 52.632 0.59 0.00 0.00 2.24
1722 1775 2.937379 CTTCTGCTCCGGCCCATGAG 62.937 65.000 0.00 1.72 37.74 2.90
1725 1778 4.247380 GCTCCGGCCCATGAGAGG 62.247 72.222 14.13 0.17 0.00 3.69
1825 1879 8.137437 CCCCAACTCAAATACAAAGCATATTAG 58.863 37.037 0.00 0.00 0.00 1.73
1848 2075 6.492254 AGGTTTTTACTTTTTACTCGCACAG 58.508 36.000 0.00 0.00 0.00 3.66
1851 2078 8.071967 GGTTTTTACTTTTTACTCGCACAGTAT 58.928 33.333 0.00 0.00 37.44 2.12
1877 2104 3.274288 GAGATGCCTTCTCCGTTGATTT 58.726 45.455 3.01 0.00 44.46 2.17
1880 2107 1.073125 TGCCTTCTCCGTTGATTTGGA 59.927 47.619 0.00 0.00 0.00 3.53
1884 2111 3.063997 CCTTCTCCGTTGATTTGGAATCG 59.936 47.826 0.00 0.00 32.89 3.34
1888 2115 6.151663 TCTCCGTTGATTTGGAATCGTATA 57.848 37.500 0.00 0.00 32.89 1.47
1890 2117 5.294356 TCCGTTGATTTGGAATCGTATAGG 58.706 41.667 0.00 0.00 0.00 2.57
1893 2120 6.872020 CCGTTGATTTGGAATCGTATAGGTAT 59.128 38.462 0.00 0.00 0.00 2.73
1916 2147 2.487265 CCGCCCACAAATAGCCTCTAAT 60.487 50.000 0.00 0.00 0.00 1.73
1920 2151 4.276926 GCCCACAAATAGCCTCTAATCTTG 59.723 45.833 0.00 0.00 0.00 3.02
1924 2155 6.038714 CCACAAATAGCCTCTAATCTTGGTTC 59.961 42.308 0.00 0.00 0.00 3.62
1991 2224 3.868757 TGTCAACATCTACTCCCTTCG 57.131 47.619 0.00 0.00 0.00 3.79
1999 2232 5.209659 ACATCTACTCCCTTCGTTCCTAAT 58.790 41.667 0.00 0.00 0.00 1.73
2000 2233 6.371278 ACATCTACTCCCTTCGTTCCTAATA 58.629 40.000 0.00 0.00 0.00 0.98
2001 2234 7.011382 ACATCTACTCCCTTCGTTCCTAATAT 58.989 38.462 0.00 0.00 0.00 1.28
2002 2235 8.168725 ACATCTACTCCCTTCGTTCCTAATATA 58.831 37.037 0.00 0.00 0.00 0.86
2004 2237 8.632906 TCTACTCCCTTCGTTCCTAATATAAG 57.367 38.462 0.00 0.00 0.00 1.73
2005 2238 6.667558 ACTCCCTTCGTTCCTAATATAAGG 57.332 41.667 0.00 0.00 38.06 2.69
2006 2239 5.011840 ACTCCCTTCGTTCCTAATATAAGGC 59.988 44.000 0.00 0.00 36.51 4.35
2008 2241 5.605488 TCCCTTCGTTCCTAATATAAGGCTT 59.395 40.000 4.58 4.58 36.51 4.35
2009 2242 6.100714 TCCCTTCGTTCCTAATATAAGGCTTT 59.899 38.462 4.45 0.00 36.51 3.51
2010 2243 6.771267 CCCTTCGTTCCTAATATAAGGCTTTT 59.229 38.462 4.45 0.00 36.51 2.27
2011 2244 7.284716 CCCTTCGTTCCTAATATAAGGCTTTTT 59.715 37.037 4.45 0.00 36.51 1.94
2132 2383 9.357161 TGTTCACTAAAAGGGCTTAAATTTAGA 57.643 29.630 10.19 0.00 38.25 2.10
2139 2390 5.892160 AGGGCTTAAATTTAGAAACGGAC 57.108 39.130 0.00 0.00 0.00 4.79
2144 2395 5.686159 TTAAATTTAGAAACGGACGGCAA 57.314 34.783 0.00 0.00 0.00 4.52
2150 2401 2.706890 AGAAACGGACGGCAATGTAAT 58.293 42.857 0.00 0.00 0.00 1.89
2279 2530 8.579850 TTAAGTAATTACAGACGGAGGAAGTA 57.420 34.615 17.65 0.00 0.00 2.24
2331 2583 8.992835 AACCTTACTAGTAAAGAACATTACCG 57.007 34.615 16.48 1.64 36.62 4.02
2383 2636 9.585099 TTTATGGTTAATTATGACTTCGTACGT 57.415 29.630 16.05 0.00 0.00 3.57
2384 2637 7.689953 ATGGTTAATTATGACTTCGTACGTC 57.310 36.000 16.05 6.28 0.00 4.34
2385 2638 6.619744 TGGTTAATTATGACTTCGTACGTCA 58.380 36.000 16.05 12.23 44.59 4.35
2386 2639 6.527722 TGGTTAATTATGACTTCGTACGTCAC 59.472 38.462 16.05 6.38 43.44 3.67
2447 2700 2.050442 CCGGGCAAACTCAAACGC 60.050 61.111 0.00 0.00 0.00 4.84
2453 2706 1.597937 GGCAAACTCAAACGCTGTGAG 60.598 52.381 8.58 8.58 46.59 3.51
2467 2720 2.876550 GCTGTGAGGTTTAACCGAGTTT 59.123 45.455 8.63 0.00 44.90 2.66
2477 2730 9.949174 GAGGTTTAACCGAGTTTATTTAAACAA 57.051 29.630 8.63 0.00 44.31 2.83
2700 3191 9.710900 TTAGTAGCATGTATTTACTCCATGATG 57.289 33.333 0.00 0.00 38.56 3.07
2765 3256 3.986996 TCTGCATGACTGGAAAGATGA 57.013 42.857 0.00 0.00 0.00 2.92
2838 3329 3.054361 ACGCAGGAGGAAAGGTGATAATT 60.054 43.478 0.00 0.00 0.00 1.40
2859 3350 1.003355 CGATGCTGTGGTTGGGTCT 60.003 57.895 0.00 0.00 0.00 3.85
2865 3356 1.799258 CTGTGGTTGGGTCTGCAAGC 61.799 60.000 0.00 0.00 0.00 4.01
2868 3359 2.328099 GGTTGGGTCTGCAAGCTCG 61.328 63.158 0.00 0.00 0.00 5.03
2929 3420 3.418944 CGACGTCTACATCATGAACATCG 59.581 47.826 14.70 0.00 0.00 3.84
2971 3462 4.313522 CACGAGTGGAAGAAGATTTTCG 57.686 45.455 0.00 0.00 38.38 3.46
3027 3518 0.811281 CCAAGGGGCTTCGACAAATC 59.189 55.000 0.00 0.00 0.00 2.17
3052 3550 3.386078 TGAACTCTATCCATGAGACTGGC 59.614 47.826 0.00 0.00 36.16 4.85
3060 3558 2.101415 TCCATGAGACTGGCTGAATACG 59.899 50.000 0.00 0.00 36.16 3.06
3098 3596 5.426833 AGTCAACATTTCTAGACCAGGCTAT 59.573 40.000 0.00 0.00 0.00 2.97
3193 3694 9.638239 CTGCTGCCTTTTTATTTATAAAGACAA 57.362 29.630 3.94 0.00 34.11 3.18
3195 3696 9.855021 GCTGCCTTTTTATTTATAAAGACAAGA 57.145 29.630 3.94 0.00 34.11 3.02
3256 3757 6.968004 TTTCGACAGTTTCATCAAATTTCG 57.032 33.333 0.00 0.00 0.00 3.46
3296 3797 9.657419 AAGCAAATCATTTAAGGTTTATGAAGG 57.343 29.630 0.00 0.00 32.54 3.46
3316 3817 8.217131 TGAAGGTTCAGATATGAAACATCATG 57.783 34.615 19.08 0.00 38.00 3.07
3318 3819 8.447924 AAGGTTCAGATATGAAACATCATGAG 57.552 34.615 19.66 0.00 37.93 2.90
3345 3846 7.283625 ACTATATACTTGCTCTCTTGACAGG 57.716 40.000 0.00 0.00 0.00 4.00
3405 3906 2.352030 CCCACAGCAAGCAATACAGTTG 60.352 50.000 0.00 0.00 0.00 3.16
3410 3911 5.344128 CACAGCAAGCAATACAGTTGATTTC 59.656 40.000 0.00 0.00 0.00 2.17
3467 3968 5.638133 AGCAATCAATATACCTTGCCATCT 58.362 37.500 10.67 0.00 43.84 2.90
3474 3975 7.345691 TCAATATACCTTGCCATCTTTTCTCA 58.654 34.615 0.00 0.00 0.00 3.27
3476 3977 8.636213 CAATATACCTTGCCATCTTTTCTCAAT 58.364 33.333 0.00 0.00 0.00 2.57
3503 4004 3.899052 AATGGCTCAAAATCCATGGTG 57.101 42.857 12.58 2.27 41.92 4.17
3514 4015 2.335681 TCCATGGTGTAGGTTCTCCA 57.664 50.000 12.58 0.00 35.82 3.86
3643 4147 4.442192 GCAATGGGTGTTGTGGTCTTAAAA 60.442 41.667 0.00 0.00 0.00 1.52
3648 4152 4.399934 GGGTGTTGTGGTCTTAAAAACTGA 59.600 41.667 0.00 0.00 0.00 3.41
3696 4200 2.315925 TGCCAAGACGGATCAAGATC 57.684 50.000 1.40 1.40 36.56 2.75
3709 4213 7.786030 ACGGATCAAGATCAAGAAGAGAAATA 58.214 34.615 11.78 0.00 39.54 1.40
3725 4229 5.701290 AGAGAAATAAAACAAGAGGTGGACG 59.299 40.000 0.00 0.00 0.00 4.79
3732 4236 4.657436 AACAAGAGGTGGACGAGATATC 57.343 45.455 0.00 0.00 0.00 1.63
3743 4247 0.038159 CGAGATATCCAAGGCGGGAC 60.038 60.000 2.98 0.00 40.44 4.46
3758 4262 1.609794 GGACGGAGACCCTCACCTT 60.610 63.158 0.00 0.00 36.03 3.50
3775 4279 0.040204 CTTGGTGCATTTCCCCCTCT 59.960 55.000 0.00 0.00 0.00 3.69
3776 4280 0.486879 TTGGTGCATTTCCCCCTCTT 59.513 50.000 0.00 0.00 0.00 2.85
3777 4281 0.039618 TGGTGCATTTCCCCCTCTTC 59.960 55.000 0.00 0.00 0.00 2.87
3787 4291 2.359967 CCCCTCTTCTCGGACCACC 61.360 68.421 0.00 0.00 0.00 4.61
3790 4294 1.609501 CTCTTCTCGGACCACCCCA 60.610 63.158 0.00 0.00 0.00 4.96
3792 4296 1.221840 CTTCTCGGACCACCCCATG 59.778 63.158 0.00 0.00 0.00 3.66
3793 4297 2.876368 CTTCTCGGACCACCCCATGC 62.876 65.000 0.00 0.00 0.00 4.06
3794 4298 4.838152 CTCGGACCACCCCATGCG 62.838 72.222 0.00 0.00 0.00 4.73
3840 4344 5.950544 ACACCTACATAGCAATTCCTACA 57.049 39.130 0.00 0.00 0.00 2.74
3841 4345 6.500589 ACACCTACATAGCAATTCCTACAT 57.499 37.500 0.00 0.00 0.00 2.29
3882 4386 4.994852 TCAGTGTTTGGTTAGAGGAAATCG 59.005 41.667 0.00 0.00 0.00 3.34
3904 4409 3.253838 AGGGGCCCACTTGCGTTA 61.254 61.111 27.72 0.00 0.00 3.18
3916 4421 2.494471 ACTTGCGTTAAATTTAGGGGGC 59.506 45.455 0.00 2.25 0.00 5.80
3924 4429 3.451402 AAATTTAGGGGGCGAAGAGTT 57.549 42.857 0.00 0.00 0.00 3.01
3928 4433 2.242882 TAGGGGGCGAAGAGTTTAGT 57.757 50.000 0.00 0.00 0.00 2.24
3941 4446 8.182227 GCGAAGAGTTTAGTTAAGGCAAATTAT 58.818 33.333 0.00 0.00 0.00 1.28
3951 4456 8.417273 AGTTAAGGCAAATTATGTAACAACCT 57.583 30.769 0.00 0.00 0.00 3.50
3958 4463 4.695217 ATTATGTAACAACCTTGCACCG 57.305 40.909 0.00 0.00 0.00 4.94
4003 4508 1.766461 CCTGCGGAGGGAAGGGTAT 60.766 63.158 16.49 0.00 35.40 2.73
4009 4514 3.181415 TGCGGAGGGAAGGGTATAGATAA 60.181 47.826 0.00 0.00 0.00 1.75
4033 4538 4.267690 GTCAATTGAGTATGATTCGCGTGA 59.732 41.667 8.80 0.00 0.00 4.35
4040 4545 3.612860 AGTATGATTCGCGTGAGACAAAC 59.387 43.478 5.77 3.75 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 137 3.231889 CTGTCCTGCTGCACCGAGT 62.232 63.158 0.00 0.00 0.00 4.18
109 139 4.007644 CCTGTCCTGCTGCACCGA 62.008 66.667 0.00 0.00 0.00 4.69
128 158 1.299648 CCGAAACTGGCCTCCATCA 59.700 57.895 3.32 0.00 30.82 3.07
337 368 1.456892 CCCACATGGCCATGCTCAT 60.457 57.895 39.74 21.78 42.39 2.90
349 380 3.069946 CAACCATGCCGCCCACAT 61.070 61.111 0.00 0.00 0.00 3.21
379 410 2.426522 CGACAATCACCACCACTGAAT 58.573 47.619 0.00 0.00 0.00 2.57
486 517 0.320073 CCCTAAAGCAACACGACGGA 60.320 55.000 0.00 0.00 0.00 4.69
646 677 2.262637 CCACCCCTACCACTACAAGAA 58.737 52.381 0.00 0.00 0.00 2.52
689 720 5.945310 ACACATACATCCAAGGCAGAATAT 58.055 37.500 0.00 0.00 0.00 1.28
693 724 3.244875 ACAACACATACATCCAAGGCAGA 60.245 43.478 0.00 0.00 0.00 4.26
703 734 3.951037 ACACACCAACACAACACATACAT 59.049 39.130 0.00 0.00 0.00 2.29
707 738 2.166829 ACACACACCAACACAACACAT 58.833 42.857 0.00 0.00 0.00 3.21
721 752 1.339824 ACAACCCGGTACAAACACACA 60.340 47.619 0.00 0.00 0.00 3.72
725 756 2.414994 TCAACAACCCGGTACAAACA 57.585 45.000 0.00 0.00 0.00 2.83
767 799 1.862827 CGAAAAAGACTTTCGTCCCGT 59.137 47.619 10.62 0.00 44.25 5.28
794 826 3.149981 TGAAAACGGGACAATACATGCA 58.850 40.909 0.00 0.00 0.00 3.96
795 827 3.190535 ACTGAAAACGGGACAATACATGC 59.809 43.478 0.00 0.00 0.00 4.06
796 828 5.371115 AACTGAAAACGGGACAATACATG 57.629 39.130 0.00 0.00 0.00 3.21
797 829 5.123344 GCTAACTGAAAACGGGACAATACAT 59.877 40.000 0.00 0.00 0.00 2.29
798 830 4.453136 GCTAACTGAAAACGGGACAATACA 59.547 41.667 0.00 0.00 0.00 2.29
799 831 4.142752 GGCTAACTGAAAACGGGACAATAC 60.143 45.833 0.00 0.00 0.00 1.89
800 832 4.004982 GGCTAACTGAAAACGGGACAATA 58.995 43.478 0.00 0.00 0.00 1.90
801 833 2.817844 GGCTAACTGAAAACGGGACAAT 59.182 45.455 0.00 0.00 0.00 2.71
802 834 2.223745 GGCTAACTGAAAACGGGACAA 58.776 47.619 0.00 0.00 0.00 3.18
803 835 1.543871 GGGCTAACTGAAAACGGGACA 60.544 52.381 0.00 0.00 0.00 4.02
804 836 1.162698 GGGCTAACTGAAAACGGGAC 58.837 55.000 0.00 0.00 0.00 4.46
805 837 0.320946 CGGGCTAACTGAAAACGGGA 60.321 55.000 0.00 0.00 0.00 5.14
806 838 0.320946 TCGGGCTAACTGAAAACGGG 60.321 55.000 0.00 0.00 0.00 5.28
807 839 1.076332 CTCGGGCTAACTGAAAACGG 58.924 55.000 0.00 0.00 33.08 4.44
808 840 1.459592 CACTCGGGCTAACTGAAAACG 59.540 52.381 0.00 0.00 33.08 3.60
809 841 1.197036 GCACTCGGGCTAACTGAAAAC 59.803 52.381 0.00 0.00 33.08 2.43
810 842 1.071699 AGCACTCGGGCTAACTGAAAA 59.928 47.619 0.00 0.00 43.70 2.29
811 843 0.685097 AGCACTCGGGCTAACTGAAA 59.315 50.000 0.00 0.00 43.70 2.69
812 844 0.685097 AAGCACTCGGGCTAACTGAA 59.315 50.000 0.00 0.00 45.07 3.02
813 845 0.685097 AAAGCACTCGGGCTAACTGA 59.315 50.000 0.00 0.00 45.07 3.41
814 846 1.523758 AAAAGCACTCGGGCTAACTG 58.476 50.000 0.00 0.00 45.07 3.16
815 847 2.271944 AAAAAGCACTCGGGCTAACT 57.728 45.000 0.00 0.00 45.07 2.24
831 863 9.834628 GGAAATATGAGACGTTGACAATAAAAA 57.165 29.630 0.00 0.00 0.00 1.94
832 864 8.455682 GGGAAATATGAGACGTTGACAATAAAA 58.544 33.333 0.00 0.00 0.00 1.52
833 865 7.201574 CGGGAAATATGAGACGTTGACAATAAA 60.202 37.037 0.00 0.00 0.00 1.40
834 866 6.256975 CGGGAAATATGAGACGTTGACAATAA 59.743 38.462 0.00 0.00 0.00 1.40
835 867 5.751509 CGGGAAATATGAGACGTTGACAATA 59.248 40.000 0.00 0.00 0.00 1.90
836 868 4.570772 CGGGAAATATGAGACGTTGACAAT 59.429 41.667 0.00 0.00 0.00 2.71
837 869 3.930229 CGGGAAATATGAGACGTTGACAA 59.070 43.478 0.00 0.00 0.00 3.18
838 870 3.193903 TCGGGAAATATGAGACGTTGACA 59.806 43.478 0.00 0.00 0.00 3.58
839 871 3.777478 TCGGGAAATATGAGACGTTGAC 58.223 45.455 0.00 0.00 0.00 3.18
840 872 3.446161 ACTCGGGAAATATGAGACGTTGA 59.554 43.478 0.00 0.00 33.93 3.18
841 873 3.551890 CACTCGGGAAATATGAGACGTTG 59.448 47.826 0.00 0.00 33.93 4.10
842 874 3.446161 TCACTCGGGAAATATGAGACGTT 59.554 43.478 0.00 0.00 33.93 3.99
843 875 3.021695 TCACTCGGGAAATATGAGACGT 58.978 45.455 0.00 0.00 33.93 4.34
844 876 3.372954 GTCACTCGGGAAATATGAGACG 58.627 50.000 0.00 0.00 33.93 4.18
845 877 3.718815 GGTCACTCGGGAAATATGAGAC 58.281 50.000 0.00 0.00 33.93 3.36
846 878 2.361119 CGGTCACTCGGGAAATATGAGA 59.639 50.000 0.00 0.00 33.93 3.27
847 879 2.361119 TCGGTCACTCGGGAAATATGAG 59.639 50.000 0.00 0.00 35.85 2.90
848 880 2.380941 TCGGTCACTCGGGAAATATGA 58.619 47.619 0.00 0.00 0.00 2.15
849 881 2.882927 TCGGTCACTCGGGAAATATG 57.117 50.000 0.00 0.00 0.00 1.78
850 882 3.899052 TTTCGGTCACTCGGGAAATAT 57.101 42.857 0.00 0.00 0.00 1.28
851 883 3.681593 TTTTCGGTCACTCGGGAAATA 57.318 42.857 0.00 0.00 0.00 1.40
852 884 2.554370 TTTTCGGTCACTCGGGAAAT 57.446 45.000 0.00 0.00 0.00 2.17
853 885 2.328819 TTTTTCGGTCACTCGGGAAA 57.671 45.000 0.00 0.00 0.00 3.13
854 886 2.554370 ATTTTTCGGTCACTCGGGAA 57.446 45.000 0.00 0.00 0.00 3.97
855 887 3.681593 TTATTTTTCGGTCACTCGGGA 57.318 42.857 0.00 0.00 0.00 5.14
856 888 3.486875 GCATTATTTTTCGGTCACTCGGG 60.487 47.826 0.00 0.00 0.00 5.14
857 889 3.126171 TGCATTATTTTTCGGTCACTCGG 59.874 43.478 0.00 0.00 0.00 4.63
858 890 4.088648 GTGCATTATTTTTCGGTCACTCG 58.911 43.478 0.00 0.00 0.00 4.18
859 891 5.296813 AGTGCATTATTTTTCGGTCACTC 57.703 39.130 0.00 0.00 0.00 3.51
860 892 7.769044 ACTATAGTGCATTATTTTTCGGTCACT 59.231 33.333 7.07 0.00 37.34 3.41
861 893 7.850982 CACTATAGTGCATTATTTTTCGGTCAC 59.149 37.037 19.55 0.00 39.39 3.67
862 894 7.915508 CACTATAGTGCATTATTTTTCGGTCA 58.084 34.615 19.55 0.00 39.39 4.02
877 909 8.957901 ACCAGTTGGCTTGTACACTATAGTGC 62.958 46.154 28.88 15.80 43.78 4.40
878 910 5.568825 ACCAGTTGGCTTGTACACTATAGTG 60.569 44.000 27.66 27.66 44.75 2.74
879 911 4.530946 ACCAGTTGGCTTGTACACTATAGT 59.469 41.667 0.00 0.00 39.32 2.12
880 912 5.086104 ACCAGTTGGCTTGTACACTATAG 57.914 43.478 0.00 0.00 39.32 1.31
881 913 5.128171 CCTACCAGTTGGCTTGTACACTATA 59.872 44.000 0.00 0.00 39.32 1.31
882 914 4.081087 CCTACCAGTTGGCTTGTACACTAT 60.081 45.833 0.00 0.00 39.32 2.12
883 915 3.259876 CCTACCAGTTGGCTTGTACACTA 59.740 47.826 0.00 0.00 39.32 2.74
884 916 2.038557 CCTACCAGTTGGCTTGTACACT 59.961 50.000 0.00 0.00 39.32 3.55
931 963 7.169308 CGTCTATGAGCGTTGTCCTTTATTTAT 59.831 37.037 0.00 0.00 0.00 1.40
932 964 6.474427 CGTCTATGAGCGTTGTCCTTTATTTA 59.526 38.462 0.00 0.00 0.00 1.40
933 965 5.291128 CGTCTATGAGCGTTGTCCTTTATTT 59.709 40.000 0.00 0.00 0.00 1.40
934 966 4.804139 CGTCTATGAGCGTTGTCCTTTATT 59.196 41.667 0.00 0.00 0.00 1.40
935 967 4.360563 CGTCTATGAGCGTTGTCCTTTAT 58.639 43.478 0.00 0.00 0.00 1.40
936 968 3.766151 CGTCTATGAGCGTTGTCCTTTA 58.234 45.455 0.00 0.00 0.00 1.85
937 969 2.607187 CGTCTATGAGCGTTGTCCTTT 58.393 47.619 0.00 0.00 0.00 3.11
969 1001 7.013083 ACGTGTGTAATGTACTAGCTAGCTTAT 59.987 37.037 24.88 13.94 0.00 1.73
1019 1054 0.392193 CATGGCGAGCTTGTCTTCCT 60.392 55.000 7.19 0.00 0.00 3.36
1020 1055 0.391661 TCATGGCGAGCTTGTCTTCC 60.392 55.000 7.19 0.00 0.00 3.46
1173 1208 1.153804 GACGAGCTCGGAAAGGGTC 60.154 63.158 36.93 21.00 44.95 4.46
1190 1225 4.585526 GGATGCCGATGTCCGCGA 62.586 66.667 8.23 0.00 36.84 5.87
1212 1247 1.375326 AAGGTTGGGGAGCTTCGTC 59.625 57.895 0.00 0.00 42.17 4.20
1233 1268 1.944234 TAAGCACTCGCATGAGCCGA 61.944 55.000 0.00 0.00 46.69 5.54
1362 1415 3.926058 ACATACTGCGGGTAAAGGAAT 57.074 42.857 0.00 0.00 33.74 3.01
1377 1430 2.031508 GTCTGAGAGAGCCGCTACATAC 60.032 54.545 0.00 0.00 0.00 2.39
1383 1436 1.815196 CATGTCTGAGAGAGCCGCT 59.185 57.895 0.00 0.00 0.00 5.52
1389 1442 1.308783 ACTCGCGCATGTCTGAGAGA 61.309 55.000 8.75 0.00 32.81 3.10
1545 1598 3.516578 CGTGAGGAGGTTCTTCACC 57.483 57.895 13.51 0.00 46.75 4.02
1566 1619 1.160946 TTAACACGCTTGCTCCGCAA 61.161 50.000 1.02 1.02 46.80 4.85
1600 1653 4.849329 GCCGACGTCCACTAGCGG 62.849 72.222 10.58 7.65 44.47 5.52
1656 1709 2.082231 CTGCACTTGAGATGTGGGAAG 58.918 52.381 0.00 0.00 36.08 3.46
1722 1775 1.810030 GGCGACGAATGTCACCCTC 60.810 63.158 0.00 0.00 45.80 4.30
1825 1879 6.260377 ACTGTGCGAGTAAAAAGTAAAAACC 58.740 36.000 0.00 0.00 30.86 3.27
1828 1882 7.359431 CGGATACTGTGCGAGTAAAAAGTAAAA 60.359 37.037 0.00 0.00 45.38 1.52
1829 1883 6.089820 CGGATACTGTGCGAGTAAAAAGTAAA 59.910 38.462 0.00 0.00 45.38 2.01
1830 1884 5.574055 CGGATACTGTGCGAGTAAAAAGTAA 59.426 40.000 0.00 0.00 45.38 2.24
1832 1886 3.924686 CGGATACTGTGCGAGTAAAAAGT 59.075 43.478 0.00 0.00 45.38 2.66
1833 1887 3.924686 ACGGATACTGTGCGAGTAAAAAG 59.075 43.478 0.00 0.00 45.38 2.27
1834 1888 3.676172 CACGGATACTGTGCGAGTAAAAA 59.324 43.478 0.00 0.00 45.38 1.94
1877 2104 3.194116 GGCGGAATACCTATACGATTCCA 59.806 47.826 12.14 0.00 46.07 3.53
1880 2107 3.056322 GTGGGCGGAATACCTATACGATT 60.056 47.826 0.00 0.00 0.00 3.34
1884 2111 3.756933 TTGTGGGCGGAATACCTATAC 57.243 47.619 0.00 0.00 0.00 1.47
1888 2115 2.748465 GCTATTTGTGGGCGGAATACCT 60.748 50.000 0.00 0.00 0.00 3.08
1890 2117 1.607148 GGCTATTTGTGGGCGGAATAC 59.393 52.381 0.00 0.00 0.00 1.89
1893 2120 0.393808 GAGGCTATTTGTGGGCGGAA 60.394 55.000 0.00 0.00 0.00 4.30
1916 2147 9.364989 CAAAGTTTTATTTTGACTGAACCAAGA 57.635 29.630 0.00 0.00 37.65 3.02
2023 2256 8.752187 TGCATATTGAAATCTCTAAAAAGCCTT 58.248 29.630 0.00 0.00 0.00 4.35
2024 2257 8.193438 GTGCATATTGAAATCTCTAAAAAGCCT 58.807 33.333 0.00 0.00 0.00 4.58
2025 2258 8.193438 AGTGCATATTGAAATCTCTAAAAAGCC 58.807 33.333 0.00 0.00 0.00 4.35
2082 2315 9.758651 ACAGATGTATATACACGCATTTTAGAA 57.241 29.630 17.69 0.00 39.30 2.10
2106 2339 9.357161 TCTAAATTTAAGCCCTTTTAGTGAACA 57.643 29.630 0.00 0.00 34.68 3.18
2118 2369 4.437794 CCGTCCGTTTCTAAATTTAAGCCC 60.438 45.833 0.00 0.00 0.00 5.19
2132 2383 2.428491 TCATTACATTGCCGTCCGTTT 58.572 42.857 0.00 0.00 0.00 3.60
2135 2386 2.675844 TCTTTCATTACATTGCCGTCCG 59.324 45.455 0.00 0.00 0.00 4.79
2220 2471 8.463930 TTCAGAAAGTTTGACCAAATGTATCT 57.536 30.769 0.00 0.00 32.36 1.98
2221 2472 9.696917 ATTTCAGAAAGTTTGACCAAATGTATC 57.303 29.630 1.28 0.00 32.36 2.24
2357 2609 9.585099 ACGTACGAAGTCATAATTAACCATAAA 57.415 29.630 24.41 0.00 43.93 1.40
2380 2633 6.511416 AGAGTAGTATATAGTGTCGTGACGT 58.489 40.000 4.40 0.00 0.00 4.34
2381 2634 7.042858 ACAAGAGTAGTATATAGTGTCGTGACG 60.043 40.741 17.15 0.00 0.00 4.35
2382 2635 8.140677 ACAAGAGTAGTATATAGTGTCGTGAC 57.859 38.462 17.15 0.00 0.00 3.67
2383 2636 8.610035 CAACAAGAGTAGTATATAGTGTCGTGA 58.390 37.037 17.15 0.00 0.00 4.35
2384 2637 8.396390 ACAACAAGAGTAGTATATAGTGTCGTG 58.604 37.037 12.28 12.28 0.00 4.35
2385 2638 8.503458 ACAACAAGAGTAGTATATAGTGTCGT 57.497 34.615 0.00 0.00 0.00 4.34
2386 2639 9.435802 GAACAACAAGAGTAGTATATAGTGTCG 57.564 37.037 0.00 0.00 0.00 4.35
2387 2640 9.733219 GGAACAACAAGAGTAGTATATAGTGTC 57.267 37.037 0.00 0.00 0.00 3.67
2388 2641 9.476928 AGGAACAACAAGAGTAGTATATAGTGT 57.523 33.333 0.00 0.00 0.00 3.55
2389 2642 9.953697 GAGGAACAACAAGAGTAGTATATAGTG 57.046 37.037 0.00 0.00 0.00 2.74
2430 2683 2.050442 GCGTTTGAGTTTGCCCGG 60.050 61.111 0.00 0.00 0.00 5.73
2447 2700 6.796705 AATAAACTCGGTTAAACCTCACAG 57.203 37.500 0.00 0.00 35.66 3.66
2574 2827 6.528537 AGCCAACAATTACATTATTGCTCA 57.471 33.333 0.00 0.00 38.74 4.26
2602 2855 8.609483 TCCCTATTAGGTCTCGTTAGTACATAT 58.391 37.037 8.91 0.00 31.93 1.78
2604 2857 6.845908 TCCCTATTAGGTCTCGTTAGTACAT 58.154 40.000 8.91 0.00 31.93 2.29
2646 2899 4.098914 AGCACATTGGTTACTTCCTTCA 57.901 40.909 0.00 0.00 0.00 3.02
2648 2901 4.980573 TGTAGCACATTGGTTACTTCCTT 58.019 39.130 0.00 0.00 0.00 3.36
2700 3191 9.372369 ACCCGAGTTATCTATACTACGTATAAC 57.628 37.037 0.00 1.35 31.69 1.89
2710 3201 6.746120 ACAACATCACCCGAGTTATCTATAC 58.254 40.000 0.00 0.00 0.00 1.47
2765 3256 5.220472 CGTCGCAATATCTTCACACAATCTT 60.220 40.000 0.00 0.00 0.00 2.40
2838 3329 0.908910 ACCCAACCACAGCATCGATA 59.091 50.000 0.00 0.00 0.00 2.92
2865 3356 0.387202 AGATGATTCCCTGCGACGAG 59.613 55.000 0.00 0.00 0.00 4.18
2868 3359 0.465705 TGGAGATGATTCCCTGCGAC 59.534 55.000 0.00 0.00 36.35 5.19
2929 3420 2.478831 GTCCTCTCGCTCAATTCCATC 58.521 52.381 0.00 0.00 0.00 3.51
2971 3462 1.464997 GTCAGTGAATCCGGCTTCAAC 59.535 52.381 21.61 13.04 36.92 3.18
3027 3518 5.990386 CCAGTCTCATGGATAGAGTTCAATG 59.010 44.000 0.00 0.00 43.57 2.82
3052 3550 0.742505 TAGGACGGGTGCGTATTCAG 59.257 55.000 0.00 0.00 0.00 3.02
3166 3664 8.802267 TGTCTTTATAAATAAAAAGGCAGCAGT 58.198 29.630 0.00 0.00 41.14 4.40
3193 3694 8.982685 CATATGAGATAGCGTAAAACACAATCT 58.017 33.333 0.00 0.00 0.00 2.40
3195 3696 7.569408 CGCATATGAGATAGCGTAAAACACAAT 60.569 37.037 6.97 0.00 44.67 2.71
3207 3708 6.587990 ACTTGATACAACGCATATGAGATAGC 59.412 38.462 13.81 6.06 0.00 2.97
3221 3722 7.184106 TGAAACTGTCGAAAACTTGATACAAC 58.816 34.615 0.00 0.00 0.00 3.32
3224 3725 7.572759 TGATGAAACTGTCGAAAACTTGATAC 58.427 34.615 0.00 0.00 0.00 2.24
3332 3833 5.967088 TCATTAAGTACCTGTCAAGAGAGC 58.033 41.667 0.00 0.00 0.00 4.09
3488 3989 5.256474 AGAACCTACACCATGGATTTTGAG 58.744 41.667 21.47 6.33 0.00 3.02
3493 3994 3.189606 TGGAGAACCTACACCATGGATT 58.810 45.455 21.47 6.94 37.04 3.01
3514 4015 6.752091 ACCAATATCCCTATGGGTTCTTTTT 58.248 36.000 2.25 0.00 38.33 1.94
3559 4061 5.701224 GGGAAAACCATAGTATCCCATGAA 58.299 41.667 9.35 0.00 45.47 2.57
3626 4130 5.570234 TCAGTTTTTAAGACCACAACACC 57.430 39.130 0.00 0.00 0.00 4.16
3627 4131 9.016623 GTATTTCAGTTTTTAAGACCACAACAC 57.983 33.333 0.00 0.00 0.00 3.32
3671 4175 5.192927 TCTTGATCCGTCTTGGCAAAATAT 58.807 37.500 0.00 0.00 37.80 1.28
3696 4200 8.078596 CCACCTCTTGTTTTATTTCTCTTCTTG 58.921 37.037 0.00 0.00 0.00 3.02
3709 4213 3.771577 ATCTCGTCCACCTCTTGTTTT 57.228 42.857 0.00 0.00 0.00 2.43
3725 4229 0.038159 CGTCCCGCCTTGGATATCTC 60.038 60.000 2.05 0.00 42.00 2.75
3732 4236 4.452733 GTCTCCGTCCCGCCTTGG 62.453 72.222 0.00 0.00 37.55 3.61
3743 4247 1.913762 ACCAAGGTGAGGGTCTCCG 60.914 63.158 0.00 0.00 35.32 4.63
3758 4262 0.039618 GAAGAGGGGGAAATGCACCA 59.960 55.000 0.00 0.00 44.24 4.17
3775 4279 2.966732 GCATGGGGTGGTCCGAGAA 61.967 63.158 0.00 0.00 36.01 2.87
3776 4280 3.399181 GCATGGGGTGGTCCGAGA 61.399 66.667 0.00 0.00 36.01 4.04
3777 4281 4.838152 CGCATGGGGTGGTCCGAG 62.838 72.222 0.89 0.00 36.01 4.63
3796 4300 4.947147 TTGCTCGGGGTTGCGCTT 62.947 61.111 9.73 0.00 0.00 4.68
3797 4301 4.722700 ATTGCTCGGGGTTGCGCT 62.723 61.111 9.73 0.00 0.00 5.92
3840 4344 8.506168 ACACTGAATCCATTACGTAAATCAAT 57.494 30.769 12.81 1.43 0.00 2.57
3841 4345 7.915293 ACACTGAATCCATTACGTAAATCAA 57.085 32.000 12.81 0.00 0.00 2.57
3862 4366 4.320870 TCCGATTTCCTCTAACCAAACAC 58.679 43.478 0.00 0.00 0.00 3.32
3882 4386 3.732849 CAAGTGGGCCCCTCCTCC 61.733 72.222 22.27 0.00 34.39 4.30
3904 4409 3.451402 AACTCTTCGCCCCCTAAATTT 57.549 42.857 0.00 0.00 0.00 1.82
3916 4421 9.490663 CATAATTTGCCTTAACTAAACTCTTCG 57.509 33.333 0.00 0.00 0.00 3.79
3928 4433 7.600752 GCAAGGTTGTTACATAATTTGCCTTAA 59.399 33.333 10.89 0.00 35.03 1.85
3941 4446 1.448922 GGCGGTGCAAGGTTGTTACA 61.449 55.000 0.00 0.00 0.00 2.41
3947 4452 4.660938 GAGGGGCGGTGCAAGGTT 62.661 66.667 0.00 0.00 0.00 3.50
3973 4478 4.452733 CGCAGGACGGGGAACTCC 62.453 72.222 0.00 0.00 38.44 3.85
3987 4492 0.559205 TCTATACCCTTCCCTCCGCA 59.441 55.000 0.00 0.00 0.00 5.69
4003 4508 9.411801 GCGAATCATACTCAATTGACTTATCTA 57.588 33.333 3.38 0.00 0.00 1.98
4009 4514 4.268644 CACGCGAATCATACTCAATTGACT 59.731 41.667 15.93 0.00 0.00 3.41
4027 4532 1.569003 TGCATGTTTGTCTCACGCG 59.431 52.632 3.53 3.53 0.00 6.01


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

AutoCloner maintained by Alex Coulton.