Multiple sequence alignment - TraesCS1A01G312000

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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 TraesCS1A01G312000 chr1A 100.000 3695 0 0 1 3695 503382435 503378741 0.000000e+00 6824.0
1 TraesCS1A01G312000 chr1A 89.809 785 77 2 1 782 519440240 519441024 0.000000e+00 1003.0
2 TraesCS1A01G312000 chr1A 93.333 75 3 1 1971 2043 353252796 353252722 3.900000e-20 110.0
3 TraesCS1A01G312000 chr1D 92.707 1138 59 12 2040 3174 407917043 407915927 0.000000e+00 1620.0
4 TraesCS1A01G312000 chr1D 91.825 1003 57 16 949 1929 407918107 407917108 0.000000e+00 1375.0
5 TraesCS1A01G312000 chr1D 89.480 789 70 7 1 782 74921089 74920307 0.000000e+00 985.0
6 TraesCS1A01G312000 chr1D 90.850 459 41 1 3172 3630 407915316 407914859 6.780000e-172 614.0
7 TraesCS1A01G312000 chr1D 95.000 80 4 0 868 947 407918162 407918083 3.870000e-25 126.0
8 TraesCS1A01G312000 chr1D 89.744 78 4 3 1971 2045 6327179 6327255 3.040000e-16 97.1
9 TraesCS1A01G312000 chr1B 91.871 1021 53 13 2040 3047 548611436 548610433 0.000000e+00 1399.0
10 TraesCS1A01G312000 chr1B 87.906 1017 74 24 949 1922 548612466 548611456 0.000000e+00 1151.0
11 TraesCS1A01G312000 chr1B 91.406 768 57 6 16 776 263553824 263553059 0.000000e+00 1044.0
12 TraesCS1A01G312000 chr1B 88.224 518 49 5 3178 3695 548549045 548548540 3.160000e-170 608.0
13 TraesCS1A01G312000 chr1B 92.800 125 8 1 3042 3165 548549772 548549648 2.930000e-41 180.0
14 TraesCS1A01G312000 chr1B 91.667 84 4 3 866 947 548612524 548612442 3.020000e-21 113.0
15 TraesCS1A01G312000 chr1B 91.892 74 2 3 1973 2042 683479854 683479781 2.350000e-17 100.0
16 TraesCS1A01G312000 chr5D 92.494 786 49 7 1 782 87190518 87191297 0.000000e+00 1116.0
17 TraesCS1A01G312000 chr7D 90.736 788 66 4 1 781 412667720 412668507 0.000000e+00 1044.0
18 TraesCS1A01G312000 chr6A 89.682 785 77 2 1 781 337209786 337209002 0.000000e+00 998.0
19 TraesCS1A01G312000 chr6A 89.286 84 5 4 1963 2043 83358631 83358713 6.530000e-18 102.0
20 TraesCS1A01G312000 chr7B 89.783 783 70 7 3 777 669973552 669974332 0.000000e+00 994.0
21 TraesCS1A01G312000 chr5B 89.308 795 67 12 1 783 645560299 645559511 0.000000e+00 981.0
22 TraesCS1A01G312000 chr4B 89.354 789 64 12 1 780 273430465 273429688 0.000000e+00 974.0
23 TraesCS1A01G312000 chr4B 92.308 78 3 3 1973 2047 191210896 191210819 1.400000e-19 108.0
24 TraesCS1A01G312000 chr2B 93.333 75 0 2 1973 2042 647445049 647444975 5.050000e-19 106.0
25 TraesCS1A01G312000 chr7A 93.151 73 2 2 1973 2042 28155621 28155549 1.820000e-18 104.0
26 TraesCS1A01G312000 chr3A 93.151 73 2 3 1973 2042 430527885 430527813 1.820000e-18 104.0
27 TraesCS1A01G312000 chrUn 87.952 83 5 4 1963 2044 27338318 27338396 3.930000e-15 93.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G312000 chr1A 503378741 503382435 3694 True 6824.000000 6824 100.000000 1 3695 1 chr1A.!!$R2 3694
1 TraesCS1A01G312000 chr1A 519440240 519441024 784 False 1003.000000 1003 89.809000 1 782 1 chr1A.!!$F1 781
2 TraesCS1A01G312000 chr1D 74920307 74921089 782 True 985.000000 985 89.480000 1 782 1 chr1D.!!$R1 781
3 TraesCS1A01G312000 chr1D 407914859 407918162 3303 True 933.750000 1620 92.595500 868 3630 4 chr1D.!!$R2 2762
4 TraesCS1A01G312000 chr1B 263553059 263553824 765 True 1044.000000 1044 91.406000 16 776 1 chr1B.!!$R1 760
5 TraesCS1A01G312000 chr1B 548610433 548612524 2091 True 887.666667 1399 90.481333 866 3047 3 chr1B.!!$R4 2181
6 TraesCS1A01G312000 chr1B 548548540 548549772 1232 True 394.000000 608 90.512000 3042 3695 2 chr1B.!!$R3 653
7 TraesCS1A01G312000 chr5D 87190518 87191297 779 False 1116.000000 1116 92.494000 1 782 1 chr5D.!!$F1 781
8 TraesCS1A01G312000 chr7D 412667720 412668507 787 False 1044.000000 1044 90.736000 1 781 1 chr7D.!!$F1 780
9 TraesCS1A01G312000 chr6A 337209002 337209786 784 True 998.000000 998 89.682000 1 781 1 chr6A.!!$R1 780
10 TraesCS1A01G312000 chr7B 669973552 669974332 780 False 994.000000 994 89.783000 3 777 1 chr7B.!!$F1 774
11 TraesCS1A01G312000 chr5B 645559511 645560299 788 True 981.000000 981 89.308000 1 783 1 chr5B.!!$R1 782
12 TraesCS1A01G312000 chr4B 273429688 273430465 777 True 974.000000 974 89.354000 1 780 1 chr4B.!!$R2 779

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
922 943 0.249322 AACACTGACGGAGACAACGG 60.249 55.0 0.00 0.00 35.23 4.44 F
1189 1238 0.318441 CTCACCGTCTTCCTGCAGAA 59.682 55.0 17.39 6.85 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2612 2720 0.687354 ACTGTCCAATCGCTTCCAGT 59.313 50.0 0.00 0.00 0.00 4.00 R
3152 3266 0.107312 CTCAGGTCCTGGAGCATTGG 60.107 60.0 26.19 13.18 31.89 3.16 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
31 33 0.908198 GAGGCTCTCACCACCATCTT 59.092 55.000 7.40 0.00 0.00 2.40
35 37 0.325933 CTCTCACCACCATCTTGGCA 59.674 55.000 0.00 0.00 42.67 4.92
85 87 1.872952 CTTATGGCAATGGATTCGCGA 59.127 47.619 3.71 3.71 0.00 5.87
87 89 0.464373 ATGGCAATGGATTCGCGACT 60.464 50.000 9.15 2.14 0.00 4.18
177 181 5.185249 GCCTGAAGAGGATACGAACCATATA 59.815 44.000 0.00 0.00 42.93 0.86
185 189 9.090103 AGAGGATACGAACCATATATTCTTCAA 57.910 33.333 0.00 0.00 46.39 2.69
193 197 6.683974 ACCATATATTCTTCAACTGTGTGC 57.316 37.500 0.00 0.00 0.00 4.57
229 233 1.062148 GGAGCTGTTTCCGCGAATTAC 59.938 52.381 8.23 0.10 0.00 1.89
258 262 1.111277 GCTGGGACCACAACAACTTT 58.889 50.000 0.00 0.00 0.00 2.66
303 308 2.985282 TTACCACCCGCGTCTCGT 60.985 61.111 4.92 0.00 36.19 4.18
310 315 2.444624 CCCGCGTCTCGTCACATTG 61.445 63.158 4.92 0.00 36.19 2.82
388 393 3.245016 TGTGATTCAGCATGTCCCTCTTT 60.245 43.478 0.00 0.00 37.40 2.52
463 469 2.040884 TTAGCCGCCCAGGGAGAT 60.041 61.111 10.89 0.00 41.48 2.75
509 515 2.887568 CTTCGCGCGATGGCTCTT 60.888 61.111 35.21 0.00 36.88 2.85
652 658 2.553028 CCCACAGCTGAACCTTGTGTAT 60.553 50.000 23.35 0.00 40.35 2.29
661 667 4.677584 TGAACCTTGTGTATTGTTTGTGC 58.322 39.130 0.00 0.00 0.00 4.57
666 672 1.865340 TGTGTATTGTTTGTGCGCGTA 59.135 42.857 8.43 0.00 0.00 4.42
744 765 0.738389 CTTTGTGCTCGGTGGTTTGT 59.262 50.000 0.00 0.00 0.00 2.83
759 780 8.578151 TCGGTGGTTTGTTTTATTTATAAAGCT 58.422 29.630 3.94 0.00 35.38 3.74
783 804 5.047847 GGACAAAAGCCTTTTTCAGTAACC 58.952 41.667 0.00 0.00 34.34 2.85
784 805 4.678622 ACAAAAGCCTTTTTCAGTAACCG 58.321 39.130 0.00 0.00 34.34 4.44
785 806 4.048504 CAAAAGCCTTTTTCAGTAACCGG 58.951 43.478 0.00 0.00 34.34 5.28
786 807 2.943036 AGCCTTTTTCAGTAACCGGA 57.057 45.000 9.46 0.00 0.00 5.14
787 808 2.779506 AGCCTTTTTCAGTAACCGGAG 58.220 47.619 9.46 0.00 0.00 4.63
788 809 1.199327 GCCTTTTTCAGTAACCGGAGC 59.801 52.381 9.46 0.00 0.00 4.70
789 810 2.500229 CCTTTTTCAGTAACCGGAGCA 58.500 47.619 9.46 0.00 0.00 4.26
790 811 2.882137 CCTTTTTCAGTAACCGGAGCAA 59.118 45.455 9.46 0.00 0.00 3.91
791 812 3.058224 CCTTTTTCAGTAACCGGAGCAAG 60.058 47.826 9.46 0.00 0.00 4.01
792 813 3.478857 TTTTCAGTAACCGGAGCAAGA 57.521 42.857 9.46 0.00 0.00 3.02
793 814 3.478857 TTTCAGTAACCGGAGCAAGAA 57.521 42.857 9.46 3.69 0.00 2.52
794 815 2.743636 TCAGTAACCGGAGCAAGAAG 57.256 50.000 9.46 0.00 0.00 2.85
795 816 1.968493 TCAGTAACCGGAGCAAGAAGT 59.032 47.619 9.46 0.00 0.00 3.01
796 817 3.159472 TCAGTAACCGGAGCAAGAAGTA 58.841 45.455 9.46 0.00 0.00 2.24
797 818 3.192844 TCAGTAACCGGAGCAAGAAGTAG 59.807 47.826 9.46 0.00 0.00 2.57
798 819 3.192844 CAGTAACCGGAGCAAGAAGTAGA 59.807 47.826 9.46 0.00 0.00 2.59
799 820 3.830755 AGTAACCGGAGCAAGAAGTAGAA 59.169 43.478 9.46 0.00 0.00 2.10
800 821 3.320673 AACCGGAGCAAGAAGTAGAAG 57.679 47.619 9.46 0.00 0.00 2.85
801 822 2.249139 ACCGGAGCAAGAAGTAGAAGT 58.751 47.619 9.46 0.00 0.00 3.01
802 823 2.633481 ACCGGAGCAAGAAGTAGAAGTT 59.367 45.455 9.46 0.00 0.00 2.66
803 824 2.996621 CCGGAGCAAGAAGTAGAAGTTG 59.003 50.000 0.00 0.00 0.00 3.16
804 825 3.306088 CCGGAGCAAGAAGTAGAAGTTGA 60.306 47.826 0.00 0.00 0.00 3.18
805 826 3.923461 CGGAGCAAGAAGTAGAAGTTGAG 59.077 47.826 0.00 0.00 0.00 3.02
806 827 4.321304 CGGAGCAAGAAGTAGAAGTTGAGA 60.321 45.833 0.00 0.00 0.00 3.27
807 828 5.542779 GGAGCAAGAAGTAGAAGTTGAGAA 58.457 41.667 0.00 0.00 0.00 2.87
808 829 5.407084 GGAGCAAGAAGTAGAAGTTGAGAAC 59.593 44.000 0.00 0.00 0.00 3.01
809 830 5.918608 AGCAAGAAGTAGAAGTTGAGAACA 58.081 37.500 0.00 0.00 0.00 3.18
810 831 6.529220 AGCAAGAAGTAGAAGTTGAGAACAT 58.471 36.000 0.00 0.00 0.00 2.71
811 832 7.671302 AGCAAGAAGTAGAAGTTGAGAACATA 58.329 34.615 0.00 0.00 0.00 2.29
812 833 7.816995 AGCAAGAAGTAGAAGTTGAGAACATAG 59.183 37.037 0.00 0.00 0.00 2.23
813 834 7.600752 GCAAGAAGTAGAAGTTGAGAACATAGT 59.399 37.037 0.00 0.00 0.00 2.12
814 835 9.134734 CAAGAAGTAGAAGTTGAGAACATAGTC 57.865 37.037 0.00 0.00 0.00 2.59
815 836 8.644374 AGAAGTAGAAGTTGAGAACATAGTCT 57.356 34.615 0.00 0.00 0.00 3.24
816 837 9.742144 AGAAGTAGAAGTTGAGAACATAGTCTA 57.258 33.333 0.00 0.00 0.00 2.59
817 838 9.997482 GAAGTAGAAGTTGAGAACATAGTCTAG 57.003 37.037 0.00 0.00 0.00 2.43
818 839 9.523168 AAGTAGAAGTTGAGAACATAGTCTAGT 57.477 33.333 0.00 0.00 0.00 2.57
819 840 9.169592 AGTAGAAGTTGAGAACATAGTCTAGTC 57.830 37.037 0.00 0.00 0.00 2.59
820 841 8.948145 GTAGAAGTTGAGAACATAGTCTAGTCA 58.052 37.037 0.00 0.00 0.00 3.41
821 842 8.050778 AGAAGTTGAGAACATAGTCTAGTCAG 57.949 38.462 0.00 0.00 0.00 3.51
822 843 7.668052 AGAAGTTGAGAACATAGTCTAGTCAGT 59.332 37.037 0.00 0.00 0.00 3.41
823 844 7.151999 AGTTGAGAACATAGTCTAGTCAGTG 57.848 40.000 0.00 0.00 0.00 3.66
824 845 6.943146 AGTTGAGAACATAGTCTAGTCAGTGA 59.057 38.462 0.00 0.00 0.00 3.41
825 846 7.448777 AGTTGAGAACATAGTCTAGTCAGTGAA 59.551 37.037 0.00 0.00 0.00 3.18
826 847 7.761038 TGAGAACATAGTCTAGTCAGTGAAA 57.239 36.000 0.00 0.00 0.00 2.69
827 848 7.594714 TGAGAACATAGTCTAGTCAGTGAAAC 58.405 38.462 0.00 0.00 0.00 2.78
828 849 7.230712 TGAGAACATAGTCTAGTCAGTGAAACA 59.769 37.037 0.00 0.00 41.43 2.83
829 850 8.128322 AGAACATAGTCTAGTCAGTGAAACAT 57.872 34.615 0.00 0.00 41.43 2.71
830 851 8.589338 AGAACATAGTCTAGTCAGTGAAACATT 58.411 33.333 0.00 0.00 41.43 2.71
831 852 8.539770 AACATAGTCTAGTCAGTGAAACATTG 57.460 34.615 0.00 0.00 41.43 2.82
832 853 7.896811 ACATAGTCTAGTCAGTGAAACATTGA 58.103 34.615 0.00 0.00 41.43 2.57
833 854 8.031864 ACATAGTCTAGTCAGTGAAACATTGAG 58.968 37.037 0.00 0.00 41.43 3.02
834 855 6.412362 AGTCTAGTCAGTGAAACATTGAGT 57.588 37.500 0.00 8.96 41.43 3.41
835 856 6.219473 AGTCTAGTCAGTGAAACATTGAGTG 58.781 40.000 12.51 5.57 41.43 3.51
836 857 5.406780 GTCTAGTCAGTGAAACATTGAGTGG 59.593 44.000 12.51 10.40 41.43 4.00
837 858 4.156455 AGTCAGTGAAACATTGAGTGGT 57.844 40.909 0.00 0.00 41.43 4.16
838 859 4.526970 AGTCAGTGAAACATTGAGTGGTT 58.473 39.130 0.00 0.00 41.48 3.67
844 865 4.178545 GAAACATTGAGTGGTTCCCATG 57.821 45.455 0.00 0.00 46.68 3.66
845 866 3.524095 AACATTGAGTGGTTCCCATGA 57.476 42.857 0.00 0.00 35.28 3.07
846 867 3.077484 ACATTGAGTGGTTCCCATGAG 57.923 47.619 0.00 0.00 35.28 2.90
847 868 2.644299 ACATTGAGTGGTTCCCATGAGA 59.356 45.455 0.00 0.00 35.28 3.27
848 869 3.267812 ACATTGAGTGGTTCCCATGAGAT 59.732 43.478 0.00 0.00 35.28 2.75
849 870 4.264083 ACATTGAGTGGTTCCCATGAGATT 60.264 41.667 0.00 0.00 35.28 2.40
850 871 4.387026 TTGAGTGGTTCCCATGAGATTT 57.613 40.909 0.00 0.00 35.28 2.17
851 872 4.387026 TGAGTGGTTCCCATGAGATTTT 57.613 40.909 0.00 0.00 35.28 1.82
852 873 4.739793 TGAGTGGTTCCCATGAGATTTTT 58.260 39.130 0.00 0.00 35.28 1.94
874 895 4.955925 TGTGTCACGTCACAAAAAGATT 57.044 36.364 7.56 0.00 43.92 2.40
888 909 1.174712 AAGATTTGTGCGGCAGCTGT 61.175 50.000 16.64 0.00 45.42 4.40
922 943 0.249322 AACACTGACGGAGACAACGG 60.249 55.000 0.00 0.00 35.23 4.44
923 944 1.105167 ACACTGACGGAGACAACGGA 61.105 55.000 0.00 0.00 35.23 4.69
924 945 0.387367 CACTGACGGAGACAACGGAG 60.387 60.000 0.00 0.00 35.23 4.63
925 946 1.444553 CTGACGGAGACAACGGAGC 60.445 63.158 0.00 0.00 35.23 4.70
926 947 2.142357 CTGACGGAGACAACGGAGCA 62.142 60.000 0.00 0.00 35.23 4.26
927 948 1.006571 GACGGAGACAACGGAGCAA 60.007 57.895 0.00 0.00 35.23 3.91
928 949 0.599204 GACGGAGACAACGGAGCAAA 60.599 55.000 0.00 0.00 35.23 3.68
929 950 0.600255 ACGGAGACAACGGAGCAAAG 60.600 55.000 0.00 0.00 35.23 2.77
930 951 0.319555 CGGAGACAACGGAGCAAAGA 60.320 55.000 0.00 0.00 0.00 2.52
931 952 1.872237 CGGAGACAACGGAGCAAAGAA 60.872 52.381 0.00 0.00 0.00 2.52
932 953 2.427506 GGAGACAACGGAGCAAAGAAT 58.572 47.619 0.00 0.00 0.00 2.40
933 954 2.160417 GGAGACAACGGAGCAAAGAATG 59.840 50.000 0.00 0.00 0.00 2.67
1054 1099 3.385384 CCGAGCCTGACTGCCAGA 61.385 66.667 0.00 0.00 45.78 3.86
1085 1130 1.152567 CCATCTCCTCGCCTCTCCT 60.153 63.158 0.00 0.00 0.00 3.69
1086 1131 0.758685 CCATCTCCTCGCCTCTCCTT 60.759 60.000 0.00 0.00 0.00 3.36
1099 1144 1.065854 CTCTCCTTCGCCAAGGTGATT 60.066 52.381 14.11 0.00 46.54 2.57
1101 1146 3.181461 CTCTCCTTCGCCAAGGTGATTAT 60.181 47.826 14.11 0.00 46.54 1.28
1114 1159 4.215908 AGGTGATTATCGCTGAACCTCTA 58.784 43.478 5.72 0.00 32.58 2.43
1115 1160 4.649674 AGGTGATTATCGCTGAACCTCTAA 59.350 41.667 5.72 0.00 32.58 2.10
1116 1161 4.985409 GGTGATTATCGCTGAACCTCTAAG 59.015 45.833 5.72 0.00 0.00 2.18
1117 1162 4.446051 GTGATTATCGCTGAACCTCTAAGC 59.554 45.833 0.00 0.00 0.00 3.09
1119 1164 4.465632 TTATCGCTGAACCTCTAAGCAA 57.534 40.909 0.00 0.00 36.73 3.91
1120 1165 3.550437 ATCGCTGAACCTCTAAGCAAT 57.450 42.857 0.00 0.00 36.73 3.56
1121 1166 2.893637 TCGCTGAACCTCTAAGCAATC 58.106 47.619 0.00 0.00 36.73 2.67
1122 1167 1.590238 CGCTGAACCTCTAAGCAATCG 59.410 52.381 0.00 0.00 36.73 3.34
1123 1168 1.328986 GCTGAACCTCTAAGCAATCGC 59.671 52.381 0.00 0.00 36.91 4.58
1162 1211 1.651770 TCCCTCCTGGTTGTATCCTCT 59.348 52.381 0.00 0.00 34.77 3.69
1173 1222 0.861155 GTATCCTCTCCTCCCCCTCA 59.139 60.000 0.00 0.00 0.00 3.86
1189 1238 0.318441 CTCACCGTCTTCCTGCAGAA 59.682 55.000 17.39 6.85 0.00 3.02
1214 1263 3.522731 CTCCTCCTCGGCGTCAGG 61.523 72.222 6.85 7.66 0.00 3.86
1296 1351 4.724602 GCGCCGTCACTGAGCTCA 62.725 66.667 17.19 17.19 0.00 4.26
1314 1369 3.418623 ATCAGGGCCCTCTCTCCCC 62.419 68.421 25.77 0.00 43.67 4.81
1354 1409 3.612371 AAGCCGTCGACGCAGAGTC 62.612 63.158 31.73 14.77 46.16 3.36
1363 1418 3.805307 CGCAGAGTCGGAGTCGCT 61.805 66.667 19.63 0.02 36.13 4.93
1379 1434 3.524759 CTTCGCAGCGTCGACGAC 61.525 66.667 39.74 28.78 43.02 4.34
1432 1487 4.033702 GCGTGCTTATTTCCTTACTGGTAC 59.966 45.833 0.00 0.00 37.07 3.34
1442 1497 0.963225 TTACTGGTACGTGCTCTGCA 59.037 50.000 3.01 0.00 35.60 4.41
1453 1514 1.066573 GTGCTCTGCAGTATGGACACT 60.067 52.381 14.67 0.00 40.08 3.55
1501 1575 3.625313 TCTTCTTTTCAATGCGTGTGACA 59.375 39.130 0.00 0.00 0.00 3.58
1519 1593 3.627577 TGACAGTCAAAGGAAACTGAAGC 59.372 43.478 0.00 0.22 44.54 3.86
1589 1663 3.354948 TGAGTAGCCAATGTGCTCAAT 57.645 42.857 0.00 0.00 41.68 2.57
1594 1668 3.077484 AGCCAATGTGCTCAATACTGT 57.923 42.857 0.00 0.00 36.75 3.55
1675 1749 3.489738 CCGACGATAAAGTTCCGTGGTAT 60.490 47.826 0.00 0.00 36.60 2.73
1679 1753 3.619483 CGATAAAGTTCCGTGGTATGCAA 59.381 43.478 0.00 0.00 0.00 4.08
1680 1754 4.093703 CGATAAAGTTCCGTGGTATGCAAA 59.906 41.667 0.00 0.00 0.00 3.68
1681 1755 5.391097 CGATAAAGTTCCGTGGTATGCAAAA 60.391 40.000 0.00 0.00 0.00 2.44
1721 1795 6.503589 AGAATAGTACCTAGATCGATGCAC 57.496 41.667 0.54 0.00 0.00 4.57
1841 1917 2.287608 CCCTTCGCTCCAACTTGAAAAC 60.288 50.000 0.00 0.00 0.00 2.43
1856 1932 8.621286 CAACTTGAAAACATAGACAAGGTAAGT 58.379 33.333 0.00 0.00 42.39 2.24
1857 1933 9.841295 AACTTGAAAACATAGACAAGGTAAGTA 57.159 29.630 0.00 0.00 42.39 2.24
1883 1959 0.968405 TTGCCTTCCCATGCAGTTTC 59.032 50.000 0.00 0.00 38.95 2.78
1909 1985 9.329913 CGCTTTGCCTAATTATATTGTACATTC 57.670 33.333 0.00 0.00 0.00 2.67
1948 2045 8.890410 ATAAGAACAGAGGTAGTACCAGTTAA 57.110 34.615 21.49 11.25 41.95 2.01
1976 2073 5.536161 ACTGCAAAAGGAATTGTGATGTACT 59.464 36.000 0.00 0.00 32.80 2.73
1977 2074 6.012658 TGCAAAAGGAATTGTGATGTACTC 57.987 37.500 0.00 0.00 32.80 2.59
1978 2075 5.048083 TGCAAAAGGAATTGTGATGTACTCC 60.048 40.000 0.00 0.00 32.80 3.85
1979 2076 5.622233 GCAAAAGGAATTGTGATGTACTCCC 60.622 44.000 0.00 0.00 32.80 4.30
1980 2077 5.520748 AAAGGAATTGTGATGTACTCCCT 57.479 39.130 0.00 0.00 0.00 4.20
1981 2078 4.762289 AGGAATTGTGATGTACTCCCTC 57.238 45.455 0.00 0.00 0.00 4.30
1982 2079 4.366267 AGGAATTGTGATGTACTCCCTCT 58.634 43.478 0.00 0.00 0.00 3.69
1983 2080 4.163078 AGGAATTGTGATGTACTCCCTCTG 59.837 45.833 0.00 0.00 0.00 3.35
1984 2081 4.080863 GGAATTGTGATGTACTCCCTCTGT 60.081 45.833 0.00 0.00 0.00 3.41
1985 2082 5.128827 GGAATTGTGATGTACTCCCTCTGTA 59.871 44.000 0.00 0.00 0.00 2.74
1986 2083 6.351881 GGAATTGTGATGTACTCCCTCTGTAA 60.352 42.308 0.00 0.00 0.00 2.41
1987 2084 6.620877 ATTGTGATGTACTCCCTCTGTAAA 57.379 37.500 0.00 0.00 0.00 2.01
1988 2085 5.401531 TGTGATGTACTCCCTCTGTAAAC 57.598 43.478 0.00 0.00 0.00 2.01
1989 2086 5.084519 TGTGATGTACTCCCTCTGTAAACT 58.915 41.667 0.00 0.00 0.00 2.66
1990 2087 6.250711 TGTGATGTACTCCCTCTGTAAACTA 58.749 40.000 0.00 0.00 0.00 2.24
1991 2088 6.722590 TGTGATGTACTCCCTCTGTAAACTAA 59.277 38.462 0.00 0.00 0.00 2.24
1992 2089 7.399191 TGTGATGTACTCCCTCTGTAAACTAAT 59.601 37.037 0.00 0.00 0.00 1.73
1993 2090 8.910944 GTGATGTACTCCCTCTGTAAACTAATA 58.089 37.037 0.00 0.00 0.00 0.98
1994 2091 9.656323 TGATGTACTCCCTCTGTAAACTAATAT 57.344 33.333 0.00 0.00 0.00 1.28
2000 2097 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
2002 2099 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
2040 2137 9.490083 ACACTTATATTAGTTTACAGAGGGAGT 57.510 33.333 0.00 0.00 0.00 3.85
2205 2302 3.944055 TTTCACTACTCTCTGCACTCC 57.056 47.619 0.00 0.00 0.00 3.85
2228 2325 5.075858 TGAAAATCATGAATGCAGGGTTC 57.924 39.130 0.00 0.00 25.70 3.62
2351 2458 6.312141 TGTTCCTTCTGATCATGACCATTA 57.688 37.500 0.00 0.00 0.00 1.90
2422 2530 2.706890 GTATTTGAAGCTCCCGTGGAA 58.293 47.619 0.00 0.00 0.00 3.53
2612 2720 0.112606 AGAGTTGGGACGTCTCTCCA 59.887 55.000 17.97 12.45 36.60 3.86
2624 2732 1.205893 GTCTCTCCACTGGAAGCGATT 59.794 52.381 0.00 0.00 37.60 3.34
2648 2756 1.134367 CAGTTATTCGTCTCGGCTCCA 59.866 52.381 0.00 0.00 0.00 3.86
2667 2775 1.799258 AAAGCAAACGGGCAGCTGAG 61.799 55.000 20.43 10.37 38.86 3.35
2738 2846 2.106131 ACGACGAGCTTGTGTGCA 59.894 55.556 12.53 0.00 34.99 4.57
2827 2935 2.825532 CCCCACCAATTGAACGATCTTT 59.174 45.455 7.12 0.00 0.00 2.52
2839 2947 2.798680 ACGATCTTTCCACGATTCTCG 58.201 47.619 0.00 0.00 46.93 4.04
2840 2948 2.120232 CGATCTTTCCACGATTCTCGG 58.880 52.381 1.29 0.00 45.59 4.63
2928 3041 4.248691 TCTTAGGATGCTCATGTGATCG 57.751 45.455 0.00 0.00 0.00 3.69
2947 3060 6.586082 GTGATCGAGTGCCATAAAAACAAATT 59.414 34.615 0.00 0.00 0.00 1.82
2957 3070 8.341173 TGCCATAAAAACAAATTTGTCATCAAC 58.659 29.630 23.47 10.33 41.31 3.18
2959 3072 8.008844 CCATAAAAACAAATTTGTCATCAACCG 58.991 33.333 23.47 8.89 41.31 4.44
3131 3245 1.140452 TGAGCAGGAGATCAAGGATGC 59.860 52.381 0.00 0.00 37.20 3.91
3139 3253 0.652592 GATCAAGGATGCGGTGTTCG 59.347 55.000 0.00 0.00 42.76 3.95
3151 3265 0.892063 GGTGTTCGCTCTCTCCTCTT 59.108 55.000 0.00 0.00 0.00 2.85
3152 3266 1.135228 GGTGTTCGCTCTCTCCTCTTC 60.135 57.143 0.00 0.00 0.00 2.87
3156 3270 2.151502 TCGCTCTCTCCTCTTCCAAT 57.848 50.000 0.00 0.00 0.00 3.16
3171 3285 0.107312 CCAATGCTCCAGGACCTGAG 60.107 60.000 23.77 17.70 32.44 3.35
3176 3910 1.743321 GCTCCAGGACCTGAGGATCG 61.743 65.000 23.77 4.93 38.61 3.69
3198 3932 2.014010 AACCCATTTGTGCATGGACT 57.986 45.000 18.75 0.00 46.18 3.85
3226 3960 2.014068 GCTGGATTTCCCTCTTCACGG 61.014 57.143 0.00 0.00 35.38 4.94
3300 4034 0.545071 CCATCCTTTTGGCCCTTGGT 60.545 55.000 0.00 0.00 40.12 3.67
3303 4037 0.486879 TCCTTTTGGCCCTTGGTGAT 59.513 50.000 0.00 0.00 40.12 3.06
3309 4043 2.048603 GGCCCTTGGTGATGTGAGC 61.049 63.158 0.00 0.00 0.00 4.26
3310 4044 1.303561 GCCCTTGGTGATGTGAGCA 60.304 57.895 0.00 0.00 0.00 4.26
3360 4094 1.337118 TCTTCCCCATTTGTTGCCAC 58.663 50.000 0.00 0.00 0.00 5.01
3417 4151 1.618074 GCCAAGATTGCTTCCTTCCCT 60.618 52.381 0.00 0.00 30.14 4.20
3438 4172 1.465387 AAGGTACCTGGGGTTGCCT 60.465 57.895 17.14 0.00 40.00 4.75
3439 4173 0.178855 AAGGTACCTGGGGTTGCCTA 60.179 55.000 17.14 0.00 38.34 3.93
3490 4224 1.377690 TCAAGGCCTCATTGGGGTTA 58.622 50.000 5.23 0.00 36.00 2.85
3537 4272 3.622263 AGGCTGGGGAGGTGGGTA 61.622 66.667 0.00 0.00 0.00 3.69
3555 4290 0.250234 TAAGCTCAATGGAGTGCGCT 59.750 50.000 9.73 0.00 41.22 5.92
3559 4294 0.460811 CTCAATGGAGTGCGCTAGCA 60.461 55.000 16.45 0.00 45.08 3.49
3583 4318 1.525995 CTCAAAGTGCGTGGGTGGT 60.526 57.895 0.00 0.00 0.00 4.16
3652 4387 1.451567 CCTAGAGGTCGTCGGCTCA 60.452 63.158 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 37 1.591768 TCTTTAAGGGGAGCCGGATT 58.408 50.000 5.05 0.00 0.00 3.01
96 98 2.592993 TTTCAGGACCTCTGCCGGG 61.593 63.158 2.18 0.00 43.06 5.73
177 181 1.238439 CGGGCACACAGTTGAAGAAT 58.762 50.000 0.00 0.00 0.00 2.40
229 233 2.352805 GTCCCAGCTTCCACCCAG 59.647 66.667 0.00 0.00 0.00 4.45
463 469 1.040646 GATGGAGGTGATGGCGTCTA 58.959 55.000 8.40 0.00 0.00 2.59
652 658 0.658368 ACACATACGCGCACAAACAA 59.342 45.000 5.73 0.00 0.00 2.83
661 667 0.442310 CAAGGTCCAACACATACGCG 59.558 55.000 3.53 3.53 0.00 6.01
666 672 1.181098 GCAGGCAAGGTCCAACACAT 61.181 55.000 0.00 0.00 0.00 3.21
744 765 9.430623 GGCTTTTGTCCAGCTTTATAAATAAAA 57.569 29.630 0.00 0.00 37.43 1.52
759 780 5.394773 GGTTACTGAAAAAGGCTTTTGTCCA 60.395 40.000 24.73 19.76 34.83 4.02
783 804 3.914312 TCAACTTCTACTTCTTGCTCCG 58.086 45.455 0.00 0.00 0.00 4.63
784 805 5.140747 TCTCAACTTCTACTTCTTGCTCC 57.859 43.478 0.00 0.00 0.00 4.70
785 806 5.986135 TGTTCTCAACTTCTACTTCTTGCTC 59.014 40.000 0.00 0.00 0.00 4.26
786 807 5.918608 TGTTCTCAACTTCTACTTCTTGCT 58.081 37.500 0.00 0.00 0.00 3.91
787 808 6.793492 ATGTTCTCAACTTCTACTTCTTGC 57.207 37.500 0.00 0.00 0.00 4.01
788 809 9.134734 GACTATGTTCTCAACTTCTACTTCTTG 57.865 37.037 0.00 0.00 0.00 3.02
789 810 9.084533 AGACTATGTTCTCAACTTCTACTTCTT 57.915 33.333 0.00 0.00 0.00 2.52
790 811 8.644374 AGACTATGTTCTCAACTTCTACTTCT 57.356 34.615 0.00 0.00 0.00 2.85
791 812 9.997482 CTAGACTATGTTCTCAACTTCTACTTC 57.003 37.037 0.00 0.00 0.00 3.01
792 813 9.523168 ACTAGACTATGTTCTCAACTTCTACTT 57.477 33.333 0.00 0.00 0.00 2.24
793 814 9.169592 GACTAGACTATGTTCTCAACTTCTACT 57.830 37.037 0.00 0.00 0.00 2.57
794 815 8.948145 TGACTAGACTATGTTCTCAACTTCTAC 58.052 37.037 0.00 0.00 0.00 2.59
795 816 9.168451 CTGACTAGACTATGTTCTCAACTTCTA 57.832 37.037 0.00 0.00 0.00 2.10
796 817 7.668052 ACTGACTAGACTATGTTCTCAACTTCT 59.332 37.037 0.00 0.00 0.00 2.85
797 818 7.753132 CACTGACTAGACTATGTTCTCAACTTC 59.247 40.741 0.00 0.00 0.00 3.01
798 819 7.448777 TCACTGACTAGACTATGTTCTCAACTT 59.551 37.037 0.00 0.00 0.00 2.66
799 820 6.943146 TCACTGACTAGACTATGTTCTCAACT 59.057 38.462 0.00 0.00 0.00 3.16
800 821 7.147143 TCACTGACTAGACTATGTTCTCAAC 57.853 40.000 0.00 0.00 0.00 3.18
801 822 7.761038 TTCACTGACTAGACTATGTTCTCAA 57.239 36.000 0.00 0.00 0.00 3.02
802 823 7.230712 TGTTTCACTGACTAGACTATGTTCTCA 59.769 37.037 0.00 0.00 0.00 3.27
803 824 7.594714 TGTTTCACTGACTAGACTATGTTCTC 58.405 38.462 0.00 0.00 0.00 2.87
804 825 7.526142 TGTTTCACTGACTAGACTATGTTCT 57.474 36.000 0.00 0.00 0.00 3.01
805 826 8.651588 CAATGTTTCACTGACTAGACTATGTTC 58.348 37.037 0.00 0.00 0.00 3.18
806 827 8.367911 TCAATGTTTCACTGACTAGACTATGTT 58.632 33.333 0.00 0.00 0.00 2.71
807 828 7.896811 TCAATGTTTCACTGACTAGACTATGT 58.103 34.615 0.00 0.00 0.00 2.29
808 829 8.031864 ACTCAATGTTTCACTGACTAGACTATG 58.968 37.037 0.00 0.00 0.00 2.23
809 830 8.031864 CACTCAATGTTTCACTGACTAGACTAT 58.968 37.037 0.00 0.00 0.00 2.12
810 831 7.371159 CACTCAATGTTTCACTGACTAGACTA 58.629 38.462 0.00 0.00 0.00 2.59
811 832 6.219473 CACTCAATGTTTCACTGACTAGACT 58.781 40.000 0.00 0.00 0.00 3.24
812 833 5.406780 CCACTCAATGTTTCACTGACTAGAC 59.593 44.000 0.00 0.00 0.00 2.59
813 834 5.070446 ACCACTCAATGTTTCACTGACTAGA 59.930 40.000 0.00 0.00 0.00 2.43
814 835 5.300752 ACCACTCAATGTTTCACTGACTAG 58.699 41.667 0.00 0.00 0.00 2.57
815 836 5.290493 ACCACTCAATGTTTCACTGACTA 57.710 39.130 0.00 0.00 0.00 2.59
816 837 4.156455 ACCACTCAATGTTTCACTGACT 57.844 40.909 0.00 0.00 0.00 3.41
817 838 4.261197 GGAACCACTCAATGTTTCACTGAC 60.261 45.833 0.00 0.00 0.00 3.51
818 839 3.882888 GGAACCACTCAATGTTTCACTGA 59.117 43.478 0.00 0.00 0.00 3.41
819 840 4.228912 GGAACCACTCAATGTTTCACTG 57.771 45.455 0.00 0.00 0.00 3.66
853 874 4.955925 AATCTTTTTGTGACGTGACACA 57.044 36.364 7.55 6.67 46.86 3.72
854 875 5.604815 CAAATCTTTTTGTGACGTGACAC 57.395 39.130 7.55 3.61 37.92 3.67
865 886 1.192980 GCTGCCGCACAAATCTTTTTG 59.807 47.619 0.00 0.00 46.27 2.44
866 887 1.069049 AGCTGCCGCACAAATCTTTTT 59.931 42.857 2.05 0.00 39.10 1.94
874 895 1.652012 GTAAACAGCTGCCGCACAA 59.348 52.632 15.27 0.00 39.10 3.33
883 904 3.806949 TCCATTTCCTGGTAAACAGCT 57.193 42.857 0.00 0.00 46.14 4.24
888 909 4.825085 GTCAGTGTTCCATTTCCTGGTAAA 59.175 41.667 0.00 0.00 46.08 2.01
934 955 1.723608 TTGCTCAACACGCCACTTGG 61.724 55.000 0.00 0.00 38.53 3.61
935 956 0.100325 TTTGCTCAACACGCCACTTG 59.900 50.000 0.00 0.00 0.00 3.16
936 957 0.381801 CTTTGCTCAACACGCCACTT 59.618 50.000 0.00 0.00 0.00 3.16
937 958 0.463654 TCTTTGCTCAACACGCCACT 60.464 50.000 0.00 0.00 0.00 4.00
938 959 0.380378 TTCTTTGCTCAACACGCCAC 59.620 50.000 0.00 0.00 0.00 5.01
939 960 1.001487 CATTCTTTGCTCAACACGCCA 60.001 47.619 0.00 0.00 0.00 5.69
940 961 1.689959 CATTCTTTGCTCAACACGCC 58.310 50.000 0.00 0.00 0.00 5.68
990 1011 0.664761 GCATGATCACATCCGGTTGG 59.335 55.000 16.70 6.13 34.15 3.77
1039 1084 2.267324 GGTCTGGCAGTCAGGCTC 59.733 66.667 15.27 0.00 46.77 4.70
1045 1090 4.083862 GGGGACGGTCTGGCAGTC 62.084 72.222 15.27 8.99 40.77 3.51
1069 1114 0.821711 CGAAGGAGAGGCGAGGAGAT 60.822 60.000 0.00 0.00 0.00 2.75
1072 1117 3.141488 GCGAAGGAGAGGCGAGGA 61.141 66.667 0.00 0.00 0.00 3.71
1085 1130 1.134521 AGCGATAATCACCTTGGCGAA 60.135 47.619 0.00 0.00 0.00 4.70
1086 1131 0.464036 AGCGATAATCACCTTGGCGA 59.536 50.000 0.00 0.00 0.00 5.54
1099 1144 4.621991 GATTGCTTAGAGGTTCAGCGATA 58.378 43.478 0.00 0.00 37.71 2.92
1101 1146 2.735444 CGATTGCTTAGAGGTTCAGCGA 60.735 50.000 0.00 0.00 36.24 4.93
1117 1162 0.526954 GCAAAGATGGGCAGCGATTG 60.527 55.000 0.00 0.00 0.00 2.67
1119 1164 0.682209 AAGCAAAGATGGGCAGCGAT 60.682 50.000 0.00 0.00 0.00 4.58
1120 1165 1.303561 AAGCAAAGATGGGCAGCGA 60.304 52.632 0.00 0.00 0.00 4.93
1121 1166 1.153901 CAAGCAAAGATGGGCAGCG 60.154 57.895 0.00 0.00 0.00 5.18
1122 1167 0.822164 ATCAAGCAAAGATGGGCAGC 59.178 50.000 0.00 0.00 0.00 5.25
1123 1168 2.159142 GGAATCAAGCAAAGATGGGCAG 60.159 50.000 0.00 0.00 0.00 4.85
1124 1169 1.826720 GGAATCAAGCAAAGATGGGCA 59.173 47.619 0.00 0.00 0.00 5.36
1126 1171 2.692041 GAGGGAATCAAGCAAAGATGGG 59.308 50.000 0.00 0.00 0.00 4.00
1127 1172 2.692041 GGAGGGAATCAAGCAAAGATGG 59.308 50.000 0.00 0.00 0.00 3.51
1129 1174 3.626729 CCAGGAGGGAATCAAGCAAAGAT 60.627 47.826 0.00 0.00 40.01 2.40
1130 1175 2.291153 CCAGGAGGGAATCAAGCAAAGA 60.291 50.000 0.00 0.00 40.01 2.52
1162 1211 2.800159 GAAGACGGTGAGGGGGAGGA 62.800 65.000 0.00 0.00 0.00 3.71
1173 1222 1.371558 GGTTCTGCAGGAAGACGGT 59.628 57.895 15.13 0.00 34.23 4.83
1189 1238 2.835431 CGAGGAGGAGGCGATGGT 60.835 66.667 0.00 0.00 0.00 3.55
1296 1351 2.288643 GGGAGAGAGGGCCCTGAT 59.711 66.667 34.59 18.99 41.31 2.90
1314 1369 1.177256 ACAGCTTGCCTTGGCTTCTG 61.177 55.000 13.18 16.65 36.59 3.02
1376 1431 1.594293 AAGAACAGCCACCACGTCG 60.594 57.895 0.00 0.00 0.00 5.12
1379 1434 0.588252 CTTCAAGAACAGCCACCACG 59.412 55.000 0.00 0.00 0.00 4.94
1432 1487 0.108662 TGTCCATACTGCAGAGCACG 60.109 55.000 23.35 3.45 33.79 5.34
1442 1497 5.255687 TGCAAATCATTCAGTGTCCATACT 58.744 37.500 0.00 0.00 0.00 2.12
1501 1575 4.273318 ACTTGCTTCAGTTTCCTTTGACT 58.727 39.130 0.00 0.00 0.00 3.41
1519 1593 5.921976 TGCTCTGAATGTGCAAATTAACTTG 59.078 36.000 0.95 0.00 41.46 3.16
1578 1652 7.495606 TGAAATCGATACAGTATTGAGCACATT 59.504 33.333 14.73 3.05 32.34 2.71
1589 1663 6.153851 TGAAGTTCCCTGAAATCGATACAGTA 59.846 38.462 22.22 12.69 0.00 2.74
1594 1668 5.422331 AGAGTGAAGTTCCCTGAAATCGATA 59.578 40.000 0.00 0.00 0.00 2.92
1721 1795 5.104259 AGTTAGTTCTTGGCAGATAAGGG 57.896 43.478 0.00 0.00 0.00 3.95
1883 1959 9.329913 GAATGTACAATATAATTAGGCAAAGCG 57.670 33.333 0.00 0.00 0.00 4.68
1909 1985 9.250624 CCTCTGTTCTTATATTTAGAAACGGAG 57.749 37.037 12.67 12.67 36.78 4.63
1948 2045 7.444299 ACATCACAATTCCTTTTGCAGTTTAT 58.556 30.769 0.00 0.00 0.00 1.40
1976 2073 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
2014 2111 9.490083 ACTCCCTCTGTAAACTAATATAAGTGT 57.510 33.333 0.00 0.00 0.00 3.55
2025 2122 8.993424 ACATATTTGATACTCCCTCTGTAAACT 58.007 33.333 0.00 0.00 0.00 2.66
2026 2123 9.046296 CACATATTTGATACTCCCTCTGTAAAC 57.954 37.037 0.00 0.00 0.00 2.01
2027 2124 8.768397 ACACATATTTGATACTCCCTCTGTAAA 58.232 33.333 0.00 0.00 0.00 2.01
2028 2125 8.319057 ACACATATTTGATACTCCCTCTGTAA 57.681 34.615 0.00 0.00 0.00 2.41
2029 2126 7.785028 AGACACATATTTGATACTCCCTCTGTA 59.215 37.037 0.00 0.00 0.00 2.74
2030 2127 6.613271 AGACACATATTTGATACTCCCTCTGT 59.387 38.462 0.00 0.00 0.00 3.41
2031 2128 7.060383 AGACACATATTTGATACTCCCTCTG 57.940 40.000 0.00 0.00 0.00 3.35
2032 2129 6.015856 CGAGACACATATTTGATACTCCCTCT 60.016 42.308 0.00 0.00 0.00 3.69
2033 2130 6.153067 CGAGACACATATTTGATACTCCCTC 58.847 44.000 0.00 0.00 0.00 4.30
2034 2131 5.598830 ACGAGACACATATTTGATACTCCCT 59.401 40.000 0.00 0.00 0.00 4.20
2035 2132 5.844004 ACGAGACACATATTTGATACTCCC 58.156 41.667 0.00 0.00 0.00 4.30
2036 2133 7.772332 AAACGAGACACATATTTGATACTCC 57.228 36.000 0.00 0.00 0.00 3.85
2102 2199 7.014711 TGCCAACATTAACCAAACAAGAAGATA 59.985 33.333 0.00 0.00 0.00 1.98
2189 2286 2.889170 TCAGGAGTGCAGAGAGTAGT 57.111 50.000 0.00 0.00 0.00 2.73
2205 2302 4.730949 ACCCTGCATTCATGATTTTCAG 57.269 40.909 0.00 3.30 0.00 3.02
2228 2325 1.578583 AAACTTTGTGTCGACCCTCG 58.421 50.000 14.12 0.26 42.10 4.63
2358 2465 2.675658 TAGCCTCAAAAGCCAAAGGT 57.324 45.000 0.00 0.00 0.00 3.50
2374 2482 6.241207 TGAAAGTAGTGCAGAAACATTAGC 57.759 37.500 0.00 0.00 0.00 3.09
2422 2530 0.764369 TCTTATGGCGATGAGGGGCT 60.764 55.000 0.67 0.00 0.00 5.19
2517 2625 6.493166 AGTGTGAAATAAGGGATGGATGAAA 58.507 36.000 0.00 0.00 0.00 2.69
2612 2720 0.687354 ACTGTCCAATCGCTTCCAGT 59.313 50.000 0.00 0.00 0.00 4.00
2624 2732 1.135199 GCCGAGACGAATAACTGTCCA 60.135 52.381 0.00 0.00 35.71 4.02
2648 2756 1.799258 CTCAGCTGCCCGTTTGCTTT 61.799 55.000 9.47 0.00 34.51 3.51
2667 2775 1.032014 TCCAAAGTTCACTTGCCAGC 58.968 50.000 0.00 0.00 36.12 4.85
2839 2947 3.439895 TGCGGTTGGTAAAAAGAAACC 57.560 42.857 0.00 0.00 38.96 3.27
2840 2948 3.552699 GGTTGCGGTTGGTAAAAAGAAAC 59.447 43.478 0.00 0.00 0.00 2.78
2895 3003 6.876257 TGAGCATCCTAAGAAAGAAAGAAGAC 59.124 38.462 0.00 0.00 0.00 3.01
2896 3004 7.009179 TGAGCATCCTAAGAAAGAAAGAAGA 57.991 36.000 0.00 0.00 0.00 2.87
2897 3005 7.336427 ACATGAGCATCCTAAGAAAGAAAGAAG 59.664 37.037 0.00 0.00 0.00 2.85
2898 3006 7.120285 CACATGAGCATCCTAAGAAAGAAAGAA 59.880 37.037 0.00 0.00 0.00 2.52
2928 3041 7.475771 TGACAAATTTGTTTTTATGGCACTC 57.524 32.000 24.02 7.87 42.43 3.51
2947 3060 5.278266 GGAGACAATTTTCGGTTGATGACAA 60.278 40.000 0.00 0.00 0.00 3.18
2957 3070 1.135575 GCTGCTGGAGACAATTTTCGG 60.136 52.381 0.00 0.00 42.06 4.30
2959 3072 1.203287 GGGCTGCTGGAGACAATTTTC 59.797 52.381 3.88 0.00 42.06 2.29
3131 3245 1.137825 GAGGAGAGAGCGAACACCG 59.862 63.158 0.00 0.00 42.21 4.94
3139 3253 1.485895 AGCATTGGAAGAGGAGAGAGC 59.514 52.381 0.00 0.00 0.00 4.09
3141 3255 2.114616 GGAGCATTGGAAGAGGAGAGA 58.885 52.381 0.00 0.00 0.00 3.10
3151 3265 0.547471 TCAGGTCCTGGAGCATTGGA 60.547 55.000 26.19 15.06 31.89 3.53
3152 3266 0.107312 CTCAGGTCCTGGAGCATTGG 60.107 60.000 26.19 13.18 31.89 3.16
3156 3270 0.689080 GATCCTCAGGTCCTGGAGCA 60.689 60.000 26.19 6.98 36.41 4.26
3171 3285 1.135112 GCACAAATGGGTTTCCGATCC 60.135 52.381 0.00 0.00 35.24 3.36
3176 3910 1.622811 TCCATGCACAAATGGGTTTCC 59.377 47.619 4.27 0.00 46.17 3.13
3226 3960 4.167554 TGGCAAAAATACCAACATCGTC 57.832 40.909 0.00 0.00 31.46 4.20
3268 4002 1.727062 AGGATGGAGGAGATCGCATT 58.273 50.000 0.00 0.00 0.00 3.56
3300 4034 1.001293 GTGACCAGACTGCTCACATCA 59.999 52.381 21.11 5.26 35.39 3.07
3303 4037 1.995376 TAGTGACCAGACTGCTCACA 58.005 50.000 25.62 13.36 37.39 3.58
3334 4068 4.592942 CAACAAATGGGGAAGATCTCAGA 58.407 43.478 0.00 0.00 0.00 3.27
3337 4071 2.428530 GGCAACAAATGGGGAAGATCTC 59.571 50.000 0.00 0.00 0.00 2.75
3360 4094 4.240888 GGATGTCATGTAGATCCATGTCG 58.759 47.826 13.13 0.00 45.50 4.35
3417 4151 1.282382 GCAACCCCAGGTACCTTCTA 58.718 55.000 13.15 0.00 33.12 2.10
3438 4172 0.391130 AAAAGCGGCGAGAGTGCATA 60.391 50.000 12.98 0.00 37.13 3.14
3439 4173 1.672356 AAAAGCGGCGAGAGTGCAT 60.672 52.632 12.98 0.00 37.13 3.96
3446 4180 1.746760 GATATTGCAAAAGCGGCGAG 58.253 50.000 12.98 0.00 0.00 5.03
3465 4199 2.816087 CCCAATGAGGCCTTGATAATCG 59.184 50.000 6.77 0.00 35.39 3.34
3490 4224 2.351276 GTGGCCTGTTGATCGGGT 59.649 61.111 3.32 0.00 44.16 5.28
3515 4249 4.316823 ACCTCCCCAGCCTCGACA 62.317 66.667 0.00 0.00 0.00 4.35
3524 4258 1.615424 GAGCTTACCCACCTCCCCA 60.615 63.158 0.00 0.00 0.00 4.96
3535 4270 0.375106 GCGCACTCCATTGAGCTTAC 59.625 55.000 0.30 0.00 42.74 2.34
3536 4271 2.767536 GCGCACTCCATTGAGCTTA 58.232 52.632 0.30 0.00 42.74 3.09
3537 4272 3.583383 GCGCACTCCATTGAGCTT 58.417 55.556 0.30 0.00 42.74 3.74
3559 4294 1.518056 CCACGCACTTTGAGCCACAT 61.518 55.000 0.00 0.00 0.00 3.21
3562 4297 2.594303 CCCACGCACTTTGAGCCA 60.594 61.111 0.00 0.00 0.00 4.75
3583 4318 0.322098 CACTTGGTCGCCCATGGTTA 60.322 55.000 11.73 0.00 41.49 2.85
3644 4379 1.227973 GGATGGGGATTGAGCCGAC 60.228 63.158 0.00 0.00 0.00 4.79
3648 4383 0.541296 CATGGGGATGGGGATTGAGC 60.541 60.000 0.00 0.00 0.00 4.26
3652 4387 4.904578 TCCATGGGGATGGGGATT 57.095 55.556 13.02 0.00 41.95 3.01


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

AutoCloner maintained by Alex Coulton.