Multiple sequence alignment - TraesCS7A01G392900

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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 TraesCS7A01G392900 chr7A 100.000 4109 0 0 1 4109 570120215 570124323 0.000000e+00 7589
1 TraesCS7A01G392900 chr7A 95.147 680 32 1 1 680 635373355 635372677 0.000000e+00 1072
2 TraesCS7A01G392900 chr7A 91.930 285 13 4 3031 3307 570141390 570141672 1.380000e-104 390
3 TraesCS7A01G392900 chr7A 81.953 338 33 17 2472 2807 570140789 570141100 1.130000e-65 261
4 TraesCS7A01G392900 chr7A 94.215 121 4 1 3298 3415 570143284 570143404 9.070000e-42 182
5 TraesCS7A01G392900 chr7A 85.380 171 13 5 2860 3030 570141106 570141264 2.540000e-37 167
6 TraesCS7A01G392900 chr7D 92.555 2243 96 19 1904 4109 502998392 503000600 0.000000e+00 3151
7 TraesCS7A01G392900 chr7D 92.165 970 59 6 2612 3579 503686493 503687447 0.000000e+00 1354
8 TraesCS7A01G392900 chr7D 95.894 682 26 2 1 681 151540752 151540072 0.000000e+00 1103
9 TraesCS7A01G392900 chr7D 90.281 854 55 18 925 1766 502997554 502998391 0.000000e+00 1092
10 TraesCS7A01G392900 chr7D 95.468 684 27 4 1 681 114467956 114467274 0.000000e+00 1088
11 TraesCS7A01G392900 chr7D 88.911 505 52 3 3088 3591 503146269 503146770 1.620000e-173 619
12 TraesCS7A01G392900 chr7D 84.814 619 58 8 3031 3648 503295998 503296581 1.270000e-164 590
13 TraesCS7A01G392900 chr7D 87.368 380 33 8 3392 3757 503039485 503039863 4.910000e-114 422
14 TraesCS7A01G392900 chr7D 88.112 286 20 9 2414 2699 503089113 503089384 1.100000e-85 327
15 TraesCS7A01G392900 chr7D 86.296 270 26 3 3033 3302 503039007 503039265 2.420000e-72 283
16 TraesCS7A01G392900 chr7D 81.437 334 35 15 2475 2806 503295401 503295709 8.820000e-62 248
17 TraesCS7A01G392900 chr7D 87.209 172 9 5 2860 3031 503038737 503038895 2.520000e-42 183
18 TraesCS7A01G392900 chr7D 86.127 173 9 6 2860 3032 503295717 503295874 5.460000e-39 172
19 TraesCS7A01G392900 chr7D 92.105 114 8 1 2700 2813 503038624 503038736 4.250000e-35 159
20 TraesCS7A01G392900 chr7D 85.430 151 22 0 2288 2438 503295251 503295401 1.530000e-34 158
21 TraesCS7A01G392900 chr7D 79.167 240 21 12 2475 2712 503030922 503031134 5.540000e-29 139
22 TraesCS7A01G392900 chr7B 94.051 1849 70 13 2279 4109 531664011 531665837 0.000000e+00 2769
23 TraesCS7A01G392900 chr7B 87.625 1398 78 34 925 2282 531662451 531663793 0.000000e+00 1535
24 TraesCS7A01G392900 chr7B 91.438 619 48 3 3031 3648 531762594 531763208 0.000000e+00 845
25 TraesCS7A01G392900 chr7B 81.503 346 31 21 2475 2813 531761991 531762310 1.900000e-63 254
26 TraesCS7A01G392900 chr7B 84.971 173 13 6 2860 3032 531762311 531762470 3.290000e-36 163
27 TraesCS7A01G392900 chr7B 80.000 250 24 19 3685 3914 531776916 531777159 1.180000e-35 161
28 TraesCS7A01G392900 chr6D 95.785 688 24 4 1 685 379092773 379093458 0.000000e+00 1105
29 TraesCS7A01G392900 chr1B 95.748 682 23 5 1 679 358031909 358031231 0.000000e+00 1094
30 TraesCS7A01G392900 chr3A 95.315 683 28 3 1 679 660861166 660861848 0.000000e+00 1081
31 TraesCS7A01G392900 chr2B 95.322 684 25 6 1 680 262902859 262903539 0.000000e+00 1079
32 TraesCS7A01G392900 chr5A 95.168 683 26 6 1 679 504754946 504754267 0.000000e+00 1072
33 TraesCS7A01G392900 chr3D 95.029 684 29 5 1 681 214959346 214958665 0.000000e+00 1070
34 TraesCS7A01G392900 chr3D 96.863 542 15 1 2619 3158 141837444 141836903 0.000000e+00 905
35 TraesCS7A01G392900 chr3D 96.795 156 5 0 1205 1360 141837595 141837440 1.130000e-65 261
36 TraesCS7A01G392900 chr3D 91.667 144 11 1 988 1131 141837733 141837591 9.010000e-47 198


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 TraesCS7A01G392900 chr7A 570120215 570124323 4108 False 7589.000000 7589 100.000000 1 4109 1 chr7A.!!$F1 4108
1 TraesCS7A01G392900 chr7A 635372677 635373355 678 True 1072.000000 1072 95.147000 1 680 1 chr7A.!!$R1 679
2 TraesCS7A01G392900 chr7A 570140789 570143404 2615 False 250.000000 390 88.369500 2472 3415 4 chr7A.!!$F2 943
3 TraesCS7A01G392900 chr7D 502997554 503000600 3046 False 2121.500000 3151 91.418000 925 4109 2 chr7D.!!$F5 3184
4 TraesCS7A01G392900 chr7D 503686493 503687447 954 False 1354.000000 1354 92.165000 2612 3579 1 chr7D.!!$F4 967
5 TraesCS7A01G392900 chr7D 151540072 151540752 680 True 1103.000000 1103 95.894000 1 681 1 chr7D.!!$R2 680
6 TraesCS7A01G392900 chr7D 114467274 114467956 682 True 1088.000000 1088 95.468000 1 681 1 chr7D.!!$R1 680
7 TraesCS7A01G392900 chr7D 503146269 503146770 501 False 619.000000 619 88.911000 3088 3591 1 chr7D.!!$F3 503
8 TraesCS7A01G392900 chr7D 503295251 503296581 1330 False 292.000000 590 84.452000 2288 3648 4 chr7D.!!$F7 1360
9 TraesCS7A01G392900 chr7D 503038624 503039863 1239 False 261.750000 422 88.244500 2700 3757 4 chr7D.!!$F6 1057
10 TraesCS7A01G392900 chr7B 531662451 531665837 3386 False 2152.000000 2769 90.838000 925 4109 2 chr7B.!!$F2 3184
11 TraesCS7A01G392900 chr7B 531761991 531763208 1217 False 420.666667 845 85.970667 2475 3648 3 chr7B.!!$F3 1173
12 TraesCS7A01G392900 chr6D 379092773 379093458 685 False 1105.000000 1105 95.785000 1 685 1 chr6D.!!$F1 684
13 TraesCS7A01G392900 chr1B 358031231 358031909 678 True 1094.000000 1094 95.748000 1 679 1 chr1B.!!$R1 678
14 TraesCS7A01G392900 chr3A 660861166 660861848 682 False 1081.000000 1081 95.315000 1 679 1 chr3A.!!$F1 678
15 TraesCS7A01G392900 chr2B 262902859 262903539 680 False 1079.000000 1079 95.322000 1 680 1 chr2B.!!$F1 679
16 TraesCS7A01G392900 chr5A 504754267 504754946 679 True 1072.000000 1072 95.168000 1 679 1 chr5A.!!$R1 678
17 TraesCS7A01G392900 chr3D 214958665 214959346 681 True 1070.000000 1070 95.029000 1 681 1 chr3D.!!$R1 680
18 TraesCS7A01G392900 chr3D 141836903 141837733 830 True 454.666667 905 95.108333 988 3158 3 chr3D.!!$R2 2170

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
948 958 0.038166 TCTCATCCCAGCCCAACAAC 59.962 55.0 0.00 0.00 0.0 3.32 F
1549 1577 0.039617 TTGCTTGTATTGGTGCGCAC 60.040 50.0 32.15 32.15 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2362 2645 0.250640 AGCACTGAAGGTCAAGGCTG 60.251 55.000 0.0 0.0 35.42 4.85 R
3507 5731 2.038007 AGCCGCTTCTCCTCCTCA 59.962 61.111 0.0 0.0 0.00 3.86 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
41 42 0.883833 AACTACAGCTGTTGCCATGC 59.116 50.000 27.06 0.00 40.80 4.06
237 240 4.853007 AGAAAGAGTTGCCATCTGCTTAT 58.147 39.130 0.00 0.00 42.00 1.73
295 298 5.726980 AACATATGGCAACTGACATGTTT 57.273 34.783 8.36 0.00 44.95 2.83
409 417 2.037367 AGAGGAGGCAGGCGTGTA 59.963 61.111 8.40 0.00 0.00 2.90
592 602 6.489675 CATACAAAATCAGCTAATTCGTGCT 58.510 36.000 0.00 0.00 40.54 4.40
612 622 5.292101 GTGCTAAGATTCGTGCAGAAGTTAT 59.708 40.000 0.00 0.00 42.92 1.89
650 660 0.840617 TGTGGGTGAGTTGGCTAACA 59.159 50.000 15.86 0.00 39.30 2.41
681 691 3.186817 TGTGGGCGTTAACATTTTCGTAG 59.813 43.478 6.39 0.00 0.00 3.51
684 694 4.514441 TGGGCGTTAACATTTTCGTAGAAA 59.486 37.500 6.39 0.00 45.90 2.52
685 695 5.008415 TGGGCGTTAACATTTTCGTAGAAAA 59.992 36.000 6.39 9.90 45.90 2.29
686 696 5.914074 GGGCGTTAACATTTTCGTAGAAAAA 59.086 36.000 11.28 0.00 45.90 1.94
724 734 9.849166 TTTCATTTACGATAAAGAAAATGGACC 57.151 29.630 6.75 0.00 38.97 4.46
725 735 7.690228 TCATTTACGATAAAGAAAATGGACCG 58.310 34.615 6.75 0.00 38.97 4.79
726 736 6.425577 TTTACGATAAAGAAAATGGACCGG 57.574 37.500 0.00 0.00 0.00 5.28
727 737 4.210724 ACGATAAAGAAAATGGACCGGA 57.789 40.909 9.46 0.00 0.00 5.14
728 738 4.777463 ACGATAAAGAAAATGGACCGGAT 58.223 39.130 9.46 0.00 0.00 4.18
729 739 4.814771 ACGATAAAGAAAATGGACCGGATC 59.185 41.667 9.46 1.18 0.00 3.36
730 740 4.084537 CGATAAAGAAAATGGACCGGATCG 60.085 45.833 9.46 3.37 0.00 3.69
731 741 3.343941 AAAGAAAATGGACCGGATCGA 57.656 42.857 9.46 0.00 0.00 3.59
732 742 3.560636 AAGAAAATGGACCGGATCGAT 57.439 42.857 9.46 0.00 0.00 3.59
733 743 2.838736 AGAAAATGGACCGGATCGATG 58.161 47.619 9.46 0.00 0.00 3.84
734 744 2.434336 AGAAAATGGACCGGATCGATGA 59.566 45.455 9.46 0.00 0.00 2.92
735 745 2.240493 AAATGGACCGGATCGATGAC 57.760 50.000 9.46 0.00 0.00 3.06
736 746 0.393077 AATGGACCGGATCGATGACC 59.607 55.000 9.46 0.00 0.00 4.02
737 747 1.472662 ATGGACCGGATCGATGACCC 61.473 60.000 9.46 0.00 0.00 4.46
738 748 2.131709 GGACCGGATCGATGACCCA 61.132 63.158 9.46 0.00 0.00 4.51
739 749 1.682451 GGACCGGATCGATGACCCAA 61.682 60.000 9.46 0.00 0.00 4.12
740 750 0.393077 GACCGGATCGATGACCCAAT 59.607 55.000 9.46 0.00 0.00 3.16
741 751 0.837272 ACCGGATCGATGACCCAATT 59.163 50.000 9.46 0.00 0.00 2.32
742 752 1.211949 ACCGGATCGATGACCCAATTT 59.788 47.619 9.46 0.00 0.00 1.82
743 753 1.603802 CCGGATCGATGACCCAATTTG 59.396 52.381 0.54 0.00 0.00 2.32
744 754 2.288666 CGGATCGATGACCCAATTTGT 58.711 47.619 0.54 0.00 0.00 2.83
745 755 3.462982 CGGATCGATGACCCAATTTGTA 58.537 45.455 0.54 0.00 0.00 2.41
746 756 4.065088 CGGATCGATGACCCAATTTGTAT 58.935 43.478 0.54 0.00 0.00 2.29
747 757 4.515191 CGGATCGATGACCCAATTTGTATT 59.485 41.667 0.54 0.00 0.00 1.89
748 758 5.699001 CGGATCGATGACCCAATTTGTATTA 59.301 40.000 0.54 0.00 0.00 0.98
749 759 6.371548 CGGATCGATGACCCAATTTGTATTAT 59.628 38.462 0.54 0.00 0.00 1.28
750 760 7.413000 CGGATCGATGACCCAATTTGTATTATC 60.413 40.741 0.54 0.00 0.00 1.75
751 761 7.607991 GGATCGATGACCCAATTTGTATTATCT 59.392 37.037 0.54 0.00 0.00 1.98
752 762 9.653287 GATCGATGACCCAATTTGTATTATCTA 57.347 33.333 0.54 0.00 0.00 1.98
767 777 9.849166 TTGTATTATCTATAATTCGCATCGTGA 57.151 29.630 0.77 0.00 34.91 4.35
772 782 7.658179 ATCTATAATTCGCATCGTGATTTGT 57.342 32.000 0.00 0.00 0.00 2.83
773 783 7.105494 TCTATAATTCGCATCGTGATTTGTC 57.895 36.000 0.00 0.00 0.00 3.18
774 784 5.991328 ATAATTCGCATCGTGATTTGTCT 57.009 34.783 0.00 0.00 0.00 3.41
775 785 4.685169 AATTCGCATCGTGATTTGTCTT 57.315 36.364 0.00 0.00 0.00 3.01
776 786 4.685169 ATTCGCATCGTGATTTGTCTTT 57.315 36.364 0.00 0.00 0.00 2.52
777 787 4.481930 TTCGCATCGTGATTTGTCTTTT 57.518 36.364 0.00 0.00 0.00 2.27
778 788 4.481930 TCGCATCGTGATTTGTCTTTTT 57.518 36.364 0.00 0.00 0.00 1.94
830 840 9.296400 TCTGATTTTAAATTTTATACAAGCGGC 57.704 29.630 0.00 0.00 0.00 6.53
831 841 8.109843 TGATTTTAAATTTTATACAAGCGGCG 57.890 30.769 0.51 0.51 0.00 6.46
832 842 5.935448 TTTAAATTTTATACAAGCGGCGC 57.065 34.783 26.86 26.86 0.00 6.53
833 843 3.775661 AAATTTTATACAAGCGGCGCT 57.224 38.095 31.35 31.35 42.56 5.92
849 859 7.764695 AGCGGCGCTTTTTAAAATTAATATT 57.235 28.000 31.35 0.00 33.89 1.28
850 860 8.192068 AGCGGCGCTTTTTAAAATTAATATTT 57.808 26.923 31.35 0.00 33.89 1.40
851 861 8.113675 AGCGGCGCTTTTTAAAATTAATATTTG 58.886 29.630 31.35 0.00 33.89 2.32
852 862 8.111224 GCGGCGCTTTTTAAAATTAATATTTGA 58.889 29.630 26.86 0.00 34.27 2.69
853 863 9.618410 CGGCGCTTTTTAAAATTAATATTTGAG 57.382 29.630 7.64 0.00 34.27 3.02
854 864 9.420966 GGCGCTTTTTAAAATTAATATTTGAGC 57.579 29.630 7.64 3.03 34.27 4.26
855 865 9.132137 GCGCTTTTTAAAATTAATATTTGAGCG 57.868 29.630 22.37 22.37 39.91 5.03
856 866 9.132137 CGCTTTTTAAAATTAATATTTGAGCGC 57.868 29.630 17.87 0.00 36.05 5.92
872 882 7.475771 TTTGAGCGCTTTTTGAAAATTATGT 57.524 28.000 13.26 0.00 0.00 2.29
873 883 6.689178 TGAGCGCTTTTTGAAAATTATGTC 57.311 33.333 13.26 0.00 0.00 3.06
874 884 5.341993 TGAGCGCTTTTTGAAAATTATGTCG 59.658 36.000 13.26 0.00 0.00 4.35
875 885 5.219633 AGCGCTTTTTGAAAATTATGTCGT 58.780 33.333 2.64 0.00 0.00 4.34
876 886 5.689961 AGCGCTTTTTGAAAATTATGTCGTT 59.310 32.000 2.64 0.00 0.00 3.85
877 887 6.200097 AGCGCTTTTTGAAAATTATGTCGTTT 59.800 30.769 2.64 0.00 0.00 3.60
878 888 6.843779 GCGCTTTTTGAAAATTATGTCGTTTT 59.156 30.769 0.00 0.00 0.00 2.43
879 889 7.372135 GCGCTTTTTGAAAATTATGTCGTTTTT 59.628 29.630 0.00 0.00 0.00 1.94
908 918 9.475620 AGGAGAAAAATAAACCAATTACCTAGG 57.524 33.333 7.41 7.41 0.00 3.02
909 919 9.470399 GGAGAAAAATAAACCAATTACCTAGGA 57.530 33.333 17.98 0.00 0.00 2.94
911 921 8.953313 AGAAAAATAAACCAATTACCTAGGACG 58.047 33.333 17.98 0.00 0.00 4.79
912 922 6.688637 AAATAAACCAATTACCTAGGACGC 57.311 37.500 17.98 0.00 0.00 5.19
913 923 2.704464 AACCAATTACCTAGGACGCC 57.296 50.000 17.98 0.00 0.00 5.68
914 924 0.835276 ACCAATTACCTAGGACGCCC 59.165 55.000 17.98 0.00 0.00 6.13
915 925 0.108019 CCAATTACCTAGGACGCCCC 59.892 60.000 17.98 0.00 0.00 5.80
916 926 0.834612 CAATTACCTAGGACGCCCCA 59.165 55.000 17.98 0.00 37.41 4.96
917 927 1.129058 AATTACCTAGGACGCCCCAG 58.871 55.000 17.98 0.00 37.41 4.45
918 928 0.763223 ATTACCTAGGACGCCCCAGG 60.763 60.000 17.98 0.00 38.44 4.45
919 929 1.877672 TTACCTAGGACGCCCCAGGA 61.878 60.000 17.98 0.00 36.97 3.86
920 930 1.877672 TACCTAGGACGCCCCAGGAA 61.878 60.000 17.98 0.00 36.97 3.36
921 931 2.435693 CCTAGGACGCCCCAGGAAG 61.436 68.421 1.05 0.00 36.13 3.46
922 932 1.381327 CTAGGACGCCCCAGGAAGA 60.381 63.158 0.00 0.00 37.41 2.87
923 933 1.381327 TAGGACGCCCCAGGAAGAG 60.381 63.158 0.00 0.00 37.41 2.85
924 934 1.870941 TAGGACGCCCCAGGAAGAGA 61.871 60.000 0.00 0.00 37.41 3.10
925 935 2.291043 GGACGCCCCAGGAAGAGAA 61.291 63.158 0.00 0.00 34.14 2.87
926 936 1.079057 GACGCCCCAGGAAGAGAAC 60.079 63.158 0.00 0.00 0.00 3.01
927 937 1.536662 ACGCCCCAGGAAGAGAACT 60.537 57.895 0.00 0.00 0.00 3.01
928 938 1.219393 CGCCCCAGGAAGAGAACTC 59.781 63.158 0.00 0.00 0.00 3.01
929 939 1.261238 CGCCCCAGGAAGAGAACTCT 61.261 60.000 0.00 0.00 42.75 3.24
948 958 0.038166 TCTCATCCCAGCCCAACAAC 59.962 55.000 0.00 0.00 0.00 3.32
960 970 0.899717 CCAACAACCCCAGGGACATG 60.900 60.000 7.25 5.27 38.96 3.21
985 996 2.344093 AAAGGGACAGGCCTCTTCTA 57.656 50.000 0.00 0.00 36.66 2.10
986 997 1.872773 AAGGGACAGGCCTCTTCTAG 58.127 55.000 0.00 0.00 36.66 2.43
1089 1114 2.046217 GAGACCTCAAACCCCCGC 60.046 66.667 0.00 0.00 0.00 6.13
1140 1165 0.904865 TAGACCAGGTGAGGGCACAG 60.905 60.000 0.00 0.00 46.96 3.66
1153 1178 0.793250 GGCACAGAACTTCGCTCTTC 59.207 55.000 0.00 0.00 0.00 2.87
1167 1192 2.251893 GCTCTTCTACGGTCTTGTTCG 58.748 52.381 0.00 0.00 0.00 3.95
1202 1228 4.612412 GTCGTTGTGGGCCGGTGA 62.612 66.667 1.90 0.00 0.00 4.02
1253 1279 2.492090 CCGGTGGAGCTCTCTTCG 59.508 66.667 14.64 12.13 0.00 3.79
1392 1418 5.341617 TCGGTCGCTTTTTGTTACAAAAAT 58.658 33.333 28.62 0.00 0.00 1.82
1426 1452 5.443431 GCGCGCTCATTAGAGTTGATATAAC 60.443 44.000 26.67 0.00 44.00 1.89
1436 1462 5.124645 AGAGTTGATATAACGTCTCCGACT 58.875 41.667 0.00 0.00 37.88 4.18
1444 1470 1.038280 ACGTCTCCGACTCCTTGTTT 58.962 50.000 0.00 0.00 37.88 2.83
1445 1471 2.233271 ACGTCTCCGACTCCTTGTTTA 58.767 47.619 0.00 0.00 37.88 2.01
1446 1472 2.824341 ACGTCTCCGACTCCTTGTTTAT 59.176 45.455 0.00 0.00 37.88 1.40
1447 1473 3.179830 CGTCTCCGACTCCTTGTTTATG 58.820 50.000 0.00 0.00 35.63 1.90
1448 1474 2.930682 GTCTCCGACTCCTTGTTTATGC 59.069 50.000 0.00 0.00 0.00 3.14
1449 1475 2.832129 TCTCCGACTCCTTGTTTATGCT 59.168 45.455 0.00 0.00 0.00 3.79
1452 1478 5.046878 TCTCCGACTCCTTGTTTATGCTAAA 60.047 40.000 0.00 0.00 0.00 1.85
1453 1479 5.741011 TCCGACTCCTTGTTTATGCTAAAT 58.259 37.500 0.00 0.00 0.00 1.40
1454 1480 6.177610 TCCGACTCCTTGTTTATGCTAAATT 58.822 36.000 0.00 0.00 0.00 1.82
1477 1505 8.986477 ATTTTGGTGTGATTTTAGCTTGTATC 57.014 30.769 0.00 0.00 0.00 2.24
1506 1534 7.012327 TCCAATGGCTCTAAGATGAATTAAACG 59.988 37.037 0.00 0.00 0.00 3.60
1508 1536 6.903883 TGGCTCTAAGATGAATTAAACGAC 57.096 37.500 0.00 0.00 0.00 4.34
1510 1538 6.757010 TGGCTCTAAGATGAATTAAACGACTC 59.243 38.462 0.00 0.00 0.00 3.36
1546 1574 5.444481 GCTTTTATTTGCTTGTATTGGTGCG 60.444 40.000 0.00 0.00 0.00 5.34
1547 1575 1.994916 ATTTGCTTGTATTGGTGCGC 58.005 45.000 0.00 0.00 0.00 6.09
1548 1576 0.670706 TTTGCTTGTATTGGTGCGCA 59.329 45.000 5.66 5.66 0.00 6.09
1549 1577 0.039617 TTGCTTGTATTGGTGCGCAC 60.040 50.000 32.15 32.15 0.00 5.34
1550 1578 1.169034 TGCTTGTATTGGTGCGCACA 61.169 50.000 38.60 22.42 0.00 4.57
1551 1579 0.039617 GCTTGTATTGGTGCGCACAA 60.040 50.000 38.60 28.88 0.00 3.33
1552 1580 1.967762 CTTGTATTGGTGCGCACAAG 58.032 50.000 38.60 27.54 41.19 3.16
1570 1598 5.335127 CACAAGGCACAATTTAGTCTATGC 58.665 41.667 0.00 0.00 0.00 3.14
1579 1607 5.181245 ACAATTTAGTCTATGCACAGCGTTT 59.819 36.000 0.00 0.00 0.00 3.60
1595 1623 1.196127 CGTTTGTTCTTAGGGGTTCGC 59.804 52.381 0.00 0.00 0.00 4.70
1610 1638 3.501950 GGTTCGCTATTTTGCCTTCTTG 58.498 45.455 0.00 0.00 0.00 3.02
1631 1659 1.963515 GAGAAGCAACAATGTTGGGGT 59.036 47.619 25.19 5.36 0.00 4.95
1644 1672 6.498651 ACAATGTTGGGGTTAATAATTCACCA 59.501 34.615 0.00 0.00 32.39 4.17
1705 1734 7.526041 AGATATTGGGGTAATAATTCTGCACA 58.474 34.615 0.00 0.00 35.03 4.57
1742 1773 9.461312 ACTGGCTTAGATGTTAAATTGTTATGA 57.539 29.630 0.00 0.00 0.00 2.15
1743 1774 9.722056 CTGGCTTAGATGTTAAATTGTTATGAC 57.278 33.333 0.00 0.00 0.00 3.06
1744 1775 8.394877 TGGCTTAGATGTTAAATTGTTATGACG 58.605 33.333 0.00 0.00 0.00 4.35
1768 1799 9.924650 ACGATCTTTCTTAAGTAGTTGTGTATT 57.075 29.630 1.63 0.00 32.98 1.89
1776 1807 4.296621 AGTAGTTGTGTATTGAACCCCC 57.703 45.455 0.00 0.00 0.00 5.40
1789 1844 2.158385 TGAACCCCCACTTTAGCAACAT 60.158 45.455 0.00 0.00 0.00 2.71
1798 1853 7.174946 CCCCCACTTTAGCAACATATTGTATAG 59.825 40.741 0.00 0.00 38.17 1.31
1817 1872 9.693739 TTGTATAGGTCCATATTTGAACATGTT 57.306 29.630 11.78 11.78 0.00 2.71
1864 1919 9.237187 TGAGTGAAATTTTAATACTGTGCCATA 57.763 29.630 0.00 0.00 0.00 2.74
1934 1989 5.565509 TGTGGAGTTATTGCCTGTTTATCA 58.434 37.500 0.00 0.00 0.00 2.15
2039 2096 5.112686 CAGAGGAATAGCTTAGGTTGTGTC 58.887 45.833 0.00 0.00 0.00 3.67
2046 2103 4.546829 AGCTTAGGTTGTGTCGGAAATA 57.453 40.909 0.00 0.00 0.00 1.40
2055 2112 8.173542 AGGTTGTGTCGGAAATAATAGTTTTT 57.826 30.769 0.00 0.00 0.00 1.94
2056 2113 8.079809 AGGTTGTGTCGGAAATAATAGTTTTTG 58.920 33.333 0.00 0.00 0.00 2.44
2105 2162 1.007118 TCTGATCAGCCTGGACTGGTA 59.993 52.381 18.36 0.00 38.26 3.25
2117 2174 1.621814 GGACTGGTAACCACTGTAGCA 59.378 52.381 0.00 0.00 0.00 3.49
2140 2197 2.214376 TTTACTGGGTGAGGCCAATG 57.786 50.000 5.01 0.00 39.65 2.82
2148 2205 2.450476 GGTGAGGCCAATGTCTGATTT 58.550 47.619 5.01 0.00 37.17 2.17
2224 2281 3.451141 TGTGTTTTGGGTTCATTCAGC 57.549 42.857 0.00 0.00 0.00 4.26
2227 2284 2.034053 TGTTTTGGGTTCATTCAGCGAC 59.966 45.455 0.00 0.00 0.00 5.19
2228 2285 1.974265 TTTGGGTTCATTCAGCGACA 58.026 45.000 0.00 0.00 0.00 4.35
2229 2286 1.974265 TTGGGTTCATTCAGCGACAA 58.026 45.000 0.00 0.00 0.00 3.18
2230 2287 1.974265 TGGGTTCATTCAGCGACAAA 58.026 45.000 0.00 0.00 0.00 2.83
2231 2288 2.302260 TGGGTTCATTCAGCGACAAAA 58.698 42.857 0.00 0.00 0.00 2.44
2232 2289 2.890311 TGGGTTCATTCAGCGACAAAAT 59.110 40.909 0.00 0.00 0.00 1.82
2310 2593 2.380064 TGTTCACCTGGGCAAGAAAT 57.620 45.000 0.00 0.00 0.00 2.17
2360 2643 5.493809 TCAAGTTGTATACTTAGTTGGGGC 58.506 41.667 18.10 0.00 45.29 5.80
2362 2645 3.201487 AGTTGTATACTTAGTTGGGGCCC 59.799 47.826 18.17 18.17 31.29 5.80
2421 2710 6.607019 ACCAATGGAGTAAACCAGAAACTAA 58.393 36.000 6.16 0.00 43.49 2.24
2439 2728 7.706607 AGAAACTAATGTCAGCAAAAAGGTTTC 59.293 33.333 0.00 0.00 0.00 2.78
3095 3522 9.203421 TGTTAGCGAAGTAATATGAACCATATG 57.797 33.333 0.00 0.00 37.17 1.78
3507 5731 0.323957 GCAGGGGGAAGAACTACGTT 59.676 55.000 0.00 0.00 0.00 3.99
3604 5828 4.150980 TGTTATTTGTCCGTGTTAGCTTCG 59.849 41.667 0.00 0.00 0.00 3.79
3655 5880 1.214367 TTTGTCGCGAAGTTCACTCC 58.786 50.000 12.06 0.00 0.00 3.85
3748 5985 3.336122 AGCAGTGCTCCCTTTTCTG 57.664 52.632 13.14 0.00 30.62 3.02
3749 5986 0.475906 AGCAGTGCTCCCTTTTCTGT 59.524 50.000 13.14 0.00 30.62 3.41
3750 5987 0.595095 GCAGTGCTCCCTTTTCTGTG 59.405 55.000 8.18 0.00 0.00 3.66
3751 5988 1.972872 CAGTGCTCCCTTTTCTGTGT 58.027 50.000 0.00 0.00 0.00 3.72
3760 6013 1.270625 CCTTTTCTGTGTGCTCCCGTA 60.271 52.381 0.00 0.00 0.00 4.02
3833 6086 4.962362 TCATAGCCATTCTTACTGGTGAGA 59.038 41.667 0.00 0.00 36.10 3.27
3846 6099 4.632153 ACTGGTGAGAATCTGTGTGTTAC 58.368 43.478 0.00 0.00 34.92 2.50
4040 6294 4.143030 CGTTCTTGATTTTCGCAGAGACAT 60.143 41.667 0.00 0.00 38.43 3.06
4067 6321 8.579006 GCATCAAATGGTATTTGGATCAGAATA 58.421 33.333 12.72 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.474478 ACTGCAGTAGATCAGACCACG 59.526 52.381 20.16 0.00 34.57 4.94
50 51 3.572632 ATCATGGCAACTGCAGTAGAT 57.427 42.857 22.01 13.25 44.36 1.98
237 240 2.674563 AAACTGCCCTAGCGTGCACA 62.675 55.000 18.64 0.00 44.31 4.57
319 327 2.372264 CCCTAGTGTGATTGCAAGCAT 58.628 47.619 21.76 7.63 0.00 3.79
379 387 0.838122 CTCCTCTCCCACACCCAAGT 60.838 60.000 0.00 0.00 0.00 3.16
409 417 3.127533 GCGTTTGCCATCTCGCCT 61.128 61.111 0.00 0.00 42.33 5.52
556 566 6.346919 GCTGATTTTGTATGCTACATAGGACG 60.347 42.308 0.00 0.00 38.68 4.79
563 573 7.279981 ACGAATTAGCTGATTTTGTATGCTACA 59.720 33.333 5.07 0.00 36.19 2.74
566 576 6.489675 CACGAATTAGCTGATTTTGTATGCT 58.510 36.000 5.07 0.00 37.72 3.79
592 602 6.312918 GTCCAATAACTTCTGCACGAATCTTA 59.687 38.462 0.00 0.00 0.00 2.10
612 622 2.668632 GCCTCCATCACCGTCCAA 59.331 61.111 0.00 0.00 0.00 3.53
698 708 9.849166 GGTCCATTTTCTTTATCGTAAATGAAA 57.151 29.630 0.00 8.41 39.26 2.69
699 709 8.178964 CGGTCCATTTTCTTTATCGTAAATGAA 58.821 33.333 0.00 0.00 39.26 2.57
700 710 7.201661 CCGGTCCATTTTCTTTATCGTAAATGA 60.202 37.037 0.00 0.00 39.26 2.57
701 711 6.910433 CCGGTCCATTTTCTTTATCGTAAATG 59.090 38.462 0.00 0.00 37.59 2.32
702 712 6.824704 TCCGGTCCATTTTCTTTATCGTAAAT 59.175 34.615 0.00 0.00 0.00 1.40
703 713 6.171921 TCCGGTCCATTTTCTTTATCGTAAA 58.828 36.000 0.00 0.00 0.00 2.01
704 714 5.732633 TCCGGTCCATTTTCTTTATCGTAA 58.267 37.500 0.00 0.00 0.00 3.18
705 715 5.341872 TCCGGTCCATTTTCTTTATCGTA 57.658 39.130 0.00 0.00 0.00 3.43
706 716 4.210724 TCCGGTCCATTTTCTTTATCGT 57.789 40.909 0.00 0.00 0.00 3.73
707 717 4.084537 CGATCCGGTCCATTTTCTTTATCG 60.085 45.833 0.00 0.00 0.00 2.92
708 718 5.054477 TCGATCCGGTCCATTTTCTTTATC 58.946 41.667 0.00 0.00 0.00 1.75
709 719 5.031066 TCGATCCGGTCCATTTTCTTTAT 57.969 39.130 0.00 0.00 0.00 1.40
710 720 4.475051 TCGATCCGGTCCATTTTCTTTA 57.525 40.909 0.00 0.00 0.00 1.85
711 721 3.343941 TCGATCCGGTCCATTTTCTTT 57.656 42.857 0.00 0.00 0.00 2.52
712 722 3.118408 TCATCGATCCGGTCCATTTTCTT 60.118 43.478 0.00 0.00 0.00 2.52
713 723 2.434336 TCATCGATCCGGTCCATTTTCT 59.566 45.455 0.00 0.00 0.00 2.52
714 724 2.544267 GTCATCGATCCGGTCCATTTTC 59.456 50.000 0.00 0.00 0.00 2.29
715 725 2.561569 GTCATCGATCCGGTCCATTTT 58.438 47.619 0.00 0.00 0.00 1.82
716 726 1.202651 GGTCATCGATCCGGTCCATTT 60.203 52.381 0.00 0.00 0.00 2.32
717 727 0.393077 GGTCATCGATCCGGTCCATT 59.607 55.000 0.00 0.00 0.00 3.16
718 728 1.472662 GGGTCATCGATCCGGTCCAT 61.473 60.000 0.00 0.00 0.00 3.41
719 729 2.131709 GGGTCATCGATCCGGTCCA 61.132 63.158 0.00 0.00 0.00 4.02
720 730 1.682451 TTGGGTCATCGATCCGGTCC 61.682 60.000 0.00 0.00 35.15 4.46
721 731 0.393077 ATTGGGTCATCGATCCGGTC 59.607 55.000 0.00 0.00 35.15 4.79
722 732 0.837272 AATTGGGTCATCGATCCGGT 59.163 50.000 0.00 0.00 35.15 5.28
723 733 1.603802 CAAATTGGGTCATCGATCCGG 59.396 52.381 0.00 0.00 35.15 5.14
724 734 2.288666 ACAAATTGGGTCATCGATCCG 58.711 47.619 0.00 0.00 35.15 4.18
725 735 7.607991 AGATAATACAAATTGGGTCATCGATCC 59.392 37.037 0.00 0.00 32.52 3.36
726 736 8.553459 AGATAATACAAATTGGGTCATCGATC 57.447 34.615 0.00 0.00 0.00 3.69
741 751 9.849166 TCACGATGCGAATTATAGATAATACAA 57.151 29.630 0.00 0.00 32.91 2.41
746 756 9.203421 ACAAATCACGATGCGAATTATAGATAA 57.797 29.630 0.00 0.00 0.00 1.75
747 757 8.757164 ACAAATCACGATGCGAATTATAGATA 57.243 30.769 0.00 0.00 0.00 1.98
748 758 7.600375 AGACAAATCACGATGCGAATTATAGAT 59.400 33.333 0.00 0.00 0.00 1.98
749 759 6.923508 AGACAAATCACGATGCGAATTATAGA 59.076 34.615 0.00 0.00 0.00 1.98
750 760 7.110179 AGACAAATCACGATGCGAATTATAG 57.890 36.000 0.00 0.00 0.00 1.31
751 761 7.477144 AAGACAAATCACGATGCGAATTATA 57.523 32.000 0.00 0.00 0.00 0.98
752 762 5.991328 AGACAAATCACGATGCGAATTAT 57.009 34.783 0.00 0.00 0.00 1.28
753 763 5.794687 AAGACAAATCACGATGCGAATTA 57.205 34.783 0.00 0.00 0.00 1.40
754 764 4.685169 AAGACAAATCACGATGCGAATT 57.315 36.364 0.00 0.00 0.00 2.17
755 765 4.685169 AAAGACAAATCACGATGCGAAT 57.315 36.364 0.00 0.00 0.00 3.34
756 766 4.481930 AAAAGACAAATCACGATGCGAA 57.518 36.364 0.00 0.00 0.00 4.70
757 767 4.481930 AAAAAGACAAATCACGATGCGA 57.518 36.364 0.00 0.00 0.00 5.10
804 814 9.296400 GCCGCTTGTATAAAATTTAAAATCAGA 57.704 29.630 0.00 0.00 0.00 3.27
805 815 8.259194 CGCCGCTTGTATAAAATTTAAAATCAG 58.741 33.333 0.00 0.00 0.00 2.90
806 816 7.253817 GCGCCGCTTGTATAAAATTTAAAATCA 60.254 33.333 0.00 0.00 0.00 2.57
807 817 7.043656 AGCGCCGCTTGTATAAAATTTAAAATC 60.044 33.333 5.39 0.00 33.89 2.17
808 818 6.754675 AGCGCCGCTTGTATAAAATTTAAAAT 59.245 30.769 5.39 0.00 33.89 1.82
809 819 6.094061 AGCGCCGCTTGTATAAAATTTAAAA 58.906 32.000 5.39 0.00 33.89 1.52
810 820 5.642686 AGCGCCGCTTGTATAAAATTTAAA 58.357 33.333 5.39 0.00 33.89 1.52
811 821 5.238006 AGCGCCGCTTGTATAAAATTTAA 57.762 34.783 5.39 0.00 33.89 1.52
812 822 4.886247 AGCGCCGCTTGTATAAAATTTA 57.114 36.364 5.39 0.00 33.89 1.40
813 823 3.775661 AGCGCCGCTTGTATAAAATTT 57.224 38.095 5.39 0.00 33.89 1.82
824 834 8.661257 AAATATTAATTTTAAAAAGCGCCGCTT 58.339 25.926 20.26 20.26 40.35 4.68
825 835 7.764695 AATATTAATTTTAAAAAGCGCCGCT 57.235 28.000 5.39 5.39 42.56 5.52
826 836 8.111224 TCAAATATTAATTTTAAAAAGCGCCGC 58.889 29.630 2.29 0.00 32.87 6.53
827 837 9.618410 CTCAAATATTAATTTTAAAAAGCGCCG 57.382 29.630 2.29 0.00 32.87 6.46
828 838 9.420966 GCTCAAATATTAATTTTAAAAAGCGCC 57.579 29.630 2.29 0.00 32.87 6.53
829 839 9.132137 CGCTCAAATATTAATTTTAAAAAGCGC 57.868 29.630 17.87 0.00 34.93 5.92
830 840 9.132137 GCGCTCAAATATTAATTTTAAAAAGCG 57.868 29.630 22.37 22.37 39.06 4.68
846 856 9.202273 ACATAATTTTCAAAAAGCGCTCAAATA 57.798 25.926 12.06 0.00 0.00 1.40
847 857 8.086851 ACATAATTTTCAAAAAGCGCTCAAAT 57.913 26.923 12.06 6.13 0.00 2.32
848 858 7.475771 ACATAATTTTCAAAAAGCGCTCAAA 57.524 28.000 12.06 3.87 0.00 2.69
849 859 6.129221 CGACATAATTTTCAAAAAGCGCTCAA 60.129 34.615 12.06 0.00 0.00 3.02
850 860 5.341993 CGACATAATTTTCAAAAAGCGCTCA 59.658 36.000 12.06 0.00 0.00 4.26
851 861 5.342259 ACGACATAATTTTCAAAAAGCGCTC 59.658 36.000 12.06 0.00 0.00 5.03
852 862 5.219633 ACGACATAATTTTCAAAAAGCGCT 58.780 33.333 2.64 2.64 0.00 5.92
853 863 5.494863 ACGACATAATTTTCAAAAAGCGC 57.505 34.783 0.00 0.00 0.00 5.92
854 864 8.746328 AAAAACGACATAATTTTCAAAAAGCG 57.254 26.923 0.00 0.00 0.00 4.68
882 892 9.475620 CCTAGGTAATTGGTTTATTTTTCTCCT 57.524 33.333 0.00 0.00 0.00 3.69
883 893 9.470399 TCCTAGGTAATTGGTTTATTTTTCTCC 57.530 33.333 9.08 0.00 0.00 3.71
885 895 8.953313 CGTCCTAGGTAATTGGTTTATTTTTCT 58.047 33.333 9.08 0.00 0.00 2.52
886 896 7.699391 GCGTCCTAGGTAATTGGTTTATTTTTC 59.301 37.037 9.08 0.00 0.00 2.29
887 897 7.363181 GGCGTCCTAGGTAATTGGTTTATTTTT 60.363 37.037 9.08 0.00 0.00 1.94
888 898 6.095860 GGCGTCCTAGGTAATTGGTTTATTTT 59.904 38.462 9.08 0.00 0.00 1.82
889 899 5.591472 GGCGTCCTAGGTAATTGGTTTATTT 59.409 40.000 9.08 0.00 0.00 1.40
890 900 5.128205 GGCGTCCTAGGTAATTGGTTTATT 58.872 41.667 9.08 0.00 0.00 1.40
891 901 4.445305 GGGCGTCCTAGGTAATTGGTTTAT 60.445 45.833 9.08 0.00 0.00 1.40
892 902 3.118298 GGGCGTCCTAGGTAATTGGTTTA 60.118 47.826 9.08 0.00 0.00 2.01
893 903 2.356432 GGGCGTCCTAGGTAATTGGTTT 60.356 50.000 9.08 0.00 0.00 3.27
894 904 1.211212 GGGCGTCCTAGGTAATTGGTT 59.789 52.381 9.08 0.00 0.00 3.67
895 905 0.835276 GGGCGTCCTAGGTAATTGGT 59.165 55.000 9.08 0.00 0.00 3.67
896 906 0.108019 GGGGCGTCCTAGGTAATTGG 59.892 60.000 5.77 0.00 0.00 3.16
897 907 0.834612 TGGGGCGTCCTAGGTAATTG 59.165 55.000 5.77 0.00 36.20 2.32
898 908 1.129058 CTGGGGCGTCCTAGGTAATT 58.871 55.000 12.35 0.00 37.92 1.40
899 909 2.836020 CTGGGGCGTCCTAGGTAAT 58.164 57.895 12.35 0.00 37.92 1.89
900 910 4.368003 CTGGGGCGTCCTAGGTAA 57.632 61.111 12.35 0.00 37.92 2.85
904 914 1.381327 TCTTCCTGGGGCGTCCTAG 60.381 63.158 13.33 13.33 40.88 3.02
905 915 1.381327 CTCTTCCTGGGGCGTCCTA 60.381 63.158 5.77 0.00 36.20 2.94
906 916 2.685380 CTCTTCCTGGGGCGTCCT 60.685 66.667 5.77 0.00 36.20 3.85
907 917 2.291043 TTCTCTTCCTGGGGCGTCC 61.291 63.158 0.00 0.00 0.00 4.79
908 918 1.079057 GTTCTCTTCCTGGGGCGTC 60.079 63.158 0.00 0.00 0.00 5.19
909 919 1.536662 AGTTCTCTTCCTGGGGCGT 60.537 57.895 0.00 0.00 0.00 5.68
910 920 1.219393 GAGTTCTCTTCCTGGGGCG 59.781 63.158 0.00 0.00 0.00 6.13
911 921 0.539518 GAGAGTTCTCTTCCTGGGGC 59.460 60.000 3.77 0.00 39.81 5.80
922 932 1.494960 GGCTGGGATGAGAGAGTTCT 58.505 55.000 0.00 0.00 36.01 3.01
923 933 0.467804 GGGCTGGGATGAGAGAGTTC 59.532 60.000 0.00 0.00 0.00 3.01
924 934 0.252881 TGGGCTGGGATGAGAGAGTT 60.253 55.000 0.00 0.00 0.00 3.01
925 935 0.252881 TTGGGCTGGGATGAGAGAGT 60.253 55.000 0.00 0.00 0.00 3.24
926 936 0.179936 GTTGGGCTGGGATGAGAGAG 59.820 60.000 0.00 0.00 0.00 3.20
927 937 0.547471 TGTTGGGCTGGGATGAGAGA 60.547 55.000 0.00 0.00 0.00 3.10
928 938 0.329261 TTGTTGGGCTGGGATGAGAG 59.671 55.000 0.00 0.00 0.00 3.20
929 939 0.038166 GTTGTTGGGCTGGGATGAGA 59.962 55.000 0.00 0.00 0.00 3.27
937 947 2.601367 CCTGGGGTTGTTGGGCTG 60.601 66.667 0.00 0.00 0.00 4.85
994 1018 3.249189 TCCGCTTGGCCTGTCCTT 61.249 61.111 3.32 0.00 35.26 3.36
1140 1165 2.162008 AGACCGTAGAAGAGCGAAGTTC 59.838 50.000 0.00 0.00 38.31 3.01
1153 1178 0.455633 CCGTCCGAACAAGACCGTAG 60.456 60.000 0.00 0.00 0.00 3.51
1167 1192 2.126424 GTCAGCGTCACTCCGTCC 60.126 66.667 0.00 0.00 0.00 4.79
1202 1228 1.705873 CGGCCCTCTTCATACCTACT 58.294 55.000 0.00 0.00 0.00 2.57
1253 1279 4.500116 GAGCTCAGGTCGTCGCCC 62.500 72.222 9.40 0.00 0.00 6.13
1392 1418 1.217001 ATGAGCGCGCAAATCGATTA 58.783 45.000 35.10 7.62 41.67 1.75
1436 1462 7.655328 CACACCAAAATTTAGCATAAACAAGGA 59.345 33.333 0.00 0.00 0.00 3.36
1448 1474 9.260002 ACAAGCTAAAATCACACCAAAATTTAG 57.740 29.630 0.00 0.00 34.87 1.85
1452 1478 8.806146 AGATACAAGCTAAAATCACACCAAAAT 58.194 29.630 0.00 0.00 0.00 1.82
1453 1479 8.081633 CAGATACAAGCTAAAATCACACCAAAA 58.918 33.333 0.00 0.00 0.00 2.44
1454 1480 7.230510 ACAGATACAAGCTAAAATCACACCAAA 59.769 33.333 0.00 0.00 0.00 3.28
1477 1505 4.412796 TCATCTTAGAGCCATTGGACAG 57.587 45.455 6.95 0.00 0.00 3.51
1546 1574 3.923017 AGACTAAATTGTGCCTTGTGC 57.077 42.857 0.00 0.00 41.77 4.57
1547 1575 5.106197 TGCATAGACTAAATTGTGCCTTGTG 60.106 40.000 3.23 0.00 0.00 3.33
1548 1576 5.009631 TGCATAGACTAAATTGTGCCTTGT 58.990 37.500 3.23 0.00 0.00 3.16
1549 1577 5.106197 TGTGCATAGACTAAATTGTGCCTTG 60.106 40.000 0.00 0.00 0.00 3.61
1550 1578 5.009631 TGTGCATAGACTAAATTGTGCCTT 58.990 37.500 0.00 0.00 0.00 4.35
1551 1579 4.588899 TGTGCATAGACTAAATTGTGCCT 58.411 39.130 0.00 0.00 0.00 4.75
1552 1580 4.731773 GCTGTGCATAGACTAAATTGTGCC 60.732 45.833 15.47 0.00 0.00 5.01
1570 1598 1.535462 CCCCTAAGAACAAACGCTGTG 59.465 52.381 0.00 0.00 38.67 3.66
1579 1607 4.563140 AAATAGCGAACCCCTAAGAACA 57.437 40.909 0.00 0.00 0.00 3.18
1610 1638 1.273327 CCCCAACATTGTTGCTTCTCC 59.727 52.381 21.55 0.00 0.00 3.71
1624 1652 7.934665 ACTTTTTGGTGAATTATTAACCCCAAC 59.065 33.333 8.90 0.00 32.70 3.77
1644 1672 8.146412 CAGGAAATCAATTCTCTTGGACTTTTT 58.854 33.333 0.00 0.00 38.18 1.94
1680 1708 7.448469 GTGTGCAGAATTATTACCCCAATATCT 59.552 37.037 0.00 0.00 0.00 1.98
1705 1734 4.699925 TCTAAGCCAGTTTGTTAGGTGT 57.300 40.909 0.00 0.00 0.00 4.16
1742 1773 9.924650 AATACACAACTACTTAAGAAAGATCGT 57.075 29.630 10.09 1.67 36.50 3.73
1768 1799 1.215673 TGTTGCTAAAGTGGGGGTTCA 59.784 47.619 0.00 0.00 0.00 3.18
1776 1807 8.774586 GGACCTATACAATATGTTGCTAAAGTG 58.225 37.037 1.57 0.00 38.96 3.16
1976 2033 6.026947 ACAAGATAAGCGGTATCTGGATAC 57.973 41.667 17.23 11.14 46.97 2.24
2055 2112 2.417651 GCGTATGCCCTAGTGTGTAACA 60.418 50.000 0.00 0.00 39.30 2.41
2056 2113 2.159142 AGCGTATGCCCTAGTGTGTAAC 60.159 50.000 2.51 0.00 44.31 2.50
2059 2116 1.771565 TAGCGTATGCCCTAGTGTGT 58.228 50.000 2.51 0.00 44.31 3.72
2066 2123 2.700897 AGAATCAGTTAGCGTATGCCCT 59.299 45.455 2.51 0.00 44.31 5.19
2069 2126 4.984785 TGATCAGAATCAGTTAGCGTATGC 59.015 41.667 0.00 0.00 36.98 3.14
2105 2162 4.518970 CCAGTAAAACATGCTACAGTGGTT 59.481 41.667 0.00 0.00 0.00 3.67
2117 2174 1.427368 TGGCCTCACCCAGTAAAACAT 59.573 47.619 3.32 0.00 37.83 2.71
2140 2197 9.554724 TCGCATAAGAATAAACAAAAATCAGAC 57.445 29.630 0.00 0.00 0.00 3.51
2148 2205 7.064609 CACTCTCCTCGCATAAGAATAAACAAA 59.935 37.037 0.00 0.00 0.00 2.83
2224 2281 3.543670 GCCATTTGCACAAATTTTGTCG 58.456 40.909 11.78 9.00 43.23 4.35
2310 2593 6.404293 GCAAACAGGTTTAAGAAACACTGAGA 60.404 38.462 18.90 0.00 43.15 3.27
2360 2643 0.607489 CACTGAAGGTCAAGGCTGGG 60.607 60.000 0.00 0.00 0.00 4.45
2362 2645 0.250640 AGCACTGAAGGTCAAGGCTG 60.251 55.000 0.00 0.00 35.42 4.85
2421 2710 5.105392 TGACTTGAAACCTTTTTGCTGACAT 60.105 36.000 0.00 0.00 0.00 3.06
2439 2728 5.066375 TGTTTGAGGACAGAAACATGACTTG 59.934 40.000 0.00 0.00 31.06 3.16
3122 3552 3.933332 CGTTAAAAGAGACCCTGACCATC 59.067 47.826 0.00 0.00 0.00 3.51
3507 5731 2.038007 AGCCGCTTCTCCTCCTCA 59.962 61.111 0.00 0.00 0.00 3.86
3655 5880 4.627467 GTGATACAGAATAAGCATAGCCCG 59.373 45.833 0.00 0.00 0.00 6.13
3736 5973 0.877743 GAGCACACAGAAAAGGGAGC 59.122 55.000 0.00 0.00 0.00 4.70
3737 5974 1.528129 GGAGCACACAGAAAAGGGAG 58.472 55.000 0.00 0.00 0.00 4.30
3738 5975 0.110486 GGGAGCACACAGAAAAGGGA 59.890 55.000 0.00 0.00 0.00 4.20
3739 5976 1.237285 CGGGAGCACACAGAAAAGGG 61.237 60.000 0.00 0.00 0.00 3.95
3740 5977 0.535102 ACGGGAGCACACAGAAAAGG 60.535 55.000 0.00 0.00 0.00 3.11
3741 5978 2.163818 TACGGGAGCACACAGAAAAG 57.836 50.000 0.00 0.00 0.00 2.27
3742 5979 2.614481 GGATACGGGAGCACACAGAAAA 60.614 50.000 0.00 0.00 0.00 2.29
3743 5980 1.066430 GGATACGGGAGCACACAGAAA 60.066 52.381 0.00 0.00 0.00 2.52
3744 5981 0.535335 GGATACGGGAGCACACAGAA 59.465 55.000 0.00 0.00 0.00 3.02
3745 5982 0.613572 TGGATACGGGAGCACACAGA 60.614 55.000 0.00 0.00 42.51 3.41
3746 5983 0.465705 ATGGATACGGGAGCACACAG 59.534 55.000 0.00 0.00 42.51 3.66
3747 5984 0.464036 GATGGATACGGGAGCACACA 59.536 55.000 0.00 0.00 42.51 3.72
3748 5985 0.753262 AGATGGATACGGGAGCACAC 59.247 55.000 0.00 0.00 42.51 3.82
3749 5986 1.412710 GAAGATGGATACGGGAGCACA 59.587 52.381 0.00 0.00 42.51 4.57
3750 5987 1.603172 CGAAGATGGATACGGGAGCAC 60.603 57.143 0.00 0.00 42.51 4.40
3751 5988 0.673985 CGAAGATGGATACGGGAGCA 59.326 55.000 0.00 0.00 42.51 4.26
3760 6013 5.304101 GGATCTATCATAGCCGAAGATGGAT 59.696 44.000 0.00 0.00 40.99 3.41
3833 6086 3.807622 CACTTCACCGTAACACACAGATT 59.192 43.478 0.00 0.00 0.00 2.40
3875 6128 1.464734 TAGTCAGCCTTCCGAGACAG 58.535 55.000 0.00 0.00 33.56 3.51
4040 6294 5.892686 TCTGATCCAAATACCATTTGATGCA 59.107 36.000 12.13 0.00 0.00 3.96
4067 6321 0.322546 GGTCACAAATCGCCTCCCTT 60.323 55.000 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.