Multiple sequence alignment - TraesCS5A01G151200

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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 TraesCS5A01G151200 chr5A 100.000 5851 0 0 1 5851 328797423 328803273 0.000000e+00 10805.0
1 TraesCS5A01G151200 chr5A 89.095 862 63 12 2 856 143593709 143594546 0.000000e+00 1042.0
2 TraesCS5A01G151200 chr5A 85.994 357 41 9 3089 3439 667026865 667027218 1.990000e-99 374.0
3 TraesCS5A01G151200 chr5A 88.085 235 22 3 5155 5389 503771650 503771422 2.080000e-69 274.0
4 TraesCS5A01G151200 chr5A 86.547 223 24 5 3222 3440 531217297 531217077 2.110000e-59 241.0
5 TraesCS5A01G151200 chr5A 88.652 141 13 2 3094 3233 531218776 531218638 1.010000e-37 169.0
6 TraesCS5A01G151200 chr5B 94.515 4959 180 39 960 5851 278005508 278010441 0.000000e+00 7566.0
7 TraesCS5A01G151200 chr5B 89.468 864 58 14 1 855 550170400 550171239 0.000000e+00 1061.0
8 TraesCS5A01G151200 chr5D 95.160 4029 130 29 960 4942 244617771 244621780 0.000000e+00 6300.0
9 TraesCS5A01G151200 chr5D 90.234 942 68 12 4926 5851 244621790 244622723 0.000000e+00 1208.0
10 TraesCS5A01G151200 chr3A 89.838 866 56 14 1 859 712722856 712723696 0.000000e+00 1083.0
11 TraesCS5A01G151200 chr3A 89.211 862 62 12 1 855 12178306 12177469 0.000000e+00 1048.0
12 TraesCS5A01G151200 chr3A 89.211 862 61 12 1 855 688890590 688891426 0.000000e+00 1048.0
13 TraesCS5A01G151200 chr3A 88.876 863 64 12 1 855 597968645 597969483 0.000000e+00 1033.0
14 TraesCS5A01G151200 chr3A 87.339 853 55 23 11 856 696640123 696639317 0.000000e+00 928.0
15 TraesCS5A01G151200 chr3A 85.501 469 43 9 395 856 67148488 67148938 3.190000e-127 466.0
16 TraesCS5A01G151200 chr6B 89.340 863 60 12 1 855 213304841 213305679 0.000000e+00 1055.0
17 TraesCS5A01G151200 chr6B 80.392 102 18 2 5185 5286 47268416 47268317 6.290000e-10 76.8
18 TraesCS5A01G151200 chr3B 89.224 863 61 12 1 855 409279300 409278462 0.000000e+00 1050.0
19 TraesCS5A01G151200 chr3B 86.775 862 58 23 1 855 552474672 552475484 0.000000e+00 909.0
20 TraesCS5A01G151200 chr1B 89.211 862 61 12 1 855 27083388 27084224 0.000000e+00 1048.0
21 TraesCS5A01G151200 chr1B 89.224 863 60 12 1 855 569979174 569980011 0.000000e+00 1048.0
22 TraesCS5A01G151200 chr2B 89.799 696 40 12 173 860 8428674 8428002 0.000000e+00 863.0
23 TraesCS5A01G151200 chr4D 88.817 465 27 9 398 855 64181649 64181203 1.110000e-151 547.0
24 TraesCS5A01G151200 chr4B 87.216 352 36 8 3094 3440 75737994 75737647 5.500000e-105 392.0
25 TraesCS5A01G151200 chr1A 85.915 355 41 8 3091 3440 65759836 65760186 2.580000e-98 370.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G151200 chr5A 328797423 328803273 5850 False 10805 10805 100.0000 1 5851 1 chr5A.!!$F2 5850
1 TraesCS5A01G151200 chr5A 143593709 143594546 837 False 1042 1042 89.0950 2 856 1 chr5A.!!$F1 854
2 TraesCS5A01G151200 chr5A 531217077 531218776 1699 True 205 241 87.5995 3094 3440 2 chr5A.!!$R2 346
3 TraesCS5A01G151200 chr5B 278005508 278010441 4933 False 7566 7566 94.5150 960 5851 1 chr5B.!!$F1 4891
4 TraesCS5A01G151200 chr5B 550170400 550171239 839 False 1061 1061 89.4680 1 855 1 chr5B.!!$F2 854
5 TraesCS5A01G151200 chr5D 244617771 244622723 4952 False 3754 6300 92.6970 960 5851 2 chr5D.!!$F1 4891
6 TraesCS5A01G151200 chr3A 712722856 712723696 840 False 1083 1083 89.8380 1 859 1 chr3A.!!$F4 858
7 TraesCS5A01G151200 chr3A 12177469 12178306 837 True 1048 1048 89.2110 1 855 1 chr3A.!!$R1 854
8 TraesCS5A01G151200 chr3A 688890590 688891426 836 False 1048 1048 89.2110 1 855 1 chr3A.!!$F3 854
9 TraesCS5A01G151200 chr3A 597968645 597969483 838 False 1033 1033 88.8760 1 855 1 chr3A.!!$F2 854
10 TraesCS5A01G151200 chr3A 696639317 696640123 806 True 928 928 87.3390 11 856 1 chr3A.!!$R2 845
11 TraesCS5A01G151200 chr6B 213304841 213305679 838 False 1055 1055 89.3400 1 855 1 chr6B.!!$F1 854
12 TraesCS5A01G151200 chr3B 409278462 409279300 838 True 1050 1050 89.2240 1 855 1 chr3B.!!$R1 854
13 TraesCS5A01G151200 chr3B 552474672 552475484 812 False 909 909 86.7750 1 855 1 chr3B.!!$F1 854
14 TraesCS5A01G151200 chr1B 27083388 27084224 836 False 1048 1048 89.2110 1 855 1 chr1B.!!$F1 854
15 TraesCS5A01G151200 chr1B 569979174 569980011 837 False 1048 1048 89.2240 1 855 1 chr1B.!!$F2 854
16 TraesCS5A01G151200 chr2B 8428002 8428674 672 True 863 863 89.7990 173 860 1 chr2B.!!$R1 687


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
892 902 0.033920 AAACACTACCGGACGGAACC 59.966 55.000 18.80 0.00 38.96 3.62 F
1007 1017 0.105760 AGAGCCGGTGAGATGGAGAT 60.106 55.000 1.90 0.00 0.00 2.75 F
1102 1112 0.949105 AAAGAAGGCGTCGAATGCGT 60.949 50.000 0.00 2.87 38.98 5.24 F
1281 1291 1.000731 GAGATGGCGAGGGAGAAGATG 59.999 57.143 0.00 0.00 0.00 2.90 F
1293 1303 1.057361 GAAGATGTTGTCGCGCGAC 59.943 57.895 46.11 46.11 44.77 5.19 F
2979 3004 1.304630 TTCGATCGTGGGGAGGTCA 60.305 57.895 15.94 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2415 2439 0.176680 CCACTTCCAGATGGGTCTCG 59.823 60.000 0.00 0.0 38.11 4.04 R
2983 3008 0.250901 GTTGTGATGGTGAGCCTGGT 60.251 55.000 0.00 0.0 35.27 4.00 R
3092 3117 2.106566 TGGGCACAAATCAAACACACT 58.893 42.857 0.00 0.0 0.00 3.55 R
3268 4645 7.016153 ACACTGATCAATCCTAGTTACCAAA 57.984 36.000 0.00 0.0 0.00 3.28 R
3315 4693 7.761038 ACAGGTGTCCCTTCTTTTTAATTAG 57.239 36.000 0.00 0.0 39.89 1.73 R
4887 6291 1.065854 ACTAGCTAGCAACAGCCTTGG 60.066 52.381 20.91 0.0 42.84 3.61 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
35 36 2.435938 GAGCGGCGGATGTTTGGA 60.436 61.111 9.78 0.00 0.00 3.53
56 57 1.971167 CGGCTGGGCTTGCTACAAA 60.971 57.895 2.80 0.00 0.00 2.83
62 63 3.004106 GCTGGGCTTGCTACAAATCATAG 59.996 47.826 0.00 0.00 0.00 2.23
65 66 2.887152 GGCTTGCTACAAATCATAGGGG 59.113 50.000 0.00 0.00 0.00 4.79
69 70 5.440610 CTTGCTACAAATCATAGGGGAAGT 58.559 41.667 0.00 0.00 0.00 3.01
89 90 0.249120 TGTCGCCGAGGACAAATCAT 59.751 50.000 6.11 0.00 43.55 2.45
128 129 7.161404 GGAAATTTTATCAAAGCTTTCAGGGT 58.839 34.615 9.23 0.00 31.16 4.34
137 138 3.370840 AGCTTTCAGGGTAATGATGCA 57.629 42.857 0.00 0.00 33.91 3.96
140 141 3.887716 GCTTTCAGGGTAATGATGCAGAT 59.112 43.478 0.00 0.00 32.63 2.90
200 201 2.161078 TATGGTGGCAGCGTCGACAA 62.161 55.000 15.66 0.00 0.00 3.18
215 216 5.677091 GCGTCGACAAATAGTAAAGGGAGTA 60.677 44.000 17.16 0.00 0.00 2.59
216 217 6.324819 CGTCGACAAATAGTAAAGGGAGTAA 58.675 40.000 17.16 0.00 0.00 2.24
217 218 6.976925 CGTCGACAAATAGTAAAGGGAGTAAT 59.023 38.462 17.16 0.00 0.00 1.89
218 219 8.131100 CGTCGACAAATAGTAAAGGGAGTAATA 58.869 37.037 17.16 0.00 0.00 0.98
219 220 9.978044 GTCGACAAATAGTAAAGGGAGTAATAT 57.022 33.333 11.55 0.00 0.00 1.28
361 362 5.066593 GGACATGGGATCCTGAAGATAAAC 58.933 45.833 12.58 0.00 34.42 2.01
440 442 5.535333 GAGACGACCGGGATGATTTTATTA 58.465 41.667 6.32 0.00 0.00 0.98
455 457 4.782019 TTTATTACTGCAGCAAGTTGGG 57.218 40.909 15.27 0.00 0.00 4.12
456 458 1.549203 ATTACTGCAGCAAGTTGGGG 58.451 50.000 15.27 0.00 0.00 4.96
483 485 4.346709 TCCAAACATCAGTGGAGTTGACTA 59.653 41.667 2.56 0.00 39.04 2.59
512 515 0.110486 AACTGCCATCAGAAACGGGT 59.890 50.000 0.00 0.00 42.95 5.28
517 520 2.290641 TGCCATCAGAAACGGGTTGTAT 60.291 45.455 0.00 0.00 0.00 2.29
548 551 5.243507 ACTCACATTGGATGCAACAACATAA 59.756 36.000 0.12 0.00 0.00 1.90
590 593 1.367840 GCGGTGGACTCAGTGAACT 59.632 57.895 0.00 0.00 0.00 3.01
593 596 2.547218 GCGGTGGACTCAGTGAACTAAA 60.547 50.000 0.00 0.00 0.00 1.85
675 685 5.650266 TGCGTCCATATCCTTTAAACATTGT 59.350 36.000 0.00 0.00 0.00 2.71
754 764 9.965824 CTAGATCTTCTAGTTTTTGAGATCCTC 57.034 37.037 0.00 0.00 41.12 3.71
755 765 8.608185 AGATCTTCTAGTTTTTGAGATCCTCT 57.392 34.615 7.76 0.00 33.31 3.69
756 766 9.707957 AGATCTTCTAGTTTTTGAGATCCTCTA 57.292 33.333 7.76 0.00 33.31 2.43
757 767 9.965824 GATCTTCTAGTTTTTGAGATCCTCTAG 57.034 37.037 0.00 0.00 0.00 2.43
758 768 8.887264 TCTTCTAGTTTTTGAGATCCTCTAGT 57.113 34.615 0.00 0.00 0.00 2.57
759 769 9.315363 TCTTCTAGTTTTTGAGATCCTCTAGTT 57.685 33.333 0.00 0.00 0.00 2.24
760 770 9.936759 CTTCTAGTTTTTGAGATCCTCTAGTTT 57.063 33.333 0.00 0.00 0.00 2.66
764 774 8.980481 AGTTTTTGAGATCCTCTAGTTTTTGA 57.020 30.769 0.00 0.00 0.00 2.69
813 823 5.587443 TCTCATCTGCTTGTAAATGACATGG 59.413 40.000 0.00 0.00 38.07 3.66
881 891 6.712301 CAACGTTGCTCTTAAAAACACTAC 57.288 37.500 16.51 0.00 0.00 2.73
882 892 5.413969 ACGTTGCTCTTAAAAACACTACC 57.586 39.130 0.00 0.00 0.00 3.18
883 893 4.025480 ACGTTGCTCTTAAAAACACTACCG 60.025 41.667 0.00 0.00 0.00 4.02
884 894 4.609783 CGTTGCTCTTAAAAACACTACCGG 60.610 45.833 0.00 0.00 0.00 5.28
885 895 4.339872 TGCTCTTAAAAACACTACCGGA 57.660 40.909 9.46 0.00 0.00 5.14
886 896 4.060205 TGCTCTTAAAAACACTACCGGAC 58.940 43.478 9.46 0.00 0.00 4.79
887 897 3.122445 GCTCTTAAAAACACTACCGGACG 59.878 47.826 9.46 0.00 0.00 4.79
888 898 3.652274 TCTTAAAAACACTACCGGACGG 58.348 45.455 9.46 9.56 42.03 4.79
889 899 3.320541 TCTTAAAAACACTACCGGACGGA 59.679 43.478 18.80 0.25 38.96 4.69
890 900 2.618442 AAAAACACTACCGGACGGAA 57.382 45.000 18.80 0.00 38.96 4.30
891 901 1.869774 AAAACACTACCGGACGGAAC 58.130 50.000 18.80 0.00 38.96 3.62
892 902 0.033920 AAACACTACCGGACGGAACC 59.966 55.000 18.80 0.00 38.96 3.62
893 903 1.820010 AACACTACCGGACGGAACCC 61.820 60.000 18.80 0.00 38.96 4.11
903 913 4.473520 CGGAACCCGCTGGCTGAT 62.474 66.667 0.00 0.00 41.17 2.90
904 914 2.044946 GGAACCCGCTGGCTGATT 60.045 61.111 0.00 0.00 33.59 2.57
905 915 2.115291 GGAACCCGCTGGCTGATTC 61.115 63.158 0.00 0.00 33.59 2.52
906 916 1.078143 GAACCCGCTGGCTGATTCT 60.078 57.895 0.00 0.00 33.59 2.40
907 917 0.178068 GAACCCGCTGGCTGATTCTA 59.822 55.000 0.00 0.00 33.59 2.10
908 918 0.179000 AACCCGCTGGCTGATTCTAG 59.821 55.000 0.00 0.00 33.59 2.43
909 919 1.070445 CCCGCTGGCTGATTCTAGG 59.930 63.158 0.00 0.00 0.00 3.02
910 920 1.690219 CCCGCTGGCTGATTCTAGGT 61.690 60.000 0.00 0.00 0.00 3.08
911 921 0.179000 CCGCTGGCTGATTCTAGGTT 59.821 55.000 0.00 0.00 0.00 3.50
912 922 1.407437 CCGCTGGCTGATTCTAGGTTT 60.407 52.381 0.00 0.00 0.00 3.27
913 923 2.359900 CGCTGGCTGATTCTAGGTTTT 58.640 47.619 0.00 0.00 0.00 2.43
914 924 2.352960 CGCTGGCTGATTCTAGGTTTTC 59.647 50.000 0.00 0.00 0.00 2.29
915 925 3.615155 GCTGGCTGATTCTAGGTTTTCT 58.385 45.455 0.00 0.00 0.00 2.52
916 926 4.013050 GCTGGCTGATTCTAGGTTTTCTT 58.987 43.478 0.00 0.00 0.00 2.52
917 927 4.460731 GCTGGCTGATTCTAGGTTTTCTTT 59.539 41.667 0.00 0.00 0.00 2.52
918 928 5.648092 GCTGGCTGATTCTAGGTTTTCTTTA 59.352 40.000 0.00 0.00 0.00 1.85
919 929 6.403746 GCTGGCTGATTCTAGGTTTTCTTTAC 60.404 42.308 0.00 0.00 0.00 2.01
920 930 6.779860 TGGCTGATTCTAGGTTTTCTTTACT 58.220 36.000 0.00 0.00 0.00 2.24
921 931 6.879458 TGGCTGATTCTAGGTTTTCTTTACTC 59.121 38.462 0.00 0.00 0.00 2.59
922 932 7.106890 GGCTGATTCTAGGTTTTCTTTACTCT 58.893 38.462 0.00 0.00 0.00 3.24
923 933 7.608376 GGCTGATTCTAGGTTTTCTTTACTCTT 59.392 37.037 0.00 0.00 0.00 2.85
924 934 8.661257 GCTGATTCTAGGTTTTCTTTACTCTTC 58.339 37.037 0.00 0.00 0.00 2.87
925 935 9.157104 CTGATTCTAGGTTTTCTTTACTCTTCC 57.843 37.037 0.00 0.00 0.00 3.46
926 936 8.101419 TGATTCTAGGTTTTCTTTACTCTTCCC 58.899 37.037 0.00 0.00 0.00 3.97
927 937 6.370186 TCTAGGTTTTCTTTACTCTTCCCC 57.630 41.667 0.00 0.00 0.00 4.81
928 938 5.847817 TCTAGGTTTTCTTTACTCTTCCCCA 59.152 40.000 0.00 0.00 0.00 4.96
929 939 4.726583 AGGTTTTCTTTACTCTTCCCCAC 58.273 43.478 0.00 0.00 0.00 4.61
930 940 3.825014 GGTTTTCTTTACTCTTCCCCACC 59.175 47.826 0.00 0.00 0.00 4.61
931 941 4.447325 GGTTTTCTTTACTCTTCCCCACCT 60.447 45.833 0.00 0.00 0.00 4.00
932 942 5.138276 GTTTTCTTTACTCTTCCCCACCTT 58.862 41.667 0.00 0.00 0.00 3.50
933 943 4.635699 TTCTTTACTCTTCCCCACCTTC 57.364 45.455 0.00 0.00 0.00 3.46
934 944 2.565834 TCTTTACTCTTCCCCACCTTCG 59.434 50.000 0.00 0.00 0.00 3.79
935 945 1.272807 TTACTCTTCCCCACCTTCGG 58.727 55.000 0.00 0.00 0.00 4.30
936 946 0.616679 TACTCTTCCCCACCTTCGGG 60.617 60.000 0.00 0.00 46.94 5.14
945 955 1.339097 CCACCTTCGGGATAGTAGGG 58.661 60.000 0.00 0.00 38.77 3.53
946 956 1.412649 CCACCTTCGGGATAGTAGGGT 60.413 57.143 0.00 0.00 38.77 4.34
947 957 2.395619 CACCTTCGGGATAGTAGGGTT 58.604 52.381 0.00 0.00 38.77 4.11
948 958 2.770232 CACCTTCGGGATAGTAGGGTTT 59.230 50.000 0.00 0.00 38.77 3.27
949 959 2.770232 ACCTTCGGGATAGTAGGGTTTG 59.230 50.000 0.00 0.00 38.77 2.93
950 960 2.484947 CCTTCGGGATAGTAGGGTTTGC 60.485 54.545 0.00 0.00 37.25 3.68
951 961 1.868713 TCGGGATAGTAGGGTTTGCA 58.131 50.000 0.00 0.00 0.00 4.08
952 962 2.404559 TCGGGATAGTAGGGTTTGCAT 58.595 47.619 0.00 0.00 0.00 3.96
953 963 3.578978 TCGGGATAGTAGGGTTTGCATA 58.421 45.455 0.00 0.00 0.00 3.14
954 964 3.576982 TCGGGATAGTAGGGTTTGCATAG 59.423 47.826 0.00 0.00 0.00 2.23
955 965 3.676093 GGGATAGTAGGGTTTGCATAGC 58.324 50.000 0.00 0.00 0.00 2.97
956 966 3.326747 GGATAGTAGGGTTTGCATAGCG 58.673 50.000 0.21 0.00 0.00 4.26
957 967 2.902705 TAGTAGGGTTTGCATAGCGG 57.097 50.000 0.21 0.00 0.00 5.52
958 968 0.463833 AGTAGGGTTTGCATAGCGGC 60.464 55.000 0.21 0.00 0.00 6.53
959 969 0.463833 GTAGGGTTTGCATAGCGGCT 60.464 55.000 7.98 7.98 34.04 5.52
960 970 1.124780 TAGGGTTTGCATAGCGGCTA 58.875 50.000 12.80 12.80 34.04 3.93
961 971 0.179045 AGGGTTTGCATAGCGGCTAG 60.179 55.000 15.78 8.66 34.04 3.42
962 972 1.166531 GGGTTTGCATAGCGGCTAGG 61.167 60.000 16.75 16.75 34.04 3.02
963 973 1.166531 GGTTTGCATAGCGGCTAGGG 61.167 60.000 21.56 14.00 34.04 3.53
983 993 1.733389 GCGACGGGAACAATCGAACTA 60.733 52.381 0.00 0.00 40.13 2.24
984 994 2.598589 CGACGGGAACAATCGAACTAA 58.401 47.619 0.00 0.00 40.13 2.24
985 995 2.343544 CGACGGGAACAATCGAACTAAC 59.656 50.000 0.00 0.00 40.13 2.34
993 1003 2.194271 CAATCGAACTAACCGAGAGCC 58.806 52.381 0.00 0.00 39.55 4.70
1007 1017 0.105760 AGAGCCGGTGAGATGGAGAT 60.106 55.000 1.90 0.00 0.00 2.75
1023 1033 1.006805 GATGGAGACGATGGAGGCG 60.007 63.158 0.00 0.00 0.00 5.52
1038 1048 1.550976 GAGGCGGGAAGAAAGAGAGAA 59.449 52.381 0.00 0.00 0.00 2.87
1102 1112 0.949105 AAAGAAGGCGTCGAATGCGT 60.949 50.000 0.00 2.87 38.98 5.24
1170 1180 2.267324 GGAAGGCTGAAGCGAGCT 59.733 61.111 5.56 0.00 43.26 4.09
1281 1291 1.000731 GAGATGGCGAGGGAGAAGATG 59.999 57.143 0.00 0.00 0.00 2.90
1293 1303 1.057361 GAAGATGTTGTCGCGCGAC 59.943 57.895 46.11 46.11 44.77 5.19
1320 1330 2.584418 CAGATGCACGCGGAGAGG 60.584 66.667 12.47 0.00 0.00 3.69
1335 1345 3.307480 CGGAGAGGCTAAGGGAAAAAGAA 60.307 47.826 0.00 0.00 0.00 2.52
1346 1356 1.617263 GGAAAAAGAAGAGAGGCCCCC 60.617 57.143 0.00 0.00 0.00 5.40
1481 1491 4.271049 TGAGCACTTCTCTTTCGTTTCTTG 59.729 41.667 0.00 0.00 42.38 3.02
1546 1556 4.985538 AGTTCATAAGCTGGGTTTCAAGA 58.014 39.130 0.00 0.00 0.00 3.02
1653 1665 4.378774 TGTTGATTTGTTCCTGCCAATTG 58.621 39.130 0.00 0.00 0.00 2.32
1692 1705 2.236893 TGAATCTCCTGTACATGCAGCA 59.763 45.455 0.00 0.00 35.28 4.41
1795 1808 1.349688 AGGTCACGGAAATAACTGGCA 59.650 47.619 0.00 0.00 0.00 4.92
1863 1876 2.476619 CGACCTGGATCATAATCGCAAC 59.523 50.000 0.00 0.00 32.24 4.17
2028 2041 2.380084 AACCGCAGAACACATATCGT 57.620 45.000 0.00 0.00 0.00 3.73
2154 2175 3.202829 ACGGGAAAGTACAACACACAT 57.797 42.857 0.00 0.00 0.00 3.21
2306 2329 7.925993 TGTATGTTGACTTAAGTTGGTTCTTG 58.074 34.615 10.02 0.00 0.00 3.02
2412 2436 4.043596 AGATTGGGTCTCATTCTAAGGCT 58.956 43.478 0.00 0.00 35.16 4.58
2415 2439 1.475930 GGGTCTCATTCTAAGGCTGGC 60.476 57.143 0.00 0.00 0.00 4.85
2426 2450 3.474570 GGCTGGCGAGACCCATCT 61.475 66.667 0.00 0.00 37.83 2.90
2568 2592 8.816894 CCTTAAGAATCATAGGCCTTCTACATA 58.183 37.037 12.58 0.00 0.00 2.29
2729 2753 5.761003 TGACTTGCATGTAGTGTTTTCATG 58.239 37.500 5.05 0.00 40.98 3.07
2979 3004 1.304630 TTCGATCGTGGGGAGGTCA 60.305 57.895 15.94 0.00 0.00 4.02
2983 3008 1.411246 CGATCGTGGGGAGGTCAATTA 59.589 52.381 7.03 0.00 0.00 1.40
3028 3053 5.922544 AGCTCAAATGTTTGCATTGAGTAAC 59.077 36.000 21.86 8.83 43.89 2.50
3033 3058 8.575589 TCAAATGTTTGCATTGAGTAACTACAT 58.424 29.630 0.66 0.00 43.89 2.29
3102 3127 6.869695 TCTGTGTTACTAAGAGTGTGTTTGA 58.130 36.000 0.00 0.00 0.00 2.69
3112 3137 2.100584 GAGTGTGTTTGATTTGTGCCCA 59.899 45.455 0.00 0.00 0.00 5.36
3315 4693 8.690840 GTGTTTAGTGTGATTGCAATTAAGTTC 58.309 33.333 14.33 0.49 0.00 3.01
3417 4799 2.096335 CACACTGCGCATCACATATGTT 59.904 45.455 12.24 0.00 0.00 2.71
3430 4812 7.862372 GCATCACATATGTTCGTGGAAATAATT 59.138 33.333 5.37 0.00 33.83 1.40
3494 4876 6.756221 AGTATAGTATTTTGATCCACGGTCC 58.244 40.000 0.00 0.00 0.00 4.46
3587 4972 0.251922 TGGTTACCGGCCTCTACACT 60.252 55.000 0.00 0.00 0.00 3.55
3691 5076 4.837972 TGGATAATCACCGAACACAATGA 58.162 39.130 0.00 0.00 0.00 2.57
3749 5134 1.593265 CATTTTCTGCACCCCTGGC 59.407 57.895 0.00 0.00 0.00 4.85
3751 5136 2.713531 ATTTTCTGCACCCCTGGCGT 62.714 55.000 0.00 0.00 0.00 5.68
3830 5215 1.243342 TTTGGCACCGATCCAAGCAG 61.243 55.000 0.00 0.00 43.67 4.24
3905 5290 1.271543 ACCAAACGTACCCTAAAGCCC 60.272 52.381 0.00 0.00 0.00 5.19
3940 5325 1.945394 CTGCCAGCACCTAACATCATC 59.055 52.381 0.00 0.00 0.00 2.92
3960 5345 3.966979 TCCATGGTATGCACTTCACATT 58.033 40.909 12.58 0.00 0.00 2.71
3966 5351 6.682423 TGGTATGCACTTCACATTGATAAG 57.318 37.500 0.00 0.00 0.00 1.73
4073 5458 6.469139 TTAAATATTCTTGTCGACGCAACA 57.531 33.333 11.62 0.00 0.00 3.33
4145 5530 2.178912 TCCACCCATTTCAGTTCGAC 57.821 50.000 0.00 0.00 0.00 4.20
4163 5548 7.595502 CAGTTCGACTCATTGTAGTTAAGTTCT 59.404 37.037 0.00 0.00 0.00 3.01
4179 5564 7.760340 AGTTAAGTTCTACTTGATGAACGGATC 59.240 37.037 2.45 0.00 44.95 3.36
4307 5692 4.447138 ACATTTGGTTCTTACAGGTCCA 57.553 40.909 0.00 0.00 0.00 4.02
4429 5814 0.109153 ATCAGCCGCTGCAATATCCA 59.891 50.000 15.98 0.00 41.13 3.41
4623 6008 2.582052 GTGTTCCCCACATGAAAGTCA 58.418 47.619 0.00 0.00 43.92 3.41
4718 6122 1.009675 CTCGTGGTTTGTGCTGTGC 60.010 57.895 0.00 0.00 0.00 4.57
4732 6136 3.044305 GTGCTGTCTCGTGGTGGC 61.044 66.667 0.00 0.00 0.00 5.01
4741 6145 2.738521 CGTGGTGGCGAGAAGGTG 60.739 66.667 0.00 0.00 0.00 4.00
4887 6291 3.497262 CGTGGTTTTTCTCTACCTTCCAC 59.503 47.826 0.00 0.00 40.13 4.02
4889 6293 3.460340 TGGTTTTTCTCTACCTTCCACCA 59.540 43.478 0.00 0.00 35.41 4.17
4938 6374 4.474651 TCATCCCATGGATCTTAACAGTGT 59.525 41.667 15.22 0.00 40.98 3.55
5001 6441 4.441356 GCTTAGAGCAACTCTAGCAGATGT 60.441 45.833 15.23 0.00 42.92 3.06
5004 6444 3.513119 AGAGCAACTCTAGCAGATGTTGA 59.487 43.478 19.64 0.00 39.28 3.18
5039 6479 1.111277 AAAACCAGTTTGCGGCTCTT 58.889 45.000 0.00 0.00 32.36 2.85
5044 6484 1.363744 CAGTTTGCGGCTCTTCCTAG 58.636 55.000 0.00 0.00 0.00 3.02
5048 6488 0.108804 TTGCGGCTCTTCCTAGAACG 60.109 55.000 0.00 0.00 35.28 3.95
5074 6514 1.400846 GCGGTATCACGAGACTTCAGA 59.599 52.381 0.00 0.00 35.47 3.27
5076 6516 2.418976 CGGTATCACGAGACTTCAGACA 59.581 50.000 0.00 0.00 35.47 3.41
5080 6520 5.163602 GGTATCACGAGACTTCAGACAGAAT 60.164 44.000 0.00 0.00 35.25 2.40
5081 6521 4.855715 TCACGAGACTTCAGACAGAATT 57.144 40.909 0.00 0.00 35.25 2.17
5143 6583 2.253758 CGGCATATGTTCCGCCTGG 61.254 63.158 8.56 0.00 43.95 4.45
5153 6593 3.941188 CCGCCTGGTCCCGCATAT 61.941 66.667 0.00 0.00 0.00 1.78
5154 6594 2.357517 CGCCTGGTCCCGCATATC 60.358 66.667 0.00 0.00 0.00 1.63
5155 6595 2.357517 GCCTGGTCCCGCATATCG 60.358 66.667 0.00 0.00 38.08 2.92
5157 6597 2.421314 CTGGTCCCGCATATCGCA 59.579 61.111 0.00 0.00 42.60 5.10
5158 6598 1.227527 CTGGTCCCGCATATCGCAA 60.228 57.895 0.00 0.00 42.60 4.85
5159 6599 0.813610 CTGGTCCCGCATATCGCAAA 60.814 55.000 0.00 0.00 42.60 3.68
5161 6601 0.517316 GGTCCCGCATATCGCAAATC 59.483 55.000 0.00 0.00 42.60 2.17
5162 6602 1.512926 GTCCCGCATATCGCAAATCT 58.487 50.000 0.00 0.00 42.60 2.40
5189 6668 9.237846 GTTTTAGTTAGATAGGCAAAATCATGC 57.762 33.333 0.00 0.00 45.67 4.06
5202 6681 7.017055 GGCAAAATCATGCTTTTGAACAATAC 58.983 34.615 29.57 14.80 44.97 1.89
5553 7056 1.817099 GGAATCGCCTGCCTGACTG 60.817 63.158 0.00 0.00 0.00 3.51
5554 7057 1.219124 GAATCGCCTGCCTGACTGA 59.781 57.895 0.00 0.00 0.00 3.41
5555 7058 0.809241 GAATCGCCTGCCTGACTGAG 60.809 60.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.485122 CCGCTTCCAAACATCCGC 59.515 61.111 0.00 0.00 0.00 5.54
56 57 1.141053 GGCGACAACTTCCCCTATGAT 59.859 52.381 0.00 0.00 0.00 2.45
62 63 2.434359 CTCGGCGACAACTTCCCC 60.434 66.667 4.99 0.00 0.00 4.81
65 66 0.599204 TTGTCCTCGGCGACAACTTC 60.599 55.000 4.99 0.00 45.49 3.01
120 121 4.858850 ACATCTGCATCATTACCCTGAAA 58.141 39.130 0.00 0.00 0.00 2.69
128 129 4.126437 CCGTTGGTACATCTGCATCATTA 58.874 43.478 0.00 0.00 39.30 1.90
137 138 1.515954 CTCCGCCGTTGGTACATCT 59.484 57.895 0.00 0.00 39.30 2.90
140 141 2.874664 AAGCTCCGCCGTTGGTACA 61.875 57.895 0.00 0.00 0.00 2.90
161 162 6.013379 ACCATATATACCATGCTGCTACAACT 60.013 38.462 0.00 0.00 0.00 3.16
215 216 4.862371 TCCGGCCTTTGGACTTTTATATT 58.138 39.130 0.00 0.00 0.00 1.28
216 217 4.513406 TCCGGCCTTTGGACTTTTATAT 57.487 40.909 0.00 0.00 0.00 0.86
217 218 4.304048 TTCCGGCCTTTGGACTTTTATA 57.696 40.909 0.00 0.00 34.56 0.98
218 219 2.891191 TCCGGCCTTTGGACTTTTAT 57.109 45.000 0.00 0.00 0.00 1.40
219 220 2.660670 TTCCGGCCTTTGGACTTTTA 57.339 45.000 0.00 0.00 34.56 1.52
350 351 5.352569 AGGAAGCATCAACGTTTATCTTCAG 59.647 40.000 22.09 4.97 32.47 3.02
361 362 4.631377 TCATACTGAAAGGAAGCATCAACG 59.369 41.667 0.00 0.00 39.30 4.10
393 394 2.031919 CGGCACCACAAGCACCTA 59.968 61.111 0.00 0.00 0.00 3.08
418 419 4.417426 AATAAAATCATCCCGGTCGTCT 57.583 40.909 0.00 0.00 0.00 4.18
440 442 1.829533 CACCCCAACTTGCTGCAGT 60.830 57.895 16.64 0.48 0.00 4.40
455 457 2.554032 CTCCACTGATGTTTGGAACACC 59.446 50.000 0.00 0.00 45.50 4.16
456 458 3.214328 ACTCCACTGATGTTTGGAACAC 58.786 45.455 0.00 0.00 45.50 3.32
483 485 1.280133 TGATGGCAGTTAGCTCAGCTT 59.720 47.619 3.31 0.00 44.79 3.74
512 515 4.586421 TCCAATGTGAGTTGCCAAATACAA 59.414 37.500 0.00 0.00 0.00 2.41
517 520 2.288948 GCATCCAATGTGAGTTGCCAAA 60.289 45.455 0.00 0.00 0.00 3.28
548 551 7.273381 CGCGAAGGAACATTCTAATTCAATTTT 59.727 33.333 0.00 0.00 0.00 1.82
562 565 1.375523 GTCCACCGCGAAGGAACAT 60.376 57.895 18.88 0.00 45.00 2.71
590 593 7.235079 TCCGGGCCTAAATAATCATCAATTTA 58.765 34.615 0.84 0.00 0.00 1.40
593 596 5.255397 TCCGGGCCTAAATAATCATCAAT 57.745 39.130 0.84 0.00 0.00 2.57
675 685 4.345257 GCCACCTGATTGACCTCTCTATAA 59.655 45.833 0.00 0.00 0.00 0.98
686 696 3.657398 ATTCATCTGCCACCTGATTGA 57.343 42.857 0.00 0.00 0.00 2.57
748 758 8.420222 TCTCATCATCTCAAAAACTAGAGGATC 58.580 37.037 0.00 0.00 40.29 3.36
749 759 8.316497 TCTCATCATCTCAAAAACTAGAGGAT 57.684 34.615 0.00 0.00 42.31 3.24
750 760 7.724490 TCTCATCATCTCAAAAACTAGAGGA 57.276 36.000 0.00 0.00 37.00 3.71
751 761 7.656948 GGATCTCATCATCTCAAAAACTAGAGG 59.343 40.741 0.00 0.00 32.76 3.69
752 762 7.656948 GGGATCTCATCATCTCAAAAACTAGAG 59.343 40.741 0.00 0.00 0.00 2.43
753 763 7.346698 AGGGATCTCATCATCTCAAAAACTAGA 59.653 37.037 0.00 0.00 0.00 2.43
754 764 7.441760 CAGGGATCTCATCATCTCAAAAACTAG 59.558 40.741 0.00 0.00 0.00 2.57
755 765 7.126268 TCAGGGATCTCATCATCTCAAAAACTA 59.874 37.037 0.00 0.00 0.00 2.24
756 766 6.069789 TCAGGGATCTCATCATCTCAAAAACT 60.070 38.462 0.00 0.00 0.00 2.66
757 767 6.118170 TCAGGGATCTCATCATCTCAAAAAC 58.882 40.000 0.00 0.00 0.00 2.43
758 768 6.317663 TCAGGGATCTCATCATCTCAAAAA 57.682 37.500 0.00 0.00 0.00 1.94
759 769 5.963214 TCAGGGATCTCATCATCTCAAAA 57.037 39.130 0.00 0.00 0.00 2.44
760 770 6.511017 AATCAGGGATCTCATCATCTCAAA 57.489 37.500 0.00 0.00 0.00 2.69
761 771 6.511017 AAATCAGGGATCTCATCATCTCAA 57.489 37.500 0.00 0.00 0.00 3.02
762 772 6.511017 AAAATCAGGGATCTCATCATCTCA 57.489 37.500 0.00 0.00 0.00 3.27
763 773 9.517868 AAATAAAATCAGGGATCTCATCATCTC 57.482 33.333 0.00 0.00 0.00 2.75
764 774 9.517868 GAAATAAAATCAGGGATCTCATCATCT 57.482 33.333 0.00 0.00 0.00 2.90
860 870 4.025480 CGGTAGTGTTTTTAAGAGCAACGT 60.025 41.667 0.00 0.00 0.00 3.99
861 871 4.451557 CGGTAGTGTTTTTAAGAGCAACG 58.548 43.478 0.00 0.00 0.00 4.10
862 872 4.512571 TCCGGTAGTGTTTTTAAGAGCAAC 59.487 41.667 0.00 0.00 0.00 4.17
863 873 4.512571 GTCCGGTAGTGTTTTTAAGAGCAA 59.487 41.667 0.00 0.00 0.00 3.91
864 874 4.060205 GTCCGGTAGTGTTTTTAAGAGCA 58.940 43.478 0.00 0.00 0.00 4.26
865 875 3.122445 CGTCCGGTAGTGTTTTTAAGAGC 59.878 47.826 0.00 0.00 0.00 4.09
866 876 3.676646 CCGTCCGGTAGTGTTTTTAAGAG 59.323 47.826 0.00 0.00 0.00 2.85
867 877 3.320541 TCCGTCCGGTAGTGTTTTTAAGA 59.679 43.478 0.00 0.00 36.47 2.10
868 878 3.652274 TCCGTCCGGTAGTGTTTTTAAG 58.348 45.455 0.00 0.00 36.47 1.85
869 879 3.742433 TCCGTCCGGTAGTGTTTTTAA 57.258 42.857 0.00 0.00 36.47 1.52
870 880 3.389221 GTTCCGTCCGGTAGTGTTTTTA 58.611 45.455 0.00 0.00 36.47 1.52
871 881 2.212652 GTTCCGTCCGGTAGTGTTTTT 58.787 47.619 0.00 0.00 36.47 1.94
872 882 1.541015 GGTTCCGTCCGGTAGTGTTTT 60.541 52.381 0.00 0.00 36.47 2.43
873 883 0.033920 GGTTCCGTCCGGTAGTGTTT 59.966 55.000 0.00 0.00 36.47 2.83
874 884 1.667722 GGTTCCGTCCGGTAGTGTT 59.332 57.895 0.00 0.00 36.47 3.32
875 885 2.278330 GGGTTCCGTCCGGTAGTGT 61.278 63.158 0.00 0.00 36.47 3.55
876 886 2.575461 GGGTTCCGTCCGGTAGTG 59.425 66.667 0.00 0.00 36.47 2.74
877 887 3.064324 CGGGTTCCGTCCGGTAGT 61.064 66.667 0.00 0.00 42.73 2.73
887 897 2.044946 AATCAGCCAGCGGGTTCC 60.045 61.111 4.36 0.00 36.17 3.62
888 898 0.178068 TAGAATCAGCCAGCGGGTTC 59.822 55.000 7.58 7.58 36.17 3.62
889 899 0.179000 CTAGAATCAGCCAGCGGGTT 59.821 55.000 4.36 0.00 36.17 4.11
890 900 1.690219 CCTAGAATCAGCCAGCGGGT 61.690 60.000 4.36 0.00 36.17 5.28
891 901 1.070445 CCTAGAATCAGCCAGCGGG 59.930 63.158 0.00 0.00 37.18 6.13
892 902 0.179000 AACCTAGAATCAGCCAGCGG 59.821 55.000 0.00 0.00 0.00 5.52
893 903 2.029838 AAACCTAGAATCAGCCAGCG 57.970 50.000 0.00 0.00 0.00 5.18
894 904 3.615155 AGAAAACCTAGAATCAGCCAGC 58.385 45.455 0.00 0.00 0.00 4.85
895 905 6.881602 AGTAAAGAAAACCTAGAATCAGCCAG 59.118 38.462 0.00 0.00 0.00 4.85
896 906 6.779860 AGTAAAGAAAACCTAGAATCAGCCA 58.220 36.000 0.00 0.00 0.00 4.75
897 907 7.106890 AGAGTAAAGAAAACCTAGAATCAGCC 58.893 38.462 0.00 0.00 0.00 4.85
898 908 8.554835 AAGAGTAAAGAAAACCTAGAATCAGC 57.445 34.615 0.00 0.00 0.00 4.26
899 909 9.157104 GGAAGAGTAAAGAAAACCTAGAATCAG 57.843 37.037 0.00 0.00 0.00 2.90
900 910 8.101419 GGGAAGAGTAAAGAAAACCTAGAATCA 58.899 37.037 0.00 0.00 0.00 2.57
901 911 7.553402 GGGGAAGAGTAAAGAAAACCTAGAATC 59.447 40.741 0.00 0.00 0.00 2.52
902 912 7.018249 TGGGGAAGAGTAAAGAAAACCTAGAAT 59.982 37.037 0.00 0.00 0.00 2.40
903 913 6.330778 TGGGGAAGAGTAAAGAAAACCTAGAA 59.669 38.462 0.00 0.00 0.00 2.10
904 914 5.847817 TGGGGAAGAGTAAAGAAAACCTAGA 59.152 40.000 0.00 0.00 0.00 2.43
905 915 5.938710 GTGGGGAAGAGTAAAGAAAACCTAG 59.061 44.000 0.00 0.00 0.00 3.02
906 916 5.221986 GGTGGGGAAGAGTAAAGAAAACCTA 60.222 44.000 0.00 0.00 0.00 3.08
907 917 4.447325 GGTGGGGAAGAGTAAAGAAAACCT 60.447 45.833 0.00 0.00 0.00 3.50
908 918 3.825014 GGTGGGGAAGAGTAAAGAAAACC 59.175 47.826 0.00 0.00 0.00 3.27
909 919 4.726583 AGGTGGGGAAGAGTAAAGAAAAC 58.273 43.478 0.00 0.00 0.00 2.43
910 920 5.382616 GAAGGTGGGGAAGAGTAAAGAAAA 58.617 41.667 0.00 0.00 0.00 2.29
911 921 4.504340 CGAAGGTGGGGAAGAGTAAAGAAA 60.504 45.833 0.00 0.00 0.00 2.52
912 922 3.007614 CGAAGGTGGGGAAGAGTAAAGAA 59.992 47.826 0.00 0.00 0.00 2.52
913 923 2.565834 CGAAGGTGGGGAAGAGTAAAGA 59.434 50.000 0.00 0.00 0.00 2.52
914 924 2.973945 CGAAGGTGGGGAAGAGTAAAG 58.026 52.381 0.00 0.00 0.00 1.85
930 940 2.169769 TGCAAACCCTACTATCCCGAAG 59.830 50.000 0.00 0.00 0.00 3.79
931 941 2.189676 TGCAAACCCTACTATCCCGAA 58.810 47.619 0.00 0.00 0.00 4.30
932 942 1.868713 TGCAAACCCTACTATCCCGA 58.131 50.000 0.00 0.00 0.00 5.14
933 943 2.930826 ATGCAAACCCTACTATCCCG 57.069 50.000 0.00 0.00 0.00 5.14
934 944 3.676093 GCTATGCAAACCCTACTATCCC 58.324 50.000 0.00 0.00 0.00 3.85
935 945 3.326747 CGCTATGCAAACCCTACTATCC 58.673 50.000 0.00 0.00 0.00 2.59
936 946 3.326747 CCGCTATGCAAACCCTACTATC 58.673 50.000 0.00 0.00 0.00 2.08
937 947 2.550208 GCCGCTATGCAAACCCTACTAT 60.550 50.000 0.00 0.00 0.00 2.12
938 948 1.202604 GCCGCTATGCAAACCCTACTA 60.203 52.381 0.00 0.00 0.00 1.82
939 949 0.463833 GCCGCTATGCAAACCCTACT 60.464 55.000 0.00 0.00 0.00 2.57
940 950 0.463833 AGCCGCTATGCAAACCCTAC 60.464 55.000 0.00 0.00 0.00 3.18
941 951 1.070134 CTAGCCGCTATGCAAACCCTA 59.930 52.381 0.00 0.00 0.00 3.53
942 952 0.179045 CTAGCCGCTATGCAAACCCT 60.179 55.000 0.00 0.00 0.00 4.34
943 953 1.166531 CCTAGCCGCTATGCAAACCC 61.167 60.000 0.00 0.00 0.00 4.11
944 954 1.166531 CCCTAGCCGCTATGCAAACC 61.167 60.000 0.00 0.00 0.00 3.27
945 955 1.786049 GCCCTAGCCGCTATGCAAAC 61.786 60.000 14.18 0.00 0.00 2.93
946 956 1.525995 GCCCTAGCCGCTATGCAAA 60.526 57.895 14.18 0.00 0.00 3.68
947 957 2.111043 GCCCTAGCCGCTATGCAA 59.889 61.111 14.18 0.00 0.00 4.08
948 958 4.299547 CGCCCTAGCCGCTATGCA 62.300 66.667 17.46 0.00 34.57 3.96
949 959 3.991051 TCGCCCTAGCCGCTATGC 61.991 66.667 0.00 6.30 34.57 3.14
950 960 2.049063 GTCGCCCTAGCCGCTATG 60.049 66.667 0.00 0.00 34.57 2.23
951 961 3.671411 CGTCGCCCTAGCCGCTAT 61.671 66.667 0.00 0.00 34.57 2.97
956 966 4.525949 GTTCCCGTCGCCCTAGCC 62.526 72.222 0.00 0.00 34.57 3.93
957 967 2.588856 ATTGTTCCCGTCGCCCTAGC 62.589 60.000 0.00 0.00 0.00 3.42
958 968 0.529992 GATTGTTCCCGTCGCCCTAG 60.530 60.000 0.00 0.00 0.00 3.02
959 969 1.518774 GATTGTTCCCGTCGCCCTA 59.481 57.895 0.00 0.00 0.00 3.53
960 970 2.267961 GATTGTTCCCGTCGCCCT 59.732 61.111 0.00 0.00 0.00 5.19
961 971 3.192922 CGATTGTTCCCGTCGCCC 61.193 66.667 0.00 0.00 0.00 6.13
962 972 1.738830 TTCGATTGTTCCCGTCGCC 60.739 57.895 0.00 0.00 35.48 5.54
963 973 1.012486 AGTTCGATTGTTCCCGTCGC 61.012 55.000 0.00 0.00 35.48 5.19
993 1003 1.339610 GTCTCCATCTCCATCTCACCG 59.660 57.143 0.00 0.00 0.00 4.94
1007 1017 3.147595 CCGCCTCCATCGTCTCCA 61.148 66.667 0.00 0.00 0.00 3.86
1023 1033 3.256136 TCAGACGTTCTCTCTTTCTTCCC 59.744 47.826 0.00 0.00 0.00 3.97
1055 1065 1.095807 CCGCTTTCTCCCCGATTTCC 61.096 60.000 0.00 0.00 0.00 3.13
1251 1261 0.107993 TCGCCATCTCTTCCTGCAAG 60.108 55.000 0.00 0.00 0.00 4.01
1252 1262 0.107993 CTCGCCATCTCTTCCTGCAA 60.108 55.000 0.00 0.00 0.00 4.08
1320 1330 3.692101 GCCTCTCTTCTTTTTCCCTTAGC 59.308 47.826 0.00 0.00 0.00 3.09
1502 1512 5.520288 ACTTTGTAGGAACATCAATCGATCG 59.480 40.000 9.36 9.36 34.97 3.69
1599 1611 8.446273 CAATCTACAATTGTTGTCAGGTTCTAG 58.554 37.037 17.78 3.35 44.12 2.43
1634 1646 3.387374 ACACAATTGGCAGGAACAAATCA 59.613 39.130 10.83 0.00 0.00 2.57
1639 1651 2.665165 AGAACACAATTGGCAGGAACA 58.335 42.857 10.83 0.00 0.00 3.18
1653 1665 8.447053 GGAGATTCAGATTCAGTAAAAGAACAC 58.553 37.037 0.00 0.00 0.00 3.32
1692 1705 1.983119 AACACATGGCGGGGATCGAT 61.983 55.000 0.00 0.00 42.43 3.59
1795 1808 0.834687 TCGAGGGGCCACTGTAAACT 60.835 55.000 15.62 0.00 0.00 2.66
1863 1876 5.007724 GTCCCTTGAGCGGTTAAAGATAATG 59.992 44.000 11.31 0.00 0.00 1.90
2133 2146 3.815856 TGTGTGTTGTACTTTCCCGTA 57.184 42.857 0.00 0.00 0.00 4.02
2135 2148 7.548196 AATATATGTGTGTTGTACTTTCCCG 57.452 36.000 0.00 0.00 0.00 5.14
2218 2240 0.604578 ACATGAACATGCTGGTTGCC 59.395 50.000 13.71 0.00 42.39 4.52
2306 2329 3.747099 AGACGCAAATACAGTTCATGC 57.253 42.857 0.00 0.00 0.00 4.06
2393 2417 2.239654 CCAGCCTTAGAATGAGACCCAA 59.760 50.000 0.00 0.00 0.00 4.12
2394 2418 1.839994 CCAGCCTTAGAATGAGACCCA 59.160 52.381 0.00 0.00 0.00 4.51
2412 2436 1.612146 TTCCAGATGGGTCTCGCCA 60.612 57.895 0.00 0.00 39.65 5.69
2415 2439 0.176680 CCACTTCCAGATGGGTCTCG 59.823 60.000 0.00 0.00 38.11 4.04
2426 2450 3.072330 TGCTTACACTTGATCCACTTCCA 59.928 43.478 0.00 0.00 0.00 3.53
2568 2592 1.271001 TGTCTGCTAATGCACTGTGCT 60.271 47.619 30.43 16.01 45.31 4.40
2729 2753 1.438651 TAACGTGCAGGCATTCAGAC 58.561 50.000 6.26 0.00 0.00 3.51
2919 2944 1.681780 GCCATCTCCCCACGATTTTCA 60.682 52.381 0.00 0.00 0.00 2.69
2979 3004 2.308570 TGTGATGGTGAGCCTGGTAATT 59.691 45.455 0.00 0.00 35.27 1.40
2983 3008 0.250901 GTTGTGATGGTGAGCCTGGT 60.251 55.000 0.00 0.00 35.27 4.00
3092 3117 2.106566 TGGGCACAAATCAAACACACT 58.893 42.857 0.00 0.00 0.00 3.55
3268 4645 7.016153 ACACTGATCAATCCTAGTTACCAAA 57.984 36.000 0.00 0.00 0.00 3.28
3315 4693 7.761038 ACAGGTGTCCCTTCTTTTTAATTAG 57.239 36.000 0.00 0.00 39.89 1.73
3417 4799 5.989477 AGGATGTCAGAATTATTTCCACGA 58.011 37.500 0.00 0.00 31.84 4.35
3430 4812 7.232737 TGTCTTAGTTCAGTAAAGGATGTCAGA 59.767 37.037 0.00 0.00 0.00 3.27
3494 4876 6.215845 CCAAGTTATCCCAGTTTCAACAAAG 58.784 40.000 0.00 0.00 0.00 2.77
3691 5076 0.319813 GTTGCCCTCGCATGCTTTTT 60.320 50.000 17.13 0.00 46.67 1.94
3830 5215 2.733956 TGGCCCATAAGATTTGGTCAC 58.266 47.619 0.00 0.00 31.99 3.67
3905 5290 4.020751 TGCTGGCAGAGAATAATAGCCTAG 60.021 45.833 20.86 0.00 45.42 3.02
3940 5325 3.695556 TCAATGTGAAGTGCATACCATGG 59.304 43.478 11.19 11.19 0.00 3.66
3960 5345 7.440198 TCAAAACATCACAAAATGGCTTATCA 58.560 30.769 0.00 0.00 0.00 2.15
3966 5351 8.505625 ACAATATTCAAAACATCACAAAATGGC 58.494 29.630 0.00 0.00 0.00 4.40
4073 5458 7.171337 ACAATTTGAGAAGCGCAAATAAATTGT 59.829 29.630 28.94 28.94 45.12 2.71
4163 5548 7.962964 GGATTATTGATCCGTTCATCAAGTA 57.037 36.000 7.49 0.64 44.21 2.24
4197 5582 9.109393 GGAACACATCTATTGAAGTAATAAGCA 57.891 33.333 0.00 0.00 31.12 3.91
4429 5814 1.267806 GCGATTTGGATGGCGATTGAT 59.732 47.619 0.00 0.00 0.00 2.57
4471 5856 1.802960 CCAGTGTGCTGAGCTTACTTG 59.197 52.381 5.83 2.36 45.28 3.16
4623 6008 1.886313 CGCCTGAATCGAGCAGCAT 60.886 57.895 11.47 0.00 32.06 3.79
4732 6136 2.266055 GCCTCCACCACCTTCTCG 59.734 66.667 0.00 0.00 0.00 4.04
4741 6145 2.574399 GACGTCTCAGCCTCCACC 59.426 66.667 8.70 0.00 0.00 4.61
4887 6291 1.065854 ACTAGCTAGCAACAGCCTTGG 60.066 52.381 20.91 0.00 42.84 3.61
4889 6293 1.065854 CCACTAGCTAGCAACAGCCTT 60.066 52.381 20.91 0.00 42.84 4.35
5039 6479 0.899720 ACCGCAAATCCGTTCTAGGA 59.100 50.000 0.00 0.00 45.54 2.94
5044 6484 1.005347 CGTGATACCGCAAATCCGTTC 60.005 52.381 0.00 0.00 0.00 3.95
5048 6488 1.859080 GTCTCGTGATACCGCAAATCC 59.141 52.381 0.00 0.00 0.00 3.01
5074 6514 1.067635 GGTTTGCGGCATCAATTCTGT 60.068 47.619 2.28 0.00 0.00 3.41
5076 6516 1.203052 CAGGTTTGCGGCATCAATTCT 59.797 47.619 2.28 0.00 0.00 2.40
5080 6520 0.878416 GTACAGGTTTGCGGCATCAA 59.122 50.000 2.28 0.00 0.00 2.57
5081 6521 0.036164 AGTACAGGTTTGCGGCATCA 59.964 50.000 2.28 0.00 0.00 3.07
5152 6592 9.046296 CCTATCTAACTAAAACAGATTTGCGAT 57.954 33.333 0.00 0.00 31.60 4.58
5153 6593 7.011109 GCCTATCTAACTAAAACAGATTTGCGA 59.989 37.037 0.00 0.00 31.60 5.10
5154 6594 7.126398 GCCTATCTAACTAAAACAGATTTGCG 58.874 38.462 0.00 0.00 31.60 4.85
5155 6595 7.985476 TGCCTATCTAACTAAAACAGATTTGC 58.015 34.615 0.00 0.00 31.60 3.68
5258 6737 9.748708 TTGCAATTAAGAGGATTATTGTATTGC 57.251 29.630 0.00 0.00 43.24 3.56
5393 6873 1.737793 GTTCCTGCCAGGTTTATGTCG 59.262 52.381 11.27 0.00 36.53 4.35
5553 7056 1.330655 TTCGTGATCCAGCCCTCCTC 61.331 60.000 0.00 0.00 0.00 3.71
5554 7057 1.306141 TTCGTGATCCAGCCCTCCT 60.306 57.895 0.00 0.00 0.00 3.69
5555 7058 1.153349 GTTCGTGATCCAGCCCTCC 60.153 63.158 0.00 0.00 0.00 4.30
5586 7089 1.531748 GGATCGATTTGGGCCCTGA 59.468 57.895 25.70 12.16 0.00 3.86



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

AutoCloner maintained by Alex Coulton.