Multiple sequence alignment - TraesCS7A01G143900

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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 TraesCS7A01G143900 chr7A 100.000 6680 0 0 1 6680 94792424 94785745 0.000000e+00 12336.0
1 TraesCS7A01G143900 chr7A 98.860 1403 10 4 3542 4942 118152143 118150745 0.000000e+00 2497.0
2 TraesCS7A01G143900 chr7A 98.439 1409 19 3 3542 4948 319590603 319592010 0.000000e+00 2477.0
3 TraesCS7A01G143900 chr7A 95.855 941 37 2 1 939 650584931 650585871 0.000000e+00 1520.0
4 TraesCS7A01G143900 chr7A 95.745 940 39 1 1 939 263292113 263293052 0.000000e+00 1513.0
5 TraesCS7A01G143900 chr7A 95.833 936 37 2 1 935 271365105 271366039 0.000000e+00 1511.0
6 TraesCS7A01G143900 chr7B 94.621 1952 83 12 1595 3541 44944385 44942451 0.000000e+00 3003.0
7 TraesCS7A01G143900 chr7B 88.192 1499 93 36 5238 6680 44942051 44940581 0.000000e+00 1711.0
8 TraesCS7A01G143900 chr7B 92.332 639 36 7 970 1605 44945059 44944431 0.000000e+00 896.0
9 TraesCS7A01G143900 chr7B 94.257 296 17 0 4947 5242 44942437 44942142 2.840000e-123 453.0
10 TraesCS7A01G143900 chr7D 94.145 1964 89 13 1595 3541 92633040 92634994 0.000000e+00 2966.0
11 TraesCS7A01G143900 chr7D 88.737 950 53 16 4947 5865 92635008 92635934 0.000000e+00 1112.0
12 TraesCS7A01G143900 chr7D 87.500 792 52 21 5930 6680 92635955 92636740 0.000000e+00 870.0
13 TraesCS7A01G143900 chr7D 90.979 654 26 12 970 1605 92632354 92632992 0.000000e+00 850.0
14 TraesCS7A01G143900 chr2A 98.998 1397 13 1 3542 4937 578391875 578390479 0.000000e+00 2501.0
15 TraesCS7A01G143900 chr2A 96.383 940 33 1 1 939 356645949 356646888 0.000000e+00 1546.0
16 TraesCS7A01G143900 chr2A 96.277 940 34 1 1 939 365905219 365906158 0.000000e+00 1541.0
17 TraesCS7A01G143900 chr2A 95.758 943 38 2 2 942 597606984 597607926 0.000000e+00 1519.0
18 TraesCS7A01G143900 chr2A 81.159 138 17 7 5934 6065 631535237 631535103 1.190000e-17 102.0
19 TraesCS7A01G143900 chr3A 98.579 1407 17 3 3542 4946 80424877 80426282 0.000000e+00 2484.0
20 TraesCS7A01G143900 chr3A 98.507 1407 19 1 3542 4946 633851801 633853207 0.000000e+00 2481.0
21 TraesCS7A01G143900 chr3A 96.064 940 36 1 1 939 589212848 589211909 0.000000e+00 1530.0
22 TraesCS7A01G143900 chr3A 95.657 944 39 2 1 942 706184821 706183878 0.000000e+00 1515.0
23 TraesCS7A01G143900 chr6A 98.509 1408 17 2 3542 4948 58016649 58015245 0.000000e+00 2481.0
24 TraesCS7A01G143900 chr6A 77.982 218 35 11 5926 6138 535425157 535424948 2.530000e-24 124.0
25 TraesCS7A01G143900 chr5A 98.174 1424 21 5 3542 4962 111615980 111614559 0.000000e+00 2481.0
26 TraesCS7A01G143900 chr5A 98.506 1406 20 1 3542 4946 611347602 611346197 0.000000e+00 2479.0
27 TraesCS7A01G143900 chr5A 96.146 934 34 2 7 939 19468376 19467444 0.000000e+00 1524.0
28 TraesCS7A01G143900 chr2D 98.366 1408 19 2 3542 4945 136425412 136426819 0.000000e+00 2470.0
29 TraesCS7A01G143900 chr4A 90.061 493 34 8 1100 1586 2949943 2949460 5.690000e-175 625.0
30 TraesCS7A01G143900 chr1B 91.667 72 5 1 5943 6013 637833559 637833630 1.530000e-16 99.0
31 TraesCS7A01G143900 chr5B 82.609 115 8 6 5936 6045 395616753 395616860 2.570000e-14 91.6


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G143900 chr7A 94785745 94792424 6679 True 12336.00 12336 100.00000 1 6680 1 chr7A.!!$R1 6679
1 TraesCS7A01G143900 chr7A 118150745 118152143 1398 True 2497.00 2497 98.86000 3542 4942 1 chr7A.!!$R2 1400
2 TraesCS7A01G143900 chr7A 319590603 319592010 1407 False 2477.00 2477 98.43900 3542 4948 1 chr7A.!!$F3 1406
3 TraesCS7A01G143900 chr7A 650584931 650585871 940 False 1520.00 1520 95.85500 1 939 1 chr7A.!!$F4 938
4 TraesCS7A01G143900 chr7A 263292113 263293052 939 False 1513.00 1513 95.74500 1 939 1 chr7A.!!$F1 938
5 TraesCS7A01G143900 chr7A 271365105 271366039 934 False 1511.00 1511 95.83300 1 935 1 chr7A.!!$F2 934
6 TraesCS7A01G143900 chr7B 44940581 44945059 4478 True 1515.75 3003 92.35050 970 6680 4 chr7B.!!$R1 5710
7 TraesCS7A01G143900 chr7D 92632354 92636740 4386 False 1449.50 2966 90.34025 970 6680 4 chr7D.!!$F1 5710
8 TraesCS7A01G143900 chr2A 578390479 578391875 1396 True 2501.00 2501 98.99800 3542 4937 1 chr2A.!!$R1 1395
9 TraesCS7A01G143900 chr2A 356645949 356646888 939 False 1546.00 1546 96.38300 1 939 1 chr2A.!!$F1 938
10 TraesCS7A01G143900 chr2A 365905219 365906158 939 False 1541.00 1541 96.27700 1 939 1 chr2A.!!$F2 938
11 TraesCS7A01G143900 chr2A 597606984 597607926 942 False 1519.00 1519 95.75800 2 942 1 chr2A.!!$F3 940
12 TraesCS7A01G143900 chr3A 80424877 80426282 1405 False 2484.00 2484 98.57900 3542 4946 1 chr3A.!!$F1 1404
13 TraesCS7A01G143900 chr3A 633851801 633853207 1406 False 2481.00 2481 98.50700 3542 4946 1 chr3A.!!$F2 1404
14 TraesCS7A01G143900 chr3A 589211909 589212848 939 True 1530.00 1530 96.06400 1 939 1 chr3A.!!$R1 938
15 TraesCS7A01G143900 chr3A 706183878 706184821 943 True 1515.00 1515 95.65700 1 942 1 chr3A.!!$R2 941
16 TraesCS7A01G143900 chr6A 58015245 58016649 1404 True 2481.00 2481 98.50900 3542 4948 1 chr6A.!!$R1 1406
17 TraesCS7A01G143900 chr5A 111614559 111615980 1421 True 2481.00 2481 98.17400 3542 4962 1 chr5A.!!$R2 1420
18 TraesCS7A01G143900 chr5A 611346197 611347602 1405 True 2479.00 2479 98.50600 3542 4946 1 chr5A.!!$R3 1404
19 TraesCS7A01G143900 chr5A 19467444 19468376 932 True 1524.00 1524 96.14600 7 939 1 chr5A.!!$R1 932
20 TraesCS7A01G143900 chr2D 136425412 136426819 1407 False 2470.00 2470 98.36600 3542 4945 1 chr2D.!!$F1 1403

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
914 917 0.035915 GGTCAAGAACCTGGCCTCTC 60.036 60.0 3.32 0.00 45.45 3.20 F
936 939 0.243095 AACTTCAGTACGTCCTCCGC 59.757 55.0 0.00 0.00 41.42 5.54 F
1819 1912 0.038744 CACTGGAAAGGTCAGGGCAT 59.961 55.0 0.00 0.00 36.62 4.40 F
2041 2135 0.671472 TCATGTGGCGTTCAGAGCAG 60.671 55.0 0.00 0.00 36.08 4.24 F
2831 2932 0.739462 TCGCACCGACATGGATGAAC 60.739 55.0 0.00 0.00 42.00 3.18 F
3468 3569 0.328258 AAGTGTGGTATGGTCCAGCC 59.672 55.0 8.03 8.03 38.23 4.85 F
4689 4808 0.175760 GAAGCTCCGGTGCATAGTGA 59.824 55.0 28.68 0.00 34.99 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1743 1824 0.535102 AGTGGTGCTGTGTTAGTGCC 60.535 55.000 0.00 0.00 0.00 5.01 R
1900 1994 0.966875 TGCACTTGATCCCCACATGC 60.967 55.000 0.00 0.00 36.75 4.06 R
3023 3124 1.388093 GCAGATGATACAGCATACGCG 59.612 52.381 3.53 3.53 45.49 6.01 R
3440 3541 3.649023 ACCATACCACACTTTGAGGTACA 59.351 43.478 4.84 0.00 44.27 2.90 R
4421 4540 0.037232 GCCGTCCTGTAGAACTTGCT 60.037 55.000 0.00 0.00 0.00 3.91 R
4960 5327 0.034337 ACAGTGCGGGTTCGTTACAT 59.966 50.000 0.00 0.00 38.89 2.29 R
5938 6438 0.389948 AACGTTCGCCAGCTAAGAGG 60.390 55.000 0.00 0.00 0.00 3.69 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
55 56 4.887655 CCACTCCTGTTTAAAGGACAACTT 59.112 41.667 0.00 0.00 41.60 2.66
111 112 3.537874 GTCCGGGCACGAGGCTAT 61.538 66.667 11.66 0.00 44.60 2.97
148 149 1.338484 ACGATTGCAGCTCAGACATGT 60.338 47.619 0.00 0.00 0.00 3.21
165 166 4.040047 ACATGTGTCCTCCATAGAATCCA 58.960 43.478 0.00 0.00 0.00 3.41
371 372 1.118356 GGAGATCTCGGATGTGGCCT 61.118 60.000 16.46 0.00 0.00 5.19
423 424 2.203015 CCAGCCCCGTATTGACCG 60.203 66.667 0.00 0.00 0.00 4.79
705 706 2.227865 TCACACACGACGATGAATGAGA 59.772 45.455 0.00 0.00 0.00 3.27
737 738 2.783288 GGACTCCGGGGCTAAGTCG 61.783 68.421 0.00 0.00 40.25 4.18
745 746 2.081462 CGGGGCTAAGTCGTGAAATTT 58.919 47.619 0.00 0.00 0.00 1.82
750 751 3.426292 GGCTAAGTCGTGAAATTTCAGCC 60.426 47.826 21.05 21.70 37.98 4.85
771 772 4.325344 GCCCATAATAATACATGAGCCCCT 60.325 45.833 0.00 0.00 0.00 4.79
772 773 5.440610 CCCATAATAATACATGAGCCCCTC 58.559 45.833 0.00 0.00 0.00 4.30
773 774 5.044919 CCCATAATAATACATGAGCCCCTCA 60.045 44.000 0.00 0.00 44.99 3.86
774 775 5.882557 CCATAATAATACATGAGCCCCTCAC 59.117 44.000 0.00 0.00 43.63 3.51
775 776 3.685139 ATAATACATGAGCCCCTCACG 57.315 47.619 0.00 0.00 43.63 4.35
776 777 1.496060 AATACATGAGCCCCTCACGA 58.504 50.000 0.00 0.00 43.63 4.35
824 827 3.653344 CGAAGGAAGTGAGACATGAACA 58.347 45.455 0.00 0.00 0.00 3.18
825 828 3.430218 CGAAGGAAGTGAGACATGAACAC 59.570 47.826 0.00 6.64 35.15 3.32
826 829 3.409026 AGGAAGTGAGACATGAACACC 57.591 47.619 0.00 1.11 35.47 4.16
827 830 2.705658 AGGAAGTGAGACATGAACACCA 59.294 45.455 0.00 0.00 35.47 4.17
828 831 3.070018 GGAAGTGAGACATGAACACCAG 58.930 50.000 0.00 0.00 35.47 4.00
829 832 3.244215 GGAAGTGAGACATGAACACCAGA 60.244 47.826 0.00 0.00 35.47 3.86
830 833 3.393089 AGTGAGACATGAACACCAGAC 57.607 47.619 0.00 0.00 35.47 3.51
831 834 2.968574 AGTGAGACATGAACACCAGACT 59.031 45.455 0.00 0.00 35.47 3.24
832 835 3.006323 AGTGAGACATGAACACCAGACTC 59.994 47.826 0.00 0.00 35.47 3.36
833 836 3.006323 GTGAGACATGAACACCAGACTCT 59.994 47.826 0.00 0.00 0.00 3.24
834 837 3.256879 TGAGACATGAACACCAGACTCTC 59.743 47.826 0.00 0.00 0.00 3.20
835 838 3.234353 AGACATGAACACCAGACTCTCA 58.766 45.455 0.00 0.00 0.00 3.27
836 839 3.837146 AGACATGAACACCAGACTCTCAT 59.163 43.478 0.00 0.00 0.00 2.90
837 840 4.081752 AGACATGAACACCAGACTCTCATC 60.082 45.833 0.00 0.00 0.00 2.92
838 841 3.185330 CATGAACACCAGACTCTCATCG 58.815 50.000 0.00 0.00 0.00 3.84
839 842 1.546029 TGAACACCAGACTCTCATCGG 59.454 52.381 0.00 0.00 0.00 4.18
840 843 0.898320 AACACCAGACTCTCATCGGG 59.102 55.000 0.00 0.00 39.62 5.14
841 844 1.142748 CACCAGACTCTCATCGGGC 59.857 63.158 0.00 0.00 37.45 6.13
842 845 1.000993 ACCAGACTCTCATCGGGCT 59.999 57.895 0.00 0.00 37.45 5.19
843 846 0.616111 ACCAGACTCTCATCGGGCTT 60.616 55.000 0.00 0.00 37.45 4.35
844 847 0.179089 CCAGACTCTCATCGGGCTTG 60.179 60.000 0.00 0.00 0.00 4.01
845 848 0.179089 CAGACTCTCATCGGGCTTGG 60.179 60.000 0.00 0.00 0.00 3.61
846 849 1.144936 GACTCTCATCGGGCTTGGG 59.855 63.158 0.00 0.00 0.00 4.12
847 850 1.306141 ACTCTCATCGGGCTTGGGA 60.306 57.895 0.00 0.00 0.00 4.37
848 851 1.333636 ACTCTCATCGGGCTTGGGAG 61.334 60.000 9.83 9.83 45.45 4.30
849 852 1.306141 TCTCATCGGGCTTGGGAGT 60.306 57.895 0.00 0.00 0.00 3.85
850 853 1.153289 CTCATCGGGCTTGGGAGTG 60.153 63.158 0.00 0.00 0.00 3.51
851 854 2.124570 CATCGGGCTTGGGAGTGG 60.125 66.667 0.00 0.00 0.00 4.00
852 855 3.411517 ATCGGGCTTGGGAGTGGG 61.412 66.667 0.00 0.00 0.00 4.61
853 856 3.943137 ATCGGGCTTGGGAGTGGGA 62.943 63.158 0.00 0.00 0.00 4.37
854 857 3.646715 CGGGCTTGGGAGTGGGAA 61.647 66.667 0.00 0.00 0.00 3.97
855 858 2.983879 CGGGCTTGGGAGTGGGAAT 61.984 63.158 0.00 0.00 0.00 3.01
856 859 1.380380 GGGCTTGGGAGTGGGAATG 60.380 63.158 0.00 0.00 0.00 2.67
857 860 1.691219 GGCTTGGGAGTGGGAATGA 59.309 57.895 0.00 0.00 0.00 2.57
858 861 0.681243 GGCTTGGGAGTGGGAATGAC 60.681 60.000 0.00 0.00 0.00 3.06
859 862 0.681243 GCTTGGGAGTGGGAATGACC 60.681 60.000 0.00 0.00 38.08 4.02
860 863 0.995024 CTTGGGAGTGGGAATGACCT 59.005 55.000 0.00 0.00 38.98 3.85
861 864 0.698238 TTGGGAGTGGGAATGACCTG 59.302 55.000 0.00 0.00 38.98 4.00
862 865 1.077429 GGGAGTGGGAATGACCTGC 60.077 63.158 0.00 0.00 38.98 4.85
863 866 1.077429 GGAGTGGGAATGACCTGCC 60.077 63.158 0.00 0.00 38.98 4.85
864 867 1.077429 GAGTGGGAATGACCTGCCC 60.077 63.158 0.00 0.00 42.38 5.36
865 868 1.542375 AGTGGGAATGACCTGCCCT 60.542 57.895 0.00 0.00 42.52 5.19
866 869 1.142688 AGTGGGAATGACCTGCCCTT 61.143 55.000 0.00 0.00 42.52 3.95
867 870 0.967380 GTGGGAATGACCTGCCCTTG 60.967 60.000 0.00 0.00 42.52 3.61
868 871 1.139498 TGGGAATGACCTGCCCTTGA 61.139 55.000 0.00 0.00 42.52 3.02
869 872 0.394899 GGGAATGACCTGCCCTTGAG 60.395 60.000 0.00 0.00 38.85 3.02
870 873 1.034292 GGAATGACCTGCCCTTGAGC 61.034 60.000 0.00 0.00 35.41 4.26
871 874 0.322816 GAATGACCTGCCCTTGAGCA 60.323 55.000 0.00 0.00 41.46 4.26
892 895 0.510359 GCAGCCTATGCGAGATTTCG 59.490 55.000 0.40 0.40 46.99 3.46
900 903 4.178861 CGAGATTTCGCCGGTCAA 57.821 55.556 1.90 0.00 40.36 3.18
901 904 1.999051 CGAGATTTCGCCGGTCAAG 59.001 57.895 1.90 0.00 40.36 3.02
902 905 0.457853 CGAGATTTCGCCGGTCAAGA 60.458 55.000 1.90 0.00 40.36 3.02
903 906 1.722011 GAGATTTCGCCGGTCAAGAA 58.278 50.000 1.90 1.26 0.00 2.52
904 907 1.393883 GAGATTTCGCCGGTCAAGAAC 59.606 52.381 1.90 0.00 0.00 3.01
905 908 0.446616 GATTTCGCCGGTCAAGAACC 59.553 55.000 1.90 0.00 45.45 3.62
906 909 0.036306 ATTTCGCCGGTCAAGAACCT 59.964 50.000 1.90 0.00 46.87 3.50
907 910 0.882927 TTTCGCCGGTCAAGAACCTG 60.883 55.000 1.90 0.00 46.87 4.00
908 911 2.725203 TTCGCCGGTCAAGAACCTGG 62.725 60.000 1.90 0.00 46.87 4.45
910 913 2.359975 CCGGTCAAGAACCTGGCC 60.360 66.667 0.00 0.00 46.87 5.36
911 914 2.750350 CGGTCAAGAACCTGGCCT 59.250 61.111 3.32 0.00 46.87 5.19
912 915 1.376037 CGGTCAAGAACCTGGCCTC 60.376 63.158 3.32 0.00 46.87 4.70
913 916 1.831652 CGGTCAAGAACCTGGCCTCT 61.832 60.000 3.32 0.00 46.87 3.69
914 917 0.035915 GGTCAAGAACCTGGCCTCTC 60.036 60.000 3.32 0.00 45.45 3.20
915 918 0.980423 GTCAAGAACCTGGCCTCTCT 59.020 55.000 3.32 0.00 0.00 3.10
916 919 1.066502 GTCAAGAACCTGGCCTCTCTC 60.067 57.143 3.32 0.00 0.00 3.20
917 920 0.979665 CAAGAACCTGGCCTCTCTCA 59.020 55.000 3.32 0.00 0.00 3.27
918 921 1.349026 CAAGAACCTGGCCTCTCTCAA 59.651 52.381 3.32 0.00 0.00 3.02
919 922 0.980423 AGAACCTGGCCTCTCTCAAC 59.020 55.000 3.32 0.00 0.00 3.18
920 923 0.980423 GAACCTGGCCTCTCTCAACT 59.020 55.000 3.32 0.00 0.00 3.16
921 924 1.349357 GAACCTGGCCTCTCTCAACTT 59.651 52.381 3.32 0.00 0.00 2.66
922 925 0.980423 ACCTGGCCTCTCTCAACTTC 59.020 55.000 3.32 0.00 0.00 3.01
923 926 0.979665 CCTGGCCTCTCTCAACTTCA 59.020 55.000 3.32 0.00 0.00 3.02
924 927 1.066286 CCTGGCCTCTCTCAACTTCAG 60.066 57.143 3.32 0.00 0.00 3.02
925 928 1.622811 CTGGCCTCTCTCAACTTCAGT 59.377 52.381 3.32 0.00 0.00 3.41
926 929 2.828520 CTGGCCTCTCTCAACTTCAGTA 59.171 50.000 3.32 0.00 0.00 2.74
927 930 2.563179 TGGCCTCTCTCAACTTCAGTAC 59.437 50.000 3.32 0.00 0.00 2.73
928 931 2.416162 GGCCTCTCTCAACTTCAGTACG 60.416 54.545 0.00 0.00 0.00 3.67
929 932 2.229302 GCCTCTCTCAACTTCAGTACGT 59.771 50.000 0.00 0.00 0.00 3.57
930 933 3.671164 GCCTCTCTCAACTTCAGTACGTC 60.671 52.174 0.00 0.00 0.00 4.34
931 934 3.119779 CCTCTCTCAACTTCAGTACGTCC 60.120 52.174 0.00 0.00 0.00 4.79
932 935 3.752665 TCTCTCAACTTCAGTACGTCCT 58.247 45.455 0.00 0.00 0.00 3.85
933 936 3.752222 TCTCTCAACTTCAGTACGTCCTC 59.248 47.826 0.00 0.00 0.00 3.71
934 937 2.818432 TCTCAACTTCAGTACGTCCTCC 59.182 50.000 0.00 0.00 0.00 4.30
935 938 1.538512 TCAACTTCAGTACGTCCTCCG 59.461 52.381 0.00 0.00 44.03 4.63
936 939 0.243095 AACTTCAGTACGTCCTCCGC 59.757 55.000 0.00 0.00 41.42 5.54
937 940 1.139095 CTTCAGTACGTCCTCCGCC 59.861 63.158 0.00 0.00 41.42 6.13
938 941 2.594119 CTTCAGTACGTCCTCCGCCG 62.594 65.000 0.00 0.00 41.42 6.46
939 942 4.189188 CAGTACGTCCTCCGCCGG 62.189 72.222 0.00 0.00 41.42 6.13
940 943 4.415150 AGTACGTCCTCCGCCGGA 62.415 66.667 5.05 5.37 41.42 5.14
941 944 3.214845 GTACGTCCTCCGCCGGAT 61.215 66.667 6.16 0.00 41.42 4.18
942 945 1.893808 GTACGTCCTCCGCCGGATA 60.894 63.158 6.16 0.00 41.42 2.59
943 946 1.598962 TACGTCCTCCGCCGGATAG 60.599 63.158 6.16 0.80 41.42 2.08
944 947 3.671411 CGTCCTCCGCCGGATAGG 61.671 72.222 6.16 5.53 44.97 2.57
945 948 2.521224 GTCCTCCGCCGGATAGGT 60.521 66.667 6.16 0.00 43.70 3.08
946 949 1.228367 GTCCTCCGCCGGATAGGTA 60.228 63.158 6.16 0.00 43.70 3.08
947 950 0.611340 GTCCTCCGCCGGATAGGTAT 60.611 60.000 6.16 0.00 43.70 2.73
948 951 0.994247 TCCTCCGCCGGATAGGTATA 59.006 55.000 6.16 0.00 43.70 1.47
949 952 1.064906 TCCTCCGCCGGATAGGTATAG 60.065 57.143 6.16 0.00 43.70 1.31
950 953 1.340795 CCTCCGCCGGATAGGTATAGT 60.341 57.143 6.16 0.00 43.70 2.12
951 954 2.092753 CCTCCGCCGGATAGGTATAGTA 60.093 54.545 6.16 0.00 43.70 1.82
952 955 3.204526 CTCCGCCGGATAGGTATAGTAG 58.795 54.545 6.16 0.00 43.70 2.57
953 956 2.840038 TCCGCCGGATAGGTATAGTAGA 59.160 50.000 5.05 0.00 43.70 2.59
954 957 3.457380 TCCGCCGGATAGGTATAGTAGAT 59.543 47.826 5.05 0.00 43.70 1.98
955 958 4.655649 TCCGCCGGATAGGTATAGTAGATA 59.344 45.833 5.05 0.00 43.70 1.98
956 959 4.996122 CCGCCGGATAGGTATAGTAGATAG 59.004 50.000 5.05 0.00 43.70 2.08
957 960 5.221601 CCGCCGGATAGGTATAGTAGATAGA 60.222 48.000 5.05 0.00 43.70 1.98
958 961 6.465948 CGCCGGATAGGTATAGTAGATAGAT 58.534 44.000 5.05 0.00 43.70 1.98
959 962 7.310299 CCGCCGGATAGGTATAGTAGATAGATA 60.310 44.444 5.05 0.00 43.70 1.98
960 963 8.259411 CGCCGGATAGGTATAGTAGATAGATAT 58.741 40.741 5.05 0.00 43.70 1.63
1006 1009 0.395312 AACGGATCAGGTGGACGTTT 59.605 50.000 0.00 0.00 44.21 3.60
1013 1016 1.418264 TCAGGTGGACGTTTGATGGAA 59.582 47.619 0.00 0.00 0.00 3.53
1113 1125 4.101448 CCCAGCTCCCAACCTCCG 62.101 72.222 0.00 0.00 0.00 4.63
1204 1216 1.019805 GCCTTCCTCACCTACAACGC 61.020 60.000 0.00 0.00 0.00 4.84
1206 1218 0.736325 CTTCCTCACCTACAACGCGG 60.736 60.000 12.47 0.00 0.00 6.46
1401 1422 3.074412 GTCATGTACCACTGGTTCAAGG 58.926 50.000 11.21 7.38 36.62 3.61
1540 1561 1.623542 GGGGCGGATCAGGTAACAGT 61.624 60.000 0.00 0.00 41.41 3.55
1546 1567 3.518590 CGGATCAGGTAACAGTAACACC 58.481 50.000 0.00 0.00 41.41 4.16
1548 1569 3.370209 GGATCAGGTAACAGTAACACCCC 60.370 52.174 0.00 0.00 41.41 4.95
1553 1574 2.097201 TAACAGTAACACCCCGCGCA 62.097 55.000 8.75 0.00 0.00 6.09
1601 1681 6.429692 GGCAATTTTATTTTTACCCTGTTGCT 59.570 34.615 0.00 0.00 38.50 3.91
1616 1697 1.880027 GTTGCTGGTTGGGTAGAGTTG 59.120 52.381 0.00 0.00 0.00 3.16
1632 1713 0.521735 GTTGTGGAGAAATGCGGGTC 59.478 55.000 0.00 0.00 0.00 4.46
1660 1741 1.006832 GGATCACGTGAATCGGTTGG 58.993 55.000 24.13 0.00 44.69 3.77
1712 1793 4.202223 ACTGTCTAGACATTGGTTCGTGTT 60.202 41.667 25.35 0.34 41.01 3.32
1713 1794 4.304110 TGTCTAGACATTGGTTCGTGTTC 58.696 43.478 21.74 0.00 36.21 3.18
1714 1795 4.038763 TGTCTAGACATTGGTTCGTGTTCT 59.961 41.667 21.74 0.00 36.21 3.01
1743 1824 5.366829 TCATGCTCAGTTTGAGTTTCATG 57.633 39.130 14.03 14.03 45.94 3.07
1744 1825 4.216902 TCATGCTCAGTTTGAGTTTCATGG 59.783 41.667 17.36 6.72 45.94 3.66
1819 1912 0.038744 CACTGGAAAGGTCAGGGCAT 59.961 55.000 0.00 0.00 36.62 4.40
1820 1913 1.281867 CACTGGAAAGGTCAGGGCATA 59.718 52.381 0.00 0.00 36.62 3.14
1821 1914 1.561542 ACTGGAAAGGTCAGGGCATAG 59.438 52.381 0.00 0.00 36.62 2.23
1878 1971 1.405105 TCTGGACAAAACAACAGCTGC 59.595 47.619 15.27 0.00 0.00 5.25
2033 2127 2.030007 CCACTTTTCATCATGTGGCGTT 60.030 45.455 0.00 0.00 42.55 4.84
2041 2135 0.671472 TCATGTGGCGTTCAGAGCAG 60.671 55.000 0.00 0.00 36.08 4.24
2084 2178 5.125578 GCCAGCTGCTAATAAACCTTTAGTT 59.874 40.000 8.66 0.00 37.35 2.24
2085 2179 6.555315 CCAGCTGCTAATAAACCTTTAGTTG 58.445 40.000 8.66 0.00 39.19 3.16
2120 2217 3.384146 TCTCTCATGATGACAGAGCCTTC 59.616 47.826 6.78 0.00 0.00 3.46
2211 2308 1.136891 TGACTGGCATACTGATGGACG 59.863 52.381 0.00 0.00 33.26 4.79
2213 2310 1.410517 ACTGGCATACTGATGGACGAG 59.589 52.381 0.00 0.00 33.26 4.18
2217 2314 1.863454 GCATACTGATGGACGAGCAAG 59.137 52.381 0.00 0.00 33.26 4.01
2274 2371 9.634021 TTAGTACCAAAACCATGCATTATATCA 57.366 29.630 0.00 0.00 0.00 2.15
2337 2435 5.376854 TGCTGCTTGTTAGAATTTTCTCC 57.623 39.130 0.00 0.00 38.70 3.71
2710 2810 6.764308 GGAAATTCTCCTGTCATCATTGAA 57.236 37.500 0.00 0.00 41.61 2.69
2714 2814 7.771927 AATTCTCCTGTCATCATTGAAAAGT 57.228 32.000 0.00 0.00 32.48 2.66
2715 2815 8.868522 AATTCTCCTGTCATCATTGAAAAGTA 57.131 30.769 0.00 0.00 32.48 2.24
2716 2816 9.471702 AATTCTCCTGTCATCATTGAAAAGTAT 57.528 29.630 0.00 0.00 32.48 2.12
2831 2932 0.739462 TCGCACCGACATGGATGAAC 60.739 55.000 0.00 0.00 42.00 3.18
2858 2959 5.734720 TCGTTAGCAATGAAGAAAGATCCT 58.265 37.500 0.00 0.00 0.00 3.24
2873 2974 5.370875 AAGATCCTGAAGCAGATAAAGCT 57.629 39.130 0.00 0.00 45.97 3.74
3023 3124 5.472137 TGCTGTTATTCTGGAAAACAGGTAC 59.528 40.000 23.05 15.07 46.50 3.34
3048 3149 4.082841 CGTATGCTGTATCATCTGCTCTCT 60.083 45.833 0.00 0.00 34.27 3.10
3299 3400 6.995364 TCTTGATGCAAAATTTCAGGATTCA 58.005 32.000 0.00 0.00 0.00 2.57
3305 3406 8.937634 ATGCAAAATTTCAGGATTCATCTTAC 57.062 30.769 0.00 0.00 0.00 2.34
3333 3434 9.136323 AGTTCATTCTTTAACCATGTTCTTCTT 57.864 29.630 0.00 0.00 0.00 2.52
3334 3435 9.399403 GTTCATTCTTTAACCATGTTCTTCTTC 57.601 33.333 0.00 0.00 0.00 2.87
3468 3569 0.328258 AAGTGTGGTATGGTCCAGCC 59.672 55.000 8.03 8.03 38.23 4.85
3482 3583 1.748122 CAGCCCTGCCTACAGCTTG 60.748 63.158 0.00 0.00 43.02 4.01
3497 3598 9.110502 GCCTACAGCTTGTAATATTAGTTTTCT 57.889 33.333 0.00 0.00 38.99 2.52
3972 4087 3.119673 AGTGATGTCGACACTGATGACTC 60.120 47.826 22.71 12.36 45.19 3.36
4421 4540 4.644685 AGAGAGTGCCACAAAAGCTAAAAA 59.355 37.500 0.00 0.00 0.00 1.94
4488 4607 2.875933 CTGAGTGTTGGCCGACTAAAAA 59.124 45.455 23.87 0.00 0.00 1.94
4496 4615 2.273557 GGCCGACTAAAAAGCGACATA 58.726 47.619 0.00 0.00 0.00 2.29
4689 4808 0.175760 GAAGCTCCGGTGCATAGTGA 59.824 55.000 28.68 0.00 34.99 3.41
4744 4863 1.648504 GGGGTAGACCGAATTTGACG 58.351 55.000 0.00 0.00 41.60 4.35
4934 5301 5.177696 GGCTTTGTTGTTGTTGTTGTTGTTA 59.822 36.000 0.00 0.00 0.00 2.41
4949 5316 8.812147 TGTTGTTGTTATTGTTGTTGTTTGTA 57.188 26.923 0.00 0.00 0.00 2.41
4980 5347 0.179078 TGTAACGAACCCGCACTGTT 60.179 50.000 0.00 0.00 39.95 3.16
5047 5414 9.016438 TCAGTACTCAGTACACATTACATAACA 57.984 33.333 17.46 0.00 41.03 2.41
5049 5416 9.239551 AGTACTCAGTACACATTACATAACAGA 57.760 33.333 17.46 0.00 41.03 3.41
5077 5444 1.418637 TCACACTTACCACAAGTCCCC 59.581 52.381 0.00 0.00 0.00 4.81
5147 5514 6.568844 GCGTATAGTGGATTTTGTGTTTTCCA 60.569 38.462 0.00 0.00 35.93 3.53
5250 5712 6.701340 TGTACAATCTGATACTTGTCAAGCT 58.299 36.000 12.66 0.13 36.92 3.74
5272 5757 1.872388 TTTTGTTCGCTCGATCACCA 58.128 45.000 2.90 0.00 0.00 4.17
5305 5790 5.361571 TGGATAAGTGGCTCATACGAGTTTA 59.638 40.000 0.00 0.00 41.71 2.01
5306 5791 6.041637 TGGATAAGTGGCTCATACGAGTTTAT 59.958 38.462 0.00 0.00 41.71 1.40
5335 5821 1.995484 CTGACTCCAAGCGTGTGTATG 59.005 52.381 0.00 0.00 0.00 2.39
5457 5943 2.821378 CAATGGAAATGAGTGTGAGGCA 59.179 45.455 0.00 0.00 0.00 4.75
5533 6019 3.587923 CTGAGTCCTTTCTGCTTCAGAG 58.412 50.000 0.00 0.00 41.75 3.35
5564 6050 4.201783 GCGTACACTGTATTTTAGGCAAGG 60.202 45.833 0.00 0.00 0.00 3.61
5579 6065 2.423373 GGCAAGGCAATGGAATCCTCTA 60.423 50.000 0.00 0.00 0.00 2.43
5624 6110 3.682696 AGAAGCTGAACTGCATGAATCA 58.317 40.909 0.00 0.00 34.99 2.57
5636 6122 7.458409 ACTGCATGAATCAAAGTATTCAAGT 57.542 32.000 0.00 1.18 46.12 3.16
5692 6179 2.576615 AGTTGCCCTTCAAGAAGTGAC 58.423 47.619 8.83 2.66 35.39 3.67
5695 6182 2.507484 TGCCCTTCAAGAAGTGACATG 58.493 47.619 8.83 0.00 35.39 3.21
5765 6259 9.337396 TGCCTACTTGGTATAAATTATCACTTG 57.663 33.333 0.00 0.00 38.35 3.16
5793 6288 8.522830 CCTACAAAAGGCTCATTTTAATCAGAA 58.477 33.333 0.00 0.00 38.97 3.02
5845 6340 5.827797 ACATAAATCACACCTTGAACACACT 59.172 36.000 0.00 0.00 37.92 3.55
5865 6360 6.754209 CACACTACATTTTGTTTTGCCTACAA 59.246 34.615 0.00 0.00 33.92 2.41
5866 6361 7.276658 CACACTACATTTTGTTTTGCCTACAAA 59.723 33.333 0.00 0.00 43.97 2.83
5938 6438 5.949952 TCCTTTGCCTTTTTAATCTAGGACC 59.050 40.000 0.00 0.00 0.00 4.46
5979 6480 2.449777 GGGAGGGGGTGGCATTTT 59.550 61.111 0.00 0.00 0.00 1.82
5995 6496 3.121778 GCATTTTGAACGATTTCACTGGC 59.878 43.478 0.00 0.00 41.64 4.85
6027 6531 2.554032 GTGAGGGGTTGACAACTTCATG 59.446 50.000 17.52 0.00 32.84 3.07
6082 6600 8.053653 ACATTTTTCGTTTAAGATTTCGCAAAC 58.946 29.630 0.00 0.00 0.00 2.93
6134 6655 1.059006 GTCATCCCCTCCCAGCTGAT 61.059 60.000 17.39 0.00 0.00 2.90
6140 6661 1.153289 CCTCCCAGCTGATGTTCGG 60.153 63.158 17.39 6.70 0.00 4.30
6165 6687 8.015658 GGCAGATAACATTACCTTAATTTAGCG 58.984 37.037 0.00 0.00 0.00 4.26
6217 6761 1.104630 CGTACTTCTCCTCCCAGTCC 58.895 60.000 0.00 0.00 0.00 3.85
6234 6778 4.564613 CCAGTCCTCTTTCTTCTTCCCTTC 60.565 50.000 0.00 0.00 0.00 3.46
6252 6800 4.512914 GCCTGCCAGATCCCACCC 62.513 72.222 0.00 0.00 0.00 4.61
6322 6870 2.693017 GCCTCCTCCTCCTCCTCA 59.307 66.667 0.00 0.00 0.00 3.86
6337 6889 4.337177 TCAATGGAACCCGCGGCA 62.337 61.111 22.85 13.33 0.00 5.69
6380 6932 4.424867 ACGGAGGCCATACCCCCA 62.425 66.667 5.01 0.00 40.58 4.96
6382 6934 2.368329 GGAGGCCATACCCCCACT 60.368 66.667 5.01 0.00 40.58 4.00
6505 7063 2.182030 GTCAAGGCGGTCCTCTCG 59.818 66.667 0.00 0.00 43.40 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 5.810587 GCAATCGTCTGGATACTCAAGTAAA 59.189 40.000 0.00 0.00 34.08 2.01
148 149 3.706594 GTGTCTGGATTCTATGGAGGACA 59.293 47.826 0.00 0.00 0.00 4.02
371 372 2.904866 GACGTGCCCCTGTTGCAA 60.905 61.111 0.00 0.00 41.06 4.08
402 403 1.117150 GTCAATACGGGGCTGGACTA 58.883 55.000 0.00 0.00 0.00 2.59
750 751 5.882557 GTGAGGGGCTCATGTATTATTATGG 59.117 44.000 0.00 0.00 42.73 2.74
771 772 2.412323 CCGACGGATCCCTTCGTGA 61.412 63.158 22.61 0.00 42.50 4.35
772 773 1.940883 TTCCGACGGATCCCTTCGTG 61.941 60.000 19.12 16.15 42.50 4.35
773 774 1.252904 TTTCCGACGGATCCCTTCGT 61.253 55.000 19.12 11.19 42.50 3.85
774 775 0.527817 CTTTCCGACGGATCCCTTCG 60.528 60.000 19.12 19.26 43.44 3.79
775 776 0.810426 GCTTTCCGACGGATCCCTTC 60.810 60.000 19.12 1.78 0.00 3.46
776 777 1.221021 GCTTTCCGACGGATCCCTT 59.779 57.895 19.12 0.00 0.00 3.95
785 788 2.189784 GGGGCTAGGCTTTCCGAC 59.810 66.667 16.80 0.00 37.47 4.79
790 793 2.680370 CCTTCGGGGGCTAGGCTTT 61.680 63.158 16.80 0.00 0.00 3.51
818 821 2.167281 CCGATGAGAGTCTGGTGTTCAT 59.833 50.000 0.00 0.00 0.00 2.57
819 822 1.546029 CCGATGAGAGTCTGGTGTTCA 59.454 52.381 0.00 0.00 0.00 3.18
820 823 1.134965 CCCGATGAGAGTCTGGTGTTC 60.135 57.143 0.00 0.00 0.00 3.18
821 824 0.898320 CCCGATGAGAGTCTGGTGTT 59.102 55.000 0.00 0.00 0.00 3.32
822 825 1.608717 GCCCGATGAGAGTCTGGTGT 61.609 60.000 0.00 0.00 0.00 4.16
823 826 1.142748 GCCCGATGAGAGTCTGGTG 59.857 63.158 0.00 0.00 0.00 4.17
824 827 0.616111 AAGCCCGATGAGAGTCTGGT 60.616 55.000 0.00 0.00 0.00 4.00
825 828 0.179089 CAAGCCCGATGAGAGTCTGG 60.179 60.000 0.00 0.00 0.00 3.86
826 829 0.179089 CCAAGCCCGATGAGAGTCTG 60.179 60.000 0.00 0.00 0.00 3.51
827 830 1.333636 CCCAAGCCCGATGAGAGTCT 61.334 60.000 0.00 0.00 0.00 3.24
828 831 1.144936 CCCAAGCCCGATGAGAGTC 59.855 63.158 0.00 0.00 0.00 3.36
829 832 1.306141 TCCCAAGCCCGATGAGAGT 60.306 57.895 0.00 0.00 0.00 3.24
830 833 1.333636 ACTCCCAAGCCCGATGAGAG 61.334 60.000 0.00 0.00 0.00 3.20
831 834 1.306141 ACTCCCAAGCCCGATGAGA 60.306 57.895 0.00 0.00 0.00 3.27
832 835 1.153289 CACTCCCAAGCCCGATGAG 60.153 63.158 0.00 0.00 0.00 2.90
833 836 2.669133 CCACTCCCAAGCCCGATGA 61.669 63.158 0.00 0.00 0.00 2.92
834 837 2.124570 CCACTCCCAAGCCCGATG 60.125 66.667 0.00 0.00 0.00 3.84
835 838 3.411517 CCCACTCCCAAGCCCGAT 61.412 66.667 0.00 0.00 0.00 4.18
836 839 4.649705 TCCCACTCCCAAGCCCGA 62.650 66.667 0.00 0.00 0.00 5.14
837 840 2.983879 ATTCCCACTCCCAAGCCCG 61.984 63.158 0.00 0.00 0.00 6.13
838 841 1.380380 CATTCCCACTCCCAAGCCC 60.380 63.158 0.00 0.00 0.00 5.19
839 842 0.681243 GTCATTCCCACTCCCAAGCC 60.681 60.000 0.00 0.00 0.00 4.35
840 843 0.681243 GGTCATTCCCACTCCCAAGC 60.681 60.000 0.00 0.00 0.00 4.01
841 844 0.995024 AGGTCATTCCCACTCCCAAG 59.005 55.000 0.00 0.00 36.75 3.61
842 845 0.698238 CAGGTCATTCCCACTCCCAA 59.302 55.000 0.00 0.00 36.75 4.12
843 846 1.852157 GCAGGTCATTCCCACTCCCA 61.852 60.000 0.00 0.00 36.75 4.37
844 847 1.077429 GCAGGTCATTCCCACTCCC 60.077 63.158 0.00 0.00 36.75 4.30
845 848 1.077429 GGCAGGTCATTCCCACTCC 60.077 63.158 0.00 0.00 36.75 3.85
846 849 1.077429 GGGCAGGTCATTCCCACTC 60.077 63.158 0.00 0.00 39.82 3.51
847 850 1.142688 AAGGGCAGGTCATTCCCACT 61.143 55.000 0.00 0.00 42.52 4.00
848 851 0.967380 CAAGGGCAGGTCATTCCCAC 60.967 60.000 0.00 0.00 42.52 4.61
849 852 1.139498 TCAAGGGCAGGTCATTCCCA 61.139 55.000 0.00 0.00 42.52 4.37
850 853 0.394899 CTCAAGGGCAGGTCATTCCC 60.395 60.000 0.00 0.00 40.36 3.97
851 854 1.034292 GCTCAAGGGCAGGTCATTCC 61.034 60.000 0.00 0.00 0.00 3.01
852 855 0.322816 TGCTCAAGGGCAGGTCATTC 60.323 55.000 0.00 0.00 37.29 2.67
853 856 1.769665 TGCTCAAGGGCAGGTCATT 59.230 52.632 0.00 0.00 37.29 2.57
854 857 3.499406 TGCTCAAGGGCAGGTCAT 58.501 55.556 0.00 0.00 37.29 3.06
864 867 1.445716 GCATAGGCTGCCTGCTCAAG 61.446 60.000 30.83 14.06 45.66 3.02
865 868 1.452651 GCATAGGCTGCCTGCTCAA 60.453 57.895 30.83 11.25 45.66 3.02
866 869 2.191375 GCATAGGCTGCCTGCTCA 59.809 61.111 30.83 11.67 45.66 4.26
884 887 1.393883 GTTCTTGACCGGCGAAATCTC 59.606 52.381 9.30 0.00 0.00 2.75
885 888 1.439679 GTTCTTGACCGGCGAAATCT 58.560 50.000 9.30 0.00 0.00 2.40
886 889 0.446616 GGTTCTTGACCGGCGAAATC 59.553 55.000 9.30 3.35 39.00 2.17
887 890 2.551644 GGTTCTTGACCGGCGAAAT 58.448 52.632 9.30 0.00 39.00 2.17
888 891 4.052519 GGTTCTTGACCGGCGAAA 57.947 55.556 9.30 0.00 39.00 3.46
896 899 0.980423 AGAGAGGCCAGGTTCTTGAC 59.020 55.000 5.01 0.00 0.00 3.18
897 900 1.270907 GAGAGAGGCCAGGTTCTTGA 58.729 55.000 5.01 0.00 0.00 3.02
898 901 0.979665 TGAGAGAGGCCAGGTTCTTG 59.020 55.000 5.01 0.00 0.00 3.02
899 902 1.349357 GTTGAGAGAGGCCAGGTTCTT 59.651 52.381 5.01 0.00 0.00 2.52
900 903 0.980423 GTTGAGAGAGGCCAGGTTCT 59.020 55.000 5.01 0.00 0.00 3.01
901 904 0.980423 AGTTGAGAGAGGCCAGGTTC 59.020 55.000 5.01 0.00 0.00 3.62
902 905 1.349357 GAAGTTGAGAGAGGCCAGGTT 59.651 52.381 5.01 0.00 0.00 3.50
903 906 0.980423 GAAGTTGAGAGAGGCCAGGT 59.020 55.000 5.01 0.00 0.00 4.00
904 907 0.979665 TGAAGTTGAGAGAGGCCAGG 59.020 55.000 5.01 0.00 0.00 4.45
905 908 1.622811 ACTGAAGTTGAGAGAGGCCAG 59.377 52.381 5.01 0.00 0.00 4.85
906 909 1.722034 ACTGAAGTTGAGAGAGGCCA 58.278 50.000 5.01 0.00 0.00 5.36
907 910 2.416162 CGTACTGAAGTTGAGAGAGGCC 60.416 54.545 0.00 0.00 0.00 5.19
908 911 2.229302 ACGTACTGAAGTTGAGAGAGGC 59.771 50.000 0.00 0.00 0.00 4.70
909 912 3.119779 GGACGTACTGAAGTTGAGAGAGG 60.120 52.174 0.00 0.00 0.00 3.69
910 913 3.754323 AGGACGTACTGAAGTTGAGAGAG 59.246 47.826 0.00 0.00 0.00 3.20
911 914 3.752222 GAGGACGTACTGAAGTTGAGAGA 59.248 47.826 4.10 0.00 0.00 3.10
912 915 3.119779 GGAGGACGTACTGAAGTTGAGAG 60.120 52.174 4.10 0.00 0.00 3.20
913 916 2.818432 GGAGGACGTACTGAAGTTGAGA 59.182 50.000 4.10 0.00 0.00 3.27
914 917 2.414293 CGGAGGACGTACTGAAGTTGAG 60.414 54.545 4.10 0.00 37.93 3.02
915 918 1.538512 CGGAGGACGTACTGAAGTTGA 59.461 52.381 4.10 0.00 37.93 3.18
916 919 1.978542 CGGAGGACGTACTGAAGTTG 58.021 55.000 4.10 0.00 37.93 3.16
917 920 0.243095 GCGGAGGACGTACTGAAGTT 59.757 55.000 4.10 0.00 46.52 2.66
918 921 1.593296 GGCGGAGGACGTACTGAAGT 61.593 60.000 4.10 0.00 46.52 3.01
919 922 1.139095 GGCGGAGGACGTACTGAAG 59.861 63.158 4.10 0.00 46.52 3.02
920 923 2.693762 CGGCGGAGGACGTACTGAA 61.694 63.158 4.10 0.00 46.52 3.02
921 924 3.129502 CGGCGGAGGACGTACTGA 61.130 66.667 4.10 0.00 46.52 3.41
922 925 4.189188 CCGGCGGAGGACGTACTG 62.189 72.222 24.41 0.00 45.55 2.74
923 926 2.329539 TATCCGGCGGAGGACGTACT 62.330 60.000 33.82 16.90 45.55 2.73
924 927 1.849976 CTATCCGGCGGAGGACGTAC 61.850 65.000 33.82 0.00 45.55 3.67
925 928 1.598962 CTATCCGGCGGAGGACGTA 60.599 63.158 33.82 19.32 45.55 3.57
926 929 2.905880 CTATCCGGCGGAGGACGT 60.906 66.667 33.82 19.23 45.55 4.34
927 930 3.671411 CCTATCCGGCGGAGGACG 61.671 72.222 33.82 19.90 46.94 4.79
928 931 0.611340 ATACCTATCCGGCGGAGGAC 60.611 60.000 33.30 0.00 44.07 3.85
929 932 0.994247 TATACCTATCCGGCGGAGGA 59.006 55.000 33.30 23.35 45.54 3.71
930 933 1.340795 ACTATACCTATCCGGCGGAGG 60.341 57.143 33.82 30.20 34.05 4.30
931 934 2.125773 ACTATACCTATCCGGCGGAG 57.874 55.000 33.82 22.42 34.05 4.63
932 935 2.840038 TCTACTATACCTATCCGGCGGA 59.160 50.000 33.10 33.10 35.61 5.54
933 936 3.272574 TCTACTATACCTATCCGGCGG 57.727 52.381 22.51 22.51 35.61 6.13
934 937 5.851720 TCTATCTACTATACCTATCCGGCG 58.148 45.833 0.00 0.00 35.61 6.46
965 968 9.326413 CCGTTTAGGATACACAAGAAAATCTAT 57.674 33.333 0.00 0.00 45.00 1.98
966 969 8.533657 TCCGTTTAGGATACACAAGAAAATCTA 58.466 33.333 0.00 0.00 45.98 1.98
967 970 7.391620 TCCGTTTAGGATACACAAGAAAATCT 58.608 34.615 0.00 0.00 45.98 2.40
968 971 7.605410 TCCGTTTAGGATACACAAGAAAATC 57.395 36.000 0.00 0.00 45.98 2.17
1006 1009 0.597568 CGCCAAGCAAACTTCCATCA 59.402 50.000 0.00 0.00 32.29 3.07
1013 1016 1.164041 AACGCTACGCCAAGCAAACT 61.164 50.000 5.84 0.00 42.91 2.66
1033 1036 0.104120 AAAGGCCAAAACTCAACGGC 59.896 50.000 5.01 0.00 44.10 5.68
1034 1037 1.599419 CGAAAGGCCAAAACTCAACGG 60.599 52.381 5.01 0.00 0.00 4.44
1035 1038 1.753956 CGAAAGGCCAAAACTCAACG 58.246 50.000 5.01 0.00 0.00 4.10
1206 1218 2.835895 GGAGCGGGAGGAGAGGAC 60.836 72.222 0.00 0.00 0.00 3.85
1540 1561 3.463728 AACTGTGCGCGGGGTGTTA 62.464 57.895 8.83 0.00 0.00 2.41
1553 1574 1.045407 TCACCTAACCGAGCAACTGT 58.955 50.000 0.00 0.00 0.00 3.55
1601 1681 1.697432 CTCCACAACTCTACCCAACCA 59.303 52.381 0.00 0.00 0.00 3.67
1616 1697 0.953960 AACGACCCGCATTTCTCCAC 60.954 55.000 0.00 0.00 0.00 4.02
1660 1741 5.352846 GGAACTTCTTTGCTGATCTTCCTAC 59.647 44.000 0.00 0.00 0.00 3.18
1712 1793 5.125356 TCAAACTGAGCATGAAACTGAAGA 58.875 37.500 0.00 0.00 0.00 2.87
1713 1794 5.428496 TCAAACTGAGCATGAAACTGAAG 57.572 39.130 0.00 0.00 0.00 3.02
1714 1795 5.428496 CTCAAACTGAGCATGAAACTGAA 57.572 39.130 0.00 0.00 37.72 3.02
1743 1824 0.535102 AGTGGTGCTGTGTTAGTGCC 60.535 55.000 0.00 0.00 0.00 5.01
1744 1825 2.163818 TAGTGGTGCTGTGTTAGTGC 57.836 50.000 0.00 0.00 0.00 4.40
1820 1913 9.770097 CATGTGTCAGTGGAATTATAATCTACT 57.230 33.333 0.00 3.78 38.94 2.57
1821 1914 9.764363 TCATGTGTCAGTGGAATTATAATCTAC 57.236 33.333 0.00 1.66 0.00 2.59
1878 1971 1.349688 TGTACACAAGGTAAGGCAGGG 59.650 52.381 0.00 0.00 32.72 4.45
1900 1994 0.966875 TGCACTTGATCCCCACATGC 60.967 55.000 0.00 0.00 36.75 4.06
2033 2127 1.489481 ATCGATGGTTCCTGCTCTGA 58.511 50.000 0.00 0.00 0.00 3.27
2041 2135 2.814336 GGCATCCTAAATCGATGGTTCC 59.186 50.000 0.00 0.00 38.05 3.62
2084 2178 5.755849 TCATGAGAGACATACTGAGTACCA 58.244 41.667 0.00 0.00 37.46 3.25
2085 2179 6.488344 TCATCATGAGAGACATACTGAGTACC 59.512 42.308 0.09 0.00 37.46 3.34
2120 2217 3.809832 CAGTGACAGTTCCACTTTACCAG 59.190 47.826 0.00 0.00 42.44 4.00
2211 2308 4.754114 ACTTTGTGAGATCTTGACTTGCTC 59.246 41.667 0.00 0.00 0.00 4.26
2213 2310 5.429957 AACTTTGTGAGATCTTGACTTGC 57.570 39.130 0.00 0.00 0.00 4.01
2217 2314 6.693113 GGTGAAAAACTTTGTGAGATCTTGAC 59.307 38.462 0.00 0.00 0.00 3.18
2292 2390 1.614903 CTGGGAACAATTTGCTGCAGA 59.385 47.619 20.43 0.00 42.06 4.26
2293 2391 1.614903 TCTGGGAACAATTTGCTGCAG 59.385 47.619 10.11 10.11 42.06 4.41
2294 2392 1.702182 TCTGGGAACAATTTGCTGCA 58.298 45.000 0.00 0.00 42.06 4.41
2295 2393 2.818130 TTCTGGGAACAATTTGCTGC 57.182 45.000 0.00 0.00 42.06 5.25
2296 2394 2.997986 GCATTCTGGGAACAATTTGCTG 59.002 45.455 0.00 0.00 42.06 4.41
2297 2395 2.901839 AGCATTCTGGGAACAATTTGCT 59.098 40.909 0.00 0.00 41.21 3.91
2337 2435 6.538021 CCTGAGATTTGGATGAACTCTGTTAG 59.462 42.308 0.00 0.00 0.00 2.34
2391 2489 3.305608 CCTTCTGGAGCCATTGAACAAAC 60.306 47.826 0.00 0.00 34.57 2.93
2625 2725 4.617223 GGAAGAATTTACGCAGCACTTTTC 59.383 41.667 0.00 0.00 0.00 2.29
2715 2815 9.590451 CTGAATATATTCCACTGCAACAAAAAT 57.410 29.630 20.29 0.00 35.97 1.82
2716 2816 8.801299 TCTGAATATATTCCACTGCAACAAAAA 58.199 29.630 20.29 0.00 35.97 1.94
2721 2821 5.528690 TGCTCTGAATATATTCCACTGCAAC 59.471 40.000 20.29 5.19 35.97 4.17
2831 2932 7.430502 GGATCTTTCTTCATTGCTAACGAAATG 59.569 37.037 0.00 0.00 37.49 2.32
2873 2974 3.454082 ACATTTCAAGAACCCAGCCAAAA 59.546 39.130 0.00 0.00 0.00 2.44
2932 3033 7.481798 CCTGATTGAAAGCTTGAACGTATTAAC 59.518 37.037 0.00 0.00 0.00 2.01
2933 3034 7.526608 CCTGATTGAAAGCTTGAACGTATTAA 58.473 34.615 0.00 0.00 0.00 1.40
2939 3040 2.589014 GCCTGATTGAAAGCTTGAACG 58.411 47.619 0.00 0.00 0.00 3.95
2991 3092 7.994425 TTTCCAGAATAACAGCATAGAAACA 57.006 32.000 0.00 0.00 0.00 2.83
2994 3095 7.121168 CCTGTTTTCCAGAATAACAGCATAGAA 59.879 37.037 19.22 0.00 44.54 2.10
3023 3124 1.388093 GCAGATGATACAGCATACGCG 59.612 52.381 3.53 3.53 45.49 6.01
3048 3149 4.163458 GTGTAAGATGTTCCCCACTCCATA 59.837 45.833 0.00 0.00 0.00 2.74
3269 3370 6.807230 CCTGAAATTTTGCATCAAGAGAGAAG 59.193 38.462 0.00 0.00 0.00 2.85
3305 3406 9.185192 GAAGAACATGGTTAAAGAATGAACTTG 57.815 33.333 0.00 0.00 0.00 3.16
3333 3434 7.501225 GCCATAAGTTAATTTGCCCTAGTTAGA 59.499 37.037 0.00 0.00 0.00 2.10
3334 3435 7.284489 TGCCATAAGTTAATTTGCCCTAGTTAG 59.716 37.037 0.00 0.00 0.00 2.34
3412 3513 4.879545 TCGGAGGTAATGGCAAATTTCTAC 59.120 41.667 0.00 0.00 0.00 2.59
3440 3541 3.649023 ACCATACCACACTTTGAGGTACA 59.351 43.478 4.84 0.00 44.27 2.90
3468 3569 6.525629 ACTAATATTACAAGCTGTAGGCAGG 58.474 40.000 0.00 0.00 44.79 4.85
3497 3598 8.934023 ATGACAAAAGTAAAGGTCCTTGAATA 57.066 30.769 4.45 0.00 0.00 1.75
3498 3599 7.839680 ATGACAAAAGTAAAGGTCCTTGAAT 57.160 32.000 4.45 0.00 0.00 2.57
3972 4087 4.855715 TGCAGTCCTATCTTAATCGGAG 57.144 45.455 0.00 0.00 27.89 4.63
4421 4540 0.037232 GCCGTCCTGTAGAACTTGCT 60.037 55.000 0.00 0.00 0.00 3.91
4451 4570 1.739466 CTCAGCGCCATACAACATTGT 59.261 47.619 2.29 2.32 44.86 2.71
4488 4607 4.870426 CACCTAACTGTTGAATATGTCGCT 59.130 41.667 2.69 0.00 0.00 4.93
4496 4615 2.151202 CGCCACACCTAACTGTTGAAT 58.849 47.619 2.69 0.00 0.00 2.57
4689 4808 3.419759 CCGCACGCTTTAGCCGTT 61.420 61.111 0.00 0.00 37.91 4.44
4744 4863 1.477295 CTCTTAACGGACTCCTCCCAC 59.523 57.143 0.00 0.00 31.93 4.61
4959 5326 1.153353 CAGTGCGGGTTCGTTACATT 58.847 50.000 0.00 0.00 38.89 2.71
4960 5327 0.034337 ACAGTGCGGGTTCGTTACAT 59.966 50.000 0.00 0.00 38.89 2.29
4965 5332 1.720694 CCAAAACAGTGCGGGTTCGT 61.721 55.000 0.00 0.00 38.89 3.85
5020 5387 9.504710 GTTATGTAATGTGTACTGAGTACTGAG 57.495 37.037 21.95 7.90 39.49 3.35
5047 5414 4.021456 TGTGGTAAGTGTGAATCATCGTCT 60.021 41.667 0.00 0.00 0.00 4.18
5049 5416 4.265904 TGTGGTAAGTGTGAATCATCGT 57.734 40.909 0.00 0.00 0.00 3.73
5147 5514 3.381272 CCATTTTCACAAGTGTCACCTGT 59.619 43.478 1.13 1.13 0.00 4.00
5250 5712 2.415168 GGTGATCGAGCGAACAAAATCA 59.585 45.455 4.42 0.00 0.00 2.57
5272 5757 1.957113 GCCACTTATCCAAGCTTGGCT 60.957 52.381 36.24 30.25 44.68 4.75
5335 5821 1.252904 TTCAGCAATCCAAGGCCAGC 61.253 55.000 5.01 0.00 0.00 4.85
5457 5943 4.082895 GCATCAAGAACAAGAGCTCAACAT 60.083 41.667 17.77 0.00 0.00 2.71
5533 6019 2.320805 TACAGTGTACGCGTGACTTC 57.679 50.000 24.59 12.56 0.00 3.01
5564 6050 7.573968 ACAAGTAAATAGAGGATTCCATTGC 57.426 36.000 5.29 0.00 0.00 3.56
5594 6080 4.256920 GCAGTTCAGCTTCTCCTCAAATA 58.743 43.478 0.00 0.00 0.00 1.40
5601 6087 2.105006 TCATGCAGTTCAGCTTCTCC 57.895 50.000 0.00 0.00 34.99 3.71
5602 6088 3.688185 TGATTCATGCAGTTCAGCTTCTC 59.312 43.478 0.00 0.00 34.99 2.87
5613 6099 8.644619 CAAACTTGAATACTTTGATTCATGCAG 58.355 33.333 10.33 4.27 43.56 4.41
5636 6122 7.825270 ACAACCACCGTTATATTACTCATCAAA 59.175 33.333 0.00 0.00 0.00 2.69
5654 6141 5.867174 GGCAACTTCATTTTATACAACCACC 59.133 40.000 0.00 0.00 0.00 4.61
5692 6179 5.648092 AGCTAAGTAAGTAAGGGCAAACATG 59.352 40.000 0.00 0.00 0.00 3.21
5695 6182 6.652062 TGTAAGCTAAGTAAGTAAGGGCAAAC 59.348 38.462 0.00 0.00 0.00 2.93
5765 6259 7.826690 TGATTAAAATGAGCCTTTTGTAGGTC 58.173 34.615 0.00 0.00 46.61 3.85
5793 6288 2.584835 TTGGCCTCTAACAACTGCAT 57.415 45.000 3.32 0.00 0.00 3.96
5877 6372 8.692710 TCGTGGTCACTTTATCTTCAGTAATAT 58.307 33.333 0.00 0.00 0.00 1.28
5882 6377 4.523173 TCTCGTGGTCACTTTATCTTCAGT 59.477 41.667 0.00 0.00 0.00 3.41
5883 6378 5.060662 TCTCGTGGTCACTTTATCTTCAG 57.939 43.478 0.00 0.00 0.00 3.02
5885 6380 6.780706 TTTTCTCGTGGTCACTTTATCTTC 57.219 37.500 0.00 0.00 0.00 2.87
5886 6381 9.449719 AATATTTTCTCGTGGTCACTTTATCTT 57.550 29.630 0.00 0.00 0.00 2.40
5887 6382 9.099454 GAATATTTTCTCGTGGTCACTTTATCT 57.901 33.333 0.00 0.00 0.00 1.98
5890 6385 8.475331 GAGAATATTTTCTCGTGGTCACTTTA 57.525 34.615 9.72 0.00 46.17 1.85
5891 6386 7.365840 GAGAATATTTTCTCGTGGTCACTTT 57.634 36.000 9.72 0.00 46.17 2.66
5921 6421 6.993308 GCTAAGAGGGTCCTAGATTAAAAAGG 59.007 42.308 0.00 0.00 0.00 3.11
5931 6431 1.044611 GCCAGCTAAGAGGGTCCTAG 58.955 60.000 0.00 0.00 0.00 3.02
5938 6438 0.389948 AACGTTCGCCAGCTAAGAGG 60.390 55.000 0.00 0.00 0.00 3.69
5964 6464 0.608130 GTTCAAAATGCCACCCCCTC 59.392 55.000 0.00 0.00 0.00 4.30
5970 6471 4.148696 CAGTGAAATCGTTCAAAATGCCAC 59.851 41.667 0.00 0.00 45.29 5.01
5979 6480 2.254546 ACTGCCAGTGAAATCGTTCA 57.745 45.000 0.00 0.00 41.57 3.18
5995 6496 4.036380 GTCAACCCCTCACAACTAAAACTG 59.964 45.833 0.00 0.00 0.00 3.16
6027 6531 5.991328 TCTGAAGAAACTGTCATGTTGTC 57.009 39.130 0.00 0.00 0.00 3.18
6059 6563 6.530534 TGGTTTGCGAAATCTTAAACGAAAAA 59.469 30.769 0.00 0.00 35.54 1.94
6064 6568 4.973663 AGTTGGTTTGCGAAATCTTAAACG 59.026 37.500 0.00 0.00 34.68 3.60
6082 6600 9.117183 ACACTTTTTCCTAGTAGTTTTAGTTGG 57.883 33.333 0.00 0.00 0.00 3.77
6134 6655 4.481368 AGGTAATGTTATCTGCCGAACA 57.519 40.909 0.00 0.00 39.74 3.18
6140 6661 8.770828 TCGCTAAATTAAGGTAATGTTATCTGC 58.229 33.333 0.00 0.00 0.00 4.26
6165 6687 8.604035 GGAATTGACTTTTCCTTTTTCTTGTTC 58.396 33.333 0.00 0.00 39.67 3.18
6217 6761 2.027653 AGGCGAAGGGAAGAAGAAAGAG 60.028 50.000 0.00 0.00 0.00 2.85
6234 6778 4.864334 GGTGGGATCTGGCAGGCG 62.864 72.222 15.73 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.