Multiple sequence alignment - TraesCS5B01G261900

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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 TraesCS5B01G261900 chr5B 100.000 2760 0 0 1 2760 446449659 446446900 0.000000e+00 5097.0
1 TraesCS5B01G261900 chr5B 90.165 1210 63 19 954 2133 447131201 447132384 0.000000e+00 1524.0
2 TraesCS5B01G261900 chr1B 97.974 839 17 0 1 839 485678391 485679229 0.000000e+00 1456.0
3 TraesCS5B01G261900 chr1B 100.000 91 0 0 861 951 485677322 485677232 4.730000e-38 169.0
4 TraesCS5B01G261900 chr1B 85.567 97 10 3 2204 2297 272383107 272383202 6.290000e-17 99.0
5 TraesCS5B01G261900 chrUn 96.531 836 29 0 4 839 326629336 326628501 0.000000e+00 1384.0
6 TraesCS5B01G261900 chrUn 81.161 844 156 3 1 842 3376186 3377028 0.000000e+00 675.0
7 TraesCS5B01G261900 chrUn 98.913 92 1 0 861 952 326630412 326630503 6.120000e-37 165.0
8 TraesCS5B01G261900 chrUn 95.238 42 2 0 2149 2190 91246996 91246955 1.770000e-07 67.6
9 TraesCS5B01G261900 chr6B 96.411 836 30 0 4 839 15841531 15840696 0.000000e+00 1378.0
10 TraesCS5B01G261900 chr6B 98.913 92 1 0 861 952 15842607 15842698 6.120000e-37 165.0
11 TraesCS5B01G261900 chr4B 94.756 839 44 0 1 839 405931337 405932175 0.000000e+00 1306.0
12 TraesCS5B01G261900 chr4B 96.703 91 2 1 861 951 405918012 405917923 1.710000e-32 150.0
13 TraesCS5B01G261900 chr7B 98.185 551 9 1 2211 2760 616744699 616744149 0.000000e+00 961.0
14 TraesCS5B01G261900 chr7B 83.017 842 141 2 1 841 728048470 728049310 0.000000e+00 761.0
15 TraesCS5B01G261900 chr5D 90.842 677 32 10 1440 2108 374516235 374516889 0.000000e+00 880.0
16 TraesCS5B01G261900 chr5D 91.014 434 24 3 964 1397 374515810 374516228 3.080000e-159 571.0
17 TraesCS5B01G261900 chr5D 88.764 89 8 2 2029 2115 374652617 374652705 1.050000e-19 108.0
18 TraesCS5B01G261900 chr6A 84.569 836 123 6 9 841 46717848 46717016 0.000000e+00 824.0
19 TraesCS5B01G261900 chr2B 96.637 446 15 0 2213 2658 446126952 446126507 0.000000e+00 741.0
20 TraesCS5B01G261900 chr2B 90.733 464 25 5 2213 2658 90293275 90292812 1.090000e-168 603.0
21 TraesCS5B01G261900 chr2B 94.253 87 5 0 2674 2760 446126525 446126439 1.720000e-27 134.0
22 TraesCS5B01G261900 chr2D 82.346 844 143 6 1 841 60172878 60173718 0.000000e+00 728.0
23 TraesCS5B01G261900 chr2A 81.517 844 150 6 1 841 692067844 692068684 0.000000e+00 689.0
24 TraesCS5B01G261900 chr2A 92.521 468 15 4 2211 2658 733138690 733139157 0.000000e+00 652.0
25 TraesCS5B01G261900 chr2A 90.909 88 7 1 2674 2760 733139139 733139226 1.740000e-22 117.0
26 TraesCS5B01G261900 chr3A 93.319 464 14 2 2212 2658 5884919 5885382 0.000000e+00 669.0
27 TraesCS5B01G261900 chr3A 92.688 465 16 3 2212 2658 5915659 5916123 0.000000e+00 654.0
28 TraesCS5B01G261900 chr3A 92.026 464 18 5 2212 2658 5953021 5953482 3.880000e-178 634.0
29 TraesCS5B01G261900 chr3A 91.026 468 24 3 2209 2658 80101746 80101279 1.400000e-172 616.0
30 TraesCS5B01G261900 chr3A 94.318 88 4 1 2674 2760 5885364 5885451 1.720000e-27 134.0
31 TraesCS5B01G261900 chr3A 93.182 88 5 1 2674 2760 5916105 5916192 8.020000e-26 128.0
32 TraesCS5B01G261900 chr3A 93.182 88 5 1 2674 2760 5953464 5953551 8.020000e-26 128.0
33 TraesCS5B01G261900 chr5A 93.243 444 30 0 954 1397 476356261 476356704 0.000000e+00 654.0
34 TraesCS5B01G261900 chr5A 93.072 332 23 0 1433 1764 476356708 476357039 1.150000e-133 486.0
35 TraesCS5B01G261900 chr5A 95.652 92 3 1 861 951 513712815 513712906 2.210000e-31 147.0
36 TraesCS5B01G261900 chr5A 93.023 43 1 2 2150 2192 633285505 633285545 8.250000e-06 62.1
37 TraesCS5B01G261900 chr3D 90.733 464 25 2 2213 2658 500195928 500196391 1.090000e-168 603.0
38 TraesCS5B01G261900 chr3D 93.182 44 3 0 2149 2192 609574309 609574266 6.380000e-07 65.8
39 TraesCS5B01G261900 chr4A 94.737 95 3 2 861 953 664232738 664232644 2.210000e-31 147.0
40 TraesCS5B01G261900 chr4A 97.436 39 1 0 2149 2187 503630553 503630591 1.770000e-07 67.6
41 TraesCS5B01G261900 chr3B 94.444 90 4 1 861 950 220978632 220978720 1.330000e-28 137.0
42 TraesCS5B01G261900 chr3B 97.500 40 1 0 2149 2188 298711789 298711828 4.930000e-08 69.4
43 TraesCS5B01G261900 chr3B 95.349 43 1 1 2146 2187 130679292 130679334 1.770000e-07 67.6
44 TraesCS5B01G261900 chr7A 90.476 84 8 0 869 952 516081917 516081834 8.080000e-21 111.0
45 TraesCS5B01G261900 chr7A 93.023 43 3 0 2149 2191 536511262 536511220 2.290000e-06 63.9
46 TraesCS5B01G261900 chr1A 88.889 90 9 1 860 949 29975919 29975831 2.910000e-20 110.0
47 TraesCS5B01G261900 chr1A 93.023 43 3 0 2149 2191 351606797 351606755 2.290000e-06 63.9
48 TraesCS5B01G261900 chr4D 94.872 39 1 1 2147 2185 501514555 501514592 2.970000e-05 60.2


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 TraesCS5B01G261900 chr5B 446446900 446449659 2759 True 5097.0 5097 100.0000 1 2760 1 chr5B.!!$R1 2759
1 TraesCS5B01G261900 chr5B 447131201 447132384 1183 False 1524.0 1524 90.1650 954 2133 1 chr5B.!!$F1 1179
2 TraesCS5B01G261900 chr1B 485678391 485679229 838 False 1456.0 1456 97.9740 1 839 1 chr1B.!!$F2 838
3 TraesCS5B01G261900 chrUn 326628501 326629336 835 True 1384.0 1384 96.5310 4 839 1 chrUn.!!$R2 835
4 TraesCS5B01G261900 chrUn 3376186 3377028 842 False 675.0 675 81.1610 1 842 1 chrUn.!!$F1 841
5 TraesCS5B01G261900 chr6B 15840696 15841531 835 True 1378.0 1378 96.4110 4 839 1 chr6B.!!$R1 835
6 TraesCS5B01G261900 chr4B 405931337 405932175 838 False 1306.0 1306 94.7560 1 839 1 chr4B.!!$F1 838
7 TraesCS5B01G261900 chr7B 616744149 616744699 550 True 961.0 961 98.1850 2211 2760 1 chr7B.!!$R1 549
8 TraesCS5B01G261900 chr7B 728048470 728049310 840 False 761.0 761 83.0170 1 841 1 chr7B.!!$F1 840
9 TraesCS5B01G261900 chr5D 374515810 374516889 1079 False 725.5 880 90.9280 964 2108 2 chr5D.!!$F2 1144
10 TraesCS5B01G261900 chr6A 46717016 46717848 832 True 824.0 824 84.5690 9 841 1 chr6A.!!$R1 832
11 TraesCS5B01G261900 chr2B 446126439 446126952 513 True 437.5 741 95.4450 2213 2760 2 chr2B.!!$R2 547
12 TraesCS5B01G261900 chr2D 60172878 60173718 840 False 728.0 728 82.3460 1 841 1 chr2D.!!$F1 840
13 TraesCS5B01G261900 chr2A 692067844 692068684 840 False 689.0 689 81.5170 1 841 1 chr2A.!!$F1 840
14 TraesCS5B01G261900 chr2A 733138690 733139226 536 False 384.5 652 91.7150 2211 2760 2 chr2A.!!$F2 549
15 TraesCS5B01G261900 chr3A 5884919 5885451 532 False 401.5 669 93.8185 2212 2760 2 chr3A.!!$F1 548
16 TraesCS5B01G261900 chr3A 5915659 5916192 533 False 391.0 654 92.9350 2212 2760 2 chr3A.!!$F2 548
17 TraesCS5B01G261900 chr3A 5953021 5953551 530 False 381.0 634 92.6040 2212 2760 2 chr3A.!!$F3 548
18 TraesCS5B01G261900 chr5A 476356261 476357039 778 False 570.0 654 93.1575 954 1764 2 chr5A.!!$F3 810

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
972 974 0.041839 GTTGCAAGTGACAGACTGCG 60.042 55.0 0.0 0.0 34.02 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 2179 2.093447 AGTGTCTCAAGCTTATTCCGGG 60.093 50.0 0.0 0.0 0.0 5.73 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
573 575 3.815856 AGCATGACATCGAGAAGACAT 57.184 42.857 0.00 0.00 0.00 3.06
664 666 3.131046 CCTTGAACTTTGCTCCACAAACT 59.869 43.478 0.00 0.00 43.35 2.66
761 763 7.004086 TGAGAGTTTCATTGGGAACATTTAGT 58.996 34.615 6.60 0.00 42.32 2.24
819 821 7.546250 ACTCCTTTACTGAAGAAGATTGAGA 57.454 36.000 0.00 0.00 37.57 3.27
862 864 9.784680 TCTTTAAATATTAGTCTCAGTCGTGTC 57.215 33.333 0.00 0.00 0.00 3.67
863 865 9.790389 CTTTAAATATTAGTCTCAGTCGTGTCT 57.210 33.333 0.00 0.00 0.00 3.41
864 866 9.569167 TTTAAATATTAGTCTCAGTCGTGTCTG 57.431 33.333 0.00 0.00 36.85 3.51
865 867 5.759506 ATATTAGTCTCAGTCGTGTCTGG 57.240 43.478 0.00 0.00 36.25 3.86
866 868 2.563261 TAGTCTCAGTCGTGTCTGGT 57.437 50.000 0.00 0.00 36.25 4.00
867 869 2.563261 AGTCTCAGTCGTGTCTGGTA 57.437 50.000 0.00 0.00 36.25 3.25
868 870 3.074675 AGTCTCAGTCGTGTCTGGTAT 57.925 47.619 0.00 0.00 36.25 2.73
869 871 2.750166 AGTCTCAGTCGTGTCTGGTATG 59.250 50.000 0.00 0.00 36.25 2.39
870 872 2.092323 TCTCAGTCGTGTCTGGTATGG 58.908 52.381 0.00 0.00 36.25 2.74
871 873 0.530744 TCAGTCGTGTCTGGTATGGC 59.469 55.000 0.00 0.00 36.25 4.40
872 874 0.246360 CAGTCGTGTCTGGTATGGCA 59.754 55.000 0.00 0.00 0.00 4.92
873 875 0.246635 AGTCGTGTCTGGTATGGCAC 59.753 55.000 0.00 0.00 0.00 5.01
883 885 2.246719 GGTATGGCACCTCTCATGAC 57.753 55.000 0.00 0.00 44.79 3.06
884 886 1.202698 GGTATGGCACCTCTCATGACC 60.203 57.143 0.00 0.00 44.79 4.02
885 887 1.131638 TATGGCACCTCTCATGACCC 58.868 55.000 0.00 0.00 0.00 4.46
886 888 0.622738 ATGGCACCTCTCATGACCCT 60.623 55.000 0.00 0.00 0.00 4.34
887 889 1.267574 TGGCACCTCTCATGACCCTC 61.268 60.000 0.00 0.00 0.00 4.30
888 890 1.142748 GCACCTCTCATGACCCTCG 59.857 63.158 0.00 0.00 0.00 4.63
889 891 1.608717 GCACCTCTCATGACCCTCGT 61.609 60.000 0.00 0.00 0.00 4.18
890 892 0.898320 CACCTCTCATGACCCTCGTT 59.102 55.000 0.00 0.00 0.00 3.85
891 893 0.898320 ACCTCTCATGACCCTCGTTG 59.102 55.000 0.00 0.00 0.00 4.10
892 894 0.898320 CCTCTCATGACCCTCGTTGT 59.102 55.000 0.00 0.00 0.00 3.32
893 895 2.100197 CCTCTCATGACCCTCGTTGTA 58.900 52.381 0.00 0.00 0.00 2.41
894 896 2.695666 CCTCTCATGACCCTCGTTGTAT 59.304 50.000 0.00 0.00 0.00 2.29
895 897 3.243569 CCTCTCATGACCCTCGTTGTATC 60.244 52.174 0.00 0.00 0.00 2.24
896 898 2.693591 TCTCATGACCCTCGTTGTATCC 59.306 50.000 0.00 0.00 0.00 2.59
897 899 1.760613 TCATGACCCTCGTTGTATCCC 59.239 52.381 0.00 0.00 0.00 3.85
898 900 1.484653 CATGACCCTCGTTGTATCCCA 59.515 52.381 0.00 0.00 0.00 4.37
899 901 0.899720 TGACCCTCGTTGTATCCCAC 59.100 55.000 0.00 0.00 0.00 4.61
900 902 0.899720 GACCCTCGTTGTATCCCACA 59.100 55.000 0.00 0.00 34.51 4.17
901 903 1.485066 GACCCTCGTTGTATCCCACAT 59.515 52.381 0.00 0.00 36.90 3.21
902 904 1.485066 ACCCTCGTTGTATCCCACATC 59.515 52.381 0.00 0.00 36.90 3.06
903 905 1.484653 CCCTCGTTGTATCCCACATCA 59.515 52.381 0.00 0.00 36.90 3.07
904 906 2.104792 CCCTCGTTGTATCCCACATCAT 59.895 50.000 0.00 0.00 36.90 2.45
905 907 3.133691 CCTCGTTGTATCCCACATCATG 58.866 50.000 0.00 0.00 36.90 3.07
906 908 3.432186 CCTCGTTGTATCCCACATCATGT 60.432 47.826 0.00 0.00 36.90 3.21
917 919 2.932498 CACATCATGTGGTTTTCGGTG 58.068 47.619 10.22 0.00 44.27 4.94
918 920 2.551887 CACATCATGTGGTTTTCGGTGA 59.448 45.455 10.22 0.00 44.27 4.02
919 921 3.191162 CACATCATGTGGTTTTCGGTGAT 59.809 43.478 10.22 0.00 44.27 3.06
920 922 3.191162 ACATCATGTGGTTTTCGGTGATG 59.809 43.478 10.59 10.59 45.06 3.07
921 923 3.133141 TCATGTGGTTTTCGGTGATGA 57.867 42.857 0.00 0.00 0.00 2.92
922 924 3.481453 TCATGTGGTTTTCGGTGATGAA 58.519 40.909 0.00 0.00 0.00 2.57
923 925 4.078537 TCATGTGGTTTTCGGTGATGAAT 58.921 39.130 0.00 0.00 0.00 2.57
924 926 5.249420 TCATGTGGTTTTCGGTGATGAATA 58.751 37.500 0.00 0.00 0.00 1.75
925 927 5.707764 TCATGTGGTTTTCGGTGATGAATAA 59.292 36.000 0.00 0.00 0.00 1.40
926 928 6.207614 TCATGTGGTTTTCGGTGATGAATAAA 59.792 34.615 0.00 0.00 0.00 1.40
927 929 6.582677 TGTGGTTTTCGGTGATGAATAAAT 57.417 33.333 0.00 0.00 0.00 1.40
928 930 6.385843 TGTGGTTTTCGGTGATGAATAAATG 58.614 36.000 0.00 0.00 0.00 2.32
929 931 6.207614 TGTGGTTTTCGGTGATGAATAAATGA 59.792 34.615 0.00 0.00 0.00 2.57
930 932 7.087639 GTGGTTTTCGGTGATGAATAAATGAA 58.912 34.615 0.00 0.00 0.00 2.57
931 933 7.759433 GTGGTTTTCGGTGATGAATAAATGAAT 59.241 33.333 0.00 0.00 0.00 2.57
932 934 8.310382 TGGTTTTCGGTGATGAATAAATGAATT 58.690 29.630 0.00 0.00 0.00 2.17
933 935 9.150348 GGTTTTCGGTGATGAATAAATGAATTT 57.850 29.630 0.00 0.00 0.00 1.82
936 938 9.920133 TTTCGGTGATGAATAAATGAATTTTCA 57.080 25.926 0.00 0.00 42.14 2.69
937 939 8.909708 TCGGTGATGAATAAATGAATTTTCAC 57.090 30.769 8.19 8.19 40.49 3.18
938 940 7.973388 TCGGTGATGAATAAATGAATTTTCACC 59.027 33.333 18.41 18.41 42.24 4.02
939 941 7.222611 CGGTGATGAATAAATGAATTTTCACCC 59.777 37.037 20.56 10.48 42.42 4.61
940 942 7.495606 GGTGATGAATAAATGAATTTTCACCCC 59.504 37.037 17.96 6.06 41.23 4.95
941 943 8.260114 GTGATGAATAAATGAATTTTCACCCCT 58.740 33.333 0.00 0.00 40.49 4.79
942 944 8.477256 TGATGAATAAATGAATTTTCACCCCTC 58.523 33.333 0.00 0.00 40.49 4.30
943 945 7.789202 TGAATAAATGAATTTTCACCCCTCA 57.211 32.000 0.00 0.00 40.49 3.86
944 946 8.200024 TGAATAAATGAATTTTCACCCCTCAA 57.800 30.769 0.00 0.00 40.49 3.02
945 947 8.654997 TGAATAAATGAATTTTCACCCCTCAAA 58.345 29.630 0.00 0.00 40.49 2.69
946 948 9.500785 GAATAAATGAATTTTCACCCCTCAAAA 57.499 29.630 0.00 0.00 40.49 2.44
947 949 9.859152 AATAAATGAATTTTCACCCCTCAAAAA 57.141 25.926 0.00 0.00 40.49 1.94
972 974 0.041839 GTTGCAAGTGACAGACTGCG 60.042 55.000 0.00 0.00 34.02 5.18
1121 1123 3.272334 GCATCGTGGGCGGATCAC 61.272 66.667 0.00 0.00 38.89 3.06
1192 1197 1.136329 AGCAAAGGCCAGGAAGGAGA 61.136 55.000 5.01 0.00 42.56 3.71
1193 1198 0.679321 GCAAAGGCCAGGAAGGAGAG 60.679 60.000 5.01 0.00 41.22 3.20
1257 1262 2.856000 AACTCCCCTGCTGCCTGT 60.856 61.111 0.00 0.00 0.00 4.00
1302 1307 1.687123 AGGTATCGTATCAGCACCACC 59.313 52.381 0.00 0.00 0.00 4.61
1418 1423 0.403271 CTGGGGGCCATAGATCCTTG 59.597 60.000 4.39 0.00 30.82 3.61
1420 1425 1.376649 GGGGGCCATAGATCCTTGAT 58.623 55.000 4.39 0.00 0.00 2.57
1421 1426 1.283321 GGGGGCCATAGATCCTTGATC 59.717 57.143 4.39 0.00 39.17 2.92
1422 1427 1.283321 GGGGCCATAGATCCTTGATCC 59.717 57.143 4.39 0.00 39.66 3.36
1423 1428 2.273619 GGGCCATAGATCCTTGATCCT 58.726 52.381 4.39 0.00 39.66 3.24
1424 1429 2.646798 GGGCCATAGATCCTTGATCCTT 59.353 50.000 4.39 0.00 39.66 3.36
1425 1430 3.308046 GGGCCATAGATCCTTGATCCTTC 60.308 52.174 4.39 0.00 39.66 3.46
1426 1431 3.308046 GGCCATAGATCCTTGATCCTTCC 60.308 52.174 0.00 0.00 39.66 3.46
1427 1432 3.586618 GCCATAGATCCTTGATCCTTCCT 59.413 47.826 0.59 0.00 39.66 3.36
1428 1433 4.042684 GCCATAGATCCTTGATCCTTCCTT 59.957 45.833 0.59 0.00 39.66 3.36
1429 1434 5.802821 GCCATAGATCCTTGATCCTTCCTTC 60.803 48.000 0.59 0.00 39.66 3.46
1435 1440 0.253044 TTGATCCTTCCTTCAGGCCG 59.747 55.000 0.00 0.00 33.35 6.13
1437 1442 0.541863 GATCCTTCCTTCAGGCCGAA 59.458 55.000 0.00 3.26 33.35 4.30
1467 1472 2.695759 CCGCGGCCTATGCAAAACA 61.696 57.895 14.67 0.00 40.13 2.83
1506 1511 2.032681 AGGCCCGTTTGAGAGTGC 59.967 61.111 0.00 0.00 0.00 4.40
1624 1629 3.056821 TCATTGTCTACAGGTGGAACGAG 60.057 47.826 0.00 0.00 38.12 4.18
1626 1631 0.601558 GTCTACAGGTGGAACGAGCA 59.398 55.000 0.00 0.00 38.12 4.26
1790 1795 7.040201 ACGTCTACACCGGTTGTATGAATATAT 60.040 37.037 2.97 0.00 40.06 0.86
1791 1796 7.272731 CGTCTACACCGGTTGTATGAATATATG 59.727 40.741 2.97 0.00 40.06 1.78
1845 1851 5.565439 GCTTTATGAAATGCAACAGTGTCCT 60.565 40.000 0.00 0.00 36.16 3.85
1846 1852 6.349280 GCTTTATGAAATGCAACAGTGTCCTA 60.349 38.462 0.00 0.00 36.16 2.94
1847 1853 7.629222 GCTTTATGAAATGCAACAGTGTCCTAT 60.629 37.037 0.00 0.00 36.16 2.57
1848 1854 5.571784 ATGAAATGCAACAGTGTCCTATG 57.428 39.130 0.00 0.00 0.00 2.23
1849 1855 4.397420 TGAAATGCAACAGTGTCCTATGT 58.603 39.130 0.00 0.00 0.00 2.29
1850 1856 4.455533 TGAAATGCAACAGTGTCCTATGTC 59.544 41.667 0.00 0.00 0.00 3.06
1851 1857 2.472695 TGCAACAGTGTCCTATGTCC 57.527 50.000 0.00 0.00 0.00 4.02
1864 1870 8.432805 AGTGTCCTATGTCCATTTATAAAGGAG 58.567 37.037 11.32 2.33 32.74 3.69
1948 1980 8.171840 GTCTAAAGATCTCGGTTGAAAAATCAG 58.828 37.037 0.00 0.00 0.00 2.90
2082 2120 4.320057 GCATGAGAACTGAACTCCACTTTG 60.320 45.833 0.00 0.00 33.95 2.77
2085 2123 3.879892 GAGAACTGAACTCCACTTTGCTT 59.120 43.478 0.00 0.00 0.00 3.91
2133 2171 7.834068 TTCACAAATGACTTAGCAGATACTC 57.166 36.000 0.00 0.00 33.38 2.59
2134 2172 6.341316 TCACAAATGACTTAGCAGATACTCC 58.659 40.000 0.00 0.00 0.00 3.85
2135 2173 5.525378 CACAAATGACTTAGCAGATACTCCC 59.475 44.000 0.00 0.00 0.00 4.30
2136 2174 5.426833 ACAAATGACTTAGCAGATACTCCCT 59.573 40.000 0.00 0.00 0.00 4.20
2137 2175 5.799827 AATGACTTAGCAGATACTCCCTC 57.200 43.478 0.00 0.00 0.00 4.30
2138 2176 3.567397 TGACTTAGCAGATACTCCCTCC 58.433 50.000 0.00 0.00 0.00 4.30
2139 2177 3.052869 TGACTTAGCAGATACTCCCTCCA 60.053 47.826 0.00 0.00 0.00 3.86
2140 2178 4.156477 GACTTAGCAGATACTCCCTCCAT 58.844 47.826 0.00 0.00 0.00 3.41
2141 2179 4.156477 ACTTAGCAGATACTCCCTCCATC 58.844 47.826 0.00 0.00 0.00 3.51
2142 2180 2.022718 AGCAGATACTCCCTCCATCC 57.977 55.000 0.00 0.00 0.00 3.51
2143 2181 0.980423 GCAGATACTCCCTCCATCCC 59.020 60.000 0.00 0.00 0.00 3.85
2144 2182 1.261480 CAGATACTCCCTCCATCCCG 58.739 60.000 0.00 0.00 0.00 5.14
2145 2183 0.115349 AGATACTCCCTCCATCCCGG 59.885 60.000 0.00 0.00 0.00 5.73
2146 2184 0.114560 GATACTCCCTCCATCCCGGA 59.885 60.000 0.73 0.00 43.61 5.14
2147 2185 0.566176 ATACTCCCTCCATCCCGGAA 59.434 55.000 0.73 0.00 45.75 4.30
2148 2186 0.566176 TACTCCCTCCATCCCGGAAT 59.434 55.000 0.73 0.00 45.75 3.01
2149 2187 0.566176 ACTCCCTCCATCCCGGAATA 59.434 55.000 0.73 0.00 45.75 1.75
2150 2188 1.061657 ACTCCCTCCATCCCGGAATAA 60.062 52.381 0.73 0.00 45.75 1.40
2151 2189 1.625818 CTCCCTCCATCCCGGAATAAG 59.374 57.143 0.73 0.00 45.75 1.73
2152 2190 0.036875 CCCTCCATCCCGGAATAAGC 59.963 60.000 0.73 0.00 45.75 3.09
2153 2191 1.059913 CCTCCATCCCGGAATAAGCT 58.940 55.000 0.73 0.00 45.75 3.74
2154 2192 1.421646 CCTCCATCCCGGAATAAGCTT 59.578 52.381 0.73 3.48 45.75 3.74
2155 2193 2.498167 CTCCATCCCGGAATAAGCTTG 58.502 52.381 9.86 0.00 45.75 4.01
2156 2194 2.104792 CTCCATCCCGGAATAAGCTTGA 59.895 50.000 9.86 0.00 45.75 3.02
2157 2195 2.104792 TCCATCCCGGAATAAGCTTGAG 59.895 50.000 9.86 0.00 42.52 3.02
2158 2196 2.104792 CCATCCCGGAATAAGCTTGAGA 59.895 50.000 9.86 0.00 36.56 3.27
2159 2197 2.981859 TCCCGGAATAAGCTTGAGAC 57.018 50.000 9.86 0.00 0.00 3.36
2160 2198 2.184533 TCCCGGAATAAGCTTGAGACA 58.815 47.619 9.86 0.00 0.00 3.41
2161 2199 2.093658 TCCCGGAATAAGCTTGAGACAC 60.094 50.000 9.86 0.00 0.00 3.67
2162 2200 2.093447 CCCGGAATAAGCTTGAGACACT 60.093 50.000 9.86 0.00 0.00 3.55
2163 2201 3.600388 CCGGAATAAGCTTGAGACACTT 58.400 45.455 9.86 0.00 0.00 3.16
2164 2202 4.382685 CCCGGAATAAGCTTGAGACACTTA 60.383 45.833 9.86 0.00 0.00 2.24
2165 2203 5.360591 CCGGAATAAGCTTGAGACACTTAT 58.639 41.667 9.86 0.00 38.04 1.73
2166 2204 5.817816 CCGGAATAAGCTTGAGACACTTATT 59.182 40.000 9.86 6.88 44.95 1.40
2167 2205 6.316390 CCGGAATAAGCTTGAGACACTTATTT 59.684 38.462 9.86 0.00 43.28 1.40
2168 2206 7.148239 CCGGAATAAGCTTGAGACACTTATTTT 60.148 37.037 9.86 0.00 43.28 1.82
2169 2207 7.693951 CGGAATAAGCTTGAGACACTTATTTTG 59.306 37.037 9.86 2.40 43.28 2.44
2170 2208 7.970614 GGAATAAGCTTGAGACACTTATTTTGG 59.029 37.037 9.86 0.00 43.28 3.28
2171 2209 5.712152 AAGCTTGAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
2172 2210 4.985538 AGCTTGAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
2173 2211 5.574188 AGCTTGAGACACTTATTTTGGGAT 58.426 37.500 0.00 0.00 0.00 3.85
2174 2212 5.416952 AGCTTGAGACACTTATTTTGGGATG 59.583 40.000 0.00 0.00 0.00 3.51
2175 2213 5.393461 GCTTGAGACACTTATTTTGGGATGG 60.393 44.000 0.00 0.00 0.00 3.51
2176 2214 5.512942 TGAGACACTTATTTTGGGATGGA 57.487 39.130 0.00 0.00 0.00 3.41
2177 2215 5.886609 TGAGACACTTATTTTGGGATGGAA 58.113 37.500 0.00 0.00 0.00 3.53
2178 2216 5.945784 TGAGACACTTATTTTGGGATGGAAG 59.054 40.000 0.00 0.00 0.00 3.46
2179 2217 5.264395 AGACACTTATTTTGGGATGGAAGG 58.736 41.667 0.00 0.00 0.00 3.46
2180 2218 5.015178 AGACACTTATTTTGGGATGGAAGGA 59.985 40.000 0.00 0.00 0.00 3.36
2181 2219 5.264395 ACACTTATTTTGGGATGGAAGGAG 58.736 41.667 0.00 0.00 0.00 3.69
2182 2220 5.222337 ACACTTATTTTGGGATGGAAGGAGT 60.222 40.000 0.00 0.00 0.00 3.85
2183 2221 6.011981 ACACTTATTTTGGGATGGAAGGAGTA 60.012 38.462 0.00 0.00 0.00 2.59
2184 2222 6.543831 CACTTATTTTGGGATGGAAGGAGTAG 59.456 42.308 0.00 0.00 0.00 2.57
2185 2223 6.217693 ACTTATTTTGGGATGGAAGGAGTAGT 59.782 38.462 0.00 0.00 0.00 2.73
2186 2224 7.404980 ACTTATTTTGGGATGGAAGGAGTAGTA 59.595 37.037 0.00 0.00 0.00 1.82
2187 2225 5.431179 TTTTGGGATGGAAGGAGTAGTAC 57.569 43.478 0.00 0.00 0.00 2.73
2188 2226 4.348020 TTGGGATGGAAGGAGTAGTACT 57.652 45.455 1.37 1.37 0.00 2.73
2189 2227 4.348020 TGGGATGGAAGGAGTAGTACTT 57.652 45.455 0.00 0.00 0.00 2.24
2190 2228 5.476950 TGGGATGGAAGGAGTAGTACTTA 57.523 43.478 0.00 0.00 0.00 2.24
2191 2229 6.039415 TGGGATGGAAGGAGTAGTACTTAT 57.961 41.667 0.00 0.00 0.00 1.73
2192 2230 6.075984 TGGGATGGAAGGAGTAGTACTTATC 58.924 44.000 0.00 0.00 0.00 1.75
2193 2231 6.075984 GGGATGGAAGGAGTAGTACTTATCA 58.924 44.000 0.00 0.00 0.00 2.15
2194 2232 6.553852 GGGATGGAAGGAGTAGTACTTATCAA 59.446 42.308 0.00 0.00 0.00 2.57
2195 2233 7.256012 GGGATGGAAGGAGTAGTACTTATCAAG 60.256 44.444 0.00 0.00 0.00 3.02
2196 2234 6.466885 TGGAAGGAGTAGTACTTATCAAGC 57.533 41.667 0.00 0.00 0.00 4.01
2197 2235 5.363005 TGGAAGGAGTAGTACTTATCAAGCC 59.637 44.000 0.00 0.00 0.00 4.35
2198 2236 5.363005 GGAAGGAGTAGTACTTATCAAGCCA 59.637 44.000 0.00 0.00 0.00 4.75
2199 2237 5.855740 AGGAGTAGTACTTATCAAGCCAC 57.144 43.478 0.00 0.00 0.00 5.01
2200 2238 5.269991 AGGAGTAGTACTTATCAAGCCACA 58.730 41.667 0.00 0.00 0.00 4.17
2201 2239 5.127356 AGGAGTAGTACTTATCAAGCCACAC 59.873 44.000 0.00 0.00 0.00 3.82
2202 2240 5.105473 GGAGTAGTACTTATCAAGCCACACA 60.105 44.000 0.00 0.00 0.00 3.72
2203 2241 6.407074 GGAGTAGTACTTATCAAGCCACACAT 60.407 42.308 0.00 0.00 0.00 3.21
2204 2242 7.201884 GGAGTAGTACTTATCAAGCCACACATA 60.202 40.741 0.00 0.00 0.00 2.29
2205 2243 7.717568 AGTAGTACTTATCAAGCCACACATAG 58.282 38.462 0.00 0.00 0.00 2.23
2206 2244 6.546428 AGTACTTATCAAGCCACACATAGT 57.454 37.500 0.00 0.00 0.00 2.12
2207 2245 6.574350 AGTACTTATCAAGCCACACATAGTC 58.426 40.000 0.00 0.00 0.00 2.59
2208 2246 5.420725 ACTTATCAAGCCACACATAGTCA 57.579 39.130 0.00 0.00 0.00 3.41
2209 2247 5.804639 ACTTATCAAGCCACACATAGTCAA 58.195 37.500 0.00 0.00 0.00 3.18
2399 2457 3.202097 CCGAATTGCAAAGGTTTGGTTT 58.798 40.909 1.71 0.00 38.57 3.27
2430 2488 3.448934 ACCAGAGATGTTGATCCTCTGT 58.551 45.455 18.73 8.92 39.68 3.41
2727 2787 3.609853 TGTTCTTGCTCAACTCTTGTGT 58.390 40.909 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
573 575 1.302752 CTGTAGCCCAAGCAGTGCA 60.303 57.895 19.20 0.00 43.56 4.57
664 666 7.608761 ACGGTGCTTTTAAATATCTAAAGGACA 59.391 33.333 20.13 7.12 45.93 4.02
761 763 6.489603 TGCAAGGTTGGAGATTAAGGATTTA 58.510 36.000 0.00 0.00 0.00 1.40
778 780 2.893489 GGAGTTCCTGAAAATGCAAGGT 59.107 45.455 1.39 0.00 0.00 3.50
842 844 5.652891 ACCAGACACGACTGAGACTAATATT 59.347 40.000 9.63 0.00 39.94 1.28
843 845 5.194432 ACCAGACACGACTGAGACTAATAT 58.806 41.667 9.63 0.00 39.94 1.28
844 846 4.586884 ACCAGACACGACTGAGACTAATA 58.413 43.478 9.63 0.00 39.94 0.98
845 847 3.422796 ACCAGACACGACTGAGACTAAT 58.577 45.455 9.63 0.00 39.94 1.73
846 848 2.860009 ACCAGACACGACTGAGACTAA 58.140 47.619 9.63 0.00 39.94 2.24
847 849 2.563261 ACCAGACACGACTGAGACTA 57.437 50.000 9.63 0.00 39.94 2.59
848 850 2.563261 TACCAGACACGACTGAGACT 57.437 50.000 9.63 0.00 39.94 3.24
849 851 2.159366 CCATACCAGACACGACTGAGAC 60.159 54.545 9.63 0.00 39.94 3.36
850 852 2.092323 CCATACCAGACACGACTGAGA 58.908 52.381 9.63 0.34 39.94 3.27
851 853 1.469940 GCCATACCAGACACGACTGAG 60.470 57.143 9.63 0.00 39.94 3.35
852 854 0.530744 GCCATACCAGACACGACTGA 59.469 55.000 9.63 0.00 39.94 3.41
853 855 0.246360 TGCCATACCAGACACGACTG 59.754 55.000 0.00 0.00 37.61 3.51
854 856 0.246635 GTGCCATACCAGACACGACT 59.753 55.000 0.00 0.00 0.00 4.18
855 857 2.750815 GTGCCATACCAGACACGAC 58.249 57.895 0.00 0.00 0.00 4.34
865 867 1.202698 GGGTCATGAGAGGTGCCATAC 60.203 57.143 0.00 0.00 0.00 2.39
866 868 1.131638 GGGTCATGAGAGGTGCCATA 58.868 55.000 0.00 0.00 0.00 2.74
867 869 0.622738 AGGGTCATGAGAGGTGCCAT 60.623 55.000 0.00 0.00 0.00 4.40
868 870 1.229625 AGGGTCATGAGAGGTGCCA 60.230 57.895 0.00 0.00 0.00 4.92
869 871 1.524482 GAGGGTCATGAGAGGTGCC 59.476 63.158 0.00 0.00 0.00 5.01
870 872 1.142748 CGAGGGTCATGAGAGGTGC 59.857 63.158 0.00 0.00 0.00 5.01
871 873 0.898320 AACGAGGGTCATGAGAGGTG 59.102 55.000 0.00 0.00 0.00 4.00
872 874 0.898320 CAACGAGGGTCATGAGAGGT 59.102 55.000 0.00 0.00 0.00 3.85
873 875 0.898320 ACAACGAGGGTCATGAGAGG 59.102 55.000 0.00 0.00 0.00 3.69
874 876 3.243569 GGATACAACGAGGGTCATGAGAG 60.244 52.174 0.00 0.00 0.00 3.20
875 877 2.693591 GGATACAACGAGGGTCATGAGA 59.306 50.000 0.00 0.00 0.00 3.27
876 878 2.224066 GGGATACAACGAGGGTCATGAG 60.224 54.545 0.00 0.00 39.74 2.90
877 879 1.760613 GGGATACAACGAGGGTCATGA 59.239 52.381 0.00 0.00 39.74 3.07
878 880 1.484653 TGGGATACAACGAGGGTCATG 59.515 52.381 0.00 0.00 39.74 3.07
879 881 1.485066 GTGGGATACAACGAGGGTCAT 59.515 52.381 0.00 0.00 39.74 3.06
880 882 0.899720 GTGGGATACAACGAGGGTCA 59.100 55.000 0.00 0.00 39.74 4.02
881 883 0.899720 TGTGGGATACAACGAGGGTC 59.100 55.000 0.00 0.00 36.06 4.46
882 884 1.485066 GATGTGGGATACAACGAGGGT 59.515 52.381 0.00 0.00 43.77 4.34
883 885 1.484653 TGATGTGGGATACAACGAGGG 59.515 52.381 0.00 0.00 43.77 4.30
884 886 2.979814 TGATGTGGGATACAACGAGG 57.020 50.000 0.00 0.00 43.77 4.63
885 887 3.557185 CACATGATGTGGGATACAACGAG 59.443 47.826 17.51 0.00 44.27 4.18
886 888 3.530535 CACATGATGTGGGATACAACGA 58.469 45.455 17.51 0.00 44.27 3.85
887 889 3.950087 CACATGATGTGGGATACAACG 57.050 47.619 17.51 0.00 44.27 4.10
898 900 2.857483 TCACCGAAAACCACATGATGT 58.143 42.857 0.00 0.00 0.00 3.06
899 901 3.439825 TCATCACCGAAAACCACATGATG 59.560 43.478 0.00 5.81 43.03 3.07
900 902 3.684908 TCATCACCGAAAACCACATGAT 58.315 40.909 0.00 0.00 0.00 2.45
901 903 3.133141 TCATCACCGAAAACCACATGA 57.867 42.857 0.00 0.00 0.00 3.07
902 904 3.913548 TTCATCACCGAAAACCACATG 57.086 42.857 0.00 0.00 0.00 3.21
903 905 6.582677 TTTATTCATCACCGAAAACCACAT 57.417 33.333 0.00 0.00 0.00 3.21
904 906 6.207614 TCATTTATTCATCACCGAAAACCACA 59.792 34.615 0.00 0.00 0.00 4.17
905 907 6.616947 TCATTTATTCATCACCGAAAACCAC 58.383 36.000 0.00 0.00 0.00 4.16
906 908 6.825944 TCATTTATTCATCACCGAAAACCA 57.174 33.333 0.00 0.00 0.00 3.67
907 909 8.702163 AATTCATTTATTCATCACCGAAAACC 57.298 30.769 0.00 0.00 0.00 3.27
910 912 9.920133 TGAAAATTCATTTATTCATCACCGAAA 57.080 25.926 0.00 0.00 31.01 3.46
911 913 9.352784 GTGAAAATTCATTTATTCATCACCGAA 57.647 29.630 0.00 0.00 39.73 4.30
912 914 7.973388 GGTGAAAATTCATTTATTCATCACCGA 59.027 33.333 13.54 0.00 40.57 4.69
913 915 7.222611 GGGTGAAAATTCATTTATTCATCACCG 59.777 37.037 18.41 0.00 44.85 4.94
914 916 7.495606 GGGGTGAAAATTCATTTATTCATCACC 59.504 37.037 17.55 17.55 44.15 4.02
915 917 8.260114 AGGGGTGAAAATTCATTTATTCATCAC 58.740 33.333 0.00 5.84 39.73 3.06
916 918 8.378115 AGGGGTGAAAATTCATTTATTCATCA 57.622 30.769 0.00 0.00 39.73 3.07
917 919 8.477256 TGAGGGGTGAAAATTCATTTATTCATC 58.523 33.333 0.00 0.00 39.73 2.92
918 920 8.378115 TGAGGGGTGAAAATTCATTTATTCAT 57.622 30.769 0.00 0.00 39.73 2.57
919 921 7.789202 TGAGGGGTGAAAATTCATTTATTCA 57.211 32.000 0.00 0.00 39.73 2.57
920 922 9.500785 TTTTGAGGGGTGAAAATTCATTTATTC 57.499 29.630 0.00 0.00 39.73 1.75
921 923 9.859152 TTTTTGAGGGGTGAAAATTCATTTATT 57.141 25.926 0.00 0.00 39.73 1.40
947 949 5.104374 CAGTCTGTCACTTGCAACATTTTT 58.896 37.500 0.00 0.00 30.26 1.94
948 950 4.675510 CAGTCTGTCACTTGCAACATTTT 58.324 39.130 0.00 0.00 30.26 1.82
949 951 3.489738 GCAGTCTGTCACTTGCAACATTT 60.490 43.478 0.00 0.00 30.26 2.32
950 952 2.033801 GCAGTCTGTCACTTGCAACATT 59.966 45.455 0.00 0.00 30.26 2.71
951 953 1.605710 GCAGTCTGTCACTTGCAACAT 59.394 47.619 0.00 0.00 30.26 2.71
952 954 1.016627 GCAGTCTGTCACTTGCAACA 58.983 50.000 0.00 0.00 30.26 3.33
972 974 1.065401 CGACTGAGACTGAGAGGATGC 59.935 57.143 0.00 0.00 0.00 3.91
1121 1123 4.554363 CGCCTCCTGTAGTCGCGG 62.554 72.222 6.13 0.00 39.20 6.46
1128 1130 2.501128 GCAGCATCGCCTCCTGTA 59.499 61.111 0.00 0.00 0.00 2.74
1154 1159 0.035725 TTCCTCCTCTGTCGTCGCTA 60.036 55.000 0.00 0.00 0.00 4.26
1192 1197 0.539051 CTCAGGCATCGTTTCCTCCT 59.461 55.000 0.00 0.00 0.00 3.69
1193 1198 0.462759 CCTCAGGCATCGTTTCCTCC 60.463 60.000 0.00 0.00 0.00 4.30
1302 1307 0.797249 GTAGTGTAGTGCGGCAGTCG 60.797 60.000 14.62 0.00 42.76 4.18
1418 1423 0.541863 TTCGGCCTGAAGGAAGGATC 59.458 55.000 0.00 0.00 40.02 3.36
1420 1425 4.225860 TTCGGCCTGAAGGAAGGA 57.774 55.556 0.00 0.00 40.02 3.36
1427 1432 1.486310 AGTCATATGCTTCGGCCTGAA 59.514 47.619 0.00 5.47 40.91 3.02
1428 1433 1.123077 AGTCATATGCTTCGGCCTGA 58.877 50.000 0.00 0.00 40.91 3.86
1429 1434 1.224075 CAGTCATATGCTTCGGCCTG 58.776 55.000 0.00 0.00 40.91 4.85
1435 1440 1.566563 CGCGGCAGTCATATGCTTC 59.433 57.895 0.00 0.00 45.75 3.86
1437 1442 2.280389 CCGCGGCAGTCATATGCT 60.280 61.111 14.67 0.00 45.75 3.79
1443 1448 4.529219 CATAGGCCGCGGCAGTCA 62.529 66.667 46.88 29.80 44.11 3.41
1467 1472 1.411651 GGAAGCTCCTCGGGCCTATT 61.412 60.000 0.84 0.00 32.53 1.73
1571 1576 2.804090 GTTCCACTCGCCGTCGAC 60.804 66.667 5.18 5.18 40.21 4.20
1587 1592 1.827399 AATGACCCCGCTCTTGTCGT 61.827 55.000 0.00 0.00 0.00 4.34
1809 1815 7.916977 TGCATTTCATAAAGCAGTATCATGTTC 59.083 33.333 0.00 0.00 32.48 3.18
1814 1820 7.094248 ACTGTTGCATTTCATAAAGCAGTATCA 60.094 33.333 0.00 0.00 38.35 2.15
1845 1851 9.442062 TGTACTCCTCCTTTATAAATGGACATA 57.558 33.333 10.55 5.45 0.00 2.29
1846 1852 8.331931 TGTACTCCTCCTTTATAAATGGACAT 57.668 34.615 10.55 6.10 0.00 3.06
1847 1853 7.743116 TGTACTCCTCCTTTATAAATGGACA 57.257 36.000 10.55 6.62 0.00 4.02
1864 1870 9.924650 TTCTTGTTCTTAACTCTATTGTACTCC 57.075 33.333 0.00 0.00 0.00 3.85
1948 1980 2.657066 GGAGAGGTTCGACCCACCC 61.657 68.421 0.39 0.00 39.75 4.61
2082 2120 4.965814 TCCATAGTCAATGATGAGGAAGC 58.034 43.478 0.00 0.00 37.86 3.86
2085 2123 9.730705 GAAATAATCCATAGTCAATGATGAGGA 57.269 33.333 0.00 0.00 37.86 3.71
2137 2175 2.104792 TCTCAAGCTTATTCCGGGATGG 59.895 50.000 5.13 0.00 40.09 3.51
2138 2176 3.134458 GTCTCAAGCTTATTCCGGGATG 58.866 50.000 5.13 0.00 0.00 3.51
2139 2177 2.771943 TGTCTCAAGCTTATTCCGGGAT 59.228 45.455 0.00 0.00 0.00 3.85
2140 2178 2.093658 GTGTCTCAAGCTTATTCCGGGA 60.094 50.000 0.00 0.00 0.00 5.14
2141 2179 2.093447 AGTGTCTCAAGCTTATTCCGGG 60.093 50.000 0.00 0.00 0.00 5.73
2142 2180 3.252974 AGTGTCTCAAGCTTATTCCGG 57.747 47.619 0.00 0.00 0.00 5.14
2143 2181 6.910536 AATAAGTGTCTCAAGCTTATTCCG 57.089 37.500 0.00 0.00 39.70 4.30
2144 2182 7.970614 CCAAAATAAGTGTCTCAAGCTTATTCC 59.029 37.037 0.00 0.00 41.65 3.01
2145 2183 7.970614 CCCAAAATAAGTGTCTCAAGCTTATTC 59.029 37.037 0.00 0.00 41.65 1.75
2146 2184 7.669722 TCCCAAAATAAGTGTCTCAAGCTTATT 59.330 33.333 0.00 0.00 43.25 1.40
2147 2185 7.175104 TCCCAAAATAAGTGTCTCAAGCTTAT 58.825 34.615 0.00 0.00 37.11 1.73
2148 2186 6.539173 TCCCAAAATAAGTGTCTCAAGCTTA 58.461 36.000 0.00 0.00 0.00 3.09
2149 2187 5.385198 TCCCAAAATAAGTGTCTCAAGCTT 58.615 37.500 0.00 0.00 0.00 3.74
2150 2188 4.985538 TCCCAAAATAAGTGTCTCAAGCT 58.014 39.130 0.00 0.00 0.00 3.74
2151 2189 5.393461 CCATCCCAAAATAAGTGTCTCAAGC 60.393 44.000 0.00 0.00 0.00 4.01
2152 2190 5.945784 TCCATCCCAAAATAAGTGTCTCAAG 59.054 40.000 0.00 0.00 0.00 3.02
2153 2191 5.886609 TCCATCCCAAAATAAGTGTCTCAA 58.113 37.500 0.00 0.00 0.00 3.02
2154 2192 5.512942 TCCATCCCAAAATAAGTGTCTCA 57.487 39.130 0.00 0.00 0.00 3.27
2155 2193 5.358160 CCTTCCATCCCAAAATAAGTGTCTC 59.642 44.000 0.00 0.00 0.00 3.36
2156 2194 5.015178 TCCTTCCATCCCAAAATAAGTGTCT 59.985 40.000 0.00 0.00 0.00 3.41
2157 2195 5.261216 TCCTTCCATCCCAAAATAAGTGTC 58.739 41.667 0.00 0.00 0.00 3.67
2158 2196 5.222337 ACTCCTTCCATCCCAAAATAAGTGT 60.222 40.000 0.00 0.00 0.00 3.55
2159 2197 5.264395 ACTCCTTCCATCCCAAAATAAGTG 58.736 41.667 0.00 0.00 0.00 3.16
2160 2198 5.536497 ACTCCTTCCATCCCAAAATAAGT 57.464 39.130 0.00 0.00 0.00 2.24
2161 2199 6.663734 ACTACTCCTTCCATCCCAAAATAAG 58.336 40.000 0.00 0.00 0.00 1.73
2162 2200 6.652205 ACTACTCCTTCCATCCCAAAATAA 57.348 37.500 0.00 0.00 0.00 1.40
2163 2201 6.906901 AGTACTACTCCTTCCATCCCAAAATA 59.093 38.462 0.00 0.00 0.00 1.40
2164 2202 5.731678 AGTACTACTCCTTCCATCCCAAAAT 59.268 40.000 0.00 0.00 0.00 1.82
2165 2203 5.098663 AGTACTACTCCTTCCATCCCAAAA 58.901 41.667 0.00 0.00 0.00 2.44
2166 2204 4.695606 AGTACTACTCCTTCCATCCCAAA 58.304 43.478 0.00 0.00 0.00 3.28
2167 2205 4.348020 AGTACTACTCCTTCCATCCCAA 57.652 45.455 0.00 0.00 0.00 4.12
2168 2206 4.348020 AAGTACTACTCCTTCCATCCCA 57.652 45.455 0.00 0.00 0.00 4.37
2169 2207 6.075984 TGATAAGTACTACTCCTTCCATCCC 58.924 44.000 0.00 0.00 0.00 3.85
2170 2208 7.598759 TTGATAAGTACTACTCCTTCCATCC 57.401 40.000 0.00 0.00 0.00 3.51
2171 2209 7.149307 GCTTGATAAGTACTACTCCTTCCATC 58.851 42.308 0.00 0.00 0.00 3.51
2172 2210 6.042208 GGCTTGATAAGTACTACTCCTTCCAT 59.958 42.308 0.00 0.00 0.00 3.41
2173 2211 5.363005 GGCTTGATAAGTACTACTCCTTCCA 59.637 44.000 0.00 0.00 0.00 3.53
2174 2212 5.363005 TGGCTTGATAAGTACTACTCCTTCC 59.637 44.000 0.00 0.00 0.00 3.46
2175 2213 6.127423 TGTGGCTTGATAAGTACTACTCCTTC 60.127 42.308 0.00 0.00 0.00 3.46
2176 2214 5.720041 TGTGGCTTGATAAGTACTACTCCTT 59.280 40.000 0.00 0.00 0.00 3.36
2177 2215 5.127356 GTGTGGCTTGATAAGTACTACTCCT 59.873 44.000 0.00 0.00 0.00 3.69
2178 2216 5.105473 TGTGTGGCTTGATAAGTACTACTCC 60.105 44.000 0.00 0.00 0.00 3.85
2179 2217 5.962433 TGTGTGGCTTGATAAGTACTACTC 58.038 41.667 0.00 0.00 0.00 2.59
2180 2218 5.995565 TGTGTGGCTTGATAAGTACTACT 57.004 39.130 0.00 0.00 0.00 2.57
2181 2219 7.490000 ACTATGTGTGGCTTGATAAGTACTAC 58.510 38.462 0.00 0.00 0.00 2.73
2182 2220 7.340999 TGACTATGTGTGGCTTGATAAGTACTA 59.659 37.037 0.00 0.00 0.00 1.82
2183 2221 6.154534 TGACTATGTGTGGCTTGATAAGTACT 59.845 38.462 0.00 0.00 0.00 2.73
2184 2222 6.338146 TGACTATGTGTGGCTTGATAAGTAC 58.662 40.000 0.00 0.00 0.00 2.73
2185 2223 6.538945 TGACTATGTGTGGCTTGATAAGTA 57.461 37.500 0.00 0.00 0.00 2.24
2186 2224 5.420725 TGACTATGTGTGGCTTGATAAGT 57.579 39.130 0.00 0.00 0.00 2.24
2187 2225 6.741992 TTTGACTATGTGTGGCTTGATAAG 57.258 37.500 0.00 0.00 0.00 1.73
2188 2226 8.046708 AGTATTTGACTATGTGTGGCTTGATAA 58.953 33.333 0.00 0.00 36.27 1.75
2189 2227 7.564793 AGTATTTGACTATGTGTGGCTTGATA 58.435 34.615 0.00 0.00 36.27 2.15
2190 2228 6.418101 AGTATTTGACTATGTGTGGCTTGAT 58.582 36.000 0.00 0.00 36.27 2.57
2191 2229 5.804639 AGTATTTGACTATGTGTGGCTTGA 58.195 37.500 0.00 0.00 36.27 3.02
2192 2230 6.238211 GCTAGTATTTGACTATGTGTGGCTTG 60.238 42.308 0.00 0.00 39.98 4.01
2193 2231 5.817816 GCTAGTATTTGACTATGTGTGGCTT 59.182 40.000 0.00 0.00 39.98 4.35
2194 2232 5.360591 GCTAGTATTTGACTATGTGTGGCT 58.639 41.667 0.00 0.00 39.98 4.75
2195 2233 4.209288 CGCTAGTATTTGACTATGTGTGGC 59.791 45.833 0.00 0.00 39.98 5.01
2196 2234 5.232202 CACGCTAGTATTTGACTATGTGTGG 59.768 44.000 13.87 0.00 41.09 4.17
2197 2235 6.261033 CACGCTAGTATTTGACTATGTGTG 57.739 41.667 10.54 10.54 39.98 3.82
2198 2236 5.962433 ACACGCTAGTATTTGACTATGTGT 58.038 37.500 13.10 13.10 45.75 3.72
2199 2237 7.165977 CACTACACGCTAGTATTTGACTATGTG 59.834 40.741 12.22 12.22 44.60 3.21
2200 2238 7.194278 CACTACACGCTAGTATTTGACTATGT 58.806 38.462 0.00 0.00 39.98 2.29
2201 2239 6.142480 GCACTACACGCTAGTATTTGACTATG 59.858 42.308 0.00 0.00 39.98 2.23
2202 2240 6.207213 GCACTACACGCTAGTATTTGACTAT 58.793 40.000 0.00 0.00 39.98 2.12
2203 2241 5.575957 GCACTACACGCTAGTATTTGACTA 58.424 41.667 0.00 0.00 39.81 2.59
2204 2242 4.421948 GCACTACACGCTAGTATTTGACT 58.578 43.478 0.00 0.00 42.69 3.41
2205 2243 3.239941 CGCACTACACGCTAGTATTTGAC 59.760 47.826 0.00 0.00 0.00 3.18
2206 2244 3.431856 CGCACTACACGCTAGTATTTGA 58.568 45.455 0.00 0.00 0.00 2.69
2207 2245 3.818385 CGCACTACACGCTAGTATTTG 57.182 47.619 0.00 0.00 0.00 2.32
2399 2457 4.528206 TCAACATCTCTGGTCTAAGAAGCA 59.472 41.667 0.00 0.00 0.00 3.91
2430 2488 6.038161 CACTACATCACAAAGACAAACCAAGA 59.962 38.462 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.