Multiple sequence alignment - TraesCS7D01G429800

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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 TraesCS7D01G429800 chr7D 100.000 2802 0 0 1 2802 549370041 549367240 0.000000e+00 5175.0
1 TraesCS7D01G429800 chr7D 89.463 949 62 21 1880 2802 549317388 549316452 0.000000e+00 1164.0
2 TraesCS7D01G429800 chr7D 92.630 787 49 4 986 1763 549318952 549318166 0.000000e+00 1123.0
3 TraesCS7D01G429800 chr7D 94.087 575 12 7 32 599 549319525 549318966 0.000000e+00 854.0
4 TraesCS7D01G429800 chr7D 84.492 187 24 3 598 783 56522217 56522399 2.220000e-41 180.0
5 TraesCS7D01G429800 chr7A 91.377 777 54 7 2028 2802 634929861 634929096 0.000000e+00 1051.0
6 TraesCS7D01G429800 chr7A 91.263 744 54 4 1031 1768 634931076 634930338 0.000000e+00 1003.0
7 TraesCS7D01G429800 chr7A 82.270 564 40 33 10 527 634933693 634933144 1.540000e-117 433.0
8 TraesCS7D01G429800 chr7A 82.178 303 39 6 602 896 723309605 723309900 2.160000e-61 246.0
9 TraesCS7D01G429800 chr7A 78.689 305 50 6 600 896 715126478 715126181 3.680000e-44 189.0
10 TraesCS7D01G429800 chr7A 91.781 73 5 1 1958 2029 634929954 634929882 1.780000e-17 100.0
11 TraesCS7D01G429800 chr7B 91.853 626 41 6 2047 2665 593556925 593556303 0.000000e+00 865.0
12 TraesCS7D01G429800 chr7B 89.034 611 29 21 10 599 593558302 593557709 0.000000e+00 723.0
13 TraesCS7D01G429800 chr7B 80.719 306 44 9 600 896 490240872 490241171 1.010000e-54 224.0
14 TraesCS7D01G429800 chr7B 89.831 177 13 3 1587 1758 593557509 593557333 3.630000e-54 222.0
15 TraesCS7D01G429800 chr7B 84.507 213 9 7 986 1194 593557695 593557503 3.680000e-44 189.0
16 TraesCS7D01G429800 chr6A 80.854 632 94 19 1113 1727 581965270 581965891 3.270000e-129 472.0
17 TraesCS7D01G429800 chr6A 78.916 166 25 8 18 176 581964521 581964683 1.370000e-18 104.0
18 TraesCS7D01G429800 chr6D 80.156 640 90 21 1113 1727 434604446 434605073 7.120000e-121 444.0
19 TraesCS7D01G429800 chr6D 100.000 34 0 0 372 405 434604081 434604114 2.330000e-06 63.9
20 TraesCS7D01G429800 chr6B 80.000 635 94 21 1113 1727 658119380 658120001 3.310000e-119 438.0
21 TraesCS7D01G429800 chr6B 80.690 290 41 8 616 896 647640585 647640868 7.860000e-51 211.0
22 TraesCS7D01G429800 chr6B 80.117 171 19 12 18 178 658118610 658118775 2.280000e-21 113.0
23 TraesCS7D01G429800 chr6B 93.617 47 1 1 372 418 658119017 658119061 5.010000e-08 69.4
24 TraesCS7D01G429800 chr5D 79.316 643 95 22 1110 1727 125778291 125777662 1.550000e-112 416.0
25 TraesCS7D01G429800 chr5D 87.736 106 8 3 73 176 125781409 125781307 4.900000e-23 119.0
26 TraesCS7D01G429800 chr5A 80.210 571 85 14 1174 1727 139893887 139893328 1.210000e-108 403.0
27 TraesCS7D01G429800 chr5A 79.054 296 41 12 602 896 706657220 706657495 1.710000e-42 183.0
28 TraesCS7D01G429800 chr5A 76.623 308 44 11 600 896 509649608 509649318 8.090000e-31 145.0
29 TraesCS7D01G429800 chr5A 88.172 93 8 2 84 176 139895007 139894918 1.060000e-19 108.0
30 TraesCS7D01G429800 chr5A 92.000 50 4 0 1110 1159 139893969 139893920 1.390000e-08 71.3
31 TraesCS7D01G429800 chr5B 80.216 556 81 18 1188 1727 138557502 138556960 9.410000e-105 390.0
32 TraesCS7D01G429800 chr5B 80.130 307 40 12 601 896 368244859 368245155 2.830000e-50 209.0
33 TraesCS7D01G429800 chr5B 88.119 101 9 1 83 183 138558404 138558307 1.760000e-22 117.0
34 TraesCS7D01G429800 chr5B 84.800 125 9 5 600 724 626016442 626016556 1.760000e-22 117.0
35 TraesCS7D01G429800 chr5B 94.000 50 3 0 1110 1159 138557601 138557552 2.990000e-10 76.8
36 TraesCS7D01G429800 chr4D 83.882 304 36 5 602 896 14434678 14434977 7.640000e-71 278.0
37 TraesCS7D01G429800 chr4D 81.323 257 28 12 583 828 404093112 404093359 1.020000e-44 191.0
38 TraesCS7D01G429800 chr2B 83.062 307 35 6 602 896 779956399 779956098 2.140000e-66 263.0
39 TraesCS7D01G429800 chr1D 82.295 305 40 9 600 896 9914203 9913905 4.630000e-63 252.0
40 TraesCS7D01G429800 chr4A 81.877 309 39 9 600 896 16477376 16477073 7.750000e-61 244.0
41 TraesCS7D01G429800 chr3D 82.085 307 34 12 600 896 15342423 15342718 2.790000e-60 243.0
42 TraesCS7D01G429800 chr3D 78.067 269 40 12 639 896 353158080 353158340 4.830000e-33 152.0
43 TraesCS7D01G429800 chr4B 80.339 295 44 6 612 896 20675854 20675564 7.860000e-51 211.0
44 TraesCS7D01G429800 chrUn 79.085 306 50 8 601 896 141430125 141429824 6.120000e-47 198.0
45 TraesCS7D01G429800 chr2A 77.474 293 42 14 617 896 495245822 495246103 1.340000e-33 154.0
46 TraesCS7D01G429800 chr2A 76.894 264 40 16 641 893 646824978 646825231 2.270000e-26 130.0
47 TraesCS7D01G429800 chr2D 81.366 161 20 6 744 896 179130667 179130825 3.790000e-24 122.0


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 TraesCS7D01G429800 chr7D 549367240 549370041 2801 True 5175.00 5175 100.00000 1 2802 1 chr7D.!!$R1 2801
1 TraesCS7D01G429800 chr7D 549316452 549319525 3073 True 1047.00 1164 92.06000 32 2802 3 chr7D.!!$R2 2770
2 TraesCS7D01G429800 chr7A 634929096 634933693 4597 True 646.75 1051 89.17275 10 2802 4 chr7A.!!$R2 2792
3 TraesCS7D01G429800 chr7B 593556303 593558302 1999 True 499.75 865 88.80625 10 2665 4 chr7B.!!$R1 2655
4 TraesCS7D01G429800 chr6A 581964521 581965891 1370 False 288.00 472 79.88500 18 1727 2 chr6A.!!$F1 1709
5 TraesCS7D01G429800 chr6D 434604081 434605073 992 False 253.95 444 90.07800 372 1727 2 chr6D.!!$F1 1355
6 TraesCS7D01G429800 chr6B 658118610 658120001 1391 False 206.80 438 84.57800 18 1727 3 chr6B.!!$F2 1709
7 TraesCS7D01G429800 chr5D 125777662 125781409 3747 True 267.50 416 83.52600 73 1727 2 chr5D.!!$R1 1654

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
973 4341 0.105555 AACCCCGGGTCCGACATATA 60.106 55.0 21.85 0.0 42.83 0.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 6860 0.314935 AGAAGGCACGCAACCATTTG 59.685 50.0 0.0 0.0 35.62 2.32 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
81 86 1.449070 TTGCTGCGCTGAGGATGAG 60.449 57.895 19.32 0.00 0.00 2.90
92 97 3.181499 GCTGAGGATGAGCTTGAATGTTG 60.181 47.826 0.00 0.00 44.09 3.33
131 140 0.882927 TGCGTGACCCTTTTTCCTCG 60.883 55.000 0.00 0.00 0.00 4.63
179 192 2.698274 ACCCAAACAACAAGAATCCACC 59.302 45.455 0.00 0.00 0.00 4.61
180 193 2.965147 CCCAAACAACAAGAATCCACCT 59.035 45.455 0.00 0.00 0.00 4.00
181 194 3.005791 CCCAAACAACAAGAATCCACCTC 59.994 47.826 0.00 0.00 0.00 3.85
182 195 3.005791 CCAAACAACAAGAATCCACCTCC 59.994 47.826 0.00 0.00 0.00 4.30
183 196 2.185004 ACAACAAGAATCCACCTCCG 57.815 50.000 0.00 0.00 0.00 4.63
184 197 1.271379 ACAACAAGAATCCACCTCCGG 60.271 52.381 0.00 0.00 0.00 5.14
185 198 0.328258 AACAAGAATCCACCTCCGGG 59.672 55.000 0.00 0.00 38.88 5.73
490 682 5.832539 TTCTCTCCACAAGAAGAAAGGAT 57.167 39.130 0.00 0.00 32.23 3.24
491 683 5.413309 TCTCTCCACAAGAAGAAAGGATC 57.587 43.478 0.00 0.00 32.23 3.36
543 3908 2.855963 CAACAAGCAAGCAACAGAGTTG 59.144 45.455 5.56 5.56 0.00 3.16
615 3983 9.790389 GATATATACTAGAAATCCAACTCGGTG 57.210 37.037 0.00 0.00 35.57 4.94
616 3984 2.973945 ACTAGAAATCCAACTCGGTGC 58.026 47.619 0.00 0.00 35.57 5.01
617 3985 2.280628 CTAGAAATCCAACTCGGTGCC 58.719 52.381 0.00 0.00 35.57 5.01
618 3986 0.322546 AGAAATCCAACTCGGTGCCC 60.323 55.000 0.00 0.00 35.57 5.36
620 3988 0.609131 AAATCCAACTCGGTGCCCAG 60.609 55.000 0.00 0.00 35.57 4.45
624 3992 4.021925 AACTCGGTGCCCAGGCTC 62.022 66.667 10.58 6.18 42.51 4.70
626 3994 3.790437 CTCGGTGCCCAGGCTCAT 61.790 66.667 10.58 0.00 42.51 2.90
627 3995 4.100084 TCGGTGCCCAGGCTCATG 62.100 66.667 10.58 3.29 42.51 3.07
628 3996 4.415150 CGGTGCCCAGGCTCATGT 62.415 66.667 10.58 0.00 42.51 3.21
629 3997 2.753043 GGTGCCCAGGCTCATGTG 60.753 66.667 10.58 0.00 42.51 3.21
630 3998 3.446570 GTGCCCAGGCTCATGTGC 61.447 66.667 11.30 11.30 42.51 4.57
632 4000 2.827642 GCCCAGGCTCATGTGCTC 60.828 66.667 18.44 9.41 38.26 4.26
633 4001 2.124403 CCCAGGCTCATGTGCTCC 60.124 66.667 18.44 4.02 0.00 4.70
634 4002 2.124403 CCAGGCTCATGTGCTCCC 60.124 66.667 18.44 3.33 0.00 4.30
636 4004 1.451567 CAGGCTCATGTGCTCCCAG 60.452 63.158 18.44 0.00 0.00 4.45
638 4006 1.451028 GGCTCATGTGCTCCCAGAC 60.451 63.158 18.44 0.00 0.00 3.51
639 4007 1.297689 GCTCATGTGCTCCCAGACA 59.702 57.895 12.42 0.00 0.00 3.41
641 4009 0.900421 CTCATGTGCTCCCAGACAGA 59.100 55.000 0.00 0.00 0.00 3.41
643 4011 1.699083 TCATGTGCTCCCAGACAGAAA 59.301 47.619 0.00 0.00 0.00 2.52
645 4013 2.727123 TGTGCTCCCAGACAGAAAAA 57.273 45.000 0.00 0.00 0.00 1.94
714 4082 7.589958 TTTTGTGTGTGGTAGATAATTTGGT 57.410 32.000 0.00 0.00 0.00 3.67
715 4083 8.693120 TTTTGTGTGTGGTAGATAATTTGGTA 57.307 30.769 0.00 0.00 0.00 3.25
716 4084 7.675962 TTGTGTGTGGTAGATAATTTGGTAC 57.324 36.000 0.00 0.00 0.00 3.34
717 4085 5.870433 TGTGTGTGGTAGATAATTTGGTACG 59.130 40.000 0.00 0.00 0.00 3.67
718 4086 5.870978 GTGTGTGGTAGATAATTTGGTACGT 59.129 40.000 0.00 0.00 0.00 3.57
719 4087 5.870433 TGTGTGGTAGATAATTTGGTACGTG 59.130 40.000 0.00 0.00 0.00 4.49
720 4088 6.101332 GTGTGGTAGATAATTTGGTACGTGA 58.899 40.000 0.00 0.00 0.00 4.35
721 4089 6.255020 GTGTGGTAGATAATTTGGTACGTGAG 59.745 42.308 0.00 0.00 0.00 3.51
722 4090 5.751990 GTGGTAGATAATTTGGTACGTGAGG 59.248 44.000 0.00 0.00 0.00 3.86
723 4091 5.422970 TGGTAGATAATTTGGTACGTGAGGT 59.577 40.000 0.00 0.00 0.00 3.85
724 4092 6.070653 TGGTAGATAATTTGGTACGTGAGGTT 60.071 38.462 0.00 0.00 0.00 3.50
725 4093 6.478016 GGTAGATAATTTGGTACGTGAGGTTC 59.522 42.308 0.00 0.00 0.00 3.62
726 4094 6.045072 AGATAATTTGGTACGTGAGGTTCA 57.955 37.500 0.00 0.00 0.00 3.18
727 4095 6.469410 AGATAATTTGGTACGTGAGGTTCAA 58.531 36.000 0.00 0.00 0.00 2.69
728 4096 7.110155 AGATAATTTGGTACGTGAGGTTCAAT 58.890 34.615 0.00 0.00 0.00 2.57
729 4097 7.610305 AGATAATTTGGTACGTGAGGTTCAATT 59.390 33.333 0.00 0.00 0.00 2.32
730 4098 5.622770 ATTTGGTACGTGAGGTTCAATTC 57.377 39.130 0.00 0.00 0.00 2.17
731 4099 3.755112 TGGTACGTGAGGTTCAATTCA 57.245 42.857 0.00 0.00 0.00 2.57
732 4100 4.074627 TGGTACGTGAGGTTCAATTCAA 57.925 40.909 0.00 0.00 0.00 2.69
733 4101 4.452825 TGGTACGTGAGGTTCAATTCAAA 58.547 39.130 0.00 0.00 0.00 2.69
734 4102 5.067273 TGGTACGTGAGGTTCAATTCAAAT 58.933 37.500 0.00 0.00 0.00 2.32
735 4103 5.533154 TGGTACGTGAGGTTCAATTCAAATT 59.467 36.000 0.00 0.00 0.00 1.82
736 4104 6.039941 TGGTACGTGAGGTTCAATTCAAATTT 59.960 34.615 0.00 0.00 0.00 1.82
737 4105 6.921307 GGTACGTGAGGTTCAATTCAAATTTT 59.079 34.615 0.00 0.00 0.00 1.82
738 4106 8.077386 GGTACGTGAGGTTCAATTCAAATTTTA 58.923 33.333 0.00 0.00 0.00 1.52
739 4107 9.453325 GTACGTGAGGTTCAATTCAAATTTTAA 57.547 29.630 0.00 0.00 0.00 1.52
740 4108 8.347729 ACGTGAGGTTCAATTCAAATTTTAAC 57.652 30.769 0.00 3.47 0.00 2.01
741 4109 8.194769 ACGTGAGGTTCAATTCAAATTTTAACT 58.805 29.630 0.00 0.00 0.00 2.24
742 4110 8.690840 CGTGAGGTTCAATTCAAATTTTAACTC 58.309 33.333 0.00 7.20 0.00 3.01
743 4111 9.528018 GTGAGGTTCAATTCAAATTTTAACTCA 57.472 29.630 8.93 8.93 0.00 3.41
755 4123 9.695526 TCAAATTTTAACTCATTTGGACATCTG 57.304 29.630 11.41 0.00 39.76 2.90
756 4124 9.695526 CAAATTTTAACTCATTTGGACATCTGA 57.304 29.630 0.00 0.00 36.93 3.27
757 4125 9.918630 AAATTTTAACTCATTTGGACATCTGAG 57.081 29.630 9.00 9.00 40.71 3.35
758 4126 6.500684 TTTAACTCATTTGGACATCTGAGC 57.499 37.500 10.00 0.00 38.94 4.26
759 4127 3.708403 ACTCATTTGGACATCTGAGCA 57.292 42.857 10.00 0.00 38.94 4.26
760 4128 4.025040 ACTCATTTGGACATCTGAGCAA 57.975 40.909 10.00 0.00 38.94 3.91
761 4129 3.755378 ACTCATTTGGACATCTGAGCAAC 59.245 43.478 10.00 0.00 38.94 4.17
762 4130 4.008330 CTCATTTGGACATCTGAGCAACT 58.992 43.478 0.00 0.00 0.00 3.16
763 4131 4.005650 TCATTTGGACATCTGAGCAACTC 58.994 43.478 0.00 0.00 0.00 3.01
764 4132 3.777106 TTTGGACATCTGAGCAACTCT 57.223 42.857 0.00 0.00 0.00 3.24
765 4133 4.890158 TTTGGACATCTGAGCAACTCTA 57.110 40.909 0.00 0.00 0.00 2.43
766 4134 4.462508 TTGGACATCTGAGCAACTCTAG 57.537 45.455 0.00 0.00 0.00 2.43
767 4135 2.762887 TGGACATCTGAGCAACTCTAGG 59.237 50.000 0.00 0.00 0.00 3.02
768 4136 2.763448 GGACATCTGAGCAACTCTAGGT 59.237 50.000 0.00 0.00 0.00 3.08
769 4137 3.954904 GGACATCTGAGCAACTCTAGGTA 59.045 47.826 0.00 0.00 0.00 3.08
770 4138 4.402793 GGACATCTGAGCAACTCTAGGTAA 59.597 45.833 0.00 0.00 0.00 2.85
771 4139 5.105310 GGACATCTGAGCAACTCTAGGTAAA 60.105 44.000 0.00 0.00 0.00 2.01
772 4140 6.360370 ACATCTGAGCAACTCTAGGTAAAA 57.640 37.500 0.00 0.00 0.00 1.52
773 4141 6.769512 ACATCTGAGCAACTCTAGGTAAAAA 58.230 36.000 0.00 0.00 0.00 1.94
789 4157 2.699251 AAAAAGACAAATCGGGTCGC 57.301 45.000 0.00 0.00 40.20 5.19
793 4161 1.735198 GACAAATCGGGTCGCGTGA 60.735 57.895 5.77 0.00 0.00 4.35
794 4162 1.286354 GACAAATCGGGTCGCGTGAA 61.286 55.000 5.77 0.00 0.00 3.18
797 4165 1.289109 AAATCGGGTCGCGTGAACAG 61.289 55.000 17.10 12.52 31.55 3.16
798 4166 2.430382 AATCGGGTCGCGTGAACAGT 62.430 55.000 17.10 0.00 31.55 3.55
802 4170 0.509929 GGGTCGCGTGAACAGTAAAC 59.490 55.000 17.10 0.00 31.55 2.01
804 4172 1.862827 GGTCGCGTGAACAGTAAACTT 59.137 47.619 9.64 0.00 0.00 2.66
805 4173 2.286025 GGTCGCGTGAACAGTAAACTTT 59.714 45.455 9.64 0.00 0.00 2.66
807 4175 4.336932 GTCGCGTGAACAGTAAACTTTTT 58.663 39.130 5.77 0.00 0.00 1.94
830 4198 9.508642 TTTTTACAAACCCTGATTTTGTCTTTT 57.491 25.926 3.83 0.00 42.26 2.27
831 4199 9.508642 TTTTACAAACCCTGATTTTGTCTTTTT 57.491 25.926 3.83 0.00 42.26 1.94
856 4224 3.944055 GAGAGCTACTCAACTGTCCAA 57.056 47.619 7.93 0.00 44.36 3.53
857 4225 4.258702 GAGAGCTACTCAACTGTCCAAA 57.741 45.455 7.93 0.00 44.36 3.28
858 4226 4.826556 GAGAGCTACTCAACTGTCCAAAT 58.173 43.478 7.93 0.00 44.36 2.32
860 4228 4.284490 AGAGCTACTCAACTGTCCAAATGA 59.716 41.667 0.00 0.00 32.06 2.57
870 4238 7.775397 CAACTGTCCAAATGAGTTGAAATTT 57.225 32.000 0.00 0.00 46.31 1.82
872 4240 8.971321 CAACTGTCCAAATGAGTTGAAATTTAG 58.029 33.333 0.00 0.00 46.31 1.85
873 4241 8.463930 ACTGTCCAAATGAGTTGAAATTTAGA 57.536 30.769 0.00 0.00 39.87 2.10
874 4242 8.912988 ACTGTCCAAATGAGTTGAAATTTAGAA 58.087 29.630 0.00 0.00 39.87 2.10
875 4243 9.918630 CTGTCCAAATGAGTTGAAATTTAGAAT 57.081 29.630 0.00 0.00 39.87 2.40
885 4253 9.543018 GAGTTGAAATTTAGAATAAACCTCACG 57.457 33.333 0.00 0.00 0.00 4.35
886 4254 8.021396 AGTTGAAATTTAGAATAAACCTCACGC 58.979 33.333 0.00 0.00 0.00 5.34
887 4255 7.441890 TGAAATTTAGAATAAACCTCACGCA 57.558 32.000 0.00 0.00 0.00 5.24
888 4256 8.050778 TGAAATTTAGAATAAACCTCACGCAT 57.949 30.769 0.00 0.00 0.00 4.73
890 4258 7.624360 AATTTAGAATAAACCTCACGCATCA 57.376 32.000 0.00 0.00 0.00 3.07
891 4259 7.624360 ATTTAGAATAAACCTCACGCATCAA 57.376 32.000 0.00 0.00 0.00 2.57
892 4260 7.441890 TTTAGAATAAACCTCACGCATCAAA 57.558 32.000 0.00 0.00 0.00 2.69
893 4261 7.624360 TTAGAATAAACCTCACGCATCAAAT 57.376 32.000 0.00 0.00 0.00 2.32
894 4262 6.515272 AGAATAAACCTCACGCATCAAATT 57.485 33.333 0.00 0.00 0.00 1.82
895 4263 7.624360 AGAATAAACCTCACGCATCAAATTA 57.376 32.000 0.00 0.00 0.00 1.40
896 4264 8.050778 AGAATAAACCTCACGCATCAAATTAA 57.949 30.769 0.00 0.00 0.00 1.40
897 4265 8.519526 AGAATAAACCTCACGCATCAAATTAAA 58.480 29.630 0.00 0.00 0.00 1.52
898 4266 9.134734 GAATAAACCTCACGCATCAAATTAAAA 57.865 29.630 0.00 0.00 0.00 1.52
899 4267 9.482627 AATAAACCTCACGCATCAAATTAAAAA 57.517 25.926 0.00 0.00 0.00 1.94
932 4300 2.592287 TTTTTCTTCGGCGCGGGT 60.592 55.556 15.48 0.00 0.00 5.28
933 4301 2.899044 TTTTTCTTCGGCGCGGGTG 61.899 57.895 15.48 8.28 0.00 4.61
953 4321 3.550431 GCTGAGCCGGGGAGCATA 61.550 66.667 2.18 0.00 34.23 3.14
954 4322 3.106986 GCTGAGCCGGGGAGCATAA 62.107 63.158 2.18 0.00 34.23 1.90
955 4323 1.526887 CTGAGCCGGGGAGCATAAA 59.473 57.895 2.18 0.00 34.23 1.40
956 4324 0.815615 CTGAGCCGGGGAGCATAAAC 60.816 60.000 2.18 0.00 34.23 2.01
957 4325 1.526225 GAGCCGGGGAGCATAAACC 60.526 63.158 2.18 0.00 34.23 3.27
958 4326 2.518587 GCCGGGGAGCATAAACCC 60.519 66.667 2.18 0.00 44.89 4.11
962 4330 2.194868 GGGAGCATAAACCCCGGG 59.805 66.667 15.80 15.80 40.19 5.73
963 4331 2.686572 GGGAGCATAAACCCCGGGT 61.687 63.158 21.85 2.03 40.19 5.28
964 4332 1.153025 GGAGCATAAACCCCGGGTC 60.153 63.158 21.85 7.39 33.12 4.46
965 4333 1.153025 GAGCATAAACCCCGGGTCC 60.153 63.158 21.85 0.00 33.12 4.46
966 4334 2.515290 GCATAAACCCCGGGTCCG 60.515 66.667 21.85 6.73 33.12 4.79
967 4335 3.033919 GCATAAACCCCGGGTCCGA 62.034 63.158 21.85 1.69 42.83 4.55
968 4336 1.153309 CATAAACCCCGGGTCCGAC 60.153 63.158 21.85 0.00 42.83 4.79
969 4337 1.613035 ATAAACCCCGGGTCCGACA 60.613 57.895 21.85 0.00 42.83 4.35
970 4338 0.984432 ATAAACCCCGGGTCCGACAT 60.984 55.000 21.85 1.47 42.83 3.06
971 4339 0.325110 TAAACCCCGGGTCCGACATA 60.325 55.000 21.85 0.00 42.83 2.29
972 4340 0.984432 AAACCCCGGGTCCGACATAT 60.984 55.000 21.85 0.00 42.83 1.78
973 4341 0.105555 AACCCCGGGTCCGACATATA 60.106 55.000 21.85 0.00 42.83 0.86
974 4342 0.115745 ACCCCGGGTCCGACATATAT 59.884 55.000 21.85 0.00 42.83 0.86
975 4343 1.358787 ACCCCGGGTCCGACATATATA 59.641 52.381 21.85 0.00 42.83 0.86
976 4344 2.023695 ACCCCGGGTCCGACATATATAT 60.024 50.000 21.85 0.00 42.83 0.86
977 4345 3.205056 ACCCCGGGTCCGACATATATATA 59.795 47.826 21.85 0.00 42.83 0.86
978 4346 3.571401 CCCCGGGTCCGACATATATATAC 59.429 52.174 21.85 0.00 42.83 1.47
979 4347 4.467769 CCCGGGTCCGACATATATATACT 58.532 47.826 14.18 0.00 42.83 2.12
980 4348 4.518211 CCCGGGTCCGACATATATATACTC 59.482 50.000 14.18 0.00 42.83 2.59
981 4349 5.374921 CCGGGTCCGACATATATATACTCT 58.625 45.833 11.39 0.00 42.83 3.24
982 4350 5.238868 CCGGGTCCGACATATATATACTCTG 59.761 48.000 11.39 0.00 42.83 3.35
983 4351 5.821470 CGGGTCCGACATATATATACTCTGT 59.179 44.000 2.83 0.00 42.83 3.41
984 4352 6.988580 CGGGTCCGACATATATATACTCTGTA 59.011 42.308 2.83 0.00 42.83 2.74
1062 5244 0.108898 TCTCTTCTCTTGCGCTCTGC 60.109 55.000 9.73 0.00 46.70 4.26
1063 5245 0.108709 CTCTTCTCTTGCGCTCTGCT 60.109 55.000 9.73 0.00 46.63 4.24
1064 5246 0.108898 TCTTCTCTTGCGCTCTGCTC 60.109 55.000 9.73 0.00 46.63 4.26
1137 5371 1.050988 CCCTCATCACCGATGACCCT 61.051 60.000 2.56 0.00 43.11 4.34
1504 5759 3.282745 GACGTCAAGCTCTCCGCCA 62.283 63.158 11.55 0.00 40.39 5.69
1511 5766 4.443266 GCTCTCCGCCACGCTCTT 62.443 66.667 0.00 0.00 0.00 2.85
1524 5788 2.995872 GCTCTTGTCGTCCTCGGCT 61.996 63.158 0.00 0.00 42.59 5.52
1538 5808 2.125106 GGCTGCGGAGGAAACGAT 60.125 61.111 5.93 0.00 0.00 3.73
1605 5875 3.322466 CTCCGGTGGAAGGTGGCT 61.322 66.667 0.00 0.00 0.00 4.75
1724 5994 0.734889 GCCACCACCATCGAATGAAG 59.265 55.000 0.00 0.00 0.00 3.02
1732 6002 4.036027 CCACCATCGAATGAAGAAATCTGG 59.964 45.833 0.00 0.00 0.00 3.86
1740 6010 3.981071 TGAAGAAATCTGGACACCGAT 57.019 42.857 0.00 0.00 0.00 4.18
1770 6040 8.995027 TCTGCATGTATAGGTGGATTTTATTT 57.005 30.769 0.00 0.00 0.00 1.40
1771 6041 9.420118 TCTGCATGTATAGGTGGATTTTATTTT 57.580 29.630 0.00 0.00 0.00 1.82
1791 6061 4.955925 TTTTGCGGTTGATGTATAGGTG 57.044 40.909 0.00 0.00 0.00 4.00
1792 6062 2.613026 TGCGGTTGATGTATAGGTGG 57.387 50.000 0.00 0.00 0.00 4.61
1793 6063 2.112190 TGCGGTTGATGTATAGGTGGA 58.888 47.619 0.00 0.00 0.00 4.02
1795 6065 3.135712 TGCGGTTGATGTATAGGTGGATT 59.864 43.478 0.00 0.00 0.00 3.01
1796 6066 4.345547 TGCGGTTGATGTATAGGTGGATTA 59.654 41.667 0.00 0.00 0.00 1.75
1797 6067 5.012664 TGCGGTTGATGTATAGGTGGATTAT 59.987 40.000 0.00 0.00 0.00 1.28
1798 6068 5.938125 GCGGTTGATGTATAGGTGGATTATT 59.062 40.000 0.00 0.00 0.00 1.40
1799 6069 7.101054 GCGGTTGATGTATAGGTGGATTATTA 58.899 38.462 0.00 0.00 0.00 0.98
1801 6071 9.496873 CGGTTGATGTATAGGTGGATTATTAAA 57.503 33.333 0.00 0.00 0.00 1.52
1811 6081 7.640597 AGGTGGATTATTAAACTACTTTGCC 57.359 36.000 1.35 0.00 0.00 4.52
1812 6082 7.179269 AGGTGGATTATTAAACTACTTTGCCA 58.821 34.615 1.35 0.00 0.00 4.92
1826 6129 1.438651 TTGCCATTAGTCGTGTGCTC 58.561 50.000 0.00 0.00 0.00 4.26
1840 6143 7.416022 AGTCGTGTGCTCAATTATACTAGTAC 58.584 38.462 4.31 0.00 0.00 2.73
1922 6857 1.070376 CGATACGTGCATGCAATCAGG 60.070 52.381 24.58 11.79 0.00 3.86
1923 6858 1.942657 GATACGTGCATGCAATCAGGT 59.057 47.619 24.58 16.80 35.74 4.00
1924 6859 1.085893 TACGTGCATGCAATCAGGTG 58.914 50.000 24.58 8.76 33.91 4.00
1925 6860 1.515519 CGTGCATGCAATCAGGTGC 60.516 57.895 24.58 6.26 45.15 5.01
1956 6895 2.131183 GTGCCTTCTCTCGCATATGTC 58.869 52.381 4.29 0.00 37.33 3.06
1965 7163 7.905493 CCTTCTCTCGCATATGTCTTTTAAAAC 59.095 37.037 4.29 0.00 0.00 2.43
1974 7172 7.524698 GCATATGTCTTTTAAAACAACTCCCCA 60.525 37.037 4.29 0.00 0.00 4.96
2155 7543 3.579586 TGATGATGCCAAGCTTTTCCTTT 59.420 39.130 0.00 0.00 0.00 3.11
2210 7599 5.549742 TCATTTGCAAGGAAAGAAACCAT 57.450 34.783 0.00 0.00 0.00 3.55
2215 7604 6.916360 TTGCAAGGAAAGAAACCATAAGAT 57.084 33.333 0.00 0.00 0.00 2.40
2295 7684 3.406200 AGGCATGCCCGAAGCTCT 61.406 61.111 33.14 9.27 44.23 4.09
2385 7774 1.959985 CCACCACACCAATGCTTGTTA 59.040 47.619 0.00 0.00 0.00 2.41
2394 7787 5.534654 ACACCAATGCTTGTTACACTTATGT 59.465 36.000 0.00 0.00 43.30 2.29
2405 7798 7.490962 TGTTACACTTATGTTCTCCACAAAG 57.509 36.000 0.00 0.00 39.50 2.77
2506 7901 1.349688 TGTAAACCTAGCCACCACCTG 59.650 52.381 0.00 0.00 0.00 4.00
2507 7902 1.350019 GTAAACCTAGCCACCACCTGT 59.650 52.381 0.00 0.00 0.00 4.00
2525 7920 6.407525 CCACCTGTTTTCCTTTGTTATTGGAA 60.408 38.462 0.00 0.00 38.00 3.53
2591 7987 8.322091 AGTAACTATCCACAAAAATAGCAGAGT 58.678 33.333 0.00 0.00 0.00 3.24
2680 8076 1.548357 ATGCTCCCGCTGAGTTGAGT 61.548 55.000 2.58 0.00 43.48 3.41
2701 8097 9.739276 TTGAGTTCAACTGGTCTGATAAAATAT 57.261 29.630 0.00 0.00 0.00 1.28
2738 8134 4.615541 GCCCGAAAACGTAAAAATCTCTTG 59.384 41.667 0.00 0.00 0.00 3.02
2750 8146 7.114247 CGTAAAAATCTCTTGCCGAAAATTTCA 59.886 33.333 6.53 0.00 0.00 2.69
2753 8149 9.657419 AAAAATCTCTTGCCGAAAATTTCATAT 57.343 25.926 6.53 0.00 0.00 1.78
2761 8157 4.338118 GCCGAAAATTTCATATGTCCCTCA 59.662 41.667 6.53 0.00 0.00 3.86
2770 8166 1.271856 TATGTCCCTCAACGCCAGAA 58.728 50.000 0.00 0.00 0.00 3.02
2781 8177 2.639286 GCCAGAAGCAACACACGG 59.361 61.111 0.00 0.00 42.97 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.709018 TCATAAGATCGATGACACCAAGTA 57.291 37.500 0.54 0.00 0.00 2.24
1 2 5.598416 TCATAAGATCGATGACACCAAGT 57.402 39.130 0.54 0.00 0.00 3.16
2 3 6.218746 TCATCATAAGATCGATGACACCAAG 58.781 40.000 0.54 3.57 42.31 3.61
3 4 6.160576 TCATCATAAGATCGATGACACCAA 57.839 37.500 0.54 0.00 42.31 3.67
92 97 4.452455 CGCATATACCAAAGTGGATTCTCC 59.548 45.833 0.18 0.00 40.96 3.71
131 140 1.195448 CGTGAGTGAACTGCCATCAAC 59.805 52.381 0.00 0.00 0.00 3.18
490 682 4.002982 CCACATCATGTTTTTCTCTCCGA 58.997 43.478 0.00 0.00 0.00 4.55
491 683 3.753272 ACCACATCATGTTTTTCTCTCCG 59.247 43.478 0.00 0.00 0.00 4.63
599 3967 0.322546 GGGCACCGAGTTGGATTTCT 60.323 55.000 2.42 0.00 40.86 2.52
613 3981 3.446570 GCACATGAGCCTGGGCAC 61.447 66.667 14.39 8.23 45.14 5.01
615 3983 2.827642 GAGCACATGAGCCTGGGC 60.828 66.667 11.77 3.00 46.19 5.36
616 3984 2.124403 GGAGCACATGAGCCTGGG 60.124 66.667 11.77 0.00 34.23 4.45
617 3985 2.124403 GGGAGCACATGAGCCTGG 60.124 66.667 11.77 0.00 34.23 4.45
618 3986 1.451567 CTGGGAGCACATGAGCCTG 60.452 63.158 11.77 0.00 34.23 4.85
620 3988 1.451028 GTCTGGGAGCACATGAGCC 60.451 63.158 11.77 3.48 34.23 4.70
622 3990 0.900421 TCTGTCTGGGAGCACATGAG 59.100 55.000 0.00 0.00 0.00 2.90
624 3992 2.189594 TTTCTGTCTGGGAGCACATG 57.810 50.000 0.00 0.00 0.00 3.21
625 3993 2.957402 TTTTCTGTCTGGGAGCACAT 57.043 45.000 0.00 0.00 0.00 3.21
626 3994 2.727123 TTTTTCTGTCTGGGAGCACA 57.273 45.000 0.00 0.00 0.00 4.57
689 4057 8.012957 ACCAAATTATCTACCACACACAAAAA 57.987 30.769 0.00 0.00 0.00 1.94
690 4058 7.589958 ACCAAATTATCTACCACACACAAAA 57.410 32.000 0.00 0.00 0.00 2.44
691 4059 7.095144 CGTACCAAATTATCTACCACACACAAA 60.095 37.037 0.00 0.00 0.00 2.83
692 4060 6.369340 CGTACCAAATTATCTACCACACACAA 59.631 38.462 0.00 0.00 0.00 3.33
693 4061 5.870433 CGTACCAAATTATCTACCACACACA 59.130 40.000 0.00 0.00 0.00 3.72
694 4062 5.870978 ACGTACCAAATTATCTACCACACAC 59.129 40.000 0.00 0.00 0.00 3.82
695 4063 5.870433 CACGTACCAAATTATCTACCACACA 59.130 40.000 0.00 0.00 0.00 3.72
696 4064 6.101332 TCACGTACCAAATTATCTACCACAC 58.899 40.000 0.00 0.00 0.00 3.82
697 4065 6.283544 TCACGTACCAAATTATCTACCACA 57.716 37.500 0.00 0.00 0.00 4.17
698 4066 5.751990 CCTCACGTACCAAATTATCTACCAC 59.248 44.000 0.00 0.00 0.00 4.16
699 4067 5.422970 ACCTCACGTACCAAATTATCTACCA 59.577 40.000 0.00 0.00 0.00 3.25
700 4068 5.910614 ACCTCACGTACCAAATTATCTACC 58.089 41.667 0.00 0.00 0.00 3.18
701 4069 7.037438 TGAACCTCACGTACCAAATTATCTAC 58.963 38.462 0.00 0.00 0.00 2.59
702 4070 7.172868 TGAACCTCACGTACCAAATTATCTA 57.827 36.000 0.00 0.00 0.00 1.98
703 4071 6.045072 TGAACCTCACGTACCAAATTATCT 57.955 37.500 0.00 0.00 0.00 1.98
704 4072 6.730960 TTGAACCTCACGTACCAAATTATC 57.269 37.500 0.00 0.00 0.00 1.75
705 4073 7.392113 TGAATTGAACCTCACGTACCAAATTAT 59.608 33.333 0.00 0.00 0.00 1.28
706 4074 6.711194 TGAATTGAACCTCACGTACCAAATTA 59.289 34.615 0.00 0.00 0.00 1.40
707 4075 5.533154 TGAATTGAACCTCACGTACCAAATT 59.467 36.000 0.00 0.00 0.00 1.82
708 4076 5.067273 TGAATTGAACCTCACGTACCAAAT 58.933 37.500 0.00 0.00 0.00 2.32
709 4077 4.452825 TGAATTGAACCTCACGTACCAAA 58.547 39.130 0.00 0.00 0.00 3.28
710 4078 4.074627 TGAATTGAACCTCACGTACCAA 57.925 40.909 0.00 0.00 0.00 3.67
711 4079 3.755112 TGAATTGAACCTCACGTACCA 57.245 42.857 0.00 0.00 0.00 3.25
712 4080 5.622770 ATTTGAATTGAACCTCACGTACC 57.377 39.130 0.00 0.00 0.00 3.34
713 4081 7.924103 AAAATTTGAATTGAACCTCACGTAC 57.076 32.000 0.00 0.00 0.00 3.67
714 4082 9.453325 GTTAAAATTTGAATTGAACCTCACGTA 57.547 29.630 0.00 0.00 0.00 3.57
715 4083 8.194769 AGTTAAAATTTGAATTGAACCTCACGT 58.805 29.630 0.00 0.00 30.86 4.49
716 4084 8.574196 AGTTAAAATTTGAATTGAACCTCACG 57.426 30.769 0.00 0.00 30.86 4.35
717 4085 9.528018 TGAGTTAAAATTTGAATTGAACCTCAC 57.472 29.630 0.00 0.00 30.86 3.51
729 4097 9.695526 CAGATGTCCAAATGAGTTAAAATTTGA 57.304 29.630 15.80 0.00 43.41 2.69
730 4098 9.695526 TCAGATGTCCAAATGAGTTAAAATTTG 57.304 29.630 10.46 10.46 41.41 2.32
731 4099 9.918630 CTCAGATGTCCAAATGAGTTAAAATTT 57.081 29.630 0.00 0.00 35.52 1.82
732 4100 8.031277 GCTCAGATGTCCAAATGAGTTAAAATT 58.969 33.333 11.46 0.00 41.00 1.82
733 4101 7.177216 TGCTCAGATGTCCAAATGAGTTAAAAT 59.823 33.333 11.46 0.00 41.00 1.82
734 4102 6.489700 TGCTCAGATGTCCAAATGAGTTAAAA 59.510 34.615 11.46 0.00 41.00 1.52
735 4103 6.003326 TGCTCAGATGTCCAAATGAGTTAAA 58.997 36.000 11.46 0.00 41.00 1.52
736 4104 5.559770 TGCTCAGATGTCCAAATGAGTTAA 58.440 37.500 11.46 0.00 41.00 2.01
737 4105 5.164620 TGCTCAGATGTCCAAATGAGTTA 57.835 39.130 11.46 2.66 41.00 2.24
738 4106 4.025040 TGCTCAGATGTCCAAATGAGTT 57.975 40.909 11.46 0.00 41.00 3.01
739 4107 3.708403 TGCTCAGATGTCCAAATGAGT 57.292 42.857 11.46 0.00 41.00 3.41
740 4108 4.008330 AGTTGCTCAGATGTCCAAATGAG 58.992 43.478 7.42 7.42 41.68 2.90
741 4109 4.005650 GAGTTGCTCAGATGTCCAAATGA 58.994 43.478 0.00 0.00 0.00 2.57
742 4110 4.008330 AGAGTTGCTCAGATGTCCAAATG 58.992 43.478 0.00 0.00 32.06 2.32
743 4111 4.298103 AGAGTTGCTCAGATGTCCAAAT 57.702 40.909 0.00 0.00 32.06 2.32
744 4112 3.777106 AGAGTTGCTCAGATGTCCAAA 57.223 42.857 0.00 0.00 32.06 3.28
745 4113 3.196469 CCTAGAGTTGCTCAGATGTCCAA 59.804 47.826 0.00 0.00 32.06 3.53
746 4114 2.762887 CCTAGAGTTGCTCAGATGTCCA 59.237 50.000 0.00 0.00 32.06 4.02
747 4115 2.763448 ACCTAGAGTTGCTCAGATGTCC 59.237 50.000 0.00 0.00 32.06 4.02
748 4116 5.584253 TTACCTAGAGTTGCTCAGATGTC 57.416 43.478 0.00 0.00 32.06 3.06
749 4117 6.360370 TTTTACCTAGAGTTGCTCAGATGT 57.640 37.500 0.00 0.00 32.06 3.06
770 4138 1.069500 CGCGACCCGATTTGTCTTTTT 60.069 47.619 0.00 0.00 40.02 1.94
771 4139 0.515564 CGCGACCCGATTTGTCTTTT 59.484 50.000 0.00 0.00 40.02 2.27
772 4140 0.601841 ACGCGACCCGATTTGTCTTT 60.602 50.000 15.93 0.00 41.02 2.52
773 4141 1.005394 ACGCGACCCGATTTGTCTT 60.005 52.632 15.93 0.00 41.02 3.01
774 4142 1.736645 CACGCGACCCGATTTGTCT 60.737 57.895 15.93 0.00 41.02 3.41
775 4143 1.286354 TTCACGCGACCCGATTTGTC 61.286 55.000 15.93 0.00 41.02 3.18
776 4144 1.301087 TTCACGCGACCCGATTTGT 60.301 52.632 15.93 0.00 41.02 2.83
777 4145 1.131826 GTTCACGCGACCCGATTTG 59.868 57.895 15.93 0.00 41.02 2.32
778 4146 1.289109 CTGTTCACGCGACCCGATTT 61.289 55.000 15.93 0.00 41.02 2.17
779 4147 1.736645 CTGTTCACGCGACCCGATT 60.737 57.895 15.93 0.00 41.02 3.34
780 4148 1.588824 TACTGTTCACGCGACCCGAT 61.589 55.000 15.93 0.00 41.02 4.18
781 4149 1.794151 TTACTGTTCACGCGACCCGA 61.794 55.000 15.93 0.00 41.02 5.14
782 4150 0.940519 TTTACTGTTCACGCGACCCG 60.941 55.000 15.93 0.00 44.21 5.28
783 4151 0.509929 GTTTACTGTTCACGCGACCC 59.490 55.000 15.93 0.00 0.00 4.46
784 4152 1.494824 AGTTTACTGTTCACGCGACC 58.505 50.000 15.93 0.00 0.00 4.79
785 4153 3.580794 AAAGTTTACTGTTCACGCGAC 57.419 42.857 15.93 0.00 0.00 5.19
786 4154 4.603231 AAAAAGTTTACTGTTCACGCGA 57.397 36.364 15.93 0.00 0.00 5.87
804 4172 9.508642 AAAAGACAAAATCAGGGTTTGTAAAAA 57.491 25.926 2.73 0.00 46.50 1.94
805 4173 9.508642 AAAAAGACAAAATCAGGGTTTGTAAAA 57.491 25.926 2.73 0.00 46.50 1.52
828 4196 4.512944 CAGTTGAGTAGCTCTCTGCAAAAA 59.487 41.667 12.45 0.00 45.94 1.94
830 4198 3.070159 ACAGTTGAGTAGCTCTCTGCAAA 59.930 43.478 12.45 0.00 45.94 3.68
831 4199 2.630098 ACAGTTGAGTAGCTCTCTGCAA 59.370 45.455 12.45 6.99 45.94 4.08
832 4200 2.230025 GACAGTTGAGTAGCTCTCTGCA 59.770 50.000 12.45 0.00 45.94 4.41
834 4202 2.822561 TGGACAGTTGAGTAGCTCTCTG 59.177 50.000 12.45 14.68 43.13 3.35
835 4203 3.162147 TGGACAGTTGAGTAGCTCTCT 57.838 47.619 12.45 3.42 43.13 3.10
836 4204 3.944055 TTGGACAGTTGAGTAGCTCTC 57.056 47.619 0.00 0.00 43.03 3.20
837 4205 4.284490 TCATTTGGACAGTTGAGTAGCTCT 59.716 41.667 0.00 0.00 0.00 4.09
838 4206 4.569943 TCATTTGGACAGTTGAGTAGCTC 58.430 43.478 0.00 0.00 0.00 4.09
839 4207 4.040952 ACTCATTTGGACAGTTGAGTAGCT 59.959 41.667 13.95 0.00 45.14 3.32
840 4208 4.319177 ACTCATTTGGACAGTTGAGTAGC 58.681 43.478 13.95 0.00 45.14 3.58
841 4209 6.233430 CAACTCATTTGGACAGTTGAGTAG 57.767 41.667 15.18 0.00 46.74 2.57
847 4215 8.912988 TCTAAATTTCAACTCATTTGGACAGTT 58.087 29.630 0.00 0.00 35.69 3.16
848 4216 8.463930 TCTAAATTTCAACTCATTTGGACAGT 57.536 30.769 0.00 0.00 35.69 3.55
849 4217 9.918630 ATTCTAAATTTCAACTCATTTGGACAG 57.081 29.630 0.00 0.00 35.69 3.51
860 4228 8.021396 GCGTGAGGTTTATTCTAAATTTCAACT 58.979 33.333 0.00 0.00 0.00 3.16
862 4230 7.877003 TGCGTGAGGTTTATTCTAAATTTCAA 58.123 30.769 0.00 0.00 0.00 2.69
863 4231 7.441890 TGCGTGAGGTTTATTCTAAATTTCA 57.558 32.000 0.00 0.00 0.00 2.69
864 4232 8.181573 TGATGCGTGAGGTTTATTCTAAATTTC 58.818 33.333 0.00 0.00 0.00 2.17
865 4233 8.050778 TGATGCGTGAGGTTTATTCTAAATTT 57.949 30.769 0.00 0.00 0.00 1.82
867 4235 7.624360 TTGATGCGTGAGGTTTATTCTAAAT 57.376 32.000 0.00 0.00 0.00 1.40
868 4236 7.441890 TTTGATGCGTGAGGTTTATTCTAAA 57.558 32.000 0.00 0.00 0.00 1.85
870 4238 7.624360 AATTTGATGCGTGAGGTTTATTCTA 57.376 32.000 0.00 0.00 0.00 2.10
872 4240 8.682128 TTTAATTTGATGCGTGAGGTTTATTC 57.318 30.769 0.00 0.00 0.00 1.75
873 4241 9.482627 TTTTTAATTTGATGCGTGAGGTTTATT 57.517 25.926 0.00 0.00 0.00 1.40
915 4283 2.592287 ACCCGCGCCGAAGAAAAA 60.592 55.556 0.00 0.00 0.00 1.94
916 4284 3.350612 CACCCGCGCCGAAGAAAA 61.351 61.111 0.00 0.00 0.00 2.29
936 4304 2.608970 TTTATGCTCCCCGGCTCAGC 62.609 60.000 9.89 9.89 0.00 4.26
937 4305 0.815615 GTTTATGCTCCCCGGCTCAG 60.816 60.000 0.00 0.00 0.00 3.35
938 4306 1.223487 GTTTATGCTCCCCGGCTCA 59.777 57.895 0.00 0.00 0.00 4.26
939 4307 1.526225 GGTTTATGCTCCCCGGCTC 60.526 63.158 0.00 0.00 0.00 4.70
940 4308 2.595655 GGTTTATGCTCCCCGGCT 59.404 61.111 0.00 0.00 0.00 5.52
941 4309 2.518587 GGGTTTATGCTCCCCGGC 60.519 66.667 0.00 0.00 37.89 6.13
945 4313 2.194868 CCCGGGGTTTATGCTCCC 59.805 66.667 14.71 0.00 42.73 4.30
946 4314 1.153025 GACCCGGGGTTTATGCTCC 60.153 63.158 27.92 0.15 35.25 4.70
947 4315 1.153025 GGACCCGGGGTTTATGCTC 60.153 63.158 27.92 10.44 35.25 4.26
948 4316 3.004090 GGACCCGGGGTTTATGCT 58.996 61.111 27.92 0.00 35.25 3.79
949 4317 2.515290 CGGACCCGGGGTTTATGC 60.515 66.667 27.92 7.57 35.25 3.14
950 4318 1.153309 GTCGGACCCGGGGTTTATG 60.153 63.158 27.92 10.63 35.25 1.90
951 4319 0.984432 ATGTCGGACCCGGGGTTTAT 60.984 55.000 27.92 1.66 35.25 1.40
952 4320 0.325110 TATGTCGGACCCGGGGTTTA 60.325 55.000 27.92 6.06 35.25 2.01
953 4321 0.984432 ATATGTCGGACCCGGGGTTT 60.984 55.000 27.92 2.66 35.25 3.27
954 4322 0.105555 TATATGTCGGACCCGGGGTT 60.106 55.000 27.92 3.65 35.25 4.11
955 4323 0.115745 ATATATGTCGGACCCGGGGT 59.884 55.000 27.92 21.21 39.44 4.95
956 4324 2.148446 TATATATGTCGGACCCGGGG 57.852 55.000 27.92 12.73 40.25 5.73
957 4325 4.467769 AGTATATATATGTCGGACCCGGG 58.532 47.826 22.25 22.25 40.25 5.73
958 4326 5.238868 CAGAGTATATATATGTCGGACCCGG 59.761 48.000 8.73 0.00 40.25 5.73
959 4327 5.821470 ACAGAGTATATATATGTCGGACCCG 59.179 44.000 5.55 1.31 41.35 5.28
960 4328 8.921353 ATACAGAGTATATATATGTCGGACCC 57.079 38.462 5.55 0.00 0.00 4.46
974 4342 9.479549 TGGATGAATGATGCTATACAGAGTATA 57.520 33.333 0.00 0.00 0.00 1.47
975 4343 8.256605 GTGGATGAATGATGCTATACAGAGTAT 58.743 37.037 0.00 0.00 0.00 2.12
976 4344 7.233348 TGTGGATGAATGATGCTATACAGAGTA 59.767 37.037 0.00 0.00 0.00 2.59
977 4345 6.042437 TGTGGATGAATGATGCTATACAGAGT 59.958 38.462 0.00 0.00 0.00 3.24
978 4346 6.461640 TGTGGATGAATGATGCTATACAGAG 58.538 40.000 0.00 0.00 0.00 3.35
979 4347 6.042437 ACTGTGGATGAATGATGCTATACAGA 59.958 38.462 0.00 0.00 36.31 3.41
980 4348 6.228995 ACTGTGGATGAATGATGCTATACAG 58.771 40.000 0.00 0.00 38.15 2.74
981 4349 6.178607 ACTGTGGATGAATGATGCTATACA 57.821 37.500 0.00 0.00 0.00 2.29
982 4350 6.226052 TGACTGTGGATGAATGATGCTATAC 58.774 40.000 0.00 0.00 0.00 1.47
983 4351 6.423776 TGACTGTGGATGAATGATGCTATA 57.576 37.500 0.00 0.00 0.00 1.31
984 4352 5.300411 TGACTGTGGATGAATGATGCTAT 57.700 39.130 0.00 0.00 0.00 2.97
992 4360 3.386078 ACGAGCTATGACTGTGGATGAAT 59.614 43.478 0.00 0.00 0.00 2.57
997 4365 2.017782 GAGACGAGCTATGACTGTGGA 58.982 52.381 0.00 0.00 0.00 4.02
1062 5244 3.304659 GCTAGCTAGCTAGTGCAAGAGAG 60.305 52.174 39.05 21.90 45.67 3.20
1063 5245 2.621055 GCTAGCTAGCTAGTGCAAGAGA 59.379 50.000 39.05 13.72 45.67 3.10
1064 5246 3.011949 GCTAGCTAGCTAGTGCAAGAG 57.988 52.381 39.05 23.14 45.67 2.85
1422 5677 1.828660 CTGGAGTCCCGCGTAGGAT 60.829 63.158 6.74 0.00 45.00 3.24
1504 5759 2.561885 CGAGGACGACAAGAGCGT 59.438 61.111 0.00 0.00 45.79 5.07
1524 5788 2.435938 GCCATCGTTTCCTCCGCA 60.436 61.111 0.00 0.00 0.00 5.69
1605 5875 3.625897 CTGCCGGACACCCAGACA 61.626 66.667 5.05 0.00 0.00 3.41
1659 5929 2.780094 CCTGAGCTGAGACGGCGAT 61.780 63.158 16.62 0.11 41.21 4.58
1724 5994 6.091441 GCAGATATAATCGGTGTCCAGATTTC 59.909 42.308 9.60 4.60 38.04 2.17
1732 6002 7.649705 CCTATACATGCAGATATAATCGGTGTC 59.350 40.741 0.00 0.00 0.00 3.67
1769 6039 4.156922 CCACCTATACATCAACCGCAAAAA 59.843 41.667 0.00 0.00 0.00 1.94
1770 6040 3.692101 CCACCTATACATCAACCGCAAAA 59.308 43.478 0.00 0.00 0.00 2.44
1771 6041 3.055021 TCCACCTATACATCAACCGCAAA 60.055 43.478 0.00 0.00 0.00 3.68
1772 6042 2.502130 TCCACCTATACATCAACCGCAA 59.498 45.455 0.00 0.00 0.00 4.85
1773 6043 2.112190 TCCACCTATACATCAACCGCA 58.888 47.619 0.00 0.00 0.00 5.69
1774 6044 2.902705 TCCACCTATACATCAACCGC 57.097 50.000 0.00 0.00 0.00 5.68
1785 6055 9.350951 GGCAAAGTAGTTTAATAATCCACCTAT 57.649 33.333 0.00 0.00 0.00 2.57
1786 6056 8.330247 TGGCAAAGTAGTTTAATAATCCACCTA 58.670 33.333 0.00 0.00 0.00 3.08
1787 6057 7.179269 TGGCAAAGTAGTTTAATAATCCACCT 58.821 34.615 0.00 0.00 0.00 4.00
1788 6058 7.399245 TGGCAAAGTAGTTTAATAATCCACC 57.601 36.000 0.00 0.00 0.00 4.61
1795 6065 8.875803 CACGACTAATGGCAAAGTAGTTTAATA 58.124 33.333 13.74 0.00 30.40 0.98
1796 6066 7.389607 ACACGACTAATGGCAAAGTAGTTTAAT 59.610 33.333 13.74 2.07 30.40 1.40
1797 6067 6.707161 ACACGACTAATGGCAAAGTAGTTTAA 59.293 34.615 13.74 0.00 30.40 1.52
1798 6068 6.146510 CACACGACTAATGGCAAAGTAGTTTA 59.853 38.462 13.74 0.00 30.40 2.01
1799 6069 5.049680 CACACGACTAATGGCAAAGTAGTTT 60.050 40.000 13.74 7.56 30.40 2.66
1801 6071 3.994392 CACACGACTAATGGCAAAGTAGT 59.006 43.478 11.52 11.52 32.64 2.73
1803 6073 2.739913 GCACACGACTAATGGCAAAGTA 59.260 45.455 5.91 0.00 0.00 2.24
1804 6074 1.535462 GCACACGACTAATGGCAAAGT 59.465 47.619 5.63 5.63 0.00 2.66
1806 6076 1.804151 GAGCACACGACTAATGGCAAA 59.196 47.619 0.00 0.00 0.00 3.68
1808 6078 0.320050 TGAGCACACGACTAATGGCA 59.680 50.000 0.00 0.00 0.00 4.92
1810 6080 5.991328 ATAATTGAGCACACGACTAATGG 57.009 39.130 0.00 0.00 0.00 3.16
1811 6081 7.700322 AGTATAATTGAGCACACGACTAATG 57.300 36.000 0.00 0.00 0.00 1.90
1812 6082 8.630917 ACTAGTATAATTGAGCACACGACTAAT 58.369 33.333 0.00 0.00 0.00 1.73
1840 6143 6.740411 AGTACAAGAACGTAGAGGAAGTAG 57.260 41.667 0.00 0.00 0.00 2.57
1878 6181 7.703621 TCGTCCATCTTTTCCTAATTAACTACG 59.296 37.037 0.00 0.00 0.00 3.51
1879 6182 8.937634 TCGTCCATCTTTTCCTAATTAACTAC 57.062 34.615 0.00 0.00 0.00 2.73
1881 6184 9.543783 GTATCGTCCATCTTTTCCTAATTAACT 57.456 33.333 0.00 0.00 0.00 2.24
1899 6834 0.937304 ATTGCATGCACGTATCGTCC 59.063 50.000 22.58 0.00 38.32 4.79
1925 6860 0.314935 AGAAGGCACGCAACCATTTG 59.685 50.000 0.00 0.00 35.62 2.32
1926 6861 0.598065 GAGAAGGCACGCAACCATTT 59.402 50.000 0.00 0.00 0.00 2.32
2124 7512 2.048444 TGGCATCATCAAGCTTCTCC 57.952 50.000 0.00 0.00 0.00 3.71
2155 7543 3.333029 TCCATGCTCGTTGATCTGAAA 57.667 42.857 0.00 0.00 0.00 2.69
2232 7621 7.681939 TTCTCTTCACACGGCTATTATTTTT 57.318 32.000 0.00 0.00 0.00 1.94
2273 7662 3.405093 CTTCGGGCATGCCTGGCTA 62.405 63.158 38.90 25.05 46.72 3.93
2295 7684 5.242069 TGTGTTTCGATGAAAAAGAAGCA 57.758 34.783 0.00 0.00 33.14 3.91
2304 7693 6.039941 ACTTTATTGGGTTGTGTTTCGATGAA 59.960 34.615 0.00 0.00 0.00 2.57
2350 7739 2.093921 GTGGTGGCTAGGAAGTCTTCTC 60.094 54.545 12.31 3.15 0.00 2.87
2357 7746 0.400213 TTGGTGTGGTGGCTAGGAAG 59.600 55.000 0.00 0.00 0.00 3.46
2385 7774 4.718961 AGCTTTGTGGAGAACATAAGTGT 58.281 39.130 0.00 0.00 38.99 3.55
2394 7787 3.462483 TGACGTTAGCTTTGTGGAGAA 57.538 42.857 0.00 0.00 0.00 2.87
2405 7798 9.533983 CATATCAATATCAATGTTGACGTTAGC 57.466 33.333 4.56 0.00 40.02 3.09
2506 7901 5.465390 GTGGCTTCCAATAACAAAGGAAAAC 59.535 40.000 0.00 0.00 40.63 2.43
2507 7902 5.454045 GGTGGCTTCCAATAACAAAGGAAAA 60.454 40.000 0.00 0.00 40.63 2.29
2538 7933 6.634805 TCTTTCTTTACATCCTGTCAGCTAG 58.365 40.000 0.00 0.00 0.00 3.42
2543 7938 5.221722 ACTGCTCTTTCTTTACATCCTGTCA 60.222 40.000 0.00 0.00 0.00 3.58
2544 7939 5.241662 ACTGCTCTTTCTTTACATCCTGTC 58.758 41.667 0.00 0.00 0.00 3.51
2545 7940 5.234466 ACTGCTCTTTCTTTACATCCTGT 57.766 39.130 0.00 0.00 0.00 4.00
2546 7941 6.876257 AGTTACTGCTCTTTCTTTACATCCTG 59.124 38.462 0.00 0.00 0.00 3.86
2563 7959 7.065803 TCTGCTATTTTTGTGGATAGTTACTGC 59.934 37.037 0.00 0.00 0.00 4.40
2680 8076 7.936496 TGCATATTTTATCAGACCAGTTGAA 57.064 32.000 0.00 0.00 0.00 2.69
2685 8081 8.162878 ACTGATTGCATATTTTATCAGACCAG 57.837 34.615 23.93 5.10 44.19 4.00
2692 8088 7.148171 GGGCCTAGACTGATTGCATATTTTATC 60.148 40.741 0.84 0.00 0.00 1.75
2701 8097 0.975556 TCGGGCCTAGACTGATTGCA 60.976 55.000 0.84 0.00 0.00 4.08
2738 8134 4.338118 TGAGGGACATATGAAATTTTCGGC 59.662 41.667 10.38 0.00 0.00 5.54
2750 8146 1.496060 TCTGGCGTTGAGGGACATAT 58.504 50.000 0.00 0.00 0.00 1.78
2753 8149 1.371183 CTTCTGGCGTTGAGGGACA 59.629 57.895 0.00 0.00 0.00 4.02
2761 8157 1.727467 GTGTGTTGCTTCTGGCGTT 59.273 52.632 0.00 0.00 45.43 4.84
2770 8166 1.302511 CTAAGCCCCGTGTGTTGCT 60.303 57.895 0.00 0.00 35.08 3.91
2781 8177 2.427506 CTTGTGACTTGTCCTAAGCCC 58.572 52.381 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.