Multiple sequence alignment - TraesCS6B01G212200

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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 TraesCS6B01G212200 chr6B 100.000 4004 0 0 1 4004 280347621 280351624 0.000000e+00 7395
1 TraesCS6B01G212200 chr6B 83.632 391 32 16 553 912 280297919 280297530 4.960000e-89 339
2 TraesCS6B01G212200 chr6B 91.518 224 19 0 577 800 309691683 309691460 3.890000e-80 309
3 TraesCS6B01G212200 chr6D 98.165 2180 40 0 935 3114 157435914 157438093 0.000000e+00 3805
4 TraesCS6B01G212200 chr6D 92.889 225 14 2 3116 3338 144895284 144895508 3.860000e-85 326
5 TraesCS6B01G212200 chr6A 98.534 1364 20 0 916 2279 215098523 215097160 0.000000e+00 2409
6 TraesCS6B01G212200 chr6A 94.570 221 12 0 3116 3336 567346309 567346529 3.830000e-90 342
7 TraesCS6B01G212200 chr2A 98.647 665 9 0 3340 4004 399916452 399915788 0.000000e+00 1179
8 TraesCS6B01G212200 chr2A 98.195 665 12 0 3340 4004 397327884 397328548 0.000000e+00 1162
9 TraesCS6B01G212200 chr2A 97.744 665 15 0 3340 4004 397338751 397339415 0.000000e+00 1146
10 TraesCS6B01G212200 chr2A 97.594 665 16 0 3340 4004 399927318 399926654 0.000000e+00 1140
11 TraesCS6B01G212200 chr4B 97.594 665 16 0 3340 4004 517175166 517175830 0.000000e+00 1140
12 TraesCS6B01G212200 chr4B 97.444 665 16 1 3340 4004 517204460 517205123 0.000000e+00 1133
13 TraesCS6B01G212200 chr4B 82.382 823 107 23 1 813 149071985 149072779 0.000000e+00 682
14 TraesCS6B01G212200 chr5B 97.297 666 18 0 3339 4004 282964360 282963695 0.000000e+00 1131
15 TraesCS6B01G212200 chr5B 97.143 665 19 0 3340 4004 275905061 275904397 0.000000e+00 1123
16 TraesCS6B01G212200 chr5B 86.286 824 88 10 1 813 268797832 268798641 0.000000e+00 872
17 TraesCS6B01G212200 chr5B 85.887 744 89 11 1 735 584711443 584712179 0.000000e+00 778
18 TraesCS6B01G212200 chr5B 92.377 223 16 1 3116 3338 479206187 479205966 2.320000e-82 316
19 TraesCS6B01G212200 chr2B 96.997 666 20 0 3339 4004 213052575 213051910 0.000000e+00 1120
20 TraesCS6B01G212200 chr2B 86.275 816 69 12 1 809 206367164 206367943 0.000000e+00 846
21 TraesCS6B01G212200 chr2B 91.064 235 21 0 579 813 206358301 206358067 6.460000e-83 318
22 TraesCS6B01G212200 chr2B 82.320 362 34 17 578 914 36336955 36336599 1.820000e-73 287
23 TraesCS6B01G212200 chr5D 86.788 825 65 17 1 813 236181039 236180247 0.000000e+00 880
24 TraesCS6B01G212200 chr5D 87.912 364 36 5 1 357 44486894 44487256 4.780000e-114 422
25 TraesCS6B01G212200 chr5D 93.304 224 15 0 3116 3339 205119041 205118818 8.290000e-87 331
26 TraesCS6B01G212200 chrUn 84.480 567 76 9 175 735 280092871 280092311 2.100000e-152 549
27 TraesCS6B01G212200 chrUn 90.331 362 31 3 175 536 339031290 339031647 4.680000e-129 472
28 TraesCS6B01G212200 chrUn 85.333 225 28 5 592 813 22359944 22359722 1.120000e-55 228
29 TraesCS6B01G212200 chrUn 93.750 128 8 0 1 128 280092999 280092872 4.080000e-45 193
30 TraesCS6B01G212200 chrUn 93.750 128 8 0 1 128 339031162 339031289 4.080000e-45 193
31 TraesCS6B01G212200 chr3B 84.211 570 72 13 175 735 740133180 740133740 4.550000e-149 538
32 TraesCS6B01G212200 chr3B 93.213 221 13 2 3120 3339 34646742 34646523 1.390000e-84 324
33 TraesCS6B01G212200 chr3B 93.750 128 8 0 1 128 740133052 740133179 4.080000e-45 193
34 TraesCS6B01G212200 chr2D 86.646 322 34 5 1 313 139781910 139782231 8.240000e-92 348
35 TraesCS6B01G212200 chr5A 94.196 224 13 0 3116 3339 244758779 244758556 3.830000e-90 342
36 TraesCS6B01G212200 chr5A 83.740 369 26 19 577 913 2313341 2313707 6.460000e-83 318
37 TraesCS6B01G212200 chr1D 93.750 224 14 0 3116 3339 326223603 326223826 1.780000e-88 337
38 TraesCS6B01G212200 chr1D 91.964 224 18 0 3116 3339 479598648 479598871 8.350000e-82 315
39 TraesCS6B01G212200 chr1D 85.778 225 27 5 592 813 1826926 1827148 2.410000e-57 233
40 TraesCS6B01G212200 chr1A 92.035 226 14 3 3116 3339 290153208 290152985 8.350000e-82 315


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 TraesCS6B01G212200 chr6B 280347621 280351624 4003 False 7395.0 7395 100.0000 1 4004 1 chr6B.!!$F1 4003
1 TraesCS6B01G212200 chr6D 157435914 157438093 2179 False 3805.0 3805 98.1650 935 3114 1 chr6D.!!$F2 2179
2 TraesCS6B01G212200 chr6A 215097160 215098523 1363 True 2409.0 2409 98.5340 916 2279 1 chr6A.!!$R1 1363
3 TraesCS6B01G212200 chr2A 399915788 399916452 664 True 1179.0 1179 98.6470 3340 4004 1 chr2A.!!$R1 664
4 TraesCS6B01G212200 chr2A 397327884 397328548 664 False 1162.0 1162 98.1950 3340 4004 1 chr2A.!!$F1 664
5 TraesCS6B01G212200 chr2A 397338751 397339415 664 False 1146.0 1146 97.7440 3340 4004 1 chr2A.!!$F2 664
6 TraesCS6B01G212200 chr2A 399926654 399927318 664 True 1140.0 1140 97.5940 3340 4004 1 chr2A.!!$R2 664
7 TraesCS6B01G212200 chr4B 517175166 517175830 664 False 1140.0 1140 97.5940 3340 4004 1 chr4B.!!$F2 664
8 TraesCS6B01G212200 chr4B 517204460 517205123 663 False 1133.0 1133 97.4440 3340 4004 1 chr4B.!!$F3 664
9 TraesCS6B01G212200 chr4B 149071985 149072779 794 False 682.0 682 82.3820 1 813 1 chr4B.!!$F1 812
10 TraesCS6B01G212200 chr5B 282963695 282964360 665 True 1131.0 1131 97.2970 3339 4004 1 chr5B.!!$R2 665
11 TraesCS6B01G212200 chr5B 275904397 275905061 664 True 1123.0 1123 97.1430 3340 4004 1 chr5B.!!$R1 664
12 TraesCS6B01G212200 chr5B 268797832 268798641 809 False 872.0 872 86.2860 1 813 1 chr5B.!!$F1 812
13 TraesCS6B01G212200 chr5B 584711443 584712179 736 False 778.0 778 85.8870 1 735 1 chr5B.!!$F2 734
14 TraesCS6B01G212200 chr2B 213051910 213052575 665 True 1120.0 1120 96.9970 3339 4004 1 chr2B.!!$R3 665
15 TraesCS6B01G212200 chr2B 206367164 206367943 779 False 846.0 846 86.2750 1 809 1 chr2B.!!$F1 808
16 TraesCS6B01G212200 chr5D 236180247 236181039 792 True 880.0 880 86.7880 1 813 1 chr5D.!!$R2 812
17 TraesCS6B01G212200 chrUn 280092311 280092999 688 True 371.0 549 89.1150 1 735 2 chrUn.!!$R2 734
18 TraesCS6B01G212200 chr3B 740133052 740133740 688 False 365.5 538 88.9805 1 735 2 chr3B.!!$F1 734

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
901 943 0.036577 CAGTGGGCAGAGGTCTCTTG 60.037 60.0 0.0 0.0 37.98 3.02 F
903 945 0.036858 GTGGGCAGAGGTCTCTTGAC 60.037 60.0 0.0 0.0 37.98 3.18 F
2391 2433 0.321298 CTGGTTACGGAAGGTGTGGG 60.321 60.0 0.0 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2379 2421 0.821711 TGCTTTTCCCACACCTTCCG 60.822 55.000 0.0 0.0 0.00 4.30 R
2787 2829 1.800586 CCCCATCGATATTGTTCAGCG 59.199 52.381 0.0 0.0 0.00 5.18 R
3318 3360 0.032615 TGGGGCATCCGGCTTTAAAT 60.033 50.000 0.0 0.0 44.01 1.40 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
144 152 4.077822 CAGAGAAGGCAACCAGAGATTTT 58.922 43.478 0.00 0.00 37.17 1.82
145 153 5.248640 CAGAGAAGGCAACCAGAGATTTTA 58.751 41.667 0.00 0.00 37.17 1.52
199 210 6.759827 GGTTGTGCGTATAAATAGAAGAGGAA 59.240 38.462 0.00 0.00 0.00 3.36
201 212 5.975344 TGTGCGTATAAATAGAAGAGGAACG 59.025 40.000 0.00 0.00 0.00 3.95
212 223 5.209818 AGAAGAGGAACGTTGTATTGTCA 57.790 39.130 5.00 0.00 0.00 3.58
277 288 1.036707 TCGTGGTGTCTCATCACACA 58.963 50.000 12.53 0.00 44.82 3.72
287 298 3.251729 GTCTCATCACACACAGCAACATT 59.748 43.478 0.00 0.00 0.00 2.71
292 303 5.472820 TCATCACACACAGCAACATTAATGA 59.527 36.000 22.16 0.00 0.00 2.57
304 315 5.336690 GCAACATTAATGATCTTGGGTGTGT 60.337 40.000 22.16 0.00 0.00 3.72
358 369 1.519455 GTGCTGTCGCTTCGGCTAT 60.519 57.895 9.53 0.00 40.06 2.97
388 399 1.743623 CAAATCACGCGGGTAGGCA 60.744 57.895 8.89 0.00 0.00 4.75
398 409 1.472662 CGGGTAGGCAGGAATCCGAT 61.473 60.000 0.00 0.00 39.83 4.18
447 461 2.817901 AGCAAAAGAAAGCAGCAACTG 58.182 42.857 0.00 0.00 34.12 3.16
515 529 4.496895 GCAACTTTCAAATCATCGGAATCG 59.503 41.667 0.00 0.00 37.82 3.34
536 551 2.483188 GGCGGAGTTTGTATCGGAATCT 60.483 50.000 0.00 0.00 0.00 2.40
667 709 2.284625 TCGGCCAGGGACAGACAT 60.285 61.111 2.24 0.00 0.00 3.06
740 782 4.671590 TCCGTCCCAGCGAGGTGA 62.672 66.667 3.61 0.00 34.66 4.02
745 787 1.533033 TCCCAGCGAGGTGAACTGA 60.533 57.895 3.61 0.00 33.10 3.41
749 791 1.373497 AGCGAGGTGAACTGAAGCG 60.373 57.895 0.00 0.00 0.00 4.68
818 860 4.803426 CCTCTCGGCGTGACCTGC 62.803 72.222 6.85 0.00 35.61 4.85
847 889 1.604604 CGAGAGGGTTCTTTTTGGCA 58.395 50.000 0.00 0.00 32.53 4.92
848 890 2.162681 CGAGAGGGTTCTTTTTGGCAT 58.837 47.619 0.00 0.00 32.53 4.40
849 891 2.558359 CGAGAGGGTTCTTTTTGGCATT 59.442 45.455 0.00 0.00 32.53 3.56
850 892 3.005791 CGAGAGGGTTCTTTTTGGCATTT 59.994 43.478 0.00 0.00 32.53 2.32
851 893 4.501400 CGAGAGGGTTCTTTTTGGCATTTT 60.501 41.667 0.00 0.00 32.53 1.82
852 894 4.960938 AGAGGGTTCTTTTTGGCATTTTC 58.039 39.130 0.00 0.00 0.00 2.29
853 895 3.727726 AGGGTTCTTTTTGGCATTTTCG 58.272 40.909 0.00 0.00 0.00 3.46
854 896 3.133901 AGGGTTCTTTTTGGCATTTTCGT 59.866 39.130 0.00 0.00 0.00 3.85
855 897 3.493129 GGGTTCTTTTTGGCATTTTCGTC 59.507 43.478 0.00 0.00 0.00 4.20
856 898 3.493129 GGTTCTTTTTGGCATTTTCGTCC 59.507 43.478 0.00 0.00 0.00 4.79
857 899 3.006659 TCTTTTTGGCATTTTCGTCCG 57.993 42.857 0.00 0.00 0.00 4.79
858 900 2.619177 TCTTTTTGGCATTTTCGTCCGA 59.381 40.909 0.00 0.00 0.00 4.55
859 901 3.066900 TCTTTTTGGCATTTTCGTCCGAA 59.933 39.130 0.00 0.00 0.00 4.30
860 902 2.697431 TTTGGCATTTTCGTCCGAAG 57.303 45.000 2.12 0.00 35.38 3.79
873 915 4.843624 CGAAGGGGGCCTTTTTCT 57.156 55.556 0.84 0.00 44.82 2.52
874 916 2.267045 CGAAGGGGGCCTTTTTCTG 58.733 57.895 0.84 0.00 44.82 3.02
875 917 1.250840 CGAAGGGGGCCTTTTTCTGG 61.251 60.000 0.84 0.00 44.82 3.86
876 918 1.536418 AAGGGGGCCTTTTTCTGGC 60.536 57.895 0.84 0.00 41.69 4.85
890 932 2.525075 TGGCAATTCCAGTGGGCA 59.475 55.556 9.92 0.00 40.72 5.36
891 933 1.607178 TGGCAATTCCAGTGGGCAG 60.607 57.895 9.92 0.00 40.72 4.85
892 934 1.304381 GGCAATTCCAGTGGGCAGA 60.304 57.895 9.92 0.00 34.01 4.26
893 935 1.318158 GGCAATTCCAGTGGGCAGAG 61.318 60.000 9.92 0.00 34.01 3.35
894 936 1.318158 GCAATTCCAGTGGGCAGAGG 61.318 60.000 9.92 0.00 0.00 3.69
895 937 0.038744 CAATTCCAGTGGGCAGAGGT 59.961 55.000 9.92 0.00 0.00 3.85
896 938 0.329596 AATTCCAGTGGGCAGAGGTC 59.670 55.000 9.92 0.00 0.00 3.85
897 939 0.548682 ATTCCAGTGGGCAGAGGTCT 60.549 55.000 9.92 0.00 0.00 3.85
898 940 1.194781 TTCCAGTGGGCAGAGGTCTC 61.195 60.000 9.92 0.00 0.00 3.36
899 941 1.611851 CCAGTGGGCAGAGGTCTCT 60.612 63.158 0.00 0.00 41.37 3.10
900 942 1.197430 CCAGTGGGCAGAGGTCTCTT 61.197 60.000 0.00 0.00 37.98 2.85
901 943 0.036577 CAGTGGGCAGAGGTCTCTTG 60.037 60.000 0.00 0.00 37.98 3.02
902 944 0.178921 AGTGGGCAGAGGTCTCTTGA 60.179 55.000 0.00 0.00 37.98 3.02
903 945 0.036858 GTGGGCAGAGGTCTCTTGAC 60.037 60.000 0.00 0.00 37.98 3.18
904 946 0.471780 TGGGCAGAGGTCTCTTGACA 60.472 55.000 0.00 0.00 44.61 3.58
905 947 0.687354 GGGCAGAGGTCTCTTGACAA 59.313 55.000 0.00 0.00 44.61 3.18
906 948 1.072331 GGGCAGAGGTCTCTTGACAAA 59.928 52.381 0.00 0.00 44.61 2.83
907 949 2.487265 GGGCAGAGGTCTCTTGACAAAA 60.487 50.000 0.00 0.00 44.61 2.44
908 950 3.214328 GGCAGAGGTCTCTTGACAAAAA 58.786 45.455 0.00 0.00 44.61 1.94
1019 1061 0.333993 ATGGTTGGCAAGCTCTCCAT 59.666 50.000 27.44 19.60 31.54 3.41
1062 1104 1.202188 CGACTCTGCAAGCTCGTATCA 60.202 52.381 0.00 0.00 0.00 2.15
1308 1350 1.210155 GGCATGCAAGGTGTTCGAC 59.790 57.895 21.36 0.00 0.00 4.20
1441 1483 1.367471 CTGCCGGACTCTGTCACAA 59.633 57.895 5.05 0.00 33.68 3.33
1545 1587 2.212652 GATCGCTATGTTGCCACATCA 58.787 47.619 6.70 0.00 43.06 3.07
1734 1776 3.127030 CCAGCGAAAAACCTAATGAGACC 59.873 47.826 0.00 0.00 0.00 3.85
1775 1817 1.157870 GCGTGCACTAGTGTGTTGGT 61.158 55.000 23.44 0.00 45.44 3.67
1779 1821 1.269883 TGCACTAGTGTGTTGGTACCG 60.270 52.381 23.44 0.00 45.44 4.02
1876 1918 8.077991 CACTCATTGACATGTACTCAAAATGTT 58.922 33.333 0.00 0.00 34.74 2.71
2379 2421 5.807011 GTGGAATGCAATGATTTCTGGTTAC 59.193 40.000 0.00 0.00 0.00 2.50
2391 2433 0.321298 CTGGTTACGGAAGGTGTGGG 60.321 60.000 0.00 0.00 0.00 4.61
2652 2694 4.908601 ACTGAAACATACTGATCCACCA 57.091 40.909 0.00 0.00 0.00 4.17
2702 2744 6.036191 GGTGCTTGTAGAAACTACTCTAATGC 59.964 42.308 9.73 4.90 29.74 3.56
2703 2745 6.036191 GTGCTTGTAGAAACTACTCTAATGCC 59.964 42.308 9.73 0.00 29.74 4.40
2713 2755 2.699954 ACTCTAATGCCGAACTTGGTG 58.300 47.619 0.00 0.00 0.00 4.17
2787 2829 9.396022 CCATGGGTAATTCTATCCAACATATAC 57.604 37.037 2.85 0.00 41.82 1.47
2867 2909 2.033328 CTCATCAAAGCTCCTGCGCG 62.033 60.000 0.00 0.00 45.42 6.86
2983 3025 5.346822 CAGCCATCTTGTCATAACAAAAAGC 59.653 40.000 0.00 0.00 44.53 3.51
3037 3079 2.244510 TCATGTCCATATGCACCCCTTT 59.755 45.455 0.00 0.00 0.00 3.11
3075 3117 6.612247 TTAGACATTTTCAGAAGTTCGCAA 57.388 33.333 0.00 0.00 0.00 4.85
3114 3156 7.387397 ACCACAAAATGTTAATTTAGGCACATG 59.613 33.333 0.00 0.00 34.84 3.21
3115 3157 7.601886 CCACAAAATGTTAATTTAGGCACATGA 59.398 33.333 0.00 0.00 34.84 3.07
3116 3158 8.986847 CACAAAATGTTAATTTAGGCACATGAA 58.013 29.630 0.00 0.00 34.84 2.57
3117 3159 9.553064 ACAAAATGTTAATTTAGGCACATGAAA 57.447 25.926 0.00 0.00 34.84 2.69
3119 3161 8.776376 AAATGTTAATTTAGGCACATGAAAGG 57.224 30.769 0.00 0.00 34.14 3.11
3120 3162 7.716799 ATGTTAATTTAGGCACATGAAAGGA 57.283 32.000 0.00 0.00 0.00 3.36
3121 3163 7.156876 TGTTAATTTAGGCACATGAAAGGAG 57.843 36.000 0.00 0.00 0.00 3.69
3122 3164 6.152661 TGTTAATTTAGGCACATGAAAGGAGG 59.847 38.462 0.00 0.00 0.00 4.30
3123 3165 4.591321 ATTTAGGCACATGAAAGGAGGA 57.409 40.909 0.00 0.00 0.00 3.71
3124 3166 4.591321 TTTAGGCACATGAAAGGAGGAT 57.409 40.909 0.00 0.00 0.00 3.24
3125 3167 5.708736 TTTAGGCACATGAAAGGAGGATA 57.291 39.130 0.00 0.00 0.00 2.59
3126 3168 5.912149 TTAGGCACATGAAAGGAGGATAT 57.088 39.130 0.00 0.00 0.00 1.63
3127 3169 7.387265 TTTAGGCACATGAAAGGAGGATATA 57.613 36.000 0.00 0.00 0.00 0.86
3128 3170 5.234466 AGGCACATGAAAGGAGGATATAC 57.766 43.478 0.00 0.00 0.00 1.47
3129 3171 4.042187 AGGCACATGAAAGGAGGATATACC 59.958 45.833 0.00 0.00 39.35 2.73
3130 3172 4.327680 GCACATGAAAGGAGGATATACCC 58.672 47.826 0.00 0.00 40.05 3.69
3131 3173 4.807643 GCACATGAAAGGAGGATATACCCC 60.808 50.000 0.00 0.00 40.05 4.95
3132 3174 3.916989 ACATGAAAGGAGGATATACCCCC 59.083 47.826 0.00 0.00 40.05 5.40
3133 3175 2.616524 TGAAAGGAGGATATACCCCCG 58.383 52.381 0.00 0.00 40.05 5.73
3134 3176 1.907255 GAAAGGAGGATATACCCCCGG 59.093 57.143 0.00 0.00 40.05 5.73
3135 3177 0.546988 AAGGAGGATATACCCCCGGC 60.547 60.000 0.00 0.00 40.05 6.13
3136 3178 1.993948 GGAGGATATACCCCCGGCC 60.994 68.421 0.00 0.00 40.05 6.13
3137 3179 1.080538 GAGGATATACCCCCGGCCT 59.919 63.158 0.00 0.00 40.05 5.19
3138 3180 0.976590 GAGGATATACCCCCGGCCTC 60.977 65.000 0.00 0.00 40.05 4.70
3139 3181 1.080538 GGATATACCCCCGGCCTCT 59.919 63.158 0.00 0.00 0.00 3.69
3140 3182 1.265454 GGATATACCCCCGGCCTCTG 61.265 65.000 0.00 0.00 0.00 3.35
3141 3183 1.900545 GATATACCCCCGGCCTCTGC 61.901 65.000 0.00 0.00 0.00 4.26
3142 3184 2.689573 ATATACCCCCGGCCTCTGCA 62.690 60.000 0.00 0.00 40.13 4.41
3143 3185 2.689573 TATACCCCCGGCCTCTGCAT 62.690 60.000 0.00 0.00 40.13 3.96
3146 3188 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
3147 3189 4.559063 CCCGGCCTCTGCATCTGG 62.559 72.222 0.00 0.00 40.13 3.86
3148 3190 4.559063 CCGGCCTCTGCATCTGGG 62.559 72.222 0.00 0.00 40.13 4.45
3151 3193 4.166888 GCCTCTGCATCTGGGCGA 62.167 66.667 0.00 0.00 37.47 5.54
3152 3194 2.827423 CCTCTGCATCTGGGCGAT 59.173 61.111 0.00 0.00 36.28 4.58
3158 3200 2.643272 CATCTGGGCGATGCATGC 59.357 61.111 11.82 11.82 42.75 4.06
3159 3201 2.190841 CATCTGGGCGATGCATGCA 61.191 57.895 25.04 25.04 42.75 3.96
3160 3202 1.897137 ATCTGGGCGATGCATGCAG 60.897 57.895 26.69 14.50 0.00 4.41
3161 3203 4.266070 CTGGGCGATGCATGCAGC 62.266 66.667 25.69 25.69 45.96 5.25
3165 3207 2.415843 GCGATGCATGCAGCCATT 59.584 55.556 28.76 10.64 44.83 3.16
3166 3208 1.227147 GCGATGCATGCAGCCATTT 60.227 52.632 28.76 9.83 44.83 2.32
3167 3209 0.808453 GCGATGCATGCAGCCATTTT 60.808 50.000 28.76 9.02 44.83 1.82
3168 3210 1.536496 GCGATGCATGCAGCCATTTTA 60.536 47.619 28.76 0.09 44.83 1.52
3169 3211 2.864882 GCGATGCATGCAGCCATTTTAT 60.865 45.455 28.76 7.39 44.83 1.40
3170 3212 3.386486 CGATGCATGCAGCCATTTTATT 58.614 40.909 28.76 6.59 44.83 1.40
3171 3213 4.548494 CGATGCATGCAGCCATTTTATTA 58.452 39.130 28.76 0.00 44.83 0.98
3172 3214 4.983538 CGATGCATGCAGCCATTTTATTAA 59.016 37.500 28.76 0.00 44.83 1.40
3173 3215 5.636121 CGATGCATGCAGCCATTTTATTAAT 59.364 36.000 28.76 5.31 44.83 1.40
3174 3216 6.146510 CGATGCATGCAGCCATTTTATTAATT 59.853 34.615 28.76 4.60 44.83 1.40
3175 3217 7.328982 CGATGCATGCAGCCATTTTATTAATTA 59.671 33.333 28.76 0.00 44.83 1.40
3176 3218 9.158233 GATGCATGCAGCCATTTTATTAATTAT 57.842 29.630 25.21 0.54 44.83 1.28
3177 3219 8.905660 TGCATGCAGCCATTTTATTAATTATT 57.094 26.923 18.46 0.00 44.83 1.40
3178 3220 8.991026 TGCATGCAGCCATTTTATTAATTATTC 58.009 29.630 18.46 0.00 44.83 1.75
3179 3221 8.991026 GCATGCAGCCATTTTATTAATTATTCA 58.009 29.630 14.21 0.00 37.23 2.57
3181 3223 8.572828 TGCAGCCATTTTATTAATTATTCACG 57.427 30.769 0.00 0.00 0.00 4.35
3182 3224 8.409371 TGCAGCCATTTTATTAATTATTCACGA 58.591 29.630 0.00 0.00 0.00 4.35
3183 3225 9.243637 GCAGCCATTTTATTAATTATTCACGAA 57.756 29.630 0.00 0.00 0.00 3.85
3202 3244 9.491675 TTCACGAAGACCTTACAAAATAATACA 57.508 29.630 0.00 0.00 0.00 2.29
3203 3245 9.661563 TCACGAAGACCTTACAAAATAATACAT 57.338 29.630 0.00 0.00 0.00 2.29
3204 3246 9.916397 CACGAAGACCTTACAAAATAATACATC 57.084 33.333 0.00 0.00 0.00 3.06
3205 3247 9.661563 ACGAAGACCTTACAAAATAATACATCA 57.338 29.630 0.00 0.00 0.00 3.07
3222 3264 2.859992 CAGTAAGCCTGAAGCCACC 58.140 57.895 0.00 0.00 44.49 4.61
3223 3265 0.036732 CAGTAAGCCTGAAGCCACCA 59.963 55.000 0.00 0.00 44.49 4.17
3224 3266 0.995024 AGTAAGCCTGAAGCCACCAT 59.005 50.000 0.00 0.00 45.47 3.55
3225 3267 1.065126 AGTAAGCCTGAAGCCACCATC 60.065 52.381 0.00 0.00 45.47 3.51
3226 3268 1.065126 GTAAGCCTGAAGCCACCATCT 60.065 52.381 0.00 0.00 45.47 2.90
3227 3269 0.407139 AAGCCTGAAGCCACCATCTT 59.593 50.000 0.00 0.00 45.47 2.40
3228 3270 0.323178 AGCCTGAAGCCACCATCTTG 60.323 55.000 0.00 0.00 45.47 3.02
3229 3271 1.318158 GCCTGAAGCCACCATCTTGG 61.318 60.000 0.00 0.00 38.59 3.61
3244 3286 3.143338 TGGCAACACCTGTCGCTA 58.857 55.556 0.00 0.00 46.17 4.26
3245 3287 1.301401 TGGCAACACCTGTCGCTAC 60.301 57.895 0.00 0.00 46.17 3.58
3246 3288 1.004918 GGCAACACCTGTCGCTACT 60.005 57.895 0.00 0.00 34.51 2.57
3247 3289 1.014564 GGCAACACCTGTCGCTACTC 61.015 60.000 0.00 0.00 34.51 2.59
3248 3290 1.014564 GCAACACCTGTCGCTACTCC 61.015 60.000 0.00 0.00 0.00 3.85
3249 3291 0.603569 CAACACCTGTCGCTACTCCT 59.396 55.000 0.00 0.00 0.00 3.69
3250 3292 1.816835 CAACACCTGTCGCTACTCCTA 59.183 52.381 0.00 0.00 0.00 2.94
3251 3293 2.427453 CAACACCTGTCGCTACTCCTAT 59.573 50.000 0.00 0.00 0.00 2.57
3252 3294 2.299521 ACACCTGTCGCTACTCCTATC 58.700 52.381 0.00 0.00 0.00 2.08
3253 3295 1.609555 CACCTGTCGCTACTCCTATCC 59.390 57.143 0.00 0.00 0.00 2.59
3254 3296 1.495574 ACCTGTCGCTACTCCTATCCT 59.504 52.381 0.00 0.00 0.00 3.24
3255 3297 2.156098 CCTGTCGCTACTCCTATCCTC 58.844 57.143 0.00 0.00 0.00 3.71
3256 3298 2.224670 CCTGTCGCTACTCCTATCCTCT 60.225 54.545 0.00 0.00 0.00 3.69
3257 3299 3.482436 CTGTCGCTACTCCTATCCTCTT 58.518 50.000 0.00 0.00 0.00 2.85
3258 3300 3.215151 TGTCGCTACTCCTATCCTCTTG 58.785 50.000 0.00 0.00 0.00 3.02
3259 3301 3.118000 TGTCGCTACTCCTATCCTCTTGA 60.118 47.826 0.00 0.00 0.00 3.02
3260 3302 4.076394 GTCGCTACTCCTATCCTCTTGAT 58.924 47.826 0.00 0.00 37.49 2.57
3261 3303 4.075682 TCGCTACTCCTATCCTCTTGATG 58.924 47.826 0.00 0.00 34.76 3.07
3262 3304 4.075682 CGCTACTCCTATCCTCTTGATGA 58.924 47.826 0.00 0.00 34.76 2.92
3263 3305 4.520874 CGCTACTCCTATCCTCTTGATGAA 59.479 45.833 0.00 0.00 34.76 2.57
3264 3306 5.335583 CGCTACTCCTATCCTCTTGATGAAG 60.336 48.000 0.00 0.00 34.76 3.02
3265 3307 5.047377 GCTACTCCTATCCTCTTGATGAAGG 60.047 48.000 0.00 0.00 34.76 3.46
3266 3308 4.230455 ACTCCTATCCTCTTGATGAAGGG 58.770 47.826 0.00 0.00 32.19 3.95
3270 3312 3.181526 CCTCTTGATGAAGGGGTGC 57.818 57.895 2.02 0.00 44.18 5.01
3271 3313 0.394899 CCTCTTGATGAAGGGGTGCC 60.395 60.000 2.02 0.00 44.18 5.01
3272 3314 0.745845 CTCTTGATGAAGGGGTGCCG 60.746 60.000 0.00 0.00 0.00 5.69
3273 3315 1.198094 TCTTGATGAAGGGGTGCCGA 61.198 55.000 0.00 0.00 0.00 5.54
3274 3316 0.322456 CTTGATGAAGGGGTGCCGAA 60.322 55.000 0.00 0.00 0.00 4.30
3275 3317 0.331278 TTGATGAAGGGGTGCCGAAT 59.669 50.000 0.00 0.00 0.00 3.34
3276 3318 0.394216 TGATGAAGGGGTGCCGAATG 60.394 55.000 0.00 0.00 0.00 2.67
3277 3319 0.394352 GATGAAGGGGTGCCGAATGT 60.394 55.000 0.00 0.00 0.00 2.71
3278 3320 0.394352 ATGAAGGGGTGCCGAATGTC 60.394 55.000 0.00 0.00 0.00 3.06
3279 3321 1.299976 GAAGGGGTGCCGAATGTCT 59.700 57.895 0.00 0.00 0.00 3.41
3280 3322 1.002134 AAGGGGTGCCGAATGTCTG 60.002 57.895 0.00 0.00 0.00 3.51
3281 3323 1.488705 AAGGGGTGCCGAATGTCTGA 61.489 55.000 0.00 0.00 0.00 3.27
3282 3324 1.450312 GGGGTGCCGAATGTCTGAG 60.450 63.158 0.00 0.00 0.00 3.35
3283 3325 2.109126 GGGTGCCGAATGTCTGAGC 61.109 63.158 0.00 0.00 0.00 4.26
3284 3326 1.078848 GGTGCCGAATGTCTGAGCT 60.079 57.895 0.00 0.00 0.00 4.09
3285 3327 1.364626 GGTGCCGAATGTCTGAGCTG 61.365 60.000 0.00 0.00 0.00 4.24
3286 3328 0.390340 GTGCCGAATGTCTGAGCTGA 60.390 55.000 0.00 0.00 0.00 4.26
3287 3329 0.321346 TGCCGAATGTCTGAGCTGAA 59.679 50.000 0.00 0.00 0.00 3.02
3288 3330 1.065926 TGCCGAATGTCTGAGCTGAAT 60.066 47.619 0.00 0.00 0.00 2.57
3289 3331 2.168313 TGCCGAATGTCTGAGCTGAATA 59.832 45.455 0.00 0.00 0.00 1.75
3290 3332 2.541762 GCCGAATGTCTGAGCTGAATAC 59.458 50.000 0.00 0.00 0.00 1.89
3291 3333 3.126831 CCGAATGTCTGAGCTGAATACC 58.873 50.000 0.00 0.00 0.00 2.73
3292 3334 3.430790 CCGAATGTCTGAGCTGAATACCA 60.431 47.826 0.00 0.00 0.00 3.25
3293 3335 4.183865 CGAATGTCTGAGCTGAATACCAA 58.816 43.478 0.00 0.00 0.00 3.67
3294 3336 4.631377 CGAATGTCTGAGCTGAATACCAAA 59.369 41.667 0.00 0.00 0.00 3.28
3295 3337 5.446473 CGAATGTCTGAGCTGAATACCAAAC 60.446 44.000 0.00 0.00 0.00 2.93
3296 3338 4.350368 TGTCTGAGCTGAATACCAAACA 57.650 40.909 0.00 0.00 0.00 2.83
3297 3339 4.318332 TGTCTGAGCTGAATACCAAACAG 58.682 43.478 0.00 0.00 35.14 3.16
3298 3340 4.040339 TGTCTGAGCTGAATACCAAACAGA 59.960 41.667 0.00 0.00 34.07 3.41
3299 3341 4.390297 GTCTGAGCTGAATACCAAACAGAC 59.610 45.833 0.00 0.00 39.48 3.51
3300 3342 4.040339 TCTGAGCTGAATACCAAACAGACA 59.960 41.667 0.00 0.00 34.07 3.41
3301 3343 4.910195 TGAGCTGAATACCAAACAGACAT 58.090 39.130 0.00 0.00 34.07 3.06
3302 3344 4.937620 TGAGCTGAATACCAAACAGACATC 59.062 41.667 0.00 0.00 34.07 3.06
3303 3345 4.910195 AGCTGAATACCAAACAGACATCA 58.090 39.130 0.00 0.00 34.07 3.07
3304 3346 4.697352 AGCTGAATACCAAACAGACATCAC 59.303 41.667 0.00 0.00 34.07 3.06
3305 3347 4.455533 GCTGAATACCAAACAGACATCACA 59.544 41.667 0.00 0.00 34.07 3.58
3306 3348 5.617751 GCTGAATACCAAACAGACATCACAC 60.618 44.000 0.00 0.00 34.07 3.82
3307 3349 4.759693 TGAATACCAAACAGACATCACACC 59.240 41.667 0.00 0.00 0.00 4.16
3308 3350 2.727123 ACCAAACAGACATCACACCA 57.273 45.000 0.00 0.00 0.00 4.17
3309 3351 3.011566 ACCAAACAGACATCACACCAA 57.988 42.857 0.00 0.00 0.00 3.67
3310 3352 3.360867 ACCAAACAGACATCACACCAAA 58.639 40.909 0.00 0.00 0.00 3.28
3311 3353 3.381272 ACCAAACAGACATCACACCAAAG 59.619 43.478 0.00 0.00 0.00 2.77
3312 3354 3.374745 CAAACAGACATCACACCAAAGC 58.625 45.455 0.00 0.00 0.00 3.51
3313 3355 1.609208 ACAGACATCACACCAAAGCC 58.391 50.000 0.00 0.00 0.00 4.35
3314 3356 1.143684 ACAGACATCACACCAAAGCCT 59.856 47.619 0.00 0.00 0.00 4.58
3315 3357 2.371841 ACAGACATCACACCAAAGCCTA 59.628 45.455 0.00 0.00 0.00 3.93
3316 3358 3.181445 ACAGACATCACACCAAAGCCTAA 60.181 43.478 0.00 0.00 0.00 2.69
3317 3359 3.189287 CAGACATCACACCAAAGCCTAAC 59.811 47.826 0.00 0.00 0.00 2.34
3318 3360 3.146066 GACATCACACCAAAGCCTAACA 58.854 45.455 0.00 0.00 0.00 2.41
3319 3361 3.758554 GACATCACACCAAAGCCTAACAT 59.241 43.478 0.00 0.00 0.00 2.71
3320 3362 4.151883 ACATCACACCAAAGCCTAACATT 58.848 39.130 0.00 0.00 0.00 2.71
3321 3363 4.588528 ACATCACACCAAAGCCTAACATTT 59.411 37.500 0.00 0.00 0.00 2.32
3322 3364 5.772672 ACATCACACCAAAGCCTAACATTTA 59.227 36.000 0.00 0.00 0.00 1.40
3323 3365 6.266558 ACATCACACCAAAGCCTAACATTTAA 59.733 34.615 0.00 0.00 0.00 1.52
3324 3366 6.716934 TCACACCAAAGCCTAACATTTAAA 57.283 33.333 0.00 0.00 0.00 1.52
3325 3367 6.744112 TCACACCAAAGCCTAACATTTAAAG 58.256 36.000 0.00 0.00 0.00 1.85
3326 3368 5.405269 CACACCAAAGCCTAACATTTAAAGC 59.595 40.000 0.00 0.00 0.00 3.51
3327 3369 4.929211 CACCAAAGCCTAACATTTAAAGCC 59.071 41.667 0.00 0.00 0.00 4.35
3328 3370 4.173256 CCAAAGCCTAACATTTAAAGCCG 58.827 43.478 0.00 0.00 0.00 5.52
3329 3371 4.173256 CAAAGCCTAACATTTAAAGCCGG 58.827 43.478 0.00 0.00 0.00 6.13
3330 3372 3.359695 AGCCTAACATTTAAAGCCGGA 57.640 42.857 5.05 0.00 0.00 5.14
3331 3373 3.898482 AGCCTAACATTTAAAGCCGGAT 58.102 40.909 5.05 0.00 0.00 4.18
3332 3374 3.632145 AGCCTAACATTTAAAGCCGGATG 59.368 43.478 5.05 0.22 0.00 3.51
3333 3375 3.795488 GCCTAACATTTAAAGCCGGATGC 60.795 47.826 5.05 0.00 41.71 3.91
3334 3376 2.959507 AACATTTAAAGCCGGATGCC 57.040 45.000 5.05 0.00 42.71 4.40
3335 3377 1.111277 ACATTTAAAGCCGGATGCCC 58.889 50.000 5.05 0.00 42.71 5.36
3336 3378 0.389025 CATTTAAAGCCGGATGCCCC 59.611 55.000 5.05 0.00 42.71 5.80
3337 3379 0.032615 ATTTAAAGCCGGATGCCCCA 60.033 50.000 5.05 0.00 42.71 4.96
3404 3446 1.202817 TGCTTGTGCGGACTAATCGTA 59.797 47.619 8.99 0.00 43.34 3.43
3420 3462 2.388735 TCGTATGCCTTGAGTCCATCT 58.611 47.619 0.00 0.00 0.00 2.90
3614 3656 2.399356 GCACTTTGGAGCTACCCGC 61.399 63.158 0.00 0.00 38.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 152 2.614520 GTGCGCATACACTCTCTCTCTA 59.385 50.000 15.91 0.00 37.58 2.43
145 153 1.403679 GTGCGCATACACTCTCTCTCT 59.596 52.381 15.91 0.00 37.58 3.10
199 210 2.475111 CGTTCTGCTGACAATACAACGT 59.525 45.455 0.00 0.00 0.00 3.99
201 212 3.741344 ACTCGTTCTGCTGACAATACAAC 59.259 43.478 0.00 0.00 0.00 3.32
277 288 5.018809 ACCCAAGATCATTAATGTTGCTGT 58.981 37.500 14.97 9.19 37.32 4.40
287 298 2.040947 TGCCACACACCCAAGATCATTA 59.959 45.455 0.00 0.00 0.00 1.90
292 303 4.500265 GTGCCACACACCCAAGAT 57.500 55.556 0.00 0.00 44.02 2.40
304 315 1.348538 CTACGCGTGATTTCGTGCCA 61.349 55.000 24.59 0.00 43.75 4.92
343 354 1.660614 CGTCTATAGCCGAAGCGACAG 60.661 57.143 0.00 0.00 46.67 3.51
358 369 1.355971 GTGATTTGCGCTTCCGTCTA 58.644 50.000 9.73 0.00 36.67 2.59
380 391 0.765510 AATCGGATTCCTGCCTACCC 59.234 55.000 0.30 0.00 0.00 3.69
383 394 2.930826 GGAAATCGGATTCCTGCCTA 57.069 50.000 3.28 0.00 44.54 3.93
398 409 3.009723 GCAAGTTCCGATGATCTGGAAA 58.990 45.455 16.35 3.56 45.35 3.13
501 515 0.105964 TCCGCCGATTCCGATGATTT 59.894 50.000 0.00 0.00 38.22 2.17
515 529 1.865340 GATTCCGATACAAACTCCGCC 59.135 52.381 0.00 0.00 0.00 6.13
536 551 4.728102 CCGGTGACTAACGGCGCA 62.728 66.667 10.83 0.00 43.96 6.09
558 573 2.962569 GGGAAAAGAAGCGGCACC 59.037 61.111 1.45 0.00 0.00 5.01
661 703 1.443407 CCTACCCTGGCGATGTCTG 59.557 63.158 0.00 0.00 0.00 3.51
662 704 2.435693 GCCTACCCTGGCGATGTCT 61.436 63.158 0.00 0.00 43.74 3.41
740 782 0.517316 GAAACGGCATCGCTTCAGTT 59.483 50.000 0.00 0.00 40.14 3.16
827 869 0.881796 GCCAAAAAGAACCCTCTCGG 59.118 55.000 0.00 0.00 37.81 4.63
828 870 1.604604 TGCCAAAAAGAACCCTCTCG 58.395 50.000 0.00 0.00 0.00 4.04
829 871 4.607293 AAATGCCAAAAAGAACCCTCTC 57.393 40.909 0.00 0.00 0.00 3.20
830 872 4.501400 CGAAAATGCCAAAAAGAACCCTCT 60.501 41.667 0.00 0.00 0.00 3.69
831 873 3.740832 CGAAAATGCCAAAAAGAACCCTC 59.259 43.478 0.00 0.00 0.00 4.30
832 874 3.133901 ACGAAAATGCCAAAAAGAACCCT 59.866 39.130 0.00 0.00 0.00 4.34
833 875 3.462982 ACGAAAATGCCAAAAAGAACCC 58.537 40.909 0.00 0.00 0.00 4.11
834 876 3.493129 GGACGAAAATGCCAAAAAGAACC 59.507 43.478 0.00 0.00 0.00 3.62
835 877 3.181575 CGGACGAAAATGCCAAAAAGAAC 59.818 43.478 0.00 0.00 0.00 3.01
836 878 3.066900 TCGGACGAAAATGCCAAAAAGAA 59.933 39.130 0.00 0.00 0.00 2.52
837 879 2.619177 TCGGACGAAAATGCCAAAAAGA 59.381 40.909 0.00 0.00 0.00 2.52
838 880 3.006659 TCGGACGAAAATGCCAAAAAG 57.993 42.857 0.00 0.00 0.00 2.27
839 881 3.376540 CTTCGGACGAAAATGCCAAAAA 58.623 40.909 8.59 0.00 33.34 1.94
840 882 2.287909 CCTTCGGACGAAAATGCCAAAA 60.288 45.455 8.59 0.00 33.34 2.44
841 883 1.268352 CCTTCGGACGAAAATGCCAAA 59.732 47.619 8.59 0.00 33.34 3.28
842 884 0.878416 CCTTCGGACGAAAATGCCAA 59.122 50.000 8.59 0.00 33.34 4.52
843 885 0.958382 CCCTTCGGACGAAAATGCCA 60.958 55.000 8.59 0.00 33.34 4.92
844 886 1.654023 CCCCTTCGGACGAAAATGCC 61.654 60.000 8.59 0.00 33.34 4.40
845 887 1.654023 CCCCCTTCGGACGAAAATGC 61.654 60.000 8.59 0.00 33.34 3.56
846 888 1.654023 GCCCCCTTCGGACGAAAATG 61.654 60.000 8.59 0.80 33.34 2.32
847 889 1.378119 GCCCCCTTCGGACGAAAAT 60.378 57.895 8.59 0.00 33.34 1.82
848 890 2.032987 GCCCCCTTCGGACGAAAA 59.967 61.111 8.59 0.00 33.34 2.29
849 891 4.024545 GGCCCCCTTCGGACGAAA 62.025 66.667 8.59 0.00 33.34 3.46
852 894 3.562732 AAAAGGCCCCCTTCGGACG 62.563 63.158 0.00 0.00 43.92 4.79
853 895 1.228769 AAAAAGGCCCCCTTCGGAC 60.229 57.895 0.00 0.00 43.92 4.79
854 896 1.076014 GAAAAAGGCCCCCTTCGGA 59.924 57.895 0.00 0.00 43.92 4.55
855 897 1.076727 AGAAAAAGGCCCCCTTCGG 59.923 57.895 0.00 0.00 43.92 4.30
856 898 1.250840 CCAGAAAAAGGCCCCCTTCG 61.251 60.000 0.00 0.00 43.92 3.79
857 899 1.544825 GCCAGAAAAAGGCCCCCTTC 61.545 60.000 0.00 0.00 43.92 3.46
859 901 2.120496 GCCAGAAAAAGGCCCCCT 59.880 61.111 0.00 0.00 46.50 4.79
873 915 1.607178 CTGCCCACTGGAATTGCCA 60.607 57.895 0.00 0.00 46.96 4.92
874 916 1.304381 TCTGCCCACTGGAATTGCC 60.304 57.895 0.00 0.00 37.10 4.52
875 917 1.318158 CCTCTGCCCACTGGAATTGC 61.318 60.000 0.00 0.00 0.00 3.56
876 918 0.038744 ACCTCTGCCCACTGGAATTG 59.961 55.000 0.00 0.00 0.00 2.32
877 919 0.329596 GACCTCTGCCCACTGGAATT 59.670 55.000 0.00 0.00 0.00 2.17
878 920 0.548682 AGACCTCTGCCCACTGGAAT 60.549 55.000 0.00 0.00 0.00 3.01
879 921 1.152030 AGACCTCTGCCCACTGGAA 60.152 57.895 0.00 0.00 0.00 3.53
880 922 1.610673 GAGACCTCTGCCCACTGGA 60.611 63.158 0.00 0.00 0.00 3.86
881 923 1.197430 AAGAGACCTCTGCCCACTGG 61.197 60.000 0.00 0.00 40.36 4.00
882 924 0.036577 CAAGAGACCTCTGCCCACTG 60.037 60.000 0.00 0.00 40.36 3.66
883 925 0.178921 TCAAGAGACCTCTGCCCACT 60.179 55.000 0.00 0.00 40.36 4.00
884 926 0.036858 GTCAAGAGACCTCTGCCCAC 60.037 60.000 0.00 0.00 40.36 4.61
885 927 0.471780 TGTCAAGAGACCTCTGCCCA 60.472 55.000 0.00 0.00 44.33 5.36
886 928 0.687354 TTGTCAAGAGACCTCTGCCC 59.313 55.000 0.00 0.00 44.33 5.36
887 929 2.550830 TTTGTCAAGAGACCTCTGCC 57.449 50.000 0.00 0.00 44.33 4.85
1062 1104 1.270678 GCTTCCTGGTAGTGTCCGTTT 60.271 52.381 2.16 0.00 0.00 3.60
1090 1132 1.451567 CGTGGGCTCGAGAGTAGGA 60.452 63.158 18.75 0.00 0.00 2.94
1308 1350 1.069500 ACGTTTCTTTCCCGCATTTCG 60.069 47.619 0.00 0.00 38.08 3.46
1441 1483 1.219124 CAGGTAGCACACTCGCCAT 59.781 57.895 0.00 0.00 0.00 4.40
1545 1587 6.240894 ACAATCCAAGTACATTGTGATGAGT 58.759 36.000 8.13 7.87 40.87 3.41
1734 1776 2.300152 TGAGAGGACTACCAGCAAAGTG 59.700 50.000 0.00 0.00 38.94 3.16
1775 1817 3.233507 ACCTCTTTACCAAGTGACGGTA 58.766 45.455 0.00 0.00 37.99 4.02
1779 1821 3.764237 TGGACCTCTTTACCAAGTGAC 57.236 47.619 0.00 0.00 0.00 3.67
1876 1918 2.037251 GGTAAGCACACTCCAGAGAACA 59.963 50.000 0.70 0.00 0.00 3.18
2314 2356 9.717942 CGATTTCCTCCTATCTTTCTCAAATAT 57.282 33.333 0.00 0.00 0.00 1.28
2328 2370 4.262635 GCTGGATCATTCGATTTCCTCCTA 60.263 45.833 0.00 0.00 29.66 2.94
2379 2421 0.821711 TGCTTTTCCCACACCTTCCG 60.822 55.000 0.00 0.00 0.00 4.30
2391 2433 5.434706 GTTTGCAATGCTAAACTGCTTTTC 58.565 37.500 18.80 0.00 37.00 2.29
2652 2694 7.373493 CAAGAAAAGAATACCACATTGAAGCT 58.627 34.615 0.00 0.00 0.00 3.74
2702 2744 2.159517 GCTGCTATTTCACCAAGTTCGG 60.160 50.000 0.00 0.00 0.00 4.30
2703 2745 2.483877 TGCTGCTATTTCACCAAGTTCG 59.516 45.455 0.00 0.00 0.00 3.95
2713 2755 7.530010 TCATAGAGTTTTGTTGCTGCTATTTC 58.470 34.615 0.00 0.00 0.00 2.17
2787 2829 1.800586 CCCCATCGATATTGTTCAGCG 59.199 52.381 0.00 0.00 0.00 5.18
3064 3106 3.438087 CCATGATTCTGTTGCGAACTTCT 59.562 43.478 0.00 0.00 0.00 2.85
3071 3113 0.179156 GGTGCCATGATTCTGTTGCG 60.179 55.000 0.00 0.00 0.00 4.85
3075 3117 2.291209 TTGTGGTGCCATGATTCTGT 57.709 45.000 0.00 0.00 0.00 3.41
3119 3161 0.976590 GAGGCCGGGGGTATATCCTC 60.977 65.000 2.18 3.91 36.25 3.71
3120 3162 1.080538 GAGGCCGGGGGTATATCCT 59.919 63.158 2.18 0.00 36.25 3.24
3121 3163 1.080538 AGAGGCCGGGGGTATATCC 59.919 63.158 2.18 0.00 0.00 2.59
3122 3164 1.900545 GCAGAGGCCGGGGGTATATC 61.901 65.000 2.18 0.00 0.00 1.63
3123 3165 1.918800 GCAGAGGCCGGGGGTATAT 60.919 63.158 2.18 0.00 0.00 0.86
3124 3166 2.525877 GCAGAGGCCGGGGGTATA 60.526 66.667 2.18 0.00 0.00 1.47
3125 3167 4.815973 TGCAGAGGCCGGGGGTAT 62.816 66.667 2.18 0.00 40.13 2.73
3126 3168 4.815973 ATGCAGAGGCCGGGGGTA 62.816 66.667 2.18 0.00 40.13 3.69
3129 3171 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
3130 3172 4.559063 CCAGATGCAGAGGCCGGG 62.559 72.222 2.18 0.00 40.13 5.73
3131 3173 4.559063 CCCAGATGCAGAGGCCGG 62.559 72.222 0.00 0.00 40.13 6.13
3134 3176 3.472943 ATCGCCCAGATGCAGAGGC 62.473 63.158 8.59 8.59 42.18 4.70
3135 3177 2.827423 ATCGCCCAGATGCAGAGG 59.173 61.111 0.00 0.00 38.36 3.69
3142 3184 1.897137 CTGCATGCATCGCCCAGAT 60.897 57.895 22.97 0.00 41.01 2.90
3143 3185 2.515290 CTGCATGCATCGCCCAGA 60.515 61.111 22.97 0.00 0.00 3.86
3144 3186 4.266070 GCTGCATGCATCGCCCAG 62.266 66.667 22.97 8.76 42.31 4.45
3147 3189 2.638330 AAATGGCTGCATGCATCGCC 62.638 55.000 33.23 33.23 45.15 5.54
3148 3190 0.808453 AAAATGGCTGCATGCATCGC 60.808 50.000 22.97 21.54 45.15 4.58
3149 3191 2.495409 TAAAATGGCTGCATGCATCG 57.505 45.000 22.97 12.00 45.15 3.84
3150 3192 7.429636 AATTAATAAAATGGCTGCATGCATC 57.570 32.000 22.97 17.75 45.15 3.91
3151 3193 9.509956 AATAATTAATAAAATGGCTGCATGCAT 57.490 25.926 22.97 6.91 45.15 3.96
3152 3194 8.905660 AATAATTAATAAAATGGCTGCATGCA 57.094 26.923 21.29 21.29 45.15 3.96
3153 3195 8.991026 TGAATAATTAATAAAATGGCTGCATGC 58.009 29.630 11.82 11.82 41.94 4.06
3155 3197 9.195411 CGTGAATAATTAATAAAATGGCTGCAT 57.805 29.630 0.50 0.00 0.00 3.96
3156 3198 8.409371 TCGTGAATAATTAATAAAATGGCTGCA 58.591 29.630 0.50 0.00 0.00 4.41
3157 3199 8.795786 TCGTGAATAATTAATAAAATGGCTGC 57.204 30.769 0.00 0.00 0.00 5.25
3176 3218 9.491675 TGTATTATTTTGTAAGGTCTTCGTGAA 57.508 29.630 0.00 0.00 0.00 3.18
3177 3219 9.661563 ATGTATTATTTTGTAAGGTCTTCGTGA 57.338 29.630 0.00 0.00 0.00 4.35
3178 3220 9.916397 GATGTATTATTTTGTAAGGTCTTCGTG 57.084 33.333 0.00 0.00 0.00 4.35
3179 3221 9.661563 TGATGTATTATTTTGTAAGGTCTTCGT 57.338 29.630 0.00 0.00 0.00 3.85
3205 3247 0.995024 ATGGTGGCTTCAGGCTTACT 59.005 50.000 1.64 0.00 41.69 2.24
3206 3248 1.065126 AGATGGTGGCTTCAGGCTTAC 60.065 52.381 1.64 0.00 41.69 2.34
3207 3249 1.289160 AGATGGTGGCTTCAGGCTTA 58.711 50.000 1.64 0.00 41.69 3.09
3208 3250 0.407139 AAGATGGTGGCTTCAGGCTT 59.593 50.000 1.64 0.00 41.69 4.35
3209 3251 0.323178 CAAGATGGTGGCTTCAGGCT 60.323 55.000 1.64 0.00 41.69 4.58
3210 3252 1.318158 CCAAGATGGTGGCTTCAGGC 61.318 60.000 0.00 0.00 41.50 4.85
3211 3253 2.877975 CCAAGATGGTGGCTTCAGG 58.122 57.895 0.00 0.00 31.35 3.86
3218 3260 0.540365 AGGTGTTGCCAAGATGGTGG 60.540 55.000 0.00 0.00 40.46 4.61
3219 3261 0.599558 CAGGTGTTGCCAAGATGGTG 59.400 55.000 0.00 0.00 40.46 4.17
3220 3262 0.185901 ACAGGTGTTGCCAAGATGGT 59.814 50.000 0.00 0.00 40.46 3.55
3221 3263 0.883833 GACAGGTGTTGCCAAGATGG 59.116 55.000 0.00 0.00 41.55 3.51
3222 3264 0.518636 CGACAGGTGTTGCCAAGATG 59.481 55.000 0.00 0.00 40.61 2.90
3223 3265 2.932663 CGACAGGTGTTGCCAAGAT 58.067 52.632 0.00 0.00 40.61 2.40
3224 3266 4.454948 CGACAGGTGTTGCCAAGA 57.545 55.556 0.00 0.00 40.61 3.02
3230 3272 0.603569 AGGAGTAGCGACAGGTGTTG 59.396 55.000 0.00 0.00 0.00 3.33
3231 3273 2.211250 TAGGAGTAGCGACAGGTGTT 57.789 50.000 0.00 0.00 0.00 3.32
3232 3274 2.299521 GATAGGAGTAGCGACAGGTGT 58.700 52.381 0.00 0.00 0.00 4.16
3233 3275 1.609555 GGATAGGAGTAGCGACAGGTG 59.390 57.143 0.00 0.00 0.00 4.00
3234 3276 1.495574 AGGATAGGAGTAGCGACAGGT 59.504 52.381 0.00 0.00 0.00 4.00
3235 3277 2.156098 GAGGATAGGAGTAGCGACAGG 58.844 57.143 0.00 0.00 0.00 4.00
3236 3278 3.134574 AGAGGATAGGAGTAGCGACAG 57.865 52.381 0.00 0.00 0.00 3.51
3237 3279 3.118000 TCAAGAGGATAGGAGTAGCGACA 60.118 47.826 0.00 0.00 0.00 4.35
3238 3280 3.478509 TCAAGAGGATAGGAGTAGCGAC 58.521 50.000 0.00 0.00 0.00 5.19
3239 3281 3.859061 TCAAGAGGATAGGAGTAGCGA 57.141 47.619 0.00 0.00 0.00 4.93
3240 3282 4.075682 TCATCAAGAGGATAGGAGTAGCG 58.924 47.826 0.00 0.00 33.95 4.26
3241 3283 5.047377 CCTTCATCAAGAGGATAGGAGTAGC 60.047 48.000 6.96 0.00 33.95 3.58
3242 3284 5.480073 CCCTTCATCAAGAGGATAGGAGTAG 59.520 48.000 11.71 0.00 33.95 2.57
3243 3285 5.398236 CCCTTCATCAAGAGGATAGGAGTA 58.602 45.833 11.71 0.00 33.95 2.59
3244 3286 4.230455 CCCTTCATCAAGAGGATAGGAGT 58.770 47.826 11.71 0.00 33.95 3.85
3245 3287 3.582208 CCCCTTCATCAAGAGGATAGGAG 59.418 52.174 11.71 0.09 28.41 3.69
3246 3288 3.051032 ACCCCTTCATCAAGAGGATAGGA 60.051 47.826 11.71 0.00 31.75 2.94
3247 3289 3.072184 CACCCCTTCATCAAGAGGATAGG 59.928 52.174 0.00 6.20 31.75 2.57
3248 3290 3.495806 GCACCCCTTCATCAAGAGGATAG 60.496 52.174 0.00 0.00 31.75 2.08
3249 3291 2.439507 GCACCCCTTCATCAAGAGGATA 59.560 50.000 0.00 0.00 31.75 2.59
3250 3292 1.213926 GCACCCCTTCATCAAGAGGAT 59.786 52.381 0.00 0.00 31.75 3.24
3251 3293 0.620556 GCACCCCTTCATCAAGAGGA 59.379 55.000 0.00 0.00 31.75 3.71
3252 3294 0.394899 GGCACCCCTTCATCAAGAGG 60.395 60.000 0.00 0.00 33.59 3.69
3253 3295 0.745845 CGGCACCCCTTCATCAAGAG 60.746 60.000 0.00 0.00 0.00 2.85
3254 3296 1.198094 TCGGCACCCCTTCATCAAGA 61.198 55.000 0.00 0.00 0.00 3.02
3255 3297 0.322456 TTCGGCACCCCTTCATCAAG 60.322 55.000 0.00 0.00 0.00 3.02
3256 3298 0.331278 ATTCGGCACCCCTTCATCAA 59.669 50.000 0.00 0.00 0.00 2.57
3257 3299 0.394216 CATTCGGCACCCCTTCATCA 60.394 55.000 0.00 0.00 0.00 3.07
3258 3300 0.394352 ACATTCGGCACCCCTTCATC 60.394 55.000 0.00 0.00 0.00 2.92
3259 3301 0.394352 GACATTCGGCACCCCTTCAT 60.394 55.000 0.00 0.00 0.00 2.57
3260 3302 1.002624 GACATTCGGCACCCCTTCA 60.003 57.895 0.00 0.00 0.00 3.02
3261 3303 1.026718 CAGACATTCGGCACCCCTTC 61.027 60.000 0.00 0.00 0.00 3.46
3262 3304 1.002134 CAGACATTCGGCACCCCTT 60.002 57.895 0.00 0.00 0.00 3.95
3263 3305 1.903877 CTCAGACATTCGGCACCCCT 61.904 60.000 0.00 0.00 0.00 4.79
3264 3306 1.450312 CTCAGACATTCGGCACCCC 60.450 63.158 0.00 0.00 0.00 4.95
3265 3307 2.109126 GCTCAGACATTCGGCACCC 61.109 63.158 0.00 0.00 0.00 4.61
3266 3308 1.078848 AGCTCAGACATTCGGCACC 60.079 57.895 0.00 0.00 0.00 5.01
3267 3309 0.390340 TCAGCTCAGACATTCGGCAC 60.390 55.000 0.00 0.00 0.00 5.01
3268 3310 0.321346 TTCAGCTCAGACATTCGGCA 59.679 50.000 0.00 0.00 0.00 5.69
3269 3311 1.661341 ATTCAGCTCAGACATTCGGC 58.339 50.000 0.00 0.00 0.00 5.54
3270 3312 3.126831 GGTATTCAGCTCAGACATTCGG 58.873 50.000 0.00 0.00 0.00 4.30
3271 3313 3.785486 TGGTATTCAGCTCAGACATTCG 58.215 45.455 0.00 0.00 0.00 3.34
3272 3314 5.412594 TGTTTGGTATTCAGCTCAGACATTC 59.587 40.000 0.00 0.00 0.00 2.67
3273 3315 5.316167 TGTTTGGTATTCAGCTCAGACATT 58.684 37.500 0.00 0.00 0.00 2.71
3274 3316 4.910195 TGTTTGGTATTCAGCTCAGACAT 58.090 39.130 0.00 0.00 0.00 3.06
3275 3317 4.040339 TCTGTTTGGTATTCAGCTCAGACA 59.960 41.667 0.00 0.00 0.00 3.41
3276 3318 4.390297 GTCTGTTTGGTATTCAGCTCAGAC 59.610 45.833 8.53 8.53 39.37 3.51
3277 3319 4.040339 TGTCTGTTTGGTATTCAGCTCAGA 59.960 41.667 0.00 0.00 0.00 3.27
3278 3320 4.318332 TGTCTGTTTGGTATTCAGCTCAG 58.682 43.478 0.00 0.00 0.00 3.35
3279 3321 4.350368 TGTCTGTTTGGTATTCAGCTCA 57.650 40.909 0.00 0.00 0.00 4.26
3280 3322 4.937620 TGATGTCTGTTTGGTATTCAGCTC 59.062 41.667 0.00 0.00 0.00 4.09
3281 3323 4.697352 GTGATGTCTGTTTGGTATTCAGCT 59.303 41.667 0.00 0.00 0.00 4.24
3282 3324 4.455533 TGTGATGTCTGTTTGGTATTCAGC 59.544 41.667 0.00 0.00 0.00 4.26
3283 3325 5.106555 GGTGTGATGTCTGTTTGGTATTCAG 60.107 44.000 0.00 0.00 0.00 3.02
3284 3326 4.759693 GGTGTGATGTCTGTTTGGTATTCA 59.240 41.667 0.00 0.00 0.00 2.57
3285 3327 4.759693 TGGTGTGATGTCTGTTTGGTATTC 59.240 41.667 0.00 0.00 0.00 1.75
3286 3328 4.724399 TGGTGTGATGTCTGTTTGGTATT 58.276 39.130 0.00 0.00 0.00 1.89
3287 3329 4.365514 TGGTGTGATGTCTGTTTGGTAT 57.634 40.909 0.00 0.00 0.00 2.73
3288 3330 3.847671 TGGTGTGATGTCTGTTTGGTA 57.152 42.857 0.00 0.00 0.00 3.25
3289 3331 2.727123 TGGTGTGATGTCTGTTTGGT 57.273 45.000 0.00 0.00 0.00 3.67
3290 3332 3.796504 GCTTTGGTGTGATGTCTGTTTGG 60.797 47.826 0.00 0.00 0.00 3.28
3291 3333 3.374745 GCTTTGGTGTGATGTCTGTTTG 58.625 45.455 0.00 0.00 0.00 2.93
3292 3334 2.362077 GGCTTTGGTGTGATGTCTGTTT 59.638 45.455 0.00 0.00 0.00 2.83
3293 3335 1.956477 GGCTTTGGTGTGATGTCTGTT 59.044 47.619 0.00 0.00 0.00 3.16
3294 3336 1.143684 AGGCTTTGGTGTGATGTCTGT 59.856 47.619 0.00 0.00 0.00 3.41
3295 3337 1.901591 AGGCTTTGGTGTGATGTCTG 58.098 50.000 0.00 0.00 0.00 3.51
3296 3338 3.181445 TGTTAGGCTTTGGTGTGATGTCT 60.181 43.478 0.00 0.00 0.00 3.41
3297 3339 3.146066 TGTTAGGCTTTGGTGTGATGTC 58.854 45.455 0.00 0.00 0.00 3.06
3298 3340 3.222173 TGTTAGGCTTTGGTGTGATGT 57.778 42.857 0.00 0.00 0.00 3.06
3299 3341 4.789012 AATGTTAGGCTTTGGTGTGATG 57.211 40.909 0.00 0.00 0.00 3.07
3300 3342 6.909550 TTAAATGTTAGGCTTTGGTGTGAT 57.090 33.333 0.00 0.00 0.00 3.06
3301 3343 6.716934 TTTAAATGTTAGGCTTTGGTGTGA 57.283 33.333 0.00 0.00 0.00 3.58
3302 3344 5.405269 GCTTTAAATGTTAGGCTTTGGTGTG 59.595 40.000 0.00 0.00 0.00 3.82
3303 3345 5.510690 GGCTTTAAATGTTAGGCTTTGGTGT 60.511 40.000 0.00 0.00 0.00 4.16
3304 3346 4.929211 GGCTTTAAATGTTAGGCTTTGGTG 59.071 41.667 0.00 0.00 0.00 4.17
3305 3347 4.321675 CGGCTTTAAATGTTAGGCTTTGGT 60.322 41.667 0.00 0.00 32.77 3.67
3306 3348 4.173256 CGGCTTTAAATGTTAGGCTTTGG 58.827 43.478 0.00 0.00 32.77 3.28
3307 3349 4.082463 TCCGGCTTTAAATGTTAGGCTTTG 60.082 41.667 0.00 0.00 32.77 2.77
3308 3350 4.083565 TCCGGCTTTAAATGTTAGGCTTT 58.916 39.130 0.00 0.00 32.77 3.51
3309 3351 3.692690 TCCGGCTTTAAATGTTAGGCTT 58.307 40.909 0.00 0.00 32.77 4.35
3310 3352 3.359695 TCCGGCTTTAAATGTTAGGCT 57.640 42.857 0.00 0.00 32.77 4.58
3311 3353 3.795488 GCATCCGGCTTTAAATGTTAGGC 60.795 47.826 0.00 0.00 40.25 3.93
3312 3354 3.243401 GGCATCCGGCTTTAAATGTTAGG 60.243 47.826 0.00 0.00 44.01 2.69
3313 3355 3.243401 GGGCATCCGGCTTTAAATGTTAG 60.243 47.826 0.00 0.00 44.01 2.34
3314 3356 2.691011 GGGCATCCGGCTTTAAATGTTA 59.309 45.455 0.00 0.00 44.01 2.41
3315 3357 1.480545 GGGCATCCGGCTTTAAATGTT 59.519 47.619 0.00 0.00 44.01 2.71
3316 3358 1.111277 GGGCATCCGGCTTTAAATGT 58.889 50.000 0.00 0.00 44.01 2.71
3317 3359 0.389025 GGGGCATCCGGCTTTAAATG 59.611 55.000 0.00 0.00 44.01 2.32
3318 3360 0.032615 TGGGGCATCCGGCTTTAAAT 60.033 50.000 0.00 0.00 44.01 1.40
3319 3361 0.682855 CTGGGGCATCCGGCTTTAAA 60.683 55.000 0.00 0.00 44.01 1.52
3320 3362 1.077068 CTGGGGCATCCGGCTTTAA 60.077 57.895 0.00 0.00 44.01 1.52
3321 3363 2.305607 ACTGGGGCATCCGGCTTTA 61.306 57.895 0.00 0.00 46.01 1.85
3322 3364 3.661648 ACTGGGGCATCCGGCTTT 61.662 61.111 0.00 0.00 46.01 3.51
3323 3365 4.431131 CACTGGGGCATCCGGCTT 62.431 66.667 0.00 0.00 46.01 4.35
3325 3367 3.338275 TTACACTGGGGCATCCGGC 62.338 63.158 0.00 0.00 46.01 6.13
3327 3369 1.153168 CCTTACACTGGGGCATCCG 60.153 63.158 0.00 0.00 38.76 4.18
3328 3370 1.227383 CCCTTACACTGGGGCATCC 59.773 63.158 0.00 0.00 40.97 3.51
3329 3371 4.986467 CCCTTACACTGGGGCATC 57.014 61.111 0.00 0.00 40.97 3.91
3333 3375 3.312736 AAATATGCCCTTACACTGGGG 57.687 47.619 0.00 0.00 44.71 4.96
3335 3377 5.010282 GGGATAAATATGCCCTTACACTGG 58.990 45.833 0.00 0.00 38.14 4.00
3404 3446 3.972638 AGTATCAGATGGACTCAAGGCAT 59.027 43.478 0.00 0.00 0.00 4.40
3614 3656 2.773487 TCCACACAACCAAGATAACGG 58.227 47.619 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.