Multiple sequence alignment - TraesCS5D01G185300

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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 TraesCS5D01G185300 chr5D 100.000 5262 0 0 1 5262 287445653 287440392 0.000000e+00 9718.0
1 TraesCS5D01G185300 chr5D 93.220 118 7 1 4626 4742 118840451 118840568 7.010000e-39 172.0
2 TraesCS5D01G185300 chr5A 93.837 3537 146 32 1139 4629 379356845 379353335 0.000000e+00 5258.0
3 TraesCS5D01G185300 chr5A 91.313 495 25 10 553 1039 379357696 379357212 0.000000e+00 660.0
4 TraesCS5D01G185300 chr5A 88.632 519 36 9 4749 5260 379353333 379352831 1.250000e-170 610.0
5 TraesCS5D01G185300 chr5A 83.248 585 59 19 1 557 379358326 379357753 7.870000e-138 501.0
6 TraesCS5D01G185300 chr5A 100.000 35 0 0 5228 5262 379352833 379352799 1.220000e-06 65.8
7 TraesCS5D01G185300 chr5B 93.556 3445 166 27 1179 4592 326575605 326572186 0.000000e+00 5081.0
8 TraesCS5D01G185300 chr5B 93.638 503 22 9 4749 5246 326572165 326571668 0.000000e+00 743.0
9 TraesCS5D01G185300 chr5B 87.356 609 38 20 547 1147 326576795 326576218 0.000000e+00 662.0
10 TraesCS5D01G185300 chr5B 92.202 436 26 6 1 432 326577429 326576998 1.250000e-170 610.0
11 TraesCS5D01G185300 chr5B 90.400 125 11 1 4626 4749 234303341 234303465 4.220000e-36 163.0
12 TraesCS5D01G185300 chr5B 91.579 95 7 1 553 646 446455197 446455103 4.280000e-26 130.0
13 TraesCS5D01G185300 chr5B 100.000 35 0 0 5228 5262 326571662 326571628 1.220000e-06 65.8
14 TraesCS5D01G185300 chr7B 91.736 121 9 1 4625 4744 81425107 81424987 3.260000e-37 167.0
15 TraesCS5D01G185300 chr6A 92.373 118 8 1 4626 4742 147303777 147303660 3.260000e-37 167.0
16 TraesCS5D01G185300 chr2A 91.736 121 9 1 4626 4745 78845572 78845692 3.260000e-37 167.0
17 TraesCS5D01G185300 chr2A 89.474 95 9 1 553 646 179846245 179846339 9.260000e-23 119.0
18 TraesCS5D01G185300 chr4B 90.476 126 10 2 4618 4742 392367899 392368023 1.170000e-36 165.0
19 TraesCS5D01G185300 chr2D 91.057 123 9 2 4626 4746 12692357 12692235 1.170000e-36 165.0
20 TraesCS5D01G185300 chr2D 90.526 95 8 1 553 646 638155620 638155714 1.990000e-24 124.0
21 TraesCS5D01G185300 chr1D 88.636 132 13 2 4626 4756 240590622 240590492 5.450000e-35 159.0
22 TraesCS5D01G185300 chr3B 88.550 131 13 2 4626 4755 829966242 829966113 1.960000e-34 158.0
23 TraesCS5D01G185300 chr6B 90.526 95 8 1 553 646 11169435 11169341 1.990000e-24 124.0
24 TraesCS5D01G185300 chr7D 90.526 95 6 3 553 645 617120965 617120872 7.160000e-24 122.0
25 TraesCS5D01G185300 chr7D 88.421 95 10 1 553 646 29789350 29789256 4.310000e-21 113.0
26 TraesCS5D01G185300 chr2B 89.474 95 9 1 553 646 646130190 646130096 9.260000e-23 119.0
27 TraesCS5D01G185300 chr6D 88.421 95 10 1 553 646 78768409 78768315 4.310000e-21 113.0
28 TraesCS5D01G185300 chr1A 88.421 95 10 1 553 646 79500108 79500202 4.310000e-21 113.0


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 TraesCS5D01G185300 chr5D 287440392 287445653 5261 True 9718.00 9718 100.0000 1 5262 1 chr5D.!!$R1 5261
1 TraesCS5D01G185300 chr5A 379352799 379358326 5527 True 1418.96 5258 91.4060 1 5262 5 chr5A.!!$R1 5261
2 TraesCS5D01G185300 chr5B 326571628 326577429 5801 True 1432.36 5081 93.3504 1 5262 5 chr5B.!!$R2 5261

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
227 234 0.109226 GCTGGACGTAGGTGACTGTC 60.109 60.0 0.00 0.0 43.88 3.51 F
1175 1551 0.387565 GTCTCATTCCCTCTCCGCTC 59.612 60.0 0.00 0.0 0.00 5.03 F
2876 3880 0.179100 GATTGTGCGCTCAGGCTCTA 60.179 55.0 12.41 0.0 36.09 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1639 2614 0.729116 GATCATCGCACCAACACCAG 59.271 55.0 0.00 0.0 0.00 4.00 R
3021 4026 0.036022 AACCTGCAGAGAAGACCAGC 59.964 55.0 17.39 0.0 0.00 4.85 R
4415 5425 0.313987 AAACGCAGCCTTAACTTGCC 59.686 50.0 0.00 0.0 34.42 4.52 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
114 115 9.561069 AGTGTCTTAAACATATTAATAGCCCAG 57.439 33.333 1.02 0.00 40.80 4.45
227 234 0.109226 GCTGGACGTAGGTGACTGTC 60.109 60.000 0.00 0.00 43.88 3.51
287 294 9.908152 TCGTCGATATGAACTTAATTGTCATAT 57.092 29.630 12.21 12.21 36.89 1.78
295 302 7.112122 TGAACTTAATTGTCATATGACCAGCT 58.888 34.615 28.64 15.15 44.15 4.24
296 303 7.611467 TGAACTTAATTGTCATATGACCAGCTT 59.389 33.333 28.64 18.92 44.15 3.74
360 367 2.289195 TGGTTCAATGTACACGGAGGAC 60.289 50.000 0.00 0.00 0.00 3.85
408 415 6.265577 AGATCAATTTGCGGCAATTAGTAAC 58.734 36.000 17.19 6.23 0.00 2.50
478 514 5.559427 AAGTCATTTGCACGCAACATATA 57.441 34.783 3.45 0.00 35.46 0.86
489 525 5.277297 GCACGCAACATATAGCAATTACAGA 60.277 40.000 0.00 0.00 0.00 3.41
510 546 6.018425 ACAGAGATATTATTGCGAGTTGCTTG 60.018 38.462 3.50 0.00 46.63 4.01
514 550 8.208718 AGATATTATTGCGAGTTGCTTGTTTA 57.791 30.769 3.50 0.00 46.63 2.01
557 655 7.383687 TCGTCTTTAATCCTTGACAGTACAAT 58.616 34.615 0.00 0.00 0.00 2.71
620 718 1.069765 CGTCGGAGCCAGGCAATAT 59.930 57.895 15.80 0.00 0.00 1.28
621 719 0.532862 CGTCGGAGCCAGGCAATATT 60.533 55.000 15.80 0.00 0.00 1.28
633 732 6.033966 GCCAGGCAATATTTGTTGTAGTAAC 58.966 40.000 6.55 0.00 0.00 2.50
667 766 8.152023 AGTCCATAGATGAAGAATAATACCCC 57.848 38.462 0.00 0.00 0.00 4.95
690 789 4.593864 GGCCGCTGGATCCGAGTC 62.594 72.222 7.39 0.00 0.00 3.36
745 844 6.326323 TCTTACACAGAGCCATCCATATACAA 59.674 38.462 0.00 0.00 0.00 2.41
849 950 3.350833 CAGCTGGCAATTAGAGTCCTTT 58.649 45.455 5.57 0.00 0.00 3.11
967 1076 0.611618 AGCCAATTTGACCATCCGCA 60.612 50.000 0.00 0.00 0.00 5.69
1055 1164 2.184167 GTCTCCTCTCCTCCTCGCG 61.184 68.421 0.00 0.00 0.00 5.87
1056 1165 2.124487 CTCCTCTCCTCCTCGCGT 60.124 66.667 5.77 0.00 0.00 6.01
1057 1166 2.124653 TCCTCTCCTCCTCGCGTC 60.125 66.667 5.77 0.00 0.00 5.19
1058 1167 3.578272 CCTCTCCTCCTCGCGTCG 61.578 72.222 5.77 0.00 0.00 5.12
1060 1169 4.779966 TCTCCTCCTCGCGTCGCT 62.780 66.667 16.36 0.00 0.00 4.93
1061 1170 2.895865 CTCCTCCTCGCGTCGCTA 60.896 66.667 16.36 2.97 0.00 4.26
1062 1171 2.437180 TCCTCCTCGCGTCGCTAA 60.437 61.111 16.36 2.17 0.00 3.09
1063 1172 1.989966 CTCCTCCTCGCGTCGCTAAA 61.990 60.000 16.36 0.00 0.00 1.85
1064 1173 1.872679 CCTCCTCGCGTCGCTAAAC 60.873 63.158 16.36 0.00 0.00 2.01
1065 1174 1.872679 CTCCTCGCGTCGCTAAACC 60.873 63.158 16.36 0.00 0.00 3.27
1066 1175 2.884207 CCTCGCGTCGCTAAACCC 60.884 66.667 16.36 0.00 0.00 4.11
1067 1176 2.884207 CTCGCGTCGCTAAACCCC 60.884 66.667 16.36 0.00 0.00 4.95
1068 1177 4.440127 TCGCGTCGCTAAACCCCC 62.440 66.667 16.36 0.00 0.00 5.40
1069 1178 4.446413 CGCGTCGCTAAACCCCCT 62.446 66.667 16.36 0.00 0.00 4.79
1167 1543 2.363795 TCCGCCGTCTCATTCCCT 60.364 61.111 0.00 0.00 0.00 4.20
1175 1551 0.387565 GTCTCATTCCCTCTCCGCTC 59.612 60.000 0.00 0.00 0.00 5.03
1266 2223 4.514577 CGCAAGATCGGTCCGGCT 62.515 66.667 12.29 6.59 43.02 5.52
1482 2452 8.911662 CGTAAATTTCTAAACTGAAAACATGGG 58.088 33.333 0.00 0.00 39.08 4.00
1544 2517 3.589641 TGTCCTAGGTGTTTGGTCCTTA 58.410 45.455 9.08 0.00 35.51 2.69
1639 2614 4.496840 CCTTGTGTTAACACTTTCCGTTCC 60.497 45.833 32.58 9.03 46.55 3.62
1876 2851 3.153369 TCCCTGCAGCAATTGTTTCTA 57.847 42.857 8.66 0.00 0.00 2.10
1890 2865 2.869801 TGTTTCTAGTTGCAACGACTGG 59.130 45.455 23.21 8.93 0.00 4.00
2175 3150 2.120909 GGTGGCCACAGCGCATAAT 61.121 57.895 35.78 0.00 41.24 1.28
2301 3288 3.067106 CGTGTGCTACAATCTTGGACTT 58.933 45.455 0.00 0.00 0.00 3.01
2352 3339 5.102313 GGTGGCATTGCTTTATTTAGTCAC 58.898 41.667 8.82 3.95 0.00 3.67
2438 3425 4.079253 TGTACTGTAGTGATGAGCTGTGA 58.921 43.478 0.00 0.00 0.00 3.58
2695 3696 2.046292 CAGGTTTGGTTTGGGTGGATT 58.954 47.619 0.00 0.00 0.00 3.01
2724 3728 5.072055 TCAGCACTCCTTCATTTTCATTGA 58.928 37.500 0.00 0.00 0.00 2.57
2725 3729 5.048504 TCAGCACTCCTTCATTTTCATTGAC 60.049 40.000 0.00 0.00 0.00 3.18
2735 3739 6.271488 TCATTTTCATTGACACATTCCTCC 57.729 37.500 0.00 0.00 0.00 4.30
2749 3753 6.016276 ACACATTCCTCCAGTTCATAAACAAC 60.016 38.462 0.00 0.00 37.88 3.32
2841 3845 8.964476 TTTAATCAGAAGTTTGAGACAACTCT 57.036 30.769 0.00 0.00 42.99 3.24
2843 3847 4.122776 TCAGAAGTTTGAGACAACTCTGC 58.877 43.478 0.00 0.00 42.99 4.26
2853 3857 4.993584 TGAGACAACTCTGCTTCTGATTTC 59.006 41.667 0.00 0.00 42.99 2.17
2876 3880 0.179100 GATTGTGCGCTCAGGCTCTA 60.179 55.000 12.41 0.00 36.09 2.43
2878 3882 0.670546 TTGTGCGCTCAGGCTCTAAC 60.671 55.000 12.41 0.00 36.09 2.34
2879 3883 1.216710 GTGCGCTCAGGCTCTAACT 59.783 57.895 9.73 0.00 36.09 2.24
2880 3884 0.456221 GTGCGCTCAGGCTCTAACTA 59.544 55.000 9.73 0.00 36.09 2.24
2882 3886 1.548719 TGCGCTCAGGCTCTAACTAAA 59.451 47.619 9.73 0.00 36.09 1.85
2883 3887 2.028476 TGCGCTCAGGCTCTAACTAAAA 60.028 45.455 9.73 0.00 36.09 1.52
2884 3888 2.348971 GCGCTCAGGCTCTAACTAAAAC 59.651 50.000 0.00 0.00 36.09 2.43
2886 3890 3.614616 CGCTCAGGCTCTAACTAAAACAG 59.385 47.826 0.00 0.00 36.09 3.16
2887 3891 3.935828 GCTCAGGCTCTAACTAAAACAGG 59.064 47.826 0.00 0.00 35.22 4.00
2888 3892 4.322801 GCTCAGGCTCTAACTAAAACAGGA 60.323 45.833 0.00 0.00 35.22 3.86
2889 3893 5.407407 TCAGGCTCTAACTAAAACAGGAG 57.593 43.478 0.00 0.00 0.00 3.69
2890 3894 3.935828 CAGGCTCTAACTAAAACAGGAGC 59.064 47.826 0.00 0.00 43.46 4.70
2891 3895 3.841255 AGGCTCTAACTAAAACAGGAGCT 59.159 43.478 11.56 0.00 43.62 4.09
2907 3911 2.820197 GGAGCTTGTCCTGGGTTTTAAG 59.180 50.000 0.00 0.00 42.99 1.85
2929 3933 2.078849 TTCAGTCGGTATGTGCACAG 57.921 50.000 25.84 11.60 0.00 3.66
2940 3944 1.155889 TGTGCACAGCTTATGTTCCG 58.844 50.000 17.42 0.00 41.41 4.30
2945 3949 1.732259 CACAGCTTATGTTCCGTGTCC 59.268 52.381 0.00 0.00 41.41 4.02
2952 3956 4.612939 GCTTATGTTCCGTGTCCTTGAAAC 60.613 45.833 0.00 0.00 0.00 2.78
2953 3957 2.404923 TGTTCCGTGTCCTTGAAACA 57.595 45.000 0.00 0.00 0.00 2.83
2968 3973 7.444487 GTCCTTGAAACATTTAAGTGTCTACCT 59.556 37.037 3.87 0.00 0.00 3.08
2972 3977 8.197592 TGAAACATTTAAGTGTCTACCTCCTA 57.802 34.615 3.87 0.00 0.00 2.94
2976 3981 8.375493 ACATTTAAGTGTCTACCTCCTATGAA 57.625 34.615 0.00 0.00 0.00 2.57
2979 3984 8.603898 TTTAAGTGTCTACCTCCTATGAATGA 57.396 34.615 0.00 0.00 0.00 2.57
3010 4015 9.539825 TTTTGCAAATGTTTGTATGAGTGTATT 57.460 25.926 13.65 0.00 40.24 1.89
3026 4031 2.224185 TGTATTTGACACACTCGCTGGT 60.224 45.455 0.00 0.00 31.20 4.00
3038 4043 1.447489 CGCTGGTCTTCTCTGCAGG 60.447 63.158 15.13 4.77 0.00 4.85
3048 4053 3.005897 TCTTCTCTGCAGGTTGTAGTCAC 59.994 47.826 15.13 0.00 31.74 3.67
3116 4121 4.558095 GCTTGTTGCACAAAGAGATGATGT 60.558 41.667 10.97 0.00 37.69 3.06
3118 4123 4.862350 TGTTGCACAAAGAGATGATGTTG 58.138 39.130 0.00 0.00 0.00 3.33
3123 4128 4.730657 CACAAAGAGATGATGTTGCCTTC 58.269 43.478 0.00 0.00 0.00 3.46
3128 4133 3.196469 AGAGATGATGTTGCCTTCTTCGA 59.804 43.478 0.00 0.00 0.00 3.71
3172 4177 1.330655 ATCCTGACGCCACCGATTCT 61.331 55.000 0.00 0.00 38.29 2.40
3196 4201 2.148768 GATGAAGATGATCGGCATGCA 58.851 47.619 21.36 0.00 37.34 3.96
3223 4228 7.006509 AGAAGGAAAAGAGAATGACAATGGAA 58.993 34.615 0.00 0.00 0.00 3.53
3247 4252 7.317722 AGTACTAGTTCCAATGAAAACCTCT 57.682 36.000 0.00 0.00 30.79 3.69
3373 4378 2.237965 ATGGGGTAAGTGGGCTGCA 61.238 57.895 0.50 0.00 0.00 4.41
3388 4393 1.604185 GCTGCAGAGATACGTGATCCC 60.604 57.143 20.43 0.00 34.80 3.85
3427 4432 2.733956 TGGATTGGCACATTTACCTCC 58.266 47.619 0.00 0.00 39.30 4.30
3517 4522 1.063642 TCTCGGTCACCTCCATCAGAT 60.064 52.381 0.00 0.00 0.00 2.90
3527 4532 3.458857 ACCTCCATCAGATCATGAAGCTT 59.541 43.478 0.00 0.00 42.53 3.74
3983 4988 2.414559 CCAATGTTCGAGTTGGATGCAC 60.415 50.000 16.78 0.00 46.15 4.57
4259 5268 6.484288 TGGAAGCTCCATCTTCTATTTTTCA 58.516 36.000 1.25 0.00 42.67 2.69
4335 5345 5.227569 TGTCATATTTCAGTGACCTGTGT 57.772 39.130 0.00 0.00 43.09 3.72
4403 5413 8.125978 AGTTCTGAGATTGCCATAAATTTTCA 57.874 30.769 0.00 0.00 0.00 2.69
4408 5418 9.252962 CTGAGATTGCCATAAATTTTCAATACC 57.747 33.333 0.00 0.00 0.00 2.73
4415 5425 6.591001 CCATAAATTTTCAATACCAAGGGGG 58.409 40.000 0.00 0.00 44.81 5.40
4513 5525 6.306356 GTGTTTAGCATCAACAAATAGCACTG 59.694 38.462 0.00 0.00 35.91 3.66
4514 5526 6.016360 TGTTTAGCATCAACAAATAGCACTGT 60.016 34.615 0.00 0.00 31.05 3.55
4515 5527 6.573664 TTAGCATCAACAAATAGCACTGTT 57.426 33.333 0.00 0.00 36.19 3.16
4564 5576 4.080863 AGGCACTGGAATACTGAGGTTTAG 60.081 45.833 0.00 0.00 37.18 1.85
4572 5584 7.792032 TGGAATACTGAGGTTTAGGATTACTG 58.208 38.462 0.00 0.00 31.64 2.74
4581 5593 6.240145 AGGTTTAGGATTACTGCGGTTTTTA 58.760 36.000 1.99 0.00 0.00 1.52
4586 5598 9.465985 TTTAGGATTACTGCGGTTTTTAAAAAG 57.534 29.630 13.58 4.50 0.00 2.27
4606 5618 2.098443 AGTTGTACTGCCAAACCAAACG 59.902 45.455 0.00 0.00 0.00 3.60
4610 5622 0.681564 ACTGCCAAACCAAACGGACA 60.682 50.000 0.00 0.00 0.00 4.02
4624 5636 6.320418 ACCAAACGGACAGAAAGATAAGTTTT 59.680 34.615 0.00 0.00 0.00 2.43
4629 5641 8.307921 ACGGACAGAAAGATAAGTTTTTACTC 57.692 34.615 0.00 0.00 0.00 2.59
4630 5642 8.148999 ACGGACAGAAAGATAAGTTTTTACTCT 58.851 33.333 0.00 0.00 0.00 3.24
4632 5644 9.713713 GGACAGAAAGATAAGTTTTTACTCTCT 57.286 33.333 0.00 0.00 0.00 3.10
4636 5648 9.984190 AGAAAGATAAGTTTTTACTCTCTTCGT 57.016 29.630 0.00 0.00 0.00 3.85
4638 5650 8.760103 AAGATAAGTTTTTACTCTCTTCGTCC 57.240 34.615 0.00 0.00 0.00 4.79
4639 5651 7.028361 AGATAAGTTTTTACTCTCTTCGTCCG 58.972 38.462 0.00 0.00 0.00 4.79
4640 5652 4.843220 AGTTTTTACTCTCTTCGTCCGA 57.157 40.909 0.00 0.00 0.00 4.55
4641 5653 5.192327 AGTTTTTACTCTCTTCGTCCGAA 57.808 39.130 1.81 1.81 0.00 4.30
4642 5654 5.594926 AGTTTTTACTCTCTTCGTCCGAAA 58.405 37.500 3.52 0.00 33.34 3.46
4643 5655 6.044682 AGTTTTTACTCTCTTCGTCCGAAAA 58.955 36.000 3.52 0.00 33.34 2.29
4644 5656 6.200475 AGTTTTTACTCTCTTCGTCCGAAAAG 59.800 38.462 3.52 0.00 33.34 2.27
4645 5657 2.067414 ACTCTCTTCGTCCGAAAAGC 57.933 50.000 3.52 0.00 33.34 3.51
4646 5658 1.614413 ACTCTCTTCGTCCGAAAAGCT 59.386 47.619 3.52 0.00 33.34 3.74
4647 5659 2.036089 ACTCTCTTCGTCCGAAAAGCTT 59.964 45.455 3.52 0.00 33.34 3.74
4648 5660 2.404215 TCTCTTCGTCCGAAAAGCTTG 58.596 47.619 0.00 0.00 33.34 4.01
4649 5661 2.135933 CTCTTCGTCCGAAAAGCTTGT 58.864 47.619 0.00 0.00 33.34 3.16
4650 5662 2.132762 TCTTCGTCCGAAAAGCTTGTC 58.867 47.619 6.56 6.56 33.34 3.18
4651 5663 1.194772 CTTCGTCCGAAAAGCTTGTCC 59.805 52.381 11.14 0.00 33.34 4.02
4652 5664 0.601841 TCGTCCGAAAAGCTTGTCCC 60.602 55.000 11.14 0.00 0.00 4.46
4653 5665 0.602905 CGTCCGAAAAGCTTGTCCCT 60.603 55.000 11.14 0.00 0.00 4.20
4654 5666 1.157585 GTCCGAAAAGCTTGTCCCTC 58.842 55.000 11.14 0.00 0.00 4.30
4655 5667 0.762418 TCCGAAAAGCTTGTCCCTCA 59.238 50.000 11.14 0.00 0.00 3.86
4656 5668 1.142060 TCCGAAAAGCTTGTCCCTCAA 59.858 47.619 11.14 0.00 34.61 3.02
4657 5669 1.953686 CCGAAAAGCTTGTCCCTCAAA 59.046 47.619 11.14 0.00 35.48 2.69
4658 5670 2.558359 CCGAAAAGCTTGTCCCTCAAAT 59.442 45.455 11.14 0.00 35.48 2.32
4659 5671 3.756434 CCGAAAAGCTTGTCCCTCAAATA 59.244 43.478 11.14 0.00 35.48 1.40
4660 5672 4.142600 CCGAAAAGCTTGTCCCTCAAATAG 60.143 45.833 11.14 0.00 35.48 1.73
4661 5673 4.695455 CGAAAAGCTTGTCCCTCAAATAGA 59.305 41.667 11.14 0.00 35.48 1.98
4662 5674 5.355350 CGAAAAGCTTGTCCCTCAAATAGAT 59.645 40.000 11.14 0.00 35.48 1.98
4663 5675 6.521151 AAAAGCTTGTCCCTCAAATAGATG 57.479 37.500 0.00 0.00 35.48 2.90
4664 5676 4.851639 AGCTTGTCCCTCAAATAGATGT 57.148 40.909 0.00 0.00 35.48 3.06
4665 5677 5.957771 AGCTTGTCCCTCAAATAGATGTA 57.042 39.130 0.00 0.00 35.48 2.29
4666 5678 6.506538 AGCTTGTCCCTCAAATAGATGTAT 57.493 37.500 0.00 0.00 35.48 2.29
4667 5679 6.529220 AGCTTGTCCCTCAAATAGATGTATC 58.471 40.000 0.00 0.00 35.48 2.24
4668 5680 6.328672 AGCTTGTCCCTCAAATAGATGTATCT 59.671 38.462 0.00 0.00 36.97 1.98
4669 5681 7.510685 AGCTTGTCCCTCAAATAGATGTATCTA 59.489 37.037 4.22 4.22 36.64 1.98
4670 5682 7.816995 GCTTGTCCCTCAAATAGATGTATCTAG 59.183 40.741 7.57 0.00 36.19 2.43
4671 5683 7.233389 TGTCCCTCAAATAGATGTATCTAGC 57.767 40.000 7.57 0.00 42.20 3.42
4672 5684 7.013220 TGTCCCTCAAATAGATGTATCTAGCT 58.987 38.462 7.57 0.00 42.20 3.32
4673 5685 7.177568 TGTCCCTCAAATAGATGTATCTAGCTC 59.822 40.741 7.57 0.00 42.20 4.09
4674 5686 6.665680 TCCCTCAAATAGATGTATCTAGCTCC 59.334 42.308 7.57 0.00 42.20 4.70
4675 5687 6.438741 CCCTCAAATAGATGTATCTAGCTCCA 59.561 42.308 7.57 0.00 42.20 3.86
4676 5688 7.038729 CCCTCAAATAGATGTATCTAGCTCCAA 60.039 40.741 7.57 0.00 42.20 3.53
4677 5689 8.034215 CCTCAAATAGATGTATCTAGCTCCAAG 58.966 40.741 7.57 0.00 42.20 3.61
4678 5690 8.484214 TCAAATAGATGTATCTAGCTCCAAGT 57.516 34.615 7.57 0.00 42.20 3.16
4679 5691 8.928448 TCAAATAGATGTATCTAGCTCCAAGTT 58.072 33.333 7.57 0.00 42.20 2.66
4682 5694 9.594936 AATAGATGTATCTAGCTCCAAGTTAGT 57.405 33.333 7.57 0.00 42.20 2.24
4683 5695 7.283625 AGATGTATCTAGCTCCAAGTTAGTG 57.716 40.000 0.00 0.00 34.85 2.74
4684 5696 5.263968 TGTATCTAGCTCCAAGTTAGTGC 57.736 43.478 0.00 0.00 31.87 4.40
4685 5697 4.709886 TGTATCTAGCTCCAAGTTAGTGCA 59.290 41.667 0.00 0.00 31.87 4.57
4686 5698 4.826274 ATCTAGCTCCAAGTTAGTGCAA 57.174 40.909 0.00 0.00 31.87 4.08
4687 5699 3.926616 TCTAGCTCCAAGTTAGTGCAAC 58.073 45.455 0.00 0.00 37.41 4.17
4688 5700 2.638480 AGCTCCAAGTTAGTGCAACA 57.362 45.000 0.00 0.00 41.43 3.33
4689 5701 3.146104 AGCTCCAAGTTAGTGCAACAT 57.854 42.857 0.00 0.00 41.43 2.71
4690 5702 4.286297 AGCTCCAAGTTAGTGCAACATA 57.714 40.909 0.00 0.00 41.43 2.29
4691 5703 4.003648 AGCTCCAAGTTAGTGCAACATAC 58.996 43.478 0.00 0.00 41.43 2.39
4692 5704 3.751175 GCTCCAAGTTAGTGCAACATACA 59.249 43.478 0.00 0.00 41.43 2.29
4693 5705 4.396166 GCTCCAAGTTAGTGCAACATACAT 59.604 41.667 0.00 0.00 41.43 2.29
4694 5706 5.447818 GCTCCAAGTTAGTGCAACATACATC 60.448 44.000 0.00 0.00 41.43 3.06
4695 5707 4.941263 TCCAAGTTAGTGCAACATACATCC 59.059 41.667 0.00 0.00 41.43 3.51
4696 5708 4.699735 CCAAGTTAGTGCAACATACATCCA 59.300 41.667 0.00 0.00 41.43 3.41
4697 5709 5.357878 CCAAGTTAGTGCAACATACATCCAT 59.642 40.000 0.00 0.00 41.43 3.41
4698 5710 6.127647 CCAAGTTAGTGCAACATACATCCATT 60.128 38.462 0.00 0.00 41.43 3.16
4699 5711 7.315142 CAAGTTAGTGCAACATACATCCATTT 58.685 34.615 0.00 0.00 41.43 2.32
4700 5712 6.855836 AGTTAGTGCAACATACATCCATTTG 58.144 36.000 0.00 0.00 41.43 2.32
4701 5713 6.658816 AGTTAGTGCAACATACATCCATTTGA 59.341 34.615 0.00 0.00 41.43 2.69
4702 5714 7.340232 AGTTAGTGCAACATACATCCATTTGAT 59.660 33.333 0.00 0.00 41.43 2.57
4704 5716 5.045215 GTGCAACATACATCCATTTGATGG 58.955 41.667 7.06 0.41 45.98 3.51
4715 5727 3.241067 CATTTGATGGACAAGCTTGGG 57.759 47.619 29.18 6.83 39.77 4.12
4716 5728 2.673775 TTTGATGGACAAGCTTGGGA 57.326 45.000 29.18 13.39 39.77 4.37
4717 5729 1.909700 TTGATGGACAAGCTTGGGAC 58.090 50.000 29.18 18.54 34.20 4.46
4718 5730 0.770499 TGATGGACAAGCTTGGGACA 59.230 50.000 29.18 23.01 0.00 4.02
4719 5731 2.424091 TTGATGGACAAGCTTGGGACAA 60.424 45.455 29.18 21.59 37.48 3.18
4720 5732 4.312039 TTGATGGACAAGCTTGGGACAAG 61.312 47.826 29.18 3.71 37.48 3.16
4721 5733 6.762480 TTGATGGACAAGCTTGGGACAAGT 62.762 45.833 29.18 11.32 37.48 3.16
4742 5754 2.730550 TTTTCGGACGGAGGAAGTAC 57.269 50.000 0.00 0.00 0.00 2.73
4743 5755 1.915141 TTTCGGACGGAGGAAGTACT 58.085 50.000 0.00 0.00 0.00 2.73
4744 5756 2.787473 TTCGGACGGAGGAAGTACTA 57.213 50.000 0.00 0.00 0.00 1.82
4745 5757 3.287867 TTCGGACGGAGGAAGTACTAT 57.712 47.619 0.00 0.00 0.00 2.12
4746 5758 3.287867 TCGGACGGAGGAAGTACTATT 57.712 47.619 0.00 0.00 0.00 1.73
4747 5759 3.624777 TCGGACGGAGGAAGTACTATTT 58.375 45.455 0.00 0.00 0.00 1.40
4795 5813 9.193806 AGAATGCCAAGTTCACTATTAATCATT 57.806 29.630 0.00 0.00 0.00 2.57
4799 5817 8.849168 TGCCAAGTTCACTATTAATCATTATGG 58.151 33.333 0.00 0.00 0.00 2.74
4800 5818 9.066892 GCCAAGTTCACTATTAATCATTATGGA 57.933 33.333 0.00 0.00 0.00 3.41
4835 5854 4.141135 CCCTACTAGTCATGAGAGGGAGAA 60.141 50.000 18.04 0.00 45.65 2.87
4946 5966 4.851558 GCTGCTACGTTTTCAGTAAAATGG 59.148 41.667 0.00 0.00 43.15 3.16
4949 5969 6.432107 TGCTACGTTTTCAGTAAAATGGAAC 58.568 36.000 0.00 0.00 43.15 3.62
4959 5979 4.218417 CAGTAAAATGGAACTGTGGGAAGG 59.782 45.833 0.00 0.00 0.00 3.46
5016 6036 1.880340 GAAGGAGATGTCGCAGCCG 60.880 63.158 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.865865 GTGCATACACATACTCGGGG 58.134 55.000 0.00 0.00 46.61 5.73
114 115 9.131791 TGGCCTCTTATTCATATTTCTTTAACC 57.868 33.333 3.32 0.00 0.00 2.85
118 119 8.699130 CCTTTGGCCTCTTATTCATATTTCTTT 58.301 33.333 3.32 0.00 0.00 2.52
199 205 0.792640 CTACGTCCAGCAGCTTTGTG 59.207 55.000 0.00 0.00 0.00 3.33
278 285 3.623703 TGCAAGCTGGTCATATGACAAT 58.376 40.909 31.51 14.74 46.47 2.71
287 294 0.890542 GTCCACATGCAAGCTGGTCA 60.891 55.000 0.00 0.00 0.00 4.02
378 385 5.384063 TTGCCGCAAATTGATCTCTTTAA 57.616 34.783 2.50 0.00 0.00 1.52
433 440 9.667107 ACTTATTAAGCACATTTTAGTAGCTCA 57.333 29.630 3.28 0.00 33.83 4.26
441 448 9.920133 TGCAAATGACTTATTAAGCACATTTTA 57.080 25.926 23.87 18.00 41.83 1.52
442 449 8.830201 TGCAAATGACTTATTAAGCACATTTT 57.170 26.923 23.87 14.81 41.83 1.82
478 514 7.875041 ACTCGCAATAATATCTCTGTAATTGCT 59.125 33.333 13.88 0.00 44.28 3.91
489 525 6.683974 AACAAGCAACTCGCAATAATATCT 57.316 33.333 0.00 0.00 46.13 1.98
528 565 9.362539 GTACTGTCAAGGATTAAAGACGAATAA 57.637 33.333 0.00 0.00 33.83 1.40
534 571 8.443937 GTGATTGTACTGTCAAGGATTAAAGAC 58.556 37.037 0.00 0.00 0.00 3.01
539 576 7.239763 TCAGTGATTGTACTGTCAAGGATTA 57.760 36.000 5.89 0.00 46.32 1.75
544 581 4.143242 CGCTTCAGTGATTGTACTGTCAAG 60.143 45.833 0.00 4.88 46.32 3.02
548 585 3.579709 CTCGCTTCAGTGATTGTACTGT 58.420 45.455 0.00 0.00 46.32 3.55
557 655 1.080501 CTTCGGCTCGCTTCAGTGA 60.081 57.895 0.00 0.00 0.00 3.41
583 681 1.771746 ATGGAGGGGCGATGATGGT 60.772 57.895 0.00 0.00 0.00 3.55
584 682 1.002868 GATGGAGGGGCGATGATGG 60.003 63.158 0.00 0.00 0.00 3.51
620 718 2.104451 TCCCGGCTGTTACTACAACAAA 59.896 45.455 0.00 0.00 32.92 2.83
621 719 1.693062 TCCCGGCTGTTACTACAACAA 59.307 47.619 0.00 0.00 32.92 2.83
633 732 1.051812 ATCTATGGACTTCCCGGCTG 58.948 55.000 0.00 0.00 37.93 4.85
667 766 3.957535 GATCCAGCGGCCAATGCG 61.958 66.667 2.24 0.00 38.85 4.73
690 789 6.201997 TGTTGTGTAGTAGTGTGCATACAAAG 59.798 38.462 16.44 0.00 38.82 2.77
903 1005 7.937394 ACACGGGCTAGAGCTTTTTATTATTAT 59.063 33.333 0.81 0.00 41.70 1.28
910 1012 2.695359 CACACGGGCTAGAGCTTTTTA 58.305 47.619 0.81 0.00 41.70 1.52
1055 1164 2.588439 GGGAGGGGGTTTAGCGAC 59.412 66.667 0.00 0.00 0.00 5.19
1056 1165 2.689771 GGGGAGGGGGTTTAGCGA 60.690 66.667 0.00 0.00 0.00 4.93
1057 1166 2.691252 AGGGGAGGGGGTTTAGCG 60.691 66.667 0.00 0.00 0.00 4.26
1058 1167 2.384433 GGAGGGGAGGGGGTTTAGC 61.384 68.421 0.00 0.00 0.00 3.09
1060 1169 2.462605 GGGAGGGGAGGGGGTTTA 59.537 66.667 0.00 0.00 0.00 2.01
1061 1170 4.714711 GGGGAGGGGAGGGGGTTT 62.715 72.222 0.00 0.00 0.00 3.27
1064 1173 4.845307 GAAGGGGAGGGGAGGGGG 62.845 77.778 0.00 0.00 0.00 5.40
1065 1174 4.845307 GGAAGGGGAGGGGAGGGG 62.845 77.778 0.00 0.00 0.00 4.79
1080 1189 3.326588 TCTCTGGTTTCTTGATTTCCGGA 59.673 43.478 0.00 0.00 33.32 5.14
1083 1192 4.697828 GGTCTCTCTGGTTTCTTGATTTCC 59.302 45.833 0.00 0.00 0.00 3.13
1148 1524 2.423898 GGGAATGAGACGGCGGAGA 61.424 63.158 13.24 0.00 0.00 3.71
1149 1525 2.107141 GGGAATGAGACGGCGGAG 59.893 66.667 13.24 0.00 0.00 4.63
1304 2261 2.113860 TTCGGCAAGAAATCAGGGAG 57.886 50.000 0.00 0.00 35.61 4.30
1305 2262 2.224769 ACTTTCGGCAAGAAATCAGGGA 60.225 45.455 6.99 0.00 46.60 4.20
1421 2391 1.339610 AGATCGGCAGAAATCCTCGAG 59.660 52.381 5.13 5.13 33.32 4.04
1523 2496 2.112279 AGGACCAAACACCTAGGACA 57.888 50.000 17.98 0.00 34.47 4.02
1524 2497 3.581770 AGTAAGGACCAAACACCTAGGAC 59.418 47.826 17.98 0.00 35.25 3.85
1525 2498 3.581332 CAGTAAGGACCAAACACCTAGGA 59.419 47.826 17.98 0.00 35.25 2.94
1639 2614 0.729116 GATCATCGCACCAACACCAG 59.271 55.000 0.00 0.00 0.00 4.00
1876 2851 2.108157 TCGCCAGTCGTTGCAACT 59.892 55.556 26.09 5.81 39.67 3.16
2031 3006 8.967918 GGGAATAAAGTATTAATATCAAGGGGC 58.032 37.037 0.00 0.00 0.00 5.80
2059 3034 9.008965 TGAACAAGCTATTGCAGTTTATTCTTA 57.991 29.630 10.25 0.00 40.27 2.10
2224 3211 4.406972 AGATGACCGGATGAAAATGAGAGA 59.593 41.667 9.46 0.00 0.00 3.10
2301 3288 3.485394 TGTGCAGGTCAGCTTTGAAATA 58.515 40.909 0.00 0.00 34.99 1.40
2352 3339 6.541969 TGTTTGAATGCATGTACGTATCTTG 58.458 36.000 0.00 3.02 0.00 3.02
2695 3696 6.545666 TGAAAATGAAGGAGTGCTGAACTTAA 59.454 34.615 0.00 0.00 40.07 1.85
2724 3728 5.630121 TGTTTATGAACTGGAGGAATGTGT 58.370 37.500 1.75 0.00 36.70 3.72
2725 3729 6.381801 GTTGTTTATGAACTGGAGGAATGTG 58.618 40.000 1.75 0.00 36.70 3.21
2735 3739 3.820467 TCTGGCTGGTTGTTTATGAACTG 59.180 43.478 1.75 0.00 36.70 3.16
2749 3753 2.935481 GAAATCTGCTTTCTGGCTGG 57.065 50.000 0.00 0.00 40.17 4.85
2841 3845 3.686241 CACAATCTCCGAAATCAGAAGCA 59.314 43.478 0.00 0.00 0.00 3.91
2843 3847 3.242220 CGCACAATCTCCGAAATCAGAAG 60.242 47.826 0.00 0.00 0.00 2.85
2853 3857 2.169789 CCTGAGCGCACAATCTCCG 61.170 63.158 11.47 0.00 0.00 4.63
2886 3890 2.579410 TAAAACCCAGGACAAGCTCC 57.421 50.000 0.00 0.00 39.81 4.70
2887 3891 3.751518 TCTTAAAACCCAGGACAAGCTC 58.248 45.455 0.00 0.00 0.00 4.09
2888 3892 3.876309 TCTTAAAACCCAGGACAAGCT 57.124 42.857 0.00 0.00 0.00 3.74
2889 3893 5.010617 TGAAATCTTAAAACCCAGGACAAGC 59.989 40.000 0.00 0.00 0.00 4.01
2890 3894 6.265422 ACTGAAATCTTAAAACCCAGGACAAG 59.735 38.462 0.00 0.00 0.00 3.16
2891 3895 6.133356 ACTGAAATCTTAAAACCCAGGACAA 58.867 36.000 0.00 0.00 0.00 3.18
2901 3905 6.428465 TGCACATACCGACTGAAATCTTAAAA 59.572 34.615 0.00 0.00 0.00 1.52
2907 3911 3.000041 TGTGCACATACCGACTGAAATC 59.000 45.455 17.42 0.00 0.00 2.17
2929 3933 2.695359 TCAAGGACACGGAACATAAGC 58.305 47.619 0.00 0.00 0.00 3.09
2940 3944 7.027778 AGACACTTAAATGTTTCAAGGACAC 57.972 36.000 0.00 0.00 31.24 3.67
2945 3949 7.661847 AGGAGGTAGACACTTAAATGTTTCAAG 59.338 37.037 0.00 0.00 31.24 3.02
2952 3956 9.265901 CATTCATAGGAGGTAGACACTTAAATG 57.734 37.037 0.00 0.00 0.00 2.32
2953 3957 9.213777 TCATTCATAGGAGGTAGACACTTAAAT 57.786 33.333 0.00 0.00 0.00 1.40
2986 3991 8.976471 CAAATACACTCATACAAACATTTGCAA 58.024 29.630 0.00 0.00 41.79 4.08
2989 3994 9.676195 TGTCAAATACACTCATACAAACATTTG 57.324 29.630 2.77 2.77 37.40 2.32
3010 4015 0.464036 AAGACCAGCGAGTGTGTCAA 59.536 50.000 0.00 0.00 31.94 3.18
3021 4026 0.036022 AACCTGCAGAGAAGACCAGC 59.964 55.000 17.39 0.00 0.00 4.85
3026 4031 3.005897 GTGACTACAACCTGCAGAGAAGA 59.994 47.826 17.39 0.00 0.00 2.87
3079 4084 3.119352 GCAACAAGCCCCTTGATCTTAAG 60.119 47.826 11.56 0.00 43.42 1.85
3080 4085 2.825532 GCAACAAGCCCCTTGATCTTAA 59.174 45.455 11.56 0.00 43.42 1.85
3081 4086 2.224992 TGCAACAAGCCCCTTGATCTTA 60.225 45.455 11.56 0.00 43.42 2.10
3082 4087 1.260544 GCAACAAGCCCCTTGATCTT 58.739 50.000 11.56 0.00 43.42 2.40
3123 4128 1.726853 AATGCGAACCTTCCTCGAAG 58.273 50.000 0.00 0.00 38.61 3.79
3172 4177 3.825143 TGCCGATCATCTTCATCAGAA 57.175 42.857 0.00 0.00 34.16 3.02
3196 4201 7.506938 TCCATTGTCATTCTCTTTTCCTTCTTT 59.493 33.333 0.00 0.00 0.00 2.52
3223 4228 7.162082 CAGAGGTTTTCATTGGAACTAGTACT 58.838 38.462 0.00 0.00 31.35 2.73
3247 4252 0.178944 TTCGAGACTTGAGGGGTCCA 60.179 55.000 0.00 0.00 34.56 4.02
3289 4294 8.924511 TCTTCTCTGTACCAATTGATTTCTTT 57.075 30.769 7.12 0.00 0.00 2.52
3373 4378 2.222886 CTCACGGGATCACGTATCTCT 58.777 52.381 24.85 0.00 46.75 3.10
3388 4393 0.673644 ATTTCCGGGTCTTGCTCACG 60.674 55.000 0.00 0.00 0.00 4.35
3453 4458 4.323477 CCCGGTTCCGTTCTGCCA 62.323 66.667 10.36 0.00 0.00 4.92
3517 4522 1.159285 CGCTGGACAAAGCTTCATGA 58.841 50.000 0.00 0.00 41.24 3.07
3527 4532 0.679505 ACAGTAGCTTCGCTGGACAA 59.320 50.000 14.33 0.00 40.10 3.18
3983 4988 5.240844 AGTCGAAACCTTCCCAATTAAGTTG 59.759 40.000 0.00 0.00 37.57 3.16
4053 5058 4.515191 TCAGAAAGACGAAAACCTCAATGG 59.485 41.667 0.00 0.00 42.93 3.16
4067 5072 3.513515 ACCCTGACATCTCTCAGAAAGAC 59.486 47.826 0.00 0.00 40.28 3.01
4123 5128 6.687081 AGACTGTACAATTTCCGACAAAAA 57.313 33.333 0.00 0.00 0.00 1.94
4278 5287 3.238108 TCGCACAAACCAACACAAAAT 57.762 38.095 0.00 0.00 0.00 1.82
4383 5393 8.756927 TGGTATTGAAAATTTATGGCAATCTCA 58.243 29.630 0.00 8.25 32.13 3.27
4415 5425 0.313987 AAACGCAGCCTTAACTTGCC 59.686 50.000 0.00 0.00 34.42 4.52
4416 5426 1.408422 CAAACGCAGCCTTAACTTGC 58.592 50.000 0.00 0.00 34.58 4.01
4459 5469 6.321848 AGTTTATAAAACCGTGGTTTCTGG 57.678 37.500 16.83 0.00 46.22 3.86
4564 5576 7.223193 ACAACTTTTTAAAAACCGCAGTAATCC 59.777 33.333 9.31 0.00 0.00 3.01
4572 5584 5.276489 GGCAGTACAACTTTTTAAAAACCGC 60.276 40.000 9.31 3.96 0.00 5.68
4581 5593 4.810191 TGGTTTGGCAGTACAACTTTTT 57.190 36.364 0.00 0.00 0.00 1.94
4586 5598 2.456010 CGTTTGGTTTGGCAGTACAAC 58.544 47.619 0.00 0.00 0.00 3.32
4606 5618 9.713713 AGAGAGTAAAAACTTATCTTTCTGTCC 57.286 33.333 0.00 0.00 0.00 4.02
4610 5622 9.984190 ACGAAGAGAGTAAAAACTTATCTTTCT 57.016 29.630 0.00 0.00 30.99 2.52
4624 5636 3.255149 AGCTTTTCGGACGAAGAGAGTAA 59.745 43.478 23.61 7.72 38.23 2.24
4629 5641 2.135933 ACAAGCTTTTCGGACGAAGAG 58.864 47.619 17.44 17.44 38.77 2.85
4630 5642 2.132762 GACAAGCTTTTCGGACGAAGA 58.867 47.619 7.25 2.48 35.38 2.87
4632 5644 1.223187 GGACAAGCTTTTCGGACGAA 58.777 50.000 6.53 2.62 0.00 3.85
4633 5645 0.601841 GGGACAAGCTTTTCGGACGA 60.602 55.000 6.53 0.00 0.00 4.20
4634 5646 0.602905 AGGGACAAGCTTTTCGGACG 60.603 55.000 6.53 0.00 0.00 4.79
4635 5647 1.157585 GAGGGACAAGCTTTTCGGAC 58.842 55.000 6.53 0.34 0.00 4.79
4636 5648 0.762418 TGAGGGACAAGCTTTTCGGA 59.238 50.000 6.53 0.00 0.00 4.55
4637 5649 1.604604 TTGAGGGACAAGCTTTTCGG 58.395 50.000 6.53 0.00 34.20 4.30
4638 5650 3.923017 ATTTGAGGGACAAGCTTTTCG 57.077 42.857 6.53 0.00 39.77 3.46
4639 5651 6.151817 ACATCTATTTGAGGGACAAGCTTTTC 59.848 38.462 3.91 3.91 39.77 2.29
4640 5652 6.012745 ACATCTATTTGAGGGACAAGCTTTT 58.987 36.000 0.00 0.00 39.77 2.27
4641 5653 5.574188 ACATCTATTTGAGGGACAAGCTTT 58.426 37.500 0.00 0.00 39.77 3.51
4642 5654 5.184892 ACATCTATTTGAGGGACAAGCTT 57.815 39.130 0.00 0.00 39.77 3.74
4643 5655 4.851639 ACATCTATTTGAGGGACAAGCT 57.148 40.909 0.00 0.00 39.77 3.74
4644 5656 6.529220 AGATACATCTATTTGAGGGACAAGC 58.471 40.000 0.00 0.00 36.19 4.01
4645 5657 7.816995 GCTAGATACATCTATTTGAGGGACAAG 59.183 40.741 0.00 0.00 38.60 3.16
4646 5658 7.510685 AGCTAGATACATCTATTTGAGGGACAA 59.489 37.037 0.00 0.00 38.60 3.18
4647 5659 7.013220 AGCTAGATACATCTATTTGAGGGACA 58.987 38.462 0.00 0.00 38.60 4.02
4648 5660 7.363443 GGAGCTAGATACATCTATTTGAGGGAC 60.363 44.444 0.00 0.00 38.60 4.46
4649 5661 6.665680 GGAGCTAGATACATCTATTTGAGGGA 59.334 42.308 0.00 0.00 38.60 4.20
4650 5662 6.438741 TGGAGCTAGATACATCTATTTGAGGG 59.561 42.308 0.00 0.00 38.60 4.30
4651 5663 7.473735 TGGAGCTAGATACATCTATTTGAGG 57.526 40.000 0.00 0.00 38.60 3.86
4652 5664 8.584157 ACTTGGAGCTAGATACATCTATTTGAG 58.416 37.037 0.00 0.00 38.60 3.02
4653 5665 8.484214 ACTTGGAGCTAGATACATCTATTTGA 57.516 34.615 0.00 0.00 38.60 2.69
4656 5668 9.594936 ACTAACTTGGAGCTAGATACATCTATT 57.405 33.333 0.00 0.00 38.60 1.73
4657 5669 9.019656 CACTAACTTGGAGCTAGATACATCTAT 57.980 37.037 0.00 0.00 38.60 1.98
4658 5670 7.040340 GCACTAACTTGGAGCTAGATACATCTA 60.040 40.741 0.00 0.00 38.32 1.98
4659 5671 6.239176 GCACTAACTTGGAGCTAGATACATCT 60.239 42.308 0.00 0.00 40.86 2.90
4660 5672 5.923684 GCACTAACTTGGAGCTAGATACATC 59.076 44.000 0.00 0.00 0.00 3.06
4661 5673 5.363868 TGCACTAACTTGGAGCTAGATACAT 59.636 40.000 0.00 0.00 0.00 2.29
4662 5674 4.709886 TGCACTAACTTGGAGCTAGATACA 59.290 41.667 0.00 0.00 0.00 2.29
4663 5675 5.263968 TGCACTAACTTGGAGCTAGATAC 57.736 43.478 0.00 0.00 0.00 2.24
4664 5676 5.186992 TGTTGCACTAACTTGGAGCTAGATA 59.813 40.000 0.00 0.00 40.05 1.98
4665 5677 4.020218 TGTTGCACTAACTTGGAGCTAGAT 60.020 41.667 0.00 0.00 40.05 1.98
4666 5678 3.323691 TGTTGCACTAACTTGGAGCTAGA 59.676 43.478 0.00 0.00 40.05 2.43
4667 5679 3.664107 TGTTGCACTAACTTGGAGCTAG 58.336 45.455 0.00 0.00 40.05 3.42
4668 5680 3.762407 TGTTGCACTAACTTGGAGCTA 57.238 42.857 0.00 0.00 40.05 3.32
4669 5681 2.638480 TGTTGCACTAACTTGGAGCT 57.362 45.000 0.00 0.00 40.05 4.09
4670 5682 3.751175 TGTATGTTGCACTAACTTGGAGC 59.249 43.478 0.00 0.00 40.05 4.70
4671 5683 5.065218 GGATGTATGTTGCACTAACTTGGAG 59.935 44.000 0.00 0.00 40.05 3.86
4672 5684 4.941263 GGATGTATGTTGCACTAACTTGGA 59.059 41.667 0.00 0.00 40.05 3.53
4673 5685 4.699735 TGGATGTATGTTGCACTAACTTGG 59.300 41.667 0.00 0.00 40.05 3.61
4674 5686 5.878332 TGGATGTATGTTGCACTAACTTG 57.122 39.130 0.00 0.00 40.05 3.16
4675 5687 7.176515 TCAAATGGATGTATGTTGCACTAACTT 59.823 33.333 0.00 0.00 40.05 2.66
4676 5688 6.658816 TCAAATGGATGTATGTTGCACTAACT 59.341 34.615 0.00 0.00 40.05 2.24
4677 5689 6.851609 TCAAATGGATGTATGTTGCACTAAC 58.148 36.000 0.00 0.00 39.80 2.34
4678 5690 7.482474 CATCAAATGGATGTATGTTGCACTAA 58.518 34.615 0.00 0.00 46.81 2.24
4679 5691 7.030075 CATCAAATGGATGTATGTTGCACTA 57.970 36.000 0.00 0.00 46.81 2.74
4680 5692 5.898174 CATCAAATGGATGTATGTTGCACT 58.102 37.500 0.00 0.00 46.81 4.40
4695 5707 2.827322 TCCCAAGCTTGTCCATCAAATG 59.173 45.455 24.35 5.47 35.48 2.32
4696 5708 2.827921 GTCCCAAGCTTGTCCATCAAAT 59.172 45.455 24.35 0.00 35.48 2.32
4697 5709 2.238521 GTCCCAAGCTTGTCCATCAAA 58.761 47.619 24.35 0.00 35.48 2.69
4698 5710 1.144708 TGTCCCAAGCTTGTCCATCAA 59.855 47.619 24.35 1.41 34.61 2.57
4699 5711 0.770499 TGTCCCAAGCTTGTCCATCA 59.230 50.000 24.35 12.85 0.00 3.07
4700 5712 1.815003 CTTGTCCCAAGCTTGTCCATC 59.185 52.381 24.35 10.65 0.00 3.51
4701 5713 1.145738 ACTTGTCCCAAGCTTGTCCAT 59.854 47.619 24.35 2.27 0.00 3.41
4702 5714 0.550914 ACTTGTCCCAAGCTTGTCCA 59.449 50.000 24.35 14.48 0.00 4.02
4703 5715 1.692411 AACTTGTCCCAAGCTTGTCC 58.308 50.000 24.35 12.15 0.00 4.02
4704 5716 3.801114 AAAACTTGTCCCAAGCTTGTC 57.199 42.857 24.35 14.49 0.00 3.18
4722 5734 2.629617 AGTACTTCCTCCGTCCGAAAAA 59.370 45.455 0.00 0.00 0.00 1.94
4723 5735 2.242043 AGTACTTCCTCCGTCCGAAAA 58.758 47.619 0.00 0.00 0.00 2.29
4724 5736 1.915141 AGTACTTCCTCCGTCCGAAA 58.085 50.000 0.00 0.00 0.00 3.46
4725 5737 2.787473 TAGTACTTCCTCCGTCCGAA 57.213 50.000 0.00 0.00 0.00 4.30
4726 5738 3.287867 AATAGTACTTCCTCCGTCCGA 57.712 47.619 0.00 0.00 0.00 4.55
4727 5739 4.818546 TCTAAATAGTACTTCCTCCGTCCG 59.181 45.833 0.00 0.00 0.00 4.79
4728 5740 6.705863 TTCTAAATAGTACTTCCTCCGTCC 57.294 41.667 0.00 0.00 0.00 4.79
4737 5749 9.095065 CGCTGGTGTAATTTCTAAATAGTACTT 57.905 33.333 0.00 0.00 0.00 2.24
4738 5750 8.255905 ACGCTGGTGTAATTTCTAAATAGTACT 58.744 33.333 0.00 0.00 0.00 2.73
4739 5751 8.325997 CACGCTGGTGTAATTTCTAAATAGTAC 58.674 37.037 0.00 0.00 39.38 2.73
4740 5752 8.415192 CACGCTGGTGTAATTTCTAAATAGTA 57.585 34.615 0.00 0.00 39.38 1.82
4741 5753 7.303634 CACGCTGGTGTAATTTCTAAATAGT 57.696 36.000 0.00 0.00 39.38 2.12
4762 5776 1.197721 GAACTTGGCATTCTCCACACG 59.802 52.381 0.00 0.00 35.50 4.49
4835 5854 8.814038 ATATAGTTCTGTTCTGGATGCTTTTT 57.186 30.769 0.00 0.00 0.00 1.94
4840 5859 8.839310 ACATTATATAGTTCTGTTCTGGATGC 57.161 34.615 0.00 0.00 0.00 3.91
4887 5906 7.015584 AGCAATTTTCCATTTTCTGGTCTAGTT 59.984 33.333 0.00 0.00 46.08 2.24
4888 5907 6.494835 AGCAATTTTCCATTTTCTGGTCTAGT 59.505 34.615 0.00 0.00 46.08 2.57
4936 5956 4.218417 CCTTCCCACAGTTCCATTTTACTG 59.782 45.833 0.00 0.00 45.61 2.74
4946 5966 2.359975 CGCCCCTTCCCACAGTTC 60.360 66.667 0.00 0.00 0.00 3.01
4969 5989 2.181021 CGTCTACTGACCACGCCC 59.819 66.667 0.00 0.00 39.94 6.13


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

AutoCloner maintained by Alex Coulton.