Multiple sequence alignment - TraesCS2A01G160300

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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 TraesCS2A01G160300 chr2A 100.000 5334 0 0 1 5334 111425468 111420135 0.000000e+00 9851
1 TraesCS2A01G160300 chr2A 92.708 192 14 0 1315 1506 111424061 111423870 1.460000e-70 278
2 TraesCS2A01G160300 chr2A 93.939 99 6 0 1501 1599 111424154 111424056 3.330000e-32 150
3 TraesCS2A01G160300 chr2D 95.368 3238 95 18 1315 4526 111334673 111331465 0.000000e+00 5097
4 TraesCS2A01G160300 chr2D 93.681 1630 55 10 1 1599 111336094 111334482 0.000000e+00 2396
5 TraesCS2A01G160300 chr2D 91.892 629 36 7 4555 5173 111331476 111330853 0.000000e+00 865
6 TraesCS2A01G160300 chr2D 93.750 192 12 0 1315 1506 111334580 111334389 6.760000e-74 289
7 TraesCS2A01G160300 chr2D 92.708 192 14 0 1408 1599 111334766 111334575 1.460000e-70 278
8 TraesCS2A01G160300 chr2D 93.939 99 6 0 1501 1599 111334766 111334668 3.330000e-32 150
9 TraesCS2A01G160300 chr2B 94.466 1825 72 12 2734 4535 161416223 161414405 0.000000e+00 2784
10 TraesCS2A01G160300 chr2B 97.540 1423 33 1 1315 2737 161417745 161416325 0.000000e+00 2433
11 TraesCS2A01G160300 chr2B 93.009 1602 74 15 14 1599 161419133 161417554 0.000000e+00 2303
12 TraesCS2A01G160300 chr2B 91.379 406 23 7 4554 4950 161414419 161414017 3.630000e-151 545
13 TraesCS2A01G160300 chr2B 93.229 192 13 0 1315 1506 161417652 161417461 3.140000e-72 283
14 TraesCS2A01G160300 chr2B 93.229 192 13 0 1408 1599 161417838 161417647 3.140000e-72 283
15 TraesCS2A01G160300 chr2B 94.949 99 5 0 1501 1599 161417838 161417740 7.150000e-34 156
16 TraesCS2A01G160300 chr2B 93.939 99 6 0 1315 1413 161417559 161417461 3.330000e-32 150
17 TraesCS2A01G160300 chr3A 83.439 948 94 31 2227 3157 687993552 687992651 0.000000e+00 822
18 TraesCS2A01G160300 chr7D 89.954 219 17 4 4956 5173 559075553 559075339 1.460000e-70 278
19 TraesCS2A01G160300 chr7D 81.169 154 25 3 5178 5328 559075294 559075142 2.610000e-23 121
20 TraesCS2A01G160300 chr4D 90.683 161 15 0 3327 3487 274221106 274221266 1.160000e-51 215
21 TraesCS2A01G160300 chr4A 90.683 161 15 0 3327 3487 255591570 255591410 1.160000e-51 215
22 TraesCS2A01G160300 chr4B 90.062 161 16 0 3327 3487 240826751 240826911 5.410000e-50 209


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 TraesCS2A01G160300 chr2A 111420135 111425468 5333 True 3426.333333 9851 95.549000 1 5334 3 chr2A.!!$R1 5333
1 TraesCS2A01G160300 chr2D 111330853 111336094 5241 True 1512.500000 5097 93.556333 1 5173 6 chr2D.!!$R1 5172
2 TraesCS2A01G160300 chr2B 161414017 161419133 5116 True 1117.125000 2784 93.967500 14 4950 8 chr2B.!!$R1 4936
3 TraesCS2A01G160300 chr3A 687992651 687993552 901 True 822.000000 822 83.439000 2227 3157 1 chr3A.!!$R1 930

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
204 211 0.558712 TAGGGTTTTGTGGCTTGGGT 59.441 50.000 0.00 0.0 0.00 4.51 F
377 385 0.798009 CCGTGCGATTTGGACATTGC 60.798 55.000 0.00 0.0 39.19 3.56 F
483 492 1.001815 AGTGGCCATTGTCGTTTTTCG 60.002 47.619 9.72 0.0 41.41 3.46 F
2272 2404 0.680921 ACCATGCAACATTCCCTCCG 60.681 55.000 0.00 0.0 0.00 4.63 F
2681 2837 4.333649 CGCATACAGTGTTGGATCATTTCT 59.666 41.667 0.00 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1336 1375 0.744874 TCTGTAGTAGCATCGGCACC 59.255 55.000 0.00 0.0 44.61 5.01 R
2272 2404 2.368439 TGCCTGCAAATCATCACCTAC 58.632 47.619 0.00 0.0 0.00 3.18 R
2433 2570 3.458831 ACTTTCCATCACATCCTCCTCT 58.541 45.455 0.00 0.0 0.00 3.69 R
3372 3654 0.453793 TAAATGGGCGCACAAATCGG 59.546 50.000 20.27 0.0 0.00 4.18 R
4404 4708 0.179034 GAAGAGAATCCGCTGGCCAT 60.179 55.000 5.51 0.0 33.66 4.40 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
204 211 0.558712 TAGGGTTTTGTGGCTTGGGT 59.441 50.000 0.00 0.00 0.00 4.51
323 330 2.505118 GTCGCGAGGTGAGCTCAC 60.505 66.667 34.25 34.25 45.72 3.51
377 385 0.798009 CCGTGCGATTTGGACATTGC 60.798 55.000 0.00 0.00 39.19 3.56
396 404 4.077300 TGCTCAGATGGTTAGGCATTAG 57.923 45.455 0.00 0.00 0.00 1.73
447 456 2.257034 GTTTAGGCGTAGGTCTGTTCG 58.743 52.381 0.00 0.00 0.00 3.95
483 492 1.001815 AGTGGCCATTGTCGTTTTTCG 60.002 47.619 9.72 0.00 41.41 3.46
599 632 8.504815 CAATTTTGTTTTATGGTGCATGAATGA 58.495 29.630 0.00 0.00 0.00 2.57
689 722 3.229276 TGCACAGTGTGAAACCTTTTG 57.771 42.857 27.37 0.00 35.23 2.44
711 744 3.334583 TTCTACATGGAGCACTTCACC 57.665 47.619 0.00 0.00 0.00 4.02
822 855 5.887754 AGTTCCTACTCCCTAAAATGCAAA 58.112 37.500 0.00 0.00 0.00 3.68
892 926 5.215903 GCAACTTAAGAAGGAAGCAGTTTC 58.784 41.667 10.09 0.00 34.93 2.78
897 935 4.907879 AAGAAGGAAGCAGTTTCACTTG 57.092 40.909 0.00 0.00 37.54 3.16
960 999 8.442384 GCTGGTAAAAATTCATGTTTAATGGTG 58.558 33.333 0.00 0.00 0.00 4.17
1003 1042 3.258872 CAGGATTTTTCCAGCCACAATGA 59.741 43.478 0.00 0.00 0.00 2.57
1336 1375 5.184096 TCTGTTACAGAGGCTAGTGAGAAAG 59.816 44.000 11.42 0.00 35.39 2.62
1372 1504 4.414337 ACAGAGGTTATTCAGGATGCTC 57.586 45.455 0.00 0.00 34.76 4.26
1459 1591 6.037281 CGATGCTACTACAGAAGTTAGTCAGA 59.963 42.308 0.00 0.00 39.80 3.27
1484 1616 5.005740 TGCTGTAGTTAGTACCGAAGAAGA 58.994 41.667 0.00 0.00 0.00 2.87
1717 1849 2.837591 TCAGCTCCAAGTGGCAGTAATA 59.162 45.455 0.00 0.00 34.44 0.98
1851 1983 4.882842 TGCCAGTACTGATGTCAAGTTA 57.117 40.909 24.68 0.00 0.00 2.24
2103 2235 1.152830 AACCGTGGCAGGGACAAAT 59.847 52.632 31.26 6.85 35.02 2.32
2272 2404 0.680921 ACCATGCAACATTCCCTCCG 60.681 55.000 0.00 0.00 0.00 4.63
2353 2485 8.645110 CCCCATTGCAAGAAATAGAATCTAAAT 58.355 33.333 4.94 0.00 0.00 1.40
2433 2570 7.584122 ACTAAATTTAGACAGGAGCTCGATA 57.416 36.000 27.92 0.00 34.84 2.92
2481 2627 7.687388 AGCATGTTGATACCATTATCAGATCT 58.313 34.615 0.00 0.00 44.03 2.75
2482 2628 7.606839 AGCATGTTGATACCATTATCAGATCTG 59.393 37.037 17.07 17.07 44.03 2.90
2483 2629 7.605309 GCATGTTGATACCATTATCAGATCTGA 59.395 37.037 27.03 27.03 44.03 3.27
2681 2837 4.333649 CGCATACAGTGTTGGATCATTTCT 59.666 41.667 0.00 0.00 0.00 2.52
2800 3081 4.917415 GTGCATGTGTAAAGTTCATTGTCC 59.083 41.667 0.00 0.00 0.00 4.02
2912 3193 6.183361 ACGGTTTTGGGAAATAGGACAATTTT 60.183 34.615 0.00 0.00 0.00 1.82
2951 3232 6.233905 AGTAAGATTTGTGGCCTTTGTTTT 57.766 33.333 3.32 0.00 0.00 2.43
3064 3345 4.574599 AAATGCAGACCAAGAAGTTGTC 57.425 40.909 0.00 0.00 30.95 3.18
3200 3481 5.606348 AAAACATTTTGTTGGCAGGTCTA 57.394 34.783 0.00 0.00 40.14 2.59
3322 3604 9.768215 TCTAATTTTTCCCCTTCTGTATTCATT 57.232 29.630 0.00 0.00 0.00 2.57
3372 3654 4.496507 GCAACAACTTCCTTGAGAGTTGAC 60.497 45.833 19.51 7.67 42.81 3.18
3518 3800 6.176975 TCATTGTCTTATTTTACCTGTGCG 57.823 37.500 0.00 0.00 0.00 5.34
3625 3907 9.191995 GTGTTACAGCTAAAATTTGCTAAATGT 57.808 29.630 2.95 1.74 37.15 2.71
3655 3937 5.048713 ACAATAGTTTGTGCTTTAGCCTGTC 60.049 40.000 0.00 0.00 44.36 3.51
3657 3939 1.602377 GTTTGTGCTTTAGCCTGTCGT 59.398 47.619 0.00 0.00 41.18 4.34
3664 3946 2.159693 GCTTTAGCCTGTCGTTGCTAAC 60.160 50.000 3.62 0.00 46.56 2.34
3715 3997 6.032956 CCTGGTAGGGGTTAATTTTTGTTC 57.967 41.667 0.00 0.00 0.00 3.18
3716 3998 5.778241 CCTGGTAGGGGTTAATTTTTGTTCT 59.222 40.000 0.00 0.00 0.00 3.01
3717 3999 6.269077 CCTGGTAGGGGTTAATTTTTGTTCTT 59.731 38.462 0.00 0.00 0.00 2.52
3775 4057 5.179533 TGTTAGCATTGTCGTGCCTTATTA 58.820 37.500 0.00 0.00 46.19 0.98
3812 4116 9.322776 GAATCTCGTGATGCATTATTTGATAAC 57.677 33.333 0.00 0.00 32.44 1.89
3851 4155 4.164030 TGCCTGCTTGTCCTATTTCTGATA 59.836 41.667 0.00 0.00 0.00 2.15
3996 4300 2.765705 ATCGAACACCCTCCCCCACT 62.766 60.000 0.00 0.00 0.00 4.00
4016 4320 2.185350 CACTGCCTACCAGCCTCG 59.815 66.667 0.00 0.00 45.78 4.63
4080 4384 1.892474 GGCTAACCAAACCATGCTTCA 59.108 47.619 0.00 0.00 35.26 3.02
4083 4387 0.673437 AACCAAACCATGCTTCACCG 59.327 50.000 0.00 0.00 0.00 4.94
4160 4464 2.653543 TACCACATCTAACCCCAGGT 57.346 50.000 0.00 0.00 37.65 4.00
4246 4550 1.194781 TCTTCAGGAGGACACAGGCC 61.195 60.000 0.00 0.00 0.00 5.19
4289 4593 1.333177 CTTATCGGAGGAGGAGGTGG 58.667 60.000 0.00 0.00 0.00 4.61
4355 4659 0.601311 GACTCAAACCTGCTGCTCGT 60.601 55.000 0.00 0.00 0.00 4.18
4404 4708 0.250945 TTATTCAGGCACAACCGGCA 60.251 50.000 0.00 0.00 46.52 5.69
4429 4733 2.104792 CCAGCGGATTCTCTTCCCAATA 59.895 50.000 0.00 0.00 31.61 1.90
4469 4773 3.077359 AGCAGTTAACATGAAGGCTGTC 58.923 45.455 8.61 0.22 0.00 3.51
4522 4829 0.751643 AAGCTTTGCACGGTCTTGGT 60.752 50.000 0.00 0.00 0.00 3.67
4527 4834 0.817634 TTGCACGGTCTTGGTCTTGG 60.818 55.000 0.00 0.00 0.00 3.61
4528 4835 1.070786 GCACGGTCTTGGTCTTGGA 59.929 57.895 0.00 0.00 0.00 3.53
4529 4836 0.534203 GCACGGTCTTGGTCTTGGAA 60.534 55.000 0.00 0.00 0.00 3.53
4530 4837 1.226746 CACGGTCTTGGTCTTGGAAC 58.773 55.000 0.00 0.00 0.00 3.62
4531 4838 1.129058 ACGGTCTTGGTCTTGGAACT 58.871 50.000 0.00 0.00 0.00 3.01
4532 4839 1.070289 ACGGTCTTGGTCTTGGAACTC 59.930 52.381 0.00 0.00 0.00 3.01
4533 4840 1.344763 CGGTCTTGGTCTTGGAACTCT 59.655 52.381 0.00 0.00 0.00 3.24
4534 4841 2.224305 CGGTCTTGGTCTTGGAACTCTT 60.224 50.000 0.00 0.00 0.00 2.85
4535 4842 3.744530 CGGTCTTGGTCTTGGAACTCTTT 60.745 47.826 0.00 0.00 0.00 2.52
4536 4843 4.207955 GGTCTTGGTCTTGGAACTCTTTT 58.792 43.478 0.00 0.00 0.00 2.27
4537 4844 4.645136 GGTCTTGGTCTTGGAACTCTTTTT 59.355 41.667 0.00 0.00 0.00 1.94
4584 4891 6.127980 TGGAACTCTTGATAACTGAGTAGTCG 60.128 42.308 0.00 0.00 39.78 4.18
4636 4943 3.040147 TGTCTGCCTAGCTGTTAACAC 57.960 47.619 3.59 2.24 0.00 3.32
4662 4969 1.396996 CGTGAATTTCCATCACCGACC 59.603 52.381 1.45 0.00 43.34 4.79
4707 5014 2.508867 CAATGTGCTGCGTGTATGTTC 58.491 47.619 0.00 0.00 0.00 3.18
4714 5022 2.285602 GCTGCGTGTATGTTCATAACCG 60.286 50.000 0.00 2.13 0.00 4.44
4725 5041 5.539582 TGTTCATAACCGTTGATGCTTAC 57.460 39.130 0.00 0.00 0.00 2.34
4726 5042 5.242434 TGTTCATAACCGTTGATGCTTACT 58.758 37.500 0.00 0.00 0.00 2.24
4728 5044 7.045416 TGTTCATAACCGTTGATGCTTACTAT 58.955 34.615 0.00 0.00 0.00 2.12
4761 5077 2.484264 GCTCTTGTTGCGGTATCAAGTT 59.516 45.455 13.98 0.00 39.36 2.66
5017 5341 6.926272 AGTAGCATCGAGAGGAATACAAATTC 59.074 38.462 0.00 0.00 40.77 2.17
5026 5350 5.018539 AGGAATACAAATTCGATCGTGGA 57.981 39.130 15.94 2.52 42.16 4.02
5044 5368 0.603065 GAGGGTGAACCAAACATGGC 59.397 55.000 1.16 0.00 43.89 4.40
5051 5375 3.451894 CCAAACATGGCGCCCCTC 61.452 66.667 26.77 0.00 0.00 4.30
5059 5384 3.717294 GGCGCCCCTCTCCAAAGA 61.717 66.667 18.11 0.00 0.00 2.52
5060 5385 2.351276 GCGCCCCTCTCCAAAGAA 59.649 61.111 0.00 0.00 0.00 2.52
5117 5442 0.239347 CAGCTCGCCCTTCAAAGTTG 59.761 55.000 0.00 0.00 0.00 3.16
5121 5446 2.747446 GCTCGCCCTTCAAAGTTGAATA 59.253 45.455 6.92 0.00 45.26 1.75
5124 5449 5.239525 GCTCGCCCTTCAAAGTTGAATATAT 59.760 40.000 6.92 0.00 45.26 0.86
5149 5474 3.546724 TGTAGTTTGTTGCTTGGTGCTA 58.453 40.909 0.00 0.00 43.37 3.49
5163 5488 7.059788 TGCTTGGTGCTATATTTCCTTAATGA 58.940 34.615 0.00 0.00 43.37 2.57
5178 5503 9.919416 TTTCCTTAATGATATGTCCATCTTTGA 57.081 29.630 0.00 0.00 0.00 2.69
5179 5504 9.565090 TTCCTTAATGATATGTCCATCTTTGAG 57.435 33.333 0.00 0.00 31.16 3.02
5180 5505 8.717717 TCCTTAATGATATGTCCATCTTTGAGT 58.282 33.333 0.00 0.00 30.22 3.41
5187 5512 8.090831 TGATATGTCCATCTTTGAGTACTATGC 58.909 37.037 0.00 0.00 0.00 3.14
5188 5513 5.675684 TGTCCATCTTTGAGTACTATGCA 57.324 39.130 0.00 0.00 0.00 3.96
5189 5514 6.048732 TGTCCATCTTTGAGTACTATGCAA 57.951 37.500 0.00 0.00 0.00 4.08
5190 5515 5.874810 TGTCCATCTTTGAGTACTATGCAAC 59.125 40.000 0.00 0.00 0.00 4.17
5191 5516 5.874810 GTCCATCTTTGAGTACTATGCAACA 59.125 40.000 0.00 0.00 0.00 3.33
5192 5517 6.371548 GTCCATCTTTGAGTACTATGCAACAA 59.628 38.462 0.00 0.00 0.00 2.83
5193 5518 7.066284 GTCCATCTTTGAGTACTATGCAACAAT 59.934 37.037 0.00 0.00 0.00 2.71
5194 5519 7.066163 TCCATCTTTGAGTACTATGCAACAATG 59.934 37.037 0.00 3.12 0.00 2.82
5195 5520 7.066163 CCATCTTTGAGTACTATGCAACAATGA 59.934 37.037 0.00 3.31 0.00 2.57
5196 5521 7.977789 TCTTTGAGTACTATGCAACAATGAA 57.022 32.000 0.00 0.00 0.00 2.57
5197 5522 8.389779 TCTTTGAGTACTATGCAACAATGAAA 57.610 30.769 0.00 0.00 0.00 2.69
5198 5523 9.013229 TCTTTGAGTACTATGCAACAATGAAAT 57.987 29.630 0.00 0.00 0.00 2.17
5199 5524 9.630098 CTTTGAGTACTATGCAACAATGAAATT 57.370 29.630 0.00 0.00 36.63 1.82
5200 5525 9.979578 TTTGAGTACTATGCAACAATGAAATTT 57.020 25.926 0.00 0.00 31.22 1.82
5201 5526 9.979578 TTGAGTACTATGCAACAATGAAATTTT 57.020 25.926 0.00 0.00 31.22 1.82
5202 5527 9.409312 TGAGTACTATGCAACAATGAAATTTTG 57.591 29.630 0.00 0.00 31.22 2.44
5203 5528 9.624697 GAGTACTATGCAACAATGAAATTTTGA 57.375 29.630 0.00 0.00 31.22 2.69
5204 5529 9.979578 AGTACTATGCAACAATGAAATTTTGAA 57.020 25.926 0.00 0.00 31.22 2.69
5206 5531 7.799784 ACTATGCAACAATGAAATTTTGAAGC 58.200 30.769 0.00 0.00 31.22 3.86
5207 5532 6.621316 ATGCAACAATGAAATTTTGAAGCA 57.379 29.167 11.73 11.73 39.58 3.91
5208 5533 6.050454 TGCAACAATGAAATTTTGAAGCAG 57.950 33.333 0.00 0.00 31.22 4.24
5209 5534 4.907582 GCAACAATGAAATTTTGAAGCAGC 59.092 37.500 0.00 0.00 31.22 5.25
5210 5535 5.504337 GCAACAATGAAATTTTGAAGCAGCA 60.504 36.000 0.00 0.00 31.22 4.41
5211 5536 6.664515 CAACAATGAAATTTTGAAGCAGCAT 58.335 32.000 0.00 0.00 31.22 3.79
5212 5537 6.476243 ACAATGAAATTTTGAAGCAGCATC 57.524 33.333 0.00 0.00 31.22 3.91
5213 5538 5.992829 ACAATGAAATTTTGAAGCAGCATCA 59.007 32.000 0.00 0.00 31.22 3.07
5214 5539 6.653320 ACAATGAAATTTTGAAGCAGCATCAT 59.347 30.769 0.14 0.00 31.22 2.45
5215 5540 7.174253 ACAATGAAATTTTGAAGCAGCATCATT 59.826 29.630 0.14 0.00 31.22 2.57
5216 5541 6.474819 TGAAATTTTGAAGCAGCATCATTG 57.525 33.333 0.14 0.00 0.00 2.82
5217 5542 5.410132 TGAAATTTTGAAGCAGCATCATTGG 59.590 36.000 0.14 0.00 0.00 3.16
5218 5543 2.373540 TTTGAAGCAGCATCATTGGC 57.626 45.000 0.14 0.00 0.00 4.52
5219 5544 0.171679 TTGAAGCAGCATCATTGGCG 59.828 50.000 0.14 0.00 36.08 5.69
5220 5545 0.677414 TGAAGCAGCATCATTGGCGA 60.677 50.000 0.00 0.00 36.08 5.54
5221 5546 0.029035 GAAGCAGCATCATTGGCGAG 59.971 55.000 0.00 0.00 36.08 5.03
5222 5547 1.381928 AAGCAGCATCATTGGCGAGG 61.382 55.000 0.00 0.00 36.08 4.63
5223 5548 2.719979 CAGCATCATTGGCGAGGC 59.280 61.111 0.00 0.00 42.88 4.70
5224 5549 2.116533 CAGCATCATTGGCGAGGCA 61.117 57.895 0.19 0.00 44.92 4.75
5225 5550 2.117156 AGCATCATTGGCGAGGCAC 61.117 57.895 0.00 0.00 44.92 5.01
5226 5551 2.409055 GCATCATTGGCGAGGCACA 61.409 57.895 0.00 0.00 42.15 4.57
5227 5552 1.936436 GCATCATTGGCGAGGCACAA 61.936 55.000 0.00 0.00 42.15 3.33
5228 5553 0.099968 CATCATTGGCGAGGCACAAG 59.900 55.000 0.00 0.00 0.00 3.16
5229 5554 1.033746 ATCATTGGCGAGGCACAAGG 61.034 55.000 0.00 0.00 0.00 3.61
5230 5555 2.361610 ATTGGCGAGGCACAAGGG 60.362 61.111 0.00 0.00 0.00 3.95
5231 5556 3.210012 ATTGGCGAGGCACAAGGGT 62.210 57.895 0.00 0.00 0.00 4.34
5232 5557 2.713531 ATTGGCGAGGCACAAGGGTT 62.714 55.000 0.00 0.00 0.00 4.11
5233 5558 3.056328 GGCGAGGCACAAGGGTTC 61.056 66.667 0.00 0.00 0.00 3.62
5234 5559 2.281484 GCGAGGCACAAGGGTTCA 60.281 61.111 0.00 0.00 0.00 3.18
5235 5560 2.617274 GCGAGGCACAAGGGTTCAC 61.617 63.158 0.00 0.00 0.00 3.18
5236 5561 2.317609 CGAGGCACAAGGGTTCACG 61.318 63.158 0.00 0.00 0.00 4.35
5237 5562 1.070786 GAGGCACAAGGGTTCACGA 59.929 57.895 0.00 0.00 0.00 4.35
5238 5563 1.227853 AGGCACAAGGGTTCACGAC 60.228 57.895 0.00 0.00 0.00 4.34
5239 5564 1.525077 GGCACAAGGGTTCACGACA 60.525 57.895 0.00 0.00 0.00 4.35
5240 5565 1.507141 GGCACAAGGGTTCACGACAG 61.507 60.000 0.00 0.00 0.00 3.51
5241 5566 1.507141 GCACAAGGGTTCACGACAGG 61.507 60.000 0.00 0.00 0.00 4.00
5242 5567 0.179056 CACAAGGGTTCACGACAGGT 60.179 55.000 0.00 0.00 0.00 4.00
5243 5568 0.544697 ACAAGGGTTCACGACAGGTT 59.455 50.000 0.00 0.00 0.00 3.50
5244 5569 1.764134 ACAAGGGTTCACGACAGGTTA 59.236 47.619 0.00 0.00 0.00 2.85
5245 5570 2.370849 ACAAGGGTTCACGACAGGTTAT 59.629 45.455 0.00 0.00 0.00 1.89
5246 5571 3.000727 CAAGGGTTCACGACAGGTTATC 58.999 50.000 0.00 0.00 0.00 1.75
5247 5572 1.203994 AGGGTTCACGACAGGTTATCG 59.796 52.381 0.00 0.00 45.17 2.92
5248 5573 0.997196 GGTTCACGACAGGTTATCGC 59.003 55.000 0.00 0.00 43.46 4.58
5249 5574 1.403780 GGTTCACGACAGGTTATCGCT 60.404 52.381 0.00 0.00 43.46 4.93
5250 5575 2.334838 GTTCACGACAGGTTATCGCTT 58.665 47.619 0.00 0.00 43.46 4.68
5251 5576 2.273370 TCACGACAGGTTATCGCTTC 57.727 50.000 0.00 0.00 43.46 3.86
5252 5577 1.135199 TCACGACAGGTTATCGCTTCC 60.135 52.381 0.00 0.00 43.46 3.46
5253 5578 0.179145 ACGACAGGTTATCGCTTCCG 60.179 55.000 0.00 0.00 43.46 4.30
5254 5579 0.870307 CGACAGGTTATCGCTTCCGG 60.870 60.000 0.00 0.00 31.96 5.14
5255 5580 1.152383 GACAGGTTATCGCTTCCGGC 61.152 60.000 0.00 0.00 34.56 6.13
5266 5591 4.947147 TTCCGGCGCTGCAACCTT 62.947 61.111 11.81 0.00 0.00 3.50
5269 5594 3.964875 CGGCGCTGCAACCTTGTT 61.965 61.111 7.64 0.00 0.00 2.83
5270 5595 2.612567 CGGCGCTGCAACCTTGTTA 61.613 57.895 7.64 0.00 0.00 2.41
5271 5596 1.657556 GGCGCTGCAACCTTGTTAA 59.342 52.632 7.64 0.00 0.00 2.01
5272 5597 0.243636 GGCGCTGCAACCTTGTTAAT 59.756 50.000 7.64 0.00 0.00 1.40
5273 5598 1.336795 GGCGCTGCAACCTTGTTAATT 60.337 47.619 7.64 0.00 0.00 1.40
5274 5599 1.985684 GCGCTGCAACCTTGTTAATTC 59.014 47.619 0.00 0.00 0.00 2.17
5275 5600 2.595386 CGCTGCAACCTTGTTAATTCC 58.405 47.619 0.00 0.00 0.00 3.01
5276 5601 2.030363 CGCTGCAACCTTGTTAATTCCA 60.030 45.455 0.00 0.00 0.00 3.53
5277 5602 3.367292 CGCTGCAACCTTGTTAATTCCAT 60.367 43.478 0.00 0.00 0.00 3.41
5278 5603 3.928375 GCTGCAACCTTGTTAATTCCATG 59.072 43.478 0.00 0.00 0.00 3.66
5279 5604 4.497300 CTGCAACCTTGTTAATTCCATGG 58.503 43.478 4.97 4.97 34.27 3.66
5280 5605 4.155709 TGCAACCTTGTTAATTCCATGGA 58.844 39.130 11.44 11.44 32.84 3.41
5281 5606 4.776837 TGCAACCTTGTTAATTCCATGGAT 59.223 37.500 17.06 3.82 32.84 3.41
5282 5607 5.111293 GCAACCTTGTTAATTCCATGGATG 58.889 41.667 17.06 7.24 34.82 3.51
5291 5616 4.929807 CCATGGATGGTAAGGGCC 57.070 61.111 5.56 0.00 43.05 5.80
5292 5617 1.228245 CCATGGATGGTAAGGGCCG 60.228 63.158 5.56 0.00 43.05 6.13
5293 5618 1.705002 CCATGGATGGTAAGGGCCGA 61.705 60.000 5.56 0.00 43.05 5.54
5294 5619 0.182537 CATGGATGGTAAGGGCCGAA 59.817 55.000 0.00 0.00 0.00 4.30
5295 5620 0.182775 ATGGATGGTAAGGGCCGAAC 59.817 55.000 0.00 0.00 0.00 3.95
5296 5621 1.202099 TGGATGGTAAGGGCCGAACA 61.202 55.000 12.44 7.58 0.00 3.18
5297 5622 0.463833 GGATGGTAAGGGCCGAACAG 60.464 60.000 12.44 0.00 0.00 3.16
5298 5623 1.077716 ATGGTAAGGGCCGAACAGC 60.078 57.895 12.44 3.37 0.00 4.40
5306 5631 3.758172 GCCGAACAGCCAAGGAAA 58.242 55.556 0.00 0.00 0.00 3.13
5307 5632 2.037871 GCCGAACAGCCAAGGAAAA 58.962 52.632 0.00 0.00 0.00 2.29
5308 5633 0.603065 GCCGAACAGCCAAGGAAAAT 59.397 50.000 0.00 0.00 0.00 1.82
5309 5634 1.669795 GCCGAACAGCCAAGGAAAATG 60.670 52.381 0.00 0.00 0.00 2.32
5310 5635 1.669795 CCGAACAGCCAAGGAAAATGC 60.670 52.381 0.00 0.00 0.00 3.56
5311 5636 1.669795 CGAACAGCCAAGGAAAATGCC 60.670 52.381 0.00 0.00 0.00 4.40
5312 5637 1.344114 GAACAGCCAAGGAAAATGCCA 59.656 47.619 0.00 0.00 0.00 4.92
5313 5638 0.971386 ACAGCCAAGGAAAATGCCAG 59.029 50.000 0.00 0.00 0.00 4.85
5314 5639 0.971386 CAGCCAAGGAAAATGCCAGT 59.029 50.000 0.00 0.00 0.00 4.00
5315 5640 1.345415 CAGCCAAGGAAAATGCCAGTT 59.655 47.619 0.00 0.00 0.00 3.16
5316 5641 1.345415 AGCCAAGGAAAATGCCAGTTG 59.655 47.619 0.00 0.00 0.00 3.16
5317 5642 1.799544 CCAAGGAAAATGCCAGTTGC 58.200 50.000 0.00 0.00 41.77 4.17
5326 5651 3.595819 GCCAGTTGCATCCCTGAC 58.404 61.111 9.43 0.00 40.77 3.51
5327 5652 1.303561 GCCAGTTGCATCCCTGACA 60.304 57.895 9.43 0.00 40.77 3.58
5328 5653 0.682209 GCCAGTTGCATCCCTGACAT 60.682 55.000 9.43 0.00 40.77 3.06
5329 5654 1.843368 CCAGTTGCATCCCTGACATT 58.157 50.000 9.43 0.00 0.00 2.71
5330 5655 1.475280 CCAGTTGCATCCCTGACATTG 59.525 52.381 9.43 0.00 0.00 2.82
5331 5656 1.135199 CAGTTGCATCCCTGACATTGC 60.135 52.381 3.18 0.00 35.67 3.56
5332 5657 1.180029 GTTGCATCCCTGACATTGCT 58.820 50.000 0.00 0.00 36.10 3.91
5333 5658 1.135199 GTTGCATCCCTGACATTGCTG 60.135 52.381 0.00 0.00 36.10 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
204 211 0.597568 CAGGCGCACCAGATCAAAAA 59.402 50.000 10.83 0.00 39.06 1.94
377 385 3.812053 GTGCTAATGCCTAACCATCTGAG 59.188 47.826 0.00 0.00 38.71 3.35
396 404 2.409870 CCCCTCAAATCCAGCGTGC 61.410 63.158 0.00 0.00 0.00 5.34
447 456 4.141482 TGGCCACTATAATTTCCTCTCACC 60.141 45.833 0.00 0.00 0.00 4.02
500 509 0.539986 TCCAGAGCATACCGAAACCC 59.460 55.000 0.00 0.00 0.00 4.11
551 579 1.753930 TAGGCCATTCATGCACACAG 58.246 50.000 5.01 0.00 0.00 3.66
599 632 7.177392 CCTCAAAACTGAAAATTCTGGATAGGT 59.823 37.037 5.26 0.00 0.00 3.08
689 722 3.437049 GGTGAAGTGCTCCATGTAGAAAC 59.563 47.826 0.00 0.00 0.00 2.78
711 744 7.497909 ACGATTGGTGGGTAAAATTATAGTCAG 59.502 37.037 0.00 0.00 0.00 3.51
822 855 7.478322 GTCAGAAGACATGAATGCATATGTTT 58.522 34.615 14.72 7.91 44.34 2.83
857 891 7.286775 TCCTTCTTAAGTTGCAGTTACCAAATT 59.713 33.333 1.63 0.00 35.13 1.82
915 953 5.218885 CCAGCATCACGAAACAAAAATGTA 58.781 37.500 0.00 0.00 0.00 2.29
929 967 7.656707 AAACATGAATTTTTACCAGCATCAC 57.343 32.000 0.00 0.00 0.00 3.06
960 999 4.186926 TGCAGTCTCATGAAATCAGCTAC 58.813 43.478 0.00 0.00 0.00 3.58
1003 1042 0.885879 TTCAGCACAGGATACGTCGT 59.114 50.000 2.21 2.21 46.39 4.34
1050 1089 1.627329 AGCTCATCCTTCAGTTCTGCA 59.373 47.619 0.00 0.00 0.00 4.41
1051 1090 2.093553 AGAGCTCATCCTTCAGTTCTGC 60.094 50.000 17.77 0.00 29.77 4.26
1053 1092 3.711863 AGAGAGCTCATCCTTCAGTTCT 58.288 45.455 17.77 2.59 33.29 3.01
1336 1375 0.744874 TCTGTAGTAGCATCGGCACC 59.255 55.000 0.00 0.00 44.61 5.01
1372 1504 8.261492 TGACTAACTTCTTCGGTACTAACTAG 57.739 38.462 0.00 0.00 0.00 2.57
1459 1591 5.909621 TCTTCGGTACTAACTACAGCATT 57.090 39.130 0.00 0.00 0.00 3.56
1717 1849 3.776969 TGTGGAGATGCTTCCTTCACTAT 59.223 43.478 11.40 0.00 38.12 2.12
2272 2404 2.368439 TGCCTGCAAATCATCACCTAC 58.632 47.619 0.00 0.00 0.00 3.18
2433 2570 3.458831 ACTTTCCATCACATCCTCCTCT 58.541 45.455 0.00 0.00 0.00 3.69
2481 2627 4.624843 GCAGTCTTTCCTCCAAGATCATCA 60.625 45.833 0.00 0.00 35.23 3.07
2482 2628 3.876320 GCAGTCTTTCCTCCAAGATCATC 59.124 47.826 0.00 0.00 35.23 2.92
2483 2629 3.681034 CGCAGTCTTTCCTCCAAGATCAT 60.681 47.826 0.00 0.00 35.23 2.45
2484 2630 2.354103 CGCAGTCTTTCCTCCAAGATCA 60.354 50.000 0.00 0.00 35.23 2.92
2485 2631 2.275318 CGCAGTCTTTCCTCCAAGATC 58.725 52.381 0.00 0.00 35.23 2.75
2486 2632 1.065854 CCGCAGTCTTTCCTCCAAGAT 60.066 52.381 0.00 0.00 35.23 2.40
2487 2633 0.321671 CCGCAGTCTTTCCTCCAAGA 59.678 55.000 0.00 0.00 0.00 3.02
2488 2634 0.035458 ACCGCAGTCTTTCCTCCAAG 59.965 55.000 0.00 0.00 0.00 3.61
2489 2635 0.472471 AACCGCAGTCTTTCCTCCAA 59.528 50.000 0.00 0.00 0.00 3.53
2996 3277 9.028284 ACATGACATGATTTCTCCATTTAAACT 57.972 29.630 22.19 0.00 0.00 2.66
3064 3345 1.819208 TTTGATGGGCTCATCCGCG 60.819 57.895 23.79 0.00 46.92 6.46
3200 3481 2.949447 ACCTCCACTTGCTGTTGAATT 58.051 42.857 0.00 0.00 0.00 2.17
3306 3587 5.124457 CACTGAACAATGAATACAGAAGGGG 59.876 44.000 0.00 0.00 33.53 4.79
3322 3604 0.836606 TGAGGAAGTGGCACTGAACA 59.163 50.000 22.83 15.63 0.00 3.18
3372 3654 0.453793 TAAATGGGCGCACAAATCGG 59.546 50.000 20.27 0.00 0.00 4.18
3518 3800 7.333528 TGAAATGCACCTCTAACAATATTCC 57.666 36.000 0.00 0.00 0.00 3.01
3635 3917 3.064207 CGACAGGCTAAAGCACAAACTA 58.936 45.455 4.07 0.00 44.36 2.24
3655 3937 4.793216 GCACCAGAATATTTGTTAGCAACG 59.207 41.667 0.00 0.00 33.82 4.10
3657 3939 6.588719 AAGCACCAGAATATTTGTTAGCAA 57.411 33.333 0.00 0.00 0.00 3.91
3713 3995 6.672218 TCCTTCATACAGAGGAATACCAAGAA 59.328 38.462 0.00 0.00 38.94 2.52
3714 3996 6.202331 TCCTTCATACAGAGGAATACCAAGA 58.798 40.000 0.00 0.00 38.94 3.02
3715 3997 6.485830 TCCTTCATACAGAGGAATACCAAG 57.514 41.667 0.00 0.00 38.94 3.61
3716 3998 6.688922 GCATCCTTCATACAGAGGAATACCAA 60.689 42.308 0.00 0.00 38.94 3.67
3717 3999 5.221722 GCATCCTTCATACAGAGGAATACCA 60.222 44.000 0.00 0.00 38.94 3.25
3775 4057 5.392380 GCATCACGAGATTCTTTGAACCAAT 60.392 40.000 0.00 0.00 30.20 3.16
3851 4155 4.152647 TCATCCACTGAAGAGTACTGTGT 58.847 43.478 0.00 0.00 36.14 3.72
3878 4182 0.833287 ACAGCATTCCTGGTAGCGAT 59.167 50.000 0.00 0.00 46.14 4.58
3880 4184 1.453155 AAACAGCATTCCTGGTAGCG 58.547 50.000 0.00 0.00 41.79 4.26
3973 4277 1.282738 GGGGGAGGGTGTTCGATTTTA 59.717 52.381 0.00 0.00 0.00 1.52
3996 4300 4.033776 GGCTGGTAGGCAGTGGCA 62.034 66.667 20.04 1.95 43.71 4.92
4016 4320 0.885196 TTTGGCGTTGTATCCTTGCC 59.115 50.000 0.00 0.00 45.91 4.52
4030 4334 1.520787 GATGGCTGCTGCATTTGGC 60.521 57.895 17.89 4.76 41.91 4.52
4094 4398 4.408821 TGACAGACCCCATGCGGC 62.409 66.667 0.00 0.00 0.00 6.53
4142 4446 1.286248 GACCTGGGGTTAGATGTGGT 58.714 55.000 0.00 0.00 35.25 4.16
4160 4464 1.677552 GAAGCACCTCCCTTTCCGA 59.322 57.895 0.00 0.00 0.00 4.55
4184 4488 1.314730 GTTTCCGGTTGCTTTGGAGA 58.685 50.000 0.00 0.00 32.39 3.71
4246 4550 4.083003 GGCAAGTAGTAGATCATCGGAGAG 60.083 50.000 0.00 0.00 43.63 3.20
4355 4659 2.360600 GCACCAACATACCGGGCA 60.361 61.111 6.32 0.00 0.00 5.36
4404 4708 0.179034 GAAGAGAATCCGCTGGCCAT 60.179 55.000 5.51 0.00 33.66 4.40
4429 4733 1.964373 GCAACACCAACGGTCGGAT 60.964 57.895 0.00 0.00 31.02 4.18
4469 4773 3.500680 ACCAACCATTACAAGCAGTAACG 59.499 43.478 4.20 0.00 44.95 3.18
4541 4848 7.124147 AGAGTTCCAAGACCAGAATTTCAAAAA 59.876 33.333 0.00 0.00 0.00 1.94
4542 4849 6.607198 AGAGTTCCAAGACCAGAATTTCAAAA 59.393 34.615 0.00 0.00 0.00 2.44
4543 4850 6.129179 AGAGTTCCAAGACCAGAATTTCAAA 58.871 36.000 0.00 0.00 0.00 2.69
4544 4851 5.694995 AGAGTTCCAAGACCAGAATTTCAA 58.305 37.500 0.00 0.00 0.00 2.69
4545 4852 5.310409 AGAGTTCCAAGACCAGAATTTCA 57.690 39.130 0.00 0.00 0.00 2.69
4546 4853 5.765182 TCAAGAGTTCCAAGACCAGAATTTC 59.235 40.000 0.00 0.00 0.00 2.17
4547 4854 5.694995 TCAAGAGTTCCAAGACCAGAATTT 58.305 37.500 0.00 0.00 0.00 1.82
4548 4855 5.310409 TCAAGAGTTCCAAGACCAGAATT 57.690 39.130 0.00 0.00 0.00 2.17
4549 4856 4.982241 TCAAGAGTTCCAAGACCAGAAT 57.018 40.909 0.00 0.00 0.00 2.40
4550 4857 4.982241 ATCAAGAGTTCCAAGACCAGAA 57.018 40.909 0.00 0.00 0.00 3.02
4551 4858 5.544176 AGTTATCAAGAGTTCCAAGACCAGA 59.456 40.000 0.00 0.00 0.00 3.86
4552 4859 5.641209 CAGTTATCAAGAGTTCCAAGACCAG 59.359 44.000 0.00 0.00 0.00 4.00
4553 4860 5.306937 TCAGTTATCAAGAGTTCCAAGACCA 59.693 40.000 0.00 0.00 0.00 4.02
4554 4861 5.794894 TCAGTTATCAAGAGTTCCAAGACC 58.205 41.667 0.00 0.00 0.00 3.85
4555 4862 6.459923 ACTCAGTTATCAAGAGTTCCAAGAC 58.540 40.000 0.00 0.00 39.45 3.01
4556 4863 6.672266 ACTCAGTTATCAAGAGTTCCAAGA 57.328 37.500 0.00 0.00 39.45 3.02
4557 4864 7.607250 ACTACTCAGTTATCAAGAGTTCCAAG 58.393 38.462 0.00 0.00 42.25 3.61
4558 4865 7.540474 ACTACTCAGTTATCAAGAGTTCCAA 57.460 36.000 0.00 0.00 42.25 3.53
4559 4866 6.127980 CGACTACTCAGTTATCAAGAGTTCCA 60.128 42.308 0.00 0.00 42.25 3.53
4560 4867 6.127952 ACGACTACTCAGTTATCAAGAGTTCC 60.128 42.308 0.00 0.00 42.25 3.62
4561 4868 6.844254 ACGACTACTCAGTTATCAAGAGTTC 58.156 40.000 0.00 0.00 42.25 3.01
4636 4943 1.196581 TGATGGAAATTCACGTGTGCG 59.803 47.619 16.51 0.00 44.93 5.34
4646 4953 1.354368 ACTGGGTCGGTGATGGAAATT 59.646 47.619 0.00 0.00 0.00 1.82
4652 4959 0.179073 GGATGACTGGGTCGGTGATG 60.179 60.000 0.00 0.00 34.95 3.07
4662 4969 3.641434 ACTGATCCAAAGGATGACTGG 57.359 47.619 2.74 0.00 43.27 4.00
4707 5014 6.706270 AGGAATAGTAAGCATCAACGGTTATG 59.294 38.462 0.00 0.00 32.00 1.90
4714 5022 4.274459 CCAGCAGGAATAGTAAGCATCAAC 59.726 45.833 0.00 0.00 36.89 3.18
4761 5077 6.573434 ACTCACGATTACATGAGAAATGCTA 58.427 36.000 0.00 0.00 44.32 3.49
4927 5251 5.074115 AGTGCTACAGTAGTCATATCCCTC 58.926 45.833 9.42 0.00 0.00 4.30
4960 5284 9.173231 TCAATACAATTTAGCTTATACCCCCTA 57.827 33.333 0.00 0.00 0.00 3.53
4980 5304 7.095857 CCTCTCGATGCTACTTTTGATCAATAC 60.096 40.741 9.40 0.00 0.00 1.89
4981 5305 6.925718 CCTCTCGATGCTACTTTTGATCAATA 59.074 38.462 9.40 3.48 0.00 1.90
5000 5324 4.976731 ACGATCGAATTTGTATTCCTCTCG 59.023 41.667 24.34 0.00 37.46 4.04
5017 5341 1.153628 GGTTCACCCTCCACGATCG 60.154 63.158 14.88 14.88 0.00 3.69
5026 5350 1.178534 CGCCATGTTTGGTTCACCCT 61.179 55.000 0.00 0.00 45.57 4.34
5044 5368 1.383523 GAATTCTTTGGAGAGGGGCG 58.616 55.000 0.00 0.00 32.44 6.13
5051 5375 6.095377 AGCTAAATTTGCGAATTCTTTGGAG 58.905 36.000 12.38 5.13 34.44 3.86
5085 5410 1.002468 GCGAGCTGTGAACACAAATGT 60.002 47.619 8.93 0.00 41.33 2.71
5089 5414 1.891919 GGGCGAGCTGTGAACACAA 60.892 57.895 8.93 0.00 41.33 3.33
5121 5446 7.574967 GCACCAAGCAACAAACTACAACTATAT 60.575 37.037 0.00 0.00 44.79 0.86
5124 5449 4.201970 GCACCAAGCAACAAACTACAACTA 60.202 41.667 0.00 0.00 44.79 2.24
5163 5488 7.966812 TGCATAGTACTCAAAGATGGACATAT 58.033 34.615 0.00 0.00 0.00 1.78
5168 5493 6.048732 TGTTGCATAGTACTCAAAGATGGA 57.951 37.500 0.00 0.00 0.00 3.41
5173 5498 9.630098 AATTTCATTGTTGCATAGTACTCAAAG 57.370 29.630 0.00 0.00 0.00 2.77
5174 5499 9.979578 AAATTTCATTGTTGCATAGTACTCAAA 57.020 25.926 0.00 0.00 0.00 2.69
5175 5500 9.979578 AAAATTTCATTGTTGCATAGTACTCAA 57.020 25.926 0.00 0.00 0.00 3.02
5176 5501 9.409312 CAAAATTTCATTGTTGCATAGTACTCA 57.591 29.630 0.00 0.00 0.00 3.41
5177 5502 9.624697 TCAAAATTTCATTGTTGCATAGTACTC 57.375 29.630 0.00 0.00 0.00 2.59
5178 5503 9.979578 TTCAAAATTTCATTGTTGCATAGTACT 57.020 25.926 0.00 0.00 0.00 2.73
5180 5505 8.924691 GCTTCAAAATTTCATTGTTGCATAGTA 58.075 29.630 0.00 0.00 32.17 1.82
5181 5506 7.441760 TGCTTCAAAATTTCATTGTTGCATAGT 59.558 29.630 0.00 0.00 34.75 2.12
5182 5507 7.798801 TGCTTCAAAATTTCATTGTTGCATAG 58.201 30.769 0.00 0.00 34.75 2.23
5183 5508 7.571613 GCTGCTTCAAAATTTCATTGTTGCATA 60.572 33.333 0.00 0.00 36.92 3.14
5184 5509 6.621316 TGCTTCAAAATTTCATTGTTGCAT 57.379 29.167 0.00 0.00 34.75 3.96
5185 5510 5.504337 GCTGCTTCAAAATTTCATTGTTGCA 60.504 36.000 0.00 1.88 36.51 4.08
5186 5511 4.907582 GCTGCTTCAAAATTTCATTGTTGC 59.092 37.500 0.00 0.00 0.00 4.17
5187 5512 6.050454 TGCTGCTTCAAAATTTCATTGTTG 57.950 33.333 0.00 0.00 0.00 3.33
5188 5513 6.483974 TGATGCTGCTTCAAAATTTCATTGTT 59.516 30.769 14.93 0.00 0.00 2.83
5189 5514 5.992829 TGATGCTGCTTCAAAATTTCATTGT 59.007 32.000 14.93 0.00 0.00 2.71
5190 5515 6.474819 TGATGCTGCTTCAAAATTTCATTG 57.525 33.333 14.93 0.00 0.00 2.82
5191 5516 7.361713 CCAATGATGCTGCTTCAAAATTTCATT 60.362 33.333 20.10 6.62 32.99 2.57
5192 5517 6.093495 CCAATGATGCTGCTTCAAAATTTCAT 59.907 34.615 20.10 0.96 0.00 2.57
5193 5518 5.410132 CCAATGATGCTGCTTCAAAATTTCA 59.590 36.000 20.10 0.00 0.00 2.69
5194 5519 5.672819 GCCAATGATGCTGCTTCAAAATTTC 60.673 40.000 20.10 6.31 0.00 2.17
5195 5520 4.155280 GCCAATGATGCTGCTTCAAAATTT 59.845 37.500 20.10 8.83 0.00 1.82
5196 5521 3.687698 GCCAATGATGCTGCTTCAAAATT 59.312 39.130 20.10 9.14 0.00 1.82
5197 5522 3.267483 GCCAATGATGCTGCTTCAAAAT 58.733 40.909 20.10 8.65 0.00 1.82
5198 5523 2.690786 GCCAATGATGCTGCTTCAAAA 58.309 42.857 20.10 0.00 0.00 2.44
5199 5524 1.403116 CGCCAATGATGCTGCTTCAAA 60.403 47.619 20.10 0.61 0.00 2.69
5200 5525 0.171679 CGCCAATGATGCTGCTTCAA 59.828 50.000 20.10 6.29 0.00 2.69
5201 5526 0.677414 TCGCCAATGATGCTGCTTCA 60.677 50.000 18.80 18.80 0.00 3.02
5202 5527 0.029035 CTCGCCAATGATGCTGCTTC 59.971 55.000 8.46 8.46 0.00 3.86
5203 5528 1.381928 CCTCGCCAATGATGCTGCTT 61.382 55.000 0.00 0.00 0.00 3.91
5204 5529 1.822613 CCTCGCCAATGATGCTGCT 60.823 57.895 0.00 0.00 0.00 4.24
5205 5530 2.719979 CCTCGCCAATGATGCTGC 59.280 61.111 0.00 0.00 0.00 5.25
5206 5531 2.116533 TGCCTCGCCAATGATGCTG 61.117 57.895 0.00 0.00 31.68 4.41
5207 5532 2.117156 GTGCCTCGCCAATGATGCT 61.117 57.895 0.00 0.00 31.68 3.79
5208 5533 1.936436 TTGTGCCTCGCCAATGATGC 61.936 55.000 0.00 0.00 0.00 3.91
5209 5534 0.099968 CTTGTGCCTCGCCAATGATG 59.900 55.000 0.00 0.00 0.00 3.07
5210 5535 1.033746 CCTTGTGCCTCGCCAATGAT 61.034 55.000 0.00 0.00 0.00 2.45
5211 5536 1.675310 CCTTGTGCCTCGCCAATGA 60.675 57.895 0.00 0.00 0.00 2.57
5212 5537 2.703798 CCCTTGTGCCTCGCCAATG 61.704 63.158 0.00 0.00 0.00 2.82
5213 5538 2.361610 CCCTTGTGCCTCGCCAAT 60.362 61.111 0.00 0.00 0.00 3.16
5214 5539 3.429372 AACCCTTGTGCCTCGCCAA 62.429 57.895 0.00 0.00 0.00 4.52
5215 5540 3.842925 GAACCCTTGTGCCTCGCCA 62.843 63.158 0.00 0.00 0.00 5.69
5216 5541 3.056328 GAACCCTTGTGCCTCGCC 61.056 66.667 0.00 0.00 0.00 5.54
5217 5542 2.281484 TGAACCCTTGTGCCTCGC 60.281 61.111 0.00 0.00 0.00 5.03
5218 5543 2.317609 CGTGAACCCTTGTGCCTCG 61.318 63.158 0.00 0.00 0.00 4.63
5219 5544 1.070786 TCGTGAACCCTTGTGCCTC 59.929 57.895 0.00 0.00 0.00 4.70
5220 5545 1.227853 GTCGTGAACCCTTGTGCCT 60.228 57.895 0.00 0.00 0.00 4.75
5221 5546 1.507141 CTGTCGTGAACCCTTGTGCC 61.507 60.000 0.00 0.00 0.00 5.01
5222 5547 1.507141 CCTGTCGTGAACCCTTGTGC 61.507 60.000 0.00 0.00 0.00 4.57
5223 5548 0.179056 ACCTGTCGTGAACCCTTGTG 60.179 55.000 0.00 0.00 0.00 3.33
5224 5549 0.544697 AACCTGTCGTGAACCCTTGT 59.455 50.000 0.00 0.00 0.00 3.16
5225 5550 2.536761 TAACCTGTCGTGAACCCTTG 57.463 50.000 0.00 0.00 0.00 3.61
5226 5551 2.353406 CGATAACCTGTCGTGAACCCTT 60.353 50.000 0.00 0.00 34.56 3.95
5227 5552 1.203994 CGATAACCTGTCGTGAACCCT 59.796 52.381 0.00 0.00 34.56 4.34
5228 5553 1.636988 CGATAACCTGTCGTGAACCC 58.363 55.000 0.00 0.00 34.56 4.11
5229 5554 0.997196 GCGATAACCTGTCGTGAACC 59.003 55.000 0.00 0.00 40.98 3.62
5230 5555 1.992170 AGCGATAACCTGTCGTGAAC 58.008 50.000 0.00 0.00 40.98 3.18
5231 5556 2.602878 GAAGCGATAACCTGTCGTGAA 58.397 47.619 0.00 0.00 40.98 3.18
5232 5557 1.135199 GGAAGCGATAACCTGTCGTGA 60.135 52.381 0.00 0.00 40.98 4.35
5233 5558 1.278238 GGAAGCGATAACCTGTCGTG 58.722 55.000 0.00 0.00 40.98 4.35
5234 5559 0.179145 CGGAAGCGATAACCTGTCGT 60.179 55.000 0.00 0.00 40.98 4.34
5235 5560 0.870307 CCGGAAGCGATAACCTGTCG 60.870 60.000 0.00 0.00 41.77 4.35
5236 5561 1.152383 GCCGGAAGCGATAACCTGTC 61.152 60.000 5.05 0.00 0.00 3.51
5237 5562 1.153429 GCCGGAAGCGATAACCTGT 60.153 57.895 5.05 0.00 0.00 4.00
5238 5563 3.719214 GCCGGAAGCGATAACCTG 58.281 61.111 5.05 0.00 0.00 4.00
5249 5574 4.947147 AAGGTTGCAGCGCCGGAA 62.947 61.111 5.05 0.00 0.00 4.30
5252 5577 2.123988 TTAACAAGGTTGCAGCGCCG 62.124 55.000 2.29 0.00 0.00 6.46
5253 5578 0.243636 ATTAACAAGGTTGCAGCGCC 59.756 50.000 2.29 0.00 0.00 6.53
5254 5579 1.985684 GAATTAACAAGGTTGCAGCGC 59.014 47.619 0.00 0.00 0.00 5.92
5255 5580 2.030363 TGGAATTAACAAGGTTGCAGCG 60.030 45.455 0.00 0.00 0.00 5.18
5256 5581 3.658757 TGGAATTAACAAGGTTGCAGC 57.341 42.857 0.00 0.00 0.00 5.25
5257 5582 4.220382 TCCATGGAATTAACAAGGTTGCAG 59.780 41.667 13.46 0.00 0.00 4.41
5258 5583 4.155709 TCCATGGAATTAACAAGGTTGCA 58.844 39.130 13.46 0.00 0.00 4.08
5259 5584 4.799564 TCCATGGAATTAACAAGGTTGC 57.200 40.909 13.46 0.00 0.00 4.17
5275 5600 0.182537 TTCGGCCCTTACCATCCATG 59.817 55.000 0.00 0.00 0.00 3.66
5276 5601 0.182775 GTTCGGCCCTTACCATCCAT 59.817 55.000 0.00 0.00 0.00 3.41
5277 5602 1.202099 TGTTCGGCCCTTACCATCCA 61.202 55.000 0.00 0.00 0.00 3.41
5278 5603 0.463833 CTGTTCGGCCCTTACCATCC 60.464 60.000 0.00 0.00 0.00 3.51
5279 5604 1.095807 GCTGTTCGGCCCTTACCATC 61.096 60.000 0.00 0.00 0.00 3.51
5280 5605 1.077716 GCTGTTCGGCCCTTACCAT 60.078 57.895 0.00 0.00 0.00 3.55
5281 5606 2.349755 GCTGTTCGGCCCTTACCA 59.650 61.111 0.00 0.00 0.00 3.25
5282 5607 2.437895 GGCTGTTCGGCCCTTACC 60.438 66.667 11.25 0.00 45.92 2.85
5289 5614 0.603065 ATTTTCCTTGGCTGTTCGGC 59.397 50.000 0.00 0.00 38.97 5.54
5290 5615 1.669795 GCATTTTCCTTGGCTGTTCGG 60.670 52.381 0.00 0.00 0.00 4.30
5291 5616 1.669795 GGCATTTTCCTTGGCTGTTCG 60.670 52.381 0.00 0.00 36.76 3.95
5292 5617 1.344114 TGGCATTTTCCTTGGCTGTTC 59.656 47.619 0.00 0.00 40.12 3.18
5293 5618 1.345415 CTGGCATTTTCCTTGGCTGTT 59.655 47.619 0.00 0.00 40.12 3.16
5294 5619 0.971386 CTGGCATTTTCCTTGGCTGT 59.029 50.000 0.00 0.00 40.12 4.40
5295 5620 0.971386 ACTGGCATTTTCCTTGGCTG 59.029 50.000 0.00 0.00 42.04 4.85
5296 5621 1.345415 CAACTGGCATTTTCCTTGGCT 59.655 47.619 0.00 0.00 40.12 4.75
5297 5622 1.799544 CAACTGGCATTTTCCTTGGC 58.200 50.000 0.00 0.00 39.89 4.52
5298 5623 1.799544 GCAACTGGCATTTTCCTTGG 58.200 50.000 0.00 0.00 43.97 3.61
5309 5634 0.682209 ATGTCAGGGATGCAACTGGC 60.682 55.000 12.42 12.42 45.13 4.85
5310 5635 1.475280 CAATGTCAGGGATGCAACTGG 59.525 52.381 14.09 0.00 35.47 4.00
5311 5636 1.135199 GCAATGTCAGGGATGCAACTG 60.135 52.381 9.41 9.41 38.63 3.16
5312 5637 1.180029 GCAATGTCAGGGATGCAACT 58.820 50.000 0.00 0.00 38.63 3.16
5313 5638 1.135199 CAGCAATGTCAGGGATGCAAC 60.135 52.381 0.00 0.00 41.18 4.17
5314 5639 1.179152 CAGCAATGTCAGGGATGCAA 58.821 50.000 0.00 0.00 41.18 4.08
5315 5640 2.876581 CAGCAATGTCAGGGATGCA 58.123 52.632 0.00 0.00 41.18 3.96


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

AutoCloner maintained by Alex Coulton.