Multiple sequence alignment - TraesCS4D01G363800

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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 TraesCS4D01G363800 chr4D 100.000 2321 0 0 1 2321 509181095 509183415 0.000000e+00 4287
1 TraesCS4D01G363800 chr5A 85.486 751 42 25 801 1537 697893887 697894584 0.000000e+00 721
2 TraesCS4D01G363800 chr5A 84.615 507 27 11 1 483 535699047 535699526 7.560000e-125 457
3 TraesCS4D01G363800 chr5A 86.301 219 22 4 561 775 697893416 697893630 4.990000e-57 231
4 TraesCS4D01G363800 chr4A 85.237 569 40 21 1 545 317037484 317036936 1.570000e-151 545
5 TraesCS4D01G363800 chr4B 83.689 515 47 19 1789 2274 657985616 657985110 3.520000e-123 451
6 TraesCS4D01G363800 chr4B 87.909 397 16 13 801 1191 657987414 657987044 2.740000e-119 438
7 TraesCS4D01G363800 chr4B 82.251 231 26 7 1538 1758 657986459 657986234 3.940000e-43 185
8 TraesCS4D01G363800 chr4B 78.997 319 32 16 1250 1537 657986811 657986497 3.940000e-43 185
9 TraesCS4D01G363800 chr6B 95.000 240 9 2 1 240 643393259 643393023 7.830000e-100 374
10 TraesCS4D01G363800 chr6B 88.026 309 20 8 240 546 643388095 643387802 1.320000e-92 350
11 TraesCS4D01G363800 chr6B 83.819 309 20 10 240 546 643392122 643391842 1.370000e-67 267
12 TraesCS4D01G363800 chr3B 90.417 240 19 4 1 240 7292377 7292612 1.730000e-81 313
13 TraesCS4D01G363800 chr2D 89.744 234 19 3 7 240 14026337 14026109 6.270000e-76 294


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 TraesCS4D01G363800 chr4D 509181095 509183415 2320 False 4287.000000 4287 100.000000 1 2321 1 chr4D.!!$F1 2320
1 TraesCS4D01G363800 chr5A 697893416 697894584 1168 False 476.000000 721 85.893500 561 1537 2 chr5A.!!$F2 976
2 TraesCS4D01G363800 chr4A 317036936 317037484 548 True 545.000000 545 85.237000 1 545 1 chr4A.!!$R1 544
3 TraesCS4D01G363800 chr4B 657985110 657987414 2304 True 314.750000 451 83.211500 801 2274 4 chr4B.!!$R1 1473
4 TraesCS4D01G363800 chr6B 643387802 643393259 5457 True 330.333333 374 88.948333 1 546 3 chr6B.!!$R1 545

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
898 6057 0.319297 GAGTTGTTGTAGTCCGCCGT 60.319 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 8109 0.179108 GCCAAGTCACCTACCTAGCG 60.179 60.0 0.0 0.0 0.0 4.26 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
31 32 1.031571 GCATGTTTCAGATCCGGCCA 61.032 55.000 2.24 0.00 0.00 5.36
171 173 7.378181 GTGATGACAAACCCATCTAAAATGTT 58.622 34.615 0.00 0.00 40.65 2.71
172 174 7.872483 GTGATGACAAACCCATCTAAAATGTTT 59.128 33.333 0.00 0.00 40.65 2.83
305 1209 1.202627 GCCAGGCAAAACCATCAACAA 60.203 47.619 6.55 0.00 43.14 2.83
312 5226 5.353956 AGGCAAAACCATCAACAAAGAAAAC 59.646 36.000 0.00 0.00 43.14 2.43
321 5235 6.018832 CCATCAACAAAGAAAACCATCAACAC 60.019 38.462 0.00 0.00 0.00 3.32
329 5243 5.486526 AGAAAACCATCAACACAGCAAAAA 58.513 33.333 0.00 0.00 0.00 1.94
330 5244 5.351189 AGAAAACCATCAACACAGCAAAAAC 59.649 36.000 0.00 0.00 0.00 2.43
331 5245 3.883830 ACCATCAACACAGCAAAAACA 57.116 38.095 0.00 0.00 0.00 2.83
332 5246 3.784338 ACCATCAACACAGCAAAAACAG 58.216 40.909 0.00 0.00 0.00 3.16
333 5247 3.446873 ACCATCAACACAGCAAAAACAGA 59.553 39.130 0.00 0.00 0.00 3.41
334 5248 4.046462 CCATCAACACAGCAAAAACAGAG 58.954 43.478 0.00 0.00 0.00 3.35
335 5249 3.149436 TCAACACAGCAAAAACAGAGC 57.851 42.857 0.00 0.00 0.00 4.09
340 5255 4.506758 ACACAGCAAAAACAGAGCAAAAT 58.493 34.783 0.00 0.00 0.00 1.82
344 5259 3.983344 AGCAAAAACAGAGCAAAATAGCG 59.017 39.130 0.00 0.00 40.15 4.26
347 5262 0.447801 AACAGAGCAAAATAGCGCGG 59.552 50.000 8.83 0.00 39.42 6.46
365 5280 0.950071 GGCAAATGTGTGCGCCAAAT 60.950 50.000 4.18 0.00 45.91 2.32
475 5392 1.270147 ACGGGCTGACACAACTAGTTC 60.270 52.381 4.77 0.00 0.00 3.01
520 5437 8.794553 AGGTGATTAAGACCATACTATAACTCG 58.205 37.037 8.73 0.00 35.76 4.18
546 5464 2.610859 AGTTCCAGGCGGTCCCAT 60.611 61.111 0.00 0.00 35.39 4.00
547 5465 1.306654 AGTTCCAGGCGGTCCCATA 60.307 57.895 0.00 0.00 35.39 2.74
548 5466 0.694444 AGTTCCAGGCGGTCCCATAT 60.694 55.000 0.00 0.00 35.39 1.78
549 5467 1.053424 GTTCCAGGCGGTCCCATATA 58.947 55.000 0.00 0.00 35.39 0.86
550 5468 1.418637 GTTCCAGGCGGTCCCATATAA 59.581 52.381 0.00 0.00 35.39 0.98
551 5469 1.809133 TCCAGGCGGTCCCATATAAA 58.191 50.000 0.00 0.00 35.39 1.40
552 5470 2.128535 TCCAGGCGGTCCCATATAAAA 58.871 47.619 0.00 0.00 35.39 1.52
553 5471 2.510382 TCCAGGCGGTCCCATATAAAAA 59.490 45.455 0.00 0.00 35.39 1.94
581 5499 7.063074 CACATGCAATTTCTTCTTCAGATTTCC 59.937 37.037 0.00 0.00 0.00 3.13
583 5501 7.053316 TGCAATTTCTTCTTCAGATTTCCAA 57.947 32.000 0.00 0.00 0.00 3.53
592 5510 7.886970 TCTTCTTCAGATTTCCAATGAATCACT 59.113 33.333 0.00 0.00 36.26 3.41
597 5515 7.855375 TCAGATTTCCAATGAATCACTAGTCT 58.145 34.615 0.00 0.00 36.26 3.24
606 5524 7.387673 CCAATGAATCACTAGTCTGTTACACAA 59.612 37.037 0.00 0.00 0.00 3.33
648 5567 4.668576 ACAACACACAAGCGATCTATTG 57.331 40.909 5.49 5.49 0.00 1.90
661 5580 3.303593 CGATCTATTGCATGTCACCAAGC 60.304 47.826 0.00 0.00 35.88 4.01
672 5591 2.877786 TGTCACCAAGCATAACACACTG 59.122 45.455 0.00 0.00 0.00 3.66
673 5592 2.226437 GTCACCAAGCATAACACACTGG 59.774 50.000 0.00 0.00 0.00 4.00
740 5662 9.624373 ACATTGATTCTACTAATGAAATCAGCT 57.376 29.630 0.00 0.00 36.09 4.24
741 5663 9.880064 CATTGATTCTACTAATGAAATCAGCTG 57.120 33.333 7.63 7.63 34.55 4.24
745 5667 3.266510 ACTAATGAAATCAGCTGCGGA 57.733 42.857 9.47 4.68 0.00 5.54
775 5697 2.517650 TAGCCCAAAAACGCCAAAAG 57.482 45.000 0.00 0.00 0.00 2.27
777 5699 0.934496 GCCCAAAAACGCCAAAAGAC 59.066 50.000 0.00 0.00 0.00 3.01
780 5702 2.418060 CCCAAAAACGCCAAAAGACACT 60.418 45.455 0.00 0.00 0.00 3.55
783 5705 2.559998 AAACGCCAAAAGACACTGTG 57.440 45.000 6.19 6.19 0.00 3.66
795 5914 8.026607 CCAAAAGACACTGTGTAAAAAGAAAGA 58.973 33.333 14.31 0.00 0.00 2.52
797 5916 9.974980 AAAAGACACTGTGTAAAAAGAAAGAAA 57.025 25.926 14.31 0.00 0.00 2.52
799 5918 8.561738 AGACACTGTGTAAAAAGAAAGAAAGA 57.438 30.769 14.31 0.00 0.00 2.52
843 5999 2.644078 CGTACTCCGTAATACCGCTTC 58.356 52.381 0.00 0.00 0.00 3.86
895 6054 1.623973 GCCGAGTTGTTGTAGTCCGC 61.624 60.000 0.00 0.00 0.00 5.54
896 6055 1.012486 CCGAGTTGTTGTAGTCCGCC 61.012 60.000 0.00 0.00 0.00 6.13
897 6056 1.342082 CGAGTTGTTGTAGTCCGCCG 61.342 60.000 0.00 0.00 0.00 6.46
898 6057 0.319297 GAGTTGTTGTAGTCCGCCGT 60.319 55.000 0.00 0.00 0.00 5.68
899 6058 0.319297 AGTTGTTGTAGTCCGCCGTC 60.319 55.000 0.00 0.00 0.00 4.79
900 6059 1.372004 TTGTTGTAGTCCGCCGTCG 60.372 57.895 0.00 0.00 0.00 5.12
915 6074 3.371063 TCGTCTCGACCCACCAGC 61.371 66.667 0.00 0.00 0.00 4.85
916 6075 3.680786 CGTCTCGACCCACCAGCA 61.681 66.667 0.00 0.00 0.00 4.41
917 6076 2.262915 GTCTCGACCCACCAGCAG 59.737 66.667 0.00 0.00 0.00 4.24
918 6077 2.203640 TCTCGACCCACCAGCAGT 60.204 61.111 0.00 0.00 0.00 4.40
922 6081 3.311110 GACCCACCAGCAGTCGGA 61.311 66.667 0.00 0.00 29.93 4.55
934 6096 0.605589 CAGTCGGAAGTTGGAACCCC 60.606 60.000 0.00 0.00 0.00 4.95
935 6097 1.670083 GTCGGAAGTTGGAACCCCG 60.670 63.158 12.27 12.27 42.93 5.73
1114 6277 3.780173 GCAAGCGCTCCTCCTCCT 61.780 66.667 12.06 0.00 34.30 3.69
1199 6362 1.153745 CGTAGGTGTGCTCTGCCTC 60.154 63.158 5.90 0.25 34.07 4.70
1200 6363 1.599606 CGTAGGTGTGCTCTGCCTCT 61.600 60.000 5.90 0.00 34.07 3.69
1202 6365 0.040351 TAGGTGTGCTCTGCCTCTCT 59.960 55.000 5.90 0.00 34.07 3.10
1203 6366 0.835543 AGGTGTGCTCTGCCTCTCTT 60.836 55.000 0.00 0.00 0.00 2.85
1205 6368 1.276421 GGTGTGCTCTGCCTCTCTTTA 59.724 52.381 0.00 0.00 0.00 1.85
1209 6372 0.179234 GCTCTGCCTCTCTTTACCCC 59.821 60.000 0.00 0.00 0.00 4.95
1210 6373 1.872773 CTCTGCCTCTCTTTACCCCT 58.127 55.000 0.00 0.00 0.00 4.79
1211 6374 1.760029 CTCTGCCTCTCTTTACCCCTC 59.240 57.143 0.00 0.00 0.00 4.30
1212 6375 1.362932 TCTGCCTCTCTTTACCCCTCT 59.637 52.381 0.00 0.00 0.00 3.69
1213 6376 1.484240 CTGCCTCTCTTTACCCCTCTG 59.516 57.143 0.00 0.00 0.00 3.35
1214 6377 0.179234 GCCTCTCTTTACCCCTCTGC 59.821 60.000 0.00 0.00 0.00 4.26
1215 6378 1.872773 CCTCTCTTTACCCCTCTGCT 58.127 55.000 0.00 0.00 0.00 4.24
1216 6379 1.760029 CCTCTCTTTACCCCTCTGCTC 59.240 57.143 0.00 0.00 0.00 4.26
1217 6380 1.407258 CTCTCTTTACCCCTCTGCTCG 59.593 57.143 0.00 0.00 0.00 5.03
1218 6381 0.179097 CTCTTTACCCCTCTGCTCGC 60.179 60.000 0.00 0.00 0.00 5.03
1219 6382 1.153349 CTTTACCCCTCTGCTCGCC 60.153 63.158 0.00 0.00 0.00 5.54
1220 6383 1.612442 TTTACCCCTCTGCTCGCCT 60.612 57.895 0.00 0.00 0.00 5.52
1221 6384 1.614241 TTTACCCCTCTGCTCGCCTC 61.614 60.000 0.00 0.00 0.00 4.70
1226 6389 4.567385 CTCTGCTCGCCTCCGCTC 62.567 72.222 0.00 0.00 0.00 5.03
1280 6617 2.607892 GCGCTTTGCTGACTCGGTT 61.608 57.895 0.00 0.00 41.73 4.44
1414 6776 1.009900 GTATCCGCGGTCTGTCTCG 60.010 63.158 27.15 0.00 0.00 4.04
1423 6785 1.254954 GGTCTGTCTCGGGTGTAGTT 58.745 55.000 0.00 0.00 0.00 2.24
1449 6817 4.874966 AGTAGCATTTCAGCTGTGAATCTC 59.125 41.667 14.67 9.18 46.11 2.75
1490 6859 2.158914 TGTCTCTGAGCAGTTGAGCAAA 60.159 45.455 0.00 0.00 36.85 3.68
1525 6894 8.595421 TGATGAAATGAAATGAAATGAAAGGGA 58.405 29.630 0.00 0.00 0.00 4.20
1572 6981 6.539173 ACCTGTACAACTTTGATTGATACCA 58.461 36.000 0.00 0.00 33.57 3.25
1579 6988 7.950512 ACAACTTTGATTGATACCATTGTCAA 58.049 30.769 0.00 0.00 37.27 3.18
1585 6994 7.885009 TGATTGATACCATTGTCAACATGAT 57.115 32.000 0.00 0.00 35.85 2.45
1597 7006 0.928505 AACATGATCCTGGGGATGCA 59.071 50.000 0.00 0.00 43.27 3.96
1598 7007 0.477204 ACATGATCCTGGGGATGCAG 59.523 55.000 0.00 0.00 43.27 4.41
1607 7016 2.356278 GGGATGCAGCCCTGAACA 59.644 61.111 33.03 0.00 45.12 3.18
1608 7017 1.751927 GGGATGCAGCCCTGAACAG 60.752 63.158 33.03 0.00 45.12 3.16
1610 7019 1.028868 GGATGCAGCCCTGAACAGTC 61.029 60.000 10.76 0.00 0.00 3.51
1653 7066 6.666980 AGCTGATCCTGATCATAGTAGCATTA 59.333 38.462 10.10 0.00 45.74 1.90
1676 7092 0.453782 GCGTTGCGTGGTGGATAAAC 60.454 55.000 0.00 0.00 0.00 2.01
1679 7095 0.956410 TTGCGTGGTGGATAAACCGG 60.956 55.000 0.00 0.00 43.73 5.28
1680 7096 1.078988 GCGTGGTGGATAAACCGGA 60.079 57.895 9.46 0.00 43.73 5.14
1691 7107 5.986741 GTGGATAAACCGGAAATGTGTTTTT 59.013 36.000 9.46 0.00 42.61 1.94
1692 7108 7.146648 GTGGATAAACCGGAAATGTGTTTTTA 58.853 34.615 9.46 0.00 42.61 1.52
1693 7109 7.327518 GTGGATAAACCGGAAATGTGTTTTTAG 59.672 37.037 9.46 0.00 42.61 1.85
1694 7110 6.309494 GGATAAACCGGAAATGTGTTTTTAGC 59.691 38.462 9.46 1.47 34.33 3.09
1696 7112 4.929819 ACCGGAAATGTGTTTTTAGCTT 57.070 36.364 9.46 0.00 0.00 3.74
1697 7113 6.394025 AACCGGAAATGTGTTTTTAGCTTA 57.606 33.333 9.46 0.00 0.00 3.09
1698 7114 5.765176 ACCGGAAATGTGTTTTTAGCTTAC 58.235 37.500 9.46 0.00 0.00 2.34
1699 7115 5.299782 ACCGGAAATGTGTTTTTAGCTTACA 59.700 36.000 9.46 0.00 0.00 2.41
1700 7116 5.627780 CCGGAAATGTGTTTTTAGCTTACAC 59.372 40.000 0.00 11.76 41.85 2.90
1705 7121 4.899516 TGTGTTTTTAGCTTACACACGTG 58.100 39.130 15.48 15.48 45.06 4.49
1706 7122 3.722289 GTGTTTTTAGCTTACACACGTGC 59.278 43.478 17.22 0.00 41.30 5.34
1707 7123 3.374367 TGTTTTTAGCTTACACACGTGCA 59.626 39.130 17.22 0.00 0.00 4.57
1708 7124 4.035792 TGTTTTTAGCTTACACACGTGCAT 59.964 37.500 17.22 6.41 0.00 3.96
1709 7125 4.398549 TTTTAGCTTACACACGTGCATC 57.601 40.909 17.22 0.00 0.00 3.91
1711 7127 1.432514 AGCTTACACACGTGCATCTG 58.567 50.000 17.22 9.02 0.00 2.90
1712 7128 1.148310 GCTTACACACGTGCATCTGT 58.852 50.000 17.22 14.86 0.00 3.41
1714 7130 2.662791 GCTTACACACGTGCATCTGTTG 60.663 50.000 17.22 7.01 0.00 3.33
1715 7131 2.232756 TACACACGTGCATCTGTTGT 57.767 45.000 17.22 12.96 0.00 3.32
1716 7132 1.378531 ACACACGTGCATCTGTTGTT 58.621 45.000 17.22 0.00 0.00 2.83
1717 7133 2.556257 ACACACGTGCATCTGTTGTTA 58.444 42.857 17.22 0.00 0.00 2.41
1718 7134 2.543848 ACACACGTGCATCTGTTGTTAG 59.456 45.455 17.22 0.00 0.00 2.34
1722 7138 3.433274 CACGTGCATCTGTTGTTAGACAT 59.567 43.478 0.82 0.00 0.00 3.06
1729 7145 7.907045 GTGCATCTGTTGTTAGACATAATCAAG 59.093 37.037 0.00 0.00 0.00 3.02
1758 7174 3.998341 TCACCGATTGGCTAGTTTGTAAC 59.002 43.478 0.00 0.00 39.70 2.50
1763 7186 4.569564 CGATTGGCTAGTTTGTAACCTACC 59.430 45.833 0.00 0.00 0.00 3.18
1768 7191 2.873094 AGTTTGTAACCTACCTGCCC 57.127 50.000 0.00 0.00 0.00 5.36
1771 7194 0.899720 TTGTAACCTACCTGCCCTCG 59.100 55.000 0.00 0.00 0.00 4.63
1782 7205 2.039879 ACCTGCCCTCGATTGTAGTTTT 59.960 45.455 0.00 0.00 0.00 2.43
1783 7206 3.081804 CCTGCCCTCGATTGTAGTTTTT 58.918 45.455 0.00 0.00 0.00 1.94
1785 7208 3.482436 TGCCCTCGATTGTAGTTTTTGT 58.518 40.909 0.00 0.00 0.00 2.83
1786 7209 3.500680 TGCCCTCGATTGTAGTTTTTGTC 59.499 43.478 0.00 0.00 0.00 3.18
1787 7210 3.500680 GCCCTCGATTGTAGTTTTTGTCA 59.499 43.478 0.00 0.00 0.00 3.58
1788 7211 4.023536 GCCCTCGATTGTAGTTTTTGTCAA 60.024 41.667 0.00 0.00 0.00 3.18
1789 7212 5.335661 GCCCTCGATTGTAGTTTTTGTCAAT 60.336 40.000 0.00 0.00 33.95 2.57
1790 7213 6.086222 CCCTCGATTGTAGTTTTTGTCAATG 58.914 40.000 0.00 0.00 31.87 2.82
1791 7214 6.086222 CCTCGATTGTAGTTTTTGTCAATGG 58.914 40.000 0.00 0.00 31.87 3.16
1792 7215 6.293955 CCTCGATTGTAGTTTTTGTCAATGGT 60.294 38.462 0.00 0.00 31.87 3.55
1793 7216 6.664515 TCGATTGTAGTTTTTGTCAATGGTC 58.335 36.000 0.00 0.00 31.87 4.02
1794 7217 6.485313 TCGATTGTAGTTTTTGTCAATGGTCT 59.515 34.615 0.00 0.00 31.87 3.85
1804 7807 0.703488 TCAATGGTCTTGGGGATGCA 59.297 50.000 0.00 0.00 0.00 3.96
1815 7818 3.050089 GGGATGCAACCCTGAACAA 57.950 52.632 24.24 0.00 45.90 2.83
1831 7834 3.130869 TGAACAATCAGCTTGCTTGTTGT 59.869 39.130 17.99 13.47 43.89 3.32
1835 7838 2.042686 TCAGCTTGCTTGTTGTCACT 57.957 45.000 0.00 0.00 0.00 3.41
1839 7842 1.202336 GCTTGCTTGTTGTCACTGCTT 60.202 47.619 0.00 0.00 0.00 3.91
1848 7851 4.507710 TGTTGTCACTGCTTATCCTGATC 58.492 43.478 0.00 0.00 0.00 2.92
1850 7853 4.128925 TGTCACTGCTTATCCTGATCAC 57.871 45.455 0.00 0.00 0.00 3.06
1864 7867 3.376234 CCTGATCACAGTAGCATTGTTGG 59.624 47.826 0.00 0.00 42.05 3.77
1865 7868 2.749076 TGATCACAGTAGCATTGTTGGC 59.251 45.455 0.00 0.00 0.00 4.52
1871 7874 1.065031 GTAGCATTGTTGGCGTTGCG 61.065 55.000 0.00 0.00 40.00 4.85
1874 7877 1.009108 CATTGTTGGCGTTGCGTGA 60.009 52.632 0.00 0.00 0.00 4.35
1896 7899 7.192913 GTGATGGATAAATCGCAAATGTGTTA 58.807 34.615 0.00 0.00 37.10 2.41
1908 7911 8.426881 TCGCAAATGTGTTATAGCTTACAATA 57.573 30.769 0.00 0.00 0.00 1.90
2014 8033 3.614870 GCCTTTTAACTTGGATGGCAGTG 60.615 47.826 0.00 0.00 38.79 3.66
2015 8034 3.056607 CCTTTTAACTTGGATGGCAGTGG 60.057 47.826 0.00 0.00 0.00 4.00
2020 8040 0.744414 CTTGGATGGCAGTGGTACCG 60.744 60.000 7.57 0.00 0.00 4.02
2040 8060 2.556622 CGTGTTTTGGTATTGCCCTCTT 59.443 45.455 0.00 0.00 36.04 2.85
2043 8063 5.587043 CGTGTTTTGGTATTGCCCTCTTATA 59.413 40.000 0.00 0.00 36.04 0.98
2047 8067 7.719633 TGTTTTGGTATTGCCCTCTTATATCTC 59.280 37.037 0.00 0.00 36.04 2.75
2048 8068 7.633018 TTTGGTATTGCCCTCTTATATCTCT 57.367 36.000 0.00 0.00 36.04 3.10
2049 8069 6.859112 TGGTATTGCCCTCTTATATCTCTC 57.141 41.667 0.00 0.00 36.04 3.20
2050 8070 6.322931 TGGTATTGCCCTCTTATATCTCTCA 58.677 40.000 0.00 0.00 36.04 3.27
2051 8071 6.787458 TGGTATTGCCCTCTTATATCTCTCAA 59.213 38.462 0.00 0.00 36.04 3.02
2052 8072 7.038729 TGGTATTGCCCTCTTATATCTCTCAAG 60.039 40.741 0.00 0.00 36.04 3.02
2053 8073 7.038658 GGTATTGCCCTCTTATATCTCTCAAGT 60.039 40.741 0.00 0.00 0.00 3.16
2055 8075 8.677870 ATTGCCCTCTTATATCTCTCAAGTAT 57.322 34.615 0.00 0.00 0.00 2.12
2056 8076 7.710676 TGCCCTCTTATATCTCTCAAGTATC 57.289 40.000 0.00 0.00 0.00 2.24
2057 8077 6.665680 TGCCCTCTTATATCTCTCAAGTATCC 59.334 42.308 0.00 0.00 0.00 2.59
2058 8078 6.183360 GCCCTCTTATATCTCTCAAGTATCCG 60.183 46.154 0.00 0.00 0.00 4.18
2059 8079 6.320164 CCCTCTTATATCTCTCAAGTATCCGG 59.680 46.154 0.00 0.00 0.00 5.14
2060 8080 7.113437 CCTCTTATATCTCTCAAGTATCCGGA 58.887 42.308 6.61 6.61 0.00 5.14
2061 8081 7.612244 CCTCTTATATCTCTCAAGTATCCGGAA 59.388 40.741 9.01 0.00 0.00 4.30
2062 8082 8.568676 TCTTATATCTCTCAAGTATCCGGAAG 57.431 38.462 9.01 0.00 0.00 3.46
2063 8083 8.383947 TCTTATATCTCTCAAGTATCCGGAAGA 58.616 37.037 9.01 4.11 0.00 2.87
2064 8084 9.184523 CTTATATCTCTCAAGTATCCGGAAGAT 57.815 37.037 9.01 12.23 39.15 2.40
2066 8086 5.521906 TCTCTCAAGTATCCGGAAGATTG 57.478 43.478 9.01 13.66 36.33 2.67
2068 8088 5.422331 TCTCTCAAGTATCCGGAAGATTGTT 59.578 40.000 9.01 0.00 36.33 2.83
2069 8089 5.419542 TCTCAAGTATCCGGAAGATTGTTG 58.580 41.667 9.01 7.10 36.33 3.33
2070 8090 5.046591 TCTCAAGTATCCGGAAGATTGTTGT 60.047 40.000 9.01 0.00 36.33 3.32
2071 8091 5.556915 TCAAGTATCCGGAAGATTGTTGTT 58.443 37.500 9.01 0.00 36.33 2.83
2072 8092 6.001460 TCAAGTATCCGGAAGATTGTTGTTT 58.999 36.000 9.01 0.00 36.33 2.83
2073 8093 6.148811 TCAAGTATCCGGAAGATTGTTGTTTC 59.851 38.462 9.01 0.00 36.33 2.78
2074 8094 5.805728 AGTATCCGGAAGATTGTTGTTTCT 58.194 37.500 9.01 0.00 36.33 2.52
2075 8095 6.238648 AGTATCCGGAAGATTGTTGTTTCTT 58.761 36.000 9.01 0.00 36.33 2.52
2077 8097 7.881232 AGTATCCGGAAGATTGTTGTTTCTTTA 59.119 33.333 9.01 0.00 36.33 1.85
2083 8103 5.108385 AGATTGTTGTTTCTTTAGCACGG 57.892 39.130 0.00 0.00 0.00 4.94
2085 8105 2.294074 TGTTGTTTCTTTAGCACGGCT 58.706 42.857 3.87 3.87 43.41 5.52
2100 8120 2.722201 GGCTGTGCGCTAGGTAGGT 61.722 63.158 9.73 0.00 39.13 3.08
2109 8134 0.902531 GCTAGGTAGGTGACTTGGCA 59.097 55.000 0.00 0.00 40.81 4.92
2119 8144 2.129607 GTGACTTGGCATTTTGCTGTG 58.870 47.619 0.00 0.00 44.28 3.66
2120 8145 1.755959 TGACTTGGCATTTTGCTGTGT 59.244 42.857 0.00 0.00 44.28 3.72
2131 8156 7.285172 TGGCATTTTGCTGTGTATGATATACTT 59.715 33.333 1.14 0.00 44.28 2.24
2135 8160 7.786178 TTTGCTGTGTATGATATACTTCCAC 57.214 36.000 1.14 0.00 0.00 4.02
2141 8166 8.185506 TGTGTATGATATACTTCCACGGTTAT 57.814 34.615 1.14 0.00 0.00 1.89
2142 8167 8.085909 TGTGTATGATATACTTCCACGGTTATG 58.914 37.037 1.14 0.00 0.00 1.90
2143 8168 7.063074 GTGTATGATATACTTCCACGGTTATGC 59.937 40.741 0.00 0.00 0.00 3.14
2144 8169 5.801531 TGATATACTTCCACGGTTATGCT 57.198 39.130 0.00 0.00 0.00 3.79
2145 8170 6.169557 TGATATACTTCCACGGTTATGCTT 57.830 37.500 0.00 0.00 0.00 3.91
2190 8219 2.098117 GCCTGTGGCTATTTTAGTGCTG 59.902 50.000 0.73 0.00 46.69 4.41
2191 8220 3.609853 CCTGTGGCTATTTTAGTGCTGA 58.390 45.455 0.00 0.00 0.00 4.26
2192 8221 4.202441 CCTGTGGCTATTTTAGTGCTGAT 58.798 43.478 0.00 0.00 0.00 2.90
2194 8223 5.237344 CCTGTGGCTATTTTAGTGCTGATAC 59.763 44.000 0.00 0.00 0.00 2.24
2197 8226 5.981315 GTGGCTATTTTAGTGCTGATACGTA 59.019 40.000 0.00 0.00 0.00 3.57
2199 8228 7.170998 GTGGCTATTTTAGTGCTGATACGTATT 59.829 37.037 9.92 0.00 0.00 1.89
2200 8229 7.170828 TGGCTATTTTAGTGCTGATACGTATTG 59.829 37.037 9.92 7.28 0.00 1.90
2224 8255 4.252971 TGAGTTCACCTTACAGTGTAGC 57.747 45.455 2.68 0.00 38.91 3.58
2251 8282 8.704668 TGGTGATTAAGCTATCTGAATAGAACA 58.295 33.333 0.00 0.00 37.63 3.18
2268 8299 1.122019 ACACGAGGCCCTTCAGTTCT 61.122 55.000 0.00 0.00 0.00 3.01
2274 8305 2.038557 GAGGCCCTTCAGTTCTGTGTTA 59.961 50.000 0.00 0.00 0.00 2.41
2275 8306 2.644798 AGGCCCTTCAGTTCTGTGTTAT 59.355 45.455 0.00 0.00 0.00 1.89
2276 8307 2.749621 GGCCCTTCAGTTCTGTGTTATG 59.250 50.000 0.00 0.00 0.00 1.90
2277 8308 3.412386 GCCCTTCAGTTCTGTGTTATGT 58.588 45.455 0.00 0.00 0.00 2.29
2278 8309 3.821033 GCCCTTCAGTTCTGTGTTATGTT 59.179 43.478 0.00 0.00 0.00 2.71
2279 8310 4.278419 GCCCTTCAGTTCTGTGTTATGTTT 59.722 41.667 0.00 0.00 0.00 2.83
2280 8311 5.221244 GCCCTTCAGTTCTGTGTTATGTTTT 60.221 40.000 0.00 0.00 0.00 2.43
2281 8312 6.682861 GCCCTTCAGTTCTGTGTTATGTTTTT 60.683 38.462 0.00 0.00 0.00 1.94
2282 8313 6.697019 CCCTTCAGTTCTGTGTTATGTTTTTG 59.303 38.462 0.00 0.00 0.00 2.44
2283 8314 7.416213 CCCTTCAGTTCTGTGTTATGTTTTTGA 60.416 37.037 0.00 0.00 0.00 2.69
2284 8315 7.432252 CCTTCAGTTCTGTGTTATGTTTTTGAC 59.568 37.037 0.00 0.00 0.00 3.18
2285 8316 7.384439 TCAGTTCTGTGTTATGTTTTTGACA 57.616 32.000 0.00 0.00 43.71 3.58
2286 8317 7.247728 TCAGTTCTGTGTTATGTTTTTGACAC 58.752 34.615 0.00 0.00 42.04 3.67
2287 8318 6.472163 CAGTTCTGTGTTATGTTTTTGACACC 59.528 38.462 3.38 0.00 42.04 4.16
2288 8319 5.508200 TCTGTGTTATGTTTTTGACACCC 57.492 39.130 3.38 0.00 42.04 4.61
2289 8320 4.339814 TCTGTGTTATGTTTTTGACACCCC 59.660 41.667 3.38 0.00 42.04 4.95
2290 8321 4.023980 TGTGTTATGTTTTTGACACCCCA 58.976 39.130 3.38 0.00 42.04 4.96
2291 8322 4.466370 TGTGTTATGTTTTTGACACCCCAA 59.534 37.500 3.38 0.00 42.04 4.12
2292 8323 5.047188 GTGTTATGTTTTTGACACCCCAAG 58.953 41.667 0.00 0.00 42.04 3.61
2293 8324 4.100189 TGTTATGTTTTTGACACCCCAAGG 59.900 41.667 0.00 0.00 42.04 3.61
2305 8336 2.741759 CCCCAAGGTTTTATGTGCAC 57.258 50.000 10.75 10.75 0.00 4.57
2306 8337 1.067915 CCCCAAGGTTTTATGTGCACG 60.068 52.381 13.13 0.00 0.00 5.34
2307 8338 1.883275 CCCAAGGTTTTATGTGCACGA 59.117 47.619 13.13 0.00 0.00 4.35
2308 8339 2.095263 CCCAAGGTTTTATGTGCACGAG 60.095 50.000 13.13 0.00 0.00 4.18
2309 8340 2.811431 CCAAGGTTTTATGTGCACGAGA 59.189 45.455 13.13 0.00 0.00 4.04
2310 8341 3.120199 CCAAGGTTTTATGTGCACGAGAG 60.120 47.826 13.13 0.00 0.00 3.20
2311 8342 2.699954 AGGTTTTATGTGCACGAGAGG 58.300 47.619 13.13 0.00 0.00 3.69
2312 8343 2.038557 AGGTTTTATGTGCACGAGAGGT 59.961 45.455 13.13 0.00 0.00 3.85
2313 8344 3.259876 AGGTTTTATGTGCACGAGAGGTA 59.740 43.478 13.13 0.00 0.00 3.08
2314 8345 3.998341 GGTTTTATGTGCACGAGAGGTAA 59.002 43.478 13.13 1.93 0.00 2.85
2315 8346 4.453136 GGTTTTATGTGCACGAGAGGTAAA 59.547 41.667 13.13 7.61 0.00 2.01
2316 8347 5.123344 GGTTTTATGTGCACGAGAGGTAAAT 59.877 40.000 13.13 0.00 0.00 1.40
2317 8348 6.314400 GGTTTTATGTGCACGAGAGGTAAATA 59.686 38.462 13.13 0.00 0.00 1.40
2318 8349 7.012044 GGTTTTATGTGCACGAGAGGTAAATAT 59.988 37.037 13.13 0.00 0.00 1.28
2319 8350 7.477144 TTTATGTGCACGAGAGGTAAATATG 57.523 36.000 13.13 0.00 0.00 1.78
2320 8351 3.194861 TGTGCACGAGAGGTAAATATGC 58.805 45.455 13.13 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 8.962884 AGCCAAGAATGTTTTTAAAGAATTGT 57.037 26.923 0.00 0.00 0.00 2.71
77 78 3.509184 ACCCTAAAAGACCGTGAGTAGTC 59.491 47.826 0.00 0.00 0.00 2.59
135 137 3.913548 TTGTCATCACGTGAATTTGGG 57.086 42.857 24.13 8.20 38.90 4.12
261 1164 2.439156 GCTCACATGACCCCAGGC 60.439 66.667 0.00 0.00 0.00 4.85
264 1167 1.556373 CCTGAGCTCACATGACCCCA 61.556 60.000 13.74 0.00 0.00 4.96
269 1172 1.297689 GGCACCTGAGCTCACATGA 59.702 57.895 21.46 0.00 34.17 3.07
305 1209 4.734398 TTGCTGTGTTGATGGTTTTCTT 57.266 36.364 0.00 0.00 0.00 2.52
312 5226 4.044336 TCTGTTTTTGCTGTGTTGATGG 57.956 40.909 0.00 0.00 0.00 3.51
321 5235 4.143473 CGCTATTTTGCTCTGTTTTTGCTG 60.143 41.667 0.00 0.00 0.00 4.41
329 5243 1.982073 GCCGCGCTATTTTGCTCTGT 61.982 55.000 5.56 0.00 0.00 3.41
330 5244 1.297893 GCCGCGCTATTTTGCTCTG 60.298 57.895 5.56 0.00 0.00 3.35
331 5245 1.305219 TTGCCGCGCTATTTTGCTCT 61.305 50.000 5.56 0.00 0.00 4.09
332 5246 0.455972 TTTGCCGCGCTATTTTGCTC 60.456 50.000 5.56 0.00 0.00 4.26
333 5247 0.173255 ATTTGCCGCGCTATTTTGCT 59.827 45.000 5.56 0.00 0.00 3.91
334 5248 0.298411 CATTTGCCGCGCTATTTTGC 59.702 50.000 5.56 0.00 0.00 3.68
335 5249 1.321148 CACATTTGCCGCGCTATTTTG 59.679 47.619 5.56 0.00 0.00 2.44
340 5255 2.866750 CACACATTTGCCGCGCTA 59.133 55.556 5.56 0.00 0.00 4.26
347 5262 0.439600 GATTTGGCGCACACATTTGC 59.560 50.000 10.83 0.00 39.28 3.68
388 5303 4.154556 CGGCCGTTTTCTGTTATTCCTTTA 59.845 41.667 19.50 0.00 0.00 1.85
475 5392 4.272748 CACCTGATGTAAGCTGATGTCATG 59.727 45.833 0.00 0.00 0.00 3.07
502 5419 5.183522 GCTAGCCGAGTTATAGTATGGTCTT 59.816 44.000 2.29 0.00 0.00 3.01
520 5437 1.153269 GCCTGGAACTCAGCTAGCC 60.153 63.158 12.13 0.00 42.05 3.93
550 5468 7.765360 TCTGAAGAAGAAATTGCATGTGTTTTT 59.235 29.630 0.00 0.00 29.54 1.94
551 5469 7.267128 TCTGAAGAAGAAATTGCATGTGTTTT 58.733 30.769 0.00 0.00 29.54 2.43
552 5470 6.808829 TCTGAAGAAGAAATTGCATGTGTTT 58.191 32.000 0.00 0.00 29.54 2.83
553 5471 6.395426 TCTGAAGAAGAAATTGCATGTGTT 57.605 33.333 0.00 0.00 29.54 3.32
554 5472 6.585695 ATCTGAAGAAGAAATTGCATGTGT 57.414 33.333 0.00 0.00 38.79 3.72
555 5473 7.063074 GGAAATCTGAAGAAGAAATTGCATGTG 59.937 37.037 0.00 0.00 38.79 3.21
556 5474 7.095270 GGAAATCTGAAGAAGAAATTGCATGT 58.905 34.615 0.00 0.00 38.79 3.21
557 5475 7.094631 TGGAAATCTGAAGAAGAAATTGCATG 58.905 34.615 0.00 0.00 38.79 4.06
558 5476 7.235935 TGGAAATCTGAAGAAGAAATTGCAT 57.764 32.000 0.00 0.00 38.79 3.96
559 5477 6.653526 TGGAAATCTGAAGAAGAAATTGCA 57.346 33.333 0.00 0.00 38.79 4.08
573 5491 7.551974 ACAGACTAGTGATTCATTGGAAATCTG 59.448 37.037 0.00 8.82 36.43 2.90
581 5499 7.889589 TGTGTAACAGACTAGTGATTCATTG 57.110 36.000 0.00 0.00 45.67 2.82
606 5524 8.147058 TGTTGTAAAATGCACACCAATATTTCT 58.853 29.630 0.00 0.00 0.00 2.52
635 5554 3.303593 GGTGACATGCAATAGATCGCTTG 60.304 47.826 0.00 6.07 38.76 4.01
636 5555 2.874701 GGTGACATGCAATAGATCGCTT 59.125 45.455 0.00 0.00 0.00 4.68
661 5580 5.957842 ATGTTTACCACCAGTGTGTTATG 57.042 39.130 0.00 0.00 41.09 1.90
672 5591 8.101654 TGAACATGTAACTAATGTTTACCACC 57.898 34.615 0.00 0.00 45.81 4.61
717 5639 7.254556 CGCAGCTGATTTCATTAGTAGAATCAA 60.255 37.037 20.43 0.00 0.00 2.57
723 5645 4.371786 TCCGCAGCTGATTTCATTAGTAG 58.628 43.478 20.43 0.00 0.00 2.57
727 5649 3.243168 GCATTCCGCAGCTGATTTCATTA 60.243 43.478 20.43 0.00 41.79 1.90
728 5650 2.480759 GCATTCCGCAGCTGATTTCATT 60.481 45.455 20.43 0.00 41.79 2.57
756 5678 2.032620 TCTTTTGGCGTTTTTGGGCTA 58.967 42.857 0.00 0.00 0.00 3.93
758 5680 0.934496 GTCTTTTGGCGTTTTTGGGC 59.066 50.000 0.00 0.00 0.00 5.36
759 5681 1.930503 GTGTCTTTTGGCGTTTTTGGG 59.069 47.619 0.00 0.00 0.00 4.12
763 5685 2.230266 ACACAGTGTCTTTTGGCGTTTT 59.770 40.909 0.00 0.00 0.00 2.43
767 5689 3.684103 TTTACACAGTGTCTTTTGGCG 57.316 42.857 10.23 0.00 0.00 5.69
775 5697 9.620660 TTTCTTTCTTTCTTTTTACACAGTGTC 57.379 29.630 10.23 0.00 0.00 3.67
777 5699 8.587111 GCTTTCTTTCTTTCTTTTTACACAGTG 58.413 33.333 0.00 0.00 0.00 3.66
780 5702 6.750039 CGGCTTTCTTTCTTTCTTTTTACACA 59.250 34.615 0.00 0.00 0.00 3.72
783 5705 5.175126 GGCGGCTTTCTTTCTTTCTTTTTAC 59.825 40.000 0.00 0.00 0.00 2.01
795 5914 1.002011 GAGGGAGGCGGCTTTCTTT 60.002 57.895 14.76 0.00 0.00 2.52
797 5916 3.775654 CGAGGGAGGCGGCTTTCT 61.776 66.667 14.76 13.88 0.00 2.52
870 6026 2.741486 TACAACAACTCGGCCCAGGC 62.741 60.000 1.31 0.00 41.06 4.85
871 6027 0.673644 CTACAACAACTCGGCCCAGG 60.674 60.000 1.31 0.00 0.00 4.45
872 6028 0.034896 ACTACAACAACTCGGCCCAG 59.965 55.000 0.00 0.00 0.00 4.45
873 6029 0.034337 GACTACAACAACTCGGCCCA 59.966 55.000 0.00 0.00 0.00 5.36
874 6030 0.672711 GGACTACAACAACTCGGCCC 60.673 60.000 0.00 0.00 0.00 5.80
875 6031 1.012486 CGGACTACAACAACTCGGCC 61.012 60.000 0.00 0.00 0.00 6.13
876 6032 1.623973 GCGGACTACAACAACTCGGC 61.624 60.000 0.00 0.00 0.00 5.54
898 6057 3.371063 GCTGGTGGGTCGAGACGA 61.371 66.667 0.00 0.00 0.00 4.20
899 6058 3.633094 CTGCTGGTGGGTCGAGACG 62.633 68.421 0.00 0.00 0.00 4.18
900 6059 2.262915 CTGCTGGTGGGTCGAGAC 59.737 66.667 0.00 0.00 0.00 3.36
913 6072 0.250338 GGTTCCAACTTCCGACTGCT 60.250 55.000 0.00 0.00 0.00 4.24
914 6073 1.235281 GGGTTCCAACTTCCGACTGC 61.235 60.000 0.00 0.00 0.00 4.40
915 6074 0.605589 GGGGTTCCAACTTCCGACTG 60.606 60.000 0.00 0.00 0.00 3.51
916 6075 1.759236 GGGGTTCCAACTTCCGACT 59.241 57.895 0.00 0.00 0.00 4.18
917 6076 1.670083 CGGGGTTCCAACTTCCGAC 60.670 63.158 15.01 0.00 43.10 4.79
918 6077 2.103339 GACGGGGTTCCAACTTCCGA 62.103 60.000 22.22 0.00 43.10 4.55
922 6081 1.070275 GACGACGGGGTTCCAACTT 59.930 57.895 0.00 0.00 0.00 2.66
934 6096 2.464865 GATTTGGATCTGGAGACGACG 58.535 52.381 0.00 0.00 0.00 5.12
935 6097 2.432510 AGGATTTGGATCTGGAGACGAC 59.567 50.000 0.00 0.00 32.66 4.34
1071 6234 2.024319 GATCATGTAGGCGAGCGGC 61.024 63.158 8.49 8.49 42.51 6.53
1161 6324 1.836802 GTCTGCTTGGAGAAGGAGGAT 59.163 52.381 0.00 0.00 45.37 3.24
1199 6362 0.179097 GCGAGCAGAGGGGTAAAGAG 60.179 60.000 0.00 0.00 0.00 2.85
1200 6363 1.614241 GGCGAGCAGAGGGGTAAAGA 61.614 60.000 0.00 0.00 0.00 2.52
1202 6365 1.612442 AGGCGAGCAGAGGGGTAAA 60.612 57.895 0.00 0.00 0.00 2.01
1203 6366 2.038975 AGGCGAGCAGAGGGGTAA 59.961 61.111 0.00 0.00 0.00 2.85
1209 6372 4.567385 GAGCGGAGGCGAGCAGAG 62.567 72.222 0.00 0.00 46.35 3.35
1280 6617 3.311110 AGGCAAACGGAGAGCGGA 61.311 61.111 0.00 0.00 0.00 5.54
1423 6785 4.056194 TTCACAGCTGAAATGCTACTGCA 61.056 43.478 23.35 0.00 41.48 4.41
1436 6798 6.389830 ACTACAGATAGAGATTCACAGCTG 57.610 41.667 13.48 13.48 32.23 4.24
1548 6954 6.539173 TGGTATCAATCAAAGTTGTACAGGT 58.461 36.000 0.00 0.00 0.00 4.00
1564 6973 6.319405 CAGGATCATGTTGACAATGGTATCAA 59.681 38.462 0.00 0.00 32.44 2.57
1572 6981 2.582172 TCCCCAGGATCATGTTGACAAT 59.418 45.455 6.62 0.00 0.00 2.71
1579 6988 0.477204 CTGCATCCCCAGGATCATGT 59.523 55.000 6.62 0.00 40.98 3.21
1607 7016 1.672881 GTGACAACAAGCAAGCTGACT 59.327 47.619 0.00 0.00 0.00 3.41
1608 7017 1.401552 TGTGACAACAAGCAAGCTGAC 59.598 47.619 0.00 0.00 31.82 3.51
1610 7019 1.862815 GCTGTGACAACAAGCAAGCTG 60.863 52.381 0.00 0.00 35.37 4.24
1616 7025 1.198637 GGATCAGCTGTGACAACAAGC 59.801 52.381 14.67 0.00 35.37 4.01
1653 7066 3.669344 CCACCACGCAACGCCAAT 61.669 61.111 0.00 0.00 0.00 3.16
1676 7092 5.627780 GTGTAAGCTAAAAACACATTTCCGG 59.372 40.000 13.60 0.00 42.40 5.14
1691 7107 2.029380 ACAGATGCACGTGTGTAAGCTA 60.029 45.455 18.38 0.00 0.00 3.32
1692 7108 1.270305 ACAGATGCACGTGTGTAAGCT 60.270 47.619 18.38 6.05 0.00 3.74
1693 7109 1.148310 ACAGATGCACGTGTGTAAGC 58.852 50.000 18.38 1.30 0.00 3.09
1694 7110 2.543848 ACAACAGATGCACGTGTGTAAG 59.456 45.455 18.38 11.58 0.00 2.34
1696 7112 2.232756 ACAACAGATGCACGTGTGTA 57.767 45.000 18.38 4.54 0.00 2.90
1697 7113 1.378531 AACAACAGATGCACGTGTGT 58.621 45.000 18.38 10.61 0.00 3.72
1698 7114 2.799978 TCTAACAACAGATGCACGTGTG 59.200 45.455 18.38 9.90 0.00 3.82
1699 7115 2.800544 GTCTAACAACAGATGCACGTGT 59.199 45.455 18.38 0.00 0.00 4.49
1700 7116 2.799978 TGTCTAACAACAGATGCACGTG 59.200 45.455 12.28 12.28 0.00 4.49
1701 7117 3.106242 TGTCTAACAACAGATGCACGT 57.894 42.857 0.00 0.00 0.00 4.49
1702 7118 5.778161 TTATGTCTAACAACAGATGCACG 57.222 39.130 0.00 0.00 31.50 5.34
1703 7119 7.307493 TGATTATGTCTAACAACAGATGCAC 57.693 36.000 0.00 0.00 31.50 4.57
1704 7120 7.823799 TCTTGATTATGTCTAACAACAGATGCA 59.176 33.333 0.00 0.00 31.50 3.96
1705 7121 8.201554 TCTTGATTATGTCTAACAACAGATGC 57.798 34.615 0.00 0.00 31.50 3.91
1708 7124 9.996554 TTCTTCTTGATTATGTCTAACAACAGA 57.003 29.630 0.00 0.00 31.50 3.41
1715 7131 9.098355 CGGTGAATTCTTCTTGATTATGTCTAA 57.902 33.333 7.05 0.00 0.00 2.10
1716 7132 8.474831 TCGGTGAATTCTTCTTGATTATGTCTA 58.525 33.333 7.05 0.00 0.00 2.59
1717 7133 7.331026 TCGGTGAATTCTTCTTGATTATGTCT 58.669 34.615 7.05 0.00 0.00 3.41
1718 7134 7.539712 TCGGTGAATTCTTCTTGATTATGTC 57.460 36.000 7.05 0.00 0.00 3.06
1722 7138 6.183360 GCCAATCGGTGAATTCTTCTTGATTA 60.183 38.462 7.05 0.00 33.28 1.75
1729 7145 4.192317 ACTAGCCAATCGGTGAATTCTTC 58.808 43.478 7.05 0.06 33.28 2.87
1740 7156 4.569564 GGTAGGTTACAAACTAGCCAATCG 59.430 45.833 5.15 0.00 32.94 3.34
1742 7158 5.497474 CAGGTAGGTTACAAACTAGCCAAT 58.503 41.667 11.58 0.00 38.18 3.16
1747 7163 3.518303 AGGGCAGGTAGGTTACAAACTAG 59.482 47.826 0.00 0.00 0.00 2.57
1758 7174 1.341531 CTACAATCGAGGGCAGGTAGG 59.658 57.143 0.00 0.00 0.00 3.18
1763 7186 3.502211 ACAAAAACTACAATCGAGGGCAG 59.498 43.478 0.00 0.00 0.00 4.85
1768 7191 6.668323 ACCATTGACAAAAACTACAATCGAG 58.332 36.000 0.00 0.00 31.85 4.04
1771 7194 7.382218 CCAAGACCATTGACAAAAACTACAATC 59.618 37.037 0.00 0.00 31.85 2.67
1782 7205 2.806434 CATCCCCAAGACCATTGACAA 58.194 47.619 0.00 0.00 0.00 3.18
1783 7206 1.616725 GCATCCCCAAGACCATTGACA 60.617 52.381 0.00 0.00 0.00 3.58
1785 7208 0.703488 TGCATCCCCAAGACCATTGA 59.297 50.000 0.00 0.00 0.00 2.57
1786 7209 1.205417 GTTGCATCCCCAAGACCATTG 59.795 52.381 0.00 0.00 0.00 2.82
1787 7210 1.560505 GTTGCATCCCCAAGACCATT 58.439 50.000 0.00 0.00 0.00 3.16
1788 7211 0.324645 GGTTGCATCCCCAAGACCAT 60.325 55.000 2.02 0.00 0.00 3.55
1789 7212 1.076549 GGTTGCATCCCCAAGACCA 59.923 57.895 2.02 0.00 0.00 4.02
1790 7213 1.682344 GGGTTGCATCCCCAAGACC 60.682 63.158 20.72 6.48 42.15 3.85
1791 7214 4.018409 GGGTTGCATCCCCAAGAC 57.982 61.111 20.72 0.00 42.15 3.01
1815 7818 2.292569 CAGTGACAACAAGCAAGCTGAT 59.707 45.455 0.00 0.00 0.00 2.90
1822 7825 2.813754 GGATAAGCAGTGACAACAAGCA 59.186 45.455 0.00 0.00 33.63 3.91
1831 7834 3.771479 ACTGTGATCAGGATAAGCAGTGA 59.229 43.478 10.97 0.00 45.14 3.41
1835 7838 3.706086 TGCTACTGTGATCAGGATAAGCA 59.294 43.478 12.97 12.97 45.14 3.91
1839 7842 5.876651 ACAATGCTACTGTGATCAGGATA 57.123 39.130 0.00 0.00 45.14 2.59
1848 7851 0.874390 ACGCCAACAATGCTACTGTG 59.126 50.000 0.00 0.00 0.00 3.66
1850 7853 1.967762 CAACGCCAACAATGCTACTG 58.032 50.000 0.00 0.00 0.00 2.74
1864 7867 2.639751 GATTTATCCATCACGCAACGC 58.360 47.619 0.00 0.00 0.00 4.84
1865 7868 2.891391 CGATTTATCCATCACGCAACG 58.109 47.619 0.00 0.00 0.00 4.10
1871 7874 5.581605 ACACATTTGCGATTTATCCATCAC 58.418 37.500 0.00 0.00 0.00 3.06
1874 7877 8.023128 GCTATAACACATTTGCGATTTATCCAT 58.977 33.333 0.00 0.00 0.00 3.41
1908 7911 9.775854 CTTGATTCTGTCTAACCATAGATTCAT 57.224 33.333 0.00 0.00 40.21 2.57
1941 7944 7.187824 AGATTAGAAAGTAGCCAATCAGTGA 57.812 36.000 0.00 0.00 0.00 3.41
1955 7958 8.190888 AGCAAACTACAATCGAGATTAGAAAG 57.809 34.615 0.00 0.00 0.00 2.62
2014 8033 2.095110 GGCAATACCAAAACACGGTACC 60.095 50.000 0.16 0.16 41.73 3.34
2015 8034 2.095110 GGGCAATACCAAAACACGGTAC 60.095 50.000 0.00 0.00 41.73 3.34
2020 8040 5.914898 ATAAGAGGGCAATACCAAAACAC 57.085 39.130 0.00 0.00 42.05 3.32
2040 8060 8.961634 CAATCTTCCGGATACTTGAGAGATATA 58.038 37.037 4.15 0.00 33.71 0.86
2043 8063 5.600484 ACAATCTTCCGGATACTTGAGAGAT 59.400 40.000 20.78 13.99 33.71 2.75
2047 8067 5.178797 ACAACAATCTTCCGGATACTTGAG 58.821 41.667 20.78 15.82 33.71 3.02
2048 8068 5.160607 ACAACAATCTTCCGGATACTTGA 57.839 39.130 20.78 9.68 33.71 3.02
2049 8069 5.880054 AACAACAATCTTCCGGATACTTG 57.120 39.130 4.15 11.68 33.71 3.16
2050 8070 6.238648 AGAAACAACAATCTTCCGGATACTT 58.761 36.000 4.15 0.00 33.71 2.24
2051 8071 5.805728 AGAAACAACAATCTTCCGGATACT 58.194 37.500 4.15 0.00 33.71 2.12
2052 8072 6.496338 AAGAAACAACAATCTTCCGGATAC 57.504 37.500 4.15 0.00 30.16 2.24
2053 8073 7.148306 GCTAAAGAAACAACAATCTTCCGGATA 60.148 37.037 4.15 0.00 34.90 2.59
2055 8075 5.048991 GCTAAAGAAACAACAATCTTCCGGA 60.049 40.000 0.00 0.00 34.90 5.14
2056 8076 5.154222 GCTAAAGAAACAACAATCTTCCGG 58.846 41.667 0.00 0.00 34.90 5.14
2057 8077 5.625311 GTGCTAAAGAAACAACAATCTTCCG 59.375 40.000 0.00 0.00 34.90 4.30
2058 8078 5.625311 CGTGCTAAAGAAACAACAATCTTCC 59.375 40.000 0.00 0.00 34.90 3.46
2059 8079 5.625311 CCGTGCTAAAGAAACAACAATCTTC 59.375 40.000 0.00 0.00 34.90 2.87
2060 8080 5.519722 CCGTGCTAAAGAAACAACAATCTT 58.480 37.500 0.00 0.00 37.49 2.40
2061 8081 4.556699 GCCGTGCTAAAGAAACAACAATCT 60.557 41.667 0.00 0.00 0.00 2.40
2062 8082 3.668656 GCCGTGCTAAAGAAACAACAATC 59.331 43.478 0.00 0.00 0.00 2.67
2063 8083 3.317993 AGCCGTGCTAAAGAAACAACAAT 59.682 39.130 0.00 0.00 36.99 2.71
2064 8084 2.685897 AGCCGTGCTAAAGAAACAACAA 59.314 40.909 0.00 0.00 36.99 2.83
2066 8086 2.032924 ACAGCCGTGCTAAAGAAACAAC 59.967 45.455 0.00 0.00 36.40 3.32
2068 8088 1.601903 CACAGCCGTGCTAAAGAAACA 59.398 47.619 0.00 0.00 36.40 2.83
2069 8089 2.316119 CACAGCCGTGCTAAAGAAAC 57.684 50.000 0.00 0.00 36.40 2.78
2085 8105 0.611062 AGTCACCTACCTAGCGCACA 60.611 55.000 11.47 0.00 0.00 4.57
2089 8109 0.179108 GCCAAGTCACCTACCTAGCG 60.179 60.000 0.00 0.00 0.00 4.26
2093 8113 3.157087 CAAAATGCCAAGTCACCTACCT 58.843 45.455 0.00 0.00 0.00 3.08
2100 8120 1.755959 ACACAGCAAAATGCCAAGTCA 59.244 42.857 0.00 0.00 46.52 3.41
2109 8134 8.840321 GTGGAAGTATATCATACACAGCAAAAT 58.160 33.333 0.00 0.00 0.00 1.82
2119 8144 7.321153 AGCATAACCGTGGAAGTATATCATAC 58.679 38.462 0.00 0.00 0.00 2.39
2120 8145 7.476540 AGCATAACCGTGGAAGTATATCATA 57.523 36.000 0.00 0.00 0.00 2.15
2131 8156 3.189702 GCAAACTTAAGCATAACCGTGGA 59.810 43.478 1.29 0.00 0.00 4.02
2135 8160 6.586082 AGAAATTGCAAACTTAAGCATAACCG 59.414 34.615 1.71 0.00 40.94 4.44
2141 8166 6.511416 TGCTAAGAAATTGCAAACTTAAGCA 58.489 32.000 23.35 23.35 36.83 3.91
2142 8167 7.329226 TGATGCTAAGAAATTGCAAACTTAAGC 59.671 33.333 1.71 16.48 42.93 3.09
2143 8168 8.746922 TGATGCTAAGAAATTGCAAACTTAAG 57.253 30.769 1.71 0.00 42.93 1.85
2144 8169 7.329226 GCTGATGCTAAGAAATTGCAAACTTAA 59.671 33.333 1.71 1.47 42.93 1.85
2145 8170 6.808212 GCTGATGCTAAGAAATTGCAAACTTA 59.192 34.615 1.71 12.53 42.93 2.24
2190 8219 5.416947 AGGTGAACTCAACCAATACGTATC 58.583 41.667 8.86 0.00 32.98 2.24
2191 8220 5.416271 AGGTGAACTCAACCAATACGTAT 57.584 39.130 1.14 1.14 32.98 3.06
2192 8221 4.877378 AGGTGAACTCAACCAATACGTA 57.123 40.909 0.00 0.00 32.98 3.57
2194 8223 4.992319 TGTAAGGTGAACTCAACCAATACG 59.008 41.667 0.00 0.00 32.98 3.06
2197 8226 4.821805 CACTGTAAGGTGAACTCAACCAAT 59.178 41.667 0.00 0.00 39.30 3.16
2199 8228 3.199071 ACACTGTAAGGTGAACTCAACCA 59.801 43.478 1.52 0.00 39.30 3.67
2200 8229 3.805207 ACACTGTAAGGTGAACTCAACC 58.195 45.455 1.52 0.00 39.30 3.77
2224 8255 9.202273 GTTCTATTCAGATAGCTTAATCACCAG 57.798 37.037 0.00 0.00 36.09 4.00
2240 8271 1.482593 AGGGCCTCGTGTTCTATTCAG 59.517 52.381 0.00 0.00 0.00 3.02
2251 8282 1.122019 ACAGAACTGAAGGGCCTCGT 61.122 55.000 6.46 1.22 0.00 4.18
2268 8299 4.023980 TGGGGTGTCAAAAACATAACACA 58.976 39.130 6.79 0.00 42.92 3.72
2274 8305 2.758130 ACCTTGGGGTGTCAAAAACAT 58.242 42.857 0.00 0.00 45.43 2.71
2275 8306 2.239681 ACCTTGGGGTGTCAAAAACA 57.760 45.000 0.00 0.00 45.43 2.83
2276 8307 3.620427 AAACCTTGGGGTGTCAAAAAC 57.380 42.857 0.00 0.00 46.67 2.43
2277 8308 5.189934 ACATAAAACCTTGGGGTGTCAAAAA 59.810 36.000 0.00 0.00 46.67 1.94
2278 8309 4.717280 ACATAAAACCTTGGGGTGTCAAAA 59.283 37.500 0.00 0.00 46.67 2.44
2279 8310 4.100189 CACATAAAACCTTGGGGTGTCAAA 59.900 41.667 0.00 0.00 46.67 2.69
2280 8311 3.639094 CACATAAAACCTTGGGGTGTCAA 59.361 43.478 0.00 0.00 46.67 3.18
2281 8312 3.226777 CACATAAAACCTTGGGGTGTCA 58.773 45.455 0.00 0.00 46.67 3.58
2282 8313 2.029380 GCACATAAAACCTTGGGGTGTC 60.029 50.000 0.00 0.00 46.67 3.67
2283 8314 1.967779 GCACATAAAACCTTGGGGTGT 59.032 47.619 0.00 0.00 46.67 4.16
2284 8315 1.967066 TGCACATAAAACCTTGGGGTG 59.033 47.619 0.00 0.00 46.67 4.61
2286 8317 1.067915 CGTGCACATAAAACCTTGGGG 60.068 52.381 18.64 0.00 38.88 4.96
2287 8318 1.883275 TCGTGCACATAAAACCTTGGG 59.117 47.619 18.64 0.00 0.00 4.12
2288 8319 2.811431 TCTCGTGCACATAAAACCTTGG 59.189 45.455 18.64 0.00 0.00 3.61
2289 8320 3.120199 CCTCTCGTGCACATAAAACCTTG 60.120 47.826 18.64 0.00 0.00 3.61
2290 8321 3.074412 CCTCTCGTGCACATAAAACCTT 58.926 45.455 18.64 0.00 0.00 3.50
2291 8322 2.038557 ACCTCTCGTGCACATAAAACCT 59.961 45.455 18.64 0.00 0.00 3.50
2292 8323 2.423577 ACCTCTCGTGCACATAAAACC 58.576 47.619 18.64 0.00 0.00 3.27
2293 8324 5.600908 TTTACCTCTCGTGCACATAAAAC 57.399 39.130 18.64 0.00 0.00 2.43
2294 8325 7.466725 GCATATTTACCTCTCGTGCACATAAAA 60.467 37.037 18.64 7.22 0.00 1.52
2295 8326 6.018262 GCATATTTACCTCTCGTGCACATAAA 60.018 38.462 18.64 10.85 0.00 1.40
2296 8327 5.465390 GCATATTTACCTCTCGTGCACATAA 59.535 40.000 18.64 0.12 0.00 1.90
2297 8328 4.988540 GCATATTTACCTCTCGTGCACATA 59.011 41.667 18.64 2.91 0.00 2.29
2298 8329 3.809832 GCATATTTACCTCTCGTGCACAT 59.190 43.478 18.64 1.56 0.00 3.21
2299 8330 3.194861 GCATATTTACCTCTCGTGCACA 58.805 45.455 18.64 3.15 0.00 4.57
2300 8331 3.861569 GCATATTTACCTCTCGTGCAC 57.138 47.619 6.82 6.82 0.00 4.57


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

AutoCloner maintained by Alex Coulton.