Multiple sequence alignment - TraesCS5D01G170600

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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 TraesCS5D01G170600 chr5D 100.000 5807 0 0 1 5807 267613538 267619344 0.000000e+00 10724
1 TraesCS5D01G170600 chr5D 85.393 267 33 5 3900 4163 7970985 7970722 7.410000e-69 272
2 TraesCS5D01G170600 chr5A 94.971 4355 150 30 2 4330 354960178 354964489 0.000000e+00 6765
3 TraesCS5D01G170600 chr5A 92.818 724 28 10 4409 5120 354964531 354965242 0.000000e+00 1027
4 TraesCS5D01G170600 chr5A 91.388 209 13 2 5117 5320 354967420 354967628 1.230000e-71 281
5 TraesCS5D01G170600 chr5B 93.884 3679 128 38 702 4331 302060468 302064098 0.000000e+00 5457
6 TraesCS5D01G170600 chr5B 90.529 1362 84 13 4395 5730 302064119 302065461 0.000000e+00 1759
7 TraesCS5D01G170600 chr4D 87.984 258 26 3 3899 4156 294346215 294346467 3.400000e-77 300
8 TraesCS5D01G170600 chr4D 86.381 257 30 4 3904 4159 65537974 65537722 5.730000e-70 276
9 TraesCS5D01G170600 chr3D 86.466 266 34 2 3899 4162 178651811 178652076 2.050000e-74 291
10 TraesCS5D01G170600 chr3B 86.090 266 35 2 3899 4162 257098941 257099206 9.520000e-73 285
11 TraesCS5D01G170600 chr6D 85.057 261 38 1 3899 4159 123124111 123123852 1.240000e-66 265
12 TraesCS5D01G170600 chr6B 85.057 261 36 3 3900 4159 217113249 217112991 4.460000e-66 263


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 TraesCS5D01G170600 chr5D 267613538 267619344 5806 False 10724 10724 100.0000 1 5807 1 chr5D.!!$F1 5806
1 TraesCS5D01G170600 chr5A 354960178 354967628 7450 False 2691 6765 93.0590 2 5320 3 chr5A.!!$F1 5318
2 TraesCS5D01G170600 chr5B 302060468 302065461 4993 False 3608 5457 92.2065 702 5730 2 chr5B.!!$F1 5028

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
521 523 0.032813 CTGGATCTGCCCAAACCCAT 60.033 55.000 0.00 0.00 35.47 4.00 F
690 693 0.536460 GGCCCTTCTTCAACGTTGGA 60.536 55.000 27.02 18.98 0.00 3.53 F
1408 1434 4.329545 TGCCCTCCTCACCAACGC 62.330 66.667 0.00 0.00 0.00 4.84 F
1730 1757 0.965439 TGCCTTGTCGAATTTTGGGG 59.035 50.000 0.00 0.00 0.00 4.96 F
1731 1758 1.253100 GCCTTGTCGAATTTTGGGGA 58.747 50.000 0.00 0.00 0.00 4.81 F
1732 1759 1.616374 GCCTTGTCGAATTTTGGGGAA 59.384 47.619 0.00 0.00 0.00 3.97 F
3377 3417 2.350522 CAGCTGCAGGTACCTTTACAG 58.649 52.381 19.71 23.37 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1408 1434 1.577328 AAAGTTGCCGTGCCGATCTG 61.577 55.000 0.0 0.0 0.00 2.90 R
1729 1756 2.021457 CCAATATGGTTCGGTGGTTCC 58.979 52.381 0.0 0.0 31.35 3.62 R
2387 2421 4.224991 TGTTACCCAGCATAAGTTACCC 57.775 45.455 0.0 0.0 0.00 3.69 R
3682 3722 2.029918 TGTCCTCTCATCAATATCGGCG 60.030 50.000 0.0 0.0 0.00 6.46 R
3753 3793 7.977789 TGTCAGTTCATAAAGTTTCTGCATA 57.022 32.000 0.0 0.0 0.00 3.14 R
3790 3830 8.428063 TCAGTCCCAAAACAATTAACATCAAAT 58.572 29.630 0.0 0.0 0.00 2.32 R
5303 7565 0.540830 TGGTGCCCATAACAACCACC 60.541 55.000 0.0 0.0 44.71 4.61 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
52 53 1.960689 TGACGAGGAAGACATCACACA 59.039 47.619 0.00 0.00 0.00 3.72
54 55 2.926200 GACGAGGAAGACATCACACATG 59.074 50.000 0.00 0.00 0.00 3.21
58 59 4.033702 CGAGGAAGACATCACACATGATTG 59.966 45.833 0.00 0.00 43.40 2.67
82 83 2.080693 CACCGCCTACATGCTTAACAA 58.919 47.619 0.00 0.00 0.00 2.83
87 88 4.165779 CGCCTACATGCTTAACAAAAAGG 58.834 43.478 0.00 0.00 0.00 3.11
88 89 4.083003 CGCCTACATGCTTAACAAAAAGGA 60.083 41.667 0.00 0.00 0.00 3.36
171 172 5.122519 TGCAAAGCCACTAAATCGATATGA 58.877 37.500 0.00 0.00 0.00 2.15
175 176 2.993899 GCCACTAAATCGATATGACCGG 59.006 50.000 0.00 0.00 0.00 5.28
182 183 7.645735 CACTAAATCGATATGACCGGATAGATG 59.354 40.741 9.46 0.00 0.00 2.90
185 186 3.628032 TCGATATGACCGGATAGATGCTC 59.372 47.826 9.46 0.00 0.00 4.26
239 240 5.739752 TCACACACACATTTCTTTCTCAG 57.260 39.130 0.00 0.00 0.00 3.35
273 274 6.382869 AGCATAAATAATGGTCTTGCTCAC 57.617 37.500 0.00 0.00 42.70 3.51
280 281 3.895232 ATGGTCTTGCTCACGTATTCT 57.105 42.857 0.00 0.00 0.00 2.40
319 320 5.997746 TCTCTACTTGTGAAACTTCAATGGG 59.002 40.000 0.00 0.00 39.21 4.00
323 324 5.200483 ACTTGTGAAACTTCAATGGGAGAA 58.800 37.500 0.00 0.00 39.21 2.87
368 369 8.353684 ACTCTAGTCATTAATCTGGTTGTATCG 58.646 37.037 0.00 0.00 0.00 2.92
369 370 7.145985 TCTAGTCATTAATCTGGTTGTATCGC 58.854 38.462 0.00 0.00 0.00 4.58
370 371 5.918608 AGTCATTAATCTGGTTGTATCGCT 58.081 37.500 0.00 0.00 0.00 4.93
373 374 7.438459 AGTCATTAATCTGGTTGTATCGCTAAC 59.562 37.037 0.00 0.00 0.00 2.34
394 395 6.920695 AACCCCTTACCCTAATTTCTACAT 57.079 37.500 0.00 0.00 0.00 2.29
399 400 8.004801 CCCCTTACCCTAATTTCTACATTGAAT 58.995 37.037 0.00 0.00 0.00 2.57
426 427 1.137825 CCTCCGCTGAAGAGACGTC 59.862 63.158 7.70 7.70 32.86 4.34
441 442 4.332268 AGAGACGTCGTAACCTCTAATCAC 59.668 45.833 10.46 0.00 34.54 3.06
450 451 7.485913 GTCGTAACCTCTAATCACGAACATTAA 59.514 37.037 0.00 0.00 42.57 1.40
466 468 7.170828 ACGAACATTAATTTTTGCCTCCTTTTC 59.829 33.333 2.08 0.00 0.00 2.29
497 499 0.460311 CTCCTCTCCGCGTATTTGGT 59.540 55.000 4.92 0.00 0.00 3.67
501 503 2.035449 CCTCTCCGCGTATTTGGTATCA 59.965 50.000 4.92 0.00 0.00 2.15
520 522 1.383799 CTGGATCTGCCCAAACCCA 59.616 57.895 0.00 0.00 35.47 4.51
521 523 0.032813 CTGGATCTGCCCAAACCCAT 60.033 55.000 0.00 0.00 35.47 4.00
531 534 7.775053 TCTGCCCAAACCCATATTTATTATC 57.225 36.000 0.00 0.00 0.00 1.75
532 535 7.301420 TCTGCCCAAACCCATATTTATTATCA 58.699 34.615 0.00 0.00 0.00 2.15
537 540 7.728083 CCCAAACCCATATTTATTATCACCTCA 59.272 37.037 0.00 0.00 0.00 3.86
588 591 3.989167 TCGACGATTAAACAATCAACCGT 59.011 39.130 0.00 0.00 0.00 4.83
591 594 5.724859 CGACGATTAAACAATCAACCGTAAC 59.275 40.000 0.00 0.00 0.00 2.50
592 595 6.400303 CGACGATTAAACAATCAACCGTAACT 60.400 38.462 0.00 0.00 0.00 2.24
608 611 7.209471 ACCGTAACTTATGAAATTTTCAGCA 57.791 32.000 16.34 5.29 43.98 4.41
647 650 8.963725 AGCAAATCTGAAATGATAATCTGTTGA 58.036 29.630 0.00 0.00 0.00 3.18
660 663 7.390440 TGATAATCTGTTGAATCTTCGGTGTTT 59.610 33.333 0.00 0.00 0.00 2.83
662 665 5.168526 TCTGTTGAATCTTCGGTGTTTTG 57.831 39.130 0.00 0.00 0.00 2.44
674 677 1.067060 GGTGTTTTGTGTCTCTTGGCC 59.933 52.381 0.00 0.00 0.00 5.36
682 685 1.072331 GTGTCTCTTGGCCCTTCTTCA 59.928 52.381 0.00 0.00 0.00 3.02
688 691 1.001378 CTTGGCCCTTCTTCAACGTTG 60.001 52.381 22.35 22.35 0.00 4.10
690 693 0.536460 GGCCCTTCTTCAACGTTGGA 60.536 55.000 27.02 18.98 0.00 3.53
716 719 5.705905 ACCTTCCAAATTTACAGCTCTGTAC 59.294 40.000 9.09 0.00 44.81 2.90
944 956 4.787280 CCGGTCCTCCTCCTGCCT 62.787 72.222 0.00 0.00 0.00 4.75
960 972 4.856607 CTCGGACCGGAAGCGCTC 62.857 72.222 12.06 4.06 0.00 5.03
1408 1434 4.329545 TGCCCTCCTCACCAACGC 62.330 66.667 0.00 0.00 0.00 4.84
1707 1734 5.790593 TCCGGTCTATTCTATTGGCATAAC 58.209 41.667 0.00 0.00 0.00 1.89
1729 1756 4.082245 ACTTATGCCTTGTCGAATTTTGGG 60.082 41.667 0.00 0.00 0.00 4.12
1730 1757 0.965439 TGCCTTGTCGAATTTTGGGG 59.035 50.000 0.00 0.00 0.00 4.96
1731 1758 1.253100 GCCTTGTCGAATTTTGGGGA 58.747 50.000 0.00 0.00 0.00 4.81
1732 1759 1.616374 GCCTTGTCGAATTTTGGGGAA 59.384 47.619 0.00 0.00 0.00 3.97
1733 1760 2.609491 GCCTTGTCGAATTTTGGGGAAC 60.609 50.000 0.00 0.00 0.00 3.62
1767 1794 7.492344 CCATATTGGAAAGTGCATTTTAAGACC 59.508 37.037 7.22 5.30 40.96 3.85
1921 1950 8.508800 ACTGCTTTCTAAGATTTACGATATCG 57.491 34.615 23.18 23.18 46.33 2.92
2049 2081 7.708322 TGACTCTTCATCTTTTAAGGATCATCG 59.292 37.037 0.00 0.00 0.00 3.84
2076 2108 4.707448 TCTGGTTGTTGTATTGTGTTTGGT 59.293 37.500 0.00 0.00 0.00 3.67
2153 2185 3.795688 TTCTTTTCAGCTGATGGGACT 57.204 42.857 19.04 0.00 0.00 3.85
2172 2204 6.323739 TGGGACTTATGCTTTGAAGAAAGTTT 59.676 34.615 0.00 0.00 40.77 2.66
2317 2350 6.349300 GGATACAAATAGATATCATGCCCGT 58.651 40.000 5.32 0.00 30.64 5.28
2377 2410 8.103305 TCTTCCAGCTCAGTGATATTTACTTTT 58.897 33.333 0.00 0.00 0.00 2.27
2378 2411 8.635765 TTCCAGCTCAGTGATATTTACTTTTT 57.364 30.769 0.00 0.00 0.00 1.94
2496 2533 9.880157 ACAATACGGTAATTTAAGTATCTGTGT 57.120 29.630 0.00 5.49 0.00 3.72
2635 2672 6.423776 AAATCCATGCAAGAAAAGAAGGAA 57.576 33.333 0.00 0.00 0.00 3.36
2754 2793 4.672899 ACAACTACAATAGGGGTGCAATT 58.327 39.130 0.00 0.00 0.00 2.32
2761 2800 5.083821 ACAATAGGGGTGCAATTGTAGTTT 58.916 37.500 11.13 0.00 40.95 2.66
2816 2855 5.409826 CCGAAATGGCTCATAATCTTCTACC 59.590 44.000 0.00 0.00 0.00 3.18
2820 2859 5.975988 TGGCTCATAATCTTCTACCCTTT 57.024 39.130 0.00 0.00 0.00 3.11
2821 2860 7.633018 ATGGCTCATAATCTTCTACCCTTTA 57.367 36.000 0.00 0.00 0.00 1.85
2824 2863 8.502738 TGGCTCATAATCTTCTACCCTTTATTT 58.497 33.333 0.00 0.00 0.00 1.40
2825 2864 9.355916 GGCTCATAATCTTCTACCCTTTATTTT 57.644 33.333 0.00 0.00 0.00 1.82
3062 3102 7.039504 AGGTTGATCTGTGATGTTAGCAAAATT 60.040 33.333 0.00 0.00 0.00 1.82
3088 3128 8.020819 TGATTTACTTATGCTTGTAACAACTGC 58.979 33.333 0.00 0.00 0.00 4.40
3111 3151 6.185511 GCAAGTTATACTCTTTTACCCCCTT 58.814 40.000 0.00 0.00 0.00 3.95
3112 3152 6.318144 GCAAGTTATACTCTTTTACCCCCTTC 59.682 42.308 0.00 0.00 0.00 3.46
3113 3153 7.631007 CAAGTTATACTCTTTTACCCCCTTCT 58.369 38.462 0.00 0.00 0.00 2.85
3377 3417 2.350522 CAGCTGCAGGTACCTTTACAG 58.649 52.381 19.71 23.37 0.00 2.74
3531 3571 8.306038 CAACAAGTATGAGAAATCATTTGGGAA 58.694 33.333 0.00 0.00 0.00 3.97
3605 3645 6.239036 GGACTTCTTACTTTGACTGGCAATTT 60.239 38.462 0.00 0.00 36.15 1.82
3753 3793 9.553064 CCTTTATGCTATGATGTAAGTTCTCTT 57.447 33.333 0.00 0.00 37.65 2.85
3887 3927 8.243289 ACTTCATTTATGTTGTTTGCAATAGC 57.757 30.769 0.00 0.00 42.57 2.97
3945 3985 7.844493 TGAAGTTCTAGGTTTGTCCTAAGTA 57.156 36.000 4.17 0.00 46.81 2.24
4136 4200 1.202770 AGGACAAACCCGGAACTTCAG 60.203 52.381 0.73 0.00 40.05 3.02
4146 4210 3.824443 CCCGGAACTTCAGTTATTTTGGT 59.176 43.478 0.73 0.00 38.56 3.67
4214 4278 5.128171 AGTTACGTAGAAATCCTGCCATGTA 59.872 40.000 0.00 0.00 0.00 2.29
4320 4384 3.684788 GTCGCAACATCATAGACCTGTTT 59.315 43.478 0.00 0.00 30.99 2.83
4326 4390 6.498304 CAACATCATAGACCTGTTTTATGCC 58.502 40.000 0.00 0.00 30.99 4.40
4331 4395 6.582636 TCATAGACCTGTTTTATGCCAGTAG 58.417 40.000 0.00 0.00 0.00 2.57
4332 4396 3.610911 AGACCTGTTTTATGCCAGTAGC 58.389 45.455 0.00 0.00 44.14 3.58
4333 4397 2.683362 GACCTGTTTTATGCCAGTAGCC 59.317 50.000 0.00 0.00 42.71 3.93
4334 4398 2.308866 ACCTGTTTTATGCCAGTAGCCT 59.691 45.455 0.00 0.00 42.71 4.58
4335 4399 2.684881 CCTGTTTTATGCCAGTAGCCTG 59.315 50.000 0.00 0.00 42.71 4.85
4336 4400 3.347216 CTGTTTTATGCCAGTAGCCTGT 58.653 45.455 0.00 0.00 42.71 4.00
4337 4401 3.758554 CTGTTTTATGCCAGTAGCCTGTT 59.241 43.478 0.00 0.00 42.71 3.16
4338 4402 4.148838 TGTTTTATGCCAGTAGCCTGTTT 58.851 39.130 0.00 0.00 42.71 2.83
4339 4403 4.217550 TGTTTTATGCCAGTAGCCTGTTTC 59.782 41.667 0.00 0.00 42.71 2.78
4340 4404 4.301072 TTTATGCCAGTAGCCTGTTTCT 57.699 40.909 0.00 0.00 42.71 2.52
4341 4405 5.429681 TTTATGCCAGTAGCCTGTTTCTA 57.570 39.130 0.00 0.00 42.71 2.10
4342 4406 5.630415 TTATGCCAGTAGCCTGTTTCTAT 57.370 39.130 0.00 0.00 42.71 1.98
4343 4407 6.740944 TTATGCCAGTAGCCTGTTTCTATA 57.259 37.500 0.00 0.00 42.71 1.31
4344 4408 5.832539 ATGCCAGTAGCCTGTTTCTATAT 57.167 39.130 0.00 0.00 42.71 0.86
4345 4409 5.630415 TGCCAGTAGCCTGTTTCTATATT 57.370 39.130 0.00 0.00 42.71 1.28
4346 4410 5.368145 TGCCAGTAGCCTGTTTCTATATTG 58.632 41.667 0.00 0.00 42.71 1.90
4347 4411 5.104527 TGCCAGTAGCCTGTTTCTATATTGT 60.105 40.000 0.00 0.00 42.71 2.71
4348 4412 6.099125 TGCCAGTAGCCTGTTTCTATATTGTA 59.901 38.462 0.00 0.00 42.71 2.41
4349 4413 6.990349 GCCAGTAGCCTGTTTCTATATTGTAA 59.010 38.462 0.00 0.00 36.95 2.41
4350 4414 7.171678 GCCAGTAGCCTGTTTCTATATTGTAAG 59.828 40.741 0.00 0.00 36.95 2.34
4351 4415 8.204836 CCAGTAGCCTGTTTCTATATTGTAAGT 58.795 37.037 0.00 0.00 36.95 2.24
4392 4456 8.738645 ATTACCTATTGTTTTCTGGATCTGTC 57.261 34.615 0.00 0.00 0.00 3.51
4393 4457 5.501156 ACCTATTGTTTTCTGGATCTGTCC 58.499 41.667 0.00 0.00 45.31 4.02
4401 4465 3.403624 GGATCTGTCCACTGGCCA 58.596 61.111 4.71 4.71 44.42 5.36
4402 4466 1.918253 GGATCTGTCCACTGGCCAT 59.082 57.895 5.51 0.00 44.42 4.40
4403 4467 0.179034 GGATCTGTCCACTGGCCATC 60.179 60.000 5.51 0.00 44.42 3.51
4404 4468 0.835941 GATCTGTCCACTGGCCATCT 59.164 55.000 5.51 0.00 0.00 2.90
4405 4469 1.211457 GATCTGTCCACTGGCCATCTT 59.789 52.381 5.51 0.00 0.00 2.40
4406 4470 1.951209 TCTGTCCACTGGCCATCTTA 58.049 50.000 5.51 0.00 0.00 2.10
4407 4471 2.481441 TCTGTCCACTGGCCATCTTAT 58.519 47.619 5.51 0.00 0.00 1.73
4473 4537 5.500234 TGGAACTGGATCAAGACAAATAGG 58.500 41.667 3.42 0.00 0.00 2.57
4544 4616 8.043710 AGTTTATAGATTCTGTAGTGCAAGCTT 58.956 33.333 0.00 0.00 0.00 3.74
4623 4695 0.829333 AGCTCGATGAATCTGCTGGT 59.171 50.000 6.80 0.00 34.61 4.00
4630 4702 1.538047 TGAATCTGCTGGTGAAAGCC 58.462 50.000 0.00 0.00 42.83 4.35
4886 4959 6.438259 AGAACATCTCTGCTTGATTCATTG 57.562 37.500 0.00 0.00 31.12 2.82
5024 5098 3.213206 TGTGCCAAAGTGAGATTCAGT 57.787 42.857 0.00 0.00 0.00 3.41
5032 5106 5.939883 CCAAAGTGAGATTCAGTGGTCAATA 59.060 40.000 0.00 0.00 28.97 1.90
5071 5145 1.672881 CATGGTTTCTCCTGATTCCGC 59.327 52.381 0.00 0.00 37.07 5.54
5080 5154 4.442706 TCTCCTGATTCCGCAAATCTTAC 58.557 43.478 9.49 0.00 43.61 2.34
5091 5167 3.367932 CGCAAATCTTACTTGAGCGAGAA 59.632 43.478 0.00 0.00 45.78 2.87
5110 5186 3.004629 AGAATTGCGCATGTTCTGTTGAA 59.995 39.130 27.59 5.25 31.41 2.69
5133 7390 5.901552 ACAACCTACACAACCATTTCAAAG 58.098 37.500 0.00 0.00 0.00 2.77
5277 7539 6.783892 TTGATTTGGATTTGCTAAACTTGC 57.216 33.333 0.00 0.00 29.24 4.01
5314 7576 6.237154 CAAATGGAAAATGGGTGGTTGTTAT 58.763 36.000 0.00 0.00 0.00 1.89
5355 7617 3.118542 GGTACAGAACGTCGAAAAGTGT 58.881 45.455 0.00 0.00 0.00 3.55
5366 7628 5.860716 ACGTCGAAAAGTGTAAATAGAGGAC 59.139 40.000 0.00 0.00 0.00 3.85
5368 7630 5.287992 GTCGAAAAGTGTAAATAGAGGACGG 59.712 44.000 0.00 0.00 0.00 4.79
5378 7640 1.944896 TAGAGGACGGGCTCCATGGA 61.945 60.000 15.27 15.27 42.46 3.41
5387 7649 3.882326 CTCCATGGAGCCCCGCAT 61.882 66.667 28.45 0.00 35.31 4.73
5394 7656 1.321805 TGGAGCCCCGCATTCAAATG 61.322 55.000 0.00 0.00 39.40 2.32
5503 7765 7.573968 ATGTGGCTTCCAAAGATAAGATAAC 57.426 36.000 0.00 0.00 34.18 1.89
5504 7766 6.480763 TGTGGCTTCCAAAGATAAGATAACA 58.519 36.000 0.00 0.00 34.18 2.41
5544 7806 2.276201 GATTATTTTTGTTGGGCCGGC 58.724 47.619 21.18 21.18 0.00 6.13
5555 7817 2.649129 GGGCCGGCATTTTGCTTCT 61.649 57.895 30.85 0.00 44.28 2.85
5556 7818 1.446618 GGCCGGCATTTTGCTTCTG 60.447 57.895 30.85 0.00 44.28 3.02
5576 7838 6.539649 TCTGTTGTGTAGCTTACAAATCAC 57.460 37.500 15.23 6.97 40.93 3.06
5610 7872 5.358298 ACAAAAGTTTACAGATCCGAAGC 57.642 39.130 0.00 0.00 0.00 3.86
5635 7897 8.765219 GCGAACATGTATAAGTCTTCACATAAT 58.235 33.333 0.00 5.22 30.66 1.28
5664 7926 8.934507 TTTCGAGTGTTTTTAAAACATGGAAT 57.065 26.923 23.37 9.77 32.23 3.01
5707 7969 3.487120 ACTTTGGCGTCTCCTAAAACT 57.513 42.857 0.00 0.00 35.26 2.66
5709 7971 4.204799 ACTTTGGCGTCTCCTAAAACTTT 58.795 39.130 0.00 0.00 35.26 2.66
5730 7992 9.840427 AACTTTGCACTTATACACATGAAATAC 57.160 29.630 0.00 0.00 0.00 1.89
5731 7993 9.231297 ACTTTGCACTTATACACATGAAATACT 57.769 29.630 0.00 0.00 0.00 2.12
5733 7995 9.838975 TTTGCACTTATACACATGAAATACTTG 57.161 29.630 0.00 0.00 0.00 3.16
5734 7996 8.560355 TGCACTTATACACATGAAATACTTGT 57.440 30.769 0.00 0.00 37.36 3.16
5735 7997 9.660180 TGCACTTATACACATGAAATACTTGTA 57.340 29.630 0.00 0.00 35.57 2.41
5742 8004 7.464830 ACACATGAAATACTTGTATCGTAGC 57.535 36.000 0.00 0.00 35.57 3.58
5743 8005 7.039270 ACACATGAAATACTTGTATCGTAGCA 58.961 34.615 0.00 0.00 35.57 3.49
5744 8006 7.547722 ACACATGAAATACTTGTATCGTAGCAA 59.452 33.333 0.00 0.00 35.57 3.91
5745 8007 8.058328 CACATGAAATACTTGTATCGTAGCAAG 58.942 37.037 0.00 11.72 45.33 4.01
5746 8008 6.583912 TGAAATACTTGTATCGTAGCAAGC 57.416 37.500 12.72 0.00 44.12 4.01
5747 8009 6.103330 TGAAATACTTGTATCGTAGCAAGCA 58.897 36.000 12.72 4.17 44.12 3.91
5748 8010 6.592220 TGAAATACTTGTATCGTAGCAAGCAA 59.408 34.615 12.72 5.28 44.12 3.91
5749 8011 6.589830 AATACTTGTATCGTAGCAAGCAAG 57.410 37.500 12.72 0.00 44.12 4.01
5750 8012 3.262420 ACTTGTATCGTAGCAAGCAAGG 58.738 45.455 12.72 0.00 44.12 3.61
5751 8013 2.309528 TGTATCGTAGCAAGCAAGGG 57.690 50.000 0.00 0.00 0.00 3.95
5752 8014 1.134521 TGTATCGTAGCAAGCAAGGGG 60.135 52.381 0.00 0.00 0.00 4.79
5753 8015 0.179056 TATCGTAGCAAGCAAGGGGC 60.179 55.000 0.00 0.00 45.30 5.80
5762 8024 3.840437 GCAAGGGGCGCATGAATA 58.160 55.556 10.83 0.00 0.00 1.75
5763 8025 1.656441 GCAAGGGGCGCATGAATAG 59.344 57.895 10.83 0.00 0.00 1.73
5764 8026 0.819259 GCAAGGGGCGCATGAATAGA 60.819 55.000 10.83 0.00 0.00 1.98
5765 8027 1.679139 CAAGGGGCGCATGAATAGAA 58.321 50.000 10.83 0.00 0.00 2.10
5766 8028 2.233271 CAAGGGGCGCATGAATAGAAT 58.767 47.619 10.83 0.00 0.00 2.40
5767 8029 2.624838 CAAGGGGCGCATGAATAGAATT 59.375 45.455 10.83 0.00 0.00 2.17
5768 8030 3.788227 AGGGGCGCATGAATAGAATTA 57.212 42.857 10.83 0.00 0.00 1.40
5769 8031 4.098914 AGGGGCGCATGAATAGAATTAA 57.901 40.909 10.83 0.00 0.00 1.40
5770 8032 4.469657 AGGGGCGCATGAATAGAATTAAA 58.530 39.130 10.83 0.00 0.00 1.52
5771 8033 5.079643 AGGGGCGCATGAATAGAATTAAAT 58.920 37.500 10.83 0.00 0.00 1.40
5772 8034 5.539955 AGGGGCGCATGAATAGAATTAAATT 59.460 36.000 10.83 0.00 0.00 1.82
5773 8035 5.863935 GGGGCGCATGAATAGAATTAAATTC 59.136 40.000 10.83 5.62 39.56 2.17
5774 8036 5.569059 GGGCGCATGAATAGAATTAAATTCG 59.431 40.000 10.83 0.00 43.92 3.34
5775 8037 6.370593 GGCGCATGAATAGAATTAAATTCGA 58.629 36.000 10.83 0.00 43.92 3.71
5776 8038 6.855914 GGCGCATGAATAGAATTAAATTCGAA 59.144 34.615 10.83 0.00 43.92 3.71
5777 8039 7.378461 GGCGCATGAATAGAATTAAATTCGAAA 59.622 33.333 10.83 0.00 43.92 3.46
5778 8040 8.742188 GCGCATGAATAGAATTAAATTCGAAAA 58.258 29.630 0.30 0.00 43.92 2.29
5792 8054 7.979444 AAATTCGAAAACATAGAGGAAGACA 57.021 32.000 0.00 0.00 0.00 3.41
5793 8055 8.567285 AAATTCGAAAACATAGAGGAAGACAT 57.433 30.769 0.00 0.00 0.00 3.06
5794 8056 9.667107 AAATTCGAAAACATAGAGGAAGACATA 57.333 29.630 0.00 0.00 0.00 2.29
5795 8057 8.649973 ATTCGAAAACATAGAGGAAGACATAC 57.350 34.615 0.00 0.00 0.00 2.39
5796 8058 7.165460 TCGAAAACATAGAGGAAGACATACA 57.835 36.000 0.00 0.00 0.00 2.29
5797 8059 7.608153 TCGAAAACATAGAGGAAGACATACAA 58.392 34.615 0.00 0.00 0.00 2.41
5798 8060 7.759886 TCGAAAACATAGAGGAAGACATACAAG 59.240 37.037 0.00 0.00 0.00 3.16
5799 8061 7.545965 CGAAAACATAGAGGAAGACATACAAGT 59.454 37.037 0.00 0.00 0.00 3.16
5800 8062 9.871238 GAAAACATAGAGGAAGACATACAAGTA 57.129 33.333 0.00 0.00 0.00 2.24
5801 8063 9.654663 AAAACATAGAGGAAGACATACAAGTAC 57.345 33.333 0.00 0.00 0.00 2.73
5802 8064 7.956328 ACATAGAGGAAGACATACAAGTACA 57.044 36.000 0.00 0.00 0.00 2.90
5803 8065 8.362464 ACATAGAGGAAGACATACAAGTACAA 57.638 34.615 0.00 0.00 0.00 2.41
5804 8066 8.251721 ACATAGAGGAAGACATACAAGTACAAC 58.748 37.037 0.00 0.00 0.00 3.32
5805 8067 5.710984 AGAGGAAGACATACAAGTACAACG 58.289 41.667 0.00 0.00 0.00 4.10
5806 8068 4.817517 AGGAAGACATACAAGTACAACGG 58.182 43.478 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.292101 CCTCGTCAAGGTATTCATCAACTTC 59.708 44.000 0.00 0.00 40.67 3.01
46 47 1.266446 CGGTGTTGCAATCATGTGTGA 59.734 47.619 0.59 0.00 39.04 3.58
52 53 1.094785 GTAGGCGGTGTTGCAATCAT 58.905 50.000 0.59 0.00 36.28 2.45
54 55 1.094785 ATGTAGGCGGTGTTGCAATC 58.905 50.000 0.59 0.00 36.28 2.67
58 59 1.586154 AAGCATGTAGGCGGTGTTGC 61.586 55.000 0.00 0.00 39.27 4.17
82 83 3.827722 TCCTTTCAACACCGATCCTTTT 58.172 40.909 0.00 0.00 0.00 2.27
87 88 8.378172 TCATATTATTCCTTTCAACACCGATC 57.622 34.615 0.00 0.00 0.00 3.69
88 89 8.924511 ATCATATTATTCCTTTCAACACCGAT 57.075 30.769 0.00 0.00 0.00 4.18
171 172 2.614259 AGAATGGAGCATCTATCCGGT 58.386 47.619 0.00 0.00 34.06 5.28
185 186 7.951121 TGCAAATTTGAATGTGCCAAGAATGG 61.951 38.462 22.31 0.00 46.75 3.16
298 299 5.997746 TCTCCCATTGAAGTTTCACAAGTAG 59.002 40.000 0.00 0.00 36.83 2.57
319 320 3.084039 TCCAAGTGCAATGACCATTCTC 58.916 45.455 2.43 0.00 0.00 2.87
323 324 4.080129 AGAGTATCCAAGTGCAATGACCAT 60.080 41.667 2.43 0.00 33.66 3.55
368 369 5.384145 AGAAATTAGGGTAAGGGGTTAGC 57.616 43.478 0.00 0.00 0.00 3.09
369 370 7.441903 TGTAGAAATTAGGGTAAGGGGTTAG 57.558 40.000 0.00 0.00 0.00 2.34
370 371 8.276477 CAATGTAGAAATTAGGGTAAGGGGTTA 58.724 37.037 0.00 0.00 0.00 2.85
373 374 6.906848 TCAATGTAGAAATTAGGGTAAGGGG 58.093 40.000 0.00 0.00 0.00 4.79
394 395 3.334583 GCGGAGGCTATATGGATTCAA 57.665 47.619 0.00 0.00 35.83 2.69
415 416 2.775890 AGAGGTTACGACGTCTCTTCA 58.224 47.619 14.70 0.00 45.23 3.02
426 427 7.745022 TTAATGTTCGTGATTAGAGGTTACG 57.255 36.000 0.00 0.00 36.20 3.18
441 442 7.420184 AAAAGGAGGCAAAAATTAATGTTCG 57.580 32.000 0.00 0.00 0.00 3.95
450 451 4.142049 TGACAACGAAAAGGAGGCAAAAAT 60.142 37.500 0.00 0.00 0.00 1.82
466 468 0.526524 GAGAGGAGCCGATGACAACG 60.527 60.000 0.00 0.00 0.00 4.10
497 499 2.092429 GGTTTGGGCAGATCCAGTGATA 60.092 50.000 0.00 0.00 38.17 2.15
501 503 1.384191 GGGTTTGGGCAGATCCAGT 59.616 57.895 0.00 0.00 38.17 4.00
520 522 6.590292 CGCCGAGTTGAGGTGATAATAAATAT 59.410 38.462 0.00 0.00 41.54 1.28
521 523 5.924254 CGCCGAGTTGAGGTGATAATAAATA 59.076 40.000 0.00 0.00 41.54 1.40
531 534 2.811317 GCTCGCCGAGTTGAGGTG 60.811 66.667 16.50 0.00 40.44 4.00
532 535 2.650116 ATGCTCGCCGAGTTGAGGT 61.650 57.895 16.50 0.00 32.78 3.85
537 540 0.108186 TGATTCATGCTCGCCGAGTT 60.108 50.000 16.50 0.63 31.39 3.01
591 594 9.801714 GTTTCATGTTGCTGAAAATTTCATAAG 57.198 29.630 9.02 0.00 44.38 1.73
592 595 9.545105 AGTTTCATGTTGCTGAAAATTTCATAA 57.455 25.926 9.02 5.33 44.38 1.90
647 650 4.451900 AGAGACACAAAACACCGAAGATT 58.548 39.130 0.00 0.00 0.00 2.40
660 663 1.140312 AGAAGGGCCAAGAGACACAA 58.860 50.000 6.18 0.00 0.00 3.33
662 665 1.072331 TGAAGAAGGGCCAAGAGACAC 59.928 52.381 6.18 0.00 0.00 3.67
674 677 2.949644 AGGTTTCCAACGTTGAAGAAGG 59.050 45.455 29.35 11.76 0.00 3.46
688 691 9.085797 ACAGAGCTGTAAATTTGGAAGGTTTCC 62.086 40.741 0.41 0.86 45.47 3.13
690 693 5.598417 ACAGAGCTGTAAATTTGGAAGGTTT 59.402 36.000 0.41 0.00 42.90 3.27
1408 1434 1.577328 AAAGTTGCCGTGCCGATCTG 61.577 55.000 0.00 0.00 0.00 2.90
1602 1628 5.814705 GTCTCTCCGAATCAAGATCATTTGT 59.185 40.000 0.00 0.00 0.00 2.83
1668 1694 6.345096 AGACCGGATCAACAATTGAAAATT 57.655 33.333 13.59 0.00 43.95 1.82
1707 1734 4.423732 CCCAAAATTCGACAAGGCATAAG 58.576 43.478 0.00 0.00 0.00 1.73
1729 1756 2.021457 CCAATATGGTTCGGTGGTTCC 58.979 52.381 0.00 0.00 31.35 3.62
1730 1757 2.993937 TCCAATATGGTTCGGTGGTTC 58.006 47.619 0.00 0.00 39.03 3.62
1731 1758 3.443145 TTCCAATATGGTTCGGTGGTT 57.557 42.857 0.00 0.00 39.03 3.67
1732 1759 3.245122 ACTTTCCAATATGGTTCGGTGGT 60.245 43.478 0.00 0.00 39.03 4.16
1733 1760 3.128589 CACTTTCCAATATGGTTCGGTGG 59.871 47.826 0.00 0.00 39.03 4.61
1734 1761 3.427503 GCACTTTCCAATATGGTTCGGTG 60.428 47.826 0.00 3.96 39.03 4.94
1735 1762 2.752903 GCACTTTCCAATATGGTTCGGT 59.247 45.455 0.00 0.00 39.03 4.69
1736 1763 2.752354 TGCACTTTCCAATATGGTTCGG 59.248 45.455 0.00 0.00 39.03 4.30
1737 1764 4.637483 ATGCACTTTCCAATATGGTTCG 57.363 40.909 0.00 0.00 39.03 3.95
2049 2081 3.315191 ACACAATACAACAACCAGAGCAC 59.685 43.478 0.00 0.00 0.00 4.40
2172 2204 4.002906 AGTGTTGGTCGCTCTGAATAAA 57.997 40.909 0.00 0.00 30.20 1.40
2377 2410 7.558444 CCCAGCATAAGTTACCCAATACTTAAA 59.442 37.037 0.00 0.00 39.51 1.52
2378 2411 7.057894 CCCAGCATAAGTTACCCAATACTTAA 58.942 38.462 0.00 0.00 39.51 1.85
2379 2412 6.159046 ACCCAGCATAAGTTACCCAATACTTA 59.841 38.462 0.00 0.00 40.14 2.24
2382 2416 4.788679 ACCCAGCATAAGTTACCCAATAC 58.211 43.478 0.00 0.00 0.00 1.89
2387 2421 4.224991 TGTTACCCAGCATAAGTTACCC 57.775 45.455 0.00 0.00 0.00 3.69
2635 2672 6.378280 GGAGAATGGTGATTGTTGAAAGGTAT 59.622 38.462 0.00 0.00 0.00 2.73
2754 2793 5.870706 TCCAACATGGTATGTCAAACTACA 58.129 37.500 0.00 0.00 44.07 2.74
2761 2800 6.376864 CCTAATTGTTCCAACATGGTATGTCA 59.623 38.462 0.00 0.00 44.07 3.58
2901 2940 8.234136 ACAATGCATGATCAAGAACAAGATAT 57.766 30.769 0.00 0.00 0.00 1.63
2921 2961 9.865321 ATCAAGGAAGATCAAACAAATACAATG 57.135 29.630 0.00 0.00 0.00 2.82
3062 3102 8.020819 GCAGTTGTTACAAGCATAAGTAAATCA 58.979 33.333 0.00 0.00 32.55 2.57
3088 3128 7.631007 AGAAGGGGGTAAAAGAGTATAACTTG 58.369 38.462 0.00 0.00 0.00 3.16
3131 3171 4.640771 ACAGGCTAATCCTCACAGAAAA 57.359 40.909 0.00 0.00 45.52 2.29
3412 3452 6.142817 CACTGGCTCAACAAACTGTTAATAC 58.857 40.000 0.00 0.00 38.77 1.89
3605 3645 7.811282 TCTGAAGCCCATTCCTACATTAAATA 58.189 34.615 0.00 0.00 37.08 1.40
3682 3722 2.029918 TGTCCTCTCATCAATATCGGCG 60.030 50.000 0.00 0.00 0.00 6.46
3753 3793 7.977789 TGTCAGTTCATAAAGTTTCTGCATA 57.022 32.000 0.00 0.00 0.00 3.14
3790 3830 8.428063 TCAGTCCCAAAACAATTAACATCAAAT 58.572 29.630 0.00 0.00 0.00 2.32
3960 4000 6.818644 GTGCATCTTTCTATAGAGTTGGTCAA 59.181 38.462 2.02 0.00 0.00 3.18
4016 4077 8.340443 TGAGATTCTTCATGAAATATGCTTTCG 58.660 33.333 9.88 0.00 38.29 3.46
4093 4154 9.810545 TCCTAAGTCAAATTTGTTTAAGTTTGG 57.189 29.630 17.47 15.49 41.28 3.28
4136 4200 8.722480 AATTACTACCTCCGTACCAAAATAAC 57.278 34.615 0.00 0.00 0.00 1.89
4146 4210 6.528537 TGCTGTTTAATTACTACCTCCGTA 57.471 37.500 0.00 0.00 0.00 4.02
4186 4250 5.128171 TGGCAGGATTTCTACGTAACTACAT 59.872 40.000 0.00 0.00 0.00 2.29
4309 4373 5.368989 GCTACTGGCATAAAACAGGTCTAT 58.631 41.667 0.00 0.00 41.35 1.98
4331 4395 7.217906 AGCCTACTTACAATATAGAAACAGGC 58.782 38.462 0.00 0.00 43.13 4.85
4332 4396 9.046296 CAAGCCTACTTACAATATAGAAACAGG 57.954 37.037 0.00 0.00 33.74 4.00
4333 4397 9.601217 ACAAGCCTACTTACAATATAGAAACAG 57.399 33.333 0.00 0.00 33.74 3.16
4368 4432 7.110155 GGACAGATCCAGAAAACAATAGGTAA 58.890 38.462 0.00 0.00 45.47 2.85
4370 4434 5.501156 GGACAGATCCAGAAAACAATAGGT 58.499 41.667 0.00 0.00 45.47 3.08
4384 4448 3.403624 TGGCCAGTGGACAGATCC 58.596 61.111 15.83 3.63 46.48 3.36
4390 4454 1.678101 GCAATAAGATGGCCAGTGGAC 59.322 52.381 15.20 12.00 0.00 4.02
4391 4455 1.284491 TGCAATAAGATGGCCAGTGGA 59.716 47.619 15.20 0.31 0.00 4.02
4392 4456 1.679680 CTGCAATAAGATGGCCAGTGG 59.320 52.381 13.05 4.20 0.00 4.00
4393 4457 2.646930 TCTGCAATAAGATGGCCAGTG 58.353 47.619 13.05 3.28 0.00 3.66
4394 4458 3.370840 TTCTGCAATAAGATGGCCAGT 57.629 42.857 13.05 0.87 0.00 4.00
4395 4459 3.255149 GGATTCTGCAATAAGATGGCCAG 59.745 47.826 13.05 0.00 0.00 4.85
4396 4460 3.225104 GGATTCTGCAATAAGATGGCCA 58.775 45.455 8.56 8.56 0.00 5.36
4397 4461 3.225104 TGGATTCTGCAATAAGATGGCC 58.775 45.455 0.00 0.00 0.00 5.36
4398 4462 5.464030 AATGGATTCTGCAATAAGATGGC 57.536 39.130 0.00 0.00 0.00 4.40
4402 4466 9.300681 CCCTAAATAATGGATTCTGCAATAAGA 57.699 33.333 0.00 0.00 0.00 2.10
4403 4467 8.031277 GCCCTAAATAATGGATTCTGCAATAAG 58.969 37.037 0.00 0.00 0.00 1.73
4404 4468 7.729881 AGCCCTAAATAATGGATTCTGCAATAA 59.270 33.333 0.00 0.00 0.00 1.40
4405 4469 7.240897 AGCCCTAAATAATGGATTCTGCAATA 58.759 34.615 0.00 0.00 0.00 1.90
4406 4470 6.080009 AGCCCTAAATAATGGATTCTGCAAT 58.920 36.000 0.00 0.00 0.00 3.56
4407 4471 5.457686 AGCCCTAAATAATGGATTCTGCAA 58.542 37.500 0.00 0.00 0.00 4.08
4574 4646 6.133356 TCAAATGGGGATTTTCCATACCTAC 58.867 40.000 0.00 0.00 43.61 3.18
4587 4659 4.042062 TCGAGCTCATAATCAAATGGGGAT 59.958 41.667 15.40 0.00 0.00 3.85
4590 4662 4.999311 TCATCGAGCTCATAATCAAATGGG 59.001 41.667 15.40 0.00 0.00 4.00
4623 4695 8.911918 TTTTAATGACTGTTACTAGGCTTTCA 57.088 30.769 0.00 0.00 0.00 2.69
4630 4702 8.083462 TGTGCACTTTTAATGACTGTTACTAG 57.917 34.615 19.41 0.00 0.00 2.57
4802 4874 6.096141 TGAAGCTGTTCCATTTACTTGTCAAA 59.904 34.615 0.00 0.00 0.00 2.69
4808 4880 4.144297 TGCTGAAGCTGTTCCATTTACTT 58.856 39.130 3.61 0.00 42.66 2.24
4821 4893 4.277921 CCTTTTCTTCTTTCTGCTGAAGCT 59.722 41.667 6.13 0.00 42.66 3.74
4828 4900 9.298774 CATATGAATTCCTTTTCTTCTTTCTGC 57.701 33.333 2.27 0.00 0.00 4.26
4869 4942 5.999600 TCACTTTCAATGAATCAAGCAGAGA 59.000 36.000 0.00 0.00 0.00 3.10
4870 4943 6.084925 GTCACTTTCAATGAATCAAGCAGAG 58.915 40.000 0.00 0.00 0.00 3.35
4886 4959 8.723942 ATGACTATAAGGAACATGTCACTTTC 57.276 34.615 16.98 10.75 37.28 2.62
5042 5116 6.070951 TCAGGAGAAACCATGAGAATGATT 57.929 37.500 0.00 0.00 42.04 2.57
5052 5126 1.281867 TGCGGAATCAGGAGAAACCAT 59.718 47.619 0.00 0.00 42.04 3.55
5071 5145 5.736358 GCAATTCTCGCTCAAGTAAGATTTG 59.264 40.000 0.00 0.00 34.56 2.32
5091 5167 2.034432 TGTTCAACAGAACATGCGCAAT 59.966 40.909 17.11 1.94 44.82 3.56
5110 5186 5.420739 ACTTTGAAATGGTTGTGTAGGTTGT 59.579 36.000 0.00 0.00 0.00 3.32
5149 7406 9.480053 AGATGTCATTGTGTTTAAAATTCTTGG 57.520 29.630 0.00 0.00 0.00 3.61
5242 7499 9.460906 GCAAATCCAAATCAATATCTTTCTCTC 57.539 33.333 0.00 0.00 0.00 3.20
5243 7500 9.198475 AGCAAATCCAAATCAATATCTTTCTCT 57.802 29.630 0.00 0.00 0.00 3.10
5251 7508 9.101655 GCAAGTTTAGCAAATCCAAATCAATAT 57.898 29.630 0.00 0.00 0.00 1.28
5252 7509 7.275341 CGCAAGTTTAGCAAATCCAAATCAATA 59.725 33.333 0.00 0.00 0.00 1.90
5253 7510 6.091169 CGCAAGTTTAGCAAATCCAAATCAAT 59.909 34.615 0.00 0.00 0.00 2.57
5277 7539 3.055719 ATTTGGACGCTGCCCACG 61.056 61.111 0.00 0.00 32.58 4.94
5303 7565 0.540830 TGGTGCCCATAACAACCACC 60.541 55.000 0.00 0.00 44.71 4.61
5314 7576 1.285280 ACTATTGCTAGTGGTGCCCA 58.715 50.000 0.00 0.00 36.81 5.36
5328 7590 4.771590 TTCGACGTTCTGTACCACTATT 57.228 40.909 0.00 0.00 0.00 1.73
5338 7600 7.329438 TCTATTTACACTTTTCGACGTTCTG 57.671 36.000 0.00 0.00 0.00 3.02
5417 7679 8.956533 AGTATACATGTGTGTGCATACATTTA 57.043 30.769 19.74 13.11 40.46 1.40
5420 7682 7.946655 GTAGTATACATGTGTGTGCATACAT 57.053 36.000 19.74 13.09 42.66 2.29
5477 7739 9.120538 GTTATCTTATCTTTGGAAGCCACATAA 57.879 33.333 0.00 0.00 30.78 1.90
5488 7750 9.093970 TCGTGTATGTTGTTATCTTATCTTTGG 57.906 33.333 0.00 0.00 0.00 3.28
5503 7765 2.730715 CGGCCCATTTTCGTGTATGTTG 60.731 50.000 0.00 0.00 0.00 3.33
5504 7766 1.470890 CGGCCCATTTTCGTGTATGTT 59.529 47.619 0.00 0.00 0.00 2.71
5544 7806 4.863491 AGCTACACAACAGAAGCAAAATG 58.137 39.130 0.00 0.00 37.44 2.32
5555 7817 6.685527 TTGTGATTTGTAAGCTACACAACA 57.314 33.333 12.13 6.46 41.20 3.33
5556 7818 9.840427 AATATTGTGATTTGTAAGCTACACAAC 57.160 29.630 12.13 4.30 45.93 3.32
5586 7848 5.625311 GCTTCGGATCTGTAAACTTTTGTTG 59.375 40.000 0.42 0.00 42.67 3.33
5593 7855 3.251571 GTTCGCTTCGGATCTGTAAACT 58.748 45.455 0.42 0.00 0.00 2.66
5594 7856 2.991190 TGTTCGCTTCGGATCTGTAAAC 59.009 45.455 0.42 1.77 0.00 2.01
5605 7867 5.515270 TGAAGACTTATACATGTTCGCTTCG 59.485 40.000 2.30 0.00 33.75 3.79
5635 7897 8.436200 CCATGTTTTAAAAACACTCGAAAACAA 58.564 29.630 13.35 1.11 46.90 2.83
5642 7904 9.631639 GAAAATTCCATGTTTTAAAAACACTCG 57.368 29.630 1.31 0.00 32.37 4.18
5683 7945 3.478857 TTAGGAGACGCCAAAGTTTCA 57.521 42.857 0.00 0.00 40.02 2.69
5684 7946 4.275196 AGTTTTAGGAGACGCCAAAGTTTC 59.725 41.667 0.00 0.00 40.02 2.78
5689 7951 3.243267 GCAAAGTTTTAGGAGACGCCAAA 60.243 43.478 0.00 0.00 40.02 3.28
5690 7952 2.292292 GCAAAGTTTTAGGAGACGCCAA 59.708 45.455 0.00 0.00 40.02 4.52
5691 7953 1.877443 GCAAAGTTTTAGGAGACGCCA 59.123 47.619 0.00 0.00 40.02 5.69
5694 7956 4.813296 AAGTGCAAAGTTTTAGGAGACG 57.187 40.909 0.00 0.00 0.00 4.18
5707 7969 9.838975 CAAGTATTTCATGTGTATAAGTGCAAA 57.161 29.630 0.00 0.00 0.00 3.68
5709 7971 8.560355 ACAAGTATTTCATGTGTATAAGTGCA 57.440 30.769 0.00 0.00 0.00 4.57
5730 7992 2.609459 CCCTTGCTTGCTACGATACAAG 59.391 50.000 10.34 10.34 44.88 3.16
5731 7993 2.627945 CCCTTGCTTGCTACGATACAA 58.372 47.619 0.00 0.00 0.00 2.41
5732 7994 1.134521 CCCCTTGCTTGCTACGATACA 60.135 52.381 0.00 0.00 0.00 2.29
5733 7995 1.583054 CCCCTTGCTTGCTACGATAC 58.417 55.000 0.00 0.00 0.00 2.24
5734 7996 0.179056 GCCCCTTGCTTGCTACGATA 60.179 55.000 0.00 0.00 36.87 2.92
5735 7997 1.452108 GCCCCTTGCTTGCTACGAT 60.452 57.895 0.00 0.00 36.87 3.73
5736 7998 2.046314 GCCCCTTGCTTGCTACGA 60.046 61.111 0.00 0.00 36.87 3.43
5737 7999 3.499737 CGCCCCTTGCTTGCTACG 61.500 66.667 0.00 0.00 38.05 3.51
5738 8000 3.815396 GCGCCCCTTGCTTGCTAC 61.815 66.667 0.00 0.00 38.05 3.58
5739 8001 3.643595 ATGCGCCCCTTGCTTGCTA 62.644 57.895 4.18 0.00 38.05 3.49
5741 8003 4.807039 CATGCGCCCCTTGCTTGC 62.807 66.667 4.18 0.00 38.05 4.01
5742 8004 1.952102 ATTCATGCGCCCCTTGCTTG 61.952 55.000 4.18 0.00 38.45 4.01
5743 8005 0.395586 TATTCATGCGCCCCTTGCTT 60.396 50.000 4.18 0.00 38.05 3.91
5744 8006 0.820891 CTATTCATGCGCCCCTTGCT 60.821 55.000 4.18 0.00 38.05 3.91
5745 8007 0.819259 TCTATTCATGCGCCCCTTGC 60.819 55.000 4.18 0.00 0.00 4.01
5746 8008 1.679139 TTCTATTCATGCGCCCCTTG 58.321 50.000 4.18 0.00 0.00 3.61
5747 8009 2.664402 ATTCTATTCATGCGCCCCTT 57.336 45.000 4.18 0.00 0.00 3.95
5748 8010 2.664402 AATTCTATTCATGCGCCCCT 57.336 45.000 4.18 0.00 0.00 4.79
5749 8011 4.846779 TTTAATTCTATTCATGCGCCCC 57.153 40.909 4.18 0.00 0.00 5.80
5750 8012 5.569059 CGAATTTAATTCTATTCATGCGCCC 59.431 40.000 14.66 0.00 37.13 6.13
5751 8013 6.370593 TCGAATTTAATTCTATTCATGCGCC 58.629 36.000 14.66 0.00 37.13 6.53
5752 8014 7.836358 TTCGAATTTAATTCTATTCATGCGC 57.164 32.000 14.66 0.00 37.13 6.09
5766 8028 9.496873 TGTCTTCCTCTATGTTTTCGAATTTAA 57.503 29.630 0.00 0.00 0.00 1.52
5767 8029 9.667107 ATGTCTTCCTCTATGTTTTCGAATTTA 57.333 29.630 0.00 0.00 0.00 1.40
5768 8030 7.979444 TGTCTTCCTCTATGTTTTCGAATTT 57.021 32.000 0.00 0.00 0.00 1.82
5769 8031 9.099454 GTATGTCTTCCTCTATGTTTTCGAATT 57.901 33.333 0.00 0.00 0.00 2.17
5770 8032 8.258007 TGTATGTCTTCCTCTATGTTTTCGAAT 58.742 33.333 0.00 0.00 0.00 3.34
5771 8033 7.608153 TGTATGTCTTCCTCTATGTTTTCGAA 58.392 34.615 0.00 0.00 0.00 3.71
5772 8034 7.165460 TGTATGTCTTCCTCTATGTTTTCGA 57.835 36.000 0.00 0.00 0.00 3.71
5773 8035 7.545965 ACTTGTATGTCTTCCTCTATGTTTTCG 59.454 37.037 0.00 0.00 0.00 3.46
5774 8036 8.779354 ACTTGTATGTCTTCCTCTATGTTTTC 57.221 34.615 0.00 0.00 0.00 2.29
5775 8037 9.654663 GTACTTGTATGTCTTCCTCTATGTTTT 57.345 33.333 0.00 0.00 0.00 2.43
5776 8038 8.812972 TGTACTTGTATGTCTTCCTCTATGTTT 58.187 33.333 0.00 0.00 0.00 2.83
5777 8039 8.362464 TGTACTTGTATGTCTTCCTCTATGTT 57.638 34.615 0.00 0.00 0.00 2.71
5778 8040 7.956328 TGTACTTGTATGTCTTCCTCTATGT 57.044 36.000 0.00 0.00 0.00 2.29
5779 8041 7.432545 CGTTGTACTTGTATGTCTTCCTCTATG 59.567 40.741 0.00 0.00 0.00 2.23
5780 8042 7.416438 CCGTTGTACTTGTATGTCTTCCTCTAT 60.416 40.741 0.00 0.00 0.00 1.98
5781 8043 6.127814 CCGTTGTACTTGTATGTCTTCCTCTA 60.128 42.308 0.00 0.00 0.00 2.43
5782 8044 5.336531 CCGTTGTACTTGTATGTCTTCCTCT 60.337 44.000 0.00 0.00 0.00 3.69
5783 8045 4.863131 CCGTTGTACTTGTATGTCTTCCTC 59.137 45.833 0.00 0.00 0.00 3.71
5784 8046 4.817517 CCGTTGTACTTGTATGTCTTCCT 58.182 43.478 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.