Multiple sequence alignment - TraesCS2A01G204400

Loading Multiple Alignment...

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 TraesCS2A01G204400 chr2A 100.000 6170 0 0 1 6170 181801699 181795530 0.000000e+00 11394
1 TraesCS2A01G204400 chr2A 86.356 623 79 5 5547 6165 374795692 374796312 0.000000e+00 675
2 TraesCS2A01G204400 chr2A 100.000 60 0 0 5488 5547 181796153 181796094 1.820000e-20 111
3 TraesCS2A01G204400 chr2D 94.997 5177 186 32 268 5412 168639492 168644627 0.000000e+00 8058
4 TraesCS2A01G204400 chr2D 94.579 535 20 4 4927 5455 168644623 168645154 0.000000e+00 819
5 TraesCS2A01G204400 chr2D 87.801 623 74 2 5547 6168 557748033 557747412 0.000000e+00 728
6 TraesCS2A01G204400 chr2D 87.599 629 73 5 5541 6165 299561034 299561661 0.000000e+00 725
7 TraesCS2A01G204400 chr2D 91.518 224 18 1 1 223 168638930 168639153 2.160000e-79 307
8 TraesCS2A01G204400 chr2B 94.141 4779 199 34 687 5435 229447964 229443237 0.000000e+00 7199
9 TraesCS2A01G204400 chr2B 91.026 702 55 6 1 701 229448676 229447982 0.000000e+00 941
10 TraesCS2A01G204400 chr4A 89.723 613 60 3 5554 6165 102992610 102992000 0.000000e+00 780
11 TraesCS2A01G204400 chr7D 87.580 628 71 4 5547 6168 509596553 509595927 0.000000e+00 721
12 TraesCS2A01G204400 chr7D 86.538 624 80 4 5547 6168 534333402 534332781 0.000000e+00 684
13 TraesCS2A01G204400 chr5D 87.319 623 76 3 5547 6168 388736890 388736270 0.000000e+00 710
14 TraesCS2A01G204400 chr5D 85.737 624 86 3 5547 6168 236455976 236455354 0.000000e+00 656
15 TraesCS2A01G204400 chr6B 85.897 624 83 5 5547 6168 377823651 377823031 0.000000e+00 660


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 TraesCS2A01G204400 chr2A 181795530 181801699 6169 True 11394.000000 11394 100.0000 1 6170 1 chr2A.!!$R1 6169
1 TraesCS2A01G204400 chr2A 374795692 374796312 620 False 675.000000 675 86.3560 5547 6165 1 chr2A.!!$F1 618
2 TraesCS2A01G204400 chr2D 168638930 168645154 6224 False 3061.333333 8058 93.6980 1 5455 3 chr2D.!!$F2 5454
3 TraesCS2A01G204400 chr2D 557747412 557748033 621 True 728.000000 728 87.8010 5547 6168 1 chr2D.!!$R1 621
4 TraesCS2A01G204400 chr2D 299561034 299561661 627 False 725.000000 725 87.5990 5541 6165 1 chr2D.!!$F1 624
5 TraesCS2A01G204400 chr2B 229443237 229448676 5439 True 4070.000000 7199 92.5835 1 5435 2 chr2B.!!$R1 5434
6 TraesCS2A01G204400 chr4A 102992000 102992610 610 True 780.000000 780 89.7230 5554 6165 1 chr4A.!!$R1 611
7 TraesCS2A01G204400 chr7D 509595927 509596553 626 True 721.000000 721 87.5800 5547 6168 1 chr7D.!!$R1 621
8 TraesCS2A01G204400 chr7D 534332781 534333402 621 True 684.000000 684 86.5380 5547 6168 1 chr7D.!!$R2 621
9 TraesCS2A01G204400 chr5D 388736270 388736890 620 True 710.000000 710 87.3190 5547 6168 1 chr5D.!!$R2 621
10 TraesCS2A01G204400 chr5D 236455354 236455976 622 True 656.000000 656 85.7370 5547 6168 1 chr5D.!!$R1 621
11 TraesCS2A01G204400 chr6B 377823031 377823651 620 True 660.000000 660 85.8970 5547 6168 1 chr6B.!!$R1 621

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
301 597 0.180642 TCGGAGCTCGTAGTCTCCAT 59.819 55.0 7.83 0.0 44.10 3.41 F
882 1210 0.672711 GCGGGTGAGTTTGGTCTACC 60.673 60.0 0.00 0.0 0.00 3.18 F
1507 1847 0.725117 CTCGGTGCGATTTGGTTACC 59.275 55.0 0.00 0.0 34.61 2.85 F
2204 2547 0.179150 CGACTGAGCTGTAGGCACTC 60.179 60.0 0.00 0.0 44.79 3.51 F
3431 3792 0.535102 AAGCTGACACAACCTTCCCG 60.535 55.0 0.00 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 2049 0.035439 TTCTCTGGGCGTTCCAATCC 60.035 55.0 1.60 0.00 46.51 3.01 R
2088 2430 0.250553 AAAACCCGCACGAATCTCCA 60.251 50.0 0.00 0.00 0.00 3.86 R
3431 3792 0.810031 ACGTCTGTGACCTGTGTTGC 60.810 55.0 0.00 0.00 0.00 4.17 R
3565 3926 0.328258 GGGTGGCCAGTGTTATCAGT 59.672 55.0 5.11 0.00 0.00 3.41 R
5178 6026 0.596600 ACTACAACCAGTGTGACGCG 60.597 55.0 3.53 3.53 41.89 6.01 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
30 31 2.229792 TCTTGCAAGGAACAATTCGCT 58.770 42.857 25.73 0.00 0.00 4.93
31 32 3.407698 TCTTGCAAGGAACAATTCGCTA 58.592 40.909 25.73 0.00 0.00 4.26
64 66 2.496111 CCAAGGCAACAACAAATGCAT 58.504 42.857 0.00 0.00 44.32 3.96
65 67 2.224549 CCAAGGCAACAACAAATGCATG 59.775 45.455 0.00 0.00 44.32 4.06
71 73 4.035441 GGCAACAACAAATGCATGAAACTT 59.965 37.500 0.00 0.00 44.32 2.66
80 82 1.535028 TGCATGAAACTTACACCGCAG 59.465 47.619 0.00 0.00 0.00 5.18
94 96 1.956170 CGCAGGTCACACTGGTCAC 60.956 63.158 0.00 0.00 38.90 3.67
123 125 0.780637 TTCACCAAGGGGCCATGTAA 59.219 50.000 4.39 0.00 37.90 2.41
126 128 0.849094 ACCAAGGGGCCATGTAAGGA 60.849 55.000 4.39 0.00 37.90 3.36
128 130 1.272985 CCAAGGGGCCATGTAAGGAAA 60.273 52.381 4.39 0.00 0.00 3.13
274 570 1.134521 CATCGCCCACTTTAGTGCCTA 60.135 52.381 4.34 0.00 44.34 3.93
301 597 0.180642 TCGGAGCTCGTAGTCTCCAT 59.819 55.000 7.83 0.00 44.10 3.41
315 611 1.984424 TCTCCATGACCCACATCAACA 59.016 47.619 0.00 0.00 37.07 3.33
316 612 2.374839 TCTCCATGACCCACATCAACAA 59.625 45.455 0.00 0.00 37.07 2.83
457 753 3.536917 CTGGGAGGCGGCGTGATA 61.537 66.667 9.37 0.00 0.00 2.15
466 762 1.809619 CGGCGTGATAGTGTGGGTG 60.810 63.158 0.00 0.00 0.00 4.61
488 784 1.858372 TTCGCTTAGCCGGGTTTTGC 61.858 55.000 13.43 13.12 0.00 3.68
549 845 2.358247 GGGTTGCGACGTGGACAT 60.358 61.111 0.11 0.00 0.00 3.06
565 861 3.118445 TGGACATAAGTGCGGATGATTGA 60.118 43.478 0.00 0.00 39.20 2.57
566 862 3.876914 GGACATAAGTGCGGATGATTGAA 59.123 43.478 0.00 0.00 0.00 2.69
621 917 6.712276 ACGAGAGATGGAACCTTATTCTTTT 58.288 36.000 0.00 0.00 0.00 2.27
673 969 2.835156 GAGAAGTAGAGACAAGGCCCTT 59.165 50.000 0.00 0.00 0.00 3.95
675 971 3.008485 AGAAGTAGAGACAAGGCCCTTTG 59.992 47.826 0.00 0.00 0.00 2.77
742 1070 8.899771 AGTTTTGGTTATTATTTAGATGGTCGG 58.100 33.333 0.00 0.00 0.00 4.79
780 1108 8.792633 GGTATGCCAATAACTATTTGCTCATTA 58.207 33.333 0.00 0.00 35.89 1.90
882 1210 0.672711 GCGGGTGAGTTTGGTCTACC 60.673 60.000 0.00 0.00 0.00 3.18
985 1325 3.293702 GCTGAAGCTCCTCCGTCT 58.706 61.111 0.00 0.00 38.21 4.18
999 1339 1.624865 CCGTCTCGTCTCGTCTCGTT 61.625 60.000 0.00 0.00 0.00 3.85
1472 1812 2.290916 TGATTCGGTGATCTCGTAGCTC 59.709 50.000 0.00 0.00 0.00 4.09
1482 1822 1.096416 CTCGTAGCTCCTCTTTCGGT 58.904 55.000 0.00 0.00 0.00 4.69
1507 1847 0.725117 CTCGGTGCGATTTGGTTACC 59.275 55.000 0.00 0.00 34.61 2.85
1515 1855 4.092968 GTGCGATTTGGTTACCAGTAGAAG 59.907 45.833 3.65 0.00 33.81 2.85
1548 1888 3.096092 TGTTATGGTTGGAGGAATTGGC 58.904 45.455 0.00 0.00 0.00 4.52
1648 1988 4.187694 GACTGTTGAAGATAGCCAGGAAG 58.812 47.826 0.00 0.00 0.00 3.46
1721 2061 2.091541 TGAATTCTGGATTGGAACGCC 58.908 47.619 7.05 0.00 0.00 5.68
1747 2087 2.278332 ACCCTCTTCCTTGCTGTTTC 57.722 50.000 0.00 0.00 0.00 2.78
1826 2166 3.259064 GCGCAACTCCATTCTTGTAGTA 58.741 45.455 0.30 0.00 0.00 1.82
1827 2167 3.307242 GCGCAACTCCATTCTTGTAGTAG 59.693 47.826 0.30 0.00 0.00 2.57
1828 2168 4.495422 CGCAACTCCATTCTTGTAGTAGT 58.505 43.478 0.00 0.00 0.00 2.73
1870 2210 3.129871 GAGAATCATGCTGCTCCTACAC 58.870 50.000 0.00 0.00 33.17 2.90
2001 2342 3.442996 GGACTGTTCCATCGGACTG 57.557 57.895 0.00 0.00 42.30 3.51
2075 2417 2.564504 AGCTCAATCGATGCTATAGCCA 59.435 45.455 21.84 10.43 41.18 4.75
2088 2430 2.715532 ATAGCCATCGGATTGCGCGT 62.716 55.000 8.43 0.00 0.00 6.01
2101 2443 3.902063 CGCGTGGAGATTCGTGCG 61.902 66.667 0.00 0.00 39.57 5.34
2195 2538 6.414408 AGTATTTTTCAATCGACTGAGCTG 57.586 37.500 0.00 0.00 0.00 4.24
2204 2547 0.179150 CGACTGAGCTGTAGGCACTC 60.179 60.000 0.00 0.00 44.79 3.51
2532 2885 2.803030 ATTGAAGCTGCTCACATCCT 57.197 45.000 1.00 0.00 0.00 3.24
2872 3227 5.105797 TGTTTGCTTGTATGCTCTATTTGGG 60.106 40.000 0.00 0.00 0.00 4.12
3000 3357 8.957466 ACATGATCATTGCAATATCCTTATCAG 58.043 33.333 12.53 10.08 0.00 2.90
3338 3699 8.478877 TCAGAGGTAGTATTTTCTTCCTTGATC 58.521 37.037 0.00 0.00 35.80 2.92
3341 3702 9.674068 GAGGTAGTATTTTCTTCCTTGATCTTT 57.326 33.333 0.00 0.00 35.80 2.52
3342 3703 9.454859 AGGTAGTATTTTCTTCCTTGATCTTTG 57.545 33.333 0.00 0.00 32.59 2.77
3371 3732 4.753610 CCTCATCTACACAGCCATGTTATG 59.246 45.833 0.00 2.19 37.65 1.90
3419 3780 8.795786 TTTCATGTGTACAAATAAAAGCTGAC 57.204 30.769 0.00 0.00 0.00 3.51
3431 3792 0.535102 AAGCTGACACAACCTTCCCG 60.535 55.000 0.00 0.00 0.00 5.14
3432 3793 2.617274 GCTGACACAACCTTCCCGC 61.617 63.158 0.00 0.00 0.00 6.13
3433 3794 1.227823 CTGACACAACCTTCCCGCA 60.228 57.895 0.00 0.00 0.00 5.69
3477 3838 2.287644 CGATGTCACTTCTGTTGTGCAA 59.712 45.455 0.00 0.00 35.58 4.08
3488 3849 3.761218 TCTGTTGTGCAAGGAAAGACAAA 59.239 39.130 0.00 0.00 30.43 2.83
3521 3882 4.067896 GTCATGATGCTTACATGGGGTAG 58.932 47.826 0.00 0.00 43.38 3.18
3522 3883 3.973305 TCATGATGCTTACATGGGGTAGA 59.027 43.478 14.52 0.00 43.38 2.59
3589 3950 0.400213 TAACACTGGCCACCCTTCTG 59.600 55.000 0.00 0.00 0.00 3.02
3609 3970 3.495331 TGAGAGCTTCTTCTGTCACTCT 58.505 45.455 0.00 0.00 37.21 3.24
3808 4169 8.518430 TTTGTATAATATGCTTTCTTGCCTCA 57.482 30.769 0.00 0.00 0.00 3.86
3837 4198 6.101650 TGCATCTGAGAGTTCTTAGACAAA 57.898 37.500 5.85 0.00 40.68 2.83
3858 4219 2.955660 AGTTCCAACTGCGGATTTTCAA 59.044 40.909 0.00 0.00 37.98 2.69
3862 4223 5.713792 TCCAACTGCGGATTTTCAATTAA 57.286 34.783 0.00 0.00 0.00 1.40
3880 4241 9.944663 TTCAATTAACAAAATATACTCGATGCC 57.055 29.630 0.00 0.00 0.00 4.40
4011 4372 2.435234 GCGACGGTACAATGGGCA 60.435 61.111 0.00 0.00 0.00 5.36
4057 4418 5.012893 GGATATGAAGGATTTGGTGATCCC 58.987 45.833 0.46 0.00 45.56 3.85
4180 4541 3.156511 TCAACTGACGATGCTGATCTC 57.843 47.619 0.00 0.00 0.00 2.75
4230 4591 2.774439 AACGTTTGGATCAGCAACAC 57.226 45.000 0.00 0.00 0.00 3.32
4329 4690 7.532571 TCATATTTTGTCTTTGATGCAGTGAG 58.467 34.615 0.00 0.00 0.00 3.51
4398 4759 9.343539 GTAATCTATTTGCCCTGAAAATCTAGT 57.656 33.333 0.00 0.00 0.00 2.57
4427 4788 9.547753 TCTTCCTATGTTTGTAAGAATATCAGC 57.452 33.333 0.00 0.00 0.00 4.26
4600 4961 4.152647 AGGATGGTAGCTACATCGAATCA 58.847 43.478 24.75 12.05 44.34 2.57
4627 4988 6.098409 CCTATGTGGAGTACTTCAAGGTATGT 59.902 42.308 5.12 0.00 38.35 2.29
4866 5227 1.227497 GGAAGAGCCGGAGCATCTG 60.227 63.158 5.05 0.00 43.56 2.90
4940 5301 5.926580 ATCTTCTCCCCAAGATGATGAAT 57.073 39.130 3.46 0.00 43.61 2.57
5006 5852 2.743538 TGCGCCTCAGCACATGTC 60.744 61.111 4.18 0.00 42.92 3.06
5025 5873 7.488150 CACATGTCGTATGTAAATACTCACACT 59.512 37.037 0.00 0.00 0.00 3.55
5144 5992 3.898741 GACCTTAGGGGAATCTGACTAGG 59.101 52.174 2.32 0.00 38.76 3.02
5348 6202 1.918800 CCCTCGAACACCCCCTCTT 60.919 63.158 0.00 0.00 0.00 2.85
5404 6258 2.460853 CCCAACCCCACTCACACCT 61.461 63.158 0.00 0.00 0.00 4.00
5436 6290 4.442893 CGTTCAGGTTTCATATCCAGCCTA 60.443 45.833 0.00 0.00 0.00 3.93
5438 6292 6.518369 CGTTCAGGTTTCATATCCAGCCTATA 60.518 42.308 0.00 0.00 0.00 1.31
5439 6293 7.398024 GTTCAGGTTTCATATCCAGCCTATAT 58.602 38.462 0.00 0.00 0.00 0.86
5440 6294 7.187824 TCAGGTTTCATATCCAGCCTATATC 57.812 40.000 0.00 0.00 0.00 1.63
5468 6322 5.979288 GGATACGGGTGTAGAAGATATGT 57.021 43.478 0.00 0.00 33.17 2.29
5469 6323 5.710984 GGATACGGGTGTAGAAGATATGTG 58.289 45.833 0.00 0.00 33.17 3.21
5470 6324 3.454371 ACGGGTGTAGAAGATATGTGC 57.546 47.619 0.00 0.00 0.00 4.57
5471 6325 2.764010 ACGGGTGTAGAAGATATGTGCA 59.236 45.455 0.00 0.00 0.00 4.57
5472 6326 3.196901 ACGGGTGTAGAAGATATGTGCAA 59.803 43.478 0.00 0.00 0.00 4.08
5473 6327 3.804325 CGGGTGTAGAAGATATGTGCAAG 59.196 47.826 0.00 0.00 0.00 4.01
5474 6328 4.680708 CGGGTGTAGAAGATATGTGCAAGT 60.681 45.833 0.00 0.00 0.00 3.16
5475 6329 4.811557 GGGTGTAGAAGATATGTGCAAGTC 59.188 45.833 0.00 0.00 0.00 3.01
5476 6330 5.419542 GGTGTAGAAGATATGTGCAAGTCA 58.580 41.667 0.00 0.00 0.00 3.41
5477 6331 6.051717 GGTGTAGAAGATATGTGCAAGTCAT 58.948 40.000 0.00 0.00 0.00 3.06
5478 6332 6.018425 GGTGTAGAAGATATGTGCAAGTCATG 60.018 42.308 0.00 0.00 0.00 3.07
5479 6333 6.758416 GTGTAGAAGATATGTGCAAGTCATGA 59.242 38.462 0.00 0.00 0.00 3.07
5480 6334 7.440556 GTGTAGAAGATATGTGCAAGTCATGAT 59.559 37.037 0.00 0.00 0.00 2.45
5481 6335 8.641541 TGTAGAAGATATGTGCAAGTCATGATA 58.358 33.333 0.00 0.00 0.00 2.15
5482 6336 9.650539 GTAGAAGATATGTGCAAGTCATGATAT 57.349 33.333 0.00 0.00 0.00 1.63
5490 6344 7.355332 TGTGCAAGTCATGATATATTGATCG 57.645 36.000 0.00 0.00 0.00 3.69
5491 6345 6.369615 TGTGCAAGTCATGATATATTGATCGG 59.630 38.462 0.00 0.00 0.00 4.18
5492 6346 5.876460 TGCAAGTCATGATATATTGATCGGG 59.124 40.000 0.00 0.00 0.00 5.14
5493 6347 5.220739 GCAAGTCATGATATATTGATCGGGC 60.221 44.000 0.00 0.00 0.00 6.13
5494 6348 4.686972 AGTCATGATATATTGATCGGGCG 58.313 43.478 0.00 0.00 0.00 6.13
5495 6349 3.246226 GTCATGATATATTGATCGGGCGC 59.754 47.826 0.00 0.00 0.00 6.53
5496 6350 3.118811 TCATGATATATTGATCGGGCGCA 60.119 43.478 10.83 0.00 0.00 6.09
5497 6351 3.541996 TGATATATTGATCGGGCGCAT 57.458 42.857 10.83 0.00 0.00 4.73
5498 6352 4.664150 TGATATATTGATCGGGCGCATA 57.336 40.909 10.83 0.00 0.00 3.14
5499 6353 5.213891 TGATATATTGATCGGGCGCATAT 57.786 39.130 10.83 4.50 0.00 1.78
5500 6354 4.990426 TGATATATTGATCGGGCGCATATG 59.010 41.667 10.83 0.00 0.00 1.78
5501 6355 1.368641 TATTGATCGGGCGCATATGC 58.631 50.000 18.08 18.08 37.78 3.14
5502 6356 0.606130 ATTGATCGGGCGCATATGCA 60.606 50.000 26.52 7.82 42.21 3.96
5503 6357 1.506309 TTGATCGGGCGCATATGCAC 61.506 55.000 26.52 17.52 42.21 4.57
5507 6361 3.966215 GGGCGCATATGCACGTAT 58.034 55.556 26.52 0.00 42.21 3.06
5508 6362 3.131326 GGGCGCATATGCACGTATA 57.869 52.632 26.52 0.00 42.21 1.47
5509 6363 0.719465 GGGCGCATATGCACGTATAC 59.281 55.000 26.52 4.59 42.21 1.47
5510 6364 1.424403 GGCGCATATGCACGTATACA 58.576 50.000 26.52 0.00 42.21 2.29
5511 6365 1.999735 GGCGCATATGCACGTATACAT 59.000 47.619 26.52 0.00 42.21 2.29
5512 6366 3.183754 GGCGCATATGCACGTATACATA 58.816 45.455 26.52 7.35 42.21 2.29
5513 6367 3.615056 GGCGCATATGCACGTATACATAA 59.385 43.478 26.52 0.00 42.21 1.90
5514 6368 4.259810 GGCGCATATGCACGTATACATAAG 60.260 45.833 26.52 7.20 42.21 1.73
5515 6369 4.326278 GCGCATATGCACGTATACATAAGT 59.674 41.667 26.52 0.00 42.21 2.24
5516 6370 5.513849 GCGCATATGCACGTATACATAAGTA 59.486 40.000 26.52 0.00 42.21 2.24
5517 6371 6.505888 GCGCATATGCACGTATACATAAGTAC 60.506 42.308 26.52 0.00 42.21 2.73
5518 6372 6.525280 CGCATATGCACGTATACATAAGTACA 59.475 38.462 26.52 0.00 42.21 2.90
5519 6373 7.220108 CGCATATGCACGTATACATAAGTACAT 59.780 37.037 26.52 6.36 42.21 2.29
5520 6374 9.511144 GCATATGCACGTATACATAAGTACATA 57.489 33.333 22.84 9.31 36.30 2.29
5524 6378 7.813645 TGCACGTATACATAAGTACATAGAGG 58.186 38.462 3.32 0.00 31.96 3.69
5525 6379 7.662669 TGCACGTATACATAAGTACATAGAGGA 59.337 37.037 3.32 0.00 31.96 3.71
5526 6380 8.176365 GCACGTATACATAAGTACATAGAGGAG 58.824 40.741 3.32 0.00 31.96 3.69
5527 6381 8.176365 CACGTATACATAAGTACATAGAGGAGC 58.824 40.741 3.32 0.00 31.96 4.70
5528 6382 7.336427 ACGTATACATAAGTACATAGAGGAGCC 59.664 40.741 3.32 0.00 31.96 4.70
5529 6383 7.336176 CGTATACATAAGTACATAGAGGAGCCA 59.664 40.741 3.32 0.00 31.96 4.75
5530 6384 5.793030 ACATAAGTACATAGAGGAGCCAC 57.207 43.478 0.00 0.00 0.00 5.01
5531 6385 4.278669 ACATAAGTACATAGAGGAGCCACG 59.721 45.833 0.00 0.00 0.00 4.94
5532 6386 2.438800 AGTACATAGAGGAGCCACGT 57.561 50.000 0.00 0.00 0.00 4.49
5533 6387 3.572632 AGTACATAGAGGAGCCACGTA 57.427 47.619 0.00 0.00 0.00 3.57
5534 6388 3.212685 AGTACATAGAGGAGCCACGTAC 58.787 50.000 0.00 0.00 0.00 3.67
5535 6389 2.438800 ACATAGAGGAGCCACGTACT 57.561 50.000 0.00 0.00 0.00 2.73
5536 6390 2.299521 ACATAGAGGAGCCACGTACTC 58.700 52.381 8.84 8.84 0.00 2.59
5537 6391 2.298610 CATAGAGGAGCCACGTACTCA 58.701 52.381 16.89 0.39 35.79 3.41
5538 6392 2.502142 TAGAGGAGCCACGTACTCAA 57.498 50.000 16.89 0.52 35.79 3.02
5539 6393 0.889306 AGAGGAGCCACGTACTCAAC 59.111 55.000 16.89 10.89 35.79 3.18
5540 6394 0.889306 GAGGAGCCACGTACTCAACT 59.111 55.000 16.89 7.81 35.79 3.16
5541 6395 2.089980 GAGGAGCCACGTACTCAACTA 58.910 52.381 16.89 0.00 35.79 2.24
5542 6396 2.688958 GAGGAGCCACGTACTCAACTAT 59.311 50.000 16.89 1.02 35.79 2.12
5543 6397 3.881688 GAGGAGCCACGTACTCAACTATA 59.118 47.826 16.89 0.00 35.79 1.31
5544 6398 3.631227 AGGAGCCACGTACTCAACTATAC 59.369 47.826 16.89 1.46 35.79 1.47
5545 6399 3.379372 GGAGCCACGTACTCAACTATACA 59.621 47.826 16.89 0.00 35.79 2.29
5552 6406 3.979495 CGTACTCAACTATACAATCGGGC 59.021 47.826 0.00 0.00 0.00 6.13
5568 6423 0.719465 GGGCGCATATGCACGTATAC 59.281 55.000 26.52 4.59 42.21 1.47
5592 6447 3.572632 AGTACATAGAGGAGCCACGTA 57.427 47.619 0.00 0.00 0.00 3.57
5705 6565 2.547855 CCATGGTCGACACAAAGACTGA 60.548 50.000 18.91 0.00 37.52 3.41
5764 6624 4.002982 TGGTCATGATGTCAGCAAACTAC 58.997 43.478 0.00 0.00 0.00 2.73
5765 6625 3.062639 GGTCATGATGTCAGCAAACTACG 59.937 47.826 0.00 0.00 0.00 3.51
5766 6626 2.672874 TCATGATGTCAGCAAACTACGC 59.327 45.455 0.00 0.00 0.00 4.42
5852 6712 3.489355 TCAATCTCAATGTGCTTGGTGT 58.511 40.909 0.12 0.00 35.43 4.16
5869 6729 0.606096 TGTGTCGATGATGAACCGGT 59.394 50.000 0.00 0.00 0.00 5.28
5874 6734 2.936498 GTCGATGATGAACCGGTTTGAT 59.064 45.455 23.22 16.48 0.00 2.57
5876 6736 2.677836 CGATGATGAACCGGTTTGATGT 59.322 45.455 23.22 8.23 0.00 3.06
5890 6750 4.160626 GGTTTGATGTAGAGGTAGACAGCT 59.839 45.833 0.00 0.00 33.17 4.24
5891 6751 5.360144 GGTTTGATGTAGAGGTAGACAGCTA 59.640 44.000 0.00 0.00 33.17 3.32
5928 6788 1.686052 GACAATGGTGGCCTTGTCAAA 59.314 47.619 23.67 0.00 46.67 2.69
5930 6790 1.411977 CAATGGTGGCCTTGTCAAACA 59.588 47.619 3.32 0.00 0.00 2.83
6044 6904 2.010145 GACAATAGGCTGTCGCTTGA 57.990 50.000 0.00 0.00 36.64 3.02
6049 6909 1.812686 TAGGCTGTCGCTTGAACGGT 61.813 55.000 0.00 0.00 36.09 4.83
6085 6946 4.085357 TGGCCAAGATAGACGCAATATT 57.915 40.909 0.61 0.00 0.00 1.28
6168 7029 1.273606 TCCAGAGAAGACGAAGCTTGG 59.726 52.381 2.10 4.94 0.00 3.61
6169 7030 1.273606 CCAGAGAAGACGAAGCTTGGA 59.726 52.381 16.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.527123 TTGGGCACGTGTCCCCTA 60.527 61.111 34.91 21.87 43.24 3.53
31 32 3.953775 CTTGGGCACGTGTCCCCT 61.954 66.667 34.91 0.00 43.24 4.79
64 66 1.139256 TGACCTGCGGTGTAAGTTTCA 59.861 47.619 4.94 0.00 35.25 2.69
65 67 1.529865 GTGACCTGCGGTGTAAGTTTC 59.470 52.381 4.94 0.00 35.25 2.78
71 73 1.365999 CAGTGTGACCTGCGGTGTA 59.634 57.895 4.94 0.00 35.25 2.90
80 82 0.033504 ACATCGTGACCAGTGTGACC 59.966 55.000 0.00 0.00 0.00 4.02
123 125 1.707427 AGGTCAATGCCTCTGTTTCCT 59.293 47.619 0.00 0.00 32.39 3.36
191 193 1.003696 TGGTGGTTATCATTGGCGTCA 59.996 47.619 0.00 0.00 0.00 4.35
244 246 2.203209 GGGCGATGTGGATGACCC 60.203 66.667 0.00 0.00 34.81 4.46
249 251 1.559682 ACTAAAGTGGGCGATGTGGAT 59.440 47.619 0.00 0.00 0.00 3.41
301 597 2.524306 GGGATTTGTTGATGTGGGTCA 58.476 47.619 0.00 0.00 0.00 4.02
315 611 4.522971 GCTTCGAGAGCGGGATTT 57.477 55.556 4.28 0.00 42.46 2.17
364 660 2.523168 CGCACCCCACCCCTTTTT 60.523 61.111 0.00 0.00 0.00 1.94
385 681 0.688087 GTCTACCCTCCTCCACCCAG 60.688 65.000 0.00 0.00 0.00 4.45
453 749 1.606994 GCGAACACACCCACACTATCA 60.607 52.381 0.00 0.00 0.00 2.15
457 753 0.466543 TAAGCGAACACACCCACACT 59.533 50.000 0.00 0.00 0.00 3.55
466 762 1.232621 AAACCCGGCTAAGCGAACAC 61.233 55.000 0.00 0.00 0.00 3.32
488 784 4.392940 CCTCCTACAATCTAAATGGCTGG 58.607 47.826 0.00 0.00 0.00 4.85
524 820 4.717313 GTCGCAACCCCACTCCCC 62.717 72.222 0.00 0.00 0.00 4.81
593 889 5.677319 ATAAGGTTCCATCTCTCGTTCAA 57.323 39.130 0.00 0.00 0.00 2.69
646 942 4.034742 GCCTTGTCTCTACTTCTCTACTCG 59.965 50.000 0.00 0.00 0.00 4.18
648 944 4.274978 GGCCTTGTCTCTACTTCTCTACT 58.725 47.826 0.00 0.00 0.00 2.57
673 969 4.562757 GCTATCCGAACATACCCTATGCAA 60.563 45.833 0.00 0.00 39.79 4.08
675 971 3.195825 AGCTATCCGAACATACCCTATGC 59.804 47.826 0.00 0.00 39.79 3.14
689 985 7.707035 GGTATGGTGAGATTTAATAGCTATCCG 59.293 40.741 6.72 0.00 0.00 4.18
740 1068 2.929398 GGCATACCAAAAGAAATTGCCG 59.071 45.455 0.00 0.00 38.82 5.69
896 1224 1.154301 GTGGTGCGGCGTGTTATTG 60.154 57.895 9.37 0.00 0.00 1.90
981 1321 0.516727 CAACGAGACGAGACGAGACG 60.517 60.000 0.00 0.00 0.00 4.18
982 1322 0.790124 GCAACGAGACGAGACGAGAC 60.790 60.000 0.00 0.00 0.00 3.36
983 1323 1.226030 TGCAACGAGACGAGACGAGA 61.226 55.000 0.00 0.00 0.00 4.04
984 1324 0.791238 CTGCAACGAGACGAGACGAG 60.791 60.000 0.00 0.00 0.00 4.18
985 1325 1.206831 CTGCAACGAGACGAGACGA 59.793 57.895 0.00 0.00 0.00 4.20
999 1339 4.408821 GGTCGGCCATGGACTGCA 62.409 66.667 18.40 0.00 34.82 4.41
1219 1559 2.669364 GTAAAGGTCGCGAGTTTGAGA 58.331 47.619 21.13 4.30 0.00 3.27
1297 1637 1.554836 CTCTCTTCCTGTCCTCTGCA 58.445 55.000 0.00 0.00 0.00 4.41
1369 1709 0.249197 CGAAGCGATCTCTGATGGCA 60.249 55.000 14.87 0.00 0.00 4.92
1408 1748 7.622893 AAAAGCAGAGGATCAGAGAATTAAC 57.377 36.000 0.00 0.00 37.82 2.01
1472 1812 0.097325 CGAGAGTCGACCGAAAGAGG 59.903 60.000 13.01 0.00 43.74 3.69
1482 1822 0.456142 CAAATCGCACCGAGAGTCGA 60.456 55.000 0.00 0.00 43.74 4.20
1515 1855 6.180472 TCCAACCATAACAGAGAAGGAAATC 58.820 40.000 0.00 0.00 0.00 2.17
1548 1888 3.921677 TCAGGTAAAAGTAAGCACGAGG 58.078 45.455 0.00 0.00 0.00 4.63
1690 2030 6.127423 CCAATCCAGAATTCATTTCTTCAGCT 60.127 38.462 8.44 0.00 42.15 4.24
1709 2049 0.035439 TTCTCTGGGCGTTCCAATCC 60.035 55.000 1.60 0.00 46.51 3.01
1747 2087 1.445582 GGACACGCAACCTCCGTAG 60.446 63.158 0.00 0.00 37.12 3.51
1870 2210 3.002348 GGAATGAATTAAGAAGGGCGTCG 59.998 47.826 0.00 0.00 0.00 5.12
1969 2310 4.381932 GGAACAGTCCAAAGCATTAATGGG 60.382 45.833 17.02 9.49 44.26 4.00
2030 2372 8.591312 GCTATAGCTATTTCTCATTCGATTGAC 58.409 37.037 17.75 0.00 38.21 3.18
2075 2417 2.369257 ATCTCCACGCGCAATCCGAT 62.369 55.000 5.73 0.00 40.02 4.18
2088 2430 0.250553 AAAACCCGCACGAATCTCCA 60.251 50.000 0.00 0.00 0.00 3.86
2171 2514 7.097192 ACAGCTCAGTCGATTGAAAAATACTA 58.903 34.615 12.02 0.00 0.00 1.82
2172 2515 5.934625 ACAGCTCAGTCGATTGAAAAATACT 59.065 36.000 12.02 0.77 0.00 2.12
2173 2516 6.170675 ACAGCTCAGTCGATTGAAAAATAC 57.829 37.500 12.02 0.00 0.00 1.89
2258 2603 7.546667 CGAAAAATCTTTGGATGTTTGGATCAT 59.453 33.333 0.00 0.00 38.93 2.45
2532 2885 3.291584 TCACAACCTTGCATGGTGTAAA 58.708 40.909 23.79 12.42 40.73 2.01
2628 2983 4.866508 TCTGAGGACGTTTCACACTTAT 57.133 40.909 0.00 0.00 0.00 1.73
2840 3195 7.533426 AGAGCATACAAGCAAACAGATTAAAG 58.467 34.615 0.00 0.00 36.85 1.85
3094 3455 5.278061 ACTCCTTAGTGGGAACATAAGCTA 58.722 41.667 0.00 0.00 46.14 3.32
3223 3584 2.039746 TCCATTTCCAGTACCTGTGGTG 59.960 50.000 0.00 0.00 36.19 4.17
3338 3699 4.631131 TGTGTAGATGAGGTGTGACAAAG 58.369 43.478 0.00 0.00 0.00 2.77
3341 3702 2.029020 GCTGTGTAGATGAGGTGTGACA 60.029 50.000 0.00 0.00 0.00 3.58
3342 3703 2.611518 GCTGTGTAGATGAGGTGTGAC 58.388 52.381 0.00 0.00 0.00 3.67
3371 3732 9.788960 GAAAATGTAGATTGTTTTGGAGGATAC 57.211 33.333 0.00 0.00 0.00 2.24
3409 3770 3.219281 GGGAAGGTTGTGTCAGCTTTTA 58.781 45.455 0.00 0.00 34.59 1.52
3413 3774 1.071471 CGGGAAGGTTGTGTCAGCT 59.929 57.895 0.00 0.00 0.00 4.24
3419 3780 1.358759 GTGTTGCGGGAAGGTTGTG 59.641 57.895 0.00 0.00 0.00 3.33
3431 3792 0.810031 ACGTCTGTGACCTGTGTTGC 60.810 55.000 0.00 0.00 0.00 4.17
3432 3793 3.362581 ACGTCTGTGACCTGTGTTG 57.637 52.632 0.00 0.00 0.00 3.33
3477 3838 6.208599 TGACACTGAAAAACTTTGTCTTTCCT 59.791 34.615 0.00 0.00 37.94 3.36
3488 3849 5.779529 AAGCATCATGACACTGAAAAACT 57.220 34.783 0.00 0.00 0.00 2.66
3521 3882 5.973565 GGCAGCATCAAACTAATACAATGTC 59.026 40.000 0.00 0.00 0.00 3.06
3522 3883 5.653769 AGGCAGCATCAAACTAATACAATGT 59.346 36.000 0.00 0.00 0.00 2.71
3552 3913 7.012894 CCAGTGTTATCAGTTGTAGTTTGGAAA 59.987 37.037 0.00 0.00 0.00 3.13
3553 3914 6.485313 CCAGTGTTATCAGTTGTAGTTTGGAA 59.515 38.462 0.00 0.00 0.00 3.53
3554 3915 5.995282 CCAGTGTTATCAGTTGTAGTTTGGA 59.005 40.000 0.00 0.00 0.00 3.53
3555 3916 5.334879 GCCAGTGTTATCAGTTGTAGTTTGG 60.335 44.000 0.00 0.00 0.00 3.28
3556 3917 5.334879 GGCCAGTGTTATCAGTTGTAGTTTG 60.335 44.000 0.00 0.00 0.00 2.93
3557 3918 4.760204 GGCCAGTGTTATCAGTTGTAGTTT 59.240 41.667 0.00 0.00 0.00 2.66
3558 3919 4.202419 TGGCCAGTGTTATCAGTTGTAGTT 60.202 41.667 0.00 0.00 0.00 2.24
3561 3922 3.558321 GGTGGCCAGTGTTATCAGTTGTA 60.558 47.826 5.11 0.00 0.00 2.41
3562 3923 2.504367 GTGGCCAGTGTTATCAGTTGT 58.496 47.619 5.11 0.00 0.00 3.32
3563 3924 1.812571 GGTGGCCAGTGTTATCAGTTG 59.187 52.381 5.11 0.00 0.00 3.16
3564 3925 1.271926 GGGTGGCCAGTGTTATCAGTT 60.272 52.381 5.11 0.00 0.00 3.16
3565 3926 0.328258 GGGTGGCCAGTGTTATCAGT 59.672 55.000 5.11 0.00 0.00 3.41
3566 3927 0.620556 AGGGTGGCCAGTGTTATCAG 59.379 55.000 5.11 0.00 0.00 2.90
3589 3950 4.519540 AAGAGTGACAGAAGAAGCTCTC 57.480 45.455 0.00 0.00 32.85 3.20
3825 4186 5.511571 GCAGTTGGAACTTTGTCTAAGAAC 58.488 41.667 0.80 0.00 37.08 3.01
3837 4198 2.582052 TGAAAATCCGCAGTTGGAACT 58.418 42.857 0.00 0.00 42.46 3.01
3874 4235 4.318121 GCACTCGAGTATTAAAAGGCATCG 60.318 45.833 19.57 1.37 0.00 3.84
3880 4241 6.093404 TCTGTCAGCACTCGAGTATTAAAAG 58.907 40.000 19.57 12.23 0.00 2.27
4011 4372 4.424842 TGGGGCAGGAACAAAAAGAATAT 58.575 39.130 0.00 0.00 0.00 1.28
4057 4418 1.662629 CAGCTGATAGTTTGCTCCACG 59.337 52.381 8.42 0.00 34.51 4.94
4147 4508 4.466370 TCGTCAGTTGAAGGACCTGAATAT 59.534 41.667 0.00 0.00 0.00 1.28
4180 4541 2.169352 ACCCTTCAGTGATCTCCATTCG 59.831 50.000 0.00 0.00 0.00 3.34
4230 4591 2.880890 ACACCTTCACTAGCAAAAGCAG 59.119 45.455 0.00 0.00 0.00 4.24
4329 4690 6.374333 TGTTGTATGAGAGTATTTTTCAGCCC 59.626 38.462 0.00 0.00 0.00 5.19
4398 4759 9.547753 GATATTCTTACAAACATAGGAAGAGCA 57.452 33.333 0.00 0.00 0.00 4.26
4427 4788 2.679336 TGCCAATGACTGATCATGAACG 59.321 45.455 0.00 0.00 45.26 3.95
4600 4961 3.775316 CCTTGAAGTACTCCACATAGGGT 59.225 47.826 0.00 0.00 38.24 4.34
4627 4988 3.053917 GGGAGCTCATGGGGTTACTTAAA 60.054 47.826 17.19 0.00 0.00 1.52
4940 5301 2.108250 CAGGGGAACAAGGGAGAAAGAA 59.892 50.000 0.00 0.00 0.00 2.52
5006 5852 7.846107 GCATTTCAGTGTGAGTATTTACATACG 59.154 37.037 0.00 0.00 40.42 3.06
5025 5873 1.298157 CGACCGCCTCTTGCATTTCA 61.298 55.000 0.00 0.00 41.33 2.69
5122 5970 3.898741 CCTAGTCAGATTCCCCTAAGGTC 59.101 52.174 0.00 0.00 36.75 3.85
5178 6026 0.596600 ACTACAACCAGTGTGACGCG 60.597 55.000 3.53 3.53 41.89 6.01
5232 6082 3.027412 AGCGGAGAACAGTACTCATCAT 58.973 45.455 0.00 0.00 36.26 2.45
5404 6258 2.223745 GAAACCTGAACGTTTGGGCTA 58.776 47.619 20.37 0.00 36.10 3.93
5455 6309 6.877236 TCATGACTTGCACATATCTTCTACA 58.123 36.000 0.00 0.00 0.00 2.74
5456 6310 7.959689 ATCATGACTTGCACATATCTTCTAC 57.040 36.000 0.00 0.00 0.00 2.59
5464 6318 9.090692 CGATCAATATATCATGACTTGCACATA 57.909 33.333 0.00 0.00 0.00 2.29
5465 6319 7.065443 CCGATCAATATATCATGACTTGCACAT 59.935 37.037 0.00 0.00 0.00 3.21
5466 6320 6.369615 CCGATCAATATATCATGACTTGCACA 59.630 38.462 0.00 0.00 0.00 4.57
5467 6321 6.183360 CCCGATCAATATATCATGACTTGCAC 60.183 42.308 0.00 0.00 0.00 4.57
5468 6322 5.876460 CCCGATCAATATATCATGACTTGCA 59.124 40.000 0.00 0.00 0.00 4.08
5469 6323 5.220739 GCCCGATCAATATATCATGACTTGC 60.221 44.000 0.00 0.00 0.00 4.01
5470 6324 5.006068 CGCCCGATCAATATATCATGACTTG 59.994 44.000 0.00 0.18 0.00 3.16
5471 6325 5.111989 CGCCCGATCAATATATCATGACTT 58.888 41.667 0.00 0.00 0.00 3.01
5472 6326 4.686972 CGCCCGATCAATATATCATGACT 58.313 43.478 0.00 0.00 0.00 3.41
5473 6327 3.246226 GCGCCCGATCAATATATCATGAC 59.754 47.826 0.00 0.00 0.00 3.06
5474 6328 3.118811 TGCGCCCGATCAATATATCATGA 60.119 43.478 4.18 0.00 0.00 3.07
5475 6329 3.197265 TGCGCCCGATCAATATATCATG 58.803 45.455 4.18 0.00 0.00 3.07
5476 6330 3.541996 TGCGCCCGATCAATATATCAT 57.458 42.857 4.18 0.00 0.00 2.45
5477 6331 3.541996 ATGCGCCCGATCAATATATCA 57.458 42.857 4.18 0.00 0.00 2.15
5478 6332 4.143030 GCATATGCGCCCGATCAATATATC 60.143 45.833 12.82 0.00 0.00 1.63
5479 6333 3.748048 GCATATGCGCCCGATCAATATAT 59.252 43.478 12.82 0.00 0.00 0.86
5480 6334 3.130633 GCATATGCGCCCGATCAATATA 58.869 45.455 12.82 0.00 0.00 0.86
5481 6335 1.942657 GCATATGCGCCCGATCAATAT 59.057 47.619 12.82 0.00 0.00 1.28
5482 6336 1.338579 TGCATATGCGCCCGATCAATA 60.339 47.619 22.21 0.00 45.83 1.90
5483 6337 0.606130 TGCATATGCGCCCGATCAAT 60.606 50.000 22.21 0.00 45.83 2.57
5484 6338 1.227793 TGCATATGCGCCCGATCAA 60.228 52.632 22.21 0.00 45.83 2.57
5485 6339 1.960763 GTGCATATGCGCCCGATCA 60.961 57.895 27.28 2.96 45.15 2.92
5486 6340 2.863153 GTGCATATGCGCCCGATC 59.137 61.111 27.28 6.61 45.15 3.69
5493 6347 6.525280 TGTACTTATGTATACGTGCATATGCG 59.475 38.462 22.21 11.74 45.83 4.73
5494 6348 7.806149 TGTACTTATGTATACGTGCATATGC 57.194 36.000 21.09 21.09 42.50 3.14
5498 6352 8.459635 CCTCTATGTACTTATGTATACGTGCAT 58.540 37.037 7.89 11.41 39.67 3.96
5499 6353 7.662669 TCCTCTATGTACTTATGTATACGTGCA 59.337 37.037 7.89 5.04 33.29 4.57
5500 6354 8.037382 TCCTCTATGTACTTATGTATACGTGC 57.963 38.462 7.89 0.00 0.00 5.34
5501 6355 8.176365 GCTCCTCTATGTACTTATGTATACGTG 58.824 40.741 7.89 0.00 0.00 4.49
5502 6356 7.336427 GGCTCCTCTATGTACTTATGTATACGT 59.664 40.741 2.56 2.56 0.00 3.57
5503 6357 7.336176 TGGCTCCTCTATGTACTTATGTATACG 59.664 40.741 0.00 0.00 0.00 3.06
5504 6358 8.460428 GTGGCTCCTCTATGTACTTATGTATAC 58.540 40.741 0.00 0.00 0.00 1.47
5505 6359 7.336176 CGTGGCTCCTCTATGTACTTATGTATA 59.664 40.741 0.00 0.00 0.00 1.47
5506 6360 6.151312 CGTGGCTCCTCTATGTACTTATGTAT 59.849 42.308 0.00 0.00 0.00 2.29
5507 6361 5.472478 CGTGGCTCCTCTATGTACTTATGTA 59.528 44.000 0.00 0.00 0.00 2.29
5508 6362 4.278669 CGTGGCTCCTCTATGTACTTATGT 59.721 45.833 0.00 0.00 0.00 2.29
5509 6363 4.278669 ACGTGGCTCCTCTATGTACTTATG 59.721 45.833 0.00 0.00 0.00 1.90
5510 6364 4.471548 ACGTGGCTCCTCTATGTACTTAT 58.528 43.478 0.00 0.00 0.00 1.73
5511 6365 3.894759 ACGTGGCTCCTCTATGTACTTA 58.105 45.455 0.00 0.00 0.00 2.24
5512 6366 2.736347 ACGTGGCTCCTCTATGTACTT 58.264 47.619 0.00 0.00 0.00 2.24
5513 6367 2.438800 ACGTGGCTCCTCTATGTACT 57.561 50.000 0.00 0.00 0.00 2.73
5514 6368 3.212685 AGTACGTGGCTCCTCTATGTAC 58.787 50.000 0.00 0.00 44.34 2.90
5515 6369 3.118149 TGAGTACGTGGCTCCTCTATGTA 60.118 47.826 15.99 0.00 32.31 2.29
5516 6370 2.299521 GAGTACGTGGCTCCTCTATGT 58.700 52.381 0.00 0.00 0.00 2.29
5517 6371 2.298610 TGAGTACGTGGCTCCTCTATG 58.701 52.381 15.99 0.00 32.31 2.23
5518 6372 2.688958 GTTGAGTACGTGGCTCCTCTAT 59.311 50.000 15.99 0.00 32.31 1.98
5519 6373 2.089980 GTTGAGTACGTGGCTCCTCTA 58.910 52.381 15.99 1.83 32.31 2.43
5520 6374 0.889306 GTTGAGTACGTGGCTCCTCT 59.111 55.000 15.99 0.00 32.31 3.69
5521 6375 0.889306 AGTTGAGTACGTGGCTCCTC 59.111 55.000 15.99 10.49 32.31 3.71
5522 6376 2.211250 TAGTTGAGTACGTGGCTCCT 57.789 50.000 15.99 10.77 32.31 3.69
5523 6377 3.379372 TGTATAGTTGAGTACGTGGCTCC 59.621 47.826 15.99 5.30 32.31 4.70
5524 6378 4.627611 TGTATAGTTGAGTACGTGGCTC 57.372 45.455 13.02 13.02 0.00 4.70
5525 6379 5.589192 GATTGTATAGTTGAGTACGTGGCT 58.411 41.667 0.00 0.00 0.00 4.75
5526 6380 4.440103 CGATTGTATAGTTGAGTACGTGGC 59.560 45.833 0.00 0.00 0.00 5.01
5527 6381 4.974275 CCGATTGTATAGTTGAGTACGTGG 59.026 45.833 0.00 0.00 0.00 4.94
5528 6382 4.974275 CCCGATTGTATAGTTGAGTACGTG 59.026 45.833 0.00 0.00 0.00 4.49
5529 6383 4.498682 GCCCGATTGTATAGTTGAGTACGT 60.499 45.833 0.00 0.00 0.00 3.57
5530 6384 3.979495 GCCCGATTGTATAGTTGAGTACG 59.021 47.826 0.00 0.00 0.00 3.67
5531 6385 3.979495 CGCCCGATTGTATAGTTGAGTAC 59.021 47.826 0.00 0.00 0.00 2.73
5532 6386 3.551454 GCGCCCGATTGTATAGTTGAGTA 60.551 47.826 0.00 0.00 0.00 2.59
5533 6387 2.802057 GCGCCCGATTGTATAGTTGAGT 60.802 50.000 0.00 0.00 0.00 3.41
5534 6388 1.792949 GCGCCCGATTGTATAGTTGAG 59.207 52.381 0.00 0.00 0.00 3.02
5535 6389 1.137282 TGCGCCCGATTGTATAGTTGA 59.863 47.619 4.18 0.00 0.00 3.18
5536 6390 1.577468 TGCGCCCGATTGTATAGTTG 58.423 50.000 4.18 0.00 0.00 3.16
5537 6391 2.543777 ATGCGCCCGATTGTATAGTT 57.456 45.000 4.18 0.00 0.00 2.24
5538 6392 3.521560 CATATGCGCCCGATTGTATAGT 58.478 45.455 4.18 0.00 0.00 2.12
5539 6393 2.285220 GCATATGCGCCCGATTGTATAG 59.715 50.000 12.82 0.00 0.00 1.31
5540 6394 2.276201 GCATATGCGCCCGATTGTATA 58.724 47.619 12.82 0.00 0.00 1.47
5541 6395 1.086696 GCATATGCGCCCGATTGTAT 58.913 50.000 12.82 0.00 0.00 2.29
5542 6396 0.250081 TGCATATGCGCCCGATTGTA 60.250 50.000 22.21 0.00 45.83 2.41
5543 6397 1.525765 TGCATATGCGCCCGATTGT 60.526 52.632 22.21 0.00 45.83 2.71
5544 6398 1.081906 GTGCATATGCGCCCGATTG 60.082 57.895 27.28 0.00 45.15 2.67
5545 6399 3.343972 GTGCATATGCGCCCGATT 58.656 55.556 27.28 0.00 45.15 3.34
5552 6406 6.525280 TGTACTTATGTATACGTGCATATGCG 59.475 38.462 22.21 11.74 45.83 4.73
5568 6423 4.278669 ACGTGGCTCCTCTATGTACTTATG 59.721 45.833 0.00 0.00 0.00 1.90
5592 6447 5.590818 TCCTCCTTCCTTGTATAGTTGAGT 58.409 41.667 0.00 0.00 0.00 3.41
5705 6565 1.477295 GTCCTTCGAGGAGTTCCGATT 59.523 52.381 0.00 0.00 46.90 3.34
5764 6624 2.519377 TACATATTCCCACTTCCGCG 57.481 50.000 0.00 0.00 0.00 6.46
5765 6625 3.311596 GTGTTACATATTCCCACTTCCGC 59.688 47.826 0.00 0.00 0.00 5.54
5766 6626 3.554324 CGTGTTACATATTCCCACTTCCG 59.446 47.826 0.00 0.00 0.00 4.30
5778 6638 2.195096 GCCATGTACGCGTGTTACATA 58.805 47.619 24.59 0.00 33.58 2.29
5852 6712 2.073056 CAAACCGGTTCATCATCGACA 58.927 47.619 22.53 0.00 0.00 4.35
5869 6729 6.890268 TCTTAGCTGTCTACCTCTACATCAAA 59.110 38.462 0.00 0.00 0.00 2.69
5874 6734 4.190001 CGTCTTAGCTGTCTACCTCTACA 58.810 47.826 0.00 0.00 0.00 2.74
5876 6736 4.484537 ACGTCTTAGCTGTCTACCTCTA 57.515 45.455 0.00 0.00 0.00 2.43
5928 6788 1.610363 TCACGAGCTCTTGTCTCTGT 58.390 50.000 18.68 0.54 0.00 3.41
5930 6790 2.509569 TCTTCACGAGCTCTTGTCTCT 58.490 47.619 18.68 0.00 0.00 3.10
5965 6825 2.717580 ACGTCGTTGCAGAGTATTCA 57.282 45.000 0.00 0.00 0.00 2.57
5969 6829 1.267533 TGCTAACGTCGTTGCAGAGTA 59.732 47.619 20.62 6.59 30.70 2.59
6044 6904 1.924731 TCACTCATCTCCTGACCGTT 58.075 50.000 0.00 0.00 0.00 4.44
6049 6909 1.126488 GGCCATCACTCATCTCCTGA 58.874 55.000 0.00 0.00 0.00 3.86
6085 6946 1.371267 CGCGTCGTTCCACTTCTGA 60.371 57.895 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.