Multiple sequence alignment - TraesCS6A01G273800

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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 TraesCS6A01G273800 chr6A 100.000 4323 0 0 1 4323 499963316 499958994 0.000000e+00 7984.0
1 TraesCS6A01G273800 chr6A 100.000 1930 0 0 4623 6552 499958694 499956765 0.000000e+00 3565.0
2 TraesCS6A01G273800 chr6A 93.911 542 33 0 21 562 499994573 499994032 0.000000e+00 819.0
3 TraesCS6A01G273800 chr6D 94.604 2650 98 22 1702 4323 357586052 357588684 0.000000e+00 4060.0
4 TraesCS6A01G273800 chr6D 88.685 1962 123 57 4623 6551 357588991 357590886 0.000000e+00 2302.0
5 TraesCS6A01G273800 chr6D 95.352 753 27 6 936 1681 357585310 357586061 0.000000e+00 1190.0
6 TraesCS6A01G273800 chr6D 81.971 771 99 15 21 761 357583304 357584064 9.330000e-173 617.0
7 TraesCS6A01G273800 chr6B 94.207 1640 59 7 2710 4323 539190172 539191801 0.000000e+00 2470.0
8 TraesCS6A01G273800 chr6B 89.232 1978 123 30 4635 6551 539192067 539194015 0.000000e+00 2390.0
9 TraesCS6A01G273800 chr6B 95.843 890 32 5 1702 2589 539189292 539190178 0.000000e+00 1434.0
10 TraesCS6A01G273800 chr6B 93.634 754 26 7 936 1682 539188564 539189302 0.000000e+00 1107.0
11 TraesCS6A01G273800 chr6B 84.335 549 55 12 245 767 539184138 539184681 5.860000e-140 508.0
12 TraesCS6A01G273800 chr6B 88.793 116 10 2 824 938 539186241 539186354 8.860000e-29 139.0
13 TraesCS6A01G273800 chr1A 84.245 768 88 17 21 763 554911396 554912155 0.000000e+00 717.0
14 TraesCS6A01G273800 chr2B 88.085 235 25 3 4645 4878 798335032 798335264 6.470000e-70 276.0
15 TraesCS6A01G273800 chr2B 82.041 245 42 2 5107 5351 798335259 798335501 2.390000e-49 207.0
16 TraesCS6A01G273800 chr5D 88.106 227 20 3 4680 4900 54776323 54776548 5.040000e-66 263.0
17 TraesCS6A01G273800 chr5D 85.714 168 17 2 28 188 80194028 80193861 3.140000e-38 171.0
18 TraesCS6A01G273800 chr4B 79.310 377 63 13 21 395 487663414 487663051 3.920000e-62 250.0
19 TraesCS6A01G273800 chr5B 100.000 28 0 0 3671 3698 307397466 307397439 1.200000e-02 52.8


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 TraesCS6A01G273800 chr6A 499956765 499963316 6551 True 5774.500000 7984 100.000000 1 6552 2 chr6A.!!$R2 6551
1 TraesCS6A01G273800 chr6A 499994032 499994573 541 True 819.000000 819 93.911000 21 562 1 chr6A.!!$R1 541
2 TraesCS6A01G273800 chr6D 357583304 357590886 7582 False 2042.250000 4060 90.153000 21 6551 4 chr6D.!!$F1 6530
3 TraesCS6A01G273800 chr6B 539184138 539194015 9877 False 1341.333333 2470 91.007333 245 6551 6 chr6B.!!$F1 6306
4 TraesCS6A01G273800 chr1A 554911396 554912155 759 False 717.000000 717 84.245000 21 763 1 chr1A.!!$F1 742

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
162 164 0.039165 GCAATTATTGGCGGGCTAGC 60.039 55.0 6.04 6.04 0.00 3.42 F
688 721 0.178995 TCAGCCATGGTTGCACTCAA 60.179 50.0 22.84 2.46 0.00 3.02 F
1498 6271 1.033202 TTATTCGCGGCTTTTCCCCC 61.033 55.0 6.13 0.00 0.00 5.40 F
2272 7047 0.608640 AAGCTGAAAGACGACGGGAT 59.391 50.0 0.00 0.00 34.07 3.85 F
3817 8618 0.035739 GCCTTGTAAACCTGGACGGA 59.964 55.0 0.00 0.00 36.31 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1366 6139 1.833934 CAAACAGCTGGGGCCAAGT 60.834 57.895 19.93 0.00 39.73 3.16 R
1502 6275 2.855963 GACATGGAGCAATTTTCGCATG 59.144 45.455 0.00 0.00 33.37 4.06 R
2996 7774 2.230508 TCGCCAGACAAACCTAGTAGTG 59.769 50.000 0.00 0.00 0.00 2.74 R
4000 8801 1.226030 GGGTACAACGGTGTGAGCAC 61.226 60.000 18.38 5.95 44.53 4.40 R
5621 10485 0.037605 GGGTACTGAGTTGACGTGGG 60.038 60.000 0.00 0.00 0.00 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
25 26 5.744345 CAGACTTAGAACCACGACACATATC 59.256 44.000 0.00 0.00 0.00 1.63
26 27 5.652891 AGACTTAGAACCACGACACATATCT 59.347 40.000 0.00 0.00 0.00 1.98
162 164 0.039165 GCAATTATTGGCGGGCTAGC 60.039 55.000 6.04 6.04 0.00 3.42
182 184 4.899502 AGCGATCCTAATTCCCATAACAG 58.100 43.478 0.00 0.00 0.00 3.16
295 302 7.067737 TGTTGGTTCCTAAGTAAGTTTTCAAGG 59.932 37.037 0.00 0.00 0.00 3.61
297 304 7.348033 TGGTTCCTAAGTAAGTTTTCAAGGAA 58.652 34.615 0.00 0.00 38.87 3.36
321 328 6.421485 AGATGTTGCCAGATCTATCAGTTTT 58.579 36.000 0.00 0.00 31.14 2.43
520 551 9.528018 TTTTCAATTTACTTGGAACATTGAGTC 57.472 29.630 0.00 0.00 39.30 3.36
597 628 1.080569 GCGCCCAACAAACTGATGG 60.081 57.895 0.00 0.00 39.70 3.51
606 637 2.086869 ACAAACTGATGGCTCCATTCG 58.913 47.619 2.53 0.56 36.70 3.34
607 638 2.290260 ACAAACTGATGGCTCCATTCGA 60.290 45.455 2.53 0.00 36.70 3.71
616 647 5.714806 TGATGGCTCCATTCGATGTAGTATA 59.285 40.000 2.53 0.00 36.70 1.47
678 711 2.933906 GCAACAAAATCATCAGCCATGG 59.066 45.455 7.63 7.63 32.64 3.66
688 721 0.178995 TCAGCCATGGTTGCACTCAA 60.179 50.000 22.84 2.46 0.00 3.02
714 747 7.177392 AGGGTATTCTCAAAATCCTTTCAACAG 59.823 37.037 0.00 0.00 0.00 3.16
724 757 1.593196 CTTTCAACAGCCACCGAGAA 58.407 50.000 0.00 0.00 0.00 2.87
725 758 1.946768 CTTTCAACAGCCACCGAGAAA 59.053 47.619 0.00 0.00 0.00 2.52
726 759 2.045561 TTCAACAGCCACCGAGAAAA 57.954 45.000 0.00 0.00 0.00 2.29
727 760 2.045561 TCAACAGCCACCGAGAAAAA 57.954 45.000 0.00 0.00 0.00 1.94
773 1789 4.458256 TCCCAATCTCCCGTAGTGTATA 57.542 45.455 0.00 0.00 0.00 1.47
795 3080 1.636988 CACGGTAGTAGCTTTTCCCG 58.363 55.000 11.55 11.55 41.09 5.14
798 3083 1.796617 CGGTAGTAGCTTTTCCCGTCG 60.797 57.143 0.00 0.00 0.00 5.12
843 3395 9.665719 TTTCCTTTTTACTTTTTGCTTGAATCT 57.334 25.926 0.00 0.00 0.00 2.40
844 3396 9.665719 TTCCTTTTTACTTTTTGCTTGAATCTT 57.334 25.926 0.00 0.00 0.00 2.40
876 3428 4.225942 AGATGATATATGGGCCGTCACAAT 59.774 41.667 0.00 0.00 0.00 2.71
877 3429 3.673902 TGATATATGGGCCGTCACAATG 58.326 45.455 0.00 0.00 0.00 2.82
878 3430 2.559698 TATATGGGCCGTCACAATGG 57.440 50.000 0.00 0.00 34.35 3.16
898 3451 4.699637 TGGAAGCGAATATAACCGAATGT 58.300 39.130 0.00 0.00 0.00 2.71
907 3460 3.637911 ATAACCGAATGTTACCTGGCA 57.362 42.857 0.00 0.00 42.06 4.92
980 5749 1.508256 CCGTCCTCCTCCCCTATTTT 58.492 55.000 0.00 0.00 0.00 1.82
1366 6139 2.520458 CCCCCTGCTGTTGTTGGA 59.480 61.111 0.00 0.00 0.00 3.53
1374 6147 2.041153 CTGTTGTTGGACTTGGCCC 58.959 57.895 0.00 0.00 0.00 5.80
1481 6254 5.699458 GGAAAGTCAAGGAAATCGTGAGTTA 59.301 40.000 0.00 0.00 43.37 2.24
1498 6271 1.033202 TTATTCGCGGCTTTTCCCCC 61.033 55.000 6.13 0.00 0.00 5.40
1502 6275 2.970639 GCGGCTTTTCCCCCTTTC 59.029 61.111 0.00 0.00 0.00 2.62
1518 6291 2.925563 CCTTTCATGCGAAAATTGCTCC 59.074 45.455 0.00 0.00 40.57 4.70
1526 6299 2.095059 GCGAAAATTGCTCCATGTCACT 60.095 45.455 0.00 0.00 0.00 3.41
1528 6301 3.189080 CGAAAATTGCTCCATGTCACTCA 59.811 43.478 0.00 0.00 0.00 3.41
1545 6318 5.064452 GTCACTCAATTCCAATGCTAGACTG 59.936 44.000 0.00 0.00 0.00 3.51
1594 6367 6.127786 GCCTTTTGAGCATTCTCTTTCTGTAT 60.128 38.462 0.00 0.00 40.03 2.29
1605 6378 9.956720 CATTCTCTTTCTGTATTGTTTGAGTTT 57.043 29.630 0.00 0.00 0.00 2.66
1623 6396 4.130118 AGTTTGCGACTTCTCTGAAATGT 58.870 39.130 0.00 0.00 33.92 2.71
1633 6406 4.679373 TCTCTGAAATGTAGAGCATCCC 57.321 45.455 0.00 0.00 41.11 3.85
1639 6412 3.845781 AATGTAGAGCATCCCATTCGT 57.154 42.857 0.00 0.00 33.49 3.85
1681 6454 1.824230 AGCTTCCTGCAACAACAACAA 59.176 42.857 0.00 0.00 45.94 2.83
1682 6455 1.926510 GCTTCCTGCAACAACAACAAC 59.073 47.619 0.00 0.00 42.31 3.32
1683 6456 2.673610 GCTTCCTGCAACAACAACAACA 60.674 45.455 0.00 0.00 42.31 3.33
1684 6457 3.583806 CTTCCTGCAACAACAACAACAA 58.416 40.909 0.00 0.00 0.00 2.83
1685 6458 3.229276 TCCTGCAACAACAACAACAAG 57.771 42.857 0.00 0.00 0.00 3.16
1686 6459 2.822561 TCCTGCAACAACAACAACAAGA 59.177 40.909 0.00 0.00 0.00 3.02
1687 6460 2.923020 CCTGCAACAACAACAACAAGAC 59.077 45.455 0.00 0.00 0.00 3.01
1688 6461 2.923020 CTGCAACAACAACAACAAGACC 59.077 45.455 0.00 0.00 0.00 3.85
1689 6462 2.560542 TGCAACAACAACAACAAGACCT 59.439 40.909 0.00 0.00 0.00 3.85
1690 6463 3.759086 TGCAACAACAACAACAAGACCTA 59.241 39.130 0.00 0.00 0.00 3.08
1691 6464 4.102649 GCAACAACAACAACAAGACCTAC 58.897 43.478 0.00 0.00 0.00 3.18
1692 6465 4.380023 GCAACAACAACAACAAGACCTACA 60.380 41.667 0.00 0.00 0.00 2.74
1693 6466 4.957759 ACAACAACAACAAGACCTACAC 57.042 40.909 0.00 0.00 0.00 2.90
1694 6467 3.372822 ACAACAACAACAAGACCTACACG 59.627 43.478 0.00 0.00 0.00 4.49
1695 6468 1.937899 ACAACAACAAGACCTACACGC 59.062 47.619 0.00 0.00 0.00 5.34
1696 6469 1.937223 CAACAACAAGACCTACACGCA 59.063 47.619 0.00 0.00 0.00 5.24
1697 6470 2.319136 ACAACAAGACCTACACGCAA 57.681 45.000 0.00 0.00 0.00 4.85
1698 6471 2.634600 ACAACAAGACCTACACGCAAA 58.365 42.857 0.00 0.00 0.00 3.68
1699 6472 3.011119 ACAACAAGACCTACACGCAAAA 58.989 40.909 0.00 0.00 0.00 2.44
1700 6473 3.440872 ACAACAAGACCTACACGCAAAAA 59.559 39.130 0.00 0.00 0.00 1.94
1745 6518 4.457257 AGAAAGCAGAGCTGTTAACATTCC 59.543 41.667 9.13 1.01 39.62 3.01
1830 6603 2.356069 TCACATCCTCGATCTTCGTGAG 59.644 50.000 0.97 0.00 41.35 3.51
1941 6714 1.302366 TGATGATGCATTGAGCCGTC 58.698 50.000 0.00 0.00 44.83 4.79
2100 6875 6.153000 ACGAGGATGAGTTAGCTAAGAAAAGA 59.847 38.462 6.38 0.00 0.00 2.52
2128 6903 4.790790 AGGTATTGAATCTTCCACCCTCTT 59.209 41.667 0.00 0.00 0.00 2.85
2206 6981 6.013379 TGCATTGGGTTTATAAGGAGAACAA 58.987 36.000 0.00 0.00 0.00 2.83
2207 6982 6.667414 TGCATTGGGTTTATAAGGAGAACAAT 59.333 34.615 0.00 0.00 0.00 2.71
2208 6983 7.180051 TGCATTGGGTTTATAAGGAGAACAATT 59.820 33.333 0.00 0.00 0.00 2.32
2272 7047 0.608640 AAGCTGAAAGACGACGGGAT 59.391 50.000 0.00 0.00 34.07 3.85
2395 7170 6.208599 TGAAAGAAAGGGCTAAAAATGATCGT 59.791 34.615 0.00 0.00 0.00 3.73
2467 7242 5.942236 TGAAGCAAAGCTGACAGAAGATTAT 59.058 36.000 6.65 0.00 39.62 1.28
2596 7371 9.298774 ACTCTGCTTAACTATTGTCGTTTATAC 57.701 33.333 0.00 0.00 0.00 1.47
2647 7422 9.504708 TGGTCAATCTTGCAATTTTCAATTATT 57.495 25.926 0.00 0.00 0.00 1.40
2662 7437 9.695526 TTTTCAATTATTTGATCAGTGTCCTTG 57.304 29.630 0.00 0.00 41.38 3.61
2664 7439 9.513906 TTCAATTATTTGATCAGTGTCCTTGTA 57.486 29.630 0.00 0.00 41.38 2.41
2680 7455 8.141268 GTGTCCTTGTATTGAAATTTTCTTCCA 58.859 33.333 10.33 0.35 0.00 3.53
2682 7457 9.196552 GTCCTTGTATTGAAATTTTCTTCCAAG 57.803 33.333 10.33 13.96 0.00 3.61
2729 7504 6.071784 TCACTTAGCGTCCTGTTTCTACATTA 60.072 38.462 0.00 0.00 32.86 1.90
2791 7566 1.347707 TGGTCTGTTTTCAGCGGAGAT 59.652 47.619 0.00 0.00 46.59 2.75
2836 7611 8.454494 AGATTTCAGATATGGATTGGGATTTCT 58.546 33.333 0.00 0.00 0.00 2.52
2996 7774 2.003301 GCACTAGCTGCTGGAGTTTAC 58.997 52.381 20.35 1.24 43.33 2.01
3316 8094 4.610122 GCAAATACGAAATCTCATGATGCG 59.390 41.667 0.00 0.00 37.34 4.73
3495 8273 7.040755 TGTTGTGTATATTCAAAACCTGACTGG 60.041 37.037 11.59 0.00 35.40 4.00
3500 8278 2.051334 TCAAAACCTGACTGGGTGTG 57.949 50.000 0.00 0.00 39.85 3.82
3560 8338 5.878406 TTTACCAAAGAAATCTTGGCCAA 57.122 34.783 19.25 19.25 36.12 4.52
3572 8350 1.614903 CTTGGCCAATCAACTTCAGCA 59.385 47.619 20.85 0.00 0.00 4.41
3621 8399 7.944061 TGTGAAGACATGTTTTCAGATTGAAT 58.056 30.769 27.00 0.00 36.11 2.57
3651 8429 1.545582 GGCTTACAAGGCTCATTTGCA 59.454 47.619 8.19 0.00 46.98 4.08
3680 8481 7.990541 TGAACAAGAAAAACATCAACATCTG 57.009 32.000 0.00 0.00 0.00 2.90
3694 8495 5.069318 TCAACATCTGCAGTACCAAATCAA 58.931 37.500 14.67 0.00 0.00 2.57
3745 8546 8.208718 TGTATTTATATGAACTTGTGGCTGTC 57.791 34.615 0.00 0.00 0.00 3.51
3781 8582 8.472683 TTGGTAAATTTGAACAAGTTTGACTG 57.527 30.769 14.90 0.00 33.31 3.51
3816 8617 0.036306 AGCCTTGTAAACCTGGACGG 59.964 55.000 0.00 0.00 39.35 4.79
3817 8618 0.035739 GCCTTGTAAACCTGGACGGA 59.964 55.000 0.00 0.00 36.31 4.69
3818 8619 1.944430 GCCTTGTAAACCTGGACGGAG 60.944 57.143 0.00 0.00 36.31 4.63
3819 8620 1.621814 CCTTGTAAACCTGGACGGAGA 59.378 52.381 0.00 0.00 36.31 3.71
3914 8715 5.860611 TCGATGAAGTTCCCTTTTCTAACA 58.139 37.500 0.00 0.00 0.00 2.41
3928 8729 7.159372 CCTTTTCTAACACTAGGAGCTGTTAA 58.841 38.462 0.00 0.00 33.50 2.01
4010 8811 5.627499 TTGAAGATATTTGTGCTCACACC 57.373 39.130 1.67 0.00 46.86 4.16
4053 8854 5.278808 CCTTGATTATGCAATGATGACAGGG 60.279 44.000 0.00 0.00 0.00 4.45
4089 8890 4.503991 CCATTAGGATCAGAGGCTGTTACC 60.504 50.000 0.00 0.00 36.89 2.85
4134 8935 3.499745 GGGCTAAGAAGTCCCAAAAAGGA 60.500 47.826 0.00 0.00 42.14 3.36
4709 9530 3.134804 ACAGTACCCATATGAGTGAAGCC 59.865 47.826 3.65 0.00 0.00 4.35
4766 9587 2.290896 TGGTGACCAATCAAGGGACATC 60.291 50.000 0.00 0.00 36.31 3.06
4906 9727 7.611213 AGTTATACTTGAACAACTACATGCC 57.389 36.000 0.00 0.00 29.67 4.40
4913 9734 2.969821 ACAACTACATGCCCAAGGAA 57.030 45.000 0.00 0.00 0.00 3.36
4923 9744 0.813821 GCCCAAGGAAGATGACAAGC 59.186 55.000 0.00 0.00 0.00 4.01
4970 9791 2.301577 AGCAGCCGAAGAAGATACAC 57.698 50.000 0.00 0.00 0.00 2.90
4997 9818 4.560311 CGGGACATAAGTGATGATCTCCTG 60.560 50.000 0.00 0.00 39.06 3.86
5003 9824 3.634218 AGTGATGATCTCCTGAGGGAT 57.366 47.619 0.00 0.00 41.36 3.85
5115 9936 1.098050 ATTGAATCCGCAGCTGTTCC 58.902 50.000 16.64 0.00 0.00 3.62
5140 9961 2.233922 AGGTGGTTGAGTACAAGATCGG 59.766 50.000 0.00 0.00 36.64 4.18
5147 9968 0.179134 AGTACAAGATCGGCGAGCAC 60.179 55.000 27.88 16.13 0.00 4.40
5209 10030 3.560068 GCGGTGTTGTAGATTTATCTGGG 59.440 47.826 2.51 0.00 37.76 4.45
5253 10074 2.038164 TGAGGCATGGCACTGAGATATC 59.962 50.000 22.64 7.21 0.00 1.63
5283 10104 2.697751 CCACCTACTTCTGATAGCAGCT 59.302 50.000 2.24 0.00 42.01 4.24
5355 10177 4.382754 GGTTCTGTCAATTTTGTTCGATGC 59.617 41.667 0.00 0.00 0.00 3.91
5362 10184 3.822594 ATTTTGTTCGATGCGTGCTTA 57.177 38.095 0.00 0.00 0.00 3.09
5385 10207 1.203994 TGTGGCGAACTTAGGTAGAGC 59.796 52.381 0.00 0.00 0.00 4.09
5405 10244 2.356125 GCATGTCCTTCAGGCCTTCTAA 60.356 50.000 0.00 0.00 46.42 2.10
5471 10310 3.243410 TCTGTACGCTTGTTTTACACACG 59.757 43.478 0.00 0.00 33.98 4.49
5477 10316 3.838550 CGCTTGTTTTACACACGCTATTC 59.161 43.478 0.00 0.00 46.24 1.75
5494 10333 5.583854 CGCTATTCAAGATGAGGGGATAATG 59.416 44.000 0.00 0.00 0.00 1.90
5511 10350 6.199393 GGATAATGTTTCGGTGCTAATTGTC 58.801 40.000 0.00 0.00 0.00 3.18
5519 10358 4.233789 TCGGTGCTAATTGTCAAAATTGC 58.766 39.130 0.00 0.00 0.00 3.56
5592 10452 4.810191 AGGTGTCTCCAGTTCATTAGTC 57.190 45.455 0.00 0.00 39.02 2.59
5598 10458 7.309867 GGTGTCTCCAGTTCATTAGTCTCTTTA 60.310 40.741 0.00 0.00 35.97 1.85
5614 10478 8.973835 AGTCTCTTTAATCAGAAACTAACTCG 57.026 34.615 0.00 0.00 0.00 4.18
5618 10482 9.574458 CTCTTTAATCAGAAACTAACTCGATGA 57.426 33.333 0.00 0.00 0.00 2.92
5621 10485 3.499048 TCAGAAACTAACTCGATGACGC 58.501 45.455 0.00 0.00 39.58 5.19
5622 10486 2.599082 CAGAAACTAACTCGATGACGCC 59.401 50.000 0.00 0.00 39.58 5.68
5625 10489 0.172803 ACTAACTCGATGACGCCCAC 59.827 55.000 0.00 0.00 39.58 4.61
5644 10510 1.612463 ACGTCAACTCAGTACCCAGAC 59.388 52.381 0.00 0.00 0.00 3.51
5654 10520 0.537653 GTACCCAGACTTCTCCTGCC 59.462 60.000 0.00 0.00 0.00 4.85
5665 10531 2.691409 TCTCCTGCCCAAGATTTACG 57.309 50.000 0.00 0.00 0.00 3.18
5700 10569 4.554586 CGTGTGTGATCAACATGTAATTGC 59.445 41.667 16.03 0.00 41.97 3.56
5726 10595 2.094762 AACGGCTGTATGGAACTGAC 57.905 50.000 0.00 0.00 0.00 3.51
5765 10634 1.640917 GGAGGGGTACAGAAGACACA 58.359 55.000 0.00 0.00 0.00 3.72
5801 10670 4.512914 GGTCCCCCAGCATCAGCC 62.513 72.222 0.00 0.00 43.56 4.85
5808 10677 0.959553 CCCAGCATCAGCCATCAATC 59.040 55.000 0.00 0.00 43.56 2.67
5811 10680 2.229062 CCAGCATCAGCCATCAATCATC 59.771 50.000 0.00 0.00 43.56 2.92
5817 10686 3.200483 TCAGCCATCAATCATCTTCACG 58.800 45.455 0.00 0.00 0.00 4.35
5863 10732 0.833949 GGTCTCATCTTCCCACCTCC 59.166 60.000 0.00 0.00 0.00 4.30
5889 10763 4.675063 ACATACCCCCATTGTTCTTCTT 57.325 40.909 0.00 0.00 0.00 2.52
5890 10764 4.600062 ACATACCCCCATTGTTCTTCTTC 58.400 43.478 0.00 0.00 0.00 2.87
5891 10765 2.604912 ACCCCCATTGTTCTTCTTCC 57.395 50.000 0.00 0.00 0.00 3.46
5896 10770 2.621668 CCCATTGTTCTTCTTCCCCTCC 60.622 54.545 0.00 0.00 0.00 4.30
5906 10780 3.551496 TTCCCCTCCAGCAACAGCG 62.551 63.158 0.00 0.00 0.00 5.18
5910 10789 2.974148 CTCCAGCAACAGCGCACA 60.974 61.111 11.47 0.00 0.00 4.57
5946 10825 5.188163 TCCGTAAATCTCATCTGTAACCCAA 59.812 40.000 0.00 0.00 0.00 4.12
5957 10836 1.182667 GTAACCCAACCATCAAGGCC 58.817 55.000 0.00 0.00 43.14 5.19
6025 10904 0.389391 AGTTCCACCAGTCACTGTCG 59.611 55.000 3.56 0.00 0.00 4.35
6054 10933 1.019805 GCACGACCTGCTTAACCTCC 61.020 60.000 0.00 0.00 43.33 4.30
6065 10944 1.479730 CTTAACCTCCCCCTACGACAC 59.520 57.143 0.00 0.00 0.00 3.67
6066 10945 0.324645 TAACCTCCCCCTACGACACC 60.325 60.000 0.00 0.00 0.00 4.16
6067 10946 2.038329 CCTCCCCCTACGACACCA 59.962 66.667 0.00 0.00 0.00 4.17
6068 10947 1.382695 CCTCCCCCTACGACACCAT 60.383 63.158 0.00 0.00 0.00 3.55
6072 10951 2.367202 CCCCTACGACACCATGCCT 61.367 63.158 0.00 0.00 0.00 4.75
6084 10963 0.963962 CCATGCCTTGCCACCATATC 59.036 55.000 0.00 0.00 0.00 1.63
6105 10984 8.834465 CATATCAATTTTCTGTAGGTTCCAGAG 58.166 37.037 0.00 0.00 39.91 3.35
6116 10995 3.329542 TTCCAGAGCCGCATCACCC 62.330 63.158 0.00 0.00 0.00 4.61
6120 10999 4.783621 GAGCCGCATCACCCAGCA 62.784 66.667 0.00 0.00 0.00 4.41
6124 11003 1.750018 CCGCATCACCCAGCATTCA 60.750 57.895 0.00 0.00 0.00 2.57
6137 11016 2.129823 GCATTCATGCGGGAATTCAG 57.870 50.000 7.93 1.72 44.67 3.02
6139 11018 1.035139 ATTCATGCGGGAATTCAGCC 58.965 50.000 18.43 6.67 33.85 4.85
6141 11020 1.454479 CATGCGGGAATTCAGCCCT 60.454 57.895 18.43 6.97 43.72 5.19
6142 11021 1.152881 ATGCGGGAATTCAGCCCTC 60.153 57.895 18.43 3.69 43.72 4.30
6177 11056 5.128992 TCCCTTCCAAAATACGCTTTTTC 57.871 39.130 0.00 0.00 0.00 2.29
6178 11057 4.830600 TCCCTTCCAAAATACGCTTTTTCT 59.169 37.500 0.00 0.00 0.00 2.52
6179 11058 5.303333 TCCCTTCCAAAATACGCTTTTTCTT 59.697 36.000 0.00 0.00 0.00 2.52
6200 11079 5.928839 TCTTCTTCTTCTTCTGAAATGTCCG 59.071 40.000 0.00 0.00 0.00 4.79
6203 11082 6.288294 TCTTCTTCTTCTGAAATGTCCGAAA 58.712 36.000 0.00 0.00 0.00 3.46
6218 11097 0.764226 CGAAAGACGCTTGCAAAACG 59.236 50.000 17.30 17.30 34.51 3.60
6259 11138 1.124477 GGACTATGGGGGAGGCAGAG 61.124 65.000 0.00 0.00 0.00 3.35
6265 11144 2.066999 GGGGGAGGCAGAGGTACAG 61.067 68.421 0.00 0.00 0.00 2.74
6270 11149 2.586792 GGCAGAGGTACAGCCCAG 59.413 66.667 6.61 0.00 43.95 4.45
6271 11150 2.124942 GCAGAGGTACAGCCCAGC 60.125 66.667 0.00 0.00 38.26 4.85
6272 11151 2.959484 GCAGAGGTACAGCCCAGCA 61.959 63.158 0.00 0.00 38.26 4.41
6273 11152 1.910722 CAGAGGTACAGCCCAGCAT 59.089 57.895 0.00 0.00 38.26 3.79
6274 11153 1.123077 CAGAGGTACAGCCCAGCATA 58.877 55.000 0.00 0.00 38.26 3.14
6288 11170 3.128764 CCCAGCATATGCATCATCATCAC 59.871 47.826 28.62 0.00 45.16 3.06
6345 11232 1.268692 CGGGATGAAATGTCATTGCCG 60.269 52.381 11.69 11.69 44.83 5.69
6346 11233 1.067516 GGGATGAAATGTCATTGCCGG 59.932 52.381 0.00 0.00 44.83 6.13
6360 11247 1.064134 GCCGGAATCGCACCAAATC 59.936 57.895 5.05 0.00 34.56 2.17
6379 11266 2.441532 CAGGGCTGGATGGGCTTG 60.442 66.667 0.00 0.00 33.25 4.01
6409 11296 3.509575 AGCCTTCAATTTTGCCGACAATA 59.490 39.130 0.00 0.00 35.21 1.90
6449 11336 2.283101 GCTGCCATCCACCCAACA 60.283 61.111 0.00 0.00 0.00 3.33
6450 11337 2.639327 GCTGCCATCCACCCAACAC 61.639 63.158 0.00 0.00 0.00 3.32
6451 11338 2.282110 TGCCATCCACCCAACACG 60.282 61.111 0.00 0.00 0.00 4.49
6452 11339 3.747976 GCCATCCACCCAACACGC 61.748 66.667 0.00 0.00 0.00 5.34
6453 11340 2.282110 CCATCCACCCAACACGCA 60.282 61.111 0.00 0.00 0.00 5.24
6459 11346 2.112198 CACCCAACACGCACACACT 61.112 57.895 0.00 0.00 0.00 3.55
6465 11352 0.391130 AACACGCACACACTCACACT 60.391 50.000 0.00 0.00 0.00 3.55
6485 11372 4.404654 CTCAAAACGCAGGCCGGC 62.405 66.667 21.18 21.18 42.52 6.13
6521 11408 1.998315 CTTTGATCAGCCTCTGACACG 59.002 52.381 0.00 0.00 43.63 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.953648 TGTGTCGTGGTTCTAAGTCTGA 59.046 45.455 0.00 0.00 0.00 3.27
1 2 3.364889 TGTGTCGTGGTTCTAAGTCTG 57.635 47.619 0.00 0.00 0.00 3.51
2 3 5.652891 AGATATGTGTCGTGGTTCTAAGTCT 59.347 40.000 0.00 0.00 0.00 3.24
3 4 5.892568 AGATATGTGTCGTGGTTCTAAGTC 58.107 41.667 0.00 0.00 0.00 3.01
4 5 5.417894 TGAGATATGTGTCGTGGTTCTAAGT 59.582 40.000 0.00 0.00 0.00 2.24
5 6 5.891451 TGAGATATGTGTCGTGGTTCTAAG 58.109 41.667 0.00 0.00 0.00 2.18
6 7 5.907866 TGAGATATGTGTCGTGGTTCTAA 57.092 39.130 0.00 0.00 0.00 2.10
7 8 5.736207 GCATGAGATATGTGTCGTGGTTCTA 60.736 44.000 10.25 0.00 35.70 2.10
8 9 4.686972 CATGAGATATGTGTCGTGGTTCT 58.313 43.478 1.31 0.00 32.52 3.01
9 10 3.246226 GCATGAGATATGTGTCGTGGTTC 59.754 47.826 10.25 0.00 35.70 3.62
10 11 3.198068 GCATGAGATATGTGTCGTGGTT 58.802 45.455 10.25 0.00 35.70 3.67
11 12 2.168313 TGCATGAGATATGTGTCGTGGT 59.832 45.455 10.25 0.00 35.70 4.16
12 13 2.825205 TGCATGAGATATGTGTCGTGG 58.175 47.619 10.25 0.00 35.70 4.94
13 14 4.053295 TGATGCATGAGATATGTGTCGTG 58.947 43.478 2.46 4.64 37.61 4.35
14 15 4.326504 TGATGCATGAGATATGTGTCGT 57.673 40.909 2.46 0.00 0.00 4.34
15 16 4.508861 TGTTGATGCATGAGATATGTGTCG 59.491 41.667 2.46 0.00 0.00 4.35
16 17 5.996669 TGTTGATGCATGAGATATGTGTC 57.003 39.130 2.46 0.00 0.00 3.67
17 18 6.544564 TGAATGTTGATGCATGAGATATGTGT 59.455 34.615 2.46 0.00 0.00 3.72
18 19 6.856426 GTGAATGTTGATGCATGAGATATGTG 59.144 38.462 2.46 0.00 0.00 3.21
19 20 6.771267 AGTGAATGTTGATGCATGAGATATGT 59.229 34.615 2.46 0.00 0.00 2.29
25 26 8.400186 TGTATAAAGTGAATGTTGATGCATGAG 58.600 33.333 2.46 0.00 0.00 2.90
26 27 8.183536 GTGTATAAAGTGAATGTTGATGCATGA 58.816 33.333 2.46 0.00 0.00 3.07
122 124 3.713288 CATTGGCGAGAAATGCAATCAT 58.287 40.909 0.00 0.00 33.53 2.45
162 164 4.899502 AGCTGTTATGGGAATTAGGATCG 58.100 43.478 0.00 0.00 0.00 3.69
168 170 5.667626 AGGAGAGAAGCTGTTATGGGAATTA 59.332 40.000 0.00 0.00 0.00 1.40
182 184 0.250901 TGGTGGCAAAGGAGAGAAGC 60.251 55.000 0.00 0.00 0.00 3.86
597 628 8.194104 AGATCAATATACTACATCGAATGGAGC 58.806 37.037 6.91 0.00 45.43 4.70
648 681 5.170021 TGATGATTTTGTTGCTGGCATAAC 58.830 37.500 7.57 7.57 0.00 1.89
649 682 5.402997 TGATGATTTTGTTGCTGGCATAA 57.597 34.783 0.00 0.00 0.00 1.90
651 684 3.857052 CTGATGATTTTGTTGCTGGCAT 58.143 40.909 0.00 0.00 0.00 4.40
652 685 2.610976 GCTGATGATTTTGTTGCTGGCA 60.611 45.455 0.00 0.00 0.00 4.92
653 686 1.997606 GCTGATGATTTTGTTGCTGGC 59.002 47.619 0.00 0.00 0.00 4.85
654 687 2.028839 TGGCTGATGATTTTGTTGCTGG 60.029 45.455 0.00 0.00 0.00 4.85
655 688 3.306917 TGGCTGATGATTTTGTTGCTG 57.693 42.857 0.00 0.00 0.00 4.41
678 711 3.674997 TGAGAATACCCTTGAGTGCAAC 58.325 45.455 0.00 0.00 0.00 4.17
688 721 7.010160 TGTTGAAAGGATTTTGAGAATACCCT 58.990 34.615 0.00 0.00 39.27 4.34
735 768 8.403292 AGATTGGGATGAGGATATAATCACAT 57.597 34.615 0.00 0.00 33.88 3.21
737 770 7.278875 GGAGATTGGGATGAGGATATAATCAC 58.721 42.308 0.00 0.00 0.00 3.06
809 3125 9.619316 GCAAAAAGTAAAAAGGAAAAACACATT 57.381 25.926 0.00 0.00 0.00 2.71
810 3126 9.008965 AGCAAAAAGTAAAAAGGAAAAACACAT 57.991 25.926 0.00 0.00 0.00 3.21
814 3130 9.885934 TTCAAGCAAAAAGTAAAAAGGAAAAAC 57.114 25.926 0.00 0.00 0.00 2.43
827 3379 6.763135 GGAGGAAAAAGATTCAAGCAAAAAGT 59.237 34.615 0.00 0.00 0.00 2.66
831 3383 5.598005 TCTGGAGGAAAAAGATTCAAGCAAA 59.402 36.000 0.00 0.00 0.00 3.68
843 3395 6.248433 GCCCATATATCATCTGGAGGAAAAA 58.752 40.000 0.00 0.00 31.38 1.94
844 3396 5.281193 GGCCCATATATCATCTGGAGGAAAA 60.281 44.000 0.00 0.00 31.38 2.29
876 3428 4.699637 ACATTCGGTTATATTCGCTTCCA 58.300 39.130 0.00 0.00 0.00 3.53
877 3429 5.668558 AACATTCGGTTATATTCGCTTCC 57.331 39.130 0.00 0.00 38.15 3.46
878 3430 6.423001 AGGTAACATTCGGTTATATTCGCTTC 59.577 38.462 0.00 0.00 43.50 3.86
925 5654 1.977293 GATGGGGGAGAGTGCTGGAC 61.977 65.000 0.00 0.00 0.00 4.02
972 5741 2.289565 GGCGACTGGAGAAAAATAGGG 58.710 52.381 0.00 0.00 0.00 3.53
980 5749 1.511305 CTAAGCGGCGACTGGAGAA 59.489 57.895 12.98 0.00 0.00 2.87
1134 5903 2.509561 GCGGCGGAAGGAGAAGAC 60.510 66.667 9.78 0.00 0.00 3.01
1366 6139 1.833934 CAAACAGCTGGGGCCAAGT 60.834 57.895 19.93 0.00 39.73 3.16
1498 6271 3.577667 TGGAGCAATTTTCGCATGAAAG 58.422 40.909 0.00 0.00 44.46 2.62
1502 6275 2.855963 GACATGGAGCAATTTTCGCATG 59.144 45.455 0.00 0.00 33.37 4.06
1518 6291 4.713824 AGCATTGGAATTGAGTGACATG 57.286 40.909 0.00 0.00 0.00 3.21
1526 6299 4.194640 GAGCAGTCTAGCATTGGAATTGA 58.805 43.478 0.00 0.00 36.85 2.57
1528 6301 3.118629 TCGAGCAGTCTAGCATTGGAATT 60.119 43.478 0.00 0.00 36.85 2.17
1545 6318 6.795593 GCGGATTAGGTAAAATAAATTCGAGC 59.204 38.462 0.00 0.00 33.15 5.03
1594 6367 3.938963 AGAGAAGTCGCAAACTCAAACAA 59.061 39.130 0.00 0.00 37.17 2.83
1605 6378 4.738124 CTCTACATTTCAGAGAAGTCGCA 58.262 43.478 0.00 0.00 41.80 5.10
1623 6396 3.452990 TGGTTAACGAATGGGATGCTCTA 59.547 43.478 0.00 0.00 0.00 2.43
1633 6406 9.781834 TCTAAGCAAATTAATGGTTAACGAATG 57.218 29.630 0.00 0.00 41.27 2.67
1698 6471 4.535526 AGCAGGTCTTGTTGTTGTTTTT 57.464 36.364 0.00 0.00 0.00 1.94
1699 6472 4.535526 AAGCAGGTCTTGTTGTTGTTTT 57.464 36.364 0.00 0.00 32.79 2.43
1700 6473 5.417580 TCTTAAGCAGGTCTTGTTGTTGTTT 59.582 36.000 0.00 0.00 36.25 2.83
1701 6474 4.947388 TCTTAAGCAGGTCTTGTTGTTGTT 59.053 37.500 0.00 0.00 36.25 2.83
1702 6475 4.523083 TCTTAAGCAGGTCTTGTTGTTGT 58.477 39.130 0.00 0.00 36.25 3.32
1703 6476 5.499139 TTCTTAAGCAGGTCTTGTTGTTG 57.501 39.130 0.00 0.00 36.25 3.33
1704 6477 6.136541 CTTTCTTAAGCAGGTCTTGTTGTT 57.863 37.500 0.00 0.00 36.25 2.83
1705 6478 5.757850 CTTTCTTAAGCAGGTCTTGTTGT 57.242 39.130 0.00 0.00 36.25 3.32
1830 6603 3.125316 CCAAATCCGTGAGTCTTTGCTAC 59.875 47.826 0.00 0.00 32.47 3.58
1892 6665 4.908736 ACGCACAGATGAAATTTTATCCG 58.091 39.130 16.88 15.13 0.00 4.18
1959 6732 7.040686 AGGGTCAACACAAAAATATGAGTGTAC 60.041 37.037 0.00 0.00 43.77 2.90
2100 6875 4.706962 GGTGGAAGATTCAATACCTGCTTT 59.293 41.667 0.00 0.00 0.00 3.51
2206 6981 8.752187 AGGTGCTTGATTAAATCATGTGTTAAT 58.248 29.630 12.96 12.96 39.39 1.40
2207 6982 8.121305 AGGTGCTTGATTAAATCATGTGTTAA 57.879 30.769 0.00 0.00 39.39 2.01
2208 6983 7.701539 AGGTGCTTGATTAAATCATGTGTTA 57.298 32.000 0.00 0.00 39.39 2.41
2272 7047 3.138884 TGCATCCTTACAAGTTCAGCA 57.861 42.857 0.00 0.00 0.00 4.41
2395 7170 7.750229 AATAGCATTCTCTTTGTTTGTCTCA 57.250 32.000 0.00 0.00 0.00 3.27
2467 7242 4.889409 AGTTCCACAAGCATTCTTCTTTCA 59.111 37.500 0.00 0.00 0.00 2.69
2564 7339 6.310467 CGACAATAGTTAAGCAGAGTAGCAAA 59.690 38.462 0.00 0.00 36.85 3.68
2571 7346 9.517609 AGTATAAACGACAATAGTTAAGCAGAG 57.482 33.333 0.00 0.00 0.00 3.35
2602 7377 9.787435 ATTGACCAAAGTAGTTATGTGACTTTA 57.213 29.630 0.00 0.00 40.54 1.85
2603 7378 8.691661 ATTGACCAAAGTAGTTATGTGACTTT 57.308 30.769 0.00 0.00 42.65 2.66
2647 7422 8.408043 AATTTCAATACAAGGACACTGATCAA 57.592 30.769 0.00 0.00 0.00 2.57
2692 7467 6.096423 AGGACGCTAAGTGATGTGTAATCTTA 59.904 38.462 0.00 0.00 0.00 2.10
2693 7468 5.105310 AGGACGCTAAGTGATGTGTAATCTT 60.105 40.000 0.00 0.00 0.00 2.40
2729 7504 7.775561 GTGAAATTAGGAAGGAAGACATGGTAT 59.224 37.037 0.00 0.00 0.00 2.73
2791 7566 9.283768 TGAAATCTAAAGCACACATAAGAAAGA 57.716 29.630 0.00 0.00 0.00 2.52
2996 7774 2.230508 TCGCCAGACAAACCTAGTAGTG 59.769 50.000 0.00 0.00 0.00 2.74
3316 8094 2.869233 ACAACATATTGCGGAATGGC 57.131 45.000 12.93 0.00 39.66 4.40
3474 8252 5.943416 CACCCAGTCAGGTTTTGAATATACA 59.057 40.000 0.00 0.00 38.39 2.29
3535 8313 6.836242 TGGCCAAGATTTCTTTGGTAAAATT 58.164 32.000 0.61 0.00 33.11 1.82
3536 8314 6.432403 TGGCCAAGATTTCTTTGGTAAAAT 57.568 33.333 0.61 0.00 33.11 1.82
3537 8315 5.878406 TGGCCAAGATTTCTTTGGTAAAA 57.122 34.783 0.61 0.00 33.11 1.52
3538 8316 5.878406 TTGGCCAAGATTTCTTTGGTAAA 57.122 34.783 16.05 0.00 33.11 2.01
3553 8331 1.702182 TGCTGAAGTTGATTGGCCAA 58.298 45.000 23.00 23.00 0.00 4.52
3560 8338 7.458409 AAACTGACATATTGCTGAAGTTGAT 57.542 32.000 0.00 0.00 31.61 2.57
3621 8399 1.347707 CCTTGTAAGCCCAGACACAGA 59.652 52.381 0.00 0.00 0.00 3.41
3680 8481 8.839310 ATCTAGTGATATTGATTTGGTACTGC 57.161 34.615 0.00 0.00 0.00 4.40
3757 8558 7.831753 TCAGTCAAACTTGTTCAAATTTACCA 58.168 30.769 0.00 0.00 0.00 3.25
3816 8617 2.680312 TGGTTGCTGCATACTCTCTC 57.320 50.000 1.84 0.00 0.00 3.20
3817 8618 3.708631 AGTATGGTTGCTGCATACTCTCT 59.291 43.478 1.84 0.00 37.53 3.10
3818 8619 3.806521 CAGTATGGTTGCTGCATACTCTC 59.193 47.826 1.84 0.00 39.34 3.20
3819 8620 3.801698 CAGTATGGTTGCTGCATACTCT 58.198 45.455 1.84 0.00 39.34 3.24
3914 8715 8.868103 ACTAGTAAAGTTTTAACAGCTCCTAGT 58.132 33.333 0.00 0.00 33.35 2.57
3941 8742 7.554959 TCTCCCTACAAAACAGAAGTATCTT 57.445 36.000 0.00 0.00 32.03 2.40
3942 8743 7.741554 ATCTCCCTACAAAACAGAAGTATCT 57.258 36.000 0.00 0.00 35.88 1.98
4000 8801 1.226030 GGGTACAACGGTGTGAGCAC 61.226 60.000 18.38 5.95 44.53 4.40
4010 8811 3.226884 CCCTGTGAAGGGTACAACG 57.773 57.895 2.38 0.00 44.08 4.10
4053 8854 2.092429 TCCTAATGGTGCAACATCTCCC 60.092 50.000 19.55 0.00 39.98 4.30
4089 8890 5.007430 CCAGTCGAAGATTTCATGGATCTTG 59.993 44.000 21.99 16.05 42.34 3.02
4134 8935 5.187186 AGCCTCATCAATGAAAAGAAGCATT 59.813 36.000 6.93 0.00 36.18 3.56
4264 9078 7.563188 TGGGCAACATAATTATACACCTCAATT 59.437 33.333 0.00 0.00 39.74 2.32
4667 9488 6.694447 ACTGTTACGCCTAGTGAATTAGAAA 58.306 36.000 0.00 0.00 0.00 2.52
4766 9587 1.021202 TGGTTGCAAGGACAAGAACG 58.979 50.000 0.00 0.00 0.00 3.95
4906 9727 1.813513 ACGCTTGTCATCTTCCTTGG 58.186 50.000 0.00 0.00 0.00 3.61
4913 9734 2.613977 CCAAGGAGAACGCTTGTCATCT 60.614 50.000 0.00 0.00 0.00 2.90
4970 9791 3.703286 TCATCACTTATGTCCCGTACG 57.297 47.619 8.69 8.69 36.89 3.67
5115 9936 0.319211 TTGTACTCAACCACCTCGCG 60.319 55.000 0.00 0.00 0.00 5.87
5209 10030 3.565307 TCAATCAGGAATAATGCCACCC 58.435 45.455 0.00 0.00 0.00 4.61
5253 10074 2.697751 CAGAAGTAGGTGGGAGGAGATG 59.302 54.545 0.00 0.00 0.00 2.90
5283 10104 8.058667 TGTCTCTACTGTAATTCGAAACCATA 57.941 34.615 0.00 0.00 0.00 2.74
5355 10177 1.666553 TTCGCCACAGGTAAGCACG 60.667 57.895 0.00 0.00 0.00 5.34
5362 10184 1.549170 CTACCTAAGTTCGCCACAGGT 59.451 52.381 0.00 0.00 42.25 4.00
5433 10272 2.572290 ACAGATTATTACCAAGGCCGC 58.428 47.619 0.00 0.00 0.00 6.53
5471 10310 6.479884 ACATTATCCCCTCATCTTGAATAGC 58.520 40.000 0.00 0.00 0.00 2.97
5477 10316 4.516698 CCGAAACATTATCCCCTCATCTTG 59.483 45.833 0.00 0.00 0.00 3.02
5494 10333 6.580476 CAATTTTGACAATTAGCACCGAAAC 58.420 36.000 0.00 0.00 0.00 2.78
5511 10350 3.492725 CAGTTCAACTGCGCAATTTTG 57.507 42.857 13.05 15.10 39.62 2.44
5538 10377 2.841442 AACCCCAGAGAAGAGAAACG 57.159 50.000 0.00 0.00 0.00 3.60
5592 10452 9.574458 TCATCGAGTTAGTTTCTGATTAAAGAG 57.426 33.333 0.00 0.00 0.00 2.85
5598 10458 4.563184 GCGTCATCGAGTTAGTTTCTGATT 59.437 41.667 0.00 0.00 39.71 2.57
5607 10467 0.866061 CGTGGGCGTCATCGAGTTAG 60.866 60.000 0.00 0.00 39.71 2.34
5621 10485 0.037605 GGGTACTGAGTTGACGTGGG 60.038 60.000 0.00 0.00 0.00 4.61
5622 10486 0.677288 TGGGTACTGAGTTGACGTGG 59.323 55.000 0.00 0.00 0.00 4.94
5625 10489 1.887198 AGTCTGGGTACTGAGTTGACG 59.113 52.381 0.00 0.00 0.00 4.35
5627 10491 3.827302 GAGAAGTCTGGGTACTGAGTTGA 59.173 47.826 0.00 0.00 38.04 3.18
5644 10510 2.939103 CGTAAATCTTGGGCAGGAGAAG 59.061 50.000 0.00 0.00 0.00 2.85
5654 10520 3.441222 GGTTTACCCACCGTAAATCTTGG 59.559 47.826 0.00 0.00 46.11 3.61
5677 10543 4.554586 GCAATTACATGTTGATCACACACG 59.445 41.667 2.30 7.43 38.61 4.49
5684 10550 6.926280 TTCAAACGCAATTACATGTTGATC 57.074 33.333 2.30 0.00 0.00 2.92
5711 10580 3.334583 TCCTTGTCAGTTCCATACAGC 57.665 47.619 0.00 0.00 0.00 4.40
5726 10595 2.423538 CCCCGTAGCTTTCATTTCCTTG 59.576 50.000 0.00 0.00 0.00 3.61
5765 10634 2.596851 ATGCTCCGGTGGCACTCTT 61.597 57.895 22.39 8.18 42.69 2.85
5811 10680 9.916397 GGAAACTACATCATTTATTACGTGAAG 57.084 33.333 0.00 0.00 0.00 3.02
5817 10686 9.712359 GGAAACGGAAACTACATCATTTATTAC 57.288 33.333 0.00 0.00 0.00 1.89
5863 10732 3.202151 AGAACAATGGGGGTATGTACCTG 59.798 47.826 8.97 2.23 45.72 4.00
5889 10763 4.020617 CGCTGTTGCTGGAGGGGA 62.021 66.667 0.00 0.00 36.97 4.81
5896 10770 0.931662 GTTCTTGTGCGCTGTTGCTG 60.932 55.000 9.73 0.00 36.97 4.41
5906 10780 3.027974 ACGGAAGACTAGTTCTTGTGC 57.972 47.619 10.94 0.40 45.24 4.57
5946 10825 2.224305 GCTATAGTTCGGCCTTGATGGT 60.224 50.000 0.00 0.00 38.35 3.55
5957 10836 3.043586 CGCTGTACTTGGCTATAGTTCG 58.956 50.000 0.84 0.00 0.00 3.95
6054 10933 1.910580 AAGGCATGGTGTCGTAGGGG 61.911 60.000 0.00 0.00 0.00 4.79
6065 10944 0.963962 GATATGGTGGCAAGGCATGG 59.036 55.000 0.00 0.00 0.00 3.66
6066 10945 1.694844 TGATATGGTGGCAAGGCATG 58.305 50.000 0.00 0.00 0.00 4.06
6067 10946 2.457813 TTGATATGGTGGCAAGGCAT 57.542 45.000 0.00 0.00 0.00 4.40
6068 10947 2.457813 ATTGATATGGTGGCAAGGCA 57.542 45.000 0.00 0.00 0.00 4.75
6072 10951 5.999205 ACAGAAAATTGATATGGTGGCAA 57.001 34.783 0.00 0.00 0.00 4.52
6084 10963 4.156739 GGCTCTGGAACCTACAGAAAATTG 59.843 45.833 0.00 0.00 43.74 2.32
6105 10984 3.129913 GAATGCTGGGTGATGCGGC 62.130 63.158 0.00 0.00 0.00 6.53
6120 10999 1.035139 GGCTGAATTCCCGCATGAAT 58.965 50.000 15.86 0.00 36.53 2.57
6128 11007 1.153147 GGTCGAGGGCTGAATTCCC 60.153 63.158 2.27 0.00 44.25 3.97
6151 11030 4.514781 AGCGTATTTTGGAAGGGAAAAC 57.485 40.909 0.00 0.00 0.00 2.43
6177 11056 5.928839 TCGGACATTTCAGAAGAAGAAGAAG 59.071 40.000 0.00 0.00 34.71 2.85
6178 11057 5.853936 TCGGACATTTCAGAAGAAGAAGAA 58.146 37.500 0.00 0.00 34.71 2.52
6179 11058 5.468540 TCGGACATTTCAGAAGAAGAAGA 57.531 39.130 0.00 0.00 34.71 2.87
6200 11079 0.498511 GCGTTTTGCAAGCGTCTTTC 59.501 50.000 20.89 6.04 45.45 2.62
6212 11091 1.681264 AGGGGAGTTTCTTGCGTTTTG 59.319 47.619 0.00 0.00 0.00 2.44
6218 11097 3.157087 TGATGAAAGGGGAGTTTCTTGC 58.843 45.455 0.00 0.00 37.34 4.01
6228 11107 2.107204 CCCATAGTCCTGATGAAAGGGG 59.893 54.545 0.00 0.00 37.96 4.79
6259 11138 0.179020 TGCATATGCTGGGCTGTACC 60.179 55.000 27.13 0.00 42.66 3.34
6265 11144 1.541379 TGATGATGCATATGCTGGGC 58.459 50.000 27.13 14.24 42.66 5.36
6270 11149 2.418976 AGCGTGATGATGATGCATATGC 59.581 45.455 21.09 21.09 42.50 3.14
6271 11150 3.181510 CCAGCGTGATGATGATGCATATG 60.182 47.826 0.00 0.00 35.47 1.78
6272 11151 3.007635 CCAGCGTGATGATGATGCATAT 58.992 45.455 0.00 0.00 35.47 1.78
6273 11152 2.419667 CCAGCGTGATGATGATGCATA 58.580 47.619 0.00 0.00 35.47 3.14
6274 11153 1.235724 CCAGCGTGATGATGATGCAT 58.764 50.000 0.00 0.00 35.47 3.96
6345 11232 0.248215 CTGCGATTTGGTGCGATTCC 60.248 55.000 0.00 0.00 0.00 3.01
6346 11233 0.248215 CCTGCGATTTGGTGCGATTC 60.248 55.000 0.00 0.00 0.00 2.52
6379 11266 3.120442 GCAAAATTGAAGGCTTGCATCAC 60.120 43.478 3.46 0.00 42.91 3.06
6409 11296 6.429078 AGCGCAAAGTGAATGATGATATGTAT 59.571 34.615 11.47 0.00 0.00 2.29
6449 11336 0.806102 GTGAGTGTGAGTGTGTGCGT 60.806 55.000 0.00 0.00 0.00 5.24
6450 11337 0.528466 AGTGAGTGTGAGTGTGTGCG 60.528 55.000 0.00 0.00 0.00 5.34
6451 11338 1.212616 GAGTGAGTGTGAGTGTGTGC 58.787 55.000 0.00 0.00 0.00 4.57
6452 11339 2.584492 TGAGTGAGTGTGAGTGTGTG 57.416 50.000 0.00 0.00 0.00 3.82
6453 11340 3.610040 TTTGAGTGAGTGTGAGTGTGT 57.390 42.857 0.00 0.00 0.00 3.72
6459 11346 1.933181 CTGCGTTTTGAGTGAGTGTGA 59.067 47.619 0.00 0.00 0.00 3.58
6465 11352 2.250939 CGGCCTGCGTTTTGAGTGA 61.251 57.895 0.00 0.00 0.00 3.41
6497 11384 0.106819 CAGAGGCTGATCAAAGGGGG 60.107 60.000 0.00 0.00 32.44 5.40
6498 11385 0.914644 TCAGAGGCTGATCAAAGGGG 59.085 55.000 0.00 0.00 35.39 4.79
6512 11399 1.730902 CGGACTGTGCGTGTCAGAG 60.731 63.158 13.79 0.00 41.48 3.35
6521 11408 1.079543 ATGTGAGAGCGGACTGTGC 60.080 57.895 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.