Multiple sequence alignment - TraesCS5D01G106200

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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 TraesCS5D01G106200 chr5D 100.000 3179 0 0 1 3179 119763030 119759852 0.000000e+00 5871.0
1 TraesCS5D01G106200 chr5B 92.279 1878 72 24 874 2701 132616162 132614308 0.000000e+00 2597.0
2 TraesCS5D01G106200 chr5B 94.377 818 30 5 2 818 133006786 133005984 0.000000e+00 1242.0
3 TraesCS5D01G106200 chr5B 91.333 150 9 4 1898 2046 135522995 135522849 5.380000e-48 202.0
4 TraesCS5D01G106200 chr5B 80.800 250 19 11 2950 3179 132614191 132613951 5.450000e-38 169.0
5 TraesCS5D01G106200 chr5A 91.856 1891 81 27 864 2701 130123644 130121774 0.000000e+00 2571.0
6 TraesCS5D01G106200 chr5A 91.090 853 27 18 6 818 130127983 130127140 0.000000e+00 1109.0
7 TraesCS5D01G106200 chr7B 82.536 418 48 15 221 632 211796789 211797187 8.440000e-91 344.0
8 TraesCS5D01G106200 chr7D 81.818 418 51 11 221 632 235578558 235578956 8.500000e-86 327.0
9 TraesCS5D01G106200 chr2A 95.205 146 5 2 2011 2155 181737176 181737320 2.470000e-56 230.0
10 TraesCS5D01G106200 chr3A 93.151 146 8 2 2011 2155 29706255 29706399 2.480000e-51 213.0
11 TraesCS5D01G106200 chr3A 100.000 51 0 0 2105 2155 552410825 552410775 9.390000e-16 95.3
12 TraesCS5D01G106200 chr4D 100.000 32 0 0 2699 2730 30199459 30199490 3.420000e-05 60.2
13 TraesCS5D01G106200 chr1D 100.000 29 0 0 613 641 28831800 28831828 2.000000e-03 54.7


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 TraesCS5D01G106200 chr5D 119759852 119763030 3178 True 5871 5871 100.0000 1 3179 1 chr5D.!!$R1 3178
1 TraesCS5D01G106200 chr5B 132613951 132616162 2211 True 1383 2597 86.5395 874 3179 2 chr5B.!!$R3 2305
2 TraesCS5D01G106200 chr5B 133005984 133006786 802 True 1242 1242 94.3770 2 818 1 chr5B.!!$R1 816
3 TraesCS5D01G106200 chr5A 130121774 130127983 6209 True 1840 2571 91.4730 6 2701 2 chr5A.!!$R1 2695

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
812 864 0.03918 GGGAATCGACAAGGGGGTTT 59.961 55.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2703 6273 0.027194 CATCGTGTGCATAGCAGTGC 59.973 55.0 7.13 7.13 40.08 4.4 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
69 72 6.921486 TCACCACATAAACTAGGAGTACAA 57.079 37.500 0.00 0.00 0.00 2.41
70 73 7.305813 TCACCACATAAACTAGGAGTACAAA 57.694 36.000 0.00 0.00 0.00 2.83
71 74 7.156673 TCACCACATAAACTAGGAGTACAAAC 58.843 38.462 0.00 0.00 0.00 2.93
72 75 7.015877 TCACCACATAAACTAGGAGTACAAACT 59.984 37.037 0.00 0.00 39.21 2.66
161 189 3.052455 TCGTTCTAGCCAAGAATGCAA 57.948 42.857 11.90 0.00 46.67 4.08
171 199 2.356535 CCAAGAATGCAAGCTACTCCCT 60.357 50.000 0.00 0.00 0.00 4.20
206 241 2.664424 CGTTGCCCAGATAAACAACACG 60.664 50.000 0.00 0.00 41.90 4.49
221 263 2.774439 ACACGGTGAATCAACAAAGC 57.226 45.000 16.29 0.00 0.00 3.51
277 319 1.416813 CGAGATGCAACGCCTCTGAC 61.417 60.000 0.00 0.00 33.95 3.51
392 434 0.716108 GTTCCGAGATTGTGTCAGCG 59.284 55.000 0.00 0.00 0.00 5.18
396 438 1.325640 CCGAGATTGTGTCAGCGATTG 59.674 52.381 0.00 0.00 0.00 2.67
431 483 2.363683 CCTGAGAAGGCAAAAGCTAGG 58.636 52.381 0.00 0.00 0.00 3.02
432 484 1.742268 CTGAGAAGGCAAAAGCTAGGC 59.258 52.381 0.00 0.00 0.00 3.93
433 485 1.352352 TGAGAAGGCAAAAGCTAGGCT 59.648 47.619 4.29 4.29 42.56 4.58
434 486 2.571653 TGAGAAGGCAAAAGCTAGGCTA 59.428 45.455 9.68 0.00 38.25 3.93
435 487 3.200825 TGAGAAGGCAAAAGCTAGGCTAT 59.799 43.478 9.68 3.32 38.25 2.97
436 488 4.203226 GAGAAGGCAAAAGCTAGGCTATT 58.797 43.478 9.68 3.47 38.25 1.73
437 489 4.604156 AGAAGGCAAAAGCTAGGCTATTT 58.396 39.130 9.68 0.00 38.25 1.40
675 727 1.227674 CGAGGCCATGGCTAGTTCC 60.228 63.158 34.70 17.88 38.98 3.62
809 861 1.984288 GAGGGGAATCGACAAGGGGG 61.984 65.000 0.00 0.00 0.00 5.40
812 864 0.039180 GGGAATCGACAAGGGGGTTT 59.961 55.000 0.00 0.00 0.00 3.27
949 4461 2.363788 TCGTGTAGTTTGGCTAGCTG 57.636 50.000 15.72 0.00 0.00 4.24
989 4501 5.622180 GAGAACTAACCCCATCCTAAATCC 58.378 45.833 0.00 0.00 0.00 3.01
1666 5193 2.047465 CTCAGCTTGCTCGTGCCT 60.047 61.111 7.05 0.00 38.71 4.75
1780 5307 2.040330 GGACAATGTTGTGCTGCCA 58.960 52.632 9.73 0.00 44.78 4.92
1782 5309 1.202510 GGACAATGTTGTGCTGCCAAA 60.203 47.619 9.73 0.00 44.78 3.28
1822 5349 2.508526 GTGAACCTTGAGGCTGACATT 58.491 47.619 0.00 0.00 39.32 2.71
1825 5352 3.181440 TGAACCTTGAGGCTGACATTCTT 60.181 43.478 0.00 0.00 39.32 2.52
1890 5417 5.796424 ACATCAAAGGCAAATTCTTGAGT 57.204 34.783 0.00 0.00 34.14 3.41
2021 5549 3.010584 GGGGGTGATATAGTTCATGCCAT 59.989 47.826 0.00 0.00 0.00 4.40
2044 5572 6.716934 TTGCCTGTTTCCATGTAAAAGTTA 57.283 33.333 0.00 0.00 0.00 2.24
2166 5695 4.687483 GCTTTTCTGGGACAACAATGAATG 59.313 41.667 0.00 0.00 38.70 2.67
2213 5742 7.514784 TTTGATCATTGCCTGACCTATATTG 57.485 36.000 0.00 0.00 36.48 1.90
2214 5743 6.191657 TGATCATTGCCTGACCTATATTGT 57.808 37.500 0.00 0.00 36.48 2.71
2215 5744 6.604171 TGATCATTGCCTGACCTATATTGTT 58.396 36.000 0.00 0.00 36.48 2.83
2216 5745 7.062322 TGATCATTGCCTGACCTATATTGTTT 58.938 34.615 0.00 0.00 36.48 2.83
2217 5746 6.698008 TCATTGCCTGACCTATATTGTTTG 57.302 37.500 0.00 0.00 0.00 2.93
2218 5747 6.422333 TCATTGCCTGACCTATATTGTTTGA 58.578 36.000 0.00 0.00 0.00 2.69
2219 5748 6.889177 TCATTGCCTGACCTATATTGTTTGAA 59.111 34.615 0.00 0.00 0.00 2.69
2220 5749 6.757897 TTGCCTGACCTATATTGTTTGAAG 57.242 37.500 0.00 0.00 0.00 3.02
2221 5750 5.192927 TGCCTGACCTATATTGTTTGAAGG 58.807 41.667 0.00 0.00 0.00 3.46
2224 5753 6.591935 CCTGACCTATATTGTTTGAAGGCTA 58.408 40.000 0.00 0.00 0.00 3.93
2238 5769 8.202137 TGTTTGAAGGCTAGTACCTGATTATAC 58.798 37.037 0.00 0.00 39.93 1.47
2248 5779 2.158827 ACCTGATTATACGGCATGCACA 60.159 45.455 21.36 3.57 0.00 4.57
2249 5780 2.877786 CCTGATTATACGGCATGCACAA 59.122 45.455 21.36 3.57 0.00 3.33
2335 5883 8.745837 CCTTTGTGTAATTATCGCATGAATTTC 58.254 33.333 0.00 0.00 0.00 2.17
2345 5893 2.479049 CGCATGAATTTCTTCTGCCAGG 60.479 50.000 0.00 0.00 34.65 4.45
2355 5903 7.909485 ATTTCTTCTGCCAGGATGATAATTT 57.091 32.000 0.00 0.00 39.69 1.82
2358 5906 9.425248 TTTCTTCTGCCAGGATGATAATTTAAT 57.575 29.630 0.00 0.00 39.69 1.40
2359 5907 8.627208 TCTTCTGCCAGGATGATAATTTAATC 57.373 34.615 0.00 0.00 39.69 1.75
2360 5908 7.667219 TCTTCTGCCAGGATGATAATTTAATCC 59.333 37.037 0.00 5.88 39.69 3.01
2361 5909 5.939883 TCTGCCAGGATGATAATTTAATCCG 59.060 40.000 0.00 4.53 43.91 4.18
2362 5910 5.630121 TGCCAGGATGATAATTTAATCCGT 58.370 37.500 0.00 0.00 43.91 4.69
2364 5912 7.227873 TGCCAGGATGATAATTTAATCCGTTA 58.772 34.615 0.00 0.00 43.91 3.18
2365 5913 7.174253 TGCCAGGATGATAATTTAATCCGTTAC 59.826 37.037 0.00 2.46 43.91 2.50
2366 5914 7.390718 GCCAGGATGATAATTTAATCCGTTACT 59.609 37.037 0.00 0.00 43.91 2.24
2367 5915 8.936864 CCAGGATGATAATTTAATCCGTTACTC 58.063 37.037 7.65 0.00 43.91 2.59
2368 5916 9.489084 CAGGATGATAATTTAATCCGTTACTCA 57.511 33.333 7.65 0.00 43.91 3.41
2473 6041 9.174166 ACTGGATTATAATGTTGGTCTTTGTAC 57.826 33.333 1.78 0.00 0.00 2.90
2488 6056 9.562408 TGGTCTTTGTACACTTAACATGAAATA 57.438 29.630 0.00 0.00 0.00 1.40
2537 6105 4.082787 TCTCTGAATTTTGCGAATGGAACC 60.083 41.667 0.00 0.00 0.00 3.62
2541 6109 3.959535 ATTTTGCGAATGGAACCATGT 57.040 38.095 7.12 0.00 36.68 3.21
2566 6134 3.252215 TGTTTGGATTAAGTTGCCTCACG 59.748 43.478 0.00 0.00 0.00 4.35
2576 6144 3.139077 AGTTGCCTCACGAACCTTTTAG 58.861 45.455 0.00 0.00 0.00 1.85
2602 6170 4.019950 GGAAACAGGGGCACTAACTAGTAA 60.020 45.833 0.00 0.00 34.13 2.24
2603 6171 4.548451 AACAGGGGCACTAACTAGTAAC 57.452 45.455 0.00 0.00 34.13 2.50
2604 6172 3.787742 ACAGGGGCACTAACTAGTAACT 58.212 45.455 0.00 0.00 34.13 2.24
2605 6173 3.768215 ACAGGGGCACTAACTAGTAACTC 59.232 47.826 0.00 0.00 34.13 3.01
2623 6191 5.983333 AACTCTGGGATGAATGGAACTAT 57.017 39.130 0.00 0.00 0.00 2.12
2633 6201 9.093458 GGGATGAATGGAACTATGGAATTTAAT 57.907 33.333 0.00 0.00 0.00 1.40
2672 6242 0.307760 GGCTTTCGTGTGTGGTGAAG 59.692 55.000 0.00 0.00 0.00 3.02
2677 6247 0.529773 TCGTGTGTGGTGAAGCAGAC 60.530 55.000 3.07 3.07 0.00 3.51
2678 6248 0.809636 CGTGTGTGGTGAAGCAGACA 60.810 55.000 8.24 8.24 0.00 3.41
2686 6256 4.081752 TGTGGTGAAGCAGACAAAACATTT 60.082 37.500 0.00 0.00 0.00 2.32
2701 6271 7.474190 ACAAAACATTTGCAATTTCCTTGAAG 58.526 30.769 0.00 0.00 36.97 3.02
2702 6272 7.336427 ACAAAACATTTGCAATTTCCTTGAAGA 59.664 29.630 0.00 0.00 36.97 2.87
2703 6273 7.486802 AAACATTTGCAATTTCCTTGAAGAG 57.513 32.000 0.00 0.00 36.97 2.85
2704 6274 4.992951 ACATTTGCAATTTCCTTGAAGAGC 59.007 37.500 0.00 0.00 36.97 4.09
2705 6275 4.669206 TTTGCAATTTCCTTGAAGAGCA 57.331 36.364 0.00 0.00 36.97 4.26
2706 6276 3.648339 TGCAATTTCCTTGAAGAGCAC 57.352 42.857 0.00 0.00 36.97 4.40
2707 6277 3.225104 TGCAATTTCCTTGAAGAGCACT 58.775 40.909 0.00 0.00 36.97 4.40
2708 6278 3.005050 TGCAATTTCCTTGAAGAGCACTG 59.995 43.478 0.00 0.00 36.97 3.66
2709 6279 3.572584 CAATTTCCTTGAAGAGCACTGC 58.427 45.455 0.00 0.00 36.97 4.40
2710 6280 2.645838 TTTCCTTGAAGAGCACTGCT 57.354 45.000 2.22 2.22 43.88 4.24
2711 6281 3.769739 TTTCCTTGAAGAGCACTGCTA 57.230 42.857 2.71 0.00 39.88 3.49
2712 6282 3.988976 TTCCTTGAAGAGCACTGCTAT 57.011 42.857 2.71 0.00 39.88 2.97
2713 6283 3.257469 TCCTTGAAGAGCACTGCTATG 57.743 47.619 2.71 0.00 39.88 2.23
2714 6284 1.669779 CCTTGAAGAGCACTGCTATGC 59.330 52.381 2.71 0.00 46.50 3.14
2720 6290 3.874873 GCACTGCTATGCACACGA 58.125 55.556 7.76 0.00 45.39 4.35
2721 6291 2.387309 GCACTGCTATGCACACGAT 58.613 52.632 7.76 0.00 45.39 3.73
2722 6292 0.027194 GCACTGCTATGCACACGATG 59.973 55.000 7.76 0.00 45.39 3.84
2731 6301 4.348081 CACACGATGCATTCACGC 57.652 55.556 0.00 0.00 0.00 5.34
2733 6303 0.790495 CACACGATGCATTCACGCAC 60.790 55.000 0.00 0.00 46.56 5.34
2734 6304 1.578367 CACGATGCATTCACGCACG 60.578 57.895 0.00 0.00 46.56 5.34
2735 6305 1.736282 ACGATGCATTCACGCACGA 60.736 52.632 0.00 0.00 46.56 4.35
2736 6306 1.296145 CGATGCATTCACGCACGAC 60.296 57.895 0.00 0.00 46.56 4.34
2737 6307 1.686566 CGATGCATTCACGCACGACT 61.687 55.000 0.00 0.00 46.56 4.18
2738 6308 0.025513 GATGCATTCACGCACGACTC 59.974 55.000 0.00 0.00 46.56 3.36
2739 6309 1.686566 ATGCATTCACGCACGACTCG 61.687 55.000 0.00 0.00 46.56 4.18
2740 6310 2.391821 CATTCACGCACGACTCGC 59.608 61.111 0.00 0.00 0.00 5.03
2747 6317 4.702826 GCACGACTCGCGCACAAC 62.703 66.667 8.75 0.00 46.04 3.32
2748 6318 3.326981 CACGACTCGCGCACAACA 61.327 61.111 8.75 0.00 46.04 3.33
2749 6319 2.583868 ACGACTCGCGCACAACAA 60.584 55.556 8.75 0.00 46.04 2.83
2750 6320 2.128128 CGACTCGCGCACAACAAC 60.128 61.111 8.75 0.00 0.00 3.32
2751 6321 2.585869 CGACTCGCGCACAACAACT 61.586 57.895 8.75 0.00 0.00 3.16
2752 6322 1.201825 GACTCGCGCACAACAACTC 59.798 57.895 8.75 0.00 0.00 3.01
2753 6323 1.487452 GACTCGCGCACAACAACTCA 61.487 55.000 8.75 0.00 0.00 3.41
2754 6324 1.083401 CTCGCGCACAACAACTCAC 60.083 57.895 8.75 0.00 0.00 3.51
2755 6325 1.761244 CTCGCGCACAACAACTCACA 61.761 55.000 8.75 0.00 0.00 3.58
2756 6326 1.651132 CGCGCACAACAACTCACAC 60.651 57.895 8.75 0.00 0.00 3.82
2757 6327 1.427419 GCGCACAACAACTCACACA 59.573 52.632 0.30 0.00 0.00 3.72
2758 6328 0.861450 GCGCACAACAACTCACACAC 60.861 55.000 0.30 0.00 0.00 3.82
2759 6329 0.445829 CGCACAACAACTCACACACA 59.554 50.000 0.00 0.00 0.00 3.72
2760 6330 1.790123 CGCACAACAACTCACACACAC 60.790 52.381 0.00 0.00 0.00 3.82
2761 6331 1.467374 GCACAACAACTCACACACACC 60.467 52.381 0.00 0.00 0.00 4.16
2762 6332 1.809547 CACAACAACTCACACACACCA 59.190 47.619 0.00 0.00 0.00 4.17
2763 6333 2.423185 CACAACAACTCACACACACCAT 59.577 45.455 0.00 0.00 0.00 3.55
2764 6334 3.088532 ACAACAACTCACACACACCATT 58.911 40.909 0.00 0.00 0.00 3.16
2765 6335 3.119531 ACAACAACTCACACACACCATTG 60.120 43.478 0.00 0.00 0.00 2.82
2766 6336 2.023673 ACAACTCACACACACCATTGG 58.976 47.619 0.00 0.00 0.00 3.16
2767 6337 2.296792 CAACTCACACACACCATTGGA 58.703 47.619 10.37 0.00 0.00 3.53
2768 6338 2.886523 CAACTCACACACACCATTGGAT 59.113 45.455 10.37 0.00 0.00 3.41
2769 6339 3.228188 ACTCACACACACCATTGGATT 57.772 42.857 10.37 0.00 0.00 3.01
2770 6340 2.886523 ACTCACACACACCATTGGATTG 59.113 45.455 10.37 8.14 0.00 2.67
2771 6341 1.612950 TCACACACACCATTGGATTGC 59.387 47.619 10.37 0.00 0.00 3.56
2772 6342 1.614903 CACACACACCATTGGATTGCT 59.385 47.619 10.37 0.00 0.00 3.91
2773 6343 2.036217 CACACACACCATTGGATTGCTT 59.964 45.455 10.37 0.00 0.00 3.91
2774 6344 2.297033 ACACACACCATTGGATTGCTTC 59.703 45.455 10.37 0.00 0.00 3.86
2775 6345 1.541147 ACACACCATTGGATTGCTTCG 59.459 47.619 10.37 0.00 0.00 3.79
2776 6346 1.135315 CACACCATTGGATTGCTTCGG 60.135 52.381 10.37 0.00 0.00 4.30
2777 6347 1.176527 CACCATTGGATTGCTTCGGT 58.823 50.000 10.37 0.00 0.00 4.69
2778 6348 1.545582 CACCATTGGATTGCTTCGGTT 59.454 47.619 10.37 0.00 0.00 4.44
2779 6349 2.029110 CACCATTGGATTGCTTCGGTTT 60.029 45.455 10.37 0.00 0.00 3.27
2780 6350 2.029110 ACCATTGGATTGCTTCGGTTTG 60.029 45.455 10.37 0.00 0.00 2.93
2781 6351 2.029110 CCATTGGATTGCTTCGGTTTGT 60.029 45.455 0.00 0.00 0.00 2.83
2782 6352 3.554752 CCATTGGATTGCTTCGGTTTGTT 60.555 43.478 0.00 0.00 0.00 2.83
2783 6353 3.810310 TTGGATTGCTTCGGTTTGTTT 57.190 38.095 0.00 0.00 0.00 2.83
2784 6354 4.920640 TTGGATTGCTTCGGTTTGTTTA 57.079 36.364 0.00 0.00 0.00 2.01
2785 6355 4.920640 TGGATTGCTTCGGTTTGTTTAA 57.079 36.364 0.00 0.00 0.00 1.52
2786 6356 5.461032 TGGATTGCTTCGGTTTGTTTAAT 57.539 34.783 0.00 0.00 0.00 1.40
2787 6357 5.465935 TGGATTGCTTCGGTTTGTTTAATC 58.534 37.500 0.00 0.00 0.00 1.75
2788 6358 5.242838 TGGATTGCTTCGGTTTGTTTAATCT 59.757 36.000 0.00 0.00 0.00 2.40
2789 6359 5.572896 GGATTGCTTCGGTTTGTTTAATCTG 59.427 40.000 0.00 0.00 0.00 2.90
2790 6360 3.896122 TGCTTCGGTTTGTTTAATCTGC 58.104 40.909 0.00 0.00 0.00 4.26
2791 6361 3.316588 TGCTTCGGTTTGTTTAATCTGCA 59.683 39.130 0.00 0.00 0.00 4.41
2792 6362 4.022416 TGCTTCGGTTTGTTTAATCTGCAT 60.022 37.500 0.00 0.00 0.00 3.96
2793 6363 4.324402 GCTTCGGTTTGTTTAATCTGCATG 59.676 41.667 0.00 0.00 0.00 4.06
2794 6364 4.433186 TCGGTTTGTTTAATCTGCATGG 57.567 40.909 0.00 0.00 0.00 3.66
2795 6365 2.923020 CGGTTTGTTTAATCTGCATGGC 59.077 45.455 0.00 0.00 0.00 4.40
2796 6366 3.367292 CGGTTTGTTTAATCTGCATGGCT 60.367 43.478 0.00 0.00 0.00 4.75
2797 6367 4.568956 GGTTTGTTTAATCTGCATGGCTT 58.431 39.130 0.00 0.00 0.00 4.35
2798 6368 4.627035 GGTTTGTTTAATCTGCATGGCTTC 59.373 41.667 0.00 0.00 0.00 3.86
2799 6369 5.473039 GTTTGTTTAATCTGCATGGCTTCT 58.527 37.500 0.00 0.00 0.00 2.85
2800 6370 6.350110 GGTTTGTTTAATCTGCATGGCTTCTA 60.350 38.462 0.00 0.00 0.00 2.10
2801 6371 5.818136 TGTTTAATCTGCATGGCTTCTAC 57.182 39.130 0.00 0.00 0.00 2.59
2802 6372 5.500234 TGTTTAATCTGCATGGCTTCTACT 58.500 37.500 0.00 0.00 0.00 2.57
2803 6373 5.586243 TGTTTAATCTGCATGGCTTCTACTC 59.414 40.000 0.00 0.00 0.00 2.59
2804 6374 2.522836 ATCTGCATGGCTTCTACTCG 57.477 50.000 0.00 0.00 0.00 4.18
2805 6375 1.186200 TCTGCATGGCTTCTACTCGT 58.814 50.000 0.00 0.00 0.00 4.18
2806 6376 1.134995 TCTGCATGGCTTCTACTCGTG 60.135 52.381 0.00 0.00 0.00 4.35
2807 6377 0.608130 TGCATGGCTTCTACTCGTGT 59.392 50.000 0.00 0.00 0.00 4.49
2808 6378 1.001974 TGCATGGCTTCTACTCGTGTT 59.998 47.619 0.00 0.00 0.00 3.32
2809 6379 1.394917 GCATGGCTTCTACTCGTGTTG 59.605 52.381 0.00 0.00 0.00 3.33
2810 6380 2.688507 CATGGCTTCTACTCGTGTTGT 58.311 47.619 0.00 0.00 0.00 3.32
2811 6381 2.433868 TGGCTTCTACTCGTGTTGTC 57.566 50.000 0.00 0.00 0.00 3.18
2812 6382 1.000506 TGGCTTCTACTCGTGTTGTCC 59.999 52.381 0.00 0.00 0.00 4.02
2813 6383 1.337821 GCTTCTACTCGTGTTGTCCG 58.662 55.000 0.00 0.00 0.00 4.79
2814 6384 1.337821 CTTCTACTCGTGTTGTCCGC 58.662 55.000 0.00 0.00 0.00 5.54
2815 6385 0.669619 TTCTACTCGTGTTGTCCGCA 59.330 50.000 0.00 0.00 0.00 5.69
2816 6386 0.669619 TCTACTCGTGTTGTCCGCAA 59.330 50.000 0.00 0.00 0.00 4.85
2817 6387 1.067364 TCTACTCGTGTTGTCCGCAAA 59.933 47.619 0.00 0.00 36.22 3.68
2818 6388 2.066262 CTACTCGTGTTGTCCGCAAAT 58.934 47.619 0.00 0.00 36.22 2.32
2819 6389 0.865769 ACTCGTGTTGTCCGCAAATC 59.134 50.000 0.00 0.00 36.22 2.17
2820 6390 0.179250 CTCGTGTTGTCCGCAAATCG 60.179 55.000 0.00 0.00 36.22 3.34
2821 6391 0.876777 TCGTGTTGTCCGCAAATCGT 60.877 50.000 0.00 0.00 36.22 3.73
2822 6392 0.721155 CGTGTTGTCCGCAAATCGTG 60.721 55.000 0.00 0.00 36.22 4.35
2836 6406 4.836455 CAAATCGTGCATAATCACATCGT 58.164 39.130 0.00 0.00 36.80 3.73
2837 6407 4.457433 AATCGTGCATAATCACATCGTG 57.543 40.909 0.00 0.00 36.80 4.35
2838 6408 2.887337 TCGTGCATAATCACATCGTGT 58.113 42.857 0.00 0.00 36.80 4.49
2842 6412 4.026330 GTGCATAATCACATCGTGTGCAC 61.026 47.826 18.57 18.57 46.75 4.57
2855 6425 1.275657 GTGCACAACACTTCCGTCG 59.724 57.895 13.17 0.00 46.41 5.12
2856 6426 1.153529 TGCACAACACTTCCGTCGT 60.154 52.632 0.00 0.00 0.00 4.34
2857 6427 0.741574 TGCACAACACTTCCGTCGTT 60.742 50.000 0.00 0.00 0.00 3.85
2858 6428 0.042448 GCACAACACTTCCGTCGTTC 60.042 55.000 0.00 0.00 0.00 3.95
2859 6429 0.580104 CACAACACTTCCGTCGTTCC 59.420 55.000 0.00 0.00 0.00 3.62
2860 6430 0.462789 ACAACACTTCCGTCGTTCCT 59.537 50.000 0.00 0.00 0.00 3.36
2861 6431 1.134610 ACAACACTTCCGTCGTTCCTT 60.135 47.619 0.00 0.00 0.00 3.36
2862 6432 1.260561 CAACACTTCCGTCGTTCCTTG 59.739 52.381 0.00 0.00 0.00 3.61
2863 6433 0.748450 ACACTTCCGTCGTTCCTTGA 59.252 50.000 0.00 0.00 0.00 3.02
2864 6434 1.137479 ACACTTCCGTCGTTCCTTGAA 59.863 47.619 0.00 0.00 0.00 2.69
2865 6435 2.224209 ACACTTCCGTCGTTCCTTGAAT 60.224 45.455 0.00 0.00 0.00 2.57
2882 6452 5.278463 CCTTGAATTGTGTGTTTGGTCCTAG 60.278 44.000 0.00 0.00 0.00 3.02
2883 6453 5.042463 TGAATTGTGTGTTTGGTCCTAGA 57.958 39.130 0.00 0.00 0.00 2.43
2884 6454 5.441500 TGAATTGTGTGTTTGGTCCTAGAA 58.558 37.500 0.00 0.00 0.00 2.10
2885 6455 5.530915 TGAATTGTGTGTTTGGTCCTAGAAG 59.469 40.000 0.00 0.00 0.00 2.85
2886 6456 3.485463 TGTGTGTTTGGTCCTAGAAGG 57.515 47.619 0.00 0.00 36.46 3.46
2888 6458 3.968649 TGTGTGTTTGGTCCTAGAAGGTA 59.031 43.478 0.00 0.00 36.53 3.08
2891 6461 5.244626 GTGTGTTTGGTCCTAGAAGGTACTA 59.755 44.000 0.00 0.00 38.49 1.82
2892 6462 5.244626 TGTGTTTGGTCCTAGAAGGTACTAC 59.755 44.000 0.00 0.00 38.49 2.73
2932 6502 6.515272 AAGGTTATTTCACATGCTACTTGG 57.485 37.500 0.00 0.00 0.00 3.61
2933 6503 5.570320 AGGTTATTTCACATGCTACTTGGT 58.430 37.500 0.00 0.00 0.00 3.67
2934 6504 6.717289 AGGTTATTTCACATGCTACTTGGTA 58.283 36.000 0.00 0.00 0.00 3.25
2935 6505 7.172342 AGGTTATTTCACATGCTACTTGGTAA 58.828 34.615 0.00 0.00 0.00 2.85
2937 6507 8.466798 GGTTATTTCACATGCTACTTGGTAATT 58.533 33.333 0.00 0.00 0.00 1.40
2938 6508 9.855021 GTTATTTCACATGCTACTTGGTAATTT 57.145 29.630 0.00 0.00 0.00 1.82
2942 6512 5.293324 TCACATGCTACTTGGTAATTTAGCG 59.707 40.000 0.00 0.00 39.92 4.26
2943 6513 5.293324 CACATGCTACTTGGTAATTTAGCGA 59.707 40.000 0.00 0.00 39.92 4.93
2944 6514 6.017934 CACATGCTACTTGGTAATTTAGCGAT 60.018 38.462 0.00 0.00 39.92 4.58
2946 6516 6.358118 TGCTACTTGGTAATTTAGCGATTG 57.642 37.500 1.52 0.00 39.92 2.67
2948 6518 7.042950 TGCTACTTGGTAATTTAGCGATTGTA 58.957 34.615 1.52 0.00 39.92 2.41
2966 6567 7.746475 GCGATTGTATAAGGTTATTTCAGATGC 59.254 37.037 0.00 0.00 0.00 3.91
2967 6568 8.993121 CGATTGTATAAGGTTATTTCAGATGCT 58.007 33.333 0.00 0.00 0.00 3.79
2982 6583 8.506168 TTTCAGATGCTACTTGGTAATTTAGG 57.494 34.615 0.00 0.00 0.00 2.69
2983 6584 6.591935 TCAGATGCTACTTGGTAATTTAGGG 58.408 40.000 0.00 0.00 0.00 3.53
2989 6590 7.863722 TGCTACTTGGTAATTTAGGGATTGTA 58.136 34.615 0.00 0.00 0.00 2.41
2991 6592 8.837389 GCTACTTGGTAATTTAGGGATTGTAAG 58.163 37.037 0.00 0.00 0.00 2.34
3040 6641 3.370103 GGTACATCATCACCCGAGGAAAA 60.370 47.826 0.00 0.00 35.20 2.29
3048 6649 4.360951 TCACCCGAGGAAAACTATGTTT 57.639 40.909 0.00 0.00 0.00 2.83
3050 6651 2.817844 ACCCGAGGAAAACTATGTTTGC 59.182 45.455 0.00 0.00 0.00 3.68
3057 6658 4.455877 AGGAAAACTATGTTTGCTTCTCCG 59.544 41.667 1.78 0.00 35.87 4.63
3059 6660 5.278315 GGAAAACTATGTTTGCTTCTCCGTT 60.278 40.000 1.78 0.00 0.00 4.44
3064 6665 0.790814 GTTTGCTTCTCCGTTCTCCG 59.209 55.000 0.00 0.00 0.00 4.63
3080 6687 1.344763 CTCCGTCACCTGAGGAAAACT 59.655 52.381 4.99 0.00 33.10 2.66
3082 6689 2.298163 TCCGTCACCTGAGGAAAACTAC 59.702 50.000 4.99 0.00 32.08 2.73
3085 6692 3.243771 CGTCACCTGAGGAAAACTACTGT 60.244 47.826 4.99 0.00 32.08 3.55
3091 6698 8.653191 TCACCTGAGGAAAACTACTGTTATTAA 58.347 33.333 4.99 0.00 34.96 1.40
3092 6699 9.280174 CACCTGAGGAAAACTACTGTTATTAAA 57.720 33.333 4.99 0.00 34.96 1.52
3093 6700 9.281371 ACCTGAGGAAAACTACTGTTATTAAAC 57.719 33.333 4.99 0.00 34.96 2.01
3095 6702 7.799784 TGAGGAAAACTACTGTTATTAAACGC 58.200 34.615 0.00 0.00 38.53 4.84
3096 6703 6.824557 AGGAAAACTACTGTTATTAAACGCG 58.175 36.000 3.53 3.53 38.53 6.01
3106 6727 6.128499 ACTGTTATTAAACGCGACAATGCTAA 60.128 34.615 15.93 0.00 38.53 3.09
3108 6729 7.244898 TGTTATTAAACGCGACAATGCTAAAT 58.755 30.769 15.93 1.86 38.53 1.40
3109 6730 7.751348 TGTTATTAAACGCGACAATGCTAAATT 59.249 29.630 15.93 0.00 38.53 1.82
3155 6776 5.345702 TCACGTGTATTGGCTACTCATAAC 58.654 41.667 16.51 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.769512 TGCAGAAAACCTTTAGATGAGTACT 58.230 36.000 0.00 0.00 0.00 2.73
4 5 6.348868 GGACTTGCAGAAAACCTTTAGATGAG 60.349 42.308 0.00 0.00 0.00 2.90
161 189 0.906756 TGAGCAGCAAGGGAGTAGCT 60.907 55.000 0.00 0.00 39.63 3.32
206 241 4.590850 AAGAAGGCTTTGTTGATTCACC 57.409 40.909 0.00 0.00 0.00 4.02
221 263 5.182001 CCTTCATGTTCACCAAGTAAGAAGG 59.818 44.000 0.00 0.00 42.27 3.46
371 413 1.338200 GCTGACACAATCTCGGAACCT 60.338 52.381 0.00 0.00 0.00 3.50
436 488 0.948678 GCTCACCGGTGCTGTAAAAA 59.051 50.000 30.25 9.01 0.00 1.94
437 489 1.225376 CGCTCACCGGTGCTGTAAAA 61.225 55.000 30.25 9.81 0.00 1.52
453 505 4.803426 CGCGGCCTCTTCTTCGCT 62.803 66.667 0.00 0.00 45.11 4.93
675 727 4.168291 GAGCAGGGCGGAGAAGGG 62.168 72.222 0.00 0.00 0.00 3.95
846 920 3.003173 TTGGAGGGCCCTCTGACG 61.003 66.667 43.34 0.00 42.38 4.35
849 923 1.492133 TTCTGTTGGAGGGCCCTCTG 61.492 60.000 43.34 28.64 42.38 3.35
850 924 0.772124 TTTCTGTTGGAGGGCCCTCT 60.772 55.000 43.34 18.43 42.38 3.69
851 925 0.609406 GTTTCTGTTGGAGGGCCCTC 60.609 60.000 39.86 39.86 42.04 4.30
852 926 1.460699 GTTTCTGTTGGAGGGCCCT 59.539 57.895 29.18 29.18 35.38 5.19
853 927 1.971695 CGTTTCTGTTGGAGGGCCC 60.972 63.158 16.46 16.46 0.00 5.80
854 928 0.955919 CTCGTTTCTGTTGGAGGGCC 60.956 60.000 0.00 0.00 0.00 5.80
855 929 0.034896 TCTCGTTTCTGTTGGAGGGC 59.965 55.000 0.00 0.00 0.00 5.19
856 930 1.797025 GTCTCGTTTCTGTTGGAGGG 58.203 55.000 0.00 0.00 0.00 4.30
857 931 1.419374 CGTCTCGTTTCTGTTGGAGG 58.581 55.000 0.00 0.00 0.00 4.30
858 932 1.419374 CCGTCTCGTTTCTGTTGGAG 58.581 55.000 0.00 0.00 0.00 3.86
859 933 0.599204 GCCGTCTCGTTTCTGTTGGA 60.599 55.000 0.00 0.00 0.00 3.53
860 934 1.566018 GGCCGTCTCGTTTCTGTTGG 61.566 60.000 0.00 0.00 0.00 3.77
861 935 0.878523 TGGCCGTCTCGTTTCTGTTG 60.879 55.000 0.00 0.00 0.00 3.33
862 936 0.034896 ATGGCCGTCTCGTTTCTGTT 59.965 50.000 0.00 0.00 0.00 3.16
1690 5217 3.222354 GACGACGGTGAGGCTGGTT 62.222 63.158 0.00 0.00 0.00 3.67
1780 5307 4.357097 ACCTTATCCCCAACCTTCTTCTTT 59.643 41.667 0.00 0.00 0.00 2.52
1782 5309 3.267031 CACCTTATCCCCAACCTTCTTCT 59.733 47.826 0.00 0.00 0.00 2.85
1822 5349 4.777896 AGCTTCACTACATACTTCCCAAGA 59.222 41.667 0.00 0.00 0.00 3.02
1890 5417 1.142667 TCATCAGTCCAACAGGCACAA 59.857 47.619 0.00 0.00 0.00 3.33
2074 5602 2.423538 GGTTAACAGATCATGCACACCC 59.576 50.000 8.10 0.00 0.00 4.61
2166 5695 6.830114 ATATAAACTCAAACGAGCACTAGC 57.170 37.500 0.00 0.00 42.56 3.42
2213 5742 7.381678 CGTATAATCAGGTACTAGCCTTCAAAC 59.618 40.741 0.00 0.00 36.02 2.93
2214 5743 7.431249 CGTATAATCAGGTACTAGCCTTCAAA 58.569 38.462 0.00 0.00 36.02 2.69
2215 5744 6.015688 CCGTATAATCAGGTACTAGCCTTCAA 60.016 42.308 0.00 0.00 36.02 2.69
2216 5745 5.475909 CCGTATAATCAGGTACTAGCCTTCA 59.524 44.000 0.00 0.00 36.02 3.02
2217 5746 5.621781 GCCGTATAATCAGGTACTAGCCTTC 60.622 48.000 0.00 0.00 36.02 3.46
2218 5747 4.220163 GCCGTATAATCAGGTACTAGCCTT 59.780 45.833 0.00 0.00 36.02 4.35
2219 5748 3.762823 GCCGTATAATCAGGTACTAGCCT 59.237 47.826 0.00 0.00 36.02 4.58
2220 5749 3.508793 TGCCGTATAATCAGGTACTAGCC 59.491 47.826 0.00 0.00 36.02 3.93
2221 5750 4.778534 TGCCGTATAATCAGGTACTAGC 57.221 45.455 0.00 0.00 36.02 3.42
2224 5753 3.323691 TGCATGCCGTATAATCAGGTACT 59.676 43.478 16.68 0.00 43.88 2.73
2238 5769 1.514657 CAACCGATTGTGCATGCCG 60.515 57.895 16.68 10.83 0.00 5.69
2248 5779 7.151308 TCACAAATTCAAAATAGCAACCGATT 58.849 30.769 0.00 0.00 0.00 3.34
2249 5780 6.686630 TCACAAATTCAAAATAGCAACCGAT 58.313 32.000 0.00 0.00 0.00 4.18
2335 5883 7.361542 CGGATTAAATTATCATCCTGGCAGAAG 60.362 40.741 17.94 5.24 35.23 2.85
2457 6006 7.633193 TGTTAAGTGTACAAAGACCAACATT 57.367 32.000 0.00 0.00 0.00 2.71
2458 6007 7.500892 TCATGTTAAGTGTACAAAGACCAACAT 59.499 33.333 0.00 5.55 36.38 2.71
2522 6090 2.625314 TCACATGGTTCCATTCGCAAAA 59.375 40.909 1.11 0.00 0.00 2.44
2526 6094 1.745087 ACATCACATGGTTCCATTCGC 59.255 47.619 1.11 0.00 33.60 4.70
2527 6095 4.168014 CAAACATCACATGGTTCCATTCG 58.832 43.478 1.11 0.00 38.32 3.34
2537 6105 5.577945 GGCAACTTAATCCAAACATCACATG 59.422 40.000 0.00 0.00 0.00 3.21
2566 6134 4.462834 CCCCTGTTTCCATCTAAAAGGTTC 59.537 45.833 0.00 0.00 0.00 3.62
2576 6144 2.092323 GTTAGTGCCCCTGTTTCCATC 58.908 52.381 0.00 0.00 0.00 3.51
2585 6153 4.024670 CAGAGTTACTAGTTAGTGCCCCT 58.975 47.826 0.00 0.00 37.10 4.79
2594 6162 5.964477 TCCATTCATCCCAGAGTTACTAGTT 59.036 40.000 0.00 0.00 0.00 2.24
2602 6170 4.103785 CCATAGTTCCATTCATCCCAGAGT 59.896 45.833 0.00 0.00 0.00 3.24
2603 6171 4.349048 TCCATAGTTCCATTCATCCCAGAG 59.651 45.833 0.00 0.00 0.00 3.35
2604 6172 4.306391 TCCATAGTTCCATTCATCCCAGA 58.694 43.478 0.00 0.00 0.00 3.86
2605 6173 4.712051 TCCATAGTTCCATTCATCCCAG 57.288 45.455 0.00 0.00 0.00 4.45
2672 6242 5.007921 AGGAAATTGCAAATGTTTTGTCTGC 59.992 36.000 1.71 0.00 0.00 4.26
2677 6247 7.695820 TCTTCAAGGAAATTGCAAATGTTTTG 58.304 30.769 1.71 6.62 38.89 2.44
2678 6248 7.467675 GCTCTTCAAGGAAATTGCAAATGTTTT 60.468 33.333 1.71 0.00 38.89 2.43
2686 6256 3.005050 CAGTGCTCTTCAAGGAAATTGCA 59.995 43.478 0.00 0.00 38.89 4.08
2701 6271 0.737367 TCGTGTGCATAGCAGTGCTC 60.737 55.000 23.64 8.26 45.27 4.26
2702 6272 0.107993 ATCGTGTGCATAGCAGTGCT 60.108 50.000 23.44 23.44 45.27 4.40
2703 6273 0.027194 CATCGTGTGCATAGCAGTGC 59.973 55.000 7.13 7.13 40.08 4.40
2714 6284 1.496835 TGCGTGAATGCATCGTGTG 59.503 52.632 0.00 0.00 40.62 3.82
2715 6285 3.964718 TGCGTGAATGCATCGTGT 58.035 50.000 0.00 0.00 40.62 4.49
2721 6291 2.371923 CGAGTCGTGCGTGAATGCA 61.372 57.895 3.82 0.00 43.95 3.96
2722 6292 2.391821 CGAGTCGTGCGTGAATGC 59.608 61.111 3.82 0.00 0.00 3.56
2723 6293 2.391821 GCGAGTCGTGCGTGAATG 59.608 61.111 15.08 0.00 0.00 2.67
2731 6301 2.866010 TTGTTGTGCGCGAGTCGTG 61.866 57.895 21.46 21.46 41.07 4.35
2732 6302 2.583868 TTGTTGTGCGCGAGTCGT 60.584 55.556 12.10 0.00 41.07 4.34
2733 6303 2.128128 GTTGTTGTGCGCGAGTCG 60.128 61.111 12.10 8.54 42.12 4.18
2734 6304 1.201825 GAGTTGTTGTGCGCGAGTC 59.798 57.895 12.10 0.00 0.00 3.36
2735 6305 1.520564 TGAGTTGTTGTGCGCGAGT 60.521 52.632 12.10 0.00 0.00 4.18
2736 6306 1.083401 GTGAGTTGTTGTGCGCGAG 60.083 57.895 12.10 0.00 0.00 5.03
2737 6307 1.811679 TGTGAGTTGTTGTGCGCGA 60.812 52.632 12.10 0.00 0.00 5.87
2738 6308 1.651132 GTGTGAGTTGTTGTGCGCG 60.651 57.895 0.00 0.00 0.00 6.86
2739 6309 0.861450 GTGTGTGAGTTGTTGTGCGC 60.861 55.000 0.00 0.00 0.00 6.09
2740 6310 0.445829 TGTGTGTGAGTTGTTGTGCG 59.554 50.000 0.00 0.00 0.00 5.34
2741 6311 1.467374 GGTGTGTGTGAGTTGTTGTGC 60.467 52.381 0.00 0.00 0.00 4.57
2742 6312 1.809547 TGGTGTGTGTGAGTTGTTGTG 59.190 47.619 0.00 0.00 0.00 3.33
2743 6313 2.192664 TGGTGTGTGTGAGTTGTTGT 57.807 45.000 0.00 0.00 0.00 3.32
2744 6314 3.437428 CAATGGTGTGTGTGAGTTGTTG 58.563 45.455 0.00 0.00 0.00 3.33
2745 6315 2.426738 CCAATGGTGTGTGTGAGTTGTT 59.573 45.455 0.00 0.00 0.00 2.83
2746 6316 2.023673 CCAATGGTGTGTGTGAGTTGT 58.976 47.619 0.00 0.00 0.00 3.32
2747 6317 2.296792 TCCAATGGTGTGTGTGAGTTG 58.703 47.619 0.00 0.00 0.00 3.16
2748 6318 2.727123 TCCAATGGTGTGTGTGAGTT 57.273 45.000 0.00 0.00 0.00 3.01
2749 6319 2.886523 CAATCCAATGGTGTGTGTGAGT 59.113 45.455 0.00 0.00 0.00 3.41
2750 6320 2.352030 GCAATCCAATGGTGTGTGTGAG 60.352 50.000 0.00 0.00 0.00 3.51
2751 6321 1.612950 GCAATCCAATGGTGTGTGTGA 59.387 47.619 0.00 0.00 0.00 3.58
2752 6322 1.614903 AGCAATCCAATGGTGTGTGTG 59.385 47.619 0.00 0.00 0.00 3.82
2753 6323 1.999648 AGCAATCCAATGGTGTGTGT 58.000 45.000 0.00 0.00 0.00 3.72
2754 6324 2.669113 CGAAGCAATCCAATGGTGTGTG 60.669 50.000 0.00 0.00 0.00 3.82
2755 6325 1.541147 CGAAGCAATCCAATGGTGTGT 59.459 47.619 0.00 0.00 0.00 3.72
2756 6326 1.135315 CCGAAGCAATCCAATGGTGTG 60.135 52.381 0.00 0.00 0.00 3.82
2757 6327 1.176527 CCGAAGCAATCCAATGGTGT 58.823 50.000 0.00 0.00 0.00 4.16
2758 6328 1.176527 ACCGAAGCAATCCAATGGTG 58.823 50.000 0.00 0.00 0.00 4.17
2759 6329 1.923356 AACCGAAGCAATCCAATGGT 58.077 45.000 0.00 0.00 0.00 3.55
2760 6330 2.029110 ACAAACCGAAGCAATCCAATGG 60.029 45.455 0.00 0.00 0.00 3.16
2761 6331 3.302365 ACAAACCGAAGCAATCCAATG 57.698 42.857 0.00 0.00 0.00 2.82
2762 6332 4.335400 AAACAAACCGAAGCAATCCAAT 57.665 36.364 0.00 0.00 0.00 3.16
2763 6333 3.810310 AAACAAACCGAAGCAATCCAA 57.190 38.095 0.00 0.00 0.00 3.53
2764 6334 4.920640 TTAAACAAACCGAAGCAATCCA 57.079 36.364 0.00 0.00 0.00 3.41
2765 6335 5.572896 CAGATTAAACAAACCGAAGCAATCC 59.427 40.000 0.00 0.00 0.00 3.01
2766 6336 5.060940 GCAGATTAAACAAACCGAAGCAATC 59.939 40.000 0.00 0.00 0.00 2.67
2767 6337 4.923281 GCAGATTAAACAAACCGAAGCAAT 59.077 37.500 0.00 0.00 0.00 3.56
2768 6338 4.202060 TGCAGATTAAACAAACCGAAGCAA 60.202 37.500 0.00 0.00 0.00 3.91
2769 6339 3.316588 TGCAGATTAAACAAACCGAAGCA 59.683 39.130 0.00 0.00 0.00 3.91
2770 6340 3.896122 TGCAGATTAAACAAACCGAAGC 58.104 40.909 0.00 0.00 0.00 3.86
2771 6341 4.858692 CCATGCAGATTAAACAAACCGAAG 59.141 41.667 0.00 0.00 0.00 3.79
2772 6342 4.804108 CCATGCAGATTAAACAAACCGAA 58.196 39.130 0.00 0.00 0.00 4.30
2773 6343 3.366883 GCCATGCAGATTAAACAAACCGA 60.367 43.478 0.00 0.00 0.00 4.69
2774 6344 2.923020 GCCATGCAGATTAAACAAACCG 59.077 45.455 0.00 0.00 0.00 4.44
2775 6345 4.192429 AGCCATGCAGATTAAACAAACC 57.808 40.909 0.00 0.00 0.00 3.27
2776 6346 5.473039 AGAAGCCATGCAGATTAAACAAAC 58.527 37.500 0.00 0.00 0.00 2.93
2777 6347 5.726980 AGAAGCCATGCAGATTAAACAAA 57.273 34.783 0.00 0.00 0.00 2.83
2778 6348 5.945784 AGTAGAAGCCATGCAGATTAAACAA 59.054 36.000 0.00 0.00 0.00 2.83
2779 6349 5.500234 AGTAGAAGCCATGCAGATTAAACA 58.500 37.500 0.00 0.00 0.00 2.83
2780 6350 5.277058 CGAGTAGAAGCCATGCAGATTAAAC 60.277 44.000 0.00 0.00 0.00 2.01
2781 6351 4.811024 CGAGTAGAAGCCATGCAGATTAAA 59.189 41.667 0.00 0.00 0.00 1.52
2782 6352 4.141937 ACGAGTAGAAGCCATGCAGATTAA 60.142 41.667 0.00 0.00 0.00 1.40
2783 6353 3.384789 ACGAGTAGAAGCCATGCAGATTA 59.615 43.478 0.00 0.00 0.00 1.75
2784 6354 2.169352 ACGAGTAGAAGCCATGCAGATT 59.831 45.455 0.00 0.00 0.00 2.40
2785 6355 1.759445 ACGAGTAGAAGCCATGCAGAT 59.241 47.619 0.00 0.00 0.00 2.90
2786 6356 1.134995 CACGAGTAGAAGCCATGCAGA 60.135 52.381 0.00 0.00 0.00 4.26
2787 6357 1.284657 CACGAGTAGAAGCCATGCAG 58.715 55.000 0.00 0.00 0.00 4.41
2788 6358 0.608130 ACACGAGTAGAAGCCATGCA 59.392 50.000 0.00 0.00 0.00 3.96
2789 6359 1.394917 CAACACGAGTAGAAGCCATGC 59.605 52.381 0.00 0.00 0.00 4.06
2790 6360 2.668457 GACAACACGAGTAGAAGCCATG 59.332 50.000 0.00 0.00 0.00 3.66
2791 6361 2.353803 GGACAACACGAGTAGAAGCCAT 60.354 50.000 0.00 0.00 0.00 4.40
2792 6362 1.000506 GGACAACACGAGTAGAAGCCA 59.999 52.381 0.00 0.00 0.00 4.75
2793 6363 1.711206 GGACAACACGAGTAGAAGCC 58.289 55.000 0.00 0.00 0.00 4.35
2794 6364 1.337821 CGGACAACACGAGTAGAAGC 58.662 55.000 0.00 0.00 0.00 3.86
2795 6365 1.335597 TGCGGACAACACGAGTAGAAG 60.336 52.381 0.00 0.00 0.00 2.85
2796 6366 0.669619 TGCGGACAACACGAGTAGAA 59.330 50.000 0.00 0.00 0.00 2.10
2797 6367 0.669619 TTGCGGACAACACGAGTAGA 59.330 50.000 0.00 0.00 0.00 2.59
2798 6368 1.493772 TTTGCGGACAACACGAGTAG 58.506 50.000 0.00 0.00 34.87 2.57
2799 6369 2.063266 GATTTGCGGACAACACGAGTA 58.937 47.619 0.00 0.00 34.87 2.59
2800 6370 0.865769 GATTTGCGGACAACACGAGT 59.134 50.000 0.00 0.00 34.87 4.18
2801 6371 0.179250 CGATTTGCGGACAACACGAG 60.179 55.000 0.00 0.00 36.99 4.18
2802 6372 0.876777 ACGATTTGCGGACAACACGA 60.877 50.000 0.00 0.00 46.49 4.35
2803 6373 0.721155 CACGATTTGCGGACAACACG 60.721 55.000 0.00 0.00 46.49 4.49
2804 6374 0.996727 GCACGATTTGCGGACAACAC 60.997 55.000 0.00 0.00 46.49 3.32
2805 6375 1.281353 GCACGATTTGCGGACAACA 59.719 52.632 0.00 0.00 46.49 3.33
2806 6376 4.130857 GCACGATTTGCGGACAAC 57.869 55.556 0.00 0.00 46.49 3.32
2813 6383 6.774241 CACGATGTGATTATGCACGATTTGC 61.774 44.000 0.00 0.00 43.34 3.68
2814 6384 4.667504 CACGATGTGATTATGCACGATTTG 59.332 41.667 0.00 0.00 41.63 2.32
2815 6385 4.332543 ACACGATGTGATTATGCACGATTT 59.667 37.500 3.61 0.00 41.63 2.17
2816 6386 3.871006 ACACGATGTGATTATGCACGATT 59.129 39.130 3.61 0.00 41.63 3.34
2817 6387 3.457234 ACACGATGTGATTATGCACGAT 58.543 40.909 3.61 0.00 41.63 3.73
2818 6388 2.887337 ACACGATGTGATTATGCACGA 58.113 42.857 3.61 0.00 41.63 4.35
2847 6417 2.806244 ACAATTCAAGGAACGACGGAAG 59.194 45.455 0.00 0.00 0.00 3.46
2848 6418 2.546368 CACAATTCAAGGAACGACGGAA 59.454 45.455 0.00 0.00 0.00 4.30
2849 6419 2.139917 CACAATTCAAGGAACGACGGA 58.860 47.619 0.00 0.00 0.00 4.69
2850 6420 1.871039 ACACAATTCAAGGAACGACGG 59.129 47.619 0.00 0.00 0.00 4.79
2851 6421 2.286833 ACACACAATTCAAGGAACGACG 59.713 45.455 0.00 0.00 0.00 5.12
2852 6422 3.963383 ACACACAATTCAAGGAACGAC 57.037 42.857 0.00 0.00 0.00 4.34
2853 6423 4.439426 CCAAACACACAATTCAAGGAACGA 60.439 41.667 0.00 0.00 0.00 3.85
2854 6424 3.796178 CCAAACACACAATTCAAGGAACG 59.204 43.478 0.00 0.00 0.00 3.95
2855 6425 4.754322 ACCAAACACACAATTCAAGGAAC 58.246 39.130 0.00 0.00 0.00 3.62
2856 6426 4.142049 GGACCAAACACACAATTCAAGGAA 60.142 41.667 0.00 0.00 0.00 3.36
2857 6427 3.383185 GGACCAAACACACAATTCAAGGA 59.617 43.478 0.00 0.00 0.00 3.36
2858 6428 3.384467 AGGACCAAACACACAATTCAAGG 59.616 43.478 0.00 0.00 0.00 3.61
2859 6429 4.654091 AGGACCAAACACACAATTCAAG 57.346 40.909 0.00 0.00 0.00 3.02
2860 6430 5.441500 TCTAGGACCAAACACACAATTCAA 58.558 37.500 0.00 0.00 0.00 2.69
2861 6431 5.042463 TCTAGGACCAAACACACAATTCA 57.958 39.130 0.00 0.00 0.00 2.57
2862 6432 5.048713 CCTTCTAGGACCAAACACACAATTC 60.049 44.000 0.00 0.00 37.67 2.17
2863 6433 4.827284 CCTTCTAGGACCAAACACACAATT 59.173 41.667 0.00 0.00 37.67 2.32
2864 6434 4.141251 ACCTTCTAGGACCAAACACACAAT 60.141 41.667 0.00 0.00 37.67 2.71
2865 6435 3.201266 ACCTTCTAGGACCAAACACACAA 59.799 43.478 0.00 0.00 37.67 3.33
2906 6476 9.337396 CCAAGTAGCATGTGAAATAACCTTATA 57.663 33.333 0.00 0.00 0.00 0.98
2907 6477 7.834181 ACCAAGTAGCATGTGAAATAACCTTAT 59.166 33.333 0.00 0.00 0.00 1.73
2908 6478 7.172342 ACCAAGTAGCATGTGAAATAACCTTA 58.828 34.615 0.00 0.00 0.00 2.69
2911 6481 5.897377 ACCAAGTAGCATGTGAAATAACC 57.103 39.130 0.00 0.00 0.00 2.85
2912 6482 9.855021 AAATTACCAAGTAGCATGTGAAATAAC 57.145 29.630 0.00 0.00 0.00 1.89
2917 6487 6.183360 CGCTAAATTACCAAGTAGCATGTGAA 60.183 38.462 5.65 0.00 39.13 3.18
2918 6488 5.293324 CGCTAAATTACCAAGTAGCATGTGA 59.707 40.000 5.65 0.00 39.13 3.58
2919 6489 5.293324 TCGCTAAATTACCAAGTAGCATGTG 59.707 40.000 5.65 0.00 39.13 3.21
2921 6491 5.984233 TCGCTAAATTACCAAGTAGCATG 57.016 39.130 5.65 0.00 39.13 4.06
2922 6492 6.542370 ACAATCGCTAAATTACCAAGTAGCAT 59.458 34.615 5.65 0.00 39.13 3.79
2924 6494 6.359480 ACAATCGCTAAATTACCAAGTAGC 57.641 37.500 0.00 0.00 36.45 3.58
2927 6497 9.052759 CCTTATACAATCGCTAAATTACCAAGT 57.947 33.333 0.00 0.00 0.00 3.16
2928 6498 9.052759 ACCTTATACAATCGCTAAATTACCAAG 57.947 33.333 0.00 0.00 0.00 3.61
2929 6499 8.967664 ACCTTATACAATCGCTAAATTACCAA 57.032 30.769 0.00 0.00 0.00 3.67
2939 6509 8.993121 CATCTGAAATAACCTTATACAATCGCT 58.007 33.333 0.00 0.00 0.00 4.93
2940 6510 7.746475 GCATCTGAAATAACCTTATACAATCGC 59.254 37.037 0.00 0.00 0.00 4.58
2948 6518 8.275040 ACCAAGTAGCATCTGAAATAACCTTAT 58.725 33.333 0.00 0.00 0.00 1.73
2966 6567 9.901172 ACTTACAATCCCTAAATTACCAAGTAG 57.099 33.333 0.00 0.00 0.00 2.57
3018 6619 1.410004 TCCTCGGGTGATGATGTACC 58.590 55.000 0.00 0.00 36.21 3.34
3040 6641 4.246458 GAGAACGGAGAAGCAAACATAGT 58.754 43.478 0.00 0.00 0.00 2.12
3064 6665 4.338379 ACAGTAGTTTTCCTCAGGTGAC 57.662 45.455 0.00 0.00 0.00 3.67
3080 6687 5.349270 AGCATTGTCGCGTTTAATAACAGTA 59.651 36.000 5.77 0.00 36.85 2.74
3082 6689 4.647964 AGCATTGTCGCGTTTAATAACAG 58.352 39.130 5.77 0.00 36.85 3.16
3085 6692 7.751348 ACAATTTAGCATTGTCGCGTTTAATAA 59.249 29.630 5.77 0.00 37.69 1.40
3091 6698 3.552604 ACAATTTAGCATTGTCGCGTT 57.447 38.095 5.77 0.00 37.69 4.84
3092 6699 3.682858 ACTACAATTTAGCATTGTCGCGT 59.317 39.130 5.77 0.00 41.81 6.01
3093 6700 4.258935 ACTACAATTTAGCATTGTCGCG 57.741 40.909 0.00 0.00 41.81 5.87
3155 6776 1.010350 GATTCTCATGGCTTGCGCG 60.010 57.895 0.00 0.00 36.88 6.86


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

AutoCloner maintained by Alex Coulton.