Multiple sequence alignment - TraesCS3D01G398800

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 TraesCS3D01G398800 chr3D 100.000 6529 0 0 1 6529 513882072 513888600 0.000000e+00 12057.0
1 TraesCS3D01G398800 chr3D 100.000 28 0 0 4832 4859 513886830 513886857 1.200000e-02 52.8
2 TraesCS3D01G398800 chr3D 100.000 28 0 0 4759 4786 513886903 513886930 1.200000e-02 52.8
3 TraesCS3D01G398800 chr3A 92.766 6262 227 78 388 6529 648853948 648860103 0.000000e+00 8846.0
4 TraesCS3D01G398800 chr3A 89.865 148 15 0 101 248 648853810 648853957 2.400000e-44 191.0
5 TraesCS3D01G398800 chr3B 88.613 3662 233 90 2938 6529 676208596 676212143 0.000000e+00 4283.0
6 TraesCS3D01G398800 chr3B 92.939 2535 115 33 388 2903 676206109 676208598 0.000000e+00 3631.0
7 TraesCS3D01G398800 chr3B 87.226 274 24 3 485 758 676204589 676204851 1.060000e-77 302.0
8 TraesCS3D01G398800 chr3B 85.714 140 17 1 108 247 676205981 676206117 1.900000e-30 145.0
9 TraesCS3D01G398800 chr3B 89.888 89 8 1 1 88 676204254 676204342 5.350000e-21 113.0
10 TraesCS3D01G398800 chr3B 85.393 89 12 1 1 88 676205844 676205932 2.510000e-14 91.6
11 TraesCS3D01G398800 chr1A 86.831 243 32 0 2110 2352 456926490 456926732 8.340000e-69 272.0
12 TraesCS3D01G398800 chr1A 85.388 219 31 1 5276 5493 456931326 456931544 6.590000e-55 226.0
13 TraesCS3D01G398800 chr1B 86.420 243 33 0 2110 2352 478711104 478711346 3.880000e-67 267.0
14 TraesCS3D01G398800 chr1B 85.000 220 32 1 5275 5493 478715521 478715740 8.520000e-54 222.0
15 TraesCS3D01G398800 chr1B 90.291 103 10 0 1006 1108 478708939 478709041 1.140000e-27 135.0
16 TraesCS3D01G398800 chr1D 86.008 243 34 0 2110 2352 356137734 356137976 1.810000e-65 261.0
17 TraesCS3D01G398800 chr1D 85.455 220 31 1 5275 5493 356141859 356142078 1.830000e-55 228.0
18 TraesCS3D01G398800 chr1D 90.291 103 10 0 1006 1108 356136039 356136141 1.140000e-27 135.0


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 TraesCS3D01G398800 chr3D 513882072 513888600 6528 False 4054.2 12057 100.000000 1 6529 3 chr3D.!!$F1 6528
1 TraesCS3D01G398800 chr3A 648853810 648860103 6293 False 4518.5 8846 91.315500 101 6529 2 chr3A.!!$F1 6428
2 TraesCS3D01G398800 chr3B 676204254 676212143 7889 False 1427.6 4283 88.295500 1 6529 6 chr3B.!!$F1 6528
3 TraesCS3D01G398800 chr1B 478708939 478711346 2407 False 201.0 267 88.355500 1006 2352 2 chr1B.!!$F2 1346
4 TraesCS3D01G398800 chr1D 356136039 356142078 6039 False 208.0 261 87.251333 1006 5493 3 chr1D.!!$F1 4487

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
599 2069 0.100146 GAAGGGAACGCGACGTCTAT 59.900 55.000 15.93 0.00 39.99 1.98 F
1808 4623 0.657840 GGGCATTAGTGACATGACGC 59.342 55.000 0.00 0.00 33.89 5.19 F
1995 4810 2.303163 TACGATTTGGTCCACATCGG 57.697 50.000 32.98 20.30 44.85 4.18 F
2727 5878 1.680735 GCCCTGTTGTGACATGAACAA 59.319 47.619 12.62 12.62 34.72 2.83 F
4444 8641 1.281899 GCCGAGTGTCTGACTAATGC 58.718 55.000 9.51 2.23 33.83 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 4653 0.313672 TGCAACGAAAGGACATTGCC 59.686 50.000 5.43 0.0 45.45 4.52 R
2699 5850 0.467290 TCACAACAGGGCCTGGAAAC 60.467 55.000 35.34 0.0 35.51 2.78 R
3147 7096 1.935873 ACCAACATCATCATCGCTTCG 59.064 47.619 0.00 0.0 0.00 3.79 R
4516 8713 0.107410 TGACAACCACGCAGGAAACT 60.107 50.000 0.93 0.0 46.44 2.66 R
6005 11074 0.254178 AGCAAGACATACAGCAGGGG 59.746 55.000 0.00 0.0 0.00 4.79 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 3.261818 AAGTGTGGTCCCTAGAGAGTT 57.738 47.619 0.00 0.00 0.00 3.01
35 36 4.157105 GTCCCTAGAGAGTTGAGTGACTTC 59.843 50.000 0.00 0.00 0.00 3.01
36 37 3.127895 CCCTAGAGAGTTGAGTGACTTCG 59.872 52.174 0.00 0.00 0.00 3.79
42 43 3.754323 AGAGTTGAGTGACTTCGGTCTAG 59.246 47.826 0.00 0.00 44.70 2.43
44 45 3.890147 AGTTGAGTGACTTCGGTCTAGTT 59.110 43.478 0.00 0.00 44.70 2.24
50 51 5.068636 AGTGACTTCGGTCTAGTTGTTAGA 58.931 41.667 0.00 0.00 44.70 2.10
85 86 8.472007 ACAATGTTTTAACTAGATGGTGGAAA 57.528 30.769 0.00 0.00 0.00 3.13
87 88 9.927668 CAATGTTTTAACTAGATGGTGGAAAAT 57.072 29.630 0.00 0.00 0.00 1.82
98 99 9.927668 CTAGATGGTGGAAAATTTACAATGTTT 57.072 29.630 0.00 0.00 0.00 2.83
103 104 9.110502 TGGTGGAAAATTTACAATGTTTTAACC 57.889 29.630 0.00 0.00 34.94 2.85
104 105 9.332502 GGTGGAAAATTTACAATGTTTTAACCT 57.667 29.630 0.00 0.00 33.35 3.50
128 159 6.947258 TGCGTATGACATGTTGATAGAATTG 58.053 36.000 0.00 0.00 0.00 2.32
137 168 8.037382 ACATGTTGATAGAATTGTGTCAAGAG 57.963 34.615 13.91 9.77 31.84 2.85
143 174 8.853077 TGATAGAATTGTGTCAAGAGAAACAT 57.147 30.769 0.00 0.00 41.51 2.71
147 178 8.627208 AGAATTGTGTCAAGAGAAACATATGT 57.373 30.769 1.41 1.41 41.51 2.29
148 179 9.071276 AGAATTGTGTCAAGAGAAACATATGTT 57.929 29.630 15.47 15.47 41.51 2.71
205 236 2.891191 TCTTAGGGTTTGGCGGAATT 57.109 45.000 0.00 0.00 0.00 2.17
209 240 0.250989 AGGGTTTGGCGGAATTCGAA 60.251 50.000 0.00 0.00 42.43 3.71
237 268 1.529796 GAGTCAACCACACCCACCA 59.470 57.895 0.00 0.00 0.00 4.17
254 285 1.027357 CCATGATGGTAAGCACTGGC 58.973 55.000 2.54 0.00 34.46 4.85
255 286 2.676142 CCATGATGGTAAGCACTGGCG 61.676 57.143 2.54 0.00 37.72 5.69
256 287 4.950208 CCATGATGGTAAGCACTGGCGA 62.950 54.545 2.54 0.00 37.72 5.54
273 304 2.918712 CGAAGCCCTACAAGGATCAT 57.081 50.000 0.00 0.00 37.67 2.45
274 305 3.199880 CGAAGCCCTACAAGGATCATT 57.800 47.619 0.00 0.00 37.67 2.57
275 306 3.545703 CGAAGCCCTACAAGGATCATTT 58.454 45.455 0.00 0.00 37.67 2.32
276 307 4.703897 CGAAGCCCTACAAGGATCATTTA 58.296 43.478 0.00 0.00 37.67 1.40
277 308 4.511826 CGAAGCCCTACAAGGATCATTTAC 59.488 45.833 0.00 0.00 37.67 2.01
278 309 5.685075 CGAAGCCCTACAAGGATCATTTACT 60.685 44.000 0.00 0.00 37.67 2.24
280 311 6.079712 AGCCCTACAAGGATCATTTACTTT 57.920 37.500 0.00 0.00 37.67 2.66
281 312 7.208064 AGCCCTACAAGGATCATTTACTTTA 57.792 36.000 0.00 0.00 37.67 1.85
284 315 8.914011 GCCCTACAAGGATCATTTACTTTATTT 58.086 33.333 0.00 0.00 37.67 1.40
301 332 8.738645 ACTTTATTTTCCTAATCTAGCCTGTG 57.261 34.615 0.00 0.00 0.00 3.66
303 334 8.732746 TTTATTTTCCTAATCTAGCCTGTGTC 57.267 34.615 0.00 0.00 0.00 3.67
304 335 5.755409 TTTTCCTAATCTAGCCTGTGTCA 57.245 39.130 0.00 0.00 0.00 3.58
306 337 5.755409 TTCCTAATCTAGCCTGTGTCAAA 57.245 39.130 0.00 0.00 0.00 2.69
307 338 5.755409 TCCTAATCTAGCCTGTGTCAAAA 57.245 39.130 0.00 0.00 0.00 2.44
308 339 6.121776 TCCTAATCTAGCCTGTGTCAAAAA 57.878 37.500 0.00 0.00 0.00 1.94
372 403 3.650950 GGCCCCTGCAGGAGTCAA 61.651 66.667 34.91 0.00 40.13 3.18
373 404 2.360475 GCCCCTGCAGGAGTCAAC 60.360 66.667 34.91 12.14 38.24 3.18
375 406 1.687612 CCCCTGCAGGAGTCAACAT 59.312 57.895 34.91 0.00 38.24 2.71
376 407 0.911769 CCCCTGCAGGAGTCAACATA 59.088 55.000 34.91 0.00 38.24 2.29
377 408 1.134280 CCCCTGCAGGAGTCAACATAG 60.134 57.143 34.91 12.69 38.24 2.23
378 409 1.556911 CCCTGCAGGAGTCAACATAGT 59.443 52.381 34.91 0.00 38.24 2.12
380 411 3.005554 CCTGCAGGAGTCAACATAGTTG 58.994 50.000 29.88 3.58 37.39 3.16
381 412 3.557898 CCTGCAGGAGTCAACATAGTTGT 60.558 47.826 29.88 0.00 35.67 3.32
382 413 3.402110 TGCAGGAGTCAACATAGTTGTG 58.598 45.455 9.43 2.27 35.83 3.33
383 414 2.160417 GCAGGAGTCAACATAGTTGTGC 59.840 50.000 9.43 7.90 35.83 4.57
384 415 2.744202 CAGGAGTCAACATAGTTGTGCC 59.256 50.000 9.43 9.16 35.83 5.01
386 417 1.128692 GAGTCAACATAGTTGTGCCGC 59.871 52.381 9.43 0.00 35.83 6.53
387 418 1.156736 GTCAACATAGTTGTGCCGCT 58.843 50.000 9.43 0.00 35.83 5.52
388 419 1.135972 GTCAACATAGTTGTGCCGCTG 60.136 52.381 9.43 0.00 35.83 5.18
389 420 1.155889 CAACATAGTTGTGCCGCTGA 58.844 50.000 1.86 0.00 35.83 4.26
390 421 1.739466 CAACATAGTTGTGCCGCTGAT 59.261 47.619 1.86 0.00 35.83 2.90
391 422 1.372582 ACATAGTTGTGCCGCTGATG 58.627 50.000 0.00 0.00 33.85 3.07
392 423 0.659427 CATAGTTGTGCCGCTGATGG 59.341 55.000 0.00 0.00 0.00 3.51
393 424 0.253044 ATAGTTGTGCCGCTGATGGT 59.747 50.000 0.00 0.00 0.00 3.55
407 1877 4.881850 CGCTGATGGTAAGATTAGGGTTTT 59.118 41.667 0.00 0.00 0.00 2.43
417 1887 9.251440 GGTAAGATTAGGGTTTTAAGGTGAAAT 57.749 33.333 0.00 0.00 0.00 2.17
424 1894 7.907841 AGGGTTTTAAGGTGAAATTGTTAGT 57.092 32.000 0.00 0.00 0.00 2.24
444 1914 0.250597 ACAACGGTTAACCAGAGCCC 60.251 55.000 24.14 0.00 35.14 5.19
445 1915 0.958876 CAACGGTTAACCAGAGCCCC 60.959 60.000 24.14 0.00 35.14 5.80
459 1929 2.918248 CCCCCATCGATGCAGGAA 59.082 61.111 26.07 0.00 0.00 3.36
473 1943 1.400242 GCAGGAACAACGATGACAAGC 60.400 52.381 0.00 0.00 0.00 4.01
478 1948 3.545633 GAACAACGATGACAAGCAAGAC 58.454 45.455 0.00 0.00 0.00 3.01
479 1949 1.873591 ACAACGATGACAAGCAAGACC 59.126 47.619 0.00 0.00 0.00 3.85
550 2020 6.070596 GGGAAGGAATGGAAAGAATCAACAAT 60.071 38.462 0.00 0.00 0.00 2.71
573 2043 1.807742 CATAAACCCTTGCCGAAACGA 59.192 47.619 0.00 0.00 0.00 3.85
583 2053 1.871039 TGCCGAAACGAAAGGAAGAAG 59.129 47.619 0.00 0.00 0.00 2.85
584 2054 1.197036 GCCGAAACGAAAGGAAGAAGG 59.803 52.381 0.00 0.00 0.00 3.46
592 2062 0.395312 AAAGGAAGAAGGGAACGCGA 59.605 50.000 15.93 0.00 0.00 5.87
599 2069 0.100146 GAAGGGAACGCGACGTCTAT 59.900 55.000 15.93 0.00 39.99 1.98
609 2079 4.925068 ACGCGACGTCTATATTTAGGTTT 58.075 39.130 15.93 0.00 33.69 3.27
610 2080 6.060028 ACGCGACGTCTATATTTAGGTTTA 57.940 37.500 15.93 0.00 33.69 2.01
611 2081 6.494842 ACGCGACGTCTATATTTAGGTTTAA 58.505 36.000 15.93 0.00 33.69 1.52
612 2082 6.972328 ACGCGACGTCTATATTTAGGTTTAAA 59.028 34.615 15.93 0.00 33.69 1.52
708 2180 2.124903 AGTCACGTTTTGTAGCACTCG 58.875 47.619 0.00 0.00 0.00 4.18
780 2253 2.885644 CCGAACGCACGATGGAGG 60.886 66.667 0.00 0.00 35.09 4.30
1316 2805 1.025041 GCCGGGGATTCTTGAATGAC 58.975 55.000 2.18 0.00 0.00 3.06
1348 2837 1.002792 GTGTTCGGCTGTTTGAGTTCC 60.003 52.381 0.00 0.00 0.00 3.62
1566 3889 1.616994 GGGTTGATTGGAACTGGGGAG 60.617 57.143 0.00 0.00 0.00 4.30
1577 3900 2.365635 TGGGGAGTCAGGGCTAGC 60.366 66.667 6.04 6.04 0.00 3.42
1585 3908 0.750249 GTCAGGGCTAGCTCTTCCTC 59.250 60.000 16.48 1.75 0.00 3.71
1702 4120 3.475566 TGCTGCTGACTAGTTGACTTT 57.524 42.857 0.00 0.00 0.00 2.66
1713 4526 5.949735 ACTAGTTGACTTTTGGTGTGTTTG 58.050 37.500 0.00 0.00 0.00 2.93
1731 4545 1.055849 TGGGTGTCTTTGCAGCTCTA 58.944 50.000 0.00 0.00 37.09 2.43
1735 4549 2.417933 GGTGTCTTTGCAGCTCTATGTG 59.582 50.000 0.00 0.00 34.39 3.21
1808 4623 0.657840 GGGCATTAGTGACATGACGC 59.342 55.000 0.00 0.00 33.89 5.19
1864 4679 4.678509 TGTCCTTTCGTTGCATTGATAC 57.321 40.909 0.00 0.00 0.00 2.24
1995 4810 2.303163 TACGATTTGGTCCACATCGG 57.697 50.000 32.98 20.30 44.85 4.18
2225 5040 3.374988 CAGCATTAGGAATCAACTTCGCA 59.625 43.478 0.00 0.00 34.45 5.10
2387 5213 3.981051 GGGTTCTTTTCCCCTCTCC 57.019 57.895 0.00 0.00 39.08 3.71
2467 5304 5.010282 GGTTCATGTGTTAGGATTCCTGTT 58.990 41.667 15.80 0.00 34.61 3.16
2473 5310 6.381498 TGTGTTAGGATTCCTGTTAATGGA 57.619 37.500 15.80 0.00 34.61 3.41
2489 5326 6.488344 TGTTAATGGATGTTAACTGTTGCTCA 59.512 34.615 7.22 0.39 42.35 4.26
2490 5327 5.376854 AATGGATGTTAACTGTTGCTCAC 57.623 39.130 7.22 0.00 0.00 3.51
2541 5551 4.281435 TCAAATGGAATGTGTTCTGTGCAT 59.719 37.500 0.00 0.00 31.84 3.96
2542 5552 5.476254 TCAAATGGAATGTGTTCTGTGCATA 59.524 36.000 0.00 0.00 31.84 3.14
2544 5554 6.534475 AATGGAATGTGTTCTGTGCATATT 57.466 33.333 0.00 0.00 34.68 1.28
2546 5556 5.953183 TGGAATGTGTTCTGTGCATATTTC 58.047 37.500 0.00 0.00 34.68 2.17
2727 5878 1.680735 GCCCTGTTGTGACATGAACAA 59.319 47.619 12.62 12.62 34.72 2.83
2734 5885 2.229792 TGTGACATGAACAAGAAGGGC 58.770 47.619 0.00 0.00 0.00 5.19
2844 5995 5.730550 GTGATTGGACACTAGAACCATGTA 58.269 41.667 0.00 0.00 37.73 2.29
3049 6992 5.707242 TGTCCTGTCTACTTTACTGTCAG 57.293 43.478 0.00 0.00 0.00 3.51
3082 7025 2.623416 GTTTGAAGTTTAGGGCACTGCT 59.377 45.455 0.00 0.00 0.00 4.24
3103 7046 9.613428 ACTGCTTATTACTTTATTAGTGCATCA 57.387 29.630 0.00 0.00 37.73 3.07
3147 7096 1.396301 GTCAGTTGTGCTGCATAGAGC 59.604 52.381 5.27 0.00 44.66 4.09
3166 7115 2.657960 CGAAGCGATGATGATGTTGG 57.342 50.000 0.00 0.00 0.00 3.77
3279 7228 8.246871 TCTCATCTTTCCTTGCTATATCATACG 58.753 37.037 0.00 0.00 0.00 3.06
3347 7445 6.568869 TGTGTGGTTCAAAAGATGGTTTTAG 58.431 36.000 0.00 0.00 0.00 1.85
3464 7562 3.903714 AGCATGGTGTATATCCACTGCTA 59.096 43.478 11.84 0.00 42.21 3.49
3580 7679 5.801380 AGTTCACCATATTAACCACTCGTT 58.199 37.500 0.00 0.00 38.57 3.85
3593 7692 3.074412 CCACTCGTTTTCTATGGCAACT 58.926 45.455 0.00 0.00 37.61 3.16
3806 7907 2.019249 GCTTGCTCTATTCCATGCACA 58.981 47.619 0.00 0.00 35.01 4.57
3807 7908 2.033049 GCTTGCTCTATTCCATGCACAG 59.967 50.000 0.00 0.00 35.01 3.66
3821 7922 4.382362 CCATGCACAGAGTCTACTGATCAA 60.382 45.833 0.00 0.00 40.63 2.57
4325 8521 8.882736 CAAAGGACTTTTGCTATTTTTCTGTTT 58.117 29.630 0.00 0.00 39.71 2.83
4444 8641 1.281899 GCCGAGTGTCTGACTAATGC 58.718 55.000 9.51 2.23 33.83 3.56
4486 8683 5.133221 AGTTGTAGCCAGAGTCAAAACAAT 58.867 37.500 0.00 0.00 0.00 2.71
4499 8696 6.275335 AGTCAAAACAATCTCACAACCATTG 58.725 36.000 0.00 0.00 34.29 2.82
4516 8713 4.104738 ACCATTGAGAAAAACAGGAGAGGA 59.895 41.667 0.00 0.00 0.00 3.71
4591 8805 2.230025 TGTTTACATGAACATTGGGCGG 59.770 45.455 0.00 0.00 34.77 6.13
4827 9044 3.807209 GCTCTGCAAAGTCTTTACCCAGA 60.807 47.826 15.81 15.81 0.00 3.86
4828 9045 4.389374 CTCTGCAAAGTCTTTACCCAGAA 58.611 43.478 16.71 7.32 0.00 3.02
4829 9046 4.389374 TCTGCAAAGTCTTTACCCAGAAG 58.611 43.478 14.96 2.19 0.00 2.85
4830 9047 4.137543 CTGCAAAGTCTTTACCCAGAAGT 58.862 43.478 11.53 0.00 0.00 3.01
4831 9048 4.134563 TGCAAAGTCTTTACCCAGAAGTC 58.865 43.478 0.00 0.00 0.00 3.01
4832 9049 4.141482 TGCAAAGTCTTTACCCAGAAGTCT 60.141 41.667 0.00 0.00 0.00 3.24
4833 9050 4.822350 GCAAAGTCTTTACCCAGAAGTCTT 59.178 41.667 0.00 0.00 35.18 3.01
4834 9051 5.299531 GCAAAGTCTTTACCCAGAAGTCTTT 59.700 40.000 0.00 0.00 40.52 2.52
4835 9052 6.729187 CAAAGTCTTTACCCAGAAGTCTTTG 58.271 40.000 16.16 16.16 44.92 2.77
4836 9053 4.390264 AGTCTTTACCCAGAAGTCTTTGC 58.610 43.478 0.00 0.00 0.00 3.68
4837 9054 4.103311 AGTCTTTACCCAGAAGTCTTTGCT 59.897 41.667 0.00 0.00 0.00 3.91
4838 9055 5.307196 AGTCTTTACCCAGAAGTCTTTGCTA 59.693 40.000 0.00 0.00 0.00 3.49
4839 9056 6.013293 AGTCTTTACCCAGAAGTCTTTGCTAT 60.013 38.462 0.00 0.00 0.00 2.97
4840 9057 6.655425 GTCTTTACCCAGAAGTCTTTGCTATT 59.345 38.462 0.00 0.00 0.00 1.73
4841 9058 7.822822 GTCTTTACCCAGAAGTCTTTGCTATTA 59.177 37.037 0.00 0.00 0.00 0.98
4842 9059 8.041323 TCTTTACCCAGAAGTCTTTGCTATTAG 58.959 37.037 0.00 0.00 0.00 1.73
4843 9060 5.104259 ACCCAGAAGTCTTTGCTATTAGG 57.896 43.478 0.00 0.00 0.00 2.69
4844 9061 4.080299 ACCCAGAAGTCTTTGCTATTAGGG 60.080 45.833 0.00 0.00 37.43 3.53
4845 9062 4.455606 CCAGAAGTCTTTGCTATTAGGGG 58.544 47.826 0.00 0.00 0.00 4.79
4846 9063 4.164221 CCAGAAGTCTTTGCTATTAGGGGA 59.836 45.833 0.00 0.00 0.00 4.81
4847 9064 5.339200 CCAGAAGTCTTTGCTATTAGGGGAA 60.339 44.000 0.00 0.00 0.00 3.97
4849 9066 6.261826 CAGAAGTCTTTGCTATTAGGGGAATG 59.738 42.308 0.00 0.00 0.00 2.67
4853 9070 2.523841 TGCTATTAGGGGAATGGGGA 57.476 50.000 0.00 0.00 0.00 4.81
4872 9089 3.563390 GGGAGCACTCTATCTGAATTTGC 59.437 47.826 0.00 0.00 0.00 3.68
4880 9913 6.370994 CACTCTATCTGAATTTGCTGTGTTCT 59.629 38.462 0.00 0.00 0.00 3.01
4989 10022 8.584157 TCCAATGTTACATTTTGATGCTACTTT 58.416 29.630 7.97 0.00 0.00 2.66
5188 10224 3.364549 CCATGGATGGTGTATTGGTGTT 58.635 45.455 5.56 0.00 43.05 3.32
5189 10225 3.768757 CCATGGATGGTGTATTGGTGTTT 59.231 43.478 5.56 0.00 43.05 2.83
5221 10257 3.539604 GCTGATCCACTCTTGCTTATGT 58.460 45.455 0.00 0.00 0.00 2.29
5318 10362 3.878519 GAGGACGAGGGCGACGAG 61.879 72.222 0.00 0.00 41.64 4.18
5658 10706 4.952460 TCCTAGTCTGTAAGCGTGTTTTT 58.048 39.130 0.00 0.00 0.00 1.94
5754 10807 0.957395 CGACTGCCAGCTGACCATTT 60.957 55.000 17.39 2.03 0.00 2.32
5775 10828 7.308229 CCATTTCTTCATTATTCGTGGATCCTC 60.308 40.741 14.23 8.71 0.00 3.71
5837 10894 1.457346 CACTGATCCTGGGTTGCTTC 58.543 55.000 0.00 0.00 0.00 3.86
5873 10931 7.333174 TGCTCTGTTGATCGAAACATATTTGTA 59.667 33.333 3.26 0.00 39.25 2.41
5908 10970 9.051679 TGGTTAATACTACAATTCCATCATTCG 57.948 33.333 0.00 0.00 0.00 3.34
5912 10974 7.891183 ATACTACAATTCCATCATTCGTAGC 57.109 36.000 0.00 0.00 0.00 3.58
5933 10995 4.460382 AGCAGTATTGACCAAACATCCTTG 59.540 41.667 0.00 0.00 0.00 3.61
5943 11005 4.776837 ACCAAACATCCTTGCAAATATGGA 59.223 37.500 19.43 14.41 0.00 3.41
5957 11019 7.853299 TGCAAATATGGAGTACTACTTTGGTA 58.147 34.615 16.12 0.60 0.00 3.25
5968 11030 2.358322 ACTTTGGTAGTTGGGTGGTG 57.642 50.000 0.00 0.00 31.29 4.17
6040 11114 2.007360 TGCTTGTGTTGCAAAACTGG 57.993 45.000 20.26 13.29 37.51 4.00
6041 11115 0.652071 GCTTGTGTTGCAAAACTGGC 59.348 50.000 20.26 18.42 36.53 4.85
6042 11116 1.289276 CTTGTGTTGCAAAACTGGCC 58.711 50.000 20.26 0.00 36.53 5.36
6044 11118 1.769026 TGTGTTGCAAAACTGGCCTA 58.231 45.000 20.26 0.00 0.00 3.93
6059 11172 0.828677 GCCTACAGGATACACGGGTT 59.171 55.000 0.00 0.00 37.39 4.11
6073 11190 1.481056 CGGGTTCCTCCTCACAGGTT 61.481 60.000 0.00 0.00 36.53 3.50
6074 11191 0.771755 GGGTTCCTCCTCACAGGTTT 59.228 55.000 0.00 0.00 36.53 3.27
6075 11192 1.145119 GGGTTCCTCCTCACAGGTTTT 59.855 52.381 0.00 0.00 36.53 2.43
6076 11193 2.424379 GGGTTCCTCCTCACAGGTTTTT 60.424 50.000 0.00 0.00 36.53 1.94
6099 11216 2.930562 GGCACCCTCCTCACAGGT 60.931 66.667 0.00 0.00 36.53 4.00
6107 11224 2.930019 CCTCACAGGTCTGGGCCA 60.930 66.667 5.85 5.85 33.05 5.36
6162 11284 0.321653 AAGCCCACCAAGTAGCGAAG 60.322 55.000 0.00 0.00 0.00 3.79
6188 11310 2.747855 CTGTCGGAGCCCAAAGCC 60.748 66.667 0.00 0.00 45.47 4.35
6251 11377 3.585990 CGCCGCATCCAACCCATC 61.586 66.667 0.00 0.00 0.00 3.51
6252 11378 3.585990 GCCGCATCCAACCCATCG 61.586 66.667 0.00 0.00 0.00 3.84
6317 11445 2.443016 CCCTCCTCCTCCGGACAG 60.443 72.222 0.00 0.00 0.00 3.51
6507 11641 1.348775 GGGGAGGATGACAAGGGAGG 61.349 65.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.110188 ACTCAACTCTCTAGGGACCACA 59.890 50.000 0.00 0.00 0.00 4.17
15 16 3.127895 CCGAAGTCACTCAACTCTCTAGG 59.872 52.174 0.00 0.00 0.00 3.02
25 26 3.220110 ACAACTAGACCGAAGTCACTCA 58.780 45.455 0.00 0.00 46.15 3.41
85 86 9.134734 CATACGCAGGTTAAAACATTGTAAATT 57.865 29.630 0.00 0.00 0.00 1.82
87 88 7.804129 GTCATACGCAGGTTAAAACATTGTAAA 59.196 33.333 0.00 0.00 0.00 2.01
89 90 6.427242 TGTCATACGCAGGTTAAAACATTGTA 59.573 34.615 0.00 0.00 0.00 2.41
91 92 5.694816 TGTCATACGCAGGTTAAAACATTG 58.305 37.500 0.00 0.00 0.00 2.82
93 94 5.414454 ACATGTCATACGCAGGTTAAAACAT 59.586 36.000 0.00 0.00 0.00 2.71
94 95 4.757657 ACATGTCATACGCAGGTTAAAACA 59.242 37.500 0.00 0.00 0.00 2.83
95 96 5.291293 ACATGTCATACGCAGGTTAAAAC 57.709 39.130 0.00 0.00 0.00 2.43
98 99 4.570930 TCAACATGTCATACGCAGGTTAA 58.429 39.130 0.00 0.00 38.54 2.01
100 101 3.052455 TCAACATGTCATACGCAGGTT 57.948 42.857 0.00 0.00 40.77 3.50
101 102 2.760634 TCAACATGTCATACGCAGGT 57.239 45.000 0.00 0.00 31.87 4.00
102 103 4.620982 TCTATCAACATGTCATACGCAGG 58.379 43.478 0.00 0.00 0.00 4.85
103 104 6.775939 ATTCTATCAACATGTCATACGCAG 57.224 37.500 0.00 0.00 0.00 5.18
104 105 6.538381 ACAATTCTATCAACATGTCATACGCA 59.462 34.615 0.00 0.00 0.00 5.24
128 159 8.764524 AGTAGAACATATGTTTCTCTTGACAC 57.235 34.615 21.63 9.75 38.56 3.67
143 174 9.871238 AAAGAGCTCGATTTTAAGTAGAACATA 57.129 29.630 8.37 0.00 0.00 2.29
147 178 8.827177 TGAAAAGAGCTCGATTTTAAGTAGAA 57.173 30.769 17.83 0.00 0.00 2.10
148 179 8.827177 TTGAAAAGAGCTCGATTTTAAGTAGA 57.173 30.769 17.83 1.36 0.00 2.59
157 188 4.227864 AGGGATTGAAAAGAGCTCGATT 57.772 40.909 8.37 7.43 0.00 3.34
205 236 1.244816 TGACTCCTTCTTCGCTTCGA 58.755 50.000 0.00 0.00 0.00 3.71
209 240 1.048601 TGGTTGACTCCTTCTTCGCT 58.951 50.000 0.00 0.00 0.00 4.93
237 268 0.541392 TCGCCAGTGCTTACCATCAT 59.459 50.000 0.00 0.00 34.43 2.45
254 285 2.918712 ATGATCCTTGTAGGGCTTCG 57.081 50.000 0.00 0.00 35.59 3.79
255 286 5.685728 AGTAAATGATCCTTGTAGGGCTTC 58.314 41.667 0.00 0.00 35.59 3.86
256 287 5.717119 AGTAAATGATCCTTGTAGGGCTT 57.283 39.130 0.00 0.00 35.59 4.35
257 288 5.717119 AAGTAAATGATCCTTGTAGGGCT 57.283 39.130 0.00 0.00 35.59 5.19
258 289 8.465273 AATAAAGTAAATGATCCTTGTAGGGC 57.535 34.615 0.00 0.00 35.59 5.19
275 306 9.832445 CACAGGCTAGATTAGGAAAATAAAGTA 57.168 33.333 0.00 0.00 0.00 2.24
276 307 8.329502 ACACAGGCTAGATTAGGAAAATAAAGT 58.670 33.333 0.00 0.00 0.00 2.66
277 308 8.738645 ACACAGGCTAGATTAGGAAAATAAAG 57.261 34.615 0.00 0.00 0.00 1.85
278 309 8.325787 TGACACAGGCTAGATTAGGAAAATAAA 58.674 33.333 0.00 0.00 0.00 1.40
280 311 7.432148 TGACACAGGCTAGATTAGGAAAATA 57.568 36.000 0.00 0.00 0.00 1.40
281 312 6.313519 TGACACAGGCTAGATTAGGAAAAT 57.686 37.500 0.00 0.00 0.00 1.82
284 315 5.755409 TTTGACACAGGCTAGATTAGGAA 57.245 39.130 0.00 0.00 0.00 3.36
285 316 5.755409 TTTTGACACAGGCTAGATTAGGA 57.245 39.130 0.00 0.00 0.00 2.94
308 339 8.284693 GCAAAACTGCAAATACATGAAGAATTT 58.715 29.630 0.00 0.00 29.93 1.82
311 342 6.279123 TGCAAAACTGCAAATACATGAAGAA 58.721 32.000 0.00 0.00 42.40 2.52
312 343 5.840715 TGCAAAACTGCAAATACATGAAGA 58.159 33.333 0.00 0.00 42.40 2.87
324 355 1.143620 GCCTTGGTGCAAAACTGCA 59.856 52.632 0.00 0.00 43.22 4.41
325 356 0.877213 CAGCCTTGGTGCAAAACTGC 60.877 55.000 0.00 0.00 0.00 4.40
328 359 1.069596 CCCAGCCTTGGTGCAAAAC 59.930 57.895 0.00 0.00 43.40 2.43
329 360 2.139484 CCCCAGCCTTGGTGCAAAA 61.139 57.895 0.00 0.00 43.40 2.44
330 361 2.523902 CCCCAGCCTTGGTGCAAA 60.524 61.111 0.00 0.00 43.40 3.68
351 382 4.517934 CTCCTGCAGGGGCCATGG 62.518 72.222 32.23 7.63 40.13 3.66
352 383 3.711059 GACTCCTGCAGGGGCCATG 62.711 68.421 33.33 15.10 40.10 3.66
353 384 3.415087 GACTCCTGCAGGGGCCAT 61.415 66.667 33.33 14.05 40.10 4.40
354 385 4.980592 TGACTCCTGCAGGGGCCA 62.981 66.667 33.33 26.51 40.10 5.36
355 386 3.650950 TTGACTCCTGCAGGGGCC 61.651 66.667 33.33 23.72 40.10 5.80
356 387 2.360475 GTTGACTCCTGCAGGGGC 60.360 66.667 33.33 24.56 40.10 5.80
357 388 0.911769 TATGTTGACTCCTGCAGGGG 59.088 55.000 31.85 31.85 42.91 4.79
358 389 1.556911 ACTATGTTGACTCCTGCAGGG 59.443 52.381 32.23 23.77 35.41 4.45
359 390 3.005554 CAACTATGTTGACTCCTGCAGG 58.994 50.000 27.87 27.87 0.00 4.85
361 392 3.402110 CACAACTATGTTGACTCCTGCA 58.598 45.455 16.04 0.00 37.82 4.41
362 393 2.160417 GCACAACTATGTTGACTCCTGC 59.840 50.000 16.04 11.07 37.82 4.85
363 394 2.744202 GGCACAACTATGTTGACTCCTG 59.256 50.000 16.04 5.74 37.82 3.86
364 395 2.612972 CGGCACAACTATGTTGACTCCT 60.613 50.000 16.04 0.00 37.82 3.69
365 396 1.732259 CGGCACAACTATGTTGACTCC 59.268 52.381 16.04 11.76 37.82 3.85
366 397 1.128692 GCGGCACAACTATGTTGACTC 59.871 52.381 16.04 5.48 37.82 3.36
367 398 1.156736 GCGGCACAACTATGTTGACT 58.843 50.000 16.04 0.00 37.82 3.41
372 403 1.372582 CATCAGCGGCACAACTATGT 58.627 50.000 1.45 0.00 41.61 2.29
373 404 0.659427 CCATCAGCGGCACAACTATG 59.341 55.000 1.45 0.00 0.00 2.23
375 406 0.899019 TACCATCAGCGGCACAACTA 59.101 50.000 1.45 0.00 0.00 2.24
376 407 0.036164 TTACCATCAGCGGCACAACT 59.964 50.000 1.45 0.00 0.00 3.16
377 408 0.447801 CTTACCATCAGCGGCACAAC 59.552 55.000 1.45 0.00 0.00 3.32
378 409 0.323302 TCTTACCATCAGCGGCACAA 59.677 50.000 1.45 0.00 0.00 3.33
380 411 1.668419 AATCTTACCATCAGCGGCAC 58.332 50.000 1.45 0.00 0.00 5.01
381 412 2.224281 CCTAATCTTACCATCAGCGGCA 60.224 50.000 1.45 0.00 0.00 5.69
382 413 2.417719 CCTAATCTTACCATCAGCGGC 58.582 52.381 0.00 0.00 0.00 6.53
383 414 2.368875 ACCCTAATCTTACCATCAGCGG 59.631 50.000 0.00 0.00 0.00 5.52
384 415 3.753294 ACCCTAATCTTACCATCAGCG 57.247 47.619 0.00 0.00 0.00 5.18
386 417 8.053355 ACCTTAAAACCCTAATCTTACCATCAG 58.947 37.037 0.00 0.00 0.00 2.90
387 418 7.832187 CACCTTAAAACCCTAATCTTACCATCA 59.168 37.037 0.00 0.00 0.00 3.07
388 419 8.050930 TCACCTTAAAACCCTAATCTTACCATC 58.949 37.037 0.00 0.00 0.00 3.51
389 420 7.935405 TCACCTTAAAACCCTAATCTTACCAT 58.065 34.615 0.00 0.00 0.00 3.55
390 421 7.332433 TCACCTTAAAACCCTAATCTTACCA 57.668 36.000 0.00 0.00 0.00 3.25
391 422 8.640063 TTTCACCTTAAAACCCTAATCTTACC 57.360 34.615 0.00 0.00 0.00 2.85
407 1877 6.991531 ACCGTTGTACTAACAATTTCACCTTA 59.008 34.615 0.00 0.00 46.84 2.69
417 1887 5.911752 TCTGGTTAACCGTTGTACTAACAA 58.088 37.500 19.65 0.00 40.17 2.83
424 1894 1.002315 GGGCTCTGGTTAACCGTTGTA 59.998 52.381 19.65 0.68 39.43 2.41
444 1914 0.734889 GTTGTTCCTGCATCGATGGG 59.265 55.000 26.00 19.10 0.00 4.00
445 1915 0.374758 CGTTGTTCCTGCATCGATGG 59.625 55.000 26.00 10.64 34.58 3.51
459 1929 1.873591 GGTCTTGCTTGTCATCGTTGT 59.126 47.619 0.00 0.00 0.00 3.32
473 1943 2.831597 GGTTTCGTACCCGGTCTTG 58.168 57.895 0.00 0.00 41.43 3.02
520 1990 1.359130 CTTTCCATTCCTTCCCACCCT 59.641 52.381 0.00 0.00 0.00 4.34
521 1991 1.357761 TCTTTCCATTCCTTCCCACCC 59.642 52.381 0.00 0.00 0.00 4.61
522 1992 2.899303 TCTTTCCATTCCTTCCCACC 57.101 50.000 0.00 0.00 0.00 4.61
524 1994 4.673328 TGATTCTTTCCATTCCTTCCCA 57.327 40.909 0.00 0.00 0.00 4.37
525 1995 4.772100 TGTTGATTCTTTCCATTCCTTCCC 59.228 41.667 0.00 0.00 0.00 3.97
550 2020 2.554893 GTTTCGGCAAGGGTTTATGACA 59.445 45.455 0.00 0.00 0.00 3.58
573 2043 0.395312 TCGCGTTCCCTTCTTCCTTT 59.605 50.000 5.77 0.00 0.00 3.11
583 2053 2.412421 AATATAGACGTCGCGTTCCC 57.588 50.000 10.46 0.00 41.37 3.97
584 2054 3.910767 CCTAAATATAGACGTCGCGTTCC 59.089 47.826 10.46 0.00 41.37 3.62
612 2082 7.720074 AGTCTCCGGTTTTATCTTCTTCTTTTT 59.280 33.333 0.00 0.00 0.00 1.94
629 2100 1.569548 TCCCTAGATCAAGTCTCCGGT 59.430 52.381 0.00 0.00 38.42 5.28
708 2180 1.680207 GAGCATGATTTCCCAAGAGGC 59.320 52.381 0.00 0.00 34.51 4.70
791 2264 2.826738 TATTTGCGCCCCGGCTTC 60.827 61.111 4.18 0.00 39.32 3.86
1316 2805 1.562575 CCGAACACGAAAAGACCCCG 61.563 60.000 0.00 0.00 0.00 5.73
1348 2837 5.856126 TCCAATCTAACACTAAAGCAACG 57.144 39.130 0.00 0.00 0.00 4.10
1566 3889 0.750249 GAGGAAGAGCTAGCCCTGAC 59.250 60.000 14.21 3.90 0.00 3.51
1577 3900 4.904241 ACAATTCCACAAGAGAGGAAGAG 58.096 43.478 0.00 0.00 45.66 2.85
1585 3908 3.369147 CGAGTGCTACAATTCCACAAGAG 59.631 47.826 0.00 0.00 32.09 2.85
1702 4120 2.223803 AAGACACCCAAACACACCAA 57.776 45.000 0.00 0.00 0.00 3.67
1713 4526 2.012673 CATAGAGCTGCAAAGACACCC 58.987 52.381 1.02 0.00 0.00 4.61
1731 4545 3.630312 ACCTAACAAAGAAACGCACACAT 59.370 39.130 0.00 0.00 0.00 3.21
1735 4549 4.281525 TGAACCTAACAAAGAAACGCAC 57.718 40.909 0.00 0.00 0.00 5.34
1808 4623 2.042230 ACTACTACCCAGCCCCGG 60.042 66.667 0.00 0.00 0.00 5.73
1838 4653 0.313672 TGCAACGAAAGGACATTGCC 59.686 50.000 5.43 0.00 45.45 4.52
1864 4679 1.345741 ACTGATATCGATGCCCTGTGG 59.654 52.381 8.54 0.00 0.00 4.17
1995 4810 7.875041 ACTAGAGTGGAATTGTCATGCATATAC 59.125 37.037 0.00 1.18 0.00 1.47
2225 5040 4.479796 TCCTTCTCATTCATTCCATCCCTT 59.520 41.667 0.00 0.00 0.00 3.95
2467 5304 6.000840 TGTGAGCAACAGTTAACATCCATTA 58.999 36.000 8.61 0.00 33.78 1.90
2473 5310 3.944650 TGTGTGTGAGCAACAGTTAACAT 59.055 39.130 8.61 0.00 40.26 2.71
2541 5551 9.613428 CATGGTCCACAGTAAGAAATAGAAATA 57.387 33.333 0.00 0.00 0.00 1.40
2542 5552 8.109634 ACATGGTCCACAGTAAGAAATAGAAAT 58.890 33.333 0.00 0.00 0.00 2.17
2544 5554 7.016153 ACATGGTCCACAGTAAGAAATAGAA 57.984 36.000 0.00 0.00 0.00 2.10
2546 5556 8.786826 TTTACATGGTCCACAGTAAGAAATAG 57.213 34.615 14.88 0.00 30.21 1.73
2686 5837 4.156739 GGCCTGGAAACTCATAACTTTCAG 59.843 45.833 0.00 0.00 0.00 3.02
2699 5850 0.467290 TCACAACAGGGCCTGGAAAC 60.467 55.000 35.34 0.00 35.51 2.78
2727 5878 1.284841 CCAGAATCCCAGGCCCTTCT 61.285 60.000 0.00 0.00 0.00 2.85
2734 5885 1.027357 CGCATTTCCAGAATCCCAGG 58.973 55.000 0.00 0.00 0.00 4.45
3022 6965 6.456501 ACAGTAAAGTAGACAGGACAATGAC 58.543 40.000 0.00 0.00 0.00 3.06
3049 6992 9.573133 CCCTAAACTTCAAACATGTCATATTTC 57.427 33.333 0.00 0.00 0.00 2.17
3103 7046 4.850680 TCCACAAAAGGTAGACACTTGTT 58.149 39.130 0.00 0.00 0.00 2.83
3104 7047 4.497291 TCCACAAAAGGTAGACACTTGT 57.503 40.909 0.00 0.00 0.00 3.16
3105 7048 4.821805 ACATCCACAAAAGGTAGACACTTG 59.178 41.667 0.00 0.00 0.00 3.16
3147 7096 1.935873 ACCAACATCATCATCGCTTCG 59.064 47.619 0.00 0.00 0.00 3.79
3151 7100 2.419673 TGTGAACCAACATCATCATCGC 59.580 45.455 0.00 0.00 0.00 4.58
3166 7115 3.374988 TGCAGCAGTAATAGCATGTGAAC 59.625 43.478 0.00 0.00 31.05 3.18
3464 7562 8.408043 TTTTCCAATATCTGTGAAATGTGAGT 57.592 30.769 0.00 0.00 29.73 3.41
3519 7618 5.016831 GGATACAAACCCTCTTCAACCATT 58.983 41.667 0.00 0.00 0.00 3.16
3580 7679 9.515226 AAACAAGATAACTAGTTGCCATAGAAA 57.485 29.630 18.56 0.00 0.00 2.52
3821 7922 6.660521 TGTTTCACAGCCAAGATTCATTCTAT 59.339 34.615 0.00 0.00 33.05 1.98
4499 8696 4.757657 GGAAACTCCTCTCCTGTTTTTCTC 59.242 45.833 0.00 0.00 34.55 2.87
4516 8713 0.107410 TGACAACCACGCAGGAAACT 60.107 50.000 0.93 0.00 46.44 2.66
4528 8725 3.248363 GCTTCAAGCCATTTTTGACAACC 59.752 43.478 0.00 0.00 34.50 3.77
4591 8805 1.070601 AGCCAACCAAGTTTTCATGCC 59.929 47.619 0.00 0.00 0.00 4.40
4827 9044 5.449553 CCATTCCCCTAATAGCAAAGACTT 58.550 41.667 0.00 0.00 0.00 3.01
4828 9045 4.141158 CCCATTCCCCTAATAGCAAAGACT 60.141 45.833 0.00 0.00 0.00 3.24
4829 9046 4.145052 CCCATTCCCCTAATAGCAAAGAC 58.855 47.826 0.00 0.00 0.00 3.01
4830 9047 3.140144 CCCCATTCCCCTAATAGCAAAGA 59.860 47.826 0.00 0.00 0.00 2.52
4831 9048 3.140144 TCCCCATTCCCCTAATAGCAAAG 59.860 47.826 0.00 0.00 0.00 2.77
4832 9049 3.135279 TCCCCATTCCCCTAATAGCAAA 58.865 45.455 0.00 0.00 0.00 3.68
4833 9050 2.716424 CTCCCCATTCCCCTAATAGCAA 59.284 50.000 0.00 0.00 0.00 3.91
4834 9051 2.348472 CTCCCCATTCCCCTAATAGCA 58.652 52.381 0.00 0.00 0.00 3.49
4835 9052 1.004862 GCTCCCCATTCCCCTAATAGC 59.995 57.143 0.00 0.00 0.00 2.97
4836 9053 2.040412 GTGCTCCCCATTCCCCTAATAG 59.960 54.545 0.00 0.00 0.00 1.73
4837 9054 2.062636 GTGCTCCCCATTCCCCTAATA 58.937 52.381 0.00 0.00 0.00 0.98
4838 9055 0.853530 GTGCTCCCCATTCCCCTAAT 59.146 55.000 0.00 0.00 0.00 1.73
4839 9056 0.253630 AGTGCTCCCCATTCCCCTAA 60.254 55.000 0.00 0.00 0.00 2.69
4840 9057 0.694444 GAGTGCTCCCCATTCCCCTA 60.694 60.000 0.00 0.00 0.00 3.53
4841 9058 2.003548 GAGTGCTCCCCATTCCCCT 61.004 63.158 0.00 0.00 0.00 4.79
4842 9059 0.694444 TAGAGTGCTCCCCATTCCCC 60.694 60.000 0.00 0.00 31.01 4.81
4843 9060 1.349357 GATAGAGTGCTCCCCATTCCC 59.651 57.143 0.00 0.00 31.01 3.97
4844 9061 2.038295 CAGATAGAGTGCTCCCCATTCC 59.962 54.545 0.00 0.00 31.01 3.01
4845 9062 2.968574 TCAGATAGAGTGCTCCCCATTC 59.031 50.000 0.00 0.00 0.00 2.67
4846 9063 3.051940 TCAGATAGAGTGCTCCCCATT 57.948 47.619 0.00 0.00 0.00 3.16
4847 9064 2.783379 TCAGATAGAGTGCTCCCCAT 57.217 50.000 0.00 0.00 0.00 4.00
4849 9066 4.133078 CAAATTCAGATAGAGTGCTCCCC 58.867 47.826 0.00 0.00 0.00 4.81
4853 9070 4.634883 CACAGCAAATTCAGATAGAGTGCT 59.365 41.667 0.00 0.00 39.69 4.40
4872 9089 7.198390 ACAAACAGATGAAAATGAGAACACAG 58.802 34.615 0.00 0.00 0.00 3.66
4907 9940 4.712051 ATAATCAGTTGCAGCAGGGATA 57.288 40.909 2.55 0.00 0.00 2.59
4989 10022 4.335315 CGCCTCCTGCACAAGAAAATAATA 59.665 41.667 0.00 0.00 41.33 0.98
5180 10216 1.067915 CGGCGATTCCAAAACACCAAT 60.068 47.619 0.00 0.00 34.01 3.16
5181 10217 0.312416 CGGCGATTCCAAAACACCAA 59.688 50.000 0.00 0.00 34.01 3.67
5185 10221 0.886938 TCAGCGGCGATTCCAAAACA 60.887 50.000 12.98 0.00 34.01 2.83
5188 10224 1.095228 GGATCAGCGGCGATTCCAAA 61.095 55.000 12.98 0.00 34.01 3.28
5189 10225 1.523711 GGATCAGCGGCGATTCCAA 60.524 57.895 12.98 0.00 34.01 3.53
5318 10362 2.043852 TCGTGCTCCTCCTCCTCC 60.044 66.667 0.00 0.00 0.00 4.30
5754 10807 5.363868 ACAGAGGATCCACGAATAATGAAGA 59.636 40.000 15.82 0.00 33.66 2.87
5775 10828 2.726760 GCAACAGAGTCACGAACTACAG 59.273 50.000 0.00 0.00 38.74 2.74
5908 10970 5.186198 AGGATGTTTGGTCAATACTGCTAC 58.814 41.667 0.00 0.00 0.00 3.58
5912 10974 4.218200 TGCAAGGATGTTTGGTCAATACTG 59.782 41.667 0.00 0.00 0.00 2.74
5933 10995 8.366671 CTACCAAAGTAGTACTCCATATTTGC 57.633 38.462 2.58 0.00 41.03 3.68
5974 11043 6.353323 TCACTCAACTATTCCAGTGTCAAAA 58.647 36.000 0.00 0.00 37.63 2.44
6005 11074 0.254178 AGCAAGACATACAGCAGGGG 59.746 55.000 0.00 0.00 0.00 4.79
6038 11112 1.046472 CCCGTGTATCCTGTAGGCCA 61.046 60.000 5.01 0.00 34.44 5.36
6040 11114 0.828677 AACCCGTGTATCCTGTAGGC 59.171 55.000 0.00 0.00 34.44 3.93
6041 11115 1.411612 GGAACCCGTGTATCCTGTAGG 59.588 57.143 0.00 0.00 0.00 3.18
6042 11116 2.361438 GAGGAACCCGTGTATCCTGTAG 59.639 54.545 6.52 0.00 43.55 2.74
6044 11118 1.192428 GAGGAACCCGTGTATCCTGT 58.808 55.000 6.52 0.00 43.55 4.00
6080 11197 3.721706 CTGTGAGGAGGGTGCCCC 61.722 72.222 3.17 2.16 45.90 5.80
6081 11198 3.721706 CCTGTGAGGAGGGTGCCC 61.722 72.222 0.00 0.00 37.67 5.36
6082 11199 2.930562 ACCTGTGAGGAGGGTGCC 60.931 66.667 0.00 0.00 37.67 5.01
6083 11200 1.915769 AGACCTGTGAGGAGGGTGC 60.916 63.158 0.00 0.00 37.67 5.01
6084 11201 1.548357 CCAGACCTGTGAGGAGGGTG 61.548 65.000 0.00 0.00 37.67 4.61
6085 11202 1.229336 CCAGACCTGTGAGGAGGGT 60.229 63.158 0.00 0.00 37.67 4.34
6086 11203 1.992277 CCCAGACCTGTGAGGAGGG 60.992 68.421 0.00 1.35 37.67 4.30
6087 11204 2.664081 GCCCAGACCTGTGAGGAGG 61.664 68.421 0.00 0.00 37.67 4.30
6088 11205 2.664081 GGCCCAGACCTGTGAGGAG 61.664 68.421 0.00 0.00 37.67 3.69
6089 11206 2.607750 GGCCCAGACCTGTGAGGA 60.608 66.667 0.00 0.00 37.67 3.71
6090 11207 2.528818 TTGGCCCAGACCTGTGAGG 61.529 63.158 0.00 0.00 42.49 3.86
6091 11208 1.302832 GTTGGCCCAGACCTGTGAG 60.303 63.158 0.00 0.00 0.00 3.51
6092 11209 2.836154 GTTGGCCCAGACCTGTGA 59.164 61.111 0.00 0.00 0.00 3.58
6093 11210 2.669569 CGTTGGCCCAGACCTGTG 60.670 66.667 0.00 0.00 0.00 3.66
6094 11211 4.643387 GCGTTGGCCCAGACCTGT 62.643 66.667 0.00 0.00 0.00 4.00
6251 11377 1.668101 CGGAGGAGGAAGGAAGGACG 61.668 65.000 0.00 0.00 0.00 4.79
6252 11378 1.962321 GCGGAGGAGGAAGGAAGGAC 61.962 65.000 0.00 0.00 0.00 3.85
6483 11617 0.179000 CTTGTCATCCTCCCCTTCGG 59.821 60.000 0.00 0.00 0.00 4.30
6484 11618 0.179000 CCTTGTCATCCTCCCCTTCG 59.821 60.000 0.00 0.00 0.00 3.79
6485 11619 0.548510 CCCTTGTCATCCTCCCCTTC 59.451 60.000 0.00 0.00 0.00 3.46
6486 11620 0.121197 TCCCTTGTCATCCTCCCCTT 59.879 55.000 0.00 0.00 0.00 3.95
6487 11621 0.327000 CTCCCTTGTCATCCTCCCCT 60.327 60.000 0.00 0.00 0.00 4.79
6507 11641 1.109609 CCCCAGGTAGTTCTCGTACC 58.890 60.000 0.00 0.00 40.42 3.34


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

AutoCloner maintained by Alex Coulton.