Multiple sequence alignment - TraesCS2D01G268800

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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 TraesCS2D01G268800 chr2D 100.000 3356 0 0 1 3356 330467232 330470587 0.000000e+00 6198.0
1 TraesCS2D01G268800 chr2D 95.634 733 31 1 2574 3305 497543370 497542638 0.000000e+00 1175.0
2 TraesCS2D01G268800 chr2D 95.851 723 29 1 2584 3305 374514128 374514850 0.000000e+00 1168.0
3 TraesCS2D01G268800 chr2D 95.429 722 33 0 2584 3305 79038617 79037896 0.000000e+00 1151.0
4 TraesCS2D01G268800 chr2D 78.193 321 53 9 5 315 70670410 70670097 4.420000e-44 189.0
5 TraesCS2D01G268800 chr2D 89.431 123 10 3 878 997 330468045 330468167 5.800000e-33 152.0
6 TraesCS2D01G268800 chr2D 89.431 123 10 3 814 936 330468109 330468228 5.800000e-33 152.0
7 TraesCS2D01G268800 chr2B 96.512 860 24 5 919 1777 398699099 398699953 0.000000e+00 1417.0
8 TraesCS2D01G268800 chr2B 93.820 534 32 1 386 918 398697233 398697766 0.000000e+00 802.0
9 TraesCS2D01G268800 chr2B 94.987 399 14 3 1777 2169 398699890 398700288 3.680000e-174 621.0
10 TraesCS2D01G268800 chr2B 90.099 404 28 4 1 396 398695503 398695902 6.420000e-142 514.0
11 TraesCS2D01G268800 chr2B 89.583 336 12 10 2159 2471 398700438 398700773 4.030000e-109 405.0
12 TraesCS2D01G268800 chr6D 96.266 723 25 2 2584 3305 86157686 86158407 0.000000e+00 1184.0
13 TraesCS2D01G268800 chr6D 100.000 53 0 0 3304 3356 296264191 296264243 7.660000e-17 99.0
14 TraesCS2D01G268800 chr6D 98.113 53 1 0 3304 3356 405007001 405006949 3.570000e-15 93.5
15 TraesCS2D01G268800 chr1D 93.528 788 36 1 2584 3356 267314410 267315197 0.000000e+00 1158.0
16 TraesCS2D01G268800 chr1D 95.574 723 30 2 2585 3305 308795833 308796555 0.000000e+00 1157.0
17 TraesCS2D01G268800 chr1D 88.053 226 17 4 107 324 319616273 319616050 3.320000e-65 259.0
18 TraesCS2D01G268800 chr1D 98.113 53 1 0 3304 3356 322593029 322592977 3.570000e-15 93.5
19 TraesCS2D01G268800 chr1D 98.113 53 1 0 3304 3356 408310041 408309989 3.570000e-15 93.5
20 TraesCS2D01G268800 chr1D 98.113 53 1 0 3304 3356 463756480 463756532 3.570000e-15 93.5
21 TraesCS2D01G268800 chr1D 83.168 101 15 2 43 141 319616370 319616270 1.280000e-14 91.6
22 TraesCS2D01G268800 chr4D 95.436 723 30 2 2585 3305 435531898 435531177 0.000000e+00 1149.0
23 TraesCS2D01G268800 chr4D 95.284 721 34 0 2585 3305 223269480 223268760 0.000000e+00 1144.0
24 TraesCS2D01G268800 chr4D 95.284 721 33 1 2584 3304 36055689 36056408 0.000000e+00 1142.0
25 TraesCS2D01G268800 chr7D 88.424 812 53 5 2585 3356 222298660 222299470 0.000000e+00 941.0
26 TraesCS2D01G268800 chr7D 79.757 247 38 9 547 782 421865676 421865431 5.760000e-38 169.0
27 TraesCS2D01G268800 chr3B 84.444 270 33 5 58 319 448495009 448494741 1.190000e-64 257.0
28 TraesCS2D01G268800 chr3A 84.647 241 33 4 547 783 481878168 481877928 1.560000e-58 237.0
29 TraesCS2D01G268800 chr3A 79.688 128 21 4 547 670 688947379 688947505 1.660000e-13 87.9
30 TraesCS2D01G268800 chr3A 80.392 102 19 1 547 648 688921216 688921116 3.590000e-10 76.8
31 TraesCS2D01G268800 chr4A 78.221 326 53 10 7 322 733101044 733100727 3.420000e-45 193.0
32 TraesCS2D01G268800 chr4A 77.982 327 53 10 7 322 733173667 733173349 1.590000e-43 187.0
33 TraesCS2D01G268800 chr4A 77.982 327 53 11 7 322 733199470 733199152 1.590000e-43 187.0
34 TraesCS2D01G268800 chr4A 79.197 274 44 8 58 322 733224211 733223942 9.570000e-41 178.0
35 TraesCS2D01G268800 chr2A 81.604 212 34 5 577 784 155158545 155158755 1.600000e-38 171.0
36 TraesCS2D01G268800 chr2A 83.660 153 13 10 2441 2583 437506291 437506441 2.100000e-27 134.0
37 TraesCS2D01G268800 chr5A 83.607 183 25 4 602 779 509722011 509722193 2.070000e-37 167.0
38 TraesCS2D01G268800 chr5B 81.159 207 29 8 582 779 485886828 485886623 1.250000e-34 158.0
39 TraesCS2D01G268800 chr3D 81.513 119 20 2 547 664 552495975 552496092 2.760000e-16 97.1
40 TraesCS2D01G268800 chr3D 98.113 53 1 0 3304 3356 526093524 526093472 3.570000e-15 93.5
41 TraesCS2D01G268800 chr3D 79.825 114 21 2 547 659 552474132 552474244 7.720000e-12 82.4
42 TraesCS2D01G268800 chr5D 98.113 53 1 0 3304 3356 236948165 236948217 3.570000e-15 93.5
43 TraesCS2D01G268800 chr5D 92.188 64 4 1 3294 3356 390059275 390059338 4.610000e-14 89.8


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 TraesCS2D01G268800 chr2D 330467232 330470587 3355 False 2167.333333 6198 92.9540 1 3356 3 chr2D.!!$F2 3355
1 TraesCS2D01G268800 chr2D 497542638 497543370 732 True 1175.000000 1175 95.6340 2574 3305 1 chr2D.!!$R3 731
2 TraesCS2D01G268800 chr2D 374514128 374514850 722 False 1168.000000 1168 95.8510 2584 3305 1 chr2D.!!$F1 721
3 TraesCS2D01G268800 chr2D 79037896 79038617 721 True 1151.000000 1151 95.4290 2584 3305 1 chr2D.!!$R2 721
4 TraesCS2D01G268800 chr2B 398695503 398700773 5270 False 751.800000 1417 93.0002 1 2471 5 chr2B.!!$F1 2470
5 TraesCS2D01G268800 chr6D 86157686 86158407 721 False 1184.000000 1184 96.2660 2584 3305 1 chr6D.!!$F1 721
6 TraesCS2D01G268800 chr1D 267314410 267315197 787 False 1158.000000 1158 93.5280 2584 3356 1 chr1D.!!$F1 772
7 TraesCS2D01G268800 chr1D 308795833 308796555 722 False 1157.000000 1157 95.5740 2585 3305 1 chr1D.!!$F2 720
8 TraesCS2D01G268800 chr4D 435531177 435531898 721 True 1149.000000 1149 95.4360 2585 3305 1 chr4D.!!$R2 720
9 TraesCS2D01G268800 chr4D 223268760 223269480 720 True 1144.000000 1144 95.2840 2585 3305 1 chr4D.!!$R1 720
10 TraesCS2D01G268800 chr4D 36055689 36056408 719 False 1142.000000 1142 95.2840 2584 3304 1 chr4D.!!$F1 720
11 TraesCS2D01G268800 chr7D 222298660 222299470 810 False 941.000000 941 88.4240 2585 3356 1 chr7D.!!$F1 771

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
927 3290 0.037232 GACTGAGTACCACCCTGCAC 60.037 60.0 0.0 0.0 0.0 4.57 F
1769 4452 0.039437 ACTACGACGACAACTGCCAG 60.039 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 5106 0.036164 TGGTCATGCCAGCTAAACGT 59.964 50.0 4.93 0.0 43.61 3.99 R
2571 5440 0.179094 TCCGACAACGCACTTGACTT 60.179 50.0 0.00 0.0 38.29 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.959553 TCACGTCAGGTTCACTCTCC 59.040 55.000 0.00 0.00 0.00 3.71
50 51 7.311360 CCTCCCTATATCTCAAAAACCCTATCC 60.311 44.444 0.00 0.00 0.00 2.59
82 83 4.329545 TGCAGCAACGGGAGGACC 62.330 66.667 0.00 0.00 0.00 4.46
86 87 1.078710 AGCAACGGGAGGACCTACT 59.921 57.895 3.00 0.00 36.97 2.57
166 174 0.537188 AGGCCACAACCTCTACATCG 59.463 55.000 5.01 0.00 33.62 3.84
176 184 4.592485 ACCTCTACATCGTCCATCAATC 57.408 45.455 0.00 0.00 0.00 2.67
183 191 0.103026 TCGTCCATCAATCTCGCCTG 59.897 55.000 0.00 0.00 0.00 4.85
203 211 0.723414 CAACGAGCAAGCGATCATGT 59.277 50.000 0.00 0.00 34.83 3.21
236 244 4.186926 GACACGTAAAGGATCCCTAAACC 58.813 47.826 8.55 0.00 31.13 3.27
241 249 3.973472 AAAGGATCCCTAAACCCATCC 57.027 47.619 8.55 0.00 35.87 3.51
244 252 1.425448 GGATCCCTAAACCCATCCCTG 59.575 57.143 0.00 0.00 30.17 4.45
255 263 4.170468 ACCCATCCCTGTTCATGTTATC 57.830 45.455 0.00 0.00 0.00 1.75
256 264 3.788142 ACCCATCCCTGTTCATGTTATCT 59.212 43.478 0.00 0.00 0.00 1.98
259 267 4.581824 CCATCCCTGTTCATGTTATCTTGG 59.418 45.833 0.00 0.00 0.00 3.61
261 269 3.591527 TCCCTGTTCATGTTATCTTGGGT 59.408 43.478 0.00 0.00 34.14 4.51
338 346 8.355169 ACCAACAATTATCAGTAATCATCATGC 58.645 33.333 0.00 0.00 30.28 4.06
377 385 6.515272 TCCATAATTTGCCTCAAGAAGTTC 57.485 37.500 0.00 0.00 0.00 3.01
387 1738 3.055747 CCTCAAGAAGTTCCAGTCTACCC 60.056 52.174 0.00 0.00 0.00 3.69
398 1749 4.362677 TCCAGTCTACCCTTCATAAGCTT 58.637 43.478 3.48 3.48 0.00 3.74
432 1783 5.292101 CCAGTTTATAAGCACAGTAGCTCAC 59.708 44.000 1.97 0.00 45.89 3.51
464 1815 7.067372 GGTCATTTCCATGATGAATACACTCAA 59.933 37.037 0.00 0.00 41.64 3.02
476 1827 9.099454 GATGAATACACTCAAAAGTAACTAGGG 57.901 37.037 0.00 0.00 33.25 3.53
478 1829 9.092338 TGAATACACTCAAAAGTAACTAGGGTA 57.908 33.333 0.00 0.00 33.25 3.69
525 1876 7.095816 GCAGTTAATTAACATCCAAAACACCAC 60.096 37.037 26.06 0.00 38.62 4.16
579 1930 1.959226 GGCTGACGTTTGCCGAGAA 60.959 57.895 15.22 0.00 39.71 2.87
592 1943 1.301677 CCGAGAAAGGAGTGGCAAGC 61.302 60.000 0.00 0.00 0.00 4.01
603 1954 1.888512 AGTGGCAAGCGAATGTCATTT 59.111 42.857 0.00 0.00 37.25 2.32
640 1991 3.367607 TGTGAAGAAAAATCAAACGGCG 58.632 40.909 4.80 4.80 0.00 6.46
677 2028 8.485591 CAAAAATGTCTTCTCTGAAGAAATTGC 58.514 33.333 20.10 7.04 40.95 3.56
685 2036 2.162208 TCTGAAGAAATTGCCATGTCGC 59.838 45.455 0.00 0.00 0.00 5.19
706 2057 0.608130 GTGAAGAAATTGCCACCCCC 59.392 55.000 0.00 0.00 0.00 5.40
710 2061 0.040204 AGAAATTGCCACCCCCTCAG 59.960 55.000 0.00 0.00 0.00 3.35
724 2075 4.105697 ACCCCCTCAGAACTAAAATTGTCA 59.894 41.667 0.00 0.00 0.00 3.58
756 2107 4.269523 GTGTGCCACCCTGCCTGA 62.270 66.667 0.00 0.00 0.00 3.86
774 2125 3.596967 CTGACGATCGTTCGCCAGTTAC 61.597 54.545 23.63 5.75 46.76 2.50
783 2134 2.572284 GCCAGTTACGAGCGTCCT 59.428 61.111 0.00 0.00 0.00 3.85
793 2144 3.717350 ACGAGCGTCCTTTAAAAATCG 57.283 42.857 0.00 0.00 35.21 3.34
822 2173 2.019249 ACACGCGTACATAGCCTCTTA 58.981 47.619 13.44 0.00 0.00 2.10
831 2182 2.565834 ACATAGCCTCTTACCACACGTT 59.434 45.455 0.00 0.00 0.00 3.99
848 2199 4.119862 CACGTTGTACTATCCTTCCATGG 58.880 47.826 4.97 4.97 0.00 3.66
857 2208 1.204146 TCCTTCCATGGCTGAGTACC 58.796 55.000 6.96 0.00 0.00 3.34
879 2230 1.657487 CTGCACGTATCCGCCGTAG 60.657 63.158 0.00 0.00 36.65 3.51
892 2243 1.003839 CCGTAGCCTCTTGCCACAA 60.004 57.895 0.00 0.00 42.71 3.33
901 2252 3.366374 GCCTCTTGCCACAAGTTGTATTC 60.366 47.826 8.49 1.52 0.00 1.75
927 3290 0.037232 GACTGAGTACCACCCTGCAC 60.037 60.000 0.00 0.00 0.00 4.57
928 3291 1.079819 CTGAGTACCACCCTGCACG 60.080 63.158 0.00 0.00 0.00 5.34
1100 3783 4.816984 TCGGTCCCTCTCCCTCGC 62.817 72.222 0.00 0.00 0.00 5.03
1133 3816 0.708918 GAAGTTCGAAACTCGCTCGG 59.291 55.000 0.00 0.00 41.91 4.63
1151 3834 2.103538 CAACATCTGCGCCATGGC 59.896 61.111 27.67 27.67 37.85 4.40
1174 3857 1.219522 CGAACAATCCCGATACGGCC 61.220 60.000 4.57 0.00 46.86 6.13
1269 3952 3.052081 GAGCACCAGGTCGTGAGT 58.948 61.111 0.00 0.00 35.68 3.41
1398 4081 2.048222 CACGATGTGGTGACCGCT 60.048 61.111 17.02 1.66 40.38 5.52
1443 4126 3.606886 GGTGCTATACCGGGACATG 57.393 57.895 6.32 0.00 40.26 3.21
1459 4142 3.004106 GGACATGCATATCAAACTGCTCC 59.996 47.826 7.38 0.00 39.16 4.70
1608 4291 1.000163 GTGTCTCTGTCCTCGCTCAAA 60.000 52.381 0.00 0.00 0.00 2.69
1701 4384 1.541588 CTCATCCATCGGAGCGTATCA 59.458 52.381 0.00 0.00 34.05 2.15
1716 4399 2.016393 TATCAGCGCCTTCCCTGTCG 62.016 60.000 2.29 0.00 0.00 4.35
1766 4449 0.110509 TCGACTACGACGACAACTGC 60.111 55.000 0.00 0.00 43.81 4.40
1767 4450 1.063951 CGACTACGACGACAACTGCC 61.064 60.000 0.00 0.00 42.66 4.85
1768 4451 0.039798 GACTACGACGACAACTGCCA 60.040 55.000 0.00 0.00 0.00 4.92
1769 4452 0.039437 ACTACGACGACAACTGCCAG 60.039 55.000 0.00 0.00 0.00 4.85
1770 4453 0.240145 CTACGACGACAACTGCCAGA 59.760 55.000 0.00 0.00 0.00 3.86
1771 4454 0.240145 TACGACGACAACTGCCAGAG 59.760 55.000 0.00 0.00 0.00 3.35
1772 4455 2.375766 CGACGACAACTGCCAGAGC 61.376 63.158 0.00 0.00 40.48 4.09
1774 4457 1.560860 GACGACAACTGCCAGAGCAC 61.561 60.000 0.00 0.00 46.52 4.40
1775 4458 2.320587 CGACAACTGCCAGAGCACC 61.321 63.158 0.00 0.00 46.52 5.01
1776 4459 1.968540 GACAACTGCCAGAGCACCC 60.969 63.158 0.00 0.00 46.52 4.61
1777 4460 2.403132 GACAACTGCCAGAGCACCCT 62.403 60.000 0.00 0.00 46.52 4.34
1778 4461 1.970114 CAACTGCCAGAGCACCCTG 60.970 63.158 0.00 0.00 46.52 4.45
1779 4462 2.455565 AACTGCCAGAGCACCCTGT 61.456 57.895 0.00 0.00 46.52 4.00
1780 4463 2.046507 CTGCCAGAGCACCCTGTC 60.047 66.667 0.00 0.00 46.52 3.51
1781 4464 3.947132 CTGCCAGAGCACCCTGTCG 62.947 68.421 0.00 0.00 46.52 4.35
1783 4466 4.767255 CCAGAGCACCCTGTCGCC 62.767 72.222 0.00 0.00 32.43 5.54
2012 4695 4.450419 CGCCTCAATCAGATCAGGTAAATC 59.550 45.833 9.29 0.00 0.00 2.17
2020 4703 4.895889 TCAGATCAGGTAAATCTCACCGAT 59.104 41.667 0.00 0.00 41.21 4.18
2113 4799 7.766278 GGTGTCTACCAATTAGCTATGATATGG 59.234 40.741 0.00 1.98 46.71 2.74
2149 4835 1.298859 CGCAGTACAAGGAGCCAACC 61.299 60.000 0.00 0.00 0.00 3.77
2175 5022 2.839486 TGGCGTGAAGAACTCAATCT 57.161 45.000 0.00 0.00 35.22 2.40
2211 5058 8.947055 ATTATTAGTGTTTTGGATTTGGATGC 57.053 30.769 0.00 0.00 0.00 3.91
2224 5071 0.829990 TGGATGCCGCAAGTGATAGA 59.170 50.000 0.00 0.00 0.00 1.98
2225 5072 1.202568 TGGATGCCGCAAGTGATAGAG 60.203 52.381 0.00 0.00 0.00 2.43
2230 5077 1.398390 GCCGCAAGTGATAGAGTTTGG 59.602 52.381 0.00 0.00 0.00 3.28
2231 5078 2.935238 GCCGCAAGTGATAGAGTTTGGA 60.935 50.000 0.00 0.00 0.00 3.53
2232 5079 2.932614 CCGCAAGTGATAGAGTTTGGAG 59.067 50.000 0.00 0.00 0.00 3.86
2251 5117 5.657474 TGGAGTATAAGAACGTTTAGCTGG 58.343 41.667 0.46 0.00 0.00 4.85
2286 5153 8.875168 TCCTATTTGGTCCATGTGTTTAAATTT 58.125 29.630 0.00 0.00 37.07 1.82
2298 5165 6.587273 TGTGTTTAAATTTTCCTCCTTTGGG 58.413 36.000 0.00 0.00 0.00 4.12
2320 5187 5.406477 GGGCAATGTCAAAGTTTGATCTTTC 59.594 40.000 20.72 11.48 42.47 2.62
2326 5193 8.862550 ATGTCAAAGTTTGATCTTTCACTTTC 57.137 30.769 20.72 4.79 42.47 2.62
2407 5274 2.820178 TCTAACATGCAGAGGTCAGGA 58.180 47.619 0.00 0.00 0.00 3.86
2493 5362 9.801714 ACTATTCACGACACTTATTTTAAAACG 57.198 29.630 1.97 3.23 0.00 3.60
2494 5363 9.257865 CTATTCACGACACTTATTTTAAAACGG 57.742 33.333 1.97 0.00 0.00 4.44
2495 5364 6.841443 TCACGACACTTATTTTAAAACGGA 57.159 33.333 1.97 0.00 0.00 4.69
2496 5365 6.879962 TCACGACACTTATTTTAAAACGGAG 58.120 36.000 1.97 4.41 0.00 4.63
2498 5367 6.572254 CACGACACTTATTTTAAAACGGAGTG 59.428 38.462 24.28 24.28 45.00 3.51
2499 5368 6.479660 ACGACACTTATTTTAAAACGGAGTGA 59.520 34.615 28.60 5.44 45.00 3.41
2500 5369 7.007697 CGACACTTATTTTAAAACGGAGTGAG 58.992 38.462 28.60 21.85 45.00 3.51
2501 5370 7.306983 CGACACTTATTTTAAAACGGAGTGAGT 60.307 37.037 28.60 17.19 45.00 3.41
2502 5371 8.891671 ACACTTATTTTAAAACGGAGTGAGTA 57.108 30.769 28.60 7.31 45.00 2.59
2503 5372 8.768019 ACACTTATTTTAAAACGGAGTGAGTAC 58.232 33.333 28.60 0.00 45.00 2.73
2504 5373 8.985805 CACTTATTTTAAAACGGAGTGAGTACT 58.014 33.333 22.92 0.00 45.00 2.73
2505 5374 9.551734 ACTTATTTTAAAACGGAGTGAGTACTT 57.448 29.630 1.97 0.00 45.00 2.24
2509 5378 8.947055 TTTTAAAACGGAGTGAGTACTTAGTT 57.053 30.769 0.00 0.00 45.00 2.24
2513 5382 8.754230 AAAACGGAGTGAGTACTTAGTTAATC 57.246 34.615 0.00 0.00 45.00 1.75
2514 5383 7.700022 AACGGAGTGAGTACTTAGTTAATCT 57.300 36.000 0.00 0.00 45.00 2.40
2515 5384 7.319142 ACGGAGTGAGTACTTAGTTAATCTC 57.681 40.000 0.00 0.00 42.51 2.75
2516 5385 7.111466 ACGGAGTGAGTACTTAGTTAATCTCT 58.889 38.462 0.00 0.00 42.51 3.10
2517 5386 7.280652 ACGGAGTGAGTACTTAGTTAATCTCTC 59.719 40.741 0.00 2.97 42.51 3.20
2518 5387 7.496591 CGGAGTGAGTACTTAGTTAATCTCTCT 59.503 40.741 15.71 12.53 37.25 3.10
2519 5388 8.833493 GGAGTGAGTACTTAGTTAATCTCTCTC 58.167 40.741 18.21 18.21 39.58 3.20
2520 5389 9.609346 GAGTGAGTACTTAGTTAATCTCTCTCT 57.391 37.037 18.64 11.85 38.43 3.10
2521 5390 9.609346 AGTGAGTACTTAGTTAATCTCTCTCTC 57.391 37.037 0.00 0.00 31.66 3.20
2522 5391 9.386010 GTGAGTACTTAGTTAATCTCTCTCTCA 57.614 37.037 0.00 0.00 0.00 3.27
2523 5392 9.961264 TGAGTACTTAGTTAATCTCTCTCTCAA 57.039 33.333 0.00 0.00 0.00 3.02
2531 5400 8.608185 AGTTAATCTCTCTCTCAATCTTTCCT 57.392 34.615 0.00 0.00 0.00 3.36
2532 5401 9.045745 AGTTAATCTCTCTCTCAATCTTTCCTT 57.954 33.333 0.00 0.00 0.00 3.36
2533 5402 9.665719 GTTAATCTCTCTCTCAATCTTTCCTTT 57.334 33.333 0.00 0.00 0.00 3.11
2534 5403 9.883142 TTAATCTCTCTCTCAATCTTTCCTTTC 57.117 33.333 0.00 0.00 0.00 2.62
2535 5404 7.738437 ATCTCTCTCTCAATCTTTCCTTTCT 57.262 36.000 0.00 0.00 0.00 2.52
2536 5405 7.169158 TCTCTCTCTCAATCTTTCCTTTCTC 57.831 40.000 0.00 0.00 0.00 2.87
2537 5406 6.154363 TCTCTCTCTCAATCTTTCCTTTCTCC 59.846 42.308 0.00 0.00 0.00 3.71
2538 5407 6.022315 TCTCTCTCAATCTTTCCTTTCTCCT 58.978 40.000 0.00 0.00 0.00 3.69
2539 5408 6.154363 TCTCTCTCAATCTTTCCTTTCTCCTC 59.846 42.308 0.00 0.00 0.00 3.71
2540 5409 6.022315 TCTCTCAATCTTTCCTTTCTCCTCT 58.978 40.000 0.00 0.00 0.00 3.69
2541 5410 6.500049 TCTCTCAATCTTTCCTTTCTCCTCTT 59.500 38.462 0.00 0.00 0.00 2.85
2542 5411 6.706295 TCTCAATCTTTCCTTTCTCCTCTTC 58.294 40.000 0.00 0.00 0.00 2.87
2543 5412 6.500049 TCTCAATCTTTCCTTTCTCCTCTTCT 59.500 38.462 0.00 0.00 0.00 2.85
2544 5413 7.017056 TCTCAATCTTTCCTTTCTCCTCTTCTT 59.983 37.037 0.00 0.00 0.00 2.52
2545 5414 7.164803 TCAATCTTTCCTTTCTCCTCTTCTTC 58.835 38.462 0.00 0.00 0.00 2.87
2546 5415 6.950860 ATCTTTCCTTTCTCCTCTTCTTCT 57.049 37.500 0.00 0.00 0.00 2.85
2547 5416 8.317679 CAATCTTTCCTTTCTCCTCTTCTTCTA 58.682 37.037 0.00 0.00 0.00 2.10
2548 5417 8.622572 ATCTTTCCTTTCTCCTCTTCTTCTAT 57.377 34.615 0.00 0.00 0.00 1.98
2549 5418 8.442660 TCTTTCCTTTCTCCTCTTCTTCTATT 57.557 34.615 0.00 0.00 0.00 1.73
2550 5419 9.548631 TCTTTCCTTTCTCCTCTTCTTCTATTA 57.451 33.333 0.00 0.00 0.00 0.98
2551 5420 9.594478 CTTTCCTTTCTCCTCTTCTTCTATTAC 57.406 37.037 0.00 0.00 0.00 1.89
2552 5421 7.663043 TCCTTTCTCCTCTTCTTCTATTACC 57.337 40.000 0.00 0.00 0.00 2.85
2553 5422 7.423341 TCCTTTCTCCTCTTCTTCTATTACCT 58.577 38.462 0.00 0.00 0.00 3.08
2554 5423 7.901861 TCCTTTCTCCTCTTCTTCTATTACCTT 59.098 37.037 0.00 0.00 0.00 3.50
2555 5424 8.544622 CCTTTCTCCTCTTCTTCTATTACCTTT 58.455 37.037 0.00 0.00 0.00 3.11
2556 5425 9.594478 CTTTCTCCTCTTCTTCTATTACCTTTC 57.406 37.037 0.00 0.00 0.00 2.62
2557 5426 8.666129 TTCTCCTCTTCTTCTATTACCTTTCA 57.334 34.615 0.00 0.00 0.00 2.69
2558 5427 8.846423 TCTCCTCTTCTTCTATTACCTTTCAT 57.154 34.615 0.00 0.00 0.00 2.57
2559 5428 9.937876 TCTCCTCTTCTTCTATTACCTTTCATA 57.062 33.333 0.00 0.00 0.00 2.15
2576 5445 9.739276 ACCTTTCATATCTGTGAATTAAAGTCA 57.261 29.630 0.00 0.00 37.88 3.41
2581 5450 8.668353 TCATATCTGTGAATTAAAGTCAAGTGC 58.332 33.333 0.00 0.00 0.00 4.40
2582 5451 5.342806 TCTGTGAATTAAAGTCAAGTGCG 57.657 39.130 0.00 0.00 0.00 5.34
2621 5490 3.204180 GGGTAGCCTAACCGACTCT 57.796 57.895 2.95 0.00 40.73 3.24
2633 5502 0.395862 CCGACTCTTCCTGGCTCCTA 60.396 60.000 0.00 0.00 0.00 2.94
2681 5552 6.663523 AGCCTTTAAACATACAAAGCATAGGT 59.336 34.615 0.00 0.00 31.69 3.08
2767 5648 6.472686 AGAAAGATACAAGATAGCCGACTT 57.527 37.500 0.00 0.00 0.00 3.01
2785 5666 4.676951 CAGGAAGCCGGCCCCAAA 62.677 66.667 30.04 0.00 0.00 3.28
2807 5688 3.068691 CCGACTCCCAGAAGCCGA 61.069 66.667 0.00 0.00 0.00 5.54
3133 6030 2.207924 AATAGCCGGCTACCTCCCG 61.208 63.158 37.53 0.00 45.17 5.14
3159 6056 1.748493 GAAACATGCGCCCCATTAAGA 59.252 47.619 4.18 0.00 29.71 2.10
3255 6152 2.279120 GTCATCAGAGGCGAGGCG 60.279 66.667 0.00 0.00 0.00 5.52
3274 6171 2.186903 CAGTAACCAGCCGCCGAT 59.813 61.111 0.00 0.00 0.00 4.18
3282 6180 3.792736 AGCCGCCGATAAAGCCCA 61.793 61.111 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.985653 TTTTGAGATATAGGGAGGAGAGTG 57.014 41.667 0.00 0.00 0.00 3.51
19 20 6.327887 GGTTTTTGAGATATAGGGAGGAGAGT 59.672 42.308 0.00 0.00 0.00 3.24
20 21 6.239743 GGGTTTTTGAGATATAGGGAGGAGAG 60.240 46.154 0.00 0.00 0.00 3.20
25 26 7.579723 CGGATAGGGTTTTTGAGATATAGGGAG 60.580 44.444 0.00 0.00 0.00 4.30
50 51 2.825836 GCAGCACCCCCAAGATCG 60.826 66.667 0.00 0.00 0.00 3.69
139 140 2.668550 GTTGTGGCCTGGACGTCC 60.669 66.667 28.17 28.17 0.00 4.79
143 144 0.036294 GTAGAGGTTGTGGCCTGGAC 60.036 60.000 3.32 0.00 39.34 4.02
166 174 0.462581 TGCAGGCGAGATTGATGGAC 60.463 55.000 0.00 0.00 0.00 4.02
183 191 0.588233 CATGATCGCTTGCTCGTTGC 60.588 55.000 0.00 0.00 43.25 4.17
203 211 1.596603 TTACGTGTCACAGAGGTCGA 58.403 50.000 0.00 0.00 0.00 4.20
211 219 2.253610 AGGGATCCTTTACGTGTCACA 58.746 47.619 12.58 0.00 0.00 3.58
212 220 4.460948 TTAGGGATCCTTTACGTGTCAC 57.539 45.455 12.58 0.00 34.61 3.67
236 244 4.581824 CCAAGATAACATGAACAGGGATGG 59.418 45.833 0.00 0.00 0.00 3.51
241 249 4.588899 TCACCCAAGATAACATGAACAGG 58.411 43.478 0.00 0.00 0.00 4.00
244 252 7.500992 TCTAGATCACCCAAGATAACATGAAC 58.499 38.462 0.00 0.00 0.00 3.18
255 263 6.461110 AAAATTGCATCTAGATCACCCAAG 57.539 37.500 1.03 0.00 0.00 3.61
256 264 7.779326 TGATAAAATTGCATCTAGATCACCCAA 59.221 33.333 1.03 4.89 0.00 4.12
259 267 8.790718 ACATGATAAAATTGCATCTAGATCACC 58.209 33.333 1.03 0.00 0.00 4.02
337 345 2.456577 TGGAAAAGCTTATGAAGGGGC 58.543 47.619 0.00 0.00 0.00 5.80
338 346 6.983906 ATTATGGAAAAGCTTATGAAGGGG 57.016 37.500 0.00 0.00 0.00 4.79
377 385 4.762289 AAGCTTATGAAGGGTAGACTGG 57.238 45.455 0.00 0.00 0.00 4.00
424 1775 4.393371 GGAAATGACCTTTCAGTGAGCTAC 59.607 45.833 5.70 0.00 44.29 3.58
432 1783 6.519679 TTCATCATGGAAATGACCTTTCAG 57.480 37.500 5.70 0.00 44.29 3.02
437 1788 6.666678 AGTGTATTCATCATGGAAATGACCT 58.333 36.000 0.00 0.00 33.01 3.85
491 1842 6.150976 TGGATGTTAATTAACTGCAGTCAAGG 59.849 38.462 21.95 0.00 37.12 3.61
525 1876 5.512082 CCGTCTCTAAAATCTTGTGTACGAG 59.488 44.000 0.00 0.00 0.00 4.18
579 1930 0.250901 ACATTCGCTTGCCACTCCTT 60.251 50.000 0.00 0.00 0.00 3.36
592 1943 3.770263 ACTGCCATCAAATGACATTCG 57.230 42.857 0.05 0.00 0.00 3.34
603 1954 5.129634 TCTTCACAACTAAAACTGCCATCA 58.870 37.500 0.00 0.00 0.00 3.07
640 1991 7.706607 AGAGAAGACATTTTTGTTTAAACTGCC 59.293 33.333 18.72 1.77 31.53 4.85
677 2028 3.495193 CAATTTCTTCACAGCGACATGG 58.505 45.455 0.00 0.00 0.00 3.66
685 2036 1.273327 GGGGTGGCAATTTCTTCACAG 59.727 52.381 0.00 0.00 32.29 3.66
706 2057 9.665264 GTTTTAGGTGACAATTTTAGTTCTGAG 57.335 33.333 0.00 0.00 0.00 3.35
710 2061 8.845942 AACGTTTTAGGTGACAATTTTAGTTC 57.154 30.769 0.00 0.00 0.00 3.01
774 2125 2.786700 GCCGATTTTTAAAGGACGCTCG 60.787 50.000 0.00 0.00 0.00 5.03
781 2132 2.491693 TGAGCTGGCCGATTTTTAAAGG 59.508 45.455 0.00 0.00 0.00 3.11
783 2134 2.887783 TGTGAGCTGGCCGATTTTTAAA 59.112 40.909 0.00 0.00 0.00 1.52
793 2144 4.735132 TACGCGTGTGAGCTGGCC 62.735 66.667 24.59 0.00 34.40 5.36
807 2158 3.703420 GTGTGGTAAGAGGCTATGTACG 58.297 50.000 0.00 0.00 0.00 3.67
822 2173 3.056322 GGAAGGATAGTACAACGTGTGGT 60.056 47.826 0.00 0.00 0.00 4.16
831 2182 3.643320 CTCAGCCATGGAAGGATAGTACA 59.357 47.826 18.40 0.00 0.00 2.90
848 2199 1.376037 GTGCAGGGTGGTACTCAGC 60.376 63.158 0.00 0.00 42.74 4.26
879 2230 1.604604 TACAACTTGTGGCAAGAGGC 58.395 50.000 14.81 0.00 43.74 4.70
892 2243 4.281182 ACTCAGTCGTGGAAGAATACAACT 59.719 41.667 0.00 0.00 0.00 3.16
901 2252 1.067776 GGTGGTACTCAGTCGTGGAAG 60.068 57.143 0.00 0.00 0.00 3.46
928 3291 0.318784 CAAGAGGCTACGGCGGATAC 60.319 60.000 13.24 0.00 39.81 2.24
1052 3735 4.871557 CCCTTCCACGTTTTCATCGTTATA 59.128 41.667 0.00 0.00 39.55 0.98
1053 3736 3.687698 CCCTTCCACGTTTTCATCGTTAT 59.312 43.478 0.00 0.00 39.55 1.89
1100 3783 3.056107 TCGAACTTCCAATCCAGGTAGTG 60.056 47.826 0.00 0.00 38.99 2.74
1151 3834 1.484356 GTATCGGGATTGTTCGGTCG 58.516 55.000 0.00 0.00 0.00 4.79
1174 3857 3.679389 AGCTTACCATCAACTTCCTGTG 58.321 45.455 0.00 0.00 0.00 3.66
1269 3952 1.893062 CGAGATGGACTGGCTGACA 59.107 57.895 0.00 0.00 0.00 3.58
1329 4012 3.731216 CGTACTGGATAGCGATGTTGAAG 59.269 47.826 0.00 0.00 0.00 3.02
1663 4346 3.223589 GGCCGGAGAGAGGAGCTC 61.224 72.222 5.05 4.71 44.29 4.09
1667 4350 2.648613 GATGAGGGCCGGAGAGAGGA 62.649 65.000 5.05 0.00 0.00 3.71
1728 4411 3.343421 GACGTTGTGTCGTGCCCC 61.343 66.667 0.00 0.00 44.21 5.80
1764 4447 4.007644 CGACAGGGTGCTCTGGCA 62.008 66.667 5.69 0.00 42.76 4.92
1766 4449 4.767255 GGCGACAGGGTGCTCTGG 62.767 72.222 3.95 0.00 38.98 3.86
1788 4471 4.953010 TGTGTCGTCCCCCGTCGA 62.953 66.667 0.00 0.00 37.94 4.20
1789 4472 3.980989 TTGTGTCGTCCCCCGTCG 61.981 66.667 0.00 0.00 37.94 5.12
1790 4473 2.356673 GTTGTGTCGTCCCCCGTC 60.357 66.667 0.00 0.00 37.94 4.79
1791 4474 4.289245 CGTTGTGTCGTCCCCCGT 62.289 66.667 0.00 0.00 37.94 5.28
1792 4475 4.289245 ACGTTGTGTCGTCCCCCG 62.289 66.667 0.00 0.00 40.04 5.73
1809 4492 1.209383 CGGCAGTCTTCGACGAAGA 59.791 57.895 31.15 31.15 45.01 2.87
1810 4493 1.801913 CCGGCAGTCTTCGACGAAG 60.802 63.158 27.81 27.81 40.65 3.79
1811 4494 1.798234 TTCCGGCAGTCTTCGACGAA 61.798 55.000 10.34 10.34 37.67 3.85
1812 4495 2.196382 CTTCCGGCAGTCTTCGACGA 62.196 60.000 0.00 0.00 37.67 4.20
1813 4496 1.801913 CTTCCGGCAGTCTTCGACG 60.802 63.158 0.00 0.00 37.67 5.12
1814 4497 2.095252 GCTTCCGGCAGTCTTCGAC 61.095 63.158 2.26 0.00 41.35 4.20
1815 4498 2.261671 GCTTCCGGCAGTCTTCGA 59.738 61.111 2.26 0.00 41.35 3.71
1836 4519 4.693532 GACATCTTGGGTCGCACA 57.306 55.556 0.00 0.00 0.00 4.57
1843 4526 3.280938 TTGGGGGCGACATCTTGGG 62.281 63.158 0.00 0.00 0.00 4.12
1892 4575 2.847234 ACCAGGAACACCGGAGCA 60.847 61.111 9.46 0.00 0.00 4.26
1919 4602 0.822164 GCTGGTACACTATGACCGGT 59.178 55.000 6.92 6.92 43.10 5.28
2020 4703 9.874215 CGTTTGTACTCTCTATACGATGATTAA 57.126 33.333 0.00 0.00 0.00 1.40
2113 4799 4.430908 ACTGCGGCTTTAGTAATACTGTC 58.569 43.478 2.68 0.00 0.00 3.51
2125 4811 0.955919 GCTCCTTGTACTGCGGCTTT 60.956 55.000 0.00 0.00 0.00 3.51
2149 4835 1.334869 AGTTCTTCACGCCAAAGCTTG 59.665 47.619 0.00 0.00 39.53 4.01
2211 5058 2.932614 CTCCAAACTCTATCACTTGCGG 59.067 50.000 0.00 0.00 0.00 5.69
2224 5071 7.331193 CAGCTAAACGTTCTTATACTCCAAACT 59.669 37.037 0.00 0.00 0.00 2.66
2225 5072 7.412672 CCAGCTAAACGTTCTTATACTCCAAAC 60.413 40.741 0.00 0.00 0.00 2.93
2230 5077 5.107133 TGCCAGCTAAACGTTCTTATACTC 58.893 41.667 0.00 0.00 0.00 2.59
2231 5078 5.080969 TGCCAGCTAAACGTTCTTATACT 57.919 39.130 0.00 0.00 0.00 2.12
2232 5079 5.522460 TCATGCCAGCTAAACGTTCTTATAC 59.478 40.000 0.00 0.00 0.00 1.47
2240 5106 0.036164 TGGTCATGCCAGCTAAACGT 59.964 50.000 4.93 0.00 43.61 3.99
2286 5153 1.146774 TGACATTGCCCAAAGGAGGAA 59.853 47.619 0.00 0.00 33.47 3.36
2298 5165 6.698766 AGTGAAAGATCAAACTTTGACATTGC 59.301 34.615 6.35 4.42 42.96 3.56
2471 5340 7.011295 ACTCCGTTTTAAAATAAGTGTCGTGAA 59.989 33.333 3.52 0.00 0.00 3.18
2472 5341 6.479660 ACTCCGTTTTAAAATAAGTGTCGTGA 59.520 34.615 3.52 1.31 0.00 4.35
2473 5342 6.572254 CACTCCGTTTTAAAATAAGTGTCGTG 59.428 38.462 20.79 11.23 0.00 4.35
2474 5343 6.479660 TCACTCCGTTTTAAAATAAGTGTCGT 59.520 34.615 24.35 8.11 35.37 4.34
2475 5344 6.879962 TCACTCCGTTTTAAAATAAGTGTCG 58.120 36.000 24.35 14.54 35.37 4.35
2476 5345 7.858583 ACTCACTCCGTTTTAAAATAAGTGTC 58.141 34.615 24.35 6.39 35.37 3.67
2477 5346 7.797038 ACTCACTCCGTTTTAAAATAAGTGT 57.203 32.000 24.35 13.69 35.37 3.55
2478 5347 8.985805 AGTACTCACTCCGTTTTAAAATAAGTG 58.014 33.333 21.96 21.96 35.20 3.16
2479 5348 9.551734 AAGTACTCACTCCGTTTTAAAATAAGT 57.448 29.630 3.52 5.61 32.29 2.24
2483 5352 9.551734 AACTAAGTACTCACTCCGTTTTAAAAT 57.448 29.630 3.52 0.00 32.29 1.82
2484 5353 8.947055 AACTAAGTACTCACTCCGTTTTAAAA 57.053 30.769 0.00 0.00 32.29 1.52
2487 5356 9.846248 GATTAACTAAGTACTCACTCCGTTTTA 57.154 33.333 0.00 0.00 32.29 1.52
2488 5357 8.583296 AGATTAACTAAGTACTCACTCCGTTTT 58.417 33.333 0.00 0.00 32.29 2.43
2489 5358 8.120140 AGATTAACTAAGTACTCACTCCGTTT 57.880 34.615 0.00 0.00 32.29 3.60
2490 5359 7.611079 AGAGATTAACTAAGTACTCACTCCGTT 59.389 37.037 0.00 0.00 32.29 4.44
2491 5360 7.111466 AGAGATTAACTAAGTACTCACTCCGT 58.889 38.462 0.00 0.00 32.29 4.69
2492 5361 7.496591 AGAGAGATTAACTAAGTACTCACTCCG 59.503 40.741 0.00 0.00 32.29 4.63
2493 5362 8.741603 AGAGAGATTAACTAAGTACTCACTCC 57.258 38.462 0.00 0.00 32.29 3.85
2494 5363 9.609346 AGAGAGAGATTAACTAAGTACTCACTC 57.391 37.037 0.00 0.00 40.00 3.51
2495 5364 9.609346 GAGAGAGAGATTAACTAAGTACTCACT 57.391 37.037 0.00 0.00 36.19 3.41
2496 5365 9.386010 TGAGAGAGAGATTAACTAAGTACTCAC 57.614 37.037 0.00 0.00 0.00 3.51
2497 5366 9.961264 TTGAGAGAGAGATTAACTAAGTACTCA 57.039 33.333 0.00 0.00 0.00 3.41
2505 5374 9.707957 AGGAAAGATTGAGAGAGAGATTAACTA 57.292 33.333 0.00 0.00 0.00 2.24
2506 5375 8.608185 AGGAAAGATTGAGAGAGAGATTAACT 57.392 34.615 0.00 0.00 0.00 2.24
2507 5376 9.665719 AAAGGAAAGATTGAGAGAGAGATTAAC 57.334 33.333 0.00 0.00 0.00 2.01
2508 5377 9.883142 GAAAGGAAAGATTGAGAGAGAGATTAA 57.117 33.333 0.00 0.00 0.00 1.40
2509 5378 9.265862 AGAAAGGAAAGATTGAGAGAGAGATTA 57.734 33.333 0.00 0.00 0.00 1.75
2510 5379 8.149631 AGAAAGGAAAGATTGAGAGAGAGATT 57.850 34.615 0.00 0.00 0.00 2.40
2511 5380 7.147672 GGAGAAAGGAAAGATTGAGAGAGAGAT 60.148 40.741 0.00 0.00 0.00 2.75
2512 5381 6.154363 GGAGAAAGGAAAGATTGAGAGAGAGA 59.846 42.308 0.00 0.00 0.00 3.10
2513 5382 6.155049 AGGAGAAAGGAAAGATTGAGAGAGAG 59.845 42.308 0.00 0.00 0.00 3.20
2514 5383 6.022315 AGGAGAAAGGAAAGATTGAGAGAGA 58.978 40.000 0.00 0.00 0.00 3.10
2515 5384 6.155049 AGAGGAGAAAGGAAAGATTGAGAGAG 59.845 42.308 0.00 0.00 0.00 3.20
2516 5385 6.022315 AGAGGAGAAAGGAAAGATTGAGAGA 58.978 40.000 0.00 0.00 0.00 3.10
2517 5386 6.298441 AGAGGAGAAAGGAAAGATTGAGAG 57.702 41.667 0.00 0.00 0.00 3.20
2518 5387 6.500049 AGAAGAGGAGAAAGGAAAGATTGAGA 59.500 38.462 0.00 0.00 0.00 3.27
2519 5388 6.710278 AGAAGAGGAGAAAGGAAAGATTGAG 58.290 40.000 0.00 0.00 0.00 3.02
2520 5389 6.694445 AGAAGAGGAGAAAGGAAAGATTGA 57.306 37.500 0.00 0.00 0.00 2.57
2521 5390 7.167535 AGAAGAAGAGGAGAAAGGAAAGATTG 58.832 38.462 0.00 0.00 0.00 2.67
2522 5391 7.328404 AGAAGAAGAGGAGAAAGGAAAGATT 57.672 36.000 0.00 0.00 0.00 2.40
2523 5392 6.950860 AGAAGAAGAGGAGAAAGGAAAGAT 57.049 37.500 0.00 0.00 0.00 2.40
2524 5393 8.442660 AATAGAAGAAGAGGAGAAAGGAAAGA 57.557 34.615 0.00 0.00 0.00 2.52
2525 5394 9.594478 GTAATAGAAGAAGAGGAGAAAGGAAAG 57.406 37.037 0.00 0.00 0.00 2.62
2526 5395 8.541234 GGTAATAGAAGAAGAGGAGAAAGGAAA 58.459 37.037 0.00 0.00 0.00 3.13
2527 5396 7.901861 AGGTAATAGAAGAAGAGGAGAAAGGAA 59.098 37.037 0.00 0.00 0.00 3.36
2528 5397 7.423341 AGGTAATAGAAGAAGAGGAGAAAGGA 58.577 38.462 0.00 0.00 0.00 3.36
2529 5398 7.669089 AGGTAATAGAAGAAGAGGAGAAAGG 57.331 40.000 0.00 0.00 0.00 3.11
2530 5399 9.594478 GAAAGGTAATAGAAGAAGAGGAGAAAG 57.406 37.037 0.00 0.00 0.00 2.62
2531 5400 9.101325 TGAAAGGTAATAGAAGAAGAGGAGAAA 57.899 33.333 0.00 0.00 0.00 2.52
2532 5401 8.666129 TGAAAGGTAATAGAAGAAGAGGAGAA 57.334 34.615 0.00 0.00 0.00 2.87
2533 5402 8.846423 ATGAAAGGTAATAGAAGAAGAGGAGA 57.154 34.615 0.00 0.00 0.00 3.71
2550 5419 9.739276 TGACTTTAATTCACAGATATGAAAGGT 57.261 29.630 0.00 0.00 41.78 3.50
2555 5424 8.668353 GCACTTGACTTTAATTCACAGATATGA 58.332 33.333 0.00 0.00 0.00 2.15
2556 5425 7.637519 CGCACTTGACTTTAATTCACAGATATG 59.362 37.037 0.00 0.00 0.00 1.78
2557 5426 7.334421 ACGCACTTGACTTTAATTCACAGATAT 59.666 33.333 0.00 0.00 0.00 1.63
2558 5427 6.649141 ACGCACTTGACTTTAATTCACAGATA 59.351 34.615 0.00 0.00 0.00 1.98
2559 5428 5.470098 ACGCACTTGACTTTAATTCACAGAT 59.530 36.000 0.00 0.00 0.00 2.90
2560 5429 4.814234 ACGCACTTGACTTTAATTCACAGA 59.186 37.500 0.00 0.00 0.00 3.41
2561 5430 5.095691 ACGCACTTGACTTTAATTCACAG 57.904 39.130 0.00 0.00 0.00 3.66
2562 5431 5.163703 ACAACGCACTTGACTTTAATTCACA 60.164 36.000 0.00 0.00 33.59 3.58
2563 5432 5.270853 ACAACGCACTTGACTTTAATTCAC 58.729 37.500 0.00 0.00 33.59 3.18
2564 5433 5.493133 ACAACGCACTTGACTTTAATTCA 57.507 34.783 0.00 0.00 33.59 2.57
2565 5434 4.607235 CGACAACGCACTTGACTTTAATTC 59.393 41.667 0.00 0.00 33.59 2.17
2566 5435 4.523813 CGACAACGCACTTGACTTTAATT 58.476 39.130 0.00 0.00 33.59 1.40
2567 5436 3.059188 CCGACAACGCACTTGACTTTAAT 60.059 43.478 0.00 0.00 38.29 1.40
2568 5437 2.285756 CCGACAACGCACTTGACTTTAA 59.714 45.455 0.00 0.00 38.29 1.52
2569 5438 1.862201 CCGACAACGCACTTGACTTTA 59.138 47.619 0.00 0.00 38.29 1.85
2570 5439 0.655733 CCGACAACGCACTTGACTTT 59.344 50.000 0.00 0.00 38.29 2.66
2571 5440 0.179094 TCCGACAACGCACTTGACTT 60.179 50.000 0.00 0.00 38.29 3.01
2572 5441 0.597637 CTCCGACAACGCACTTGACT 60.598 55.000 0.00 0.00 38.29 3.41
2573 5442 0.874607 ACTCCGACAACGCACTTGAC 60.875 55.000 0.00 0.00 38.29 3.18
2574 5443 0.669619 TACTCCGACAACGCACTTGA 59.330 50.000 0.00 0.00 38.29 3.02
2575 5444 1.493772 TTACTCCGACAACGCACTTG 58.506 50.000 0.00 0.00 38.29 3.16
2576 5445 2.228138 TTTACTCCGACAACGCACTT 57.772 45.000 0.00 0.00 38.29 3.16
2577 5446 2.450609 ATTTACTCCGACAACGCACT 57.549 45.000 0.00 0.00 38.29 4.40
2578 5447 2.028883 GCTATTTACTCCGACAACGCAC 59.971 50.000 0.00 0.00 38.29 5.34
2579 5448 2.264813 GCTATTTACTCCGACAACGCA 58.735 47.619 0.00 0.00 38.29 5.24
2580 5449 1.591619 GGCTATTTACTCCGACAACGC 59.408 52.381 0.00 0.00 38.29 4.84
2581 5450 2.601763 GTGGCTATTTACTCCGACAACG 59.398 50.000 0.00 0.00 39.43 4.10
2582 5451 2.601763 CGTGGCTATTTACTCCGACAAC 59.398 50.000 0.00 0.00 0.00 3.32
2662 5533 4.573201 GCGGACCTATGCTTTGTATGTTTA 59.427 41.667 0.00 0.00 0.00 2.01
2665 5536 2.561569 GCGGACCTATGCTTTGTATGT 58.438 47.619 0.00 0.00 0.00 2.29
2785 5666 1.545706 GCTTCTGGGAGTCGGTCCTT 61.546 60.000 4.92 0.00 46.06 3.36
2807 5688 2.668550 GCCGGCTTTCTTCGTGGT 60.669 61.111 22.15 0.00 0.00 4.16
2839 5736 1.071699 GTCTTGGTGGGTGCAGTCTTA 59.928 52.381 0.00 0.00 0.00 2.10
3054 5951 2.302260 CCGCCTTCAGATGTCTCTCTA 58.698 52.381 0.00 0.00 0.00 2.43
3133 6030 2.401195 GGCGCATGTTTCGAGAGC 59.599 61.111 10.83 0.00 0.00 4.09
3135 6032 2.435938 GGGGCGCATGTTTCGAGA 60.436 61.111 10.83 0.00 0.00 4.04
3159 6056 2.249139 AGCCTTACCTCGTCTTGTCTT 58.751 47.619 0.00 0.00 0.00 3.01
3255 6152 2.573609 ATCGGCGGCTGGTTACTGTC 62.574 60.000 7.21 0.00 0.00 3.51
3274 6171 4.073052 CACCGCTTGTGGGCTTTA 57.927 55.556 5.16 0.00 41.52 1.85


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

AutoCloner maintained by Alex Coulton.