Multiple sequence alignment - TraesCS5B01G457700

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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 TraesCS5B01G457700 chr5B 100.000 4431 0 0 980 5410 632152829 632157259 0.000000e+00 8183.0
1 TraesCS5B01G457700 chr5B 100.000 626 0 0 1 626 632151850 632152475 0.000000e+00 1157.0
2 TraesCS5B01G457700 chr5B 88.333 60 6 1 1764 1822 134911287 134911346 2.700000e-08 71.3
3 TraesCS5B01G457700 chr5D 95.293 1721 55 10 2526 4223 503671284 503673001 0.000000e+00 2706.0
4 TraesCS5B01G457700 chr5D 99.058 955 8 1 4217 5170 503673035 503673989 0.000000e+00 1712.0
5 TraesCS5B01G457700 chr5D 93.534 897 44 6 986 1880 503669748 503670632 0.000000e+00 1323.0
6 TraesCS5B01G457700 chr5D 87.898 628 30 22 1 609 503669123 503669723 0.000000e+00 697.0
7 TraesCS5B01G457700 chr5D 88.008 517 45 14 1963 2474 503670780 503671284 3.610000e-166 595.0
8 TraesCS5B01G457700 chr5A 92.807 1418 74 17 1966 3371 631665410 631666811 0.000000e+00 2028.0
9 TraesCS5B01G457700 chr5A 91.500 1000 53 15 986 1966 631664298 631665284 0.000000e+00 1347.0
10 TraesCS5B01G457700 chr5A 92.216 758 40 11 4250 4994 631668179 631668930 0.000000e+00 1055.0
11 TraesCS5B01G457700 chr5A 90.816 294 20 4 3330 3620 631666813 631667102 2.360000e-103 387.0
12 TraesCS5B01G457700 chr5A 80.037 546 65 27 3711 4223 631667578 631668112 1.110000e-96 364.0
13 TraesCS5B01G457700 chr5A 87.342 316 9 13 247 532 631663656 631663970 3.120000e-87 333.0
14 TraesCS5B01G457700 chr5A 94.074 135 6 2 1 135 631663289 631663421 2.550000e-48 204.0
15 TraesCS5B01G457700 chr3B 91.119 1171 66 15 2526 3677 212887590 212886439 0.000000e+00 1552.0
16 TraesCS5B01G457700 chr3B 89.808 991 53 15 986 1966 212889171 212888219 0.000000e+00 1227.0
17 TraesCS5B01G457700 chr3B 87.967 482 50 8 1997 2474 212888067 212887590 3.660000e-156 562.0
18 TraesCS5B01G457700 chr3B 96.356 247 8 1 5164 5409 497096328 497096574 6.520000e-109 405.0
19 TraesCS5B01G457700 chr3B 96.296 243 9 0 5168 5410 742450160 742449918 3.040000e-107 399.0
20 TraesCS5B01G457700 chr3B 91.870 123 3 3 3673 3788 212886241 212886119 1.210000e-36 165.0
21 TraesCS5B01G457700 chr2A 96.327 245 9 0 5165 5409 84977773 84977529 2.350000e-108 403.0
22 TraesCS5B01G457700 chr2A 96.680 241 8 0 5169 5409 478914601 478914841 8.440000e-108 401.0
23 TraesCS5B01G457700 chr2A 96.680 241 8 0 5169 5409 753083163 753083403 8.440000e-108 401.0
24 TraesCS5B01G457700 chr1A 96.311 244 9 0 5166 5409 536345210 536345453 8.440000e-108 401.0
25 TraesCS5B01G457700 chr1A 93.103 116 7 1 4997 5112 590673612 590673726 9.320000e-38 169.0
26 TraesCS5B01G457700 chr6B 95.918 245 10 0 5166 5410 21064540 21064784 1.090000e-106 398.0
27 TraesCS5B01G457700 chr3A 96.266 241 9 0 5169 5409 697028268 697028508 3.930000e-106 396.0
28 TraesCS5B01G457700 chr3A 95.528 246 11 0 5165 5410 449125692 449125447 1.410000e-105 394.0
29 TraesCS5B01G457700 chr4A 95.495 111 5 0 5002 5112 21047607 21047497 1.550000e-40 178.0
30 TraesCS5B01G457700 chr4A 79.024 205 38 5 1015 1218 15655005 15654805 9.450000e-28 135.0
31 TraesCS5B01G457700 chr4D 79.188 197 36 5 1015 1210 451279440 451279632 1.220000e-26 132.0
32 TraesCS5B01G457700 chr4B 79.330 179 35 2 1015 1192 564866507 564866684 2.050000e-24 124.0
33 TraesCS5B01G457700 chr4B 89.831 59 5 1 1764 1821 612342133 612342191 2.090000e-09 75.0
34 TraesCS5B01G457700 chr2B 88.889 63 6 1 1764 1825 634672739 634672677 5.810000e-10 76.8
35 TraesCS5B01G457700 chr1B 88.889 63 6 1 1764 1825 660959486 660959424 5.810000e-10 76.8


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 TraesCS5B01G457700 chr5B 632151850 632157259 5409 False 4670.000000 8183 100.000000 1 5410 2 chr5B.!!$F2 5409
1 TraesCS5B01G457700 chr5D 503669123 503673989 4866 False 1406.600000 2706 92.758200 1 5170 5 chr5D.!!$F1 5169
2 TraesCS5B01G457700 chr5A 631663289 631668930 5641 False 816.857143 2028 89.827429 1 4994 7 chr5A.!!$F1 4993
3 TraesCS5B01G457700 chr3B 212886119 212889171 3052 True 876.500000 1552 90.191000 986 3788 4 chr3B.!!$R2 2802

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
67 68 0.179048 TTGATGCTACAGCCCATCCG 60.179 55.0 0.00 0.0 41.18 4.18 F
141 142 0.675633 GCACCCATCACACAAGCTTT 59.324 50.0 0.00 0.0 0.00 3.51 F
1495 1657 0.713883 CGGTCAATTCGAGTTCGGTG 59.286 55.0 1.26 0.0 40.29 4.94 F
2040 2353 0.815734 GCATTGATCTGCAAGCACCT 59.184 50.0 2.23 0.0 41.87 4.00 F
3516 3894 2.200373 ATTGAAGCAGTTAAGCCGGT 57.800 45.0 1.90 0.0 34.23 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1077 1237 0.110486 AGGCGATGGTGGTGAAGTTT 59.890 50.000 0.00 0.0 0.00 2.66 R
1541 1705 1.414181 CCCATAGGCGTGTGAGAAGAT 59.586 52.381 4.57 0.0 0.00 2.40 R
2851 3182 0.110238 CTGATTCAACGGCAACCACG 60.110 55.000 0.00 0.0 37.36 4.94 R
3620 3998 0.550147 AGCCCTCACTAACACCCCAT 60.550 55.000 0.00 0.0 0.00 4.00 R
5181 6289 0.040425 GCGGGCGCACTATATTTTGG 60.040 55.000 8.62 0.0 41.49 3.28 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
62 63 1.533625 TGTGTTTGATGCTACAGCCC 58.466 50.000 0.00 0.00 41.18 5.19
67 68 0.179048 TTGATGCTACAGCCCATCCG 60.179 55.000 0.00 0.00 41.18 4.18
70 71 1.276421 GATGCTACAGCCCATCCGTAT 59.724 52.381 0.00 0.00 41.18 3.06
86 87 1.790123 CGTATGCGCCAACATCACAAC 60.790 52.381 4.18 0.00 0.00 3.32
127 128 5.493133 TCATTTCATACAATTACGCACCC 57.507 39.130 0.00 0.00 0.00 4.61
135 136 1.809547 CAATTACGCACCCATCACACA 59.190 47.619 0.00 0.00 0.00 3.72
136 137 2.192664 ATTACGCACCCATCACACAA 57.807 45.000 0.00 0.00 0.00 3.33
137 138 1.518325 TTACGCACCCATCACACAAG 58.482 50.000 0.00 0.00 0.00 3.16
138 139 0.953471 TACGCACCCATCACACAAGC 60.953 55.000 0.00 0.00 0.00 4.01
139 140 1.968017 CGCACCCATCACACAAGCT 60.968 57.895 0.00 0.00 0.00 3.74
140 141 1.518056 CGCACCCATCACACAAGCTT 61.518 55.000 0.00 0.00 0.00 3.74
141 142 0.675633 GCACCCATCACACAAGCTTT 59.324 50.000 0.00 0.00 0.00 3.51
142 143 1.336240 GCACCCATCACACAAGCTTTC 60.336 52.381 0.00 0.00 0.00 2.62
143 144 2.233271 CACCCATCACACAAGCTTTCT 58.767 47.619 0.00 0.00 0.00 2.52
144 145 3.411446 CACCCATCACACAAGCTTTCTA 58.589 45.455 0.00 0.00 0.00 2.10
145 146 3.820467 CACCCATCACACAAGCTTTCTAA 59.180 43.478 0.00 0.00 0.00 2.10
146 147 4.074970 ACCCATCACACAAGCTTTCTAAG 58.925 43.478 0.00 0.00 0.00 2.18
148 149 5.221843 ACCCATCACACAAGCTTTCTAAGTA 60.222 40.000 0.00 0.00 0.00 2.24
151 152 6.595326 CCATCACACAAGCTTTCTAAGTATCA 59.405 38.462 0.00 0.00 0.00 2.15
152 153 7.201591 CCATCACACAAGCTTTCTAAGTATCAG 60.202 40.741 0.00 0.00 0.00 2.90
153 154 6.759272 TCACACAAGCTTTCTAAGTATCAGT 58.241 36.000 0.00 0.00 0.00 3.41
154 155 7.892609 TCACACAAGCTTTCTAAGTATCAGTA 58.107 34.615 0.00 0.00 0.00 2.74
155 156 8.364894 TCACACAAGCTTTCTAAGTATCAGTAA 58.635 33.333 0.00 0.00 0.00 2.24
156 157 9.155975 CACACAAGCTTTCTAAGTATCAGTAAT 57.844 33.333 0.00 0.00 0.00 1.89
157 158 9.726438 ACACAAGCTTTCTAAGTATCAGTAATT 57.274 29.630 0.00 0.00 0.00 1.40
186 293 4.666512 AGGCAAACTTGTGGTAATCTGAT 58.333 39.130 0.00 0.00 0.00 2.90
201 308 6.370166 GGTAATCTGATTGTATTAGCAGGAGC 59.630 42.308 13.01 0.00 36.52 4.70
212 319 2.197283 AGCAGGAGCAGAAAAGAAGG 57.803 50.000 0.00 0.00 45.49 3.46
222 329 6.403746 GGAGCAGAAAAGAAGGTAAATACTGC 60.404 42.308 0.00 0.00 45.30 4.40
228 335 9.606631 AGAAAAGAAGGTAAATACTGCAGATAG 57.393 33.333 23.35 0.00 0.00 2.08
229 336 9.601217 GAAAAGAAGGTAAATACTGCAGATAGA 57.399 33.333 23.35 2.54 0.00 1.98
231 338 9.771534 AAAGAAGGTAAATACTGCAGATAGATC 57.228 33.333 23.35 6.43 0.00 2.75
232 339 7.598278 AGAAGGTAAATACTGCAGATAGATCG 58.402 38.462 23.35 0.00 0.00 3.69
233 340 7.448777 AGAAGGTAAATACTGCAGATAGATCGA 59.551 37.037 23.35 0.00 0.00 3.59
235 342 8.809468 AGGTAAATACTGCAGATAGATCGATA 57.191 34.615 23.35 0.00 0.00 2.92
236 343 8.898761 AGGTAAATACTGCAGATAGATCGATAG 58.101 37.037 23.35 0.00 0.00 2.08
237 344 8.679100 GGTAAATACTGCAGATAGATCGATAGT 58.321 37.037 23.35 0.00 37.40 2.12
310 440 3.198068 CGAGCCAGCTAAGCTAATCAAA 58.802 45.455 10.24 0.00 41.75 2.69
311 441 3.001736 CGAGCCAGCTAAGCTAATCAAAC 59.998 47.826 10.24 0.00 41.75 2.93
535 695 3.922305 TTTCCCCCTTCCCCTCCCC 62.922 68.421 0.00 0.00 0.00 4.81
538 698 4.845307 CCCCTTCCCCTCCCCCTC 62.845 77.778 0.00 0.00 0.00 4.30
539 699 4.845307 CCCTTCCCCTCCCCCTCC 62.845 77.778 0.00 0.00 0.00 4.30
540 700 4.845307 CCTTCCCCTCCCCCTCCC 62.845 77.778 0.00 0.00 0.00 4.30
541 701 4.845307 CTTCCCCTCCCCCTCCCC 62.845 77.778 0.00 0.00 0.00 4.81
582 742 3.142393 CCGAGATCCAATCCGGCT 58.858 61.111 0.00 0.00 36.71 5.52
1201 1361 2.435059 GCTTCAGTGAGTCGCCCC 60.435 66.667 0.00 0.00 0.00 5.80
1202 1362 2.125912 CTTCAGTGAGTCGCCCCG 60.126 66.667 0.00 0.00 0.00 5.73
1203 1363 4.373116 TTCAGTGAGTCGCCCCGC 62.373 66.667 0.00 0.00 0.00 6.13
1246 1407 4.918201 CCCGCCCGATCCTTGCTC 62.918 72.222 0.00 0.00 0.00 4.26
1286 1447 3.696426 GCGTGATCTGATCCGCGC 61.696 66.667 27.63 27.63 42.18 6.86
1482 1644 1.216977 CACGCTGGGTATCGGTCAA 59.783 57.895 0.00 0.00 0.00 3.18
1495 1657 0.713883 CGGTCAATTCGAGTTCGGTG 59.286 55.000 1.26 0.00 40.29 4.94
1535 1699 3.316029 TGCTATGCAGTCAATATTGTGGC 59.684 43.478 14.97 15.82 33.32 5.01
1546 1710 6.261826 AGTCAATATTGTGGCTGCTAATCTTC 59.738 38.462 14.97 0.00 30.49 2.87
1549 1713 3.701205 TTGTGGCTGCTAATCTTCTCA 57.299 42.857 0.00 0.00 0.00 3.27
1574 1739 1.416401 CCTATGGGGCAGTCGTTGTAT 59.584 52.381 0.00 0.00 0.00 2.29
1575 1740 2.548067 CCTATGGGGCAGTCGTTGTATC 60.548 54.545 0.00 0.00 0.00 2.24
1587 1752 2.416202 TCGTTGTATCACAGCTGCAATG 59.584 45.455 15.27 14.36 0.00 2.82
1693 1862 2.803479 GGCTTGCTAGGCATGTGC 59.197 61.111 16.52 0.00 45.79 4.57
1697 1866 1.385528 CTTGCTAGGCATGTGCATCA 58.614 50.000 7.36 0.00 44.36 3.07
1717 1886 7.576750 CATCAAATGCCAGCACATATTTATC 57.423 36.000 0.00 0.00 0.00 1.75
1719 1888 5.834742 TCAAATGCCAGCACATATTTATCCT 59.165 36.000 0.00 0.00 0.00 3.24
1720 1889 7.003482 TCAAATGCCAGCACATATTTATCCTA 58.997 34.615 0.00 0.00 0.00 2.94
1721 1890 7.505248 TCAAATGCCAGCACATATTTATCCTAA 59.495 33.333 0.00 0.00 0.00 2.69
1722 1891 7.838079 AATGCCAGCACATATTTATCCTAAA 57.162 32.000 0.00 0.00 0.00 1.85
1864 2042 6.354130 TGGTATAGGTTTCCAGATAAGCAAC 58.646 40.000 0.00 0.00 0.00 4.17
1928 2110 2.747446 CCGAGTTTTCTAATGGGTGTGG 59.253 50.000 0.00 0.00 0.00 4.17
1931 2113 4.563993 CGAGTTTTCTAATGGGTGTGGGTA 60.564 45.833 0.00 0.00 0.00 3.69
1967 2154 8.477419 TTTTCATACCCTTGATCTTTTTGAGT 57.523 30.769 0.00 0.00 0.00 3.41
1968 2155 8.477419 TTTCATACCCTTGATCTTTTTGAGTT 57.523 30.769 0.00 0.00 0.00 3.01
1969 2156 8.477419 TTCATACCCTTGATCTTTTTGAGTTT 57.523 30.769 0.00 0.00 0.00 2.66
1970 2157 7.885297 TCATACCCTTGATCTTTTTGAGTTTG 58.115 34.615 0.00 0.00 0.00 2.93
1971 2158 7.505585 TCATACCCTTGATCTTTTTGAGTTTGT 59.494 33.333 0.00 0.00 0.00 2.83
1972 2159 8.792633 CATACCCTTGATCTTTTTGAGTTTGTA 58.207 33.333 0.00 0.00 0.00 2.41
1973 2160 7.839680 ACCCTTGATCTTTTTGAGTTTGTAT 57.160 32.000 0.00 0.00 0.00 2.29
1975 2162 9.362151 ACCCTTGATCTTTTTGAGTTTGTATAA 57.638 29.630 0.00 0.00 0.00 0.98
1976 2163 9.846248 CCCTTGATCTTTTTGAGTTTGTATAAG 57.154 33.333 0.00 0.00 0.00 1.73
2040 2353 0.815734 GCATTGATCTGCAAGCACCT 59.184 50.000 2.23 0.00 41.87 4.00
2116 2429 4.220821 TGTTCCTCTCTGATTGGACTGTAC 59.779 45.833 0.00 0.00 0.00 2.90
2150 2463 7.573627 CACTTGTTAGTTAAGTGTAGCCTTTC 58.426 38.462 9.14 0.00 46.13 2.62
2165 2478 2.472816 CCTTTCGCACTTTGCAACAAT 58.527 42.857 0.00 0.00 45.36 2.71
2173 2487 3.243367 GCACTTTGCAACAATACTGGTCA 60.243 43.478 0.00 0.00 44.26 4.02
2331 2645 4.380233 GCATTTTACTGAGCACAGAAGCAT 60.380 41.667 18.54 1.99 46.03 3.79
2374 2690 8.768501 ATCAGTAGAGTACATCTCATTACCAA 57.231 34.615 0.00 0.00 44.98 3.67
2378 2694 8.855110 AGTAGAGTACATCTCATTACCAATCTG 58.145 37.037 0.00 0.00 44.98 2.90
2386 2702 6.252599 TCTCATTACCAATCTGGCAATACT 57.747 37.500 0.00 0.00 42.67 2.12
2387 2703 6.662755 TCTCATTACCAATCTGGCAATACTT 58.337 36.000 0.00 0.00 42.67 2.24
2449 2773 8.740123 TGTGAAACCTTCATTAGTTAAAGTCA 57.260 30.769 0.00 0.00 42.47 3.41
2489 2813 4.934001 TGTGTACTGAGGTAGTAGAAGACG 59.066 45.833 0.00 0.00 42.37 4.18
2524 2848 8.974060 ATGTAGTGGAAATTAACATTACCGAT 57.026 30.769 10.43 0.46 31.25 4.18
2610 2935 2.978978 CCTTCAAACCCCCTTTTCCAAT 59.021 45.455 0.00 0.00 0.00 3.16
2714 3043 5.772825 TTTTTGCAGACATAGCACTTCTT 57.227 34.783 0.00 0.00 42.54 2.52
2767 3097 8.752005 TCCTTGGTTGAATTATAATTCCAGAG 57.248 34.615 27.53 19.02 43.19 3.35
3034 3366 8.224720 TGGGGCTATTTATAATATATGGCCTTC 58.775 37.037 17.57 12.62 41.30 3.46
3035 3367 7.670140 GGGGCTATTTATAATATATGGCCTTCC 59.330 40.741 17.57 10.68 41.30 3.46
3516 3894 2.200373 ATTGAAGCAGTTAAGCCGGT 57.800 45.000 1.90 0.00 34.23 5.28
3620 3998 5.586243 GGTGCTCTTGATATGCTCAAACTAA 59.414 40.000 0.00 0.00 43.20 2.24
4506 5605 6.715347 ATGGTGCTTAGTTCTTTTCTTGTT 57.285 33.333 0.00 0.00 0.00 2.83
4742 5844 0.751643 GTGTGGGTGTGTCTGCCTTT 60.752 55.000 0.00 0.00 0.00 3.11
4984 6091 2.350458 GGCAATCCATGGGCGTGTT 61.350 57.895 13.02 0.00 0.00 3.32
5065 6172 4.367023 GCCTGGCGTGGACGTGTA 62.367 66.667 1.35 0.00 42.22 2.90
5170 6278 3.069729 CCATCTACAGGCTTGGGTAGTAC 59.930 52.174 0.00 0.00 38.46 2.73
5171 6279 3.752359 TCTACAGGCTTGGGTAGTACT 57.248 47.619 0.00 0.00 38.46 2.73
5172 6280 3.629087 TCTACAGGCTTGGGTAGTACTC 58.371 50.000 0.00 0.00 38.46 2.59
5173 6281 1.569653 ACAGGCTTGGGTAGTACTCC 58.430 55.000 0.00 0.27 0.00 3.85
5174 6282 0.831307 CAGGCTTGGGTAGTACTCCC 59.169 60.000 18.49 18.49 44.81 4.30
5175 6283 0.717196 AGGCTTGGGTAGTACTCCCT 59.283 55.000 23.01 8.11 44.84 4.20
5176 6284 1.121378 GGCTTGGGTAGTACTCCCTC 58.879 60.000 23.01 15.07 44.84 4.30
5177 6285 1.121378 GCTTGGGTAGTACTCCCTCC 58.879 60.000 23.01 12.44 44.84 4.30
5178 6286 1.621622 GCTTGGGTAGTACTCCCTCCA 60.622 57.143 23.01 14.02 44.84 3.86
5179 6287 2.960104 GCTTGGGTAGTACTCCCTCCAT 60.960 54.545 23.01 0.00 44.84 3.41
5180 6288 3.385115 CTTGGGTAGTACTCCCTCCATT 58.615 50.000 23.01 0.00 44.84 3.16
5181 6289 3.042059 TGGGTAGTACTCCCTCCATTC 57.958 52.381 23.01 1.74 44.84 2.67
5182 6290 2.327373 GGGTAGTACTCCCTCCATTCC 58.673 57.143 18.19 2.79 41.58 3.01
5183 6291 2.359994 GGGTAGTACTCCCTCCATTCCA 60.360 54.545 18.19 0.00 41.58 3.53
5184 6292 3.381335 GGTAGTACTCCCTCCATTCCAA 58.619 50.000 0.00 0.00 0.00 3.53
5185 6293 3.778629 GGTAGTACTCCCTCCATTCCAAA 59.221 47.826 0.00 0.00 0.00 3.28
5186 6294 4.226620 GGTAGTACTCCCTCCATTCCAAAA 59.773 45.833 0.00 0.00 0.00 2.44
5187 6295 5.104067 GGTAGTACTCCCTCCATTCCAAAAT 60.104 44.000 0.00 0.00 0.00 1.82
5188 6296 6.100714 GGTAGTACTCCCTCCATTCCAAAATA 59.899 42.308 0.00 0.00 0.00 1.40
5189 6297 6.848562 AGTACTCCCTCCATTCCAAAATAT 57.151 37.500 0.00 0.00 0.00 1.28
5190 6298 7.947782 AGTACTCCCTCCATTCCAAAATATA 57.052 36.000 0.00 0.00 0.00 0.86
5191 6299 7.978925 AGTACTCCCTCCATTCCAAAATATAG 58.021 38.462 0.00 0.00 0.00 1.31
5192 6300 6.848562 ACTCCCTCCATTCCAAAATATAGT 57.151 37.500 0.00 0.00 0.00 2.12
5193 6301 6.605119 ACTCCCTCCATTCCAAAATATAGTG 58.395 40.000 0.00 0.00 0.00 2.74
5194 6302 5.385198 TCCCTCCATTCCAAAATATAGTGC 58.615 41.667 0.00 0.00 0.00 4.40
5195 6303 4.216257 CCCTCCATTCCAAAATATAGTGCG 59.784 45.833 0.00 0.00 0.00 5.34
5196 6304 4.320494 CCTCCATTCCAAAATATAGTGCGC 60.320 45.833 0.00 0.00 0.00 6.09
5197 6305 3.568007 TCCATTCCAAAATATAGTGCGCC 59.432 43.478 4.18 0.00 0.00 6.53
5198 6306 3.305335 CCATTCCAAAATATAGTGCGCCC 60.305 47.826 4.18 0.00 0.00 6.13
5199 6307 1.588674 TCCAAAATATAGTGCGCCCG 58.411 50.000 4.18 0.00 0.00 6.13
5200 6308 0.040425 CCAAAATATAGTGCGCCCGC 60.040 55.000 4.18 5.60 42.35 6.13
5201 6309 0.384230 CAAAATATAGTGCGCCCGCG 60.384 55.000 4.18 4.36 45.51 6.46
5215 6323 2.736995 CGCGCTTTTCGAGGTCCA 60.737 61.111 5.56 0.00 41.67 4.02
5216 6324 2.314647 CGCGCTTTTCGAGGTCCAA 61.315 57.895 5.56 0.00 41.67 3.53
5217 6325 1.206831 GCGCTTTTCGAGGTCCAAC 59.793 57.895 0.00 0.00 41.67 3.77
5218 6326 1.228657 GCGCTTTTCGAGGTCCAACT 61.229 55.000 0.00 0.00 41.67 3.16
5219 6327 1.226746 CGCTTTTCGAGGTCCAACTT 58.773 50.000 0.00 0.00 41.67 2.66
5220 6328 1.602377 CGCTTTTCGAGGTCCAACTTT 59.398 47.619 0.00 0.00 41.67 2.66
5221 6329 2.602217 CGCTTTTCGAGGTCCAACTTTG 60.602 50.000 0.00 0.00 41.67 2.77
5222 6330 2.616842 GCTTTTCGAGGTCCAACTTTGA 59.383 45.455 0.00 0.00 0.00 2.69
5223 6331 3.548214 GCTTTTCGAGGTCCAACTTTGAC 60.548 47.826 0.00 0.00 0.00 3.18
5224 6332 2.249844 TTCGAGGTCCAACTTTGACC 57.750 50.000 4.16 4.16 39.18 4.02
5225 6333 1.124780 TCGAGGTCCAACTTTGACCA 58.875 50.000 13.24 0.00 41.22 4.02
5226 6334 1.697432 TCGAGGTCCAACTTTGACCAT 59.303 47.619 13.24 0.72 41.22 3.55
5227 6335 2.901192 TCGAGGTCCAACTTTGACCATA 59.099 45.455 13.24 0.00 41.22 2.74
5228 6336 3.325425 TCGAGGTCCAACTTTGACCATAA 59.675 43.478 13.24 0.00 41.22 1.90
5229 6337 4.069304 CGAGGTCCAACTTTGACCATAAA 58.931 43.478 13.24 0.00 41.22 1.40
5230 6338 4.700213 CGAGGTCCAACTTTGACCATAAAT 59.300 41.667 13.24 0.00 41.22 1.40
5231 6339 5.183140 CGAGGTCCAACTTTGACCATAAATT 59.817 40.000 13.24 0.00 41.22 1.82
5232 6340 6.294508 CGAGGTCCAACTTTGACCATAAATTT 60.295 38.462 13.24 0.00 41.22 1.82
5233 6341 7.094549 CGAGGTCCAACTTTGACCATAAATTTA 60.095 37.037 13.24 0.00 41.22 1.40
5234 6342 8.485578 AGGTCCAACTTTGACCATAAATTTAA 57.514 30.769 13.24 0.00 41.22 1.52
5235 6343 8.364894 AGGTCCAACTTTGACCATAAATTTAAC 58.635 33.333 13.24 0.00 41.22 2.01
5236 6344 7.601130 GGTCCAACTTTGACCATAAATTTAACC 59.399 37.037 1.21 0.00 38.76 2.85
5237 6345 8.145122 GTCCAACTTTGACCATAAATTTAACCA 58.855 33.333 1.21 0.00 0.00 3.67
5238 6346 8.705594 TCCAACTTTGACCATAAATTTAACCAA 58.294 29.630 1.21 2.19 0.00 3.67
5239 6347 8.769891 CCAACTTTGACCATAAATTTAACCAAC 58.230 33.333 1.21 0.00 0.00 3.77
5240 6348 8.484008 CAACTTTGACCATAAATTTAACCAACG 58.516 33.333 1.21 5.06 0.00 4.10
5241 6349 7.942990 ACTTTGACCATAAATTTAACCAACGA 58.057 30.769 1.21 0.00 0.00 3.85
5242 6350 8.079809 ACTTTGACCATAAATTTAACCAACGAG 58.920 33.333 1.21 3.35 0.00 4.18
5243 6351 7.747155 TTGACCATAAATTTAACCAACGAGA 57.253 32.000 1.21 0.00 0.00 4.04
5244 6352 7.136289 TGACCATAAATTTAACCAACGAGAC 57.864 36.000 1.21 0.00 0.00 3.36
5245 6353 6.149807 TGACCATAAATTTAACCAACGAGACC 59.850 38.462 1.21 0.00 0.00 3.85
5246 6354 6.005198 ACCATAAATTTAACCAACGAGACCA 58.995 36.000 1.21 0.00 0.00 4.02
5247 6355 6.490721 ACCATAAATTTAACCAACGAGACCAA 59.509 34.615 1.21 0.00 0.00 3.67
5248 6356 6.804783 CCATAAATTTAACCAACGAGACCAAC 59.195 38.462 1.21 0.00 0.00 3.77
5249 6357 7.308951 CCATAAATTTAACCAACGAGACCAACT 60.309 37.037 1.21 0.00 0.00 3.16
5250 6358 5.432885 AATTTAACCAACGAGACCAACTG 57.567 39.130 0.00 0.00 0.00 3.16
5251 6359 1.873698 TAACCAACGAGACCAACTGC 58.126 50.000 0.00 0.00 0.00 4.40
5252 6360 1.157870 AACCAACGAGACCAACTGCG 61.158 55.000 0.00 0.00 0.00 5.18
5253 6361 2.317609 CCAACGAGACCAACTGCGG 61.318 63.158 0.00 0.00 0.00 5.69
5254 6362 2.665185 AACGAGACCAACTGCGGC 60.665 61.111 0.00 0.00 0.00 6.53
5261 6369 4.697756 CCAACTGCGGCGGGAGAA 62.698 66.667 19.55 0.00 35.29 2.87
5262 6370 2.668212 CAACTGCGGCGGGAGAAA 60.668 61.111 19.55 0.00 35.29 2.52
5263 6371 2.112297 AACTGCGGCGGGAGAAAA 59.888 55.556 19.55 0.00 35.29 2.29
5264 6372 1.527380 AACTGCGGCGGGAGAAAAA 60.527 52.632 19.55 0.00 35.29 1.94
5304 6412 9.450807 AAACTTCTTTCGAATACAAATTCACTG 57.549 29.630 0.00 0.00 41.44 3.66
5305 6413 8.378172 ACTTCTTTCGAATACAAATTCACTGA 57.622 30.769 0.00 0.00 41.44 3.41
5306 6414 9.003658 ACTTCTTTCGAATACAAATTCACTGAT 57.996 29.630 0.00 0.00 41.44 2.90
5321 6429 9.822185 AAATTCACTGATATAATTTTTGCTCCC 57.178 29.630 0.00 0.00 30.62 4.30
5322 6430 6.618287 TCACTGATATAATTTTTGCTCCCG 57.382 37.500 0.00 0.00 0.00 5.14
5323 6431 5.008613 TCACTGATATAATTTTTGCTCCCGC 59.991 40.000 0.00 0.00 0.00 6.13
5324 6432 4.278419 ACTGATATAATTTTTGCTCCCGCC 59.722 41.667 0.00 0.00 34.43 6.13
5325 6433 3.252215 TGATATAATTTTTGCTCCCGCCG 59.748 43.478 0.00 0.00 34.43 6.46
5326 6434 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.000 0.00 0.00 34.43 6.53
5327 6435 1.244697 TAATTTTTGCTCCCGCCGCA 61.245 50.000 0.00 0.00 35.22 5.69
5328 6436 2.093537 AATTTTTGCTCCCGCCGCAA 62.094 50.000 0.00 0.00 44.83 4.85
5329 6437 1.887344 ATTTTTGCTCCCGCCGCAAT 61.887 50.000 5.33 0.00 45.67 3.56
5330 6438 2.485188 TTTTTGCTCCCGCCGCAATC 62.485 55.000 5.33 0.00 45.67 2.67
5346 6454 5.712217 CGCAATCGGTCTTGATAGTTAAA 57.288 39.130 0.00 0.00 0.00 1.52
5347 6455 6.287107 CGCAATCGGTCTTGATAGTTAAAT 57.713 37.500 0.00 0.00 0.00 1.40
5348 6456 6.715464 CGCAATCGGTCTTGATAGTTAAATT 58.285 36.000 0.00 0.00 0.00 1.82
5349 6457 7.186804 CGCAATCGGTCTTGATAGTTAAATTT 58.813 34.615 0.00 0.00 0.00 1.82
5350 6458 8.332464 CGCAATCGGTCTTGATAGTTAAATTTA 58.668 33.333 0.00 0.00 0.00 1.40
5351 6459 9.434559 GCAATCGGTCTTGATAGTTAAATTTAC 57.565 33.333 0.00 0.00 0.00 2.01
5352 6460 9.632969 CAATCGGTCTTGATAGTTAAATTTACG 57.367 33.333 0.00 0.00 0.00 3.18
5353 6461 7.760131 TCGGTCTTGATAGTTAAATTTACGG 57.240 36.000 0.00 0.00 0.00 4.02
5354 6462 7.322664 TCGGTCTTGATAGTTAAATTTACGGT 58.677 34.615 0.00 0.00 0.00 4.83
5355 6463 7.489113 TCGGTCTTGATAGTTAAATTTACGGTC 59.511 37.037 0.00 0.00 0.00 4.79
5356 6464 7.276218 CGGTCTTGATAGTTAAATTTACGGTCA 59.724 37.037 0.00 0.00 0.00 4.02
5357 6465 8.938906 GGTCTTGATAGTTAAATTTACGGTCAA 58.061 33.333 0.00 6.02 0.00 3.18
5366 6474 9.292846 AGTTAAATTTACGGTCAAAGTTGAAAC 57.707 29.630 0.00 0.00 39.21 2.78
5367 6475 9.074443 GTTAAATTTACGGTCAAAGTTGAAACA 57.926 29.630 0.00 0.00 39.21 2.83
5368 6476 7.514573 AAATTTACGGTCAAAGTTGAAACAC 57.485 32.000 0.00 0.00 39.21 3.32
5369 6477 2.817538 ACGGTCAAAGTTGAAACACG 57.182 45.000 0.00 2.00 39.21 4.49
5370 6478 2.078392 ACGGTCAAAGTTGAAACACGT 58.922 42.857 0.00 2.58 39.21 4.49
5371 6479 2.159626 ACGGTCAAAGTTGAAACACGTG 60.160 45.455 15.48 15.48 39.21 4.49
5372 6480 2.094575 CGGTCAAAGTTGAAACACGTGA 59.905 45.455 25.01 0.00 39.21 4.35
5373 6481 3.425094 CGGTCAAAGTTGAAACACGTGAA 60.425 43.478 25.01 2.35 39.21 3.18
5374 6482 4.668289 GGTCAAAGTTGAAACACGTGAAT 58.332 39.130 25.01 10.29 39.21 2.57
5375 6483 5.502706 CGGTCAAAGTTGAAACACGTGAATA 60.503 40.000 25.01 2.33 39.21 1.75
5376 6484 5.907391 GGTCAAAGTTGAAACACGTGAATAG 59.093 40.000 25.01 0.00 39.21 1.73
5377 6485 6.238266 GGTCAAAGTTGAAACACGTGAATAGA 60.238 38.462 25.01 1.86 39.21 1.98
5378 6486 7.352739 GTCAAAGTTGAAACACGTGAATAGAT 58.647 34.615 25.01 0.00 39.21 1.98
5379 6487 7.321271 GTCAAAGTTGAAACACGTGAATAGATG 59.679 37.037 25.01 9.63 39.21 2.90
5380 6488 7.225734 TCAAAGTTGAAACACGTGAATAGATGA 59.774 33.333 25.01 11.70 33.55 2.92
5381 6489 7.490962 AAGTTGAAACACGTGAATAGATGAA 57.509 32.000 25.01 0.78 0.00 2.57
5382 6490 7.121974 AGTTGAAACACGTGAATAGATGAAG 57.878 36.000 25.01 0.00 0.00 3.02
5383 6491 5.530519 TGAAACACGTGAATAGATGAAGC 57.469 39.130 25.01 0.00 0.00 3.86
5384 6492 4.994217 TGAAACACGTGAATAGATGAAGCA 59.006 37.500 25.01 0.00 0.00 3.91
5385 6493 4.928661 AACACGTGAATAGATGAAGCAC 57.071 40.909 25.01 0.00 0.00 4.40
5386 6494 4.193826 ACACGTGAATAGATGAAGCACT 57.806 40.909 25.01 0.00 0.00 4.40
5387 6495 5.324784 ACACGTGAATAGATGAAGCACTA 57.675 39.130 25.01 0.00 0.00 2.74
5388 6496 5.103000 ACACGTGAATAGATGAAGCACTAC 58.897 41.667 25.01 0.00 0.00 2.73
5389 6497 5.102313 CACGTGAATAGATGAAGCACTACA 58.898 41.667 10.90 0.00 0.00 2.74
5390 6498 5.750547 CACGTGAATAGATGAAGCACTACAT 59.249 40.000 10.90 0.00 0.00 2.29
5391 6499 6.256539 CACGTGAATAGATGAAGCACTACATT 59.743 38.462 10.90 0.00 0.00 2.71
5392 6500 7.435192 CACGTGAATAGATGAAGCACTACATTA 59.565 37.037 10.90 0.00 0.00 1.90
5393 6501 8.144478 ACGTGAATAGATGAAGCACTACATTAT 58.856 33.333 0.00 0.00 0.00 1.28
5394 6502 8.430828 CGTGAATAGATGAAGCACTACATTATG 58.569 37.037 0.00 0.00 0.00 1.90
5395 6503 8.715998 GTGAATAGATGAAGCACTACATTATGG 58.284 37.037 0.00 0.00 0.00 2.74
5396 6504 8.650490 TGAATAGATGAAGCACTACATTATGGA 58.350 33.333 0.00 0.00 0.00 3.41
5397 6505 9.494271 GAATAGATGAAGCACTACATTATGGAA 57.506 33.333 0.00 0.00 0.00 3.53
5399 6507 7.741027 AGATGAAGCACTACATTATGGAATG 57.259 36.000 0.00 0.00 46.77 2.67
5400 6508 6.713903 AGATGAAGCACTACATTATGGAATGG 59.286 38.462 0.00 0.00 45.83 3.16
5401 6509 6.000246 TGAAGCACTACATTATGGAATGGA 58.000 37.500 0.00 0.00 45.83 3.41
5407 6515 5.832539 CTACATTATGGAATGGAGGGAGT 57.167 43.478 2.44 0.00 46.58 3.85
5408 6516 6.935240 CTACATTATGGAATGGAGGGAGTA 57.065 41.667 2.44 0.00 46.58 2.59
5409 6517 5.832539 ACATTATGGAATGGAGGGAGTAG 57.167 43.478 0.00 0.00 45.83 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 0.235665 GATGTTGGCGCATACGGATG 59.764 55.000 10.83 2.22 40.57 3.51
67 68 1.467374 GGTTGTGATGTTGGCGCATAC 60.467 52.381 10.83 6.99 0.00 2.39
70 71 1.106351 AAGGTTGTGATGTTGGCGCA 61.106 50.000 10.83 0.00 0.00 6.09
86 87 0.179001 AAACTGGGGGTCAACGAAGG 60.179 55.000 0.00 0.00 0.00 3.46
127 128 7.332926 ACTGATACTTAGAAAGCTTGTGTGATG 59.667 37.037 0.00 0.00 0.00 3.07
151 152 9.705290 CCACAAGTTTGCCTATTAAAAATTACT 57.295 29.630 0.00 0.00 0.00 2.24
152 153 9.483916 ACCACAAGTTTGCCTATTAAAAATTAC 57.516 29.630 0.00 0.00 0.00 1.89
156 157 9.699703 GATTACCACAAGTTTGCCTATTAAAAA 57.300 29.630 0.00 0.00 0.00 1.94
157 158 9.084533 AGATTACCACAAGTTTGCCTATTAAAA 57.915 29.630 0.00 0.00 0.00 1.52
166 273 5.772521 ACAATCAGATTACCACAAGTTTGC 58.227 37.500 0.00 0.00 0.00 3.68
186 293 5.804639 TCTTTTCTGCTCCTGCTAATACAA 58.195 37.500 0.00 0.00 40.48 2.41
193 300 1.423161 ACCTTCTTTTCTGCTCCTGCT 59.577 47.619 0.00 0.00 40.48 4.24
201 308 7.672983 TCTGCAGTATTTACCTTCTTTTCTG 57.327 36.000 14.67 0.00 0.00 3.02
228 335 8.487970 TCGATGCTTGATTTTTAACTATCGATC 58.512 33.333 0.00 0.00 38.94 3.69
229 336 8.276325 GTCGATGCTTGATTTTTAACTATCGAT 58.724 33.333 2.16 2.16 43.49 3.59
231 338 6.566427 CGTCGATGCTTGATTTTTAACTATCG 59.434 38.462 0.00 0.00 37.00 2.92
232 339 6.846283 CCGTCGATGCTTGATTTTTAACTATC 59.154 38.462 0.00 0.00 0.00 2.08
233 340 6.315393 ACCGTCGATGCTTGATTTTTAACTAT 59.685 34.615 0.00 0.00 0.00 2.12
235 342 4.454504 ACCGTCGATGCTTGATTTTTAACT 59.545 37.500 0.00 0.00 0.00 2.24
236 343 4.719040 ACCGTCGATGCTTGATTTTTAAC 58.281 39.130 0.00 0.00 0.00 2.01
237 344 5.444877 CGTACCGTCGATGCTTGATTTTTAA 60.445 40.000 0.00 0.00 0.00 1.52
239 346 3.181524 CGTACCGTCGATGCTTGATTTTT 60.182 43.478 0.00 0.00 0.00 1.94
240 347 2.347452 CGTACCGTCGATGCTTGATTTT 59.653 45.455 0.00 0.00 0.00 1.82
248 372 2.948840 CTTCCCCGTACCGTCGATGC 62.949 65.000 0.00 0.00 0.00 3.91
293 417 3.620488 TGGGTTTGATTAGCTTAGCTGG 58.380 45.455 17.97 0.00 40.10 4.85
310 440 1.632965 GGGTTAAGCGAGGGATGGGT 61.633 60.000 0.00 0.00 0.00 4.51
311 441 1.148498 GGGTTAAGCGAGGGATGGG 59.852 63.158 0.00 0.00 0.00 4.00
490 640 0.882927 TTCGCTTTGGAGTGGAACGG 60.883 55.000 0.00 0.00 45.86 4.44
491 641 0.941542 TTTCGCTTTGGAGTGGAACG 59.058 50.000 0.00 0.00 45.86 3.95
493 643 1.314730 GGTTTCGCTTTGGAGTGGAA 58.685 50.000 0.00 0.00 34.13 3.53
494 644 0.882927 CGGTTTCGCTTTGGAGTGGA 60.883 55.000 0.00 0.00 34.13 4.02
497 647 0.883370 GGTCGGTTTCGCTTTGGAGT 60.883 55.000 0.00 0.00 36.13 3.85
499 649 0.179040 AAGGTCGGTTTCGCTTTGGA 60.179 50.000 0.00 0.00 36.13 3.53
1053 1213 1.174078 TGAACTCGGTGTACTCGGCA 61.174 55.000 8.77 2.06 0.00 5.69
1077 1237 0.110486 AGGCGATGGTGGTGAAGTTT 59.890 50.000 0.00 0.00 0.00 2.66
1482 1644 3.194968 ACCAAGTATCACCGAACTCGAAT 59.805 43.478 0.00 0.00 43.02 3.34
1495 1657 6.183360 GCATAGCACGATATTGACCAAGTATC 60.183 42.308 0.00 0.00 0.00 2.24
1535 1699 1.929836 GGCGTGTGAGAAGATTAGCAG 59.070 52.381 0.00 0.00 0.00 4.24
1540 1704 2.158900 CCCATAGGCGTGTGAGAAGATT 60.159 50.000 4.57 0.00 0.00 2.40
1541 1705 1.414181 CCCATAGGCGTGTGAGAAGAT 59.586 52.381 4.57 0.00 0.00 2.40
1567 1732 2.476686 CCATTGCAGCTGTGATACAACG 60.477 50.000 16.64 2.85 0.00 4.10
1574 1739 3.057548 CGGCCATTGCAGCTGTGA 61.058 61.111 16.64 4.48 40.13 3.58
1575 1740 3.057548 TCGGCCATTGCAGCTGTG 61.058 61.111 16.64 5.66 40.13 3.66
1693 1862 6.588756 GGATAAATATGTGCTGGCATTTGATG 59.411 38.462 0.00 0.00 0.00 3.07
1697 1866 7.838079 TTAGGATAAATATGTGCTGGCATTT 57.162 32.000 0.00 0.00 0.00 2.32
1717 1886 6.816140 ACAAATGAACCGCCAAATTATTTAGG 59.184 34.615 0.00 0.00 0.00 2.69
1719 1888 7.360438 GCAACAAATGAACCGCCAAATTATTTA 60.360 33.333 0.00 0.00 0.00 1.40
1720 1889 6.567511 GCAACAAATGAACCGCCAAATTATTT 60.568 34.615 0.00 0.00 0.00 1.40
1721 1890 5.106752 GCAACAAATGAACCGCCAAATTATT 60.107 36.000 0.00 0.00 0.00 1.40
1722 1891 4.391523 GCAACAAATGAACCGCCAAATTAT 59.608 37.500 0.00 0.00 0.00 1.28
1820 1996 3.485711 CCATGCATAAATATACGCTGCCG 60.486 47.826 0.00 0.00 41.14 5.69
1891 2073 3.733337 ACTCGGAAATGCTGATACATCC 58.267 45.455 0.00 0.00 0.00 3.51
1901 2083 4.157840 ACCCATTAGAAAACTCGGAAATGC 59.842 41.667 0.00 0.00 0.00 3.56
1975 2162 9.177608 TGAAATGCTTATACAAACTTAGATGCT 57.822 29.630 0.00 0.00 0.00 3.79
1976 2163 9.226345 GTGAAATGCTTATACAAACTTAGATGC 57.774 33.333 0.00 0.00 0.00 3.91
2040 2353 7.564660 ACCATGCAAGGGAATATTCATTCTTAA 59.435 33.333 17.07 9.10 43.46 1.85
2074 2387 9.512435 GAGGAACATCTATGTGAATTGATTTTG 57.488 33.333 0.00 0.00 41.61 2.44
2116 2429 6.803320 CACTTAACTAACAAGTGCATCCAATG 59.197 38.462 2.59 0.00 44.49 2.82
2165 2478 2.225491 GCGACAAAAGCAATGACCAGTA 59.775 45.455 0.00 0.00 34.19 2.74
2173 2487 1.421382 GCATGTGCGACAAAAGCAAT 58.579 45.000 0.00 0.00 46.97 3.56
2304 2618 3.926527 TCTGTGCTCAGTAAAATGCTACG 59.073 43.478 15.01 0.00 41.91 3.51
2374 2690 9.407380 TGTAATGTATGAAAAGTATTGCCAGAT 57.593 29.630 0.00 0.00 0.00 2.90
2489 2813 6.949352 AATTTCCACTACATCATCACATCC 57.051 37.500 0.00 0.00 0.00 3.51
2524 2848 9.632807 AGAAACGCAGCAATATAACAAAATTAA 57.367 25.926 0.00 0.00 0.00 1.40
2566 2891 8.259049 AGGAATTGTGCATTAAAATTCACATG 57.741 30.769 19.72 0.00 41.03 3.21
2714 3043 9.959749 AGAAACAAGCATTATCTTCGTTTTTAA 57.040 25.926 0.00 0.00 0.00 1.52
2767 3097 7.411804 GCAACACCAACAAATGAAATATAGTGC 60.412 37.037 0.00 0.00 0.00 4.40
2777 3107 5.451242 GGAAGTTAGCAACACCAACAAATGA 60.451 40.000 0.00 0.00 32.84 2.57
2851 3182 0.110238 CTGATTCAACGGCAACCACG 60.110 55.000 0.00 0.00 37.36 4.94
2971 3302 3.057734 CACGTACCCAAACTCTCTGTTC 58.942 50.000 0.00 0.00 38.03 3.18
3034 3366 6.676950 TCACACACAAAGTTAGCATAAATGG 58.323 36.000 0.00 0.00 0.00 3.16
3035 3367 8.746922 ATTCACACACAAAGTTAGCATAAATG 57.253 30.769 0.00 0.00 0.00 2.32
3040 3372 9.840427 GTAAATATTCACACACAAAGTTAGCAT 57.160 29.630 0.00 0.00 0.00 3.79
3047 3379 9.515020 ACAAACAGTAAATATTCACACACAAAG 57.485 29.630 0.00 0.00 0.00 2.77
3088 3420 1.081892 CACAGTACTGCATGTGCTCC 58.918 55.000 22.90 0.00 39.61 4.70
3371 3746 2.304221 AGTACAGTGCCCAGTACAGA 57.696 50.000 4.82 0.00 42.26 3.41
3620 3998 0.550147 AGCCCTCACTAACACCCCAT 60.550 55.000 0.00 0.00 0.00 4.00
4021 5070 5.708948 TGATTCCCAAATTTAAGAACAGCG 58.291 37.500 4.64 0.00 0.00 5.18
4711 5813 2.439507 ACACCCACACAATTCTGACTCT 59.560 45.455 0.00 0.00 0.00 3.24
4742 5844 1.774217 AGCCCCCAACAAGAGGACA 60.774 57.895 0.00 0.00 0.00 4.02
4984 6091 2.551270 AGCTCCAAATGTCCCTCAGTA 58.449 47.619 0.00 0.00 0.00 2.74
5170 6278 5.474876 GCACTATATTTTGGAATGGAGGGAG 59.525 44.000 0.00 0.00 0.00 4.30
5171 6279 5.385198 GCACTATATTTTGGAATGGAGGGA 58.615 41.667 0.00 0.00 0.00 4.20
5172 6280 4.216257 CGCACTATATTTTGGAATGGAGGG 59.784 45.833 0.00 0.00 0.00 4.30
5173 6281 4.320494 GCGCACTATATTTTGGAATGGAGG 60.320 45.833 0.30 0.00 0.00 4.30
5174 6282 4.320494 GGCGCACTATATTTTGGAATGGAG 60.320 45.833 10.83 0.00 0.00 3.86
5175 6283 3.568007 GGCGCACTATATTTTGGAATGGA 59.432 43.478 10.83 0.00 0.00 3.41
5176 6284 3.305335 GGGCGCACTATATTTTGGAATGG 60.305 47.826 10.83 0.00 0.00 3.16
5177 6285 3.609175 CGGGCGCACTATATTTTGGAATG 60.609 47.826 8.62 0.00 0.00 2.67
5178 6286 2.552315 CGGGCGCACTATATTTTGGAAT 59.448 45.455 8.62 0.00 0.00 3.01
5179 6287 1.944024 CGGGCGCACTATATTTTGGAA 59.056 47.619 8.62 0.00 0.00 3.53
5180 6288 1.588674 CGGGCGCACTATATTTTGGA 58.411 50.000 8.62 0.00 0.00 3.53
5181 6289 0.040425 GCGGGCGCACTATATTTTGG 60.040 55.000 8.62 0.00 41.49 3.28
5182 6290 0.384230 CGCGGGCGCACTATATTTTG 60.384 55.000 8.62 0.00 42.06 2.44
5183 6291 1.938861 CGCGGGCGCACTATATTTT 59.061 52.632 8.62 0.00 42.06 1.82
5184 6292 3.637714 CGCGGGCGCACTATATTT 58.362 55.556 8.62 0.00 42.06 1.40
5198 6306 2.314647 TTGGACCTCGAAAAGCGCG 61.315 57.895 0.00 0.00 40.61 6.86
5199 6307 1.206831 GTTGGACCTCGAAAAGCGC 59.793 57.895 0.00 0.00 40.61 5.92
5200 6308 1.226746 AAGTTGGACCTCGAAAAGCG 58.773 50.000 0.00 0.00 42.69 4.68
5201 6309 2.616842 TCAAAGTTGGACCTCGAAAAGC 59.383 45.455 0.00 0.00 0.00 3.51
5202 6310 4.210832 GTCAAAGTTGGACCTCGAAAAG 57.789 45.455 0.00 0.00 0.00 2.27
5211 6319 8.145122 TGGTTAAATTTATGGTCAAAGTTGGAC 58.855 33.333 1.31 1.31 29.44 4.02
5212 6320 8.251383 TGGTTAAATTTATGGTCAAAGTTGGA 57.749 30.769 0.00 0.00 29.44 3.53
5213 6321 8.769891 GTTGGTTAAATTTATGGTCAAAGTTGG 58.230 33.333 0.00 0.00 29.44 3.77
5214 6322 8.484008 CGTTGGTTAAATTTATGGTCAAAGTTG 58.516 33.333 0.00 0.00 29.44 3.16
5215 6323 8.414778 TCGTTGGTTAAATTTATGGTCAAAGTT 58.585 29.630 0.00 0.00 31.36 2.66
5216 6324 7.942990 TCGTTGGTTAAATTTATGGTCAAAGT 58.057 30.769 0.00 0.00 0.00 2.66
5217 6325 8.293867 TCTCGTTGGTTAAATTTATGGTCAAAG 58.706 33.333 0.00 4.88 0.00 2.77
5218 6326 8.077386 GTCTCGTTGGTTAAATTTATGGTCAAA 58.923 33.333 0.00 0.00 0.00 2.69
5219 6327 7.308710 GGTCTCGTTGGTTAAATTTATGGTCAA 60.309 37.037 0.00 0.00 0.00 3.18
5220 6328 6.149807 GGTCTCGTTGGTTAAATTTATGGTCA 59.850 38.462 0.00 0.00 0.00 4.02
5221 6329 6.149807 TGGTCTCGTTGGTTAAATTTATGGTC 59.850 38.462 0.00 0.00 0.00 4.02
5222 6330 6.005198 TGGTCTCGTTGGTTAAATTTATGGT 58.995 36.000 0.00 0.00 0.00 3.55
5223 6331 6.503589 TGGTCTCGTTGGTTAAATTTATGG 57.496 37.500 0.00 0.00 0.00 2.74
5224 6332 7.537306 CAGTTGGTCTCGTTGGTTAAATTTATG 59.463 37.037 0.00 0.00 0.00 1.90
5225 6333 7.590279 CAGTTGGTCTCGTTGGTTAAATTTAT 58.410 34.615 0.00 0.00 0.00 1.40
5226 6334 6.513720 GCAGTTGGTCTCGTTGGTTAAATTTA 60.514 38.462 0.00 0.00 0.00 1.40
5227 6335 5.735070 GCAGTTGGTCTCGTTGGTTAAATTT 60.735 40.000 0.00 0.00 0.00 1.82
5228 6336 4.261447 GCAGTTGGTCTCGTTGGTTAAATT 60.261 41.667 0.00 0.00 0.00 1.82
5229 6337 3.252458 GCAGTTGGTCTCGTTGGTTAAAT 59.748 43.478 0.00 0.00 0.00 1.40
5230 6338 2.614983 GCAGTTGGTCTCGTTGGTTAAA 59.385 45.455 0.00 0.00 0.00 1.52
5231 6339 2.215196 GCAGTTGGTCTCGTTGGTTAA 58.785 47.619 0.00 0.00 0.00 2.01
5232 6340 1.870580 CGCAGTTGGTCTCGTTGGTTA 60.871 52.381 0.00 0.00 0.00 2.85
5233 6341 1.157870 CGCAGTTGGTCTCGTTGGTT 61.158 55.000 0.00 0.00 0.00 3.67
5234 6342 1.594293 CGCAGTTGGTCTCGTTGGT 60.594 57.895 0.00 0.00 0.00 3.67
5235 6343 2.317609 CCGCAGTTGGTCTCGTTGG 61.318 63.158 0.00 0.00 0.00 3.77
5236 6344 2.954753 GCCGCAGTTGGTCTCGTTG 61.955 63.158 0.00 0.00 0.00 4.10
5237 6345 2.665185 GCCGCAGTTGGTCTCGTT 60.665 61.111 0.00 0.00 0.00 3.85
5244 6352 4.697756 TTCTCCCGCCGCAGTTGG 62.698 66.667 0.00 0.00 0.00 3.77
5245 6353 1.791103 TTTTTCTCCCGCCGCAGTTG 61.791 55.000 0.00 0.00 0.00 3.16
5246 6354 1.527380 TTTTTCTCCCGCCGCAGTT 60.527 52.632 0.00 0.00 0.00 3.16
5247 6355 2.112297 TTTTTCTCCCGCCGCAGT 59.888 55.556 0.00 0.00 0.00 4.40
5295 6403 9.822185 GGGAGCAAAAATTATATCAGTGAATTT 57.178 29.630 0.00 0.00 34.94 1.82
5296 6404 8.137437 CGGGAGCAAAAATTATATCAGTGAATT 58.863 33.333 0.00 0.00 0.00 2.17
5297 6405 7.651808 CGGGAGCAAAAATTATATCAGTGAAT 58.348 34.615 0.00 0.00 0.00 2.57
5298 6406 7.026631 CGGGAGCAAAAATTATATCAGTGAA 57.973 36.000 0.00 0.00 0.00 3.18
5299 6407 6.618287 CGGGAGCAAAAATTATATCAGTGA 57.382 37.500 0.00 0.00 0.00 3.41
5324 6432 5.712217 TTTAACTATCAAGACCGATTGCG 57.288 39.130 0.00 0.00 37.24 4.85
5325 6433 9.434559 GTAAATTTAACTATCAAGACCGATTGC 57.565 33.333 0.00 0.00 0.00 3.56
5326 6434 9.632969 CGTAAATTTAACTATCAAGACCGATTG 57.367 33.333 0.00 0.00 0.00 2.67
5327 6435 8.823818 CCGTAAATTTAACTATCAAGACCGATT 58.176 33.333 0.00 0.00 0.00 3.34
5328 6436 7.983484 ACCGTAAATTTAACTATCAAGACCGAT 59.017 33.333 0.00 0.00 0.00 4.18
5329 6437 7.322664 ACCGTAAATTTAACTATCAAGACCGA 58.677 34.615 0.00 0.00 0.00 4.69
5330 6438 7.276218 TGACCGTAAATTTAACTATCAAGACCG 59.724 37.037 0.00 0.00 0.00 4.79
5331 6439 8.483307 TGACCGTAAATTTAACTATCAAGACC 57.517 34.615 0.00 0.00 0.00 3.85
5340 6448 9.292846 GTTTCAACTTTGACCGTAAATTTAACT 57.707 29.630 0.00 0.00 36.83 2.24
5341 6449 9.074443 TGTTTCAACTTTGACCGTAAATTTAAC 57.926 29.630 0.00 0.00 36.83 2.01
5342 6450 9.074443 GTGTTTCAACTTTGACCGTAAATTTAA 57.926 29.630 0.00 0.00 36.83 1.52
5343 6451 7.428761 CGTGTTTCAACTTTGACCGTAAATTTA 59.571 33.333 0.00 0.00 36.83 1.40
5344 6452 6.251801 CGTGTTTCAACTTTGACCGTAAATTT 59.748 34.615 0.00 0.00 36.83 1.82
5345 6453 5.740099 CGTGTTTCAACTTTGACCGTAAATT 59.260 36.000 0.00 0.00 36.83 1.82
5346 6454 5.163733 ACGTGTTTCAACTTTGACCGTAAAT 60.164 36.000 0.00 0.00 36.83 1.40
5347 6455 4.153835 ACGTGTTTCAACTTTGACCGTAAA 59.846 37.500 0.00 0.00 36.83 2.01
5348 6456 3.683822 ACGTGTTTCAACTTTGACCGTAA 59.316 39.130 0.00 0.00 36.83 3.18
5349 6457 3.062369 CACGTGTTTCAACTTTGACCGTA 59.938 43.478 7.58 0.00 36.83 4.02
5350 6458 2.078392 ACGTGTTTCAACTTTGACCGT 58.922 42.857 0.00 0.00 36.83 4.83
5351 6459 2.094575 TCACGTGTTTCAACTTTGACCG 59.905 45.455 16.51 0.00 36.83 4.79
5352 6460 3.750639 TCACGTGTTTCAACTTTGACC 57.249 42.857 16.51 0.00 36.83 4.02
5353 6461 6.711579 TCTATTCACGTGTTTCAACTTTGAC 58.288 36.000 16.51 0.00 36.83 3.18
5354 6462 6.912203 TCTATTCACGTGTTTCAACTTTGA 57.088 33.333 16.51 0.00 34.92 2.69
5355 6463 7.351981 TCATCTATTCACGTGTTTCAACTTTG 58.648 34.615 16.51 4.40 0.00 2.77
5356 6464 7.490962 TCATCTATTCACGTGTTTCAACTTT 57.509 32.000 16.51 0.00 0.00 2.66
5357 6465 7.490962 TTCATCTATTCACGTGTTTCAACTT 57.509 32.000 16.51 0.00 0.00 2.66
5358 6466 6.347725 GCTTCATCTATTCACGTGTTTCAACT 60.348 38.462 16.51 0.00 0.00 3.16
5359 6467 5.790495 GCTTCATCTATTCACGTGTTTCAAC 59.210 40.000 16.51 0.00 0.00 3.18
5360 6468 5.468409 TGCTTCATCTATTCACGTGTTTCAA 59.532 36.000 16.51 2.25 0.00 2.69
5361 6469 4.994217 TGCTTCATCTATTCACGTGTTTCA 59.006 37.500 16.51 0.00 0.00 2.69
5362 6470 5.120830 AGTGCTTCATCTATTCACGTGTTTC 59.879 40.000 16.51 0.00 33.28 2.78
5363 6471 4.997395 AGTGCTTCATCTATTCACGTGTTT 59.003 37.500 16.51 6.83 33.28 2.83
5364 6472 4.569943 AGTGCTTCATCTATTCACGTGTT 58.430 39.130 16.51 7.21 33.28 3.32
5365 6473 4.193826 AGTGCTTCATCTATTCACGTGT 57.806 40.909 16.51 0.00 33.28 4.49
5366 6474 5.102313 TGTAGTGCTTCATCTATTCACGTG 58.898 41.667 9.94 9.94 33.28 4.49
5367 6475 5.324784 TGTAGTGCTTCATCTATTCACGT 57.675 39.130 0.00 0.00 33.28 4.49
5368 6476 6.834959 AATGTAGTGCTTCATCTATTCACG 57.165 37.500 0.00 0.00 33.28 4.35
5369 6477 8.715998 CCATAATGTAGTGCTTCATCTATTCAC 58.284 37.037 0.00 0.00 0.00 3.18
5370 6478 8.650490 TCCATAATGTAGTGCTTCATCTATTCA 58.350 33.333 0.00 0.00 0.00 2.57
5371 6479 9.494271 TTCCATAATGTAGTGCTTCATCTATTC 57.506 33.333 0.00 0.00 0.00 1.75
5373 6481 9.445878 CATTCCATAATGTAGTGCTTCATCTAT 57.554 33.333 0.00 0.00 38.15 1.98
5374 6482 7.879677 CCATTCCATAATGTAGTGCTTCATCTA 59.120 37.037 0.00 0.00 40.84 1.98
5375 6483 6.713903 CCATTCCATAATGTAGTGCTTCATCT 59.286 38.462 0.00 0.00 40.84 2.90
5376 6484 6.712095 TCCATTCCATAATGTAGTGCTTCATC 59.288 38.462 0.00 0.00 40.84 2.92
5377 6485 6.604171 TCCATTCCATAATGTAGTGCTTCAT 58.396 36.000 0.00 0.00 40.84 2.57
5378 6486 6.000246 TCCATTCCATAATGTAGTGCTTCA 58.000 37.500 0.00 0.00 40.84 3.02
5379 6487 5.471456 CCTCCATTCCATAATGTAGTGCTTC 59.529 44.000 0.00 0.00 40.84 3.86
5380 6488 5.380043 CCTCCATTCCATAATGTAGTGCTT 58.620 41.667 0.00 0.00 40.84 3.91
5381 6489 4.202503 CCCTCCATTCCATAATGTAGTGCT 60.203 45.833 0.00 0.00 40.84 4.40
5382 6490 4.074970 CCCTCCATTCCATAATGTAGTGC 58.925 47.826 0.00 0.00 40.84 4.40
5383 6491 5.072329 ACTCCCTCCATTCCATAATGTAGTG 59.928 44.000 0.00 0.00 40.84 2.74
5384 6492 5.227593 ACTCCCTCCATTCCATAATGTAGT 58.772 41.667 0.00 0.00 40.84 2.73
5385 6493 5.832539 ACTCCCTCCATTCCATAATGTAG 57.167 43.478 0.00 0.00 40.84 2.74
5386 6494 6.935240 CTACTCCCTCCATTCCATAATGTA 57.065 41.667 0.00 0.00 40.84 2.29
5387 6495 5.832539 CTACTCCCTCCATTCCATAATGT 57.167 43.478 0.00 0.00 40.84 2.71


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

AutoCloner maintained by Alex Coulton.