Multiple sequence alignment - TraesCS2D01G124700

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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 TraesCS2D01G124700 chr2D 100.000 4323 0 0 1838 6160 73005509 73001187 0.000000e+00 7984.0
1 TraesCS2D01G124700 chr2D 100.000 1262 0 0 1 1262 73007346 73006085 0.000000e+00 2331.0
2 TraesCS2D01G124700 chr2B 93.192 3966 194 36 1838 5754 110412472 110408534 0.000000e+00 5758.0
3 TraesCS2D01G124700 chr2B 87.410 1247 122 24 1 1217 110413812 110412571 0.000000e+00 1400.0
4 TraesCS2D01G124700 chr2B 100.000 36 0 0 1227 1262 110412545 110412510 3.980000e-07 67.6
5 TraesCS2D01G124700 chr2A 93.200 3706 168 27 1838 5494 71592958 71589288 0.000000e+00 5371.0
6 TraesCS2D01G124700 chr2A 91.678 709 49 10 510 1217 71593756 71593057 0.000000e+00 974.0
7 TraesCS2D01G124700 chr2A 90.969 454 24 6 5690 6127 71589291 71588839 4.110000e-166 595.0
8 TraesCS2D01G124700 chr3B 77.765 868 139 42 2355 3201 681207548 681206714 9.280000e-133 484.0
9 TraesCS2D01G124700 chr3B 82.333 300 43 6 3645 3936 681206342 681206045 1.030000e-62 252.0
10 TraesCS2D01G124700 chr3B 90.244 41 4 0 291 331 23686903 23686863 3.000000e-03 54.7
11 TraesCS2D01G124700 chr3D 82.058 379 49 16 2831 3201 517485239 517484872 7.760000e-79 305.0
12 TraesCS2D01G124700 chr3D 80.153 393 60 14 4491 4870 517483454 517483067 1.690000e-70 278.0
13 TraesCS2D01G124700 chr3D 83.793 290 42 5 2358 2643 517485733 517485445 2.830000e-68 270.0
14 TraesCS2D01G124700 chr3A 83.596 317 43 9 2355 2665 653326821 653326508 7.810000e-74 289.0
15 TraesCS2D01G124700 chr3A 83.121 314 36 12 2898 3200 653326369 653326062 2.830000e-68 270.0
16 TraesCS2D01G124700 chr3A 76.726 507 84 26 4366 4841 653324509 653324006 1.030000e-62 252.0
17 TraesCS2D01G124700 chr3A 77.746 355 58 15 3400 3750 653325938 653325601 1.350000e-46 198.0
18 TraesCS2D01G124700 chr7A 78.750 240 43 5 477 711 651057709 651057473 2.970000e-33 154.0
19 TraesCS2D01G124700 chr7D 78.481 237 47 3 480 713 565187753 565187518 1.070000e-32 152.0
20 TraesCS2D01G124700 chr6D 78.571 210 43 2 477 684 1580503 1580712 2.990000e-28 137.0


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 TraesCS2D01G124700 chr2D 73001187 73007346 6159 True 5157.500000 7984 100.000000 1 6160 2 chr2D.!!$R1 6159
1 TraesCS2D01G124700 chr2B 110408534 110413812 5278 True 2408.533333 5758 93.534000 1 5754 3 chr2B.!!$R1 5753
2 TraesCS2D01G124700 chr2A 71588839 71593756 4917 True 2313.333333 5371 91.949000 510 6127 3 chr2A.!!$R1 5617
3 TraesCS2D01G124700 chr3B 681206045 681207548 1503 True 368.000000 484 80.049000 2355 3936 2 chr3B.!!$R2 1581
4 TraesCS2D01G124700 chr3D 517483067 517485733 2666 True 284.333333 305 82.001333 2358 4870 3 chr3D.!!$R1 2512
5 TraesCS2D01G124700 chr3A 653324006 653326821 2815 True 252.250000 289 80.297250 2355 4841 4 chr3A.!!$R1 2486

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
281 293 0.034476 GGACCCGAAGAAAAGACGGT 59.966 55.000 0.00 0.00 44.34 4.83 F
329 342 0.535335 TAGCTAACCAGTCTTGCCGG 59.465 55.000 0.00 0.00 0.00 6.13 F
1224 1253 0.322975 CCCAATCTAGATGGAGCCCG 59.677 60.000 17.78 0.00 40.56 6.13 F
1225 1254 1.342074 CCAATCTAGATGGAGCCCGA 58.658 55.000 8.84 0.00 40.56 5.14 F
2913 3046 1.923356 TTTGGAAGGTCTTGGCATCC 58.077 50.000 0.00 0.00 0.00 3.51 F
2947 3080 0.661483 GAACAAGTGCAAAGCGGCTC 60.661 55.000 1.45 0.00 34.04 4.70 F
3362 3515 1.190763 CAAAGTTCTTGCATGCAACGC 59.809 47.619 28.80 19.72 0.00 4.84 F
4514 5449 3.185246 TGCACTAGCCTCTCTTATTGC 57.815 47.619 0.00 0.00 41.13 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1225 1254 1.271840 TTACAGGATTGGCTCGGGCT 61.272 55.000 7.48 0.00 38.73 5.19 R
2139 2197 1.459592 GCCTAGTGCGCATTTATACGG 59.540 52.381 15.91 8.84 0.00 4.02 R
2913 3046 0.667993 TGTTCTCAAGCCGCTTTTGG 59.332 50.000 1.86 0.00 0.00 3.28 R
2936 3069 2.018324 GCTTGTTGAGCCGCTTTGC 61.018 57.895 0.00 0.00 46.01 3.68 R
4514 5449 0.592637 TTGCCGCTGATGAACACAAG 59.407 50.000 0.00 0.00 0.00 3.16 R
4720 5665 4.667573 TGCCCACAAATAAATACTGGTGA 58.332 39.130 0.00 0.00 0.00 4.02 R
5015 5968 1.466167 CAGCATGGAACGAACAGGAAG 59.534 52.381 0.00 0.00 0.00 3.46 R
5500 6459 0.039074 CTCCTGACTTGCGTTCGAGT 60.039 55.000 0.00 0.00 39.61 4.18 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
34 35 5.405935 ACTTTGGATAAGGATGTTTTGGC 57.594 39.130 0.00 0.00 0.00 4.52
38 39 3.245586 TGGATAAGGATGTTTTGGCCACT 60.246 43.478 3.88 0.00 0.00 4.00
39 40 4.017958 TGGATAAGGATGTTTTGGCCACTA 60.018 41.667 3.88 0.00 0.00 2.74
42 43 6.948309 GGATAAGGATGTTTTGGCCACTATAT 59.052 38.462 3.88 0.00 0.00 0.86
48 49 8.227507 AGGATGTTTTGGCCACTATATAAAGAT 58.772 33.333 3.88 6.28 0.00 2.40
49 50 9.515226 GGATGTTTTGGCCACTATATAAAGATA 57.485 33.333 3.88 0.00 0.00 1.98
79 80 4.699637 TGAACTCTAACCAACATCGTGTT 58.300 39.130 0.00 0.00 42.08 3.32
136 137 2.019249 CATGGCCACAATTCGACATCT 58.981 47.619 8.16 0.00 0.00 2.90
141 142 4.081365 TGGCCACAATTCGACATCTAGTTA 60.081 41.667 0.00 0.00 0.00 2.24
216 217 8.945057 CCATAATTGTTTTCTTTAAACCCATGG 58.055 33.333 4.14 4.14 44.49 3.66
234 235 0.170339 GGCCGAACCAAAGAAATCCG 59.830 55.000 0.00 0.00 38.86 4.18
235 236 0.879090 GCCGAACCAAAGAAATCCGT 59.121 50.000 0.00 0.00 0.00 4.69
250 262 3.782889 ATCCGTAAGCAAAGCCAAATC 57.217 42.857 0.00 0.00 0.00 2.17
258 270 2.094545 AGCAAAGCCAAATCGTCCAATC 60.095 45.455 0.00 0.00 0.00 2.67
260 272 3.676873 GCAAAGCCAAATCGTCCAATCAT 60.677 43.478 0.00 0.00 0.00 2.45
263 275 1.002468 GCCAAATCGTCCAATCATCGG 60.002 52.381 0.00 0.00 0.00 4.18
278 290 3.900446 TCGGACCCGAAGAAAAGAC 57.100 52.632 8.91 0.00 46.01 3.01
279 291 0.038892 TCGGACCCGAAGAAAAGACG 60.039 55.000 8.91 0.00 46.01 4.18
281 293 0.034476 GGACCCGAAGAAAAGACGGT 59.966 55.000 0.00 0.00 44.34 4.83
282 294 1.145803 GACCCGAAGAAAAGACGGTG 58.854 55.000 0.00 0.00 44.34 4.94
283 295 0.754472 ACCCGAAGAAAAGACGGTGA 59.246 50.000 0.00 0.00 44.34 4.02
284 296 1.139455 ACCCGAAGAAAAGACGGTGAA 59.861 47.619 0.00 0.00 44.34 3.18
298 311 5.734720 AGACGGTGAATGATAGTTGATTGT 58.265 37.500 0.00 0.00 0.00 2.71
320 333 7.624360 TGTTGGTTTTATGATAGCTAACCAG 57.376 36.000 13.27 0.00 46.22 4.00
329 342 0.535335 TAGCTAACCAGTCTTGCCGG 59.465 55.000 0.00 0.00 0.00 6.13
330 343 2.399356 GCTAACCAGTCTTGCCGGC 61.399 63.158 22.73 22.73 0.00 6.13
331 344 1.745489 CTAACCAGTCTTGCCGGCC 60.745 63.158 26.77 8.39 0.00 6.13
332 345 3.599285 TAACCAGTCTTGCCGGCCG 62.599 63.158 26.77 21.04 0.00 6.13
341 354 4.992511 TGCCGGCCGTGGTTACAC 62.993 66.667 26.77 3.14 44.23 2.90
344 357 2.740826 CGGCCGTGGTTACACTGG 60.741 66.667 19.50 0.00 45.50 4.00
355 368 4.273480 GTGGTTACACTGGCATGATGTATC 59.727 45.833 0.00 6.69 44.29 2.24
356 369 4.080638 TGGTTACACTGGCATGATGTATCA 60.081 41.667 0.00 0.00 41.70 2.15
378 394 7.265599 TCATGTTGTCTATTTTCCTAGGGAA 57.734 36.000 9.46 2.79 40.27 3.97
381 397 7.510675 TGTTGTCTATTTTCCTAGGGAAGAT 57.489 36.000 9.46 5.89 43.06 2.40
382 398 7.565680 TGTTGTCTATTTTCCTAGGGAAGATC 58.434 38.462 9.46 0.00 43.06 2.75
393 409 8.989045 TTCCTAGGGAAGATCATTATGGATAA 57.011 34.615 9.46 0.00 36.71 1.75
394 410 8.989045 TCCTAGGGAAGATCATTATGGATAAA 57.011 34.615 9.46 0.00 0.00 1.40
432 448 6.503589 AGTAAGGATACATCATCTACGAGC 57.496 41.667 0.00 0.00 41.41 5.03
445 462 7.803279 TCATCTACGAGCTTAGTAATCAGAA 57.197 36.000 0.00 0.00 0.00 3.02
466 489 1.917872 ATCTAGAGGCTCGTCCATCC 58.082 55.000 9.22 0.00 37.29 3.51
483 506 5.179555 GTCCATCCATAAACTAGCGGAAATC 59.820 44.000 0.00 0.00 0.00 2.17
488 511 7.696992 TCCATAAACTAGCGGAAATCTTTTT 57.303 32.000 0.00 0.00 0.00 1.94
514 539 0.613853 ACGTTCGATGGGAGAGGGAA 60.614 55.000 0.00 0.00 0.00 3.97
623 648 5.162075 ACAGAAACTGTAATGTCGCTCTAC 58.838 41.667 2.43 0.00 43.46 2.59
629 654 7.435068 AACTGTAATGTCGCTCTACAAAAAT 57.565 32.000 0.00 0.00 32.02 1.82
635 660 5.090652 TGTCGCTCTACAAAAATTGTCAC 57.909 39.130 0.00 0.00 44.12 3.67
653 678 4.582656 TGTCACCCCTCACAACTAAAATTG 59.417 41.667 0.00 0.00 35.59 2.32
654 679 4.022329 GTCACCCCTCACAACTAAAATTGG 60.022 45.833 0.00 0.00 33.63 3.16
667 692 3.840890 AAAATTGGCAGCGAAATCGTA 57.159 38.095 4.59 0.00 42.22 3.43
709 734 1.000145 GAAAGTTCGCGAGCTAAGGG 59.000 55.000 26.02 0.00 0.00 3.95
713 738 1.681327 TTCGCGAGCTAAGGGGTCT 60.681 57.895 9.59 0.00 40.01 3.85
721 747 4.514401 CGAGCTAAGGGGTCTAAAACAAT 58.486 43.478 0.00 0.00 40.01 2.71
774 800 6.035866 GCACATGTCTGTTTTTGATTTCAACA 59.964 34.615 0.00 0.00 32.01 3.33
777 803 8.819974 ACATGTCTGTTTTTGATTTCAACATTC 58.180 29.630 0.00 0.00 30.85 2.67
922 950 3.475774 CGCTGCGTACCACCGTTC 61.476 66.667 14.93 0.00 0.00 3.95
1217 1246 5.822519 TGAAATTCGAACCCCAATCTAGATG 59.177 40.000 5.86 0.76 0.00 2.90
1218 1247 3.838244 TTCGAACCCCAATCTAGATGG 57.162 47.619 5.86 9.75 37.71 3.51
1220 1249 2.965831 TCGAACCCCAATCTAGATGGAG 59.034 50.000 17.78 10.46 40.56 3.86
1222 1251 1.439543 ACCCCAATCTAGATGGAGCC 58.560 55.000 17.78 0.00 40.56 4.70
1223 1252 0.695347 CCCCAATCTAGATGGAGCCC 59.305 60.000 17.78 0.00 40.56 5.19
1224 1253 0.322975 CCCAATCTAGATGGAGCCCG 59.677 60.000 17.78 0.00 40.56 6.13
1225 1254 1.342074 CCAATCTAGATGGAGCCCGA 58.658 55.000 8.84 0.00 40.56 5.14
1874 1919 7.391554 TGAATAAGATGCATGGGTTATAGCTTC 59.608 37.037 2.46 1.40 0.00 3.86
1897 1942 4.150980 CGCTAGTACTAATCTCGACCTGAG 59.849 50.000 3.76 0.00 46.72 3.35
2060 2115 4.771590 TCCAATGTTTCATCTGTCTTGC 57.228 40.909 0.00 0.00 0.00 4.01
2070 2125 3.056536 TCATCTGTCTTGCGAGTTTAGCT 60.057 43.478 0.00 0.00 35.28 3.32
2112 2170 3.181521 CGCATGTCTAGTTTTCATCGCAA 60.182 43.478 0.00 0.00 0.00 4.85
2139 2197 7.329588 CCATTGACTTGGTAAACTATAACCC 57.670 40.000 0.00 0.00 34.69 4.11
2140 2198 6.320418 CCATTGACTTGGTAAACTATAACCCC 59.680 42.308 0.00 0.00 34.69 4.95
2147 2205 8.767436 ACTTGGTAAACTATAACCCCGTATAAA 58.233 33.333 0.00 0.00 34.69 1.40
2153 2211 2.616634 TAACCCCGTATAAATGCGCA 57.383 45.000 14.96 14.96 34.50 6.09
2178 2236 3.942130 GCCTTGCCATTTAGTGACTTT 57.058 42.857 0.00 0.00 0.00 2.66
2179 2237 3.578688 GCCTTGCCATTTAGTGACTTTG 58.421 45.455 0.00 0.00 0.00 2.77
2180 2238 3.255642 GCCTTGCCATTTAGTGACTTTGA 59.744 43.478 0.00 0.00 0.00 2.69
2181 2239 4.261994 GCCTTGCCATTTAGTGACTTTGAA 60.262 41.667 0.00 0.00 0.00 2.69
2182 2240 5.738783 GCCTTGCCATTTAGTGACTTTGAAA 60.739 40.000 0.00 0.00 0.00 2.69
2183 2241 6.279882 CCTTGCCATTTAGTGACTTTGAAAA 58.720 36.000 0.00 0.00 0.00 2.29
2184 2242 6.760770 CCTTGCCATTTAGTGACTTTGAAAAA 59.239 34.615 0.00 0.00 0.00 1.94
2185 2243 7.042523 CCTTGCCATTTAGTGACTTTGAAAAAG 60.043 37.037 0.00 0.00 0.00 2.27
2186 2244 7.106439 TGCCATTTAGTGACTTTGAAAAAGA 57.894 32.000 6.73 0.00 0.00 2.52
2187 2245 7.551585 TGCCATTTAGTGACTTTGAAAAAGAA 58.448 30.769 6.73 0.00 0.00 2.52
2213 2271 3.828451 AGTGTGTGCAAATTAAGCTCCAT 59.172 39.130 0.00 0.00 0.00 3.41
2216 2274 4.463539 TGTGTGCAAATTAAGCTCCATCAT 59.536 37.500 0.00 0.00 0.00 2.45
2278 2365 6.409704 TGTTTCTATGAGTAGCTCAAAGCAT 58.590 36.000 2.80 0.00 45.56 3.79
2279 2366 6.536582 TGTTTCTATGAGTAGCTCAAAGCATC 59.463 38.462 2.80 0.00 45.56 3.91
2280 2367 6.477053 TTCTATGAGTAGCTCAAAGCATCT 57.523 37.500 2.80 0.00 45.56 2.90
2281 2368 7.588497 TTCTATGAGTAGCTCAAAGCATCTA 57.412 36.000 2.80 0.00 45.56 1.98
2299 2386 8.095937 AGCATCTACATTATGATGACATTGTG 57.904 34.615 4.20 0.00 41.69 3.33
2748 2844 5.865085 ACAGTCCTTGCTACATGTTCTTTA 58.135 37.500 2.30 0.00 0.00 1.85
2753 2849 6.599638 GTCCTTGCTACATGTTCTTTAGGATT 59.400 38.462 2.30 0.00 32.42 3.01
2757 2853 7.759489 TGCTACATGTTCTTTAGGATTTTGT 57.241 32.000 2.30 0.00 0.00 2.83
2824 2922 2.498441 TGTTGGGCCTCCCTGTATAAT 58.502 47.619 4.53 0.00 45.70 1.28
2835 2966 9.528489 GGCCTCCCTGTATAATTATTTAAATGA 57.472 33.333 11.05 2.82 0.00 2.57
2857 2989 6.541969 TGAAAATGTGAGCGTGTTATACATG 58.458 36.000 0.00 0.00 38.13 3.21
2913 3046 1.923356 TTTGGAAGGTCTTGGCATCC 58.077 50.000 0.00 0.00 0.00 3.51
2943 3076 2.378806 CTTGAGAACAAGTGCAAAGCG 58.621 47.619 0.00 0.00 45.73 4.68
2947 3080 0.661483 GAACAAGTGCAAAGCGGCTC 60.661 55.000 1.45 0.00 34.04 4.70
2980 3113 6.707608 TGATGCTGACTGGTAATCATGTTATC 59.292 38.462 0.00 0.00 0.00 1.75
2981 3114 5.368145 TGCTGACTGGTAATCATGTTATCC 58.632 41.667 0.00 0.00 0.00 2.59
2982 3115 5.104569 TGCTGACTGGTAATCATGTTATCCA 60.105 40.000 0.00 0.00 0.00 3.41
2983 3116 6.000219 GCTGACTGGTAATCATGTTATCCAT 59.000 40.000 0.00 0.00 0.00 3.41
2985 3118 7.661437 GCTGACTGGTAATCATGTTATCCATAA 59.339 37.037 0.00 0.00 30.71 1.90
2988 3121 9.209175 GACTGGTAATCATGTTATCCATAACTC 57.791 37.037 10.17 0.00 42.32 3.01
3115 3259 2.251642 ACGTGAAGCCCTGAAACGC 61.252 57.895 0.00 0.00 37.76 4.84
3142 3286 9.371136 CGTAAATCATATGCTGTAGGTATCATT 57.629 33.333 0.00 0.00 0.00 2.57
3203 3347 6.710597 CACTATTTAGCTACAGTGTAGGGA 57.289 41.667 27.48 0.00 34.91 4.20
3206 3350 6.896307 ACTATTTAGCTACAGTGTAGGGAGTT 59.104 38.462 27.48 8.63 0.00 3.01
3215 3359 2.567615 AGTGTAGGGAGTTACTTGCTGG 59.432 50.000 0.00 0.00 0.00 4.85
3254 3398 3.210227 TCTGGTGGTGTGTAATGTGTTG 58.790 45.455 0.00 0.00 0.00 3.33
3362 3515 1.190763 CAAAGTTCTTGCATGCAACGC 59.809 47.619 28.80 19.72 0.00 4.84
3930 4452 3.414549 TTTGTCTCACCAGCGTTTTTC 57.585 42.857 0.00 0.00 0.00 2.29
3943 4465 5.920273 CCAGCGTTTTTCATCTTTTGTGTAT 59.080 36.000 0.00 0.00 0.00 2.29
4106 4867 5.163663 GCTGCCATACTAAGCAATAAACACA 60.164 40.000 0.00 0.00 38.82 3.72
4107 4868 6.189677 TGCCATACTAAGCAATAAACACAC 57.810 37.500 0.00 0.00 35.69 3.82
4118 4879 5.869888 AGCAATAAACACACTAGTAGTCAGC 59.130 40.000 0.00 0.00 0.00 4.26
4147 5010 4.142790 CCTTTATGACCGAGTAGAGGCTA 58.857 47.826 0.00 0.00 0.00 3.93
4262 5156 6.127281 TGGCATCATAGAAGCACATTTCAATT 60.127 34.615 0.00 0.00 0.00 2.32
4307 5221 4.511826 GGGTGGTAATTTTCTAGCGATGAG 59.488 45.833 0.00 0.00 0.00 2.90
4323 5237 3.406764 GATGAGAAGTTCAGCCACTTGT 58.593 45.455 5.50 0.00 39.68 3.16
4514 5449 3.185246 TGCACTAGCCTCTCTTATTGC 57.815 47.619 0.00 0.00 41.13 3.56
4675 5617 9.462606 GATCTAGAAGGAAAGGTAAAATTGGAA 57.537 33.333 0.00 0.00 0.00 3.53
4932 5884 4.790878 CACTATGGCATGCACATAATCAC 58.209 43.478 21.36 0.00 31.02 3.06
4949 5901 8.865090 ACATAATCACTGGAGAAATAGAGTAGG 58.135 37.037 0.00 0.00 0.00 3.18
5025 5978 4.436242 TCTAGTAAGTGCTTCCTGTTCG 57.564 45.455 0.00 0.00 0.00 3.95
5032 5985 1.197721 GTGCTTCCTGTTCGTTCCATG 59.802 52.381 0.00 0.00 0.00 3.66
5199 6152 0.106708 GCACCGGGCTTGATGAGATA 59.893 55.000 6.32 0.00 40.25 1.98
5265 6221 0.665835 ATGCGCGTTTGAACCTTCAA 59.334 45.000 8.43 0.00 44.78 2.69
5273 6229 3.426191 CGTTTGAACCTTCAATGCATGTG 59.574 43.478 0.00 0.98 45.65 3.21
5410 6369 2.240493 TAGCCGAGAGCCTAAATTGC 57.760 50.000 0.00 0.00 45.47 3.56
5500 6459 3.817084 CCAGTTGAGTTCTGATGCTTCAA 59.183 43.478 3.65 0.00 35.20 2.69
5526 6485 1.364626 CGCAAGTCAGGAGATGCCAC 61.365 60.000 0.00 0.00 40.02 5.01
5533 6492 1.555075 TCAGGAGATGCCACACTTACC 59.445 52.381 0.00 0.00 40.02 2.85
5537 6496 1.204941 GAGATGCCACACTTACCGTCT 59.795 52.381 0.00 0.00 0.00 4.18
5553 6513 5.007385 ACCGTCTTGATTGTACATCCTAC 57.993 43.478 0.00 0.00 0.00 3.18
5586 6546 3.997021 AGTTTGGACTCTGTAAATCTGCG 59.003 43.478 0.00 0.00 0.00 5.18
5587 6547 2.010145 TGGACTCTGTAAATCTGCGC 57.990 50.000 0.00 0.00 0.00 6.09
5599 6559 0.179134 ATCTGCGCCTCAGTTCGTAC 60.179 55.000 4.18 0.00 43.32 3.67
5618 6578 6.578944 TCGTACTTAATGGTGCTTGTATCAT 58.421 36.000 0.00 0.00 0.00 2.45
5635 6595 5.474532 TGTATCATCTCAAATATTGCCAGGC 59.525 40.000 3.66 3.66 0.00 4.85
5722 6682 1.333619 GAGACACTCGGCTCTCATCTC 59.666 57.143 0.00 0.00 34.21 2.75
5743 6703 2.237143 CTGGGCAAGTTCTCAGGTATGA 59.763 50.000 0.00 0.00 0.00 2.15
5757 6717 3.503831 GGTATGAAACCTCGGGTCCCG 62.504 61.905 25.31 25.31 45.75 5.14
5782 6742 3.201708 ACCTCTTCTTCATCTTCCCATGG 59.798 47.826 4.14 4.14 0.00 3.66
5798 6758 3.436906 CCCATGGCCTGAATGGATCTTTA 60.437 47.826 19.78 0.00 46.44 1.85
5800 6760 4.461781 CCATGGCCTGAATGGATCTTTATC 59.538 45.833 14.18 0.00 46.44 1.75
5812 6772 7.931578 ATGGATCTTTATCTACGTCTAGAGG 57.068 40.000 10.86 10.86 32.24 3.69
5816 6776 7.444792 GGATCTTTATCTACGTCTAGAGGTCAA 59.555 40.741 20.74 11.09 32.24 3.18
5827 6787 5.063944 CGTCTAGAGGTCAAACAATCATTGG 59.936 44.000 1.58 0.00 34.12 3.16
5843 6803 9.872684 ACAATCATTGGAGTTTTAGATGGATAT 57.127 29.630 1.58 0.00 34.12 1.63
5847 6807 7.939039 TCATTGGAGTTTTAGATGGATATGACC 59.061 37.037 0.00 0.00 0.00 4.02
5898 6858 2.238646 GGATTGGAGTACCATCACACCA 59.761 50.000 0.00 0.00 46.34 4.17
5991 6951 6.092122 CCATCTTTAGTTGATTGCGTACTTCA 59.908 38.462 0.00 0.00 0.00 3.02
6008 6968 5.869753 ACTTCATCAACTATCTTGTGTGC 57.130 39.130 0.00 0.00 0.00 4.57
6010 6970 6.701340 ACTTCATCAACTATCTTGTGTGCTA 58.299 36.000 0.00 0.00 0.00 3.49
6016 6976 4.891992 ACTATCTTGTGTGCTACCAGTT 57.108 40.909 0.00 0.00 0.00 3.16
6021 6981 4.566004 TCTTGTGTGCTACCAGTTACATC 58.434 43.478 0.00 0.00 0.00 3.06
6022 6982 2.954316 TGTGTGCTACCAGTTACATCG 58.046 47.619 0.00 0.00 0.00 3.84
6044 7019 6.340522 TCGACTGAGATCATGCAAAATCTTA 58.659 36.000 13.61 9.76 32.43 2.10
6060 7035 7.534918 GCAAAATCTTAAATGAAAACACATGGC 59.465 33.333 0.00 0.00 0.00 4.40
6109 7084 0.478507 AGAAGGAACCCCACCAAGTG 59.521 55.000 0.00 0.00 33.88 3.16
6113 7088 1.826487 GAACCCCACCAAGTGCGTT 60.826 57.895 0.00 0.00 30.87 4.84
6119 7094 0.586319 CCACCAAGTGCGTTGTACTG 59.414 55.000 0.00 0.00 33.87 2.74
6124 7099 1.800586 CAAGTGCGTTGTACTGCATCT 59.199 47.619 10.39 7.53 43.96 2.90
6125 7100 1.432514 AGTGCGTTGTACTGCATCTG 58.567 50.000 10.39 0.00 43.96 2.90
6126 7101 1.148310 GTGCGTTGTACTGCATCTGT 58.852 50.000 10.39 0.00 43.96 3.41
6127 7102 1.126846 GTGCGTTGTACTGCATCTGTC 59.873 52.381 10.39 0.00 43.96 3.51
6128 7103 1.000843 TGCGTTGTACTGCATCTGTCT 59.999 47.619 4.28 0.00 35.90 3.41
6129 7104 1.656095 GCGTTGTACTGCATCTGTCTC 59.344 52.381 0.00 0.00 0.00 3.36
6130 7105 2.263077 CGTTGTACTGCATCTGTCTCC 58.737 52.381 0.00 0.00 0.00 3.71
6131 7106 2.352715 CGTTGTACTGCATCTGTCTCCA 60.353 50.000 0.00 0.00 0.00 3.86
6132 7107 2.996621 GTTGTACTGCATCTGTCTCCAC 59.003 50.000 0.00 0.00 0.00 4.02
6133 7108 2.529632 TGTACTGCATCTGTCTCCACT 58.470 47.619 0.00 0.00 0.00 4.00
6134 7109 2.232208 TGTACTGCATCTGTCTCCACTG 59.768 50.000 0.00 0.00 0.00 3.66
6135 7110 1.346062 ACTGCATCTGTCTCCACTGT 58.654 50.000 0.00 0.00 0.00 3.55
6136 7111 1.696336 ACTGCATCTGTCTCCACTGTT 59.304 47.619 0.00 0.00 0.00 3.16
6137 7112 2.105477 ACTGCATCTGTCTCCACTGTTT 59.895 45.455 0.00 0.00 0.00 2.83
6138 7113 3.144506 CTGCATCTGTCTCCACTGTTTT 58.855 45.455 0.00 0.00 0.00 2.43
6139 7114 4.202357 ACTGCATCTGTCTCCACTGTTTTA 60.202 41.667 0.00 0.00 0.00 1.52
6140 7115 4.713553 TGCATCTGTCTCCACTGTTTTAA 58.286 39.130 0.00 0.00 0.00 1.52
6141 7116 4.756642 TGCATCTGTCTCCACTGTTTTAAG 59.243 41.667 0.00 0.00 0.00 1.85
6142 7117 4.757149 GCATCTGTCTCCACTGTTTTAAGT 59.243 41.667 0.00 0.00 0.00 2.24
6143 7118 5.106908 GCATCTGTCTCCACTGTTTTAAGTC 60.107 44.000 0.00 0.00 0.00 3.01
6144 7119 5.607939 TCTGTCTCCACTGTTTTAAGTCA 57.392 39.130 0.00 0.00 0.00 3.41
6145 7120 5.357257 TCTGTCTCCACTGTTTTAAGTCAC 58.643 41.667 0.00 0.00 0.00 3.67
6146 7121 5.092554 TGTCTCCACTGTTTTAAGTCACA 57.907 39.130 0.00 0.00 0.00 3.58
6147 7122 5.116180 TGTCTCCACTGTTTTAAGTCACAG 58.884 41.667 9.04 9.04 45.15 3.66
6148 7123 5.105106 TGTCTCCACTGTTTTAAGTCACAGA 60.105 40.000 14.99 0.00 42.74 3.41
6149 7124 5.234543 GTCTCCACTGTTTTAAGTCACAGAC 59.765 44.000 14.99 0.00 42.74 3.51
6150 7125 5.092554 TCCACTGTTTTAAGTCACAGACA 57.907 39.130 14.99 0.00 42.74 3.41
6151 7126 5.492895 TCCACTGTTTTAAGTCACAGACAA 58.507 37.500 14.99 1.82 42.74 3.18
6152 7127 6.119536 TCCACTGTTTTAAGTCACAGACAAT 58.880 36.000 14.99 0.00 42.74 2.71
6153 7128 7.276658 TCCACTGTTTTAAGTCACAGACAATA 58.723 34.615 14.99 0.00 42.74 1.90
6154 7129 7.225931 TCCACTGTTTTAAGTCACAGACAATAC 59.774 37.037 14.99 0.00 42.74 1.89
6155 7130 7.011950 CCACTGTTTTAAGTCACAGACAATACA 59.988 37.037 14.99 0.00 42.74 2.29
6156 7131 7.850982 CACTGTTTTAAGTCACAGACAATACAC 59.149 37.037 14.99 0.00 42.74 2.90
6157 7132 6.939627 TGTTTTAAGTCACAGACAATACACG 58.060 36.000 0.00 0.00 34.60 4.49
6158 7133 6.535865 TGTTTTAAGTCACAGACAATACACGT 59.464 34.615 0.00 0.00 34.60 4.49
6159 7134 7.064847 TGTTTTAAGTCACAGACAATACACGTT 59.935 33.333 0.00 0.00 34.60 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.222810 GGCCAAAACATCCTTATCCAAAGT 59.777 41.667 0.00 0.00 0.00 2.66
48 49 7.297936 TGTTGGTTAGAGTTCAAGATCACTA 57.702 36.000 0.00 0.00 0.00 2.74
49 50 6.174720 TGTTGGTTAGAGTTCAAGATCACT 57.825 37.500 0.00 0.00 0.00 3.41
60 61 6.032956 TCATAACACGATGTTGGTTAGAGT 57.967 37.500 11.90 0.00 41.30 3.24
199 200 3.231818 TCGGCCATGGGTTTAAAGAAAA 58.768 40.909 15.13 0.00 0.00 2.29
207 208 2.523530 TGGTTCGGCCATGGGTTT 59.476 55.556 15.13 0.00 43.61 3.27
216 217 0.879090 ACGGATTTCTTTGGTTCGGC 59.121 50.000 0.00 0.00 0.00 5.54
227 228 3.569250 TTGGCTTTGCTTACGGATTTC 57.431 42.857 0.00 0.00 0.00 2.17
229 230 3.427503 CGATTTGGCTTTGCTTACGGATT 60.428 43.478 0.00 0.00 0.00 3.01
231 232 1.466950 CGATTTGGCTTTGCTTACGGA 59.533 47.619 0.00 0.00 0.00 4.69
232 233 1.199097 ACGATTTGGCTTTGCTTACGG 59.801 47.619 0.00 0.00 0.00 4.02
234 235 2.227865 TGGACGATTTGGCTTTGCTTAC 59.772 45.455 0.00 0.00 0.00 2.34
235 236 2.509569 TGGACGATTTGGCTTTGCTTA 58.490 42.857 0.00 0.00 0.00 3.09
275 287 5.734720 ACAATCAACTATCATTCACCGTCT 58.265 37.500 0.00 0.00 0.00 4.18
276 288 6.250819 CAACAATCAACTATCATTCACCGTC 58.749 40.000 0.00 0.00 0.00 4.79
277 289 5.123820 CCAACAATCAACTATCATTCACCGT 59.876 40.000 0.00 0.00 0.00 4.83
278 290 5.123820 ACCAACAATCAACTATCATTCACCG 59.876 40.000 0.00 0.00 0.00 4.94
279 291 6.515272 ACCAACAATCAACTATCATTCACC 57.485 37.500 0.00 0.00 0.00 4.02
298 311 7.630082 AGACTGGTTAGCTATCATAAAACCAA 58.370 34.615 14.31 1.91 46.51 3.67
320 333 3.887335 TAACCACGGCCGGCAAGAC 62.887 63.158 31.76 9.91 0.00 3.01
330 343 0.321210 TCATGCCAGTGTAACCACGG 60.321 55.000 0.00 0.00 46.56 4.94
331 344 1.398041 CATCATGCCAGTGTAACCACG 59.602 52.381 0.00 0.00 46.56 4.94
332 345 2.436417 ACATCATGCCAGTGTAACCAC 58.564 47.619 0.00 0.00 42.17 4.16
334 347 4.450976 TGATACATCATGCCAGTGTAACC 58.549 43.478 0.00 0.00 37.80 2.85
355 368 7.338710 TCTTCCCTAGGAAAATAGACAACATG 58.661 38.462 11.48 0.00 41.54 3.21
356 369 7.510675 TCTTCCCTAGGAAAATAGACAACAT 57.489 36.000 11.48 0.00 41.54 2.71
359 372 7.749377 TGATCTTCCCTAGGAAAATAGACAA 57.251 36.000 11.48 0.00 41.54 3.18
366 379 7.705912 TCCATAATGATCTTCCCTAGGAAAA 57.294 36.000 11.48 3.23 41.54 2.29
414 430 6.503589 ACTAAGCTCGTAGATGATGTATCC 57.496 41.667 0.00 0.00 36.40 2.59
416 432 9.232473 TGATTACTAAGCTCGTAGATGATGTAT 57.768 33.333 0.00 0.00 33.89 2.29
418 434 7.445707 TCTGATTACTAAGCTCGTAGATGATGT 59.554 37.037 0.00 0.00 33.89 3.06
422 438 8.858003 TTTTCTGATTACTAAGCTCGTAGATG 57.142 34.615 0.00 0.00 33.89 2.90
423 439 9.685828 GATTTTCTGATTACTAAGCTCGTAGAT 57.314 33.333 0.00 0.00 33.89 1.98
432 448 9.691362 GAGCCTCTAGATTTTCTGATTACTAAG 57.309 37.037 0.00 0.00 0.00 2.18
445 462 2.630580 GGATGGACGAGCCTCTAGATTT 59.369 50.000 0.00 0.00 37.63 2.17
488 511 2.821378 TCTCCCATCGAACGTTAGACAA 59.179 45.455 13.50 0.00 0.00 3.18
489 512 2.422479 CTCTCCCATCGAACGTTAGACA 59.578 50.000 13.50 0.00 0.00 3.41
492 515 1.067212 CCCTCTCCCATCGAACGTTAG 59.933 57.143 0.00 0.00 0.00 2.34
493 516 1.108776 CCCTCTCCCATCGAACGTTA 58.891 55.000 0.00 0.00 0.00 3.18
495 518 0.613853 TTCCCTCTCCCATCGAACGT 60.614 55.000 0.00 0.00 0.00 3.99
496 519 0.103208 CTTCCCTCTCCCATCGAACG 59.897 60.000 0.00 0.00 0.00 3.95
497 520 1.137282 GTCTTCCCTCTCCCATCGAAC 59.863 57.143 0.00 0.00 0.00 3.95
498 521 1.273041 TGTCTTCCCTCTCCCATCGAA 60.273 52.381 0.00 0.00 0.00 3.71
499 522 0.335019 TGTCTTCCCTCTCCCATCGA 59.665 55.000 0.00 0.00 0.00 3.59
500 523 1.195115 TTGTCTTCCCTCTCCCATCG 58.805 55.000 0.00 0.00 0.00 3.84
514 539 3.007473 TCAAAAGGGGTTCGTTTGTCT 57.993 42.857 0.00 0.00 42.63 3.41
599 624 5.386958 AGAGCGACATTACAGTTTCTGTA 57.613 39.130 5.64 5.64 43.46 2.74
611 636 6.142817 GTGACAATTTTTGTAGAGCGACATT 58.857 36.000 0.00 0.00 45.52 2.71
623 648 4.119136 GTTGTGAGGGGTGACAATTTTTG 58.881 43.478 0.00 0.00 0.00 2.44
629 654 3.935818 TTTAGTTGTGAGGGGTGACAA 57.064 42.857 0.00 0.00 0.00 3.18
635 660 2.896685 TGCCAATTTTAGTTGTGAGGGG 59.103 45.455 0.00 0.00 0.00 4.79
667 692 0.324275 ATAAGGGGTGGCATTTGCGT 60.324 50.000 0.00 0.00 43.26 5.24
861 889 2.683362 GGCCCAAACCTTATCTTTCTCG 59.317 50.000 0.00 0.00 0.00 4.04
894 922 0.393402 TACGCAGCGAGGGAGAAGTA 60.393 55.000 24.65 0.00 0.00 2.24
947 975 2.279073 CGAGGTAGGGCAGGGAGA 59.721 66.667 0.00 0.00 0.00 3.71
1222 1251 4.918201 GGATTGGCTCGGGCTCGG 62.918 72.222 7.48 0.00 38.73 4.63
1223 1252 3.854669 AGGATTGGCTCGGGCTCG 61.855 66.667 7.48 0.00 38.73 5.03
1224 1253 1.686325 TACAGGATTGGCTCGGGCTC 61.686 60.000 7.48 0.00 38.73 4.70
1225 1254 1.271840 TTACAGGATTGGCTCGGGCT 61.272 55.000 7.48 0.00 38.73 5.19
1874 1919 4.056740 TCAGGTCGAGATTAGTACTAGCG 58.943 47.826 2.23 6.48 0.00 4.26
1973 2018 7.307455 GCCTCCTCGAATGTTCAATAGAATTAC 60.307 40.741 0.00 0.00 35.92 1.89
2021 2076 4.402616 TGGAACATTCTTCTGGGGAAAT 57.597 40.909 0.00 0.00 0.00 2.17
2060 2115 6.312426 AATCAGTTGATCAAGAGCTAAACTCG 59.688 38.462 8.80 0.00 41.33 4.18
2070 2125 3.064408 GCGCATGAATCAGTTGATCAAGA 59.936 43.478 8.80 3.98 32.75 3.02
2131 2189 4.092383 GTGCGCATTTATACGGGGTTATAG 59.908 45.833 15.91 0.00 0.00 1.31
2139 2197 1.459592 GCCTAGTGCGCATTTATACGG 59.540 52.381 15.91 8.84 0.00 4.02
2140 2198 1.459592 GGCCTAGTGCGCATTTATACG 59.540 52.381 15.91 0.00 42.61 3.06
2147 2205 2.825836 GCAAGGCCTAGTGCGCAT 60.826 61.111 15.91 5.37 42.61 4.73
2172 2230 9.352784 CACACACTTAATTCTTTTTCAAAGTCA 57.647 29.630 0.00 0.00 0.00 3.41
2177 2235 8.539770 TTTGCACACACTTAATTCTTTTTCAA 57.460 26.923 0.00 0.00 0.00 2.69
2178 2236 8.715191 ATTTGCACACACTTAATTCTTTTTCA 57.285 26.923 0.00 0.00 0.00 2.69
2182 2240 8.764287 GCTTAATTTGCACACACTTAATTCTTT 58.236 29.630 0.00 0.00 0.00 2.52
2183 2241 8.143835 AGCTTAATTTGCACACACTTAATTCTT 58.856 29.630 0.00 0.00 0.00 2.52
2184 2242 7.661040 AGCTTAATTTGCACACACTTAATTCT 58.339 30.769 0.00 0.00 0.00 2.40
2185 2243 7.062255 GGAGCTTAATTTGCACACACTTAATTC 59.938 37.037 0.00 0.00 0.00 2.17
2186 2244 6.868339 GGAGCTTAATTTGCACACACTTAATT 59.132 34.615 0.00 0.00 0.00 1.40
2187 2245 6.015519 TGGAGCTTAATTTGCACACACTTAAT 60.016 34.615 0.00 0.00 0.00 1.40
2213 2271 9.829507 AACAATTTGAGTTTGAAATAACCATGA 57.170 25.926 2.79 0.00 0.00 3.07
2216 2274 9.883142 AAGAACAATTTGAGTTTGAAATAACCA 57.117 25.926 2.79 0.00 0.00 3.67
2259 2342 6.743110 TGTAGATGCTTTGAGCTACTCATAG 58.257 40.000 9.78 9.78 42.97 2.23
2281 2368 9.617523 TTCATCTACACAATGTCATCATAATGT 57.382 29.630 0.00 0.00 36.70 2.71
2299 2386 6.252441 CCGAGAAGATATGCGAATTCATCTAC 59.748 42.308 6.22 2.09 0.00 2.59
2305 2392 2.413453 GGCCGAGAAGATATGCGAATTC 59.587 50.000 0.00 0.00 0.00 2.17
2485 2576 3.629398 GGTCACAGAGCTCCCATTAATTG 59.371 47.826 10.93 1.61 0.00 2.32
2718 2814 6.476378 ACATGTAGCAAGGACTGTTTAAGAT 58.524 36.000 0.00 0.00 0.00 2.40
2728 2824 5.488341 TCCTAAAGAACATGTAGCAAGGAC 58.512 41.667 0.00 0.00 0.00 3.85
2824 2922 9.469807 AACACGCTCACATTTTCATTTAAATAA 57.530 25.926 0.00 0.00 0.00 1.40
2835 2966 6.494893 ACATGTATAACACGCTCACATTTT 57.505 33.333 0.00 0.00 0.00 1.82
2876 3008 9.382275 CCTTCCAAAACAAAAATCCATATTAGG 57.618 33.333 0.00 0.00 0.00 2.69
2881 3013 7.610580 AGACCTTCCAAAACAAAAATCCATA 57.389 32.000 0.00 0.00 0.00 2.74
2913 3046 0.667993 TGTTCTCAAGCCGCTTTTGG 59.332 50.000 1.86 0.00 0.00 3.28
2936 3069 2.018324 GCTTGTTGAGCCGCTTTGC 61.018 57.895 0.00 0.00 46.01 3.68
2980 3113 7.201652 GGCTCAAAGTAAGCTTTAGAGTTATGG 60.202 40.741 3.20 0.00 42.54 2.74
2981 3114 7.201652 GGGCTCAAAGTAAGCTTTAGAGTTATG 60.202 40.741 3.20 0.00 42.54 1.90
2982 3115 6.824196 GGGCTCAAAGTAAGCTTTAGAGTTAT 59.176 38.462 3.20 0.00 42.54 1.89
2983 3116 6.171213 GGGCTCAAAGTAAGCTTTAGAGTTA 58.829 40.000 3.20 0.00 42.54 2.24
2985 3118 4.565861 GGGGCTCAAAGTAAGCTTTAGAGT 60.566 45.833 3.20 0.00 42.54 3.24
2988 3121 3.686016 TGGGGCTCAAAGTAAGCTTTAG 58.314 45.455 3.20 0.00 42.54 1.85
3033 3175 6.700520 CCTCCGATACCTACAATTGTAAGAAC 59.299 42.308 18.89 9.35 0.00 3.01
3115 3259 7.320399 TGATACCTACAGCATATGATTTACGG 58.680 38.462 6.97 4.31 0.00 4.02
3930 4452 8.703336 CGGACATGATACTATACACAAAAGATG 58.297 37.037 0.00 0.00 0.00 2.90
3943 4465 5.410132 CCACAAAAACACGGACATGATACTA 59.590 40.000 0.00 0.00 0.00 1.82
4307 5221 3.003378 GGTTGTACAAGTGGCTGAACTTC 59.997 47.826 8.98 0.00 38.34 3.01
4323 5237 3.300852 TCGAAGTTATGTGCGGTTGTA 57.699 42.857 0.00 0.00 0.00 2.41
4514 5449 0.592637 TTGCCGCTGATGAACACAAG 59.407 50.000 0.00 0.00 0.00 3.16
4675 5617 9.297037 AGGAATGTTACTAAAAAGTATGCAGTT 57.703 29.630 0.00 0.00 0.00 3.16
4720 5665 4.667573 TGCCCACAAATAAATACTGGTGA 58.332 39.130 0.00 0.00 0.00 4.02
4932 5884 7.473735 TGCATATCCTACTCTATTTCTCCAG 57.526 40.000 0.00 0.00 0.00 3.86
4949 5901 7.027760 CAGCTTATGATCCATGTTTGCATATC 58.972 38.462 0.00 0.00 33.30 1.63
5015 5968 1.466167 CAGCATGGAACGAACAGGAAG 59.534 52.381 0.00 0.00 0.00 3.46
5016 5969 1.522668 CAGCATGGAACGAACAGGAA 58.477 50.000 0.00 0.00 0.00 3.36
5025 5978 5.954296 ATTATAGTCATGCAGCATGGAAC 57.046 39.130 30.92 23.19 42.43 3.62
5190 6143 5.538053 GGGTTCTCTGACTGATATCTCATCA 59.462 44.000 3.98 4.42 0.00 3.07
5199 6152 2.630889 TCTGGGGTTCTCTGACTGAT 57.369 50.000 0.00 0.00 0.00 2.90
5265 6221 4.405116 ACCACAAAAGAAACACATGCAT 57.595 36.364 0.00 0.00 0.00 3.96
5273 6229 7.865889 CCTTCATACCTTTACCACAAAAGAAAC 59.134 37.037 0.00 0.00 38.50 2.78
5382 6341 1.067915 GGCTCTCGGCTAAGCTCTATG 60.068 57.143 0.00 0.00 41.46 2.23
5445 6404 9.868277 GGGTCAAATTTTTCATACATGTTATGA 57.132 29.630 2.30 8.63 32.63 2.15
5500 6459 0.039074 CTCCTGACTTGCGTTCGAGT 60.039 55.000 0.00 0.00 39.61 4.18
5526 6485 5.291128 GGATGTACAATCAAGACGGTAAGTG 59.709 44.000 0.00 0.00 0.00 3.16
5533 6492 5.263968 AGGTAGGATGTACAATCAAGACG 57.736 43.478 0.00 0.00 0.00 4.18
5537 6496 6.636454 AAAGGAGGTAGGATGTACAATCAA 57.364 37.500 0.00 0.00 0.00 2.57
5553 6513 3.149981 GAGTCCAAACTCCAAAAGGAGG 58.850 50.000 15.36 0.00 45.26 4.30
5586 6546 3.617263 CACCATTAAGTACGAACTGAGGC 59.383 47.826 0.00 0.00 35.62 4.70
5587 6547 3.617263 GCACCATTAAGTACGAACTGAGG 59.383 47.826 0.00 0.00 35.62 3.86
5599 6559 7.558161 TTGAGATGATACAAGCACCATTAAG 57.442 36.000 0.00 0.00 0.00 1.85
5618 6578 3.650281 TCTGCCTGGCAATATTTGAGA 57.350 42.857 23.51 10.76 38.41 3.27
5664 6624 0.588252 GTTACTGTGTGGTGCAGCAG 59.412 55.000 20.85 10.19 37.47 4.24
5669 6629 3.127895 TCAACTTTGTTACTGTGTGGTGC 59.872 43.478 0.00 0.00 0.00 5.01
5670 6630 4.955925 TCAACTTTGTTACTGTGTGGTG 57.044 40.909 0.00 0.00 0.00 4.17
5671 6631 6.995686 TGATATCAACTTTGTTACTGTGTGGT 59.004 34.615 1.98 0.00 0.00 4.16
5722 6682 2.237143 TCATACCTGAGAACTTGCCCAG 59.763 50.000 0.00 0.00 0.00 4.45
5757 6717 3.261897 TGGGAAGATGAAGAAGAGGTGTC 59.738 47.826 0.00 0.00 0.00 3.67
5782 6742 5.542779 ACGTAGATAAAGATCCATTCAGGC 58.457 41.667 0.00 0.00 37.29 4.85
5798 6758 6.377429 TGATTGTTTGACCTCTAGACGTAGAT 59.623 38.462 0.00 0.00 34.63 1.98
5800 6760 5.950883 TGATTGTTTGACCTCTAGACGTAG 58.049 41.667 0.00 0.00 0.00 3.51
5812 6772 9.132521 CATCTAAAACTCCAATGATTGTTTGAC 57.867 33.333 4.27 0.00 33.61 3.18
5816 6776 8.599624 ATCCATCTAAAACTCCAATGATTGTT 57.400 30.769 4.27 0.00 0.00 2.83
5827 6787 5.703130 GCCAGGTCATATCCATCTAAAACTC 59.297 44.000 0.00 0.00 0.00 3.01
5843 6803 6.372104 TGGATAAATTCAATATGCCAGGTCA 58.628 36.000 0.00 0.00 0.00 4.02
5898 6858 4.961438 TTAACTCGAACACCTTAACCCT 57.039 40.909 0.00 0.00 0.00 4.34
5991 6951 5.046304 ACTGGTAGCACACAAGATAGTTGAT 60.046 40.000 0.16 0.00 31.88 2.57
6008 6968 5.297029 TGATCTCAGTCGATGTAACTGGTAG 59.703 44.000 3.65 0.00 43.48 3.18
6010 6970 4.017126 TGATCTCAGTCGATGTAACTGGT 58.983 43.478 3.65 0.00 43.48 4.00
6016 6976 4.654091 TTGCATGATCTCAGTCGATGTA 57.346 40.909 0.00 0.00 0.00 2.29
6021 6981 5.481200 AAGATTTTGCATGATCTCAGTCG 57.519 39.130 11.44 0.00 31.63 4.18
6022 6982 9.234384 CATTTAAGATTTTGCATGATCTCAGTC 57.766 33.333 11.44 0.00 31.63 3.51
6044 7019 6.489127 CATGATTGCCATGTGTTTTCATTT 57.511 33.333 0.00 0.00 45.83 2.32
6060 7035 3.181493 GCTTACTCCAGCAACCATGATTG 60.181 47.826 0.00 0.00 39.83 2.67
6109 7084 1.656095 GAGACAGATGCAGTACAACGC 59.344 52.381 0.00 0.00 0.00 4.84
6113 7088 2.232208 CAGTGGAGACAGATGCAGTACA 59.768 50.000 0.00 0.00 44.46 2.90
6119 7094 4.757149 ACTTAAAACAGTGGAGACAGATGC 59.243 41.667 0.00 0.00 44.46 3.91
6124 7099 5.092554 TGTGACTTAAAACAGTGGAGACA 57.907 39.130 0.00 0.00 38.70 3.41
6125 7100 5.234543 GTCTGTGACTTAAAACAGTGGAGAC 59.765 44.000 10.68 0.00 43.49 3.36
6126 7101 5.105106 TGTCTGTGACTTAAAACAGTGGAGA 60.105 40.000 10.68 0.00 43.49 3.71
6127 7102 5.116180 TGTCTGTGACTTAAAACAGTGGAG 58.884 41.667 10.68 0.00 43.49 3.86
6128 7103 5.092554 TGTCTGTGACTTAAAACAGTGGA 57.907 39.130 10.68 0.00 43.49 4.02
6129 7104 5.811399 TTGTCTGTGACTTAAAACAGTGG 57.189 39.130 10.68 0.00 43.49 4.00
6130 7105 7.850982 GTGTATTGTCTGTGACTTAAAACAGTG 59.149 37.037 10.68 0.00 43.49 3.66
6131 7106 7.254319 CGTGTATTGTCTGTGACTTAAAACAGT 60.254 37.037 10.68 0.00 43.49 3.55
6132 7107 7.063456 CGTGTATTGTCTGTGACTTAAAACAG 58.937 38.462 6.36 6.36 44.23 3.16
6133 7108 6.535865 ACGTGTATTGTCTGTGACTTAAAACA 59.464 34.615 0.00 0.00 33.15 2.83
6134 7109 6.940714 ACGTGTATTGTCTGTGACTTAAAAC 58.059 36.000 0.00 0.00 33.15 2.43
6135 7110 7.542534 AACGTGTATTGTCTGTGACTTAAAA 57.457 32.000 0.00 0.00 33.15 1.52


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

AutoCloner maintained by Alex Coulton.