Multiple sequence alignment - TraesCS5A01G006200

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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 TraesCS5A01G006200 chr5A 100.000 4976 0 0 779 5754 3524333 3529308 0.000000e+00 9190
1 TraesCS5A01G006200 chr5A 100.000 369 0 0 1 369 3523555 3523923 0.000000e+00 682
2 TraesCS5A01G006200 chr5A 100.000 190 0 0 180 369 3523556 3523745 9.170000e-93 351
3 TraesCS5A01G006200 chr5A 100.000 190 0 0 2 191 3523734 3523923 9.170000e-93 351
4 TraesCS5A01G006200 chr5D 92.395 4471 232 47 779 5190 5174589 5170168 0.000000e+00 6274
5 TraesCS5A01G006200 chr5D 93.182 572 13 5 5188 5754 5170100 5169550 0.000000e+00 817
6 TraesCS5A01G006200 chr5D 89.779 362 25 5 779 1131 5201590 5201232 2.440000e-123 453
7 TraesCS5A01G006200 chr5D 89.779 362 25 5 779 1131 5212009 5211651 2.440000e-123 453
8 TraesCS5A01G006200 chr5D 89.503 362 26 5 779 1131 5179342 5178984 1.140000e-121 448
9 TraesCS5A01G006200 chr5D 89.503 362 26 5 779 1131 5193080 5192722 1.140000e-121 448
10 TraesCS5A01G006200 chr5D 89.227 362 27 5 779 1131 5210195 5209837 5.290000e-120 442
11 TraesCS5A01G006200 chr5D 89.227 362 26 6 779 1131 5192320 5191963 1.900000e-119 440
12 TraesCS5A01G006200 chr5D 89.227 362 26 6 779 1131 5216197 5215840 1.900000e-119 440
13 TraesCS5A01G006200 chr5D 88.950 362 27 6 779 1131 5209438 5209081 8.850000e-118 435
14 TraesCS5A01G006200 chr5D 90.110 182 14 4 182 360 5176971 5176791 3.470000e-57 233
15 TraesCS5A01G006200 chr5D 90.110 182 14 4 4 182 5176971 5176791 3.470000e-57 233
16 TraesCS5A01G006200 chr5D 87.912 182 18 4 182 360 5207239 5207059 1.620000e-50 211
17 TraesCS5A01G006200 chr5D 87.912 182 18 4 4 182 5207239 5207059 1.620000e-50 211
18 TraesCS5A01G006200 chr5B 91.260 2723 153 46 2514 5190 6651891 6654574 0.000000e+00 3631
19 TraesCS5A01G006200 chr5B 92.062 1688 77 23 883 2528 6650043 6651715 0.000000e+00 2322
20 TraesCS5A01G006200 chr4A 89.247 93 4 5 4417 4504 706851060 706850969 1.690000e-20 111


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 TraesCS5A01G006200 chr5A 3523555 3529308 5753 False 2643.500000 9190 100.0000 1 5754 4 chr5A.!!$F1 5753
1 TraesCS5A01G006200 chr5D 5169550 5179342 9792 True 1601.000000 6274 91.0600 4 5754 5 chr5D.!!$R2 5750
2 TraesCS5A01G006200 chr5D 5191963 5193080 1117 True 444.000000 448 89.3650 779 1131 2 chr5D.!!$R3 352
3 TraesCS5A01G006200 chr5D 5207059 5216197 9138 True 365.333333 453 88.8345 4 1131 6 chr5D.!!$R4 1127
4 TraesCS5A01G006200 chr5B 6650043 6654574 4531 False 2976.500000 3631 91.6610 883 5190 2 chr5B.!!$F1 4307

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
367 934 0.174845 TAGCATCACACCTGTACCGC 59.825 55.0 0.00 0.0 0.00 5.68 F
953 7055 0.185175 GTCCTCCTCCTCCTCCTCTC 59.815 65.0 0.00 0.0 0.00 3.20 F
1372 9363 0.527113 TGGTTGATTGATGCTTGCGG 59.473 50.0 0.00 0.0 0.00 5.69 F
3298 12201 0.327000 CCCTCCCTTCTGGTGAGGAT 60.327 60.0 16.08 0.0 45.64 3.24 F
4368 13291 1.928868 ACTTCTGGGCCCTTTCATTG 58.071 50.0 25.70 9.1 0.00 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1946 10292 0.192566 TGAGGACTAGGGTGGTGGTT 59.807 55.000 0.0 0.0 0.00 3.67 R
2154 10501 1.154301 CGGACAAAAATGACCCGCG 60.154 57.895 0.0 0.0 33.47 6.46 R
3337 12242 0.409484 AGGATTCAAACAGGGGTGGG 59.591 55.000 0.0 0.0 0.00 4.61 R
4559 13486 1.222567 GATGGATGGGGGTTACTGGT 58.777 55.000 0.0 0.0 0.00 4.00 R
5732 14800 0.033228 CATCAGTCTCTCGCCCCATC 59.967 60.000 0.0 0.0 0.00 3.51 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
111 678 5.869344 CACATTACGATTTGTCTCTCCTTCA 59.131 40.000 0.00 0.00 0.00 3.02
134 701 8.085720 TCAATCAAAAACATAATTTGGCACAG 57.914 30.769 0.00 0.00 42.39 3.66
167 734 3.539604 AGCAGCATCTTGATGGTACTTC 58.460 45.455 13.87 5.58 43.09 3.01
182 749 3.134804 GGTACTTCCATAGCATCACACCT 59.865 47.826 0.00 0.00 35.97 4.00
183 750 3.272574 ACTTCCATAGCATCACACCTG 57.727 47.619 0.00 0.00 0.00 4.00
184 751 2.573462 ACTTCCATAGCATCACACCTGT 59.427 45.455 0.00 0.00 0.00 4.00
185 752 3.774766 ACTTCCATAGCATCACACCTGTA 59.225 43.478 0.00 0.00 0.00 2.74
186 753 3.819564 TCCATAGCATCACACCTGTAC 57.180 47.619 0.00 0.00 0.00 2.90
188 755 2.473816 CATAGCATCACACCTGTACCG 58.526 52.381 0.00 0.00 0.00 4.02
191 758 1.809619 CATCACACCTGTACCGCCG 60.810 63.158 0.00 0.00 0.00 6.46
197 764 4.514577 CCTGTACCGCCGCCAGAG 62.515 72.222 0.00 0.00 0.00 3.35
209 776 4.559063 CCAGAGCTGGGGCATCCG 62.559 72.222 8.69 0.00 46.81 4.18
232 799 2.043046 CCCGCCCCAATGGTCAAT 60.043 61.111 0.00 0.00 36.04 2.57
233 800 1.685421 CCCGCCCCAATGGTCAATT 60.685 57.895 0.00 0.00 36.04 2.32
234 801 1.264045 CCCGCCCCAATGGTCAATTT 61.264 55.000 0.00 0.00 36.04 1.82
235 802 0.612744 CCGCCCCAATGGTCAATTTT 59.387 50.000 0.00 0.00 36.04 1.82
236 803 1.003003 CCGCCCCAATGGTCAATTTTT 59.997 47.619 0.00 0.00 36.04 1.94
250 817 2.637025 TTTTTGCAGAGGCGTCGC 59.363 55.556 9.22 9.22 45.35 5.19
283 850 3.937814 TGGCACATTACGATTTGTCTCT 58.062 40.909 0.00 0.00 0.00 3.10
284 851 3.932710 TGGCACATTACGATTTGTCTCTC 59.067 43.478 0.00 0.00 0.00 3.20
285 852 3.309954 GGCACATTACGATTTGTCTCTCC 59.690 47.826 0.00 0.00 0.00 3.71
286 853 4.184629 GCACATTACGATTTGTCTCTCCT 58.815 43.478 0.00 0.00 0.00 3.69
287 854 4.631813 GCACATTACGATTTGTCTCTCCTT 59.368 41.667 0.00 0.00 0.00 3.36
288 855 5.220491 GCACATTACGATTTGTCTCTCCTTC 60.220 44.000 0.00 0.00 0.00 3.46
289 856 5.869344 CACATTACGATTTGTCTCTCCTTCA 59.131 40.000 0.00 0.00 0.00 3.02
290 857 6.368791 CACATTACGATTTGTCTCTCCTTCAA 59.631 38.462 0.00 0.00 0.00 2.69
291 858 7.065085 CACATTACGATTTGTCTCTCCTTCAAT 59.935 37.037 0.00 0.00 0.00 2.57
292 859 7.278868 ACATTACGATTTGTCTCTCCTTCAATC 59.721 37.037 0.00 0.00 0.00 2.67
293 860 5.152623 ACGATTTGTCTCTCCTTCAATCA 57.847 39.130 0.00 0.00 0.00 2.57
294 861 5.551233 ACGATTTGTCTCTCCTTCAATCAA 58.449 37.500 0.00 0.00 0.00 2.57
295 862 5.997746 ACGATTTGTCTCTCCTTCAATCAAA 59.002 36.000 0.00 0.00 0.00 2.69
296 863 6.486657 ACGATTTGTCTCTCCTTCAATCAAAA 59.513 34.615 0.00 0.00 0.00 2.44
297 864 7.013274 ACGATTTGTCTCTCCTTCAATCAAAAA 59.987 33.333 0.00 0.00 0.00 1.94
298 865 7.324616 CGATTTGTCTCTCCTTCAATCAAAAAC 59.675 37.037 0.00 0.00 0.00 2.43
299 866 7.403312 TTTGTCTCTCCTTCAATCAAAAACA 57.597 32.000 0.00 0.00 0.00 2.83
300 867 7.587037 TTGTCTCTCCTTCAATCAAAAACAT 57.413 32.000 0.00 0.00 0.00 2.71
301 868 8.690203 TTGTCTCTCCTTCAATCAAAAACATA 57.310 30.769 0.00 0.00 0.00 2.29
302 869 8.690203 TGTCTCTCCTTCAATCAAAAACATAA 57.310 30.769 0.00 0.00 0.00 1.90
303 870 9.300681 TGTCTCTCCTTCAATCAAAAACATAAT 57.699 29.630 0.00 0.00 0.00 1.28
307 874 9.709495 TCTCCTTCAATCAAAAACATAATTTGG 57.291 29.630 0.00 0.00 38.12 3.28
308 875 8.321650 TCCTTCAATCAAAAACATAATTTGGC 57.678 30.769 0.00 0.00 38.12 4.52
309 876 7.935755 TCCTTCAATCAAAAACATAATTTGGCA 59.064 29.630 0.00 0.00 38.12 4.92
310 877 8.016801 CCTTCAATCAAAAACATAATTTGGCAC 58.983 33.333 0.00 0.00 38.12 5.01
311 878 8.442632 TTCAATCAAAAACATAATTTGGCACA 57.557 26.923 0.00 0.00 38.12 4.57
312 879 8.085720 TCAATCAAAAACATAATTTGGCACAG 57.914 30.769 0.00 0.00 42.39 3.66
313 880 7.714377 TCAATCAAAAACATAATTTGGCACAGT 59.286 29.630 0.00 0.00 42.39 3.55
314 881 6.841443 TCAAAAACATAATTTGGCACAGTG 57.159 33.333 0.00 0.00 42.39 3.66
315 882 5.236047 TCAAAAACATAATTTGGCACAGTGC 59.764 36.000 17.97 17.97 42.39 4.40
329 896 4.511636 GTGCCTCTCACTAGCAGC 57.488 61.111 0.00 0.00 42.38 5.25
330 897 1.593787 GTGCCTCTCACTAGCAGCA 59.406 57.895 0.00 0.00 42.38 4.41
331 898 0.177604 GTGCCTCTCACTAGCAGCAT 59.822 55.000 0.00 0.00 42.38 3.79
332 899 0.463204 TGCCTCTCACTAGCAGCATC 59.537 55.000 0.00 0.00 31.65 3.91
333 900 0.752054 GCCTCTCACTAGCAGCATCT 59.248 55.000 0.00 0.00 0.00 2.90
334 901 1.138661 GCCTCTCACTAGCAGCATCTT 59.861 52.381 0.00 0.00 0.00 2.40
335 902 2.823984 CCTCTCACTAGCAGCATCTTG 58.176 52.381 0.00 0.00 0.00 3.02
336 903 2.429971 CCTCTCACTAGCAGCATCTTGA 59.570 50.000 0.00 0.00 0.00 3.02
337 904 3.069872 CCTCTCACTAGCAGCATCTTGAT 59.930 47.826 0.00 0.00 0.00 2.57
338 905 4.052608 CTCTCACTAGCAGCATCTTGATG 58.947 47.826 6.27 6.27 36.74 3.07
339 906 3.132160 CTCACTAGCAGCATCTTGATGG 58.868 50.000 11.91 0.00 33.75 3.51
340 907 2.502947 TCACTAGCAGCATCTTGATGGT 59.497 45.455 9.22 9.22 46.71 3.55
341 908 3.706086 TCACTAGCAGCATCTTGATGGTA 59.294 43.478 13.87 6.35 43.09 3.25
342 909 3.806521 CACTAGCAGCATCTTGATGGTAC 59.193 47.826 13.87 9.43 43.09 3.34
343 910 3.708631 ACTAGCAGCATCTTGATGGTACT 59.291 43.478 16.54 16.54 43.09 2.73
344 911 3.641434 AGCAGCATCTTGATGGTACTT 57.359 42.857 13.87 2.15 43.09 2.24
345 912 3.539604 AGCAGCATCTTGATGGTACTTC 58.460 45.455 13.87 5.58 43.09 3.01
346 913 2.615912 GCAGCATCTTGATGGTACTTCC 59.384 50.000 13.87 0.00 33.75 3.46
347 914 6.151510 AGCAGCATCTTGATGGTACTTCCA 62.152 45.833 13.87 0.00 43.09 3.53
358 925 4.137116 TGGTACTTCCATAGCATCACAC 57.863 45.455 0.00 0.00 41.93 3.82
359 926 3.118408 TGGTACTTCCATAGCATCACACC 60.118 47.826 0.00 0.00 41.93 4.16
360 927 3.134804 GGTACTTCCATAGCATCACACCT 59.865 47.826 0.00 0.00 35.97 4.00
361 928 3.272574 ACTTCCATAGCATCACACCTG 57.727 47.619 0.00 0.00 0.00 4.00
362 929 2.573462 ACTTCCATAGCATCACACCTGT 59.427 45.455 0.00 0.00 0.00 4.00
363 930 3.774766 ACTTCCATAGCATCACACCTGTA 59.225 43.478 0.00 0.00 0.00 2.74
364 931 3.819564 TCCATAGCATCACACCTGTAC 57.180 47.619 0.00 0.00 0.00 2.90
365 932 2.434336 TCCATAGCATCACACCTGTACC 59.566 50.000 0.00 0.00 0.00 3.34
366 933 2.473816 CATAGCATCACACCTGTACCG 58.526 52.381 0.00 0.00 0.00 4.02
367 934 0.174845 TAGCATCACACCTGTACCGC 59.825 55.000 0.00 0.00 0.00 5.68
368 935 2.106683 GCATCACACCTGTACCGCC 61.107 63.158 0.00 0.00 0.00 6.13
807 1374 9.650714 ACACCTCTTAAGTTTTAAATTTAGGGT 57.349 29.630 1.63 6.77 0.00 4.34
953 7055 0.185175 GTCCTCCTCCTCCTCCTCTC 59.815 65.000 0.00 0.00 0.00 3.20
990 8828 2.359967 CCTTCCTCTCCACGGACCC 61.360 68.421 0.00 0.00 0.00 4.46
1312 9164 1.620819 CCCCTCCCTGTCTATGATTCG 59.379 57.143 0.00 0.00 0.00 3.34
1313 9165 2.320781 CCCTCCCTGTCTATGATTCGT 58.679 52.381 0.00 0.00 0.00 3.85
1366 9357 3.493699 CCCCATGATTGGTTGATTGATGC 60.494 47.826 0.00 0.00 41.91 3.91
1367 9358 3.386726 CCCATGATTGGTTGATTGATGCT 59.613 43.478 0.00 0.00 41.91 3.79
1369 9360 4.808895 CCATGATTGGTTGATTGATGCTTG 59.191 41.667 0.00 0.00 38.30 4.01
1370 9361 3.852286 TGATTGGTTGATTGATGCTTGC 58.148 40.909 0.00 0.00 0.00 4.01
1372 9363 0.527113 TGGTTGATTGATGCTTGCGG 59.473 50.000 0.00 0.00 0.00 5.69
1378 9381 1.111116 ATTGATGCTTGCGGGATGGG 61.111 55.000 0.00 0.00 0.00 4.00
1405 9408 2.002586 CGGACTAGTTGTTGCCTGATG 58.997 52.381 0.00 0.00 0.00 3.07
1608 9737 5.613358 GCACTTGCACACTTAGTTATCTT 57.387 39.130 0.00 0.00 41.59 2.40
1609 9738 6.721571 GCACTTGCACACTTAGTTATCTTA 57.278 37.500 0.00 0.00 41.59 2.10
1771 9943 4.010349 GCTTAGGTAAACTCCATTGTGCT 58.990 43.478 0.00 0.00 0.00 4.40
1841 10186 2.360165 CCTCCATGCCAGTGCTTATTTC 59.640 50.000 0.00 0.00 38.71 2.17
1946 10292 3.872511 TCCATTCGTTAGCGGAAAGTA 57.127 42.857 0.00 0.00 38.89 2.24
2014 10360 0.865769 CGACACGGTTTAGCTGCTTT 59.134 50.000 7.79 0.00 0.00 3.51
2016 10362 2.477375 CGACACGGTTTAGCTGCTTTAA 59.523 45.455 7.79 0.00 0.00 1.52
2154 10501 3.423154 CCGCTGACCTTGTTCGGC 61.423 66.667 0.00 0.00 43.46 5.54
2185 10532 2.349755 GTCCGGTTTGGGCAGCTA 59.650 61.111 0.00 0.00 44.04 3.32
2266 10613 4.929808 GCAGTTTTTAGAGTAGCTGCACTA 59.070 41.667 4.12 4.57 45.83 2.74
2269 10616 7.361286 GCAGTTTTTAGAGTAGCTGCACTATTT 60.361 37.037 9.56 0.00 45.83 1.40
2362 10709 3.433306 TGACCTTGTAAATGGAGGTGG 57.567 47.619 0.00 0.00 32.35 4.61
2446 10794 2.672195 GCTGACCTTGTTAAATGCAGGC 60.672 50.000 0.00 0.00 0.00 4.85
2576 11119 7.268199 TGAATGCCTCATCTTTTGCTATTAG 57.732 36.000 0.00 0.00 0.00 1.73
2597 11140 7.547285 TTAGAAATCAATTTGTTTTCTCGCG 57.453 32.000 26.92 0.00 42.28 5.87
2611 11154 8.075593 TGTTTTCTCGCGTTTAACTAAACTAT 57.924 30.769 5.77 0.00 42.46 2.12
2617 11160 8.400947 TCTCGCGTTTAACTAAACTATCTATGT 58.599 33.333 5.77 0.00 42.46 2.29
2682 11226 6.215845 GTCAACAGACATTTTTGGTTGCTAT 58.784 36.000 0.00 0.00 38.87 2.97
2720 11279 7.009179 TCAAGTCAAAGTGGATAATCTGTCT 57.991 36.000 0.00 0.00 0.00 3.41
2724 11283 6.071334 AGTCAAAGTGGATAATCTGTCTTCGA 60.071 38.462 0.00 0.00 0.00 3.71
2726 11285 6.813649 TCAAAGTGGATAATCTGTCTTCGAAG 59.186 38.462 19.35 19.35 0.00 3.79
2732 11291 7.278868 GTGGATAATCTGTCTTCGAAGTGAAAT 59.721 37.037 23.85 16.29 35.79 2.17
2733 11292 8.474831 TGGATAATCTGTCTTCGAAGTGAAATA 58.525 33.333 23.85 16.20 35.79 1.40
2740 11299 7.655732 TCTGTCTTCGAAGTGAAATATTCAACA 59.344 33.333 23.85 14.60 42.15 3.33
2751 11310 8.859090 AGTGAAATATTCAACAACTTTCCATGA 58.141 29.630 0.00 0.00 42.15 3.07
2787 11346 8.854614 ATGTTAGCAGGATATAACTGAATTCC 57.145 34.615 2.27 0.00 38.20 3.01
2850 11409 6.813649 TCGCTATTCATGAATATACCAAGCTC 59.186 38.462 24.77 5.29 33.29 4.09
2891 11455 8.052621 TCTTATAATAAAATAGGCAGGTGGGT 57.947 34.615 0.00 0.00 0.00 4.51
2892 11456 7.942341 TCTTATAATAAAATAGGCAGGTGGGTG 59.058 37.037 0.00 0.00 0.00 4.61
2893 11457 2.818751 TAAAATAGGCAGGTGGGTGG 57.181 50.000 0.00 0.00 0.00 4.61
2999 11563 9.880064 CTTGCTGATAATCACAATATCAAAGAG 57.120 33.333 0.00 0.00 38.82 2.85
3001 11565 7.040892 TGCTGATAATCACAATATCAAAGAGCC 60.041 37.037 0.00 0.00 38.82 4.70
3038 11602 8.642935 TTCCATCATTCCAGTTTAAATGTACA 57.357 30.769 0.00 0.00 35.02 2.90
3061 11625 6.095440 ACACTATAATTCATTGTCAACCCAGC 59.905 38.462 0.00 0.00 0.00 4.85
3075 11639 1.219124 CCAGCGTGGTAGCATCACT 59.781 57.895 0.00 0.00 40.15 3.41
3144 11708 1.677576 CAGTTTGCAACTCAGCTTCCA 59.322 47.619 0.00 0.00 40.46 3.53
3173 11740 2.694109 CAGTAAGGTACCCCAGCTAGTC 59.306 54.545 8.74 0.00 33.59 2.59
3297 12200 1.081092 CCCTCCCTTCTGGTGAGGA 59.919 63.158 16.08 0.00 45.64 3.71
3298 12201 0.327000 CCCTCCCTTCTGGTGAGGAT 60.327 60.000 16.08 0.00 45.64 3.24
3326 12229 6.998968 ATGAACATGAAATTGGAGTCTCTC 57.001 37.500 0.00 0.00 0.00 3.20
3327 12230 5.868454 TGAACATGAAATTGGAGTCTCTCA 58.132 37.500 0.00 0.00 31.08 3.27
3330 12233 4.699257 ACATGAAATTGGAGTCTCTCAAGC 59.301 41.667 0.00 0.00 31.08 4.01
3337 12242 2.563179 TGGAGTCTCTCAAGCACCTAAC 59.437 50.000 0.00 0.00 31.08 2.34
3362 12267 4.021456 CACCCCTGTTTGAATCCTAAAACC 60.021 45.833 0.00 0.00 35.80 3.27
3364 12269 4.021456 CCCCTGTTTGAATCCTAAAACCAC 60.021 45.833 0.00 0.00 35.80 4.16
3402 12307 2.031495 AGCACCTTCCCTACTGACTT 57.969 50.000 0.00 0.00 0.00 3.01
3433 12338 6.007076 TGGTTCATGTGGTTATTTGCTAAGA 58.993 36.000 0.00 0.00 0.00 2.10
3517 12422 9.046296 GGGTGTGAGTTAAAGAGATATACAATG 57.954 37.037 0.00 0.00 0.00 2.82
3532 12437 9.174166 AGATATACAATGTTTGGGTGTCTAAAC 57.826 33.333 0.00 0.00 42.39 2.01
3553 12458 4.137543 ACTTTGAAGCTTTGAGTGTAGGG 58.862 43.478 0.00 0.00 0.00 3.53
3815 12730 3.935203 ACAGCTGCACATATGACACTTAC 59.065 43.478 15.27 0.00 0.00 2.34
3838 12753 9.594478 TTACATATATGATTTTGTCGACTGTGT 57.406 29.630 19.63 9.77 0.00 3.72
3871 12787 4.696877 TGTGATCTCTGCCACACAAATTAG 59.303 41.667 0.00 0.00 39.70 1.73
3956 12879 5.232414 GGACGTATAGCAGTGCTCTTTAAAG 59.768 44.000 23.64 9.04 40.44 1.85
4009 12932 6.029346 ACCCAGATTGCTTAGTTCAAATTG 57.971 37.500 0.00 0.00 0.00 2.32
4022 12945 5.240121 AGTTCAAATTGATTTGTCCCATGC 58.760 37.500 14.22 0.00 45.49 4.06
4039 12962 4.365723 CCATGCCTGTTTTAGCATCAATC 58.634 43.478 0.00 0.00 46.58 2.67
4083 13006 4.051922 GGGCTATGAAGATCTGTAACACG 58.948 47.826 0.00 0.00 0.00 4.49
4104 13027 3.502211 CGGATAATACCCTGTCAATTGCC 59.498 47.826 0.00 0.00 0.00 4.52
4147 13070 4.940046 TCTGAAGCCACTGAATTTGAGATC 59.060 41.667 0.00 0.00 0.00 2.75
4153 13076 4.159135 GCCACTGAATTTGAGATCCAATGT 59.841 41.667 0.00 0.00 34.23 2.71
4171 13094 7.946207 TCCAATGTAGCTGAAAAATGTTTGTA 58.054 30.769 0.00 0.00 0.00 2.41
4216 13139 5.426504 AGACCTGTAAATCAGCAAGATCAG 58.573 41.667 0.00 0.00 42.38 2.90
4287 13210 7.348080 AGGAAGAACTTACCCTTTTCTTTTG 57.652 36.000 0.00 0.00 39.22 2.44
4368 13291 1.928868 ACTTCTGGGCCCTTTCATTG 58.071 50.000 25.70 9.10 0.00 2.82
4407 13331 6.479972 TCTATGATTGTGAACGAATAGGGT 57.520 37.500 0.00 0.00 0.00 4.34
4459 13386 9.389755 AGATAAAAAGGTTCTGCTTCTCTTATC 57.610 33.333 0.00 0.00 0.00 1.75
4523 13450 6.701340 TGTAAGTTCAGTCTGTATCAGCATT 58.299 36.000 0.00 0.00 0.00 3.56
4559 13486 1.234615 GCTCGCCAGCAAAGGTTACA 61.235 55.000 0.00 0.00 46.06 2.41
4563 13490 0.598065 GCCAGCAAAGGTTACACCAG 59.402 55.000 0.00 0.00 41.95 4.00
4580 13507 2.021441 ACCAGTAACCCCCATCCATCTA 60.021 50.000 0.00 0.00 0.00 1.98
4588 13515 2.636005 CCCCATCCATCTATCCCTTCA 58.364 52.381 0.00 0.00 0.00 3.02
4604 13531 4.875536 TCCCTTCATCACATATCAAACACG 59.124 41.667 0.00 0.00 0.00 4.49
4611 13538 6.818142 TCATCACATATCAAACACGATGTTCT 59.182 34.615 0.00 0.00 40.14 3.01
4641 13568 5.340803 TGTTCTCTTACTAGCTACGCATTG 58.659 41.667 0.00 0.00 0.00 2.82
4767 13741 2.329267 AGTATGAGGGGCATCGAATCA 58.671 47.619 0.00 0.00 38.44 2.57
4814 13788 1.077429 CCAGCCAGCCTTCCTTACC 60.077 63.158 0.00 0.00 0.00 2.85
4970 13949 5.627780 TGTCGAAACGTGAATATATCATCGG 59.372 40.000 0.00 0.00 40.97 4.18
5086 14070 4.569943 ACATTGTTTCGTGCTATCTGTCT 58.430 39.130 0.00 0.00 0.00 3.41
5196 14259 3.886123 ACAAGTCCAGTGTGCTTTTAGT 58.114 40.909 0.00 0.00 0.00 2.24
5221 14284 8.337532 GTTTGGATAAATTTGATGCTAAATGCC 58.662 33.333 0.00 0.00 42.00 4.40
5223 14286 8.476064 TGGATAAATTTGATGCTAAATGCCTA 57.524 30.769 0.00 0.00 42.00 3.93
5245 14308 7.093945 GCCTATTGTGGACAAGAAAATTCCTTA 60.094 37.037 0.00 0.00 39.47 2.69
5356 14419 1.021968 ACAAGAACACAAGGAACGGC 58.978 50.000 0.00 0.00 0.00 5.68
5507 14570 5.238432 TGTTGCGACATCAGAGTTATTTTGT 59.762 36.000 1.50 0.00 0.00 2.83
5510 14573 5.929415 TGCGACATCAGAGTTATTTTGTGTA 59.071 36.000 0.00 0.00 0.00 2.90
5513 14576 8.056571 GCGACATCAGAGTTATTTTGTGTATAC 58.943 37.037 0.00 0.00 0.00 1.47
5514 14577 9.083080 CGACATCAGAGTTATTTTGTGTATACA 57.917 33.333 0.08 0.08 34.31 2.29
5545 14611 6.561737 TTGTTTTGAATTGCATGCATGATT 57.438 29.167 30.64 20.55 0.00 2.57
5553 14619 7.149307 TGAATTGCATGCATGATTGTTATAGG 58.851 34.615 30.64 0.00 0.00 2.57
5562 14628 5.359576 GCATGATTGTTATAGGTTGTTCCCA 59.640 40.000 0.00 0.00 36.75 4.37
5563 14629 6.040842 GCATGATTGTTATAGGTTGTTCCCAT 59.959 38.462 0.00 0.00 36.75 4.00
5564 14630 7.651808 CATGATTGTTATAGGTTGTTCCCATC 58.348 38.462 0.00 0.00 36.75 3.51
5565 14631 6.969043 TGATTGTTATAGGTTGTTCCCATCT 58.031 36.000 0.00 0.00 36.75 2.90
5566 14632 6.828273 TGATTGTTATAGGTTGTTCCCATCTG 59.172 38.462 0.00 0.00 36.75 2.90
5567 14633 5.772393 TGTTATAGGTTGTTCCCATCTGT 57.228 39.130 0.00 0.00 36.75 3.41
5568 14634 5.496556 TGTTATAGGTTGTTCCCATCTGTG 58.503 41.667 0.00 0.00 36.75 3.66
5569 14635 5.249622 TGTTATAGGTTGTTCCCATCTGTGA 59.750 40.000 0.00 0.00 36.75 3.58
5570 14636 2.867109 AGGTTGTTCCCATCTGTGAG 57.133 50.000 0.00 0.00 36.75 3.51
5571 14637 2.338809 AGGTTGTTCCCATCTGTGAGA 58.661 47.619 0.00 0.00 36.75 3.27
5572 14638 2.915604 AGGTTGTTCCCATCTGTGAGAT 59.084 45.455 0.00 0.00 34.74 2.75
5646 14714 0.825425 TCCAACCATCAAGGCGCAAA 60.825 50.000 10.83 0.00 43.14 3.68
5708 14776 5.872617 CACTACCACCTTCGATGTATTTTGA 59.127 40.000 0.00 0.00 0.00 2.69
5712 14780 7.227049 ACCACCTTCGATGTATTTTGATTTT 57.773 32.000 0.00 0.00 0.00 1.82
5736 14804 4.878439 CCATCAAATGGTAAGCATGATGG 58.122 43.478 16.12 16.12 45.54 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.514577 CTCTGGCGGCGGTACAGG 62.515 72.222 18.34 0.91 33.19 4.00
92 659 6.280855 TGATTGAAGGAGAGACAAATCGTA 57.719 37.500 0.00 0.00 0.00 3.43
95 662 8.137437 TGTTTTTGATTGAAGGAGAGACAAATC 58.863 33.333 0.00 0.00 0.00 2.17
111 678 7.520292 GCACTGTGCCAAATTATGTTTTTGATT 60.520 33.333 21.78 0.00 37.42 2.57
146 713 3.539604 GAAGTACCATCAAGATGCTGCT 58.460 45.455 0.00 0.00 37.49 4.24
167 734 2.803133 CGGTACAGGTGTGATGCTATGG 60.803 54.545 0.00 0.00 0.00 2.74
233 800 2.637025 GCGACGCCTCTGCAAAAA 59.363 55.556 9.14 0.00 37.32 1.94
234 801 3.353836 GGCGACGCCTCTGCAAAA 61.354 61.111 31.30 0.00 46.69 2.44
251 818 4.738998 TGTGCCATGGCGAAGGGG 62.739 66.667 30.87 0.00 45.51 4.79
252 819 0.751277 TAATGTGCCATGGCGAAGGG 60.751 55.000 30.87 0.00 45.51 3.95
253 820 0.381801 GTAATGTGCCATGGCGAAGG 59.618 55.000 30.87 0.00 45.51 3.46
254 821 0.027979 CGTAATGTGCCATGGCGAAG 59.972 55.000 30.87 13.94 45.51 3.79
255 822 0.391793 TCGTAATGTGCCATGGCGAA 60.392 50.000 30.87 21.84 45.51 4.70
256 823 0.179059 ATCGTAATGTGCCATGGCGA 60.179 50.000 30.87 20.68 45.51 5.54
257 824 0.662619 AATCGTAATGTGCCATGGCG 59.337 50.000 30.87 15.26 45.51 5.69
258 825 2.159254 ACAAATCGTAATGTGCCATGGC 60.159 45.455 30.54 30.54 42.35 4.40
259 826 3.378112 AGACAAATCGTAATGTGCCATGG 59.622 43.478 7.63 7.63 0.00 3.66
260 827 4.333649 AGAGACAAATCGTAATGTGCCATG 59.666 41.667 0.00 0.00 0.00 3.66
261 828 4.517285 AGAGACAAATCGTAATGTGCCAT 58.483 39.130 0.00 0.00 0.00 4.40
262 829 3.932710 GAGAGACAAATCGTAATGTGCCA 59.067 43.478 0.00 0.00 0.00 4.92
263 830 3.309954 GGAGAGACAAATCGTAATGTGCC 59.690 47.826 0.00 0.00 0.00 5.01
264 831 4.184629 AGGAGAGACAAATCGTAATGTGC 58.815 43.478 0.00 0.00 0.00 4.57
265 832 5.869344 TGAAGGAGAGACAAATCGTAATGTG 59.131 40.000 0.00 0.00 0.00 3.21
266 833 6.037786 TGAAGGAGAGACAAATCGTAATGT 57.962 37.500 0.00 0.00 0.00 2.71
267 834 6.968131 TTGAAGGAGAGACAAATCGTAATG 57.032 37.500 0.00 0.00 0.00 1.90
268 835 7.331026 TGATTGAAGGAGAGACAAATCGTAAT 58.669 34.615 0.00 0.00 0.00 1.89
269 836 6.697395 TGATTGAAGGAGAGACAAATCGTAA 58.303 36.000 0.00 0.00 0.00 3.18
270 837 6.280855 TGATTGAAGGAGAGACAAATCGTA 57.719 37.500 0.00 0.00 0.00 3.43
271 838 5.152623 TGATTGAAGGAGAGACAAATCGT 57.847 39.130 0.00 0.00 0.00 3.73
272 839 6.486253 TTTGATTGAAGGAGAGACAAATCG 57.514 37.500 0.00 0.00 0.00 3.34
273 840 8.137437 TGTTTTTGATTGAAGGAGAGACAAATC 58.863 33.333 0.00 0.00 0.00 2.17
274 841 8.010733 TGTTTTTGATTGAAGGAGAGACAAAT 57.989 30.769 0.00 0.00 0.00 2.32
275 842 7.403312 TGTTTTTGATTGAAGGAGAGACAAA 57.597 32.000 0.00 0.00 0.00 2.83
276 843 7.587037 ATGTTTTTGATTGAAGGAGAGACAA 57.413 32.000 0.00 0.00 0.00 3.18
277 844 8.690203 TTATGTTTTTGATTGAAGGAGAGACA 57.310 30.769 0.00 0.00 0.00 3.41
281 848 9.709495 CCAAATTATGTTTTTGATTGAAGGAGA 57.291 29.630 0.00 0.00 36.40 3.71
282 849 8.445493 GCCAAATTATGTTTTTGATTGAAGGAG 58.555 33.333 0.00 0.00 36.40 3.69
283 850 7.935755 TGCCAAATTATGTTTTTGATTGAAGGA 59.064 29.630 0.00 0.00 36.40 3.36
284 851 8.016801 GTGCCAAATTATGTTTTTGATTGAAGG 58.983 33.333 0.00 0.00 36.40 3.46
285 852 8.557864 TGTGCCAAATTATGTTTTTGATTGAAG 58.442 29.630 0.00 0.00 36.40 3.02
286 853 8.442632 TGTGCCAAATTATGTTTTTGATTGAA 57.557 26.923 0.00 0.00 36.40 2.69
287 854 7.714377 ACTGTGCCAAATTATGTTTTTGATTGA 59.286 29.630 0.00 0.00 36.40 2.57
288 855 7.799447 CACTGTGCCAAATTATGTTTTTGATTG 59.201 33.333 0.00 0.00 36.40 2.67
289 856 7.520292 GCACTGTGCCAAATTATGTTTTTGATT 60.520 33.333 21.78 0.00 37.42 2.57
290 857 6.073112 GCACTGTGCCAAATTATGTTTTTGAT 60.073 34.615 21.78 0.00 37.42 2.57
291 858 5.236047 GCACTGTGCCAAATTATGTTTTTGA 59.764 36.000 21.78 0.00 37.42 2.69
292 859 5.442402 GCACTGTGCCAAATTATGTTTTTG 58.558 37.500 21.78 0.00 37.42 2.44
293 860 5.671742 GCACTGTGCCAAATTATGTTTTT 57.328 34.783 21.78 0.00 37.42 1.94
313 880 0.463204 GATGCTGCTAGTGAGAGGCA 59.537 55.000 0.00 0.00 36.58 4.75
314 881 0.752054 AGATGCTGCTAGTGAGAGGC 59.248 55.000 0.00 0.00 0.00 4.70
315 882 2.429971 TCAAGATGCTGCTAGTGAGAGG 59.570 50.000 0.00 0.00 0.00 3.69
316 883 3.797451 TCAAGATGCTGCTAGTGAGAG 57.203 47.619 0.00 0.00 0.00 3.20
317 884 3.181468 CCATCAAGATGCTGCTAGTGAGA 60.181 47.826 0.00 0.00 37.49 3.27
318 885 3.132160 CCATCAAGATGCTGCTAGTGAG 58.868 50.000 0.00 0.00 37.49 3.51
319 886 2.502947 ACCATCAAGATGCTGCTAGTGA 59.497 45.455 0.00 0.00 37.49 3.41
320 887 2.915349 ACCATCAAGATGCTGCTAGTG 58.085 47.619 0.00 0.00 37.49 2.74
321 888 3.708631 AGTACCATCAAGATGCTGCTAGT 59.291 43.478 0.00 0.00 37.49 2.57
322 889 4.333913 AGTACCATCAAGATGCTGCTAG 57.666 45.455 0.00 0.00 37.49 3.42
323 890 4.443457 GGAAGTACCATCAAGATGCTGCTA 60.443 45.833 0.00 0.00 37.49 3.49
324 891 3.539604 GAAGTACCATCAAGATGCTGCT 58.460 45.455 0.00 0.00 37.49 4.24
325 892 2.615912 GGAAGTACCATCAAGATGCTGC 59.384 50.000 4.53 0.00 37.49 5.25
326 893 3.877559 TGGAAGTACCATCAAGATGCTG 58.122 45.455 4.53 0.00 44.64 4.41
338 905 3.134804 AGGTGTGATGCTATGGAAGTACC 59.865 47.826 0.00 0.00 39.54 3.34
339 906 4.122776 CAGGTGTGATGCTATGGAAGTAC 58.877 47.826 0.00 0.00 0.00 2.73
340 907 3.774766 ACAGGTGTGATGCTATGGAAGTA 59.225 43.478 0.00 0.00 0.00 2.24
341 908 2.573462 ACAGGTGTGATGCTATGGAAGT 59.427 45.455 0.00 0.00 0.00 3.01
342 909 3.272574 ACAGGTGTGATGCTATGGAAG 57.727 47.619 0.00 0.00 0.00 3.46
343 910 3.118408 GGTACAGGTGTGATGCTATGGAA 60.118 47.826 0.00 0.00 0.00 3.53
344 911 2.434336 GGTACAGGTGTGATGCTATGGA 59.566 50.000 0.00 0.00 0.00 3.41
345 912 2.803133 CGGTACAGGTGTGATGCTATGG 60.803 54.545 0.00 0.00 0.00 2.74
346 913 2.473816 CGGTACAGGTGTGATGCTATG 58.526 52.381 0.00 0.00 0.00 2.23
347 914 1.202533 GCGGTACAGGTGTGATGCTAT 60.203 52.381 0.00 0.00 0.00 2.97
348 915 0.174845 GCGGTACAGGTGTGATGCTA 59.825 55.000 0.00 0.00 0.00 3.49
349 916 1.079127 GCGGTACAGGTGTGATGCT 60.079 57.895 0.00 0.00 0.00 3.79
350 917 2.106683 GGCGGTACAGGTGTGATGC 61.107 63.158 0.00 0.00 0.00 3.91
351 918 4.201951 GGCGGTACAGGTGTGATG 57.798 61.111 0.00 0.00 0.00 3.07
825 5872 8.809468 ATCTTTTTGAGTACCTAAATTCCTCC 57.191 34.615 0.00 0.00 0.00 4.30
953 7055 1.208706 GGGAAGGGAAAGAGGAGAGG 58.791 60.000 0.00 0.00 0.00 3.69
990 8828 3.902063 CTCGTCATGGCGCGTTCG 61.902 66.667 16.44 1.89 39.07 3.95
1305 9157 3.809832 CCCGCAAGAATCTAACGAATCAT 59.190 43.478 6.44 0.00 43.02 2.45
1355 9346 0.810648 TCCCGCAAGCATCAATCAAC 59.189 50.000 0.00 0.00 0.00 3.18
1366 9357 3.583882 AACCCACCCATCCCGCAAG 62.584 63.158 0.00 0.00 0.00 4.01
1367 9358 3.577334 GAACCCACCCATCCCGCAA 62.577 63.158 0.00 0.00 0.00 4.85
1370 9361 4.483243 CCGAACCCACCCATCCCG 62.483 72.222 0.00 0.00 0.00 5.14
1372 9363 0.979187 TAGTCCGAACCCACCCATCC 60.979 60.000 0.00 0.00 0.00 3.51
1378 9381 2.140717 CAACAACTAGTCCGAACCCAC 58.859 52.381 0.00 0.00 0.00 4.61
1405 9408 5.988287 TGCCCATGGAAAATAATTTCTTCC 58.012 37.500 15.22 6.12 43.65 3.46
1771 9943 3.157252 GAGGGGATGAGAGGCGCA 61.157 66.667 10.83 0.00 0.00 6.09
1841 10186 6.017934 ACACCATATGCAAAGTTAGCTAATCG 60.018 38.462 9.88 0.09 0.00 3.34
1946 10292 0.192566 TGAGGACTAGGGTGGTGGTT 59.807 55.000 0.00 0.00 0.00 3.67
2014 10360 5.168647 TGGAAAGGAAAGGCGAGTTATTA 57.831 39.130 0.00 0.00 0.00 0.98
2016 10362 3.713826 TGGAAAGGAAAGGCGAGTTAT 57.286 42.857 0.00 0.00 0.00 1.89
2074 10421 2.560981 TCTGCATCTAACAAGGTCGTGA 59.439 45.455 0.00 0.00 0.00 4.35
2154 10501 1.154301 CGGACAAAAATGACCCGCG 60.154 57.895 0.00 0.00 33.47 6.46
2266 10613 3.951663 AGGCGAGTTAAAGCACCTAAAT 58.048 40.909 0.00 0.00 34.54 1.40
2269 10616 3.412237 AAAGGCGAGTTAAAGCACCTA 57.588 42.857 0.00 0.00 34.54 3.08
2362 10709 1.264288 ACTTAGACGCAAAGCACAAGC 59.736 47.619 0.00 0.00 42.56 4.01
2543 11086 4.260170 AGATGAGGCATTCAAGAGAACAC 58.740 43.478 0.00 0.00 39.77 3.32
2550 11093 4.451629 AGCAAAAGATGAGGCATTCAAG 57.548 40.909 0.00 0.00 39.77 3.02
2557 11100 7.934457 TGATTTCTAATAGCAAAAGATGAGGC 58.066 34.615 0.00 0.00 0.00 4.70
2576 11119 5.806089 ACGCGAGAAAACAAATTGATTTC 57.194 34.783 15.93 17.40 38.80 2.17
2617 11160 6.880484 TCCGTTACATAGGCTATCTTTTTCA 58.120 36.000 3.47 0.00 0.00 2.69
2638 11182 1.927174 CGTAGCTGAATGGAAGTTCCG 59.073 52.381 17.13 3.50 40.17 4.30
2682 11226 8.724229 CACTTTGACTTGATATGATTTGACAGA 58.276 33.333 0.00 0.00 0.00 3.41
2720 11279 9.445786 GAAAGTTGTTGAATATTTCACTTCGAA 57.554 29.630 0.00 0.00 39.87 3.71
2724 11283 9.480053 CATGGAAAGTTGTTGAATATTTCACTT 57.520 29.630 0.00 0.00 39.87 3.16
2726 11285 9.474920 TTCATGGAAAGTTGTTGAATATTTCAC 57.525 29.630 0.00 0.00 39.87 3.18
2732 11291 7.950512 ACATGTTCATGGAAAGTTGTTGAATA 58.049 30.769 15.71 0.00 0.00 1.75
2733 11292 6.819284 ACATGTTCATGGAAAGTTGTTGAAT 58.181 32.000 15.71 0.00 0.00 2.57
2774 11333 5.116084 AGCTGCAAGGGAATTCAGTTATA 57.884 39.130 7.93 0.00 0.00 0.98
2787 11346 2.803956 CAACATTGGAAAAGCTGCAAGG 59.196 45.455 1.02 0.00 42.24 3.61
2843 11402 8.779354 AGATTTAGTTAGTAGTTTGAGCTTGG 57.221 34.615 0.00 0.00 0.00 3.61
2891 11455 4.956700 TGGTGTTTTCATTTGAGGTTACCA 59.043 37.500 3.51 0.00 32.56 3.25
2892 11456 5.068591 ACTGGTGTTTTCATTTGAGGTTACC 59.931 40.000 0.00 0.00 0.00 2.85
2893 11457 6.144078 ACTGGTGTTTTCATTTGAGGTTAC 57.856 37.500 0.00 0.00 0.00 2.50
2999 11563 2.562298 TGATGGAAATGGACAAACAGGC 59.438 45.455 0.00 0.00 0.00 4.85
3001 11565 5.047164 TGGAATGATGGAAATGGACAAACAG 60.047 40.000 0.00 0.00 0.00 3.16
3038 11602 5.296780 CGCTGGGTTGACAATGAATTATAGT 59.703 40.000 0.00 0.00 0.00 2.12
3075 11639 5.696270 CACTGAGTTACTGACAATTGCAGTA 59.304 40.000 25.62 25.62 44.27 2.74
3173 11740 2.210116 AGCACAAACTACTTGTCACCG 58.790 47.619 0.00 0.00 45.50 4.94
3217 11784 4.366684 CCAGTGGGGCAGGGTTCC 62.367 72.222 0.00 0.00 0.00 3.62
3326 12229 1.304134 GGGGTGGGTTAGGTGCTTG 60.304 63.158 0.00 0.00 0.00 4.01
3327 12230 1.465387 AGGGGTGGGTTAGGTGCTT 60.465 57.895 0.00 0.00 0.00 3.91
3330 12233 0.481128 AAACAGGGGTGGGTTAGGTG 59.519 55.000 0.00 0.00 0.00 4.00
3337 12242 0.409484 AGGATTCAAACAGGGGTGGG 59.591 55.000 0.00 0.00 0.00 4.61
3362 12267 5.184864 TGCTTGTTTTATTCACATAGGGGTG 59.815 40.000 0.00 0.00 40.16 4.61
3364 12269 5.394115 GGTGCTTGTTTTATTCACATAGGGG 60.394 44.000 0.00 0.00 0.00 4.79
3402 12307 6.662865 AATAACCACATGAACCAAATGTCA 57.337 33.333 0.00 0.00 36.10 3.58
3433 12338 6.638021 AACAGAATAACCCCTACTAGCTTT 57.362 37.500 0.00 0.00 0.00 3.51
3517 12422 5.041287 GCTTCAAAGTTTAGACACCCAAAC 58.959 41.667 0.00 0.00 35.36 2.93
3532 12437 4.137543 ACCCTACACTCAAAGCTTCAAAG 58.862 43.478 0.00 0.00 0.00 2.77
3553 12458 0.322456 TGTGAGCATGCCCCTGTTAC 60.322 55.000 15.66 2.80 0.00 2.50
3815 12730 9.249457 ACTACACAGTCGACAAAATCATATATG 57.751 33.333 19.50 6.36 0.00 1.78
3835 12750 5.398169 CAGAGATCACACTGAGAACTACAC 58.602 45.833 8.28 0.00 36.98 2.90
3838 12753 3.445450 GGCAGAGATCACACTGAGAACTA 59.555 47.826 15.32 0.00 36.98 2.24
3871 12787 6.076981 TGAACATTCAGCCTCTTCTTTTTC 57.923 37.500 0.00 0.00 32.50 2.29
3973 12896 7.195374 AGCAATCTGGGTCTATAACAAACTA 57.805 36.000 0.00 0.00 0.00 2.24
4022 12945 6.750501 CACTTCATGATTGATGCTAAAACAGG 59.249 38.462 0.00 0.00 31.80 4.00
4039 12962 6.102663 CCCTTCAGTTACTACTCACTTCATG 58.897 44.000 0.00 0.00 30.26 3.07
4083 13006 4.729868 AGGCAATTGACAGGGTATTATCC 58.270 43.478 15.18 0.00 0.00 2.59
4147 13070 8.586570 TTACAAACATTTTTCAGCTACATTGG 57.413 30.769 0.00 0.00 0.00 3.16
4216 13139 4.548669 ACCTAGGGGAGTCAGAAGATTAC 58.451 47.826 14.81 0.00 36.25 1.89
4334 13257 6.770785 GGCCCAGAAGTACATTTATATTGTGA 59.229 38.462 0.00 0.00 0.00 3.58
4355 13278 6.323739 TCATAAGAATAACAATGAAAGGGCCC 59.676 38.462 16.46 16.46 0.00 5.80
4387 13311 6.411376 TGTAACCCTATTCGTTCACAATCAT 58.589 36.000 0.00 0.00 0.00 2.45
4396 13320 7.544217 GCAAAATCAATTGTAACCCTATTCGTT 59.456 33.333 5.13 0.00 32.80 3.85
4435 13362 9.171877 CAGATAAGAGAAGCAGAACCTTTTTAT 57.828 33.333 0.00 0.00 0.00 1.40
4559 13486 1.222567 GATGGATGGGGGTTACTGGT 58.777 55.000 0.00 0.00 0.00 4.00
4563 13490 2.576648 GGGATAGATGGATGGGGGTTAC 59.423 54.545 0.00 0.00 0.00 2.50
4573 13500 6.961721 TGATATGTGATGAAGGGATAGATGGA 59.038 38.462 0.00 0.00 0.00 3.41
4580 13507 5.528690 CGTGTTTGATATGTGATGAAGGGAT 59.471 40.000 0.00 0.00 0.00 3.85
4588 13515 7.615582 AAGAACATCGTGTTTGATATGTGAT 57.384 32.000 5.14 0.00 41.28 3.06
4604 13531 7.643579 AGTAAGAGAACAAGCAAAAGAACATC 58.356 34.615 0.00 0.00 0.00 3.06
4611 13538 6.365247 CGTAGCTAGTAAGAGAACAAGCAAAA 59.635 38.462 0.00 0.00 32.42 2.44
4641 13568 3.296628 CGTTGCTGTTGTTGACCAATAC 58.703 45.455 0.00 0.00 35.02 1.89
4814 13788 4.154918 CCCTTGGAAGAGATTTCTTTCACG 59.845 45.833 6.47 5.27 46.31 4.35
4970 13949 8.645730 TTCTATATATCTCTCATCGTCGGTAC 57.354 38.462 0.00 0.00 0.00 3.34
5086 14070 4.199310 CAGGCTAGCAAAGTTTATAGGCA 58.801 43.478 23.94 3.50 41.78 4.75
5356 14419 3.865745 CACTAGTGGCCATTTACTTCTCG 59.134 47.826 9.72 0.00 0.00 4.04
5458 14521 9.341899 CAAAGAAACTACAGGATTTTTAATCCG 57.658 33.333 11.65 9.61 42.87 4.18
5513 14576 8.683774 GCATGCAATTCAAAACAAAATTTACTG 58.316 29.630 14.21 0.00 0.00 2.74
5514 14577 8.404000 TGCATGCAATTCAAAACAAAATTTACT 58.596 25.926 20.30 0.00 0.00 2.24
5562 14628 7.121382 ACAAATAATCCAACCATCTCACAGAT 58.879 34.615 0.00 0.00 34.74 2.90
5563 14629 6.484288 ACAAATAATCCAACCATCTCACAGA 58.516 36.000 0.00 0.00 0.00 3.41
5564 14630 6.600822 AGACAAATAATCCAACCATCTCACAG 59.399 38.462 0.00 0.00 0.00 3.66
5565 14631 6.484288 AGACAAATAATCCAACCATCTCACA 58.516 36.000 0.00 0.00 0.00 3.58
5566 14632 7.253422 CAAGACAAATAATCCAACCATCTCAC 58.747 38.462 0.00 0.00 0.00 3.51
5567 14633 6.127647 GCAAGACAAATAATCCAACCATCTCA 60.128 38.462 0.00 0.00 0.00 3.27
5568 14634 6.127647 TGCAAGACAAATAATCCAACCATCTC 60.128 38.462 0.00 0.00 0.00 2.75
5569 14635 5.716228 TGCAAGACAAATAATCCAACCATCT 59.284 36.000 0.00 0.00 0.00 2.90
5570 14636 5.964758 TGCAAGACAAATAATCCAACCATC 58.035 37.500 0.00 0.00 0.00 3.51
5571 14637 5.999205 TGCAAGACAAATAATCCAACCAT 57.001 34.783 0.00 0.00 0.00 3.55
5572 14638 5.716228 AGATGCAAGACAAATAATCCAACCA 59.284 36.000 0.00 0.00 0.00 3.67
5573 14639 6.212888 AGATGCAAGACAAATAATCCAACC 57.787 37.500 0.00 0.00 0.00 3.77
5574 14640 7.814107 TGAAAGATGCAAGACAAATAATCCAAC 59.186 33.333 0.00 0.00 0.00 3.77
5575 14641 7.814107 GTGAAAGATGCAAGACAAATAATCCAA 59.186 33.333 0.00 0.00 0.00 3.53
5576 14642 7.315142 GTGAAAGATGCAAGACAAATAATCCA 58.685 34.615 0.00 0.00 0.00 3.41
5577 14643 6.753744 GGTGAAAGATGCAAGACAAATAATCC 59.246 38.462 0.00 0.00 0.00 3.01
5578 14644 7.487189 CAGGTGAAAGATGCAAGACAAATAATC 59.513 37.037 0.00 0.00 0.00 1.75
5579 14645 7.318141 CAGGTGAAAGATGCAAGACAAATAAT 58.682 34.615 0.00 0.00 0.00 1.28
5580 14646 6.680810 CAGGTGAAAGATGCAAGACAAATAA 58.319 36.000 0.00 0.00 0.00 1.40
5581 14647 5.335897 GCAGGTGAAAGATGCAAGACAAATA 60.336 40.000 0.00 0.00 39.75 1.40
5646 14714 4.705991 TGCCACATTCACAACATGATGTAT 59.294 37.500 8.43 0.00 37.11 2.29
5732 14800 0.033228 CATCAGTCTCTCGCCCCATC 59.967 60.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.