Multiple sequence alignment - TraesCS5D01G447600

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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 TraesCS5D01G447600 chr5D 100.000 3418 0 0 1 3418 497819250 497822667 0.000000e+00 6312.0
1 TraesCS5D01G447600 chr5D 76.395 1470 246 64 1022 2459 423535354 423533954 0.000000e+00 699.0
2 TraesCS5D01G447600 chr5D 75.398 1569 288 69 1065 2574 47531058 47532587 0.000000e+00 669.0
3 TraesCS5D01G447600 chr5D 80.423 189 25 9 3233 3418 497814953 497815132 2.140000e-27 134.0
4 TraesCS5D01G447600 chr5D 81.651 109 15 2 3313 3417 497810728 497810835 6.080000e-13 86.1
5 TraesCS5D01G447600 chr5A 90.582 2920 188 44 1 2899 621846455 621849308 0.000000e+00 3788.0
6 TraesCS5D01G447600 chr5A 75.876 1484 254 68 1161 2577 37935201 37936647 0.000000e+00 662.0
7 TraesCS5D01G447600 chr5A 75.093 1618 278 80 875 2459 537125123 537123598 1.030000e-179 640.0
8 TraesCS5D01G447600 chr5A 83.333 222 22 10 3175 3394 621849464 621849672 1.250000e-44 191.0
9 TraesCS5D01G447600 chr5A 85.165 182 23 3 33 213 492627306 492627484 2.090000e-42 183.0
10 TraesCS5D01G447600 chr5B 95.618 890 35 3 749 1636 616957966 616958853 0.000000e+00 1424.0
11 TraesCS5D01G447600 chr5B 86.906 863 82 15 2105 2956 616958850 616959692 0.000000e+00 939.0
12 TraesCS5D01G447600 chr5B 88.696 115 11 2 421 535 616956212 616956324 4.600000e-29 139.0
13 TraesCS5D01G447600 chr6A 78.201 1312 211 38 1070 2345 17947374 17946102 0.000000e+00 769.0
14 TraesCS5D01G447600 chr3A 74.529 1700 291 69 936 2567 696348378 696346753 8.110000e-171 610.0
15 TraesCS5D01G447600 chr3A 79.279 222 33 12 1 213 661873842 661874059 3.560000e-30 143.0
16 TraesCS5D01G447600 chr6B 80.095 839 123 29 1523 2345 30341692 30340882 4.920000e-163 584.0
17 TraesCS5D01G447600 chr6B 88.235 255 30 0 1612 1866 718253189 718253443 4.290000e-79 305.0
18 TraesCS5D01G447600 chr1B 74.734 1409 262 57 1167 2529 630820226 630821586 8.340000e-151 544.0
19 TraesCS5D01G447600 chr7B 77.907 946 142 37 1609 2519 661720011 661719098 8.400000e-146 527.0
20 TraesCS5D01G447600 chr7B 73.696 920 206 22 1065 1963 620679108 620678204 3.290000e-85 326.0
21 TraesCS5D01G447600 chr7B 76.106 565 108 21 1015 1568 661724546 661723998 1.560000e-68 270.0
22 TraesCS5D01G447600 chr7D 74.780 1134 213 48 746 1847 602291535 602292627 3.130000e-120 442.0
23 TraesCS5D01G447600 chrUn 77.171 806 150 23 1064 1850 87219811 87220601 4.050000e-119 438.0
24 TraesCS5D01G447600 chr2B 84.494 316 43 6 14 326 655518252 655517940 1.190000e-79 307.0
25 TraesCS5D01G447600 chr2B 81.761 318 43 10 12 317 5810490 5810804 5.660000e-63 252.0
26 TraesCS5D01G447600 chr2D 84.365 307 42 6 14 319 548600157 548599856 2.580000e-76 296.0
27 TraesCS5D01G447600 chr7A 83.391 289 37 9 1 284 56711853 56711571 1.220000e-64 257.0
28 TraesCS5D01G447600 chr1D 81.231 325 45 15 1 317 40799702 40800018 7.320000e-62 248.0
29 TraesCS5D01G447600 chr4B 78.899 327 41 20 1 309 546275684 546276000 2.690000e-46 196.0
30 TraesCS5D01G447600 chr3D 81.865 193 20 11 1 183 432543930 432543743 7.640000e-32 148.0


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 TraesCS5D01G447600 chr5D 497819250 497822667 3417 False 6312.0 6312 100.000000 1 3418 1 chr5D.!!$F4 3417
1 TraesCS5D01G447600 chr5D 423533954 423535354 1400 True 699.0 699 76.395000 1022 2459 1 chr5D.!!$R1 1437
2 TraesCS5D01G447600 chr5D 47531058 47532587 1529 False 669.0 669 75.398000 1065 2574 1 chr5D.!!$F1 1509
3 TraesCS5D01G447600 chr5A 621846455 621849672 3217 False 1989.5 3788 86.957500 1 3394 2 chr5A.!!$F3 3393
4 TraesCS5D01G447600 chr5A 37935201 37936647 1446 False 662.0 662 75.876000 1161 2577 1 chr5A.!!$F1 1416
5 TraesCS5D01G447600 chr5A 537123598 537125123 1525 True 640.0 640 75.093000 875 2459 1 chr5A.!!$R1 1584
6 TraesCS5D01G447600 chr5B 616956212 616959692 3480 False 834.0 1424 90.406667 421 2956 3 chr5B.!!$F1 2535
7 TraesCS5D01G447600 chr6A 17946102 17947374 1272 True 769.0 769 78.201000 1070 2345 1 chr6A.!!$R1 1275
8 TraesCS5D01G447600 chr3A 696346753 696348378 1625 True 610.0 610 74.529000 936 2567 1 chr3A.!!$R1 1631
9 TraesCS5D01G447600 chr6B 30340882 30341692 810 True 584.0 584 80.095000 1523 2345 1 chr6B.!!$R1 822
10 TraesCS5D01G447600 chr1B 630820226 630821586 1360 False 544.0 544 74.734000 1167 2529 1 chr1B.!!$F1 1362
11 TraesCS5D01G447600 chr7B 661719098 661724546 5448 True 398.5 527 77.006500 1015 2519 2 chr7B.!!$R2 1504
12 TraesCS5D01G447600 chr7B 620678204 620679108 904 True 326.0 326 73.696000 1065 1963 1 chr7B.!!$R1 898
13 TraesCS5D01G447600 chr7D 602291535 602292627 1092 False 442.0 442 74.780000 746 1847 1 chr7D.!!$F1 1101
14 TraesCS5D01G447600 chrUn 87219811 87220601 790 False 438.0 438 77.171000 1064 1850 1 chrUn.!!$F1 786


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
288 290 0.108756 GGTACTGTTCGTCCAGGAGC 60.109 60.0 0.00 6.04 36.69 4.70 F
294 296 0.169009 GTTCGTCCAGGAGCAAATGC 59.831 55.0 0.00 0.00 42.49 3.56 F
343 345 0.325933 ATCTGCAGCTAACCAGTGCA 59.674 50.0 9.47 0.00 44.80 4.57 F
344 346 0.325933 TCTGCAGCTAACCAGTGCAT 59.674 50.0 9.47 0.00 45.77 3.96 F
720 1864 0.470268 ACCCTAGCTAGCTGTAGGCC 60.470 60.0 27.68 0.00 43.05 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2060 7624 0.103208 CCACCGAGCTCACACCTATC 59.897 60.000 15.40 0.0 0.0 2.08 R
2108 7672 4.002982 CCTCTTTCAATCCACGACAATGA 58.997 43.478 0.00 0.0 0.0 2.57 R
2310 7880 2.965831 AGCTTAGTGTCACTTGAGGTCA 59.034 45.455 11.54 0.0 0.0 4.02 R
2357 7937 4.442706 CAAAACACACACAGAGACTACCT 58.557 43.478 0.00 0.0 0.0 3.08 R
2475 8074 2.991190 GTTGATGCTTGCACCTGAATTG 59.009 45.455 0.00 0.0 0.0 2.32 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
73 75 8.519526 CATCCAAATACTACCTGCAAAGTTTTA 58.480 33.333 1.78 0.00 0.00 1.52
80 82 4.479786 ACCTGCAAAGTTTTAGGCAAAA 57.520 36.364 13.25 0.00 35.59 2.44
143 145 7.368198 ACACCAAATGTTACCCTAAATTTGT 57.632 32.000 0.00 0.00 38.98 2.83
167 169 4.566545 TTTCACCGACGAAACACTACTA 57.433 40.909 0.00 0.00 30.00 1.82
169 171 2.226437 TCACCGACGAAACACTACTACC 59.774 50.000 0.00 0.00 0.00 3.18
179 181 2.601905 ACACTACTACCCCGTTTCACT 58.398 47.619 0.00 0.00 0.00 3.41
217 219 5.616866 GCATAGTTGCGACACTAACACAAAT 60.617 40.000 6.90 0.00 39.49 2.32
225 227 5.670341 GCGACACTAACACAAATATCCACAC 60.670 44.000 0.00 0.00 0.00 3.82
226 228 5.407084 CGACACTAACACAAATATCCACACA 59.593 40.000 0.00 0.00 0.00 3.72
227 229 6.073494 CGACACTAACACAAATATCCACACAA 60.073 38.462 0.00 0.00 0.00 3.33
228 230 7.519168 CGACACTAACACAAATATCCACACAAA 60.519 37.037 0.00 0.00 0.00 2.83
229 231 8.001881 ACACTAACACAAATATCCACACAAAA 57.998 30.769 0.00 0.00 0.00 2.44
230 232 8.470805 ACACTAACACAAATATCCACACAAAAA 58.529 29.630 0.00 0.00 0.00 1.94
234 236 8.954950 AACACAAATATCCACACAAAAATTCA 57.045 26.923 0.00 0.00 0.00 2.57
235 237 8.592105 ACACAAATATCCACACAAAAATTCAG 57.408 30.769 0.00 0.00 0.00 3.02
236 238 8.420222 ACACAAATATCCACACAAAAATTCAGA 58.580 29.630 0.00 0.00 0.00 3.27
237 239 9.258826 CACAAATATCCACACAAAAATTCAGAA 57.741 29.630 0.00 0.00 0.00 3.02
288 290 0.108756 GGTACTGTTCGTCCAGGAGC 60.109 60.000 0.00 6.04 36.69 4.70
294 296 0.169009 GTTCGTCCAGGAGCAAATGC 59.831 55.000 0.00 0.00 42.49 3.56
313 315 3.373565 CCCAGAGCCAAAACGCCC 61.374 66.667 0.00 0.00 0.00 6.13
317 319 2.034221 GAGCCAAAACGCCCCTCT 59.966 61.111 0.00 0.00 0.00 3.69
319 321 3.431725 GCCAAAACGCCCCTCTCG 61.432 66.667 0.00 0.00 0.00 4.04
340 342 0.617413 AGCATCTGCAGCTAACCAGT 59.383 50.000 9.47 0.00 45.16 4.00
341 343 0.731417 GCATCTGCAGCTAACCAGTG 59.269 55.000 9.47 0.00 41.59 3.66
342 344 0.731417 CATCTGCAGCTAACCAGTGC 59.269 55.000 9.47 0.00 37.73 4.40
343 345 0.325933 ATCTGCAGCTAACCAGTGCA 59.674 50.000 9.47 0.00 44.80 4.57
344 346 0.325933 TCTGCAGCTAACCAGTGCAT 59.674 50.000 9.47 0.00 45.77 3.96
353 356 3.369471 GCTAACCAGTGCATAGAGACCAA 60.369 47.826 0.00 0.00 0.00 3.67
385 388 3.994392 GAGTGGCTCTTAACATGTCGAAA 59.006 43.478 0.00 0.00 0.00 3.46
386 389 4.385825 AGTGGCTCTTAACATGTCGAAAA 58.614 39.130 0.00 0.00 0.00 2.29
450 453 6.016777 ACAGATGCAGAAAGTTTTAACCTCAG 60.017 38.462 0.00 0.00 0.00 3.35
504 507 2.708216 TCAGTCAAGTGCTGTTTGGA 57.292 45.000 0.00 0.00 35.60 3.53
594 1734 7.432350 TTTGTTGTTGTTGAAAATTCAGCTT 57.568 28.000 10.64 0.00 38.92 3.74
693 1837 2.095466 ACGTGGTGAGTTGTTGTTGTTG 60.095 45.455 0.00 0.00 0.00 3.33
694 1838 2.095466 CGTGGTGAGTTGTTGTTGTTGT 60.095 45.455 0.00 0.00 0.00 3.32
695 1839 3.610585 CGTGGTGAGTTGTTGTTGTTGTT 60.611 43.478 0.00 0.00 0.00 2.83
696 1840 4.378563 CGTGGTGAGTTGTTGTTGTTGTTA 60.379 41.667 0.00 0.00 0.00 2.41
697 1841 5.462405 GTGGTGAGTTGTTGTTGTTGTTAA 58.538 37.500 0.00 0.00 0.00 2.01
698 1842 5.343860 GTGGTGAGTTGTTGTTGTTGTTAAC 59.656 40.000 0.00 0.00 0.00 2.01
699 1843 4.860352 GGTGAGTTGTTGTTGTTGTTAACC 59.140 41.667 2.48 0.00 0.00 2.85
717 1861 2.389715 ACCAACCCTAGCTAGCTGTAG 58.610 52.381 27.68 17.00 0.00 2.74
718 1862 1.689273 CCAACCCTAGCTAGCTGTAGG 59.311 57.143 27.68 24.57 36.33 3.18
719 1863 1.069358 CAACCCTAGCTAGCTGTAGGC 59.931 57.143 27.68 0.00 35.37 3.93
720 1864 0.470268 ACCCTAGCTAGCTGTAGGCC 60.470 60.000 27.68 0.00 43.05 5.19
823 2277 4.980805 TCTTGCGGCGGCGACTTT 62.981 61.111 36.87 0.00 44.10 2.66
1370 2889 1.374343 CCGATGTCGACGAGGAGGAA 61.374 60.000 15.86 0.00 43.02 3.36
1553 3075 6.826231 TGATATGTGATTGTTTTACCATCCGT 59.174 34.615 0.00 0.00 0.00 4.69
1653 3211 7.502120 TTTAGCAATCTCCTTGATGATAAGC 57.498 36.000 0.00 0.00 36.97 3.09
1754 3312 0.550914 TCAGGGCACAACTCTTTGGT 59.449 50.000 0.00 0.00 37.00 3.67
1925 7420 4.090761 TGAGGAACAAGAACAAGCAGAT 57.909 40.909 0.00 0.00 0.00 2.90
2060 7624 1.327764 GAAAAGCGGTTATCTGAGCGG 59.672 52.381 0.00 0.00 40.59 5.52
2108 7672 2.765135 TCTTGCTCTAGCTGAGAAGCAT 59.235 45.455 14.86 0.00 45.39 3.79
2280 7847 2.092968 TCAAGGCGGAAGTAATGCTCAT 60.093 45.455 0.00 0.00 0.00 2.90
2310 7880 9.273016 GCATATATATGGTACGCATATTCCTTT 57.727 33.333 21.50 2.18 34.32 3.11
2357 7937 7.066142 GCATATATGGGATCCTCTAGAGAGAA 58.934 42.308 21.76 6.62 44.74 2.87
2366 7946 5.881923 TCCTCTAGAGAGAAGGTAGTCTC 57.118 47.826 21.76 0.00 44.74 3.36
2579 8184 5.247862 TCTGTGCATTGATTGTGTCATACT 58.752 37.500 0.00 0.00 36.54 2.12
2662 8270 0.911769 TGGTCTGGGTTAGCCATGAG 59.088 55.000 2.75 0.00 36.17 2.90
2774 8382 4.100707 CATGAGCATCGTTTTCATGGTT 57.899 40.909 5.93 0.00 42.69 3.67
2822 8431 2.105766 GGGAAGCAAAGCAATGGAGAT 58.894 47.619 0.00 0.00 0.00 2.75
2843 8453 1.065782 ACGTGCATGCACTAATACCCA 60.066 47.619 39.46 6.09 44.16 4.51
2899 8509 3.645268 CTGGGGCAGGGGTGTAAGC 62.645 68.421 0.00 0.00 0.00 3.09
2901 8511 4.796495 GGGCAGGGGTGTAAGCGG 62.796 72.222 0.00 0.00 33.03 5.52
2922 8532 2.447250 CGCGCTTCGTAGTTAATCTCA 58.553 47.619 5.56 0.00 0.00 3.27
2923 8533 2.850060 CGCGCTTCGTAGTTAATCTCAA 59.150 45.455 5.56 0.00 0.00 3.02
2956 8566 2.895404 TCTAGCTTGAGTTACACGGGTT 59.105 45.455 0.00 0.00 0.00 4.11
2957 8567 2.632987 AGCTTGAGTTACACGGGTTT 57.367 45.000 0.00 0.00 0.00 3.27
2958 8568 2.218603 AGCTTGAGTTACACGGGTTTG 58.781 47.619 0.00 0.00 0.00 2.93
2959 8569 1.944709 GCTTGAGTTACACGGGTTTGT 59.055 47.619 0.00 0.00 0.00 2.83
2960 8570 2.356695 GCTTGAGTTACACGGGTTTGTT 59.643 45.455 0.00 0.00 0.00 2.83
2961 8571 3.790789 GCTTGAGTTACACGGGTTTGTTG 60.791 47.826 0.00 0.00 0.00 3.33
2962 8572 3.263489 TGAGTTACACGGGTTTGTTGA 57.737 42.857 0.00 0.00 0.00 3.18
2963 8573 3.607741 TGAGTTACACGGGTTTGTTGAA 58.392 40.909 0.00 0.00 0.00 2.69
2964 8574 3.623960 TGAGTTACACGGGTTTGTTGAAG 59.376 43.478 0.00 0.00 0.00 3.02
2965 8575 3.613030 AGTTACACGGGTTTGTTGAAGT 58.387 40.909 0.00 0.00 0.00 3.01
2966 8576 4.011698 AGTTACACGGGTTTGTTGAAGTT 58.988 39.130 0.00 0.00 0.00 2.66
2967 8577 2.931512 ACACGGGTTTGTTGAAGTTG 57.068 45.000 0.00 0.00 0.00 3.16
2968 8578 1.135228 ACACGGGTTTGTTGAAGTTGC 60.135 47.619 0.00 0.00 0.00 4.17
2969 8579 1.135257 CACGGGTTTGTTGAAGTTGCA 60.135 47.619 0.00 0.00 0.00 4.08
2970 8580 1.135228 ACGGGTTTGTTGAAGTTGCAC 60.135 47.619 0.00 0.00 0.00 4.57
2971 8581 1.134175 CGGGTTTGTTGAAGTTGCACT 59.866 47.619 0.00 0.00 0.00 4.40
2972 8582 2.356382 CGGGTTTGTTGAAGTTGCACTA 59.644 45.455 0.00 0.00 0.00 2.74
2973 8583 3.548014 CGGGTTTGTTGAAGTTGCACTAG 60.548 47.826 0.00 0.00 0.00 2.57
2974 8584 3.380320 GGGTTTGTTGAAGTTGCACTAGT 59.620 43.478 0.00 0.00 0.00 2.57
2975 8585 4.577283 GGGTTTGTTGAAGTTGCACTAGTA 59.423 41.667 0.00 0.00 0.00 1.82
2976 8586 5.277828 GGGTTTGTTGAAGTTGCACTAGTAG 60.278 44.000 0.00 0.00 0.00 2.57
2977 8587 5.277828 GGTTTGTTGAAGTTGCACTAGTAGG 60.278 44.000 1.45 0.00 0.00 3.18
2978 8588 3.399330 TGTTGAAGTTGCACTAGTAGGC 58.601 45.455 1.45 0.00 0.00 3.93
2979 8589 3.071023 TGTTGAAGTTGCACTAGTAGGCT 59.929 43.478 6.73 0.00 0.00 4.58
2980 8590 3.319137 TGAAGTTGCACTAGTAGGCTG 57.681 47.619 0.00 0.00 0.00 4.85
2981 8591 2.632996 TGAAGTTGCACTAGTAGGCTGT 59.367 45.455 0.00 0.00 0.00 4.40
2982 8592 3.254892 GAAGTTGCACTAGTAGGCTGTC 58.745 50.000 0.00 0.00 0.00 3.51
2983 8593 1.202582 AGTTGCACTAGTAGGCTGTCG 59.797 52.381 0.00 0.00 0.00 4.35
2984 8594 0.108804 TTGCACTAGTAGGCTGTCGC 60.109 55.000 0.00 0.00 0.00 5.19
3010 8620 4.521062 GACGCCGCTCTGCATCCT 62.521 66.667 0.00 0.00 0.00 3.24
3011 8621 4.087892 ACGCCGCTCTGCATCCTT 62.088 61.111 0.00 0.00 0.00 3.36
3012 8622 2.106938 CGCCGCTCTGCATCCTTA 59.893 61.111 0.00 0.00 0.00 2.69
3013 8623 2.240500 CGCCGCTCTGCATCCTTAC 61.241 63.158 0.00 0.00 0.00 2.34
3014 8624 1.889573 GCCGCTCTGCATCCTTACC 60.890 63.158 0.00 0.00 0.00 2.85
3015 8625 1.227674 CCGCTCTGCATCCTTACCC 60.228 63.158 0.00 0.00 0.00 3.69
3016 8626 1.690219 CCGCTCTGCATCCTTACCCT 61.690 60.000 0.00 0.00 0.00 4.34
3017 8627 0.531532 CGCTCTGCATCCTTACCCTG 60.532 60.000 0.00 0.00 0.00 4.45
3018 8628 0.179034 GCTCTGCATCCTTACCCTGG 60.179 60.000 0.00 0.00 0.00 4.45
3019 8629 1.500474 CTCTGCATCCTTACCCTGGA 58.500 55.000 0.00 0.00 38.06 3.86
3020 8630 1.415659 CTCTGCATCCTTACCCTGGAG 59.584 57.143 0.00 0.00 36.99 3.86
3021 8631 0.471617 CTGCATCCTTACCCTGGAGG 59.528 60.000 0.00 0.00 43.78 4.30
3023 8633 2.620234 CATCCTTACCCTGGAGGCA 58.380 57.895 0.00 0.00 40.58 4.75
3024 8634 0.918983 CATCCTTACCCTGGAGGCAA 59.081 55.000 0.00 0.00 40.58 4.52
3025 8635 1.284785 CATCCTTACCCTGGAGGCAAA 59.715 52.381 0.00 0.00 40.58 3.68
3026 8636 1.451449 TCCTTACCCTGGAGGCAAAA 58.549 50.000 0.00 0.00 40.58 2.44
3027 8637 1.354368 TCCTTACCCTGGAGGCAAAAG 59.646 52.381 0.00 0.00 40.58 2.27
3028 8638 1.177401 CTTACCCTGGAGGCAAAAGC 58.823 55.000 0.00 0.00 40.58 3.51
3029 8639 0.777446 TTACCCTGGAGGCAAAAGCT 59.223 50.000 0.00 0.00 40.58 3.74
3030 8640 1.663911 TACCCTGGAGGCAAAAGCTA 58.336 50.000 0.00 0.00 40.58 3.32
3031 8641 0.329596 ACCCTGGAGGCAAAAGCTAG 59.670 55.000 0.00 0.00 40.58 3.42
3032 8642 1.034292 CCCTGGAGGCAAAAGCTAGC 61.034 60.000 6.62 6.62 0.00 3.42
3033 8643 0.322816 CCTGGAGGCAAAAGCTAGCA 60.323 55.000 18.83 0.00 0.00 3.49
3034 8644 1.093159 CTGGAGGCAAAAGCTAGCAG 58.907 55.000 18.83 4.81 0.00 4.24
3035 8645 0.692476 TGGAGGCAAAAGCTAGCAGA 59.308 50.000 18.83 0.00 0.00 4.26
3036 8646 1.073763 TGGAGGCAAAAGCTAGCAGAA 59.926 47.619 18.83 0.00 0.00 3.02
3037 8647 2.162681 GGAGGCAAAAGCTAGCAGAAA 58.837 47.619 18.83 0.00 0.00 2.52
3038 8648 2.558359 GGAGGCAAAAGCTAGCAGAAAA 59.442 45.455 18.83 0.00 0.00 2.29
3039 8649 3.194329 GGAGGCAAAAGCTAGCAGAAAAT 59.806 43.478 18.83 0.00 0.00 1.82
3040 8650 4.419280 GAGGCAAAAGCTAGCAGAAAATC 58.581 43.478 18.83 2.84 0.00 2.17
3041 8651 3.828451 AGGCAAAAGCTAGCAGAAAATCA 59.172 39.130 18.83 0.00 0.00 2.57
3042 8652 3.922850 GGCAAAAGCTAGCAGAAAATCAC 59.077 43.478 18.83 0.00 0.00 3.06
3043 8653 4.321527 GGCAAAAGCTAGCAGAAAATCACT 60.322 41.667 18.83 0.00 0.00 3.41
3044 8654 4.855937 GCAAAAGCTAGCAGAAAATCACTC 59.144 41.667 18.83 0.00 0.00 3.51
3045 8655 5.563475 GCAAAAGCTAGCAGAAAATCACTCA 60.563 40.000 18.83 0.00 0.00 3.41
3046 8656 5.619625 AAAGCTAGCAGAAAATCACTCAC 57.380 39.130 18.83 0.00 0.00 3.51
3047 8657 4.550076 AGCTAGCAGAAAATCACTCACT 57.450 40.909 18.83 0.00 0.00 3.41
3048 8658 4.252073 AGCTAGCAGAAAATCACTCACTG 58.748 43.478 18.83 0.00 0.00 3.66
3051 8661 3.198863 GCAGAAAATCACTCACTGCTG 57.801 47.619 0.00 0.00 46.66 4.41
3052 8662 2.095364 GCAGAAAATCACTCACTGCTGG 60.095 50.000 0.00 0.00 46.66 4.85
3053 8663 3.405831 CAGAAAATCACTCACTGCTGGA 58.594 45.455 0.00 0.00 0.00 3.86
3054 8664 3.817084 CAGAAAATCACTCACTGCTGGAA 59.183 43.478 0.00 0.00 0.00 3.53
3055 8665 3.817647 AGAAAATCACTCACTGCTGGAAC 59.182 43.478 0.00 0.00 0.00 3.62
3056 8666 3.498774 AAATCACTCACTGCTGGAACT 57.501 42.857 0.00 0.00 0.00 3.01
3057 8667 2.469274 ATCACTCACTGCTGGAACTG 57.531 50.000 0.00 0.00 0.00 3.16
3058 8668 0.394192 TCACTCACTGCTGGAACTGG 59.606 55.000 0.00 0.00 0.00 4.00
3059 8669 0.107456 CACTCACTGCTGGAACTGGT 59.893 55.000 0.00 0.00 0.00 4.00
3060 8670 0.394565 ACTCACTGCTGGAACTGGTC 59.605 55.000 0.00 0.00 0.00 4.02
3069 8679 3.633361 GGAACTGGTCCTGGTGAAG 57.367 57.895 3.98 0.00 43.98 3.02
3070 8680 1.056660 GGAACTGGTCCTGGTGAAGA 58.943 55.000 3.98 0.00 43.98 2.87
3071 8681 1.420138 GGAACTGGTCCTGGTGAAGAA 59.580 52.381 3.98 0.00 43.98 2.52
3072 8682 2.158667 GGAACTGGTCCTGGTGAAGAAA 60.159 50.000 3.98 0.00 43.98 2.52
3073 8683 3.551846 GAACTGGTCCTGGTGAAGAAAA 58.448 45.455 0.33 0.00 0.00 2.29
3074 8684 3.214696 ACTGGTCCTGGTGAAGAAAAG 57.785 47.619 0.33 0.00 0.00 2.27
3075 8685 2.777692 ACTGGTCCTGGTGAAGAAAAGA 59.222 45.455 0.33 0.00 0.00 2.52
3076 8686 3.202151 ACTGGTCCTGGTGAAGAAAAGAA 59.798 43.478 0.33 0.00 0.00 2.52
3077 8687 4.207165 CTGGTCCTGGTGAAGAAAAGAAA 58.793 43.478 0.00 0.00 0.00 2.52
3078 8688 3.951680 TGGTCCTGGTGAAGAAAAGAAAC 59.048 43.478 0.00 0.00 0.00 2.78
3079 8689 3.003378 GGTCCTGGTGAAGAAAAGAAACG 59.997 47.826 0.00 0.00 0.00 3.60
3080 8690 3.875134 GTCCTGGTGAAGAAAAGAAACGA 59.125 43.478 0.00 0.00 0.00 3.85
3081 8691 4.024809 GTCCTGGTGAAGAAAAGAAACGAG 60.025 45.833 0.00 0.00 0.00 4.18
3082 8692 3.251004 CCTGGTGAAGAAAAGAAACGAGG 59.749 47.826 0.00 0.00 31.68 4.63
3097 8707 1.379642 CGAGGAGAATTGCTTGGGGC 61.380 60.000 0.00 0.00 42.22 5.80
3113 8723 2.183555 GCTGCTTGGCCTGAATGC 59.816 61.111 3.32 0.00 0.00 3.56
3151 8761 1.662044 CTCAAGGCCAAACACCAGC 59.338 57.895 5.01 0.00 0.00 4.85
3167 8777 1.517242 CAGCTGGTTCTGAAGACCAC 58.483 55.000 5.57 0.00 36.19 4.16
3169 8779 1.202698 AGCTGGTTCTGAAGACCACAC 60.203 52.381 0.00 0.00 0.00 3.82
3172 8782 1.837439 TGGTTCTGAAGACCACACACT 59.163 47.619 0.00 0.00 0.00 3.55
3196 8842 9.032624 ACTAACTGGAAAATGCTTCTAGTACTA 57.967 33.333 1.89 1.89 38.95 1.82
3220 8866 9.712305 CTATTATCTGTGTCTTATTCCGGAAAT 57.288 33.333 23.08 12.31 0.00 2.17
3226 8872 6.851609 TGTGTCTTATTCCGGAAATGAATTG 58.148 36.000 23.08 7.57 34.43 2.32
3230 8876 8.044309 TGTCTTATTCCGGAAATGAATTGTAGA 58.956 33.333 23.08 10.03 34.43 2.59
3232 8878 9.056005 TCTTATTCCGGAAATGAATTGTAGATG 57.944 33.333 23.08 2.20 34.43 2.90
3233 8879 5.499139 TTCCGGAAATGAATTGTAGATGC 57.501 39.130 16.28 0.00 0.00 3.91
3238 8884 5.527214 CGGAAATGAATTGTAGATGCTGGTA 59.473 40.000 0.00 0.00 0.00 3.25
3241 8887 8.416329 GGAAATGAATTGTAGATGCTGGTAAAT 58.584 33.333 0.00 0.00 0.00 1.40
3242 8888 9.807649 GAAATGAATTGTAGATGCTGGTAAATT 57.192 29.630 0.00 0.00 0.00 1.82
3270 8917 3.939592 TCACCACGTGTGTTAATTTCACA 59.060 39.130 15.65 10.65 45.61 3.58
3303 8958 8.191446 GCTATATGTATGTATGTACTGACCCAG 58.809 40.741 0.00 0.00 37.52 4.45
3305 8960 6.808321 ATGTATGTATGTACTGACCCAGTT 57.192 37.500 4.85 0.00 42.59 3.16
3306 8961 5.972935 TGTATGTATGTACTGACCCAGTTG 58.027 41.667 4.85 0.00 42.59 3.16
3307 8962 5.717654 TGTATGTATGTACTGACCCAGTTGA 59.282 40.000 4.85 0.00 42.59 3.18
3308 8963 5.755409 ATGTATGTACTGACCCAGTTGAA 57.245 39.130 4.85 0.00 42.59 2.69
3309 8964 5.554437 TGTATGTACTGACCCAGTTGAAA 57.446 39.130 4.85 0.00 42.59 2.69
3310 8965 5.547465 TGTATGTACTGACCCAGTTGAAAG 58.453 41.667 4.85 0.00 42.59 2.62
3311 8966 4.706842 ATGTACTGACCCAGTTGAAAGT 57.293 40.909 4.85 0.00 42.59 2.66
3312 8967 5.818678 ATGTACTGACCCAGTTGAAAGTA 57.181 39.130 4.85 0.00 42.59 2.24
3313 8968 5.209818 TGTACTGACCCAGTTGAAAGTAG 57.790 43.478 4.85 0.00 42.59 2.57
3314 8969 4.652421 TGTACTGACCCAGTTGAAAGTAGT 59.348 41.667 4.85 0.00 42.59 2.73
3315 8970 4.338379 ACTGACCCAGTTGAAAGTAGTC 57.662 45.455 0.00 0.00 42.59 2.59
3316 8971 3.709653 ACTGACCCAGTTGAAAGTAGTCA 59.290 43.478 0.00 0.00 42.59 3.41
3317 8972 4.163458 ACTGACCCAGTTGAAAGTAGTCAA 59.837 41.667 0.00 0.00 42.59 3.18
3318 8973 5.105567 TGACCCAGTTGAAAGTAGTCAAA 57.894 39.130 0.00 0.00 39.18 2.69
3349 9004 7.985184 GGTGTTAAAACCATTCTTTTCTTCCTT 59.015 33.333 10.17 0.00 40.22 3.36
3359 9014 7.381408 CCATTCTTTTCTTCCTTTTCCGTTTAC 59.619 37.037 0.00 0.00 0.00 2.01
3365 9020 5.001232 TCTTCCTTTTCCGTTTACCTCATG 58.999 41.667 0.00 0.00 0.00 3.07
3370 9025 5.183140 CCTTTTCCGTTTACCTCATGTCAAT 59.817 40.000 0.00 0.00 0.00 2.57
3371 9026 6.294508 CCTTTTCCGTTTACCTCATGTCAATT 60.295 38.462 0.00 0.00 0.00 2.32
3372 9027 5.621197 TTCCGTTTACCTCATGTCAATTG 57.379 39.130 0.00 0.00 0.00 2.32
3373 9028 4.900684 TCCGTTTACCTCATGTCAATTGA 58.099 39.130 3.38 3.38 0.00 2.57
3374 9029 5.309638 TCCGTTTACCTCATGTCAATTGAA 58.690 37.500 10.35 1.23 0.00 2.69
3375 9030 5.180492 TCCGTTTACCTCATGTCAATTGAAC 59.820 40.000 10.35 5.46 0.00 3.18
3376 9031 5.079406 CGTTTACCTCATGTCAATTGAACG 58.921 41.667 10.35 8.54 0.00 3.95
3377 9032 4.678509 TTACCTCATGTCAATTGAACGC 57.321 40.909 10.35 0.00 0.00 4.84
3378 9033 2.503331 ACCTCATGTCAATTGAACGCA 58.497 42.857 10.35 4.62 0.00 5.24
3379 9034 2.884012 ACCTCATGTCAATTGAACGCAA 59.116 40.909 10.35 0.00 38.60 4.85
3380 9035 3.058016 ACCTCATGTCAATTGAACGCAAG 60.058 43.478 10.35 1.65 37.45 4.01
3394 9049 0.942962 CGCAAGGAGATGAAGATGGC 59.057 55.000 0.00 0.00 0.00 4.40
3395 9050 1.744798 CGCAAGGAGATGAAGATGGCA 60.745 52.381 0.00 0.00 0.00 4.92
3396 9051 1.948145 GCAAGGAGATGAAGATGGCAG 59.052 52.381 0.00 0.00 0.00 4.85
3397 9052 2.421107 GCAAGGAGATGAAGATGGCAGA 60.421 50.000 0.00 0.00 0.00 4.26
3398 9053 3.468770 CAAGGAGATGAAGATGGCAGAG 58.531 50.000 0.00 0.00 0.00 3.35
3399 9054 1.417145 AGGAGATGAAGATGGCAGAGC 59.583 52.381 0.00 0.00 0.00 4.09
3400 9055 1.500108 GAGATGAAGATGGCAGAGCG 58.500 55.000 0.00 0.00 0.00 5.03
3401 9056 0.532417 AGATGAAGATGGCAGAGCGC 60.532 55.000 0.00 0.00 41.28 5.92
3402 9057 1.829349 GATGAAGATGGCAGAGCGCG 61.829 60.000 0.00 0.00 43.84 6.86
3403 9058 2.510238 GAAGATGGCAGAGCGCGT 60.510 61.111 8.43 0.00 43.84 6.01
3404 9059 2.806856 GAAGATGGCAGAGCGCGTG 61.807 63.158 8.43 4.89 43.84 5.34
3405 9060 4.827087 AGATGGCAGAGCGCGTGG 62.827 66.667 8.43 3.14 43.84 4.94
3406 9061 4.819761 GATGGCAGAGCGCGTGGA 62.820 66.667 8.43 0.00 43.84 4.02
3411 9066 3.250323 CAGAGCGCGTGGACGATG 61.250 66.667 8.43 0.00 43.02 3.84
3417 9072 3.700961 GCGTGGACGATGCGTATT 58.299 55.556 2.73 0.00 41.37 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 58 3.827722 TGCCTAAAACTTTGCAGGTAGT 58.172 40.909 0.00 0.00 0.00 2.73
60 62 5.296531 ACATTTTTGCCTAAAACTTTGCAGG 59.703 36.000 0.00 0.00 38.48 4.85
121 123 9.688091 AAAAACAAATTTAGGGTAACATTTGGT 57.312 25.926 6.32 0.00 39.79 3.67
162 164 3.947910 TCAAGTGAAACGGGGTAGTAG 57.052 47.619 0.00 0.00 45.86 2.57
167 169 3.449377 ACAATTTTCAAGTGAAACGGGGT 59.551 39.130 5.98 1.03 45.86 4.95
169 171 4.677584 TGACAATTTTCAAGTGAAACGGG 58.322 39.130 5.98 2.04 45.86 5.28
197 199 5.121768 GGATATTTGTGTTAGTGTCGCAACT 59.878 40.000 0.00 0.00 35.50 3.16
198 200 5.106869 TGGATATTTGTGTTAGTGTCGCAAC 60.107 40.000 0.00 0.00 35.50 4.17
203 205 6.795098 TGTGTGGATATTTGTGTTAGTGTC 57.205 37.500 0.00 0.00 0.00 3.67
210 212 8.420222 TCTGAATTTTTGTGTGGATATTTGTGT 58.580 29.630 0.00 0.00 0.00 3.72
264 266 0.104487 TGGACGAACAGTACCGCAAA 59.896 50.000 0.00 0.00 30.72 3.68
265 267 0.319211 CTGGACGAACAGTACCGCAA 60.319 55.000 0.00 0.00 33.81 4.85
266 268 1.287815 CTGGACGAACAGTACCGCA 59.712 57.895 0.00 0.00 33.81 5.69
267 269 1.445582 CCTGGACGAACAGTACCGC 60.446 63.158 9.53 0.00 36.75 5.68
268 270 0.170561 CTCCTGGACGAACAGTACCG 59.829 60.000 0.00 0.00 36.75 4.02
269 271 0.108756 GCTCCTGGACGAACAGTACC 60.109 60.000 0.00 0.00 36.75 3.34
270 272 0.601558 TGCTCCTGGACGAACAGTAC 59.398 55.000 0.00 0.00 36.75 2.73
271 273 1.334160 TTGCTCCTGGACGAACAGTA 58.666 50.000 0.00 0.00 36.75 2.74
272 274 0.468226 TTTGCTCCTGGACGAACAGT 59.532 50.000 0.00 0.00 36.75 3.55
273 275 1.466167 CATTTGCTCCTGGACGAACAG 59.534 52.381 0.00 0.00 38.21 3.16
274 276 1.522668 CATTTGCTCCTGGACGAACA 58.477 50.000 0.00 0.00 0.00 3.18
275 277 0.169009 GCATTTGCTCCTGGACGAAC 59.831 55.000 0.00 0.00 38.21 3.95
276 278 2.555123 GCATTTGCTCCTGGACGAA 58.445 52.632 0.00 0.00 38.21 3.85
277 279 4.301505 GCATTTGCTCCTGGACGA 57.698 55.556 0.00 0.00 38.21 4.20
294 296 2.335712 GGCGTTTTGGCTCTGGGAG 61.336 63.158 0.00 0.00 40.72 4.30
313 315 0.597118 GCTGCAGATGCTACGAGAGG 60.597 60.000 20.43 0.00 42.66 3.69
317 319 1.202417 GGTTAGCTGCAGATGCTACGA 60.202 52.381 20.43 0.00 41.95 3.43
319 321 2.208431 CTGGTTAGCTGCAGATGCTAC 58.792 52.381 20.43 11.32 41.95 3.58
340 342 1.570813 CGCGATTTGGTCTCTATGCA 58.429 50.000 0.00 0.00 0.00 3.96
341 343 0.233332 GCGCGATTTGGTCTCTATGC 59.767 55.000 12.10 0.00 0.00 3.14
342 344 0.861837 GGCGCGATTTGGTCTCTATG 59.138 55.000 12.10 0.00 0.00 2.23
343 345 0.249911 GGGCGCGATTTGGTCTCTAT 60.250 55.000 12.10 0.00 0.00 1.98
344 346 1.143183 GGGCGCGATTTGGTCTCTA 59.857 57.895 12.10 0.00 0.00 2.43
391 394 1.676006 CAGGGTTGTTCTTTGCGTTCT 59.324 47.619 0.00 0.00 0.00 3.01
398 401 8.528044 TTTACATAAACTCAGGGTTGTTCTTT 57.472 30.769 0.00 0.00 38.29 2.52
572 809 6.162079 TCAAGCTGAATTTTCAACAACAACA 58.838 32.000 0.00 0.00 36.64 3.33
576 813 8.816144 TGTAAATCAAGCTGAATTTTCAACAAC 58.184 29.630 10.77 4.51 36.64 3.32
579 816 8.482429 CAGTGTAAATCAAGCTGAATTTTCAAC 58.518 33.333 10.77 5.60 36.64 3.18
693 1837 3.055312 ACAGCTAGCTAGGGTTGGTTAAC 60.055 47.826 18.86 0.00 36.04 2.01
694 1838 3.178865 ACAGCTAGCTAGGGTTGGTTAA 58.821 45.455 18.86 0.00 0.00 2.01
695 1839 2.829023 ACAGCTAGCTAGGGTTGGTTA 58.171 47.619 18.86 0.00 0.00 2.85
696 1840 1.657804 ACAGCTAGCTAGGGTTGGTT 58.342 50.000 18.86 0.00 0.00 3.67
697 1841 2.389715 CTACAGCTAGCTAGGGTTGGT 58.610 52.381 18.86 11.77 0.00 3.67
698 1842 1.689273 CCTACAGCTAGCTAGGGTTGG 59.311 57.143 21.60 18.66 0.00 3.77
699 1843 1.069358 GCCTACAGCTAGCTAGGGTTG 59.931 57.143 27.54 17.84 38.99 3.77
1370 2889 3.199946 TGAAACTGAACTTCACCTCCACT 59.800 43.478 0.00 0.00 0.00 4.00
1504 3026 2.360475 GGGACTGCTCAAGGGTGC 60.360 66.667 0.00 0.00 0.00 5.01
1553 3075 0.957362 TGCAAACCATGATGTCGCAA 59.043 45.000 0.00 0.00 0.00 4.85
1653 3211 0.892755 AATGCCACATCAGCACCAAG 59.107 50.000 0.00 0.00 44.40 3.61
1754 3312 1.229951 AGTGCCCTCCTTCATGGGA 60.230 57.895 1.75 0.00 46.15 4.37
1925 7420 5.180680 CACAGCTTCTGACATTTCATCTTCA 59.819 40.000 0.29 0.00 35.18 3.02
2060 7624 0.103208 CCACCGAGCTCACACCTATC 59.897 60.000 15.40 0.00 0.00 2.08
2108 7672 4.002982 CCTCTTTCAATCCACGACAATGA 58.997 43.478 0.00 0.00 0.00 2.57
2280 7847 9.476202 GAATATGCGTACCATATATATGCAGAA 57.524 33.333 16.08 5.17 45.28 3.02
2310 7880 2.965831 AGCTTAGTGTCACTTGAGGTCA 59.034 45.455 11.54 0.00 0.00 4.02
2357 7937 4.442706 CAAAACACACACAGAGACTACCT 58.557 43.478 0.00 0.00 0.00 3.08
2366 7946 4.737054 AGAGAAAAGCAAAACACACACAG 58.263 39.130 0.00 0.00 0.00 3.66
2408 7992 6.126968 TGGATTCTTCAGATTCAGCATACAGA 60.127 38.462 0.00 0.00 0.00 3.41
2459 8052 9.347240 CACCTGAATTGATAAACTATCCATTCT 57.653 33.333 15.79 1.34 42.91 2.40
2475 8074 2.991190 GTTGATGCTTGCACCTGAATTG 59.009 45.455 0.00 0.00 0.00 2.32
2579 8184 6.699642 GGCTACTAGAAAAACAACAAATGCAA 59.300 34.615 0.00 0.00 0.00 4.08
2774 8382 5.947228 AACAGAAGCAGATTTCGAAATCA 57.053 34.783 38.54 11.72 45.59 2.57
2843 8453 1.938657 CTCGTCACAGCATCTCCGGT 61.939 60.000 0.00 0.00 0.00 5.28
2899 8509 1.477030 ATTAACTACGAAGCGCGCCG 61.477 55.000 30.33 27.05 46.04 6.46
2901 8511 1.187487 GAGATTAACTACGAAGCGCGC 59.813 52.381 26.66 26.66 46.04 6.86
2923 8533 9.863845 GTAACTCAAGCTAGAACTAATTTCTCT 57.136 33.333 0.00 0.00 44.02 3.10
2948 8558 1.135228 GCAACTTCAACAAACCCGTGT 60.135 47.619 0.00 0.00 0.00 4.49
2963 8573 4.600712 GCGACAGCCTACTAGTGCAACT 62.601 54.545 5.39 0.00 44.66 3.16
2964 8574 1.630148 CGACAGCCTACTAGTGCAAC 58.370 55.000 5.39 0.00 0.00 4.17
2965 8575 0.108804 GCGACAGCCTACTAGTGCAA 60.109 55.000 5.39 0.00 37.42 4.08
2966 8576 1.511305 GCGACAGCCTACTAGTGCA 59.489 57.895 5.39 0.00 37.42 4.57
2967 8577 4.403976 GCGACAGCCTACTAGTGC 57.596 61.111 5.39 0.66 37.42 4.40
2993 8603 2.629050 TAAGGATGCAGAGCGGCGTC 62.629 60.000 9.37 10.57 46.62 5.19
2994 8604 2.721167 TAAGGATGCAGAGCGGCGT 61.721 57.895 9.37 0.00 36.28 5.68
2995 8605 2.106938 TAAGGATGCAGAGCGGCG 59.893 61.111 0.51 0.51 36.28 6.46
2996 8606 1.889573 GGTAAGGATGCAGAGCGGC 60.890 63.158 0.00 0.00 0.00 6.53
2997 8607 1.227674 GGGTAAGGATGCAGAGCGG 60.228 63.158 0.00 0.00 0.00 5.52
2998 8608 0.531532 CAGGGTAAGGATGCAGAGCG 60.532 60.000 0.00 0.00 0.00 5.03
2999 8609 0.179034 CCAGGGTAAGGATGCAGAGC 60.179 60.000 0.00 0.00 0.00 4.09
3000 8610 1.415659 CTCCAGGGTAAGGATGCAGAG 59.584 57.143 0.00 0.00 33.99 3.35
3001 8611 1.500474 CTCCAGGGTAAGGATGCAGA 58.500 55.000 0.00 0.00 33.99 4.26
3002 8612 0.471617 CCTCCAGGGTAAGGATGCAG 59.528 60.000 0.00 0.00 34.35 4.41
3003 8613 1.635817 GCCTCCAGGGTAAGGATGCA 61.636 60.000 4.89 0.00 43.59 3.96
3004 8614 1.149401 GCCTCCAGGGTAAGGATGC 59.851 63.158 0.00 0.00 39.12 3.91
3005 8615 0.918983 TTGCCTCCAGGGTAAGGATG 59.081 55.000 0.00 0.00 34.78 3.51
3006 8616 1.681229 TTTGCCTCCAGGGTAAGGAT 58.319 50.000 0.00 0.00 40.62 3.24
3007 8617 1.354368 CTTTTGCCTCCAGGGTAAGGA 59.646 52.381 0.00 0.00 40.62 3.36
3008 8618 1.839424 CTTTTGCCTCCAGGGTAAGG 58.161 55.000 0.00 0.00 40.62 2.69
3009 8619 1.177401 GCTTTTGCCTCCAGGGTAAG 58.823 55.000 0.00 0.00 40.62 2.34
3010 8620 3.356814 GCTTTTGCCTCCAGGGTAA 57.643 52.632 0.00 0.00 40.15 2.85
3022 8632 5.855395 GTGAGTGATTTTCTGCTAGCTTTTG 59.145 40.000 17.23 3.90 0.00 2.44
3023 8633 5.767168 AGTGAGTGATTTTCTGCTAGCTTTT 59.233 36.000 17.23 0.00 0.00 2.27
3024 8634 5.180868 CAGTGAGTGATTTTCTGCTAGCTTT 59.819 40.000 17.23 0.00 0.00 3.51
3025 8635 4.694509 CAGTGAGTGATTTTCTGCTAGCTT 59.305 41.667 17.23 0.00 0.00 3.74
3026 8636 4.252073 CAGTGAGTGATTTTCTGCTAGCT 58.748 43.478 17.23 0.00 0.00 3.32
3027 8637 3.181512 GCAGTGAGTGATTTTCTGCTAGC 60.182 47.826 8.10 8.10 45.14 3.42
3028 8638 4.596801 GCAGTGAGTGATTTTCTGCTAG 57.403 45.455 7.98 0.00 45.14 3.42
3032 8642 3.405831 TCCAGCAGTGAGTGATTTTCTG 58.594 45.455 0.00 0.00 0.00 3.02
3033 8643 3.777106 TCCAGCAGTGAGTGATTTTCT 57.223 42.857 0.00 0.00 0.00 2.52
3034 8644 3.817647 AGTTCCAGCAGTGAGTGATTTTC 59.182 43.478 0.00 0.00 0.00 2.29
3035 8645 3.567164 CAGTTCCAGCAGTGAGTGATTTT 59.433 43.478 0.00 0.00 0.00 1.82
3036 8646 3.144506 CAGTTCCAGCAGTGAGTGATTT 58.855 45.455 0.00 0.00 0.00 2.17
3037 8647 2.551721 CCAGTTCCAGCAGTGAGTGATT 60.552 50.000 0.00 0.00 0.00 2.57
3038 8648 1.002888 CCAGTTCCAGCAGTGAGTGAT 59.997 52.381 0.00 0.00 0.00 3.06
3039 8649 0.394192 CCAGTTCCAGCAGTGAGTGA 59.606 55.000 0.00 0.00 0.00 3.41
3040 8650 0.107456 ACCAGTTCCAGCAGTGAGTG 59.893 55.000 0.00 0.00 0.00 3.51
3041 8651 0.394565 GACCAGTTCCAGCAGTGAGT 59.605 55.000 0.00 0.00 0.00 3.41
3042 8652 0.321122 GGACCAGTTCCAGCAGTGAG 60.321 60.000 0.00 0.00 45.10 3.51
3043 8653 1.754745 GGACCAGTTCCAGCAGTGA 59.245 57.895 0.00 0.00 45.10 3.41
3044 8654 4.386413 GGACCAGTTCCAGCAGTG 57.614 61.111 0.00 0.00 45.10 3.66
3051 8661 1.056660 TCTTCACCAGGACCAGTTCC 58.943 55.000 0.00 0.00 46.33 3.62
3052 8662 2.930826 TTCTTCACCAGGACCAGTTC 57.069 50.000 0.00 0.00 0.00 3.01
3053 8663 3.202151 TCTTTTCTTCACCAGGACCAGTT 59.798 43.478 0.00 0.00 0.00 3.16
3054 8664 2.777692 TCTTTTCTTCACCAGGACCAGT 59.222 45.455 0.00 0.00 0.00 4.00
3055 8665 3.492102 TCTTTTCTTCACCAGGACCAG 57.508 47.619 0.00 0.00 0.00 4.00
3056 8666 3.943671 TTCTTTTCTTCACCAGGACCA 57.056 42.857 0.00 0.00 0.00 4.02
3057 8667 3.003378 CGTTTCTTTTCTTCACCAGGACC 59.997 47.826 0.00 0.00 0.00 4.46
3058 8668 3.875134 TCGTTTCTTTTCTTCACCAGGAC 59.125 43.478 0.00 0.00 0.00 3.85
3059 8669 4.127171 CTCGTTTCTTTTCTTCACCAGGA 58.873 43.478 0.00 0.00 0.00 3.86
3060 8670 3.251004 CCTCGTTTCTTTTCTTCACCAGG 59.749 47.826 0.00 0.00 0.00 4.45
3061 8671 4.127171 TCCTCGTTTCTTTTCTTCACCAG 58.873 43.478 0.00 0.00 0.00 4.00
3062 8672 4.127171 CTCCTCGTTTCTTTTCTTCACCA 58.873 43.478 0.00 0.00 0.00 4.17
3063 8673 4.377897 TCTCCTCGTTTCTTTTCTTCACC 58.622 43.478 0.00 0.00 0.00 4.02
3064 8674 5.986004 TTCTCCTCGTTTCTTTTCTTCAC 57.014 39.130 0.00 0.00 0.00 3.18
3065 8675 6.513393 GCAATTCTCCTCGTTTCTTTTCTTCA 60.513 38.462 0.00 0.00 0.00 3.02
3066 8676 5.853810 GCAATTCTCCTCGTTTCTTTTCTTC 59.146 40.000 0.00 0.00 0.00 2.87
3067 8677 5.532779 AGCAATTCTCCTCGTTTCTTTTCTT 59.467 36.000 0.00 0.00 0.00 2.52
3068 8678 5.066593 AGCAATTCTCCTCGTTTCTTTTCT 58.933 37.500 0.00 0.00 0.00 2.52
3069 8679 5.363979 AGCAATTCTCCTCGTTTCTTTTC 57.636 39.130 0.00 0.00 0.00 2.29
3070 8680 5.507985 CCAAGCAATTCTCCTCGTTTCTTTT 60.508 40.000 0.00 0.00 0.00 2.27
3071 8681 4.022849 CCAAGCAATTCTCCTCGTTTCTTT 60.023 41.667 0.00 0.00 0.00 2.52
3072 8682 3.503748 CCAAGCAATTCTCCTCGTTTCTT 59.496 43.478 0.00 0.00 0.00 2.52
3073 8683 3.077359 CCAAGCAATTCTCCTCGTTTCT 58.923 45.455 0.00 0.00 0.00 2.52
3074 8684 2.162408 CCCAAGCAATTCTCCTCGTTTC 59.838 50.000 0.00 0.00 0.00 2.78
3075 8685 2.162681 CCCAAGCAATTCTCCTCGTTT 58.837 47.619 0.00 0.00 0.00 3.60
3076 8686 1.614317 CCCCAAGCAATTCTCCTCGTT 60.614 52.381 0.00 0.00 0.00 3.85
3077 8687 0.035056 CCCCAAGCAATTCTCCTCGT 60.035 55.000 0.00 0.00 0.00 4.18
3078 8688 1.379642 GCCCCAAGCAATTCTCCTCG 61.380 60.000 0.00 0.00 42.97 4.63
3079 8689 2.498077 GCCCCAAGCAATTCTCCTC 58.502 57.895 0.00 0.00 42.97 3.71
3080 8690 4.772678 GCCCCAAGCAATTCTCCT 57.227 55.556 0.00 0.00 42.97 3.69
3124 8734 2.686106 GGCCTTGAGGTACGGGGA 60.686 66.667 0.00 0.00 37.57 4.81
3128 8738 0.872388 GTGTTTGGCCTTGAGGTACG 59.128 55.000 3.32 0.00 37.57 3.67
3131 8741 0.468029 CTGGTGTTTGGCCTTGAGGT 60.468 55.000 3.32 0.00 37.57 3.85
3151 8761 2.158900 AGTGTGTGGTCTTCAGAACCAG 60.159 50.000 0.00 0.00 33.74 4.00
3163 8773 3.317993 GCATTTTCCAGTTAGTGTGTGGT 59.682 43.478 0.00 0.00 32.73 4.16
3167 8777 5.695851 AGAAGCATTTTCCAGTTAGTGTG 57.304 39.130 0.00 0.00 0.00 3.82
3169 8779 7.819900 AGTACTAGAAGCATTTTCCAGTTAGTG 59.180 37.037 0.00 0.00 0.00 2.74
3196 8842 8.210946 TCATTTCCGGAATAAGACACAGATAAT 58.789 33.333 19.62 0.00 0.00 1.28
3210 8856 5.829924 AGCATCTACAATTCATTTCCGGAAT 59.170 36.000 19.62 5.48 36.57 3.01
3214 8860 4.336433 ACCAGCATCTACAATTCATTTCCG 59.664 41.667 0.00 0.00 0.00 4.30
3226 8872 9.516314 GGTGAAAAATAATTTACCAGCATCTAC 57.484 33.333 0.00 0.00 38.47 2.59
3230 8876 6.811170 CGTGGTGAAAAATAATTTACCAGCAT 59.189 34.615 4.17 0.00 46.02 3.79
3232 8878 6.088883 CACGTGGTGAAAAATAATTTACCAGC 59.911 38.462 7.95 1.07 46.02 4.85
3233 8879 7.142680 ACACGTGGTGAAAAATAATTTACCAG 58.857 34.615 21.57 2.73 46.02 4.00
3274 8921 9.737427 GGTCAGTACATACATACATATAGCATC 57.263 37.037 0.00 0.00 0.00 3.91
3303 8958 5.585047 ACACCTGAGTTTGACTACTTTCAAC 59.415 40.000 0.00 0.00 35.18 3.18
3304 8959 5.741011 ACACCTGAGTTTGACTACTTTCAA 58.259 37.500 0.00 0.00 33.55 2.69
3305 8960 5.353394 ACACCTGAGTTTGACTACTTTCA 57.647 39.130 0.00 0.00 0.00 2.69
3306 8961 7.781548 TTAACACCTGAGTTTGACTACTTTC 57.218 36.000 0.00 0.00 33.07 2.62
3307 8962 8.456471 GTTTTAACACCTGAGTTTGACTACTTT 58.544 33.333 0.00 0.00 33.07 2.66
3308 8963 7.066645 GGTTTTAACACCTGAGTTTGACTACTT 59.933 37.037 3.41 0.00 33.50 2.24
3309 8964 6.541278 GGTTTTAACACCTGAGTTTGACTACT 59.459 38.462 3.41 0.00 33.50 2.57
3310 8965 6.316890 TGGTTTTAACACCTGAGTTTGACTAC 59.683 38.462 11.94 0.00 37.75 2.73
3311 8966 6.416415 TGGTTTTAACACCTGAGTTTGACTA 58.584 36.000 11.94 0.00 37.75 2.59
3312 8967 5.258051 TGGTTTTAACACCTGAGTTTGACT 58.742 37.500 11.94 0.00 37.75 3.41
3313 8968 5.570234 TGGTTTTAACACCTGAGTTTGAC 57.430 39.130 11.94 0.00 37.75 3.18
3314 8969 6.605594 AGAATGGTTTTAACACCTGAGTTTGA 59.394 34.615 11.94 0.00 37.75 2.69
3315 8970 6.805713 AGAATGGTTTTAACACCTGAGTTTG 58.194 36.000 11.94 0.00 37.75 2.93
3316 8971 7.418337 AAGAATGGTTTTAACACCTGAGTTT 57.582 32.000 11.94 0.00 37.75 2.66
3317 8972 7.418337 AAAGAATGGTTTTAACACCTGAGTT 57.582 32.000 11.94 2.53 37.75 3.01
3318 8973 7.342026 AGAAAAGAATGGTTTTAACACCTGAGT 59.658 33.333 11.94 0.00 37.75 3.41
3349 9004 5.765677 TCAATTGACATGAGGTAAACGGAAA 59.234 36.000 3.38 0.00 0.00 3.13
3359 9014 3.495193 CTTGCGTTCAATTGACATGAGG 58.505 45.455 7.89 0.32 0.00 3.86
3365 9020 3.436704 TCATCTCCTTGCGTTCAATTGAC 59.563 43.478 7.89 2.92 0.00 3.18
3370 9025 3.401033 TCTTCATCTCCTTGCGTTCAA 57.599 42.857 0.00 0.00 0.00 2.69
3371 9026 3.264947 CATCTTCATCTCCTTGCGTTCA 58.735 45.455 0.00 0.00 0.00 3.18
3372 9027 2.611292 CCATCTTCATCTCCTTGCGTTC 59.389 50.000 0.00 0.00 0.00 3.95
3373 9028 2.636830 CCATCTTCATCTCCTTGCGTT 58.363 47.619 0.00 0.00 0.00 4.84
3374 9029 1.745141 GCCATCTTCATCTCCTTGCGT 60.745 52.381 0.00 0.00 0.00 5.24
3375 9030 0.942962 GCCATCTTCATCTCCTTGCG 59.057 55.000 0.00 0.00 0.00 4.85
3376 9031 1.948145 CTGCCATCTTCATCTCCTTGC 59.052 52.381 0.00 0.00 0.00 4.01
3377 9032 3.468770 CTCTGCCATCTTCATCTCCTTG 58.531 50.000 0.00 0.00 0.00 3.61
3378 9033 2.158784 GCTCTGCCATCTTCATCTCCTT 60.159 50.000 0.00 0.00 0.00 3.36
3379 9034 1.417145 GCTCTGCCATCTTCATCTCCT 59.583 52.381 0.00 0.00 0.00 3.69
3380 9035 1.873069 CGCTCTGCCATCTTCATCTCC 60.873 57.143 0.00 0.00 0.00 3.71
3394 9049 3.250323 CATCGTCCACGCGCTCTG 61.250 66.667 5.73 0.00 39.60 3.35
3400 9055 3.700961 AATACGCATCGTCCACGC 58.299 55.556 0.00 0.00 41.54 5.34



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

AutoCloner maintained by Alex Coulton.