Multiple sequence alignment - TraesCS4D01G276600

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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 TraesCS4D01G276600 chr4D 100.000 4459 0 0 1 4459 447909336 447913794 0.000000e+00 8235
1 TraesCS4D01G276600 chr4B 92.579 2978 97 50 1194 4083 560663436 560666377 0.000000e+00 4161
2 TraesCS4D01G276600 chr4B 94.163 771 36 3 432 1202 560662507 560663268 0.000000e+00 1166
3 TraesCS4D01G276600 chr4B 92.355 484 22 7 1 472 560662030 560662510 0.000000e+00 675
4 TraesCS4D01G276600 chr4B 89.844 128 10 1 4092 4219 560666753 560666877 1.280000e-35 161
5 TraesCS4D01G276600 chr4A 92.472 1634 65 15 327 1943 19447151 19448743 0.000000e+00 2283
6 TraesCS4D01G276600 chr4A 88.315 1181 66 40 2907 4035 19449761 19450921 0.000000e+00 1351
7 TraesCS4D01G276600 chr4A 86.393 926 46 31 2033 2897 19448887 19449793 0.000000e+00 939
8 TraesCS4D01G276600 chr4A 96.677 331 7 3 1 328 19446604 19446933 8.430000e-152 547
9 TraesCS4D01G276600 chr7D 93.878 245 14 1 4215 4459 422346606 422346849 7.050000e-98 368
10 TraesCS4D01G276600 chr7D 94.215 242 13 1 4218 4459 605537740 605537500 7.050000e-98 368
11 TraesCS4D01G276600 chr7D 92.562 242 15 2 4218 4459 414430723 414430485 1.190000e-90 344
12 TraesCS4D01G276600 chr7D 91.736 242 17 3 4218 4459 27230310 27230072 2.570000e-87 333
13 TraesCS4D01G276600 chr1A 92.623 244 15 2 4216 4459 535305487 535305727 9.180000e-92 348
14 TraesCS4D01G276600 chr1A 92.149 242 16 2 4218 4459 571781750 571781512 5.520000e-89 339
15 TraesCS4D01G276600 chr2B 92.562 242 16 2 4218 4459 235076321 235076560 3.300000e-91 346
16 TraesCS4D01G276600 chr1D 92.181 243 16 3 4218 4459 451046586 451046346 1.540000e-89 340
17 TraesCS4D01G276600 chr3B 91.736 242 18 2 4218 4459 738127457 738127696 7.150000e-88 335
18 TraesCS4D01G276600 chr2D 86.822 129 14 2 392 519 122864231 122864105 1.670000e-29 141
19 TraesCS4D01G276600 chr2A 86.992 123 13 3 392 513 549290306 549290426 7.780000e-28 135
20 TraesCS4D01G276600 chr2A 85.271 129 16 2 392 519 127198287 127198161 3.620000e-26 130
21 TraesCS4D01G276600 chr5D 86.667 120 14 1 392 511 164604967 164604850 1.010000e-26 132
22 TraesCS4D01G276600 chr5D 86.179 123 14 2 392 513 285256745 285256865 3.620000e-26 130
23 TraesCS4D01G276600 chr3A 86.777 121 13 2 395 514 310692050 310691932 1.010000e-26 132
24 TraesCS4D01G276600 chr6D 86.179 123 14 2 392 513 410398399 410398279 3.620000e-26 130


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 TraesCS4D01G276600 chr4D 447909336 447913794 4458 False 8235.00 8235 100.00000 1 4459 1 chr4D.!!$F1 4458
1 TraesCS4D01G276600 chr4B 560662030 560666877 4847 False 1540.75 4161 92.23525 1 4219 4 chr4B.!!$F1 4218
2 TraesCS4D01G276600 chr4A 19446604 19450921 4317 False 1280.00 2283 90.96425 1 4035 4 chr4A.!!$F1 4034

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
415 646 3.872511 TTTTCCTGCTTCGGACGTATA 57.127 42.857 0.00 0.00 31.44 1.47 F
1016 1286 0.820482 TCGATGGATGCCATGCAAGG 60.820 55.000 2.09 2.86 45.26 3.61 F
1068 1338 1.128136 CAGAGCTCGTGCATTGTGAAG 59.872 52.381 12.58 0.00 42.74 3.02 F
2208 2735 0.035439 TTGGATCCTCAACCTTCGGC 60.035 55.000 14.23 0.00 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 2413 0.100503 CGGCCTTAATTCAAAGCCGG 59.899 55.0 18.29 0.00 39.92 6.13 R
2208 2735 0.311165 GCAGCAGCTTCATGGCTATG 59.689 55.0 3.17 3.17 41.00 2.23 R
2340 2867 0.410663 TCTTCCCGGTCACCTCCTTA 59.589 55.0 0.00 0.00 0.00 2.69 R
4249 5263 0.031994 AAAAAGCGGACAAAGCGCAT 59.968 45.0 11.47 0.00 40.04 4.73 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
353 580 7.553881 AAAGTACTCCATCCGTTCATTATTG 57.446 36.000 0.00 0.00 0.00 1.90
407 638 5.500771 GCAAAAAGAACTTTTTCCTGCTTCG 60.501 40.000 18.40 9.10 46.30 3.79
415 646 3.872511 TTTTCCTGCTTCGGACGTATA 57.127 42.857 0.00 0.00 31.44 1.47
528 794 5.281349 GGAGGGGTATTAGTTTCCTTTTCCA 60.281 44.000 0.00 0.00 0.00 3.53
624 890 4.250464 TGTAAGCTGTCCCTTTACATTCG 58.750 43.478 0.00 0.00 0.00 3.34
808 1078 4.253685 GTTTGTGCCTACATCTAGCTTCA 58.746 43.478 0.00 0.00 36.53 3.02
940 1210 4.326826 CAAGGAGAGAGCGATAGAGAGAT 58.673 47.826 0.00 0.00 39.76 2.75
1016 1286 0.820482 TCGATGGATGCCATGCAAGG 60.820 55.000 2.09 2.86 45.26 3.61
1068 1338 1.128136 CAGAGCTCGTGCATTGTGAAG 59.872 52.381 12.58 0.00 42.74 3.02
1587 2033 4.918360 AGGGTGCTGGTGGTGGGA 62.918 66.667 0.00 0.00 0.00 4.37
1809 2261 4.017126 CCTGGAGTTTCAATAGTTTCCCC 58.983 47.826 0.00 0.00 0.00 4.81
1822 2274 2.047061 GTTTCCCCCTTTGCCTTTCTT 58.953 47.619 0.00 0.00 0.00 2.52
1823 2275 2.009681 TTCCCCCTTTGCCTTTCTTC 57.990 50.000 0.00 0.00 0.00 2.87
1824 2276 1.158007 TCCCCCTTTGCCTTTCTTCT 58.842 50.000 0.00 0.00 0.00 2.85
1825 2277 2.354328 TCCCCCTTTGCCTTTCTTCTA 58.646 47.619 0.00 0.00 0.00 2.10
1826 2278 2.926329 TCCCCCTTTGCCTTTCTTCTAT 59.074 45.455 0.00 0.00 0.00 1.98
1827 2279 4.116113 TCCCCCTTTGCCTTTCTTCTATA 58.884 43.478 0.00 0.00 0.00 1.31
1828 2280 4.731929 TCCCCCTTTGCCTTTCTTCTATAT 59.268 41.667 0.00 0.00 0.00 0.86
1904 2359 7.308782 AGTATGCTAGTGTGCTTTTTGATAC 57.691 36.000 0.00 0.00 0.00 2.24
1907 2362 9.046296 GTATGCTAGTGTGCTTTTTGATACTAT 57.954 33.333 0.00 0.00 0.00 2.12
1909 2364 8.648557 TGCTAGTGTGCTTTTTGATACTATAG 57.351 34.615 0.00 0.00 0.00 1.31
1910 2365 8.258007 TGCTAGTGTGCTTTTTGATACTATAGT 58.742 33.333 10.87 10.87 0.00 2.12
1911 2366 8.756864 GCTAGTGTGCTTTTTGATACTATAGTC 58.243 37.037 9.12 0.00 0.00 2.59
1912 2367 9.250624 CTAGTGTGCTTTTTGATACTATAGTCC 57.749 37.037 9.12 3.51 0.00 3.85
1914 2369 8.978472 AGTGTGCTTTTTGATACTATAGTCCTA 58.022 33.333 9.12 0.00 0.00 2.94
1915 2370 9.765795 GTGTGCTTTTTGATACTATAGTCCTAT 57.234 33.333 9.12 0.00 0.00 2.57
1916 2371 9.764363 TGTGCTTTTTGATACTATAGTCCTATG 57.236 33.333 9.12 0.00 0.00 2.23
1917 2372 9.982651 GTGCTTTTTGATACTATAGTCCTATGA 57.017 33.333 9.12 0.00 0.00 2.15
1942 2397 4.580995 CGATATATGCTACTCCCTCCGATT 59.419 45.833 0.00 0.00 0.00 3.34
1956 2413 6.472887 TCCCTCCGATTCATAATAAATGTCC 58.527 40.000 0.00 0.00 0.00 4.02
1988 2445 4.476628 TTAAGGCCGAACTAACCTTAGG 57.523 45.455 0.00 0.00 44.60 2.69
1995 2452 3.683340 CCGAACTAACCTTAGGTCAAAGC 59.317 47.826 3.62 0.00 45.60 3.51
2009 2515 2.531508 GTCAAAGCTGCGACACTTTTTG 59.468 45.455 10.19 0.00 33.92 2.44
2019 2525 4.508492 TGCGACACTTTTTGTTTAGATCGA 59.492 37.500 0.00 0.00 39.17 3.59
2038 2544 4.712476 TCGAAGGGAGTACTGGTATCTAC 58.288 47.826 0.00 0.00 0.00 2.59
2202 2729 2.570135 GAGATGCTTGGATCCTCAACC 58.430 52.381 14.23 5.38 0.00 3.77
2208 2735 0.035439 TTGGATCCTCAACCTTCGGC 60.035 55.000 14.23 0.00 0.00 5.54
2255 2782 0.035439 CCGGTAAAGCTGGTGGACAT 60.035 55.000 0.00 0.00 38.84 3.06
2339 2866 2.044551 GCTGGGGCCTTTGGAGAG 60.045 66.667 0.84 0.00 0.00 3.20
2340 2867 2.911926 GCTGGGGCCTTTGGAGAGT 61.912 63.158 0.84 0.00 0.00 3.24
2379 2906 2.347490 CCTGTTCTGGACGTGGGG 59.653 66.667 0.00 0.00 0.00 4.96
2391 2918 2.362889 GTGGGGGCATGGTCCTTG 60.363 66.667 0.22 0.22 0.00 3.61
2404 2931 2.307392 TGGTCCTTGATCAAATCCGGAA 59.693 45.455 9.01 0.00 32.13 4.30
2420 2947 2.943033 CCGGAAACATCAAGGTATGGTC 59.057 50.000 0.00 0.00 0.00 4.02
2444 2977 7.554835 GTCATGGTTACTTCTCTCTTCTCTCTA 59.445 40.741 0.00 0.00 0.00 2.43
2445 2978 7.554835 TCATGGTTACTTCTCTCTTCTCTCTAC 59.445 40.741 0.00 0.00 0.00 2.59
2446 2979 7.023171 TGGTTACTTCTCTCTTCTCTCTACT 57.977 40.000 0.00 0.00 0.00 2.57
2447 2980 8.148437 TGGTTACTTCTCTCTTCTCTCTACTA 57.852 38.462 0.00 0.00 0.00 1.82
2488 3027 2.568623 AGTGGTTGGCGAAGAAGAAT 57.431 45.000 0.00 0.00 0.00 2.40
2573 3112 2.144482 ACAACGTTCTACCTCGGTTG 57.856 50.000 0.00 1.08 0.00 3.77
2583 3123 2.930826 ACCTCGGTTGATCTTGTTGT 57.069 45.000 0.00 0.00 0.00 3.32
2604 3144 5.305585 TGTTGAGTGGAGTGAGATTTTACC 58.694 41.667 0.00 0.00 0.00 2.85
2606 3146 3.056107 TGAGTGGAGTGAGATTTTACCGG 60.056 47.826 0.00 0.00 0.00 5.28
2616 3156 5.579904 GTGAGATTTTACCGGTTTACCTCTC 59.420 44.000 15.04 17.88 31.70 3.20
2618 3158 5.731591 AGATTTTACCGGTTTACCTCTCTG 58.268 41.667 15.04 0.00 0.00 3.35
2621 3161 1.713297 ACCGGTTTACCTCTCTGTGT 58.287 50.000 0.00 0.00 0.00 3.72
2629 3179 0.472734 ACCTCTCTGTGTCTGGCCTT 60.473 55.000 3.32 0.00 0.00 4.35
2632 3182 2.354203 CCTCTCTGTGTCTGGCCTTTAC 60.354 54.545 3.32 0.00 0.00 2.01
2683 3256 3.367025 CGTGTGTACTTTTGGTAGCTAGC 59.633 47.826 16.08 16.08 0.00 3.42
2687 3260 5.105473 TGTGTACTTTTGGTAGCTAGCTAGG 60.105 44.000 24.78 8.33 0.00 3.02
2772 3345 1.600957 CGAGCGCAATCTCCAATGATT 59.399 47.619 11.47 0.00 37.16 2.57
2852 3430 4.475944 GTGTGTGCACATTCTATTTGACC 58.524 43.478 24.69 5.75 43.97 4.02
2853 3431 4.216257 GTGTGTGCACATTCTATTTGACCT 59.784 41.667 24.69 0.00 43.97 3.85
2854 3432 4.216042 TGTGTGCACATTCTATTTGACCTG 59.784 41.667 24.69 0.00 36.21 4.00
2855 3433 4.455533 GTGTGCACATTCTATTTGACCTGA 59.544 41.667 24.69 0.00 0.00 3.86
2856 3434 5.048782 GTGTGCACATTCTATTTGACCTGAA 60.049 40.000 24.69 0.00 0.00 3.02
2857 3435 5.534278 TGTGCACATTCTATTTGACCTGAAA 59.466 36.000 17.42 0.00 0.00 2.69
2858 3436 6.088824 GTGCACATTCTATTTGACCTGAAAG 58.911 40.000 13.17 0.00 0.00 2.62
2861 3439 6.583806 GCACATTCTATTTGACCTGAAAGTTG 59.416 38.462 0.00 0.00 0.00 3.16
2888 3466 3.708631 ACCTCTCTCTCTCTCTCTCTCTG 59.291 52.174 0.00 0.00 0.00 3.35
2906 3492 5.766590 TCTCTGTCTCTCTCTCTCTCTCTA 58.233 45.833 0.00 0.00 0.00 2.43
2925 3511 2.525105 ACACCTCTCCCTCTCTCTTC 57.475 55.000 0.00 0.00 0.00 2.87
2926 3512 2.000048 ACACCTCTCCCTCTCTCTTCT 59.000 52.381 0.00 0.00 0.00 2.85
2927 3513 2.025321 ACACCTCTCCCTCTCTCTTCTC 60.025 54.545 0.00 0.00 0.00 2.87
2928 3514 2.242196 CACCTCTCCCTCTCTCTTCTCT 59.758 54.545 0.00 0.00 0.00 3.10
2929 3515 2.926329 ACCTCTCCCTCTCTCTTCTCTT 59.074 50.000 0.00 0.00 0.00 2.85
2933 3519 4.850680 TCTCCCTCTCTCTTCTCTTGTAC 58.149 47.826 0.00 0.00 0.00 2.90
2936 3522 3.130340 CCCTCTCTCTTCTCTTGTACAGC 59.870 52.174 0.00 0.00 0.00 4.40
2982 3570 1.904852 CTGGCATGTGCACGTCTGAC 61.905 60.000 9.07 10.61 44.36 3.51
3137 3729 0.462047 CCGTCATGGCTCCAGGTAAC 60.462 60.000 0.00 0.00 0.00 2.50
3141 3733 0.254178 CATGGCTCCAGGTAACAGCT 59.746 55.000 0.00 0.00 41.41 4.24
3180 3772 1.476488 AGCAAACGCTTTCCACAAACT 59.524 42.857 0.00 0.00 35.79 2.66
3182 3774 2.108700 CAAACGCTTTCCACAAACTCG 58.891 47.619 0.00 0.00 0.00 4.18
3185 3777 0.111266 CGCTTTCCACAAACTCGACG 60.111 55.000 0.00 0.00 0.00 5.12
3187 3779 0.234884 CTTTCCACAAACTCGACGGC 59.765 55.000 0.00 0.00 0.00 5.68
3213 3805 3.627395 TTACTGATGCCATTCCGTTCT 57.373 42.857 0.00 0.00 0.00 3.01
3494 4089 4.954970 AGGGCGGTGGTGTTGCAG 62.955 66.667 0.00 0.00 0.00 4.41
3890 4535 2.038033 GCCACTAGTTCCCAGTGTAACA 59.962 50.000 0.00 0.00 41.52 2.41
3913 4558 1.288419 TGTCCAGTTACACATGCGCG 61.288 55.000 0.00 0.00 0.00 6.86
3981 4628 5.343249 GCAGTCACAACTTCTTCATTTTGT 58.657 37.500 0.00 0.00 31.71 2.83
3982 4629 5.807011 GCAGTCACAACTTCTTCATTTTGTT 59.193 36.000 0.00 0.00 31.71 2.83
3983 4630 6.237648 GCAGTCACAACTTCTTCATTTTGTTG 60.238 38.462 0.00 0.00 42.31 3.33
4037 4684 2.818291 TTTACGCCCCCGCTTTACCC 62.818 60.000 0.00 0.00 38.22 3.69
4040 4687 2.920636 GCCCCCGCTTTACCCATA 59.079 61.111 0.00 0.00 0.00 2.74
4083 4730 5.739161 GTCTTACAACAGTTCAAAGTGCAAG 59.261 40.000 0.00 0.00 32.54 4.01
4084 4731 2.879826 ACAACAGTTCAAAGTGCAAGC 58.120 42.857 0.00 0.00 32.54 4.01
4085 4732 1.847999 CAACAGTTCAAAGTGCAAGCG 59.152 47.619 0.00 0.00 32.54 4.68
4086 4733 1.378531 ACAGTTCAAAGTGCAAGCGA 58.621 45.000 0.00 0.00 32.54 4.93
4087 4734 1.742831 ACAGTTCAAAGTGCAAGCGAA 59.257 42.857 0.00 0.00 32.54 4.70
4088 4735 2.163412 ACAGTTCAAAGTGCAAGCGAAA 59.837 40.909 0.00 0.00 32.54 3.46
4089 4736 3.178267 CAGTTCAAAGTGCAAGCGAAAA 58.822 40.909 0.00 0.00 0.00 2.29
4090 4737 3.798337 CAGTTCAAAGTGCAAGCGAAAAT 59.202 39.130 0.00 0.00 0.00 1.82
4094 5108 6.533367 AGTTCAAAGTGCAAGCGAAAATAAAA 59.467 30.769 0.00 0.00 0.00 1.52
4096 5110 7.475771 TCAAAGTGCAAGCGAAAATAAAAAT 57.524 28.000 0.00 0.00 0.00 1.82
4146 5160 3.716006 CGAAGCGCACACCCACAG 61.716 66.667 11.47 0.00 0.00 3.66
4152 5166 0.382515 GCGCACACCCACAGTTTTTA 59.617 50.000 0.30 0.00 0.00 1.52
4153 5167 1.862411 GCGCACACCCACAGTTTTTAC 60.862 52.381 0.30 0.00 0.00 2.01
4154 5168 1.268845 CGCACACCCACAGTTTTTACC 60.269 52.381 0.00 0.00 0.00 2.85
4157 5171 3.118920 GCACACCCACAGTTTTTACCTTT 60.119 43.478 0.00 0.00 0.00 3.11
4162 5176 5.810074 CACCCACAGTTTTTACCTTTCTTTG 59.190 40.000 0.00 0.00 0.00 2.77
4177 5191 4.846779 TTCTTTGGGAAACGGAGAAATG 57.153 40.909 0.00 0.00 0.00 2.32
4193 5207 4.067896 AGAAATGAAGGCACACACAGTAG 58.932 43.478 0.00 0.00 0.00 2.57
4198 5212 1.037493 AGGCACACACAGTAGACGAA 58.963 50.000 0.00 0.00 0.00 3.85
4219 5233 0.911769 ATGGTTTCGGCTGGATGAGA 59.088 50.000 0.00 0.00 0.00 3.27
4220 5234 0.250234 TGGTTTCGGCTGGATGAGAG 59.750 55.000 0.00 0.00 0.00 3.20
4221 5235 1.092345 GGTTTCGGCTGGATGAGAGC 61.092 60.000 0.00 0.00 35.57 4.09
4222 5236 0.391661 GTTTCGGCTGGATGAGAGCA 60.392 55.000 0.00 0.00 38.27 4.26
4223 5237 0.324614 TTTCGGCTGGATGAGAGCAA 59.675 50.000 0.00 0.00 38.27 3.91
4224 5238 0.391661 TTCGGCTGGATGAGAGCAAC 60.392 55.000 0.00 0.00 38.27 4.17
4225 5239 1.220206 CGGCTGGATGAGAGCAACT 59.780 57.895 0.00 0.00 38.27 3.16
4226 5240 0.809241 CGGCTGGATGAGAGCAACTC 60.809 60.000 0.00 4.35 45.11 3.01
4227 5241 0.463474 GGCTGGATGAGAGCAACTCC 60.463 60.000 8.13 0.00 44.34 3.85
4228 5242 0.251354 GCTGGATGAGAGCAACTCCA 59.749 55.000 8.13 0.00 44.34 3.86
4229 5243 1.339438 GCTGGATGAGAGCAACTCCAA 60.339 52.381 8.13 0.00 44.34 3.53
4230 5244 2.354259 CTGGATGAGAGCAACTCCAAC 58.646 52.381 8.13 0.68 44.34 3.77
4231 5245 1.338105 TGGATGAGAGCAACTCCAACG 60.338 52.381 8.13 0.00 44.34 4.10
4232 5246 1.363744 GATGAGAGCAACTCCAACGG 58.636 55.000 8.13 0.00 44.34 4.44
4233 5247 0.036010 ATGAGAGCAACTCCAACGGG 60.036 55.000 8.13 0.00 44.34 5.28
4234 5248 1.376037 GAGAGCAACTCCAACGGGG 60.376 63.158 0.33 0.00 39.53 5.73
4235 5249 3.056328 GAGCAACTCCAACGGGGC 61.056 66.667 0.00 0.00 36.21 5.80
4238 5252 3.047877 CAACTCCAACGGGGCGAC 61.048 66.667 0.00 0.00 36.21 5.19
4250 5264 4.415783 GGCGACCCAAAAGGACAT 57.584 55.556 0.00 0.00 39.89 3.06
4251 5265 1.883021 GGCGACCCAAAAGGACATG 59.117 57.895 0.00 0.00 39.89 3.21
4252 5266 1.212751 GCGACCCAAAAGGACATGC 59.787 57.895 0.00 0.00 39.89 4.06
4253 5267 1.501741 CGACCCAAAAGGACATGCG 59.498 57.895 0.00 0.00 39.89 4.73
4254 5268 1.212751 GACCCAAAAGGACATGCGC 59.787 57.895 0.00 0.00 39.89 6.09
4255 5269 1.228552 ACCCAAAAGGACATGCGCT 60.229 52.632 9.73 0.00 39.89 5.92
4256 5270 0.827507 ACCCAAAAGGACATGCGCTT 60.828 50.000 9.73 0.00 39.89 4.68
4257 5271 0.318120 CCCAAAAGGACATGCGCTTT 59.682 50.000 9.73 0.00 38.24 3.51
4258 5272 1.421382 CCAAAAGGACATGCGCTTTG 58.579 50.000 9.73 9.00 0.00 2.77
4259 5273 1.269726 CCAAAAGGACATGCGCTTTGT 60.270 47.619 14.97 14.97 0.00 2.83
4260 5274 2.053627 CAAAAGGACATGCGCTTTGTC 58.946 47.619 26.05 26.05 42.20 3.18
4270 5284 3.250220 CGCTTTGTCCGCTTTTTGT 57.750 47.368 0.00 0.00 0.00 2.83
4271 5285 1.120437 CGCTTTGTCCGCTTTTTGTC 58.880 50.000 0.00 0.00 0.00 3.18
4272 5286 1.487482 GCTTTGTCCGCTTTTTGTCC 58.513 50.000 0.00 0.00 0.00 4.02
4273 5287 1.753956 CTTTGTCCGCTTTTTGTCCG 58.246 50.000 0.00 0.00 0.00 4.79
4274 5288 1.064952 CTTTGTCCGCTTTTTGTCCGT 59.935 47.619 0.00 0.00 0.00 4.69
4275 5289 1.096416 TTGTCCGCTTTTTGTCCGTT 58.904 45.000 0.00 0.00 0.00 4.44
4276 5290 1.096416 TGTCCGCTTTTTGTCCGTTT 58.904 45.000 0.00 0.00 0.00 3.60
4277 5291 1.202200 TGTCCGCTTTTTGTCCGTTTG 60.202 47.619 0.00 0.00 0.00 2.93
4278 5292 0.382515 TCCGCTTTTTGTCCGTTTGG 59.617 50.000 0.00 0.00 0.00 3.28
4279 5293 0.596341 CCGCTTTTTGTCCGTTTGGG 60.596 55.000 0.00 0.00 35.24 4.12
4280 5294 0.101579 CGCTTTTTGTCCGTTTGGGT 59.898 50.000 0.00 0.00 37.00 4.51
4281 5295 1.847818 GCTTTTTGTCCGTTTGGGTC 58.152 50.000 0.00 0.00 37.00 4.46
4282 5296 1.862411 GCTTTTTGTCCGTTTGGGTCG 60.862 52.381 0.00 0.00 37.00 4.79
4284 5298 1.726533 TTTTGTCCGTTTGGGTCGGC 61.727 55.000 0.00 0.00 46.49 5.54
4285 5299 4.629523 TGTCCGTTTGGGTCGGCC 62.630 66.667 0.00 0.00 46.49 6.13
4310 5324 2.773480 CGTGCGCGTCCGTATTTT 59.227 55.556 12.43 0.00 36.67 1.82
4311 5325 1.989918 CGTGCGCGTCCGTATTTTA 59.010 52.632 12.43 0.00 36.67 1.52
4312 5326 0.366196 CGTGCGCGTCCGTATTTTAA 59.634 50.000 12.43 0.00 36.67 1.52
4313 5327 1.201790 CGTGCGCGTCCGTATTTTAAA 60.202 47.619 12.43 0.00 36.67 1.52
4314 5328 2.721193 CGTGCGCGTCCGTATTTTAAAA 60.721 45.455 12.43 2.51 36.67 1.52
4315 5329 3.419004 GTGCGCGTCCGTATTTTAAAAT 58.581 40.909 17.18 17.18 36.67 1.82
4316 5330 3.847457 GTGCGCGTCCGTATTTTAAAATT 59.153 39.130 18.14 3.85 36.67 1.82
4317 5331 3.846896 TGCGCGTCCGTATTTTAAAATTG 59.153 39.130 18.14 11.28 36.67 2.32
4318 5332 3.238798 GCGCGTCCGTATTTTAAAATTGG 59.761 43.478 18.14 18.55 36.67 3.16
4319 5333 4.405196 CGCGTCCGTATTTTAAAATTGGT 58.595 39.130 18.14 0.00 0.00 3.67
4320 5334 4.492998 CGCGTCCGTATTTTAAAATTGGTC 59.507 41.667 18.14 15.52 0.00 4.02
4321 5335 4.492998 GCGTCCGTATTTTAAAATTGGTCG 59.507 41.667 27.30 27.30 37.34 4.79
4322 5336 5.023286 CGTCCGTATTTTAAAATTGGTCGG 58.977 41.667 25.73 24.89 34.28 4.79
4323 5337 4.794762 GTCCGTATTTTAAAATTGGTCGGC 59.205 41.667 24.59 19.68 36.16 5.54
4324 5338 4.701171 TCCGTATTTTAAAATTGGTCGGCT 59.299 37.500 24.59 6.12 36.16 5.52
4325 5339 5.183522 TCCGTATTTTAAAATTGGTCGGCTT 59.816 36.000 24.59 5.59 36.16 4.35
4326 5340 5.287513 CCGTATTTTAAAATTGGTCGGCTTG 59.712 40.000 18.14 3.98 0.00 4.01
4327 5341 6.087522 CGTATTTTAAAATTGGTCGGCTTGA 58.912 36.000 18.14 0.00 0.00 3.02
4348 5362 3.846430 CCTAACGGGGAGGCCGAC 61.846 72.222 0.00 0.00 34.52 4.79
4349 5363 3.846430 CTAACGGGGAGGCCGACC 61.846 72.222 12.59 12.59 34.52 4.79
4355 5369 3.326900 GGGAGGCCGACCCAAATA 58.673 61.111 28.20 0.00 46.05 1.40
4356 5370 1.844130 GGGAGGCCGACCCAAATAT 59.156 57.895 28.20 0.00 46.05 1.28
4357 5371 0.537371 GGGAGGCCGACCCAAATATG 60.537 60.000 28.20 0.00 46.05 1.78
4358 5372 1.172812 GGAGGCCGACCCAAATATGC 61.173 60.000 10.32 0.00 36.11 3.14
4359 5373 1.152756 AGGCCGACCCAAATATGCC 60.153 57.895 0.00 0.00 39.17 4.40
4360 5374 2.551912 GGCCGACCCAAATATGCCG 61.552 63.158 0.00 0.00 0.00 5.69
4361 5375 2.551912 GCCGACCCAAATATGCCGG 61.552 63.158 0.00 0.00 36.35 6.13
4362 5376 2.551912 CCGACCCAAATATGCCGGC 61.552 63.158 22.73 22.73 0.00 6.13
4363 5377 2.892334 CGACCCAAATATGCCGGCG 61.892 63.158 23.90 7.09 0.00 6.46
4364 5378 1.822186 GACCCAAATATGCCGGCGT 60.822 57.895 27.04 27.04 0.00 5.68
4365 5379 2.058829 GACCCAAATATGCCGGCGTG 62.059 60.000 31.45 17.73 0.00 5.34
4366 5380 1.821759 CCCAAATATGCCGGCGTGA 60.822 57.895 31.45 14.60 0.00 4.35
4367 5381 1.380403 CCCAAATATGCCGGCGTGAA 61.380 55.000 31.45 13.04 0.00 3.18
4368 5382 0.453793 CCAAATATGCCGGCGTGAAA 59.546 50.000 31.45 12.20 0.00 2.69
4369 5383 1.135257 CCAAATATGCCGGCGTGAAAA 60.135 47.619 31.45 11.78 0.00 2.29
4370 5384 2.600731 CAAATATGCCGGCGTGAAAAA 58.399 42.857 31.45 11.34 0.00 1.94
4416 5430 8.696410 AAACATAATTAAACATAAAGTGGCCG 57.304 30.769 0.00 0.00 0.00 6.13
4417 5431 6.801575 ACATAATTAAACATAAAGTGGCCGG 58.198 36.000 0.00 0.00 0.00 6.13
4418 5432 6.378848 ACATAATTAAACATAAAGTGGCCGGT 59.621 34.615 1.90 0.00 0.00 5.28
4419 5433 4.976224 ATTAAACATAAAGTGGCCGGTC 57.024 40.909 0.00 0.00 0.00 4.79
4420 5434 2.279935 AAACATAAAGTGGCCGGTCA 57.720 45.000 3.51 3.51 0.00 4.02
4421 5435 2.279935 AACATAAAGTGGCCGGTCAA 57.720 45.000 12.16 0.00 0.00 3.18
4422 5436 2.279935 ACATAAAGTGGCCGGTCAAA 57.720 45.000 12.16 0.00 0.00 2.69
4423 5437 1.883926 ACATAAAGTGGCCGGTCAAAC 59.116 47.619 12.16 0.00 0.00 2.93
4424 5438 1.135803 CATAAAGTGGCCGGTCAAACG 60.136 52.381 12.16 0.00 0.00 3.60
4425 5439 1.508808 TAAAGTGGCCGGTCAAACGC 61.509 55.000 12.16 0.00 0.00 4.84
4433 5447 3.597728 GGTCAAACGCCGGCCAAA 61.598 61.111 23.46 0.00 0.00 3.28
4434 5448 2.413765 GTCAAACGCCGGCCAAAA 59.586 55.556 23.46 0.00 0.00 2.44
4435 5449 1.660264 GTCAAACGCCGGCCAAAAG 60.660 57.895 23.46 9.08 0.00 2.27
4436 5450 2.122167 TCAAACGCCGGCCAAAAGT 61.122 52.632 23.46 9.87 0.00 2.66
4437 5451 1.660264 CAAACGCCGGCCAAAAGTC 60.660 57.895 23.46 0.00 0.00 3.01
4438 5452 2.852180 AAACGCCGGCCAAAAGTCC 61.852 57.895 23.46 0.00 0.00 3.85
4439 5453 4.572571 ACGCCGGCCAAAAGTCCA 62.573 61.111 23.46 0.00 0.00 4.02
4440 5454 4.038080 CGCCGGCCAAAAGTCCAC 62.038 66.667 23.46 0.00 0.00 4.02
4441 5455 3.680786 GCCGGCCAAAAGTCCACC 61.681 66.667 18.11 0.00 0.00 4.61
4442 5456 2.115266 CCGGCCAAAAGTCCACCT 59.885 61.111 2.24 0.00 0.00 4.00
4443 5457 1.377229 CCGGCCAAAAGTCCACCTA 59.623 57.895 2.24 0.00 0.00 3.08
4444 5458 0.250989 CCGGCCAAAAGTCCACCTAA 60.251 55.000 2.24 0.00 0.00 2.69
4445 5459 1.611519 CGGCCAAAAGTCCACCTAAA 58.388 50.000 2.24 0.00 0.00 1.85
4446 5460 2.167662 CGGCCAAAAGTCCACCTAAAT 58.832 47.619 2.24 0.00 0.00 1.40
4447 5461 2.163613 CGGCCAAAAGTCCACCTAAATC 59.836 50.000 2.24 0.00 0.00 2.17
4448 5462 3.431415 GGCCAAAAGTCCACCTAAATCT 58.569 45.455 0.00 0.00 0.00 2.40
4449 5463 4.595986 GGCCAAAAGTCCACCTAAATCTA 58.404 43.478 0.00 0.00 0.00 1.98
4450 5464 5.014202 GGCCAAAAGTCCACCTAAATCTAA 58.986 41.667 0.00 0.00 0.00 2.10
4451 5465 5.656859 GGCCAAAAGTCCACCTAAATCTAAT 59.343 40.000 0.00 0.00 0.00 1.73
4452 5466 6.831868 GGCCAAAAGTCCACCTAAATCTAATA 59.168 38.462 0.00 0.00 0.00 0.98
4453 5467 7.340999 GGCCAAAAGTCCACCTAAATCTAATAA 59.659 37.037 0.00 0.00 0.00 1.40
4454 5468 8.745590 GCCAAAAGTCCACCTAAATCTAATAAA 58.254 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 4.020751 TGTTGGATCTGCATATCTAGAGGC 60.021 45.833 11.43 2.72 0.00 4.70
390 617 2.349532 CGTCCGAAGCAGGAAAAAGTTC 60.350 50.000 0.00 0.00 42.77 3.01
497 763 2.823959 ACTAATACCCCTCCGTTCACA 58.176 47.619 0.00 0.00 0.00 3.58
528 794 9.883142 TGAAAACCAATCTTTTCAGTACAAAAT 57.117 25.926 0.00 0.00 42.55 1.82
808 1078 5.719085 TCTTCTTTGCCTCTAGTCTCTGAAT 59.281 40.000 0.00 0.00 0.00 2.57
929 1199 7.008719 CACAAACACACAACTATCTCTCTATCG 59.991 40.741 0.00 0.00 0.00 2.92
930 1200 7.815068 ACACAAACACACAACTATCTCTCTATC 59.185 37.037 0.00 0.00 0.00 2.08
940 1210 2.437413 TGGCACACAAACACACAACTA 58.563 42.857 0.00 0.00 0.00 2.24
981 1251 2.734755 TCGATCAATGGCCCAAGAAT 57.265 45.000 0.00 0.00 0.00 2.40
1016 1286 1.340017 TGCCACCATTACCTTGCTCTC 60.340 52.381 0.00 0.00 0.00 3.20
1068 1338 4.626081 CCGACGATGATGGGGCCC 62.626 72.222 18.17 18.17 0.00 5.80
1587 2033 2.048023 CATGCCGGAGTTGCCACAT 61.048 57.895 5.05 0.00 34.35 3.21
1907 2362 9.713713 GAGTAGCATATATCGATCATAGGACTA 57.286 37.037 0.00 4.57 0.00 2.59
1908 2363 7.663905 GGAGTAGCATATATCGATCATAGGACT 59.336 40.741 0.00 0.00 0.00 3.85
1909 2364 7.094549 GGGAGTAGCATATATCGATCATAGGAC 60.095 44.444 0.00 0.00 0.00 3.85
1910 2365 6.943146 GGGAGTAGCATATATCGATCATAGGA 59.057 42.308 0.00 0.00 0.00 2.94
1911 2366 6.945435 AGGGAGTAGCATATATCGATCATAGG 59.055 42.308 0.00 2.01 0.00 2.57
1912 2367 7.120579 GGAGGGAGTAGCATATATCGATCATAG 59.879 44.444 0.00 0.00 0.00 2.23
1914 2369 5.772672 GGAGGGAGTAGCATATATCGATCAT 59.227 44.000 0.00 0.00 0.00 2.45
1915 2370 5.133941 GGAGGGAGTAGCATATATCGATCA 58.866 45.833 0.00 0.00 0.00 2.92
1916 2371 4.214545 CGGAGGGAGTAGCATATATCGATC 59.785 50.000 0.00 0.00 0.00 3.69
1917 2372 4.138290 CGGAGGGAGTAGCATATATCGAT 58.862 47.826 2.16 2.16 0.00 3.59
1918 2373 3.199289 TCGGAGGGAGTAGCATATATCGA 59.801 47.826 0.00 0.00 0.00 3.59
1919 2374 3.542648 TCGGAGGGAGTAGCATATATCG 58.457 50.000 0.00 0.00 0.00 2.92
1942 2397 5.441500 TCAAAGCCGGGACATTTATTATGA 58.558 37.500 2.18 0.00 0.00 2.15
1956 2413 0.100503 CGGCCTTAATTCAAAGCCGG 59.899 55.000 18.29 0.00 39.92 6.13
1974 2431 4.389077 CAGCTTTGACCTAAGGTTAGTTCG 59.611 45.833 0.00 0.00 35.25 3.95
1988 2445 2.475200 AAAAGTGTCGCAGCTTTGAC 57.525 45.000 7.93 7.93 35.40 3.18
1995 2452 4.840772 CGATCTAAACAAAAAGTGTCGCAG 59.159 41.667 0.00 0.00 40.60 5.18
2009 2515 4.401837 ACCAGTACTCCCTTCGATCTAAAC 59.598 45.833 0.00 0.00 0.00 2.01
2038 2544 9.073475 AGAAGCAGAGTTCTAATATACTACTGG 57.927 37.037 0.00 0.00 34.90 4.00
2147 2674 1.621107 CACCTGTTTCATCATTGCGC 58.379 50.000 0.00 0.00 0.00 6.09
2148 2675 1.068402 TGCACCTGTTTCATCATTGCG 60.068 47.619 0.00 0.00 32.42 4.85
2208 2735 0.311165 GCAGCAGCTTCATGGCTATG 59.689 55.000 3.17 3.17 41.00 2.23
2255 2782 1.059584 TGCAACCAGGAGGAGGAACA 61.060 55.000 0.00 0.00 38.69 3.18
2339 2866 0.535797 CTTCCCGGTCACCTCCTTAC 59.464 60.000 0.00 0.00 0.00 2.34
2340 2867 0.410663 TCTTCCCGGTCACCTCCTTA 59.589 55.000 0.00 0.00 0.00 2.69
2379 2906 2.363359 GGATTTGATCAAGGACCATGCC 59.637 50.000 8.41 0.27 0.00 4.40
2391 2918 4.399303 ACCTTGATGTTTCCGGATTTGATC 59.601 41.667 4.15 5.67 0.00 2.92
2404 2931 4.591321 ACCATGACCATACCTTGATGTT 57.409 40.909 0.00 0.00 0.00 2.71
2420 2947 6.773976 AGAGAGAAGAGAGAAGTAACCATG 57.226 41.667 0.00 0.00 0.00 3.66
2444 2977 5.736951 CTAGCAAGCATATCCTTCCTAGT 57.263 43.478 0.00 0.00 31.49 2.57
2488 3027 5.596361 AGAAACAAGTCTCTCTCTTGACTCA 59.404 40.000 11.72 0.00 42.02 3.41
2573 3112 4.380531 TCACTCCACTCAACAACAAGATC 58.619 43.478 0.00 0.00 0.00 2.75
2583 3123 4.562757 CCGGTAAAATCTCACTCCACTCAA 60.563 45.833 0.00 0.00 0.00 3.02
2604 3144 2.352814 CCAGACACAGAGAGGTAAACCG 60.353 54.545 0.00 0.00 42.08 4.44
2606 3146 2.613223 GGCCAGACACAGAGAGGTAAAC 60.613 54.545 0.00 0.00 0.00 2.01
2616 3156 3.751698 GGTAAAGTAAAGGCCAGACACAG 59.248 47.826 5.01 0.00 0.00 3.66
2618 3158 3.501062 GTGGTAAAGTAAAGGCCAGACAC 59.499 47.826 5.01 0.00 0.00 3.67
2621 3161 4.103469 TCAAGTGGTAAAGTAAAGGCCAGA 59.897 41.667 5.01 0.00 0.00 3.86
2629 3179 5.012664 TCAGGCAGATCAAGTGGTAAAGTAA 59.987 40.000 0.00 0.00 0.00 2.24
2632 3182 3.942829 TCAGGCAGATCAAGTGGTAAAG 58.057 45.455 0.00 0.00 0.00 1.85
2660 3210 2.140717 AGCTACCAAAAGTACACACGC 58.859 47.619 0.00 0.00 0.00 5.34
2683 3256 3.449737 TCCCACACGTCTAATTTCCCTAG 59.550 47.826 0.00 0.00 0.00 3.02
2687 3260 3.404899 TGTTCCCACACGTCTAATTTCC 58.595 45.455 0.00 0.00 0.00 3.13
2759 3332 6.039493 GCATGAGTGAGAAATCATTGGAGATT 59.961 38.462 0.00 0.00 39.81 2.40
2772 3345 3.244078 ACAAGGTTACGCATGAGTGAGAA 60.244 43.478 12.80 0.00 0.00 2.87
2845 3423 5.422012 AGGTGTTTCAACTTTCAGGTCAAAT 59.578 36.000 0.00 0.00 0.00 2.32
2852 3430 5.363939 AGAGAGAGGTGTTTCAACTTTCAG 58.636 41.667 7.80 0.00 35.17 3.02
2853 3431 5.129485 AGAGAGAGAGGTGTTTCAACTTTCA 59.871 40.000 7.80 0.00 35.17 2.69
2854 3432 5.606505 AGAGAGAGAGGTGTTTCAACTTTC 58.393 41.667 0.00 0.00 33.25 2.62
2855 3433 5.365314 AGAGAGAGAGAGGTGTTTCAACTTT 59.635 40.000 0.00 0.00 28.17 2.66
2856 3434 4.898861 AGAGAGAGAGAGGTGTTTCAACTT 59.101 41.667 0.00 0.00 28.17 2.66
2857 3435 4.479158 AGAGAGAGAGAGGTGTTTCAACT 58.521 43.478 0.00 0.00 32.17 3.16
2858 3436 4.522789 AGAGAGAGAGAGAGGTGTTTCAAC 59.477 45.833 0.00 0.00 0.00 3.18
2861 3439 4.589908 AGAGAGAGAGAGAGAGGTGTTTC 58.410 47.826 0.00 0.00 0.00 2.78
2888 3466 4.406003 AGGTGTAGAGAGAGAGAGAGAGAC 59.594 50.000 0.00 0.00 0.00 3.36
2906 3492 2.000048 AGAAGAGAGAGGGAGAGGTGT 59.000 52.381 0.00 0.00 0.00 4.16
2982 3570 1.399440 CACAAGCCATCCATCAGAACG 59.601 52.381 0.00 0.00 0.00 3.95
3137 3729 1.209998 CATGCATGTCGAGAGAGCTG 58.790 55.000 18.91 4.03 43.49 4.24
3141 3733 0.249955 TTGCCATGCATGTCGAGAGA 59.750 50.000 24.58 1.49 38.76 3.10
3180 3772 1.803922 CAGTAATGCGTGCCGTCGA 60.804 57.895 0.00 0.00 0.00 4.20
3182 3774 0.301687 CATCAGTAATGCGTGCCGTC 59.698 55.000 0.00 0.00 0.00 4.79
3398 3990 1.690633 TGCCACCATCTCCTCCTCC 60.691 63.158 0.00 0.00 0.00 4.30
3477 4072 4.954970 CTGCAACACCACCGCCCT 62.955 66.667 0.00 0.00 0.00 5.19
3494 4089 1.153086 CATAGCTCACAGGGGTGCC 60.153 63.158 0.00 0.00 44.87 5.01
3495 4090 1.821332 GCATAGCTCACAGGGGTGC 60.821 63.158 0.00 0.00 44.87 5.01
3890 4535 2.677902 CGCATGTGTAACTGGACAGGAT 60.678 50.000 4.14 0.00 38.04 3.24
3913 4558 2.952310 ACCCAACTGTTTTCTCTTCTGC 59.048 45.455 0.00 0.00 0.00 4.26
3981 4628 4.082300 TGCAACAGAAACTTCTTCAAGCAA 60.082 37.500 0.00 0.00 34.74 3.91
3982 4629 3.443329 TGCAACAGAAACTTCTTCAAGCA 59.557 39.130 0.00 0.00 34.74 3.91
3983 4630 4.032703 TGCAACAGAAACTTCTTCAAGC 57.967 40.909 0.00 0.00 34.74 4.01
4037 4684 3.002246 CCCGATCGATGTGTTGGTTTATG 59.998 47.826 18.66 0.00 0.00 1.90
4040 4687 1.271163 ACCCGATCGATGTGTTGGTTT 60.271 47.619 18.66 0.00 0.00 3.27
4146 5160 5.521010 CCGTTTCCCAAAGAAAGGTAAAAAC 59.479 40.000 6.99 0.00 45.11 2.43
4152 5166 2.173996 TCTCCGTTTCCCAAAGAAAGGT 59.826 45.455 6.99 0.00 45.11 3.50
4153 5167 2.858745 TCTCCGTTTCCCAAAGAAAGG 58.141 47.619 1.84 1.84 45.11 3.11
4154 5168 4.911514 TTTCTCCGTTTCCCAAAGAAAG 57.088 40.909 0.00 0.00 45.11 2.62
4157 5171 4.093472 TCATTTCTCCGTTTCCCAAAGA 57.907 40.909 0.00 0.00 0.00 2.52
4162 5176 1.472878 GCCTTCATTTCTCCGTTTCCC 59.527 52.381 0.00 0.00 0.00 3.97
4177 5191 1.000607 TCGTCTACTGTGTGTGCCTTC 60.001 52.381 0.00 0.00 0.00 3.46
4193 5207 0.721718 CAGCCGAAACCATCTTCGTC 59.278 55.000 5.17 0.00 45.31 4.20
4198 5212 0.911769 TCATCCAGCCGAAACCATCT 59.088 50.000 0.00 0.00 0.00 2.90
4209 5223 0.251354 TGGAGTTGCTCTCATCCAGC 59.749 55.000 10.56 0.00 44.40 4.85
4221 5235 3.047877 GTCGCCCCGTTGGAGTTG 61.048 66.667 0.00 0.00 35.07 3.16
4222 5236 4.324991 GGTCGCCCCGTTGGAGTT 62.325 66.667 0.00 0.00 35.07 3.01
4232 5246 1.304134 ATGTCCTTTTGGGTCGCCC 60.304 57.895 7.87 7.87 45.71 6.13
4233 5247 1.883021 CATGTCCTTTTGGGTCGCC 59.117 57.895 0.00 0.00 40.87 5.54
4234 5248 1.212751 GCATGTCCTTTTGGGTCGC 59.787 57.895 0.00 0.00 40.87 5.19
4235 5249 1.501741 CGCATGTCCTTTTGGGTCG 59.498 57.895 0.00 0.00 40.87 4.79
4236 5250 1.212751 GCGCATGTCCTTTTGGGTC 59.787 57.895 0.30 0.00 40.87 4.46
4237 5251 0.827507 AAGCGCATGTCCTTTTGGGT 60.828 50.000 11.47 0.00 40.87 4.51
4238 5252 0.318120 AAAGCGCATGTCCTTTTGGG 59.682 50.000 11.47 0.00 40.87 4.12
4239 5253 1.269726 ACAAAGCGCATGTCCTTTTGG 60.270 47.619 11.47 0.00 42.21 3.28
4240 5254 2.053627 GACAAAGCGCATGTCCTTTTG 58.946 47.619 26.73 20.06 41.02 2.44
4241 5255 2.422276 GACAAAGCGCATGTCCTTTT 57.578 45.000 26.73 8.60 41.02 2.27
4246 5260 2.187599 AAGCGGACAAAGCGCATGTC 62.188 55.000 28.19 28.19 45.08 3.06
4247 5261 1.795170 AAAGCGGACAAAGCGCATGT 61.795 50.000 17.34 17.34 40.04 3.21
4248 5262 0.664166 AAAAGCGGACAAAGCGCATG 60.664 50.000 11.47 11.29 40.04 4.06
4249 5263 0.031994 AAAAAGCGGACAAAGCGCAT 59.968 45.000 11.47 0.00 40.04 4.73
4250 5264 0.869454 CAAAAAGCGGACAAAGCGCA 60.869 50.000 11.47 0.00 40.04 6.09
4251 5265 0.869880 ACAAAAAGCGGACAAAGCGC 60.870 50.000 0.00 0.00 40.04 5.92
4252 5266 1.120437 GACAAAAAGCGGACAAAGCG 58.880 50.000 0.00 0.00 40.04 4.68
4253 5267 1.487482 GGACAAAAAGCGGACAAAGC 58.513 50.000 0.00 0.00 0.00 3.51
4254 5268 1.064952 ACGGACAAAAAGCGGACAAAG 59.935 47.619 0.00 0.00 0.00 2.77
4255 5269 1.096416 ACGGACAAAAAGCGGACAAA 58.904 45.000 0.00 0.00 0.00 2.83
4256 5270 1.096416 AACGGACAAAAAGCGGACAA 58.904 45.000 0.00 0.00 0.00 3.18
4257 5271 1.096416 AAACGGACAAAAAGCGGACA 58.904 45.000 0.00 0.00 0.00 4.02
4258 5272 1.472990 CAAACGGACAAAAAGCGGAC 58.527 50.000 0.00 0.00 0.00 4.79
4259 5273 0.382515 CCAAACGGACAAAAAGCGGA 59.617 50.000 0.00 0.00 0.00 5.54
4260 5274 0.596341 CCCAAACGGACAAAAAGCGG 60.596 55.000 0.00 0.00 0.00 5.52
4261 5275 0.101579 ACCCAAACGGACAAAAAGCG 59.898 50.000 0.00 0.00 34.64 4.68
4262 5276 1.847818 GACCCAAACGGACAAAAAGC 58.152 50.000 0.00 0.00 34.64 3.51
4263 5277 2.113910 CGACCCAAACGGACAAAAAG 57.886 50.000 0.00 0.00 34.64 2.27
4294 5308 2.507275 TTTAAAATACGGACGCGCAC 57.493 45.000 5.73 0.00 0.00 5.34
4295 5309 3.743567 ATTTTAAAATACGGACGCGCA 57.256 38.095 11.76 0.00 0.00 6.09
4296 5310 3.238798 CCAATTTTAAAATACGGACGCGC 59.761 43.478 18.30 0.00 0.00 6.86
4297 5311 4.405196 ACCAATTTTAAAATACGGACGCG 58.595 39.130 25.33 3.53 0.00 6.01
4298 5312 4.492998 CGACCAATTTTAAAATACGGACGC 59.507 41.667 25.66 17.20 34.92 5.19
4299 5313 5.023286 CCGACCAATTTTAAAATACGGACG 58.977 41.667 27.71 27.71 38.12 4.79
4300 5314 4.794762 GCCGACCAATTTTAAAATACGGAC 59.205 41.667 30.07 23.41 35.33 4.79
4301 5315 4.701171 AGCCGACCAATTTTAAAATACGGA 59.299 37.500 30.07 5.55 35.33 4.69
4302 5316 4.989044 AGCCGACCAATTTTAAAATACGG 58.011 39.130 26.07 26.07 35.84 4.02
4303 5317 6.033091 GTCAAGCCGACCAATTTTAAAATACG 59.967 38.462 13.68 15.02 38.85 3.06
4304 5318 7.273188 GTCAAGCCGACCAATTTTAAAATAC 57.727 36.000 13.68 5.79 38.85 1.89
4337 5351 1.716028 ATATTTGGGTCGGCCTCCCC 61.716 60.000 24.16 21.11 44.00 4.81
4338 5352 0.537371 CATATTTGGGTCGGCCTCCC 60.537 60.000 21.54 21.54 44.81 4.30
4339 5353 1.172812 GCATATTTGGGTCGGCCTCC 61.173 60.000 5.77 2.82 34.45 4.30
4340 5354 1.172812 GGCATATTTGGGTCGGCCTC 61.173 60.000 5.77 0.00 38.37 4.70
4341 5355 1.152756 GGCATATTTGGGTCGGCCT 60.153 57.895 5.77 0.00 38.37 5.19
4342 5356 2.551912 CGGCATATTTGGGTCGGCC 61.552 63.158 0.00 0.00 38.04 6.13
4343 5357 2.551912 CCGGCATATTTGGGTCGGC 61.552 63.158 0.00 0.00 46.07 5.54
4344 5358 3.744559 CCGGCATATTTGGGTCGG 58.255 61.111 0.00 0.00 46.67 4.79
4345 5359 2.892334 CGCCGGCATATTTGGGTCG 61.892 63.158 28.98 0.37 0.00 4.79
4346 5360 1.822186 ACGCCGGCATATTTGGGTC 60.822 57.895 28.98 0.00 0.00 4.46
4347 5361 2.118404 CACGCCGGCATATTTGGGT 61.118 57.895 28.98 10.68 0.00 4.51
4348 5362 1.380403 TTCACGCCGGCATATTTGGG 61.380 55.000 28.98 10.34 0.00 4.12
4349 5363 0.453793 TTTCACGCCGGCATATTTGG 59.546 50.000 28.98 10.77 0.00 3.28
4350 5364 2.270275 TTTTCACGCCGGCATATTTG 57.730 45.000 28.98 14.48 0.00 2.32
4390 5404 9.790389 CGGCCACTTTATGTTTAATTATGTTTA 57.210 29.630 2.24 0.00 0.00 2.01
4391 5405 7.762159 CCGGCCACTTTATGTTTAATTATGTTT 59.238 33.333 2.24 0.00 0.00 2.83
4392 5406 7.093684 ACCGGCCACTTTATGTTTAATTATGTT 60.094 33.333 0.00 0.00 0.00 2.71
4393 5407 6.378848 ACCGGCCACTTTATGTTTAATTATGT 59.621 34.615 0.00 0.00 0.00 2.29
4394 5408 6.801575 ACCGGCCACTTTATGTTTAATTATG 58.198 36.000 0.00 0.00 0.00 1.90
4395 5409 6.603997 TGACCGGCCACTTTATGTTTAATTAT 59.396 34.615 0.00 0.00 0.00 1.28
4396 5410 5.944599 TGACCGGCCACTTTATGTTTAATTA 59.055 36.000 0.00 0.00 0.00 1.40
4397 5411 4.767928 TGACCGGCCACTTTATGTTTAATT 59.232 37.500 0.00 0.00 0.00 1.40
4398 5412 4.337145 TGACCGGCCACTTTATGTTTAAT 58.663 39.130 0.00 0.00 0.00 1.40
4399 5413 3.752665 TGACCGGCCACTTTATGTTTAA 58.247 40.909 0.00 0.00 0.00 1.52
4400 5414 3.420300 TGACCGGCCACTTTATGTTTA 57.580 42.857 0.00 0.00 0.00 2.01
4401 5415 2.279935 TGACCGGCCACTTTATGTTT 57.720 45.000 0.00 0.00 0.00 2.83
4402 5416 2.279935 TTGACCGGCCACTTTATGTT 57.720 45.000 0.00 0.00 0.00 2.71
4403 5417 1.883926 GTTTGACCGGCCACTTTATGT 59.116 47.619 0.00 0.00 0.00 2.29
4404 5418 1.135803 CGTTTGACCGGCCACTTTATG 60.136 52.381 0.00 0.00 0.00 1.90
4405 5419 1.161843 CGTTTGACCGGCCACTTTAT 58.838 50.000 0.00 0.00 0.00 1.40
4406 5420 1.508808 GCGTTTGACCGGCCACTTTA 61.509 55.000 0.00 0.00 0.00 1.85
4407 5421 2.841160 GCGTTTGACCGGCCACTTT 61.841 57.895 0.00 0.00 0.00 2.66
4408 5422 3.284449 GCGTTTGACCGGCCACTT 61.284 61.111 0.00 0.00 0.00 3.16
4416 5430 3.140225 TTTTGGCCGGCGTTTGACC 62.140 57.895 22.54 4.79 0.00 4.02
4417 5431 1.660264 CTTTTGGCCGGCGTTTGAC 60.660 57.895 22.54 5.65 0.00 3.18
4418 5432 2.065906 GACTTTTGGCCGGCGTTTGA 62.066 55.000 22.54 4.04 0.00 2.69
4419 5433 1.660264 GACTTTTGGCCGGCGTTTG 60.660 57.895 22.54 11.78 0.00 2.93
4420 5434 2.725641 GACTTTTGGCCGGCGTTT 59.274 55.556 22.54 0.04 0.00 3.60
4421 5435 3.292159 GGACTTTTGGCCGGCGTT 61.292 61.111 22.54 0.00 38.22 4.84
4428 5442 6.775594 ATTAGATTTAGGTGGACTTTTGGC 57.224 37.500 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.