Multiple sequence alignment - TraesCS4B01G302800

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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 TraesCS4B01G302800 chr4B 100.000 3293 0 0 1 3293 590137800 590141092 0.000000e+00 6082.0
1 TraesCS4B01G302800 chr4D 94.063 2358 86 25 819 3151 469562491 469564819 0.000000e+00 3530.0
2 TraesCS4B01G302800 chr4D 85.542 166 8 7 7 172 469559922 469560071 3.400000e-35 159.0
3 TraesCS4B01G302800 chr4A 91.059 2058 109 32 260 2296 1914631 1912628 0.000000e+00 2712.0
4 TraesCS4B01G302800 chr4A 89.394 198 13 2 2493 2686 1912489 1912296 3.280000e-60 243.0
5 TraesCS4B01G302800 chr4A 87.293 181 16 6 1 175 1914887 1914708 2.000000e-47 200.0
6 TraesCS4B01G302800 chr4A 86.986 146 2 6 2321 2452 1912631 1912489 7.360000e-32 148.0
7 TraesCS4B01G302800 chr4A 88.462 52 5 1 2695 2745 1912300 1912249 9.870000e-06 62.1
8 TraesCS4B01G302800 chr7D 88.406 138 16 0 3152 3289 7188926 7189063 2.030000e-37 167.0
9 TraesCS4B01G302800 chr7A 83.562 73 9 3 1891 1963 589238167 589238098 7.630000e-07 65.8
10 TraesCS4B01G302800 chr7B 91.304 46 1 3 1891 1936 546252221 546252179 3.550000e-05 60.2


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 TraesCS4B01G302800 chr4B 590137800 590141092 3292 False 6082.00 6082 100.0000 1 3293 1 chr4B.!!$F1 3292
1 TraesCS4B01G302800 chr4D 469559922 469564819 4897 False 1844.50 3530 89.8025 7 3151 2 chr4D.!!$F1 3144
2 TraesCS4B01G302800 chr4A 1912249 1914887 2638 True 673.02 2712 88.6388 1 2745 5 chr4A.!!$R1 2744

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
40 41 0.179081 AAACCCGCGGATTCTAGAGC 60.179 55.0 30.73 0.0 0.00 4.09 F
505 2025 0.529992 GGGATAGCCGGAGTTGTTCG 60.530 60.0 5.05 0.0 33.83 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 3535 1.144969 AGACGCCGTTGTACATGTTG 58.855 50.0 2.30 0.0 0.0 3.33 R
2303 4175 0.935196 AACACGTGAAGAAAGGTCGC 59.065 50.0 25.01 0.0 0.0 5.19 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
40 41 0.179081 AAACCCGCGGATTCTAGAGC 60.179 55.000 30.73 0.00 0.00 4.09
89 90 2.124901 TAAACCCGGCCGCATCAG 60.125 61.111 22.85 5.30 0.00 2.90
105 106 5.211454 CGCATCAGTCATCAACTAGACTAG 58.789 45.833 8.00 8.00 42.87 2.57
106 107 5.008118 CGCATCAGTCATCAACTAGACTAGA 59.992 44.000 16.55 0.00 42.87 2.43
107 108 6.293900 CGCATCAGTCATCAACTAGACTAGAT 60.294 42.308 16.55 0.98 42.87 1.98
139 145 0.670162 ATTCATGCAATGTAGGCGGC 59.330 50.000 0.00 0.00 46.80 6.53
165 171 6.126565 GGATTCCAGTTTACCAGGGTTACTAT 60.127 42.308 0.00 0.00 0.00 2.12
172 178 7.021251 AGTTTACCAGGGTTACTATATAGGGG 58.979 42.308 14.25 6.20 0.00 4.79
173 179 4.431158 ACCAGGGTTACTATATAGGGGG 57.569 50.000 14.25 6.80 0.00 5.40
174 180 4.006273 ACCAGGGTTACTATATAGGGGGA 58.994 47.826 14.25 0.00 0.00 4.81
175 181 4.428100 ACCAGGGTTACTATATAGGGGGAA 59.572 45.833 14.25 0.51 0.00 3.97
176 182 5.102081 ACCAGGGTTACTATATAGGGGGAAA 60.102 44.000 14.25 0.00 0.00 3.13
178 184 6.333435 CCAGGGTTACTATATAGGGGGAAAAA 59.667 42.308 14.25 0.00 0.00 1.94
217 1492 6.636562 TTTTACCGAAAAACTGGCAAGATA 57.363 33.333 0.00 0.00 32.05 1.98
221 1496 3.751175 CCGAAAAACTGGCAAGATAGACA 59.249 43.478 0.00 0.00 0.00 3.41
244 1519 3.803082 CACACAAGCGGGATGGCG 61.803 66.667 0.00 0.00 38.18 5.69
262 1537 3.888323 TGGCGTGATATGCATGGTTAAAT 59.112 39.130 10.16 0.00 33.98 1.40
263 1538 4.340666 TGGCGTGATATGCATGGTTAAATT 59.659 37.500 10.16 0.00 33.98 1.82
264 1539 4.917415 GGCGTGATATGCATGGTTAAATTC 59.083 41.667 10.16 0.00 33.98 2.17
265 1540 5.507149 GGCGTGATATGCATGGTTAAATTCA 60.507 40.000 10.16 0.00 33.98 2.57
266 1541 5.976534 GCGTGATATGCATGGTTAAATTCAA 59.023 36.000 10.16 0.00 33.98 2.69
267 1542 6.074888 GCGTGATATGCATGGTTAAATTCAAC 60.075 38.462 10.16 0.00 33.98 3.18
319 1821 5.795441 GGTATCAGAATCTTTTTGTTGCGTC 59.205 40.000 0.00 0.00 0.00 5.19
322 1824 3.423206 CAGAATCTTTTTGTTGCGTCAGC 59.577 43.478 0.00 0.00 45.41 4.26
357 1874 1.655654 CTGAGCGTGCGGTATCTCG 60.656 63.158 0.00 0.00 0.00 4.04
377 1894 2.610479 CGCAAGAGTAGAAGCAACCTCA 60.610 50.000 0.00 0.00 43.02 3.86
378 1895 2.739379 GCAAGAGTAGAAGCAACCTCAC 59.261 50.000 0.00 0.00 0.00 3.51
394 1911 0.756294 TCACCGGAGAAGAAGCAACA 59.244 50.000 9.46 0.00 0.00 3.33
410 1927 7.721402 AGAAGCAACACCACTATCTATCTTAG 58.279 38.462 0.00 0.00 0.00 2.18
432 1952 2.561478 ATGTAAGGGTGCAGTTTCGT 57.439 45.000 0.00 0.00 0.00 3.85
466 1986 5.046950 GCAACCTCACTATCTATCTTAGGGG 60.047 48.000 0.00 0.00 0.00 4.79
467 1987 5.952161 ACCTCACTATCTATCTTAGGGGT 57.048 43.478 0.00 0.00 0.00 4.95
468 1988 5.646215 ACCTCACTATCTATCTTAGGGGTG 58.354 45.833 0.00 0.00 0.00 4.61
469 1989 4.464597 CCTCACTATCTATCTTAGGGGTGC 59.535 50.000 0.00 0.00 0.00 5.01
470 1990 4.079970 TCACTATCTATCTTAGGGGTGCG 58.920 47.826 0.00 0.00 0.00 5.34
471 1991 3.193691 CACTATCTATCTTAGGGGTGCGG 59.806 52.174 0.00 0.00 0.00 5.69
472 1992 2.696526 ATCTATCTTAGGGGTGCGGA 57.303 50.000 0.00 0.00 0.00 5.54
489 2009 4.918360 AGTGTGGGGTGCAGGGGA 62.918 66.667 0.00 0.00 0.00 4.81
491 2011 2.126142 TGTGGGGTGCAGGGGATA 59.874 61.111 0.00 0.00 0.00 2.59
498 2018 2.844362 TGCAGGGGATAGCCGGAG 60.844 66.667 5.05 0.00 33.83 4.63
505 2025 0.529992 GGGATAGCCGGAGTTGTTCG 60.530 60.000 5.05 0.00 33.83 3.95
506 2026 1.152383 GGATAGCCGGAGTTGTTCGC 61.152 60.000 5.05 0.00 0.00 4.70
512 2032 3.727146 GGAGTTGTTCGCCGTTGT 58.273 55.556 0.00 0.00 0.00 3.32
514 2034 1.368850 GAGTTGTTCGCCGTTGTGC 60.369 57.895 0.00 0.00 0.00 4.57
530 2050 0.815615 GTGCGGCTTAGAGGAATGGG 60.816 60.000 0.00 0.00 0.00 4.00
535 2055 1.227973 CTTAGAGGAATGGGCGGGC 60.228 63.158 0.00 0.00 0.00 6.13
569 2089 2.670148 GCGGTGGGAGGAGGTTGAT 61.670 63.158 0.00 0.00 0.00 2.57
576 2096 0.621862 GGAGGAGGTTGATGGGAGGT 60.622 60.000 0.00 0.00 0.00 3.85
578 2098 1.210722 GAGGAGGTTGATGGGAGGTTC 59.789 57.143 0.00 0.00 0.00 3.62
587 2107 2.436824 GGGAGGTTCGGAGCAAGC 60.437 66.667 0.00 0.00 0.00 4.01
588 2108 2.436824 GGAGGTTCGGAGCAAGCC 60.437 66.667 0.00 0.00 0.00 4.35
601 2121 2.034879 CAAGCCGGTGCACAGTAGG 61.035 63.158 20.43 16.24 41.13 3.18
610 2130 3.706373 CACAGTAGGCCCCGCAGT 61.706 66.667 0.00 0.00 0.00 4.40
611 2131 2.928396 ACAGTAGGCCCCGCAGTT 60.928 61.111 0.00 0.00 0.00 3.16
691 2211 6.529220 AGGAAGAAGATGAATAGTATGTGGC 58.471 40.000 0.00 0.00 0.00 5.01
692 2212 5.703130 GGAAGAAGATGAATAGTATGTGGCC 59.297 44.000 0.00 0.00 0.00 5.36
715 2235 0.690192 TTCAGGCCGTTGGATGAAGA 59.310 50.000 0.00 0.00 30.34 2.87
716 2236 0.911769 TCAGGCCGTTGGATGAAGAT 59.088 50.000 0.00 0.00 0.00 2.40
719 2239 1.134280 AGGCCGTTGGATGAAGATCTG 60.134 52.381 0.00 0.00 0.00 2.90
722 2242 3.209410 GCCGTTGGATGAAGATCTGAAT 58.791 45.455 0.00 0.00 0.00 2.57
723 2243 4.380531 GCCGTTGGATGAAGATCTGAATA 58.619 43.478 0.00 0.00 0.00 1.75
724 2244 4.212214 GCCGTTGGATGAAGATCTGAATAC 59.788 45.833 0.00 0.00 0.00 1.89
725 2245 4.445718 CCGTTGGATGAAGATCTGAATACG 59.554 45.833 0.00 0.85 0.00 3.06
726 2246 4.445718 CGTTGGATGAAGATCTGAATACGG 59.554 45.833 0.00 0.00 0.00 4.02
727 2247 5.360591 GTTGGATGAAGATCTGAATACGGT 58.639 41.667 0.00 0.00 0.00 4.83
728 2248 5.614324 TGGATGAAGATCTGAATACGGTT 57.386 39.130 0.00 0.00 0.00 4.44
729 2249 5.989477 TGGATGAAGATCTGAATACGGTTT 58.011 37.500 0.00 0.00 0.00 3.27
730 2250 7.119709 TGGATGAAGATCTGAATACGGTTTA 57.880 36.000 0.00 0.00 0.00 2.01
731 2251 7.210174 TGGATGAAGATCTGAATACGGTTTAG 58.790 38.462 0.00 0.00 0.00 1.85
732 2252 7.069455 TGGATGAAGATCTGAATACGGTTTAGA 59.931 37.037 0.00 0.97 0.00 2.10
733 2253 8.091449 GGATGAAGATCTGAATACGGTTTAGAT 58.909 37.037 0.00 8.98 0.00 1.98
742 2262 7.122204 TCTGAATACGGTTTAGATGAGAACTGA 59.878 37.037 2.39 0.00 36.03 3.41
754 2274 3.807553 TGAGAACTGACTGATGCAACAA 58.192 40.909 0.00 0.00 0.00 2.83
760 2280 6.698766 AGAACTGACTGATGCAACAATTTTTC 59.301 34.615 0.00 0.00 0.00 2.29
775 2295 2.337879 TTTTCCAGGTGCACGCTCCT 62.338 55.000 11.45 6.82 40.17 3.69
841 2706 7.938563 TTTTGTTTGTAGATTTTGGAATCCG 57.061 32.000 0.00 0.00 42.16 4.18
842 2707 6.642707 TTGTTTGTAGATTTTGGAATCCGT 57.357 33.333 0.00 0.00 42.16 4.69
843 2708 6.642707 TGTTTGTAGATTTTGGAATCCGTT 57.357 33.333 0.00 0.00 42.16 4.44
844 2709 7.747155 TGTTTGTAGATTTTGGAATCCGTTA 57.253 32.000 0.00 0.00 42.16 3.18
908 2774 4.295051 CAAGACCCCAAAATGTACAAACG 58.705 43.478 0.00 0.00 0.00 3.60
997 2864 1.021390 GCTCAAGCTAAGCTCCGCAA 61.021 55.000 12.56 0.00 38.25 4.85
1080 2950 1.549170 GACCTGTCCGTCTACCACAAT 59.451 52.381 0.00 0.00 0.00 2.71
1091 2961 0.988832 TACCACAATGTCCACCCTCC 59.011 55.000 0.00 0.00 0.00 4.30
1665 3535 4.767255 CTGCTGTCCCAGGTCGGC 62.767 72.222 7.68 7.68 36.39 5.54
1787 3657 1.447140 GGTACACGCCGATGCTGAA 60.447 57.895 0.00 0.00 34.43 3.02
1797 3667 0.107017 CGATGCTGAAGAACCCCCAT 60.107 55.000 0.00 0.00 0.00 4.00
2303 4175 0.320374 TGCAACTAGTTCCCACGAGG 59.680 55.000 4.77 0.00 30.11 4.63
2308 4180 2.280823 CTAGTTCCCACGAGGCGACC 62.281 65.000 0.00 0.00 34.51 4.79
2323 4195 1.070776 GCGACCTTTCTTCACGTGTTC 60.071 52.381 16.51 0.14 0.00 3.18
2324 4196 1.189446 CGACCTTTCTTCACGTGTTCG 59.811 52.381 16.51 5.34 43.34 3.95
2408 4298 7.148154 TGTGATTGTTAATTTGCGGCTTAGTAT 60.148 33.333 0.00 0.00 0.00 2.12
2452 4342 3.435105 TGTGGCATCAAAGTTTGTCAC 57.565 42.857 15.08 16.92 46.15 3.67
2477 4367 4.235025 TGCGCGTGTGTTGTGCTG 62.235 61.111 8.43 0.00 43.10 4.41
2479 4369 2.876879 GCGCGTGTGTTGTGCTGTA 61.877 57.895 8.43 0.00 39.67 2.74
2480 4370 1.083657 CGCGTGTGTTGTGCTGTAC 60.084 57.895 0.00 0.00 0.00 2.90
2481 4371 1.487452 CGCGTGTGTTGTGCTGTACT 61.487 55.000 0.00 0.00 0.00 2.73
2482 4372 1.493772 GCGTGTGTTGTGCTGTACTA 58.506 50.000 0.00 0.00 0.00 1.82
2582 4476 3.249917 CTTGTTTGTTTCGTTTGGCTGT 58.750 40.909 0.00 0.00 0.00 4.40
2599 4493 0.249363 TGTTGCGCAAGGTGTACGTA 60.249 50.000 25.78 0.00 38.28 3.57
2600 4494 0.162294 GTTGCGCAAGGTGTACGTAC 59.838 55.000 25.78 18.90 38.28 3.67
2601 4495 1.276820 TTGCGCAAGGTGTACGTACG 61.277 55.000 21.02 15.01 38.28 3.67
2602 4496 1.730547 GCGCAAGGTGTACGTACGT 60.731 57.895 25.98 25.98 38.28 3.57
2680 4574 2.125512 GGAGTGTACTGGCAGCCG 60.126 66.667 15.89 4.22 0.00 5.52
2726 4620 1.152984 CACAGTGCCCAGACCAACA 60.153 57.895 0.00 0.00 0.00 3.33
2746 4640 1.452651 GGCTAGCATGCAAGCTCCA 60.453 57.895 21.34 2.59 45.26 3.86
2747 4641 0.822532 GGCTAGCATGCAAGCTCCAT 60.823 55.000 21.34 0.00 45.26 3.41
2748 4642 0.311165 GCTAGCATGCAAGCTCCATG 59.689 55.000 21.34 18.19 45.26 3.66
2749 4643 0.952280 CTAGCATGCAAGCTCCATGG 59.048 55.000 21.34 4.97 45.26 3.66
2750 4644 1.105167 TAGCATGCAAGCTCCATGGC 61.105 55.000 21.34 15.93 45.26 4.40
2751 4645 2.717044 GCATGCAAGCTCCATGGCA 61.717 57.895 21.78 12.43 40.24 4.92
2752 4646 4.699192 ATGCAAGCTCCATGGCAT 57.301 50.000 6.96 2.66 41.81 4.40
2753 4647 0.464036 CATGCAAGCTCCATGGCATT 59.536 50.000 6.96 0.00 43.97 3.56
2754 4648 0.464036 ATGCAAGCTCCATGGCATTG 59.536 50.000 6.96 12.40 43.97 2.82
2755 4649 1.520787 GCAAGCTCCATGGCATTGC 60.521 57.895 23.61 23.61 38.26 3.56
2771 4665 3.368843 GCATTGCCTCCTTTCGAAATTTG 59.631 43.478 11.70 3.59 0.00 2.32
2785 4679 9.971744 CTTTCGAAATTTGAAGTTTGAACAATT 57.028 25.926 11.70 0.00 36.46 2.32
2806 4700 9.908152 ACAATTATGTTGCTCATGATGATATTG 57.092 29.630 0.00 2.17 35.91 1.90
2826 4720 2.498481 TGTCGAAATAGGACCGATGGTT 59.502 45.455 0.00 0.00 35.25 3.67
2848 4742 8.671921 TGGTTGTTTAATACTAACGTTTTGACA 58.328 29.630 5.91 2.13 0.00 3.58
2862 4756 5.971202 ACGTTTTGACAATTAGTTCTTGCAG 59.029 36.000 0.00 0.00 0.00 4.41
2881 4785 7.391554 TCTTGCAGCTTCTTTATTAAGTCATGT 59.608 33.333 0.00 0.00 32.98 3.21
2908 4812 9.372369 AGTTTCTACTTTAGAGTGCATATTCAC 57.628 33.333 0.00 0.00 36.60 3.18
3071 4982 2.136026 GGGTGGTAGGGGAATGAGAAT 58.864 52.381 0.00 0.00 0.00 2.40
3111 5022 1.559368 AGCCAAGTTTGCATGCCATA 58.441 45.000 16.68 0.00 0.00 2.74
3123 5034 2.353406 GCATGCCATATTCAGAATGGGC 60.353 50.000 24.02 24.02 43.53 5.36
3151 5062 5.480073 TCCCTGTTCATTACCATTTGGAAAG 59.520 40.000 3.01 0.00 38.94 2.62
3152 5063 5.480073 CCCTGTTCATTACCATTTGGAAAGA 59.520 40.000 3.01 0.00 38.94 2.52
3153 5064 6.350445 CCCTGTTCATTACCATTTGGAAAGAG 60.350 42.308 3.01 0.00 38.94 2.85
3154 5065 6.209391 CCTGTTCATTACCATTTGGAAAGAGT 59.791 38.462 3.01 0.00 38.94 3.24
3155 5066 7.255942 CCTGTTCATTACCATTTGGAAAGAGTT 60.256 37.037 3.01 0.00 38.94 3.01
3156 5067 8.698973 TGTTCATTACCATTTGGAAAGAGTTA 57.301 30.769 3.01 0.00 38.94 2.24
3157 5068 9.137459 TGTTCATTACCATTTGGAAAGAGTTAA 57.863 29.630 3.01 0.00 38.94 2.01
3158 5069 9.974980 GTTCATTACCATTTGGAAAGAGTTAAA 57.025 29.630 3.01 0.00 38.94 1.52
3164 5075 7.892609 ACCATTTGGAAAGAGTTAAATACACC 58.107 34.615 3.01 0.00 38.94 4.16
3165 5076 7.507616 ACCATTTGGAAAGAGTTAAATACACCA 59.492 33.333 3.01 0.00 38.94 4.17
3166 5077 7.812669 CCATTTGGAAAGAGTTAAATACACCAC 59.187 37.037 0.00 0.00 37.39 4.16
3167 5078 6.548441 TTGGAAAGAGTTAAATACACCACG 57.452 37.500 0.00 0.00 0.00 4.94
3168 5079 5.856156 TGGAAAGAGTTAAATACACCACGA 58.144 37.500 0.00 0.00 0.00 4.35
3169 5080 5.929992 TGGAAAGAGTTAAATACACCACGAG 59.070 40.000 0.00 0.00 0.00 4.18
3170 5081 5.930569 GGAAAGAGTTAAATACACCACGAGT 59.069 40.000 0.00 0.00 0.00 4.18
3179 5090 3.606886 CACCACGAGTGCCTTAACT 57.393 52.632 0.00 0.00 40.28 2.24
3180 5091 1.878953 CACCACGAGTGCCTTAACTT 58.121 50.000 0.00 0.00 40.28 2.66
3181 5092 1.531149 CACCACGAGTGCCTTAACTTG 59.469 52.381 0.00 0.00 40.28 3.16
3182 5093 1.140252 ACCACGAGTGCCTTAACTTGT 59.860 47.619 0.00 0.00 44.15 3.16
3183 5094 1.798813 CCACGAGTGCCTTAACTTGTC 59.201 52.381 0.00 0.00 41.90 3.18
3184 5095 1.798813 CACGAGTGCCTTAACTTGTCC 59.201 52.381 0.00 0.00 41.90 4.02
3185 5096 1.692519 ACGAGTGCCTTAACTTGTCCT 59.307 47.619 0.00 0.00 40.14 3.85
3186 5097 2.895404 ACGAGTGCCTTAACTTGTCCTA 59.105 45.455 0.00 0.00 40.14 2.94
3187 5098 3.514309 ACGAGTGCCTTAACTTGTCCTAT 59.486 43.478 0.00 0.00 40.14 2.57
3188 5099 3.865745 CGAGTGCCTTAACTTGTCCTATG 59.134 47.826 0.00 0.00 0.00 2.23
3189 5100 3.610911 AGTGCCTTAACTTGTCCTATGC 58.389 45.455 0.00 0.00 0.00 3.14
3190 5101 2.351726 GTGCCTTAACTTGTCCTATGCG 59.648 50.000 0.00 0.00 0.00 4.73
3191 5102 2.235155 TGCCTTAACTTGTCCTATGCGA 59.765 45.455 0.00 0.00 0.00 5.10
3192 5103 3.118408 TGCCTTAACTTGTCCTATGCGAT 60.118 43.478 0.00 0.00 0.00 4.58
3193 5104 3.495001 GCCTTAACTTGTCCTATGCGATC 59.505 47.826 0.00 0.00 0.00 3.69
3194 5105 4.693283 CCTTAACTTGTCCTATGCGATCA 58.307 43.478 0.00 0.00 0.00 2.92
3195 5106 5.116180 CCTTAACTTGTCCTATGCGATCAA 58.884 41.667 0.00 0.00 0.00 2.57
3196 5107 5.760253 CCTTAACTTGTCCTATGCGATCAAT 59.240 40.000 0.00 0.00 0.00 2.57
3197 5108 6.260936 CCTTAACTTGTCCTATGCGATCAATT 59.739 38.462 0.00 0.00 0.00 2.32
3198 5109 7.201732 CCTTAACTTGTCCTATGCGATCAATTT 60.202 37.037 0.00 0.00 0.00 1.82
3199 5110 5.490139 ACTTGTCCTATGCGATCAATTTG 57.510 39.130 0.00 0.00 0.00 2.32
3200 5111 5.185454 ACTTGTCCTATGCGATCAATTTGA 58.815 37.500 0.75 0.75 0.00 2.69
3201 5112 5.824624 ACTTGTCCTATGCGATCAATTTGAT 59.175 36.000 11.64 11.64 40.34 2.57
3202 5113 5.678132 TGTCCTATGCGATCAATTTGATG 57.322 39.130 16.41 9.78 37.20 3.07
3203 5114 5.125356 TGTCCTATGCGATCAATTTGATGT 58.875 37.500 16.41 0.00 37.20 3.06
3204 5115 5.237127 TGTCCTATGCGATCAATTTGATGTC 59.763 40.000 16.41 8.24 37.20 3.06
3205 5116 5.468072 GTCCTATGCGATCAATTTGATGTCT 59.532 40.000 16.41 0.00 37.20 3.41
3206 5117 6.646653 GTCCTATGCGATCAATTTGATGTCTA 59.353 38.462 16.41 1.46 37.20 2.59
3207 5118 7.171508 GTCCTATGCGATCAATTTGATGTCTAA 59.828 37.037 16.41 0.00 37.20 2.10
3208 5119 7.714813 TCCTATGCGATCAATTTGATGTCTAAA 59.285 33.333 16.41 0.00 37.20 1.85
3209 5120 8.013947 CCTATGCGATCAATTTGATGTCTAAAG 58.986 37.037 16.41 6.87 37.20 1.85
3210 5121 6.741992 TGCGATCAATTTGATGTCTAAAGT 57.258 33.333 16.41 0.00 37.20 2.66
3211 5122 7.144722 TGCGATCAATTTGATGTCTAAAGTT 57.855 32.000 16.41 0.00 37.20 2.66
3212 5123 7.022979 TGCGATCAATTTGATGTCTAAAGTTG 58.977 34.615 16.41 0.00 37.20 3.16
3213 5124 7.023575 GCGATCAATTTGATGTCTAAAGTTGT 58.976 34.615 16.41 0.00 37.20 3.32
3214 5125 7.007725 GCGATCAATTTGATGTCTAAAGTTGTG 59.992 37.037 16.41 0.00 37.20 3.33
3215 5126 8.229811 CGATCAATTTGATGTCTAAAGTTGTGA 58.770 33.333 16.41 0.00 37.20 3.58
3216 5127 9.897744 GATCAATTTGATGTCTAAAGTTGTGAA 57.102 29.630 16.41 0.00 37.20 3.18
3237 5148 9.863845 TGTGAAATACATAAAAGTGATACTCGA 57.136 29.630 0.00 0.00 33.42 4.04
3243 5154 9.871238 ATACATAAAAGTGATACTCGAACTTGT 57.129 29.630 0.40 0.00 34.46 3.16
3244 5155 8.240883 ACATAAAAGTGATACTCGAACTTGTC 57.759 34.615 0.40 0.00 34.46 3.18
3245 5156 8.088981 ACATAAAAGTGATACTCGAACTTGTCT 58.911 33.333 0.40 0.00 34.46 3.41
3246 5157 6.771188 AAAAGTGATACTCGAACTTGTCTG 57.229 37.500 0.40 0.00 34.46 3.51
3247 5158 3.839293 AGTGATACTCGAACTTGTCTGC 58.161 45.455 0.00 0.00 0.00 4.26
3248 5159 2.594654 GTGATACTCGAACTTGTCTGCG 59.405 50.000 0.00 0.00 0.00 5.18
3249 5160 1.584308 GATACTCGAACTTGTCTGCGC 59.416 52.381 0.00 0.00 0.00 6.09
3250 5161 0.728129 TACTCGAACTTGTCTGCGCG 60.728 55.000 0.00 0.00 0.00 6.86
3251 5162 2.016704 CTCGAACTTGTCTGCGCGT 61.017 57.895 8.43 0.00 0.00 6.01
3252 5163 2.168621 CGAACTTGTCTGCGCGTG 59.831 61.111 8.43 0.68 0.00 5.34
3253 5164 2.127609 GAACTTGTCTGCGCGTGC 60.128 61.111 15.48 15.48 43.20 5.34
3263 5174 3.981303 GCGCGTGCAAATATGGTG 58.019 55.556 17.66 0.00 42.15 4.17
3264 5175 2.223549 GCGCGTGCAAATATGGTGC 61.224 57.895 17.66 4.96 42.15 5.01
3265 5176 1.586042 CGCGTGCAAATATGGTGCC 60.586 57.895 0.00 1.35 41.49 5.01
3266 5177 1.809207 GCGTGCAAATATGGTGCCT 59.191 52.632 8.71 0.00 41.49 4.75
3267 5178 0.248621 GCGTGCAAATATGGTGCCTC 60.249 55.000 8.71 2.87 41.49 4.70
3268 5179 0.381801 CGTGCAAATATGGTGCCTCC 59.618 55.000 8.71 0.00 41.49 4.30
3269 5180 1.767759 GTGCAAATATGGTGCCTCCT 58.232 50.000 8.71 0.00 41.49 3.69
3270 5181 1.406539 GTGCAAATATGGTGCCTCCTG 59.593 52.381 8.71 0.00 41.49 3.86
3271 5182 1.005805 TGCAAATATGGTGCCTCCTGT 59.994 47.619 8.71 0.00 41.49 4.00
3272 5183 1.678101 GCAAATATGGTGCCTCCTGTC 59.322 52.381 0.99 0.00 35.91 3.51
3273 5184 1.942657 CAAATATGGTGCCTCCTGTCG 59.057 52.381 0.00 0.00 37.07 4.35
3274 5185 1.204146 AATATGGTGCCTCCTGTCGT 58.796 50.000 0.00 0.00 37.07 4.34
3275 5186 2.082140 ATATGGTGCCTCCTGTCGTA 57.918 50.000 0.00 0.00 37.07 3.43
3276 5187 2.082140 TATGGTGCCTCCTGTCGTAT 57.918 50.000 0.00 0.00 37.07 3.06
3277 5188 0.753262 ATGGTGCCTCCTGTCGTATC 59.247 55.000 0.00 0.00 37.07 2.24
3278 5189 1.327690 TGGTGCCTCCTGTCGTATCC 61.328 60.000 0.00 0.00 37.07 2.59
3279 5190 1.442148 GTGCCTCCTGTCGTATCCC 59.558 63.158 0.00 0.00 0.00 3.85
3280 5191 2.125326 TGCCTCCTGTCGTATCCCG 61.125 63.158 0.00 0.00 38.13 5.14
3281 5192 2.857744 GCCTCCTGTCGTATCCCGG 61.858 68.421 0.00 0.00 37.11 5.73
3282 5193 1.455217 CCTCCTGTCGTATCCCGGT 60.455 63.158 0.00 0.00 37.11 5.28
3283 5194 1.734137 CTCCTGTCGTATCCCGGTG 59.266 63.158 0.00 0.00 37.11 4.94
3284 5195 1.000521 TCCTGTCGTATCCCGGTGT 60.001 57.895 0.00 0.00 37.11 4.16
3285 5196 0.255604 TCCTGTCGTATCCCGGTGTA 59.744 55.000 0.00 0.00 37.11 2.90
3286 5197 0.383231 CCTGTCGTATCCCGGTGTAC 59.617 60.000 0.00 1.79 37.11 2.90
3287 5198 0.028505 CTGTCGTATCCCGGTGTACG 59.971 60.000 22.66 22.66 43.61 3.67
3288 5199 1.298638 GTCGTATCCCGGTGTACGC 60.299 63.158 23.42 17.01 42.38 4.42
3289 5200 1.451927 TCGTATCCCGGTGTACGCT 60.452 57.895 23.42 0.00 42.38 5.07
3290 5201 1.031571 TCGTATCCCGGTGTACGCTT 61.032 55.000 23.42 0.00 42.38 4.68
3291 5202 0.179129 CGTATCCCGGTGTACGCTTT 60.179 55.000 18.82 0.00 42.52 3.51
3292 5203 1.283736 GTATCCCGGTGTACGCTTTG 58.716 55.000 6.35 0.00 42.52 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 123 3.117794 CCGCCTACATTGCATGAATTTG 58.882 45.455 0.00 0.00 0.00 2.32
121 127 1.713937 CGCCGCCTACATTGCATGAA 61.714 55.000 0.00 0.00 0.00 2.57
134 140 1.450669 TAAACTGGAATCCGCCGCC 60.451 57.895 0.00 0.00 0.00 6.13
139 145 1.280998 ACCCTGGTAAACTGGAATCCG 59.719 52.381 0.00 0.00 40.42 4.18
195 1470 5.998981 TCTATCTTGCCAGTTTTTCGGTAAA 59.001 36.000 0.00 0.00 0.00 2.01
197 1472 4.933400 GTCTATCTTGCCAGTTTTTCGGTA 59.067 41.667 0.00 0.00 0.00 4.02
198 1473 3.751698 GTCTATCTTGCCAGTTTTTCGGT 59.248 43.478 0.00 0.00 0.00 4.69
204 1479 4.718961 AGTTGTGTCTATCTTGCCAGTTT 58.281 39.130 0.00 0.00 0.00 2.66
217 1492 1.290203 CGCTTGTGTGAGTTGTGTCT 58.710 50.000 0.00 0.00 0.00 3.41
221 1496 0.108585 ATCCCGCTTGTGTGAGTTGT 59.891 50.000 0.00 0.00 0.00 3.32
244 1519 7.975616 AGTGTTGAATTTAACCATGCATATCAC 59.024 33.333 10.29 0.00 0.00 3.06
294 1796 5.473504 ACGCAACAAAAAGATTCTGATACCT 59.526 36.000 0.00 0.00 0.00 3.08
301 1803 3.550842 GGCTGACGCAACAAAAAGATTCT 60.551 43.478 0.00 0.00 38.10 2.40
302 1804 2.726241 GGCTGACGCAACAAAAAGATTC 59.274 45.455 0.00 0.00 38.10 2.52
305 1807 1.098869 TGGCTGACGCAACAAAAAGA 58.901 45.000 0.00 0.00 38.10 2.52
357 1874 2.739379 GTGAGGTTGCTTCTACTCTTGC 59.261 50.000 0.00 0.00 0.00 4.01
359 1876 2.028930 CGGTGAGGTTGCTTCTACTCTT 60.029 50.000 0.00 0.00 0.00 2.85
364 1881 0.895530 CTCCGGTGAGGTTGCTTCTA 59.104 55.000 0.00 0.00 41.99 2.10
377 1894 0.250338 GGTGTTGCTTCTTCTCCGGT 60.250 55.000 0.00 0.00 0.00 5.28
378 1895 0.250295 TGGTGTTGCTTCTTCTCCGG 60.250 55.000 0.00 0.00 0.00 5.14
410 1927 3.252458 ACGAAACTGCACCCTTACATTTC 59.748 43.478 0.00 0.00 0.00 2.17
432 1952 2.436109 GAGGTTGCTGCTCCCCAA 59.564 61.111 0.00 0.00 0.00 4.12
469 1989 4.704833 CCTGCACCCCACACTCCG 62.705 72.222 0.00 0.00 0.00 4.63
470 1990 4.351054 CCCTGCACCCCACACTCC 62.351 72.222 0.00 0.00 0.00 3.85
471 1991 4.351054 CCCCTGCACCCCACACTC 62.351 72.222 0.00 0.00 0.00 3.51
472 1992 2.781258 TATCCCCTGCACCCCACACT 62.781 60.000 0.00 0.00 0.00 3.55
489 2009 1.153429 GGCGAACAACTCCGGCTAT 60.153 57.895 0.00 0.00 45.94 2.97
509 2029 1.678728 CCATTCCTCTAAGCCGCACAA 60.679 52.381 0.00 0.00 0.00 3.33
512 2032 1.526887 CCCATTCCTCTAAGCCGCA 59.473 57.895 0.00 0.00 0.00 5.69
514 2034 1.595382 CGCCCATTCCTCTAAGCCG 60.595 63.158 0.00 0.00 0.00 5.52
569 2089 3.068881 CTTGCTCCGAACCTCCCA 58.931 61.111 0.00 0.00 0.00 4.37
587 2107 4.778143 GGGCCTACTGTGCACCGG 62.778 72.222 15.69 10.55 0.00 5.28
588 2108 4.778143 GGGGCCTACTGTGCACCG 62.778 72.222 15.69 11.05 43.57 4.94
594 2114 2.928396 AACTGCGGGGCCTACTGT 60.928 61.111 0.84 3.14 0.00 3.55
608 2128 3.823330 CTCTACCGCCCGCGAACT 61.823 66.667 8.23 0.00 42.83 3.01
618 2138 0.314302 CCAATAGCCGACCTCTACCG 59.686 60.000 0.00 0.00 0.00 4.02
622 2142 2.444256 GCCCCAATAGCCGACCTCT 61.444 63.158 0.00 0.00 0.00 3.69
627 2147 3.488569 CCCAGCCCCAATAGCCGA 61.489 66.667 0.00 0.00 0.00 5.54
692 2212 0.523072 CATCCAACGGCCTGAAACAG 59.477 55.000 0.00 0.00 0.00 3.16
715 2235 7.923344 CAGTTCTCATCTAAACCGTATTCAGAT 59.077 37.037 0.00 0.00 0.00 2.90
716 2236 7.122204 TCAGTTCTCATCTAAACCGTATTCAGA 59.878 37.037 0.00 0.00 0.00 3.27
719 2239 7.221067 CAGTCAGTTCTCATCTAAACCGTATTC 59.779 40.741 0.00 0.00 0.00 1.75
722 2242 5.708697 TCAGTCAGTTCTCATCTAAACCGTA 59.291 40.000 0.00 0.00 0.00 4.02
723 2243 4.523173 TCAGTCAGTTCTCATCTAAACCGT 59.477 41.667 0.00 0.00 0.00 4.83
724 2244 5.060662 TCAGTCAGTTCTCATCTAAACCG 57.939 43.478 0.00 0.00 0.00 4.44
725 2245 5.293079 GCATCAGTCAGTTCTCATCTAAACC 59.707 44.000 0.00 0.00 0.00 3.27
726 2246 5.871524 TGCATCAGTCAGTTCTCATCTAAAC 59.128 40.000 0.00 0.00 0.00 2.01
727 2247 6.041423 TGCATCAGTCAGTTCTCATCTAAA 57.959 37.500 0.00 0.00 0.00 1.85
728 2248 5.665916 TGCATCAGTCAGTTCTCATCTAA 57.334 39.130 0.00 0.00 0.00 2.10
729 2249 5.047092 TGTTGCATCAGTCAGTTCTCATCTA 60.047 40.000 0.00 0.00 0.00 1.98
730 2250 4.252073 GTTGCATCAGTCAGTTCTCATCT 58.748 43.478 0.00 0.00 0.00 2.90
731 2251 3.999001 TGTTGCATCAGTCAGTTCTCATC 59.001 43.478 0.00 0.00 0.00 2.92
732 2252 4.011966 TGTTGCATCAGTCAGTTCTCAT 57.988 40.909 0.00 0.00 0.00 2.90
733 2253 3.473923 TGTTGCATCAGTCAGTTCTCA 57.526 42.857 0.00 0.00 0.00 3.27
742 2262 4.101430 ACCTGGAAAAATTGTTGCATCAGT 59.899 37.500 2.70 0.00 0.00 3.41
754 2274 0.598065 GAGCGTGCACCTGGAAAAAT 59.402 50.000 12.15 0.00 0.00 1.82
760 2280 1.455383 AAAAAGGAGCGTGCACCTGG 61.455 55.000 12.15 0.00 37.12 4.45
844 2709 8.917088 CCATCCCTGTTGAAAGTTTGATATTAT 58.083 33.333 0.00 0.00 0.00 1.28
855 2720 5.726980 TTCATTTCCATCCCTGTTGAAAG 57.273 39.130 0.00 0.00 30.96 2.62
908 2774 6.183360 GGTTTATATAGGGGTTTGGCCTTTTC 60.183 42.308 3.32 0.00 37.43 2.29
1006 2873 2.352805 GAGAGGCAACCTGGTGGG 59.647 66.667 0.00 0.00 41.89 4.61
1065 2935 1.274167 TGGACATTGTGGTAGACGGAC 59.726 52.381 0.00 0.00 0.00 4.79
1596 3466 1.374947 CTGCTTCGGGAGGTTGGAA 59.625 57.895 0.00 0.00 0.00 3.53
1665 3535 1.144969 AGACGCCGTTGTACATGTTG 58.855 50.000 2.30 0.00 0.00 3.33
1787 3657 2.284405 ACGACCGATGGGGGTTCT 60.284 61.111 0.00 0.00 41.40 3.01
1797 3667 1.686566 CGTAGTACAGCGACGACCGA 61.687 60.000 0.00 0.00 46.68 4.69
2303 4175 0.935196 AACACGTGAAGAAAGGTCGC 59.065 50.000 25.01 0.00 0.00 5.19
2323 4195 4.903638 ATGATTCGATTATAACCGCACG 57.096 40.909 0.00 0.00 0.00 5.34
2324 4196 6.241385 GCTAATGATTCGATTATAACCGCAC 58.759 40.000 0.00 0.00 0.00 5.34
2408 4298 5.843673 TCCTTATTGCACACACTGAAAAA 57.156 34.783 0.00 0.00 0.00 1.94
2477 4367 6.915300 TCTCTAGTTCTATCGACACGTAGTAC 59.085 42.308 0.00 0.00 41.61 2.73
2480 4370 6.825284 TTCTCTAGTTCTATCGACACGTAG 57.175 41.667 0.00 0.00 0.00 3.51
2481 4371 7.783090 AATTCTCTAGTTCTATCGACACGTA 57.217 36.000 0.00 0.00 0.00 3.57
2482 4372 6.680874 AATTCTCTAGTTCTATCGACACGT 57.319 37.500 0.00 0.00 0.00 4.49
2512 4402 6.749118 CACCAGTAAATAGTTACGACCAGTAC 59.251 42.308 7.38 0.00 43.78 2.73
2514 4404 5.244626 ACACCAGTAAATAGTTACGACCAGT 59.755 40.000 7.38 2.39 43.78 4.00
2515 4405 5.575606 CACACCAGTAAATAGTTACGACCAG 59.424 44.000 7.38 1.85 43.78 4.00
2517 4407 5.713025 TCACACCAGTAAATAGTTACGACC 58.287 41.667 7.38 0.00 43.78 4.79
2582 4476 1.276820 CGTACGTACACCTTGCGCAA 61.277 55.000 23.48 23.48 36.67 4.85
2599 4493 0.030369 AGCGTGAAAGTCTCGAACGT 59.970 50.000 5.56 0.00 35.64 3.99
2600 4494 0.431233 CAGCGTGAAAGTCTCGAACG 59.569 55.000 4.08 0.00 35.64 3.95
2601 4495 0.161870 GCAGCGTGAAAGTCTCGAAC 59.838 55.000 4.08 0.00 35.64 3.95
2602 4496 0.249280 TGCAGCGTGAAAGTCTCGAA 60.249 50.000 4.08 0.00 35.64 3.71
2726 4620 1.153005 GAGCTTGCATGCTAGCCCT 60.153 57.895 38.59 27.11 44.17 5.19
2749 4643 2.947448 ATTTCGAAAGGAGGCAATGC 57.053 45.000 16.80 0.00 0.00 3.56
2750 4644 4.808558 TCAAATTTCGAAAGGAGGCAATG 58.191 39.130 16.80 6.28 0.00 2.82
2751 4645 5.011023 ACTTCAAATTTCGAAAGGAGGCAAT 59.989 36.000 16.80 0.00 0.00 3.56
2752 4646 4.340950 ACTTCAAATTTCGAAAGGAGGCAA 59.659 37.500 16.80 3.66 0.00 4.52
2753 4647 3.888930 ACTTCAAATTTCGAAAGGAGGCA 59.111 39.130 16.80 0.00 0.00 4.75
2754 4648 4.505313 ACTTCAAATTTCGAAAGGAGGC 57.495 40.909 16.80 0.00 0.00 4.70
2755 4649 6.503524 TCAAACTTCAAATTTCGAAAGGAGG 58.496 36.000 16.80 14.96 0.00 4.30
2756 4650 7.487829 TGTTCAAACTTCAAATTTCGAAAGGAG 59.512 33.333 16.80 9.30 0.00 3.69
2757 4651 7.316640 TGTTCAAACTTCAAATTTCGAAAGGA 58.683 30.769 16.80 10.65 0.00 3.36
2758 4652 7.518731 TGTTCAAACTTCAAATTTCGAAAGG 57.481 32.000 16.80 8.49 0.00 3.11
2759 4653 9.971744 AATTGTTCAAACTTCAAATTTCGAAAG 57.028 25.926 16.80 3.72 0.00 2.62
2771 4665 7.928908 TGAGCAACATAATTGTTCAAACTTC 57.071 32.000 4.02 0.00 44.24 3.01
2785 4679 7.153985 TCGACAATATCATCATGAGCAACATA 58.846 34.615 0.09 0.00 37.46 2.29
2786 4680 5.993441 TCGACAATATCATCATGAGCAACAT 59.007 36.000 0.09 0.00 40.17 2.71
2801 4695 5.011738 ACCATCGGTCCTATTTCGACAATAT 59.988 40.000 0.00 0.00 35.70 1.28
2804 4698 2.498481 ACCATCGGTCCTATTTCGACAA 59.502 45.455 0.00 0.00 35.70 3.18
2806 4700 2.864343 CAACCATCGGTCCTATTTCGAC 59.136 50.000 0.00 0.00 33.12 4.20
2873 4767 9.915629 CACTCTAAAGTAGAAACTACATGACTT 57.084 33.333 0.00 0.00 33.75 3.01
3033 4937 7.161715 ACCACCCTTCCATATGTACATTATT 57.838 36.000 14.77 0.00 0.00 1.40
3036 4940 5.073144 CCTACCACCCTTCCATATGTACATT 59.927 44.000 14.77 0.00 0.00 2.71
3123 5034 6.014669 TCCAAATGGTAATGAACAGGGAAAAG 60.015 38.462 0.00 0.00 36.34 2.27
3151 5062 3.370061 GGCACTCGTGGTGTATTTAACTC 59.630 47.826 11.43 0.00 46.86 3.01
3152 5063 3.007614 AGGCACTCGTGGTGTATTTAACT 59.992 43.478 11.43 0.00 46.86 2.24
3153 5064 3.332034 AGGCACTCGTGGTGTATTTAAC 58.668 45.455 11.43 0.00 46.86 2.01
3154 5065 3.688694 AGGCACTCGTGGTGTATTTAA 57.311 42.857 11.43 0.00 46.86 1.52
3155 5066 3.688694 AAGGCACTCGTGGTGTATTTA 57.311 42.857 11.43 0.00 46.86 1.40
3156 5067 2.561478 AAGGCACTCGTGGTGTATTT 57.439 45.000 11.43 3.62 46.86 1.40
3157 5068 3.007614 AGTTAAGGCACTCGTGGTGTATT 59.992 43.478 11.43 9.30 46.86 1.89
3158 5069 2.565834 AGTTAAGGCACTCGTGGTGTAT 59.434 45.455 11.43 3.45 46.86 2.29
3159 5070 1.965643 AGTTAAGGCACTCGTGGTGTA 59.034 47.619 11.43 0.00 46.86 2.90
3160 5071 0.756903 AGTTAAGGCACTCGTGGTGT 59.243 50.000 11.43 0.00 46.86 4.16
3162 5073 1.140252 ACAAGTTAAGGCACTCGTGGT 59.860 47.619 0.00 0.00 38.49 4.16
3163 5074 1.798813 GACAAGTTAAGGCACTCGTGG 59.201 52.381 0.00 0.00 38.49 4.94
3164 5075 1.798813 GGACAAGTTAAGGCACTCGTG 59.201 52.381 0.00 0.00 38.49 4.35
3165 5076 1.692519 AGGACAAGTTAAGGCACTCGT 59.307 47.619 0.00 0.00 38.49 4.18
3166 5077 2.457366 AGGACAAGTTAAGGCACTCG 57.543 50.000 0.00 0.00 38.49 4.18
3167 5078 3.623510 GCATAGGACAAGTTAAGGCACTC 59.376 47.826 0.00 0.00 38.49 3.51
3169 5080 2.351726 CGCATAGGACAAGTTAAGGCAC 59.648 50.000 0.00 0.00 0.00 5.01
3170 5081 2.235155 TCGCATAGGACAAGTTAAGGCA 59.765 45.455 0.00 0.00 0.00 4.75
3171 5082 2.901249 TCGCATAGGACAAGTTAAGGC 58.099 47.619 0.00 0.00 0.00 4.35
3172 5083 4.693283 TGATCGCATAGGACAAGTTAAGG 58.307 43.478 0.00 0.00 0.00 2.69
3173 5084 6.851222 ATTGATCGCATAGGACAAGTTAAG 57.149 37.500 0.00 0.00 0.00 1.85
3174 5085 7.335673 TCAAATTGATCGCATAGGACAAGTTAA 59.664 33.333 0.00 0.00 30.04 2.01
3175 5086 6.821160 TCAAATTGATCGCATAGGACAAGTTA 59.179 34.615 0.00 0.00 30.04 2.24
3176 5087 5.647658 TCAAATTGATCGCATAGGACAAGTT 59.352 36.000 0.00 0.00 30.94 2.66
3177 5088 5.185454 TCAAATTGATCGCATAGGACAAGT 58.815 37.500 0.00 0.00 0.00 3.16
3178 5089 5.739752 TCAAATTGATCGCATAGGACAAG 57.260 39.130 0.00 0.00 0.00 3.16
3179 5090 5.589855 ACATCAAATTGATCGCATAGGACAA 59.410 36.000 5.36 0.00 34.28 3.18
3180 5091 5.125356 ACATCAAATTGATCGCATAGGACA 58.875 37.500 5.36 0.00 34.28 4.02
3181 5092 5.468072 AGACATCAAATTGATCGCATAGGAC 59.532 40.000 5.36 0.00 34.28 3.85
3182 5093 5.614308 AGACATCAAATTGATCGCATAGGA 58.386 37.500 5.36 0.00 34.28 2.94
3183 5094 5.936686 AGACATCAAATTGATCGCATAGG 57.063 39.130 5.36 0.00 34.28 2.57
3184 5095 8.554528 ACTTTAGACATCAAATTGATCGCATAG 58.445 33.333 5.36 2.93 34.28 2.23
3185 5096 8.437360 ACTTTAGACATCAAATTGATCGCATA 57.563 30.769 5.36 0.00 34.28 3.14
3186 5097 7.325660 ACTTTAGACATCAAATTGATCGCAT 57.674 32.000 5.36 0.00 34.28 4.73
3187 5098 6.741992 ACTTTAGACATCAAATTGATCGCA 57.258 33.333 5.36 0.00 34.28 5.10
3188 5099 7.007725 CACAACTTTAGACATCAAATTGATCGC 59.992 37.037 5.36 1.28 34.28 4.58
3189 5100 8.229811 TCACAACTTTAGACATCAAATTGATCG 58.770 33.333 5.36 4.91 34.28 3.69
3190 5101 9.897744 TTCACAACTTTAGACATCAAATTGATC 57.102 29.630 5.36 0.00 34.28 2.92
3211 5122 9.863845 TCGAGTATCACTTTTATGTATTTCACA 57.136 29.630 0.00 0.00 36.86 3.58
3217 5128 9.871238 ACAAGTTCGAGTATCACTTTTATGTAT 57.129 29.630 0.00 0.00 29.96 2.29
3218 5129 9.350357 GACAAGTTCGAGTATCACTTTTATGTA 57.650 33.333 0.00 0.00 29.96 2.29
3219 5130 8.088981 AGACAAGTTCGAGTATCACTTTTATGT 58.911 33.333 0.00 0.00 29.96 2.29
3220 5131 8.376203 CAGACAAGTTCGAGTATCACTTTTATG 58.624 37.037 0.00 0.00 29.96 1.90
3221 5132 7.063544 GCAGACAAGTTCGAGTATCACTTTTAT 59.936 37.037 0.00 0.00 29.96 1.40
3222 5133 6.365247 GCAGACAAGTTCGAGTATCACTTTTA 59.635 38.462 0.00 0.00 29.96 1.52
3223 5134 5.177696 GCAGACAAGTTCGAGTATCACTTTT 59.822 40.000 0.00 0.00 29.96 2.27
3224 5135 4.686554 GCAGACAAGTTCGAGTATCACTTT 59.313 41.667 0.00 0.00 29.96 2.66
3225 5136 4.238514 GCAGACAAGTTCGAGTATCACTT 58.761 43.478 0.00 0.00 32.27 3.16
3226 5137 3.670895 CGCAGACAAGTTCGAGTATCACT 60.671 47.826 0.00 0.00 33.17 3.41
3227 5138 2.594654 CGCAGACAAGTTCGAGTATCAC 59.405 50.000 0.00 0.00 33.17 3.06
3228 5139 2.863739 CGCAGACAAGTTCGAGTATCA 58.136 47.619 0.00 0.00 33.17 2.15
3229 5140 1.584308 GCGCAGACAAGTTCGAGTATC 59.416 52.381 0.30 0.00 0.00 2.24
3230 5141 1.630148 GCGCAGACAAGTTCGAGTAT 58.370 50.000 0.30 0.00 0.00 2.12
3231 5142 0.728129 CGCGCAGACAAGTTCGAGTA 60.728 55.000 8.75 0.00 0.00 2.59
3232 5143 2.016704 CGCGCAGACAAGTTCGAGT 61.017 57.895 8.75 0.00 0.00 4.18
3233 5144 2.016704 ACGCGCAGACAAGTTCGAG 61.017 57.895 5.73 0.00 0.00 4.04
3234 5145 2.027024 ACGCGCAGACAAGTTCGA 59.973 55.556 5.73 0.00 0.00 3.71
3235 5146 2.168621 CACGCGCAGACAAGTTCG 59.831 61.111 5.73 0.00 0.00 3.95
3236 5147 2.127609 GCACGCGCAGACAAGTTC 60.128 61.111 5.73 0.00 38.36 3.01
3237 5148 2.894879 TGCACGCGCAGACAAGTT 60.895 55.556 5.73 0.00 45.36 2.66
3246 5157 2.223549 GCACCATATTTGCACGCGC 61.224 57.895 5.73 0.00 39.93 6.86
3247 5158 1.586042 GGCACCATATTTGCACGCG 60.586 57.895 3.53 3.53 42.12 6.01
3248 5159 0.248621 GAGGCACCATATTTGCACGC 60.249 55.000 8.08 0.00 42.12 5.34
3249 5160 0.381801 GGAGGCACCATATTTGCACG 59.618 55.000 8.08 0.00 42.12 5.34
3250 5161 1.406539 CAGGAGGCACCATATTTGCAC 59.593 52.381 3.18 2.54 42.12 4.57
3251 5162 1.005805 ACAGGAGGCACCATATTTGCA 59.994 47.619 3.18 0.00 42.12 4.08
3252 5163 1.678101 GACAGGAGGCACCATATTTGC 59.322 52.381 3.18 0.00 42.04 3.68
3253 5164 1.942657 CGACAGGAGGCACCATATTTG 59.057 52.381 3.18 0.00 42.04 2.32
3254 5165 1.559682 ACGACAGGAGGCACCATATTT 59.440 47.619 3.18 0.00 42.04 1.40
3255 5166 1.204146 ACGACAGGAGGCACCATATT 58.796 50.000 3.18 0.00 42.04 1.28
3256 5167 2.082140 TACGACAGGAGGCACCATAT 57.918 50.000 3.18 0.00 42.04 1.78
3257 5168 1.961394 GATACGACAGGAGGCACCATA 59.039 52.381 3.18 0.00 42.04 2.74
3258 5169 0.753262 GATACGACAGGAGGCACCAT 59.247 55.000 3.18 0.00 42.04 3.55
3259 5170 1.327690 GGATACGACAGGAGGCACCA 61.328 60.000 3.18 0.00 42.04 4.17
3260 5171 1.442148 GGATACGACAGGAGGCACC 59.558 63.158 0.00 0.00 39.35 5.01
3261 5172 1.442148 GGGATACGACAGGAGGCAC 59.558 63.158 0.00 0.00 37.60 5.01
3262 5173 3.950232 GGGATACGACAGGAGGCA 58.050 61.111 0.00 0.00 37.60 4.75
3272 5183 0.179129 AAAGCGTACACCGGGATACG 60.179 55.000 26.63 26.63 45.45 3.06
3273 5184 1.283736 CAAAGCGTACACCGGGATAC 58.716 55.000 6.32 6.87 36.94 2.24
3274 5185 3.744941 CAAAGCGTACACCGGGATA 57.255 52.632 6.32 0.00 36.94 2.59
3275 5186 4.609995 CAAAGCGTACACCGGGAT 57.390 55.556 6.32 0.00 36.94 3.85


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

AutoCloner maintained by Alex Coulton.