Multiple sequence alignment - TraesCS6D01G184500

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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 TraesCS6D01G184500 chr6D 100.000 3251 0 0 1 3251 232742759 232746009 0.000000e+00 6004.0
1 TraesCS6D01G184500 chr6D 90.000 220 19 3 2571 2789 131604155 131603938 6.870000e-72 281.0
2 TraesCS6D01G184500 chr6D 97.059 34 0 1 3129 3161 232745802 232745835 4.530000e-04 56.5
3 TraesCS6D01G184500 chr6A 95.385 2882 101 15 1 2876 306766963 306764108 0.000000e+00 4556.0
4 TraesCS6D01G184500 chr6A 79.909 219 29 9 54 260 540333501 540333286 2.610000e-31 147.0
5 TraesCS6D01G184500 chr6A 78.431 153 24 9 15 161 127574876 127575025 1.240000e-14 91.6
6 TraesCS6D01G184500 chr6B 97.543 1750 28 4 838 2576 369527807 369526062 0.000000e+00 2979.0
7 TraesCS6D01G184500 chr6B 87.196 781 78 20 1 777 369531181 369530419 0.000000e+00 869.0
8 TraesCS6D01G184500 chr6B 84.810 237 20 5 2877 3112 83737063 83736842 1.170000e-54 224.0
9 TraesCS6D01G184500 chr6B 92.500 80 3 3 767 845 369530117 369530040 9.530000e-21 111.0
10 TraesCS6D01G184500 chr2B 85.000 260 15 8 2877 3117 701361601 701361347 3.240000e-60 243.0
11 TraesCS6D01G184500 chr2B 84.810 237 20 5 2877 3112 774402931 774402710 1.170000e-54 224.0
12 TraesCS6D01G184500 chr2B 79.870 154 28 3 15 167 630769519 630769670 3.430000e-20 110.0
13 TraesCS6D01G184500 chr5A 85.124 242 20 7 2877 3117 446692460 446692234 1.950000e-57 233.0
14 TraesCS6D01G184500 chrUn 84.810 237 20 5 2877 3112 407816336 407816557 1.170000e-54 224.0
15 TraesCS6D01G184500 chr1B 84.810 237 20 5 2877 3112 17186724 17186503 1.170000e-54 224.0
16 TraesCS6D01G184500 chr1B 84.810 237 20 5 2877 3112 117872318 117872097 1.170000e-54 224.0
17 TraesCS6D01G184500 chr1B 91.566 83 7 0 3166 3248 207023092 207023174 7.370000e-22 115.0
18 TraesCS6D01G184500 chr7B 84.810 237 19 5 2877 3112 230624911 230625131 4.220000e-54 222.0
19 TraesCS6D01G184500 chr4B 84.388 237 21 5 2877 3112 275698011 275698232 5.460000e-53 219.0
20 TraesCS6D01G184500 chr1A 84.388 237 21 5 2877 3112 423371449 423371670 5.460000e-53 219.0
21 TraesCS6D01G184500 chr7A 86.022 186 15 2 2893 3078 226724478 226724652 4.280000e-44 189.0
22 TraesCS6D01G184500 chr5B 81.818 242 28 6 2877 3117 57697904 57697678 4.280000e-44 189.0


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 TraesCS6D01G184500 chr6D 232742759 232746009 3250 False 3030.250000 6004 98.5295 1 3251 2 chr6D.!!$F1 3250
1 TraesCS6D01G184500 chr6A 306764108 306766963 2855 True 4556.000000 4556 95.3850 1 2876 1 chr6A.!!$R1 2875
2 TraesCS6D01G184500 chr6B 369526062 369531181 5119 True 1319.666667 2979 92.4130 1 2576 3 chr6B.!!$R2 2575

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
596 601 0.238289 CGCACAGCCTACCAAAAGTG 59.762 55.0 0.00 0.0 0.00 3.16 F
628 633 1.073768 GCTCGTGAAGGAGAACTCGC 61.074 60.0 4.26 0.0 36.08 5.03 F
663 668 1.799544 CCTTGCACCATTTCCTTTGC 58.200 50.0 0.00 0.0 35.45 3.68 F
2167 4735 1.093972 CAATGTTGGTGCTGCGGATA 58.906 50.0 0.00 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 4622 1.304630 TGATTGCTGCTGGCCATGT 60.305 52.632 5.51 0.0 40.92 3.21 R
2167 4735 1.602237 CACTACCAATGCCTCCGGT 59.398 57.895 0.00 0.0 36.79 5.28 R
2211 4779 3.374042 TCGTCTTCCATCTCTTCCTCT 57.626 47.619 0.00 0.0 0.00 3.69 R
3093 5661 0.454600 TTGATCCGGTCGTGTAGCTC 59.545 55.000 0.00 0.0 0.00 4.09 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
191 193 4.876107 CCACGAGAAGTAAATATGTGCCTT 59.124 41.667 0.00 0.00 0.00 4.35
202 204 1.549203 ATGTGCCTTTTGCGGAAGAT 58.451 45.000 0.82 0.00 45.60 2.40
213 217 6.256757 CCTTTTGCGGAAGATAAAAACACAAA 59.743 34.615 0.82 0.00 31.56 2.83
219 223 7.492669 TGCGGAAGATAAAAACACAAATTTTCA 59.507 29.630 0.00 0.00 31.35 2.69
274 278 3.624777 AGTAAATCCGTACCTCCTCGAA 58.375 45.455 0.00 0.00 0.00 3.71
358 362 5.466058 GCATGACTATGACTCTCATGAAAGG 59.534 44.000 10.36 0.00 42.65 3.11
364 368 8.088463 ACTATGACTCTCATGAAAGGAAATCT 57.912 34.615 0.21 0.00 37.70 2.40
380 384 7.396540 AGGAAATCTGTGCCTACATTTAAAG 57.603 36.000 0.00 0.00 35.97 1.85
385 389 6.569179 TCTGTGCCTACATTTAAAGGAAAC 57.431 37.500 6.90 0.00 35.97 2.78
386 390 6.303839 TCTGTGCCTACATTTAAAGGAAACT 58.696 36.000 6.90 0.00 38.26 2.66
461 466 6.563222 TTGTCCAAAACCTAAGAATAACGG 57.437 37.500 0.00 0.00 0.00 4.44
466 471 8.136800 GTCCAAAACCTAAGAATAACGGAAAAA 58.863 33.333 0.00 0.00 0.00 1.94
469 474 7.585579 AAACCTAAGAATAACGGAAAAACCA 57.414 32.000 0.00 0.00 38.90 3.67
556 561 2.593026 ACAAAATTCGAAGGAAGCCCA 58.407 42.857 3.35 0.00 35.19 5.36
596 601 0.238289 CGCACAGCCTACCAAAAGTG 59.762 55.000 0.00 0.00 0.00 3.16
628 633 1.073768 GCTCGTGAAGGAGAACTCGC 61.074 60.000 4.26 0.00 36.08 5.03
639 644 2.229302 GGAGAACTCGCTGAGTAGTTGT 59.771 50.000 10.81 3.70 42.59 3.32
663 668 1.799544 CCTTGCACCATTTCCTTTGC 58.200 50.000 0.00 0.00 35.45 3.68
839 1157 5.067936 CGGATAGGTCACTCAAGAATGTACT 59.932 44.000 0.00 0.00 0.00 2.73
2167 4735 1.093972 CAATGTTGGTGCTGCGGATA 58.906 50.000 0.00 0.00 0.00 2.59
2211 4779 3.811031 TTCCGGCAACAAGGAAGAA 57.189 47.368 0.00 0.00 41.19 2.52
2493 5061 7.036996 TGTTTGTGCTTTTGATGTGATTCTA 57.963 32.000 0.00 0.00 0.00 2.10
2494 5062 7.487484 TGTTTGTGCTTTTGATGTGATTCTAA 58.513 30.769 0.00 0.00 0.00 2.10
2646 5214 6.201425 TGTTTGAGTAACATACGTCCTGTTTC 59.799 38.462 18.17 14.18 41.73 2.78
2703 5271 7.284034 GTGAATTGTAATGGAGATCATCAGGTT 59.716 37.037 0.00 0.00 34.44 3.50
2755 5323 9.512588 ACTCTCTTCAATAAGTGTGATTCATTT 57.487 29.630 0.00 0.00 34.13 2.32
2808 5376 2.938956 ACTTTACTGTGAGCAAGGCT 57.061 45.000 0.00 0.00 43.88 4.58
2876 5444 4.095334 TCATGAAAAGGAATGCATCACTCG 59.905 41.667 0.00 0.00 0.00 4.18
2877 5445 2.162208 TGAAAAGGAATGCATCACTCGC 59.838 45.455 0.00 0.00 0.00 5.03
2878 5446 1.098050 AAAGGAATGCATCACTCGCC 58.902 50.000 0.00 0.00 0.00 5.54
2879 5447 0.254178 AAGGAATGCATCACTCGCCT 59.746 50.000 0.00 0.00 0.00 5.52
2880 5448 1.123077 AGGAATGCATCACTCGCCTA 58.877 50.000 0.00 0.00 0.00 3.93
2881 5449 1.069823 AGGAATGCATCACTCGCCTAG 59.930 52.381 0.00 0.00 0.00 3.02
2882 5450 1.202580 GGAATGCATCACTCGCCTAGT 60.203 52.381 0.00 0.00 39.81 2.57
2883 5451 2.555199 GAATGCATCACTCGCCTAGTT 58.445 47.619 0.00 0.00 35.76 2.24
2884 5452 2.698855 ATGCATCACTCGCCTAGTTT 57.301 45.000 0.00 0.00 35.76 2.66
2885 5453 1.725641 TGCATCACTCGCCTAGTTTG 58.274 50.000 0.00 0.00 35.76 2.93
2886 5454 1.009829 GCATCACTCGCCTAGTTTGG 58.990 55.000 0.00 0.00 35.76 3.28
2887 5455 1.676014 GCATCACTCGCCTAGTTTGGT 60.676 52.381 0.00 0.00 35.76 3.67
2888 5456 2.418197 GCATCACTCGCCTAGTTTGGTA 60.418 50.000 0.00 0.00 35.76 3.25
2889 5457 3.448686 CATCACTCGCCTAGTTTGGTAG 58.551 50.000 0.00 0.00 35.76 3.18
2890 5458 1.203994 TCACTCGCCTAGTTTGGTAGC 59.796 52.381 0.00 0.00 35.76 3.58
2891 5459 0.172803 ACTCGCCTAGTTTGGTAGCG 59.827 55.000 0.00 0.00 33.35 4.26
2892 5460 1.146358 CTCGCCTAGTTTGGTAGCGC 61.146 60.000 0.00 0.00 0.00 5.92
2893 5461 1.447140 CGCCTAGTTTGGTAGCGCA 60.447 57.895 11.47 0.00 0.00 6.09
2894 5462 1.421410 CGCCTAGTTTGGTAGCGCAG 61.421 60.000 11.47 0.00 0.00 5.18
2895 5463 0.391263 GCCTAGTTTGGTAGCGCAGT 60.391 55.000 11.47 0.00 0.00 4.40
2896 5464 1.944430 GCCTAGTTTGGTAGCGCAGTT 60.944 52.381 11.47 0.00 0.00 3.16
2897 5465 2.423577 CCTAGTTTGGTAGCGCAGTTT 58.576 47.619 11.47 0.00 0.00 2.66
2898 5466 2.812011 CCTAGTTTGGTAGCGCAGTTTT 59.188 45.455 11.47 0.00 0.00 2.43
2899 5467 3.252458 CCTAGTTTGGTAGCGCAGTTTTT 59.748 43.478 11.47 0.00 0.00 1.94
2900 5468 4.453136 CCTAGTTTGGTAGCGCAGTTTTTA 59.547 41.667 11.47 0.00 0.00 1.52
2901 5469 4.904253 AGTTTGGTAGCGCAGTTTTTAA 57.096 36.364 11.47 0.00 0.00 1.52
2902 5470 5.251601 AGTTTGGTAGCGCAGTTTTTAAA 57.748 34.783 11.47 0.00 0.00 1.52
2903 5471 5.652518 AGTTTGGTAGCGCAGTTTTTAAAA 58.347 33.333 11.47 0.00 0.00 1.52
2904 5472 5.517411 AGTTTGGTAGCGCAGTTTTTAAAAC 59.483 36.000 11.47 12.16 0.00 2.43
2905 5473 4.634184 TGGTAGCGCAGTTTTTAAAACA 57.366 36.364 20.62 0.00 0.00 2.83
2906 5474 4.352887 TGGTAGCGCAGTTTTTAAAACAC 58.647 39.130 20.62 12.04 0.00 3.32
2907 5475 3.732219 GGTAGCGCAGTTTTTAAAACACC 59.268 43.478 20.62 14.32 0.00 4.16
2908 5476 2.816689 AGCGCAGTTTTTAAAACACCC 58.183 42.857 20.62 8.63 0.00 4.61
2909 5477 2.429250 AGCGCAGTTTTTAAAACACCCT 59.571 40.909 20.62 8.62 0.00 4.34
2910 5478 3.633065 AGCGCAGTTTTTAAAACACCCTA 59.367 39.130 20.62 0.00 0.00 3.53
2911 5479 3.978855 GCGCAGTTTTTAAAACACCCTAG 59.021 43.478 20.62 8.20 0.00 3.02
2912 5480 4.498513 GCGCAGTTTTTAAAACACCCTAGT 60.499 41.667 20.62 0.00 0.00 2.57
2913 5481 5.277925 GCGCAGTTTTTAAAACACCCTAGTA 60.278 40.000 20.62 0.00 0.00 1.82
2914 5482 6.569035 GCGCAGTTTTTAAAACACCCTAGTAT 60.569 38.462 20.62 0.00 0.00 2.12
2915 5483 7.364970 CGCAGTTTTTAAAACACCCTAGTATT 58.635 34.615 20.62 0.00 0.00 1.89
2916 5484 7.863877 CGCAGTTTTTAAAACACCCTAGTATTT 59.136 33.333 20.62 0.00 0.00 1.40
2917 5485 9.188588 GCAGTTTTTAAAACACCCTAGTATTTC 57.811 33.333 20.62 0.00 0.00 2.17
2926 5494 6.796705 ACACCCTAGTATTTCAAAACTTCG 57.203 37.500 0.00 0.00 0.00 3.79
2927 5495 5.704053 ACACCCTAGTATTTCAAAACTTCGG 59.296 40.000 0.00 0.00 0.00 4.30
2928 5496 5.704053 CACCCTAGTATTTCAAAACTTCGGT 59.296 40.000 0.00 0.00 0.00 4.69
2929 5497 6.875195 CACCCTAGTATTTCAAAACTTCGGTA 59.125 38.462 0.00 0.00 29.57 4.02
2930 5498 7.551617 CACCCTAGTATTTCAAAACTTCGGTAT 59.448 37.037 0.00 0.00 29.57 2.73
2931 5499 8.105197 ACCCTAGTATTTCAAAACTTCGGTATT 58.895 33.333 0.00 0.00 29.13 1.89
2932 5500 8.395633 CCCTAGTATTTCAAAACTTCGGTATTG 58.604 37.037 0.00 0.00 0.00 1.90
2933 5501 7.908601 CCTAGTATTTCAAAACTTCGGTATTGC 59.091 37.037 0.00 0.00 0.00 3.56
2934 5502 7.209471 AGTATTTCAAAACTTCGGTATTGCA 57.791 32.000 0.00 0.00 0.00 4.08
2935 5503 7.653647 AGTATTTCAAAACTTCGGTATTGCAA 58.346 30.769 0.00 0.00 0.00 4.08
2936 5504 8.303876 AGTATTTCAAAACTTCGGTATTGCAAT 58.696 29.630 17.56 17.56 0.00 3.56
2937 5505 6.761731 TTTCAAAACTTCGGTATTGCAATG 57.238 33.333 22.27 5.54 0.00 2.82
2938 5506 4.233789 TCAAAACTTCGGTATTGCAATGC 58.766 39.130 22.27 20.14 0.00 3.56
2939 5507 4.022416 TCAAAACTTCGGTATTGCAATGCT 60.022 37.500 24.03 4.13 0.00 3.79
2940 5508 4.519540 AAACTTCGGTATTGCAATGCTT 57.480 36.364 24.03 9.76 0.00 3.91
2941 5509 3.492421 ACTTCGGTATTGCAATGCTTG 57.508 42.857 24.03 17.45 0.00 4.01
2942 5510 2.164219 ACTTCGGTATTGCAATGCTTGG 59.836 45.455 24.03 14.87 0.00 3.61
2943 5511 1.102154 TCGGTATTGCAATGCTTGGG 58.898 50.000 24.03 12.78 0.00 4.12
2944 5512 0.528249 CGGTATTGCAATGCTTGGGC 60.528 55.000 24.03 8.68 39.26 5.36
2954 5522 3.642938 TGCTTGGGCAACGAATACT 57.357 47.368 0.00 0.00 46.36 2.12
2955 5523 2.772077 TGCTTGGGCAACGAATACTA 57.228 45.000 0.00 0.00 46.36 1.82
2956 5524 2.352388 TGCTTGGGCAACGAATACTAC 58.648 47.619 0.00 0.00 46.36 2.73
2957 5525 2.289756 TGCTTGGGCAACGAATACTACA 60.290 45.455 0.00 0.00 46.36 2.74
2958 5526 2.351726 GCTTGGGCAACGAATACTACAG 59.648 50.000 0.00 0.00 38.54 2.74
2959 5527 3.596214 CTTGGGCAACGAATACTACAGT 58.404 45.455 0.00 0.00 32.20 3.55
2960 5528 3.688694 TGGGCAACGAATACTACAGTT 57.311 42.857 0.00 0.00 37.60 3.16
2961 5529 4.010667 TGGGCAACGAATACTACAGTTT 57.989 40.909 0.00 0.00 37.60 2.66
2962 5530 4.391155 TGGGCAACGAATACTACAGTTTT 58.609 39.130 0.00 0.00 37.60 2.43
2963 5531 4.822896 TGGGCAACGAATACTACAGTTTTT 59.177 37.500 0.00 0.00 37.60 1.94
2994 5562 7.760131 TTTTTGAAAACTGCAATTCTCTCAG 57.240 32.000 7.73 0.00 0.00 3.35
2995 5563 6.455360 TTTGAAAACTGCAATTCTCTCAGT 57.545 33.333 7.73 0.00 42.28 3.41
3001 5569 6.566197 AACTGCAATTCTCTCAGTTTTAGG 57.434 37.500 1.47 0.00 45.55 2.69
3002 5570 5.869579 ACTGCAATTCTCTCAGTTTTAGGA 58.130 37.500 0.00 0.00 37.78 2.94
3003 5571 6.299141 ACTGCAATTCTCTCAGTTTTAGGAA 58.701 36.000 0.00 0.00 37.78 3.36
3004 5572 6.772716 ACTGCAATTCTCTCAGTTTTAGGAAA 59.227 34.615 0.00 0.00 37.78 3.13
3005 5573 7.285401 ACTGCAATTCTCTCAGTTTTAGGAAAA 59.715 33.333 0.00 0.00 37.78 2.29
3022 5590 6.759497 AGGAAAACTACTGATATGTTTGGC 57.241 37.500 0.00 0.00 34.63 4.52
3023 5591 6.485171 AGGAAAACTACTGATATGTTTGGCT 58.515 36.000 0.00 0.00 34.63 4.75
3024 5592 6.375455 AGGAAAACTACTGATATGTTTGGCTG 59.625 38.462 0.00 0.00 34.63 4.85
3025 5593 6.404734 GGAAAACTACTGATATGTTTGGCTGG 60.405 42.308 0.00 0.00 34.63 4.85
3026 5594 4.844349 ACTACTGATATGTTTGGCTGGT 57.156 40.909 0.00 0.00 0.00 4.00
3027 5595 4.517285 ACTACTGATATGTTTGGCTGGTG 58.483 43.478 0.00 0.00 0.00 4.17
3028 5596 3.439857 ACTGATATGTTTGGCTGGTGT 57.560 42.857 0.00 0.00 0.00 4.16
3029 5597 3.766545 ACTGATATGTTTGGCTGGTGTT 58.233 40.909 0.00 0.00 0.00 3.32
3030 5598 3.507233 ACTGATATGTTTGGCTGGTGTTG 59.493 43.478 0.00 0.00 0.00 3.33
3031 5599 3.495331 TGATATGTTTGGCTGGTGTTGT 58.505 40.909 0.00 0.00 0.00 3.32
3032 5600 3.894427 TGATATGTTTGGCTGGTGTTGTT 59.106 39.130 0.00 0.00 0.00 2.83
3033 5601 4.343526 TGATATGTTTGGCTGGTGTTGTTT 59.656 37.500 0.00 0.00 0.00 2.83
3034 5602 3.625649 ATGTTTGGCTGGTGTTGTTTT 57.374 38.095 0.00 0.00 0.00 2.43
3035 5603 4.744795 ATGTTTGGCTGGTGTTGTTTTA 57.255 36.364 0.00 0.00 0.00 1.52
3036 5604 3.851098 TGTTTGGCTGGTGTTGTTTTAC 58.149 40.909 0.00 0.00 0.00 2.01
3037 5605 3.511934 TGTTTGGCTGGTGTTGTTTTACT 59.488 39.130 0.00 0.00 0.00 2.24
3038 5606 3.791973 TTGGCTGGTGTTGTTTTACTG 57.208 42.857 0.00 0.00 0.00 2.74
3039 5607 2.729194 TGGCTGGTGTTGTTTTACTGT 58.271 42.857 0.00 0.00 0.00 3.55
3040 5608 3.887352 TGGCTGGTGTTGTTTTACTGTA 58.113 40.909 0.00 0.00 0.00 2.74
3041 5609 3.880490 TGGCTGGTGTTGTTTTACTGTAG 59.120 43.478 0.00 0.00 0.00 2.74
3042 5610 3.881089 GGCTGGTGTTGTTTTACTGTAGT 59.119 43.478 0.00 0.00 0.00 2.73
3043 5611 4.337274 GGCTGGTGTTGTTTTACTGTAGTT 59.663 41.667 0.00 0.00 0.00 2.24
3044 5612 5.163591 GGCTGGTGTTGTTTTACTGTAGTTT 60.164 40.000 0.00 0.00 0.00 2.66
3045 5613 6.327154 GCTGGTGTTGTTTTACTGTAGTTTT 58.673 36.000 0.00 0.00 0.00 2.43
3046 5614 6.252655 GCTGGTGTTGTTTTACTGTAGTTTTG 59.747 38.462 0.00 0.00 0.00 2.44
3047 5615 7.450124 TGGTGTTGTTTTACTGTAGTTTTGA 57.550 32.000 0.00 0.00 0.00 2.69
3048 5616 7.306953 TGGTGTTGTTTTACTGTAGTTTTGAC 58.693 34.615 0.00 0.00 0.00 3.18
3049 5617 6.748658 GGTGTTGTTTTACTGTAGTTTTGACC 59.251 38.462 0.00 0.00 0.00 4.02
3050 5618 7.306953 GTGTTGTTTTACTGTAGTTTTGACCA 58.693 34.615 0.00 0.00 0.00 4.02
3051 5619 7.808856 GTGTTGTTTTACTGTAGTTTTGACCAA 59.191 33.333 0.00 0.00 0.00 3.67
3052 5620 8.524487 TGTTGTTTTACTGTAGTTTTGACCAAT 58.476 29.630 0.00 0.00 0.00 3.16
3061 5629 9.344772 ACTGTAGTTTTGACCAATAATTACACA 57.655 29.630 0.00 0.00 0.00 3.72
3063 5631 9.953697 TGTAGTTTTGACCAATAATTACACAAC 57.046 29.630 0.00 0.00 0.00 3.32
3094 5662 9.632638 ATCTAAGTTAATTACTACACCTACGGA 57.367 33.333 0.00 0.00 35.54 4.69
3095 5663 9.113838 TCTAAGTTAATTACTACACCTACGGAG 57.886 37.037 0.00 0.00 35.54 4.63
3096 5664 6.141560 AGTTAATTACTACACCTACGGAGC 57.858 41.667 0.00 0.00 34.56 4.70
3097 5665 5.890419 AGTTAATTACTACACCTACGGAGCT 59.110 40.000 0.00 0.00 34.56 4.09
3098 5666 7.056635 AGTTAATTACTACACCTACGGAGCTA 58.943 38.462 0.00 0.00 34.56 3.32
3099 5667 5.764487 AATTACTACACCTACGGAGCTAC 57.236 43.478 0.00 0.00 0.00 3.58
3100 5668 2.795231 ACTACACCTACGGAGCTACA 57.205 50.000 0.00 0.00 0.00 2.74
3101 5669 2.363683 ACTACACCTACGGAGCTACAC 58.636 52.381 0.00 0.00 0.00 2.90
3102 5670 1.329906 CTACACCTACGGAGCTACACG 59.670 57.143 0.00 0.00 0.00 4.49
3103 5671 0.321919 ACACCTACGGAGCTACACGA 60.322 55.000 11.30 0.00 0.00 4.35
3104 5672 0.098376 CACCTACGGAGCTACACGAC 59.902 60.000 11.30 0.00 0.00 4.34
3105 5673 1.028868 ACCTACGGAGCTACACGACC 61.029 60.000 11.30 0.00 0.00 4.79
3108 5676 3.129502 CGGAGCTACACGACCGGA 61.130 66.667 9.46 0.00 41.41 5.14
3109 5677 2.478890 CGGAGCTACACGACCGGAT 61.479 63.158 9.46 0.00 41.41 4.18
3110 5678 1.359475 GGAGCTACACGACCGGATC 59.641 63.158 9.46 0.32 0.00 3.36
3111 5679 1.381928 GGAGCTACACGACCGGATCA 61.382 60.000 9.46 0.00 0.00 2.92
3112 5680 0.454600 GAGCTACACGACCGGATCAA 59.545 55.000 9.46 0.00 0.00 2.57
3113 5681 1.067212 GAGCTACACGACCGGATCAAT 59.933 52.381 9.46 0.00 0.00 2.57
3114 5682 1.480954 AGCTACACGACCGGATCAATT 59.519 47.619 9.46 0.00 0.00 2.32
3115 5683 2.691526 AGCTACACGACCGGATCAATTA 59.308 45.455 9.46 0.00 0.00 1.40
3116 5684 3.050619 GCTACACGACCGGATCAATTAG 58.949 50.000 9.46 2.34 0.00 1.73
3117 5685 3.243301 GCTACACGACCGGATCAATTAGA 60.243 47.826 9.46 0.00 0.00 2.10
3118 5686 3.438297 ACACGACCGGATCAATTAGAG 57.562 47.619 9.46 0.00 0.00 2.43
3119 5687 2.128035 CACGACCGGATCAATTAGAGC 58.872 52.381 9.46 0.00 0.00 4.09
3120 5688 1.754803 ACGACCGGATCAATTAGAGCA 59.245 47.619 9.46 0.00 33.23 4.26
3121 5689 2.365617 ACGACCGGATCAATTAGAGCAT 59.634 45.455 9.46 0.00 33.23 3.79
3122 5690 2.733552 CGACCGGATCAATTAGAGCATG 59.266 50.000 9.46 0.00 33.23 4.06
3123 5691 3.070018 GACCGGATCAATTAGAGCATGG 58.930 50.000 9.46 0.00 36.23 3.66
3124 5692 2.439507 ACCGGATCAATTAGAGCATGGT 59.560 45.455 9.46 0.00 37.88 3.55
3125 5693 3.117888 ACCGGATCAATTAGAGCATGGTT 60.118 43.478 9.46 0.00 39.10 3.67
3126 5694 4.102524 ACCGGATCAATTAGAGCATGGTTA 59.897 41.667 9.46 0.00 39.10 2.85
3127 5695 4.452455 CCGGATCAATTAGAGCATGGTTAC 59.548 45.833 0.00 0.00 33.23 2.50
3128 5696 5.300752 CGGATCAATTAGAGCATGGTTACT 58.699 41.667 0.00 0.00 33.23 2.24
3129 5697 5.760253 CGGATCAATTAGAGCATGGTTACTT 59.240 40.000 0.00 0.00 33.23 2.24
3130 5698 6.260936 CGGATCAATTAGAGCATGGTTACTTT 59.739 38.462 0.00 0.00 33.23 2.66
3131 5699 7.441157 CGGATCAATTAGAGCATGGTTACTTTA 59.559 37.037 0.00 0.00 33.23 1.85
3132 5700 8.560374 GGATCAATTAGAGCATGGTTACTTTAC 58.440 37.037 0.00 0.00 33.23 2.01
3133 5701 7.859325 TCAATTAGAGCATGGTTACTTTACC 57.141 36.000 0.00 0.00 38.73 2.85
3167 5735 8.962679 ACACAACTTTAATCTAAGTTTTGACCA 58.037 29.630 17.37 0.00 43.85 4.02
3168 5736 9.796120 CACAACTTTAATCTAAGTTTTGACCAA 57.204 29.630 8.83 0.00 43.85 3.67
3169 5737 9.797556 ACAACTTTAATCTAAGTTTTGACCAAC 57.202 29.630 0.00 0.00 43.85 3.77
3170 5738 9.244799 CAACTTTAATCTAAGTTTTGACCAACC 57.755 33.333 0.00 0.00 43.85 3.77
3171 5739 7.645402 ACTTTAATCTAAGTTTTGACCAACCG 58.355 34.615 0.00 0.00 34.81 4.44
3172 5740 7.283807 ACTTTAATCTAAGTTTTGACCAACCGT 59.716 33.333 0.00 0.00 34.81 4.83
3173 5741 7.571080 TTAATCTAAGTTTTGACCAACCGTT 57.429 32.000 0.00 0.00 0.00 4.44
3174 5742 4.886247 TCTAAGTTTTGACCAACCGTTG 57.114 40.909 4.12 4.12 0.00 4.10
3186 5754 4.616181 CCAACCGTTGGCTATAAGAAAG 57.384 45.455 17.33 0.00 45.17 2.62
3187 5755 4.007659 CCAACCGTTGGCTATAAGAAAGT 58.992 43.478 17.33 0.00 45.17 2.66
3188 5756 4.142687 CCAACCGTTGGCTATAAGAAAGTG 60.143 45.833 17.33 0.00 45.17 3.16
3189 5757 4.281898 ACCGTTGGCTATAAGAAAGTGT 57.718 40.909 0.00 0.00 0.00 3.55
3190 5758 4.251268 ACCGTTGGCTATAAGAAAGTGTC 58.749 43.478 0.00 0.00 0.00 3.67
3191 5759 4.250464 CCGTTGGCTATAAGAAAGTGTCA 58.750 43.478 0.00 0.00 0.00 3.58
3192 5760 4.876107 CCGTTGGCTATAAGAAAGTGTCAT 59.124 41.667 0.00 0.00 0.00 3.06
3193 5761 5.220662 CCGTTGGCTATAAGAAAGTGTCATG 60.221 44.000 0.00 0.00 0.00 3.07
3194 5762 5.351465 CGTTGGCTATAAGAAAGTGTCATGT 59.649 40.000 0.00 0.00 0.00 3.21
3195 5763 6.455646 CGTTGGCTATAAGAAAGTGTCATGTC 60.456 42.308 0.00 0.00 0.00 3.06
3196 5764 6.048732 TGGCTATAAGAAAGTGTCATGTCA 57.951 37.500 0.00 0.00 0.00 3.58
3197 5765 6.653020 TGGCTATAAGAAAGTGTCATGTCAT 58.347 36.000 0.00 0.00 0.00 3.06
3198 5766 7.112122 TGGCTATAAGAAAGTGTCATGTCATT 58.888 34.615 0.00 0.00 0.00 2.57
3199 5767 7.611467 TGGCTATAAGAAAGTGTCATGTCATTT 59.389 33.333 0.00 0.00 0.00 2.32
3200 5768 9.109393 GGCTATAAGAAAGTGTCATGTCATTTA 57.891 33.333 1.47 0.00 0.00 1.40
3206 5774 8.862325 AGAAAGTGTCATGTCATTTATAACCA 57.138 30.769 1.47 0.00 0.00 3.67
3207 5775 9.295825 AGAAAGTGTCATGTCATTTATAACCAA 57.704 29.630 1.47 0.00 0.00 3.67
3210 5778 9.466497 AAGTGTCATGTCATTTATAACCAATCT 57.534 29.630 0.00 0.00 0.00 2.40
3211 5779 9.466497 AGTGTCATGTCATTTATAACCAATCTT 57.534 29.630 0.00 0.00 0.00 2.40
3224 5792 9.860650 TTATAACCAATCTTATAGCCAACATGT 57.139 29.630 0.00 0.00 0.00 3.21
3228 5796 8.848474 ACCAATCTTATAGCCAACATGTATAC 57.152 34.615 0.00 0.00 0.00 1.47
3229 5797 7.883311 ACCAATCTTATAGCCAACATGTATACC 59.117 37.037 0.00 0.00 0.00 2.73
3230 5798 7.882791 CCAATCTTATAGCCAACATGTATACCA 59.117 37.037 0.00 0.00 0.00 3.25
3231 5799 9.283768 CAATCTTATAGCCAACATGTATACCAA 57.716 33.333 0.00 0.00 0.00 3.67
3236 5804 7.687941 ATAGCCAACATGTATACCAATTAGC 57.312 36.000 0.00 0.00 0.00 3.09
3237 5805 5.694995 AGCCAACATGTATACCAATTAGCT 58.305 37.500 0.00 0.00 0.00 3.32
3238 5806 6.837312 AGCCAACATGTATACCAATTAGCTA 58.163 36.000 0.00 0.00 0.00 3.32
3239 5807 7.461749 AGCCAACATGTATACCAATTAGCTAT 58.538 34.615 0.00 0.00 0.00 2.97
3240 5808 8.602424 AGCCAACATGTATACCAATTAGCTATA 58.398 33.333 0.00 0.00 0.00 1.31
3241 5809 9.226606 GCCAACATGTATACCAATTAGCTATAA 57.773 33.333 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 3.575256 TGAAGGCATGAATTTGCTTCTGT 59.425 39.130 0.00 0.00 42.38 3.41
70 71 5.473846 AGAGACACTGATTTACTTCTCGTGA 59.526 40.000 0.00 0.00 35.64 4.35
144 146 2.811317 CTTCCGCGAGAGGCACAC 60.811 66.667 8.23 0.00 43.84 3.82
191 193 7.778470 AATTTGTGTTTTTATCTTCCGCAAA 57.222 28.000 0.00 0.00 39.12 3.68
213 217 3.119849 CGTGCCTCTCGGAAAATGAAAAT 60.120 43.478 0.00 0.00 0.00 1.82
219 223 2.009774 CAATCGTGCCTCTCGGAAAAT 58.990 47.619 0.00 0.00 0.00 1.82
224 228 1.084370 GGAACAATCGTGCCTCTCGG 61.084 60.000 0.00 0.00 37.94 4.63
255 259 4.463891 ACTTTTCGAGGAGGTACGGATTTA 59.536 41.667 2.74 0.00 0.00 1.40
264 268 3.260128 ACGGATTTACTTTTCGAGGAGGT 59.740 43.478 2.74 0.00 0.00 3.85
274 278 3.435671 CGCTTGAAGGACGGATTTACTTT 59.564 43.478 0.00 0.00 0.00 2.66
322 326 4.101585 TCATAGTCATGCCTCTCGGAAAAT 59.898 41.667 0.00 0.00 31.73 1.82
358 362 7.391148 TCCTTTAAATGTAGGCACAGATTTC 57.609 36.000 0.00 0.00 38.30 2.17
364 368 6.322712 ACAAGTTTCCTTTAAATGTAGGCACA 59.677 34.615 0.00 0.00 39.52 4.57
461 466 6.099341 TGTTTCTCAGCTTTTCTGGTTTTTC 58.901 36.000 0.00 0.00 43.06 2.29
466 471 5.659440 TTTTGTTTCTCAGCTTTTCTGGT 57.341 34.783 0.00 0.00 43.06 4.00
550 555 1.522569 GGTCGTGCTCTATGGGCTT 59.477 57.895 0.00 0.00 0.00 4.35
596 601 3.787001 CGAGCCCTCCCAAGGTCC 61.787 72.222 0.00 0.00 41.59 4.46
628 633 2.481952 GCAAGGCAGAACAACTACTCAG 59.518 50.000 0.00 0.00 0.00 3.35
639 644 0.968405 GGAAATGGTGCAAGGCAGAA 59.032 50.000 0.00 0.00 40.08 3.02
800 1118 9.057089 GTGACCTATCCGATATTTTCATTTCTT 57.943 33.333 0.00 0.00 0.00 2.52
814 1132 4.023980 ACATTCTTGAGTGACCTATCCGA 58.976 43.478 0.20 0.00 0.00 4.55
857 3414 3.312697 GCGATGGGAGGTGTTTATCTTTC 59.687 47.826 0.00 0.00 0.00 2.62
1209 3777 2.507102 CAGGCGTCGATCAGCGTT 60.507 61.111 0.00 0.00 41.80 4.84
1752 4320 3.869272 CGAATCGCCTGTGCCAGC 61.869 66.667 0.00 0.00 0.00 4.85
1878 4446 3.326006 TCTGCATCTTGAGGAAGAACTGT 59.674 43.478 0.00 0.00 41.64 3.55
2054 4622 1.304630 TGATTGCTGCTGGCCATGT 60.305 52.632 5.51 0.00 40.92 3.21
2167 4735 1.602237 CACTACCAATGCCTCCGGT 59.398 57.895 0.00 0.00 36.79 5.28
2211 4779 3.374042 TCGTCTTCCATCTCTTCCTCT 57.626 47.619 0.00 0.00 0.00 3.69
2523 5091 8.820933 CCATATAACTAATCATGCTACATTCGG 58.179 37.037 0.00 0.00 0.00 4.30
2646 5214 4.355437 CATAGGCTACTGTTGAGAACTCG 58.645 47.826 0.00 0.00 0.00 4.18
2703 5271 6.823182 ACATATAACATAAGCAGCACAGTTCA 59.177 34.615 0.00 0.00 0.00 3.18
2755 5323 2.170607 GCCACAATAACCTCTCCTGCTA 59.829 50.000 0.00 0.00 0.00 3.49
2822 5390 5.126396 AGCCTTGCTATTTTCTCAACAAC 57.874 39.130 0.00 0.00 36.99 3.32
2823 5391 5.789643 AAGCCTTGCTATTTTCTCAACAA 57.210 34.783 0.00 0.00 38.25 2.83
2824 5392 5.767665 TGTAAGCCTTGCTATTTTCTCAACA 59.232 36.000 0.00 0.00 38.25 3.33
2825 5393 6.254281 TGTAAGCCTTGCTATTTTCTCAAC 57.746 37.500 0.00 0.00 38.25 3.18
2876 5444 0.391263 ACTGCGCTACCAAACTAGGC 60.391 55.000 9.73 0.00 0.00 3.93
2877 5445 2.094762 AACTGCGCTACCAAACTAGG 57.905 50.000 9.73 0.00 0.00 3.02
2878 5446 4.483476 AAAAACTGCGCTACCAAACTAG 57.517 40.909 9.73 0.00 0.00 2.57
2879 5447 6.374565 TTTAAAAACTGCGCTACCAAACTA 57.625 33.333 9.73 0.00 0.00 2.24
2880 5448 4.904253 TTAAAAACTGCGCTACCAAACT 57.096 36.364 9.73 0.00 0.00 2.66
2881 5449 5.288952 TGTTTTAAAAACTGCGCTACCAAAC 59.711 36.000 9.73 7.65 0.00 2.93
2882 5450 5.288952 GTGTTTTAAAAACTGCGCTACCAAA 59.711 36.000 9.73 0.00 0.00 3.28
2883 5451 4.799428 GTGTTTTAAAAACTGCGCTACCAA 59.201 37.500 9.73 0.00 0.00 3.67
2884 5452 4.352887 GTGTTTTAAAAACTGCGCTACCA 58.647 39.130 9.73 0.00 0.00 3.25
2885 5453 3.732219 GGTGTTTTAAAAACTGCGCTACC 59.268 43.478 9.73 0.00 0.00 3.18
2886 5454 3.732219 GGGTGTTTTAAAAACTGCGCTAC 59.268 43.478 9.73 0.00 0.00 3.58
2887 5455 3.633065 AGGGTGTTTTAAAAACTGCGCTA 59.367 39.130 9.73 0.00 0.00 4.26
2888 5456 2.429250 AGGGTGTTTTAAAAACTGCGCT 59.571 40.909 9.73 4.54 0.00 5.92
2889 5457 2.816689 AGGGTGTTTTAAAAACTGCGC 58.183 42.857 0.00 0.00 0.00 6.09
2890 5458 5.177725 ACTAGGGTGTTTTAAAAACTGCG 57.822 39.130 1.31 0.00 0.00 5.18
2891 5459 9.188588 GAAATACTAGGGTGTTTTAAAAACTGC 57.811 33.333 1.31 0.00 37.00 4.40
2900 5468 8.132995 CGAAGTTTTGAAATACTAGGGTGTTTT 58.867 33.333 0.00 0.00 37.00 2.43
2901 5469 7.255346 CCGAAGTTTTGAAATACTAGGGTGTTT 60.255 37.037 0.00 0.00 39.00 2.83
2902 5470 6.206048 CCGAAGTTTTGAAATACTAGGGTGTT 59.794 38.462 0.00 0.00 0.00 3.32
2903 5471 5.704053 CCGAAGTTTTGAAATACTAGGGTGT 59.296 40.000 0.00 0.00 0.00 4.16
2904 5472 5.704053 ACCGAAGTTTTGAAATACTAGGGTG 59.296 40.000 0.00 0.00 32.25 4.61
2905 5473 5.872963 ACCGAAGTTTTGAAATACTAGGGT 58.127 37.500 0.00 10.88 30.90 4.34
2906 5474 8.395633 CAATACCGAAGTTTTGAAATACTAGGG 58.604 37.037 0.00 10.50 37.17 3.53
2907 5475 7.908601 GCAATACCGAAGTTTTGAAATACTAGG 59.091 37.037 0.00 0.00 37.17 3.02
2908 5476 8.447833 TGCAATACCGAAGTTTTGAAATACTAG 58.552 33.333 1.34 0.00 37.17 2.57
2909 5477 8.325421 TGCAATACCGAAGTTTTGAAATACTA 57.675 30.769 1.34 0.00 37.17 1.82
2910 5478 7.209471 TGCAATACCGAAGTTTTGAAATACT 57.791 32.000 1.34 0.00 37.17 2.12
2911 5479 7.861176 TTGCAATACCGAAGTTTTGAAATAC 57.139 32.000 0.00 0.00 37.17 1.89
2912 5480 7.062839 GCATTGCAATACCGAAGTTTTGAAATA 59.937 33.333 12.53 0.00 39.69 1.40
2913 5481 6.128580 GCATTGCAATACCGAAGTTTTGAAAT 60.129 34.615 12.53 0.01 41.34 2.17
2914 5482 5.176590 GCATTGCAATACCGAAGTTTTGAAA 59.823 36.000 12.53 0.00 37.03 2.69
2915 5483 4.683781 GCATTGCAATACCGAAGTTTTGAA 59.316 37.500 12.53 0.00 37.17 2.69
2916 5484 4.022416 AGCATTGCAATACCGAAGTTTTGA 60.022 37.500 12.53 0.00 37.17 2.69
2917 5485 4.236935 AGCATTGCAATACCGAAGTTTTG 58.763 39.130 12.53 0.00 37.81 2.44
2918 5486 4.519540 AGCATTGCAATACCGAAGTTTT 57.480 36.364 12.53 0.00 0.00 2.43
2919 5487 4.236935 CAAGCATTGCAATACCGAAGTTT 58.763 39.130 12.53 0.00 40.39 2.66
2920 5488 3.836949 CAAGCATTGCAATACCGAAGTT 58.163 40.909 12.53 0.00 40.39 2.66
2921 5489 3.492421 CAAGCATTGCAATACCGAAGT 57.508 42.857 12.53 0.00 40.39 3.01
2937 5505 2.351726 CTGTAGTATTCGTTGCCCAAGC 59.648 50.000 0.00 0.00 40.48 4.01
2938 5506 3.596214 ACTGTAGTATTCGTTGCCCAAG 58.404 45.455 0.00 0.00 0.00 3.61
2939 5507 3.688694 ACTGTAGTATTCGTTGCCCAA 57.311 42.857 0.00 0.00 0.00 4.12
2940 5508 3.688694 AACTGTAGTATTCGTTGCCCA 57.311 42.857 0.00 0.00 0.00 5.36
2941 5509 5.366829 AAAAACTGTAGTATTCGTTGCCC 57.633 39.130 0.00 0.00 0.00 5.36
2970 5538 7.322664 ACTGAGAGAATTGCAGTTTTCAAAAA 58.677 30.769 13.79 0.00 39.69 1.94
2971 5539 6.866480 ACTGAGAGAATTGCAGTTTTCAAAA 58.134 32.000 13.79 0.06 39.69 2.44
2972 5540 6.455360 ACTGAGAGAATTGCAGTTTTCAAA 57.545 33.333 13.79 2.17 39.69 2.69
2979 5547 5.869579 TCCTAAAACTGAGAGAATTGCAGT 58.130 37.500 0.00 0.00 44.15 4.40
2980 5548 6.808008 TTCCTAAAACTGAGAGAATTGCAG 57.192 37.500 0.00 0.00 35.81 4.41
2981 5549 7.425606 GTTTTCCTAAAACTGAGAGAATTGCA 58.574 34.615 7.78 0.00 45.55 4.08
2982 5550 7.859613 GTTTTCCTAAAACTGAGAGAATTGC 57.140 36.000 7.78 0.00 45.55 3.56
2996 5564 8.736244 GCCAAACATATCAGTAGTTTTCCTAAA 58.264 33.333 0.00 0.00 33.54 1.85
2997 5565 8.107095 AGCCAAACATATCAGTAGTTTTCCTAA 58.893 33.333 0.00 0.00 33.54 2.69
2998 5566 7.552687 CAGCCAAACATATCAGTAGTTTTCCTA 59.447 37.037 0.00 0.00 33.54 2.94
2999 5567 6.375455 CAGCCAAACATATCAGTAGTTTTCCT 59.625 38.462 0.00 0.00 33.54 3.36
3000 5568 6.404734 CCAGCCAAACATATCAGTAGTTTTCC 60.405 42.308 0.00 0.00 33.54 3.13
3001 5569 6.151144 ACCAGCCAAACATATCAGTAGTTTTC 59.849 38.462 0.00 0.00 33.54 2.29
3002 5570 6.010219 ACCAGCCAAACATATCAGTAGTTTT 58.990 36.000 0.00 0.00 33.54 2.43
3003 5571 5.415701 CACCAGCCAAACATATCAGTAGTTT 59.584 40.000 0.00 0.00 36.00 2.66
3004 5572 4.943705 CACCAGCCAAACATATCAGTAGTT 59.056 41.667 0.00 0.00 0.00 2.24
3005 5573 4.019321 ACACCAGCCAAACATATCAGTAGT 60.019 41.667 0.00 0.00 0.00 2.73
3006 5574 4.517285 ACACCAGCCAAACATATCAGTAG 58.483 43.478 0.00 0.00 0.00 2.57
3007 5575 4.568072 ACACCAGCCAAACATATCAGTA 57.432 40.909 0.00 0.00 0.00 2.74
3008 5576 3.439857 ACACCAGCCAAACATATCAGT 57.560 42.857 0.00 0.00 0.00 3.41
3009 5577 3.507233 ACAACACCAGCCAAACATATCAG 59.493 43.478 0.00 0.00 0.00 2.90
3010 5578 3.495331 ACAACACCAGCCAAACATATCA 58.505 40.909 0.00 0.00 0.00 2.15
3011 5579 4.519540 AACAACACCAGCCAAACATATC 57.480 40.909 0.00 0.00 0.00 1.63
3012 5580 4.953940 AAACAACACCAGCCAAACATAT 57.046 36.364 0.00 0.00 0.00 1.78
3013 5581 4.744795 AAAACAACACCAGCCAAACATA 57.255 36.364 0.00 0.00 0.00 2.29
3014 5582 3.625649 AAAACAACACCAGCCAAACAT 57.374 38.095 0.00 0.00 0.00 2.71
3015 5583 3.511934 AGTAAAACAACACCAGCCAAACA 59.488 39.130 0.00 0.00 0.00 2.83
3016 5584 3.862845 CAGTAAAACAACACCAGCCAAAC 59.137 43.478 0.00 0.00 0.00 2.93
3017 5585 3.511934 ACAGTAAAACAACACCAGCCAAA 59.488 39.130 0.00 0.00 0.00 3.28
3018 5586 3.093057 ACAGTAAAACAACACCAGCCAA 58.907 40.909 0.00 0.00 0.00 4.52
3019 5587 2.729194 ACAGTAAAACAACACCAGCCA 58.271 42.857 0.00 0.00 0.00 4.75
3020 5588 3.881089 ACTACAGTAAAACAACACCAGCC 59.119 43.478 0.00 0.00 0.00 4.85
3021 5589 5.494632 AACTACAGTAAAACAACACCAGC 57.505 39.130 0.00 0.00 0.00 4.85
3022 5590 7.483691 GTCAAAACTACAGTAAAACAACACCAG 59.516 37.037 0.00 0.00 0.00 4.00
3023 5591 7.306953 GTCAAAACTACAGTAAAACAACACCA 58.693 34.615 0.00 0.00 0.00 4.17
3024 5592 6.748658 GGTCAAAACTACAGTAAAACAACACC 59.251 38.462 0.00 0.00 0.00 4.16
3025 5593 7.306953 TGGTCAAAACTACAGTAAAACAACAC 58.693 34.615 0.00 0.00 0.00 3.32
3026 5594 7.450124 TGGTCAAAACTACAGTAAAACAACA 57.550 32.000 0.00 0.00 0.00 3.33
3027 5595 8.920509 ATTGGTCAAAACTACAGTAAAACAAC 57.079 30.769 0.00 0.00 0.00 3.32
3035 5603 9.344772 TGTGTAATTATTGGTCAAAACTACAGT 57.655 29.630 0.00 0.00 0.00 3.55
3037 5605 9.953697 GTTGTGTAATTATTGGTCAAAACTACA 57.046 29.630 0.00 0.00 0.00 2.74
3088 5656 1.351012 CGGTCGTGTAGCTCCGTAG 59.649 63.158 0.00 0.00 38.45 3.51
3089 5657 2.108514 CCGGTCGTGTAGCTCCGTA 61.109 63.158 8.30 0.00 41.17 4.02
3090 5658 3.437795 CCGGTCGTGTAGCTCCGT 61.438 66.667 8.30 0.00 41.17 4.69
3091 5659 2.389866 GATCCGGTCGTGTAGCTCCG 62.390 65.000 0.00 2.41 42.22 4.63
3092 5660 1.359475 GATCCGGTCGTGTAGCTCC 59.641 63.158 0.00 0.00 0.00 4.70
3093 5661 0.454600 TTGATCCGGTCGTGTAGCTC 59.545 55.000 0.00 0.00 0.00 4.09
3094 5662 1.112113 ATTGATCCGGTCGTGTAGCT 58.888 50.000 0.00 0.00 0.00 3.32
3095 5663 1.935933 AATTGATCCGGTCGTGTAGC 58.064 50.000 0.00 0.00 0.00 3.58
3096 5664 4.537965 CTCTAATTGATCCGGTCGTGTAG 58.462 47.826 0.00 0.00 0.00 2.74
3097 5665 3.243301 GCTCTAATTGATCCGGTCGTGTA 60.243 47.826 0.00 0.00 0.00 2.90
3098 5666 2.481449 GCTCTAATTGATCCGGTCGTGT 60.481 50.000 0.00 0.00 0.00 4.49
3099 5667 2.128035 GCTCTAATTGATCCGGTCGTG 58.872 52.381 0.00 0.00 0.00 4.35
3100 5668 1.754803 TGCTCTAATTGATCCGGTCGT 59.245 47.619 0.00 0.00 0.00 4.34
3101 5669 2.509052 TGCTCTAATTGATCCGGTCG 57.491 50.000 0.00 0.00 0.00 4.79
3102 5670 3.070018 CCATGCTCTAATTGATCCGGTC 58.930 50.000 0.00 0.00 0.00 4.79
3103 5671 2.439507 ACCATGCTCTAATTGATCCGGT 59.560 45.455 0.00 0.00 0.00 5.28
3104 5672 3.131709 ACCATGCTCTAATTGATCCGG 57.868 47.619 0.00 0.00 0.00 5.14
3105 5673 5.300752 AGTAACCATGCTCTAATTGATCCG 58.699 41.667 0.00 0.00 0.00 4.18
3106 5674 7.573968 AAAGTAACCATGCTCTAATTGATCC 57.426 36.000 0.00 0.00 0.00 3.36
3107 5675 8.560374 GGTAAAGTAACCATGCTCTAATTGATC 58.440 37.037 0.00 0.00 39.50 2.92
3108 5676 8.052748 TGGTAAAGTAACCATGCTCTAATTGAT 58.947 33.333 0.00 0.00 44.68 2.57
3109 5677 7.398829 TGGTAAAGTAACCATGCTCTAATTGA 58.601 34.615 0.00 0.00 44.68 2.57
3110 5678 7.624360 TGGTAAAGTAACCATGCTCTAATTG 57.376 36.000 0.00 0.00 44.68 2.32
3143 5711 9.797556 GTTGGTCAAAACTTAGATTAAAGTTGT 57.202 29.630 2.97 0.00 46.40 3.32
3144 5712 9.244799 GGTTGGTCAAAACTTAGATTAAAGTTG 57.755 33.333 2.97 0.00 46.40 3.16
3146 5714 7.283807 ACGGTTGGTCAAAACTTAGATTAAAGT 59.716 33.333 0.00 0.00 41.46 2.66
3147 5715 7.645402 ACGGTTGGTCAAAACTTAGATTAAAG 58.355 34.615 0.00 0.00 0.00 1.85
3148 5716 7.571080 ACGGTTGGTCAAAACTTAGATTAAA 57.429 32.000 0.00 0.00 0.00 1.52
3149 5717 7.419204 CAACGGTTGGTCAAAACTTAGATTAA 58.581 34.615 13.03 0.00 0.00 1.40
3150 5718 6.016943 CCAACGGTTGGTCAAAACTTAGATTA 60.017 38.462 27.87 0.00 45.93 1.75
3151 5719 5.221165 CCAACGGTTGGTCAAAACTTAGATT 60.221 40.000 27.87 0.00 45.93 2.40
3152 5720 4.277423 CCAACGGTTGGTCAAAACTTAGAT 59.723 41.667 27.87 0.00 45.93 1.98
3153 5721 3.628487 CCAACGGTTGGTCAAAACTTAGA 59.372 43.478 27.87 0.00 45.93 2.10
3154 5722 3.959943 CCAACGGTTGGTCAAAACTTAG 58.040 45.455 27.87 1.84 45.93 2.18
3156 5724 2.951457 CCAACGGTTGGTCAAAACTT 57.049 45.000 27.87 0.00 45.93 2.66
3166 5734 4.454504 ACACTTTCTTATAGCCAACGGTTG 59.545 41.667 13.86 13.86 0.00 3.77
3167 5735 4.648651 ACACTTTCTTATAGCCAACGGTT 58.351 39.130 0.00 0.00 0.00 4.44
3168 5736 4.251268 GACACTTTCTTATAGCCAACGGT 58.749 43.478 0.00 0.00 0.00 4.83
3169 5737 4.250464 TGACACTTTCTTATAGCCAACGG 58.750 43.478 0.00 0.00 0.00 4.44
3170 5738 5.351465 ACATGACACTTTCTTATAGCCAACG 59.649 40.000 0.00 0.00 0.00 4.10
3171 5739 6.371548 TGACATGACACTTTCTTATAGCCAAC 59.628 38.462 0.00 0.00 0.00 3.77
3172 5740 6.472016 TGACATGACACTTTCTTATAGCCAA 58.528 36.000 0.00 0.00 0.00 4.52
3173 5741 6.048732 TGACATGACACTTTCTTATAGCCA 57.951 37.500 0.00 0.00 0.00 4.75
3174 5742 7.559590 AATGACATGACACTTTCTTATAGCC 57.440 36.000 0.00 0.00 0.00 3.93
3180 5748 9.295825 TGGTTATAAATGACATGACACTTTCTT 57.704 29.630 0.00 0.00 0.00 2.52
3181 5749 8.862325 TGGTTATAAATGACATGACACTTTCT 57.138 30.769 0.00 0.00 0.00 2.52
3184 5752 9.466497 AGATTGGTTATAAATGACATGACACTT 57.534 29.630 0.00 0.00 0.00 3.16
3185 5753 9.466497 AAGATTGGTTATAAATGACATGACACT 57.534 29.630 0.00 0.00 0.00 3.55
3198 5766 9.860650 ACATGTTGGCTATAAGATTGGTTATAA 57.139 29.630 0.00 0.00 0.00 0.98
3202 5770 9.284968 GTATACATGTTGGCTATAAGATTGGTT 57.715 33.333 2.30 0.00 0.00 3.67
3203 5771 7.883311 GGTATACATGTTGGCTATAAGATTGGT 59.117 37.037 2.30 0.00 0.00 3.67
3204 5772 7.882791 TGGTATACATGTTGGCTATAAGATTGG 59.117 37.037 2.30 0.00 0.00 3.16
3205 5773 8.846943 TGGTATACATGTTGGCTATAAGATTG 57.153 34.615 2.30 0.00 0.00 2.67
3210 5778 9.226606 GCTAATTGGTATACATGTTGGCTATAA 57.773 33.333 2.30 0.00 32.56 0.98
3211 5779 8.602424 AGCTAATTGGTATACATGTTGGCTATA 58.398 33.333 16.75 0.00 38.86 1.31
3212 5780 7.461749 AGCTAATTGGTATACATGTTGGCTAT 58.538 34.615 16.75 0.00 38.86 2.97
3213 5781 6.837312 AGCTAATTGGTATACATGTTGGCTA 58.163 36.000 16.75 0.00 38.86 3.93
3214 5782 5.694995 AGCTAATTGGTATACATGTTGGCT 58.305 37.500 2.30 14.19 37.19 4.75
3215 5783 7.687941 ATAGCTAATTGGTATACATGTTGGC 57.312 36.000 2.30 8.94 37.56 4.52


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

AutoCloner maintained by Alex Coulton.