Multiple sequence alignment - TraesCS7B01G152800

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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 TraesCS7B01G152800 chr7B 100.000 4241 0 0 1 4241 203030886 203026646 0.000000e+00 7832.0
1 TraesCS7B01G152800 chr7D 87.757 4370 313 115 1 4241 232410589 232406313 0.000000e+00 4902.0
2 TraesCS7B01G152800 chr7A 86.466 3783 245 109 1 3655 244606146 244602503 0.000000e+00 3903.0
3 TraesCS7B01G152800 chr7A 90.291 103 3 4 4146 4241 244602428 244602326 1.240000e-25 128.0
4 TraesCS7B01G152800 chr7A 87.838 74 6 2 3679 3752 244602503 244602433 2.720000e-12 84.2


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 TraesCS7B01G152800 chr7B 203026646 203030886 4240 True 7832.000000 7832 100.000000 1 4241 1 chr7B.!!$R1 4240
1 TraesCS7B01G152800 chr7D 232406313 232410589 4276 True 4902.000000 4902 87.757000 1 4241 1 chr7D.!!$R1 4240
2 TraesCS7B01G152800 chr7A 244602326 244606146 3820 True 1371.733333 3903 88.198333 1 4241 3 chr7A.!!$R1 4240

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
905 943 0.250209 CTCCTCCAGCATCCATTCCG 60.250 60.0 0.00 0.00 0.00 4.30 F
1459 1528 0.240411 GTGAGCAGAGCTTGGCTTTG 59.760 55.0 13.45 5.82 42.55 2.77 F
2887 3036 0.098376 GTACTGCACTCCCTCGTACG 59.902 60.0 9.53 9.53 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2887 3036 0.231534 CAGCGACGACATCATCATGC 59.768 55.0 0.0 0.0 32.57 4.06 R
2978 3139 0.105224 TCCTTGTTCCGTTCAGCGAA 59.895 50.0 0.0 0.0 44.77 4.70 R
3775 3962 0.171903 CGGGGTGTACAGTTCGGTAG 59.828 60.0 0.0 0.0 0.00 3.18 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
19 20 0.250295 CCTCGAAGTTGGCCTTGACA 60.250 55.000 3.32 0.00 32.03 3.58
61 62 2.198304 GACCCGGCCACCAGAGAAAT 62.198 60.000 2.24 0.00 0.00 2.17
62 63 1.000896 CCCGGCCACCAGAGAAATT 60.001 57.895 2.24 0.00 0.00 1.82
63 64 0.611896 CCCGGCCACCAGAGAAATTT 60.612 55.000 2.24 0.00 0.00 1.82
84 85 1.596477 GCATGAGGATGGAGCGGAC 60.596 63.158 0.00 0.00 0.00 4.79
130 131 3.512516 GCAGCTCCCACCAATCGC 61.513 66.667 0.00 0.00 0.00 4.58
194 195 3.558505 CAGCAAGCAACAACACTATGAC 58.441 45.455 0.00 0.00 0.00 3.06
201 202 2.508439 AACACTATGACGCGGGCG 60.508 61.111 12.47 12.04 46.03 6.13
202 203 4.508128 ACACTATGACGCGGGCGG 62.508 66.667 18.03 1.36 44.69 6.13
221 222 1.717348 CATGCGATGTGTGCGATGT 59.283 52.632 0.00 0.00 34.24 3.06
222 223 0.587985 CATGCGATGTGTGCGATGTG 60.588 55.000 0.00 0.00 34.24 3.21
234 235 3.499737 GATGTGTTCGGCAGCGGG 61.500 66.667 0.00 0.00 0.00 6.13
236 237 2.845752 GATGTGTTCGGCAGCGGGTA 62.846 60.000 0.00 0.00 0.00 3.69
252 253 1.202382 GGGTAAGGACTCGTGATTCCG 60.202 57.143 1.14 0.00 35.53 4.30
253 254 1.747355 GGTAAGGACTCGTGATTCCGA 59.253 52.381 1.14 0.00 35.53 4.55
256 257 1.872679 GGACTCGTGATTCCGACGC 60.873 63.158 0.00 0.00 36.75 5.19
257 258 2.202440 ACTCGTGATTCCGACGCG 60.202 61.111 3.53 3.53 41.61 6.01
298 300 2.080693 CCACAAGGCGCATAACAACTA 58.919 47.619 10.83 0.00 0.00 2.24
318 334 9.445786 ACAACTATTTGACGAAATGTAAGTTTG 57.554 29.630 0.00 0.00 36.48 2.93
322 338 9.530129 CTATTTGACGAAATGTAAGTTTGACTC 57.470 33.333 0.00 0.00 33.63 3.36
334 351 8.715191 TGTAAGTTTGACTCCGTTAAGTTTAA 57.285 30.769 0.00 0.00 0.00 1.52
337 354 5.761726 AGTTTGACTCCGTTAAGTTTAAGGG 59.238 40.000 14.27 14.27 45.42 3.95
354 371 8.225416 AGTTTAAGGGATTGGTTAGAAAAGACT 58.775 33.333 0.00 0.00 0.00 3.24
381 398 8.650143 TTTTTAGGAGAGCAAATGTATTCCTT 57.350 30.769 0.00 0.00 36.51 3.36
388 405 8.907885 GGAGAGCAAATGTATTCCTTTAAAGAT 58.092 33.333 16.98 5.77 0.00 2.40
425 444 4.513692 ACTCCTCTAAATCGAGATGAGACG 59.486 45.833 11.24 0.00 39.35 4.18
435 454 0.955178 AGATGAGACGAGCCATACCG 59.045 55.000 0.00 0.00 0.00 4.02
437 456 1.878088 GATGAGACGAGCCATACCGTA 59.122 52.381 0.00 0.00 39.30 4.02
444 463 5.045872 AGACGAGCCATACCGTATTTTAAC 58.954 41.667 0.00 0.00 39.30 2.01
584 609 1.539827 GGAATTCCACGTGTTTCCCAG 59.460 52.381 20.04 5.41 33.08 4.45
590 617 1.960689 CCACGTGTTTCCCAGGAAATT 59.039 47.619 15.65 0.00 44.52 1.82
616 643 4.329801 GCGAAAATCCATGTGAAAAATCCC 59.670 41.667 0.00 0.00 0.00 3.85
720 754 1.024579 CAGAATTACTGCCGCCGGTT 61.025 55.000 4.45 0.00 39.86 4.44
905 943 0.250209 CTCCTCCAGCATCCATTCCG 60.250 60.000 0.00 0.00 0.00 4.30
917 955 1.626356 CCATTCCGCCTCCTCCTTCA 61.626 60.000 0.00 0.00 0.00 3.02
927 965 2.234296 CCTCCTTCACCCCCAAGCT 61.234 63.158 0.00 0.00 0.00 3.74
928 966 1.001641 CTCCTTCACCCCCAAGCTG 60.002 63.158 0.00 0.00 0.00 4.24
1012 1062 3.832981 CGTAAAGGAACGACGCGT 58.167 55.556 13.85 13.85 45.68 6.01
1016 1066 0.592637 TAAAGGAACGACGCGTCTCA 59.407 50.000 33.94 9.56 39.99 3.27
1038 1095 4.324991 GGGCGGTTCTTGGACGGT 62.325 66.667 0.00 0.00 0.00 4.83
1039 1096 3.047877 GGCGGTTCTTGGACGGTG 61.048 66.667 0.00 0.00 0.00 4.94
1040 1097 2.280592 GCGGTTCTTGGACGGTGT 60.281 61.111 0.00 0.00 0.00 4.16
1041 1098 2.315386 GCGGTTCTTGGACGGTGTC 61.315 63.158 0.00 0.00 0.00 3.67
1277 1340 3.797353 GGGCTCTTCGGGATGCCA 61.797 66.667 3.39 0.00 46.53 4.92
1459 1528 0.240411 GTGAGCAGAGCTTGGCTTTG 59.760 55.000 13.45 5.82 42.55 2.77
1502 1571 1.526686 CTGCTGATGCCCGCCATTA 60.527 57.895 0.00 0.00 38.71 1.90
1567 1636 4.070552 GCAGAAGGAGGCGGACGT 62.071 66.667 0.00 0.00 0.00 4.34
1586 1655 2.526873 AAGAGGTGCAGGACGGGT 60.527 61.111 0.00 0.00 0.00 5.28
1796 1876 3.003793 CCTGAATGATCATGCTGCTTCTG 59.996 47.826 14.96 9.23 34.37 3.02
1917 1997 3.263261 GAAATTTCTCCAGGACCTCGTC 58.737 50.000 11.05 0.00 0.00 4.20
1947 2027 7.702348 GGATGCAACAAGGTAATTAGTCATTTC 59.298 37.037 0.00 0.00 0.00 2.17
1948 2028 7.517614 TGCAACAAGGTAATTAGTCATTTCA 57.482 32.000 0.00 0.00 0.00 2.69
1950 2030 8.584157 TGCAACAAGGTAATTAGTCATTTCATT 58.416 29.630 0.00 0.00 0.00 2.57
1951 2031 9.076596 GCAACAAGGTAATTAGTCATTTCATTC 57.923 33.333 0.00 0.00 0.00 2.67
1999 2080 6.404074 CCAAAATGAGAAATCGGAAAGAGGAG 60.404 42.308 0.00 0.00 0.00 3.69
2072 2197 6.047231 AGACAGTCTTTGTGTACAAGGTTAC 58.953 40.000 0.00 0.00 41.05 2.50
2075 2200 5.236478 CAGTCTTTGTGTACAAGGTTACCAG 59.764 44.000 3.51 0.00 37.15 4.00
2092 2217 6.370442 GGTTACCAGTTAAATTGGCCAAATTC 59.630 38.462 24.71 9.57 37.51 2.17
2189 2314 2.094442 GCAAGTCGAGGTAAGAAGAGCT 60.094 50.000 0.00 0.00 0.00 4.09
2190 2315 3.506810 CAAGTCGAGGTAAGAAGAGCTG 58.493 50.000 0.00 0.00 0.00 4.24
2191 2316 3.074675 AGTCGAGGTAAGAAGAGCTGA 57.925 47.619 0.00 0.00 0.00 4.26
2192 2317 3.422796 AGTCGAGGTAAGAAGAGCTGAA 58.577 45.455 0.00 0.00 0.00 3.02
2193 2318 3.827302 AGTCGAGGTAAGAAGAGCTGAAA 59.173 43.478 0.00 0.00 0.00 2.69
2194 2319 4.082463 AGTCGAGGTAAGAAGAGCTGAAAG 60.082 45.833 0.00 0.00 0.00 2.62
2219 2346 1.967319 AACCATCCGATGCCATGTAC 58.033 50.000 2.53 0.00 0.00 2.90
2221 2348 1.202687 ACCATCCGATGCCATGTACTG 60.203 52.381 2.53 0.00 0.00 2.74
2233 2360 2.259618 CATGTACTGGTAGTGACGTGC 58.740 52.381 0.00 0.00 0.00 5.34
2274 2405 1.072331 TCCTCCTCTGTTTCTGTTGCC 59.928 52.381 0.00 0.00 0.00 4.52
2350 2481 0.957395 CCACGCTCCTGCACAAAGAT 60.957 55.000 0.00 0.00 39.64 2.40
2373 2504 2.612251 CCCAAAACCCACCCCTGT 59.388 61.111 0.00 0.00 0.00 4.00
2477 2609 1.515304 GAGCTCGGTGTTCTCGCTC 60.515 63.158 0.00 0.00 40.07 5.03
2654 2789 4.681978 ACGGCCAGCACGAACCTC 62.682 66.667 2.24 0.00 34.93 3.85
2693 2831 4.290155 CCTTGAGAATTTCGTGGTTGTTG 58.710 43.478 0.00 0.00 0.00 3.33
2694 2832 4.202010 CCTTGAGAATTTCGTGGTTGTTGT 60.202 41.667 0.00 0.00 0.00 3.32
2727 2865 5.688348 CGAAAGAATCGTTAGAGACCTTG 57.312 43.478 0.00 0.00 46.52 3.61
2729 2870 5.061064 CGAAAGAATCGTTAGAGACCTTGTG 59.939 44.000 0.00 0.00 46.52 3.33
2752 2898 2.219903 TGATACAGTTTCGTTGTGCGTG 59.780 45.455 0.00 0.00 42.13 5.34
2836 2985 1.335132 GCCAGGATAACGGGGTCTCA 61.335 60.000 0.00 0.00 34.66 3.27
2860 3009 2.633481 AGAGAGCTTCCACGGTTAGTTT 59.367 45.455 0.00 0.00 0.00 2.66
2861 3010 3.071167 AGAGAGCTTCCACGGTTAGTTTT 59.929 43.478 0.00 0.00 0.00 2.43
2862 3011 3.400255 AGAGCTTCCACGGTTAGTTTTC 58.600 45.455 0.00 0.00 0.00 2.29
2863 3012 3.071167 AGAGCTTCCACGGTTAGTTTTCT 59.929 43.478 0.00 0.00 0.00 2.52
2864 3013 4.282703 AGAGCTTCCACGGTTAGTTTTCTA 59.717 41.667 0.00 0.00 0.00 2.10
2865 3014 4.964593 AGCTTCCACGGTTAGTTTTCTAA 58.035 39.130 0.00 0.00 39.72 2.10
2866 3015 5.370679 AGCTTCCACGGTTAGTTTTCTAAA 58.629 37.500 0.00 0.00 42.99 1.85
2867 3016 5.824097 AGCTTCCACGGTTAGTTTTCTAAAA 59.176 36.000 0.00 0.00 42.99 1.52
2869 3018 6.238566 GCTTCCACGGTTAGTTTTCTAAAAGT 60.239 38.462 1.48 1.48 42.99 2.66
2870 3019 7.041848 GCTTCCACGGTTAGTTTTCTAAAAGTA 60.042 37.037 0.00 0.00 42.99 2.24
2871 3020 7.713764 TCCACGGTTAGTTTTCTAAAAGTAC 57.286 36.000 2.88 0.00 42.99 2.73
2873 3022 7.439056 TCCACGGTTAGTTTTCTAAAAGTACTG 59.561 37.037 0.00 6.25 42.99 2.74
2874 3023 7.067728 CACGGTTAGTTTTCTAAAAGTACTGC 58.932 38.462 0.00 0.00 42.99 4.40
2875 3024 6.762661 ACGGTTAGTTTTCTAAAAGTACTGCA 59.237 34.615 0.00 0.00 42.99 4.41
2876 3025 7.067728 CGGTTAGTTTTCTAAAAGTACTGCAC 58.932 38.462 0.00 0.22 42.99 4.57
2877 3026 7.042254 CGGTTAGTTTTCTAAAAGTACTGCACT 60.042 37.037 0.00 0.00 42.99 4.40
2878 3027 8.281194 GGTTAGTTTTCTAAAAGTACTGCACTC 58.719 37.037 0.00 0.00 42.99 3.51
2879 3028 6.862711 AGTTTTCTAAAAGTACTGCACTCC 57.137 37.500 0.00 0.00 36.04 3.85
2880 3029 5.763698 AGTTTTCTAAAAGTACTGCACTCCC 59.236 40.000 0.00 0.00 36.04 4.30
2881 3030 5.562298 TTTCTAAAAGTACTGCACTCCCT 57.438 39.130 0.00 0.00 36.04 4.20
2882 3031 4.803098 TCTAAAAGTACTGCACTCCCTC 57.197 45.455 0.00 0.00 36.04 4.30
2883 3032 2.457366 AAAAGTACTGCACTCCCTCG 57.543 50.000 0.00 0.00 36.04 4.63
2884 3033 1.339097 AAAGTACTGCACTCCCTCGT 58.661 50.000 0.00 0.00 36.04 4.18
2886 3035 1.461559 AGTACTGCACTCCCTCGTAC 58.538 55.000 0.00 2.79 28.33 3.67
2887 3036 0.098376 GTACTGCACTCCCTCGTACG 59.902 60.000 9.53 9.53 0.00 3.67
2888 3037 1.651240 TACTGCACTCCCTCGTACGC 61.651 60.000 11.24 0.00 0.00 4.42
2896 3057 1.270826 CTCCCTCGTACGCATGATGAT 59.729 52.381 11.24 0.00 0.00 2.45
2897 3058 1.000274 TCCCTCGTACGCATGATGATG 60.000 52.381 11.24 0.00 0.00 3.07
2903 3064 1.448308 GTACGCATGATGATGTCGTCG 59.552 52.381 15.12 3.69 40.44 5.12
2908 3069 1.520174 CATGATGATGTCGTCGCTGAC 59.480 52.381 0.00 0.50 39.37 3.51
2926 3087 2.277247 GCGCGCGCATTGTGTAAT 60.277 55.556 46.11 0.00 41.49 1.89
2927 3088 2.278887 GCGCGCGCATTGTGTAATC 61.279 57.895 46.11 15.04 41.49 1.75
2928 3089 1.348250 CGCGCGCATTGTGTAATCT 59.652 52.632 32.61 0.00 0.00 2.40
2929 3090 0.920766 CGCGCGCATTGTGTAATCTG 60.921 55.000 32.61 5.56 0.00 2.90
2930 3091 1.196130 GCGCGCATTGTGTAATCTGC 61.196 55.000 29.10 0.00 0.00 4.26
2973 3134 5.189180 GCCAGATGAAAATGGAGTTCTAGT 58.811 41.667 0.00 0.00 39.02 2.57
2978 3139 3.260884 TGAAAATGGAGTTCTAGTCGGCT 59.739 43.478 0.00 0.00 0.00 5.52
2987 3148 0.170561 TCTAGTCGGCTTCGCTGAAC 59.829 55.000 0.00 0.00 46.01 3.18
2989 3151 2.537792 TAGTCGGCTTCGCTGAACGG 62.538 60.000 0.00 0.00 46.01 4.44
2992 3154 2.861006 GGCTTCGCTGAACGGAAC 59.139 61.111 0.00 0.00 43.89 3.62
2995 3157 0.110644 GCTTCGCTGAACGGAACAAG 60.111 55.000 0.00 0.00 43.89 3.16
2997 3159 0.105224 TTCGCTGAACGGAACAAGGA 59.895 50.000 0.00 0.00 43.89 3.36
3024 3194 9.035890 TCTGTACATAGGAAGAATCAAGAAGAA 57.964 33.333 0.00 0.00 0.00 2.52
3025 3195 9.829507 CTGTACATAGGAAGAATCAAGAAGAAT 57.170 33.333 0.00 0.00 0.00 2.40
3029 3199 9.790344 ACATAGGAAGAATCAAGAAGAATATGG 57.210 33.333 0.00 0.00 0.00 2.74
3032 3202 8.977267 AGGAAGAATCAAGAAGAATATGGAAG 57.023 34.615 0.00 0.00 0.00 3.46
3033 3203 7.501892 AGGAAGAATCAAGAAGAATATGGAAGC 59.498 37.037 0.00 0.00 0.00 3.86
3034 3204 7.284034 GGAAGAATCAAGAAGAATATGGAAGCA 59.716 37.037 0.00 0.00 0.00 3.91
3035 3205 7.804843 AGAATCAAGAAGAATATGGAAGCAG 57.195 36.000 0.00 0.00 0.00 4.24
3036 3206 7.344913 AGAATCAAGAAGAATATGGAAGCAGT 58.655 34.615 0.00 0.00 0.00 4.40
3037 3207 7.498570 AGAATCAAGAAGAATATGGAAGCAGTC 59.501 37.037 0.00 0.00 0.00 3.51
3086 3256 5.303078 TCTCAACTCTGAAGCTAACAGTCTT 59.697 40.000 16.72 9.08 36.81 3.01
3098 3268 6.472887 AGCTAACAGTCTTTGTAATTAGGCA 58.527 36.000 0.00 0.00 39.73 4.75
3104 3274 7.097834 ACAGTCTTTGTAATTAGGCACTACTC 58.902 38.462 0.00 0.00 38.53 2.59
3109 3279 7.618512 TCTTTGTAATTAGGCACTACTCCTACT 59.381 37.037 0.00 0.00 42.67 2.57
3110 3280 8.827832 TTTGTAATTAGGCACTACTCCTACTA 57.172 34.615 0.00 0.00 42.67 1.82
3111 3281 7.814264 TGTAATTAGGCACTACTCCTACTAC 57.186 40.000 0.00 0.00 42.67 2.73
3112 3282 7.580910 TGTAATTAGGCACTACTCCTACTACT 58.419 38.462 0.00 0.00 42.67 2.57
3113 3283 8.057623 TGTAATTAGGCACTACTCCTACTACTT 58.942 37.037 0.00 0.00 42.67 2.24
3123 3293 5.184892 ACTCCTACTACTTAAGGGACGAA 57.815 43.478 7.53 0.00 33.40 3.85
3127 3297 6.870769 TCCTACTACTTAAGGGACGAATTTG 58.129 40.000 7.53 0.00 33.40 2.32
3129 3299 6.755607 CCTACTACTTAAGGGACGAATTTGTC 59.244 42.308 16.39 16.39 38.17 3.18
3130 3300 6.105397 ACTACTTAAGGGACGAATTTGTCA 57.895 37.500 24.11 4.09 40.72 3.58
3136 3306 3.074412 AGGGACGAATTTGTCATGTCAC 58.926 45.455 24.11 8.22 40.72 3.67
3137 3307 2.159707 GGGACGAATTTGTCATGTCACG 60.160 50.000 24.11 1.58 40.72 4.35
3139 3309 3.423123 GGACGAATTTGTCATGTCACGTC 60.423 47.826 24.11 18.55 44.81 4.34
3146 3316 1.016130 GTCATGTCACGTCCTGCCTG 61.016 60.000 0.00 0.00 0.00 4.85
3166 3336 0.908910 TAGGGCGGTGTGATGTGATT 59.091 50.000 0.00 0.00 0.00 2.57
3167 3337 0.392998 AGGGCGGTGTGATGTGATTC 60.393 55.000 0.00 0.00 0.00 2.52
3168 3338 1.376609 GGGCGGTGTGATGTGATTCC 61.377 60.000 0.00 0.00 0.00 3.01
3169 3339 0.392998 GGCGGTGTGATGTGATTCCT 60.393 55.000 0.00 0.00 0.00 3.36
3170 3340 1.009829 GCGGTGTGATGTGATTCCTC 58.990 55.000 0.00 0.00 0.00 3.71
3255 3432 0.467804 TCAGTTGCAGCCTGTGTGTA 59.532 50.000 13.30 0.00 0.00 2.90
3265 3442 2.159184 AGCCTGTGTGTATGATGAGACG 60.159 50.000 0.00 0.00 0.00 4.18
3287 3464 2.923655 CGGTGCAGATATTATACAGGCG 59.076 50.000 0.00 0.00 0.00 5.52
3338 3516 9.766277 CTGCTCTTCAAAGTTTTAATATCTGTC 57.234 33.333 0.00 0.00 0.00 3.51
3362 3540 3.617284 GATGAAAACCCCCGTCAGTATT 58.383 45.455 0.00 0.00 0.00 1.89
3363 3541 4.681244 CGATGAAAACCCCCGTCAGTATTA 60.681 45.833 0.00 0.00 0.00 0.98
3364 3542 3.941573 TGAAAACCCCCGTCAGTATTAC 58.058 45.455 0.00 0.00 0.00 1.89
3365 3543 3.273434 GAAAACCCCCGTCAGTATTACC 58.727 50.000 0.00 0.00 0.00 2.85
3366 3544 1.206878 AACCCCCGTCAGTATTACCC 58.793 55.000 0.00 0.00 0.00 3.69
3367 3545 0.692083 ACCCCCGTCAGTATTACCCC 60.692 60.000 0.00 0.00 0.00 4.95
3368 3546 1.413256 CCCCCGTCAGTATTACCCCC 61.413 65.000 0.00 0.00 0.00 5.40
3369 3547 1.744014 CCCGTCAGTATTACCCCCG 59.256 63.158 0.00 0.00 0.00 5.73
3370 3548 1.044790 CCCGTCAGTATTACCCCCGT 61.045 60.000 0.00 0.00 0.00 5.28
3371 3549 0.386838 CCGTCAGTATTACCCCCGTC 59.613 60.000 0.00 0.00 0.00 4.79
3372 3550 1.105457 CGTCAGTATTACCCCCGTCA 58.895 55.000 0.00 0.00 0.00 4.35
3373 3551 1.066605 CGTCAGTATTACCCCCGTCAG 59.933 57.143 0.00 0.00 0.00 3.51
3374 3552 2.105766 GTCAGTATTACCCCCGTCAGT 58.894 52.381 0.00 0.00 0.00 3.41
3375 3553 3.290710 GTCAGTATTACCCCCGTCAGTA 58.709 50.000 0.00 0.00 0.00 2.74
3376 3554 3.893813 GTCAGTATTACCCCCGTCAGTAT 59.106 47.826 0.00 0.00 0.00 2.12
3420 3598 2.573609 TTCTCTCCGCCTTAAGCCGC 62.574 60.000 0.00 0.00 38.78 6.53
3464 3648 3.243201 GGTGCTACCTTACGCTACGTATT 60.243 47.826 0.00 0.00 41.97 1.89
3494 3678 1.661821 CCCGGCGATTAGAGCGAAG 60.662 63.158 9.30 0.00 35.00 3.79
3574 3758 1.146957 ATCCGTCTCGTCTCGTCTCG 61.147 60.000 0.00 0.00 0.00 4.04
3652 3836 6.390721 GTTCTTCAGCTCTGTATACTTCACA 58.609 40.000 4.17 0.00 0.00 3.58
3660 3844 5.425577 TCTGTATACTTCACAGATCGAGC 57.574 43.478 4.17 0.00 45.68 5.03
3661 3845 5.126779 TCTGTATACTTCACAGATCGAGCT 58.873 41.667 0.00 0.00 45.68 4.09
3662 3846 6.289064 TCTGTATACTTCACAGATCGAGCTA 58.711 40.000 1.25 0.00 45.68 3.32
3663 3847 6.425417 TCTGTATACTTCACAGATCGAGCTAG 59.575 42.308 1.25 0.00 45.68 3.42
3664 3848 6.289064 TGTATACTTCACAGATCGAGCTAGA 58.711 40.000 1.25 1.31 0.00 2.43
3665 3849 6.766467 TGTATACTTCACAGATCGAGCTAGAA 59.234 38.462 1.25 10.07 0.00 2.10
3666 3850 6.701145 ATACTTCACAGATCGAGCTAGAAA 57.299 37.500 15.62 5.82 0.00 2.52
3667 3851 5.392767 ACTTCACAGATCGAGCTAGAAAA 57.607 39.130 15.62 3.83 0.00 2.29
3668 3852 5.784177 ACTTCACAGATCGAGCTAGAAAAA 58.216 37.500 15.62 2.38 0.00 1.94
3669 3853 5.635700 ACTTCACAGATCGAGCTAGAAAAAC 59.364 40.000 15.62 0.00 0.00 2.43
3670 3854 4.495422 TCACAGATCGAGCTAGAAAAACC 58.505 43.478 1.25 0.00 0.00 3.27
3674 3858 1.992170 TCGAGCTAGAAAAACCGAGC 58.008 50.000 0.00 0.00 35.07 5.03
3720 3907 6.722129 AGTTTCTTCAGAGATACTGTACCACT 59.278 38.462 0.00 0.00 45.86 4.00
3724 3911 7.173032 TCTTCAGAGATACTGTACCACTGTAA 58.827 38.462 6.53 0.87 45.86 2.41
3738 3925 3.124921 GTAACTGCATGCGGGCGT 61.125 61.111 29.43 16.64 36.28 5.68
3743 3930 3.716856 CTGCATGCGGGCGTTTACG 62.717 63.158 19.33 0.00 43.27 3.18
3764 3951 3.860930 TTCACAAGGGCGGGAAGGC 62.861 63.158 0.00 0.00 45.91 4.35
3765 3952 4.351054 CACAAGGGCGGGAAGGCT 62.351 66.667 0.00 0.00 45.89 4.58
3766 3953 4.351054 ACAAGGGCGGGAAGGCTG 62.351 66.667 0.00 0.00 45.89 4.85
3772 3959 4.496336 GCGGGAAGGCTGCCATCT 62.496 66.667 22.65 4.36 30.82 2.90
3773 3960 3.106986 GCGGGAAGGCTGCCATCTA 62.107 63.158 22.65 0.00 30.82 1.98
3774 3961 1.526887 CGGGAAGGCTGCCATCTAA 59.473 57.895 22.65 0.00 30.82 2.10
3775 3962 0.815615 CGGGAAGGCTGCCATCTAAC 60.816 60.000 22.65 11.76 30.82 2.34
3779 3966 2.485657 GGAAGGCTGCCATCTAACTACC 60.486 54.545 22.65 0.23 0.00 3.18
3780 3967 0.753262 AGGCTGCCATCTAACTACCG 59.247 55.000 22.65 0.00 0.00 4.02
3782 3969 1.138266 GGCTGCCATCTAACTACCGAA 59.862 52.381 15.17 0.00 0.00 4.30
3787 3981 4.018490 TGCCATCTAACTACCGAACTGTA 58.982 43.478 0.00 0.00 0.00 2.74
3791 3985 5.338365 CATCTAACTACCGAACTGTACACC 58.662 45.833 0.00 0.00 0.00 4.16
3797 3991 1.661480 CGAACTGTACACCCCGTCA 59.339 57.895 0.00 0.00 0.00 4.35
3851 4050 2.980378 TACGCGCGACAGGCTGTTA 61.980 57.895 39.36 12.26 40.44 2.41
3861 4060 3.504863 GACAGGCTGTTACGACGAAATA 58.495 45.455 22.98 0.00 0.00 1.40
3925 4124 1.499007 ACAGCAAAAGGGAGGAAGGAA 59.501 47.619 0.00 0.00 0.00 3.36
3951 4150 1.743995 GCCCGTCGCTTTACACCAT 60.744 57.895 0.00 0.00 0.00 3.55
3954 4153 0.390603 CCGTCGCTTTACACCATCCA 60.391 55.000 0.00 0.00 0.00 3.41
3960 4159 3.131396 CGCTTTACACCATCCAGATACC 58.869 50.000 0.00 0.00 0.00 2.73
3974 4173 4.340097 TCCAGATACCACCAACTGTATACG 59.660 45.833 0.00 0.00 0.00 3.06
3981 4180 3.244156 CACCAACTGTATACGCACGTAA 58.756 45.455 7.02 0.00 33.99 3.18
4000 4201 1.463674 AGTACGTACCGGGGTTACTG 58.536 55.000 21.80 0.00 0.00 2.74
4002 4203 0.323360 TACGTACCGGGGTTACTGCT 60.323 55.000 6.32 0.00 0.00 4.24
4017 4218 3.851976 ACTGCTACAGTACAGTACAGC 57.148 47.619 13.37 12.92 45.09 4.40
4018 4219 3.154710 ACTGCTACAGTACAGTACAGCA 58.845 45.455 18.47 18.47 45.09 4.41
4019 4220 3.763902 CTGCTACAGTACAGTACAGCAG 58.236 50.000 25.67 25.67 42.77 4.24
4020 4221 3.154710 TGCTACAGTACAGTACAGCAGT 58.845 45.455 16.55 10.30 32.44 4.40
4021 4222 4.329392 TGCTACAGTACAGTACAGCAGTA 58.671 43.478 16.55 5.36 32.44 2.74
4022 4223 4.948004 TGCTACAGTACAGTACAGCAGTAT 59.052 41.667 16.55 0.00 32.44 2.12
4023 4224 6.117488 TGCTACAGTACAGTACAGCAGTATA 58.883 40.000 16.55 0.00 32.44 1.47
4024 4225 6.037940 TGCTACAGTACAGTACAGCAGTATAC 59.962 42.308 16.55 0.00 32.44 1.47
4025 4226 6.037940 GCTACAGTACAGTACAGCAGTATACA 59.962 42.308 13.37 0.00 31.84 2.29
4026 4227 6.438259 ACAGTACAGTACAGCAGTATACAG 57.562 41.667 13.37 0.00 31.84 2.74
4037 4238 1.672363 CAGTATACAGTGGGCGTCGTA 59.328 52.381 5.50 0.00 0.00 3.43
4040 4241 1.317431 ATACAGTGGGCGTCGTAGCA 61.317 55.000 7.12 0.00 39.27 3.49
4046 4250 2.879462 GGCGTCGTAGCAAGGTCG 60.879 66.667 7.12 0.00 39.27 4.79
4052 4256 3.854459 GTAGCAAGGTCGCTGCGC 61.854 66.667 18.65 12.39 44.75 6.09
4073 4280 2.049433 ACACGCCTCGTCGAAAGG 60.049 61.111 10.16 10.16 38.32 3.11
4100 4307 2.729467 CGTATTCATCCTCGATCGGAGC 60.729 54.545 16.41 0.00 41.71 4.70
4101 4308 1.626686 ATTCATCCTCGATCGGAGCT 58.373 50.000 16.41 0.00 41.71 4.09
4102 4309 2.271944 TTCATCCTCGATCGGAGCTA 57.728 50.000 16.41 3.31 41.71 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.599204 GGGTCTTGACTTCGTCGCAA 60.599 55.000 0.61 0.00 34.95 4.85
35 36 2.430367 GTGGCCGGGTCTTGACTT 59.570 61.111 2.18 0.00 0.00 3.01
37 38 3.901797 CTGGTGGCCGGGTCTTGAC 62.902 68.421 2.18 0.00 0.00 3.18
43 44 1.789576 AATTTCTCTGGTGGCCGGGT 61.790 55.000 2.18 0.00 0.00 5.28
44 45 0.611896 AAATTTCTCTGGTGGCCGGG 60.612 55.000 2.18 0.00 0.00 5.73
61 62 1.477553 GCTCCATCCTCATGCCAAAA 58.522 50.000 0.00 0.00 0.00 2.44
62 63 0.749091 CGCTCCATCCTCATGCCAAA 60.749 55.000 0.00 0.00 0.00 3.28
63 64 1.153107 CGCTCCATCCTCATGCCAA 60.153 57.895 0.00 0.00 0.00 4.52
133 134 2.338620 CTTGGTGGACGTCGAGCA 59.661 61.111 25.54 25.54 0.00 4.26
201 202 2.827051 ATCGCACACATCGCATGCC 61.827 57.895 13.15 0.00 35.91 4.40
202 203 1.653232 CATCGCACACATCGCATGC 60.653 57.895 7.91 7.91 35.96 4.06
204 205 1.020861 ACACATCGCACACATCGCAT 61.021 50.000 0.00 0.00 0.00 4.73
221 222 2.047655 CTTACCCGCTGCCGAACA 60.048 61.111 0.00 0.00 36.29 3.18
222 223 2.818274 CCTTACCCGCTGCCGAAC 60.818 66.667 0.00 0.00 36.29 3.95
234 235 2.790468 CGTCGGAATCACGAGTCCTTAC 60.790 54.545 11.42 8.41 44.42 2.34
236 237 0.170561 CGTCGGAATCACGAGTCCTT 59.829 55.000 11.42 0.00 44.42 3.36
252 253 3.400590 GACGTTGGTCACCGCGTC 61.401 66.667 22.45 22.45 43.00 5.19
298 300 7.360361 GGAGTCAAACTTACATTTCGTCAAAT 58.640 34.615 0.00 0.00 31.91 2.32
318 334 5.353400 CCAATCCCTTAAACTTAACGGAGTC 59.647 44.000 6.24 0.00 45.00 3.36
322 338 5.970317 AACCAATCCCTTAAACTTAACGG 57.030 39.130 0.00 0.00 0.00 4.44
334 351 7.914427 AAAAAGTCTTTTCTAACCAATCCCT 57.086 32.000 10.95 0.00 28.09 4.20
359 376 9.747898 TTTAAAGGAATACATTTGCTCTCCTAA 57.252 29.630 0.00 0.00 32.94 2.69
362 379 8.281212 TCTTTAAAGGAATACATTTGCTCTCC 57.719 34.615 15.13 0.00 32.34 3.71
376 393 4.186159 CCGCCGAGTAATCTTTAAAGGAA 58.814 43.478 15.13 0.00 0.00 3.36
381 398 5.723295 AGTAAACCGCCGAGTAATCTTTAA 58.277 37.500 0.00 0.00 0.00 1.52
388 405 1.474077 GAGGAGTAAACCGCCGAGTAA 59.526 52.381 0.00 0.00 34.73 2.24
488 509 8.587952 ACCAGTGCAAAGTATTAAATTTTGTC 57.412 30.769 0.00 5.25 34.98 3.18
516 540 6.108687 TGTGATGCAGAGTAATTACAAGGAG 58.891 40.000 17.65 4.22 0.00 3.69
565 590 1.539827 CCTGGGAAACACGTGGAATTC 59.460 52.381 21.57 19.10 0.00 2.17
584 609 4.563976 CACATGGATTTTCGCTGAATTTCC 59.436 41.667 0.00 10.38 0.00 3.13
590 617 4.844998 TTTTCACATGGATTTTCGCTGA 57.155 36.364 0.00 0.00 0.00 4.26
643 671 4.435970 TCGACGGAGGGCTGGCTA 62.436 66.667 0.00 0.00 0.00 3.93
662 690 0.746563 CGGTCTCGCTCTCCTTCTCT 60.747 60.000 0.00 0.00 0.00 3.10
714 748 1.952635 CGGCTCCGTAATAACCGGC 60.953 63.158 0.00 0.00 45.09 6.13
720 754 3.608662 CCCGCCGGCTCCGTAATA 61.609 66.667 26.68 0.00 37.81 0.98
848 886 2.983592 GGGTCAAAGTGGCGGTGG 60.984 66.667 0.00 0.00 0.00 4.61
905 943 3.412408 GGGGGTGAAGGAGGAGGC 61.412 72.222 0.00 0.00 0.00 4.70
927 965 2.039624 GAGGTGGAGGAGGAGGCA 59.960 66.667 0.00 0.00 0.00 4.75
928 966 2.766229 GGAGGTGGAGGAGGAGGC 60.766 72.222 0.00 0.00 0.00 4.70
984 1034 2.618839 CTTTACGCGGCGAATCGG 59.381 61.111 30.94 10.67 0.00 4.18
1012 1062 1.768684 AAGAACCGCCCAAGCTGAGA 61.769 55.000 0.00 0.00 36.60 3.27
1016 1066 2.282462 CCAAGAACCGCCCAAGCT 60.282 61.111 0.00 0.00 36.60 3.74
1173 1236 1.544314 GCAGAACTTCTCCAGGCAGTT 60.544 52.381 0.00 0.00 33.32 3.16
1485 1554 1.077140 TTAATGGCGGGCATCAGCA 60.077 52.632 17.96 1.06 44.61 4.41
1486 1555 1.360192 GTTAATGGCGGGCATCAGC 59.640 57.895 17.96 1.06 41.10 4.26
1487 1556 1.648720 CGTTAATGGCGGGCATCAG 59.351 57.895 17.96 5.90 0.00 2.90
1488 1557 2.477176 GCGTTAATGGCGGGCATCA 61.477 57.895 17.96 0.00 0.00 3.07
1489 1558 2.186826 AGCGTTAATGGCGGGCATC 61.187 57.895 17.96 4.83 35.00 3.91
1490 1559 2.124320 AGCGTTAATGGCGGGCAT 60.124 55.556 11.73 11.73 35.00 4.40
1491 1560 3.130819 CAGCGTTAATGGCGGGCA 61.131 61.111 6.74 6.74 35.00 5.36
1492 1561 2.822255 TCAGCGTTAATGGCGGGC 60.822 61.111 0.00 0.00 35.00 6.13
1493 1562 2.469516 GGTCAGCGTTAATGGCGGG 61.470 63.158 0.00 0.00 35.00 6.13
1494 1563 1.302383 TTGGTCAGCGTTAATGGCGG 61.302 55.000 0.00 0.00 35.00 6.13
1495 1564 0.096976 CTTGGTCAGCGTTAATGGCG 59.903 55.000 0.00 0.00 35.00 5.69
1496 1565 0.179163 GCTTGGTCAGCGTTAATGGC 60.179 55.000 0.00 0.00 39.29 4.40
1497 1566 3.996825 GCTTGGTCAGCGTTAATGG 57.003 52.632 0.00 0.00 39.29 3.16
1567 1636 2.583441 CCCGTCCTGCACCTCTTGA 61.583 63.158 0.00 0.00 0.00 3.02
1586 1655 1.176619 TCACCTTCTTCTCGGCGTCA 61.177 55.000 6.85 0.00 0.00 4.35
1796 1876 4.008539 GCAACAACATGCTACTAGAAGC 57.991 45.455 0.00 0.00 43.06 3.86
1917 1997 2.214376 TTACCTTGTTGCATCCTGGG 57.786 50.000 0.00 0.00 0.00 4.45
1966 2046 7.839907 TCCGATTTCTCATTTTGGATGAAAAT 58.160 30.769 0.00 0.00 43.77 1.82
1967 2047 7.225784 TCCGATTTCTCATTTTGGATGAAAA 57.774 32.000 0.00 0.00 37.93 2.29
1974 2054 5.415701 TCCTCTTTCCGATTTCTCATTTTGG 59.584 40.000 0.00 0.00 0.00 3.28
1989 2069 3.632145 TGTGCTTGTTTTCTCCTCTTTCC 59.368 43.478 0.00 0.00 0.00 3.13
1999 2080 8.804743 CATCAAGATTATCATGTGCTTGTTTTC 58.195 33.333 0.00 0.00 37.71 2.29
2072 2197 5.409214 CACAGAATTTGGCCAATTTAACTGG 59.591 40.000 27.97 19.61 35.02 4.00
2075 2200 5.757808 ACACACAGAATTTGGCCAATTTAAC 59.242 36.000 21.26 10.94 35.02 2.01
2189 2314 1.073125 TCGGATGGTTTCAGGCTTTCA 59.927 47.619 0.00 0.00 0.00 2.69
2190 2315 1.821216 TCGGATGGTTTCAGGCTTTC 58.179 50.000 0.00 0.00 0.00 2.62
2191 2316 2.094675 CATCGGATGGTTTCAGGCTTT 58.905 47.619 10.18 0.00 0.00 3.51
2192 2317 1.755179 CATCGGATGGTTTCAGGCTT 58.245 50.000 10.18 0.00 0.00 4.35
2193 2318 0.749454 GCATCGGATGGTTTCAGGCT 60.749 55.000 18.96 0.00 0.00 4.58
2194 2319 1.728490 GGCATCGGATGGTTTCAGGC 61.728 60.000 18.96 2.40 0.00 4.85
2230 2357 1.596727 GATCAGAATTCAGAGCGGCAC 59.403 52.381 8.44 0.00 0.00 5.01
2231 2358 1.207811 TGATCAGAATTCAGAGCGGCA 59.792 47.619 8.44 0.50 0.00 5.69
2233 2360 3.529533 AGTTGATCAGAATTCAGAGCGG 58.470 45.455 8.44 0.00 0.00 5.52
2274 2405 2.500910 AGCTTCATGGAGAGGAACTGAG 59.499 50.000 4.75 0.00 41.55 3.35
2350 2481 1.456705 GGTGGGTTTTGGGCTCACA 60.457 57.895 0.00 0.00 38.99 3.58
2357 2488 0.689412 ACAACAGGGGTGGGTTTTGG 60.689 55.000 0.00 0.00 0.00 3.28
2373 2504 1.665169 CGCGATGGTGATGATGAACAA 59.335 47.619 0.00 0.00 0.00 2.83
2418 2549 2.679450 CATTCGACACGGACAAGGTAA 58.321 47.619 0.00 0.00 0.00 2.85
2654 2789 0.323178 AGGCAAGAATCACCTGCTGG 60.323 55.000 8.29 8.29 39.83 4.85
2675 2813 3.001939 ACGACAACAACCACGAAATTCTC 59.998 43.478 0.00 0.00 0.00 2.87
2727 2865 3.799035 CACAACGAAACTGTATCAGCAC 58.201 45.455 0.00 0.00 34.37 4.40
2729 2870 2.839474 GCACAACGAAACTGTATCAGC 58.161 47.619 0.00 0.00 34.37 4.26
2860 3009 4.321750 CGAGGGAGTGCAGTACTTTTAGAA 60.322 45.833 3.17 0.00 40.53 2.10
2861 3010 3.192844 CGAGGGAGTGCAGTACTTTTAGA 59.807 47.826 3.17 0.00 40.53 2.10
2862 3011 3.056749 ACGAGGGAGTGCAGTACTTTTAG 60.057 47.826 3.17 0.00 40.53 1.85
2863 3012 2.895404 ACGAGGGAGTGCAGTACTTTTA 59.105 45.455 3.17 0.00 40.53 1.52
2864 3013 1.692519 ACGAGGGAGTGCAGTACTTTT 59.307 47.619 3.17 0.00 40.53 2.27
2865 3014 1.339097 ACGAGGGAGTGCAGTACTTT 58.661 50.000 3.17 0.00 40.53 2.66
2866 3015 1.817447 GTACGAGGGAGTGCAGTACTT 59.183 52.381 3.17 0.00 40.53 2.24
2867 3016 1.461559 GTACGAGGGAGTGCAGTACT 58.538 55.000 3.17 0.41 44.02 2.73
2869 3018 1.651240 GCGTACGAGGGAGTGCAGTA 61.651 60.000 21.65 0.00 0.00 2.74
2870 3019 2.991076 GCGTACGAGGGAGTGCAGT 61.991 63.158 21.65 0.00 0.00 4.40
2871 3020 2.202623 GCGTACGAGGGAGTGCAG 60.203 66.667 21.65 0.00 0.00 4.41
2873 3022 1.878522 CATGCGTACGAGGGAGTGC 60.879 63.158 21.65 0.00 0.00 4.40
2874 3023 0.385751 ATCATGCGTACGAGGGAGTG 59.614 55.000 21.65 7.47 0.00 3.51
2875 3024 0.385751 CATCATGCGTACGAGGGAGT 59.614 55.000 21.65 0.00 0.00 3.85
2876 3025 0.668535 TCATCATGCGTACGAGGGAG 59.331 55.000 21.65 3.56 0.00 4.30
2877 3026 1.000274 CATCATCATGCGTACGAGGGA 60.000 52.381 21.65 12.39 0.00 4.20
2878 3027 1.269778 ACATCATCATGCGTACGAGGG 60.270 52.381 21.65 6.81 32.57 4.30
2879 3028 2.054363 GACATCATCATGCGTACGAGG 58.946 52.381 21.65 7.20 32.57 4.63
2880 3029 1.710773 CGACATCATCATGCGTACGAG 59.289 52.381 21.65 7.99 32.57 4.18
2881 3030 1.064952 ACGACATCATCATGCGTACGA 59.935 47.619 21.65 4.52 39.44 3.43
2882 3031 1.448308 GACGACATCATCATGCGTACG 59.552 52.381 11.84 11.84 40.51 3.67
2883 3032 1.448308 CGACGACATCATCATGCGTAC 59.552 52.381 0.00 0.00 40.51 3.67
2884 3033 1.753956 CGACGACATCATCATGCGTA 58.246 50.000 0.00 0.00 40.51 4.42
2886 3035 1.200103 GCGACGACATCATCATGCG 59.800 57.895 0.00 0.00 36.33 4.73
2887 3036 0.231534 CAGCGACGACATCATCATGC 59.768 55.000 0.00 0.00 32.57 4.06
2888 3037 1.520174 GTCAGCGACGACATCATCATG 59.480 52.381 0.00 0.00 35.88 3.07
2908 3069 4.785569 TTACACAATGCGCGCGCG 62.786 61.111 45.73 45.73 45.51 6.86
2909 3070 2.277247 ATTACACAATGCGCGCGC 60.277 55.556 45.02 45.02 42.35 6.86
2910 3071 0.920766 CAGATTACACAATGCGCGCG 60.921 55.000 28.44 28.44 0.00 6.86
2912 3073 2.845600 GCAGATTACACAATGCGCG 58.154 52.632 0.00 0.00 0.00 6.86
2915 3076 1.532505 CCTGCGCAGATTACACAATGC 60.533 52.381 38.06 0.00 35.32 3.56
2916 3077 1.739466 ACCTGCGCAGATTACACAATG 59.261 47.619 38.06 19.04 0.00 2.82
2918 3079 1.155889 CACCTGCGCAGATTACACAA 58.844 50.000 38.06 0.00 0.00 3.33
2919 3080 0.320050 TCACCTGCGCAGATTACACA 59.680 50.000 38.06 11.62 0.00 3.72
2920 3081 1.594862 GATCACCTGCGCAGATTACAC 59.405 52.381 38.06 19.42 0.00 2.90
2921 3082 1.482182 AGATCACCTGCGCAGATTACA 59.518 47.619 38.06 16.91 0.00 2.41
2922 3083 1.863454 CAGATCACCTGCGCAGATTAC 59.137 52.381 38.06 22.56 35.89 1.89
2923 3084 2.229675 CAGATCACCTGCGCAGATTA 57.770 50.000 38.06 21.81 35.89 1.75
2924 3085 3.076104 CAGATCACCTGCGCAGATT 57.924 52.632 38.06 21.63 35.89 2.40
2925 3086 4.850822 CAGATCACCTGCGCAGAT 57.149 55.556 38.06 21.54 35.89 2.90
2945 3106 3.094572 CTCCATTTTCATCTGGCCTGTT 58.905 45.455 3.32 0.00 32.30 3.16
2946 3107 2.042162 ACTCCATTTTCATCTGGCCTGT 59.958 45.455 3.32 0.00 32.30 4.00
2978 3139 0.105224 TCCTTGTTCCGTTCAGCGAA 59.895 50.000 0.00 0.00 44.77 4.70
2987 3148 4.341235 TCCTATGTACAGATCCTTGTTCCG 59.659 45.833 0.33 0.00 32.56 4.30
2989 3151 7.113658 TCTTCCTATGTACAGATCCTTGTTC 57.886 40.000 0.33 0.00 32.56 3.18
2992 3154 7.730084 TGATTCTTCCTATGTACAGATCCTTG 58.270 38.462 0.33 0.00 0.00 3.61
2995 3157 7.957002 TCTTGATTCTTCCTATGTACAGATCC 58.043 38.462 0.33 0.00 0.00 3.36
2997 3159 9.206690 TCTTCTTGATTCTTCCTATGTACAGAT 57.793 33.333 0.33 0.00 0.00 2.90
3024 3194 2.421107 CCACTGCTGACTGCTTCCATAT 60.421 50.000 5.87 0.00 43.37 1.78
3025 3195 1.065926 CCACTGCTGACTGCTTCCATA 60.066 52.381 5.87 0.00 43.37 2.74
3026 3196 0.322277 CCACTGCTGACTGCTTCCAT 60.322 55.000 5.87 0.00 43.37 3.41
3027 3197 1.071987 CCACTGCTGACTGCTTCCA 59.928 57.895 5.87 0.00 43.37 3.53
3028 3198 2.331132 GCCACTGCTGACTGCTTCC 61.331 63.158 5.87 0.00 43.37 3.46
3029 3199 2.675056 CGCCACTGCTGACTGCTTC 61.675 63.158 5.87 0.00 43.37 3.86
3030 3200 2.667536 CGCCACTGCTGACTGCTT 60.668 61.111 5.87 0.00 43.37 3.91
3031 3201 3.586461 CTCGCCACTGCTGACTGCT 62.586 63.158 5.87 0.00 43.37 4.24
3032 3202 3.117171 CTCGCCACTGCTGACTGC 61.117 66.667 0.00 0.00 43.25 4.40
3033 3203 2.025969 CACTCGCCACTGCTGACTG 61.026 63.158 0.00 0.00 34.43 3.51
3034 3204 1.748329 TTCACTCGCCACTGCTGACT 61.748 55.000 0.00 0.00 34.43 3.41
3035 3205 1.287730 CTTCACTCGCCACTGCTGAC 61.288 60.000 0.00 0.00 34.43 3.51
3036 3206 1.005748 CTTCACTCGCCACTGCTGA 60.006 57.895 0.00 0.00 34.43 4.26
3037 3207 2.675056 GCTTCACTCGCCACTGCTG 61.675 63.158 0.00 0.00 34.43 4.41
3067 3237 5.283457 ACAAAGACTGTTAGCTTCAGAGT 57.717 39.130 20.35 9.70 32.99 3.24
3086 3256 8.057623 AGTAGTAGGAGTAGTGCCTAATTACAA 58.942 37.037 0.28 0.00 39.58 2.41
3098 3268 5.426833 TCGTCCCTTAAGTAGTAGGAGTAGT 59.573 44.000 0.97 0.00 33.13 2.73
3104 3274 6.637657 ACAAATTCGTCCCTTAAGTAGTAGG 58.362 40.000 0.97 0.00 0.00 3.18
3109 3279 6.469410 ACATGACAAATTCGTCCCTTAAGTA 58.531 36.000 0.00 0.00 34.88 2.24
3110 3280 5.313712 ACATGACAAATTCGTCCCTTAAGT 58.686 37.500 0.00 0.00 34.88 2.24
3111 3281 5.411361 TGACATGACAAATTCGTCCCTTAAG 59.589 40.000 0.00 0.00 34.88 1.85
3112 3282 5.180492 GTGACATGACAAATTCGTCCCTTAA 59.820 40.000 0.00 0.00 34.88 1.85
3113 3283 4.693566 GTGACATGACAAATTCGTCCCTTA 59.306 41.667 0.00 0.00 34.88 2.69
3123 3293 1.806542 GCAGGACGTGACATGACAAAT 59.193 47.619 0.00 0.00 0.00 2.32
3127 3297 1.016130 CAGGCAGGACGTGACATGAC 61.016 60.000 3.41 0.00 36.10 3.06
3129 3299 0.246360 TACAGGCAGGACGTGACATG 59.754 55.000 3.41 3.63 36.10 3.21
3130 3300 0.532573 CTACAGGCAGGACGTGACAT 59.467 55.000 3.41 0.00 36.10 3.06
3146 3316 0.178068 ATCACATCACACCGCCCTAC 59.822 55.000 0.00 0.00 0.00 3.18
3166 3336 3.691575 CCAGCGATATTAGAGGAGAGGA 58.308 50.000 0.00 0.00 0.00 3.71
3167 3337 2.165437 GCCAGCGATATTAGAGGAGAGG 59.835 54.545 0.00 0.00 0.00 3.69
3168 3338 2.822561 TGCCAGCGATATTAGAGGAGAG 59.177 50.000 0.00 0.00 0.00 3.20
3169 3339 2.558795 GTGCCAGCGATATTAGAGGAGA 59.441 50.000 0.00 0.00 0.00 3.71
3170 3340 2.560542 AGTGCCAGCGATATTAGAGGAG 59.439 50.000 0.00 0.00 0.00 3.69
3217 3388 7.667283 CAACTGATCGTTCCGCTATATTAATC 58.333 38.462 0.00 0.00 32.27 1.75
3242 3419 1.938577 CTCATCATACACACAGGCTGC 59.061 52.381 15.89 0.00 0.00 5.25
3246 3423 2.196749 GCGTCTCATCATACACACAGG 58.803 52.381 0.00 0.00 0.00 4.00
3247 3424 1.848608 CGCGTCTCATCATACACACAG 59.151 52.381 0.00 0.00 0.00 3.66
3255 3432 1.520120 CTGCACCGCGTCTCATCAT 60.520 57.895 4.92 0.00 0.00 2.45
3265 3442 2.673368 GCCTGTATAATATCTGCACCGC 59.327 50.000 0.00 0.00 0.00 5.68
3287 3464 0.839946 TTAGGATTGGCAGGAGAGGC 59.160 55.000 0.00 0.00 0.00 4.70
3338 3516 2.744709 ACGGGGGTTTTCATCGCG 60.745 61.111 0.00 0.00 41.51 5.87
3371 3549 5.988561 GCTCCAAGGAAGATTCAGTATACTG 59.011 44.000 24.37 24.37 45.08 2.74
3372 3550 5.902431 AGCTCCAAGGAAGATTCAGTATACT 59.098 40.000 0.00 0.00 0.00 2.12
3373 3551 6.168270 AGCTCCAAGGAAGATTCAGTATAC 57.832 41.667 0.00 0.00 0.00 1.47
3374 3552 6.814954 AAGCTCCAAGGAAGATTCAGTATA 57.185 37.500 0.00 0.00 0.00 1.47
3375 3553 5.707066 AAGCTCCAAGGAAGATTCAGTAT 57.293 39.130 0.00 0.00 0.00 2.12
3376 3554 5.395768 GCTAAGCTCCAAGGAAGATTCAGTA 60.396 44.000 0.00 0.00 0.00 2.74
3420 3598 1.656263 CAGCACAGCACGCAACAAG 60.656 57.895 0.00 0.00 0.00 3.16
3522 3706 4.229876 ACTAAAAGCGACGTGTAACCTAC 58.770 43.478 0.00 0.00 0.00 3.18
3569 3753 1.745864 TCCAGCGAGGAGACGAGAC 60.746 63.158 0.00 0.00 43.07 3.36
3629 3813 6.434340 TCTGTGAAGTATACAGAGCTGAAGAA 59.566 38.462 5.50 0.00 46.92 2.52
3652 3836 3.735514 GCTCGGTTTTTCTAGCTCGATCT 60.736 47.826 0.00 0.00 32.18 2.75
3654 3838 2.541556 GCTCGGTTTTTCTAGCTCGAT 58.458 47.619 0.00 0.00 32.18 3.59
3655 3839 1.731424 CGCTCGGTTTTTCTAGCTCGA 60.731 52.381 0.00 0.00 32.73 4.04
3657 3841 0.370615 GCGCTCGGTTTTTCTAGCTC 59.629 55.000 0.00 0.00 32.73 4.09
3659 3843 1.296056 TGGCGCTCGGTTTTTCTAGC 61.296 55.000 7.64 0.00 0.00 3.42
3660 3844 0.721718 CTGGCGCTCGGTTTTTCTAG 59.278 55.000 7.64 0.00 0.00 2.43
3661 3845 1.296056 GCTGGCGCTCGGTTTTTCTA 61.296 55.000 7.64 0.00 0.00 2.10
3662 3846 2.617274 GCTGGCGCTCGGTTTTTCT 61.617 57.895 7.64 0.00 0.00 2.52
3663 3847 2.126850 GCTGGCGCTCGGTTTTTC 60.127 61.111 7.64 0.00 0.00 2.29
3664 3848 2.594592 AGCTGGCGCTCGGTTTTT 60.595 55.556 7.64 0.00 45.15 1.94
3717 3904 1.796151 CCCGCATGCAGTTACAGTG 59.204 57.895 19.57 0.00 0.00 3.66
3720 3907 3.124270 CGCCCGCATGCAGTTACA 61.124 61.111 19.57 0.00 0.00 2.41
3724 3911 2.359354 TAAACGCCCGCATGCAGT 60.359 55.556 19.57 8.83 0.00 4.40
3738 3925 0.945813 CGCCCTTGTGAAACCGTAAA 59.054 50.000 0.00 0.00 34.36 2.01
3743 3930 1.524008 CTTCCCGCCCTTGTGAAACC 61.524 60.000 0.00 0.00 34.36 3.27
3764 3951 3.119101 ACAGTTCGGTAGTTAGATGGCAG 60.119 47.826 0.00 0.00 0.00 4.85
3765 3952 2.829720 ACAGTTCGGTAGTTAGATGGCA 59.170 45.455 0.00 0.00 0.00 4.92
3766 3953 3.521947 ACAGTTCGGTAGTTAGATGGC 57.478 47.619 0.00 0.00 0.00 4.40
3768 3955 5.338365 GGTGTACAGTTCGGTAGTTAGATG 58.662 45.833 0.00 0.00 0.00 2.90
3769 3956 4.400567 GGGTGTACAGTTCGGTAGTTAGAT 59.599 45.833 0.00 0.00 0.00 1.98
3770 3957 3.758554 GGGTGTACAGTTCGGTAGTTAGA 59.241 47.826 0.00 0.00 0.00 2.10
3771 3958 3.119352 GGGGTGTACAGTTCGGTAGTTAG 60.119 52.174 0.00 0.00 0.00 2.34
3772 3959 2.825532 GGGGTGTACAGTTCGGTAGTTA 59.174 50.000 0.00 0.00 0.00 2.24
3773 3960 1.620323 GGGGTGTACAGTTCGGTAGTT 59.380 52.381 0.00 0.00 0.00 2.24
3774 3961 1.260544 GGGGTGTACAGTTCGGTAGT 58.739 55.000 0.00 0.00 0.00 2.73
3775 3962 0.171903 CGGGGTGTACAGTTCGGTAG 59.828 60.000 0.00 0.00 0.00 3.18
3779 3966 0.665369 GTGACGGGGTGTACAGTTCG 60.665 60.000 0.00 2.86 0.00 3.95
3780 3967 0.320160 GGTGACGGGGTGTACAGTTC 60.320 60.000 0.00 0.00 0.00 3.01
3782 3969 3.463345 GGTGACGGGGTGTACAGT 58.537 61.111 0.00 0.00 0.00 3.55
3851 4050 7.480542 GCTATCATTTTGTTTGTATTTCGTCGT 59.519 33.333 0.00 0.00 0.00 4.34
3861 4060 4.343526 TGGTGGTGCTATCATTTTGTTTGT 59.656 37.500 0.00 0.00 0.00 2.83
3894 4093 1.266175 CTTTTGCTGTCAGTCAGGCTG 59.734 52.381 8.58 8.58 46.34 4.85
3899 4098 1.202806 CCTCCCTTTTGCTGTCAGTCA 60.203 52.381 0.93 0.00 0.00 3.41
3951 4150 4.340097 CGTATACAGTTGGTGGTATCTGGA 59.660 45.833 3.32 0.00 32.72 3.86
3954 4153 3.702548 TGCGTATACAGTTGGTGGTATCT 59.297 43.478 3.32 0.00 32.72 1.98
3960 4159 1.705256 ACGTGCGTATACAGTTGGTG 58.295 50.000 3.32 0.00 0.00 4.17
3986 4185 1.135721 CTGTAGCAGTAACCCCGGTAC 59.864 57.143 0.00 0.00 34.89 3.34
3987 4186 1.272648 ACTGTAGCAGTAACCCCGGTA 60.273 52.381 0.00 0.00 43.46 4.02
4000 4201 3.851976 ACTGCTGTACTGTACTGTAGC 57.148 47.619 29.01 23.46 41.57 3.58
4002 4203 7.065443 CACTGTATACTGCTGTACTGTACTGTA 59.935 40.741 21.03 17.20 35.76 2.74
4017 4218 0.454600 ACGACGCCCACTGTATACTG 59.545 55.000 8.11 8.11 0.00 2.74
4018 4219 1.945394 CTACGACGCCCACTGTATACT 59.055 52.381 4.17 0.00 0.00 2.12
4019 4220 1.598924 GCTACGACGCCCACTGTATAC 60.599 57.143 0.00 0.00 0.00 1.47
4020 4221 0.664761 GCTACGACGCCCACTGTATA 59.335 55.000 0.00 0.00 0.00 1.47
4021 4222 1.317431 TGCTACGACGCCCACTGTAT 61.317 55.000 0.00 0.00 0.00 2.29
4022 4223 1.525718 TTGCTACGACGCCCACTGTA 61.526 55.000 0.00 0.00 0.00 2.74
4023 4224 2.765250 CTTGCTACGACGCCCACTGT 62.765 60.000 0.00 0.00 0.00 3.55
4024 4225 2.048597 TTGCTACGACGCCCACTG 60.049 61.111 0.00 0.00 0.00 3.66
4025 4226 2.261671 CTTGCTACGACGCCCACT 59.738 61.111 0.00 0.00 0.00 4.00
4026 4227 2.813908 CCTTGCTACGACGCCCAC 60.814 66.667 0.00 0.00 0.00 4.61
4052 4256 0.937699 TTTCGACGAGGCGTGTGAAG 60.938 55.000 0.00 0.00 41.37 3.02
4073 4280 2.658707 GAGGATGAATACGCGCGCC 61.659 63.158 32.58 20.99 0.00 6.53


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

AutoCloner maintained by Alex Coulton.