Multiple sequence alignment - TraesCS1D01G093000

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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 TraesCS1D01G093000 chr1D 100.000 3092 0 0 1 3092 79090341 79093432 0.000000e+00 5710.0
1 TraesCS1D01G093000 chr1A 93.204 1913 74 20 800 2663 96365760 96363855 0.000000e+00 2761.0
2 TraesCS1D01G093000 chr1A 94.545 275 11 4 2664 2936 96363793 96363521 3.690000e-114 422.0
3 TraesCS1D01G093000 chr1A 81.797 423 55 15 1 417 96368395 96367989 4.940000e-88 335.0
4 TraesCS1D01G093000 chr1B 90.100 2091 145 25 785 2835 129998397 130000465 0.000000e+00 2658.0
5 TraesCS1D01G093000 chr1B 88.889 162 11 5 559 719 129998175 129998330 3.150000e-45 193.0
6 TraesCS1D01G093000 chr1B 84.252 127 13 6 2431 2552 623945800 623945924 1.950000e-22 117.0
7 TraesCS1D01G093000 chr1B 92.308 39 3 0 2835 2873 130000493 130000531 4.310000e-04 56.5
8 TraesCS1D01G093000 chr5A 89.147 129 14 0 2435 2563 610378906 610378778 8.870000e-36 161.0
9 TraesCS1D01G093000 chr3A 88.372 129 15 0 2435 2563 597624259 597624131 4.130000e-34 156.0
10 TraesCS1D01G093000 chr3A 84.892 139 20 1 2425 2563 6788573 6788710 4.160000e-29 139.0
11 TraesCS1D01G093000 chr6D 90.083 121 9 3 2445 2563 436674967 436674848 1.480000e-33 154.0
12 TraesCS1D01G093000 chr5D 83.544 158 24 2 2935 3092 305849157 305849312 2.480000e-31 147.0
13 TraesCS1D01G093000 chr5D 85.612 139 20 0 2425 2563 437358929 437358791 2.480000e-31 147.0
14 TraesCS1D01G093000 chr7D 84.892 139 21 0 2425 2563 455434009 455433871 1.160000e-29 141.0
15 TraesCS1D01G093000 chr6A 83.036 112 19 0 2946 3057 97722067 97721956 5.450000e-18 102.0


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 TraesCS1D01G093000 chr1D 79090341 79093432 3091 False 5710.000000 5710 100.000000 1 3092 1 chr1D.!!$F1 3091
1 TraesCS1D01G093000 chr1A 96363521 96368395 4874 True 1172.666667 2761 89.848667 1 2936 3 chr1A.!!$R1 2935
2 TraesCS1D01G093000 chr1B 129998175 130000531 2356 False 969.166667 2658 90.432333 559 2873 3 chr1B.!!$F2 2314

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
453 864 0.170116 CGTGTTTGTGCACAACCTGT 59.83 50.0 31.17 0.0 39.19 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2341 4295 0.249489 ACTGACTCGTGTGCCTGAAC 60.249 55.0 0.0 0.0 0.0 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
34 36 3.021269 TGACGTGTTGTGTGATCCTAC 57.979 47.619 0.00 0.00 0.00 3.18
35 37 2.362717 TGACGTGTTGTGTGATCCTACA 59.637 45.455 0.00 0.00 0.00 2.74
36 38 3.006430 TGACGTGTTGTGTGATCCTACAT 59.994 43.478 0.00 0.00 32.43 2.29
72 74 0.473326 ATGAGAGGGATGAGCCAAGC 59.527 55.000 0.00 0.00 38.95 4.01
76 78 3.424105 GGGATGAGCCAAGCCCCT 61.424 66.667 0.00 0.00 38.95 4.79
84 86 2.225242 TGAGCCAAGCCCCTTTGATTAA 60.225 45.455 0.00 0.00 0.00 1.40
95 97 7.586349 AGCCCCTTTGATTAAGAAGATATTGA 58.414 34.615 0.00 0.00 35.80 2.57
97 99 7.285401 GCCCCTTTGATTAAGAAGATATTGACA 59.715 37.037 0.00 0.00 35.80 3.58
116 118 8.859236 ATTGACATAATCATTAGACCTCATGG 57.141 34.615 0.00 0.00 37.11 3.66
117 119 7.616528 TGACATAATCATTAGACCTCATGGA 57.383 36.000 0.00 0.00 32.38 3.41
156 158 3.937814 AGCATTTCTTGATGTGTACCGA 58.062 40.909 0.00 0.00 0.00 4.69
166 168 6.368791 TCTTGATGTGTACCGAAAGATTGAAG 59.631 38.462 0.00 0.00 0.00 3.02
169 171 4.312443 TGTGTACCGAAAGATTGAAGACC 58.688 43.478 0.00 0.00 0.00 3.85
170 172 3.367025 GTGTACCGAAAGATTGAAGACCG 59.633 47.826 0.00 0.00 0.00 4.79
171 173 3.256383 TGTACCGAAAGATTGAAGACCGA 59.744 43.478 0.00 0.00 0.00 4.69
172 174 2.960819 ACCGAAAGATTGAAGACCGAG 58.039 47.619 0.00 0.00 0.00 4.63
177 179 0.827368 AGATTGAAGACCGAGCCTCC 59.173 55.000 0.00 0.00 0.00 4.30
179 181 1.627297 ATTGAAGACCGAGCCTCCCC 61.627 60.000 0.00 0.00 0.00 4.81
182 184 3.239627 AAGACCGAGCCTCCCCTCA 62.240 63.158 0.00 0.00 0.00 3.86
187 189 2.828145 GAGCCTCCCCTCATCAGC 59.172 66.667 0.00 0.00 0.00 4.26
188 190 2.771762 AGCCTCCCCTCATCAGCC 60.772 66.667 0.00 0.00 0.00 4.85
189 191 3.092511 GCCTCCCCTCATCAGCCA 61.093 66.667 0.00 0.00 0.00 4.75
195 197 0.332632 CCCCTCATCAGCCAAAGGAA 59.667 55.000 0.00 0.00 0.00 3.36
198 200 2.232208 CCCTCATCAGCCAAAGGAAAAC 59.768 50.000 0.00 0.00 0.00 2.43
199 201 2.892852 CCTCATCAGCCAAAGGAAAACA 59.107 45.455 0.00 0.00 0.00 2.83
202 204 4.151121 TCATCAGCCAAAGGAAAACATCA 58.849 39.130 0.00 0.00 0.00 3.07
204 206 2.627699 TCAGCCAAAGGAAAACATCACC 59.372 45.455 0.00 0.00 0.00 4.02
205 207 2.364970 CAGCCAAAGGAAAACATCACCA 59.635 45.455 0.00 0.00 0.00 4.17
212 214 6.222389 CAAAGGAAAACATCACCAAGCATAA 58.778 36.000 0.00 0.00 0.00 1.90
213 215 6.610075 AAGGAAAACATCACCAAGCATAAT 57.390 33.333 0.00 0.00 0.00 1.28
214 216 6.212888 AGGAAAACATCACCAAGCATAATC 57.787 37.500 0.00 0.00 0.00 1.75
215 217 5.716228 AGGAAAACATCACCAAGCATAATCA 59.284 36.000 0.00 0.00 0.00 2.57
216 218 6.038356 GGAAAACATCACCAAGCATAATCAG 58.962 40.000 0.00 0.00 0.00 2.90
217 219 4.644103 AACATCACCAAGCATAATCAGC 57.356 40.909 0.00 0.00 0.00 4.26
218 220 3.623703 ACATCACCAAGCATAATCAGCA 58.376 40.909 0.00 0.00 0.00 4.41
219 221 3.630769 ACATCACCAAGCATAATCAGCAG 59.369 43.478 0.00 0.00 0.00 4.24
220 222 2.019249 TCACCAAGCATAATCAGCAGC 58.981 47.619 0.00 0.00 0.00 5.25
221 223 2.022195 CACCAAGCATAATCAGCAGCT 58.978 47.619 0.00 0.00 39.37 4.24
222 224 3.118298 TCACCAAGCATAATCAGCAGCTA 60.118 43.478 0.00 0.00 36.07 3.32
223 225 3.250280 CACCAAGCATAATCAGCAGCTAG 59.750 47.826 0.00 0.00 36.07 3.42
224 226 3.135348 ACCAAGCATAATCAGCAGCTAGA 59.865 43.478 0.00 0.00 36.07 2.43
225 227 4.202440 ACCAAGCATAATCAGCAGCTAGAT 60.202 41.667 0.00 0.00 36.07 1.98
240 242 6.496565 AGCAGCTAGATGGAGATAGTAATGTT 59.503 38.462 10.52 0.00 0.00 2.71
429 840 9.784531 AATATATATGAAAGCCGCATTATAGCT 57.215 29.630 0.00 0.00 38.88 3.32
434 845 3.320673 AAGCCGCATTATAGCTACTCC 57.679 47.619 0.00 0.00 35.30 3.85
435 846 1.202582 AGCCGCATTATAGCTACTCCG 59.797 52.381 0.00 0.00 34.38 4.63
441 852 4.085055 CGCATTATAGCTACTCCGTGTTTG 60.085 45.833 0.00 0.00 0.00 2.93
442 853 4.809426 GCATTATAGCTACTCCGTGTTTGT 59.191 41.667 0.00 0.00 0.00 2.83
452 863 0.525242 CCGTGTTTGTGCACAACCTG 60.525 55.000 31.17 19.68 39.19 4.00
453 864 0.170116 CGTGTTTGTGCACAACCTGT 59.830 50.000 31.17 0.00 39.19 4.00
469 880 0.729116 CTGTGTAGCCTCCAAATGCG 59.271 55.000 0.00 0.00 0.00 4.73
472 883 1.664151 GTGTAGCCTCCAAATGCGTAC 59.336 52.381 0.00 0.00 0.00 3.67
473 884 1.553248 TGTAGCCTCCAAATGCGTACT 59.447 47.619 0.00 0.00 0.00 2.73
474 885 2.202566 GTAGCCTCCAAATGCGTACTC 58.797 52.381 0.00 0.00 0.00 2.59
475 886 0.905357 AGCCTCCAAATGCGTACTCT 59.095 50.000 0.00 0.00 0.00 3.24
476 887 1.009829 GCCTCCAAATGCGTACTCTG 58.990 55.000 0.00 0.00 0.00 3.35
477 888 1.009829 CCTCCAAATGCGTACTCTGC 58.990 55.000 0.00 0.00 0.00 4.26
478 889 1.406069 CCTCCAAATGCGTACTCTGCT 60.406 52.381 0.00 0.00 0.00 4.24
479 890 2.159099 CCTCCAAATGCGTACTCTGCTA 60.159 50.000 0.00 0.00 0.00 3.49
480 891 3.119291 CTCCAAATGCGTACTCTGCTAG 58.881 50.000 0.00 0.00 0.00 3.42
481 892 2.758423 TCCAAATGCGTACTCTGCTAGA 59.242 45.455 0.00 0.00 0.00 2.43
514 925 2.160417 GCTTCATATGCGTTATGGAGGC 59.840 50.000 13.77 8.89 42.27 4.70
518 929 0.467804 TATGCGTTATGGAGGCTGCA 59.532 50.000 12.23 12.23 39.81 4.41
523 934 2.554032 GCGTTATGGAGGCTGCAAATAT 59.446 45.455 14.16 0.00 36.26 1.28
531 942 0.740737 GGCTGCAAATATGGCGACTT 59.259 50.000 0.50 0.00 0.00 3.01
540 951 2.225068 TATGGCGACTTTGCTAGAGC 57.775 50.000 0.00 0.00 42.50 4.09
546 957 1.135141 CGACTTTGCTAGAGCTGCTCT 60.135 52.381 32.31 32.31 43.83 4.09
549 960 4.111916 GACTTTGCTAGAGCTGCTCTTAG 58.888 47.826 34.42 26.66 41.50 2.18
562 973 1.474143 GCTCTTAGGTCTCCACATGCC 60.474 57.143 0.00 0.00 0.00 4.40
749 1172 4.865925 GTGGTAAAAGGTTTTGTGTTGGAC 59.134 41.667 0.00 0.00 0.00 4.02
855 2762 0.323302 TGGCAAGCGGTAGACAATGA 59.677 50.000 0.00 0.00 0.00 2.57
887 2794 3.064958 CGTAGCTCGGTCTCTTTGATACA 59.935 47.826 0.00 0.00 35.71 2.29
888 2795 3.512033 AGCTCGGTCTCTTTGATACAC 57.488 47.619 0.00 0.00 0.00 2.90
908 2815 2.282745 AGCAACCCAAGCCAGCTC 60.283 61.111 0.00 0.00 0.00 4.09
909 2816 3.741476 GCAACCCAAGCCAGCTCG 61.741 66.667 0.00 0.00 0.00 5.03
910 2817 2.281761 CAACCCAAGCCAGCTCGT 60.282 61.111 0.00 0.00 0.00 4.18
1540 3459 1.727535 CGAATCGCATTGTTTTCGCCA 60.728 47.619 0.00 0.00 35.18 5.69
1596 3515 4.248859 TCATTTTCGAGGAGCTGAAGAAG 58.751 43.478 0.00 0.00 0.00 2.85
1623 3542 2.079158 AGATGCTTGGATGTTGTCACG 58.921 47.619 0.00 0.00 0.00 4.35
1656 3575 3.055094 TCTTGGACATGCTAGGAAAGGTC 60.055 47.826 0.00 5.78 0.00 3.85
1678 3597 0.250553 TCGGGTGGACGAAATGCTTT 60.251 50.000 0.00 0.00 40.34 3.51
1680 3599 0.958822 GGGTGGACGAAATGCTTTGT 59.041 50.000 0.00 0.00 0.00 2.83
1721 3640 2.508526 ACTTGGCATTTCTCCTGACAC 58.491 47.619 0.00 0.00 29.34 3.67
1770 3689 2.359900 CTGCGTAGGCTTGGAAGATTT 58.640 47.619 9.11 0.00 40.82 2.17
1941 3860 5.983720 CCAACCTTCGATTTATGTCTATCGT 59.016 40.000 0.00 0.00 43.03 3.73
1987 3906 2.399356 GGGCGGTTTGAGCTAGCAC 61.399 63.158 18.83 11.88 34.52 4.40
2019 3938 3.875727 CCGATGAGATGAATTCAAGTGCT 59.124 43.478 13.09 7.63 0.00 4.40
2048 3967 4.380843 TGTTAGGCCCTGAAGATTTCAA 57.619 40.909 0.00 0.00 39.58 2.69
2050 3969 2.521547 AGGCCCTGAAGATTTCAAGG 57.478 50.000 0.00 2.72 42.89 3.61
2079 3998 2.310052 CAAGGGAAGAAGGGTCAGGAAT 59.690 50.000 0.00 0.00 0.00 3.01
2120 4039 5.123027 CAGAAAAGTTATCTTCCAGGTCTGC 59.877 44.000 0.00 0.00 32.90 4.26
2161 4080 0.877071 CAACAGCTGCTGGTACCAAG 59.123 55.000 31.00 12.62 35.51 3.61
2162 4081 0.474184 AACAGCTGCTGGTACCAAGT 59.526 50.000 31.00 6.95 35.51 3.16
2163 4082 0.474184 ACAGCTGCTGGTACCAAGTT 59.526 50.000 31.00 6.59 35.51 2.66
2178 4097 2.880890 CCAAGTTGTTCCAGACTTCCAG 59.119 50.000 1.45 0.00 34.04 3.86
2279 4218 8.043113 TGACAGTAGCTTGATGATTACAAAGAT 58.957 33.333 0.00 0.00 0.00 2.40
2341 4295 6.430308 CCATTACTGATCCATGATTCAAGAGG 59.570 42.308 0.00 0.00 0.00 3.69
2391 4345 4.866486 GCAGCAATTCCCAGTTAAGAAATG 59.134 41.667 0.00 0.00 0.00 2.32
2441 4395 0.250597 GGTGCCCGTTACTGGAAAGT 60.251 55.000 0.00 0.00 0.00 2.66
2489 4446 5.055812 GGTGTCAAATTTCAGCATTTTCCA 58.944 37.500 4.66 0.00 33.12 3.53
2500 4457 3.924686 CAGCATTTTCCATTGCTCTTCAC 59.075 43.478 0.00 0.00 45.83 3.18
2702 4723 1.753930 TGGTGTGATGCCATGTCATC 58.246 50.000 9.79 9.79 42.33 2.92
2716 4737 2.287769 TGTCATCCCATGTAATGTGCG 58.712 47.619 0.00 0.00 44.81 5.34
2752 4773 0.039035 GTTGTTGGGGGTGCTGGATA 59.961 55.000 0.00 0.00 0.00 2.59
2791 4812 3.769844 TGCTCTCCTAGGGACTAACTTTG 59.230 47.826 9.46 0.00 42.17 2.77
2898 4952 9.594478 TTTTCAGAATGTATGCTCGTATTTAGA 57.406 29.630 0.00 0.00 37.40 2.10
2903 4957 7.815068 AGAATGTATGCTCGTATTTAGATCACC 59.185 37.037 0.00 0.00 0.00 4.02
2908 4962 4.565166 TGCTCGTATTTAGATCACCAAACG 59.435 41.667 0.00 0.00 0.00 3.60
2909 4963 4.025979 GCTCGTATTTAGATCACCAAACGG 60.026 45.833 0.00 0.00 0.00 4.44
2926 4980 1.071228 ACGGTACAAAGTCCTGAACCC 59.929 52.381 0.00 0.00 0.00 4.11
2927 4981 1.804601 GGTACAAAGTCCTGAACCCG 58.195 55.000 0.00 0.00 0.00 5.28
2928 4982 1.071228 GGTACAAAGTCCTGAACCCGT 59.929 52.381 0.00 0.00 0.00 5.28
2929 4983 2.299867 GGTACAAAGTCCTGAACCCGTA 59.700 50.000 0.00 0.00 0.00 4.02
2930 4984 2.538512 ACAAAGTCCTGAACCCGTAC 57.461 50.000 0.00 0.00 0.00 3.67
2932 4986 2.171027 ACAAAGTCCTGAACCCGTACAA 59.829 45.455 0.00 0.00 0.00 2.41
2933 4987 2.806244 CAAAGTCCTGAACCCGTACAAG 59.194 50.000 0.00 0.00 0.00 3.16
2934 4988 0.320697 AGTCCTGAACCCGTACAAGC 59.679 55.000 0.00 0.00 0.00 4.01
2935 4989 0.034337 GTCCTGAACCCGTACAAGCA 59.966 55.000 0.00 0.00 0.00 3.91
2936 4990 0.034337 TCCTGAACCCGTACAAGCAC 59.966 55.000 0.00 0.00 0.00 4.40
2937 4991 0.953960 CCTGAACCCGTACAAGCACC 60.954 60.000 0.00 0.00 0.00 5.01
2938 4992 0.953960 CTGAACCCGTACAAGCACCC 60.954 60.000 0.00 0.00 0.00 4.61
2939 4993 1.071814 GAACCCGTACAAGCACCCA 59.928 57.895 0.00 0.00 0.00 4.51
2940 4994 1.228033 AACCCGTACAAGCACCCAC 60.228 57.895 0.00 0.00 0.00 4.61
2941 4995 1.702022 AACCCGTACAAGCACCCACT 61.702 55.000 0.00 0.00 0.00 4.00
2942 4996 0.832983 ACCCGTACAAGCACCCACTA 60.833 55.000 0.00 0.00 0.00 2.74
2943 4997 0.322322 CCCGTACAAGCACCCACTAA 59.678 55.000 0.00 0.00 0.00 2.24
2944 4998 1.674817 CCCGTACAAGCACCCACTAAG 60.675 57.143 0.00 0.00 0.00 2.18
2945 4999 1.274167 CCGTACAAGCACCCACTAAGA 59.726 52.381 0.00 0.00 0.00 2.10
2946 5000 2.334838 CGTACAAGCACCCACTAAGAC 58.665 52.381 0.00 0.00 0.00 3.01
2947 5001 2.696506 GTACAAGCACCCACTAAGACC 58.303 52.381 0.00 0.00 0.00 3.85
2948 5002 1.435256 ACAAGCACCCACTAAGACCT 58.565 50.000 0.00 0.00 0.00 3.85
2949 5003 1.774856 ACAAGCACCCACTAAGACCTT 59.225 47.619 0.00 0.00 0.00 3.50
2950 5004 2.154462 CAAGCACCCACTAAGACCTTG 58.846 52.381 0.00 0.00 0.00 3.61
2951 5005 1.435256 AGCACCCACTAAGACCTTGT 58.565 50.000 0.00 0.00 0.00 3.16
2952 5006 1.072331 AGCACCCACTAAGACCTTGTG 59.928 52.381 0.00 0.00 0.00 3.33
2953 5007 1.071699 GCACCCACTAAGACCTTGTGA 59.928 52.381 11.28 0.00 33.95 3.58
2954 5008 2.486548 GCACCCACTAAGACCTTGTGAA 60.487 50.000 11.28 0.00 33.95 3.18
2955 5009 3.815809 CACCCACTAAGACCTTGTGAAA 58.184 45.455 11.28 0.00 33.95 2.69
2956 5010 3.815401 CACCCACTAAGACCTTGTGAAAG 59.185 47.826 11.28 0.00 33.95 2.62
2957 5011 3.714798 ACCCACTAAGACCTTGTGAAAGA 59.285 43.478 11.28 0.00 33.95 2.52
2958 5012 4.065789 CCCACTAAGACCTTGTGAAAGAC 58.934 47.826 11.28 0.00 33.95 3.01
2959 5013 4.202367 CCCACTAAGACCTTGTGAAAGACT 60.202 45.833 11.28 0.00 33.95 3.24
2960 5014 4.991687 CCACTAAGACCTTGTGAAAGACTC 59.008 45.833 11.28 0.00 33.95 3.36
2961 5015 4.681942 CACTAAGACCTTGTGAAAGACTCG 59.318 45.833 6.53 0.00 33.95 4.18
2962 5016 3.821421 AAGACCTTGTGAAAGACTCGT 57.179 42.857 0.00 0.00 0.00 4.18
2963 5017 3.099267 AGACCTTGTGAAAGACTCGTG 57.901 47.619 0.00 0.00 0.00 4.35
2964 5018 1.527311 GACCTTGTGAAAGACTCGTGC 59.473 52.381 0.00 0.00 0.00 5.34
2965 5019 0.868406 CCTTGTGAAAGACTCGTGCC 59.132 55.000 0.00 0.00 0.00 5.01
2966 5020 1.581934 CTTGTGAAAGACTCGTGCCA 58.418 50.000 0.00 0.00 0.00 4.92
2967 5021 1.261619 CTTGTGAAAGACTCGTGCCAC 59.738 52.381 0.00 0.00 0.00 5.01
2968 5022 0.176910 TGTGAAAGACTCGTGCCACA 59.823 50.000 0.00 0.00 32.87 4.17
2969 5023 1.295792 GTGAAAGACTCGTGCCACAA 58.704 50.000 0.00 0.00 0.00 3.33
2970 5024 1.668751 GTGAAAGACTCGTGCCACAAA 59.331 47.619 0.00 0.00 0.00 2.83
2971 5025 2.096819 GTGAAAGACTCGTGCCACAAAA 59.903 45.455 0.00 0.00 0.00 2.44
2972 5026 2.354510 TGAAAGACTCGTGCCACAAAAG 59.645 45.455 0.00 0.00 0.00 2.27
2973 5027 2.325583 AAGACTCGTGCCACAAAAGA 57.674 45.000 0.00 0.00 0.00 2.52
2974 5028 2.325583 AGACTCGTGCCACAAAAGAA 57.674 45.000 0.00 0.00 0.00 2.52
2975 5029 2.851195 AGACTCGTGCCACAAAAGAAT 58.149 42.857 0.00 0.00 0.00 2.40
2976 5030 2.808543 AGACTCGTGCCACAAAAGAATC 59.191 45.455 0.00 0.00 0.00 2.52
2977 5031 2.808543 GACTCGTGCCACAAAAGAATCT 59.191 45.455 0.00 0.00 0.00 2.40
2978 5032 2.549754 ACTCGTGCCACAAAAGAATCTG 59.450 45.455 0.00 0.00 0.00 2.90
2979 5033 2.549754 CTCGTGCCACAAAAGAATCTGT 59.450 45.455 0.00 0.00 0.00 3.41
2980 5034 2.290367 TCGTGCCACAAAAGAATCTGTG 59.710 45.455 0.00 0.00 42.14 3.66
2981 5035 2.290367 CGTGCCACAAAAGAATCTGTGA 59.710 45.455 3.83 0.00 44.68 3.58
2982 5036 3.632189 GTGCCACAAAAGAATCTGTGAC 58.368 45.455 3.83 0.00 44.68 3.67
2983 5037 2.622942 TGCCACAAAAGAATCTGTGACC 59.377 45.455 3.83 0.00 44.68 4.02
2984 5038 2.622942 GCCACAAAAGAATCTGTGACCA 59.377 45.455 3.83 0.00 44.68 4.02
2985 5039 3.304928 GCCACAAAAGAATCTGTGACCAG 60.305 47.826 3.83 0.00 44.68 4.00
2993 5047 1.754745 TCTGTGACCAGACCCAAGC 59.245 57.895 0.00 0.00 42.80 4.01
2994 5048 1.053835 TCTGTGACCAGACCCAAGCA 61.054 55.000 0.00 0.00 42.80 3.91
2995 5049 0.179020 CTGTGACCAGACCCAAGCAA 60.179 55.000 0.00 0.00 41.50 3.91
2996 5050 0.179020 TGTGACCAGACCCAAGCAAG 60.179 55.000 0.00 0.00 0.00 4.01
2997 5051 0.108585 GTGACCAGACCCAAGCAAGA 59.891 55.000 0.00 0.00 0.00 3.02
2998 5052 0.108585 TGACCAGACCCAAGCAAGAC 59.891 55.000 0.00 0.00 0.00 3.01
2999 5053 0.108585 GACCAGACCCAAGCAAGACA 59.891 55.000 0.00 0.00 0.00 3.41
3000 5054 0.773644 ACCAGACCCAAGCAAGACAT 59.226 50.000 0.00 0.00 0.00 3.06
3001 5055 1.271597 ACCAGACCCAAGCAAGACATC 60.272 52.381 0.00 0.00 0.00 3.06
3002 5056 1.271543 CCAGACCCAAGCAAGACATCA 60.272 52.381 0.00 0.00 0.00 3.07
3003 5057 2.619849 CCAGACCCAAGCAAGACATCAT 60.620 50.000 0.00 0.00 0.00 2.45
3004 5058 2.681848 CAGACCCAAGCAAGACATCATC 59.318 50.000 0.00 0.00 0.00 2.92
3005 5059 2.575279 AGACCCAAGCAAGACATCATCT 59.425 45.455 0.00 0.00 40.46 2.90
3007 5061 3.350833 ACCCAAGCAAGACATCATCTTC 58.649 45.455 0.00 0.00 44.99 2.87
3008 5062 3.245016 ACCCAAGCAAGACATCATCTTCA 60.245 43.478 0.00 0.00 44.99 3.02
3009 5063 3.760151 CCCAAGCAAGACATCATCTTCAA 59.240 43.478 0.00 0.00 44.99 2.69
3010 5064 4.380233 CCCAAGCAAGACATCATCTTCAAC 60.380 45.833 0.00 0.00 44.99 3.18
3011 5065 4.380233 CCAAGCAAGACATCATCTTCAACC 60.380 45.833 0.00 0.00 44.99 3.77
3012 5066 4.025040 AGCAAGACATCATCTTCAACCA 57.975 40.909 0.00 0.00 44.99 3.67
3013 5067 3.755378 AGCAAGACATCATCTTCAACCAC 59.245 43.478 0.00 0.00 44.99 4.16
3014 5068 3.503363 GCAAGACATCATCTTCAACCACA 59.497 43.478 0.00 0.00 44.99 4.17
3015 5069 4.022935 GCAAGACATCATCTTCAACCACAA 60.023 41.667 0.00 0.00 44.99 3.33
3016 5070 5.455392 CAAGACATCATCTTCAACCACAAC 58.545 41.667 0.00 0.00 44.99 3.32
3017 5071 4.717877 AGACATCATCTTCAACCACAACA 58.282 39.130 0.00 0.00 31.62 3.33
3018 5072 5.319453 AGACATCATCTTCAACCACAACAT 58.681 37.500 0.00 0.00 31.62 2.71
3019 5073 5.413833 AGACATCATCTTCAACCACAACATC 59.586 40.000 0.00 0.00 31.62 3.06
3020 5074 5.072055 ACATCATCTTCAACCACAACATCA 58.928 37.500 0.00 0.00 0.00 3.07
3021 5075 5.713389 ACATCATCTTCAACCACAACATCAT 59.287 36.000 0.00 0.00 0.00 2.45
3022 5076 5.885230 TCATCTTCAACCACAACATCATC 57.115 39.130 0.00 0.00 0.00 2.92
3023 5077 5.315348 TCATCTTCAACCACAACATCATCA 58.685 37.500 0.00 0.00 0.00 3.07
3024 5078 5.181811 TCATCTTCAACCACAACATCATCAC 59.818 40.000 0.00 0.00 0.00 3.06
3025 5079 3.820467 TCTTCAACCACAACATCATCACC 59.180 43.478 0.00 0.00 0.00 4.02
3026 5080 3.220674 TCAACCACAACATCATCACCA 57.779 42.857 0.00 0.00 0.00 4.17
3027 5081 2.884012 TCAACCACAACATCATCACCAC 59.116 45.455 0.00 0.00 0.00 4.16
3028 5082 1.909700 ACCACAACATCATCACCACC 58.090 50.000 0.00 0.00 0.00 4.61
3029 5083 1.144708 ACCACAACATCATCACCACCA 59.855 47.619 0.00 0.00 0.00 4.17
3030 5084 1.541147 CCACAACATCATCACCACCAC 59.459 52.381 0.00 0.00 0.00 4.16
3031 5085 2.228925 CACAACATCATCACCACCACA 58.771 47.619 0.00 0.00 0.00 4.17
3032 5086 2.030893 CACAACATCATCACCACCACAC 60.031 50.000 0.00 0.00 0.00 3.82
3033 5087 2.158623 ACAACATCATCACCACCACACT 60.159 45.455 0.00 0.00 0.00 3.55
3034 5088 2.189594 ACATCATCACCACCACACTG 57.810 50.000 0.00 0.00 0.00 3.66
3035 5089 0.806868 CATCATCACCACCACACTGC 59.193 55.000 0.00 0.00 0.00 4.40
3036 5090 0.694771 ATCATCACCACCACACTGCT 59.305 50.000 0.00 0.00 0.00 4.24
3037 5091 1.347062 TCATCACCACCACACTGCTA 58.653 50.000 0.00 0.00 0.00 3.49
3038 5092 1.001974 TCATCACCACCACACTGCTAC 59.998 52.381 0.00 0.00 0.00 3.58
3039 5093 1.055849 ATCACCACCACACTGCTACA 58.944 50.000 0.00 0.00 0.00 2.74
3040 5094 1.055849 TCACCACCACACTGCTACAT 58.944 50.000 0.00 0.00 0.00 2.29
3041 5095 1.001974 TCACCACCACACTGCTACATC 59.998 52.381 0.00 0.00 0.00 3.06
3042 5096 1.002430 CACCACCACACTGCTACATCT 59.998 52.381 0.00 0.00 0.00 2.90
3043 5097 1.699634 ACCACCACACTGCTACATCTT 59.300 47.619 0.00 0.00 0.00 2.40
3044 5098 2.106511 ACCACCACACTGCTACATCTTT 59.893 45.455 0.00 0.00 0.00 2.52
3045 5099 3.149196 CCACCACACTGCTACATCTTTT 58.851 45.455 0.00 0.00 0.00 2.27
3046 5100 3.189287 CCACCACACTGCTACATCTTTTC 59.811 47.826 0.00 0.00 0.00 2.29
3047 5101 4.067896 CACCACACTGCTACATCTTTTCT 58.932 43.478 0.00 0.00 0.00 2.52
3048 5102 4.516698 CACCACACTGCTACATCTTTTCTT 59.483 41.667 0.00 0.00 0.00 2.52
3049 5103 5.009010 CACCACACTGCTACATCTTTTCTTT 59.991 40.000 0.00 0.00 0.00 2.52
3050 5104 5.009010 ACCACACTGCTACATCTTTTCTTTG 59.991 40.000 0.00 0.00 0.00 2.77
3051 5105 4.913924 CACACTGCTACATCTTTTCTTTGC 59.086 41.667 0.00 0.00 0.00 3.68
3052 5106 4.823989 ACACTGCTACATCTTTTCTTTGCT 59.176 37.500 0.00 0.00 0.00 3.91
3053 5107 5.049129 ACACTGCTACATCTTTTCTTTGCTC 60.049 40.000 0.00 0.00 0.00 4.26
3054 5108 4.457257 ACTGCTACATCTTTTCTTTGCTCC 59.543 41.667 0.00 0.00 0.00 4.70
3055 5109 3.436704 TGCTACATCTTTTCTTTGCTCCG 59.563 43.478 0.00 0.00 0.00 4.63
3056 5110 3.181506 GCTACATCTTTTCTTTGCTCCGG 60.182 47.826 0.00 0.00 0.00 5.14
3057 5111 2.863809 ACATCTTTTCTTTGCTCCGGT 58.136 42.857 0.00 0.00 0.00 5.28
3058 5112 2.554032 ACATCTTTTCTTTGCTCCGGTG 59.446 45.455 0.00 0.00 0.00 4.94
3059 5113 0.951558 TCTTTTCTTTGCTCCGGTGC 59.048 50.000 21.41 21.41 0.00 5.01
3060 5114 0.039165 CTTTTCTTTGCTCCGGTGCC 60.039 55.000 24.73 8.35 0.00 5.01
3061 5115 0.753479 TTTTCTTTGCTCCGGTGCCA 60.753 50.000 24.73 12.27 0.00 4.92
3062 5116 0.753479 TTTCTTTGCTCCGGTGCCAA 60.753 50.000 24.73 18.91 0.00 4.52
3063 5117 0.753479 TTCTTTGCTCCGGTGCCAAA 60.753 50.000 24.73 20.90 0.00 3.28
3064 5118 0.753479 TCTTTGCTCCGGTGCCAAAA 60.753 50.000 24.73 17.58 0.00 2.44
3065 5119 0.318955 CTTTGCTCCGGTGCCAAAAG 60.319 55.000 24.73 22.12 0.00 2.27
3066 5120 1.743321 TTTGCTCCGGTGCCAAAAGG 61.743 55.000 24.73 0.00 0.00 3.11
3067 5121 2.282180 GCTCCGGTGCCAAAAGGA 60.282 61.111 17.73 0.00 0.00 3.36
3068 5122 2.626780 GCTCCGGTGCCAAAAGGAC 61.627 63.158 17.73 0.00 35.74 3.85
3069 5123 1.228124 CTCCGGTGCCAAAAGGACA 60.228 57.895 0.00 0.00 38.89 4.02
3070 5124 0.821711 CTCCGGTGCCAAAAGGACAA 60.822 55.000 0.00 0.00 38.89 3.18
3071 5125 0.821711 TCCGGTGCCAAAAGGACAAG 60.822 55.000 0.00 0.00 38.89 3.16
3072 5126 1.659794 CGGTGCCAAAAGGACAAGG 59.340 57.895 0.00 0.00 38.89 3.61
3073 5127 0.821711 CGGTGCCAAAAGGACAAGGA 60.822 55.000 0.00 0.00 38.89 3.36
3074 5128 0.673985 GGTGCCAAAAGGACAAGGAC 59.326 55.000 0.00 0.00 38.89 3.85
3075 5129 1.398692 GTGCCAAAAGGACAAGGACA 58.601 50.000 0.00 0.00 36.67 4.02
3076 5130 1.067060 GTGCCAAAAGGACAAGGACAC 59.933 52.381 0.00 0.00 36.67 3.67
3077 5131 1.341482 TGCCAAAAGGACAAGGACACA 60.341 47.619 0.00 0.00 0.00 3.72
3078 5132 1.067060 GCCAAAAGGACAAGGACACAC 59.933 52.381 0.00 0.00 0.00 3.82
3079 5133 2.654863 CCAAAAGGACAAGGACACACT 58.345 47.619 0.00 0.00 0.00 3.55
3080 5134 3.023832 CCAAAAGGACAAGGACACACTT 58.976 45.455 0.00 0.00 0.00 3.16
3081 5135 4.204012 CCAAAAGGACAAGGACACACTTA 58.796 43.478 0.00 0.00 0.00 2.24
3082 5136 4.827284 CCAAAAGGACAAGGACACACTTAT 59.173 41.667 0.00 0.00 0.00 1.73
3083 5137 5.278463 CCAAAAGGACAAGGACACACTTATG 60.278 44.000 0.00 0.00 0.00 1.90
3084 5138 3.059352 AGGACAAGGACACACTTATGC 57.941 47.619 0.00 0.00 0.00 3.14
3085 5139 2.371841 AGGACAAGGACACACTTATGCA 59.628 45.455 0.00 0.00 0.00 3.96
3086 5140 3.009473 AGGACAAGGACACACTTATGCAT 59.991 43.478 3.79 3.79 0.00 3.96
3087 5141 3.375299 GGACAAGGACACACTTATGCATC 59.625 47.826 0.19 0.00 0.00 3.91
3088 5142 3.347216 ACAAGGACACACTTATGCATCC 58.653 45.455 0.19 0.00 34.60 3.51
3089 5143 3.244875 ACAAGGACACACTTATGCATCCA 60.245 43.478 0.19 0.00 36.16 3.41
3090 5144 3.719268 AGGACACACTTATGCATCCAA 57.281 42.857 0.19 0.00 36.16 3.53
3091 5145 3.347216 AGGACACACTTATGCATCCAAC 58.653 45.455 0.19 0.00 36.16 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 8.887036 TCATATTATGTAGGATCACACAACAC 57.113 34.615 3.67 0.00 0.00 3.32
49 51 2.485659 TGGCTCATCCCTCTCATTCTT 58.514 47.619 0.00 0.00 0.00 2.52
52 54 1.133853 GCTTGGCTCATCCCTCTCATT 60.134 52.381 0.00 0.00 0.00 2.57
56 58 2.381941 GGGCTTGGCTCATCCCTCT 61.382 63.158 0.00 0.00 35.87 3.69
65 67 2.042979 TCTTAATCAAAGGGGCTTGGCT 59.957 45.455 0.00 0.00 35.75 4.75
72 74 8.752005 TGTCAATATCTTCTTAATCAAAGGGG 57.248 34.615 0.00 0.00 35.75 4.79
95 97 7.147497 TGTGTCCATGAGGTCTAATGATTATGT 60.147 37.037 0.00 0.00 35.89 2.29
97 99 7.147497 TGTGTGTCCATGAGGTCTAATGATTAT 60.147 37.037 0.00 0.00 35.89 1.28
99 101 5.045651 TGTGTGTCCATGAGGTCTAATGATT 60.046 40.000 0.00 0.00 35.89 2.57
107 109 2.768253 TCATGTGTGTCCATGAGGTC 57.232 50.000 0.00 0.00 44.70 3.85
113 115 3.358118 TGAATGCATCATGTGTGTCCAT 58.642 40.909 0.00 0.00 31.50 3.41
115 117 3.766151 CTTGAATGCATCATGTGTGTCC 58.234 45.455 0.00 0.00 38.03 4.02
116 118 3.176708 GCTTGAATGCATCATGTGTGTC 58.823 45.455 0.00 0.00 38.03 3.67
117 119 2.559231 TGCTTGAATGCATCATGTGTGT 59.441 40.909 0.00 0.00 38.03 3.72
149 151 3.256383 TCGGTCTTCAATCTTTCGGTACA 59.744 43.478 0.00 0.00 0.00 2.90
152 154 2.931320 GCTCGGTCTTCAATCTTTCGGT 60.931 50.000 0.00 0.00 0.00 4.69
153 155 1.661112 GCTCGGTCTTCAATCTTTCGG 59.339 52.381 0.00 0.00 0.00 4.30
156 158 2.355209 GGAGGCTCGGTCTTCAATCTTT 60.355 50.000 8.69 0.00 0.00 2.52
166 168 2.444895 ATGAGGGGAGGCTCGGTC 60.445 66.667 8.69 5.48 0.00 4.79
169 171 3.136750 CTGATGAGGGGAGGCTCG 58.863 66.667 8.69 0.00 0.00 5.03
170 172 2.817056 GGCTGATGAGGGGAGGCTC 61.817 68.421 5.78 5.78 0.00 4.70
171 173 2.771762 GGCTGATGAGGGGAGGCT 60.772 66.667 0.00 0.00 0.00 4.58
172 174 2.215451 TTTGGCTGATGAGGGGAGGC 62.215 60.000 0.00 0.00 0.00 4.70
177 179 2.220653 TTTCCTTTGGCTGATGAGGG 57.779 50.000 0.00 0.00 0.00 4.30
179 181 4.219070 TGATGTTTTCCTTTGGCTGATGAG 59.781 41.667 0.00 0.00 0.00 2.90
182 184 3.259123 GGTGATGTTTTCCTTTGGCTGAT 59.741 43.478 0.00 0.00 0.00 2.90
187 189 3.181467 TGCTTGGTGATGTTTTCCTTTGG 60.181 43.478 0.00 0.00 0.00 3.28
188 190 4.057406 TGCTTGGTGATGTTTTCCTTTG 57.943 40.909 0.00 0.00 0.00 2.77
189 191 4.961438 ATGCTTGGTGATGTTTTCCTTT 57.039 36.364 0.00 0.00 0.00 3.11
195 197 4.463539 TGCTGATTATGCTTGGTGATGTTT 59.536 37.500 0.00 0.00 0.00 2.83
198 200 3.550233 GCTGCTGATTATGCTTGGTGATG 60.550 47.826 0.00 0.00 0.00 3.07
199 201 2.621998 GCTGCTGATTATGCTTGGTGAT 59.378 45.455 0.00 0.00 0.00 3.06
202 204 2.431954 AGCTGCTGATTATGCTTGGT 57.568 45.000 0.00 0.00 30.96 3.67
204 206 4.154375 CCATCTAGCTGCTGATTATGCTTG 59.846 45.833 13.43 1.87 37.02 4.01
205 207 4.041321 TCCATCTAGCTGCTGATTATGCTT 59.959 41.667 13.43 0.00 37.02 3.91
212 214 4.676109 ACTATCTCCATCTAGCTGCTGAT 58.324 43.478 13.43 10.26 0.00 2.90
213 215 4.111255 ACTATCTCCATCTAGCTGCTGA 57.889 45.455 13.43 8.28 0.00 4.26
214 216 5.973899 TTACTATCTCCATCTAGCTGCTG 57.026 43.478 13.43 2.51 0.00 4.41
215 217 6.015918 ACATTACTATCTCCATCTAGCTGCT 58.984 40.000 7.57 7.57 0.00 4.24
216 218 6.279513 ACATTACTATCTCCATCTAGCTGC 57.720 41.667 0.00 0.00 0.00 5.25
407 410 7.782049 AGTAGCTATAATGCGGCTTTCATATA 58.218 34.615 4.22 0.00 37.50 0.86
419 830 4.809426 ACAAACACGGAGTAGCTATAATGC 59.191 41.667 0.00 0.00 41.61 3.56
429 840 1.666700 GTTGTGCACAAACACGGAGTA 59.333 47.619 32.61 5.04 43.74 2.59
434 845 0.170116 ACAGGTTGTGCACAAACACG 59.830 50.000 40.51 33.09 45.61 4.49
435 846 1.627879 CACAGGTTGTGCACAAACAC 58.372 50.000 40.51 28.56 45.61 3.32
452 863 1.664151 GTACGCATTTGGAGGCTACAC 59.336 52.381 0.00 0.00 0.00 2.90
453 864 1.553248 AGTACGCATTTGGAGGCTACA 59.447 47.619 0.00 0.00 0.00 2.74
469 880 7.474772 CGCTCTAGCAACTCTAGCAGAGTAC 62.475 52.000 16.02 12.36 46.87 2.73
472 883 2.286950 CGCTCTAGCAACTCTAGCAGAG 60.287 54.545 10.48 10.48 43.55 3.35
473 884 1.673400 CGCTCTAGCAACTCTAGCAGA 59.327 52.381 2.44 0.00 43.55 4.26
474 885 1.863624 GCGCTCTAGCAACTCTAGCAG 60.864 57.143 0.00 0.00 43.55 4.24
475 886 0.101399 GCGCTCTAGCAACTCTAGCA 59.899 55.000 0.00 0.00 43.55 3.49
476 887 0.383949 AGCGCTCTAGCAACTCTAGC 59.616 55.000 2.64 0.00 43.55 3.42
477 888 2.098280 TGAAGCGCTCTAGCAACTCTAG 59.902 50.000 12.06 0.00 44.90 2.43
478 889 2.092323 TGAAGCGCTCTAGCAACTCTA 58.908 47.619 12.06 0.00 42.21 2.43
479 890 0.891373 TGAAGCGCTCTAGCAACTCT 59.109 50.000 12.06 0.00 42.21 3.24
480 891 1.933247 ATGAAGCGCTCTAGCAACTC 58.067 50.000 12.06 1.69 42.21 3.01
481 892 3.388308 CATATGAAGCGCTCTAGCAACT 58.612 45.455 12.06 0.00 42.21 3.16
482 893 2.096516 GCATATGAAGCGCTCTAGCAAC 60.097 50.000 12.06 0.00 42.21 4.17
483 894 2.138320 GCATATGAAGCGCTCTAGCAA 58.862 47.619 12.06 0.00 42.21 3.91
484 895 1.788258 GCATATGAAGCGCTCTAGCA 58.212 50.000 12.06 7.59 42.21 3.49
496 907 2.871637 GCAGCCTCCATAACGCATATGA 60.872 50.000 6.97 0.00 43.52 2.15
504 915 3.305608 GCCATATTTGCAGCCTCCATAAC 60.306 47.826 0.00 0.00 0.00 1.89
518 929 3.561725 GCTCTAGCAAAGTCGCCATATTT 59.438 43.478 0.00 0.00 41.59 1.40
523 934 0.390340 CAGCTCTAGCAAAGTCGCCA 60.390 55.000 4.54 0.00 45.16 5.69
531 942 2.428890 GACCTAAGAGCAGCTCTAGCAA 59.571 50.000 25.66 10.42 40.28 3.91
540 951 2.741228 GCATGTGGAGACCTAAGAGCAG 60.741 54.545 0.00 0.00 0.00 4.24
546 957 0.535335 GTCGGCATGTGGAGACCTAA 59.465 55.000 0.00 0.00 0.00 2.69
549 960 1.003839 TTGTCGGCATGTGGAGACC 60.004 57.895 0.00 0.00 33.04 3.85
555 966 1.065401 ACACAAACTTGTCGGCATGTG 59.935 47.619 17.46 17.46 39.91 3.21
562 973 7.728895 AGAAAAATGAAAACACAAACTTGTCG 58.271 30.769 0.00 0.00 39.91 4.35
720 1143 8.989980 CAACACAAAACCTTTTACCACTAAAAA 58.010 29.630 0.00 0.00 32.55 1.94
721 1144 7.603024 CCAACACAAAACCTTTTACCACTAAAA 59.397 33.333 0.00 0.00 32.11 1.52
722 1145 7.039223 TCCAACACAAAACCTTTTACCACTAAA 60.039 33.333 0.00 0.00 0.00 1.85
723 1146 6.436532 TCCAACACAAAACCTTTTACCACTAA 59.563 34.615 0.00 0.00 0.00 2.24
724 1147 5.950549 TCCAACACAAAACCTTTTACCACTA 59.049 36.000 0.00 0.00 0.00 2.74
725 1148 4.773149 TCCAACACAAAACCTTTTACCACT 59.227 37.500 0.00 0.00 0.00 4.00
726 1149 4.865925 GTCCAACACAAAACCTTTTACCAC 59.134 41.667 0.00 0.00 0.00 4.16
727 1150 4.527038 TGTCCAACACAAAACCTTTTACCA 59.473 37.500 0.00 0.00 29.30 3.25
728 1151 5.074584 TGTCCAACACAAAACCTTTTACC 57.925 39.130 0.00 0.00 29.30 2.85
762 1185 8.689972 ACATTATAAGGAGCAAAAATCCAGAAG 58.310 33.333 3.76 0.00 39.47 2.85
797 1220 2.000701 CCAGGGCCAGGTCCATACA 61.001 63.158 14.32 0.00 0.00 2.29
798 1221 2.919043 CCAGGGCCAGGTCCATAC 59.081 66.667 14.32 0.00 0.00 2.39
843 2750 0.880278 CGGCCCATCATTGTCTACCG 60.880 60.000 0.00 0.00 0.00 4.02
855 2762 4.530857 GAGCTACGCACGGCCCAT 62.531 66.667 0.00 0.00 0.00 4.00
887 2794 3.850098 CTGGCTTGGGTTGCTCCGT 62.850 63.158 0.00 0.00 37.00 4.69
888 2795 3.058160 CTGGCTTGGGTTGCTCCG 61.058 66.667 0.00 0.00 37.00 4.63
908 2815 3.047807 ATCCATGGGCCTGTGGACG 62.048 63.158 26.41 5.85 46.55 4.79
909 2816 1.454479 CATCCATGGGCCTGTGGAC 60.454 63.158 26.41 0.00 46.55 4.02
1092 3011 3.400590 GTCGTTGTCGTCGGCCAC 61.401 66.667 2.24 0.00 38.33 5.01
1093 3012 3.902086 TGTCGTTGTCGTCGGCCA 61.902 61.111 2.24 0.00 38.33 5.36
1094 3013 3.400590 GTGTCGTTGTCGTCGGCC 61.401 66.667 0.00 0.00 38.33 6.13
1095 3014 3.400590 GGTGTCGTTGTCGTCGGC 61.401 66.667 0.00 0.00 38.33 5.54
1096 3015 2.732094 GGGTGTCGTTGTCGTCGG 60.732 66.667 0.00 0.00 38.33 4.79
1119 3038 3.519930 GCGAGACGGGAGGAGGAC 61.520 72.222 0.00 0.00 0.00 3.85
1540 3459 2.129785 GGTGCCCGTATCTACCCGT 61.130 63.158 0.00 0.00 0.00 5.28
1596 3515 5.128919 ACAACATCCAAGCATCTCTTATCC 58.871 41.667 0.00 0.00 32.74 2.59
1623 3542 3.548818 GCATGTCCAAGACAGTGTTGAAC 60.549 47.826 12.01 2.17 46.04 3.18
1656 3575 2.098233 CATTTCGTCCACCCGACCG 61.098 63.158 0.00 0.00 38.36 4.79
1678 3597 1.277273 CTCCATCAGCTTCACCTCACA 59.723 52.381 0.00 0.00 0.00 3.58
1680 3599 0.907486 CCTCCATCAGCTTCACCTCA 59.093 55.000 0.00 0.00 0.00 3.86
2019 3938 4.042809 TCTTCAGGGCCTAACAAATCAGAA 59.957 41.667 5.28 0.88 0.00 3.02
2048 3967 2.723530 TCTTCCCTTGGACTTCTCCT 57.276 50.000 0.00 0.00 37.48 3.69
2050 3969 2.026729 CCCTTCTTCCCTTGGACTTCTC 60.027 54.545 0.00 0.00 0.00 2.87
2079 3998 2.179427 TCTGCTTCTTACCTGCTGCTA 58.821 47.619 0.00 0.00 0.00 3.49
2120 4039 3.852205 GCATCGCATGTGAAGGAATCATG 60.852 47.826 13.91 5.49 40.97 3.07
2178 4097 3.350219 ACCAACATGACCAGTATCCAC 57.650 47.619 0.00 0.00 0.00 4.02
2191 4110 5.624159 TCTTCTGAAGATGTCAACCAACAT 58.376 37.500 15.82 0.00 42.49 2.71
2251 4190 7.543947 TTGTAATCATCAAGCTACTGTCATG 57.456 36.000 0.00 0.00 0.00 3.07
2279 4218 2.016604 GCCATTCAGGTCATTGCGGTA 61.017 52.381 0.00 0.00 40.61 4.02
2321 4275 5.045359 TGAACCTCTTGAATCATGGATCAGT 60.045 40.000 0.00 0.00 0.00 3.41
2341 4295 0.249489 ACTGACTCGTGTGCCTGAAC 60.249 55.000 0.00 0.00 0.00 3.18
2391 4345 0.527565 AATCCAGCGATGCACCAAAC 59.472 50.000 0.00 0.00 0.00 2.93
2441 4395 4.600576 TCAGAGCACAACGGCGCA 62.601 61.111 10.83 0.00 39.27 6.09
2489 4446 2.556144 TCAGTGCAGTGAAGAGCAAT 57.444 45.000 21.91 0.00 43.20 3.56
2500 4457 6.981762 AGATTTCACTATTCTTCAGTGCAG 57.018 37.500 0.00 0.00 42.58 4.41
2648 4606 3.302344 GTTTGTGCACCGGCCCAT 61.302 61.111 15.69 0.00 40.13 4.00
2702 4723 1.543802 ACAAACCGCACATTACATGGG 59.456 47.619 0.00 0.00 36.54 4.00
2716 4737 5.120053 CCAACAACAGAAACTTCAACAAACC 59.880 40.000 0.00 0.00 0.00 3.27
2752 4773 1.004044 AGCATGCAGTAAACAGCCTCT 59.996 47.619 21.98 0.00 0.00 3.69
2791 4812 8.650714 GTTTGCATTCACTTGATTAAATCTTCC 58.349 33.333 0.00 0.00 0.00 3.46
2903 4957 3.002965 GGTTCAGGACTTTGTACCGTTTG 59.997 47.826 0.00 0.00 30.42 2.93
2908 4962 1.071228 ACGGGTTCAGGACTTTGTACC 59.929 52.381 0.00 0.00 37.67 3.34
2909 4963 2.538512 ACGGGTTCAGGACTTTGTAC 57.461 50.000 0.00 0.00 0.00 2.90
2926 4980 2.334838 GTCTTAGTGGGTGCTTGTACG 58.665 52.381 0.00 0.00 0.00 3.67
2927 4981 2.302157 AGGTCTTAGTGGGTGCTTGTAC 59.698 50.000 0.00 0.00 0.00 2.90
2928 4982 2.616524 AGGTCTTAGTGGGTGCTTGTA 58.383 47.619 0.00 0.00 0.00 2.41
2929 4983 1.435256 AGGTCTTAGTGGGTGCTTGT 58.565 50.000 0.00 0.00 0.00 3.16
2930 4984 2.154462 CAAGGTCTTAGTGGGTGCTTG 58.846 52.381 0.00 0.00 0.00 4.01
2932 4986 1.072331 CACAAGGTCTTAGTGGGTGCT 59.928 52.381 0.00 0.00 0.00 4.40
2933 4987 1.071699 TCACAAGGTCTTAGTGGGTGC 59.928 52.381 10.81 0.00 34.17 5.01
2934 4988 3.485463 TTCACAAGGTCTTAGTGGGTG 57.515 47.619 10.81 0.00 34.17 4.61
2935 4989 3.714798 TCTTTCACAAGGTCTTAGTGGGT 59.285 43.478 10.81 0.00 34.17 4.51
2936 4990 4.065789 GTCTTTCACAAGGTCTTAGTGGG 58.934 47.826 10.81 0.00 34.17 4.61
2937 4991 4.962155 AGTCTTTCACAAGGTCTTAGTGG 58.038 43.478 10.81 0.00 34.17 4.00
2938 4992 4.681942 CGAGTCTTTCACAAGGTCTTAGTG 59.318 45.833 0.00 0.00 34.67 2.74
2939 4993 4.341520 ACGAGTCTTTCACAAGGTCTTAGT 59.658 41.667 0.00 0.00 0.00 2.24
2940 4994 4.681942 CACGAGTCTTTCACAAGGTCTTAG 59.318 45.833 0.00 0.00 0.00 2.18
2941 4995 4.617959 CACGAGTCTTTCACAAGGTCTTA 58.382 43.478 0.00 0.00 0.00 2.10
2942 4996 3.458189 CACGAGTCTTTCACAAGGTCTT 58.542 45.455 0.00 0.00 0.00 3.01
2943 4997 2.803492 GCACGAGTCTTTCACAAGGTCT 60.803 50.000 0.00 0.00 0.00 3.85
2944 4998 1.527311 GCACGAGTCTTTCACAAGGTC 59.473 52.381 0.00 0.00 0.00 3.85
2945 4999 1.583054 GCACGAGTCTTTCACAAGGT 58.417 50.000 0.00 0.00 0.00 3.50
2946 5000 0.868406 GGCACGAGTCTTTCACAAGG 59.132 55.000 0.00 0.00 0.00 3.61
2947 5001 1.261619 GTGGCACGAGTCTTTCACAAG 59.738 52.381 0.00 0.00 0.00 3.16
2948 5002 1.295792 GTGGCACGAGTCTTTCACAA 58.704 50.000 0.00 0.00 0.00 3.33
2949 5003 0.176910 TGTGGCACGAGTCTTTCACA 59.823 50.000 13.77 0.00 33.48 3.58
2950 5004 1.295792 TTGTGGCACGAGTCTTTCAC 58.704 50.000 13.77 0.00 0.00 3.18
2951 5005 2.031258 TTTGTGGCACGAGTCTTTCA 57.969 45.000 13.77 0.00 0.00 2.69
2952 5006 2.612212 TCTTTTGTGGCACGAGTCTTTC 59.388 45.455 13.77 0.00 0.00 2.62
2953 5007 2.639065 TCTTTTGTGGCACGAGTCTTT 58.361 42.857 13.77 0.00 0.00 2.52
2954 5008 2.325583 TCTTTTGTGGCACGAGTCTT 57.674 45.000 13.77 0.00 0.00 3.01
2955 5009 2.325583 TTCTTTTGTGGCACGAGTCT 57.674 45.000 13.77 0.00 0.00 3.24
2956 5010 2.808543 AGATTCTTTTGTGGCACGAGTC 59.191 45.455 13.77 9.97 0.00 3.36
2957 5011 2.549754 CAGATTCTTTTGTGGCACGAGT 59.450 45.455 13.77 0.34 0.00 4.18
2958 5012 2.549754 ACAGATTCTTTTGTGGCACGAG 59.450 45.455 13.77 10.78 0.00 4.18
2959 5013 2.290367 CACAGATTCTTTTGTGGCACGA 59.710 45.455 13.77 8.59 40.69 4.35
2960 5014 2.290367 TCACAGATTCTTTTGTGGCACG 59.710 45.455 13.77 0.00 43.69 5.34
2961 5015 3.632189 GTCACAGATTCTTTTGTGGCAC 58.368 45.455 11.55 11.55 46.35 5.01
2962 5016 3.988379 GTCACAGATTCTTTTGTGGCA 57.012 42.857 4.52 0.00 46.35 4.92
2963 5017 2.622942 TGGTCACAGATTCTTTTGTGGC 59.377 45.455 4.95 2.98 46.37 5.01
2976 5030 0.179020 TTGCTTGGGTCTGGTCACAG 60.179 55.000 0.00 0.00 46.30 3.66
2977 5031 0.179020 CTTGCTTGGGTCTGGTCACA 60.179 55.000 0.00 0.00 0.00 3.58
2978 5032 0.108585 TCTTGCTTGGGTCTGGTCAC 59.891 55.000 0.00 0.00 0.00 3.67
2979 5033 0.108585 GTCTTGCTTGGGTCTGGTCA 59.891 55.000 0.00 0.00 0.00 4.02
2980 5034 0.108585 TGTCTTGCTTGGGTCTGGTC 59.891 55.000 0.00 0.00 0.00 4.02
2981 5035 0.773644 ATGTCTTGCTTGGGTCTGGT 59.226 50.000 0.00 0.00 0.00 4.00
2982 5036 1.271543 TGATGTCTTGCTTGGGTCTGG 60.272 52.381 0.00 0.00 0.00 3.86
2983 5037 2.189594 TGATGTCTTGCTTGGGTCTG 57.810 50.000 0.00 0.00 0.00 3.51
2984 5038 2.575279 AGATGATGTCTTGCTTGGGTCT 59.425 45.455 0.00 0.00 31.47 3.85
2985 5039 2.996631 AGATGATGTCTTGCTTGGGTC 58.003 47.619 0.00 0.00 31.47 4.46
2986 5040 3.446442 AAGATGATGTCTTGCTTGGGT 57.554 42.857 0.00 0.00 45.38 4.51
2995 5049 4.717877 TGTTGTGGTTGAAGATGATGTCT 58.282 39.130 0.00 0.00 39.43 3.41
2996 5050 5.181811 TGATGTTGTGGTTGAAGATGATGTC 59.818 40.000 0.00 0.00 0.00 3.06
2997 5051 5.072055 TGATGTTGTGGTTGAAGATGATGT 58.928 37.500 0.00 0.00 0.00 3.06
2998 5052 5.632244 TGATGTTGTGGTTGAAGATGATG 57.368 39.130 0.00 0.00 0.00 3.07
2999 5053 5.947566 TGATGATGTTGTGGTTGAAGATGAT 59.052 36.000 0.00 0.00 0.00 2.45
3000 5054 5.181811 GTGATGATGTTGTGGTTGAAGATGA 59.818 40.000 0.00 0.00 0.00 2.92
3001 5055 5.396484 GTGATGATGTTGTGGTTGAAGATG 58.604 41.667 0.00 0.00 0.00 2.90
3002 5056 4.460382 GGTGATGATGTTGTGGTTGAAGAT 59.540 41.667 0.00 0.00 0.00 2.40
3003 5057 3.820467 GGTGATGATGTTGTGGTTGAAGA 59.180 43.478 0.00 0.00 0.00 2.87
3004 5058 3.569277 TGGTGATGATGTTGTGGTTGAAG 59.431 43.478 0.00 0.00 0.00 3.02
3005 5059 3.317711 GTGGTGATGATGTTGTGGTTGAA 59.682 43.478 0.00 0.00 0.00 2.69
3006 5060 2.884012 GTGGTGATGATGTTGTGGTTGA 59.116 45.455 0.00 0.00 0.00 3.18
3007 5061 2.030007 GGTGGTGATGATGTTGTGGTTG 60.030 50.000 0.00 0.00 0.00 3.77
3008 5062 2.238521 GGTGGTGATGATGTTGTGGTT 58.761 47.619 0.00 0.00 0.00 3.67
3009 5063 1.144708 TGGTGGTGATGATGTTGTGGT 59.855 47.619 0.00 0.00 0.00 4.16
3010 5064 1.541147 GTGGTGGTGATGATGTTGTGG 59.459 52.381 0.00 0.00 0.00 4.17
3011 5065 2.030893 GTGTGGTGGTGATGATGTTGTG 60.031 50.000 0.00 0.00 0.00 3.33
3012 5066 2.158623 AGTGTGGTGGTGATGATGTTGT 60.159 45.455 0.00 0.00 0.00 3.32
3013 5067 2.227149 CAGTGTGGTGGTGATGATGTTG 59.773 50.000 0.00 0.00 0.00 3.33
3014 5068 2.507484 CAGTGTGGTGGTGATGATGTT 58.493 47.619 0.00 0.00 0.00 2.71
3015 5069 1.883638 GCAGTGTGGTGGTGATGATGT 60.884 52.381 0.00 0.00 0.00 3.06
3016 5070 0.806868 GCAGTGTGGTGGTGATGATG 59.193 55.000 0.00 0.00 0.00 3.07
3017 5071 0.694771 AGCAGTGTGGTGGTGATGAT 59.305 50.000 0.00 0.00 0.00 2.45
3018 5072 1.001974 GTAGCAGTGTGGTGGTGATGA 59.998 52.381 0.00 0.00 0.00 2.92
3019 5073 1.270785 TGTAGCAGTGTGGTGGTGATG 60.271 52.381 0.00 0.00 0.00 3.07
3020 5074 1.055849 TGTAGCAGTGTGGTGGTGAT 58.944 50.000 0.00 0.00 0.00 3.06
3021 5075 1.001974 GATGTAGCAGTGTGGTGGTGA 59.998 52.381 0.00 0.00 0.00 4.02
3022 5076 1.002430 AGATGTAGCAGTGTGGTGGTG 59.998 52.381 0.00 0.00 0.00 4.17
3023 5077 1.352083 AGATGTAGCAGTGTGGTGGT 58.648 50.000 0.00 0.00 0.00 4.16
3024 5078 2.479566 AAGATGTAGCAGTGTGGTGG 57.520 50.000 0.00 0.00 0.00 4.61
3025 5079 4.067896 AGAAAAGATGTAGCAGTGTGGTG 58.932 43.478 0.00 0.00 0.00 4.17
3026 5080 4.357918 AGAAAAGATGTAGCAGTGTGGT 57.642 40.909 0.00 0.00 0.00 4.16
3027 5081 5.455392 CAAAGAAAAGATGTAGCAGTGTGG 58.545 41.667 0.00 0.00 0.00 4.17
3028 5082 4.913924 GCAAAGAAAAGATGTAGCAGTGTG 59.086 41.667 0.00 0.00 0.00 3.82
3029 5083 4.823989 AGCAAAGAAAAGATGTAGCAGTGT 59.176 37.500 0.00 0.00 0.00 3.55
3030 5084 5.368256 AGCAAAGAAAAGATGTAGCAGTG 57.632 39.130 0.00 0.00 0.00 3.66
3031 5085 4.457257 GGAGCAAAGAAAAGATGTAGCAGT 59.543 41.667 0.00 0.00 0.00 4.40
3032 5086 4.436584 CGGAGCAAAGAAAAGATGTAGCAG 60.437 45.833 0.00 0.00 0.00 4.24
3033 5087 3.436704 CGGAGCAAAGAAAAGATGTAGCA 59.563 43.478 0.00 0.00 0.00 3.49
3034 5088 3.181506 CCGGAGCAAAGAAAAGATGTAGC 60.182 47.826 0.00 0.00 0.00 3.58
3035 5089 4.003648 ACCGGAGCAAAGAAAAGATGTAG 58.996 43.478 9.46 0.00 0.00 2.74
3036 5090 3.751175 CACCGGAGCAAAGAAAAGATGTA 59.249 43.478 9.46 0.00 0.00 2.29
3037 5091 2.554032 CACCGGAGCAAAGAAAAGATGT 59.446 45.455 9.46 0.00 0.00 3.06
3038 5092 2.669391 GCACCGGAGCAAAGAAAAGATG 60.669 50.000 19.70 0.00 0.00 2.90
3039 5093 1.541588 GCACCGGAGCAAAGAAAAGAT 59.458 47.619 19.70 0.00 0.00 2.40
3040 5094 0.951558 GCACCGGAGCAAAGAAAAGA 59.048 50.000 19.70 0.00 0.00 2.52
3041 5095 0.039165 GGCACCGGAGCAAAGAAAAG 60.039 55.000 25.48 0.00 35.83 2.27
3042 5096 0.753479 TGGCACCGGAGCAAAGAAAA 60.753 50.000 25.48 0.00 35.83 2.29
3043 5097 0.753479 TTGGCACCGGAGCAAAGAAA 60.753 50.000 25.48 8.40 35.83 2.52
3044 5098 0.753479 TTTGGCACCGGAGCAAAGAA 60.753 50.000 25.48 10.69 35.83 2.52
3045 5099 0.753479 TTTTGGCACCGGAGCAAAGA 60.753 50.000 25.48 13.21 35.83 2.52
3046 5100 0.318955 CTTTTGGCACCGGAGCAAAG 60.319 55.000 25.48 21.06 35.83 2.77
3047 5101 1.739049 CTTTTGGCACCGGAGCAAA 59.261 52.632 25.48 18.23 35.83 3.68
3048 5102 2.199652 CCTTTTGGCACCGGAGCAA 61.200 57.895 25.48 12.24 35.83 3.91
3049 5103 2.597217 CCTTTTGGCACCGGAGCA 60.597 61.111 25.48 8.95 35.83 4.26
3050 5104 2.282180 TCCTTTTGGCACCGGAGC 60.282 61.111 16.31 16.31 40.12 4.70
3051 5105 0.821711 TTGTCCTTTTGGCACCGGAG 60.822 55.000 9.46 0.00 40.12 4.63
3052 5106 0.821711 CTTGTCCTTTTGGCACCGGA 60.822 55.000 9.46 0.00 40.12 5.14
3053 5107 1.659794 CTTGTCCTTTTGGCACCGG 59.340 57.895 0.00 0.00 40.12 5.28
3054 5108 0.821711 TCCTTGTCCTTTTGGCACCG 60.822 55.000 0.00 0.00 40.12 4.94
3055 5109 0.673985 GTCCTTGTCCTTTTGGCACC 59.326 55.000 0.00 0.00 40.12 5.01
3056 5110 1.067060 GTGTCCTTGTCCTTTTGGCAC 59.933 52.381 0.00 0.00 40.12 5.01
3057 5111 1.341482 TGTGTCCTTGTCCTTTTGGCA 60.341 47.619 0.00 0.00 40.12 4.92
3058 5112 1.067060 GTGTGTCCTTGTCCTTTTGGC 59.933 52.381 0.00 0.00 40.12 4.52
3059 5113 2.654863 AGTGTGTCCTTGTCCTTTTGG 58.345 47.619 0.00 0.00 42.21 3.28
3060 5114 5.762045 CATAAGTGTGTCCTTGTCCTTTTG 58.238 41.667 0.00 0.00 0.00 2.44
3061 5115 4.278419 GCATAAGTGTGTCCTTGTCCTTTT 59.722 41.667 0.00 0.00 0.00 2.27
3062 5116 3.821033 GCATAAGTGTGTCCTTGTCCTTT 59.179 43.478 0.00 0.00 0.00 3.11
3063 5117 3.181445 TGCATAAGTGTGTCCTTGTCCTT 60.181 43.478 0.00 0.00 0.00 3.36
3064 5118 2.371841 TGCATAAGTGTGTCCTTGTCCT 59.628 45.455 0.00 0.00 0.00 3.85
3065 5119 2.778299 TGCATAAGTGTGTCCTTGTCC 58.222 47.619 0.00 0.00 0.00 4.02
3066 5120 3.375299 GGATGCATAAGTGTGTCCTTGTC 59.625 47.826 0.00 0.00 32.04 3.18
3067 5121 3.244875 TGGATGCATAAGTGTGTCCTTGT 60.245 43.478 0.00 0.00 34.29 3.16
3068 5122 3.346315 TGGATGCATAAGTGTGTCCTTG 58.654 45.455 0.00 0.00 34.29 3.61
3069 5123 3.719268 TGGATGCATAAGTGTGTCCTT 57.281 42.857 0.00 0.00 34.29 3.36
3070 5124 3.347216 GTTGGATGCATAAGTGTGTCCT 58.653 45.455 0.00 0.00 34.29 3.85
3071 5125 3.764885 GTTGGATGCATAAGTGTGTCC 57.235 47.619 0.00 0.00 33.98 4.02


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

AutoCloner maintained by Alex Coulton.