Multiple sequence alignment - TraesCS5D01G243400

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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 TraesCS5D01G243400 chr5D 100.000 6033 0 0 1 6033 351482824 351476792 0.000000e+00 11141
1 TraesCS5D01G243400 chr5B 92.099 4164 174 66 588 4667 412690728 412686636 0.000000e+00 5723
2 TraesCS5D01G243400 chr5B 92.961 1378 63 6 4666 6033 412686482 412685129 0.000000e+00 1977
3 TraesCS5D01G243400 chr5B 91.139 237 9 7 359 594 412691396 412691171 1.630000e-80 311
4 TraesCS5D01G243400 chr5B 93.289 149 7 1 217 362 412691829 412691681 3.660000e-52 217
5 TraesCS5D01G243400 chr5A 93.696 3236 113 22 2419 5617 451887854 451884673 0.000000e+00 4761
6 TraesCS5D01G243400 chr5A 91.723 1631 73 27 219 1812 451890536 451888931 0.000000e+00 2207
7 TraesCS5D01G243400 chr5A 89.107 560 30 11 1870 2422 451888804 451888269 0.000000e+00 667
8 TraesCS5D01G243400 chr5A 93.927 247 11 1 5790 6032 451884054 451883808 2.660000e-98 370
9 TraesCS5D01G243400 chr5A 90.789 152 10 2 5646 5797 451884276 451884129 3.690000e-47 200


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 TraesCS5D01G243400 chr5D 351476792 351482824 6032 True 11141 11141 100.0000 1 6033 1 chr5D.!!$R1 6032
1 TraesCS5D01G243400 chr5B 412685129 412691829 6700 True 2057 5723 92.3720 217 6033 4 chr5B.!!$R1 5816
2 TraesCS5D01G243400 chr5A 451883808 451890536 6728 True 1641 4761 91.8484 219 6032 5 chr5A.!!$R1 5813

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
563 857 0.032615 TGGTTGGGAAAGCAAGGTGT 60.033 50.000 0.0 0.0 0.00 4.16 F
624 1368 0.108851 GGCGATGCCCAAACGAAAAT 60.109 50.000 0.0 0.0 44.06 1.82 F
1959 2843 0.671781 ATTCCAGACGTGACTGCTGC 60.672 55.000 0.0 0.0 36.67 5.25 F
2815 4125 0.465460 GAAGTGCCACAGACCCACAA 60.465 55.000 0.0 0.0 32.09 3.33 F
3841 5152 1.134220 GGCATCGGTGTTAGATGGGAA 60.134 52.381 0.0 0.0 44.06 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 2418 0.486879 ATTGCCTTCAAACCCCAGGA 59.513 50.000 0.00 0.0 35.56 3.86 R
2565 3874 1.002087 CTGGTTAGACTTCCAGGCGTT 59.998 52.381 14.78 0.0 45.11 4.84 R
3539 4850 1.032114 GGGTCTGTGCTTGCCCATAC 61.032 60.000 0.00 0.0 40.76 2.39 R
4172 5483 1.074889 GCTGGAGGAAAGGGGTTACAA 59.925 52.381 0.00 0.0 0.00 2.41 R
5626 7133 0.264657 AGGCTTCCCACCAAGGTTTT 59.735 50.000 0.00 0.0 34.66 2.43 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
37 38 8.797266 ATATTTTTCTTTGAAACGTGAAGGAC 57.203 30.769 0.00 0.00 0.00 3.85
38 39 5.890424 TTTTCTTTGAAACGTGAAGGACT 57.110 34.783 0.00 0.00 0.00 3.85
39 40 4.875544 TTCTTTGAAACGTGAAGGACTG 57.124 40.909 0.00 0.00 0.00 3.51
40 41 4.131649 TCTTTGAAACGTGAAGGACTGA 57.868 40.909 0.00 0.00 0.00 3.41
41 42 4.703897 TCTTTGAAACGTGAAGGACTGAT 58.296 39.130 0.00 0.00 0.00 2.90
42 43 5.123227 TCTTTGAAACGTGAAGGACTGATT 58.877 37.500 0.00 0.00 0.00 2.57
43 44 5.236478 TCTTTGAAACGTGAAGGACTGATTC 59.764 40.000 0.00 0.00 0.00 2.52
44 45 3.399330 TGAAACGTGAAGGACTGATTCC 58.601 45.455 0.00 0.00 46.33 3.01
77 78 9.543231 AGGAATATATAAGAATCCGTTCCTACA 57.457 33.333 7.82 0.00 41.61 2.74
85 86 7.668525 AAGAATCCGTTCCTACAAACTAAAG 57.331 36.000 0.00 0.00 34.81 1.85
86 87 5.642491 AGAATCCGTTCCTACAAACTAAAGC 59.358 40.000 0.00 0.00 34.81 3.51
87 88 4.339872 TCCGTTCCTACAAACTAAAGCA 57.660 40.909 0.00 0.00 0.00 3.91
88 89 4.312443 TCCGTTCCTACAAACTAAAGCAG 58.688 43.478 0.00 0.00 0.00 4.24
89 90 4.062991 CCGTTCCTACAAACTAAAGCAGT 58.937 43.478 0.00 0.00 40.05 4.40
105 106 9.651913 ACTAAAGCAGTTCAAAGAAAATTTTCA 57.348 25.926 28.00 8.82 35.16 2.69
161 162 9.713713 GAGGGATCCTCTAATATTTCTACAAAC 57.286 37.037 12.58 0.00 46.41 2.93
162 163 8.661345 AGGGATCCTCTAATATTTCTACAAACC 58.339 37.037 12.58 0.00 0.00 3.27
163 164 8.437575 GGGATCCTCTAATATTTCTACAAACCA 58.562 37.037 12.58 0.00 0.00 3.67
164 165 9.847224 GGATCCTCTAATATTTCTACAAACCAA 57.153 33.333 3.84 0.00 0.00 3.67
172 173 5.977489 ATTTCTACAAACCAAAGTAGGCC 57.023 39.130 0.00 0.00 38.54 5.19
173 174 4.717279 TTCTACAAACCAAAGTAGGCCT 57.283 40.909 11.78 11.78 38.54 5.19
174 175 5.829062 TTCTACAAACCAAAGTAGGCCTA 57.171 39.130 8.91 8.91 38.54 3.93
175 176 5.829062 TCTACAAACCAAAGTAGGCCTAA 57.171 39.130 15.83 0.00 38.54 2.69
176 177 6.190346 TCTACAAACCAAAGTAGGCCTAAA 57.810 37.500 15.83 0.00 38.54 1.85
177 178 6.786122 TCTACAAACCAAAGTAGGCCTAAAT 58.214 36.000 15.83 3.07 38.54 1.40
178 179 5.722021 ACAAACCAAAGTAGGCCTAAATG 57.278 39.130 15.83 13.34 0.00 2.32
179 180 5.144832 ACAAACCAAAGTAGGCCTAAATGT 58.855 37.500 15.83 7.95 0.00 2.71
180 181 6.308566 ACAAACCAAAGTAGGCCTAAATGTA 58.691 36.000 15.83 0.00 0.00 2.29
181 182 6.778559 ACAAACCAAAGTAGGCCTAAATGTAA 59.221 34.615 15.83 0.00 0.00 2.41
182 183 7.288158 ACAAACCAAAGTAGGCCTAAATGTAAA 59.712 33.333 15.83 0.00 0.00 2.01
183 184 7.842887 AACCAAAGTAGGCCTAAATGTAAAA 57.157 32.000 15.83 0.00 0.00 1.52
184 185 7.842887 ACCAAAGTAGGCCTAAATGTAAAAA 57.157 32.000 15.83 0.00 0.00 1.94
221 222 5.592688 ACATTTATATTGTGGAACGGAAGGG 59.407 40.000 0.00 0.00 42.39 3.95
227 228 2.262637 TGTGGAACGGAAGGGATACTT 58.737 47.619 0.00 0.00 42.39 2.24
239 240 5.522824 GGAAGGGATACTTTTGCTTACTACG 59.477 44.000 0.00 0.00 40.21 3.51
247 248 2.074547 TTGCTTACTACGCCTGTCAC 57.925 50.000 0.00 0.00 0.00 3.67
474 766 0.387367 CGAGTGACCTGTGACGAAGG 60.387 60.000 0.00 0.00 40.93 3.46
475 767 0.667792 GAGTGACCTGTGACGAAGGC 60.668 60.000 0.00 0.00 38.48 4.35
486 778 2.284798 GACGAAGGCGATGAGAGGCA 62.285 60.000 0.00 0.00 41.64 4.75
488 780 1.150567 CGAAGGCGATGAGAGGCAAG 61.151 60.000 0.00 0.00 40.82 4.01
489 781 1.435408 GAAGGCGATGAGAGGCAAGC 61.435 60.000 0.00 0.00 36.55 4.01
492 786 1.712977 GGCGATGAGAGGCAAGCAAG 61.713 60.000 0.00 0.00 36.38 4.01
504 798 3.389002 AGGCAAGCAAGGAAAAGAAATGT 59.611 39.130 0.00 0.00 0.00 2.71
548 842 1.603455 CTCACATGCCCGGTTGGTT 60.603 57.895 0.00 0.00 36.04 3.67
563 857 0.032615 TGGTTGGGAAAGCAAGGTGT 60.033 50.000 0.00 0.00 0.00 4.16
623 1367 1.287503 GGCGATGCCCAAACGAAAA 59.712 52.632 0.00 0.00 44.06 2.29
624 1368 0.108851 GGCGATGCCCAAACGAAAAT 60.109 50.000 0.00 0.00 44.06 1.82
625 1369 1.133407 GGCGATGCCCAAACGAAAATA 59.867 47.619 0.00 0.00 44.06 1.40
689 1433 2.282701 TCGTACCCTAACACGAATGC 57.717 50.000 0.00 0.00 43.63 3.56
694 1438 4.384846 CGTACCCTAACACGAATGCATATC 59.615 45.833 0.00 0.00 40.56 1.63
695 1439 3.740115 ACCCTAACACGAATGCATATCC 58.260 45.455 0.00 0.00 0.00 2.59
744 1492 2.233271 CTGAGCAAAGCAAAGAGGGAA 58.767 47.619 0.00 0.00 0.00 3.97
745 1493 2.624838 CTGAGCAAAGCAAAGAGGGAAA 59.375 45.455 0.00 0.00 0.00 3.13
746 1494 3.030291 TGAGCAAAGCAAAGAGGGAAAA 58.970 40.909 0.00 0.00 0.00 2.29
747 1495 3.450457 TGAGCAAAGCAAAGAGGGAAAAA 59.550 39.130 0.00 0.00 0.00 1.94
778 1529 0.676782 AAGCTCCCCGTCAAAATCCG 60.677 55.000 0.00 0.00 0.00 4.18
1244 2031 2.757508 TGAGCTCTCCGCCTCCAG 60.758 66.667 16.19 0.00 40.39 3.86
1258 2045 1.480954 CCTCCAGCCGCTTAAGTTCTA 59.519 52.381 4.02 0.00 0.00 2.10
1276 2063 5.647225 AGTTCTACTTCCTCGTGGTTACTAG 59.353 44.000 2.99 0.00 34.23 2.57
1277 2064 5.171339 TCTACTTCCTCGTGGTTACTAGT 57.829 43.478 0.00 0.00 34.23 2.57
1279 2066 6.711277 TCTACTTCCTCGTGGTTACTAGTAA 58.289 40.000 11.38 11.38 34.23 2.24
1280 2067 7.168219 TCTACTTCCTCGTGGTTACTAGTAAA 58.832 38.462 16.82 0.00 34.23 2.01
1281 2068 6.655078 ACTTCCTCGTGGTTACTAGTAAAA 57.345 37.500 16.82 6.09 34.23 1.52
1282 2069 6.685657 ACTTCCTCGTGGTTACTAGTAAAAG 58.314 40.000 16.82 15.06 34.23 2.27
1283 2070 5.649782 TCCTCGTGGTTACTAGTAAAAGG 57.350 43.478 16.82 16.32 34.23 3.11
1284 2071 4.463891 TCCTCGTGGTTACTAGTAAAAGGG 59.536 45.833 16.82 12.50 34.23 3.95
1285 2072 4.221482 CCTCGTGGTTACTAGTAAAAGGGT 59.779 45.833 16.82 0.00 0.00 4.34
1286 2073 5.279657 CCTCGTGGTTACTAGTAAAAGGGTT 60.280 44.000 16.82 0.00 0.00 4.11
1287 2074 6.173427 TCGTGGTTACTAGTAAAAGGGTTT 57.827 37.500 16.82 0.00 0.00 3.27
1288 2075 5.990996 TCGTGGTTACTAGTAAAAGGGTTTG 59.009 40.000 16.82 3.03 0.00 2.93
1289 2076 5.179929 CGTGGTTACTAGTAAAAGGGTTTGG 59.820 44.000 16.82 0.00 0.00 3.28
1290 2077 6.064060 GTGGTTACTAGTAAAAGGGTTTGGT 58.936 40.000 16.82 0.00 0.00 3.67
1311 2098 4.319984 GGTGATTCGTTGGTTTAGTTGGTC 60.320 45.833 0.00 0.00 0.00 4.02
1312 2099 4.514066 GTGATTCGTTGGTTTAGTTGGTCT 59.486 41.667 0.00 0.00 0.00 3.85
1313 2100 5.697633 GTGATTCGTTGGTTTAGTTGGTCTA 59.302 40.000 0.00 0.00 0.00 2.59
1345 2132 2.734723 CGTGGGTGCAGTGACGAG 60.735 66.667 5.59 0.00 33.64 4.18
1408 2195 1.203523 GACTGCGAGTTCATCACCTCT 59.796 52.381 0.00 0.00 0.00 3.69
1530 2317 2.673368 CTCTGGTTGGTGAACGATTAGC 59.327 50.000 0.00 0.00 32.28 3.09
1537 2324 5.109903 GTTGGTGAACGATTAGCTGTCTAT 58.890 41.667 0.00 0.00 0.00 1.98
1569 2356 8.284945 TCTTGTAATGAATTTCAGATTCTGGG 57.715 34.615 13.59 0.00 31.51 4.45
1631 2418 8.807948 AGTTCATATAGGTTTTGCTGTTATGT 57.192 30.769 0.00 0.00 0.00 2.29
1669 2456 5.276489 GGCAATTGTTATGATTGATGCAACG 60.276 40.000 7.40 0.00 36.78 4.10
1694 2481 7.962918 CGTAAAAGTTATTCCTGGAAATGTCTG 59.037 37.037 14.03 0.00 0.00 3.51
1793 2581 5.549742 TGATTTGCTCTTTCATGGGTTTT 57.450 34.783 0.00 0.00 0.00 2.43
1820 2640 1.398390 CACAGGGCGTAGAATTCTTGC 59.602 52.381 14.36 17.20 0.00 4.01
1931 2815 2.009774 GCATAAGCTGGTGGTAGTGTG 58.990 52.381 0.00 0.00 37.91 3.82
1932 2816 2.615493 GCATAAGCTGGTGGTAGTGTGT 60.615 50.000 0.00 0.00 37.91 3.72
1959 2843 0.671781 ATTCCAGACGTGACTGCTGC 60.672 55.000 0.00 0.00 36.67 5.25
1966 2850 1.219522 ACGTGACTGCTGCGTTTACC 61.220 55.000 0.00 0.00 35.11 2.85
2028 2912 3.614159 CCATACATGTCATTGGCTTCG 57.386 47.619 0.00 0.00 0.00 3.79
2088 2979 8.903820 GGCTATGGATTAATTACAAGTGTTCTT 58.096 33.333 0.00 0.00 0.00 2.52
2276 3167 8.803799 GCGTAAAATATGGTTATTGTTCTTTGG 58.196 33.333 0.00 0.00 0.00 3.28
2282 3173 4.415596 TGGTTATTGTTCTTTGGCCAGAT 58.584 39.130 5.11 0.00 0.00 2.90
2288 3179 8.416329 GTTATTGTTCTTTGGCCAGATCATAAT 58.584 33.333 5.11 7.47 0.00 1.28
2327 3218 2.818751 TTGGGACCTGTTTGAAGTGT 57.181 45.000 0.00 0.00 0.00 3.55
2369 3260 9.778993 ATTCTCAAACTCGTCATATTTTTCATG 57.221 29.630 0.00 0.00 0.00 3.07
2371 3262 8.443160 TCTCAAACTCGTCATATTTTTCATGAC 58.557 33.333 0.00 5.57 45.76 3.06
2544 3853 2.633509 CCAGGCTGCTGCTTTCCAC 61.634 63.158 15.64 0.00 39.59 4.02
2565 3874 3.157881 CGATCCAGGCTACCAGAATAGA 58.842 50.000 0.00 0.00 0.00 1.98
2650 3960 7.286546 TCATGAATCTAACCAAACAAAGACCAA 59.713 33.333 0.00 0.00 0.00 3.67
2709 4019 0.549469 AAGGACCCGAACCAAACACT 59.451 50.000 0.00 0.00 0.00 3.55
2740 4050 2.406130 CTCGCATTTGTGGCACATTTT 58.594 42.857 22.73 6.40 44.52 1.82
2751 4061 3.306703 GTGGCACATTTTTGTCAAGTGTG 59.693 43.478 13.86 16.97 44.52 3.82
2757 4067 6.183360 GCACATTTTTGTCAAGTGTGTTTGAT 60.183 34.615 19.89 0.00 41.53 2.57
2765 4075 4.065088 TCAAGTGTGTTTGATCTGTAGCC 58.935 43.478 0.00 0.00 32.39 3.93
2805 4115 3.414700 CGTCTGCGGAAGTGCCAC 61.415 66.667 0.00 0.00 35.94 5.01
2809 4119 2.280797 TGCGGAAGTGCCACAGAC 60.281 61.111 0.00 0.00 35.94 3.51
2810 4120 3.050275 GCGGAAGTGCCACAGACC 61.050 66.667 0.00 0.00 35.94 3.85
2811 4121 2.358737 CGGAAGTGCCACAGACCC 60.359 66.667 0.00 0.00 35.94 4.46
2812 4122 2.836154 GGAAGTGCCACAGACCCA 59.164 61.111 0.00 0.00 36.34 4.51
2813 4123 1.600916 GGAAGTGCCACAGACCCAC 60.601 63.158 0.00 0.00 36.34 4.61
2814 4124 1.148273 GAAGTGCCACAGACCCACA 59.852 57.895 0.00 0.00 32.09 4.17
2815 4125 0.465460 GAAGTGCCACAGACCCACAA 60.465 55.000 0.00 0.00 32.09 3.33
2871 4181 9.520204 CAAACCATTACTAGCAATCCTATTTTG 57.480 33.333 0.00 0.00 0.00 2.44
2923 4234 1.547820 TGTGCCAAACTCAACAAAGCA 59.452 42.857 0.00 0.00 0.00 3.91
3113 4424 5.829924 TCTTTTCTCTGGTTCAGCTGAAATT 59.170 36.000 29.99 0.00 35.51 1.82
3539 4850 2.189594 TCCTGTGCAATCTGGTTCTG 57.810 50.000 0.00 0.00 0.00 3.02
3716 5027 7.174426 GGTATTATTACCGATTTAGCTGGCTTT 59.826 37.037 0.00 0.00 38.69 3.51
3785 5096 9.064706 AGAATATATTTGCAGTTCAGGAATGAG 57.935 33.333 0.00 0.00 0.00 2.90
3841 5152 1.134220 GGCATCGGTGTTAGATGGGAA 60.134 52.381 0.00 0.00 44.06 3.97
4066 5377 5.401531 TCTACAAGTGTACCACCATCTTC 57.598 43.478 0.00 0.00 34.49 2.87
4172 5483 3.834231 CCCCTTGTTTTCCATGTTCTGAT 59.166 43.478 0.00 0.00 0.00 2.90
4206 5517 2.123428 CCAGCTGGTAGGCCAATGC 61.123 63.158 25.53 1.36 45.51 3.56
4249 5560 1.228094 GCCCTAAGCTGCCTCCATC 60.228 63.158 0.00 0.00 38.99 3.51
4287 5598 0.920763 ATCTGCTGTTCCATCCCCCA 60.921 55.000 0.00 0.00 0.00 4.96
4321 5644 2.661176 TACCTTCCTCCAATCCCTGT 57.339 50.000 0.00 0.00 0.00 4.00
4324 5647 1.289160 CTTCCTCCAATCCCTGTCCA 58.711 55.000 0.00 0.00 0.00 4.02
4551 5879 6.812998 TGTAGCATGTACTTAGGGTTGTATC 58.187 40.000 0.00 0.00 0.00 2.24
4639 5967 2.061773 ACTTGCGAATTGAGACACTCG 58.938 47.619 0.00 0.00 32.35 4.18
4651 5980 4.580868 TGAGACACTCGAGAATCTACTGT 58.419 43.478 21.68 11.04 32.35 3.55
4652 5981 4.393371 TGAGACACTCGAGAATCTACTGTG 59.607 45.833 21.68 6.78 32.35 3.66
4656 5985 4.169508 CACTCGAGAATCTACTGTGTTGG 58.830 47.826 21.68 0.00 0.00 3.77
4876 6377 9.362539 GTTAGTGAAATTGCATTGATTGAATCT 57.637 29.630 6.73 0.00 0.00 2.40
4952 6453 4.524316 ATGTGCTGCTTCAATTTGCTTA 57.476 36.364 0.00 0.00 0.00 3.09
5046 6547 4.566278 CCATTCCTGAAGTGATGGTCAGAA 60.566 45.833 2.28 0.00 32.38 3.02
5047 6548 4.705110 TTCCTGAAGTGATGGTCAGAAA 57.295 40.909 2.28 0.00 32.38 2.52
5048 6549 4.705110 TCCTGAAGTGATGGTCAGAAAA 57.295 40.909 2.28 0.00 32.38 2.29
5070 6571 4.712476 ACTTCCAATGTATCTGCTCCATC 58.288 43.478 0.00 0.00 0.00 3.51
5080 6581 2.143122 TCTGCTCCATCGTTCACAAAC 58.857 47.619 0.00 0.00 0.00 2.93
5146 6647 2.770164 ACTTCCTGAACTGGGAATCG 57.230 50.000 0.00 0.00 41.34 3.34
5165 6666 2.944349 TCGCAATATGATGCTGCAAAGA 59.056 40.909 6.36 0.00 44.21 2.52
5305 6806 0.663153 GCTGCCTTATGCCTTTACCG 59.337 55.000 0.00 0.00 40.16 4.02
5342 6843 0.185175 GAAGGGTTGGGGACTTGTGT 59.815 55.000 0.00 0.00 0.00 3.72
5448 6949 7.555965 TGTGACATATTCAGCATACTACAACT 58.444 34.615 0.00 0.00 33.71 3.16
5450 6951 6.918022 TGACATATTCAGCATACTACAACTCG 59.082 38.462 0.00 0.00 0.00 4.18
5572 7073 4.737578 AGTTAGGTCACAGAGGTTACAGA 58.262 43.478 0.00 0.00 0.00 3.41
5617 7124 5.420739 GCTTCACCTTGGTGGGAATAAAATA 59.579 40.000 18.45 0.00 41.11 1.40
5618 7125 6.627287 GCTTCACCTTGGTGGGAATAAAATAC 60.627 42.308 18.45 0.00 41.11 1.89
5619 7126 5.265989 TCACCTTGGTGGGAATAAAATACC 58.734 41.667 18.45 0.00 41.11 2.73
5620 7127 4.404394 CACCTTGGTGGGAATAAAATACCC 59.596 45.833 11.72 0.00 43.51 3.69
5621 7128 3.964688 CCTTGGTGGGAATAAAATACCCC 59.035 47.826 0.00 0.00 42.65 4.95
5622 7129 4.326610 CCTTGGTGGGAATAAAATACCCCT 60.327 45.833 0.00 0.00 42.65 4.79
5623 7130 5.103430 CCTTGGTGGGAATAAAATACCCCTA 60.103 44.000 0.00 0.00 42.65 3.53
5624 7131 6.418964 TTGGTGGGAATAAAATACCCCTAA 57.581 37.500 0.00 0.00 42.65 2.69
5625 7132 6.418964 TGGTGGGAATAAAATACCCCTAAA 57.581 37.500 0.00 0.00 42.65 1.85
5626 7133 6.812649 TGGTGGGAATAAAATACCCCTAAAA 58.187 36.000 0.00 0.00 42.65 1.52
5627 7134 7.254164 TGGTGGGAATAAAATACCCCTAAAAA 58.746 34.615 0.00 0.00 42.65 1.94
5674 7572 3.577848 TGGCCAAGCTGTCAACATTATTT 59.422 39.130 0.61 0.00 0.00 1.40
5695 7593 2.028130 ACTCAAAAACGGAATGGTGCA 58.972 42.857 0.00 0.00 0.00 4.57
5739 7637 2.874014 TGGTGCCACATTTGATCAGAA 58.126 42.857 0.00 0.00 0.00 3.02
5744 7642 5.105797 GGTGCCACATTTGATCAGAATTACA 60.106 40.000 0.00 0.00 0.00 2.41
5769 7667 3.824414 AAATAAAGGCGGAACTTCACG 57.176 42.857 0.00 0.00 0.00 4.35
5899 7879 7.590279 TCCCATATCAAGAAAAGAAAAACGAC 58.410 34.615 0.00 0.00 0.00 4.34
5965 7945 0.317854 GGCGCGCAACTTTCTTCTTT 60.318 50.000 34.42 0.00 0.00 2.52
5983 7966 1.110442 TTTTGAACACAGGTGCCCAG 58.890 50.000 0.00 0.00 0.00 4.45
5990 7973 3.560636 ACACAGGTGCCCAGTATATTC 57.439 47.619 0.00 0.00 0.00 1.75
5997 7980 2.226437 GTGCCCAGTATATTCATTGGCG 59.774 50.000 0.00 0.00 40.25 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.887406 GTCCTTCACGTTTCAAAGAAAAATATA 57.113 29.630 0.00 0.00 0.00 0.86
12 13 8.630037 AGTCCTTCACGTTTCAAAGAAAAATAT 58.370 29.630 0.00 0.00 0.00 1.28
13 14 7.913297 CAGTCCTTCACGTTTCAAAGAAAAATA 59.087 33.333 0.00 0.00 0.00 1.40
14 15 6.751888 CAGTCCTTCACGTTTCAAAGAAAAAT 59.248 34.615 0.00 0.00 0.00 1.82
15 16 6.072397 TCAGTCCTTCACGTTTCAAAGAAAAA 60.072 34.615 0.00 0.00 0.00 1.94
16 17 5.413213 TCAGTCCTTCACGTTTCAAAGAAAA 59.587 36.000 0.00 0.00 0.00 2.29
17 18 4.938832 TCAGTCCTTCACGTTTCAAAGAAA 59.061 37.500 0.00 0.00 0.00 2.52
18 19 4.509616 TCAGTCCTTCACGTTTCAAAGAA 58.490 39.130 0.00 0.00 0.00 2.52
19 20 4.131649 TCAGTCCTTCACGTTTCAAAGA 57.868 40.909 0.00 0.00 0.00 2.52
20 21 5.424121 AATCAGTCCTTCACGTTTCAAAG 57.576 39.130 0.00 0.00 0.00 2.77
21 22 4.274950 GGAATCAGTCCTTCACGTTTCAAA 59.725 41.667 0.00 0.00 43.98 2.69
22 23 3.813166 GGAATCAGTCCTTCACGTTTCAA 59.187 43.478 0.00 0.00 43.98 2.69
23 24 3.399330 GGAATCAGTCCTTCACGTTTCA 58.601 45.455 0.00 0.00 43.98 2.69
51 52 9.543231 TGTAGGAACGGATTCTTATATATTCCT 57.457 33.333 12.41 12.41 45.16 3.36
59 60 9.379791 CTTTAGTTTGTAGGAACGGATTCTTAT 57.620 33.333 0.00 0.00 34.98 1.73
60 61 7.332678 GCTTTAGTTTGTAGGAACGGATTCTTA 59.667 37.037 0.00 0.00 34.98 2.10
61 62 6.148976 GCTTTAGTTTGTAGGAACGGATTCTT 59.851 38.462 0.00 0.00 34.98 2.52
62 63 5.642491 GCTTTAGTTTGTAGGAACGGATTCT 59.358 40.000 0.00 0.00 34.98 2.40
63 64 5.410439 TGCTTTAGTTTGTAGGAACGGATTC 59.590 40.000 0.00 0.00 34.74 2.52
64 65 5.310451 TGCTTTAGTTTGTAGGAACGGATT 58.690 37.500 0.00 0.00 34.74 3.01
65 66 4.901868 TGCTTTAGTTTGTAGGAACGGAT 58.098 39.130 0.00 0.00 34.74 4.18
66 67 4.202284 ACTGCTTTAGTTTGTAGGAACGGA 60.202 41.667 0.00 0.00 35.67 4.69
67 68 4.062991 ACTGCTTTAGTTTGTAGGAACGG 58.937 43.478 0.00 0.00 35.67 4.44
79 80 9.651913 TGAAAATTTTCTTTGAACTGCTTTAGT 57.348 25.926 26.73 0.00 38.48 2.24
136 137 8.661345 GGTTTGTAGAAATATTAGAGGATCCCT 58.339 37.037 8.55 8.06 36.03 4.20
137 138 8.437575 TGGTTTGTAGAAATATTAGAGGATCCC 58.562 37.037 8.55 0.00 33.66 3.85
138 139 9.847224 TTGGTTTGTAGAAATATTAGAGGATCC 57.153 33.333 2.48 2.48 33.66 3.36
146 147 9.181061 GGCCTACTTTGGTTTGTAGAAATATTA 57.819 33.333 0.00 0.00 38.62 0.98
147 148 7.893833 AGGCCTACTTTGGTTTGTAGAAATATT 59.106 33.333 1.29 0.00 38.62 1.28
148 149 7.410991 AGGCCTACTTTGGTTTGTAGAAATAT 58.589 34.615 1.29 0.00 38.62 1.28
149 150 6.786122 AGGCCTACTTTGGTTTGTAGAAATA 58.214 36.000 1.29 0.00 38.62 1.40
150 151 5.641155 AGGCCTACTTTGGTTTGTAGAAAT 58.359 37.500 1.29 0.00 38.62 2.17
151 152 5.056553 AGGCCTACTTTGGTTTGTAGAAA 57.943 39.130 1.29 0.00 38.62 2.52
152 153 4.717279 AGGCCTACTTTGGTTTGTAGAA 57.283 40.909 1.29 0.00 38.62 2.10
153 154 5.829062 TTAGGCCTACTTTGGTTTGTAGA 57.171 39.130 13.46 0.00 38.62 2.59
154 155 6.433093 ACATTTAGGCCTACTTTGGTTTGTAG 59.567 38.462 13.46 0.00 36.75 2.74
155 156 6.308566 ACATTTAGGCCTACTTTGGTTTGTA 58.691 36.000 13.46 0.00 0.00 2.41
156 157 5.144832 ACATTTAGGCCTACTTTGGTTTGT 58.855 37.500 13.46 4.81 0.00 2.83
157 158 5.722021 ACATTTAGGCCTACTTTGGTTTG 57.278 39.130 13.46 4.20 0.00 2.93
158 159 7.842887 TTTACATTTAGGCCTACTTTGGTTT 57.157 32.000 13.46 0.00 0.00 3.27
159 160 7.842887 TTTTACATTTAGGCCTACTTTGGTT 57.157 32.000 13.46 0.00 0.00 3.67
160 161 7.842887 TTTTTACATTTAGGCCTACTTTGGT 57.157 32.000 13.46 9.26 0.00 3.67
190 191 8.670135 CCGTTCCACAATATAAATGTGTAAAGA 58.330 33.333 16.42 7.50 45.23 2.52
191 192 8.670135 TCCGTTCCACAATATAAATGTGTAAAG 58.330 33.333 16.42 11.25 45.23 1.85
192 193 8.563123 TCCGTTCCACAATATAAATGTGTAAA 57.437 30.769 16.42 10.13 45.23 2.01
193 194 8.563123 TTCCGTTCCACAATATAAATGTGTAA 57.437 30.769 16.42 8.04 45.23 2.41
194 195 7.281324 CCTTCCGTTCCACAATATAAATGTGTA 59.719 37.037 16.42 3.25 45.23 2.90
195 196 6.094881 CCTTCCGTTCCACAATATAAATGTGT 59.905 38.462 16.42 0.26 45.23 3.72
196 197 6.459573 CCCTTCCGTTCCACAATATAAATGTG 60.460 42.308 12.71 12.71 46.05 3.21
197 198 5.592688 CCCTTCCGTTCCACAATATAAATGT 59.407 40.000 0.00 0.00 0.00 2.71
198 199 5.825679 TCCCTTCCGTTCCACAATATAAATG 59.174 40.000 0.00 0.00 0.00 2.32
199 200 6.008696 TCCCTTCCGTTCCACAATATAAAT 57.991 37.500 0.00 0.00 0.00 1.40
200 201 5.438698 TCCCTTCCGTTCCACAATATAAA 57.561 39.130 0.00 0.00 0.00 1.40
201 202 5.640158 ATCCCTTCCGTTCCACAATATAA 57.360 39.130 0.00 0.00 0.00 0.98
202 203 5.842328 AGTATCCCTTCCGTTCCACAATATA 59.158 40.000 0.00 0.00 0.00 0.86
203 204 4.658901 AGTATCCCTTCCGTTCCACAATAT 59.341 41.667 0.00 0.00 0.00 1.28
204 205 4.035112 AGTATCCCTTCCGTTCCACAATA 58.965 43.478 0.00 0.00 0.00 1.90
205 206 2.844348 AGTATCCCTTCCGTTCCACAAT 59.156 45.455 0.00 0.00 0.00 2.71
206 207 2.262637 AGTATCCCTTCCGTTCCACAA 58.737 47.619 0.00 0.00 0.00 3.33
207 208 1.946984 AGTATCCCTTCCGTTCCACA 58.053 50.000 0.00 0.00 0.00 4.17
208 209 3.345508 AAAGTATCCCTTCCGTTCCAC 57.654 47.619 0.00 0.00 31.27 4.02
209 210 3.681593 CAAAAGTATCCCTTCCGTTCCA 58.318 45.455 0.00 0.00 31.27 3.53
210 211 2.422479 GCAAAAGTATCCCTTCCGTTCC 59.578 50.000 0.00 0.00 31.27 3.62
211 212 3.344515 AGCAAAAGTATCCCTTCCGTTC 58.655 45.455 0.00 0.00 31.27 3.95
212 213 3.434940 AGCAAAAGTATCCCTTCCGTT 57.565 42.857 0.00 0.00 31.27 4.44
213 214 3.434940 AAGCAAAAGTATCCCTTCCGT 57.565 42.857 0.00 0.00 31.27 4.69
214 215 4.514401 AGTAAGCAAAAGTATCCCTTCCG 58.486 43.478 0.00 0.00 31.27 4.30
215 216 5.522824 CGTAGTAAGCAAAAGTATCCCTTCC 59.477 44.000 0.00 0.00 31.27 3.46
221 222 4.868734 ACAGGCGTAGTAAGCAAAAGTATC 59.131 41.667 10.30 0.00 36.08 2.24
227 228 2.224090 TGTGACAGGCGTAGTAAGCAAA 60.224 45.455 10.30 0.00 36.08 3.68
239 240 2.126734 GCGCAATGTGTGACAGGC 60.127 61.111 0.30 0.00 0.00 4.85
247 248 1.512522 CGTGATGTGGCGCAATGTG 60.513 57.895 10.83 0.00 0.00 3.21
337 341 2.355244 GCCGCGATAGACTGGCTC 60.355 66.667 8.23 0.00 44.16 4.70
456 748 0.667792 GCCTTCGTCACAGGTCACTC 60.668 60.000 0.00 0.00 33.40 3.51
474 766 1.712977 CCTTGCTTGCCTCTCATCGC 61.713 60.000 0.00 0.00 0.00 4.58
475 767 0.107993 TCCTTGCTTGCCTCTCATCG 60.108 55.000 0.00 0.00 0.00 3.84
486 778 6.044682 CACTTGACATTTCTTTTCCTTGCTT 58.955 36.000 0.00 0.00 0.00 3.91
488 780 5.591099 TCACTTGACATTTCTTTTCCTTGC 58.409 37.500 0.00 0.00 0.00 4.01
489 781 6.183360 ACCTCACTTGACATTTCTTTTCCTTG 60.183 38.462 0.00 0.00 0.00 3.61
492 786 5.774498 ACCTCACTTGACATTTCTTTTCC 57.226 39.130 0.00 0.00 0.00 3.13
504 798 2.656069 GGCGGGCTACCTCACTTGA 61.656 63.158 0.00 0.00 33.28 3.02
548 842 2.364970 CAAATCACACCTTGCTTTCCCA 59.635 45.455 0.00 0.00 0.00 4.37
623 1367 4.101119 AGGAGTGTATTTTACTGCGGCTAT 59.899 41.667 0.00 0.00 40.84 2.97
624 1368 3.449737 AGGAGTGTATTTTACTGCGGCTA 59.550 43.478 0.00 0.00 40.84 3.93
625 1369 2.236395 AGGAGTGTATTTTACTGCGGCT 59.764 45.455 0.00 0.00 40.84 5.52
745 1493 3.501349 GGGAGCTTTCTCTTCCCTTTTT 58.499 45.455 1.55 0.00 39.31 1.94
746 1494 2.225142 GGGGAGCTTTCTCTTCCCTTTT 60.225 50.000 8.56 0.00 37.65 2.27
747 1495 1.356059 GGGGAGCTTTCTCTTCCCTTT 59.644 52.381 8.56 0.00 37.65 3.11
748 1496 0.995803 GGGGAGCTTTCTCTTCCCTT 59.004 55.000 8.56 0.00 37.65 3.95
749 1497 1.268283 CGGGGAGCTTTCTCTTCCCT 61.268 60.000 8.56 0.00 38.16 4.20
750 1498 1.222113 CGGGGAGCTTTCTCTTCCC 59.778 63.158 0.03 0.03 39.31 3.97
751 1499 0.108089 GACGGGGAGCTTTCTCTTCC 60.108 60.000 0.00 0.00 39.31 3.46
752 1500 0.608640 TGACGGGGAGCTTTCTCTTC 59.391 55.000 0.00 0.00 39.31 2.87
778 1529 2.112815 GGGTGCCAAGTATGCGGAC 61.113 63.158 0.00 0.00 0.00 4.79
1189 1976 1.378119 CGCTGGAAAGGTAACCCCC 60.378 63.158 0.00 0.00 37.17 5.40
1190 1977 0.675837 GTCGCTGGAAAGGTAACCCC 60.676 60.000 0.00 0.00 37.17 4.95
1244 2031 3.188492 GAGGAAGTAGAACTTAAGCGGC 58.812 50.000 1.29 0.00 38.80 6.53
1258 2045 6.294955 CCTTTTACTAGTAACCACGAGGAAGT 60.295 42.308 14.96 3.74 32.52 3.01
1276 2063 4.841443 ACGAATCACCAAACCCTTTTAC 57.159 40.909 0.00 0.00 0.00 2.01
1277 2064 4.038162 CCAACGAATCACCAAACCCTTTTA 59.962 41.667 0.00 0.00 0.00 1.52
1279 2066 2.364002 CCAACGAATCACCAAACCCTTT 59.636 45.455 0.00 0.00 0.00 3.11
1280 2067 1.960689 CCAACGAATCACCAAACCCTT 59.039 47.619 0.00 0.00 0.00 3.95
1281 2068 1.133606 ACCAACGAATCACCAAACCCT 60.134 47.619 0.00 0.00 0.00 4.34
1282 2069 1.324383 ACCAACGAATCACCAAACCC 58.676 50.000 0.00 0.00 0.00 4.11
1283 2070 3.446310 AAACCAACGAATCACCAAACC 57.554 42.857 0.00 0.00 0.00 3.27
1284 2071 5.177725 ACTAAACCAACGAATCACCAAAC 57.822 39.130 0.00 0.00 0.00 2.93
1285 2072 5.450688 CCAACTAAACCAACGAATCACCAAA 60.451 40.000 0.00 0.00 0.00 3.28
1286 2073 4.036971 CCAACTAAACCAACGAATCACCAA 59.963 41.667 0.00 0.00 0.00 3.67
1287 2074 3.566322 CCAACTAAACCAACGAATCACCA 59.434 43.478 0.00 0.00 0.00 4.17
1288 2075 3.566742 ACCAACTAAACCAACGAATCACC 59.433 43.478 0.00 0.00 0.00 4.02
1289 2076 4.514066 AGACCAACTAAACCAACGAATCAC 59.486 41.667 0.00 0.00 0.00 3.06
1290 2077 4.710324 AGACCAACTAAACCAACGAATCA 58.290 39.130 0.00 0.00 0.00 2.57
1345 2132 4.260702 CCGTCTAAGTCCTAATCGACTGAC 60.261 50.000 0.00 0.00 42.35 3.51
1352 2139 1.952296 TCCGCCGTCTAAGTCCTAATC 59.048 52.381 0.00 0.00 0.00 1.75
1359 2146 0.747283 AGTCGATCCGCCGTCTAAGT 60.747 55.000 0.00 0.00 0.00 2.24
1408 2195 1.300971 GAAGCATCGAACAGCAGCCA 61.301 55.000 9.96 0.00 0.00 4.75
1569 2356 9.708092 ACTATCTAAGTAAGGTTTCAACTGAAC 57.292 33.333 0.00 0.00 36.36 3.18
1603 2390 5.954335 ACAGCAAAACCTATATGAACTTGC 58.046 37.500 0.00 0.00 38.33 4.01
1631 2418 0.486879 ATTGCCTTCAAACCCCAGGA 59.513 50.000 0.00 0.00 35.56 3.86
1669 2456 8.244113 CCAGACATTTCCAGGAATAACTTTTAC 58.756 37.037 1.58 0.00 0.00 2.01
1694 2481 3.367321 AGTGACCTCTAAGGCTCTAACC 58.633 50.000 0.00 0.00 39.63 2.85
1793 2581 1.913778 TCTACGCCCTGTGTGTTAGA 58.086 50.000 0.00 0.00 38.91 2.10
1820 2640 7.134815 CACATCTAACTTTGACAGAAACAAGG 58.865 38.462 0.00 0.00 0.00 3.61
1931 2815 4.106197 GTCACGTCTGGAATCATCAGTAC 58.894 47.826 0.00 0.00 34.15 2.73
1932 2816 4.017126 AGTCACGTCTGGAATCATCAGTA 58.983 43.478 0.00 0.00 34.15 2.74
1959 2843 1.002773 ACAGGCAGGGTAAGGTAAACG 59.997 52.381 0.00 0.00 0.00 3.60
1966 2850 4.040952 AGCATCTTATACAGGCAGGGTAAG 59.959 45.833 0.00 0.00 0.00 2.34
2028 2912 3.119029 ACCATGCAATGCCAGTGATAAAC 60.119 43.478 1.53 0.00 44.97 2.01
2088 2979 9.814507 CACGTAAACACTTAATAGCAAAATACA 57.185 29.630 0.00 0.00 0.00 2.29
2223 3114 6.301169 AGAATGTGTTCCTCCCTAAACTAG 57.699 41.667 0.00 0.00 34.81 2.57
2327 3218 3.071457 TGAGAATGTGAGGTTGCTCAAGA 59.929 43.478 0.00 0.00 34.88 3.02
2369 3260 5.753921 CAGGTGAGAACCCTATTAAATCGTC 59.246 44.000 0.00 0.00 0.00 4.20
2371 3262 5.671493 ACAGGTGAGAACCCTATTAAATCG 58.329 41.667 0.00 0.00 0.00 3.34
2477 3786 3.827008 ACAGGCCAGTATGTCAGTATG 57.173 47.619 5.01 0.00 37.54 2.39
2544 3853 3.157881 TCTATTCTGGTAGCCTGGATCG 58.842 50.000 0.00 0.00 0.00 3.69
2565 3874 1.002087 CTGGTTAGACTTCCAGGCGTT 59.998 52.381 14.78 0.00 45.11 4.84
2688 3998 0.547075 TGTTTGGTTCGGGTCCTTGA 59.453 50.000 0.00 0.00 0.00 3.02
2709 4019 0.909610 AAATGCGAGGGACTGGGAGA 60.910 55.000 0.00 0.00 38.16 3.71
2740 4050 5.007626 GCTACAGATCAAACACACTTGACAA 59.992 40.000 0.00 0.00 38.12 3.18
2751 4061 6.262496 GGGGTATAAAAGGCTACAGATCAAAC 59.738 42.308 0.00 0.00 0.00 2.93
2757 4067 5.785123 ACTAGGGGTATAAAAGGCTACAGA 58.215 41.667 0.00 0.00 0.00 3.41
2765 4075 4.347292 GGGGAGTGACTAGGGGTATAAAAG 59.653 50.000 0.00 0.00 0.00 2.27
2805 4115 5.009911 TCAACAAAGAATCATTGTGGGTCTG 59.990 40.000 4.55 0.00 39.98 3.51
2808 4118 4.895297 AGTCAACAAAGAATCATTGTGGGT 59.105 37.500 4.55 0.00 39.98 4.51
2809 4119 5.224888 CAGTCAACAAAGAATCATTGTGGG 58.775 41.667 4.55 1.46 39.98 4.61
2810 4120 5.221303 ACCAGTCAACAAAGAATCATTGTGG 60.221 40.000 4.55 1.99 39.98 4.17
2811 4121 5.835257 ACCAGTCAACAAAGAATCATTGTG 58.165 37.500 4.55 0.56 39.98 3.33
2812 4122 6.127366 ACAACCAGTCAACAAAGAATCATTGT 60.127 34.615 0.00 0.00 42.56 2.71
2813 4123 6.275335 ACAACCAGTCAACAAAGAATCATTG 58.725 36.000 0.00 0.00 0.00 2.82
2814 4124 6.469782 ACAACCAGTCAACAAAGAATCATT 57.530 33.333 0.00 0.00 0.00 2.57
2815 4125 6.469782 AACAACCAGTCAACAAAGAATCAT 57.530 33.333 0.00 0.00 0.00 2.45
2871 4181 9.526713 GTAGAAGTAAATAACTAACCTAGTGGC 57.473 37.037 0.00 0.00 39.39 5.01
2898 4208 4.630894 TTGTTGAGTTTGGCACAGTTAG 57.369 40.909 0.00 0.00 42.39 2.34
2899 4209 4.676723 GCTTTGTTGAGTTTGGCACAGTTA 60.677 41.667 0.00 0.00 42.39 2.24
2923 4234 4.482990 AGATGAAGGGACAATGTGGTTTT 58.517 39.130 0.00 0.00 0.00 2.43
3113 4424 1.065345 TCCAACGTGAAACCAACCTGA 60.065 47.619 0.00 0.00 0.00 3.86
3245 4556 1.180029 CCAATGGTGAAGGCAGAAGG 58.820 55.000 0.00 0.00 0.00 3.46
3539 4850 1.032114 GGGTCTGTGCTTGCCCATAC 61.032 60.000 0.00 0.00 40.76 2.39
3730 5041 7.601886 GCATGTATATGATAGACAGTGAGCTTT 59.398 37.037 6.09 0.00 36.36 3.51
3752 5063 7.645402 TGAACTGCAAATATATTCTCTGCATG 58.355 34.615 18.85 15.56 41.81 4.06
3806 5117 1.336125 GATGCCTCAATAGTTGCTGGC 59.664 52.381 14.86 14.86 44.45 4.85
4066 5377 2.202797 CACTCCCAGATGGCGACG 60.203 66.667 0.00 0.00 0.00 5.12
4172 5483 1.074889 GCTGGAGGAAAGGGGTTACAA 59.925 52.381 0.00 0.00 0.00 2.41
4206 5517 2.316108 ACCAAAGCAGGGTGGTTTTAG 58.684 47.619 1.44 0.31 46.17 1.85
4249 5560 1.174078 TGGCTGTGGTGAATGCACAG 61.174 55.000 6.08 0.00 46.96 3.66
4287 5598 6.388619 AGGAAGGTATGGTTTATGAACTGT 57.611 37.500 0.00 0.00 36.03 3.55
4321 5644 2.495383 GGATGGGGAGGATCTACATGGA 60.495 54.545 0.00 0.00 33.08 3.41
4324 5647 1.804672 AGGGATGGGGAGGATCTACAT 59.195 52.381 0.00 0.00 34.96 2.29
4524 5850 5.425539 ACAACCCTAAGTACATGCTACAGAT 59.574 40.000 0.00 0.00 0.00 2.90
4623 5951 2.264109 TCTCGAGTGTCTCAATTCGC 57.736 50.000 13.13 0.00 33.36 4.70
4639 5967 7.819900 AGATACAAACCAACACAGTAGATTCTC 59.180 37.037 0.00 0.00 0.00 2.87
4876 6377 7.038659 CAGTACTTGTGGGTTTTGAAAATTCA 58.961 34.615 0.00 0.00 34.92 2.57
5000 6501 3.084786 GGAGAGCTGCAAGTTTACCATT 58.915 45.455 1.02 0.00 35.30 3.16
5002 6503 1.699634 AGGAGAGCTGCAAGTTTACCA 59.300 47.619 1.02 0.00 35.30 3.25
5003 6504 2.351455 GAGGAGAGCTGCAAGTTTACC 58.649 52.381 1.02 0.00 35.30 2.85
5046 6547 4.922206 TGGAGCAGATACATTGGAAGTTT 58.078 39.130 0.00 0.00 0.00 2.66
5047 6548 4.574674 TGGAGCAGATACATTGGAAGTT 57.425 40.909 0.00 0.00 0.00 2.66
5048 6549 4.712476 GATGGAGCAGATACATTGGAAGT 58.288 43.478 0.00 0.00 30.07 3.01
5070 6571 5.005394 CGTATTCAGGATAGGTTTGTGAACG 59.995 44.000 0.00 0.00 36.61 3.95
5080 6581 3.409570 TCGACCTCGTATTCAGGATAGG 58.590 50.000 0.00 0.00 40.80 2.57
5146 6647 3.040795 CGTCTTTGCAGCATCATATTGC 58.959 45.455 0.00 0.00 43.09 3.56
5295 6796 4.004982 GACCTTACAATTCGGTAAAGGCA 58.995 43.478 0.00 0.00 33.18 4.75
5305 6806 3.933332 CCTTCGGTGAGACCTTACAATTC 59.067 47.826 0.00 0.00 35.66 2.17
5342 6843 9.310449 ACCTTAAGAGTACACATTCTTCTCTAA 57.690 33.333 3.36 0.00 34.91 2.10
5448 6949 1.753930 ATGCCACATCAAAGATGCGA 58.246 45.000 6.90 0.00 0.00 5.10
5450 6951 3.852286 TGAAATGCCACATCAAAGATGC 58.148 40.909 6.90 0.00 0.00 3.91
5572 7073 3.404899 CACATGAAAGGCAAGCCAAAAT 58.595 40.909 14.40 0.00 38.92 1.82
5625 7132 1.128200 GGCTTCCCACCAAGGTTTTT 58.872 50.000 0.00 0.00 34.66 1.94
5626 7133 0.264657 AGGCTTCCCACCAAGGTTTT 59.735 50.000 0.00 0.00 34.66 2.43
5627 7134 1.154430 TAGGCTTCCCACCAAGGTTT 58.846 50.000 0.00 0.00 34.66 3.27
5628 7135 1.382914 ATAGGCTTCCCACCAAGGTT 58.617 50.000 0.00 0.00 34.66 3.50
5629 7136 2.280308 TATAGGCTTCCCACCAAGGT 57.720 50.000 0.00 0.00 34.66 3.50
5630 7137 3.884037 AATATAGGCTTCCCACCAAGG 57.116 47.619 0.00 0.00 37.03 3.61
5631 7138 4.342092 CCAAAATATAGGCTTCCCACCAAG 59.658 45.833 0.00 0.00 0.00 3.61
5632 7139 4.285863 CCAAAATATAGGCTTCCCACCAA 58.714 43.478 0.00 0.00 0.00 3.67
5633 7140 3.909732 CCAAAATATAGGCTTCCCACCA 58.090 45.455 0.00 0.00 0.00 4.17
5674 7572 3.215151 TGCACCATTCCGTTTTTGAGTA 58.785 40.909 0.00 0.00 0.00 2.59
5695 7593 8.147704 CCAACCTAGTTCAACATACCAAATTTT 58.852 33.333 0.00 0.00 0.00 1.82
5739 7637 6.379988 AGTTCCGCCTTTATTTTCCATGTAAT 59.620 34.615 0.00 0.00 0.00 1.89
5744 7642 4.770010 TGAAGTTCCGCCTTTATTTTCCAT 59.230 37.500 0.00 0.00 0.00 3.41
5769 7667 4.747810 ACTTGATCGGATGCCAAATTTTC 58.252 39.130 0.00 0.00 0.00 2.29
5899 7879 5.221322 CCCTTTCTCCCTGAAGTTCTTTTTG 60.221 44.000 4.17 0.00 35.89 2.44
5997 7980 4.811557 GGATAAGATCTACTGTTGTGGCAC 59.188 45.833 11.55 11.55 0.00 5.01


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

AutoCloner maintained by Alex Coulton.