Multiple sequence alignment - TraesCS5A01G025700

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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 TraesCS5A01G025700 chr5A 100.000 7171 0 0 1 7171 20822935 20815765 0.000000e+00 13243
1 TraesCS5A01G025700 chr5A 86.111 180 19 5 6993 7171 645417845 645417671 9.500000e-44 189
2 TraesCS5A01G025700 chr5B 95.708 7037 236 32 1 7003 23892457 23885453 0.000000e+00 11261
3 TraesCS5A01G025700 chr5B 84.239 184 23 6 6990 7171 701501429 701501608 2.660000e-39 174
4 TraesCS5A01G025700 chr5D 96.892 3990 115 7 3022 7003 32154052 32150064 0.000000e+00 6673
5 TraesCS5A01G025700 chr5D 95.831 3046 90 14 1 3028 32157343 32154317 0.000000e+00 4887
6 TraesCS5A01G025700 chr3D 85.946 185 20 3 6993 7171 547932673 547932489 7.340000e-45 193
7 TraesCS5A01G025700 chr7D 84.699 183 22 5 6990 7171 75312676 75312853 2.060000e-40 178
8 TraesCS5A01G025700 chr7D 82.123 179 21 7 7000 7171 99380069 99380243 7.500000e-30 143
9 TraesCS5A01G025700 chr7B 85.542 166 17 4 7012 7171 543322238 543322402 4.450000e-37 167
10 TraesCS5A01G025700 chr1B 83.978 181 21 5 6998 7171 114487161 114487340 4.450000e-37 167
11 TraesCS5A01G025700 chr7A 82.564 195 24 5 6986 7171 579730139 579730332 5.760000e-36 163
12 TraesCS5A01G025700 chr1A 81.818 187 26 4 6993 7171 454532793 454532607 4.480000e-32 150


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 TraesCS5A01G025700 chr5A 20815765 20822935 7170 True 13243 13243 100.0000 1 7171 1 chr5A.!!$R1 7170
1 TraesCS5A01G025700 chr5B 23885453 23892457 7004 True 11261 11261 95.7080 1 7003 1 chr5B.!!$R1 7002
2 TraesCS5A01G025700 chr5D 32150064 32157343 7279 True 5780 6673 96.3615 1 7003 2 chr5D.!!$R1 7002

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
519 531 1.373497 AAAGTCTCCGCTGCGACAG 60.373 57.895 25.45 18.14 32.68 3.51 F
1896 1928 0.178068 GCGGCACTTCTTGGGAGATA 59.822 55.000 0.00 0.00 0.00 1.98 F
3399 3704 0.250234 TAATGAGCAGAACGCCAGCT 59.750 50.000 0.00 0.00 44.04 4.24 F
4007 4314 2.224769 TGAGAGGCTTAGGTTGTTTGGG 60.225 50.000 0.00 0.00 0.00 4.12 F
4636 4943 6.524734 TGGTATGTATGCTTCTTATGTGGAG 58.475 40.000 0.00 0.00 0.00 3.86 F
5410 5718 2.934553 GGTACAAAGATTAGGTGCGACC 59.065 50.000 0.00 0.00 38.99 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2277 2309 0.038159 AGCCGCTTGTCAGTACTCAC 60.038 55.000 0.00 0.00 0.00 3.51 R
3458 3763 2.364970 TGAACAAACCAAAGCCCAGATG 59.635 45.455 0.00 0.00 0.00 2.90 R
4511 4818 0.029167 TGTGCACGTTGTTCTGCATG 59.971 50.000 13.13 0.00 44.93 4.06 R
5003 5311 0.243636 GTAACCATTGGTGCACAGGC 59.756 55.000 20.43 1.36 35.34 4.85 R
5742 6050 0.535102 CATCGTACTCATTGGGGGCC 60.535 60.000 0.00 0.00 0.00 5.80 R
7014 7334 0.041663 ACAAATGCGTCGTCCGTTTG 60.042 50.000 12.96 12.96 42.19 2.93 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
104 105 2.507102 ACGGCGAGCTCAATCACG 60.507 61.111 16.62 12.08 0.00 4.35
444 456 4.668576 CGTAGAACGGTAGAAGTGTACA 57.331 45.455 0.00 0.00 38.08 2.90
445 457 5.227238 CGTAGAACGGTAGAAGTGTACAT 57.773 43.478 0.00 0.00 38.08 2.29
446 458 6.349973 CGTAGAACGGTAGAAGTGTACATA 57.650 41.667 0.00 0.00 38.08 2.29
447 459 6.188175 CGTAGAACGGTAGAAGTGTACATAC 58.812 44.000 0.00 0.00 38.08 2.39
448 460 5.227238 AGAACGGTAGAAGTGTACATACG 57.773 43.478 0.00 0.00 0.00 3.06
519 531 1.373497 AAAGTCTCCGCTGCGACAG 60.373 57.895 25.45 18.14 32.68 3.51
620 637 1.535202 AGATCGGAGATGGGAGGCC 60.535 63.158 0.00 0.00 45.12 5.19
830 847 2.943653 GTGTCCTGGTTTTCGCCG 59.056 61.111 0.00 0.00 0.00 6.46
834 851 2.032071 CCTGGTTTTCGCCGTCCT 59.968 61.111 0.00 0.00 0.00 3.85
843 860 1.879737 TTCGCCGTCCTCCGAAATGA 61.880 55.000 0.00 0.00 40.11 2.57
854 871 2.160853 CGAAATGAGAGAGCGCGCA 61.161 57.895 35.10 12.17 0.00 6.09
890 907 2.114670 CGGTTCGCCATCCATTGCT 61.115 57.895 0.00 0.00 37.00 3.91
1014 1034 2.968574 TGAGATCATGGAGGTAAGGCTC 59.031 50.000 0.00 0.00 0.00 4.70
1022 1042 1.200484 GGAGGTAAGGCTCGATCGATC 59.800 57.143 19.78 14.83 0.00 3.69
1033 1053 1.006102 GATCGATCGCCGGATGGTT 60.006 57.895 11.09 0.00 39.14 3.67
1052 1072 0.756294 TGATTGGTCGGTGTGTGAGT 59.244 50.000 0.00 0.00 0.00 3.41
1259 1291 3.573772 CTCGCACGAGCTCAACCCA 62.574 63.158 15.40 0.00 39.10 4.51
1681 1713 4.803426 GCTCAGCGGCTACTGCGT 62.803 66.667 0.26 0.00 40.82 5.24
1682 1714 2.125912 CTCAGCGGCTACTGCGTT 60.126 61.111 0.26 0.00 40.82 4.84
1685 1717 1.811266 CAGCGGCTACTGCGTTGAT 60.811 57.895 0.26 0.00 40.82 2.57
1688 1720 1.811266 CGGCTACTGCGTTGATGCT 60.811 57.895 0.00 0.00 40.82 3.79
1766 1798 1.150536 ATTGCAGTCCACCAACGGT 59.849 52.632 0.00 0.00 35.62 4.83
1896 1928 0.178068 GCGGCACTTCTTGGGAGATA 59.822 55.000 0.00 0.00 0.00 1.98
2040 2072 0.834612 AACCAGGAACAAGGTCGACA 59.165 50.000 18.91 0.00 38.03 4.35
2111 2143 1.219393 GGCTTCTCTTGGGGACTCG 59.781 63.158 0.00 0.00 0.00 4.18
2192 2224 3.870538 AAGCCAAGGATGATATGCAGA 57.129 42.857 0.00 0.00 0.00 4.26
2277 2309 2.398554 CGGTGTGATTCCAAGGGCG 61.399 63.158 0.00 0.00 0.00 6.13
2641 2673 7.174253 GTCACCATTATTGACACCAAGAACTAA 59.826 37.037 0.00 0.00 42.58 2.24
2840 2872 5.288952 GCAGGTCGAAAGTTTACTGACTATC 59.711 44.000 12.28 1.04 0.00 2.08
2988 3020 5.975988 TGGAAGAAGGATAGCCAAGTTAT 57.024 39.130 0.00 0.00 36.29 1.89
3088 3391 3.243873 TGCACTTCTGTGACTCTAGTTGG 60.244 47.826 0.00 0.00 46.55 3.77
3312 3617 8.281212 ACTTCGAAATTATAAAGCCAATCAGT 57.719 30.769 0.00 0.00 0.00 3.41
3399 3704 0.250234 TAATGAGCAGAACGCCAGCT 59.750 50.000 0.00 0.00 44.04 4.24
3427 3732 5.841957 ATGCTAATTCCTTCACAATGTCC 57.158 39.130 0.00 0.00 0.00 4.02
3528 3834 6.645790 ATTCCAAGCTCCTTATAGCATTTG 57.354 37.500 0.00 0.00 45.30 2.32
3862 4169 3.005050 AGTTGAATGTTCAGCATGGTGTG 59.995 43.478 23.35 0.00 40.36 3.82
4007 4314 2.224769 TGAGAGGCTTAGGTTGTTTGGG 60.225 50.000 0.00 0.00 0.00 4.12
4636 4943 6.524734 TGGTATGTATGCTTCTTATGTGGAG 58.475 40.000 0.00 0.00 0.00 3.86
4659 4967 7.277760 GGAGCATGTTTTGACTTAAAAGTGTTT 59.722 33.333 0.00 0.00 39.88 2.83
4923 5231 6.919662 AGCAATGTTATTGTTCAGAACAGTTG 59.080 34.615 15.81 14.36 39.95 3.16
5003 5311 8.673275 GTCGAAATGATTTGCTATTTATTCACG 58.327 33.333 0.00 0.00 0.00 4.35
5018 5326 2.985282 ACGCCTGTGCACCAATGG 60.985 61.111 15.69 12.16 37.32 3.16
5377 5685 4.935352 TTGTTTTCATGCTAGGTTGCTT 57.065 36.364 0.00 0.00 0.00 3.91
5410 5718 2.934553 GGTACAAAGATTAGGTGCGACC 59.065 50.000 0.00 0.00 38.99 4.79
5619 5927 4.670221 GCAACTAAAAGACTGCCTCGAATG 60.670 45.833 0.00 0.00 0.00 2.67
5703 6011 8.807948 AATATGATACAAGTTACTTTGCCTGT 57.192 30.769 0.00 0.00 0.00 4.00
5742 6050 1.923204 GCTGATGAGCAAGTCACTACG 59.077 52.381 0.00 0.00 45.46 3.51
5760 6068 1.837090 GGCCCCCAATGAGTACGAT 59.163 57.895 0.00 0.00 0.00 3.73
5838 6146 9.601971 GACTACGAAGAAGATGTATAACAGATC 57.398 37.037 0.00 0.00 0.00 2.75
5865 6173 5.013391 TCCCTCTTAACTTCCCGTTGTAATT 59.987 40.000 0.00 0.00 37.05 1.40
5878 6186 7.270047 TCCCGTTGTAATTAGAGTAATCCAAG 58.730 38.462 0.00 0.00 0.00 3.61
5880 6188 7.224167 CCCGTTGTAATTAGAGTAATCCAAGTC 59.776 40.741 0.00 0.00 0.00 3.01
6017 6326 5.009610 GCAACTTCTCATTCAAGGTAACCAA 59.990 40.000 0.00 0.00 37.17 3.67
6078 6387 4.262617 GGTGAGTTAACATCTTTCCCTCC 58.737 47.826 8.61 0.00 0.00 4.30
6115 6424 0.964700 TCCCAGCTAGCATCGATGAG 59.035 55.000 29.20 18.42 0.00 2.90
6197 6506 0.905357 AGGACAGACCAATTCCCTCG 59.095 55.000 0.00 0.00 42.04 4.63
6246 6555 5.674052 AGCTGACATCATCTTACTCTTGT 57.326 39.130 0.00 0.00 0.00 3.16
6278 6587 6.512741 CGGTGTACAAAAAGTAAGACTGCATT 60.513 38.462 0.00 0.00 33.72 3.56
6333 6645 0.608856 TTGTCATGCAGGCAACGGAT 60.609 50.000 0.00 0.00 36.80 4.18
6374 6687 4.095632 GCTAGCAGCGAGTGATATGATAGA 59.904 45.833 10.63 0.00 34.41 1.98
6427 6740 3.181448 TGCGGGTTTCCTCTAGAACTTTT 60.181 43.478 0.00 0.00 32.95 2.27
6446 6759 1.332195 TATGAGGATCGACCAGCCAG 58.668 55.000 6.78 0.00 42.04 4.85
6461 6774 1.873591 AGCCAGACAAGCACTTTAACG 59.126 47.619 0.00 0.00 0.00 3.18
6476 6789 1.997669 TAACGTGCATATGTGTCGCA 58.002 45.000 4.29 0.00 0.00 5.10
6524 6838 3.388024 AGTTAGTCAGTGTTTGCTCAGGA 59.612 43.478 0.00 0.00 0.00 3.86
6587 6901 0.445436 CATCTCTTGCCGTTGCTGAC 59.555 55.000 0.00 0.00 38.71 3.51
6805 7122 0.682209 GGTGATGCCTTGGATGCACT 60.682 55.000 0.00 0.00 42.38 4.40
6850 7167 0.536460 GTCGTGGGGTCAACATTGGT 60.536 55.000 0.00 0.00 0.00 3.67
6940 7259 4.261801 CCAAATCCACTTATTGTCGGACT 58.738 43.478 9.88 0.00 31.90 3.85
6966 7286 8.918202 TGTCTTCTATTTTAATGTTGACAGGT 57.082 30.769 0.00 0.00 0.00 4.00
6994 7314 4.585879 GGTCATAGTTTTGGCACCTTAGA 58.414 43.478 0.00 0.00 0.00 2.10
6995 7315 5.193679 GGTCATAGTTTTGGCACCTTAGAT 58.806 41.667 0.00 0.00 0.00 1.98
6998 7318 6.374333 GTCATAGTTTTGGCACCTTAGATCAA 59.626 38.462 0.00 0.00 0.00 2.57
7003 7323 2.265367 TGGCACCTTAGATCAACTCCA 58.735 47.619 0.00 0.00 0.00 3.86
7004 7324 2.642311 TGGCACCTTAGATCAACTCCAA 59.358 45.455 0.00 0.00 0.00 3.53
7005 7325 3.073798 TGGCACCTTAGATCAACTCCAAA 59.926 43.478 0.00 0.00 0.00 3.28
7006 7326 3.691609 GGCACCTTAGATCAACTCCAAAG 59.308 47.826 0.00 0.00 0.00 2.77
7007 7327 3.691609 GCACCTTAGATCAACTCCAAAGG 59.308 47.826 0.00 0.00 40.77 3.11
7008 7328 3.691609 CACCTTAGATCAACTCCAAAGGC 59.308 47.826 0.00 0.00 39.52 4.35
7009 7329 3.282885 CCTTAGATCAACTCCAAAGGCC 58.717 50.000 0.00 0.00 33.24 5.19
7010 7330 3.054065 CCTTAGATCAACTCCAAAGGCCT 60.054 47.826 0.00 0.00 33.24 5.19
7011 7331 4.164221 CCTTAGATCAACTCCAAAGGCCTA 59.836 45.833 5.16 0.00 33.24 3.93
7012 7332 3.636153 AGATCAACTCCAAAGGCCTAC 57.364 47.619 5.16 0.00 0.00 3.18
7013 7333 2.239907 AGATCAACTCCAAAGGCCTACC 59.760 50.000 5.16 0.00 0.00 3.18
7014 7334 0.696501 TCAACTCCAAAGGCCTACCC 59.303 55.000 5.16 0.00 36.11 3.69
7015 7335 0.404040 CAACTCCAAAGGCCTACCCA 59.596 55.000 5.16 0.00 36.11 4.51
7016 7336 1.154430 AACTCCAAAGGCCTACCCAA 58.846 50.000 5.16 0.00 36.11 4.12
7017 7337 1.154430 ACTCCAAAGGCCTACCCAAA 58.846 50.000 5.16 0.00 36.11 3.28
7018 7338 1.203013 ACTCCAAAGGCCTACCCAAAC 60.203 52.381 5.16 0.00 36.11 2.93
7019 7339 0.250989 TCCAAAGGCCTACCCAAACG 60.251 55.000 5.16 0.00 36.11 3.60
7020 7340 1.248101 CCAAAGGCCTACCCAAACGG 61.248 60.000 5.16 0.00 36.11 4.44
7021 7341 0.250989 CAAAGGCCTACCCAAACGGA 60.251 55.000 5.16 0.00 36.11 4.69
7022 7342 0.251033 AAAGGCCTACCCAAACGGAC 60.251 55.000 5.16 0.00 36.11 4.79
7023 7343 2.435410 GGCCTACCCAAACGGACG 60.435 66.667 0.00 0.00 34.64 4.79
7024 7344 2.658422 GCCTACCCAAACGGACGA 59.342 61.111 0.00 0.00 34.64 4.20
7025 7345 1.739196 GCCTACCCAAACGGACGAC 60.739 63.158 0.00 0.00 34.64 4.34
7035 7355 3.856508 CGGACGACGCATTTGTCT 58.143 55.556 0.00 0.00 38.57 3.41
7036 7356 1.416049 CGGACGACGCATTTGTCTG 59.584 57.895 0.00 0.94 38.57 3.51
7037 7357 1.132640 GGACGACGCATTTGTCTGC 59.867 57.895 0.00 0.00 38.57 4.26
7038 7358 1.132640 GACGACGCATTTGTCTGCC 59.867 57.895 0.00 0.00 39.00 4.85
7039 7359 1.291877 GACGACGCATTTGTCTGCCT 61.292 55.000 0.00 0.00 39.00 4.75
7040 7360 0.884704 ACGACGCATTTGTCTGCCTT 60.885 50.000 0.00 0.00 39.00 4.35
7041 7361 0.238289 CGACGCATTTGTCTGCCTTT 59.762 50.000 0.00 0.00 39.00 3.11
7042 7362 1.334960 CGACGCATTTGTCTGCCTTTT 60.335 47.619 0.00 0.00 39.00 2.27
7043 7363 2.053627 GACGCATTTGTCTGCCTTTTG 58.946 47.619 0.00 0.00 39.00 2.44
7044 7364 1.408702 ACGCATTTGTCTGCCTTTTGT 59.591 42.857 0.00 0.00 39.00 2.83
7045 7365 2.159114 ACGCATTTGTCTGCCTTTTGTT 60.159 40.909 0.00 0.00 39.00 2.83
7046 7366 2.865551 CGCATTTGTCTGCCTTTTGTTT 59.134 40.909 0.00 0.00 39.00 2.83
7047 7367 3.302610 CGCATTTGTCTGCCTTTTGTTTG 60.303 43.478 0.00 0.00 39.00 2.93
7048 7368 3.622612 GCATTTGTCTGCCTTTTGTTTGT 59.377 39.130 0.00 0.00 36.10 2.83
7049 7369 4.094739 GCATTTGTCTGCCTTTTGTTTGTT 59.905 37.500 0.00 0.00 36.10 2.83
7050 7370 5.391843 GCATTTGTCTGCCTTTTGTTTGTTT 60.392 36.000 0.00 0.00 36.10 2.83
7051 7371 5.604010 TTTGTCTGCCTTTTGTTTGTTTG 57.396 34.783 0.00 0.00 0.00 2.93
7052 7372 3.594134 TGTCTGCCTTTTGTTTGTTTGG 58.406 40.909 0.00 0.00 0.00 3.28
7053 7373 2.935849 GTCTGCCTTTTGTTTGTTTGGG 59.064 45.455 0.00 0.00 0.00 4.12
7054 7374 2.569404 TCTGCCTTTTGTTTGTTTGGGT 59.431 40.909 0.00 0.00 0.00 4.51
7055 7375 2.935849 CTGCCTTTTGTTTGTTTGGGTC 59.064 45.455 0.00 0.00 0.00 4.46
7056 7376 1.930503 GCCTTTTGTTTGTTTGGGTCG 59.069 47.619 0.00 0.00 0.00 4.79
7057 7377 2.545731 CCTTTTGTTTGTTTGGGTCGG 58.454 47.619 0.00 0.00 0.00 4.79
7058 7378 1.930503 CTTTTGTTTGTTTGGGTCGGC 59.069 47.619 0.00 0.00 0.00 5.54
7059 7379 0.175989 TTTGTTTGTTTGGGTCGGCC 59.824 50.000 0.00 0.00 0.00 6.13
7060 7380 2.005960 TTGTTTGTTTGGGTCGGCCG 62.006 55.000 22.12 22.12 34.97 6.13
7061 7381 3.597728 TTTGTTTGGGTCGGCCGC 61.598 61.111 23.51 16.04 34.97 6.53
7094 7414 4.895854 CCAATTTTGGCTCGGCAG 57.104 55.556 0.00 0.00 42.21 4.85
7095 7415 1.966762 CCAATTTTGGCTCGGCAGT 59.033 52.632 0.00 0.00 42.21 4.40
7096 7416 0.388907 CCAATTTTGGCTCGGCAGTG 60.389 55.000 0.00 0.00 42.21 3.66
7097 7417 1.010419 CAATTTTGGCTCGGCAGTGC 61.010 55.000 6.55 6.55 36.24 4.40
7098 7418 2.476534 AATTTTGGCTCGGCAGTGCG 62.477 55.000 9.45 4.79 37.71 5.34
7118 7438 3.732892 CAACGCGCCGACCCATTT 61.733 61.111 5.73 0.00 0.00 2.32
7119 7439 3.428282 AACGCGCCGACCCATTTC 61.428 61.111 5.73 0.00 0.00 2.17
7120 7440 4.690719 ACGCGCCGACCCATTTCA 62.691 61.111 5.73 0.00 0.00 2.69
7121 7441 3.202001 CGCGCCGACCCATTTCAT 61.202 61.111 0.00 0.00 0.00 2.57
7122 7442 2.408835 GCGCCGACCCATTTCATG 59.591 61.111 0.00 0.00 0.00 3.07
7123 7443 2.406616 GCGCCGACCCATTTCATGT 61.407 57.895 0.00 0.00 0.00 3.21
7124 7444 1.721487 CGCCGACCCATTTCATGTC 59.279 57.895 0.00 0.00 0.00 3.06
7125 7445 1.714899 CGCCGACCCATTTCATGTCC 61.715 60.000 0.00 0.00 0.00 4.02
7126 7446 1.714899 GCCGACCCATTTCATGTCCG 61.715 60.000 0.00 0.00 0.00 4.79
7127 7447 1.714899 CCGACCCATTTCATGTCCGC 61.715 60.000 0.00 0.00 0.00 5.54
7128 7448 1.024046 CGACCCATTTCATGTCCGCA 61.024 55.000 0.00 0.00 0.00 5.69
7129 7449 1.392589 GACCCATTTCATGTCCGCAT 58.607 50.000 0.00 0.00 35.32 4.73
7130 7450 1.750778 GACCCATTTCATGTCCGCATT 59.249 47.619 0.00 0.00 31.99 3.56
7131 7451 1.750778 ACCCATTTCATGTCCGCATTC 59.249 47.619 0.00 0.00 31.99 2.67
7132 7452 1.750206 CCCATTTCATGTCCGCATTCA 59.250 47.619 0.00 0.00 31.99 2.57
7133 7453 2.166050 CCCATTTCATGTCCGCATTCAA 59.834 45.455 0.00 0.00 31.99 2.69
7134 7454 3.181397 CCATTTCATGTCCGCATTCAAC 58.819 45.455 0.00 0.00 31.99 3.18
7135 7455 3.119388 CCATTTCATGTCCGCATTCAACT 60.119 43.478 0.00 0.00 31.99 3.16
7136 7456 4.487948 CATTTCATGTCCGCATTCAACTT 58.512 39.130 0.00 0.00 31.99 2.66
7137 7457 4.582701 TTTCATGTCCGCATTCAACTTT 57.417 36.364 0.00 0.00 31.99 2.66
7138 7458 4.582701 TTCATGTCCGCATTCAACTTTT 57.417 36.364 0.00 0.00 31.99 2.27
7139 7459 5.697473 TTCATGTCCGCATTCAACTTTTA 57.303 34.783 0.00 0.00 31.99 1.52
7140 7460 5.697473 TCATGTCCGCATTCAACTTTTAA 57.303 34.783 0.00 0.00 31.99 1.52
7141 7461 6.078202 TCATGTCCGCATTCAACTTTTAAA 57.922 33.333 0.00 0.00 31.99 1.52
7142 7462 6.686630 TCATGTCCGCATTCAACTTTTAAAT 58.313 32.000 0.00 0.00 31.99 1.40
7143 7463 7.821652 TCATGTCCGCATTCAACTTTTAAATA 58.178 30.769 0.00 0.00 31.99 1.40
7144 7464 8.300286 TCATGTCCGCATTCAACTTTTAAATAA 58.700 29.630 0.00 0.00 31.99 1.40
7145 7465 8.920665 CATGTCCGCATTCAACTTTTAAATAAA 58.079 29.630 0.00 0.00 31.99 1.40
7146 7466 8.873215 TGTCCGCATTCAACTTTTAAATAAAA 57.127 26.923 0.00 0.00 34.35 1.52
7147 7467 9.314321 TGTCCGCATTCAACTTTTAAATAAAAA 57.686 25.926 0.55 0.00 35.04 1.94
7163 7483 2.927553 AAAAATGCTCGTGGCTGATC 57.072 45.000 5.00 0.00 42.39 2.92
7164 7484 1.825090 AAAATGCTCGTGGCTGATCA 58.175 45.000 0.00 0.00 42.39 2.92
7165 7485 2.048444 AAATGCTCGTGGCTGATCAT 57.952 45.000 0.00 0.00 42.39 2.45
7166 7486 1.306148 AATGCTCGTGGCTGATCATG 58.694 50.000 0.00 0.00 42.39 3.07
7167 7487 1.164662 ATGCTCGTGGCTGATCATGC 61.165 55.000 0.00 2.02 42.39 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
368 372 2.186125 GCTGGGGCGTAGGTGTAC 59.814 66.667 0.00 0.00 0.00 2.90
391 403 0.665369 ATCGGTTCACGTCCGTTGAC 60.665 55.000 13.17 0.00 46.86 3.18
394 406 1.443194 CGATCGGTTCACGTCCGTT 60.443 57.895 7.38 5.83 46.86 4.44
430 442 2.369600 CGCGTATGTACACTTCTACCG 58.630 52.381 0.00 0.00 0.00 4.02
431 443 2.114825 GCGCGTATGTACACTTCTACC 58.885 52.381 8.43 0.00 0.00 3.18
435 447 1.268946 GCGCGCGTATGTACACTTC 59.731 57.895 32.35 5.70 0.00 3.01
437 449 2.947621 CGCGCGCGTATGTACACT 60.948 61.111 42.49 0.00 34.35 3.55
519 531 0.863119 GCGAACATTCAAGGCGATGC 60.863 55.000 0.00 0.00 0.00 3.91
527 539 1.866237 GCTCCGTGCGAACATTCAA 59.134 52.632 0.00 0.00 0.00 2.69
636 653 3.459063 AACTACCGCCGCCTCCTC 61.459 66.667 0.00 0.00 0.00 3.71
637 654 3.771160 CAACTACCGCCGCCTCCT 61.771 66.667 0.00 0.00 0.00 3.69
779 796 1.265905 GAATTTATAAGTGCCGCGGGG 59.734 52.381 29.38 15.40 0.00 5.73
830 847 1.535015 CGCTCTCTCATTTCGGAGGAC 60.535 57.143 0.00 0.00 35.58 3.85
834 851 1.226688 CGCGCTCTCTCATTTCGGA 60.227 57.895 5.56 0.00 0.00 4.55
871 888 2.112198 GCAATGGATGGCGAACCGA 61.112 57.895 0.00 0.00 39.70 4.69
872 889 2.114670 AGCAATGGATGGCGAACCG 61.115 57.895 0.00 0.00 39.70 4.44
890 907 2.571212 CCCTCGCATTAAACTATGGCA 58.429 47.619 0.00 0.00 0.00 4.92
931 948 3.434454 GAGGATCCTCCGTCGTCC 58.566 66.667 28.84 3.71 42.75 4.79
1022 1042 1.714899 GACCAATCAACCATCCGGCG 61.715 60.000 0.00 0.00 34.57 6.46
1025 1045 0.392461 ACCGACCAATCAACCATCCG 60.392 55.000 0.00 0.00 0.00 4.18
1028 1048 1.202879 ACACACCGACCAATCAACCAT 60.203 47.619 0.00 0.00 0.00 3.55
1030 1050 0.591170 CACACACCGACCAATCAACC 59.409 55.000 0.00 0.00 0.00 3.77
1033 1053 0.756294 ACTCACACACCGACCAATCA 59.244 50.000 0.00 0.00 0.00 2.57
1052 1072 2.190170 AAACACAACGCCGGCATCA 61.190 52.632 28.98 0.00 0.00 3.07
1091 1111 4.680237 TCCTTCTGCACGCACCGG 62.680 66.667 0.00 0.00 0.00 5.28
1511 1543 0.969894 ACTTGACCCAGAACTCCTCG 59.030 55.000 0.00 0.00 0.00 4.63
1541 1573 4.671590 TCGTCGAGGGCCTGGACA 62.672 66.667 37.11 25.40 38.76 4.02
1688 1720 4.560743 TGCTGGTGCTTGCCGTCA 62.561 61.111 0.00 0.00 40.48 4.35
1766 1798 2.439701 CCTAGGTCCGTCGAGCCA 60.440 66.667 0.00 0.00 37.19 4.75
1805 1837 0.537653 GCCTCTCCTTAAGCTCGGTT 59.462 55.000 0.00 0.00 0.00 4.44
2040 2072 5.908562 ATCCTCTCAACAATCTCATCCAT 57.091 39.130 0.00 0.00 0.00 3.41
2111 2143 3.308323 GTGAAATCTCGATCTTGACTGCC 59.692 47.826 0.00 0.00 0.00 4.85
2192 2224 2.874701 CGGGATCTCAAAATCGCAGATT 59.125 45.455 0.00 0.00 45.12 2.40
2277 2309 0.038159 AGCCGCTTGTCAGTACTCAC 60.038 55.000 0.00 0.00 0.00 3.51
2444 2476 5.467735 CACTGTCAACAGATGAGACAAATCA 59.532 40.000 16.71 0.00 46.59 2.57
2609 2641 3.435327 GTGTCAATAATGGTGACTGCGAA 59.565 43.478 6.17 0.00 44.70 4.70
2641 2673 1.344438 TCAGCTGTGATTCTTCGTGGT 59.656 47.619 14.67 0.00 0.00 4.16
3088 3391 8.196378 AGAGTCAGGGTAATATTTCAGGTATC 57.804 38.462 0.00 0.00 0.00 2.24
3312 3617 3.361158 CGCCCAAATGCACCACGA 61.361 61.111 0.00 0.00 0.00 4.35
3399 3704 7.560991 ACATTGTGAAGGAATTAGCATATGGAA 59.439 33.333 4.56 0.00 0.00 3.53
3427 3732 8.948631 TTCAATGTTCAGTATAAAGGAGCTAG 57.051 34.615 0.00 0.00 0.00 3.42
3458 3763 2.364970 TGAACAAACCAAAGCCCAGATG 59.635 45.455 0.00 0.00 0.00 2.90
3557 3863 9.403110 GCAAGTCATCCATTTAATAACATCATC 57.597 33.333 0.00 0.00 0.00 2.92
3564 3870 8.806429 TCTTGAGCAAGTCATCCATTTAATAA 57.194 30.769 9.79 0.00 39.38 1.40
3862 4169 6.231211 TGGAAGTTAAGTGAAGTCCAGAATC 58.769 40.000 0.00 0.00 31.53 2.52
4007 4314 9.539825 CTATATATGTCCTTGCCATATCTTCAC 57.460 37.037 0.00 0.00 36.93 3.18
4368 4675 5.353394 AAATCCAAATCATTCTGCAGCAT 57.647 34.783 9.47 0.00 0.00 3.79
4511 4818 0.029167 TGTGCACGTTGTTCTGCATG 59.971 50.000 13.13 0.00 44.93 4.06
5003 5311 0.243636 GTAACCATTGGTGCACAGGC 59.756 55.000 20.43 1.36 35.34 4.85
5066 5374 4.977963 GCAACCAATATTGTTGATGATCGG 59.022 41.667 23.39 7.09 31.83 4.18
5377 5685 5.687166 ATCTTTGTACCGGGTTCTCAATA 57.313 39.130 4.31 2.05 0.00 1.90
5410 5718 0.681564 AGAGTACCTCTCCAGCACCG 60.682 60.000 0.00 0.00 43.71 4.94
5467 5775 6.525629 AGCATATTTCAGTTAGCGAGGTTAT 58.474 36.000 0.00 0.00 0.00 1.89
5473 5781 8.972262 CTCTAATAGCATATTTCAGTTAGCGA 57.028 34.615 0.00 0.00 0.00 4.93
5658 5966 3.801114 TCATCGTCTGTACAGGGAATG 57.199 47.619 22.48 20.00 0.00 2.67
5733 6041 1.615424 ATTGGGGGCCGTAGTGACT 60.615 57.895 0.00 0.00 0.00 3.41
5742 6050 0.535102 CATCGTACTCATTGGGGGCC 60.535 60.000 0.00 0.00 0.00 5.80
5760 6068 4.652822 TGCTACTAGTCTCACTTCTGTCA 58.347 43.478 0.00 0.00 0.00 3.58
5838 6146 3.629142 ACGGGAAGTTAAGAGGGATTG 57.371 47.619 0.00 0.00 0.00 2.67
5878 6186 5.874810 TGTGAGGTGACTGCTATAAAATGAC 59.125 40.000 0.00 0.00 44.43 3.06
5880 6188 6.932356 ATGTGAGGTGACTGCTATAAAATG 57.068 37.500 0.00 0.00 44.43 2.32
5887 6196 4.350368 TGAAAATGTGAGGTGACTGCTA 57.650 40.909 0.00 0.00 44.43 3.49
5922 6231 4.581824 CCACATTCATCTCCCTGTTAATGG 59.418 45.833 0.00 0.00 0.00 3.16
6017 6326 0.907704 TGTGGCAAGTCGGATAGGGT 60.908 55.000 0.00 0.00 0.00 4.34
6026 6335 5.382618 AGATTCAAAGATTGTGGCAAGTC 57.617 39.130 0.00 0.00 0.00 3.01
6027 6336 5.069516 ACAAGATTCAAAGATTGTGGCAAGT 59.930 36.000 0.00 0.00 34.71 3.16
6078 6387 3.244146 TGGGAAATGTTCTGGTTGCAATG 60.244 43.478 0.59 0.00 0.00 2.82
6115 6424 7.505646 GTTATGCTTCGTCATCAGATCATAAC 58.494 38.462 10.72 10.72 37.32 1.89
6197 6506 0.737219 GAGATGCTGGTCATGTTGCC 59.263 55.000 0.00 0.00 35.05 4.52
6246 6555 6.766944 TCTTACTTTTTGTACACCGGATCAAA 59.233 34.615 9.46 10.90 0.00 2.69
6278 6587 4.216257 GCAGTAGAATCAGGTTTTTGCTCA 59.784 41.667 0.00 0.00 0.00 4.26
6284 6596 4.082125 CAAGGGCAGTAGAATCAGGTTTT 58.918 43.478 0.00 0.00 0.00 2.43
6352 6664 5.809719 TCTATCATATCACTCGCTGCTAG 57.190 43.478 0.00 0.00 0.00 3.42
6374 6687 3.118542 GTCTTCGACCGTTACACACTTT 58.881 45.455 0.00 0.00 0.00 2.66
6427 6740 1.133482 TCTGGCTGGTCGATCCTCATA 60.133 52.381 0.00 0.00 37.07 2.15
6461 6774 2.270923 TCTTCTGCGACACATATGCAC 58.729 47.619 1.58 0.00 34.42 4.57
6470 6783 1.289066 CGTCCCTTCTTCTGCGACA 59.711 57.895 0.00 0.00 0.00 4.35
6472 6785 2.970639 CCGTCCCTTCTTCTGCGA 59.029 61.111 0.00 0.00 0.00 5.10
6476 6789 3.391382 CCCGCCGTCCCTTCTTCT 61.391 66.667 0.00 0.00 0.00 2.85
6524 6838 3.631250 ACCTATGGAAAATGGCACGAAT 58.369 40.909 0.00 0.00 0.00 3.34
6607 6921 8.475639 GGTTCCTGTCTAGTATCTCAAATGTTA 58.524 37.037 0.00 0.00 0.00 2.41
6805 7122 2.620585 TGAAAACATGCGACCATTGTCA 59.379 40.909 0.00 0.00 41.85 3.58
6850 7167 3.494254 AGCCCCAAACCGACCACA 61.494 61.111 0.00 0.00 0.00 4.17
6940 7259 9.349713 ACCTGTCAACATTAAAATAGAAGACAA 57.650 29.630 0.00 0.00 33.67 3.18
6966 7286 2.147958 GCCAAAACTATGACCGTCACA 58.852 47.619 2.57 0.00 0.00 3.58
6994 7314 1.285078 GGGTAGGCCTTTGGAGTTGAT 59.715 52.381 12.58 0.00 34.45 2.57
6995 7315 0.696501 GGGTAGGCCTTTGGAGTTGA 59.303 55.000 12.58 0.00 34.45 3.18
6998 7318 1.154430 TTTGGGTAGGCCTTTGGAGT 58.846 50.000 12.58 0.00 34.45 3.85
7003 7323 0.251033 GTCCGTTTGGGTAGGCCTTT 60.251 55.000 12.58 0.00 37.00 3.11
7004 7324 1.377612 GTCCGTTTGGGTAGGCCTT 59.622 57.895 12.58 0.00 37.00 4.35
7005 7325 2.951101 CGTCCGTTTGGGTAGGCCT 61.951 63.158 11.78 11.78 37.00 5.19
7006 7326 2.435410 CGTCCGTTTGGGTAGGCC 60.435 66.667 0.00 0.00 37.00 5.19
7007 7327 1.739196 GTCGTCCGTTTGGGTAGGC 60.739 63.158 0.00 0.00 37.00 3.93
7008 7328 1.444895 CGTCGTCCGTTTGGGTAGG 60.445 63.158 0.00 0.00 37.00 3.18
7009 7329 2.090524 GCGTCGTCCGTTTGGGTAG 61.091 63.158 0.00 0.00 39.32 3.18
7010 7330 2.049248 GCGTCGTCCGTTTGGGTA 60.049 61.111 0.00 0.00 39.32 3.69
7011 7331 2.999739 AATGCGTCGTCCGTTTGGGT 63.000 55.000 0.00 0.00 39.32 4.51
7012 7332 1.847890 AAATGCGTCGTCCGTTTGGG 61.848 55.000 0.00 0.00 39.32 4.12
7013 7333 0.724453 CAAATGCGTCGTCCGTTTGG 60.724 55.000 8.74 0.00 36.20 3.28
7014 7334 0.041663 ACAAATGCGTCGTCCGTTTG 60.042 50.000 12.96 12.96 42.19 2.93
7015 7335 0.233848 GACAAATGCGTCGTCCGTTT 59.766 50.000 0.00 0.00 39.32 3.60
7016 7336 0.599204 AGACAAATGCGTCGTCCGTT 60.599 50.000 5.13 0.00 40.98 4.44
7017 7337 1.006571 AGACAAATGCGTCGTCCGT 60.007 52.632 5.13 0.00 40.98 4.69
7018 7338 1.416049 CAGACAAATGCGTCGTCCG 59.584 57.895 5.13 0.00 40.98 4.79
7019 7339 1.132640 GCAGACAAATGCGTCGTCC 59.867 57.895 5.13 0.00 40.98 4.79
7020 7340 4.725758 GCAGACAAATGCGTCGTC 57.274 55.556 0.00 1.12 40.98 4.20
7026 7346 3.622612 ACAAACAAAAGGCAGACAAATGC 59.377 39.130 0.00 0.00 45.74 3.56
7027 7347 5.799681 AACAAACAAAAGGCAGACAAATG 57.200 34.783 0.00 0.00 0.00 2.32
7028 7348 5.123661 CCAAACAAACAAAAGGCAGACAAAT 59.876 36.000 0.00 0.00 0.00 2.32
7029 7349 4.453819 CCAAACAAACAAAAGGCAGACAAA 59.546 37.500 0.00 0.00 0.00 2.83
7030 7350 3.999663 CCAAACAAACAAAAGGCAGACAA 59.000 39.130 0.00 0.00 0.00 3.18
7031 7351 3.594134 CCAAACAAACAAAAGGCAGACA 58.406 40.909 0.00 0.00 0.00 3.41
7032 7352 2.935849 CCCAAACAAACAAAAGGCAGAC 59.064 45.455 0.00 0.00 0.00 3.51
7033 7353 2.569404 ACCCAAACAAACAAAAGGCAGA 59.431 40.909 0.00 0.00 0.00 4.26
7034 7354 2.935849 GACCCAAACAAACAAAAGGCAG 59.064 45.455 0.00 0.00 0.00 4.85
7035 7355 2.675317 CGACCCAAACAAACAAAAGGCA 60.675 45.455 0.00 0.00 0.00 4.75
7036 7356 1.930503 CGACCCAAACAAACAAAAGGC 59.069 47.619 0.00 0.00 0.00 4.35
7037 7357 2.545731 CCGACCCAAACAAACAAAAGG 58.454 47.619 0.00 0.00 0.00 3.11
7038 7358 1.930503 GCCGACCCAAACAAACAAAAG 59.069 47.619 0.00 0.00 0.00 2.27
7039 7359 1.405661 GGCCGACCCAAACAAACAAAA 60.406 47.619 0.00 0.00 0.00 2.44
7040 7360 0.175989 GGCCGACCCAAACAAACAAA 59.824 50.000 0.00 0.00 0.00 2.83
7041 7361 1.817209 GGCCGACCCAAACAAACAA 59.183 52.632 0.00 0.00 0.00 2.83
7042 7362 2.482333 CGGCCGACCCAAACAAACA 61.482 57.895 24.07 0.00 0.00 2.83
7043 7363 2.333581 CGGCCGACCCAAACAAAC 59.666 61.111 24.07 0.00 0.00 2.93
7044 7364 3.597728 GCGGCCGACCCAAACAAA 61.598 61.111 33.48 0.00 0.00 2.83
7069 7389 4.576993 CCAAAATTGGGCAGACGC 57.423 55.556 4.18 0.00 44.70 5.19
7078 7398 1.010419 GCACTGCCGAGCCAAAATTG 61.010 55.000 0.00 0.00 0.00 2.32
7079 7399 1.290009 GCACTGCCGAGCCAAAATT 59.710 52.632 0.00 0.00 0.00 1.82
7080 7400 2.964978 GCACTGCCGAGCCAAAAT 59.035 55.556 0.00 0.00 0.00 1.82
7081 7401 3.659092 CGCACTGCCGAGCCAAAA 61.659 61.111 0.00 0.00 0.00 2.44
7101 7421 3.661025 GAAATGGGTCGGCGCGTTG 62.661 63.158 12.62 0.00 36.96 4.10
7102 7422 3.428282 GAAATGGGTCGGCGCGTT 61.428 61.111 8.43 5.61 38.23 4.84
7103 7423 3.969250 ATGAAATGGGTCGGCGCGT 62.969 57.895 8.43 0.00 0.00 6.01
7104 7424 3.202001 ATGAAATGGGTCGGCGCG 61.202 61.111 0.00 0.00 0.00 6.86
7105 7425 2.408835 CATGAAATGGGTCGGCGC 59.591 61.111 0.00 0.00 41.79 6.53
7115 7435 4.789012 AAGTTGAATGCGGACATGAAAT 57.211 36.364 0.00 0.00 36.36 2.17
7116 7436 4.582701 AAAGTTGAATGCGGACATGAAA 57.417 36.364 0.00 0.00 36.36 2.69
7117 7437 4.582701 AAAAGTTGAATGCGGACATGAA 57.417 36.364 0.00 0.00 36.36 2.57
7118 7438 5.697473 TTAAAAGTTGAATGCGGACATGA 57.303 34.783 0.00 0.00 36.36 3.07
7119 7439 6.949578 ATTTAAAAGTTGAATGCGGACATG 57.050 33.333 0.00 0.00 36.36 3.21
7120 7440 9.482627 TTTTATTTAAAAGTTGAATGCGGACAT 57.517 25.926 0.00 0.00 32.92 3.06
7121 7441 8.873215 TTTTATTTAAAAGTTGAATGCGGACA 57.127 26.923 0.00 0.00 32.00 4.02
7150 7470 3.020627 GCATGATCAGCCACGAGC 58.979 61.111 0.09 0.00 44.25 5.03


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

AutoCloner maintained by Alex Coulton.