Multiple sequence alignment - TraesCS1D01G436900

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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 TraesCS1D01G436900 chr1D 100.000 6909 0 0 1 6909 484398047 484404955 0.000000e+00 12759
1 TraesCS1D01G436900 chr1D 90.071 141 13 1 1001 1140 476442868 476442728 1.530000e-41 182
2 TraesCS1D01G436900 chr1A 94.904 6535 199 64 303 6773 581580008 581586472 0.000000e+00 10100
3 TraesCS1D01G436900 chr1A 89.899 297 22 6 1 296 581578166 581578455 6.540000e-100 375
4 TraesCS1D01G436900 chr1A 91.633 251 11 4 6669 6909 581758723 581758973 8.580000e-89 339
5 TraesCS1D01G436900 chr1A 90.071 141 13 1 1001 1140 572212805 572212665 1.530000e-41 182
6 TraesCS1D01G436900 chr1A 94.030 67 3 1 6788 6854 581588714 581588779 4.410000e-17 100
7 TraesCS1D01G436900 chr1B 91.885 6174 310 78 302 6371 674627405 674633491 0.000000e+00 8449
8 TraesCS1D01G436900 chr1B 94.853 136 5 2 6522 6656 674656735 674656869 1.950000e-50 211
9 TraesCS1D01G436900 chr1B 87.821 156 15 4 1001 1154 662671414 662671261 5.510000e-41 180
10 TraesCS1D01G436900 chr1B 95.536 112 5 0 6411 6522 674633491 674633602 5.510000e-41 180
11 TraesCS1D01G436900 chr7A 81.778 450 52 23 4243 4680 80851430 80850999 3.970000e-92 350
12 TraesCS1D01G436900 chr3D 86.885 244 32 0 4586 4829 315482782 315483025 2.460000e-69 274
13 TraesCS1D01G436900 chr3B 86.475 244 33 0 4586 4829 404828102 404827859 1.140000e-67 268
14 TraesCS1D01G436900 chr7B 91.964 112 8 1 4320 4431 23439855 23439745 9.280000e-34 156


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 TraesCS1D01G436900 chr1D 484398047 484404955 6908 False 12759.0 12759 100.000000 1 6909 1 chr1D.!!$F1 6908
1 TraesCS1D01G436900 chr1A 581578166 581588779 10613 False 3525.0 10100 92.944333 1 6854 3 chr1A.!!$F2 6853
2 TraesCS1D01G436900 chr1B 674627405 674633602 6197 False 4314.5 8449 93.710500 302 6522 2 chr1B.!!$F2 6220

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
255 257 0.250166 ACCTGACCAAACGCCTACAC 60.250 55.000 0.00 0.0 0.00 2.90 F
269 271 0.949105 CTACACGTGGGTCCACTTGC 60.949 60.000 21.57 0.0 46.03 4.01 F
2083 3737 0.182775 GGTGGCGAGGTATTGGGATT 59.817 55.000 0.00 0.0 0.00 3.01 F
2770 4428 0.322008 CAAGCCACTTCCTCCAGACC 60.322 60.000 0.00 0.0 0.00 3.85 F
3549 5219 1.002773 ACCCGTCCAACTTACCATGTC 59.997 52.381 0.00 0.0 0.00 3.06 F
3802 5473 2.212869 TTGCTGTTACGGGTATAGCG 57.787 50.000 0.00 0.0 37.20 4.26 F
5566 7257 1.451207 CGGCGTCCAATTCCATCCA 60.451 57.895 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 3255 0.739813 GAATCCCTCCGGAACACACG 60.740 60.000 5.23 0.0 43.10 4.49 R
2264 3918 1.004745 CATTAAGCAGGAGGTGGTGGT 59.995 52.381 0.00 0.0 36.83 4.16 R
3875 5554 0.836606 TGTGTGCTTTCTGGTCCTGA 59.163 50.000 0.00 0.0 0.00 3.86 R
4582 6264 1.106285 AGCGCCCTGGAATGAAAATC 58.894 50.000 2.29 0.0 0.00 2.17 R
4966 6648 1.561076 ACCATATGTGAGCTCAAGGCA 59.439 47.619 20.19 13.2 44.79 4.75 R
5648 7339 1.142870 TGTTTGCTGTAGCTTCCCACT 59.857 47.619 5.38 0.0 42.66 4.00 R
6873 10811 0.602638 TACAACGTCAAGGCAGCAGG 60.603 55.000 0.00 0.0 0.00 4.85 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
53 54 7.384439 TGAACAACTATGAAACTTGTGAACA 57.616 32.000 0.00 0.00 0.00 3.18
130 131 9.696917 AACACTCCTTAAATTCATGAATGTTTC 57.303 29.630 21.39 0.00 0.00 2.78
206 208 7.920738 ACCGAGAAGCATTTTAATAGAATGTC 58.079 34.615 5.59 0.00 36.96 3.06
240 242 5.097742 TGTTATGTTAGACCCATGACCTG 57.902 43.478 0.00 0.00 30.19 4.00
243 245 1.906574 TGTTAGACCCATGACCTGACC 59.093 52.381 0.00 0.00 0.00 4.02
244 246 1.906574 GTTAGACCCATGACCTGACCA 59.093 52.381 0.00 0.00 0.00 4.02
245 247 2.304761 GTTAGACCCATGACCTGACCAA 59.695 50.000 0.00 0.00 0.00 3.67
246 248 1.444933 AGACCCATGACCTGACCAAA 58.555 50.000 0.00 0.00 0.00 3.28
247 249 1.073923 AGACCCATGACCTGACCAAAC 59.926 52.381 0.00 0.00 0.00 2.93
248 250 0.250727 ACCCATGACCTGACCAAACG 60.251 55.000 0.00 0.00 0.00 3.60
249 251 1.586154 CCCATGACCTGACCAAACGC 61.586 60.000 0.00 0.00 0.00 4.84
250 252 1.586154 CCATGACCTGACCAAACGCC 61.586 60.000 0.00 0.00 0.00 5.68
255 257 0.250166 ACCTGACCAAACGCCTACAC 60.250 55.000 0.00 0.00 0.00 2.90
269 271 0.949105 CTACACGTGGGTCCACTTGC 60.949 60.000 21.57 0.00 46.03 4.01
315 1862 7.623630 TCATCCATGATCTGTAAAGTTTGAGA 58.376 34.615 0.00 0.11 0.00 3.27
319 1866 7.550551 TCCATGATCTGTAAAGTTTGAGATGAC 59.449 37.037 13.80 4.81 0.00 3.06
327 1874 6.486320 TGTAAAGTTTGAGATGACAATGAGCA 59.514 34.615 0.00 0.00 0.00 4.26
368 1915 9.768662 AGTTAAAGATGAAATTGCAAGTCAAAT 57.231 25.926 16.91 8.06 38.34 2.32
402 1950 7.771183 ACTAATGCTTCTTTGAGTTTGTTTCA 58.229 30.769 0.00 0.00 0.00 2.69
435 1985 3.868757 ACAAGCACGTTGAGCTAGATA 57.131 42.857 0.00 0.00 42.53 1.98
460 2010 4.798574 TGATTCGTCATCCGATATCACAG 58.201 43.478 3.12 0.00 46.75 3.66
482 2032 6.016276 ACAGTTACATTTGTTTCTCATGACCC 60.016 38.462 0.00 0.00 0.00 4.46
485 2035 4.222336 ACATTTGTTTCTCATGACCCCAA 58.778 39.130 0.00 0.00 0.00 4.12
502 2052 6.900186 TGACCCCAATATCATAAACAACCATT 59.100 34.615 0.00 0.00 0.00 3.16
527 2077 8.117813 TCTACATGGACATATCGCATAAGTTA 57.882 34.615 0.00 0.00 0.00 2.24
566 2117 9.309516 TGTTTTCTTATATTGGTACTGTCGATC 57.690 33.333 0.00 0.00 0.00 3.69
567 2118 8.762426 GTTTTCTTATATTGGTACTGTCGATCC 58.238 37.037 0.00 0.00 0.00 3.36
578 2129 3.518590 ACTGTCGATCCCACGTTTATTC 58.481 45.455 0.00 0.00 34.70 1.75
587 2160 5.026038 TCCCACGTTTATTCCATACGAAT 57.974 39.130 0.00 0.00 43.79 3.34
604 2177 8.889717 CCATACGAATACATAGTTTGTTTTCCT 58.110 33.333 9.92 3.76 40.90 3.36
611 2184 6.237313 ACATAGTTTGTTTTCCTTAGACGC 57.763 37.500 0.00 0.00 33.74 5.19
620 2193 2.074547 TCCTTAGACGCGGTTTTGAG 57.925 50.000 12.47 0.00 0.00 3.02
673 2260 9.699410 TCCAAATAGAGACCATAATTTTGATGT 57.301 29.630 0.00 0.00 0.00 3.06
674 2261 9.956720 CCAAATAGAGACCATAATTTTGATGTC 57.043 33.333 0.00 0.00 0.00 3.06
713 2301 6.878923 TGTGACATTCTAGGGTCAAACATAAG 59.121 38.462 12.34 0.00 44.83 1.73
965 2554 3.744719 CGTTGGCGGACGAGAGGA 61.745 66.667 7.35 0.00 45.47 3.71
984 2573 1.528309 GGGGCGGAGAGAGAGAGAG 60.528 68.421 0.00 0.00 0.00 3.20
990 2579 1.166531 GGAGAGAGAGAGAGAGGCGC 61.167 65.000 0.00 0.00 0.00 6.53
1174 2763 2.124653 TCCGCCGAGAGAGAGACC 60.125 66.667 0.00 0.00 0.00 3.85
1175 2764 3.578272 CCGCCGAGAGAGAGACCG 61.578 72.222 0.00 0.00 0.00 4.79
1453 3068 2.606108 CAGCCAACCTTTTATTTCGCC 58.394 47.619 0.00 0.00 0.00 5.54
1456 3071 2.029380 GCCAACCTTTTATTTCGCCTGT 60.029 45.455 0.00 0.00 0.00 4.00
1487 3102 6.887626 TTGTCCATGGATCATATTGATGTG 57.112 37.500 19.62 0.00 37.20 3.21
1492 3107 7.392393 GTCCATGGATCATATTGATGTGAATCA 59.608 37.037 19.62 0.00 37.20 2.57
1541 3159 2.622436 GTCCTCAGTGCTGTTGTATCC 58.378 52.381 0.00 0.00 0.00 2.59
1630 3255 0.957888 GTTTCTGTGCTGGAGGCCTC 60.958 60.000 25.59 25.59 40.92 4.70
1770 3399 7.535489 ACTCGGATTAGTTTGTTTATGCTAC 57.465 36.000 0.00 0.00 0.00 3.58
2080 3734 0.535102 GATGGTGGCGAGGTATTGGG 60.535 60.000 0.00 0.00 0.00 4.12
2083 3737 0.182775 GGTGGCGAGGTATTGGGATT 59.817 55.000 0.00 0.00 0.00 3.01
2149 3803 9.099071 AGATCTGTTCAGTTGATATAGCCTTAT 57.901 33.333 0.00 0.00 0.00 1.73
2165 3819 3.891366 GCCTTATATTGTTGCAGGTGGAT 59.109 43.478 0.00 0.00 0.00 3.41
2213 3867 5.386958 TTCTAGACATTAAGCTGACACGT 57.613 39.130 0.00 0.00 0.00 4.49
2264 3918 2.224426 CCAGGTGTGCAACTACAACCTA 60.224 50.000 0.00 0.00 39.07 3.08
2265 3919 2.806244 CAGGTGTGCAACTACAACCTAC 59.194 50.000 0.00 0.00 39.07 3.18
2266 3920 2.148768 GGTGTGCAACTACAACCTACC 58.851 52.381 0.00 0.00 38.04 3.18
2306 3964 3.947834 GGCAATGTCAAACTATAGCTGGT 59.052 43.478 0.00 0.00 0.00 4.00
2330 3988 4.448732 TCGGATAATGTTCATGCTGAATCG 59.551 41.667 2.61 0.00 38.79 3.34
2632 4290 8.962857 TGTGCATTTGTAAATATGTGTTGTAG 57.037 30.769 0.00 0.00 0.00 2.74
2770 4428 0.322008 CAAGCCACTTCCTCCAGACC 60.322 60.000 0.00 0.00 0.00 3.85
2884 4545 3.495331 TGTCCCACACATTACAAATGCT 58.505 40.909 0.00 0.00 0.00 3.79
3003 4664 8.515414 AGGTGCAAGAGATAACTTTTAACATTC 58.485 33.333 0.00 0.00 0.00 2.67
3045 4708 7.153985 TCTCTTTGCTTACAATTCATTTTGGG 58.846 34.615 0.00 0.00 35.21 4.12
3305 4975 6.166982 GTGAGCAGGTAAGTAAACTTCTCAT 58.833 40.000 11.89 0.00 35.61 2.90
3496 5166 1.378531 TGGTCTCACGCCAAATATGC 58.621 50.000 0.00 0.00 32.29 3.14
3532 5202 4.838904 ACTAAGGTTAGTCAATGGACCC 57.161 45.455 0.00 0.00 45.48 4.46
3549 5219 1.002773 ACCCGTCCAACTTACCATGTC 59.997 52.381 0.00 0.00 0.00 3.06
3568 5239 4.503910 TGTCTCTGACCCGTATTGATTTG 58.496 43.478 0.00 0.00 0.00 2.32
3734 5405 2.699846 TGAATTCTTTTGGTTGCAGGCT 59.300 40.909 7.05 0.00 0.00 4.58
3749 5420 4.272489 TGCAGGCTGCTAATATTTTCACT 58.728 39.130 36.50 0.00 45.31 3.41
3802 5473 2.212869 TTGCTGTTACGGGTATAGCG 57.787 50.000 0.00 0.00 37.20 4.26
3968 5647 4.853924 TGAGGTTTTCTTCCAAAGATGC 57.146 40.909 0.00 0.00 37.38 3.91
4095 5774 4.580580 ACAGGATGAAGTTGGTTTCTGTTC 59.419 41.667 0.00 0.00 39.69 3.18
4103 5782 4.014406 AGTTGGTTTCTGTTCGTCCTTTT 58.986 39.130 0.00 0.00 0.00 2.27
4146 5825 5.953548 GGAAACCTTTACTTAGGCCCAATTA 59.046 40.000 0.00 0.00 38.99 1.40
4247 5926 2.928334 AGGTGAGATGATCATTGTGGC 58.072 47.619 10.14 0.00 40.92 5.01
4582 6264 7.490962 TTTACAATTTGTACCTGTCTGACAG 57.509 36.000 26.94 26.94 45.53 3.51
4700 6382 4.675063 AAACAATGTCCCCTATCTTGGT 57.325 40.909 0.00 0.00 0.00 3.67
5000 6683 8.850156 GCTCACATATGGTTCCTTACAATTTAT 58.150 33.333 7.80 0.00 0.00 1.40
5092 6778 4.072131 TCAAGGTTACTGACTGCAAATCC 58.928 43.478 0.00 0.00 0.00 3.01
5566 7257 1.451207 CGGCGTCCAATTCCATCCA 60.451 57.895 0.00 0.00 0.00 3.41
5620 7311 4.504858 CTCCATTTGTCGGTAAGCTACTT 58.495 43.478 0.00 0.00 0.00 2.24
5648 7339 5.546499 ACTTACTGGAAACTATCTTGGTCCA 59.454 40.000 0.00 0.00 36.90 4.02
5695 7387 1.511850 TCTGCTCAAACATCCACACG 58.488 50.000 0.00 0.00 0.00 4.49
5794 7488 0.949105 CGGCTAAACACAAGCTCGGT 60.949 55.000 0.00 0.00 39.97 4.69
5806 7500 2.640302 GCTCGGTGACAGCTCCTCA 61.640 63.158 2.72 0.00 33.48 3.86
5911 7605 0.107848 GCAGTACCCATGGTTAGCGT 60.108 55.000 11.73 3.24 37.09 5.07
6140 7838 3.603770 CGAATGTTTTTGATCCTTGCGTC 59.396 43.478 0.00 0.00 0.00 5.19
6157 7855 6.202954 CCTTGCGTCTGGACTAAATAATAAGG 59.797 42.308 0.00 0.00 0.00 2.69
6163 7861 8.081025 CGTCTGGACTAAATAATAAGGTAGACC 58.919 40.741 0.00 0.00 0.00 3.85
6182 7880 8.407832 GGTAGACCATCTTAGAAAGTCTTAGTC 58.592 40.741 18.31 9.78 38.65 2.59
6204 7903 1.228894 TCGAGACAGAGCCTGGGTT 60.229 57.895 0.00 0.00 35.51 4.11
6565 8265 3.382865 TCACACATTGCCAAACTTTGCTA 59.617 39.130 0.00 0.00 0.00 3.49
6567 8267 3.131933 ACACATTGCCAAACTTTGCTACA 59.868 39.130 0.00 0.00 0.00 2.74
6583 8283 1.470098 CTACAAATGTGGCAGTGGCTC 59.530 52.381 18.53 14.88 40.87 4.70
6603 8303 4.437659 GCTCGTGGTTTGTTTGTTTCACTA 60.438 41.667 0.00 0.00 0.00 2.74
6625 8325 0.609131 ATAGTTGTGCCCTGCCACAC 60.609 55.000 0.00 0.00 44.72 3.82
6773 8484 8.536340 AACCATAAGTTAACCCACAAAAAGTA 57.464 30.769 0.88 0.00 36.74 2.24
6774 8485 8.715190 ACCATAAGTTAACCCACAAAAAGTAT 57.285 30.769 0.88 0.00 0.00 2.12
6775 8486 8.799367 ACCATAAGTTAACCCACAAAAAGTATC 58.201 33.333 0.88 0.00 0.00 2.24
6776 8487 8.798402 CCATAAGTTAACCCACAAAAAGTATCA 58.202 33.333 0.88 0.00 0.00 2.15
6780 8491 4.434713 AACCCACAAAAAGTATCATCGC 57.565 40.909 0.00 0.00 0.00 4.58
6781 8492 3.686016 ACCCACAAAAAGTATCATCGCT 58.314 40.909 0.00 0.00 0.00 4.93
6782 8493 4.079253 ACCCACAAAAAGTATCATCGCTT 58.921 39.130 0.00 0.00 0.00 4.68
6783 8494 4.522789 ACCCACAAAAAGTATCATCGCTTT 59.477 37.500 0.00 0.00 36.60 3.51
6784 8495 5.095490 CCCACAAAAAGTATCATCGCTTTC 58.905 41.667 0.00 0.00 34.26 2.62
6785 8496 4.788100 CCACAAAAAGTATCATCGCTTTCG 59.212 41.667 0.00 0.00 34.26 3.46
6822 10760 2.022240 GAGAGCCATCGTCCTCCACC 62.022 65.000 0.00 0.00 0.00 4.61
6848 10786 0.779997 AAGCCCACAATCCCAACTCT 59.220 50.000 0.00 0.00 0.00 3.24
6850 10788 0.681243 GCCCACAATCCCAACTCTCC 60.681 60.000 0.00 0.00 0.00 3.71
6851 10789 0.392998 CCCACAATCCCAACTCTCCG 60.393 60.000 0.00 0.00 0.00 4.63
6852 10790 0.613260 CCACAATCCCAACTCTCCGA 59.387 55.000 0.00 0.00 0.00 4.55
6853 10791 1.676014 CCACAATCCCAACTCTCCGAC 60.676 57.143 0.00 0.00 0.00 4.79
6854 10792 1.001974 CACAATCCCAACTCTCCGACA 59.998 52.381 0.00 0.00 0.00 4.35
6855 10793 1.909302 ACAATCCCAACTCTCCGACAT 59.091 47.619 0.00 0.00 0.00 3.06
6856 10794 2.093447 ACAATCCCAACTCTCCGACATC 60.093 50.000 0.00 0.00 0.00 3.06
6857 10795 1.866015 ATCCCAACTCTCCGACATCA 58.134 50.000 0.00 0.00 0.00 3.07
6858 10796 1.866015 TCCCAACTCTCCGACATCAT 58.134 50.000 0.00 0.00 0.00 2.45
6859 10797 1.482182 TCCCAACTCTCCGACATCATG 59.518 52.381 0.00 0.00 0.00 3.07
6860 10798 1.473965 CCCAACTCTCCGACATCATGG 60.474 57.143 0.00 0.00 0.00 3.66
6861 10799 1.473965 CCAACTCTCCGACATCATGGG 60.474 57.143 0.00 0.00 0.00 4.00
6862 10800 0.833287 AACTCTCCGACATCATGGGG 59.167 55.000 0.00 0.00 0.00 4.96
6863 10801 0.325671 ACTCTCCGACATCATGGGGT 60.326 55.000 0.00 0.00 0.00 4.95
6864 10802 0.105593 CTCTCCGACATCATGGGGTG 59.894 60.000 0.00 0.00 0.00 4.61
6865 10803 0.617535 TCTCCGACATCATGGGGTGT 60.618 55.000 0.00 0.00 0.00 4.16
6866 10804 0.462581 CTCCGACATCATGGGGTGTG 60.463 60.000 4.43 0.00 0.00 3.82
6867 10805 2.114670 CCGACATCATGGGGTGTGC 61.115 63.158 4.43 0.00 0.00 4.57
6868 10806 2.463620 CGACATCATGGGGTGTGCG 61.464 63.158 4.43 4.92 0.00 5.34
6869 10807 2.045045 ACATCATGGGGTGTGCGG 60.045 61.111 0.00 0.00 0.00 5.69
6870 10808 2.271821 CATCATGGGGTGTGCGGA 59.728 61.111 0.00 0.00 0.00 5.54
6871 10809 1.378382 CATCATGGGGTGTGCGGAA 60.378 57.895 0.00 0.00 0.00 4.30
6872 10810 1.077501 ATCATGGGGTGTGCGGAAG 60.078 57.895 0.00 0.00 0.00 3.46
6884 10822 3.437795 CGGAAGCCTGCTGCCTTG 61.438 66.667 14.24 0.00 39.68 3.61
6885 10823 2.034687 GGAAGCCTGCTGCCTTGA 59.965 61.111 9.04 0.00 42.71 3.02
6886 10824 2.338785 GGAAGCCTGCTGCCTTGAC 61.339 63.158 9.04 0.00 42.71 3.18
6887 10825 2.670934 AAGCCTGCTGCCTTGACG 60.671 61.111 0.00 0.00 42.71 4.35
6888 10826 3.482232 AAGCCTGCTGCCTTGACGT 62.482 57.895 0.00 0.00 42.71 4.34
6889 10827 2.965716 AAGCCTGCTGCCTTGACGTT 62.966 55.000 0.00 0.00 42.71 3.99
6890 10828 2.949106 CCTGCTGCCTTGACGTTG 59.051 61.111 0.00 0.00 0.00 4.10
6891 10829 1.893808 CCTGCTGCCTTGACGTTGT 60.894 57.895 0.00 0.00 0.00 3.32
6892 10830 0.602638 CCTGCTGCCTTGACGTTGTA 60.603 55.000 0.00 0.00 0.00 2.41
6893 10831 1.442769 CTGCTGCCTTGACGTTGTAT 58.557 50.000 0.00 0.00 0.00 2.29
6894 10832 1.394917 CTGCTGCCTTGACGTTGTATC 59.605 52.381 0.00 0.00 0.00 2.24
6895 10833 1.270571 TGCTGCCTTGACGTTGTATCA 60.271 47.619 0.00 0.00 0.00 2.15
6896 10834 2.009774 GCTGCCTTGACGTTGTATCAT 58.990 47.619 0.00 0.00 0.00 2.45
6897 10835 2.223112 GCTGCCTTGACGTTGTATCATG 60.223 50.000 0.00 0.00 0.00 3.07
6898 10836 2.352651 CTGCCTTGACGTTGTATCATGG 59.647 50.000 0.00 0.00 41.91 3.66
6899 10837 2.027653 TGCCTTGACGTTGTATCATGGA 60.028 45.455 10.25 0.00 41.67 3.41
6900 10838 3.206150 GCCTTGACGTTGTATCATGGAT 58.794 45.455 10.25 0.00 41.67 3.41
6901 10839 4.141824 TGCCTTGACGTTGTATCATGGATA 60.142 41.667 10.25 0.00 41.67 2.59
6902 10840 4.449068 GCCTTGACGTTGTATCATGGATAG 59.551 45.833 10.25 0.00 41.67 2.08
6903 10841 4.991056 CCTTGACGTTGTATCATGGATAGG 59.009 45.833 0.00 0.00 41.67 2.57
6904 10842 5.453339 CCTTGACGTTGTATCATGGATAGGT 60.453 44.000 0.00 0.00 41.67 3.08
6905 10843 5.607939 TGACGTTGTATCATGGATAGGTT 57.392 39.130 0.00 0.00 0.00 3.50
6906 10844 6.718522 TGACGTTGTATCATGGATAGGTTA 57.281 37.500 0.00 0.00 0.00 2.85
6907 10845 6.745116 TGACGTTGTATCATGGATAGGTTAG 58.255 40.000 0.00 0.00 0.00 2.34
6908 10846 5.539048 ACGTTGTATCATGGATAGGTTAGC 58.461 41.667 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.800155 TCACAAGTTTCATAGTTGTTCATGA 57.200 32.000 0.00 0.00 45.92 3.07
101 102 9.739276 ACATTCATGAATTTAAGGAGTGTTAGA 57.261 29.630 18.41 0.00 0.00 2.10
183 185 7.065894 CCGACATTCTATTAAAATGCTTCTCG 58.934 38.462 0.00 1.91 37.58 4.04
184 186 7.920738 ACCGACATTCTATTAAAATGCTTCTC 58.079 34.615 0.00 0.00 37.58 2.87
206 208 6.237755 GGTCTAACATAACAAGATCGAAACCG 60.238 42.308 0.00 0.00 0.00 4.44
225 227 2.335681 TGGTCAGGTCATGGGTCTAA 57.664 50.000 0.00 0.00 0.00 2.10
227 229 1.073923 GTTTGGTCAGGTCATGGGTCT 59.926 52.381 0.00 0.00 0.00 3.85
240 242 1.562575 CCACGTGTAGGCGTTTGGTC 61.563 60.000 15.65 0.00 43.83 4.02
243 245 1.562575 GACCCACGTGTAGGCGTTTG 61.563 60.000 15.65 0.00 43.83 2.93
244 246 1.301165 GACCCACGTGTAGGCGTTT 60.301 57.895 15.65 0.00 43.83 3.60
245 247 2.341176 GACCCACGTGTAGGCGTT 59.659 61.111 15.65 0.00 43.83 4.84
246 248 3.688159 GGACCCACGTGTAGGCGT 61.688 66.667 15.65 2.02 46.88 5.68
247 249 3.687102 TGGACCCACGTGTAGGCG 61.687 66.667 15.65 0.00 37.94 5.52
248 250 2.047560 GTGGACCCACGTGTAGGC 60.048 66.667 15.65 7.51 37.19 3.93
292 294 8.270030 TCATCTCAAACTTTACAGATCATGGAT 58.730 33.333 0.00 0.00 0.00 3.41
293 295 7.550551 GTCATCTCAAACTTTACAGATCATGGA 59.449 37.037 0.00 0.00 0.00 3.41
295 297 8.260270 TGTCATCTCAAACTTTACAGATCATG 57.740 34.615 0.00 0.00 0.00 3.07
297 299 8.724229 CATTGTCATCTCAAACTTTACAGATCA 58.276 33.333 0.00 0.00 0.00 2.92
298 300 8.939929 TCATTGTCATCTCAAACTTTACAGATC 58.060 33.333 0.00 0.00 0.00 2.75
299 301 8.853077 TCATTGTCATCTCAAACTTTACAGAT 57.147 30.769 0.00 0.00 0.00 2.90
315 1862 7.014326 AGCTTATCATTCATTGCTCATTGTCAT 59.986 33.333 0.00 0.00 0.00 3.06
319 1866 7.872881 ACTAGCTTATCATTCATTGCTCATTG 58.127 34.615 0.00 0.00 32.72 2.82
390 1938 5.568685 TTCGGATGTTTGAAACAAACTCA 57.431 34.783 15.31 8.71 45.86 3.41
402 1950 3.112580 CGTGCTTGTTTTTCGGATGTTT 58.887 40.909 0.00 0.00 0.00 2.83
460 2010 5.242838 TGGGGTCATGAGAAACAAATGTAAC 59.757 40.000 0.00 0.00 0.00 2.50
502 2052 6.590234 ACTTATGCGATATGTCCATGTAGA 57.410 37.500 0.00 0.00 0.00 2.59
551 2102 1.136305 CGTGGGATCGACAGTACCAAT 59.864 52.381 0.00 0.00 32.19 3.16
561 2112 3.830744 ATGGAATAAACGTGGGATCGA 57.169 42.857 0.00 0.00 34.70 3.59
566 2117 5.754406 TGTATTCGTATGGAATAAACGTGGG 59.246 40.000 0.00 0.00 46.39 4.61
567 2118 6.831727 TGTATTCGTATGGAATAAACGTGG 57.168 37.500 0.00 0.00 46.39 4.94
578 2129 8.889717 AGGAAAACAAACTATGTATTCGTATGG 58.110 33.333 0.00 0.00 42.99 2.74
587 2160 6.089820 CGCGTCTAAGGAAAACAAACTATGTA 59.910 38.462 0.00 0.00 42.99 2.29
604 2177 4.199840 GTTTTCTCAAAACCGCGTCTAA 57.800 40.909 4.92 0.00 43.78 2.10
605 2178 3.865224 GTTTTCTCAAAACCGCGTCTA 57.135 42.857 4.92 0.00 43.78 2.59
636 2218 5.476945 GGTCTCTATTTGGAAGGAGCAAAAA 59.523 40.000 0.00 0.00 0.00 1.94
637 2219 5.010282 GGTCTCTATTTGGAAGGAGCAAAA 58.990 41.667 0.00 0.00 0.00 2.44
638 2220 4.042809 TGGTCTCTATTTGGAAGGAGCAAA 59.957 41.667 0.00 0.00 0.00 3.68
639 2221 3.587061 TGGTCTCTATTTGGAAGGAGCAA 59.413 43.478 0.00 0.00 0.00 3.91
640 2222 3.181329 TGGTCTCTATTTGGAAGGAGCA 58.819 45.455 0.00 0.00 0.00 4.26
641 2223 3.914426 TGGTCTCTATTTGGAAGGAGC 57.086 47.619 0.00 0.00 0.00 4.70
642 2224 8.986929 AAATTATGGTCTCTATTTGGAAGGAG 57.013 34.615 0.00 0.00 0.00 3.69
656 2238 6.332976 AGAGGGACATCAAAATTATGGTCT 57.667 37.500 0.00 0.00 0.00 3.85
772 2360 1.224381 CTTTCCCCCTCTATCCCCTCT 59.776 57.143 0.00 0.00 0.00 3.69
950 2539 3.068691 CCTCCTCTCGTCCGCCAA 61.069 66.667 0.00 0.00 0.00 4.52
957 2546 4.824515 CTCCGCCCCTCCTCTCGT 62.825 72.222 0.00 0.00 0.00 4.18
965 2554 1.994885 CTCTCTCTCTCTCCGCCCCT 61.995 65.000 0.00 0.00 0.00 4.79
970 2559 0.880278 CGCCTCTCTCTCTCTCTCCG 60.880 65.000 0.00 0.00 0.00 4.63
971 2560 1.166531 GCGCCTCTCTCTCTCTCTCC 61.167 65.000 0.00 0.00 0.00 3.71
972 2561 1.166531 GGCGCCTCTCTCTCTCTCTC 61.167 65.000 22.15 0.00 0.00 3.20
990 2579 1.067582 GTACTTCATCTCGCCGGGG 59.932 63.158 13.31 13.31 0.00 5.73
1044 2633 4.410400 CTGGCCGTCACCCCCTTC 62.410 72.222 0.00 0.00 0.00 3.46
1453 3068 1.739466 CCATGGACAAATCACGGACAG 59.261 52.381 5.56 0.00 0.00 3.51
1456 3071 2.238395 TGATCCATGGACAAATCACGGA 59.762 45.455 18.99 0.00 0.00 4.69
1487 3102 7.255416 GGCTAATTCTTGATCCTTTCCTGATTC 60.255 40.741 0.00 0.00 0.00 2.52
1492 3107 4.455606 CGGCTAATTCTTGATCCTTTCCT 58.544 43.478 0.00 0.00 0.00 3.36
1541 3159 4.097892 GGCCACCTTGTACCATTTAGATTG 59.902 45.833 0.00 0.00 0.00 2.67
1630 3255 0.739813 GAATCCCTCCGGAACACACG 60.740 60.000 5.23 0.00 43.10 4.49
1770 3399 8.883731 AGAAACCAATAACTATCAAACGATGAG 58.116 33.333 0.00 0.00 42.53 2.90
2134 3788 8.454106 CCTGCAACAATATAAGGCTATATCAAC 58.546 37.037 0.00 0.00 30.73 3.18
2149 3803 3.772387 TCCAAATCCACCTGCAACAATA 58.228 40.909 0.00 0.00 0.00 1.90
2152 3806 2.170166 GATCCAAATCCACCTGCAACA 58.830 47.619 0.00 0.00 0.00 3.33
2165 3819 5.163405 CCTCTCATAGTTTCCGAGATCCAAA 60.163 44.000 0.00 0.00 35.35 3.28
2213 3867 7.276658 TCTTTCCAGTAGTTATGTTGTTGTCA 58.723 34.615 0.00 0.00 0.00 3.58
2264 3918 1.004745 CATTAAGCAGGAGGTGGTGGT 59.995 52.381 0.00 0.00 36.83 4.16
2265 3919 1.683011 CCATTAAGCAGGAGGTGGTGG 60.683 57.143 0.00 0.00 36.83 4.61
2266 3920 1.755179 CCATTAAGCAGGAGGTGGTG 58.245 55.000 0.00 0.00 36.83 4.17
2330 3988 5.156355 CAGTGATGTTGAAATACAGCCAAC 58.844 41.667 0.00 0.00 40.22 3.77
2372 4030 4.534500 ACCTTGTATGGACCAAGTCATACA 59.466 41.667 0.00 10.84 38.07 2.29
2385 4043 7.389053 GGATAAGAAGCTAATGACCTTGTATGG 59.611 40.741 0.00 0.00 0.00 2.74
2572 4230 5.703130 GCCACTATTCTGAGTTTCTCACTTT 59.297 40.000 0.00 0.00 35.39 2.66
2632 4290 6.525976 GCAAGATCAGACTATTTTGCAACTTC 59.474 38.462 0.00 0.00 43.11 3.01
2796 4456 6.403866 AGAAATGTTCAATGTAAGTTGCCA 57.596 33.333 0.00 0.00 0.00 4.92
2884 4545 5.670485 ACACGCTCAATCCAATCTTGTATA 58.330 37.500 0.00 0.00 0.00 1.47
3003 4664 8.348507 AGCAAAGAGAGTCTTAAAAATGAACAG 58.651 33.333 0.00 0.00 35.27 3.16
3305 4975 5.559770 TGGCATTATGAACTGACTGAGAAA 58.440 37.500 0.00 0.00 0.00 2.52
3496 5166 9.223557 ACTAACCTTAGTACTGCGACAAGCTAG 62.224 44.444 5.39 6.84 43.43 3.42
3532 5202 3.056821 TCAGAGACATGGTAAGTTGGACG 60.057 47.826 0.00 0.00 0.00 4.79
3549 5219 6.594159 AGTTAACAAATCAATACGGGTCAGAG 59.406 38.462 8.61 0.00 0.00 3.35
3568 5239 7.750903 GTCACCAATAAAGCATGAGAAGTTAAC 59.249 37.037 0.00 0.00 0.00 2.01
3776 5447 3.706600 ACCCGTAACAGCAAAGGAATA 57.293 42.857 0.00 0.00 0.00 1.75
3829 5500 8.975663 ATATCATATAGTGCATGGGAAAGATG 57.024 34.615 0.00 0.00 0.00 2.90
3830 5501 9.986157 AAATATCATATAGTGCATGGGAAAGAT 57.014 29.630 0.00 0.00 0.00 2.40
3871 5550 2.886523 TGTGCTTTCTGGTCCTGAAATG 59.113 45.455 20.55 15.88 32.56 2.32
3872 5551 2.887152 GTGTGCTTTCTGGTCCTGAAAT 59.113 45.455 20.55 0.00 32.56 2.17
3873 5552 2.297701 GTGTGCTTTCTGGTCCTGAAA 58.702 47.619 19.49 19.49 32.18 2.69
3874 5553 1.211703 TGTGTGCTTTCTGGTCCTGAA 59.788 47.619 7.09 7.09 0.00 3.02
3875 5554 0.836606 TGTGTGCTTTCTGGTCCTGA 59.163 50.000 0.00 0.00 0.00 3.86
3876 5555 1.679139 TTGTGTGCTTTCTGGTCCTG 58.321 50.000 0.00 0.00 0.00 3.86
3951 5630 3.681417 GCATGGCATCTTTGGAAGAAAAC 59.319 43.478 0.00 0.00 41.63 2.43
3983 5662 6.581171 AACATGGGAAAGAAGATTCAGAAC 57.419 37.500 0.00 0.00 0.00 3.01
3984 5663 6.517194 GCAAACATGGGAAAGAAGATTCAGAA 60.517 38.462 0.00 0.00 0.00 3.02
4095 5774 8.076178 AGACAGATAAAACAATTGAAAAGGACG 58.924 33.333 13.59 0.00 0.00 4.79
4103 5782 7.505585 AGGTTTCCAGACAGATAAAACAATTGA 59.494 33.333 13.59 0.00 32.75 2.57
4146 5825 3.565482 CACCTGAAACAACAGTGCAGTAT 59.435 43.478 0.00 0.00 36.30 2.12
4247 5926 8.647143 ATTTAACAACAAGACTGAAACAATGG 57.353 30.769 0.00 0.00 0.00 3.16
4582 6264 1.106285 AGCGCCCTGGAATGAAAATC 58.894 50.000 2.29 0.00 0.00 2.17
4966 6648 1.561076 ACCATATGTGAGCTCAAGGCA 59.439 47.619 20.19 13.20 44.79 4.75
5092 6778 2.962827 CTGCACTCACAGCTTGGCG 61.963 63.158 0.00 0.00 0.00 5.69
5566 7257 2.158957 TGAAGGCGTTGACTTGAACTCT 60.159 45.455 0.00 0.00 26.99 3.24
5620 7311 6.042781 ACCAAGATAGTTTCCAGTAAGTGTCA 59.957 38.462 0.00 0.00 0.00 3.58
5648 7339 1.142870 TGTTTGCTGTAGCTTCCCACT 59.857 47.619 5.38 0.00 42.66 4.00
5695 7387 2.202566 GCGATTAGTCCTGTAGGCAAC 58.797 52.381 0.00 0.00 34.44 4.17
5722 7416 1.748122 CTGATCCAGCTGCCCACAC 60.748 63.158 8.66 0.00 0.00 3.82
5725 7419 2.611800 ACCTGATCCAGCTGCCCA 60.612 61.111 8.66 4.49 0.00 5.36
5731 7425 2.045634 TGCAGCACCTGATCCAGC 60.046 61.111 0.00 0.00 32.44 4.85
5737 7431 2.745698 CTGTCCTGCAGCACCTGA 59.254 61.111 8.66 0.00 38.52 3.86
5794 7488 1.754745 GGGTGTTGAGGAGCTGTCA 59.245 57.895 0.00 0.00 0.00 3.58
5806 7500 2.636403 GTTCTGGTGTACTAGGGGTGTT 59.364 50.000 0.00 0.00 0.00 3.32
5911 7605 1.373246 CTTGGCGAAACCGACGGTA 60.373 57.895 22.06 0.00 43.94 4.02
5981 7677 2.744202 CTGATAAGTTGCTCAGCCGTTT 59.256 45.455 0.00 0.00 33.12 3.60
6140 7838 9.930693 GATGGTCTACCTTATTATTTAGTCCAG 57.069 37.037 0.02 0.00 34.58 3.86
6157 7855 9.181061 AGACTAAGACTTTCTAAGATGGTCTAC 57.819 37.037 0.00 0.00 36.42 2.59
6163 7861 8.237949 TCGACAAGACTAAGACTTTCTAAGATG 58.762 37.037 0.00 0.00 0.00 2.90
6182 7880 0.108898 CCAGGCTCTGTCTCGACAAG 60.109 60.000 1.02 3.73 41.33 3.16
6204 7903 4.339814 GGAAATCAAAGTACACACCCAACA 59.660 41.667 0.00 0.00 0.00 3.33
6347 8047 1.280133 AGTGCTGTACTGCCATGTGAT 59.720 47.619 20.46 0.00 38.49 3.06
6541 8241 3.560896 GCAAAGTTTGGCAATGTGTGAAT 59.439 39.130 17.11 0.00 0.00 2.57
6542 8242 2.935201 GCAAAGTTTGGCAATGTGTGAA 59.065 40.909 17.11 0.00 0.00 3.18
6543 8243 2.168106 AGCAAAGTTTGGCAATGTGTGA 59.832 40.909 17.11 0.00 0.00 3.58
6565 8265 1.518056 CGAGCCACTGCCACATTTGT 61.518 55.000 0.00 0.00 38.69 2.83
6567 8267 1.228245 ACGAGCCACTGCCACATTT 60.228 52.632 0.00 0.00 38.69 2.32
6583 8283 5.574082 TGATAGTGAAACAAACAAACCACG 58.426 37.500 0.00 0.00 41.43 4.94
6603 8303 0.625316 TGGCAGGGCACAACTATGAT 59.375 50.000 0.00 0.00 0.00 2.45
6828 10766 0.890683 GAGTTGGGATTGTGGGCTTG 59.109 55.000 0.00 0.00 0.00 4.01
6839 10777 1.482182 CATGATGTCGGAGAGTTGGGA 59.518 52.381 0.00 0.00 36.95 4.37
6848 10786 1.601703 CACACCCCATGATGTCGGA 59.398 57.895 0.00 0.00 0.00 4.55
6850 10788 2.463620 CGCACACCCCATGATGTCG 61.464 63.158 0.00 0.00 0.00 4.35
6851 10789 2.114670 CCGCACACCCCATGATGTC 61.115 63.158 0.00 0.00 0.00 3.06
6852 10790 2.045045 CCGCACACCCCATGATGT 60.045 61.111 0.00 0.00 0.00 3.06
6853 10791 1.378382 TTCCGCACACCCCATGATG 60.378 57.895 0.00 0.00 0.00 3.07
6854 10792 1.077501 CTTCCGCACACCCCATGAT 60.078 57.895 0.00 0.00 0.00 2.45
6855 10793 2.350895 CTTCCGCACACCCCATGA 59.649 61.111 0.00 0.00 0.00 3.07
6856 10794 3.443045 GCTTCCGCACACCCCATG 61.443 66.667 0.00 0.00 35.78 3.66
6857 10795 4.740822 GGCTTCCGCACACCCCAT 62.741 66.667 0.00 0.00 38.10 4.00
6862 10800 3.730761 CAGCAGGCTTCCGCACAC 61.731 66.667 0.00 0.00 38.10 3.82
6872 10810 2.980233 AACGTCAAGGCAGCAGGC 60.980 61.111 0.00 0.00 43.74 4.85
6873 10811 0.602638 TACAACGTCAAGGCAGCAGG 60.603 55.000 0.00 0.00 0.00 4.85
6874 10812 1.394917 GATACAACGTCAAGGCAGCAG 59.605 52.381 0.00 0.00 0.00 4.24
6875 10813 1.270571 TGATACAACGTCAAGGCAGCA 60.271 47.619 0.00 0.00 0.00 4.41
6876 10814 1.438651 TGATACAACGTCAAGGCAGC 58.561 50.000 0.00 0.00 0.00 5.25
6877 10815 2.352651 CCATGATACAACGTCAAGGCAG 59.647 50.000 0.00 0.00 28.99 4.85
6878 10816 2.027653 TCCATGATACAACGTCAAGGCA 60.028 45.455 0.00 0.00 35.11 4.75
6879 10817 2.627945 TCCATGATACAACGTCAAGGC 58.372 47.619 0.00 0.00 35.11 4.35
6880 10818 4.991056 CCTATCCATGATACAACGTCAAGG 59.009 45.833 0.00 0.00 36.15 3.61
6881 10819 5.601662 ACCTATCCATGATACAACGTCAAG 58.398 41.667 0.00 0.00 0.00 3.02
6882 10820 5.607939 ACCTATCCATGATACAACGTCAA 57.392 39.130 0.00 0.00 0.00 3.18
6883 10821 5.607939 AACCTATCCATGATACAACGTCA 57.392 39.130 0.00 0.00 0.00 4.35
6884 10822 5.634020 GCTAACCTATCCATGATACAACGTC 59.366 44.000 0.00 0.00 0.00 4.34
6885 10823 5.539048 GCTAACCTATCCATGATACAACGT 58.461 41.667 0.00 0.00 0.00 3.99


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

AutoCloner maintained by Alex Coulton.