Multiple sequence alignment - TraesCS5B01G377500

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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 TraesCS5B01G377500 chr5B 100.000 5919 0 0 1 5919 555120098 555126016 0.000000e+00 10931.0
1 TraesCS5B01G377500 chr5D 93.962 5565 198 49 139 5638 454169095 454174586 0.000000e+00 8288.0
2 TraesCS5B01G377500 chr5D 91.571 261 11 7 5635 5894 454175958 454176208 3.390000e-92 350.0
3 TraesCS5B01G377500 chr5D 95.062 81 3 1 1 81 454169014 454169093 6.230000e-25 126.0
4 TraesCS5B01G377500 chr5A 95.859 2946 99 14 1797 4731 573559565 573562498 0.000000e+00 4743.0
5 TraesCS5B01G377500 chr5A 95.552 1776 57 7 1 1763 573557801 573559567 0.000000e+00 2822.0
6 TraesCS5B01G377500 chr5A 85.983 478 25 15 5186 5639 573563054 573563513 1.930000e-129 473.0
7 TraesCS5B01G377500 chr5A 85.714 378 23 11 4740 5109 573562618 573562972 2.610000e-98 370.0
8 TraesCS5B01G377500 chr5A 83.929 224 10 12 5642 5865 573563781 573563978 2.180000e-44 191.0
9 TraesCS5B01G377500 chr6D 83.648 159 16 1 3602 3760 449760385 449760237 2.220000e-29 141.0
10 TraesCS5B01G377500 chr4A 97.222 36 1 0 2911 2946 618564344 618564379 1.780000e-05 62.1


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 TraesCS5B01G377500 chr5B 555120098 555126016 5918 False 10931.000000 10931 100.000000 1 5919 1 chr5B.!!$F1 5918
1 TraesCS5B01G377500 chr5D 454169014 454176208 7194 False 2921.333333 8288 93.531667 1 5894 3 chr5D.!!$F1 5893
2 TraesCS5B01G377500 chr5A 573557801 573563978 6177 False 1719.800000 4743 89.407400 1 5865 5 chr5A.!!$F1 5864

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
893 910 2.365293 AGCACTCGCCATCATACATGTA 59.635 45.455 8.27 8.27 39.83 2.29 F
1945 1975 1.471287 TCGTGTATGGGTTGTCTCGAG 59.529 52.381 5.93 5.93 0.00 4.04 F
2600 2631 1.039233 CCTGGGTTGGCTAAGCATGG 61.039 60.000 14.20 10.62 36.03 3.66 F
3481 3514 0.687920 TTCCGTGGGCATGTGAAGTA 59.312 50.000 0.00 0.00 0.00 2.24 F
4424 4462 1.542915 CCCCTCTGAAACTGCATGTTG 59.457 52.381 0.00 0.00 39.13 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2414 2444 0.255890 TCAGGTAGGGCATGGCTTTC 59.744 55.000 19.78 9.42 0.0 2.62 R
2999 3032 1.398390 GTTTAACGCTGCTCCATGAGG 59.602 52.381 0.00 0.00 0.0 3.86 R
4403 4440 0.038744 ACATGCAGTTTCAGAGGGGG 59.961 55.000 0.00 0.00 0.0 5.40 R
4897 5050 0.106819 AAGACTGGGCCATGATCTGC 60.107 55.000 6.72 0.00 0.0 4.26 R
5865 7467 0.676466 TCCTGTGCAATACAAGGCGG 60.676 55.000 0.00 0.00 39.2 6.13 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
41 42 3.776969 ACAGAGATGGTGGAGCAAATAGA 59.223 43.478 0.00 0.00 0.00 1.98
53 54 7.010460 GGTGGAGCAAATAGATTTGTTAAATGC 59.990 37.037 14.72 1.73 46.63 3.56
62 63 3.859411 TTTGTTAAATGCCCCATCGTC 57.141 42.857 0.00 0.00 0.00 4.20
82 83 9.196552 CATCGTCATTGCTCTTATTAGTTATGA 57.803 33.333 0.00 0.00 0.00 2.15
219 227 4.091509 ACTTGTCGACGTAGCAATGAAATC 59.908 41.667 11.62 0.00 0.00 2.17
236 249 9.499585 CAATGAAATCTGTCATGTATCAAACTC 57.500 33.333 0.00 0.00 38.28 3.01
355 368 3.062042 CCGAAGATGCATCGAATGATCA 58.938 45.455 20.67 0.00 42.76 2.92
369 382 5.291858 TCGAATGATCAAAGTCACTACATGC 59.708 40.000 0.00 0.00 0.00 4.06
573 586 9.726232 CAAATGTGTATCACTAAGGAAATGATG 57.274 33.333 1.72 0.00 34.86 3.07
720 734 8.894768 ATATGAAAGTTGCTATGAACCTAGTC 57.105 34.615 0.00 0.00 0.00 2.59
729 743 7.539034 TGCTATGAACCTAGTCTATTGCATA 57.461 36.000 0.00 0.00 0.00 3.14
754 768 2.456577 ACCAAAAAGGCGGCTATGAAT 58.543 42.857 13.71 0.00 43.14 2.57
893 910 2.365293 AGCACTCGCCATCATACATGTA 59.635 45.455 8.27 8.27 39.83 2.29
894 911 2.733552 GCACTCGCCATCATACATGTAG 59.266 50.000 11.91 4.09 0.00 2.74
895 912 3.800261 GCACTCGCCATCATACATGTAGT 60.800 47.826 11.91 0.00 0.00 2.73
1092 1109 1.678970 GGGAAGTTGGCGCCTGATT 60.679 57.895 29.70 18.68 0.00 2.57
1102 1119 3.351740 TGGCGCCTGATTTTGAAAGATA 58.648 40.909 29.70 0.00 0.00 1.98
1104 1121 4.219507 TGGCGCCTGATTTTGAAAGATAAA 59.780 37.500 29.70 0.00 0.00 1.40
1110 1127 7.809806 CGCCTGATTTTGAAAGATAAAGACTTT 59.190 33.333 5.62 5.62 39.76 2.66
1167 1184 8.843885 ATCTAAAGGTTAGAACTGTTTACACC 57.156 34.615 2.04 1.44 0.00 4.16
1194 1211 4.431809 TGCATTTTTGTTGAGGTCACTTG 58.568 39.130 0.00 0.00 0.00 3.16
1200 1217 2.564771 TGTTGAGGTCACTTGCTTCAG 58.435 47.619 0.00 0.00 0.00 3.02
1370 1387 4.464244 CGAATCAGGCTCTATGGATAAGGA 59.536 45.833 0.00 0.00 0.00 3.36
1382 1399 2.026262 TGGATAAGGAAAGGACTGCCAC 60.026 50.000 0.00 0.00 36.29 5.01
1608 1626 4.890158 ACTTGTCACACAGTGATATCCA 57.110 40.909 7.81 0.00 44.63 3.41
1609 1627 5.227569 ACTTGTCACACAGTGATATCCAA 57.772 39.130 7.81 3.64 44.63 3.53
1610 1628 5.240891 ACTTGTCACACAGTGATATCCAAG 58.759 41.667 18.61 18.61 44.63 3.61
1611 1629 5.012046 ACTTGTCACACAGTGATATCCAAGA 59.988 40.000 23.39 1.35 44.63 3.02
1612 1630 5.482163 TGTCACACAGTGATATCCAAGAA 57.518 39.130 7.81 0.00 44.63 2.52
1945 1975 1.471287 TCGTGTATGGGTTGTCTCGAG 59.529 52.381 5.93 5.93 0.00 4.04
2035 2065 9.442047 CACCACAAAGAGAGAAAAATAGTATCT 57.558 33.333 0.00 0.00 0.00 1.98
2214 2244 3.120923 GCAATTTTCCGTTGTGCAATCAG 60.121 43.478 0.00 0.00 35.28 2.90
2404 2434 3.960102 TGAATCAGTTTTCTTGCCTTGGT 59.040 39.130 0.00 0.00 0.00 3.67
2414 2444 2.125106 GCCTTGGTAGACTGGCCG 60.125 66.667 0.00 0.00 39.49 6.13
2480 2510 6.596888 TCAGCTACTGATCCATCTTTTCTTTG 59.403 38.462 0.00 0.00 35.39 2.77
2493 2523 6.092955 TCTTTTCTTTGATGAATTGCTGCT 57.907 33.333 0.00 0.00 0.00 4.24
2506 2537 2.664402 TGCTGCTTCCTTTCTTTCCT 57.336 45.000 0.00 0.00 0.00 3.36
2520 2551 6.422100 CCTTTCTTTCCTCTTTGCTAAAAAGC 59.578 38.462 0.00 0.00 0.00 3.51
2527 2558 4.418392 CTCTTTGCTAAAAAGCATGCGAT 58.582 39.130 13.01 2.11 44.94 4.58
2535 2566 2.540265 AAAGCATGCGATAGAGAGGG 57.460 50.000 13.01 0.00 39.76 4.30
2583 2614 2.909217 AGAGTAAGGAGGCTCAAACCT 58.091 47.619 17.69 6.28 45.04 3.50
2600 2631 1.039233 CCTGGGTTGGCTAAGCATGG 61.039 60.000 14.20 10.62 36.03 3.66
2690 2721 4.926238 ACTTCTTGTAGAGCTTTGATGTCG 59.074 41.667 0.00 0.00 0.00 4.35
2707 2738 4.066646 TGTCGTTTTGAAGAGATGACCA 57.933 40.909 0.00 0.00 0.00 4.02
2802 2833 8.322906 TCACCTTTCATGTGATAACTTTACTG 57.677 34.615 0.00 0.00 37.80 2.74
2842 2873 3.392616 AGGAATATTGGCCACCTAGTGAG 59.607 47.826 3.88 0.00 35.23 3.51
2854 2885 4.441495 CCACCTAGTGAGTTTGATCGCATA 60.441 45.833 0.00 0.00 35.23 3.14
2922 2953 5.746284 AGAGGTAATGCCCTTTTAGTTCTC 58.254 41.667 0.00 0.00 38.26 2.87
2933 2964 7.669722 TGCCCTTTTAGTTCTCAACTTCATATT 59.330 33.333 0.00 0.00 42.81 1.28
2999 3032 2.041216 AGGTGGAACTATTTGGTCACCC 59.959 50.000 0.00 0.00 35.54 4.61
3015 3048 2.270205 CCCTCATGGAGCAGCGTT 59.730 61.111 0.00 0.00 35.39 4.84
3085 3118 8.868522 TGGAAGACTAATTTCATTCAACTGAT 57.131 30.769 0.00 0.00 0.00 2.90
3156 3189 9.188588 CTACAAATCATTTCCAATATGTGCATC 57.811 33.333 0.00 0.00 0.00 3.91
3251 3284 4.669206 ACAAGAACAATGCCAAACATGA 57.331 36.364 0.00 0.00 39.60 3.07
3282 3315 9.289303 CAGATAACACCAATTAGTTTTGCATAC 57.711 33.333 0.00 0.00 0.00 2.39
3481 3514 0.687920 TTCCGTGGGCATGTGAAGTA 59.312 50.000 0.00 0.00 0.00 2.24
3711 3744 5.609423 CCCCAGAAAATAGAGAGTGATGAG 58.391 45.833 0.00 0.00 0.00 2.90
3722 3755 5.995446 AGAGAGTGATGAGATTAAAACCCC 58.005 41.667 0.00 0.00 0.00 4.95
3742 3775 6.314917 ACCCCTACAAAATCTCAAGTTGATT 58.685 36.000 5.91 0.00 35.88 2.57
3743 3776 6.782494 ACCCCTACAAAATCTCAAGTTGATTT 59.218 34.615 5.91 2.29 43.44 2.17
3775 3808 3.307410 GGATATGATAACCATGACCGCCA 60.307 47.826 0.00 0.00 36.71 5.69
3924 3957 3.391049 AGCAGTAAGGAACAGAAACGTC 58.609 45.455 0.00 0.00 0.00 4.34
3986 4019 3.256631 ACATGTCCAATGGTGCTTCTTTC 59.743 43.478 0.00 0.00 0.00 2.62
3988 4021 2.622942 TGTCCAATGGTGCTTCTTTCAC 59.377 45.455 0.00 0.00 0.00 3.18
3996 4029 2.288395 GGTGCTTCTTTCACATGTTGGG 60.288 50.000 0.00 0.00 36.22 4.12
4109 4142 9.543783 ACTTATGGAGTAAGATTACGATTTTCC 57.456 33.333 0.00 0.32 41.99 3.13
4173 4206 5.539574 CACTCATGCATTATATTTCCCCCAA 59.460 40.000 0.00 0.00 0.00 4.12
4191 4224 9.507381 TTCCCCCAATCAAACCATATTATTTTA 57.493 29.630 0.00 0.00 0.00 1.52
4256 4293 9.774742 GAAAATGTTATGAGTAAAGACACCATC 57.225 33.333 0.00 0.00 0.00 3.51
4261 4298 8.783093 TGTTATGAGTAAAGACACCATCAAAAG 58.217 33.333 0.00 0.00 0.00 2.27
4262 4299 8.999431 GTTATGAGTAAAGACACCATCAAAAGA 58.001 33.333 0.00 0.00 0.00 2.52
4263 4300 9.739276 TTATGAGTAAAGACACCATCAAAAGAT 57.261 29.630 0.00 0.00 0.00 2.40
4264 4301 7.439157 TGAGTAAAGACACCATCAAAAGATG 57.561 36.000 0.00 0.00 0.00 2.90
4403 4440 3.701205 ATTTGAGGCCATGGGAAAAAC 57.299 42.857 15.13 0.00 0.00 2.43
4418 4456 1.704641 AAAACCCCCTCTGAAACTGC 58.295 50.000 0.00 0.00 0.00 4.40
4424 4462 1.542915 CCCCTCTGAAACTGCATGTTG 59.457 52.381 0.00 0.00 39.13 3.33
4473 4511 4.137543 ACTTGACCAGGTTTTGATGAGTC 58.862 43.478 0.00 0.00 0.00 3.36
4562 4600 6.878317 TCTGATCGAACTGTCAAGGATTTAT 58.122 36.000 0.00 0.00 0.00 1.40
4580 4618 2.859165 ATATCAGGCATTACCACGGG 57.141 50.000 0.00 0.00 43.14 5.28
4582 4620 1.920734 ATCAGGCATTACCACGGGCA 61.921 55.000 0.00 0.00 43.14 5.36
4583 4621 1.677300 CAGGCATTACCACGGGCAA 60.677 57.895 0.00 0.00 43.14 4.52
4619 4658 1.747355 CTGACCAAATCATGACCAGGC 59.253 52.381 0.00 0.00 36.48 4.85
4776 4927 4.727507 TCAAAGCTCTCTGAGGTGATAC 57.272 45.455 4.59 0.00 39.62 2.24
4777 4928 4.348486 TCAAAGCTCTCTGAGGTGATACT 58.652 43.478 4.59 0.00 39.62 2.12
4778 4929 5.510430 TCAAAGCTCTCTGAGGTGATACTA 58.490 41.667 4.59 0.00 39.62 1.82
4780 4931 4.098914 AGCTCTCTGAGGTGATACTAGG 57.901 50.000 4.59 0.00 39.04 3.02
4781 4932 3.461831 AGCTCTCTGAGGTGATACTAGGT 59.538 47.826 4.59 0.00 39.04 3.08
4782 4933 3.568007 GCTCTCTGAGGTGATACTAGGTG 59.432 52.174 4.59 0.00 0.00 4.00
4783 4934 4.687494 GCTCTCTGAGGTGATACTAGGTGA 60.687 50.000 4.59 0.00 0.00 4.02
4784 4935 5.441500 CTCTCTGAGGTGATACTAGGTGAA 58.558 45.833 4.59 0.00 0.00 3.18
4785 4936 6.019656 TCTCTGAGGTGATACTAGGTGAAT 57.980 41.667 4.59 0.00 0.00 2.57
4786 4937 6.436027 TCTCTGAGGTGATACTAGGTGAATT 58.564 40.000 4.59 0.00 0.00 2.17
4787 4938 6.322456 TCTCTGAGGTGATACTAGGTGAATTG 59.678 42.308 4.59 0.00 0.00 2.32
4790 4941 7.068348 TCTGAGGTGATACTAGGTGAATTGTAC 59.932 40.741 0.00 0.00 0.00 2.90
4820 4971 5.910637 ATTTATTTTAAGCGCATGCATGG 57.089 34.783 27.34 17.93 46.23 3.66
4880 5033 2.368221 CTCCATGAGATTCTGACTCCCC 59.632 54.545 0.00 0.00 33.95 4.81
4893 5046 2.025981 TGACTCCCCTCATTCATGTTGG 60.026 50.000 0.00 0.00 0.00 3.77
4895 5048 2.291153 ACTCCCCTCATTCATGTTGGTG 60.291 50.000 0.00 0.00 0.00 4.17
4896 5049 0.819582 CCCCTCATTCATGTTGGTGC 59.180 55.000 0.00 0.00 0.00 5.01
4897 5050 0.452987 CCCTCATTCATGTTGGTGCG 59.547 55.000 0.00 0.00 0.00 5.34
4898 5051 0.179156 CCTCATTCATGTTGGTGCGC 60.179 55.000 0.00 0.00 0.00 6.09
4899 5052 0.522626 CTCATTCATGTTGGTGCGCA 59.477 50.000 5.66 5.66 0.00 6.09
4900 5053 0.522626 TCATTCATGTTGGTGCGCAG 59.477 50.000 12.22 0.00 0.00 5.18
4901 5054 0.522626 CATTCATGTTGGTGCGCAGA 59.477 50.000 12.22 0.00 0.00 4.26
4902 5055 1.133598 CATTCATGTTGGTGCGCAGAT 59.866 47.619 12.22 0.00 0.00 2.90
4903 5056 0.804364 TTCATGTTGGTGCGCAGATC 59.196 50.000 12.22 4.05 0.00 2.75
5000 5156 4.261447 GCCGTACCTCACACTTGAATTTTT 60.261 41.667 0.00 0.00 0.00 1.94
5009 5165 6.279882 TCACACTTGAATTTTTGGTTGGATC 58.720 36.000 0.00 0.00 0.00 3.36
5014 5170 7.065563 CACTTGAATTTTTGGTTGGATCAACAA 59.934 33.333 12.06 0.00 45.11 2.83
5061 5222 5.868801 TCTTCTTCAAAAACAAAACAGCCAG 59.131 36.000 0.00 0.00 0.00 4.85
5113 5278 1.006571 GCAATGCAGCAACAGCAGT 60.007 52.632 0.00 0.00 46.36 4.40
5116 5281 2.430382 AATGCAGCAACAGCAGTGCC 62.430 55.000 12.58 0.00 46.36 5.01
5117 5282 4.353437 GCAGCAACAGCAGTGCCC 62.353 66.667 12.58 0.00 0.00 5.36
5118 5283 3.677648 CAGCAACAGCAGTGCCCC 61.678 66.667 12.58 0.00 0.00 5.80
5119 5284 3.894638 AGCAACAGCAGTGCCCCT 61.895 61.111 12.58 0.00 0.00 4.79
5157 5322 2.285083 TGCATACCGTTTGTAGCATCC 58.715 47.619 0.00 0.00 32.38 3.51
5178 5343 3.305094 CCATCATTCACGCTGCATTTTTC 59.695 43.478 0.00 0.00 0.00 2.29
5180 5345 3.567530 TCATTCACGCTGCATTTTTCTG 58.432 40.909 0.00 0.00 0.00 3.02
5182 5347 4.215185 TCATTCACGCTGCATTTTTCTGTA 59.785 37.500 0.00 0.00 0.00 2.74
5263 5456 2.668550 GTGGTGGAACAGGCCGAC 60.669 66.667 0.00 0.00 41.80 4.79
5268 5461 3.998672 GGAACAGGCCGACGGACA 61.999 66.667 24.57 0.00 29.21 4.02
5277 5470 0.802607 GCCGACGGACAAGATGAGAC 60.803 60.000 20.50 0.00 0.00 3.36
5342 5539 2.927856 TGGGATGTGGGTGCGTCT 60.928 61.111 0.00 0.00 0.00 4.18
5454 5651 1.101331 GTGGTCTCGGACGGATAACT 58.899 55.000 0.00 0.00 32.65 2.24
5467 5664 4.517285 ACGGATAACTGTCAGATTGCATT 58.483 39.130 6.91 0.00 0.00 3.56
5470 5682 4.641989 GGATAACTGTCAGATTGCATTGGT 59.358 41.667 6.91 0.00 0.00 3.67
5537 5756 1.262151 GATTGTGTTGTTACCGTGCGT 59.738 47.619 0.00 0.00 0.00 5.24
5549 5768 3.353836 GTGCGTGTTGGTGCCGAT 61.354 61.111 0.00 0.00 0.00 4.18
5587 5807 1.760029 TGCTTCCGGCTATGATGTGTA 59.240 47.619 0.00 0.00 42.39 2.90
5605 5833 3.768215 GTGTAGAGTAGTGTAGGGCCTTT 59.232 47.826 13.45 0.00 0.00 3.11
5606 5834 4.222366 GTGTAGAGTAGTGTAGGGCCTTTT 59.778 45.833 13.45 0.00 0.00 2.27
5607 5835 3.983044 AGAGTAGTGTAGGGCCTTTTG 57.017 47.619 13.45 0.00 0.00 2.44
5608 5836 2.572104 AGAGTAGTGTAGGGCCTTTTGG 59.428 50.000 13.45 0.00 44.18 3.28
5609 5837 2.570302 GAGTAGTGTAGGGCCTTTTGGA 59.430 50.000 13.45 0.00 44.07 3.53
5610 5838 2.983898 AGTAGTGTAGGGCCTTTTGGAA 59.016 45.455 13.45 0.00 44.07 3.53
5650 7252 7.031372 CACAATTTTGTCATGGACTTGGATAG 58.969 38.462 0.00 0.00 39.91 2.08
5819 7421 2.202797 CCCGATGTGCTCGTGAGG 60.203 66.667 0.00 0.00 46.18 3.86
5840 7442 0.505655 GTGACGTACGGCTCAAACAC 59.494 55.000 23.82 6.99 0.00 3.32
5873 7475 1.432251 CGTCGTATCTCCGCCTTGT 59.568 57.895 0.00 0.00 0.00 3.16
5888 7490 2.945440 GCCTTGTATTGCACAGGATGGA 60.945 50.000 0.00 0.00 43.62 3.41
5894 7496 1.896220 TTGCACAGGATGGACTTCAC 58.104 50.000 0.00 0.00 43.62 3.18
5895 7497 1.059098 TGCACAGGATGGACTTCACT 58.941 50.000 0.00 0.00 43.62 3.41
5896 7498 2.256306 TGCACAGGATGGACTTCACTA 58.744 47.619 0.00 0.00 43.62 2.74
5897 7499 2.637382 TGCACAGGATGGACTTCACTAA 59.363 45.455 0.00 0.00 43.62 2.24
5898 7500 3.264193 TGCACAGGATGGACTTCACTAAT 59.736 43.478 0.00 0.00 43.62 1.73
5899 7501 3.873952 GCACAGGATGGACTTCACTAATC 59.126 47.826 0.00 0.00 43.62 1.75
5900 7502 4.623886 GCACAGGATGGACTTCACTAATCA 60.624 45.833 0.00 0.00 43.62 2.57
5901 7503 4.872691 CACAGGATGGACTTCACTAATCAC 59.127 45.833 0.00 0.00 43.62 3.06
5902 7504 4.780021 ACAGGATGGACTTCACTAATCACT 59.220 41.667 0.00 0.00 43.62 3.41
5903 7505 5.958380 ACAGGATGGACTTCACTAATCACTA 59.042 40.000 0.00 0.00 43.62 2.74
5904 7506 6.613271 ACAGGATGGACTTCACTAATCACTAT 59.387 38.462 0.00 0.00 43.62 2.12
5905 7507 7.151308 CAGGATGGACTTCACTAATCACTATC 58.849 42.308 0.00 0.00 0.00 2.08
5906 7508 7.015098 CAGGATGGACTTCACTAATCACTATCT 59.985 40.741 0.00 0.00 0.00 1.98
5907 7509 7.566879 AGGATGGACTTCACTAATCACTATCTT 59.433 37.037 0.00 0.00 0.00 2.40
5908 7510 7.870445 GGATGGACTTCACTAATCACTATCTTC 59.130 40.741 0.00 0.00 0.00 2.87
5909 7511 7.113658 TGGACTTCACTAATCACTATCTTCC 57.886 40.000 0.00 0.00 0.00 3.46
5910 7512 6.897966 TGGACTTCACTAATCACTATCTTCCT 59.102 38.462 0.00 0.00 0.00 3.36
5911 7513 7.068839 TGGACTTCACTAATCACTATCTTCCTC 59.931 40.741 0.00 0.00 0.00 3.71
5912 7514 7.354751 ACTTCACTAATCACTATCTTCCTCC 57.645 40.000 0.00 0.00 0.00 4.30
5913 7515 6.897966 ACTTCACTAATCACTATCTTCCTCCA 59.102 38.462 0.00 0.00 0.00 3.86
5914 7516 7.400339 ACTTCACTAATCACTATCTTCCTCCAA 59.600 37.037 0.00 0.00 0.00 3.53
5915 7517 7.921041 TCACTAATCACTATCTTCCTCCAAT 57.079 36.000 0.00 0.00 0.00 3.16
5916 7518 9.434275 TTCACTAATCACTATCTTCCTCCAATA 57.566 33.333 0.00 0.00 0.00 1.90
5917 7519 8.861086 TCACTAATCACTATCTTCCTCCAATAC 58.139 37.037 0.00 0.00 0.00 1.89
5918 7520 8.642432 CACTAATCACTATCTTCCTCCAATACA 58.358 37.037 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.766591 TGACGATGGGGCATTTAACAAAT 59.233 39.130 0.00 0.00 0.00 2.32
53 54 2.620251 TAAGAGCAATGACGATGGGG 57.380 50.000 0.00 0.00 0.00 4.96
62 63 9.035607 ACTTCGTCATAACTAATAAGAGCAATG 57.964 33.333 0.00 0.00 0.00 2.82
106 107 1.663695 GTGCTGATAAGGGCGCTAAA 58.336 50.000 7.64 0.00 36.23 1.85
131 139 8.682128 AAACATAAAACGTAGCCATGTTTATG 57.318 30.769 20.06 19.21 44.03 1.90
219 227 7.664082 AGAAACAGAGTTTGATACATGACAG 57.336 36.000 0.00 0.00 0.00 3.51
236 249 8.347035 TGGTCTTCCGTTATTAAAAAGAAACAG 58.653 33.333 0.00 0.00 36.30 3.16
355 368 7.615403 TCAGATAGAAAGCATGTAGTGACTTT 58.385 34.615 0.00 0.00 37.09 2.66
573 586 3.625764 TCGCTCATTGTAAAATACAGCCC 59.374 43.478 4.02 0.00 40.24 5.19
640 654 7.449395 CCATCTGAAATCTGGGCAAATCTATAA 59.551 37.037 0.00 0.00 0.00 0.98
720 734 7.042791 CCGCCTTTTTGGTTAATTATGCAATAG 60.043 37.037 0.00 0.00 38.35 1.73
729 743 4.464597 TCATAGCCGCCTTTTTGGTTAATT 59.535 37.500 0.00 0.00 38.35 1.40
893 910 6.449635 TCAATACTTGCAGAACAAACAACT 57.550 33.333 0.00 0.00 37.96 3.16
894 911 7.518731 TTTCAATACTTGCAGAACAAACAAC 57.481 32.000 0.00 0.00 37.96 3.32
895 912 8.602328 CATTTTCAATACTTGCAGAACAAACAA 58.398 29.630 0.00 0.00 37.96 2.83
959 976 6.262193 TCTGTCAGATACAATACGAACACA 57.738 37.500 0.00 0.00 37.74 3.72
1102 1119 6.429385 CAGCTCAAGATGGAACTAAAGTCTTT 59.571 38.462 2.81 2.81 0.00 2.52
1104 1121 5.486526 CAGCTCAAGATGGAACTAAAGTCT 58.513 41.667 0.00 0.00 0.00 3.24
1110 1127 1.134699 CGGCAGCTCAAGATGGAACTA 60.135 52.381 0.00 0.00 31.02 2.24
1167 1184 4.202040 TGACCTCAACAAAAATGCAGTGAG 60.202 41.667 0.00 0.00 0.00 3.51
1194 1211 0.255890 TGGATGGCCCTTACTGAAGC 59.744 55.000 0.00 0.00 35.38 3.86
1200 1217 4.711846 AGAGAAATTTTGGATGGCCCTTAC 59.288 41.667 0.00 0.00 35.38 2.34
1370 1387 1.416401 TCTTCTTCGTGGCAGTCCTTT 59.584 47.619 0.00 0.00 0.00 3.11
1382 1399 0.389166 AGCAGCTCGGTTCTTCTTCG 60.389 55.000 0.00 0.00 0.00 3.79
1436 1453 4.627035 CGTCATCAACATCAGAAGCAACTA 59.373 41.667 0.00 0.00 0.00 2.24
1575 1592 7.011016 CACTGTGTGACAAGTAATAACTGTCAA 59.989 37.037 5.75 0.00 41.31 3.18
1608 1626 9.247861 AGCATCCATAATAACTTGTCTTTTCTT 57.752 29.630 0.00 0.00 0.00 2.52
1609 1627 8.814038 AGCATCCATAATAACTTGTCTTTTCT 57.186 30.769 0.00 0.00 0.00 2.52
1610 1628 9.508567 GAAGCATCCATAATAACTTGTCTTTTC 57.491 33.333 0.00 0.00 0.00 2.29
1611 1629 9.023962 TGAAGCATCCATAATAACTTGTCTTTT 57.976 29.630 0.00 0.00 0.00 2.27
1612 1630 8.462016 GTGAAGCATCCATAATAACTTGTCTTT 58.538 33.333 0.00 0.00 0.00 2.52
2035 2065 6.508030 TCATTTACTGCCCATTAGTCCATA 57.492 37.500 0.00 0.00 0.00 2.74
2214 2244 8.397906 CAGCAGATAGAAGAGACTATAGTATGC 58.602 40.741 4.38 0.00 33.85 3.14
2414 2444 0.255890 TCAGGTAGGGCATGGCTTTC 59.744 55.000 19.78 9.42 0.00 2.62
2480 2510 4.715527 AGAAAGGAAGCAGCAATTCATC 57.284 40.909 0.00 0.00 0.00 2.92
2493 2523 7.654022 TTTTAGCAAAGAGGAAAGAAAGGAA 57.346 32.000 0.00 0.00 0.00 3.36
2520 2551 1.543802 GTCTCCCCTCTCTATCGCATG 59.456 57.143 0.00 0.00 0.00 4.06
2527 2558 0.989602 TGTGACGTCTCCCCTCTCTA 59.010 55.000 17.92 0.00 0.00 2.43
2535 2566 1.813178 TGAGATCTGTGTGACGTCTCC 59.187 52.381 17.92 7.96 35.58 3.71
2583 2614 1.682005 GCCATGCTTAGCCAACCCA 60.682 57.895 0.29 0.00 0.00 4.51
2600 2631 2.656560 AGTGTCTAGACCATGAACGC 57.343 50.000 20.11 0.72 0.00 4.84
2690 2721 5.403466 GCAAACATGGTCATCTCTTCAAAAC 59.597 40.000 0.00 0.00 0.00 2.43
2707 2738 1.708341 AAGGGAGCAACTGCAAACAT 58.292 45.000 4.22 0.00 45.16 2.71
2802 2833 2.844348 TCCTCCTATTTGGAACCAGGTC 59.156 50.000 0.00 0.00 45.63 3.85
2842 2873 4.277257 TGCAGACAATATGCGATCAAAC 57.723 40.909 0.00 0.00 46.87 2.93
2854 2885 2.887152 GTCCTTCAGGTTTGCAGACAAT 59.113 45.455 9.87 0.00 35.21 2.71
2999 3032 1.398390 GTTTAACGCTGCTCCATGAGG 59.602 52.381 0.00 0.00 0.00 3.86
3085 3118 2.346766 ATGCCATCGATGCCAACTAA 57.653 45.000 20.25 0.00 0.00 2.24
3134 3167 9.321562 GAAAGATGCACATATTGGAAATGATTT 57.678 29.630 0.00 0.00 0.00 2.17
3251 3284 7.480760 AAACTAATTGGTGTTATCTGGCATT 57.519 32.000 0.00 0.00 0.00 3.56
3282 3315 6.458751 CCACATGAAACCGAATAGGAAATCAG 60.459 42.308 0.00 0.00 45.00 2.90
3335 3368 9.088987 ACACTTCCACCATTTTAGTTCAAATAT 57.911 29.630 0.00 0.00 0.00 1.28
3481 3514 2.941480 CCATTCCTCATGGCTTAAGCT 58.059 47.619 25.88 5.35 46.59 3.74
3540 3573 8.728596 AATGGCCTGTAGTCTATACTCTTAAT 57.271 34.615 3.32 0.00 37.15 1.40
3541 3574 8.548880 AAATGGCCTGTAGTCTATACTCTTAA 57.451 34.615 3.32 0.00 37.15 1.85
3542 3575 8.548880 AAAATGGCCTGTAGTCTATACTCTTA 57.451 34.615 3.32 0.00 37.15 2.10
3711 3744 8.803235 ACTTGAGATTTTGTAGGGGTTTTAATC 58.197 33.333 0.00 0.00 0.00 1.75
3742 3775 5.830457 TGGTTATCATATCCGCCAATTCAAA 59.170 36.000 0.00 0.00 0.00 2.69
3743 3776 5.380900 TGGTTATCATATCCGCCAATTCAA 58.619 37.500 0.00 0.00 0.00 2.69
3775 3808 1.748122 CAGCGGATGCAGCCTCTTT 60.748 57.895 20.58 0.00 46.23 2.52
3924 3957 3.914426 AGGGCTATTACCAGTTCTGTG 57.086 47.619 0.00 0.00 0.00 3.66
3996 4029 9.516314 GGTTACTGAGAAATTATAAAACATGGC 57.484 33.333 0.00 0.00 0.00 4.40
4261 4298 7.775120 ACATTCCAGAAATGATGTAAACCATC 58.225 34.615 4.86 0.00 46.54 3.51
4262 4299 7.722949 ACATTCCAGAAATGATGTAAACCAT 57.277 32.000 4.86 0.00 46.54 3.55
4263 4300 7.667635 TGTACATTCCAGAAATGATGTAAACCA 59.332 33.333 4.86 0.00 46.54 3.67
4264 4301 8.050778 TGTACATTCCAGAAATGATGTAAACC 57.949 34.615 4.86 0.00 46.54 3.27
4327 4364 4.527564 AGCGACGATTTTTGTTTCTCAAG 58.472 39.130 0.00 0.00 37.35 3.02
4403 4440 0.038744 ACATGCAGTTTCAGAGGGGG 59.961 55.000 0.00 0.00 0.00 5.40
4405 4442 2.227388 GACAACATGCAGTTTCAGAGGG 59.773 50.000 0.00 0.00 38.74 4.30
4418 4456 5.700832 TGTTTCTGGCTAACTAGACAACATG 59.299 40.000 0.00 0.00 41.63 3.21
4424 4462 4.315803 TGCTTGTTTCTGGCTAACTAGAC 58.684 43.478 0.00 0.00 32.47 2.59
4473 4511 8.483218 CACTATTCGACTAAATCAATAGCACAG 58.517 37.037 0.00 0.00 34.77 3.66
4535 4573 3.056536 TCCTTGACAGTTCGATCAGAAGG 60.057 47.826 0.00 0.00 39.95 3.46
4542 4580 7.875041 CCTGATATAAATCCTTGACAGTTCGAT 59.125 37.037 0.00 0.00 0.00 3.59
4562 4600 0.107831 GCCCGTGGTAATGCCTGATA 59.892 55.000 0.00 0.00 38.35 2.15
4590 4628 7.016563 TGGTCATGATTTGGTCAGCTATAGTAT 59.983 37.037 0.00 0.00 40.92 2.12
4619 4658 4.931002 CCACTTGCTTCATGTTTTTATGGG 59.069 41.667 0.00 0.00 0.00 4.00
4651 4690 5.068198 AGGTCAAAAGGCACAAGCATATATG 59.932 40.000 8.45 8.45 44.61 1.78
4737 4777 9.674824 GAGCTTTGATGTCAAGATAATTAATGG 57.325 33.333 0.00 0.00 37.15 3.16
4764 4915 5.958380 ACAATTCACCTAGTATCACCTCAGA 59.042 40.000 0.00 0.00 0.00 3.27
4790 4941 9.530129 GCATGCGCTTAAAATAAATACTACTAG 57.470 33.333 9.73 0.00 34.30 2.57
4798 4949 4.211794 GCCATGCATGCGCTTAAAATAAAT 59.788 37.500 21.69 0.00 39.64 1.40
4801 4952 2.361757 AGCCATGCATGCGCTTAAAATA 59.638 40.909 27.05 0.00 39.64 1.40
4820 4971 6.973229 ATAATCTTTCAACAATGCCAAAGC 57.027 33.333 0.00 0.00 40.48 3.51
4880 5033 0.522626 TGCGCACCAACATGAATGAG 59.477 50.000 5.66 0.00 0.00 2.90
4893 5046 3.589881 GGGCCATGATCTGCGCAC 61.590 66.667 5.66 0.00 39.90 5.34
4895 5048 3.285215 CTGGGCCATGATCTGCGC 61.285 66.667 6.72 0.00 40.49 6.09
4896 5049 1.890979 GACTGGGCCATGATCTGCG 60.891 63.158 6.72 0.00 0.00 5.18
4897 5050 0.106819 AAGACTGGGCCATGATCTGC 60.107 55.000 6.72 0.00 0.00 4.26
4898 5051 1.211212 TCAAGACTGGGCCATGATCTG 59.789 52.381 6.72 1.27 0.00 2.90
4899 5052 1.588239 TCAAGACTGGGCCATGATCT 58.412 50.000 6.72 8.06 0.00 2.75
4900 5053 2.228059 CATCAAGACTGGGCCATGATC 58.772 52.381 15.69 10.27 0.00 2.92
4901 5054 1.753141 GCATCAAGACTGGGCCATGAT 60.753 52.381 6.72 10.92 0.00 2.45
4902 5055 0.394762 GCATCAAGACTGGGCCATGA 60.395 55.000 6.72 8.61 0.00 3.07
4903 5056 0.395311 AGCATCAAGACTGGGCCATG 60.395 55.000 6.72 1.70 0.00 3.66
4948 5104 3.818787 CCTGCGTCAATGCTGGGC 61.819 66.667 11.22 0.00 46.71 5.36
5000 5156 1.327303 GGCTGTTGTTGATCCAACCA 58.673 50.000 11.01 0.00 42.96 3.67
5009 5165 3.365265 GGAGGGCGGCTGTTGTTG 61.365 66.667 9.56 0.00 0.00 3.33
5014 5170 1.603739 GAAAAAGGAGGGCGGCTGT 60.604 57.895 9.56 0.00 0.00 4.40
5061 5222 2.328099 CGCTGGTGAAACTGGAGCC 61.328 63.158 0.00 0.00 36.74 4.70
5092 5257 1.006571 GCTGTTGCTGCATTGCTGT 60.007 52.632 15.71 0.00 36.03 4.40
5116 5281 1.509548 AATTGGTGGGTGAGGGAGGG 61.510 60.000 0.00 0.00 0.00 4.30
5117 5282 0.409484 AAATTGGTGGGTGAGGGAGG 59.591 55.000 0.00 0.00 0.00 4.30
5118 5283 1.895131 CAAAATTGGTGGGTGAGGGAG 59.105 52.381 0.00 0.00 0.00 4.30
5119 5284 2.008242 CAAAATTGGTGGGTGAGGGA 57.992 50.000 0.00 0.00 0.00 4.20
5157 5322 4.031314 CAGAAAAATGCAGCGTGAATGATG 59.969 41.667 0.00 0.00 0.00 3.07
5178 5343 2.304401 TGCGCCACGACGTTTACAG 61.304 57.895 4.18 0.00 34.88 2.74
5180 5345 2.169327 GTGCGCCACGACGTTTAC 59.831 61.111 4.18 0.00 34.88 2.01
5263 5456 2.520979 GTTCTCGTCTCATCTTGTCCG 58.479 52.381 0.00 0.00 0.00 4.79
5277 5470 2.735134 CCTAAAGGTCAAACGGTTCTCG 59.265 50.000 0.00 0.00 45.88 4.04
5342 5539 3.931247 CGACGGGGGTGGTTGACA 61.931 66.667 0.00 0.00 0.00 3.58
5399 5596 2.954989 GCCCTACTACCACTACCACTAC 59.045 54.545 0.00 0.00 0.00 2.73
5400 5597 2.582172 TGCCCTACTACCACTACCACTA 59.418 50.000 0.00 0.00 0.00 2.74
5401 5598 1.360162 TGCCCTACTACCACTACCACT 59.640 52.381 0.00 0.00 0.00 4.00
5402 5599 1.856629 TGCCCTACTACCACTACCAC 58.143 55.000 0.00 0.00 0.00 4.16
5403 5600 2.181975 GTTGCCCTACTACCACTACCA 58.818 52.381 0.00 0.00 0.00 3.25
5404 5601 2.093816 GTGTTGCCCTACTACCACTACC 60.094 54.545 0.00 0.00 0.00 3.18
5454 5651 1.805943 CACGACCAATGCAATCTGACA 59.194 47.619 0.00 0.00 0.00 3.58
5537 5756 2.047655 GGTCGATCGGCACCAACA 60.048 61.111 22.85 0.00 32.33 3.33
5548 5767 1.078848 GCAAGCAGGTGAGGTCGAT 60.079 57.895 0.00 0.00 0.00 3.59
5549 5768 2.210013 AGCAAGCAGGTGAGGTCGA 61.210 57.895 0.00 0.00 0.00 4.20
5587 5807 2.572104 CCAAAAGGCCCTACACTACTCT 59.428 50.000 0.00 0.00 0.00 3.24
5605 5833 2.218603 GTTCGAGCTTCCAAGTTCCAA 58.781 47.619 0.00 0.00 33.29 3.53
5606 5834 1.140052 TGTTCGAGCTTCCAAGTTCCA 59.860 47.619 0.00 0.00 33.29 3.53
5607 5835 1.531578 GTGTTCGAGCTTCCAAGTTCC 59.468 52.381 0.00 0.00 33.29 3.62
5608 5836 2.210116 TGTGTTCGAGCTTCCAAGTTC 58.790 47.619 0.00 0.00 33.51 3.01
5609 5837 2.325583 TGTGTTCGAGCTTCCAAGTT 57.674 45.000 0.00 0.00 0.00 2.66
5610 5838 2.325583 TTGTGTTCGAGCTTCCAAGT 57.674 45.000 0.00 0.00 0.00 3.16
5650 7252 2.265073 TACGTTAGCCGGCGGTGTAC 62.265 60.000 28.82 20.00 42.24 2.90
5747 7349 3.531059 TCTATGCTATGCCCCAGGTTAT 58.469 45.455 0.00 0.00 0.00 1.89
5748 7350 2.984672 TCTATGCTATGCCCCAGGTTA 58.015 47.619 0.00 0.00 0.00 2.85
5749 7351 1.819753 TCTATGCTATGCCCCAGGTT 58.180 50.000 0.00 0.00 0.00 3.50
5782 7384 5.666718 TCGGGGAAACTAATAAACCATCCTA 59.333 40.000 0.00 0.00 0.00 2.94
5791 7393 4.448210 GAGCACATCGGGGAAACTAATAA 58.552 43.478 0.00 0.00 0.00 1.40
5792 7394 4.067972 GAGCACATCGGGGAAACTAATA 57.932 45.455 0.00 0.00 0.00 0.98
5793 7395 2.919228 GAGCACATCGGGGAAACTAAT 58.081 47.619 0.00 0.00 0.00 1.73
5865 7467 0.676466 TCCTGTGCAATACAAGGCGG 60.676 55.000 0.00 0.00 39.20 6.13
5866 7468 1.064505 CATCCTGTGCAATACAAGGCG 59.935 52.381 0.00 0.00 39.20 5.52
5867 7469 1.406539 CCATCCTGTGCAATACAAGGC 59.593 52.381 0.00 0.00 39.20 4.35
5873 7475 3.264193 AGTGAAGTCCATCCTGTGCAATA 59.736 43.478 0.00 0.00 0.00 1.90
5888 7490 6.897966 TGGAGGAAGATAGTGATTAGTGAAGT 59.102 38.462 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.