Multiple sequence alignment - TraesCS6B01G211800

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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 TraesCS6B01G211800 chr6B 100.000 6203 0 0 1 6203 280044932 280051134 0.000000e+00 11455.0
1 TraesCS6B01G211800 chr6B 96.499 857 29 1 74 929 657252752 657253608 0.000000e+00 1415.0
2 TraesCS6B01G211800 chr6B 96.163 860 32 1 74 932 289779870 289779011 0.000000e+00 1404.0
3 TraesCS6B01G211800 chr6B 100.000 75 0 0 1 75 24996895 24996969 8.380000e-29 139.0
4 TraesCS6B01G211800 chr6B 84.733 131 15 2 1645 1771 570132201 570132072 6.530000e-25 126.0
5 TraesCS6B01G211800 chr6A 92.889 5372 240 68 927 6203 215532079 215526755 0.000000e+00 7673.0
6 TraesCS6B01G211800 chr6D 97.093 1789 35 3 930 2701 157163990 157165778 0.000000e+00 3000.0
7 TraesCS6B01G211800 chr6D 93.167 2005 59 33 3436 5395 157166524 157168495 0.000000e+00 2872.0
8 TraesCS6B01G211800 chr6D 91.521 401 9 4 2728 3110 157165778 157166171 4.260000e-146 529.0
9 TraesCS6B01G211800 chr6D 91.946 298 11 7 3141 3425 157166171 157166468 7.490000e-109 405.0
10 TraesCS6B01G211800 chr1B 96.963 856 26 0 74 929 365450962 365450107 0.000000e+00 1437.0
11 TraesCS6B01G211800 chr2B 96.495 856 30 0 74 929 724751626 724752481 0.000000e+00 1415.0
12 TraesCS6B01G211800 chr2B 100.000 76 0 0 1 76 724751177 724751252 2.330000e-29 141.0
13 TraesCS6B01G211800 chr2B 100.000 75 0 0 1 75 732021519 732021593 8.380000e-29 139.0
14 TraesCS6B01G211800 chr5B 96.495 856 28 2 74 929 553182896 553182043 0.000000e+00 1413.0
15 TraesCS6B01G211800 chr5B 100.000 75 0 0 1 75 551463626 551463700 8.380000e-29 139.0
16 TraesCS6B01G211800 chr4B 96.495 856 29 1 74 929 29628461 29627607 0.000000e+00 1413.0
17 TraesCS6B01G211800 chr4B 96.379 856 30 1 74 929 611023880 611023026 0.000000e+00 1408.0
18 TraesCS6B01G211800 chr4B 96.262 856 31 1 74 929 29622542 29621688 0.000000e+00 1402.0
19 TraesCS6B01G211800 chr4B 98.684 76 1 0 1 76 204402042 204402117 1.080000e-27 135.0
20 TraesCS6B01G211800 chr4B 97.468 79 2 0 1 79 419821215 419821137 1.080000e-27 135.0
21 TraesCS6B01G211800 chr4B 98.684 76 1 0 1 76 493531915 493531990 1.080000e-27 135.0
22 TraesCS6B01G211800 chr4B 98.684 76 1 0 1 76 656971455 656971530 1.080000e-27 135.0
23 TraesCS6B01G211800 chr4A 96.145 856 33 0 74 929 660466165 660465310 0.000000e+00 1399.0
24 TraesCS6B01G211800 chr7D 75.978 716 151 17 4060 4765 459872774 459873478 3.560000e-92 350.0
25 TraesCS6B01G211800 chr7D 96.970 33 1 0 5489 5521 45001531 45001563 8.690000e-04 56.5
26 TraesCS6B01G211800 chr7A 75.524 715 154 18 4060 4764 539652770 539652067 1.290000e-86 331.0
27 TraesCS6B01G211800 chr7A 100.000 31 0 0 6173 6203 230891957 230891927 2.420000e-04 58.4
28 TraesCS6B01G211800 chr7B 75.522 719 149 22 4060 4765 482175193 482175897 1.670000e-85 327.0
29 TraesCS6B01G211800 chrUn 98.734 79 1 0 1 79 47879039 47878961 2.330000e-29 141.0
30 TraesCS6B01G211800 chr2D 88.406 69 6 2 5454 5521 595155845 595155778 1.430000e-11 82.4
31 TraesCS6B01G211800 chr5D 88.889 63 7 0 5454 5516 482005490 482005428 1.850000e-10 78.7
32 TraesCS6B01G211800 chr3B 91.304 46 4 0 6156 6201 597860577 597860622 5.190000e-06 63.9
33 TraesCS6B01G211800 chr3A 100.000 31 0 0 6166 6196 203631681 203631651 2.420000e-04 58.4
34 TraesCS6B01G211800 chr1A 100.000 28 0 0 5494 5521 5827553 5827526 1.100000e-02 52.8


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 TraesCS6B01G211800 chr6B 280044932 280051134 6202 False 11455.0 11455 100.00000 1 6203 1 chr6B.!!$F2 6202
1 TraesCS6B01G211800 chr6B 657252752 657253608 856 False 1415.0 1415 96.49900 74 929 1 chr6B.!!$F3 855
2 TraesCS6B01G211800 chr6B 289779011 289779870 859 True 1404.0 1404 96.16300 74 932 1 chr6B.!!$R1 858
3 TraesCS6B01G211800 chr6A 215526755 215532079 5324 True 7673.0 7673 92.88900 927 6203 1 chr6A.!!$R1 5276
4 TraesCS6B01G211800 chr6D 157163990 157168495 4505 False 1701.5 3000 93.43175 930 5395 4 chr6D.!!$F1 4465
5 TraesCS6B01G211800 chr1B 365450107 365450962 855 True 1437.0 1437 96.96300 74 929 1 chr1B.!!$R1 855
6 TraesCS6B01G211800 chr2B 724751177 724752481 1304 False 778.0 1415 98.24750 1 929 2 chr2B.!!$F2 928
7 TraesCS6B01G211800 chr5B 553182043 553182896 853 True 1413.0 1413 96.49500 74 929 1 chr5B.!!$R1 855
8 TraesCS6B01G211800 chr4B 29627607 29628461 854 True 1413.0 1413 96.49500 74 929 1 chr4B.!!$R2 855
9 TraesCS6B01G211800 chr4B 611023026 611023880 854 True 1408.0 1408 96.37900 74 929 1 chr4B.!!$R4 855
10 TraesCS6B01G211800 chr4B 29621688 29622542 854 True 1402.0 1402 96.26200 74 929 1 chr4B.!!$R1 855
11 TraesCS6B01G211800 chr4A 660465310 660466165 855 True 1399.0 1399 96.14500 74 929 1 chr4A.!!$R1 855
12 TraesCS6B01G211800 chr7D 459872774 459873478 704 False 350.0 350 75.97800 4060 4765 1 chr7D.!!$F2 705
13 TraesCS6B01G211800 chr7A 539652067 539652770 703 True 331.0 331 75.52400 4060 4764 1 chr7A.!!$R2 704
14 TraesCS6B01G211800 chr7B 482175193 482175897 704 False 327.0 327 75.52200 4060 4765 1 chr7B.!!$F1 705

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
938 1317 1.415659 CTGGAGATGCCTAAGGACCTG 59.584 57.143 0.0 0.00 37.63 4.00 F
1434 1828 1.195115 TTGGCGAGGAGTATGAGCTT 58.805 50.000 0.0 0.00 0.00 3.74 F
3000 3426 1.217882 AGGTTTCTTGTCTTGCGTCG 58.782 50.000 0.0 0.00 0.00 5.12 F
3719 4234 0.037512 TATTTTTCCGCCGGACGTGA 60.038 50.000 4.7 5.54 41.42 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 2264 0.245266 TCGCCTTCAATACGTCTGCA 59.755 50.000 0.00 0.0 0.00 4.41 R
3413 3852 1.339929 TGCTGCTCTCTGTTCGTGTAA 59.660 47.619 0.00 0.0 0.00 2.41 R
4502 5036 0.037326 ACATGGTGATCAACGCGTCT 60.037 50.000 14.44 0.0 0.00 4.18 R
5395 5953 0.040781 AAACGAACGTTCATTGGCGG 60.041 50.000 26.71 11.7 37.35 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
690 1068 2.025359 GATGCGAGGGAAAAGCGTCG 62.025 60.000 0.00 0.00 37.20 5.12
846 1225 4.371975 CGAAAAACGGGCTCCTGA 57.628 55.556 1.01 0.00 38.46 3.86
938 1317 1.415659 CTGGAGATGCCTAAGGACCTG 59.584 57.143 0.00 0.00 37.63 4.00
1075 1469 1.538666 CCCTCCCCAGCCATAAAGG 59.461 63.158 0.00 0.00 41.84 3.11
1396 1790 1.734477 CAGTCCGAGCTCAACCACG 60.734 63.158 15.40 0.00 0.00 4.94
1434 1828 1.195115 TTGGCGAGGAGTATGAGCTT 58.805 50.000 0.00 0.00 0.00 3.74
1537 1931 1.678970 GTGCACCCCCTGGTTGATC 60.679 63.158 5.22 0.00 44.75 2.92
1551 1945 5.336213 CCTGGTTGATCTGTGAGGAATTTTG 60.336 44.000 0.00 0.00 0.00 2.44
1627 2021 3.544684 TCAGTGAAGCAAAAGCTCAAGA 58.455 40.909 0.00 0.00 0.00 3.02
1650 2044 1.427072 ATTATCTTGGCCTCCCGGGG 61.427 60.000 23.50 6.77 35.12 5.73
1867 2261 6.596888 TGTCAGATTTCATTCTTGATCCTGAC 59.403 38.462 0.00 0.00 43.71 3.51
1870 2264 7.832685 TCAGATTTCATTCTTGATCCTGACAAT 59.167 33.333 0.00 0.00 32.17 2.71
1914 2308 8.877864 AAAATTCTTGTGATGGAGGTATTACA 57.122 30.769 0.00 0.00 0.00 2.41
1919 2313 7.275183 TCTTGTGATGGAGGTATTACATCTTG 58.725 38.462 8.26 0.00 41.12 3.02
1967 2361 9.908152 AACTTCCATTTTATTAACAGTAGCAAC 57.092 29.630 0.00 0.00 0.00 4.17
2097 2492 3.129287 AGCTGCAATTAAACGAATCCTGG 59.871 43.478 1.02 0.00 0.00 4.45
2194 2589 6.035368 TCCTATTATTGATCTGCTGAGCTC 57.965 41.667 6.82 6.82 0.00 4.09
2321 2726 7.912056 TTGTCTGTCATAGGAAAGAAAGATG 57.088 36.000 0.00 0.00 39.11 2.90
2692 3099 3.865011 TGTGACAAAGCACAACATGTT 57.135 38.095 4.92 4.92 45.08 2.71
2706 3113 6.145858 GCACAACATGTTGATGATGCTAAAAA 59.854 34.615 38.30 0.00 42.93 1.94
2770 3177 6.015940 GCTCTGTGAAAATCCCCTATATTTGG 60.016 42.308 0.00 0.00 0.00 3.28
2837 3244 4.155709 TCATCAGACATCCAGACCTATCC 58.844 47.826 0.00 0.00 0.00 2.59
2838 3245 3.981516 TCAGACATCCAGACCTATCCT 57.018 47.619 0.00 0.00 0.00 3.24
2839 3246 4.271807 TCAGACATCCAGACCTATCCTT 57.728 45.455 0.00 0.00 0.00 3.36
2840 3247 4.624913 TCAGACATCCAGACCTATCCTTT 58.375 43.478 0.00 0.00 0.00 3.11
2841 3248 4.651503 TCAGACATCCAGACCTATCCTTTC 59.348 45.833 0.00 0.00 0.00 2.62
2896 3304 9.255304 CAGATTCCTAATACTAGAGTTGCTTTC 57.745 37.037 0.00 0.00 0.00 2.62
2995 3421 7.540055 GCATCTGAAATTAGGTTTCTTGTCTTG 59.460 37.037 2.67 0.00 45.22 3.02
3000 3426 1.217882 AGGTTTCTTGTCTTGCGTCG 58.782 50.000 0.00 0.00 0.00 5.12
3009 3435 2.658285 TGTCTTGCGTCGAAACTAGAC 58.342 47.619 17.69 17.69 35.41 2.59
3036 3462 7.360113 ACAAAATGTCTGTATTTTTCACCCT 57.640 32.000 0.00 0.00 37.97 4.34
3092 3518 5.281314 AGGTTCTTGACATGTCCCTAGTAT 58.719 41.667 22.85 2.07 0.00 2.12
3120 3546 7.949690 ATTCATCTGGAATTCTGTGAAATGA 57.050 32.000 5.23 4.37 43.76 2.57
3126 3552 6.373495 TCTGGAATTCTGTGAAATGATGACTG 59.627 38.462 5.23 0.00 0.00 3.51
3142 3568 5.527214 TGATGACTGGTTTAGTTGAGTGTTG 59.473 40.000 0.00 0.00 40.53 3.33
3250 3676 4.868067 ACAAGCTGCATTTCTTTCTGAAG 58.132 39.130 1.02 0.00 35.89 3.02
3303 3731 2.342910 ACAAGAGCGGTTACAGTACG 57.657 50.000 0.00 0.00 0.00 3.67
3385 3818 6.451393 CGAGGAAGAAGAAGAAGAAGAAGAA 58.549 40.000 0.00 0.00 0.00 2.52
3389 3822 8.150296 AGGAAGAAGAAGAAGAAGAAGAAGAAG 58.850 37.037 0.00 0.00 0.00 2.85
3393 3826 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
3395 3828 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
3396 3829 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
3397 3830 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
3399 3832 9.898152 AGAAGAAGAAGAAGAAGAAGAAGAAAA 57.102 29.630 0.00 0.00 0.00 2.29
3401 3834 8.153479 AGAAGAAGAAGAAGAAGAAGAAAAGC 57.847 34.615 0.00 0.00 0.00 3.51
3403 3836 7.872113 AGAAGAAGAAGAAGAAGAAAAGCAA 57.128 32.000 0.00 0.00 0.00 3.91
3413 3852 8.401490 AGAAGAAGAAAAGCAAGTACATTGAT 57.599 30.769 8.63 0.85 41.83 2.57
3444 3928 0.264359 AGAGCAGCAGACCCTCCTAT 59.736 55.000 0.00 0.00 0.00 2.57
3452 3936 3.142977 AGCAGACCCTCCTATATTCCTCA 59.857 47.826 0.00 0.00 0.00 3.86
3573 4088 1.133792 GCTTGGCAGGTATGGTATGGT 60.134 52.381 0.00 0.00 0.00 3.55
3574 4089 2.105821 GCTTGGCAGGTATGGTATGGTA 59.894 50.000 0.00 0.00 0.00 3.25
3575 4090 3.807209 GCTTGGCAGGTATGGTATGGTAG 60.807 52.174 0.00 0.00 0.00 3.18
3576 4091 2.334977 TGGCAGGTATGGTATGGTAGG 58.665 52.381 0.00 0.00 0.00 3.18
3577 4092 1.628846 GGCAGGTATGGTATGGTAGGG 59.371 57.143 0.00 0.00 0.00 3.53
3672 4187 2.362120 CCCTGGCTTGGGCTTGAG 60.362 66.667 3.38 0.00 40.84 3.02
3719 4234 0.037512 TATTTTTCCGCCGGACGTGA 60.038 50.000 4.70 5.54 41.42 4.35
3725 4240 2.180769 CGCCGGACGTGATGAAGA 59.819 61.111 5.05 0.00 36.87 2.87
3819 4334 2.743928 CTTGGTCGCCTGCTCCAC 60.744 66.667 3.14 0.00 0.00 4.02
3820 4335 4.680237 TTGGTCGCCTGCTCCACG 62.680 66.667 3.14 0.00 0.00 4.94
3822 4337 4.681978 GGTCGCCTGCTCCACGTT 62.682 66.667 0.00 0.00 0.00 3.99
3824 4339 2.664851 TCGCCTGCTCCACGTTTG 60.665 61.111 0.00 0.00 0.00 2.93
3825 4340 2.664851 CGCCTGCTCCACGTTTGA 60.665 61.111 0.00 0.00 0.00 2.69
3865 4395 9.557061 TTTGAATTGATGATTTGATTTGAACCA 57.443 25.926 0.00 0.00 0.00 3.67
3866 4396 9.727859 TTGAATTGATGATTTGATTTGAACCAT 57.272 25.926 0.00 0.00 0.00 3.55
3867 4397 9.157104 TGAATTGATGATTTGATTTGAACCATG 57.843 29.630 0.00 0.00 0.00 3.66
3868 4398 9.158233 GAATTGATGATTTGATTTGAACCATGT 57.842 29.630 0.00 0.00 0.00 3.21
3869 4399 9.509956 AATTGATGATTTGATTTGAACCATGTT 57.490 25.926 0.00 0.00 0.00 2.71
3871 4401 6.874664 TGATGATTTGATTTGAACCATGTTGG 59.125 34.615 0.00 0.00 45.02 3.77
3872 4402 5.549347 TGATTTGATTTGAACCATGTTGGG 58.451 37.500 0.00 0.00 43.37 4.12
3873 4403 5.071519 TGATTTGATTTGAACCATGTTGGGT 59.928 36.000 0.00 0.00 42.68 4.51
3874 4404 4.333913 TTGATTTGAACCATGTTGGGTG 57.666 40.909 0.00 0.00 37.76 4.61
3875 4405 2.632028 TGATTTGAACCATGTTGGGTGG 59.368 45.455 0.00 0.00 37.76 4.61
3876 4406 2.461300 TTTGAACCATGTTGGGTGGA 57.539 45.000 0.00 0.00 37.76 4.02
3877 4407 2.692709 TTGAACCATGTTGGGTGGAT 57.307 45.000 0.00 0.00 37.76 3.41
3879 4409 3.364460 TGAACCATGTTGGGTGGATAG 57.636 47.619 0.00 0.00 37.76 2.08
3881 4411 3.527253 TGAACCATGTTGGGTGGATAGAT 59.473 43.478 0.00 0.00 37.76 1.98
3882 4412 3.582998 ACCATGTTGGGTGGATAGATG 57.417 47.619 0.00 0.00 43.37 2.90
3884 4414 4.044308 ACCATGTTGGGTGGATAGATGTA 58.956 43.478 0.00 0.00 43.37 2.29
3885 4415 4.665009 ACCATGTTGGGTGGATAGATGTAT 59.335 41.667 0.00 0.00 43.37 2.29
3886 4416 5.221925 ACCATGTTGGGTGGATAGATGTATC 60.222 44.000 1.18 1.18 43.37 2.24
3912 4446 0.841289 AGGAGGAGGAGAGGACGTAG 59.159 60.000 0.00 0.00 0.00 3.51
3913 4447 0.179012 GGAGGAGGAGAGGACGTAGG 60.179 65.000 0.00 0.00 0.00 3.18
3914 4448 0.547553 GAGGAGGAGAGGACGTAGGT 59.452 60.000 0.00 0.00 0.00 3.08
3915 4449 1.767681 GAGGAGGAGAGGACGTAGGTA 59.232 57.143 0.00 0.00 0.00 3.08
4128 4662 0.617413 CTGCATCACCTTGTCCTCCT 59.383 55.000 0.00 0.00 0.00 3.69
4129 4663 0.615331 TGCATCACCTTGTCCTCCTC 59.385 55.000 0.00 0.00 0.00 3.71
4135 4669 0.547954 ACCTTGTCCTCCTCCTTCCC 60.548 60.000 0.00 0.00 0.00 3.97
4136 4670 0.547712 CCTTGTCCTCCTCCTTCCCA 60.548 60.000 0.00 0.00 0.00 4.37
4140 4674 1.075226 TCCTCCTCCTTCCCATCGG 60.075 63.158 0.00 0.00 0.00 4.18
4253 4787 2.808543 GTCCTCGCAATTATCCATGGAC 59.191 50.000 18.99 1.61 36.42 4.02
4502 5036 2.898612 GCTCTGGATGATGATCTCCTGA 59.101 50.000 14.68 14.68 37.22 3.86
4526 5060 1.656652 CGTTGATCACCATGTCCCTC 58.343 55.000 0.00 0.00 0.00 4.30
4622 5156 3.598715 TCGTTGGCGTCGGTCACT 61.599 61.111 0.00 0.00 39.49 3.41
4774 5308 2.744709 CGGGCCCGTGTACTTTGG 60.745 66.667 36.64 3.38 34.35 3.28
4796 5330 3.612004 GCTTCTTCGACTTCTTCTCCGAA 60.612 47.826 0.00 0.00 38.49 4.30
4797 5331 4.739195 CTTCTTCGACTTCTTCTCCGAAT 58.261 43.478 0.00 0.00 39.76 3.34
4829 5363 2.184579 GGGCTAGTCGACCTGCAC 59.815 66.667 24.90 20.49 38.04 4.57
4899 5433 2.351060 CCACTCACTCGCTACAACGTAA 60.351 50.000 0.00 0.00 0.00 3.18
4900 5434 2.655474 CACTCACTCGCTACAACGTAAC 59.345 50.000 0.00 0.00 0.00 2.50
4901 5435 2.551459 ACTCACTCGCTACAACGTAACT 59.449 45.455 0.00 0.00 0.00 2.24
4902 5436 3.748048 ACTCACTCGCTACAACGTAACTA 59.252 43.478 0.00 0.00 0.00 2.24
4903 5437 4.070581 TCACTCGCTACAACGTAACTAC 57.929 45.455 0.00 0.00 0.00 2.73
4905 5439 3.844657 CACTCGCTACAACGTAACTACAG 59.155 47.826 0.00 0.00 0.00 2.74
4906 5440 3.499918 ACTCGCTACAACGTAACTACAGT 59.500 43.478 0.00 0.00 0.00 3.55
4907 5441 4.690748 ACTCGCTACAACGTAACTACAGTA 59.309 41.667 0.00 0.00 0.00 2.74
4908 5442 5.163913 ACTCGCTACAACGTAACTACAGTAG 60.164 44.000 6.00 6.00 33.04 2.57
4987 5538 3.723348 GCGCGGTTGAAGTGGTCC 61.723 66.667 8.83 0.00 0.00 4.46
5222 5780 0.179111 CCTATCGCTTGCGTGGAAGA 60.179 55.000 14.70 0.00 0.00 2.87
5225 5783 0.037326 ATCGCTTGCGTGGAAGAGAA 60.037 50.000 14.70 0.00 35.70 2.87
5253 5811 3.890147 GGCCTATATACGTAGGAGGATGG 59.110 52.174 19.31 8.63 43.27 3.51
5331 5889 7.008021 AGGAGACAAATTGTTTTGCCAATAT 57.992 32.000 0.00 0.00 45.01 1.28
5334 5892 8.016801 GGAGACAAATTGTTTTGCCAATATTTG 58.983 33.333 0.00 0.00 45.01 2.32
5395 5953 1.523758 AGACAAGGGAACGCATGAAC 58.476 50.000 0.00 0.00 0.00 3.18
5396 5954 0.521735 GACAAGGGAACGCATGAACC 59.478 55.000 0.00 0.00 0.00 3.62
5414 5974 0.040781 CCGCCAATGAACGTTCGTTT 60.041 50.000 28.63 18.99 34.34 3.60
5418 5978 2.646250 CCAATGAACGTTCGTTTGGTC 58.354 47.619 33.48 12.07 37.85 4.02
5426 5986 1.189446 CGTTCGTTTGGTCGACTCAAG 59.811 52.381 16.46 7.44 39.58 3.02
5438 5998 4.501058 GGTCGACTCAAGGTTACTTTGAGT 60.501 45.833 32.79 32.79 42.42 3.41
5439 5999 5.048507 GTCGACTCAAGGTTACTTTGAGTT 58.951 41.667 32.74 21.34 41.15 3.01
5477 6037 2.171027 ACGTTACAACCAAAGTCCCTCA 59.829 45.455 0.00 0.00 0.00 3.86
5481 6041 2.586425 ACAACCAAAGTCCCTCACATG 58.414 47.619 0.00 0.00 0.00 3.21
5500 6060 2.215907 GCACGAGCATACACTCATCT 57.784 50.000 0.00 0.00 41.58 2.90
5515 6075 3.181490 ACTCATCTCTATAAACGCACGCA 60.181 43.478 0.00 0.00 0.00 5.24
5516 6076 3.977427 TCATCTCTATAAACGCACGCAT 58.023 40.909 0.00 0.00 0.00 4.73
5517 6077 3.735746 TCATCTCTATAAACGCACGCATG 59.264 43.478 0.00 0.00 0.00 4.06
5542 6102 2.163810 ACGCACACCCTACCCTATTA 57.836 50.000 0.00 0.00 0.00 0.98
5625 6185 5.774498 AAGTTTTACTCCCAAGAGCAAAG 57.226 39.130 0.00 0.00 44.65 2.77
5630 6190 1.215423 ACTCCCAAGAGCAAAGGTTGT 59.785 47.619 0.00 0.00 44.65 3.32
5711 6271 6.152154 TGCTTTTTGTAACCTTATCTTAGGGC 59.848 38.462 0.00 0.00 39.76 5.19
5727 6287 0.106521 GGGCATGTTTGGTTGCTTGT 59.893 50.000 0.00 0.00 38.88 3.16
5733 6293 3.090952 TGTTTGGTTGCTTGTGTATGC 57.909 42.857 0.00 0.00 0.00 3.14
5737 6297 0.447801 GGTTGCTTGTGTATGCCTCG 59.552 55.000 0.00 0.00 0.00 4.63
5740 6300 0.391130 TGCTTGTGTATGCCTCGGTC 60.391 55.000 0.00 0.00 0.00 4.79
5791 6351 4.242811 AGGATGCCTGACCTATATCCAAA 58.757 43.478 0.00 0.00 39.76 3.28
5819 6379 3.688673 GCTCATTCTTTCCTCTCAACCAG 59.311 47.826 0.00 0.00 0.00 4.00
5835 6395 1.008538 CAGGTGTTCGGCTTGCAAC 60.009 57.895 0.00 0.00 0.00 4.17
5877 6437 0.883370 TCATGCGAGCTGATGGATGC 60.883 55.000 0.00 0.00 34.36 3.91
5908 6468 1.153353 GCGTGTCCCTGAAAAATCGA 58.847 50.000 0.00 0.00 0.00 3.59
5909 6469 1.136057 GCGTGTCCCTGAAAAATCGAC 60.136 52.381 0.00 0.00 0.00 4.20
5922 6482 4.301072 AAAATCGACTGGAGGAATTGGA 57.699 40.909 0.00 0.00 0.00 3.53
5945 6505 0.305922 CCTCTCGCCAATTTGATCGC 59.694 55.000 0.00 0.00 0.00 4.58
6033 6594 2.522638 CGGGCGTATTCTTCACCGC 61.523 63.158 0.00 0.00 45.05 5.68
6043 6604 4.373116 TTCACCGCCGAGCAGGTC 62.373 66.667 8.54 0.00 43.70 3.85
6104 6665 4.323409 CCTTCTTCTTCCTCTTCTTCCCTG 60.323 50.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 462 2.857744 CGACGCCCCATCTCTACCC 61.858 68.421 0.00 0.00 0.00 3.69
255 632 3.733344 ATGGGGTTCATCGTCGCCG 62.733 63.158 0.00 0.00 39.12 6.46
690 1068 1.873863 CCTTTTCCCGCCGTTTCTC 59.126 57.895 0.00 0.00 0.00 2.87
929 1308 3.053842 ACGGAGATACAGACAGGTCCTTA 60.054 47.826 0.00 0.00 0.00 2.69
930 1309 2.291670 ACGGAGATACAGACAGGTCCTT 60.292 50.000 0.00 0.00 0.00 3.36
932 1311 1.765230 ACGGAGATACAGACAGGTCC 58.235 55.000 0.00 0.00 0.00 4.46
933 1312 5.067413 TGAATTACGGAGATACAGACAGGTC 59.933 44.000 0.00 0.00 0.00 3.85
938 1317 5.258456 TGGTGAATTACGGAGATACAGAC 57.742 43.478 0.00 0.00 0.00 3.51
1257 1651 2.040606 ACGTACATGGGGAGGCCT 59.959 61.111 3.86 3.86 0.00 5.19
1396 1790 4.131088 GTCGAGTGGGACGAGGGC 62.131 72.222 0.00 0.00 40.37 5.19
1434 1828 2.091055 CCTGACCTTGAGATCCCTCCTA 60.091 54.545 0.00 0.00 38.66 2.94
1537 1931 2.997986 GCCATTGCAAAATTCCTCACAG 59.002 45.455 1.71 0.00 37.47 3.66
1551 1945 2.137523 CACTTTCAACCAAGCCATTGC 58.862 47.619 0.00 0.00 34.91 3.56
1627 2021 1.421646 CGGGAGGCCAAGATAATCCTT 59.578 52.381 5.01 0.00 0.00 3.36
1650 2044 3.425492 GCTTCAACCTTTTGATCTCGCTC 60.425 47.826 0.00 0.00 41.50 5.03
1727 2121 7.824779 ACAACTCTTGGTAGATTCTGATTTACC 59.175 37.037 0.00 0.00 41.28 2.85
1744 2138 6.084277 CACATGATCACATCAACAACTCTTG 58.916 40.000 0.00 0.00 43.50 3.02
1867 2261 2.537529 CGCCTTCAATACGTCTGCATTG 60.538 50.000 0.00 0.00 34.17 2.82
1870 2264 0.245266 TCGCCTTCAATACGTCTGCA 59.755 50.000 0.00 0.00 0.00 4.41
1914 2308 7.066284 GGTTATATGATGATAAAGCGGCAAGAT 59.934 37.037 1.45 0.00 0.00 2.40
1919 2313 6.149474 AGTTGGTTATATGATGATAAAGCGGC 59.851 38.462 0.00 0.00 0.00 6.53
1960 2354 3.630312 TGGAGACAAAAACTGGTTGCTAC 59.370 43.478 0.00 0.00 37.44 3.58
2040 2435 7.678218 GCACATGAGTTTTTCCTAGATGTGATC 60.678 40.741 15.66 0.00 37.47 2.92
2097 2492 5.239525 AGAAGTGAAACATGCTTCTAACCAC 59.760 40.000 10.07 0.74 44.74 4.16
2169 2564 6.229733 AGCTCAGCAGATCAATAATAGGAAC 58.770 40.000 0.00 0.00 0.00 3.62
2321 2726 6.572167 AAGCACTATTACGGATACTAGGTC 57.428 41.667 0.00 0.00 0.00 3.85
2770 3177 8.119226 CAGATTTACTTACAAAGCATGTAGAGC 58.881 37.037 0.00 0.00 43.63 4.09
2839 3246 9.990360 AGTTTTCTTTTTCTTTTACACAAGGAA 57.010 25.926 0.00 0.00 0.00 3.36
2840 3247 9.418045 CAGTTTTCTTTTTCTTTTACACAAGGA 57.582 29.630 0.00 0.00 0.00 3.36
2841 3248 8.168626 GCAGTTTTCTTTTTCTTTTACACAAGG 58.831 33.333 0.00 0.00 0.00 3.61
2896 3304 3.359033 TCCCTGCATCAATTTCCTGAAG 58.641 45.455 0.00 0.00 0.00 3.02
3000 3426 6.945072 ACAGACATTTTGTTCGTCTAGTTTC 58.055 36.000 0.00 0.00 37.92 2.78
3009 3435 7.096230 GGGTGAAAAATACAGACATTTTGTTCG 60.096 37.037 0.00 0.00 37.97 3.95
3036 3462 4.642885 GGCATACCATACAAGCAAGGTTTA 59.357 41.667 0.00 0.00 35.62 2.01
3120 3546 5.680619 TCAACACTCAACTAAACCAGTCAT 58.319 37.500 0.00 0.00 36.04 3.06
3126 3552 7.480810 AGACAAAATCAACACTCAACTAAACC 58.519 34.615 0.00 0.00 0.00 3.27
3142 3568 6.586344 TCTCCCATCTCACATAGACAAAATC 58.414 40.000 0.00 0.00 36.93 2.17
3385 3818 8.348507 CAATGTACTTGCTTTTCTTCTTCTTCT 58.651 33.333 0.00 0.00 0.00 2.85
3393 3826 7.803189 CGTGTAATCAATGTACTTGCTTTTCTT 59.197 33.333 0.00 0.00 34.66 2.52
3395 3828 7.295201 TCGTGTAATCAATGTACTTGCTTTTC 58.705 34.615 0.00 0.00 34.66 2.29
3396 3829 7.197071 TCGTGTAATCAATGTACTTGCTTTT 57.803 32.000 0.00 0.00 34.66 2.27
3397 3830 6.795098 TCGTGTAATCAATGTACTTGCTTT 57.205 33.333 0.00 0.00 34.66 3.51
3399 3832 5.699001 TGTTCGTGTAATCAATGTACTTGCT 59.301 36.000 0.00 0.00 34.66 3.91
3400 3833 5.922546 TGTTCGTGTAATCAATGTACTTGC 58.077 37.500 0.00 0.00 34.66 4.01
3401 3834 7.328493 TCTCTGTTCGTGTAATCAATGTACTTG 59.672 37.037 0.00 0.00 36.09 3.16
3403 3836 6.920817 TCTCTGTTCGTGTAATCAATGTACT 58.079 36.000 0.00 0.00 0.00 2.73
3413 3852 1.339929 TGCTGCTCTCTGTTCGTGTAA 59.660 47.619 0.00 0.00 0.00 2.41
3444 3928 5.557576 AAGCATGCATAGAGTGAGGAATA 57.442 39.130 21.98 0.00 0.00 1.75
3452 3936 1.541233 GGCCGTAAGCATGCATAGAGT 60.541 52.381 21.98 0.00 46.50 3.24
3555 4070 2.708861 CCTACCATACCATACCTGCCAA 59.291 50.000 0.00 0.00 0.00 4.52
3573 4088 1.153188 TGATCGTCGCCGTACCCTA 60.153 57.895 0.00 0.00 35.01 3.53
3574 4089 2.438975 TGATCGTCGCCGTACCCT 60.439 61.111 0.00 0.00 35.01 4.34
3575 4090 2.025727 CTGATCGTCGCCGTACCC 59.974 66.667 0.00 0.00 35.01 3.69
3576 4091 2.654404 GCTGATCGTCGCCGTACC 60.654 66.667 0.00 0.00 35.01 3.34
3577 4092 1.939785 CTGCTGATCGTCGCCGTAC 60.940 63.158 0.00 0.00 35.01 3.67
3672 4187 0.108281 GCTCAACGGTAAGGACCTCC 60.108 60.000 0.00 0.00 44.46 4.30
3699 4214 0.797542 CACGTCCGGCGGAAAAATAA 59.202 50.000 32.91 2.96 46.52 1.40
3719 4234 3.857052 TGATAAACGACGCCTTCTTCAT 58.143 40.909 0.00 0.00 0.00 2.57
3725 4240 2.093658 ACCTGATGATAAACGACGCCTT 60.094 45.455 0.00 0.00 0.00 4.35
3758 4273 0.472471 TGGAAGAACTGGGTGTGGAC 59.528 55.000 0.00 0.00 0.00 4.02
3865 4395 4.020218 CCGATACATCTATCCACCCAACAT 60.020 45.833 0.00 0.00 0.00 2.71
3866 4396 3.323691 CCGATACATCTATCCACCCAACA 59.676 47.826 0.00 0.00 0.00 3.33
3867 4397 3.576982 TCCGATACATCTATCCACCCAAC 59.423 47.826 0.00 0.00 0.00 3.77
3868 4398 3.832490 CTCCGATACATCTATCCACCCAA 59.168 47.826 0.00 0.00 0.00 4.12
3869 4399 3.181422 ACTCCGATACATCTATCCACCCA 60.181 47.826 0.00 0.00 0.00 4.51
3871 4401 4.079970 TCACTCCGATACATCTATCCACC 58.920 47.826 0.00 0.00 0.00 4.61
3872 4402 4.156922 CCTCACTCCGATACATCTATCCAC 59.843 50.000 0.00 0.00 0.00 4.02
3873 4403 4.042934 TCCTCACTCCGATACATCTATCCA 59.957 45.833 0.00 0.00 0.00 3.41
3874 4404 4.590918 TCCTCACTCCGATACATCTATCC 58.409 47.826 0.00 0.00 0.00 2.59
3875 4405 4.638421 CCTCCTCACTCCGATACATCTATC 59.362 50.000 0.00 0.00 0.00 2.08
3876 4406 4.289934 TCCTCCTCACTCCGATACATCTAT 59.710 45.833 0.00 0.00 0.00 1.98
3877 4407 3.651423 TCCTCCTCACTCCGATACATCTA 59.349 47.826 0.00 0.00 0.00 1.98
3879 4409 2.817258 CTCCTCCTCACTCCGATACATC 59.183 54.545 0.00 0.00 0.00 3.06
3881 4411 1.133761 CCTCCTCCTCACTCCGATACA 60.134 57.143 0.00 0.00 0.00 2.29
3882 4412 1.143277 TCCTCCTCCTCACTCCGATAC 59.857 57.143 0.00 0.00 0.00 2.24
3884 4414 0.184933 CTCCTCCTCCTCACTCCGAT 59.815 60.000 0.00 0.00 0.00 4.18
3885 4415 0.914902 TCTCCTCCTCCTCACTCCGA 60.915 60.000 0.00 0.00 0.00 4.55
3886 4416 0.465460 CTCTCCTCCTCCTCACTCCG 60.465 65.000 0.00 0.00 0.00 4.63
3912 4446 1.926426 ATGGCTGCCAAGGAGGTACC 61.926 60.000 27.24 2.73 36.95 3.34
3913 4447 0.749454 CATGGCTGCCAAGGAGGTAC 60.749 60.000 27.24 0.00 36.95 3.34
3914 4448 1.207488 ACATGGCTGCCAAGGAGGTA 61.207 55.000 27.24 0.00 36.95 3.08
3915 4449 2.085343 AACATGGCTGCCAAGGAGGT 62.085 55.000 27.24 15.35 36.95 3.85
4140 4674 3.567797 GATGCTCTTCGGCGCCAC 61.568 66.667 28.98 8.43 34.52 5.01
4316 4850 1.911766 AACCCACTCCACGATCCGT 60.912 57.895 0.00 0.00 42.36 4.69
4502 5036 0.037326 ACATGGTGATCAACGCGTCT 60.037 50.000 14.44 0.00 0.00 4.18
4526 5060 1.815212 CGCTGTGGATCATCTTCGCG 61.815 60.000 0.00 0.00 31.65 5.87
4622 5156 3.071602 GGCTCAAGGGCAAGATCTACATA 59.928 47.826 0.00 0.00 40.53 2.29
4774 5308 2.095161 TCGGAGAAGAAGTCGAAGAAGC 60.095 50.000 0.00 0.00 39.69 3.86
4829 5363 3.827784 GTAGTGAGCGTGCGTGCG 61.828 66.667 0.00 0.00 40.67 5.34
4966 5517 3.645975 CACTTCAACCGCGCCGTT 61.646 61.111 8.36 8.36 0.00 4.44
4987 5538 2.181021 GACCCCTACAGCGTCGTG 59.819 66.667 0.00 0.00 0.00 4.35
5182 5736 3.655384 GGTTGTCCCCTCTCTACCTATT 58.345 50.000 0.00 0.00 0.00 1.73
5212 5770 1.270305 CCTTGTCTTCTCTTCCACGCA 60.270 52.381 0.00 0.00 0.00 5.24
5222 5780 5.711036 CCTACGTATATAGGCCTTGTCTTCT 59.289 44.000 12.58 0.00 35.54 2.85
5225 5783 5.252586 TCCTACGTATATAGGCCTTGTCT 57.747 43.478 12.58 0.00 41.51 3.41
5253 5811 2.521105 AATAATACCACCTCGACGGC 57.479 50.000 0.00 0.00 35.61 5.68
5331 5889 6.071391 GGCCAGACCAAGAATAGAAAATCAAA 60.071 38.462 0.00 0.00 38.86 2.69
5334 5892 5.506686 GGCCAGACCAAGAATAGAAAATC 57.493 43.478 0.00 0.00 38.86 2.17
5395 5953 0.040781 AAACGAACGTTCATTGGCGG 60.041 50.000 26.71 11.70 37.35 6.13
5396 5954 1.041726 CAAACGAACGTTCATTGGCG 58.958 50.000 26.71 15.21 37.35 5.69
5414 5974 3.385433 TCAAAGTAACCTTGAGTCGACCA 59.615 43.478 13.01 7.31 0.00 4.02
5418 5978 5.986004 AAACTCAAAGTAACCTTGAGTCG 57.014 39.130 18.09 0.00 37.72 4.18
5439 5999 9.545611 GTTGTAACGTGTTTAGAAGAAGAAAAA 57.454 29.630 0.00 0.00 0.00 1.94
5444 6004 6.592798 TGGTTGTAACGTGTTTAGAAGAAG 57.407 37.500 0.00 0.00 0.00 2.85
5458 6018 3.547746 TGTGAGGGACTTTGGTTGTAAC 58.452 45.455 0.00 0.00 41.55 2.50
5481 6041 2.123342 GAGATGAGTGTATGCTCGTGC 58.877 52.381 1.71 1.71 38.28 5.34
5498 6058 1.858458 GCATGCGTGCGTTTATAGAGA 59.142 47.619 16.43 0.00 42.28 3.10
5516 6076 2.562876 TAGGGTGTGCGTACGTGCA 61.563 57.895 17.90 12.99 43.95 4.57
5517 6077 2.090524 GTAGGGTGTGCGTACGTGC 61.091 63.158 17.90 10.45 0.00 5.34
5518 6078 1.444895 GGTAGGGTGTGCGTACGTG 60.445 63.158 17.90 0.00 0.00 4.49
5519 6079 2.639327 GGGTAGGGTGTGCGTACGT 61.639 63.158 17.90 0.00 0.00 3.57
5520 6080 1.031571 TAGGGTAGGGTGTGCGTACG 61.032 60.000 11.84 11.84 0.00 3.67
5521 6081 1.406903 ATAGGGTAGGGTGTGCGTAC 58.593 55.000 0.00 0.00 0.00 3.67
5522 6082 2.163810 AATAGGGTAGGGTGTGCGTA 57.836 50.000 0.00 0.00 0.00 4.42
5542 6102 2.039216 TGTCATCAATACCACAACCCGT 59.961 45.455 0.00 0.00 0.00 5.28
5546 6106 4.764679 TGCTTGTCATCAATACCACAAC 57.235 40.909 0.00 0.00 32.82 3.32
5611 6171 1.882623 GACAACCTTTGCTCTTGGGAG 59.117 52.381 0.00 0.00 42.18 4.30
5625 6185 2.032634 TTGCCGATGCTCGACAACC 61.033 57.895 7.07 0.00 43.74 3.77
5630 6190 4.467084 GGGGTTGCCGATGCTCGA 62.467 66.667 7.07 0.00 43.74 4.04
5711 6271 3.429543 GCATACACAAGCAACCAAACATG 59.570 43.478 0.00 0.00 0.00 3.21
5737 6297 0.181350 CCACATTCCTAGGCCTGACC 59.819 60.000 17.99 0.00 39.61 4.02
5740 6300 4.567318 GCCACATTCCTAGGCCTG 57.433 61.111 17.99 5.26 42.58 4.85
5769 6329 3.567375 TGGATATAGGTCAGGCATCCT 57.433 47.619 0.00 0.00 36.83 3.24
5791 6351 6.257994 TGAGAGGAAAGAATGAGCCAATAT 57.742 37.500 0.00 0.00 0.00 1.28
5799 6359 3.652869 ACCTGGTTGAGAGGAAAGAATGA 59.347 43.478 0.00 0.00 34.37 2.57
5802 6362 2.777692 ACACCTGGTTGAGAGGAAAGAA 59.222 45.455 0.00 0.00 34.37 2.52
5819 6379 2.051345 CGTTGCAAGCCGAACACC 60.051 61.111 0.00 0.00 0.00 4.16
5867 6427 2.252346 GGCTCGCAGCATCCATCAG 61.252 63.158 9.78 0.00 44.75 2.90
5870 6430 3.800833 TGGGCTCGCAGCATCCAT 61.801 61.111 9.78 0.00 44.75 3.41
5908 6468 2.507471 GAGGTGATCCAATTCCTCCAGT 59.493 50.000 0.00 0.00 40.14 4.00
5909 6469 2.776536 AGAGGTGATCCAATTCCTCCAG 59.223 50.000 5.27 0.00 45.16 3.86
5922 6482 2.787473 TCAAATTGGCGAGAGGTGAT 57.213 45.000 0.00 0.00 0.00 3.06
5945 6505 1.070289 GTGGACGAGGGCTAAATAGGG 59.930 57.143 0.00 0.00 0.00 3.53
6033 6594 4.056125 TGTCGCTGACCTGCTCGG 62.056 66.667 6.30 0.00 39.35 4.63
6073 6634 1.751924 AGGAAGAAGAAGGATCGACGG 59.248 52.381 0.00 0.00 0.00 4.79
6076 6637 4.605183 AGAAGAGGAAGAAGAAGGATCGA 58.395 43.478 0.00 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.