Multiple sequence alignment - TraesCS2A01G201900

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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 TraesCS2A01G201900 chr2A 100.000 5655 0 0 1 5655 176075692 176081346 0.000000e+00 10443.0
1 TraesCS2A01G201900 chr2B 92.594 3713 133 56 267 3897 223729059 223732711 0.000000e+00 5203.0
2 TraesCS2A01G201900 chr2B 91.407 1862 66 29 3818 5646 223732709 223734509 0.000000e+00 2466.0
3 TraesCS2A01G201900 chr2B 91.964 112 9 0 141 252 223728232 223728343 2.110000e-34 158.0
4 TraesCS2A01G201900 chr2B 90.588 85 5 3 53 137 223727779 223727860 5.990000e-20 110.0
5 TraesCS2A01G201900 chr2D 92.574 3636 133 54 11 3561 175590867 175594450 0.000000e+00 5092.0
6 TraesCS2A01G201900 chr2D 95.722 1309 48 6 3560 4863 175594531 175595836 0.000000e+00 2100.0
7 TraesCS2A01G201900 chr2D 86.935 597 26 18 5074 5646 175605202 175605770 1.730000e-174 623.0
8 TraesCS2A01G201900 chr2D 82.558 172 7 8 4857 5028 175604849 175604997 4.600000e-26 130.0
9 TraesCS2A01G201900 chr2D 82.222 135 17 5 3174 3303 5553550 5553682 5.990000e-20 110.0
10 TraesCS2A01G201900 chr7D 85.385 130 16 3 3174 3303 519785590 519785464 1.280000e-26 132.0
11 TraesCS2A01G201900 chrUn 80.303 132 19 4 3132 3261 79968699 79968573 6.030000e-15 93.5
12 TraesCS2A01G201900 chr5A 90.000 70 7 0 3235 3304 607563272 607563341 2.170000e-14 91.6
13 TraesCS2A01G201900 chr5B 91.111 45 1 1 3252 3296 434667040 434666999 2.200000e-04 58.4


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 TraesCS2A01G201900 chr2A 176075692 176081346 5654 False 10443.00 10443 100.00000 1 5655 1 chr2A.!!$F1 5654
1 TraesCS2A01G201900 chr2B 223727779 223734509 6730 False 1984.25 5203 91.63825 53 5646 4 chr2B.!!$F1 5593
2 TraesCS2A01G201900 chr2D 175590867 175595836 4969 False 3596.00 5092 94.14800 11 4863 2 chr2D.!!$F2 4852
3 TraesCS2A01G201900 chr2D 175604849 175605770 921 False 376.50 623 84.74650 4857 5646 2 chr2D.!!$F3 789

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
252 621 0.512952 CGCCAGTGCAGTTTCTGTAC 59.487 55.000 9.32 9.32 45.10 2.90 F
494 1571 1.202188 GCTTGTTTATTCCTCGCAGCC 60.202 52.381 0.00 0.00 0.00 4.85 F
675 1782 1.225704 CATCAACCAGGGGCCTCTC 59.774 63.158 0.00 0.00 0.00 3.20 F
2170 3344 1.067000 CCGACGGGGTAATTACACACA 60.067 52.381 19.28 0.00 0.00 3.72 F
2238 3415 1.166531 GGTCATTCCTATGTGCCCGC 61.167 60.000 0.00 0.00 33.34 6.13 F
3405 4601 1.067776 GTGGTTGAGGGAGTAGTCGTG 60.068 57.143 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 3038 0.251742 TCCCAGGACCAAAATGGCTG 60.252 55.0 0.00 0.00 42.67 4.85 R
2100 3274 0.979665 TGAGAGGCCAGTGGAAGAAG 59.020 55.0 15.20 0.00 0.00 2.85 R
2238 3415 1.354040 GGACAGACTCAGACATTGCG 58.646 55.0 0.00 0.00 0.00 4.85 R
2986 4180 0.172352 GAAGCACAGAGTCTCCCGAG 59.828 60.0 0.00 0.00 0.00 4.63 R
3622 4903 0.251354 TCCTGCCTCTGCACTGATTC 59.749 55.0 0.00 0.00 44.23 2.52 R
5275 6838 0.037605 GTACGTACTTGCCAGCCAGT 60.038 55.0 18.47 1.71 0.00 4.00 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
74 75 1.262824 CGGAAAGATACTCGCTCGCG 61.263 60.000 0.00 0.00 41.35 5.87
177 546 1.214367 TCCACACGCTTCTTTTCGTC 58.786 50.000 0.00 0.00 36.73 4.20
223 592 1.372087 CGCTGCCTCTCCAATTGGAC 61.372 60.000 23.63 13.94 39.78 4.02
252 621 0.512952 CGCCAGTGCAGTTTCTGTAC 59.487 55.000 9.32 9.32 45.10 2.90
347 1421 1.326548 GCAAGTCGTAATTACCTGCCG 59.673 52.381 10.01 0.00 0.00 5.69
351 1425 2.234414 AGTCGTAATTACCTGCCGGAAA 59.766 45.455 5.05 0.00 0.00 3.13
365 1439 1.591248 CGGAAATGAACGCTTGAACG 58.409 50.000 0.00 0.00 39.50 3.95
426 1503 7.605309 TGATATACTACTACTACCACCACATCG 59.395 40.741 0.00 0.00 0.00 3.84
446 1523 3.338676 GATCCGTTCGATGCCCGC 61.339 66.667 0.00 0.00 38.37 6.13
447 1524 4.910585 ATCCGTTCGATGCCCGCC 62.911 66.667 0.00 0.00 38.37 6.13
494 1571 1.202188 GCTTGTTTATTCCTCGCAGCC 60.202 52.381 0.00 0.00 0.00 4.85
530 1607 2.125753 AAAGCTCAGCTCCTCGCG 60.126 61.111 0.00 0.00 45.59 5.87
550 1635 3.743534 TACATTACCTGCCGCGGCC 62.744 63.158 44.42 27.83 41.09 6.13
570 1655 4.200092 GCCTAGTTAATCAGGAAAGGTGG 58.800 47.826 9.00 0.00 33.42 4.61
581 1668 2.061028 GGAAAGGTGGTACGTTACGTG 58.939 52.381 21.22 0.00 41.39 4.49
605 1692 4.152580 GGAGTAAAACAACAGAGCAGCTAC 59.847 45.833 0.00 0.00 0.00 3.58
606 1693 4.962155 AGTAAAACAACAGAGCAGCTACT 58.038 39.130 0.00 0.00 0.00 2.57
675 1782 1.225704 CATCAACCAGGGGCCTCTC 59.774 63.158 0.00 0.00 0.00 3.20
786 1900 2.449189 CGCAGCGCAATAAATAAGCAA 58.551 42.857 11.47 0.00 0.00 3.91
802 1916 4.312152 AACCCTCCGTCCCGACCT 62.312 66.667 0.00 0.00 0.00 3.85
803 1917 4.755507 ACCCTCCGTCCCGACCTC 62.756 72.222 0.00 0.00 0.00 3.85
810 1924 3.745803 GTCCCGACCTCGCTCGTT 61.746 66.667 0.00 0.00 38.18 3.85
811 1925 2.987547 TCCCGACCTCGCTCGTTT 60.988 61.111 0.00 0.00 38.18 3.60
840 1954 1.227674 GCCTCGTCCATGGGATGAC 60.228 63.158 13.02 0.99 42.15 3.06
896 2010 3.842923 CATCTGCGACTCCCGGCT 61.843 66.667 0.00 0.00 39.04 5.52
897 2011 3.532155 ATCTGCGACTCCCGGCTC 61.532 66.667 0.00 0.00 39.04 4.70
1232 2380 2.866351 TGTAAGCTAACAAACCACCCC 58.134 47.619 0.00 0.00 0.00 4.95
1250 2398 3.143338 GAGAATCGCTCCCCCTCC 58.857 66.667 0.00 0.00 37.69 4.30
1251 2399 2.840102 AGAATCGCTCCCCCTCCG 60.840 66.667 0.00 0.00 0.00 4.63
1252 2400 4.610714 GAATCGCTCCCCCTCCGC 62.611 72.222 0.00 0.00 0.00 5.54
1603 2759 3.479269 GCTCGTACGTGGCACTGC 61.479 66.667 23.01 5.66 0.00 4.40
1638 2797 5.481824 TCACATACCATGATACATCTCTCCC 59.518 44.000 0.00 0.00 0.00 4.30
1674 2833 6.152932 AGCAGAAATGTCAAATCACTTGTT 57.847 33.333 0.00 0.00 36.34 2.83
1879 3038 5.291293 ACGCCACTACACACAATTAATTC 57.709 39.130 0.00 0.00 0.00 2.17
1883 3042 5.640732 CCACTACACACAATTAATTCAGCC 58.359 41.667 0.00 0.00 0.00 4.85
1910 3084 2.222027 GTCCTGGGACTTTCTGTGTTG 58.778 52.381 12.09 0.00 41.57 3.33
1917 3091 2.614057 GGACTTTCTGTGTTGACACCAG 59.386 50.000 11.42 8.94 45.88 4.00
2100 3274 2.202756 GTCATCTCGGTGCCGGAC 60.203 66.667 5.05 6.41 40.25 4.79
2170 3344 1.067000 CCGACGGGGTAATTACACACA 60.067 52.381 19.28 0.00 0.00 3.72
2238 3415 1.166531 GGTCATTCCTATGTGCCCGC 61.167 60.000 0.00 0.00 33.34 6.13
2308 3494 4.802039 TCGGAGCTACTTAAATTAGTTGCG 59.198 41.667 12.25 12.25 46.72 4.85
2342 3528 1.436606 GTCACACTTTCGCGTTCGC 60.437 57.895 5.77 7.14 35.26 4.70
2381 3567 1.754234 ATGGCGGGCCTTGAACATC 60.754 57.895 11.55 0.00 36.94 3.06
2556 3742 2.415090 GCCTTTGTGACTTGCTGCATAG 60.415 50.000 1.84 6.72 0.00 2.23
2603 3789 2.244436 CTTTGCTGCATCGTCACCCG 62.244 60.000 1.84 0.00 38.13 5.28
2706 3892 2.793790 GCGACATCATGAGCAGTTAGAG 59.206 50.000 0.09 0.00 0.00 2.43
2783 3976 6.319048 TGATCCATAGCTTCTTTCCTTCTT 57.681 37.500 0.00 0.00 0.00 2.52
2825 4018 2.165301 GTCGATTTCCAGCGGACCG 61.165 63.158 10.29 10.29 0.00 4.79
2840 4033 3.550842 GCGGACCGGTTCGTACTAATAAT 60.551 47.826 34.54 0.00 0.00 1.28
2841 4034 4.320202 GCGGACCGGTTCGTACTAATAATA 60.320 45.833 34.54 0.00 0.00 0.98
2842 4035 5.147162 CGGACCGGTTCGTACTAATAATAC 58.853 45.833 27.65 0.00 0.00 1.89
2844 4037 6.513393 CGGACCGGTTCGTACTAATAATACTT 60.513 42.308 27.65 0.00 0.00 2.24
2845 4038 7.307751 CGGACCGGTTCGTACTAATAATACTTA 60.308 40.741 27.65 0.00 0.00 2.24
2846 4039 8.017946 GGACCGGTTCGTACTAATAATACTTAG 58.982 40.741 9.42 0.00 35.31 2.18
2847 4040 8.451908 ACCGGTTCGTACTAATAATACTTAGT 57.548 34.615 0.00 2.45 42.89 2.24
2848 4041 9.555727 ACCGGTTCGTACTAATAATACTTAGTA 57.444 33.333 0.00 0.00 41.16 1.82
2889 4082 2.025981 TGATCCATGACTCCCTGTTTGG 60.026 50.000 0.00 0.00 35.09 3.28
2919 4112 9.691362 TTTTAGTTATGAACTTCTGCCATTTTC 57.309 29.630 0.00 0.00 42.81 2.29
2937 4131 9.860898 GCCATTTTCTTAGTTCATTAACTTGAT 57.139 29.630 0.00 0.00 43.60 2.57
3053 4249 4.510038 TTGCTTGCTCTCTTTTGATTCC 57.490 40.909 0.00 0.00 0.00 3.01
3067 4263 8.028652 TCTTTTGATTCCACCAAATTAAGGTT 57.971 30.769 0.00 0.00 37.23 3.50
3162 4358 3.921677 TGCGGAAGAAATCGAGTTAGTT 58.078 40.909 0.00 0.00 0.00 2.24
3170 4366 6.342338 AGAAATCGAGTTAGTTGTAGGTGT 57.658 37.500 0.00 0.00 0.00 4.16
3171 4367 6.756221 AGAAATCGAGTTAGTTGTAGGTGTT 58.244 36.000 0.00 0.00 0.00 3.32
3212 4408 5.743636 AATGGTTCATATGTGGTTGCTTT 57.256 34.783 1.90 0.00 0.00 3.51
3250 4446 8.073768 TGCTTAATAATTAATAAGAACGGCTGC 58.926 33.333 19.97 7.05 32.10 5.25
3360 4556 1.265905 GTCGCGACCCATCAAAGTTTT 59.734 47.619 28.61 0.00 0.00 2.43
3363 4559 3.058777 TCGCGACCCATCAAAGTTTTAAC 60.059 43.478 3.71 0.00 0.00 2.01
3402 4598 2.028930 CACTGTGGTTGAGGGAGTAGTC 60.029 54.545 0.00 0.00 0.00 2.59
3405 4601 1.067776 GTGGTTGAGGGAGTAGTCGTG 60.068 57.143 0.00 0.00 0.00 4.35
3409 4605 2.363925 AGGGAGTAGTCGTGGGGC 60.364 66.667 0.00 0.00 0.00 5.80
3431 4628 3.732212 TGCTACTTCATTGCATATCGCT 58.268 40.909 0.00 0.00 43.06 4.93
3478 4675 4.077822 CTCTGGTGCTGATTTTTCCTCTT 58.922 43.478 0.00 0.00 0.00 2.85
3506 4703 2.751259 CCTTGCTGTGTTCAGTGCATAT 59.249 45.455 0.00 0.00 43.05 1.78
3548 4745 2.143122 TGCCAGTTATAGCGCTAATGC 58.857 47.619 22.98 16.70 0.00 3.56
3622 4903 4.959596 AGCAAACTTATGACTCTGCATG 57.040 40.909 0.00 0.00 32.21 4.06
3628 4909 6.922247 AACTTATGACTCTGCATGAATCAG 57.078 37.500 0.00 0.00 34.23 2.90
3707 4988 3.190535 CACCATGTTAAAAGTTCCCTCCG 59.809 47.826 0.00 0.00 0.00 4.63
3828 5112 5.429957 AAGCAAGATGTTGTCTTCTGTTC 57.570 39.130 4.33 0.00 45.35 3.18
3842 5126 3.188159 TCTGTTCACCTTTGTAAGCGT 57.812 42.857 0.00 0.00 0.00 5.07
4125 5487 9.924650 TTCTTTATAGTTGTACTTCAGGAAGAC 57.075 33.333 15.51 9.54 40.79 3.01
4138 5500 5.426689 TCAGGAAGACATACAAGCTGAAT 57.573 39.130 0.00 0.00 0.00 2.57
4140 5502 6.341316 TCAGGAAGACATACAAGCTGAATAC 58.659 40.000 0.00 0.00 0.00 1.89
4154 5516 5.439721 AGCTGAATACATACTTGATTGGCA 58.560 37.500 0.00 0.00 0.00 4.92
4325 5687 2.597578 AACCAAGTACCCAACATCCC 57.402 50.000 0.00 0.00 0.00 3.85
4417 5779 3.434641 CGTCCATGGATAACATCAGCATC 59.565 47.826 19.62 0.00 37.84 3.91
4777 6139 1.888512 TGGAACAGGCTTCTGATTTGC 59.111 47.619 0.00 0.00 40.86 3.68
4786 6148 2.288030 GCTTCTGATTTGCTGTTGTGCT 60.288 45.455 0.00 0.00 0.00 4.40
4810 6172 2.282462 CCTGGCAAGCCTTCCGTT 60.282 61.111 12.96 0.00 36.94 4.44
4811 6173 2.629656 CCTGGCAAGCCTTCCGTTG 61.630 63.158 12.96 0.00 36.94 4.10
4836 6198 1.730446 GCTTGGAATTCGAGCTGTTGC 60.730 52.381 19.50 4.77 46.85 4.17
4884 6246 7.828717 TGTATATCTTGAATGACAAAAGGCTCA 59.171 33.333 0.00 0.00 38.08 4.26
4887 6249 4.828939 TCTTGAATGACAAAAGGCTCACAT 59.171 37.500 0.00 0.00 38.08 3.21
4917 6279 5.107453 GGGTGTCGCTCGATTATTTATGAAG 60.107 44.000 0.00 0.00 0.00 3.02
4955 6318 5.403897 TCGAGGACGAAAATCAATATTGC 57.596 39.130 10.76 0.00 45.74 3.56
4956 6319 4.873259 TCGAGGACGAAAATCAATATTGCA 59.127 37.500 10.76 0.63 45.74 4.08
4957 6320 5.527214 TCGAGGACGAAAATCAATATTGCAT 59.473 36.000 10.76 2.97 45.74 3.96
4981 6344 3.622163 TGCCTTTTGTTTCAAATGTGCAG 59.378 39.130 13.85 3.70 0.00 4.41
5028 6391 1.253593 ACGATCCTGAGCAGAGCACA 61.254 55.000 0.00 0.00 0.00 4.57
5030 6393 0.536260 GATCCTGAGCAGAGCACAGT 59.464 55.000 13.77 0.00 43.68 3.55
5031 6394 0.249676 ATCCTGAGCAGAGCACAGTG 59.750 55.000 13.77 0.00 43.68 3.66
5032 6395 1.375652 CCTGAGCAGAGCACAGTGG 60.376 63.158 13.77 0.00 43.68 4.00
5033 6396 1.375652 CTGAGCAGAGCACAGTGGG 60.376 63.158 1.84 0.00 41.12 4.61
5034 6397 2.745492 GAGCAGAGCACAGTGGGC 60.745 66.667 10.12 10.12 0.00 5.36
5035 6398 4.694233 AGCAGAGCACAGTGGGCG 62.694 66.667 12.68 0.00 36.08 6.13
5036 6399 4.996434 GCAGAGCACAGTGGGCGT 62.996 66.667 12.68 0.00 36.08 5.68
5037 6400 3.046087 CAGAGCACAGTGGGCGTG 61.046 66.667 12.68 10.12 37.43 5.34
5038 6401 4.320456 AGAGCACAGTGGGCGTGG 62.320 66.667 12.68 0.00 34.85 4.94
5039 6402 4.314440 GAGCACAGTGGGCGTGGA 62.314 66.667 12.68 0.00 34.85 4.02
5040 6403 4.320456 AGCACAGTGGGCGTGGAG 62.320 66.667 12.68 0.00 34.85 3.86
5085 6623 4.935808 GGGATAATATCATTGTCGGGTGAC 59.064 45.833 2.41 0.00 45.71 3.67
5086 6624 5.280011 GGGATAATATCATTGTCGGGTGACT 60.280 44.000 2.41 0.00 45.70 3.41
5129 6672 4.159506 ACTTGGCTTTGTAGCTTTTGTTGA 59.840 37.500 0.00 0.00 46.90 3.18
5130 6673 4.040445 TGGCTTTGTAGCTTTTGTTGAC 57.960 40.909 0.00 0.00 46.90 3.18
5131 6674 3.445450 TGGCTTTGTAGCTTTTGTTGACA 59.555 39.130 0.00 0.00 46.90 3.58
5132 6675 4.044426 GGCTTTGTAGCTTTTGTTGACAG 58.956 43.478 0.00 0.00 46.90 3.51
5133 6676 4.202010 GGCTTTGTAGCTTTTGTTGACAGA 60.202 41.667 0.00 0.00 46.90 3.41
5175 6728 1.817357 GGGTTTGCTAGCCGTTTACT 58.183 50.000 13.29 0.00 34.09 2.24
5176 6729 2.976589 GGGTTTGCTAGCCGTTTACTA 58.023 47.619 13.29 0.00 34.09 1.82
5177 6730 3.538591 GGGTTTGCTAGCCGTTTACTAT 58.461 45.455 13.29 0.00 34.09 2.12
5178 6731 3.311596 GGGTTTGCTAGCCGTTTACTATG 59.688 47.826 13.29 0.00 34.09 2.23
5180 6733 2.234300 TGCTAGCCGTTTACTATGCC 57.766 50.000 13.29 0.00 0.00 4.40
5243 6806 1.446272 CGACGAGGAAGGAACTGGC 60.446 63.158 0.00 0.00 40.86 4.85
5268 6831 2.104792 ACCCCGGTGTGAATATGATGAG 59.895 50.000 0.00 0.00 0.00 2.90
5270 6833 3.433598 CCCCGGTGTGAATATGATGAGTT 60.434 47.826 0.00 0.00 0.00 3.01
5272 6835 4.441792 CCGGTGTGAATATGATGAGTTGA 58.558 43.478 0.00 0.00 0.00 3.18
5273 6836 5.059161 CCGGTGTGAATATGATGAGTTGAT 58.941 41.667 0.00 0.00 0.00 2.57
5274 6837 5.049886 CCGGTGTGAATATGATGAGTTGATG 60.050 44.000 0.00 0.00 0.00 3.07
5275 6838 5.754890 CGGTGTGAATATGATGAGTTGATGA 59.245 40.000 0.00 0.00 0.00 2.92
5310 6875 3.103793 CGTACCTGACGCATTTTCTTG 57.896 47.619 0.00 0.00 46.27 3.02
5403 6994 1.251527 ACGGAGAATGGAGCACTCGT 61.252 55.000 0.00 0.00 0.00 4.18
5428 7019 3.871594 CGTGGTCAAGAAACAGAAACTCT 59.128 43.478 0.00 0.00 0.00 3.24
5429 7020 4.332819 CGTGGTCAAGAAACAGAAACTCTT 59.667 41.667 0.00 0.00 0.00 2.85
5457 7048 2.015587 ACTAGTTCTAGTTCTCGGCCG 58.984 52.381 22.12 22.12 0.00 6.13
5520 7111 1.503347 ACCTGACCCACCCAAGAATTT 59.497 47.619 0.00 0.00 0.00 1.82
5534 7125 3.561120 AATTTCTGGGCCCGCGACA 62.561 57.895 19.37 9.85 0.00 4.35
5535 7126 2.837031 AATTTCTGGGCCCGCGACAT 62.837 55.000 19.37 11.88 0.00 3.06
5600 7191 3.373130 TGAAGATTTCGCTGATTGAGCTG 59.627 43.478 0.00 0.00 46.64 4.24
5601 7192 1.669779 AGATTTCGCTGATTGAGCTGC 59.330 47.619 0.00 0.00 46.64 5.25
5602 7193 1.669779 GATTTCGCTGATTGAGCTGCT 59.330 47.619 0.00 0.00 46.64 4.24
5603 7194 0.800631 TTTCGCTGATTGAGCTGCTG 59.199 50.000 7.01 0.00 46.64 4.41
5604 7195 0.321034 TTCGCTGATTGAGCTGCTGT 60.321 50.000 7.01 0.00 46.64 4.40
5605 7196 1.017701 TCGCTGATTGAGCTGCTGTG 61.018 55.000 7.01 0.00 46.64 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.076044 AGCCCGGCCAAGCATTTAT 60.076 52.632 15.84 0.00 0.00 1.40
16 17 3.070576 GAGCCCGGCCAAGCATTT 61.071 61.111 15.84 0.00 0.00 2.32
20 21 4.547367 ATACGAGCCCGGCCAAGC 62.547 66.667 5.55 4.33 40.78 4.01
21 22 2.280186 GATACGAGCCCGGCCAAG 60.280 66.667 5.55 0.00 40.78 3.61
22 23 3.857038 GGATACGAGCCCGGCCAA 61.857 66.667 5.55 0.00 40.78 4.52
23 24 4.853142 AGGATACGAGCCCGGCCA 62.853 66.667 5.55 0.00 46.39 5.36
24 25 3.992317 GAGGATACGAGCCCGGCC 61.992 72.222 5.55 0.00 46.39 6.13
25 26 3.992317 GGAGGATACGAGCCCGGC 61.992 72.222 0.00 0.00 46.39 6.13
177 546 5.817816 AGTCCGCTACAAGATTCTTTAATGG 59.182 40.000 0.00 0.00 0.00 3.16
223 592 2.103143 CACTGGCGCTCTACTCCG 59.897 66.667 7.64 0.00 0.00 4.63
234 603 1.884235 AGTACAGAAACTGCACTGGC 58.116 50.000 6.95 0.32 36.80 4.85
327 1401 1.326548 CGGCAGGTAATTACGACTTGC 59.673 52.381 17.52 17.52 46.15 4.01
347 1421 2.961522 TCGTTCAAGCGTTCATTTCC 57.038 45.000 0.00 0.00 0.00 3.13
351 1425 3.369147 CAGAGATTCGTTCAAGCGTTCAT 59.631 43.478 0.00 0.00 0.00 2.57
365 1439 3.637229 TCCCTCCGTAATCACAGAGATTC 59.363 47.826 0.00 0.00 43.42 2.52
426 1503 1.887707 GGGCATCGAACGGATCACC 60.888 63.158 0.00 0.00 31.28 4.02
446 1523 4.899239 GGCGATGGTCAGAGCGGG 62.899 72.222 0.00 0.00 0.00 6.13
494 1571 2.090524 GTTTACTGACGGGTCGCGG 61.091 63.158 14.28 0.00 0.00 6.46
550 1635 6.040878 CGTACCACCTTTCCTGATTAACTAG 58.959 44.000 0.00 0.00 0.00 2.57
570 1655 4.295051 TGTTTTACTCCCACGTAACGTAC 58.705 43.478 0.00 0.00 38.32 3.67
581 1668 2.226674 GCTGCTCTGTTGTTTTACTCCC 59.773 50.000 0.00 0.00 0.00 4.30
605 1692 0.179187 CACGACGACCTCACTGCTAG 60.179 60.000 0.00 0.00 0.00 3.42
606 1693 1.583495 CCACGACGACCTCACTGCTA 61.583 60.000 0.00 0.00 0.00 3.49
753 1860 2.588596 CTGCGGCAGTGACACACA 60.589 61.111 21.60 0.00 36.74 3.72
802 1916 1.088306 GAGAGGAGAGAAACGAGCGA 58.912 55.000 0.00 0.00 0.00 4.93
803 1917 0.247894 CGAGAGGAGAGAAACGAGCG 60.248 60.000 0.00 0.00 0.00 5.03
804 1918 0.524604 GCGAGAGGAGAGAAACGAGC 60.525 60.000 0.00 0.00 0.00 5.03
805 1919 0.099791 GGCGAGAGGAGAGAAACGAG 59.900 60.000 0.00 0.00 0.00 4.18
806 1920 0.322636 AGGCGAGAGGAGAGAAACGA 60.323 55.000 0.00 0.00 0.00 3.85
807 1921 0.099791 GAGGCGAGAGGAGAGAAACG 59.900 60.000 0.00 0.00 0.00 3.60
808 1922 0.099791 CGAGGCGAGAGGAGAGAAAC 59.900 60.000 0.00 0.00 0.00 2.78
809 1923 0.322636 ACGAGGCGAGAGGAGAGAAA 60.323 55.000 0.00 0.00 0.00 2.52
810 1924 0.745128 GACGAGGCGAGAGGAGAGAA 60.745 60.000 0.00 0.00 0.00 2.87
811 1925 1.153329 GACGAGGCGAGAGGAGAGA 60.153 63.158 0.00 0.00 0.00 3.10
895 2009 1.345741 TGTTGCTTGTCTCAGGAGGAG 59.654 52.381 0.00 0.00 45.49 3.69
896 2010 1.423584 TGTTGCTTGTCTCAGGAGGA 58.576 50.000 0.00 0.00 0.00 3.71
897 2011 2.149578 CTTGTTGCTTGTCTCAGGAGG 58.850 52.381 0.00 0.00 0.00 4.30
968 2098 2.256461 GCCAGCCAGCAAGAAACG 59.744 61.111 0.00 0.00 0.00 3.60
1232 2380 2.731374 GAGGGGGAGCGATTCTCG 59.269 66.667 0.00 0.00 42.82 4.04
1254 2402 3.765257 ATGGGAGGCGGAGAGGAGG 62.765 68.421 0.00 0.00 0.00 4.30
1344 2500 2.589442 GTCGAACACCCCGCACAA 60.589 61.111 0.00 0.00 0.00 3.33
1603 2759 1.157870 GGTATGTGAATGTCCGGCGG 61.158 60.000 22.51 22.51 0.00 6.13
1674 2833 3.720002 ACAAAGAGGGGGTCAGAACTAAA 59.280 43.478 0.00 0.00 0.00 1.85
1879 3038 0.251742 TCCCAGGACCAAAATGGCTG 60.252 55.000 0.00 0.00 42.67 4.85
1883 3042 3.256631 CAGAAAGTCCCAGGACCAAAATG 59.743 47.826 13.27 3.21 45.59 2.32
1910 3084 3.649277 ATCGCAGACCGCTGGTGTC 62.649 63.158 4.94 0.00 42.51 3.67
1917 3091 2.887568 CCTGACATCGCAGACCGC 60.888 66.667 0.00 0.00 42.51 5.68
2100 3274 0.979665 TGAGAGGCCAGTGGAAGAAG 59.020 55.000 15.20 0.00 0.00 2.85
2170 3344 5.527026 AATGGGAGAAAGGAGTGAAAGAT 57.473 39.130 0.00 0.00 0.00 2.40
2238 3415 1.354040 GGACAGACTCAGACATTGCG 58.646 55.000 0.00 0.00 0.00 4.85
2279 3465 6.812160 ACTAATTTAAGTAGCTCCGACAACAG 59.188 38.462 0.00 0.00 0.00 3.16
2280 3466 6.694447 ACTAATTTAAGTAGCTCCGACAACA 58.306 36.000 0.00 0.00 0.00 3.33
2308 3494 4.997395 AGTGTGACAGATTGACATTACACC 59.003 41.667 0.00 0.00 0.00 4.16
2342 3528 3.774066 TGTGAGACTAATCAGTGCATCG 58.226 45.455 0.00 0.00 34.21 3.84
2467 3653 1.812571 AGCAACCAATACGGAAAGCTG 59.187 47.619 0.00 0.00 37.94 4.24
2556 3742 7.227512 AGTGTGTTAAGCTGGCTAATCATTATC 59.772 37.037 0.00 0.00 0.00 1.75
2603 3789 1.734465 GTACAGCAGATGACAACAGGC 59.266 52.381 0.00 0.00 0.00 4.85
2706 3892 1.961277 CACTCGCCACACCCAGTTC 60.961 63.158 0.00 0.00 0.00 3.01
2717 3903 1.975363 GCAATGAGCAGTCACTCGCC 61.975 60.000 0.00 0.00 44.79 5.54
2762 3949 8.095452 TCTTAAGAAGGAAAGAAGCTATGGAT 57.905 34.615 1.68 0.00 0.00 3.41
2763 3950 7.496346 TCTTAAGAAGGAAAGAAGCTATGGA 57.504 36.000 1.68 0.00 0.00 3.41
2764 3951 8.744568 AATCTTAAGAAGGAAAGAAGCTATGG 57.255 34.615 9.71 0.00 35.47 2.74
2765 3952 8.547069 CGAATCTTAAGAAGGAAAGAAGCTATG 58.453 37.037 9.71 0.00 35.47 2.23
2766 3953 8.478877 TCGAATCTTAAGAAGGAAAGAAGCTAT 58.521 33.333 9.71 0.00 35.47 2.97
2767 3954 7.837863 TCGAATCTTAAGAAGGAAAGAAGCTA 58.162 34.615 9.71 0.00 35.47 3.32
2783 3976 8.837788 ACATTATTCAGATGCATCGAATCTTA 57.162 30.769 31.43 23.30 34.45 2.10
2870 4063 1.995542 ACCAAACAGGGAGTCATGGAT 59.004 47.619 0.00 0.00 43.89 3.41
2901 4094 7.231317 TGAACTAAGAAAATGGCAGAAGTTCAT 59.769 33.333 5.50 4.57 43.81 2.57
2903 4096 6.970484 TGAACTAAGAAAATGGCAGAAGTTC 58.030 36.000 0.00 0.00 41.09 3.01
2986 4180 0.172352 GAAGCACAGAGTCTCCCGAG 59.828 60.000 0.00 0.00 0.00 4.63
3053 4249 6.573664 TGACATCTGAACCTTAATTTGGTG 57.426 37.500 3.96 0.00 37.93 4.17
3067 4263 8.969260 AATTATAGAAATGTGCTGACATCTGA 57.031 30.769 0.00 0.00 42.30 3.27
3299 4495 6.398918 TCTGTGAGTTACTAGATGCCTTTTC 58.601 40.000 0.00 0.00 0.00 2.29
3360 4556 0.321210 CCGTCCATGGTGCACAGTTA 60.321 55.000 20.43 1.75 0.00 2.24
3363 4559 3.434319 GCCGTCCATGGTGCACAG 61.434 66.667 20.43 7.70 0.00 3.66
3402 4598 0.392998 AATGAAGTAGCAGCCCCACG 60.393 55.000 0.00 0.00 0.00 4.94
3405 4601 0.680921 TGCAATGAAGTAGCAGCCCC 60.681 55.000 0.00 0.00 33.75 5.80
3409 4605 4.062853 GCGATATGCAATGAAGTAGCAG 57.937 45.455 0.00 0.00 45.45 4.24
3431 4628 0.623723 GCTGTCCCATAGAACCCCAA 59.376 55.000 0.00 0.00 0.00 4.12
3506 4703 8.731605 TGGCATAGAAAAATAAACATAACGTCA 58.268 29.630 0.00 0.00 0.00 4.35
3548 4745 2.556189 ACTGTCTCCTAGATAGCATGCG 59.444 50.000 13.01 0.00 37.01 4.73
3622 4903 0.251354 TCCTGCCTCTGCACTGATTC 59.749 55.000 0.00 0.00 44.23 2.52
3628 4909 3.604582 GGATAATATCCTGCCTCTGCAC 58.395 50.000 11.91 0.00 46.19 4.57
3707 4988 5.631096 GCAAAAGGTGTCTTCAAGATTAAGC 59.369 40.000 0.00 0.00 31.82 3.09
3842 5126 5.855925 CACGCAAACTACAATCATTAAGCAA 59.144 36.000 0.00 0.00 0.00 3.91
4125 5487 9.874215 CAATCAAGTATGTATTCAGCTTGTATG 57.126 33.333 14.45 11.89 39.34 2.39
4417 5779 1.066152 TCTGCGACTGAATCATCCTCG 59.934 52.381 0.00 2.05 0.00 4.63
4564 5926 2.100631 GCCCGACCAGTTGTGATCG 61.101 63.158 0.00 0.00 0.00 3.69
4764 6126 2.669364 CACAACAGCAAATCAGAAGCC 58.331 47.619 0.00 0.00 0.00 4.35
4777 6139 0.309922 CAGGCAGTGAAGCACAACAG 59.690 55.000 0.00 0.00 36.74 3.16
4786 6148 2.598394 GGCTTGCCAGGCAGTGAA 60.598 61.111 15.50 0.00 45.26 3.18
4810 6172 1.159285 CTCGAATTCCAAGCACAGCA 58.841 50.000 0.00 0.00 0.00 4.41
4811 6173 0.179179 GCTCGAATTCCAAGCACAGC 60.179 55.000 18.09 4.37 36.06 4.40
4830 6192 0.973632 GGGGTAAAAAGGGGCAACAG 59.026 55.000 0.00 0.00 39.74 3.16
4833 6195 0.472161 GGTGGGGTAAAAAGGGGCAA 60.472 55.000 0.00 0.00 0.00 4.52
4836 6198 2.104669 TTTGGTGGGGTAAAAAGGGG 57.895 50.000 0.00 0.00 0.00 4.79
4884 6246 0.872388 GAGCGACACCCGAAAAATGT 59.128 50.000 0.00 0.00 41.76 2.71
4887 6249 0.320073 ATCGAGCGACACCCGAAAAA 60.320 50.000 0.00 0.00 41.76 1.94
4937 6300 6.308766 GGCATATGCAATATTGATTTTCGTCC 59.691 38.462 28.07 6.07 37.44 4.79
4938 6301 7.086376 AGGCATATGCAATATTGATTTTCGTC 58.914 34.615 28.07 5.39 37.44 4.20
4940 6303 7.878477 AAGGCATATGCAATATTGATTTTCG 57.122 32.000 28.07 3.61 37.44 3.46
4941 6304 9.872757 CAAAAGGCATATGCAATATTGATTTTC 57.127 29.630 28.07 6.82 37.44 2.29
4942 6305 9.398538 ACAAAAGGCATATGCAATATTGATTTT 57.601 25.926 28.07 16.28 37.44 1.82
4943 6306 8.967664 ACAAAAGGCATATGCAATATTGATTT 57.032 26.923 28.07 13.20 37.44 2.17
4944 6307 8.967664 AACAAAAGGCATATGCAATATTGATT 57.032 26.923 28.07 17.54 37.44 2.57
4945 6308 8.967664 AAACAAAAGGCATATGCAATATTGAT 57.032 26.923 28.07 17.39 37.44 2.57
4946 6309 8.039538 TGAAACAAAAGGCATATGCAATATTGA 58.960 29.630 28.07 9.13 37.44 2.57
4947 6310 8.199176 TGAAACAAAAGGCATATGCAATATTG 57.801 30.769 28.07 24.64 37.44 1.90
4948 6311 8.789825 TTGAAACAAAAGGCATATGCAATATT 57.210 26.923 28.07 14.30 37.44 1.28
4949 6312 8.789825 TTTGAAACAAAAGGCATATGCAATAT 57.210 26.923 28.07 9.50 41.02 1.28
4950 6313 8.666573 CATTTGAAACAAAAGGCATATGCAATA 58.333 29.630 28.07 0.00 44.36 1.90
4951 6314 7.175293 ACATTTGAAACAAAAGGCATATGCAAT 59.825 29.630 28.07 13.97 44.36 3.56
4952 6315 6.485984 ACATTTGAAACAAAAGGCATATGCAA 59.514 30.769 28.07 10.19 44.36 4.08
4953 6316 5.996513 ACATTTGAAACAAAAGGCATATGCA 59.003 32.000 28.07 4.04 44.36 3.96
4954 6317 6.308675 CACATTTGAAACAAAAGGCATATGC 58.691 36.000 19.79 19.79 41.14 3.14
4955 6318 6.073167 TGCACATTTGAAACAAAAGGCATATG 60.073 34.615 0.00 0.00 0.00 1.78
4956 6319 5.996513 TGCACATTTGAAACAAAAGGCATAT 59.003 32.000 12.78 0.00 0.00 1.78
4957 6320 5.363101 TGCACATTTGAAACAAAAGGCATA 58.637 33.333 12.78 0.00 0.00 3.14
4981 6344 2.929161 GCCCGATTTAACCCAGCAAAAC 60.929 50.000 0.00 0.00 0.00 2.43
4997 6360 2.508439 GATCGTCGCTTTGCCCGA 60.508 61.111 0.00 0.00 34.12 5.14
5085 6623 1.381165 CCGGCCGGGGAATTTACAAG 61.381 60.000 37.42 5.42 0.00 3.16
5086 6624 1.378778 CCGGCCGGGGAATTTACAA 60.379 57.895 37.42 0.00 0.00 2.41
5129 6672 0.877071 CGCATTGCCTTCTGTTCTGT 59.123 50.000 2.41 0.00 0.00 3.41
5130 6673 0.455633 GCGCATTGCCTTCTGTTCTG 60.456 55.000 0.30 0.00 37.76 3.02
5131 6674 1.878775 GCGCATTGCCTTCTGTTCT 59.121 52.632 0.30 0.00 37.76 3.01
5132 6675 4.465413 GCGCATTGCCTTCTGTTC 57.535 55.556 0.30 0.00 37.76 3.18
5174 6727 4.929808 ACACGTGTCTAAGAAAAGGCATAG 59.070 41.667 17.22 0.00 32.82 2.23
5175 6728 4.890088 ACACGTGTCTAAGAAAAGGCATA 58.110 39.130 17.22 0.00 32.82 3.14
5176 6729 3.740115 ACACGTGTCTAAGAAAAGGCAT 58.260 40.909 17.22 0.00 32.82 4.40
5177 6730 3.188159 ACACGTGTCTAAGAAAAGGCA 57.812 42.857 17.22 0.00 0.00 4.75
5178 6731 4.272748 AGAAACACGTGTCTAAGAAAAGGC 59.727 41.667 23.61 0.00 0.00 4.35
5180 6733 6.258068 AGGAAGAAACACGTGTCTAAGAAAAG 59.742 38.462 23.61 0.00 0.00 2.27
5243 6806 0.177141 ATATTCACACCGGGGTGACG 59.823 55.000 38.69 13.36 46.76 4.35
5268 6831 0.524862 CTTGCCAGCCAGTCATCAAC 59.475 55.000 0.00 0.00 0.00 3.18
5270 6833 0.983467 TACTTGCCAGCCAGTCATCA 59.017 50.000 0.00 0.00 0.00 3.07
5272 6835 0.391661 CGTACTTGCCAGCCAGTCAT 60.392 55.000 0.00 0.00 0.00 3.06
5273 6836 1.005037 CGTACTTGCCAGCCAGTCA 60.005 57.895 0.00 0.00 0.00 3.41
5274 6837 0.245539 TACGTACTTGCCAGCCAGTC 59.754 55.000 0.00 0.00 0.00 3.51
5275 6838 0.037605 GTACGTACTTGCCAGCCAGT 60.038 55.000 18.47 1.71 0.00 4.00
5403 6994 2.971660 TCTGTTTCTTGACCACGACA 57.028 45.000 0.00 0.00 0.00 4.35
5428 7019 2.168496 ACTAGAACTAGTGCGGCAGAA 58.832 47.619 12.83 0.00 44.11 3.02
5429 7020 1.835494 ACTAGAACTAGTGCGGCAGA 58.165 50.000 12.83 0.00 44.11 4.26
5457 7048 3.656045 CCAACACGACCGGCAACC 61.656 66.667 0.00 0.00 0.00 3.77
5520 7111 3.561120 AAAATGTCGCGGGCCCAGA 62.561 57.895 24.92 18.17 0.00 3.86
5534 7125 1.332144 ATGCGGGCATGCTGGAAAAT 61.332 50.000 18.92 1.62 35.03 1.82
5535 7126 1.983481 ATGCGGGCATGCTGGAAAA 60.983 52.632 18.92 0.00 35.03 2.29
5600 7191 3.807538 CCATCGCACAGCCACAGC 61.808 66.667 0.00 0.00 40.32 4.40
5601 7192 1.518056 AAACCATCGCACAGCCACAG 61.518 55.000 0.00 0.00 0.00 3.66
5602 7193 1.528076 AAACCATCGCACAGCCACA 60.528 52.632 0.00 0.00 0.00 4.17
5603 7194 1.081242 CAAACCATCGCACAGCCAC 60.081 57.895 0.00 0.00 0.00 5.01
5604 7195 1.228094 TCAAACCATCGCACAGCCA 60.228 52.632 0.00 0.00 0.00 4.75
5605 7196 0.955428 TCTCAAACCATCGCACAGCC 60.955 55.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.