Multiple sequence alignment - TraesCS2D01G369000

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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 TraesCS2D01G369000 chr2D 100.000 6732 0 0 1 6732 473280804 473287535 0.000000e+00 12432.0
1 TraesCS2D01G369000 chr2D 93.548 155 10 0 2563 2717 33931114 33931268 1.460000e-56 231.0
2 TraesCS2D01G369000 chr2D 93.548 155 10 0 2563 2717 630265859 630265705 1.460000e-56 231.0
3 TraesCS2D01G369000 chr2B 94.440 3903 118 26 512 4363 553618299 553622153 0.000000e+00 5914.0
4 TraesCS2D01G369000 chr2B 91.686 1323 53 28 4739 6020 553622512 553623818 0.000000e+00 1781.0
5 TraesCS2D01G369000 chr2B 93.536 526 19 8 6183 6703 553629553 553630068 0.000000e+00 769.0
6 TraesCS2D01G369000 chr2B 95.513 468 17 1 1 468 553617836 553618299 0.000000e+00 745.0
7 TraesCS2D01G369000 chr2B 96.970 363 7 2 4319 4680 553622153 553622512 2.080000e-169 606.0
8 TraesCS2D01G369000 chr2B 99.020 102 1 0 6014 6115 553623864 553623965 4.150000e-42 183.0
9 TraesCS2D01G369000 chr2B 93.750 64 2 1 6130 6191 553623949 553624012 2.000000e-15 95.3
10 TraesCS2D01G369000 chr2A 92.125 3619 169 45 2452 6020 615351971 615355523 0.000000e+00 4998.0
11 TraesCS2D01G369000 chr2A 91.978 2518 123 22 1 2466 615349301 615351791 0.000000e+00 3458.0
12 TraesCS2D01G369000 chr2A 85.762 604 49 21 6139 6725 615355683 615356266 7.470000e-169 604.0
13 TraesCS2D01G369000 chrUn 93.548 155 10 0 2563 2717 432961906 432962060 1.460000e-56 231.0
14 TraesCS2D01G369000 chr5D 93.548 155 10 0 2563 2717 503329504 503329350 1.460000e-56 231.0
15 TraesCS2D01G369000 chr1D 93.548 155 10 0 2563 2717 254475592 254475438 1.460000e-56 231.0
16 TraesCS2D01G369000 chr1D 92.903 155 11 0 2563 2717 244767081 244766927 6.790000e-55 226.0
17 TraesCS2D01G369000 chr1A 93.548 155 10 0 2563 2717 554449352 554449506 1.460000e-56 231.0


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 TraesCS2D01G369000 chr2D 473280804 473287535 6731 False 12432.00 12432 100.000000 1 6732 1 chr2D.!!$F2 6731
1 TraesCS2D01G369000 chr2B 553617836 553624012 6176 False 1554.05 5914 95.229833 1 6191 6 chr2B.!!$F2 6190
2 TraesCS2D01G369000 chr2B 553629553 553630068 515 False 769.00 769 93.536000 6183 6703 1 chr2B.!!$F1 520
3 TraesCS2D01G369000 chr2A 615349301 615356266 6965 False 3020.00 4998 89.955000 1 6725 3 chr2A.!!$F1 6724

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
953 983 0.407918 CAACTGGGCCCTAGGGAAAA 59.592 55.000 33.21 14.0 37.50 2.29 F
1841 1878 0.248990 GTGTGTCGTGTTACGGTGGA 60.249 55.000 1.24 0.0 42.81 4.02 F
1982 2038 0.393537 AAGCTCCCTGAAATCGCTGG 60.394 55.000 0.00 0.0 0.00 4.85 F
2105 2166 0.950555 ACACACTACTGCCGCACATG 60.951 55.000 0.00 0.0 0.00 3.21 F
2430 2506 2.093764 AGATGAGCACGGAAGAAGGAAG 60.094 50.000 0.00 0.0 0.00 3.46 F
2634 2904 3.760151 TGGAGAAGTGCTGATTTTCATGG 59.240 43.478 0.00 0.0 0.00 3.66 F
3857 4132 3.895232 AGGAGTATGTTACTGTGCTGG 57.105 47.619 0.00 0.0 39.59 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2022 0.745845 CCACCAGCGATTTCAGGGAG 60.746 60.000 0.00 0.00 0.00 4.30 R
3313 3587 2.944129 AGCACCATGTAAAACAGTGGT 58.056 42.857 0.00 7.77 39.13 4.16 R
3774 4049 3.202001 CCTGTGGGCGCATTACCG 61.202 66.667 10.83 0.87 0.00 4.02 R
3857 4132 6.913170 TCCAGAAACTCAAGTAATTTCATGC 58.087 36.000 0.00 0.00 35.26 4.06 R
4321 4596 2.028476 TGAGTGGAACATAGGTCGGTTG 60.028 50.000 0.00 0.00 44.52 3.77 R
4628 4948 6.319048 AGGATGAGAATAGGAGCAGAAAAA 57.681 37.500 0.00 0.00 0.00 1.94 R
5856 6232 0.108041 CCTAAGGGTTAAAGCGCCGA 60.108 55.000 2.29 0.00 0.00 5.54 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
67 68 8.923270 TCAAACAAGGAGAAAAGGTAAATCAAT 58.077 29.630 0.00 0.00 0.00 2.57
534 535 4.107051 GTGTGCGAGGTGGCATGC 62.107 66.667 9.90 9.90 45.99 4.06
618 619 3.654143 TCCTCCGTCCTGTCCCGA 61.654 66.667 0.00 0.00 0.00 5.14
756 757 0.808847 GCAAACCTCGTACGGGATCC 60.809 60.000 18.83 1.92 0.00 3.36
836 844 1.454539 CGAGGTGGGAGGTTTGGTT 59.545 57.895 0.00 0.00 0.00 3.67
869 891 3.764466 AGACAGGGGCGCGAGAAG 61.764 66.667 12.10 0.00 0.00 2.85
953 983 0.407918 CAACTGGGCCCTAGGGAAAA 59.592 55.000 33.21 14.00 37.50 2.29
978 1008 2.539953 GCTATCTCGTTCTCACACTCGG 60.540 54.545 0.00 0.00 0.00 4.63
979 1009 0.811915 ATCTCGTTCTCACACTCGGG 59.188 55.000 0.00 0.00 0.00 5.14
980 1010 1.444553 CTCGTTCTCACACTCGGGC 60.445 63.158 0.00 0.00 0.00 6.13
981 1011 2.142357 CTCGTTCTCACACTCGGGCA 62.142 60.000 0.00 0.00 0.00 5.36
982 1012 2.022129 CGTTCTCACACTCGGGCAC 61.022 63.158 0.00 0.00 0.00 5.01
983 1013 1.367840 GTTCTCACACTCGGGCACT 59.632 57.895 0.00 0.00 0.00 4.40
984 1014 0.667792 GTTCTCACACTCGGGCACTC 60.668 60.000 0.00 0.00 0.00 3.51
985 1015 2.126307 CTCACACTCGGGCACTCG 60.126 66.667 0.00 0.00 0.00 4.18
986 1016 3.633094 CTCACACTCGGGCACTCGG 62.633 68.421 0.00 0.00 0.00 4.63
1048 1078 2.403987 CCGCTCTCGATCGTTCGT 59.596 61.111 15.94 0.00 45.65 3.85
1049 1079 1.651730 CCGCTCTCGATCGTTCGTC 60.652 63.158 15.94 1.40 45.65 4.20
1050 1080 1.651730 CGCTCTCGATCGTTCGTCC 60.652 63.158 15.94 0.00 45.65 4.79
1268 1304 1.738099 CAAAGAGGCGTGACGAGGG 60.738 63.158 10.10 0.00 0.00 4.30
1553 1589 3.954258 GAGAAGAGGAAGAGGAAGGAGAG 59.046 52.174 0.00 0.00 0.00 3.20
1572 1608 4.711055 AGAGGGAGAGGGAAAAGGATAAA 58.289 43.478 0.00 0.00 0.00 1.40
1620 1656 0.336392 AGGATTTGGGGAAGAAGGCC 59.664 55.000 0.00 0.00 0.00 5.19
1761 1797 5.335191 GGTTTTCACAAGCCAAGATGTAGAG 60.335 44.000 0.00 0.00 33.44 2.43
1763 1799 3.930336 TCACAAGCCAAGATGTAGAGTG 58.070 45.455 0.00 0.00 0.00 3.51
1815 1852 6.233905 TGCATGAGGCTATGTTAGTTAAGA 57.766 37.500 0.00 0.00 45.15 2.10
1836 1873 4.208460 AGAATGAAAGTGTGTCGTGTTACG 59.792 41.667 0.00 0.00 44.19 3.18
1837 1874 2.195096 TGAAAGTGTGTCGTGTTACGG 58.805 47.619 1.24 0.00 42.81 4.02
1838 1875 2.195922 GAAAGTGTGTCGTGTTACGGT 58.804 47.619 1.24 0.00 42.81 4.83
1839 1876 1.563111 AAGTGTGTCGTGTTACGGTG 58.437 50.000 1.24 0.00 42.81 4.94
1840 1877 0.249155 AGTGTGTCGTGTTACGGTGG 60.249 55.000 1.24 0.00 42.81 4.61
1841 1878 0.248990 GTGTGTCGTGTTACGGTGGA 60.249 55.000 1.24 0.00 42.81 4.02
1842 1879 0.675083 TGTGTCGTGTTACGGTGGAT 59.325 50.000 1.24 0.00 42.81 3.41
1879 1934 2.922950 CGCACTGCCCAGCAAACAT 61.923 57.895 0.00 0.00 38.41 2.71
1890 1945 0.824595 AGCAAACATCCTGCAGCACA 60.825 50.000 8.66 0.00 42.48 4.57
1901 1957 1.008079 GCAGCACACACCTCTTTGC 60.008 57.895 0.00 0.00 35.08 3.68
1902 1958 1.450531 GCAGCACACACCTCTTTGCT 61.451 55.000 0.00 0.00 46.27 3.91
1903 1959 1.882912 CAGCACACACCTCTTTGCTA 58.117 50.000 0.00 0.00 43.49 3.49
1911 1967 3.251004 CACACCTCTTTGCTACCTTTGAC 59.749 47.826 0.00 0.00 0.00 3.18
1912 1968 3.118038 ACACCTCTTTGCTACCTTTGACA 60.118 43.478 0.00 0.00 0.00 3.58
1921 1977 4.469657 TGCTACCTTTGACAAGTGGATTT 58.530 39.130 13.93 0.00 0.00 2.17
1929 1985 2.158623 TGACAAGTGGATTTGGTGAGCT 60.159 45.455 0.00 0.00 32.32 4.09
1943 1999 4.144297 TGGTGAGCTTGCAAACTAGAAAT 58.856 39.130 1.52 0.00 0.00 2.17
1966 2022 7.766219 ATAATTTTGCACAGATCAATGAAGC 57.234 32.000 0.00 0.00 0.00 3.86
1976 2032 4.888239 CAGATCAATGAAGCTCCCTGAAAT 59.112 41.667 0.00 0.00 0.00 2.17
1977 2033 5.008811 CAGATCAATGAAGCTCCCTGAAATC 59.991 44.000 0.00 0.00 0.00 2.17
1982 2038 0.393537 AAGCTCCCTGAAATCGCTGG 60.394 55.000 0.00 0.00 0.00 4.85
2004 2060 1.205893 GGTTGCGGACTGATCTTCTCT 59.794 52.381 0.00 0.00 0.00 3.10
2005 2061 2.266554 GTTGCGGACTGATCTTCTCTG 58.733 52.381 0.00 0.00 0.00 3.35
2034 2090 8.181573 GCTAGCTAGTATGTTGATCTATCACTC 58.818 40.741 21.62 0.00 36.36 3.51
2035 2091 9.225436 CTAGCTAGTATGTTGATCTATCACTCA 57.775 37.037 12.92 0.00 36.36 3.41
2037 2093 7.040062 AGCTAGTATGTTGATCTATCACTCACC 60.040 40.741 0.00 0.00 36.36 4.02
2038 2094 7.255625 GCTAGTATGTTGATCTATCACTCACCA 60.256 40.741 0.00 0.00 36.36 4.17
2039 2095 7.423844 AGTATGTTGATCTATCACTCACCAA 57.576 36.000 0.00 0.00 36.36 3.67
2040 2096 8.027524 AGTATGTTGATCTATCACTCACCAAT 57.972 34.615 0.00 0.00 36.36 3.16
2041 2097 7.930325 AGTATGTTGATCTATCACTCACCAATG 59.070 37.037 0.00 0.00 36.36 2.82
2042 2098 6.053632 TGTTGATCTATCACTCACCAATGT 57.946 37.500 0.00 0.00 36.36 2.71
2046 2102 6.892485 TGATCTATCACTCACCAATGTCAAT 58.108 36.000 0.00 0.00 0.00 2.57
2056 2112 6.149973 ACTCACCAATGTCAATGTGTTATCTG 59.850 38.462 0.00 0.00 0.00 2.90
2060 2116 6.660521 ACCAATGTCAATGTGTTATCTGTCAT 59.339 34.615 0.00 0.00 0.00 3.06
2070 2126 8.754230 ATGTGTTATCTGTCATCTATTCATCG 57.246 34.615 0.00 0.00 0.00 3.84
2101 2162 1.826340 ATCCACACACTACTGCCGCA 61.826 55.000 0.00 0.00 0.00 5.69
2105 2166 0.950555 ACACACTACTGCCGCACATG 60.951 55.000 0.00 0.00 0.00 3.21
2121 2182 3.058708 GCACATGCACGCTGATATATTGT 60.059 43.478 0.00 0.00 41.59 2.71
2182 2243 8.755696 TGCATAAATACAGAAAAATGTTCACC 57.244 30.769 0.00 0.00 34.56 4.02
2183 2244 7.540400 TGCATAAATACAGAAAAATGTTCACCG 59.460 33.333 0.00 0.00 34.56 4.94
2199 2260 7.806014 AATGTTCACCGTCATTATGTTGTAAAC 59.194 33.333 0.00 0.00 38.63 2.01
2430 2506 2.093764 AGATGAGCACGGAAGAAGGAAG 60.094 50.000 0.00 0.00 0.00 3.46
2580 2850 5.125367 ACCTAAGTCTTTGTCCAAAAGGT 57.875 39.130 7.09 7.09 33.83 3.50
2632 2902 6.350780 GGATTTGGAGAAGTGCTGATTTTCAT 60.351 38.462 0.00 0.00 0.00 2.57
2634 2904 3.760151 TGGAGAAGTGCTGATTTTCATGG 59.240 43.478 0.00 0.00 0.00 3.66
3103 3376 8.798859 AGAGTGCAGACAATCAAATTAATACT 57.201 30.769 0.00 0.00 43.32 2.12
3284 3557 6.278172 TGGATAACTTATGTGCATGCAAAA 57.722 33.333 24.58 14.69 0.00 2.44
3285 3558 6.695429 TGGATAACTTATGTGCATGCAAAAA 58.305 32.000 24.58 15.37 0.00 1.94
3313 3587 4.225717 GGGTCAGGGTAAACAAGGTGTATA 59.774 45.833 0.00 0.00 0.00 1.47
3567 3841 7.331934 GCCCAATTTAGAGTTTCTTCCAATTTC 59.668 37.037 0.00 0.00 0.00 2.17
3857 4132 3.895232 AGGAGTATGTTACTGTGCTGG 57.105 47.619 0.00 0.00 39.59 4.85
4321 4596 7.711339 CCTGTAGACCTTTGGTATTGAACTATC 59.289 40.741 0.00 0.00 35.25 2.08
4363 4638 8.531146 CACTCATTTTGGGTAATAGAATGGTTT 58.469 33.333 0.00 0.00 24.29 3.27
4449 4768 7.323049 TCCACAGAAAGACAATTACGAAAAA 57.677 32.000 0.00 0.00 0.00 1.94
4710 5033 2.035066 GCTCATTGGCAGTGTCTTGTTT 59.965 45.455 9.95 0.00 0.00 2.83
4712 5035 4.685924 CTCATTGGCAGTGTCTTGTTTTT 58.314 39.130 9.95 0.00 0.00 1.94
4807 5135 7.432869 TGCATTGTTAGCATACAAGTTCTTTT 58.567 30.769 9.14 0.00 40.99 2.27
4870 5198 3.490348 AGTTGTGAATTCTGTCTTGGGG 58.510 45.455 7.05 0.00 0.00 4.96
4879 5209 0.673644 CTGTCTTGGGGCCGTACTTG 60.674 60.000 0.00 0.00 0.00 3.16
5007 5345 2.713967 GCCATGTGCTCGGCCATTT 61.714 57.895 2.24 0.00 42.82 2.32
5008 5346 1.383456 GCCATGTGCTCGGCCATTTA 61.383 55.000 2.24 0.00 42.82 1.40
5009 5347 1.321474 CCATGTGCTCGGCCATTTAT 58.679 50.000 2.24 0.00 0.00 1.40
5010 5348 1.001048 CCATGTGCTCGGCCATTTATG 60.001 52.381 2.24 0.00 0.00 1.90
5011 5349 1.677576 CATGTGCTCGGCCATTTATGT 59.322 47.619 2.24 0.00 0.00 2.29
5013 5351 2.992593 TGTGCTCGGCCATTTATGTTA 58.007 42.857 2.24 0.00 0.00 2.41
5133 5472 6.656314 TTGTTAGGTGTATGCTATTGAACG 57.344 37.500 0.00 0.00 0.00 3.95
5221 5560 6.889301 ATGGATTATTATGCAGACACCAAG 57.111 37.500 0.00 0.00 35.44 3.61
5411 5754 5.364778 ACCAACCCTTACAAAAATTTCAGC 58.635 37.500 0.00 0.00 0.00 4.26
5443 5786 1.369625 GCACGCTACTTATGCCAAGT 58.630 50.000 6.13 6.13 33.06 3.16
5520 5876 1.002142 TCAATAGGCGTCGACATACCG 60.002 52.381 17.16 1.71 0.00 4.02
5601 5957 8.153411 CGCAGTTTATTTGCACAAAAAGTATAC 58.847 33.333 0.00 0.00 41.59 1.47
5706 6065 5.981088 ATGCATCAGTTTGGTACATTGAA 57.019 34.783 0.00 0.00 39.30 2.69
5753 6118 4.785346 ACTCCATAGGCATCTCATTGTT 57.215 40.909 0.00 0.00 0.00 2.83
5791 6167 1.470098 GGCATCTGATTGTTTGTCGCT 59.530 47.619 0.00 0.00 0.00 4.93
5803 6179 1.723608 TTGTCGCTTGGTGTGGCAAG 61.724 55.000 0.00 0.00 44.59 4.01
5808 6184 1.648720 CTTGGTGTGGCAAGTCGTG 59.351 57.895 0.00 0.00 0.00 4.35
5809 6185 1.078072 TTGGTGTGGCAAGTCGTGT 60.078 52.632 0.00 0.00 0.00 4.49
5810 6186 1.092921 TTGGTGTGGCAAGTCGTGTC 61.093 55.000 0.00 0.00 0.00 3.67
5811 6187 1.522806 GGTGTGGCAAGTCGTGTCA 60.523 57.895 0.00 0.00 40.39 3.58
5812 6188 1.498865 GGTGTGGCAAGTCGTGTCAG 61.499 60.000 0.00 0.00 44.30 3.51
5813 6189 0.810031 GTGTGGCAAGTCGTGTCAGT 60.810 55.000 0.00 0.00 44.30 3.41
5814 6190 0.529773 TGTGGCAAGTCGTGTCAGTC 60.530 55.000 0.00 0.00 44.30 3.51
5815 6191 0.249489 GTGGCAAGTCGTGTCAGTCT 60.249 55.000 0.00 0.00 44.30 3.24
5856 6232 2.945668 GGGCTTTCAATGATTCGTAGCT 59.054 45.455 0.00 0.00 0.00 3.32
5889 6265 3.267031 ACCCTTAGGCTGTCAGCTTTTAT 59.733 43.478 23.68 8.22 41.99 1.40
5890 6266 4.473559 ACCCTTAGGCTGTCAGCTTTTATA 59.526 41.667 23.68 7.33 41.99 0.98
5891 6267 5.132816 ACCCTTAGGCTGTCAGCTTTTATAT 59.867 40.000 23.68 3.58 41.99 0.86
5892 6268 6.064717 CCCTTAGGCTGTCAGCTTTTATATT 58.935 40.000 23.68 3.52 41.99 1.28
5893 6269 6.547510 CCCTTAGGCTGTCAGCTTTTATATTT 59.452 38.462 23.68 2.60 41.99 1.40
5894 6270 7.719633 CCCTTAGGCTGTCAGCTTTTATATTTA 59.280 37.037 23.68 0.00 41.99 1.40
5929 6308 1.449726 ATGTACGAGGGTATGCGCGA 61.450 55.000 12.10 0.00 0.00 5.87
6098 6559 1.737735 CGCTGTGAACGCCAGATGA 60.738 57.895 0.00 0.00 31.38 2.92
6099 6560 1.291184 CGCTGTGAACGCCAGATGAA 61.291 55.000 0.00 0.00 31.38 2.57
6100 6561 0.874390 GCTGTGAACGCCAGATGAAA 59.126 50.000 0.00 0.00 31.38 2.69
6101 6562 1.470098 GCTGTGAACGCCAGATGAAAT 59.530 47.619 0.00 0.00 31.38 2.17
6102 6563 2.677836 GCTGTGAACGCCAGATGAAATA 59.322 45.455 0.00 0.00 31.38 1.40
6103 6564 3.485877 GCTGTGAACGCCAGATGAAATAC 60.486 47.826 0.00 0.00 31.38 1.89
6104 6565 3.935203 CTGTGAACGCCAGATGAAATACT 59.065 43.478 0.00 0.00 31.38 2.12
6105 6566 3.684305 TGTGAACGCCAGATGAAATACTG 59.316 43.478 0.00 0.00 0.00 2.74
6106 6567 3.684788 GTGAACGCCAGATGAAATACTGT 59.315 43.478 0.00 0.00 32.93 3.55
6107 6568 4.154195 GTGAACGCCAGATGAAATACTGTT 59.846 41.667 0.00 0.00 32.93 3.16
6108 6569 4.154015 TGAACGCCAGATGAAATACTGTTG 59.846 41.667 0.00 0.00 32.93 3.33
6109 6570 3.009723 ACGCCAGATGAAATACTGTTGG 58.990 45.455 0.00 0.00 32.93 3.77
6110 6571 2.223340 CGCCAGATGAAATACTGTTGGC 60.223 50.000 5.93 5.93 44.59 4.52
6111 6572 2.754552 GCCAGATGAAATACTGTTGGCA 59.245 45.455 10.18 0.00 46.64 4.92
6112 6573 3.181493 GCCAGATGAAATACTGTTGGCAG 60.181 47.826 10.18 0.00 46.64 4.85
6113 6574 3.379372 CCAGATGAAATACTGTTGGCAGG 59.621 47.826 0.00 0.00 46.62 4.85
6114 6575 4.012374 CAGATGAAATACTGTTGGCAGGT 58.988 43.478 0.00 0.00 46.62 4.00
6115 6576 4.095483 CAGATGAAATACTGTTGGCAGGTC 59.905 45.833 0.00 0.00 46.62 3.85
6116 6577 2.790433 TGAAATACTGTTGGCAGGTCC 58.210 47.619 0.00 0.00 46.62 4.46
6117 6578 1.737793 GAAATACTGTTGGCAGGTCCG 59.262 52.381 0.00 0.00 46.62 4.79
6118 6579 0.690762 AATACTGTTGGCAGGTCCGT 59.309 50.000 0.00 0.00 46.62 4.69
6119 6580 0.690762 ATACTGTTGGCAGGTCCGTT 59.309 50.000 0.00 0.00 46.62 4.44
6120 6581 0.470766 TACTGTTGGCAGGTCCGTTT 59.529 50.000 0.00 0.00 46.62 3.60
6121 6582 0.818040 ACTGTTGGCAGGTCCGTTTC 60.818 55.000 0.00 0.00 46.62 2.78
6122 6583 0.817634 CTGTTGGCAGGTCCGTTTCA 60.818 55.000 0.00 0.00 39.01 2.69
6123 6584 0.394488 TGTTGGCAGGTCCGTTTCAA 60.394 50.000 0.00 0.00 37.80 2.69
6124 6585 0.741915 GTTGGCAGGTCCGTTTCAAA 59.258 50.000 0.00 0.00 37.80 2.69
6125 6586 1.135333 GTTGGCAGGTCCGTTTCAAAA 59.865 47.619 0.00 0.00 37.80 2.44
6126 6587 1.475403 TGGCAGGTCCGTTTCAAAAA 58.525 45.000 0.00 0.00 37.80 1.94
6206 6670 2.569853 TGATCACCTCATAACGTTGGGT 59.430 45.455 11.99 10.72 0.00 4.51
6217 6681 2.131776 ACGTTGGGTGGAAAAAGACA 57.868 45.000 0.00 0.00 0.00 3.41
6223 6687 2.834549 TGGGTGGAAAAAGACAAAAGCA 59.165 40.909 0.00 0.00 0.00 3.91
6287 6752 7.370383 TCAGAAATTCACAATAAACTTGAGGC 58.630 34.615 0.00 0.00 0.00 4.70
6304 6769 2.816672 GAGGCAAGGAAGAAGAACAAGG 59.183 50.000 0.00 0.00 0.00 3.61
6307 6772 3.496870 GGCAAGGAAGAAGAACAAGGAGA 60.497 47.826 0.00 0.00 0.00 3.71
6310 6775 4.632327 AGGAAGAAGAACAAGGAGAAGG 57.368 45.455 0.00 0.00 0.00 3.46
6394 6868 5.451908 GCGATTCTTCACATCAAAAGTTGA 58.548 37.500 0.00 0.00 45.01 3.18
6398 6872 7.518848 CGATTCTTCACATCAAAAGTTGACTCA 60.519 37.037 0.00 0.00 43.48 3.41
6435 6909 2.461695 ACCAAATCACAACCACAACCA 58.538 42.857 0.00 0.00 0.00 3.67
6436 6910 2.430332 ACCAAATCACAACCACAACCAG 59.570 45.455 0.00 0.00 0.00 4.00
6437 6911 2.692557 CCAAATCACAACCACAACCAGA 59.307 45.455 0.00 0.00 0.00 3.86
6725 7207 1.144936 CGGAGAGGATTCCTGTGGC 59.855 63.158 10.74 0.00 34.96 5.01
6726 7208 1.333636 CGGAGAGGATTCCTGTGGCT 61.334 60.000 10.74 0.01 34.96 4.75
6727 7209 0.467804 GGAGAGGATTCCTGTGGCTC 59.532 60.000 10.74 10.04 31.76 4.70
6728 7210 0.103937 GAGAGGATTCCTGTGGCTCG 59.896 60.000 10.74 0.00 31.76 5.03
6729 7211 1.522580 GAGGATTCCTGTGGCTCGC 60.523 63.158 10.74 0.00 31.76 5.03
6730 7212 1.965754 GAGGATTCCTGTGGCTCGCT 61.966 60.000 10.74 0.00 31.76 4.93
6731 7213 1.817099 GGATTCCTGTGGCTCGCTG 60.817 63.158 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 5.738619 TCAACCTTACTCTGCATTGTCTA 57.261 39.130 0.00 0.00 0.00 2.59
278 279 3.423154 GAGCGCAACAGGAACCGG 61.423 66.667 11.47 0.00 0.00 5.28
498 499 0.825425 CCTGCGCCATCTCTCCTCTA 60.825 60.000 4.18 0.00 0.00 2.43
534 535 0.176680 AGGTGAGCTCGTATGCCAAG 59.823 55.000 9.64 0.00 0.00 3.61
618 619 1.079127 CTTGGCGATGTCGAGGGTT 60.079 57.895 6.60 0.00 43.02 4.11
716 717 2.663188 CCTTATCAGCTCGCGGGC 60.663 66.667 26.87 26.87 0.00 6.13
836 844 1.429299 TGTCTGTCTCCCTCTCCTTCA 59.571 52.381 0.00 0.00 0.00 3.02
867 889 0.460311 CACGTATTCCTCCTCGGCTT 59.540 55.000 0.00 0.00 0.00 4.35
869 891 1.027357 TACACGTATTCCTCCTCGGC 58.973 55.000 0.00 0.00 0.00 5.54
870 892 2.019249 TGTACACGTATTCCTCCTCGG 58.981 52.381 0.00 0.00 0.00 4.63
871 893 2.033049 CCTGTACACGTATTCCTCCTCG 59.967 54.545 0.00 0.00 0.00 4.63
945 972 3.371965 ACGAGATAGCCTGTTTTCCCTA 58.628 45.455 0.00 0.00 0.00 3.53
946 973 2.188817 ACGAGATAGCCTGTTTTCCCT 58.811 47.619 0.00 0.00 0.00 4.20
953 983 2.164624 GTGTGAGAACGAGATAGCCTGT 59.835 50.000 0.00 0.00 0.00 4.00
1060 1090 1.356527 CCTAGGGTTTCGCCGTTTCG 61.357 60.000 0.00 0.00 38.44 3.46
1118 1148 4.738998 CCTTGCCGGCACCATCCA 62.739 66.667 32.95 13.16 0.00 3.41
1242 1278 1.961277 ACGCCTCTTTGACTTGCCG 60.961 57.895 0.00 0.00 0.00 5.69
1268 1304 2.123897 AGCTCTCGCTCTCCTCCC 60.124 66.667 0.00 0.00 45.15 4.30
1390 1426 2.011222 GTAGGACGACTCAGACTCTGG 58.989 57.143 6.20 0.24 31.51 3.86
1553 1589 5.827756 TCTTTTTATCCTTTTCCCTCTCCC 58.172 41.667 0.00 0.00 0.00 4.30
1572 1608 3.771577 TCCTTCCGCTTCTTCTTCTTT 57.228 42.857 0.00 0.00 0.00 2.52
1620 1656 2.310233 CCACGAGTTGGTCACTGCG 61.310 63.158 0.00 0.00 41.10 5.18
1706 1742 9.896645 ACTAAGAAATGATGATCTAGAAGCAAA 57.103 29.630 0.00 0.00 0.00 3.68
1815 1852 3.246699 CCGTAACACGACACACTTTCATT 59.753 43.478 0.00 0.00 46.05 2.57
1836 1873 1.973281 CACAGCACCACCATCCACC 60.973 63.158 0.00 0.00 0.00 4.61
1837 1874 2.629656 GCACAGCACCACCATCCAC 61.630 63.158 0.00 0.00 0.00 4.02
1838 1875 2.282391 GCACAGCACCACCATCCA 60.282 61.111 0.00 0.00 0.00 3.41
1839 1876 1.604593 AAGCACAGCACCACCATCC 60.605 57.895 0.00 0.00 0.00 3.51
1840 1877 1.582968 CAAGCACAGCACCACCATC 59.417 57.895 0.00 0.00 0.00 3.51
1841 1878 1.904865 CCAAGCACAGCACCACCAT 60.905 57.895 0.00 0.00 0.00 3.55
1842 1879 2.519063 CCAAGCACAGCACCACCA 60.519 61.111 0.00 0.00 0.00 4.17
1879 1934 1.699054 AAGAGGTGTGTGCTGCAGGA 61.699 55.000 17.12 10.66 0.00 3.86
1890 1945 3.118038 TGTCAAAGGTAGCAAAGAGGTGT 60.118 43.478 0.00 0.00 0.00 4.16
1901 1957 4.827284 ACCAAATCCACTTGTCAAAGGTAG 59.173 41.667 4.21 0.00 37.76 3.18
1902 1958 4.582656 CACCAAATCCACTTGTCAAAGGTA 59.417 41.667 4.21 0.00 37.76 3.08
1903 1959 3.384467 CACCAAATCCACTTGTCAAAGGT 59.616 43.478 4.21 0.00 37.76 3.50
1911 1967 2.608752 GCAAGCTCACCAAATCCACTTG 60.609 50.000 0.00 0.00 36.87 3.16
1912 1968 1.615392 GCAAGCTCACCAAATCCACTT 59.385 47.619 0.00 0.00 0.00 3.16
1921 1977 2.928801 TCTAGTTTGCAAGCTCACCA 57.071 45.000 19.79 1.02 0.00 4.17
1943 1999 6.927416 AGCTTCATTGATCTGTGCAAAATTA 58.073 32.000 0.00 0.00 0.00 1.40
1955 2011 4.024218 CGATTTCAGGGAGCTTCATTGATC 60.024 45.833 0.00 0.00 0.00 2.92
1957 2013 3.273434 CGATTTCAGGGAGCTTCATTGA 58.727 45.455 0.00 0.00 0.00 2.57
1965 2021 1.078143 ACCAGCGATTTCAGGGAGC 60.078 57.895 0.00 0.00 0.00 4.70
1966 2022 0.745845 CCACCAGCGATTTCAGGGAG 60.746 60.000 0.00 0.00 0.00 4.30
1982 2038 1.079503 GAAGATCAGTCCGCAACCAC 58.920 55.000 0.00 0.00 0.00 4.16
2004 2060 3.040655 TCAACATACTAGCTAGCCCCA 57.959 47.619 20.91 4.13 0.00 4.96
2005 2061 3.835395 AGATCAACATACTAGCTAGCCCC 59.165 47.826 20.91 0.61 0.00 5.80
2034 2090 6.072563 TGACAGATAACACATTGACATTGGTG 60.073 38.462 2.63 0.00 37.29 4.17
2035 2091 6.003326 TGACAGATAACACATTGACATTGGT 58.997 36.000 2.63 0.00 0.00 3.67
2037 2093 7.982224 AGATGACAGATAACACATTGACATTG 58.018 34.615 0.00 0.00 0.00 2.82
2038 2094 9.842775 ATAGATGACAGATAACACATTGACATT 57.157 29.630 0.00 0.00 0.00 2.71
2039 2095 9.842775 AATAGATGACAGATAACACATTGACAT 57.157 29.630 0.00 0.00 0.00 3.06
2040 2096 9.317936 GAATAGATGACAGATAACACATTGACA 57.682 33.333 0.00 0.00 0.00 3.58
2041 2097 9.317936 TGAATAGATGACAGATAACACATTGAC 57.682 33.333 0.00 0.00 0.00 3.18
2046 2102 7.716612 ACGATGAATAGATGACAGATAACACA 58.283 34.615 0.00 0.00 0.00 3.72
2060 2116 6.349694 GGATGTGCTCATCTACGATGAATAGA 60.350 42.308 23.83 0.34 46.74 1.98
2085 2141 0.950555 ATGTGCGGCAGTAGTGTGTG 60.951 55.000 1.18 0.00 0.00 3.82
2101 2162 6.165577 TCATACAATATATCAGCGTGCATGT 58.834 36.000 7.93 0.00 0.00 3.21
2105 2166 7.294676 TGATTCATACAATATATCAGCGTGC 57.705 36.000 0.00 0.00 0.00 5.34
2217 2278 7.639113 ATGAACTTTTTGGTTAGTGAGAACA 57.361 32.000 0.00 0.00 0.00 3.18
2580 2850 4.469945 AGACAGACGGAATTCCAGGATTAA 59.530 41.667 24.09 0.00 35.14 1.40
2632 2902 5.469760 CACCATATCATAAGATTTGCGTCCA 59.530 40.000 0.00 0.00 35.67 4.02
2634 2904 5.106555 CCCACCATATCATAAGATTTGCGTC 60.107 44.000 0.00 0.00 35.67 5.19
3036 3309 7.284034 GTCACAGGGATTCATCACTTAAATCAT 59.716 37.037 0.00 0.00 38.84 2.45
3285 3558 3.964688 CCTTGTTTACCCTGACCCTTTTT 59.035 43.478 0.00 0.00 0.00 1.94
3313 3587 2.944129 AGCACCATGTAAAACAGTGGT 58.056 42.857 0.00 7.77 39.13 4.16
3381 3655 8.677148 AATAAGCTCAACTGAAAGAACACTAA 57.323 30.769 0.00 0.00 37.43 2.24
3567 3841 6.208204 CCAAAATAAGATCCAATAGGGCAGAG 59.792 42.308 0.00 0.00 36.21 3.35
3774 4049 3.202001 CCTGTGGGCGCATTACCG 61.202 66.667 10.83 0.87 0.00 4.02
3857 4132 6.913170 TCCAGAAACTCAAGTAATTTCATGC 58.087 36.000 0.00 0.00 35.26 4.06
3996 4271 8.958119 ACACTAACAGTCTATGAAAAGAAACA 57.042 30.769 0.00 0.00 0.00 2.83
4321 4596 2.028476 TGAGTGGAACATAGGTCGGTTG 60.028 50.000 0.00 0.00 44.52 3.77
4628 4948 6.319048 AGGATGAGAATAGGAGCAGAAAAA 57.681 37.500 0.00 0.00 0.00 1.94
4683 5004 2.089980 ACACTGCCAATGAGCATTCTC 58.910 47.619 0.00 0.00 43.09 2.87
4710 5033 9.005777 ACACTTTTTAGCGTAGATATTGGAAAA 57.994 29.630 0.00 0.00 0.00 2.29
4712 5035 8.038944 AGACACTTTTTAGCGTAGATATTGGAA 58.961 33.333 0.00 0.00 0.00 3.53
4807 5135 8.768501 AGACTGAACAACATCTAGGATACATA 57.231 34.615 0.00 0.00 41.41 2.29
4827 5155 5.639506 ACTACGTTTCATTCATGGAAGACTG 59.360 40.000 0.00 0.00 0.00 3.51
4855 5183 0.322546 ACGGCCCCAAGACAGAATTC 60.323 55.000 0.00 0.00 0.00 2.17
4857 5185 0.252197 GTACGGCCCCAAGACAGAAT 59.748 55.000 0.00 0.00 0.00 2.40
4879 5209 1.398390 CTTGGCATCAAGTAACCGAGC 59.602 52.381 0.00 0.00 43.92 5.03
4900 5230 9.683069 CAGAAATATGAACATAAATTAGTGCCC 57.317 33.333 0.00 0.00 0.00 5.36
5008 5346 9.051259 ACAGGAAGATGCACCTATATATAACAT 57.949 33.333 0.00 0.00 34.87 2.71
5009 5347 8.435931 ACAGGAAGATGCACCTATATATAACA 57.564 34.615 0.00 0.00 34.87 2.41
5010 5348 9.726438 AAACAGGAAGATGCACCTATATATAAC 57.274 33.333 0.00 0.00 34.87 1.89
5078 5416 7.506261 TGGATTAGGTAAACCTTACAAAGCAAA 59.494 33.333 7.04 0.00 46.09 3.68
5221 5560 4.916983 TCATGTAAACCCATGCTAATGC 57.083 40.909 0.00 0.00 41.60 3.56
5388 5731 5.130311 AGCTGAAATTTTTGTAAGGGTTGGT 59.870 36.000 0.00 0.00 0.00 3.67
5411 5754 1.359848 AGCGTGCGTTTTCCATCTAG 58.640 50.000 0.00 0.00 0.00 2.43
5601 5957 1.403780 GCATTTTCCAAGCCAGCTCAG 60.404 52.381 0.00 0.00 0.00 3.35
5733 6092 6.461110 AAAAACAATGAGATGCCTATGGAG 57.539 37.500 0.00 0.00 0.00 3.86
5762 6127 8.701908 ACAAACAATCAGATGCCTATATGAAT 57.298 30.769 0.00 0.00 37.99 2.57
5765 6130 6.596703 CGACAAACAATCAGATGCCTATATG 58.403 40.000 0.00 0.00 0.00 1.78
5766 6131 5.180117 GCGACAAACAATCAGATGCCTATAT 59.820 40.000 0.00 0.00 0.00 0.86
5767 6132 4.511454 GCGACAAACAATCAGATGCCTATA 59.489 41.667 0.00 0.00 0.00 1.31
5778 6154 2.384382 CACACCAAGCGACAAACAATC 58.616 47.619 0.00 0.00 0.00 2.67
5791 6167 1.078072 ACACGACTTGCCACACCAA 60.078 52.632 0.00 0.00 0.00 3.67
5803 6179 1.333931 TCACTGACAGACTGACACGAC 59.666 52.381 10.08 0.00 0.00 4.34
5808 6184 3.254411 TCATGAGTCACTGACAGACTGAC 59.746 47.826 10.08 13.23 45.79 3.51
5809 6185 3.490348 TCATGAGTCACTGACAGACTGA 58.510 45.455 10.08 0.00 45.79 3.41
5810 6186 3.255395 ACTCATGAGTCACTGACAGACTG 59.745 47.826 22.89 0.00 45.79 3.51
5812 6188 3.932545 ACTCATGAGTCACTGACAGAC 57.067 47.619 22.89 0.00 36.92 3.51
5813 6189 3.006217 CCAACTCATGAGTCACTGACAGA 59.994 47.826 28.01 3.36 41.58 3.41
5814 6190 3.324117 CCAACTCATGAGTCACTGACAG 58.676 50.000 28.01 7.46 41.58 3.51
5815 6191 2.037641 CCCAACTCATGAGTCACTGACA 59.962 50.000 28.01 0.00 41.58 3.58
5856 6232 0.108041 CCTAAGGGTTAAAGCGCCGA 60.108 55.000 2.29 0.00 0.00 5.54
5894 6270 9.760077 CCCTCGTACATGAATATAGTTTAGTTT 57.240 33.333 0.00 0.00 0.00 2.66
5929 6308 3.406764 CAGCACTAAAAGCCAAGAGTCT 58.593 45.455 0.00 0.00 0.00 3.24
5960 6339 3.539172 ACAACGTTAAAACAAGCGAAACG 59.461 39.130 0.00 4.54 46.11 3.60
5965 6344 2.446282 AGCACAACGTTAAAACAAGCG 58.554 42.857 0.00 0.00 0.00 4.68
6098 6559 1.073284 ACGGACCTGCCAACAGTATTT 59.927 47.619 0.00 0.00 42.81 1.40
6099 6560 0.690762 ACGGACCTGCCAACAGTATT 59.309 50.000 0.00 0.00 42.81 1.89
6100 6561 0.690762 AACGGACCTGCCAACAGTAT 59.309 50.000 0.00 0.00 42.81 2.12
6101 6562 0.470766 AAACGGACCTGCCAACAGTA 59.529 50.000 0.00 0.00 42.81 2.74
6102 6563 0.818040 GAAACGGACCTGCCAACAGT 60.818 55.000 0.00 0.00 42.81 3.55
6103 6564 0.817634 TGAAACGGACCTGCCAACAG 60.818 55.000 0.00 0.00 44.05 3.16
6104 6565 0.394488 TTGAAACGGACCTGCCAACA 60.394 50.000 0.00 0.00 35.94 3.33
6105 6566 0.741915 TTTGAAACGGACCTGCCAAC 59.258 50.000 0.00 0.00 35.94 3.77
6106 6567 1.475403 TTTTGAAACGGACCTGCCAA 58.525 45.000 0.00 0.00 35.94 4.52
6107 6568 1.475403 TTTTTGAAACGGACCTGCCA 58.525 45.000 0.00 0.00 35.94 4.92
6206 6670 5.850557 TGAGATGCTTTTGTCTTTTTCCA 57.149 34.783 0.00 0.00 0.00 3.53
6217 6681 9.836864 TCATATATGTGTAGTTGAGATGCTTTT 57.163 29.630 12.42 0.00 0.00 2.27
6274 6739 6.306987 TCTTCTTCCTTGCCTCAAGTTTATT 58.693 36.000 5.92 0.00 39.58 1.40
6287 6752 4.759183 CCTTCTCCTTGTTCTTCTTCCTTG 59.241 45.833 0.00 0.00 0.00 3.61
6377 6847 8.375465 GTTTTTGAGTCAACTTTTGATGTGAAG 58.625 33.333 4.68 0.00 42.47 3.02
6394 6868 5.186797 TGGTTTGTTGGATCTGTTTTTGAGT 59.813 36.000 0.00 0.00 0.00 3.41
6398 6872 7.065683 GTGATTTGGTTTGTTGGATCTGTTTTT 59.934 33.333 0.00 0.00 0.00 1.94
6447 6921 1.739562 CGTCTGGCCTTGTGCTCTC 60.740 63.158 3.32 0.00 40.92 3.20


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

AutoCloner maintained by Alex Coulton.