Multiple sequence alignment - TraesCS5A01G371900

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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 TraesCS5A01G371900 chr5A 100.000 4052 0 0 1 4052 570509414 570505363 0.000000e+00 7483.0
1 TraesCS5A01G371900 chr5A 100.000 1780 0 0 4342 6121 570505073 570503294 0.000000e+00 3288.0
2 TraesCS5A01G371900 chr5D 96.767 2165 61 7 1755 3915 451683286 451681127 0.000000e+00 3602.0
3 TraesCS5A01G371900 chr5D 92.378 1758 79 22 1 1721 451685024 451683285 0.000000e+00 2453.0
4 TraesCS5A01G371900 chr5D 90.033 1836 88 39 4342 6121 451677542 451675746 0.000000e+00 2289.0
5 TraesCS5A01G371900 chr5D 96.078 102 3 1 3898 3999 451677927 451677827 1.360000e-36 165.0
6 TraesCS5A01G371900 chr5B 90.757 1558 77 23 1 1519 551509800 551508271 0.000000e+00 2017.0
7 TraesCS5A01G371900 chr5B 82.816 1513 177 48 2578 4036 551507174 551505691 0.000000e+00 1277.0
8 TraesCS5A01G371900 chr5B 90.754 822 51 13 5313 6121 551504277 551503468 0.000000e+00 1074.0
9 TraesCS5A01G371900 chr5B 87.596 911 76 16 4377 5277 551505358 551504475 0.000000e+00 1022.0
10 TraesCS5A01G371900 chr5B 87.117 326 23 11 2008 2318 551507709 551507388 9.760000e-93 351.0
11 TraesCS5A01G371900 chr5B 85.714 189 16 6 1534 1715 551508175 551507991 8.100000e-44 189.0
12 TraesCS5A01G371900 chr5B 93.182 44 2 1 5959 6002 551503591 551503549 5.120000e-06 63.9


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 TraesCS5A01G371900 chr5A 570503294 570509414 6120 True 5385.500000 7483 100.000000 1 6121 2 chr5A.!!$R1 6120
1 TraesCS5A01G371900 chr5D 451675746 451685024 9278 True 2127.250000 3602 93.814000 1 6121 4 chr5D.!!$R1 6120
2 TraesCS5A01G371900 chr5B 551503468 551509800 6332 True 856.271429 2017 88.276571 1 6121 7 chr5B.!!$R1 6120

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
845 858 0.930726 AGAGAGGGAGGGATTCGTCT 59.069 55.000 0.00 0.0 0.00 4.18 F
1014 1052 1.694133 CCTCCATGTCCTCCTCCAGC 61.694 65.000 0.00 0.0 0.00 4.85 F
1741 1882 0.394565 AAGGCGCTGTTCTGAAGTCT 59.605 50.000 7.64 0.0 0.00 3.24 F
1743 1884 1.202698 AGGCGCTGTTCTGAAGTCTTT 60.203 47.619 7.64 0.0 0.00 2.52 F
2836 3052 1.471684 CAAGTTGGCTTGCCTGAGATC 59.528 52.381 13.18 0.0 44.54 2.75 F
4451 8067 3.181329 TCAAGCTGAACTTCTCCCCATA 58.819 45.455 0.00 0.0 36.04 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 1863 0.394565 AGACTTCAGAACAGCGCCTT 59.605 50.000 2.29 0.00 0.00 4.35 R
2017 2189 1.080638 AATCAGGGGCCAAGGTACAA 58.919 50.000 4.39 0.00 0.00 2.41 R
2564 2766 5.306419 TGTCTAATAGCTTCAGCAGGATGAT 59.694 40.000 0.75 0.00 45.16 2.45 R
3215 3434 6.313905 AGAAACAATCCACGAATCATAGACAC 59.686 38.462 0.00 0.00 0.00 3.67 R
4690 8306 0.647410 GAGTTCCATGTGACGCGATG 59.353 55.000 15.93 5.70 0.00 3.84 R
5662 9463 0.035820 TATCGCGGGCCTGAGTTTTT 60.036 50.000 18.31 1.96 0.00 1.94 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
27 28 0.959372 GCACAGCTTCAGATGGCAGT 60.959 55.000 0.00 0.00 35.42 4.40
57 58 5.997129 GGAGATCAATTCCTTCTCAATCTCC 59.003 44.000 11.51 11.51 46.12 3.71
100 101 2.209273 TGTCAACAATCACACAGACCG 58.791 47.619 0.00 0.00 0.00 4.79
102 103 1.414550 TCAACAATCACACAGACCGGA 59.585 47.619 9.46 0.00 0.00 5.14
190 191 3.595428 ATCCCCACGTCGGAGGACA 62.595 63.158 0.00 0.00 43.61 4.02
486 487 1.075970 CTCCGTGATCTCCTCCCCA 60.076 63.158 0.00 0.00 0.00 4.96
799 812 1.195115 CGACATTCTCTCCCAAGGGA 58.805 55.000 7.77 7.77 42.90 4.20
813 826 2.926838 CCAAGGGAAACAAACACAAACG 59.073 45.455 0.00 0.00 0.00 3.60
814 827 2.287393 AGGGAAACAAACACAAACGC 57.713 45.000 0.00 0.00 0.00 4.84
815 828 1.134936 AGGGAAACAAACACAAACGCC 60.135 47.619 0.00 0.00 0.00 5.68
816 829 1.282817 GGAAACAAACACAAACGCCC 58.717 50.000 0.00 0.00 0.00 6.13
817 830 1.134936 GGAAACAAACACAAACGCCCT 60.135 47.619 0.00 0.00 0.00 5.19
818 831 2.099427 GGAAACAAACACAAACGCCCTA 59.901 45.455 0.00 0.00 0.00 3.53
819 832 2.855660 AACAAACACAAACGCCCTAC 57.144 45.000 0.00 0.00 0.00 3.18
820 833 1.752683 ACAAACACAAACGCCCTACA 58.247 45.000 0.00 0.00 0.00 2.74
821 834 1.673920 ACAAACACAAACGCCCTACAG 59.326 47.619 0.00 0.00 0.00 2.74
822 835 1.673920 CAAACACAAACGCCCTACAGT 59.326 47.619 0.00 0.00 0.00 3.55
823 836 2.873472 CAAACACAAACGCCCTACAGTA 59.127 45.455 0.00 0.00 0.00 2.74
824 837 2.914695 ACACAAACGCCCTACAGTAA 57.085 45.000 0.00 0.00 0.00 2.24
825 838 2.762745 ACACAAACGCCCTACAGTAAG 58.237 47.619 0.00 0.00 0.00 2.34
826 839 2.366266 ACACAAACGCCCTACAGTAAGA 59.634 45.455 0.00 0.00 0.00 2.10
827 840 2.993899 CACAAACGCCCTACAGTAAGAG 59.006 50.000 0.00 0.00 0.00 2.85
831 844 2.645802 ACGCCCTACAGTAAGAGAGAG 58.354 52.381 0.00 0.00 0.00 3.20
833 846 2.312390 GCCCTACAGTAAGAGAGAGGG 58.688 57.143 0.12 0.12 45.57 4.30
838 851 2.289467 ACAGTAAGAGAGAGGGAGGGA 58.711 52.381 0.00 0.00 0.00 4.20
844 857 1.133606 AGAGAGAGGGAGGGATTCGTC 60.134 57.143 0.00 0.00 0.00 4.20
845 858 0.930726 AGAGAGGGAGGGATTCGTCT 59.069 55.000 0.00 0.00 0.00 4.18
866 880 4.418328 TCCGGCCCACCATTTCGG 62.418 66.667 0.00 0.00 41.80 4.30
966 980 3.751246 CGCCGGAACCCTACGACA 61.751 66.667 5.05 0.00 0.00 4.35
1014 1052 1.694133 CCTCCATGTCCTCCTCCAGC 61.694 65.000 0.00 0.00 0.00 4.85
1016 1054 2.202987 CATGTCCTCCTCCAGCGC 60.203 66.667 0.00 0.00 0.00 5.92
1133 1171 3.449227 CGCCAGTCTCACCGCCTA 61.449 66.667 0.00 0.00 0.00 3.93
1134 1172 2.786495 CGCCAGTCTCACCGCCTAT 61.786 63.158 0.00 0.00 0.00 2.57
1152 1190 2.180946 ATGTGGCCTCTGTCTATGGA 57.819 50.000 3.32 0.00 0.00 3.41
1159 1198 3.282021 GCCTCTGTCTATGGATTTGCAA 58.718 45.455 0.00 0.00 0.00 4.08
1163 1202 5.238868 CCTCTGTCTATGGATTTGCAATCTG 59.761 44.000 0.00 0.00 0.00 2.90
1165 1204 6.417258 TCTGTCTATGGATTTGCAATCTGAA 58.583 36.000 0.00 0.00 0.00 3.02
1170 1209 7.446625 GTCTATGGATTTGCAATCTGAATAGGT 59.553 37.037 0.00 0.00 0.00 3.08
1193 1232 5.255397 TCTTCCATTGGTGTAGGTGATTT 57.745 39.130 1.86 0.00 0.00 2.17
1305 1344 2.043115 TGGGAGCTTAGGACTTCAGAGA 59.957 50.000 0.00 0.00 0.00 3.10
1415 1456 1.741770 GGAGGCGTTGTTCGAGCAT 60.742 57.895 1.75 0.00 42.86 3.79
1489 1530 4.125703 CTCATGGAAGAATGGTGAGTAGC 58.874 47.826 0.00 0.00 33.42 3.58
1688 1827 6.173339 CCACATGGTTTGTCAGTCTAATAGT 58.827 40.000 0.00 0.00 36.00 2.12
1728 1869 8.964420 TTGCATATTATTCTATTTAAAGGCGC 57.036 30.769 0.00 0.00 0.00 6.53
1729 1870 8.335532 TGCATATTATTCTATTTAAAGGCGCT 57.664 30.769 7.64 0.00 0.00 5.92
1730 1871 8.236586 TGCATATTATTCTATTTAAAGGCGCTG 58.763 33.333 7.64 0.00 0.00 5.18
1731 1872 8.237267 GCATATTATTCTATTTAAAGGCGCTGT 58.763 33.333 7.64 0.00 0.00 4.40
1734 1875 7.859325 TTATTCTATTTAAAGGCGCTGTTCT 57.141 32.000 7.64 0.00 0.00 3.01
1735 1876 5.545658 TTCTATTTAAAGGCGCTGTTCTG 57.454 39.130 7.64 0.00 0.00 3.02
1736 1877 4.827692 TCTATTTAAAGGCGCTGTTCTGA 58.172 39.130 7.64 0.00 0.00 3.27
1737 1878 5.242434 TCTATTTAAAGGCGCTGTTCTGAA 58.758 37.500 7.64 0.00 0.00 3.02
1738 1879 3.896648 TTTAAAGGCGCTGTTCTGAAG 57.103 42.857 7.64 0.00 0.00 3.02
1739 1880 2.543777 TAAAGGCGCTGTTCTGAAGT 57.456 45.000 7.64 0.00 0.00 3.01
1740 1881 1.230324 AAAGGCGCTGTTCTGAAGTC 58.770 50.000 7.64 0.00 0.00 3.01
1741 1882 0.394565 AAGGCGCTGTTCTGAAGTCT 59.605 50.000 7.64 0.00 0.00 3.24
1742 1883 0.394565 AGGCGCTGTTCTGAAGTCTT 59.605 50.000 7.64 0.00 0.00 3.01
1743 1884 1.202698 AGGCGCTGTTCTGAAGTCTTT 60.203 47.619 7.64 0.00 0.00 2.52
1744 1885 1.604278 GGCGCTGTTCTGAAGTCTTTT 59.396 47.619 7.64 0.00 0.00 2.27
1745 1886 2.033424 GGCGCTGTTCTGAAGTCTTTTT 59.967 45.455 7.64 0.00 0.00 1.94
1746 1887 3.250040 GGCGCTGTTCTGAAGTCTTTTTA 59.750 43.478 7.64 0.00 0.00 1.52
1747 1888 4.261031 GGCGCTGTTCTGAAGTCTTTTTAA 60.261 41.667 7.64 0.00 0.00 1.52
1748 1889 5.270853 GCGCTGTTCTGAAGTCTTTTTAAA 58.729 37.500 0.00 0.00 0.00 1.52
1749 1890 5.396654 GCGCTGTTCTGAAGTCTTTTTAAAG 59.603 40.000 0.00 0.00 37.36 1.85
1750 1891 6.715464 CGCTGTTCTGAAGTCTTTTTAAAGA 58.285 36.000 0.89 0.89 42.41 2.52
1751 1892 7.355778 CGCTGTTCTGAAGTCTTTTTAAAGAT 58.644 34.615 8.07 0.00 45.83 2.40
1752 1893 8.495949 CGCTGTTCTGAAGTCTTTTTAAAGATA 58.504 33.333 8.07 0.00 45.83 1.98
1753 1894 9.818796 GCTGTTCTGAAGTCTTTTTAAAGATAG 57.181 33.333 8.07 5.66 45.83 2.08
1774 1915 2.680339 GTTTGTATTCTGCTGCCTCCTC 59.320 50.000 0.00 0.00 0.00 3.71
1797 1938 2.778299 AGTTAGCAGACGCCAATTCAA 58.222 42.857 0.00 0.00 39.83 2.69
1813 1954 5.916883 CCAATTCAAGTGTGATCAGTTTCAC 59.083 40.000 0.00 0.18 45.05 3.18
1831 1972 5.818136 TTCACAAACAGTTCTCTCAAAGG 57.182 39.130 0.00 0.00 0.00 3.11
1845 1986 7.523293 TCTCTCAAAGGAAAATGCACATTAA 57.477 32.000 0.00 0.00 0.00 1.40
1952 2093 6.971527 TTTGATGTTTTCATGCCATTGATC 57.028 33.333 0.00 0.00 41.05 2.92
2030 2202 2.026636 TCTGTGTATTGTACCTTGGCCC 60.027 50.000 0.00 0.00 0.00 5.80
2247 2433 4.657814 AGGGTTTGATGGTGTACTCATT 57.342 40.909 0.00 0.00 0.00 2.57
2289 2475 6.785466 ACTTTTGTCCCTGGTTATTTTGGTAT 59.215 34.615 0.00 0.00 0.00 2.73
2307 2494 4.342951 TGGTATGGTTAAGTCCATCGGTAG 59.657 45.833 1.02 0.00 45.67 3.18
2324 2511 8.291032 CCATCGGTAGTTATTTTGTTGTGTTAA 58.709 33.333 0.00 0.00 0.00 2.01
2325 2512 9.325150 CATCGGTAGTTATTTTGTTGTGTTAAG 57.675 33.333 0.00 0.00 0.00 1.85
2327 2514 8.767085 TCGGTAGTTATTTTGTTGTGTTAAGAG 58.233 33.333 0.00 0.00 0.00 2.85
2505 2707 2.805845 CTTTTGGCTGTGCATATGAGC 58.194 47.619 6.97 6.62 0.00 4.26
2652 2854 7.780745 TGTAATTTTCCCTTGGTCTGTTTCTTA 59.219 33.333 0.00 0.00 0.00 2.10
2708 2910 6.767902 TGGAATCTTTCATATTCTAGGCACAC 59.232 38.462 0.00 0.00 34.43 3.82
2836 3052 1.471684 CAAGTTGGCTTGCCTGAGATC 59.528 52.381 13.18 0.00 44.54 2.75
2884 3102 5.700402 ATGAACCTCTGTTATGGCTAGTT 57.300 39.130 0.00 0.00 33.97 2.24
2907 3125 6.292649 GTTTAATAAAACCCTGCAACTGTTGC 60.293 38.462 32.58 32.58 46.03 4.17
3027 3245 3.873952 GCAGACATCATTGAGGAGGTAAC 59.126 47.826 5.16 0.00 31.00 2.50
3176 3395 6.887002 AGAATGGTCTTTAATGAAGAGGGTTC 59.113 38.462 0.00 0.00 44.78 3.62
3330 3551 8.783093 CAGTTGTCCTACATTGAACAAATTCTA 58.217 33.333 0.00 0.00 35.69 2.10
3436 3662 5.245526 GGACCTTTGTCTAAAGACCACTCTA 59.754 44.000 7.63 0.00 44.87 2.43
3479 3707 6.499000 TCCGTTGATATGGATACCCTTTATCA 59.501 38.462 0.00 0.00 36.93 2.15
3530 3758 5.470437 TGATGATAACACTTGTTTACGCCAA 59.530 36.000 0.00 0.00 39.31 4.52
3812 4041 6.434302 TGGATTCCTGTATGTGAATTTCCAT 58.566 36.000 3.95 0.58 29.18 3.41
3844 4081 5.697633 GCCTTTTGCTTGATTCATTCAAAGA 59.302 36.000 11.25 5.61 43.64 2.52
4025 7641 8.851541 AACCGAGTAAATTACTAAACAATCCA 57.148 30.769 5.55 0.00 39.59 3.41
4032 7648 9.797556 GTAAATTACTAAACAATCCAATGGGTC 57.202 33.333 0.00 0.00 34.93 4.46
4041 7657 8.551682 AAACAATCCAATGGGTCATATACATT 57.448 30.769 0.00 0.00 35.36 2.71
4432 8048 5.048364 CCCATGACGTACTTTCCAAAATTCA 60.048 40.000 0.00 0.00 0.00 2.57
4451 8067 3.181329 TCAAGCTGAACTTCTCCCCATA 58.819 45.455 0.00 0.00 36.04 2.74
4690 8306 4.834357 AACCAATGCAAGCCAAAATTTC 57.166 36.364 0.00 0.00 0.00 2.17
4694 8310 4.436317 CCAATGCAAGCCAAAATTTCATCG 60.436 41.667 0.00 0.00 0.00 3.84
4794 8411 7.769272 TCAAACTTTGACTGCTAATTTTTGG 57.231 32.000 0.00 0.00 34.08 3.28
4797 8414 8.663911 CAAACTTTGACTGCTAATTTTTGGAAA 58.336 29.630 0.00 0.00 0.00 3.13
4798 8415 8.424274 AACTTTGACTGCTAATTTTTGGAAAG 57.576 30.769 0.00 0.00 0.00 2.62
4799 8416 6.479990 ACTTTGACTGCTAATTTTTGGAAAGC 59.520 34.615 0.00 0.00 0.00 3.51
4801 8418 5.911752 TGACTGCTAATTTTTGGAAAGCAA 58.088 33.333 0.00 0.00 0.00 3.91
4802 8419 5.984926 TGACTGCTAATTTTTGGAAAGCAAG 59.015 36.000 0.00 0.00 0.00 4.01
4842 8459 6.854496 TGTTTAATAACAGGTGTGAGTGAC 57.146 37.500 0.00 0.00 39.29 3.67
4843 8460 6.350103 TGTTTAATAACAGGTGTGAGTGACA 58.650 36.000 0.00 0.00 39.29 3.58
4844 8461 6.481976 TGTTTAATAACAGGTGTGAGTGACAG 59.518 38.462 0.00 0.00 39.29 3.51
4851 8468 2.037772 AGGTGTGAGTGACAGGATTCAC 59.962 50.000 0.00 0.00 45.45 3.18
4884 8501 7.274033 ACAGATTTATGCATCAATTGACAAACG 59.726 33.333 11.07 0.00 0.00 3.60
4910 8527 4.560513 CGGTTTTGCAGGAATACCAACATT 60.561 41.667 13.46 0.00 38.94 2.71
4975 8593 8.768397 TGTTTATCTGGTGAGATATGGTTTAGT 58.232 33.333 0.00 0.00 40.27 2.24
4979 8597 7.108841 TCTGGTGAGATATGGTTTAGTACAC 57.891 40.000 0.00 0.00 0.00 2.90
4993 8611 7.499563 TGGTTTAGTACACTGCAATCACTTTAA 59.500 33.333 0.00 0.00 0.00 1.52
5031 8650 4.515567 CACCTTGTTTAGTTCCCAGTTCTC 59.484 45.833 0.00 0.00 0.00 2.87
5137 8756 4.120589 CCTTAACCGAGTCATCTTTAGCC 58.879 47.826 0.00 0.00 0.00 3.93
5197 8817 4.276431 CCCGAAACTTGCTAACTTGGTAAA 59.724 41.667 0.00 0.00 0.00 2.01
5390 9183 7.335422 CCAGCTTAACTACAGAAAGATTGTGAT 59.665 37.037 0.00 0.00 0.00 3.06
5391 9184 8.725148 CAGCTTAACTACAGAAAGATTGTGATT 58.275 33.333 0.00 0.00 0.00 2.57
5392 9185 8.725148 AGCTTAACTACAGAAAGATTGTGATTG 58.275 33.333 0.00 0.00 0.00 2.67
5393 9186 8.507249 GCTTAACTACAGAAAGATTGTGATTGT 58.493 33.333 0.00 0.00 0.00 2.71
5394 9187 9.817365 CTTAACTACAGAAAGATTGTGATTGTG 57.183 33.333 0.00 0.00 0.00 3.33
5395 9188 9.554395 TTAACTACAGAAAGATTGTGATTGTGA 57.446 29.630 0.00 0.00 0.00 3.58
5521 9317 1.555075 TCCTGGCTGTTACATCACTCC 59.445 52.381 0.00 0.00 0.00 3.85
5578 9374 7.410728 CGACTATGACAATTTTTCAAATGCACC 60.411 37.037 0.00 0.00 0.00 5.01
5599 9395 8.916062 TGCACCATTATATTCAGACAAATCAAT 58.084 29.630 0.00 0.00 0.00 2.57
5625 9421 8.254508 TGGTTTTTCTAGCGGCAAAATTATATT 58.745 29.630 1.45 0.00 0.00 1.28
5662 9463 9.478768 TGTGACGAAATGAGTTACTACAAATTA 57.521 29.630 0.00 0.00 0.00 1.40
5709 9510 6.308371 TGTTCTCTACCGAAAATTCCAAAC 57.692 37.500 0.00 0.00 0.00 2.93
5710 9511 5.239963 TGTTCTCTACCGAAAATTCCAAACC 59.760 40.000 0.00 0.00 0.00 3.27
5731 9532 3.996363 CCTGCCCTGCAAATTAAGAAAAC 59.004 43.478 0.00 0.00 38.41 2.43
5738 9539 5.526846 CCTGCAAATTAAGAAAACAAAGCCA 59.473 36.000 0.00 0.00 0.00 4.75
5757 9558 6.949352 AGCCAGTATTCATCAAAAGGTATG 57.051 37.500 0.00 0.00 0.00 2.39
5817 9620 2.389059 CGAGATCACATGACGATCCAC 58.611 52.381 19.54 14.90 40.17 4.02
5845 9648 2.042686 TGGAGGATGCTTTTGATCCG 57.957 50.000 0.00 0.00 43.78 4.18
5851 9654 3.196254 AGGATGCTTTTGATCCGCATTTT 59.804 39.130 9.33 1.42 43.77 1.82
6007 9818 5.458041 AAGTTTCAGCAACAGCATTACAT 57.542 34.783 0.00 0.00 37.93 2.29
6112 9940 6.417930 GCATACAGAAACAAGGTCAAAACTTC 59.582 38.462 0.00 0.00 0.00 3.01
6118 9946 7.698130 CAGAAACAAGGTCAAAACTTCAGTAAG 59.302 37.037 0.00 0.00 38.77 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.107072 AGAAGGAATTGATCTCCACTGGA 58.893 43.478 0.00 0.00 35.20 3.86
57 58 1.413445 CTGGGGAAGATGAGCAGAGAG 59.587 57.143 0.00 0.00 0.00 3.20
100 101 2.320587 CGCAGCACCTGTTCACTCC 61.321 63.158 0.00 0.00 33.43 3.85
102 103 2.281070 CCGCAGCACCTGTTCACT 60.281 61.111 0.00 0.00 33.43 3.41
375 376 2.202987 CTGGTCATCAGGCGAGGC 60.203 66.667 0.00 0.00 39.76 4.70
510 511 3.358076 CTTCCCGGTGCTCGAGTCC 62.358 68.421 15.13 15.34 42.43 3.85
686 687 3.068691 CTCCCTCGAAGCCGACCA 61.069 66.667 0.00 0.00 40.30 4.02
694 695 0.919780 TCCTCCTCCTCTCCCTCGAA 60.920 60.000 0.00 0.00 0.00 3.71
695 696 1.307953 TCCTCCTCCTCTCCCTCGA 60.308 63.158 0.00 0.00 0.00 4.04
743 747 3.470888 ACCTCCTCCGCATTCCCG 61.471 66.667 0.00 0.00 0.00 5.14
744 748 2.190578 CACCTCCTCCGCATTCCC 59.809 66.667 0.00 0.00 0.00 3.97
745 749 2.190578 CCACCTCCTCCGCATTCC 59.809 66.667 0.00 0.00 0.00 3.01
747 751 4.473520 CGCCACCTCCTCCGCATT 62.474 66.667 0.00 0.00 0.00 3.56
799 812 2.492484 TGTAGGGCGTTTGTGTTTGTTT 59.508 40.909 0.00 0.00 0.00 2.83
813 826 2.091775 TCCCTCTCTCTTACTGTAGGGC 60.092 54.545 4.93 0.00 42.91 5.19
814 827 3.435890 CCTCCCTCTCTCTTACTGTAGGG 60.436 56.522 3.60 3.60 44.29 3.53
815 828 3.435890 CCCTCCCTCTCTCTTACTGTAGG 60.436 56.522 0.00 0.00 0.00 3.18
816 829 3.460340 TCCCTCCCTCTCTCTTACTGTAG 59.540 52.174 0.00 0.00 0.00 2.74
817 830 3.471879 TCCCTCCCTCTCTCTTACTGTA 58.528 50.000 0.00 0.00 0.00 2.74
818 831 2.289467 TCCCTCCCTCTCTCTTACTGT 58.711 52.381 0.00 0.00 0.00 3.55
819 832 3.611025 ATCCCTCCCTCTCTCTTACTG 57.389 52.381 0.00 0.00 0.00 2.74
820 833 3.435890 CGAATCCCTCCCTCTCTCTTACT 60.436 52.174 0.00 0.00 0.00 2.24
821 834 2.888414 CGAATCCCTCCCTCTCTCTTAC 59.112 54.545 0.00 0.00 0.00 2.34
822 835 2.514582 ACGAATCCCTCCCTCTCTCTTA 59.485 50.000 0.00 0.00 0.00 2.10
823 836 1.289530 ACGAATCCCTCCCTCTCTCTT 59.710 52.381 0.00 0.00 0.00 2.85
824 837 0.930726 ACGAATCCCTCCCTCTCTCT 59.069 55.000 0.00 0.00 0.00 3.10
825 838 1.133606 AGACGAATCCCTCCCTCTCTC 60.134 57.143 0.00 0.00 0.00 3.20
826 839 0.930726 AGACGAATCCCTCCCTCTCT 59.069 55.000 0.00 0.00 0.00 3.10
827 840 1.410882 CAAGACGAATCCCTCCCTCTC 59.589 57.143 0.00 0.00 0.00 3.20
831 844 0.179070 GAGCAAGACGAATCCCTCCC 60.179 60.000 0.00 0.00 0.00 4.30
833 846 0.528684 CGGAGCAAGACGAATCCCTC 60.529 60.000 0.00 0.00 0.00 4.30
838 851 2.125106 GGCCGGAGCAAGACGAAT 60.125 61.111 5.05 0.00 42.56 3.34
844 857 3.944250 AATGGTGGGCCGGAGCAAG 62.944 63.158 5.05 0.00 42.56 4.01
845 858 3.521765 AAATGGTGGGCCGGAGCAA 62.522 57.895 5.05 0.00 42.56 3.91
858 871 0.395586 TGGGCCTCATTCCGAAATGG 60.396 55.000 4.53 0.00 42.19 3.16
866 880 1.162800 GCTCGTCATGGGCCTCATTC 61.163 60.000 4.53 0.01 32.92 2.67
993 1031 1.383803 GGAGGAGGACATGGAGGCT 60.384 63.158 0.00 0.00 0.00 4.58
1118 1156 0.179100 CACATAGGCGGTGAGACTGG 60.179 60.000 1.52 0.00 39.66 4.00
1120 1158 2.202866 CCACATAGGCGGTGAGACT 58.797 57.895 8.27 0.00 43.68 3.24
1133 1171 2.180946 TCCATAGACAGAGGCCACAT 57.819 50.000 5.01 0.00 0.00 3.21
1134 1172 2.180946 ATCCATAGACAGAGGCCACA 57.819 50.000 5.01 0.00 0.00 4.17
1140 1178 6.053650 TCAGATTGCAAATCCATAGACAGAG 58.946 40.000 1.71 0.00 0.00 3.35
1144 1182 7.446625 ACCTATTCAGATTGCAAATCCATAGAC 59.553 37.037 1.71 0.00 0.00 2.59
1152 1190 6.664816 TGGAAGAACCTATTCAGATTGCAAAT 59.335 34.615 1.71 0.00 37.29 2.32
1159 1198 6.125029 CACCAATGGAAGAACCTATTCAGAT 58.875 40.000 6.16 0.00 37.29 2.90
1163 1202 5.823045 CCTACACCAATGGAAGAACCTATTC 59.177 44.000 6.16 0.00 39.86 1.75
1165 1204 4.788617 ACCTACACCAATGGAAGAACCTAT 59.211 41.667 6.16 0.00 39.86 2.57
1170 1209 4.927267 ATCACCTACACCAATGGAAGAA 57.073 40.909 6.16 0.00 0.00 2.52
1305 1344 2.905415 TGCCCTCAGGACAATTCAAT 57.095 45.000 0.00 0.00 33.47 2.57
1404 1445 1.612199 GGGGTGGTAATGCTCGAACAA 60.612 52.381 0.00 0.00 0.00 2.83
1415 1456 2.168458 TGATCTCGATGGGGTGGTAA 57.832 50.000 0.00 0.00 0.00 2.85
1614 1752 1.812571 CCAATGTACAAGCACCACCTC 59.187 52.381 0.00 0.00 0.00 3.85
1615 1753 1.144913 ACCAATGTACAAGCACCACCT 59.855 47.619 0.00 0.00 0.00 4.00
1721 1862 1.202698 AGACTTCAGAACAGCGCCTTT 60.203 47.619 2.29 0.00 0.00 3.11
1722 1863 0.394565 AGACTTCAGAACAGCGCCTT 59.605 50.000 2.29 0.00 0.00 4.35
1723 1864 0.394565 AAGACTTCAGAACAGCGCCT 59.605 50.000 2.29 0.00 0.00 5.52
1724 1865 1.230324 AAAGACTTCAGAACAGCGCC 58.770 50.000 2.29 0.00 0.00 6.53
1725 1866 3.340337 AAAAAGACTTCAGAACAGCGC 57.660 42.857 0.00 0.00 0.00 5.92
1726 1867 6.715464 TCTTTAAAAAGACTTCAGAACAGCG 58.285 36.000 1.00 0.00 39.95 5.18
1727 1868 9.818796 CTATCTTTAAAAAGACTTCAGAACAGC 57.181 33.333 7.29 0.00 46.80 4.40
1742 1883 9.840427 GCAGCAGAATACAAACTATCTTTAAAA 57.160 29.630 0.00 0.00 0.00 1.52
1743 1884 8.458843 GGCAGCAGAATACAAACTATCTTTAAA 58.541 33.333 0.00 0.00 0.00 1.52
1744 1885 7.829211 AGGCAGCAGAATACAAACTATCTTTAA 59.171 33.333 0.00 0.00 0.00 1.52
1745 1886 7.338710 AGGCAGCAGAATACAAACTATCTTTA 58.661 34.615 0.00 0.00 0.00 1.85
1746 1887 6.183347 AGGCAGCAGAATACAAACTATCTTT 58.817 36.000 0.00 0.00 0.00 2.52
1747 1888 5.749462 AGGCAGCAGAATACAAACTATCTT 58.251 37.500 0.00 0.00 0.00 2.40
1748 1889 5.363939 GAGGCAGCAGAATACAAACTATCT 58.636 41.667 0.00 0.00 0.00 1.98
1749 1890 4.513318 GGAGGCAGCAGAATACAAACTATC 59.487 45.833 0.00 0.00 0.00 2.08
1750 1891 4.164988 AGGAGGCAGCAGAATACAAACTAT 59.835 41.667 0.00 0.00 0.00 2.12
1751 1892 3.519510 AGGAGGCAGCAGAATACAAACTA 59.480 43.478 0.00 0.00 0.00 2.24
1752 1893 2.307098 AGGAGGCAGCAGAATACAAACT 59.693 45.455 0.00 0.00 0.00 2.66
1753 1894 2.680339 GAGGAGGCAGCAGAATACAAAC 59.320 50.000 0.00 0.00 0.00 2.93
1754 1895 2.677902 CGAGGAGGCAGCAGAATACAAA 60.678 50.000 0.00 0.00 0.00 2.83
1774 1915 1.922570 ATTGGCGTCTGCTAACTACG 58.077 50.000 0.00 0.00 44.83 3.51
1813 1954 6.199719 GCATTTTCCTTTGAGAGAACTGTTTG 59.800 38.462 0.00 0.00 0.00 2.93
2004 2145 5.648092 GCCAAGGTACAATACACAGAATCTT 59.352 40.000 0.00 0.00 0.00 2.40
2017 2189 1.080638 AATCAGGGGCCAAGGTACAA 58.919 50.000 4.39 0.00 0.00 2.41
2030 2202 5.882557 ACCTGTAGCAAGTAATGAAATCAGG 59.117 40.000 0.00 0.00 39.13 3.86
2099 2271 5.009010 CAGCCACCGATTTCTTTATAGCATT 59.991 40.000 0.00 0.00 0.00 3.56
2101 2273 3.876914 CAGCCACCGATTTCTTTATAGCA 59.123 43.478 0.00 0.00 0.00 3.49
2247 2433 7.151999 ACAAAAGTAAATATGCATGTTCCGA 57.848 32.000 10.16 0.00 0.00 4.55
2289 2475 6.549433 AATAACTACCGATGGACTTAACCA 57.451 37.500 0.00 0.00 44.41 3.67
2505 2707 1.256376 CGCGAGAAGATGAATTCCACG 59.744 52.381 0.00 0.00 34.72 4.94
2557 2759 5.994250 AGCTTCAGCAGGATGATTACTTTA 58.006 37.500 0.75 0.00 45.16 1.85
2561 2763 7.330700 GTCTAATAGCTTCAGCAGGATGATTAC 59.669 40.741 0.75 0.00 45.16 1.89
2564 2766 5.306419 TGTCTAATAGCTTCAGCAGGATGAT 59.694 40.000 0.75 0.00 45.16 2.45
2572 2774 6.857777 ATGAATGTGTCTAATAGCTTCAGC 57.142 37.500 0.00 0.00 42.49 4.26
2652 2854 7.792032 TGATATAAACAGAAGACGGGAAAGAT 58.208 34.615 0.00 0.00 0.00 2.40
2708 2910 9.567848 ACATATTCTTTGTTGCCTAAAATAACG 57.432 29.630 0.00 0.00 0.00 3.18
2836 3052 6.316140 TCTTCATATCTCCCGAAAATGTTGTG 59.684 38.462 0.00 0.00 0.00 3.33
3027 3245 7.200455 ACATTTGGTTTCGTTCCTTTTAGAAG 58.800 34.615 0.00 0.00 0.00 2.85
3176 3395 9.696917 AAAAATCACCTTTAAATGCTACAAGAG 57.303 29.630 0.00 0.00 0.00 2.85
3215 3434 6.313905 AGAAACAATCCACGAATCATAGACAC 59.686 38.462 0.00 0.00 0.00 3.67
3436 3662 9.778741 ATCAACGGAGATACACAATACAAATAT 57.221 29.630 0.00 0.00 0.00 1.28
3530 3758 8.814038 ATGAGAAGGTAAGAAAAATGCATACT 57.186 30.769 0.00 0.00 0.00 2.12
3896 4146 8.866093 TGACCAAATCCATCGAATATAGACTTA 58.134 33.333 0.00 0.00 0.00 2.24
3944 7411 3.756963 GGAGTTGTCCCCACATTTTCTAC 59.243 47.826 0.00 0.00 36.76 2.59
3956 7423 1.834263 AGTATCAGCAGGAGTTGTCCC 59.166 52.381 0.00 0.00 45.26 4.46
3999 7551 8.938906 TGGATTGTTTAGTAATTTACTCGGTTC 58.061 33.333 12.26 4.58 40.14 3.62
4432 8048 3.525199 ACATATGGGGAGAAGTTCAGCTT 59.475 43.478 7.80 0.00 40.76 3.74
4497 8113 2.726760 CACGTCTAACTCACACTTCTGC 59.273 50.000 0.00 0.00 0.00 4.26
4554 8170 4.768968 AGCAATTTATGTCCAGAGCTTGTT 59.231 37.500 0.00 0.00 0.00 2.83
4690 8306 0.647410 GAGTTCCATGTGACGCGATG 59.353 55.000 15.93 5.70 0.00 3.84
4694 8310 4.693532 TGGAGTTCCATGTGACGC 57.306 55.556 0.00 0.00 42.01 5.19
4778 8395 5.528043 TGCTTTCCAAAAATTAGCAGTCA 57.472 34.783 0.00 0.00 0.00 3.41
4779 8396 5.985530 ACTTGCTTTCCAAAAATTAGCAGTC 59.014 36.000 0.00 0.00 31.94 3.51
4798 8415 4.567959 ACAAGATTTGAACAAAGCACTTGC 59.432 37.500 24.79 0.00 39.89 4.01
4799 8416 6.651755 AACAAGATTTGAACAAAGCACTTG 57.348 33.333 24.10 24.10 39.00 3.16
4801 8418 8.947055 ATTAAACAAGATTTGAACAAAGCACT 57.053 26.923 15.87 7.95 39.00 4.40
4815 8432 7.936847 TCACTCACACCTGTTATTAAACAAGAT 59.063 33.333 0.00 0.00 44.79 2.40
4818 8435 6.824196 TGTCACTCACACCTGTTATTAAACAA 59.176 34.615 0.00 0.00 44.79 2.83
4842 8459 8.834465 CATAAATCTGTAGGAAAGTGAATCCTG 58.166 37.037 5.36 0.00 46.72 3.86
4844 8461 7.283127 TGCATAAATCTGTAGGAAAGTGAATCC 59.717 37.037 0.00 0.00 37.22 3.01
4851 8468 9.459640 CAATTGATGCATAAATCTGTAGGAAAG 57.540 33.333 9.84 0.00 0.00 2.62
4884 8501 1.471287 GGTATTCCTGCAAAACCGGTC 59.529 52.381 8.04 0.00 0.00 4.79
4935 8552 6.014327 ACCAGATAAACAATGTCAAATGCCTT 60.014 34.615 0.00 0.00 0.00 4.35
4973 8591 9.448438 TGATAATTAAAGTGATTGCAGTGTACT 57.552 29.630 0.00 0.00 0.00 2.73
5031 8650 8.501580 GTTGAATCACCATAGACATATGATGTG 58.498 37.037 10.38 6.14 45.03 3.21
5137 8756 3.430929 CCAGATTTCAGGGTCTAGGTTCG 60.431 52.174 0.00 0.00 0.00 3.95
5162 8782 5.246203 AGCAAGTTTCGGGCATAGATAGATA 59.754 40.000 0.00 0.00 0.00 1.98
5163 8783 4.040952 AGCAAGTTTCGGGCATAGATAGAT 59.959 41.667 0.00 0.00 0.00 1.98
5165 8785 3.733337 AGCAAGTTTCGGGCATAGATAG 58.267 45.455 0.00 0.00 0.00 2.08
5243 8863 8.863086 AGGAATTGGGTACATCATAATCATTTG 58.137 33.333 0.00 0.00 0.00 2.32
5325 9112 0.387929 TTGTGAGCGACTTCGACCTT 59.612 50.000 2.02 0.00 43.02 3.50
5332 9119 8.773404 AGTATTTACTATTTTGTGAGCGACTT 57.227 30.769 0.00 0.00 34.13 3.01
5393 9186 7.684317 TTATACTATGTGAATGTCCCCTTCA 57.316 36.000 0.00 0.00 0.00 3.02
5394 9187 8.837389 GTTTTATACTATGTGAATGTCCCCTTC 58.163 37.037 0.00 0.00 0.00 3.46
5395 9188 8.557450 AGTTTTATACTATGTGAATGTCCCCTT 58.443 33.333 0.00 0.00 34.56 3.95
5521 9317 7.215789 ACTTGGTCAGAATATGATTAGCTCAG 58.784 38.462 0.00 0.00 40.92 3.35
5599 9395 4.329462 AATTTTGCCGCTAGAAAAACCA 57.671 36.364 0.00 0.00 0.00 3.67
5625 9421 4.994217 TCATTTCGTCACATGCTGACTTTA 59.006 37.500 19.39 9.49 46.50 1.85
5662 9463 0.035820 TATCGCGGGCCTGAGTTTTT 60.036 50.000 18.31 1.96 0.00 1.94
5709 9510 3.959535 TTTCTTAATTTGCAGGGCAGG 57.040 42.857 0.00 0.00 40.61 4.85
5710 9511 4.630111 TGTTTTCTTAATTTGCAGGGCAG 58.370 39.130 0.00 0.00 40.61 4.85
5731 9532 6.029346 ACCTTTTGATGAATACTGGCTTTG 57.971 37.500 0.00 0.00 0.00 2.77
5757 9558 7.816640 TGTTAAATGGCAGTTGATTCTTCTAC 58.183 34.615 10.91 0.00 0.00 2.59
5817 9620 6.225318 TCAAAAGCATCCTCCAATCTTTTTG 58.775 36.000 0.00 0.00 35.52 2.44
5845 9648 1.080974 ACGAGCTGCTGCAAAATGC 60.081 52.632 18.42 3.39 45.29 3.56
6007 9818 2.270352 AAATGACTGCCCGTTCTTGA 57.730 45.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.