Multiple sequence alignment - TraesCS6A01G040200

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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 TraesCS6A01G040200 chr6A 100.000 2417 0 0 1 2417 20870114 20872530 0.000000e+00 4464.0
1 TraesCS6A01G040200 chr6A 90.476 189 17 1 1 188 20865402 20865590 5.160000e-62 248.0
2 TraesCS6A01G040200 chr6D 87.031 933 76 18 936 1832 20780548 20781471 0.000000e+00 1011.0
3 TraesCS6A01G040200 chr6D 84.350 984 95 22 1396 2358 20781717 20782662 0.000000e+00 909.0
4 TraesCS6A01G040200 chr6D 86.832 805 40 22 194 942 20779727 20780521 0.000000e+00 839.0
5 TraesCS6A01G040200 chr6D 88.948 561 46 10 945 1496 20818708 20818155 0.000000e+00 678.0
6 TraesCS6A01G040200 chr6D 89.474 190 17 2 1 189 20779364 20779551 1.120000e-58 237.0
7 TraesCS6A01G040200 chr6D 95.620 137 6 0 763 899 20833515 20833379 1.120000e-53 220.0
8 TraesCS6A01G040200 chr6D 82.609 138 18 5 769 902 20834213 20834078 1.520000e-22 117.0
9 TraesCS6A01G040200 chr6D 86.250 80 10 1 1838 1917 20848911 20848833 4.280000e-13 86.1
10 TraesCS6A01G040200 chr6D 81.333 75 12 2 1838 1912 20817843 20817771 2.600000e-05 60.2
11 TraesCS6A01G040200 chr7B 97.136 419 12 0 999 1417 662311475 662311057 0.000000e+00 708.0
12 TraesCS6A01G040200 chr7B 96.852 413 13 0 999 1411 661716683 661717095 0.000000e+00 691.0
13 TraesCS6A01G040200 chr7B 96.209 422 16 0 999 1420 662009955 662009534 0.000000e+00 691.0
14 TraesCS6A01G040200 chr7B 96.610 413 14 0 999 1411 661999014 661999426 0.000000e+00 686.0
15 TraesCS6A01G040200 chr7B 89.873 79 6 2 2104 2182 100737010 100736934 1.530000e-17 100.0
16 TraesCS6A01G040200 chr7A 96.610 413 14 0 999 1411 680244597 680245009 0.000000e+00 686.0
17 TraesCS6A01G040200 chr7A 95.498 422 19 0 999 1420 680264524 680264103 0.000000e+00 675.0
18 TraesCS6A01G040200 chr7A 89.873 79 6 2 2104 2182 136807486 136807410 1.530000e-17 100.0
19 TraesCS6A01G040200 chr7D 95.327 428 20 0 984 1411 588409294 588409721 0.000000e+00 680.0
20 TraesCS6A01G040200 chr7D 89.873 79 6 2 2104 2182 136998208 136998132 1.530000e-17 100.0
21 TraesCS6A01G040200 chr7D 85.246 61 6 2 1561 1619 521644146 521644205 2.600000e-05 60.2
22 TraesCS6A01G040200 chr6B 90.761 184 17 0 763 946 35628854 35629037 1.860000e-61 246.0
23 TraesCS6A01G040200 chrUn 94.444 36 1 1 1485 1519 163376413 163376448 1.000000e-03 54.7


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 TraesCS6A01G040200 chr6A 20870114 20872530 2416 False 4464.0 4464 100.00000 1 2417 1 chr6A.!!$F2 2416
1 TraesCS6A01G040200 chr6D 20779364 20782662 3298 False 749.0 1011 86.92175 1 2358 4 chr6D.!!$F1 2357
2 TraesCS6A01G040200 chr6D 20817771 20818708 937 True 369.1 678 85.14050 945 1912 2 chr6D.!!$R2 967

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
82 83 0.038618 TAAGCACACGCGATGTCAGT 60.039 50.0 15.93 3.33 45.49 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 2786 0.034574 AGTGGCCTCACAACACAACA 60.035 50.0 3.32 0.0 45.91 3.33 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
54 55 9.553064 GACAAGACAATCTAATGACATAGGATT 57.447 33.333 8.91 8.91 0.00 3.01
70 71 7.112122 ACATAGGATTGTTTGATCTAAGCACA 58.888 34.615 0.00 0.00 0.00 4.57
75 76 1.724623 GTTTGATCTAAGCACACGCGA 59.275 47.619 15.93 0.00 45.49 5.87
78 79 1.135112 TGATCTAAGCACACGCGATGT 60.135 47.619 15.93 11.14 45.49 3.06
82 83 0.038618 TAAGCACACGCGATGTCAGT 60.039 50.000 15.93 3.33 45.49 3.41
116 117 1.812922 TCGACCGACGCCTAGAGTC 60.813 63.158 7.88 7.88 42.26 3.36
121 122 3.902086 GACGCCTAGAGTCGGCCC 61.902 72.222 0.00 0.00 44.73 5.80
131 132 1.143073 AGAGTCGGCCCTTCAAAAAGT 59.857 47.619 0.00 0.00 0.00 2.66
133 134 1.029681 GTCGGCCCTTCAAAAAGTGT 58.970 50.000 0.00 0.00 0.00 3.55
147 148 6.050432 TCAAAAAGTGTGTGTAACGTATCCT 58.950 36.000 0.00 0.00 42.39 3.24
148 149 5.917541 AAAAGTGTGTGTAACGTATCCTG 57.082 39.130 0.00 0.00 42.39 3.86
149 150 2.955614 AGTGTGTGTAACGTATCCTGC 58.044 47.619 0.00 0.00 42.39 4.85
170 171 3.957383 AAAAATGTGTGTGGTCCGC 57.043 47.368 0.00 0.00 0.00 5.54
172 173 0.467290 AAAATGTGTGTGGTCCGCCT 60.467 50.000 0.00 0.00 35.27 5.52
191 192 4.083155 GGGAGCCCCTATTCCACA 57.917 61.111 3.16 0.00 41.34 4.17
323 496 8.138074 TGTACAAATTTTGAATCCGATGAACAA 58.862 29.630 15.81 0.00 0.00 2.83
328 501 8.606040 AATTTTGAATCCGATGAACAATTTGT 57.394 26.923 0.00 0.00 0.00 2.83
341 514 6.871844 TGAACAATTTGTGAACTTGATGGAA 58.128 32.000 2.13 0.00 0.00 3.53
343 516 7.986320 TGAACAATTTGTGAACTTGATGGAAAT 59.014 29.630 2.13 0.00 0.00 2.17
344 517 8.735692 AACAATTTGTGAACTTGATGGAAATT 57.264 26.923 2.13 0.00 0.00 1.82
345 518 8.735692 ACAATTTGTGAACTTGATGGAAATTT 57.264 26.923 0.15 0.00 0.00 1.82
346 519 8.829612 ACAATTTGTGAACTTGATGGAAATTTC 58.170 29.630 9.83 9.83 0.00 2.17
349 522 9.617523 ATTTGTGAACTTGATGGAAATTTCTTT 57.382 25.926 17.42 5.72 0.00 2.52
470 644 7.104326 ACAAATTTCGTATTTGTTGCACATC 57.896 32.000 18.82 0.00 46.45 3.06
520 694 9.958234 TGAATTTGATGAACGTTTTCTAAATCA 57.042 25.926 15.86 15.86 32.36 2.57
636 810 8.237811 AGAGAAAATAAAGAGGCAAACAGAAA 57.762 30.769 0.00 0.00 0.00 2.52
646 820 4.769688 AGGCAAACAGAAAAGAAAAAGGG 58.230 39.130 0.00 0.00 0.00 3.95
679 853 7.016858 GGGTTTAGGGAAGGATTTAAAACCTTT 59.983 37.037 25.41 15.26 45.08 3.11
688 869 5.186992 AGGATTTAAAACCTTTCGGATTGGG 59.813 40.000 11.06 0.00 31.95 4.12
758 964 2.411535 CTGGTACATGCATGGCCAG 58.588 57.895 36.11 36.11 43.32 4.85
759 965 1.076850 TGGTACATGCATGGCCAGG 60.077 57.895 29.55 14.45 33.94 4.45
760 966 1.227102 GGTACATGCATGGCCAGGA 59.773 57.895 29.41 10.38 0.00 3.86
761 967 0.178981 GGTACATGCATGGCCAGGAT 60.179 55.000 29.41 12.39 0.00 3.24
762 968 1.242076 GTACATGCATGGCCAGGATC 58.758 55.000 29.41 4.58 0.00 3.36
763 969 0.250424 TACATGCATGGCCAGGATCG 60.250 55.000 29.41 10.27 0.00 3.69
764 970 1.527611 CATGCATGGCCAGGATCGT 60.528 57.895 24.18 2.21 0.00 3.73
765 971 1.105167 CATGCATGGCCAGGATCGTT 61.105 55.000 24.18 0.00 0.00 3.85
920 1148 3.118223 CCTTCCTCCATCCAGTTTCCTAC 60.118 52.174 0.00 0.00 0.00 3.18
935 1163 1.961394 TCCTACATAAATCTCGCCGCT 59.039 47.619 0.00 0.00 0.00 5.52
949 1208 4.796231 CGCTCCCTCCGTTCACCG 62.796 72.222 0.00 0.00 0.00 4.94
961 1220 1.792006 GTTCACCGTCGATCCAAACT 58.208 50.000 0.00 0.00 0.00 2.66
964 1224 1.548719 TCACCGTCGATCCAAACTCAT 59.451 47.619 0.00 0.00 0.00 2.90
990 1250 0.179000 ACACCCTCGAATCATCAGCC 59.821 55.000 0.00 0.00 0.00 4.85
991 1251 0.467384 CACCCTCGAATCATCAGCCT 59.533 55.000 0.00 0.00 0.00 4.58
1051 1314 1.258445 GGAGAAGGCCGAGAAGACCA 61.258 60.000 0.00 0.00 0.00 4.02
1054 1317 1.874345 GAAGGCCGAGAAGACCACGA 61.874 60.000 0.00 0.00 0.00 4.35
1058 1321 2.504244 CGAGAAGACCACGACGGC 60.504 66.667 0.00 0.00 39.03 5.68
1066 1329 2.257371 CCACGACGGCGAAGAAGA 59.743 61.111 22.49 0.00 41.64 2.87
1176 1439 5.275067 AGATCTACATCTTCAAGGTGCTC 57.725 43.478 0.00 0.00 35.67 4.26
1179 1442 5.227569 TCTACATCTTCAAGGTGCTCAAA 57.772 39.130 0.00 0.00 0.00 2.69
1241 1504 4.815308 GTCCATCATGAACTCCTTCATCAG 59.185 45.833 0.00 0.00 44.04 2.90
1311 1574 0.606401 ACAAGAAGCCCACCATCACG 60.606 55.000 0.00 0.00 0.00 4.35
1314 1577 1.003839 GAAGCCCACCATCACGTCA 60.004 57.895 0.00 0.00 0.00 4.35
1434 1697 2.682155 AGGCTTCATCCTCGTTTCTC 57.318 50.000 0.00 0.00 0.00 2.87
1437 1700 3.054802 AGGCTTCATCCTCGTTTCTCAAT 60.055 43.478 0.00 0.00 0.00 2.57
1446 1709 2.409975 TCGTTTCTCAATCCGTTGGAC 58.590 47.619 0.00 0.00 32.98 4.02
1462 1725 5.035443 CGTTGGACTCTGTATGTAGTTAGC 58.965 45.833 0.00 0.00 0.00 3.09
1474 1737 5.808042 ATGTAGTTAGCTGCAAGATTGTG 57.192 39.130 1.02 0.00 40.57 3.33
1483 1746 3.918591 GCTGCAAGATTGTGTTCTGAATG 59.081 43.478 0.00 0.00 34.07 2.67
1487 1750 5.530543 TGCAAGATTGTGTTCTGAATGTGTA 59.469 36.000 0.00 0.00 0.00 2.90
1504 1767 3.003585 TGTGTAATCTTGTGCTGCTTGTG 59.996 43.478 0.00 0.00 0.00 3.33
1511 1774 1.227943 GTGCTGCTTGTGGGTCTGA 60.228 57.895 0.00 0.00 0.00 3.27
1518 1781 4.326826 CTGCTTGTGGGTCTGAAGAAATA 58.673 43.478 0.00 0.00 0.00 1.40
1524 1787 7.283127 GCTTGTGGGTCTGAAGAAATATTCATA 59.717 37.037 0.00 0.00 38.47 2.15
1530 1793 7.659390 GGGTCTGAAGAAATATTCATAGGACTG 59.341 40.741 7.91 0.00 38.47 3.51
1531 1794 7.659390 GGTCTGAAGAAATATTCATAGGACTGG 59.341 40.741 7.91 0.00 38.47 4.00
1549 1812 7.555965 AGGACTGGTTAATGAATATTTTTGCC 58.444 34.615 0.00 0.00 0.00 4.52
1597 1861 3.811497 TCAGATTCTTCTTGCTGTGTGTG 59.189 43.478 0.00 0.00 0.00 3.82
1602 1866 5.888691 TTCTTCTTGCTGTGTGTGTTTTA 57.111 34.783 0.00 0.00 0.00 1.52
1610 1874 3.183775 GCTGTGTGTGTTTTACTACTCGG 59.816 47.826 0.00 0.00 0.00 4.63
1625 1889 1.279271 ACTCGGTTTCATCTGGAAGGG 59.721 52.381 0.00 0.00 36.72 3.95
1629 1893 2.447443 GGTTTCATCTGGAAGGGGTTC 58.553 52.381 0.00 0.00 36.72 3.62
1630 1894 2.225017 GGTTTCATCTGGAAGGGGTTCA 60.225 50.000 0.00 0.00 36.72 3.18
1633 1897 1.565759 TCATCTGGAAGGGGTTCATGG 59.434 52.381 0.00 0.00 0.00 3.66
1634 1898 0.929244 ATCTGGAAGGGGTTCATGGG 59.071 55.000 0.00 0.00 0.00 4.00
1682 2254 3.934068 TCTTTGTACCTTTCCCTTAGCG 58.066 45.455 0.00 0.00 0.00 4.26
1695 2267 1.634702 CTTAGCGAACAGTCTCTGCC 58.365 55.000 0.00 0.00 34.37 4.85
1699 2271 1.416813 GCGAACAGTCTCTGCCGATG 61.417 60.000 13.23 0.00 34.49 3.84
1737 2715 0.884514 GGAGCTTGCCTTTGTTCTCC 59.115 55.000 0.00 0.00 34.13 3.71
1792 2781 5.929697 TTCTGTTGATTCTTGTAGTGCTG 57.070 39.130 0.00 0.00 0.00 4.41
1793 2782 4.960938 TCTGTTGATTCTTGTAGTGCTGT 58.039 39.130 0.00 0.00 0.00 4.40
1795 2784 5.466728 TCTGTTGATTCTTGTAGTGCTGTTC 59.533 40.000 0.00 0.00 0.00 3.18
1796 2785 4.211164 TGTTGATTCTTGTAGTGCTGTTCG 59.789 41.667 0.00 0.00 0.00 3.95
1797 2786 3.990092 TGATTCTTGTAGTGCTGTTCGT 58.010 40.909 0.00 0.00 0.00 3.85
1798 2787 3.740832 TGATTCTTGTAGTGCTGTTCGTG 59.259 43.478 0.00 0.00 0.00 4.35
1799 2788 2.882927 TCTTGTAGTGCTGTTCGTGT 57.117 45.000 0.00 0.00 0.00 4.49
1813 2805 1.092921 TCGTGTTGTGTTGTGAGGCC 61.093 55.000 0.00 0.00 0.00 5.19
1814 2806 1.372838 CGTGTTGTGTTGTGAGGCCA 61.373 55.000 5.01 0.00 0.00 5.36
1831 2824 3.201708 AGGCCACTAGCTTTGAATCAGAT 59.798 43.478 5.01 0.00 43.05 2.90
1838 2831 7.187480 CACTAGCTTTGAATCAGATGAACATG 58.813 38.462 0.00 0.00 0.00 3.21
1840 2833 4.110482 GCTTTGAATCAGATGAACATGCC 58.890 43.478 0.00 0.00 0.00 4.40
1843 2836 3.812262 TGAATCAGATGAACATGCCGAT 58.188 40.909 0.00 0.00 0.00 4.18
1877 2919 2.108075 TGTTCCACAATGTGATGGAGGT 59.892 45.455 15.91 0.00 45.66 3.85
1883 2925 2.106338 ACAATGTGATGGAGGTGTGACA 59.894 45.455 0.00 0.00 0.00 3.58
1888 2930 2.037772 GTGATGGAGGTGTGACAGTTCT 59.962 50.000 0.00 0.00 0.00 3.01
1899 2941 5.411361 GGTGTGACAGTTCTATATGCACAAA 59.589 40.000 0.00 0.00 36.19 2.83
1905 2947 6.109359 ACAGTTCTATATGCACAAAGGAGAC 58.891 40.000 0.00 0.00 0.00 3.36
1915 2957 3.620821 GCACAAAGGAGACTCTGAATAGC 59.379 47.826 1.74 0.00 42.68 2.97
1916 2958 4.825422 CACAAAGGAGACTCTGAATAGCA 58.175 43.478 1.74 0.00 42.68 3.49
1917 2959 5.426504 CACAAAGGAGACTCTGAATAGCAT 58.573 41.667 1.74 0.00 42.68 3.79
1918 2960 6.577103 CACAAAGGAGACTCTGAATAGCATA 58.423 40.000 1.74 0.00 42.68 3.14
1919 2961 6.700960 CACAAAGGAGACTCTGAATAGCATAG 59.299 42.308 1.74 0.00 42.68 2.23
1920 2962 6.382570 ACAAAGGAGACTCTGAATAGCATAGT 59.617 38.462 1.74 0.00 42.68 2.12
1921 2963 6.403866 AAGGAGACTCTGAATAGCATAGTG 57.596 41.667 1.74 0.00 42.68 2.74
1922 2964 5.700183 AGGAGACTCTGAATAGCATAGTGA 58.300 41.667 1.74 0.00 34.45 3.41
1923 2965 6.314120 AGGAGACTCTGAATAGCATAGTGAT 58.686 40.000 1.74 0.00 34.45 3.06
1924 2966 7.465960 AGGAGACTCTGAATAGCATAGTGATA 58.534 38.462 1.74 0.00 34.45 2.15
1925 2967 7.947332 AGGAGACTCTGAATAGCATAGTGATAA 59.053 37.037 1.74 0.00 34.45 1.75
1951 2993 9.486497 ACATCATTACAAGAGCTATGTTATCTG 57.514 33.333 9.67 8.48 32.27 2.90
1958 3000 5.804944 AGAGCTATGTTATCTGTCTGCAT 57.195 39.130 0.00 0.00 0.00 3.96
1961 3003 6.705381 AGAGCTATGTTATCTGTCTGCATTTC 59.295 38.462 0.00 0.00 0.00 2.17
1976 3018 3.575256 TGCATTTCTCTTGCACCAAATCT 59.425 39.130 0.00 0.00 44.73 2.40
1978 3020 4.321452 GCATTTCTCTTGCACCAAATCTGA 60.321 41.667 0.00 0.00 39.90 3.27
2029 3071 6.150140 ACTGCAACATTCCAGTAGAATTTCTC 59.850 38.462 1.27 0.00 42.86 2.87
2032 3074 7.025963 GCAACATTCCAGTAGAATTTCTCAAG 58.974 38.462 1.27 0.00 42.86 3.02
2056 3098 6.267242 AGTTTTTCGAGGGAAGTAGAAGTACT 59.733 38.462 0.00 0.00 41.61 2.73
2063 3121 5.520751 AGGGAAGTAGAAGTACTGTATGCT 58.479 41.667 0.00 0.00 39.60 3.79
2080 3138 6.845302 TGTATGCTTAGTTGCAAGATTTCTG 58.155 36.000 0.00 0.00 46.61 3.02
2081 3139 4.164822 TGCTTAGTTGCAAGATTTCTGC 57.835 40.909 0.00 0.00 40.29 4.26
2116 3174 6.995091 AGTCTCTTTTAACAGTTGCAGAATCT 59.005 34.615 0.00 0.00 0.00 2.40
2134 3192 2.358737 GGTGGCGTCCAGGTCTTG 60.359 66.667 0.00 0.00 32.34 3.02
2135 3193 3.050275 GTGGCGTCCAGGTCTTGC 61.050 66.667 0.00 0.00 32.34 4.01
2160 3218 4.225942 TGACCTTATCAGTTCAAGCCATCT 59.774 41.667 0.00 0.00 31.91 2.90
2161 3219 5.184892 ACCTTATCAGTTCAAGCCATCTT 57.815 39.130 0.00 0.00 0.00 2.40
2229 3289 9.567776 TTTGTTCAAAGTTCTATCCAGTAATCA 57.432 29.630 0.00 0.00 0.00 2.57
2243 3303 5.487488 TCCAGTAATCACATTACCCAAGACT 59.513 40.000 3.29 0.00 44.77 3.24
2260 3320 6.135290 CAAGACTGGTTTCTTGTTTCATCA 57.865 37.500 4.94 0.00 45.12 3.07
2278 3338 3.084536 TCATCTGCTAAATGTTGCCCA 57.915 42.857 0.00 0.00 0.00 5.36
2292 3352 1.105457 TGCCCAGTTTATGCATCAGC 58.895 50.000 0.19 0.00 42.57 4.26
2293 3353 0.029834 GCCCAGTTTATGCATCAGCG 59.970 55.000 0.19 0.00 46.23 5.18
2334 3394 4.936891 AGCGAAAGTGCTCTTTTGATTTT 58.063 34.783 25.69 9.75 42.95 1.82
2358 3418 9.667107 TTTCCGTGAGATAAAAACAGATTAGAT 57.333 29.630 0.00 0.00 0.00 1.98
2359 3419 9.667107 TTCCGTGAGATAAAAACAGATTAGATT 57.333 29.630 0.00 0.00 0.00 2.40
2385 3445 7.253422 AGATGTTTATAGCACTGTTTTCATGC 58.747 34.615 0.00 0.00 35.86 4.06
2386 3446 6.324561 TGTTTATAGCACTGTTTTCATGCA 57.675 33.333 0.00 0.00 37.06 3.96
2387 3447 6.148948 TGTTTATAGCACTGTTTTCATGCAC 58.851 36.000 0.00 0.00 37.06 4.57
2388 3448 5.956068 TTATAGCACTGTTTTCATGCACA 57.044 34.783 0.00 0.00 37.06 4.57
2389 3449 4.852134 ATAGCACTGTTTTCATGCACAA 57.148 36.364 0.00 0.00 37.06 3.33
2390 3450 2.813061 AGCACTGTTTTCATGCACAAC 58.187 42.857 0.00 0.00 37.06 3.32
2391 3451 1.518102 GCACTGTTTTCATGCACAACG 59.482 47.619 0.00 0.00 35.77 4.10
2392 3452 1.518102 CACTGTTTTCATGCACAACGC 59.482 47.619 0.00 0.00 42.89 4.84
2403 3463 1.597742 GCACAACGCATGGATATCCT 58.402 50.000 22.35 5.66 41.79 3.24
2404 3464 1.532868 GCACAACGCATGGATATCCTC 59.467 52.381 22.35 10.54 41.79 3.71
2405 3465 2.146342 CACAACGCATGGATATCCTCC 58.854 52.381 22.35 9.56 45.19 4.30
2406 3466 1.072331 ACAACGCATGGATATCCTCCC 59.928 52.381 22.35 9.23 44.23 4.30
2407 3467 1.349026 CAACGCATGGATATCCTCCCT 59.651 52.381 22.35 2.42 44.23 4.20
2408 3468 1.734655 ACGCATGGATATCCTCCCTT 58.265 50.000 22.35 1.89 44.23 3.95
2409 3469 2.057922 ACGCATGGATATCCTCCCTTT 58.942 47.619 22.35 0.32 44.23 3.11
2410 3470 2.039084 ACGCATGGATATCCTCCCTTTC 59.961 50.000 22.35 4.43 44.23 2.62
2411 3471 2.038952 CGCATGGATATCCTCCCTTTCA 59.961 50.000 22.35 0.00 44.23 2.69
2412 3472 3.496692 CGCATGGATATCCTCCCTTTCAA 60.497 47.826 22.35 0.00 44.23 2.69
2413 3473 4.473444 GCATGGATATCCTCCCTTTCAAA 58.527 43.478 22.35 0.00 44.23 2.69
2414 3474 5.082425 GCATGGATATCCTCCCTTTCAAAT 58.918 41.667 22.35 0.87 44.23 2.32
2415 3475 5.541484 GCATGGATATCCTCCCTTTCAAATT 59.459 40.000 22.35 0.00 44.23 1.82
2416 3476 6.294955 GCATGGATATCCTCCCTTTCAAATTC 60.295 42.308 22.35 0.00 44.23 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.671190 TGTCTCGAATTCGACTACAAAAGTA 58.329 36.000 26.90 11.77 44.22 2.24
15 16 5.366829 TTGTCTTGTCTCGAATTCGACTA 57.633 39.130 25.96 14.43 44.22 2.59
19 20 6.871044 TTAGATTGTCTTGTCTCGAATTCG 57.129 37.500 21.78 21.78 41.45 3.34
54 55 1.459209 CGCGTGTGCTTAGATCAAACA 59.541 47.619 0.00 0.00 39.65 2.83
70 71 2.370281 ATTTCAGACTGACATCGCGT 57.630 45.000 5.77 0.00 0.00 6.01
75 76 2.489329 CGCCCAAATTTCAGACTGACAT 59.511 45.455 4.15 0.74 0.00 3.06
78 79 1.202879 ACCGCCCAAATTTCAGACTGA 60.203 47.619 0.00 0.00 0.00 3.41
82 83 0.035598 TCGACCGCCCAAATTTCAGA 59.964 50.000 0.00 0.00 0.00 3.27
109 110 2.762535 TTTTGAAGGGCCGACTCTAG 57.237 50.000 0.00 0.00 0.00 2.43
116 117 0.744281 ACACACTTTTTGAAGGGCCG 59.256 50.000 0.00 0.00 0.00 6.13
121 122 6.849305 GGATACGTTACACACACTTTTTGAAG 59.151 38.462 0.00 0.00 0.00 3.02
131 132 3.388345 TTGCAGGATACGTTACACACA 57.612 42.857 0.00 0.00 46.39 3.72
157 158 2.579657 CCTAGGCGGACCACACACA 61.580 63.158 0.00 0.00 39.06 3.72
299 472 9.703892 AATTGTTCATCGGATTCAAAATTTGTA 57.296 25.926 5.56 0.00 0.00 2.41
323 496 9.617523 AAAGAAATTTCCATCAAGTTCACAAAT 57.382 25.926 14.61 0.00 33.99 2.32
433 607 9.703892 AATACGAAATTTGTTCATCCATTTTCA 57.296 25.926 0.00 0.00 0.00 2.69
462 636 3.917380 CGCCGAATTTAAAAGATGTGCAA 59.083 39.130 0.00 0.00 0.00 4.08
470 644 7.114247 TCAGAATTTGTTCGCCGAATTTAAAAG 59.886 33.333 1.55 0.00 37.29 2.27
559 733 4.573201 TGCGAATTTTCTTACCTAATCCGG 59.427 41.667 0.00 0.00 0.00 5.14
623 797 4.811024 CCCTTTTTCTTTTCTGTTTGCCTC 59.189 41.667 0.00 0.00 0.00 4.70
653 827 6.021030 AGGTTTTAAATCCTTCCCTAAACCC 58.979 40.000 11.40 0.00 42.34 4.11
679 853 1.376683 CGGCTTTCACCCAATCCGA 60.377 57.895 0.00 0.00 39.23 4.55
688 869 0.165295 GCGTACCTTTCGGCTTTCAC 59.835 55.000 0.00 0.00 0.00 3.18
758 964 0.442699 GGCTGAAACGTGAACGATCC 59.557 55.000 10.26 0.00 43.02 3.36
759 965 1.136336 GTGGCTGAAACGTGAACGATC 60.136 52.381 10.26 7.97 43.02 3.69
760 966 0.865769 GTGGCTGAAACGTGAACGAT 59.134 50.000 10.26 0.00 43.02 3.73
761 967 1.484227 CGTGGCTGAAACGTGAACGA 61.484 55.000 10.26 0.00 43.02 3.85
762 968 1.083657 CGTGGCTGAAACGTGAACG 60.084 57.895 0.40 0.40 46.33 3.95
763 969 4.893241 CGTGGCTGAAACGTGAAC 57.107 55.556 0.00 0.00 36.31 3.18
815 1043 1.303236 TCGGCTGATGTTTGGGGTG 60.303 57.895 0.00 0.00 0.00 4.61
820 1048 2.480555 GCCGTCGGCTGATGTTTG 59.519 61.111 28.98 0.00 46.69 2.93
874 1102 1.302832 GGCTGTGGTTGGTGGAGAG 60.303 63.158 0.00 0.00 0.00 3.20
907 1135 5.992217 GCGAGATTTATGTAGGAAACTGGAT 59.008 40.000 0.00 0.00 43.88 3.41
920 1148 0.034059 AGGGAGCGGCGAGATTTATG 59.966 55.000 12.98 0.00 0.00 1.90
942 1170 1.725164 GAGTTTGGATCGACGGTGAAC 59.275 52.381 0.00 0.00 0.00 3.18
949 1208 2.483889 GGGGAGATGAGTTTGGATCGAC 60.484 54.545 0.00 0.00 0.00 4.20
961 1220 1.685765 CGAGGGTGTGGGGAGATGA 60.686 63.158 0.00 0.00 0.00 2.92
964 1224 0.976073 GATTCGAGGGTGTGGGGAGA 60.976 60.000 0.00 0.00 0.00 3.71
1033 1296 0.108567 GTGGTCTTCTCGGCCTTCTC 60.109 60.000 0.00 0.00 0.00 2.87
1034 1297 1.878656 CGTGGTCTTCTCGGCCTTCT 61.879 60.000 0.00 0.00 0.00 2.85
1035 1298 1.446272 CGTGGTCTTCTCGGCCTTC 60.446 63.158 0.00 0.00 0.00 3.46
1036 1299 1.906824 TCGTGGTCTTCTCGGCCTT 60.907 57.895 0.00 0.00 0.00 4.35
1037 1300 2.282958 TCGTGGTCTTCTCGGCCT 60.283 61.111 0.00 0.00 0.00 5.19
1038 1301 2.126031 GTCGTGGTCTTCTCGGCC 60.126 66.667 0.00 0.00 0.00 6.13
1039 1302 2.504244 CGTCGTGGTCTTCTCGGC 60.504 66.667 0.00 0.00 0.00 5.54
1051 1314 2.079020 TTGGTCTTCTTCGCCGTCGT 62.079 55.000 0.00 0.00 36.96 4.34
1054 1317 1.004918 CCTTGGTCTTCTTCGCCGT 60.005 57.895 0.00 0.00 0.00 5.68
1058 1321 0.737715 CTCGGCCTTGGTCTTCTTCG 60.738 60.000 0.00 0.00 0.00 3.79
1176 1439 2.203280 TCCGGGTGCACCTGTTTG 60.203 61.111 36.69 24.52 40.86 2.93
1179 1442 3.249189 ATGTCCGGGTGCACCTGT 61.249 61.111 36.69 20.20 40.86 4.00
1311 1574 1.760029 GAGGTCTGGATCTCCCTTGAC 59.240 57.143 0.00 0.56 37.92 3.18
1434 1697 3.861840 ACATACAGAGTCCAACGGATTG 58.138 45.455 0.00 0.00 32.73 2.67
1437 1700 3.693807 ACTACATACAGAGTCCAACGGA 58.306 45.455 0.00 0.00 0.00 4.69
1446 1709 5.895928 TCTTGCAGCTAACTACATACAGAG 58.104 41.667 0.00 0.00 0.00 3.35
1462 1725 4.915667 CACATTCAGAACACAATCTTGCAG 59.084 41.667 0.00 0.00 0.00 4.41
1474 1737 6.082338 CAGCACAAGATTACACATTCAGAAC 58.918 40.000 0.00 0.00 0.00 3.01
1483 1746 3.558505 CACAAGCAGCACAAGATTACAC 58.441 45.455 0.00 0.00 0.00 2.90
1487 1750 0.963962 CCCACAAGCAGCACAAGATT 59.036 50.000 0.00 0.00 0.00 2.40
1504 1767 7.659390 CAGTCCTATGAATATTTCTTCAGACCC 59.341 40.741 0.00 0.00 38.47 4.46
1524 1787 7.555965 GGCAAAAATATTCATTAACCAGTCCT 58.444 34.615 0.00 0.00 0.00 3.85
1530 1793 6.533367 TCAAGCGGCAAAAATATTCATTAACC 59.467 34.615 1.45 0.00 0.00 2.85
1531 1794 7.518731 TCAAGCGGCAAAAATATTCATTAAC 57.481 32.000 1.45 0.00 0.00 2.01
1539 1802 8.819974 CAATATTTCTTCAAGCGGCAAAAATAT 58.180 29.630 1.45 5.78 32.21 1.28
1540 1803 7.816995 ACAATATTTCTTCAAGCGGCAAAAATA 59.183 29.630 1.45 3.82 0.00 1.40
1541 1804 6.650390 ACAATATTTCTTCAAGCGGCAAAAAT 59.350 30.769 1.45 1.76 0.00 1.82
1543 1806 5.404968 CACAATATTTCTTCAAGCGGCAAAA 59.595 36.000 1.45 0.00 0.00 2.44
1546 1809 3.505680 ACACAATATTTCTTCAAGCGGCA 59.494 39.130 1.45 0.00 0.00 5.69
1547 1810 3.853671 CACACAATATTTCTTCAAGCGGC 59.146 43.478 0.00 0.00 0.00 6.53
1548 1811 5.046910 ACACACAATATTTCTTCAAGCGG 57.953 39.130 0.00 0.00 0.00 5.52
1549 1812 5.565259 GTGACACACAATATTTCTTCAAGCG 59.435 40.000 0.00 0.00 34.08 4.68
1597 1861 6.161381 TCCAGATGAAACCGAGTAGTAAAAC 58.839 40.000 0.00 0.00 0.00 2.43
1602 1866 3.195825 CCTTCCAGATGAAACCGAGTAGT 59.804 47.826 0.00 0.00 31.06 2.73
1610 1874 3.154827 TGAACCCCTTCCAGATGAAAC 57.845 47.619 0.00 0.00 31.06 2.78
1658 1942 5.557866 GCTAAGGGAAAGGTACAAAGAAGA 58.442 41.667 0.00 0.00 0.00 2.87
1664 1948 3.071312 TGTTCGCTAAGGGAAAGGTACAA 59.929 43.478 0.00 0.00 36.32 2.41
1682 2254 0.108424 AGCATCGGCAGAGACTGTTC 60.108 55.000 0.00 0.00 44.61 3.18
1695 2267 0.725686 CAACTTCAGAGGCAGCATCG 59.274 55.000 0.42 0.00 0.00 3.84
1699 2271 0.170561 CATGCAACTTCAGAGGCAGC 59.829 55.000 0.00 0.00 39.95 5.25
1782 2771 2.350192 CACAACACGAACAGCACTACAA 59.650 45.455 0.00 0.00 0.00 2.41
1789 2778 1.129624 TCACAACACAACACGAACAGC 59.870 47.619 0.00 0.00 0.00 4.40
1792 2781 1.531058 GCCTCACAACACAACACGAAC 60.531 52.381 0.00 0.00 0.00 3.95
1793 2782 0.730265 GCCTCACAACACAACACGAA 59.270 50.000 0.00 0.00 0.00 3.85
1795 2784 1.355210 GGCCTCACAACACAACACG 59.645 57.895 0.00 0.00 0.00 4.49
1796 2785 0.100503 GTGGCCTCACAACACAACAC 59.899 55.000 3.32 0.00 43.13 3.32
1797 2786 0.034574 AGTGGCCTCACAACACAACA 60.035 50.000 3.32 0.00 45.91 3.33
1798 2787 1.873591 CTAGTGGCCTCACAACACAAC 59.126 52.381 3.32 0.00 45.91 3.32
1799 2788 1.813862 GCTAGTGGCCTCACAACACAA 60.814 52.381 3.32 0.00 45.91 3.33
1813 2805 6.732531 TGTTCATCTGATTCAAAGCTAGTG 57.267 37.500 0.00 0.00 0.00 2.74
1814 2806 6.183360 GCATGTTCATCTGATTCAAAGCTAGT 60.183 38.462 0.00 0.00 0.00 2.57
1831 2824 3.724508 ACACAAAAATCGGCATGTTCA 57.275 38.095 0.00 0.00 0.00 3.18
1838 2831 3.626028 ACAGAGAACACAAAAATCGGC 57.374 42.857 0.00 0.00 0.00 5.54
1840 2833 4.970003 GTGGAACAGAGAACACAAAAATCG 59.030 41.667 0.00 0.00 41.80 3.34
1877 2919 5.643348 CCTTTGTGCATATAGAACTGTCACA 59.357 40.000 2.51 0.00 31.96 3.58
1883 2925 6.382570 AGAGTCTCCTTTGTGCATATAGAACT 59.617 38.462 2.51 3.63 0.00 3.01
1888 2930 6.544928 TTCAGAGTCTCCTTTGTGCATATA 57.455 37.500 0.00 0.00 0.00 0.86
1899 2941 5.700183 TCACTATGCTATTCAGAGTCTCCT 58.300 41.667 0.00 0.00 43.21 3.69
1905 2947 9.872721 ATGATGTTATCACTATGCTATTCAGAG 57.127 33.333 0.00 0.00 43.01 3.35
1915 2957 9.486497 AGCTCTTGTAATGATGTTATCACTATG 57.514 33.333 0.00 0.00 43.01 2.23
1918 2960 9.486497 CATAGCTCTTGTAATGATGTTATCACT 57.514 33.333 0.00 0.00 43.01 3.41
1919 2961 9.265901 ACATAGCTCTTGTAATGATGTTATCAC 57.734 33.333 0.00 0.00 43.01 3.06
1920 2962 9.836864 AACATAGCTCTTGTAATGATGTTATCA 57.163 29.630 4.33 0.00 44.55 2.15
1925 2967 9.486497 CAGATAACATAGCTCTTGTAATGATGT 57.514 33.333 0.00 0.00 0.00 3.06
1942 2984 6.183360 GCAAGAGAAATGCAGACAGATAACAT 60.183 38.462 0.00 0.00 43.29 2.71
1958 3000 4.717877 TCTCAGATTTGGTGCAAGAGAAA 58.282 39.130 0.00 0.00 0.00 2.52
1961 3003 3.672808 ACTCTCAGATTTGGTGCAAGAG 58.327 45.455 5.02 5.02 35.90 2.85
1997 3039 2.620115 CTGGAATGTTGCAGTGTCAACT 59.380 45.455 22.36 10.21 44.83 3.16
1998 3040 3.004024 CTGGAATGTTGCAGTGTCAAC 57.996 47.619 17.98 17.98 44.80 3.18
2010 3052 8.697507 AAACTTGAGAAATTCTACTGGAATGT 57.302 30.769 0.00 0.00 43.17 2.71
2013 3055 8.342634 CGAAAAACTTGAGAAATTCTACTGGAA 58.657 33.333 0.00 0.00 38.41 3.53
2029 3071 5.758784 ACTTCTACTTCCCTCGAAAAACTTG 59.241 40.000 0.00 0.00 0.00 3.16
2032 3074 6.365518 CAGTACTTCTACTTCCCTCGAAAAAC 59.634 42.308 0.00 0.00 30.03 2.43
2056 3098 6.623549 GCAGAAATCTTGCAACTAAGCATACA 60.624 38.462 0.00 0.00 45.19 2.29
2063 3121 4.397420 TCCTGCAGAAATCTTGCAACTAA 58.603 39.130 17.39 0.00 38.15 2.24
2080 3138 8.568794 ACTGTTAAAAGAGACTTTATTTCCTGC 58.431 33.333 0.00 0.00 0.00 4.85
2096 3154 5.916883 CACCAGATTCTGCAACTGTTAAAAG 59.083 40.000 8.23 0.00 0.00 2.27
2116 3174 2.847234 AAGACCTGGACGCCACCA 60.847 61.111 0.00 0.00 38.33 4.17
2135 3193 4.326826 TGGCTTGAACTGATAAGGTCAAG 58.673 43.478 27.74 27.74 36.14 3.02
2160 3218 5.699001 TCTTGCGCTAGAATAAAAGTGTCAA 59.301 36.000 19.24 0.00 0.00 3.18
2161 3219 5.234752 TCTTGCGCTAGAATAAAAGTGTCA 58.765 37.500 19.24 0.00 0.00 3.58
2175 3233 3.059665 CACGATTGCATATTCTTGCGCTA 60.060 43.478 9.73 0.00 45.77 4.26
2220 3280 5.586243 CAGTCTTGGGTAATGTGATTACTGG 59.414 44.000 6.46 0.00 43.53 4.00
2223 3283 5.944007 AACCAGTCTTGGGTAATGTGATTAC 59.056 40.000 0.00 0.00 44.69 1.89
2226 3286 4.657814 AACCAGTCTTGGGTAATGTGAT 57.342 40.909 0.00 0.00 44.69 3.06
2229 3289 4.724279 AGAAACCAGTCTTGGGTAATGT 57.276 40.909 0.00 0.00 46.25 2.71
2243 3303 4.828939 AGCAGATGATGAAACAAGAAACCA 59.171 37.500 0.00 0.00 0.00 3.67
2260 3320 3.091633 ACTGGGCAACATTTAGCAGAT 57.908 42.857 0.00 0.00 39.74 2.90
2278 3338 5.049405 GGCTATTTACGCTGATGCATAAACT 60.049 40.000 0.00 0.00 39.20 2.66
2292 3352 3.372954 CTTCCTCTGTCGGCTATTTACG 58.627 50.000 0.00 0.00 0.00 3.18
2293 3353 3.124560 GCTTCCTCTGTCGGCTATTTAC 58.875 50.000 0.00 0.00 0.00 2.01
2359 3419 8.397906 GCATGAAAACAGTGCTATAAACATCTA 58.602 33.333 0.00 0.00 36.02 1.98
2360 3420 7.094248 TGCATGAAAACAGTGCTATAAACATCT 60.094 33.333 0.00 0.00 39.52 2.90
2361 3421 7.008628 GTGCATGAAAACAGTGCTATAAACATC 59.991 37.037 0.00 0.00 39.52 3.06
2362 3422 6.808212 GTGCATGAAAACAGTGCTATAAACAT 59.192 34.615 0.00 0.00 39.52 2.71
2363 3423 6.148948 GTGCATGAAAACAGTGCTATAAACA 58.851 36.000 0.00 0.00 39.52 2.83
2364 3424 6.148948 TGTGCATGAAAACAGTGCTATAAAC 58.851 36.000 0.00 0.00 39.52 2.01
2365 3425 6.324561 TGTGCATGAAAACAGTGCTATAAA 57.675 33.333 0.00 0.00 39.52 1.40
2366 3426 5.956068 TGTGCATGAAAACAGTGCTATAA 57.044 34.783 0.00 0.00 39.52 0.98
2367 3427 5.616645 CGTTGTGCATGAAAACAGTGCTATA 60.617 40.000 0.00 0.00 39.52 1.31
2368 3428 4.549458 GTTGTGCATGAAAACAGTGCTAT 58.451 39.130 0.00 0.00 39.52 2.97
2369 3429 3.547813 CGTTGTGCATGAAAACAGTGCTA 60.548 43.478 0.00 0.00 39.52 3.49
2370 3430 2.795681 CGTTGTGCATGAAAACAGTGCT 60.796 45.455 0.00 0.00 39.52 4.40
2371 3431 1.518102 CGTTGTGCATGAAAACAGTGC 59.482 47.619 0.00 0.00 39.26 4.40
2372 3432 1.518102 GCGTTGTGCATGAAAACAGTG 59.482 47.619 0.00 0.00 45.45 3.66
2373 3433 1.838913 GCGTTGTGCATGAAAACAGT 58.161 45.000 0.00 0.00 45.45 3.55
2384 3444 1.532868 GAGGATATCCATGCGTTGTGC 59.467 52.381 23.81 0.00 40.97 4.57


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

AutoCloner maintained by Alex Coulton.