Multiple sequence alignment - TraesCS7D01G168600

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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 TraesCS7D01G168600 chr7D 100.000 2704 0 0 1 2704 119106987 119104284 0.000000e+00 4994.0
1 TraesCS7D01G168600 chr7D 93.058 677 18 11 1 652 403771127 403770455 0.000000e+00 963.0
2 TraesCS7D01G168600 chr7D 84.795 171 16 4 1 169 579818027 579818189 2.150000e-36 163.0
3 TraesCS7D01G168600 chr7D 80.791 177 20 8 1 169 70111657 70111487 2.830000e-25 126.0
4 TraesCS7D01G168600 chr7D 94.203 69 3 1 651 718 403770421 403770353 1.320000e-18 104.0
5 TraesCS7D01G168600 chr7B 89.125 1177 66 28 717 1859 80514655 80513507 0.000000e+00 1408.0
6 TraesCS7D01G168600 chr7A 91.148 723 38 10 1182 1884 123264988 123264272 0.000000e+00 957.0
7 TraesCS7D01G168600 chr7A 94.521 219 5 1 717 935 123270884 123270673 5.580000e-87 331.0
8 TraesCS7D01G168600 chr7A 89.474 247 25 1 2153 2399 123263599 123263354 7.270000e-81 311.0
9 TraesCS7D01G168600 chr7A 85.354 198 22 3 1957 2149 123264267 123264072 5.910000e-47 198.0
10 TraesCS7D01G168600 chr7A 73.308 517 77 36 1 493 95945182 95945661 1.690000e-27 134.0
11 TraesCS7D01G168600 chr7A 86.250 80 7 3 2059 2136 50264117 50264040 1.730000e-12 84.2
12 TraesCS7D01G168600 chr1B 91.069 683 28 16 1 652 303883356 303882676 0.000000e+00 893.0
13 TraesCS7D01G168600 chr1B 94.513 565 22 6 1 558 303887165 303886603 0.000000e+00 863.0
14 TraesCS7D01G168600 chr1B 85.246 244 28 7 995 1231 581412188 581412430 7.480000e-61 244.0
15 TraesCS7D01G168600 chr1B 96.809 94 3 0 559 652 303886574 303886481 1.000000e-34 158.0
16 TraesCS7D01G168600 chr1B 93.651 63 2 2 655 715 303882636 303882574 2.870000e-15 93.5
17 TraesCS7D01G168600 chr5A 88.774 677 47 15 1 652 447204250 447204922 0.000000e+00 802.0
18 TraesCS7D01G168600 chr5A 95.588 68 3 0 651 718 447204959 447205026 2.850000e-20 110.0
19 TraesCS7D01G168600 chr5A 85.897 78 11 0 2059 2136 611345200 611345277 1.730000e-12 84.2
20 TraesCS7D01G168600 chr1D 85.656 244 27 6 995 1231 430466519 430466761 1.610000e-62 250.0
21 TraesCS7D01G168600 chr1A 85.656 244 27 6 995 1231 528063723 528063965 1.610000e-62 250.0
22 TraesCS7D01G168600 chr1A 100.000 29 0 0 2569 2597 60706069 60706097 1.000000e-03 54.7
23 TraesCS7D01G168600 chr4A 90.123 81 7 1 2056 2136 96535639 96535560 1.320000e-18 104.0
24 TraesCS7D01G168600 chr4A 88.732 71 7 1 2068 2137 117950303 117950233 4.800000e-13 86.1
25 TraesCS7D01G168600 chr4A 85.714 77 10 1 94 169 201172819 201172895 2.230000e-11 80.5
26 TraesCS7D01G168600 chr6B 92.308 65 4 1 2057 2121 457410641 457410704 1.030000e-14 91.6
27 TraesCS7D01G168600 chr4D 91.667 60 5 0 2071 2130 259496375 259496316 1.730000e-12 84.2
28 TraesCS7D01G168600 chr5B 94.340 53 2 1 2064 2115 642938849 642938901 2.230000e-11 80.5
29 TraesCS7D01G168600 chr2D 90.323 62 5 1 2060 2121 621941217 621941277 2.230000e-11 80.5
30 TraesCS7D01G168600 chr6D 80.769 104 12 7 2494 2595 115634903 115634806 1.040000e-09 75.0
31 TraesCS7D01G168600 chr3A 89.091 55 3 3 654 705 381017414 381017468 6.250000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G168600 chr7D 119104284 119106987 2703 True 4994.000000 4994 100.000000 1 2704 1 chr7D.!!$R2 2703
1 TraesCS7D01G168600 chr7D 403770353 403771127 774 True 533.500000 963 93.630500 1 718 2 chr7D.!!$R3 717
2 TraesCS7D01G168600 chr7B 80513507 80514655 1148 True 1408.000000 1408 89.125000 717 1859 1 chr7B.!!$R1 1142
3 TraesCS7D01G168600 chr7A 123263354 123264988 1634 True 488.666667 957 88.658667 1182 2399 3 chr7A.!!$R3 1217
4 TraesCS7D01G168600 chr1B 303882574 303887165 4591 True 501.875000 893 94.010500 1 715 4 chr1B.!!$R1 714
5 TraesCS7D01G168600 chr5A 447204250 447205026 776 False 456.000000 802 92.181000 1 718 2 chr5A.!!$F2 717

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
856 4743 0.175073 ATACGGAAGAACACGGCTCC 59.825 55.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 5972 0.110486 ACGTTTGCTGACTCCCCATT 59.89 50.0 0.0 0.0 0.0 3.16 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
474 4288 3.869246 AGCTCGTTAATTTACACGGGATG 59.131 43.478 8.20 0.00 39.36 3.51
609 4452 2.161012 CGTGAGCTTAGTTAGTGGACGA 59.839 50.000 0.00 0.00 0.00 4.20
691 4572 7.283625 TGCTAAAATCTTAAACCATGTGTGT 57.716 32.000 0.00 0.00 0.00 3.72
730 4612 0.469144 ACGGGCCAATCCAAGTTTGT 60.469 50.000 4.39 0.00 36.21 2.83
741 4623 6.468956 CCAATCCAAGTTTGTATTCGATTTCG 59.531 38.462 0.00 0.00 41.45 3.46
745 4627 6.369340 TCCAAGTTTGTATTCGATTTCGCTAA 59.631 34.615 0.00 0.00 39.60 3.09
756 4638 3.245990 CGATTTCGCTAAGCATGTCATCA 59.754 43.478 0.00 0.00 0.00 3.07
759 4642 2.554142 TCGCTAAGCATGTCATCAAGG 58.446 47.619 0.00 0.00 0.00 3.61
765 4648 5.452496 GCTAAGCATGTCATCAAGGACTCTA 60.452 44.000 0.00 0.00 38.61 2.43
773 4656 5.127845 TGTCATCAAGGACTCTAGAACATCC 59.872 44.000 8.66 8.66 38.61 3.51
782 4665 6.903534 AGGACTCTAGAACATCCTATTTCCAA 59.096 38.462 15.21 0.00 39.89 3.53
832 4719 1.003233 GGAAGGCTCCGTGAAGCTT 60.003 57.895 0.00 0.00 42.13 3.74
852 4739 0.999406 CAGCATACGGAAGAACACGG 59.001 55.000 0.00 0.00 0.00 4.94
854 4741 0.739813 GCATACGGAAGAACACGGCT 60.740 55.000 0.00 0.00 0.00 5.52
855 4742 1.278238 CATACGGAAGAACACGGCTC 58.722 55.000 0.00 0.00 0.00 4.70
856 4743 0.175073 ATACGGAAGAACACGGCTCC 59.825 55.000 0.00 0.00 0.00 4.70
857 4744 2.203972 TACGGAAGAACACGGCTCCG 62.204 60.000 6.79 6.79 45.13 4.63
868 4755 2.753043 GGCTCCGTCCTCCGTGTA 60.753 66.667 0.00 0.00 33.66 2.90
869 4756 2.125961 GGCTCCGTCCTCCGTGTAT 61.126 63.158 0.00 0.00 33.66 2.29
902 4789 3.459378 CTCGCGATGCCATTGCCAC 62.459 63.158 10.36 0.00 36.27 5.01
922 4809 1.929230 GAGCTTCTCGTCCTAAAGCC 58.071 55.000 2.91 0.00 45.09 4.35
924 4811 1.205893 AGCTTCTCGTCCTAAAGCCTG 59.794 52.381 2.91 0.00 45.09 4.85
936 4823 0.411058 AAAGCCTGCTCCCATTTCCT 59.589 50.000 0.00 0.00 0.00 3.36
939 4826 1.755783 CCTGCTCCCATTTCCTGCC 60.756 63.158 0.00 0.00 0.00 4.85
940 4827 1.305623 CTGCTCCCATTTCCTGCCT 59.694 57.895 0.00 0.00 0.00 4.75
941 4828 1.000521 TGCTCCCATTTCCTGCCTG 60.001 57.895 0.00 0.00 0.00 4.85
943 4830 0.750911 GCTCCCATTTCCTGCCTGAG 60.751 60.000 0.00 0.00 0.00 3.35
944 4831 0.622665 CTCCCATTTCCTGCCTGAGT 59.377 55.000 0.00 0.00 0.00 3.41
1302 5189 3.426903 CGGTCTCCGGTATCCCTAA 57.573 57.895 0.00 0.00 44.15 2.69
1306 5193 2.317973 GTCTCCGGTATCCCTAAGCTT 58.682 52.381 3.48 3.48 0.00 3.74
1427 5314 1.509004 GAGACCAGCTCGTGAGTCC 59.491 63.158 0.00 0.00 33.17 3.85
1430 5317 1.939769 GACCAGCTCGTGAGTCCTCC 61.940 65.000 0.00 0.00 0.00 4.30
1431 5318 1.979155 CCAGCTCGTGAGTCCTCCA 60.979 63.158 0.00 0.00 0.00 3.86
1445 5358 3.519913 AGTCCTCCACCTGAATTAACTCC 59.480 47.826 0.00 0.00 0.00 3.85
1677 5590 1.271163 TGGAGTCGTGGGAATTGGTTC 60.271 52.381 0.00 0.00 0.00 3.62
1679 5592 2.500229 GAGTCGTGGGAATTGGTTCAA 58.500 47.619 0.00 0.00 36.01 2.69
1728 5641 0.741927 GTTTGCTCCCAATGCATGCC 60.742 55.000 16.68 0.00 40.34 4.40
1755 5684 0.589708 CATGCTGCCATGTATCCACG 59.410 55.000 0.00 0.00 43.07 4.94
1763 5692 1.327460 CCATGTATCCACGTTTGCGAG 59.673 52.381 0.00 0.00 42.00 5.03
1775 5704 2.964123 CGTTTGCGAGTTATGTTGTGTG 59.036 45.455 0.00 0.00 41.33 3.82
1842 5775 9.354673 CCTTCTGCTTGGAATAAGGAAATAATA 57.645 33.333 0.00 0.00 39.26 0.98
1881 5823 8.447053 GGTTTTTGTCTTCTTAAATGTGCAAAA 58.553 29.630 0.00 0.00 34.25 2.44
1909 5851 8.566008 AAATTCAAATCTTTTGTGAGAACTCG 57.434 30.769 0.39 0.00 0.00 4.18
1910 5852 5.095691 TCAAATCTTTTGTGAGAACTCGC 57.904 39.130 8.23 8.23 40.32 5.03
1911 5853 4.574421 TCAAATCTTTTGTGAGAACTCGCA 59.426 37.500 13.04 13.04 46.99 5.10
1918 5860 3.607422 TGTGAGAACTCGCAAAACATG 57.393 42.857 14.39 0.00 45.85 3.21
1919 5861 2.942376 TGTGAGAACTCGCAAAACATGT 59.058 40.909 14.39 0.00 45.85 3.21
1920 5862 3.376859 TGTGAGAACTCGCAAAACATGTT 59.623 39.130 14.39 4.92 45.85 2.71
1921 5863 4.572795 TGTGAGAACTCGCAAAACATGTTA 59.427 37.500 12.39 0.00 45.85 2.41
1922 5864 5.238432 TGTGAGAACTCGCAAAACATGTTAT 59.762 36.000 12.39 0.00 45.85 1.89
1923 5865 5.565259 GTGAGAACTCGCAAAACATGTTATG 59.435 40.000 12.39 2.37 39.72 1.90
1924 5866 5.468409 TGAGAACTCGCAAAACATGTTATGA 59.532 36.000 12.39 6.66 0.00 2.15
1925 5867 6.149308 TGAGAACTCGCAAAACATGTTATGAT 59.851 34.615 12.39 0.00 0.00 2.45
1926 5868 6.913170 AGAACTCGCAAAACATGTTATGATT 58.087 32.000 12.39 0.00 0.00 2.57
1927 5869 7.023575 AGAACTCGCAAAACATGTTATGATTC 58.976 34.615 12.39 9.49 0.00 2.52
1928 5870 6.252967 ACTCGCAAAACATGTTATGATTCA 57.747 33.333 12.39 0.00 0.00 2.57
1929 5871 6.317088 ACTCGCAAAACATGTTATGATTCAG 58.683 36.000 12.39 5.12 0.00 3.02
1930 5872 5.639757 TCGCAAAACATGTTATGATTCAGG 58.360 37.500 12.39 0.00 0.00 3.86
1931 5873 5.182950 TCGCAAAACATGTTATGATTCAGGT 59.817 36.000 12.39 0.00 0.00 4.00
1932 5874 5.512788 CGCAAAACATGTTATGATTCAGGTC 59.487 40.000 12.39 0.00 0.00 3.85
1933 5875 5.512788 GCAAAACATGTTATGATTCAGGTCG 59.487 40.000 12.39 0.00 0.00 4.79
1934 5876 6.611381 CAAAACATGTTATGATTCAGGTCGT 58.389 36.000 12.39 0.00 0.00 4.34
1935 5877 7.625395 GCAAAACATGTTATGATTCAGGTCGTA 60.625 37.037 12.39 0.00 0.00 3.43
1936 5878 6.903883 AACATGTTATGATTCAGGTCGTAC 57.096 37.500 9.97 0.00 0.00 3.67
1937 5879 5.972935 ACATGTTATGATTCAGGTCGTACA 58.027 37.500 0.00 0.00 0.00 2.90
1938 5880 6.042777 ACATGTTATGATTCAGGTCGTACAG 58.957 40.000 0.00 0.00 0.00 2.74
1939 5881 5.907866 TGTTATGATTCAGGTCGTACAGA 57.092 39.130 0.00 0.00 0.00 3.41
1940 5882 6.465439 TGTTATGATTCAGGTCGTACAGAT 57.535 37.500 0.00 0.00 0.00 2.90
1941 5883 6.873997 TGTTATGATTCAGGTCGTACAGATT 58.126 36.000 0.00 0.00 0.00 2.40
1942 5884 8.002984 TGTTATGATTCAGGTCGTACAGATTA 57.997 34.615 0.00 0.00 0.00 1.75
1943 5885 7.919091 TGTTATGATTCAGGTCGTACAGATTAC 59.081 37.037 0.00 0.00 0.00 1.89
1944 5886 6.716934 ATGATTCAGGTCGTACAGATTACT 57.283 37.500 0.00 0.00 0.00 2.24
1945 5887 6.525578 TGATTCAGGTCGTACAGATTACTT 57.474 37.500 0.00 0.00 0.00 2.24
1946 5888 7.634671 TGATTCAGGTCGTACAGATTACTTA 57.365 36.000 0.00 0.00 0.00 2.24
1947 5889 7.478322 TGATTCAGGTCGTACAGATTACTTAC 58.522 38.462 0.00 0.00 0.00 2.34
1948 5890 7.338703 TGATTCAGGTCGTACAGATTACTTACT 59.661 37.037 0.00 0.00 0.00 2.24
1949 5891 7.458409 TTCAGGTCGTACAGATTACTTACTT 57.542 36.000 0.00 0.00 0.00 2.24
1950 5892 7.458409 TCAGGTCGTACAGATTACTTACTTT 57.542 36.000 0.00 0.00 0.00 2.66
1951 5893 7.889469 TCAGGTCGTACAGATTACTTACTTTT 58.111 34.615 0.00 0.00 0.00 2.27
1952 5894 8.362639 TCAGGTCGTACAGATTACTTACTTTTT 58.637 33.333 0.00 0.00 0.00 1.94
2039 5981 1.771255 GCTCATAGGACAATGGGGAGT 59.229 52.381 0.00 0.00 0.00 3.85
2049 5991 0.110486 AATGGGGAGTCAGCAAACGT 59.890 50.000 0.00 0.00 0.00 3.99
2063 6005 3.915437 CAAACGTGCACCCTATTTTCT 57.085 42.857 12.15 0.00 0.00 2.52
2120 6067 7.898014 AGGATCATAGTACAAGTCACATACA 57.102 36.000 0.00 0.00 0.00 2.29
2123 6070 7.435488 GGATCATAGTACAAGTCACATACACAC 59.565 40.741 0.00 0.00 0.00 3.82
2124 6071 6.627243 TCATAGTACAAGTCACATACACACC 58.373 40.000 0.00 0.00 0.00 4.16
2125 6072 4.948341 AGTACAAGTCACATACACACCA 57.052 40.909 0.00 0.00 0.00 4.17
2131 6078 2.151202 GTCACATACACACCAACCTGG 58.849 52.381 0.00 0.00 45.02 4.45
2136 6083 1.394618 TACACACCAACCTGGCAAAC 58.605 50.000 0.00 0.00 42.67 2.93
2137 6084 1.065600 CACACCAACCTGGCAAACG 59.934 57.895 0.00 0.00 42.67 3.60
2149 6096 4.038080 CAAACGCGCACCCTTCCC 62.038 66.667 5.73 0.00 0.00 3.97
2158 6574 2.689771 ACCCTTCCCCGGCGTTAT 60.690 61.111 6.01 0.00 0.00 1.89
2191 6607 2.166459 AGATTGCACTGCGTTAGCTAGA 59.834 45.455 0.00 0.00 45.42 2.43
2206 6622 0.734253 CTAGAGAGCAAACGCGCACT 60.734 55.000 5.73 0.00 35.39 4.40
2267 6683 3.190327 TCGCCATGTGTTTATCTGGTTTG 59.810 43.478 0.00 0.00 0.00 2.93
2281 6697 4.750941 TCTGGTTTGGGGATTTTCTCAAT 58.249 39.130 0.00 0.00 0.00 2.57
2284 6700 6.784969 TCTGGTTTGGGGATTTTCTCAATAAA 59.215 34.615 0.00 0.00 0.00 1.40
2312 6728 1.244816 GGTTTTGGGAAGGTTCTCCG 58.755 55.000 0.00 0.00 36.21 4.63
2313 6729 0.596577 GTTTTGGGAAGGTTCTCCGC 59.403 55.000 0.00 0.00 36.21 5.54
2342 6758 6.699642 CCAGTTTTGTTTTACTTATGGGTGTG 59.300 38.462 0.00 0.00 0.00 3.82
2354 6770 0.045623 TGGGTGTGGGTATCCCTGAT 59.954 55.000 6.38 0.00 45.70 2.90
2357 6773 1.507140 GTGTGGGTATCCCTGATCCA 58.493 55.000 6.38 0.00 45.70 3.41
2364 6780 2.505819 GGTATCCCTGATCCAGTGTGTT 59.494 50.000 0.00 0.00 0.00 3.32
2366 6782 4.163458 GGTATCCCTGATCCAGTGTGTTTA 59.837 45.833 0.00 0.00 0.00 2.01
2368 6784 4.927267 TCCCTGATCCAGTGTGTTTATT 57.073 40.909 0.00 0.00 0.00 1.40
2377 6793 4.702612 TCCAGTGTGTTTATTTGTGTGTGT 59.297 37.500 0.00 0.00 0.00 3.72
2409 6825 2.962786 GCGTGTGCGTGTGTACCA 60.963 61.111 0.00 0.00 40.81 3.25
2410 6826 2.938823 GCGTGTGCGTGTGTACCAG 61.939 63.158 0.00 0.00 40.81 4.00
2411 6827 1.590525 CGTGTGCGTGTGTACCAGT 60.591 57.895 0.00 0.00 0.00 4.00
2412 6828 1.149361 CGTGTGCGTGTGTACCAGTT 61.149 55.000 0.00 0.00 0.00 3.16
2413 6829 1.011333 GTGTGCGTGTGTACCAGTTT 58.989 50.000 0.00 0.00 0.00 2.66
2414 6830 1.399089 GTGTGCGTGTGTACCAGTTTT 59.601 47.619 0.00 0.00 0.00 2.43
2415 6831 2.085320 TGTGCGTGTGTACCAGTTTTT 58.915 42.857 0.00 0.00 0.00 1.94
2509 6925 9.506018 TCTGAGTACATTTTTCAGATTCATGAA 57.494 29.630 11.26 11.26 41.62 2.57
2510 6926 9.552114 CTGAGTACATTTTTCAGATTCATGAAC 57.448 33.333 11.07 5.15 40.54 3.18
2511 6927 8.229811 TGAGTACATTTTTCAGATTCATGAACG 58.770 33.333 11.07 2.60 38.87 3.95
2512 6928 8.099364 AGTACATTTTTCAGATTCATGAACGT 57.901 30.769 11.07 0.00 38.87 3.99
2513 6929 8.567948 AGTACATTTTTCAGATTCATGAACGTT 58.432 29.630 11.07 0.00 38.87 3.99
2514 6930 9.180678 GTACATTTTTCAGATTCATGAACGTTT 57.819 29.630 11.07 0.00 38.87 3.60
2515 6931 8.647143 ACATTTTTCAGATTCATGAACGTTTT 57.353 26.923 11.07 0.00 38.87 2.43
2516 6932 9.743057 ACATTTTTCAGATTCATGAACGTTTTA 57.257 25.926 11.07 0.00 38.87 1.52
2524 6940 9.712410 CAGATTCATGAACGTTTTAAAATTTCG 57.288 29.630 11.07 5.95 0.00 3.46
2525 6941 9.672086 AGATTCATGAACGTTTTAAAATTTCGA 57.328 25.926 11.07 7.28 0.00 3.71
2526 6942 9.922951 GATTCATGAACGTTTTAAAATTTCGAG 57.077 29.630 11.07 11.01 0.00 4.04
2527 6943 9.672086 ATTCATGAACGTTTTAAAATTTCGAGA 57.328 25.926 11.07 12.53 0.00 4.04
2528 6944 9.504710 TTCATGAACGTTTTAAAATTTCGAGAA 57.495 25.926 14.18 16.01 0.00 2.87
2529 6945 9.672086 TCATGAACGTTTTAAAATTTCGAGAAT 57.328 25.926 14.18 4.25 0.00 2.40
2667 7083 9.945904 AAACTCGAGATTCTTTATTTAGAAGGT 57.054 29.630 21.68 0.00 37.55 3.50
2687 7103 8.478066 AGAAGGTATTTAATGAAAAATCAGCCC 58.522 33.333 0.00 0.00 31.63 5.19
2688 7104 7.732222 AGGTATTTAATGAAAAATCAGCCCA 57.268 32.000 0.00 0.00 31.63 5.36
2689 7105 8.322905 AGGTATTTAATGAAAAATCAGCCCAT 57.677 30.769 0.00 0.00 31.63 4.00
2690 7106 9.432982 AGGTATTTAATGAAAAATCAGCCCATA 57.567 29.630 0.00 0.00 31.63 2.74
2691 7107 9.696917 GGTATTTAATGAAAAATCAGCCCATAG 57.303 33.333 0.00 0.00 31.63 2.23
2694 7110 8.593945 TTTAATGAAAAATCAGCCCATAGACT 57.406 30.769 0.00 0.00 0.00 3.24
2695 7111 8.593945 TTAATGAAAAATCAGCCCATAGACTT 57.406 30.769 0.00 0.00 0.00 3.01
2696 7112 7.486407 AATGAAAAATCAGCCCATAGACTTT 57.514 32.000 0.00 0.00 0.00 2.66
2697 7113 8.593945 AATGAAAAATCAGCCCATAGACTTTA 57.406 30.769 0.00 0.00 0.00 1.85
2698 7114 8.773033 ATGAAAAATCAGCCCATAGACTTTAT 57.227 30.769 0.00 0.00 0.00 1.40
2699 7115 9.866655 ATGAAAAATCAGCCCATAGACTTTATA 57.133 29.630 0.00 0.00 0.00 0.98
2700 7116 9.693739 TGAAAAATCAGCCCATAGACTTTATAA 57.306 29.630 0.00 0.00 0.00 0.98
2703 7119 9.700831 AAAATCAGCCCATAGACTTTATAAACT 57.299 29.630 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
328 4140 5.654603 ATGACGTGTCTGTGTTATAGGAA 57.345 39.130 0.00 0.00 0.00 3.36
374 4188 1.002624 CCGAAAGCTGGCCCAGTAA 60.003 57.895 13.35 0.00 33.43 2.24
474 4288 7.759489 TGGAGACATATATAAAATTGGTGGC 57.241 36.000 0.00 0.00 33.40 5.01
609 4452 2.028130 CCTCTAAGCTCATCCTCACGT 58.972 52.381 0.00 0.00 0.00 4.49
730 4612 5.047188 TGACATGCTTAGCGAAATCGAATA 58.953 37.500 7.06 0.00 43.02 1.75
741 4623 3.539604 AGTCCTTGATGACATGCTTAGC 58.460 45.455 0.00 0.00 37.73 3.09
745 4627 4.285020 TCTAGAGTCCTTGATGACATGCT 58.715 43.478 0.00 0.00 37.73 3.79
756 4638 6.903534 TGGAAATAGGATGTTCTAGAGTCCTT 59.096 38.462 21.40 9.65 41.22 3.36
759 4642 7.496263 GGTTTGGAAATAGGATGTTCTAGAGTC 59.504 40.741 0.00 0.00 0.00 3.36
782 4665 1.385347 TGACTGTGGACCCCAGGTT 60.385 57.895 8.95 0.00 35.25 3.50
832 4719 1.403647 CCGTGTTCTTCCGTATGCTGA 60.404 52.381 0.00 0.00 0.00 4.26
857 4744 3.808174 GCCTGAAATAATACACGGAGGAC 59.192 47.826 0.00 0.00 0.00 3.85
858 4745 3.452990 TGCCTGAAATAATACACGGAGGA 59.547 43.478 0.00 0.00 0.00 3.71
859 4746 3.804036 TGCCTGAAATAATACACGGAGG 58.196 45.455 0.00 0.00 0.00 4.30
860 4747 3.248602 GCTGCCTGAAATAATACACGGAG 59.751 47.826 0.00 0.00 0.00 4.63
861 4748 3.118408 AGCTGCCTGAAATAATACACGGA 60.118 43.478 0.00 0.00 0.00 4.69
862 4749 3.206150 AGCTGCCTGAAATAATACACGG 58.794 45.455 0.00 0.00 0.00 4.94
863 4750 4.122776 AGAGCTGCCTGAAATAATACACG 58.877 43.478 0.00 0.00 0.00 4.49
864 4751 4.210120 CGAGAGCTGCCTGAAATAATACAC 59.790 45.833 0.00 0.00 0.00 2.90
865 4752 4.371786 CGAGAGCTGCCTGAAATAATACA 58.628 43.478 0.00 0.00 0.00 2.29
866 4753 4.981389 CGAGAGCTGCCTGAAATAATAC 57.019 45.455 0.00 0.00 0.00 1.89
915 4802 2.027385 GGAAATGGGAGCAGGCTTTAG 58.973 52.381 0.00 0.00 0.00 1.85
916 4803 1.640670 AGGAAATGGGAGCAGGCTTTA 59.359 47.619 0.00 0.00 0.00 1.85
917 4804 0.411058 AGGAAATGGGAGCAGGCTTT 59.589 50.000 0.00 0.00 0.00 3.51
922 4809 1.035932 CAGGCAGGAAATGGGAGCAG 61.036 60.000 0.00 0.00 0.00 4.24
924 4811 0.750911 CTCAGGCAGGAAATGGGAGC 60.751 60.000 0.00 0.00 0.00 4.70
936 4823 1.607801 CGGATGTCAGGACTCAGGCA 61.608 60.000 0.65 0.00 0.00 4.75
939 4826 0.457851 GGTCGGATGTCAGGACTCAG 59.542 60.000 0.65 0.00 0.00 3.35
940 4827 1.313091 CGGTCGGATGTCAGGACTCA 61.313 60.000 0.65 0.00 0.00 3.41
941 4828 1.433879 CGGTCGGATGTCAGGACTC 59.566 63.158 0.65 0.00 0.00 3.36
943 4830 2.202756 GCGGTCGGATGTCAGGAC 60.203 66.667 0.00 0.00 0.00 3.85
944 4831 3.822192 CGCGGTCGGATGTCAGGA 61.822 66.667 0.00 0.00 0.00 3.86
992 4879 2.611800 TGAGGTCCATGCTGGCCT 60.612 61.111 3.32 13.73 43.50 5.19
1062 4949 2.915659 AGAAGGCGTCGGTGGACA 60.916 61.111 0.00 0.00 43.61 4.02
1302 5189 1.749033 GCGCAGATAGGGGTAAGCT 59.251 57.895 0.30 0.00 0.00 3.74
1306 5193 2.915659 CCGGCGCAGATAGGGGTA 60.916 66.667 10.83 0.00 0.00 3.69
1403 5290 0.453793 CACGAGCTGGTCTCTGGTAG 59.546 60.000 0.00 0.00 39.70 3.18
1427 5314 3.611766 ACGGAGTTAATTCAGGTGGAG 57.388 47.619 3.40 0.00 37.78 3.86
1484 5397 1.594518 GGCACGTACGCTGCAATTATG 60.595 52.381 29.99 15.52 36.27 1.90
1677 5590 1.605710 CTTCTGAAGGTGGCACAGTTG 59.394 52.381 20.82 5.33 41.80 3.16
1679 5592 1.131638 TCTTCTGAAGGTGGCACAGT 58.868 50.000 20.82 5.92 41.80 3.55
1752 5681 2.964123 CACAACATAACTCGCAAACGTG 59.036 45.455 0.00 0.00 41.18 4.49
1754 5683 2.964123 CACACAACATAACTCGCAAACG 59.036 45.455 0.00 0.00 42.01 3.60
1755 5684 2.719046 GCACACAACATAACTCGCAAAC 59.281 45.455 0.00 0.00 0.00 2.93
1763 5692 5.579384 TTACTACACGCACACAACATAAC 57.421 39.130 0.00 0.00 0.00 1.89
1775 5704 8.578308 TTATACATGTGGTTATTACTACACGC 57.422 34.615 9.11 0.00 46.63 5.34
1802 5731 2.203938 AAGGGCTCCGGGAGACAA 60.204 61.111 30.32 0.00 39.95 3.18
1842 5775 9.990868 AGAAGACAAAAACCCCTATATTACATT 57.009 29.630 0.00 0.00 0.00 2.71
1843 5776 9.990868 AAGAAGACAAAAACCCCTATATTACAT 57.009 29.630 0.00 0.00 0.00 2.29
1853 5786 5.465390 GCACATTTAAGAAGACAAAAACCCC 59.535 40.000 0.00 0.00 0.00 4.95
1884 5826 7.168135 GCGAGTTCTCACAAAAGATTTGAATTT 59.832 33.333 9.62 0.00 0.00 1.82
1886 5828 6.145535 GCGAGTTCTCACAAAAGATTTGAAT 58.854 36.000 9.62 0.00 0.00 2.57
1888 5830 4.574421 TGCGAGTTCTCACAAAAGATTTGA 59.426 37.500 9.62 0.00 0.00 2.69
1889 5831 4.847633 TGCGAGTTCTCACAAAAGATTTG 58.152 39.130 1.47 1.47 0.00 2.32
1890 5832 5.499139 TTGCGAGTTCTCACAAAAGATTT 57.501 34.783 1.49 0.00 0.00 2.17
1891 5833 5.499139 TTTGCGAGTTCTCACAAAAGATT 57.501 34.783 11.82 0.00 0.00 2.40
1892 5834 5.163663 TGTTTTGCGAGTTCTCACAAAAGAT 60.164 36.000 21.22 0.00 41.26 2.40
1893 5835 4.155099 TGTTTTGCGAGTTCTCACAAAAGA 59.845 37.500 21.22 18.72 41.26 2.52
1894 5836 4.411327 TGTTTTGCGAGTTCTCACAAAAG 58.589 39.130 21.22 0.00 41.26 2.27
1895 5837 4.427096 TGTTTTGCGAGTTCTCACAAAA 57.573 36.364 18.52 18.52 39.09 2.44
1896 5838 4.142491 ACATGTTTTGCGAGTTCTCACAAA 60.142 37.500 10.62 10.62 0.00 2.83
1897 5839 3.376859 ACATGTTTTGCGAGTTCTCACAA 59.623 39.130 0.00 0.00 0.00 3.33
1898 5840 2.942376 ACATGTTTTGCGAGTTCTCACA 59.058 40.909 0.00 0.00 0.00 3.58
1899 5841 3.609103 ACATGTTTTGCGAGTTCTCAC 57.391 42.857 0.00 0.00 0.00 3.51
1900 5842 5.468409 TCATAACATGTTTTGCGAGTTCTCA 59.532 36.000 17.78 0.00 0.00 3.27
1901 5843 5.927030 TCATAACATGTTTTGCGAGTTCTC 58.073 37.500 17.78 0.00 0.00 2.87
1902 5844 5.940192 TCATAACATGTTTTGCGAGTTCT 57.060 34.783 17.78 0.00 0.00 3.01
1903 5845 6.801377 TGAATCATAACATGTTTTGCGAGTTC 59.199 34.615 17.78 17.92 0.00 3.01
1904 5846 6.676950 TGAATCATAACATGTTTTGCGAGTT 58.323 32.000 17.78 11.24 0.00 3.01
1905 5847 6.252967 TGAATCATAACATGTTTTGCGAGT 57.747 33.333 17.78 7.56 0.00 4.18
1906 5848 5.740569 CCTGAATCATAACATGTTTTGCGAG 59.259 40.000 17.78 11.45 0.00 5.03
1907 5849 5.182950 ACCTGAATCATAACATGTTTTGCGA 59.817 36.000 17.78 8.69 0.00 5.10
1908 5850 5.401550 ACCTGAATCATAACATGTTTTGCG 58.598 37.500 17.78 3.30 0.00 4.85
1909 5851 5.512788 CGACCTGAATCATAACATGTTTTGC 59.487 40.000 17.78 7.22 0.00 3.68
1910 5852 6.611381 ACGACCTGAATCATAACATGTTTTG 58.389 36.000 17.78 18.75 0.00 2.44
1911 5853 6.817765 ACGACCTGAATCATAACATGTTTT 57.182 33.333 17.78 5.99 0.00 2.43
1912 5854 6.876789 TGTACGACCTGAATCATAACATGTTT 59.123 34.615 17.78 0.00 0.00 2.83
1913 5855 6.403049 TGTACGACCTGAATCATAACATGTT 58.597 36.000 16.68 16.68 0.00 2.71
1914 5856 5.972935 TGTACGACCTGAATCATAACATGT 58.027 37.500 0.00 0.00 0.00 3.21
1915 5857 6.273071 TCTGTACGACCTGAATCATAACATG 58.727 40.000 0.00 0.00 0.00 3.21
1916 5858 6.465439 TCTGTACGACCTGAATCATAACAT 57.535 37.500 0.00 0.00 0.00 2.71
1917 5859 5.907866 TCTGTACGACCTGAATCATAACA 57.092 39.130 0.00 0.00 0.00 2.41
1918 5860 8.136165 AGTAATCTGTACGACCTGAATCATAAC 58.864 37.037 0.00 0.00 0.00 1.89
1919 5861 8.234136 AGTAATCTGTACGACCTGAATCATAA 57.766 34.615 0.00 0.00 0.00 1.90
1920 5862 7.818997 AGTAATCTGTACGACCTGAATCATA 57.181 36.000 0.00 0.00 0.00 2.15
1921 5863 6.716934 AGTAATCTGTACGACCTGAATCAT 57.283 37.500 0.00 0.00 0.00 2.45
1922 5864 6.525578 AAGTAATCTGTACGACCTGAATCA 57.474 37.500 0.00 0.00 0.00 2.57
1923 5865 7.705214 AGTAAGTAATCTGTACGACCTGAATC 58.295 38.462 0.00 0.00 0.00 2.52
1924 5866 7.642082 AGTAAGTAATCTGTACGACCTGAAT 57.358 36.000 0.00 0.00 0.00 2.57
1925 5867 7.458409 AAGTAAGTAATCTGTACGACCTGAA 57.542 36.000 0.00 0.00 0.00 3.02
1926 5868 7.458409 AAAGTAAGTAATCTGTACGACCTGA 57.542 36.000 0.00 0.00 0.00 3.86
1927 5869 8.530269 AAAAAGTAAGTAATCTGTACGACCTG 57.470 34.615 0.00 0.00 0.00 4.00
2018 5960 0.758734 TCCCCATTGTCCTATGAGCG 59.241 55.000 0.00 0.00 0.00 5.03
2023 5965 1.771255 GCTGACTCCCCATTGTCCTAT 59.229 52.381 0.00 0.00 32.67 2.57
2030 5972 0.110486 ACGTTTGCTGACTCCCCATT 59.890 50.000 0.00 0.00 0.00 3.16
2049 5991 8.602472 ATTACCATAAAAGAAAATAGGGTGCA 57.398 30.769 0.00 0.00 36.87 4.57
2110 6057 2.224523 CCAGGTTGGTGTGTATGTGACT 60.225 50.000 0.00 0.00 31.35 3.41
2111 6058 2.151202 CCAGGTTGGTGTGTATGTGAC 58.849 52.381 0.00 0.00 31.35 3.67
2116 6063 1.960689 GTTTGCCAGGTTGGTGTGTAT 59.039 47.619 0.00 0.00 40.46 2.29
2120 6067 2.781158 GCGTTTGCCAGGTTGGTGT 61.781 57.895 0.00 0.00 40.46 4.16
2123 6070 4.999939 GCGCGTTTGCCAGGTTGG 63.000 66.667 8.43 0.00 41.55 3.77
2124 6071 4.263209 TGCGCGTTTGCCAGGTTG 62.263 61.111 8.43 0.00 38.08 3.77
2125 6072 4.264638 GTGCGCGTTTGCCAGGTT 62.265 61.111 8.43 0.00 38.08 3.50
2131 6078 4.700365 GGAAGGGTGCGCGTTTGC 62.700 66.667 8.43 0.00 37.91 3.68
2145 6092 2.203470 AAAAAGATAACGCCGGGGAA 57.797 45.000 27.23 13.13 0.00 3.97
2174 6590 1.133216 CTCTCTAGCTAACGCAGTGCA 59.867 52.381 16.83 0.00 45.00 4.57
2191 6607 3.044305 GGAGTGCGCGTTTGCTCT 61.044 61.111 8.43 0.00 41.06 4.09
2202 6618 2.350522 CCATGTAGTGTTGAGGAGTGC 58.649 52.381 0.00 0.00 0.00 4.40
2206 6622 0.618458 GGCCCATGTAGTGTTGAGGA 59.382 55.000 0.00 0.00 0.00 3.71
2246 6662 3.500982 CAAACCAGATAAACACATGGCG 58.499 45.455 0.00 0.00 36.21 5.69
2290 6706 2.424379 GGAGAACCTTCCCAAAACCAGT 60.424 50.000 0.00 0.00 0.00 4.00
2312 6728 6.143278 CCATAAGTAAAACAAAACTGGTTCGC 59.857 38.462 0.00 0.00 0.00 4.70
2313 6729 6.639279 CCCATAAGTAAAACAAAACTGGTTCG 59.361 38.462 0.00 0.00 0.00 3.95
2319 6735 6.183360 CCCACACCCATAAGTAAAACAAAACT 60.183 38.462 0.00 0.00 0.00 2.66
2354 6770 4.702612 ACACACACAAATAAACACACTGGA 59.297 37.500 0.00 0.00 0.00 3.86
2357 6773 5.048364 ACACACACACACAAATAAACACACT 60.048 36.000 0.00 0.00 0.00 3.55
2364 6780 3.763902 GTGCACACACACACACAAATAA 58.236 40.909 13.17 0.00 46.61 1.40
2366 6782 2.276472 GTGCACACACACACACAAAT 57.724 45.000 13.17 0.00 46.61 2.32
2391 6807 2.962786 GGTACACACGCACACGCA 60.963 61.111 0.00 0.00 45.53 5.24
2484 6900 9.552114 GTTCATGAATCTGAAAAATGTACTCAG 57.448 33.333 12.12 3.30 36.92 3.35
2485 6901 8.229811 CGTTCATGAATCTGAAAAATGTACTCA 58.770 33.333 12.12 0.00 36.92 3.41
2486 6902 8.230486 ACGTTCATGAATCTGAAAAATGTACTC 58.770 33.333 12.12 0.00 36.92 2.59
2487 6903 8.099364 ACGTTCATGAATCTGAAAAATGTACT 57.901 30.769 12.12 0.00 36.92 2.73
2488 6904 8.728088 AACGTTCATGAATCTGAAAAATGTAC 57.272 30.769 12.12 0.00 36.92 2.90
2489 6905 9.743057 AAAACGTTCATGAATCTGAAAAATGTA 57.257 25.926 12.12 0.00 36.92 2.29
2490 6906 8.647143 AAAACGTTCATGAATCTGAAAAATGT 57.353 26.923 12.12 0.00 36.92 2.71
2498 6914 9.712410 CGAAATTTTAAAACGTTCATGAATCTG 57.288 29.630 12.12 7.52 0.00 2.90
2499 6915 9.672086 TCGAAATTTTAAAACGTTCATGAATCT 57.328 25.926 12.12 0.00 0.00 2.40
2500 6916 9.922951 CTCGAAATTTTAAAACGTTCATGAATC 57.077 29.630 12.12 4.81 0.00 2.52
2501 6917 9.672086 TCTCGAAATTTTAAAACGTTCATGAAT 57.328 25.926 12.12 0.00 0.00 2.57
2502 6918 9.504710 TTCTCGAAATTTTAAAACGTTCATGAA 57.495 25.926 18.97 3.38 0.00 2.57
2503 6919 9.672086 ATTCTCGAAATTTTAAAACGTTCATGA 57.328 25.926 18.97 14.57 0.00 3.07
2641 7057 9.945904 ACCTTCTAAATAAAGAATCTCGAGTTT 57.054 29.630 13.13 10.65 35.04 2.66
2661 7077 8.478066 GGGCTGATTTTTCATTAAATACCTTCT 58.522 33.333 0.00 0.00 0.00 2.85
2662 7078 8.257306 TGGGCTGATTTTTCATTAAATACCTTC 58.743 33.333 0.00 0.00 0.00 3.46
2663 7079 8.144862 TGGGCTGATTTTTCATTAAATACCTT 57.855 30.769 0.00 0.00 0.00 3.50
2664 7080 7.732222 TGGGCTGATTTTTCATTAAATACCT 57.268 32.000 0.00 0.00 0.00 3.08
2665 7081 9.696917 CTATGGGCTGATTTTTCATTAAATACC 57.303 33.333 0.00 0.00 0.00 2.73
2668 7084 9.205513 AGTCTATGGGCTGATTTTTCATTAAAT 57.794 29.630 0.00 0.00 0.00 1.40
2669 7085 8.593945 AGTCTATGGGCTGATTTTTCATTAAA 57.406 30.769 0.00 0.00 0.00 1.52
2670 7086 8.593945 AAGTCTATGGGCTGATTTTTCATTAA 57.406 30.769 0.00 0.00 0.00 1.40
2671 7087 8.593945 AAAGTCTATGGGCTGATTTTTCATTA 57.406 30.769 0.00 0.00 0.00 1.90
2672 7088 7.486407 AAAGTCTATGGGCTGATTTTTCATT 57.514 32.000 0.00 0.00 0.00 2.57
2673 7089 8.773033 ATAAAGTCTATGGGCTGATTTTTCAT 57.227 30.769 0.00 0.00 0.00 2.57
2674 7090 9.693739 TTATAAAGTCTATGGGCTGATTTTTCA 57.306 29.630 0.00 0.00 0.00 2.69
2677 7093 9.700831 AGTTTATAAAGTCTATGGGCTGATTTT 57.299 29.630 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.