Multiple sequence alignment - TraesCS5D01G033900

Loading Multiple Alignment...

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 TraesCS5D01G033900 chr5D 100.000 2532 0 0 1 2532 32700326 32697795 0.000000e+00 4676.0
1 TraesCS5D01G033900 chr5D 92.227 952 74 0 1 952 64808129 64807178 0.000000e+00 1349.0
2 TraesCS5D01G033900 chr5D 91.912 952 77 0 1 952 503459447 503458496 0.000000e+00 1332.0
3 TraesCS5D01G033900 chr5D 86.439 848 95 7 954 1791 32810812 32811649 0.000000e+00 911.0
4 TraesCS5D01G033900 chr5D 100.000 179 0 0 2784 2962 32697543 32697365 6.120000e-87 331.0
5 TraesCS5D01G033900 chr6A 94.643 952 51 0 1 952 421627727 421626776 0.000000e+00 1476.0
6 TraesCS5D01G033900 chr5A 91.246 971 61 14 953 1916 21414412 21413459 0.000000e+00 1301.0
7 TraesCS5D01G033900 chr5A 86.101 849 98 7 954 1792 21419312 21420150 0.000000e+00 896.0
8 TraesCS5D01G033900 chr5A 94.186 86 5 0 2021 2106 21413404 21413319 6.660000e-27 132.0
9 TraesCS5D01G033900 chrUn 95.990 773 31 0 1 773 289443668 289442896 0.000000e+00 1256.0
10 TraesCS5D01G033900 chrUn 94.558 147 8 0 808 954 289442895 289442749 8.260000e-56 228.0
11 TraesCS5D01G033900 chr7B 88.038 953 111 3 1 952 271295195 271296145 0.000000e+00 1125.0
12 TraesCS5D01G033900 chr3B 84.211 950 147 3 1 949 328720894 328721841 0.000000e+00 920.0
13 TraesCS5D01G033900 chr3B 78.195 853 136 38 949 1775 79979622 79980450 1.590000e-137 499.0
14 TraesCS5D01G033900 chr3B 76.555 836 155 27 986 1799 126302302 126301486 1.270000e-113 420.0
15 TraesCS5D01G033900 chr3B 76.152 868 151 34 953 1792 126310239 126309400 3.550000e-109 405.0
16 TraesCS5D01G033900 chr6D 81.885 955 163 9 1 952 365626595 365627542 0.000000e+00 797.0
17 TraesCS5D01G033900 chr2D 83.705 853 103 15 954 1796 605386701 605385875 0.000000e+00 773.0
18 TraesCS5D01G033900 chr6B 84.525 769 98 9 1035 1792 683372241 683372999 0.000000e+00 741.0
19 TraesCS5D01G033900 chr6B 86.607 448 53 3 1348 1788 683317391 683317838 3.430000e-134 488.0
20 TraesCS5D01G033900 chr6B 89.062 64 7 0 954 1017 683372182 683372245 2.450000e-11 80.5
21 TraesCS5D01G033900 chr4A 81.279 860 157 4 2 859 651209559 651210416 0.000000e+00 693.0
22 TraesCS5D01G033900 chr4A 81.029 875 162 4 2 874 651466895 651467767 0.000000e+00 693.0
23 TraesCS5D01G033900 chr4A 73.126 707 146 26 1096 1783 665318170 665317489 2.310000e-51 213.0
24 TraesCS5D01G033900 chr2A 83.225 769 93 10 1039 1799 38613909 38613169 0.000000e+00 673.0
25 TraesCS5D01G033900 chr2A 87.500 64 8 0 954 1017 38613973 38613910 1.140000e-09 75.0
26 TraesCS5D01G033900 chr5B 91.096 438 29 4 979 1415 24104702 24104274 4.250000e-163 584.0
27 TraesCS5D01G033900 chr5B 93.818 275 7 6 2268 2532 24102604 24102330 3.550000e-109 405.0
28 TraesCS5D01G033900 chr5B 92.248 258 17 1 1620 1877 24104276 24104022 2.170000e-96 363.0
29 TraesCS5D01G033900 chr5B 96.089 179 7 0 2784 2962 24102321 24102143 2.890000e-75 292.0
30 TraesCS5D01G033900 chr5B 92.208 154 9 3 2811 2962 24096118 24095966 6.430000e-52 215.0
31 TraesCS5D01G033900 chr5B 94.118 136 8 0 2109 2244 24102734 24102599 1.080000e-49 207.0
32 TraesCS5D01G033900 chr5B 92.958 71 5 0 2431 2501 24096276 24096206 1.450000e-18 104.0
33 TraesCS5D01G033900 chr3A 77.844 835 142 29 980 1791 63485867 63486681 7.430000e-131 477.0
34 TraesCS5D01G033900 chr3A 74.168 871 143 53 953 1792 94102451 94103270 1.340000e-73 287.0
35 TraesCS5D01G033900 chr3D 77.129 822 147 28 980 1781 50425521 50426321 3.500000e-119 438.0
36 TraesCS5D01G033900 chr3D 76.675 836 154 28 986 1799 80478187 80477371 2.730000e-115 425.0
37 TraesCS5D01G033900 chr7D 72.848 825 161 43 967 1764 50428358 50427570 1.070000e-54 224.0
38 TraesCS5D01G033900 chr7D 72.429 700 146 31 1100 1783 50641058 50640390 2.350000e-41 180.0
39 TraesCS5D01G033900 chr7A 73.208 530 106 27 955 1472 53520718 53520213 3.060000e-35 159.0
40 TraesCS5D01G033900 chr7A 97.059 34 1 0 2858 2891 178608893 178608926 1.150000e-04 58.4
41 TraesCS5D01G033900 chr1D 100.000 34 0 0 2858 2891 390214874 390214841 2.460000e-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 TraesCS5D01G033900 chr5D 32697365 32700326 2961 True 2503.50 4676 100.0000 1 2962 2 chr5D.!!$R3 2961
1 TraesCS5D01G033900 chr5D 64807178 64808129 951 True 1349.00 1349 92.2270 1 952 1 chr5D.!!$R1 951
2 TraesCS5D01G033900 chr5D 503458496 503459447 951 True 1332.00 1332 91.9120 1 952 1 chr5D.!!$R2 951
3 TraesCS5D01G033900 chr5D 32810812 32811649 837 False 911.00 911 86.4390 954 1791 1 chr5D.!!$F1 837
4 TraesCS5D01G033900 chr6A 421626776 421627727 951 True 1476.00 1476 94.6430 1 952 1 chr6A.!!$R1 951
5 TraesCS5D01G033900 chr5A 21419312 21420150 838 False 896.00 896 86.1010 954 1792 1 chr5A.!!$F1 838
6 TraesCS5D01G033900 chr5A 21413319 21414412 1093 True 716.50 1301 92.7160 953 2106 2 chr5A.!!$R1 1153
7 TraesCS5D01G033900 chrUn 289442749 289443668 919 True 742.00 1256 95.2740 1 954 2 chrUn.!!$R1 953
8 TraesCS5D01G033900 chr7B 271295195 271296145 950 False 1125.00 1125 88.0380 1 952 1 chr7B.!!$F1 951
9 TraesCS5D01G033900 chr3B 328720894 328721841 947 False 920.00 920 84.2110 1 949 1 chr3B.!!$F2 948
10 TraesCS5D01G033900 chr3B 79979622 79980450 828 False 499.00 499 78.1950 949 1775 1 chr3B.!!$F1 826
11 TraesCS5D01G033900 chr3B 126301486 126302302 816 True 420.00 420 76.5550 986 1799 1 chr3B.!!$R1 813
12 TraesCS5D01G033900 chr3B 126309400 126310239 839 True 405.00 405 76.1520 953 1792 1 chr3B.!!$R2 839
13 TraesCS5D01G033900 chr6D 365626595 365627542 947 False 797.00 797 81.8850 1 952 1 chr6D.!!$F1 951
14 TraesCS5D01G033900 chr2D 605385875 605386701 826 True 773.00 773 83.7050 954 1796 1 chr2D.!!$R1 842
15 TraesCS5D01G033900 chr6B 683372182 683372999 817 False 410.75 741 86.7935 954 1792 2 chr6B.!!$F2 838
16 TraesCS5D01G033900 chr4A 651209559 651210416 857 False 693.00 693 81.2790 2 859 1 chr4A.!!$F1 857
17 TraesCS5D01G033900 chr4A 651466895 651467767 872 False 693.00 693 81.0290 2 874 1 chr4A.!!$F2 872
18 TraesCS5D01G033900 chr4A 665317489 665318170 681 True 213.00 213 73.1260 1096 1783 1 chr4A.!!$R1 687
19 TraesCS5D01G033900 chr2A 38613169 38613973 804 True 374.00 673 85.3625 954 1799 2 chr2A.!!$R1 845
20 TraesCS5D01G033900 chr5B 24102143 24104702 2559 True 370.20 584 93.4738 979 2962 5 chr5B.!!$R2 1983
21 TraesCS5D01G033900 chr3A 63485867 63486681 814 False 477.00 477 77.8440 980 1791 1 chr3A.!!$F1 811
22 TraesCS5D01G033900 chr3A 94102451 94103270 819 False 287.00 287 74.1680 953 1792 1 chr3A.!!$F2 839
23 TraesCS5D01G033900 chr3D 50425521 50426321 800 False 438.00 438 77.1290 980 1781 1 chr3D.!!$F1 801
24 TraesCS5D01G033900 chr3D 80477371 80478187 816 True 425.00 425 76.6750 986 1799 1 chr3D.!!$R1 813
25 TraesCS5D01G033900 chr7D 50427570 50428358 788 True 224.00 224 72.8480 967 1764 1 chr7D.!!$R1 797

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
61 62 2.623418 TTCTGGTCTGCCTCCTTCTA 57.377 50.0 0.00 0.00 35.27 2.10 F
1153 1178 0.103026 CTCATCAACCAGATCGGCGA 59.897 55.0 13.87 13.87 39.03 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 1832 0.029989 GGGGAGGGGTAAGATCTGGT 60.030 60.0 0.0 0.0 0.00 4.00 R
1976 2087 0.388649 CGCGTCCAGCTAAGAGTTGT 60.389 55.0 0.0 0.0 45.59 3.32 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
61 62 2.623418 TTCTGGTCTGCCTCCTTCTA 57.377 50.000 0.00 0.00 35.27 2.10
137 138 6.008331 ACTTTATTCCAGTTAAACACCCCTC 58.992 40.000 0.00 0.00 0.00 4.30
290 291 7.924541 ACTGGGACAACCTTAAATATGAGTAA 58.075 34.615 0.00 0.00 38.70 2.24
310 311 3.619900 ATGCCTATCACCCTGAGACTA 57.380 47.619 0.00 0.00 0.00 2.59
366 367 8.429493 TTGAGTGTTATCTCAGATGCTTTATG 57.571 34.615 0.00 0.00 43.85 1.90
789 790 4.299978 GTGAAGTAGCCTATCGATTGGAC 58.700 47.826 27.09 17.43 0.00 4.02
1094 1119 1.071471 CACCACCTTCCACTTCGCT 59.929 57.895 0.00 0.00 0.00 4.93
1153 1178 0.103026 CTCATCAACCAGATCGGCGA 59.897 55.000 13.87 13.87 39.03 5.54
1345 1370 1.074951 CCCTCAGGGTTGGGAACAC 59.925 63.158 0.00 0.00 46.15 3.32
1346 1371 1.074951 CCTCAGGGTTGGGAACACC 59.925 63.158 0.00 0.00 42.67 4.16
1347 1372 1.302511 CTCAGGGTTGGGAACACCG 60.303 63.158 0.00 0.00 44.64 4.94
1348 1373 1.764571 CTCAGGGTTGGGAACACCGA 61.765 60.000 0.00 0.00 44.64 4.69
1349 1374 1.149627 CAGGGTTGGGAACACCGAA 59.850 57.895 0.00 0.00 44.64 4.30
1350 1375 1.149854 AGGGTTGGGAACACCGAAC 59.850 57.895 0.00 0.00 44.64 3.95
1351 1376 1.152922 GGGTTGGGAACACCGAACA 60.153 57.895 13.99 0.00 42.77 3.18
1369 1400 1.522355 ACGATCATCAAGCTGCCGG 60.522 57.895 0.00 0.00 0.00 6.13
1452 1484 3.842923 CCATCGTGGAGGCGCTCT 61.843 66.667 7.64 1.93 40.96 4.09
1553 1618 1.150536 GCTGGACAAGGTGTTCCCA 59.849 57.895 0.00 0.00 34.66 4.37
1731 1799 2.821366 TCGGCTACGACCTCGACC 60.821 66.667 0.78 0.00 45.59 4.79
1735 1803 2.697761 GCTACGACCTCGACCAGCA 61.698 63.158 0.78 0.00 43.02 4.41
1738 1806 1.174078 TACGACCTCGACCAGCACAA 61.174 55.000 0.78 0.00 43.02 3.33
1742 1810 0.973632 ACCTCGACCAGCACAACATA 59.026 50.000 0.00 0.00 0.00 2.29
1813 1881 0.320160 GTGTCACCACGTTAGGGTCC 60.320 60.000 0.00 0.00 36.19 4.46
1821 1889 1.068127 CACGTTAGGGTCCCTAATCGG 59.932 57.143 32.85 26.20 46.16 4.18
1831 1899 2.557490 GTCCCTAATCGGCAGGTAGTAG 59.443 54.545 0.00 0.00 0.00 2.57
1842 1910 6.066690 TCGGCAGGTAGTAGTAATAATCACT 58.933 40.000 0.00 0.00 0.00 3.41
1843 1911 7.226441 TCGGCAGGTAGTAGTAATAATCACTA 58.774 38.462 0.00 0.00 0.00 2.74
1844 1912 7.886970 TCGGCAGGTAGTAGTAATAATCACTAT 59.113 37.037 0.00 0.00 31.46 2.12
1907 1979 2.526432 ACCACGAGTGTCTATTGGACT 58.474 47.619 1.69 0.00 44.74 3.85
1939 2050 9.581099 TTTGACTGAAATAAAAGGTTGAAGAAC 57.419 29.630 0.00 0.00 0.00 3.01
1940 2051 7.414436 TGACTGAAATAAAAGGTTGAAGAACG 58.586 34.615 0.00 0.00 32.28 3.95
1941 2052 6.206498 ACTGAAATAAAAGGTTGAAGAACGC 58.794 36.000 0.00 0.00 32.28 4.84
1942 2053 6.137794 TGAAATAAAAGGTTGAAGAACGCA 57.862 33.333 0.00 0.00 32.28 5.24
1943 2054 6.565234 TGAAATAAAAGGTTGAAGAACGCAA 58.435 32.000 0.00 0.00 32.28 4.85
1944 2055 7.206687 TGAAATAAAAGGTTGAAGAACGCAAT 58.793 30.769 0.00 0.00 32.28 3.56
1945 2056 8.353684 TGAAATAAAAGGTTGAAGAACGCAATA 58.646 29.630 0.00 0.00 32.28 1.90
1946 2057 9.187455 GAAATAAAAGGTTGAAGAACGCAATAA 57.813 29.630 0.00 0.00 32.28 1.40
1947 2058 9.535878 AAATAAAAGGTTGAAGAACGCAATAAA 57.464 25.926 0.00 0.00 32.28 1.40
1948 2059 9.535878 AATAAAAGGTTGAAGAACGCAATAAAA 57.464 25.926 0.00 0.00 32.28 1.52
1949 2060 9.705290 ATAAAAGGTTGAAGAACGCAATAAAAT 57.295 25.926 0.00 0.00 32.28 1.82
1951 2062 8.742554 AAAGGTTGAAGAACGCAATAAAATAG 57.257 30.769 0.00 0.00 32.28 1.73
1952 2063 7.681939 AGGTTGAAGAACGCAATAAAATAGA 57.318 32.000 0.00 0.00 32.28 1.98
1953 2064 7.752695 AGGTTGAAGAACGCAATAAAATAGAG 58.247 34.615 0.00 0.00 32.28 2.43
1954 2065 6.469275 GGTTGAAGAACGCAATAAAATAGAGC 59.531 38.462 0.00 0.00 32.28 4.09
1955 2066 6.735678 TGAAGAACGCAATAAAATAGAGCA 57.264 33.333 0.00 0.00 0.00 4.26
1956 2067 7.139896 TGAAGAACGCAATAAAATAGAGCAA 57.860 32.000 0.00 0.00 0.00 3.91
1957 2068 7.761409 TGAAGAACGCAATAAAATAGAGCAAT 58.239 30.769 0.00 0.00 0.00 3.56
1958 2069 8.888716 TGAAGAACGCAATAAAATAGAGCAATA 58.111 29.630 0.00 0.00 0.00 1.90
1959 2070 9.716507 GAAGAACGCAATAAAATAGAGCAATAA 57.283 29.630 0.00 0.00 0.00 1.40
1960 2071 9.503427 AAGAACGCAATAAAATAGAGCAATAAC 57.497 29.630 0.00 0.00 0.00 1.89
1961 2072 7.850982 AGAACGCAATAAAATAGAGCAATAACG 59.149 33.333 0.00 0.00 0.00 3.18
1962 2073 6.427150 ACGCAATAAAATAGAGCAATAACGG 58.573 36.000 0.00 0.00 0.00 4.44
1963 2074 5.851177 CGCAATAAAATAGAGCAATAACGGG 59.149 40.000 0.00 0.00 0.00 5.28
1964 2075 5.629435 GCAATAAAATAGAGCAATAACGGGC 59.371 40.000 0.00 0.00 0.00 6.13
1965 2076 6.515035 GCAATAAAATAGAGCAATAACGGGCT 60.515 38.462 0.00 0.00 44.48 5.19
1966 2077 4.900635 AAAATAGAGCAATAACGGGCTG 57.099 40.909 0.00 0.00 41.22 4.85
1967 2078 3.838244 AATAGAGCAATAACGGGCTGA 57.162 42.857 0.00 0.00 41.22 4.26
1968 2079 3.838244 ATAGAGCAATAACGGGCTGAA 57.162 42.857 0.00 0.00 41.22 3.02
1969 2080 2.489938 AGAGCAATAACGGGCTGAAA 57.510 45.000 0.00 0.00 41.22 2.69
1970 2081 2.790433 AGAGCAATAACGGGCTGAAAA 58.210 42.857 0.00 0.00 41.22 2.29
1971 2082 3.153919 AGAGCAATAACGGGCTGAAAAA 58.846 40.909 0.00 0.00 41.22 1.94
1990 2101 5.668558 AAAAACGTACAACTCTTAGCTGG 57.331 39.130 0.00 0.00 0.00 4.85
1991 2102 4.595762 AAACGTACAACTCTTAGCTGGA 57.404 40.909 0.00 0.00 0.00 3.86
1992 2103 3.572604 ACGTACAACTCTTAGCTGGAC 57.427 47.619 0.00 0.00 0.00 4.02
1993 2104 2.516923 CGTACAACTCTTAGCTGGACG 58.483 52.381 0.00 1.12 41.46 4.79
1994 2105 2.260481 GTACAACTCTTAGCTGGACGC 58.740 52.381 0.00 0.00 39.57 5.19
1995 2106 0.388649 ACAACTCTTAGCTGGACGCG 60.389 55.000 3.53 3.53 45.59 6.01
1996 2107 1.446272 AACTCTTAGCTGGACGCGC 60.446 57.895 5.73 0.00 45.59 6.86
1997 2108 2.951745 CTCTTAGCTGGACGCGCG 60.952 66.667 30.96 30.96 45.59 6.86
1998 2109 3.685214 CTCTTAGCTGGACGCGCGT 62.685 63.158 38.52 38.52 45.59 6.01
1999 2110 3.545481 CTTAGCTGGACGCGCGTG 61.545 66.667 42.90 27.13 45.59 5.34
2023 2134 2.307686 AGGGAAGATAACAAAGCCGGAA 59.692 45.455 5.05 0.00 0.00 4.30
2033 2144 8.403236 AGATAACAAAGCCGGAATAATAACAAC 58.597 33.333 5.05 0.00 0.00 3.32
2037 2148 4.230745 AGCCGGAATAATAACAACCAGT 57.769 40.909 5.05 0.00 0.00 4.00
2091 2205 9.904198 AAGAAATCAAATCCAAAAGAAAGGAAA 57.096 25.926 0.00 0.00 37.48 3.13
2106 2220 4.731313 AAGGAAACAAAGAGACCAGGAT 57.269 40.909 0.00 0.00 0.00 3.24
2107 2221 4.026356 AGGAAACAAAGAGACCAGGATG 57.974 45.455 0.00 0.00 0.00 3.51
2142 3433 4.445448 GGAGGCATCAGAGATTACCAACAT 60.445 45.833 0.00 0.00 0.00 2.71
2144 3435 4.080129 AGGCATCAGAGATTACCAACATGT 60.080 41.667 0.00 0.00 0.00 3.21
2159 3450 4.330250 CAACATGTCAAGATCCTTCCTGT 58.670 43.478 0.00 0.00 0.00 4.00
2212 3503 1.998315 CTCTGCGTCTTCTTCCATGTG 59.002 52.381 0.00 0.00 0.00 3.21
2222 3513 6.564328 GTCTTCTTCCATGTGTTGAAAAAGT 58.436 36.000 0.00 0.00 0.00 2.66
2238 3529 1.975660 AAGTTAAAAGTGCCGGCTGA 58.024 45.000 29.70 4.80 0.00 4.26
2239 3530 1.975660 AGTTAAAAGTGCCGGCTGAA 58.024 45.000 29.70 3.84 0.00 3.02
2240 3531 2.303175 AGTTAAAAGTGCCGGCTGAAA 58.697 42.857 29.70 3.37 0.00 2.69
2241 3532 2.034179 AGTTAAAAGTGCCGGCTGAAAC 59.966 45.455 29.70 17.69 0.00 2.78
2242 3533 1.975660 TAAAAGTGCCGGCTGAAACT 58.024 45.000 29.70 19.90 0.00 2.66
2243 3534 1.111277 AAAAGTGCCGGCTGAAACTT 58.889 45.000 29.70 24.62 34.40 2.66
2244 3535 0.385390 AAAGTGCCGGCTGAAACTTG 59.615 50.000 29.70 0.00 33.30 3.16
2245 3536 1.455383 AAGTGCCGGCTGAAACTTGG 61.455 55.000 29.70 0.00 31.82 3.61
2246 3537 1.896660 GTGCCGGCTGAAACTTGGA 60.897 57.895 29.70 0.00 0.00 3.53
2247 3538 1.152860 TGCCGGCTGAAACTTGGAA 60.153 52.632 29.70 0.00 0.00 3.53
2248 3539 1.172180 TGCCGGCTGAAACTTGGAAG 61.172 55.000 29.70 0.00 0.00 3.46
2249 3540 1.172812 GCCGGCTGAAACTTGGAAGT 61.173 55.000 22.15 0.00 42.04 3.01
2299 3590 5.920273 AGTGCTAACAAATGAAATTCCAACG 59.080 36.000 0.00 0.00 33.67 4.10
2311 3602 4.974368 AATTCCAACGAACAAACACTCA 57.026 36.364 0.00 0.00 0.00 3.41
2330 3621 9.896645 AACACTCAGATGAAATTCATATACACT 57.103 29.630 8.64 0.00 37.20 3.55
2348 3639 7.944729 ATACACTGAGGCTGAAATTATTGTT 57.055 32.000 0.00 0.00 0.00 2.83
2384 3678 6.819146 TGATTCTACACACATTAAACGCCATA 59.181 34.615 0.00 0.00 0.00 2.74
2438 3738 6.745116 TCGACAGAACACAAAGAGAAGATTA 58.255 36.000 0.00 0.00 0.00 1.75
2472 3773 8.609176 CAAGCTATAAATTTACTACGCAAGGAA 58.391 33.333 0.00 0.00 46.39 3.36
2845 4146 3.668447 AGTCAAGTACAATCCAGCTGTG 58.332 45.455 13.81 7.14 0.00 3.66
2863 4164 7.160049 CAGCTGTGAATCAACTATGGATCTAT 58.840 38.462 5.25 0.00 0.00 1.98
2917 4218 9.736023 AGTGAAAATTCAACTTCATTTCAGTAC 57.264 29.630 5.37 0.00 40.18 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 5.105635 CCACCATAATGCAGTCAAAGTGATT 60.106 40.000 0.00 0.00 0.00 2.57
137 138 4.707030 TCAGCAATCTTAACAGCATTGG 57.293 40.909 0.00 0.00 0.00 3.16
290 291 2.485966 AGTCTCAGGGTGATAGGCAT 57.514 50.000 0.00 0.00 0.00 4.40
310 311 5.998363 GGTTAACTCTCTCAGTTTGACCATT 59.002 40.000 5.42 0.00 43.38 3.16
366 367 0.329596 ATTTCCTGGGGTGAGCAGAC 59.670 55.000 0.00 0.00 0.00 3.51
430 431 1.604604 TTTCCCAAAGAAGAGTGCCG 58.395 50.000 0.00 0.00 35.40 5.69
757 758 1.084370 GCTACTTCACCGATGCGCTT 61.084 55.000 9.73 0.55 0.00 4.68
789 790 3.574826 GCACCTTACTATCAGGAGGTAGG 59.425 52.174 0.00 0.00 40.42 3.18
983 984 2.227388 GTCGTCGAAGGTGAAGGTCTTA 59.773 50.000 0.00 0.00 0.00 2.10
1345 1370 1.325640 CAGCTTGATGATCGTGTTCGG 59.674 52.381 0.00 0.00 37.69 4.30
1346 1371 1.267235 GCAGCTTGATGATCGTGTTCG 60.267 52.381 0.00 0.00 38.55 3.95
1347 1372 1.063174 GGCAGCTTGATGATCGTGTTC 59.937 52.381 0.00 0.00 0.00 3.18
1348 1373 1.089920 GGCAGCTTGATGATCGTGTT 58.910 50.000 0.00 0.00 0.00 3.32
1349 1374 1.086067 CGGCAGCTTGATGATCGTGT 61.086 55.000 0.00 0.00 0.00 4.49
1350 1375 1.640069 CGGCAGCTTGATGATCGTG 59.360 57.895 0.00 0.00 0.00 4.35
1351 1376 1.522355 CCGGCAGCTTGATGATCGT 60.522 57.895 0.00 0.00 0.00 3.73
1678 1746 1.153188 ATGATGTTGCCGATCGCCA 60.153 52.632 10.32 0.63 36.24 5.69
1731 1799 1.135689 GGCGAAGGTTATGTTGTGCTG 60.136 52.381 0.00 0.00 0.00 4.41
1735 1803 0.696501 AGGGGCGAAGGTTATGTTGT 59.303 50.000 0.00 0.00 0.00 3.32
1738 1806 1.077716 GCAGGGGCGAAGGTTATGT 60.078 57.895 0.00 0.00 0.00 2.29
1764 1832 0.029989 GGGGAGGGGTAAGATCTGGT 60.030 60.000 0.00 0.00 0.00 4.00
1813 1881 5.979288 ATTACTACTACCTGCCGATTAGG 57.021 43.478 0.00 0.00 44.97 2.69
1842 1910 6.238731 CGATTACTGGTGACCCTAACGTAATA 60.239 42.308 0.00 0.00 0.00 0.98
1843 1911 5.450965 CGATTACTGGTGACCCTAACGTAAT 60.451 44.000 0.00 4.83 0.00 1.89
1844 1912 4.142403 CGATTACTGGTGACCCTAACGTAA 60.142 45.833 0.00 0.00 0.00 3.18
1925 2036 9.191995 CTATTTTATTGCGTTCTTCAACCTTTT 57.808 29.630 0.00 0.00 0.00 2.27
1927 2038 8.106247 TCTATTTTATTGCGTTCTTCAACCTT 57.894 30.769 0.00 0.00 0.00 3.50
1928 2039 7.626452 GCTCTATTTTATTGCGTTCTTCAACCT 60.626 37.037 0.00 0.00 0.00 3.50
1929 2040 6.469275 GCTCTATTTTATTGCGTTCTTCAACC 59.531 38.462 0.00 0.00 0.00 3.77
1930 2041 7.021196 TGCTCTATTTTATTGCGTTCTTCAAC 58.979 34.615 0.00 0.00 0.00 3.18
1931 2042 7.139896 TGCTCTATTTTATTGCGTTCTTCAA 57.860 32.000 0.00 0.00 0.00 2.69
1932 2043 6.735678 TGCTCTATTTTATTGCGTTCTTCA 57.264 33.333 0.00 0.00 0.00 3.02
1933 2044 9.716507 TTATTGCTCTATTTTATTGCGTTCTTC 57.283 29.630 0.00 0.00 0.00 2.87
1934 2045 9.503427 GTTATTGCTCTATTTTATTGCGTTCTT 57.497 29.630 0.00 0.00 0.00 2.52
1935 2046 7.850982 CGTTATTGCTCTATTTTATTGCGTTCT 59.149 33.333 0.00 0.00 0.00 3.01
1936 2047 7.111593 CCGTTATTGCTCTATTTTATTGCGTTC 59.888 37.037 0.00 0.00 0.00 3.95
1937 2048 6.910433 CCGTTATTGCTCTATTTTATTGCGTT 59.090 34.615 0.00 0.00 0.00 4.84
1938 2049 6.427150 CCGTTATTGCTCTATTTTATTGCGT 58.573 36.000 0.00 0.00 0.00 5.24
1939 2050 5.851177 CCCGTTATTGCTCTATTTTATTGCG 59.149 40.000 0.00 0.00 0.00 4.85
1940 2051 5.629435 GCCCGTTATTGCTCTATTTTATTGC 59.371 40.000 0.00 0.00 0.00 3.56
1941 2052 6.857964 CAGCCCGTTATTGCTCTATTTTATTG 59.142 38.462 0.00 0.00 35.12 1.90
1942 2053 6.770785 TCAGCCCGTTATTGCTCTATTTTATT 59.229 34.615 0.00 0.00 35.12 1.40
1943 2054 6.296026 TCAGCCCGTTATTGCTCTATTTTAT 58.704 36.000 0.00 0.00 35.12 1.40
1944 2055 5.676552 TCAGCCCGTTATTGCTCTATTTTA 58.323 37.500 0.00 0.00 35.12 1.52
1945 2056 4.523083 TCAGCCCGTTATTGCTCTATTTT 58.477 39.130 0.00 0.00 35.12 1.82
1946 2057 4.150897 TCAGCCCGTTATTGCTCTATTT 57.849 40.909 0.00 0.00 35.12 1.40
1947 2058 3.838244 TCAGCCCGTTATTGCTCTATT 57.162 42.857 0.00 0.00 35.12 1.73
1948 2059 3.838244 TTCAGCCCGTTATTGCTCTAT 57.162 42.857 0.00 0.00 35.12 1.98
1949 2060 3.620427 TTTCAGCCCGTTATTGCTCTA 57.380 42.857 0.00 0.00 35.12 2.43
1950 2061 2.489938 TTTCAGCCCGTTATTGCTCT 57.510 45.000 0.00 0.00 35.12 4.09
1951 2062 3.569250 TTTTTCAGCCCGTTATTGCTC 57.431 42.857 0.00 0.00 35.12 4.26
1968 2079 5.235831 GTCCAGCTAAGAGTTGTACGTTTTT 59.764 40.000 0.00 0.00 0.00 1.94
1969 2080 4.748600 GTCCAGCTAAGAGTTGTACGTTTT 59.251 41.667 0.00 0.00 0.00 2.43
1970 2081 4.304939 GTCCAGCTAAGAGTTGTACGTTT 58.695 43.478 0.00 0.00 0.00 3.60
1971 2082 3.611057 CGTCCAGCTAAGAGTTGTACGTT 60.611 47.826 0.00 0.00 34.96 3.99
1972 2083 2.095364 CGTCCAGCTAAGAGTTGTACGT 60.095 50.000 0.00 0.00 34.96 3.57
1973 2084 2.516923 CGTCCAGCTAAGAGTTGTACG 58.483 52.381 0.00 0.00 33.34 3.67
1974 2085 2.260481 GCGTCCAGCTAAGAGTTGTAC 58.740 52.381 0.00 0.00 44.04 2.90
1975 2086 1.135489 CGCGTCCAGCTAAGAGTTGTA 60.135 52.381 0.00 0.00 45.59 2.41
1976 2087 0.388649 CGCGTCCAGCTAAGAGTTGT 60.389 55.000 0.00 0.00 45.59 3.32
1977 2088 1.687494 GCGCGTCCAGCTAAGAGTTG 61.687 60.000 8.43 0.00 45.59 3.16
1978 2089 1.446272 GCGCGTCCAGCTAAGAGTT 60.446 57.895 8.43 0.00 45.59 3.01
1979 2090 2.182030 GCGCGTCCAGCTAAGAGT 59.818 61.111 8.43 0.00 45.59 3.24
1980 2091 2.951745 CGCGCGTCCAGCTAAGAG 60.952 66.667 24.19 0.00 45.59 2.85
1981 2092 3.744719 ACGCGCGTCCAGCTAAGA 61.745 61.111 32.73 0.00 45.59 2.10
1982 2093 3.545481 CACGCGCGTCCAGCTAAG 61.545 66.667 35.61 15.89 45.59 2.18
1992 2103 2.622903 TATCTTCCCTTCCACGCGCG 62.623 60.000 30.96 30.96 0.00 6.86
1993 2104 0.461339 TTATCTTCCCTTCCACGCGC 60.461 55.000 5.73 0.00 0.00 6.86
1994 2105 1.287425 GTTATCTTCCCTTCCACGCG 58.713 55.000 3.53 3.53 0.00 6.01
1995 2106 2.396590 TGTTATCTTCCCTTCCACGC 57.603 50.000 0.00 0.00 0.00 5.34
1996 2107 3.127030 GCTTTGTTATCTTCCCTTCCACG 59.873 47.826 0.00 0.00 0.00 4.94
1997 2108 3.444034 GGCTTTGTTATCTTCCCTTCCAC 59.556 47.826 0.00 0.00 0.00 4.02
1998 2109 3.697166 GGCTTTGTTATCTTCCCTTCCA 58.303 45.455 0.00 0.00 0.00 3.53
1999 2110 2.683362 CGGCTTTGTTATCTTCCCTTCC 59.317 50.000 0.00 0.00 0.00 3.46
2000 2111 2.683362 CCGGCTTTGTTATCTTCCCTTC 59.317 50.000 0.00 0.00 0.00 3.46
2001 2112 2.307686 TCCGGCTTTGTTATCTTCCCTT 59.692 45.455 0.00 0.00 0.00 3.95
2002 2113 1.913419 TCCGGCTTTGTTATCTTCCCT 59.087 47.619 0.00 0.00 0.00 4.20
2003 2114 2.413310 TCCGGCTTTGTTATCTTCCC 57.587 50.000 0.00 0.00 0.00 3.97
2004 2115 6.635030 ATTATTCCGGCTTTGTTATCTTCC 57.365 37.500 0.00 0.00 0.00 3.46
2005 2116 8.617809 TGTTATTATTCCGGCTTTGTTATCTTC 58.382 33.333 0.00 0.00 0.00 2.87
2006 2117 8.514330 TGTTATTATTCCGGCTTTGTTATCTT 57.486 30.769 0.00 0.00 0.00 2.40
2007 2118 8.403236 GTTGTTATTATTCCGGCTTTGTTATCT 58.597 33.333 0.00 0.00 0.00 1.98
2008 2119 7.646526 GGTTGTTATTATTCCGGCTTTGTTATC 59.353 37.037 0.00 0.00 0.00 1.75
2023 2134 8.934697 TCTTATCCTGCTACTGGTTGTTATTAT 58.065 33.333 0.00 0.00 0.00 1.28
2033 2144 5.501156 ACCTTTTTCTTATCCTGCTACTGG 58.499 41.667 0.00 0.00 0.00 4.00
2037 2148 6.156256 TCTGCTACCTTTTTCTTATCCTGCTA 59.844 38.462 0.00 0.00 0.00 3.49
2091 2205 3.008485 GTCCTTCATCCTGGTCTCTTTGT 59.992 47.826 0.00 0.00 0.00 2.83
2106 2220 3.003173 CCTCCTGCCCGTCCTTCA 61.003 66.667 0.00 0.00 0.00 3.02
2107 2221 4.475135 GCCTCCTGCCCGTCCTTC 62.475 72.222 0.00 0.00 0.00 3.46
2142 3433 1.909302 GGGACAGGAAGGATCTTGACA 59.091 52.381 0.00 0.00 36.24 3.58
2144 3435 2.342406 TGGGACAGGAAGGATCTTGA 57.658 50.000 0.00 0.00 36.24 3.02
2159 3450 8.428063 TGCTTTCTTTTCAAAATTTAGATGGGA 58.572 29.630 0.00 0.00 0.00 4.37
2187 3478 3.621558 TGGAAGAAGACGCAGAGATCTA 58.378 45.455 0.00 0.00 0.00 1.98
2189 3480 2.949451 TGGAAGAAGACGCAGAGATC 57.051 50.000 0.00 0.00 0.00 2.75
2195 3486 1.872952 CAACACATGGAAGAAGACGCA 59.127 47.619 0.00 0.00 0.00 5.24
2212 3503 4.260051 GCCGGCACTTTTAACTTTTTCAAC 60.260 41.667 24.80 0.00 0.00 3.18
2222 3513 2.303175 AGTTTCAGCCGGCACTTTTAA 58.697 42.857 31.54 10.66 0.00 1.52
2245 3536 7.175119 AGTTTGAAGCCTACTGGAAATAACTTC 59.825 37.037 0.00 0.00 34.57 3.01
2246 3537 7.004691 AGTTTGAAGCCTACTGGAAATAACTT 58.995 34.615 0.00 0.00 34.57 2.66
2247 3538 6.543735 AGTTTGAAGCCTACTGGAAATAACT 58.456 36.000 0.00 0.00 34.57 2.24
2248 3539 6.819397 AGTTTGAAGCCTACTGGAAATAAC 57.181 37.500 0.00 0.00 34.57 1.89
2249 3540 7.940137 TGTAAGTTTGAAGCCTACTGGAAATAA 59.060 33.333 0.00 0.00 34.57 1.40
2250 3541 7.455058 TGTAAGTTTGAAGCCTACTGGAAATA 58.545 34.615 0.00 0.00 34.57 1.40
2251 3542 6.303839 TGTAAGTTTGAAGCCTACTGGAAAT 58.696 36.000 0.00 0.00 34.57 2.17
2252 3543 5.686753 TGTAAGTTTGAAGCCTACTGGAAA 58.313 37.500 0.00 0.00 34.57 3.13
2253 3544 5.298989 TGTAAGTTTGAAGCCTACTGGAA 57.701 39.130 0.00 0.00 34.57 3.53
2254 3545 4.894784 CTGTAAGTTTGAAGCCTACTGGA 58.105 43.478 0.00 0.00 34.57 3.86
2311 3602 7.660617 CAGCCTCAGTGTATATGAATTTCATCT 59.339 37.037 14.99 8.62 38.26 2.90
2330 3621 5.643379 GGTGAACAATAATTTCAGCCTCA 57.357 39.130 3.44 0.00 42.90 3.86
2395 3689 6.931838 TGTCGATTGAACTAGGAGTTACATT 58.068 36.000 0.00 0.00 38.80 2.71
2438 3738 9.984190 GTAGTAAATTTATAGCTTGCTCCTAGT 57.016 33.333 0.31 0.00 0.00 2.57
2472 3773 6.758886 CCTAGCTTATCTCGTCATTTCTGTTT 59.241 38.462 0.00 0.00 0.00 2.83
2863 4164 9.650714 TTCAGGTACTCCTTTTAGCTGTATATA 57.349 33.333 0.00 0.00 43.07 0.86
2878 4179 7.272037 TGAATTTTCACTTTTCAGGTACTCC 57.728 36.000 0.00 0.00 29.63 3.85
2899 4200 7.502226 AGTGATTGGTACTGAAATGAAGTTGAA 59.498 33.333 0.00 0.00 0.00 2.69
2900 4201 6.998074 AGTGATTGGTACTGAAATGAAGTTGA 59.002 34.615 0.00 0.00 0.00 3.18
2917 4218 7.819415 TCTGAACTACATCTTGTTAGTGATTGG 59.181 37.037 0.00 0.00 0.00 3.16
2921 4222 8.122472 TGATCTGAACTACATCTTGTTAGTGA 57.878 34.615 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.