Multiple sequence alignment - TraesCS2D01G384100

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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 TraesCS2D01G384100 chr2D 100.000 2696 0 0 1 2696 488473507 488470812 0.000000e+00 4979.0
1 TraesCS2D01G384100 chr2D 96.535 1847 51 5 4 1847 488365442 488363606 0.000000e+00 3044.0
2 TraesCS2D01G384100 chr2D 82.407 648 77 17 2078 2696 489401996 489401357 5.110000e-147 531.0
3 TraesCS2D01G384100 chr2D 78.061 196 40 3 92 285 488473201 488473007 1.310000e-23 121.0
4 TraesCS2D01G384100 chr2D 78.061 196 40 3 307 501 488473416 488473223 1.310000e-23 121.0
5 TraesCS2D01G384100 chr2D 78.261 184 37 3 307 489 488365354 488365173 6.100000e-22 115.0
6 TraesCS2D01G384100 chr2D 91.667 60 4 1 515 573 575354252 575354193 6.190000e-12 82.4
7 TraesCS2D01G384100 chr2A 90.892 1087 49 21 970 2027 632929205 632928140 0.000000e+00 1413.0
8 TraesCS2D01G384100 chr2A 93.103 145 7 2 830 971 632929392 632929248 2.720000e-50 209.0
9 TraesCS2D01G384100 chr2A 91.156 147 6 5 668 809 632929645 632929501 2.740000e-45 193.0
10 TraesCS2D01G384100 chr2B 93.961 828 34 2 966 1777 572678827 572678000 0.000000e+00 1238.0
11 TraesCS2D01G384100 chr2B 89.836 974 50 21 4 971 572679793 572678863 0.000000e+00 1205.0
12 TraesCS2D01G384100 chr2B 83.790 438 52 13 2030 2455 572775683 572775253 5.410000e-107 398.0
13 TraesCS2D01G384100 chr2B 85.268 224 19 7 2486 2696 572757746 572757524 4.520000e-53 219.0
14 TraesCS2D01G384100 chr2B 83.058 242 14 14 1804 2027 572678008 572677776 7.620000e-46 195.0
15 TraesCS2D01G384100 chr2B 84.000 200 18 6 2192 2389 248453056 248453243 2.130000e-41 180.0
16 TraesCS2D01G384100 chr2B 90.000 60 6 0 514 573 729528011 729527952 8.000000e-11 78.7
17 TraesCS2D01G384100 chr2B 100.000 30 0 0 922 951 572678976 572678947 3.750000e-04 56.5
18 TraesCS2D01G384100 chr6B 84.252 508 69 10 1129 1629 515022057 515022560 4.040000e-133 484.0
19 TraesCS2D01G384100 chr6D 82.959 534 67 18 1135 1647 311582634 311582104 6.800000e-126 460.0
20 TraesCS2D01G384100 chr6D 95.205 146 7 0 1368 1513 414098779 414098924 5.800000e-57 231.0
21 TraesCS2D01G384100 chr6A 81.888 519 67 18 1135 1629 448351817 448351302 1.930000e-111 412.0
22 TraesCS2D01G384100 chr6A 93.103 58 3 1 517 573 502715132 502715189 1.720000e-12 84.2
23 TraesCS2D01G384100 chr1B 96.400 250 9 0 1267 1516 378858372 378858123 1.930000e-111 412.0
24 TraesCS2D01G384100 chr7D 82.439 410 54 14 1135 1529 126880291 126879885 2.570000e-90 342.0
25 TraesCS2D01G384100 chr7D 90.164 61 5 1 514 573 498229926 498229866 8.000000e-11 78.7
26 TraesCS2D01G384100 chr7D 86.667 60 8 0 2424 2483 626138816 626138757 1.730000e-07 67.6
27 TraesCS2D01G384100 chr5A 93.966 116 7 0 1356 1471 540474874 540474989 2.760000e-40 176.0
28 TraesCS2D01G384100 chr5A 90.000 60 4 2 307 364 38170576 38170635 2.880000e-10 76.8
29 TraesCS2D01G384100 chr5D 79.878 164 27 5 5 165 51021789 51021629 6.100000e-22 115.0
30 TraesCS2D01G384100 chr5D 82.895 76 13 0 307 382 51021703 51021628 4.820000e-08 69.4
31 TraesCS2D01G384100 chr4A 76.961 204 40 5 1159 1357 503236421 503236220 2.840000e-20 110.0
32 TraesCS2D01G384100 chr4A 80.435 138 18 8 10 142 631672585 631672452 2.210000e-16 97.1
33 TraesCS2D01G384100 chr4A 93.333 45 3 0 307 351 620781782 620781826 1.730000e-07 67.6
34 TraesCS2D01G384100 chr3B 90.411 73 7 0 2229 2301 79114772 79114700 2.210000e-16 97.1
35 TraesCS2D01G384100 chr3B 90.000 70 4 3 2240 2307 79114206 79114274 1.330000e-13 87.9
36 TraesCS2D01G384100 chr3B 88.060 67 5 3 509 573 43045557 43045622 2.880000e-10 76.8
37 TraesCS2D01G384100 chr7B 81.667 120 17 4 40 156 526233371 526233488 7.950000e-16 95.3
38 TraesCS2D01G384100 chr7B 91.667 60 4 1 515 573 173865878 173865819 6.190000e-12 82.4
39 TraesCS2D01G384100 chr1D 93.103 58 3 1 517 573 338936269 338936212 1.720000e-12 84.2
40 TraesCS2D01G384100 chr1D 81.553 103 15 4 25 125 897660 897760 6.190000e-12 82.4
41 TraesCS2D01G384100 chr1D 94.737 38 0 2 2262 2297 344741090 344741127 1.040000e-04 58.4
42 TraesCS2D01G384100 chr1A 83.158 95 12 4 28 120 551318713 551318621 1.720000e-12 84.2
43 TraesCS2D01G384100 chr1A 84.706 85 9 4 50 132 549229817 549229899 6.190000e-12 82.4
44 TraesCS2D01G384100 chr1A 97.500 40 1 0 307 346 2547976 2547937 4.820000e-08 69.4
45 TraesCS2D01G384100 chr5B 86.667 75 5 5 295 364 51329978 51330052 8.000000e-11 78.7
46 TraesCS2D01G384100 chr7A 90.909 55 5 0 2238 2292 705982393 705982447 1.040000e-09 75.0
47 TraesCS2D01G384100 chr7A 90.909 55 5 0 2238 2292 706007621 706007675 1.040000e-09 75.0
48 TraesCS2D01G384100 chrUn 94.737 38 0 2 2262 2297 209975700 209975737 1.040000e-04 58.4


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 TraesCS2D01G384100 chr2D 488470812 488473507 2695 True 1740.333333 4979 85.37400 1 2696 3 chr2D.!!$R4 2695
1 TraesCS2D01G384100 chr2D 488363606 488365442 1836 True 1579.500000 3044 87.39800 4 1847 2 chr2D.!!$R3 1843
2 TraesCS2D01G384100 chr2D 489401357 489401996 639 True 531.000000 531 82.40700 2078 2696 1 chr2D.!!$R1 618
3 TraesCS2D01G384100 chr2A 632928140 632929645 1505 True 605.000000 1413 91.71700 668 2027 3 chr2A.!!$R1 1359
4 TraesCS2D01G384100 chr2B 572677776 572679793 2017 True 673.625000 1238 91.71375 4 2027 4 chr2B.!!$R4 2023
5 TraesCS2D01G384100 chr6B 515022057 515022560 503 False 484.000000 484 84.25200 1129 1629 1 chr6B.!!$F1 500
6 TraesCS2D01G384100 chr6D 311582104 311582634 530 True 460.000000 460 82.95900 1135 1647 1 chr6D.!!$R1 512
7 TraesCS2D01G384100 chr6A 448351302 448351817 515 True 412.000000 412 81.88800 1135 1629 1 chr6A.!!$R1 494

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
288 292 0.0982 GAAAGAATAACGTGCCCGCC 59.902 55.0 0.0 0.0 37.7 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 1973 0.033504 CCCGCGCACCAGATATAAGT 59.966 55.0 8.75 0.0 0.0 2.24 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
64 67 6.964807 AATGGAGCTAATTAATGCACATGA 57.035 33.333 0.00 0.00 32.41 3.07
81 84 5.517770 GCACATGAAATTAAATCTCTGGCAC 59.482 40.000 0.00 0.00 0.00 5.01
169 173 1.317613 TGTCTGCATGTGAAACCACC 58.682 50.000 0.00 0.00 34.36 4.61
250 254 5.408299 GGCGCTCAGTTTCCAAATTATTTTT 59.592 36.000 7.64 0.00 0.00 1.94
277 281 0.388778 TGACCGCGTGCGAAAGAATA 60.389 50.000 16.91 0.00 42.83 1.75
288 292 0.098200 GAAAGAATAACGTGCCCGCC 59.902 55.000 0.00 0.00 37.70 6.13
493 497 6.766452 TTAATGAATGTGTACGAAACGACA 57.234 33.333 0.00 0.00 0.00 4.35
695 702 0.894835 AAAATTTGGCGGTGGGCTAG 59.105 50.000 0.00 0.00 42.94 3.42
696 703 0.251608 AAATTTGGCGGTGGGCTAGT 60.252 50.000 0.00 0.00 42.94 2.57
697 704 0.621609 AATTTGGCGGTGGGCTAGTA 59.378 50.000 0.00 0.00 42.94 1.82
698 705 0.107361 ATTTGGCGGTGGGCTAGTAC 60.107 55.000 0.00 0.00 42.94 2.73
1012 1165 1.897473 TGGATCCATGGACCATCACT 58.103 50.000 24.08 6.70 0.00 3.41
1374 1563 2.507102 CAGATCAAGCGCGACGGT 60.507 61.111 12.10 0.00 40.00 4.83
1608 1797 1.541620 GGGGTTCAGGGTCCTCCTT 60.542 63.158 0.00 0.00 45.47 3.36
1686 1875 0.038618 CCCACATTCACGTCTCGTCA 60.039 55.000 0.00 0.00 38.32 4.35
1691 1880 1.061131 CATTCACGTCTCGTCATTGGC 59.939 52.381 0.00 0.00 38.32 4.52
1700 1889 0.032815 TCGTCATTGGCGTGAAGTGA 59.967 50.000 10.85 0.00 0.00 3.41
1781 1970 2.354704 GCTAGCTGTGTCAATGGGTACA 60.355 50.000 7.70 0.00 0.00 2.90
1782 1971 2.185004 AGCTGTGTCAATGGGTACAC 57.815 50.000 0.00 0.00 44.97 2.90
1783 1972 1.699634 AGCTGTGTCAATGGGTACACT 59.300 47.619 0.00 0.00 44.99 3.55
1784 1973 2.903784 AGCTGTGTCAATGGGTACACTA 59.096 45.455 0.00 0.00 44.99 2.74
1796 1985 7.787904 TCAATGGGTACACTACTTATATCTGGT 59.212 37.037 0.00 0.00 0.00 4.00
1802 1991 2.030185 ACTACTTATATCTGGTGCGCGG 60.030 50.000 8.83 0.00 0.00 6.46
1913 2115 2.722094 TGGTGGCAATGTAAGGCTAAG 58.278 47.619 0.00 0.00 0.00 2.18
1931 2133 6.581171 GCTAAGCCAGGCTAATGAAAATAT 57.419 37.500 16.56 0.00 38.25 1.28
1951 2153 9.546428 AAAATATTATGCTCTTTTACCAATGGC 57.454 29.630 0.00 0.00 0.00 4.40
1952 2154 8.482852 AATATTATGCTCTTTTACCAATGGCT 57.517 30.769 0.00 0.00 0.00 4.75
1955 2157 1.545582 GCTCTTTTACCAATGGCTGCA 59.454 47.619 0.00 0.00 0.00 4.41
1956 2158 2.167075 GCTCTTTTACCAATGGCTGCAT 59.833 45.455 0.00 0.00 0.00 3.96
1957 2159 3.777478 CTCTTTTACCAATGGCTGCATG 58.223 45.455 0.00 0.00 0.00 4.06
1958 2160 2.496871 TCTTTTACCAATGGCTGCATGG 59.503 45.455 14.39 14.39 40.16 3.66
1961 2163 2.816777 TACCAATGGCTGCATGGTTA 57.183 45.000 23.01 10.85 44.92 2.85
1964 2166 3.225104 ACCAATGGCTGCATGGTTATAG 58.775 45.455 15.49 0.00 44.92 1.31
1974 2186 2.099098 GCATGGTTATAGTGTTGCACCC 59.901 50.000 0.00 0.00 34.49 4.61
1975 2187 2.102070 TGGTTATAGTGTTGCACCCG 57.898 50.000 0.00 0.00 34.49 5.28
1981 2193 2.264005 TAGTGTTGCACCCGTGAAAT 57.736 45.000 0.00 0.00 34.49 2.17
1982 2194 0.667993 AGTGTTGCACCCGTGAAATG 59.332 50.000 0.00 0.00 34.49 2.32
1983 2195 0.383949 GTGTTGCACCCGTGAAATGT 59.616 50.000 0.00 0.00 29.51 2.71
1984 2196 1.107114 TGTTGCACCCGTGAAATGTT 58.893 45.000 0.00 0.00 29.51 2.71
1985 2197 1.478510 TGTTGCACCCGTGAAATGTTT 59.521 42.857 0.00 0.00 29.51 2.83
1986 2198 2.124122 GTTGCACCCGTGAAATGTTTC 58.876 47.619 0.00 0.00 37.69 2.78
2015 2227 1.750193 AATGGGATCGATTGCAACGT 58.250 45.000 16.97 8.10 0.00 3.99
2027 2239 6.143496 TCGATTGCAACGTAAATGCTAAAAA 58.857 32.000 11.66 0.00 44.14 1.94
2028 2240 6.804295 TCGATTGCAACGTAAATGCTAAAAAT 59.196 30.769 11.66 3.53 44.14 1.82
2029 2241 6.888797 CGATTGCAACGTAAATGCTAAAAATG 59.111 34.615 11.66 0.00 44.14 2.32
2030 2242 6.459257 TTGCAACGTAAATGCTAAAAATGG 57.541 33.333 11.66 0.00 44.14 3.16
2031 2243 5.773575 TGCAACGTAAATGCTAAAAATGGA 58.226 33.333 11.66 0.00 44.14 3.41
2032 2244 5.861251 TGCAACGTAAATGCTAAAAATGGAG 59.139 36.000 11.66 0.00 44.14 3.86
2033 2245 5.288472 GCAACGTAAATGCTAAAAATGGAGG 59.712 40.000 3.46 0.00 40.64 4.30
2034 2246 6.616947 CAACGTAAATGCTAAAAATGGAGGA 58.383 36.000 0.00 0.00 0.00 3.71
2035 2247 6.190954 ACGTAAATGCTAAAAATGGAGGAC 57.809 37.500 0.00 0.00 0.00 3.85
2036 2248 5.163794 ACGTAAATGCTAAAAATGGAGGACG 60.164 40.000 0.00 0.00 0.00 4.79
2037 2249 4.718940 AAATGCTAAAAATGGAGGACGG 57.281 40.909 0.00 0.00 0.00 4.79
2038 2250 3.644966 ATGCTAAAAATGGAGGACGGA 57.355 42.857 0.00 0.00 0.00 4.69
2039 2251 2.985896 TGCTAAAAATGGAGGACGGAG 58.014 47.619 0.00 0.00 0.00 4.63
2040 2252 2.289565 GCTAAAAATGGAGGACGGAGG 58.710 52.381 0.00 0.00 0.00 4.30
2041 2253 2.093128 GCTAAAAATGGAGGACGGAGGA 60.093 50.000 0.00 0.00 0.00 3.71
2042 2254 2.789409 AAAAATGGAGGACGGAGGAG 57.211 50.000 0.00 0.00 0.00 3.69
2043 2255 1.952621 AAAATGGAGGACGGAGGAGA 58.047 50.000 0.00 0.00 0.00 3.71
2044 2256 1.490574 AAATGGAGGACGGAGGAGAG 58.509 55.000 0.00 0.00 0.00 3.20
2045 2257 0.631753 AATGGAGGACGGAGGAGAGA 59.368 55.000 0.00 0.00 0.00 3.10
2046 2258 0.184933 ATGGAGGACGGAGGAGAGAG 59.815 60.000 0.00 0.00 0.00 3.20
2047 2259 0.914902 TGGAGGACGGAGGAGAGAGA 60.915 60.000 0.00 0.00 0.00 3.10
2048 2260 0.179029 GGAGGACGGAGGAGAGAGAG 60.179 65.000 0.00 0.00 0.00 3.20
2049 2261 0.834612 GAGGACGGAGGAGAGAGAGA 59.165 60.000 0.00 0.00 0.00 3.10
2050 2262 0.837272 AGGACGGAGGAGAGAGAGAG 59.163 60.000 0.00 0.00 0.00 3.20
2051 2263 0.179029 GGACGGAGGAGAGAGAGAGG 60.179 65.000 0.00 0.00 0.00 3.69
2052 2264 0.834612 GACGGAGGAGAGAGAGAGGA 59.165 60.000 0.00 0.00 0.00 3.71
2053 2265 0.837272 ACGGAGGAGAGAGAGAGGAG 59.163 60.000 0.00 0.00 0.00 3.69
2054 2266 0.108585 CGGAGGAGAGAGAGAGGAGG 59.891 65.000 0.00 0.00 0.00 4.30
2055 2267 0.478507 GGAGGAGAGAGAGAGGAGGG 59.521 65.000 0.00 0.00 0.00 4.30
2056 2268 1.518367 GAGGAGAGAGAGAGGAGGGA 58.482 60.000 0.00 0.00 0.00 4.20
2057 2269 1.421646 GAGGAGAGAGAGAGGAGGGAG 59.578 61.905 0.00 0.00 0.00 4.30
2058 2270 0.478507 GGAGAGAGAGAGGAGGGAGG 59.521 65.000 0.00 0.00 0.00 4.30
2059 2271 1.518367 GAGAGAGAGAGGAGGGAGGA 58.482 60.000 0.00 0.00 0.00 3.71
2060 2272 1.421646 GAGAGAGAGAGGAGGGAGGAG 59.578 61.905 0.00 0.00 0.00 3.69
2061 2273 0.478507 GAGAGAGAGGAGGGAGGAGG 59.521 65.000 0.00 0.00 0.00 4.30
2062 2274 0.998945 AGAGAGAGGAGGGAGGAGGG 60.999 65.000 0.00 0.00 0.00 4.30
2063 2275 1.230819 AGAGAGGAGGGAGGAGGGT 60.231 63.158 0.00 0.00 0.00 4.34
2064 2276 1.075600 GAGAGGAGGGAGGAGGGTG 60.076 68.421 0.00 0.00 0.00 4.61
2065 2277 2.041405 GAGGAGGGAGGAGGGTGG 60.041 72.222 0.00 0.00 0.00 4.61
2066 2278 4.423209 AGGAGGGAGGAGGGTGGC 62.423 72.222 0.00 0.00 0.00 5.01
2105 2325 2.200092 GGCGAGAGGAGGAGGGAT 59.800 66.667 0.00 0.00 0.00 3.85
2112 2332 3.237741 GGAGGAGGGATGAGGGCG 61.238 72.222 0.00 0.00 0.00 6.13
2129 2349 3.157949 GGCGGGAGAAGGAGGGAG 61.158 72.222 0.00 0.00 0.00 4.30
2130 2350 3.157949 GCGGGAGAAGGAGGGAGG 61.158 72.222 0.00 0.00 0.00 4.30
2131 2351 2.690452 CGGGAGAAGGAGGGAGGA 59.310 66.667 0.00 0.00 0.00 3.71
2132 2352 1.456705 CGGGAGAAGGAGGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
2133 2353 1.074850 GGGAGAAGGAGGGAGGAGG 60.075 68.421 0.00 0.00 0.00 4.30
2134 2354 1.074850 GGAGAAGGAGGGAGGAGGG 60.075 68.421 0.00 0.00 0.00 4.30
2135 2355 1.707200 GAGAAGGAGGGAGGAGGGT 59.293 63.158 0.00 0.00 0.00 4.34
2136 2356 0.689412 GAGAAGGAGGGAGGAGGGTG 60.689 65.000 0.00 0.00 0.00 4.61
2137 2357 1.690985 GAAGGAGGGAGGAGGGTGG 60.691 68.421 0.00 0.00 0.00 4.61
2138 2358 3.952799 AAGGAGGGAGGAGGGTGGC 62.953 68.421 0.00 0.00 0.00 5.01
2145 2365 2.366972 AGGAGGGTGGCGGCTTAT 60.367 61.111 11.43 0.00 0.00 1.73
2161 2381 2.565391 GCTTATAGAGGAAGGAGGAGGC 59.435 54.545 0.00 0.00 0.00 4.70
2162 2382 3.169908 CTTATAGAGGAAGGAGGAGGCC 58.830 54.545 0.00 0.00 0.00 5.19
2163 2383 0.944999 ATAGAGGAAGGAGGAGGCCA 59.055 55.000 5.01 0.00 0.00 5.36
2165 2385 2.041928 AGGAAGGAGGAGGCCAGG 59.958 66.667 5.01 0.00 0.00 4.45
2167 2387 2.041265 GAAGGAGGAGGCCAGGGA 59.959 66.667 5.01 0.00 0.00 4.20
2168 2388 2.285743 AAGGAGGAGGCCAGGGAC 60.286 66.667 5.01 0.00 0.00 4.46
2169 2389 3.194025 AAGGAGGAGGCCAGGGACA 62.194 63.158 5.01 0.00 0.00 4.02
2170 2390 2.610859 GGAGGAGGCCAGGGACAA 60.611 66.667 5.01 0.00 0.00 3.18
2171 2391 2.671682 GAGGAGGCCAGGGACAAC 59.328 66.667 5.01 0.00 0.00 3.32
2172 2392 2.121963 AGGAGGCCAGGGACAACA 60.122 61.111 5.01 0.00 0.00 3.33
2174 2394 2.352805 GAGGCCAGGGACAACAGG 59.647 66.667 5.01 0.00 0.00 4.00
2175 2395 2.121963 AGGCCAGGGACAACAGGA 60.122 61.111 5.01 0.00 0.00 3.86
2178 2398 2.224159 GCCAGGGACAACAGGAGGA 61.224 63.158 0.00 0.00 0.00 3.71
2209 2437 2.004589 AGTAGAGGGAGTGAGAGGGTT 58.995 52.381 0.00 0.00 0.00 4.11
2212 2440 1.364328 AGAGGGAGTGAGAGGGTTGAT 59.636 52.381 0.00 0.00 0.00 2.57
2250 2478 1.589196 GTGCCTTAGGAGTAGCGCG 60.589 63.158 0.69 0.00 0.00 6.86
2282 2510 0.815615 GCGCTACTGCTAAGCCCATT 60.816 55.000 0.00 0.00 36.60 3.16
2292 2520 3.054728 TGCTAAGCCCATTAGTTGTAGCA 60.055 43.478 0.00 0.00 42.57 3.49
2293 2521 4.137543 GCTAAGCCCATTAGTTGTAGCAT 58.862 43.478 0.00 0.00 42.57 3.79
2323 2551 1.965930 CCAACGTTGCTGCTAGGCA 60.966 57.895 22.93 0.00 40.74 4.75
2360 2588 1.066002 GCGCCCGTGTATCTACAGTAA 59.934 52.381 0.00 0.00 36.78 2.24
2366 2594 4.156915 CCGTGTATCTACAGTAATAGCGC 58.843 47.826 0.00 0.00 36.78 5.92
2370 2598 2.115348 TCTACAGTAATAGCGCGTGC 57.885 50.000 14.39 14.39 43.24 5.34
2406 2634 2.262774 CTTCTGTGGCCAGCCCCTAG 62.263 65.000 5.11 2.06 38.66 3.02
2422 2650 0.475044 CTAGAGGCTCGGTAGGGACT 59.525 60.000 9.22 0.00 40.53 3.85
2448 2676 1.537814 TAGTAGTGCGGGTGTGGTGG 61.538 60.000 0.00 0.00 0.00 4.61
2449 2677 3.632080 TAGTGCGGGTGTGGTGGG 61.632 66.667 0.00 0.00 0.00 4.61
2468 2696 1.830145 CCCCCGCTACTGCTAATGT 59.170 57.895 0.00 0.00 36.97 2.71
2475 2703 2.555199 GCTACTGCTAATGTCCACCTG 58.445 52.381 0.00 0.00 36.03 4.00
2479 2707 0.692476 TGCTAATGTCCACCTGCAGT 59.308 50.000 13.81 0.00 0.00 4.40
2521 2761 0.648958 GTAGCGCGACACATTTACCC 59.351 55.000 16.21 0.00 0.00 3.69
2529 2769 2.748647 ACATTTACCCCGCGCCAC 60.749 61.111 0.00 0.00 0.00 5.01
2553 2793 7.690952 CTGTTACCAGTCTATCTATAGGGTC 57.309 44.000 0.00 0.00 33.80 4.46
2555 2795 7.460071 TGTTACCAGTCTATCTATAGGGTCTC 58.540 42.308 0.00 0.00 0.00 3.36
2558 2798 7.891825 ACCAGTCTATCTATAGGGTCTCTTA 57.108 40.000 0.00 0.00 0.00 2.10
2559 2799 8.290463 ACCAGTCTATCTATAGGGTCTCTTAA 57.710 38.462 0.00 0.00 0.00 1.85
2560 2800 8.734763 ACCAGTCTATCTATAGGGTCTCTTAAA 58.265 37.037 0.00 0.00 0.00 1.52
2561 2801 9.016438 CCAGTCTATCTATAGGGTCTCTTAAAC 57.984 40.741 0.00 0.00 0.00 2.01
2573 2813 7.510407 AGGGTCTCTTAAACAAATCTATAGGC 58.490 38.462 0.00 0.00 0.00 3.93
2591 2831 4.576330 AGGCTTTTTCTAGTAGTGGCAT 57.424 40.909 0.00 0.00 0.00 4.40
2594 2834 4.142600 GGCTTTTTCTAGTAGTGGCATGTG 60.143 45.833 0.00 0.00 0.00 3.21
2595 2835 4.672801 GCTTTTTCTAGTAGTGGCATGTGC 60.673 45.833 0.00 0.00 41.14 4.57
2621 2867 0.525311 CTCTGCGAGCTCTGAGTCAA 59.475 55.000 12.85 0.00 0.00 3.18
2645 2891 1.337118 GGAGGGGAAAAACATGCACA 58.663 50.000 0.00 0.00 0.00 4.57
2649 2895 2.158827 AGGGGAAAAACATGCACAAACC 60.159 45.455 0.00 0.00 0.00 3.27
2651 2897 3.540617 GGGAAAAACATGCACAAACCTT 58.459 40.909 0.00 0.00 0.00 3.50
2655 2901 4.420522 AAAACATGCACAAACCTTCCAT 57.579 36.364 0.00 0.00 0.00 3.41
2656 2902 3.389925 AACATGCACAAACCTTCCATG 57.610 42.857 0.00 0.00 39.23 3.66
2657 2903 2.596346 ACATGCACAAACCTTCCATGA 58.404 42.857 0.00 0.00 37.36 3.07
2662 2908 3.640498 TGCACAAACCTTCCATGAATTCA 59.360 39.130 11.26 11.26 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.729467 CGCCGAATTAATTTGGAACGCA 60.729 45.455 31.03 0.00 42.84 5.24
1 2 1.843753 CGCCGAATTAATTTGGAACGC 59.156 47.619 31.03 17.61 42.84 4.84
2 3 1.843753 GCGCCGAATTAATTTGGAACG 59.156 47.619 31.03 25.69 42.84 3.95
64 67 9.101655 GCAATTAATGTGCCAGAGATTTAATTT 57.898 29.630 9.95 0.00 35.91 1.82
169 173 9.823647 ACTCTATTAAACAGGAGTTGATATGTG 57.176 33.333 0.00 0.00 38.17 3.21
250 254 0.924777 CGCACGCGGTCATTAATGTA 59.075 50.000 12.47 0.00 35.56 2.29
288 292 7.464178 GCCACTAATCTATATTATGAAACGGCG 60.464 40.741 4.80 4.80 0.00 6.46
376 380 3.605634 CGGTTGGTACATCATCCTTTCA 58.394 45.455 0.00 0.00 39.30 2.69
562 566 9.109393 TCAAGGAATCAATTCGGTTTAGATTAG 57.891 33.333 0.00 0.00 37.67 1.73
695 702 1.994779 CACGGGTCCAAATGTACGTAC 59.005 52.381 18.90 18.90 32.85 3.67
696 703 1.617850 ACACGGGTCCAAATGTACGTA 59.382 47.619 0.00 0.00 32.85 3.57
697 704 0.393820 ACACGGGTCCAAATGTACGT 59.606 50.000 0.00 0.00 34.61 3.57
698 705 2.367030 TACACGGGTCCAAATGTACG 57.633 50.000 0.00 0.00 0.00 3.67
1012 1165 3.691342 CACGTGGGAGGAGCCGAA 61.691 66.667 7.95 0.00 37.63 4.30
1686 1875 1.070786 ACGGTCACTTCACGCCAAT 59.929 52.632 0.00 0.00 0.00 3.16
1691 1880 2.310233 CCAGCACGGTCACTTCACG 61.310 63.158 0.00 0.00 0.00 4.35
1715 1904 1.201429 ATCACTCCACCCACCACCTC 61.201 60.000 0.00 0.00 0.00 3.85
1775 1964 5.564259 CGCACCAGATATAAGTAGTGTACCC 60.564 48.000 0.00 0.00 0.00 3.69
1781 1970 2.030185 CCGCGCACCAGATATAAGTAGT 60.030 50.000 8.75 0.00 0.00 2.73
1782 1971 2.596452 CCGCGCACCAGATATAAGTAG 58.404 52.381 8.75 0.00 0.00 2.57
1783 1972 1.271379 CCCGCGCACCAGATATAAGTA 59.729 52.381 8.75 0.00 0.00 2.24
1784 1973 0.033504 CCCGCGCACCAGATATAAGT 59.966 55.000 8.75 0.00 0.00 2.24
1796 1985 3.032667 TAGCCATTAACCCCGCGCA 62.033 57.895 8.75 0.00 0.00 6.09
1866 2066 4.502604 GGAGCCATTACACTATAAGCCGAA 60.503 45.833 0.00 0.00 0.00 4.30
1867 2067 3.006537 GGAGCCATTACACTATAAGCCGA 59.993 47.826 0.00 0.00 0.00 5.54
1868 2068 3.244078 TGGAGCCATTACACTATAAGCCG 60.244 47.826 0.00 0.00 0.00 5.52
1869 2069 4.202367 ACTGGAGCCATTACACTATAAGCC 60.202 45.833 0.00 0.00 0.00 4.35
1870 2070 4.962155 ACTGGAGCCATTACACTATAAGC 58.038 43.478 0.00 0.00 0.00 3.09
1871 2071 5.760253 CCAACTGGAGCCATTACACTATAAG 59.240 44.000 0.00 0.00 37.39 1.73
1872 2072 5.190925 ACCAACTGGAGCCATTACACTATAA 59.809 40.000 1.86 0.00 38.94 0.98
1913 2115 6.928520 AGCATAATATTTTCATTAGCCTGGC 58.071 36.000 11.65 11.65 0.00 4.85
1931 2133 4.142182 GCAGCCATTGGTAAAAGAGCATAA 60.142 41.667 4.26 0.00 34.92 1.90
1942 2144 2.816777 TAACCATGCAGCCATTGGTA 57.183 45.000 9.29 0.00 34.15 3.25
1943 2145 2.163810 ATAACCATGCAGCCATTGGT 57.836 45.000 3.00 3.00 35.65 3.67
1945 2147 3.633525 ACACTATAACCATGCAGCCATTG 59.366 43.478 0.00 0.00 0.00 2.82
1946 2148 3.902218 ACACTATAACCATGCAGCCATT 58.098 40.909 0.00 0.00 0.00 3.16
1947 2149 3.582998 ACACTATAACCATGCAGCCAT 57.417 42.857 0.00 0.00 0.00 4.40
1949 2151 2.223572 GCAACACTATAACCATGCAGCC 60.224 50.000 0.00 0.00 34.10 4.85
1950 2152 2.423185 TGCAACACTATAACCATGCAGC 59.577 45.455 0.00 0.00 38.73 5.25
1951 2153 3.181497 GGTGCAACACTATAACCATGCAG 60.181 47.826 0.00 0.00 43.62 4.41
1952 2154 2.752354 GGTGCAACACTATAACCATGCA 59.248 45.455 0.00 0.00 41.08 3.96
1955 2157 2.026636 ACGGGTGCAACACTATAACCAT 60.027 45.455 3.06 0.00 38.93 3.55
1956 2158 1.348366 ACGGGTGCAACACTATAACCA 59.652 47.619 3.06 0.00 38.93 3.67
1957 2159 1.735571 CACGGGTGCAACACTATAACC 59.264 52.381 3.06 0.00 38.93 2.85
1958 2160 2.690786 TCACGGGTGCAACACTATAAC 58.309 47.619 3.06 0.00 38.93 1.89
1959 2161 3.404224 TTCACGGGTGCAACACTATAA 57.596 42.857 3.06 0.00 38.93 0.98
1961 2163 2.264005 TTTCACGGGTGCAACACTAT 57.736 45.000 3.06 0.00 38.93 2.12
1964 2166 0.383949 ACATTTCACGGGTGCAACAC 59.616 50.000 3.06 0.00 39.98 3.32
1974 2186 0.591170 ACCGGCTGAAACATTTCACG 59.409 50.000 0.00 6.66 41.88 4.35
1975 2187 3.907894 TTACCGGCTGAAACATTTCAC 57.092 42.857 0.00 1.70 41.88 3.18
1981 2193 1.889829 CCCATTTTACCGGCTGAAACA 59.110 47.619 0.00 0.00 0.00 2.83
1982 2194 2.164338 TCCCATTTTACCGGCTGAAAC 58.836 47.619 0.00 0.00 0.00 2.78
1983 2195 2.588464 TCCCATTTTACCGGCTGAAA 57.412 45.000 0.00 0.00 0.00 2.69
1984 2196 2.650322 GATCCCATTTTACCGGCTGAA 58.350 47.619 0.00 0.00 0.00 3.02
1985 2197 1.474320 CGATCCCATTTTACCGGCTGA 60.474 52.381 0.00 0.00 0.00 4.26
1986 2198 0.944386 CGATCCCATTTTACCGGCTG 59.056 55.000 0.00 0.00 0.00 4.85
2015 2227 5.502079 TCCGTCCTCCATTTTTAGCATTTA 58.498 37.500 0.00 0.00 0.00 1.40
2027 2239 0.184933 CTCTCTCCTCCGTCCTCCAT 59.815 60.000 0.00 0.00 0.00 3.41
2028 2240 0.914902 TCTCTCTCCTCCGTCCTCCA 60.915 60.000 0.00 0.00 0.00 3.86
2029 2241 0.179029 CTCTCTCTCCTCCGTCCTCC 60.179 65.000 0.00 0.00 0.00 4.30
2030 2242 0.834612 TCTCTCTCTCCTCCGTCCTC 59.165 60.000 0.00 0.00 0.00 3.71
2031 2243 0.837272 CTCTCTCTCTCCTCCGTCCT 59.163 60.000 0.00 0.00 0.00 3.85
2032 2244 0.179029 CCTCTCTCTCTCCTCCGTCC 60.179 65.000 0.00 0.00 0.00 4.79
2033 2245 0.834612 TCCTCTCTCTCTCCTCCGTC 59.165 60.000 0.00 0.00 0.00 4.79
2034 2246 0.837272 CTCCTCTCTCTCTCCTCCGT 59.163 60.000 0.00 0.00 0.00 4.69
2035 2247 0.108585 CCTCCTCTCTCTCTCCTCCG 59.891 65.000 0.00 0.00 0.00 4.63
2036 2248 0.478507 CCCTCCTCTCTCTCTCCTCC 59.521 65.000 0.00 0.00 0.00 4.30
2037 2249 1.421646 CTCCCTCCTCTCTCTCTCCTC 59.578 61.905 0.00 0.00 0.00 3.71
2038 2250 1.522900 CTCCCTCCTCTCTCTCTCCT 58.477 60.000 0.00 0.00 0.00 3.69
2039 2251 0.478507 CCTCCCTCCTCTCTCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
2040 2252 1.421646 CTCCTCCCTCCTCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
2041 2253 1.522900 CTCCTCCCTCCTCTCTCTCT 58.477 60.000 0.00 0.00 0.00 3.10
2042 2254 0.478507 CCTCCTCCCTCCTCTCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
2043 2255 0.998945 CCCTCCTCCCTCCTCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
2044 2256 1.293683 ACCCTCCTCCCTCCTCTCTC 61.294 65.000 0.00 0.00 0.00 3.20
2045 2257 1.230819 ACCCTCCTCCCTCCTCTCT 60.231 63.158 0.00 0.00 0.00 3.10
2046 2258 1.075600 CACCCTCCTCCCTCCTCTC 60.076 68.421 0.00 0.00 0.00 3.20
2047 2259 2.641746 CCACCCTCCTCCCTCCTCT 61.642 68.421 0.00 0.00 0.00 3.69
2048 2260 2.041405 CCACCCTCCTCCCTCCTC 60.041 72.222 0.00 0.00 0.00 3.71
2049 2261 4.423209 GCCACCCTCCTCCCTCCT 62.423 72.222 0.00 0.00 0.00 3.69
2066 2278 3.430497 TCCTCCCTCCTCCTCCGG 61.430 72.222 0.00 0.00 0.00 5.14
2067 2279 2.197324 CTCCTCCCTCCTCCTCCG 59.803 72.222 0.00 0.00 0.00 4.63
2068 2280 2.612251 CCTCCTCCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
2069 2281 2.612251 CCCTCCTCCCTCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
2070 2282 3.773154 GCCCTCCTCCCTCCTCCT 61.773 72.222 0.00 0.00 0.00 3.69
2090 2302 0.539438 CCTCATCCCTCCTCCTCTCG 60.539 65.000 0.00 0.00 0.00 4.04
2091 2303 0.178935 CCCTCATCCCTCCTCCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
2092 2304 1.945447 CCCTCATCCCTCCTCCTCT 59.055 63.158 0.00 0.00 0.00 3.69
2112 2332 3.157949 CTCCCTCCTTCTCCCGCC 61.158 72.222 0.00 0.00 0.00 6.13
2120 2340 2.456840 CCACCCTCCTCCCTCCTT 59.543 66.667 0.00 0.00 0.00 3.36
2127 2347 1.119574 TATAAGCCGCCACCCTCCTC 61.120 60.000 0.00 0.00 0.00 3.71
2128 2348 1.074775 TATAAGCCGCCACCCTCCT 60.075 57.895 0.00 0.00 0.00 3.69
2129 2349 1.119574 TCTATAAGCCGCCACCCTCC 61.120 60.000 0.00 0.00 0.00 4.30
2130 2350 0.318762 CTCTATAAGCCGCCACCCTC 59.681 60.000 0.00 0.00 0.00 4.30
2131 2351 1.122019 CCTCTATAAGCCGCCACCCT 61.122 60.000 0.00 0.00 0.00 4.34
2132 2352 1.119574 TCCTCTATAAGCCGCCACCC 61.120 60.000 0.00 0.00 0.00 4.61
2133 2353 0.756903 TTCCTCTATAAGCCGCCACC 59.243 55.000 0.00 0.00 0.00 4.61
2134 2354 1.270358 CCTTCCTCTATAAGCCGCCAC 60.270 57.143 0.00 0.00 0.00 5.01
2135 2355 1.048601 CCTTCCTCTATAAGCCGCCA 58.951 55.000 0.00 0.00 0.00 5.69
2136 2356 1.273886 CTCCTTCCTCTATAAGCCGCC 59.726 57.143 0.00 0.00 0.00 6.13
2137 2357 1.273886 CCTCCTTCCTCTATAAGCCGC 59.726 57.143 0.00 0.00 0.00 6.53
2138 2358 2.823154 CTCCTCCTTCCTCTATAAGCCG 59.177 54.545 0.00 0.00 0.00 5.52
2139 2359 3.169908 CCTCCTCCTTCCTCTATAAGCC 58.830 54.545 0.00 0.00 0.00 4.35
2140 2360 2.565391 GCCTCCTCCTTCCTCTATAAGC 59.435 54.545 0.00 0.00 0.00 3.09
2145 2365 0.263172 CTGGCCTCCTCCTTCCTCTA 59.737 60.000 3.32 0.00 0.00 2.43
2161 2381 1.557269 CCTCCTCCTGTTGTCCCTGG 61.557 65.000 0.00 0.00 0.00 4.45
2162 2382 0.545309 TCCTCCTCCTGTTGTCCCTG 60.545 60.000 0.00 0.00 0.00 4.45
2163 2383 0.252467 CTCCTCCTCCTGTTGTCCCT 60.252 60.000 0.00 0.00 0.00 4.20
2165 2385 1.190643 CTCTCCTCCTCCTGTTGTCC 58.809 60.000 0.00 0.00 0.00 4.02
2167 2387 0.907230 GCCTCTCCTCCTCCTGTTGT 60.907 60.000 0.00 0.00 0.00 3.32
2168 2388 0.906756 TGCCTCTCCTCCTCCTGTTG 60.907 60.000 0.00 0.00 0.00 3.33
2169 2389 0.178891 TTGCCTCTCCTCCTCCTGTT 60.179 55.000 0.00 0.00 0.00 3.16
2170 2390 0.178891 TTTGCCTCTCCTCCTCCTGT 60.179 55.000 0.00 0.00 0.00 4.00
2171 2391 0.540923 CTTTGCCTCTCCTCCTCCTG 59.459 60.000 0.00 0.00 0.00 3.86
2172 2392 0.118144 ACTTTGCCTCTCCTCCTCCT 59.882 55.000 0.00 0.00 0.00 3.69
2174 2394 2.693074 CTCTACTTTGCCTCTCCTCCTC 59.307 54.545 0.00 0.00 0.00 3.71
2175 2395 2.625617 CCTCTACTTTGCCTCTCCTCCT 60.626 54.545 0.00 0.00 0.00 3.69
2178 2398 1.362932 TCCCTCTACTTTGCCTCTCCT 59.637 52.381 0.00 0.00 0.00 3.69
2209 2437 1.081481 TATCCCTCTCCCGCCTATCA 58.919 55.000 0.00 0.00 0.00 2.15
2212 2440 0.114560 CCTTATCCCTCTCCCGCCTA 59.885 60.000 0.00 0.00 0.00 3.93
2339 2567 1.299926 CTGTAGATACACGGGCGCC 60.300 63.158 21.18 21.18 31.93 6.53
2340 2568 0.664761 TACTGTAGATACACGGGCGC 59.335 55.000 0.00 0.00 31.93 6.53
2341 2569 3.637998 ATTACTGTAGATACACGGGCG 57.362 47.619 0.00 0.00 31.93 6.13
2360 2588 2.278857 CTCCTTCGCACGCGCTAT 60.279 61.111 5.73 0.00 39.59 2.97
2406 2634 0.183252 AGTAGTCCCTACCGAGCCTC 59.817 60.000 0.00 0.00 37.65 4.70
2422 2650 3.691118 CACACCCGCACTACTACTAAGTA 59.309 47.826 0.00 0.00 37.15 2.24
2455 2683 2.555199 CAGGTGGACATTAGCAGTAGC 58.445 52.381 0.00 0.00 42.56 3.58
2459 2687 1.376543 CTGCAGGTGGACATTAGCAG 58.623 55.000 5.57 0.00 42.69 4.24
2462 2690 1.089920 GCACTGCAGGTGGACATTAG 58.910 55.000 19.93 0.00 45.44 1.73
2468 2696 2.113774 CCAAGCACTGCAGGTGGA 59.886 61.111 19.93 0.00 45.44 4.02
2475 2703 2.386661 TAGTAGAAGCCAAGCACTGC 57.613 50.000 0.00 0.00 0.00 4.40
2479 2707 3.513912 TGCTACTTAGTAGAAGCCAAGCA 59.486 43.478 22.14 10.46 38.29 3.91
2509 2749 2.757056 GGCGCGGGGTAAATGTGTC 61.757 63.158 8.83 0.00 0.00 3.67
2510 2750 2.748647 GGCGCGGGGTAAATGTGT 60.749 61.111 8.83 0.00 0.00 3.72
2512 2752 2.748647 GTGGCGCGGGGTAAATGT 60.749 61.111 8.83 0.00 0.00 2.71
2514 2754 2.437716 CAGTGGCGCGGGGTAAAT 60.438 61.111 8.83 0.00 0.00 1.40
2565 2805 6.610020 TGCCACTACTAGAAAAAGCCTATAGA 59.390 38.462 0.00 0.00 0.00 1.98
2566 2806 6.817184 TGCCACTACTAGAAAAAGCCTATAG 58.183 40.000 0.00 0.00 0.00 1.31
2567 2807 6.801718 TGCCACTACTAGAAAAAGCCTATA 57.198 37.500 0.00 0.00 0.00 1.31
2568 2808 5.693769 TGCCACTACTAGAAAAAGCCTAT 57.306 39.130 0.00 0.00 0.00 2.57
2569 2809 5.045869 ACATGCCACTACTAGAAAAAGCCTA 60.046 40.000 0.00 0.00 0.00 3.93
2570 2810 4.263506 ACATGCCACTACTAGAAAAAGCCT 60.264 41.667 0.00 0.00 0.00 4.58
2573 2813 4.974591 GCACATGCCACTACTAGAAAAAG 58.025 43.478 0.00 0.00 34.31 2.27
2603 2843 0.961753 TTTGACTCAGAGCTCGCAGA 59.038 50.000 18.72 12.62 0.00 4.26
2604 2844 2.007360 ATTTGACTCAGAGCTCGCAG 57.993 50.000 8.37 10.61 0.00 5.18
2605 2845 2.341257 GAATTTGACTCAGAGCTCGCA 58.659 47.619 8.37 0.00 0.00 5.10
2621 2867 2.233676 GCATGTTTTTCCCCTCCGAATT 59.766 45.455 0.00 0.00 0.00 2.17
2645 2891 5.307716 ACAATGGTGAATTCATGGAAGGTTT 59.692 36.000 12.12 0.00 0.00 3.27
2662 2908 4.324563 CCTGTTAAGAGGGATCACAATGGT 60.325 45.833 10.88 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.