Multiple sequence alignment - TraesCS5B01G178000

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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 TraesCS5B01G178000 chr5B 100.000 2840 0 0 1 2840 325552466 325549627 0.000000e+00 5245.0
1 TraesCS5B01G178000 chr5B 95.856 917 33 4 4 918 684757826 684758739 0.000000e+00 1478.0
2 TraesCS5B01G178000 chr5B 95.402 87 4 0 1186 1272 325551200 325551114 3.820000e-29 139.0
3 TraesCS5B01G178000 chr5B 95.402 87 4 0 1267 1353 325551281 325551195 3.820000e-29 139.0
4 TraesCS5B01G178000 chr1B 97.059 918 25 1 1 916 73038239 73037322 0.000000e+00 1544.0
5 TraesCS5B01G178000 chr3B 96.630 920 29 1 1 918 810540189 810539270 0.000000e+00 1526.0
6 TraesCS5B01G178000 chr3B 96.820 912 28 1 1 911 36536100 36537011 0.000000e+00 1522.0
7 TraesCS5B01G178000 chr6B 96.518 919 30 1 1 917 5875346 5876264 0.000000e+00 1519.0
8 TraesCS5B01G178000 chr6A 96.605 913 29 1 1 911 563702795 563703707 0.000000e+00 1513.0
9 TraesCS5B01G178000 chr7B 96.601 912 30 1 1 912 738599766 738598856 0.000000e+00 1511.0
10 TraesCS5B01G178000 chr7B 95.861 918 37 1 1 917 23072638 23071721 0.000000e+00 1483.0
11 TraesCS5B01G178000 chr2B 96.276 913 32 1 1 911 355193095 355192183 0.000000e+00 1496.0
12 TraesCS5B01G178000 chr5A 91.815 1014 49 12 929 1934 378728056 378727069 0.000000e+00 1382.0
13 TraesCS5B01G178000 chr5D 92.295 610 14 9 1395 1977 286455818 286455215 0.000000e+00 835.0
14 TraesCS5B01G178000 chr7D 85.327 811 71 11 2039 2840 506799492 506798721 0.000000e+00 795.0
15 TraesCS5B01G178000 chr4A 81.063 301 27 13 2546 2837 446481378 446481657 2.220000e-51 213.0
16 TraesCS5B01G178000 chr4A 100.000 31 0 0 2157 2187 446481292 446481322 1.100000e-04 58.4
17 TraesCS5B01G178000 chr6D 88.679 53 6 0 2693 2745 80391633 80391685 6.570000e-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 TraesCS5B01G178000 chr5B 325549627 325552466 2839 True 1841 5245 96.934667 1 2840 3 chr5B.!!$R1 2839
1 TraesCS5B01G178000 chr5B 684757826 684758739 913 False 1478 1478 95.856000 4 918 1 chr5B.!!$F1 914
2 TraesCS5B01G178000 chr1B 73037322 73038239 917 True 1544 1544 97.059000 1 916 1 chr1B.!!$R1 915
3 TraesCS5B01G178000 chr3B 810539270 810540189 919 True 1526 1526 96.630000 1 918 1 chr3B.!!$R1 917
4 TraesCS5B01G178000 chr3B 36536100 36537011 911 False 1522 1522 96.820000 1 911 1 chr3B.!!$F1 910
5 TraesCS5B01G178000 chr6B 5875346 5876264 918 False 1519 1519 96.518000 1 917 1 chr6B.!!$F1 916
6 TraesCS5B01G178000 chr6A 563702795 563703707 912 False 1513 1513 96.605000 1 911 1 chr6A.!!$F1 910
7 TraesCS5B01G178000 chr7B 738598856 738599766 910 True 1511 1511 96.601000 1 912 1 chr7B.!!$R2 911
8 TraesCS5B01G178000 chr7B 23071721 23072638 917 True 1483 1483 95.861000 1 917 1 chr7B.!!$R1 916
9 TraesCS5B01G178000 chr2B 355192183 355193095 912 True 1496 1496 96.276000 1 911 1 chr2B.!!$R1 910
10 TraesCS5B01G178000 chr5A 378727069 378728056 987 True 1382 1382 91.815000 929 1934 1 chr5A.!!$R1 1005
11 TraesCS5B01G178000 chr5D 286455215 286455818 603 True 835 835 92.295000 1395 1977 1 chr5D.!!$R1 582
12 TraesCS5B01G178000 chr7D 506798721 506799492 771 True 795 795 85.327000 2039 2840 1 chr7D.!!$R1 801

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
196 197 0.768221 AAGGGAGTGGCTTGGACAGA 60.768 55.0 0.0 0.0 0.0 3.41 F
1234 1238 0.464036 TTATGAGCCGCCGTCAGAAT 59.536 50.0 0.0 0.0 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 1381 0.036765 GTTGTACGGGCACATGAGGA 60.037 55.0 0.0 0.0 0.00 3.71 R
2392 2426 0.039074 CTACGTCGATCAGGGGATGC 60.039 60.0 0.0 0.0 32.67 3.91 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
196 197 0.768221 AAGGGAGTGGCTTGGACAGA 60.768 55.000 0.00 0.00 0.00 3.41
493 494 2.281070 CTGTGTGGTGGCGAGCTT 60.281 61.111 0.00 0.00 0.00 3.74
918 921 2.703536 AGGAAACCCTTTTTCGGCAATT 59.296 40.909 0.00 0.00 0.00 2.32
919 922 3.135712 AGGAAACCCTTTTTCGGCAATTT 59.864 39.130 0.00 0.00 0.00 1.82
920 923 4.345547 AGGAAACCCTTTTTCGGCAATTTA 59.654 37.500 0.00 0.00 0.00 1.40
921 924 4.449743 GGAAACCCTTTTTCGGCAATTTAC 59.550 41.667 0.00 0.00 0.00 2.01
922 925 4.948341 AACCCTTTTTCGGCAATTTACT 57.052 36.364 0.00 0.00 0.00 2.24
923 926 4.514781 ACCCTTTTTCGGCAATTTACTC 57.485 40.909 0.00 0.00 0.00 2.59
924 927 3.892588 ACCCTTTTTCGGCAATTTACTCA 59.107 39.130 0.00 0.00 0.00 3.41
925 928 4.342665 ACCCTTTTTCGGCAATTTACTCAA 59.657 37.500 0.00 0.00 0.00 3.02
926 929 4.923281 CCCTTTTTCGGCAATTTACTCAAG 59.077 41.667 0.00 0.00 0.00 3.02
927 930 5.508994 CCCTTTTTCGGCAATTTACTCAAGT 60.509 40.000 0.00 0.00 0.00 3.16
985 988 6.384886 TCCTTTCCTATATAAACCCAGACGTT 59.615 38.462 0.00 0.00 0.00 3.99
1071 1075 1.206610 AGCAAGTGATCGAGCATGTCT 59.793 47.619 6.66 0.00 0.00 3.41
1166 1170 0.529992 CCTGAACCTTATCCGCCGAC 60.530 60.000 0.00 0.00 0.00 4.79
1234 1238 0.464036 TTATGAGCCGCCGTCAGAAT 59.536 50.000 0.00 0.00 0.00 2.40
1243 1247 1.648467 GCCGTCAGAATTGGTGCCTC 61.648 60.000 0.00 0.00 0.00 4.70
1304 1308 1.071605 CGAGCGCCTTATTATCAGCC 58.928 55.000 2.29 0.00 0.00 4.85
1332 1336 2.092538 AGAATTGGTGCCTCCTCATCAG 60.093 50.000 0.00 0.00 37.07 2.90
1341 1345 2.202797 CCTCATCAGGTGTCGCCG 60.203 66.667 0.00 0.00 43.70 6.46
1389 1393 1.153549 GACGACTCCTCATGTGCCC 60.154 63.158 0.00 0.00 0.00 5.36
1392 1396 1.663379 CGACTCCTCATGTGCCCGTA 61.663 60.000 0.00 0.00 0.00 4.02
1627 1631 3.458579 CGTCGCAACCGTCGTCTG 61.459 66.667 0.00 0.00 40.23 3.51
1628 1632 3.764049 GTCGCAACCGTCGTCTGC 61.764 66.667 5.87 5.87 35.54 4.26
1721 1731 2.737376 GCCTCCGTCGACACCAAC 60.737 66.667 17.16 0.00 0.00 3.77
1772 1782 3.474570 GGCGCCTCACCCTCATCT 61.475 66.667 22.15 0.00 0.00 2.90
1782 1792 2.418910 CCCTCATCTCGGCGACACT 61.419 63.158 4.99 0.00 0.00 3.55
1846 1863 6.369065 CCATCAAGAATACTATTAGGTTCGGC 59.631 42.308 0.00 0.00 0.00 5.54
1939 1972 4.142381 GCATGGACCTTAATTTGACTCACC 60.142 45.833 0.00 0.00 0.00 4.02
1957 1990 4.140536 TCACCACTGCATTGATGTGTTAA 58.859 39.130 5.49 0.00 0.00 2.01
1958 1991 4.766373 TCACCACTGCATTGATGTGTTAAT 59.234 37.500 5.49 0.00 0.00 1.40
1959 1992 4.860352 CACCACTGCATTGATGTGTTAATG 59.140 41.667 5.49 0.00 37.35 1.90
1965 1998 3.956233 CATTGATGTGTTAATGCCTCCG 58.044 45.455 0.00 0.00 0.00 4.63
1977 2010 7.225931 GTGTTAATGCCTCCGTTCAAGAATATA 59.774 37.037 0.00 0.00 0.00 0.86
1978 2011 7.771361 TGTTAATGCCTCCGTTCAAGAATATAA 59.229 33.333 0.00 0.00 0.00 0.98
1979 2012 8.784043 GTTAATGCCTCCGTTCAAGAATATAAT 58.216 33.333 0.00 0.00 0.00 1.28
1980 2013 7.823745 AATGCCTCCGTTCAAGAATATAATT 57.176 32.000 0.00 0.00 0.00 1.40
1981 2014 8.918202 AATGCCTCCGTTCAAGAATATAATTA 57.082 30.769 0.00 0.00 0.00 1.40
1982 2015 9.520515 AATGCCTCCGTTCAAGAATATAATTAT 57.479 29.630 2.97 2.97 0.00 1.28
1983 2016 8.547967 TGCCTCCGTTCAAGAATATAATTATC 57.452 34.615 0.00 0.00 0.00 1.75
1984 2017 8.375506 TGCCTCCGTTCAAGAATATAATTATCT 58.624 33.333 0.00 0.00 0.00 1.98
1985 2018 8.660373 GCCTCCGTTCAAGAATATAATTATCTG 58.340 37.037 0.00 0.00 0.00 2.90
1986 2019 9.929180 CCTCCGTTCAAGAATATAATTATCTGA 57.071 33.333 0.00 0.00 0.00 3.27
1998 2031 6.857777 ATAATTATCTGACACTTGCTCAGC 57.142 37.500 0.00 0.00 35.95 4.26
1999 2032 3.683365 TTATCTGACACTTGCTCAGCA 57.317 42.857 0.00 0.00 35.95 4.41
2000 2033 1.805869 ATCTGACACTTGCTCAGCAC 58.194 50.000 0.00 0.00 38.71 4.40
2001 2034 0.465287 TCTGACACTTGCTCAGCACA 59.535 50.000 0.00 0.00 38.71 4.57
2002 2035 1.071228 TCTGACACTTGCTCAGCACAT 59.929 47.619 0.00 0.00 38.71 3.21
2003 2036 1.878088 CTGACACTTGCTCAGCACATT 59.122 47.619 0.00 0.00 38.71 2.71
2004 2037 2.292569 CTGACACTTGCTCAGCACATTT 59.707 45.455 0.00 0.00 38.71 2.32
2005 2038 2.689471 TGACACTTGCTCAGCACATTTT 59.311 40.909 0.00 0.00 38.71 1.82
2006 2039 3.243168 TGACACTTGCTCAGCACATTTTC 60.243 43.478 0.00 0.00 38.71 2.29
2007 2040 2.287188 ACACTTGCTCAGCACATTTTCG 60.287 45.455 0.00 0.00 38.71 3.46
2008 2041 1.949525 ACTTGCTCAGCACATTTTCGT 59.050 42.857 0.00 0.00 38.71 3.85
2009 2042 2.031682 ACTTGCTCAGCACATTTTCGTC 60.032 45.455 0.00 0.00 38.71 4.20
2010 2043 1.592064 TGCTCAGCACATTTTCGTCA 58.408 45.000 0.00 0.00 31.71 4.35
2011 2044 1.946081 TGCTCAGCACATTTTCGTCAA 59.054 42.857 0.00 0.00 31.71 3.18
2012 2045 2.357323 TGCTCAGCACATTTTCGTCAAA 59.643 40.909 0.00 0.00 31.71 2.69
2013 2046 3.181492 TGCTCAGCACATTTTCGTCAAAA 60.181 39.130 0.00 0.00 32.74 2.44
2014 2047 3.180387 GCTCAGCACATTTTCGTCAAAAC 59.820 43.478 0.00 0.00 34.24 2.43
2015 2048 4.601019 CTCAGCACATTTTCGTCAAAACT 58.399 39.130 0.00 0.00 34.24 2.66
2016 2049 4.992688 TCAGCACATTTTCGTCAAAACTT 58.007 34.783 0.00 0.00 34.24 2.66
2017 2050 5.406649 TCAGCACATTTTCGTCAAAACTTT 58.593 33.333 0.00 0.00 34.24 2.66
2018 2051 5.288232 TCAGCACATTTTCGTCAAAACTTTG 59.712 36.000 0.00 0.00 34.24 2.77
2019 2052 4.566360 AGCACATTTTCGTCAAAACTTTGG 59.434 37.500 2.49 0.00 38.66 3.28
2020 2053 4.781883 GCACATTTTCGTCAAAACTTTGGC 60.782 41.667 2.49 0.00 39.31 4.52
2021 2054 4.328440 CACATTTTCGTCAAAACTTTGGCA 59.672 37.500 7.49 0.00 42.66 4.92
2022 2055 4.328712 ACATTTTCGTCAAAACTTTGGCAC 59.671 37.500 7.49 0.00 42.66 5.01
2023 2056 3.577649 TTTCGTCAAAACTTTGGCACA 57.422 38.095 7.49 0.00 42.66 4.57
2024 2057 2.553079 TCGTCAAAACTTTGGCACAC 57.447 45.000 7.49 0.00 42.66 3.82
2025 2058 1.813178 TCGTCAAAACTTTGGCACACA 59.187 42.857 7.49 0.00 42.66 3.72
2026 2059 2.159448 TCGTCAAAACTTTGGCACACAG 60.159 45.455 7.49 0.00 42.66 3.66
2027 2060 2.539476 GTCAAAACTTTGGCACACAGG 58.461 47.619 1.96 0.00 41.03 4.00
2028 2061 2.165437 GTCAAAACTTTGGCACACAGGA 59.835 45.455 1.96 0.00 41.03 3.86
2029 2062 3.030291 TCAAAACTTTGGCACACAGGAT 58.970 40.909 2.49 0.00 41.03 3.24
2030 2063 3.068024 TCAAAACTTTGGCACACAGGATC 59.932 43.478 2.49 0.00 41.03 3.36
2031 2064 1.620822 AACTTTGGCACACAGGATCC 58.379 50.000 2.48 2.48 41.03 3.36
2032 2065 0.251341 ACTTTGGCACACAGGATCCC 60.251 55.000 8.55 0.00 41.03 3.85
2033 2066 0.038744 CTTTGGCACACAGGATCCCT 59.961 55.000 8.55 0.00 39.29 4.20
2034 2067 1.281867 CTTTGGCACACAGGATCCCTA 59.718 52.381 8.55 0.00 39.29 3.53
2035 2068 1.595311 TTGGCACACAGGATCCCTAT 58.405 50.000 8.55 0.00 39.29 2.57
2036 2069 1.131638 TGGCACACAGGATCCCTATC 58.868 55.000 8.55 0.00 29.64 2.08
2037 2070 3.821067 TTGGCACACAGGATCCCTATCC 61.821 54.545 8.55 3.32 46.13 2.59
2048 2081 0.179001 TCCCTATCCGCGACTGATGA 60.179 55.000 8.23 0.00 0.00 2.92
2104 2137 1.091771 CCAGCAGCGTCCGATTCATT 61.092 55.000 0.00 0.00 0.00 2.57
2127 2160 6.901081 TCATATACAACCGTCAGATCTGAT 57.099 37.500 27.51 13.45 42.18 2.90
2128 2161 6.681777 TCATATACAACCGTCAGATCTGATG 58.318 40.000 30.40 30.40 44.14 3.07
2131 2164 1.134580 CAACCGTCAGATCTGATGCCT 60.135 52.381 31.49 20.46 43.41 4.75
2149 2183 2.416162 GCCTCCTACAGTCGTCTTCTTG 60.416 54.545 0.00 0.00 0.00 3.02
2161 2195 0.318441 TCTTCTTGCTCCTCACACCG 59.682 55.000 0.00 0.00 0.00 4.94
2177 2211 4.760047 CGTTCCCCACGCTCCCAG 62.760 72.222 0.00 0.00 43.37 4.45
2252 2286 2.825836 CGGTGGCCAATGAGCTCC 60.826 66.667 7.24 0.42 0.00 4.70
2253 2287 2.356278 GGTGGCCAATGAGCTCCA 59.644 61.111 7.24 0.00 0.00 3.86
2275 2309 4.629523 GGTCCCGTCCGTTGCCAA 62.630 66.667 0.00 0.00 0.00 4.52
2300 2334 0.884259 TCACATCACGGTTGCCAGTG 60.884 55.000 0.00 0.00 39.55 3.66
2301 2335 2.260869 ACATCACGGTTGCCAGTGC 61.261 57.895 0.00 0.00 38.19 4.40
2308 2342 4.643387 GTTGCCAGTGCGTCCCCT 62.643 66.667 0.00 0.00 41.78 4.79
2321 2355 1.911269 TCCCCTAGCGTGCAGTCAA 60.911 57.895 0.00 0.00 0.00 3.18
2322 2356 1.741770 CCCCTAGCGTGCAGTCAAC 60.742 63.158 0.00 0.00 0.00 3.18
2336 2370 2.032634 TCAACGACGGATTGCAGCC 61.033 57.895 0.00 0.00 0.00 4.85
2356 2390 1.230050 TAAACCACCCCCTCCCCTC 60.230 63.158 0.00 0.00 0.00 4.30
2357 2391 2.793484 TAAACCACCCCCTCCCCTCC 62.793 65.000 0.00 0.00 0.00 4.30
2392 2426 2.267351 TGGTTCGCCATGGTTGCAG 61.267 57.895 14.67 0.37 43.56 4.41
2401 2435 1.380785 ATGGTTGCAGCATCCCCTG 60.381 57.895 18.31 0.00 28.87 4.45
2410 2444 0.467474 AGCATCCCCTGATCGACGTA 60.467 55.000 0.00 0.00 0.00 3.57
2455 2489 2.476051 GCTTGCATCGTGGTGTCG 59.524 61.111 0.00 0.00 0.00 4.35
2456 2490 2.027073 GCTTGCATCGTGGTGTCGA 61.027 57.895 0.00 0.00 43.86 4.20
2457 2491 1.565156 GCTTGCATCGTGGTGTCGAA 61.565 55.000 0.00 0.00 42.99 3.71
2458 2492 0.163788 CTTGCATCGTGGTGTCGAAC 59.836 55.000 0.00 0.00 42.99 3.95
2502 2536 2.446435 ACAAAATCCTTCCATGGTCGG 58.554 47.619 12.58 13.28 0.00 4.79
2519 2553 6.189677 TGGTCGGTTGAAGCAAAATATTAG 57.810 37.500 0.00 0.00 0.00 1.73
2549 2583 2.101415 AGCAAACAAAAGCTCCAGTTCC 59.899 45.455 0.00 0.00 36.00 3.62
2587 2621 7.491048 GTCCAGTTCTAGCAAAAACAAATTCAA 59.509 33.333 0.00 0.00 0.00 2.69
2592 2626 8.977505 GTTCTAGCAAAAACAAATTCAATAGCA 58.022 29.630 0.00 0.00 0.00 3.49
2593 2627 9.539825 TTCTAGCAAAAACAAATTCAATAGCAA 57.460 25.926 0.00 0.00 0.00 3.91
2621 2655 2.222596 GCTTCAGTCGTCATTTGTAGCG 60.223 50.000 0.00 0.00 0.00 4.26
2649 2691 2.192664 TCCAGCAAAAGATTACGCCA 57.807 45.000 0.00 0.00 0.00 5.69
2650 2692 2.509569 TCCAGCAAAAGATTACGCCAA 58.490 42.857 0.00 0.00 0.00 4.52
2656 2698 3.859386 GCAAAAGATTACGCCAATTCCAG 59.141 43.478 0.00 0.00 0.00 3.86
2670 2712 5.561339 GCCAATTCCAGCAAAACAAATTCAG 60.561 40.000 0.00 0.00 0.00 3.02
2671 2713 5.759273 CCAATTCCAGCAAAACAAATTCAGA 59.241 36.000 0.00 0.00 0.00 3.27
2672 2714 6.260493 CCAATTCCAGCAAAACAAATTCAGAA 59.740 34.615 0.00 0.00 0.00 3.02
2673 2715 7.349711 CAATTCCAGCAAAACAAATTCAGAAG 58.650 34.615 0.00 0.00 0.00 2.85
2674 2716 5.596836 TCCAGCAAAACAAATTCAGAAGT 57.403 34.783 0.00 0.00 0.00 3.01
2675 2717 5.350633 TCCAGCAAAACAAATTCAGAAGTG 58.649 37.500 0.00 0.00 0.00 3.16
2676 2718 5.126869 TCCAGCAAAACAAATTCAGAAGTGA 59.873 36.000 4.06 0.00 0.00 3.41
2677 2719 5.811613 CCAGCAAAACAAATTCAGAAGTGAA 59.188 36.000 4.06 0.00 46.81 3.18
2678 2720 6.237915 CCAGCAAAACAAATTCAGAAGTGAAC 60.238 38.462 4.06 0.00 45.58 3.18
2679 2721 6.310956 CAGCAAAACAAATTCAGAAGTGAACA 59.689 34.615 4.06 0.00 45.58 3.18
2680 2722 6.873076 AGCAAAACAAATTCAGAAGTGAACAA 59.127 30.769 4.06 0.00 45.58 2.83
2681 2723 6.955407 GCAAAACAAATTCAGAAGTGAACAAC 59.045 34.615 4.06 0.00 45.58 3.32
2682 2724 7.148590 GCAAAACAAATTCAGAAGTGAACAACT 60.149 33.333 4.06 0.00 45.58 3.16
2683 2725 8.375465 CAAAACAAATTCAGAAGTGAACAACTC 58.625 33.333 4.06 0.00 45.58 3.01
2684 2726 6.136541 ACAAATTCAGAAGTGAACAACTCC 57.863 37.500 4.06 0.00 45.58 3.85
2685 2727 5.652014 ACAAATTCAGAAGTGAACAACTCCA 59.348 36.000 4.06 0.00 45.58 3.86
2697 2739 0.324943 CAACTCCAGGGGTCGATTGT 59.675 55.000 0.00 0.00 0.00 2.71
2729 2771 7.833285 AGAAAAGGTAGTTCCAGCAAAATAA 57.167 32.000 0.00 0.00 39.02 1.40
2768 2810 4.681978 ACCTCGCAACCAGCCGAC 62.682 66.667 0.00 0.00 41.38 4.79
2794 2836 1.337074 ACAGTGCCGCCAAAAATCATG 60.337 47.619 0.00 0.00 0.00 3.07
2795 2837 0.390209 AGTGCCGCCAAAAATCATGC 60.390 50.000 0.00 0.00 0.00 4.06
2822 2864 2.540769 CGCCGACAGTCACAAAACAAAT 60.541 45.455 0.41 0.00 0.00 2.32
2824 2866 4.219033 GCCGACAGTCACAAAACAAATAG 58.781 43.478 0.41 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
239 240 0.036671 CTCCGAGGCCCGTAAAGTTT 60.037 55.000 0.00 0.00 36.31 2.66
354 355 4.539083 AGCAACACCGTCGGCACA 62.539 61.111 12.28 0.00 0.00 4.57
493 494 0.984230 CTCCACCTTAGGCACTCCAA 59.016 55.000 0.00 0.00 41.75 3.53
918 921 5.721232 GCTTAGTGAGCCTAACTTGAGTAA 58.279 41.667 0.00 0.00 46.01 2.24
919 922 5.326200 GCTTAGTGAGCCTAACTTGAGTA 57.674 43.478 0.00 0.00 46.01 2.59
920 923 4.195225 GCTTAGTGAGCCTAACTTGAGT 57.805 45.455 0.00 0.00 46.01 3.41
985 988 2.373836 AGTACCTGGCCACATGTTTACA 59.626 45.455 0.00 0.00 0.00 2.41
1042 1046 4.442733 GCTCGATCACTTGCTCTTATGTAC 59.557 45.833 0.00 0.00 0.00 2.90
1043 1047 4.097892 TGCTCGATCACTTGCTCTTATGTA 59.902 41.667 0.00 0.00 0.00 2.29
1044 1048 3.118992 TGCTCGATCACTTGCTCTTATGT 60.119 43.478 0.00 0.00 0.00 2.29
1045 1049 3.451526 TGCTCGATCACTTGCTCTTATG 58.548 45.455 0.00 0.00 0.00 1.90
1071 1075 2.435805 GAGGGTAAGAGATGGACATGCA 59.564 50.000 0.00 0.00 0.00 3.96
1234 1238 0.842030 ACCTGATGAGGAGGCACCAA 60.842 55.000 4.75 0.00 42.93 3.67
1243 1247 2.202797 CGGCGACACCTGATGAGG 60.203 66.667 0.00 0.00 46.21 3.86
1281 1285 3.511699 CTGATAATAAGGCGCTCGCATA 58.488 45.455 16.36 8.76 44.11 3.14
1304 1308 2.480555 GCACCAATTCTGACGGCG 59.519 61.111 4.80 4.80 0.00 6.46
1376 1380 0.249120 TTGTACGGGCACATGAGGAG 59.751 55.000 0.00 0.00 0.00 3.69
1377 1381 0.036765 GTTGTACGGGCACATGAGGA 60.037 55.000 0.00 0.00 0.00 3.71
1378 1382 1.024579 GGTTGTACGGGCACATGAGG 61.025 60.000 0.00 0.00 0.00 3.86
1439 1443 4.481112 GCACGGCGGCAGGAATTG 62.481 66.667 13.24 0.00 0.00 2.32
1558 1562 1.436983 GGCGGCTCGTATTTCTTGGG 61.437 60.000 0.00 0.00 0.00 4.12
1623 1627 2.476051 CATGTTGTCCGCGCAGAC 59.524 61.111 16.89 16.89 37.28 3.51
1628 1632 3.499737 GAGGCCATGTTGTCCGCG 61.500 66.667 5.01 0.00 0.00 6.46
1629 1633 3.134127 GGAGGCCATGTTGTCCGC 61.134 66.667 5.01 0.00 0.00 5.54
1721 1731 1.521010 CCATGAGCACGAGGAGCTG 60.521 63.158 0.00 0.00 43.58 4.24
1782 1792 1.971505 AAGATTCGATGCGGGGCTCA 61.972 55.000 0.00 0.00 0.00 4.26
1846 1863 2.743752 CCCTCGCGCAGACATGTTG 61.744 63.158 8.75 1.64 0.00 3.33
1957 1990 9.167311 GATAATTATATTCTTGAACGGAGGCAT 57.833 33.333 0.00 0.00 0.00 4.40
1958 1991 8.375506 AGATAATTATATTCTTGAACGGAGGCA 58.624 33.333 0.00 0.00 0.00 4.75
1959 1992 8.660373 CAGATAATTATATTCTTGAACGGAGGC 58.340 37.037 0.00 0.00 0.00 4.70
1960 1993 9.929180 TCAGATAATTATATTCTTGAACGGAGG 57.071 33.333 0.00 0.00 0.00 4.30
1977 2010 4.394300 GTGCTGAGCAAGTGTCAGATAATT 59.606 41.667 9.51 0.00 43.65 1.40
1978 2011 3.937706 GTGCTGAGCAAGTGTCAGATAAT 59.062 43.478 9.51 0.00 43.65 1.28
1979 2012 3.244181 TGTGCTGAGCAAGTGTCAGATAA 60.244 43.478 9.51 0.00 43.65 1.75
1980 2013 2.299867 TGTGCTGAGCAAGTGTCAGATA 59.700 45.455 9.51 0.00 43.65 1.98
1981 2014 1.071228 TGTGCTGAGCAAGTGTCAGAT 59.929 47.619 9.51 0.00 43.65 2.90
1982 2015 0.465287 TGTGCTGAGCAAGTGTCAGA 59.535 50.000 9.51 0.00 43.65 3.27
1983 2016 1.520494 ATGTGCTGAGCAAGTGTCAG 58.480 50.000 9.51 0.00 41.47 3.51
1984 2017 1.971481 AATGTGCTGAGCAAGTGTCA 58.029 45.000 9.51 2.29 41.47 3.58
1985 2018 3.303406 GAAAATGTGCTGAGCAAGTGTC 58.697 45.455 9.51 0.00 41.47 3.67
1986 2019 2.287188 CGAAAATGTGCTGAGCAAGTGT 60.287 45.455 9.51 0.00 41.47 3.55
1987 2020 2.287188 ACGAAAATGTGCTGAGCAAGTG 60.287 45.455 9.51 0.00 41.47 3.16
1988 2021 1.949525 ACGAAAATGTGCTGAGCAAGT 59.050 42.857 9.51 0.00 41.47 3.16
1989 2022 2.031769 TGACGAAAATGTGCTGAGCAAG 60.032 45.455 9.51 0.00 41.47 4.01
1990 2023 1.946081 TGACGAAAATGTGCTGAGCAA 59.054 42.857 9.51 0.00 41.47 3.91
1991 2024 1.592064 TGACGAAAATGTGCTGAGCA 58.408 45.000 1.40 1.40 35.60 4.26
1992 2025 2.686558 TTGACGAAAATGTGCTGAGC 57.313 45.000 0.00 0.00 0.00 4.26
1993 2026 4.601019 AGTTTTGACGAAAATGTGCTGAG 58.399 39.130 0.00 0.00 33.63 3.35
1994 2027 4.630894 AGTTTTGACGAAAATGTGCTGA 57.369 36.364 0.00 0.00 33.63 4.26
1995 2028 5.483213 CAAAGTTTTGACGAAAATGTGCTG 58.517 37.500 0.00 0.00 40.55 4.41
1996 2029 4.566360 CCAAAGTTTTGACGAAAATGTGCT 59.434 37.500 6.18 0.00 40.55 4.40
1997 2030 4.781883 GCCAAAGTTTTGACGAAAATGTGC 60.782 41.667 6.18 0.00 40.55 4.57
1998 2031 4.328440 TGCCAAAGTTTTGACGAAAATGTG 59.672 37.500 6.18 0.00 40.55 3.21
1999 2032 4.328712 GTGCCAAAGTTTTGACGAAAATGT 59.671 37.500 6.18 0.00 40.55 2.71
2000 2033 4.328440 TGTGCCAAAGTTTTGACGAAAATG 59.672 37.500 6.18 0.00 40.55 2.32
2001 2034 4.328712 GTGTGCCAAAGTTTTGACGAAAAT 59.671 37.500 6.18 0.00 40.55 1.82
2002 2035 3.675698 GTGTGCCAAAGTTTTGACGAAAA 59.324 39.130 6.18 0.00 40.55 2.29
2003 2036 3.246619 GTGTGCCAAAGTTTTGACGAAA 58.753 40.909 6.18 0.00 40.55 3.46
2004 2037 2.229062 TGTGTGCCAAAGTTTTGACGAA 59.771 40.909 6.18 0.00 40.55 3.85
2005 2038 1.813178 TGTGTGCCAAAGTTTTGACGA 59.187 42.857 6.18 0.00 40.55 4.20
2006 2039 2.184448 CTGTGTGCCAAAGTTTTGACG 58.816 47.619 6.18 0.00 40.55 4.35
2007 2040 2.165437 TCCTGTGTGCCAAAGTTTTGAC 59.835 45.455 6.18 0.00 40.55 3.18
2008 2041 2.451490 TCCTGTGTGCCAAAGTTTTGA 58.549 42.857 6.18 0.00 40.55 2.69
2009 2042 2.957491 TCCTGTGTGCCAAAGTTTTG 57.043 45.000 0.00 0.00 37.90 2.44
2010 2043 2.365293 GGATCCTGTGTGCCAAAGTTTT 59.635 45.455 3.84 0.00 0.00 2.43
2011 2044 1.963515 GGATCCTGTGTGCCAAAGTTT 59.036 47.619 3.84 0.00 0.00 2.66
2012 2045 1.620822 GGATCCTGTGTGCCAAAGTT 58.379 50.000 3.84 0.00 0.00 2.66
2013 2046 0.251341 GGGATCCTGTGTGCCAAAGT 60.251 55.000 12.58 0.00 0.00 2.66
2014 2047 0.038744 AGGGATCCTGTGTGCCAAAG 59.961 55.000 12.58 0.00 29.57 2.77
2015 2048 1.367346 TAGGGATCCTGTGTGCCAAA 58.633 50.000 12.58 0.00 34.61 3.28
2016 2049 1.490490 GATAGGGATCCTGTGTGCCAA 59.510 52.381 12.58 0.00 34.61 4.52
2017 2050 1.131638 GATAGGGATCCTGTGTGCCA 58.868 55.000 12.58 0.00 34.61 4.92
2027 2060 1.135257 CATCAGTCGCGGATAGGGATC 60.135 57.143 6.13 0.00 43.89 3.36
2028 2061 0.891373 CATCAGTCGCGGATAGGGAT 59.109 55.000 6.13 0.00 43.89 3.85
2029 2062 0.179001 TCATCAGTCGCGGATAGGGA 60.179 55.000 6.13 0.00 39.67 4.20
2030 2063 0.242286 CTCATCAGTCGCGGATAGGG 59.758 60.000 6.13 0.00 0.00 3.53
2031 2064 0.387878 GCTCATCAGTCGCGGATAGG 60.388 60.000 6.13 0.00 0.00 2.57
2032 2065 0.727457 CGCTCATCAGTCGCGGATAG 60.727 60.000 6.13 1.80 42.88 2.08
2033 2066 1.282875 CGCTCATCAGTCGCGGATA 59.717 57.895 6.13 0.00 42.88 2.59
2034 2067 2.026734 CGCTCATCAGTCGCGGAT 59.973 61.111 6.13 0.00 42.88 4.18
2035 2068 4.854784 GCGCTCATCAGTCGCGGA 62.855 66.667 6.13 0.00 46.31 5.54
2091 2124 5.389516 GGTTGTATATGAATGAATCGGACGC 60.390 44.000 0.00 0.00 0.00 5.19
2104 2137 6.681777 CATCAGATCTGACGGTTGTATATGA 58.318 40.000 27.37 0.60 43.11 2.15
2127 2160 1.174783 GAAGACGACTGTAGGAGGCA 58.825 55.000 0.00 0.00 0.00 4.75
2128 2161 1.465794 AGAAGACGACTGTAGGAGGC 58.534 55.000 0.00 0.00 0.00 4.70
2131 2164 2.488545 GAGCAAGAAGACGACTGTAGGA 59.511 50.000 0.00 0.00 0.00 2.94
2149 2183 2.047179 GGGAACGGTGTGAGGAGC 60.047 66.667 0.00 0.00 0.00 4.70
2161 2195 2.804828 CTTCTGGGAGCGTGGGGAAC 62.805 65.000 0.00 0.00 0.00 3.62
2177 2211 2.899339 GGGGCGATGCTCTGCTTC 60.899 66.667 0.00 0.00 0.00 3.86
2235 2269 2.825836 GGAGCTCATTGGCCACCG 60.826 66.667 17.19 0.00 0.00 4.94
2236 2270 1.751927 CTGGAGCTCATTGGCCACC 60.752 63.158 17.19 1.05 0.00 4.61
2237 2271 2.413142 GCTGGAGCTCATTGGCCAC 61.413 63.158 17.19 0.00 38.21 5.01
2241 2275 2.515523 CCCGCTGGAGCTCATTGG 60.516 66.667 17.19 11.01 39.32 3.16
2243 2277 3.011517 ACCCCGCTGGAGCTCATT 61.012 61.111 17.19 0.00 39.32 2.57
2244 2278 3.474570 GACCCCGCTGGAGCTCAT 61.475 66.667 17.19 0.00 39.32 2.90
2268 2302 0.451783 GATGTGATCCCGTTGGCAAC 59.548 55.000 20.27 20.27 0.00 4.17
2275 2309 0.391130 CAACCGTGATGTGATCCCGT 60.391 55.000 0.00 0.00 0.00 5.28
2277 2311 1.376609 GGCAACCGTGATGTGATCCC 61.377 60.000 0.00 0.00 0.00 3.85
2281 2315 0.884259 CACTGGCAACCGTGATGTGA 60.884 55.000 0.00 0.00 32.71 3.58
2282 2316 1.575922 CACTGGCAACCGTGATGTG 59.424 57.895 0.00 0.00 32.71 3.21
2292 2326 2.925706 TAGGGGACGCACTGGCAA 60.926 61.111 0.00 0.00 41.24 4.52
2293 2327 3.390521 CTAGGGGACGCACTGGCA 61.391 66.667 0.00 0.00 41.24 4.92
2294 2328 4.840005 GCTAGGGGACGCACTGGC 62.840 72.222 0.00 0.00 34.10 4.85
2301 2335 3.701604 GACTGCACGCTAGGGGACG 62.702 68.421 11.95 0.00 0.00 4.79
2308 2342 1.728074 CGTCGTTGACTGCACGCTA 60.728 57.895 0.00 0.00 0.00 4.26
2321 2355 1.895020 TTAGGGCTGCAATCCGTCGT 61.895 55.000 0.50 0.00 0.00 4.34
2322 2356 0.742990 TTTAGGGCTGCAATCCGTCG 60.743 55.000 0.50 0.00 0.00 5.12
2336 2370 2.314215 GGGGAGGGGGTGGTTTAGG 61.314 68.421 0.00 0.00 0.00 2.69
2392 2426 0.039074 CTACGTCGATCAGGGGATGC 60.039 60.000 0.00 0.00 32.67 3.91
2492 2526 0.109532 TTGCTTCAACCGACCATGGA 59.890 50.000 21.47 0.00 0.00 3.41
2502 2536 8.736244 TGGAACCTACTAATATTTTGCTTCAAC 58.264 33.333 0.00 0.00 0.00 3.18
2519 2553 3.068165 AGCTTTTGTTTGCTGGAACCTAC 59.932 43.478 0.00 0.00 38.21 3.18
2559 2593 3.219281 TGTTTTTGCTAGAACTGGACCC 58.781 45.455 0.00 0.00 0.00 4.46
2560 2594 4.911514 TTGTTTTTGCTAGAACTGGACC 57.088 40.909 0.00 0.00 0.00 4.46
2561 2595 6.978080 TGAATTTGTTTTTGCTAGAACTGGAC 59.022 34.615 0.00 0.00 0.00 4.02
2562 2596 7.106439 TGAATTTGTTTTTGCTAGAACTGGA 57.894 32.000 0.00 0.00 0.00 3.86
2563 2597 7.769272 TTGAATTTGTTTTTGCTAGAACTGG 57.231 32.000 0.00 0.00 0.00 4.00
2565 2599 9.196552 GCTATTGAATTTGTTTTTGCTAGAACT 57.803 29.630 0.00 0.00 0.00 3.01
2566 2600 8.977505 TGCTATTGAATTTGTTTTTGCTAGAAC 58.022 29.630 0.00 0.00 0.00 3.01
2567 2601 9.539825 TTGCTATTGAATTTGTTTTTGCTAGAA 57.460 25.926 0.00 0.00 0.00 2.10
2568 2602 9.539825 TTTGCTATTGAATTTGTTTTTGCTAGA 57.460 25.926 0.00 0.00 0.00 2.43
2603 2637 3.291809 TTCGCTACAAATGACGACTGA 57.708 42.857 0.00 0.00 33.69 3.41
2628 2662 2.682856 TGGCGTAATCTTTTGCTGGATC 59.317 45.455 0.00 0.00 0.00 3.36
2642 2684 2.362397 TGTTTTGCTGGAATTGGCGTAA 59.638 40.909 0.00 0.00 0.00 3.18
2649 2691 7.011669 CACTTCTGAATTTGTTTTGCTGGAATT 59.988 33.333 0.00 0.00 0.00 2.17
2650 2692 6.480981 CACTTCTGAATTTGTTTTGCTGGAAT 59.519 34.615 0.00 0.00 0.00 3.01
2656 2698 6.645700 TGTTCACTTCTGAATTTGTTTTGC 57.354 33.333 0.00 0.00 38.69 3.68
2670 2712 1.143073 ACCCCTGGAGTTGTTCACTTC 59.857 52.381 0.00 0.00 35.01 3.01
2671 2713 1.143073 GACCCCTGGAGTTGTTCACTT 59.857 52.381 0.00 0.00 35.01 3.16
2672 2714 0.765510 GACCCCTGGAGTTGTTCACT 59.234 55.000 0.00 0.00 39.07 3.41
2673 2715 0.602905 CGACCCCTGGAGTTGTTCAC 60.603 60.000 0.00 0.00 0.00 3.18
2674 2716 0.761323 TCGACCCCTGGAGTTGTTCA 60.761 55.000 0.00 0.00 0.00 3.18
2675 2717 0.613777 ATCGACCCCTGGAGTTGTTC 59.386 55.000 0.00 0.00 0.00 3.18
2676 2718 1.064825 AATCGACCCCTGGAGTTGTT 58.935 50.000 0.00 0.00 0.00 2.83
2677 2719 0.324943 CAATCGACCCCTGGAGTTGT 59.675 55.000 0.00 0.00 0.00 3.32
2678 2720 0.324943 ACAATCGACCCCTGGAGTTG 59.675 55.000 0.00 0.00 0.00 3.16
2679 2721 1.831736 CTACAATCGACCCCTGGAGTT 59.168 52.381 0.00 0.00 0.00 3.01
2680 2722 1.486211 CTACAATCGACCCCTGGAGT 58.514 55.000 0.00 0.00 0.00 3.85
2681 2723 0.105039 GCTACAATCGACCCCTGGAG 59.895 60.000 0.00 0.00 0.00 3.86
2682 2724 0.616395 TGCTACAATCGACCCCTGGA 60.616 55.000 0.00 0.00 0.00 3.86
2683 2725 0.251916 TTGCTACAATCGACCCCTGG 59.748 55.000 0.00 0.00 0.00 4.45
2684 2726 2.107950 TTTGCTACAATCGACCCCTG 57.892 50.000 0.00 0.00 0.00 4.45
2685 2727 2.871096 TTTTGCTACAATCGACCCCT 57.129 45.000 0.00 0.00 0.00 4.79
2697 2739 6.238925 GCTGGAACTACCTTTTCTTTTTGCTA 60.239 38.462 0.00 0.00 39.86 3.49
2735 2777 1.754226 GAGGTGTTTTTGCTGGAACCA 59.246 47.619 0.00 0.00 0.00 3.67
2741 2783 1.199624 GTTGCGAGGTGTTTTTGCTG 58.800 50.000 0.00 0.00 0.00 4.41
2775 2817 1.352114 CATGATTTTTGGCGGCACTG 58.648 50.000 12.92 0.00 0.00 3.66
2777 2819 1.360931 GGCATGATTTTTGGCGGCAC 61.361 55.000 12.92 0.00 0.00 5.01
2806 2848 6.998074 TGGAGATCTATTTGTTTTGTGACTGT 59.002 34.615 0.00 0.00 0.00 3.55
2808 2850 6.150140 GCTGGAGATCTATTTGTTTTGTGACT 59.850 38.462 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.