Multiple sequence alignment - TraesCS7A01G181100

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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 TraesCS7A01G181100 chr7A 100.000 2654 0 0 1 2654 135902807 135900154 0.000000e+00 4902.0
1 TraesCS7A01G181100 chr7A 82.609 253 38 4 75 322 542705927 542705676 4.450000e-53 219.0
2 TraesCS7A01G181100 chr7D 91.654 1941 94 16 2 1903 136254666 136252755 0.000000e+00 2625.0
3 TraesCS7A01G181100 chr7D 95.077 650 26 4 2006 2654 136252763 136252119 0.000000e+00 1018.0
4 TraesCS7A01G181100 chr7D 82.609 276 40 6 53 322 234793424 234793151 1.230000e-58 237.0
5 TraesCS7A01G181100 chr7D 78.388 273 52 4 54 322 608824799 608824530 1.260000e-38 171.0
6 TraesCS7A01G181100 chr7D 84.348 115 17 1 321 435 178144662 178144549 7.770000e-21 111.0
7 TraesCS7A01G181100 chr7B 92.446 1165 44 11 777 1903 99131347 99130189 0.000000e+00 1624.0
8 TraesCS7A01G181100 chr7B 92.542 657 32 9 2006 2654 99130197 99129550 0.000000e+00 926.0
9 TraesCS7A01G181100 chr7B 95.192 104 4 1 1910 2012 673218725 673218828 2.110000e-36 163.0
10 TraesCS7A01G181100 chr7B 94.175 103 5 1 1910 2012 648478317 648478418 3.540000e-34 156.0
11 TraesCS7A01G181100 chr7B 80.342 117 14 8 320 433 733485264 733485374 2.190000e-11 80.5
12 TraesCS7A01G181100 chr5B 84.800 250 36 2 1313 1561 430680028 430679780 1.580000e-62 250.0
13 TraesCS7A01G181100 chr5B 93.333 60 3 1 320 379 682540335 682540277 1.310000e-13 87.9
14 TraesCS7A01G181100 chr5A 82.000 300 44 7 29 322 409330641 409330936 2.040000e-61 246.0
15 TraesCS7A01G181100 chr5A 83.200 250 40 2 1313 1561 465996825 465996577 7.390000e-56 228.0
16 TraesCS7A01G181100 chr5A 88.608 79 5 4 320 397 349620592 349620517 2.810000e-15 93.5
17 TraesCS7A01G181100 chr5D 84.400 250 37 2 1313 1561 364670755 364670507 7.340000e-61 244.0
18 TraesCS7A01G181100 chr2A 85.043 234 31 2 92 322 598642930 598643162 4.420000e-58 235.0
19 TraesCS7A01G181100 chr4D 80.205 293 51 5 30 317 35593293 35593003 2.070000e-51 213.0
20 TraesCS7A01G181100 chrUn 81.633 245 41 2 80 320 92182510 92182266 1.610000e-47 200.0
21 TraesCS7A01G181100 chrUn 96.907 97 3 0 1910 2006 105364991 105365087 2.110000e-36 163.0
22 TraesCS7A01G181100 chr2D 81.452 248 36 7 79 320 48209602 48209359 7.500000e-46 195.0
23 TraesCS7A01G181100 chr2D 94.286 105 5 1 1910 2013 33317815 33317919 2.730000e-35 159.0
24 TraesCS7A01G181100 chr6D 96.907 97 3 0 1910 2006 83157648 83157744 2.110000e-36 163.0
25 TraesCS7A01G181100 chr6D 83.168 101 12 5 320 419 427745847 427745943 1.310000e-13 87.9
26 TraesCS7A01G181100 chr1A 95.960 99 4 0 1910 2008 548464343 548464441 7.600000e-36 161.0
27 TraesCS7A01G181100 chr6B 94.231 104 6 0 1902 2005 154370359 154370462 2.730000e-35 159.0
28 TraesCS7A01G181100 chr6B 92.661 109 5 3 1910 2018 38014847 38014742 1.270000e-33 154.0
29 TraesCS7A01G181100 chr3D 93.333 105 7 0 1902 2006 536239350 536239454 3.540000e-34 156.0
30 TraesCS7A01G181100 chr4A 82.707 133 21 1 320 450 87969087 87968955 1.670000e-22 117.0
31 TraesCS7A01G181100 chr4A 96.875 32 1 0 546 577 672740633 672740664 1.000000e-03 54.7
32 TraesCS7A01G181100 chr4A 96.875 32 1 0 546 577 672885953 672885984 1.000000e-03 54.7
33 TraesCS7A01G181100 chr4A 96.875 32 1 0 546 577 672929954 672929985 1.000000e-03 54.7
34 TraesCS7A01G181100 chr4A 96.875 32 1 0 546 577 672950958 672950989 1.000000e-03 54.7
35 TraesCS7A01G181100 chr1D 85.714 70 9 1 320 389 376771997 376771929 3.660000e-09 73.1
36 TraesCS7A01G181100 chr3A 89.474 57 5 1 320 376 719271177 719271122 1.320000e-08 71.3


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 TraesCS7A01G181100 chr7A 135900154 135902807 2653 True 4902.0 4902 100.0000 1 2654 1 chr7A.!!$R1 2653
1 TraesCS7A01G181100 chr7D 136252119 136254666 2547 True 1821.5 2625 93.3655 2 2654 2 chr7D.!!$R4 2652
2 TraesCS7A01G181100 chr7B 99129550 99131347 1797 True 1275.0 1624 92.4940 777 2654 2 chr7B.!!$R1 1877

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
48 49 0.03601 GACCAGTCCACAGACATGGG 60.036 60.0 0.0 6.77 46.15 4.00 F
413 417 0.24636 CCGCCAGGGTCAAAATTTCC 59.754 55.0 0.0 0.00 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1024 1055 0.251077 AGGAAGTGGAAGCTGGCAAG 60.251 55.0 0.0 0.0 0.0 4.01 R
2125 2185 0.385390 CACCCGCATTATGGAAAGCC 59.615 55.0 0.0 0.0 0.0 4.35 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
29 30 3.734902 GCAAATTTTCTACCGCATCCAGG 60.735 47.826 0.00 0.00 0.00 4.45
33 34 0.616395 TTCTACCGCATCCAGGACCA 60.616 55.000 0.00 0.00 0.00 4.02
48 49 0.036010 GACCAGTCCACAGACATGGG 60.036 60.000 0.00 6.77 46.15 4.00
52 53 1.623311 CAGTCCACAGACATGGGTGTA 59.377 52.381 11.75 0.00 46.15 2.90
60 61 0.460311 GACATGGGTGTAGGAGGACG 59.540 60.000 0.00 0.00 39.09 4.79
75 76 4.329545 ACGCCATCCAACCGCAGT 62.330 61.111 0.00 0.00 0.00 4.40
106 107 6.579666 ACATTTCGAACCGCATTTTAACTAAC 59.420 34.615 0.00 0.00 0.00 2.34
107 108 4.666928 TCGAACCGCATTTTAACTAACC 57.333 40.909 0.00 0.00 0.00 2.85
121 122 9.804758 ATTTTAACTAACCGAACAAAATTCACA 57.195 25.926 0.00 0.00 0.00 3.58
172 173 9.504708 TTTGGATAAAATGAAGCACAAATCATT 57.495 25.926 0.00 0.00 45.61 2.57
173 174 8.706492 TGGATAAAATGAAGCACAAATCATTC 57.294 30.769 1.88 0.00 43.54 2.67
185 186 7.368059 AGCACAAATCATTCATATGTAGCATG 58.632 34.615 1.90 2.25 33.34 4.06
268 272 1.518515 CATCAACGGATCATGTCGTCG 59.481 52.381 10.64 5.74 38.78 5.12
288 292 2.481568 CGCATACATACTGCCCATTCAG 59.518 50.000 0.00 0.00 39.86 3.02
295 299 4.641989 ACATACTGCCCATTCAGTTTCATC 59.358 41.667 1.55 0.00 44.26 2.92
325 329 0.248990 TGTACGTAAATAGCCGGGCG 60.249 55.000 14.39 0.00 0.00 6.13
326 330 0.249031 GTACGTAAATAGCCGGGCGT 60.249 55.000 14.39 6.03 36.52 5.68
348 352 2.292192 CCCCATATCCGCCCCATATTTT 60.292 50.000 0.00 0.00 0.00 1.82
349 353 2.760092 CCCATATCCGCCCCATATTTTG 59.240 50.000 0.00 0.00 0.00 2.44
350 354 2.760092 CCATATCCGCCCCATATTTTGG 59.240 50.000 0.00 0.00 46.00 3.28
383 387 2.819117 GATGTCTGTCAGTCCGCGCA 62.819 60.000 8.75 0.00 0.00 6.09
389 393 0.882484 TGTCAGTCCGCGCATTTGAA 60.882 50.000 8.75 0.00 0.00 2.69
413 417 0.246360 CCGCCAGGGTCAAAATTTCC 59.754 55.000 0.00 0.00 0.00 3.13
451 468 1.894756 CGTTTGAGGCGGGTTTGGA 60.895 57.895 0.00 0.00 0.00 3.53
452 469 1.658114 GTTTGAGGCGGGTTTGGAC 59.342 57.895 0.00 0.00 0.00 4.02
499 516 8.579850 AACTCTAGCTCCATATAAGATCTCAG 57.420 38.462 0.00 0.00 0.00 3.35
520 537 8.325787 TCTCAGCATAGTTTTACCTTAATCCAA 58.674 33.333 0.00 0.00 0.00 3.53
602 620 3.363341 TCCGGTTTCAATGAAGTTTGC 57.637 42.857 0.00 0.00 0.00 3.68
606 624 2.035321 GGTTTCAATGAAGTTTGCCCGA 59.965 45.455 0.00 0.00 0.00 5.14
607 625 3.049912 GTTTCAATGAAGTTTGCCCGAC 58.950 45.455 0.00 0.00 0.00 4.79
639 657 2.945447 TTGAATTGTATGCTGGCAGC 57.055 45.000 31.91 31.91 42.82 5.25
664 682 3.936203 GCCCGTATCCCGCATCCA 61.936 66.667 0.00 0.00 34.38 3.41
665 683 2.030562 CCCGTATCCCGCATCCAC 59.969 66.667 0.00 0.00 34.38 4.02
666 684 2.030562 CCGTATCCCGCATCCACC 59.969 66.667 0.00 0.00 34.38 4.61
667 685 2.030562 CGTATCCCGCATCCACCC 59.969 66.667 0.00 0.00 0.00 4.61
668 686 2.802724 CGTATCCCGCATCCACCCA 61.803 63.158 0.00 0.00 0.00 4.51
669 687 1.761174 GTATCCCGCATCCACCCAT 59.239 57.895 0.00 0.00 0.00 4.00
670 688 0.981183 GTATCCCGCATCCACCCATA 59.019 55.000 0.00 0.00 0.00 2.74
671 689 1.559682 GTATCCCGCATCCACCCATAT 59.440 52.381 0.00 0.00 0.00 1.78
672 690 0.620556 ATCCCGCATCCACCCATATC 59.379 55.000 0.00 0.00 0.00 1.63
673 691 1.002134 CCCGCATCCACCCATATCC 60.002 63.158 0.00 0.00 0.00 2.59
674 692 1.002134 CCGCATCCACCCATATCCC 60.002 63.158 0.00 0.00 0.00 3.85
675 693 1.375908 CGCATCCACCCATATCCCG 60.376 63.158 0.00 0.00 0.00 5.14
676 694 1.675641 GCATCCACCCATATCCCGC 60.676 63.158 0.00 0.00 0.00 6.13
677 695 1.760527 CATCCACCCATATCCCGCA 59.239 57.895 0.00 0.00 0.00 5.69
678 696 0.329261 CATCCACCCATATCCCGCAT 59.671 55.000 0.00 0.00 0.00 4.73
679 697 0.620556 ATCCACCCATATCCCGCATC 59.379 55.000 0.00 0.00 0.00 3.91
680 698 0.473694 TCCACCCATATCCCGCATCT 60.474 55.000 0.00 0.00 0.00 2.90
694 712 0.457853 GCATCTGTGTCCGCGAACTA 60.458 55.000 8.23 0.00 0.00 2.24
723 741 4.444838 CGTGGACGGATGCGGGAA 62.445 66.667 12.44 0.00 35.37 3.97
757 775 5.413833 AGGTCAATGTTGAAGATGCACTAAG 59.586 40.000 0.00 0.00 39.21 2.18
931 962 0.531532 CCTCGTCTGCCATAGCCAAG 60.532 60.000 0.00 0.00 38.69 3.61
989 1020 5.573337 GCCATAAGCAAAGAAGAGACAAT 57.427 39.130 0.00 0.00 42.97 2.71
1024 1055 0.381801 CCACCATAACAATGGCGAGC 59.618 55.000 4.31 0.00 45.47 5.03
1077 1108 1.650528 CTTCCTCCTCCTTCACCACT 58.349 55.000 0.00 0.00 0.00 4.00
1131 1162 1.272554 CCTACTTCCCGCCCTCCTTT 61.273 60.000 0.00 0.00 0.00 3.11
1157 1188 3.862402 CGCTCTACTCGCCGACGT 61.862 66.667 0.00 0.00 41.18 4.34
1185 1216 4.959446 GCAGCAGCCTTTGAGTTG 57.041 55.556 0.00 0.00 33.58 3.16
1359 1390 2.708865 GGTCTCGAACCGGGAGTCC 61.709 68.421 6.32 6.57 36.89 3.85
1471 1502 2.669569 AGCTCAACCGCGCATTGT 60.670 55.556 18.02 4.98 34.40 2.71
1484 1515 3.049674 ATTGTGCGAGTGTGCCGG 61.050 61.111 0.00 0.00 0.00 6.13
1600 1652 0.390866 CTCGAGCAATCACAGTGGCT 60.391 55.000 0.00 1.19 39.75 4.75
1746 1805 9.482627 AGATTATAAGAGCATGTGTTACTAAGC 57.517 33.333 0.00 0.00 0.00 3.09
1886 1946 9.793259 GTTGATAAATTAACATGGATAGGAGGA 57.207 33.333 0.00 0.00 0.00 3.71
1892 1952 8.511748 AATTAACATGGATAGGAGGATGTAGT 57.488 34.615 0.00 0.00 0.00 2.73
1893 1953 5.815233 AACATGGATAGGAGGATGTAGTG 57.185 43.478 0.00 0.00 0.00 2.74
1894 1954 3.580458 ACATGGATAGGAGGATGTAGTGC 59.420 47.826 0.00 0.00 0.00 4.40
1895 1955 3.619900 TGGATAGGAGGATGTAGTGCT 57.380 47.619 0.00 0.00 0.00 4.40
1896 1956 4.741928 TGGATAGGAGGATGTAGTGCTA 57.258 45.455 0.00 0.00 0.00 3.49
1897 1957 5.276694 TGGATAGGAGGATGTAGTGCTAT 57.723 43.478 0.00 0.00 30.65 2.97
1898 1958 6.402981 TGGATAGGAGGATGTAGTGCTATA 57.597 41.667 0.00 0.00 28.36 1.31
1899 1959 6.986391 TGGATAGGAGGATGTAGTGCTATAT 58.014 40.000 0.00 0.00 28.36 0.86
1900 1960 8.114301 TGGATAGGAGGATGTAGTGCTATATA 57.886 38.462 0.00 0.00 28.36 0.86
1901 1961 8.737633 TGGATAGGAGGATGTAGTGCTATATAT 58.262 37.037 0.00 0.00 28.36 0.86
1902 1962 9.594936 GGATAGGAGGATGTAGTGCTATATATT 57.405 37.037 0.00 0.00 28.36 1.28
1904 1964 7.575414 AGGAGGATGTAGTGCTATATATTCG 57.425 40.000 0.00 0.00 0.00 3.34
1905 1965 7.347252 AGGAGGATGTAGTGCTATATATTCGA 58.653 38.462 0.00 0.00 0.00 3.71
1906 1966 7.500892 AGGAGGATGTAGTGCTATATATTCGAG 59.499 40.741 0.00 0.00 0.00 4.04
1907 1967 7.499563 GGAGGATGTAGTGCTATATATTCGAGA 59.500 40.741 0.00 0.00 0.00 4.04
1908 1968 8.988546 AGGATGTAGTGCTATATATTCGAGAT 57.011 34.615 0.00 0.00 0.00 2.75
1916 1976 5.691815 GCTATATATTCGAGATAGCCGACC 58.308 45.833 14.81 0.00 45.75 4.79
1917 1977 5.238868 GCTATATATTCGAGATAGCCGACCA 59.761 44.000 14.81 0.00 45.75 4.02
1918 1978 3.851976 ATATTCGAGATAGCCGACCAC 57.148 47.619 0.00 0.00 35.61 4.16
1919 1979 0.674534 ATTCGAGATAGCCGACCACC 59.325 55.000 0.00 0.00 35.61 4.61
1920 1980 1.389609 TTCGAGATAGCCGACCACCC 61.390 60.000 0.00 0.00 35.61 4.61
1921 1981 2.125326 CGAGATAGCCGACCACCCA 61.125 63.158 0.00 0.00 0.00 4.51
1922 1982 1.464376 CGAGATAGCCGACCACCCAT 61.464 60.000 0.00 0.00 0.00 4.00
1923 1983 0.759346 GAGATAGCCGACCACCCATT 59.241 55.000 0.00 0.00 0.00 3.16
1924 1984 1.141053 GAGATAGCCGACCACCCATTT 59.859 52.381 0.00 0.00 0.00 2.32
1925 1985 2.367567 GAGATAGCCGACCACCCATTTA 59.632 50.000 0.00 0.00 0.00 1.40
1926 1986 2.368875 AGATAGCCGACCACCCATTTAG 59.631 50.000 0.00 0.00 0.00 1.85
1927 1987 1.575419 TAGCCGACCACCCATTTAGT 58.425 50.000 0.00 0.00 0.00 2.24
1928 1988 1.575419 AGCCGACCACCCATTTAGTA 58.425 50.000 0.00 0.00 0.00 1.82
1929 1989 1.485066 AGCCGACCACCCATTTAGTAG 59.515 52.381 0.00 0.00 0.00 2.57
1930 1990 1.208776 GCCGACCACCCATTTAGTAGT 59.791 52.381 0.00 0.00 0.00 2.73
1931 1991 2.355412 GCCGACCACCCATTTAGTAGTT 60.355 50.000 0.00 0.00 0.00 2.24
1932 1992 3.118665 GCCGACCACCCATTTAGTAGTTA 60.119 47.826 0.00 0.00 0.00 2.24
1933 1993 4.443881 GCCGACCACCCATTTAGTAGTTAT 60.444 45.833 0.00 0.00 0.00 1.89
1934 1994 5.295152 CCGACCACCCATTTAGTAGTTATC 58.705 45.833 0.00 0.00 0.00 1.75
1935 1995 5.070047 CCGACCACCCATTTAGTAGTTATCT 59.930 44.000 0.00 0.00 0.00 1.98
1936 1996 5.983720 CGACCACCCATTTAGTAGTTATCTG 59.016 44.000 0.00 0.00 0.00 2.90
1937 1997 6.183360 CGACCACCCATTTAGTAGTTATCTGA 60.183 42.308 0.00 0.00 0.00 3.27
1938 1998 7.125792 ACCACCCATTTAGTAGTTATCTGAG 57.874 40.000 0.00 0.00 0.00 3.35
1939 1999 6.901300 ACCACCCATTTAGTAGTTATCTGAGA 59.099 38.462 0.00 0.00 0.00 3.27
1940 2000 7.402071 ACCACCCATTTAGTAGTTATCTGAGAA 59.598 37.037 0.00 0.00 0.00 2.87
1941 2001 8.265055 CCACCCATTTAGTAGTTATCTGAGAAA 58.735 37.037 0.00 0.00 0.00 2.52
1942 2002 9.667107 CACCCATTTAGTAGTTATCTGAGAAAA 57.333 33.333 0.00 0.00 0.00 2.29
1980 2040 4.456662 TTTTTGGAACCCTAGGCTGTAA 57.543 40.909 2.05 0.00 0.00 2.41
1981 2041 4.456662 TTTTGGAACCCTAGGCTGTAAA 57.543 40.909 2.05 0.00 0.00 2.01
1982 2042 3.713826 TTGGAACCCTAGGCTGTAAAG 57.286 47.619 2.05 0.00 0.00 1.85
1983 2043 2.627933 TGGAACCCTAGGCTGTAAAGT 58.372 47.619 2.05 0.00 0.00 2.66
1984 2044 3.793712 TGGAACCCTAGGCTGTAAAGTA 58.206 45.455 2.05 0.00 0.00 2.24
1985 2045 3.773119 TGGAACCCTAGGCTGTAAAGTAG 59.227 47.826 2.05 0.00 0.00 2.57
1986 2046 3.773667 GGAACCCTAGGCTGTAAAGTAGT 59.226 47.826 2.05 0.00 0.00 2.73
1987 2047 4.958581 GGAACCCTAGGCTGTAAAGTAGTA 59.041 45.833 2.05 0.00 0.00 1.82
1988 2048 5.068855 GGAACCCTAGGCTGTAAAGTAGTAG 59.931 48.000 2.05 0.00 0.00 2.57
1989 2049 5.204131 ACCCTAGGCTGTAAAGTAGTAGT 57.796 43.478 2.05 0.00 0.00 2.73
1990 2050 5.587861 ACCCTAGGCTGTAAAGTAGTAGTT 58.412 41.667 2.05 0.00 0.00 2.24
1991 2051 6.021672 ACCCTAGGCTGTAAAGTAGTAGTTT 58.978 40.000 2.05 8.04 0.00 2.66
1992 2052 6.499699 ACCCTAGGCTGTAAAGTAGTAGTTTT 59.500 38.462 2.05 0.00 0.00 2.43
1993 2053 7.675619 ACCCTAGGCTGTAAAGTAGTAGTTTTA 59.324 37.037 2.05 0.00 0.00 1.52
1994 2054 8.702819 CCCTAGGCTGTAAAGTAGTAGTTTTAT 58.297 37.037 2.05 0.00 0.00 1.40
1995 2055 9.530633 CCTAGGCTGTAAAGTAGTAGTTTTATG 57.469 37.037 8.25 1.37 0.00 1.90
1996 2056 7.845066 AGGCTGTAAAGTAGTAGTTTTATGC 57.155 36.000 8.25 9.52 0.00 3.14
1997 2057 7.621796 AGGCTGTAAAGTAGTAGTTTTATGCT 58.378 34.615 8.25 0.38 0.00 3.79
1998 2058 8.755977 AGGCTGTAAAGTAGTAGTTTTATGCTA 58.244 33.333 8.25 0.00 0.00 3.49
1999 2059 9.543783 GGCTGTAAAGTAGTAGTTTTATGCTAT 57.456 33.333 8.25 0.00 0.00 2.97
2101 2161 5.816777 GTGAGAGATCAAGGAAGGATCAAAG 59.183 44.000 0.00 0.00 42.84 2.77
2125 2185 1.597663 GGTGAGGACGACAAGTGTTTG 59.402 52.381 0.00 0.00 40.24 2.93
2145 2205 0.385390 GCTTTCCATAATGCGGGTGG 59.615 55.000 0.00 0.00 0.00 4.61
2186 2247 4.600692 AGTGCATTCCACCCTTTTTAAC 57.399 40.909 0.00 0.00 45.83 2.01
2342 2403 1.014044 TCTTTGGCAGCTAAGTCGCG 61.014 55.000 0.00 0.00 34.40 5.87
2399 2462 7.646526 CGAACAAGGTTCGACATATGTATCTAA 59.353 37.037 22.84 0.00 43.97 2.10
2609 2678 7.591407 CATAAGCGTGAATGTTTTGTTAATCG 58.409 34.615 0.00 0.00 0.00 3.34
2613 2682 6.141685 AGCGTGAATGTTTTGTTAATCGAAAC 59.858 34.615 0.00 11.15 45.63 2.78
2623 2692 6.788684 TTGTTAATCGAAACGGAGAATGAA 57.211 33.333 0.00 0.00 31.76 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.461081 TGCGGTAGAAAATTTGCAGGTTAT 59.539 37.500 0.00 0.00 0.00 1.89
8 9 3.694072 TCCTGGATGCGGTAGAAAATTTG 59.306 43.478 0.00 0.00 0.00 2.32
29 30 0.036010 CCCATGTCTGTGGACTGGTC 60.036 60.000 0.00 0.00 42.02 4.02
33 34 1.902508 CTACACCCATGTCTGTGGACT 59.097 52.381 10.75 0.00 42.02 3.85
40 41 1.867363 GTCCTCCTACACCCATGTCT 58.133 55.000 0.00 0.00 40.48 3.41
43 44 1.144057 GCGTCCTCCTACACCCATG 59.856 63.158 0.00 0.00 0.00 3.66
48 49 1.442148 GGATGGCGTCCTCCTACAC 59.558 63.158 18.69 0.00 44.16 2.90
60 61 3.499737 CGACTGCGGTTGGATGGC 61.500 66.667 4.84 0.00 0.00 4.40
75 76 0.648441 GCGGTTCGAAATGTATGCGA 59.352 50.000 0.00 0.00 0.00 5.10
106 107 3.241784 CGGTTTGTGTGAATTTTGTTCGG 59.758 43.478 0.00 0.00 0.00 4.30
107 108 3.241784 CCGGTTTGTGTGAATTTTGTTCG 59.758 43.478 0.00 0.00 0.00 3.95
121 122 2.218603 GATGAATATCGGCCGGTTTGT 58.781 47.619 27.83 6.59 0.00 2.83
142 143 7.945033 TTGTGCTTCATTTTATCCAAACTTC 57.055 32.000 0.00 0.00 0.00 3.01
157 158 7.067251 TGCTACATATGAATGATTTGTGCTTCA 59.933 33.333 10.38 0.00 36.54 3.02
172 173 9.428097 CTAGACTTATTTGCATGCTACATATGA 57.572 33.333 20.33 0.00 0.00 2.15
173 174 9.212641 ACTAGACTTATTTGCATGCTACATATG 57.787 33.333 20.33 14.92 0.00 1.78
229 230 7.425606 GTTGATGAAAAACTTGTACATCTGGT 58.574 34.615 0.00 0.00 38.36 4.00
268 272 3.480470 ACTGAATGGGCAGTATGTATGC 58.520 45.455 0.00 0.00 46.67 3.14
288 292 4.961551 CGTACACACACTGTTTGATGAAAC 59.038 41.667 0.27 0.27 41.72 2.78
295 299 6.068931 GCTATTTACGTACACACACTGTTTG 58.931 40.000 0.00 0.00 33.91 2.93
325 329 0.912487 TATGGGGCGGATATGGGGAC 60.912 60.000 0.00 0.00 0.00 4.46
326 330 0.045623 ATATGGGGCGGATATGGGGA 59.954 55.000 0.00 0.00 0.00 4.81
348 352 1.365293 CATCCCTCATATCCAGCCCA 58.635 55.000 0.00 0.00 0.00 5.36
349 353 1.280421 GACATCCCTCATATCCAGCCC 59.720 57.143 0.00 0.00 0.00 5.19
350 354 2.027377 CAGACATCCCTCATATCCAGCC 60.027 54.545 0.00 0.00 0.00 4.85
383 387 3.443045 CTGGCGGGCGCTTCAAAT 61.443 61.111 7.64 0.00 41.60 2.32
397 401 3.942130 GTCAGGAAATTTTGACCCTGG 57.058 47.619 18.62 5.69 44.66 4.45
413 417 2.047844 CGGTCACTGGCAGGTCAG 60.048 66.667 20.34 5.84 40.40 3.51
443 460 3.961414 TCCGGGCAGTCCAAACCC 61.961 66.667 0.00 0.00 40.51 4.11
451 468 0.033405 TAGCTTAGAGTCCGGGCAGT 60.033 55.000 9.71 0.00 0.00 4.40
452 469 0.386113 GTAGCTTAGAGTCCGGGCAG 59.614 60.000 9.71 0.00 0.00 4.85
458 475 3.281158 AGAGTTCGGTAGCTTAGAGTCC 58.719 50.000 0.00 0.00 0.00 3.85
459 476 4.024641 GCTAGAGTTCGGTAGCTTAGAGTC 60.025 50.000 0.00 0.00 38.92 3.36
563 581 8.792830 AACCGGATGATATTCATATAAACCAG 57.207 34.615 9.46 0.00 37.20 4.00
602 620 7.651704 ACAATTCAAAATTTTAGACAAGTCGGG 59.348 33.333 2.44 0.00 34.09 5.14
639 657 1.597027 GGGATACGGGCATCCAACG 60.597 63.158 13.09 0.00 45.52 4.10
664 682 0.397941 CACAGATGCGGGATATGGGT 59.602 55.000 8.94 0.00 0.00 4.51
665 683 0.397941 ACACAGATGCGGGATATGGG 59.602 55.000 4.75 4.75 32.48 4.00
666 684 1.609061 GGACACAGATGCGGGATATGG 60.609 57.143 8.94 0.91 0.00 2.74
667 685 1.800805 GGACACAGATGCGGGATATG 58.199 55.000 2.40 2.40 0.00 1.78
668 686 0.318441 CGGACACAGATGCGGGATAT 59.682 55.000 0.00 0.00 0.00 1.63
669 687 1.739667 CGGACACAGATGCGGGATA 59.260 57.895 0.00 0.00 0.00 2.59
670 688 2.501128 CGGACACAGATGCGGGAT 59.499 61.111 0.00 0.00 0.00 3.85
671 689 4.451150 GCGGACACAGATGCGGGA 62.451 66.667 0.00 0.00 0.00 5.14
675 693 0.457853 TAGTTCGCGGACACAGATGC 60.458 55.000 21.79 0.00 0.00 3.91
676 694 1.990799 TTAGTTCGCGGACACAGATG 58.009 50.000 21.79 0.00 0.00 2.90
677 695 2.961526 ATTAGTTCGCGGACACAGAT 57.038 45.000 21.79 4.74 0.00 2.90
678 696 3.192001 AGTTATTAGTTCGCGGACACAGA 59.808 43.478 21.79 0.00 0.00 3.41
679 697 3.508762 AGTTATTAGTTCGCGGACACAG 58.491 45.455 21.79 0.00 0.00 3.66
680 698 3.192001 AGAGTTATTAGTTCGCGGACACA 59.808 43.478 21.79 5.62 0.00 3.72
723 741 5.534207 TCAACATTGACCTGCAAATTCTT 57.466 34.783 0.00 0.00 40.48 2.52
734 752 5.627499 TTAGTGCATCTTCAACATTGACC 57.373 39.130 0.00 0.00 36.83 4.02
739 757 4.380233 GCAAGCTTAGTGCATCTTCAACAT 60.380 41.667 0.00 0.00 45.94 2.71
740 758 3.058016 GCAAGCTTAGTGCATCTTCAACA 60.058 43.478 0.00 0.00 45.94 3.33
757 775 4.261614 GGTAGCTTACAAATATGGGCAAGC 60.262 45.833 0.00 4.44 38.87 4.01
826 844 7.969690 TGGTTTCTCTTCTCTCTCTCATATT 57.030 36.000 0.00 0.00 0.00 1.28
828 846 7.617329 TCAATGGTTTCTCTTCTCTCTCTCATA 59.383 37.037 0.00 0.00 0.00 2.15
931 962 8.675504 TGTAGTAGCACTAGTAGATCTTGTTTC 58.324 37.037 0.00 0.00 30.12 2.78
989 1020 2.980379 TGGTGGTACATGGTCCTGTTTA 59.020 45.455 0.00 0.00 44.52 2.01
1024 1055 0.251077 AGGAAGTGGAAGCTGGCAAG 60.251 55.000 0.00 0.00 0.00 4.01
1077 1108 1.908344 CCATGTTCATGTGGTGGTGA 58.092 50.000 11.13 0.00 0.00 4.02
1131 1162 1.448119 CGAGTAGAGCGGCAGGATCA 61.448 60.000 1.45 0.00 32.03 2.92
1157 1188 4.700365 CTGCTGCCACGTCGTCGA 62.700 66.667 9.47 0.00 40.62 4.20
1200 1231 1.375268 GTGAGCCGCTTCTTCTGCT 60.375 57.895 0.00 0.00 36.62 4.24
1201 1232 2.394563 GGTGAGCCGCTTCTTCTGC 61.395 63.158 0.00 0.00 0.00 4.26
1202 1233 0.739112 GAGGTGAGCCGCTTCTTCTG 60.739 60.000 0.00 0.00 40.50 3.02
1203 1234 1.594310 GAGGTGAGCCGCTTCTTCT 59.406 57.895 0.00 0.00 40.50 2.85
1552 1583 2.173669 CCGGTGCCGATTGCTGTAG 61.174 63.158 12.71 0.00 42.83 2.74
1554 1585 3.958147 CTCCGGTGCCGATTGCTGT 62.958 63.158 12.71 0.00 42.83 4.40
1720 1779 9.482627 GCTTAGTAACACATGCTCTTATAATCT 57.517 33.333 0.00 0.00 0.00 2.40
1774 1834 2.441532 GCATGCATGACCCCAGCT 60.442 61.111 30.64 0.00 0.00 4.24
1805 1865 6.192970 ACATATTCCTGATAGGGAAACTGG 57.807 41.667 0.00 0.00 46.73 4.00
1886 1946 8.788806 GGCTATCTCGAATATATAGCACTACAT 58.211 37.037 20.92 0.00 46.42 2.29
1887 1947 7.041984 CGGCTATCTCGAATATATAGCACTACA 60.042 40.741 20.92 0.00 46.42 2.74
1890 1950 6.017770 GTCGGCTATCTCGAATATATAGCACT 60.018 42.308 20.92 0.00 46.42 4.40
1891 1951 6.137415 GTCGGCTATCTCGAATATATAGCAC 58.863 44.000 20.92 12.86 46.42 4.40
1892 1952 5.238868 GGTCGGCTATCTCGAATATATAGCA 59.761 44.000 20.92 7.41 46.42 3.49
1893 1953 5.238868 TGGTCGGCTATCTCGAATATATAGC 59.761 44.000 15.27 15.27 44.74 2.97
1894 1954 6.293516 GGTGGTCGGCTATCTCGAATATATAG 60.294 46.154 0.00 0.00 38.42 1.31
1895 1955 5.530171 GGTGGTCGGCTATCTCGAATATATA 59.470 44.000 0.00 0.00 38.42 0.86
1896 1956 4.338682 GGTGGTCGGCTATCTCGAATATAT 59.661 45.833 0.00 0.00 38.42 0.86
1897 1957 3.693085 GGTGGTCGGCTATCTCGAATATA 59.307 47.826 0.00 0.00 38.42 0.86
1898 1958 2.492484 GGTGGTCGGCTATCTCGAATAT 59.508 50.000 0.00 0.00 38.42 1.28
1899 1959 1.884579 GGTGGTCGGCTATCTCGAATA 59.115 52.381 0.00 0.00 38.42 1.75
1900 1960 0.674534 GGTGGTCGGCTATCTCGAAT 59.325 55.000 0.00 0.00 38.42 3.34
1901 1961 1.389609 GGGTGGTCGGCTATCTCGAA 61.390 60.000 0.00 0.00 38.42 3.71
1902 1962 1.826921 GGGTGGTCGGCTATCTCGA 60.827 63.158 0.00 0.00 0.00 4.04
1903 1963 1.464376 ATGGGTGGTCGGCTATCTCG 61.464 60.000 0.00 0.00 0.00 4.04
1904 1964 0.759346 AATGGGTGGTCGGCTATCTC 59.241 55.000 0.00 0.00 0.00 2.75
1905 1965 1.213296 AAATGGGTGGTCGGCTATCT 58.787 50.000 0.00 0.00 0.00 1.98
1906 1966 2.104281 ACTAAATGGGTGGTCGGCTATC 59.896 50.000 0.00 0.00 0.00 2.08
1907 1967 2.124411 ACTAAATGGGTGGTCGGCTAT 58.876 47.619 0.00 0.00 0.00 2.97
1908 1968 1.575419 ACTAAATGGGTGGTCGGCTA 58.425 50.000 0.00 0.00 0.00 3.93
1909 1969 1.485066 CTACTAAATGGGTGGTCGGCT 59.515 52.381 0.00 0.00 0.00 5.52
1910 1970 1.208776 ACTACTAAATGGGTGGTCGGC 59.791 52.381 0.00 0.00 0.00 5.54
1911 1971 3.622166 AACTACTAAATGGGTGGTCGG 57.378 47.619 0.00 0.00 0.00 4.79
1912 1972 5.983720 CAGATAACTACTAAATGGGTGGTCG 59.016 44.000 0.00 0.00 0.00 4.79
1913 1973 7.069578 TCTCAGATAACTACTAAATGGGTGGTC 59.930 40.741 0.00 0.00 0.00 4.02
1914 1974 6.901300 TCTCAGATAACTACTAAATGGGTGGT 59.099 38.462 0.00 0.00 0.00 4.16
1915 1975 7.361457 TCTCAGATAACTACTAAATGGGTGG 57.639 40.000 0.00 0.00 0.00 4.61
1916 1976 9.667107 TTTTCTCAGATAACTACTAAATGGGTG 57.333 33.333 0.00 0.00 0.00 4.61
1959 2019 4.456662 TTACAGCCTAGGGTTCCAAAAA 57.543 40.909 11.77 0.00 0.00 1.94
1960 2020 4.141111 ACTTTACAGCCTAGGGTTCCAAAA 60.141 41.667 11.77 8.41 0.00 2.44
1961 2021 3.396611 ACTTTACAGCCTAGGGTTCCAAA 59.603 43.478 11.77 10.46 0.00 3.28
1962 2022 2.983898 ACTTTACAGCCTAGGGTTCCAA 59.016 45.455 11.77 2.58 0.00 3.53
1963 2023 2.627933 ACTTTACAGCCTAGGGTTCCA 58.372 47.619 11.77 0.00 0.00 3.53
1964 2024 3.773667 ACTACTTTACAGCCTAGGGTTCC 59.226 47.826 11.77 0.00 0.00 3.62
1965 2025 5.655974 ACTACTACTTTACAGCCTAGGGTTC 59.344 44.000 11.77 0.00 0.00 3.62
1966 2026 5.587861 ACTACTACTTTACAGCCTAGGGTT 58.412 41.667 11.77 5.84 0.00 4.11
1967 2027 5.204131 ACTACTACTTTACAGCCTAGGGT 57.796 43.478 7.93 7.93 0.00 4.34
1968 2028 6.541934 AAACTACTACTTTACAGCCTAGGG 57.458 41.667 11.72 0.00 0.00 3.53
1969 2029 9.530633 CATAAAACTACTACTTTACAGCCTAGG 57.469 37.037 3.67 3.67 0.00 3.02
1970 2030 9.032420 GCATAAAACTACTACTTTACAGCCTAG 57.968 37.037 0.00 0.00 0.00 3.02
1971 2031 8.755977 AGCATAAAACTACTACTTTACAGCCTA 58.244 33.333 0.00 0.00 0.00 3.93
1972 2032 7.621796 AGCATAAAACTACTACTTTACAGCCT 58.378 34.615 0.00 0.00 0.00 4.58
1973 2033 7.845066 AGCATAAAACTACTACTTTACAGCC 57.155 36.000 0.00 0.00 0.00 4.85
2101 2161 1.080705 CTTGTCGTCCTCACCGGTC 60.081 63.158 2.59 0.00 0.00 4.79
2111 2171 2.540973 GGAAAGCCAAACACTTGTCGTC 60.541 50.000 0.00 0.00 0.00 4.20
2125 2185 0.385390 CACCCGCATTATGGAAAGCC 59.615 55.000 0.00 0.00 0.00 4.35
2342 2403 3.772932 TGCAAAAACTATAGCATGCTGC 58.227 40.909 30.42 21.21 45.46 5.25
2399 2462 6.876155 TGCTACAATCATATGCCAAAATTGT 58.124 32.000 18.36 18.36 41.83 2.71
2524 2588 3.573598 TGCATGCGTAGATTTGTTTTGG 58.426 40.909 14.09 0.00 0.00 3.28
2558 2623 7.094975 GCACGTGGCAATGGAATTTATATACTA 60.095 37.037 18.88 0.00 43.97 1.82
2559 2624 6.293955 GCACGTGGCAATGGAATTTATATACT 60.294 38.462 18.88 0.00 43.97 2.12
2560 2625 5.856455 GCACGTGGCAATGGAATTTATATAC 59.144 40.000 18.88 0.00 43.97 1.47
2580 2645 2.525750 AACATTCACGCTTATGCACG 57.474 45.000 0.00 0.00 39.64 5.34
2588 2653 5.351233 TCGATTAACAAAACATTCACGCT 57.649 34.783 0.00 0.00 0.00 5.07
2589 2654 6.278861 GTTTCGATTAACAAAACATTCACGC 58.721 36.000 0.00 0.00 33.97 5.34
2609 2678 4.315803 TCCTGAAGTTCATTCTCCGTTTC 58.684 43.478 5.91 0.00 38.83 2.78
2613 2682 3.601443 ACTCCTGAAGTTCATTCTCCG 57.399 47.619 5.91 0.00 38.83 4.63
2617 2686 7.606456 TGTAATACCAACTCCTGAAGTTCATTC 59.394 37.037 5.91 0.00 45.28 2.67
2623 2692 4.286032 TGCTGTAATACCAACTCCTGAAGT 59.714 41.667 0.00 0.00 41.10 3.01


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

AutoCloner maintained by Alex Coulton.