Multiple sequence alignment - TraesCS6B01G165500

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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 TraesCS6B01G165500 chr6B 100.000 2727 0 0 1 2727 172322884 172325610 0.000000e+00 5036.0
1 TraesCS6B01G165500 chr6B 89.427 227 22 2 1265 1490 172265141 172265366 4.440000e-73 285.0
2 TraesCS6B01G165500 chr6A 91.571 1127 47 21 802 1911 108201181 108202276 0.000000e+00 1511.0
3 TraesCS6B01G165500 chr6A 92.282 298 15 5 2435 2724 108202654 108202951 1.510000e-112 416.0
4 TraesCS6B01G165500 chr6A 87.603 363 35 5 2047 2406 108202301 108202656 1.950000e-111 412.0
5 TraesCS6B01G165500 chr6A 89.091 220 23 1 1265 1483 108179913 108180132 3.460000e-69 272.0
6 TraesCS6B01G165500 chr7A 98.876 801 9 0 1 801 712592263 712591463 0.000000e+00 1430.0
7 TraesCS6B01G165500 chr7A 89.286 140 15 0 2486 2625 649425147 649425286 2.790000e-40 176.0
8 TraesCS6B01G165500 chr4A 98.502 801 12 0 1 801 181639411 181640211 0.000000e+00 1413.0
9 TraesCS6B01G165500 chr4A 98.502 801 11 1 1 801 115553755 115552956 0.000000e+00 1411.0
10 TraesCS6B01G165500 chr4A 81.609 87 12 3 1909 1995 731354461 731354543 4.870000e-08 69.4
11 TraesCS6B01G165500 chr3A 98.737 792 9 1 1 792 470841426 470842216 0.000000e+00 1406.0
12 TraesCS6B01G165500 chr7B 98.005 802 15 1 1 802 697265903 697265103 0.000000e+00 1391.0
13 TraesCS6B01G165500 chr7B 97.378 801 20 1 1 801 589946916 589947715 0.000000e+00 1362.0
14 TraesCS6B01G165500 chr7B 89.286 140 15 0 2486 2625 614220473 614220612 2.790000e-40 176.0
15 TraesCS6B01G165500 chr7B 92.000 50 1 2 1999 2046 513813886 513813934 1.750000e-07 67.6
16 TraesCS6B01G165500 chr1A 97.878 801 17 0 1 801 593269333 593270133 0.000000e+00 1386.0
17 TraesCS6B01G165500 chr2B 97.631 802 14 1 1 802 650414934 650415730 0.000000e+00 1371.0
18 TraesCS6B01G165500 chr1B 97.503 801 20 0 1 801 296747469 296748269 0.000000e+00 1369.0
19 TraesCS6B01G165500 chr6D 91.053 950 31 21 954 1871 89822476 89823403 0.000000e+00 1234.0
20 TraesCS6B01G165500 chr6D 97.832 692 12 1 2039 2727 89823419 89824110 0.000000e+00 1192.0
21 TraesCS6B01G165500 chr6D 89.868 227 21 2 1265 1490 89734113 89734338 9.550000e-75 291.0
22 TraesCS6B01G165500 chr6D 97.368 114 3 0 802 915 89822350 89822463 7.700000e-46 195.0
23 TraesCS6B01G165500 chr7D 89.286 140 15 0 2486 2625 563825504 563825365 2.790000e-40 176.0
24 TraesCS6B01G165500 chr7D 83.516 91 11 2 1915 2005 562247964 562248050 6.260000e-12 82.4
25 TraesCS6B01G165500 chr1D 88.571 140 16 0 2486 2625 421494138 421493999 1.300000e-38 171.0
26 TraesCS6B01G165500 chr2D 87.857 140 17 0 2486 2625 558943578 558943717 6.040000e-37 165.0
27 TraesCS6B01G165500 chr2D 90.741 54 1 3 1999 2049 421789950 421789898 4.870000e-08 69.4
28 TraesCS6B01G165500 chr3D 86.429 140 19 0 2486 2625 577441834 577441695 1.310000e-33 154.0
29 TraesCS6B01G165500 chr5B 85.106 94 11 3 1913 2005 591655429 591655338 2.890000e-15 93.5
30 TraesCS6B01G165500 chr5B 92.000 50 0 4 1999 2045 522929037 522929085 1.750000e-07 67.6
31 TraesCS6B01G165500 chr5B 87.719 57 2 4 1999 2053 318405839 318405892 8.150000e-06 62.1
32 TraesCS6B01G165500 chr5A 83.168 101 12 3 1913 2012 570006128 570006224 1.350000e-13 87.9
33 TraesCS6B01G165500 chr5A 83.696 92 12 3 1913 2004 570006215 570006127 1.740000e-12 84.2
34 TraesCS6B01G165500 chr5A 92.157 51 1 2 2002 2049 474539908 474539858 4.870000e-08 69.4
35 TraesCS6B01G165500 chr4B 84.337 83 12 1 1913 1995 657468647 657468728 2.250000e-11 80.5
36 TraesCS6B01G165500 chr4B 84.615 78 11 1 1928 2005 657468721 657468645 2.910000e-10 76.8
37 TraesCS6B01G165500 chr4B 93.750 48 0 2 1999 2044 322692986 322692940 4.870000e-08 69.4
38 TraesCS6B01G165500 chr2A 81.818 99 15 3 1909 2004 555925680 555925778 2.250000e-11 80.5
39 TraesCS6B01G165500 chr2A 90.566 53 2 2 1999 2049 16133199 16133148 1.750000e-07 67.6
40 TraesCS6B01G165500 chr3B 81.250 96 16 2 1910 2004 502805091 502804997 2.910000e-10 76.8
41 TraesCS6B01G165500 chr5D 89.286 56 1 3 1999 2052 352456327 352456275 6.300000e-07 65.8
42 TraesCS6B01G165500 chr5D 87.719 57 2 4 1999 2053 280788420 280788473 8.150000e-06 62.1
43 TraesCS6B01G165500 chrUn 85.484 62 5 3 2006 2065 97740105 97740046 8.150000e-06 62.1


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 TraesCS6B01G165500 chr6B 172322884 172325610 2726 False 5036.000000 5036 100.000000 1 2727 1 chr6B.!!$F2 2726
1 TraesCS6B01G165500 chr6A 108201181 108202951 1770 False 779.666667 1511 90.485333 802 2724 3 chr6A.!!$F2 1922
2 TraesCS6B01G165500 chr7A 712591463 712592263 800 True 1430.000000 1430 98.876000 1 801 1 chr7A.!!$R1 800
3 TraesCS6B01G165500 chr4A 181639411 181640211 800 False 1413.000000 1413 98.502000 1 801 1 chr4A.!!$F1 800
4 TraesCS6B01G165500 chr4A 115552956 115553755 799 True 1411.000000 1411 98.502000 1 801 1 chr4A.!!$R1 800
5 TraesCS6B01G165500 chr3A 470841426 470842216 790 False 1406.000000 1406 98.737000 1 792 1 chr3A.!!$F1 791
6 TraesCS6B01G165500 chr7B 697265103 697265903 800 True 1391.000000 1391 98.005000 1 802 1 chr7B.!!$R1 801
7 TraesCS6B01G165500 chr7B 589946916 589947715 799 False 1362.000000 1362 97.378000 1 801 1 chr7B.!!$F2 800
8 TraesCS6B01G165500 chr1A 593269333 593270133 800 False 1386.000000 1386 97.878000 1 801 1 chr1A.!!$F1 800
9 TraesCS6B01G165500 chr2B 650414934 650415730 796 False 1371.000000 1371 97.631000 1 802 1 chr2B.!!$F1 801
10 TraesCS6B01G165500 chr1B 296747469 296748269 800 False 1369.000000 1369 97.503000 1 801 1 chr1B.!!$F1 800
11 TraesCS6B01G165500 chr6D 89822350 89824110 1760 False 873.666667 1234 95.417667 802 2727 3 chr6D.!!$F2 1925

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
938 940 0.824109 CCGCCTCCAGAGAATGTGTA 59.176 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2112 2161 0.250038 AGCTGTGCTTCGCTTCAGAA 60.25 50.0 12.74 0.0 33.89 3.02 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
101 102 9.646336 GCTAGATTAAACAATACCATTAACACG 57.354 33.333 0.00 0.00 0.00 4.49
504 506 0.958091 CGGCGAATCAGAGAGAGGAT 59.042 55.000 0.00 0.00 0.00 3.24
769 771 3.693085 TGGTACTGATTCGTGAGTAGGTC 59.307 47.826 0.00 0.00 0.00 3.85
916 918 4.989279 ACGACTACAAATACGTACCCAT 57.011 40.909 0.00 0.00 37.22 4.00
917 919 4.675510 ACGACTACAAATACGTACCCATG 58.324 43.478 0.00 0.00 37.22 3.66
918 920 4.046462 CGACTACAAATACGTACCCATGG 58.954 47.826 4.14 4.14 0.00 3.66
930 932 4.559063 CCATGGCCGCCTCCAGAG 62.559 72.222 11.61 0.00 39.89 3.35
931 933 3.473647 CATGGCCGCCTCCAGAGA 61.474 66.667 11.61 0.00 39.89 3.10
932 934 2.688666 ATGGCCGCCTCCAGAGAA 60.689 61.111 11.61 0.00 39.89 2.87
933 935 2.074948 ATGGCCGCCTCCAGAGAAT 61.075 57.895 11.61 0.00 39.89 2.40
934 936 2.203126 GGCCGCCTCCAGAGAATG 60.203 66.667 0.71 0.00 0.00 2.67
935 937 2.586792 GCCGCCTCCAGAGAATGT 59.413 61.111 0.00 0.00 0.00 2.71
936 938 1.817099 GCCGCCTCCAGAGAATGTG 60.817 63.158 0.00 0.00 0.00 3.21
937 939 1.599047 CCGCCTCCAGAGAATGTGT 59.401 57.895 0.00 0.00 0.00 3.72
938 940 0.824109 CCGCCTCCAGAGAATGTGTA 59.176 55.000 0.00 0.00 0.00 2.90
939 941 1.414181 CCGCCTCCAGAGAATGTGTAT 59.586 52.381 0.00 0.00 0.00 2.29
940 942 2.628178 CCGCCTCCAGAGAATGTGTATA 59.372 50.000 0.00 0.00 0.00 1.47
941 943 3.553096 CCGCCTCCAGAGAATGTGTATAC 60.553 52.174 0.00 0.00 0.00 1.47
951 953 5.477291 AGAGAATGTGTATACTACCCATCGG 59.523 44.000 4.17 0.00 0.00 4.18
970 972 2.221169 GGCCAATACAAGCATCATCGA 58.779 47.619 0.00 0.00 0.00 3.59
1027 1035 2.267174 CCATAGATCTTGTGGCCTGG 57.733 55.000 3.32 0.00 0.00 4.45
1028 1036 1.492176 CCATAGATCTTGTGGCCTGGT 59.508 52.381 3.32 0.00 0.00 4.00
1029 1037 2.569059 CATAGATCTTGTGGCCTGGTG 58.431 52.381 3.32 0.00 0.00 4.17
1030 1038 0.911769 TAGATCTTGTGGCCTGGTGG 59.088 55.000 3.32 0.00 0.00 4.61
1031 1039 1.136329 AGATCTTGTGGCCTGGTGGT 61.136 55.000 3.32 0.00 35.27 4.16
1201 1209 3.123674 GGTACGTGACTTCCTGCTG 57.876 57.895 0.00 0.00 0.00 4.41
1202 1210 1.014564 GGTACGTGACTTCCTGCTGC 61.015 60.000 0.00 0.00 0.00 5.25
1203 1211 0.038159 GTACGTGACTTCCTGCTGCT 60.038 55.000 0.00 0.00 0.00 4.24
1204 1212 0.679505 TACGTGACTTCCTGCTGCTT 59.320 50.000 0.00 0.00 0.00 3.91
1205 1213 0.882042 ACGTGACTTCCTGCTGCTTG 60.882 55.000 0.00 0.00 0.00 4.01
1206 1214 1.578423 GTGACTTCCTGCTGCTTGC 59.422 57.895 0.00 0.00 43.25 4.01
1238 1270 1.132640 GGTGACGCGACTTTGATGC 59.867 57.895 15.93 0.00 0.00 3.91
1248 1280 0.662619 ACTTTGATGCGTGTGTGTGG 59.337 50.000 0.00 0.00 0.00 4.17
1368 1410 2.061773 CACCTACGACAAGCAGTTCAG 58.938 52.381 0.00 0.00 0.00 3.02
1580 1622 2.597217 CGCCAAACTCCCCAGCAA 60.597 61.111 0.00 0.00 0.00 3.91
1601 1643 3.814268 CAAATGCTCCGGCGGGTG 61.814 66.667 27.98 19.90 42.25 4.61
1602 1644 4.028490 AAATGCTCCGGCGGGTGA 62.028 61.111 27.98 10.26 42.25 4.02
1603 1645 3.976701 AAATGCTCCGGCGGGTGAG 62.977 63.158 27.98 17.59 42.25 3.51
1772 1814 0.179004 TGCTCCTTTTCAAAGCCGGA 60.179 50.000 5.05 0.00 35.12 5.14
1801 1843 0.884514 GCTCCTTTTCAGAGGGCAAC 59.115 55.000 0.00 0.00 37.41 4.17
1876 1920 3.118261 TGGTTCCTGAATGAGATAGCACC 60.118 47.826 0.00 0.00 0.00 5.01
1877 1921 3.135530 GGTTCCTGAATGAGATAGCACCT 59.864 47.826 0.00 0.00 0.00 4.00
1911 1957 7.254829 GCATTCCAGCAGCATATTATCAGATAG 60.255 40.741 0.00 0.00 0.00 2.08
1913 1959 6.871844 TCCAGCAGCATATTATCAGATAGAC 58.128 40.000 0.00 0.00 0.00 2.59
1915 1961 6.979817 CCAGCAGCATATTATCAGATAGACTC 59.020 42.308 0.00 0.00 0.00 3.36
1917 1963 6.098124 AGCAGCATATTATCAGATAGACTCCC 59.902 42.308 0.00 0.00 0.00 4.30
1918 1964 6.098124 GCAGCATATTATCAGATAGACTCCCT 59.902 42.308 0.00 0.00 0.00 4.20
1919 1965 7.684187 GCAGCATATTATCAGATAGACTCCCTC 60.684 44.444 0.00 0.00 0.00 4.30
1920 1966 6.838612 AGCATATTATCAGATAGACTCCCTCC 59.161 42.308 0.00 0.00 0.00 4.30
1922 1968 7.289782 GCATATTATCAGATAGACTCCCTCCAT 59.710 40.741 0.00 0.00 0.00 3.41
1923 1969 9.874195 CATATTATCAGATAGACTCCCTCCATA 57.126 37.037 0.00 0.00 0.00 2.74
1926 1972 5.004361 TCAGATAGACTCCCTCCATAAGG 57.996 47.826 0.00 0.00 45.77 2.69
1940 1986 5.914033 CTCCATAAGGAAATACTTGTCGGA 58.086 41.667 0.00 0.00 45.19 4.55
1941 1987 6.302535 TCCATAAGGAAATACTTGTCGGAA 57.697 37.500 0.00 0.00 42.23 4.30
1942 1988 6.713276 TCCATAAGGAAATACTTGTCGGAAA 58.287 36.000 0.00 0.00 42.23 3.13
1943 1989 7.169591 TCCATAAGGAAATACTTGTCGGAAAA 58.830 34.615 0.00 0.00 42.23 2.29
1944 1990 7.666388 TCCATAAGGAAATACTTGTCGGAAAAA 59.334 33.333 0.00 0.00 42.23 1.94
1945 1991 8.466798 CCATAAGGAAATACTTGTCGGAAAAAT 58.533 33.333 0.00 0.00 36.89 1.82
1946 1992 9.289303 CATAAGGAAATACTTGTCGGAAAAATG 57.711 33.333 0.00 0.00 32.02 2.32
1947 1993 6.267496 AGGAAATACTTGTCGGAAAAATGG 57.733 37.500 0.00 0.00 0.00 3.16
1948 1994 6.007703 AGGAAATACTTGTCGGAAAAATGGA 58.992 36.000 0.00 0.00 0.00 3.41
1949 1995 6.663523 AGGAAATACTTGTCGGAAAAATGGAT 59.336 34.615 0.00 0.00 0.00 3.41
1950 1996 7.832187 AGGAAATACTTGTCGGAAAAATGGATA 59.168 33.333 0.00 0.00 0.00 2.59
1951 1997 8.463607 GGAAATACTTGTCGGAAAAATGGATAA 58.536 33.333 0.00 0.00 0.00 1.75
1952 1998 9.285770 GAAATACTTGTCGGAAAAATGGATAAC 57.714 33.333 0.00 0.00 0.00 1.89
1953 1999 7.931578 ATACTTGTCGGAAAAATGGATAACA 57.068 32.000 0.00 0.00 0.00 2.41
1954 2000 6.009115 ACTTGTCGGAAAAATGGATAACAC 57.991 37.500 0.00 0.00 0.00 3.32
1955 2001 5.533154 ACTTGTCGGAAAAATGGATAACACA 59.467 36.000 0.00 0.00 0.00 3.72
1956 2002 6.208599 ACTTGTCGGAAAAATGGATAACACAT 59.791 34.615 0.00 0.00 0.00 3.21
1957 2003 6.189677 TGTCGGAAAAATGGATAACACATC 57.810 37.500 0.00 0.00 0.00 3.06
1958 2004 5.943416 TGTCGGAAAAATGGATAACACATCT 59.057 36.000 0.00 0.00 0.00 2.90
1959 2005 6.432783 TGTCGGAAAAATGGATAACACATCTT 59.567 34.615 0.00 0.00 0.00 2.40
1960 2006 6.967199 GTCGGAAAAATGGATAACACATCTTC 59.033 38.462 0.00 0.00 0.00 2.87
1961 2007 6.884295 TCGGAAAAATGGATAACACATCTTCT 59.116 34.615 0.00 0.00 0.00 2.85
1962 2008 7.393234 TCGGAAAAATGGATAACACATCTTCTT 59.607 33.333 0.00 0.00 0.00 2.52
1963 2009 8.028938 CGGAAAAATGGATAACACATCTTCTTT 58.971 33.333 0.00 0.00 0.00 2.52
1964 2010 9.710900 GGAAAAATGGATAACACATCTTCTTTT 57.289 29.630 0.00 0.00 0.00 2.27
1971 2017 9.699410 TGGATAACACATCTTCTTTTATCCATT 57.301 29.630 14.55 0.00 46.91 3.16
1977 2023 9.865321 ACACATCTTCTTTTATCCATTTTGATG 57.135 29.630 0.00 0.00 35.23 3.07
1983 2029 9.918630 CTTCTTTTATCCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
1990 2036 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
1991 2037 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
1992 2038 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
1993 2039 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
1994 2040 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
1995 2041 3.193903 TGATGACAAGTATTTCCGGACGA 59.806 43.478 1.83 0.00 0.00 4.20
1996 2042 3.663995 TGACAAGTATTTCCGGACGAA 57.336 42.857 1.83 0.00 0.00 3.85
1997 2043 3.581755 TGACAAGTATTTCCGGACGAAG 58.418 45.455 1.83 0.00 0.00 3.79
1998 2044 3.256383 TGACAAGTATTTCCGGACGAAGA 59.744 43.478 1.83 0.00 0.00 2.87
1999 2045 3.846360 ACAAGTATTTCCGGACGAAGAG 58.154 45.455 1.83 0.00 0.00 2.85
2000 2046 3.508793 ACAAGTATTTCCGGACGAAGAGA 59.491 43.478 1.83 0.00 0.00 3.10
2001 2047 4.106197 CAAGTATTTCCGGACGAAGAGAG 58.894 47.826 1.83 0.00 0.00 3.20
2002 2048 3.354467 AGTATTTCCGGACGAAGAGAGT 58.646 45.455 1.83 0.00 0.00 3.24
2003 2049 4.521146 AGTATTTCCGGACGAAGAGAGTA 58.479 43.478 1.83 0.00 0.00 2.59
2004 2050 3.779271 ATTTCCGGACGAAGAGAGTAC 57.221 47.619 1.83 0.00 0.00 2.73
2005 2051 2.189594 TTCCGGACGAAGAGAGTACA 57.810 50.000 1.83 0.00 0.00 2.90
2006 2052 2.414994 TCCGGACGAAGAGAGTACAT 57.585 50.000 0.00 0.00 0.00 2.29
2007 2053 2.286872 TCCGGACGAAGAGAGTACATC 58.713 52.381 0.00 0.00 0.00 3.06
2008 2054 1.334243 CCGGACGAAGAGAGTACATCC 59.666 57.143 0.00 0.00 0.00 3.51
2009 2055 2.014857 CGGACGAAGAGAGTACATCCA 58.985 52.381 0.00 0.00 0.00 3.41
2010 2056 2.619177 CGGACGAAGAGAGTACATCCAT 59.381 50.000 0.00 0.00 0.00 3.41
2011 2057 3.066900 CGGACGAAGAGAGTACATCCATT 59.933 47.826 0.00 0.00 0.00 3.16
2012 2058 4.440250 CGGACGAAGAGAGTACATCCATTT 60.440 45.833 0.00 0.00 0.00 2.32
2013 2059 5.044558 GGACGAAGAGAGTACATCCATTTC 58.955 45.833 0.00 0.00 0.00 2.17
2014 2060 5.163499 GGACGAAGAGAGTACATCCATTTCT 60.163 44.000 0.00 0.00 0.00 2.52
2015 2061 6.287589 ACGAAGAGAGTACATCCATTTCTT 57.712 37.500 0.00 0.00 0.00 2.52
2016 2062 6.334202 ACGAAGAGAGTACATCCATTTCTTC 58.666 40.000 0.00 0.00 37.04 2.87
2017 2063 6.820470 GAAGAGAGTACATCCATTTCTTCG 57.180 41.667 0.00 0.00 32.58 3.79
2018 2064 6.531503 AAGAGAGTACATCCATTTCTTCGA 57.468 37.500 0.00 0.00 0.00 3.71
2019 2065 5.897050 AGAGAGTACATCCATTTCTTCGAC 58.103 41.667 0.00 0.00 0.00 4.20
2020 2066 5.419155 AGAGAGTACATCCATTTCTTCGACA 59.581 40.000 0.00 0.00 0.00 4.35
2021 2067 6.037786 AGAGTACATCCATTTCTTCGACAA 57.962 37.500 0.00 0.00 0.00 3.18
2022 2068 6.102663 AGAGTACATCCATTTCTTCGACAAG 58.897 40.000 0.00 0.00 0.00 3.16
2023 2069 5.794894 AGTACATCCATTTCTTCGACAAGT 58.205 37.500 0.00 0.00 0.00 3.16
2024 2070 6.931838 AGTACATCCATTTCTTCGACAAGTA 58.068 36.000 0.00 0.00 0.00 2.24
2025 2071 7.556844 AGTACATCCATTTCTTCGACAAGTAT 58.443 34.615 0.00 0.00 0.00 2.12
2026 2072 8.041323 AGTACATCCATTTCTTCGACAAGTATT 58.959 33.333 0.00 0.00 0.00 1.89
2027 2073 7.687941 ACATCCATTTCTTCGACAAGTATTT 57.312 32.000 0.00 0.00 0.00 1.40
2028 2074 7.752695 ACATCCATTTCTTCGACAAGTATTTC 58.247 34.615 0.00 0.00 0.00 2.17
2029 2075 6.737254 TCCATTTCTTCGACAAGTATTTCC 57.263 37.500 0.00 0.00 0.00 3.13
2030 2076 5.350365 TCCATTTCTTCGACAAGTATTTCCG 59.650 40.000 0.00 0.00 0.00 4.30
2031 2077 5.447279 CCATTTCTTCGACAAGTATTTCCGG 60.447 44.000 0.00 0.00 0.00 5.14
2032 2078 4.524316 TTCTTCGACAAGTATTTCCGGA 57.476 40.909 0.00 0.00 0.00 5.14
2033 2079 3.841643 TCTTCGACAAGTATTTCCGGAC 58.158 45.455 1.83 0.00 0.00 4.79
2034 2080 3.256383 TCTTCGACAAGTATTTCCGGACA 59.744 43.478 1.83 0.00 0.00 4.02
2035 2081 3.226346 TCGACAAGTATTTCCGGACAG 57.774 47.619 1.83 0.00 0.00 3.51
2036 2082 2.094390 TCGACAAGTATTTCCGGACAGG 60.094 50.000 1.83 0.00 42.97 4.00
2037 2083 2.629051 GACAAGTATTTCCGGACAGGG 58.371 52.381 1.83 0.00 41.52 4.45
2038 2084 2.235402 GACAAGTATTTCCGGACAGGGA 59.765 50.000 1.83 0.00 41.52 4.20
2039 2085 2.236395 ACAAGTATTTCCGGACAGGGAG 59.764 50.000 1.83 0.00 41.52 4.30
2056 2102 8.145122 GGACAGGGAGTATTACTTATCAGAAAG 58.855 40.741 0.00 0.00 0.00 2.62
2072 2118 5.835257 TCAGAAAGCATAATAAAGGCATGC 58.165 37.500 9.90 9.90 44.29 4.06
2088 2137 2.348591 GCATGCGCGGACTAATACTTTC 60.349 50.000 8.83 0.00 0.00 2.62
2112 2161 5.050490 GCATAAATACACGACCAGAGATGT 58.950 41.667 0.00 0.00 0.00 3.06
2407 2456 4.400884 ACCACAATGAAACAGCAAAGTACA 59.599 37.500 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 5.552178 AGTGTAAGATTCTGTCCAAACTCC 58.448 41.667 0.00 0.00 0.00 3.85
494 496 0.843309 TCGCTCTCCATCCTCTCTCT 59.157 55.000 0.00 0.00 0.00 3.10
504 506 0.326595 ACTCTCACTCTCGCTCTCCA 59.673 55.000 0.00 0.00 0.00 3.86
769 771 0.586319 CGTTGGTACCACACTTGCTG 59.414 55.000 16.04 0.11 0.00 4.41
873 875 2.435762 ACATGCATGCCGCGTACA 60.436 55.556 26.53 2.86 46.97 2.90
916 918 2.688666 ATTCTCTGGAGGCGGCCA 60.689 61.111 23.09 0.00 36.30 5.36
917 919 2.203126 CATTCTCTGGAGGCGGCC 60.203 66.667 12.11 12.11 0.00 6.13
918 920 1.817099 CACATTCTCTGGAGGCGGC 60.817 63.158 0.00 0.00 0.00 6.53
935 937 2.385135 TGGCCGATGGGTAGTATACA 57.615 50.000 5.50 0.00 45.43 2.29
936 938 3.975168 ATTGGCCGATGGGTAGTATAC 57.025 47.619 4.07 0.00 42.04 1.47
937 939 4.418359 TGTATTGGCCGATGGGTAGTATA 58.582 43.478 16.45 0.00 34.97 1.47
938 940 3.244582 TGTATTGGCCGATGGGTAGTAT 58.755 45.455 16.45 0.00 34.97 2.12
939 941 2.680251 TGTATTGGCCGATGGGTAGTA 58.320 47.619 16.45 0.00 34.97 1.82
940 942 1.502690 TGTATTGGCCGATGGGTAGT 58.497 50.000 16.45 0.00 34.97 2.73
941 943 2.494059 CTTGTATTGGCCGATGGGTAG 58.506 52.381 16.45 4.04 34.97 3.18
951 953 3.561310 TCTTCGATGATGCTTGTATTGGC 59.439 43.478 0.00 0.00 0.00 4.52
970 972 5.467063 GCTACAAAGTAGAAACTGCACTCTT 59.533 40.000 8.29 0.00 35.62 2.85
1072 1080 2.732094 GACGTTGTACTGCGCCGT 60.732 61.111 10.01 10.01 0.00 5.68
1205 1213 4.915110 CGTCACCGAGATGCAAATGTGC 62.915 54.545 0.00 0.00 43.73 4.57
1206 1214 1.201954 CGTCACCGAGATGCAAATGTG 60.202 52.381 0.00 0.00 35.63 3.21
1207 1215 1.078709 CGTCACCGAGATGCAAATGT 58.921 50.000 0.00 0.00 35.63 2.71
1222 1254 3.155424 CGCATCAAAGTCGCGTCA 58.845 55.556 5.77 0.00 43.86 4.35
1227 1259 0.581529 ACACACACGCATCAAAGTCG 59.418 50.000 0.00 0.00 0.00 4.18
1230 1262 0.040157 CCCACACACACGCATCAAAG 60.040 55.000 0.00 0.00 0.00 2.77
1238 1270 1.948508 CATGAACCCCACACACACG 59.051 57.895 0.00 0.00 0.00 4.49
1601 1643 2.360794 GCGTTGAGTTACTCGCCTC 58.639 57.895 7.92 0.00 42.33 4.70
1602 1644 4.573162 GCGTTGAGTTACTCGCCT 57.427 55.556 7.92 0.00 42.33 5.52
1604 1646 2.442188 CCGGCGTTGAGTTACTCGC 61.442 63.158 6.01 8.05 46.42 5.03
1605 1647 2.442188 GCCGGCGTTGAGTTACTCG 61.442 63.158 12.58 0.00 32.35 4.18
1606 1648 2.098831 GGCCGGCGTTGAGTTACTC 61.099 63.158 22.54 5.27 0.00 2.59
1607 1649 2.047560 GGCCGGCGTTGAGTTACT 60.048 61.111 22.54 0.00 0.00 2.24
1608 1650 1.908066 CTTGGCCGGCGTTGAGTTAC 61.908 60.000 22.54 3.09 0.00 2.50
1609 1651 1.669760 CTTGGCCGGCGTTGAGTTA 60.670 57.895 22.54 0.00 0.00 2.24
1750 1792 2.151202 CGGCTTTGAAAAGGAGCAGTA 58.849 47.619 5.02 0.00 38.14 2.74
1772 1814 5.942826 CCTCTGAAAAGGAGCAAATAGTCTT 59.057 40.000 0.00 0.00 38.87 3.01
1801 1843 2.937469 AGAATCTGAGCAGAGACACG 57.063 50.000 6.34 0.00 41.33 4.49
1876 1920 1.337071 CTGCTGGAATGCCAATGCTAG 59.663 52.381 5.59 0.00 45.41 3.42
1877 1921 1.395635 CTGCTGGAATGCCAATGCTA 58.604 50.000 5.59 0.00 45.41 3.49
1911 1957 6.126739 ACAAGTATTTCCTTATGGAGGGAGTC 60.127 42.308 0.00 0.00 46.31 3.36
1913 1959 6.253946 ACAAGTATTTCCTTATGGAGGGAG 57.746 41.667 0.00 0.00 46.31 4.30
1915 1961 5.057149 CGACAAGTATTTCCTTATGGAGGG 58.943 45.833 0.00 0.00 46.31 4.30
1917 1963 5.914033 TCCGACAAGTATTTCCTTATGGAG 58.086 41.667 0.00 0.00 44.24 3.86
1918 1964 5.943349 TCCGACAAGTATTTCCTTATGGA 57.057 39.130 0.00 0.00 41.36 3.41
1919 1965 6.995511 TTTCCGACAAGTATTTCCTTATGG 57.004 37.500 0.00 0.00 0.00 2.74
1920 1966 9.289303 CATTTTTCCGACAAGTATTTCCTTATG 57.711 33.333 0.00 0.00 0.00 1.90
1922 1968 7.666388 TCCATTTTTCCGACAAGTATTTCCTTA 59.334 33.333 0.00 0.00 0.00 2.69
1923 1969 6.492087 TCCATTTTTCCGACAAGTATTTCCTT 59.508 34.615 0.00 0.00 0.00 3.36
1926 1972 9.285770 GTTATCCATTTTTCCGACAAGTATTTC 57.714 33.333 0.00 0.00 0.00 2.17
1927 1973 8.798402 TGTTATCCATTTTTCCGACAAGTATTT 58.202 29.630 0.00 0.00 0.00 1.40
1930 1976 6.711194 TGTGTTATCCATTTTTCCGACAAGTA 59.289 34.615 0.00 0.00 0.00 2.24
1931 1977 5.533154 TGTGTTATCCATTTTTCCGACAAGT 59.467 36.000 0.00 0.00 0.00 3.16
1932 1978 6.007936 TGTGTTATCCATTTTTCCGACAAG 57.992 37.500 0.00 0.00 0.00 3.16
1934 1980 5.943416 AGATGTGTTATCCATTTTTCCGACA 59.057 36.000 0.00 0.00 0.00 4.35
1935 1981 6.436843 AGATGTGTTATCCATTTTTCCGAC 57.563 37.500 0.00 0.00 0.00 4.79
1936 1982 6.884295 AGAAGATGTGTTATCCATTTTTCCGA 59.116 34.615 0.00 0.00 0.00 4.55
1937 1983 7.088589 AGAAGATGTGTTATCCATTTTTCCG 57.911 36.000 0.00 0.00 0.00 4.30
1938 1984 9.710900 AAAAGAAGATGTGTTATCCATTTTTCC 57.289 29.630 0.00 0.00 0.00 3.13
1951 1997 9.865321 CATCAAAATGGATAAAAGAAGATGTGT 57.135 29.630 0.00 0.00 0.00 3.72
1957 2003 9.918630 ACTTGTCATCAAAATGGATAAAAGAAG 57.081 29.630 0.00 0.00 33.42 2.85
1964 2010 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
1965 2011 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
1966 2012 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
1967 2013 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
1968 2014 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
1969 2015 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
1970 2016 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
1971 2017 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
1972 2018 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
1973 2019 3.193903 TCGTCCGGAAATACTTGTCATCA 59.806 43.478 5.23 0.00 0.00 3.07
1974 2020 3.777478 TCGTCCGGAAATACTTGTCATC 58.223 45.455 5.23 0.00 0.00 2.92
1975 2021 3.880047 TCGTCCGGAAATACTTGTCAT 57.120 42.857 5.23 0.00 0.00 3.06
1976 2022 3.256383 TCTTCGTCCGGAAATACTTGTCA 59.744 43.478 5.23 0.00 33.34 3.58
1977 2023 3.841643 TCTTCGTCCGGAAATACTTGTC 58.158 45.455 5.23 0.00 33.34 3.18
1978 2024 3.508793 TCTCTTCGTCCGGAAATACTTGT 59.491 43.478 5.23 0.00 33.34 3.16
1979 2025 4.106029 TCTCTTCGTCCGGAAATACTTG 57.894 45.455 5.23 0.00 33.34 3.16
1980 2026 3.762823 ACTCTCTTCGTCCGGAAATACTT 59.237 43.478 5.23 0.00 33.34 2.24
1981 2027 3.354467 ACTCTCTTCGTCCGGAAATACT 58.646 45.455 5.23 0.00 33.34 2.12
1982 2028 3.779271 ACTCTCTTCGTCCGGAAATAC 57.221 47.619 5.23 0.00 33.34 1.89
1983 2029 4.264253 TGTACTCTCTTCGTCCGGAAATA 58.736 43.478 5.23 0.00 33.34 1.40
1984 2030 3.087031 TGTACTCTCTTCGTCCGGAAAT 58.913 45.455 5.23 0.00 33.34 2.17
1985 2031 2.507484 TGTACTCTCTTCGTCCGGAAA 58.493 47.619 5.23 0.00 33.34 3.13
1986 2032 2.189594 TGTACTCTCTTCGTCCGGAA 57.810 50.000 5.23 0.00 0.00 4.30
1987 2033 2.286872 GATGTACTCTCTTCGTCCGGA 58.713 52.381 0.00 0.00 0.00 5.14
1988 2034 1.334243 GGATGTACTCTCTTCGTCCGG 59.666 57.143 0.00 0.00 0.00 5.14
1989 2035 2.014857 TGGATGTACTCTCTTCGTCCG 58.985 52.381 0.00 0.00 39.36 4.79
1990 2036 4.657436 AATGGATGTACTCTCTTCGTCC 57.343 45.455 0.00 0.00 37.66 4.79
1991 2037 5.897050 AGAAATGGATGTACTCTCTTCGTC 58.103 41.667 0.00 0.00 0.00 4.20
1992 2038 5.923733 AGAAATGGATGTACTCTCTTCGT 57.076 39.130 0.00 0.00 0.00 3.85
1993 2039 6.820470 GAAGAAATGGATGTACTCTCTTCG 57.180 41.667 0.00 0.00 31.10 3.79
1994 2040 6.474102 GTCGAAGAAATGGATGTACTCTCTTC 59.526 42.308 0.00 0.00 39.69 2.87
1995 2041 6.071334 TGTCGAAGAAATGGATGTACTCTCTT 60.071 38.462 0.00 0.00 39.69 2.85
1996 2042 5.419155 TGTCGAAGAAATGGATGTACTCTCT 59.581 40.000 0.00 0.00 39.69 3.10
1997 2043 5.651530 TGTCGAAGAAATGGATGTACTCTC 58.348 41.667 0.00 0.00 39.69 3.20
1998 2044 5.661056 TGTCGAAGAAATGGATGTACTCT 57.339 39.130 0.00 0.00 39.69 3.24
1999 2045 5.869888 ACTTGTCGAAGAAATGGATGTACTC 59.130 40.000 0.00 0.00 39.69 2.59
2000 2046 5.794894 ACTTGTCGAAGAAATGGATGTACT 58.205 37.500 0.00 0.00 39.69 2.73
2001 2047 7.772332 ATACTTGTCGAAGAAATGGATGTAC 57.228 36.000 0.00 0.00 39.69 2.90
2002 2048 8.786826 AAATACTTGTCGAAGAAATGGATGTA 57.213 30.769 0.00 0.00 39.69 2.29
2003 2049 7.148239 GGAAATACTTGTCGAAGAAATGGATGT 60.148 37.037 0.00 0.00 39.69 3.06
2004 2050 7.189512 GGAAATACTTGTCGAAGAAATGGATG 58.810 38.462 0.00 0.00 39.69 3.51
2005 2051 6.037172 CGGAAATACTTGTCGAAGAAATGGAT 59.963 38.462 0.00 0.00 39.69 3.41
2006 2052 5.350365 CGGAAATACTTGTCGAAGAAATGGA 59.650 40.000 0.00 0.00 39.69 3.41
2007 2053 5.447279 CCGGAAATACTTGTCGAAGAAATGG 60.447 44.000 0.00 0.00 39.69 3.16
2008 2054 5.350365 TCCGGAAATACTTGTCGAAGAAATG 59.650 40.000 0.00 0.00 39.69 2.32
2009 2055 5.350640 GTCCGGAAATACTTGTCGAAGAAAT 59.649 40.000 5.23 0.00 39.69 2.17
2010 2056 4.687483 GTCCGGAAATACTTGTCGAAGAAA 59.313 41.667 5.23 0.00 39.69 2.52
2011 2057 4.240096 GTCCGGAAATACTTGTCGAAGAA 58.760 43.478 5.23 0.00 39.69 2.52
2012 2058 3.256383 TGTCCGGAAATACTTGTCGAAGA 59.744 43.478 5.23 0.00 32.98 2.87
2013 2059 3.581755 TGTCCGGAAATACTTGTCGAAG 58.418 45.455 5.23 0.00 35.07 3.79
2014 2060 3.581755 CTGTCCGGAAATACTTGTCGAA 58.418 45.455 5.23 0.00 0.00 3.71
2015 2061 2.094390 CCTGTCCGGAAATACTTGTCGA 60.094 50.000 5.23 0.00 33.16 4.20
2016 2062 2.268298 CCTGTCCGGAAATACTTGTCG 58.732 52.381 5.23 0.00 33.16 4.35
2017 2063 2.235402 TCCCTGTCCGGAAATACTTGTC 59.765 50.000 5.23 0.00 33.16 3.18
2018 2064 2.236395 CTCCCTGTCCGGAAATACTTGT 59.764 50.000 5.23 0.00 33.16 3.16
2019 2065 2.236395 ACTCCCTGTCCGGAAATACTTG 59.764 50.000 5.23 0.00 33.16 3.16
2020 2066 2.547990 ACTCCCTGTCCGGAAATACTT 58.452 47.619 5.23 0.00 33.16 2.24
2021 2067 2.249309 ACTCCCTGTCCGGAAATACT 57.751 50.000 5.23 0.00 33.16 2.12
2022 2068 4.684484 AATACTCCCTGTCCGGAAATAC 57.316 45.455 5.23 0.00 33.16 1.89
2023 2069 5.461327 AGTAATACTCCCTGTCCGGAAATA 58.539 41.667 5.23 0.00 33.16 1.40
2024 2070 4.296056 AGTAATACTCCCTGTCCGGAAAT 58.704 43.478 5.23 0.00 33.16 2.17
2025 2071 3.716431 AGTAATACTCCCTGTCCGGAAA 58.284 45.455 5.23 0.00 33.16 3.13
2026 2072 3.393426 AGTAATACTCCCTGTCCGGAA 57.607 47.619 5.23 0.00 33.16 4.30
2027 2073 3.393426 AAGTAATACTCCCTGTCCGGA 57.607 47.619 0.00 0.00 33.16 5.14
2028 2074 4.831155 TGATAAGTAATACTCCCTGTCCGG 59.169 45.833 0.00 0.00 0.00 5.14
2029 2075 5.768662 TCTGATAAGTAATACTCCCTGTCCG 59.231 44.000 0.00 0.00 0.00 4.79
2030 2076 7.598759 TTCTGATAAGTAATACTCCCTGTCC 57.401 40.000 0.00 0.00 0.00 4.02
2031 2077 7.654116 GCTTTCTGATAAGTAATACTCCCTGTC 59.346 40.741 0.00 0.00 0.00 3.51
2032 2078 7.125811 TGCTTTCTGATAAGTAATACTCCCTGT 59.874 37.037 0.00 0.00 0.00 4.00
2033 2079 7.500992 TGCTTTCTGATAAGTAATACTCCCTG 58.499 38.462 0.00 0.00 0.00 4.45
2034 2080 7.676683 TGCTTTCTGATAAGTAATACTCCCT 57.323 36.000 0.00 0.00 0.00 4.20
2035 2081 9.998106 TTATGCTTTCTGATAAGTAATACTCCC 57.002 33.333 0.00 0.00 0.00 4.30
2056 2102 1.330306 CGCGCATGCCTTTATTATGC 58.670 50.000 13.15 5.19 42.75 3.14
2072 2118 1.552226 TGCGAAAGTATTAGTCCGCG 58.448 50.000 0.00 0.00 44.76 6.46
2088 2137 3.702330 TCTCTGGTCGTGTATTTATGCG 58.298 45.455 0.00 0.00 0.00 4.73
2112 2161 0.250038 AGCTGTGCTTCGCTTCAGAA 60.250 50.000 12.74 0.00 33.89 3.02
2217 2266 5.003160 TCATGGTCGTCATCAAGAATTTGT 58.997 37.500 0.00 0.00 35.73 2.83
2650 2707 4.223144 ACTATTTTCTGTTTGGGTGCCTT 58.777 39.130 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.