Multiple sequence alignment - TraesCS2D01G157700

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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 TraesCS2D01G157700 chr2D 100.000 2882 0 0 1 2882 101337277 101334396 0.000000e+00 5323.0
1 TraesCS2D01G157700 chr2D 95.604 819 35 1 2064 2882 215923180 215923997 0.000000e+00 1312.0
2 TraesCS2D01G157700 chr2D 94.247 817 47 0 2066 2882 226274466 226273650 0.000000e+00 1249.0
3 TraesCS2D01G157700 chr2D 73.239 355 81 14 235 582 350615489 350615836 1.810000e-22 117.0
4 TraesCS2D01G157700 chr2B 96.981 1921 54 4 1 1919 373098811 373096893 0.000000e+00 3223.0
5 TraesCS2D01G157700 chr2B 96.632 950 32 0 964 1913 8228577 8227628 0.000000e+00 1578.0
6 TraesCS2D01G157700 chr2B 96.421 950 34 0 964 1913 8072823 8071874 0.000000e+00 1567.0
7 TraesCS2D01G157700 chr2A 96.776 1923 55 7 1 1918 50051962 50050042 0.000000e+00 3201.0
8 TraesCS2D01G157700 chr2A 95.935 1919 68 6 1 1911 767549292 767551208 0.000000e+00 3103.0
9 TraesCS2D01G157700 chr2A 94.153 838 42 4 1 835 463258841 463259674 0.000000e+00 1269.0
10 TraesCS2D01G157700 chr6D 96.516 1923 55 6 1 1919 433503969 433502055 0.000000e+00 3169.0
11 TraesCS2D01G157700 chr6D 77.713 1032 221 8 3 1029 188890291 188889264 8.770000e-175 623.0
12 TraesCS2D01G157700 chr6D 72.194 392 93 16 238 621 6858308 6857925 3.930000e-19 106.0
13 TraesCS2D01G157700 chr5B 94.141 1536 83 6 383 1914 587457859 587459391 0.000000e+00 2331.0
14 TraesCS2D01G157700 chr3A 92.503 907 63 4 1009 1915 162754890 162755791 0.000000e+00 1293.0
15 TraesCS2D01G157700 chr3A 86.928 153 10 3 1913 2063 193901268 193901412 2.300000e-36 163.0
16 TraesCS2D01G157700 chr3A 87.248 149 9 3 1915 2061 193893085 193893225 8.260000e-36 161.0
17 TraesCS2D01G157700 chr3A 85.714 161 12 4 1906 2063 336059087 336059239 2.970000e-35 159.0
18 TraesCS2D01G157700 chr5D 94.750 819 42 1 2065 2882 279041027 279041845 0.000000e+00 1273.0
19 TraesCS2D01G157700 chr5D 93.529 819 52 1 2065 2882 279094720 279095538 0.000000e+00 1218.0
20 TraesCS2D01G157700 chr5D 77.852 149 27 5 269 414 12757273 12757128 1.420000e-13 87.9
21 TraesCS2D01G157700 chr5D 81.081 111 19 2 239 348 103642593 103642702 1.420000e-13 87.9
22 TraesCS2D01G157700 chr3D 94.303 825 42 4 2060 2882 439192990 439193811 0.000000e+00 1258.0
23 TraesCS2D01G157700 chr3D 93.635 817 49 2 2064 2880 439199463 439200276 0.000000e+00 1218.0
24 TraesCS2D01G157700 chr3D 75.806 930 212 12 1 924 125680778 125679856 2.620000e-125 459.0
25 TraesCS2D01G157700 chr7D 94.017 819 48 1 2064 2882 91540293 91541110 0.000000e+00 1240.0
26 TraesCS2D01G157700 chr7D 93.780 820 47 4 2064 2882 581760592 581759776 0.000000e+00 1229.0
27 TraesCS2D01G157700 chr7D 93.171 820 55 1 2063 2882 91533820 91534638 0.000000e+00 1203.0
28 TraesCS2D01G157700 chr7D 88.820 161 6 5 1906 2063 511985214 511985365 1.360000e-43 187.0
29 TraesCS2D01G157700 chr7D 72.959 392 91 15 238 621 615489819 615489435 3.900000e-24 122.0
30 TraesCS2D01G157700 chr5A 93.646 661 42 0 1255 1915 97566405 97565745 0.000000e+00 989.0
31 TraesCS2D01G157700 chr5A 78.697 1136 234 8 1 1132 491717439 491716308 0.000000e+00 750.0
32 TraesCS2D01G157700 chr5A 79.415 1025 201 9 1 1020 34490394 34491413 0.000000e+00 715.0
33 TraesCS2D01G157700 chr5A 85.802 162 11 5 1906 2063 133860669 133860822 8.260000e-36 161.0
34 TraesCS2D01G157700 chr6B 75.628 1912 447 18 1 1902 118685361 118683459 0.000000e+00 931.0
35 TraesCS2D01G157700 chr6B 75.024 1029 234 21 3 1020 18403402 18404418 3.390000e-124 455.0
36 TraesCS2D01G157700 chr6B 74.402 961 220 25 72 1019 87654389 87653442 3.480000e-104 388.0
37 TraesCS2D01G157700 chr6B 88.462 156 9 2 1909 2063 83229305 83229158 2.280000e-41 180.0
38 TraesCS2D01G157700 chr6B 85.714 161 12 4 1906 2063 400696126 400696278 2.970000e-35 159.0
39 TraesCS2D01G157700 chr3B 93.294 507 31 2 1 505 736186802 736186297 0.000000e+00 745.0
40 TraesCS2D01G157700 chr4A 75.016 1569 356 30 351 1899 71249324 71247772 0.000000e+00 693.0
41 TraesCS2D01G157700 chr1D 79.154 993 202 5 122 1112 103354388 103353399 0.000000e+00 682.0
42 TraesCS2D01G157700 chr7B 73.910 1284 303 30 610 1875 336468038 336466769 1.200000e-133 486.0
43 TraesCS2D01G157700 chr7B 76.225 694 144 18 173 855 710481813 710481130 5.910000e-92 348.0
44 TraesCS2D01G157700 chr7B 76.117 649 145 10 404 1047 727488663 727488020 5.950000e-87 331.0
45 TraesCS2D01G157700 chr7B 75.878 427 90 11 24 445 586628664 586628246 3.760000e-49 206.0
46 TraesCS2D01G157700 chr4B 87.821 156 10 2 1909 2063 545964174 545964027 1.060000e-39 174.0
47 TraesCS2D01G157700 chr4B 71.982 439 109 14 161 592 658976153 658975722 1.810000e-22 117.0
48 TraesCS2D01G157700 chr1B 87.234 141 9 2 1924 2063 156667733 156667865 4.970000e-33 152.0
49 TraesCS2D01G157700 chr4D 81.443 97 14 3 239 333 234448079 234448173 3.080000e-10 76.8


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 TraesCS2D01G157700 chr2D 101334396 101337277 2881 True 5323 5323 100.000 1 2882 1 chr2D.!!$R1 2881
1 TraesCS2D01G157700 chr2D 215923180 215923997 817 False 1312 1312 95.604 2064 2882 1 chr2D.!!$F1 818
2 TraesCS2D01G157700 chr2D 226273650 226274466 816 True 1249 1249 94.247 2066 2882 1 chr2D.!!$R2 816
3 TraesCS2D01G157700 chr2B 373096893 373098811 1918 True 3223 3223 96.981 1 1919 1 chr2B.!!$R3 1918
4 TraesCS2D01G157700 chr2B 8227628 8228577 949 True 1578 1578 96.632 964 1913 1 chr2B.!!$R2 949
5 TraesCS2D01G157700 chr2B 8071874 8072823 949 True 1567 1567 96.421 964 1913 1 chr2B.!!$R1 949
6 TraesCS2D01G157700 chr2A 50050042 50051962 1920 True 3201 3201 96.776 1 1918 1 chr2A.!!$R1 1917
7 TraesCS2D01G157700 chr2A 767549292 767551208 1916 False 3103 3103 95.935 1 1911 1 chr2A.!!$F2 1910
8 TraesCS2D01G157700 chr2A 463258841 463259674 833 False 1269 1269 94.153 1 835 1 chr2A.!!$F1 834
9 TraesCS2D01G157700 chr6D 433502055 433503969 1914 True 3169 3169 96.516 1 1919 1 chr6D.!!$R3 1918
10 TraesCS2D01G157700 chr6D 188889264 188890291 1027 True 623 623 77.713 3 1029 1 chr6D.!!$R2 1026
11 TraesCS2D01G157700 chr5B 587457859 587459391 1532 False 2331 2331 94.141 383 1914 1 chr5B.!!$F1 1531
12 TraesCS2D01G157700 chr3A 162754890 162755791 901 False 1293 1293 92.503 1009 1915 1 chr3A.!!$F1 906
13 TraesCS2D01G157700 chr5D 279041027 279041845 818 False 1273 1273 94.750 2065 2882 1 chr5D.!!$F2 817
14 TraesCS2D01G157700 chr5D 279094720 279095538 818 False 1218 1218 93.529 2065 2882 1 chr5D.!!$F3 817
15 TraesCS2D01G157700 chr3D 439192990 439193811 821 False 1258 1258 94.303 2060 2882 1 chr3D.!!$F1 822
16 TraesCS2D01G157700 chr3D 439199463 439200276 813 False 1218 1218 93.635 2064 2880 1 chr3D.!!$F2 816
17 TraesCS2D01G157700 chr3D 125679856 125680778 922 True 459 459 75.806 1 924 1 chr3D.!!$R1 923
18 TraesCS2D01G157700 chr7D 91540293 91541110 817 False 1240 1240 94.017 2064 2882 1 chr7D.!!$F2 818
19 TraesCS2D01G157700 chr7D 581759776 581760592 816 True 1229 1229 93.780 2064 2882 1 chr7D.!!$R1 818
20 TraesCS2D01G157700 chr7D 91533820 91534638 818 False 1203 1203 93.171 2063 2882 1 chr7D.!!$F1 819
21 TraesCS2D01G157700 chr5A 97565745 97566405 660 True 989 989 93.646 1255 1915 1 chr5A.!!$R1 660
22 TraesCS2D01G157700 chr5A 491716308 491717439 1131 True 750 750 78.697 1 1132 1 chr5A.!!$R2 1131
23 TraesCS2D01G157700 chr5A 34490394 34491413 1019 False 715 715 79.415 1 1020 1 chr5A.!!$F1 1019
24 TraesCS2D01G157700 chr6B 118683459 118685361 1902 True 931 931 75.628 1 1902 1 chr6B.!!$R3 1901
25 TraesCS2D01G157700 chr6B 18403402 18404418 1016 False 455 455 75.024 3 1020 1 chr6B.!!$F1 1017
26 TraesCS2D01G157700 chr6B 87653442 87654389 947 True 388 388 74.402 72 1019 1 chr6B.!!$R2 947
27 TraesCS2D01G157700 chr3B 736186297 736186802 505 True 745 745 93.294 1 505 1 chr3B.!!$R1 504
28 TraesCS2D01G157700 chr4A 71247772 71249324 1552 True 693 693 75.016 351 1899 1 chr4A.!!$R1 1548
29 TraesCS2D01G157700 chr1D 103353399 103354388 989 True 682 682 79.154 122 1112 1 chr1D.!!$R1 990
30 TraesCS2D01G157700 chr7B 336466769 336468038 1269 True 486 486 73.910 610 1875 1 chr7B.!!$R1 1265
31 TraesCS2D01G157700 chr7B 710481130 710481813 683 True 348 348 76.225 173 855 1 chr7B.!!$R3 682
32 TraesCS2D01G157700 chr7B 727488020 727488663 643 True 331 331 76.117 404 1047 1 chr7B.!!$R4 643

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
315 323 0.910088 GTGTGCCTAAGGAGAGGGGT 60.91 60.0 0.0 0.0 37.06 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2038 0.037232 GTTCGTGAACAGGGGAGGAG 60.037 60.0 7.83 0.0 40.84 3.69 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
315 323 0.910088 GTGTGCCTAAGGAGAGGGGT 60.910 60.000 0.00 0.00 37.06 4.95
513 521 4.102524 AGTCTGTGGAGTGGTATTCAAACA 59.897 41.667 0.00 0.00 0.00 2.83
678 687 2.007608 GCTGAAAATAGGACGTGGGAC 58.992 52.381 0.00 0.00 0.00 4.46
731 744 7.073883 CCTATTGATGTGCAACGAATTATGAG 58.926 38.462 0.00 0.00 42.39 2.90
760 773 2.700354 TGGCAGTGGGTATGATGGATA 58.300 47.619 0.00 0.00 0.00 2.59
787 800 5.437289 TGTCTCATGGCACTTTAACAAAG 57.563 39.130 0.00 0.00 44.10 2.77
890 905 4.082679 AGTTCAAGCCTCAAGTACTAGTCG 60.083 45.833 0.00 0.00 0.00 4.18
926 941 2.622011 GGAAATTGCGTGTGCCGGA 61.622 57.895 5.05 0.00 41.78 5.14
1189 1213 3.265791 GTGCTACTGTCCAGGAATCAAG 58.734 50.000 0.00 0.00 0.00 3.02
1264 1288 0.321298 GTATGTGTGGTGGGAGCGTT 60.321 55.000 0.00 0.00 0.00 4.84
1318 1345 1.128136 CAACGAGATCAGCACAAGCAG 59.872 52.381 0.00 0.00 45.49 4.24
1430 1458 9.890629 TCTAGTTAAACTCAATGTTGATGCTAT 57.109 29.630 0.00 0.00 39.13 2.97
1445 1473 7.121611 TGTTGATGCTATGTTTGATCAAGACAT 59.878 33.333 25.59 25.59 35.91 3.06
1518 1546 3.628942 TGGCTGCATCTTGTGTTGATATC 59.371 43.478 0.50 0.00 0.00 1.63
1534 1562 5.567037 TGATATCCCGTTCATGGAAGATT 57.433 39.130 0.00 0.00 35.03 2.40
1535 1563 5.308014 TGATATCCCGTTCATGGAAGATTG 58.692 41.667 0.00 0.00 35.03 2.67
1541 1569 1.672881 GTTCATGGAAGATTGCGGGAG 59.327 52.381 0.00 0.00 0.00 4.30
1650 1678 5.824624 GGAGGTAATTGAGATCATGCAGAAA 59.175 40.000 0.00 0.00 0.00 2.52
1768 1796 4.079446 CCAATATGGCGGCGGATT 57.921 55.556 9.78 3.20 0.00 3.01
1812 1840 5.123227 ACTTCTCGAACAATTGTCTGGAAA 58.877 37.500 12.39 3.82 0.00 3.13
1956 1984 8.967664 ATAAAAACAAAACTAAAGAAACCCCC 57.032 30.769 0.00 0.00 0.00 5.40
1957 1985 6.375830 AAAACAAAACTAAAGAAACCCCCA 57.624 33.333 0.00 0.00 0.00 4.96
1958 1986 5.347620 AACAAAACTAAAGAAACCCCCAC 57.652 39.130 0.00 0.00 0.00 4.61
1959 1987 3.707611 ACAAAACTAAAGAAACCCCCACC 59.292 43.478 0.00 0.00 0.00 4.61
1960 1988 2.688902 AACTAAAGAAACCCCCACCC 57.311 50.000 0.00 0.00 0.00 4.61
1961 1989 0.781920 ACTAAAGAAACCCCCACCCC 59.218 55.000 0.00 0.00 0.00 4.95
1962 1990 1.081481 CTAAAGAAACCCCCACCCCT 58.919 55.000 0.00 0.00 0.00 4.79
1963 1991 1.005569 CTAAAGAAACCCCCACCCCTC 59.994 57.143 0.00 0.00 0.00 4.30
1964 1992 0.704813 AAAGAAACCCCCACCCCTCT 60.705 55.000 0.00 0.00 0.00 3.69
1965 1993 1.435346 AAGAAACCCCCACCCCTCTG 61.435 60.000 0.00 0.00 0.00 3.35
1966 1994 2.863988 AAACCCCCACCCCTCTGG 60.864 66.667 0.00 0.00 41.37 3.86
1972 2000 4.366684 CCACCCCTCTGGCCCAAC 62.367 72.222 0.00 0.00 37.83 3.77
1973 2001 3.260100 CACCCCTCTGGCCCAACT 61.260 66.667 0.00 0.00 37.83 3.16
1974 2002 3.260100 ACCCCTCTGGCCCAACTG 61.260 66.667 0.00 0.00 37.83 3.16
1975 2003 4.052518 CCCCTCTGGCCCAACTGG 62.053 72.222 0.00 0.00 37.09 4.00
1976 2004 2.935481 CCCTCTGGCCCAACTGGA 60.935 66.667 0.00 0.00 37.39 3.86
1977 2005 2.352805 CCTCTGGCCCAACTGGAC 59.647 66.667 0.00 0.00 45.71 4.02
1978 2006 2.352805 CTCTGGCCCAACTGGACC 59.647 66.667 0.00 0.00 44.34 4.46
1979 2007 2.449518 TCTGGCCCAACTGGACCA 60.450 61.111 3.54 3.54 44.34 4.02
1980 2008 2.067932 CTCTGGCCCAACTGGACCAA 62.068 60.000 5.22 0.00 44.34 3.67
1981 2009 1.604593 CTGGCCCAACTGGACCAAG 60.605 63.158 5.22 0.00 44.34 3.61
1982 2010 2.991540 GGCCCAACTGGACCAAGC 60.992 66.667 0.00 0.00 35.25 4.01
1983 2011 3.365265 GCCCAACTGGACCAAGCG 61.365 66.667 0.00 0.00 37.39 4.68
1984 2012 2.672996 CCCAACTGGACCAAGCGG 60.673 66.667 0.00 0.00 37.39 5.52
1985 2013 3.365265 CCAACTGGACCAAGCGGC 61.365 66.667 0.00 0.00 37.39 6.53
1986 2014 3.365265 CAACTGGACCAAGCGGCC 61.365 66.667 0.00 0.00 34.57 6.13
1987 2015 3.884774 AACTGGACCAAGCGGCCA 61.885 61.111 2.24 0.00 37.08 5.36
1988 2016 4.643387 ACTGGACCAAGCGGCCAC 62.643 66.667 2.24 0.00 35.44 5.01
2010 2038 4.394712 CCAGGCACACCCCTCGTC 62.395 72.222 0.00 0.00 36.11 4.20
2011 2039 3.314331 CAGGCACACCCCTCGTCT 61.314 66.667 0.00 0.00 36.11 4.18
2012 2040 2.997897 AGGCACACCCCTCGTCTC 60.998 66.667 0.00 0.00 36.11 3.36
2013 2041 4.083862 GGCACACCCCTCGTCTCC 62.084 72.222 0.00 0.00 0.00 3.71
2014 2042 2.997897 GCACACCCCTCGTCTCCT 60.998 66.667 0.00 0.00 0.00 3.69
2015 2043 3.007973 GCACACCCCTCGTCTCCTC 62.008 68.421 0.00 0.00 0.00 3.71
2016 2044 2.037527 ACACCCCTCGTCTCCTCC 59.962 66.667 0.00 0.00 0.00 4.30
2017 2045 2.760385 CACCCCTCGTCTCCTCCC 60.760 72.222 0.00 0.00 0.00 4.30
2018 2046 4.077180 ACCCCTCGTCTCCTCCCC 62.077 72.222 0.00 0.00 0.00 4.81
2019 2047 3.756783 CCCCTCGTCTCCTCCCCT 61.757 72.222 0.00 0.00 0.00 4.79
2020 2048 2.443016 CCCTCGTCTCCTCCCCTG 60.443 72.222 0.00 0.00 0.00 4.45
2021 2049 2.360980 CCTCGTCTCCTCCCCTGT 59.639 66.667 0.00 0.00 0.00 4.00
2022 2050 1.305381 CCTCGTCTCCTCCCCTGTT 60.305 63.158 0.00 0.00 0.00 3.16
2023 2051 1.324005 CCTCGTCTCCTCCCCTGTTC 61.324 65.000 0.00 0.00 0.00 3.18
2024 2052 0.612174 CTCGTCTCCTCCCCTGTTCA 60.612 60.000 0.00 0.00 0.00 3.18
2025 2053 0.898789 TCGTCTCCTCCCCTGTTCAC 60.899 60.000 0.00 0.00 0.00 3.18
2026 2054 1.592223 GTCTCCTCCCCTGTTCACG 59.408 63.158 0.00 0.00 0.00 4.35
2027 2055 0.898789 GTCTCCTCCCCTGTTCACGA 60.899 60.000 0.00 0.00 0.00 4.35
2028 2056 0.178944 TCTCCTCCCCTGTTCACGAA 60.179 55.000 0.00 0.00 0.00 3.85
2029 2057 0.037232 CTCCTCCCCTGTTCACGAAC 60.037 60.000 2.89 2.89 41.50 3.95
2030 2058 1.003718 CCTCCCCTGTTCACGAACC 60.004 63.158 7.43 0.00 40.46 3.62
2031 2059 1.752198 CTCCCCTGTTCACGAACCA 59.248 57.895 7.43 0.00 40.46 3.67
2032 2060 0.602905 CTCCCCTGTTCACGAACCAC 60.603 60.000 7.43 0.00 40.46 4.16
2033 2061 1.599797 CCCCTGTTCACGAACCACC 60.600 63.158 7.43 0.00 40.46 4.61
2034 2062 1.599797 CCCTGTTCACGAACCACCC 60.600 63.158 7.43 0.00 40.46 4.61
2035 2063 1.599797 CCTGTTCACGAACCACCCC 60.600 63.158 7.43 0.00 40.46 4.95
2036 2064 1.959226 CTGTTCACGAACCACCCCG 60.959 63.158 7.43 0.00 40.46 5.73
2037 2065 2.109593 GTTCACGAACCACCCCGT 59.890 61.111 0.00 0.00 39.88 5.28
2087 2115 1.402787 GATCATGGGTTCCGGCAAAT 58.597 50.000 0.00 0.00 0.00 2.32
2114 2142 1.525077 GTTCGAACACTGGGGTGCA 60.525 57.895 23.12 0.00 46.57 4.57
2116 2144 2.203139 CGAACACTGGGGTGCACA 60.203 61.111 20.43 0.00 46.57 4.57
2150 2178 1.271271 CCTACCGATCTACGCCCTAGT 60.271 57.143 0.00 0.00 41.07 2.57
2213 2241 7.913789 ACACAAGGGACACAAGATTTATACTA 58.086 34.615 0.00 0.00 0.00 1.82
2226 2254 2.457813 TATACTAGTTCGGGCCACCA 57.542 50.000 4.39 0.00 36.13 4.17
2273 2301 0.678048 GTGGTGGTGGATTGCCTCTC 60.678 60.000 0.00 0.00 34.31 3.20
2312 2340 0.685097 CAAGGGGAAGAACGACCTCA 59.315 55.000 0.00 0.00 31.69 3.86
2344 2372 2.160813 GTGTTCTTGTGTTCGGTGTGTT 59.839 45.455 0.00 0.00 0.00 3.32
2353 2381 1.529865 GTTCGGTGTGTTGCTAAGGAC 59.470 52.381 0.00 0.00 0.00 3.85
2366 2394 0.615331 TAAGGACTGGCTCAAGGCTG 59.385 55.000 8.59 8.59 43.43 4.85
2552 2581 2.035442 GCGAAAGGGCTCTGGTGAC 61.035 63.158 0.00 0.00 0.00 3.67
2556 2585 1.407656 AAAGGGCTCTGGTGACGACA 61.408 55.000 0.00 0.00 0.00 4.35
2589 2618 2.675423 CGGTGACCTCCGTCCTGA 60.675 66.667 0.00 0.00 44.77 3.86
2611 2640 0.957888 GCCTGCTGGTCTTGGTCTTC 60.958 60.000 11.69 0.00 35.27 2.87
2732 2761 2.767445 CCGCCTGGTGTCGATCGTA 61.767 63.158 15.94 2.69 0.00 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
315 323 0.627451 AATCTCTGAAGCCCATGCCA 59.373 50.000 0.00 0.00 38.69 4.92
513 521 4.780815 TCCAAATATGTCCTCGCTTGAAT 58.219 39.130 0.00 0.00 0.00 2.57
643 652 8.195436 CCTATTTTCAGCATCAATGAGTTCATT 58.805 33.333 1.58 1.58 46.62 2.57
644 653 7.558807 TCCTATTTTCAGCATCAATGAGTTCAT 59.441 33.333 0.00 0.00 38.41 2.57
731 744 2.353610 CCCACTGCCAAAGGGATGC 61.354 63.158 0.00 0.00 45.80 3.91
760 773 6.815089 TGTTAAAGTGCCATGAGACAAAATT 58.185 32.000 0.00 0.00 0.00 1.82
799 812 2.596904 TGGTAAGCCGATCTAACAGC 57.403 50.000 0.00 0.00 37.67 4.40
890 905 1.644786 CCAAATGGTTCGCCGGACTC 61.645 60.000 5.05 0.00 41.18 3.36
1189 1213 0.531974 TCAGCCACCAACGACTGAAC 60.532 55.000 0.00 0.00 36.27 3.18
1430 1458 6.406370 CCAGTACCTATGTCTTGATCAAACA 58.594 40.000 19.03 19.03 0.00 2.83
1445 1473 1.064463 CACCCGTACTCCCAGTACCTA 60.064 57.143 8.00 0.00 46.27 3.08
1518 1546 0.378257 CGCAATCTTCCATGAACGGG 59.622 55.000 0.00 0.00 0.00 5.28
1650 1678 1.745489 GCCGAGTGAATTTCCGCCT 60.745 57.895 0.00 0.00 0.00 5.52
1768 1796 5.507637 AGTCTCCGAGTTCCTAGACAATAA 58.492 41.667 0.00 0.00 40.65 1.40
1869 1897 5.119931 TCATGGCGGTTTATATTTCATGC 57.880 39.130 0.00 0.00 32.93 4.06
1930 1958 9.398538 GGGGGTTTCTTTAGTTTTGTTTTTATT 57.601 29.630 0.00 0.00 0.00 1.40
1931 1959 8.549731 TGGGGGTTTCTTTAGTTTTGTTTTTAT 58.450 29.630 0.00 0.00 0.00 1.40
1932 1960 7.823310 GTGGGGGTTTCTTTAGTTTTGTTTTTA 59.177 33.333 0.00 0.00 0.00 1.52
1933 1961 6.655848 GTGGGGGTTTCTTTAGTTTTGTTTTT 59.344 34.615 0.00 0.00 0.00 1.94
1934 1962 6.174760 GTGGGGGTTTCTTTAGTTTTGTTTT 58.825 36.000 0.00 0.00 0.00 2.43
1935 1963 5.338544 GGTGGGGGTTTCTTTAGTTTTGTTT 60.339 40.000 0.00 0.00 0.00 2.83
1936 1964 4.162698 GGTGGGGGTTTCTTTAGTTTTGTT 59.837 41.667 0.00 0.00 0.00 2.83
1937 1965 3.707611 GGTGGGGGTTTCTTTAGTTTTGT 59.292 43.478 0.00 0.00 0.00 2.83
1938 1966 3.070446 GGGTGGGGGTTTCTTTAGTTTTG 59.930 47.826 0.00 0.00 0.00 2.44
1939 1967 3.311091 GGGTGGGGGTTTCTTTAGTTTT 58.689 45.455 0.00 0.00 0.00 2.43
1940 1968 2.426708 GGGGTGGGGGTTTCTTTAGTTT 60.427 50.000 0.00 0.00 0.00 2.66
1941 1969 1.148446 GGGGTGGGGGTTTCTTTAGTT 59.852 52.381 0.00 0.00 0.00 2.24
1942 1970 0.781920 GGGGTGGGGGTTTCTTTAGT 59.218 55.000 0.00 0.00 0.00 2.24
1943 1971 1.005569 GAGGGGTGGGGGTTTCTTTAG 59.994 57.143 0.00 0.00 0.00 1.85
1944 1972 1.078115 GAGGGGTGGGGGTTTCTTTA 58.922 55.000 0.00 0.00 0.00 1.85
1945 1973 0.704813 AGAGGGGTGGGGGTTTCTTT 60.705 55.000 0.00 0.00 0.00 2.52
1946 1974 1.072143 AGAGGGGTGGGGGTTTCTT 60.072 57.895 0.00 0.00 0.00 2.52
1947 1975 1.852626 CAGAGGGGTGGGGGTTTCT 60.853 63.158 0.00 0.00 0.00 2.52
1948 1976 2.763902 CAGAGGGGTGGGGGTTTC 59.236 66.667 0.00 0.00 0.00 2.78
1949 1977 2.863988 CCAGAGGGGTGGGGGTTT 60.864 66.667 0.00 0.00 33.46 3.27
1955 1983 4.366684 GTTGGGCCAGAGGGGTGG 62.367 72.222 6.23 0.00 41.01 4.61
1956 1984 3.260100 AGTTGGGCCAGAGGGGTG 61.260 66.667 6.23 0.00 39.65 4.61
1957 1985 3.260100 CAGTTGGGCCAGAGGGGT 61.260 66.667 6.23 0.00 39.65 4.95
1958 1986 4.052518 CCAGTTGGGCCAGAGGGG 62.053 72.222 6.23 3.61 40.85 4.79
1959 1987 2.935481 TCCAGTTGGGCCAGAGGG 60.935 66.667 17.49 14.79 36.21 4.30
1960 1988 2.352805 GTCCAGTTGGGCCAGAGG 59.647 66.667 6.23 10.51 36.21 3.69
1966 1994 3.365265 CGCTTGGTCCAGTTGGGC 61.365 66.667 0.00 0.00 39.63 5.36
1967 1995 2.672996 CCGCTTGGTCCAGTTGGG 60.673 66.667 0.00 0.00 35.41 4.12
1968 1996 3.365265 GCCGCTTGGTCCAGTTGG 61.365 66.667 0.00 0.00 34.16 3.77
1969 1997 3.365265 GGCCGCTTGGTCCAGTTG 61.365 66.667 0.00 0.00 34.16 3.16
1970 1998 3.884774 TGGCCGCTTGGTCCAGTT 61.885 61.111 0.00 0.00 36.12 3.16
1971 1999 4.643387 GTGGCCGCTTGGTCCAGT 62.643 66.667 9.68 0.00 38.89 4.00
1993 2021 4.394712 GACGAGGGGTGTGCCTGG 62.395 72.222 0.00 0.00 34.45 4.45
1994 2022 3.302347 GAGACGAGGGGTGTGCCTG 62.302 68.421 0.00 0.00 34.45 4.85
1995 2023 2.997897 GAGACGAGGGGTGTGCCT 60.998 66.667 0.00 0.00 34.45 4.75
1996 2024 4.083862 GGAGACGAGGGGTGTGCC 62.084 72.222 0.00 0.00 0.00 5.01
1997 2025 2.997897 AGGAGACGAGGGGTGTGC 60.998 66.667 0.00 0.00 0.00 4.57
1998 2026 2.352032 GGAGGAGACGAGGGGTGTG 61.352 68.421 0.00 0.00 0.00 3.82
1999 2027 2.037527 GGAGGAGACGAGGGGTGT 59.962 66.667 0.00 0.00 0.00 4.16
2000 2028 2.760385 GGGAGGAGACGAGGGGTG 60.760 72.222 0.00 0.00 0.00 4.61
2001 2029 4.077180 GGGGAGGAGACGAGGGGT 62.077 72.222 0.00 0.00 0.00 4.95
2002 2030 3.756783 AGGGGAGGAGACGAGGGG 61.757 72.222 0.00 0.00 0.00 4.79
2003 2031 2.443016 CAGGGGAGGAGACGAGGG 60.443 72.222 0.00 0.00 0.00 4.30
2004 2032 1.305381 AACAGGGGAGGAGACGAGG 60.305 63.158 0.00 0.00 0.00 4.63
2005 2033 0.612174 TGAACAGGGGAGGAGACGAG 60.612 60.000 0.00 0.00 0.00 4.18
2006 2034 0.898789 GTGAACAGGGGAGGAGACGA 60.899 60.000 0.00 0.00 0.00 4.20
2007 2035 1.592223 GTGAACAGGGGAGGAGACG 59.408 63.158 0.00 0.00 0.00 4.18
2008 2036 0.898789 TCGTGAACAGGGGAGGAGAC 60.899 60.000 0.00 0.00 0.00 3.36
2009 2037 0.178944 TTCGTGAACAGGGGAGGAGA 60.179 55.000 0.00 0.00 0.00 3.71
2010 2038 0.037232 GTTCGTGAACAGGGGAGGAG 60.037 60.000 7.83 0.00 40.84 3.69
2011 2039 1.477685 GGTTCGTGAACAGGGGAGGA 61.478 60.000 14.16 0.00 42.85 3.71
2012 2040 1.003718 GGTTCGTGAACAGGGGAGG 60.004 63.158 14.16 0.00 42.85 4.30
2013 2041 0.602905 GTGGTTCGTGAACAGGGGAG 60.603 60.000 14.16 0.00 42.85 4.30
2014 2042 1.448497 GTGGTTCGTGAACAGGGGA 59.552 57.895 14.16 0.00 42.85 4.81
2015 2043 1.599797 GGTGGTTCGTGAACAGGGG 60.600 63.158 14.16 0.00 42.85 4.79
2016 2044 1.599797 GGGTGGTTCGTGAACAGGG 60.600 63.158 14.16 0.00 42.85 4.45
2017 2045 1.599797 GGGGTGGTTCGTGAACAGG 60.600 63.158 14.16 0.00 42.85 4.00
2018 2046 1.959226 CGGGGTGGTTCGTGAACAG 60.959 63.158 14.16 0.00 42.85 3.16
2019 2047 2.109387 CGGGGTGGTTCGTGAACA 59.891 61.111 14.16 0.00 42.85 3.18
2020 2048 2.109593 ACGGGGTGGTTCGTGAAC 59.890 61.111 4.15 4.15 38.25 3.18
2055 2083 3.740128 ATGATCCGACAGCCGTGGC 62.740 63.158 1.67 1.67 42.33 5.01
2056 2084 1.884464 CATGATCCGACAGCCGTGG 60.884 63.158 0.00 0.00 36.31 4.94
2057 2085 1.884464 CCATGATCCGACAGCCGTG 60.884 63.158 0.00 0.00 36.31 4.94
2058 2086 2.501128 CCATGATCCGACAGCCGT 59.499 61.111 0.00 0.00 36.31 5.68
2061 2089 0.815615 GGAACCCATGATCCGACAGC 60.816 60.000 0.00 0.00 0.00 4.40
2087 2115 2.038033 CCAGTGTTCGAACCTTAAGGGA 59.962 50.000 25.31 10.45 40.27 4.20
2213 2241 1.603455 CACAATGGTGGCCCGAACT 60.603 57.895 0.00 0.00 41.45 3.01
2273 2301 0.174845 TACGGTTCTTCATCAGCCCG 59.825 55.000 0.00 0.00 40.65 6.13
2312 2340 3.117888 ACACAAGAACACCTCAACCTCAT 60.118 43.478 0.00 0.00 0.00 2.90
2344 2372 0.615331 CCTTGAGCCAGTCCTTAGCA 59.385 55.000 0.00 0.00 0.00 3.49
2353 2381 2.035312 AAGCCAGCCTTGAGCCAG 59.965 61.111 0.00 0.00 45.47 4.85
2552 2581 2.432628 GAGCCCAAGACGGTGTCG 60.433 66.667 0.00 0.00 37.67 4.35
2556 2585 4.003788 CGTGGAGCCCAAGACGGT 62.004 66.667 1.83 0.00 35.05 4.83
2589 2618 2.357836 CCAAGACCAGCAGGCCAT 59.642 61.111 5.01 0.00 39.06 4.40
2611 2640 5.404946 CAAAGGTTTCCATATCAGTGCAAG 58.595 41.667 0.00 0.00 0.00 4.01
2732 2761 0.109086 CTCTCGTGACGTGAGCCATT 60.109 55.000 21.58 0.00 39.80 3.16
2764 2793 1.374758 GAGATATCAAGGCGGGGCG 60.375 63.158 5.32 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.