Multiple sequence alignment - TraesCS4B01G172400

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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 TraesCS4B01G172400 chr4B 100.000 2570 0 0 1 2570 377373690 377376259 0.000000e+00 4747
1 TraesCS4B01G172400 chr4B 90.667 900 55 6 4 874 523184562 523183663 0.000000e+00 1170
2 TraesCS4B01G172400 chr4A 93.255 1186 38 12 883 2055 177618072 177616916 0.000000e+00 1709
3 TraesCS4B01G172400 chr4A 90.852 317 15 8 2257 2570 177616914 177616609 1.840000e-111 412
4 TraesCS4B01G172400 chr4D 91.916 1138 40 19 883 2013 302398992 302400084 0.000000e+00 1544
5 TraesCS4B01G172400 chr4D 88.312 231 11 6 2346 2570 302400191 302400411 1.960000e-66 263
6 TraesCS4B01G172400 chr4D 91.566 166 14 0 2086 2251 62120470 62120635 1.990000e-56 230
7 TraesCS4B01G172400 chr6B 92.597 878 35 5 23 870 209592066 209591189 0.000000e+00 1234
8 TraesCS4B01G172400 chr6B 89.647 879 60 11 20 867 673874733 673875611 0.000000e+00 1090
9 TraesCS4B01G172400 chr6B 88.348 884 61 17 24 875 8619138 8620011 0.000000e+00 1024
10 TraesCS4B01G172400 chr1B 91.648 886 42 7 23 877 82740155 82739271 0.000000e+00 1197
11 TraesCS4B01G172400 chr1B 91.081 897 51 10 4 871 340978823 340977927 0.000000e+00 1186
12 TraesCS4B01G172400 chr1B 89.314 889 52 16 20 878 671068605 671069480 0.000000e+00 1075
13 TraesCS4B01G172400 chr3B 91.051 894 52 10 4 870 193604435 193605327 0.000000e+00 1182
14 TraesCS4B01G172400 chr7B 91.344 878 42 12 23 870 726142249 726141376 0.000000e+00 1170
15 TraesCS4B01G172400 chr7B 88.155 878 70 12 23 870 667388850 667387977 0.000000e+00 1014
16 TraesCS4B01G172400 chr7B 91.176 170 13 2 2086 2255 563740014 563739847 1.990000e-56 230
17 TraesCS4B01G172400 chr7B 88.021 192 16 7 2067 2257 734431251 734431066 1.200000e-53 220
18 TraesCS4B01G172400 chrUn 89.444 881 61 12 27 875 200662952 200662072 0.000000e+00 1083
19 TraesCS4B01G172400 chrUn 89.318 880 63 11 27 875 317027046 317026167 0.000000e+00 1075
20 TraesCS4B01G172400 chr7A 88.571 875 92 5 4 875 668095299 668096168 0.000000e+00 1055
21 TraesCS4B01G172400 chr7A 91.617 167 14 0 2087 2253 443397632 443397798 5.530000e-57 231
22 TraesCS4B01G172400 chr7A 89.385 179 18 1 2074 2251 16718380 16718202 9.250000e-55 224
23 TraesCS4B01G172400 chr2A 81.836 523 84 5 1045 1560 57176236 57175718 1.830000e-116 429
24 TraesCS4B01G172400 chr2D 81.262 523 87 5 1045 1560 55764783 55764265 1.840000e-111 412
25 TraesCS4B01G172400 chr2D 90.698 172 16 0 2087 2258 515460882 515460711 1.990000e-56 230
26 TraesCS4B01G172400 chr2B 81.262 523 87 6 1045 1560 88434970 88434452 1.840000e-111 412
27 TraesCS4B01G172400 chr2B 91.124 169 15 0 2087 2255 781778728 781778560 1.990000e-56 230
28 TraesCS4B01G172400 chr3D 92.727 165 12 0 2087 2251 105119306 105119470 3.300000e-59 239
29 TraesCS4B01G172400 chr6D 90.116 172 17 0 2087 2258 94051915 94052086 9.250000e-55 224


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 TraesCS4B01G172400 chr4B 377373690 377376259 2569 False 4747.0 4747 100.0000 1 2570 1 chr4B.!!$F1 2569
1 TraesCS4B01G172400 chr4B 523183663 523184562 899 True 1170.0 1170 90.6670 4 874 1 chr4B.!!$R1 870
2 TraesCS4B01G172400 chr4A 177616609 177618072 1463 True 1060.5 1709 92.0535 883 2570 2 chr4A.!!$R1 1687
3 TraesCS4B01G172400 chr4D 302398992 302400411 1419 False 903.5 1544 90.1140 883 2570 2 chr4D.!!$F2 1687
4 TraesCS4B01G172400 chr6B 209591189 209592066 877 True 1234.0 1234 92.5970 23 870 1 chr6B.!!$R1 847
5 TraesCS4B01G172400 chr6B 673874733 673875611 878 False 1090.0 1090 89.6470 20 867 1 chr6B.!!$F2 847
6 TraesCS4B01G172400 chr6B 8619138 8620011 873 False 1024.0 1024 88.3480 24 875 1 chr6B.!!$F1 851
7 TraesCS4B01G172400 chr1B 82739271 82740155 884 True 1197.0 1197 91.6480 23 877 1 chr1B.!!$R1 854
8 TraesCS4B01G172400 chr1B 340977927 340978823 896 True 1186.0 1186 91.0810 4 871 1 chr1B.!!$R2 867
9 TraesCS4B01G172400 chr1B 671068605 671069480 875 False 1075.0 1075 89.3140 20 878 1 chr1B.!!$F1 858
10 TraesCS4B01G172400 chr3B 193604435 193605327 892 False 1182.0 1182 91.0510 4 870 1 chr3B.!!$F1 866
11 TraesCS4B01G172400 chr7B 726141376 726142249 873 True 1170.0 1170 91.3440 23 870 1 chr7B.!!$R3 847
12 TraesCS4B01G172400 chr7B 667387977 667388850 873 True 1014.0 1014 88.1550 23 870 1 chr7B.!!$R2 847
13 TraesCS4B01G172400 chrUn 200662072 200662952 880 True 1083.0 1083 89.4440 27 875 1 chrUn.!!$R1 848
14 TraesCS4B01G172400 chrUn 317026167 317027046 879 True 1075.0 1075 89.3180 27 875 1 chrUn.!!$R2 848
15 TraesCS4B01G172400 chr7A 668095299 668096168 869 False 1055.0 1055 88.5710 4 875 1 chr7A.!!$F2 871
16 TraesCS4B01G172400 chr2A 57175718 57176236 518 True 429.0 429 81.8360 1045 1560 1 chr2A.!!$R1 515
17 TraesCS4B01G172400 chr2D 55764265 55764783 518 True 412.0 412 81.2620 1045 1560 1 chr2D.!!$R1 515
18 TraesCS4B01G172400 chr2B 88434452 88434970 518 True 412.0 412 81.2620 1045 1560 1 chr2B.!!$R1 515

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
922 961 0.452122 CCAACGTTTTAAGCGCTCCG 60.452 55.0 12.06 11.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2065 2146 0.803117 CTTGCATGCTGTCTCACTGG 59.197 55.0 20.33 0.0 0.0 4.0 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
158 162 4.318689 GCAAACACAAATTCGAACCAATGG 60.319 41.667 0.00 0.00 0.00 3.16
280 285 2.695359 GACGAAACTATCCAGTGCCAA 58.305 47.619 0.00 0.00 34.36 4.52
407 417 1.186200 GGAAATGCAGGAAGGGGTTC 58.814 55.000 0.00 0.00 0.00 3.62
491 516 4.166011 GCACCATCGACGGCTTGC 62.166 66.667 0.00 0.00 0.00 4.01
523 561 1.208052 CTTCGCCTTCTCCTCCAATGA 59.792 52.381 0.00 0.00 0.00 2.57
616 654 2.326550 GGTGTGCGACGTGTTTGG 59.673 61.111 0.00 0.00 0.00 3.28
675 714 2.992689 TTCCACCGCACGCCTCTA 60.993 61.111 0.00 0.00 0.00 2.43
720 759 2.112297 AACCAACGTGCGGGTGAT 59.888 55.556 7.49 0.00 37.50 3.06
848 887 3.771978 GGTGGTGAACGCCCAAAT 58.228 55.556 0.00 0.00 44.24 2.32
922 961 0.452122 CCAACGTTTTAAGCGCTCCG 60.452 55.000 12.06 11.00 0.00 4.63
927 972 1.723701 CGTTTTAAGCGCTCCGGAAAC 60.724 52.381 12.06 17.23 0.00 2.78
941 986 2.162681 CGGAAACCATTCTCAAAGCCT 58.837 47.619 0.00 0.00 35.79 4.58
942 987 3.343617 CGGAAACCATTCTCAAAGCCTA 58.656 45.455 0.00 0.00 35.79 3.93
943 988 3.947834 CGGAAACCATTCTCAAAGCCTAT 59.052 43.478 0.00 0.00 35.79 2.57
944 989 5.123227 CGGAAACCATTCTCAAAGCCTATA 58.877 41.667 0.00 0.00 35.79 1.31
999 1044 2.110213 ACCGGCGAACTCAAAGCA 59.890 55.556 9.30 0.00 0.00 3.91
1230 1281 3.537874 GTCGGCGCCTACATCCCT 61.538 66.667 24.96 0.00 0.00 4.20
1309 1360 2.045045 CGCTCTTTGGCCCCATCA 60.045 61.111 0.00 0.00 0.00 3.07
1332 1383 3.717294 GAGGAGCCCGGCAAGGAA 61.717 66.667 13.15 0.00 45.00 3.36
1570 1630 2.429930 CCGTGTGGGGAGCTTGAA 59.570 61.111 0.00 0.00 0.00 2.69
1571 1631 1.672356 CCGTGTGGGGAGCTTGAAG 60.672 63.158 0.00 0.00 0.00 3.02
1572 1632 1.672356 CGTGTGGGGAGCTTGAAGG 60.672 63.158 0.00 0.00 0.00 3.46
1573 1633 1.973812 GTGTGGGGAGCTTGAAGGC 60.974 63.158 0.00 0.00 0.00 4.35
1574 1634 2.747855 GTGGGGAGCTTGAAGGCG 60.748 66.667 0.00 0.00 37.29 5.52
1575 1635 4.033776 TGGGGAGCTTGAAGGCGG 62.034 66.667 0.00 0.00 37.29 6.13
1617 1692 3.024547 CGTCCCTCTCCTGTTTCTCATA 58.975 50.000 0.00 0.00 0.00 2.15
1618 1693 3.639094 CGTCCCTCTCCTGTTTCTCATAT 59.361 47.826 0.00 0.00 0.00 1.78
1619 1694 4.500545 CGTCCCTCTCCTGTTTCTCATATG 60.501 50.000 0.00 0.00 0.00 1.78
1620 1695 4.651503 GTCCCTCTCCTGTTTCTCATATGA 59.348 45.833 5.07 5.07 0.00 2.15
1656 1731 6.607019 TCCTAGACATTTTTGTTTAGGGTGT 58.393 36.000 17.69 0.00 43.13 4.16
1762 1838 5.862924 TCACAGCAAGCAGTAATTAGTTC 57.137 39.130 0.00 0.00 0.00 3.01
1767 1843 5.412594 CAGCAAGCAGTAATTAGTTCCTTCA 59.587 40.000 0.00 0.00 0.00 3.02
1804 1880 7.858583 AGTTCTTGTTAATTCGGAAACTGTAC 58.141 34.615 0.00 0.00 0.00 2.90
1805 1881 7.713942 AGTTCTTGTTAATTCGGAAACTGTACT 59.286 33.333 0.00 0.00 0.00 2.73
1806 1882 8.981647 GTTCTTGTTAATTCGGAAACTGTACTA 58.018 33.333 0.00 0.00 0.00 1.82
1847 1923 5.073827 GCCTCCCCTAAAAATATTCTCTCCT 59.926 44.000 0.00 0.00 0.00 3.69
1892 1968 1.003118 CTGCCTAACCTGTTACTGCCA 59.997 52.381 5.04 0.00 0.00 4.92
1907 1983 3.017656 GCCATTGCGCGTTGACGTA 62.018 57.895 8.43 0.00 42.22 3.57
1931 2012 5.880332 ACGGTACTACATTTGCTCATTTGAT 59.120 36.000 0.00 0.00 0.00 2.57
1932 2013 6.183360 ACGGTACTACATTTGCTCATTTGATG 60.183 38.462 0.00 0.00 0.00 3.07
1933 2014 6.037062 CGGTACTACATTTGCTCATTTGATGA 59.963 38.462 0.00 0.00 37.76 2.92
2016 2097 6.226052 GTTCTCCTTTGGCAAGAAATTTGAT 58.774 36.000 0.00 0.00 31.26 2.57
2019 2100 6.493115 TCTCCTTTGGCAAGAAATTTGATACA 59.507 34.615 0.00 0.00 30.57 2.29
2027 2108 7.099120 GGCAAGAAATTTGATACATGTTCCTT 58.901 34.615 2.30 0.00 0.00 3.36
2083 2164 0.607217 CCCAGTGAGACAGCATGCAA 60.607 55.000 21.98 0.00 42.53 4.08
2084 2165 0.803117 CCAGTGAGACAGCATGCAAG 59.197 55.000 21.98 14.52 42.53 4.01
2086 2167 2.357075 CAGTGAGACAGCATGCAAGAT 58.643 47.619 21.98 2.44 42.53 2.40
2087 2168 3.528532 CAGTGAGACAGCATGCAAGATA 58.471 45.455 21.98 0.00 42.53 1.98
2088 2169 3.309138 CAGTGAGACAGCATGCAAGATAC 59.691 47.826 21.98 11.24 42.53 2.24
2089 2170 3.197333 AGTGAGACAGCATGCAAGATACT 59.803 43.478 21.98 13.31 42.53 2.12
2090 2171 3.555139 GTGAGACAGCATGCAAGATACTC 59.445 47.826 21.98 19.59 42.53 2.59
2091 2172 3.129871 GAGACAGCATGCAAGATACTCC 58.870 50.000 21.98 0.00 42.53 3.85
2092 2173 2.158842 AGACAGCATGCAAGATACTCCC 60.159 50.000 21.98 0.00 42.53 4.30
2093 2174 1.842562 ACAGCATGCAAGATACTCCCT 59.157 47.619 21.98 0.00 42.53 4.20
2094 2175 2.158842 ACAGCATGCAAGATACTCCCTC 60.159 50.000 21.98 0.00 42.53 4.30
2095 2176 1.419387 AGCATGCAAGATACTCCCTCC 59.581 52.381 21.98 0.00 0.00 4.30
2096 2177 1.875576 GCATGCAAGATACTCCCTCCG 60.876 57.143 14.21 0.00 0.00 4.63
2097 2178 1.414181 CATGCAAGATACTCCCTCCGT 59.586 52.381 0.00 0.00 0.00 4.69
2098 2179 1.568504 TGCAAGATACTCCCTCCGTT 58.431 50.000 0.00 0.00 0.00 4.44
2099 2180 1.906574 TGCAAGATACTCCCTCCGTTT 59.093 47.619 0.00 0.00 0.00 3.60
2100 2181 2.093658 TGCAAGATACTCCCTCCGTTTC 60.094 50.000 0.00 0.00 0.00 2.78
2101 2182 2.168728 GCAAGATACTCCCTCCGTTTCT 59.831 50.000 0.00 0.00 0.00 2.52
2102 2183 3.383825 GCAAGATACTCCCTCCGTTTCTA 59.616 47.826 0.00 0.00 0.00 2.10
2103 2184 4.142004 GCAAGATACTCCCTCCGTTTCTAA 60.142 45.833 0.00 0.00 0.00 2.10
2104 2185 5.626116 GCAAGATACTCCCTCCGTTTCTAAA 60.626 44.000 0.00 0.00 0.00 1.85
2105 2186 6.583562 CAAGATACTCCCTCCGTTTCTAAAT 58.416 40.000 0.00 0.00 0.00 1.40
2106 2187 7.686127 GCAAGATACTCCCTCCGTTTCTAAATA 60.686 40.741 0.00 0.00 0.00 1.40
2107 2188 8.368668 CAAGATACTCCCTCCGTTTCTAAATAT 58.631 37.037 0.00 0.00 0.00 1.28
2108 2189 9.597681 AAGATACTCCCTCCGTTTCTAAATATA 57.402 33.333 0.00 0.00 0.00 0.86
2109 2190 9.597681 AGATACTCCCTCCGTTTCTAAATATAA 57.402 33.333 0.00 0.00 0.00 0.98
2110 2191 9.857957 GATACTCCCTCCGTTTCTAAATATAAG 57.142 37.037 0.00 0.00 0.00 1.73
2111 2192 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
2112 2193 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
2113 2194 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
2114 2195 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
2115 2196 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
2116 2197 9.392259 CCCTCCGTTTCTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 0.00 2.27
2135 2216 9.883142 AGTCTTTTTAAACATTTCAAATGGACA 57.117 25.926 14.70 0.00 29.40 4.02
2141 2222 8.777865 TTAAACATTTCAAATGGACAACAACA 57.222 26.923 14.70 0.00 0.00 3.33
2142 2223 7.862512 AAACATTTCAAATGGACAACAACAT 57.137 28.000 14.70 0.00 0.00 2.71
2143 2224 8.954950 AAACATTTCAAATGGACAACAACATA 57.045 26.923 14.70 0.00 0.00 2.29
2144 2225 8.954950 AACATTTCAAATGGACAACAACATAA 57.045 26.923 14.70 0.00 0.00 1.90
2145 2226 8.592105 ACATTTCAAATGGACAACAACATAAG 57.408 30.769 14.70 0.00 0.00 1.73
2146 2227 8.420222 ACATTTCAAATGGACAACAACATAAGA 58.580 29.630 14.70 0.00 0.00 2.10
2147 2228 9.258826 CATTTCAAATGGACAACAACATAAGAA 57.741 29.630 1.73 0.00 0.00 2.52
2149 2230 8.815141 TTCAAATGGACAACAACATAAGAATG 57.185 30.769 0.00 0.00 39.17 2.67
2151 2232 9.072375 TCAAATGGACAACAACATAAGAATGTA 57.928 29.630 0.00 0.00 45.79 2.29
2152 2233 9.859427 CAAATGGACAACAACATAAGAATGTAT 57.141 29.630 0.00 0.00 45.79 2.29
2153 2234 9.859427 AAATGGACAACAACATAAGAATGTATG 57.141 29.630 0.00 0.00 45.79 2.39
2154 2235 7.994425 TGGACAACAACATAAGAATGTATGT 57.006 32.000 0.00 0.00 45.79 2.29
2155 2236 9.679661 ATGGACAACAACATAAGAATGTATGTA 57.320 29.630 0.00 0.00 45.79 2.29
2156 2237 9.161629 TGGACAACAACATAAGAATGTATGTAG 57.838 33.333 0.00 0.00 45.79 2.74
2157 2238 9.378551 GGACAACAACATAAGAATGTATGTAGA 57.621 33.333 0.00 0.00 45.79 2.59
2159 2240 9.719355 ACAACAACATAAGAATGTATGTAGACA 57.281 29.630 0.00 0.00 45.79 3.41
2192 2273 9.331282 AGAGTGTATATTCACTAATTTTGCTCC 57.669 33.333 14.24 0.00 46.81 4.70
2193 2274 9.109393 GAGTGTATATTCACTAATTTTGCTCCA 57.891 33.333 14.24 0.00 46.81 3.86
2194 2275 9.632638 AGTGTATATTCACTAATTTTGCTCCAT 57.367 29.630 12.81 0.00 45.31 3.41
2201 2282 9.632638 ATTCACTAATTTTGCTCCATATGTAGT 57.367 29.630 1.24 0.00 0.00 2.73
2202 2283 8.662781 TCACTAATTTTGCTCCATATGTAGTC 57.337 34.615 1.24 0.00 0.00 2.59
2203 2284 8.264347 TCACTAATTTTGCTCCATATGTAGTCA 58.736 33.333 1.24 0.00 0.00 3.41
2204 2285 8.338259 CACTAATTTTGCTCCATATGTAGTCAC 58.662 37.037 1.24 0.00 0.00 3.67
2205 2286 8.267894 ACTAATTTTGCTCCATATGTAGTCACT 58.732 33.333 1.24 0.00 0.00 3.41
2206 2287 6.932356 ATTTTGCTCCATATGTAGTCACTG 57.068 37.500 1.24 0.00 0.00 3.66
2207 2288 4.406648 TTGCTCCATATGTAGTCACTGG 57.593 45.455 1.24 0.00 33.54 4.00
2208 2289 3.374764 TGCTCCATATGTAGTCACTGGT 58.625 45.455 1.24 0.00 33.80 4.00
2209 2290 3.774766 TGCTCCATATGTAGTCACTGGTT 59.225 43.478 1.24 0.00 33.80 3.67
2210 2291 4.959839 TGCTCCATATGTAGTCACTGGTTA 59.040 41.667 1.24 0.00 33.80 2.85
2211 2292 5.069119 TGCTCCATATGTAGTCACTGGTTAG 59.931 44.000 1.24 0.00 33.80 2.34
2212 2293 5.302059 GCTCCATATGTAGTCACTGGTTAGA 59.698 44.000 1.24 0.00 33.80 2.10
2213 2294 6.183360 GCTCCATATGTAGTCACTGGTTAGAA 60.183 42.308 1.24 0.00 33.80 2.10
2214 2295 7.472100 GCTCCATATGTAGTCACTGGTTAGAAT 60.472 40.741 1.24 0.00 33.80 2.40
2215 2296 7.952671 TCCATATGTAGTCACTGGTTAGAATC 58.047 38.462 1.24 0.00 33.80 2.52
2216 2297 7.785028 TCCATATGTAGTCACTGGTTAGAATCT 59.215 37.037 1.24 0.00 33.80 2.40
2217 2298 8.424918 CCATATGTAGTCACTGGTTAGAATCTT 58.575 37.037 1.24 0.00 0.00 2.40
2218 2299 9.823647 CATATGTAGTCACTGGTTAGAATCTTT 57.176 33.333 0.00 0.00 0.00 2.52
2221 2302 8.185506 TGTAGTCACTGGTTAGAATCTTTACA 57.814 34.615 0.00 0.00 0.00 2.41
2222 2303 8.644216 TGTAGTCACTGGTTAGAATCTTTACAA 58.356 33.333 0.00 0.00 0.00 2.41
2223 2304 9.485206 GTAGTCACTGGTTAGAATCTTTACAAA 57.515 33.333 0.00 0.00 0.00 2.83
2224 2305 8.608844 AGTCACTGGTTAGAATCTTTACAAAG 57.391 34.615 0.00 0.00 37.36 2.77
2226 2307 8.496751 GTCACTGGTTAGAATCTTTACAAAGAC 58.503 37.037 6.56 0.00 46.80 3.01
2227 2308 8.429641 TCACTGGTTAGAATCTTTACAAAGACT 58.570 33.333 6.56 3.84 46.80 3.24
2228 2309 9.057089 CACTGGTTAGAATCTTTACAAAGACTT 57.943 33.333 6.56 3.58 46.80 3.01
2245 2326 9.379791 ACAAAGACTTATATTTAAGAACGGAGG 57.620 33.333 9.58 0.00 38.56 4.30
2246 2327 8.827677 CAAAGACTTATATTTAAGAACGGAGGG 58.172 37.037 9.58 0.00 38.56 4.30
2247 2328 7.909485 AGACTTATATTTAAGAACGGAGGGA 57.091 36.000 9.58 0.00 38.56 4.20
2248 2329 7.953752 AGACTTATATTTAAGAACGGAGGGAG 58.046 38.462 9.58 0.00 38.56 4.30
2249 2330 7.564292 AGACTTATATTTAAGAACGGAGGGAGT 59.436 37.037 9.58 0.00 38.56 3.85
2250 2331 8.773033 ACTTATATTTAAGAACGGAGGGAGTA 57.227 34.615 9.58 0.00 38.56 2.59
2251 2332 8.637099 ACTTATATTTAAGAACGGAGGGAGTAC 58.363 37.037 9.58 0.00 38.56 2.73
2252 2333 8.773033 TTATATTTAAGAACGGAGGGAGTACT 57.227 34.615 0.00 0.00 0.00 2.73
2269 2352 8.624670 AGGGAGTACTATATAGGATTCACATGA 58.375 37.037 19.07 0.00 29.28 3.07
2282 2365 7.180663 AGGATTCACATGAGGAATTTTTCTCT 58.819 34.615 15.16 7.08 35.23 3.10
2298 2381 8.594881 ATTTTTCTCTGCGATTAGTATGGTAG 57.405 34.615 0.00 0.00 0.00 3.18
2299 2382 6.710597 TTTCTCTGCGATTAGTATGGTAGT 57.289 37.500 0.00 0.00 0.00 2.73
2300 2383 5.690997 TCTCTGCGATTAGTATGGTAGTG 57.309 43.478 0.00 0.00 0.00 2.74
2321 2409 5.523013 TGCAAACTAGCACAAAAACAAAC 57.477 34.783 0.00 0.00 40.11 2.93
2322 2410 4.991056 TGCAAACTAGCACAAAAACAAACA 59.009 33.333 0.00 0.00 40.11 2.83
2325 2413 6.302078 GCAAACTAGCACAAAAACAAACAAAC 59.698 34.615 0.00 0.00 0.00 2.93
2327 2415 7.484035 AACTAGCACAAAAACAAACAAACAA 57.516 28.000 0.00 0.00 0.00 2.83
2328 2416 7.484035 ACTAGCACAAAAACAAACAAACAAA 57.516 28.000 0.00 0.00 0.00 2.83
2329 2417 7.920738 ACTAGCACAAAAACAAACAAACAAAA 58.079 26.923 0.00 0.00 0.00 2.44
2330 2418 8.398665 ACTAGCACAAAAACAAACAAACAAAAA 58.601 25.926 0.00 0.00 0.00 1.94
2331 2419 9.392021 CTAGCACAAAAACAAACAAACAAAAAT 57.608 25.926 0.00 0.00 0.00 1.82
2387 2477 9.582431 CTCGTCAAAAAGAAGAATAGTATGGTA 57.418 33.333 0.00 0.00 34.30 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.280628 GAGGCGAACTTGGTAGATTGG 58.719 52.381 0.00 0.00 0.00 3.16
94 96 6.729690 ATTTTGAGGGTGAATTTGAAGTCA 57.270 33.333 0.00 0.00 0.00 3.41
158 162 1.291906 CCCCGGTTTGTTTGATGCC 59.708 57.895 0.00 0.00 0.00 4.40
270 275 0.457851 CCGTTTTTGTTGGCACTGGA 59.542 50.000 0.00 0.00 0.00 3.86
280 285 1.961793 TGTCTGCTAGCCGTTTTTGT 58.038 45.000 13.29 0.00 0.00 2.83
407 417 0.595588 ATGCTCGCTACATCTCTCGG 59.404 55.000 0.00 0.00 0.00 4.63
504 529 1.275666 TCATTGGAGGAGAAGGCGAA 58.724 50.000 0.00 0.00 0.00 4.70
523 561 1.608590 CAACCCACTCGCACTTCAAAT 59.391 47.619 0.00 0.00 0.00 2.32
586 624 1.847968 CACACCCCTCCACCCTCTT 60.848 63.158 0.00 0.00 0.00 2.85
675 714 2.594592 GGTCAGCGGTTGCCACTT 60.595 61.111 0.00 0.00 44.31 3.16
717 756 1.212751 CGGTGTGCGAGTCAGATCA 59.787 57.895 0.00 0.00 0.00 2.92
846 885 4.201970 CGGAAATGTTAACGCCCATACATT 60.202 41.667 0.26 0.00 41.55 2.71
848 887 2.678836 CGGAAATGTTAACGCCCATACA 59.321 45.455 0.26 0.00 0.00 2.29
878 917 3.149981 GCCATGGTTTTATAGAGGAGCC 58.850 50.000 14.67 0.00 0.00 4.70
879 918 4.068599 GAGCCATGGTTTTATAGAGGAGC 58.931 47.826 14.67 0.00 0.00 4.70
880 919 4.505742 GGGAGCCATGGTTTTATAGAGGAG 60.506 50.000 14.67 0.00 0.00 3.69
881 920 3.394606 GGGAGCCATGGTTTTATAGAGGA 59.605 47.826 14.67 0.00 0.00 3.71
922 961 8.870075 ATATATAGGCTTTGAGAATGGTTTCC 57.130 34.615 0.00 0.00 31.84 3.13
927 972 9.453572 TGCTTTATATATAGGCTTTGAGAATGG 57.546 33.333 15.77 0.00 0.00 3.16
944 989 9.950496 TTTCTCTCTGTTCTTTCTGCTTTATAT 57.050 29.630 0.00 0.00 0.00 0.86
1021 1066 2.076863 CTTGGACAAGGACGGCTTAAG 58.923 52.381 4.15 0.00 34.87 1.85
1022 1067 1.695242 TCTTGGACAAGGACGGCTTAA 59.305 47.619 11.76 0.00 38.88 1.85
1299 1350 4.731853 TCCTCGGTGATGGGGCCA 62.732 66.667 4.39 0.00 0.00 5.36
1340 1391 0.526524 CTTCATGTCCTCGTCCTCGC 60.527 60.000 0.00 0.00 36.96 5.03
1579 1639 3.855853 GAGAGGAAGAGGCCGGGC 61.856 72.222 22.67 22.67 0.00 6.13
1580 1640 3.532155 CGAGAGGAAGAGGCCGGG 61.532 72.222 2.18 0.00 0.00 5.73
1581 1641 2.756283 ACGAGAGGAAGAGGCCGG 60.756 66.667 0.00 0.00 0.00 6.13
1582 1642 2.776913 GGACGAGAGGAAGAGGCCG 61.777 68.421 0.00 0.00 0.00 6.13
1583 1643 2.428085 GGGACGAGAGGAAGAGGCC 61.428 68.421 0.00 0.00 0.00 5.19
1584 1644 1.380650 AGGGACGAGAGGAAGAGGC 60.381 63.158 0.00 0.00 0.00 4.70
1585 1645 0.257616 AGAGGGACGAGAGGAAGAGG 59.742 60.000 0.00 0.00 0.00 3.69
1586 1646 1.675552 GAGAGGGACGAGAGGAAGAG 58.324 60.000 0.00 0.00 0.00 2.85
1587 1647 0.256464 GGAGAGGGACGAGAGGAAGA 59.744 60.000 0.00 0.00 0.00 2.87
1588 1648 0.257616 AGGAGAGGGACGAGAGGAAG 59.742 60.000 0.00 0.00 0.00 3.46
1589 1649 0.033991 CAGGAGAGGGACGAGAGGAA 60.034 60.000 0.00 0.00 0.00 3.36
1590 1650 1.208844 ACAGGAGAGGGACGAGAGGA 61.209 60.000 0.00 0.00 0.00 3.71
1591 1651 0.323908 AACAGGAGAGGGACGAGAGG 60.324 60.000 0.00 0.00 0.00 3.69
1592 1652 1.474879 GAAACAGGAGAGGGACGAGAG 59.525 57.143 0.00 0.00 0.00 3.20
1593 1653 1.075698 AGAAACAGGAGAGGGACGAGA 59.924 52.381 0.00 0.00 0.00 4.04
1594 1654 1.474879 GAGAAACAGGAGAGGGACGAG 59.525 57.143 0.00 0.00 0.00 4.18
1595 1655 1.203013 TGAGAAACAGGAGAGGGACGA 60.203 52.381 0.00 0.00 0.00 4.20
1661 1736 4.082787 GGTGGAAAGCTCGATCATGAAAAA 60.083 41.667 0.00 0.00 0.00 1.94
1662 1737 3.440173 GGTGGAAAGCTCGATCATGAAAA 59.560 43.478 0.00 0.00 0.00 2.29
1663 1738 3.009723 GGTGGAAAGCTCGATCATGAAA 58.990 45.455 0.00 0.00 0.00 2.69
1780 1856 7.858583 AGTACAGTTTCCGAATTAACAAGAAC 58.141 34.615 0.00 0.00 0.00 3.01
1781 1857 9.715121 ATAGTACAGTTTCCGAATTAACAAGAA 57.285 29.630 0.00 0.00 0.00 2.52
1804 1880 3.054802 AGGCTGGTCAAGGTCTTTGATAG 60.055 47.826 0.18 4.53 46.85 2.08
1805 1881 2.912956 AGGCTGGTCAAGGTCTTTGATA 59.087 45.455 0.18 0.00 46.85 2.15
1806 1882 1.707427 AGGCTGGTCAAGGTCTTTGAT 59.293 47.619 0.18 0.00 46.85 2.57
1847 1923 1.503818 GGAAAGCCGCACGAAACTGA 61.504 55.000 0.00 0.00 0.00 3.41
1892 1968 2.722731 CCGTACGTCAACGCGCAAT 61.723 57.895 15.21 0.00 44.43 3.56
1907 1983 5.242434 TCAAATGAGCAAATGTAGTACCGT 58.758 37.500 0.00 0.00 0.00 4.83
1956 2037 8.470040 AACATTCATGAACATATTTGCTTCAC 57.530 30.769 11.07 0.00 30.84 3.18
2016 2097 7.444183 CCTAGTGTTTTTCAGAAGGAACATGTA 59.556 37.037 13.99 9.76 34.56 2.29
2019 2100 6.486993 GTCCTAGTGTTTTTCAGAAGGAACAT 59.513 38.462 13.99 8.38 38.83 2.71
2055 2136 6.252599 TGCTGTCTCACTGGGATTAATAAT 57.747 37.500 0.00 0.00 0.00 1.28
2056 2137 5.692115 TGCTGTCTCACTGGGATTAATAA 57.308 39.130 0.00 0.00 0.00 1.40
2057 2138 5.614308 CATGCTGTCTCACTGGGATTAATA 58.386 41.667 0.00 0.00 0.00 0.98
2058 2139 4.458397 CATGCTGTCTCACTGGGATTAAT 58.542 43.478 0.00 0.00 0.00 1.40
2059 2140 3.877559 CATGCTGTCTCACTGGGATTAA 58.122 45.455 0.00 0.00 0.00 1.40
2060 2141 2.420547 GCATGCTGTCTCACTGGGATTA 60.421 50.000 11.37 0.00 0.00 1.75
2065 2146 0.803117 CTTGCATGCTGTCTCACTGG 59.197 55.000 20.33 0.00 0.00 4.00
2069 2150 3.431346 GGAGTATCTTGCATGCTGTCTCA 60.431 47.826 20.33 0.00 33.73 3.27
2076 2157 1.875576 CGGAGGGAGTATCTTGCATGC 60.876 57.143 11.82 11.82 33.73 4.06
2083 2164 9.597681 TTATATTTAGAAACGGAGGGAGTATCT 57.402 33.333 0.00 0.00 33.73 1.98
2084 2165 9.857957 CTTATATTTAGAAACGGAGGGAGTATC 57.142 37.037 0.00 0.00 0.00 2.24
2086 2167 8.773033 ACTTATATTTAGAAACGGAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
2087 2168 7.564292 AGACTTATATTTAGAAACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
2088 2169 7.953752 AGACTTATATTTAGAAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
2089 2170 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
2090 2171 8.959705 AAAGACTTATATTTAGAAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
2109 2190 9.883142 TGTCCATTTGAAATGTTTAAAAAGACT 57.117 25.926 15.93 0.00 33.41 3.24
2115 2196 9.219603 TGTTGTTGTCCATTTGAAATGTTTAAA 57.780 25.926 15.93 3.49 0.00 1.52
2116 2197 8.777865 TGTTGTTGTCCATTTGAAATGTTTAA 57.222 26.923 15.93 5.71 0.00 1.52
2117 2198 8.954950 ATGTTGTTGTCCATTTGAAATGTTTA 57.045 26.923 15.93 0.00 0.00 2.01
2118 2199 7.862512 ATGTTGTTGTCCATTTGAAATGTTT 57.137 28.000 15.93 0.00 0.00 2.83
2119 2200 8.954950 TTATGTTGTTGTCCATTTGAAATGTT 57.045 26.923 15.93 0.00 0.00 2.71
2120 2201 8.420222 TCTTATGTTGTTGTCCATTTGAAATGT 58.580 29.630 15.93 0.00 0.00 2.71
2121 2202 8.815141 TCTTATGTTGTTGTCCATTTGAAATG 57.185 30.769 10.84 10.84 0.00 2.32
2123 2204 9.258826 CATTCTTATGTTGTTGTCCATTTGAAA 57.741 29.630 0.00 0.00 0.00 2.69
2124 2205 8.420222 ACATTCTTATGTTGTTGTCCATTTGAA 58.580 29.630 0.00 0.00 42.29 2.69
2125 2206 7.950512 ACATTCTTATGTTGTTGTCCATTTGA 58.049 30.769 0.00 0.00 42.29 2.69
2126 2207 9.859427 ATACATTCTTATGTTGTTGTCCATTTG 57.141 29.630 0.00 0.00 42.29 2.32
2127 2208 9.859427 CATACATTCTTATGTTGTTGTCCATTT 57.141 29.630 0.00 0.00 42.29 2.32
2128 2209 9.023962 ACATACATTCTTATGTTGTTGTCCATT 57.976 29.630 0.00 0.00 42.29 3.16
2129 2210 8.579850 ACATACATTCTTATGTTGTTGTCCAT 57.420 30.769 0.00 0.00 42.29 3.41
2130 2211 7.994425 ACATACATTCTTATGTTGTTGTCCA 57.006 32.000 0.00 0.00 42.29 4.02
2131 2212 9.378551 TCTACATACATTCTTATGTTGTTGTCC 57.621 33.333 1.33 0.00 42.29 4.02
2133 2214 9.719355 TGTCTACATACATTCTTATGTTGTTGT 57.281 29.630 1.33 0.00 42.29 3.32
2166 2247 9.331282 GGAGCAAAATTAGTGAATATACACTCT 57.669 33.333 4.63 0.00 46.36 3.24
2167 2248 9.109393 TGGAGCAAAATTAGTGAATATACACTC 57.891 33.333 4.63 0.00 46.36 3.51
2175 2256 9.632638 ACTACATATGGAGCAAAATTAGTGAAT 57.367 29.630 15.30 0.00 0.00 2.57
2176 2257 9.109393 GACTACATATGGAGCAAAATTAGTGAA 57.891 33.333 15.30 0.00 0.00 3.18
2177 2258 8.264347 TGACTACATATGGAGCAAAATTAGTGA 58.736 33.333 15.30 0.00 0.00 3.41
2178 2259 8.338259 GTGACTACATATGGAGCAAAATTAGTG 58.662 37.037 15.30 0.00 0.00 2.74
2179 2260 8.267894 AGTGACTACATATGGAGCAAAATTAGT 58.732 33.333 15.30 5.78 0.00 2.24
2180 2261 8.554528 CAGTGACTACATATGGAGCAAAATTAG 58.445 37.037 15.30 2.60 0.00 1.73
2181 2262 7.498900 CCAGTGACTACATATGGAGCAAAATTA 59.501 37.037 15.30 0.00 37.70 1.40
2182 2263 6.319658 CCAGTGACTACATATGGAGCAAAATT 59.680 38.462 15.30 0.00 37.70 1.82
2183 2264 5.824624 CCAGTGACTACATATGGAGCAAAAT 59.175 40.000 15.30 0.00 37.70 1.82
2184 2265 5.185454 CCAGTGACTACATATGGAGCAAAA 58.815 41.667 15.30 0.00 37.70 2.44
2185 2266 4.225042 ACCAGTGACTACATATGGAGCAAA 59.775 41.667 15.30 0.00 38.36 3.68
2186 2267 3.774766 ACCAGTGACTACATATGGAGCAA 59.225 43.478 15.30 0.16 38.36 3.91
2187 2268 3.374764 ACCAGTGACTACATATGGAGCA 58.625 45.455 15.30 10.95 38.36 4.26
2188 2269 4.408182 AACCAGTGACTACATATGGAGC 57.592 45.455 15.30 8.47 38.36 4.70
2189 2270 6.961360 TCTAACCAGTGACTACATATGGAG 57.039 41.667 13.77 13.77 38.36 3.86
2190 2271 7.785028 AGATTCTAACCAGTGACTACATATGGA 59.215 37.037 7.80 0.00 38.36 3.41
2191 2272 7.957002 AGATTCTAACCAGTGACTACATATGG 58.043 38.462 7.80 0.00 39.79 2.74
2192 2273 9.823647 AAAGATTCTAACCAGTGACTACATATG 57.176 33.333 0.00 0.00 0.00 1.78
2195 2276 8.812972 TGTAAAGATTCTAACCAGTGACTACAT 58.187 33.333 0.00 0.00 0.00 2.29
2196 2277 8.185506 TGTAAAGATTCTAACCAGTGACTACA 57.814 34.615 0.00 0.00 0.00 2.74
2197 2278 9.485206 TTTGTAAAGATTCTAACCAGTGACTAC 57.515 33.333 0.00 0.00 0.00 2.73
2198 2279 9.706691 CTTTGTAAAGATTCTAACCAGTGACTA 57.293 33.333 0.00 0.00 38.28 2.59
2199 2280 8.429641 TCTTTGTAAAGATTCTAACCAGTGACT 58.570 33.333 3.05 0.00 39.95 3.41
2200 2281 8.496751 GTCTTTGTAAAGATTCTAACCAGTGAC 58.503 37.037 9.98 0.00 45.83 3.67
2201 2282 8.429641 AGTCTTTGTAAAGATTCTAACCAGTGA 58.570 33.333 9.98 0.00 45.83 3.41
2202 2283 8.608844 AGTCTTTGTAAAGATTCTAACCAGTG 57.391 34.615 9.98 0.00 45.83 3.66
2219 2300 9.379791 CCTCCGTTCTTAAATATAAGTCTTTGT 57.620 33.333 0.00 0.00 39.65 2.83
2220 2301 8.827677 CCCTCCGTTCTTAAATATAAGTCTTTG 58.172 37.037 0.00 0.00 39.65 2.77
2221 2302 8.765517 TCCCTCCGTTCTTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 39.65 2.52
2222 2303 8.315220 TCCCTCCGTTCTTAAATATAAGTCTT 57.685 34.615 0.00 0.00 39.65 3.01
2223 2304 7.564292 ACTCCCTCCGTTCTTAAATATAAGTCT 59.436 37.037 0.00 0.00 39.65 3.24
2224 2305 7.724287 ACTCCCTCCGTTCTTAAATATAAGTC 58.276 38.462 0.00 0.00 39.65 3.01
2225 2306 7.672122 ACTCCCTCCGTTCTTAAATATAAGT 57.328 36.000 0.00 0.00 39.65 2.24
2226 2307 8.858094 AGTACTCCCTCCGTTCTTAAATATAAG 58.142 37.037 0.00 0.00 39.97 1.73
2227 2308 8.773033 AGTACTCCCTCCGTTCTTAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
2229 2310 8.953223 ATAGTACTCCCTCCGTTCTTAAATAT 57.047 34.615 0.00 0.00 0.00 1.28
2231 2312 8.953223 ATATAGTACTCCCTCCGTTCTTAAAT 57.047 34.615 0.00 0.00 0.00 1.40
2232 2313 9.512588 CTATATAGTACTCCCTCCGTTCTTAAA 57.487 37.037 0.00 0.00 0.00 1.52
2233 2314 8.105829 CCTATATAGTACTCCCTCCGTTCTTAA 58.894 40.741 0.00 0.00 0.00 1.85
2234 2315 7.459125 TCCTATATAGTACTCCCTCCGTTCTTA 59.541 40.741 0.00 0.00 0.00 2.10
2235 2316 6.274200 TCCTATATAGTACTCCCTCCGTTCTT 59.726 42.308 0.00 0.00 0.00 2.52
2236 2317 5.789575 TCCTATATAGTACTCCCTCCGTTCT 59.210 44.000 0.00 0.00 0.00 3.01
2237 2318 6.059787 TCCTATATAGTACTCCCTCCGTTC 57.940 45.833 0.00 0.00 0.00 3.95
2238 2319 6.655376 ATCCTATATAGTACTCCCTCCGTT 57.345 41.667 0.00 0.00 0.00 4.44
2239 2320 6.217074 TGAATCCTATATAGTACTCCCTCCGT 59.783 42.308 0.00 0.00 0.00 4.69
2240 2321 6.543100 GTGAATCCTATATAGTACTCCCTCCG 59.457 46.154 0.00 0.00 0.00 4.63
2241 2322 7.411808 TGTGAATCCTATATAGTACTCCCTCC 58.588 42.308 0.00 0.00 0.00 4.30
2242 2323 8.908903 CATGTGAATCCTATATAGTACTCCCTC 58.091 40.741 0.00 0.00 0.00 4.30
2243 2324 8.624670 TCATGTGAATCCTATATAGTACTCCCT 58.375 37.037 0.00 0.00 0.00 4.20
2244 2325 8.824756 TCATGTGAATCCTATATAGTACTCCC 57.175 38.462 0.00 0.00 0.00 4.30
2245 2326 8.908903 CCTCATGTGAATCCTATATAGTACTCC 58.091 40.741 0.00 0.00 0.00 3.85
2246 2327 9.688091 TCCTCATGTGAATCCTATATAGTACTC 57.312 37.037 0.00 2.86 0.00 2.59
2269 2352 7.227512 CCATACTAATCGCAGAGAAAAATTCCT 59.772 37.037 0.00 0.00 43.63 3.36
2278 2361 4.023107 GCACTACCATACTAATCGCAGAGA 60.023 45.833 0.00 0.00 43.63 3.10
2282 2365 4.394439 TTGCACTACCATACTAATCGCA 57.606 40.909 0.00 0.00 0.00 5.10
2299 2382 4.991056 TGTTTGTTTTTGTGCTAGTTTGCA 59.009 33.333 0.00 0.00 41.05 4.08
2300 2383 5.523013 TGTTTGTTTTTGTGCTAGTTTGC 57.477 34.783 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.