Multiple sequence alignment - TraesCS7B01G317200
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 | TraesCS7B01G317200 | chr7B | 100.000 | 3050 | 0 | 0 | 1 | 3050 | 567567298 | 567570347 | 0.000000e+00 | 5633.0 |
1 | TraesCS7B01G317200 | chr7A | 95.726 | 1240 | 53 | 0 | 908 | 2147 | 608922507 | 608923746 | 0.000000e+00 | 1997.0 |
2 | TraesCS7B01G317200 | chr7A | 89.547 | 574 | 41 | 8 | 344 | 912 | 608921558 | 608922117 | 0.000000e+00 | 710.0 |
3 | TraesCS7B01G317200 | chr7A | 94.242 | 330 | 17 | 1 | 2723 | 3050 | 608923893 | 608924222 | 1.260000e-138 | 503.0 |
4 | TraesCS7B01G317200 | chr7A | 97.887 | 142 | 3 | 0 | 2193 | 2334 | 608923745 | 608923886 | 2.350000e-61 | 246.0 |
5 | TraesCS7B01G317200 | chr7A | 93.617 | 47 | 3 | 0 | 1 | 47 | 608921511 | 608921557 | 1.520000e-08 | 71.3 |
6 | TraesCS7B01G317200 | chr7D | 94.679 | 996 | 41 | 4 | 1730 | 2719 | 529602978 | 529603967 | 0.000000e+00 | 1535.0 |
7 | TraesCS7B01G317200 | chr7D | 95.783 | 830 | 35 | 0 | 908 | 1737 | 529586467 | 529587296 | 0.000000e+00 | 1339.0 |
8 | TraesCS7B01G317200 | chr7D | 93.706 | 429 | 21 | 6 | 1 | 426 | 529582617 | 529583042 | 3.320000e-179 | 638.0 |
9 | TraesCS7B01G317200 | chr7D | 95.122 | 328 | 16 | 0 | 2723 | 3050 | 529604024 | 529604351 | 4.510000e-143 | 518.0 |
10 | TraesCS7B01G317200 | chr5D | 92.378 | 328 | 25 | 0 | 2723 | 3050 | 169974981 | 169975308 | 4.600000e-128 | 468.0 |
11 | TraesCS7B01G317200 | chr5B | 90.854 | 328 | 30 | 0 | 2723 | 3050 | 593661953 | 593662280 | 1.000000e-119 | 440.0 |
12 | TraesCS7B01G317200 | chr2D | 90.244 | 328 | 32 | 0 | 2723 | 3050 | 386815293 | 386815620 | 2.170000e-116 | 429.0 |
13 | TraesCS7B01G317200 | chr2D | 85.662 | 272 | 38 | 1 | 2780 | 3050 | 110069329 | 110069058 | 4.980000e-73 | 285.0 |
14 | TraesCS7B01G317200 | chr2B | 89.024 | 328 | 36 | 0 | 2723 | 3050 | 458106142 | 458106469 | 1.020000e-109 | 407.0 |
15 | TraesCS7B01G317200 | chr2A | 86.066 | 244 | 31 | 3 | 2473 | 2715 | 106124648 | 106124889 | 3.020000e-65 | 259.0 |
16 | TraesCS7B01G317200 | chr3B | 83.784 | 259 | 41 | 1 | 2793 | 3050 | 663414911 | 663415169 | 8.450000e-61 | 244.0 |
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 | TraesCS7B01G317200 | chr7B | 567567298 | 567570347 | 3049 | False | 5633.00 | 5633 | 100.0000 | 1 | 3050 | 1 | chr7B.!!$F1 | 3049 |
1 | TraesCS7B01G317200 | chr7A | 608921511 | 608924222 | 2711 | False | 705.46 | 1997 | 94.2038 | 1 | 3050 | 5 | chr7A.!!$F1 | 3049 |
2 | TraesCS7B01G317200 | chr7D | 529602978 | 529604351 | 1373 | False | 1026.50 | 1535 | 94.9005 | 1730 | 3050 | 2 | chr7D.!!$F2 | 1320 |
3 | TraesCS7B01G317200 | chr7D | 529582617 | 529587296 | 4679 | False | 988.50 | 1339 | 94.7445 | 1 | 1737 | 2 | chr7D.!!$F1 | 1736 |
AutoCloner calculated primer pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
493 | 3873 | 0.107017 | CCTGGTCATCCGAGGCAAAT | 60.107 | 55.0 | 0.0 | 0.0 | 36.3 | 2.32 | F |
1133 | 4911 | 0.106708 | ATCCGTGGCATAATCAGCGT | 59.893 | 50.0 | 0.0 | 0.0 | 0.0 | 5.07 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1371 | 5149 | 0.035439 | AGGCAACATAGACGGTTGGG | 60.035 | 55.0 | 7.31 | 0.0 | 44.41 | 4.12 | R |
2780 | 6664 | 0.234106 | CGCTGTCTTCACTTGCACAG | 59.766 | 55.0 | 0.00 | 0.0 | 39.47 | 3.66 | R |
All possible primersListed 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. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
28 | 29 | 2.280628 | CAGTCTCTATTTTCCACGGCC | 58.719 | 52.381 | 0.00 | 0.00 | 0.00 | 6.13 |
29 | 30 | 1.906574 | AGTCTCTATTTTCCACGGCCA | 59.093 | 47.619 | 2.24 | 0.00 | 0.00 | 5.36 |
47 | 48 | 2.802247 | GCCAAAACATGTTTTCCAGCTC | 59.198 | 45.455 | 29.21 | 13.33 | 40.45 | 4.09 |
56 | 57 | 3.153919 | TGTTTTCCAGCTCCCACATTAC | 58.846 | 45.455 | 0.00 | 0.00 | 0.00 | 1.89 |
57 | 58 | 2.492088 | GTTTTCCAGCTCCCACATTACC | 59.508 | 50.000 | 0.00 | 0.00 | 0.00 | 2.85 |
100 | 102 | 8.807667 | ATGAAATAAAAAGACTGCAGTGAAAG | 57.192 | 30.769 | 27.27 | 0.00 | 0.00 | 2.62 |
112 | 114 | 2.643551 | CAGTGAAAGGTGTGTCTTGGT | 58.356 | 47.619 | 0.00 | 0.00 | 0.00 | 3.67 |
186 | 189 | 3.328931 | AGACATCTGAGTGGGAACAACAT | 59.671 | 43.478 | 0.00 | 0.00 | 46.06 | 2.71 |
428 | 3807 | 6.538021 | TGTTTGAATTGTGTTTTCCTGATTGG | 59.462 | 34.615 | 0.00 | 0.00 | 37.10 | 3.16 |
478 | 3858 | 8.809468 | TCTAGTTGTCTATATATGTAGCCTGG | 57.191 | 38.462 | 1.74 | 0.00 | 0.00 | 4.45 |
490 | 3870 | 3.785859 | GCCTGGTCATCCGAGGCA | 61.786 | 66.667 | 10.05 | 0.00 | 46.90 | 4.75 |
493 | 3873 | 0.107017 | CCTGGTCATCCGAGGCAAAT | 60.107 | 55.000 | 0.00 | 0.00 | 36.30 | 2.32 |
504 | 3884 | 7.591426 | GTCATCCGAGGCAAATAAATTGATAAC | 59.409 | 37.037 | 0.00 | 0.00 | 41.85 | 1.89 |
531 | 3911 | 7.386848 | AGACATTTTCTCATGCTCAATTTTTGG | 59.613 | 33.333 | 0.00 | 0.00 | 0.00 | 3.28 |
533 | 3913 | 4.603989 | TTCTCATGCTCAATTTTTGGCA | 57.396 | 36.364 | 6.07 | 6.07 | 39.77 | 4.92 |
538 | 3918 | 4.467082 | TCATGCTCAATTTTTGGCATAGGT | 59.533 | 37.500 | 12.58 | 0.00 | 41.98 | 3.08 |
539 | 3919 | 4.888326 | TGCTCAATTTTTGGCATAGGTT | 57.112 | 36.364 | 0.00 | 0.00 | 33.81 | 3.50 |
540 | 3920 | 4.819769 | TGCTCAATTTTTGGCATAGGTTC | 58.180 | 39.130 | 0.00 | 0.00 | 33.81 | 3.62 |
554 | 3934 | 5.241728 | GGCATAGGTTCTTCTTTTTGTGACT | 59.758 | 40.000 | 0.00 | 0.00 | 0.00 | 3.41 |
558 | 3938 | 6.319141 | AGGTTCTTCTTTTTGTGACTATGC | 57.681 | 37.500 | 0.00 | 0.00 | 0.00 | 3.14 |
637 | 4017 | 5.944013 | GAAGTTTTGCTTCCTGAATACTCC | 58.056 | 41.667 | 0.00 | 0.00 | 45.95 | 3.85 |
638 | 4018 | 4.003648 | AGTTTTGCTTCCTGAATACTCCG | 58.996 | 43.478 | 0.00 | 0.00 | 0.00 | 4.63 |
639 | 4019 | 3.695830 | TTTGCTTCCTGAATACTCCGT | 57.304 | 42.857 | 0.00 | 0.00 | 0.00 | 4.69 |
640 | 4020 | 4.811969 | TTTGCTTCCTGAATACTCCGTA | 57.188 | 40.909 | 0.00 | 0.00 | 0.00 | 4.02 |
647 | 4027 | 5.899120 | TCCTGAATACTCCGTATATGCTC | 57.101 | 43.478 | 0.00 | 0.00 | 0.00 | 4.26 |
788 | 4171 | 1.079543 | AGTGCTCTGCTTGCTACCG | 60.080 | 57.895 | 0.00 | 0.00 | 0.00 | 4.02 |
791 | 4174 | 1.374758 | GCTCTGCTTGCTACCGTGT | 60.375 | 57.895 | 0.00 | 0.00 | 0.00 | 4.49 |
849 | 4232 | 3.326836 | TTGTTGTCGCATGACCTATCA | 57.673 | 42.857 | 0.00 | 0.00 | 44.86 | 2.15 |
859 | 4242 | 7.598869 | TGTCGCATGACCTATCATTCTATTTAC | 59.401 | 37.037 | 0.00 | 0.00 | 43.40 | 2.01 |
864 | 4247 | 5.305902 | TGACCTATCATTCTATTTACGGCCA | 59.694 | 40.000 | 2.24 | 0.00 | 0.00 | 5.36 |
878 | 4261 | 0.321653 | CGGCCAGTCTTTGCCTAGTT | 60.322 | 55.000 | 2.24 | 0.00 | 45.71 | 2.24 |
920 | 4698 | 6.691818 | CCTAGTCTGTATTTGTCGTGTCATAC | 59.308 | 42.308 | 0.00 | 0.00 | 0.00 | 2.39 |
945 | 4723 | 6.978659 | CGTACTGTGAGCTAGAATTTCCATTA | 59.021 | 38.462 | 0.00 | 0.00 | 0.00 | 1.90 |
974 | 4752 | 2.355108 | CGATTGTTCCTCACCCACAGAT | 60.355 | 50.000 | 0.00 | 0.00 | 0.00 | 2.90 |
1133 | 4911 | 0.106708 | ATCCGTGGCATAATCAGCGT | 59.893 | 50.000 | 0.00 | 0.00 | 0.00 | 5.07 |
1164 | 4942 | 2.970324 | GCCACCTGCGTGTTCGAA | 60.970 | 61.111 | 0.00 | 0.00 | 38.41 | 3.71 |
1341 | 5119 | 1.757306 | CAGTGAGGTGCCTCTGGTT | 59.243 | 57.895 | 17.96 | 0.35 | 43.12 | 3.67 |
1633 | 5411 | 0.770499 | TCACTTCCTTGTGGCATCCA | 59.230 | 50.000 | 0.00 | 0.00 | 38.40 | 3.41 |
1639 | 5417 | 1.171308 | CCTTGTGGCATCCAGTGAAG | 58.829 | 55.000 | 0.00 | 0.00 | 32.34 | 3.02 |
1683 | 5461 | 1.860078 | CTTTCGTGGACGGTTCTGC | 59.140 | 57.895 | 0.00 | 0.00 | 40.29 | 4.26 |
1686 | 5464 | 3.103911 | CGTGGACGGTTCTGCGAC | 61.104 | 66.667 | 0.00 | 0.00 | 35.37 | 5.19 |
1692 | 5470 | 1.214367 | GACGGTTCTGCGACTTCAAA | 58.786 | 50.000 | 0.00 | 0.00 | 0.00 | 2.69 |
1743 | 5521 | 2.092323 | TGGTCACCTCTAGATGACACG | 58.908 | 52.381 | 22.08 | 0.00 | 45.83 | 4.49 |
1779 | 5557 | 2.037772 | CAGCTGGTTTCTGTACAGAGGT | 59.962 | 50.000 | 23.97 | 15.33 | 38.88 | 3.85 |
1854 | 5632 | 3.625897 | CAGTGGGGTGGCTCGACA | 61.626 | 66.667 | 0.00 | 0.00 | 0.00 | 4.35 |
1998 | 5776 | 0.400213 | TCCCGGCTTCAATTGTGACT | 59.600 | 50.000 | 5.13 | 0.00 | 31.90 | 3.41 |
2016 | 5794 | 1.372087 | CTGAGGAACGGCATTGGCTC | 61.372 | 60.000 | 8.71 | 0.00 | 40.87 | 4.70 |
2145 | 5923 | 8.210265 | AGGAAGATTTTATTGTTTTGCTTTGGA | 58.790 | 29.630 | 0.00 | 0.00 | 0.00 | 3.53 |
2146 | 5924 | 8.835439 | GGAAGATTTTATTGTTTTGCTTTGGAA | 58.165 | 29.630 | 0.00 | 0.00 | 0.00 | 3.53 |
2150 | 5928 | 8.854979 | ATTTTATTGTTTTGCTTTGGAAAAGC | 57.145 | 26.923 | 15.99 | 15.99 | 43.29 | 3.51 |
2157 | 5935 | 2.888834 | GCTTTGGAAAAGCAGGTTCA | 57.111 | 45.000 | 17.52 | 0.00 | 42.56 | 3.18 |
2158 | 5936 | 3.177997 | GCTTTGGAAAAGCAGGTTCAA | 57.822 | 42.857 | 17.52 | 0.00 | 42.56 | 2.69 |
2159 | 5937 | 2.866156 | GCTTTGGAAAAGCAGGTTCAAC | 59.134 | 45.455 | 17.52 | 0.00 | 42.56 | 3.18 |
2160 | 5938 | 3.678529 | GCTTTGGAAAAGCAGGTTCAACA | 60.679 | 43.478 | 17.52 | 0.00 | 42.56 | 3.33 |
2161 | 5939 | 4.502962 | CTTTGGAAAAGCAGGTTCAACAA | 58.497 | 39.130 | 0.00 | 0.00 | 0.00 | 2.83 |
2162 | 5940 | 3.518634 | TGGAAAAGCAGGTTCAACAAC | 57.481 | 42.857 | 0.00 | 0.00 | 0.00 | 3.32 |
2163 | 5941 | 2.828520 | TGGAAAAGCAGGTTCAACAACA | 59.171 | 40.909 | 0.00 | 0.00 | 33.70 | 3.33 |
2164 | 5942 | 3.450457 | TGGAAAAGCAGGTTCAACAACAT | 59.550 | 39.130 | 0.00 | 0.00 | 33.70 | 2.71 |
2165 | 5943 | 4.081198 | TGGAAAAGCAGGTTCAACAACATT | 60.081 | 37.500 | 0.00 | 0.00 | 33.70 | 2.71 |
2166 | 5944 | 4.270808 | GGAAAAGCAGGTTCAACAACATTG | 59.729 | 41.667 | 0.00 | 0.00 | 33.70 | 2.82 |
2167 | 5945 | 4.734398 | AAAGCAGGTTCAACAACATTGA | 57.266 | 36.364 | 0.00 | 0.00 | 33.70 | 2.57 |
2168 | 5946 | 4.942761 | AAGCAGGTTCAACAACATTGAT | 57.057 | 36.364 | 0.00 | 0.00 | 33.70 | 2.57 |
2169 | 5947 | 4.942761 | AGCAGGTTCAACAACATTGATT | 57.057 | 36.364 | 0.00 | 0.00 | 33.70 | 2.57 |
2170 | 5948 | 4.624015 | AGCAGGTTCAACAACATTGATTG | 58.376 | 39.130 | 0.00 | 0.45 | 33.70 | 2.67 |
2171 | 5949 | 4.341806 | AGCAGGTTCAACAACATTGATTGA | 59.658 | 37.500 | 0.00 | 2.69 | 33.70 | 2.57 |
2172 | 5950 | 5.011329 | AGCAGGTTCAACAACATTGATTGAT | 59.989 | 36.000 | 0.00 | 0.00 | 33.70 | 2.57 |
2173 | 5951 | 5.119588 | GCAGGTTCAACAACATTGATTGATG | 59.880 | 40.000 | 0.00 | 2.87 | 34.58 | 3.07 |
2174 | 5952 | 6.218019 | CAGGTTCAACAACATTGATTGATGT | 58.782 | 36.000 | 0.00 | 0.00 | 42.56 | 3.06 |
2175 | 5953 | 7.369607 | CAGGTTCAACAACATTGATTGATGTA | 58.630 | 34.615 | 0.00 | 0.00 | 40.14 | 2.29 |
2176 | 5954 | 7.326789 | CAGGTTCAACAACATTGATTGATGTAC | 59.673 | 37.037 | 0.00 | 1.70 | 40.14 | 2.90 |
2177 | 5955 | 7.014134 | AGGTTCAACAACATTGATTGATGTACA | 59.986 | 33.333 | 0.00 | 0.00 | 40.14 | 2.90 |
2178 | 5956 | 7.326789 | GGTTCAACAACATTGATTGATGTACAG | 59.673 | 37.037 | 0.33 | 0.00 | 40.14 | 2.74 |
2179 | 5957 | 7.509141 | TCAACAACATTGATTGATGTACAGT | 57.491 | 32.000 | 0.33 | 0.00 | 40.14 | 3.55 |
2180 | 5958 | 7.939782 | TCAACAACATTGATTGATGTACAGTT | 58.060 | 30.769 | 0.33 | 0.00 | 40.14 | 3.16 |
2181 | 5959 | 9.061435 | TCAACAACATTGATTGATGTACAGTTA | 57.939 | 29.630 | 0.33 | 0.00 | 40.14 | 2.24 |
2182 | 5960 | 9.117145 | CAACAACATTGATTGATGTACAGTTAC | 57.883 | 33.333 | 0.33 | 0.00 | 40.14 | 2.50 |
2183 | 5961 | 8.621532 | ACAACATTGATTGATGTACAGTTACT | 57.378 | 30.769 | 0.33 | 0.00 | 39.34 | 2.24 |
2184 | 5962 | 8.721478 | ACAACATTGATTGATGTACAGTTACTC | 58.279 | 33.333 | 0.33 | 0.00 | 39.34 | 2.59 |
2185 | 5963 | 8.939929 | CAACATTGATTGATGTACAGTTACTCT | 58.060 | 33.333 | 0.33 | 0.00 | 39.25 | 3.24 |
2186 | 5964 | 9.507329 | AACATTGATTGATGTACAGTTACTCTT | 57.493 | 29.630 | 0.33 | 0.00 | 39.25 | 2.85 |
2191 | 5969 | 9.803315 | TGATTGATGTACAGTTACTCTTATCAC | 57.197 | 33.333 | 0.33 | 0.00 | 0.00 | 3.06 |
2306 | 6132 | 2.158534 | TGTTGCTAGACCAACCACCATT | 60.159 | 45.455 | 9.80 | 0.00 | 43.36 | 3.16 |
2391 | 6217 | 4.381411 | GCTGAAGTGAAGAACCTTGTAGT | 58.619 | 43.478 | 0.00 | 0.00 | 0.00 | 2.73 |
2392 | 6218 | 4.449405 | GCTGAAGTGAAGAACCTTGTAGTC | 59.551 | 45.833 | 0.00 | 0.00 | 0.00 | 2.59 |
2393 | 6219 | 5.601662 | CTGAAGTGAAGAACCTTGTAGTCA | 58.398 | 41.667 | 0.00 | 0.00 | 0.00 | 3.41 |
2394 | 6220 | 6.174720 | TGAAGTGAAGAACCTTGTAGTCAT | 57.825 | 37.500 | 0.00 | 0.00 | 0.00 | 3.06 |
2395 | 6221 | 7.297936 | TGAAGTGAAGAACCTTGTAGTCATA | 57.702 | 36.000 | 0.00 | 0.00 | 0.00 | 2.15 |
2396 | 6222 | 7.378966 | TGAAGTGAAGAACCTTGTAGTCATAG | 58.621 | 38.462 | 0.00 | 0.00 | 0.00 | 2.23 |
2480 | 6306 | 2.619147 | TCCAAATTGGATGCAAATGCG | 58.381 | 42.857 | 11.23 | 1.85 | 42.67 | 4.73 |
2491 | 6317 | 2.411904 | TGCAAATGCGGGAAATGAAAC | 58.588 | 42.857 | 0.35 | 0.00 | 45.83 | 2.78 |
2538 | 6364 | 9.277783 | GTCATTCTATTGGCTATCTTTGTATGT | 57.722 | 33.333 | 0.00 | 0.00 | 0.00 | 2.29 |
2546 | 6372 | 9.950680 | ATTGGCTATCTTTGTATGTAATTTTCG | 57.049 | 29.630 | 0.00 | 0.00 | 0.00 | 3.46 |
2577 | 6403 | 4.346418 | AGCGAGAAGGGAGAATACATGAAT | 59.654 | 41.667 | 0.00 | 0.00 | 0.00 | 2.57 |
2585 | 6411 | 7.083062 | AGGGAGAATACATGAATATCAGCAA | 57.917 | 36.000 | 0.00 | 0.00 | 0.00 | 3.91 |
2668 | 6499 | 5.503927 | TCTGAAGGAATCAAATTCTGGAGG | 58.496 | 41.667 | 0.18 | 0.00 | 37.67 | 4.30 |
2669 | 6500 | 4.019174 | TGAAGGAATCAAATTCTGGAGGC | 58.981 | 43.478 | 0.18 | 0.00 | 39.24 | 4.70 |
2719 | 6550 | 4.227197 | AGTATGGTAATAGCAGCTGGAGT | 58.773 | 43.478 | 17.12 | 0.00 | 0.00 | 3.85 |
2720 | 6551 | 3.760580 | ATGGTAATAGCAGCTGGAGTC | 57.239 | 47.619 | 17.12 | 0.00 | 0.00 | 3.36 |
2721 | 6552 | 2.752030 | TGGTAATAGCAGCTGGAGTCT | 58.248 | 47.619 | 17.12 | 6.32 | 0.00 | 3.24 |
2758 | 6642 | 3.065787 | ATCCAGATGGGCTGCCACC | 62.066 | 63.158 | 22.05 | 8.51 | 43.50 | 4.61 |
2778 | 6662 | 4.035091 | CACCGAGTGATTGTGAAAACTGAA | 59.965 | 41.667 | 0.00 | 0.00 | 35.23 | 3.02 |
2780 | 6664 | 5.049405 | ACCGAGTGATTGTGAAAACTGAATC | 60.049 | 40.000 | 0.00 | 0.00 | 0.00 | 2.52 |
2788 | 6672 | 4.923893 | TGTGAAAACTGAATCTGTGCAAG | 58.076 | 39.130 | 0.00 | 0.00 | 0.00 | 4.01 |
2960 | 6844 | 4.341235 | TGCGTATGATGCTAAACTAGGAGT | 59.659 | 41.667 | 0.00 | 0.00 | 0.00 | 3.85 |
2963 | 6847 | 5.175856 | CGTATGATGCTAAACTAGGAGTTGC | 59.824 | 44.000 | 0.00 | 0.00 | 38.66 | 4.17 |
3011 | 6895 | 4.819105 | ATCCAGACCTTGTAAATGACGA | 57.181 | 40.909 | 0.00 | 0.00 | 0.00 | 4.20 |
3022 | 6906 | 3.818210 | TGTAAATGACGATGTTGTTGGCT | 59.182 | 39.130 | 0.00 | 0.00 | 0.00 | 4.75 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
28 | 29 | 3.181467 | TGGGAGCTGGAAAACATGTTTTG | 60.181 | 43.478 | 34.88 | 23.25 | 42.26 | 2.44 |
29 | 30 | 3.037549 | TGGGAGCTGGAAAACATGTTTT | 58.962 | 40.909 | 31.40 | 31.40 | 44.59 | 2.43 |
77 | 79 | 7.168135 | CACCTTTCACTGCAGTCTTTTTATTTC | 59.832 | 37.037 | 18.64 | 0.00 | 0.00 | 2.17 |
81 | 83 | 4.947388 | ACACCTTTCACTGCAGTCTTTTTA | 59.053 | 37.500 | 18.64 | 0.00 | 0.00 | 1.52 |
82 | 84 | 3.763897 | ACACCTTTCACTGCAGTCTTTTT | 59.236 | 39.130 | 18.64 | 0.00 | 0.00 | 1.94 |
100 | 102 | 4.759693 | TGATCATGTTTACCAAGACACACC | 59.240 | 41.667 | 0.00 | 0.00 | 0.00 | 4.16 |
171 | 174 | 2.172505 | AGTGACATGTTGTTCCCACTCA | 59.827 | 45.455 | 9.22 | 0.00 | 30.23 | 3.41 |
186 | 189 | 1.423541 | ACTTGGTGCCCAATAGTGACA | 59.576 | 47.619 | 7.06 | 0.00 | 43.07 | 3.58 |
203 | 206 | 3.844211 | TGCATGGTAGGGAAACTAGACTT | 59.156 | 43.478 | 0.00 | 0.00 | 30.77 | 3.01 |
212 | 215 | 2.685106 | TGGTTTTGCATGGTAGGGAA | 57.315 | 45.000 | 0.00 | 0.00 | 0.00 | 3.97 |
308 | 311 | 4.644685 | CCTTGGTGGAAAGTTTCTCAGAAA | 59.355 | 41.667 | 15.05 | 0.00 | 38.35 | 2.52 |
378 | 381 | 0.539438 | AGTGATGAGGCGGGCAAAAA | 60.539 | 50.000 | 3.78 | 0.00 | 0.00 | 1.94 |
428 | 3807 | 2.450476 | GACCATGGGGGCATGATTATC | 58.550 | 52.381 | 18.09 | 0.00 | 44.16 | 1.75 |
438 | 3817 | 4.166144 | ACAACTAGAATAAGACCATGGGGG | 59.834 | 45.833 | 18.09 | 0.00 | 44.81 | 5.40 |
478 | 3858 | 5.499139 | TCAATTTATTTGCCTCGGATGAC | 57.501 | 39.130 | 0.00 | 0.00 | 35.16 | 3.06 |
504 | 3884 | 7.884816 | AAAATTGAGCATGAGAAAATGTCTG | 57.115 | 32.000 | 0.00 | 0.00 | 36.41 | 3.51 |
514 | 3894 | 5.047847 | CCTATGCCAAAAATTGAGCATGAG | 58.952 | 41.667 | 19.86 | 14.91 | 42.96 | 2.90 |
518 | 3898 | 4.527816 | AGAACCTATGCCAAAAATTGAGCA | 59.472 | 37.500 | 8.11 | 8.11 | 39.77 | 4.26 |
531 | 3911 | 6.319141 | AGTCACAAAAAGAAGAACCTATGC | 57.681 | 37.500 | 0.00 | 0.00 | 0.00 | 3.14 |
533 | 3913 | 7.885399 | AGCATAGTCACAAAAAGAAGAACCTAT | 59.115 | 33.333 | 0.00 | 0.00 | 0.00 | 2.57 |
538 | 3918 | 6.942532 | ACAGCATAGTCACAAAAAGAAGAA | 57.057 | 33.333 | 0.00 | 0.00 | 0.00 | 2.52 |
539 | 3919 | 6.942532 | AACAGCATAGTCACAAAAAGAAGA | 57.057 | 33.333 | 0.00 | 0.00 | 0.00 | 2.87 |
540 | 3920 | 7.992180 | AAAACAGCATAGTCACAAAAAGAAG | 57.008 | 32.000 | 0.00 | 0.00 | 0.00 | 2.85 |
676 | 4056 | 8.094798 | AGTTAGCAAATCAGTTTTCATCGTAA | 57.905 | 30.769 | 0.00 | 0.00 | 0.00 | 3.18 |
829 | 4212 | 3.326836 | TGATAGGTCATGCGACAACAA | 57.673 | 42.857 | 0.00 | 0.00 | 44.54 | 2.83 |
831 | 4214 | 4.122776 | AGAATGATAGGTCATGCGACAAC | 58.877 | 43.478 | 0.00 | 0.00 | 44.01 | 3.32 |
832 | 4215 | 4.406648 | AGAATGATAGGTCATGCGACAA | 57.593 | 40.909 | 0.00 | 0.00 | 44.01 | 3.18 |
834 | 4217 | 7.201359 | CGTAAATAGAATGATAGGTCATGCGAC | 60.201 | 40.741 | 0.00 | 0.00 | 44.01 | 5.19 |
835 | 4218 | 6.806739 | CGTAAATAGAATGATAGGTCATGCGA | 59.193 | 38.462 | 0.00 | 0.00 | 44.01 | 5.10 |
837 | 4220 | 6.183360 | GCCGTAAATAGAATGATAGGTCATGC | 60.183 | 42.308 | 0.00 | 0.00 | 44.20 | 4.06 |
838 | 4221 | 6.313905 | GGCCGTAAATAGAATGATAGGTCATG | 59.686 | 42.308 | 0.00 | 0.00 | 44.20 | 3.07 |
839 | 4222 | 6.013725 | TGGCCGTAAATAGAATGATAGGTCAT | 60.014 | 38.462 | 0.00 | 0.00 | 46.91 | 3.06 |
840 | 4223 | 5.305902 | TGGCCGTAAATAGAATGATAGGTCA | 59.694 | 40.000 | 0.00 | 0.00 | 39.04 | 4.02 |
842 | 4225 | 5.307196 | ACTGGCCGTAAATAGAATGATAGGT | 59.693 | 40.000 | 0.00 | 0.00 | 0.00 | 3.08 |
843 | 4226 | 5.794894 | ACTGGCCGTAAATAGAATGATAGG | 58.205 | 41.667 | 0.00 | 0.00 | 0.00 | 2.57 |
849 | 4232 | 4.335594 | GCAAAGACTGGCCGTAAATAGAAT | 59.664 | 41.667 | 0.00 | 0.00 | 0.00 | 2.40 |
887 | 4271 | 4.949856 | ACAAATACAGACTAGGCAATTGGG | 59.050 | 41.667 | 7.72 | 0.00 | 0.00 | 4.12 |
920 | 4698 | 4.744570 | TGGAAATTCTAGCTCACAGTACG | 58.255 | 43.478 | 0.00 | 0.00 | 0.00 | 3.67 |
945 | 4723 | 4.504858 | GGTGAGGAACAATCGATTAGTGT | 58.495 | 43.478 | 10.97 | 2.51 | 38.23 | 3.55 |
974 | 4752 | 8.112822 | TGATGAAACCCAATTTCTTACCAGATA | 58.887 | 33.333 | 1.48 | 0.00 | 46.05 | 1.98 |
1164 | 4942 | 4.684134 | AGCAGCCACCCGCCATTT | 62.684 | 61.111 | 0.00 | 0.00 | 38.78 | 2.32 |
1341 | 5119 | 0.105778 | TGGTCTCAATGCACACGACA | 59.894 | 50.000 | 0.00 | 0.00 | 0.00 | 4.35 |
1371 | 5149 | 0.035439 | AGGCAACATAGACGGTTGGG | 60.035 | 55.000 | 7.31 | 0.00 | 44.41 | 4.12 |
1381 | 5159 | 2.682846 | CCCAGGGCAGGCAACATA | 59.317 | 61.111 | 0.00 | 0.00 | 41.41 | 2.29 |
1633 | 5411 | 4.314121 | GAGATGAGCACAACTTCTTCACT | 58.686 | 43.478 | 0.00 | 0.00 | 29.49 | 3.41 |
1639 | 5417 | 1.127582 | GCACGAGATGAGCACAACTTC | 59.872 | 52.381 | 0.00 | 0.00 | 33.95 | 3.01 |
1683 | 5461 | 4.214119 | TCCAGCTTGAAGAATTTGAAGTCG | 59.786 | 41.667 | 0.00 | 0.00 | 0.00 | 4.18 |
1686 | 5464 | 4.863131 | GCATCCAGCTTGAAGAATTTGAAG | 59.137 | 41.667 | 0.00 | 0.00 | 41.15 | 3.02 |
1743 | 5521 | 0.964358 | AGCTGCAACCATCAAGCTCC | 60.964 | 55.000 | 1.02 | 0.00 | 0.00 | 4.70 |
1998 | 5776 | 1.377202 | GAGCCAATGCCGTTCCTCA | 60.377 | 57.895 | 0.00 | 0.00 | 38.69 | 3.86 |
2016 | 5794 | 1.337823 | CCACCAAAGACACTAGACCGG | 60.338 | 57.143 | 0.00 | 0.00 | 0.00 | 5.28 |
2088 | 5866 | 7.531716 | CAAGTTTGTGTTGGTACTCAAGTTTA | 58.468 | 34.615 | 0.00 | 0.00 | 38.54 | 2.01 |
2145 | 5923 | 5.083533 | TCAATGTTGTTGAACCTGCTTTT | 57.916 | 34.783 | 0.00 | 0.00 | 0.00 | 2.27 |
2146 | 5924 | 4.734398 | TCAATGTTGTTGAACCTGCTTT | 57.266 | 36.364 | 0.00 | 0.00 | 0.00 | 3.51 |
2147 | 5925 | 4.942761 | ATCAATGTTGTTGAACCTGCTT | 57.057 | 36.364 | 0.00 | 0.00 | 31.55 | 3.91 |
2148 | 5926 | 4.341806 | TCAATCAATGTTGTTGAACCTGCT | 59.658 | 37.500 | 0.00 | 0.00 | 30.79 | 4.24 |
2149 | 5927 | 4.619973 | TCAATCAATGTTGTTGAACCTGC | 58.380 | 39.130 | 0.00 | 0.00 | 30.79 | 4.85 |
2150 | 5928 | 6.218019 | ACATCAATCAATGTTGTTGAACCTG | 58.782 | 36.000 | 11.74 | 9.52 | 38.51 | 4.00 |
2151 | 5929 | 6.409524 | ACATCAATCAATGTTGTTGAACCT | 57.590 | 33.333 | 11.74 | 0.00 | 38.51 | 3.50 |
2152 | 5930 | 7.144661 | TGTACATCAATCAATGTTGTTGAACC | 58.855 | 34.615 | 0.00 | 0.00 | 41.20 | 3.62 |
2153 | 5931 | 7.862372 | ACTGTACATCAATCAATGTTGTTGAAC | 59.138 | 33.333 | 0.00 | 0.00 | 41.20 | 3.18 |
2154 | 5932 | 7.939782 | ACTGTACATCAATCAATGTTGTTGAA | 58.060 | 30.769 | 0.00 | 0.00 | 41.20 | 2.69 |
2155 | 5933 | 7.509141 | ACTGTACATCAATCAATGTTGTTGA | 57.491 | 32.000 | 0.00 | 10.75 | 41.20 | 3.18 |
2156 | 5934 | 9.117145 | GTAACTGTACATCAATCAATGTTGTTG | 57.883 | 33.333 | 0.00 | 0.00 | 41.20 | 3.33 |
2157 | 5935 | 9.066892 | AGTAACTGTACATCAATCAATGTTGTT | 57.933 | 29.630 | 0.00 | 0.00 | 41.20 | 2.83 |
2158 | 5936 | 8.621532 | AGTAACTGTACATCAATCAATGTTGT | 57.378 | 30.769 | 0.00 | 0.00 | 42.94 | 3.32 |
2159 | 5937 | 8.939929 | AGAGTAACTGTACATCAATCAATGTTG | 58.060 | 33.333 | 0.00 | 0.00 | 40.32 | 3.33 |
2160 | 5938 | 9.507329 | AAGAGTAACTGTACATCAATCAATGTT | 57.493 | 29.630 | 0.00 | 0.00 | 40.32 | 2.71 |
2165 | 5943 | 9.803315 | GTGATAAGAGTAACTGTACATCAATCA | 57.197 | 33.333 | 0.00 | 2.24 | 32.12 | 2.57 |
2166 | 5944 | 9.803315 | TGTGATAAGAGTAACTGTACATCAATC | 57.197 | 33.333 | 0.00 | 0.00 | 32.12 | 2.67 |
2168 | 5946 | 9.639601 | CTTGTGATAAGAGTAACTGTACATCAA | 57.360 | 33.333 | 0.00 | 0.00 | 32.12 | 2.57 |
2169 | 5947 | 8.803235 | ACTTGTGATAAGAGTAACTGTACATCA | 58.197 | 33.333 | 0.00 | 0.00 | 32.12 | 3.07 |
2170 | 5948 | 9.640963 | AACTTGTGATAAGAGTAACTGTACATC | 57.359 | 33.333 | 0.00 | 0.00 | 32.12 | 3.06 |
2171 | 5949 | 9.640963 | GAACTTGTGATAAGAGTAACTGTACAT | 57.359 | 33.333 | 0.00 | 0.00 | 32.12 | 2.29 |
2172 | 5950 | 8.635328 | TGAACTTGTGATAAGAGTAACTGTACA | 58.365 | 33.333 | 0.00 | 0.00 | 32.12 | 2.90 |
2173 | 5951 | 8.913656 | GTGAACTTGTGATAAGAGTAACTGTAC | 58.086 | 37.037 | 0.00 | 0.00 | 0.00 | 2.90 |
2174 | 5952 | 8.635328 | TGTGAACTTGTGATAAGAGTAACTGTA | 58.365 | 33.333 | 0.00 | 0.00 | 0.00 | 2.74 |
2175 | 5953 | 7.497595 | TGTGAACTTGTGATAAGAGTAACTGT | 58.502 | 34.615 | 0.00 | 0.00 | 0.00 | 3.55 |
2176 | 5954 | 7.946655 | TGTGAACTTGTGATAAGAGTAACTG | 57.053 | 36.000 | 0.00 | 0.00 | 0.00 | 3.16 |
2177 | 5955 | 8.958119 | TTTGTGAACTTGTGATAAGAGTAACT | 57.042 | 30.769 | 0.00 | 0.00 | 0.00 | 2.24 |
2178 | 5956 | 8.827677 | ACTTTGTGAACTTGTGATAAGAGTAAC | 58.172 | 33.333 | 0.00 | 0.00 | 0.00 | 2.50 |
2179 | 5957 | 8.958119 | ACTTTGTGAACTTGTGATAAGAGTAA | 57.042 | 30.769 | 0.00 | 0.00 | 0.00 | 2.24 |
2180 | 5958 | 8.421784 | AGACTTTGTGAACTTGTGATAAGAGTA | 58.578 | 33.333 | 0.00 | 0.00 | 0.00 | 2.59 |
2181 | 5959 | 7.275920 | AGACTTTGTGAACTTGTGATAAGAGT | 58.724 | 34.615 | 0.00 | 0.00 | 0.00 | 3.24 |
2182 | 5960 | 7.721286 | AGACTTTGTGAACTTGTGATAAGAG | 57.279 | 36.000 | 0.00 | 0.00 | 0.00 | 2.85 |
2183 | 5961 | 7.467267 | GCAAGACTTTGTGAACTTGTGATAAGA | 60.467 | 37.037 | 0.00 | 0.00 | 40.88 | 2.10 |
2184 | 5962 | 6.634436 | GCAAGACTTTGTGAACTTGTGATAAG | 59.366 | 38.462 | 0.00 | 0.00 | 40.88 | 1.73 |
2185 | 5963 | 6.094742 | TGCAAGACTTTGTGAACTTGTGATAA | 59.905 | 34.615 | 0.00 | 0.00 | 40.88 | 1.75 |
2186 | 5964 | 5.588246 | TGCAAGACTTTGTGAACTTGTGATA | 59.412 | 36.000 | 0.00 | 0.00 | 40.88 | 2.15 |
2187 | 5965 | 4.398988 | TGCAAGACTTTGTGAACTTGTGAT | 59.601 | 37.500 | 0.00 | 0.00 | 40.88 | 3.06 |
2188 | 5966 | 3.755905 | TGCAAGACTTTGTGAACTTGTGA | 59.244 | 39.130 | 0.00 | 0.00 | 40.88 | 3.58 |
2189 | 5967 | 4.095410 | TGCAAGACTTTGTGAACTTGTG | 57.905 | 40.909 | 0.00 | 0.00 | 40.88 | 3.33 |
2190 | 5968 | 4.737054 | CTTGCAAGACTTTGTGAACTTGT | 58.263 | 39.130 | 22.31 | 0.00 | 40.88 | 3.16 |
2191 | 5969 | 3.549070 | GCTTGCAAGACTTTGTGAACTTG | 59.451 | 43.478 | 30.39 | 0.00 | 41.46 | 3.16 |
2306 | 6132 | 9.379770 | TCCACTTGAGATGATATACAGGATTTA | 57.620 | 33.333 | 0.00 | 0.00 | 0.00 | 1.40 |
2365 | 6191 | 0.235926 | GGTTCTTCACTTCAGCGTGC | 59.764 | 55.000 | 0.00 | 0.00 | 34.92 | 5.34 |
2440 | 6266 | 3.309954 | GGAAGTGCCGTAGTGATGATTTC | 59.690 | 47.826 | 0.00 | 0.00 | 0.00 | 2.17 |
2480 | 6306 | 4.343814 | TCAGAAGGTTTGGTTTCATTTCCC | 59.656 | 41.667 | 0.00 | 0.00 | 0.00 | 3.97 |
2491 | 6317 | 7.452880 | TGACAGATTTTATCAGAAGGTTTGG | 57.547 | 36.000 | 0.00 | 0.00 | 0.00 | 3.28 |
2509 | 6335 | 7.568349 | ACAAAGATAGCCAATAGAATGACAGA | 58.432 | 34.615 | 0.00 | 0.00 | 0.00 | 3.41 |
2524 | 6350 | 9.651718 | CCTTCGAAAATTACATACAAAGATAGC | 57.348 | 33.333 | 0.00 | 0.00 | 0.00 | 2.97 |
2538 | 6364 | 6.091713 | CCTTCTCGCTTTACCTTCGAAAATTA | 59.908 | 38.462 | 0.00 | 0.00 | 0.00 | 1.40 |
2539 | 6365 | 5.106673 | CCTTCTCGCTTTACCTTCGAAAATT | 60.107 | 40.000 | 0.00 | 0.00 | 0.00 | 1.82 |
2546 | 6372 | 2.496470 | TCTCCCTTCTCGCTTTACCTTC | 59.504 | 50.000 | 0.00 | 0.00 | 0.00 | 3.46 |
2577 | 6403 | 4.949856 | GGACCATCTTTCCTTTTGCTGATA | 59.050 | 41.667 | 0.00 | 0.00 | 0.00 | 2.15 |
2585 | 6411 | 2.491675 | GTCCGGACCATCTTTCCTTT | 57.508 | 50.000 | 24.75 | 0.00 | 0.00 | 3.11 |
2613 | 6439 | 6.639686 | CCATCAGTGTTGACTTTCAAGATTTG | 59.360 | 38.462 | 2.63 | 0.00 | 37.00 | 2.32 |
2614 | 6440 | 6.322201 | ACCATCAGTGTTGACTTTCAAGATTT | 59.678 | 34.615 | 2.63 | 0.00 | 37.00 | 2.17 |
2645 | 6471 | 5.503927 | CCTCCAGAATTTGATTCCTTCAGA | 58.496 | 41.667 | 0.00 | 0.00 | 40.13 | 3.27 |
2665 | 6496 | 1.340991 | TGATAACAAAGCCCCAGCCTC | 60.341 | 52.381 | 0.00 | 0.00 | 41.25 | 4.70 |
2668 | 6499 | 1.106285 | CCTGATAACAAAGCCCCAGC | 58.894 | 55.000 | 0.00 | 0.00 | 40.32 | 4.85 |
2669 | 6500 | 2.755103 | GTTCCTGATAACAAAGCCCCAG | 59.245 | 50.000 | 0.00 | 0.00 | 0.00 | 4.45 |
2700 | 6531 | 3.312890 | AGACTCCAGCTGCTATTACCAT | 58.687 | 45.455 | 8.66 | 0.00 | 0.00 | 3.55 |
2751 | 6635 | 0.320683 | TCACAATCACTCGGTGGCAG | 60.321 | 55.000 | 0.00 | 0.00 | 33.87 | 4.85 |
2758 | 6642 | 6.075918 | CAGATTCAGTTTTCACAATCACTCG | 58.924 | 40.000 | 0.00 | 0.00 | 0.00 | 4.18 |
2778 | 6662 | 2.149578 | GCTGTCTTCACTTGCACAGAT | 58.850 | 47.619 | 2.11 | 0.00 | 38.90 | 2.90 |
2780 | 6664 | 0.234106 | CGCTGTCTTCACTTGCACAG | 59.766 | 55.000 | 0.00 | 0.00 | 39.47 | 3.66 |
2788 | 6672 | 0.880278 | TTGCTCACCGCTGTCTTCAC | 60.880 | 55.000 | 0.00 | 0.00 | 40.11 | 3.18 |
2905 | 6789 | 6.892658 | ATGTGCAACTAAATTACAAGTCCA | 57.107 | 33.333 | 0.00 | 0.00 | 38.04 | 4.02 |
3011 | 6895 | 3.149196 | CTGGACAAGTAGCCAACAACAT | 58.851 | 45.455 | 0.00 | 0.00 | 32.95 | 2.71 |
3022 | 6906 | 2.616524 | AGTACAAGGGCTGGACAAGTA | 58.383 | 47.619 | 0.00 | 0.00 | 42.01 | 2.24 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.