Multiple sequence alignment - TraesCS1B01G192600
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 | TraesCS1B01G192600 | chr1B | 100.000 | 4898 | 0 | 0 | 1 | 4898 | 344842927 | 344838030 | 0.000000e+00 | 9046.0 |
1 | TraesCS1B01G192600 | chr1A | 94.518 | 2955 | 124 | 18 | 1847 | 4775 | 334451724 | 334448782 | 0.000000e+00 | 4525.0 |
2 | TraesCS1B01G192600 | chr1A | 94.050 | 1042 | 38 | 12 | 710 | 1733 | 334452842 | 334451807 | 0.000000e+00 | 1559.0 |
3 | TraesCS1B01G192600 | chr1A | 94.173 | 635 | 31 | 4 | 4268 | 4896 | 334416718 | 334416084 | 0.000000e+00 | 963.0 |
4 | TraesCS1B01G192600 | chr1A | 93.651 | 252 | 12 | 3 | 410 | 661 | 334453094 | 334452847 | 1.660000e-99 | 374.0 |
5 | TraesCS1B01G192600 | chr1A | 90.435 | 115 | 6 | 3 | 1747 | 1856 | 584082913 | 584082799 | 3.950000e-31 | 147.0 |
6 | TraesCS1B01G192600 | chr1A | 89.024 | 82 | 8 | 1 | 2519 | 2600 | 334451125 | 334451045 | 3.120000e-17 | 100.0 |
7 | TraesCS1B01G192600 | chr1D | 93.984 | 2959 | 135 | 20 | 1845 | 4775 | 267986754 | 267989697 | 0.000000e+00 | 4438.0 |
8 | TraesCS1B01G192600 | chr1D | 95.131 | 1068 | 31 | 11 | 681 | 1733 | 267985612 | 267986673 | 0.000000e+00 | 1664.0 |
9 | TraesCS1B01G192600 | chr1D | 89.000 | 400 | 35 | 5 | 4219 | 4616 | 268461813 | 268462205 | 2.050000e-133 | 486.0 |
10 | TraesCS1B01G192600 | chr1D | 94.805 | 231 | 11 | 1 | 410 | 640 | 267985368 | 267985597 | 4.660000e-95 | 359.0 |
11 | TraesCS1B01G192600 | chr1D | 85.714 | 231 | 16 | 5 | 5 | 220 | 267984812 | 267985040 | 1.370000e-55 | 228.0 |
12 | TraesCS1B01G192600 | chr1D | 81.145 | 297 | 29 | 16 | 4612 | 4883 | 268467360 | 268467654 | 3.840000e-51 | 213.0 |
13 | TraesCS1B01G192600 | chr1D | 91.463 | 82 | 6 | 1 | 2519 | 2600 | 267987355 | 267987435 | 1.440000e-20 | 111.0 |
14 | TraesCS1B01G192600 | chr6A | 98.913 | 92 | 0 | 1 | 1758 | 1848 | 503767444 | 503767535 | 3.920000e-36 | 163.0 |
15 | TraesCS1B01G192600 | chr4A | 97.826 | 92 | 2 | 0 | 1753 | 1844 | 59254318 | 59254227 | 5.070000e-35 | 159.0 |
16 | TraesCS1B01G192600 | chr3B | 96.842 | 95 | 2 | 1 | 1755 | 1849 | 447014633 | 447014540 | 1.830000e-34 | 158.0 |
17 | TraesCS1B01G192600 | chr5D | 94.949 | 99 | 5 | 0 | 1744 | 1842 | 364250210 | 364250308 | 6.560000e-34 | 156.0 |
18 | TraesCS1B01G192600 | chr6D | 95.876 | 97 | 1 | 3 | 1752 | 1846 | 79346548 | 79346453 | 2.360000e-33 | 154.0 |
19 | TraesCS1B01G192600 | chr6B | 95.789 | 95 | 4 | 0 | 1750 | 1844 | 546656566 | 546656660 | 2.360000e-33 | 154.0 |
20 | TraesCS1B01G192600 | chr7B | 88.793 | 116 | 11 | 2 | 1749 | 1864 | 20241016 | 20240903 | 1.840000e-29 | 141.0 |
21 | TraesCS1B01G192600 | chr3D | 91.346 | 104 | 6 | 3 | 1744 | 1846 | 414368803 | 414368702 | 6.610000e-29 | 139.0 |
22 | TraesCS1B01G192600 | chr2A | 85.714 | 84 | 11 | 1 | 307 | 389 | 706531654 | 706531571 | 2.430000e-13 | 87.9 |
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 | TraesCS1B01G192600 | chr1B | 344838030 | 344842927 | 4897 | True | 9046.0 | 9046 | 100.00000 | 1 | 4898 | 1 | chr1B.!!$R1 | 4897 |
1 | TraesCS1B01G192600 | chr1A | 334448782 | 334453094 | 4312 | True | 1639.5 | 4525 | 92.81075 | 410 | 4775 | 4 | chr1A.!!$R3 | 4365 |
2 | TraesCS1B01G192600 | chr1A | 334416084 | 334416718 | 634 | True | 963.0 | 963 | 94.17300 | 4268 | 4896 | 1 | chr1A.!!$R1 | 628 |
3 | TraesCS1B01G192600 | chr1D | 267984812 | 267989697 | 4885 | False | 1360.0 | 4438 | 92.21940 | 5 | 4775 | 5 | chr1D.!!$F3 | 4770 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
267 | 413 | 0.893270 | CACCGGGCATGGAAAAGACA | 60.893 | 55.0 | 6.32 | 0.0 | 0.00 | 3.41 | F |
268 | 414 | 0.893727 | ACCGGGCATGGAAAAGACAC | 60.894 | 55.0 | 6.32 | 0.0 | 0.00 | 3.67 | F |
269 | 415 | 0.893270 | CCGGGCATGGAAAAGACACA | 60.893 | 55.0 | 0.00 | 0.0 | 0.00 | 3.72 | F |
2003 | 2203 | 0.530744 | GTCATAGGGTCGAGTGTGCA | 59.469 | 55.0 | 0.00 | 0.0 | 0.00 | 4.57 | F |
2139 | 2339 | 0.257328 | TGGGCTTTGTTGTCCACTCA | 59.743 | 50.0 | 0.00 | 0.0 | 36.71 | 3.41 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1858 | 2058 | 0.184451 | CTGGGTAGGGCCGTACTCTA | 59.816 | 60.000 | 30.30 | 18.84 | 38.44 | 2.43 | R |
1944 | 2144 | 5.011533 | TCCCTATGCTTCTAGATGCTTCTTC | 59.988 | 44.000 | 25.75 | 2.78 | 33.17 | 2.87 | R |
2139 | 2339 | 5.247110 | AGGAATGACTGACAGTGTGAGTATT | 59.753 | 40.000 | 15.74 | 14.20 | 28.74 | 1.89 | R |
3774 | 3996 | 1.228124 | CGGGCAAGTGGGTTCTTCA | 60.228 | 57.895 | 0.00 | 0.00 | 0.00 | 3.02 | R |
4093 | 4318 | 4.165372 | GGTCCAGGTAGATATTTGGTTCCA | 59.835 | 45.833 | 0.00 | 0.00 | 32.51 | 3.53 | 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 |
---|---|---|---|---|---|---|---|---|---|
41 | 42 | 4.673441 | ACATGTGTATGAAGTCGCTACTC | 58.327 | 43.478 | 0.00 | 0.00 | 37.73 | 2.59 |
56 | 57 | 3.066760 | CGCTACTCCATCAGTGATACACA | 59.933 | 47.826 | 5.03 | 0.00 | 36.74 | 3.72 |
87 | 89 | 2.286184 | CCGTTATGAAGTATTGCGGTGC | 60.286 | 50.000 | 0.00 | 0.00 | 33.23 | 5.01 |
98 | 114 | 3.423154 | GCGGTGCGAAGAAGGTGG | 61.423 | 66.667 | 0.00 | 0.00 | 0.00 | 4.61 |
100 | 116 | 2.032681 | GGTGCGAAGAAGGTGGCT | 59.967 | 61.111 | 0.00 | 0.00 | 0.00 | 4.75 |
122 | 138 | 3.719144 | GGCGCGCGTTTAGGTGTT | 61.719 | 61.111 | 32.35 | 0.00 | 0.00 | 3.32 |
177 | 193 | 4.097741 | TGCAACTATGTTAACCCATCATGC | 59.902 | 41.667 | 2.48 | 7.63 | 32.69 | 4.06 |
207 | 223 | 3.900966 | TGAGAGAAGACCCATCACATG | 57.099 | 47.619 | 0.00 | 0.00 | 0.00 | 3.21 |
220 | 236 | 4.400251 | CCCATCACATGCAATTCTTGTACT | 59.600 | 41.667 | 0.00 | 0.00 | 32.52 | 2.73 |
221 | 237 | 5.589855 | CCCATCACATGCAATTCTTGTACTA | 59.410 | 40.000 | 0.00 | 0.00 | 32.52 | 1.82 |
222 | 238 | 6.095300 | CCCATCACATGCAATTCTTGTACTAA | 59.905 | 38.462 | 0.00 | 0.00 | 32.52 | 2.24 |
223 | 239 | 6.968904 | CCATCACATGCAATTCTTGTACTAAC | 59.031 | 38.462 | 0.00 | 0.00 | 32.52 | 2.34 |
224 | 240 | 7.361971 | CCATCACATGCAATTCTTGTACTAACA | 60.362 | 37.037 | 0.00 | 0.00 | 32.52 | 2.41 |
225 | 241 | 7.686438 | TCACATGCAATTCTTGTACTAACAT | 57.314 | 32.000 | 0.00 | 0.00 | 34.97 | 2.71 |
226 | 242 | 7.529158 | TCACATGCAATTCTTGTACTAACATG | 58.471 | 34.615 | 0.00 | 0.00 | 38.59 | 3.21 |
253 | 399 | 2.912771 | TGTAATTCACTATGCCACCGG | 58.087 | 47.619 | 0.00 | 0.00 | 0.00 | 5.28 |
264 | 410 | 3.287445 | CCACCGGGCATGGAAAAG | 58.713 | 61.111 | 6.32 | 0.00 | 39.87 | 2.27 |
265 | 411 | 1.304052 | CCACCGGGCATGGAAAAGA | 60.304 | 57.895 | 6.32 | 0.00 | 39.87 | 2.52 |
266 | 412 | 1.595093 | CCACCGGGCATGGAAAAGAC | 61.595 | 60.000 | 6.32 | 0.00 | 39.87 | 3.01 |
267 | 413 | 0.893270 | CACCGGGCATGGAAAAGACA | 60.893 | 55.000 | 6.32 | 0.00 | 0.00 | 3.41 |
268 | 414 | 0.893727 | ACCGGGCATGGAAAAGACAC | 60.894 | 55.000 | 6.32 | 0.00 | 0.00 | 3.67 |
269 | 415 | 0.893270 | CCGGGCATGGAAAAGACACA | 60.893 | 55.000 | 0.00 | 0.00 | 0.00 | 3.72 |
270 | 416 | 1.176527 | CGGGCATGGAAAAGACACAT | 58.823 | 50.000 | 0.00 | 0.00 | 0.00 | 3.21 |
271 | 417 | 1.133025 | CGGGCATGGAAAAGACACATC | 59.867 | 52.381 | 0.00 | 0.00 | 0.00 | 3.06 |
272 | 418 | 2.450476 | GGGCATGGAAAAGACACATCT | 58.550 | 47.619 | 0.00 | 0.00 | 36.42 | 2.90 |
273 | 419 | 2.165030 | GGGCATGGAAAAGACACATCTG | 59.835 | 50.000 | 0.00 | 0.00 | 34.48 | 2.90 |
274 | 420 | 2.821969 | GGCATGGAAAAGACACATCTGT | 59.178 | 45.455 | 0.00 | 0.00 | 34.48 | 3.41 |
275 | 421 | 3.256631 | GGCATGGAAAAGACACATCTGTT | 59.743 | 43.478 | 0.00 | 0.00 | 34.85 | 3.16 |
276 | 422 | 4.262164 | GGCATGGAAAAGACACATCTGTTT | 60.262 | 41.667 | 0.00 | 0.00 | 32.04 | 2.83 |
277 | 423 | 5.291971 | GCATGGAAAAGACACATCTGTTTT | 58.708 | 37.500 | 0.00 | 0.00 | 32.04 | 2.43 |
278 | 424 | 5.754890 | GCATGGAAAAGACACATCTGTTTTT | 59.245 | 36.000 | 0.00 | 0.00 | 36.50 | 1.94 |
308 | 454 | 2.294233 | AGACACATCTTTGTTTGCGCAT | 59.706 | 40.909 | 12.75 | 0.00 | 32.34 | 4.73 |
309 | 455 | 2.396601 | ACACATCTTTGTTTGCGCATG | 58.603 | 42.857 | 12.75 | 6.34 | 32.34 | 4.06 |
482 | 661 | 3.859961 | CACAACTCACGGTGTATCATCTC | 59.140 | 47.826 | 8.17 | 0.00 | 0.00 | 2.75 |
571 | 750 | 7.336931 | GCAGTTTCTTACAATAAAGGATGGAGA | 59.663 | 37.037 | 0.00 | 0.00 | 0.00 | 3.71 |
623 | 802 | 1.485124 | AGGTGTGTATGATCTCGCCA | 58.515 | 50.000 | 0.00 | 0.00 | 34.98 | 5.69 |
624 | 803 | 1.831106 | AGGTGTGTATGATCTCGCCAA | 59.169 | 47.619 | 0.00 | 0.00 | 34.98 | 4.52 |
657 | 837 | 6.127366 | GGTGTGTATGGACCATCATCATTTTT | 60.127 | 38.462 | 11.17 | 0.00 | 31.97 | 1.94 |
658 | 838 | 6.974622 | GTGTGTATGGACCATCATCATTTTTC | 59.025 | 38.462 | 11.17 | 0.00 | 0.00 | 2.29 |
660 | 840 | 7.396907 | TGTGTATGGACCATCATCATTTTTCTT | 59.603 | 33.333 | 11.17 | 0.00 | 0.00 | 2.52 |
661 | 841 | 8.253113 | GTGTATGGACCATCATCATTTTTCTTT | 58.747 | 33.333 | 11.17 | 0.00 | 0.00 | 2.52 |
662 | 842 | 8.814931 | TGTATGGACCATCATCATTTTTCTTTT | 58.185 | 29.630 | 11.17 | 0.00 | 0.00 | 2.27 |
757 | 937 | 7.775561 | GCAAATGGGATATTTACCCCTATCTAG | 59.224 | 40.741 | 0.00 | 0.00 | 46.21 | 2.43 |
758 | 938 | 8.836735 | CAAATGGGATATTTACCCCTATCTAGT | 58.163 | 37.037 | 0.00 | 0.00 | 46.21 | 2.57 |
760 | 940 | 9.503369 | AATGGGATATTTACCCCTATCTAGTAC | 57.497 | 37.037 | 0.00 | 0.00 | 46.21 | 2.73 |
950 | 1132 | 2.271777 | CAACCCTAGAACCCAACCCTA | 58.728 | 52.381 | 0.00 | 0.00 | 0.00 | 3.53 |
956 | 1138 | 3.309994 | CCTAGAACCCAACCCTACTCTCT | 60.310 | 52.174 | 0.00 | 0.00 | 0.00 | 3.10 |
1212 | 1400 | 2.445274 | CGCGGATTATATGCGTGCT | 58.555 | 52.632 | 0.00 | 0.00 | 46.67 | 4.40 |
1247 | 1435 | 2.857618 | CGAATCCGAGCTGCTATCTAC | 58.142 | 52.381 | 0.15 | 0.00 | 38.22 | 2.59 |
1493 | 1690 | 1.196808 | GCGTTTGACAACCACATCGAT | 59.803 | 47.619 | 0.00 | 0.00 | 0.00 | 3.59 |
1554 | 1751 | 5.526479 | CACATGGACCATGAGAATGTAAGAG | 59.474 | 44.000 | 35.91 | 9.45 | 43.81 | 2.85 |
1559 | 1756 | 5.940470 | GGACCATGAGAATGTAAGAGTTGTT | 59.060 | 40.000 | 0.00 | 0.00 | 0.00 | 2.83 |
1594 | 1792 | 6.667007 | TGTTGACATGTATAGTGATTGCTG | 57.333 | 37.500 | 0.00 | 0.00 | 0.00 | 4.41 |
1595 | 1793 | 6.172630 | TGTTGACATGTATAGTGATTGCTGT | 58.827 | 36.000 | 0.00 | 0.00 | 0.00 | 4.40 |
1606 | 1804 | 2.549754 | GTGATTGCTGTGTGTACTTGCT | 59.450 | 45.455 | 0.00 | 0.00 | 0.00 | 3.91 |
1622 | 1820 | 4.504858 | ACTTGCTGTACCACTATAAGTGC | 58.495 | 43.478 | 1.43 | 0.00 | 44.63 | 4.40 |
1631 | 1829 | 2.679837 | CCACTATAAGTGCTTGCTGTGG | 59.320 | 50.000 | 13.23 | 13.23 | 44.63 | 4.17 |
1714 | 1912 | 4.625742 | TGTGAACGCTGCTCTTATTAGTTC | 59.374 | 41.667 | 0.00 | 2.16 | 37.56 | 3.01 |
1720 | 1918 | 5.351740 | ACGCTGCTCTTATTAGTTCCTTTTC | 59.648 | 40.000 | 0.00 | 0.00 | 0.00 | 2.29 |
1723 | 1923 | 7.024171 | GCTGCTCTTATTAGTTCCTTTTCAAC | 58.976 | 38.462 | 0.00 | 0.00 | 0.00 | 3.18 |
1736 | 1936 | 9.508642 | AGTTCCTTTTCAACACCAAATTTAAAA | 57.491 | 25.926 | 0.00 | 0.00 | 0.00 | 1.52 |
1739 | 1939 | 9.898152 | TCCTTTTCAACACCAAATTTAAAATCT | 57.102 | 25.926 | 0.00 | 0.00 | 0.00 | 2.40 |
1743 | 1943 | 8.514136 | TTCAACACCAAATTTAAAATCTAGCG | 57.486 | 30.769 | 0.00 | 0.00 | 0.00 | 4.26 |
1744 | 1944 | 7.087639 | TCAACACCAAATTTAAAATCTAGCGG | 58.912 | 34.615 | 0.00 | 0.00 | 0.00 | 5.52 |
1745 | 1945 | 6.584185 | ACACCAAATTTAAAATCTAGCGGT | 57.416 | 33.333 | 0.00 | 0.00 | 0.00 | 5.68 |
1746 | 1946 | 6.386654 | ACACCAAATTTAAAATCTAGCGGTG | 58.613 | 36.000 | 12.79 | 12.79 | 44.49 | 4.94 |
1747 | 1947 | 6.207810 | ACACCAAATTTAAAATCTAGCGGTGA | 59.792 | 34.615 | 18.49 | 0.00 | 42.16 | 4.02 |
1748 | 1948 | 7.093945 | ACACCAAATTTAAAATCTAGCGGTGAT | 60.094 | 33.333 | 18.49 | 0.00 | 42.16 | 3.06 |
1750 | 1950 | 8.311109 | ACCAAATTTAAAATCTAGCGGTGATTT | 58.689 | 29.630 | 14.87 | 14.87 | 43.44 | 2.17 |
1761 | 1961 | 9.640963 | AATCTAGCGGTGATTTAATATGTACTC | 57.359 | 33.333 | 0.00 | 0.00 | 30.84 | 2.59 |
1762 | 1962 | 7.600065 | TCTAGCGGTGATTTAATATGTACTCC | 58.400 | 38.462 | 0.00 | 0.00 | 0.00 | 3.85 |
1763 | 1963 | 5.548406 | AGCGGTGATTTAATATGTACTCCC | 58.452 | 41.667 | 0.00 | 0.00 | 0.00 | 4.30 |
1765 | 1965 | 5.638234 | GCGGTGATTTAATATGTACTCCCTC | 59.362 | 44.000 | 0.00 | 0.00 | 0.00 | 4.30 |
1767 | 1967 | 6.868864 | CGGTGATTTAATATGTACTCCCTCTG | 59.131 | 42.308 | 0.00 | 0.00 | 0.00 | 3.35 |
1768 | 1968 | 7.471539 | CGGTGATTTAATATGTACTCCCTCTGT | 60.472 | 40.741 | 0.00 | 0.00 | 0.00 | 3.41 |
1784 | 1984 | 8.862085 | ACTCCCTCTGTAAACTAATATAAGAGC | 58.138 | 37.037 | 0.00 | 0.00 | 0.00 | 4.09 |
1786 | 1986 | 9.381038 | TCCCTCTGTAAACTAATATAAGAGCAT | 57.619 | 33.333 | 0.00 | 0.00 | 0.00 | 3.79 |
1815 | 2015 | 9.733219 | AGATCACTAACTTAGTAATCTAAACGC | 57.267 | 33.333 | 11.59 | 0.00 | 41.03 | 4.84 |
1816 | 2016 | 9.733219 | GATCACTAACTTAGTAATCTAAACGCT | 57.267 | 33.333 | 5.18 | 0.00 | 37.23 | 5.07 |
1817 | 2017 | 9.733219 | ATCACTAACTTAGTAATCTAAACGCTC | 57.267 | 33.333 | 0.95 | 0.00 | 37.23 | 5.03 |
1818 | 2018 | 8.954350 | TCACTAACTTAGTAATCTAAACGCTCT | 58.046 | 33.333 | 0.95 | 0.00 | 37.23 | 4.09 |
1819 | 2019 | 9.570488 | CACTAACTTAGTAATCTAAACGCTCTT | 57.430 | 33.333 | 0.95 | 0.00 | 37.23 | 2.85 |
1833 | 2033 | 9.669353 | TCTAAACGCTCTTATATTAGTTTACGG | 57.331 | 33.333 | 0.00 | 0.00 | 34.29 | 4.02 |
1834 | 2034 | 9.669353 | CTAAACGCTCTTATATTAGTTTACGGA | 57.331 | 33.333 | 0.00 | 0.00 | 34.29 | 4.69 |
1835 | 2035 | 8.571461 | AAACGCTCTTATATTAGTTTACGGAG | 57.429 | 34.615 | 0.00 | 0.00 | 31.14 | 4.63 |
1836 | 2036 | 6.675987 | ACGCTCTTATATTAGTTTACGGAGG | 58.324 | 40.000 | 0.00 | 0.00 | 0.00 | 4.30 |
1837 | 2037 | 6.091437 | CGCTCTTATATTAGTTTACGGAGGG | 58.909 | 44.000 | 0.00 | 0.00 | 0.00 | 4.30 |
1838 | 2038 | 6.072286 | CGCTCTTATATTAGTTTACGGAGGGA | 60.072 | 42.308 | 0.00 | 0.00 | 34.63 | 4.20 |
1839 | 2039 | 7.314393 | GCTCTTATATTAGTTTACGGAGGGAG | 58.686 | 42.308 | 0.00 | 0.00 | 0.00 | 4.30 |
1840 | 2040 | 7.039853 | GCTCTTATATTAGTTTACGGAGGGAGT | 60.040 | 40.741 | 0.00 | 0.00 | 0.00 | 3.85 |
1841 | 2041 | 9.512588 | CTCTTATATTAGTTTACGGAGGGAGTA | 57.487 | 37.037 | 0.00 | 0.00 | 0.00 | 2.59 |
1842 | 2042 | 9.289782 | TCTTATATTAGTTTACGGAGGGAGTAC | 57.710 | 37.037 | 0.00 | 0.00 | 0.00 | 2.73 |
1843 | 2043 | 9.294614 | CTTATATTAGTTTACGGAGGGAGTACT | 57.705 | 37.037 | 0.00 | 0.00 | 0.00 | 2.73 |
1858 | 2058 | 8.706521 | GGAGGGAGTACTTAGAATGTAAATCTT | 58.293 | 37.037 | 0.00 | 0.00 | 0.00 | 2.40 |
1944 | 2144 | 8.997621 | TGTGGTAATACTTAAGCTTCTTACTG | 57.002 | 34.615 | 0.00 | 0.00 | 0.00 | 2.74 |
2003 | 2203 | 0.530744 | GTCATAGGGTCGAGTGTGCA | 59.469 | 55.000 | 0.00 | 0.00 | 0.00 | 4.57 |
2011 | 2211 | 0.577269 | GTCGAGTGTGCACTGACAAC | 59.423 | 55.000 | 19.41 | 7.30 | 42.66 | 3.32 |
2050 | 2250 | 6.036844 | GGCTTCTACTAGTGGTTTTATTTCCG | 59.963 | 42.308 | 5.39 | 0.00 | 0.00 | 4.30 |
2139 | 2339 | 0.257328 | TGGGCTTTGTTGTCCACTCA | 59.743 | 50.000 | 0.00 | 0.00 | 36.71 | 3.41 |
2290 | 2490 | 4.002906 | TGTTACTGAGTTGATGGACACC | 57.997 | 45.455 | 0.00 | 0.00 | 0.00 | 4.16 |
2293 | 2493 | 1.000955 | ACTGAGTTGATGGACACCGAC | 59.999 | 52.381 | 0.00 | 0.00 | 0.00 | 4.79 |
2299 | 2499 | 4.480480 | ATGGACACCGACCTCCAT | 57.520 | 55.556 | 2.76 | 2.76 | 41.67 | 3.41 |
2371 | 2571 | 1.975407 | CCTCCTGCTTGTGCCAAGG | 60.975 | 63.158 | 14.32 | 2.25 | 38.71 | 3.61 |
2407 | 2607 | 5.830912 | TGCTGGAATTGTAGTTGAAACAAG | 58.169 | 37.500 | 0.00 | 0.00 | 40.00 | 3.16 |
2454 | 2654 | 5.538118 | TCGATTGACATGTACTCACAGTTT | 58.462 | 37.500 | 0.00 | 0.00 | 38.30 | 2.66 |
2519 | 2719 | 6.183360 | GCTTTGTCCTCCAGAAATCATAAGTC | 60.183 | 42.308 | 0.00 | 0.00 | 0.00 | 3.01 |
2554 | 2754 | 5.238583 | TCTGTGCCTTCTTTAGTTCTTAGC | 58.761 | 41.667 | 0.00 | 0.00 | 0.00 | 3.09 |
2570 | 2770 | 7.625469 | AGTTCTTAGCTTAGGTTTATGAGCTT | 58.375 | 34.615 | 0.00 | 0.00 | 42.46 | 3.74 |
2574 | 2774 | 9.765795 | TCTTAGCTTAGGTTTATGAGCTTTATC | 57.234 | 33.333 | 0.00 | 0.00 | 42.46 | 1.75 |
2602 | 2802 | 8.243426 | TCCAGCAATCATAAGTTACATGTTTTC | 58.757 | 33.333 | 2.30 | 0.00 | 0.00 | 2.29 |
2760 | 2960 | 1.609072 | GCAAGGACCACTTCAGAAACC | 59.391 | 52.381 | 0.00 | 0.00 | 37.29 | 3.27 |
2841 | 3041 | 4.836825 | ACTGTTCACAATATACTGCTGCT | 58.163 | 39.130 | 0.00 | 0.00 | 0.00 | 4.24 |
2865 | 3065 | 1.072331 | GATGTCTGGTCAGTTGGGTGT | 59.928 | 52.381 | 0.00 | 0.00 | 0.00 | 4.16 |
2898 | 3098 | 7.043565 | GTGAAATTATTACTCGTCAACCCCTA | 58.956 | 38.462 | 0.00 | 0.00 | 0.00 | 3.53 |
2966 | 3166 | 0.382636 | GGTTTGTTCAACTCGTCGCG | 60.383 | 55.000 | 0.00 | 0.00 | 35.46 | 5.87 |
2969 | 3169 | 0.525882 | TTGTTCAACTCGTCGCGTGA | 60.526 | 50.000 | 5.77 | 4.67 | 0.00 | 4.35 |
2970 | 3170 | 0.318360 | TGTTCAACTCGTCGCGTGAT | 60.318 | 50.000 | 5.77 | 0.00 | 0.00 | 3.06 |
3030 | 3230 | 6.971184 | GTCTATTTGGAAGCTGTCAATCAATG | 59.029 | 38.462 | 3.30 | 0.00 | 0.00 | 2.82 |
3037 | 3237 | 4.634184 | AGCTGTCAATCAATGAAGATGC | 57.366 | 40.909 | 0.00 | 0.00 | 40.50 | 3.91 |
3059 | 3259 | 4.143221 | GCGTCTGTTTCTGAGCTTCTTTAG | 60.143 | 45.833 | 0.00 | 0.00 | 0.00 | 1.85 |
3108 | 3330 | 9.665719 | TTGAAACAATAGCATCTGACTGTATTA | 57.334 | 29.630 | 0.00 | 0.00 | 0.00 | 0.98 |
3147 | 3369 | 6.583806 | GCATCTTGTGTTTGAATAGAAGTTGG | 59.416 | 38.462 | 9.07 | 0.00 | 0.00 | 3.77 |
3160 | 3382 | 7.441760 | TGAATAGAAGTTGGTTACTTTTACGCA | 59.558 | 33.333 | 0.00 | 0.00 | 47.00 | 5.24 |
3202 | 3424 | 6.118852 | TGTATTTTGCATCTGGTAGCATGTA | 58.881 | 36.000 | 0.00 | 0.00 | 40.94 | 2.29 |
3286 | 3508 | 2.485814 | GCAAGTTTCTGTGGATGTCTCC | 59.514 | 50.000 | 0.00 | 0.00 | 42.45 | 3.71 |
3345 | 3567 | 6.144402 | GGTTGTTTTCTGTGCAATACATTCTG | 59.856 | 38.462 | 0.00 | 0.00 | 38.92 | 3.02 |
3356 | 3578 | 7.121020 | TGTGCAATACATTCTGAGCTTCAAATA | 59.879 | 33.333 | 0.00 | 0.00 | 33.42 | 1.40 |
3371 | 3593 | 9.989869 | GAGCTTCAAATAGACCATTTTTAGTAC | 57.010 | 33.333 | 0.00 | 0.00 | 34.49 | 2.73 |
3376 | 3598 | 8.387813 | TCAAATAGACCATTTTTAGTACCCACT | 58.612 | 33.333 | 0.00 | 0.00 | 34.49 | 4.00 |
3394 | 3616 | 3.434299 | CCACTGAATGCATTTTTGCTTCC | 59.566 | 43.478 | 14.33 | 0.00 | 35.49 | 3.46 |
3450 | 3672 | 7.259290 | TCAAATATTAATCAGTCCTTTCCGC | 57.741 | 36.000 | 0.00 | 0.00 | 0.00 | 5.54 |
3496 | 3718 | 1.137675 | TCACCAGATGATTCGAGCCTG | 59.862 | 52.381 | 0.00 | 0.00 | 29.99 | 4.85 |
3514 | 3736 | 2.622436 | CTGGGATTTCTTCGGAGTGAC | 58.378 | 52.381 | 0.00 | 0.00 | 0.00 | 3.67 |
3613 | 3835 | 4.350368 | TGGTGCAGTTGATCTGTTAGAA | 57.650 | 40.909 | 0.00 | 0.00 | 45.23 | 2.10 |
3729 | 3951 | 7.853524 | TCAAAATCATTTTTCATGCAGTTGAC | 58.146 | 30.769 | 0.00 | 0.00 | 32.72 | 3.18 |
3741 | 3963 | 1.005630 | AGTTGACGAGGCTCTGCAC | 60.006 | 57.895 | 13.50 | 4.08 | 0.00 | 4.57 |
3774 | 3996 | 4.851843 | TGGCTTCTCTTCATGACATCAAT | 58.148 | 39.130 | 0.00 | 0.00 | 0.00 | 2.57 |
3915 | 4137 | 5.499004 | ACTAAGAGCCAAGGTTTGTATCA | 57.501 | 39.130 | 0.00 | 0.00 | 0.00 | 2.15 |
4010 | 4233 | 5.613698 | ATCTAGATCCTGGAATCCTGAGA | 57.386 | 43.478 | 7.81 | 2.70 | 0.00 | 3.27 |
4012 | 4235 | 5.975113 | TCTAGATCCTGGAATCCTGAGAAT | 58.025 | 41.667 | 7.81 | 0.00 | 0.00 | 2.40 |
4089 | 4314 | 9.087424 | GTAATTTAGATCTTGAAAATTGCACCC | 57.913 | 33.333 | 18.68 | 4.61 | 36.11 | 4.61 |
4093 | 4318 | 6.178607 | AGATCTTGAAAATTGCACCCTTTT | 57.821 | 33.333 | 0.00 | 0.00 | 0.00 | 2.27 |
4095 | 4320 | 4.450053 | TCTTGAAAATTGCACCCTTTTGG | 58.550 | 39.130 | 5.76 | 0.00 | 41.37 | 3.28 |
4109 | 4334 | 6.627287 | GCACCCTTTTGGAACCAAATATCTAC | 60.627 | 42.308 | 17.86 | 5.74 | 44.14 | 2.59 |
4115 | 4340 | 5.367945 | TGGAACCAAATATCTACCTGGAC | 57.632 | 43.478 | 0.00 | 0.00 | 32.97 | 4.02 |
4129 | 4354 | 6.317312 | TCTACCTGGACCAGTAAGACTTTAA | 58.683 | 40.000 | 20.24 | 0.00 | 0.00 | 1.52 |
4152 | 4377 | 7.961326 | AATTTGAGAACATACCCTGCTTAAT | 57.039 | 32.000 | 0.00 | 0.00 | 0.00 | 1.40 |
4205 | 4431 | 1.531677 | CGTTTCTTGTGTGTGTGCCAG | 60.532 | 52.381 | 0.00 | 0.00 | 0.00 | 4.85 |
4594 | 4821 | 9.559732 | TTAAACATCCCATGTATATCTGAGTTG | 57.440 | 33.333 | 0.00 | 0.00 | 44.07 | 3.16 |
4659 | 4891 | 2.806244 | GTGCCAGTCGTATTGAAGTTGT | 59.194 | 45.455 | 0.00 | 0.00 | 0.00 | 3.32 |
4668 | 4900 | 8.279800 | CAGTCGTATTGAAGTTGTTGATACAAA | 58.720 | 33.333 | 0.00 | 0.00 | 45.33 | 2.83 |
4706 | 4939 | 3.414759 | TCACTGGTAGGTGTATCCCAT | 57.585 | 47.619 | 0.00 | 0.00 | 38.28 | 4.00 |
4786 | 5021 | 3.200825 | TCCTTAAGCTTCCATTAGCAGCT | 59.799 | 43.478 | 0.00 | 0.00 | 46.12 | 4.24 |
4800 | 5035 | 3.413846 | AGCAGCTTTCTCATGACTTGA | 57.586 | 42.857 | 0.00 | 0.00 | 0.00 | 3.02 |
4801 | 5036 | 3.748083 | AGCAGCTTTCTCATGACTTGAA | 58.252 | 40.909 | 0.00 | 0.00 | 32.78 | 2.69 |
4802 | 5037 | 3.752222 | AGCAGCTTTCTCATGACTTGAAG | 59.248 | 43.478 | 0.00 | 0.00 | 32.78 | 3.02 |
4803 | 5038 | 3.750130 | GCAGCTTTCTCATGACTTGAAGA | 59.250 | 43.478 | 0.00 | 0.00 | 32.78 | 2.87 |
4804 | 5039 | 4.378253 | GCAGCTTTCTCATGACTTGAAGAC | 60.378 | 45.833 | 0.00 | 0.00 | 32.78 | 3.01 |
4805 | 5040 | 4.753610 | CAGCTTTCTCATGACTTGAAGACA | 59.246 | 41.667 | 0.00 | 0.00 | 32.78 | 3.41 |
4818 | 5054 | 5.139727 | ACTTGAAGACATGAATGGAACCAA | 58.860 | 37.500 | 0.00 | 0.00 | 0.00 | 3.67 |
4822 | 5058 | 3.087031 | AGACATGAATGGAACCAAGCAG | 58.913 | 45.455 | 0.00 | 0.00 | 0.00 | 4.24 |
4851 | 5087 | 5.418840 | GGGTGATTAAACTGATCCATTGTGT | 59.581 | 40.000 | 0.00 | 0.00 | 0.00 | 3.72 |
4885 | 5122 | 9.220767 | ACAGTGAATAGACTTTATTCCTCAAAC | 57.779 | 33.333 | 0.00 | 0.00 | 34.06 | 2.93 |
4886 | 5123 | 9.219603 | CAGTGAATAGACTTTATTCCTCAAACA | 57.780 | 33.333 | 4.89 | 0.00 | 34.06 | 2.83 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
15 | 16 | 7.944002 | GAGTAGCGACTTCATACACATGTATGT | 60.944 | 40.741 | 24.42 | 11.19 | 45.21 | 2.29 |
16 | 17 | 6.360947 | GAGTAGCGACTTCATACACATGTATG | 59.639 | 42.308 | 21.17 | 21.17 | 45.71 | 2.39 |
41 | 42 | 7.754924 | GGTGTTTAAATTGTGTATCACTGATGG | 59.245 | 37.037 | 1.42 | 0.00 | 35.11 | 3.51 |
56 | 57 | 9.349145 | GCAATACTTCATAACGGTGTTTAAATT | 57.651 | 29.630 | 0.00 | 0.00 | 0.00 | 1.82 |
87 | 89 | 1.153628 | CCGGTAGCCACCTTCTTCG | 60.154 | 63.158 | 0.00 | 0.00 | 43.33 | 3.79 |
106 | 122 | 0.585519 | CATAACACCTAAACGCGCGC | 60.586 | 55.000 | 32.58 | 23.91 | 0.00 | 6.86 |
107 | 123 | 0.993532 | TCATAACACCTAAACGCGCG | 59.006 | 50.000 | 30.96 | 30.96 | 0.00 | 6.86 |
144 | 160 | 7.094549 | GGGTTAACATAGTTGCATGTTACAAGA | 60.095 | 37.037 | 9.57 | 0.00 | 46.10 | 3.02 |
147 | 163 | 6.004574 | TGGGTTAACATAGTTGCATGTTACA | 58.995 | 36.000 | 9.57 | 3.72 | 46.10 | 2.41 |
177 | 193 | 3.139850 | GGTCTTCTCTCATGCATGATGG | 58.860 | 50.000 | 28.81 | 22.30 | 36.02 | 3.51 |
190 | 206 | 2.408271 | TGCATGTGATGGGTCTTCTC | 57.592 | 50.000 | 0.00 | 0.00 | 0.00 | 2.87 |
220 | 236 | 6.832520 | AGTGAATTACATGGTTGCATGTTA | 57.167 | 33.333 | 0.00 | 0.00 | 42.56 | 2.41 |
221 | 237 | 5.726980 | AGTGAATTACATGGTTGCATGTT | 57.273 | 34.783 | 0.00 | 0.00 | 42.56 | 2.71 |
222 | 238 | 6.681120 | GCATAGTGAATTACATGGTTGCATGT | 60.681 | 38.462 | 0.00 | 0.00 | 46.35 | 3.21 |
223 | 239 | 5.688621 | GCATAGTGAATTACATGGTTGCATG | 59.311 | 40.000 | 0.00 | 0.00 | 38.46 | 4.06 |
224 | 240 | 5.221303 | GGCATAGTGAATTACATGGTTGCAT | 60.221 | 40.000 | 0.00 | 0.00 | 0.00 | 3.96 |
225 | 241 | 4.097741 | GGCATAGTGAATTACATGGTTGCA | 59.902 | 41.667 | 0.00 | 0.00 | 0.00 | 4.08 |
226 | 242 | 4.097741 | TGGCATAGTGAATTACATGGTTGC | 59.902 | 41.667 | 0.00 | 0.00 | 0.00 | 4.17 |
253 | 399 | 2.821969 | ACAGATGTGTCTTTTCCATGCC | 59.178 | 45.455 | 0.00 | 0.00 | 30.42 | 4.40 |
278 | 424 | 9.243637 | GCAAACAAAGATGTGTCTATGTTAAAA | 57.756 | 29.630 | 0.00 | 0.00 | 40.46 | 1.52 |
279 | 425 | 7.589587 | CGCAAACAAAGATGTGTCTATGTTAAA | 59.410 | 33.333 | 0.00 | 0.00 | 40.46 | 1.52 |
280 | 426 | 7.075121 | CGCAAACAAAGATGTGTCTATGTTAA | 58.925 | 34.615 | 0.00 | 0.00 | 40.46 | 2.01 |
281 | 427 | 6.598525 | CGCAAACAAAGATGTGTCTATGTTA | 58.401 | 36.000 | 0.00 | 0.00 | 40.46 | 2.41 |
282 | 428 | 5.451908 | CGCAAACAAAGATGTGTCTATGTT | 58.548 | 37.500 | 0.00 | 0.00 | 40.46 | 2.71 |
283 | 429 | 4.613622 | GCGCAAACAAAGATGTGTCTATGT | 60.614 | 41.667 | 0.30 | 0.00 | 40.46 | 2.29 |
284 | 430 | 3.848019 | GCGCAAACAAAGATGTGTCTATG | 59.152 | 43.478 | 0.30 | 0.00 | 40.46 | 2.23 |
285 | 431 | 3.501828 | TGCGCAAACAAAGATGTGTCTAT | 59.498 | 39.130 | 8.16 | 0.00 | 40.46 | 1.98 |
286 | 432 | 2.875317 | TGCGCAAACAAAGATGTGTCTA | 59.125 | 40.909 | 8.16 | 0.00 | 40.46 | 2.59 |
287 | 433 | 1.675483 | TGCGCAAACAAAGATGTGTCT | 59.325 | 42.857 | 8.16 | 0.00 | 40.46 | 3.41 |
288 | 434 | 2.118228 | TGCGCAAACAAAGATGTGTC | 57.882 | 45.000 | 8.16 | 0.00 | 40.46 | 3.67 |
515 | 694 | 7.844009 | ACGTCTTACATTAAGGGACAAAGATA | 58.156 | 34.615 | 0.00 | 0.00 | 36.45 | 1.98 |
571 | 750 | 6.120905 | TCTAACGCCTTTACAGATCTACTCT | 58.879 | 40.000 | 0.00 | 0.00 | 33.14 | 3.24 |
821 | 1002 | 4.292178 | GGATGGGAGCGAGCGGAG | 62.292 | 72.222 | 0.00 | 0.00 | 0.00 | 4.63 |
950 | 1132 | 3.011885 | CCGAGGAGGGGAGAGAGT | 58.988 | 66.667 | 0.00 | 0.00 | 35.97 | 3.24 |
956 | 1138 | 4.144727 | GAGGAGCCGAGGAGGGGA | 62.145 | 72.222 | 0.00 | 0.00 | 41.48 | 4.81 |
1212 | 1400 | 2.872245 | GGATTCGCTATTAACTGCAGCA | 59.128 | 45.455 | 15.27 | 0.00 | 34.94 | 4.41 |
1247 | 1435 | 5.582269 | CGGAATATTCTACACATGGCATAGG | 59.418 | 44.000 | 14.95 | 0.00 | 0.00 | 2.57 |
1312 | 1500 | 4.817464 | ACTTTATGCCTAAAACGTCACACA | 59.183 | 37.500 | 0.00 | 0.00 | 0.00 | 3.72 |
1554 | 1751 | 9.312146 | CATGTCAACAAACTAAAAACAAACAAC | 57.688 | 29.630 | 0.00 | 0.00 | 0.00 | 3.32 |
1566 | 1763 | 8.664798 | GCAATCACTATACATGTCAACAAACTA | 58.335 | 33.333 | 0.00 | 0.00 | 0.00 | 2.24 |
1568 | 1765 | 7.482743 | CAGCAATCACTATACATGTCAACAAAC | 59.517 | 37.037 | 0.00 | 0.00 | 0.00 | 2.93 |
1571 | 1768 | 6.092533 | CACAGCAATCACTATACATGTCAACA | 59.907 | 38.462 | 0.00 | 0.00 | 0.00 | 3.33 |
1572 | 1769 | 6.092670 | ACACAGCAATCACTATACATGTCAAC | 59.907 | 38.462 | 0.00 | 0.00 | 0.00 | 3.18 |
1612 | 1810 | 2.305927 | ACCCACAGCAAGCACTTATAGT | 59.694 | 45.455 | 0.00 | 0.00 | 0.00 | 2.12 |
1622 | 1820 | 5.200368 | AGAAATGTAAAACCCACAGCAAG | 57.800 | 39.130 | 0.00 | 0.00 | 0.00 | 4.01 |
1687 | 1885 | 1.160137 | AAGAGCAGCGTTCACAATCC | 58.840 | 50.000 | 0.00 | 0.00 | 0.00 | 3.01 |
1688 | 1886 | 4.606457 | AATAAGAGCAGCGTTCACAATC | 57.394 | 40.909 | 0.00 | 0.00 | 0.00 | 2.67 |
1720 | 1918 | 6.866248 | ACCGCTAGATTTTAAATTTGGTGTTG | 59.134 | 34.615 | 0.00 | 0.00 | 0.00 | 3.33 |
1723 | 1923 | 6.616947 | TCACCGCTAGATTTTAAATTTGGTG | 58.383 | 36.000 | 15.14 | 15.14 | 43.37 | 4.17 |
1734 | 1934 | 9.998106 | AGTACATATTAAATCACCGCTAGATTT | 57.002 | 29.630 | 11.07 | 11.07 | 45.05 | 2.17 |
1735 | 1935 | 9.640963 | GAGTACATATTAAATCACCGCTAGATT | 57.359 | 33.333 | 0.00 | 0.00 | 37.30 | 2.40 |
1736 | 1936 | 8.251721 | GGAGTACATATTAAATCACCGCTAGAT | 58.748 | 37.037 | 0.00 | 0.00 | 0.00 | 1.98 |
1737 | 1937 | 7.309621 | GGGAGTACATATTAAATCACCGCTAGA | 60.310 | 40.741 | 0.00 | 0.00 | 0.00 | 2.43 |
1738 | 1938 | 6.812160 | GGGAGTACATATTAAATCACCGCTAG | 59.188 | 42.308 | 0.00 | 0.00 | 0.00 | 3.42 |
1739 | 1939 | 6.495872 | AGGGAGTACATATTAAATCACCGCTA | 59.504 | 38.462 | 0.00 | 0.00 | 0.00 | 4.26 |
1740 | 1940 | 5.307196 | AGGGAGTACATATTAAATCACCGCT | 59.693 | 40.000 | 0.00 | 0.00 | 0.00 | 5.52 |
1743 | 1943 | 7.736893 | ACAGAGGGAGTACATATTAAATCACC | 58.263 | 38.462 | 0.00 | 0.00 | 0.00 | 4.02 |
1758 | 1958 | 8.862085 | GCTCTTATATTAGTTTACAGAGGGAGT | 58.138 | 37.037 | 0.00 | 0.00 | 0.00 | 3.85 |
1790 | 1990 | 9.733219 | AGCGTTTAGATTACTAAGTTAGTGATC | 57.267 | 33.333 | 28.08 | 28.08 | 46.38 | 2.92 |
1791 | 1991 | 9.733219 | GAGCGTTTAGATTACTAAGTTAGTGAT | 57.267 | 33.333 | 23.14 | 20.31 | 39.81 | 3.06 |
1792 | 1992 | 8.954350 | AGAGCGTTTAGATTACTAAGTTAGTGA | 58.046 | 33.333 | 23.14 | 16.63 | 39.81 | 3.41 |
1793 | 1993 | 9.570488 | AAGAGCGTTTAGATTACTAAGTTAGTG | 57.430 | 33.333 | 23.14 | 6.38 | 39.81 | 2.74 |
1807 | 2007 | 9.669353 | CCGTAAACTAATATAAGAGCGTTTAGA | 57.331 | 33.333 | 0.00 | 0.00 | 30.36 | 2.10 |
1808 | 2008 | 9.669353 | TCCGTAAACTAATATAAGAGCGTTTAG | 57.331 | 33.333 | 0.00 | 0.00 | 30.36 | 1.85 |
1811 | 2011 | 7.144000 | CCTCCGTAAACTAATATAAGAGCGTT | 58.856 | 38.462 | 0.00 | 0.00 | 0.00 | 4.84 |
1812 | 2012 | 6.294397 | CCCTCCGTAAACTAATATAAGAGCGT | 60.294 | 42.308 | 0.00 | 0.00 | 0.00 | 5.07 |
1813 | 2013 | 6.072286 | TCCCTCCGTAAACTAATATAAGAGCG | 60.072 | 42.308 | 0.00 | 0.00 | 0.00 | 5.03 |
1814 | 2014 | 7.039853 | ACTCCCTCCGTAAACTAATATAAGAGC | 60.040 | 40.741 | 0.00 | 0.00 | 0.00 | 4.09 |
1815 | 2015 | 8.406730 | ACTCCCTCCGTAAACTAATATAAGAG | 57.593 | 38.462 | 0.00 | 0.00 | 0.00 | 2.85 |
1816 | 2016 | 9.289782 | GTACTCCCTCCGTAAACTAATATAAGA | 57.710 | 37.037 | 0.00 | 0.00 | 0.00 | 2.10 |
1817 | 2017 | 9.294614 | AGTACTCCCTCCGTAAACTAATATAAG | 57.705 | 37.037 | 0.00 | 0.00 | 0.00 | 1.73 |
1818 | 2018 | 9.646522 | AAGTACTCCCTCCGTAAACTAATATAA | 57.353 | 33.333 | 0.00 | 0.00 | 0.00 | 0.98 |
1820 | 2020 | 9.294614 | CTAAGTACTCCCTCCGTAAACTAATAT | 57.705 | 37.037 | 0.00 | 0.00 | 0.00 | 1.28 |
1821 | 2021 | 8.494433 | TCTAAGTACTCCCTCCGTAAACTAATA | 58.506 | 37.037 | 0.00 | 0.00 | 0.00 | 0.98 |
1822 | 2022 | 7.349598 | TCTAAGTACTCCCTCCGTAAACTAAT | 58.650 | 38.462 | 0.00 | 0.00 | 0.00 | 1.73 |
1823 | 2023 | 6.721318 | TCTAAGTACTCCCTCCGTAAACTAA | 58.279 | 40.000 | 0.00 | 0.00 | 0.00 | 2.24 |
1824 | 2024 | 6.313519 | TCTAAGTACTCCCTCCGTAAACTA | 57.686 | 41.667 | 0.00 | 0.00 | 0.00 | 2.24 |
1825 | 2025 | 5.184892 | TCTAAGTACTCCCTCCGTAAACT | 57.815 | 43.478 | 0.00 | 0.00 | 0.00 | 2.66 |
1826 | 2026 | 5.904362 | TTCTAAGTACTCCCTCCGTAAAC | 57.096 | 43.478 | 0.00 | 0.00 | 0.00 | 2.01 |
1827 | 2027 | 5.954150 | ACATTCTAAGTACTCCCTCCGTAAA | 59.046 | 40.000 | 0.00 | 0.00 | 0.00 | 2.01 |
1828 | 2028 | 5.513233 | ACATTCTAAGTACTCCCTCCGTAA | 58.487 | 41.667 | 0.00 | 0.00 | 0.00 | 3.18 |
1829 | 2029 | 5.121380 | ACATTCTAAGTACTCCCTCCGTA | 57.879 | 43.478 | 0.00 | 0.00 | 0.00 | 4.02 |
1830 | 2030 | 3.978610 | ACATTCTAAGTACTCCCTCCGT | 58.021 | 45.455 | 0.00 | 0.00 | 0.00 | 4.69 |
1831 | 2031 | 6.461110 | TTTACATTCTAAGTACTCCCTCCG | 57.539 | 41.667 | 0.00 | 0.00 | 0.00 | 4.63 |
1832 | 2032 | 8.252624 | AGATTTACATTCTAAGTACTCCCTCC | 57.747 | 38.462 | 0.00 | 0.00 | 0.00 | 4.30 |
1842 | 2042 | 9.182933 | GCCGTACTCTAAGATTTACATTCTAAG | 57.817 | 37.037 | 0.00 | 0.00 | 0.00 | 2.18 |
1843 | 2043 | 8.139989 | GGCCGTACTCTAAGATTTACATTCTAA | 58.860 | 37.037 | 0.00 | 0.00 | 0.00 | 2.10 |
1858 | 2058 | 0.184451 | CTGGGTAGGGCCGTACTCTA | 59.816 | 60.000 | 30.30 | 18.84 | 38.44 | 2.43 |
1944 | 2144 | 5.011533 | TCCCTATGCTTCTAGATGCTTCTTC | 59.988 | 44.000 | 25.75 | 2.78 | 33.17 | 2.87 |
2050 | 2250 | 6.985059 | ACACCACTTCTAGAAACTTAGACAAC | 59.015 | 38.462 | 6.63 | 0.00 | 29.67 | 3.32 |
2139 | 2339 | 5.247110 | AGGAATGACTGACAGTGTGAGTATT | 59.753 | 40.000 | 15.74 | 14.20 | 28.74 | 1.89 |
2290 | 2490 | 2.670479 | CGAATGATCTGATGGAGGTCG | 58.330 | 52.381 | 0.00 | 0.00 | 34.02 | 4.79 |
2293 | 2493 | 2.036862 | TGAGCGAATGATCTGATGGAGG | 59.963 | 50.000 | 0.00 | 0.00 | 0.00 | 4.30 |
2299 | 2499 | 5.818857 | TGATTGATTTGAGCGAATGATCTGA | 59.181 | 36.000 | 0.00 | 0.00 | 0.00 | 3.27 |
2371 | 2571 | 9.722056 | CTACAATTCCAGCAAATACATAAGAAC | 57.278 | 33.333 | 0.00 | 0.00 | 0.00 | 3.01 |
2407 | 2607 | 8.959058 | CGATATCTACATTAGTCACAACAAGAC | 58.041 | 37.037 | 0.34 | 0.00 | 36.26 | 3.01 |
2454 | 2654 | 7.391148 | AAGAACTAAAGAAAGCACAGAACAA | 57.609 | 32.000 | 0.00 | 0.00 | 0.00 | 2.83 |
2536 | 2736 | 6.408035 | ACCTAAGCTAAGAACTAAAGAAGGC | 58.592 | 40.000 | 0.00 | 0.00 | 0.00 | 4.35 |
2554 | 2754 | 8.964476 | TGGAAGATAAAGCTCATAAACCTAAG | 57.036 | 34.615 | 0.00 | 0.00 | 0.00 | 2.18 |
2570 | 2770 | 9.851686 | ATGTAACTTATGATTGCTGGAAGATAA | 57.148 | 29.630 | 0.00 | 0.00 | 34.07 | 1.75 |
2574 | 2774 | 7.325660 | ACATGTAACTTATGATTGCTGGAAG | 57.674 | 36.000 | 0.00 | 0.00 | 0.00 | 3.46 |
2602 | 2802 | 5.877012 | ACTGATACAAGAAGTACTGCAATGG | 59.123 | 40.000 | 3.00 | 0.00 | 35.05 | 3.16 |
2760 | 2960 | 4.037327 | ACCACATACTCTGTCATGAGATCG | 59.963 | 45.833 | 0.00 | 0.00 | 35.29 | 3.69 |
2841 | 3041 | 3.587061 | ACCCAACTGACCAGACATCAATA | 59.413 | 43.478 | 3.76 | 0.00 | 0.00 | 1.90 |
2898 | 3098 | 6.581388 | TGGATGTAATCTCTTCCAGGAAAT | 57.419 | 37.500 | 2.72 | 0.00 | 44.71 | 2.17 |
2986 | 3186 | 5.895636 | AGACAACAACATGACTTGTCAAA | 57.104 | 34.783 | 23.99 | 0.00 | 44.17 | 2.69 |
3030 | 3230 | 2.093467 | GCTCAGAAACAGACGCATCTTC | 59.907 | 50.000 | 0.00 | 0.00 | 30.42 | 2.87 |
3037 | 3237 | 4.985409 | ACTAAAGAAGCTCAGAAACAGACG | 59.015 | 41.667 | 0.00 | 0.00 | 0.00 | 4.18 |
3078 | 3278 | 8.671921 | ACAGTCAGATGCTATTGTTTCAAATAG | 58.328 | 33.333 | 0.00 | 0.00 | 41.27 | 1.73 |
3108 | 3330 | 4.393062 | CACAAGATGCGAAACAGGTCTAAT | 59.607 | 41.667 | 0.00 | 0.00 | 0.00 | 1.73 |
3147 | 3369 | 7.673810 | AATTCAGTGTTTGCGTAAAAGTAAC | 57.326 | 32.000 | 0.00 | 0.00 | 0.00 | 2.50 |
3202 | 3424 | 1.269448 | CAGTAAAATGTTGCCGCACCT | 59.731 | 47.619 | 0.00 | 0.00 | 0.00 | 4.00 |
3208 | 3430 | 7.320443 | TCTGATGATACAGTAAAATGTTGCC | 57.680 | 36.000 | 0.00 | 0.00 | 38.79 | 4.52 |
3325 | 3547 | 5.474532 | AGCTCAGAATGTATTGCACAGAAAA | 59.525 | 36.000 | 0.00 | 0.00 | 41.51 | 2.29 |
3345 | 3567 | 9.989869 | GTACTAAAAATGGTCTATTTGAAGCTC | 57.010 | 33.333 | 0.00 | 0.00 | 38.93 | 4.09 |
3356 | 3578 | 5.836024 | TCAGTGGGTACTAAAAATGGTCT | 57.164 | 39.130 | 0.00 | 0.00 | 34.74 | 3.85 |
3371 | 3593 | 3.048337 | AGCAAAAATGCATTCAGTGGG | 57.952 | 42.857 | 13.38 | 1.12 | 37.25 | 4.61 |
3376 | 3598 | 6.696441 | AAAAAGGAAGCAAAAATGCATTCA | 57.304 | 29.167 | 13.38 | 0.00 | 37.25 | 2.57 |
3496 | 3718 | 2.762535 | TGTCACTCCGAAGAAATCCC | 57.237 | 50.000 | 0.00 | 0.00 | 0.00 | 3.85 |
3514 | 3736 | 4.201841 | TGCTTCATGTATCTTCGTGCATTG | 60.202 | 41.667 | 0.00 | 0.00 | 0.00 | 2.82 |
3690 | 3912 | 5.484173 | TGATTTTGAGCCATAGTAAAGCG | 57.516 | 39.130 | 0.00 | 0.00 | 0.00 | 4.68 |
3729 | 3951 | 4.767255 | GGGTGGTGCAGAGCCTCG | 62.767 | 72.222 | 6.63 | 0.00 | 0.00 | 4.63 |
3774 | 3996 | 1.228124 | CGGGCAAGTGGGTTCTTCA | 60.228 | 57.895 | 0.00 | 0.00 | 0.00 | 3.02 |
3915 | 4137 | 9.321562 | ACGAAATATTTTCAACCAGACGTATAT | 57.678 | 29.630 | 1.43 | 0.00 | 0.00 | 0.86 |
4085 | 4308 | 6.127451 | GGTAGATATTTGGTTCCAAAAGGGTG | 60.127 | 42.308 | 18.85 | 0.00 | 39.05 | 4.61 |
4086 | 4309 | 5.955959 | GGTAGATATTTGGTTCCAAAAGGGT | 59.044 | 40.000 | 18.85 | 7.13 | 39.05 | 4.34 |
4089 | 4314 | 6.889722 | TCCAGGTAGATATTTGGTTCCAAAAG | 59.110 | 38.462 | 18.85 | 3.77 | 39.05 | 2.27 |
4093 | 4318 | 4.165372 | GGTCCAGGTAGATATTTGGTTCCA | 59.835 | 45.833 | 0.00 | 0.00 | 32.51 | 3.53 |
4095 | 4320 | 5.104485 | ACTGGTCCAGGTAGATATTTGGTTC | 60.104 | 44.000 | 23.06 | 0.00 | 35.51 | 3.62 |
4109 | 4334 | 6.940298 | TCAAATTAAAGTCTTACTGGTCCAGG | 59.060 | 38.462 | 23.06 | 5.58 | 35.51 | 4.45 |
4129 | 4354 | 9.646522 | AATATTAAGCAGGGTATGTTCTCAAAT | 57.353 | 29.630 | 0.00 | 0.00 | 0.00 | 2.32 |
4205 | 4431 | 6.610741 | AAATGAACTGAGACAACAGAGAAC | 57.389 | 37.500 | 0.00 | 0.00 | 40.63 | 3.01 |
4525 | 4751 | 6.769512 | ACAAGCCTTAGATACACAAGAAGAA | 58.230 | 36.000 | 0.00 | 0.00 | 0.00 | 2.52 |
4594 | 4821 | 9.617975 | GCTTGAGATAATAAAAGGCAATATGTC | 57.382 | 33.333 | 0.00 | 0.00 | 0.00 | 3.06 |
4659 | 4891 | 7.894708 | TGGAATTTCAGAGCAATTTGTATCAA | 58.105 | 30.769 | 0.00 | 0.00 | 0.00 | 2.57 |
4668 | 4900 | 5.962433 | CAGTGAATGGAATTTCAGAGCAAT | 58.038 | 37.500 | 0.00 | 0.00 | 36.07 | 3.56 |
4757 | 4990 | 7.880195 | TGCTAATGGAAGCTTAAGGATAAGATC | 59.120 | 37.037 | 0.00 | 0.00 | 43.19 | 2.75 |
4759 | 4992 | 7.136822 | TGCTAATGGAAGCTTAAGGATAAGA | 57.863 | 36.000 | 0.00 | 0.00 | 43.19 | 2.10 |
4775 | 5010 | 4.197750 | AGTCATGAGAAAGCTGCTAATGG | 58.802 | 43.478 | 0.90 | 0.00 | 0.00 | 3.16 |
4779 | 5014 | 4.541973 | TCAAGTCATGAGAAAGCTGCTA | 57.458 | 40.909 | 0.90 | 0.00 | 33.04 | 3.49 |
4786 | 5021 | 7.094506 | CCATTCATGTCTTCAAGTCATGAGAAA | 60.095 | 37.037 | 21.57 | 11.85 | 46.03 | 2.52 |
4800 | 5035 | 3.499338 | TGCTTGGTTCCATTCATGTCTT | 58.501 | 40.909 | 0.00 | 0.00 | 0.00 | 3.01 |
4801 | 5036 | 3.087031 | CTGCTTGGTTCCATTCATGTCT | 58.913 | 45.455 | 0.00 | 0.00 | 0.00 | 3.41 |
4802 | 5037 | 2.416431 | GCTGCTTGGTTCCATTCATGTC | 60.416 | 50.000 | 0.00 | 0.00 | 0.00 | 3.06 |
4803 | 5038 | 1.547372 | GCTGCTTGGTTCCATTCATGT | 59.453 | 47.619 | 0.00 | 0.00 | 0.00 | 3.21 |
4804 | 5039 | 1.134907 | GGCTGCTTGGTTCCATTCATG | 60.135 | 52.381 | 0.00 | 0.00 | 0.00 | 3.07 |
4805 | 5040 | 1.188863 | GGCTGCTTGGTTCCATTCAT | 58.811 | 50.000 | 0.00 | 0.00 | 0.00 | 2.57 |
4818 | 5054 | 2.171003 | GTTTAATCACCCAAGGCTGCT | 58.829 | 47.619 | 0.00 | 0.00 | 0.00 | 4.24 |
4822 | 5058 | 3.381590 | GGATCAGTTTAATCACCCAAGGC | 59.618 | 47.826 | 0.00 | 0.00 | 0.00 | 4.35 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.