Multiple sequence alignment - TraesCS7D01G554300

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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 TraesCS7D01G554300 chr7D 100.000 3026 0 0 1 3026 638298016 638294991 0.000000e+00 5589.0
1 TraesCS7D01G554300 chr7D 88.928 858 48 18 95 937 638289424 638288599 0.000000e+00 1014.0
2 TraesCS7D01G554300 chr7D 87.786 655 76 4 1054 1707 638288515 638287864 0.000000e+00 763.0
3 TraesCS7D01G554300 chr7D 87.138 311 28 8 1833 2142 638287669 638287370 2.890000e-90 342.0
4 TraesCS7D01G554300 chr7D 78.378 518 88 16 1054 1565 638274436 638273937 6.300000e-82 315.0
5 TraesCS7D01G554300 chr7D 85.959 292 26 8 2736 3026 638286765 638286488 6.340000e-77 298.0
6 TraesCS7D01G554300 chr7D 82.418 364 36 11 2184 2547 638287361 638287026 2.950000e-75 292.0
7 TraesCS7D01G554300 chr7B 84.347 1693 151 49 78 1711 734406751 734408388 0.000000e+00 1554.0
8 TraesCS7D01G554300 chr7B 90.000 290 27 1 2737 3026 734409930 734410217 1.020000e-99 374.0
9 TraesCS7D01G554300 chr7B 79.142 513 88 14 1055 1565 734426486 734426981 1.340000e-88 337.0
10 TraesCS7D01G554300 chr7B 76.268 493 90 18 1216 1685 734360560 734361048 1.400000e-58 237.0
11 TraesCS7D01G554300 chr7B 87.654 162 20 0 1404 1565 734417022 734417183 3.980000e-44 189.0
12 TraesCS7D01G554300 chr7A 93.156 1052 55 8 661 1703 727773250 727774293 0.000000e+00 1528.0
13 TraesCS7D01G554300 chr7A 87.995 808 65 16 965 1744 727787879 727788682 0.000000e+00 926.0
14 TraesCS7D01G554300 chr7A 87.949 473 48 7 215 680 727772751 727773221 1.590000e-152 549.0
15 TraesCS7D01G554300 chr7A 82.547 636 95 11 1054 1681 727721792 727722419 2.050000e-151 545.0
16 TraesCS7D01G554300 chr7A 86.061 495 40 13 449 927 727787040 727787521 3.480000e-139 505.0
17 TraesCS7D01G554300 chr7A 87.077 325 30 8 1819 2142 727774674 727774987 1.030000e-94 357.0
18 TraesCS7D01G554300 chr7A 85.852 311 29 8 1833 2142 727788845 727789141 1.750000e-82 316.0
19 TraesCS7D01G554300 chr7A 94.444 180 10 0 2847 3026 727789649 727789828 8.260000e-71 278.0
20 TraesCS7D01G554300 chr7A 95.425 153 6 1 2 153 727772600 727772752 3.010000e-60 243.0
21 TraesCS7D01G554300 chr7A 88.718 195 21 1 2351 2544 727789289 727789483 1.400000e-58 237.0
22 TraesCS7D01G554300 chr7A 77.866 253 34 4 2774 3026 727776145 727776375 1.460000e-28 137.0
23 TraesCS7D01G554300 chr7A 89.610 77 4 2 2567 2639 727789479 727789555 8.930000e-16 95.3
24 TraesCS7D01G554300 chr2B 100.000 48 0 0 2139 2186 123281184 123281231 4.160000e-14 89.8
25 TraesCS7D01G554300 chr1D 100.000 48 0 0 2139 2186 46393552 46393505 4.160000e-14 89.8
26 TraesCS7D01G554300 chr1B 100.000 47 0 0 2140 2186 298248778 298248824 1.490000e-13 87.9
27 TraesCS7D01G554300 chr1B 98.000 50 0 1 2138 2186 60376334 60376383 5.380000e-13 86.1
28 TraesCS7D01G554300 chrUn 100.000 46 0 0 2141 2186 290333115 290333070 5.380000e-13 86.1
29 TraesCS7D01G554300 chrUn 100.000 46 0 0 2141 2186 290338879 290338834 5.380000e-13 86.1
30 TraesCS7D01G554300 chrUn 100.000 46 0 0 2141 2186 468333314 468333359 5.380000e-13 86.1
31 TraesCS7D01G554300 chr6D 98.000 50 0 1 2138 2186 32295416 32295367 5.380000e-13 86.1
32 TraesCS7D01G554300 chr2A 91.935 62 2 3 2128 2186 705992949 705992888 1.930000e-12 84.2


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 TraesCS7D01G554300 chr7D 638294991 638298016 3025 True 5589.000000 5589 100.0000 1 3026 1 chr7D.!!$R2 3025
1 TraesCS7D01G554300 chr7D 638286488 638289424 2936 True 541.800000 1014 86.4458 95 3026 5 chr7D.!!$R3 2931
2 TraesCS7D01G554300 chr7B 734406751 734410217 3466 False 964.000000 1554 87.1735 78 3026 2 chr7B.!!$F4 2948
3 TraesCS7D01G554300 chr7A 727772600 727776375 3775 False 562.800000 1528 88.2946 2 3026 5 chr7A.!!$F2 3024
4 TraesCS7D01G554300 chr7A 727721792 727722419 627 False 545.000000 545 82.5470 1054 1681 1 chr7A.!!$F1 627
5 TraesCS7D01G554300 chr7A 727787040 727789828 2788 False 392.883333 926 88.7800 449 3026 6 chr7A.!!$F3 2577

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
195 199 1.523758 AACCTGGCTTTAGACAAGCG 58.476 50.0 0.0 0.0 43.89 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2177 3105 0.109781 CTTGAACGGCAATCGGTTGG 60.11 55.0 11.04 0.0 39.92 3.77 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
23 24 3.885297 ACAAGCTATACATGTCCAATGGC 59.115 43.478 0.00 4.29 0.00 4.40
28 29 5.010314 AGCTATACATGTCCAATGGCAAATG 59.990 40.000 15.28 0.76 30.27 2.32
170 173 6.435277 GGCAAATTCATGATATATGTCCTGGT 59.565 38.462 0.00 0.00 0.00 4.00
195 199 1.523758 AACCTGGCTTTAGACAAGCG 58.476 50.000 0.00 0.00 43.89 4.68
204 210 5.086727 GGCTTTAGACAAGCGTATTTGTTC 58.913 41.667 0.65 0.00 43.89 3.18
207 213 6.856426 GCTTTAGACAAGCGTATTTGTTCTTT 59.144 34.615 4.13 0.00 41.15 2.52
245 258 7.696992 TCTGTATTTTGGGGACTGTATTTTC 57.303 36.000 0.00 0.00 0.00 2.29
277 292 4.777366 CACAAAGAATTACCTGGGGGAATT 59.223 41.667 6.48 6.48 36.25 2.17
302 317 7.620458 CTAGCATAGTAAGTGGCCTATCGGC 62.620 52.000 3.32 0.00 44.36 5.54
346 364 2.606272 GTCCAGTGAACGAAAACGTTCT 59.394 45.455 26.92 12.22 45.80 3.01
616 640 3.066760 CGCAAGTTTTCCTCTTCTTTGGT 59.933 43.478 0.00 0.00 0.00 3.67
802 889 6.510799 CGAATCCACGTAGTACTGGTACTAAG 60.511 46.154 22.51 22.51 46.55 2.18
1315 1772 2.121538 CGATCACGCTCCTCCTCCA 61.122 63.158 0.00 0.00 0.00 3.86
1558 2018 2.741985 CGTGCTCCCATCGTTGCA 60.742 61.111 0.00 0.00 0.00 4.08
1724 2193 6.390721 TGTAGTATTGTTCTTGTGCTCTCTC 58.609 40.000 0.00 0.00 0.00 3.20
1726 2195 5.719173 AGTATTGTTCTTGTGCTCTCTCTC 58.281 41.667 0.00 0.00 0.00 3.20
1727 2196 4.888326 ATTGTTCTTGTGCTCTCTCTCT 57.112 40.909 0.00 0.00 0.00 3.10
1737 2206 2.101415 TGCTCTCTCTCTCTCTCTCTCG 59.899 54.545 0.00 0.00 0.00 4.04
1740 2209 2.362397 TCTCTCTCTCTCTCTCTCGCTC 59.638 54.545 0.00 0.00 0.00 5.03
1741 2210 2.363680 CTCTCTCTCTCTCTCTCGCTCT 59.636 54.545 0.00 0.00 0.00 4.09
1742 2211 2.362397 TCTCTCTCTCTCTCTCGCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
1743 2212 2.363680 CTCTCTCTCTCTCTCGCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
1744 2213 2.362397 TCTCTCTCTCTCTCGCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
1745 2214 2.363680 CTCTCTCTCTCTCGCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
1748 2217 0.529773 TCTCTCTCGCTCTCTCTCGC 60.530 60.000 0.00 0.00 0.00 5.03
1749 2218 0.530650 CTCTCTCGCTCTCTCTCGCT 60.531 60.000 0.00 0.00 0.00 4.93
1750 2219 0.529773 TCTCTCGCTCTCTCTCGCTC 60.530 60.000 0.00 0.00 0.00 5.03
1752 2221 0.529773 TCTCGCTCTCTCTCGCTCTC 60.530 60.000 0.00 0.00 0.00 3.20
1753 2222 0.530650 CTCGCTCTCTCTCGCTCTCT 60.531 60.000 0.00 0.00 0.00 3.10
1754 2223 0.529773 TCGCTCTCTCTCGCTCTCTC 60.530 60.000 0.00 0.00 0.00 3.20
1755 2224 0.530650 CGCTCTCTCTCGCTCTCTCT 60.531 60.000 0.00 0.00 0.00 3.10
1756 2225 1.221414 GCTCTCTCTCGCTCTCTCTC 58.779 60.000 0.00 0.00 0.00 3.20
1757 2226 1.202580 GCTCTCTCTCGCTCTCTCTCT 60.203 57.143 0.00 0.00 0.00 3.10
1758 2227 2.748605 CTCTCTCTCGCTCTCTCTCTC 58.251 57.143 0.00 0.00 0.00 3.20
1759 2228 2.363680 CTCTCTCTCGCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
1760 2229 2.362397 TCTCTCTCGCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
1761 2230 2.363680 CTCTCTCGCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
1762 2231 2.362397 TCTCTCGCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
1763 2232 2.363680 CTCTCGCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
1764 2233 2.362397 TCTCGCTCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
1765 2234 2.363680 CTCGCTCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
1766 2235 2.362397 TCGCTCTCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
1767 2236 2.363680 CGCTCTCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
1768 2237 3.551863 CGCTCTCTCTCTCTCTCTCTCTC 60.552 56.522 0.00 0.00 0.00 3.20
1769 2238 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
1770 2239 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
1771 2240 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
1772 2241 4.078922 TCTCTCTCTCTCTCTCTCTCTCCT 60.079 50.000 0.00 0.00 0.00 3.69
1773 2242 4.219115 TCTCTCTCTCTCTCTCTCTCCTC 58.781 52.174 0.00 0.00 0.00 3.71
1774 2243 4.078922 TCTCTCTCTCTCTCTCTCTCCTCT 60.079 50.000 0.00 0.00 0.00 3.69
1775 2244 4.624913 TCTCTCTCTCTCTCTCTCCTCTT 58.375 47.826 0.00 0.00 0.00 2.85
1776 2245 5.032846 TCTCTCTCTCTCTCTCTCCTCTTT 58.967 45.833 0.00 0.00 0.00 2.52
1777 2246 5.102953 TCTCTCTCTCTCTCTCCTCTTTG 57.897 47.826 0.00 0.00 0.00 2.77
1778 2247 3.620488 TCTCTCTCTCTCTCCTCTTTGC 58.380 50.000 0.00 0.00 0.00 3.68
1779 2248 2.355756 CTCTCTCTCTCTCCTCTTTGCG 59.644 54.545 0.00 0.00 0.00 4.85
1780 2249 2.026729 TCTCTCTCTCTCCTCTTTGCGA 60.027 50.000 0.00 0.00 0.00 5.10
1781 2250 2.951642 CTCTCTCTCTCCTCTTTGCGAT 59.048 50.000 0.00 0.00 0.00 4.58
1782 2251 4.133820 CTCTCTCTCTCCTCTTTGCGATA 58.866 47.826 0.00 0.00 0.00 2.92
1783 2252 4.724399 TCTCTCTCTCCTCTTTGCGATAT 58.276 43.478 0.00 0.00 0.00 1.63
1784 2253 5.136828 TCTCTCTCTCCTCTTTGCGATATT 58.863 41.667 0.00 0.00 0.00 1.28
1785 2254 5.240623 TCTCTCTCTCCTCTTTGCGATATTC 59.759 44.000 0.00 0.00 0.00 1.75
1786 2255 4.889995 TCTCTCTCCTCTTTGCGATATTCA 59.110 41.667 0.00 0.00 0.00 2.57
1787 2256 4.938080 TCTCTCCTCTTTGCGATATTCAC 58.062 43.478 0.00 0.00 0.00 3.18
1788 2257 4.054671 CTCTCCTCTTTGCGATATTCACC 58.945 47.826 0.00 0.00 0.00 4.02
1789 2258 3.706594 TCTCCTCTTTGCGATATTCACCT 59.293 43.478 0.00 0.00 0.00 4.00
1790 2259 4.054671 CTCCTCTTTGCGATATTCACCTC 58.945 47.826 0.00 0.00 0.00 3.85
1791 2260 3.706594 TCCTCTTTGCGATATTCACCTCT 59.293 43.478 0.00 0.00 0.00 3.69
1792 2261 3.806521 CCTCTTTGCGATATTCACCTCTG 59.193 47.826 0.00 0.00 0.00 3.35
1793 2262 3.198068 TCTTTGCGATATTCACCTCTGC 58.802 45.455 0.00 0.00 0.00 4.26
1794 2263 1.570813 TTGCGATATTCACCTCTGCG 58.429 50.000 0.00 0.00 0.00 5.18
1795 2264 0.744281 TGCGATATTCACCTCTGCGA 59.256 50.000 0.00 0.00 0.00 5.10
1796 2265 1.341209 TGCGATATTCACCTCTGCGAT 59.659 47.619 0.00 0.00 0.00 4.58
1797 2266 2.556622 TGCGATATTCACCTCTGCGATA 59.443 45.455 0.00 0.00 0.00 2.92
1798 2267 3.193479 TGCGATATTCACCTCTGCGATAT 59.807 43.478 0.00 0.00 0.00 1.63
1799 2268 4.177026 GCGATATTCACCTCTGCGATATT 58.823 43.478 0.00 0.00 0.00 1.28
1800 2269 4.627467 GCGATATTCACCTCTGCGATATTT 59.373 41.667 0.00 0.00 0.00 1.40
1801 2270 5.220303 GCGATATTCACCTCTGCGATATTTC 60.220 44.000 0.00 0.00 0.00 2.17
1802 2271 6.096036 CGATATTCACCTCTGCGATATTTCT 58.904 40.000 0.00 0.00 0.00 2.52
1803 2272 6.034363 CGATATTCACCTCTGCGATATTTCTG 59.966 42.308 0.00 0.00 0.00 3.02
1804 2273 2.826428 TCACCTCTGCGATATTTCTGC 58.174 47.619 0.00 0.00 0.00 4.26
1805 2274 1.524355 CACCTCTGCGATATTTCTGCG 59.476 52.381 0.00 0.00 0.00 5.18
1806 2275 1.409064 ACCTCTGCGATATTTCTGCGA 59.591 47.619 0.00 0.00 0.00 5.10
1807 2276 2.036475 ACCTCTGCGATATTTCTGCGAT 59.964 45.455 0.00 0.00 0.00 4.58
1808 2277 3.255888 ACCTCTGCGATATTTCTGCGATA 59.744 43.478 0.00 0.00 0.00 2.92
1809 2278 4.081972 ACCTCTGCGATATTTCTGCGATAT 60.082 41.667 0.00 0.00 0.00 1.63
1810 2279 4.867047 CCTCTGCGATATTTCTGCGATATT 59.133 41.667 0.00 0.00 0.00 1.28
1811 2280 5.005203 CCTCTGCGATATTTCTGCGATATTC 59.995 44.000 0.00 0.00 0.00 1.75
1812 2281 5.469479 TCTGCGATATTTCTGCGATATTCA 58.531 37.500 0.00 0.00 0.00 2.57
1813 2282 5.346011 TCTGCGATATTTCTGCGATATTCAC 59.654 40.000 0.00 0.00 0.00 3.18
1814 2283 4.388773 TGCGATATTTCTGCGATATTCACC 59.611 41.667 0.00 0.00 0.00 4.02
1815 2284 4.627467 GCGATATTTCTGCGATATTCACCT 59.373 41.667 0.00 0.00 0.00 4.00
1816 2285 5.220303 GCGATATTTCTGCGATATTCACCTC 60.220 44.000 0.00 0.00 0.00 3.85
1817 2286 6.096036 CGATATTTCTGCGATATTCACCTCT 58.904 40.000 0.00 0.00 0.00 3.69
1818 2287 6.587990 CGATATTTCTGCGATATTCACCTCTT 59.412 38.462 0.00 0.00 0.00 2.85
1819 2288 5.998454 ATTTCTGCGATATTCACCTCTTG 57.002 39.130 0.00 0.00 0.00 3.02
1820 2289 2.826428 TCTGCGATATTCACCTCTTGC 58.174 47.619 0.00 0.00 0.00 4.01
1821 2290 1.524355 CTGCGATATTCACCTCTTGCG 59.476 52.381 0.00 0.00 0.00 4.85
1822 2291 1.136110 TGCGATATTCACCTCTTGCGA 59.864 47.619 0.00 0.00 0.00 5.10
1823 2292 2.201732 GCGATATTCACCTCTTGCGAA 58.798 47.619 0.00 0.00 0.00 4.70
1824 2293 2.607635 GCGATATTCACCTCTTGCGAAA 59.392 45.455 0.00 0.00 0.00 3.46
1825 2294 3.063452 GCGATATTCACCTCTTGCGAAAA 59.937 43.478 0.00 0.00 0.00 2.29
1826 2295 4.260784 GCGATATTCACCTCTTGCGAAAAT 60.261 41.667 0.00 0.00 0.00 1.82
1827 2296 5.050363 GCGATATTCACCTCTTGCGAAAATA 60.050 40.000 0.00 0.00 0.00 1.40
1828 2297 6.355638 CGATATTCACCTCTTGCGAAAATAC 58.644 40.000 0.00 0.00 0.00 1.89
1849 2777 5.579564 ACTCCGTGTATTTCTCTACCTTC 57.420 43.478 0.00 0.00 0.00 3.46
1868 2796 2.826428 TCTGCGATATTCACCTCTTGC 58.174 47.619 0.00 0.00 0.00 4.01
1870 2798 1.209261 TGCGATATTCACCTCTTGCCA 59.791 47.619 0.00 0.00 0.00 4.92
1871 2799 1.599542 GCGATATTCACCTCTTGCCAC 59.400 52.381 0.00 0.00 0.00 5.01
1872 2800 1.860950 CGATATTCACCTCTTGCCACG 59.139 52.381 0.00 0.00 0.00 4.94
1874 2802 2.380084 TATTCACCTCTTGCCACGTC 57.620 50.000 0.00 0.00 0.00 4.34
1875 2803 0.687354 ATTCACCTCTTGCCACGTCT 59.313 50.000 0.00 0.00 0.00 4.18
1876 2804 0.468226 TTCACCTCTTGCCACGTCTT 59.532 50.000 0.00 0.00 0.00 3.01
1877 2805 0.468226 TCACCTCTTGCCACGTCTTT 59.532 50.000 0.00 0.00 0.00 2.52
1878 2806 0.588252 CACCTCTTGCCACGTCTTTG 59.412 55.000 0.00 0.00 0.00 2.77
1889 2817 3.546218 GCCACGTCTTTGTCTTCTTCAAC 60.546 47.826 0.00 0.00 0.00 3.18
1900 2828 6.194796 TGTCTTCTTCAACCTTGAACAAAG 57.805 37.500 0.00 4.68 41.88 2.77
1914 2842 4.965814 TGAACAAAGAACTGAGCATCTCT 58.034 39.130 0.00 0.00 34.92 3.10
1918 2846 7.663081 TGAACAAAGAACTGAGCATCTCTATTT 59.337 33.333 0.00 0.00 34.92 1.40
1920 2848 9.507329 AACAAAGAACTGAGCATCTCTATTTAA 57.493 29.630 0.00 0.00 34.92 1.52
1921 2849 9.160496 ACAAAGAACTGAGCATCTCTATTTAAG 57.840 33.333 0.00 0.00 34.92 1.85
1923 2851 7.667575 AGAACTGAGCATCTCTATTTAAGGA 57.332 36.000 0.00 0.00 34.92 3.36
1926 2854 8.499403 AACTGAGCATCTCTATTTAAGGAAAC 57.501 34.615 0.00 0.00 34.92 2.78
1928 2856 7.768120 ACTGAGCATCTCTATTTAAGGAAACAG 59.232 37.037 0.00 0.00 34.92 3.16
1949 2877 7.111247 ACAGAACTTCAATTTCATTTGGACA 57.889 32.000 0.00 0.00 0.00 4.02
1975 2903 3.960102 TGAATATTTGCTGGGTGGAATCC 59.040 43.478 0.00 0.00 0.00 3.01
1987 2915 3.517500 GGGTGGAATCCATTGCCTTTTTA 59.482 43.478 4.81 0.00 35.28 1.52
1993 2921 7.174772 GTGGAATCCATTGCCTTTTTAATTGTT 59.825 33.333 4.81 0.00 35.28 2.83
2027 2955 6.263168 GCTGCACCTGGTATAGTCAATAAAAT 59.737 38.462 0.00 0.00 0.00 1.82
2132 3060 6.012421 AGGAAAACTAAAGTGGAAGGATAGCT 60.012 38.462 0.00 0.00 0.00 3.32
2154 3082 4.407365 TCATCCTGAGAAAAAGGGTTTCC 58.593 43.478 0.00 0.00 35.35 3.13
2155 3083 3.238788 TCCTGAGAAAAAGGGTTTCCC 57.761 47.619 0.00 0.00 45.90 3.97
2164 3092 2.203582 GGGTTTCCCCCGCTTTGT 60.204 61.111 0.00 0.00 45.80 2.83
2165 3093 1.075305 GGGTTTCCCCCGCTTTGTA 59.925 57.895 0.00 0.00 45.80 2.41
2166 3094 0.323999 GGGTTTCCCCCGCTTTGTAT 60.324 55.000 0.00 0.00 45.80 2.29
2167 3095 1.552578 GGTTTCCCCCGCTTTGTATT 58.447 50.000 0.00 0.00 0.00 1.89
2168 3096 1.475280 GGTTTCCCCCGCTTTGTATTC 59.525 52.381 0.00 0.00 0.00 1.75
2169 3097 1.475280 GTTTCCCCCGCTTTGTATTCC 59.525 52.381 0.00 0.00 0.00 3.01
2170 3098 0.699399 TTCCCCCGCTTTGTATTCCA 59.301 50.000 0.00 0.00 0.00 3.53
2171 3099 0.699399 TCCCCCGCTTTGTATTCCAA 59.301 50.000 0.00 0.00 0.00 3.53
2172 3100 1.075698 TCCCCCGCTTTGTATTCCAAA 59.924 47.619 0.00 0.00 40.71 3.28
2182 3110 4.329462 TTGTATTCCAAAGCAACCAACC 57.671 40.909 0.00 0.00 0.00 3.77
2203 3131 3.564511 CGATTGCCGTTCAAGTTTGATT 58.435 40.909 0.00 0.00 38.22 2.57
2246 3174 3.466836 AGCTGACACGAATTTCAGTCAA 58.533 40.909 17.28 6.88 41.24 3.18
2274 3202 9.453572 TGATAAATAGCCATGGACTATGAAATC 57.546 33.333 18.40 20.36 39.21 2.17
2298 3226 2.558359 GACACCTGTTGGCAGCTTTAAT 59.442 45.455 2.28 0.00 41.26 1.40
2309 3237 6.441093 TGGCAGCTTTAATGTTTGATCTAG 57.559 37.500 0.00 0.00 0.00 2.43
2412 3341 8.259411 TCTTTAAATTAATTGATGCATGCACCT 58.741 29.630 25.37 8.32 0.00 4.00
2425 3378 9.348476 TGATGCATGCACCTTATTTTATTACTA 57.652 29.630 25.37 0.00 0.00 1.82
2465 3418 6.664515 TCATGTCGTGGTTTAGTTCAAATTC 58.335 36.000 0.00 0.00 0.00 2.17
2466 3419 6.261158 TCATGTCGTGGTTTAGTTCAAATTCA 59.739 34.615 0.00 0.00 0.00 2.57
2478 3431 6.149129 AGTTCAAATTCAAAACAGAGGGAC 57.851 37.500 0.00 0.00 0.00 4.46
2479 3432 5.656416 AGTTCAAATTCAAAACAGAGGGACA 59.344 36.000 0.00 0.00 0.00 4.02
2487 3440 5.070001 TCAAAACAGAGGGACAATAAGGTG 58.930 41.667 0.00 0.00 0.00 4.00
2490 3443 3.248024 ACAGAGGGACAATAAGGTGACA 58.752 45.455 0.00 0.00 0.00 3.58
2547 3538 8.450964 ACATGTACTAACATTTATGCAAGTCAC 58.549 33.333 0.00 0.00 44.07 3.67
2564 3555 4.936891 AGTCACCAGTGAAAGCAAAAATC 58.063 39.130 1.23 0.00 41.85 2.17
2565 3556 4.402155 AGTCACCAGTGAAAGCAAAAATCA 59.598 37.500 1.23 0.00 41.85 2.57
2566 3557 4.741676 GTCACCAGTGAAAGCAAAAATCAG 59.258 41.667 1.23 0.00 41.85 2.90
2601 3594 7.439955 ACATATGTTTGTCGAGTTACTGTTTCA 59.560 33.333 1.41 0.00 0.00 2.69
2615 3612 1.271379 TGTTTCACCGCATCTAGTCGT 59.729 47.619 0.00 0.00 0.00 4.34
2639 3821 7.534239 CGTGGAAGAAGACTTAAAGCATAAAAC 59.466 37.037 0.00 0.00 36.39 2.43
2640 3822 8.349983 GTGGAAGAAGACTTAAAGCATAAAACA 58.650 33.333 0.00 0.00 36.39 2.83
2641 3823 9.077885 TGGAAGAAGACTTAAAGCATAAAACAT 57.922 29.630 0.00 0.00 36.39 2.71
2680 3930 4.802051 GCGCCCCCTCTGCAATGA 62.802 66.667 0.00 0.00 0.00 2.57
2681 3931 2.825836 CGCCCCCTCTGCAATGAC 60.826 66.667 0.00 0.00 0.00 3.06
2682 3932 2.440980 GCCCCCTCTGCAATGACC 60.441 66.667 0.00 0.00 0.00 4.02
2683 3933 2.124570 CCCCCTCTGCAATGACCG 60.125 66.667 0.00 0.00 0.00 4.79
2684 3934 2.671070 CCCCTCTGCAATGACCGT 59.329 61.111 0.00 0.00 0.00 4.83
2685 3935 1.746615 CCCCTCTGCAATGACCGTG 60.747 63.158 0.00 0.00 0.00 4.94
2686 3936 1.746615 CCCTCTGCAATGACCGTGG 60.747 63.158 0.00 0.00 0.00 4.94
2687 3937 1.003355 CCTCTGCAATGACCGTGGT 60.003 57.895 0.00 0.00 0.00 4.16
2688 3938 0.249120 CCTCTGCAATGACCGTGGTA 59.751 55.000 0.00 0.00 0.00 3.25
2689 3939 1.645034 CTCTGCAATGACCGTGGTAG 58.355 55.000 0.00 0.00 0.00 3.18
2690 3940 0.249120 TCTGCAATGACCGTGGTAGG 59.751 55.000 0.00 0.00 37.30 3.18
2691 3941 0.249120 CTGCAATGACCGTGGTAGGA 59.751 55.000 0.00 0.00 34.73 2.94
2692 3942 0.036765 TGCAATGACCGTGGTAGGAC 60.037 55.000 0.00 0.00 34.73 3.85
2693 3943 1.082117 GCAATGACCGTGGTAGGACG 61.082 60.000 0.00 0.00 39.13 4.79
2694 3944 0.245539 CAATGACCGTGGTAGGACGT 59.754 55.000 0.00 0.00 37.66 4.34
2695 3945 0.971386 AATGACCGTGGTAGGACGTT 59.029 50.000 0.00 0.00 37.66 3.99
2696 3946 0.245539 ATGACCGTGGTAGGACGTTG 59.754 55.000 0.00 0.00 37.66 4.10
2697 3947 0.822944 TGACCGTGGTAGGACGTTGA 60.823 55.000 0.00 0.00 37.66 3.18
2698 3948 0.529378 GACCGTGGTAGGACGTTGAT 59.471 55.000 0.00 0.00 37.66 2.57
2699 3949 0.971386 ACCGTGGTAGGACGTTGATT 59.029 50.000 0.00 0.00 37.66 2.57
2700 3950 1.337447 ACCGTGGTAGGACGTTGATTG 60.337 52.381 0.00 0.00 37.66 2.67
2701 3951 1.337447 CCGTGGTAGGACGTTGATTGT 60.337 52.381 0.00 0.00 37.66 2.71
2702 3952 2.409975 CGTGGTAGGACGTTGATTGTT 58.590 47.619 0.00 0.00 34.56 2.83
2703 3953 3.577667 CGTGGTAGGACGTTGATTGTTA 58.422 45.455 0.00 0.00 34.56 2.41
2704 3954 3.365820 CGTGGTAGGACGTTGATTGTTAC 59.634 47.826 0.00 0.00 34.56 2.50
2705 3955 3.681417 GTGGTAGGACGTTGATTGTTACC 59.319 47.826 0.00 0.00 0.00 2.85
2706 3956 3.324268 TGGTAGGACGTTGATTGTTACCA 59.676 43.478 0.00 0.00 37.37 3.25
2707 3957 3.681417 GGTAGGACGTTGATTGTTACCAC 59.319 47.826 0.00 0.00 31.61 4.16
2708 3958 2.409975 AGGACGTTGATTGTTACCACG 58.590 47.619 0.00 0.00 0.00 4.94
2709 3959 2.137523 GGACGTTGATTGTTACCACGT 58.862 47.619 0.00 0.00 34.98 4.49
2710 3960 2.156310 GGACGTTGATTGTTACCACGTC 59.844 50.000 13.35 13.35 44.95 4.34
2711 3961 1.788308 ACGTTGATTGTTACCACGTCG 59.212 47.619 0.00 0.00 0.00 5.12
2712 3962 2.052891 CGTTGATTGTTACCACGTCGA 58.947 47.619 0.00 0.00 0.00 4.20
2713 3963 2.664568 CGTTGATTGTTACCACGTCGAT 59.335 45.455 0.00 0.00 0.00 3.59
2714 3964 3.853103 CGTTGATTGTTACCACGTCGATA 59.147 43.478 0.00 0.00 0.00 2.92
2715 3965 4.259135 CGTTGATTGTTACCACGTCGATAC 60.259 45.833 0.00 0.00 0.00 2.24
2716 3966 4.437772 TGATTGTTACCACGTCGATACA 57.562 40.909 0.00 0.00 0.00 2.29
2717 3967 5.001237 TGATTGTTACCACGTCGATACAT 57.999 39.130 0.00 0.00 0.00 2.29
2718 3968 5.412640 TGATTGTTACCACGTCGATACATT 58.587 37.500 0.00 0.00 0.00 2.71
2719 3969 5.289917 TGATTGTTACCACGTCGATACATTG 59.710 40.000 0.00 0.00 0.00 2.82
2720 3970 4.177165 TGTTACCACGTCGATACATTGT 57.823 40.909 0.00 0.00 0.00 2.71
2721 3971 5.307926 TGTTACCACGTCGATACATTGTA 57.692 39.130 0.00 0.00 0.00 2.41
2722 3972 5.334319 TGTTACCACGTCGATACATTGTAG 58.666 41.667 0.00 0.00 0.00 2.74
2723 3973 3.431922 ACCACGTCGATACATTGTAGG 57.568 47.619 0.00 0.00 0.00 3.18
2724 3974 2.124903 CCACGTCGATACATTGTAGGC 58.875 52.381 0.00 0.00 0.00 3.93
2725 3975 2.480587 CCACGTCGATACATTGTAGGCA 60.481 50.000 0.00 0.00 0.00 4.75
2726 3976 3.183754 CACGTCGATACATTGTAGGCAA 58.816 45.455 0.00 0.00 39.16 4.52
2727 3977 3.242944 CACGTCGATACATTGTAGGCAAG 59.757 47.826 0.00 0.00 38.10 4.01
2728 3978 3.129813 ACGTCGATACATTGTAGGCAAGA 59.870 43.478 0.00 0.00 38.10 3.02
2729 3979 3.486108 CGTCGATACATTGTAGGCAAGAC 59.514 47.826 2.53 6.34 38.10 3.01
2730 3980 3.486108 GTCGATACATTGTAGGCAAGACG 59.514 47.826 2.53 0.00 38.10 4.18
2731 3981 2.218759 CGATACATTGTAGGCAAGACGC 59.781 50.000 2.53 0.00 38.10 5.19
2732 3982 2.753055 TACATTGTAGGCAAGACGCA 57.247 45.000 0.00 0.00 45.17 5.24
2733 3983 1.156736 ACATTGTAGGCAAGACGCAC 58.843 50.000 0.00 0.00 45.17 5.34
2734 3984 1.155889 CATTGTAGGCAAGACGCACA 58.844 50.000 0.00 0.00 45.17 4.57
2738 4016 1.535028 TGTAGGCAAGACGCACAAATG 59.465 47.619 0.00 0.00 45.17 2.32
2804 4593 3.110358 TCGACTGTAGAAACAACACACG 58.890 45.455 0.00 0.00 34.49 4.49
2809 4598 2.353269 TGTAGAAACAACACACGCCAAG 59.647 45.455 0.00 0.00 30.91 3.61
2811 4600 0.248866 GAAACAACACACGCCAAGGG 60.249 55.000 0.00 0.00 0.00 3.95
2820 4610 2.161609 CACACGCCAAGGGAAATAGAAC 59.838 50.000 0.00 0.00 0.00 3.01
2855 4645 2.101770 CGTCGACGGCTAGGGTTC 59.898 66.667 29.70 0.00 35.37 3.62
2864 4654 4.204799 GACGGCTAGGGTTCCAATTAAAT 58.795 43.478 0.00 0.00 0.00 1.40
2870 4660 7.041721 GGCTAGGGTTCCAATTAAATTTTCAG 58.958 38.462 0.00 0.00 0.00 3.02
2906 4696 5.476599 TCATTACAGGGACAAACATGGAAAG 59.523 40.000 0.00 0.00 0.00 2.62
2942 4732 1.226974 CGGTACAGCTGCGCACTAT 60.227 57.895 15.27 0.26 0.00 2.12
3010 4800 1.269569 GGAACTTTTCGGCAAAGGTGG 60.270 52.381 5.18 0.00 42.99 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.023707 GCCATTGGACATGTATAGCTTGTC 60.024 45.833 6.95 6.90 45.86 3.18
5 6 4.916983 TTTGCCATTGGACATGTATAGC 57.083 40.909 6.95 0.00 0.00 2.97
23 24 9.384682 GAACAAAAATATTTCCTGCAACATTTG 57.615 29.630 0.10 1.34 0.00 2.32
178 182 2.380084 TACGCTTGTCTAAAGCCAGG 57.620 50.000 4.59 0.00 40.02 4.45
181 185 4.680171 ACAAATACGCTTGTCTAAAGCC 57.320 40.909 4.59 0.00 40.02 4.35
182 186 5.928153 AGAACAAATACGCTTGTCTAAAGC 58.072 37.500 0.00 0.00 38.59 3.51
183 187 8.283291 AGAAAGAACAAATACGCTTGTCTAAAG 58.717 33.333 0.00 0.00 38.59 1.85
245 258 5.466393 CAGGTAATTCTTTGTGCCAAAAAGG 59.534 40.000 7.50 0.00 41.84 3.11
277 292 4.700692 CGATAGGCCACTTACTATGCTAGA 59.299 45.833 5.01 0.00 30.43 2.43
302 317 3.190849 CTCCAGCGCATCACACGG 61.191 66.667 11.47 0.00 0.00 4.94
304 319 2.821366 CCCTCCAGCGCATCACAC 60.821 66.667 11.47 0.00 0.00 3.82
306 321 2.045926 AACCCTCCAGCGCATCAC 60.046 61.111 11.47 0.00 0.00 3.06
308 323 2.825836 CCAACCCTCCAGCGCATC 60.826 66.667 11.47 0.00 0.00 3.91
309 324 3.628646 GACCAACCCTCCAGCGCAT 62.629 63.158 11.47 0.00 0.00 4.73
346 364 7.170828 CGTCCGATTTAGGATGTTTGATCAATA 59.829 37.037 9.40 2.07 43.04 1.90
539 563 0.727398 GAAAGGGATTCGAAGCACCG 59.273 55.000 12.91 0.00 0.00 4.94
616 640 7.333528 ACTTCTTTTGACATCTGCTTTGTTA 57.666 32.000 0.00 0.00 0.00 2.41
802 889 4.404654 CGCGTGGCTCCTTTTGGC 62.405 66.667 0.00 0.00 40.12 4.52
959 1046 1.792632 GCGTGGGTTTTTATAGCGTGC 60.793 52.381 0.00 0.00 0.00 5.34
1315 1772 0.836400 TCTTCTTGAGGCCCTTCGGT 60.836 55.000 0.00 0.00 0.00 4.69
1410 1867 0.457443 CAGGCAGATCGCACACTCTA 59.543 55.000 10.82 0.00 45.17 2.43
1724 2193 2.363680 AGAGAGAGCGAGAGAGAGAGAG 59.636 54.545 0.00 0.00 0.00 3.20
1726 2195 2.748605 GAGAGAGAGCGAGAGAGAGAG 58.251 57.143 0.00 0.00 0.00 3.20
1727 2196 1.067060 CGAGAGAGAGCGAGAGAGAGA 59.933 57.143 0.00 0.00 0.00 3.10
1737 2206 1.202580 AGAGAGAGAGCGAGAGAGAGC 60.203 57.143 0.00 0.00 0.00 4.09
1740 2209 2.363680 AGAGAGAGAGAGAGCGAGAGAG 59.636 54.545 0.00 0.00 0.00 3.20
1741 2210 2.362397 GAGAGAGAGAGAGAGCGAGAGA 59.638 54.545 0.00 0.00 0.00 3.10
1742 2211 2.363680 AGAGAGAGAGAGAGAGCGAGAG 59.636 54.545 0.00 0.00 0.00 3.20
1743 2212 2.362397 GAGAGAGAGAGAGAGAGCGAGA 59.638 54.545 0.00 0.00 0.00 4.04
1744 2213 2.363680 AGAGAGAGAGAGAGAGAGCGAG 59.636 54.545 0.00 0.00 0.00 5.03
1745 2214 2.362397 GAGAGAGAGAGAGAGAGAGCGA 59.638 54.545 0.00 0.00 0.00 4.93
1748 2217 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
1749 2218 4.078922 AGGAGAGAGAGAGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
1750 2219 4.222336 AGGAGAGAGAGAGAGAGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
1752 2221 4.222336 AGAGGAGAGAGAGAGAGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
1753 2222 4.271807 AGAGGAGAGAGAGAGAGAGAGA 57.728 50.000 0.00 0.00 0.00 3.10
1754 2223 5.121811 CAAAGAGGAGAGAGAGAGAGAGAG 58.878 50.000 0.00 0.00 0.00 3.20
1755 2224 4.626287 GCAAAGAGGAGAGAGAGAGAGAGA 60.626 50.000 0.00 0.00 0.00 3.10
1756 2225 3.629398 GCAAAGAGGAGAGAGAGAGAGAG 59.371 52.174 0.00 0.00 0.00 3.20
1757 2226 3.620488 GCAAAGAGGAGAGAGAGAGAGA 58.380 50.000 0.00 0.00 0.00 3.10
1758 2227 2.355756 CGCAAAGAGGAGAGAGAGAGAG 59.644 54.545 0.00 0.00 0.00 3.20
1759 2228 2.026729 TCGCAAAGAGGAGAGAGAGAGA 60.027 50.000 0.00 0.00 0.00 3.10
1760 2229 2.364632 TCGCAAAGAGGAGAGAGAGAG 58.635 52.381 0.00 0.00 0.00 3.20
1761 2230 2.498644 TCGCAAAGAGGAGAGAGAGA 57.501 50.000 0.00 0.00 0.00 3.10
1762 2231 5.009510 TGAATATCGCAAAGAGGAGAGAGAG 59.990 44.000 0.00 0.00 0.00 3.20
1763 2232 4.889995 TGAATATCGCAAAGAGGAGAGAGA 59.110 41.667 0.00 0.00 0.00 3.10
1764 2233 4.981674 GTGAATATCGCAAAGAGGAGAGAG 59.018 45.833 0.00 0.00 0.00 3.20
1765 2234 4.202161 GGTGAATATCGCAAAGAGGAGAGA 60.202 45.833 0.00 0.00 0.00 3.10
1766 2235 4.054671 GGTGAATATCGCAAAGAGGAGAG 58.945 47.826 0.00 0.00 0.00 3.20
1767 2236 3.706594 AGGTGAATATCGCAAAGAGGAGA 59.293 43.478 0.00 0.00 0.00 3.71
1768 2237 4.054671 GAGGTGAATATCGCAAAGAGGAG 58.945 47.826 0.00 0.00 0.00 3.69
1769 2238 3.706594 AGAGGTGAATATCGCAAAGAGGA 59.293 43.478 0.00 0.00 0.00 3.71
1770 2239 3.806521 CAGAGGTGAATATCGCAAAGAGG 59.193 47.826 0.00 0.00 0.00 3.69
1771 2240 3.247173 GCAGAGGTGAATATCGCAAAGAG 59.753 47.826 0.00 0.00 0.00 2.85
1772 2241 3.198068 GCAGAGGTGAATATCGCAAAGA 58.802 45.455 0.00 0.00 0.00 2.52
1773 2242 2.033407 CGCAGAGGTGAATATCGCAAAG 60.033 50.000 0.00 0.00 0.00 2.77
1774 2243 1.933181 CGCAGAGGTGAATATCGCAAA 59.067 47.619 0.00 0.00 0.00 3.68
1775 2244 1.136110 TCGCAGAGGTGAATATCGCAA 59.864 47.619 0.00 0.00 0.00 4.85
1776 2245 0.744281 TCGCAGAGGTGAATATCGCA 59.256 50.000 0.00 0.00 0.00 5.10
1777 2246 2.071688 ATCGCAGAGGTGAATATCGC 57.928 50.000 0.00 0.00 43.63 4.58
1778 2247 6.034363 CAGAAATATCGCAGAGGTGAATATCG 59.966 42.308 0.00 0.00 43.63 2.92
1779 2248 6.183360 GCAGAAATATCGCAGAGGTGAATATC 60.183 42.308 0.00 0.00 43.63 1.63
1780 2249 5.641209 GCAGAAATATCGCAGAGGTGAATAT 59.359 40.000 0.00 0.00 43.63 1.28
1781 2250 4.991056 GCAGAAATATCGCAGAGGTGAATA 59.009 41.667 0.00 0.00 43.63 1.75
1782 2251 3.812053 GCAGAAATATCGCAGAGGTGAAT 59.188 43.478 0.00 0.00 43.63 2.57
1783 2252 3.198068 GCAGAAATATCGCAGAGGTGAA 58.802 45.455 0.00 0.00 43.63 3.18
1784 2253 2.799562 CGCAGAAATATCGCAGAGGTGA 60.800 50.000 0.00 0.00 43.63 4.02
1785 2254 1.524355 CGCAGAAATATCGCAGAGGTG 59.476 52.381 0.00 0.00 43.63 4.00
1786 2255 1.409064 TCGCAGAAATATCGCAGAGGT 59.591 47.619 0.00 0.00 43.63 3.85
1787 2256 2.140065 TCGCAGAAATATCGCAGAGG 57.860 50.000 0.00 0.00 43.63 3.69
1788 2257 5.574443 TGAATATCGCAGAAATATCGCAGAG 59.426 40.000 0.00 0.00 40.54 3.35
1789 2258 5.346011 GTGAATATCGCAGAAATATCGCAGA 59.654 40.000 0.00 0.00 43.58 4.26
1790 2259 5.445142 GGTGAATATCGCAGAAATATCGCAG 60.445 44.000 0.00 0.00 43.58 5.18
1791 2260 4.388773 GGTGAATATCGCAGAAATATCGCA 59.611 41.667 0.00 0.00 43.58 5.10
1792 2261 4.627467 AGGTGAATATCGCAGAAATATCGC 59.373 41.667 0.00 0.00 43.58 4.58
1793 2262 6.096036 AGAGGTGAATATCGCAGAAATATCG 58.904 40.000 0.00 0.00 43.58 2.92
1794 2263 7.623089 GCAAGAGGTGAATATCGCAGAAATATC 60.623 40.741 0.00 0.00 43.58 1.63
1795 2264 6.148480 GCAAGAGGTGAATATCGCAGAAATAT 59.852 38.462 0.00 0.00 43.58 1.28
1796 2265 5.466728 GCAAGAGGTGAATATCGCAGAAATA 59.533 40.000 0.00 0.00 43.58 1.40
1797 2266 4.274459 GCAAGAGGTGAATATCGCAGAAAT 59.726 41.667 0.00 0.00 43.58 2.17
1798 2267 3.623060 GCAAGAGGTGAATATCGCAGAAA 59.377 43.478 0.00 0.00 43.58 2.52
1799 2268 3.198068 GCAAGAGGTGAATATCGCAGAA 58.802 45.455 0.00 0.00 43.58 3.02
1800 2269 2.799562 CGCAAGAGGTGAATATCGCAGA 60.800 50.000 0.00 0.00 41.23 4.26
1801 2270 1.524355 CGCAAGAGGTGAATATCGCAG 59.476 52.381 0.00 0.00 43.02 5.18
1802 2271 1.136110 TCGCAAGAGGTGAATATCGCA 59.864 47.619 0.00 0.00 45.01 5.10
1803 2272 1.852942 TCGCAAGAGGTGAATATCGC 58.147 50.000 0.00 0.00 45.01 4.58
1807 2276 9.664275 ACGGAGTATTTTCGCAAGAGGTGAATA 62.664 40.741 0.00 0.00 46.67 1.75
1808 2277 8.957901 ACGGAGTATTTTCGCAAGAGGTGAAT 62.958 42.308 0.00 0.00 46.67 2.57
1809 2278 7.751450 ACGGAGTATTTTCGCAAGAGGTGAA 62.751 44.000 0.00 0.00 46.67 3.18
1810 2279 6.357404 ACGGAGTATTTTCGCAAGAGGTGA 62.357 45.833 0.00 0.00 46.67 4.02
1811 2280 4.167685 ACGGAGTATTTTCGCAAGAGGTG 61.168 47.826 0.00 0.00 46.67 4.00
1812 2281 2.028385 ACGGAGTATTTTCGCAAGAGGT 60.028 45.455 0.00 0.00 46.67 3.85
1813 2282 2.348666 CACGGAGTATTTTCGCAAGAGG 59.651 50.000 0.00 0.00 46.82 3.69
1814 2283 2.993899 ACACGGAGTATTTTCGCAAGAG 59.006 45.455 0.00 0.00 46.82 2.85
1815 2284 3.034721 ACACGGAGTATTTTCGCAAGA 57.965 42.857 0.00 0.00 44.40 3.02
1825 2294 7.013464 CAGAAGGTAGAGAAATACACGGAGTAT 59.987 40.741 0.00 0.00 45.27 2.12
1826 2295 6.318144 CAGAAGGTAGAGAAATACACGGAGTA 59.682 42.308 0.00 0.00 41.61 2.59
1828 2297 5.583495 CAGAAGGTAGAGAAATACACGGAG 58.417 45.833 0.00 0.00 0.00 4.63
1849 2777 1.869767 GGCAAGAGGTGAATATCGCAG 59.130 52.381 0.00 0.00 0.00 5.18
1868 2796 3.002348 GGTTGAAGAAGACAAAGACGTGG 59.998 47.826 0.00 0.00 0.00 4.94
1870 2798 4.138487 AGGTTGAAGAAGACAAAGACGT 57.862 40.909 0.00 0.00 0.00 4.34
1871 2799 4.570772 TCAAGGTTGAAGAAGACAAAGACG 59.429 41.667 0.00 0.00 33.55 4.18
1872 2800 6.128007 TGTTCAAGGTTGAAGAAGACAAAGAC 60.128 38.462 5.38 0.00 46.80 3.01
1874 2802 6.194796 TGTTCAAGGTTGAAGAAGACAAAG 57.805 37.500 5.38 0.00 46.80 2.77
1875 2803 6.582677 TTGTTCAAGGTTGAAGAAGACAAA 57.417 33.333 10.16 0.00 46.80 2.83
1876 2804 6.432783 TCTTTGTTCAAGGTTGAAGAAGACAA 59.567 34.615 18.38 12.03 46.57 3.18
1877 2805 5.943416 TCTTTGTTCAAGGTTGAAGAAGACA 59.057 36.000 18.38 7.98 46.57 3.41
1878 2806 6.436843 TCTTTGTTCAAGGTTGAAGAAGAC 57.563 37.500 18.38 6.06 46.57 3.01
1889 2817 4.518211 AGATGCTCAGTTCTTTGTTCAAGG 59.482 41.667 0.00 0.00 32.64 3.61
1900 2828 8.608317 GTTTCCTTAAATAGAGATGCTCAGTTC 58.392 37.037 0.00 0.00 32.06 3.01
1920 2848 7.712205 CCAAATGAAATTGAAGTTCTGTTTCCT 59.288 33.333 20.71 13.63 36.10 3.36
1921 2849 7.710475 TCCAAATGAAATTGAAGTTCTGTTTCC 59.290 33.333 20.71 10.56 36.10 3.13
1923 2851 8.040132 TGTCCAAATGAAATTGAAGTTCTGTTT 58.960 29.630 6.92 5.24 36.10 2.83
1926 2854 7.205297 AGTGTCCAAATGAAATTGAAGTTCTG 58.795 34.615 6.92 0.00 36.10 3.02
1928 2856 9.132521 CATAGTGTCCAAATGAAATTGAAGTTC 57.867 33.333 0.00 0.00 36.10 3.01
1949 2877 5.387113 TCCACCCAGCAAATATTCATAGT 57.613 39.130 0.00 0.00 0.00 2.12
2005 2933 9.869757 AAAAATTTTATTGACTATACCAGGTGC 57.130 29.630 0.76 0.00 0.00 5.01
2027 2955 7.222805 CGAATCGATTCTGATGGAGACTAAAAA 59.777 37.037 29.97 0.00 34.69 1.94
2149 3077 1.475280 GGAATACAAAGCGGGGGAAAC 59.525 52.381 0.00 0.00 0.00 2.78
2150 3078 1.075698 TGGAATACAAAGCGGGGGAAA 59.924 47.619 0.00 0.00 0.00 3.13
2151 3079 0.699399 TGGAATACAAAGCGGGGGAA 59.301 50.000 0.00 0.00 0.00 3.97
2152 3080 0.699399 TTGGAATACAAAGCGGGGGA 59.301 50.000 0.00 0.00 35.79 4.81
2153 3081 1.551452 TTTGGAATACAAAGCGGGGG 58.449 50.000 0.00 0.00 43.81 5.40
2160 3088 4.698575 GGTTGGTTGCTTTGGAATACAAA 58.301 39.130 0.00 0.00 46.34 2.83
2161 3089 3.243569 CGGTTGGTTGCTTTGGAATACAA 60.244 43.478 0.00 0.00 37.28 2.41
2162 3090 2.294791 CGGTTGGTTGCTTTGGAATACA 59.705 45.455 0.00 0.00 0.00 2.29
2163 3091 2.554893 TCGGTTGGTTGCTTTGGAATAC 59.445 45.455 0.00 0.00 0.00 1.89
2164 3092 2.865079 TCGGTTGGTTGCTTTGGAATA 58.135 42.857 0.00 0.00 0.00 1.75
2165 3093 1.698506 TCGGTTGGTTGCTTTGGAAT 58.301 45.000 0.00 0.00 0.00 3.01
2166 3094 1.698506 ATCGGTTGGTTGCTTTGGAA 58.301 45.000 0.00 0.00 0.00 3.53
2167 3095 1.339610 CAATCGGTTGGTTGCTTTGGA 59.660 47.619 0.00 0.00 0.00 3.53
2168 3096 1.782044 CAATCGGTTGGTTGCTTTGG 58.218 50.000 0.00 0.00 0.00 3.28
2169 3097 1.139163 GCAATCGGTTGGTTGCTTTG 58.861 50.000 11.04 0.00 45.41 2.77
2170 3098 3.586430 GCAATCGGTTGGTTGCTTT 57.414 47.368 11.04 0.00 45.41 3.51
2174 3102 0.386731 GAACGGCAATCGGTTGGTTG 60.387 55.000 11.04 0.00 39.92 3.77
2175 3103 0.820074 TGAACGGCAATCGGTTGGTT 60.820 50.000 11.04 6.65 39.92 3.67
2176 3104 0.820074 TTGAACGGCAATCGGTTGGT 60.820 50.000 11.04 0.00 39.92 3.67
2177 3105 0.109781 CTTGAACGGCAATCGGTTGG 60.110 55.000 11.04 0.00 39.92 3.77
2178 3106 0.591170 ACTTGAACGGCAATCGGTTG 59.409 50.000 3.38 3.38 39.92 3.77
2179 3107 1.314730 AACTTGAACGGCAATCGGTT 58.685 45.000 0.00 0.00 39.92 4.44
2180 3108 1.001815 CAAACTTGAACGGCAATCGGT 60.002 47.619 0.00 0.00 44.24 4.69
2181 3109 1.265635 TCAAACTTGAACGGCAATCGG 59.734 47.619 0.00 0.00 36.23 4.18
2182 3110 2.679355 TCAAACTTGAACGGCAATCG 57.321 45.000 0.00 0.00 37.28 3.34
2203 3131 0.321346 ACATCACGTCCACATCAGCA 59.679 50.000 0.00 0.00 0.00 4.41
2246 3174 9.812347 TTTCATAGTCCATGGCTATTTATCAAT 57.188 29.630 19.86 0.00 35.16 2.57
2261 3189 5.045651 ACAGGTGTCATGATTTCATAGTCCA 60.046 40.000 0.00 0.00 34.26 4.02
2274 3202 1.582968 GCTGCCAACAGGTGTCATG 59.417 57.895 0.00 0.00 44.63 3.07
2298 3226 6.061441 TGCTGGAAAAGTTCTAGATCAAACA 58.939 36.000 5.63 0.00 40.34 2.83
2309 3237 7.631717 ATTAACTATCCTGCTGGAAAAGTTC 57.368 36.000 30.33 0.00 46.80 3.01
2317 3245 7.872113 AGAGAAAAATTAACTATCCTGCTGG 57.128 36.000 2.58 2.58 0.00 4.85
2391 3320 8.967664 AATAAGGTGCATGCATCAATTAATTT 57.032 26.923 31.54 17.50 0.00 1.82
2392 3321 8.967664 AAATAAGGTGCATGCATCAATTAATT 57.032 26.923 31.54 17.93 0.00 1.40
2465 3418 5.048713 GTCACCTTATTGTCCCTCTGTTTTG 60.049 44.000 0.00 0.00 0.00 2.44
2466 3419 5.070685 GTCACCTTATTGTCCCTCTGTTTT 58.929 41.667 0.00 0.00 0.00 2.43
2478 3431 6.618287 TTTGTGAGAACTGTCACCTTATTG 57.382 37.500 4.70 0.00 45.42 1.90
2479 3432 7.054124 TCTTTTGTGAGAACTGTCACCTTATT 58.946 34.615 4.70 0.00 45.42 1.40
2487 3440 8.742554 TTTTCTTTTCTTTTGTGAGAACTGTC 57.257 30.769 0.00 0.00 35.50 3.51
2490 3443 8.585018 TCCTTTTTCTTTTCTTTTGTGAGAACT 58.415 29.630 0.00 0.00 35.50 3.01
2545 3536 3.492011 GCTGATTTTTGCTTTCACTGGTG 59.508 43.478 0.00 0.00 0.00 4.17
2547 3538 3.719924 TGCTGATTTTTGCTTTCACTGG 58.280 40.909 0.00 0.00 0.00 4.00
2601 3594 0.456221 CTTCCACGACTAGATGCGGT 59.544 55.000 0.00 0.00 0.00 5.68
2615 3612 8.458573 TGTTTTATGCTTTAAGTCTTCTTCCA 57.541 30.769 0.00 0.00 35.36 3.53
2663 3913 4.802051 TCATTGCAGAGGGGGCGC 62.802 66.667 0.00 0.00 0.00 6.53
2670 3920 1.645034 CTACCACGGTCATTGCAGAG 58.355 55.000 0.00 0.00 0.00 3.35
2680 3930 0.971386 AATCAACGTCCTACCACGGT 59.029 50.000 0.00 0.00 44.41 4.83
2681 3931 1.337447 ACAATCAACGTCCTACCACGG 60.337 52.381 0.00 0.00 44.41 4.94
2682 3932 2.074547 ACAATCAACGTCCTACCACG 57.925 50.000 0.00 0.00 45.65 4.94
2683 3933 3.681417 GGTAACAATCAACGTCCTACCAC 59.319 47.826 0.00 0.00 0.00 4.16
2684 3934 3.929094 GGTAACAATCAACGTCCTACCA 58.071 45.455 0.00 0.00 0.00 3.25
2700 3950 4.736793 CCTACAATGTATCGACGTGGTAAC 59.263 45.833 0.00 0.00 31.75 2.50
2701 3951 4.734402 GCCTACAATGTATCGACGTGGTAA 60.734 45.833 0.00 0.00 31.75 2.85
2702 3952 3.243168 GCCTACAATGTATCGACGTGGTA 60.243 47.826 0.00 0.00 30.87 3.25
2703 3953 2.480759 GCCTACAATGTATCGACGTGGT 60.481 50.000 0.00 0.00 33.10 4.16
2704 3954 2.124903 GCCTACAATGTATCGACGTGG 58.875 52.381 0.00 0.00 0.00 4.94
2705 3955 2.804647 TGCCTACAATGTATCGACGTG 58.195 47.619 0.00 0.00 0.00 4.49
2706 3956 3.129813 TCTTGCCTACAATGTATCGACGT 59.870 43.478 0.00 0.00 34.61 4.34
2707 3957 3.486108 GTCTTGCCTACAATGTATCGACG 59.514 47.826 0.00 0.00 34.61 5.12
2708 3958 3.486108 CGTCTTGCCTACAATGTATCGAC 59.514 47.826 0.00 0.00 34.61 4.20
2709 3959 3.702330 CGTCTTGCCTACAATGTATCGA 58.298 45.455 0.00 0.00 34.61 3.59
2710 3960 2.218759 GCGTCTTGCCTACAATGTATCG 59.781 50.000 0.00 0.00 37.76 2.92
2711 3961 3.001330 GTGCGTCTTGCCTACAATGTATC 59.999 47.826 0.00 0.00 45.60 2.24
2712 3962 2.936498 GTGCGTCTTGCCTACAATGTAT 59.064 45.455 0.00 0.00 45.60 2.29
2713 3963 2.289133 TGTGCGTCTTGCCTACAATGTA 60.289 45.455 0.00 0.00 45.60 2.29
2714 3964 1.156736 GTGCGTCTTGCCTACAATGT 58.843 50.000 0.00 0.00 45.60 2.71
2715 3965 1.155889 TGTGCGTCTTGCCTACAATG 58.844 50.000 0.00 0.00 45.60 2.82
2716 3966 1.890876 TTGTGCGTCTTGCCTACAAT 58.109 45.000 0.00 0.00 45.60 2.71
2717 3967 1.669604 TTTGTGCGTCTTGCCTACAA 58.330 45.000 0.00 0.00 45.60 2.41
2718 3968 1.535028 CATTTGTGCGTCTTGCCTACA 59.465 47.619 0.00 0.00 45.60 2.74
2719 3969 1.535462 ACATTTGTGCGTCTTGCCTAC 59.465 47.619 0.00 0.00 45.60 3.18
2720 3970 1.890876 ACATTTGTGCGTCTTGCCTA 58.109 45.000 0.00 0.00 45.60 3.93
2721 3971 1.890876 TACATTTGTGCGTCTTGCCT 58.109 45.000 0.00 0.00 45.60 4.75
2722 3972 2.287308 TGTTACATTTGTGCGTCTTGCC 60.287 45.455 0.00 0.00 45.60 4.52
2723 3973 2.993545 TGTTACATTTGTGCGTCTTGC 58.006 42.857 0.00 0.00 46.70 4.01
2724 3974 9.502145 AATTATATGTTACATTTGTGCGTCTTG 57.498 29.630 2.23 0.00 0.00 3.02
2757 4537 2.165641 TCGCGGGACCATAGCTAATATG 59.834 50.000 6.13 0.00 40.96 1.78
2804 4593 3.344515 AGTTCGTTCTATTTCCCTTGGC 58.655 45.455 0.00 0.00 0.00 4.52
2809 4598 5.192327 TCCGATAGTTCGTTCTATTTCCC 57.808 43.478 0.00 0.00 43.97 3.97
2811 4600 7.695869 ATGTTCCGATAGTTCGTTCTATTTC 57.304 36.000 0.00 0.00 43.97 2.17
2870 4660 7.050377 TGTCCCTGTAATGAATGATTTCTCTC 58.950 38.462 0.00 0.00 32.78 3.20
2890 4680 1.273327 CTGGCTTTCCATGTTTGTCCC 59.727 52.381 0.00 0.00 42.51 4.46
2906 4696 1.442526 CGATCATGCAAGGACCTGGC 61.443 60.000 14.62 14.62 0.00 4.85
2942 4732 3.442273 GCCAATCGTTCCACAATTTCCTA 59.558 43.478 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.