Multiple sequence alignment - TraesCS3A01G174900

Loading Multiple Alignment...

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 TraesCS3A01G174900 chr3A 100.000 3776 0 0 2457 6232 194707737 194703962 0.000000e+00 6974.0
1 TraesCS3A01G174900 chr3A 100.000 2054 0 0 1 2054 194710193 194708140 0.000000e+00 3794.0
2 TraesCS3A01G174900 chr3A 88.103 311 28 6 1675 1982 194708444 194708140 1.650000e-95 361.0
3 TraesCS3A01G174900 chr3A 88.103 311 28 6 1750 2054 194708519 194708212 1.650000e-95 361.0
4 TraesCS3A01G174900 chr3A 92.000 150 12 0 2460 2609 194707656 194707507 1.760000e-50 211.0
5 TraesCS3A01G174900 chr3A 92.000 150 12 0 2538 2687 194707734 194707585 1.760000e-50 211.0
6 TraesCS3A01G174900 chr3A 91.667 48 4 0 5774 5821 108468004 108467957 4.030000e-07 67.6
7 TraesCS3A01G174900 chr3A 97.059 34 1 0 3967 4000 194706155 194706122 2.430000e-04 58.4
8 TraesCS3A01G174900 chr3A 97.059 34 1 0 4039 4072 194706227 194706194 2.430000e-04 58.4
9 TraesCS3A01G174900 chr3B 95.591 3720 119 17 2460 6164 239310124 239306435 0.000000e+00 5919.0
10 TraesCS3A01G174900 chr3B 91.267 1626 81 24 313 1916 239312063 239310477 0.000000e+00 2159.0
11 TraesCS3A01G174900 chr3B 89.172 314 28 1 1 314 239323479 239323172 2.720000e-103 387.0
12 TraesCS3A01G174900 chr3B 93.103 261 14 3 4185 4443 422225608 422225350 4.560000e-101 379.0
13 TraesCS3A01G174900 chr3B 87.308 260 27 1 1732 1991 239310175 239309922 6.110000e-75 292.0
14 TraesCS3A01G174900 chr3B 84.859 284 37 2 1680 1960 239310152 239309872 1.320000e-71 281.0
15 TraesCS3A01G174900 chr3B 87.402 254 17 9 1807 2054 239310175 239309931 1.710000e-70 278.0
16 TraesCS3A01G174900 chr3B 92.941 170 9 1 1885 2054 239310175 239310009 1.740000e-60 244.0
17 TraesCS3A01G174900 chr3B 84.058 207 27 2 1682 1882 239310078 239309872 1.770000e-45 195.0
18 TraesCS3A01G174900 chr3B 91.579 95 5 1 1963 2054 239310175 239310081 1.820000e-25 128.0
19 TraesCS3A01G174900 chr3B 97.561 41 1 0 6189 6229 239306452 239306412 3.120000e-08 71.3
20 TraesCS3A01G174900 chr3B 97.059 34 1 0 4039 4072 239308635 239308602 2.430000e-04 58.4
21 TraesCS3A01G174900 chr3D 94.897 3684 158 14 2495 6163 162409866 162406198 0.000000e+00 5734.0
22 TraesCS3A01G174900 chr3D 94.080 2010 83 17 1 1991 162412105 162410113 0.000000e+00 3020.0
23 TraesCS3A01G174900 chr3D 90.820 305 22 3 1750 2054 162410420 162410122 2.710000e-108 403.0
24 TraesCS3A01G174900 chr3D 87.023 262 22 5 1802 2054 162410452 162410194 1.020000e-72 285.0
25 TraesCS3A01G174900 chr3D 88.038 209 19 2 2460 2668 162410387 162410185 6.240000e-60 243.0
26 TraesCS3A01G174900 chr3D 85.388 219 19 8 2510 2728 162410415 162410210 1.360000e-51 215.0
27 TraesCS3A01G174900 chr3D 84.305 223 26 5 1744 1960 162409865 162409646 6.330000e-50 209.0
28 TraesCS3A01G174900 chr3D 84.951 206 28 1 1680 1882 162409851 162409646 8.190000e-49 206.0
29 TraesCS3A01G174900 chr3D 89.506 162 14 1 1896 2054 162409866 162409705 1.060000e-47 202.0
30 TraesCS3A01G174900 chr3D 90.667 150 11 1 2460 2609 162409823 162409677 4.930000e-46 196.0
31 TraesCS3A01G174900 chr3D 84.932 146 16 5 2573 2718 162409866 162409727 6.510000e-30 143.0
32 TraesCS3A01G174900 chr5B 92.720 261 15 3 4185 4443 452131827 452132085 2.120000e-99 374.0
33 TraesCS3A01G174900 chr7A 89.655 174 13 4 4272 4443 642738396 642738566 3.780000e-52 217.0
34 TraesCS3A01G174900 chr2A 89.017 173 14 4 4272 4442 687064262 687064431 6.330000e-50 209.0
35 TraesCS3A01G174900 chr2A 90.090 111 11 0 4186 4296 687064143 687064253 1.810000e-30 145.0
36 TraesCS3A01G174900 chr6D 97.872 47 1 0 5771 5817 411950556 411950602 1.440000e-11 82.4
37 TraesCS3A01G174900 chr2B 97.872 47 1 0 5771 5817 645479737 645479691 1.440000e-11 82.4
38 TraesCS3A01G174900 chr7D 97.674 43 1 0 5772 5814 388039031 388038989 2.410000e-09 75.0
39 TraesCS3A01G174900 chr1A 97.674 43 1 0 5773 5815 247339026 247339068 2.410000e-09 75.0
40 TraesCS3A01G174900 chr1A 97.619 42 1 0 5774 5815 129728253 129728212 8.670000e-09 73.1
41 TraesCS3A01G174900 chr1D 86.667 60 5 3 5758 5817 238493658 238493602 5.220000e-06 63.9


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 TraesCS3A01G174900 chr3A 194703962 194710193 6231 True 1503.600000 6974 94.290500 1 6232 8 chr3A.!!$R2 6231
1 TraesCS3A01G174900 chr3B 239306412 239312063 5651 True 962.570000 5919 90.962500 313 6229 10 chr3B.!!$R3 5916
2 TraesCS3A01G174900 chr3D 162406198 162412105 5907 True 986.909091 5734 88.600636 1 6163 11 chr3D.!!$R1 6162

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
769 796 0.890683 AAATCTGCTTTTGGAGGGCG 59.109 50.0 0.0 0.0 38.51 6.13 F
1885 2304 0.244721 GCAGAAGAATGTTGTGGGGC 59.755 55.0 0.0 0.0 0.00 5.80 F
2487 2906 0.244721 GAAGAATGTTGTGCAGCCCC 59.755 55.0 0.0 0.0 0.00 5.80 F
3130 3555 0.256464 GAGAAGGACGAGGAGGAGGA 59.744 60.0 0.0 0.0 0.00 3.71 F
3131 3556 0.257616 AGAAGGACGAGGAGGAGGAG 59.742 60.0 0.0 0.0 0.00 3.69 F
3363 3788 0.545309 TCTTGAGGAGGAGGTGGTGG 60.545 60.0 0.0 0.0 0.00 4.61 F
3364 3789 0.545309 CTTGAGGAGGAGGTGGTGGA 60.545 60.0 0.0 0.0 0.00 4.02 F
3365 3790 0.545309 TTGAGGAGGAGGTGGTGGAG 60.545 60.0 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 2372 0.108585 GTTCAGAGGGCTCCACAACA 59.891 55.000 0.00 0.00 0.00 3.33 R
2757 3179 0.543174 TTTTTGCCACGGCCCCTTAT 60.543 50.000 5.42 0.00 41.09 1.73 R
3767 4198 1.198759 TCCTTCCAACCCTTCCTCGG 61.199 60.000 0.00 0.00 0.00 4.63 R
4109 4540 1.269448 CTTGTTGTGTTGGGGATTCCG 59.731 52.381 0.00 0.00 38.76 4.30 R
4620 5051 1.270147 ACCTTCTCGGTAAGCACACAC 60.270 52.381 0.00 0.00 46.73 3.82 R
5125 5559 2.975489 ACCCTCTGAGAGCTCTTTGAAA 59.025 45.455 19.36 1.53 0.00 2.69 R
5161 5595 8.463930 AAAGTTCTCAGAACATTGGATAAACA 57.536 30.769 19.89 0.00 0.00 2.83 R
5553 5994 7.736893 ACATTGTTCCTAGACAAAGTAGAACT 58.263 34.615 4.01 0.00 42.29 3.01 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
21 22 1.553690 CCTCCACCTCGACCACCAAT 61.554 60.000 0.00 0.00 0.00 3.16
65 66 6.227298 ACAATAGTCGATTGACCATCTTCT 57.773 37.500 12.07 0.00 46.94 2.85
132 133 2.094649 CCACTACTCTTCCTTGACGGTC 60.095 54.545 0.00 0.00 0.00 4.79
181 182 2.101965 GTGTGTGCACGCAAAGCA 59.898 55.556 33.01 9.06 41.22 3.91
192 193 1.067749 GCAAAGCATGGTGTGTGCA 59.932 52.632 16.22 0.00 44.87 4.57
212 213 4.729595 GCATGTGCATGTATATGGATGTG 58.270 43.478 19.26 3.48 40.80 3.21
213 214 4.216902 GCATGTGCATGTATATGGATGTGT 59.783 41.667 19.26 0.00 40.80 3.72
214 215 5.695818 CATGTGCATGTATATGGATGTGTG 58.304 41.667 11.84 0.00 36.99 3.82
215 216 4.779696 TGTGCATGTATATGGATGTGTGT 58.220 39.130 1.33 0.00 36.99 3.72
216 217 4.575645 TGTGCATGTATATGGATGTGTGTG 59.424 41.667 1.33 0.00 36.99 3.82
243 244 6.578545 GTGTGTAAATGTGATGTTGCTAACTG 59.421 38.462 0.00 0.00 0.00 3.16
247 248 9.008965 TGTAAATGTGATGTTGCTAACTGTAAT 57.991 29.630 0.00 0.00 0.00 1.89
287 288 1.092348 GACATGCTGCTGCTTGATGA 58.908 50.000 29.76 6.04 44.17 2.92
309 310 3.056250 AGTTGCGCTGCTATATATGCTCT 60.056 43.478 9.73 0.00 0.00 4.09
347 348 8.087750 TGAAGAACATGTGAAAAGTGAAAACTT 58.912 29.630 0.00 0.00 0.00 2.66
574 577 8.316046 CGTTTTCGTGTTCATATTTACGTCTAT 58.684 33.333 0.00 0.00 37.74 1.98
622 629 5.279106 GGTTAACCAACATAAACCAAGGGTC 60.279 44.000 20.12 0.00 40.89 4.46
665 672 5.578336 ACAACTCATGTCACAATCTCATACG 59.422 40.000 0.00 0.00 37.96 3.06
672 687 3.248602 GTCACAATCTCATACGGCAATCC 59.751 47.826 0.00 0.00 0.00 3.01
692 707 2.968655 CCTTTAAAAGAACGAAACGGCG 59.031 45.455 4.80 4.80 37.29 6.46
724 751 6.161381 CAGTTTCCTGAAATCTGATTTTGGG 58.839 40.000 23.43 21.70 41.50 4.12
728 755 5.018809 TCCTGAAATCTGATTTTGGGGAAG 58.981 41.667 23.43 13.30 31.47 3.46
744 771 2.431454 GGAAGGTGGAGCTGAAAAGAG 58.569 52.381 0.00 0.00 0.00 2.85
745 772 2.224646 GGAAGGTGGAGCTGAAAAGAGT 60.225 50.000 0.00 0.00 0.00 3.24
769 796 0.890683 AAATCTGCTTTTGGAGGGCG 59.109 50.000 0.00 0.00 38.51 6.13
856 883 1.062148 TCGTATTCTCTCTCACGCACG 59.938 52.381 0.00 0.00 34.50 5.34
896 923 2.592308 GCTCCGCTCCCCTGATTT 59.408 61.111 0.00 0.00 0.00 2.17
897 924 1.821332 GCTCCGCTCCCCTGATTTG 60.821 63.158 0.00 0.00 0.00 2.32
898 925 1.604378 CTCCGCTCCCCTGATTTGT 59.396 57.895 0.00 0.00 0.00 2.83
902 929 1.243342 CGCTCCCCTGATTTGTTGCA 61.243 55.000 0.00 0.00 0.00 4.08
1221 1253 2.431023 CGATCTCGGGTCCTCCAAT 58.569 57.895 0.00 0.00 35.37 3.16
1305 1337 2.483013 CCTAATCAAGGTCGGCGATTCA 60.483 50.000 14.79 0.00 40.94 2.57
1546 1578 1.303643 GAGAAGCCCCAGGTGGTTG 60.304 63.158 0.00 0.00 0.00 3.77
1609 1644 4.406972 CCCTATTTGAGATGGAGACTGTGA 59.593 45.833 0.00 0.00 0.00 3.58
1809 1901 1.178534 ACAAGAATGTTGTGGGGCCG 61.179 55.000 0.00 0.00 35.91 6.13
1837 2256 2.387757 CAGAGAAGGAAGAGGAGGAGG 58.612 57.143 0.00 0.00 0.00 4.30
1838 2257 2.024464 CAGAGAAGGAAGAGGAGGAGGA 60.024 54.545 0.00 0.00 0.00 3.71
1839 2258 2.244769 AGAGAAGGAAGAGGAGGAGGAG 59.755 54.545 0.00 0.00 0.00 3.69
1880 2299 1.251251 GGCAGGCAGAAGAATGTTGT 58.749 50.000 0.00 0.00 0.00 3.32
1881 2300 1.068055 GGCAGGCAGAAGAATGTTGTG 60.068 52.381 0.00 0.00 0.00 3.33
1882 2301 1.068055 GCAGGCAGAAGAATGTTGTGG 60.068 52.381 0.00 0.00 0.00 4.17
1883 2302 1.542915 CAGGCAGAAGAATGTTGTGGG 59.457 52.381 0.00 0.00 0.00 4.61
1884 2303 0.890683 GGCAGAAGAATGTTGTGGGG 59.109 55.000 0.00 0.00 0.00 4.96
1885 2304 0.244721 GCAGAAGAATGTTGTGGGGC 59.755 55.000 0.00 0.00 0.00 5.80
1886 2305 0.890683 CAGAAGAATGTTGTGGGGCC 59.109 55.000 0.00 0.00 0.00 5.80
1887 2306 0.251787 AGAAGAATGTTGTGGGGCCC 60.252 55.000 18.17 18.17 0.00 5.80
1888 2307 0.251787 GAAGAATGTTGTGGGGCCCT 60.252 55.000 25.93 0.00 0.00 5.19
1889 2308 0.251787 AAGAATGTTGTGGGGCCCTC 60.252 55.000 25.93 21.68 0.00 4.30
1890 2309 1.142688 AGAATGTTGTGGGGCCCTCT 61.143 55.000 25.93 13.49 0.00 3.69
1891 2310 0.967380 GAATGTTGTGGGGCCCTCTG 60.967 60.000 25.93 0.00 0.00 3.35
1892 2311 1.434513 AATGTTGTGGGGCCCTCTGA 61.435 55.000 25.93 10.56 0.00 3.27
1893 2312 1.434513 ATGTTGTGGGGCCCTCTGAA 61.435 55.000 25.93 8.78 0.00 3.02
1894 2313 1.603739 GTTGTGGGGCCCTCTGAAC 60.604 63.158 25.93 17.08 0.00 3.18
1895 2314 2.840753 TTGTGGGGCCCTCTGAACC 61.841 63.158 25.93 2.81 0.00 3.62
1896 2315 3.256960 GTGGGGCCCTCTGAACCA 61.257 66.667 25.93 6.07 0.00 3.67
1897 2316 2.935481 TGGGGCCCTCTGAACCAG 60.935 66.667 25.93 0.00 0.00 4.00
1898 2317 2.610859 GGGGCCCTCTGAACCAGA 60.611 66.667 24.38 0.00 38.25 3.86
1909 2328 3.169099 TCTGAACCAGAGAAGGAAGAGG 58.831 50.000 0.00 0.00 35.39 3.69
1910 2329 3.169099 CTGAACCAGAGAAGGAAGAGGA 58.831 50.000 0.00 0.00 32.44 3.71
1911 2330 3.169099 TGAACCAGAGAAGGAAGAGGAG 58.831 50.000 0.00 0.00 0.00 3.69
1912 2331 2.246091 ACCAGAGAAGGAAGAGGAGG 57.754 55.000 0.00 0.00 0.00 4.30
1913 2332 1.719378 ACCAGAGAAGGAAGAGGAGGA 59.281 52.381 0.00 0.00 0.00 3.71
1914 2333 2.292192 ACCAGAGAAGGAAGAGGAGGAG 60.292 54.545 0.00 0.00 0.00 3.69
1915 2334 2.387757 CAGAGAAGGAAGAGGAGGAGG 58.612 57.143 0.00 0.00 0.00 4.30
1916 2335 2.024464 CAGAGAAGGAAGAGGAGGAGGA 60.024 54.545 0.00 0.00 0.00 3.71
1917 2336 2.244769 AGAGAAGGAAGAGGAGGAGGAG 59.755 54.545 0.00 0.00 0.00 3.69
1918 2337 1.290732 AGAAGGAAGAGGAGGAGGAGG 59.709 57.143 0.00 0.00 0.00 4.30
1919 2338 0.326143 AAGGAAGAGGAGGAGGAGGC 60.326 60.000 0.00 0.00 0.00 4.70
1920 2339 1.764454 GGAAGAGGAGGAGGAGGCC 60.764 68.421 0.00 0.00 0.00 5.19
1921 2340 1.002274 GAAGAGGAGGAGGAGGCCA 59.998 63.158 5.01 0.00 0.00 5.36
1922 2341 0.399806 GAAGAGGAGGAGGAGGCCAT 60.400 60.000 5.01 0.00 0.00 4.40
1923 2342 0.693767 AAGAGGAGGAGGAGGCCATG 60.694 60.000 5.01 0.00 0.00 3.66
1924 2343 2.040043 AGGAGGAGGAGGCCATGG 60.040 66.667 7.63 7.63 0.00 3.66
1925 2344 3.883549 GGAGGAGGAGGCCATGGC 61.884 72.222 29.47 29.47 41.06 4.40
1926 2345 4.247380 GAGGAGGAGGCCATGGCG 62.247 72.222 29.90 0.00 43.06 5.69
1929 2348 4.864334 GAGGAGGCCATGGCGGTG 62.864 72.222 29.90 0.00 43.06 4.94
1932 2351 4.408821 GAGGCCATGGCGGTGACA 62.409 66.667 29.90 0.00 43.06 3.58
1933 2352 4.722700 AGGCCATGGCGGTGACAC 62.723 66.667 29.90 14.42 43.06 3.67
1952 2371 2.032528 CCGTGGCAGGCAGAAGAA 59.967 61.111 0.00 0.00 0.00 2.52
1953 2372 1.377725 CCGTGGCAGGCAGAAGAAT 60.378 57.895 0.00 0.00 0.00 2.40
1954 2373 1.651240 CCGTGGCAGGCAGAAGAATG 61.651 60.000 0.00 0.00 0.00 2.67
1955 2374 0.957395 CGTGGCAGGCAGAAGAATGT 60.957 55.000 0.00 0.00 0.00 2.71
1956 2375 1.251251 GTGGCAGGCAGAAGAATGTT 58.749 50.000 0.00 0.00 0.00 2.71
1957 2376 1.068055 GTGGCAGGCAGAAGAATGTTG 60.068 52.381 0.00 0.00 0.00 3.33
1958 2377 1.251251 GGCAGGCAGAAGAATGTTGT 58.749 50.000 0.00 0.00 0.00 3.32
1992 2411 0.829990 CAGAGAAGGAAGAGGAGGCC 59.170 60.000 0.00 0.00 0.00 5.19
2473 2892 4.749323 CCATGGCAGGCAGAAGAA 57.251 55.556 0.00 0.00 0.00 2.52
2474 2893 3.202548 CCATGGCAGGCAGAAGAAT 57.797 52.632 0.00 0.00 0.00 2.40
2475 2894 0.744874 CCATGGCAGGCAGAAGAATG 59.255 55.000 0.00 0.00 0.00 2.67
2476 2895 1.471119 CATGGCAGGCAGAAGAATGT 58.529 50.000 1.89 0.00 0.00 2.71
2477 2896 1.822990 CATGGCAGGCAGAAGAATGTT 59.177 47.619 1.89 0.00 0.00 2.71
2478 2897 1.250328 TGGCAGGCAGAAGAATGTTG 58.750 50.000 0.00 0.00 0.00 3.33
2479 2898 1.251251 GGCAGGCAGAAGAATGTTGT 58.749 50.000 0.00 0.00 0.00 3.32
2480 2899 1.068055 GGCAGGCAGAAGAATGTTGTG 60.068 52.381 0.00 0.00 0.00 3.33
2481 2900 1.668047 GCAGGCAGAAGAATGTTGTGC 60.668 52.381 3.63 3.63 37.89 4.57
2482 2901 1.610038 CAGGCAGAAGAATGTTGTGCA 59.390 47.619 13.78 0.00 40.04 4.57
2483 2902 1.884579 AGGCAGAAGAATGTTGTGCAG 59.115 47.619 13.78 0.00 40.04 4.41
2484 2903 1.668047 GGCAGAAGAATGTTGTGCAGC 60.668 52.381 13.78 0.00 40.04 5.25
2485 2904 1.668047 GCAGAAGAATGTTGTGCAGCC 60.668 52.381 7.37 0.00 38.41 4.85
2486 2905 1.068055 CAGAAGAATGTTGTGCAGCCC 60.068 52.381 0.00 0.00 0.00 5.19
2487 2906 0.244721 GAAGAATGTTGTGCAGCCCC 59.755 55.000 0.00 0.00 0.00 5.80
2488 2907 1.187567 AAGAATGTTGTGCAGCCCCC 61.188 55.000 0.00 0.00 0.00 5.40
2489 2908 1.607467 GAATGTTGTGCAGCCCCCT 60.607 57.895 0.00 0.00 0.00 4.79
2490 2909 1.880819 GAATGTTGTGCAGCCCCCTG 61.881 60.000 0.00 0.00 42.13 4.45
2491 2910 2.370459 AATGTTGTGCAGCCCCCTGA 62.370 55.000 0.00 0.00 41.77 3.86
2492 2911 2.203480 GTTGTGCAGCCCCCTGAA 60.203 61.111 0.00 0.00 41.77 3.02
2493 2912 2.203480 TTGTGCAGCCCCCTGAAC 60.203 61.111 0.00 0.00 46.23 3.18
2554 2973 1.509923 GTGGCAGGCAGAAGAATGC 59.490 57.895 0.00 0.00 45.74 3.56
2593 3015 3.177228 CAGAGAAGGAAAAGGAGGAGGA 58.823 50.000 0.00 0.00 0.00 3.71
2594 3016 3.197549 CAGAGAAGGAAAAGGAGGAGGAG 59.802 52.174 0.00 0.00 0.00 3.69
2595 3017 2.503765 GAGAAGGAAAAGGAGGAGGAGG 59.496 54.545 0.00 0.00 0.00 4.30
2618 3040 2.970324 GTGGTGACGCGCTTTGGA 60.970 61.111 5.73 0.00 0.00 3.53
2672 3094 2.666317 GAGAAGGAAGAGGAGGAGGAG 58.334 57.143 0.00 0.00 0.00 3.69
2710 3132 2.042706 ACCGTAGAGGGAGGAAGAAGAA 59.957 50.000 0.00 0.00 46.96 2.52
2757 3179 2.901975 CCTCCGAAGATGAGGTCCA 58.098 57.895 0.00 0.00 43.68 4.02
2782 3204 1.212751 GCCGTGGCAAAAAGGCTAG 59.787 57.895 5.89 0.00 45.67 3.42
2817 3239 3.261897 GGTTCTTGAGGATGTGGAAGAGA 59.738 47.826 0.00 0.00 0.00 3.10
2848 3270 2.977914 TGAGTTGGCTGTATCAAGAGC 58.022 47.619 0.00 0.00 41.23 4.09
2874 3296 0.319555 TGAGGACTTGCTCGTTTCGG 60.320 55.000 0.00 0.00 0.00 4.30
2890 3312 1.671054 CGGCGACATTGAAGGGTGT 60.671 57.895 0.00 0.00 0.00 4.16
2897 3319 3.421844 GACATTGAAGGGTGTTAAGGCT 58.578 45.455 0.00 0.00 0.00 4.58
2934 3356 1.348008 GGCATCTGGGGATGGAGACA 61.348 60.000 7.89 0.00 46.77 3.41
3017 3439 1.299541 CCGCTTTCGATAATGGTGCT 58.700 50.000 0.00 0.00 38.10 4.40
3091 3513 0.972983 CGAGGGAGGCAGAAGAAGGA 60.973 60.000 0.00 0.00 0.00 3.36
3130 3555 0.256464 GAGAAGGACGAGGAGGAGGA 59.744 60.000 0.00 0.00 0.00 3.71
3131 3556 0.257616 AGAAGGACGAGGAGGAGGAG 59.742 60.000 0.00 0.00 0.00 3.69
3132 3557 0.753848 GAAGGACGAGGAGGAGGAGG 60.754 65.000 0.00 0.00 0.00 4.30
3253 3678 0.794605 GGCGCAACGAAGAAGAATGC 60.795 55.000 10.83 0.00 0.00 3.56
3258 3683 2.021931 CGAAGAAGAATGCGGCGC 59.978 61.111 27.44 27.44 0.00 6.53
3358 3783 1.974236 CACAGTTCTTGAGGAGGAGGT 59.026 52.381 0.00 0.00 0.00 3.85
3359 3784 1.974236 ACAGTTCTTGAGGAGGAGGTG 59.026 52.381 0.00 0.00 0.00 4.00
3360 3785 1.277557 CAGTTCTTGAGGAGGAGGTGG 59.722 57.143 0.00 0.00 0.00 4.61
3361 3786 1.132689 AGTTCTTGAGGAGGAGGTGGT 60.133 52.381 0.00 0.00 0.00 4.16
3362 3787 1.002544 GTTCTTGAGGAGGAGGTGGTG 59.997 57.143 0.00 0.00 0.00 4.17
3363 3788 0.545309 TCTTGAGGAGGAGGTGGTGG 60.545 60.000 0.00 0.00 0.00 4.61
3364 3789 0.545309 CTTGAGGAGGAGGTGGTGGA 60.545 60.000 0.00 0.00 0.00 4.02
3365 3790 0.545309 TTGAGGAGGAGGTGGTGGAG 60.545 60.000 0.00 0.00 0.00 3.86
3366 3791 1.687493 GAGGAGGAGGTGGTGGAGG 60.687 68.421 0.00 0.00 0.00 4.30
3452 3883 2.438392 GACGGTGAAGAAGGGGGATAAT 59.562 50.000 0.00 0.00 0.00 1.28
3492 3923 3.067320 AGAGGTCAAAAGAACTGCAAAGC 59.933 43.478 0.00 0.00 0.00 3.51
3664 4095 6.041865 CCTGAACTAGAGAATGATGAGGATGT 59.958 42.308 0.00 0.00 0.00 3.06
3767 4198 1.274703 TGATGAGGTCTGGAAGGGGC 61.275 60.000 0.00 0.00 0.00 5.80
3791 4222 1.560146 GGAAGGGTTGGAAGGACTAGG 59.440 57.143 0.00 0.00 0.00 3.02
4020 4451 3.901797 GAGGAACAGGGTGGTGCGG 62.902 68.421 0.00 0.00 27.51 5.69
4022 4453 2.351276 GAACAGGGTGGTGCGGAT 59.649 61.111 0.00 0.00 0.00 4.18
4092 4523 2.930682 GGTGCGAATGGTTCTTCTAGAC 59.069 50.000 0.00 0.00 0.00 2.59
4109 4540 8.908903 TCTTCTAGACTTGATTCAGGATCTAAC 58.091 37.037 2.39 0.00 35.69 2.34
4620 5051 2.568956 TGAGGAGGGACTGAACTTGATG 59.431 50.000 0.00 0.00 41.55 3.07
4772 5206 4.067192 GGGCTTGCTGTTTCATTTTGATT 58.933 39.130 0.00 0.00 0.00 2.57
4798 5232 5.388599 TCTATCCTTCATCCTTTTTCCCC 57.611 43.478 0.00 0.00 0.00 4.81
4812 5246 3.374042 TTTCCCCACTCACACTTCAAA 57.626 42.857 0.00 0.00 0.00 2.69
4822 5256 7.362834 CCCACTCACACTTCAAAATGCATTATA 60.363 37.037 13.39 0.00 0.00 0.98
4859 5293 4.978083 ATTCAGCATTCTTGGCTACTTG 57.022 40.909 0.00 0.00 40.23 3.16
5071 5505 4.960938 TCTGCAGAATATAGGTGCGAATT 58.039 39.130 15.67 0.00 40.23 2.17
5125 5559 5.236282 CACTCTTCACTGACTGTCATTGAT 58.764 41.667 25.23 12.20 36.23 2.57
5161 5595 6.043243 TCTCAGAGGGTTCTAACAACATTTCT 59.957 38.462 0.00 0.00 30.73 2.52
5348 5788 7.279615 TGTGTTCAAAACTCTAGGAGATTCAA 58.720 34.615 1.31 0.00 33.32 2.69
5553 5994 5.719563 TGAGTTTGATGTGTGGATAGGAGTA 59.280 40.000 0.00 0.00 0.00 2.59
5579 6020 7.873505 AGTTCTACTTTGTCTAGGAACAATGTC 59.126 37.037 15.06 5.81 42.86 3.06
5600 6041 6.561614 TGTCTCGTAGATTTAGATTGTGGAC 58.438 40.000 0.00 0.00 33.89 4.02
5634 6075 8.868522 ATTTTGTCTACATTGAATTGGAGAGA 57.131 30.769 0.00 0.00 37.25 3.10
5732 6174 1.891150 CTGAGCAAGATGGTTTGGCTT 59.109 47.619 0.00 0.00 0.00 4.35
5831 6277 4.223255 GGAGTATATCTTACCAAGAGGGGC 59.777 50.000 0.00 0.00 41.61 5.80
5928 6377 2.286872 GCATGATCAAGACAGTCCTGG 58.713 52.381 0.00 0.00 34.19 4.45
5948 6397 4.072131 TGGTTGCTTCACAGTTAGGATTC 58.928 43.478 0.00 0.00 0.00 2.52
5999 6448 4.811969 TGCTTTCATTCCTTGCATCATT 57.188 36.364 0.00 0.00 0.00 2.57
6000 6449 4.751060 TGCTTTCATTCCTTGCATCATTC 58.249 39.130 0.00 0.00 0.00 2.67
6002 6451 5.653330 TGCTTTCATTCCTTGCATCATTCTA 59.347 36.000 0.00 0.00 0.00 2.10
6066 6517 4.846779 TTAAACTGGCTGAATGTTCACC 57.153 40.909 0.00 0.40 32.90 4.02
6146 6597 4.519906 AGAGAAAACACCAAAGGAAGGA 57.480 40.909 0.00 0.00 0.00 3.36
6164 6615 3.545703 AGGATATCAAAGGCGAAGGTTG 58.454 45.455 4.83 0.00 0.00 3.77
6165 6616 3.054361 AGGATATCAAAGGCGAAGGTTGT 60.054 43.478 4.83 0.00 0.00 3.32
6166 6617 3.065371 GGATATCAAAGGCGAAGGTTGTG 59.935 47.826 4.83 0.00 0.00 3.33
6167 6618 2.270352 ATCAAAGGCGAAGGTTGTGA 57.730 45.000 0.00 0.00 0.00 3.58
6168 6619 2.270352 TCAAAGGCGAAGGTTGTGAT 57.730 45.000 0.00 0.00 0.00 3.06
6169 6620 3.410631 TCAAAGGCGAAGGTTGTGATA 57.589 42.857 0.00 0.00 0.00 2.15
6170 6621 3.950397 TCAAAGGCGAAGGTTGTGATAT 58.050 40.909 0.00 0.00 0.00 1.63
6171 6622 3.938963 TCAAAGGCGAAGGTTGTGATATC 59.061 43.478 0.00 0.00 0.00 1.63
6172 6623 3.627395 AAGGCGAAGGTTGTGATATCA 57.373 42.857 0.00 0.00 0.00 2.15
6173 6624 3.627395 AGGCGAAGGTTGTGATATCAA 57.373 42.857 7.07 0.00 0.00 2.57
6174 6625 3.950397 AGGCGAAGGTTGTGATATCAAA 58.050 40.909 7.07 0.00 0.00 2.69
6175 6626 3.941483 AGGCGAAGGTTGTGATATCAAAG 59.059 43.478 7.07 0.00 0.00 2.77
6176 6627 3.065371 GGCGAAGGTTGTGATATCAAAGG 59.935 47.826 7.07 0.00 0.00 3.11
6177 6628 3.487544 GCGAAGGTTGTGATATCAAAGGC 60.488 47.826 7.07 0.00 0.00 4.35
6178 6629 3.242413 CGAAGGTTGTGATATCAAAGGCG 60.242 47.826 7.07 2.02 0.00 5.52
6179 6630 3.627395 AGGTTGTGATATCAAAGGCGA 57.373 42.857 7.07 0.00 0.00 5.54
6180 6631 3.950397 AGGTTGTGATATCAAAGGCGAA 58.050 40.909 7.07 0.00 0.00 4.70
6181 6632 3.941483 AGGTTGTGATATCAAAGGCGAAG 59.059 43.478 7.07 0.00 0.00 3.79
6182 6633 3.065371 GGTTGTGATATCAAAGGCGAAGG 59.935 47.826 7.07 0.00 0.00 3.46
6183 6634 3.627395 TGTGATATCAAAGGCGAAGGT 57.373 42.857 7.07 0.00 0.00 3.50
6184 6635 3.950397 TGTGATATCAAAGGCGAAGGTT 58.050 40.909 7.07 0.00 0.00 3.50
6185 6636 3.689161 TGTGATATCAAAGGCGAAGGTTG 59.311 43.478 7.07 0.00 0.00 3.77
6186 6637 2.682856 TGATATCAAAGGCGAAGGTTGC 59.317 45.455 1.98 0.00 0.00 4.17
6192 6643 3.406559 GGCGAAGGTTGCCGTATC 58.593 61.111 0.00 0.00 43.70 2.24
6193 6644 1.448893 GGCGAAGGTTGCCGTATCA 60.449 57.895 0.00 0.00 43.70 2.15
6194 6645 1.022451 GGCGAAGGTTGCCGTATCAA 61.022 55.000 0.00 0.00 43.70 2.57
6195 6646 0.800012 GCGAAGGTTGCCGTATCAAA 59.200 50.000 0.00 0.00 0.00 2.69
6196 6647 1.202031 GCGAAGGTTGCCGTATCAAAG 60.202 52.381 0.00 0.00 0.00 2.77
6197 6648 1.396996 CGAAGGTTGCCGTATCAAAGG 59.603 52.381 0.00 0.00 0.00 3.11
6203 6654 2.014594 GCCGTATCAAAGGCGAAGG 58.985 57.895 0.00 0.00 44.22 3.46
6204 6655 0.743345 GCCGTATCAAAGGCGAAGGT 60.743 55.000 0.00 0.00 44.22 3.50
6205 6656 1.734163 CCGTATCAAAGGCGAAGGTT 58.266 50.000 0.00 0.00 0.00 3.50
6223 6674 7.465513 GCGAAGGTTACAACAGAAGGTAATATG 60.466 40.741 0.00 0.00 32.63 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.071542 TGAGGCTTCCAATCACAACGA 59.928 47.619 0.00 0.00 0.00 3.85
116 117 1.289380 GCGACCGTCAAGGAAGAGT 59.711 57.895 0.00 0.00 45.00 3.24
132 133 0.962356 AAATGAGTTGGGCAGAGGCG 60.962 55.000 0.00 0.00 42.47 5.52
192 193 5.239963 CACACACATCCATATACATGCACAT 59.760 40.000 0.00 0.00 0.00 3.21
201 202 5.159273 ACACACACACACACATCCATATA 57.841 39.130 0.00 0.00 0.00 0.86
211 212 4.637977 ACATCACATTTACACACACACACA 59.362 37.500 0.00 0.00 0.00 3.72
212 213 5.168526 ACATCACATTTACACACACACAC 57.831 39.130 0.00 0.00 0.00 3.82
213 214 5.576895 CAACATCACATTTACACACACACA 58.423 37.500 0.00 0.00 0.00 3.72
214 215 4.440758 GCAACATCACATTTACACACACAC 59.559 41.667 0.00 0.00 0.00 3.82
215 216 4.337836 AGCAACATCACATTTACACACACA 59.662 37.500 0.00 0.00 0.00 3.72
216 217 4.858935 AGCAACATCACATTTACACACAC 58.141 39.130 0.00 0.00 0.00 3.82
243 244 6.365050 CAAAAGCAAAACATCAAGCCATTAC 58.635 36.000 0.00 0.00 0.00 1.89
247 248 3.118482 TCCAAAAGCAAAACATCAAGCCA 60.118 39.130 0.00 0.00 0.00 4.75
287 288 3.056250 AGAGCATATATAGCAGCGCAACT 60.056 43.478 11.47 9.06 0.00 3.16
347 348 2.627221 TGCAACTTGGCATGCTTTTAGA 59.373 40.909 18.92 0.00 42.97 2.10
462 463 4.451891 TTGACATGGCATGTATACCCAT 57.548 40.909 31.48 7.91 45.03 4.00
537 540 6.893759 TGAACACGAAAACGATATGAACATT 58.106 32.000 0.00 0.00 0.00 2.71
574 577 8.898761 ACCAATGCGAGTAATTTCATATTGTTA 58.101 29.630 0.00 0.00 0.00 2.41
622 629 7.488150 TGAGTTGTATGCTGAAACGTCTATAAG 59.512 37.037 0.00 0.00 0.00 1.73
665 672 5.116528 CGTTTCGTTCTTTTAAAGGATTGCC 59.883 40.000 4.77 0.00 0.00 4.52
672 687 2.968655 CCGCCGTTTCGTTCTTTTAAAG 59.031 45.455 0.00 0.00 0.00 1.85
724 751 2.224646 ACTCTTTTCAGCTCCACCTTCC 60.225 50.000 0.00 0.00 0.00 3.46
728 755 1.611936 GGGACTCTTTTCAGCTCCACC 60.612 57.143 0.00 0.00 0.00 4.61
767 794 4.803426 CCACTCTCGGCTCCACGC 62.803 72.222 0.00 0.00 38.13 5.34
787 814 1.519408 GAGGCCAAGTGCGAACTAAA 58.481 50.000 5.01 0.00 42.61 1.85
788 815 0.321298 GGAGGCCAAGTGCGAACTAA 60.321 55.000 5.01 0.00 42.61 2.24
884 911 0.968405 TTGCAACAAATCAGGGGAGC 59.032 50.000 0.00 0.00 0.00 4.70
902 929 1.098712 TCGGGCGTTTTGAGCACTTT 61.099 50.000 0.00 0.00 35.51 2.66
970 1001 1.527370 GGGATCGGAGGGTTTCCTG 59.473 63.158 0.00 0.00 45.05 3.86
1024 1056 4.785453 CTTCTCCACCGCCAGGGC 62.785 72.222 0.00 0.00 43.47 5.19
1221 1253 3.636231 CCGTTGAGGAGGGTGCCA 61.636 66.667 0.00 0.00 45.00 4.92
1305 1337 4.719369 GAGACGGCGAGCACGGTT 62.719 66.667 16.62 0.00 40.15 4.44
1650 1685 1.552337 TCCTCATTCTCTGGTGCAGAC 59.448 52.381 0.00 0.00 35.39 3.51
1742 1834 3.108376 GCCTCCTCCTTTTCCTTCTCTA 58.892 50.000 0.00 0.00 0.00 2.43
1788 1880 1.039856 GCCCCACAACATTCTTGTGT 58.960 50.000 11.27 0.00 46.05 3.72
1805 1897 0.390472 CTTCTCTGGTTCAGACGGCC 60.390 60.000 0.00 0.00 35.39 6.13
1809 1901 3.056179 CCTCTTCCTTCTCTGGTTCAGAC 60.056 52.174 0.00 0.00 35.39 3.51
1880 2299 2.935481 CTGGTTCAGAGGGCCCCA 60.935 66.667 21.43 6.28 32.44 4.96
1881 2300 2.610859 TCTGGTTCAGAGGGCCCC 60.611 66.667 21.43 10.60 35.39 5.80
1888 2307 3.169099 CCTCTTCCTTCTCTGGTTCAGA 58.831 50.000 0.00 0.00 38.25 3.27
1889 2308 3.169099 TCCTCTTCCTTCTCTGGTTCAG 58.831 50.000 0.00 0.00 0.00 3.02
1890 2309 3.169099 CTCCTCTTCCTTCTCTGGTTCA 58.831 50.000 0.00 0.00 0.00 3.18
1891 2310 2.499693 CCTCCTCTTCCTTCTCTGGTTC 59.500 54.545 0.00 0.00 0.00 3.62
1892 2311 2.112691 TCCTCCTCTTCCTTCTCTGGTT 59.887 50.000 0.00 0.00 0.00 3.67
1893 2312 1.719378 TCCTCCTCTTCCTTCTCTGGT 59.281 52.381 0.00 0.00 0.00 4.00
1894 2313 2.387757 CTCCTCCTCTTCCTTCTCTGG 58.612 57.143 0.00 0.00 0.00 3.86
1895 2314 2.024464 TCCTCCTCCTCTTCCTTCTCTG 60.024 54.545 0.00 0.00 0.00 3.35
1896 2315 2.244769 CTCCTCCTCCTCTTCCTTCTCT 59.755 54.545 0.00 0.00 0.00 3.10
1897 2316 2.666317 CTCCTCCTCCTCTTCCTTCTC 58.334 57.143 0.00 0.00 0.00 2.87
1898 2317 1.290732 CCTCCTCCTCCTCTTCCTTCT 59.709 57.143 0.00 0.00 0.00 2.85
1899 2318 1.788229 CCTCCTCCTCCTCTTCCTTC 58.212 60.000 0.00 0.00 0.00 3.46
1900 2319 0.326143 GCCTCCTCCTCCTCTTCCTT 60.326 60.000 0.00 0.00 0.00 3.36
1901 2320 1.313129 GCCTCCTCCTCCTCTTCCT 59.687 63.158 0.00 0.00 0.00 3.36
1902 2321 1.764454 GGCCTCCTCCTCCTCTTCC 60.764 68.421 0.00 0.00 0.00 3.46
1903 2322 0.399806 ATGGCCTCCTCCTCCTCTTC 60.400 60.000 3.32 0.00 0.00 2.87
1904 2323 0.693767 CATGGCCTCCTCCTCCTCTT 60.694 60.000 3.32 0.00 0.00 2.85
1905 2324 1.074623 CATGGCCTCCTCCTCCTCT 60.075 63.158 3.32 0.00 0.00 3.69
1906 2325 2.146061 CCATGGCCTCCTCCTCCTC 61.146 68.421 3.32 0.00 0.00 3.71
1907 2326 2.040043 CCATGGCCTCCTCCTCCT 60.040 66.667 3.32 0.00 0.00 3.69
1908 2327 3.883549 GCCATGGCCTCCTCCTCC 61.884 72.222 27.24 0.00 34.56 4.30
1909 2328 4.247380 CGCCATGGCCTCCTCCTC 62.247 72.222 30.79 0.24 37.98 3.71
1912 2331 4.864334 CACCGCCATGGCCTCCTC 62.864 72.222 30.79 2.65 43.94 3.71
1915 2334 4.408821 TGTCACCGCCATGGCCTC 62.409 66.667 30.79 16.03 43.94 4.70
1916 2335 4.722700 GTGTCACCGCCATGGCCT 62.723 66.667 30.79 13.60 43.94 5.19
1935 2354 1.377725 ATTCTTCTGCCTGCCACGG 60.378 57.895 0.00 0.00 0.00 4.94
1936 2355 0.957395 ACATTCTTCTGCCTGCCACG 60.957 55.000 0.00 0.00 0.00 4.94
1937 2356 1.068055 CAACATTCTTCTGCCTGCCAC 60.068 52.381 0.00 0.00 0.00 5.01
1938 2357 1.250328 CAACATTCTTCTGCCTGCCA 58.750 50.000 0.00 0.00 0.00 4.92
1939 2358 1.068055 CACAACATTCTTCTGCCTGCC 60.068 52.381 0.00 0.00 0.00 4.85
1940 2359 1.068055 CCACAACATTCTTCTGCCTGC 60.068 52.381 0.00 0.00 0.00 4.85
1941 2360 2.486982 CTCCACAACATTCTTCTGCCTG 59.513 50.000 0.00 0.00 0.00 4.85
1942 2361 2.787994 CTCCACAACATTCTTCTGCCT 58.212 47.619 0.00 0.00 0.00 4.75
1943 2362 1.200948 GCTCCACAACATTCTTCTGCC 59.799 52.381 0.00 0.00 0.00 4.85
1944 2363 1.200948 GGCTCCACAACATTCTTCTGC 59.799 52.381 0.00 0.00 0.00 4.26
1945 2364 1.815003 GGGCTCCACAACATTCTTCTG 59.185 52.381 0.00 0.00 0.00 3.02
1946 2365 1.707427 AGGGCTCCACAACATTCTTCT 59.293 47.619 0.00 0.00 0.00 2.85
1947 2366 2.087646 GAGGGCTCCACAACATTCTTC 58.912 52.381 0.00 0.00 0.00 2.87
1948 2367 1.707427 AGAGGGCTCCACAACATTCTT 59.293 47.619 0.00 0.00 0.00 2.52
1949 2368 1.004044 CAGAGGGCTCCACAACATTCT 59.996 52.381 0.00 0.00 0.00 2.40
1950 2369 1.003580 TCAGAGGGCTCCACAACATTC 59.996 52.381 0.00 0.00 0.00 2.67
1951 2370 1.067295 TCAGAGGGCTCCACAACATT 58.933 50.000 0.00 0.00 0.00 2.71
1952 2371 1.067295 TTCAGAGGGCTCCACAACAT 58.933 50.000 0.00 0.00 0.00 2.71
1953 2372 0.108585 GTTCAGAGGGCTCCACAACA 59.891 55.000 0.00 0.00 0.00 3.33
1954 2373 0.606673 GGTTCAGAGGGCTCCACAAC 60.607 60.000 0.00 0.00 0.00 3.32
1955 2374 1.059584 TGGTTCAGAGGGCTCCACAA 61.060 55.000 0.00 0.00 0.00 3.33
1956 2375 1.461268 TGGTTCAGAGGGCTCCACA 60.461 57.895 0.00 0.00 0.00 4.17
1957 2376 1.194781 TCTGGTTCAGAGGGCTCCAC 61.195 60.000 0.00 0.00 35.39 4.02
1958 2377 1.158466 TCTGGTTCAGAGGGCTCCA 59.842 57.895 0.00 0.00 35.39 3.86
2456 2875 0.744874 CATTCTTCTGCCTGCCATGG 59.255 55.000 7.63 7.63 0.00 3.66
2457 2876 1.471119 ACATTCTTCTGCCTGCCATG 58.529 50.000 0.00 0.00 0.00 3.66
2458 2877 1.822990 CAACATTCTTCTGCCTGCCAT 59.177 47.619 0.00 0.00 0.00 4.40
2459 2878 1.250328 CAACATTCTTCTGCCTGCCA 58.750 50.000 0.00 0.00 0.00 4.92
2460 2879 1.068055 CACAACATTCTTCTGCCTGCC 60.068 52.381 0.00 0.00 0.00 4.85
2461 2880 1.668047 GCACAACATTCTTCTGCCTGC 60.668 52.381 0.00 0.00 0.00 4.85
2462 2881 1.610038 TGCACAACATTCTTCTGCCTG 59.390 47.619 0.00 0.00 0.00 4.85
2463 2882 1.884579 CTGCACAACATTCTTCTGCCT 59.115 47.619 0.00 0.00 0.00 4.75
2464 2883 1.668047 GCTGCACAACATTCTTCTGCC 60.668 52.381 0.00 0.00 0.00 4.85
2465 2884 1.668047 GGCTGCACAACATTCTTCTGC 60.668 52.381 0.50 0.00 0.00 4.26
2466 2885 1.068055 GGGCTGCACAACATTCTTCTG 60.068 52.381 0.50 0.00 0.00 3.02
2467 2886 1.251251 GGGCTGCACAACATTCTTCT 58.749 50.000 0.50 0.00 0.00 2.85
2468 2887 0.244721 GGGGCTGCACAACATTCTTC 59.755 55.000 3.46 0.00 0.00 2.87
2469 2888 1.187567 GGGGGCTGCACAACATTCTT 61.188 55.000 3.46 0.00 0.00 2.52
2470 2889 1.607467 GGGGGCTGCACAACATTCT 60.607 57.895 3.46 0.00 0.00 2.40
2471 2890 1.607467 AGGGGGCTGCACAACATTC 60.607 57.895 3.46 0.00 0.00 2.67
2472 2891 1.909781 CAGGGGGCTGCACAACATT 60.910 57.895 3.46 0.00 0.00 2.71
2473 2892 2.283388 CAGGGGGCTGCACAACAT 60.283 61.111 3.46 0.00 0.00 2.71
2474 2893 3.067084 TTCAGGGGGCTGCACAACA 62.067 57.895 3.46 0.00 0.00 3.33
2475 2894 2.203480 TTCAGGGGGCTGCACAAC 60.203 61.111 3.46 0.00 0.00 3.32
2476 2895 2.203480 GTTCAGGGGGCTGCACAA 60.203 61.111 3.46 0.00 0.00 3.33
2477 2896 4.284550 GGTTCAGGGGGCTGCACA 62.285 66.667 3.46 0.00 0.00 4.57
2478 2897 4.284550 TGGTTCAGGGGGCTGCAC 62.285 66.667 0.50 0.00 0.00 4.57
2479 2898 3.970410 CTGGTTCAGGGGGCTGCA 61.970 66.667 0.50 0.00 0.00 4.41
2480 2899 3.635268 CTCTGGTTCAGGGGGCTGC 62.635 68.421 0.00 0.00 31.51 5.25
2481 2900 1.492133 TTCTCTGGTTCAGGGGGCTG 61.492 60.000 0.00 0.00 31.91 4.85
2482 2901 1.151810 TTCTCTGGTTCAGGGGGCT 60.152 57.895 0.00 0.00 31.91 5.19
2483 2902 1.301293 CTTCTCTGGTTCAGGGGGC 59.699 63.158 0.00 0.00 31.91 5.80
2484 2903 0.547712 TCCTTCTCTGGTTCAGGGGG 60.548 60.000 0.00 0.00 31.91 5.40
2485 2904 1.362224 TTCCTTCTCTGGTTCAGGGG 58.638 55.000 0.00 0.00 31.91 4.79
2486 2905 3.416156 CTTTTCCTTCTCTGGTTCAGGG 58.584 50.000 0.00 0.00 32.35 4.45
2487 2906 3.073062 TCCTTTTCCTTCTCTGGTTCAGG 59.927 47.826 0.00 0.00 31.51 3.86
2488 2907 4.322567 CTCCTTTTCCTTCTCTGGTTCAG 58.677 47.826 0.00 0.00 0.00 3.02
2489 2908 3.073062 CCTCCTTTTCCTTCTCTGGTTCA 59.927 47.826 0.00 0.00 0.00 3.18
2490 2909 3.328050 TCCTCCTTTTCCTTCTCTGGTTC 59.672 47.826 0.00 0.00 0.00 3.62
2491 2910 3.327439 TCCTCCTTTTCCTTCTCTGGTT 58.673 45.455 0.00 0.00 0.00 3.67
2492 2911 2.909662 CTCCTCCTTTTCCTTCTCTGGT 59.090 50.000 0.00 0.00 0.00 4.00
2493 2912 2.238395 CCTCCTCCTTTTCCTTCTCTGG 59.762 54.545 0.00 0.00 0.00 3.86
2554 2973 2.674380 GTTCAGGGGGCTGCACAG 60.674 66.667 3.46 0.00 0.00 3.66
2563 2982 1.362224 TTCCTTCTCTGGTTCAGGGG 58.638 55.000 0.00 0.00 31.91 4.79
2593 3015 4.626081 GCGTCACCACTGTGGCCT 62.626 66.667 26.20 5.36 44.39 5.19
2613 3035 3.960102 ACAACATTCTTCTGCCTTCCAAA 59.040 39.130 0.00 0.00 0.00 3.28
2614 3036 3.318839 CACAACATTCTTCTGCCTTCCAA 59.681 43.478 0.00 0.00 0.00 3.53
2618 3040 3.152341 CTCCACAACATTCTTCTGCCTT 58.848 45.455 0.00 0.00 0.00 4.35
2672 3094 4.589675 TTTGTCACCACCGGGGCC 62.590 66.667 6.32 0.00 42.05 5.80
2693 3115 4.033709 CCACATTCTTCTTCCTCCCTCTA 58.966 47.826 0.00 0.00 0.00 2.43
2710 3132 4.388499 GGGCGTCCGTCACCACAT 62.388 66.667 0.00 0.00 0.00 3.21
2756 3178 1.254284 TTTTGCCACGGCCCCTTATG 61.254 55.000 5.42 0.00 41.09 1.90
2757 3179 0.543174 TTTTTGCCACGGCCCCTTAT 60.543 50.000 5.42 0.00 41.09 1.73
2782 3204 0.593128 AAGAACCATGTCGCTTGCAC 59.407 50.000 0.00 0.00 0.00 4.57
2817 3239 1.713078 AGCCAACTCATTTCCTCCCTT 59.287 47.619 0.00 0.00 0.00 3.95
2862 3284 1.225376 AATGTCGCCGAAACGAGCAA 61.225 50.000 0.00 0.00 43.89 3.91
2874 3296 2.161609 CCTTAACACCCTTCAATGTCGC 59.838 50.000 0.00 0.00 0.00 5.19
2890 3312 4.656112 CCTTATCCCTCTTCTGAGCCTTAA 59.344 45.833 0.00 0.00 38.93 1.85
2897 3319 2.119495 GCCACCTTATCCCTCTTCTGA 58.881 52.381 0.00 0.00 0.00 3.27
2934 3356 0.543749 GACACTGCAGCCCCTTCTAT 59.456 55.000 15.27 0.00 0.00 1.98
3031 3453 1.590932 CTCCATCTCTTCAATGGGCG 58.409 55.000 2.51 0.00 43.30 6.13
3082 3504 2.698797 TGAGGTTCAACGTCCTTCTTCT 59.301 45.455 7.75 0.00 32.42 2.85
3091 3513 2.104111 TCTGGTTCATGAGGTTCAACGT 59.896 45.455 0.00 0.00 0.00 3.99
3130 3555 2.436109 GTGTCACCACCATGGCCT 59.564 61.111 13.04 0.00 42.67 5.19
3131 3556 3.055719 CGTGTCACCACCATGGCC 61.056 66.667 13.04 0.00 42.67 5.36
3132 3557 2.281484 ACGTGTCACCACCATGGC 60.281 61.111 13.04 0.00 42.67 4.40
3258 3683 2.625737 CAGTGATACAGGAGCAACTGG 58.374 52.381 11.63 0.00 42.75 4.00
3330 3755 4.780815 TCCTCAAGAACTGTGTTCATTGT 58.219 39.130 12.16 0.00 0.00 2.71
3358 3783 2.284921 CCTGCTCCTCCTCCACCA 60.285 66.667 0.00 0.00 0.00 4.17
3359 3784 3.086600 CCCTGCTCCTCCTCCACC 61.087 72.222 0.00 0.00 0.00 4.61
3360 3785 3.086600 CCCCTGCTCCTCCTCCAC 61.087 72.222 0.00 0.00 0.00 4.02
3361 3786 4.421554 CCCCCTGCTCCTCCTCCA 62.422 72.222 0.00 0.00 0.00 3.86
3452 3883 2.360726 CCATCCACAGCTGCTGCA 60.361 61.111 28.39 13.72 42.74 4.41
3492 3923 3.343941 TGGTAATTTCTCCTCCAACGG 57.656 47.619 0.00 0.00 0.00 4.44
3570 4001 1.558756 CTCCATCTCTTCAGTGGGCTT 59.441 52.381 0.00 0.00 33.78 4.35
3767 4198 1.198759 TCCTTCCAACCCTTCCTCGG 61.199 60.000 0.00 0.00 0.00 4.63
3791 4222 2.678336 CTCAGGAACGTTATTCCTTGCC 59.322 50.000 0.00 0.00 46.21 4.52
3892 4323 1.635817 ATCCTCACCCCCATTCACCG 61.636 60.000 0.00 0.00 0.00 4.94
4020 4451 4.187694 CTGGCAACTCTAGAAGAACCATC 58.812 47.826 0.00 0.00 37.61 3.51
4022 4453 2.972713 ACTGGCAACTCTAGAAGAACCA 59.027 45.455 0.00 0.00 37.61 3.67
4092 4523 5.698545 GGATTCCGTTAGATCCTGAATCAAG 59.301 44.000 15.87 0.00 41.82 3.02
4109 4540 1.269448 CTTGTTGTGTTGGGGATTCCG 59.731 52.381 0.00 0.00 38.76 4.30
4211 4642 9.330063 CAGTTTTCTATCCTGCAACAGATAATA 57.670 33.333 0.00 0.00 32.44 0.98
4481 4912 9.392021 CAAAGTAAAAACACAAACAAGCATTTT 57.608 25.926 0.00 0.00 0.00 1.82
4620 5051 1.270147 ACCTTCTCGGTAAGCACACAC 60.270 52.381 0.00 0.00 46.73 3.82
4752 5186 6.535274 AGAAATCAAAATGAAACAGCAAGC 57.465 33.333 0.00 0.00 0.00 4.01
4772 5206 7.119387 GGGAAAAAGGATGAAGGATAGAAGAA 58.881 38.462 0.00 0.00 0.00 2.52
4798 5232 9.577110 AATATAATGCATTTTGAAGTGTGAGTG 57.423 29.630 18.75 0.00 0.00 3.51
4836 5270 5.105997 ACAAGTAGCCAAGAATGCTGAATTC 60.106 40.000 0.00 0.00 44.44 2.17
4859 5293 3.626028 ATTTGGACAGTTTGAGCGAAC 57.374 42.857 0.00 0.00 0.00 3.95
5071 5505 8.902806 AGACACTTTTGATCATACACTGAAAAA 58.097 29.630 0.00 0.00 37.44 1.94
5125 5559 2.975489 ACCCTCTGAGAGCTCTTTGAAA 59.025 45.455 19.36 1.53 0.00 2.69
5161 5595 8.463930 AAAGTTCTCAGAACATTGGATAAACA 57.536 30.769 19.89 0.00 0.00 2.83
5553 5994 7.736893 ACATTGTTCCTAGACAAAGTAGAACT 58.263 34.615 4.01 0.00 42.29 3.01
5579 6020 5.163447 TGGGTCCACAATCTAAATCTACGAG 60.163 44.000 0.00 0.00 0.00 4.18
5600 6041 8.830201 TTCAATGTAGACAAAATTCAATTGGG 57.170 30.769 5.42 0.00 32.02 4.12
5634 6075 0.178981 AGCACAGGCAAGGAACATGT 60.179 50.000 0.00 0.00 44.61 3.21
5675 6116 5.469760 TGTATATAGACGCATGCAAGCATTT 59.530 36.000 19.57 0.00 33.90 2.32
5831 6277 6.017400 AGGTGATTTGCATAAACTTCAGTG 57.983 37.500 0.00 0.00 0.00 3.66
5928 6377 3.125316 CGGAATCCTAACTGTGAAGCAAC 59.875 47.826 0.00 0.00 0.00 4.17
5948 6397 2.205074 GAGACCTCATAATGCACACGG 58.795 52.381 0.00 0.00 0.00 4.94
6066 6517 5.597813 ACTTGAATGAGCAGTTAAACGAG 57.402 39.130 0.00 0.00 0.00 4.18
6146 6597 3.950397 TCACAACCTTCGCCTTTGATAT 58.050 40.909 0.00 0.00 0.00 1.63
6164 6615 3.487544 GCAACCTTCGCCTTTGATATCAC 60.488 47.826 4.48 0.00 0.00 3.06
6165 6616 2.682856 GCAACCTTCGCCTTTGATATCA 59.317 45.455 0.00 0.00 0.00 2.15
6166 6617 2.033424 GGCAACCTTCGCCTTTGATATC 59.967 50.000 0.00 0.00 46.56 1.63
6167 6618 2.024414 GGCAACCTTCGCCTTTGATAT 58.976 47.619 0.00 0.00 46.56 1.63
6168 6619 1.459450 GGCAACCTTCGCCTTTGATA 58.541 50.000 0.00 0.00 46.56 2.15
6169 6620 2.267045 GGCAACCTTCGCCTTTGAT 58.733 52.632 0.00 0.00 46.56 2.57
6170 6621 3.758172 GGCAACCTTCGCCTTTGA 58.242 55.556 0.00 0.00 46.56 2.69
6175 6626 1.022451 TTGATACGGCAACCTTCGCC 61.022 55.000 0.00 0.00 46.62 5.54
6176 6627 0.800012 TTTGATACGGCAACCTTCGC 59.200 50.000 0.00 0.00 0.00 4.70
6177 6628 1.396996 CCTTTGATACGGCAACCTTCG 59.603 52.381 0.00 0.00 0.00 3.79
6178 6629 1.132453 GCCTTTGATACGGCAACCTTC 59.868 52.381 0.00 0.00 45.59 3.46
6179 6630 1.173913 GCCTTTGATACGGCAACCTT 58.826 50.000 0.00 0.00 45.59 3.50
6180 6631 1.024579 CGCCTTTGATACGGCAACCT 61.025 55.000 0.00 0.00 46.62 3.50
6181 6632 1.022451 TCGCCTTTGATACGGCAACC 61.022 55.000 0.00 0.00 46.62 3.77
6182 6633 0.800012 TTCGCCTTTGATACGGCAAC 59.200 50.000 0.00 0.00 46.62 4.17
6183 6634 1.083489 CTTCGCCTTTGATACGGCAA 58.917 50.000 0.00 0.00 46.62 4.52
6184 6635 0.742990 CCTTCGCCTTTGATACGGCA 60.743 55.000 0.00 0.00 46.62 5.69
6185 6636 0.743345 ACCTTCGCCTTTGATACGGC 60.743 55.000 0.00 0.00 42.86 5.68
6186 6637 1.734163 AACCTTCGCCTTTGATACGG 58.266 50.000 0.00 0.00 0.00 4.02
6187 6638 3.255725 TGTAACCTTCGCCTTTGATACG 58.744 45.455 0.00 0.00 0.00 3.06
6188 6639 4.453136 TGTTGTAACCTTCGCCTTTGATAC 59.547 41.667 0.00 0.00 0.00 2.24
6189 6640 4.643463 TGTTGTAACCTTCGCCTTTGATA 58.357 39.130 0.00 0.00 0.00 2.15
6190 6641 3.482436 TGTTGTAACCTTCGCCTTTGAT 58.518 40.909 0.00 0.00 0.00 2.57
6191 6642 2.875933 CTGTTGTAACCTTCGCCTTTGA 59.124 45.455 0.00 0.00 0.00 2.69
6192 6643 2.875933 TCTGTTGTAACCTTCGCCTTTG 59.124 45.455 0.00 0.00 0.00 2.77
6193 6644 3.202829 TCTGTTGTAACCTTCGCCTTT 57.797 42.857 0.00 0.00 0.00 3.11
6194 6645 2.922740 TCTGTTGTAACCTTCGCCTT 57.077 45.000 0.00 0.00 0.00 4.35
6195 6646 2.550208 CCTTCTGTTGTAACCTTCGCCT 60.550 50.000 0.00 0.00 0.00 5.52
6196 6647 1.804748 CCTTCTGTTGTAACCTTCGCC 59.195 52.381 0.00 0.00 0.00 5.54
6197 6648 2.490991 ACCTTCTGTTGTAACCTTCGC 58.509 47.619 0.00 0.00 0.00 4.70
6198 6649 7.762615 TCATATTACCTTCTGTTGTAACCTTCG 59.237 37.037 0.00 0.00 30.35 3.79
6199 6650 9.614792 ATCATATTACCTTCTGTTGTAACCTTC 57.385 33.333 0.00 0.00 30.35 3.46
6200 6651 9.614792 GATCATATTACCTTCTGTTGTAACCTT 57.385 33.333 0.00 0.00 30.35 3.50
6201 6652 8.993424 AGATCATATTACCTTCTGTTGTAACCT 58.007 33.333 0.00 0.00 30.35 3.50


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

AutoCloner maintained by Alex Coulton.