Multiple sequence alignment - TraesCS7B01G204700

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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 TraesCS7B01G204700 chr7B 100.000 4655 0 0 1 4655 374987498 374982844 0.000000e+00 8597.0
1 TraesCS7B01G204700 chr7D 87.161 1768 156 35 1961 3695 379828450 379826721 0.000000e+00 1941.0
2 TraesCS7B01G204700 chr7D 89.379 1450 93 29 403 1831 379830019 379828610 0.000000e+00 1768.0
3 TraesCS7B01G204700 chr7D 92.086 973 50 14 3693 4655 379826639 379825684 0.000000e+00 1345.0
4 TraesCS7B01G204700 chr7D 80.052 381 60 15 30 398 496169118 496169494 7.680000e-68 268.0
5 TraesCS7B01G204700 chr7A 90.037 1355 76 30 2950 4284 428342747 428341432 0.000000e+00 1700.0
6 TraesCS7B01G204700 chr7A 92.186 1011 59 15 833 1831 428345067 428344065 0.000000e+00 1411.0
7 TraesCS7B01G204700 chr7A 85.840 1024 98 24 1886 2880 428343959 428342954 0.000000e+00 1044.0
8 TraesCS7B01G204700 chr7A 94.947 376 19 0 4280 4655 428341472 428341097 1.440000e-164 590.0
9 TraesCS7B01G204700 chr7A 82.867 572 73 19 2 560 428386161 428385602 1.510000e-134 490.0
10 TraesCS7B01G204700 chr7A 89.908 218 19 2 555 770 428385422 428385206 1.280000e-70 278.0
11 TraesCS7B01G204700 chr7A 79.894 378 58 16 30 392 64474738 64475112 1.280000e-65 261.0
12 TraesCS7B01G204700 chr2D 81.994 361 48 14 3 351 298839349 298839704 1.640000e-74 291.0
13 TraesCS7B01G204700 chr2D 79.211 380 62 12 29 395 101904014 101903639 1.000000e-61 248.0
14 TraesCS7B01G204700 chr4B 80.147 408 62 15 15 410 53162286 53162686 2.120000e-73 287.0
15 TraesCS7B01G204700 chr1B 80.749 374 61 9 30 396 278613196 278613565 9.860000e-72 281.0
16 TraesCS7B01G204700 chr3A 80.153 393 59 17 15 395 25996038 25995653 4.590000e-70 276.0
17 TraesCS7B01G204700 chr3D 79.016 386 65 14 30 404 428605975 428605595 2.780000e-62 250.0
18 TraesCS7B01G204700 chr2A 81.443 97 17 1 489 585 608873971 608873876 1.390000e-10 78.7


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 TraesCS7B01G204700 chr7B 374982844 374987498 4654 True 8597.000000 8597 100.0000 1 4655 1 chr7B.!!$R1 4654
1 TraesCS7B01G204700 chr7D 379825684 379830019 4335 True 1684.666667 1941 89.5420 403 4655 3 chr7D.!!$R1 4252
2 TraesCS7B01G204700 chr7A 428341097 428345067 3970 True 1186.250000 1700 90.7525 833 4655 4 chr7A.!!$R1 3822
3 TraesCS7B01G204700 chr7A 428385206 428386161 955 True 384.000000 490 86.3875 2 770 2 chr7A.!!$R2 768

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
372 383 0.108774 TGACCGGGTGTAAATGTGCA 59.891 50.0 3.30 0.0 0.0 4.57 F
1572 1806 0.388006 TCTGTGGTCGTACGCATGTG 60.388 55.0 11.24 4.3 0.0 3.21 F
2227 2521 0.110486 GAGTGGTTGGTGGTGGATGT 59.890 55.0 0.00 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2208 2502 0.110486 ACATCCACCACCAACCACTC 59.890 55.0 0.00 0.0 0.0 3.51 R
3076 3587 0.178981 AAGCCCTGCAGAACACACAT 60.179 50.0 17.39 0.0 0.0 3.21 R
4191 4800 0.033991 CTGGAGGAGACGAGGAAGGA 60.034 60.0 0.00 0.0 0.0 3.36 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
26 27 2.051941 CAGCAATTTGGTGCCCAGT 58.948 52.632 14.97 0.00 46.14 4.00
38 39 1.451028 GCCCAGTCTCATCTGCACC 60.451 63.158 0.00 0.00 34.47 5.01
42 43 2.187946 GTCTCATCTGCACCCCCG 59.812 66.667 0.00 0.00 0.00 5.73
45 46 1.227764 CTCATCTGCACCCCCGATG 60.228 63.158 6.56 6.56 36.70 3.84
125 126 4.776349 TGGTAGATAATTTGGTGCGTGAT 58.224 39.130 0.00 0.00 0.00 3.06
129 130 2.627863 TAATTTGGTGCGTGATGTGC 57.372 45.000 0.00 0.00 0.00 4.57
130 131 0.672889 AATTTGGTGCGTGATGTGCA 59.327 45.000 0.00 0.00 40.70 4.57
137 138 1.207593 GCGTGATGTGCACTCCAAC 59.792 57.895 19.41 10.04 45.49 3.77
141 142 2.349817 CGTGATGTGCACTCCAACTTTC 60.350 50.000 19.41 3.00 45.49 2.62
152 153 5.706916 CACTCCAACTTTCAGATCATTTGG 58.293 41.667 0.00 0.00 35.75 3.28
154 155 6.152323 CACTCCAACTTTCAGATCATTTGGAT 59.848 38.462 1.49 0.00 41.21 3.41
160 161 8.350722 CAACTTTCAGATCATTTGGATATCTGG 58.649 37.037 10.68 0.05 44.37 3.86
167 168 5.912149 TCATTTGGATATCTGGGTAGCTT 57.088 39.130 2.05 0.00 0.00 3.74
169 170 6.672593 TCATTTGGATATCTGGGTAGCTTTT 58.327 36.000 2.05 0.00 0.00 2.27
192 195 4.164221 TGGCAAAAAGACAAATTTGGGGTA 59.836 37.500 21.74 0.00 37.09 3.69
233 236 7.566760 TTCATGTACTGTTCTGACACAAATT 57.433 32.000 0.00 0.00 0.00 1.82
235 238 5.168526 TGTACTGTTCTGACACAAATTGC 57.831 39.130 0.00 0.00 0.00 3.56
270 273 4.870426 AGCACTACTCGTATGTCCAAATTG 59.130 41.667 0.00 0.00 0.00 2.32
275 278 4.253685 ACTCGTATGTCCAAATTGTCTGG 58.746 43.478 0.00 0.00 35.05 3.86
277 280 4.900684 TCGTATGTCCAAATTGTCTGGAA 58.099 39.130 0.00 0.00 44.55 3.53
287 290 2.270352 TTGTCTGGAATTTGGAGCGT 57.730 45.000 0.00 0.00 0.00 5.07
288 291 1.522668 TGTCTGGAATTTGGAGCGTG 58.477 50.000 0.00 0.00 0.00 5.34
289 292 1.202758 TGTCTGGAATTTGGAGCGTGT 60.203 47.619 0.00 0.00 0.00 4.49
294 297 2.151202 GGAATTTGGAGCGTGTCTCAA 58.849 47.619 0.00 0.00 43.70 3.02
309 312 5.580691 CGTGTCTCAAGCACCAAATTATCTA 59.419 40.000 0.00 0.00 33.61 1.98
310 313 6.258727 CGTGTCTCAAGCACCAAATTATCTAT 59.741 38.462 0.00 0.00 33.61 1.98
369 380 3.495434 TTCTTGACCGGGTGTAAATGT 57.505 42.857 3.30 0.00 0.00 2.71
372 383 0.108774 TGACCGGGTGTAAATGTGCA 59.891 50.000 3.30 0.00 0.00 4.57
374 385 1.132262 GACCGGGTGTAAATGTGCATG 59.868 52.381 3.30 0.00 0.00 4.06
459 471 8.801715 TTTTCTAACGATTTGTTACGACTAGT 57.198 30.769 0.00 0.00 42.09 2.57
496 508 5.227908 TCTGGTCTACATCAACGACTTTTC 58.772 41.667 0.00 0.00 0.00 2.29
564 761 2.109181 GTGGAGACCCATAGGCGC 59.891 66.667 0.00 0.00 45.68 6.53
770 973 4.923281 GGCAGCATAGTACCAAAGTTTTTG 59.077 41.667 0.00 0.00 0.00 2.44
799 1023 0.441145 GCGTACAACGGGACATGTTC 59.559 55.000 0.00 0.00 42.82 3.18
800 1024 1.938016 GCGTACAACGGGACATGTTCT 60.938 52.381 3.62 0.00 42.82 3.01
802 1026 2.156891 CGTACAACGGGACATGTTCTTG 59.843 50.000 3.62 4.36 38.08 3.02
804 1028 1.142060 ACAACGGGACATGTTCTTGGA 59.858 47.619 3.62 0.00 0.00 3.53
811 1035 2.519013 GACATGTTCTTGGAAAGGCCT 58.481 47.619 0.00 0.00 46.24 5.19
812 1036 3.561313 GGACATGTTCTTGGAAAGGCCTA 60.561 47.826 5.16 0.00 46.24 3.93
813 1037 4.079253 GACATGTTCTTGGAAAGGCCTAA 58.921 43.478 5.16 0.00 46.24 2.69
814 1038 4.479158 ACATGTTCTTGGAAAGGCCTAAA 58.521 39.130 5.16 0.00 46.24 1.85
815 1039 5.086621 ACATGTTCTTGGAAAGGCCTAAAT 58.913 37.500 5.16 0.00 46.24 1.40
816 1040 5.543790 ACATGTTCTTGGAAAGGCCTAAATT 59.456 36.000 5.16 0.00 46.24 1.82
817 1041 5.467035 TGTTCTTGGAAAGGCCTAAATTG 57.533 39.130 5.16 0.00 46.24 2.32
818 1042 4.898861 TGTTCTTGGAAAGGCCTAAATTGT 59.101 37.500 5.16 0.00 46.24 2.71
819 1043 5.365314 TGTTCTTGGAAAGGCCTAAATTGTT 59.635 36.000 5.16 0.00 46.24 2.83
820 1044 6.126911 TGTTCTTGGAAAGGCCTAAATTGTTT 60.127 34.615 5.16 0.00 46.24 2.83
821 1045 6.493189 TCTTGGAAAGGCCTAAATTGTTTT 57.507 33.333 5.16 0.00 46.24 2.43
822 1046 6.894682 TCTTGGAAAGGCCTAAATTGTTTTT 58.105 32.000 5.16 0.00 46.24 1.94
853 1077 4.981806 TGGAAAGGCCTTAATGAAATCG 57.018 40.909 20.84 0.00 37.63 3.34
1018 1242 2.764547 CCGTCTCCCTCTTCCCCC 60.765 72.222 0.00 0.00 0.00 5.40
1036 1260 1.066918 CGCGGCGTATCTAGGGTTT 59.933 57.895 15.36 0.00 0.00 3.27
1037 1261 0.529119 CGCGGCGTATCTAGGGTTTT 60.529 55.000 15.36 0.00 0.00 2.43
1146 1370 2.988684 GCCATGGCGTCCACCAAA 60.989 61.111 23.48 0.00 44.65 3.28
1412 1646 2.419574 GGACGGTTGGCTTGAGCTAATA 60.420 50.000 5.08 0.00 43.26 0.98
1506 1740 4.516698 GGGTCGTATCATCGTAAGTTCCTA 59.483 45.833 0.00 0.00 39.48 2.94
1572 1806 0.388006 TCTGTGGTCGTACGCATGTG 60.388 55.000 11.24 4.30 0.00 3.21
1588 1822 5.008217 ACGCATGTGTGTTAAGTGTAATGTT 59.992 36.000 11.96 0.00 34.75 2.71
1662 1896 1.537202 CTTGTGTCTAAGCAAGTGGGC 59.463 52.381 0.00 0.00 37.78 5.36
1683 1917 7.225931 GTGGGCGTGAATTGATTAATACTCTAA 59.774 37.037 0.00 0.00 0.00 2.10
1735 1974 8.707839 ACACATCTGTTGTTTGTTTTGTTAAAG 58.292 29.630 0.00 0.00 36.00 1.85
1738 1977 5.639931 TCTGTTGTTTGTTTTGTTAAAGGCC 59.360 36.000 0.00 0.00 0.00 5.19
1761 2000 4.877378 ACATGAAAATGTGTTGGCATCT 57.123 36.364 0.00 0.00 32.79 2.90
1792 2031 6.704819 CAAGAATTGGTAAACACTTGCAAAC 58.295 36.000 0.00 0.00 43.94 2.93
1812 2051 2.230508 ACAAATCTGCATGCTCAACAGG 59.769 45.455 20.33 5.76 32.19 4.00
1817 2056 1.884579 CTGCATGCTCAACAGGAAAGT 59.115 47.619 20.33 0.00 29.21 2.66
1831 2070 8.736244 TCAACAGGAAAGTATTAATTAAGTGCC 58.264 33.333 3.94 0.00 0.00 5.01
1832 2071 8.519526 CAACAGGAAAGTATTAATTAAGTGCCA 58.480 33.333 3.94 0.00 0.00 4.92
1833 2072 8.644374 ACAGGAAAGTATTAATTAAGTGCCAA 57.356 30.769 3.94 0.00 0.00 4.52
1835 2074 8.739972 CAGGAAAGTATTAATTAAGTGCCAAGT 58.260 33.333 3.94 0.00 0.00 3.16
1837 2076 7.908601 GGAAAGTATTAATTAAGTGCCAAGTCG 59.091 37.037 3.94 0.00 0.00 4.18
1838 2077 7.916914 AAGTATTAATTAAGTGCCAAGTCGT 57.083 32.000 3.94 0.00 0.00 4.34
1839 2078 7.303634 AGTATTAATTAAGTGCCAAGTCGTG 57.696 36.000 3.94 0.00 0.00 4.35
1840 2079 7.101054 AGTATTAATTAAGTGCCAAGTCGTGA 58.899 34.615 3.94 0.00 0.00 4.35
1841 2080 7.769044 AGTATTAATTAAGTGCCAAGTCGTGAT 59.231 33.333 3.94 0.00 0.00 3.06
1842 2081 4.685169 AATTAAGTGCCAAGTCGTGATG 57.315 40.909 0.00 0.00 0.00 3.07
1844 2083 1.237285 AAGTGCCAAGTCGTGATGCC 61.237 55.000 0.00 0.00 0.00 4.40
1845 2084 2.359850 TGCCAAGTCGTGATGCCC 60.360 61.111 0.00 0.00 0.00 5.36
1846 2085 3.134127 GCCAAGTCGTGATGCCCC 61.134 66.667 0.00 0.00 0.00 5.80
1847 2086 2.438434 CCAAGTCGTGATGCCCCC 60.438 66.667 0.00 0.00 0.00 5.40
1862 2101 2.699938 CCCCCACCCCCAATAGCT 60.700 66.667 0.00 0.00 0.00 3.32
1865 2104 1.427072 CCCCACCCCCAATAGCTAGG 61.427 65.000 0.00 0.00 0.00 3.02
1874 2139 5.965091 ACCCCCAATAGCTAGGTAATAGATC 59.035 44.000 5.62 0.00 32.76 2.75
1878 2143 6.154706 CCCAATAGCTAGGTAATAGATCGGTT 59.845 42.308 5.62 0.00 32.76 4.44
1879 2144 7.310485 CCCAATAGCTAGGTAATAGATCGGTTT 60.310 40.741 5.62 0.00 32.76 3.27
1880 2145 8.095169 CCAATAGCTAGGTAATAGATCGGTTTT 58.905 37.037 5.62 0.00 32.76 2.43
1881 2146 9.141400 CAATAGCTAGGTAATAGATCGGTTTTC 57.859 37.037 5.62 0.00 32.76 2.29
1883 2148 5.839606 AGCTAGGTAATAGATCGGTTTTCCT 59.160 40.000 0.00 8.01 33.75 3.36
1884 2149 6.015265 AGCTAGGTAATAGATCGGTTTTCCTC 60.015 42.308 0.00 0.00 33.75 3.71
1888 2178 5.236695 GGTAATAGATCGGTTTTCCTCTTGC 59.763 44.000 0.00 0.00 37.95 4.01
1908 2198 3.266772 TGCCTGTTCAAGAGGGACATAAT 59.733 43.478 2.10 0.00 0.00 1.28
1921 2211 5.685728 AGGGACATAATCTAGTTTCAAGCC 58.314 41.667 0.00 0.00 0.00 4.35
1925 2215 7.226918 GGGACATAATCTAGTTTCAAGCCTTAC 59.773 40.741 0.00 0.00 0.00 2.34
1926 2216 7.988028 GGACATAATCTAGTTTCAAGCCTTACT 59.012 37.037 0.00 0.00 0.00 2.24
1927 2217 9.384764 GACATAATCTAGTTTCAAGCCTTACTT 57.615 33.333 0.00 0.00 40.05 2.24
1932 2222 8.691661 ATCTAGTTTCAAGCCTTACTTTTTCA 57.308 30.769 0.00 0.00 36.04 2.69
1934 2224 6.775594 AGTTTCAAGCCTTACTTTTTCAGT 57.224 33.333 0.00 0.00 36.04 3.41
1935 2225 6.564328 AGTTTCAAGCCTTACTTTTTCAGTG 58.436 36.000 0.00 0.00 36.04 3.66
1939 2229 8.911918 TTCAAGCCTTACTTTTTCAGTGTATA 57.088 30.769 0.00 0.00 36.04 1.47
1964 2254 3.655615 TGTAACACTGAAACCAACCCT 57.344 42.857 0.00 0.00 0.00 4.34
1969 2259 3.408634 ACACTGAAACCAACCCTAATCG 58.591 45.455 0.00 0.00 0.00 3.34
1971 2261 3.435671 CACTGAAACCAACCCTAATCGTC 59.564 47.826 0.00 0.00 0.00 4.20
1989 2279 6.743575 ATCGTCACCTTTAAAATCAAGGAG 57.256 37.500 5.70 0.00 43.32 3.69
2068 2361 3.866651 CCCAGTCAGAACTTCACCATAG 58.133 50.000 0.00 0.00 31.71 2.23
2079 2372 8.349245 CAGAACTTCACCATAGTAGATACTGAG 58.651 40.741 2.72 0.00 37.10 3.35
2087 2380 5.986135 CCATAGTAGATACTGAGGTGTTTGC 59.014 44.000 2.72 0.00 37.10 3.68
2093 2386 4.284490 AGATACTGAGGTGTTTGCAGAAGA 59.716 41.667 0.00 0.00 33.94 2.87
2171 2465 6.406370 TGAGTTTTGAAGATCATCGGTGTAT 58.594 36.000 0.00 0.00 0.00 2.29
2175 2469 7.174946 AGTTTTGAAGATCATCGGTGTATGTTT 59.825 33.333 0.00 0.00 0.00 2.83
2195 2489 7.187244 TGTTTGTGGTAATTTGATTGCAATG 57.813 32.000 18.59 0.00 33.25 2.82
2196 2490 5.859521 TTGTGGTAATTTGATTGCAATGC 57.140 34.783 18.59 9.15 33.25 3.56
2203 2497 5.856126 AATTTGATTGCAATGCAGACAAG 57.144 34.783 18.59 0.00 40.61 3.16
2208 2502 3.374220 TTGCAATGCAGACAAGGAAAG 57.626 42.857 8.31 0.00 40.61 2.62
2220 2514 1.956477 CAAGGAAAGAGTGGTTGGTGG 59.044 52.381 0.00 0.00 0.00 4.61
2227 2521 0.110486 GAGTGGTTGGTGGTGGATGT 59.890 55.000 0.00 0.00 0.00 3.06
2243 2537 2.671396 GGATGTTAACCACTAGTGTGCG 59.329 50.000 21.18 8.93 42.54 5.34
2247 2541 2.989166 GTTAACCACTAGTGTGCGTACC 59.011 50.000 21.18 0.00 42.54 3.34
2248 2542 1.335145 AACCACTAGTGTGCGTACCT 58.665 50.000 21.18 0.49 42.54 3.08
2260 2554 4.738740 GTGTGCGTACCTAGTCAATGATAC 59.261 45.833 0.00 0.00 0.00 2.24
2261 2555 4.399934 TGTGCGTACCTAGTCAATGATACA 59.600 41.667 0.00 0.00 0.00 2.29
2263 2557 5.983720 GTGCGTACCTAGTCAATGATACAAT 59.016 40.000 0.00 0.00 0.00 2.71
2264 2558 7.143340 GTGCGTACCTAGTCAATGATACAATA 58.857 38.462 0.00 0.00 0.00 1.90
2265 2559 7.326305 GTGCGTACCTAGTCAATGATACAATAG 59.674 40.741 0.00 0.00 0.00 1.73
2266 2560 7.013942 TGCGTACCTAGTCAATGATACAATAGT 59.986 37.037 0.00 0.00 0.00 2.12
2292 2586 9.787435 TTTTTATCCTTAGAAGTTAGCTTGTCA 57.213 29.630 0.00 0.00 34.61 3.58
2304 2598 7.277174 AGTTAGCTTGTCATAACTTTTTGCT 57.723 32.000 0.00 0.00 38.73 3.91
2306 2600 7.229506 AGTTAGCTTGTCATAACTTTTTGCTCT 59.770 33.333 0.00 0.00 38.73 4.09
2307 2601 5.766222 AGCTTGTCATAACTTTTTGCTCTG 58.234 37.500 0.00 0.00 0.00 3.35
2308 2602 5.532406 AGCTTGTCATAACTTTTTGCTCTGA 59.468 36.000 0.00 0.00 0.00 3.27
2324 2618 1.132849 TCTGAGTTCAGGACCTTCCCA 60.133 52.381 9.13 0.00 43.91 4.37
2334 2628 3.758554 CAGGACCTTCCCATTGTAACTTG 59.241 47.826 0.00 0.00 37.19 3.16
2350 2644 7.328277 TGTAACTTGCTGTTAGTCAAACATT 57.672 32.000 3.72 0.00 46.81 2.71
2375 2669 3.389656 TGTTTGGTGTGTCCTGTCTCATA 59.610 43.478 0.00 0.00 37.07 2.15
2376 2670 4.041567 TGTTTGGTGTGTCCTGTCTCATAT 59.958 41.667 0.00 0.00 37.07 1.78
2416 2711 5.047021 TGTGTTGTTTTGAATCACCCTCAAA 60.047 36.000 0.00 0.00 40.21 2.69
2427 2722 1.756538 CACCCTCAAAACTTGCAACCT 59.243 47.619 0.00 0.00 0.00 3.50
2430 2725 2.310538 CCTCAAAACTTGCAACCTCCT 58.689 47.619 0.00 0.00 0.00 3.69
2431 2726 2.695147 CCTCAAAACTTGCAACCTCCTT 59.305 45.455 0.00 0.00 0.00 3.36
2490 2785 7.352739 GTGATTGTGTTTGGACAACTAAGTAG 58.647 38.462 0.00 0.00 38.64 2.57
2527 2822 9.261180 GGCCTAAAAATGCCTTTATTTTAGATC 57.739 33.333 15.23 8.70 43.98 2.75
2589 2884 3.471680 CATAGGTTGCTTCCTAAGGCTC 58.528 50.000 10.51 0.00 42.42 4.70
2590 2885 1.662686 AGGTTGCTTCCTAAGGCTCT 58.337 50.000 0.00 0.00 35.87 4.09
2594 2889 0.615331 TGCTTCCTAAGGCTCTGGTG 59.385 55.000 5.78 2.74 0.00 4.17
2597 2892 1.484240 CTTCCTAAGGCTCTGGTGAGG 59.516 57.143 5.78 0.00 40.53 3.86
2625 2921 5.690865 TCTCTTGTCATGGTTTGGTTTACT 58.309 37.500 0.00 0.00 0.00 2.24
2629 2925 4.527944 TGTCATGGTTTGGTTTACTGACA 58.472 39.130 0.00 0.00 39.18 3.58
2639 2935 4.575885 TGGTTTACTGACAGGTGATAAGC 58.424 43.478 7.51 3.98 0.00 3.09
2651 2947 5.643777 ACAGGTGATAAGCTTACAATGTGAC 59.356 40.000 8.70 0.00 0.00 3.67
2652 2948 5.643348 CAGGTGATAAGCTTACAATGTGACA 59.357 40.000 8.70 0.00 0.00 3.58
2653 2949 5.643777 AGGTGATAAGCTTACAATGTGACAC 59.356 40.000 8.70 0.00 0.00 3.67
2660 2956 3.374058 GCTTACAATGTGACACGCCTATT 59.626 43.478 0.22 0.00 0.00 1.73
2673 2976 1.667724 CGCCTATTCTGCTTCAGTTGG 59.332 52.381 0.00 0.00 32.61 3.77
2678 2981 5.253330 CCTATTCTGCTTCAGTTGGGTTTA 58.747 41.667 0.00 0.00 32.61 2.01
2710 3027 9.301153 CTTTCCAGTTTACATGTAATAAATGCC 57.699 33.333 18.69 2.52 0.00 4.40
2723 3040 0.680921 AAATGCCCCACATGGTCTCG 60.681 55.000 0.00 0.00 39.60 4.04
2738 3055 3.064931 GGTCTCGTGGGTTTTTCAGTAG 58.935 50.000 0.00 0.00 0.00 2.57
2743 3060 2.940410 CGTGGGTTTTTCAGTAGTGTGT 59.060 45.455 0.00 0.00 0.00 3.72
2754 3071 9.990360 TTTTTCAGTAGTGTGTCTGTCATATTA 57.010 29.630 0.00 0.00 33.89 0.98
2758 3075 8.749354 TCAGTAGTGTGTCTGTCATATTATTGT 58.251 33.333 0.00 0.00 33.89 2.71
2766 3083 8.786898 GTGTCTGTCATATTATTGTTGCCATAT 58.213 33.333 0.00 0.00 0.00 1.78
2769 3086 7.611467 TCTGTCATATTATTGTTGCCATATCCC 59.389 37.037 0.00 0.00 0.00 3.85
2770 3087 7.469343 TGTCATATTATTGTTGCCATATCCCT 58.531 34.615 0.00 0.00 0.00 4.20
2771 3088 7.611467 TGTCATATTATTGTTGCCATATCCCTC 59.389 37.037 0.00 0.00 0.00 4.30
2772 3089 6.823182 TCATATTATTGTTGCCATATCCCTCG 59.177 38.462 0.00 0.00 0.00 4.63
2810 3127 3.003394 TGTTGCCATATCCCTTGTCAG 57.997 47.619 0.00 0.00 0.00 3.51
2811 3128 2.575735 TGTTGCCATATCCCTTGTCAGA 59.424 45.455 0.00 0.00 0.00 3.27
2817 3134 4.202398 GCCATATCCCTTGTCAGATTCTCA 60.202 45.833 0.00 0.00 0.00 3.27
2834 3151 8.112449 CAGATTCTCAAACTTTTGCTTTTGAAC 58.888 33.333 0.00 0.00 40.36 3.18
2835 3152 7.818930 AGATTCTCAAACTTTTGCTTTTGAACA 59.181 29.630 0.00 0.00 40.36 3.18
2839 3156 7.059448 TCAAACTTTTGCTTTTGAACATGTC 57.941 32.000 0.00 0.00 38.48 3.06
2843 3160 6.576185 ACTTTTGCTTTTGAACATGTCAGAT 58.424 32.000 0.00 0.00 37.61 2.90
2845 3162 4.508461 TGCTTTTGAACATGTCAGATGG 57.492 40.909 0.00 0.00 37.61 3.51
2914 3407 7.874940 TCATTTCAATGAGACAAAGTTAGTGG 58.125 34.615 0.00 0.00 40.32 4.00
2915 3408 7.719193 TCATTTCAATGAGACAAAGTTAGTGGA 59.281 33.333 0.00 0.00 40.32 4.02
2917 3410 5.551233 TCAATGAGACAAAGTTAGTGGAGG 58.449 41.667 0.00 0.00 0.00 4.30
2918 3411 5.071788 TCAATGAGACAAAGTTAGTGGAGGT 59.928 40.000 0.00 0.00 0.00 3.85
2919 3412 6.269077 TCAATGAGACAAAGTTAGTGGAGGTA 59.731 38.462 0.00 0.00 0.00 3.08
2920 3413 5.464030 TGAGACAAAGTTAGTGGAGGTAC 57.536 43.478 0.00 0.00 0.00 3.34
2921 3414 4.282703 TGAGACAAAGTTAGTGGAGGTACC 59.717 45.833 2.73 2.73 39.54 3.34
2922 3415 3.257624 AGACAAAGTTAGTGGAGGTACCG 59.742 47.826 6.18 0.00 42.61 4.02
2929 3431 4.411540 AGTTAGTGGAGGTACCGAGAGATA 59.588 45.833 6.18 0.00 42.61 1.98
2973 3475 4.022416 TGAAGCGTGCCAATAACAGATTTT 60.022 37.500 0.00 0.00 0.00 1.82
2978 3480 5.229887 GCGTGCCAATAACAGATTTTACATG 59.770 40.000 0.00 0.00 0.00 3.21
2979 3481 6.321717 CGTGCCAATAACAGATTTTACATGT 58.678 36.000 2.69 2.69 0.00 3.21
3033 3543 6.580963 TTGAATGTTTTTGTACATGTGTGC 57.419 33.333 9.11 0.00 38.69 4.57
3036 3546 6.475076 TGAATGTTTTTGTACATGTGTGCTTC 59.525 34.615 9.11 0.54 38.69 3.86
3040 3550 6.815641 TGTTTTTGTACATGTGTGCTTCATTT 59.184 30.769 9.11 0.00 0.00 2.32
3041 3551 6.825284 TTTTGTACATGTGTGCTTCATTTG 57.175 33.333 9.11 0.00 0.00 2.32
3043 3553 3.255395 TGTACATGTGTGCTTCATTTGGG 59.745 43.478 9.11 0.00 0.00 4.12
3045 3555 0.609662 ATGTGTGCTTCATTTGGGCC 59.390 50.000 0.00 0.00 0.00 5.80
3046 3556 1.080569 GTGTGCTTCATTTGGGCCG 60.081 57.895 0.00 0.00 0.00 6.13
3054 3565 2.799126 TCATTTGGGCCGTATTGAGT 57.201 45.000 0.00 0.00 0.00 3.41
3076 3587 8.322828 TGAGTAATGCTGGGTTTTTATACTGTA 58.677 33.333 0.00 0.00 0.00 2.74
3205 3716 4.680171 AACCAAGCTTTATCGTAACAGC 57.320 40.909 0.00 0.00 0.00 4.40
3211 3722 5.578005 AGCTTTATCGTAACAGCACTAGA 57.422 39.130 0.00 0.00 34.49 2.43
3335 3848 3.515602 AAGTCAAAGAGCCATGAACCT 57.484 42.857 0.00 0.00 0.00 3.50
3352 3865 7.095102 CCATGAACCTTTGAATCCATGTTTTTC 60.095 37.037 0.00 0.00 32.01 2.29
3397 3910 3.567585 GGCCTCTAAATTCTGCAATCTCC 59.432 47.826 0.00 0.00 0.00 3.71
3461 3974 1.373748 GCTGGCGTTGTCGTTCCTA 60.374 57.895 0.00 0.00 39.49 2.94
3470 3983 1.990799 TGTCGTTCCTATGTTGAGCG 58.009 50.000 0.00 0.00 37.73 5.03
3504 4017 0.252696 TGTACTCCACCCAGGCTGAT 60.253 55.000 17.94 0.00 37.29 2.90
3531 4044 2.224185 TGTAGCTTGTCGTTGTGGTCAT 60.224 45.455 0.00 0.00 0.00 3.06
3532 4045 1.967319 AGCTTGTCGTTGTGGTCATT 58.033 45.000 0.00 0.00 0.00 2.57
3557 4070 5.007385 AGGATATGTAACGTCTGTTGTCC 57.993 43.478 0.00 0.00 39.12 4.02
3593 4106 4.785376 AGACCCAGTAAATCCATTCTGTCT 59.215 41.667 0.00 0.00 0.00 3.41
3632 4145 8.515695 TGTTTGATCAAGATGATGAGCTTATT 57.484 30.769 8.41 0.00 37.20 1.40
3661 4174 8.394971 TGTGTTTAAGATTGACATGAACAGAT 57.605 30.769 0.00 0.00 0.00 2.90
3663 4176 7.965107 GTGTTTAAGATTGACATGAACAGATCC 59.035 37.037 0.00 0.00 0.00 3.36
3700 4301 5.575606 TGTTGAGCTTATTAGTTACGACTGC 59.424 40.000 0.00 0.00 36.60 4.40
3818 4419 7.441157 CCAGATGACTCGGCAAAGTTAATTATA 59.559 37.037 0.00 0.00 0.00 0.98
3819 4420 8.491152 CAGATGACTCGGCAAAGTTAATTATAG 58.509 37.037 0.00 0.00 0.00 1.31
3825 4426 9.998106 ACTCGGCAAAGTTAATTATAGACATAT 57.002 29.630 0.00 0.00 0.00 1.78
3929 4531 8.587952 ACAGAATCGGTTTTAAAATCTTTTGG 57.412 30.769 9.44 3.15 0.00 3.28
3936 4540 9.122779 TCGGTTTTAAAATCTTTTGGAGACTTA 57.877 29.630 9.44 0.00 37.17 2.24
3998 4604 5.648960 TGTTCATCAGAGATAGCAATGCAAA 59.351 36.000 8.35 0.00 0.00 3.68
4010 4616 7.937942 AGATAGCAATGCAAACTCATAATCTCT 59.062 33.333 8.35 0.00 0.00 3.10
4081 4687 4.176271 TCATGAGATCAAACTGTGTAGCG 58.824 43.478 0.00 0.00 0.00 4.26
4083 4689 2.271800 GAGATCAAACTGTGTAGCGGG 58.728 52.381 0.00 0.00 0.00 6.13
4085 4691 0.324943 ATCAAACTGTGTAGCGGGCT 59.675 50.000 0.00 0.00 0.00 5.19
4086 4692 0.970640 TCAAACTGTGTAGCGGGCTA 59.029 50.000 0.00 0.00 0.00 3.93
4094 4703 0.186630 TGTAGCGGGCTAGGGATACA 59.813 55.000 0.00 0.00 39.74 2.29
4163 4772 1.073897 GAACCACCTGCTCTTGGCT 59.926 57.895 0.00 0.00 42.39 4.75
4191 4800 4.715792 TCTTCTTGCTCATCATCTCCTTCT 59.284 41.667 0.00 0.00 0.00 2.85
4192 4801 4.669206 TCTTGCTCATCATCTCCTTCTC 57.331 45.455 0.00 0.00 0.00 2.87
4197 4806 3.244181 GCTCATCATCTCCTTCTCCTTCC 60.244 52.174 0.00 0.00 0.00 3.46
4200 4809 2.660572 TCATCTCCTTCTCCTTCCTCG 58.339 52.381 0.00 0.00 0.00 4.63
4201 4810 2.024846 TCATCTCCTTCTCCTTCCTCGT 60.025 50.000 0.00 0.00 0.00 4.18
4319 4931 3.240606 CTTGTGGTCGGCGTTGCTG 62.241 63.158 6.85 0.00 36.06 4.41
4445 5057 1.980052 CCGCACCCTTGTCTCCTTA 59.020 57.895 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.222936 GGGTGCAGATGAGACTGGG 59.777 63.158 0.00 0.00 38.22 4.45
26 27 1.383109 ATCGGGGGTGCAGATGAGA 60.383 57.895 0.00 0.00 0.00 3.27
91 92 9.603921 CCAAATTATCTACCATGCAAAAGAATT 57.396 29.630 0.00 0.00 0.00 2.17
92 93 8.761689 ACCAAATTATCTACCATGCAAAAGAAT 58.238 29.630 0.00 0.00 0.00 2.40
93 94 8.034215 CACCAAATTATCTACCATGCAAAAGAA 58.966 33.333 0.00 0.00 0.00 2.52
94 95 7.546358 CACCAAATTATCTACCATGCAAAAGA 58.454 34.615 0.00 0.00 0.00 2.52
95 96 6.256321 GCACCAAATTATCTACCATGCAAAAG 59.744 38.462 0.00 0.00 0.00 2.27
96 97 6.105333 GCACCAAATTATCTACCATGCAAAA 58.895 36.000 0.00 0.00 0.00 2.44
100 101 3.315191 ACGCACCAAATTATCTACCATGC 59.685 43.478 0.00 0.00 0.00 4.06
104 105 4.574828 ACATCACGCACCAAATTATCTACC 59.425 41.667 0.00 0.00 0.00 3.18
125 126 2.708216 TCTGAAAGTTGGAGTGCACA 57.292 45.000 21.04 0.00 33.76 4.57
129 130 5.474532 TCCAAATGATCTGAAAGTTGGAGTG 59.525 40.000 16.76 0.00 39.58 3.51
130 131 5.634118 TCCAAATGATCTGAAAGTTGGAGT 58.366 37.500 16.76 0.00 39.58 3.85
137 138 7.002879 ACCCAGATATCCAAATGATCTGAAAG 58.997 38.462 11.70 4.25 46.31 2.62
141 142 5.879223 GCTACCCAGATATCCAAATGATCTG 59.121 44.000 0.00 4.47 44.09 2.90
152 153 3.820557 TGCCAAAAGCTACCCAGATATC 58.179 45.455 0.00 0.00 44.23 1.63
154 155 3.730215 TTGCCAAAAGCTACCCAGATA 57.270 42.857 0.00 0.00 44.23 1.98
160 161 4.053469 TGTCTTTTTGCCAAAAGCTACC 57.947 40.909 16.21 6.53 46.01 3.18
167 168 4.400567 CCCCAAATTTGTCTTTTTGCCAAA 59.599 37.500 16.73 0.00 32.68 3.28
169 170 3.054065 ACCCCAAATTTGTCTTTTTGCCA 60.054 39.130 16.73 0.00 32.68 4.92
203 206 9.936759 TGTGTCAGAACAGTACATGAAATATAA 57.063 29.630 0.00 0.00 35.64 0.98
207 210 7.566760 TTTGTGTCAGAACAGTACATGAAAT 57.433 32.000 0.00 0.00 35.64 2.17
208 211 6.993786 TTTGTGTCAGAACAGTACATGAAA 57.006 33.333 0.00 0.00 35.64 2.69
214 217 4.275936 AGGCAATTTGTGTCAGAACAGTAC 59.724 41.667 0.00 0.00 35.64 2.73
217 220 3.996150 AGGCAATTTGTGTCAGAACAG 57.004 42.857 0.00 0.00 35.64 3.16
243 246 2.541999 GGACATACGAGTAGTGCTCAGC 60.542 54.545 9.04 0.00 44.33 4.26
249 252 6.035005 CAGACAATTTGGACATACGAGTAGTG 59.965 42.308 0.78 0.00 0.00 2.74
250 253 6.100004 CAGACAATTTGGACATACGAGTAGT 58.900 40.000 0.78 0.00 0.00 2.73
270 273 1.464997 GACACGCTCCAAATTCCAGAC 59.535 52.381 0.00 0.00 0.00 3.51
275 278 2.413371 GCTTGAGACACGCTCCAAATTC 60.413 50.000 0.00 0.00 43.26 2.17
277 280 1.160137 GCTTGAGACACGCTCCAAAT 58.840 50.000 0.00 0.00 43.26 2.32
285 288 4.393062 AGATAATTTGGTGCTTGAGACACG 59.607 41.667 0.00 0.00 38.98 4.49
287 290 7.337938 TGATAGATAATTTGGTGCTTGAGACA 58.662 34.615 0.00 0.00 0.00 3.41
288 291 7.792374 TGATAGATAATTTGGTGCTTGAGAC 57.208 36.000 0.00 0.00 0.00 3.36
289 292 7.040892 GCATGATAGATAATTTGGTGCTTGAGA 60.041 37.037 0.00 0.00 0.00 3.27
294 297 6.964807 TTGCATGATAGATAATTTGGTGCT 57.035 33.333 0.00 0.00 0.00 4.40
365 376 1.927487 TTTCTGAGCCCATGCACATT 58.073 45.000 0.00 0.00 37.45 2.71
369 380 0.332293 TCCATTTCTGAGCCCATGCA 59.668 50.000 0.00 0.00 41.13 3.96
372 383 4.042062 TCGAATATCCATTTCTGAGCCCAT 59.958 41.667 0.00 0.00 0.00 4.00
374 385 3.999663 CTCGAATATCCATTTCTGAGCCC 59.000 47.826 0.00 0.00 0.00 5.19
458 470 1.154225 CAGAAATTGCCGGCGACAC 60.154 57.895 21.40 13.27 0.00 3.67
459 471 2.331893 CCAGAAATTGCCGGCGACA 61.332 57.895 21.40 6.93 0.00 4.35
496 508 1.065701 AGCTTGTAGATGTAGCGGTCG 59.934 52.381 0.00 0.00 39.82 4.79
498 510 1.409427 GGAGCTTGTAGATGTAGCGGT 59.591 52.381 0.00 0.00 39.82 5.68
506 518 9.606631 CTTGTTTAAATCTAGGAGCTTGTAGAT 57.393 33.333 11.30 11.30 37.56 1.98
581 778 1.630148 CGTAGTCTTCTTCCTTGCCG 58.370 55.000 0.00 0.00 0.00 5.69
585 782 2.168728 GGATGCCGTAGTCTTCTTCCTT 59.831 50.000 0.00 0.00 0.00 3.36
770 973 3.494251 TCCCGTTGTACGCTAAAAGTTTC 59.506 43.478 0.00 0.00 40.91 2.78
777 1001 1.273048 ACATGTCCCGTTGTACGCTAA 59.727 47.619 0.00 0.00 40.91 3.09
820 1044 2.637382 GGCCTTTCCATTCCCTGAAAAA 59.363 45.455 0.00 0.00 30.65 1.94
821 1045 2.158173 AGGCCTTTCCATTCCCTGAAAA 60.158 45.455 0.00 0.00 37.29 2.29
822 1046 1.432807 AGGCCTTTCCATTCCCTGAAA 59.567 47.619 0.00 0.00 37.29 2.69
823 1047 1.084018 AGGCCTTTCCATTCCCTGAA 58.916 50.000 0.00 0.00 37.29 3.02
824 1048 1.084018 AAGGCCTTTCCATTCCCTGA 58.916 50.000 13.78 0.00 37.29 3.86
825 1049 2.826674 TAAGGCCTTTCCATTCCCTG 57.173 50.000 26.08 0.00 37.29 4.45
826 1050 3.272020 TCATTAAGGCCTTTCCATTCCCT 59.728 43.478 26.08 0.00 37.29 4.20
827 1051 3.642141 TCATTAAGGCCTTTCCATTCCC 58.358 45.455 26.08 0.00 37.29 3.97
828 1052 5.675684 TTTCATTAAGGCCTTTCCATTCC 57.324 39.130 26.08 0.00 37.29 3.01
829 1053 5.979517 CGATTTCATTAAGGCCTTTCCATTC 59.020 40.000 26.08 11.24 37.29 2.67
830 1054 5.682212 GCGATTTCATTAAGGCCTTTCCATT 60.682 40.000 26.08 0.00 37.29 3.16
831 1055 4.202151 GCGATTTCATTAAGGCCTTTCCAT 60.202 41.667 26.08 10.96 37.29 3.41
832 1056 3.130340 GCGATTTCATTAAGGCCTTTCCA 59.870 43.478 26.08 8.85 37.29 3.53
833 1057 3.490933 GGCGATTTCATTAAGGCCTTTCC 60.491 47.826 26.08 7.11 36.71 3.13
834 1058 3.706698 GGCGATTTCATTAAGGCCTTTC 58.293 45.455 26.08 12.23 36.71 2.62
835 1059 2.099098 CGGCGATTTCATTAAGGCCTTT 59.901 45.455 26.08 2.84 37.22 3.11
836 1060 1.676006 CGGCGATTTCATTAAGGCCTT 59.324 47.619 24.18 24.18 37.22 4.35
837 1061 1.308998 CGGCGATTTCATTAAGGCCT 58.691 50.000 0.00 0.00 37.22 5.19
838 1062 0.317854 GCGGCGATTTCATTAAGGCC 60.318 55.000 12.98 0.00 36.45 5.19
839 1063 0.317854 GGCGGCGATTTCATTAAGGC 60.318 55.000 12.98 0.00 0.00 4.35
840 1064 1.021202 TGGCGGCGATTTCATTAAGG 58.979 50.000 12.98 0.00 0.00 2.69
904 1128 0.266152 AAGGGTCCGGATCAGAGGAT 59.734 55.000 18.43 0.00 38.97 3.24
1018 1242 0.529119 AAAACCCTAGATACGCCGCG 60.529 55.000 12.14 12.14 0.00 6.46
1036 1260 1.738830 CGGAGCGCGGAGGTAAAAA 60.739 57.895 8.83 0.00 0.00 1.94
1037 1261 2.125832 CGGAGCGCGGAGGTAAAA 60.126 61.111 8.83 0.00 0.00 1.52
1069 1293 2.492484 TCTAGAAGCTTCTGGACGGAAC 59.508 50.000 31.84 2.54 39.47 3.62
1146 1370 0.753262 GGGTCATGATACGCTGGACT 59.247 55.000 0.00 0.00 0.00 3.85
1272 1499 2.745884 CGCACCAAGGATTCGCCA 60.746 61.111 0.00 0.00 40.02 5.69
1412 1646 6.418057 TTTCTGCACCAAAATTAGAACCAT 57.582 33.333 0.00 0.00 0.00 3.55
1506 1740 6.142818 TCAATTTGAACAAGAAATCGGTGT 57.857 33.333 0.00 0.00 0.00 4.16
1588 1822 5.453198 CCACATGGTATGCAGATACACAGTA 60.453 44.000 0.00 0.00 36.85 2.74
1647 1881 0.320421 TCACGCCCACTTGCTTAGAC 60.320 55.000 0.00 0.00 0.00 2.59
1692 1926 4.530710 TGTGTTCTGCTAAGTTATCGGT 57.469 40.909 0.00 0.00 0.00 4.69
1693 1927 5.233050 CAGATGTGTTCTGCTAAGTTATCGG 59.767 44.000 0.00 0.00 45.16 4.18
1694 1928 6.266203 CAGATGTGTTCTGCTAAGTTATCG 57.734 41.667 0.00 0.00 45.16 2.92
1758 1997 9.750125 GTGTTTACCAATTCTTGAGAAAAAGAT 57.250 29.630 0.00 0.00 36.12 2.40
1761 2000 9.364989 CAAGTGTTTACCAATTCTTGAGAAAAA 57.635 29.630 0.00 0.00 37.61 1.94
1792 2031 2.490509 TCCTGTTGAGCATGCAGATTTG 59.509 45.455 21.98 5.63 32.39 2.32
1812 2051 8.448615 ACGACTTGGCACTTAATTAATACTTTC 58.551 33.333 0.00 0.00 0.00 2.62
1817 2056 7.466725 GCATCACGACTTGGCACTTAATTAATA 60.467 37.037 0.00 0.00 0.00 0.98
1845 2084 1.386772 TAGCTATTGGGGGTGGGGG 60.387 63.158 0.00 0.00 0.00 5.40
1846 2085 1.427072 CCTAGCTATTGGGGGTGGGG 61.427 65.000 0.00 0.00 0.00 4.96
1847 2086 0.697854 ACCTAGCTATTGGGGGTGGG 60.698 60.000 1.00 0.00 38.49 4.61
1848 2087 2.112279 TACCTAGCTATTGGGGGTGG 57.888 55.000 10.99 1.45 0.00 4.61
1849 2088 5.091552 TCTATTACCTAGCTATTGGGGGTG 58.908 45.833 10.99 0.00 0.00 4.61
1850 2089 5.364620 TCTATTACCTAGCTATTGGGGGT 57.635 43.478 6.81 6.81 0.00 4.95
1852 2091 5.069251 CCGATCTATTACCTAGCTATTGGGG 59.931 48.000 4.20 0.00 0.00 4.96
1853 2092 5.657302 ACCGATCTATTACCTAGCTATTGGG 59.343 44.000 4.20 0.28 0.00 4.12
1855 2094 9.141400 GAAAACCGATCTATTACCTAGCTATTG 57.859 37.037 0.00 0.00 0.00 1.90
1856 2095 8.312564 GGAAAACCGATCTATTACCTAGCTATT 58.687 37.037 0.00 0.00 0.00 1.73
1857 2096 7.674772 AGGAAAACCGATCTATTACCTAGCTAT 59.325 37.037 0.00 0.00 0.00 2.97
1858 2097 7.008941 AGGAAAACCGATCTATTACCTAGCTA 58.991 38.462 0.00 0.00 0.00 3.32
1859 2098 5.839606 AGGAAAACCGATCTATTACCTAGCT 59.160 40.000 0.00 0.00 0.00 3.32
1860 2099 6.015265 AGAGGAAAACCGATCTATTACCTAGC 60.015 42.308 0.00 0.00 0.00 3.42
1861 2100 7.527568 AGAGGAAAACCGATCTATTACCTAG 57.472 40.000 0.00 0.00 0.00 3.02
1862 2101 7.686127 GCAAGAGGAAAACCGATCTATTACCTA 60.686 40.741 0.00 0.00 0.00 3.08
1865 2104 5.236695 GGCAAGAGGAAAACCGATCTATTAC 59.763 44.000 0.00 0.00 0.00 1.89
1874 2139 1.266989 GAACAGGCAAGAGGAAAACCG 59.733 52.381 0.00 0.00 0.00 4.44
1878 2143 3.576078 TCTTGAACAGGCAAGAGGAAA 57.424 42.857 0.00 0.00 46.73 3.13
1884 2149 1.202806 TGTCCCTCTTGAACAGGCAAG 60.203 52.381 0.00 0.00 45.10 4.01
1888 2178 5.365021 AGATTATGTCCCTCTTGAACAGG 57.635 43.478 0.00 0.00 0.00 4.00
1908 2198 7.773690 ACTGAAAAAGTAAGGCTTGAAACTAGA 59.226 33.333 10.69 0.00 37.36 2.43
1934 2224 9.562408 TTGGTTTCAGTGTTACAAAGATATACA 57.438 29.630 0.00 0.00 0.00 2.29
1935 2225 9.821662 GTTGGTTTCAGTGTTACAAAGATATAC 57.178 33.333 0.00 0.00 0.00 1.47
1939 2229 5.068591 GGGTTGGTTTCAGTGTTACAAAGAT 59.931 40.000 0.00 0.00 0.00 2.40
1964 2254 7.148306 GCTCCTTGATTTTAAAGGTGACGATTA 60.148 37.037 8.13 0.00 43.97 1.75
1969 2259 5.705609 TGCTCCTTGATTTTAAAGGTGAC 57.294 39.130 8.13 1.83 43.97 3.67
1971 2261 6.089249 ACTTGCTCCTTGATTTTAAAGGTG 57.911 37.500 2.35 1.61 43.97 4.00
1989 2279 6.149633 CACAAGGAACCAAATAACTACTTGC 58.850 40.000 0.00 0.00 38.02 4.01
2068 2361 5.073311 TCTGCAAACACCTCAGTATCTAC 57.927 43.478 0.00 0.00 0.00 2.59
2079 2372 7.370383 TCAAGAAAATATCTTCTGCAAACACC 58.630 34.615 0.00 0.00 45.42 4.16
2087 2380 8.954350 AGGAACACATCAAGAAAATATCTTCTG 58.046 33.333 0.00 0.00 45.42 3.02
2093 2386 8.096414 CCCAAAAGGAACACATCAAGAAAATAT 58.904 33.333 0.00 0.00 38.24 1.28
2152 2446 6.429692 ACAAACATACACCGATGATCTTCAAA 59.570 34.615 9.10 0.00 0.00 2.69
2153 2447 5.937540 ACAAACATACACCGATGATCTTCAA 59.062 36.000 9.10 0.00 0.00 2.69
2158 2452 3.938963 ACCACAAACATACACCGATGATC 59.061 43.478 0.00 0.00 0.00 2.92
2171 2465 6.293298 GCATTGCAATCAAATTACCACAAACA 60.293 34.615 9.53 0.00 35.56 2.83
2175 2469 4.891260 TGCATTGCAATCAAATTACCACA 58.109 34.783 9.53 0.00 34.76 4.17
2195 2489 2.262423 ACCACTCTTTCCTTGTCTGC 57.738 50.000 0.00 0.00 0.00 4.26
2196 2490 2.880890 CCAACCACTCTTTCCTTGTCTG 59.119 50.000 0.00 0.00 0.00 3.51
2203 2497 1.318576 CACCACCAACCACTCTTTCC 58.681 55.000 0.00 0.00 0.00 3.13
2208 2502 0.110486 ACATCCACCACCAACCACTC 59.890 55.000 0.00 0.00 0.00 3.51
2227 2521 2.892852 AGGTACGCACACTAGTGGTTAA 59.107 45.455 26.12 5.55 45.98 2.01
2235 2529 4.011698 TCATTGACTAGGTACGCACACTA 58.988 43.478 0.00 0.00 0.00 2.74
2264 2558 9.794719 ACAAGCTAACTTCTAAGGATAAAAACT 57.205 29.630 0.00 0.00 32.29 2.66
2266 2560 9.787435 TGACAAGCTAACTTCTAAGGATAAAAA 57.213 29.630 0.00 0.00 32.29 1.94
2272 2566 8.135382 AGTTATGACAAGCTAACTTCTAAGGA 57.865 34.615 0.00 0.00 35.22 3.36
2281 2575 7.324616 CAGAGCAAAAAGTTATGACAAGCTAAC 59.675 37.037 0.00 0.00 0.00 2.34
2289 2583 6.959361 TGAACTCAGAGCAAAAAGTTATGAC 58.041 36.000 0.00 0.00 32.34 3.06
2292 2586 6.205658 GTCCTGAACTCAGAGCAAAAAGTTAT 59.794 38.462 8.33 0.00 46.59 1.89
2304 2598 1.132849 TGGGAAGGTCCTGAACTCAGA 60.133 52.381 8.33 0.00 46.59 3.27
2306 2600 2.040278 CAATGGGAAGGTCCTGAACTCA 59.960 50.000 0.00 0.00 36.57 3.41
2307 2601 2.040412 ACAATGGGAAGGTCCTGAACTC 59.960 50.000 0.00 0.00 36.57 3.01
2308 2602 2.065799 ACAATGGGAAGGTCCTGAACT 58.934 47.619 0.00 0.00 36.57 3.01
2324 2618 7.328277 TGTTTGACTAACAGCAAGTTACAAT 57.672 32.000 0.00 0.00 41.73 2.71
2350 2644 2.088423 GACAGGACACACCAAACACAA 58.912 47.619 0.00 0.00 42.04 3.33
2389 2684 6.322456 TGAGGGTGATTCAAAACAACACATAA 59.678 34.615 0.00 0.00 33.82 1.90
2416 2711 2.587522 GAGGAAAGGAGGTTGCAAGTT 58.412 47.619 0.00 0.00 0.00 2.66
2427 2722 0.499147 TTACCAGGGGGAGGAAAGGA 59.501 55.000 0.00 0.00 38.05 3.36
2430 2725 1.835895 TTGTTACCAGGGGGAGGAAA 58.164 50.000 0.00 0.00 38.05 3.13
2431 2726 1.835895 TTTGTTACCAGGGGGAGGAA 58.164 50.000 0.00 0.00 38.05 3.36
2448 2743 9.288576 ACACAATCACCGATATGAATCATATTT 57.711 29.630 16.02 3.95 37.20 1.40
2457 2752 4.634004 GTCCAAACACAATCACCGATATGA 59.366 41.667 0.00 0.00 0.00 2.15
2459 2754 4.584874 TGTCCAAACACAATCACCGATAT 58.415 39.130 0.00 0.00 0.00 1.63
2490 2785 3.945640 TTTTTAGGCCCCTGGACTATC 57.054 47.619 0.00 0.00 43.67 2.08
2524 2819 8.821894 GTGTAGGATGAAGAATTTAGTGTGATC 58.178 37.037 0.00 0.00 0.00 2.92
2527 2822 7.905604 TGTGTAGGATGAAGAATTTAGTGTG 57.094 36.000 0.00 0.00 0.00 3.82
2537 2832 8.816894 AGTTCTAGAAAATGTGTAGGATGAAGA 58.183 33.333 6.78 0.00 0.00 2.87
2538 2833 8.877779 CAGTTCTAGAAAATGTGTAGGATGAAG 58.122 37.037 6.78 0.00 0.00 3.02
2579 2874 0.413832 ACCTCACCAGAGCCTTAGGA 59.586 55.000 0.69 0.00 40.68 2.94
2589 2884 4.199310 TGACAAGAGAAAAACCTCACCAG 58.801 43.478 0.00 0.00 35.68 4.00
2590 2885 4.229304 TGACAAGAGAAAAACCTCACCA 57.771 40.909 0.00 0.00 35.68 4.17
2594 2889 5.774498 AACCATGACAAGAGAAAAACCTC 57.226 39.130 0.00 0.00 0.00 3.85
2597 2892 5.660460 ACCAAACCATGACAAGAGAAAAAC 58.340 37.500 0.00 0.00 0.00 2.43
2625 2921 5.643348 CACATTGTAAGCTTATCACCTGTCA 59.357 40.000 9.88 0.00 0.00 3.58
2629 2925 5.643777 GTGTCACATTGTAAGCTTATCACCT 59.356 40.000 9.88 0.00 0.00 4.00
2639 2935 4.870426 AGAATAGGCGTGTCACATTGTAAG 59.130 41.667 3.42 0.00 0.00 2.34
2651 2947 2.015736 ACTGAAGCAGAATAGGCGTG 57.984 50.000 0.82 0.00 35.18 5.34
2652 2948 2.350522 CAACTGAAGCAGAATAGGCGT 58.649 47.619 0.82 0.00 35.18 5.68
2653 2949 1.667724 CCAACTGAAGCAGAATAGGCG 59.332 52.381 0.82 0.00 35.18 5.52
2660 2956 3.569194 TGTAAACCCAACTGAAGCAGA 57.431 42.857 0.82 0.00 35.18 4.26
2673 2976 9.191995 CATGTAAACTGGAAAGAAATGTAAACC 57.808 33.333 0.00 0.00 0.00 3.27
2723 3040 4.035208 CAGACACACTACTGAAAAACCCAC 59.965 45.833 0.00 0.00 36.38 4.61
2738 3055 6.258160 GGCAACAATAATATGACAGACACAC 58.742 40.000 0.00 0.00 0.00 3.82
2758 3075 1.496060 ACTGACGAGGGATATGGCAA 58.504 50.000 0.00 0.00 0.00 4.52
2766 3083 1.887198 GTCTGAGAAACTGACGAGGGA 59.113 52.381 0.00 0.00 37.62 4.20
2769 3086 4.806247 ACAAAAGTCTGAGAAACTGACGAG 59.194 41.667 0.00 0.00 46.95 4.18
2770 3087 4.755411 ACAAAAGTCTGAGAAACTGACGA 58.245 39.130 0.00 0.00 46.95 4.20
2771 3088 5.258622 CAACAAAAGTCTGAGAAACTGACG 58.741 41.667 0.00 0.00 46.95 4.35
2772 3089 5.030936 GCAACAAAAGTCTGAGAAACTGAC 58.969 41.667 0.00 0.00 44.24 3.51
2810 3127 7.962917 TGTTCAAAAGCAAAAGTTTGAGAATC 58.037 30.769 7.96 0.00 42.86 2.52
2811 3128 7.903995 TGTTCAAAAGCAAAAGTTTGAGAAT 57.096 28.000 7.96 0.00 42.86 2.40
2817 3134 6.873076 TCTGACATGTTCAAAAGCAAAAGTTT 59.127 30.769 0.00 0.00 32.21 2.66
2834 3151 8.447924 AATAATCTGTTCTTCCATCTGACATG 57.552 34.615 0.00 0.00 0.00 3.21
2835 3152 8.900781 CAAATAATCTGTTCTTCCATCTGACAT 58.099 33.333 0.00 0.00 0.00 3.06
2839 3156 7.636150 ACCAAATAATCTGTTCTTCCATCTG 57.364 36.000 0.00 0.00 0.00 2.90
2843 3160 8.877864 ATACAACCAAATAATCTGTTCTTCCA 57.122 30.769 0.00 0.00 0.00 3.53
2893 3386 5.997746 CCTCCACTAACTTTGTCTCATTGAA 59.002 40.000 0.00 0.00 0.00 2.69
2906 3399 2.575279 TCTCTCGGTACCTCCACTAACT 59.425 50.000 10.90 0.00 35.57 2.24
2907 3400 2.996631 TCTCTCGGTACCTCCACTAAC 58.003 52.381 10.90 0.00 35.57 2.34
2909 3402 3.072184 GGTATCTCTCGGTACCTCCACTA 59.928 52.174 10.90 0.00 37.85 2.74
2910 3403 2.158638 GGTATCTCTCGGTACCTCCACT 60.159 54.545 10.90 0.00 37.85 4.00
2911 3404 2.228925 GGTATCTCTCGGTACCTCCAC 58.771 57.143 10.90 0.00 37.85 4.02
2912 3405 1.848388 TGGTATCTCTCGGTACCTCCA 59.152 52.381 10.90 3.10 40.78 3.86
2913 3406 2.653234 TGGTATCTCTCGGTACCTCC 57.347 55.000 10.90 0.61 40.78 4.30
2914 3407 7.774157 TGATATAATGGTATCTCTCGGTACCTC 59.226 40.741 10.90 0.00 40.78 3.85
2915 3408 7.640313 TGATATAATGGTATCTCTCGGTACCT 58.360 38.462 10.90 0.00 40.78 3.08
2917 3410 8.399425 CACTGATATAATGGTATCTCTCGGTAC 58.601 40.741 0.00 0.00 33.26 3.34
2918 3411 8.326529 TCACTGATATAATGGTATCTCTCGGTA 58.673 37.037 0.00 0.00 33.26 4.02
2919 3412 7.175797 TCACTGATATAATGGTATCTCTCGGT 58.824 38.462 0.00 0.00 33.26 4.69
2920 3413 7.631717 TCACTGATATAATGGTATCTCTCGG 57.368 40.000 0.00 0.00 33.26 4.63
2921 3414 8.735315 ACTTCACTGATATAATGGTATCTCTCG 58.265 37.037 0.00 0.00 33.26 4.04
2940 3442 1.605712 GGCACGCTTCAGTACTTCACT 60.606 52.381 0.00 0.00 38.32 3.41
2956 3458 8.458843 ACTACATGTAAAATCTGTTATTGGCAC 58.541 33.333 7.06 0.00 0.00 5.01
3020 3530 4.261952 CCCAAATGAAGCACACATGTACAA 60.262 41.667 0.00 0.00 0.00 2.41
3033 3543 3.016736 ACTCAATACGGCCCAAATGAAG 58.983 45.455 0.00 0.00 0.00 3.02
3036 3546 4.792704 GCATTACTCAATACGGCCCAAATG 60.793 45.833 0.00 0.00 0.00 2.32
3040 3550 1.488812 AGCATTACTCAATACGGCCCA 59.511 47.619 0.00 0.00 0.00 5.36
3041 3551 1.873591 CAGCATTACTCAATACGGCCC 59.126 52.381 0.00 0.00 0.00 5.80
3043 3553 1.873591 CCCAGCATTACTCAATACGGC 59.126 52.381 0.00 0.00 0.00 5.68
3045 3555 5.560966 AAAACCCAGCATTACTCAATACG 57.439 39.130 0.00 0.00 0.00 3.06
3046 3556 9.946165 GTATAAAAACCCAGCATTACTCAATAC 57.054 33.333 0.00 0.00 0.00 1.89
3054 3565 8.898761 CACATACAGTATAAAAACCCAGCATTA 58.101 33.333 0.00 0.00 0.00 1.90
3076 3587 0.178981 AAGCCCTGCAGAACACACAT 60.179 50.000 17.39 0.00 0.00 3.21
3319 3832 4.589216 TTCAAAGGTTCATGGCTCTTTG 57.411 40.909 19.75 19.75 44.17 2.77
3335 3848 5.602145 ACAGGAGGAAAAACATGGATTCAAA 59.398 36.000 0.00 0.00 0.00 2.69
3352 3865 1.398390 GTTGCTTGCGATTACAGGAGG 59.602 52.381 0.00 0.00 0.00 4.30
3404 3917 3.675775 GCTTCACTTTCCACTGCAACAAA 60.676 43.478 0.00 0.00 0.00 2.83
3461 3974 2.479566 ATCACAGGAACGCTCAACAT 57.520 45.000 0.00 0.00 0.00 2.71
3470 3983 5.638234 GTGGAGTACAAAGTATCACAGGAAC 59.362 44.000 0.00 0.00 0.00 3.62
3504 4017 3.370672 CACAACGACAAGCTACATGCATA 59.629 43.478 0.00 0.00 45.94 3.14
3531 4044 6.460781 ACAACAGACGTTACATATCCTCAAA 58.539 36.000 0.00 0.00 32.75 2.69
3532 4045 6.032956 ACAACAGACGTTACATATCCTCAA 57.967 37.500 0.00 0.00 32.75 3.02
3557 4070 2.774234 ACTGGGTCTGGGTTCATAGATG 59.226 50.000 0.00 0.00 0.00 2.90
3593 4106 3.394674 TCAAACATCTTGCACGGAGTA 57.605 42.857 0.00 0.00 41.61 2.59
3632 4145 6.951062 TCATGTCAATCTTAAACACAACCA 57.049 33.333 0.00 0.00 0.00 3.67
3661 4174 3.128589 GCTCAACAAACAAGTCAACAGGA 59.871 43.478 0.00 0.00 0.00 3.86
3663 4176 4.361451 AGCTCAACAAACAAGTCAACAG 57.639 40.909 0.00 0.00 0.00 3.16
3718 4319 6.254589 GTGTCTCACTCATAACTCATAAGCAC 59.745 42.308 0.00 0.00 0.00 4.40
3722 4323 8.122472 TCAAGTGTCTCACTCATAACTCATAA 57.878 34.615 2.86 0.00 44.62 1.90
3723 4324 7.703058 TCAAGTGTCTCACTCATAACTCATA 57.297 36.000 2.86 0.00 44.62 2.15
3724 4325 6.596309 TCAAGTGTCTCACTCATAACTCAT 57.404 37.500 2.86 0.00 44.62 2.90
3725 4326 6.596309 ATCAAGTGTCTCACTCATAACTCA 57.404 37.500 2.86 0.00 44.62 3.41
3726 4327 7.064016 GGAAATCAAGTGTCTCACTCATAACTC 59.936 40.741 2.86 0.00 44.62 3.01
3727 4328 6.876257 GGAAATCAAGTGTCTCACTCATAACT 59.124 38.462 2.86 0.00 44.62 2.24
3728 4329 6.092807 GGGAAATCAAGTGTCTCACTCATAAC 59.907 42.308 2.86 0.00 44.62 1.89
3907 4509 8.912658 GTCTCCAAAAGATTTTAAAACCGATTC 58.087 33.333 1.97 0.00 36.11 2.52
3936 4540 9.431887 GCAATTGCAATTGATATTTCCTGATAT 57.568 29.630 42.21 9.14 46.72 1.63
3972 4576 5.238650 TGCATTGCTATCTCTGATGAACATG 59.761 40.000 10.49 0.00 0.00 3.21
4023 4629 6.380274 AGAATCCAGCAAGTGAATTCAATCAT 59.620 34.615 10.35 0.00 0.00 2.45
4030 4636 4.282703 AGCAAAGAATCCAGCAAGTGAATT 59.717 37.500 0.00 0.00 0.00 2.17
4073 4679 0.186630 TATCCCTAGCCCGCTACACA 59.813 55.000 0.00 0.00 0.00 3.72
4074 4680 0.602060 GTATCCCTAGCCCGCTACAC 59.398 60.000 0.00 0.00 0.00 2.90
4075 4681 0.186630 TGTATCCCTAGCCCGCTACA 59.813 55.000 0.00 0.00 0.00 2.74
4076 4682 1.477295 GATGTATCCCTAGCCCGCTAC 59.523 57.143 0.00 0.00 0.00 3.58
4077 4683 1.358103 AGATGTATCCCTAGCCCGCTA 59.642 52.381 0.00 0.00 0.00 4.26
4078 4684 0.115349 AGATGTATCCCTAGCCCGCT 59.885 55.000 0.00 0.00 0.00 5.52
4080 4686 2.872038 GCAAAGATGTATCCCTAGCCCG 60.872 54.545 0.00 0.00 0.00 6.13
4081 4687 2.373502 AGCAAAGATGTATCCCTAGCCC 59.626 50.000 0.00 0.00 0.00 5.19
4083 4689 4.274459 CACAAGCAAAGATGTATCCCTAGC 59.726 45.833 0.00 0.00 0.00 3.42
4085 4691 5.692115 TCACAAGCAAAGATGTATCCCTA 57.308 39.130 0.00 0.00 0.00 3.53
4086 4692 4.574674 TCACAAGCAAAGATGTATCCCT 57.425 40.909 0.00 0.00 0.00 4.20
4094 4703 7.937394 TGATCTCATATCATCACAAGCAAAGAT 59.063 33.333 0.00 0.00 0.00 2.40
4163 4772 5.413833 GGAGATGATGAGCAAGAAGAACAAA 59.586 40.000 0.00 0.00 0.00 2.83
4191 4800 0.033991 CTGGAGGAGACGAGGAAGGA 60.034 60.000 0.00 0.00 0.00 3.36
4192 4801 0.323908 ACTGGAGGAGACGAGGAAGG 60.324 60.000 0.00 0.00 0.00 3.46
4197 4806 0.814457 CTGGAACTGGAGGAGACGAG 59.186 60.000 0.00 0.00 0.00 4.18
4200 4809 1.822371 GAGACTGGAACTGGAGGAGAC 59.178 57.143 0.00 0.00 0.00 3.36
4201 4810 1.713647 AGAGACTGGAACTGGAGGAGA 59.286 52.381 0.00 0.00 0.00 3.71
4436 5048 1.065709 GTTTGCCCGGATAAGGAGACA 60.066 52.381 0.73 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.