Multiple sequence alignment - TraesCS5B01G274900

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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 TraesCS5B01G274900 chr5B 100.000 2225 0 0 1 2225 460679690 460681914 0.000000e+00 4109.0
1 TraesCS5B01G274900 chr5B 82.870 432 50 10 891 1307 398158957 398159379 1.260000e-97 366.0
2 TraesCS5B01G274900 chr5D 93.265 1069 49 12 777 1843 384075933 384076980 0.000000e+00 1554.0
3 TraesCS5B01G274900 chr5D 82.759 435 52 18 888 1307 339112852 339113278 1.260000e-97 366.0
4 TraesCS5B01G274900 chr5D 90.323 217 10 3 556 772 384072390 384072595 7.830000e-70 274.0
5 TraesCS5B01G274900 chr5D 91.720 157 12 1 260 416 384071941 384072096 1.340000e-52 217.0
6 TraesCS5B01G274900 chr5D 83.146 178 22 6 559 729 339112390 339112566 2.960000e-34 156.0
7 TraesCS5B01G274900 chr5D 90.123 81 8 0 479 559 384072096 384072176 3.020000e-19 106.0
8 TraesCS5B01G274900 chr5D 84.337 83 9 3 2145 2225 483707941 483707861 6.590000e-11 78.7
9 TraesCS5B01G274900 chr5D 97.297 37 1 0 4 40 384071596 384071632 1.840000e-06 63.9
10 TraesCS5B01G274900 chr5A 87.719 1026 87 31 804 1813 484559611 484560613 0.000000e+00 1160.0
11 TraesCS5B01G274900 chr5A 89.967 299 19 5 264 559 484558648 484558938 2.090000e-100 375.0
12 TraesCS5B01G274900 chr5A 82.339 436 51 20 888 1307 439877749 439878174 2.720000e-94 355.0
13 TraesCS5B01G274900 chr5A 92.391 184 12 2 557 739 484558984 484559166 6.090000e-66 261.0
14 TraesCS5B01G274900 chr5A 90.580 138 8 2 1919 2054 484561591 484561725 6.310000e-41 178.0
15 TraesCS5B01G274900 chr5A 81.690 213 32 5 1 206 484558114 484558326 1.060000e-38 171.0
16 TraesCS5B01G274900 chr5A 82.540 189 25 5 556 737 439877292 439877479 2.290000e-35 159.0
17 TraesCS5B01G274900 chr2D 82.540 126 15 6 1273 1394 34379172 34379050 1.090000e-18 104.0
18 TraesCS5B01G274900 chr6D 87.013 77 10 0 2146 2222 3599707 3599783 1.090000e-13 87.9
19 TraesCS5B01G274900 chr3A 85.185 81 8 3 2144 2222 567569160 567569238 1.830000e-11 80.5


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 TraesCS5B01G274900 chr5B 460679690 460681914 2224 False 4109.00 4109 100.0000 1 2225 1 chr5B.!!$F2 2224
1 TraesCS5B01G274900 chr5D 384071596 384076980 5384 False 442.98 1554 92.5456 4 1843 5 chr5D.!!$F2 1839
2 TraesCS5B01G274900 chr5D 339112390 339113278 888 False 261.00 366 82.9525 559 1307 2 chr5D.!!$F1 748
3 TraesCS5B01G274900 chr5A 484558114 484561725 3611 False 429.00 1160 88.4694 1 2054 5 chr5A.!!$F2 2053
4 TraesCS5B01G274900 chr5A 439877292 439878174 882 False 257.00 355 82.4395 556 1307 2 chr5A.!!$F1 751

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
995 5119 0.178958 ACAGACCGGTCCTTCTGACT 60.179 55.0 30.82 6.96 43.89 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2197 7224 0.037734 GGTAGAACCAACCCACCAGG 59.962 60.0 0.0 0.0 38.42 4.45 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
62 65 2.519963 GCTCAAAACTAAAGCCGCATC 58.480 47.619 0.00 0.00 0.00 3.91
63 66 2.732282 GCTCAAAACTAAAGCCGCATCC 60.732 50.000 0.00 0.00 0.00 3.51
64 67 1.816224 TCAAAACTAAAGCCGCATCCC 59.184 47.619 0.00 0.00 0.00 3.85
71 74 2.439553 AAAGCCGCATCCCCCTCAAA 62.440 55.000 0.00 0.00 0.00 2.69
72 75 2.362375 GCCGCATCCCCCTCAAAA 60.362 61.111 0.00 0.00 0.00 2.44
73 76 1.981853 GCCGCATCCCCCTCAAAAA 60.982 57.895 0.00 0.00 0.00 1.94
103 106 2.990066 AACTAAAGCCGGAGATCAGG 57.010 50.000 5.05 0.00 0.00 3.86
105 108 2.035632 ACTAAAGCCGGAGATCAGGAG 58.964 52.381 5.05 0.00 32.68 3.69
106 109 1.342819 CTAAAGCCGGAGATCAGGAGG 59.657 57.143 5.05 0.00 32.68 4.30
147 176 1.539165 CCGGAGATCAGGAGGAGGA 59.461 63.158 0.00 0.00 32.68 3.71
229 287 7.082972 ACTAGGAATCCCACCAGTTTATAGAT 58.917 38.462 0.00 0.00 33.88 1.98
239 297 4.227300 ACCAGTTTATAGATGTTGGCCTCA 59.773 41.667 3.32 3.67 0.00 3.86
261 555 7.141758 TCAGCAGATTCATCTAGGGTTAAAT 57.858 36.000 0.00 0.00 34.85 1.40
292 586 4.631131 TGTACCTCGCCATGATAAAGATG 58.369 43.478 0.00 0.00 0.00 2.90
374 669 0.319040 CATATCAGTGGCTCGGGTCG 60.319 60.000 0.00 0.00 0.00 4.79
466 762 6.777091 TCAGGGGTTTATGATTGATGGTAATG 59.223 38.462 0.00 0.00 0.00 1.90
470 766 7.926018 GGGGTTTATGATTGATGGTAATGTTTC 59.074 37.037 0.00 0.00 0.00 2.78
481 777 4.016444 TGGTAATGTTTCCTGAAGATGGC 58.984 43.478 0.00 0.00 0.00 4.40
597 1111 7.283354 CCATAAATCAGTTTCTCCTTACTTCCC 59.717 40.741 0.00 0.00 0.00 3.97
744 1314 7.490962 TGTTAAGACACAATGGAGTACAAAG 57.509 36.000 0.00 0.00 0.00 2.77
982 5106 1.677552 CACAGGGTGGGTACAGACC 59.322 63.158 4.30 4.30 46.13 3.85
995 5119 0.178958 ACAGACCGGTCCTTCTGACT 60.179 55.000 30.82 6.96 43.89 3.41
1059 5195 4.947147 GGTGGTGGCGGCACAAGA 62.947 66.667 38.28 21.61 0.00 3.02
1195 5331 2.358737 GTTCTGTCAGCCCCACCG 60.359 66.667 0.00 0.00 0.00 4.94
1328 5467 4.154918 CCTGTCTGCAACTCTGGTTAATTC 59.845 45.833 0.00 0.00 33.88 2.17
1334 5473 4.168760 GCAACTCTGGTTAATTCACATGC 58.831 43.478 0.00 0.00 33.88 4.06
1413 5554 6.667007 ATTTTGTTCAAGTTGAAAGCCAAG 57.333 33.333 19.63 0.00 38.22 3.61
1420 5561 2.309613 AGTTGAAAGCCAAGCATGACA 58.690 42.857 0.00 0.00 35.03 3.58
1421 5562 2.035066 AGTTGAAAGCCAAGCATGACAC 59.965 45.455 0.00 0.00 35.03 3.67
1422 5563 1.985473 TGAAAGCCAAGCATGACACT 58.015 45.000 0.00 0.00 0.00 3.55
1423 5564 1.610038 TGAAAGCCAAGCATGACACTG 59.390 47.619 0.00 0.00 0.00 3.66
1424 5565 1.610522 GAAAGCCAAGCATGACACTGT 59.389 47.619 0.00 0.00 0.00 3.55
1427 5568 0.665369 GCCAAGCATGACACTGTTGC 60.665 55.000 0.00 0.00 36.63 4.17
1429 5570 1.335597 CCAAGCATGACACTGTTGCTG 60.336 52.381 8.77 4.51 45.54 4.41
1437 5587 1.007734 CACTGTTGCTGCTTGCTGG 60.008 57.895 0.00 0.00 43.37 4.85
1447 5597 1.734465 CTGCTTGCTGGTAGTGTTAGC 59.266 52.381 0.00 0.00 37.93 3.09
1452 5602 3.247006 TGCTGGTAGTGTTAGCTTAGC 57.753 47.619 0.00 0.00 38.25 3.09
1512 5663 8.502387 GCTGCTTTGGAGAGACATTAATATAAG 58.498 37.037 0.00 0.00 0.00 1.73
1573 5724 7.180229 TCCTACATACAGAGAAAGAAACCATGA 59.820 37.037 0.00 0.00 0.00 3.07
1581 5732 6.875726 CAGAGAAAGAAACCATGACATCTGTA 59.124 38.462 0.00 0.00 0.00 2.74
1592 5744 8.553459 ACCATGACATCTGTAAACTTCTAAAG 57.447 34.615 0.00 0.00 0.00 1.85
1627 5779 5.760484 TCGGTTGGTATAGTTTTAAGGGT 57.240 39.130 0.00 0.00 0.00 4.34
1651 5805 5.571784 ATTATGACTGAAACATGGTGCTG 57.428 39.130 0.00 0.00 0.00 4.41
1678 5832 1.202879 TGGTGCAGGTACAAAAGGAGG 60.203 52.381 0.00 0.00 0.00 4.30
1692 5846 0.768221 AGGAGGCCTGAAACACTGGA 60.768 55.000 12.00 0.00 39.52 3.86
1696 5850 1.202818 AGGCCTGAAACACTGGAGTTC 60.203 52.381 3.11 0.00 39.52 3.01
1717 5871 2.160721 TGCTGGGGTGGTTTTACAAA 57.839 45.000 0.00 0.00 0.00 2.83
1779 5933 5.582269 CACGAATGGTCATGTGAAAGATAGT 59.418 40.000 0.00 0.00 34.29 2.12
1844 5998 4.905429 TGTCACTGCTGTGTATGGTATTT 58.095 39.130 21.35 0.00 44.14 1.40
1846 6000 4.695455 GTCACTGCTGTGTATGGTATTTGT 59.305 41.667 21.35 0.00 44.14 2.83
1847 6001 5.181245 GTCACTGCTGTGTATGGTATTTGTT 59.819 40.000 21.35 0.00 44.14 2.83
1848 6002 5.181056 TCACTGCTGTGTATGGTATTTGTTG 59.819 40.000 21.35 0.00 44.14 3.33
1849 6003 4.458989 ACTGCTGTGTATGGTATTTGTTGG 59.541 41.667 0.00 0.00 0.00 3.77
1850 6004 4.402829 TGCTGTGTATGGTATTTGTTGGT 58.597 39.130 0.00 0.00 0.00 3.67
1851 6005 4.217334 TGCTGTGTATGGTATTTGTTGGTG 59.783 41.667 0.00 0.00 0.00 4.17
1853 6007 5.697473 TGTGTATGGTATTTGTTGGTGTG 57.303 39.130 0.00 0.00 0.00 3.82
1854 6008 4.520874 TGTGTATGGTATTTGTTGGTGTGG 59.479 41.667 0.00 0.00 0.00 4.17
1855 6009 4.762765 GTGTATGGTATTTGTTGGTGTGGA 59.237 41.667 0.00 0.00 0.00 4.02
1857 6011 5.833667 TGTATGGTATTTGTTGGTGTGGAAA 59.166 36.000 0.00 0.00 0.00 3.13
1859 6013 7.670140 TGTATGGTATTTGTTGGTGTGGAAATA 59.330 33.333 0.00 0.00 0.00 1.40
1860 6014 6.978674 TGGTATTTGTTGGTGTGGAAATAA 57.021 33.333 0.00 0.00 0.00 1.40
1862 6016 5.867174 GGTATTTGTTGGTGTGGAAATAAGC 59.133 40.000 0.00 0.00 0.00 3.09
1863 6017 5.543507 ATTTGTTGGTGTGGAAATAAGCA 57.456 34.783 0.00 0.00 0.00 3.91
1864 6018 5.543507 TTTGTTGGTGTGGAAATAAGCAT 57.456 34.783 0.00 0.00 0.00 3.79
1865 6019 5.543507 TTGTTGGTGTGGAAATAAGCATT 57.456 34.783 0.00 0.00 0.00 3.56
1866 6020 4.880759 TGTTGGTGTGGAAATAAGCATTG 58.119 39.130 0.00 0.00 0.00 2.82
1868 6022 2.233431 TGGTGTGGAAATAAGCATTGCC 59.767 45.455 4.70 0.00 40.06 4.52
1874 6028 5.226194 TGGAAATAAGCATTGCCAAAACT 57.774 34.783 4.70 0.00 45.54 2.66
1875 6029 5.237048 TGGAAATAAGCATTGCCAAAACTC 58.763 37.500 4.70 0.00 45.54 3.01
1876 6030 5.011943 TGGAAATAAGCATTGCCAAAACTCT 59.988 36.000 4.70 0.00 45.54 3.24
1877 6031 5.349543 GGAAATAAGCATTGCCAAAACTCTG 59.650 40.000 4.70 0.00 39.48 3.35
1878 6032 5.726980 AATAAGCATTGCCAAAACTCTGA 57.273 34.783 4.70 0.00 0.00 3.27
1879 6033 5.726980 ATAAGCATTGCCAAAACTCTGAA 57.273 34.783 4.70 0.00 0.00 3.02
1880 6034 4.405116 AAGCATTGCCAAAACTCTGAAA 57.595 36.364 4.70 0.00 0.00 2.69
1881 6035 3.721035 AGCATTGCCAAAACTCTGAAAC 58.279 40.909 4.70 0.00 0.00 2.78
1882 6036 3.385755 AGCATTGCCAAAACTCTGAAACT 59.614 39.130 4.70 0.00 0.00 2.66
1884 6038 3.691049 TTGCCAAAACTCTGAAACTCG 57.309 42.857 0.00 0.00 0.00 4.18
1886 6040 3.476552 TGCCAAAACTCTGAAACTCGAT 58.523 40.909 0.00 0.00 0.00 3.59
1887 6041 3.250762 TGCCAAAACTCTGAAACTCGATG 59.749 43.478 0.00 0.00 0.00 3.84
1889 6043 4.611581 GCCAAAACTCTGAAACTCGATGTC 60.612 45.833 0.00 0.00 0.00 3.06
1890 6044 4.511454 CCAAAACTCTGAAACTCGATGTCA 59.489 41.667 0.00 0.00 0.00 3.58
1892 6046 5.659048 AAACTCTGAAACTCGATGTCAAC 57.341 39.130 0.00 0.00 0.00 3.18
1893 6047 4.322080 ACTCTGAAACTCGATGTCAACA 57.678 40.909 0.00 0.00 0.00 3.33
1894 6048 4.887748 ACTCTGAAACTCGATGTCAACAT 58.112 39.130 0.00 0.00 39.70 2.71
1895 6049 6.025749 ACTCTGAAACTCGATGTCAACATA 57.974 37.500 0.00 0.00 36.57 2.29
1896 6050 6.096036 ACTCTGAAACTCGATGTCAACATAG 58.904 40.000 0.00 0.00 36.57 2.23
1897 6051 4.864806 TCTGAAACTCGATGTCAACATAGC 59.135 41.667 0.00 0.00 36.57 2.97
1898 6052 3.612423 TGAAACTCGATGTCAACATAGCG 59.388 43.478 0.00 0.00 36.57 4.26
1899 6053 3.503827 AACTCGATGTCAACATAGCGA 57.496 42.857 6.71 6.71 36.57 4.93
1900 6054 3.503827 ACTCGATGTCAACATAGCGAA 57.496 42.857 7.89 0.00 36.57 4.70
1901 6055 4.046938 ACTCGATGTCAACATAGCGAAT 57.953 40.909 7.89 0.00 36.57 3.34
1902 6056 5.183014 ACTCGATGTCAACATAGCGAATA 57.817 39.130 7.89 0.00 36.57 1.75
1903 6057 5.215903 ACTCGATGTCAACATAGCGAATAG 58.784 41.667 7.89 1.59 36.57 1.73
1904 6058 3.981416 TCGATGTCAACATAGCGAATAGC 59.019 43.478 4.91 0.00 40.83 2.97
1929 6954 5.184892 AGCTACCAGAATCACCATTTTCT 57.815 39.130 0.00 0.00 32.48 2.52
1932 6957 5.415701 GCTACCAGAATCACCATTTTCTTCA 59.584 40.000 0.00 0.00 29.85 3.02
1944 6969 5.529060 ACCATTTTCTTCAGTGAGTCACTTC 59.471 40.000 23.33 0.00 42.59 3.01
1945 6970 5.762218 CCATTTTCTTCAGTGAGTCACTTCT 59.238 40.000 23.33 0.00 42.59 2.85
1946 6971 6.261826 CCATTTTCTTCAGTGAGTCACTTCTT 59.738 38.462 23.33 0.00 42.59 2.52
1956 6981 1.072505 TCACTTCTTGGAACGGGCC 59.927 57.895 0.00 0.00 0.00 5.80
1993 7020 5.620206 TCACAATTTGGAGTCTCAAGCTTA 58.380 37.500 0.00 0.00 0.00 3.09
2003 7030 5.483811 GAGTCTCAAGCTTAGCCTAGTTTT 58.516 41.667 0.00 0.00 0.00 2.43
2042 7069 8.457261 GGATAATATGCACCTGATTCAAAGATC 58.543 37.037 0.00 0.00 0.00 2.75
2047 7074 4.828939 TGCACCTGATTCAAAGATCTTGTT 59.171 37.500 9.17 0.00 0.00 2.83
2054 7081 6.240894 TGATTCAAAGATCTTGTTAGGTGCT 58.759 36.000 9.17 0.00 0.00 4.40
2055 7082 6.716628 TGATTCAAAGATCTTGTTAGGTGCTT 59.283 34.615 9.17 0.00 0.00 3.91
2056 7083 6.959639 TTCAAAGATCTTGTTAGGTGCTTT 57.040 33.333 9.17 0.00 0.00 3.51
2057 7084 6.317789 TCAAAGATCTTGTTAGGTGCTTTG 57.682 37.500 9.17 0.00 41.01 2.77
2058 7085 5.827797 TCAAAGATCTTGTTAGGTGCTTTGT 59.172 36.000 9.17 0.00 40.69 2.83
2059 7086 6.321181 TCAAAGATCTTGTTAGGTGCTTTGTT 59.679 34.615 9.17 0.00 40.69 2.83
2060 7087 6.715347 AAGATCTTGTTAGGTGCTTTGTTT 57.285 33.333 7.30 0.00 0.00 2.83
2061 7088 6.715347 AGATCTTGTTAGGTGCTTTGTTTT 57.285 33.333 0.00 0.00 0.00 2.43
2062 7089 7.112452 AGATCTTGTTAGGTGCTTTGTTTTT 57.888 32.000 0.00 0.00 0.00 1.94
2063 7090 7.203218 AGATCTTGTTAGGTGCTTTGTTTTTC 58.797 34.615 0.00 0.00 0.00 2.29
2064 7091 5.656480 TCTTGTTAGGTGCTTTGTTTTTCC 58.344 37.500 0.00 0.00 0.00 3.13
2065 7092 5.420739 TCTTGTTAGGTGCTTTGTTTTTCCT 59.579 36.000 0.00 0.00 0.00 3.36
2066 7093 5.669164 TGTTAGGTGCTTTGTTTTTCCTT 57.331 34.783 0.00 0.00 0.00 3.36
2067 7094 5.415221 TGTTAGGTGCTTTGTTTTTCCTTG 58.585 37.500 0.00 0.00 0.00 3.61
2068 7095 3.541996 AGGTGCTTTGTTTTTCCTTGG 57.458 42.857 0.00 0.00 0.00 3.61
2069 7096 2.837591 AGGTGCTTTGTTTTTCCTTGGT 59.162 40.909 0.00 0.00 0.00 3.67
2070 7097 4.027437 AGGTGCTTTGTTTTTCCTTGGTA 58.973 39.130 0.00 0.00 0.00 3.25
2071 7098 4.468153 AGGTGCTTTGTTTTTCCTTGGTAA 59.532 37.500 0.00 0.00 0.00 2.85
2072 7099 4.808895 GGTGCTTTGTTTTTCCTTGGTAAG 59.191 41.667 0.00 0.00 0.00 2.34
2073 7100 5.416083 GTGCTTTGTTTTTCCTTGGTAAGT 58.584 37.500 0.00 0.00 0.00 2.24
2074 7101 5.290885 GTGCTTTGTTTTTCCTTGGTAAGTG 59.709 40.000 0.00 0.00 0.00 3.16
2075 7102 4.808895 GCTTTGTTTTTCCTTGGTAAGTGG 59.191 41.667 0.00 0.00 0.00 4.00
2076 7103 5.625886 GCTTTGTTTTTCCTTGGTAAGTGGT 60.626 40.000 0.00 0.00 0.00 4.16
2077 7104 4.993029 TGTTTTTCCTTGGTAAGTGGTG 57.007 40.909 0.00 0.00 0.00 4.17
2078 7105 4.345854 TGTTTTTCCTTGGTAAGTGGTGT 58.654 39.130 0.00 0.00 0.00 4.16
2079 7106 4.773149 TGTTTTTCCTTGGTAAGTGGTGTT 59.227 37.500 0.00 0.00 0.00 3.32
2080 7107 4.993029 TTTTCCTTGGTAAGTGGTGTTG 57.007 40.909 0.00 0.00 0.00 3.33
2081 7108 3.935818 TTCCTTGGTAAGTGGTGTTGA 57.064 42.857 0.00 0.00 0.00 3.18
2082 7109 3.202829 TCCTTGGTAAGTGGTGTTGAC 57.797 47.619 0.00 0.00 0.00 3.18
2083 7110 2.506231 TCCTTGGTAAGTGGTGTTGACA 59.494 45.455 0.00 0.00 0.00 3.58
2084 7111 3.054287 TCCTTGGTAAGTGGTGTTGACAA 60.054 43.478 0.00 0.00 0.00 3.18
2085 7112 3.888930 CCTTGGTAAGTGGTGTTGACAAT 59.111 43.478 0.00 0.00 0.00 2.71
2086 7113 4.340950 CCTTGGTAAGTGGTGTTGACAATT 59.659 41.667 0.00 0.00 0.00 2.32
2087 7114 5.507315 CCTTGGTAAGTGGTGTTGACAATTC 60.507 44.000 0.00 0.00 0.00 2.17
2088 7115 4.787551 TGGTAAGTGGTGTTGACAATTCT 58.212 39.130 0.00 0.00 0.00 2.40
2089 7116 5.931294 TGGTAAGTGGTGTTGACAATTCTA 58.069 37.500 0.00 0.00 0.00 2.10
2090 7117 6.539173 TGGTAAGTGGTGTTGACAATTCTAT 58.461 36.000 0.00 0.00 0.00 1.98
2091 7118 7.001674 TGGTAAGTGGTGTTGACAATTCTATT 58.998 34.615 0.00 0.00 0.00 1.73
2092 7119 7.504238 TGGTAAGTGGTGTTGACAATTCTATTT 59.496 33.333 0.00 0.00 0.00 1.40
2093 7120 8.357402 GGTAAGTGGTGTTGACAATTCTATTTT 58.643 33.333 0.00 0.00 0.00 1.82
2094 7121 9.744468 GTAAGTGGTGTTGACAATTCTATTTTT 57.256 29.630 0.00 0.00 0.00 1.94
2112 7139 4.789095 TTTTTAACACAGACGCAGACTC 57.211 40.909 0.00 0.00 0.00 3.36
2113 7140 2.433868 TTAACACAGACGCAGACTCC 57.566 50.000 0.00 0.00 0.00 3.85
2114 7141 1.324383 TAACACAGACGCAGACTCCA 58.676 50.000 0.00 0.00 0.00 3.86
2115 7142 0.249489 AACACAGACGCAGACTCCAC 60.249 55.000 0.00 0.00 0.00 4.02
2116 7143 1.730902 CACAGACGCAGACTCCACG 60.731 63.158 0.00 0.00 0.00 4.94
2117 7144 2.194212 ACAGACGCAGACTCCACGT 61.194 57.895 0.00 0.00 43.83 4.49
2118 7145 1.007271 CAGACGCAGACTCCACGTT 60.007 57.895 0.00 0.00 40.69 3.99
2119 7146 0.597637 CAGACGCAGACTCCACGTTT 60.598 55.000 0.00 0.00 40.69 3.60
2120 7147 0.597637 AGACGCAGACTCCACGTTTG 60.598 55.000 0.00 0.00 40.69 2.93
2121 7148 2.159272 GACGCAGACTCCACGTTTGC 62.159 60.000 0.00 0.00 46.92 3.68
2122 7149 4.049393 GCAGACTCCACGTTTGCT 57.951 55.556 0.00 0.00 46.88 3.91
2123 7150 1.862806 GCAGACTCCACGTTTGCTC 59.137 57.895 0.00 0.00 46.88 4.26
2124 7151 1.569479 GCAGACTCCACGTTTGCTCC 61.569 60.000 0.00 0.00 46.88 4.70
2125 7152 0.951040 CAGACTCCACGTTTGCTCCC 60.951 60.000 0.00 0.00 0.00 4.30
2126 7153 1.070786 GACTCCACGTTTGCTCCCA 59.929 57.895 0.00 0.00 0.00 4.37
2127 7154 1.227853 ACTCCACGTTTGCTCCCAC 60.228 57.895 0.00 0.00 0.00 4.61
2128 7155 1.071471 CTCCACGTTTGCTCCCACT 59.929 57.895 0.00 0.00 0.00 4.00
2129 7156 0.951040 CTCCACGTTTGCTCCCACTC 60.951 60.000 0.00 0.00 0.00 3.51
2130 7157 1.227823 CCACGTTTGCTCCCACTCA 60.228 57.895 0.00 0.00 0.00 3.41
2131 7158 1.230635 CCACGTTTGCTCCCACTCAG 61.231 60.000 0.00 0.00 0.00 3.35
2132 7159 1.598130 ACGTTTGCTCCCACTCAGC 60.598 57.895 0.00 0.00 37.40 4.26
2133 7160 1.302033 CGTTTGCTCCCACTCAGCT 60.302 57.895 0.00 0.00 37.79 4.24
2134 7161 0.886490 CGTTTGCTCCCACTCAGCTT 60.886 55.000 0.00 0.00 37.79 3.74
2135 7162 1.608025 CGTTTGCTCCCACTCAGCTTA 60.608 52.381 0.00 0.00 37.79 3.09
2136 7163 1.807142 GTTTGCTCCCACTCAGCTTAC 59.193 52.381 0.00 0.00 37.79 2.34
2137 7164 1.055849 TTGCTCCCACTCAGCTTACA 58.944 50.000 0.00 0.00 37.79 2.41
2138 7165 1.279496 TGCTCCCACTCAGCTTACAT 58.721 50.000 0.00 0.00 37.79 2.29
2139 7166 2.466846 TGCTCCCACTCAGCTTACATA 58.533 47.619 0.00 0.00 37.79 2.29
2140 7167 2.837591 TGCTCCCACTCAGCTTACATAA 59.162 45.455 0.00 0.00 37.79 1.90
2141 7168 3.455910 TGCTCCCACTCAGCTTACATAAT 59.544 43.478 0.00 0.00 37.79 1.28
2142 7169 4.061596 GCTCCCACTCAGCTTACATAATC 58.938 47.826 0.00 0.00 33.75 1.75
2143 7170 4.636249 CTCCCACTCAGCTTACATAATCC 58.364 47.826 0.00 0.00 0.00 3.01
2144 7171 3.391296 TCCCACTCAGCTTACATAATCCC 59.609 47.826 0.00 0.00 0.00 3.85
2145 7172 3.392616 CCCACTCAGCTTACATAATCCCT 59.607 47.826 0.00 0.00 0.00 4.20
2146 7173 4.384056 CCACTCAGCTTACATAATCCCTG 58.616 47.826 0.00 0.00 0.00 4.45
2147 7174 4.101585 CCACTCAGCTTACATAATCCCTGA 59.898 45.833 0.00 0.00 0.00 3.86
2148 7175 5.396772 CCACTCAGCTTACATAATCCCTGAA 60.397 44.000 0.00 0.00 0.00 3.02
2149 7176 6.115446 CACTCAGCTTACATAATCCCTGAAA 58.885 40.000 0.00 0.00 0.00 2.69
2150 7177 6.769822 CACTCAGCTTACATAATCCCTGAAAT 59.230 38.462 0.00 0.00 0.00 2.17
2151 7178 7.933577 CACTCAGCTTACATAATCCCTGAAATA 59.066 37.037 0.00 0.00 0.00 1.40
2152 7179 8.494433 ACTCAGCTTACATAATCCCTGAAATAA 58.506 33.333 0.00 0.00 0.00 1.40
2153 7180 9.342308 CTCAGCTTACATAATCCCTGAAATAAA 57.658 33.333 0.00 0.00 0.00 1.40
2154 7181 9.866655 TCAGCTTACATAATCCCTGAAATAAAT 57.133 29.630 0.00 0.00 0.00 1.40
2167 7194 8.726988 TCCCTGAAATAAATAGAGAAAAACACG 58.273 33.333 0.00 0.00 0.00 4.49
2168 7195 8.726988 CCCTGAAATAAATAGAGAAAAACACGA 58.273 33.333 0.00 0.00 0.00 4.35
2169 7196 9.760660 CCTGAAATAAATAGAGAAAAACACGAG 57.239 33.333 0.00 0.00 0.00 4.18
2170 7197 9.267096 CTGAAATAAATAGAGAAAAACACGAGC 57.733 33.333 0.00 0.00 0.00 5.03
2171 7198 8.779303 TGAAATAAATAGAGAAAAACACGAGCA 58.221 29.630 0.00 0.00 0.00 4.26
2172 7199 8.950403 AAATAAATAGAGAAAAACACGAGCAC 57.050 30.769 0.00 0.00 0.00 4.40
2173 7200 5.358298 AAATAGAGAAAAACACGAGCACC 57.642 39.130 0.00 0.00 0.00 5.01
2174 7201 2.325583 AGAGAAAAACACGAGCACCA 57.674 45.000 0.00 0.00 0.00 4.17
2175 7202 2.639065 AGAGAAAAACACGAGCACCAA 58.361 42.857 0.00 0.00 0.00 3.67
2176 7203 3.214328 AGAGAAAAACACGAGCACCAAT 58.786 40.909 0.00 0.00 0.00 3.16
2177 7204 3.003689 AGAGAAAAACACGAGCACCAATG 59.996 43.478 0.00 0.00 0.00 2.82
2190 7217 3.774066 GCACCAATGCCAAATCTAGAAC 58.226 45.455 0.00 0.00 46.97 3.01
2191 7218 3.445096 GCACCAATGCCAAATCTAGAACT 59.555 43.478 0.00 0.00 46.97 3.01
2192 7219 4.082026 GCACCAATGCCAAATCTAGAACTT 60.082 41.667 0.00 0.00 46.97 2.66
2193 7220 5.404946 CACCAATGCCAAATCTAGAACTTG 58.595 41.667 0.00 3.76 0.00 3.16
2194 7221 5.183713 CACCAATGCCAAATCTAGAACTTGA 59.816 40.000 15.95 2.11 0.00 3.02
2195 7222 5.774690 ACCAATGCCAAATCTAGAACTTGAA 59.225 36.000 15.95 7.31 0.00 2.69
2196 7223 6.095377 CCAATGCCAAATCTAGAACTTGAAC 58.905 40.000 15.95 10.01 0.00 3.18
2197 7224 5.904362 ATGCCAAATCTAGAACTTGAACC 57.096 39.130 15.95 7.44 0.00 3.62
2198 7225 4.079253 TGCCAAATCTAGAACTTGAACCC 58.921 43.478 15.95 5.70 0.00 4.11
2199 7226 4.202567 TGCCAAATCTAGAACTTGAACCCT 60.203 41.667 15.95 0.00 0.00 4.34
2200 7227 4.156739 GCCAAATCTAGAACTTGAACCCTG 59.843 45.833 15.95 3.63 0.00 4.45
2201 7228 4.702131 CCAAATCTAGAACTTGAACCCTGG 59.298 45.833 15.95 0.37 0.00 4.45
2202 7229 5.316987 CAAATCTAGAACTTGAACCCTGGT 58.683 41.667 10.91 0.00 0.00 4.00
2203 7230 4.559862 ATCTAGAACTTGAACCCTGGTG 57.440 45.455 0.00 0.00 0.00 4.17
2204 7231 2.637872 TCTAGAACTTGAACCCTGGTGG 59.362 50.000 0.00 0.00 41.37 4.61
2215 7242 3.644861 CCTGGTGGGTTGGTTCTAC 57.355 57.895 0.00 0.00 0.00 2.59
2216 7243 0.037734 CCTGGTGGGTTGGTTCTACC 59.962 60.000 0.00 0.00 39.22 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 43 0.454452 GCGGCTTTAGTTTTGAGCGG 60.454 55.000 0.00 0.00 39.05 5.52
81 84 4.010349 CCTGATCTCCGGCTTTAGTTTTT 58.990 43.478 0.00 0.00 0.00 1.94
82 85 3.263425 TCCTGATCTCCGGCTTTAGTTTT 59.737 43.478 0.00 0.00 0.00 2.43
83 86 2.838202 TCCTGATCTCCGGCTTTAGTTT 59.162 45.455 0.00 0.00 0.00 2.66
84 87 2.432510 CTCCTGATCTCCGGCTTTAGTT 59.567 50.000 0.00 0.00 0.00 2.24
85 88 2.035632 CTCCTGATCTCCGGCTTTAGT 58.964 52.381 0.00 0.00 0.00 2.24
86 89 1.342819 CCTCCTGATCTCCGGCTTTAG 59.657 57.143 0.00 0.00 0.00 1.85
95 98 2.503382 GGTCCGGCCTCCTGATCTC 61.503 68.421 0.00 0.00 0.00 2.75
97 100 3.917760 CGGTCCGGCCTCCTGATC 61.918 72.222 2.34 0.00 34.25 2.92
98 101 3.976490 TTCGGTCCGGCCTCCTGAT 62.976 63.158 12.29 0.00 34.25 2.90
99 102 3.976490 ATTCGGTCCGGCCTCCTGA 62.976 63.158 12.29 0.00 34.25 3.86
101 104 3.155167 GATTCGGTCCGGCCTCCT 61.155 66.667 12.29 0.00 34.25 3.69
147 176 1.306568 GCTGGTCTCCCTTCCTCCT 60.307 63.158 0.00 0.00 0.00 3.69
183 212 1.870580 CGCCGTGTTACCTGAGTGAAA 60.871 52.381 0.00 0.00 0.00 2.69
229 287 0.401356 TGAATCTGCTGAGGCCAACA 59.599 50.000 5.01 3.66 37.74 3.33
239 297 8.884323 TGATATTTAACCCTAGATGAATCTGCT 58.116 33.333 2.99 0.00 37.76 4.24
261 555 4.830600 TCATGGCGAGGTACATAAGTGATA 59.169 41.667 0.00 0.00 0.00 2.15
274 568 2.497138 TGCATCTTTATCATGGCGAGG 58.503 47.619 0.00 0.00 0.00 4.63
292 586 4.809426 ACTACAGCTAATTCACGGTTATGC 59.191 41.667 0.00 0.00 0.00 3.14
358 653 3.461773 CCGACCCGAGCCACTGAT 61.462 66.667 0.00 0.00 0.00 2.90
374 669 3.500680 TCTCACATTTAGTTTCGCCAACC 59.499 43.478 0.00 0.00 35.77 3.77
447 743 9.520204 CAGGAAACATTACCATCAATCATAAAC 57.480 33.333 0.00 0.00 0.00 2.01
466 762 4.379918 GCTTGTAAGCCATCTTCAGGAAAC 60.380 45.833 5.30 0.00 46.20 2.78
481 777 1.661178 CGTTGCTGCTGTGCTTGTAAG 60.661 52.381 0.00 0.00 0.00 2.34
542 839 9.732130 GGCTTTCTAGACAGATATCCATAATTT 57.268 33.333 10.15 0.00 0.00 1.82
550 847 6.902771 TGGTAGGCTTTCTAGACAGATATC 57.097 41.667 10.15 3.10 0.00 1.63
597 1111 9.872757 AGATTTTAACATTTACACACTTACACG 57.127 29.630 0.00 0.00 0.00 4.49
631 1145 9.186837 AGGAAGATGTTAAAGATTAGACGAGTA 57.813 33.333 0.00 0.00 0.00 2.59
744 1314 5.049129 GCCATTTCATCTGCTTATCCACTAC 60.049 44.000 0.00 0.00 0.00 2.73
809 4856 2.735134 GCAAACGATCGGGGATACATAC 59.265 50.000 20.98 0.00 39.74 2.39
852 4931 4.445452 AACCAACATGCATCTGCTTTAG 57.555 40.909 0.00 0.00 42.66 1.85
995 5119 4.503910 CCAACCTTGAGTTATCATCACGA 58.496 43.478 0.00 0.00 36.18 4.35
1055 5191 3.737663 CGCCTTCTTCTCATCTCCTCTTG 60.738 52.174 0.00 0.00 0.00 3.02
1059 5195 1.118838 CCGCCTTCTTCTCATCTCCT 58.881 55.000 0.00 0.00 0.00 3.69
1089 5225 4.662961 CGCAGTGCCTCCACGTCA 62.663 66.667 10.11 0.00 46.62 4.35
1195 5331 2.203294 ACGTTGGTTGGAGGTGGC 60.203 61.111 0.00 0.00 0.00 5.01
1204 5340 0.672401 CATACGCTGGGACGTTGGTT 60.672 55.000 0.00 0.00 45.75 3.67
1413 5554 0.313043 AAGCAGCAACAGTGTCATGC 59.687 50.000 11.28 11.28 40.34 4.06
1427 5568 1.734465 GCTAACACTACCAGCAAGCAG 59.266 52.381 0.00 0.00 35.35 4.24
1428 5569 1.347707 AGCTAACACTACCAGCAAGCA 59.652 47.619 0.00 0.00 37.78 3.91
1429 5570 2.100605 AGCTAACACTACCAGCAAGC 57.899 50.000 0.00 0.00 37.78 4.01
1437 5587 5.012328 AGTGATGGCTAAGCTAACACTAC 57.988 43.478 10.06 0.00 46.92 2.73
1447 5597 2.503356 AGACCTTGGAGTGATGGCTAAG 59.497 50.000 0.00 0.00 0.00 2.18
1452 5602 4.026744 TCTAGAAGACCTTGGAGTGATGG 58.973 47.826 0.00 0.00 0.00 3.51
1581 5732 8.983724 CGATTCAGAGAAAGTCTTTAGAAGTTT 58.016 33.333 0.00 0.00 30.64 2.66
1592 5744 3.665190 ACCAACCGATTCAGAGAAAGTC 58.335 45.455 0.00 0.00 0.00 3.01
1605 5757 5.760484 ACCCTTAAAACTATACCAACCGA 57.240 39.130 0.00 0.00 0.00 4.69
1627 5779 6.658816 ACAGCACCATGTTTCAGTCATAATTA 59.341 34.615 0.00 0.00 0.00 1.40
1633 5787 2.346766 ACAGCACCATGTTTCAGTCA 57.653 45.000 0.00 0.00 0.00 3.41
1651 5805 3.512033 TTGTACCTGCACCAACAAAAC 57.488 42.857 1.55 0.00 0.00 2.43
1678 5832 2.262423 AGAACTCCAGTGTTTCAGGC 57.738 50.000 0.00 0.00 0.00 4.85
1692 5846 0.261696 AAACCACCCCAGCAAGAACT 59.738 50.000 0.00 0.00 0.00 3.01
1696 5850 1.698506 TGTAAAACCACCCCAGCAAG 58.301 50.000 0.00 0.00 0.00 4.01
1737 5891 0.321475 TGCAGTCGCACCATTCATCA 60.321 50.000 0.00 0.00 45.36 3.07
1756 5910 5.734720 ACTATCTTTCACATGACCATTCGT 58.265 37.500 0.00 0.00 0.00 3.85
1807 5961 7.542130 ACAGCAGTGACAAAGAAAGTTAAAAAG 59.458 33.333 0.00 0.00 0.00 2.27
1844 5998 4.798924 GCAATGCTTATTTCCACACCAACA 60.799 41.667 0.00 0.00 0.00 3.33
1846 6000 3.306641 GGCAATGCTTATTTCCACACCAA 60.307 43.478 4.82 0.00 0.00 3.67
1847 6001 2.233431 GGCAATGCTTATTTCCACACCA 59.767 45.455 4.82 0.00 0.00 4.17
1848 6002 2.233431 TGGCAATGCTTATTTCCACACC 59.767 45.455 4.82 0.00 0.00 4.16
1849 6003 3.591196 TGGCAATGCTTATTTCCACAC 57.409 42.857 4.82 0.00 0.00 3.82
1850 6004 4.613925 TTTGGCAATGCTTATTTCCACA 57.386 36.364 4.82 0.00 0.00 4.17
1851 6005 4.996758 AGTTTTGGCAATGCTTATTTCCAC 59.003 37.500 4.82 0.00 0.00 4.02
1853 6007 5.349543 CAGAGTTTTGGCAATGCTTATTTCC 59.650 40.000 4.82 0.00 0.00 3.13
1854 6008 6.158598 TCAGAGTTTTGGCAATGCTTATTTC 58.841 36.000 4.82 0.00 0.00 2.17
1855 6009 6.100404 TCAGAGTTTTGGCAATGCTTATTT 57.900 33.333 4.82 0.00 0.00 1.40
1857 6011 5.726980 TTCAGAGTTTTGGCAATGCTTAT 57.273 34.783 4.82 0.00 0.00 1.73
1859 6013 4.122046 GTTTCAGAGTTTTGGCAATGCTT 58.878 39.130 4.82 0.00 0.00 3.91
1860 6014 3.385755 AGTTTCAGAGTTTTGGCAATGCT 59.614 39.130 4.82 1.89 0.00 3.79
1862 6016 3.976942 CGAGTTTCAGAGTTTTGGCAATG 59.023 43.478 0.00 0.00 0.00 2.82
1863 6017 3.882888 TCGAGTTTCAGAGTTTTGGCAAT 59.117 39.130 0.00 0.00 0.00 3.56
1864 6018 3.275143 TCGAGTTTCAGAGTTTTGGCAA 58.725 40.909 0.00 0.00 0.00 4.52
1865 6019 2.912771 TCGAGTTTCAGAGTTTTGGCA 58.087 42.857 0.00 0.00 0.00 4.92
1866 6020 3.251004 ACATCGAGTTTCAGAGTTTTGGC 59.749 43.478 0.00 0.00 0.00 4.52
1868 6022 5.657470 TGACATCGAGTTTCAGAGTTTTG 57.343 39.130 0.00 0.00 0.00 2.44
1870 6024 5.116180 TGTTGACATCGAGTTTCAGAGTTT 58.884 37.500 0.00 0.00 0.00 2.66
1871 6025 4.693283 TGTTGACATCGAGTTTCAGAGTT 58.307 39.130 0.00 0.00 0.00 3.01
1872 6026 4.322080 TGTTGACATCGAGTTTCAGAGT 57.678 40.909 0.00 0.00 0.00 3.24
1874 6028 4.864806 GCTATGTTGACATCGAGTTTCAGA 59.135 41.667 0.00 0.00 37.76 3.27
1875 6029 4.259570 CGCTATGTTGACATCGAGTTTCAG 60.260 45.833 0.00 0.00 37.76 3.02
1876 6030 3.612423 CGCTATGTTGACATCGAGTTTCA 59.388 43.478 0.00 0.00 37.76 2.69
1877 6031 3.857665 TCGCTATGTTGACATCGAGTTTC 59.142 43.478 0.00 0.00 37.76 2.78
1878 6032 3.845178 TCGCTATGTTGACATCGAGTTT 58.155 40.909 0.00 0.00 37.76 2.66
1879 6033 3.503827 TCGCTATGTTGACATCGAGTT 57.496 42.857 0.00 0.00 37.76 3.01
1880 6034 3.503827 TTCGCTATGTTGACATCGAGT 57.496 42.857 0.00 0.00 35.19 4.18
1881 6035 4.089208 GCTATTCGCTATGTTGACATCGAG 59.911 45.833 0.00 0.00 35.19 4.04
1882 6036 3.981416 GCTATTCGCTATGTTGACATCGA 59.019 43.478 0.00 2.19 37.76 3.59
1896 6050 3.644884 TCTGGTAGCTAAGCTATTCGC 57.355 47.619 0.00 0.00 43.30 4.70
1897 6051 5.631512 GTGATTCTGGTAGCTAAGCTATTCG 59.368 44.000 0.00 0.00 43.30 3.34
1898 6052 5.929415 GGTGATTCTGGTAGCTAAGCTATTC 59.071 44.000 0.00 0.00 43.30 1.75
1899 6053 5.366768 TGGTGATTCTGGTAGCTAAGCTATT 59.633 40.000 0.00 0.00 43.30 1.73
1900 6054 4.901849 TGGTGATTCTGGTAGCTAAGCTAT 59.098 41.667 0.00 0.00 43.30 2.97
1901 6055 4.286707 TGGTGATTCTGGTAGCTAAGCTA 58.713 43.478 0.00 0.00 40.44 3.32
1902 6056 3.107601 TGGTGATTCTGGTAGCTAAGCT 58.892 45.455 0.00 0.00 43.41 3.74
1903 6057 3.543680 TGGTGATTCTGGTAGCTAAGC 57.456 47.619 0.00 0.00 0.00 3.09
1904 6058 6.825721 AGAAAATGGTGATTCTGGTAGCTAAG 59.174 38.462 0.00 0.00 34.70 2.18
1905 6059 6.721318 AGAAAATGGTGATTCTGGTAGCTAA 58.279 36.000 0.00 0.00 34.70 3.09
1906 6060 6.313519 AGAAAATGGTGATTCTGGTAGCTA 57.686 37.500 0.00 0.00 34.70 3.32
1908 6062 5.415701 TGAAGAAAATGGTGATTCTGGTAGC 59.584 40.000 0.00 0.00 36.09 3.58
1910 6064 6.430925 CACTGAAGAAAATGGTGATTCTGGTA 59.569 38.462 0.00 0.00 36.09 3.25
1911 6065 5.242393 CACTGAAGAAAATGGTGATTCTGGT 59.758 40.000 0.00 0.00 36.09 4.00
1912 6066 5.474532 TCACTGAAGAAAATGGTGATTCTGG 59.525 40.000 0.00 0.00 36.09 3.86
1915 6069 6.205464 TGACTCACTGAAGAAAATGGTGATTC 59.795 38.462 0.00 0.00 37.22 2.52
1929 6954 4.442706 GTTCCAAGAAGTGACTCACTGAA 58.557 43.478 12.59 8.34 44.62 3.02
1956 6981 0.602638 TTGTGAAGTAGCCCAGCACG 60.603 55.000 0.00 0.00 32.39 5.34
1962 6987 3.421844 ACTCCAAATTGTGAAGTAGCCC 58.578 45.455 0.00 0.00 0.00 5.19
1993 7020 3.577805 AACACCAGACAAAACTAGGCT 57.422 42.857 0.00 0.00 0.00 4.58
2003 7030 5.948758 TGCATATTATCCAAAACACCAGACA 59.051 36.000 0.00 0.00 0.00 3.41
2042 7069 5.660460 AGGAAAAACAAAGCACCTAACAAG 58.340 37.500 0.00 0.00 0.00 3.16
2047 7074 4.027437 ACCAAGGAAAAACAAAGCACCTA 58.973 39.130 0.00 0.00 0.00 3.08
2054 7081 5.246429 ACACCACTTACCAAGGAAAAACAAA 59.754 36.000 0.00 0.00 0.00 2.83
2055 7082 4.773149 ACACCACTTACCAAGGAAAAACAA 59.227 37.500 0.00 0.00 0.00 2.83
2056 7083 4.345854 ACACCACTTACCAAGGAAAAACA 58.654 39.130 0.00 0.00 0.00 2.83
2057 7084 4.994907 ACACCACTTACCAAGGAAAAAC 57.005 40.909 0.00 0.00 0.00 2.43
2058 7085 5.017490 TCAACACCACTTACCAAGGAAAAA 58.983 37.500 0.00 0.00 0.00 1.94
2059 7086 4.399934 GTCAACACCACTTACCAAGGAAAA 59.600 41.667 0.00 0.00 0.00 2.29
2060 7087 3.949113 GTCAACACCACTTACCAAGGAAA 59.051 43.478 0.00 0.00 0.00 3.13
2061 7088 3.054287 TGTCAACACCACTTACCAAGGAA 60.054 43.478 0.00 0.00 0.00 3.36
2062 7089 2.506231 TGTCAACACCACTTACCAAGGA 59.494 45.455 0.00 0.00 0.00 3.36
2063 7090 2.925724 TGTCAACACCACTTACCAAGG 58.074 47.619 0.00 0.00 0.00 3.61
2064 7091 5.299279 AGAATTGTCAACACCACTTACCAAG 59.701 40.000 0.00 0.00 0.00 3.61
2065 7092 5.197451 AGAATTGTCAACACCACTTACCAA 58.803 37.500 0.00 0.00 0.00 3.67
2066 7093 4.787551 AGAATTGTCAACACCACTTACCA 58.212 39.130 0.00 0.00 0.00 3.25
2067 7094 7.448748 AATAGAATTGTCAACACCACTTACC 57.551 36.000 0.00 0.00 0.00 2.85
2068 7095 9.744468 AAAAATAGAATTGTCAACACCACTTAC 57.256 29.630 0.00 0.00 0.00 2.34
2091 7118 3.558418 GGAGTCTGCGTCTGTGTTAAAAA 59.442 43.478 0.00 0.00 0.00 1.94
2092 7119 3.128349 GGAGTCTGCGTCTGTGTTAAAA 58.872 45.455 0.00 0.00 0.00 1.52
2093 7120 2.101750 TGGAGTCTGCGTCTGTGTTAAA 59.898 45.455 0.00 0.00 0.00 1.52
2094 7121 1.684450 TGGAGTCTGCGTCTGTGTTAA 59.316 47.619 0.00 0.00 0.00 2.01
2095 7122 1.000607 GTGGAGTCTGCGTCTGTGTTA 60.001 52.381 0.00 0.00 0.00 2.41
2096 7123 0.249489 GTGGAGTCTGCGTCTGTGTT 60.249 55.000 0.00 0.00 0.00 3.32
2097 7124 1.364171 GTGGAGTCTGCGTCTGTGT 59.636 57.895 0.00 0.00 0.00 3.72
2098 7125 1.730902 CGTGGAGTCTGCGTCTGTG 60.731 63.158 0.00 0.00 0.00 3.66
2099 7126 1.735376 AACGTGGAGTCTGCGTCTGT 61.735 55.000 11.57 0.00 37.92 3.41
2100 7127 0.597637 AAACGTGGAGTCTGCGTCTG 60.598 55.000 11.57 0.00 37.92 3.51
2101 7128 0.597637 CAAACGTGGAGTCTGCGTCT 60.598 55.000 11.57 0.00 37.92 4.18
2102 7129 1.853319 CAAACGTGGAGTCTGCGTC 59.147 57.895 11.57 0.00 37.92 5.19
2103 7130 2.244651 GCAAACGTGGAGTCTGCGT 61.245 57.895 6.69 6.69 37.04 5.24
2104 7131 2.551270 GCAAACGTGGAGTCTGCG 59.449 61.111 0.00 5.58 37.04 5.18
2105 7132 1.569479 GGAGCAAACGTGGAGTCTGC 61.569 60.000 0.00 0.00 46.76 4.26
2106 7133 0.951040 GGGAGCAAACGTGGAGTCTG 60.951 60.000 0.00 0.00 0.00 3.51
2107 7134 1.371558 GGGAGCAAACGTGGAGTCT 59.628 57.895 0.00 0.00 0.00 3.24
2108 7135 1.070786 TGGGAGCAAACGTGGAGTC 59.929 57.895 0.00 0.00 0.00 3.36
2109 7136 1.227853 GTGGGAGCAAACGTGGAGT 60.228 57.895 0.00 0.00 0.00 3.85
2110 7137 0.951040 GAGTGGGAGCAAACGTGGAG 60.951 60.000 0.00 0.00 0.00 3.86
2111 7138 1.070786 GAGTGGGAGCAAACGTGGA 59.929 57.895 0.00 0.00 0.00 4.02
2112 7139 1.227823 TGAGTGGGAGCAAACGTGG 60.228 57.895 0.00 0.00 0.00 4.94
2113 7140 1.845809 GCTGAGTGGGAGCAAACGTG 61.846 60.000 0.00 0.00 36.40 4.49
2114 7141 1.598130 GCTGAGTGGGAGCAAACGT 60.598 57.895 0.00 0.00 36.40 3.99
2115 7142 0.886490 AAGCTGAGTGGGAGCAAACG 60.886 55.000 0.00 0.00 39.05 3.60
2116 7143 1.807142 GTAAGCTGAGTGGGAGCAAAC 59.193 52.381 0.00 0.00 39.05 2.93
2117 7144 1.419762 TGTAAGCTGAGTGGGAGCAAA 59.580 47.619 0.00 0.00 39.05 3.68
2118 7145 1.055849 TGTAAGCTGAGTGGGAGCAA 58.944 50.000 0.00 0.00 39.05 3.91
2119 7146 1.279496 ATGTAAGCTGAGTGGGAGCA 58.721 50.000 0.00 0.00 39.05 4.26
2120 7147 3.543680 TTATGTAAGCTGAGTGGGAGC 57.456 47.619 0.00 0.00 36.65 4.70
2121 7148 4.503991 GGGATTATGTAAGCTGAGTGGGAG 60.504 50.000 0.00 0.00 0.00 4.30
2122 7149 3.391296 GGGATTATGTAAGCTGAGTGGGA 59.609 47.826 0.00 0.00 0.00 4.37
2123 7150 3.392616 AGGGATTATGTAAGCTGAGTGGG 59.607 47.826 0.00 0.00 0.00 4.61
2124 7151 4.101585 TCAGGGATTATGTAAGCTGAGTGG 59.898 45.833 0.00 0.00 0.00 4.00
2125 7152 5.282055 TCAGGGATTATGTAAGCTGAGTG 57.718 43.478 0.00 0.00 0.00 3.51
2126 7153 5.957771 TTCAGGGATTATGTAAGCTGAGT 57.042 39.130 0.00 0.00 0.00 3.41
2127 7154 8.908786 TTATTTCAGGGATTATGTAAGCTGAG 57.091 34.615 0.00 0.00 0.00 3.35
2128 7155 9.866655 ATTTATTTCAGGGATTATGTAAGCTGA 57.133 29.630 0.00 0.00 0.00 4.26
2141 7168 8.726988 CGTGTTTTTCTCTATTTATTTCAGGGA 58.273 33.333 0.00 0.00 0.00 4.20
2142 7169 8.726988 TCGTGTTTTTCTCTATTTATTTCAGGG 58.273 33.333 0.00 0.00 0.00 4.45
2143 7170 9.760660 CTCGTGTTTTTCTCTATTTATTTCAGG 57.239 33.333 0.00 0.00 0.00 3.86
2144 7171 9.267096 GCTCGTGTTTTTCTCTATTTATTTCAG 57.733 33.333 0.00 0.00 0.00 3.02
2145 7172 8.779303 TGCTCGTGTTTTTCTCTATTTATTTCA 58.221 29.630 0.00 0.00 0.00 2.69
2146 7173 9.052080 GTGCTCGTGTTTTTCTCTATTTATTTC 57.948 33.333 0.00 0.00 0.00 2.17
2147 7174 8.021396 GGTGCTCGTGTTTTTCTCTATTTATTT 58.979 33.333 0.00 0.00 0.00 1.40
2148 7175 7.174253 TGGTGCTCGTGTTTTTCTCTATTTATT 59.826 33.333 0.00 0.00 0.00 1.40
2149 7176 6.653320 TGGTGCTCGTGTTTTTCTCTATTTAT 59.347 34.615 0.00 0.00 0.00 1.40
2150 7177 5.992829 TGGTGCTCGTGTTTTTCTCTATTTA 59.007 36.000 0.00 0.00 0.00 1.40
2151 7178 4.819630 TGGTGCTCGTGTTTTTCTCTATTT 59.180 37.500 0.00 0.00 0.00 1.40
2152 7179 4.385825 TGGTGCTCGTGTTTTTCTCTATT 58.614 39.130 0.00 0.00 0.00 1.73
2153 7180 4.002906 TGGTGCTCGTGTTTTTCTCTAT 57.997 40.909 0.00 0.00 0.00 1.98
2154 7181 3.462483 TGGTGCTCGTGTTTTTCTCTA 57.538 42.857 0.00 0.00 0.00 2.43
2155 7182 2.325583 TGGTGCTCGTGTTTTTCTCT 57.674 45.000 0.00 0.00 0.00 3.10
2156 7183 3.300009 CATTGGTGCTCGTGTTTTTCTC 58.700 45.455 0.00 0.00 0.00 2.87
2157 7184 3.354089 CATTGGTGCTCGTGTTTTTCT 57.646 42.857 0.00 0.00 0.00 2.52
2170 7197 5.183713 TCAAGTTCTAGATTTGGCATTGGTG 59.816 40.000 14.19 0.00 0.00 4.17
2171 7198 5.324409 TCAAGTTCTAGATTTGGCATTGGT 58.676 37.500 14.19 0.00 0.00 3.67
2172 7199 5.902613 TCAAGTTCTAGATTTGGCATTGG 57.097 39.130 14.19 0.00 0.00 3.16
2173 7200 6.095377 GGTTCAAGTTCTAGATTTGGCATTG 58.905 40.000 14.19 4.57 0.00 2.82
2174 7201 5.185828 GGGTTCAAGTTCTAGATTTGGCATT 59.814 40.000 14.19 0.00 0.00 3.56
2175 7202 4.706962 GGGTTCAAGTTCTAGATTTGGCAT 59.293 41.667 14.19 0.00 0.00 4.40
2176 7203 4.079253 GGGTTCAAGTTCTAGATTTGGCA 58.921 43.478 14.19 0.00 0.00 4.92
2177 7204 4.156739 CAGGGTTCAAGTTCTAGATTTGGC 59.843 45.833 14.19 9.39 0.00 4.52
2178 7205 4.702131 CCAGGGTTCAAGTTCTAGATTTGG 59.298 45.833 14.19 0.00 0.00 3.28
2179 7206 5.182001 CACCAGGGTTCAAGTTCTAGATTTG 59.818 44.000 9.95 9.95 0.00 2.32
2180 7207 5.316987 CACCAGGGTTCAAGTTCTAGATTT 58.683 41.667 0.00 0.00 0.00 2.17
2181 7208 4.263506 CCACCAGGGTTCAAGTTCTAGATT 60.264 45.833 0.00 0.00 0.00 2.40
2182 7209 3.264450 CCACCAGGGTTCAAGTTCTAGAT 59.736 47.826 0.00 0.00 0.00 1.98
2183 7210 2.637872 CCACCAGGGTTCAAGTTCTAGA 59.362 50.000 0.00 0.00 0.00 2.43
2184 7211 3.059352 CCACCAGGGTTCAAGTTCTAG 57.941 52.381 0.00 0.00 0.00 2.43
2197 7224 0.037734 GGTAGAACCAACCCACCAGG 59.962 60.000 0.00 0.00 38.42 4.45
2198 7225 3.644861 GGTAGAACCAACCCACCAG 57.355 57.895 0.00 0.00 38.42 4.00


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

AutoCloner maintained by Alex Coulton.