Multiple sequence alignment - TraesCS6B01G339500

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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 TraesCS6B01G339500 chr6B 100.000 2333 0 0 1 2333 599073842 599071510 0.000000e+00 4309
1 TraesCS6B01G339500 chr6B 81.502 919 83 40 463 1343 604597419 604598288 0.000000e+00 675
2 TraesCS6B01G339500 chr6D 89.586 1450 67 34 392 1797 400078381 400076972 0.000000e+00 1764
3 TraesCS6B01G339500 chr6D 80.804 448 35 26 1901 2333 400076937 400076526 1.050000e-78 303
4 TraesCS6B01G339500 chr6A 84.392 1826 116 69 58 1802 545831232 545829495 0.000000e+00 1637
5 TraesCS6B01G339500 chr6A 89.904 208 11 3 2126 2333 545829294 545829097 2.300000e-65 259
6 TraesCS6B01G339500 chr2D 80.215 839 72 59 847 1621 163022901 163022093 5.670000e-151 544
7 TraesCS6B01G339500 chr2B 83.048 643 46 42 767 1387 224645772 224646373 2.050000e-145 525
8 TraesCS6B01G339500 chr2A 78.170 907 92 71 767 1621 176655353 176656205 4.510000e-132 481
9 TraesCS6B01G339500 chr1D 85.784 408 27 23 995 1387 1836839 1836448 1.000000e-108 403


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 TraesCS6B01G339500 chr6B 599071510 599073842 2332 True 4309.0 4309 100.000 1 2333 1 chr6B.!!$R1 2332
1 TraesCS6B01G339500 chr6B 604597419 604598288 869 False 675.0 675 81.502 463 1343 1 chr6B.!!$F1 880
2 TraesCS6B01G339500 chr6D 400076526 400078381 1855 True 1033.5 1764 85.195 392 2333 2 chr6D.!!$R1 1941
3 TraesCS6B01G339500 chr6A 545829097 545831232 2135 True 948.0 1637 87.148 58 2333 2 chr6A.!!$R1 2275
4 TraesCS6B01G339500 chr2D 163022093 163022901 808 True 544.0 544 80.215 847 1621 1 chr2D.!!$R1 774
5 TraesCS6B01G339500 chr2B 224645772 224646373 601 False 525.0 525 83.048 767 1387 1 chr2B.!!$F1 620
6 TraesCS6B01G339500 chr2A 176655353 176656205 852 False 481.0 481 78.170 767 1621 1 chr2A.!!$F1 854

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
806 907 0.178891 TCCTAGCTCCCATCCCATCC 60.179 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2298 2552 0.041312 GTGTTATGGCGCGCCTATTG 60.041 55.0 45.79 0.0 36.94 1.9 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
22 23 4.756502 GGTAATAACAGAGACTGTCCACC 58.243 47.826 3.76 6.63 44.62 4.61
23 24 4.466726 GGTAATAACAGAGACTGTCCACCT 59.533 45.833 3.76 0.00 44.62 4.00
24 25 4.543590 AATAACAGAGACTGTCCACCTG 57.456 45.455 16.03 16.03 44.62 4.00
25 26 0.394565 AACAGAGACTGTCCACCTGC 59.605 55.000 16.99 0.00 44.62 4.85
26 27 0.470833 ACAGAGACTGTCCACCTGCT 60.471 55.000 16.99 6.89 41.21 4.24
27 28 1.203063 ACAGAGACTGTCCACCTGCTA 60.203 52.381 16.99 0.00 41.21 3.49
28 29 1.203523 CAGAGACTGTCCACCTGCTAC 59.796 57.143 3.76 0.00 0.00 3.58
29 30 1.076350 AGAGACTGTCCACCTGCTACT 59.924 52.381 3.76 0.00 0.00 2.57
30 31 1.474879 GAGACTGTCCACCTGCTACTC 59.525 57.143 3.76 0.00 0.00 2.59
31 32 1.076350 AGACTGTCCACCTGCTACTCT 59.924 52.381 3.76 0.00 0.00 3.24
32 33 1.896465 GACTGTCCACCTGCTACTCTT 59.104 52.381 0.00 0.00 0.00 2.85
33 34 1.896465 ACTGTCCACCTGCTACTCTTC 59.104 52.381 0.00 0.00 0.00 2.87
34 35 0.888619 TGTCCACCTGCTACTCTTCG 59.111 55.000 0.00 0.00 0.00 3.79
35 36 1.174783 GTCCACCTGCTACTCTTCGA 58.825 55.000 0.00 0.00 0.00 3.71
36 37 1.135344 GTCCACCTGCTACTCTTCGAC 60.135 57.143 0.00 0.00 0.00 4.20
37 38 0.888619 CCACCTGCTACTCTTCGACA 59.111 55.000 0.00 0.00 0.00 4.35
38 39 1.272490 CCACCTGCTACTCTTCGACAA 59.728 52.381 0.00 0.00 0.00 3.18
39 40 2.093973 CCACCTGCTACTCTTCGACAAT 60.094 50.000 0.00 0.00 0.00 2.71
40 41 2.926200 CACCTGCTACTCTTCGACAATG 59.074 50.000 0.00 0.00 0.00 2.82
41 42 2.563179 ACCTGCTACTCTTCGACAATGT 59.437 45.455 0.00 0.00 0.00 2.71
42 43 3.006967 ACCTGCTACTCTTCGACAATGTT 59.993 43.478 0.00 0.00 0.00 2.71
43 44 3.997021 CCTGCTACTCTTCGACAATGTTT 59.003 43.478 0.00 0.00 0.00 2.83
44 45 4.452455 CCTGCTACTCTTCGACAATGTTTT 59.548 41.667 0.00 0.00 0.00 2.43
45 46 5.049405 CCTGCTACTCTTCGACAATGTTTTT 60.049 40.000 0.00 0.00 0.00 1.94
84 85 3.585990 GCCCAACCATGCGATCGG 61.586 66.667 18.30 2.04 0.00 4.18
94 95 4.208686 GCGATCGGCGGAAGACCT 62.209 66.667 18.30 0.00 41.29 3.85
97 98 2.042843 ATCGGCGGAAGACCTCCT 60.043 61.111 7.21 0.00 42.85 3.69
103 104 4.070552 GGAAGACCTCCTGCGCGT 62.071 66.667 8.43 0.00 41.61 6.01
107 108 2.493907 AAGACCTCCTGCGCGTCTTC 62.494 60.000 18.20 4.06 41.82 2.87
129 130 1.795768 TCACAAGTTCATCCACTCGC 58.204 50.000 0.00 0.00 0.00 5.03
130 131 0.798776 CACAAGTTCATCCACTCGCC 59.201 55.000 0.00 0.00 0.00 5.54
136 137 2.202919 CATCCACTCGCCGCATCA 60.203 61.111 0.00 0.00 0.00 3.07
148 149 1.080569 CGCATCACCTTTTGCACCC 60.081 57.895 0.00 0.00 38.80 4.61
154 155 0.829990 CACCTTTTGCACCCTTGGTT 59.170 50.000 0.00 0.00 31.02 3.67
157 158 1.202639 CCTTTTGCACCCTTGGTTTCC 60.203 52.381 0.00 0.00 31.02 3.13
158 159 1.762370 CTTTTGCACCCTTGGTTTCCT 59.238 47.619 0.00 0.00 31.02 3.36
159 160 2.757894 TTTGCACCCTTGGTTTCCTA 57.242 45.000 0.00 0.00 31.02 2.94
161 162 2.757894 TGCACCCTTGGTTTCCTAAA 57.242 45.000 0.00 0.00 31.02 1.85
162 163 2.312390 TGCACCCTTGGTTTCCTAAAC 58.688 47.619 0.00 0.00 40.65 2.01
163 164 1.268625 GCACCCTTGGTTTCCTAAACG 59.731 52.381 0.00 0.00 42.29 3.60
164 165 2.853705 CACCCTTGGTTTCCTAAACGA 58.146 47.619 0.00 0.00 42.29 3.85
165 166 3.215975 CACCCTTGGTTTCCTAAACGAA 58.784 45.455 0.00 1.05 42.29 3.85
166 167 3.633065 CACCCTTGGTTTCCTAAACGAAA 59.367 43.478 0.00 0.00 42.29 3.46
167 168 3.887110 ACCCTTGGTTTCCTAAACGAAAG 59.113 43.478 0.00 5.84 42.29 2.62
168 169 4.629449 ACCCTTGGTTTCCTAAACGAAAGT 60.629 41.667 0.00 6.43 42.29 2.66
169 170 5.397786 ACCCTTGGTTTCCTAAACGAAAGTA 60.398 40.000 0.00 0.00 42.29 2.24
170 171 7.188385 ACCCTTGGTTTCCTAAACGAAAGTAG 61.188 42.308 0.00 8.00 42.29 2.57
171 172 9.268491 ACCCTTGGTTTCCTAAACGAAAGTAGA 62.268 40.741 0.00 0.00 42.29 2.59
182 183 2.753452 ACGAAAGTAGAGAATCGCTCCA 59.247 45.455 0.00 0.00 46.88 3.86
184 185 2.880963 AAGTAGAGAATCGCTCCAGC 57.119 50.000 0.00 0.00 45.10 4.85
186 187 1.680735 AGTAGAGAATCGCTCCAGCAG 59.319 52.381 0.00 0.00 45.10 4.24
187 188 0.387202 TAGAGAATCGCTCCAGCAGC 59.613 55.000 0.00 0.00 45.10 5.25
188 189 1.886777 GAGAATCGCTCCAGCAGCC 60.887 63.158 0.00 0.00 46.74 4.85
189 190 2.124983 GAATCGCTCCAGCAGCCA 60.125 61.111 0.00 0.00 46.74 4.75
190 191 2.124819 AATCGCTCCAGCAGCCAG 60.125 61.111 0.00 0.00 46.74 4.85
191 192 2.866085 GAATCGCTCCAGCAGCCAGT 62.866 60.000 0.00 0.00 46.74 4.00
227 228 6.127842 ACGACAAACATGGTAAATAATCCCAC 60.128 38.462 0.00 0.00 0.00 4.61
228 229 6.127869 CGACAAACATGGTAAATAATCCCACA 60.128 38.462 0.00 0.00 0.00 4.17
230 231 6.154363 ACAAACATGGTAAATAATCCCACAGG 59.846 38.462 0.00 0.00 0.00 4.00
231 232 4.803452 ACATGGTAAATAATCCCACAGGG 58.197 43.478 0.00 0.00 46.11 4.45
243 244 1.689243 CCACAGGGATCGGATCAGCA 61.689 60.000 18.99 0.00 35.59 4.41
250 251 1.139853 GGATCGGATCAGCAGGAAGTT 59.860 52.381 18.99 0.00 0.00 2.66
257 258 4.579869 GGATCAGCAGGAAGTTTGTTCTA 58.420 43.478 0.00 0.00 0.00 2.10
263 264 5.455525 CAGCAGGAAGTTTGTTCTAAAAACG 59.544 40.000 0.00 0.00 41.41 3.60
268 269 4.205323 AGTTTGTTCTAAAAACGAGCCG 57.795 40.909 0.00 0.00 41.41 5.52
286 287 2.009774 CCGCATTTTCGAGTCTTCCAT 58.990 47.619 0.00 0.00 0.00 3.41
333 336 4.341366 AGATTTTGGCTGTCCCTTTTTG 57.659 40.909 0.00 0.00 0.00 2.44
335 338 0.467804 TTTGGCTGTCCCTTTTTGCC 59.532 50.000 0.00 0.00 43.49 4.52
336 339 1.406860 TTGGCTGTCCCTTTTTGCCC 61.407 55.000 0.00 0.00 42.62 5.36
342 345 0.321346 GTCCCTTTTTGCCCACCATG 59.679 55.000 0.00 0.00 0.00 3.66
350 353 2.307496 TTGCCCACCATGAAAGTGAT 57.693 45.000 0.00 0.00 37.42 3.06
351 354 2.307496 TGCCCACCATGAAAGTGATT 57.693 45.000 0.00 0.00 37.42 2.57
365 375 5.306937 TGAAAGTGATTACTCTCCAACCAGA 59.693 40.000 0.00 0.00 35.69 3.86
384 395 2.158755 AGACCAGTTGTTTCAGGTGGAG 60.159 50.000 0.00 0.00 33.77 3.86
483 525 2.239291 GCGCTATAAAGAGCAGGCC 58.761 57.895 0.00 0.00 46.68 5.19
488 530 1.072965 CTATAAAGAGCAGGCCAGGGG 59.927 57.143 5.01 0.00 0.00 4.79
556 599 2.294078 CGCAGGGTCCCTCTTCCTT 61.294 63.158 7.76 0.00 0.00 3.36
598 646 2.468532 CGTACGACGCAAGCAACC 59.531 61.111 10.44 0.00 45.62 3.77
599 647 2.304401 CGTACGACGCAAGCAACCA 61.304 57.895 10.44 0.00 45.62 3.67
600 648 1.823260 CGTACGACGCAAGCAACCAA 61.823 55.000 10.44 0.00 45.62 3.67
601 649 0.383860 GTACGACGCAAGCAACCAAC 60.384 55.000 0.00 0.00 45.62 3.77
664 723 3.405592 CTTTCCCGCGTCCGATCGA 62.406 63.158 18.66 0.00 36.29 3.59
802 903 1.143889 CCTTTTCCTAGCTCCCATCCC 59.856 57.143 0.00 0.00 0.00 3.85
803 904 1.846439 CTTTTCCTAGCTCCCATCCCA 59.154 52.381 0.00 0.00 0.00 4.37
804 905 2.212752 TTTCCTAGCTCCCATCCCAT 57.787 50.000 0.00 0.00 0.00 4.00
805 906 1.734655 TTCCTAGCTCCCATCCCATC 58.265 55.000 0.00 0.00 0.00 3.51
806 907 0.178891 TCCTAGCTCCCATCCCATCC 60.179 60.000 0.00 0.00 0.00 3.51
807 908 1.204113 CCTAGCTCCCATCCCATCCC 61.204 65.000 0.00 0.00 0.00 3.85
811 912 4.514594 TCCCATCCCATCCCGCCT 62.515 66.667 0.00 0.00 0.00 5.52
873 981 1.183549 CGCCTCTATATAAGCCCGGT 58.816 55.000 0.00 0.00 0.00 5.28
878 986 0.606604 CTATATAAGCCCGGTGCGGT 59.393 55.000 0.00 0.16 46.80 5.68
880 988 2.391724 ATATAAGCCCGGTGCGGTGG 62.392 60.000 0.00 0.00 46.80 4.61
918 1032 0.929824 CACAACGAAAGCAACAGCCG 60.930 55.000 0.00 0.00 0.00 5.52
936 1050 2.959071 GCGATCGAGACAGCAGCC 60.959 66.667 21.57 0.00 0.00 4.85
978 1122 0.932585 GCTAGTCGCGATCACAGCTC 60.933 60.000 14.06 0.00 0.00 4.09
981 1125 1.875813 GTCGCGATCACAGCTCAGG 60.876 63.158 14.06 0.00 0.00 3.86
1386 1547 1.066918 ACGTTACGCCCATCGATCC 59.933 57.895 4.09 0.00 41.67 3.36
1398 1586 2.093973 CCATCGATCCATGGGTAGCTAC 60.094 54.545 15.88 15.88 39.95 3.58
1399 1587 2.677542 TCGATCCATGGGTAGCTACT 57.322 50.000 22.74 1.33 0.00 2.57
1400 1588 3.801307 TCGATCCATGGGTAGCTACTA 57.199 47.619 22.74 12.97 0.00 1.82
1409 1597 1.989706 GGTAGCTACTAGCCTGCTCT 58.010 55.000 22.74 0.00 43.77 4.09
1416 1608 4.280677 AGCTACTAGCCTGCTCTAAATCAG 59.719 45.833 4.32 0.00 43.77 2.90
1448 1641 9.581099 GCTAGCTTTTGGTTGCTATAATAAAAA 57.419 29.630 7.70 0.00 43.31 1.94
1519 1741 2.283086 TGTCGACGTTTTGTGTGTGATC 59.717 45.455 11.62 0.00 0.00 2.92
1587 1812 1.134521 TCCATCGCATACCTCGCTTTT 60.135 47.619 0.00 0.00 0.00 2.27
1613 1840 6.992063 TTGTTGTTGCCAATAATGTGTTTT 57.008 29.167 0.00 0.00 32.11 2.43
1675 1904 7.813645 TGATGAAGTATTATGCATGATGAAGC 58.186 34.615 13.89 2.53 0.00 3.86
1730 1960 9.678260 AACAAGCTTGTATAGATGAAAGAAGAT 57.322 29.630 31.31 7.55 41.31 2.40
1737 1967 8.613060 TGTATAGATGAAAGAAGATCCATTGC 57.387 34.615 0.00 0.00 0.00 3.56
1759 1989 4.201822 GCTCGGTCCAATCATAGTGAAAAC 60.202 45.833 0.00 0.00 0.00 2.43
1774 2004 6.581171 AGTGAAAACCTGAATTTGATCCTC 57.419 37.500 0.00 0.00 0.00 3.71
1776 2006 5.048713 GTGAAAACCTGAATTTGATCCTCGT 60.049 40.000 0.00 0.00 0.00 4.18
1789 2019 0.529378 TCCTCGTTTAGAAGGGACGC 59.471 55.000 0.00 0.00 36.77 5.19
1791 2021 1.747355 CCTCGTTTAGAAGGGACGCTA 59.253 52.381 0.00 0.00 36.77 4.26
1799 2029 3.268023 AGAAGGGACGCTATTTTCAGG 57.732 47.619 0.00 0.00 0.00 3.86
1802 2032 1.486726 AGGGACGCTATTTTCAGGGAG 59.513 52.381 0.00 0.00 33.01 4.30
1804 2034 1.406887 GGACGCTATTTTCAGGGAGCA 60.407 52.381 0.00 0.00 34.49 4.26
1805 2035 1.936547 GACGCTATTTTCAGGGAGCAG 59.063 52.381 0.00 0.00 34.49 4.24
1806 2036 0.659957 CGCTATTTTCAGGGAGCAGC 59.340 55.000 0.00 0.00 34.49 5.25
1807 2037 1.028130 GCTATTTTCAGGGAGCAGCC 58.972 55.000 0.00 0.00 34.96 4.85
1808 2038 1.683011 GCTATTTTCAGGGAGCAGCCA 60.683 52.381 0.00 0.00 38.95 4.75
1809 2039 2.019984 CTATTTTCAGGGAGCAGCCAC 58.980 52.381 0.00 0.00 38.95 5.01
1810 2040 0.613012 ATTTTCAGGGAGCAGCCACC 60.613 55.000 0.00 0.00 38.95 4.61
1811 2041 1.719063 TTTTCAGGGAGCAGCCACCT 61.719 55.000 0.00 0.00 38.95 4.00
1812 2042 0.840288 TTTCAGGGAGCAGCCACCTA 60.840 55.000 5.21 0.00 38.95 3.08
1813 2043 0.621571 TTCAGGGAGCAGCCACCTAT 60.622 55.000 5.21 0.00 38.95 2.57
1814 2044 0.621571 TCAGGGAGCAGCCACCTATT 60.622 55.000 5.21 0.00 38.95 1.73
1816 2046 1.490490 CAGGGAGCAGCCACCTATTTA 59.510 52.381 5.21 0.00 38.95 1.40
1817 2047 1.771255 AGGGAGCAGCCACCTATTTAG 59.229 52.381 3.66 0.00 38.95 1.85
1818 2048 1.490910 GGGAGCAGCCACCTATTTAGT 59.509 52.381 6.25 0.00 38.95 2.24
1819 2049 2.704065 GGGAGCAGCCACCTATTTAGTA 59.296 50.000 6.25 0.00 38.95 1.82
1820 2050 3.244249 GGGAGCAGCCACCTATTTAGTAG 60.244 52.174 6.25 0.00 38.95 2.57
1832 2062 5.810080 CTATTTAGTAGGAAGGAGGGGTG 57.190 47.826 0.00 0.00 0.00 4.61
1833 2063 3.858696 TTTAGTAGGAAGGAGGGGTGA 57.141 47.619 0.00 0.00 0.00 4.02
1834 2064 3.399952 TTAGTAGGAAGGAGGGGTGAG 57.600 52.381 0.00 0.00 0.00 3.51
1835 2065 1.394532 AGTAGGAAGGAGGGGTGAGA 58.605 55.000 0.00 0.00 0.00 3.27
1836 2066 1.007359 AGTAGGAAGGAGGGGTGAGAC 59.993 57.143 0.00 0.00 0.00 3.36
1837 2067 1.007359 GTAGGAAGGAGGGGTGAGACT 59.993 57.143 0.00 0.00 0.00 3.24
1838 2068 0.494095 AGGAAGGAGGGGTGAGACTT 59.506 55.000 0.00 0.00 0.00 3.01
1839 2069 1.132365 AGGAAGGAGGGGTGAGACTTT 60.132 52.381 0.00 0.00 0.00 2.66
1840 2070 1.279558 GGAAGGAGGGGTGAGACTTTC 59.720 57.143 0.00 0.00 0.00 2.62
1841 2071 2.261729 GAAGGAGGGGTGAGACTTTCT 58.738 52.381 0.00 0.00 0.00 2.52
1842 2072 3.442076 GAAGGAGGGGTGAGACTTTCTA 58.558 50.000 0.00 0.00 0.00 2.10
1843 2073 3.108847 AGGAGGGGTGAGACTTTCTAG 57.891 52.381 0.00 0.00 0.00 2.43
1844 2074 2.112190 GGAGGGGTGAGACTTTCTAGG 58.888 57.143 0.00 0.00 0.00 3.02
1845 2075 2.112190 GAGGGGTGAGACTTTCTAGGG 58.888 57.143 0.00 0.00 0.00 3.53
1846 2076 1.722851 AGGGGTGAGACTTTCTAGGGA 59.277 52.381 0.00 0.00 0.00 4.20
1847 2077 1.832366 GGGGTGAGACTTTCTAGGGAC 59.168 57.143 0.00 0.00 0.00 4.46
1848 2078 2.560158 GGGGTGAGACTTTCTAGGGACT 60.560 54.545 0.00 0.00 46.37 3.85
1849 2079 3.309701 GGGGTGAGACTTTCTAGGGACTA 60.310 52.174 0.00 0.00 41.75 2.59
1865 2095 4.941873 AGGGACTAGCGACTTTTTAATTGG 59.058 41.667 0.00 0.00 36.02 3.16
1866 2096 4.095932 GGGACTAGCGACTTTTTAATTGGG 59.904 45.833 0.00 0.00 0.00 4.12
1867 2097 4.939439 GGACTAGCGACTTTTTAATTGGGA 59.061 41.667 0.00 0.00 0.00 4.37
1868 2098 5.413523 GGACTAGCGACTTTTTAATTGGGAA 59.586 40.000 0.00 0.00 0.00 3.97
1869 2099 6.095021 GGACTAGCGACTTTTTAATTGGGAAT 59.905 38.462 0.00 0.00 0.00 3.01
1870 2100 7.281549 GGACTAGCGACTTTTTAATTGGGAATA 59.718 37.037 0.00 0.00 0.00 1.75
1871 2101 8.570068 ACTAGCGACTTTTTAATTGGGAATAA 57.430 30.769 0.00 0.00 0.00 1.40
1872 2102 9.016438 ACTAGCGACTTTTTAATTGGGAATAAA 57.984 29.630 0.00 0.00 0.00 1.40
1873 2103 9.849166 CTAGCGACTTTTTAATTGGGAATAAAA 57.151 29.630 0.00 0.00 0.00 1.52
1898 2128 8.926715 AAAATTCTAAGACTTGTGAACCAAAC 57.073 30.769 0.00 0.00 31.20 2.93
1899 2129 7.639113 AATTCTAAGACTTGTGAACCAAACA 57.361 32.000 0.00 0.00 31.20 2.83
1908 2138 0.109532 TGAACCAAACATCGCCCTGA 59.890 50.000 0.00 0.00 0.00 3.86
1913 2143 2.290641 ACCAAACATCGCCCTGATAACA 60.291 45.455 0.00 0.00 34.83 2.41
1936 2166 5.010012 CAGCTTTTCTGGGAGTGTAATGTTT 59.990 40.000 0.00 0.00 39.15 2.83
1946 2176 8.096621 TGGGAGTGTAATGTTTTAGATGGATA 57.903 34.615 0.00 0.00 0.00 2.59
1947 2177 8.553153 TGGGAGTGTAATGTTTTAGATGGATAA 58.447 33.333 0.00 0.00 0.00 1.75
1948 2178 9.574516 GGGAGTGTAATGTTTTAGATGGATAAT 57.425 33.333 0.00 0.00 0.00 1.28
1963 2193 8.489676 AGATGGATAATCTAGTTGACACTCAT 57.510 34.615 0.00 0.00 44.22 2.90
2026 2256 5.421693 TGGCAAATGTAAGCTCCATGTTAAT 59.578 36.000 0.00 0.00 0.00 1.40
2027 2257 6.605194 TGGCAAATGTAAGCTCCATGTTAATA 59.395 34.615 0.00 0.00 0.00 0.98
2029 2259 8.143835 GGCAAATGTAAGCTCCATGTTAATATT 58.856 33.333 0.00 0.00 0.00 1.28
2030 2260 9.533253 GCAAATGTAAGCTCCATGTTAATATTT 57.467 29.630 0.00 0.00 0.00 1.40
2032 2262 9.950680 AAATGTAAGCTCCATGTTAATATTTCG 57.049 29.630 0.00 0.00 0.00 3.46
2033 2263 8.902540 ATGTAAGCTCCATGTTAATATTTCGA 57.097 30.769 0.00 0.00 0.00 3.71
2034 2264 8.725405 TGTAAGCTCCATGTTAATATTTCGAA 57.275 30.769 0.00 0.00 0.00 3.71
2035 2265 8.609176 TGTAAGCTCCATGTTAATATTTCGAAC 58.391 33.333 0.00 0.00 0.00 3.95
2036 2266 6.619801 AGCTCCATGTTAATATTTCGAACC 57.380 37.500 0.00 0.00 0.00 3.62
2037 2267 6.119536 AGCTCCATGTTAATATTTCGAACCA 58.880 36.000 0.00 0.00 0.00 3.67
2038 2268 6.772716 AGCTCCATGTTAATATTTCGAACCAT 59.227 34.615 0.00 0.00 0.00 3.55
2039 2269 6.857964 GCTCCATGTTAATATTTCGAACCATG 59.142 38.462 0.00 2.40 0.00 3.66
2040 2270 6.734137 TCCATGTTAATATTTCGAACCATGC 58.266 36.000 0.00 0.00 0.00 4.06
2041 2271 6.319911 TCCATGTTAATATTTCGAACCATGCA 59.680 34.615 0.00 0.00 0.00 3.96
2042 2272 6.417635 CCATGTTAATATTTCGAACCATGCAC 59.582 38.462 0.00 0.00 0.00 4.57
2043 2273 6.502136 TGTTAATATTTCGAACCATGCACA 57.498 33.333 0.00 0.00 0.00 4.57
2044 2274 6.318628 TGTTAATATTTCGAACCATGCACAC 58.681 36.000 0.00 0.00 0.00 3.82
2045 2275 3.673746 ATATTTCGAACCATGCACACG 57.326 42.857 0.00 0.00 0.00 4.49
2046 2276 0.521291 ATTTCGAACCATGCACACGG 59.479 50.000 0.00 0.00 0.00 4.94
2047 2277 0.533085 TTTCGAACCATGCACACGGA 60.533 50.000 0.00 0.00 0.00 4.69
2048 2278 0.533085 TTCGAACCATGCACACGGAA 60.533 50.000 5.68 0.00 0.00 4.30
2049 2279 0.948623 TCGAACCATGCACACGGAAG 60.949 55.000 5.68 0.00 0.00 3.46
2070 2300 5.455056 AGTACAACACAGTCCTAAGACAG 57.545 43.478 0.00 0.00 46.15 3.51
2084 2314 6.427242 GTCCTAAGACAGAAAAGGAAAACGAT 59.573 38.462 0.00 0.00 42.99 3.73
2215 2469 5.648092 AGAGCTGAATTTAACGCATAAGGTT 59.352 36.000 0.00 0.00 0.00 3.50
2226 2480 8.830201 TTAACGCATAAGGTTAACTTAGACAA 57.170 30.769 5.42 0.00 44.43 3.18
2249 2503 5.547465 AGATTGATGACCAAGTTTCACGTA 58.453 37.500 0.00 0.00 38.31 3.57
2250 2504 5.408604 AGATTGATGACCAAGTTTCACGTAC 59.591 40.000 0.00 0.00 38.31 3.67
2251 2505 4.061357 TGATGACCAAGTTTCACGTACA 57.939 40.909 0.00 0.00 0.00 2.90
2252 2506 4.055360 TGATGACCAAGTTTCACGTACAG 58.945 43.478 0.00 0.00 0.00 2.74
2253 2507 3.530265 TGACCAAGTTTCACGTACAGT 57.470 42.857 0.00 0.00 0.00 3.55
2269 2523 6.970613 CACGTACAGTAGCAATTAGTGATGTA 59.029 38.462 0.00 0.00 36.40 2.29
2294 2548 1.135489 CACAGAGCAATTCAAGCGCAT 60.135 47.619 11.47 0.00 37.01 4.73
2295 2549 1.131883 ACAGAGCAATTCAAGCGCATC 59.868 47.619 11.47 0.00 37.01 3.91
2296 2550 1.131693 CAGAGCAATTCAAGCGCATCA 59.868 47.619 11.47 0.00 37.01 3.07
2297 2551 2.022195 AGAGCAATTCAAGCGCATCAT 58.978 42.857 11.47 0.00 37.01 2.45
2298 2552 2.033049 AGAGCAATTCAAGCGCATCATC 59.967 45.455 11.47 0.00 37.01 2.92
2299 2553 1.746787 AGCAATTCAAGCGCATCATCA 59.253 42.857 11.47 0.00 37.01 3.07
2302 2556 4.037089 AGCAATTCAAGCGCATCATCAATA 59.963 37.500 11.47 0.00 37.01 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.466726 AGGTGGACAGTCTCTGTTATTACC 59.533 45.833 0.00 9.60 45.44 2.85
1 2 5.411781 CAGGTGGACAGTCTCTGTTATTAC 58.588 45.833 0.00 2.36 45.44 1.89
2 3 4.081642 GCAGGTGGACAGTCTCTGTTATTA 60.082 45.833 15.42 0.00 45.44 0.98
3 4 3.307059 GCAGGTGGACAGTCTCTGTTATT 60.307 47.826 15.42 0.00 45.44 1.40
4 5 2.234908 GCAGGTGGACAGTCTCTGTTAT 59.765 50.000 15.42 0.00 45.44 1.89
5 6 1.618837 GCAGGTGGACAGTCTCTGTTA 59.381 52.381 15.42 0.00 45.44 2.41
6 7 0.394565 GCAGGTGGACAGTCTCTGTT 59.605 55.000 15.42 0.00 45.44 3.16
8 9 1.203523 GTAGCAGGTGGACAGTCTCTG 59.796 57.143 0.00 7.48 37.52 3.35
9 10 1.076350 AGTAGCAGGTGGACAGTCTCT 59.924 52.381 0.00 0.00 0.00 3.10
10 11 1.474879 GAGTAGCAGGTGGACAGTCTC 59.525 57.143 0.00 0.00 0.00 3.36
11 12 1.076350 AGAGTAGCAGGTGGACAGTCT 59.924 52.381 0.00 0.00 0.00 3.24
12 13 1.551452 AGAGTAGCAGGTGGACAGTC 58.449 55.000 0.00 0.00 0.00 3.51
13 14 1.896465 GAAGAGTAGCAGGTGGACAGT 59.104 52.381 0.00 0.00 0.00 3.55
14 15 1.135257 CGAAGAGTAGCAGGTGGACAG 60.135 57.143 0.00 0.00 0.00 3.51
15 16 0.888619 CGAAGAGTAGCAGGTGGACA 59.111 55.000 0.00 0.00 0.00 4.02
16 17 1.135344 GTCGAAGAGTAGCAGGTGGAC 60.135 57.143 0.00 0.00 36.95 4.02
17 18 1.174783 GTCGAAGAGTAGCAGGTGGA 58.825 55.000 0.00 0.00 36.95 4.02
18 19 0.888619 TGTCGAAGAGTAGCAGGTGG 59.111 55.000 0.00 0.00 36.95 4.61
19 20 2.724977 TTGTCGAAGAGTAGCAGGTG 57.275 50.000 0.00 0.00 36.95 4.00
20 21 2.563179 ACATTGTCGAAGAGTAGCAGGT 59.437 45.455 0.00 0.00 36.95 4.00
21 22 3.238108 ACATTGTCGAAGAGTAGCAGG 57.762 47.619 0.00 0.00 36.95 4.85
22 23 5.597813 AAAACATTGTCGAAGAGTAGCAG 57.402 39.130 0.00 0.00 36.95 4.24
45 46 2.507471 ACCAACATTGCCCAAGGAAAAA 59.493 40.909 0.00 0.00 0.00 1.94
46 47 2.122768 ACCAACATTGCCCAAGGAAAA 58.877 42.857 0.00 0.00 0.00 2.29
47 48 1.415659 CACCAACATTGCCCAAGGAAA 59.584 47.619 0.00 0.00 0.00 3.13
48 49 1.047002 CACCAACATTGCCCAAGGAA 58.953 50.000 0.00 0.00 0.00 3.36
49 50 1.470996 GCACCAACATTGCCCAAGGA 61.471 55.000 0.00 0.00 33.58 3.36
50 51 1.004679 GCACCAACATTGCCCAAGG 60.005 57.895 0.00 0.00 33.58 3.61
51 52 4.679412 GCACCAACATTGCCCAAG 57.321 55.556 0.00 0.00 33.58 3.61
78 79 2.026301 GAGGTCTTCCGCCGATCG 59.974 66.667 8.51 8.51 39.05 3.69
94 95 2.261671 GAAGGAAGACGCGCAGGA 59.738 61.111 5.73 0.00 0.00 3.86
97 98 1.221466 CTTGTGAAGGAAGACGCGCA 61.221 55.000 5.73 0.00 0.00 6.09
103 104 4.103153 AGTGGATGAACTTGTGAAGGAAGA 59.897 41.667 0.00 0.00 0.00 2.87
107 108 2.738846 CGAGTGGATGAACTTGTGAAGG 59.261 50.000 0.00 0.00 0.00 3.46
129 130 1.080569 GGTGCAAAAGGTGATGCGG 60.081 57.895 0.00 0.00 45.47 5.69
130 131 1.080569 GGGTGCAAAAGGTGATGCG 60.081 57.895 0.00 0.00 45.47 4.73
136 137 1.484653 GAAACCAAGGGTGCAAAAGGT 59.515 47.619 0.00 0.00 35.34 3.50
148 149 6.927381 TCTCTACTTTCGTTTAGGAAACCAAG 59.073 38.462 0.00 6.94 38.14 3.61
154 155 5.803967 GCGATTCTCTACTTTCGTTTAGGAA 59.196 40.000 0.00 0.00 34.24 3.36
157 158 5.456173 GGAGCGATTCTCTACTTTCGTTTAG 59.544 44.000 0.00 0.00 41.60 1.85
158 159 5.106038 TGGAGCGATTCTCTACTTTCGTTTA 60.106 40.000 0.00 0.00 41.60 2.01
159 160 4.174762 GGAGCGATTCTCTACTTTCGTTT 58.825 43.478 0.00 0.00 41.60 3.60
161 162 2.753452 TGGAGCGATTCTCTACTTTCGT 59.247 45.455 0.00 0.00 41.60 3.85
162 163 3.367607 CTGGAGCGATTCTCTACTTTCG 58.632 50.000 0.00 0.00 41.60 3.46
163 164 3.120041 GCTGGAGCGATTCTCTACTTTC 58.880 50.000 0.00 0.00 41.60 2.62
164 165 2.497675 TGCTGGAGCGATTCTCTACTTT 59.502 45.455 0.00 0.00 45.83 2.66
165 166 2.100584 CTGCTGGAGCGATTCTCTACTT 59.899 50.000 0.00 0.00 45.83 2.24
166 167 1.680735 CTGCTGGAGCGATTCTCTACT 59.319 52.381 0.00 0.00 45.83 2.57
167 168 1.867698 GCTGCTGGAGCGATTCTCTAC 60.868 57.143 5.14 0.00 45.83 2.59
168 169 0.387202 GCTGCTGGAGCGATTCTCTA 59.613 55.000 5.14 0.00 45.83 2.43
169 170 1.143620 GCTGCTGGAGCGATTCTCT 59.856 57.895 5.14 0.00 45.83 3.10
170 171 3.716585 GCTGCTGGAGCGATTCTC 58.283 61.111 5.14 0.00 45.83 2.87
182 183 4.341783 GGCTCACCACTGGCTGCT 62.342 66.667 0.00 0.00 35.26 4.24
202 203 5.946972 TGGGATTATTTACCATGTTTGTCGT 59.053 36.000 0.00 0.00 0.00 4.34
227 228 1.117749 TCCTGCTGATCCGATCCCTG 61.118 60.000 5.91 1.99 0.00 4.45
228 229 0.399091 TTCCTGCTGATCCGATCCCT 60.399 55.000 5.91 0.00 0.00 4.20
230 231 0.755686 ACTTCCTGCTGATCCGATCC 59.244 55.000 5.91 0.00 0.00 3.36
231 232 2.611225 AACTTCCTGCTGATCCGATC 57.389 50.000 1.01 1.01 0.00 3.69
232 233 2.026822 ACAAACTTCCTGCTGATCCGAT 60.027 45.455 0.00 0.00 0.00 4.18
233 234 1.347707 ACAAACTTCCTGCTGATCCGA 59.652 47.619 0.00 0.00 0.00 4.55
234 235 1.813513 ACAAACTTCCTGCTGATCCG 58.186 50.000 0.00 0.00 0.00 4.18
243 244 5.220989 GGCTCGTTTTTAGAACAAACTTCCT 60.221 40.000 0.00 0.00 32.79 3.36
250 251 1.941294 TGCGGCTCGTTTTTAGAACAA 59.059 42.857 0.00 0.00 0.00 2.83
257 258 1.002251 TCGAAAATGCGGCTCGTTTTT 60.002 42.857 8.64 6.32 42.29 1.94
263 264 1.061276 GAAGACTCGAAAATGCGGCTC 59.939 52.381 0.00 0.00 0.00 4.70
268 269 4.154918 ACTTGATGGAAGACTCGAAAATGC 59.845 41.667 0.00 0.00 35.42 3.56
286 287 0.749818 TTGCTTTGTGCCGGACTTGA 60.750 50.000 5.05 0.00 42.00 3.02
315 318 1.134250 GGCAAAAAGGGACAGCCAAAA 60.134 47.619 0.00 0.00 44.59 2.44
333 336 3.356290 AGTAATCACTTTCATGGTGGGC 58.644 45.455 0.00 0.00 35.61 5.36
335 338 4.878397 GGAGAGTAATCACTTTCATGGTGG 59.122 45.833 0.00 0.00 37.58 4.61
336 339 5.491070 TGGAGAGTAATCACTTTCATGGTG 58.509 41.667 0.00 0.00 37.58 4.17
342 345 5.639931 GTCTGGTTGGAGAGTAATCACTTTC 59.360 44.000 0.00 0.00 35.61 2.62
350 353 2.972348 ACTGGTCTGGTTGGAGAGTAA 58.028 47.619 0.00 0.00 0.00 2.24
351 354 2.632996 CAACTGGTCTGGTTGGAGAGTA 59.367 50.000 0.00 0.00 39.97 2.59
365 375 1.564348 ACTCCACCTGAAACAACTGGT 59.436 47.619 0.00 0.00 41.52 4.00
384 395 3.194755 GTGTGGGGGATTTTCCAATGTAC 59.805 47.826 0.00 0.00 38.64 2.90
565 608 1.783140 GTACGTATCGTTCGATTGGGC 59.217 52.381 12.77 2.02 41.54 5.36
578 626 0.986992 GTTGCTTGCGTCGTACGTAT 59.013 50.000 16.05 0.00 44.73 3.06
596 644 1.381165 GCGGTTGAGTTGGTGTTGGT 61.381 55.000 0.00 0.00 0.00 3.67
597 645 1.358759 GCGGTTGAGTTGGTGTTGG 59.641 57.895 0.00 0.00 0.00 3.77
598 646 1.010125 CGCGGTTGAGTTGGTGTTG 60.010 57.895 0.00 0.00 0.00 3.33
599 647 2.830285 GCGCGGTTGAGTTGGTGTT 61.830 57.895 8.83 0.00 0.00 3.32
600 648 3.276846 GCGCGGTTGAGTTGGTGT 61.277 61.111 8.83 0.00 0.00 4.16
601 649 4.368808 CGCGCGGTTGAGTTGGTG 62.369 66.667 24.84 0.00 0.00 4.17
664 723 1.614385 GTGTGAATGACGTCGACGAT 58.386 50.000 41.52 26.13 43.02 3.73
873 981 0.739462 GATGTTGATCGACCACCGCA 60.739 55.000 10.69 0.00 38.37 5.69
878 986 2.419990 GGTGGATGATGTTGATCGACCA 60.420 50.000 10.69 2.72 44.18 4.02
880 988 2.609459 GTGGTGGATGATGTTGATCGAC 59.391 50.000 6.11 6.11 0.00 4.20
918 1032 2.959071 GCTGCTGTCTCGATCGCC 60.959 66.667 11.09 1.07 0.00 5.54
936 1050 0.901124 AGTAGCCAAGTGAGCCTCTG 59.099 55.000 0.00 0.00 0.00 3.35
959 1085 0.932585 GAGCTGTGATCGCGACTAGC 60.933 60.000 12.93 18.43 43.95 3.42
981 1125 1.516603 GTCGACCGAGTGGCTAAGC 60.517 63.158 3.51 0.00 39.70 3.09
983 1127 0.172578 CATGTCGACCGAGTGGCTAA 59.827 55.000 14.12 0.00 39.70 3.09
1090 1237 1.194781 ACCGCATCCTCCTTCACTGT 61.195 55.000 0.00 0.00 0.00 3.55
1092 1239 0.904865 TCACCGCATCCTCCTTCACT 60.905 55.000 0.00 0.00 0.00 3.41
1094 1241 0.250234 CTTCACCGCATCCTCCTTCA 59.750 55.000 0.00 0.00 0.00 3.02
1119 1275 1.305381 CCCCTCCTGGAACGTCTCT 60.305 63.158 0.00 0.00 35.39 3.10
1386 1547 1.001406 GCAGGCTAGTAGCTACCCATG 59.999 57.143 20.31 16.39 41.99 3.66
1398 1586 4.813697 GGAAACTGATTTAGAGCAGGCTAG 59.186 45.833 3.37 0.00 43.50 3.42
1399 1587 4.680708 CGGAAACTGATTTAGAGCAGGCTA 60.681 45.833 3.37 0.00 43.50 3.93
1400 1588 3.615155 GGAAACTGATTTAGAGCAGGCT 58.385 45.455 3.37 0.00 43.50 4.58
1408 1596 5.803020 AAAGCTAGCGGAAACTGATTTAG 57.197 39.130 9.55 0.00 0.00 1.85
1409 1597 5.106317 CCAAAAGCTAGCGGAAACTGATTTA 60.106 40.000 9.55 0.00 0.00 1.40
1416 1608 2.661594 CAACCAAAAGCTAGCGGAAAC 58.338 47.619 9.55 0.00 0.00 2.78
1471 1676 1.553654 GCACGCAGTCGCTAATACG 59.446 57.895 0.00 0.00 41.61 3.06
1519 1741 0.179100 CCATACAGGCACACTCTCCG 60.179 60.000 0.00 0.00 0.00 4.63
1578 1803 2.535574 GCAACAACAAAGAAAAGCGAGG 59.464 45.455 0.00 0.00 0.00 4.63
1730 1960 0.617935 TGATTGGACCGAGCAATGGA 59.382 50.000 0.00 0.00 0.00 3.41
1737 1967 4.332819 GGTTTTCACTATGATTGGACCGAG 59.667 45.833 0.00 0.00 0.00 4.63
1759 1989 6.037610 CCTTCTAAACGAGGATCAAATTCAGG 59.962 42.308 0.00 0.00 33.17 3.86
1774 2004 4.628333 TGAAAATAGCGTCCCTTCTAAACG 59.372 41.667 0.00 0.00 39.33 3.60
1776 2006 5.183228 CCTGAAAATAGCGTCCCTTCTAAA 58.817 41.667 0.00 0.00 0.00 1.85
1789 2019 2.019984 GTGGCTGCTCCCTGAAAATAG 58.980 52.381 0.00 0.00 0.00 1.73
1791 2021 0.613012 GGTGGCTGCTCCCTGAAAAT 60.613 55.000 0.00 0.00 0.00 1.82
1799 2029 3.244249 CCTACTAAATAGGTGGCTGCTCC 60.244 52.174 0.00 2.90 45.15 4.70
1810 2040 5.464984 TCACCCCTCCTTCCTACTAAATAG 58.535 45.833 0.00 0.00 0.00 1.73
1811 2041 5.197189 TCTCACCCCTCCTTCCTACTAAATA 59.803 44.000 0.00 0.00 0.00 1.40
1812 2042 4.015541 TCTCACCCCTCCTTCCTACTAAAT 60.016 45.833 0.00 0.00 0.00 1.40
1813 2043 3.338824 TCTCACCCCTCCTTCCTACTAAA 59.661 47.826 0.00 0.00 0.00 1.85
1814 2044 2.931088 TCTCACCCCTCCTTCCTACTAA 59.069 50.000 0.00 0.00 0.00 2.24
1816 2046 1.007359 GTCTCACCCCTCCTTCCTACT 59.993 57.143 0.00 0.00 0.00 2.57
1817 2047 1.007359 AGTCTCACCCCTCCTTCCTAC 59.993 57.143 0.00 0.00 0.00 3.18
1818 2048 1.394532 AGTCTCACCCCTCCTTCCTA 58.605 55.000 0.00 0.00 0.00 2.94
1819 2049 0.494095 AAGTCTCACCCCTCCTTCCT 59.506 55.000 0.00 0.00 0.00 3.36
1820 2050 1.279558 GAAAGTCTCACCCCTCCTTCC 59.720 57.143 0.00 0.00 0.00 3.46
1821 2051 2.261729 AGAAAGTCTCACCCCTCCTTC 58.738 52.381 0.00 0.00 0.00 3.46
1822 2052 2.424684 AGAAAGTCTCACCCCTCCTT 57.575 50.000 0.00 0.00 0.00 3.36
1824 2054 2.112190 CCTAGAAAGTCTCACCCCTCC 58.888 57.143 0.00 0.00 0.00 4.30
1826 2056 1.722851 TCCCTAGAAAGTCTCACCCCT 59.277 52.381 0.00 0.00 0.00 4.79
1827 2057 1.832366 GTCCCTAGAAAGTCTCACCCC 59.168 57.143 0.00 0.00 0.00 4.95
1829 2059 3.382227 GCTAGTCCCTAGAAAGTCTCACC 59.618 52.174 2.51 0.00 36.26 4.02
1831 2061 3.054582 TCGCTAGTCCCTAGAAAGTCTCA 60.055 47.826 2.51 0.00 36.26 3.27
1832 2062 3.313249 GTCGCTAGTCCCTAGAAAGTCTC 59.687 52.174 2.51 0.00 36.26 3.36
1833 2063 3.054213 AGTCGCTAGTCCCTAGAAAGTCT 60.054 47.826 2.51 0.00 36.26 3.24
1834 2064 3.281158 AGTCGCTAGTCCCTAGAAAGTC 58.719 50.000 2.51 0.00 36.26 3.01
1835 2065 3.369242 AGTCGCTAGTCCCTAGAAAGT 57.631 47.619 2.51 0.00 36.26 2.66
1836 2066 4.722361 AAAGTCGCTAGTCCCTAGAAAG 57.278 45.455 2.51 0.00 36.26 2.62
1837 2067 5.479124 AAAAAGTCGCTAGTCCCTAGAAA 57.521 39.130 2.51 0.00 36.26 2.52
1838 2068 6.594788 TTAAAAAGTCGCTAGTCCCTAGAA 57.405 37.500 2.51 0.00 36.26 2.10
1839 2069 6.786967 ATTAAAAAGTCGCTAGTCCCTAGA 57.213 37.500 2.51 0.00 36.26 2.43
1840 2070 6.258068 CCAATTAAAAAGTCGCTAGTCCCTAG 59.742 42.308 0.00 0.00 37.16 3.02
1841 2071 6.110707 CCAATTAAAAAGTCGCTAGTCCCTA 58.889 40.000 0.00 0.00 0.00 3.53
1842 2072 4.941873 CCAATTAAAAAGTCGCTAGTCCCT 59.058 41.667 0.00 0.00 0.00 4.20
1843 2073 4.095932 CCCAATTAAAAAGTCGCTAGTCCC 59.904 45.833 0.00 0.00 0.00 4.46
1844 2074 4.939439 TCCCAATTAAAAAGTCGCTAGTCC 59.061 41.667 0.00 0.00 0.00 3.85
1845 2075 6.490566 TTCCCAATTAAAAAGTCGCTAGTC 57.509 37.500 0.00 0.00 0.00 2.59
1846 2076 8.570068 TTATTCCCAATTAAAAAGTCGCTAGT 57.430 30.769 0.00 0.00 0.00 2.57
1847 2077 9.849166 TTTTATTCCCAATTAAAAAGTCGCTAG 57.151 29.630 0.00 0.00 0.00 3.42
1872 2102 9.366216 GTTTGGTTCACAAGTCTTAGAATTTTT 57.634 29.630 0.00 0.00 40.82 1.94
1873 2103 8.527810 TGTTTGGTTCACAAGTCTTAGAATTTT 58.472 29.630 0.00 0.00 40.82 1.82
1874 2104 8.062065 TGTTTGGTTCACAAGTCTTAGAATTT 57.938 30.769 0.00 0.00 40.82 1.82
1875 2105 7.639113 TGTTTGGTTCACAAGTCTTAGAATT 57.361 32.000 0.00 0.00 40.82 2.17
1876 2106 7.307989 CGATGTTTGGTTCACAAGTCTTAGAAT 60.308 37.037 3.73 0.00 40.82 2.40
1877 2107 6.018262 CGATGTTTGGTTCACAAGTCTTAGAA 60.018 38.462 0.00 0.00 40.82 2.10
1878 2108 5.465390 CGATGTTTGGTTCACAAGTCTTAGA 59.535 40.000 0.00 0.00 40.82 2.10
1879 2109 5.679906 CGATGTTTGGTTCACAAGTCTTAG 58.320 41.667 0.00 0.00 40.82 2.18
1880 2110 4.024387 GCGATGTTTGGTTCACAAGTCTTA 60.024 41.667 0.00 0.00 40.82 2.10
1881 2111 3.243068 GCGATGTTTGGTTCACAAGTCTT 60.243 43.478 0.00 0.00 40.82 3.01
1882 2112 2.290641 GCGATGTTTGGTTCACAAGTCT 59.709 45.455 0.00 0.00 40.82 3.24
1883 2113 2.604614 GGCGATGTTTGGTTCACAAGTC 60.605 50.000 0.00 0.00 40.82 3.01
1884 2114 1.336755 GGCGATGTTTGGTTCACAAGT 59.663 47.619 0.00 0.00 40.82 3.16
1885 2115 1.335872 GGGCGATGTTTGGTTCACAAG 60.336 52.381 0.00 0.00 40.82 3.16
1886 2116 0.671251 GGGCGATGTTTGGTTCACAA 59.329 50.000 0.00 0.00 37.28 3.33
1887 2117 0.179004 AGGGCGATGTTTGGTTCACA 60.179 50.000 0.00 0.00 0.00 3.58
1888 2118 0.240945 CAGGGCGATGTTTGGTTCAC 59.759 55.000 0.00 0.00 0.00 3.18
1889 2119 0.109532 TCAGGGCGATGTTTGGTTCA 59.890 50.000 0.00 0.00 0.00 3.18
1890 2120 1.463674 ATCAGGGCGATGTTTGGTTC 58.536 50.000 0.00 0.00 31.20 3.62
1891 2121 2.752903 GTTATCAGGGCGATGTTTGGTT 59.247 45.455 0.00 0.00 35.39 3.67
1892 2122 2.290641 TGTTATCAGGGCGATGTTTGGT 60.291 45.455 0.00 0.00 35.39 3.67
1893 2123 2.355756 CTGTTATCAGGGCGATGTTTGG 59.644 50.000 0.00 0.00 37.97 3.28
1894 2124 2.223340 GCTGTTATCAGGGCGATGTTTG 60.223 50.000 3.05 0.00 41.57 2.93
1895 2125 2.017049 GCTGTTATCAGGGCGATGTTT 58.983 47.619 3.05 0.00 41.57 2.83
1896 2126 1.210478 AGCTGTTATCAGGGCGATGTT 59.790 47.619 3.05 0.00 41.57 2.71
1897 2127 0.833287 AGCTGTTATCAGGGCGATGT 59.167 50.000 3.05 0.00 41.57 3.06
1898 2128 1.959042 AAGCTGTTATCAGGGCGATG 58.041 50.000 3.05 0.00 41.57 3.84
1899 2129 2.717639 AAAGCTGTTATCAGGGCGAT 57.282 45.000 3.05 0.00 41.57 4.58
1908 2138 4.373156 ACACTCCCAGAAAAGCTGTTAT 57.627 40.909 0.00 0.00 43.33 1.89
1913 2143 4.373156 ACATTACACTCCCAGAAAAGCT 57.627 40.909 0.00 0.00 0.00 3.74
1936 2166 9.421399 TGAGTGTCAACTAGATTATCCATCTAA 57.579 33.333 0.00 0.00 42.90 2.10
1994 2224 5.192327 AGCTTACATTTGCCATATGAAGC 57.808 39.130 16.57 16.57 36.94 3.86
2026 2256 1.735018 CCGTGTGCATGGTTCGAAATA 59.265 47.619 0.00 0.00 32.81 1.40
2027 2257 0.521291 CCGTGTGCATGGTTCGAAAT 59.479 50.000 0.00 0.00 32.81 2.17
2029 2259 0.533085 TTCCGTGTGCATGGTTCGAA 60.533 50.000 9.94 0.00 38.61 3.71
2030 2260 0.948623 CTTCCGTGTGCATGGTTCGA 60.949 55.000 9.94 0.00 38.61 3.71
2031 2261 1.227999 ACTTCCGTGTGCATGGTTCG 61.228 55.000 9.94 3.47 38.61 3.95
2032 2262 1.463444 GTACTTCCGTGTGCATGGTTC 59.537 52.381 9.94 0.00 38.61 3.62
2033 2263 1.202710 TGTACTTCCGTGTGCATGGTT 60.203 47.619 9.94 0.22 38.61 3.67
2034 2264 0.394938 TGTACTTCCGTGTGCATGGT 59.605 50.000 9.94 0.00 38.61 3.55
2035 2265 1.196808 GTTGTACTTCCGTGTGCATGG 59.803 52.381 4.11 4.11 38.85 3.66
2036 2266 1.870402 TGTTGTACTTCCGTGTGCATG 59.130 47.619 0.00 0.00 32.97 4.06
2037 2267 1.871039 GTGTTGTACTTCCGTGTGCAT 59.129 47.619 0.00 0.00 32.97 3.96
2038 2268 1.292061 GTGTTGTACTTCCGTGTGCA 58.708 50.000 0.00 0.00 0.00 4.57
2039 2269 1.260561 CTGTGTTGTACTTCCGTGTGC 59.739 52.381 0.00 0.00 0.00 4.57
2040 2270 2.538449 GACTGTGTTGTACTTCCGTGTG 59.462 50.000 0.00 0.00 0.00 3.82
2041 2271 2.482490 GGACTGTGTTGTACTTCCGTGT 60.482 50.000 0.00 0.00 0.00 4.49
2042 2272 2.132762 GGACTGTGTTGTACTTCCGTG 58.867 52.381 0.00 0.00 0.00 4.94
2043 2273 2.037144 AGGACTGTGTTGTACTTCCGT 58.963 47.619 0.00 0.00 37.29 4.69
2044 2274 2.814280 AGGACTGTGTTGTACTTCCG 57.186 50.000 0.00 0.00 37.29 4.30
2045 2275 5.221382 TGTCTTAGGACTGTGTTGTACTTCC 60.221 44.000 6.54 0.00 42.54 3.46
2046 2276 5.839621 TGTCTTAGGACTGTGTTGTACTTC 58.160 41.667 6.54 0.00 42.54 3.01
2047 2277 5.597182 TCTGTCTTAGGACTGTGTTGTACTT 59.403 40.000 6.54 0.00 42.54 2.24
2048 2278 5.138276 TCTGTCTTAGGACTGTGTTGTACT 58.862 41.667 6.54 0.00 42.54 2.73
2049 2279 5.449107 TCTGTCTTAGGACTGTGTTGTAC 57.551 43.478 6.54 0.00 42.54 2.90
2050 2280 6.474140 TTTCTGTCTTAGGACTGTGTTGTA 57.526 37.500 6.54 0.00 42.54 2.41
2051 2281 5.353394 TTTCTGTCTTAGGACTGTGTTGT 57.647 39.130 6.54 0.00 42.54 3.32
2052 2282 5.237344 CCTTTTCTGTCTTAGGACTGTGTTG 59.763 44.000 6.54 0.32 42.54 3.33
2056 2286 5.888982 TTCCTTTTCTGTCTTAGGACTGT 57.111 39.130 6.54 0.00 42.54 3.55
2057 2287 6.292919 CGTTTTCCTTTTCTGTCTTAGGACTG 60.293 42.308 6.54 6.06 42.54 3.51
2070 2300 8.850452 CATGCTTAAACTATCGTTTTCCTTTTC 58.150 33.333 0.18 0.00 42.91 2.29
2084 2314 4.651778 ACACAAGAGGCATGCTTAAACTA 58.348 39.130 18.92 0.00 0.00 2.24
2088 2318 4.014569 TGTACACAAGAGGCATGCTTAA 57.985 40.909 18.92 0.00 0.00 1.85
2097 2337 2.412870 TGAACGCATGTACACAAGAGG 58.587 47.619 0.00 0.00 0.00 3.69
2122 2376 0.390735 AAGGACGCGTGTGGGTTATC 60.391 55.000 20.70 0.00 41.99 1.75
2124 2378 1.301087 CAAGGACGCGTGTGGGTTA 60.301 57.895 20.70 0.00 41.99 2.85
2187 2441 2.742053 TGCGTTAAATTCAGCTCTGGTC 59.258 45.455 0.00 0.00 0.00 4.02
2215 2469 8.375506 ACTTGGTCATCAATCTTGTCTAAGTTA 58.624 33.333 0.00 0.00 34.45 2.24
2226 2480 4.389374 ACGTGAAACTTGGTCATCAATCT 58.611 39.130 0.00 0.00 34.45 2.40
2249 2503 6.947464 AGGTTACATCACTAATTGCTACTGT 58.053 36.000 0.00 0.00 0.00 3.55
2250 2504 7.010552 GTGAGGTTACATCACTAATTGCTACTG 59.989 40.741 20.81 0.00 43.03 2.74
2251 2505 7.042335 GTGAGGTTACATCACTAATTGCTACT 58.958 38.462 20.81 0.00 43.03 2.57
2252 2506 6.816640 TGTGAGGTTACATCACTAATTGCTAC 59.183 38.462 26.46 1.53 45.87 3.58
2253 2507 6.941857 TGTGAGGTTACATCACTAATTGCTA 58.058 36.000 26.46 5.27 45.87 3.49
2269 2523 2.555757 GCTTGAATTGCTCTGTGAGGTT 59.444 45.455 0.00 0.00 0.00 3.50
2294 2548 0.320050 TATGGCGCGCCTATTGATGA 59.680 50.000 45.79 27.14 36.94 2.92
2295 2549 1.135972 GTTATGGCGCGCCTATTGATG 60.136 52.381 45.79 0.00 36.94 3.07
2296 2550 1.156736 GTTATGGCGCGCCTATTGAT 58.843 50.000 45.79 33.29 36.94 2.57
2297 2551 0.179070 TGTTATGGCGCGCCTATTGA 60.179 50.000 45.79 29.48 36.94 2.57
2298 2552 0.041312 GTGTTATGGCGCGCCTATTG 60.041 55.000 45.79 0.00 36.94 1.90
2299 2553 0.462937 TGTGTTATGGCGCGCCTATT 60.463 50.000 45.79 32.55 36.94 1.73
2302 2556 2.819595 CTGTGTTATGGCGCGCCT 60.820 61.111 45.79 33.35 36.94 5.52


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

AutoCloner maintained by Alex Coulton.