Multiple sequence alignment - TraesCS5B01G420200

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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 TraesCS5B01G420200 chr5B 100.000 3563 0 0 1 3563 595662481 595658919 0.000000e+00 6580.0
1 TraesCS5B01G420200 chr5B 86.621 583 66 11 2983 3563 378816531 378815959 5.020000e-178 634.0
2 TraesCS5B01G420200 chr5B 91.429 105 8 1 2391 2495 700333712 700333609 3.710000e-30 143.0
3 TraesCS5B01G420200 chr5B 100.000 28 0 0 2292 2319 610376292 610376265 6.000000e-03 52.8
4 TraesCS5B01G420200 chr5D 85.847 1936 144 46 3 1844 484578426 484576527 0.000000e+00 1938.0
5 TraesCS5B01G420200 chr5D 95.169 1097 44 7 2472 3563 484575473 484574381 0.000000e+00 1724.0
6 TraesCS5B01G420200 chr5D 85.236 657 77 15 2915 3563 326370201 326369557 0.000000e+00 658.0
7 TraesCS5B01G420200 chr5D 92.000 150 8 3 2239 2385 484575644 484575496 1.300000e-49 207.0
8 TraesCS5B01G420200 chr5D 85.789 190 17 9 2024 2205 484576380 484576193 3.630000e-45 193.0
9 TraesCS5B01G420200 chr5A 95.364 1100 42 7 2466 3563 606160711 606159619 0.000000e+00 1740.0
10 TraesCS5B01G420200 chr5A 85.610 1640 137 41 1 1608 606162910 606161338 0.000000e+00 1629.0
11 TraesCS5B01G420200 chr5A 85.584 659 76 15 2912 3563 430246306 430246952 0.000000e+00 673.0
12 TraesCS5B01G420200 chr2B 84.000 500 70 6 2966 3460 55913653 55913159 4.160000e-129 472.0
13 TraesCS5B01G420200 chr2B 81.818 495 80 8 2969 3458 55924274 55923785 1.190000e-109 407.0
14 TraesCS5B01G420200 chr2B 100.000 28 0 0 2292 2319 152507630 152507657 6.000000e-03 52.8
15 TraesCS5B01G420200 chr2A 83.567 499 73 7 2967 3460 36672351 36672845 3.240000e-125 459.0
16 TraesCS5B01G420200 chr2D 82.016 506 75 11 2966 3463 33878719 33878222 1.980000e-112 416.0
17 TraesCS5B01G420200 chr7D 93.617 94 5 1 2391 2483 159174441 159174534 4.800000e-29 139.0
18 TraesCS5B01G420200 chr7B 93.617 94 5 1 2391 2483 90139280 90139373 4.800000e-29 139.0
19 TraesCS5B01G420200 chr4D 93.617 94 5 1 2391 2483 414548696 414548603 4.800000e-29 139.0
20 TraesCS5B01G420200 chr4B 93.617 94 5 1 2391 2483 178963385 178963478 4.800000e-29 139.0
21 TraesCS5B01G420200 chr4A 93.617 94 5 1 2391 2483 1988894 1988987 4.800000e-29 139.0
22 TraesCS5B01G420200 chr4A 94.366 71 4 0 3458 3528 208811987 208812057 3.760000e-20 110.0
23 TraesCS5B01G420200 chr3D 93.617 94 5 1 2391 2483 489232945 489233038 4.800000e-29 139.0
24 TraesCS5B01G420200 chr3D 95.775 71 3 0 3458 3528 404558899 404558969 8.080000e-22 115.0
25 TraesCS5B01G420200 chr1B 93.617 94 5 1 2391 2483 402895946 402895853 4.800000e-29 139.0
26 TraesCS5B01G420200 chr1A 93.617 94 5 1 2391 2483 401930040 401930133 4.800000e-29 139.0
27 TraesCS5B01G420200 chr3A 95.775 71 3 0 3458 3528 402138461 402138391 8.080000e-22 115.0
28 TraesCS5B01G420200 chr6A 92.958 71 5 0 3458 3528 234140442 234140372 1.750000e-18 104.0


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 TraesCS5B01G420200 chr5B 595658919 595662481 3562 True 6580.0 6580 100.00000 1 3563 1 chr5B.!!$R2 3562
1 TraesCS5B01G420200 chr5B 378815959 378816531 572 True 634.0 634 86.62100 2983 3563 1 chr5B.!!$R1 580
2 TraesCS5B01G420200 chr5D 484574381 484578426 4045 True 1015.5 1938 89.70125 3 3563 4 chr5D.!!$R2 3560
3 TraesCS5B01G420200 chr5D 326369557 326370201 644 True 658.0 658 85.23600 2915 3563 1 chr5D.!!$R1 648
4 TraesCS5B01G420200 chr5A 606159619 606162910 3291 True 1684.5 1740 90.48700 1 3563 2 chr5A.!!$R1 3562
5 TraesCS5B01G420200 chr5A 430246306 430246952 646 False 673.0 673 85.58400 2912 3563 1 chr5A.!!$F1 651

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
479 502 0.239347 CCTAGTTTGTGTGCTGCAGC 59.761 55.0 31.89 31.89 42.50 5.25 F
1862 2024 0.109597 GCAACACCACTGCTACATGC 60.110 55.0 0.00 0.00 43.25 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 2116 0.106268 TTGTGCCCTGCCAAGAAGAA 60.106 50.0 0.00 0.0 0.00 2.52 R
2897 3623 0.816825 GGTGCACCTGATGATCGCAT 60.817 55.0 29.12 0.0 37.47 4.73 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
44 45 5.762218 TGTTTTATTTCAGGCAATTGTTGGG 59.238 36.000 7.40 0.00 0.00 4.12
51 52 0.467804 GGCAATTGTTGGGTTGTGGT 59.532 50.000 7.40 0.00 0.00 4.16
89 90 2.519013 AGCTGGTTCAATTTCCTGACC 58.481 47.619 0.00 0.00 0.00 4.02
92 93 2.884639 CTGGTTCAATTTCCTGACCGTT 59.115 45.455 0.00 0.00 0.00 4.44
109 110 7.334921 CCTGACCGTTATTTACATTGGTAAGAA 59.665 37.037 0.00 0.00 40.40 2.52
110 111 8.259049 TGACCGTTATTTACATTGGTAAGAAG 57.741 34.615 0.00 0.00 40.40 2.85
111 112 7.080353 ACCGTTATTTACATTGGTAAGAAGC 57.920 36.000 0.00 0.00 40.40 3.86
114 115 9.052759 CCGTTATTTACATTGGTAAGAAGCTAT 57.947 33.333 0.00 0.00 40.40 2.97
132 133 9.785982 AGAAGCTATAACATTTATTTCTCTCCC 57.214 33.333 0.00 0.00 0.00 4.30
169 180 7.506114 ACTGAGAAACAACATAACTGTTCCTA 58.494 34.615 0.00 0.00 43.76 2.94
179 190 5.640357 ACATAACTGTTCCTATTTCGCGAAA 59.360 36.000 33.83 33.83 28.70 3.46
203 214 1.798725 CGTTCCGCTGCTTGCATTG 60.799 57.895 0.00 0.00 43.06 2.82
210 221 2.330286 CGCTGCTTGCATTGATGAAAA 58.670 42.857 0.00 0.00 43.06 2.29
213 224 3.495377 GCTGCTTGCATTGATGAAAACAA 59.505 39.130 0.00 0.00 42.31 2.83
214 225 4.609783 GCTGCTTGCATTGATGAAAACAAC 60.610 41.667 0.00 0.00 42.31 3.32
215 226 4.439968 TGCTTGCATTGATGAAAACAACA 58.560 34.783 0.00 0.00 28.93 3.33
216 227 4.270566 TGCTTGCATTGATGAAAACAACAC 59.729 37.500 0.00 0.00 28.93 3.32
220 231 3.742369 GCATTGATGAAAACAACACCTGG 59.258 43.478 0.00 0.00 28.93 4.45
222 233 5.358922 CATTGATGAAAACAACACCTGGTT 58.641 37.500 0.00 0.00 41.47 3.67
224 235 5.413309 TGATGAAAACAACACCTGGTTTT 57.587 34.783 0.00 0.00 45.25 2.43
225 236 5.174395 TGATGAAAACAACACCTGGTTTTG 58.826 37.500 21.02 21.02 45.25 2.44
249 260 1.724582 GAACAGGGTTTGTGTGCGCT 61.725 55.000 9.73 0.00 40.74 5.92
267 278 2.281070 CACACGCTCCCTGTGCTT 60.281 61.111 0.00 0.00 41.03 3.91
393 404 3.071602 CCACCAAGAGGAACAAGAAGAGA 59.928 47.826 0.00 0.00 38.69 3.10
401 412 5.944007 AGAGGAACAAGAAGAGAGAGTAGAC 59.056 44.000 0.00 0.00 0.00 2.59
448 471 6.707608 TCATGATTTATCGAGTGAAATCCCTG 59.292 38.462 19.52 17.16 40.04 4.45
449 472 4.816385 TGATTTATCGAGTGAAATCCCTGC 59.184 41.667 19.52 4.47 40.04 4.85
450 473 4.487714 TTTATCGAGTGAAATCCCTGCT 57.512 40.909 0.00 0.00 0.00 4.24
451 474 5.607939 TTTATCGAGTGAAATCCCTGCTA 57.392 39.130 0.00 0.00 0.00 3.49
452 475 5.808366 TTATCGAGTGAAATCCCTGCTAT 57.192 39.130 0.00 0.00 0.00 2.97
453 476 4.696479 ATCGAGTGAAATCCCTGCTATT 57.304 40.909 0.00 0.00 0.00 1.73
454 477 5.808366 ATCGAGTGAAATCCCTGCTATTA 57.192 39.130 0.00 0.00 0.00 0.98
455 478 5.808366 TCGAGTGAAATCCCTGCTATTAT 57.192 39.130 0.00 0.00 0.00 1.28
479 502 0.239347 CCTAGTTTGTGTGCTGCAGC 59.761 55.000 31.89 31.89 42.50 5.25
497 520 2.027745 CAGCCCTGTAGTGTGTCTCAAT 60.028 50.000 0.00 0.00 0.00 2.57
514 537 5.123502 GTCTCAATTGTCATGTGAGAGCATT 59.876 40.000 11.98 0.00 46.32 3.56
617 643 1.340889 GTGGGATGCTGCTCAACAAAA 59.659 47.619 0.00 0.00 0.00 2.44
618 644 2.028748 GTGGGATGCTGCTCAACAAAAT 60.029 45.455 0.00 0.00 0.00 1.82
647 673 7.169982 GTGAGACCATAAGTTGTCTGCATATAC 59.830 40.741 0.00 0.00 41.74 1.47
703 749 0.524862 AAAGAATTGCTCGCTGCCAG 59.475 50.000 0.00 0.00 42.00 4.85
715 761 0.681175 GCTGCCAGGTCCAAATTTGT 59.319 50.000 16.73 0.00 0.00 2.83
736 785 3.966218 GTGATCGCGATTTTATTTTCGGG 59.034 43.478 24.55 3.38 46.06 5.14
742 791 4.496673 CGCGATTTTATTTTCGGGGATTGA 60.497 41.667 0.00 0.00 42.48 2.57
775 824 4.566070 CCATTCTGTCCATGCCCAAATTTT 60.566 41.667 0.00 0.00 0.00 1.82
840 889 1.101331 CAGATTTGGGAGGCAGAAGC 58.899 55.000 0.00 0.00 41.10 3.86
848 897 1.078567 GAGGCAGAAGCTGACCCAG 60.079 63.158 0.00 0.00 41.11 4.45
876 925 2.010582 TTTTCAGGTGGTGTTGCGGC 62.011 55.000 0.00 0.00 0.00 6.53
909 958 2.903635 ATGCACCCTGAGCTGCTGT 61.904 57.895 7.01 0.00 34.29 4.40
1022 1072 0.466555 TAAAACCTGCGTTGCCCACT 60.467 50.000 0.00 0.00 30.72 4.00
1024 1074 4.643387 ACCTGCGTTGCCCACTCC 62.643 66.667 0.00 0.00 0.00 3.85
1030 1080 2.286523 CGTTGCCCACTCCTCTCCT 61.287 63.158 0.00 0.00 0.00 3.69
1031 1081 1.599576 GTTGCCCACTCCTCTCCTC 59.400 63.158 0.00 0.00 0.00 3.71
1178 1236 2.878429 CCTCCTCCACGACGACAG 59.122 66.667 0.00 0.00 0.00 3.51
1491 1558 4.335647 ATGCCCGGGATGCCGATC 62.336 66.667 28.88 17.78 34.88 3.69
1626 1762 1.869690 GTTCAGCTTCAAGCCGGAC 59.130 57.895 5.05 0.00 43.77 4.79
1742 1884 2.196229 CAACCCCAACCCCAACGA 59.804 61.111 0.00 0.00 0.00 3.85
1757 1899 2.202797 CGAGGCCATCCACTGACG 60.203 66.667 5.01 0.00 33.74 4.35
1766 1908 1.135915 CATCCACTGACGAGGAAGGAG 59.864 57.143 0.00 0.00 37.48 3.69
1767 1909 0.404426 TCCACTGACGAGGAAGGAGA 59.596 55.000 0.00 0.00 0.00 3.71
1768 1910 1.203013 TCCACTGACGAGGAAGGAGAA 60.203 52.381 0.00 0.00 0.00 2.87
1769 1911 1.203523 CCACTGACGAGGAAGGAGAAG 59.796 57.143 0.00 0.00 0.00 2.85
1770 1912 2.163509 CACTGACGAGGAAGGAGAAGA 58.836 52.381 0.00 0.00 0.00 2.87
1771 1913 2.558795 CACTGACGAGGAAGGAGAAGAA 59.441 50.000 0.00 0.00 0.00 2.52
1772 1914 2.823154 ACTGACGAGGAAGGAGAAGAAG 59.177 50.000 0.00 0.00 0.00 2.85
1773 1915 2.823154 CTGACGAGGAAGGAGAAGAAGT 59.177 50.000 0.00 0.00 0.00 3.01
1774 1916 2.558795 TGACGAGGAAGGAGAAGAAGTG 59.441 50.000 0.00 0.00 0.00 3.16
1775 1917 1.896465 ACGAGGAAGGAGAAGAAGTGG 59.104 52.381 0.00 0.00 0.00 4.00
1776 1918 1.404851 CGAGGAAGGAGAAGAAGTGGC 60.405 57.143 0.00 0.00 0.00 5.01
1805 1949 1.340405 GCATCAATCACCTGACCTGGT 60.340 52.381 0.00 0.00 41.77 4.00
1817 1961 3.129502 CCTGGTGTCATGGCGCAG 61.130 66.667 13.71 8.10 0.00 5.18
1819 1963 4.720902 TGGTGTCATGGCGCAGGG 62.721 66.667 13.71 0.00 0.00 4.45
1820 1964 4.722700 GGTGTCATGGCGCAGGGT 62.723 66.667 13.71 0.00 0.00 4.34
1821 1965 3.434319 GTGTCATGGCGCAGGGTG 61.434 66.667 10.83 1.58 0.00 4.61
1822 1966 3.952508 TGTCATGGCGCAGGGTGT 61.953 61.111 10.83 0.00 0.00 4.16
1846 2008 4.079787 AGCCCAGGATCATTTTACTAGCAA 60.080 41.667 0.00 0.00 0.00 3.91
1849 2011 5.066505 CCCAGGATCATTTTACTAGCAACAC 59.933 44.000 0.00 0.00 0.00 3.32
1862 2024 0.109597 GCAACACCACTGCTACATGC 60.110 55.000 0.00 0.00 43.25 4.06
1864 2026 0.110295 AACACCACTGCTACATGCCA 59.890 50.000 0.00 0.00 42.00 4.92
1865 2027 0.329261 ACACCACTGCTACATGCCAT 59.671 50.000 0.00 0.00 42.00 4.40
1866 2028 0.736636 CACCACTGCTACATGCCATG 59.263 55.000 2.40 2.40 42.00 3.66
1867 2029 0.620030 ACCACTGCTACATGCCATGA 59.380 50.000 12.53 0.00 42.00 3.07
1868 2030 1.019673 CCACTGCTACATGCCATGAC 58.980 55.000 12.53 1.00 42.00 3.06
1869 2031 1.407851 CCACTGCTACATGCCATGACT 60.408 52.381 12.53 0.00 42.00 3.41
1873 2035 3.452264 ACTGCTACATGCCATGACTCTTA 59.548 43.478 12.53 0.00 42.00 2.10
1882 2044 8.579850 ACATGCCATGACTCTTAGAAAAATTA 57.420 30.769 12.53 0.00 0.00 1.40
1888 2050 8.669243 CCATGACTCTTAGAAAAATTACTCCAC 58.331 37.037 0.00 0.00 0.00 4.02
1899 2061 4.623932 AATTACTCCACACAGAAGCAGA 57.376 40.909 0.00 0.00 0.00 4.26
1901 2063 4.415881 TTACTCCACACAGAAGCAGAAA 57.584 40.909 0.00 0.00 0.00 2.52
1902 2064 2.565841 ACTCCACACAGAAGCAGAAAC 58.434 47.619 0.00 0.00 0.00 2.78
1903 2065 2.171448 ACTCCACACAGAAGCAGAAACT 59.829 45.455 0.00 0.00 0.00 2.66
1904 2066 3.209410 CTCCACACAGAAGCAGAAACTT 58.791 45.455 0.00 0.00 0.00 2.66
1905 2067 3.206150 TCCACACAGAAGCAGAAACTTC 58.794 45.455 0.00 0.00 45.29 3.01
1906 2068 2.291741 CCACACAGAAGCAGAAACTTCC 59.708 50.000 0.83 0.00 45.95 3.46
1907 2069 2.945008 CACACAGAAGCAGAAACTTCCA 59.055 45.455 0.83 0.00 45.95 3.53
1908 2070 3.378112 CACACAGAAGCAGAAACTTCCAA 59.622 43.478 0.83 0.00 45.95 3.53
1909 2071 4.016444 ACACAGAAGCAGAAACTTCCAAA 58.984 39.130 0.83 0.00 45.95 3.28
1910 2072 4.096984 ACACAGAAGCAGAAACTTCCAAAG 59.903 41.667 0.83 0.00 45.95 2.77
1911 2073 4.096984 CACAGAAGCAGAAACTTCCAAAGT 59.903 41.667 0.83 0.00 45.95 2.66
1912 2074 4.336713 ACAGAAGCAGAAACTTCCAAAGTC 59.663 41.667 0.83 0.00 45.95 3.01
1950 2112 4.870221 ACATTTCCTTTTATACGCCGTC 57.130 40.909 0.00 0.00 0.00 4.79
1951 2113 4.510571 ACATTTCCTTTTATACGCCGTCT 58.489 39.130 0.00 0.00 0.00 4.18
1952 2114 4.569564 ACATTTCCTTTTATACGCCGTCTC 59.430 41.667 0.00 0.00 0.00 3.36
1954 2116 4.460948 TTCCTTTTATACGCCGTCTCTT 57.539 40.909 0.00 0.00 0.00 2.85
1955 2117 4.460948 TCCTTTTATACGCCGTCTCTTT 57.539 40.909 0.00 0.00 0.00 2.52
1956 2118 4.427312 TCCTTTTATACGCCGTCTCTTTC 58.573 43.478 0.00 0.00 0.00 2.62
1959 2121 5.005490 CCTTTTATACGCCGTCTCTTTCTTC 59.995 44.000 0.00 0.00 0.00 2.87
1966 2128 2.072298 CCGTCTCTTTCTTCTTGGCAG 58.928 52.381 0.00 0.00 0.00 4.85
1975 2137 2.133742 CTTCTTGGCAGGGCACAACG 62.134 60.000 0.00 0.00 0.00 4.10
1992 2154 0.626916 ACGGCCTCCTCTAGAGTCTT 59.373 55.000 18.42 0.00 41.47 3.01
1993 2155 1.006162 ACGGCCTCCTCTAGAGTCTTT 59.994 52.381 18.42 0.00 41.47 2.52
1995 2157 2.498078 CGGCCTCCTCTAGAGTCTTTTT 59.502 50.000 18.42 0.00 41.47 1.94
2015 2177 2.282887 TTTTTGCGAGGGGCCTCC 60.283 61.111 0.00 0.00 42.61 4.30
2023 2185 4.215391 AGGGGCCTCCTCTAGAGT 57.785 61.111 18.42 0.00 44.06 3.24
2024 2186 1.935191 AGGGGCCTCCTCTAGAGTC 59.065 63.158 18.42 4.77 44.06 3.36
2025 2187 0.629270 AGGGGCCTCCTCTAGAGTCT 60.629 60.000 18.42 0.00 44.06 3.24
2026 2188 1.150872 GGGGCCTCCTCTAGAGTCTA 58.849 60.000 18.42 0.00 41.47 2.59
2027 2189 1.074889 GGGGCCTCCTCTAGAGTCTAG 59.925 61.905 19.55 19.55 41.47 2.43
2028 2190 1.074889 GGGCCTCCTCTAGAGTCTAGG 59.925 61.905 23.96 19.88 41.47 3.02
2029 2191 1.546998 GGCCTCCTCTAGAGTCTAGGC 60.547 61.905 31.33 31.33 41.47 3.93
2030 2192 1.144093 GCCTCCTCTAGAGTCTAGGCA 59.856 57.143 32.74 7.71 42.10 4.75
2031 2193 2.814097 GCCTCCTCTAGAGTCTAGGCAG 60.814 59.091 32.74 15.75 42.10 4.85
2032 2194 2.224769 CCTCCTCTAGAGTCTAGGCAGG 60.225 59.091 23.96 22.55 41.47 4.85
2033 2195 1.144093 TCCTCTAGAGTCTAGGCAGGC 59.856 57.143 23.96 0.00 0.00 4.85
2034 2196 1.616159 CTCTAGAGTCTAGGCAGGCC 58.384 60.000 23.96 0.97 0.00 5.19
2035 2197 0.927029 TCTAGAGTCTAGGCAGGCCA 59.073 55.000 23.96 3.19 38.92 5.36
2083 2245 3.986996 TCATGGATTTCAGCAGAGTCA 57.013 42.857 0.00 0.00 0.00 3.41
2085 2247 4.259356 TCATGGATTTCAGCAGAGTCAAG 58.741 43.478 0.00 0.00 0.00 3.02
2089 2251 5.668471 TGGATTTCAGCAGAGTCAAGATAG 58.332 41.667 0.00 0.00 0.00 2.08
2101 2263 3.636300 AGTCAAGATAGCAGCTGTAGAGG 59.364 47.826 16.64 0.00 0.00 3.69
2105 2267 0.671251 ATAGCAGCTGTAGAGGTCGC 59.329 55.000 16.64 0.00 0.00 5.19
2108 2270 1.819229 CAGCTGTAGAGGTCGCCAT 59.181 57.895 5.25 0.00 0.00 4.40
2113 2275 2.743183 GCTGTAGAGGTCGCCATGAATT 60.743 50.000 0.00 0.00 0.00 2.17
2114 2276 3.535561 CTGTAGAGGTCGCCATGAATTT 58.464 45.455 0.00 0.00 0.00 1.82
2115 2277 3.531538 TGTAGAGGTCGCCATGAATTTC 58.468 45.455 0.00 0.00 0.00 2.17
2116 2278 3.197766 TGTAGAGGTCGCCATGAATTTCT 59.802 43.478 0.00 0.00 0.00 2.52
2117 2279 2.911484 AGAGGTCGCCATGAATTTCTC 58.089 47.619 0.00 0.00 0.00 2.87
2119 2281 2.869192 GAGGTCGCCATGAATTTCTCTC 59.131 50.000 0.00 0.00 0.00 3.20
2120 2282 1.594862 GGTCGCCATGAATTTCTCTCG 59.405 52.381 0.00 0.00 0.00 4.04
2170 2337 6.126409 ACTCTTCACAATCAGTACCCAAAAA 58.874 36.000 0.00 0.00 0.00 1.94
2172 2339 6.980593 TCTTCACAATCAGTACCCAAAAATG 58.019 36.000 0.00 0.00 0.00 2.32
2190 2357 4.707030 AATGATGATGCACACGAAACAT 57.293 36.364 0.00 0.00 0.00 2.71
2191 2358 5.816449 AATGATGATGCACACGAAACATA 57.184 34.783 0.00 0.00 0.00 2.29
2195 2362 2.482336 TGATGCACACGAAACATACCAC 59.518 45.455 0.00 0.00 0.00 4.16
2233 2440 1.135046 CTGAGTCACAGCACAACTCG 58.865 55.000 0.00 0.00 41.84 4.18
2245 2452 3.630312 AGCACAACTCGGTAACAAAACAT 59.370 39.130 0.00 0.00 0.00 2.71
2247 2454 4.439776 GCACAACTCGGTAACAAAACATTC 59.560 41.667 0.00 0.00 0.00 2.67
2248 2455 5.732247 GCACAACTCGGTAACAAAACATTCT 60.732 40.000 0.00 0.00 0.00 2.40
2249 2456 6.512091 GCACAACTCGGTAACAAAACATTCTA 60.512 38.462 0.00 0.00 0.00 2.10
2387 3112 8.925161 TTGGTGATTTTAAAAGAGTGAACTTG 57.075 30.769 6.79 0.00 0.00 3.16
2388 3113 8.062065 TGGTGATTTTAAAAGAGTGAACTTGT 57.938 30.769 6.79 0.00 0.00 3.16
2390 3115 9.366216 GGTGATTTTAAAAGAGTGAACTTGTTT 57.634 29.630 6.79 0.00 0.00 2.83
2423 3148 8.547967 ACTAAAATGTGACTTGATACATTCGT 57.452 30.769 0.00 0.00 44.32 3.85
2424 3149 9.647797 ACTAAAATGTGACTTGATACATTCGTA 57.352 29.630 0.00 0.00 44.32 3.43
2431 3156 9.297586 TGTGACTTGATACATTCGTATTTAGAC 57.702 33.333 0.00 0.00 38.48 2.59
2432 3157 9.297586 GTGACTTGATACATTCGTATTTAGACA 57.702 33.333 0.00 0.00 38.48 3.41
2433 3158 9.863845 TGACTTGATACATTCGTATTTAGACAA 57.136 29.630 0.00 0.00 38.48 3.18
2454 3179 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2455 3180 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2456 3181 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2457 3182 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2458 3183 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2459 3184 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2460 3185 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2461 3186 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2462 3187 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2463 3188 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2464 3189 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2469 3194 0.613853 TTGGGACGGAGGGAGTACTG 60.614 60.000 0.00 0.00 0.00 2.74
2521 3246 1.089920 GCTCACGTGAATCCAAGCAT 58.910 50.000 20.49 0.00 0.00 3.79
2522 3247 1.063174 GCTCACGTGAATCCAAGCATC 59.937 52.381 20.49 0.00 0.00 3.91
2570 3295 4.399303 CACAGGGGCTACAGGATTAAAAAG 59.601 45.833 0.00 0.00 0.00 2.27
2579 3304 8.352942 GGCTACAGGATTAAAAAGAACATATGG 58.647 37.037 7.80 0.00 0.00 2.74
2627 3352 4.318618 GCACACGATATGCAGATTCAGAAG 60.319 45.833 0.00 0.00 42.88 2.85
2693 3418 2.363680 ACAATCATCTCGGGTCAGCTAG 59.636 50.000 0.00 0.00 0.00 3.42
2694 3419 2.625314 CAATCATCTCGGGTCAGCTAGA 59.375 50.000 0.00 0.00 0.00 2.43
2715 3440 8.821894 GCTAGAATCAAGGACTAACAACAATAG 58.178 37.037 0.00 0.00 0.00 1.73
2716 3441 7.617041 AGAATCAAGGACTAACAACAATAGC 57.383 36.000 0.00 0.00 0.00 2.97
2731 3456 8.587952 ACAACAATAGCAAAACAAAATACTCC 57.412 30.769 0.00 0.00 0.00 3.85
2750 3475 1.263217 CCTAACACACGTTGCTCCAAC 59.737 52.381 0.00 0.00 40.54 3.77
2783 3509 9.092876 GCACTAATAATGTCTGATAGATAAGCC 57.907 37.037 0.00 0.00 0.00 4.35
2952 3678 2.635915 AGGACCAGTTACCACGAATGAA 59.364 45.455 0.00 0.00 0.00 2.57
3097 3830 2.884639 CCTTTCGGTCAGAAAACCATGT 59.115 45.455 0.00 0.00 46.98 3.21
3206 3940 3.764160 GATCCTGCCCTCCTTGCCG 62.764 68.421 0.00 0.00 0.00 5.69
3297 4032 6.364976 GGCATACAAGTTATTGGTGTCAAAAC 59.635 38.462 0.00 0.00 40.97 2.43
3547 4285 2.103432 TGTGCCTGACCTTTTTAGACGA 59.897 45.455 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.356751 TGCCTGAAATAAAACATAGCGTGAT 59.643 36.000 0.00 0.00 0.00 3.06
18 19 7.605691 CCCAACAATTGCCTGAAATAAAACATA 59.394 33.333 5.05 0.00 0.00 2.29
68 69 3.686016 GGTCAGGAAATTGAACCAGCTA 58.314 45.455 0.00 0.00 0.00 3.32
80 81 6.005198 ACCAATGTAAATAACGGTCAGGAAA 58.995 36.000 0.00 0.00 0.00 3.13
109 110 8.281529 AGGGGAGAGAAATAAATGTTATAGCT 57.718 34.615 0.00 0.00 0.00 3.32
110 111 8.926092 AAGGGGAGAGAAATAAATGTTATAGC 57.074 34.615 0.00 0.00 0.00 2.97
159 170 3.120304 GCTTTCGCGAAATAGGAACAGTT 60.120 43.478 32.28 0.00 0.00 3.16
191 202 3.061322 TGTTTTCATCAATGCAAGCAGC 58.939 40.909 0.00 0.00 45.96 5.25
192 203 4.508492 TGTTGTTTTCATCAATGCAAGCAG 59.492 37.500 0.00 0.00 28.09 4.24
193 204 4.270566 GTGTTGTTTTCATCAATGCAAGCA 59.729 37.500 0.00 0.00 32.31 3.91
194 205 4.318974 GGTGTTGTTTTCATCAATGCAAGC 60.319 41.667 0.00 0.00 32.31 4.01
199 210 4.947645 ACCAGGTGTTGTTTTCATCAATG 58.052 39.130 0.00 0.00 32.31 2.82
203 214 4.033932 GCAAAACCAGGTGTTGTTTTCATC 59.966 41.667 21.79 1.83 41.40 2.92
210 221 0.823460 CAGGCAAAACCAGGTGTTGT 59.177 50.000 21.79 2.25 43.14 3.32
213 224 0.032615 TTCCAGGCAAAACCAGGTGT 60.033 50.000 0.00 0.00 45.46 4.16
214 225 0.389025 GTTCCAGGCAAAACCAGGTG 59.611 55.000 0.00 0.00 45.46 4.00
215 226 0.032615 TGTTCCAGGCAAAACCAGGT 60.033 50.000 0.00 0.00 45.46 4.00
216 227 0.675633 CTGTTCCAGGCAAAACCAGG 59.324 55.000 0.00 0.00 46.66 4.45
267 278 3.005554 CTGGTCCTCGTACTTCTCGTAA 58.994 50.000 0.00 0.00 0.00 3.18
327 338 1.891150 TCGAGTTTCTGGTACTGGTCC 59.109 52.381 0.00 0.00 0.00 4.46
330 341 2.927014 GCTGTCGAGTTTCTGGTACTGG 60.927 54.545 0.00 0.00 0.00 4.00
393 404 7.237471 TCCATCTGATCTGATCTAGTCTACTCT 59.763 40.741 17.82 0.00 0.00 3.24
401 412 5.769162 TGAGTGTCCATCTGATCTGATCTAG 59.231 44.000 17.82 13.09 0.00 2.43
448 471 6.719365 CACACAAACTAGGCAGAATAATAGC 58.281 40.000 0.00 0.00 0.00 2.97
449 472 6.540189 AGCACACAAACTAGGCAGAATAATAG 59.460 38.462 0.00 0.00 0.00 1.73
450 473 6.316140 CAGCACACAAACTAGGCAGAATAATA 59.684 38.462 0.00 0.00 0.00 0.98
451 474 5.124457 CAGCACACAAACTAGGCAGAATAAT 59.876 40.000 0.00 0.00 0.00 1.28
452 475 4.455533 CAGCACACAAACTAGGCAGAATAA 59.544 41.667 0.00 0.00 0.00 1.40
453 476 4.002982 CAGCACACAAACTAGGCAGAATA 58.997 43.478 0.00 0.00 0.00 1.75
454 477 2.816087 CAGCACACAAACTAGGCAGAAT 59.184 45.455 0.00 0.00 0.00 2.40
455 478 2.221169 CAGCACACAAACTAGGCAGAA 58.779 47.619 0.00 0.00 0.00 3.02
479 502 3.997021 GACAATTGAGACACACTACAGGG 59.003 47.826 13.59 0.00 0.00 4.45
497 520 4.492791 CACAAATGCTCTCACATGACAA 57.507 40.909 0.00 0.00 0.00 3.18
514 537 4.481195 GGAAGCACCTGAGCACAA 57.519 55.556 0.00 0.00 36.85 3.33
523 546 1.239347 GGTTCTGTTCAGGAAGCACC 58.761 55.000 0.00 0.00 39.88 5.01
630 656 7.182817 ACTTCCAGTATATGCAGACAACTTA 57.817 36.000 0.00 0.00 0.00 2.24
647 673 3.499918 ACGAATTTGAGCTCAACTTCCAG 59.500 43.478 35.13 28.35 40.33 3.86
703 749 1.466950 TCGCGATCACAAATTTGGACC 59.533 47.619 21.74 6.99 0.00 4.46
715 761 3.002862 CCCCGAAAATAAAATCGCGATCA 59.997 43.478 23.92 11.22 37.73 2.92
736 785 5.689564 ACAGAATGGATGTGGATCTCAATCC 60.690 44.000 11.78 11.78 46.62 3.01
742 791 3.117745 TGGACAGAATGGATGTGGATCT 58.882 45.455 0.00 0.00 43.62 2.75
752 801 1.559368 TTTGGGCATGGACAGAATGG 58.441 50.000 0.00 0.00 43.62 3.16
775 824 5.221224 ACCAGATTTTTCGACAGAATGCAAA 60.221 36.000 0.00 0.00 42.53 3.68
792 841 1.425066 TCTGCACCCTTTGACCAGATT 59.575 47.619 0.00 0.00 0.00 2.40
833 882 1.073897 AACCTGGGTCAGCTTCTGC 59.926 57.895 0.00 0.00 40.05 4.26
840 889 4.204012 TGAAAACTAACAACCTGGGTCAG 58.796 43.478 0.00 0.00 0.00 3.51
848 897 3.697542 ACACCACCTGAAAACTAACAACC 59.302 43.478 0.00 0.00 0.00 3.77
931 980 1.372087 CTGCCCTGCACTCCGATTTC 61.372 60.000 0.00 0.00 33.79 2.17
986 1036 7.307811 GCAGGTTTTATAGCGAGGTAATTTAGG 60.308 40.741 0.00 0.00 0.00 2.69
988 1038 7.486802 GCAGGTTTTATAGCGAGGTAATTTA 57.513 36.000 0.00 0.00 0.00 1.40
1013 1063 1.599576 GAGGAGAGGAGTGGGCAAC 59.400 63.158 0.00 0.00 0.00 4.17
1014 1064 1.613630 GGAGGAGAGGAGTGGGCAA 60.614 63.158 0.00 0.00 0.00 4.52
1022 1072 1.149782 AGGTGGTGAGGAGGAGAGGA 61.150 60.000 0.00 0.00 0.00 3.71
1024 1074 1.034838 CGAGGTGGTGAGGAGGAGAG 61.035 65.000 0.00 0.00 0.00 3.20
1049 1099 0.676151 CTGGCTCCTTGGCTGTTCTC 60.676 60.000 0.00 0.00 42.34 2.87
1405 1472 2.998279 GCCACCACTTCATGCTGCC 61.998 63.158 0.00 0.00 0.00 4.85
1557 1624 3.211865 CATAGGCATAGGCATAGGCATG 58.788 50.000 17.33 8.95 39.97 4.06
1558 1625 3.572632 CATAGGCATAGGCATAGGCAT 57.427 47.619 17.33 12.60 39.97 4.40
1562 1629 2.421107 CCTGGCATAGGCATAGGCATAG 60.421 54.545 17.33 13.33 39.97 2.23
1563 1630 1.561076 CCTGGCATAGGCATAGGCATA 59.439 52.381 17.33 0.00 40.47 3.14
1720 1862 4.280019 GGGGTTGGGGTTGTCGCT 62.280 66.667 0.00 0.00 0.00 4.93
1742 1884 2.362369 CCTCGTCAGTGGATGGCCT 61.362 63.158 3.32 0.00 32.98 5.19
1757 1899 1.625818 TGCCACTTCTTCTCCTTCCTC 59.374 52.381 0.00 0.00 0.00 3.71
1766 1908 0.310854 CCGGTGTTTGCCACTTCTTC 59.689 55.000 0.00 0.00 43.94 2.87
1767 1909 1.734388 GCCGGTGTTTGCCACTTCTT 61.734 55.000 1.90 0.00 43.94 2.52
1768 1910 2.193536 GCCGGTGTTTGCCACTTCT 61.194 57.895 1.90 0.00 43.94 2.85
1769 1911 1.805428 ATGCCGGTGTTTGCCACTTC 61.805 55.000 1.90 0.00 43.94 3.01
1770 1912 1.805428 GATGCCGGTGTTTGCCACTT 61.805 55.000 1.90 0.00 43.94 3.16
1771 1913 2.203480 ATGCCGGTGTTTGCCACT 60.203 55.556 1.90 0.00 43.94 4.00
1772 1914 2.081425 TTGATGCCGGTGTTTGCCAC 62.081 55.000 1.90 0.00 43.74 5.01
1773 1915 1.184322 ATTGATGCCGGTGTTTGCCA 61.184 50.000 1.90 0.00 0.00 4.92
1774 1916 0.458370 GATTGATGCCGGTGTTTGCC 60.458 55.000 1.90 0.00 0.00 4.52
1775 1917 0.243365 TGATTGATGCCGGTGTTTGC 59.757 50.000 1.90 0.00 0.00 3.68
1776 1918 1.402720 GGTGATTGATGCCGGTGTTTG 60.403 52.381 1.90 0.00 0.00 2.93
1782 1926 1.097547 GGTCAGGTGATTGATGCCGG 61.098 60.000 0.00 0.00 0.00 6.13
1783 1927 0.107508 AGGTCAGGTGATTGATGCCG 60.108 55.000 0.00 0.00 0.00 5.69
1805 1949 2.520465 CTACACCCTGCGCCATGACA 62.520 60.000 4.18 0.00 0.00 3.58
1806 1950 1.815421 CTACACCCTGCGCCATGAC 60.815 63.158 4.18 0.00 0.00 3.06
1807 1951 2.584064 CTACACCCTGCGCCATGA 59.416 61.111 4.18 0.00 0.00 3.07
1809 1953 4.489771 GGCTACACCCTGCGCCAT 62.490 66.667 4.18 0.00 37.26 4.40
1819 1963 4.781934 AGTAAAATGATCCTGGGCTACAC 58.218 43.478 0.00 0.00 0.00 2.90
1820 1964 5.454755 GCTAGTAAAATGATCCTGGGCTACA 60.455 44.000 0.00 0.00 0.00 2.74
1821 1965 4.998033 GCTAGTAAAATGATCCTGGGCTAC 59.002 45.833 0.00 0.00 0.00 3.58
1822 1966 4.658435 TGCTAGTAAAATGATCCTGGGCTA 59.342 41.667 0.00 0.00 0.00 3.93
1830 1976 6.546395 CAGTGGTGTTGCTAGTAAAATGATC 58.454 40.000 0.00 0.00 0.00 2.92
1834 1980 4.766404 GCAGTGGTGTTGCTAGTAAAAT 57.234 40.909 0.00 0.00 38.51 1.82
1860 2022 7.336931 GGAGTAATTTTTCTAAGAGTCATGGCA 59.663 37.037 0.00 0.00 0.00 4.92
1861 2023 7.336931 TGGAGTAATTTTTCTAAGAGTCATGGC 59.663 37.037 0.00 0.00 0.00 4.40
1862 2024 8.669243 GTGGAGTAATTTTTCTAAGAGTCATGG 58.331 37.037 0.00 0.00 0.00 3.66
1864 2026 9.220767 GTGTGGAGTAATTTTTCTAAGAGTCAT 57.779 33.333 0.00 0.00 0.00 3.06
1865 2027 8.208224 TGTGTGGAGTAATTTTTCTAAGAGTCA 58.792 33.333 0.00 0.00 0.00 3.41
1866 2028 8.603242 TGTGTGGAGTAATTTTTCTAAGAGTC 57.397 34.615 0.00 0.00 0.00 3.36
1867 2029 8.429641 TCTGTGTGGAGTAATTTTTCTAAGAGT 58.570 33.333 0.00 0.00 0.00 3.24
1868 2030 8.833231 TCTGTGTGGAGTAATTTTTCTAAGAG 57.167 34.615 0.00 0.00 0.00 2.85
1869 2031 9.273016 CTTCTGTGTGGAGTAATTTTTCTAAGA 57.727 33.333 0.00 0.00 0.00 2.10
1873 2035 5.827797 TGCTTCTGTGTGGAGTAATTTTTCT 59.172 36.000 0.00 0.00 0.00 2.52
1882 2044 2.171448 AGTTTCTGCTTCTGTGTGGAGT 59.829 45.455 0.00 0.00 0.00 3.85
1888 2050 4.096984 ACTTTGGAAGTTTCTGCTTCTGTG 59.903 41.667 5.90 0.00 43.13 3.66
1899 2061 9.447157 TCATTTTGAATTTGACTTTGGAAGTTT 57.553 25.926 0.00 0.00 43.03 2.66
1901 2063 9.048446 CATCATTTTGAATTTGACTTTGGAAGT 57.952 29.630 0.00 0.00 46.38 3.01
1902 2064 9.263538 TCATCATTTTGAATTTGACTTTGGAAG 57.736 29.630 0.00 0.00 0.00 3.46
1903 2065 9.610705 TTCATCATTTTGAATTTGACTTTGGAA 57.389 25.926 0.00 0.00 30.82 3.53
1904 2066 9.044150 GTTCATCATTTTGAATTTGACTTTGGA 57.956 29.630 0.00 0.00 37.88 3.53
1905 2067 8.828644 TGTTCATCATTTTGAATTTGACTTTGG 58.171 29.630 0.00 0.00 37.88 3.28
1932 2094 4.460948 AGAGACGGCGTATAAAAGGAAA 57.539 40.909 14.74 0.00 0.00 3.13
1936 2098 5.805994 AGAAGAAAGAGACGGCGTATAAAAG 59.194 40.000 14.74 0.00 0.00 2.27
1943 2105 1.605712 CCAAGAAGAAAGAGACGGCGT 60.606 52.381 14.65 14.65 0.00 5.68
1950 2112 1.172175 GCCCTGCCAAGAAGAAAGAG 58.828 55.000 0.00 0.00 0.00 2.85
1951 2113 0.478072 TGCCCTGCCAAGAAGAAAGA 59.522 50.000 0.00 0.00 0.00 2.52
1952 2114 0.600057 GTGCCCTGCCAAGAAGAAAG 59.400 55.000 0.00 0.00 0.00 2.62
1954 2116 0.106268 TTGTGCCCTGCCAAGAAGAA 60.106 50.000 0.00 0.00 0.00 2.52
1955 2117 0.823356 GTTGTGCCCTGCCAAGAAGA 60.823 55.000 0.00 0.00 0.00 2.87
1956 2118 1.662044 GTTGTGCCCTGCCAAGAAG 59.338 57.895 0.00 0.00 0.00 2.85
1959 2121 3.673484 CCGTTGTGCCCTGCCAAG 61.673 66.667 0.00 0.00 0.00 3.61
1998 2160 2.282887 GGAGGCCCCTCGCAAAAA 60.283 61.111 0.00 0.00 43.59 1.94
1999 2161 3.256960 AGGAGGCCCCTCGCAAAA 61.257 61.111 0.00 0.00 43.31 2.44
2007 2169 4.611119 GACTCTAGAGGAGGCCCC 57.389 66.667 23.50 0.00 44.14 5.80
2011 2173 2.224769 CCTGCCTAGACTCTAGAGGAGG 60.225 59.091 23.50 23.58 45.83 4.30
2012 2174 2.814097 GCCTGCCTAGACTCTAGAGGAG 60.814 59.091 23.50 16.04 46.87 3.69
2013 2175 1.144093 GCCTGCCTAGACTCTAGAGGA 59.856 57.143 23.50 7.78 31.45 3.71
2014 2176 1.616159 GCCTGCCTAGACTCTAGAGG 58.384 60.000 23.50 13.57 0.00 3.69
2015 2177 1.133637 TGGCCTGCCTAGACTCTAGAG 60.134 57.143 18.49 18.49 36.94 2.43
2016 2178 0.927029 TGGCCTGCCTAGACTCTAGA 59.073 55.000 13.90 0.00 36.94 2.43
2017 2179 2.008242 ATGGCCTGCCTAGACTCTAG 57.992 55.000 9.97 6.14 36.94 2.43
2018 2180 2.435805 CAAATGGCCTGCCTAGACTCTA 59.564 50.000 9.97 0.00 36.94 2.43
2019 2181 1.211457 CAAATGGCCTGCCTAGACTCT 59.789 52.381 9.97 0.00 36.94 3.24
2020 2182 1.673168 CAAATGGCCTGCCTAGACTC 58.327 55.000 9.97 0.00 36.94 3.36
2021 2183 0.394899 GCAAATGGCCTGCCTAGACT 60.395 55.000 9.97 0.00 36.11 3.24
2022 2184 2.110296 GCAAATGGCCTGCCTAGAC 58.890 57.895 9.97 0.00 36.11 2.59
2023 2185 4.664062 GCAAATGGCCTGCCTAGA 57.336 55.556 9.97 0.00 36.11 2.43
2032 2194 4.796314 TTGGCAAAGGCAAATGGC 57.204 50.000 0.00 0.00 44.79 4.40
2063 2225 3.986996 TGACTCTGCTGAAATCCATGA 57.013 42.857 0.00 0.00 0.00 3.07
2071 2233 3.678252 GCTGCTATCTTGACTCTGCTGAA 60.678 47.826 0.00 0.00 0.00 3.02
2075 2237 2.203401 CAGCTGCTATCTTGACTCTGC 58.797 52.381 0.00 0.00 0.00 4.26
2076 2238 3.523606 ACAGCTGCTATCTTGACTCTG 57.476 47.619 15.27 0.00 0.00 3.35
2079 2241 3.636300 CCTCTACAGCTGCTATCTTGACT 59.364 47.826 15.27 0.00 0.00 3.41
2083 2245 2.621055 CGACCTCTACAGCTGCTATCTT 59.379 50.000 15.27 0.00 0.00 2.40
2085 2247 1.335506 GCGACCTCTACAGCTGCTATC 60.336 57.143 15.27 2.34 0.00 2.08
2089 2251 2.202810 GGCGACCTCTACAGCTGC 60.203 66.667 15.27 0.00 0.00 5.25
2101 2263 2.271800 ACGAGAGAAATTCATGGCGAC 58.728 47.619 0.00 0.00 0.00 5.19
2105 2267 6.758416 TCAGTGATAACGAGAGAAATTCATGG 59.242 38.462 0.00 0.00 0.00 3.66
2108 2270 6.100004 GGTCAGTGATAACGAGAGAAATTCA 58.900 40.000 0.00 0.00 0.00 2.57
2113 2275 3.427573 TGGGTCAGTGATAACGAGAGAA 58.572 45.455 0.00 0.00 0.00 2.87
2114 2276 3.081710 TGGGTCAGTGATAACGAGAGA 57.918 47.619 0.00 0.00 0.00 3.10
2115 2277 3.512680 GTTGGGTCAGTGATAACGAGAG 58.487 50.000 0.00 0.00 0.00 3.20
2116 2278 2.094906 CGTTGGGTCAGTGATAACGAGA 60.095 50.000 24.00 0.00 44.76 4.04
2117 2279 2.094906 TCGTTGGGTCAGTGATAACGAG 60.095 50.000 25.57 10.38 45.32 4.18
2119 2281 1.990563 GTCGTTGGGTCAGTGATAACG 59.009 52.381 23.08 23.08 43.73 3.18
2120 2282 3.251571 GAGTCGTTGGGTCAGTGATAAC 58.748 50.000 0.00 2.19 0.00 1.89
2170 2337 4.035558 GGTATGTTTCGTGTGCATCATCAT 59.964 41.667 0.00 0.00 0.00 2.45
2172 2339 3.373748 TGGTATGTTTCGTGTGCATCATC 59.626 43.478 0.00 0.00 0.00 2.92
2190 2357 1.371183 GTGGCTGAGCAGTGTGGTA 59.629 57.895 6.82 0.00 0.00 3.25
2191 2358 2.111878 GTGGCTGAGCAGTGTGGT 59.888 61.111 6.82 0.00 0.00 4.16
2195 2362 1.526686 TTGTGGTGGCTGAGCAGTG 60.527 57.895 6.82 0.00 30.97 3.66
2229 2436 8.441312 TTCTTTAGAATGTTTTGTTACCGAGT 57.559 30.769 0.00 0.00 0.00 4.18
2245 2452 7.148639 GCTCACGTGTCATTGTATTCTTTAGAA 60.149 37.037 16.51 0.00 38.56 2.10
2247 2454 6.311445 AGCTCACGTGTCATTGTATTCTTTAG 59.689 38.462 16.51 0.29 0.00 1.85
2248 2455 6.163476 AGCTCACGTGTCATTGTATTCTTTA 58.837 36.000 16.51 0.00 0.00 1.85
2249 2456 4.997395 AGCTCACGTGTCATTGTATTCTTT 59.003 37.500 16.51 0.00 0.00 2.52
2327 3051 3.008485 TGTGTAGCCCATGTGTCAATGTA 59.992 43.478 0.00 0.00 0.00 2.29
2397 3122 9.647797 ACGAATGTATCAAGTCACATTTTAGTA 57.352 29.630 1.86 0.00 43.58 1.82
2398 3123 8.547967 ACGAATGTATCAAGTCACATTTTAGT 57.452 30.769 1.86 1.50 43.58 2.24
2405 3130 9.297586 GTCTAAATACGAATGTATCAAGTCACA 57.702 33.333 0.00 0.00 40.42 3.58
2406 3131 9.297586 TGTCTAAATACGAATGTATCAAGTCAC 57.702 33.333 0.00 0.00 40.42 3.67
2407 3132 9.863845 TTGTCTAAATACGAATGTATCAAGTCA 57.136 29.630 0.00 0.00 40.42 3.41
2428 3153 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2429 3154 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2430 3155 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2431 3156 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2432 3157 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2433 3158 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2434 3159 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2435 3160 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2436 3161 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2437 3162 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2438 3163 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2439 3164 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2440 3165 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2441 3166 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2442 3167 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2443 3168 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2444 3169 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2445 3170 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2446 3171 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2447 3172 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2448 3173 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2449 3174 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
2450 3175 0.613853 CAGTACTCCCTCCGTCCCAA 60.614 60.000 0.00 0.00 0.00 4.12
2451 3176 1.000019 CAGTACTCCCTCCGTCCCA 60.000 63.158 0.00 0.00 0.00 4.37
2452 3177 0.257039 TACAGTACTCCCTCCGTCCC 59.743 60.000 0.00 0.00 0.00 4.46
2453 3178 2.361643 ATACAGTACTCCCTCCGTCC 57.638 55.000 0.00 0.00 0.00 4.79
2454 3179 5.126061 TGTTTTATACAGTACTCCCTCCGTC 59.874 44.000 0.00 0.00 31.68 4.79
2455 3180 5.018809 TGTTTTATACAGTACTCCCTCCGT 58.981 41.667 0.00 0.00 31.68 4.69
2456 3181 5.587388 TGTTTTATACAGTACTCCCTCCG 57.413 43.478 0.00 0.00 31.68 4.63
2457 3182 8.044908 TCATTTGTTTTATACAGTACTCCCTCC 58.955 37.037 0.00 0.00 38.19 4.30
2458 3183 9.614792 ATCATTTGTTTTATACAGTACTCCCTC 57.385 33.333 0.00 0.00 38.19 4.30
2459 3184 9.975218 AATCATTTGTTTTATACAGTACTCCCT 57.025 29.630 0.00 0.00 38.19 4.20
2513 3238 0.958091 CCGGTGTTTTGATGCTTGGA 59.042 50.000 0.00 0.00 0.00 3.53
2521 3246 1.021202 CAGCTTGTCCGGTGTTTTGA 58.979 50.000 0.00 0.00 0.00 2.69
2522 3247 0.594796 GCAGCTTGTCCGGTGTTTTG 60.595 55.000 0.00 0.00 34.99 2.44
2570 3295 7.534239 GTCGTCTTTTCTTTTGTCCATATGTTC 59.466 37.037 1.24 0.00 0.00 3.18
2604 3329 3.126073 TCTGAATCTGCATATCGTGTGC 58.874 45.455 0.00 3.19 42.81 4.57
2605 3330 5.045872 TCTTCTGAATCTGCATATCGTGTG 58.954 41.667 0.00 0.00 0.00 3.82
2606 3331 5.268118 TCTTCTGAATCTGCATATCGTGT 57.732 39.130 0.00 0.00 0.00 4.49
2638 3363 4.014406 GGTTTAAGTCTGGTTACCATGGG 58.986 47.826 18.09 0.00 30.82 4.00
2693 3418 7.377766 TGCTATTGTTGTTAGTCCTTGATTC 57.622 36.000 0.00 0.00 0.00 2.52
2694 3419 7.759489 TTGCTATTGTTGTTAGTCCTTGATT 57.241 32.000 0.00 0.00 0.00 2.57
2715 3440 6.141685 CGTGTGTTAGGAGTATTTTGTTTTGC 59.858 38.462 0.00 0.00 0.00 3.68
2716 3441 7.190871 ACGTGTGTTAGGAGTATTTTGTTTTG 58.809 34.615 0.00 0.00 0.00 2.44
2731 3456 1.937223 TGTTGGAGCAACGTGTGTTAG 59.063 47.619 0.00 0.00 46.13 2.34
2750 3475 9.803130 CTATCAGACATTATTAGTGCGAAATTG 57.197 33.333 0.00 0.00 0.00 2.32
2783 3509 2.229675 TCTGCATCTGTATTGAGGCG 57.770 50.000 0.00 0.00 45.37 5.52
2897 3623 0.816825 GGTGCACCTGATGATCGCAT 60.817 55.000 29.12 0.00 37.47 4.73
2945 3671 2.205074 ACGCAGAAGGCTATTCATTCG 58.795 47.619 0.00 6.95 40.19 3.34
2952 3678 4.141937 TGAGTGAATAACGCAGAAGGCTAT 60.142 41.667 0.00 0.00 41.67 2.97
3097 3830 5.071250 ACCTATTTGCCACACTAATCCGATA 59.929 40.000 0.00 0.00 0.00 2.92
3206 3940 6.422776 AATGTGACGAATAATCCAGTTGAC 57.577 37.500 0.00 0.00 0.00 3.18
3297 4032 5.615925 AACAACTATACTTCCTGCCCTAG 57.384 43.478 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.