Multiple sequence alignment - TraesCS2A01G590700

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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 TraesCS2A01G590700 chr2A 100.000 2690 0 0 1 2690 778759047 778761736 0.000000e+00 4968.0
1 TraesCS2A01G590700 chr2A 88.874 746 33 24 1187 1925 778789150 778789852 0.000000e+00 872.0
2 TraesCS2A01G590700 chr2A 80.169 1185 112 54 785 1897 778876133 778877266 0.000000e+00 773.0
3 TraesCS2A01G590700 chr2A 80.855 1076 99 53 775 1767 778914506 778915557 0.000000e+00 747.0
4 TraesCS2A01G590700 chr2A 83.089 751 77 31 1182 1912 778827501 778828221 2.920000e-179 638.0
5 TraesCS2A01G590700 chr2A 82.617 512 79 9 2184 2690 734108035 734107529 6.830000e-121 444.0
6 TraesCS2A01G590700 chr2A 83.333 306 25 17 756 1036 778827030 778827334 2.660000e-65 259.0
7 TraesCS2A01G590700 chr2A 79.725 291 24 18 766 1037 778788655 778788929 7.650000e-41 178.0
8 TraesCS2A01G590700 chr2A 86.667 75 7 2 756 830 778814253 778814324 2.220000e-11 80.5
9 TraesCS2A01G590700 chr2B 86.015 1852 112 57 1 1812 777659868 777658124 0.000000e+00 1849.0
10 TraesCS2A01G590700 chr2B 88.196 754 33 19 682 1409 777635485 777634762 0.000000e+00 848.0
11 TraesCS2A01G590700 chr2B 78.956 1245 116 66 766 1927 777619154 777617973 0.000000e+00 713.0
12 TraesCS2A01G590700 chr2B 85.417 720 58 22 1089 1774 777549395 777548689 0.000000e+00 704.0
13 TraesCS2A01G590700 chr2B 82.042 813 86 38 756 1531 777522176 777521387 2.920000e-179 638.0
14 TraesCS2A01G590700 chr2B 91.908 346 26 1 1405 1750 777634018 777633675 1.450000e-132 483.0
15 TraesCS2A01G590700 chr2B 89.779 362 29 4 263 619 777642962 777642604 8.780000e-125 457.0
16 TraesCS2A01G590700 chr2B 88.608 237 11 2 1 233 777643248 777643024 9.490000e-70 274.0
17 TraesCS2A01G590700 chr2B 88.235 102 4 1 1828 1921 777657845 777657744 6.090000e-22 115.0
18 TraesCS2A01G590700 chr2B 79.747 158 31 1 2030 2187 157690662 157690818 2.190000e-21 113.0
19 TraesCS2A01G590700 chr2B 95.082 61 3 0 629 689 777635559 777635499 2.200000e-16 97.1
20 TraesCS2A01G590700 chr2D 88.291 1580 80 41 421 1914 634659444 634657884 0.000000e+00 1796.0
21 TraesCS2A01G590700 chr2D 81.752 1107 87 57 756 1762 634482709 634481618 0.000000e+00 819.0
22 TraesCS2A01G590700 chr2D 89.597 596 40 9 1181 1760 634575292 634574703 0.000000e+00 737.0
23 TraesCS2A01G590700 chr2D 83.757 511 73 9 2185 2690 88404332 88403827 2.420000e-130 475.0
24 TraesCS2A01G590700 chr2D 82.812 512 79 8 2184 2690 192667653 192667146 1.470000e-122 449.0
25 TraesCS2A01G590700 chr2D 96.528 144 2 1 50 193 634659742 634659602 4.480000e-58 235.0
26 TraesCS2A01G590700 chr2D 83.516 182 14 10 520 696 634576023 634575853 3.590000e-34 156.0
27 TraesCS2A01G590700 chr2D 85.430 151 15 3 85 233 634576532 634576387 1.670000e-32 150.0
28 TraesCS2A01G590700 chr2D 81.481 189 27 8 875 1061 634556666 634556484 6.000000e-32 148.0
29 TraesCS2A01G590700 chr2D 95.294 85 4 0 230 314 634659526 634659442 4.670000e-28 135.0
30 TraesCS2A01G590700 chr2D 74.336 339 41 22 392 696 634483149 634482823 4.740000e-18 102.0
31 TraesCS2A01G590700 chr5A 83.789 512 73 8 2184 2690 79208263 79207757 6.740000e-131 477.0
32 TraesCS2A01G590700 chr6D 83.730 504 76 5 2189 2690 382794686 382795185 3.130000e-129 472.0
33 TraesCS2A01G590700 chr6D 82.779 511 83 4 2182 2690 433361714 433362221 4.080000e-123 451.0
34 TraesCS2A01G590700 chr6D 81.757 148 25 2 2030 2176 468881204 468881058 3.640000e-24 122.0
35 TraesCS2A01G590700 chr6D 78.689 183 34 4 1989 2170 1426233 1426411 1.690000e-22 117.0
36 TraesCS2A01G590700 chr6D 82.400 125 20 2 2073 2196 411925021 411924898 1.020000e-19 108.0
37 TraesCS2A01G590700 chr3D 83.562 511 76 7 2184 2690 409031493 409031999 3.130000e-129 472.0
38 TraesCS2A01G590700 chr5D 83.600 500 77 4 2193 2690 564225004 564224508 5.250000e-127 464.0
39 TraesCS2A01G590700 chr5D 78.571 182 37 2 2016 2196 344835301 344835121 4.700000e-23 119.0
40 TraesCS2A01G590700 chr1A 82.937 504 78 8 2184 2683 580150529 580150030 5.280000e-122 448.0
41 TraesCS2A01G590700 chr7D 80.952 147 24 3 2043 2189 628535636 628535778 2.190000e-21 113.0
42 TraesCS2A01G590700 chr7A 80.000 155 29 2 2042 2196 207895557 207895405 2.190000e-21 113.0
43 TraesCS2A01G590700 chr7B 77.778 189 32 9 1989 2174 490890928 490891109 1.020000e-19 108.0
44 TraesCS2A01G590700 chr4B 73.163 313 58 16 1935 2241 357954266 357953974 3.690000e-14 89.8
45 TraesCS2A01G590700 chr4B 77.070 157 33 3 2041 2196 57804588 57804742 1.330000e-13 87.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G590700 chr2A 778759047 778761736 2689 False 4968.000000 4968 100.000000 1 2690 1 chr2A.!!$F1 2689
1 TraesCS2A01G590700 chr2A 778876133 778877266 1133 False 773.000000 773 80.169000 785 1897 1 chr2A.!!$F3 1112
2 TraesCS2A01G590700 chr2A 778914506 778915557 1051 False 747.000000 747 80.855000 775 1767 1 chr2A.!!$F4 992
3 TraesCS2A01G590700 chr2A 778788655 778789852 1197 False 525.000000 872 84.299500 766 1925 2 chr2A.!!$F5 1159
4 TraesCS2A01G590700 chr2A 778827030 778828221 1191 False 448.500000 638 83.211000 756 1912 2 chr2A.!!$F6 1156
5 TraesCS2A01G590700 chr2A 734107529 734108035 506 True 444.000000 444 82.617000 2184 2690 1 chr2A.!!$R1 506
6 TraesCS2A01G590700 chr2B 777657744 777659868 2124 True 982.000000 1849 87.125000 1 1921 2 chr2B.!!$R6 1920
7 TraesCS2A01G590700 chr2B 777617973 777619154 1181 True 713.000000 713 78.956000 766 1927 1 chr2B.!!$R3 1161
8 TraesCS2A01G590700 chr2B 777548689 777549395 706 True 704.000000 704 85.417000 1089 1774 1 chr2B.!!$R2 685
9 TraesCS2A01G590700 chr2B 777521387 777522176 789 True 638.000000 638 82.042000 756 1531 1 chr2B.!!$R1 775
10 TraesCS2A01G590700 chr2B 777633675 777635559 1884 True 476.033333 848 91.728667 629 1750 3 chr2B.!!$R4 1121
11 TraesCS2A01G590700 chr2B 777642604 777643248 644 True 365.500000 457 89.193500 1 619 2 chr2B.!!$R5 618
12 TraesCS2A01G590700 chr2D 634657884 634659742 1858 True 722.000000 1796 93.371000 50 1914 3 chr2D.!!$R6 1864
13 TraesCS2A01G590700 chr2D 88403827 88404332 505 True 475.000000 475 83.757000 2185 2690 1 chr2D.!!$R1 505
14 TraesCS2A01G590700 chr2D 634481618 634483149 1531 True 460.500000 819 78.044000 392 1762 2 chr2D.!!$R4 1370
15 TraesCS2A01G590700 chr2D 192667146 192667653 507 True 449.000000 449 82.812000 2184 2690 1 chr2D.!!$R2 506
16 TraesCS2A01G590700 chr2D 634574703 634576532 1829 True 347.666667 737 86.181000 85 1760 3 chr2D.!!$R5 1675
17 TraesCS2A01G590700 chr5A 79207757 79208263 506 True 477.000000 477 83.789000 2184 2690 1 chr5A.!!$R1 506
18 TraesCS2A01G590700 chr6D 433361714 433362221 507 False 451.000000 451 82.779000 2182 2690 1 chr6D.!!$F3 508
19 TraesCS2A01G590700 chr3D 409031493 409031999 506 False 472.000000 472 83.562000 2184 2690 1 chr3D.!!$F1 506

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
134 141 0.174617 CCCTTTGTCCTCTCTCTCGC 59.825 60.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 3592 0.036294 GAGACCCGTTTAAGCAGGCT 60.036 55.0 0.0 0.0 0.0 4.58 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 27 1.033746 CATCGGCCAGCCATGAAACT 61.034 55.000 9.78 0.00 35.37 2.66
37 42 2.483877 TGAAACTAACCTCGCAGCAATG 59.516 45.455 0.00 0.00 0.00 2.82
131 138 3.408251 CCCCCTTTGTCCTCTCTCT 57.592 57.895 0.00 0.00 0.00 3.10
132 139 1.199615 CCCCCTTTGTCCTCTCTCTC 58.800 60.000 0.00 0.00 0.00 3.20
133 140 0.820871 CCCCTTTGTCCTCTCTCTCG 59.179 60.000 0.00 0.00 0.00 4.04
134 141 0.174617 CCCTTTGTCCTCTCTCTCGC 59.825 60.000 0.00 0.00 0.00 5.03
135 142 0.174617 CCTTTGTCCTCTCTCTCGCC 59.825 60.000 0.00 0.00 0.00 5.54
136 143 1.181786 CTTTGTCCTCTCTCTCGCCT 58.818 55.000 0.00 0.00 0.00 5.52
137 144 1.134175 CTTTGTCCTCTCTCTCGCCTC 59.866 57.143 0.00 0.00 0.00 4.70
138 145 0.681564 TTGTCCTCTCTCTCGCCTCC 60.682 60.000 0.00 0.00 0.00 4.30
139 146 1.826487 GTCCTCTCTCTCGCCTCCC 60.826 68.421 0.00 0.00 0.00 4.30
140 147 2.277072 CCTCTCTCTCGCCTCCCA 59.723 66.667 0.00 0.00 0.00 4.37
141 148 1.827789 CCTCTCTCTCGCCTCCCAG 60.828 68.421 0.00 0.00 0.00 4.45
258 338 3.945434 CTGGATGCATGCGTCGGC 61.945 66.667 28.80 18.66 40.52 5.54
319 410 4.569023 CAGTCGCGGCGCTGGATA 62.569 66.667 30.54 6.98 31.35 2.59
326 417 1.212751 CGGCGCTGGATATCGATGA 59.787 57.895 8.83 0.00 0.00 2.92
362 454 2.160219 GCCCATCGATCACGTACGTATA 59.840 50.000 22.34 12.85 40.69 1.47
369 461 7.412237 CCATCGATCACGTACGTATATACAGAA 60.412 40.741 22.34 1.24 40.69 3.02
370 462 7.586714 TCGATCACGTACGTATATACAGAAT 57.413 36.000 22.34 3.70 40.69 2.40
408 502 3.549625 GGGTTACGTCGATCACAGTATCC 60.550 52.174 0.00 2.37 0.00 2.59
417 511 0.613572 TCACAGTATCCCGGCACAGA 60.614 55.000 0.00 0.00 0.00 3.41
509 633 1.200484 GAAGACGAGCCGAGAACTCTT 59.800 52.381 1.50 0.42 31.71 2.85
720 923 3.204827 GCATCCTTGCCGCGTCAT 61.205 61.111 4.92 0.00 43.38 3.06
807 1080 0.879400 CGTCAGCTCCATCATCTGGC 60.879 60.000 0.00 0.00 45.52 4.85
815 1088 1.826921 CATCATCTGGCTGCCACCC 60.827 63.158 19.30 0.00 0.00 4.61
842 1131 1.549620 CACATCCAGCTCAGACTGACT 59.450 52.381 0.00 1.52 40.25 3.41
871 1183 1.996291 TCACTCTCTCCTTCCTCTCCA 59.004 52.381 0.00 0.00 0.00 3.86
959 1304 1.738830 CTCGTTTTAAGCCGGCCGA 60.739 57.895 30.73 22.20 0.00 5.54
1100 1523 1.077123 GACTGCATGCTCACTCTGTG 58.923 55.000 20.33 0.66 34.45 3.66
1118 1555 2.759973 TCCTCTCCGGCAAGCGAT 60.760 61.111 0.00 0.00 0.00 4.58
1119 1556 2.279784 CCTCTCCGGCAAGCGATC 60.280 66.667 0.00 0.00 0.00 3.69
1139 1576 0.726256 TACGTACGTACTGATGCGCA 59.274 50.000 23.60 14.96 37.46 6.09
1559 2810 4.082523 CTGGACACCGGCGACCAT 62.083 66.667 14.01 0.00 0.00 3.55
1703 2975 3.243873 GGGAACTGATCAGCGTCATCATA 60.244 47.826 22.83 0.00 29.78 2.15
1704 2976 4.562347 GGGAACTGATCAGCGTCATCATAT 60.562 45.833 22.83 0.00 29.78 1.78
1707 2979 4.953667 ACTGATCAGCGTCATCATATGTT 58.046 39.130 22.83 0.00 29.78 2.71
1763 3035 2.820059 TTATCATCGCAGCCTCGATT 57.180 45.000 7.83 0.00 45.81 3.34
1780 3054 3.318275 TCGATTCGAGGCTAATAGTGCTT 59.682 43.478 4.29 0.00 0.00 3.91
1822 3102 5.312079 ACGTCTCCTGTTTACAGTAGTACT 58.688 41.667 0.00 0.00 42.27 2.73
1823 3103 6.467677 ACGTCTCCTGTTTACAGTAGTACTA 58.532 40.000 1.57 0.00 42.27 1.82
1921 3490 5.936956 GGATATGGCTAGAAAGTTCATGAGG 59.063 44.000 0.00 0.00 0.00 3.86
1927 3496 4.813697 GCTAGAAAGTTCATGAGGATCCAC 59.186 45.833 15.82 8.65 0.00 4.02
1928 3497 5.396213 GCTAGAAAGTTCATGAGGATCCACT 60.396 44.000 15.82 4.26 0.00 4.00
1929 3498 4.841422 AGAAAGTTCATGAGGATCCACTG 58.159 43.478 15.82 8.16 0.00 3.66
1930 3499 4.288105 AGAAAGTTCATGAGGATCCACTGT 59.712 41.667 15.82 1.89 0.00 3.55
1931 3500 5.485353 AGAAAGTTCATGAGGATCCACTGTA 59.515 40.000 15.82 0.00 0.00 2.74
1932 3501 4.744795 AGTTCATGAGGATCCACTGTAC 57.255 45.455 15.82 11.41 0.00 2.90
1933 3502 3.131223 AGTTCATGAGGATCCACTGTACG 59.869 47.826 15.82 0.00 0.00 3.67
1934 3503 2.735151 TCATGAGGATCCACTGTACGT 58.265 47.619 15.82 0.00 0.00 3.57
1935 3504 3.096852 TCATGAGGATCCACTGTACGTT 58.903 45.455 15.82 0.00 0.00 3.99
1936 3505 4.274978 TCATGAGGATCCACTGTACGTTA 58.725 43.478 15.82 0.00 0.00 3.18
1937 3506 4.338400 TCATGAGGATCCACTGTACGTTAG 59.662 45.833 15.82 0.00 0.00 2.34
1938 3507 3.959293 TGAGGATCCACTGTACGTTAGA 58.041 45.455 15.82 0.00 0.00 2.10
1939 3508 3.945921 TGAGGATCCACTGTACGTTAGAG 59.054 47.826 15.82 0.00 0.00 2.43
1940 3509 2.688958 AGGATCCACTGTACGTTAGAGC 59.311 50.000 15.82 0.00 0.00 4.09
1941 3510 2.426024 GGATCCACTGTACGTTAGAGCA 59.574 50.000 6.95 0.00 0.00 4.26
1942 3511 3.068307 GGATCCACTGTACGTTAGAGCAT 59.932 47.826 6.95 0.00 0.00 3.79
1943 3512 3.777465 TCCACTGTACGTTAGAGCATC 57.223 47.619 0.00 0.00 0.00 3.91
1958 3527 4.873746 GAGCATCTATACAGCACCCTAA 57.126 45.455 0.00 0.00 0.00 2.69
1959 3528 5.215252 GAGCATCTATACAGCACCCTAAA 57.785 43.478 0.00 0.00 0.00 1.85
1960 3529 4.962155 AGCATCTATACAGCACCCTAAAC 58.038 43.478 0.00 0.00 0.00 2.01
1961 3530 4.065789 GCATCTATACAGCACCCTAAACC 58.934 47.826 0.00 0.00 0.00 3.27
1962 3531 4.642429 CATCTATACAGCACCCTAAACCC 58.358 47.826 0.00 0.00 0.00 4.11
1963 3532 4.003584 TCTATACAGCACCCTAAACCCT 57.996 45.455 0.00 0.00 0.00 4.34
1964 3533 3.965347 TCTATACAGCACCCTAAACCCTC 59.035 47.826 0.00 0.00 0.00 4.30
1965 3534 1.282382 TACAGCACCCTAAACCCTCC 58.718 55.000 0.00 0.00 0.00 4.30
1966 3535 0.475828 ACAGCACCCTAAACCCTCCT 60.476 55.000 0.00 0.00 0.00 3.69
1967 3536 0.253327 CAGCACCCTAAACCCTCCTC 59.747 60.000 0.00 0.00 0.00 3.71
1968 3537 0.178873 AGCACCCTAAACCCTCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
1969 3538 0.696501 GCACCCTAAACCCTCCTCAA 59.303 55.000 0.00 0.00 0.00 3.02
1970 3539 1.074889 GCACCCTAAACCCTCCTCAAA 59.925 52.381 0.00 0.00 0.00 2.69
1971 3540 2.291605 GCACCCTAAACCCTCCTCAAAT 60.292 50.000 0.00 0.00 0.00 2.32
1972 3541 3.621558 CACCCTAAACCCTCCTCAAATC 58.378 50.000 0.00 0.00 0.00 2.17
1973 3542 2.581246 ACCCTAAACCCTCCTCAAATCC 59.419 50.000 0.00 0.00 0.00 3.01
1974 3543 2.853077 CCCTAAACCCTCCTCAAATCCT 59.147 50.000 0.00 0.00 0.00 3.24
1975 3544 3.269643 CCCTAAACCCTCCTCAAATCCTT 59.730 47.826 0.00 0.00 0.00 3.36
1976 3545 4.527944 CCTAAACCCTCCTCAAATCCTTC 58.472 47.826 0.00 0.00 0.00 3.46
1977 3546 2.789409 AACCCTCCTCAAATCCTTCG 57.211 50.000 0.00 0.00 0.00 3.79
1978 3547 0.912486 ACCCTCCTCAAATCCTTCGG 59.088 55.000 0.00 0.00 0.00 4.30
1979 3548 0.181350 CCCTCCTCAAATCCTTCGGG 59.819 60.000 0.00 0.00 0.00 5.14
1980 3549 0.464554 CCTCCTCAAATCCTTCGGGC 60.465 60.000 0.00 0.00 34.44 6.13
1981 3550 0.811616 CTCCTCAAATCCTTCGGGCG 60.812 60.000 0.00 0.00 34.44 6.13
1982 3551 2.472909 CCTCAAATCCTTCGGGCGC 61.473 63.158 0.00 0.00 34.44 6.53
1983 3552 2.813179 CTCAAATCCTTCGGGCGCG 61.813 63.158 18.21 18.21 34.44 6.86
1984 3553 4.536687 CAAATCCTTCGGGCGCGC 62.537 66.667 25.94 25.94 34.44 6.86
1985 3554 4.778143 AAATCCTTCGGGCGCGCT 62.778 61.111 32.29 4.96 34.44 5.92
1986 3555 3.379865 AAATCCTTCGGGCGCGCTA 62.380 57.895 32.29 14.31 34.44 4.26
1987 3556 2.660258 AAATCCTTCGGGCGCGCTAT 62.660 55.000 32.29 10.15 34.44 2.97
1988 3557 3.575351 ATCCTTCGGGCGCGCTATC 62.575 63.158 32.29 19.07 34.44 2.08
1995 3564 4.570663 GGCGCGCTATCGGTCACT 62.571 66.667 32.29 0.00 35.95 3.41
1996 3565 3.323136 GCGCGCTATCGGTCACTG 61.323 66.667 26.67 0.00 35.95 3.66
1997 3566 2.407616 CGCGCTATCGGTCACTGA 59.592 61.111 5.56 0.00 35.95 3.41
1998 3567 1.939785 CGCGCTATCGGTCACTGAC 60.940 63.158 5.56 0.00 35.95 3.51
2012 3581 5.695851 GTCACTGACCAGTCATGATTTTT 57.304 39.130 0.00 0.00 40.20 1.94
2013 3582 5.693814 GTCACTGACCAGTCATGATTTTTC 58.306 41.667 0.00 0.00 40.20 2.29
2014 3583 5.239306 GTCACTGACCAGTCATGATTTTTCA 59.761 40.000 0.00 0.00 40.20 2.69
2015 3584 5.827267 TCACTGACCAGTCATGATTTTTCAA 59.173 36.000 0.00 0.00 40.20 2.69
2016 3585 5.916883 CACTGACCAGTCATGATTTTTCAAC 59.083 40.000 0.00 0.00 40.20 3.18
2017 3586 5.010012 ACTGACCAGTCATGATTTTTCAACC 59.990 40.000 0.00 0.00 36.92 3.77
2018 3587 4.280677 TGACCAGTCATGATTTTTCAACCC 59.719 41.667 0.00 0.00 34.14 4.11
2019 3588 4.222336 ACCAGTCATGATTTTTCAACCCA 58.778 39.130 0.00 0.00 0.00 4.51
2020 3589 4.653341 ACCAGTCATGATTTTTCAACCCAA 59.347 37.500 0.00 0.00 0.00 4.12
2021 3590 5.130145 ACCAGTCATGATTTTTCAACCCAAA 59.870 36.000 0.00 0.00 0.00 3.28
2022 3591 5.466393 CCAGTCATGATTTTTCAACCCAAAC 59.534 40.000 0.00 0.00 0.00 2.93
2023 3592 6.047870 CAGTCATGATTTTTCAACCCAAACA 58.952 36.000 0.00 0.00 0.00 2.83
2024 3593 6.201425 CAGTCATGATTTTTCAACCCAAACAG 59.799 38.462 0.00 0.00 0.00 3.16
2025 3594 5.050159 GTCATGATTTTTCAACCCAAACAGC 60.050 40.000 0.00 0.00 0.00 4.40
2026 3595 3.802866 TGATTTTTCAACCCAAACAGCC 58.197 40.909 0.00 0.00 0.00 4.85
2027 3596 3.454082 TGATTTTTCAACCCAAACAGCCT 59.546 39.130 0.00 0.00 0.00 4.58
2028 3597 2.977772 TTTTCAACCCAAACAGCCTG 57.022 45.000 0.00 0.00 0.00 4.85
2029 3598 0.463620 TTTCAACCCAAACAGCCTGC 59.536 50.000 0.00 0.00 0.00 4.85
2030 3599 0.396974 TTCAACCCAAACAGCCTGCT 60.397 50.000 0.00 0.00 0.00 4.24
2031 3600 0.396974 TCAACCCAAACAGCCTGCTT 60.397 50.000 0.00 0.00 0.00 3.91
2032 3601 1.133637 TCAACCCAAACAGCCTGCTTA 60.134 47.619 0.00 0.00 0.00 3.09
2033 3602 1.686052 CAACCCAAACAGCCTGCTTAA 59.314 47.619 0.00 0.00 0.00 1.85
2034 3603 2.080654 ACCCAAACAGCCTGCTTAAA 57.919 45.000 0.00 0.00 0.00 1.52
2035 3604 1.686587 ACCCAAACAGCCTGCTTAAAC 59.313 47.619 0.00 0.00 0.00 2.01
2036 3605 1.335872 CCCAAACAGCCTGCTTAAACG 60.336 52.381 0.00 0.00 0.00 3.60
2037 3606 1.335872 CCAAACAGCCTGCTTAAACGG 60.336 52.381 0.00 0.00 0.00 4.44
2038 3607 0.958822 AAACAGCCTGCTTAAACGGG 59.041 50.000 0.00 0.00 39.28 5.28
2039 3608 0.179001 AACAGCCTGCTTAAACGGGT 60.179 50.000 5.63 0.00 38.45 5.28
2040 3609 0.605589 ACAGCCTGCTTAAACGGGTC 60.606 55.000 5.63 0.00 38.45 4.46
2041 3610 0.321653 CAGCCTGCTTAAACGGGTCT 60.322 55.000 5.63 1.05 38.45 3.85
2042 3611 0.036294 AGCCTGCTTAAACGGGTCTC 60.036 55.000 5.63 0.00 38.45 3.36
2043 3612 0.321298 GCCTGCTTAAACGGGTCTCA 60.321 55.000 5.63 0.00 38.45 3.27
2044 3613 1.880646 GCCTGCTTAAACGGGTCTCAA 60.881 52.381 5.63 0.00 38.45 3.02
2045 3614 2.500229 CCTGCTTAAACGGGTCTCAAA 58.500 47.619 0.00 0.00 0.00 2.69
2046 3615 2.225727 CCTGCTTAAACGGGTCTCAAAC 59.774 50.000 0.00 0.00 0.00 2.93
2047 3616 1.868498 TGCTTAAACGGGTCTCAAACG 59.132 47.619 0.00 0.00 0.00 3.60
2048 3617 1.399343 GCTTAAACGGGTCTCAAACGC 60.399 52.381 0.00 0.00 37.46 4.84
2049 3618 2.140717 CTTAAACGGGTCTCAAACGCT 58.859 47.619 0.00 0.00 38.63 5.07
2050 3619 1.787012 TAAACGGGTCTCAAACGCTC 58.213 50.000 0.00 0.00 38.63 5.03
2051 3620 1.219522 AAACGGGTCTCAAACGCTCG 61.220 55.000 0.00 0.00 38.63 5.03
2052 3621 2.079020 AACGGGTCTCAAACGCTCGA 62.079 55.000 0.00 0.00 38.63 4.04
2053 3622 1.372499 CGGGTCTCAAACGCTCGAA 60.372 57.895 0.00 0.00 38.63 3.71
2054 3623 1.615107 CGGGTCTCAAACGCTCGAAC 61.615 60.000 0.00 0.00 38.63 3.95
2055 3624 0.319641 GGGTCTCAAACGCTCGAACT 60.320 55.000 0.00 0.00 37.81 3.01
2056 3625 0.784778 GGTCTCAAACGCTCGAACTG 59.215 55.000 0.00 0.00 0.00 3.16
2057 3626 1.602165 GGTCTCAAACGCTCGAACTGA 60.602 52.381 0.00 0.00 0.00 3.41
2065 3634 3.867771 CTCGAACTGAGCTGCACC 58.132 61.111 1.02 0.00 38.03 5.01
2066 3635 1.291588 CTCGAACTGAGCTGCACCT 59.708 57.895 1.02 0.00 38.03 4.00
2067 3636 0.320247 CTCGAACTGAGCTGCACCTT 60.320 55.000 1.02 0.00 38.03 3.50
2068 3637 0.106708 TCGAACTGAGCTGCACCTTT 59.893 50.000 1.02 0.00 0.00 3.11
2069 3638 0.514691 CGAACTGAGCTGCACCTTTC 59.485 55.000 1.02 0.30 0.00 2.62
2070 3639 1.597742 GAACTGAGCTGCACCTTTCA 58.402 50.000 1.02 0.00 0.00 2.69
2071 3640 2.157738 GAACTGAGCTGCACCTTTCAT 58.842 47.619 1.02 0.00 0.00 2.57
2072 3641 2.283145 ACTGAGCTGCACCTTTCATT 57.717 45.000 1.02 0.00 0.00 2.57
2073 3642 3.423539 ACTGAGCTGCACCTTTCATTA 57.576 42.857 1.02 0.00 0.00 1.90
2074 3643 3.960571 ACTGAGCTGCACCTTTCATTAT 58.039 40.909 1.02 0.00 0.00 1.28
2075 3644 3.944015 ACTGAGCTGCACCTTTCATTATC 59.056 43.478 1.02 0.00 0.00 1.75
2076 3645 3.282021 TGAGCTGCACCTTTCATTATCC 58.718 45.455 1.02 0.00 0.00 2.59
2077 3646 3.282021 GAGCTGCACCTTTCATTATCCA 58.718 45.455 1.02 0.00 0.00 3.41
2078 3647 3.285484 AGCTGCACCTTTCATTATCCAG 58.715 45.455 1.02 0.00 0.00 3.86
2079 3648 2.223665 GCTGCACCTTTCATTATCCAGC 60.224 50.000 0.00 0.00 37.82 4.85
2080 3649 2.360165 CTGCACCTTTCATTATCCAGCC 59.640 50.000 0.00 0.00 0.00 4.85
2081 3650 2.025037 TGCACCTTTCATTATCCAGCCT 60.025 45.455 0.00 0.00 0.00 4.58
2082 3651 3.201930 TGCACCTTTCATTATCCAGCCTA 59.798 43.478 0.00 0.00 0.00 3.93
2083 3652 4.207165 GCACCTTTCATTATCCAGCCTAA 58.793 43.478 0.00 0.00 0.00 2.69
2084 3653 4.644685 GCACCTTTCATTATCCAGCCTAAA 59.355 41.667 0.00 0.00 0.00 1.85
2085 3654 5.302823 GCACCTTTCATTATCCAGCCTAAAT 59.697 40.000 0.00 0.00 0.00 1.40
2086 3655 6.490040 GCACCTTTCATTATCCAGCCTAAATA 59.510 38.462 0.00 0.00 0.00 1.40
2087 3656 7.177392 GCACCTTTCATTATCCAGCCTAAATAT 59.823 37.037 0.00 0.00 0.00 1.28
2088 3657 8.517878 CACCTTTCATTATCCAGCCTAAATATG 58.482 37.037 0.00 0.00 0.00 1.78
2089 3658 7.671398 ACCTTTCATTATCCAGCCTAAATATGG 59.329 37.037 0.00 0.00 35.30 2.74
2090 3659 7.123247 CCTTTCATTATCCAGCCTAAATATGGG 59.877 40.741 0.00 0.00 34.71 4.00
2091 3660 6.078456 TCATTATCCAGCCTAAATATGGGG 57.922 41.667 0.00 0.00 34.71 4.96
2092 3661 2.907458 ATCCAGCCTAAATATGGGGC 57.093 50.000 5.92 5.92 45.57 5.80
2100 3669 4.273318 GCCTAAATATGGGGCAGATAAGG 58.727 47.826 8.42 0.00 44.69 2.69
2101 3670 4.860022 CCTAAATATGGGGCAGATAAGGG 58.140 47.826 0.00 0.00 0.00 3.95
2102 3671 3.833559 AAATATGGGGCAGATAAGGGG 57.166 47.619 0.00 0.00 0.00 4.79
2103 3672 1.002857 ATATGGGGCAGATAAGGGGC 58.997 55.000 0.00 0.00 0.00 5.80
2104 3673 1.488705 TATGGGGCAGATAAGGGGCG 61.489 60.000 0.00 0.00 0.00 6.13
2105 3674 4.956932 GGGGCAGATAAGGGGCGC 62.957 72.222 0.00 0.00 39.47 6.53
2106 3675 3.878667 GGGCAGATAAGGGGCGCT 61.879 66.667 7.64 0.00 37.49 5.92
2107 3676 2.281139 GGCAGATAAGGGGCGCTC 60.281 66.667 7.64 1.18 0.00 5.03
2108 3677 2.663188 GCAGATAAGGGGCGCTCG 60.663 66.667 7.64 0.00 0.00 5.03
2109 3678 2.029666 CAGATAAGGGGCGCTCGG 59.970 66.667 7.64 0.00 0.00 4.63
2110 3679 3.234730 AGATAAGGGGCGCTCGGG 61.235 66.667 7.64 0.00 0.00 5.14
2111 3680 4.990553 GATAAGGGGCGCTCGGGC 62.991 72.222 7.64 0.00 41.35 6.13
2160 3729 3.809013 GCCCATCCGACCCCACAT 61.809 66.667 0.00 0.00 0.00 3.21
2161 3730 2.448582 GCCCATCCGACCCCACATA 61.449 63.158 0.00 0.00 0.00 2.29
2162 3731 1.779061 GCCCATCCGACCCCACATAT 61.779 60.000 0.00 0.00 0.00 1.78
2163 3732 1.651737 CCCATCCGACCCCACATATA 58.348 55.000 0.00 0.00 0.00 0.86
2164 3733 2.196595 CCCATCCGACCCCACATATAT 58.803 52.381 0.00 0.00 0.00 0.86
2165 3734 2.576191 CCCATCCGACCCCACATATATT 59.424 50.000 0.00 0.00 0.00 1.28
2166 3735 3.370527 CCCATCCGACCCCACATATATTC 60.371 52.174 0.00 0.00 0.00 1.75
2167 3736 3.370527 CCATCCGACCCCACATATATTCC 60.371 52.174 0.00 0.00 0.00 3.01
2168 3737 3.269592 TCCGACCCCACATATATTCCT 57.730 47.619 0.00 0.00 0.00 3.36
2169 3738 3.170717 TCCGACCCCACATATATTCCTC 58.829 50.000 0.00 0.00 0.00 3.71
2170 3739 3.173965 CCGACCCCACATATATTCCTCT 58.826 50.000 0.00 0.00 0.00 3.69
2171 3740 3.195825 CCGACCCCACATATATTCCTCTC 59.804 52.174 0.00 0.00 0.00 3.20
2172 3741 4.090090 CGACCCCACATATATTCCTCTCT 58.910 47.826 0.00 0.00 0.00 3.10
2173 3742 5.262009 CGACCCCACATATATTCCTCTCTA 58.738 45.833 0.00 0.00 0.00 2.43
2174 3743 5.894393 CGACCCCACATATATTCCTCTCTAT 59.106 44.000 0.00 0.00 0.00 1.98
2175 3744 6.039941 CGACCCCACATATATTCCTCTCTATC 59.960 46.154 0.00 0.00 0.00 2.08
2176 3745 7.062584 ACCCCACATATATTCCTCTCTATCT 57.937 40.000 0.00 0.00 0.00 1.98
2177 3746 6.900186 ACCCCACATATATTCCTCTCTATCTG 59.100 42.308 0.00 0.00 0.00 2.90
2178 3747 6.183360 CCCCACATATATTCCTCTCTATCTGC 60.183 46.154 0.00 0.00 0.00 4.26
2179 3748 6.610830 CCCACATATATTCCTCTCTATCTGCT 59.389 42.308 0.00 0.00 0.00 4.24
2180 3749 7.125507 CCCACATATATTCCTCTCTATCTGCTT 59.874 40.741 0.00 0.00 0.00 3.91
2181 3750 7.980662 CCACATATATTCCTCTCTATCTGCTTG 59.019 40.741 0.00 0.00 0.00 4.01
2182 3751 7.492020 CACATATATTCCTCTCTATCTGCTTGC 59.508 40.741 0.00 0.00 0.00 4.01
2183 3752 3.767902 ATTCCTCTCTATCTGCTTGCC 57.232 47.619 0.00 0.00 0.00 4.52
2184 3753 1.035923 TCCTCTCTATCTGCTTGCCG 58.964 55.000 0.00 0.00 0.00 5.69
2185 3754 0.033228 CCTCTCTATCTGCTTGCCGG 59.967 60.000 0.00 0.00 0.00 6.13
2186 3755 1.035923 CTCTCTATCTGCTTGCCGGA 58.964 55.000 5.05 0.00 0.00 5.14
2191 3760 1.609635 TATCTGCTTGCCGGACCGAA 61.610 55.000 17.49 0.97 0.00 4.30
2229 3798 2.835431 CGACCCCGAGCTCATCCT 60.835 66.667 15.40 0.00 38.22 3.24
2230 3799 2.851071 CGACCCCGAGCTCATCCTC 61.851 68.421 15.40 1.58 38.22 3.71
2235 3804 2.279120 CGAGCTCATCCTCCACGC 60.279 66.667 15.40 0.00 0.00 5.34
2236 3805 2.279120 GAGCTCATCCTCCACGCG 60.279 66.667 9.40 3.53 0.00 6.01
2237 3806 3.781770 GAGCTCATCCTCCACGCGG 62.782 68.421 12.47 0.00 0.00 6.46
2257 3826 3.157252 TGAGGAGGAGATGGCCGC 61.157 66.667 0.00 0.00 0.00 6.53
2360 3930 1.149361 GCACAAATGGCGCATGGATG 61.149 55.000 10.83 3.64 0.00 3.51
2361 3931 0.456628 CACAAATGGCGCATGGATGA 59.543 50.000 10.83 0.00 0.00 2.92
2362 3932 1.067974 CACAAATGGCGCATGGATGAT 59.932 47.619 10.83 0.00 0.00 2.45
2418 3989 2.783288 GGGTCCTTCTAGCGTCCGG 61.783 68.421 0.00 0.00 0.00 5.14
2460 4031 1.594293 CTCCGTTGACGTGCCAAGT 60.594 57.895 0.00 0.00 37.74 3.16
2593 4164 2.893398 GGAGTCGCATTCTCCGGT 59.107 61.111 0.00 0.00 41.36 5.28
2618 4189 1.146041 TATGGTGCATCAGTCCGGC 59.854 57.895 5.59 0.00 0.00 6.13
2646 4217 1.958715 CGCATTGTGGTGGACGTCA 60.959 57.895 18.91 0.27 0.00 4.35
2686 4257 1.182667 TCCATCACCGATCTGACGTT 58.817 50.000 0.00 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 27 0.245266 TCGTCATTGCTGCGAGGTTA 59.755 50.000 1.01 0.00 0.00 2.85
37 42 0.580104 CGTGGGTTTTGTCTGTCGTC 59.420 55.000 0.00 0.00 0.00 4.20
134 141 4.785453 GGTTGGCGAGCTGGGAGG 62.785 72.222 0.00 0.00 0.00 4.30
135 142 3.672295 GAGGTTGGCGAGCTGGGAG 62.672 68.421 11.97 0.00 35.91 4.30
136 143 3.706373 GAGGTTGGCGAGCTGGGA 61.706 66.667 11.97 0.00 35.91 4.37
137 144 4.785453 GGAGGTTGGCGAGCTGGG 62.785 72.222 11.97 0.00 35.91 4.45
221 243 0.752376 TGTTTGTTTGGGGACGGACC 60.752 55.000 0.00 0.00 38.08 4.46
343 434 6.035327 TCTGTATATACGTACGTGATCGATGG 59.965 42.308 30.25 13.66 40.62 3.51
362 454 6.351371 CCGGTGGATCAAGCTATATTCTGTAT 60.351 42.308 0.00 0.00 0.00 2.29
369 461 2.621070 ACCCGGTGGATCAAGCTATAT 58.379 47.619 0.00 0.00 34.81 0.86
370 462 2.097110 ACCCGGTGGATCAAGCTATA 57.903 50.000 0.00 0.00 34.81 1.31
377 469 1.892338 GACGTAACCCGGTGGATCA 59.108 57.895 0.00 0.00 42.24 2.92
462 571 0.734889 GTGTGGATGGAATCTTGCGG 59.265 55.000 0.00 0.00 44.71 5.69
496 612 0.902516 AGGCTGAAGAGTTCTCGGCT 60.903 55.000 3.83 0.80 34.05 5.52
509 633 1.670949 GATCGTGCAGAGGAGGCTGA 61.671 60.000 0.00 0.00 38.14 4.26
823 1104 1.549620 CAGTCAGTCTGAGCTGGATGT 59.450 52.381 17.76 0.00 46.27 3.06
842 1131 1.279558 AGGAGAGAGTGAGACGTAGCA 59.720 52.381 0.00 0.00 0.00 3.49
1067 1474 1.301244 CAGTCACTGACCTGCGCTT 60.301 57.895 9.73 0.00 32.44 4.68
1100 1523 2.962697 GATCGCTTGCCGGAGAGGAC 62.963 65.000 5.05 0.00 45.00 3.85
1118 1555 1.004610 GCGCATCAGTACGTACGTAGA 60.005 52.381 27.48 21.48 0.00 2.59
1119 1556 1.267682 TGCGCATCAGTACGTACGTAG 60.268 52.381 27.48 17.07 0.00 3.51
1139 1576 1.299541 CTGACAAGTTCACCAAGCGT 58.700 50.000 0.00 0.00 0.00 5.07
1239 1730 5.869888 GCTGTAGTTGTTGTAGTAGCAGAAT 59.130 40.000 0.00 0.00 0.00 2.40
1434 2679 3.708220 GAGAAGGCGCGTCTCCTGG 62.708 68.421 16.36 0.00 36.33 4.45
1448 2696 3.379445 GCGGGTGGTCGGAGAGAA 61.379 66.667 0.00 0.00 36.95 2.87
1559 2810 1.676635 CCGTCGTAGAGGTGGTCCA 60.677 63.158 0.00 0.00 41.34 4.02
1725 2997 2.100879 AAACAGGAGCCTCGAACGCT 62.101 55.000 6.38 6.38 39.95 5.07
1763 3035 3.887621 AACAAGCACTATTAGCCTCGA 57.112 42.857 0.00 0.00 0.00 4.04
1780 3054 3.823873 ACGTAGAATTTCCCATGCAAACA 59.176 39.130 0.00 0.00 0.00 2.83
1921 3490 3.777465 TGCTCTAACGTACAGTGGATC 57.223 47.619 0.00 0.00 0.00 3.36
1927 3496 6.081049 GCTGTATAGATGCTCTAACGTACAG 58.919 44.000 17.38 17.38 40.06 2.74
1928 3497 5.529800 TGCTGTATAGATGCTCTAACGTACA 59.470 40.000 0.00 0.00 31.96 2.90
1929 3498 5.852229 GTGCTGTATAGATGCTCTAACGTAC 59.148 44.000 0.00 0.00 31.96 3.67
1930 3499 5.048921 GGTGCTGTATAGATGCTCTAACGTA 60.049 44.000 0.00 0.00 31.96 3.57
1931 3500 4.261656 GGTGCTGTATAGATGCTCTAACGT 60.262 45.833 0.00 0.00 31.96 3.99
1932 3501 4.230657 GGTGCTGTATAGATGCTCTAACG 58.769 47.826 0.00 0.00 31.96 3.18
1933 3502 4.282195 AGGGTGCTGTATAGATGCTCTAAC 59.718 45.833 0.00 0.00 31.96 2.34
1934 3503 4.483950 AGGGTGCTGTATAGATGCTCTAA 58.516 43.478 0.00 0.00 31.96 2.10
1935 3504 4.119556 AGGGTGCTGTATAGATGCTCTA 57.880 45.455 0.00 0.00 32.87 2.43
1936 3505 2.969628 AGGGTGCTGTATAGATGCTCT 58.030 47.619 0.00 0.00 0.00 4.09
1937 3506 4.873746 TTAGGGTGCTGTATAGATGCTC 57.126 45.455 0.00 0.00 0.00 4.26
1938 3507 4.202367 GGTTTAGGGTGCTGTATAGATGCT 60.202 45.833 0.00 0.00 0.00 3.79
1939 3508 4.065789 GGTTTAGGGTGCTGTATAGATGC 58.934 47.826 0.00 0.00 0.00 3.91
1940 3509 4.348168 AGGGTTTAGGGTGCTGTATAGATG 59.652 45.833 0.00 0.00 0.00 2.90
1941 3510 4.567857 AGGGTTTAGGGTGCTGTATAGAT 58.432 43.478 0.00 0.00 0.00 1.98
1942 3511 3.965347 GAGGGTTTAGGGTGCTGTATAGA 59.035 47.826 0.00 0.00 0.00 1.98
1943 3512 3.071167 GGAGGGTTTAGGGTGCTGTATAG 59.929 52.174 0.00 0.00 0.00 1.31
1944 3513 3.043418 GGAGGGTTTAGGGTGCTGTATA 58.957 50.000 0.00 0.00 0.00 1.47
1945 3514 1.844497 GGAGGGTTTAGGGTGCTGTAT 59.156 52.381 0.00 0.00 0.00 2.29
1946 3515 1.203389 AGGAGGGTTTAGGGTGCTGTA 60.203 52.381 0.00 0.00 0.00 2.74
1947 3516 0.475828 AGGAGGGTTTAGGGTGCTGT 60.476 55.000 0.00 0.00 0.00 4.40
1948 3517 0.253327 GAGGAGGGTTTAGGGTGCTG 59.747 60.000 0.00 0.00 0.00 4.41
1949 3518 0.178873 TGAGGAGGGTTTAGGGTGCT 60.179 55.000 0.00 0.00 0.00 4.40
1950 3519 0.696501 TTGAGGAGGGTTTAGGGTGC 59.303 55.000 0.00 0.00 0.00 5.01
1951 3520 3.621558 GATTTGAGGAGGGTTTAGGGTG 58.378 50.000 0.00 0.00 0.00 4.61
1952 3521 2.581246 GGATTTGAGGAGGGTTTAGGGT 59.419 50.000 0.00 0.00 0.00 4.34
1953 3522 2.853077 AGGATTTGAGGAGGGTTTAGGG 59.147 50.000 0.00 0.00 0.00 3.53
1954 3523 4.527944 GAAGGATTTGAGGAGGGTTTAGG 58.472 47.826 0.00 0.00 0.00 2.69
1955 3524 4.192317 CGAAGGATTTGAGGAGGGTTTAG 58.808 47.826 0.00 0.00 0.00 1.85
1956 3525 4.216411 CGAAGGATTTGAGGAGGGTTTA 57.784 45.455 0.00 0.00 0.00 2.01
1957 3526 3.073274 CGAAGGATTTGAGGAGGGTTT 57.927 47.619 0.00 0.00 0.00 3.27
1958 3527 2.789409 CGAAGGATTTGAGGAGGGTT 57.211 50.000 0.00 0.00 0.00 4.11
1978 3547 4.570663 AGTGACCGATAGCGCGCC 62.571 66.667 30.33 12.17 35.83 6.53
1979 3548 3.323136 CAGTGACCGATAGCGCGC 61.323 66.667 26.66 26.66 35.83 6.86
1980 3549 1.939785 GTCAGTGACCGATAGCGCG 60.940 63.158 12.54 0.00 35.83 6.86
1981 3550 1.589196 GGTCAGTGACCGATAGCGC 60.589 63.158 26.12 0.00 43.14 5.92
1982 3551 4.711980 GGTCAGTGACCGATAGCG 57.288 61.111 26.12 0.00 43.14 4.26
1990 3559 5.239306 TGAAAAATCATGACTGGTCAGTGAC 59.761 40.000 15.24 15.24 43.61 3.67
1991 3560 5.375773 TGAAAAATCATGACTGGTCAGTGA 58.624 37.500 8.49 11.94 43.61 3.41
1992 3561 5.694231 TGAAAAATCATGACTGGTCAGTG 57.306 39.130 8.49 7.81 43.61 3.66
1993 3562 5.010012 GGTTGAAAAATCATGACTGGTCAGT 59.990 40.000 0.00 2.94 43.61 3.41
1994 3563 5.464168 GGTTGAAAAATCATGACTGGTCAG 58.536 41.667 0.00 0.00 43.61 3.51
1995 3564 4.280677 GGGTTGAAAAATCATGACTGGTCA 59.719 41.667 0.00 5.87 44.59 4.02
1996 3565 4.280677 TGGGTTGAAAAATCATGACTGGTC 59.719 41.667 0.00 0.00 0.00 4.02
1997 3566 4.222336 TGGGTTGAAAAATCATGACTGGT 58.778 39.130 0.00 0.00 0.00 4.00
1998 3567 4.870123 TGGGTTGAAAAATCATGACTGG 57.130 40.909 0.00 0.00 0.00 4.00
1999 3568 6.047870 TGTTTGGGTTGAAAAATCATGACTG 58.952 36.000 0.00 0.00 0.00 3.51
2000 3569 6.232581 TGTTTGGGTTGAAAAATCATGACT 57.767 33.333 0.00 0.00 0.00 3.41
2001 3570 5.050159 GCTGTTTGGGTTGAAAAATCATGAC 60.050 40.000 0.00 0.00 0.00 3.06
2002 3571 5.055812 GCTGTTTGGGTTGAAAAATCATGA 58.944 37.500 0.00 0.00 0.00 3.07
2003 3572 4.213906 GGCTGTTTGGGTTGAAAAATCATG 59.786 41.667 0.00 0.00 0.00 3.07
2004 3573 4.102996 AGGCTGTTTGGGTTGAAAAATCAT 59.897 37.500 0.00 0.00 0.00 2.45
2005 3574 3.454082 AGGCTGTTTGGGTTGAAAAATCA 59.546 39.130 0.00 0.00 0.00 2.57
2006 3575 3.809279 CAGGCTGTTTGGGTTGAAAAATC 59.191 43.478 6.28 0.00 0.00 2.17
2007 3576 3.807553 CAGGCTGTTTGGGTTGAAAAAT 58.192 40.909 6.28 0.00 0.00 1.82
2008 3577 2.679349 GCAGGCTGTTTGGGTTGAAAAA 60.679 45.455 17.16 0.00 0.00 1.94
2009 3578 1.134551 GCAGGCTGTTTGGGTTGAAAA 60.135 47.619 17.16 0.00 0.00 2.29
2010 3579 0.463620 GCAGGCTGTTTGGGTTGAAA 59.536 50.000 17.16 0.00 0.00 2.69
2011 3580 0.396974 AGCAGGCTGTTTGGGTTGAA 60.397 50.000 17.16 0.00 0.00 2.69
2012 3581 0.396974 AAGCAGGCTGTTTGGGTTGA 60.397 50.000 16.14 0.00 0.00 3.18
2013 3582 1.327303 TAAGCAGGCTGTTTGGGTTG 58.673 50.000 24.47 0.00 0.00 3.77
2014 3583 2.080654 TTAAGCAGGCTGTTTGGGTT 57.919 45.000 24.47 8.93 0.00 4.11
2015 3584 1.686587 GTTTAAGCAGGCTGTTTGGGT 59.313 47.619 24.47 2.71 0.00 4.51
2016 3585 1.335872 CGTTTAAGCAGGCTGTTTGGG 60.336 52.381 24.47 8.56 0.00 4.12
2017 3586 1.335872 CCGTTTAAGCAGGCTGTTTGG 60.336 52.381 24.47 14.07 0.00 3.28
2018 3587 1.335872 CCCGTTTAAGCAGGCTGTTTG 60.336 52.381 24.47 9.17 0.00 2.93
2019 3588 0.958822 CCCGTTTAAGCAGGCTGTTT 59.041 50.000 20.41 20.41 0.00 2.83
2020 3589 0.179001 ACCCGTTTAAGCAGGCTGTT 60.179 50.000 17.16 7.32 0.00 3.16
2021 3590 0.605589 GACCCGTTTAAGCAGGCTGT 60.606 55.000 17.16 0.00 0.00 4.40
2022 3591 0.321653 AGACCCGTTTAAGCAGGCTG 60.322 55.000 10.94 10.94 0.00 4.85
2023 3592 0.036294 GAGACCCGTTTAAGCAGGCT 60.036 55.000 0.00 0.00 0.00 4.58
2024 3593 0.321298 TGAGACCCGTTTAAGCAGGC 60.321 55.000 0.00 0.00 0.00 4.85
2025 3594 2.178912 TTGAGACCCGTTTAAGCAGG 57.821 50.000 0.00 0.00 0.00 4.85
2026 3595 2.096417 CGTTTGAGACCCGTTTAAGCAG 60.096 50.000 0.00 0.00 0.00 4.24
2027 3596 1.868498 CGTTTGAGACCCGTTTAAGCA 59.132 47.619 0.00 0.00 0.00 3.91
2028 3597 1.399343 GCGTTTGAGACCCGTTTAAGC 60.399 52.381 0.00 0.00 0.00 3.09
2029 3598 2.140717 AGCGTTTGAGACCCGTTTAAG 58.859 47.619 0.00 0.00 0.00 1.85
2030 3599 2.137523 GAGCGTTTGAGACCCGTTTAA 58.862 47.619 0.00 0.00 0.00 1.52
2031 3600 1.787012 GAGCGTTTGAGACCCGTTTA 58.213 50.000 0.00 0.00 0.00 2.01
2032 3601 1.219522 CGAGCGTTTGAGACCCGTTT 61.220 55.000 0.00 0.00 0.00 3.60
2033 3602 1.663702 CGAGCGTTTGAGACCCGTT 60.664 57.895 0.00 0.00 0.00 4.44
2034 3603 2.049433 CGAGCGTTTGAGACCCGT 60.049 61.111 0.00 0.00 0.00 5.28
2035 3604 1.372499 TTCGAGCGTTTGAGACCCG 60.372 57.895 0.00 0.00 0.00 5.28
2036 3605 0.319641 AGTTCGAGCGTTTGAGACCC 60.320 55.000 0.00 0.00 0.00 4.46
2037 3606 0.784778 CAGTTCGAGCGTTTGAGACC 59.215 55.000 0.00 0.00 0.00 3.85
2038 3607 1.716581 CTCAGTTCGAGCGTTTGAGAC 59.283 52.381 10.31 0.00 37.96 3.36
2039 3608 2.051879 CTCAGTTCGAGCGTTTGAGA 57.948 50.000 10.31 0.00 37.96 3.27
2048 3617 0.320247 AAGGTGCAGCTCAGTTCGAG 60.320 55.000 20.46 0.00 45.37 4.04
2049 3618 0.106708 AAAGGTGCAGCTCAGTTCGA 59.893 50.000 20.46 0.00 0.00 3.71
2050 3619 0.514691 GAAAGGTGCAGCTCAGTTCG 59.485 55.000 20.46 0.00 0.00 3.95
2051 3620 1.597742 TGAAAGGTGCAGCTCAGTTC 58.402 50.000 20.46 18.85 0.00 3.01
2052 3621 2.283145 ATGAAAGGTGCAGCTCAGTT 57.717 45.000 20.46 10.14 0.00 3.16
2053 3622 2.283145 AATGAAAGGTGCAGCTCAGT 57.717 45.000 20.46 10.60 0.00 3.41
2054 3623 3.314635 GGATAATGAAAGGTGCAGCTCAG 59.685 47.826 20.46 0.00 0.00 3.35
2055 3624 3.282021 GGATAATGAAAGGTGCAGCTCA 58.718 45.455 20.46 14.55 0.00 4.26
2056 3625 3.282021 TGGATAATGAAAGGTGCAGCTC 58.718 45.455 20.46 8.62 0.00 4.09
2057 3626 3.285484 CTGGATAATGAAAGGTGCAGCT 58.715 45.455 13.85 13.85 0.00 4.24
2058 3627 2.223665 GCTGGATAATGAAAGGTGCAGC 60.224 50.000 8.11 8.11 46.02 5.25
2059 3628 2.360165 GGCTGGATAATGAAAGGTGCAG 59.640 50.000 0.00 0.00 33.78 4.41
2060 3629 2.025037 AGGCTGGATAATGAAAGGTGCA 60.025 45.455 0.00 0.00 0.00 4.57
2061 3630 2.659428 AGGCTGGATAATGAAAGGTGC 58.341 47.619 0.00 0.00 0.00 5.01
2062 3631 6.966534 ATTTAGGCTGGATAATGAAAGGTG 57.033 37.500 0.00 0.00 0.00 4.00
2063 3632 7.671398 CCATATTTAGGCTGGATAATGAAAGGT 59.329 37.037 0.00 0.00 31.38 3.50
2064 3633 7.123247 CCCATATTTAGGCTGGATAATGAAAGG 59.877 40.741 0.00 0.00 31.38 3.11
2065 3634 7.123247 CCCCATATTTAGGCTGGATAATGAAAG 59.877 40.741 0.00 0.00 31.38 2.62
2066 3635 6.953520 CCCCATATTTAGGCTGGATAATGAAA 59.046 38.462 0.00 0.00 31.38 2.69
2067 3636 6.493166 CCCCATATTTAGGCTGGATAATGAA 58.507 40.000 0.00 0.00 31.38 2.57
2068 3637 5.575571 GCCCCATATTTAGGCTGGATAATGA 60.576 44.000 0.00 0.00 43.62 2.57
2069 3638 4.646492 GCCCCATATTTAGGCTGGATAATG 59.354 45.833 0.00 0.00 43.62 1.90
2070 3639 4.871822 GCCCCATATTTAGGCTGGATAAT 58.128 43.478 0.00 0.00 43.62 1.28
2071 3640 4.316025 GCCCCATATTTAGGCTGGATAA 57.684 45.455 0.00 0.00 43.62 1.75
2073 3642 2.907458 GCCCCATATTTAGGCTGGAT 57.093 50.000 0.00 0.00 43.62 3.41
2079 3648 4.325344 CCCCTTATCTGCCCCATATTTAGG 60.325 50.000 0.00 0.00 0.00 2.69
2080 3649 4.860022 CCCCTTATCTGCCCCATATTTAG 58.140 47.826 0.00 0.00 0.00 1.85
2081 3650 3.011257 GCCCCTTATCTGCCCCATATTTA 59.989 47.826 0.00 0.00 0.00 1.40
2082 3651 2.225369 GCCCCTTATCTGCCCCATATTT 60.225 50.000 0.00 0.00 0.00 1.40
2083 3652 1.359130 GCCCCTTATCTGCCCCATATT 59.641 52.381 0.00 0.00 0.00 1.28
2084 3653 1.002857 GCCCCTTATCTGCCCCATAT 58.997 55.000 0.00 0.00 0.00 1.78
2085 3654 1.488705 CGCCCCTTATCTGCCCCATA 61.489 60.000 0.00 0.00 0.00 2.74
2086 3655 2.833913 CGCCCCTTATCTGCCCCAT 61.834 63.158 0.00 0.00 0.00 4.00
2087 3656 3.488569 CGCCCCTTATCTGCCCCA 61.489 66.667 0.00 0.00 0.00 4.96
2088 3657 4.956932 GCGCCCCTTATCTGCCCC 62.957 72.222 0.00 0.00 0.00 5.80
2089 3658 3.834013 GAGCGCCCCTTATCTGCCC 62.834 68.421 2.29 0.00 0.00 5.36
2090 3659 2.281139 GAGCGCCCCTTATCTGCC 60.281 66.667 2.29 0.00 0.00 4.85
2091 3660 2.663188 CGAGCGCCCCTTATCTGC 60.663 66.667 2.29 0.00 0.00 4.26
2092 3661 2.029666 CCGAGCGCCCCTTATCTG 59.970 66.667 2.29 0.00 0.00 2.90
2093 3662 3.234730 CCCGAGCGCCCCTTATCT 61.235 66.667 2.29 0.00 0.00 1.98
2094 3663 4.990553 GCCCGAGCGCCCCTTATC 62.991 72.222 2.29 0.00 0.00 1.75
2143 3712 1.779061 ATATGTGGGGTCGGATGGGC 61.779 60.000 0.00 0.00 0.00 5.36
2144 3713 1.651737 TATATGTGGGGTCGGATGGG 58.348 55.000 0.00 0.00 0.00 4.00
2145 3714 3.370527 GGAATATATGTGGGGTCGGATGG 60.371 52.174 0.00 0.00 0.00 3.51
2146 3715 3.519510 AGGAATATATGTGGGGTCGGATG 59.480 47.826 0.00 0.00 0.00 3.51
2147 3716 3.775316 GAGGAATATATGTGGGGTCGGAT 59.225 47.826 0.00 0.00 0.00 4.18
2148 3717 3.170717 GAGGAATATATGTGGGGTCGGA 58.829 50.000 0.00 0.00 0.00 4.55
2149 3718 3.173965 AGAGGAATATATGTGGGGTCGG 58.826 50.000 0.00 0.00 0.00 4.79
2150 3719 4.090090 AGAGAGGAATATATGTGGGGTCG 58.910 47.826 0.00 0.00 0.00 4.79
2151 3720 7.069331 CAGATAGAGAGGAATATATGTGGGGTC 59.931 44.444 0.00 0.00 0.00 4.46
2152 3721 6.900186 CAGATAGAGAGGAATATATGTGGGGT 59.100 42.308 0.00 0.00 0.00 4.95
2153 3722 6.183360 GCAGATAGAGAGGAATATATGTGGGG 60.183 46.154 0.00 0.00 0.00 4.96
2154 3723 6.610830 AGCAGATAGAGAGGAATATATGTGGG 59.389 42.308 0.00 0.00 0.00 4.61
2155 3724 7.658525 AGCAGATAGAGAGGAATATATGTGG 57.341 40.000 0.00 0.00 0.00 4.17
2156 3725 7.492020 GCAAGCAGATAGAGAGGAATATATGTG 59.508 40.741 0.00 0.00 0.00 3.21
2157 3726 7.364585 GGCAAGCAGATAGAGAGGAATATATGT 60.365 40.741 0.00 0.00 0.00 2.29
2158 3727 6.985645 GGCAAGCAGATAGAGAGGAATATATG 59.014 42.308 0.00 0.00 0.00 1.78
2159 3728 6.183360 CGGCAAGCAGATAGAGAGGAATATAT 60.183 42.308 0.00 0.00 0.00 0.86
2160 3729 5.126222 CGGCAAGCAGATAGAGAGGAATATA 59.874 44.000 0.00 0.00 0.00 0.86
2161 3730 4.081752 CGGCAAGCAGATAGAGAGGAATAT 60.082 45.833 0.00 0.00 0.00 1.28
2162 3731 3.256879 CGGCAAGCAGATAGAGAGGAATA 59.743 47.826 0.00 0.00 0.00 1.75
2163 3732 2.036992 CGGCAAGCAGATAGAGAGGAAT 59.963 50.000 0.00 0.00 0.00 3.01
2164 3733 1.410517 CGGCAAGCAGATAGAGAGGAA 59.589 52.381 0.00 0.00 0.00 3.36
2165 3734 1.035923 CGGCAAGCAGATAGAGAGGA 58.964 55.000 0.00 0.00 0.00 3.71
2166 3735 0.033228 CCGGCAAGCAGATAGAGAGG 59.967 60.000 0.00 0.00 0.00 3.69
2167 3736 1.035923 TCCGGCAAGCAGATAGAGAG 58.964 55.000 0.00 0.00 0.00 3.20
2168 3737 0.747255 GTCCGGCAAGCAGATAGAGA 59.253 55.000 0.00 0.00 0.00 3.10
2169 3738 0.249657 GGTCCGGCAAGCAGATAGAG 60.250 60.000 0.00 0.00 0.00 2.43
2170 3739 1.823295 GGTCCGGCAAGCAGATAGA 59.177 57.895 0.00 0.00 0.00 1.98
2171 3740 1.592669 CGGTCCGGCAAGCAGATAG 60.593 63.158 2.34 0.00 0.00 2.08
2172 3741 1.609635 TTCGGTCCGGCAAGCAGATA 61.610 55.000 12.29 0.00 0.00 1.98
2173 3742 2.257409 ATTCGGTCCGGCAAGCAGAT 62.257 55.000 12.29 0.00 0.00 2.90
2174 3743 2.852495 GATTCGGTCCGGCAAGCAGA 62.852 60.000 12.29 0.00 0.00 4.26
2175 3744 2.436646 ATTCGGTCCGGCAAGCAG 60.437 61.111 12.29 0.00 0.00 4.24
2176 3745 2.435938 GATTCGGTCCGGCAAGCA 60.436 61.111 12.29 0.00 0.00 3.91
2177 3746 3.202706 GGATTCGGTCCGGCAAGC 61.203 66.667 12.29 1.56 37.23 4.01
2191 3760 1.343478 ACGGATCTGGAGGTGAAGGAT 60.343 52.381 6.47 0.00 0.00 3.24
2235 3804 2.506061 CCATCTCCTCCTCAGGCCG 61.506 68.421 0.00 0.00 40.12 6.13
2236 3805 2.817056 GCCATCTCCTCCTCAGGCC 61.817 68.421 0.00 0.00 40.12 5.19
2237 3806 2.817056 GGCCATCTCCTCCTCAGGC 61.817 68.421 0.00 0.00 40.12 4.85
2343 3913 1.067974 CATCATCCATGCGCCATTTGT 59.932 47.619 4.18 0.00 0.00 2.83
2460 4031 1.544537 GGCCCATTATGTGTGCCGATA 60.545 52.381 0.00 0.00 41.59 2.92
2466 4037 1.299541 GACGAGGCCCATTATGTGTG 58.700 55.000 0.00 0.00 0.00 3.82
2472 4043 2.777972 CGTCGGACGAGGCCCATTA 61.778 63.158 25.29 0.00 46.05 1.90
2473 4044 4.143333 CGTCGGACGAGGCCCATT 62.143 66.667 25.29 0.00 46.05 3.16
2557 4128 3.770040 CCTCGCCGACATCCACCA 61.770 66.667 0.00 0.00 0.00 4.17
2626 4197 2.358125 CGTCCACCACAATGCGGA 60.358 61.111 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.