Multiple sequence alignment - TraesCS7A01G550200

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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 TraesCS7A01G550200 chr7A 100.000 5017 0 0 1 5017 724132025 724127009 0.000000e+00 9265
1 TraesCS7A01G550200 chr7A 90.476 105 9 1 4138 4242 129876933 129877036 2.440000e-28 137
2 TraesCS7A01G550200 chrUn 97.463 2286 45 9 2097 4380 92741030 92738756 0.000000e+00 3888
3 TraesCS7A01G550200 chrUn 89.957 1165 77 24 829 1976 92742183 92741042 0.000000e+00 1467
4 TraesCS7A01G550200 chrUn 97.500 640 13 1 4378 5017 92738633 92737997 0.000000e+00 1090
5 TraesCS7A01G550200 chrUn 87.727 220 24 3 3760 3979 92727350 92727134 2.320000e-63 254
6 TraesCS7A01G550200 chrUn 87.500 184 18 1 4834 5017 92726584 92726406 1.830000e-49 207
7 TraesCS7A01G550200 chr7B 96.702 1607 49 4 2091 3696 730171825 730170222 0.000000e+00 2671
8 TraesCS7A01G550200 chr7B 84.622 1190 106 34 835 1991 730172965 730171820 0.000000e+00 1112
9 TraesCS7A01G550200 chr7B 96.861 446 11 2 3693 4136 730170152 730169708 0.000000e+00 743
10 TraesCS7A01G550200 chr7B 93.409 440 29 0 4578 5017 730165979 730165540 0.000000e+00 652
11 TraesCS7A01G550200 chr7B 95.623 297 11 2 4283 4578 730166431 730166136 4.540000e-130 475
12 TraesCS7A01G550200 chr7B 82.544 401 43 13 3751 4148 730164669 730164293 1.350000e-85 327
13 TraesCS7A01G550200 chr7B 87.500 184 18 1 4834 5017 730163861 730163683 1.830000e-49 207
14 TraesCS7A01G550200 chr7B 93.243 74 5 0 4225 4298 730169706 730169633 5.310000e-20 110
15 TraesCS7A01G550200 chr3A 93.502 831 48 6 1 826 309884121 309883292 0.000000e+00 1230
16 TraesCS7A01G550200 chr3A 92.745 827 53 6 5 826 318201634 318202458 0.000000e+00 1188
17 TraesCS7A01G550200 chr3A 88.785 107 10 2 4143 4249 629669410 629669306 4.080000e-26 130
18 TraesCS7A01G550200 chr1A 92.900 831 50 9 1 826 170159016 170159842 0.000000e+00 1199
19 TraesCS7A01G550200 chr1A 91.176 136 10 2 1985 2120 376756342 376756209 3.080000e-42 183
20 TraesCS7A01G550200 chr6A 92.597 824 55 5 5 823 295346661 295347483 0.000000e+00 1179
21 TraesCS7A01G550200 chr6A 93.284 134 7 2 1964 2096 477910900 477910768 3.960000e-46 196
22 TraesCS7A01G550200 chr6A 96.610 118 3 1 1977 2093 475435172 475435055 1.430000e-45 195
23 TraesCS7A01G550200 chr2A 92.364 825 57 6 6 826 320573458 320572636 0.000000e+00 1170
24 TraesCS7A01G550200 chr2A 91.576 831 60 9 1 823 417919135 417918307 0.000000e+00 1138
25 TraesCS7A01G550200 chr2A 90.789 836 65 10 1 826 334741584 334742417 0.000000e+00 1107
26 TraesCS7A01G550200 chr2A 99.091 110 1 0 1986 2095 96153218 96153109 1.100000e-46 198
27 TraesCS7A01G550200 chr2A 94.355 124 3 3 1969 2092 138184292 138184411 2.380000e-43 187
28 TraesCS7A01G550200 chr7D 91.637 837 54 14 1 825 329226943 329227775 0.000000e+00 1144
29 TraesCS7A01G550200 chr7D 92.553 94 7 0 4136 4229 506141361 506141454 8.760000e-28 135
30 TraesCS7A01G550200 chr5A 91.325 830 63 7 1 823 351417002 351417829 0.000000e+00 1125
31 TraesCS7A01G550200 chr4D 85.325 477 61 5 2928 3404 497247369 497246902 7.550000e-133 484
32 TraesCS7A01G550200 chr4D 86.228 334 40 5 2179 2512 497248108 497247781 1.720000e-94 357
33 TraesCS7A01G550200 chr4D 84.559 136 21 0 3812 3947 497243624 497243489 8.760000e-28 135
34 TraesCS7A01G550200 chr3B 99.099 111 1 0 1985 2095 12156860 12156970 3.060000e-47 200
35 TraesCS7A01G550200 chr3B 91.837 98 7 1 4131 4228 804117473 804117569 8.760000e-28 135
36 TraesCS7A01G550200 chr3B 91.667 96 7 1 4140 4235 452283205 452283111 1.130000e-26 132
37 TraesCS7A01G550200 chr2D 95.902 122 4 1 1986 2107 640202155 640202275 3.960000e-46 196
38 TraesCS7A01G550200 chr3D 95.833 120 3 2 1986 2104 302930195 302930313 5.130000e-45 193
39 TraesCS7A01G550200 chr3D 94.505 91 5 0 4138 4228 509255107 509255197 1.880000e-29 141
40 TraesCS7A01G550200 chr5B 94.309 123 6 1 1972 2093 50531818 50531940 2.380000e-43 187
41 TraesCS7A01G550200 chr5B 92.708 96 5 2 4139 4234 83789840 83789747 2.440000e-28 137
42 TraesCS7A01G550200 chr2B 91.753 97 6 2 4132 4228 46846072 46846166 3.150000e-27 134


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 TraesCS7A01G550200 chr7A 724127009 724132025 5016 True 9265.000000 9265 100.000000 1 5017 1 chr7A.!!$R1 5016
1 TraesCS7A01G550200 chrUn 92737997 92742183 4186 True 2148.333333 3888 94.973333 829 5017 3 chrUn.!!$R2 4188
2 TraesCS7A01G550200 chrUn 92726406 92727350 944 True 230.500000 254 87.613500 3760 5017 2 chrUn.!!$R1 1257
3 TraesCS7A01G550200 chr7B 730163683 730172965 9282 True 787.125000 2671 91.313000 835 5017 8 chr7B.!!$R1 4182
4 TraesCS7A01G550200 chr3A 309883292 309884121 829 True 1230.000000 1230 93.502000 1 826 1 chr3A.!!$R1 825
5 TraesCS7A01G550200 chr3A 318201634 318202458 824 False 1188.000000 1188 92.745000 5 826 1 chr3A.!!$F1 821
6 TraesCS7A01G550200 chr1A 170159016 170159842 826 False 1199.000000 1199 92.900000 1 826 1 chr1A.!!$F1 825
7 TraesCS7A01G550200 chr6A 295346661 295347483 822 False 1179.000000 1179 92.597000 5 823 1 chr6A.!!$F1 818
8 TraesCS7A01G550200 chr2A 320572636 320573458 822 True 1170.000000 1170 92.364000 6 826 1 chr2A.!!$R2 820
9 TraesCS7A01G550200 chr2A 417918307 417919135 828 True 1138.000000 1138 91.576000 1 823 1 chr2A.!!$R3 822
10 TraesCS7A01G550200 chr2A 334741584 334742417 833 False 1107.000000 1107 90.789000 1 826 1 chr2A.!!$F2 825
11 TraesCS7A01G550200 chr7D 329226943 329227775 832 False 1144.000000 1144 91.637000 1 825 1 chr7D.!!$F1 824
12 TraesCS7A01G550200 chr5A 351417002 351417829 827 False 1125.000000 1125 91.325000 1 823 1 chr5A.!!$F1 822
13 TraesCS7A01G550200 chr4D 497243489 497248108 4619 True 325.333333 484 85.370667 2179 3947 3 chr4D.!!$R1 1768

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
879 901 0.675837 GGCCGTAACAGTTTCCCCTC 60.676 60.000 0.0 0.0 0.0 4.30 F
1907 1967 0.037590 CAACCCAAAGACCCGATCCA 59.962 55.000 0.0 0.0 0.0 3.41 F
2013 2078 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2140 0.033796 ATGTACTCCCTCCGTTCCGA 60.034 55.0 0.0 0.0 0.0 4.55 R
3734 7107 1.661341 ACTTGCGATCCTCATTCTGC 58.339 50.0 0.0 0.0 0.0 4.26 R
4151 7526 7.931578 AAAAACGTCTTACATTATGGGATGA 57.068 32.0 0.0 0.0 0.0 2.92 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
189 193 2.298729 GAGCAAAATGGGTTAGGTTGCA 59.701 45.455 9.13 0.00 45.47 4.08
215 221 3.146066 GCTATGGTGGATTTTGCGGATA 58.854 45.455 0.00 0.00 0.00 2.59
336 344 2.058798 CTCAACGAGCTAAAGAACGCA 58.941 47.619 0.00 0.00 0.00 5.24
386 394 2.614481 GGGCGAAATGGTGAAGTACTCA 60.614 50.000 0.00 0.00 0.00 3.41
466 478 2.993264 CGGTACAGGTCCGTGGGT 60.993 66.667 0.00 0.00 42.62 4.51
655 669 4.751767 TCCACTTGAAACCAAGCAAATT 57.248 36.364 5.20 0.00 43.61 1.82
690 705 5.046529 TCCAACAAAACATCATCAAAACCG 58.953 37.500 0.00 0.00 0.00 4.44
752 772 9.996554 AGGAATTTTTGAATTTAGGACGAAATT 57.003 25.926 3.34 3.34 40.81 1.82
783 805 2.986728 AGGCTAGAAAACAAAGAGGGGA 59.013 45.455 0.00 0.00 0.00 4.81
787 809 3.602205 AGAAAACAAAGAGGGGAGCTT 57.398 42.857 0.00 0.00 0.00 3.74
823 845 4.188937 ACCATGGCTCATGATACCAAAT 57.811 40.909 18.58 7.20 43.81 2.32
824 846 3.893200 ACCATGGCTCATGATACCAAATG 59.107 43.478 18.58 13.81 43.81 2.32
826 848 3.949586 TGGCTCATGATACCAAATGGA 57.050 42.857 13.74 0.00 38.94 3.41
827 849 3.554934 TGGCTCATGATACCAAATGGAC 58.445 45.455 13.74 0.00 38.94 4.02
828 850 2.549754 GGCTCATGATACCAAATGGACG 59.450 50.000 6.42 0.00 38.94 4.79
829 851 2.031682 GCTCATGATACCAAATGGACGC 60.032 50.000 6.42 0.00 38.94 5.19
830 852 2.549754 CTCATGATACCAAATGGACGCC 59.450 50.000 6.42 0.00 38.94 5.68
831 853 1.264020 CATGATACCAAATGGACGCCG 59.736 52.381 6.42 0.00 38.94 6.46
832 854 1.092921 TGATACCAAATGGACGCCGC 61.093 55.000 6.42 0.00 38.94 6.53
833 855 1.782028 GATACCAAATGGACGCCGCC 61.782 60.000 6.42 0.00 38.94 6.13
879 901 0.675837 GGCCGTAACAGTTTCCCCTC 60.676 60.000 0.00 0.00 0.00 4.30
912 934 2.127534 CCGAACGGAAAAACGGCG 60.128 61.111 4.80 4.80 38.98 6.46
961 983 1.973760 TCGTCCCCCGAAAAATCGA 59.026 52.632 0.00 0.00 44.03 3.59
987 1009 4.060667 CCACCCCCATCACCCCAC 62.061 72.222 0.00 0.00 0.00 4.61
988 1010 4.060667 CACCCCCATCACCCCACC 62.061 72.222 0.00 0.00 0.00 4.61
989 1011 4.301662 ACCCCCATCACCCCACCT 62.302 66.667 0.00 0.00 0.00 4.00
990 1012 3.420482 CCCCCATCACCCCACCTC 61.420 72.222 0.00 0.00 0.00 3.85
991 1013 3.420482 CCCCATCACCCCACCTCC 61.420 72.222 0.00 0.00 0.00 4.30
992 1014 2.613696 CCCATCACCCCACCTCCA 60.614 66.667 0.00 0.00 0.00 3.86
1163 1188 2.860628 CGCACGCGCACTCTTATCC 61.861 63.158 5.73 0.00 38.40 2.59
1260 1289 1.595993 TTCCTTCCTCGCTCCTGACG 61.596 60.000 0.00 0.00 0.00 4.35
1261 1290 2.046864 CCTTCCTCGCTCCTGACGA 61.047 63.158 0.00 0.00 38.02 4.20
1393 1422 1.507174 CCAGACTCTCCGTTCCGAC 59.493 63.158 0.00 0.00 0.00 4.79
1419 1454 0.247854 GCCGCGCTTGAAATTCTCTC 60.248 55.000 5.56 0.00 0.00 3.20
1430 1465 3.935203 TGAAATTCTCTCATTCTGACGCC 59.065 43.478 0.00 0.00 0.00 5.68
1431 1466 3.616956 AATTCTCTCATTCTGACGCCA 57.383 42.857 0.00 0.00 0.00 5.69
1438 1473 1.278985 TCATTCTGACGCCACCTTCAT 59.721 47.619 0.00 0.00 0.00 2.57
1449 1484 0.597568 CACCTTCATTTTCCAGCGCA 59.402 50.000 11.47 0.00 0.00 6.09
1719 1760 0.398239 TCTGCTGCCCAGAGATAGCT 60.398 55.000 0.00 0.00 45.44 3.32
1721 1762 1.901159 CTGCTGCCCAGAGATAGCTAT 59.099 52.381 5.76 5.76 44.64 2.97
1725 1766 0.820871 GCCCAGAGATAGCTATCCGG 59.179 60.000 26.65 23.04 33.17 5.14
1730 1771 1.181786 GAGATAGCTATCCGGCTGCT 58.818 55.000 26.65 17.14 43.01 4.24
1742 1783 1.534595 CCGGCTGCTGAAATTGTATGC 60.535 52.381 10.70 0.00 0.00 3.14
1744 1785 1.477700 GGCTGCTGAAATTGTATGCCA 59.522 47.619 0.00 0.00 38.99 4.92
1753 1794 6.147492 GCTGAAATTGTATGCCATGAACAAAA 59.853 34.615 0.00 0.00 36.75 2.44
1756 1797 9.716531 TGAAATTGTATGCCATGAACAAAAATA 57.283 25.926 0.00 0.00 36.75 1.40
1782 1842 7.817418 TTGGCTCACTGTTTTAGTTTCTAAT 57.183 32.000 0.00 0.00 37.60 1.73
1823 1883 5.717178 TCTTCTGTTATGGTAGCAAGAGACT 59.283 40.000 0.00 0.00 0.00 3.24
1825 1885 4.772624 TCTGTTATGGTAGCAAGAGACTGT 59.227 41.667 0.00 0.00 0.00 3.55
1837 1897 1.005332 AGAGACTGTAGAGGAGCAGCA 59.995 52.381 0.00 0.00 36.26 4.41
1843 1903 0.742635 GTAGAGGAGCAGCAACTGGC 60.743 60.000 0.00 0.00 45.30 4.85
1845 1905 4.711949 AGGAGCAGCAACTGGCCG 62.712 66.667 0.00 0.00 46.50 6.13
1866 1926 2.159282 GCTGGATCAGAAGCCAACAATG 60.159 50.000 0.00 0.00 41.34 2.82
1873 1933 4.681744 TCAGAAGCCAACAATGTTTCAAC 58.318 39.130 0.00 0.00 0.00 3.18
1907 1967 0.037590 CAACCCAAAGACCCGATCCA 59.962 55.000 0.00 0.00 0.00 3.41
1976 2041 7.315247 TGTTTTGTAAGATGGTGGATATTCG 57.685 36.000 0.00 0.00 0.00 3.34
1978 2043 7.392113 TGTTTTGTAAGATGGTGGATATTCGTT 59.608 33.333 0.00 0.00 0.00 3.85
1979 2044 7.548196 TTTGTAAGATGGTGGATATTCGTTC 57.452 36.000 0.00 0.00 0.00 3.95
1980 2045 6.228616 TGTAAGATGGTGGATATTCGTTCA 57.771 37.500 0.00 0.00 0.00 3.18
1982 2047 6.929049 TGTAAGATGGTGGATATTCGTTCATC 59.071 38.462 0.00 0.00 0.00 2.92
1983 2048 5.815233 AGATGGTGGATATTCGTTCATCT 57.185 39.130 7.39 7.39 36.17 2.90
1984 2049 6.179906 AGATGGTGGATATTCGTTCATCTT 57.820 37.500 7.39 0.00 37.24 2.40
1985 2050 6.595682 AGATGGTGGATATTCGTTCATCTTT 58.404 36.000 7.39 0.00 37.24 2.52
1986 2051 7.735917 AGATGGTGGATATTCGTTCATCTTTA 58.264 34.615 7.39 0.00 37.24 1.85
1987 2052 7.657761 AGATGGTGGATATTCGTTCATCTTTAC 59.342 37.037 7.39 0.00 37.24 2.01
1988 2053 6.884832 TGGTGGATATTCGTTCATCTTTACT 58.115 36.000 0.00 0.00 0.00 2.24
1989 2054 7.335627 TGGTGGATATTCGTTCATCTTTACTT 58.664 34.615 0.00 0.00 0.00 2.24
1990 2055 7.494625 TGGTGGATATTCGTTCATCTTTACTTC 59.505 37.037 0.00 0.00 0.00 3.01
1991 2056 7.041984 GGTGGATATTCGTTCATCTTTACTTCC 60.042 40.741 0.00 0.00 0.00 3.46
1992 2057 7.711339 GTGGATATTCGTTCATCTTTACTTCCT 59.289 37.037 0.00 0.00 0.00 3.36
1993 2058 7.926555 TGGATATTCGTTCATCTTTACTTCCTC 59.073 37.037 0.00 0.00 0.00 3.71
1994 2059 7.385478 GGATATTCGTTCATCTTTACTTCCTCC 59.615 40.741 0.00 0.00 0.00 4.30
1995 2060 4.106029 TCGTTCATCTTTACTTCCTCCG 57.894 45.455 0.00 0.00 0.00 4.63
1996 2061 3.508793 TCGTTCATCTTTACTTCCTCCGT 59.491 43.478 0.00 0.00 0.00 4.69
1997 2062 4.021719 TCGTTCATCTTTACTTCCTCCGTT 60.022 41.667 0.00 0.00 0.00 4.44
1998 2063 4.326548 CGTTCATCTTTACTTCCTCCGTTC 59.673 45.833 0.00 0.00 0.00 3.95
1999 2064 4.467198 TCATCTTTACTTCCTCCGTTCC 57.533 45.455 0.00 0.00 0.00 3.62
2000 2065 3.835978 TCATCTTTACTTCCTCCGTTCCA 59.164 43.478 0.00 0.00 0.00 3.53
2001 2066 4.285003 TCATCTTTACTTCCTCCGTTCCAA 59.715 41.667 0.00 0.00 0.00 3.53
2002 2067 4.693042 TCTTTACTTCCTCCGTTCCAAA 57.307 40.909 0.00 0.00 0.00 3.28
2003 2068 5.237236 TCTTTACTTCCTCCGTTCCAAAT 57.763 39.130 0.00 0.00 0.00 2.32
2004 2069 5.627135 TCTTTACTTCCTCCGTTCCAAATT 58.373 37.500 0.00 0.00 0.00 1.82
2005 2070 6.771573 TCTTTACTTCCTCCGTTCCAAATTA 58.228 36.000 0.00 0.00 0.00 1.40
2006 2071 6.652062 TCTTTACTTCCTCCGTTCCAAATTAC 59.348 38.462 0.00 0.00 0.00 1.89
2007 2072 4.635699 ACTTCCTCCGTTCCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
2008 2073 4.576879 ACTTCCTCCGTTCCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
2009 2074 3.241067 TCCTCCGTTCCAAATTACTCG 57.759 47.619 0.00 0.00 0.00 4.18
2010 2075 2.564062 TCCTCCGTTCCAAATTACTCGT 59.436 45.455 0.00 0.00 0.00 4.18
2011 2076 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2012 2077 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2013 2078 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
2014 2079 1.722464 CGTTCCAAATTACTCGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
2015 2080 2.222508 CGTTCCAAATTACTCGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
2016 2081 2.991190 GTTCCAAATTACTCGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
2017 2082 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
2018 2083 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
2019 2084 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
2020 2085 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
2021 2086 4.334443 CAAATTACTCGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
2022 2087 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
2023 2088 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
2024 2089 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
2025 2090 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
2026 2091 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
2027 2092 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
2028 2093 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
2029 2094 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
2030 2095 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
2031 2096 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
2032 2097 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
2033 2098 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
2034 2099 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
2035 2100 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
2036 2101 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
2037 2102 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
2038 2103 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
2064 2129 6.537453 ACATCTAGATACATCCATACCTGC 57.463 41.667 4.54 0.00 0.00 4.85
2065 2130 5.126222 ACATCTAGATACATCCATACCTGCG 59.874 44.000 4.54 0.00 0.00 5.18
2066 2131 4.918588 TCTAGATACATCCATACCTGCGA 58.081 43.478 0.00 0.00 0.00 5.10
2067 2132 3.944055 AGATACATCCATACCTGCGAC 57.056 47.619 0.00 0.00 0.00 5.19
2068 2133 3.230976 AGATACATCCATACCTGCGACA 58.769 45.455 0.00 0.00 0.00 4.35
2069 2134 3.641436 AGATACATCCATACCTGCGACAA 59.359 43.478 0.00 0.00 0.00 3.18
2070 2135 2.315925 ACATCCATACCTGCGACAAG 57.684 50.000 0.00 0.00 0.00 3.16
2071 2136 1.555075 ACATCCATACCTGCGACAAGT 59.445 47.619 0.00 0.00 0.00 3.16
2072 2137 2.764010 ACATCCATACCTGCGACAAGTA 59.236 45.455 0.00 0.00 0.00 2.24
2073 2138 3.196901 ACATCCATACCTGCGACAAGTAA 59.803 43.478 0.00 0.00 0.00 2.24
2074 2139 4.141711 ACATCCATACCTGCGACAAGTAAT 60.142 41.667 0.00 0.00 0.00 1.89
2075 2140 4.481368 TCCATACCTGCGACAAGTAATT 57.519 40.909 0.00 0.00 0.00 1.40
2076 2141 4.439057 TCCATACCTGCGACAAGTAATTC 58.561 43.478 0.00 0.00 0.00 2.17
2077 2142 3.245284 CCATACCTGCGACAAGTAATTCG 59.755 47.826 0.00 0.00 38.31 3.34
2078 2143 1.722011 ACCTGCGACAAGTAATTCGG 58.278 50.000 0.00 0.00 35.73 4.30
2079 2144 1.274167 ACCTGCGACAAGTAATTCGGA 59.726 47.619 0.00 0.00 35.73 4.55
2080 2145 2.289195 ACCTGCGACAAGTAATTCGGAA 60.289 45.455 0.00 0.00 35.02 4.30
2081 2146 2.093783 CCTGCGACAAGTAATTCGGAAC 59.906 50.000 0.00 0.00 35.02 3.62
2128 2193 4.349636 TCTGGTTCACTCCCTAAATTGTCA 59.650 41.667 0.00 0.00 0.00 3.58
2134 2199 4.041567 TCACTCCCTAAATTGTCAAGCTCA 59.958 41.667 0.00 0.00 0.00 4.26
2147 2212 5.643664 TGTCAAGCTCATATTCATTGTTGC 58.356 37.500 0.00 0.00 0.00 4.17
2333 2400 3.525199 ACAATATCTGGAGGCAGGAGTTT 59.475 43.478 0.00 0.00 0.00 2.66
2539 2606 7.690256 AGGTACTTCATTTTACACCTCTGAAT 58.310 34.615 0.00 0.00 27.25 2.57
2540 2607 8.164070 AGGTACTTCATTTTACACCTCTGAATT 58.836 33.333 0.00 0.00 27.25 2.17
2541 2608 8.793592 GGTACTTCATTTTACACCTCTGAATTT 58.206 33.333 0.00 0.00 0.00 1.82
2570 2637 7.390440 TCAGACTTTTCTTCAGTTTCTTGTTCA 59.610 33.333 0.00 0.00 0.00 3.18
2585 2652 1.269174 TGTTCACATTGGCATGGAACG 59.731 47.619 12.94 0.00 40.23 3.95
2593 2660 2.481289 TGGCATGGAACGATGTGTTA 57.519 45.000 0.00 0.00 42.09 2.41
2597 2664 5.129634 TGGCATGGAACGATGTGTTATATT 58.870 37.500 0.00 0.00 42.09 1.28
2602 2669 8.503196 GCATGGAACGATGTGTTATATTTATCA 58.497 33.333 0.00 0.00 42.09 2.15
3107 3479 2.125512 CGCCCTGCTACTGTCCAC 60.126 66.667 0.00 0.00 0.00 4.02
3194 3566 2.926838 GTCAGCTCGTCTCAAGGAATTC 59.073 50.000 0.00 0.00 0.00 2.17
3728 7101 6.456501 TGGTTTCACTTACTAAGAGAAGCTC 58.543 40.000 16.63 10.70 38.88 4.09
4151 7526 8.090788 TCTTGTGCTTAATAATCTACTCCCTT 57.909 34.615 0.00 0.00 0.00 3.95
4201 7576 3.123804 ACTGCACTAGTGTCAAAAGACG 58.876 45.455 23.44 11.15 38.49 4.18
4265 7643 5.611796 TCAACTACATGCACAGTGATTTC 57.388 39.130 4.15 0.00 0.00 2.17
4322 10917 9.656040 TCATTCAAGGATACAAAAATGAATTGG 57.344 29.630 0.00 0.00 37.05 3.16
4426 11161 9.998106 AGTATGGAGTAATTATGCGTAAGAATT 57.002 29.630 4.43 0.00 36.57 2.17
4461 11196 7.865706 TGGAGTAATTTTTCTATGCCTTCTC 57.134 36.000 0.00 0.00 0.00 2.87
4502 11237 4.416516 TGAGAGTGGAGAATGAACAGGTA 58.583 43.478 0.00 0.00 0.00 3.08
4638 11531 2.590821 ACCTGAAGTTGCAGCAAGAAT 58.409 42.857 8.49 0.00 34.56 2.40
4677 11570 1.953686 GTGCTTCAACAAAGGTGGCTA 59.046 47.619 0.00 0.00 35.37 3.93
4776 11669 8.098220 ACAGCACCCATTTTAATTGAATTTTC 57.902 30.769 0.00 0.00 0.00 2.29
4920 13670 3.064820 CCTTGTTAATCGGCATGTGGTAC 59.935 47.826 0.00 0.00 0.00 3.34
5012 13762 0.945743 CTGCAGCAGCGTCACTTGTA 60.946 55.000 10.14 0.00 46.23 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 193 3.026694 GCAAAATCCACCATAGCCTTCT 58.973 45.455 0.00 0.00 0.00 2.85
215 221 5.987019 TTAACTAGGCCTTCCACCATATT 57.013 39.130 12.58 0.00 33.74 1.28
386 394 2.603776 GACCCCCAGGACAGTCGT 60.604 66.667 0.00 0.00 36.73 4.34
389 397 2.923035 CACGACCCCCAGGACAGT 60.923 66.667 0.00 0.00 36.73 3.55
466 478 0.113776 AAGTCTCTGGACACCCCGTA 59.886 55.000 0.00 0.00 44.36 4.02
723 741 8.348285 TCGTCCTAAATTCAAAAATTCCTCAT 57.652 30.769 0.00 0.00 33.93 2.90
726 745 9.996554 AATTTCGTCCTAAATTCAAAAATTCCT 57.003 25.926 0.00 0.00 34.71 3.36
752 772 9.398538 TCTTTGTTTTCTAGCCTAGTTTTGTTA 57.601 29.630 0.00 0.00 0.00 2.41
783 805 3.882888 TGGTTTCTCACGAAATTGAAGCT 59.117 39.130 0.00 0.00 40.91 3.74
787 809 3.057596 GCCATGGTTTCTCACGAAATTGA 60.058 43.478 14.67 0.00 40.91 2.57
830 852 3.545124 TACACCCAAGGCAGTGGCG 62.545 63.158 11.51 0.00 42.47 5.69
831 853 1.971695 GTACACCCAAGGCAGTGGC 60.972 63.158 9.02 9.02 38.34 5.01
832 854 1.303317 GGTACACCCAAGGCAGTGG 60.303 63.158 0.00 0.40 38.34 4.00
833 855 1.454104 TGGTACACCCAAGGCAGTG 59.546 57.895 0.00 0.00 41.50 3.66
879 901 2.534019 CGGATCGCAACGGGAATGG 61.534 63.158 0.00 0.00 0.00 3.16
975 997 2.613696 TGGAGGTGGGGTGATGGG 60.614 66.667 0.00 0.00 0.00 4.00
979 1001 2.203938 GGAGTGGAGGTGGGGTGA 60.204 66.667 0.00 0.00 0.00 4.02
987 1009 2.914289 GCCATGGAGGAGTGGAGG 59.086 66.667 18.40 0.00 41.22 4.30
988 1010 2.503061 CGCCATGGAGGAGTGGAG 59.497 66.667 18.40 0.00 41.22 3.86
1146 1171 2.526120 GGGATAAGAGTGCGCGTGC 61.526 63.158 15.48 15.48 43.20 5.34
1152 1177 1.149401 GGGCAGGGGATAAGAGTGC 59.851 63.158 0.00 0.00 0.00 4.40
1158 1183 3.168528 GGCGAGGGCAGGGGATAA 61.169 66.667 0.00 0.00 42.47 1.75
1235 1260 0.684805 GAGCGAGGAAGGAAGGAGGA 60.685 60.000 0.00 0.00 0.00 3.71
1369 1398 4.069232 CGGAGAGTCTGGCGGCAA 62.069 66.667 14.48 0.99 0.00 4.52
1419 1454 1.742761 ATGAAGGTGGCGTCAGAATG 58.257 50.000 0.00 0.00 37.54 2.67
1430 1465 0.597568 TGCGCTGGAAAATGAAGGTG 59.402 50.000 9.73 0.00 0.00 4.00
1431 1466 0.598065 GTGCGCTGGAAAATGAAGGT 59.402 50.000 9.73 0.00 0.00 3.50
1438 1473 2.668212 CTCCCGTGCGCTGGAAAA 60.668 61.111 19.05 5.16 0.00 2.29
1719 1760 2.418368 ACAATTTCAGCAGCCGGATA 57.582 45.000 5.05 0.00 0.00 2.59
1721 1762 2.016318 CATACAATTTCAGCAGCCGGA 58.984 47.619 5.05 0.00 0.00 5.14
1725 1766 2.945447 TGGCATACAATTTCAGCAGC 57.055 45.000 0.00 0.00 0.00 5.25
1730 1771 8.618702 ATTTTTGTTCATGGCATACAATTTCA 57.381 26.923 14.69 0.19 32.39 2.69
1742 1783 6.875195 AGTGAGCCAAATATTTTTGTTCATGG 59.125 34.615 13.59 5.95 40.55 3.66
1744 1785 7.444299 ACAGTGAGCCAAATATTTTTGTTCAT 58.556 30.769 13.59 4.93 40.55 2.57
1753 1794 8.860088 AGAAACTAAAACAGTGAGCCAAATATT 58.140 29.630 0.00 0.00 37.63 1.28
1756 1797 6.715347 AGAAACTAAAACAGTGAGCCAAAT 57.285 33.333 0.00 0.00 37.63 2.32
1760 1801 8.100508 AGAATTAGAAACTAAAACAGTGAGCC 57.899 34.615 0.00 0.00 37.63 4.70
1763 1804 9.052759 GGTGAGAATTAGAAACTAAAACAGTGA 57.947 33.333 0.00 0.00 37.63 3.41
1764 1805 8.009974 CGGTGAGAATTAGAAACTAAAACAGTG 58.990 37.037 0.00 0.00 37.63 3.66
1765 1806 7.172703 CCGGTGAGAATTAGAAACTAAAACAGT 59.827 37.037 0.00 0.00 40.05 3.55
1767 1808 6.993902 ACCGGTGAGAATTAGAAACTAAAACA 59.006 34.615 6.12 0.00 0.00 2.83
1768 1809 7.295930 CACCGGTGAGAATTAGAAACTAAAAC 58.704 38.462 31.31 0.00 0.00 2.43
1782 1842 1.420430 AGAAGAACCACCGGTGAGAA 58.580 50.000 36.07 0.00 35.34 2.87
1788 1848 2.256117 AACAGAAGAAGAACCACCGG 57.744 50.000 0.00 0.00 0.00 5.28
1823 1883 0.610174 CCAGTTGCTGCTCCTCTACA 59.390 55.000 0.00 0.00 0.00 2.74
1825 1885 1.599047 GCCAGTTGCTGCTCCTCTA 59.401 57.895 0.00 0.00 36.87 2.43
1837 1897 1.841302 TTCTGATCCAGCGGCCAGTT 61.841 55.000 2.24 0.00 0.00 3.16
1843 1903 1.078214 TTGGCTTCTGATCCAGCGG 60.078 57.895 0.00 0.00 36.85 5.52
1845 1905 1.538047 TTGTTGGCTTCTGATCCAGC 58.462 50.000 6.43 6.43 33.32 4.85
1866 1926 1.477105 GAAACCGCTGCAGTTGAAAC 58.523 50.000 16.64 0.00 0.00 2.78
1873 1933 3.659092 TTGCCGAAACCGCTGCAG 61.659 61.111 10.11 10.11 34.81 4.41
1907 1967 5.086104 TGACCTCTCGCTTTAGCTTTATT 57.914 39.130 0.00 0.00 39.32 1.40
1976 2041 4.630505 GGAACGGAGGAAGTAAAGATGAAC 59.369 45.833 0.00 0.00 0.00 3.18
1978 2043 3.835978 TGGAACGGAGGAAGTAAAGATGA 59.164 43.478 0.00 0.00 0.00 2.92
1979 2044 4.202245 TGGAACGGAGGAAGTAAAGATG 57.798 45.455 0.00 0.00 0.00 2.90
1980 2045 4.903045 TTGGAACGGAGGAAGTAAAGAT 57.097 40.909 0.00 0.00 0.00 2.40
1982 2047 5.959618 AATTTGGAACGGAGGAAGTAAAG 57.040 39.130 0.00 0.00 0.00 1.85
1983 2048 6.536447 AGTAATTTGGAACGGAGGAAGTAAA 58.464 36.000 0.00 0.00 0.00 2.01
1984 2049 6.117975 AGTAATTTGGAACGGAGGAAGTAA 57.882 37.500 0.00 0.00 0.00 2.24
1985 2050 5.622914 CGAGTAATTTGGAACGGAGGAAGTA 60.623 44.000 0.00 0.00 0.00 2.24
1986 2051 4.576879 GAGTAATTTGGAACGGAGGAAGT 58.423 43.478 0.00 0.00 0.00 3.01
1987 2052 3.617263 CGAGTAATTTGGAACGGAGGAAG 59.383 47.826 0.00 0.00 0.00 3.46
1988 2053 3.007182 ACGAGTAATTTGGAACGGAGGAA 59.993 43.478 0.00 0.00 0.00 3.36
1989 2054 2.564062 ACGAGTAATTTGGAACGGAGGA 59.436 45.455 0.00 0.00 0.00 3.71
1990 2055 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1991 2056 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
1992 2057 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
1993 2058 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
1994 2059 1.722464 TGCGACGAGTAATTTGGAACG 59.278 47.619 0.00 0.00 0.00 3.95
1995 2060 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
1996 2061 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
1997 2062 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
1998 2063 4.334443 CATTTCTGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
1999 2064 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
2000 2065 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
2001 2066 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
2002 2067 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
2003 2068 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
2004 2069 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
2005 2070 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
2006 2071 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
2007 2072 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
2008 2073 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
2009 2074 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
2010 2075 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
2011 2076 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
2012 2077 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
2038 2103 8.700051 GCAGGTATGGATGTATCTAGATGTATT 58.300 37.037 15.79 0.00 0.00 1.89
2039 2104 7.013750 CGCAGGTATGGATGTATCTAGATGTAT 59.986 40.741 15.79 9.11 0.00 2.29
2040 2105 6.318900 CGCAGGTATGGATGTATCTAGATGTA 59.681 42.308 15.79 4.44 0.00 2.29
2041 2106 5.126222 CGCAGGTATGGATGTATCTAGATGT 59.874 44.000 15.79 1.25 0.00 3.06
2042 2107 5.358160 TCGCAGGTATGGATGTATCTAGATG 59.642 44.000 15.79 0.00 0.00 2.90
2043 2108 5.358442 GTCGCAGGTATGGATGTATCTAGAT 59.642 44.000 10.73 10.73 0.00 1.98
2044 2109 4.700692 GTCGCAGGTATGGATGTATCTAGA 59.299 45.833 0.00 0.00 0.00 2.43
2045 2110 4.459337 TGTCGCAGGTATGGATGTATCTAG 59.541 45.833 0.00 0.00 0.00 2.43
2046 2111 4.403734 TGTCGCAGGTATGGATGTATCTA 58.596 43.478 0.00 0.00 0.00 1.98
2047 2112 3.230976 TGTCGCAGGTATGGATGTATCT 58.769 45.455 0.00 0.00 0.00 1.98
2048 2113 3.660501 TGTCGCAGGTATGGATGTATC 57.339 47.619 0.00 0.00 0.00 2.24
2049 2114 3.388024 ACTTGTCGCAGGTATGGATGTAT 59.612 43.478 0.00 0.00 0.00 2.29
2050 2115 2.764010 ACTTGTCGCAGGTATGGATGTA 59.236 45.455 0.00 0.00 0.00 2.29
2051 2116 1.555075 ACTTGTCGCAGGTATGGATGT 59.445 47.619 0.00 0.00 0.00 3.06
2052 2117 2.315925 ACTTGTCGCAGGTATGGATG 57.684 50.000 0.00 0.00 0.00 3.51
2053 2118 4.689612 ATTACTTGTCGCAGGTATGGAT 57.310 40.909 3.46 0.00 0.00 3.41
2054 2119 4.439057 GAATTACTTGTCGCAGGTATGGA 58.561 43.478 3.46 0.00 0.00 3.41
2055 2120 3.245284 CGAATTACTTGTCGCAGGTATGG 59.755 47.826 3.46 0.00 0.00 2.74
2056 2121 3.245284 CCGAATTACTTGTCGCAGGTATG 59.755 47.826 3.46 0.00 35.93 2.39
2057 2122 3.131577 TCCGAATTACTTGTCGCAGGTAT 59.868 43.478 3.46 0.00 35.93 2.73
2058 2123 2.492881 TCCGAATTACTTGTCGCAGGTA 59.507 45.455 0.00 0.00 35.93 3.08
2059 2124 1.274167 TCCGAATTACTTGTCGCAGGT 59.726 47.619 0.00 0.91 35.93 4.00
2060 2125 2.004583 TCCGAATTACTTGTCGCAGG 57.995 50.000 0.00 0.00 35.93 4.85
2061 2126 2.222508 CGTTCCGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 35.93 5.18
2062 2127 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
2063 2128 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
2064 2129 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
2065 2130 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2066 2131 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2067 2132 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2068 2133 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2069 2134 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2070 2135 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2071 2136 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2072 2137 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
2073 2138 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
2074 2139 0.251297 TGTACTCCCTCCGTTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
2075 2140 0.033796 ATGTACTCCCTCCGTTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
2076 2141 0.384669 GATGTACTCCCTCCGTTCCG 59.615 60.000 0.00 0.00 0.00 4.30
2077 2142 0.384669 CGATGTACTCCCTCCGTTCC 59.615 60.000 0.00 0.00 0.00 3.62
2078 2143 0.248949 GCGATGTACTCCCTCCGTTC 60.249 60.000 0.00 0.00 0.00 3.95
2079 2144 0.968901 TGCGATGTACTCCCTCCGTT 60.969 55.000 0.00 0.00 0.00 4.44
2080 2145 0.968901 TTGCGATGTACTCCCTCCGT 60.969 55.000 0.00 0.00 0.00 4.69
2081 2146 0.249073 CTTGCGATGTACTCCCTCCG 60.249 60.000 0.00 0.00 0.00 4.63
2082 2147 0.824759 ACTTGCGATGTACTCCCTCC 59.175 55.000 0.00 0.00 0.00 4.30
2083 2148 1.204941 ACACTTGCGATGTACTCCCTC 59.795 52.381 0.00 0.00 0.00 4.30
2084 2149 1.267121 ACACTTGCGATGTACTCCCT 58.733 50.000 0.00 0.00 0.00 4.20
2085 2150 2.094762 AACACTTGCGATGTACTCCC 57.905 50.000 0.00 0.00 0.00 4.30
2086 2151 3.123621 CAGAAACACTTGCGATGTACTCC 59.876 47.826 0.00 0.00 0.00 3.85
2087 2152 3.123621 CCAGAAACACTTGCGATGTACTC 59.876 47.826 0.00 0.00 0.00 2.59
2088 2153 3.067106 CCAGAAACACTTGCGATGTACT 58.933 45.455 0.00 0.00 0.00 2.73
2089 2154 2.806244 ACCAGAAACACTTGCGATGTAC 59.194 45.455 0.00 0.00 0.00 2.90
2090 2155 3.120321 ACCAGAAACACTTGCGATGTA 57.880 42.857 0.00 0.00 0.00 2.29
2091 2156 1.967319 ACCAGAAACACTTGCGATGT 58.033 45.000 0.00 0.00 0.00 3.06
2092 2157 2.290367 TGAACCAGAAACACTTGCGATG 59.710 45.455 0.00 0.00 0.00 3.84
2093 2158 2.290641 GTGAACCAGAAACACTTGCGAT 59.709 45.455 0.00 0.00 0.00 4.58
2128 2193 3.489738 GCGGCAACAATGAATATGAGCTT 60.490 43.478 0.00 0.00 0.00 3.74
2134 2199 2.760092 ACAAGGCGGCAACAATGAATAT 59.240 40.909 13.08 0.00 0.00 1.28
2144 2209 1.103803 TGTTTACAACAAGGCGGCAA 58.896 45.000 13.08 0.00 38.72 4.52
2147 2212 2.292016 TGTGATGTTTACAACAAGGCGG 59.708 45.455 0.00 0.00 45.86 6.13
2165 2230 0.036388 ATACCTGCAGGAACCGTGTG 60.036 55.000 39.19 9.60 38.94 3.82
2166 2231 0.690762 AATACCTGCAGGAACCGTGT 59.309 50.000 39.19 17.30 38.94 4.49
2318 2385 0.322008 GGTGAAACTCCTGCCTCCAG 60.322 60.000 0.00 0.00 36.42 3.86
2333 2400 3.389656 TGGAGTCTGTATTTGTGTGGTGA 59.610 43.478 0.00 0.00 0.00 4.02
2540 2607 9.410556 CAAGAAACTGAAGAAAAGTCTGAAAAA 57.589 29.630 0.00 0.00 33.05 1.94
2541 2608 8.576442 ACAAGAAACTGAAGAAAAGTCTGAAAA 58.424 29.630 0.00 0.00 33.05 2.29
2570 2637 1.473677 CACATCGTTCCATGCCAATGT 59.526 47.619 0.00 0.00 31.27 2.71
2593 2660 6.995091 GCAGAACAAGAGAGGGTGATAAATAT 59.005 38.462 0.00 0.00 0.00 1.28
2597 2664 3.582647 TGCAGAACAAGAGAGGGTGATAA 59.417 43.478 0.00 0.00 0.00 1.75
2602 2669 0.036022 GCTGCAGAACAAGAGAGGGT 59.964 55.000 20.43 0.00 0.00 4.34
3107 3479 5.107109 TGAAATTGTCAATGTTCTCCACG 57.893 39.130 0.00 0.00 31.51 4.94
3194 3566 4.000988 ACGGGTCATGTGCTTTAAAGTAG 58.999 43.478 16.38 1.31 0.00 2.57
3645 6944 5.422666 CCGTAGACATAACATACACGGTA 57.577 43.478 0.00 0.00 41.81 4.02
3667 6966 6.128661 TGACAAGCGATTGTTGTAAGATACAC 60.129 38.462 21.37 3.57 38.26 2.90
3728 7101 2.223433 GCGATCCTCATTCTGCCAAAAG 60.223 50.000 0.00 0.00 0.00 2.27
3734 7107 1.661341 ACTTGCGATCCTCATTCTGC 58.339 50.000 0.00 0.00 0.00 4.26
4151 7526 7.931578 AAAAACGTCTTACATTATGGGATGA 57.068 32.000 0.00 0.00 0.00 2.92
4198 7573 3.067180 TCCGTCCCATAATGTAAGACGTC 59.933 47.826 7.70 7.70 46.62 4.34
4201 7576 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
4461 11196 7.329226 CACTCTCAGCTTCTCTTTTCTTCTTAG 59.671 40.741 0.00 0.00 0.00 2.18
4502 11237 1.151668 CAAGCTCTACGCAAACAGCT 58.848 50.000 0.00 0.00 44.28 4.24
4638 11531 3.017442 CACTATCCCTCGTTGACTCAGA 58.983 50.000 0.00 0.00 0.00 3.27
4677 11570 6.461509 CCAGAGTTACCTTTTGTTGCATTTCT 60.462 38.462 0.00 0.00 0.00 2.52
4776 11669 5.695851 AAAAAGGTGCTACATGTGAAGAG 57.304 39.130 9.11 0.00 0.00 2.85
4920 13670 8.245491 TCATGTCAAATCATATGAACAAACCAG 58.755 33.333 9.99 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.