Multiple sequence alignment - TraesCS3B01G189700

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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 TraesCS3B01G189700 chr3B 100.000 5796 0 0 1 5796 201869420 201875215 0.000000e+00 10704.0
1 TraesCS3B01G189700 chr3B 90.323 186 16 2 1 185 49121262 49121078 5.800000e-60 243.0
2 TraesCS3B01G189700 chr3B 89.730 185 16 2 1 185 232009741 232009922 3.490000e-57 233.0
3 TraesCS3B01G189700 chr3B 87.912 91 11 0 2739 2829 486386622 486386712 2.210000e-19 108.0
4 TraesCS3B01G189700 chr3D 95.135 4851 157 25 446 5263 138885057 138889861 0.000000e+00 7577.0
5 TraesCS3B01G189700 chr3D 94.371 533 21 7 5267 5796 138889950 138890476 0.000000e+00 809.0
6 TraesCS3B01G189700 chr3D 84.810 79 12 0 2751 2829 603997459 603997537 4.810000e-11 80.5
7 TraesCS3B01G189700 chr3A 94.689 2994 112 20 2826 5790 157024154 157027129 0.000000e+00 4604.0
8 TraesCS3B01G189700 chr3A 94.859 2587 89 15 180 2746 157021592 157024154 0.000000e+00 4000.0
9 TraesCS3B01G189700 chr5B 92.737 179 12 1 1 178 395913665 395913487 2.070000e-64 257.0
10 TraesCS3B01G189700 chr7B 91.351 185 14 2 1 184 680866976 680867159 9.640000e-63 252.0
11 TraesCS3B01G189700 chr7B 83.908 87 12 2 2744 2829 442094283 442094198 1.340000e-11 82.4
12 TraesCS3B01G189700 chr7B 84.091 88 10 3 2744 2829 457143785 457143700 1.340000e-11 82.4
13 TraesCS3B01G189700 chr7B 81.720 93 15 2 2738 2829 291457985 291458076 6.230000e-10 76.8
14 TraesCS3B01G189700 chr6D 90.957 188 14 2 1 187 427316434 427316619 3.470000e-62 250.0
15 TraesCS3B01G189700 chr6D 91.011 178 14 2 1 178 422032749 422032574 7.510000e-59 239.0
16 TraesCS3B01G189700 chr1A 90.710 183 14 2 1 182 117881856 117882036 2.090000e-59 241.0
17 TraesCS3B01G189700 chr1A 90.526 95 7 2 2745 2837 474384832 474384738 2.190000e-24 124.0
18 TraesCS3B01G189700 chr7D 91.061 179 13 2 1 178 77497520 77497696 7.510000e-59 239.0
19 TraesCS3B01G189700 chr1D 89.617 183 16 2 1 182 53253358 53253538 4.520000e-56 230.0
20 TraesCS3B01G189700 chr4B 87.209 86 11 0 2745 2830 660583541 660583456 1.330000e-16 99.0
21 TraesCS3B01G189700 chr7A 83.333 90 9 5 2745 2831 21837935 21837849 1.730000e-10 78.7


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 TraesCS3B01G189700 chr3B 201869420 201875215 5795 False 10704 10704 100.000 1 5796 1 chr3B.!!$F1 5795
1 TraesCS3B01G189700 chr3D 138885057 138890476 5419 False 4193 7577 94.753 446 5796 2 chr3D.!!$F2 5350
2 TraesCS3B01G189700 chr3A 157021592 157027129 5537 False 4302 4604 94.774 180 5790 2 chr3A.!!$F1 5610

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
149 150 0.035598 TCTTCGATTTTGGACCGCCA 59.964 50.000 0.00 0.00 44.17 5.69 F
782 789 1.001068 TCCTGCCATTTGTTGCACATG 59.999 47.619 0.00 0.00 33.17 3.21 F
2031 2040 0.032815 TTCATCGTCACGCACCTTCA 59.967 50.000 0.00 0.00 0.00 3.02 F
2985 3033 0.313672 ATTTTGACACACGCGGCATT 59.686 45.000 12.47 0.00 0.00 3.56 F
4086 4137 0.035534 TTTTGATGCGAGGCTGCCTA 60.036 50.000 23.44 6.65 31.76 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 2027 0.321653 AGGGATTGAAGGTGCGTGAC 60.322 55.000 0.00 0.0 0.0 3.67 R
2680 2722 0.322975 CTGGTTGCTGCCTGTACTCT 59.677 55.000 0.00 0.0 0.0 3.24 R
3724 3774 1.140852 TGTAGATTCATGGCTTCCCGG 59.859 52.381 0.00 0.0 0.0 5.73 R
4343 4394 0.257039 ATCCACCCATTCCTCTGTGC 59.743 55.000 0.00 0.0 0.0 4.57 R
5433 5580 0.032615 ACTGCCCTTTGGTCCAACAA 60.033 50.000 2.98 0.0 0.0 2.83 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
26 27 5.792741 GTTTTGGACCATGAATTTGGATCA 58.207 37.500 3.10 0.00 39.25 2.92
27 28 6.408869 GTTTTGGACCATGAATTTGGATCAT 58.591 36.000 3.10 0.00 39.25 2.45
28 29 5.857471 TTGGACCATGAATTTGGATCATC 57.143 39.130 3.10 0.00 39.25 2.92
29 30 5.133383 TGGACCATGAATTTGGATCATCT 57.867 39.130 3.10 0.00 39.25 2.90
30 31 6.264771 TGGACCATGAATTTGGATCATCTA 57.735 37.500 3.10 0.00 39.25 1.98
31 32 6.855667 TGGACCATGAATTTGGATCATCTAT 58.144 36.000 3.10 0.00 39.25 1.98
32 33 7.299896 TGGACCATGAATTTGGATCATCTATT 58.700 34.615 3.10 0.00 39.25 1.73
33 34 7.231925 TGGACCATGAATTTGGATCATCTATTG 59.768 37.037 3.10 0.00 39.25 1.90
34 35 7.309621 GGACCATGAATTTGGATCATCTATTGG 60.310 40.741 3.10 0.00 39.25 3.16
35 36 7.299896 ACCATGAATTTGGATCATCTATTGGA 58.700 34.615 3.10 0.00 39.25 3.53
36 37 7.450634 ACCATGAATTTGGATCATCTATTGGAG 59.549 37.037 3.10 0.00 39.25 3.86
37 38 7.450634 CCATGAATTTGGATCATCTATTGGAGT 59.549 37.037 0.00 0.00 39.25 3.85
38 39 8.857098 CATGAATTTGGATCATCTATTGGAGTT 58.143 33.333 0.00 0.00 35.38 3.01
39 40 8.229253 TGAATTTGGATCATCTATTGGAGTTG 57.771 34.615 0.00 0.00 0.00 3.16
40 41 7.286087 TGAATTTGGATCATCTATTGGAGTTGG 59.714 37.037 0.00 0.00 0.00 3.77
41 42 5.715439 TTGGATCATCTATTGGAGTTGGT 57.285 39.130 0.00 0.00 0.00 3.67
42 43 5.296151 TGGATCATCTATTGGAGTTGGTC 57.704 43.478 0.00 0.00 35.15 4.02
43 44 4.971282 TGGATCATCTATTGGAGTTGGTCT 59.029 41.667 0.00 0.00 35.90 3.85
44 45 5.429762 TGGATCATCTATTGGAGTTGGTCTT 59.570 40.000 0.00 0.00 35.90 3.01
45 46 6.069440 TGGATCATCTATTGGAGTTGGTCTTT 60.069 38.462 0.00 0.00 35.90 2.52
46 47 6.830838 GGATCATCTATTGGAGTTGGTCTTTT 59.169 38.462 0.00 0.00 35.90 2.27
47 48 7.201767 GGATCATCTATTGGAGTTGGTCTTTTG 60.202 40.741 0.00 0.00 35.90 2.44
48 49 5.945784 TCATCTATTGGAGTTGGTCTTTTGG 59.054 40.000 0.00 0.00 0.00 3.28
49 50 5.576563 TCTATTGGAGTTGGTCTTTTGGA 57.423 39.130 0.00 0.00 0.00 3.53
50 51 5.313712 TCTATTGGAGTTGGTCTTTTGGAC 58.686 41.667 0.00 0.00 43.79 4.02
62 63 5.126396 GTCTTTTGGACCAGGAGAATTTG 57.874 43.478 9.68 0.00 38.93 2.32
63 64 4.021981 GTCTTTTGGACCAGGAGAATTTGG 60.022 45.833 9.68 0.00 38.93 3.28
64 65 3.893753 TTTGGACCAGGAGAATTTGGA 57.106 42.857 0.00 0.00 37.89 3.53
65 66 2.879103 TGGACCAGGAGAATTTGGAC 57.121 50.000 0.00 0.00 37.89 4.02
66 67 1.354368 TGGACCAGGAGAATTTGGACC 59.646 52.381 8.06 8.06 45.64 4.46
67 68 1.354368 GGACCAGGAGAATTTGGACCA 59.646 52.381 9.63 0.00 45.05 4.02
68 69 2.024941 GGACCAGGAGAATTTGGACCAT 60.025 50.000 9.63 0.00 45.05 3.55
69 70 3.282885 GACCAGGAGAATTTGGACCATC 58.717 50.000 0.00 0.00 37.89 3.51
70 71 2.922283 ACCAGGAGAATTTGGACCATCT 59.078 45.455 0.00 0.00 37.89 2.90
71 72 3.285484 CCAGGAGAATTTGGACCATCTG 58.715 50.000 0.65 0.00 36.55 2.90
72 73 3.308688 CCAGGAGAATTTGGACCATCTGT 60.309 47.826 0.65 0.00 36.55 3.41
73 74 4.338879 CAGGAGAATTTGGACCATCTGTT 58.661 43.478 0.65 0.00 0.00 3.16
74 75 4.157289 CAGGAGAATTTGGACCATCTGTTG 59.843 45.833 0.65 0.00 0.00 3.33
84 85 3.658398 CATCTGTTGGAGTTGGCCT 57.342 52.632 3.32 0.00 0.00 5.19
85 86 1.915141 CATCTGTTGGAGTTGGCCTT 58.085 50.000 3.32 0.00 0.00 4.35
86 87 2.242043 CATCTGTTGGAGTTGGCCTTT 58.758 47.619 3.32 0.00 0.00 3.11
87 88 2.452600 TCTGTTGGAGTTGGCCTTTT 57.547 45.000 3.32 0.00 0.00 2.27
88 89 2.745968 TCTGTTGGAGTTGGCCTTTTT 58.254 42.857 3.32 0.00 0.00 1.94
89 90 2.693074 TCTGTTGGAGTTGGCCTTTTTC 59.307 45.455 3.32 0.00 0.00 2.29
90 91 1.407258 TGTTGGAGTTGGCCTTTTTCG 59.593 47.619 3.32 0.00 0.00 3.46
91 92 1.679153 GTTGGAGTTGGCCTTTTTCGA 59.321 47.619 3.32 0.00 0.00 3.71
92 93 2.060050 TGGAGTTGGCCTTTTTCGAA 57.940 45.000 3.32 0.00 0.00 3.71
93 94 1.953686 TGGAGTTGGCCTTTTTCGAAG 59.046 47.619 3.32 0.00 0.00 3.79
94 95 1.335964 GGAGTTGGCCTTTTTCGAAGC 60.336 52.381 3.32 0.00 0.00 3.86
95 96 1.609072 GAGTTGGCCTTTTTCGAAGCT 59.391 47.619 3.32 0.00 0.00 3.74
96 97 2.031870 AGTTGGCCTTTTTCGAAGCTT 58.968 42.857 3.32 0.00 0.00 3.74
97 98 2.034685 AGTTGGCCTTTTTCGAAGCTTC 59.965 45.455 16.84 16.84 0.00 3.86
98 99 1.686355 TGGCCTTTTTCGAAGCTTCA 58.314 45.000 25.47 10.50 0.00 3.02
99 100 2.028130 TGGCCTTTTTCGAAGCTTCAA 58.972 42.857 25.47 15.51 0.00 2.69
100 101 2.428890 TGGCCTTTTTCGAAGCTTCAAA 59.571 40.909 25.47 19.76 0.00 2.69
101 102 3.118956 TGGCCTTTTTCGAAGCTTCAAAA 60.119 39.130 25.47 23.43 0.00 2.44
102 103 3.245284 GGCCTTTTTCGAAGCTTCAAAAC 59.755 43.478 25.47 16.30 0.00 2.43
103 104 3.061205 GCCTTTTTCGAAGCTTCAAAACG 60.061 43.478 25.47 22.50 0.00 3.60
104 105 3.061205 CCTTTTTCGAAGCTTCAAAACGC 60.061 43.478 25.47 0.00 0.00 4.84
105 106 2.834574 TTTCGAAGCTTCAAAACGCA 57.165 40.000 25.47 0.00 0.00 5.24
106 107 2.099633 TTCGAAGCTTCAAAACGCAC 57.900 45.000 25.47 0.00 0.00 5.34
107 108 1.295792 TCGAAGCTTCAAAACGCACT 58.704 45.000 25.47 0.00 0.00 4.40
108 109 1.668751 TCGAAGCTTCAAAACGCACTT 59.331 42.857 25.47 0.00 0.00 3.16
109 110 2.096819 TCGAAGCTTCAAAACGCACTTT 59.903 40.909 25.47 0.00 0.00 2.66
110 111 2.851824 CGAAGCTTCAAAACGCACTTTT 59.148 40.909 25.47 0.00 31.77 2.27
111 112 3.303229 CGAAGCTTCAAAACGCACTTTTT 59.697 39.130 25.47 0.00 28.85 1.94
112 113 4.568077 GAAGCTTCAAAACGCACTTTTTG 58.432 39.130 21.67 6.11 44.52 2.44
116 117 2.520979 TCAAAACGCACTTTTTGACGG 58.479 42.857 10.05 0.00 45.99 4.79
117 118 2.095161 TCAAAACGCACTTTTTGACGGT 60.095 40.909 10.05 0.00 45.99 4.83
118 119 2.640346 AAACGCACTTTTTGACGGTT 57.360 40.000 0.00 0.00 32.19 4.44
119 120 2.182904 AACGCACTTTTTGACGGTTC 57.817 45.000 0.00 0.00 0.00 3.62
120 121 1.088306 ACGCACTTTTTGACGGTTCA 58.912 45.000 0.00 0.00 0.00 3.18
121 122 1.469308 ACGCACTTTTTGACGGTTCAA 59.531 42.857 0.00 0.00 40.14 2.69
134 135 8.568732 TTTGACGGTTCAAATTTTACATCTTC 57.431 30.769 0.00 0.00 45.08 2.87
135 136 6.367421 TGACGGTTCAAATTTTACATCTTCG 58.633 36.000 0.00 0.00 0.00 3.79
136 137 6.203145 TGACGGTTCAAATTTTACATCTTCGA 59.797 34.615 0.00 0.00 0.00 3.71
137 138 7.094975 TGACGGTTCAAATTTTACATCTTCGAT 60.095 33.333 0.00 0.00 0.00 3.59
138 139 7.590279 ACGGTTCAAATTTTACATCTTCGATT 58.410 30.769 0.00 0.00 0.00 3.34
139 140 8.079809 ACGGTTCAAATTTTACATCTTCGATTT 58.920 29.630 0.00 0.00 0.00 2.17
140 141 8.911662 CGGTTCAAATTTTACATCTTCGATTTT 58.088 29.630 0.00 0.00 0.00 1.82
143 144 9.973450 TTCAAATTTTACATCTTCGATTTTGGA 57.027 25.926 0.00 0.00 0.00 3.53
144 145 9.405587 TCAAATTTTACATCTTCGATTTTGGAC 57.594 29.630 0.00 0.00 0.00 4.02
145 146 8.647226 CAAATTTTACATCTTCGATTTTGGACC 58.353 33.333 0.00 0.00 0.00 4.46
146 147 5.539582 TTTACATCTTCGATTTTGGACCG 57.460 39.130 0.00 0.00 0.00 4.79
147 148 1.737793 ACATCTTCGATTTTGGACCGC 59.262 47.619 0.00 0.00 0.00 5.68
148 149 1.064060 CATCTTCGATTTTGGACCGCC 59.936 52.381 0.00 0.00 0.00 6.13
149 150 0.035598 TCTTCGATTTTGGACCGCCA 59.964 50.000 0.00 0.00 44.17 5.69
159 160 2.517650 TGGACCGCCAAATTTTGAAC 57.482 45.000 10.72 1.92 42.49 3.18
160 161 1.069358 TGGACCGCCAAATTTTGAACC 59.931 47.619 10.72 6.82 42.49 3.62
161 162 1.069358 GGACCGCCAAATTTTGAACCA 59.931 47.619 10.72 0.00 0.00 3.67
162 163 2.289382 GGACCGCCAAATTTTGAACCAT 60.289 45.455 10.72 0.00 0.00 3.55
163 164 2.993220 GACCGCCAAATTTTGAACCATC 59.007 45.455 10.72 0.00 0.00 3.51
164 165 2.632512 ACCGCCAAATTTTGAACCATCT 59.367 40.909 10.72 0.00 0.00 2.90
165 166 3.829601 ACCGCCAAATTTTGAACCATCTA 59.170 39.130 10.72 0.00 0.00 1.98
166 167 4.466015 ACCGCCAAATTTTGAACCATCTAT 59.534 37.500 10.72 0.00 0.00 1.98
167 168 5.046663 ACCGCCAAATTTTGAACCATCTATT 60.047 36.000 10.72 0.00 0.00 1.73
168 169 5.291614 CCGCCAAATTTTGAACCATCTATTG 59.708 40.000 10.72 0.00 0.00 1.90
169 170 6.098679 CGCCAAATTTTGAACCATCTATTGA 58.901 36.000 10.72 0.00 0.00 2.57
170 171 6.589523 CGCCAAATTTTGAACCATCTATTGAA 59.410 34.615 10.72 0.00 0.00 2.69
171 172 7.201461 CGCCAAATTTTGAACCATCTATTGAAG 60.201 37.037 10.72 0.00 0.00 3.02
172 173 7.818930 GCCAAATTTTGAACCATCTATTGAAGA 59.181 33.333 10.72 0.00 39.02 2.87
173 174 9.880157 CCAAATTTTGAACCATCTATTGAAGAT 57.120 29.630 10.72 0.00 46.36 2.40
184 185 5.720371 TCTATTGAAGATGCTCCTAGCTC 57.280 43.478 0.00 0.00 42.97 4.09
187 188 1.952990 TGAAGATGCTCCTAGCTCGAG 59.047 52.381 8.45 8.45 42.97 4.04
238 239 2.046892 CGGCCCACTCAGACCTTG 60.047 66.667 0.00 0.00 0.00 3.61
266 273 3.710722 CTTCTGCCGAGGCCCAGT 61.711 66.667 12.05 0.00 41.09 4.00
356 363 2.726822 AAACCCTCTCCGCCGAACAC 62.727 60.000 0.00 0.00 0.00 3.32
444 451 4.332543 TCCCCACCTCCTCCGCTT 62.333 66.667 0.00 0.00 0.00 4.68
482 489 1.369321 GGAGATCCATCCGCACCTC 59.631 63.158 0.00 0.00 35.64 3.85
536 543 1.880027 CTGCTTATATTGCCCGGGAAC 59.120 52.381 29.31 8.20 0.00 3.62
540 547 4.139038 GCTTATATTGCCCGGGAACTTTA 58.861 43.478 29.31 4.44 0.00 1.85
641 648 1.749334 CTAGGTCCGTCCCTGGATGC 61.749 65.000 0.00 0.00 40.91 3.91
686 693 6.537301 TGTTATGTATTGGTAGCAAGCACTAC 59.463 38.462 13.51 10.63 41.54 2.73
715 722 4.696479 TCCTCTTAGAAATCCTGGCATC 57.304 45.455 0.00 0.00 0.00 3.91
737 744 3.990469 CAGAAGTAGCACGTTTGATCTGT 59.010 43.478 0.00 0.00 0.00 3.41
738 745 4.449068 CAGAAGTAGCACGTTTGATCTGTT 59.551 41.667 0.00 0.00 0.00 3.16
739 746 4.449068 AGAAGTAGCACGTTTGATCTGTTG 59.551 41.667 0.00 0.00 0.00 3.33
744 751 2.642995 CACGTTTGATCTGTTGCTGTG 58.357 47.619 0.00 0.00 0.00 3.66
768 775 2.123428 GGATGTGCCATGTCCTGCC 61.123 63.158 0.00 0.00 36.34 4.85
782 789 1.001068 TCCTGCCATTTGTTGCACATG 59.999 47.619 0.00 0.00 33.17 3.21
788 795 2.985809 CCATTTGTTGCACATGTAACCG 59.014 45.455 9.88 0.00 39.42 4.44
809 816 4.142622 CCGTATTTGTCATGTGATGCTGTT 60.143 41.667 0.00 0.00 0.00 3.16
810 817 5.393124 CGTATTTGTCATGTGATGCTGTTT 58.607 37.500 0.00 0.00 0.00 2.83
845 854 9.595823 GGTTACTTGAGTGCTATAAATCTGTAA 57.404 33.333 0.00 0.00 0.00 2.41
849 858 9.372369 ACTTGAGTGCTATAAATCTGTAAGTTC 57.628 33.333 0.00 0.00 33.76 3.01
850 859 9.371136 CTTGAGTGCTATAAATCTGTAAGTTCA 57.629 33.333 0.00 0.00 33.76 3.18
851 860 9.890629 TTGAGTGCTATAAATCTGTAAGTTCAT 57.109 29.630 0.00 0.00 33.76 2.57
852 861 9.890629 TGAGTGCTATAAATCTGTAAGTTCATT 57.109 29.630 0.00 0.00 33.76 2.57
882 891 2.382882 TCTTGTTGTGACAATTGGGCA 58.617 42.857 10.83 4.77 44.30 5.36
891 900 2.953648 TGACAATTGGGCAGCTGATATG 59.046 45.455 20.43 9.17 0.00 1.78
892 901 3.216800 GACAATTGGGCAGCTGATATGA 58.783 45.455 20.43 0.00 0.00 2.15
893 902 3.825014 GACAATTGGGCAGCTGATATGAT 59.175 43.478 20.43 0.84 0.00 2.45
894 903 4.989277 ACAATTGGGCAGCTGATATGATA 58.011 39.130 20.43 0.00 0.00 2.15
895 904 5.577100 ACAATTGGGCAGCTGATATGATAT 58.423 37.500 20.43 0.00 0.00 1.63
896 905 6.014647 ACAATTGGGCAGCTGATATGATATT 58.985 36.000 20.43 4.11 0.00 1.28
916 925 9.923143 TGATATTTTGGTACTAGATAATGGTCG 57.077 33.333 0.00 0.00 0.00 4.79
962 971 7.915923 GGCACAGTAGCTAATTTCTTATTTTCC 59.084 37.037 0.00 0.00 34.17 3.13
974 983 5.505181 TCTTATTTTCCTTGGTGCTCTCT 57.495 39.130 0.00 0.00 0.00 3.10
1149 1158 4.303282 GAGTTCCTCTTATCCGCATTCTC 58.697 47.826 0.00 0.00 0.00 2.87
1176 1185 4.878397 CCTACTGAGAAATGTGGGAATGTC 59.122 45.833 0.00 0.00 37.03 3.06
1491 1500 4.627611 AAATGATGATTCCTCTGTTGCG 57.372 40.909 0.00 0.00 0.00 4.85
1743 1752 4.822026 TCCGAGTTTCAAAGGAGAATCTC 58.178 43.478 0.71 0.71 39.37 2.75
1795 1804 6.263168 ACTTTGTCAGGTAGATTTTTCCAGTG 59.737 38.462 0.00 0.00 0.00 3.66
1801 1810 4.762251 AGGTAGATTTTTCCAGTGCTGAAC 59.238 41.667 0.02 0.00 0.00 3.18
1838 1847 9.290988 TGTTCCTTGCAATTATCTTTTGTAGTA 57.709 29.630 0.00 0.00 0.00 1.82
1868 1877 9.223099 CCAAGATTTTGCTTTTGGAAGATTATT 57.777 29.630 0.00 0.00 42.05 1.40
2018 2027 3.599343 TGTTCATCCTTCTGGTTCATCG 58.401 45.455 0.00 0.00 34.23 3.84
2031 2040 0.032815 TTCATCGTCACGCACCTTCA 59.967 50.000 0.00 0.00 0.00 3.02
2035 2044 0.669318 TCGTCACGCACCTTCAATCC 60.669 55.000 0.00 0.00 0.00 3.01
2129 2138 4.956075 GGACCTTTTGATACCATTGACCAT 59.044 41.667 0.00 0.00 0.00 3.55
2279 2288 6.151144 GGCTATTATGTTCAAGTGACAAGGTT 59.849 38.462 0.00 0.00 0.00 3.50
2433 2442 7.674471 ACAACCTTACTTTTCTCTTGATAGC 57.326 36.000 0.00 0.00 0.00 2.97
2488 2519 2.231716 ACCCCTTTAGCCCATGTTTC 57.768 50.000 0.00 0.00 0.00 2.78
2671 2713 4.875561 TGGCACACTTGTATACAGTACA 57.124 40.909 5.56 1.81 0.00 2.90
2680 2722 9.772973 ACACTTGTATACAGTACAATTTCTTGA 57.227 29.630 5.56 0.00 36.90 3.02
2753 2795 9.448587 AACTTATGGTAATATTGTACTCCCTCT 57.551 33.333 0.00 0.00 0.00 3.69
2783 2825 4.568152 ATGTAAGACGTTTTTGCAAGCT 57.432 36.364 0.00 0.00 0.00 3.74
2784 2826 3.947626 TGTAAGACGTTTTTGCAAGCTC 58.052 40.909 0.00 0.00 0.00 4.09
2816 2858 7.561021 TTGCAAAAGCGTCTTATATTATGGA 57.439 32.000 0.00 0.00 0.00 3.41
2884 2932 2.942376 TGCATTAGAAGGTTGTATGGCG 59.058 45.455 0.00 0.00 0.00 5.69
2899 2947 1.118356 TGGCGCAAGAATTTTGGGGT 61.118 50.000 10.83 0.00 43.02 4.95
2940 2988 4.100373 ACTTCTTTCCTCATACTCTGCCT 58.900 43.478 0.00 0.00 0.00 4.75
2942 2990 4.478206 TCTTTCCTCATACTCTGCCTTG 57.522 45.455 0.00 0.00 0.00 3.61
2953 3001 4.639135 ACTCTGCCTTGAGTTTTTCAAC 57.361 40.909 0.00 0.00 44.01 3.18
2957 3005 4.462483 TCTGCCTTGAGTTTTTCAACTGTT 59.538 37.500 0.00 0.00 43.79 3.16
2977 3025 8.460831 ACTGTTTGTTTCTTATTTTGACACAC 57.539 30.769 0.00 0.00 0.00 3.82
2984 3032 1.160989 TATTTTGACACACGCGGCAT 58.839 45.000 12.47 0.00 0.00 4.40
2985 3033 0.313672 ATTTTGACACACGCGGCATT 59.686 45.000 12.47 0.00 0.00 3.56
2986 3034 0.317436 TTTTGACACACGCGGCATTC 60.317 50.000 12.47 1.68 0.00 2.67
2987 3035 1.440145 TTTGACACACGCGGCATTCA 61.440 50.000 12.47 4.72 0.00 2.57
2988 3036 1.233950 TTGACACACGCGGCATTCAT 61.234 50.000 12.47 0.00 0.00 2.57
2989 3037 1.233950 TGACACACGCGGCATTCATT 61.234 50.000 12.47 0.00 0.00 2.57
2990 3038 0.794229 GACACACGCGGCATTCATTG 60.794 55.000 12.47 0.00 0.00 2.82
2991 3039 1.209898 CACACGCGGCATTCATTGT 59.790 52.632 12.47 0.00 0.00 2.71
2992 3040 0.387112 CACACGCGGCATTCATTGTT 60.387 50.000 12.47 0.00 0.00 2.83
2993 3041 1.135831 CACACGCGGCATTCATTGTTA 60.136 47.619 12.47 0.00 0.00 2.41
3356 3405 2.783135 TGAGCAAAGACAAGATCCCAC 58.217 47.619 0.00 0.00 0.00 4.61
3426 3475 8.908786 TGGATTGAACAGATCCTATTTATCAC 57.091 34.615 4.91 0.00 42.88 3.06
3724 3774 3.119352 GGATCCTCAGTTTGGTGCATTTC 60.119 47.826 3.84 0.00 0.00 2.17
3731 3781 0.965439 TTTGGTGCATTTCCGGGAAG 59.035 50.000 9.80 0.44 0.00 3.46
3878 3928 5.898174 TCCAATATTTTCTTGAGCATGCTG 58.102 37.500 28.27 11.47 0.00 4.41
3891 3941 2.012673 GCATGCTGTAAGAGGAACAGG 58.987 52.381 11.37 0.00 43.71 4.00
3958 4008 3.420893 TGTTGGACATCCTAAGCAAAGG 58.579 45.455 0.00 0.00 38.06 3.11
3976 4026 5.592054 CAAAGGTCCTCTTTCTTTGGAAAC 58.408 41.667 0.00 0.00 43.32 2.78
3984 4034 9.764363 GTCCTCTTTCTTTGGAAACATTTTAAT 57.236 29.630 0.00 0.00 42.32 1.40
4079 4129 1.469703 TGCATGAGTTTTGATGCGAGG 59.530 47.619 0.00 0.00 46.66 4.63
4086 4137 0.035534 TTTTGATGCGAGGCTGCCTA 60.036 50.000 23.44 6.65 31.76 3.93
4122 4173 4.719026 AATCTATGAGTCATGGCACCAT 57.281 40.909 16.15 5.26 37.08 3.55
4204 4255 9.918630 GCTGCATTGGATTGTAGATTATTAATT 57.081 29.630 0.00 0.00 31.72 1.40
4232 4283 6.339730 CAAATGGCTTTAATGCACCATAAGA 58.660 36.000 14.56 0.00 42.06 2.10
4288 4339 5.708697 TCGTGATCCTACTCTCAACTTTGTA 59.291 40.000 0.00 0.00 0.00 2.41
4385 4436 5.576447 TTTCTGGGTTTGTTTCTTGTCTC 57.424 39.130 0.00 0.00 0.00 3.36
4390 4441 3.242641 GGGTTTGTTTCTTGTCTCGTGTC 60.243 47.826 0.00 0.00 0.00 3.67
4585 4636 0.872388 GCGAGGTTTGTGTCCGAAAT 59.128 50.000 0.00 0.00 0.00 2.17
4660 4718 8.641498 ATTAATCCTATATGCAGTTTTCAGGG 57.359 34.615 0.00 0.00 0.00 4.45
4705 4763 3.257393 GCTAGCTGATTCCATGGATACG 58.743 50.000 17.06 5.90 42.51 3.06
4803 4861 1.572415 ACCTGCCCCATGAGATTTCAT 59.428 47.619 0.00 0.00 44.87 2.57
4860 4918 4.423913 TGATCCTTCTGGGGAGATCATAG 58.576 47.826 0.00 0.00 40.03 2.23
5011 5069 3.165875 CAGTGGTGGAACTTCTCTAGGA 58.834 50.000 0.00 0.00 36.74 2.94
5014 5072 3.024547 TGGTGGAACTTCTCTAGGATCG 58.975 50.000 0.00 0.00 36.74 3.69
5079 5137 6.766944 GCATTATAGCTGCCTGAATCTATCAT 59.233 38.462 0.00 0.00 37.44 2.45
5137 5195 6.243148 TCTAACCTTTTTGTATGAGAACCCC 58.757 40.000 0.00 0.00 0.00 4.95
5143 5201 6.155049 CCTTTTTGTATGAGAACCCCATCATT 59.845 38.462 0.00 0.00 37.36 2.57
5163 5221 7.294676 TCATTCGATGTTGTGAACTTCTATG 57.705 36.000 0.00 0.00 34.44 2.23
5188 5246 8.148351 TGAAGGGAAATAACCTATTAGTGATCG 58.852 37.037 0.00 0.00 37.35 3.69
5222 5280 7.936496 TTGGTCTGACATCTGCATTATTAAA 57.064 32.000 10.38 0.00 0.00 1.52
5263 5321 3.322828 TCGCTGGACCAATACCCTAATAC 59.677 47.826 0.00 0.00 0.00 1.89
5308 5454 9.909644 ATAGTACCTACACATATCAAATCGTTC 57.090 33.333 0.00 0.00 0.00 3.95
5314 5460 5.057149 ACACATATCAAATCGTTCCCTAGC 58.943 41.667 0.00 0.00 0.00 3.42
5332 5478 6.208204 TCCCTAGCGTCCTGTATTAATTACTC 59.792 42.308 0.00 0.00 0.00 2.59
5387 5533 2.925563 GCCTTTGCAGTGACATATTTGC 59.074 45.455 0.00 0.00 37.47 3.68
5433 5580 3.252701 GCAGCAGCTTGATATATTGCACT 59.747 43.478 8.61 0.00 37.24 4.40
5453 5600 0.032615 TGTTGGACCAAAGGGCAGTT 60.033 50.000 8.94 0.00 37.90 3.16
5521 5670 3.011818 CAACACTGCTCTAATGATGGCA 58.988 45.455 0.00 0.00 0.00 4.92
5602 5751 9.855021 GTCTTGCTGGTTATATGTTGTATTTTT 57.145 29.630 0.00 0.00 0.00 1.94
5644 5801 9.973246 GGACATACATTTTTATGTATATCTGCG 57.027 33.333 13.28 4.15 43.63 5.18
5791 5948 7.278424 CCCTTAATGCTGTATGTTTTTCCATTG 59.722 37.037 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.792741 TGATCCAAATTCATGGTCCAAAAC 58.207 37.500 0.00 0.00 41.46 2.43
4 5 6.441284 AGATGATCCAAATTCATGGTCCAAAA 59.559 34.615 0.00 0.00 41.46 2.44
6 7 5.521696 AGATGATCCAAATTCATGGTCCAA 58.478 37.500 0.00 0.00 41.46 3.53
7 8 5.133383 AGATGATCCAAATTCATGGTCCA 57.867 39.130 0.00 0.00 41.46 4.02
8 9 7.309621 CCAATAGATGATCCAAATTCATGGTCC 60.310 40.741 0.00 0.00 41.46 4.46
9 10 7.449395 TCCAATAGATGATCCAAATTCATGGTC 59.551 37.037 0.00 0.00 41.46 4.02
10 11 7.299896 TCCAATAGATGATCCAAATTCATGGT 58.700 34.615 0.00 0.00 41.46 3.55
11 12 7.450634 ACTCCAATAGATGATCCAAATTCATGG 59.549 37.037 0.00 0.00 42.12 3.66
12 13 8.405418 ACTCCAATAGATGATCCAAATTCATG 57.595 34.615 0.00 0.00 34.03 3.07
13 14 8.857098 CAACTCCAATAGATGATCCAAATTCAT 58.143 33.333 0.00 0.00 36.54 2.57
14 15 7.286087 CCAACTCCAATAGATGATCCAAATTCA 59.714 37.037 0.00 0.00 29.65 2.57
15 16 7.286316 ACCAACTCCAATAGATGATCCAAATTC 59.714 37.037 0.00 0.00 29.65 2.17
16 17 7.128077 ACCAACTCCAATAGATGATCCAAATT 58.872 34.615 0.00 0.00 29.65 1.82
17 18 6.676558 ACCAACTCCAATAGATGATCCAAAT 58.323 36.000 0.00 0.00 29.65 2.32
18 19 6.069440 AGACCAACTCCAATAGATGATCCAAA 60.069 38.462 0.00 0.00 29.65 3.28
19 20 5.429762 AGACCAACTCCAATAGATGATCCAA 59.570 40.000 0.00 0.00 29.65 3.53
20 21 4.971282 AGACCAACTCCAATAGATGATCCA 59.029 41.667 0.00 0.00 29.65 3.41
21 22 5.559148 AGACCAACTCCAATAGATGATCC 57.441 43.478 0.00 0.00 29.65 3.36
22 23 7.201767 CCAAAAGACCAACTCCAATAGATGATC 60.202 40.741 0.00 0.00 29.65 2.92
23 24 6.604795 CCAAAAGACCAACTCCAATAGATGAT 59.395 38.462 0.00 0.00 29.65 2.45
24 25 5.945784 CCAAAAGACCAACTCCAATAGATGA 59.054 40.000 0.00 0.00 29.65 2.92
25 26 5.945784 TCCAAAAGACCAACTCCAATAGATG 59.054 40.000 0.00 0.00 0.00 2.90
26 27 5.946377 GTCCAAAAGACCAACTCCAATAGAT 59.054 40.000 0.00 0.00 39.84 1.98
27 28 5.313712 GTCCAAAAGACCAACTCCAATAGA 58.686 41.667 0.00 0.00 39.84 1.98
28 29 5.629079 GTCCAAAAGACCAACTCCAATAG 57.371 43.478 0.00 0.00 39.84 1.73
40 41 4.021981 CCAAATTCTCCTGGTCCAAAAGAC 60.022 45.833 2.93 0.00 45.51 3.01
41 42 4.141041 TCCAAATTCTCCTGGTCCAAAAGA 60.141 41.667 0.00 0.00 34.11 2.52
42 43 4.021981 GTCCAAATTCTCCTGGTCCAAAAG 60.022 45.833 0.00 0.00 34.11 2.27
43 44 3.895041 GTCCAAATTCTCCTGGTCCAAAA 59.105 43.478 0.00 0.00 34.11 2.44
44 45 3.496331 GTCCAAATTCTCCTGGTCCAAA 58.504 45.455 0.00 0.00 34.11 3.28
45 46 2.225017 GGTCCAAATTCTCCTGGTCCAA 60.225 50.000 5.58 0.00 39.77 3.53
46 47 1.354368 GGTCCAAATTCTCCTGGTCCA 59.646 52.381 5.58 0.00 39.77 4.02
47 48 1.354368 TGGTCCAAATTCTCCTGGTCC 59.646 52.381 3.90 3.90 40.24 4.46
48 49 2.879103 TGGTCCAAATTCTCCTGGTC 57.121 50.000 0.00 0.00 34.11 4.02
49 50 2.922283 AGATGGTCCAAATTCTCCTGGT 59.078 45.455 0.00 0.00 34.11 4.00
50 51 3.285484 CAGATGGTCCAAATTCTCCTGG 58.715 50.000 0.00 0.00 0.00 4.45
51 52 3.960571 ACAGATGGTCCAAATTCTCCTG 58.039 45.455 0.00 0.00 0.00 3.86
52 53 4.338879 CAACAGATGGTCCAAATTCTCCT 58.661 43.478 0.00 0.00 0.00 3.69
53 54 3.445096 CCAACAGATGGTCCAAATTCTCC 59.555 47.826 0.00 0.00 44.85 3.71
54 55 4.708726 CCAACAGATGGTCCAAATTCTC 57.291 45.455 0.00 0.00 44.85 2.87
66 67 1.915141 AAGGCCAACTCCAACAGATG 58.085 50.000 5.01 0.00 0.00 2.90
67 68 2.683211 AAAGGCCAACTCCAACAGAT 57.317 45.000 5.01 0.00 0.00 2.90
68 69 2.452600 AAAAGGCCAACTCCAACAGA 57.547 45.000 5.01 0.00 0.00 3.41
69 70 2.543653 CGAAAAAGGCCAACTCCAACAG 60.544 50.000 5.01 0.00 0.00 3.16
70 71 1.407258 CGAAAAAGGCCAACTCCAACA 59.593 47.619 5.01 0.00 0.00 3.33
71 72 1.679153 TCGAAAAAGGCCAACTCCAAC 59.321 47.619 5.01 0.00 0.00 3.77
72 73 2.060050 TCGAAAAAGGCCAACTCCAA 57.940 45.000 5.01 0.00 0.00 3.53
73 74 1.953686 CTTCGAAAAAGGCCAACTCCA 59.046 47.619 5.01 0.00 0.00 3.86
74 75 1.335964 GCTTCGAAAAAGGCCAACTCC 60.336 52.381 5.01 0.00 0.00 3.85
75 76 1.609072 AGCTTCGAAAAAGGCCAACTC 59.391 47.619 5.01 0.00 0.00 3.01
76 77 1.692411 AGCTTCGAAAAAGGCCAACT 58.308 45.000 5.01 0.00 0.00 3.16
77 78 2.223711 TGAAGCTTCGAAAAAGGCCAAC 60.224 45.455 21.11 0.00 0.00 3.77
78 79 2.028130 TGAAGCTTCGAAAAAGGCCAA 58.972 42.857 21.11 0.00 0.00 4.52
79 80 1.686355 TGAAGCTTCGAAAAAGGCCA 58.314 45.000 21.11 0.00 0.00 5.36
80 81 2.793278 TTGAAGCTTCGAAAAAGGCC 57.207 45.000 21.11 0.00 0.00 5.19
81 82 3.061205 CGTTTTGAAGCTTCGAAAAAGGC 60.061 43.478 33.48 23.06 41.01 4.35
82 83 3.061205 GCGTTTTGAAGCTTCGAAAAAGG 60.061 43.478 33.48 28.89 41.01 3.11
83 84 3.545873 TGCGTTTTGAAGCTTCGAAAAAG 59.454 39.130 33.48 29.38 41.01 2.27
84 85 3.302170 GTGCGTTTTGAAGCTTCGAAAAA 59.698 39.130 33.48 24.93 41.01 1.94
85 86 2.849473 GTGCGTTTTGAAGCTTCGAAAA 59.151 40.909 33.48 27.21 41.01 2.29
86 87 2.096819 AGTGCGTTTTGAAGCTTCGAAA 59.903 40.909 29.98 29.98 38.03 3.46
87 88 1.668751 AGTGCGTTTTGAAGCTTCGAA 59.331 42.857 22.78 22.78 0.00 3.71
88 89 1.295792 AGTGCGTTTTGAAGCTTCGA 58.704 45.000 21.11 17.11 0.00 3.71
89 90 2.105323 AAGTGCGTTTTGAAGCTTCG 57.895 45.000 21.11 10.81 0.00 3.79
90 91 4.568077 CAAAAAGTGCGTTTTGAAGCTTC 58.432 39.130 19.89 19.89 46.77 3.86
91 92 4.582441 CAAAAAGTGCGTTTTGAAGCTT 57.418 36.364 14.88 0.00 46.77 3.74
97 98 2.255316 ACCGTCAAAAAGTGCGTTTTG 58.745 42.857 14.16 14.16 45.71 2.44
98 99 2.640346 ACCGTCAAAAAGTGCGTTTT 57.360 40.000 0.00 0.00 40.26 2.43
99 100 2.095161 TGAACCGTCAAAAAGTGCGTTT 60.095 40.909 0.00 0.00 0.00 3.60
100 101 1.469308 TGAACCGTCAAAAAGTGCGTT 59.531 42.857 0.00 0.00 0.00 4.84
101 102 1.088306 TGAACCGTCAAAAAGTGCGT 58.912 45.000 0.00 0.00 0.00 5.24
102 103 2.181426 TTGAACCGTCAAAAAGTGCG 57.819 45.000 0.00 0.00 40.87 5.34
110 111 6.853872 CGAAGATGTAAAATTTGAACCGTCAA 59.146 34.615 0.00 0.00 42.12 3.18
111 112 6.203145 TCGAAGATGTAAAATTTGAACCGTCA 59.797 34.615 0.00 0.00 0.00 4.35
112 113 6.595794 TCGAAGATGTAAAATTTGAACCGTC 58.404 36.000 0.00 0.00 0.00 4.79
113 114 6.548441 TCGAAGATGTAAAATTTGAACCGT 57.452 33.333 0.00 0.00 0.00 4.83
114 115 8.447787 AAATCGAAGATGTAAAATTTGAACCG 57.552 30.769 0.00 0.00 45.12 4.44
117 118 9.973450 TCCAAAATCGAAGATGTAAAATTTGAA 57.027 25.926 0.00 0.00 45.12 2.69
118 119 9.405587 GTCCAAAATCGAAGATGTAAAATTTGA 57.594 29.630 0.00 0.00 45.12 2.69
119 120 8.647226 GGTCCAAAATCGAAGATGTAAAATTTG 58.353 33.333 0.00 0.00 45.12 2.32
120 121 7.540745 CGGTCCAAAATCGAAGATGTAAAATTT 59.459 33.333 0.00 0.00 45.12 1.82
121 122 7.027161 CGGTCCAAAATCGAAGATGTAAAATT 58.973 34.615 0.00 0.00 45.12 1.82
122 123 6.551736 CGGTCCAAAATCGAAGATGTAAAAT 58.448 36.000 0.00 0.00 45.12 1.82
123 124 5.618195 GCGGTCCAAAATCGAAGATGTAAAA 60.618 40.000 0.00 0.00 45.12 1.52
124 125 4.142773 GCGGTCCAAAATCGAAGATGTAAA 60.143 41.667 0.00 0.00 45.12 2.01
125 126 3.372822 GCGGTCCAAAATCGAAGATGTAA 59.627 43.478 0.00 0.00 45.12 2.41
126 127 2.933906 GCGGTCCAAAATCGAAGATGTA 59.066 45.455 0.00 0.00 45.12 2.29
127 128 1.737793 GCGGTCCAAAATCGAAGATGT 59.262 47.619 0.00 0.00 45.12 3.06
128 129 1.064060 GGCGGTCCAAAATCGAAGATG 59.936 52.381 0.00 0.00 45.12 2.90
129 130 1.339631 TGGCGGTCCAAAATCGAAGAT 60.340 47.619 0.00 0.00 40.00 2.40
130 131 0.035598 TGGCGGTCCAAAATCGAAGA 59.964 50.000 0.00 0.00 39.99 2.87
131 132 2.550487 TGGCGGTCCAAAATCGAAG 58.450 52.632 0.00 0.00 39.99 3.79
132 133 4.802678 TGGCGGTCCAAAATCGAA 57.197 50.000 0.00 0.00 39.99 3.71
140 141 1.069358 GGTTCAAAATTTGGCGGTCCA 59.931 47.619 5.83 0.00 41.55 4.02
141 142 1.069358 TGGTTCAAAATTTGGCGGTCC 59.931 47.619 5.83 3.05 0.00 4.46
142 143 2.517650 TGGTTCAAAATTTGGCGGTC 57.482 45.000 5.83 0.00 0.00 4.79
143 144 2.632512 AGATGGTTCAAAATTTGGCGGT 59.367 40.909 5.83 0.00 0.00 5.68
144 145 3.317603 AGATGGTTCAAAATTTGGCGG 57.682 42.857 5.83 0.00 0.00 6.13
145 146 6.098679 TCAATAGATGGTTCAAAATTTGGCG 58.901 36.000 5.83 0.00 0.00 5.69
146 147 7.818930 TCTTCAATAGATGGTTCAAAATTTGGC 59.181 33.333 5.83 0.00 0.00 4.52
147 148 9.880157 ATCTTCAATAGATGGTTCAAAATTTGG 57.120 29.630 5.83 0.00 42.11 3.28
161 162 5.105797 CGAGCTAGGAGCATCTTCAATAGAT 60.106 44.000 0.64 0.00 45.56 1.98
162 163 4.217334 CGAGCTAGGAGCATCTTCAATAGA 59.783 45.833 0.64 0.00 45.56 1.98
163 164 4.217334 TCGAGCTAGGAGCATCTTCAATAG 59.783 45.833 0.64 0.00 45.56 1.73
164 165 4.145052 TCGAGCTAGGAGCATCTTCAATA 58.855 43.478 0.64 0.00 45.56 1.90
165 166 2.961741 TCGAGCTAGGAGCATCTTCAAT 59.038 45.455 0.64 0.00 45.56 2.57
166 167 2.360483 CTCGAGCTAGGAGCATCTTCAA 59.640 50.000 0.00 0.00 45.56 2.69
167 168 1.952990 CTCGAGCTAGGAGCATCTTCA 59.047 52.381 0.00 0.00 45.56 3.02
168 169 1.269448 CCTCGAGCTAGGAGCATCTTC 59.731 57.143 6.99 0.00 45.56 2.87
169 170 1.133637 TCCTCGAGCTAGGAGCATCTT 60.134 52.381 6.99 0.00 45.56 2.40
170 171 0.476338 TCCTCGAGCTAGGAGCATCT 59.524 55.000 6.99 0.00 45.56 2.90
171 172 1.323412 TTCCTCGAGCTAGGAGCATC 58.677 55.000 6.99 0.00 46.29 3.91
172 173 2.008242 ATTCCTCGAGCTAGGAGCAT 57.992 50.000 6.99 0.00 46.29 3.79
173 174 1.410517 CAATTCCTCGAGCTAGGAGCA 59.589 52.381 6.99 0.00 46.29 4.26
174 175 1.270041 CCAATTCCTCGAGCTAGGAGC 60.270 57.143 6.99 0.00 46.29 4.70
175 176 2.295909 CTCCAATTCCTCGAGCTAGGAG 59.704 54.545 6.99 13.85 46.29 3.69
176 177 2.091830 TCTCCAATTCCTCGAGCTAGGA 60.092 50.000 6.99 0.72 44.12 2.94
177 178 2.295909 CTCTCCAATTCCTCGAGCTAGG 59.704 54.545 6.99 4.16 38.06 3.02
178 179 2.295909 CCTCTCCAATTCCTCGAGCTAG 59.704 54.545 6.99 0.00 0.00 3.42
184 185 1.147153 GGCCCTCTCCAATTCCTCG 59.853 63.158 0.00 0.00 0.00 4.63
187 188 1.342672 TACCGGCCCTCTCCAATTCC 61.343 60.000 0.00 0.00 0.00 3.01
238 239 0.992802 CGGCAGAAGCTCGTAACTTC 59.007 55.000 0.00 6.70 43.16 3.01
444 451 0.101759 GCTCCACGGCGATACTGTAA 59.898 55.000 16.62 0.00 35.54 2.41
482 489 5.796935 CGTTGCCAACAGAAGAAATCAATAG 59.203 40.000 8.51 0.00 0.00 1.73
536 543 5.182760 ACAGAGAGCAGGCAAAAGAATAAAG 59.817 40.000 0.00 0.00 0.00 1.85
540 547 3.151912 ACAGAGAGCAGGCAAAAGAAT 57.848 42.857 0.00 0.00 0.00 2.40
641 648 1.062810 AGGCCCTAGTTCCTAGACCTG 60.063 57.143 0.00 0.00 38.27 4.00
686 693 5.645497 CAGGATTTCTAAGAGGAAACCACAG 59.355 44.000 0.00 0.00 37.91 3.66
715 722 3.990469 ACAGATCAAACGTGCTACTTCTG 59.010 43.478 0.00 10.23 36.35 3.02
737 744 2.300433 GCACATCCATATCCACAGCAA 58.700 47.619 0.00 0.00 0.00 3.91
738 745 1.477377 GGCACATCCATATCCACAGCA 60.477 52.381 0.00 0.00 34.01 4.41
739 746 1.242076 GGCACATCCATATCCACAGC 58.758 55.000 0.00 0.00 34.01 4.40
782 789 5.064707 AGCATCACATGACAAATACGGTTAC 59.935 40.000 0.00 0.00 0.00 2.50
788 795 7.642071 AAAAACAGCATCACATGACAAATAC 57.358 32.000 0.00 0.00 0.00 1.89
817 826 7.766278 ACAGATTTATAGCACTCAAGTAACCAG 59.234 37.037 0.00 0.00 0.00 4.00
845 854 9.850628 CACAACAAGATGATAATTGAATGAACT 57.149 29.630 0.00 0.00 0.00 3.01
849 858 9.628746 TTGTCACAACAAGATGATAATTGAATG 57.371 29.630 0.00 0.13 40.45 2.67
891 900 9.924650 ACGACCATTATCTAGTACCAAAATATC 57.075 33.333 0.00 0.00 0.00 1.63
916 925 6.131389 GTGCCAATAACCGACGAATAAATAC 58.869 40.000 0.00 0.00 0.00 1.89
1014 1023 3.118223 GGAATGGTCTCTTGGAAGGGTAG 60.118 52.174 0.00 0.00 0.00 3.18
1149 1158 2.636830 CCACATTTCTCAGTAGGGCAG 58.363 52.381 0.00 0.00 0.00 4.85
1176 1185 4.269183 TGATGCTACCACCTTTACCAATG 58.731 43.478 0.00 0.00 0.00 2.82
1289 1298 3.932089 GCTAGCTTCTTTGTCCTTCTCAG 59.068 47.826 7.70 0.00 0.00 3.35
1491 1500 4.578928 TCTGGCTCCAACTTTGTAGTTTTC 59.421 41.667 0.00 0.00 41.85 2.29
1743 1752 6.817765 TCTTTGAGTAAAGCACATAAAGGG 57.182 37.500 0.00 0.00 42.40 3.95
1795 1804 6.378710 AGGAACAAGAAAACTAAGTTCAGC 57.621 37.500 0.00 0.00 40.11 4.26
1801 1810 9.696917 ATAATTGCAAGGAACAAGAAAACTAAG 57.303 29.630 4.94 0.00 0.00 2.18
1838 1847 5.549742 TCCAAAAGCAAAATCTTGGACAT 57.450 34.783 0.00 0.00 41.83 3.06
1840 1849 5.600696 TCTTCCAAAAGCAAAATCTTGGAC 58.399 37.500 1.93 0.00 45.36 4.02
1896 1905 4.637534 GTCAAGCTCTCCATTAATCTGCAA 59.362 41.667 0.00 0.00 0.00 4.08
1925 1934 2.486982 CACTGCATTCAGACCTTTCCTG 59.513 50.000 0.00 0.00 42.95 3.86
2018 2027 0.321653 AGGGATTGAAGGTGCGTGAC 60.322 55.000 0.00 0.00 0.00 3.67
2031 2040 3.044894 GAGGAAGACCATCTGAGGGATT 58.955 50.000 16.28 9.16 38.94 3.01
2035 2044 1.761784 CTGGAGGAAGACCATCTGAGG 59.238 57.143 0.00 0.00 38.94 3.86
2129 2138 2.008242 AAGGTGCAACATTTGGCCTA 57.992 45.000 3.64 0.00 37.74 3.93
2279 2288 4.911522 CCACCCTTCCCTATAATACTTCCA 59.088 45.833 0.00 0.00 0.00 3.53
2433 2442 6.386654 ACTGGGTTTATTTAATGAAACTGCG 58.613 36.000 10.76 0.00 36.12 5.18
2488 2519 3.367703 CCTTAAATGCCTTCACTGCCAAG 60.368 47.826 0.00 0.00 0.00 3.61
2651 2693 6.737254 AATTGTACTGTATACAAGTGTGCC 57.263 37.500 7.06 0.00 40.27 5.01
2652 2694 8.029642 AGAAATTGTACTGTATACAAGTGTGC 57.970 34.615 7.06 6.02 40.27 4.57
2653 2695 9.811655 CAAGAAATTGTACTGTATACAAGTGTG 57.188 33.333 7.06 0.00 40.27 3.82
2654 2696 9.772973 TCAAGAAATTGTACTGTATACAAGTGT 57.227 29.630 7.06 4.35 40.27 3.55
2662 2704 9.862371 CTGTACTCTCAAGAAATTGTACTGTAT 57.138 33.333 0.00 0.00 33.59 2.29
2663 2705 8.304596 CCTGTACTCTCAAGAAATTGTACTGTA 58.695 37.037 0.00 0.00 33.59 2.74
2664 2706 7.155328 CCTGTACTCTCAAGAAATTGTACTGT 58.845 38.462 0.00 0.00 33.59 3.55
2671 2713 4.006319 GCTGCCTGTACTCTCAAGAAATT 58.994 43.478 0.00 0.00 0.00 1.82
2680 2722 0.322975 CTGGTTGCTGCCTGTACTCT 59.677 55.000 0.00 0.00 0.00 3.24
2731 2773 8.232412 AGACAGAGGGAGTACAATATTACCATA 58.768 37.037 0.00 0.00 0.00 2.74
2732 2774 7.076446 AGACAGAGGGAGTACAATATTACCAT 58.924 38.462 0.00 0.00 0.00 3.55
2753 2795 7.041712 TGCAAAAACGTCTTACATTATGAGACA 60.042 33.333 12.46 0.00 42.74 3.41
2816 2858 4.402793 ACCAGATTATGTACTCGCTCTGTT 59.597 41.667 12.09 0.33 0.00 3.16
2819 2861 6.710597 TTTACCAGATTATGTACTCGCTCT 57.289 37.500 0.00 0.00 0.00 4.09
2884 2932 5.639082 CAGAAATGTACCCCAAAATTCTTGC 59.361 40.000 0.00 0.00 0.00 4.01
2899 2947 8.514330 AAGAAGTACAAAACACCAGAAATGTA 57.486 30.769 0.00 0.00 0.00 2.29
2940 2988 8.655651 AAGAAACAAACAGTTGAAAAACTCAA 57.344 26.923 0.00 0.00 41.19 3.02
2953 3001 7.600039 CGTGTGTCAAAATAAGAAACAAACAG 58.400 34.615 0.00 0.00 35.15 3.16
2957 3005 4.731000 CGCGTGTGTCAAAATAAGAAACAA 59.269 37.500 0.00 0.00 35.15 2.83
2977 3025 3.063670 TGAATAACAATGAATGCCGCG 57.936 42.857 0.00 0.00 0.00 6.46
3356 3405 4.006989 TCATCAATTTCTTGTACACCCCG 58.993 43.478 0.00 0.00 33.87 5.73
3504 3554 8.836268 AAAGTGTCGTACAAAAATATCCAGTA 57.164 30.769 0.00 0.00 0.00 2.74
3517 3567 7.333921 TGGAAAAGAAACTAAAAGTGTCGTACA 59.666 33.333 0.00 0.00 37.53 2.90
3522 3572 7.096884 ACCTGGAAAAGAAACTAAAAGTGTC 57.903 36.000 0.00 0.00 32.53 3.67
3535 3585 7.001674 TCTGCAGTTAATTAACCTGGAAAAGA 58.998 34.615 21.92 13.33 36.88 2.52
3568 3618 6.329197 TCAGAATCCCCGGTTATCTAAAAGAT 59.671 38.462 0.00 0.00 38.70 2.40
3724 3774 1.140852 TGTAGATTCATGGCTTCCCGG 59.859 52.381 0.00 0.00 0.00 5.73
3731 3781 4.774726 TCCTAGGAGATGTAGATTCATGGC 59.225 45.833 7.62 0.00 0.00 4.40
3878 3928 4.930405 GCTGTAAACTCCTGTTCCTCTTAC 59.070 45.833 0.00 0.00 34.96 2.34
3891 3941 5.405331 AAAGAACTGAACGCTGTAAACTC 57.595 39.130 0.00 0.00 0.00 3.01
3958 4008 9.764363 ATTAAAATGTTTCCAAAGAAAGAGGAC 57.236 29.630 0.00 0.00 42.60 3.85
3984 4034 8.623903 CAGCCAAACTAATCATTATAAGCAGAA 58.376 33.333 0.00 0.00 0.00 3.02
4001 4051 3.352512 TTGGTCCCCAGCCAAACT 58.647 55.556 0.00 0.00 42.39 2.66
4018 4068 3.888930 CCACACTAACTGGTGACCAAATT 59.111 43.478 5.53 5.88 40.13 1.82
4063 4113 1.159285 CAGCCTCGCATCAAAACTCA 58.841 50.000 0.00 0.00 0.00 3.41
4079 4129 7.761249 AGATTAATTCACAACAAATTAGGCAGC 59.239 33.333 0.00 0.00 31.97 5.25
4122 4173 7.269316 TGTTAATCAGATGGCGACTACAATTA 58.731 34.615 0.00 0.00 0.00 1.40
4204 4255 3.118811 GGTGCATTAAAGCCATTTGCCTA 60.119 43.478 0.00 0.00 42.71 3.93
4222 4273 7.707893 AGCAAAAACATTATGATCTTATGGTGC 59.292 33.333 0.00 4.89 0.00 5.01
4232 4283 8.482852 AGGGCTATAAGCAAAAACATTATGAT 57.517 30.769 0.00 0.00 44.75 2.45
4288 4339 1.380785 CCAACATCCTGCATGCCCT 60.381 57.895 16.68 0.00 35.65 5.19
4343 4394 0.257039 ATCCACCCATTCCTCTGTGC 59.743 55.000 0.00 0.00 0.00 4.57
4385 4436 7.918562 TCAAAAGGGAAGAAAATTTAAGACACG 59.081 33.333 0.00 0.00 0.00 4.49
4585 4636 5.744171 ACCAGATATGCTACATGACACAAA 58.256 37.500 0.00 0.00 0.00 2.83
4660 4718 5.107453 CGGTTCATCGATTGTTATCTTAGCC 60.107 44.000 0.00 0.00 0.00 3.93
4705 4763 3.499918 GTGTGCCAGATATCATAACAGGC 59.500 47.826 5.32 1.70 40.93 4.85
4803 4861 3.326006 GGGATGCATCACCTTCAGAGATA 59.674 47.826 27.25 0.00 0.00 1.98
4860 4918 1.607467 AAACAGCATCACCTGGGCC 60.607 57.895 0.00 0.00 37.16 5.80
5011 5069 8.458843 CACAACTTTGGGAGATTATAAAACGAT 58.541 33.333 0.00 0.00 31.80 3.73
5014 5072 6.811665 GCCACAACTTTGGGAGATTATAAAAC 59.188 38.462 0.00 0.00 37.10 2.43
5143 5201 5.869344 CCTTCATAGAAGTTCACAACATCGA 59.131 40.000 5.50 0.00 34.50 3.59
5163 5221 8.148999 ACGATCACTAATAGGTTATTTCCCTTC 58.851 37.037 0.00 0.00 33.35 3.46
5188 5246 6.749118 GCAGATGTCAGACCAAAATTCATAAC 59.251 38.462 0.00 0.00 0.00 1.89
5222 5280 3.429547 GCGAATAGTGGTCATGTCAGTCT 60.430 47.826 0.00 0.00 0.00 3.24
5308 5454 6.208994 AGAGTAATTAATACAGGACGCTAGGG 59.791 42.308 5.05 5.05 36.94 3.53
5314 5460 8.867112 TTGCTAAGAGTAATTAATACAGGACG 57.133 34.615 0.00 0.00 36.94 4.79
5332 5478 7.440523 AGTTGTTCTACCTGAATTTGCTAAG 57.559 36.000 0.00 0.00 36.99 2.18
5347 5493 3.039011 GGCCTCTGGGATAGTTGTTCTA 58.961 50.000 0.00 0.00 33.58 2.10
5421 5568 6.449635 TTGGTCCAACAAGTGCAATATATC 57.550 37.500 0.00 0.00 0.00 1.63
5433 5580 0.032615 ACTGCCCTTTGGTCCAACAA 60.033 50.000 2.98 0.00 0.00 2.83
5478 5625 5.257262 TGTATGCAGTATGTTAGGGCAAAA 58.743 37.500 0.00 0.00 39.31 2.44
5482 5629 4.035208 GTGTTGTATGCAGTATGTTAGGGC 59.965 45.833 0.00 0.00 39.31 5.19
5483 5630 5.294306 CAGTGTTGTATGCAGTATGTTAGGG 59.706 44.000 0.00 0.00 39.31 3.53
5484 5631 5.220662 GCAGTGTTGTATGCAGTATGTTAGG 60.221 44.000 0.00 0.00 42.11 2.69
5521 5670 8.537728 TGATCATATTAATCCAAGCAAGGTTT 57.462 30.769 0.00 0.00 0.00 3.27
5644 5801 3.787634 TGTCGCGATACATAACGAACTTC 59.212 43.478 14.06 0.00 36.14 3.01
5647 5804 4.201242 CGTATGTCGCGATACATAACGAAC 60.201 45.833 22.84 14.12 42.43 3.95


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

AutoCloner maintained by Alex Coulton.