Multiple sequence alignment - TraesCS3A01G373200

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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 TraesCS3A01G373200 chr3A 100.000 2894 0 0 1 2894 623353505 623356398 0.000000e+00 5345
1 TraesCS3A01G373200 chr3A 91.685 2333 148 18 599 2894 623361844 623364167 0.000000e+00 3192
2 TraesCS3A01G373200 chr3A 87.996 2066 214 20 838 2894 623229455 623231495 0.000000e+00 2410
3 TraesCS3A01G373200 chr3A 90.707 1302 110 6 600 1895 623389237 623390533 0.000000e+00 1724
4 TraesCS3A01G373200 chr3A 94.457 451 22 3 1 449 11512703 11513152 0.000000e+00 691
5 TraesCS3A01G373200 chr3A 86.679 548 47 7 2314 2861 623341927 623342448 4.160000e-163 584
6 TraesCS3A01G373200 chr3D 90.969 2126 146 21 796 2891 480357801 480359910 0.000000e+00 2820
7 TraesCS3A01G373200 chr3D 90.230 1914 157 13 1001 2894 480157929 480159832 0.000000e+00 2471
8 TraesCS3A01G373200 chr3D 89.468 1709 126 25 600 2295 480366345 480368012 0.000000e+00 2109
9 TraesCS3A01G373200 chr3D 91.527 1310 92 8 599 1895 480375412 480376715 0.000000e+00 1786
10 TraesCS3A01G373200 chr3D 90.826 545 46 3 2314 2858 480371418 480371958 0.000000e+00 726
11 TraesCS3A01G373200 chr3D 95.291 446 18 3 1 446 584700562 584700120 0.000000e+00 704
12 TraesCS3A01G373200 chr3D 82.500 720 71 23 2197 2894 480311089 480311775 5.380000e-162 580
13 TraesCS3A01G373200 chr3D 91.400 407 20 2 1996 2387 480310690 480311096 7.050000e-151 544
14 TraesCS3A01G373200 chr3D 91.566 83 7 0 448 530 480366145 480366227 6.550000e-22 115
15 TraesCS3A01G373200 chr3B 88.741 2336 185 36 600 2894 640700301 640702599 0.000000e+00 2785
16 TraesCS3A01G373200 chr3B 88.873 2049 188 23 870 2894 640693399 640695431 0.000000e+00 2484
17 TraesCS3A01G373200 chr3B 90.218 1513 116 12 796 2296 640708125 640709617 0.000000e+00 1945
18 TraesCS3A01G373200 chr3B 95.000 80 4 0 450 529 640810092 640810171 3.030000e-25 126
19 TraesCS3A01G373200 chr3B 90.244 82 8 0 2314 2395 640710070 640710151 1.100000e-19 108
20 TraesCS3A01G373200 chr7D 95.672 439 17 2 1 439 637694736 637694300 0.000000e+00 704
21 TraesCS3A01G373200 chr7D 94.619 446 22 2 1 445 497561735 497562179 0.000000e+00 689
22 TraesCS3A01G373200 chr2D 95.270 444 19 2 3 445 73126040 73125598 0.000000e+00 702
23 TraesCS3A01G373200 chr2D 94.619 446 22 2 1 445 36803945 36803501 0.000000e+00 689
24 TraesCS3A01G373200 chr6D 95.067 446 20 2 1 445 142135862 142135418 0.000000e+00 701
25 TraesCS3A01G373200 chr1D 94.843 446 21 2 1 445 60170986 60170542 0.000000e+00 695
26 TraesCS3A01G373200 chr2A 94.457 451 19 3 1 451 551452456 551452012 0.000000e+00 689


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 TraesCS3A01G373200 chr3A 623353505 623356398 2893 False 5345.0 5345 100.00000 1 2894 1 chr3A.!!$F4 2893
1 TraesCS3A01G373200 chr3A 623361844 623364167 2323 False 3192.0 3192 91.68500 599 2894 1 chr3A.!!$F5 2295
2 TraesCS3A01G373200 chr3A 623229455 623231495 2040 False 2410.0 2410 87.99600 838 2894 1 chr3A.!!$F2 2056
3 TraesCS3A01G373200 chr3A 623389237 623390533 1296 False 1724.0 1724 90.70700 600 1895 1 chr3A.!!$F6 1295
4 TraesCS3A01G373200 chr3A 623341927 623342448 521 False 584.0 584 86.67900 2314 2861 1 chr3A.!!$F3 547
5 TraesCS3A01G373200 chr3D 480357801 480359910 2109 False 2820.0 2820 90.96900 796 2891 1 chr3D.!!$F2 2095
6 TraesCS3A01G373200 chr3D 480157929 480159832 1903 False 2471.0 2471 90.23000 1001 2894 1 chr3D.!!$F1 1893
7 TraesCS3A01G373200 chr3D 480366145 480376715 10570 False 1184.0 2109 90.84675 448 2858 4 chr3D.!!$F4 2410
8 TraesCS3A01G373200 chr3D 480310690 480311775 1085 False 562.0 580 86.95000 1996 2894 2 chr3D.!!$F3 898
9 TraesCS3A01G373200 chr3B 640700301 640702599 2298 False 2785.0 2785 88.74100 600 2894 1 chr3B.!!$F2 2294
10 TraesCS3A01G373200 chr3B 640693399 640695431 2032 False 2484.0 2484 88.87300 870 2894 1 chr3B.!!$F1 2024
11 TraesCS3A01G373200 chr3B 640708125 640710151 2026 False 1026.5 1945 90.23100 796 2395 2 chr3B.!!$F4 1599

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
129 130 0.032678 AGCGACGATCATCACCATCC 59.967 55.0 0.0 0.0 0.0 3.51 F
368 369 0.042731 AAGACGGAGAGGATGGGGAA 59.957 55.0 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1036 1108 0.251653 AGTGCTACGAAGAGGGTGGA 60.252 55.0 0.00 0.0 0.00 4.02 R
2233 2311 0.169672 CCAGTTGCAAGATGGCGAAG 59.830 55.0 15.71 0.0 36.28 3.79 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
17 18 3.089784 CCGAAACCCGCGAAGATG 58.910 61.111 8.23 0.00 36.84 2.90
18 19 1.447140 CCGAAACCCGCGAAGATGA 60.447 57.895 8.23 0.00 36.84 2.92
19 20 1.017177 CCGAAACCCGCGAAGATGAA 61.017 55.000 8.23 0.00 36.84 2.57
20 21 0.793861 CGAAACCCGCGAAGATGAAA 59.206 50.000 8.23 0.00 0.00 2.69
21 22 1.201921 CGAAACCCGCGAAGATGAAAG 60.202 52.381 8.23 0.00 0.00 2.62
22 23 2.073816 GAAACCCGCGAAGATGAAAGA 58.926 47.619 8.23 0.00 0.00 2.52
23 24 1.726853 AACCCGCGAAGATGAAAGAG 58.273 50.000 8.23 0.00 0.00 2.85
24 25 0.741221 ACCCGCGAAGATGAAAGAGC 60.741 55.000 8.23 0.00 0.00 4.09
25 26 1.432270 CCCGCGAAGATGAAAGAGCC 61.432 60.000 8.23 0.00 0.00 4.70
26 27 0.740868 CCGCGAAGATGAAAGAGCCA 60.741 55.000 8.23 0.00 0.00 4.75
27 28 1.293924 CGCGAAGATGAAAGAGCCAT 58.706 50.000 0.00 0.00 0.00 4.40
28 29 1.004185 CGCGAAGATGAAAGAGCCATG 60.004 52.381 0.00 0.00 0.00 3.66
29 30 1.332997 GCGAAGATGAAAGAGCCATGG 59.667 52.381 7.63 7.63 0.00 3.66
30 31 1.945394 CGAAGATGAAAGAGCCATGGG 59.055 52.381 15.13 0.00 0.00 4.00
31 32 2.305009 GAAGATGAAAGAGCCATGGGG 58.695 52.381 15.13 0.00 37.18 4.96
47 48 4.920828 GGCTCAACCCACCAGAAA 57.079 55.556 0.00 0.00 0.00 2.52
48 49 2.646121 GGCTCAACCCACCAGAAAG 58.354 57.895 0.00 0.00 0.00 2.62
49 50 0.895559 GGCTCAACCCACCAGAAAGG 60.896 60.000 0.00 0.00 45.67 3.11
50 51 0.110486 GCTCAACCCACCAGAAAGGA 59.890 55.000 0.00 0.00 41.22 3.36
51 52 1.884067 GCTCAACCCACCAGAAAGGAG 60.884 57.143 0.00 0.00 41.22 3.69
52 53 0.771127 TCAACCCACCAGAAAGGAGG 59.229 55.000 0.00 0.00 46.82 4.30
59 60 3.988976 CACCAGAAAGGAGGATCAAGA 57.011 47.619 0.00 0.00 41.22 3.02
60 61 4.292186 CACCAGAAAGGAGGATCAAGAA 57.708 45.455 0.00 0.00 41.22 2.52
61 62 4.260170 CACCAGAAAGGAGGATCAAGAAG 58.740 47.826 0.00 0.00 41.22 2.85
62 63 4.019860 CACCAGAAAGGAGGATCAAGAAGA 60.020 45.833 0.00 0.00 41.22 2.87
63 64 4.599241 ACCAGAAAGGAGGATCAAGAAGAA 59.401 41.667 0.00 0.00 41.22 2.52
64 65 4.940654 CCAGAAAGGAGGATCAAGAAGAAC 59.059 45.833 0.00 0.00 41.22 3.01
65 66 5.280419 CCAGAAAGGAGGATCAAGAAGAACT 60.280 44.000 0.00 0.00 41.22 3.01
66 67 5.874261 CAGAAAGGAGGATCAAGAAGAACTC 59.126 44.000 0.00 0.00 36.25 3.01
67 68 4.835284 AAGGAGGATCAAGAAGAACTCC 57.165 45.455 0.00 0.00 46.65 3.85
69 70 4.835284 GGAGGATCAAGAAGAACTCCTT 57.165 45.455 0.00 0.00 44.65 3.36
70 71 4.512484 GGAGGATCAAGAAGAACTCCTTG 58.488 47.826 0.00 0.00 44.65 3.61
71 72 4.019771 GGAGGATCAAGAAGAACTCCTTGT 60.020 45.833 0.00 0.00 44.65 3.16
72 73 5.187967 GGAGGATCAAGAAGAACTCCTTGTA 59.812 44.000 0.00 0.00 44.65 2.41
73 74 6.293004 AGGATCAAGAAGAACTCCTTGTAG 57.707 41.667 1.21 0.00 40.32 2.74
74 75 6.019748 AGGATCAAGAAGAACTCCTTGTAGA 58.980 40.000 1.21 0.00 40.32 2.59
75 76 6.671779 AGGATCAAGAAGAACTCCTTGTAGAT 59.328 38.462 1.21 0.00 40.32 1.98
76 77 6.983890 GGATCAAGAAGAACTCCTTGTAGATC 59.016 42.308 1.21 0.00 40.32 2.75
77 78 7.147742 GGATCAAGAAGAACTCCTTGTAGATCT 60.148 40.741 0.00 0.00 40.32 2.75
78 79 7.164230 TCAAGAAGAACTCCTTGTAGATCTC 57.836 40.000 0.00 0.00 40.32 2.75
79 80 6.153680 TCAAGAAGAACTCCTTGTAGATCTCC 59.846 42.308 0.00 0.00 40.32 3.71
80 81 5.584913 AGAAGAACTCCTTGTAGATCTCCA 58.415 41.667 0.00 0.00 34.68 3.86
81 82 5.656416 AGAAGAACTCCTTGTAGATCTCCAG 59.344 44.000 0.00 0.00 34.68 3.86
82 83 5.199982 AGAACTCCTTGTAGATCTCCAGA 57.800 43.478 0.00 0.00 0.00 3.86
83 84 4.953579 AGAACTCCTTGTAGATCTCCAGAC 59.046 45.833 0.00 0.00 0.00 3.51
84 85 3.283751 ACTCCTTGTAGATCTCCAGACG 58.716 50.000 0.00 0.00 0.00 4.18
85 86 3.283751 CTCCTTGTAGATCTCCAGACGT 58.716 50.000 0.00 0.00 0.00 4.34
86 87 3.280295 TCCTTGTAGATCTCCAGACGTC 58.720 50.000 7.70 7.70 0.00 4.34
87 88 2.032302 CCTTGTAGATCTCCAGACGTCG 59.968 54.545 10.46 5.16 0.00 5.12
88 89 2.685850 TGTAGATCTCCAGACGTCGA 57.314 50.000 10.46 1.17 0.00 4.20
89 90 2.981898 TGTAGATCTCCAGACGTCGAA 58.018 47.619 10.46 0.00 0.00 3.71
90 91 3.542648 TGTAGATCTCCAGACGTCGAAT 58.457 45.455 10.46 0.47 0.00 3.34
91 92 3.560481 TGTAGATCTCCAGACGTCGAATC 59.440 47.826 10.46 9.71 0.00 2.52
92 93 1.950909 AGATCTCCAGACGTCGAATCC 59.049 52.381 10.46 0.00 0.00 3.01
93 94 1.676529 GATCTCCAGACGTCGAATCCA 59.323 52.381 10.46 0.00 0.00 3.41
94 95 1.541379 TCTCCAGACGTCGAATCCAA 58.459 50.000 10.46 0.00 0.00 3.53
95 96 1.201647 TCTCCAGACGTCGAATCCAAC 59.798 52.381 10.46 0.00 0.00 3.77
96 97 0.109458 TCCAGACGTCGAATCCAACG 60.109 55.000 10.46 1.94 44.22 4.10
97 98 0.109458 CCAGACGTCGAATCCAACGA 60.109 55.000 10.46 0.00 41.29 3.85
98 99 1.469251 CCAGACGTCGAATCCAACGAT 60.469 52.381 10.46 0.00 41.29 3.73
99 100 1.846782 CAGACGTCGAATCCAACGATC 59.153 52.381 10.46 4.40 41.29 3.69
100 101 1.197910 GACGTCGAATCCAACGATCC 58.802 55.000 0.00 0.00 41.29 3.36
101 102 0.524816 ACGTCGAATCCAACGATCCG 60.525 55.000 9.36 0.00 41.29 4.18
102 103 0.248336 CGTCGAATCCAACGATCCGA 60.248 55.000 0.00 0.00 41.29 4.55
103 104 1.197910 GTCGAATCCAACGATCCGAC 58.802 55.000 0.00 0.00 41.62 4.79
104 105 0.248336 TCGAATCCAACGATCCGACG 60.248 55.000 0.00 0.00 34.85 5.12
106 107 0.921347 GAATCCAACGATCCGACGTG 59.079 55.000 0.00 0.00 45.83 4.49
107 108 0.459585 AATCCAACGATCCGACGTGG 60.460 55.000 0.00 0.00 45.83 4.94
108 109 2.901051 ATCCAACGATCCGACGTGGC 62.901 60.000 0.00 0.00 45.83 5.01
109 110 3.186047 CAACGATCCGACGTGGCC 61.186 66.667 0.00 0.00 45.83 5.36
110 111 3.687102 AACGATCCGACGTGGCCA 61.687 61.111 0.00 0.00 45.83 5.36
111 112 3.642778 AACGATCCGACGTGGCCAG 62.643 63.158 5.11 2.58 45.83 4.85
121 122 2.202932 GTGGCCAGCGACGATCAT 60.203 61.111 5.11 0.00 0.00 2.45
122 123 2.106938 TGGCCAGCGACGATCATC 59.893 61.111 0.00 0.00 0.00 2.92
123 124 2.106938 GGCCAGCGACGATCATCA 59.893 61.111 0.00 0.00 0.00 3.07
124 125 2.240500 GGCCAGCGACGATCATCAC 61.241 63.158 0.00 0.00 0.00 3.06
125 126 2.240500 GCCAGCGACGATCATCACC 61.241 63.158 0.00 0.00 0.00 4.02
126 127 1.141665 CCAGCGACGATCATCACCA 59.858 57.895 0.00 0.00 0.00 4.17
127 128 0.249615 CCAGCGACGATCATCACCAT 60.250 55.000 0.00 0.00 0.00 3.55
128 129 1.135046 CAGCGACGATCATCACCATC 58.865 55.000 0.00 0.00 0.00 3.51
129 130 0.032678 AGCGACGATCATCACCATCC 59.967 55.000 0.00 0.00 0.00 3.51
130 131 0.946221 GCGACGATCATCACCATCCC 60.946 60.000 0.00 0.00 0.00 3.85
131 132 0.664466 CGACGATCATCACCATCCCG 60.664 60.000 0.00 0.00 0.00 5.14
132 133 0.946221 GACGATCATCACCATCCCGC 60.946 60.000 0.00 0.00 0.00 6.13
133 134 2.023771 CGATCATCACCATCCCGCG 61.024 63.158 0.00 0.00 0.00 6.46
134 135 1.669115 GATCATCACCATCCCGCGG 60.669 63.158 21.04 21.04 0.00 6.46
135 136 3.832237 ATCATCACCATCCCGCGGC 62.832 63.158 22.85 0.00 0.00 6.53
153 154 3.407967 GGCCTGATGGGGTCCGAA 61.408 66.667 0.00 0.00 35.12 4.30
154 155 2.190578 GCCTGATGGGGTCCGAAG 59.809 66.667 0.00 0.00 35.12 3.79
155 156 2.367202 GCCTGATGGGGTCCGAAGA 61.367 63.158 0.00 0.00 35.12 2.87
156 157 1.910580 GCCTGATGGGGTCCGAAGAA 61.911 60.000 0.00 0.00 35.12 2.52
157 158 0.618458 CCTGATGGGGTCCGAAGAAA 59.382 55.000 0.00 0.00 0.00 2.52
158 159 1.407437 CCTGATGGGGTCCGAAGAAAG 60.407 57.143 0.00 0.00 0.00 2.62
159 160 0.618458 TGATGGGGTCCGAAGAAAGG 59.382 55.000 0.00 0.00 0.00 3.11
160 161 0.909623 GATGGGGTCCGAAGAAAGGA 59.090 55.000 0.00 0.00 34.99 3.36
161 162 1.490910 GATGGGGTCCGAAGAAAGGAT 59.509 52.381 0.00 0.00 40.30 3.24
162 163 1.368374 TGGGGTCCGAAGAAAGGATT 58.632 50.000 0.00 0.00 40.30 3.01
163 164 1.280998 TGGGGTCCGAAGAAAGGATTC 59.719 52.381 0.00 0.00 40.30 2.52
164 165 1.280998 GGGGTCCGAAGAAAGGATTCA 59.719 52.381 0.00 0.00 40.30 2.57
165 166 2.633488 GGGTCCGAAGAAAGGATTCAG 58.367 52.381 0.00 0.00 40.30 3.02
166 167 2.236395 GGGTCCGAAGAAAGGATTCAGA 59.764 50.000 0.00 0.00 40.30 3.27
167 168 3.118223 GGGTCCGAAGAAAGGATTCAGAT 60.118 47.826 0.00 0.00 40.30 2.90
168 169 3.873952 GGTCCGAAGAAAGGATTCAGATG 59.126 47.826 0.00 0.00 40.30 2.90
169 170 3.873952 GTCCGAAGAAAGGATTCAGATGG 59.126 47.826 0.00 0.00 40.30 3.51
170 171 3.774766 TCCGAAGAAAGGATTCAGATGGA 59.225 43.478 0.00 0.00 38.06 3.41
171 172 4.410228 TCCGAAGAAAGGATTCAGATGGAT 59.590 41.667 0.00 0.00 38.06 3.41
172 173 4.754114 CCGAAGAAAGGATTCAGATGGATC 59.246 45.833 0.00 0.00 38.06 3.36
173 174 5.454471 CCGAAGAAAGGATTCAGATGGATCT 60.454 44.000 1.24 0.00 38.06 2.75
174 175 6.239430 CCGAAGAAAGGATTCAGATGGATCTA 60.239 42.308 1.24 0.00 38.06 1.98
175 176 7.212976 CGAAGAAAGGATTCAGATGGATCTAA 58.787 38.462 1.24 0.00 38.06 2.10
176 177 7.877097 CGAAGAAAGGATTCAGATGGATCTAAT 59.123 37.037 1.24 0.00 38.06 1.73
177 178 9.218440 GAAGAAAGGATTCAGATGGATCTAATC 57.782 37.037 1.24 0.00 38.06 1.75
178 179 8.508969 AGAAAGGATTCAGATGGATCTAATCT 57.491 34.615 1.24 5.84 38.06 2.40
184 185 7.197901 ATTCAGATGGATCTAATCTGGATCC 57.802 40.000 25.61 4.20 43.91 3.36
187 188 2.682155 GGATCTAATCTGGATCCGGC 57.318 55.000 16.48 0.00 46.24 6.13
188 189 1.134965 GGATCTAATCTGGATCCGGCG 60.135 57.143 16.48 0.00 46.24 6.46
189 190 0.898320 ATCTAATCTGGATCCGGCGG 59.102 55.000 22.51 22.51 0.00 6.13
190 191 1.374758 CTAATCTGGATCCGGCGGC 60.375 63.158 23.83 8.24 0.00 6.53
191 192 2.099652 CTAATCTGGATCCGGCGGCA 62.100 60.000 23.83 13.12 0.00 5.69
192 193 2.377628 TAATCTGGATCCGGCGGCAC 62.378 60.000 23.83 17.01 0.00 5.01
215 216 4.265056 ACCACCGGTCAGGCCAAC 62.265 66.667 2.59 1.87 46.52 3.77
228 229 4.954970 CCAACGCAGCCACCACCT 62.955 66.667 0.00 0.00 0.00 4.00
229 230 3.357079 CAACGCAGCCACCACCTC 61.357 66.667 0.00 0.00 0.00 3.85
230 231 3.872603 AACGCAGCCACCACCTCA 61.873 61.111 0.00 0.00 0.00 3.86
231 232 4.626081 ACGCAGCCACCACCTCAC 62.626 66.667 0.00 0.00 0.00 3.51
233 234 4.314440 GCAGCCACCACCTCACGA 62.314 66.667 0.00 0.00 0.00 4.35
234 235 2.357517 CAGCCACCACCTCACGAC 60.358 66.667 0.00 0.00 0.00 4.34
235 236 2.842462 AGCCACCACCTCACGACA 60.842 61.111 0.00 0.00 0.00 4.35
236 237 2.665185 GCCACCACCTCACGACAC 60.665 66.667 0.00 0.00 0.00 3.67
237 238 2.355837 CCACCACCTCACGACACG 60.356 66.667 0.00 0.00 0.00 4.49
238 239 3.036084 CACCACCTCACGACACGC 61.036 66.667 0.00 0.00 0.00 5.34
239 240 3.224324 ACCACCTCACGACACGCT 61.224 61.111 0.00 0.00 0.00 5.07
240 241 2.734723 CCACCTCACGACACGCTG 60.735 66.667 0.00 0.00 0.00 5.18
241 242 2.734723 CACCTCACGACACGCTGG 60.735 66.667 0.00 0.00 0.00 4.85
242 243 3.224324 ACCTCACGACACGCTGGT 61.224 61.111 0.00 0.00 0.00 4.00
243 244 2.430921 CCTCACGACACGCTGGTC 60.431 66.667 0.00 0.00 34.42 4.02
278 279 3.822192 CACGACGCCGATGGGAGA 61.822 66.667 4.13 0.00 39.50 3.71
279 280 3.823330 ACGACGCCGATGGGAGAC 61.823 66.667 4.13 0.00 39.50 3.36
280 281 4.570663 CGACGCCGATGGGAGACC 62.571 72.222 4.13 0.00 45.57 3.85
328 329 3.470888 CCCGGCGTTCCTCTGGAT 61.471 66.667 6.01 0.00 31.56 3.41
329 330 2.107141 CCGGCGTTCCTCTGGATC 59.893 66.667 6.01 0.00 31.56 3.36
330 331 2.107141 CGGCGTTCCTCTGGATCC 59.893 66.667 4.20 4.20 0.00 3.36
331 332 2.506472 GGCGTTCCTCTGGATCCC 59.494 66.667 9.90 0.00 0.00 3.85
332 333 2.107141 GCGTTCCTCTGGATCCCG 59.893 66.667 9.90 2.27 0.00 5.14
333 334 2.107141 CGTTCCTCTGGATCCCGC 59.893 66.667 9.90 0.00 0.00 6.13
334 335 2.427245 CGTTCCTCTGGATCCCGCT 61.427 63.158 9.90 0.00 0.00 5.52
335 336 1.144936 GTTCCTCTGGATCCCGCTG 59.855 63.158 9.90 0.00 0.00 5.18
336 337 1.306141 TTCCTCTGGATCCCGCTGT 60.306 57.895 9.90 0.00 0.00 4.40
337 338 1.330655 TTCCTCTGGATCCCGCTGTC 61.331 60.000 9.90 0.00 0.00 3.51
338 339 2.801631 CCTCTGGATCCCGCTGTCC 61.802 68.421 9.90 0.00 35.02 4.02
339 340 2.764128 TCTGGATCCCGCTGTCCC 60.764 66.667 9.90 0.00 33.45 4.46
340 341 4.227134 CTGGATCCCGCTGTCCCG 62.227 72.222 9.90 0.00 33.45 5.14
358 359 4.069232 CGCCAGCCAAGACGGAGA 62.069 66.667 0.00 0.00 36.56 3.71
359 360 2.125350 GCCAGCCAAGACGGAGAG 60.125 66.667 0.00 0.00 36.56 3.20
360 361 2.581354 CCAGCCAAGACGGAGAGG 59.419 66.667 0.00 0.00 36.56 3.69
361 362 1.984570 CCAGCCAAGACGGAGAGGA 60.985 63.158 0.00 0.00 36.56 3.71
362 363 1.333636 CCAGCCAAGACGGAGAGGAT 61.334 60.000 0.00 0.00 36.56 3.24
363 364 0.179089 CAGCCAAGACGGAGAGGATG 60.179 60.000 0.00 0.00 36.56 3.51
364 365 1.144936 GCCAAGACGGAGAGGATGG 59.855 63.158 0.00 0.00 36.56 3.51
365 366 1.826024 CCAAGACGGAGAGGATGGG 59.174 63.158 0.00 0.00 36.56 4.00
366 367 1.690219 CCAAGACGGAGAGGATGGGG 61.690 65.000 0.00 0.00 36.56 4.96
367 368 0.687757 CAAGACGGAGAGGATGGGGA 60.688 60.000 0.00 0.00 0.00 4.81
368 369 0.042731 AAGACGGAGAGGATGGGGAA 59.957 55.000 0.00 0.00 0.00 3.97
369 370 0.042731 AGACGGAGAGGATGGGGAAA 59.957 55.000 0.00 0.00 0.00 3.13
370 371 0.909623 GACGGAGAGGATGGGGAAAA 59.090 55.000 0.00 0.00 0.00 2.29
371 372 0.912486 ACGGAGAGGATGGGGAAAAG 59.088 55.000 0.00 0.00 0.00 2.27
372 373 0.464554 CGGAGAGGATGGGGAAAAGC 60.465 60.000 0.00 0.00 0.00 3.51
373 374 0.106469 GGAGAGGATGGGGAAAAGCC 60.106 60.000 0.00 0.00 0.00 4.35
429 430 4.647615 CTATGGACGGCGGCGAGG 62.648 72.222 38.93 15.61 0.00 4.63
443 444 4.144727 GAGGAGGGGCGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
444 445 4.150454 AGGAGGGGCGAGGAGGAG 62.150 72.222 0.00 0.00 0.00 3.69
445 446 4.144727 GGAGGGGCGAGGAGGAGA 62.145 72.222 0.00 0.00 0.00 3.71
446 447 2.835895 GAGGGGCGAGGAGGAGAC 60.836 72.222 0.00 0.00 0.00 3.36
460 461 2.243810 AGGAGACTCGAAAGCTCACTT 58.756 47.619 9.99 0.00 32.90 3.16
462 463 3.827302 AGGAGACTCGAAAGCTCACTTTA 59.173 43.478 9.99 0.00 41.25 1.85
466 467 4.278669 AGACTCGAAAGCTCACTTTAGTCA 59.721 41.667 17.34 0.00 45.65 3.41
481 482 8.133627 TCACTTTAGTCACTATATACGCCTTTC 58.866 37.037 0.00 0.00 0.00 2.62
482 483 7.113124 CACTTTAGTCACTATATACGCCTTTCG 59.887 40.741 0.00 0.00 45.38 3.46
518 519 7.770433 TGGTCACTGAGTATAATCATCAAAAGG 59.230 37.037 2.91 0.00 0.00 3.11
580 612 6.767524 AGTGAACTTTGGACACAAAATACA 57.232 33.333 0.00 0.00 45.27 2.29
581 613 7.164230 AGTGAACTTTGGACACAAAATACAA 57.836 32.000 0.00 0.00 45.27 2.41
582 614 7.257722 AGTGAACTTTGGACACAAAATACAAG 58.742 34.615 0.00 0.00 45.27 3.16
583 615 6.475402 GTGAACTTTGGACACAAAATACAAGG 59.525 38.462 0.00 0.00 45.27 3.61
584 616 5.529581 ACTTTGGACACAAAATACAAGGG 57.470 39.130 0.00 0.00 45.27 3.95
585 617 4.959839 ACTTTGGACACAAAATACAAGGGT 59.040 37.500 0.00 0.00 45.27 4.34
586 618 4.927978 TTGGACACAAAATACAAGGGTG 57.072 40.909 0.00 0.00 32.66 4.61
588 620 2.890945 GGACACAAAATACAAGGGTGCT 59.109 45.455 0.00 0.00 32.89 4.40
589 621 3.305335 GGACACAAAATACAAGGGTGCTG 60.305 47.826 0.00 0.00 32.89 4.41
591 623 2.035704 CACAAAATACAAGGGTGCTGCA 59.964 45.455 0.00 0.00 0.00 4.41
592 624 2.697751 ACAAAATACAAGGGTGCTGCAA 59.302 40.909 2.77 0.00 0.00 4.08
593 625 3.243839 ACAAAATACAAGGGTGCTGCAAG 60.244 43.478 2.77 0.00 0.00 4.01
621 673 1.727880 GCTGCGTATACGTTTTGTCCA 59.272 47.619 25.04 12.23 42.22 4.02
636 688 3.790437 CCAGCACTCTGCCGGGAT 61.790 66.667 2.18 0.00 46.52 3.85
657 716 3.760580 AGGAAACAGAGGAGTTGAGTG 57.239 47.619 0.00 0.00 0.00 3.51
708 767 2.921754 CCGTTTCACTAATCTGTCCGAC 59.078 50.000 0.00 0.00 0.00 4.79
732 791 3.934457 ATTAAGCAAGGAAACAACCCG 57.066 42.857 0.00 0.00 0.00 5.28
773 832 2.983898 ACCCCTCAGCTTTACTTAACCA 59.016 45.455 0.00 0.00 0.00 3.67
789 848 9.532494 TTACTTAACCATAACCACTCTACTACA 57.468 33.333 0.00 0.00 0.00 2.74
896 958 7.763985 CCCAAACCACTATAAAATCCAAACATC 59.236 37.037 0.00 0.00 0.00 3.06
944 1009 0.099791 GAGCACGTCTCCTCACTAGC 59.900 60.000 0.00 0.00 35.77 3.42
949 1014 1.440938 CGTCTCCTCACTAGCCTCCG 61.441 65.000 0.00 0.00 0.00 4.63
1024 1096 2.182030 GCCGTTCTCTCACTCCCG 59.818 66.667 0.00 0.00 0.00 5.14
1036 1108 1.534235 ACTCCCGTCCAGCTCACTT 60.534 57.895 0.00 0.00 0.00 3.16
1180 1252 2.227194 TCCTCGCTTTTCTCCCAAAAC 58.773 47.619 0.00 0.00 0.00 2.43
1396 1468 0.250597 GAACAACTACCTGGGCGGTT 60.251 55.000 0.00 0.00 46.37 4.44
1783 1855 4.421479 CCGGCGAGCTCACTTCGT 62.421 66.667 15.40 0.00 0.00 3.85
1935 2007 8.880878 ATTTGGTTTGGTTGAGTTGTTATTAC 57.119 30.769 0.00 0.00 0.00 1.89
1957 2029 5.368145 ACTGTGTGTCTTGTGTCATGTATT 58.632 37.500 0.00 0.00 0.00 1.89
2063 2141 7.893302 TCTTTGAACCAAGTCCCATATTACATT 59.107 33.333 0.00 0.00 0.00 2.71
2225 2303 5.696724 ACATGACACCTCGACTTTTTAAGAG 59.303 40.000 0.00 0.00 0.00 2.85
2233 2311 8.654215 CACCTCGACTTTTTAAGAGTAATAACC 58.346 37.037 0.00 0.00 0.00 2.85
2251 2329 0.169672 CCTTCGCCATCTTGCAACTG 59.830 55.000 0.00 0.00 0.00 3.16
2256 2532 0.529378 GCCATCTTGCAACTGGAAGG 59.471 55.000 21.98 13.72 42.71 3.46
2342 6429 8.736097 ATAACTTTTTGGAAAATACTCCCCTT 57.264 30.769 0.00 0.00 34.22 3.95
2348 6436 8.728596 TTTTGGAAAATACTCCCCTTGAATTA 57.271 30.769 0.00 0.00 34.22 1.40
2453 6541 9.632638 TTTTCTTGGATGATTAAGGGAGAATAG 57.367 33.333 0.00 0.00 0.00 1.73
2454 6542 7.937700 TCTTGGATGATTAAGGGAGAATAGT 57.062 36.000 0.00 0.00 0.00 2.12
2480 6569 7.663493 TCGGCCAGATTTATTTTCCAAAATTTT 59.337 29.630 2.24 0.00 39.24 1.82
2481 6570 7.750014 CGGCCAGATTTATTTTCCAAAATTTTG 59.250 33.333 21.65 21.65 39.24 2.44
2523 6612 4.523083 ACAACTGAACTAGCCAACAAAGA 58.477 39.130 0.00 0.00 0.00 2.52
2657 6749 6.320672 AGGTTGCCTCATCTTCATTTATCAAG 59.679 38.462 0.00 0.00 0.00 3.02
2697 6793 4.495690 TGTTCGGTTGGGAATATGATCA 57.504 40.909 0.00 0.00 0.00 2.92
2701 6797 5.567037 TCGGTTGGGAATATGATCAAGAT 57.433 39.130 0.00 0.00 0.00 2.40
2784 6880 6.712095 TCAATATCATCTTGACATAGGTTGGC 59.288 38.462 0.00 0.00 0.00 4.52
2786 6882 1.331756 CATCTTGACATAGGTTGGCGC 59.668 52.381 0.00 0.00 35.37 6.53
2849 6946 4.450976 TGATAACAATCGCTAGCCATTGT 58.549 39.130 28.33 28.33 43.61 2.71
2868 6965 6.349033 CCATTGTGGATATGAGCACACATATG 60.349 42.308 13.12 0.00 42.66 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.073816 TCTTTCATCTTCGCGGGTTTC 58.926 47.619 6.13 0.00 0.00 2.78
3 4 2.076863 CTCTTTCATCTTCGCGGGTTT 58.923 47.619 6.13 0.00 0.00 3.27
8 9 1.004185 CATGGCTCTTTCATCTTCGCG 60.004 52.381 0.00 0.00 0.00 5.87
9 10 1.332997 CCATGGCTCTTTCATCTTCGC 59.667 52.381 0.00 0.00 0.00 4.70
10 11 1.945394 CCCATGGCTCTTTCATCTTCG 59.055 52.381 6.09 0.00 0.00 3.79
11 12 2.305009 CCCCATGGCTCTTTCATCTTC 58.695 52.381 6.09 0.00 0.00 2.87
12 13 2.449137 CCCCATGGCTCTTTCATCTT 57.551 50.000 6.09 0.00 0.00 2.40
30 31 0.895559 CCTTTCTGGTGGGTTGAGCC 60.896 60.000 0.00 0.00 0.00 4.70
31 32 0.110486 TCCTTTCTGGTGGGTTGAGC 59.890 55.000 0.00 0.00 37.07 4.26
32 33 1.271597 CCTCCTTTCTGGTGGGTTGAG 60.272 57.143 0.00 0.00 43.83 3.02
33 34 0.771127 CCTCCTTTCTGGTGGGTTGA 59.229 55.000 0.00 0.00 43.83 3.18
34 35 0.771127 TCCTCCTTTCTGGTGGGTTG 59.229 55.000 3.39 0.00 46.67 3.77
35 36 1.636003 GATCCTCCTTTCTGGTGGGTT 59.364 52.381 3.39 0.00 46.67 4.11
36 37 1.290134 GATCCTCCTTTCTGGTGGGT 58.710 55.000 3.39 0.00 46.67 4.51
37 38 1.289160 TGATCCTCCTTTCTGGTGGG 58.711 55.000 3.39 0.00 46.67 4.61
39 40 3.988976 TCTTGATCCTCCTTTCTGGTG 57.011 47.619 0.00 0.00 37.07 4.17
40 41 4.171234 TCTTCTTGATCCTCCTTTCTGGT 58.829 43.478 0.00 0.00 37.07 4.00
41 42 4.833478 TCTTCTTGATCCTCCTTTCTGG 57.167 45.455 0.00 0.00 37.10 3.86
42 43 5.803552 AGTTCTTCTTGATCCTCCTTTCTG 58.196 41.667 0.00 0.00 0.00 3.02
43 44 5.045942 GGAGTTCTTCTTGATCCTCCTTTCT 60.046 44.000 0.00 0.00 38.82 2.52
44 45 5.045942 AGGAGTTCTTCTTGATCCTCCTTTC 60.046 44.000 6.99 0.00 44.42 2.62
45 46 4.849235 AGGAGTTCTTCTTGATCCTCCTTT 59.151 41.667 6.99 0.00 44.42 3.11
46 47 4.434195 AGGAGTTCTTCTTGATCCTCCTT 58.566 43.478 6.99 0.00 44.42 3.36
47 48 4.073425 AGGAGTTCTTCTTGATCCTCCT 57.927 45.455 6.99 6.99 43.19 3.69
48 49 4.019771 ACAAGGAGTTCTTCTTGATCCTCC 60.020 45.833 22.85 0.00 41.94 4.30
49 50 5.159273 ACAAGGAGTTCTTCTTGATCCTC 57.841 43.478 22.85 0.00 41.94 3.71
50 51 6.019748 TCTACAAGGAGTTCTTCTTGATCCT 58.980 40.000 22.85 7.21 41.94 3.24
51 52 6.287589 TCTACAAGGAGTTCTTCTTGATCC 57.712 41.667 22.85 0.00 41.94 3.36
52 53 7.781056 AGATCTACAAGGAGTTCTTCTTGATC 58.219 38.462 22.85 16.02 41.94 2.92
53 54 7.147742 GGAGATCTACAAGGAGTTCTTCTTGAT 60.148 40.741 22.85 9.63 41.94 2.57
54 55 6.153680 GGAGATCTACAAGGAGTTCTTCTTGA 59.846 42.308 22.85 9.28 41.94 3.02
55 56 6.071108 TGGAGATCTACAAGGAGTTCTTCTTG 60.071 42.308 16.57 16.57 44.14 3.02
56 57 6.019748 TGGAGATCTACAAGGAGTTCTTCTT 58.980 40.000 4.73 0.00 32.41 2.52
57 58 5.584913 TGGAGATCTACAAGGAGTTCTTCT 58.415 41.667 4.73 0.00 32.41 2.85
58 59 5.654650 TCTGGAGATCTACAAGGAGTTCTTC 59.345 44.000 9.45 0.00 32.41 2.87
59 60 5.420739 GTCTGGAGATCTACAAGGAGTTCTT 59.579 44.000 9.45 0.00 35.79 2.52
60 61 4.953579 GTCTGGAGATCTACAAGGAGTTCT 59.046 45.833 9.45 0.00 0.00 3.01
61 62 4.201970 CGTCTGGAGATCTACAAGGAGTTC 60.202 50.000 9.45 0.00 0.00 3.01
62 63 3.697045 CGTCTGGAGATCTACAAGGAGTT 59.303 47.826 9.45 0.00 0.00 3.01
63 64 3.283751 CGTCTGGAGATCTACAAGGAGT 58.716 50.000 9.45 0.00 0.00 3.85
64 65 3.283751 ACGTCTGGAGATCTACAAGGAG 58.716 50.000 9.45 3.66 0.00 3.69
65 66 3.280295 GACGTCTGGAGATCTACAAGGA 58.720 50.000 9.45 0.49 0.00 3.36
66 67 2.032302 CGACGTCTGGAGATCTACAAGG 59.968 54.545 14.70 8.37 0.00 3.61
67 68 2.937149 TCGACGTCTGGAGATCTACAAG 59.063 50.000 14.70 6.17 0.00 3.16
68 69 2.981898 TCGACGTCTGGAGATCTACAA 58.018 47.619 14.70 0.00 0.00 2.41
69 70 2.685850 TCGACGTCTGGAGATCTACA 57.314 50.000 14.70 7.60 0.00 2.74
70 71 3.058777 GGATTCGACGTCTGGAGATCTAC 60.059 52.174 14.70 0.00 0.00 2.59
71 72 3.139850 GGATTCGACGTCTGGAGATCTA 58.860 50.000 14.70 0.00 0.00 1.98
72 73 1.950909 GGATTCGACGTCTGGAGATCT 59.049 52.381 14.70 0.00 0.00 2.75
73 74 1.676529 TGGATTCGACGTCTGGAGATC 59.323 52.381 14.70 9.00 0.00 2.75
74 75 1.763968 TGGATTCGACGTCTGGAGAT 58.236 50.000 14.70 0.04 0.00 2.75
75 76 1.201647 GTTGGATTCGACGTCTGGAGA 59.798 52.381 14.70 0.00 0.00 3.71
76 77 1.630148 GTTGGATTCGACGTCTGGAG 58.370 55.000 14.70 0.00 0.00 3.86
77 78 0.109458 CGTTGGATTCGACGTCTGGA 60.109 55.000 14.70 1.01 43.72 3.86
78 79 2.359792 CGTTGGATTCGACGTCTGG 58.640 57.895 14.70 0.00 43.72 3.86
87 88 0.921347 CACGTCGGATCGTTGGATTC 59.079 55.000 0.00 0.00 42.27 2.52
88 89 0.459585 CCACGTCGGATCGTTGGATT 60.460 55.000 0.00 0.00 42.27 3.01
89 90 1.141019 CCACGTCGGATCGTTGGAT 59.859 57.895 0.00 0.00 42.27 3.41
90 91 2.569657 CCACGTCGGATCGTTGGA 59.430 61.111 0.00 0.00 42.27 3.53
91 92 3.186047 GCCACGTCGGATCGTTGG 61.186 66.667 8.04 0.00 42.27 3.77
92 93 3.186047 GGCCACGTCGGATCGTTG 61.186 66.667 0.00 2.56 42.27 4.10
93 94 3.642778 CTGGCCACGTCGGATCGTT 62.643 63.158 0.00 0.00 42.27 3.85
94 95 4.129737 CTGGCCACGTCGGATCGT 62.130 66.667 0.00 0.85 45.10 3.73
101 102 4.796231 ATCGTCGCTGGCCACGTC 62.796 66.667 21.61 16.90 37.30 4.34
102 103 4.796231 GATCGTCGCTGGCCACGT 62.796 66.667 21.61 7.64 37.30 4.49
103 104 4.794439 TGATCGTCGCTGGCCACG 62.794 66.667 18.07 18.07 37.36 4.94
104 105 2.202932 ATGATCGTCGCTGGCCAC 60.203 61.111 0.00 0.00 0.00 5.01
105 106 2.106938 GATGATCGTCGCTGGCCA 59.893 61.111 4.71 4.71 0.00 5.36
106 107 2.106938 TGATGATCGTCGCTGGCC 59.893 61.111 10.32 0.00 0.00 5.36
107 108 2.240500 GGTGATGATCGTCGCTGGC 61.241 63.158 23.97 7.74 0.00 4.85
108 109 0.249615 ATGGTGATGATCGTCGCTGG 60.250 55.000 23.97 0.00 0.00 4.85
109 110 1.135046 GATGGTGATGATCGTCGCTG 58.865 55.000 23.97 0.00 0.00 5.18
110 111 0.032678 GGATGGTGATGATCGTCGCT 59.967 55.000 23.97 8.88 0.00 4.93
111 112 0.946221 GGGATGGTGATGATCGTCGC 60.946 60.000 18.40 18.40 0.00 5.19
112 113 0.664466 CGGGATGGTGATGATCGTCG 60.664 60.000 10.32 0.00 0.00 5.12
113 114 0.946221 GCGGGATGGTGATGATCGTC 60.946 60.000 8.06 8.06 0.00 4.20
114 115 1.069765 GCGGGATGGTGATGATCGT 59.930 57.895 0.00 0.00 0.00 3.73
115 116 2.023771 CGCGGGATGGTGATGATCG 61.024 63.158 0.00 0.00 0.00 3.69
116 117 1.669115 CCGCGGGATGGTGATGATC 60.669 63.158 20.10 0.00 0.00 2.92
117 118 2.427320 CCGCGGGATGGTGATGAT 59.573 61.111 20.10 0.00 0.00 2.45
118 119 4.545706 GCCGCGGGATGGTGATGA 62.546 66.667 29.38 0.00 0.00 2.92
136 137 3.406595 CTTCGGACCCCATCAGGCC 62.407 68.421 0.00 0.00 0.00 5.19
137 138 1.910580 TTCTTCGGACCCCATCAGGC 61.911 60.000 0.00 0.00 0.00 4.85
138 139 0.618458 TTTCTTCGGACCCCATCAGG 59.382 55.000 0.00 0.00 0.00 3.86
139 140 1.407437 CCTTTCTTCGGACCCCATCAG 60.407 57.143 0.00 0.00 0.00 2.90
140 141 0.618458 CCTTTCTTCGGACCCCATCA 59.382 55.000 0.00 0.00 0.00 3.07
141 142 0.909623 TCCTTTCTTCGGACCCCATC 59.090 55.000 0.00 0.00 0.00 3.51
142 143 1.596496 ATCCTTTCTTCGGACCCCAT 58.404 50.000 0.00 0.00 32.41 4.00
143 144 1.280998 GAATCCTTTCTTCGGACCCCA 59.719 52.381 0.00 0.00 32.41 4.96
144 145 1.280998 TGAATCCTTTCTTCGGACCCC 59.719 52.381 0.00 0.00 32.41 4.95
145 146 2.236395 TCTGAATCCTTTCTTCGGACCC 59.764 50.000 0.00 0.00 34.01 4.46
146 147 3.611766 TCTGAATCCTTTCTTCGGACC 57.388 47.619 0.00 0.00 34.01 4.46
147 148 3.873952 CCATCTGAATCCTTTCTTCGGAC 59.126 47.826 0.00 0.00 39.99 4.79
148 149 3.774766 TCCATCTGAATCCTTTCTTCGGA 59.225 43.478 0.00 0.00 41.08 4.55
149 150 4.142609 TCCATCTGAATCCTTTCTTCGG 57.857 45.455 0.00 0.00 32.78 4.30
150 151 5.609423 AGATCCATCTGAATCCTTTCTTCG 58.391 41.667 0.00 0.00 35.42 3.79
151 152 9.218440 GATTAGATCCATCTGAATCCTTTCTTC 57.782 37.037 0.00 0.00 37.76 2.87
152 153 8.947305 AGATTAGATCCATCTGAATCCTTTCTT 58.053 33.333 4.53 0.00 37.76 2.52
153 154 8.508969 AGATTAGATCCATCTGAATCCTTTCT 57.491 34.615 4.53 0.00 37.76 2.52
169 170 1.134965 CCGCCGGATCCAGATTAGATC 60.135 57.143 13.41 0.00 39.57 2.75
170 171 0.898320 CCGCCGGATCCAGATTAGAT 59.102 55.000 13.41 0.00 0.00 1.98
171 172 1.816863 GCCGCCGGATCCAGATTAGA 61.817 60.000 7.68 0.00 0.00 2.10
172 173 1.374758 GCCGCCGGATCCAGATTAG 60.375 63.158 7.68 0.00 0.00 1.73
173 174 2.137528 TGCCGCCGGATCCAGATTA 61.138 57.895 7.68 0.00 0.00 1.75
174 175 3.479203 TGCCGCCGGATCCAGATT 61.479 61.111 7.68 0.00 0.00 2.40
175 176 4.241555 GTGCCGCCGGATCCAGAT 62.242 66.667 7.68 0.00 0.00 2.90
198 199 4.265056 GTTGGCCTGACCGGTGGT 62.265 66.667 14.63 0.00 43.94 4.16
211 212 4.954970 AGGTGGTGGCTGCGTTGG 62.955 66.667 0.00 0.00 0.00 3.77
212 213 3.357079 GAGGTGGTGGCTGCGTTG 61.357 66.667 0.00 0.00 0.00 4.10
213 214 3.872603 TGAGGTGGTGGCTGCGTT 61.873 61.111 0.00 0.00 0.00 4.84
214 215 4.626081 GTGAGGTGGTGGCTGCGT 62.626 66.667 0.00 0.00 0.00 5.24
216 217 4.314440 TCGTGAGGTGGTGGCTGC 62.314 66.667 0.00 0.00 0.00 5.25
217 218 2.357517 GTCGTGAGGTGGTGGCTG 60.358 66.667 0.00 0.00 0.00 4.85
218 219 2.842462 TGTCGTGAGGTGGTGGCT 60.842 61.111 0.00 0.00 0.00 4.75
219 220 2.665185 GTGTCGTGAGGTGGTGGC 60.665 66.667 0.00 0.00 0.00 5.01
220 221 2.355837 CGTGTCGTGAGGTGGTGG 60.356 66.667 0.00 0.00 0.00 4.61
221 222 3.036084 GCGTGTCGTGAGGTGGTG 61.036 66.667 0.00 0.00 0.00 4.17
222 223 3.224324 AGCGTGTCGTGAGGTGGT 61.224 61.111 0.00 0.00 0.00 4.16
223 224 2.734723 CAGCGTGTCGTGAGGTGG 60.735 66.667 0.00 0.00 0.00 4.61
224 225 2.734723 CCAGCGTGTCGTGAGGTG 60.735 66.667 0.00 0.00 0.00 4.00
225 226 3.208884 GACCAGCGTGTCGTGAGGT 62.209 63.158 0.00 0.00 32.43 3.85
226 227 2.430921 GACCAGCGTGTCGTGAGG 60.431 66.667 0.00 0.00 0.00 3.86
261 262 3.822192 TCTCCCATCGGCGTCGTG 61.822 66.667 10.18 7.19 37.69 4.35
262 263 3.823330 GTCTCCCATCGGCGTCGT 61.823 66.667 10.18 0.00 37.69 4.34
263 264 4.570663 GGTCTCCCATCGGCGTCG 62.571 72.222 1.15 1.15 37.82 5.12
264 265 4.222847 GGGTCTCCCATCGGCGTC 62.223 72.222 6.85 0.00 44.65 5.19
311 312 3.447025 GATCCAGAGGAACGCCGGG 62.447 68.421 2.18 0.00 39.96 5.73
312 313 2.107141 GATCCAGAGGAACGCCGG 59.893 66.667 0.00 0.00 39.96 6.13
313 314 2.107141 GGATCCAGAGGAACGCCG 59.893 66.667 6.95 0.00 39.96 6.46
314 315 2.506472 GGGATCCAGAGGAACGCC 59.494 66.667 15.23 0.00 34.34 5.68
315 316 2.107141 CGGGATCCAGAGGAACGC 59.893 66.667 15.23 1.09 34.34 4.84
316 317 2.107141 GCGGGATCCAGAGGAACG 59.893 66.667 16.86 8.00 34.34 3.95
317 318 1.144936 CAGCGGGATCCAGAGGAAC 59.855 63.158 16.86 0.00 34.34 3.62
318 319 1.306141 ACAGCGGGATCCAGAGGAA 60.306 57.895 16.86 0.00 34.34 3.36
319 320 1.758514 GACAGCGGGATCCAGAGGA 60.759 63.158 16.86 0.00 35.55 3.71
320 321 2.801631 GGACAGCGGGATCCAGAGG 61.802 68.421 16.86 8.75 34.87 3.69
321 322 2.801631 GGGACAGCGGGATCCAGAG 61.802 68.421 16.86 9.47 36.65 3.35
322 323 2.764128 GGGACAGCGGGATCCAGA 60.764 66.667 16.86 0.00 36.65 3.86
323 324 4.227134 CGGGACAGCGGGATCCAG 62.227 72.222 15.23 11.38 36.65 3.86
341 342 3.997064 CTCTCCGTCTTGGCTGGCG 62.997 68.421 0.00 0.00 37.80 5.69
342 343 2.125350 CTCTCCGTCTTGGCTGGC 60.125 66.667 0.00 0.00 37.80 4.85
343 344 1.333636 ATCCTCTCCGTCTTGGCTGG 61.334 60.000 0.00 0.00 37.80 4.85
344 345 0.179089 CATCCTCTCCGTCTTGGCTG 60.179 60.000 0.00 0.00 37.80 4.85
345 346 1.333636 CCATCCTCTCCGTCTTGGCT 61.334 60.000 0.00 0.00 37.80 4.75
346 347 1.144936 CCATCCTCTCCGTCTTGGC 59.855 63.158 0.00 0.00 37.80 4.52
347 348 1.690219 CCCCATCCTCTCCGTCTTGG 61.690 65.000 0.00 0.00 40.09 3.61
348 349 0.687757 TCCCCATCCTCTCCGTCTTG 60.688 60.000 0.00 0.00 0.00 3.02
349 350 0.042731 TTCCCCATCCTCTCCGTCTT 59.957 55.000 0.00 0.00 0.00 3.01
350 351 0.042731 TTTCCCCATCCTCTCCGTCT 59.957 55.000 0.00 0.00 0.00 4.18
351 352 0.909623 TTTTCCCCATCCTCTCCGTC 59.090 55.000 0.00 0.00 0.00 4.79
352 353 0.912486 CTTTTCCCCATCCTCTCCGT 59.088 55.000 0.00 0.00 0.00 4.69
353 354 0.464554 GCTTTTCCCCATCCTCTCCG 60.465 60.000 0.00 0.00 0.00 4.63
354 355 0.106469 GGCTTTTCCCCATCCTCTCC 60.106 60.000 0.00 0.00 0.00 3.71
355 356 3.503998 GGCTTTTCCCCATCCTCTC 57.496 57.895 0.00 0.00 0.00 3.20
412 413 4.647615 CCTCGCCGCCGTCCATAG 62.648 72.222 0.00 0.00 35.54 2.23
426 427 4.144727 TCCTCCTCGCCCCTCCTC 62.145 72.222 0.00 0.00 0.00 3.71
427 428 4.150454 CTCCTCCTCGCCCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
428 429 4.144727 TCTCCTCCTCGCCCCTCC 62.145 72.222 0.00 0.00 0.00 4.30
429 430 2.835895 GTCTCCTCCTCGCCCCTC 60.836 72.222 0.00 0.00 0.00 4.30
430 431 3.351885 AGTCTCCTCCTCGCCCCT 61.352 66.667 0.00 0.00 0.00 4.79
431 432 2.835895 GAGTCTCCTCCTCGCCCC 60.836 72.222 0.00 0.00 0.00 5.80
432 433 3.213402 CGAGTCTCCTCCTCGCCC 61.213 72.222 0.00 0.00 44.42 6.13
436 437 1.404035 GAGCTTTCGAGTCTCCTCCTC 59.596 57.143 0.00 0.00 33.93 3.71
437 438 1.272203 TGAGCTTTCGAGTCTCCTCCT 60.272 52.381 0.00 0.00 33.93 3.69
438 439 1.135228 GTGAGCTTTCGAGTCTCCTCC 60.135 57.143 0.00 0.00 33.93 4.30
439 440 1.816224 AGTGAGCTTTCGAGTCTCCTC 59.184 52.381 0.00 0.00 0.00 3.71
440 441 1.917872 AGTGAGCTTTCGAGTCTCCT 58.082 50.000 0.00 3.49 0.00 3.69
441 442 2.734276 AAGTGAGCTTTCGAGTCTCC 57.266 50.000 0.00 1.79 0.00 3.71
442 443 4.800784 ACTAAAGTGAGCTTTCGAGTCTC 58.199 43.478 0.00 4.37 43.28 3.36
443 444 4.278669 TGACTAAAGTGAGCTTTCGAGTCT 59.721 41.667 16.94 0.00 43.68 3.24
444 445 4.383351 GTGACTAAAGTGAGCTTTCGAGTC 59.617 45.833 12.48 12.48 43.64 3.36
445 446 4.038162 AGTGACTAAAGTGAGCTTTCGAGT 59.962 41.667 0.00 0.00 43.28 4.18
446 447 4.551388 AGTGACTAAAGTGAGCTTTCGAG 58.449 43.478 0.00 0.00 43.28 4.04
481 482 5.201713 ACTCAGTGACCATATAATCACCG 57.798 43.478 12.67 5.52 45.28 4.94
511 512 5.321102 ACGGCCAATATATATGCCTTTTGA 58.679 37.500 17.54 0.00 41.80 2.69
518 519 8.458843 ACTCAAAAATACGGCCAATATATATGC 58.541 33.333 2.24 0.00 0.00 3.14
538 570 8.527810 AGTTCACTTTGGTCATTTTTACTCAAA 58.472 29.630 0.00 0.00 0.00 2.69
560 592 5.983118 CCCTTGTATTTTGTGTCCAAAGTTC 59.017 40.000 0.00 0.00 41.37 3.01
572 604 3.319755 CTTGCAGCACCCTTGTATTTTG 58.680 45.455 0.00 0.00 0.00 2.44
574 606 1.273327 GCTTGCAGCACCCTTGTATTT 59.727 47.619 0.00 0.00 41.89 1.40
575 607 0.890683 GCTTGCAGCACCCTTGTATT 59.109 50.000 0.00 0.00 41.89 1.89
577 609 0.890542 CAGCTTGCAGCACCCTTGTA 60.891 55.000 0.00 0.00 45.56 2.41
578 610 2.196776 AGCTTGCAGCACCCTTGT 59.803 55.556 0.00 0.00 45.56 3.16
579 611 2.649034 CAGCTTGCAGCACCCTTG 59.351 61.111 0.00 0.00 45.56 3.61
580 612 3.300765 GCAGCTTGCAGCACCCTT 61.301 61.111 0.00 0.00 45.56 3.95
595 627 0.390603 AACGTATACGCAGCTTGGCA 60.391 50.000 24.64 0.00 44.43 4.92
596 628 0.725117 AAACGTATACGCAGCTTGGC 59.275 50.000 24.64 0.00 44.43 4.52
597 629 2.158841 ACAAAACGTATACGCAGCTTGG 59.841 45.455 24.64 12.65 44.43 3.61
621 673 2.136878 CCTATCCCGGCAGAGTGCT 61.137 63.158 0.00 0.00 44.28 4.40
636 688 3.006967 GCACTCAACTCCTCTGTTTCCTA 59.993 47.826 0.00 0.00 0.00 2.94
673 732 2.356382 TGAAACGGACTGCGTTCAAATT 59.644 40.909 8.90 0.00 0.00 1.82
708 767 5.861787 CGGGTTGTTTCCTTGCTTAATTTAG 59.138 40.000 0.00 0.00 0.00 1.85
753 812 3.713826 TGGTTAAGTAAAGCTGAGGGG 57.286 47.619 0.00 0.00 36.51 4.79
802 861 3.873361 TCCGCTTCTGCATCTGAATTTAG 59.127 43.478 0.00 0.00 39.64 1.85
859 919 2.430367 GTTTGGGGAGCGTCAGGT 59.570 61.111 0.00 0.00 0.00 4.00
869 929 6.014156 TGTTTGGATTTTATAGTGGTTTGGGG 60.014 38.462 0.00 0.00 0.00 4.96
896 958 1.024271 CGTTGTGATGGCTATTGGGG 58.976 55.000 0.00 0.00 0.00 4.96
944 1009 1.445716 CTAGTACAGGACGGCGGAGG 61.446 65.000 13.24 0.00 0.00 4.30
982 1054 1.750206 CATTGTTGGGATCAATCGGCA 59.250 47.619 0.00 0.00 33.92 5.69
1024 1096 1.003233 GGGTGGAAGTGAGCTGGAC 60.003 63.158 0.00 0.00 0.00 4.02
1036 1108 0.251653 AGTGCTACGAAGAGGGTGGA 60.252 55.000 0.00 0.00 0.00 4.02
1396 1468 2.441532 GGGACCGGACGAGGATGA 60.442 66.667 9.46 0.00 34.73 2.92
1783 1855 0.817229 TTGATGAGCGGCAACACACA 60.817 50.000 1.45 4.16 0.00 3.72
1935 2007 5.237127 ACAATACATGACACAAGACACACAG 59.763 40.000 0.00 0.00 0.00 3.66
1957 2029 6.706716 TCAAACAATTAACACACGATCCTACA 59.293 34.615 0.00 0.00 0.00 2.74
2225 2303 3.625764 TGCAAGATGGCGAAGGTTATTAC 59.374 43.478 0.00 0.00 36.28 1.89
2233 2311 0.169672 CCAGTTGCAAGATGGCGAAG 59.830 55.000 15.71 0.00 36.28 3.79
2251 2329 8.433421 TCAACATCGTCTATAAAATTCCTTCC 57.567 34.615 0.00 0.00 0.00 3.46
2348 6436 7.255569 CAAGTGCACATGAATAACTGAATCAT 58.744 34.615 21.04 0.00 34.22 2.45
2431 6519 6.870965 CGACTATTCTCCCTTAATCATCCAAG 59.129 42.308 0.00 0.00 0.00 3.61
2433 6521 5.246203 CCGACTATTCTCCCTTAATCATCCA 59.754 44.000 0.00 0.00 0.00 3.41
2451 6539 5.105567 TGGAAAATAAATCTGGCCGACTA 57.894 39.130 0.00 0.00 0.00 2.59
2453 6541 4.712122 TTGGAAAATAAATCTGGCCGAC 57.288 40.909 0.00 0.00 0.00 4.79
2454 6542 5.730296 TTTTGGAAAATAAATCTGGCCGA 57.270 34.783 0.00 0.00 0.00 5.54
2480 6569 7.994334 AGTTGTATTGTAAACTTTGTACTCCCA 59.006 33.333 0.00 0.00 32.75 4.37
2481 6570 8.287503 CAGTTGTATTGTAAACTTTGTACTCCC 58.712 37.037 0.00 0.00 34.41 4.30
2523 6612 8.608844 TTTTGTTGTTTGAATAGTGTTTTGGT 57.391 26.923 0.00 0.00 0.00 3.67
2701 6797 9.440773 GGACACATAATCATCTCTATAATTGCA 57.559 33.333 0.00 0.00 0.00 4.08
2754 6850 8.373981 ACCTATGTCAAGATGATATTGAAGGAG 58.626 37.037 20.07 10.76 38.34 3.69
2868 6965 7.087007 TCGACAGATGATATGCTAATCTTCAC 58.913 38.462 13.41 6.85 34.23 3.18


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

AutoCloner maintained by Alex Coulton.