Multiple sequence alignment - TraesCS5A01G161500

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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 TraesCS5A01G161500 chr5A 100.000 4559 0 0 1 4559 343962197 343957639 0.000000e+00 8419.0
1 TraesCS5A01G161500 chr5B 92.774 3543 164 52 313 3827 293211368 293207890 0.000000e+00 5040.0
2 TraesCS5A01G161500 chr5B 90.544 698 48 10 3875 4559 293207885 293207193 0.000000e+00 907.0
3 TraesCS5A01G161500 chr5D 96.223 3018 97 7 888 3903 259236535 259233533 0.000000e+00 4926.0
4 TraesCS5A01G161500 chr5D 92.961 483 22 9 4079 4559 259233541 259233069 0.000000e+00 693.0
5 TraesCS5A01G161500 chr5D 87.950 556 21 9 313 837 259237460 259236920 8.380000e-172 614.0
6 TraesCS5A01G161500 chr5D 85.955 178 18 2 3906 4076 457284329 457284506 2.800000e-42 183.0
7 TraesCS5A01G161500 chr7A 94.212 311 16 1 3 313 132623017 132622709 1.480000e-129 473.0
8 TraesCS5A01G161500 chr4A 92.283 311 24 0 1 311 143725875 143725565 4.190000e-120 442.0
9 TraesCS5A01G161500 chr4A 84.669 287 42 2 1 286 67889175 67889460 7.460000e-73 285.0
10 TraesCS5A01G161500 chr4A 85.714 77 7 4 2746 2820 491689078 491689152 1.360000e-10 78.7
11 TraesCS5A01G161500 chr4A 97.222 36 0 1 2919 2954 562483509 562483475 4.930000e-05 60.2
12 TraesCS5A01G161500 chr4B 91.987 312 24 1 3 313 14534590 14534901 1.950000e-118 436.0
13 TraesCS5A01G161500 chr4B 88.629 299 34 0 3 301 578036224 578035926 9.320000e-97 364.0
14 TraesCS5A01G161500 chr4B 92.857 42 1 2 2913 2954 55704977 55705016 4.930000e-05 60.2
15 TraesCS5A01G161500 chr2A 91.167 317 24 2 1 313 448565267 448564951 1.170000e-115 427.0
16 TraesCS5A01G161500 chr3B 90.735 313 29 0 1 313 744030850 744031162 7.050000e-113 418.0
17 TraesCS5A01G161500 chr7D 78.864 317 57 9 1 313 637731092 637731402 5.980000e-49 206.0
18 TraesCS5A01G161500 chr3A 78.947 171 23 6 3906 4063 675361223 675361393 2.240000e-18 104.0
19 TraesCS5A01G161500 chr3D 88.889 72 5 2 3906 3977 590171361 590171429 8.130000e-13 86.1
20 TraesCS5A01G161500 chr6A 78.295 129 28 0 1 129 581269710 581269838 2.920000e-12 84.2
21 TraesCS5A01G161500 chr4D 84.416 77 8 4 2746 2820 81908777 81908851 6.330000e-09 73.1
22 TraesCS5A01G161500 chr4D 92.857 42 1 2 2913 2954 38304759 38304798 4.930000e-05 60.2


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 TraesCS5A01G161500 chr5A 343957639 343962197 4558 True 8419.000000 8419 100.000 1 4559 1 chr5A.!!$R1 4558
1 TraesCS5A01G161500 chr5B 293207193 293211368 4175 True 2973.500000 5040 91.659 313 4559 2 chr5B.!!$R1 4246
2 TraesCS5A01G161500 chr5D 259233069 259237460 4391 True 2077.666667 4926 92.378 313 4559 3 chr5D.!!$R1 4246

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
111 112 0.040425 GGTCACGCAGCGTTTTGATT 60.040 50.000 20.29 0.0 38.32 2.57 F
116 117 0.159345 CGCAGCGTTTTGATTGCAAC 59.841 50.000 6.65 0.0 36.37 4.17 F
281 282 0.173481 TGCGCGAATGCTAGTCTTCT 59.827 50.000 12.10 0.0 39.65 2.85 F
283 284 1.005557 GCGCGAATGCTAGTCTTCTTG 60.006 52.381 12.10 0.0 39.65 3.02 F
583 596 1.184970 AGGTGGCCGGAAAACCATTG 61.185 55.000 19.24 0.0 38.46 2.82 F
584 597 1.374125 GTGGCCGGAAAACCATTGC 60.374 57.895 5.05 0.0 38.46 3.56 F
2483 2871 1.406887 GGGTGAGAATAAGAGCGGCAA 60.407 52.381 1.45 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 2191 0.386478 GCAGCACCTCGAGCTTTTTG 60.386 55.000 6.99 2.53 41.14 2.44 R
2091 2479 1.588597 GGCTTTGAGCAGCTTTCCC 59.411 57.895 0.00 0.00 44.75 3.97 R
2376 2764 2.049526 ATGTGCTTCGTCGACGCA 60.050 55.556 32.19 23.25 39.60 5.24 R
2421 2809 0.179161 CGTCTTCTGCGGTGAGGTAG 60.179 60.000 0.00 0.00 0.00 3.18 R
2430 2818 2.811317 GACCTGCCGTCTTCTGCG 60.811 66.667 0.00 0.00 38.57 5.18 R
2973 3361 3.849953 GCCGCCGACGTGATGTTC 61.850 66.667 0.00 0.00 37.70 3.18 R
3972 4365 0.037590 CCACCCCACCTGAAAATCGA 59.962 55.000 0.00 0.00 0.00 3.59 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
42 43 9.986833 TGTTCAACATATATCAGAAAATGTTCG 57.013 29.630 5.74 3.84 39.80 3.95
46 47 9.603298 CAACATATATCAGAAAATGTTCGATGG 57.397 33.333 11.09 4.07 39.80 3.51
47 48 8.908786 ACATATATCAGAAAATGTTCGATGGT 57.091 30.769 11.09 0.00 38.90 3.55
48 49 8.993121 ACATATATCAGAAAATGTTCGATGGTC 58.007 33.333 11.09 0.00 38.90 4.02
49 50 8.992073 CATATATCAGAAAATGTTCGATGGTCA 58.008 33.333 11.09 0.00 38.90 4.02
50 51 7.864108 ATATCAGAAAATGTTCGATGGTCAA 57.136 32.000 11.09 0.00 38.90 3.18
51 52 6.764308 ATCAGAAAATGTTCGATGGTCAAT 57.236 33.333 3.21 0.00 38.90 2.57
52 53 6.573664 TCAGAAAATGTTCGATGGTCAATT 57.426 33.333 0.00 0.00 38.90 2.32
53 54 6.980593 TCAGAAAATGTTCGATGGTCAATTT 58.019 32.000 0.00 0.00 38.90 1.82
54 55 7.432869 TCAGAAAATGTTCGATGGTCAATTTT 58.567 30.769 0.00 0.00 38.90 1.82
55 56 7.925483 TCAGAAAATGTTCGATGGTCAATTTTT 59.075 29.630 0.00 0.00 38.90 1.94
83 84 8.662781 TTTTTGGATCAGTCAGTACATATAGC 57.337 34.615 0.00 0.00 0.00 2.97
84 85 7.603180 TTTGGATCAGTCAGTACATATAGCT 57.397 36.000 0.00 0.00 0.00 3.32
85 86 6.825944 TGGATCAGTCAGTACATATAGCTC 57.174 41.667 0.00 0.00 0.00 4.09
86 87 6.547402 TGGATCAGTCAGTACATATAGCTCT 58.453 40.000 0.00 0.00 0.00 4.09
87 88 6.657117 TGGATCAGTCAGTACATATAGCTCTC 59.343 42.308 0.00 0.00 0.00 3.20
88 89 6.657117 GGATCAGTCAGTACATATAGCTCTCA 59.343 42.308 0.00 0.00 0.00 3.27
89 90 7.175816 GGATCAGTCAGTACATATAGCTCTCAA 59.824 40.741 0.00 0.00 0.00 3.02
90 91 7.503521 TCAGTCAGTACATATAGCTCTCAAG 57.496 40.000 0.00 0.00 0.00 3.02
91 92 7.057264 TCAGTCAGTACATATAGCTCTCAAGT 58.943 38.462 0.00 0.00 0.00 3.16
92 93 7.012799 TCAGTCAGTACATATAGCTCTCAAGTG 59.987 40.741 0.00 0.00 0.00 3.16
93 94 6.264292 AGTCAGTACATATAGCTCTCAAGTGG 59.736 42.308 0.00 0.00 0.00 4.00
94 95 6.039941 GTCAGTACATATAGCTCTCAAGTGGT 59.960 42.308 0.00 0.00 0.00 4.16
95 96 6.263392 TCAGTACATATAGCTCTCAAGTGGTC 59.737 42.308 0.00 0.00 0.00 4.02
96 97 6.039829 CAGTACATATAGCTCTCAAGTGGTCA 59.960 42.308 0.00 0.00 0.00 4.02
97 98 5.269505 ACATATAGCTCTCAAGTGGTCAC 57.730 43.478 0.00 0.00 0.00 3.67
98 99 2.949451 ATAGCTCTCAAGTGGTCACG 57.051 50.000 0.00 0.00 36.20 4.35
99 100 0.243907 TAGCTCTCAAGTGGTCACGC 59.756 55.000 0.00 0.00 36.20 5.34
100 101 1.300931 GCTCTCAAGTGGTCACGCA 60.301 57.895 0.00 0.00 36.20 5.24
101 102 1.287730 GCTCTCAAGTGGTCACGCAG 61.288 60.000 0.00 0.00 36.20 5.18
102 103 1.287730 CTCTCAAGTGGTCACGCAGC 61.288 60.000 0.00 0.00 36.20 5.25
103 104 2.661537 TCAAGTGGTCACGCAGCG 60.662 61.111 14.82 14.82 36.20 5.18
104 105 2.967076 CAAGTGGTCACGCAGCGT 60.967 61.111 16.61 16.61 42.36 5.07
105 106 2.203015 AAGTGGTCACGCAGCGTT 60.203 55.556 20.29 0.00 38.32 4.84
106 107 1.817941 AAGTGGTCACGCAGCGTTT 60.818 52.632 20.29 6.03 38.32 3.60
107 108 1.373590 AAGTGGTCACGCAGCGTTTT 61.374 50.000 20.29 3.33 38.32 2.43
108 109 1.654137 GTGGTCACGCAGCGTTTTG 60.654 57.895 20.29 7.75 38.32 2.44
109 110 1.815840 TGGTCACGCAGCGTTTTGA 60.816 52.632 20.29 10.40 38.32 2.69
110 111 1.163420 TGGTCACGCAGCGTTTTGAT 61.163 50.000 20.29 0.00 38.32 2.57
111 112 0.040425 GGTCACGCAGCGTTTTGATT 60.040 50.000 20.29 0.00 38.32 2.57
112 113 1.044725 GTCACGCAGCGTTTTGATTG 58.955 50.000 20.29 5.21 38.32 2.67
113 114 0.660005 TCACGCAGCGTTTTGATTGC 60.660 50.000 20.29 0.00 38.32 3.56
114 115 0.933973 CACGCAGCGTTTTGATTGCA 60.934 50.000 20.29 0.00 38.32 4.08
115 116 0.248825 ACGCAGCGTTTTGATTGCAA 60.249 45.000 16.61 0.00 36.35 4.08
116 117 0.159345 CGCAGCGTTTTGATTGCAAC 59.841 50.000 6.65 0.00 36.37 4.17
117 118 1.490621 GCAGCGTTTTGATTGCAACT 58.509 45.000 0.00 0.00 36.59 3.16
118 119 2.660490 GCAGCGTTTTGATTGCAACTA 58.340 42.857 0.00 0.00 36.59 2.24
119 120 2.405025 GCAGCGTTTTGATTGCAACTAC 59.595 45.455 0.00 0.00 36.59 2.73
120 121 2.651703 CAGCGTTTTGATTGCAACTACG 59.348 45.455 0.00 8.64 41.48 3.51
122 123 2.645163 CGTTTTGATTGCAACTACGCA 58.355 42.857 0.00 0.00 41.03 5.24
123 124 2.651703 CGTTTTGATTGCAACTACGCAG 59.348 45.455 0.00 0.00 44.14 5.18
124 125 2.330231 TTTGATTGCAACTACGCAGC 57.670 45.000 0.00 0.00 44.14 5.25
125 126 1.233919 TTGATTGCAACTACGCAGCA 58.766 45.000 0.00 0.00 44.14 4.41
126 127 0.798159 TGATTGCAACTACGCAGCAG 59.202 50.000 0.00 0.00 44.14 4.24
127 128 0.522076 GATTGCAACTACGCAGCAGC 60.522 55.000 0.00 0.00 44.14 5.25
128 129 0.957395 ATTGCAACTACGCAGCAGCT 60.957 50.000 0.00 0.00 44.14 4.24
129 130 1.568612 TTGCAACTACGCAGCAGCTC 61.569 55.000 0.00 0.00 44.14 4.09
130 131 2.744768 GCAACTACGCAGCAGCTCC 61.745 63.158 0.00 0.00 39.10 4.70
131 132 1.374631 CAACTACGCAGCAGCTCCA 60.375 57.895 0.00 0.00 39.10 3.86
132 133 1.079543 AACTACGCAGCAGCTCCAG 60.080 57.895 0.00 0.00 39.10 3.86
133 134 1.821061 AACTACGCAGCAGCTCCAGT 61.821 55.000 0.00 0.00 39.10 4.00
134 135 1.808799 CTACGCAGCAGCTCCAGTG 60.809 63.158 0.00 0.00 39.10 3.66
135 136 3.300934 TACGCAGCAGCTCCAGTGG 62.301 63.158 1.40 1.40 39.10 4.00
136 137 4.694233 CGCAGCAGCTCCAGTGGT 62.694 66.667 9.54 0.00 39.10 4.16
137 138 2.665000 GCAGCAGCTCCAGTGGTA 59.335 61.111 9.54 0.00 37.91 3.25
138 139 1.003355 GCAGCAGCTCCAGTGGTAA 60.003 57.895 9.54 0.00 37.91 2.85
139 140 1.023513 GCAGCAGCTCCAGTGGTAAG 61.024 60.000 9.54 0.68 37.91 2.34
140 141 0.392193 CAGCAGCTCCAGTGGTAAGG 60.392 60.000 9.54 0.00 0.00 2.69
141 142 0.545309 AGCAGCTCCAGTGGTAAGGA 60.545 55.000 9.54 0.00 0.00 3.36
145 146 1.153549 CTCCAGTGGTAAGGAGCGC 60.154 63.158 9.54 0.00 44.37 5.92
146 147 1.608717 CTCCAGTGGTAAGGAGCGCT 61.609 60.000 11.27 11.27 44.37 5.92
147 148 0.323999 TCCAGTGGTAAGGAGCGCTA 60.324 55.000 11.50 0.00 41.92 4.26
148 149 0.535335 CCAGTGGTAAGGAGCGCTAA 59.465 55.000 11.50 0.00 41.92 3.09
149 150 1.641577 CAGTGGTAAGGAGCGCTAAC 58.358 55.000 11.50 6.70 41.92 2.34
150 151 1.204941 CAGTGGTAAGGAGCGCTAACT 59.795 52.381 11.50 9.48 41.92 2.24
151 152 1.477295 AGTGGTAAGGAGCGCTAACTC 59.523 52.381 11.50 0.00 42.02 3.01
152 153 1.477295 GTGGTAAGGAGCGCTAACTCT 59.523 52.381 11.50 2.68 36.87 3.24
153 154 1.749634 TGGTAAGGAGCGCTAACTCTC 59.250 52.381 11.50 8.46 36.87 3.20
154 155 2.025898 GGTAAGGAGCGCTAACTCTCT 58.974 52.381 11.50 0.00 36.87 3.10
155 156 3.212685 GGTAAGGAGCGCTAACTCTCTA 58.787 50.000 11.50 0.00 36.87 2.43
156 157 3.822167 GGTAAGGAGCGCTAACTCTCTAT 59.178 47.826 11.50 0.00 36.87 1.98
157 158 4.083164 GGTAAGGAGCGCTAACTCTCTATC 60.083 50.000 11.50 0.00 36.87 2.08
158 159 2.147958 AGGAGCGCTAACTCTCTATCG 58.852 52.381 11.50 0.00 36.87 2.92
159 160 1.874872 GGAGCGCTAACTCTCTATCGT 59.125 52.381 11.50 0.00 36.87 3.73
160 161 2.291190 GGAGCGCTAACTCTCTATCGTT 59.709 50.000 11.50 0.00 36.87 3.85
161 162 3.293262 GAGCGCTAACTCTCTATCGTTG 58.707 50.000 11.50 0.00 33.69 4.10
162 163 2.033550 AGCGCTAACTCTCTATCGTTGG 59.966 50.000 8.99 0.00 0.00 3.77
163 164 2.859032 GCGCTAACTCTCTATCGTTGGG 60.859 54.545 0.00 0.00 0.00 4.12
164 165 2.358267 CGCTAACTCTCTATCGTTGGGT 59.642 50.000 0.00 0.00 0.00 4.51
165 166 3.181489 CGCTAACTCTCTATCGTTGGGTT 60.181 47.826 0.00 0.00 0.00 4.11
166 167 4.113354 GCTAACTCTCTATCGTTGGGTTG 58.887 47.826 0.00 0.00 0.00 3.77
167 168 3.611766 AACTCTCTATCGTTGGGTTGG 57.388 47.619 0.00 0.00 0.00 3.77
168 169 1.831736 ACTCTCTATCGTTGGGTTGGG 59.168 52.381 0.00 0.00 0.00 4.12
169 170 2.108168 CTCTCTATCGTTGGGTTGGGA 58.892 52.381 0.00 0.00 0.00 4.37
170 171 2.101582 CTCTCTATCGTTGGGTTGGGAG 59.898 54.545 0.00 0.00 0.00 4.30
171 172 1.831736 CTCTATCGTTGGGTTGGGAGT 59.168 52.381 0.00 0.00 0.00 3.85
172 173 2.236395 CTCTATCGTTGGGTTGGGAGTT 59.764 50.000 0.00 0.00 0.00 3.01
173 174 2.640826 TCTATCGTTGGGTTGGGAGTTT 59.359 45.455 0.00 0.00 0.00 2.66
174 175 1.616159 ATCGTTGGGTTGGGAGTTTG 58.384 50.000 0.00 0.00 0.00 2.93
175 176 0.547075 TCGTTGGGTTGGGAGTTTGA 59.453 50.000 0.00 0.00 0.00 2.69
176 177 1.144093 TCGTTGGGTTGGGAGTTTGAT 59.856 47.619 0.00 0.00 0.00 2.57
177 178 1.960689 CGTTGGGTTGGGAGTTTGATT 59.039 47.619 0.00 0.00 0.00 2.57
178 179 2.030274 CGTTGGGTTGGGAGTTTGATTC 60.030 50.000 0.00 0.00 0.00 2.52
179 180 2.299013 GTTGGGTTGGGAGTTTGATTCC 59.701 50.000 0.00 0.00 0.00 3.01
180 181 1.786441 TGGGTTGGGAGTTTGATTCCT 59.214 47.619 0.00 0.00 35.01 3.36
181 182 2.990284 TGGGTTGGGAGTTTGATTCCTA 59.010 45.455 0.00 0.00 35.01 2.94
182 183 3.245122 TGGGTTGGGAGTTTGATTCCTAC 60.245 47.826 0.00 0.00 35.01 3.18
183 184 3.007635 GGTTGGGAGTTTGATTCCTACG 58.992 50.000 0.00 0.00 35.01 3.51
184 185 3.558533 GGTTGGGAGTTTGATTCCTACGT 60.559 47.826 0.00 0.00 35.01 3.57
185 186 4.322953 GGTTGGGAGTTTGATTCCTACGTA 60.323 45.833 0.00 0.00 35.01 3.57
186 187 4.460948 TGGGAGTTTGATTCCTACGTAC 57.539 45.455 0.00 0.00 35.01 3.67
187 188 3.833650 TGGGAGTTTGATTCCTACGTACA 59.166 43.478 0.00 0.00 35.01 2.90
188 189 4.081862 TGGGAGTTTGATTCCTACGTACAG 60.082 45.833 0.00 0.00 35.01 2.74
189 190 3.864003 GGAGTTTGATTCCTACGTACAGC 59.136 47.826 0.00 0.00 0.00 4.40
190 191 4.491676 GAGTTTGATTCCTACGTACAGCA 58.508 43.478 0.00 0.00 0.00 4.41
191 192 5.086104 AGTTTGATTCCTACGTACAGCAT 57.914 39.130 0.00 0.00 0.00 3.79
192 193 5.488341 AGTTTGATTCCTACGTACAGCATT 58.512 37.500 0.00 0.00 0.00 3.56
193 194 5.581085 AGTTTGATTCCTACGTACAGCATTC 59.419 40.000 0.00 0.00 0.00 2.67
194 195 5.339008 TTGATTCCTACGTACAGCATTCT 57.661 39.130 0.00 0.00 0.00 2.40
195 196 5.339008 TGATTCCTACGTACAGCATTCTT 57.661 39.130 0.00 0.00 0.00 2.52
196 197 5.730550 TGATTCCTACGTACAGCATTCTTT 58.269 37.500 0.00 0.00 0.00 2.52
197 198 6.170506 TGATTCCTACGTACAGCATTCTTTT 58.829 36.000 0.00 0.00 0.00 2.27
198 199 6.653320 TGATTCCTACGTACAGCATTCTTTTT 59.347 34.615 0.00 0.00 0.00 1.94
216 217 2.252976 TTTGGGATTTTTGGCACTGC 57.747 45.000 0.00 0.00 0.00 4.40
240 241 1.871077 GGTAACGCCAAGAAACGGG 59.129 57.895 0.00 0.00 37.17 5.28
241 242 1.208358 GTAACGCCAAGAAACGGGC 59.792 57.895 0.00 0.00 46.80 6.13
275 276 3.643978 GCCCTGCGCGAATGCTAG 61.644 66.667 12.10 0.00 39.65 3.42
276 277 2.202932 CCCTGCGCGAATGCTAGT 60.203 61.111 12.10 0.00 39.65 2.57
277 278 2.240500 CCCTGCGCGAATGCTAGTC 61.241 63.158 12.10 0.00 39.65 2.59
278 279 1.227089 CCTGCGCGAATGCTAGTCT 60.227 57.895 12.10 0.00 39.65 3.24
279 280 0.807667 CCTGCGCGAATGCTAGTCTT 60.808 55.000 12.10 0.00 39.65 3.01
280 281 0.574454 CTGCGCGAATGCTAGTCTTC 59.426 55.000 12.10 0.00 39.65 2.87
281 282 0.173481 TGCGCGAATGCTAGTCTTCT 59.827 50.000 12.10 0.00 39.65 2.85
282 283 1.281899 GCGCGAATGCTAGTCTTCTT 58.718 50.000 12.10 0.00 39.65 2.52
283 284 1.005557 GCGCGAATGCTAGTCTTCTTG 60.006 52.381 12.10 0.00 39.65 3.02
284 285 2.530177 CGCGAATGCTAGTCTTCTTGA 58.470 47.619 0.00 0.00 39.65 3.02
285 286 2.280183 CGCGAATGCTAGTCTTCTTGAC 59.720 50.000 0.00 0.00 41.73 3.18
286 287 2.280183 GCGAATGCTAGTCTTCTTGACG 59.720 50.000 0.00 0.00 43.55 4.35
287 288 5.342528 GCGAATGCTAGTCTTCTTGACGC 62.343 52.174 0.00 0.00 43.55 5.19
292 293 2.465920 GTCTTCTTGACGCACGCG 59.534 61.111 10.36 10.36 46.03 6.01
293 294 2.014554 GTCTTCTTGACGCACGCGA 61.015 57.895 19.66 0.00 42.83 5.87
294 295 1.729484 TCTTCTTGACGCACGCGAG 60.729 57.895 19.66 5.97 42.83 5.03
295 296 3.340721 CTTCTTGACGCACGCGAGC 62.341 63.158 18.99 18.99 42.83 5.03
339 340 4.275936 CCCGACATTGACTGAAAGAAAACT 59.724 41.667 0.00 0.00 37.43 2.66
404 407 7.172532 CACATTGCTAGAACCGGCTTATTATAA 59.827 37.037 0.00 0.00 0.00 0.98
409 412 6.092259 GCTAGAACCGGCTTATTATAACCATG 59.908 42.308 0.00 0.00 0.00 3.66
415 427 4.935808 CGGCTTATTATAACCATGGGAGAC 59.064 45.833 18.09 1.94 0.00 3.36
440 452 5.110598 TCATAAATAGCGGCTAACGTTGAA 58.889 37.500 14.54 0.00 46.52 2.69
448 460 3.623863 CGGCTAACGTTGAAACAAACAT 58.376 40.909 11.99 0.00 37.93 2.71
463 475 2.028190 CATCTAGCGAGCACCGGG 59.972 66.667 6.32 0.00 39.04 5.73
583 596 1.184970 AGGTGGCCGGAAAACCATTG 61.185 55.000 19.24 0.00 38.46 2.82
584 597 1.374125 GTGGCCGGAAAACCATTGC 60.374 57.895 5.05 0.00 38.46 3.56
613 649 2.124942 GCGGCCTCTCCCTTTCAG 60.125 66.667 0.00 0.00 0.00 3.02
622 658 2.677875 CCCTTTCAGCCAGCACCC 60.678 66.667 0.00 0.00 0.00 4.61
623 659 2.677875 CCTTTCAGCCAGCACCCC 60.678 66.667 0.00 0.00 0.00 4.95
624 660 2.677875 CTTTCAGCCAGCACCCCC 60.678 66.667 0.00 0.00 0.00 5.40
795 845 2.170817 GTGTCACCTTCCTTCCTATCCC 59.829 54.545 0.00 0.00 0.00 3.85
856 906 4.776322 CGCGCACTCCCCATTCCA 62.776 66.667 8.75 0.00 0.00 3.53
857 907 2.124151 GCGCACTCCCCATTCCAT 60.124 61.111 0.30 0.00 0.00 3.41
1086 1474 2.477845 GACGACCACGACGACGAT 59.522 61.111 15.32 0.00 42.66 3.73
1215 1603 2.202756 GAGGACATGGACGGCGTC 60.203 66.667 30.72 30.72 0.00 5.19
1224 1612 2.694760 GGACGGCGTCTACGAGGTT 61.695 63.158 35.42 0.00 43.02 3.50
1230 1618 2.582978 GTCTACGAGGTTGGGGCC 59.417 66.667 0.00 0.00 0.00 5.80
1395 1783 4.012895 GTGGCCGTCAAGTGCGTG 62.013 66.667 0.00 0.00 0.00 5.34
1428 1816 4.480031 GACCGCTTCGAGAAGTCC 57.520 61.111 13.58 0.00 40.45 3.85
1816 2204 1.866853 GCCCACCAAAAAGCTCGAGG 61.867 60.000 15.58 0.00 0.00 4.63
2133 2521 2.186903 CGTAAGCTGCCGGATGGT 59.813 61.111 5.05 0.00 37.67 3.55
2376 2764 3.247648 AGCACAGCCACCTCTGCT 61.248 61.111 0.00 0.00 38.33 4.24
2430 2818 1.761198 GGTACCACCATCTACCTCACC 59.239 57.143 7.15 0.00 38.42 4.02
2483 2871 1.406887 GGGTGAGAATAAGAGCGGCAA 60.407 52.381 1.45 0.00 0.00 4.52
3296 3684 4.436998 GGAGCAGGACGTCCGTGG 62.437 72.222 28.26 21.69 42.08 4.94
3607 3995 7.701539 ATGTAAGCTGACAATTTACATTCCA 57.298 32.000 8.32 0.00 42.34 3.53
3619 4007 6.814954 ATTTACATTCCAGAGAAGAGGCTA 57.185 37.500 0.00 0.00 34.86 3.93
3622 4010 3.320541 ACATTCCAGAGAAGAGGCTATCG 59.679 47.826 0.00 0.00 34.86 2.92
3637 4025 6.535508 AGAGGCTATCGTATGTTTCTTTGTTC 59.464 38.462 0.00 0.00 0.00 3.18
3643 4031 9.586150 CTATCGTATGTTTCTTTGTTCATATGC 57.414 33.333 0.00 0.00 32.87 3.14
3647 4035 8.910666 CGTATGTTTCTTTGTTCATATGCAAAA 58.089 29.630 9.04 4.37 34.68 2.44
3683 4071 5.948758 TCTGGTGCATTTTGTGTGGATATTA 59.051 36.000 0.00 0.00 0.00 0.98
3812 4204 7.499292 TCACATTGTTCAAAGGTTCAAATCAT 58.501 30.769 0.00 0.00 0.00 2.45
3815 4207 8.420222 ACATTGTTCAAAGGTTCAAATCATACA 58.580 29.630 0.00 0.00 0.00 2.29
3860 4253 6.073548 CGAAAATAAGTTCTTGTGTGCTCTCT 60.074 38.462 0.00 0.00 0.00 3.10
3863 4256 1.071385 AGTTCTTGTGTGCTCTCTGGG 59.929 52.381 0.00 0.00 0.00 4.45
3900 4293 6.475402 CACGAACTTTGAAGCAAAATAAAGGT 59.525 34.615 0.00 0.00 35.13 3.50
3904 4297 9.308318 GAACTTTGAAGCAAAATAAAGGTTACA 57.692 29.630 0.00 0.00 35.13 2.41
3905 4298 9.660180 AACTTTGAAGCAAAATAAAGGTTACAA 57.340 25.926 0.00 0.00 35.13 2.41
3921 4314 7.677454 AGGTTACAAAAATCCTAAACCTACG 57.323 36.000 2.82 0.00 43.65 3.51
3925 4318 8.558700 GTTACAAAAATCCTAAACCTACGAACA 58.441 33.333 0.00 0.00 0.00 3.18
3931 4324 3.127548 TCCTAAACCTACGAACAGCTACG 59.872 47.826 0.00 5.77 0.00 3.51
3972 4365 4.229582 TCCAACTAATCTAAACATGCCCCT 59.770 41.667 0.00 0.00 0.00 4.79
3973 4366 4.580580 CCAACTAATCTAAACATGCCCCTC 59.419 45.833 0.00 0.00 0.00 4.30
3983 4384 1.027357 CATGCCCCTCGATTTTCAGG 58.973 55.000 0.00 0.00 0.00 3.86
3987 4388 0.394352 CCCCTCGATTTTCAGGTGGG 60.394 60.000 0.00 0.00 0.00 4.61
3989 4390 0.328258 CCTCGATTTTCAGGTGGGGT 59.672 55.000 0.00 0.00 0.00 4.95
3991 4392 0.037590 TCGATTTTCAGGTGGGGTGG 59.962 55.000 0.00 0.00 0.00 4.61
3992 4393 0.965363 CGATTTTCAGGTGGGGTGGG 60.965 60.000 0.00 0.00 0.00 4.61
3993 4394 0.114364 GATTTTCAGGTGGGGTGGGT 59.886 55.000 0.00 0.00 0.00 4.51
4006 4412 2.290768 GGGGTGGGTCTTCTCCTTTAAC 60.291 54.545 0.00 0.00 0.00 2.01
4027 4433 4.906618 ACCCAATCAAATAGTCTCACGTT 58.093 39.130 0.00 0.00 0.00 3.99
4037 4443 8.304596 TCAAATAGTCTCACGTTAGATCAGTTT 58.695 33.333 2.21 0.73 0.00 2.66
4047 4453 8.308931 TCACGTTAGATCAGTTTGTAACCTTAT 58.691 33.333 0.00 0.00 0.00 1.73
4063 4469 8.093307 TGTAACCTTATGTAAACCATTACGTGA 58.907 33.333 0.00 0.00 43.59 4.35
4070 4476 9.656040 TTATGTAAACCATTACGTGAATGTAGT 57.344 29.630 0.00 0.00 43.59 2.73
4183 4589 4.610680 GCGTGCTTTAACTTTGGACAGTAG 60.611 45.833 0.00 0.00 0.00 2.57
4404 4810 9.967346 TCTGAAGGTGTCTATTTTATATCTTCG 57.033 33.333 0.00 0.00 33.08 3.79
4405 4811 9.197694 CTGAAGGTGTCTATTTTATATCTTCGG 57.802 37.037 0.00 0.00 33.08 4.30
4468 4874 4.211125 TGGACTAATTGTTGGACAAAGCA 58.789 39.130 0.00 0.00 41.96 3.91
4476 4882 7.571080 AATTGTTGGACAAAGCATGAAATTT 57.429 28.000 0.00 0.00 41.96 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.986833 CGAACATTTTCTGATATATGTTGAACA 57.013 29.630 0.00 0.00 40.29 3.18
20 21 9.603298 CCATCGAACATTTTCTGATATATGTTG 57.397 33.333 13.66 8.70 40.29 3.33
21 22 9.342308 ACCATCGAACATTTTCTGATATATGTT 57.658 29.630 10.42 10.42 42.22 2.71
22 23 8.908786 ACCATCGAACATTTTCTGATATATGT 57.091 30.769 0.00 0.00 32.89 2.29
23 24 8.992073 TGACCATCGAACATTTTCTGATATATG 58.008 33.333 0.00 0.00 0.00 1.78
24 25 9.559732 TTGACCATCGAACATTTTCTGATATAT 57.440 29.630 0.00 0.00 0.00 0.86
25 26 8.956533 TTGACCATCGAACATTTTCTGATATA 57.043 30.769 0.00 0.00 0.00 0.86
26 27 7.864108 TTGACCATCGAACATTTTCTGATAT 57.136 32.000 0.00 0.00 0.00 1.63
27 28 7.864108 ATTGACCATCGAACATTTTCTGATA 57.136 32.000 0.00 0.00 0.00 2.15
28 29 6.764308 ATTGACCATCGAACATTTTCTGAT 57.236 33.333 0.00 0.00 0.00 2.90
29 30 6.573664 AATTGACCATCGAACATTTTCTGA 57.426 33.333 0.00 0.00 0.00 3.27
30 31 7.642071 AAAATTGACCATCGAACATTTTCTG 57.358 32.000 0.00 0.00 0.00 3.02
57 58 9.277783 GCTATATGTACTGACTGATCCAAAAAT 57.722 33.333 0.00 0.00 0.00 1.82
58 59 8.486210 AGCTATATGTACTGACTGATCCAAAAA 58.514 33.333 0.00 0.00 0.00 1.94
59 60 8.023021 AGCTATATGTACTGACTGATCCAAAA 57.977 34.615 0.00 0.00 0.00 2.44
60 61 7.507277 AGAGCTATATGTACTGACTGATCCAAA 59.493 37.037 0.00 0.00 0.00 3.28
61 62 7.007116 AGAGCTATATGTACTGACTGATCCAA 58.993 38.462 0.00 0.00 0.00 3.53
62 63 6.547402 AGAGCTATATGTACTGACTGATCCA 58.453 40.000 0.00 0.00 0.00 3.41
63 64 6.657117 TGAGAGCTATATGTACTGACTGATCC 59.343 42.308 0.00 0.00 0.00 3.36
64 65 7.680442 TGAGAGCTATATGTACTGACTGATC 57.320 40.000 0.00 0.00 0.00 2.92
65 66 7.723616 ACTTGAGAGCTATATGTACTGACTGAT 59.276 37.037 0.00 0.00 0.00 2.90
66 67 7.012799 CACTTGAGAGCTATATGTACTGACTGA 59.987 40.741 0.00 0.00 0.00 3.41
67 68 7.138081 CACTTGAGAGCTATATGTACTGACTG 58.862 42.308 0.00 0.00 0.00 3.51
68 69 6.264292 CCACTTGAGAGCTATATGTACTGACT 59.736 42.308 0.00 0.00 0.00 3.41
69 70 6.039941 ACCACTTGAGAGCTATATGTACTGAC 59.960 42.308 0.00 0.00 0.00 3.51
70 71 6.129874 ACCACTTGAGAGCTATATGTACTGA 58.870 40.000 0.00 0.00 0.00 3.41
71 72 6.039829 TGACCACTTGAGAGCTATATGTACTG 59.960 42.308 0.00 0.00 0.00 2.74
72 73 6.039941 GTGACCACTTGAGAGCTATATGTACT 59.960 42.308 0.00 0.00 0.00 2.73
73 74 6.210078 GTGACCACTTGAGAGCTATATGTAC 58.790 44.000 0.00 0.00 0.00 2.90
74 75 5.008712 CGTGACCACTTGAGAGCTATATGTA 59.991 44.000 0.00 0.00 0.00 2.29
75 76 4.202060 CGTGACCACTTGAGAGCTATATGT 60.202 45.833 0.00 0.00 0.00 2.29
76 77 4.294232 CGTGACCACTTGAGAGCTATATG 58.706 47.826 0.00 0.00 0.00 1.78
77 78 3.243569 GCGTGACCACTTGAGAGCTATAT 60.244 47.826 0.00 0.00 0.00 0.86
78 79 2.099263 GCGTGACCACTTGAGAGCTATA 59.901 50.000 0.00 0.00 0.00 1.31
79 80 1.134965 GCGTGACCACTTGAGAGCTAT 60.135 52.381 0.00 0.00 0.00 2.97
80 81 0.243907 GCGTGACCACTTGAGAGCTA 59.756 55.000 0.00 0.00 0.00 3.32
81 82 1.005630 GCGTGACCACTTGAGAGCT 60.006 57.895 0.00 0.00 0.00 4.09
82 83 1.287730 CTGCGTGACCACTTGAGAGC 61.288 60.000 0.00 0.00 0.00 4.09
83 84 1.287730 GCTGCGTGACCACTTGAGAG 61.288 60.000 0.00 0.00 0.00 3.20
84 85 1.300931 GCTGCGTGACCACTTGAGA 60.301 57.895 0.00 0.00 0.00 3.27
85 86 2.661566 CGCTGCGTGACCACTTGAG 61.662 63.158 14.93 0.00 0.00 3.02
86 87 2.661537 CGCTGCGTGACCACTTGA 60.662 61.111 14.93 0.00 0.00 3.02
87 88 2.047151 AAACGCTGCGTGACCACTTG 62.047 55.000 29.63 0.00 39.99 3.16
88 89 1.373590 AAAACGCTGCGTGACCACTT 61.374 50.000 29.63 14.97 39.99 3.16
89 90 1.817941 AAAACGCTGCGTGACCACT 60.818 52.632 29.63 8.91 39.99 4.00
90 91 1.654137 CAAAACGCTGCGTGACCAC 60.654 57.895 29.63 0.00 39.99 4.16
91 92 1.163420 ATCAAAACGCTGCGTGACCA 61.163 50.000 29.63 13.65 39.99 4.02
92 93 0.040425 AATCAAAACGCTGCGTGACC 60.040 50.000 29.63 0.00 39.99 4.02
93 94 1.044725 CAATCAAAACGCTGCGTGAC 58.955 50.000 29.63 0.00 39.99 3.67
94 95 0.660005 GCAATCAAAACGCTGCGTGA 60.660 50.000 29.63 21.34 39.99 4.35
95 96 0.933973 TGCAATCAAAACGCTGCGTG 60.934 50.000 29.63 16.46 39.99 5.34
96 97 0.248825 TTGCAATCAAAACGCTGCGT 60.249 45.000 23.57 23.57 43.97 5.24
97 98 0.159345 GTTGCAATCAAAACGCTGCG 59.841 50.000 21.91 21.91 37.62 5.18
98 99 1.490621 AGTTGCAATCAAAACGCTGC 58.509 45.000 0.59 0.00 33.37 5.25
99 100 2.651703 CGTAGTTGCAATCAAAACGCTG 59.348 45.455 0.59 0.00 37.18 5.18
100 101 2.916111 CGTAGTTGCAATCAAAACGCT 58.084 42.857 0.59 0.00 37.18 5.07
102 103 2.645163 TGCGTAGTTGCAATCAAAACG 58.355 42.857 0.59 9.70 43.02 3.60
103 104 2.405025 GCTGCGTAGTTGCAATCAAAAC 59.595 45.455 0.59 0.00 45.74 2.43
104 105 2.033927 TGCTGCGTAGTTGCAATCAAAA 59.966 40.909 0.59 0.00 45.74 2.44
105 106 1.606189 TGCTGCGTAGTTGCAATCAAA 59.394 42.857 0.59 0.00 45.74 2.69
106 107 1.197492 CTGCTGCGTAGTTGCAATCAA 59.803 47.619 0.59 0.00 45.74 2.57
107 108 0.798159 CTGCTGCGTAGTTGCAATCA 59.202 50.000 0.59 0.00 45.74 2.57
108 109 0.522076 GCTGCTGCGTAGTTGCAATC 60.522 55.000 0.59 0.00 45.74 2.67
109 110 0.957395 AGCTGCTGCGTAGTTGCAAT 60.957 50.000 17.88 0.00 45.74 3.56
110 111 1.568612 GAGCTGCTGCGTAGTTGCAA 61.569 55.000 7.01 0.00 45.74 4.08
111 112 2.029288 GAGCTGCTGCGTAGTTGCA 61.029 57.895 7.01 4.54 45.42 4.08
112 113 2.744768 GGAGCTGCTGCGTAGTTGC 61.745 63.158 7.01 7.05 45.42 4.17
113 114 1.357258 CTGGAGCTGCTGCGTAGTTG 61.357 60.000 16.44 0.00 45.42 3.16
114 115 1.079543 CTGGAGCTGCTGCGTAGTT 60.080 57.895 16.44 0.00 45.42 2.24
115 116 2.279069 ACTGGAGCTGCTGCGTAGT 61.279 57.895 16.44 11.99 45.42 2.73
116 117 1.808799 CACTGGAGCTGCTGCGTAG 60.809 63.158 16.44 11.35 45.42 3.51
117 118 2.262603 CACTGGAGCTGCTGCGTA 59.737 61.111 16.44 0.00 45.42 4.42
118 119 4.694233 CCACTGGAGCTGCTGCGT 62.694 66.667 16.44 13.61 45.42 5.24
119 120 2.786539 TTACCACTGGAGCTGCTGCG 62.787 60.000 16.44 13.00 45.42 5.18
120 121 1.003355 TTACCACTGGAGCTGCTGC 60.003 57.895 14.73 14.73 40.05 5.25
121 122 0.392193 CCTTACCACTGGAGCTGCTG 60.392 60.000 7.01 10.59 0.00 4.41
122 123 0.545309 TCCTTACCACTGGAGCTGCT 60.545 55.000 6.82 0.00 0.00 4.24
123 124 0.107945 CTCCTTACCACTGGAGCTGC 60.108 60.000 0.71 0.00 42.62 5.25
128 129 0.323999 TAGCGCTCCTTACCACTGGA 60.324 55.000 16.34 0.00 0.00 3.86
129 130 0.535335 TTAGCGCTCCTTACCACTGG 59.465 55.000 16.34 0.00 0.00 4.00
130 131 1.204941 AGTTAGCGCTCCTTACCACTG 59.795 52.381 16.34 0.00 0.00 3.66
131 132 1.477295 GAGTTAGCGCTCCTTACCACT 59.523 52.381 16.34 5.66 0.00 4.00
132 133 1.477295 AGAGTTAGCGCTCCTTACCAC 59.523 52.381 16.34 5.97 36.20 4.16
133 134 1.749634 GAGAGTTAGCGCTCCTTACCA 59.250 52.381 16.34 0.00 35.84 3.25
134 135 2.025898 AGAGAGTTAGCGCTCCTTACC 58.974 52.381 16.34 0.17 41.58 2.85
135 136 4.377635 CGATAGAGAGTTAGCGCTCCTTAC 60.378 50.000 16.34 8.57 41.58 2.34
136 137 3.747010 CGATAGAGAGTTAGCGCTCCTTA 59.253 47.826 16.34 1.10 41.58 2.69
137 138 2.550606 CGATAGAGAGTTAGCGCTCCTT 59.449 50.000 16.34 0.00 41.58 3.36
138 139 2.147958 CGATAGAGAGTTAGCGCTCCT 58.852 52.381 16.34 11.93 41.58 3.69
139 140 1.874872 ACGATAGAGAGTTAGCGCTCC 59.125 52.381 16.34 5.93 41.58 4.70
140 141 3.293262 CAACGATAGAGAGTTAGCGCTC 58.707 50.000 16.34 0.00 41.07 5.03
141 142 2.033550 CCAACGATAGAGAGTTAGCGCT 59.966 50.000 17.26 17.26 35.99 5.92
142 143 2.386249 CCAACGATAGAGAGTTAGCGC 58.614 52.381 0.00 0.00 35.99 5.92
143 144 2.358267 ACCCAACGATAGAGAGTTAGCG 59.642 50.000 0.00 0.00 38.32 4.26
144 145 4.113354 CAACCCAACGATAGAGAGTTAGC 58.887 47.826 0.00 0.00 41.38 3.09
145 146 4.441634 CCCAACCCAACGATAGAGAGTTAG 60.442 50.000 0.00 0.00 41.38 2.34
146 147 3.449737 CCCAACCCAACGATAGAGAGTTA 59.550 47.826 0.00 0.00 41.38 2.24
147 148 2.236395 CCCAACCCAACGATAGAGAGTT 59.764 50.000 0.00 0.00 41.38 3.01
148 149 1.831736 CCCAACCCAACGATAGAGAGT 59.168 52.381 0.00 0.00 41.38 3.24
149 150 2.101582 CTCCCAACCCAACGATAGAGAG 59.898 54.545 0.00 0.00 41.38 3.20
150 151 2.108168 CTCCCAACCCAACGATAGAGA 58.892 52.381 0.00 0.00 41.38 3.10
151 152 1.831736 ACTCCCAACCCAACGATAGAG 59.168 52.381 0.00 0.00 41.38 2.43
152 153 1.946984 ACTCCCAACCCAACGATAGA 58.053 50.000 0.00 0.00 41.38 1.98
153 154 2.747446 CAAACTCCCAACCCAACGATAG 59.253 50.000 0.00 0.00 46.19 2.08
154 155 2.372504 TCAAACTCCCAACCCAACGATA 59.627 45.455 0.00 0.00 0.00 2.92
155 156 1.144093 TCAAACTCCCAACCCAACGAT 59.856 47.619 0.00 0.00 0.00 3.73
156 157 0.547075 TCAAACTCCCAACCCAACGA 59.453 50.000 0.00 0.00 0.00 3.85
157 158 1.616159 ATCAAACTCCCAACCCAACG 58.384 50.000 0.00 0.00 0.00 4.10
158 159 2.299013 GGAATCAAACTCCCAACCCAAC 59.701 50.000 0.00 0.00 0.00 3.77
159 160 2.178984 AGGAATCAAACTCCCAACCCAA 59.821 45.455 0.00 0.00 32.95 4.12
160 161 1.786441 AGGAATCAAACTCCCAACCCA 59.214 47.619 0.00 0.00 32.95 4.51
161 162 2.604912 AGGAATCAAACTCCCAACCC 57.395 50.000 0.00 0.00 32.95 4.11
162 163 3.007635 CGTAGGAATCAAACTCCCAACC 58.992 50.000 0.00 0.00 32.95 3.77
163 164 3.671716 ACGTAGGAATCAAACTCCCAAC 58.328 45.455 0.00 0.00 32.95 3.77
164 165 4.283978 TGTACGTAGGAATCAAACTCCCAA 59.716 41.667 0.00 0.00 32.95 4.12
165 166 3.833650 TGTACGTAGGAATCAAACTCCCA 59.166 43.478 0.00 0.00 32.95 4.37
166 167 4.430908 CTGTACGTAGGAATCAAACTCCC 58.569 47.826 0.00 0.00 32.95 4.30
167 168 3.864003 GCTGTACGTAGGAATCAAACTCC 59.136 47.826 0.00 0.00 0.00 3.85
168 169 4.491676 TGCTGTACGTAGGAATCAAACTC 58.508 43.478 0.00 0.00 0.00 3.01
169 170 4.530710 TGCTGTACGTAGGAATCAAACT 57.469 40.909 0.00 0.00 0.00 2.66
170 171 5.581085 AGAATGCTGTACGTAGGAATCAAAC 59.419 40.000 0.00 0.00 0.00 2.93
171 172 5.730550 AGAATGCTGTACGTAGGAATCAAA 58.269 37.500 0.00 0.00 0.00 2.69
172 173 5.339008 AGAATGCTGTACGTAGGAATCAA 57.661 39.130 0.00 0.00 0.00 2.57
173 174 5.339008 AAGAATGCTGTACGTAGGAATCA 57.661 39.130 0.00 0.00 0.00 2.57
174 175 6.663944 AAAAGAATGCTGTACGTAGGAATC 57.336 37.500 0.00 0.00 0.00 2.52
195 196 2.948315 GCAGTGCCAAAAATCCCAAAAA 59.052 40.909 2.85 0.00 0.00 1.94
196 197 2.570135 GCAGTGCCAAAAATCCCAAAA 58.430 42.857 2.85 0.00 0.00 2.44
197 198 2.252976 GCAGTGCCAAAAATCCCAAA 57.747 45.000 2.85 0.00 0.00 3.28
221 222 1.494189 CCGTTTCTTGGCGTTACCG 59.506 57.895 0.00 0.00 43.94 4.02
222 223 1.871077 CCCGTTTCTTGGCGTTACC 59.129 57.895 0.00 0.00 39.84 2.85
223 224 1.208358 GCCCGTTTCTTGGCGTTAC 59.792 57.895 0.00 0.00 38.00 2.50
224 225 3.658048 GCCCGTTTCTTGGCGTTA 58.342 55.556 0.00 0.00 38.00 3.18
258 259 3.643978 CTAGCATTCGCGCAGGGC 61.644 66.667 8.75 5.08 45.49 5.19
259 260 2.202932 ACTAGCATTCGCGCAGGG 60.203 61.111 8.75 0.00 45.49 4.45
260 261 0.807667 AAGACTAGCATTCGCGCAGG 60.808 55.000 8.75 0.00 45.49 4.85
261 262 0.574454 GAAGACTAGCATTCGCGCAG 59.426 55.000 8.75 0.00 45.49 5.18
262 263 0.173481 AGAAGACTAGCATTCGCGCA 59.827 50.000 8.75 0.00 45.49 6.09
263 264 1.005557 CAAGAAGACTAGCATTCGCGC 60.006 52.381 0.00 0.00 45.49 6.86
264 265 2.280183 GTCAAGAAGACTAGCATTCGCG 59.720 50.000 0.00 0.00 44.09 5.87
265 266 2.280183 CGTCAAGAAGACTAGCATTCGC 59.720 50.000 0.00 0.00 45.32 4.70
266 267 2.280183 GCGTCAAGAAGACTAGCATTCG 59.720 50.000 0.00 0.00 45.32 3.34
267 268 3.061429 GTGCGTCAAGAAGACTAGCATTC 59.939 47.826 0.00 0.00 42.72 2.67
268 269 2.996621 GTGCGTCAAGAAGACTAGCATT 59.003 45.455 0.00 0.00 42.72 3.56
269 270 2.611518 GTGCGTCAAGAAGACTAGCAT 58.388 47.619 0.00 0.00 42.72 3.79
270 271 1.666023 CGTGCGTCAAGAAGACTAGCA 60.666 52.381 0.00 0.00 45.32 3.49
271 272 0.985549 CGTGCGTCAAGAAGACTAGC 59.014 55.000 0.00 0.00 45.32 3.42
272 273 0.985549 GCGTGCGTCAAGAAGACTAG 59.014 55.000 0.00 0.00 45.32 2.57
273 274 0.728129 CGCGTGCGTCAAGAAGACTA 60.728 55.000 6.00 0.00 45.32 2.59
274 275 2.016704 CGCGTGCGTCAAGAAGACT 61.017 57.895 6.00 0.00 45.32 3.24
275 276 1.935065 CTCGCGTGCGTCAAGAAGAC 61.935 60.000 14.47 0.00 44.02 3.01
276 277 1.729484 CTCGCGTGCGTCAAGAAGA 60.729 57.895 14.47 0.00 40.74 2.87
277 278 2.765785 CTCGCGTGCGTCAAGAAG 59.234 61.111 14.47 0.00 40.74 2.85
278 279 3.403057 GCTCGCGTGCGTCAAGAA 61.403 61.111 18.06 0.00 40.74 2.52
289 290 4.914420 CCCTAGCTCACGCTCGCG 62.914 72.222 10.06 10.06 45.15 5.87
290 291 4.577246 CCCCTAGCTCACGCTCGC 62.577 72.222 0.00 0.00 45.15 5.03
291 292 4.577246 GCCCCTAGCTCACGCTCG 62.577 72.222 0.00 0.00 45.15 5.03
300 301 3.253061 GGGATGGGAGCCCCTAGC 61.253 72.222 11.10 0.00 45.70 3.42
306 307 2.757124 AATGTCGGGGATGGGAGCC 61.757 63.158 0.00 0.00 0.00 4.70
307 308 1.526917 CAATGTCGGGGATGGGAGC 60.527 63.158 0.00 0.00 0.00 4.70
308 309 0.179045 GTCAATGTCGGGGATGGGAG 60.179 60.000 0.00 0.00 0.00 4.30
309 310 0.620410 AGTCAATGTCGGGGATGGGA 60.620 55.000 0.00 0.00 0.00 4.37
310 311 0.464373 CAGTCAATGTCGGGGATGGG 60.464 60.000 0.00 0.00 0.00 4.00
311 312 0.541392 TCAGTCAATGTCGGGGATGG 59.459 55.000 0.00 0.00 0.00 3.51
404 407 5.564550 GCTATTTATGATGTCTCCCATGGT 58.435 41.667 11.73 0.00 32.56 3.55
409 412 3.003480 GCCGCTATTTATGATGTCTCCC 58.997 50.000 0.00 0.00 0.00 4.30
415 427 5.176774 TCAACGTTAGCCGCTATTTATGATG 59.823 40.000 0.00 0.00 41.42 3.07
426 438 1.776897 GTTTGTTTCAACGTTAGCCGC 59.223 47.619 0.00 0.00 41.42 6.53
440 452 2.076863 GGTGCTCGCTAGATGTTTGTT 58.923 47.619 0.00 0.00 0.00 2.83
448 460 2.678934 AACCCGGTGCTCGCTAGA 60.679 61.111 0.00 0.00 37.59 2.43
463 475 7.115520 CGTCTCCTATGATATGATTGTGTCAAC 59.884 40.741 0.00 0.00 40.97 3.18
606 642 2.677875 GGGGTGCTGGCTGAAAGG 60.678 66.667 0.00 0.00 0.00 3.11
644 680 1.361668 CTCGGTTGACTTGGATGGCG 61.362 60.000 0.00 0.00 0.00 5.69
855 905 5.364446 TCTTGATCAATGGGGAATGGAAATG 59.636 40.000 8.96 0.00 0.00 2.32
856 906 5.364735 GTCTTGATCAATGGGGAATGGAAAT 59.635 40.000 8.96 0.00 0.00 2.17
857 907 4.711355 GTCTTGATCAATGGGGAATGGAAA 59.289 41.667 8.96 0.00 0.00 3.13
1190 1578 1.612146 TCCATGTCCTCGAAGCCCA 60.612 57.895 0.00 0.00 0.00 5.36
1215 1603 2.584608 CTGGCCCCAACCTCGTAG 59.415 66.667 0.00 0.00 0.00 3.51
1224 1612 0.984961 CTCTGATCTTCCTGGCCCCA 60.985 60.000 0.00 0.00 0.00 4.96
1230 1618 1.591059 CGCGCCTCTGATCTTCCTG 60.591 63.158 0.00 0.00 0.00 3.86
1305 1693 1.219124 GCCGAGCACCTCTTGATCA 59.781 57.895 0.00 0.00 41.01 2.92
1362 1750 4.760047 ACCGTGGTGCCATCGCTC 62.760 66.667 0.00 0.00 35.36 5.03
1701 2089 0.593128 GCATGACGTTGCTGGTCTTT 59.407 50.000 4.97 0.00 39.57 2.52
1803 2191 0.386478 GCAGCACCTCGAGCTTTTTG 60.386 55.000 6.99 2.53 41.14 2.44
2091 2479 1.588597 GGCTTTGAGCAGCTTTCCC 59.411 57.895 0.00 0.00 44.75 3.97
2376 2764 2.049526 ATGTGCTTCGTCGACGCA 60.050 55.556 32.19 23.25 39.60 5.24
2421 2809 0.179161 CGTCTTCTGCGGTGAGGTAG 60.179 60.000 0.00 0.00 0.00 3.18
2430 2818 2.811317 GACCTGCCGTCTTCTGCG 60.811 66.667 0.00 0.00 38.57 5.18
2973 3361 3.849953 GCCGCCGACGTGATGTTC 61.850 66.667 0.00 0.00 37.70 3.18
3042 3430 3.800604 GCTCGTTTCTTGACAGGAACTCT 60.801 47.826 0.00 0.00 36.44 3.24
3252 3640 1.739562 CTGCACCTTCCTCACGAGC 60.740 63.158 0.00 0.00 0.00 5.03
3607 3995 5.830991 AGAAACATACGATAGCCTCTTCTCT 59.169 40.000 0.00 0.00 42.67 3.10
3619 4007 7.984391 TGCATATGAACAAAGAAACATACGAT 58.016 30.769 6.97 0.00 0.00 3.73
3652 4040 5.524646 CACACAAAATGCACCAGATCTTTTT 59.475 36.000 0.00 0.00 0.00 1.94
3653 4041 5.051816 CACACAAAATGCACCAGATCTTTT 58.948 37.500 0.00 0.00 0.00 2.27
3654 4042 4.501915 CCACACAAAATGCACCAGATCTTT 60.502 41.667 0.00 0.00 0.00 2.52
3655 4043 3.006110 CCACACAAAATGCACCAGATCTT 59.994 43.478 0.00 0.00 0.00 2.40
3656 4044 2.559668 CCACACAAAATGCACCAGATCT 59.440 45.455 0.00 0.00 0.00 2.75
3657 4045 2.557924 TCCACACAAAATGCACCAGATC 59.442 45.455 0.00 0.00 0.00 2.75
3658 4046 2.596346 TCCACACAAAATGCACCAGAT 58.404 42.857 0.00 0.00 0.00 2.90
3664 4052 8.965819 ACAGTATTAATATCCACACAAAATGCA 58.034 29.630 0.00 0.00 0.00 3.96
3683 4071 7.868922 TCACTACAAAATCACACGTACAGTATT 59.131 33.333 0.00 0.00 0.00 1.89
3724 4112 9.148879 ACTTACCAATATAGTCAACTGAGCTAT 57.851 33.333 0.00 0.00 0.00 2.97
3725 4113 8.414003 CACTTACCAATATAGTCAACTGAGCTA 58.586 37.037 0.00 0.00 0.00 3.32
3726 4114 7.093289 ACACTTACCAATATAGTCAACTGAGCT 60.093 37.037 0.00 0.00 0.00 4.09
3841 4233 3.244215 CCCAGAGAGCACACAAGAACTTA 60.244 47.826 0.00 0.00 0.00 2.24
3846 4239 1.423584 TTCCCAGAGAGCACACAAGA 58.576 50.000 0.00 0.00 0.00 3.02
3860 4253 2.459060 TCGTGCGACTATTTTTCCCA 57.541 45.000 0.00 0.00 0.00 4.37
3863 4256 5.437263 TCAAAGTTCGTGCGACTATTTTTC 58.563 37.500 0.00 0.00 0.00 2.29
3900 4293 8.674263 TGTTCGTAGGTTTAGGATTTTTGTAA 57.326 30.769 0.00 0.00 0.00 2.41
3904 4297 6.002082 AGCTGTTCGTAGGTTTAGGATTTTT 58.998 36.000 0.00 0.00 0.00 1.94
3905 4298 5.557866 AGCTGTTCGTAGGTTTAGGATTTT 58.442 37.500 0.00 0.00 0.00 1.82
3931 4324 3.323243 TGGAAGTTTTCGTAGCAGCTAC 58.677 45.455 21.13 21.13 33.99 3.58
3942 4335 9.129209 GCATGTTTAGATTAGTTGGAAGTTTTC 57.871 33.333 0.00 0.00 0.00 2.29
3950 4343 4.536765 AGGGGCATGTTTAGATTAGTTGG 58.463 43.478 0.00 0.00 0.00 3.77
3972 4365 0.037590 CCACCCCACCTGAAAATCGA 59.962 55.000 0.00 0.00 0.00 3.59
3973 4366 0.965363 CCCACCCCACCTGAAAATCG 60.965 60.000 0.00 0.00 0.00 3.34
3983 4384 1.134438 AAGGAGAAGACCCACCCCAC 61.134 60.000 0.00 0.00 0.00 4.61
3987 4388 3.069079 GGTTAAAGGAGAAGACCCACC 57.931 52.381 0.00 0.00 0.00 4.61
3991 4392 4.918588 TGATTGGGTTAAAGGAGAAGACC 58.081 43.478 0.00 0.00 0.00 3.85
3992 4393 6.894339 TTTGATTGGGTTAAAGGAGAAGAC 57.106 37.500 0.00 0.00 0.00 3.01
3993 4394 8.390921 ACTATTTGATTGGGTTAAAGGAGAAGA 58.609 33.333 0.00 0.00 0.00 2.87
4006 4412 6.338146 TCTAACGTGAGACTATTTGATTGGG 58.662 40.000 0.00 0.00 0.00 4.12
4037 4443 8.093307 TCACGTAATGGTTTACATAAGGTTACA 58.907 33.333 0.00 0.00 39.40 2.41
4159 4565 2.017782 TGTCCAAAGTTAAAGCACGCA 58.982 42.857 0.00 0.00 0.00 5.24
4183 4589 6.876257 AGATCCTCATAGCATTCGGAAATTAC 59.124 38.462 0.00 0.00 0.00 1.89
4361 4767 8.195436 CACCTTCAGATTGATATTCAAAAGCAT 58.805 33.333 0.00 0.00 40.12 3.79
4381 4787 9.760077 TTCCGAAGATATAAAATAGACACCTTC 57.240 33.333 0.00 0.00 0.00 3.46
4468 4874 5.801947 GCGCAGTTTGACTATCAAATTTCAT 59.198 36.000 0.30 0.00 46.55 2.57
4476 4882 2.472695 AAGGCGCAGTTTGACTATCA 57.527 45.000 10.83 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.