Multiple sequence alignment - TraesCS5B01G226100

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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 TraesCS5B01G226100 chr5B 100.000 3185 0 0 1 3185 402752661 402749477 0.000000e+00 5882.0
1 TraesCS5B01G226100 chr5B 90.370 135 13 0 1000 1134 266501406 266501540 9.080000e-41 178.0
2 TraesCS5B01G226100 chr5B 94.949 99 5 0 39 137 402758903 402758805 4.250000e-34 156.0
3 TraesCS5B01G226100 chr5B 89.000 100 11 0 1493 1592 266501783 266501882 1.200000e-24 124.0
4 TraesCS5B01G226100 chr5B 85.714 84 12 0 1492 1575 704916514 704916597 4.380000e-14 89.8
5 TraesCS5B01G226100 chr5A 93.944 2873 106 31 323 3164 443743478 443740643 0.000000e+00 4279.0
6 TraesCS5B01G226100 chr5A 95.041 121 6 0 140 260 70499603 70499723 1.170000e-44 191.0
7 TraesCS5B01G226100 chr5A 91.111 135 12 0 1000 1134 316085020 316085154 1.950000e-42 183.0
8 TraesCS5B01G226100 chr5A 88.235 102 12 0 1491 1592 316085398 316085499 4.310000e-24 122.0
9 TraesCS5B01G226100 chr5D 93.296 2834 95 41 334 3124 342713785 342711004 0.000000e+00 4093.0
10 TraesCS5B01G226100 chr5D 95.522 134 4 2 129 260 433184106 433183973 2.490000e-51 213.0
11 TraesCS5B01G226100 chr5D 91.111 135 12 0 1000 1134 238557792 238557658 1.950000e-42 183.0
12 TraesCS5B01G226100 chr5D 90.722 97 9 0 1496 1592 238557411 238557315 2.580000e-26 130.0
13 TraesCS5B01G226100 chr5D 90.244 41 2 2 257 296 433183966 433183927 6.000000e-03 52.8
14 TraesCS5B01G226100 chr2D 94.203 138 8 0 1243 1380 108313296 108313433 8.950000e-51 211.0
15 TraesCS5B01G226100 chr2D 86.709 158 11 1 138 285 313817442 313817285 1.970000e-37 167.0
16 TraesCS5B01G226100 chr2D 95.960 99 4 0 39 137 91231727 91231629 9.140000e-36 161.0
17 TraesCS5B01G226100 chr2B 94.203 138 8 0 1243 1380 158146584 158146721 8.950000e-51 211.0
18 TraesCS5B01G226100 chr2A 93.662 142 8 1 1239 1380 104450619 104450759 8.950000e-51 211.0
19 TraesCS5B01G226100 chr2A 77.419 155 34 1 988 1141 572487844 572487690 1.220000e-14 91.6
20 TraesCS5B01G226100 chr6D 96.748 123 4 0 138 260 154498774 154498896 4.160000e-49 206.0
21 TraesCS5B01G226100 chr6D 82.051 117 19 2 999 1114 309718608 309718723 7.270000e-17 99.0
22 TraesCS5B01G226100 chr7B 95.122 123 6 0 138 260 155476714 155476592 9.010000e-46 195.0
23 TraesCS5B01G226100 chr7B 93.548 124 7 1 137 260 657374061 657373939 1.950000e-42 183.0
24 TraesCS5B01G226100 chr3D 94.400 125 7 0 136 260 482232702 482232826 3.240000e-45 193.0
25 TraesCS5B01G226100 chr7D 94.309 123 7 0 138 260 614171963 614172085 4.190000e-44 189.0
26 TraesCS5B01G226100 chr4A 94.355 124 6 1 138 260 632912010 632912133 4.190000e-44 189.0
27 TraesCS5B01G226100 chr4A 90.426 94 7 2 1493 1585 468603626 468603718 4.310000e-24 122.0
28 TraesCS5B01G226100 chr3B 94.309 123 7 0 138 260 480864194 480864316 4.190000e-44 189.0
29 TraesCS5B01G226100 chr1B 95.876 97 4 0 41 137 328965732 328965828 1.180000e-34 158.0
30 TraesCS5B01G226100 chr1A 94.949 99 5 0 39 137 166260310 166260212 4.250000e-34 156.0
31 TraesCS5B01G226100 chr1A 93.939 99 6 0 39 137 71288672 71288770 1.980000e-32 150.0
32 TraesCS5B01G226100 chrUn 93.939 99 6 0 39 137 36923950 36923852 1.980000e-32 150.0
33 TraesCS5B01G226100 chrUn 93.939 99 6 0 39 137 196706686 196706784 1.980000e-32 150.0
34 TraesCS5B01G226100 chrUn 93.939 99 6 0 39 137 359104186 359104088 1.980000e-32 150.0
35 TraesCS5B01G226100 chrUn 93.939 99 6 0 39 137 359106292 359106194 1.980000e-32 150.0
36 TraesCS5B01G226100 chrUn 100.000 28 0 0 257 284 12169355 12169382 6.000000e-03 52.8
37 TraesCS5B01G226100 chr4D 92.308 91 5 2 1496 1585 107710356 107710267 9.270000e-26 128.0
38 TraesCS5B01G226100 chr4B 90.426 94 7 2 1493 1585 168985244 168985336 4.310000e-24 122.0
39 TraesCS5B01G226100 chr6B 82.051 117 19 2 999 1114 477689272 477689387 7.270000e-17 99.0
40 TraesCS5B01G226100 chr6A 82.051 117 19 2 999 1114 446520785 446520900 7.270000e-17 99.0


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 TraesCS5B01G226100 chr5B 402749477 402752661 3184 True 5882 5882 100.000 1 3185 1 chr5B.!!$R1 3184
1 TraesCS5B01G226100 chr5A 443740643 443743478 2835 True 4279 4279 93.944 323 3164 1 chr5A.!!$R1 2841
2 TraesCS5B01G226100 chr5D 342711004 342713785 2781 True 4093 4093 93.296 334 3124 1 chr5D.!!$R1 2790

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
47 48 0.107214 TTTGCGGGGATCTAGCCTTG 60.107 55.0 0.0 0.0 0.0 3.61 F
280 281 0.249489 CCTACATGCCAGCTACGTCC 60.249 60.0 0.0 0.0 0.0 4.79 F
282 283 0.686441 TACATGCCAGCTACGTCCCT 60.686 55.0 0.0 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1190 1205 1.234615 AATTCCAGTTCACCCGCACG 61.235 55.000 0.0 0.0 0.00 5.34 R
1237 1261 2.270257 GCATCAGCCCTGCAACACA 61.270 57.895 0.0 0.0 39.46 3.72 R
2206 2234 3.031013 TGCTCTAGTCGATCAATTCCCA 58.969 45.455 0.0 0.0 0.00 4.37 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
44 45 3.184736 TTTTTGCGGGGATCTAGCC 57.815 52.632 0.00 0.00 0.00 3.93
45 46 0.623723 TTTTTGCGGGGATCTAGCCT 59.376 50.000 0.00 0.00 0.00 4.58
46 47 0.623723 TTTTGCGGGGATCTAGCCTT 59.376 50.000 0.00 0.00 0.00 4.35
47 48 0.107214 TTTGCGGGGATCTAGCCTTG 60.107 55.000 0.00 0.00 0.00 3.61
48 49 1.271840 TTGCGGGGATCTAGCCTTGT 61.272 55.000 0.00 0.00 0.00 3.16
49 50 0.397957 TGCGGGGATCTAGCCTTGTA 60.398 55.000 0.00 0.00 0.00 2.41
50 51 0.977395 GCGGGGATCTAGCCTTGTAT 59.023 55.000 0.00 0.00 0.00 2.29
51 52 2.176889 GCGGGGATCTAGCCTTGTATA 58.823 52.381 0.00 0.00 0.00 1.47
52 53 2.565834 GCGGGGATCTAGCCTTGTATAA 59.434 50.000 0.00 0.00 0.00 0.98
53 54 3.197983 GCGGGGATCTAGCCTTGTATAAT 59.802 47.826 0.00 0.00 0.00 1.28
54 55 4.323562 GCGGGGATCTAGCCTTGTATAATT 60.324 45.833 0.00 0.00 0.00 1.40
55 56 5.178797 CGGGGATCTAGCCTTGTATAATTG 58.821 45.833 0.00 0.00 0.00 2.32
56 57 5.046591 CGGGGATCTAGCCTTGTATAATTGA 60.047 44.000 0.00 0.00 0.00 2.57
57 58 6.174049 GGGGATCTAGCCTTGTATAATTGAC 58.826 44.000 0.00 0.00 0.00 3.18
58 59 6.013293 GGGGATCTAGCCTTGTATAATTGACT 60.013 42.308 0.00 0.00 0.00 3.41
59 60 7.454225 GGGATCTAGCCTTGTATAATTGACTT 58.546 38.462 0.00 0.00 0.00 3.01
60 61 7.604545 GGGATCTAGCCTTGTATAATTGACTTC 59.395 40.741 0.00 0.00 0.00 3.01
61 62 8.371699 GGATCTAGCCTTGTATAATTGACTTCT 58.628 37.037 0.00 0.00 0.00 2.85
64 65 9.642343 TCTAGCCTTGTATAATTGACTTCTAGA 57.358 33.333 0.00 0.00 0.00 2.43
65 66 9.906660 CTAGCCTTGTATAATTGACTTCTAGAG 57.093 37.037 0.00 0.00 0.00 2.43
66 67 8.540507 AGCCTTGTATAATTGACTTCTAGAGA 57.459 34.615 0.00 0.00 0.00 3.10
67 68 9.153479 AGCCTTGTATAATTGACTTCTAGAGAT 57.847 33.333 0.00 0.00 0.00 2.75
85 86 9.463902 TCTAGAGATATGGTAGTATTAGTTGGC 57.536 37.037 0.00 0.00 0.00 4.52
86 87 9.469097 CTAGAGATATGGTAGTATTAGTTGGCT 57.531 37.037 0.00 0.00 0.00 4.75
87 88 8.728596 AGAGATATGGTAGTATTAGTTGGCTT 57.271 34.615 0.00 0.00 0.00 4.35
88 89 8.589338 AGAGATATGGTAGTATTAGTTGGCTTG 58.411 37.037 0.00 0.00 0.00 4.01
89 90 8.263854 AGATATGGTAGTATTAGTTGGCTTGT 57.736 34.615 0.00 0.00 0.00 3.16
90 91 8.368668 AGATATGGTAGTATTAGTTGGCTTGTC 58.631 37.037 0.00 0.00 0.00 3.18
91 92 5.748670 TGGTAGTATTAGTTGGCTTGTCA 57.251 39.130 0.00 0.00 0.00 3.58
92 93 5.484715 TGGTAGTATTAGTTGGCTTGTCAC 58.515 41.667 0.00 0.00 0.00 3.67
93 94 4.565564 GGTAGTATTAGTTGGCTTGTCACG 59.434 45.833 0.00 0.00 0.00 4.35
94 95 3.000727 AGTATTAGTTGGCTTGTCACGC 58.999 45.455 0.00 0.00 0.00 5.34
95 96 1.890876 ATTAGTTGGCTTGTCACGCA 58.109 45.000 3.49 0.00 0.00 5.24
96 97 1.669604 TTAGTTGGCTTGTCACGCAA 58.330 45.000 3.49 0.00 35.50 4.85
106 107 3.503827 TTGTCACGCAAGATATCTCGT 57.496 42.857 12.35 12.35 43.62 4.18
115 116 8.842942 CACGCAAGATATCTCGTGTATATATT 57.157 34.615 26.81 0.24 44.84 1.28
116 117 8.737648 CACGCAAGATATCTCGTGTATATATTG 58.262 37.037 26.81 11.65 44.84 1.90
117 118 8.459635 ACGCAAGATATCTCGTGTATATATTGT 58.540 33.333 16.21 0.00 39.24 2.71
118 119 8.737648 CGCAAGATATCTCGTGTATATATTGTG 58.262 37.037 5.51 15.20 40.08 3.33
119 120 9.788960 GCAAGATATCTCGTGTATATATTGTGA 57.211 33.333 5.51 0.00 39.24 3.58
122 123 9.462606 AGATATCTCGTGTATATATTGTGACCA 57.537 33.333 0.00 0.00 0.00 4.02
124 125 9.856488 ATATCTCGTGTATATATTGTGACCAAC 57.144 33.333 0.00 0.00 32.26 3.77
125 126 7.342769 TCTCGTGTATATATTGTGACCAACT 57.657 36.000 0.00 0.00 32.26 3.16
126 127 7.423199 TCTCGTGTATATATTGTGACCAACTC 58.577 38.462 0.00 0.00 32.26 3.01
127 128 6.509656 TCGTGTATATATTGTGACCAACTCC 58.490 40.000 0.00 0.00 32.26 3.85
128 129 5.401376 CGTGTATATATTGTGACCAACTCCG 59.599 44.000 0.00 0.00 32.26 4.63
129 130 6.509656 GTGTATATATTGTGACCAACTCCGA 58.490 40.000 0.00 0.00 32.26 4.55
130 131 6.641314 GTGTATATATTGTGACCAACTCCGAG 59.359 42.308 0.00 0.00 32.26 4.63
131 132 3.543680 ATATTGTGACCAACTCCGAGG 57.456 47.619 0.00 0.00 32.26 4.63
132 133 1.348064 ATTGTGACCAACTCCGAGGA 58.652 50.000 0.00 0.00 32.26 3.71
133 134 1.124780 TTGTGACCAACTCCGAGGAA 58.875 50.000 0.00 0.00 0.00 3.36
134 135 1.348064 TGTGACCAACTCCGAGGAAT 58.652 50.000 0.00 0.00 0.00 3.01
135 136 2.531771 TGTGACCAACTCCGAGGAATA 58.468 47.619 0.00 0.00 0.00 1.75
136 137 2.232941 TGTGACCAACTCCGAGGAATAC 59.767 50.000 0.00 0.00 0.00 1.89
137 138 1.829222 TGACCAACTCCGAGGAATACC 59.171 52.381 0.00 0.00 0.00 2.73
138 139 1.829222 GACCAACTCCGAGGAATACCA 59.171 52.381 0.00 0.00 38.94 3.25
139 140 1.831736 ACCAACTCCGAGGAATACCAG 59.168 52.381 0.00 0.00 38.94 4.00
140 141 1.139058 CCAACTCCGAGGAATACCAGG 59.861 57.143 0.00 0.00 38.94 4.45
141 142 1.139058 CAACTCCGAGGAATACCAGGG 59.861 57.143 0.00 0.00 38.94 4.45
142 143 0.635009 ACTCCGAGGAATACCAGGGA 59.365 55.000 0.00 0.00 37.42 4.20
143 144 1.041437 CTCCGAGGAATACCAGGGAC 58.959 60.000 0.00 0.00 35.75 4.46
144 145 0.754217 TCCGAGGAATACCAGGGACG 60.754 60.000 0.00 0.00 35.75 4.79
145 146 0.754217 CCGAGGAATACCAGGGACGA 60.754 60.000 0.00 0.00 38.94 4.20
146 147 1.108776 CGAGGAATACCAGGGACGAA 58.891 55.000 0.00 0.00 38.94 3.85
147 148 1.067212 CGAGGAATACCAGGGACGAAG 59.933 57.143 0.00 0.00 38.94 3.79
148 149 0.831307 AGGAATACCAGGGACGAAGC 59.169 55.000 0.00 0.00 38.94 3.86
149 150 0.831307 GGAATACCAGGGACGAAGCT 59.169 55.000 0.00 0.00 35.97 3.74
150 151 2.037144 GGAATACCAGGGACGAAGCTA 58.963 52.381 0.00 0.00 35.97 3.32
151 152 2.036089 GGAATACCAGGGACGAAGCTAG 59.964 54.545 0.00 0.00 35.97 3.42
152 153 2.750141 ATACCAGGGACGAAGCTAGA 57.250 50.000 0.00 0.00 0.00 2.43
153 154 2.519771 TACCAGGGACGAAGCTAGAA 57.480 50.000 0.00 0.00 0.00 2.10
154 155 1.640917 ACCAGGGACGAAGCTAGAAA 58.359 50.000 0.00 0.00 0.00 2.52
155 156 1.975680 ACCAGGGACGAAGCTAGAAAA 59.024 47.619 0.00 0.00 0.00 2.29
156 157 2.370849 ACCAGGGACGAAGCTAGAAAAA 59.629 45.455 0.00 0.00 0.00 1.94
176 177 5.859205 AAAAAGCTTGATGGGGTCATATC 57.141 39.130 0.00 0.00 36.54 1.63
177 178 3.515602 AAGCTTGATGGGGTCATATCC 57.484 47.619 0.00 0.00 36.54 2.59
178 179 2.421725 AGCTTGATGGGGTCATATCCA 58.578 47.619 0.00 0.00 36.54 3.41
179 180 2.991713 AGCTTGATGGGGTCATATCCAT 59.008 45.455 0.00 0.00 45.57 3.41
180 181 3.087031 GCTTGATGGGGTCATATCCATG 58.913 50.000 0.00 0.00 43.20 3.66
181 182 3.693807 CTTGATGGGGTCATATCCATGG 58.306 50.000 4.97 4.97 43.20 3.66
182 183 1.355381 TGATGGGGTCATATCCATGGC 59.645 52.381 6.96 0.00 43.20 4.40
183 184 1.355381 GATGGGGTCATATCCATGGCA 59.645 52.381 6.96 0.00 43.20 4.92
184 185 1.230074 TGGGGTCATATCCATGGCAA 58.770 50.000 6.96 0.00 38.60 4.52
185 186 1.788295 TGGGGTCATATCCATGGCAAT 59.212 47.619 6.96 0.00 38.60 3.56
186 187 2.173519 GGGGTCATATCCATGGCAATG 58.826 52.381 6.96 12.92 38.60 2.82
187 188 2.225091 GGGGTCATATCCATGGCAATGA 60.225 50.000 19.36 19.36 38.60 2.57
188 189 3.087031 GGGTCATATCCATGGCAATGAG 58.913 50.000 22.22 5.93 38.60 2.90
189 190 3.087031 GGTCATATCCATGGCAATGAGG 58.913 50.000 22.22 3.59 38.60 3.86
190 191 3.499202 GGTCATATCCATGGCAATGAGGT 60.499 47.826 22.22 0.00 38.60 3.85
191 192 3.755378 GTCATATCCATGGCAATGAGGTC 59.245 47.826 22.22 11.81 36.73 3.85
192 193 3.395273 TCATATCCATGGCAATGAGGTCA 59.605 43.478 19.36 3.60 35.67 4.02
193 194 4.043686 TCATATCCATGGCAATGAGGTCAT 59.956 41.667 19.36 3.30 35.67 3.06
194 195 2.353357 TCCATGGCAATGAGGTCATC 57.647 50.000 6.96 0.00 35.67 2.92
195 196 1.848388 TCCATGGCAATGAGGTCATCT 59.152 47.619 6.96 0.00 35.67 2.90
196 197 2.242965 TCCATGGCAATGAGGTCATCTT 59.757 45.455 6.96 0.00 35.67 2.40
197 198 2.621998 CCATGGCAATGAGGTCATCTTC 59.378 50.000 1.41 0.00 35.67 2.87
198 199 3.552875 CATGGCAATGAGGTCATCTTCT 58.447 45.455 0.00 0.00 35.67 2.85
199 200 4.445305 CCATGGCAATGAGGTCATCTTCTA 60.445 45.833 1.41 0.00 35.67 2.10
200 201 5.314529 CATGGCAATGAGGTCATCTTCTAT 58.685 41.667 0.00 0.00 35.67 1.98
201 202 6.470278 CATGGCAATGAGGTCATCTTCTATA 58.530 40.000 0.00 0.00 35.67 1.31
202 203 6.499106 TGGCAATGAGGTCATCTTCTATAA 57.501 37.500 0.00 0.00 35.10 0.98
203 204 6.899089 TGGCAATGAGGTCATCTTCTATAAA 58.101 36.000 0.00 0.00 35.10 1.40
204 205 7.520798 TGGCAATGAGGTCATCTTCTATAAAT 58.479 34.615 0.00 0.00 35.10 1.40
205 206 7.663081 TGGCAATGAGGTCATCTTCTATAAATC 59.337 37.037 0.00 0.00 35.10 2.17
206 207 7.663081 GGCAATGAGGTCATCTTCTATAAATCA 59.337 37.037 0.00 0.00 35.10 2.57
207 208 9.060347 GCAATGAGGTCATCTTCTATAAATCAA 57.940 33.333 0.00 0.00 35.10 2.57
257 258 8.852671 AGGATTTAATAATTTCATTGGGGTCA 57.147 30.769 0.00 0.00 0.00 4.02
258 259 9.278011 AGGATTTAATAATTTCATTGGGGTCAA 57.722 29.630 0.00 0.00 37.28 3.18
268 269 2.142356 TTGGGGTCAATGCCTACATG 57.858 50.000 0.00 0.00 36.36 3.21
269 270 0.395586 TGGGGTCAATGCCTACATGC 60.396 55.000 0.00 0.00 36.36 4.06
270 271 1.109323 GGGGTCAATGCCTACATGCC 61.109 60.000 0.00 0.00 36.36 4.40
271 272 0.395586 GGGTCAATGCCTACATGCCA 60.396 55.000 0.00 0.00 36.36 4.92
272 273 1.027357 GGTCAATGCCTACATGCCAG 58.973 55.000 0.00 0.00 36.36 4.85
273 274 0.383231 GTCAATGCCTACATGCCAGC 59.617 55.000 0.00 0.00 36.36 4.85
274 275 0.256752 TCAATGCCTACATGCCAGCT 59.743 50.000 0.00 0.00 36.36 4.24
275 276 1.490069 TCAATGCCTACATGCCAGCTA 59.510 47.619 0.00 0.00 36.36 3.32
276 277 1.605710 CAATGCCTACATGCCAGCTAC 59.394 52.381 0.00 0.00 36.36 3.58
277 278 0.250038 ATGCCTACATGCCAGCTACG 60.250 55.000 0.00 0.00 34.35 3.51
278 279 1.144057 GCCTACATGCCAGCTACGT 59.856 57.895 0.00 0.00 0.00 3.57
279 280 0.876342 GCCTACATGCCAGCTACGTC 60.876 60.000 0.00 0.00 0.00 4.34
280 281 0.249489 CCTACATGCCAGCTACGTCC 60.249 60.000 0.00 0.00 0.00 4.79
281 282 0.249489 CTACATGCCAGCTACGTCCC 60.249 60.000 0.00 0.00 0.00 4.46
282 283 0.686441 TACATGCCAGCTACGTCCCT 60.686 55.000 0.00 0.00 0.00 4.20
283 284 1.522355 CATGCCAGCTACGTCCCTG 60.522 63.158 0.00 0.00 0.00 4.45
284 285 1.685765 ATGCCAGCTACGTCCCTGA 60.686 57.895 14.82 0.00 0.00 3.86
285 286 1.680522 ATGCCAGCTACGTCCCTGAG 61.681 60.000 14.82 7.77 0.00 3.35
286 287 3.082579 GCCAGCTACGTCCCTGAGG 62.083 68.421 14.82 0.00 0.00 3.86
287 288 1.379977 CCAGCTACGTCCCTGAGGA 60.380 63.158 14.82 0.00 41.08 3.71
288 289 0.970937 CCAGCTACGTCCCTGAGGAA 60.971 60.000 14.82 0.00 46.38 3.36
289 290 1.115467 CAGCTACGTCCCTGAGGAAT 58.885 55.000 0.00 0.00 46.38 3.01
290 291 2.307768 CAGCTACGTCCCTGAGGAATA 58.692 52.381 0.00 0.00 46.38 1.75
291 292 2.034812 CAGCTACGTCCCTGAGGAATAC 59.965 54.545 0.00 0.00 46.38 1.89
292 293 2.029623 GCTACGTCCCTGAGGAATACA 58.970 52.381 0.00 0.00 46.38 2.29
293 294 2.429610 GCTACGTCCCTGAGGAATACAA 59.570 50.000 0.00 0.00 46.38 2.41
294 295 3.069729 GCTACGTCCCTGAGGAATACAAT 59.930 47.826 0.00 0.00 46.38 2.71
295 296 4.443034 GCTACGTCCCTGAGGAATACAATT 60.443 45.833 0.00 0.00 46.38 2.32
296 297 3.873910 ACGTCCCTGAGGAATACAATTG 58.126 45.455 0.00 3.24 46.38 2.32
297 298 3.517901 ACGTCCCTGAGGAATACAATTGA 59.482 43.478 13.59 0.00 46.38 2.57
298 299 4.122776 CGTCCCTGAGGAATACAATTGAG 58.877 47.826 13.59 0.00 46.38 3.02
299 300 4.383118 CGTCCCTGAGGAATACAATTGAGT 60.383 45.833 13.59 0.00 46.38 3.41
300 301 5.501156 GTCCCTGAGGAATACAATTGAGTT 58.499 41.667 13.59 6.12 46.38 3.01
301 302 5.946377 GTCCCTGAGGAATACAATTGAGTTT 59.054 40.000 13.59 2.24 46.38 2.66
302 303 6.094186 GTCCCTGAGGAATACAATTGAGTTTC 59.906 42.308 13.59 11.07 46.38 2.78
303 304 5.945784 CCCTGAGGAATACAATTGAGTTTCA 59.054 40.000 13.59 7.11 33.47 2.69
304 305 6.604795 CCCTGAGGAATACAATTGAGTTTCAT 59.395 38.462 13.59 9.22 33.47 2.57
305 306 7.201767 CCCTGAGGAATACAATTGAGTTTCATC 60.202 40.741 13.59 16.86 33.47 2.92
306 307 7.201767 CCTGAGGAATACAATTGAGTTTCATCC 60.202 40.741 13.59 9.26 0.00 3.51
307 308 6.603201 TGAGGAATACAATTGAGTTTCATCCC 59.397 38.462 13.59 3.80 0.00 3.85
308 309 5.590259 AGGAATACAATTGAGTTTCATCCCG 59.410 40.000 13.59 0.00 0.00 5.14
309 310 5.357032 GGAATACAATTGAGTTTCATCCCGT 59.643 40.000 13.59 0.00 0.00 5.28
310 311 6.540914 GGAATACAATTGAGTTTCATCCCGTA 59.459 38.462 13.59 0.00 0.00 4.02
311 312 7.228706 GGAATACAATTGAGTTTCATCCCGTAT 59.771 37.037 13.59 0.00 0.00 3.06
312 313 7.730364 ATACAATTGAGTTTCATCCCGTATC 57.270 36.000 13.59 0.00 0.00 2.24
313 314 5.745227 ACAATTGAGTTTCATCCCGTATCT 58.255 37.500 13.59 0.00 0.00 1.98
314 315 6.180472 ACAATTGAGTTTCATCCCGTATCTT 58.820 36.000 13.59 0.00 0.00 2.40
315 316 6.659242 ACAATTGAGTTTCATCCCGTATCTTT 59.341 34.615 13.59 0.00 0.00 2.52
316 317 7.176690 ACAATTGAGTTTCATCCCGTATCTTTT 59.823 33.333 13.59 0.00 0.00 2.27
317 318 6.737254 TTGAGTTTCATCCCGTATCTTTTC 57.263 37.500 0.00 0.00 0.00 2.29
318 319 6.049955 TGAGTTTCATCCCGTATCTTTTCT 57.950 37.500 0.00 0.00 0.00 2.52
319 320 7.177832 TGAGTTTCATCCCGTATCTTTTCTA 57.822 36.000 0.00 0.00 0.00 2.10
320 321 7.792032 TGAGTTTCATCCCGTATCTTTTCTAT 58.208 34.615 0.00 0.00 0.00 1.98
321 322 8.920174 TGAGTTTCATCCCGTATCTTTTCTATA 58.080 33.333 0.00 0.00 0.00 1.31
526 531 5.108187 AGATACAGCACAATTCACTCCAT 57.892 39.130 0.00 0.00 0.00 3.41
619 624 2.269023 ACCCATCACCAGATTCACTCA 58.731 47.619 0.00 0.00 30.20 3.41
699 704 3.058016 CCTTCTCATTTTCGTGTGCATGT 60.058 43.478 0.00 0.00 0.00 3.21
700 705 4.154015 CCTTCTCATTTTCGTGTGCATGTA 59.846 41.667 0.00 0.00 0.00 2.29
701 706 4.926860 TCTCATTTTCGTGTGCATGTAG 57.073 40.909 0.00 0.00 0.00 2.74
702 707 4.314961 TCTCATTTTCGTGTGCATGTAGT 58.685 39.130 0.00 0.00 0.00 2.73
703 708 5.474825 TCTCATTTTCGTGTGCATGTAGTA 58.525 37.500 0.00 0.00 0.00 1.82
704 709 5.347635 TCTCATTTTCGTGTGCATGTAGTAC 59.652 40.000 0.00 0.00 0.00 2.73
812 818 4.033709 TGGTAGCTAGCATTTCTCCTTCT 58.966 43.478 21.35 0.00 0.00 2.85
1170 1177 2.918712 AGGGATCATGGATCGTTCAC 57.081 50.000 0.00 0.00 39.72 3.18
1195 1210 2.508891 GGACTCGATCTTGCGTGCG 61.509 63.158 0.00 0.00 0.00 5.34
1216 1231 3.367292 CGGGTGAACTGGAATTGGAATTG 60.367 47.826 0.00 0.00 0.00 2.32
1237 1261 3.450457 TGACAAGCTTTGTTGATTTGGGT 59.550 39.130 0.00 0.00 45.52 4.51
1239 1263 3.197549 ACAAGCTTTGTTGATTTGGGTGT 59.802 39.130 0.00 0.00 42.22 4.16
1296 1321 1.346722 CTTCGGTGGACCAACTACCTT 59.653 52.381 8.18 0.00 46.07 3.50
1365 1390 4.767255 GTCCACCTCCAGGCGCTG 62.767 72.222 7.64 3.34 39.32 5.18
1563 1588 3.650942 TCAAGAACTACTGGAACACCCAT 59.349 43.478 0.00 0.00 45.57 4.00
2103 2131 1.030488 CCATGCTGGAGAACTGGCTG 61.030 60.000 0.00 0.00 40.96 4.85
2121 2149 2.819595 CTTGACGACGGCATGGGG 60.820 66.667 3.10 0.00 0.00 4.96
2254 2282 5.666462 ACAAAAATTTAAGAAAGGCGTGGT 58.334 33.333 0.00 0.00 0.00 4.16
2384 2423 5.352643 TTTTAAGTAGTTGCTCTTTCCGC 57.647 39.130 0.00 0.00 0.00 5.54
2402 2441 4.258543 TCCGCTGTTAATTAGGGTTTGAG 58.741 43.478 6.18 0.00 0.00 3.02
2435 2474 2.158900 CCTAAATGGATCGTGCAGGAGT 60.159 50.000 15.18 3.38 38.35 3.85
2446 2485 4.637276 TCGTGCAGGAGTGATAAAGAAAA 58.363 39.130 4.68 0.00 0.00 2.29
2561 2613 6.768483 TCCCATCGAGCTGAAATAAATCATA 58.232 36.000 0.00 0.00 0.00 2.15
2628 2684 5.614308 TGATCATATGCAGTTAAGTGGAGG 58.386 41.667 12.19 3.93 0.00 4.30
2631 2687 5.815581 TCATATGCAGTTAAGTGGAGGTTT 58.184 37.500 12.19 0.00 0.00 3.27
2633 2689 7.398829 TCATATGCAGTTAAGTGGAGGTTTAA 58.601 34.615 12.19 0.00 0.00 1.52
2677 2733 7.435305 TGTTTTCAAGATCAGATGCATCAAAA 58.565 30.769 27.81 18.35 0.00 2.44
2678 2734 8.092068 TGTTTTCAAGATCAGATGCATCAAAAT 58.908 29.630 27.81 17.06 0.00 1.82
2680 2736 6.144078 TCAAGATCAGATGCATCAAAATGG 57.856 37.500 27.81 11.74 33.19 3.16
2681 2737 5.889289 TCAAGATCAGATGCATCAAAATGGA 59.111 36.000 27.81 14.65 37.65 3.41
2683 2739 4.583489 AGATCAGATGCATCAAAATGGACC 59.417 41.667 27.81 7.04 35.91 4.46
2684 2740 3.972133 TCAGATGCATCAAAATGGACCT 58.028 40.909 27.81 0.51 35.91 3.85
2685 2741 3.949754 TCAGATGCATCAAAATGGACCTC 59.050 43.478 27.81 0.00 35.91 3.85
2687 2743 4.401519 CAGATGCATCAAAATGGACCTCTT 59.598 41.667 27.81 0.00 35.91 2.85
2688 2744 5.591472 CAGATGCATCAAAATGGACCTCTTA 59.409 40.000 27.81 0.00 35.91 2.10
2689 2745 6.264744 CAGATGCATCAAAATGGACCTCTTAT 59.735 38.462 27.81 0.00 35.91 1.73
2690 2746 6.489361 AGATGCATCAAAATGGACCTCTTATC 59.511 38.462 27.81 0.00 35.91 1.75
2691 2747 5.508567 TGCATCAAAATGGACCTCTTATCA 58.491 37.500 0.00 0.00 33.19 2.15
2695 2751 7.818930 GCATCAAAATGGACCTCTTATCAAAAA 59.181 33.333 0.00 0.00 33.19 1.94
2787 2844 7.461182 AAAAATATTTGGTTCGTCCATGAGA 57.539 32.000 0.39 0.00 46.60 3.27
2796 2853 3.712016 TCGTCCATGAGATTCCCAAAA 57.288 42.857 0.00 0.00 0.00 2.44
2813 2877 0.890996 AAAGCGCCAAGTCCCTCAAG 60.891 55.000 2.29 0.00 0.00 3.02
2823 2887 4.644685 CCAAGTCCCTCAAGAAAAAGTTCA 59.355 41.667 0.00 0.00 36.09 3.18
2833 2897 8.899771 CCTCAAGAAAAAGTTCAGGTTAAACTA 58.100 33.333 0.00 0.00 35.96 2.24
2873 2937 5.170021 TCATGCATGTTTGTAATTTCTGCC 58.830 37.500 25.43 0.00 0.00 4.85
2906 2970 7.118723 ACATATCAAAATGAGTGGAAGGCTTA 58.881 34.615 0.00 0.00 0.00 3.09
2923 2987 6.354794 AGGCTTAAAGTTCCCAAATTTACC 57.645 37.500 0.00 0.00 0.00 2.85
2925 2989 7.243091 AGGCTTAAAGTTCCCAAATTTACCTA 58.757 34.615 0.00 0.00 0.00 3.08
2928 2992 8.745590 GCTTAAAGTTCCCAAATTTACCTATGA 58.254 33.333 0.00 0.00 0.00 2.15
2935 2999 8.803235 GTTCCCAAATTTACCTATGAAAGAACT 58.197 33.333 0.00 0.00 0.00 3.01
3061 3125 4.153958 TGAAAATCACATGTTGTACCGC 57.846 40.909 0.00 0.00 0.00 5.68
3119 3183 8.937634 TCTTTTAGGGACATCGATAGTTAAAC 57.062 34.615 0.00 0.00 37.40 2.01
3120 3184 8.533657 TCTTTTAGGGACATCGATAGTTAAACA 58.466 33.333 0.00 0.00 37.40 2.83
3121 3185 9.326413 CTTTTAGGGACATCGATAGTTAAACAT 57.674 33.333 0.00 0.00 37.40 2.71
3180 3246 8.677148 AAACTCACATATATATTTTCGGTGCT 57.323 30.769 0.00 0.00 0.00 4.40
3181 3247 9.772973 AAACTCACATATATATTTTCGGTGCTA 57.227 29.630 0.00 0.00 0.00 3.49
3182 3248 9.772973 AACTCACATATATATTTTCGGTGCTAA 57.227 29.630 0.00 0.00 0.00 3.09
3183 3249 9.204570 ACTCACATATATATTTTCGGTGCTAAC 57.795 33.333 0.00 0.00 0.00 2.34
3184 3250 9.424319 CTCACATATATATTTTCGGTGCTAACT 57.576 33.333 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.623723 AGGCTAGATCCCCGCAAAAA 59.376 50.000 0.00 0.00 0.00 1.94
27 28 0.623723 AAGGCTAGATCCCCGCAAAA 59.376 50.000 0.00 0.00 0.00 2.44
28 29 0.107214 CAAGGCTAGATCCCCGCAAA 60.107 55.000 0.00 0.00 0.00 3.68
29 30 1.271840 ACAAGGCTAGATCCCCGCAA 61.272 55.000 0.00 0.00 0.00 4.85
30 31 0.397957 TACAAGGCTAGATCCCCGCA 60.398 55.000 0.00 0.00 0.00 5.69
31 32 0.977395 ATACAAGGCTAGATCCCCGC 59.023 55.000 0.00 0.00 0.00 6.13
32 33 5.046591 TCAATTATACAAGGCTAGATCCCCG 60.047 44.000 0.00 0.00 0.00 5.73
33 34 6.013293 AGTCAATTATACAAGGCTAGATCCCC 60.013 42.308 0.00 0.00 0.00 4.81
34 35 7.010339 AGTCAATTATACAAGGCTAGATCCC 57.990 40.000 0.00 0.00 0.00 3.85
35 36 8.371699 AGAAGTCAATTATACAAGGCTAGATCC 58.628 37.037 0.00 0.00 0.00 3.36
38 39 9.642343 TCTAGAAGTCAATTATACAAGGCTAGA 57.358 33.333 0.00 0.00 0.00 2.43
39 40 9.906660 CTCTAGAAGTCAATTATACAAGGCTAG 57.093 37.037 0.00 0.00 0.00 3.42
40 41 9.642343 TCTCTAGAAGTCAATTATACAAGGCTA 57.358 33.333 0.00 0.00 0.00 3.93
41 42 8.540507 TCTCTAGAAGTCAATTATACAAGGCT 57.459 34.615 0.00 0.00 0.00 4.58
59 60 9.463902 GCCAACTAATACTACCATATCTCTAGA 57.536 37.037 0.00 0.00 0.00 2.43
60 61 9.469097 AGCCAACTAATACTACCATATCTCTAG 57.531 37.037 0.00 0.00 0.00 2.43
61 62 9.824216 AAGCCAACTAATACTACCATATCTCTA 57.176 33.333 0.00 0.00 0.00 2.43
62 63 8.589338 CAAGCCAACTAATACTACCATATCTCT 58.411 37.037 0.00 0.00 0.00 3.10
63 64 8.368668 ACAAGCCAACTAATACTACCATATCTC 58.631 37.037 0.00 0.00 0.00 2.75
64 65 8.263854 ACAAGCCAACTAATACTACCATATCT 57.736 34.615 0.00 0.00 0.00 1.98
65 66 8.148351 TGACAAGCCAACTAATACTACCATATC 58.852 37.037 0.00 0.00 0.00 1.63
66 67 7.931948 GTGACAAGCCAACTAATACTACCATAT 59.068 37.037 0.00 0.00 0.00 1.78
67 68 7.270047 GTGACAAGCCAACTAATACTACCATA 58.730 38.462 0.00 0.00 0.00 2.74
68 69 6.113411 GTGACAAGCCAACTAATACTACCAT 58.887 40.000 0.00 0.00 0.00 3.55
69 70 5.484715 GTGACAAGCCAACTAATACTACCA 58.515 41.667 0.00 0.00 0.00 3.25
70 71 4.565564 CGTGACAAGCCAACTAATACTACC 59.434 45.833 0.00 0.00 0.00 3.18
71 72 4.032558 GCGTGACAAGCCAACTAATACTAC 59.967 45.833 1.44 0.00 0.00 2.73
72 73 4.178540 GCGTGACAAGCCAACTAATACTA 58.821 43.478 1.44 0.00 0.00 1.82
73 74 3.000727 GCGTGACAAGCCAACTAATACT 58.999 45.455 1.44 0.00 0.00 2.12
74 75 2.739913 TGCGTGACAAGCCAACTAATAC 59.260 45.455 10.95 0.00 0.00 1.89
75 76 3.046968 TGCGTGACAAGCCAACTAATA 57.953 42.857 10.95 0.00 0.00 0.98
76 77 1.890876 TGCGTGACAAGCCAACTAAT 58.109 45.000 10.95 0.00 0.00 1.73
77 78 1.669604 TTGCGTGACAAGCCAACTAA 58.330 45.000 10.95 0.00 33.24 2.24
78 79 3.388272 TTGCGTGACAAGCCAACTA 57.612 47.368 10.95 0.00 33.24 2.24
79 80 4.234019 TTGCGTGACAAGCCAACT 57.766 50.000 10.95 0.00 33.24 3.16
86 87 3.503827 ACGAGATATCTTGCGTGACAA 57.496 42.857 18.44 0.00 35.44 3.18
91 92 8.459635 ACAATATATACACGAGATATCTTGCGT 58.540 33.333 18.44 17.20 37.48 5.24
92 93 8.737648 CACAATATATACACGAGATATCTTGCG 58.262 37.037 18.44 14.65 31.43 4.85
93 94 9.788960 TCACAATATATACACGAGATATCTTGC 57.211 33.333 18.44 0.84 31.43 4.01
96 97 9.462606 TGGTCACAATATATACACGAGATATCT 57.537 33.333 4.47 4.47 0.00 1.98
98 99 9.856488 GTTGGTCACAATATATACACGAGATAT 57.144 33.333 0.00 0.00 39.13 1.63
99 100 9.074576 AGTTGGTCACAATATATACACGAGATA 57.925 33.333 0.00 0.00 39.13 1.98
100 101 7.952671 AGTTGGTCACAATATATACACGAGAT 58.047 34.615 0.00 0.00 39.13 2.75
101 102 7.342769 AGTTGGTCACAATATATACACGAGA 57.657 36.000 0.00 0.00 39.13 4.04
102 103 6.641314 GGAGTTGGTCACAATATATACACGAG 59.359 42.308 0.00 0.00 39.13 4.18
103 104 6.509656 GGAGTTGGTCACAATATATACACGA 58.490 40.000 0.00 0.00 39.13 4.35
104 105 5.401376 CGGAGTTGGTCACAATATATACACG 59.599 44.000 0.00 0.00 39.13 4.49
105 106 6.509656 TCGGAGTTGGTCACAATATATACAC 58.490 40.000 0.00 0.00 39.13 2.90
106 107 6.239204 CCTCGGAGTTGGTCACAATATATACA 60.239 42.308 4.02 0.00 39.13 2.29
107 108 6.015688 TCCTCGGAGTTGGTCACAATATATAC 60.016 42.308 4.02 0.00 39.13 1.47
108 109 6.072649 TCCTCGGAGTTGGTCACAATATATA 58.927 40.000 4.02 0.00 39.13 0.86
109 110 4.899457 TCCTCGGAGTTGGTCACAATATAT 59.101 41.667 4.02 0.00 39.13 0.86
110 111 4.283337 TCCTCGGAGTTGGTCACAATATA 58.717 43.478 4.02 0.00 39.13 0.86
111 112 3.104512 TCCTCGGAGTTGGTCACAATAT 58.895 45.455 4.02 0.00 39.13 1.28
112 113 2.531771 TCCTCGGAGTTGGTCACAATA 58.468 47.619 4.02 0.00 39.13 1.90
113 114 1.348064 TCCTCGGAGTTGGTCACAAT 58.652 50.000 4.02 0.00 39.13 2.71
114 115 1.124780 TTCCTCGGAGTTGGTCACAA 58.875 50.000 4.02 0.00 0.00 3.33
115 116 1.348064 ATTCCTCGGAGTTGGTCACA 58.652 50.000 4.02 0.00 0.00 3.58
116 117 2.418334 GGTATTCCTCGGAGTTGGTCAC 60.418 54.545 4.02 0.00 0.00 3.67
117 118 1.829222 GGTATTCCTCGGAGTTGGTCA 59.171 52.381 4.02 0.00 0.00 4.02
118 119 1.829222 TGGTATTCCTCGGAGTTGGTC 59.171 52.381 4.02 0.00 34.23 4.02
119 120 1.831736 CTGGTATTCCTCGGAGTTGGT 59.168 52.381 4.02 0.00 34.23 3.67
120 121 1.139058 CCTGGTATTCCTCGGAGTTGG 59.861 57.143 4.02 0.00 34.23 3.77
121 122 1.139058 CCCTGGTATTCCTCGGAGTTG 59.861 57.143 4.02 0.00 34.23 3.16
122 123 1.007963 TCCCTGGTATTCCTCGGAGTT 59.992 52.381 4.02 0.00 31.36 3.01
123 124 0.635009 TCCCTGGTATTCCTCGGAGT 59.365 55.000 4.02 0.00 31.36 3.85
124 125 1.041437 GTCCCTGGTATTCCTCGGAG 58.959 60.000 0.00 0.00 34.13 4.63
125 126 0.754217 CGTCCCTGGTATTCCTCGGA 60.754 60.000 0.00 0.00 34.23 4.55
126 127 0.754217 TCGTCCCTGGTATTCCTCGG 60.754 60.000 0.00 0.00 34.23 4.63
127 128 1.067212 CTTCGTCCCTGGTATTCCTCG 59.933 57.143 0.00 0.00 34.23 4.63
128 129 1.202545 GCTTCGTCCCTGGTATTCCTC 60.203 57.143 0.00 0.00 34.23 3.71
129 130 0.831307 GCTTCGTCCCTGGTATTCCT 59.169 55.000 0.00 0.00 34.23 3.36
130 131 0.831307 AGCTTCGTCCCTGGTATTCC 59.169 55.000 0.00 0.00 0.00 3.01
131 132 2.957006 TCTAGCTTCGTCCCTGGTATTC 59.043 50.000 0.00 0.00 0.00 1.75
132 133 3.028094 TCTAGCTTCGTCCCTGGTATT 57.972 47.619 0.00 0.00 0.00 1.89
133 134 2.750141 TCTAGCTTCGTCCCTGGTAT 57.250 50.000 0.00 0.00 0.00 2.73
134 135 2.519771 TTCTAGCTTCGTCCCTGGTA 57.480 50.000 0.00 0.00 0.00 3.25
135 136 1.640917 TTTCTAGCTTCGTCCCTGGT 58.359 50.000 0.00 0.00 0.00 4.00
136 137 2.762535 TTTTCTAGCTTCGTCCCTGG 57.237 50.000 0.00 0.00 0.00 4.45
154 155 4.651045 GGATATGACCCCATCAAGCTTTTT 59.349 41.667 0.00 0.00 41.93 1.94
155 156 4.218312 GGATATGACCCCATCAAGCTTTT 58.782 43.478 0.00 0.00 41.93 2.27
156 157 3.205056 TGGATATGACCCCATCAAGCTTT 59.795 43.478 0.00 0.00 41.93 3.51
157 158 2.785269 TGGATATGACCCCATCAAGCTT 59.215 45.455 0.00 0.00 41.93 3.74
158 159 2.421725 TGGATATGACCCCATCAAGCT 58.578 47.619 0.00 0.00 41.93 3.74
159 160 2.957402 TGGATATGACCCCATCAAGC 57.043 50.000 0.00 0.00 41.93 4.01
160 161 3.693807 CCATGGATATGACCCCATCAAG 58.306 50.000 5.56 0.00 41.93 3.02
161 162 2.225091 GCCATGGATATGACCCCATCAA 60.225 50.000 18.40 0.00 41.93 2.57
162 163 1.355381 GCCATGGATATGACCCCATCA 59.645 52.381 18.40 0.00 40.95 3.07
163 164 1.355381 TGCCATGGATATGACCCCATC 59.645 52.381 18.40 0.00 40.95 3.51
164 165 1.459117 TGCCATGGATATGACCCCAT 58.541 50.000 18.40 0.00 43.51 4.00
165 166 1.230074 TTGCCATGGATATGACCCCA 58.770 50.000 18.40 0.00 36.36 4.96
166 167 2.173519 CATTGCCATGGATATGACCCC 58.826 52.381 18.40 0.00 36.36 4.95
167 168 3.087031 CTCATTGCCATGGATATGACCC 58.913 50.000 18.40 0.00 36.36 4.46
168 169 3.087031 CCTCATTGCCATGGATATGACC 58.913 50.000 18.40 0.00 36.36 4.02
169 170 3.755378 GACCTCATTGCCATGGATATGAC 59.245 47.826 18.40 7.72 36.36 3.06
170 171 3.395273 TGACCTCATTGCCATGGATATGA 59.605 43.478 18.40 20.27 36.36 2.15
171 172 3.758425 TGACCTCATTGCCATGGATATG 58.242 45.455 18.40 17.15 0.00 1.78
172 173 4.291513 AGATGACCTCATTGCCATGGATAT 59.708 41.667 18.40 4.37 36.57 1.63
173 174 3.654321 AGATGACCTCATTGCCATGGATA 59.346 43.478 18.40 1.58 36.57 2.59
174 175 2.445905 AGATGACCTCATTGCCATGGAT 59.554 45.455 18.40 0.00 36.57 3.41
175 176 1.848388 AGATGACCTCATTGCCATGGA 59.152 47.619 18.40 0.00 36.57 3.41
176 177 2.359981 AGATGACCTCATTGCCATGG 57.640 50.000 7.63 7.63 36.57 3.66
177 178 3.552875 AGAAGATGACCTCATTGCCATG 58.447 45.455 0.00 0.00 36.57 3.66
178 179 3.947612 AGAAGATGACCTCATTGCCAT 57.052 42.857 0.00 0.00 36.57 4.40
179 180 6.499106 TTATAGAAGATGACCTCATTGCCA 57.501 37.500 0.00 0.00 36.57 4.92
180 181 7.663081 TGATTTATAGAAGATGACCTCATTGCC 59.337 37.037 0.00 0.00 36.57 4.52
181 182 8.613060 TGATTTATAGAAGATGACCTCATTGC 57.387 34.615 0.00 0.00 36.57 3.56
231 232 9.278011 TGACCCCAATGAAATTATTAAATCCTT 57.722 29.630 0.00 0.00 32.46 3.36
232 233 8.852671 TGACCCCAATGAAATTATTAAATCCT 57.147 30.769 0.00 0.00 32.46 3.24
248 249 2.669781 CATGTAGGCATTGACCCCAAT 58.330 47.619 0.00 0.00 43.37 3.16
249 250 1.959508 GCATGTAGGCATTGACCCCAA 60.960 52.381 0.00 0.00 36.61 4.12
250 251 0.395586 GCATGTAGGCATTGACCCCA 60.396 55.000 0.00 0.00 31.99 4.96
251 252 1.109323 GGCATGTAGGCATTGACCCC 61.109 60.000 0.00 0.00 43.51 4.95
252 253 2.419057 GGCATGTAGGCATTGACCC 58.581 57.895 0.00 0.00 43.51 4.46
260 261 0.876342 GACGTAGCTGGCATGTAGGC 60.876 60.000 0.00 0.00 44.50 3.93
261 262 0.249489 GGACGTAGCTGGCATGTAGG 60.249 60.000 0.00 0.00 0.00 3.18
262 263 0.249489 GGGACGTAGCTGGCATGTAG 60.249 60.000 0.00 0.00 0.00 2.74
263 264 0.686441 AGGGACGTAGCTGGCATGTA 60.686 55.000 0.00 0.00 0.00 2.29
264 265 1.990060 AGGGACGTAGCTGGCATGT 60.990 57.895 0.00 0.00 0.00 3.21
265 266 1.522355 CAGGGACGTAGCTGGCATG 60.522 63.158 0.00 0.00 0.00 4.06
266 267 1.680522 CTCAGGGACGTAGCTGGCAT 61.681 60.000 0.00 0.00 0.00 4.40
267 268 2.283604 TCAGGGACGTAGCTGGCA 60.284 61.111 0.00 0.00 0.00 4.92
268 269 2.496817 CTCAGGGACGTAGCTGGC 59.503 66.667 0.00 0.00 0.00 4.85
269 270 0.970937 TTCCTCAGGGACGTAGCTGG 60.971 60.000 0.00 0.00 42.05 4.85
270 271 1.115467 ATTCCTCAGGGACGTAGCTG 58.885 55.000 0.00 0.00 42.05 4.24
271 272 2.308690 GTATTCCTCAGGGACGTAGCT 58.691 52.381 0.00 0.00 42.05 3.32
272 273 2.029623 TGTATTCCTCAGGGACGTAGC 58.970 52.381 0.00 0.00 42.05 3.58
273 274 4.939052 ATTGTATTCCTCAGGGACGTAG 57.061 45.455 0.00 0.00 42.05 3.51
274 275 4.712829 TCAATTGTATTCCTCAGGGACGTA 59.287 41.667 5.13 0.00 42.05 3.57
275 276 3.517901 TCAATTGTATTCCTCAGGGACGT 59.482 43.478 5.13 0.00 42.05 4.34
276 277 4.122776 CTCAATTGTATTCCTCAGGGACG 58.877 47.826 5.13 0.00 42.05 4.79
277 278 5.104259 ACTCAATTGTATTCCTCAGGGAC 57.896 43.478 5.13 0.00 42.05 4.46
278 279 5.779241 AACTCAATTGTATTCCTCAGGGA 57.221 39.130 5.13 0.00 40.36 4.20
279 280 5.945784 TGAAACTCAATTGTATTCCTCAGGG 59.054 40.000 5.13 0.00 0.00 4.45
280 281 7.201767 GGATGAAACTCAATTGTATTCCTCAGG 60.202 40.741 5.13 0.00 0.00 3.86
281 282 7.201767 GGGATGAAACTCAATTGTATTCCTCAG 60.202 40.741 5.13 0.00 0.00 3.35
282 283 6.603201 GGGATGAAACTCAATTGTATTCCTCA 59.397 38.462 5.13 3.85 0.00 3.86
283 284 6.238484 CGGGATGAAACTCAATTGTATTCCTC 60.238 42.308 5.13 10.17 0.00 3.71
284 285 5.590259 CGGGATGAAACTCAATTGTATTCCT 59.410 40.000 5.13 2.41 0.00 3.36
285 286 5.357032 ACGGGATGAAACTCAATTGTATTCC 59.643 40.000 5.13 4.05 0.00 3.01
286 287 6.436843 ACGGGATGAAACTCAATTGTATTC 57.563 37.500 5.13 9.03 0.00 1.75
287 288 7.993183 AGATACGGGATGAAACTCAATTGTATT 59.007 33.333 5.13 0.00 0.00 1.89
288 289 7.509546 AGATACGGGATGAAACTCAATTGTAT 58.490 34.615 5.13 0.00 0.00 2.29
289 290 6.884832 AGATACGGGATGAAACTCAATTGTA 58.115 36.000 5.13 0.00 0.00 2.41
290 291 5.745227 AGATACGGGATGAAACTCAATTGT 58.255 37.500 5.13 0.00 0.00 2.71
291 292 6.683974 AAGATACGGGATGAAACTCAATTG 57.316 37.500 0.00 0.00 0.00 2.32
292 293 7.611855 AGAAAAGATACGGGATGAAACTCAATT 59.388 33.333 0.00 0.00 0.00 2.32
293 294 7.112779 AGAAAAGATACGGGATGAAACTCAAT 58.887 34.615 0.00 0.00 0.00 2.57
294 295 6.472887 AGAAAAGATACGGGATGAAACTCAA 58.527 36.000 0.00 0.00 0.00 3.02
295 296 6.049955 AGAAAAGATACGGGATGAAACTCA 57.950 37.500 0.00 0.00 0.00 3.41
296 297 9.413048 CTATAGAAAAGATACGGGATGAAACTC 57.587 37.037 0.00 0.00 0.00 3.01
297 298 8.925338 ACTATAGAAAAGATACGGGATGAAACT 58.075 33.333 6.78 0.00 0.00 2.66
298 299 9.543783 AACTATAGAAAAGATACGGGATGAAAC 57.456 33.333 6.78 0.00 0.00 2.78
301 302 9.542462 CAAAACTATAGAAAAGATACGGGATGA 57.458 33.333 6.78 0.00 0.00 2.92
302 303 9.542462 TCAAAACTATAGAAAAGATACGGGATG 57.458 33.333 6.78 0.00 0.00 3.51
303 304 9.543783 GTCAAAACTATAGAAAAGATACGGGAT 57.456 33.333 6.78 0.00 0.00 3.85
304 305 7.703621 CGTCAAAACTATAGAAAAGATACGGGA 59.296 37.037 6.78 0.00 0.00 5.14
305 306 7.703621 TCGTCAAAACTATAGAAAAGATACGGG 59.296 37.037 6.78 0.00 0.00 5.28
306 307 8.624701 TCGTCAAAACTATAGAAAAGATACGG 57.375 34.615 6.78 0.00 0.00 4.02
315 316 8.227791 GCAGTCAAATTCGTCAAAACTATAGAA 58.772 33.333 6.78 0.00 0.00 2.10
316 317 7.148474 GGCAGTCAAATTCGTCAAAACTATAGA 60.148 37.037 6.78 0.00 0.00 1.98
317 318 6.961554 GGCAGTCAAATTCGTCAAAACTATAG 59.038 38.462 0.00 0.00 0.00 1.31
318 319 6.653320 AGGCAGTCAAATTCGTCAAAACTATA 59.347 34.615 0.00 0.00 0.00 1.31
319 320 5.473504 AGGCAGTCAAATTCGTCAAAACTAT 59.526 36.000 0.00 0.00 0.00 2.12
320 321 4.819630 AGGCAGTCAAATTCGTCAAAACTA 59.180 37.500 0.00 0.00 0.00 2.24
321 322 3.632145 AGGCAGTCAAATTCGTCAAAACT 59.368 39.130 0.00 0.00 0.00 2.66
373 375 9.226606 CATCTAGGTTACTATCTCCAGTTCTAG 57.773 40.741 0.00 0.00 31.25 2.43
374 376 7.666388 GCATCTAGGTTACTATCTCCAGTTCTA 59.334 40.741 0.00 0.00 0.00 2.10
375 377 6.492087 GCATCTAGGTTACTATCTCCAGTTCT 59.508 42.308 0.00 0.00 0.00 3.01
376 378 6.265649 TGCATCTAGGTTACTATCTCCAGTTC 59.734 42.308 0.00 0.00 0.00 3.01
377 379 6.136857 TGCATCTAGGTTACTATCTCCAGTT 58.863 40.000 0.00 0.00 0.00 3.16
378 380 5.706447 TGCATCTAGGTTACTATCTCCAGT 58.294 41.667 0.00 0.00 0.00 4.00
619 624 3.627577 CAGCAGAATTATTGTAACCCGCT 59.372 43.478 0.00 0.00 0.00 5.52
1190 1205 1.234615 AATTCCAGTTCACCCGCACG 61.235 55.000 0.00 0.00 0.00 5.34
1195 1210 3.831911 TCAATTCCAATTCCAGTTCACCC 59.168 43.478 0.00 0.00 0.00 4.61
1216 1231 3.803778 CACCCAAATCAACAAAGCTTGTC 59.196 43.478 0.00 0.00 44.59 3.18
1237 1261 2.270257 GCATCAGCCCTGCAACACA 61.270 57.895 0.00 0.00 39.46 3.72
1239 1263 3.057548 CGCATCAGCCCTGCAACA 61.058 61.111 3.98 0.00 39.64 3.33
1563 1588 5.798125 TCTTCTTGAGCTTCTTCTTGAGA 57.202 39.130 0.00 0.00 0.00 3.27
2103 2131 3.499737 CCCATGCCGTCGTCAAGC 61.500 66.667 0.00 0.00 0.00 4.01
2206 2234 3.031013 TGCTCTAGTCGATCAATTCCCA 58.969 45.455 0.00 0.00 0.00 4.37
2368 2407 1.797025 ACAGCGGAAAGAGCAACTAC 58.203 50.000 0.00 0.00 37.01 2.73
2381 2420 4.094442 GTCTCAAACCCTAATTAACAGCGG 59.906 45.833 0.00 0.00 0.00 5.52
2384 2423 7.824289 TGATCAGTCTCAAACCCTAATTAACAG 59.176 37.037 0.00 0.00 0.00 3.16
2529 2581 1.115467 AGCTCGATGGGAGAAACGAT 58.885 50.000 0.00 0.00 46.23 3.73
2532 2584 2.386661 TTCAGCTCGATGGGAGAAAC 57.613 50.000 0.00 0.00 46.23 2.78
2696 2752 9.995003 TCTTTACCAAATTATTCAAAACAGCAT 57.005 25.926 0.00 0.00 0.00 3.79
2778 2835 2.098117 CGCTTTTGGGAATCTCATGGAC 59.902 50.000 0.00 0.00 33.84 4.02
2787 2844 0.603065 GACTTGGCGCTTTTGGGAAT 59.397 50.000 7.64 0.00 33.84 3.01
2796 2853 1.768684 TTCTTGAGGGACTTGGCGCT 61.769 55.000 7.64 0.00 41.55 5.92
2813 2877 9.286170 AGATCCTAGTTTAACCTGAACTTTTTC 57.714 33.333 0.00 0.00 38.28 2.29
2823 2887 7.918076 TCACAAATGAGATCCTAGTTTAACCT 58.082 34.615 0.00 0.00 0.00 3.50
2833 2897 5.198207 TGCATGATTCACAAATGAGATCCT 58.802 37.500 0.00 0.00 35.83 3.24
2906 2970 9.374711 TCTTTCATAGGTAAATTTGGGAACTTT 57.625 29.630 0.00 0.00 0.00 2.66
2923 2987 9.079833 CATTTTAATGTGGCAGTTCTTTCATAG 57.920 33.333 0.00 0.00 0.00 2.23
2925 2989 6.875195 CCATTTTAATGTGGCAGTTCTTTCAT 59.125 34.615 0.00 0.00 34.60 2.57
2928 2992 6.173427 ACCATTTTAATGTGGCAGTTCTTT 57.827 33.333 6.56 0.00 39.13 2.52
2935 2999 5.505780 AGCTAGTACCATTTTAATGTGGCA 58.494 37.500 6.56 0.00 39.13 4.92
3061 3125 6.998968 ATCAGCTGAAGTAAAGAAAGGATG 57.001 37.500 22.50 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.