Multiple sequence alignment - TraesCS1B01G390700

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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 TraesCS1B01G390700 chr1B 100.000 2138 0 0 1 2138 624018089 624020226 0.000000e+00 3949.0
1 TraesCS1B01G390700 chr1B 83.992 506 58 16 948 1436 623990647 623991146 4.160000e-127 464.0
2 TraesCS1B01G390700 chr1B 87.975 316 24 5 1822 2136 623991374 623991676 5.610000e-96 361.0
3 TraesCS1B01G390700 chr1B 85.404 322 35 6 1822 2136 623996597 623996913 7.360000e-85 324.0
4 TraesCS1B01G390700 chr1B 87.108 287 26 5 1822 2104 623993093 623993372 4.430000e-82 315.0
5 TraesCS1B01G390700 chr1B 100.000 38 0 0 3 40 279905777 279905740 1.060000e-08 71.3
6 TraesCS1B01G390700 chr1D 91.498 1635 86 19 535 2138 453573186 453574798 0.000000e+00 2200.0
7 TraesCS1B01G390700 chr1D 81.882 850 68 31 629 1453 453554854 453555642 2.310000e-179 638.0
8 TraesCS1B01G390700 chr1D 86.207 319 27 6 1822 2136 453555906 453556211 1.580000e-86 329.0
9 TraesCS1B01G390700 chr1D 85.538 325 30 8 1822 2134 453563681 453564000 7.360000e-85 324.0
10 TraesCS1B01G390700 chr1D 80.804 224 32 7 310 525 453571911 453572131 4.720000e-37 165.0
11 TraesCS1B01G390700 chr1A 89.359 1748 103 34 443 2138 548453921 548455637 0.000000e+00 2121.0
12 TraesCS1B01G390700 chr1A 80.482 871 79 37 629 1453 548445184 548446009 1.100000e-162 582.0
13 TraesCS1B01G390700 chr1A 83.648 318 37 9 1822 2133 548446271 548446579 3.470000e-73 285.0
14 TraesCS1B01G390700 chr1A 83.385 325 26 9 1822 2134 548447983 548448291 2.090000e-70 276.0
15 TraesCS1B01G390700 chr1A 83.969 131 15 4 997 1127 547949908 547950032 1.040000e-23 121.0
16 TraesCS1B01G390700 chr1A 89.041 73 5 2 860 932 548441701 548441770 1.050000e-13 87.9
17 TraesCS1B01G390700 chr1A 100.000 36 0 0 5 40 23067018 23067053 1.370000e-07 67.6
18 TraesCS1B01G390700 chr3A 77.210 724 79 51 781 1449 34583493 34582801 5.650000e-91 344.0
19 TraesCS1B01G390700 chr3B 77.206 680 69 54 781 1411 42707571 42706929 3.420000e-83 318.0
20 TraesCS1B01G390700 chr3B 79.429 350 39 25 1001 1326 42714677 42714337 1.280000e-52 217.0
21 TraesCS1B01G390700 chr3B 80.000 245 30 12 911 1138 42690276 42690034 1.700000e-36 163.0
22 TraesCS1B01G390700 chr3B 82.517 143 17 6 1267 1403 42689921 42689781 3.730000e-23 119.0
23 TraesCS1B01G390700 chr3B 100.000 40 0 0 1 40 5814355 5814394 8.180000e-10 75.0
24 TraesCS1B01G390700 chr3B 100.000 38 0 0 3 40 426087086 426087123 1.060000e-08 71.3
25 TraesCS1B01G390700 chr3D 77.778 495 56 31 897 1347 25190581 25190097 2.720000e-64 255.0
26 TraesCS1B01G390700 chr3D 89.189 74 7 1 1292 1364 25150919 25150846 8.130000e-15 91.6
27 TraesCS1B01G390700 chr3D 100.000 36 0 0 5 40 471418483 471418518 1.370000e-07 67.6
28 TraesCS1B01G390700 chrUn 100.000 38 0 0 3 40 31720094 31720057 1.060000e-08 71.3
29 TraesCS1B01G390700 chr7B 100.000 38 0 0 3 40 613461650 613461687 1.060000e-08 71.3
30 TraesCS1B01G390700 chr5B 93.478 46 1 2 5 49 273597641 273597597 1.370000e-07 67.6
31 TraesCS1B01G390700 chr2D 100.000 36 0 0 5 40 1642393 1642358 1.370000e-07 67.6


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 TraesCS1B01G390700 chr1B 624018089 624020226 2137 False 3949.000 3949 100.00000 1 2138 1 chr1B.!!$F1 2137
1 TraesCS1B01G390700 chr1B 623990647 623996913 6266 False 366.000 464 86.11975 948 2136 4 chr1B.!!$F2 1188
2 TraesCS1B01G390700 chr1D 453571911 453574798 2887 False 1182.500 2200 86.15100 310 2138 2 chr1D.!!$F3 1828
3 TraesCS1B01G390700 chr1D 453554854 453556211 1357 False 483.500 638 84.04450 629 2136 2 chr1D.!!$F2 1507
4 TraesCS1B01G390700 chr1A 548453921 548455637 1716 False 2121.000 2121 89.35900 443 2138 1 chr1A.!!$F3 1695
5 TraesCS1B01G390700 chr1A 548441701 548448291 6590 False 307.725 582 84.13900 629 2134 4 chr1A.!!$F4 1505
6 TraesCS1B01G390700 chr3A 34582801 34583493 692 True 344.000 344 77.21000 781 1449 1 chr3A.!!$R1 668
7 TraesCS1B01G390700 chr3B 42706929 42707571 642 True 318.000 318 77.20600 781 1411 1 chr3B.!!$R1 630

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
158 159 0.099968 TTTCGTACTCGGCCATCTCG 59.9 55.0 2.24 0.35 37.69 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1281 5070 0.036388 AGGAGCACCACATTACACCG 60.036 55.0 2.07 0.0 38.94 4.94 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 2.123077 CCAGGGAGGGCGAGAGAT 60.123 66.667 0.00 0.00 0.00 2.75
46 47 2.123077 AGGGAGGGCGAGAGATGG 60.123 66.667 0.00 0.00 0.00 3.51
48 49 2.123251 GGAGGGCGAGAGATGGGA 60.123 66.667 0.00 0.00 0.00 4.37
49 50 1.762460 GGAGGGCGAGAGATGGGAA 60.762 63.158 0.00 0.00 0.00 3.97
51 52 0.105778 GAGGGCGAGAGATGGGAAAG 59.894 60.000 0.00 0.00 0.00 2.62
52 53 1.147153 GGGCGAGAGATGGGAAAGG 59.853 63.158 0.00 0.00 0.00 3.11
54 55 0.253327 GGCGAGAGATGGGAAAGGTT 59.747 55.000 0.00 0.00 0.00 3.50
55 56 1.340114 GGCGAGAGATGGGAAAGGTTT 60.340 52.381 0.00 0.00 0.00 3.27
59 60 4.443598 GCGAGAGATGGGAAAGGTTTATCT 60.444 45.833 0.00 0.00 0.00 1.98
60 61 5.675538 CGAGAGATGGGAAAGGTTTATCTT 58.324 41.667 0.00 0.00 0.00 2.40
61 62 6.685620 GCGAGAGATGGGAAAGGTTTATCTTA 60.686 42.308 0.00 0.00 0.00 2.10
63 64 7.600752 CGAGAGATGGGAAAGGTTTATCTTATC 59.399 40.741 0.00 0.00 0.00 1.75
64 65 8.574309 AGAGATGGGAAAGGTTTATCTTATCT 57.426 34.615 0.00 0.00 0.00 1.98
66 67 8.574309 AGATGGGAAAGGTTTATCTTATCTCT 57.426 34.615 0.00 0.00 0.00 3.10
67 68 9.008584 AGATGGGAAAGGTTTATCTTATCTCTT 57.991 33.333 0.00 0.00 0.00 2.85
68 69 8.986929 ATGGGAAAGGTTTATCTTATCTCTTG 57.013 34.615 0.00 0.00 0.00 3.02
70 71 6.263392 GGGAAAGGTTTATCTTATCTCTTGGC 59.737 42.308 0.00 0.00 0.00 4.52
71 72 6.828785 GGAAAGGTTTATCTTATCTCTTGGCA 59.171 38.462 0.00 0.00 0.00 4.92
73 74 8.829373 AAAGGTTTATCTTATCTCTTGGCATT 57.171 30.769 0.00 0.00 0.00 3.56
74 75 8.457238 AAGGTTTATCTTATCTCTTGGCATTC 57.543 34.615 0.00 0.00 0.00 2.67
76 77 6.073003 GGTTTATCTTATCTCTTGGCATTCCG 60.073 42.308 0.00 0.00 34.14 4.30
79 80 4.843728 TCTTATCTCTTGGCATTCCGTTT 58.156 39.130 0.00 0.00 34.14 3.60
80 81 5.253330 TCTTATCTCTTGGCATTCCGTTTT 58.747 37.500 0.00 0.00 34.14 2.43
82 83 6.882140 TCTTATCTCTTGGCATTCCGTTTTTA 59.118 34.615 0.00 0.00 34.14 1.52
83 84 7.556275 TCTTATCTCTTGGCATTCCGTTTTTAT 59.444 33.333 0.00 0.00 34.14 1.40
84 85 5.309323 TCTCTTGGCATTCCGTTTTTATG 57.691 39.130 0.00 0.00 34.14 1.90
85 86 5.007034 TCTCTTGGCATTCCGTTTTTATGA 58.993 37.500 0.00 0.00 34.14 2.15
86 87 5.652014 TCTCTTGGCATTCCGTTTTTATGAT 59.348 36.000 0.00 0.00 34.14 2.45
87 88 6.152661 TCTCTTGGCATTCCGTTTTTATGATT 59.847 34.615 0.00 0.00 34.14 2.57
88 89 6.696411 TCTTGGCATTCCGTTTTTATGATTT 58.304 32.000 0.00 0.00 34.14 2.17
90 91 5.788450 TGGCATTCCGTTTTTATGATTTGT 58.212 33.333 0.00 0.00 34.14 2.83
91 92 6.925211 TGGCATTCCGTTTTTATGATTTGTA 58.075 32.000 0.00 0.00 34.14 2.41
92 93 6.809196 TGGCATTCCGTTTTTATGATTTGTAC 59.191 34.615 0.00 0.00 34.14 2.90
94 95 7.009174 GGCATTCCGTTTTTATGATTTGTACTG 59.991 37.037 0.00 0.00 0.00 2.74
95 96 7.540745 GCATTCCGTTTTTATGATTTGTACTGT 59.459 33.333 0.00 0.00 0.00 3.55
96 97 9.061610 CATTCCGTTTTTATGATTTGTACTGTC 57.938 33.333 0.00 0.00 0.00 3.51
97 98 6.823531 TCCGTTTTTATGATTTGTACTGTCG 58.176 36.000 0.00 0.00 0.00 4.35
98 99 6.019152 CCGTTTTTATGATTTGTACTGTCGG 58.981 40.000 0.00 0.00 0.00 4.79
101 102 6.417191 TTTTATGATTTGTACTGTCGGAGC 57.583 37.500 0.00 0.00 0.00 4.70
106 107 3.610040 TTTGTACTGTCGGAGCATGAT 57.390 42.857 0.00 0.00 0.00 2.45
107 108 2.871182 TGTACTGTCGGAGCATGATC 57.129 50.000 1.26 1.26 0.00 2.92
108 109 2.379005 TGTACTGTCGGAGCATGATCT 58.621 47.619 11.34 0.00 0.00 2.75
109 110 2.760650 TGTACTGTCGGAGCATGATCTT 59.239 45.455 11.34 0.00 0.00 2.40
110 111 3.195610 TGTACTGTCGGAGCATGATCTTT 59.804 43.478 11.34 0.00 0.00 2.52
112 113 1.938577 CTGTCGGAGCATGATCTTTGG 59.061 52.381 11.34 0.00 0.00 3.28
113 114 1.278985 TGTCGGAGCATGATCTTTGGT 59.721 47.619 11.34 0.00 0.00 3.67
114 115 1.936547 GTCGGAGCATGATCTTTGGTC 59.063 52.381 11.34 15.67 40.11 4.02
115 116 1.833630 TCGGAGCATGATCTTTGGTCT 59.166 47.619 20.29 3.45 40.54 3.85
116 117 2.159043 TCGGAGCATGATCTTTGGTCTC 60.159 50.000 20.29 13.18 40.54 3.36
117 118 2.158986 CGGAGCATGATCTTTGGTCTCT 60.159 50.000 20.29 2.64 40.54 3.10
119 120 3.118482 GGAGCATGATCTTTGGTCTCTGA 60.118 47.826 20.29 0.00 40.54 3.27
121 122 3.518705 AGCATGATCTTTGGTCTCTGACT 59.481 43.478 0.00 0.00 32.47 3.41
122 123 4.713814 AGCATGATCTTTGGTCTCTGACTA 59.286 41.667 0.00 0.00 32.47 2.59
124 125 4.727507 TGATCTTTGGTCTCTGACTAGC 57.272 45.455 0.00 0.00 32.47 3.42
125 126 4.348486 TGATCTTTGGTCTCTGACTAGCT 58.652 43.478 0.00 0.00 32.47 3.32
128 129 4.663334 TCTTTGGTCTCTGACTAGCTACA 58.337 43.478 0.00 0.00 32.47 2.74
129 130 5.077564 TCTTTGGTCTCTGACTAGCTACAA 58.922 41.667 0.00 0.00 32.47 2.41
131 132 5.801531 TTGGTCTCTGACTAGCTACAAAA 57.198 39.130 0.00 0.00 32.47 2.44
132 133 5.135508 TGGTCTCTGACTAGCTACAAAAC 57.864 43.478 0.00 0.00 32.47 2.43
133 134 4.021368 TGGTCTCTGACTAGCTACAAAACC 60.021 45.833 0.00 0.00 32.47 3.27
135 136 5.404096 GTCTCTGACTAGCTACAAAACCTC 58.596 45.833 0.00 0.00 0.00 3.85
136 137 5.184287 GTCTCTGACTAGCTACAAAACCTCT 59.816 44.000 0.00 0.00 0.00 3.69
137 138 5.184096 TCTCTGACTAGCTACAAAACCTCTG 59.816 44.000 0.00 0.00 0.00 3.35
138 139 4.833380 TCTGACTAGCTACAAAACCTCTGT 59.167 41.667 0.00 0.00 0.00 3.41
139 140 5.304614 TCTGACTAGCTACAAAACCTCTGTT 59.695 40.000 0.00 0.00 35.82 3.16
140 141 5.925509 TGACTAGCTACAAAACCTCTGTTT 58.074 37.500 0.00 0.00 46.50 2.83
151 152 1.336609 ACCTCTGTTTTCGTACTCGGC 60.337 52.381 0.00 0.00 37.69 5.54
152 153 1.347320 CTCTGTTTTCGTACTCGGCC 58.653 55.000 0.00 0.00 37.69 6.13
153 154 0.675083 TCTGTTTTCGTACTCGGCCA 59.325 50.000 2.24 0.00 37.69 5.36
155 156 1.659098 CTGTTTTCGTACTCGGCCATC 59.341 52.381 2.24 0.00 37.69 3.51
156 157 1.274167 TGTTTTCGTACTCGGCCATCT 59.726 47.619 2.24 0.00 37.69 2.90
157 158 1.925185 GTTTTCGTACTCGGCCATCTC 59.075 52.381 2.24 0.00 37.69 2.75
158 159 0.099968 TTTCGTACTCGGCCATCTCG 59.900 55.000 2.24 0.35 37.69 4.04
159 160 1.721664 TTCGTACTCGGCCATCTCGG 61.722 60.000 2.24 0.00 37.69 4.63
161 162 1.359475 GTACTCGGCCATCTCGGTC 59.641 63.158 2.24 0.00 36.97 4.79
162 163 1.102222 GTACTCGGCCATCTCGGTCT 61.102 60.000 2.24 0.00 37.17 3.85
163 164 1.101635 TACTCGGCCATCTCGGTCTG 61.102 60.000 2.24 0.00 37.17 3.51
164 165 2.044352 TCGGCCATCTCGGTCTGA 60.044 61.111 2.24 0.00 37.17 3.27
165 166 2.069465 CTCGGCCATCTCGGTCTGAG 62.069 65.000 2.24 1.83 46.72 3.35
166 167 2.818132 GGCCATCTCGGTCTGAGG 59.182 66.667 8.86 0.00 45.32 3.86
167 168 2.107953 GCCATCTCGGTCTGAGGC 59.892 66.667 8.86 1.81 45.32 4.70
168 169 2.415010 CCATCTCGGTCTGAGGCG 59.585 66.667 8.86 0.61 45.32 5.52
170 171 2.121538 CATCTCGGTCTGAGGCGGA 61.122 63.158 8.86 0.00 45.32 5.54
171 172 1.379977 ATCTCGGTCTGAGGCGGAA 60.380 57.895 8.86 0.00 45.32 4.30
174 175 1.878656 CTCGGTCTGAGGCGGAAAGT 61.879 60.000 0.11 0.00 41.29 2.66
178 179 1.207329 GGTCTGAGGCGGAAAGTACAT 59.793 52.381 0.00 0.00 0.00 2.29
179 180 2.354805 GGTCTGAGGCGGAAAGTACATT 60.355 50.000 0.00 0.00 0.00 2.71
180 181 3.335579 GTCTGAGGCGGAAAGTACATTT 58.664 45.455 0.00 0.00 0.00 2.32
188 189 0.730840 GAAAGTACATTTCGGCCGGG 59.269 55.000 27.83 15.07 38.11 5.73
189 190 0.325602 AAAGTACATTTCGGCCGGGA 59.674 50.000 27.83 14.97 0.00 5.14
191 192 0.325602 AGTACATTTCGGCCGGGAAA 59.674 50.000 27.83 19.92 39.96 3.13
192 193 1.166989 GTACATTTCGGCCGGGAAAA 58.833 50.000 27.83 19.13 39.19 2.29
194 195 2.131776 ACATTTCGGCCGGGAAAATA 57.868 45.000 27.83 0.00 39.19 1.40
195 196 2.021457 ACATTTCGGCCGGGAAAATAG 58.979 47.619 27.83 18.33 39.19 1.73
196 197 2.294074 CATTTCGGCCGGGAAAATAGA 58.706 47.619 27.83 0.00 39.19 1.98
197 198 2.721425 TTTCGGCCGGGAAAATAGAT 57.279 45.000 27.83 0.00 33.23 1.98
198 199 2.721425 TTCGGCCGGGAAAATAGATT 57.279 45.000 27.83 0.00 0.00 2.40
199 200 2.721425 TCGGCCGGGAAAATAGATTT 57.279 45.000 27.83 0.00 0.00 2.17
200 201 3.007473 TCGGCCGGGAAAATAGATTTT 57.993 42.857 27.83 0.00 42.24 1.82
201 202 2.685897 TCGGCCGGGAAAATAGATTTTG 59.314 45.455 27.83 0.00 39.86 2.44
203 204 2.764010 GGCCGGGAAAATAGATTTTGGT 59.236 45.455 2.18 0.00 39.86 3.67
204 205 3.196901 GGCCGGGAAAATAGATTTTGGTT 59.803 43.478 2.18 0.00 39.86 3.67
205 206 4.403113 GGCCGGGAAAATAGATTTTGGTTA 59.597 41.667 2.18 0.00 39.86 2.85
206 207 5.105269 GGCCGGGAAAATAGATTTTGGTTAA 60.105 40.000 2.18 0.00 39.86 2.01
207 208 6.399743 GCCGGGAAAATAGATTTTGGTTAAA 58.600 36.000 2.18 0.00 39.86 1.52
209 210 7.551262 GCCGGGAAAATAGATTTTGGTTAAATT 59.449 33.333 2.18 0.00 39.86 1.82
210 211 9.443323 CCGGGAAAATAGATTTTGGTTAAATTT 57.557 29.630 4.98 0.00 39.86 1.82
222 223 8.824781 ATTTTGGTTAAATTTGGCAAATTTTGC 58.175 25.926 39.96 32.31 46.01 3.68
237 238 6.957150 CAAATTTTGCTCAAATTACAGGCAA 58.043 32.000 7.38 0.00 43.20 4.52
239 240 7.748691 AATTTTGCTCAAATTACAGGCAAAT 57.251 28.000 15.95 5.57 47.00 2.32
240 241 7.748691 ATTTTGCTCAAATTACAGGCAAATT 57.251 28.000 15.95 12.00 47.00 1.82
242 243 7.565323 TTTGCTCAAATTACAGGCAAATTTT 57.435 28.000 13.10 0.00 44.37 1.82
243 244 7.565323 TTGCTCAAATTACAGGCAAATTTTT 57.435 28.000 0.00 0.00 39.45 1.94
244 245 6.957150 TGCTCAAATTACAGGCAAATTTTTG 58.043 32.000 0.00 0.00 41.03 2.44
246 247 7.281774 TGCTCAAATTACAGGCAAATTTTTGAA 59.718 29.630 7.21 0.00 40.55 2.69
247 248 8.127954 GCTCAAATTACAGGCAAATTTTTGAAA 58.872 29.630 7.21 0.00 40.55 2.69
251 252 9.747293 AAATTACAGGCAAATTTTTGAAAATGG 57.253 25.926 7.21 0.98 40.55 3.16
252 253 5.185668 ACAGGCAAATTTTTGAAAATGGC 57.814 34.783 7.21 7.86 40.55 4.40
254 255 3.563508 GGCAAATTTTTGAAAATGGCCG 58.436 40.909 20.08 6.36 43.47 6.13
255 256 3.251972 GGCAAATTTTTGAAAATGGCCGA 59.748 39.130 20.08 0.00 43.47 5.54
256 257 4.261363 GGCAAATTTTTGAAAATGGCCGAA 60.261 37.500 20.08 0.00 43.47 4.30
257 258 5.277047 GCAAATTTTTGAAAATGGCCGAAA 58.723 33.333 7.21 0.00 40.55 3.46
259 260 6.493978 CAAATTTTTGAAAATGGCCGAAACT 58.506 32.000 0.00 0.00 40.55 2.66
260 261 5.922739 ATTTTTGAAAATGGCCGAAACTC 57.077 34.783 0.00 0.00 37.24 3.01
261 262 2.697431 TTGAAAATGGCCGAAACTCG 57.303 45.000 0.00 0.00 40.07 4.18
270 271 3.693245 CGAAACTCGGGCATCTCG 58.307 61.111 0.00 0.00 36.00 4.04
271 272 1.878522 CGAAACTCGGGCATCTCGG 60.879 63.158 0.00 0.00 36.00 4.63
273 274 2.852495 GAAACTCGGGCATCTCGGCA 62.852 60.000 0.00 0.00 43.60 5.69
274 275 2.257409 AAACTCGGGCATCTCGGCAT 62.257 55.000 0.00 0.00 43.60 4.40
275 276 2.664185 CTCGGGCATCTCGGCATG 60.664 66.667 0.00 0.00 43.60 4.06
276 277 4.240103 TCGGGCATCTCGGCATGG 62.240 66.667 0.00 0.00 43.60 3.66
278 279 4.962836 GGGCATCTCGGCATGGGG 62.963 72.222 0.00 0.00 43.60 4.96
289 290 2.153366 GGCATGGGGCGAAAATAATG 57.847 50.000 0.00 0.00 46.16 1.90
290 291 1.686052 GGCATGGGGCGAAAATAATGA 59.314 47.619 0.00 0.00 46.16 2.57
293 294 3.430098 GCATGGGGCGAAAATAATGACAA 60.430 43.478 0.00 0.00 0.00 3.18
294 295 4.753233 CATGGGGCGAAAATAATGACAAA 58.247 39.130 0.00 0.00 0.00 2.83
295 296 4.181309 TGGGGCGAAAATAATGACAAAC 57.819 40.909 0.00 0.00 0.00 2.93
296 297 3.056465 TGGGGCGAAAATAATGACAAACC 60.056 43.478 0.00 0.00 0.00 3.27
298 299 3.175929 GGCGAAAATAATGACAAACCGG 58.824 45.455 0.00 0.00 0.00 5.28
299 300 3.119779 GGCGAAAATAATGACAAACCGGA 60.120 43.478 9.46 0.00 0.00 5.14
300 301 4.477780 GCGAAAATAATGACAAACCGGAA 58.522 39.130 9.46 0.00 0.00 4.30
301 302 4.918583 GCGAAAATAATGACAAACCGGAAA 59.081 37.500 9.46 0.00 0.00 3.13
302 303 5.575218 GCGAAAATAATGACAAACCGGAAAT 59.425 36.000 9.46 0.00 0.00 2.17
304 305 6.804295 CGAAAATAATGACAAACCGGAAATCA 59.196 34.615 9.46 6.69 0.00 2.57
305 306 7.327275 CGAAAATAATGACAAACCGGAAATCAA 59.673 33.333 9.46 0.00 0.00 2.57
306 307 8.894768 AAAATAATGACAAACCGGAAATCAAA 57.105 26.923 9.46 0.00 0.00 2.69
307 308 8.894768 AAATAATGACAAACCGGAAATCAAAA 57.105 26.923 9.46 0.00 0.00 2.44
308 309 7.883229 ATAATGACAAACCGGAAATCAAAAC 57.117 32.000 9.46 0.00 0.00 2.43
312 313 4.932146 ACAAACCGGAAATCAAAACTCTG 58.068 39.130 9.46 0.00 0.00 3.35
317 318 4.069304 CCGGAAATCAAAACTCTGTACCA 58.931 43.478 0.00 0.00 0.00 3.25
341 343 3.228188 TGTGAATGGAATATGCCTCCC 57.772 47.619 0.11 0.00 31.32 4.30
365 367 1.192534 GGAGTGTTCTTGCTTCGTTCG 59.807 52.381 0.00 0.00 0.00 3.95
369 371 3.059597 AGTGTTCTTGCTTCGTTCGATTG 60.060 43.478 0.00 0.00 0.00 2.67
370 372 2.223144 TGTTCTTGCTTCGTTCGATTGG 59.777 45.455 0.00 0.00 0.00 3.16
373 375 1.128692 CTTGCTTCGTTCGATTGGACC 59.871 52.381 0.00 0.00 0.00 4.46
376 378 0.721718 CTTCGTTCGATTGGACCAGC 59.278 55.000 0.00 0.00 0.00 4.85
385 387 2.283101 TGGACCAGCCATGCCAAC 60.283 61.111 0.00 0.00 43.33 3.77
386 388 3.443045 GGACCAGCCATGCCAACG 61.443 66.667 0.00 0.00 36.34 4.10
387 389 2.359850 GACCAGCCATGCCAACGA 60.360 61.111 0.00 0.00 0.00 3.85
388 390 1.750399 GACCAGCCATGCCAACGAT 60.750 57.895 0.00 0.00 0.00 3.73
391 393 0.179129 CCAGCCATGCCAACGATTTC 60.179 55.000 0.00 0.00 0.00 2.17
400 402 3.379240 TGCCAACGATTTCAAACACATG 58.621 40.909 0.00 0.00 0.00 3.21
408 410 4.618927 CGATTTCAAACACATGGCCATCTT 60.619 41.667 17.61 2.22 0.00 2.40
439 441 3.590311 CATTTCGCGAATACACGTTACC 58.410 45.455 24.05 0.00 35.59 2.85
455 457 3.304928 CGTTACCGTCAAGAGTAGGTTGT 60.305 47.826 0.00 0.00 38.12 3.32
463 465 6.204108 CCGTCAAGAGTAGGTTGTAAATTTGT 59.796 38.462 0.00 0.00 0.00 2.83
466 468 8.837389 GTCAAGAGTAGGTTGTAAATTTGTTCT 58.163 33.333 0.00 0.00 0.00 3.01
506 514 6.595716 ACGAGCAGATTAAGCTTTGTTTAGAT 59.404 34.615 3.20 0.00 43.58 1.98
525 533 8.718734 GTTTAGATGAACGACCAGATTTAGTTT 58.281 33.333 0.00 0.00 0.00 2.66
579 597 7.992754 AGATATTATCATTCCTGAAGTTGGC 57.007 36.000 6.46 0.00 34.37 4.52
580 598 7.520798 AGATATTATCATTCCTGAAGTTGGCA 58.479 34.615 6.46 0.00 34.37 4.92
581 599 7.664731 AGATATTATCATTCCTGAAGTTGGCAG 59.335 37.037 6.46 0.00 34.37 4.85
583 601 4.574674 ATCATTCCTGAAGTTGGCAGTA 57.425 40.909 0.00 0.00 34.37 2.74
584 602 4.365514 TCATTCCTGAAGTTGGCAGTAA 57.634 40.909 0.00 0.00 0.00 2.24
589 607 6.478512 TTCCTGAAGTTGGCAGTAAAATTT 57.521 33.333 0.00 0.00 0.00 1.82
590 608 6.084326 TCCTGAAGTTGGCAGTAAAATTTC 57.916 37.500 0.00 0.00 0.00 2.17
594 612 4.600692 AGTTGGCAGTAAAATTTCCACC 57.399 40.909 0.00 0.00 0.00 4.61
595 613 3.964031 AGTTGGCAGTAAAATTTCCACCA 59.036 39.130 0.00 0.00 0.00 4.17
596 614 4.592778 AGTTGGCAGTAAAATTTCCACCAT 59.407 37.500 0.00 0.00 0.00 3.55
597 615 4.533919 TGGCAGTAAAATTTCCACCATG 57.466 40.909 0.00 0.00 0.00 3.66
599 617 3.055891 GGCAGTAAAATTTCCACCATGCT 60.056 43.478 12.70 0.00 0.00 3.79
604 622 7.201548 GCAGTAAAATTTCCACCATGCTAAATG 60.202 37.037 0.00 0.00 0.00 2.32
605 623 7.278424 CAGTAAAATTTCCACCATGCTAAATGG 59.722 37.037 2.79 2.79 44.54 3.16
614 632 4.552166 CCATGCTAAATGGTTTACTCGG 57.448 45.455 0.00 0.00 34.56 4.63
615 633 4.196193 CCATGCTAAATGGTTTACTCGGA 58.804 43.478 0.00 0.00 34.56 4.55
616 634 4.273480 CCATGCTAAATGGTTTACTCGGAG 59.727 45.833 2.83 2.83 34.56 4.63
619 637 6.229936 TGCTAAATGGTTTACTCGGAGTAT 57.770 37.500 17.96 4.78 29.64 2.12
627 645 7.828508 TGGTTTACTCGGAGTATATGTATGT 57.171 36.000 17.96 0.00 29.64 2.29
649 4338 3.356529 AGTTCAGTATTCAGGGGCAAG 57.643 47.619 0.00 0.00 0.00 4.01
657 4346 3.806949 ATTCAGGGGCAAGTTTACTCA 57.193 42.857 0.00 0.00 0.00 3.41
916 4639 1.134759 CCACAGCAGAGACAGATCCAG 60.135 57.143 0.00 0.00 0.00 3.86
932 4665 1.744368 CAGCCAGCAGTAGCAGTGG 60.744 63.158 0.00 0.00 45.49 4.00
933 4666 1.915266 AGCCAGCAGTAGCAGTGGA 60.915 57.895 0.00 0.00 45.49 4.02
1089 4836 1.301165 GCAACAAAAGGCCAGGCTG 60.301 57.895 12.43 7.75 0.00 4.85
1104 4851 3.369381 GCTGTACATCATCCAGCGT 57.631 52.632 0.00 0.00 41.80 5.07
1144 4891 2.700371 TGCTACCATGACTGACCATAGG 59.300 50.000 0.00 0.00 0.00 2.57
1145 4892 2.700897 GCTACCATGACTGACCATAGGT 59.299 50.000 0.00 0.00 39.44 3.08
1149 4904 3.273434 CCATGACTGACCATAGGTGTTG 58.727 50.000 0.00 0.00 35.25 3.33
1242 5030 8.698210 TGTAAGTAGTTCAGAAGTTTCAGGTTA 58.302 33.333 0.00 0.00 0.00 2.85
1281 5070 0.380378 TTGGTGTTGAAGTTCTGCGC 59.620 50.000 0.00 0.00 0.00 6.09
1406 5205 8.388484 TGGAAGATCTCAGAAAAAGAAAGAAG 57.612 34.615 0.00 0.00 0.00 2.85
1421 5220 9.710900 AAAAGAAAGAAGAAAACAGTGTGAAAT 57.289 25.926 0.00 0.00 0.00 2.17
1472 5273 6.327365 TCCCATCATTGTATGATCAGTACTGT 59.673 38.462 21.99 9.95 46.62 3.55
1473 5274 6.994496 CCCATCATTGTATGATCAGTACTGTT 59.006 38.462 21.99 14.38 46.62 3.16
1474 5275 8.150296 CCCATCATTGTATGATCAGTACTGTTA 58.850 37.037 21.99 10.30 46.62 2.41
1475 5276 9.546428 CCATCATTGTATGATCAGTACTGTTAA 57.454 33.333 21.99 8.10 46.62 2.01
1583 5384 4.007659 GGATTGGGTATGTTGTTCGACTT 58.992 43.478 0.00 0.00 0.00 3.01
1630 5445 2.226200 GGTGTGCATTTTGGGAATTTGC 59.774 45.455 0.00 0.00 0.00 3.68
1636 5451 0.319125 TTTTGGGAATTTGCGGCGAC 60.319 50.000 12.98 2.02 0.00 5.19
1712 5532 7.883229 AGTTTTACACACAACCAAAAGAAAG 57.117 32.000 0.00 0.00 0.00 2.62
1777 5597 2.916702 TGCTGACAGCTTTCTCTGAA 57.083 45.000 26.94 1.51 42.97 3.02
1821 5641 6.224584 ACCTCAACTTAGAACTTAGAACTGC 58.775 40.000 0.00 0.00 0.00 4.40
1943 5777 7.446319 CCTTGCTCATGGTTCATTCTATATCAA 59.554 37.037 0.00 0.00 0.00 2.57
1981 5816 7.495135 AATGCCTCAAAAATGTTTGGTAAAG 57.505 32.000 8.51 0.00 43.70 1.85
2129 5965 4.095610 GGTGCTATTGTGCGTTGTTATTC 58.904 43.478 0.00 0.00 35.36 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.123077 ATCTCTCGCCCTCCCTGG 60.123 66.667 0.00 0.00 0.00 4.45
28 29 2.506061 CCATCTCTCGCCCTCCCTG 61.506 68.421 0.00 0.00 0.00 4.45
29 30 2.123077 CCATCTCTCGCCCTCCCT 60.123 66.667 0.00 0.00 0.00 4.20
31 32 1.338136 TTTCCCATCTCTCGCCCTCC 61.338 60.000 0.00 0.00 0.00 4.30
32 33 0.105778 CTTTCCCATCTCTCGCCCTC 59.894 60.000 0.00 0.00 0.00 4.30
34 35 1.147153 CCTTTCCCATCTCTCGCCC 59.853 63.158 0.00 0.00 0.00 6.13
35 36 0.253327 AACCTTTCCCATCTCTCGCC 59.747 55.000 0.00 0.00 0.00 5.54
36 37 2.115343 AAACCTTTCCCATCTCTCGC 57.885 50.000 0.00 0.00 0.00 5.03
38 39 8.655901 AGATAAGATAAACCTTTCCCATCTCTC 58.344 37.037 0.00 0.00 0.00 3.20
40 41 8.655901 AGAGATAAGATAAACCTTTCCCATCTC 58.344 37.037 0.00 0.00 36.51 2.75
43 44 8.001292 CCAAGAGATAAGATAAACCTTTCCCAT 58.999 37.037 0.00 0.00 0.00 4.00
44 45 7.346471 CCAAGAGATAAGATAAACCTTTCCCA 58.654 38.462 0.00 0.00 0.00 4.37
46 47 6.828785 TGCCAAGAGATAAGATAAACCTTTCC 59.171 38.462 0.00 0.00 0.00 3.13
48 49 8.829373 AATGCCAAGAGATAAGATAAACCTTT 57.171 30.769 0.00 0.00 0.00 3.11
49 50 7.503902 GGAATGCCAAGAGATAAGATAAACCTT 59.496 37.037 0.00 0.00 0.00 3.50
51 52 6.073003 CGGAATGCCAAGAGATAAGATAAACC 60.073 42.308 0.00 0.00 0.00 3.27
52 53 6.483640 ACGGAATGCCAAGAGATAAGATAAAC 59.516 38.462 0.00 0.00 0.00 2.01
54 55 6.174720 ACGGAATGCCAAGAGATAAGATAA 57.825 37.500 0.00 0.00 0.00 1.75
55 56 5.808366 ACGGAATGCCAAGAGATAAGATA 57.192 39.130 0.00 0.00 0.00 1.98
59 60 5.975693 AAAAACGGAATGCCAAGAGATAA 57.024 34.783 0.00 0.00 0.00 1.75
60 61 6.826231 TCATAAAAACGGAATGCCAAGAGATA 59.174 34.615 0.00 0.00 0.00 1.98
61 62 5.652014 TCATAAAAACGGAATGCCAAGAGAT 59.348 36.000 0.00 0.00 0.00 2.75
63 64 5.309323 TCATAAAAACGGAATGCCAAGAG 57.691 39.130 0.00 0.00 0.00 2.85
64 65 5.913137 ATCATAAAAACGGAATGCCAAGA 57.087 34.783 0.00 0.00 0.00 3.02
66 67 6.226787 ACAAATCATAAAAACGGAATGCCAA 58.773 32.000 0.00 0.00 0.00 4.52
67 68 5.788450 ACAAATCATAAAAACGGAATGCCA 58.212 33.333 0.00 0.00 0.00 4.92
68 69 7.009174 CAGTACAAATCATAAAAACGGAATGCC 59.991 37.037 0.00 0.00 0.00 4.40
70 71 8.964420 ACAGTACAAATCATAAAAACGGAATG 57.036 30.769 0.00 0.00 0.00 2.67
71 72 7.960738 CGACAGTACAAATCATAAAAACGGAAT 59.039 33.333 0.00 0.00 0.00 3.01
73 74 6.128499 CCGACAGTACAAATCATAAAAACGGA 60.128 38.462 0.00 0.00 36.05 4.69
74 75 6.019152 CCGACAGTACAAATCATAAAAACGG 58.981 40.000 0.00 0.00 0.00 4.44
76 77 6.741358 GCTCCGACAGTACAAATCATAAAAAC 59.259 38.462 0.00 0.00 0.00 2.43
79 80 5.483811 TGCTCCGACAGTACAAATCATAAA 58.516 37.500 0.00 0.00 0.00 1.40
80 81 5.079689 TGCTCCGACAGTACAAATCATAA 57.920 39.130 0.00 0.00 0.00 1.90
82 83 3.610040 TGCTCCGACAGTACAAATCAT 57.390 42.857 0.00 0.00 0.00 2.45
83 84 3.056179 TCATGCTCCGACAGTACAAATCA 60.056 43.478 0.00 0.00 0.00 2.57
84 85 3.521560 TCATGCTCCGACAGTACAAATC 58.478 45.455 0.00 0.00 0.00 2.17
85 86 3.610040 TCATGCTCCGACAGTACAAAT 57.390 42.857 0.00 0.00 0.00 2.32
86 87 3.195610 AGATCATGCTCCGACAGTACAAA 59.804 43.478 0.00 0.00 0.00 2.83
87 88 2.760650 AGATCATGCTCCGACAGTACAA 59.239 45.455 0.00 0.00 0.00 2.41
88 89 2.379005 AGATCATGCTCCGACAGTACA 58.621 47.619 0.00 0.00 0.00 2.90
90 91 3.430790 CCAAAGATCATGCTCCGACAGTA 60.431 47.826 0.00 0.00 0.00 2.74
91 92 2.625737 CAAAGATCATGCTCCGACAGT 58.374 47.619 0.00 0.00 0.00 3.55
92 93 1.938577 CCAAAGATCATGCTCCGACAG 59.061 52.381 0.00 0.00 0.00 3.51
94 95 1.936547 GACCAAAGATCATGCTCCGAC 59.063 52.381 0.00 0.00 0.00 4.79
95 96 1.833630 AGACCAAAGATCATGCTCCGA 59.166 47.619 0.00 0.00 0.00 4.55
96 97 2.158986 AGAGACCAAAGATCATGCTCCG 60.159 50.000 0.00 0.00 0.00 4.63
97 98 3.118482 TCAGAGACCAAAGATCATGCTCC 60.118 47.826 0.00 0.00 0.00 4.70
98 99 3.870419 GTCAGAGACCAAAGATCATGCTC 59.130 47.826 0.00 0.00 0.00 4.26
101 102 5.049167 GCTAGTCAGAGACCAAAGATCATG 58.951 45.833 0.00 0.00 32.18 3.07
106 107 4.663334 TGTAGCTAGTCAGAGACCAAAGA 58.337 43.478 0.00 0.00 32.18 2.52
107 108 5.392767 TTGTAGCTAGTCAGAGACCAAAG 57.607 43.478 0.00 0.00 32.18 2.77
108 109 5.801531 TTTGTAGCTAGTCAGAGACCAAA 57.198 39.130 0.00 0.00 32.18 3.28
109 110 5.510861 GGTTTTGTAGCTAGTCAGAGACCAA 60.511 44.000 0.00 0.00 32.18 3.67
110 111 4.021368 GGTTTTGTAGCTAGTCAGAGACCA 60.021 45.833 0.00 0.00 32.18 4.02
112 113 5.184287 AGAGGTTTTGTAGCTAGTCAGAGAC 59.816 44.000 0.00 0.00 33.94 3.36
113 114 5.184096 CAGAGGTTTTGTAGCTAGTCAGAGA 59.816 44.000 0.00 0.00 33.94 3.10
114 115 5.047660 ACAGAGGTTTTGTAGCTAGTCAGAG 60.048 44.000 0.00 0.00 33.94 3.35
115 116 4.833380 ACAGAGGTTTTGTAGCTAGTCAGA 59.167 41.667 0.00 0.00 33.94 3.27
116 117 5.140747 ACAGAGGTTTTGTAGCTAGTCAG 57.859 43.478 0.00 0.00 33.94 3.51
117 118 5.546621 AACAGAGGTTTTGTAGCTAGTCA 57.453 39.130 0.00 0.00 33.94 3.41
129 130 3.387397 CCGAGTACGAAAACAGAGGTTT 58.613 45.455 0.00 0.00 41.61 3.27
131 132 1.336609 GCCGAGTACGAAAACAGAGGT 60.337 52.381 0.00 0.00 42.66 3.85
132 133 1.347320 GCCGAGTACGAAAACAGAGG 58.653 55.000 0.00 0.00 42.66 3.69
133 134 1.336517 TGGCCGAGTACGAAAACAGAG 60.337 52.381 0.00 0.00 42.66 3.35
135 136 1.659098 GATGGCCGAGTACGAAAACAG 59.341 52.381 0.00 0.00 42.66 3.16
136 137 1.274167 AGATGGCCGAGTACGAAAACA 59.726 47.619 0.00 0.00 42.66 2.83
137 138 1.925185 GAGATGGCCGAGTACGAAAAC 59.075 52.381 0.00 0.00 42.66 2.43
138 139 1.468565 CGAGATGGCCGAGTACGAAAA 60.469 52.381 0.00 0.00 42.66 2.29
139 140 0.099968 CGAGATGGCCGAGTACGAAA 59.900 55.000 0.00 0.00 42.66 3.46
140 141 1.721664 CCGAGATGGCCGAGTACGAA 61.722 60.000 0.00 0.00 42.66 3.85
143 144 1.102222 AGACCGAGATGGCCGAGTAC 61.102 60.000 0.00 0.00 43.94 2.73
144 145 1.101635 CAGACCGAGATGGCCGAGTA 61.102 60.000 0.00 0.00 43.94 2.59
145 146 2.043852 AGACCGAGATGGCCGAGT 60.044 61.111 0.00 0.00 43.94 4.18
146 147 2.069465 CTCAGACCGAGATGGCCGAG 62.069 65.000 0.00 0.00 45.45 4.63
147 148 2.044352 TCAGACCGAGATGGCCGA 60.044 61.111 0.00 0.00 43.94 5.54
148 149 2.415010 CTCAGACCGAGATGGCCG 59.585 66.667 0.00 0.00 45.45 6.13
149 150 2.818132 CCTCAGACCGAGATGGCC 59.182 66.667 0.00 0.00 45.45 5.36
151 152 2.415010 CGCCTCAGACCGAGATGG 59.585 66.667 0.00 0.00 45.45 3.51
152 153 1.667154 TTCCGCCTCAGACCGAGATG 61.667 60.000 0.00 0.00 45.45 2.90
153 154 0.970937 TTTCCGCCTCAGACCGAGAT 60.971 55.000 0.00 0.00 45.45 2.75
155 156 1.153745 CTTTCCGCCTCAGACCGAG 60.154 63.158 0.00 0.00 41.89 4.63
156 157 0.609957 TACTTTCCGCCTCAGACCGA 60.610 55.000 0.00 0.00 0.00 4.69
157 158 0.458025 GTACTTTCCGCCTCAGACCG 60.458 60.000 0.00 0.00 0.00 4.79
158 159 0.606604 TGTACTTTCCGCCTCAGACC 59.393 55.000 0.00 0.00 0.00 3.85
159 160 2.674796 ATGTACTTTCCGCCTCAGAC 57.325 50.000 0.00 0.00 0.00 3.51
161 162 2.348666 CGAAATGTACTTTCCGCCTCAG 59.651 50.000 10.34 0.00 40.19 3.35
162 163 2.343101 CGAAATGTACTTTCCGCCTCA 58.657 47.619 10.34 0.00 40.19 3.86
163 164 1.664151 CCGAAATGTACTTTCCGCCTC 59.336 52.381 10.34 0.00 40.19 4.70
164 165 1.734163 CCGAAATGTACTTTCCGCCT 58.266 50.000 10.34 0.00 40.19 5.52
165 166 0.098200 GCCGAAATGTACTTTCCGCC 59.902 55.000 14.21 0.00 40.22 6.13
166 167 0.098200 GGCCGAAATGTACTTTCCGC 59.902 55.000 15.62 15.62 43.25 5.54
167 168 0.372334 CGGCCGAAATGTACTTTCCG 59.628 55.000 24.07 8.00 40.19 4.30
168 169 0.730840 CCGGCCGAAATGTACTTTCC 59.269 55.000 30.73 1.39 40.19 3.13
170 171 0.325602 TCCCGGCCGAAATGTACTTT 59.674 50.000 30.73 0.00 0.00 2.66
171 172 0.325602 TTCCCGGCCGAAATGTACTT 59.674 50.000 30.73 0.00 0.00 2.24
174 175 2.131776 ATTTTCCCGGCCGAAATGTA 57.868 45.000 30.73 5.64 32.00 2.29
178 179 2.721425 ATCTATTTTCCCGGCCGAAA 57.279 45.000 30.73 20.15 0.00 3.46
179 180 2.721425 AATCTATTTTCCCGGCCGAA 57.279 45.000 30.73 13.96 0.00 4.30
180 181 2.685897 CAAAATCTATTTTCCCGGCCGA 59.314 45.455 30.73 6.25 37.86 5.54
182 183 2.764010 ACCAAAATCTATTTTCCCGGCC 59.236 45.455 0.00 0.00 37.86 6.13
183 184 4.465632 AACCAAAATCTATTTTCCCGGC 57.534 40.909 0.00 0.00 37.86 6.13
184 185 9.443323 AAATTTAACCAAAATCTATTTTCCCGG 57.557 29.630 0.00 0.00 37.86 5.73
213 214 6.542574 TGCCTGTAATTTGAGCAAAATTTG 57.457 33.333 13.36 0.57 44.41 2.32
214 215 7.565323 TTTGCCTGTAATTTGAGCAAAATTT 57.435 28.000 13.36 0.00 46.95 1.82
219 220 7.281774 TCAAAAATTTGCCTGTAATTTGAGCAA 59.718 29.630 0.98 0.00 41.39 3.91
221 222 7.188468 TCAAAAATTTGCCTGTAATTTGAGC 57.812 32.000 0.98 0.00 35.85 4.26
225 226 9.747293 CCATTTTCAAAAATTTGCCTGTAATTT 57.253 25.926 0.98 0.00 36.52 1.82
227 228 7.369607 GCCATTTTCAAAAATTTGCCTGTAAT 58.630 30.769 0.98 0.00 36.52 1.89
228 229 6.238869 GGCCATTTTCAAAAATTTGCCTGTAA 60.239 34.615 20.77 0.00 43.55 2.41
229 230 5.240403 GGCCATTTTCAAAAATTTGCCTGTA 59.760 36.000 20.77 0.00 43.55 2.74
230 231 4.037803 GGCCATTTTCAAAAATTTGCCTGT 59.962 37.500 20.77 0.00 43.55 4.00
231 232 4.548494 GGCCATTTTCAAAAATTTGCCTG 58.452 39.130 20.77 4.99 43.55 4.85
232 233 3.252944 CGGCCATTTTCAAAAATTTGCCT 59.747 39.130 23.08 0.00 44.10 4.75
233 234 3.251972 TCGGCCATTTTCAAAAATTTGCC 59.748 39.130 19.34 19.34 43.50 4.52
234 235 4.480386 TCGGCCATTTTCAAAAATTTGC 57.520 36.364 2.24 9.43 36.52 3.68
235 236 6.493978 AGTTTCGGCCATTTTCAAAAATTTG 58.506 32.000 2.24 0.00 36.52 2.32
237 238 5.050431 CGAGTTTCGGCCATTTTCAAAAATT 60.050 36.000 2.24 0.00 34.90 1.82
239 240 3.799420 CGAGTTTCGGCCATTTTCAAAAA 59.201 39.130 2.24 0.00 36.00 1.94
240 241 3.376540 CGAGTTTCGGCCATTTTCAAAA 58.623 40.909 2.24 0.00 36.00 2.44
242 243 2.697431 CGAGTTTCGGCCATTTTCAA 57.303 45.000 2.24 0.00 36.00 2.69
254 255 2.174319 GCCGAGATGCCCGAGTTTC 61.174 63.158 0.00 0.00 0.00 2.78
255 256 2.125106 GCCGAGATGCCCGAGTTT 60.125 61.111 0.00 0.00 0.00 2.66
256 257 2.735772 ATGCCGAGATGCCCGAGTT 61.736 57.895 0.00 0.00 0.00 3.01
257 258 3.157252 ATGCCGAGATGCCCGAGT 61.157 61.111 0.00 0.00 0.00 4.18
259 260 4.240103 CCATGCCGAGATGCCCGA 62.240 66.667 0.00 0.00 0.00 5.14
261 262 4.962836 CCCCATGCCGAGATGCCC 62.963 72.222 0.00 0.00 0.00 5.36
264 265 3.755526 TTCGCCCCATGCCGAGATG 62.756 63.158 0.00 0.00 36.24 2.90
265 266 2.550699 TTTTCGCCCCATGCCGAGAT 62.551 55.000 0.00 0.00 36.24 2.75
266 267 2.550699 ATTTTCGCCCCATGCCGAGA 62.551 55.000 0.00 0.00 36.24 4.04
268 269 0.394488 TTATTTTCGCCCCATGCCGA 60.394 50.000 0.00 0.00 36.24 5.54
270 271 1.686052 TCATTATTTTCGCCCCATGCC 59.314 47.619 0.00 0.00 36.24 4.40
271 272 2.100584 TGTCATTATTTTCGCCCCATGC 59.899 45.455 0.00 0.00 0.00 4.06
273 274 4.382577 GGTTTGTCATTATTTTCGCCCCAT 60.383 41.667 0.00 0.00 0.00 4.00
274 275 3.056465 GGTTTGTCATTATTTTCGCCCCA 60.056 43.478 0.00 0.00 0.00 4.96
275 276 3.517602 GGTTTGTCATTATTTTCGCCCC 58.482 45.455 0.00 0.00 0.00 5.80
276 277 3.175929 CGGTTTGTCATTATTTTCGCCC 58.824 45.455 0.00 0.00 0.00 6.13
278 279 4.086199 TCCGGTTTGTCATTATTTTCGC 57.914 40.909 0.00 0.00 0.00 4.70
279 280 6.804295 TGATTTCCGGTTTGTCATTATTTTCG 59.196 34.615 0.00 0.00 0.00 3.46
281 282 8.894768 TTTGATTTCCGGTTTGTCATTATTTT 57.105 26.923 0.00 0.00 0.00 1.82
282 283 8.769891 GTTTTGATTTCCGGTTTGTCATTATTT 58.230 29.630 0.00 0.00 0.00 1.40
283 284 8.147704 AGTTTTGATTTCCGGTTTGTCATTATT 58.852 29.630 0.00 0.00 0.00 1.40
284 285 7.666623 AGTTTTGATTTCCGGTTTGTCATTAT 58.333 30.769 0.00 0.00 0.00 1.28
285 286 7.013846 AGAGTTTTGATTTCCGGTTTGTCATTA 59.986 33.333 0.00 0.00 0.00 1.90
286 287 5.912892 AGTTTTGATTTCCGGTTTGTCATT 58.087 33.333 0.00 0.00 0.00 2.57
287 288 5.301805 AGAGTTTTGATTTCCGGTTTGTCAT 59.698 36.000 0.00 0.00 0.00 3.06
288 289 4.642885 AGAGTTTTGATTTCCGGTTTGTCA 59.357 37.500 0.00 0.00 0.00 3.58
289 290 4.976116 CAGAGTTTTGATTTCCGGTTTGTC 59.024 41.667 0.00 0.00 0.00 3.18
290 291 4.401202 ACAGAGTTTTGATTTCCGGTTTGT 59.599 37.500 0.00 0.00 0.00 2.83
293 294 4.517832 GGTACAGAGTTTTGATTTCCGGTT 59.482 41.667 0.00 0.00 0.00 4.44
294 295 4.070009 GGTACAGAGTTTTGATTTCCGGT 58.930 43.478 0.00 0.00 0.00 5.28
295 296 4.069304 TGGTACAGAGTTTTGATTTCCGG 58.931 43.478 0.00 0.00 0.00 5.14
296 297 5.682943 TTGGTACAGAGTTTTGATTTCCG 57.317 39.130 0.00 0.00 42.39 4.30
298 299 8.755018 CACAATTTGGTACAGAGTTTTGATTTC 58.245 33.333 0.78 0.00 42.39 2.17
299 300 8.474025 TCACAATTTGGTACAGAGTTTTGATTT 58.526 29.630 0.78 0.00 42.39 2.17
300 301 8.006298 TCACAATTTGGTACAGAGTTTTGATT 57.994 30.769 0.78 0.00 42.39 2.57
301 302 7.581213 TCACAATTTGGTACAGAGTTTTGAT 57.419 32.000 0.78 0.00 42.39 2.57
302 303 7.397892 TTCACAATTTGGTACAGAGTTTTGA 57.602 32.000 0.78 0.00 42.39 2.69
304 305 7.069331 TCCATTCACAATTTGGTACAGAGTTTT 59.931 33.333 0.78 0.00 42.39 2.43
305 306 6.549364 TCCATTCACAATTTGGTACAGAGTTT 59.451 34.615 0.78 0.00 42.39 2.66
306 307 6.068010 TCCATTCACAATTTGGTACAGAGTT 58.932 36.000 0.78 0.00 42.39 3.01
307 308 5.630121 TCCATTCACAATTTGGTACAGAGT 58.370 37.500 0.78 0.00 42.39 3.24
308 309 6.573664 TTCCATTCACAATTTGGTACAGAG 57.426 37.500 0.78 0.00 42.39 3.35
312 313 6.701400 GGCATATTCCATTCACAATTTGGTAC 59.299 38.462 0.78 0.00 0.00 3.34
317 318 5.070847 GGGAGGCATATTCCATTCACAATTT 59.929 40.000 0.00 0.00 36.40 1.82
341 343 1.528129 GAAGCAAGAACACTCCCCAG 58.472 55.000 0.00 0.00 0.00 4.45
369 371 3.443045 CGTTGGCATGGCTGGTCC 61.443 66.667 21.08 0.00 0.00 4.46
370 372 1.315257 AATCGTTGGCATGGCTGGTC 61.315 55.000 21.08 7.09 0.00 4.02
373 375 0.527113 TGAAATCGTTGGCATGGCTG 59.473 50.000 21.08 10.33 0.00 4.85
376 378 2.730928 GTGTTTGAAATCGTTGGCATGG 59.269 45.455 0.00 0.00 0.00 3.66
378 380 3.724508 TGTGTTTGAAATCGTTGGCAT 57.275 38.095 0.00 0.00 0.00 4.40
382 384 2.730928 GGCCATGTGTTTGAAATCGTTG 59.269 45.455 0.00 0.00 0.00 4.10
383 385 2.363680 TGGCCATGTGTTTGAAATCGTT 59.636 40.909 0.00 0.00 0.00 3.85
384 386 1.959985 TGGCCATGTGTTTGAAATCGT 59.040 42.857 0.00 0.00 0.00 3.73
385 387 2.721274 TGGCCATGTGTTTGAAATCG 57.279 45.000 0.00 0.00 0.00 3.34
386 388 4.460948 AGATGGCCATGTGTTTGAAATC 57.539 40.909 26.56 4.46 0.00 2.17
387 389 4.283978 TCAAGATGGCCATGTGTTTGAAAT 59.716 37.500 26.56 0.00 0.00 2.17
388 390 3.640498 TCAAGATGGCCATGTGTTTGAAA 59.360 39.130 26.56 4.79 0.00 2.69
391 393 3.581755 CTTCAAGATGGCCATGTGTTTG 58.418 45.455 26.56 20.20 0.00 2.93
400 402 2.476320 GCTCGCCTTCAAGATGGCC 61.476 63.158 18.03 0.00 45.71 5.36
434 436 4.248691 ACAACCTACTCTTGACGGTAAC 57.751 45.455 0.00 0.00 0.00 2.50
439 441 7.186021 ACAAATTTACAACCTACTCTTGACG 57.814 36.000 0.00 0.00 0.00 4.35
441 443 8.974060 AGAACAAATTTACAACCTACTCTTGA 57.026 30.769 0.00 0.00 0.00 3.02
463 465 8.248253 TCTGCTCGTGTTACATATCTTTTAGAA 58.752 33.333 0.00 0.00 0.00 2.10
466 468 8.942338 AATCTGCTCGTGTTACATATCTTTTA 57.058 30.769 0.00 0.00 0.00 1.52
470 472 6.642950 GCTTAATCTGCTCGTGTTACATATCT 59.357 38.462 0.00 0.00 0.00 1.98
472 474 6.516718 AGCTTAATCTGCTCGTGTTACATAT 58.483 36.000 0.00 0.00 35.67 1.78
473 475 5.902681 AGCTTAATCTGCTCGTGTTACATA 58.097 37.500 0.00 0.00 35.67 2.29
506 514 7.094975 CCATGTAAAACTAAATCTGGTCGTTCA 60.095 37.037 0.00 0.00 0.00 3.18
557 575 7.293073 ACTGCCAACTTCAGGAATGATAATAT 58.707 34.615 0.00 0.00 35.94 1.28
563 581 2.957402 ACTGCCAACTTCAGGAATGA 57.043 45.000 0.00 0.00 35.94 2.57
564 582 5.452078 TTTTACTGCCAACTTCAGGAATG 57.548 39.130 0.00 0.00 34.62 2.67
565 583 6.670695 AATTTTACTGCCAACTTCAGGAAT 57.329 33.333 0.00 0.00 34.62 3.01
567 585 5.010617 GGAAATTTTACTGCCAACTTCAGGA 59.989 40.000 0.00 0.00 35.94 3.86
568 586 5.221422 TGGAAATTTTACTGCCAACTTCAGG 60.221 40.000 0.00 0.00 35.94 3.86
572 590 4.407296 TGGTGGAAATTTTACTGCCAACTT 59.593 37.500 11.08 0.00 37.24 2.66
575 593 4.802248 GCATGGTGGAAATTTTACTGCCAA 60.802 41.667 10.69 0.00 0.00 4.52
576 594 3.306641 GCATGGTGGAAATTTTACTGCCA 60.307 43.478 9.54 9.54 0.00 4.92
579 597 7.278424 CCATTTAGCATGGTGGAAATTTTACTG 59.722 37.037 7.89 0.00 34.56 2.74
580 598 7.330262 CCATTTAGCATGGTGGAAATTTTACT 58.670 34.615 7.89 0.00 34.56 2.24
581 599 7.538303 CCATTTAGCATGGTGGAAATTTTAC 57.462 36.000 7.89 0.00 34.56 2.01
594 612 4.876107 ACTCCGAGTAAACCATTTAGCATG 59.124 41.667 0.00 0.00 0.00 4.06
595 613 5.099042 ACTCCGAGTAAACCATTTAGCAT 57.901 39.130 0.00 0.00 0.00 3.79
596 614 4.546829 ACTCCGAGTAAACCATTTAGCA 57.453 40.909 0.00 0.00 0.00 3.49
597 615 7.871463 ACATATACTCCGAGTAAACCATTTAGC 59.129 37.037 12.26 0.00 33.89 3.09
604 622 9.837525 CTAACATACATATACTCCGAGTAAACC 57.162 37.037 12.26 0.00 33.89 3.27
608 626 9.783081 TGAACTAACATACATATACTCCGAGTA 57.217 33.333 10.70 10.70 34.82 2.59
610 628 8.784994 ACTGAACTAACATACATATACTCCGAG 58.215 37.037 0.00 0.00 0.00 4.63
619 637 8.647796 CCCCTGAATACTGAACTAACATACATA 58.352 37.037 0.00 0.00 0.00 2.29
624 642 4.227300 TGCCCCTGAATACTGAACTAACAT 59.773 41.667 0.00 0.00 0.00 2.71
627 645 4.288626 ACTTGCCCCTGAATACTGAACTAA 59.711 41.667 0.00 0.00 0.00 2.24
631 649 3.806949 AACTTGCCCCTGAATACTGAA 57.193 42.857 0.00 0.00 0.00 3.02
649 4338 5.120830 ACAGCTGATTCGAATGTGAGTAAAC 59.879 40.000 23.35 0.00 0.00 2.01
657 4346 2.027745 AGGTGACAGCTGATTCGAATGT 60.028 45.455 23.35 8.34 0.00 2.71
916 4639 1.449246 CTCCACTGCTACTGCTGGC 60.449 63.158 0.00 0.00 41.57 4.85
932 4665 1.381056 TCCCTGCTCTGCTCTCCTC 60.381 63.158 0.00 0.00 0.00 3.71
933 4666 1.381599 CTCCCTGCTCTGCTCTCCT 60.382 63.158 0.00 0.00 0.00 3.69
1012 4753 3.064987 GCTTGCTGCCATGGCTCTG 62.065 63.158 35.53 25.08 42.51 3.35
1036 4777 2.225624 TGATCCTTCCTCTTCCTGACCA 60.226 50.000 0.00 0.00 0.00 4.02
1089 4836 0.301687 CGCAACGCTGGATGATGTAC 59.698 55.000 0.00 0.00 0.00 2.90
1104 4851 1.446099 GAGGAGCATGACGACGCAA 60.446 57.895 0.00 0.00 0.00 4.85
1144 4891 5.424121 AGCTACAAATGAGAACACAACAC 57.576 39.130 0.00 0.00 0.00 3.32
1145 4892 5.700832 CCTAGCTACAAATGAGAACACAACA 59.299 40.000 0.00 0.00 0.00 3.33
1149 4904 4.508662 AGCCTAGCTACAAATGAGAACAC 58.491 43.478 0.00 0.00 36.99 3.32
1176 4947 5.991606 CACCAAAGAATCTGTCAAGTACTCA 59.008 40.000 0.00 0.00 0.00 3.41
1178 4949 5.760253 CACACCAAAGAATCTGTCAAGTACT 59.240 40.000 0.00 0.00 0.00 2.73
1179 4950 5.527582 ACACACCAAAGAATCTGTCAAGTAC 59.472 40.000 0.00 0.00 0.00 2.73
1242 5030 5.047188 CCAAAACTAACCGTCAGCAAAATT 58.953 37.500 0.00 0.00 0.00 1.82
1281 5070 0.036388 AGGAGCACCACATTACACCG 60.036 55.000 2.07 0.00 38.94 4.94
1406 5205 8.687824 TTTCTGAGAAATTTCACACTGTTTTC 57.312 30.769 19.99 6.21 0.00 2.29
1411 5210 6.382869 ACCTTTCTGAGAAATTTCACACTG 57.617 37.500 19.99 13.43 0.00 3.66
1421 5220 5.940470 GCCAAGAGATAACCTTTCTGAGAAA 59.060 40.000 7.49 7.49 0.00 2.52
1583 5384 6.233905 TGAGATAGCCTTGTGTGCTAAATA 57.766 37.500 0.00 0.00 43.96 1.40
1630 5445 3.884581 TTTCACCTCGACGTCGCCG 62.885 63.158 32.19 24.57 39.60 6.46
1636 5451 3.110178 GCCGGTTTCACCTCGACG 61.110 66.667 1.90 0.00 35.66 5.12
1637 5452 1.566018 CTTGCCGGTTTCACCTCGAC 61.566 60.000 1.90 0.00 35.66 4.20
1650 5465 1.703438 GATGCAGACTGCTCTTGCCG 61.703 60.000 26.94 0.00 45.31 5.69
1750 5570 3.088044 GCTGTCAGCATCAGCGAC 58.912 61.111 20.16 0.00 46.39 5.19
1792 5612 9.194271 GTTCTAAGTTCTAAGTTGAGGTTACTG 57.806 37.037 0.00 0.00 0.00 2.74
1821 5641 3.106738 GGGAATCCCATGAGCACTG 57.893 57.895 14.67 0.00 44.65 3.66
1981 5816 3.414700 CGTCCAGTGCTGTTCGGC 61.415 66.667 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.