Multiple sequence alignment - TraesCS3D01G167700

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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 TraesCS3D01G167700 chr3D 100.000 3622 0 0 1 3622 141779050 141782671 0.000000e+00 6689.0
1 TraesCS3D01G167700 chr3D 86.471 510 56 7 2574 3074 141789270 141789775 6.840000e-152 547.0
2 TraesCS3D01G167700 chr3D 97.895 190 4 0 3093 3282 141786947 141787136 2.700000e-86 329.0
3 TraesCS3D01G167700 chr3A 90.833 2618 120 50 316 2870 160506265 160508825 0.000000e+00 3395.0
4 TraesCS3D01G167700 chr3A 88.489 139 13 2 3484 3622 701759096 701758961 8.050000e-37 165.0
5 TraesCS3D01G167700 chr3B 88.420 2841 167 74 303 3077 203871347 203874091 0.000000e+00 3275.0
6 TraesCS3D01G167700 chr3B 90.909 209 18 1 2 210 106701162 106701369 2.750000e-71 279.0
7 TraesCS3D01G167700 chr3B 90.909 209 18 1 2 210 536901269 536901062 2.750000e-71 279.0
8 TraesCS3D01G167700 chr5D 97.358 530 13 1 3093 3622 483514872 483514344 0.000000e+00 900.0
9 TraesCS3D01G167700 chr5D 93.909 197 8 1 3093 3285 483497462 483497266 9.840000e-76 294.0
10 TraesCS3D01G167700 chr7D 95.857 531 20 2 3092 3622 58935947 58935419 0.000000e+00 857.0
11 TraesCS3D01G167700 chr7D 96.842 190 6 0 3096 3285 58931039 58930850 5.840000e-83 318.0
12 TraesCS3D01G167700 chr7D 95.876 194 8 0 3093 3286 3189662 3189469 7.550000e-82 315.0
13 TraesCS3D01G167700 chr5A 91.388 209 17 1 2 210 704867035 704867242 5.920000e-73 285.0
14 TraesCS3D01G167700 chr5A 90.909 209 18 1 2 210 139481464 139481257 2.750000e-71 279.0
15 TraesCS3D01G167700 chr5A 97.436 39 1 0 2040 2078 636598865 636598827 2.330000e-07 67.6
16 TraesCS3D01G167700 chrUn 90.909 209 18 1 2 210 287542494 287542701 2.750000e-71 279.0
17 TraesCS3D01G167700 chrUn 90.385 208 19 1 2 209 404649309 404649515 4.610000e-69 272.0
18 TraesCS3D01G167700 chrUn 89.091 55 5 1 210 263 50087477 50087531 2.330000e-07 67.6
19 TraesCS3D01G167700 chrUn 95.349 43 1 1 222 263 50119882 50119840 2.330000e-07 67.6
20 TraesCS3D01G167700 chr6A 90.909 209 18 1 2 210 57972790 57972583 2.750000e-71 279.0
21 TraesCS3D01G167700 chr1B 90.909 209 18 1 2 210 371440263 371440056 2.750000e-71 279.0
22 TraesCS3D01G167700 chr4D 90.476 210 19 1 1 210 62483512 62483720 3.560000e-70 276.0
23 TraesCS3D01G167700 chr4A 89.062 128 14 0 3495 3622 309205189 309205062 3.740000e-35 159.0
24 TraesCS3D01G167700 chr4A 93.878 49 3 0 216 264 710017863 710017911 1.390000e-09 75.0
25 TraesCS3D01G167700 chr5B 92.593 54 4 0 210 263 543222941 543222994 1.080000e-10 78.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G167700 chr3D 141779050 141782671 3621 False 6689 6689 100.000 1 3622 1 chr3D.!!$F1 3621
1 TraesCS3D01G167700 chr3D 141786947 141789775 2828 False 438 547 92.183 2574 3282 2 chr3D.!!$F2 708
2 TraesCS3D01G167700 chr3A 160506265 160508825 2560 False 3395 3395 90.833 316 2870 1 chr3A.!!$F1 2554
3 TraesCS3D01G167700 chr3B 203871347 203874091 2744 False 3275 3275 88.420 303 3077 1 chr3B.!!$F2 2774
4 TraesCS3D01G167700 chr5D 483514344 483514872 528 True 900 900 97.358 3093 3622 1 chr5D.!!$R2 529
5 TraesCS3D01G167700 chr7D 58935419 58935947 528 True 857 857 95.857 3092 3622 1 chr7D.!!$R3 530

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
142 143 0.168788 CGCCTACGGTGACTTCGTAA 59.831 55.000 0.00 0.0 41.62 3.18 F
183 184 0.251386 TCAGTCTCTCGGAGGTGCTT 60.251 55.000 4.96 0.0 0.00 3.91 F
715 746 0.392461 GATACAACAAGGGCAGGCGA 60.392 55.000 0.00 0.0 0.00 5.54 F
1009 1059 1.150081 CAGATCACCATGGGCTCCC 59.850 63.158 18.09 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1472 1528 0.031449 GAGTCATAGGCTCCACTCGC 59.969 60.000 0.0 0.0 0.0 5.03 R
1520 1599 1.520174 CAGTCATTGATAGTGCGAGCG 59.480 52.381 0.0 0.0 0.0 5.03 R
2499 2586 0.384230 CAACGCACACACACGAATCC 60.384 55.000 0.0 0.0 0.0 3.01 R
2943 3063 0.390603 CTCCCGCATCACCGTTTACA 60.391 55.000 0.0 0.0 0.0 2.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.305314 GGGACAGTGGTATCGCCA 58.695 61.111 0.00 0.00 46.95 5.69
24 25 3.792736 TGGTATCGCCAGCCCACC 61.793 66.667 0.00 0.00 43.61 4.61
25 26 3.792736 GGTATCGCCAGCCCACCA 61.793 66.667 0.00 0.00 37.17 4.17
26 27 2.203070 GTATCGCCAGCCCACCAG 60.203 66.667 0.00 0.00 0.00 4.00
27 28 3.479203 TATCGCCAGCCCACCAGG 61.479 66.667 0.00 0.00 39.47 4.45
43 44 0.890996 CAGGGTTCAAGTCCTGGTGC 60.891 60.000 0.00 0.00 44.99 5.01
44 45 1.062488 AGGGTTCAAGTCCTGGTGCT 61.062 55.000 0.00 0.00 31.11 4.40
45 46 0.606673 GGGTTCAAGTCCTGGTGCTC 60.607 60.000 0.00 0.00 0.00 4.26
46 47 0.951040 GGTTCAAGTCCTGGTGCTCG 60.951 60.000 0.00 0.00 0.00 5.03
48 49 2.031012 CAAGTCCTGGTGCTCGCA 59.969 61.111 0.00 0.00 0.00 5.10
49 50 1.376424 CAAGTCCTGGTGCTCGCAT 60.376 57.895 0.00 0.00 0.00 4.73
50 51 0.957395 CAAGTCCTGGTGCTCGCATT 60.957 55.000 0.00 0.00 0.00 3.56
52 53 0.833287 AGTCCTGGTGCTCGCATTAT 59.167 50.000 0.00 0.00 0.00 1.28
53 54 1.210478 AGTCCTGGTGCTCGCATTATT 59.790 47.619 0.00 0.00 0.00 1.40
54 55 2.017049 GTCCTGGTGCTCGCATTATTT 58.983 47.619 0.00 0.00 0.00 1.40
55 56 2.032178 GTCCTGGTGCTCGCATTATTTC 59.968 50.000 0.00 0.00 0.00 2.17
56 57 2.092968 TCCTGGTGCTCGCATTATTTCT 60.093 45.455 0.00 0.00 0.00 2.52
57 58 2.032550 CCTGGTGCTCGCATTATTTCTG 59.967 50.000 0.00 0.00 0.00 3.02
59 60 2.288666 GGTGCTCGCATTATTTCTGGA 58.711 47.619 0.00 0.00 0.00 3.86
60 61 2.880890 GGTGCTCGCATTATTTCTGGAT 59.119 45.455 0.00 0.00 0.00 3.41
61 62 3.316308 GGTGCTCGCATTATTTCTGGATT 59.684 43.478 0.00 0.00 0.00 3.01
62 63 4.202050 GGTGCTCGCATTATTTCTGGATTT 60.202 41.667 0.00 0.00 0.00 2.17
63 64 5.008613 GGTGCTCGCATTATTTCTGGATTTA 59.991 40.000 0.00 0.00 0.00 1.40
64 65 6.294176 GGTGCTCGCATTATTTCTGGATTTAT 60.294 38.462 0.00 0.00 0.00 1.40
66 67 7.649306 GTGCTCGCATTATTTCTGGATTTATTT 59.351 33.333 0.00 0.00 0.00 1.40
67 68 7.862372 TGCTCGCATTATTTCTGGATTTATTTC 59.138 33.333 0.00 0.00 0.00 2.17
68 69 7.862372 GCTCGCATTATTTCTGGATTTATTTCA 59.138 33.333 0.00 0.00 0.00 2.69
69 70 9.390795 CTCGCATTATTTCTGGATTTATTTCAG 57.609 33.333 0.00 0.00 0.00 3.02
70 71 8.352201 TCGCATTATTTCTGGATTTATTTCAGG 58.648 33.333 0.00 0.00 0.00 3.86
71 72 8.352201 CGCATTATTTCTGGATTTATTTCAGGA 58.648 33.333 0.00 0.00 0.00 3.86
77 78 9.807649 ATTTCTGGATTTATTTCAGGATTTTCG 57.192 29.630 0.00 0.00 0.00 3.46
78 79 8.574251 TTCTGGATTTATTTCAGGATTTTCGA 57.426 30.769 0.00 0.00 0.00 3.71
79 80 7.985476 TCTGGATTTATTTCAGGATTTTCGAC 58.015 34.615 0.00 0.00 0.00 4.20
81 82 6.596106 TGGATTTATTTCAGGATTTTCGACGA 59.404 34.615 0.00 0.00 0.00 4.20
82 83 7.282224 TGGATTTATTTCAGGATTTTCGACGAT 59.718 33.333 0.00 0.00 0.00 3.73
83 84 7.587757 GGATTTATTTCAGGATTTTCGACGATG 59.412 37.037 0.00 0.00 0.00 3.84
85 86 2.378445 TCAGGATTTTCGACGATGCA 57.622 45.000 0.00 0.00 0.00 3.96
86 87 1.999735 TCAGGATTTTCGACGATGCAC 59.000 47.619 0.00 0.00 0.00 4.57
89 90 3.074412 AGGATTTTCGACGATGCACTTT 58.926 40.909 0.00 0.00 0.00 2.66
91 92 3.120338 GGATTTTCGACGATGCACTTTCA 60.120 43.478 0.00 0.00 0.00 2.69
92 93 3.519908 TTTTCGACGATGCACTTTCAG 57.480 42.857 0.00 0.00 0.00 3.02
93 94 2.148916 TTCGACGATGCACTTTCAGT 57.851 45.000 0.00 0.00 0.00 3.41
96 97 0.716108 GACGATGCACTTTCAGTCGG 59.284 55.000 8.33 0.00 36.68 4.79
97 98 0.317160 ACGATGCACTTTCAGTCGGA 59.683 50.000 8.33 0.00 36.68 4.55
98 99 0.994995 CGATGCACTTTCAGTCGGAG 59.005 55.000 0.00 0.00 0.00 4.63
99 100 1.363744 GATGCACTTTCAGTCGGAGG 58.636 55.000 0.00 0.00 0.00 4.30
100 101 0.976641 ATGCACTTTCAGTCGGAGGA 59.023 50.000 0.00 0.00 0.00 3.71
101 102 0.318441 TGCACTTTCAGTCGGAGGAG 59.682 55.000 0.00 0.00 0.00 3.69
102 103 0.603569 GCACTTTCAGTCGGAGGAGA 59.396 55.000 0.00 0.00 0.00 3.71
104 105 2.886081 CACTTTCAGTCGGAGGAGATG 58.114 52.381 0.00 0.00 0.00 2.90
106 107 2.900546 ACTTTCAGTCGGAGGAGATGTT 59.099 45.455 0.00 0.00 0.00 2.71
107 108 3.056465 ACTTTCAGTCGGAGGAGATGTTC 60.056 47.826 0.00 0.00 0.00 3.18
108 109 2.516227 TCAGTCGGAGGAGATGTTCT 57.484 50.000 0.00 0.00 0.00 3.01
109 110 2.370349 TCAGTCGGAGGAGATGTTCTC 58.630 52.381 0.00 0.00 42.66 2.87
110 111 1.064803 CAGTCGGAGGAGATGTTCTCG 59.935 57.143 0.00 0.00 44.28 4.04
111 112 1.096416 GTCGGAGGAGATGTTCTCGT 58.904 55.000 0.00 0.00 44.28 4.18
115 116 2.461897 GAGGAGATGTTCTCGTCGAC 57.538 55.000 5.18 5.18 44.90 4.20
116 117 0.727970 AGGAGATGTTCTCGTCGACG 59.272 55.000 31.30 31.30 44.28 5.12
117 118 0.725686 GGAGATGTTCTCGTCGACGA 59.274 55.000 35.66 35.66 44.28 4.20
130 131 4.883300 GACGACGAGGCGCCTACG 62.883 72.222 32.91 32.91 44.07 3.51
135 136 4.849329 CGAGGCGCCTACGGTGAC 62.849 72.222 32.97 14.51 42.50 3.67
138 139 2.508663 GGCGCCTACGGTGACTTC 60.509 66.667 22.15 0.00 38.38 3.01
139 140 2.879462 GCGCCTACGGTGACTTCG 60.879 66.667 0.00 0.00 40.57 3.79
142 143 0.168788 CGCCTACGGTGACTTCGTAA 59.831 55.000 0.00 0.00 41.62 3.18
145 146 2.856557 GCCTACGGTGACTTCGTAAATC 59.143 50.000 0.00 0.00 41.62 2.17
147 148 4.349501 CCTACGGTGACTTCGTAAATCTC 58.650 47.826 0.00 0.00 41.62 2.75
148 149 3.928727 ACGGTGACTTCGTAAATCTCA 57.071 42.857 0.00 0.00 39.22 3.27
150 151 4.235360 ACGGTGACTTCGTAAATCTCAAG 58.765 43.478 0.00 0.00 39.22 3.02
151 152 4.022589 ACGGTGACTTCGTAAATCTCAAGA 60.023 41.667 0.00 0.00 39.22 3.02
154 155 6.100004 GGTGACTTCGTAAATCTCAAGATGA 58.900 40.000 0.00 0.00 34.49 2.92
155 156 6.758886 GGTGACTTCGTAAATCTCAAGATGAT 59.241 38.462 0.00 0.00 34.49 2.45
156 157 7.921214 GGTGACTTCGTAAATCTCAAGATGATA 59.079 37.037 0.00 0.00 34.49 2.15
157 158 9.469807 GTGACTTCGTAAATCTCAAGATGATAT 57.530 33.333 0.00 0.00 34.49 1.63
158 159 9.468532 TGACTTCGTAAATCTCAAGATGATATG 57.531 33.333 0.00 0.00 34.49 1.78
159 160 9.469807 GACTTCGTAAATCTCAAGATGATATGT 57.530 33.333 0.00 0.00 34.49 2.29
169 170 9.979578 ATCTCAAGATGATATGTTAACTCAGTC 57.020 33.333 7.22 1.18 32.68 3.51
170 171 9.194972 TCTCAAGATGATATGTTAACTCAGTCT 57.805 33.333 7.22 5.22 0.00 3.24
172 173 9.194972 TCAAGATGATATGTTAACTCAGTCTCT 57.805 33.333 7.22 0.49 0.00 3.10
173 174 9.462174 CAAGATGATATGTTAACTCAGTCTCTC 57.538 37.037 7.22 0.00 0.00 3.20
174 175 7.870826 AGATGATATGTTAACTCAGTCTCTCG 58.129 38.462 7.22 0.00 0.00 4.04
177 178 4.974368 ATGTTAACTCAGTCTCTCGGAG 57.026 45.455 7.22 0.00 42.53 4.63
178 179 3.082548 TGTTAACTCAGTCTCTCGGAGG 58.917 50.000 7.22 0.00 41.46 4.30
180 181 1.540267 AACTCAGTCTCTCGGAGGTG 58.460 55.000 4.96 0.00 41.46 4.00
182 183 0.679640 CTCAGTCTCTCGGAGGTGCT 60.680 60.000 4.96 0.00 35.32 4.40
183 184 0.251386 TCAGTCTCTCGGAGGTGCTT 60.251 55.000 4.96 0.00 0.00 3.91
184 185 1.004394 TCAGTCTCTCGGAGGTGCTTA 59.996 52.381 4.96 0.00 0.00 3.09
186 187 3.118000 TCAGTCTCTCGGAGGTGCTTATA 60.118 47.826 4.96 0.00 0.00 0.98
187 188 3.252215 CAGTCTCTCGGAGGTGCTTATAG 59.748 52.174 4.96 0.00 0.00 1.31
188 189 2.554893 GTCTCTCGGAGGTGCTTATAGG 59.445 54.545 4.96 0.00 0.00 2.57
189 190 1.889829 CTCTCGGAGGTGCTTATAGGG 59.110 57.143 4.96 0.00 0.00 3.53
191 192 2.110188 TCTCGGAGGTGCTTATAGGGAT 59.890 50.000 4.96 0.00 0.00 3.85
192 193 3.332783 TCTCGGAGGTGCTTATAGGGATA 59.667 47.826 4.96 0.00 0.00 2.59
193 194 3.697045 CTCGGAGGTGCTTATAGGGATAG 59.303 52.174 0.00 0.00 0.00 2.08
194 195 2.761208 CGGAGGTGCTTATAGGGATAGG 59.239 54.545 0.00 0.00 0.00 2.57
195 196 2.502130 GGAGGTGCTTATAGGGATAGGC 59.498 54.545 0.00 0.00 40.25 3.93
196 197 2.166664 GAGGTGCTTATAGGGATAGGCG 59.833 54.545 0.00 0.00 42.19 5.52
197 198 1.405661 GGTGCTTATAGGGATAGGCGC 60.406 57.143 0.00 0.00 45.61 6.53
198 199 1.550976 GTGCTTATAGGGATAGGCGCT 59.449 52.381 7.64 0.00 43.94 5.92
199 200 2.028020 GTGCTTATAGGGATAGGCGCTT 60.028 50.000 7.64 0.52 43.94 4.68
200 201 2.028112 TGCTTATAGGGATAGGCGCTTG 60.028 50.000 7.64 0.00 42.19 4.01
202 203 0.530744 TATAGGGATAGGCGCTTGCG 59.469 55.000 7.64 10.90 40.66 4.85
206 207 2.240500 GGATAGGCGCTTGCGTCTG 61.241 63.158 28.68 0.00 40.46 3.51
207 208 1.519455 GATAGGCGCTTGCGTCTGT 60.519 57.895 28.68 23.46 40.46 3.41
208 209 1.756375 GATAGGCGCTTGCGTCTGTG 61.756 60.000 28.68 0.00 40.46 3.66
211 212 3.112075 GCGCTTGCGTCTGTGCTA 61.112 61.111 16.38 0.00 36.83 3.49
212 213 2.456119 GCGCTTGCGTCTGTGCTAT 61.456 57.895 16.38 0.00 36.83 2.97
216 217 1.926561 CTTGCGTCTGTGCTATGCTA 58.073 50.000 0.00 0.00 35.36 3.49
217 218 2.270923 CTTGCGTCTGTGCTATGCTAA 58.729 47.619 0.00 0.00 35.36 3.09
218 219 2.378445 TGCGTCTGTGCTATGCTAAA 57.622 45.000 0.00 0.00 35.36 1.85
219 220 2.694213 TGCGTCTGTGCTATGCTAAAA 58.306 42.857 0.00 0.00 35.36 1.52
220 221 3.070748 TGCGTCTGTGCTATGCTAAAAA 58.929 40.909 0.00 0.00 35.36 1.94
247 248 9.289303 ACATGATTGTTATTGAATAAAAGTCGC 57.711 29.630 0.00 0.00 29.55 5.19
249 250 8.050778 TGATTGTTATTGAATAAAAGTCGCCT 57.949 30.769 0.00 0.00 0.00 5.52
251 252 9.997482 GATTGTTATTGAATAAAAGTCGCCTTA 57.003 29.630 0.00 0.00 0.00 2.69
257 258 7.915293 TTGAATAAAAGTCGCCTTAATCTCA 57.085 32.000 0.00 0.00 0.00 3.27
259 260 8.330466 TGAATAAAAGTCGCCTTAATCTCAAA 57.670 30.769 0.00 0.00 0.00 2.69
260 261 8.788806 TGAATAAAAGTCGCCTTAATCTCAAAA 58.211 29.630 0.00 0.00 0.00 2.44
261 262 9.620660 GAATAAAAGTCGCCTTAATCTCAAAAA 57.379 29.630 0.00 0.00 0.00 1.94
292 293 2.567169 CTCCAGTTACCACTCACCATCA 59.433 50.000 0.00 0.00 0.00 3.07
293 294 2.976185 TCCAGTTACCACTCACCATCAA 59.024 45.455 0.00 0.00 0.00 2.57
294 295 3.587061 TCCAGTTACCACTCACCATCAAT 59.413 43.478 0.00 0.00 0.00 2.57
295 296 3.941483 CCAGTTACCACTCACCATCAATC 59.059 47.826 0.00 0.00 0.00 2.67
299 300 1.004745 ACCACTCACCATCAATCCCAC 59.995 52.381 0.00 0.00 0.00 4.61
300 301 1.004628 CCACTCACCATCAATCCCACA 59.995 52.381 0.00 0.00 0.00 4.17
301 302 2.086869 CACTCACCATCAATCCCACAC 58.913 52.381 0.00 0.00 0.00 3.82
323 324 1.235724 CGTGGAAAAACCTGAGGACC 58.764 55.000 4.99 1.06 39.86 4.46
333 338 0.995024 CCTGAGGACCTGGTTTCCAT 59.005 55.000 0.00 0.00 35.33 3.41
339 344 2.572104 AGGACCTGGTTTCCATGTCTAC 59.428 50.000 18.33 7.73 44.67 2.59
340 345 2.572104 GGACCTGGTTTCCATGTCTACT 59.428 50.000 18.33 0.00 44.67 2.57
343 348 5.453480 GGACCTGGTTTCCATGTCTACTATC 60.453 48.000 18.33 3.51 44.67 2.08
345 350 4.656112 CCTGGTTTCCATGTCTACTATCCT 59.344 45.833 0.00 0.00 30.82 3.24
346 351 5.453903 CCTGGTTTCCATGTCTACTATCCTG 60.454 48.000 0.00 0.00 30.82 3.86
347 352 5.030147 TGGTTTCCATGTCTACTATCCTGT 58.970 41.667 0.00 0.00 0.00 4.00
363 368 0.959553 CTGTACCGGTATCCGCATCT 59.040 55.000 19.19 0.00 46.86 2.90
398 403 4.564116 CGCCGCCTACCACTACCG 62.564 72.222 0.00 0.00 0.00 4.02
401 406 2.493030 CGCCTACCACTACCGGTG 59.507 66.667 19.93 10.05 44.96 4.94
405 410 1.153628 CTACCACTACCGGTGCAGC 60.154 63.158 19.93 5.64 44.08 5.25
431 440 1.228063 ATCCATCCATGCTCCACGC 60.228 57.895 0.00 0.00 39.77 5.34
432 441 1.703014 ATCCATCCATGCTCCACGCT 61.703 55.000 0.00 0.00 40.11 5.07
434 443 1.890979 CATCCATGCTCCACGCTCC 60.891 63.158 0.00 0.00 40.11 4.70
435 444 2.369633 ATCCATGCTCCACGCTCCA 61.370 57.895 0.00 0.00 40.11 3.86
436 445 2.599645 ATCCATGCTCCACGCTCCAC 62.600 60.000 0.00 0.00 40.11 4.02
531 540 1.588082 GAGTGGGCCGTCGTTTCTA 59.412 57.895 0.00 0.00 0.00 2.10
715 746 0.392461 GATACAACAAGGGCAGGCGA 60.392 55.000 0.00 0.00 0.00 5.54
767 800 4.838486 CGCGCTCCGTCTCCACTC 62.838 72.222 5.56 0.00 0.00 3.51
768 801 3.444805 GCGCTCCGTCTCCACTCT 61.445 66.667 0.00 0.00 0.00 3.24
1009 1059 1.150081 CAGATCACCATGGGCTCCC 59.850 63.158 18.09 0.00 0.00 4.30
1055 1105 3.741476 CCTGAGGTTTGCTGCGCC 61.741 66.667 4.18 0.00 0.00 6.53
1083 1134 1.302949 GTTGGGCTGGCTCATGGTA 59.697 57.895 0.00 0.00 0.00 3.25
1093 1144 3.119319 TGGCTCATGGTATTTCCCTACA 58.881 45.455 0.00 0.00 34.77 2.74
1129 1181 3.253188 TCGATTTGTTTTTGCTCTCAGGG 59.747 43.478 0.00 0.00 0.00 4.45
1136 1188 1.207791 TTTGCTCTCAGGGGAGGATC 58.792 55.000 0.00 0.00 41.69 3.36
1176 1228 1.677217 GGGTGCAGATGTGAGTTCCTC 60.677 57.143 0.00 0.00 0.00 3.71
1181 1233 2.465813 CAGATGTGAGTTCCTCCTCCT 58.534 52.381 0.00 0.00 0.00 3.69
1204 1256 2.414481 CTCCTCAATTTGTGACAGAGCG 59.586 50.000 0.12 0.00 29.23 5.03
1250 1302 1.332997 CTTGATCTGCATCGGCCTTTC 59.667 52.381 0.00 0.00 40.13 2.62
1290 1342 5.493133 TGTCTGACACGCAACTAAAATTT 57.507 34.783 6.36 0.00 0.00 1.82
1291 1343 5.270083 TGTCTGACACGCAACTAAAATTTG 58.730 37.500 6.36 0.00 0.00 2.32
1293 1345 6.142817 GTCTGACACGCAACTAAAATTTGAT 58.857 36.000 2.24 0.00 0.00 2.57
1457 1513 5.697633 CACAAATCTAAATGCAAAACAGCCT 59.302 36.000 0.00 0.00 0.00 4.58
1468 1524 9.586435 AAATGCAAAACAGCCTAAATAATACTC 57.414 29.630 0.00 0.00 0.00 2.59
1470 1526 7.761409 TGCAAAACAGCCTAAATAATACTCAG 58.239 34.615 0.00 0.00 0.00 3.35
1471 1527 7.393234 TGCAAAACAGCCTAAATAATACTCAGT 59.607 33.333 0.00 0.00 0.00 3.41
1472 1528 7.698130 GCAAAACAGCCTAAATAATACTCAGTG 59.302 37.037 0.00 0.00 0.00 3.66
1473 1529 6.927294 AACAGCCTAAATAATACTCAGTGC 57.073 37.500 0.00 0.00 0.00 4.40
1520 1599 3.715618 TGTTTGCGTCGATCAACATAC 57.284 42.857 0.00 1.24 0.00 2.39
1529 1608 1.560923 GATCAACATACGCTCGCACT 58.439 50.000 0.00 0.00 0.00 4.40
1537 1624 3.243401 ACATACGCTCGCACTATCAATGA 60.243 43.478 0.00 0.00 0.00 2.57
1639 1726 4.760047 TCGAGCTTCTTGGGCGGC 62.760 66.667 0.00 0.00 34.52 6.53
1643 1730 3.880846 GCTTCTTGGGCGGCATCG 61.881 66.667 12.47 0.00 39.81 3.84
1765 1852 2.485582 CTCGACACGCACCTCGAT 59.514 61.111 0.00 0.00 38.22 3.59
2227 2314 1.880340 CGACAAGATCCTCAGCGGC 60.880 63.158 0.00 0.00 0.00 6.53
2467 2554 1.873572 GGAACGAATTGGCATGCGC 60.874 57.895 12.44 0.00 34.29 6.09
2482 2569 2.514592 CGCCCATGGATCGTTGCT 60.515 61.111 15.22 0.00 0.00 3.91
2497 2584 4.363999 TCGTTGCTTTTGGTTGGTTAATG 58.636 39.130 0.00 0.00 0.00 1.90
2498 2585 4.098044 TCGTTGCTTTTGGTTGGTTAATGA 59.902 37.500 0.00 0.00 0.00 2.57
2499 2586 4.444056 CGTTGCTTTTGGTTGGTTAATGAG 59.556 41.667 0.00 0.00 0.00 2.90
2501 2588 4.219115 TGCTTTTGGTTGGTTAATGAGGA 58.781 39.130 0.00 0.00 0.00 3.71
2745 2840 5.517411 CGTACTGTTTGTCACTTGACTTGTA 59.483 40.000 10.63 4.41 44.99 2.41
2747 2842 6.422776 ACTGTTTGTCACTTGACTTGTAAG 57.577 37.500 10.63 4.98 44.99 2.34
2748 2843 5.938125 ACTGTTTGTCACTTGACTTGTAAGT 59.062 36.000 10.63 0.00 44.99 2.24
2791 2895 1.592669 GCCGGATGGATGACTCACG 60.593 63.158 5.05 0.00 37.49 4.35
2854 2969 3.216800 AGAAATGATACACATGCGGCAT 58.783 40.909 10.23 10.23 39.39 4.40
2883 2998 3.194116 ACGGGTTAACGAAGATGCTTAGA 59.806 43.478 0.00 0.00 37.61 2.10
2930 3050 2.494471 AGGACATCGTATTTGTGACCGA 59.506 45.455 0.00 0.00 33.81 4.69
2937 3057 2.858344 CGTATTTGTGACCGATGAGGAC 59.142 50.000 0.00 0.00 45.00 3.85
2943 3063 1.482593 GTGACCGATGAGGACCAATCT 59.517 52.381 0.00 0.00 45.00 2.40
2945 3065 1.482593 GACCGATGAGGACCAATCTGT 59.517 52.381 0.00 0.00 45.00 3.41
2948 3068 3.517901 ACCGATGAGGACCAATCTGTAAA 59.482 43.478 0.00 0.00 45.00 2.01
2981 3101 1.383456 GCCGGCCATTCAACTGCATA 61.383 55.000 18.11 0.00 0.00 3.14
2990 3110 5.626543 GCCATTCAACTGCATATCATAAACG 59.373 40.000 0.00 0.00 0.00 3.60
3000 3120 4.963953 GCATATCATAAACGTTCACACAGC 59.036 41.667 0.00 0.00 0.00 4.40
3004 3124 1.493772 TAAACGTTCACACAGCTCCG 58.506 50.000 0.00 0.00 0.00 4.63
3013 3133 4.200838 TCACACAGCTCCGATCAATTTA 57.799 40.909 0.00 0.00 0.00 1.40
3050 3170 3.992643 TCGTCCGATTACAACCAAAAGA 58.007 40.909 0.00 0.00 0.00 2.52
3052 3172 4.815308 TCGTCCGATTACAACCAAAAGAAA 59.185 37.500 0.00 0.00 0.00 2.52
3057 3177 7.275999 GTCCGATTACAACCAAAAGAAAACAAA 59.724 33.333 0.00 0.00 0.00 2.83
3078 3198 8.687824 ACAAATATGCAGTGTATACTTTTTGC 57.312 30.769 18.16 8.97 34.07 3.68
3079 3199 7.759433 ACAAATATGCAGTGTATACTTTTTGCC 59.241 33.333 18.16 0.00 34.07 4.52
3080 3200 4.718940 ATGCAGTGTATACTTTTTGCCC 57.281 40.909 4.17 0.00 34.07 5.36
3081 3201 2.486203 TGCAGTGTATACTTTTTGCCCG 59.514 45.455 4.17 0.00 34.07 6.13
3082 3202 2.745281 GCAGTGTATACTTTTTGCCCGA 59.255 45.455 4.17 0.00 34.07 5.14
3083 3203 3.377172 GCAGTGTATACTTTTTGCCCGAT 59.623 43.478 4.17 0.00 34.07 4.18
3084 3204 4.495844 GCAGTGTATACTTTTTGCCCGATC 60.496 45.833 4.17 0.00 34.07 3.69
3085 3205 4.876107 CAGTGTATACTTTTTGCCCGATCT 59.124 41.667 4.17 0.00 34.07 2.75
3086 3206 5.006746 CAGTGTATACTTTTTGCCCGATCTC 59.993 44.000 4.17 0.00 34.07 2.75
3087 3207 4.272748 GTGTATACTTTTTGCCCGATCTCC 59.727 45.833 4.17 0.00 0.00 3.71
3088 3208 3.644966 ATACTTTTTGCCCGATCTCCA 57.355 42.857 0.00 0.00 0.00 3.86
3089 3209 2.286365 ACTTTTTGCCCGATCTCCAA 57.714 45.000 0.00 0.00 0.00 3.53
3090 3210 2.593026 ACTTTTTGCCCGATCTCCAAA 58.407 42.857 0.00 0.00 0.00 3.28
3257 3377 5.801350 ATGTGTAACTGTGTGTATGATGC 57.199 39.130 0.00 0.00 38.04 3.91
3288 3408 4.278419 GTGAATTACACCTTTCAGCTTGGT 59.722 41.667 0.00 0.00 43.05 3.67
3445 3566 3.399046 CCCCCTTCGACCATGACA 58.601 61.111 0.00 0.00 0.00 3.58
3449 3570 0.608130 CCCTTCGACCATGACAGTGA 59.392 55.000 0.00 0.00 0.00 3.41
3451 3572 2.544685 CCTTCGACCATGACAGTGATC 58.455 52.381 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.144057 CTGGCGATACCACTGTCCC 59.856 63.158 0.00 0.00 46.36 4.46
2 3 1.521681 GGCTGGCGATACCACTGTC 60.522 63.158 0.00 0.00 46.36 3.51
3 4 2.584608 GGCTGGCGATACCACTGT 59.415 61.111 0.00 0.00 46.36 3.55
4 5 2.203070 GGGCTGGCGATACCACTG 60.203 66.667 0.00 0.00 46.36 3.66
5 6 2.687200 TGGGCTGGCGATACCACT 60.687 61.111 0.00 0.00 46.36 4.00
6 7 2.513897 GTGGGCTGGCGATACCAC 60.514 66.667 6.28 6.28 46.36 4.16
9 10 2.203070 CTGGTGGGCTGGCGATAC 60.203 66.667 0.00 0.00 0.00 2.24
10 11 3.479203 CCTGGTGGGCTGGCGATA 61.479 66.667 0.00 0.00 0.00 2.92
20 21 0.250901 CAGGACTTGAACCCTGGTGG 60.251 60.000 0.00 0.00 44.68 4.61
25 26 1.062488 AGCACCAGGACTTGAACCCT 61.062 55.000 0.00 0.00 0.00 4.34
26 27 0.606673 GAGCACCAGGACTTGAACCC 60.607 60.000 0.00 0.00 0.00 4.11
27 28 0.951040 CGAGCACCAGGACTTGAACC 60.951 60.000 0.00 0.00 0.00 3.62
29 30 1.301716 GCGAGCACCAGGACTTGAA 60.302 57.895 0.00 0.00 0.00 2.69
30 31 1.830587 ATGCGAGCACCAGGACTTGA 61.831 55.000 0.00 0.00 0.00 3.02
32 33 0.613260 TAATGCGAGCACCAGGACTT 59.387 50.000 0.00 0.00 0.00 3.01
39 40 2.288666 TCCAGAAATAATGCGAGCACC 58.711 47.619 0.00 0.00 0.00 5.01
40 41 4.558538 AATCCAGAAATAATGCGAGCAC 57.441 40.909 0.00 0.00 0.00 4.40
41 42 6.882610 ATAAATCCAGAAATAATGCGAGCA 57.117 33.333 0.00 0.00 0.00 4.26
43 44 9.390795 CTGAAATAAATCCAGAAATAATGCGAG 57.609 33.333 0.00 0.00 0.00 5.03
44 45 8.352201 CCTGAAATAAATCCAGAAATAATGCGA 58.648 33.333 0.00 0.00 0.00 5.10
45 46 8.352201 TCCTGAAATAAATCCAGAAATAATGCG 58.648 33.333 0.00 0.00 0.00 4.73
52 53 9.019656 TCGAAAATCCTGAAATAAATCCAGAAA 57.980 29.630 0.00 0.00 0.00 2.52
53 54 8.458843 GTCGAAAATCCTGAAATAAATCCAGAA 58.541 33.333 0.00 0.00 0.00 3.02
54 55 7.201609 CGTCGAAAATCCTGAAATAAATCCAGA 60.202 37.037 0.00 0.00 0.00 3.86
55 56 6.907212 CGTCGAAAATCCTGAAATAAATCCAG 59.093 38.462 0.00 0.00 0.00 3.86
56 57 6.596106 TCGTCGAAAATCCTGAAATAAATCCA 59.404 34.615 0.00 0.00 0.00 3.41
57 58 7.011828 TCGTCGAAAATCCTGAAATAAATCC 57.988 36.000 0.00 0.00 0.00 3.01
59 60 6.912591 GCATCGTCGAAAATCCTGAAATAAAT 59.087 34.615 0.00 0.00 0.00 1.40
60 61 6.128145 TGCATCGTCGAAAATCCTGAAATAAA 60.128 34.615 0.00 0.00 0.00 1.40
61 62 5.352846 TGCATCGTCGAAAATCCTGAAATAA 59.647 36.000 0.00 0.00 0.00 1.40
62 63 4.873259 TGCATCGTCGAAAATCCTGAAATA 59.127 37.500 0.00 0.00 0.00 1.40
63 64 3.689161 TGCATCGTCGAAAATCCTGAAAT 59.311 39.130 0.00 0.00 0.00 2.17
64 65 3.070748 TGCATCGTCGAAAATCCTGAAA 58.929 40.909 0.00 0.00 0.00 2.69
66 67 1.999735 GTGCATCGTCGAAAATCCTGA 59.000 47.619 0.00 0.00 0.00 3.86
67 68 2.002586 AGTGCATCGTCGAAAATCCTG 58.997 47.619 0.00 0.00 0.00 3.86
68 69 2.386661 AGTGCATCGTCGAAAATCCT 57.613 45.000 0.00 0.00 0.00 3.24
69 70 3.120338 TGAAAGTGCATCGTCGAAAATCC 60.120 43.478 0.00 0.00 0.00 3.01
70 71 4.065423 TGAAAGTGCATCGTCGAAAATC 57.935 40.909 0.00 0.00 0.00 2.17
71 72 4.070581 CTGAAAGTGCATCGTCGAAAAT 57.929 40.909 0.00 0.00 0.00 1.82
72 73 3.519908 CTGAAAGTGCATCGTCGAAAA 57.480 42.857 0.00 0.00 0.00 2.29
85 86 7.067210 GAGAACATCTCCTCCGACTGAAAGT 62.067 48.000 0.00 0.00 43.95 2.66
86 87 3.194542 AGAACATCTCCTCCGACTGAAAG 59.805 47.826 0.00 0.00 42.29 2.62
89 90 2.370349 GAGAACATCTCCTCCGACTGA 58.630 52.381 0.00 0.00 37.55 3.41
91 92 1.340211 ACGAGAACATCTCCTCCGACT 60.340 52.381 1.98 0.00 40.34 4.18
92 93 1.064357 GACGAGAACATCTCCTCCGAC 59.936 57.143 1.98 0.00 40.34 4.79
93 94 1.380524 GACGAGAACATCTCCTCCGA 58.619 55.000 1.98 0.00 40.34 4.55
96 97 1.267632 CGTCGACGAGAACATCTCCTC 60.268 57.143 33.35 0.08 40.34 3.71
97 98 0.727970 CGTCGACGAGAACATCTCCT 59.272 55.000 33.35 0.00 40.34 3.69
98 99 0.725686 TCGTCGACGAGAACATCTCC 59.274 55.000 34.97 0.00 44.22 3.71
112 113 4.883300 GTAGGCGCCTCGTCGTCG 62.883 72.222 36.73 0.00 39.34 5.12
113 114 4.883300 CGTAGGCGCCTCGTCGTC 62.883 72.222 36.73 15.88 36.23 4.20
126 127 4.978186 TGAGATTTACGAAGTCACCGTAG 58.022 43.478 0.00 0.00 43.93 3.51
127 128 5.181811 TCTTGAGATTTACGAAGTCACCGTA 59.818 40.000 0.00 0.00 43.93 4.02
128 129 3.928727 TGAGATTTACGAAGTCACCGT 57.071 42.857 0.00 0.00 43.93 4.83
129 130 4.482386 TCTTGAGATTTACGAAGTCACCG 58.518 43.478 0.00 0.00 43.93 4.94
130 131 6.100004 TCATCTTGAGATTTACGAAGTCACC 58.900 40.000 0.00 0.00 35.39 4.02
131 132 7.763172 ATCATCTTGAGATTTACGAAGTCAC 57.237 36.000 0.00 0.00 35.39 3.67
134 135 9.823647 AACATATCATCTTGAGATTTACGAAGT 57.176 29.630 0.00 0.00 37.29 3.01
145 146 9.462174 GAGACTGAGTTAACATATCATCTTGAG 57.538 37.037 8.61 0.00 0.00 3.02
147 148 9.462174 GAGAGACTGAGTTAACATATCATCTTG 57.538 37.037 8.61 0.00 0.00 3.02
148 149 8.349245 CGAGAGACTGAGTTAACATATCATCTT 58.651 37.037 8.61 0.00 0.00 2.40
150 151 7.041030 TCCGAGAGACTGAGTTAACATATCATC 60.041 40.741 8.61 3.77 0.00 2.92
151 152 6.773200 TCCGAGAGACTGAGTTAACATATCAT 59.227 38.462 8.61 0.00 0.00 2.45
154 155 5.533154 CCTCCGAGAGACTGAGTTAACATAT 59.467 44.000 8.61 0.00 0.00 1.78
155 156 4.882427 CCTCCGAGAGACTGAGTTAACATA 59.118 45.833 8.61 0.00 0.00 2.29
156 157 3.697045 CCTCCGAGAGACTGAGTTAACAT 59.303 47.826 8.61 0.00 0.00 2.71
157 158 3.082548 CCTCCGAGAGACTGAGTTAACA 58.917 50.000 8.61 0.00 0.00 2.41
158 159 3.083293 ACCTCCGAGAGACTGAGTTAAC 58.917 50.000 0.00 0.00 0.00 2.01
159 160 3.082548 CACCTCCGAGAGACTGAGTTAA 58.917 50.000 0.00 0.00 0.00 2.01
161 162 1.540267 CACCTCCGAGAGACTGAGTT 58.460 55.000 0.00 0.00 0.00 3.01
163 164 0.679640 AGCACCTCCGAGAGACTGAG 60.680 60.000 0.00 0.00 0.00 3.35
164 165 0.251386 AAGCACCTCCGAGAGACTGA 60.251 55.000 0.00 0.00 0.00 3.41
167 168 2.554893 CCTATAAGCACCTCCGAGAGAC 59.445 54.545 0.00 0.00 0.00 3.36
168 169 2.489255 CCCTATAAGCACCTCCGAGAGA 60.489 54.545 0.00 0.00 0.00 3.10
169 170 1.889829 CCCTATAAGCACCTCCGAGAG 59.110 57.143 0.00 0.00 0.00 3.20
170 171 1.497716 TCCCTATAAGCACCTCCGAGA 59.502 52.381 0.00 0.00 0.00 4.04
172 173 2.696526 ATCCCTATAAGCACCTCCGA 57.303 50.000 0.00 0.00 0.00 4.55
173 174 2.761208 CCTATCCCTATAAGCACCTCCG 59.239 54.545 0.00 0.00 0.00 4.63
174 175 2.502130 GCCTATCCCTATAAGCACCTCC 59.498 54.545 0.00 0.00 0.00 4.30
177 178 1.405661 GCGCCTATCCCTATAAGCACC 60.406 57.143 0.00 0.00 0.00 5.01
178 179 1.550976 AGCGCCTATCCCTATAAGCAC 59.449 52.381 2.29 0.00 0.00 4.40
180 181 2.622436 CAAGCGCCTATCCCTATAAGC 58.378 52.381 2.29 0.00 0.00 3.09
182 183 1.067142 CGCAAGCGCCTATCCCTATAA 60.067 52.381 2.29 0.00 33.11 0.98
183 184 0.530744 CGCAAGCGCCTATCCCTATA 59.469 55.000 2.29 0.00 33.11 1.31
184 185 1.293498 CGCAAGCGCCTATCCCTAT 59.707 57.895 2.29 0.00 33.11 2.57
186 187 3.447025 GACGCAAGCGCCTATCCCT 62.447 63.158 15.09 0.00 44.19 4.20
187 188 2.967615 GACGCAAGCGCCTATCCC 60.968 66.667 15.09 0.00 44.19 3.85
188 189 2.107141 AGACGCAAGCGCCTATCC 59.893 61.111 15.09 0.00 44.19 2.59
189 190 1.519455 ACAGACGCAAGCGCCTATC 60.519 57.895 15.09 4.52 44.19 2.08
191 192 2.432456 CACAGACGCAAGCGCCTA 60.432 61.111 15.09 0.00 44.19 3.93
194 195 2.456119 ATAGCACAGACGCAAGCGC 61.456 57.895 15.09 0.00 44.19 5.92
195 196 1.346197 CATAGCACAGACGCAAGCG 59.654 57.895 13.50 13.50 46.03 4.68
196 197 1.061570 GCATAGCACAGACGCAAGC 59.938 57.895 0.00 0.00 45.62 4.01
198 199 2.378445 TTAGCATAGCACAGACGCAA 57.622 45.000 0.00 0.00 0.00 4.85
199 200 2.378445 TTTAGCATAGCACAGACGCA 57.622 45.000 0.00 0.00 0.00 5.24
200 201 3.740044 TTTTTAGCATAGCACAGACGC 57.260 42.857 0.00 0.00 0.00 5.19
221 222 9.289303 GCGACTTTTATTCAATAACAATCATGT 57.711 29.630 0.00 0.00 43.14 3.21
222 223 8.745837 GGCGACTTTTATTCAATAACAATCATG 58.254 33.333 0.00 0.00 0.00 3.07
223 224 8.686334 AGGCGACTTTTATTCAATAACAATCAT 58.314 29.630 0.00 0.00 37.44 2.45
224 225 8.050778 AGGCGACTTTTATTCAATAACAATCA 57.949 30.769 0.00 0.00 37.44 2.57
266 267 4.204799 GGTGAGTGGTAACTGGAGTTTTT 58.795 43.478 0.00 0.00 39.31 1.94
267 268 3.201266 TGGTGAGTGGTAACTGGAGTTTT 59.799 43.478 0.00 0.00 39.31 2.43
268 269 2.775384 TGGTGAGTGGTAACTGGAGTTT 59.225 45.455 0.00 0.00 39.31 2.66
269 270 2.404559 TGGTGAGTGGTAACTGGAGTT 58.595 47.619 0.00 0.00 41.73 3.01
270 271 2.097110 TGGTGAGTGGTAACTGGAGT 57.903 50.000 0.00 0.00 36.52 3.85
271 272 2.567169 TGATGGTGAGTGGTAACTGGAG 59.433 50.000 0.00 0.00 36.52 3.86
272 273 2.615391 TGATGGTGAGTGGTAACTGGA 58.385 47.619 0.00 0.00 36.52 3.86
273 274 3.417069 TTGATGGTGAGTGGTAACTGG 57.583 47.619 0.00 0.00 36.52 4.00
274 275 3.941483 GGATTGATGGTGAGTGGTAACTG 59.059 47.826 0.00 0.00 36.52 3.16
275 276 3.054361 GGGATTGATGGTGAGTGGTAACT 60.054 47.826 0.00 0.00 40.21 2.24
276 277 3.279434 GGGATTGATGGTGAGTGGTAAC 58.721 50.000 0.00 0.00 0.00 2.50
277 278 2.916269 TGGGATTGATGGTGAGTGGTAA 59.084 45.455 0.00 0.00 0.00 2.85
278 279 2.238646 GTGGGATTGATGGTGAGTGGTA 59.761 50.000 0.00 0.00 0.00 3.25
279 280 1.004745 GTGGGATTGATGGTGAGTGGT 59.995 52.381 0.00 0.00 0.00 4.16
280 281 1.004628 TGTGGGATTGATGGTGAGTGG 59.995 52.381 0.00 0.00 0.00 4.00
282 283 1.339055 CGTGTGGGATTGATGGTGAGT 60.339 52.381 0.00 0.00 0.00 3.41
283 284 1.372582 CGTGTGGGATTGATGGTGAG 58.627 55.000 0.00 0.00 0.00 3.51
286 287 1.378514 GCCGTGTGGGATTGATGGT 60.379 57.895 0.00 0.00 38.47 3.55
299 300 1.008995 CAGGTTTTTCCACGCCGTG 60.009 57.895 10.95 10.95 39.02 4.94
300 301 1.153127 TCAGGTTTTTCCACGCCGT 60.153 52.632 0.00 0.00 39.02 5.68
301 302 1.574428 CTCAGGTTTTTCCACGCCG 59.426 57.895 0.00 0.00 39.02 6.46
323 324 5.129485 ACAGGATAGTAGACATGGAAACCAG 59.871 44.000 0.00 0.00 36.75 4.00
333 338 3.939740 ACCGGTACAGGATAGTAGACA 57.060 47.619 19.63 0.00 34.73 3.41
393 398 2.510238 GAGCAGCTGCACCGGTAG 60.510 66.667 38.24 2.57 45.16 3.18
401 406 1.897615 GATGGATGGGAGCAGCTGC 60.898 63.158 31.53 31.53 42.49 5.25
405 410 0.894184 GCATGGATGGATGGGAGCAG 60.894 60.000 0.00 0.00 0.00 4.24
465 474 2.546645 TATCGCGGCGTTTCGACCTT 62.547 55.000 22.90 0.00 37.55 3.50
531 540 2.125512 GTCGCTCGCTGGTGGAAT 60.126 61.111 0.00 0.00 0.00 3.01
582 596 1.810030 CTTTCTCCTACGCGGTGGC 60.810 63.158 12.47 0.00 0.00 5.01
764 797 2.584391 GGGCAACGTGGGAGAGAGT 61.584 63.158 0.00 0.00 37.60 3.24
765 798 2.266055 GGGCAACGTGGGAGAGAG 59.734 66.667 0.00 0.00 37.60 3.20
766 799 3.691342 CGGGCAACGTGGGAGAGA 61.691 66.667 0.00 0.00 37.93 3.10
795 828 8.611051 ATGGTCTAACAGAAAAGATAGGTAGT 57.389 34.615 0.00 0.00 0.00 2.73
1009 1059 1.502231 CTCAACTCACCCTGAACGTG 58.498 55.000 0.00 0.00 0.00 4.49
1055 1105 1.283793 CAGCCCAACAACAAGCTCG 59.716 57.895 0.00 0.00 31.93 5.03
1061 1111 1.153524 ATGAGCCAGCCCAACAACA 59.846 52.632 0.00 0.00 0.00 3.33
1083 1134 4.971924 AGATCAGGTAAGCTGTAGGGAAAT 59.028 41.667 0.00 0.00 0.00 2.17
1093 1144 5.091261 ACAAATCGAAGATCAGGTAAGCT 57.909 39.130 0.00 0.00 45.12 3.74
1129 1181 0.688087 AGACGGGGACTTGATCCTCC 60.688 60.000 0.00 0.00 46.92 4.30
1136 1188 2.545952 CCGATTCATAGACGGGGACTTG 60.546 54.545 0.00 0.00 42.48 3.16
1176 1228 2.573462 TCACAAATTGAGGAGGAGGAGG 59.427 50.000 0.00 0.00 0.00 4.30
1181 1233 3.557898 GCTCTGTCACAAATTGAGGAGGA 60.558 47.826 0.00 0.00 36.50 3.71
1204 1256 5.236263 GCTTTTCTCTAGCTAGATTGGCTTC 59.764 44.000 23.48 7.40 40.74 3.86
1290 1342 2.363306 AAGTTGGTGGCAGTTCATCA 57.637 45.000 0.00 0.00 0.00 3.07
1291 1343 3.383761 CAAAAGTTGGTGGCAGTTCATC 58.616 45.455 0.00 0.00 0.00 2.92
1293 1345 1.480137 CCAAAAGTTGGTGGCAGTTCA 59.520 47.619 0.00 0.00 45.93 3.18
1313 1365 1.194495 CCGACAAAGTATACCGACGC 58.806 55.000 0.00 0.00 0.00 5.19
1357 1409 4.656112 AGTGAAAGGAGAAACAGAAGAGGA 59.344 41.667 0.00 0.00 0.00 3.71
1362 1414 3.627577 GCACAGTGAAAGGAGAAACAGAA 59.372 43.478 4.15 0.00 0.00 3.02
1428 1480 8.498054 TGTTTTGCATTTAGATTTGTGGAAAA 57.502 26.923 0.00 0.00 38.80 2.29
1468 1524 0.529337 CATAGGCTCCACTCGCACTG 60.529 60.000 0.00 0.00 0.00 3.66
1470 1526 0.528684 GTCATAGGCTCCACTCGCAC 60.529 60.000 0.00 0.00 0.00 5.34
1471 1527 0.684479 AGTCATAGGCTCCACTCGCA 60.684 55.000 0.00 0.00 0.00 5.10
1472 1528 0.031449 GAGTCATAGGCTCCACTCGC 59.969 60.000 0.00 0.00 0.00 5.03
1473 1529 1.686355 AGAGTCATAGGCTCCACTCG 58.314 55.000 12.31 0.00 40.27 4.18
1477 1533 2.573462 AGCAAAAGAGTCATAGGCTCCA 59.427 45.455 0.00 0.00 33.69 3.86
1478 1534 3.274095 AGCAAAAGAGTCATAGGCTCC 57.726 47.619 0.00 0.00 33.69 4.70
1520 1599 1.520174 CAGTCATTGATAGTGCGAGCG 59.480 52.381 0.00 0.00 0.00 5.03
1524 1603 2.892374 TGGACAGTCATTGATAGTGCG 58.108 47.619 2.17 0.00 0.00 5.34
1529 1608 3.243873 GCCGAGATGGACAGTCATTGATA 60.244 47.826 2.17 0.00 42.00 2.15
1537 1624 4.498520 CGCGCCGAGATGGACAGT 62.499 66.667 0.00 0.00 42.00 3.55
1639 1726 4.530857 GCCGGGTCCAGGACGATG 62.531 72.222 12.94 5.51 32.65 3.84
1643 1730 4.489771 CATGGCCGGGTCCAGGAC 62.490 72.222 12.94 11.70 40.11 3.85
2467 2554 1.135024 CCAAAAGCAACGATCCATGGG 60.135 52.381 13.02 0.00 0.00 4.00
2482 2569 5.536916 ACGAATCCTCATTAACCAACCAAAA 59.463 36.000 0.00 0.00 0.00 2.44
2497 2584 0.944311 ACGCACACACACGAATCCTC 60.944 55.000 0.00 0.00 0.00 3.71
2498 2585 0.531974 AACGCACACACACGAATCCT 60.532 50.000 0.00 0.00 0.00 3.24
2499 2586 0.384230 CAACGCACACACACGAATCC 60.384 55.000 0.00 0.00 0.00 3.01
2501 2588 1.092921 ACCAACGCACACACACGAAT 61.093 50.000 0.00 0.00 0.00 3.34
2667 2762 0.598942 TGTACACGCACGAACATGCT 60.599 50.000 0.00 0.00 43.80 3.79
2671 2766 2.143008 ATCTTGTACACGCACGAACA 57.857 45.000 0.00 0.00 0.00 3.18
2711 2806 2.159352 ACAAACAGTACGGGCAACAAAC 60.159 45.455 0.00 0.00 39.74 2.93
2745 2840 7.549134 CACACATACCACAGTTATACATGACTT 59.451 37.037 0.00 0.00 0.00 3.01
2747 2842 6.816640 ACACACATACCACAGTTATACATGAC 59.183 38.462 0.00 0.00 0.00 3.06
2748 2843 6.816140 CACACACATACCACAGTTATACATGA 59.184 38.462 0.00 0.00 0.00 3.07
2750 2845 5.584649 GCACACACATACCACAGTTATACAT 59.415 40.000 0.00 0.00 0.00 2.29
2791 2895 8.608844 AGACCCAAGATCGTATTATTCATTTC 57.391 34.615 0.00 0.00 0.00 2.17
2854 2969 6.594937 AGCATCTTCGTTAACCCGTAAAATTA 59.405 34.615 0.00 0.00 0.00 1.40
2930 3050 3.263425 ACCGTTTACAGATTGGTCCTCAT 59.737 43.478 0.00 0.00 0.00 2.90
2937 3057 2.223021 CGCATCACCGTTTACAGATTGG 60.223 50.000 0.00 0.00 0.00 3.16
2943 3063 0.390603 CTCCCGCATCACCGTTTACA 60.391 55.000 0.00 0.00 0.00 2.41
2945 3065 1.448893 GCTCCCGCATCACCGTTTA 60.449 57.895 0.00 0.00 35.78 2.01
2981 3101 3.684788 GGAGCTGTGTGAACGTTTATGAT 59.315 43.478 0.46 0.00 0.00 2.45
2990 3110 1.795768 TTGATCGGAGCTGTGTGAAC 58.204 50.000 0.00 0.00 0.00 3.18
3029 3149 3.992643 TCTTTTGGTTGTAATCGGACGA 58.007 40.909 0.00 0.00 0.00 4.20
3032 3152 6.452494 TGTTTTCTTTTGGTTGTAATCGGA 57.548 33.333 0.00 0.00 0.00 4.55
3038 3158 8.948631 TGCATATTTGTTTTCTTTTGGTTGTA 57.051 26.923 0.00 0.00 0.00 2.41
3052 3172 9.139174 GCAAAAAGTATACACTGCATATTTGTT 57.861 29.630 5.50 0.00 34.36 2.83
3057 3177 5.008613 CGGGCAAAAAGTATACACTGCATAT 59.991 40.000 5.50 0.00 34.36 1.78
3077 3197 0.804989 CAACACTTTGGAGATCGGGC 59.195 55.000 0.00 0.00 0.00 6.13
3087 3207 0.310854 GGGCGTCTTCCAACACTTTG 59.689 55.000 0.00 0.00 0.00 2.77
3088 3208 1.164041 CGGGCGTCTTCCAACACTTT 61.164 55.000 0.00 0.00 0.00 2.66
3089 3209 1.597027 CGGGCGTCTTCCAACACTT 60.597 57.895 0.00 0.00 0.00 3.16
3090 3210 2.030562 CGGGCGTCTTCCAACACT 59.969 61.111 0.00 0.00 0.00 3.55
3288 3408 5.514169 TGAGAAGAGAAGAGGCTCTGATAA 58.486 41.667 19.53 0.00 44.18 1.75
3437 3558 2.260639 AGAGGGATCACTGTCATGGT 57.739 50.000 0.00 0.00 0.00 3.55
3445 3566 2.628290 GGGAGGAAGAAGAGGGATCACT 60.628 54.545 0.00 0.00 0.00 3.41
3449 3570 0.029577 GGGGGAGGAAGAAGAGGGAT 60.030 60.000 0.00 0.00 0.00 3.85
3451 3572 0.985490 CAGGGGGAGGAAGAAGAGGG 60.985 65.000 0.00 0.00 0.00 4.30
3490 3611 1.566231 GGGATGGTGGTGGAAGAAGAT 59.434 52.381 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.