Multiple sequence alignment - TraesCS2B01G569200

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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 TraesCS2B01G569200 chr2B 100.000 2589 0 0 1 2589 759764394 759766982 0.000000e+00 4782.0
1 TraesCS2B01G569200 chr2B 77.419 775 104 44 1045 1765 759817788 759818545 1.870000e-106 396.0
2 TraesCS2B01G569200 chr2B 80.464 517 56 23 1099 1589 759757078 759757575 1.140000e-93 353.0
3 TraesCS2B01G569200 chr2B 84.024 338 46 5 1970 2302 759889615 759889281 4.160000e-83 318.0
4 TraesCS2B01G569200 chr2B 89.189 111 11 1 1781 1890 17892494 17892384 1.250000e-28 137.0
5 TraesCS2B01G569200 chr2B 82.857 70 10 2 2176 2245 759743177 759743244 7.740000e-06 62.1
6 TraesCS2B01G569200 chr2D 92.088 1087 60 12 1048 2112 620193740 620194822 0.000000e+00 1507.0
7 TraesCS2B01G569200 chr2D 85.813 578 44 18 472 1044 620193151 620193695 1.730000e-161 579.0
8 TraesCS2B01G569200 chr2D 79.785 559 57 31 1075 1601 620198959 620199493 3.170000e-94 355.0
9 TraesCS2B01G569200 chr2D 85.538 325 26 9 1271 1592 620160292 620160598 1.160000e-83 320.0
10 TraesCS2B01G569200 chr2D 96.273 161 3 3 2136 2296 620194815 620194972 7.110000e-66 261.0
11 TraesCS2B01G569200 chr2D 90.741 108 4 2 239 340 620192901 620193008 3.470000e-29 139.0
12 TraesCS2B01G569200 chr2D 92.405 79 6 0 1099 1177 620160046 620160124 2.110000e-21 113.0
13 TraesCS2B01G569200 chr2D 92.647 68 5 0 2325 2392 620194974 620195041 5.900000e-17 99.0
14 TraesCS2B01G569200 chr2D 76.087 184 22 14 2175 2355 620154985 620155149 2.760000e-10 76.8
15 TraesCS2B01G569200 chr2A 84.605 1507 113 63 432 1884 751608412 751609853 0.000000e+00 1387.0
16 TraesCS2B01G569200 chr2A 86.914 512 47 11 1893 2392 751609813 751610316 8.090000e-155 556.0
17 TraesCS2B01G569200 chr2A 80.059 682 79 38 1066 1723 751662670 751663318 1.090000e-123 453.0
18 TraesCS2B01G569200 chr2A 79.740 385 60 9 1077 1458 751546720 751547089 1.980000e-66 263.0
19 TraesCS2B01G569200 chr2A 81.143 350 47 12 1099 1444 751552950 751553284 1.980000e-66 263.0
20 TraesCS2B01G569200 chr2A 86.364 66 8 1 2175 2240 751548002 751548066 1.290000e-08 71.3
21 TraesCS2B01G569200 chrUn 77.938 485 56 25 1267 1733 23148850 23148399 3.310000e-64 255.0
22 TraesCS2B01G569200 chr1D 78.698 169 26 9 2414 2579 454304308 454304147 1.270000e-18 104.0


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 TraesCS2B01G569200 chr2B 759764394 759766982 2588 False 4782.0 4782 100.000000 1 2589 1 chr2B.!!$F3 2588
1 TraesCS2B01G569200 chr2B 759817788 759818545 757 False 396.0 396 77.419000 1045 1765 1 chr2B.!!$F4 720
2 TraesCS2B01G569200 chr2D 620192901 620199493 6592 False 490.0 1507 89.557833 239 2392 6 chr2D.!!$F3 2153
3 TraesCS2B01G569200 chr2D 620160046 620160598 552 False 216.5 320 88.971500 1099 1592 2 chr2D.!!$F2 493
4 TraesCS2B01G569200 chr2A 751608412 751610316 1904 False 971.5 1387 85.759500 432 2392 2 chr2A.!!$F4 1960
5 TraesCS2B01G569200 chr2A 751662670 751663318 648 False 453.0 453 80.059000 1066 1723 1 chr2A.!!$F2 657

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
178 179 0.040958 CGCAGTCTGTTCTTGGTTGC 60.041 55.0 0.93 0.0 0.0 4.17 F
516 575 0.109597 CTCGCAATCAAAGCCACCAC 60.110 55.0 0.00 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1096 1229 0.670162 CCAACTTCAGCACAACCTGG 59.330 55.0 0.00 0.00 33.64 4.45 R
2343 2683 0.164217 GGTTAACGAAATGCGCACGA 59.836 50.0 23.36 1.29 46.04 4.35 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
20 21 1.234821 TGCAGTGTTGAATCGTTCCC 58.765 50.000 0.00 0.00 0.00 3.97
21 22 0.521735 GCAGTGTTGAATCGTTCCCC 59.478 55.000 0.00 0.00 0.00 4.81
22 23 1.890876 CAGTGTTGAATCGTTCCCCA 58.109 50.000 0.00 0.00 0.00 4.96
23 24 1.535462 CAGTGTTGAATCGTTCCCCAC 59.465 52.381 0.00 0.00 32.57 4.61
24 25 1.142060 AGTGTTGAATCGTTCCCCACA 59.858 47.619 13.68 5.67 33.95 4.17
25 26 2.159382 GTGTTGAATCGTTCCCCACAT 58.841 47.619 9.68 0.00 32.64 3.21
26 27 2.095263 GTGTTGAATCGTTCCCCACATG 60.095 50.000 0.00 0.00 32.64 3.21
27 28 1.472480 GTTGAATCGTTCCCCACATGG 59.528 52.381 0.00 0.00 0.00 3.66
28 29 0.679640 TGAATCGTTCCCCACATGGC 60.680 55.000 0.00 0.00 0.00 4.40
29 30 1.714899 GAATCGTTCCCCACATGGCG 61.715 60.000 0.00 0.00 0.00 5.69
30 31 3.697439 ATCGTTCCCCACATGGCGG 62.697 63.158 0.00 0.00 0.00 6.13
37 38 4.676951 CCACATGGCGGGGTTGGT 62.677 66.667 0.00 0.00 0.00 3.67
38 39 3.372730 CACATGGCGGGGTTGGTG 61.373 66.667 0.00 0.00 0.00 4.17
60 61 4.794439 CGTGCAGGACGGATCGCA 62.794 66.667 6.56 0.00 44.85 5.10
61 62 2.434185 GTGCAGGACGGATCGCAA 60.434 61.111 0.00 0.00 35.87 4.85
62 63 2.434185 TGCAGGACGGATCGCAAC 60.434 61.111 0.00 0.00 0.00 4.17
63 64 3.554692 GCAGGACGGATCGCAACG 61.555 66.667 0.00 0.00 0.00 4.10
64 65 2.180769 CAGGACGGATCGCAACGA 59.819 61.111 0.00 0.00 41.13 3.85
66 67 1.226974 AGGACGGATCGCAACGATG 60.227 57.895 7.28 0.00 47.00 3.84
67 68 2.621000 GACGGATCGCAACGATGC 59.379 61.111 7.72 7.72 47.00 3.91
75 76 3.814268 GCAACGATGCGCACCCAT 61.814 61.111 14.90 0.00 43.83 4.00
76 77 2.468670 GCAACGATGCGCACCCATA 61.469 57.895 14.90 0.00 43.83 2.74
77 78 1.643292 CAACGATGCGCACCCATAG 59.357 57.895 14.90 0.00 0.00 2.23
78 79 1.523711 AACGATGCGCACCCATAGG 60.524 57.895 14.90 0.00 40.04 2.57
79 80 3.349006 CGATGCGCACCCATAGGC 61.349 66.667 14.90 0.00 36.11 3.93
80 81 2.980233 GATGCGCACCCATAGGCC 60.980 66.667 14.90 0.00 36.11 5.19
81 82 4.935495 ATGCGCACCCATAGGCCG 62.935 66.667 14.90 0.00 36.11 6.13
84 85 4.856801 CGCACCCATAGGCCGCTT 62.857 66.667 0.00 0.00 36.11 4.68
85 86 2.440247 GCACCCATAGGCCGCTTT 60.440 61.111 0.00 0.00 36.11 3.51
86 87 2.052104 GCACCCATAGGCCGCTTTT 61.052 57.895 0.00 0.00 36.11 2.27
87 88 1.604147 GCACCCATAGGCCGCTTTTT 61.604 55.000 0.00 0.00 36.11 1.94
88 89 0.455815 CACCCATAGGCCGCTTTTTC 59.544 55.000 0.00 0.00 36.11 2.29
89 90 0.331616 ACCCATAGGCCGCTTTTTCT 59.668 50.000 0.00 0.00 36.11 2.52
90 91 1.272480 ACCCATAGGCCGCTTTTTCTT 60.272 47.619 0.00 0.00 36.11 2.52
91 92 1.134946 CCCATAGGCCGCTTTTTCTTG 59.865 52.381 0.00 0.00 0.00 3.02
92 93 1.818674 CCATAGGCCGCTTTTTCTTGT 59.181 47.619 0.00 0.00 0.00 3.16
93 94 2.415893 CCATAGGCCGCTTTTTCTTGTG 60.416 50.000 0.00 0.00 0.00 3.33
94 95 0.596082 TAGGCCGCTTTTTCTTGTGC 59.404 50.000 0.00 0.00 0.00 4.57
95 96 2.016165 GGCCGCTTTTTCTTGTGCG 61.016 57.895 0.00 0.00 46.74 5.34
96 97 1.299089 GCCGCTTTTTCTTGTGCGT 60.299 52.632 0.00 0.00 45.90 5.24
97 98 0.869880 GCCGCTTTTTCTTGTGCGTT 60.870 50.000 0.00 0.00 45.90 4.84
98 99 0.845768 CCGCTTTTTCTTGTGCGTTG 59.154 50.000 0.00 0.00 45.90 4.10
99 100 1.532921 CCGCTTTTTCTTGTGCGTTGA 60.533 47.619 0.00 0.00 45.90 3.18
100 101 2.384382 CGCTTTTTCTTGTGCGTTGAT 58.616 42.857 0.00 0.00 42.93 2.57
101 102 2.401720 CGCTTTTTCTTGTGCGTTGATC 59.598 45.455 0.00 0.00 42.93 2.92
102 103 2.401720 GCTTTTTCTTGTGCGTTGATCG 59.598 45.455 0.00 0.00 43.12 3.69
103 104 3.848191 GCTTTTTCTTGTGCGTTGATCGA 60.848 43.478 0.00 0.00 42.86 3.59
104 105 4.466828 CTTTTTCTTGTGCGTTGATCGAT 58.533 39.130 0.00 0.00 42.86 3.59
105 106 3.722555 TTTCTTGTGCGTTGATCGATC 57.277 42.857 18.72 18.72 42.86 3.69
106 107 2.654749 TCTTGTGCGTTGATCGATCT 57.345 45.000 25.02 0.00 42.86 2.75
107 108 2.959516 TCTTGTGCGTTGATCGATCTT 58.040 42.857 25.02 0.00 42.86 2.40
108 109 2.923655 TCTTGTGCGTTGATCGATCTTC 59.076 45.455 25.02 16.26 42.86 2.87
109 110 2.654749 TGTGCGTTGATCGATCTTCT 57.345 45.000 25.02 0.00 42.86 2.85
110 111 2.959516 TGTGCGTTGATCGATCTTCTT 58.040 42.857 25.02 0.00 42.86 2.52
111 112 2.667969 TGTGCGTTGATCGATCTTCTTG 59.332 45.455 25.02 11.93 42.86 3.02
112 113 1.660607 TGCGTTGATCGATCTTCTTGC 59.339 47.619 25.02 19.91 42.86 4.01
113 114 1.929836 GCGTTGATCGATCTTCTTGCT 59.070 47.619 25.02 0.00 42.86 3.91
114 115 2.285486 GCGTTGATCGATCTTCTTGCTG 60.285 50.000 25.02 8.35 42.86 4.41
115 116 2.285486 CGTTGATCGATCTTCTTGCTGC 60.285 50.000 25.02 0.00 42.86 5.25
116 117 1.945387 TGATCGATCTTCTTGCTGCC 58.055 50.000 25.02 0.00 0.00 4.85
117 118 1.483827 TGATCGATCTTCTTGCTGCCT 59.516 47.619 25.02 0.00 0.00 4.75
118 119 2.093288 TGATCGATCTTCTTGCTGCCTT 60.093 45.455 25.02 0.00 0.00 4.35
119 120 1.730501 TCGATCTTCTTGCTGCCTTG 58.269 50.000 0.00 0.00 0.00 3.61
120 121 1.276138 TCGATCTTCTTGCTGCCTTGA 59.724 47.619 0.00 0.00 0.00 3.02
121 122 1.396301 CGATCTTCTTGCTGCCTTGAC 59.604 52.381 0.00 0.00 0.00 3.18
122 123 1.742268 GATCTTCTTGCTGCCTTGACC 59.258 52.381 0.00 0.00 0.00 4.02
123 124 0.250901 TCTTCTTGCTGCCTTGACCC 60.251 55.000 0.00 0.00 0.00 4.46
124 125 0.251077 CTTCTTGCTGCCTTGACCCT 60.251 55.000 0.00 0.00 0.00 4.34
125 126 0.250901 TTCTTGCTGCCTTGACCCTC 60.251 55.000 0.00 0.00 0.00 4.30
126 127 2.032528 TTGCTGCCTTGACCCTCG 59.967 61.111 0.00 0.00 0.00 4.63
127 128 2.454832 CTTGCTGCCTTGACCCTCGA 62.455 60.000 0.00 0.00 0.00 4.04
128 129 2.125350 GCTGCCTTGACCCTCGAG 60.125 66.667 5.13 5.13 0.00 4.04
132 133 2.266055 CCTTGACCCTCGAGGCAC 59.734 66.667 26.87 20.46 40.92 5.01
133 134 2.125912 CTTGACCCTCGAGGCACG 60.126 66.667 26.87 15.15 40.58 5.34
134 135 3.649277 CTTGACCCTCGAGGCACGG 62.649 68.421 26.87 14.76 42.82 4.94
135 136 4.988716 TGACCCTCGAGGCACGGT 62.989 66.667 26.87 18.11 42.82 4.83
136 137 3.692406 GACCCTCGAGGCACGGTT 61.692 66.667 26.87 4.82 42.82 4.44
137 138 3.934391 GACCCTCGAGGCACGGTTG 62.934 68.421 26.87 12.85 42.82 3.77
150 151 3.066190 GGTTGCTAAACCGGGGGC 61.066 66.667 6.32 4.75 46.32 5.80
151 152 3.066190 GTTGCTAAACCGGGGGCC 61.066 66.667 6.32 0.00 0.00 5.80
166 167 4.112341 GCCGGTCGTACGCAGTCT 62.112 66.667 11.24 0.00 43.93 3.24
167 168 2.202440 CCGGTCGTACGCAGTCTG 60.202 66.667 11.24 5.98 43.93 3.51
168 169 2.559840 CGGTCGTACGCAGTCTGT 59.440 61.111 11.24 0.00 43.93 3.41
169 170 1.081641 CGGTCGTACGCAGTCTGTT 60.082 57.895 11.24 0.00 43.93 3.16
170 171 1.063951 CGGTCGTACGCAGTCTGTTC 61.064 60.000 11.24 0.00 43.93 3.18
171 172 0.240411 GGTCGTACGCAGTCTGTTCT 59.760 55.000 11.24 0.00 43.93 3.01
172 173 1.335689 GGTCGTACGCAGTCTGTTCTT 60.336 52.381 11.24 0.00 43.93 2.52
173 174 1.714460 GTCGTACGCAGTCTGTTCTTG 59.286 52.381 11.24 0.00 43.93 3.02
174 175 1.060713 CGTACGCAGTCTGTTCTTGG 58.939 55.000 0.52 0.00 43.93 3.61
175 176 1.602165 CGTACGCAGTCTGTTCTTGGT 60.602 52.381 0.52 0.00 43.93 3.67
176 177 2.480845 GTACGCAGTCTGTTCTTGGTT 58.519 47.619 0.93 0.00 43.93 3.67
177 178 1.299541 ACGCAGTCTGTTCTTGGTTG 58.700 50.000 0.93 0.00 29.74 3.77
178 179 0.040958 CGCAGTCTGTTCTTGGTTGC 60.041 55.000 0.93 0.00 0.00 4.17
179 180 1.312815 GCAGTCTGTTCTTGGTTGCT 58.687 50.000 0.93 0.00 0.00 3.91
180 181 2.494059 GCAGTCTGTTCTTGGTTGCTA 58.506 47.619 0.93 0.00 0.00 3.49
181 182 2.224314 GCAGTCTGTTCTTGGTTGCTAC 59.776 50.000 0.93 0.00 0.00 3.58
182 183 3.466836 CAGTCTGTTCTTGGTTGCTACA 58.533 45.455 0.00 0.00 0.00 2.74
183 184 3.876914 CAGTCTGTTCTTGGTTGCTACAA 59.123 43.478 0.00 0.00 0.00 2.41
184 185 4.335315 CAGTCTGTTCTTGGTTGCTACAAA 59.665 41.667 0.00 0.00 0.00 2.83
185 186 4.947388 AGTCTGTTCTTGGTTGCTACAAAA 59.053 37.500 0.00 0.00 0.00 2.44
186 187 5.417580 AGTCTGTTCTTGGTTGCTACAAAAA 59.582 36.000 0.00 0.00 0.00 1.94
187 188 5.743872 GTCTGTTCTTGGTTGCTACAAAAAG 59.256 40.000 0.00 1.50 0.00 2.27
188 189 5.650266 TCTGTTCTTGGTTGCTACAAAAAGA 59.350 36.000 0.00 3.79 0.00 2.52
189 190 6.321181 TCTGTTCTTGGTTGCTACAAAAAGAT 59.679 34.615 0.00 0.00 0.00 2.40
190 191 6.872920 TGTTCTTGGTTGCTACAAAAAGATT 58.127 32.000 0.00 0.00 0.00 2.40
191 192 7.327214 TGTTCTTGGTTGCTACAAAAAGATTT 58.673 30.769 0.00 0.00 0.00 2.17
192 193 7.491048 TGTTCTTGGTTGCTACAAAAAGATTTC 59.509 33.333 0.00 2.46 0.00 2.17
193 194 7.346751 TCTTGGTTGCTACAAAAAGATTTCT 57.653 32.000 0.00 0.00 0.00 2.52
194 195 8.458573 TCTTGGTTGCTACAAAAAGATTTCTA 57.541 30.769 0.00 0.00 0.00 2.10
195 196 8.349983 TCTTGGTTGCTACAAAAAGATTTCTAC 58.650 33.333 0.00 0.00 0.00 2.59
196 197 6.664515 TGGTTGCTACAAAAAGATTTCTACG 58.335 36.000 0.00 0.00 0.00 3.51
197 198 6.261381 TGGTTGCTACAAAAAGATTTCTACGT 59.739 34.615 0.00 0.00 0.00 3.57
198 199 7.441760 TGGTTGCTACAAAAAGATTTCTACGTA 59.558 33.333 0.00 0.00 0.00 3.57
199 200 8.448615 GGTTGCTACAAAAAGATTTCTACGTAT 58.551 33.333 0.00 0.00 0.00 3.06
200 201 9.474249 GTTGCTACAAAAAGATTTCTACGTATC 57.526 33.333 0.00 0.00 0.00 2.24
201 202 8.193250 TGCTACAAAAAGATTTCTACGTATCC 57.807 34.615 0.00 0.00 0.00 2.59
202 203 7.009815 TGCTACAAAAAGATTTCTACGTATCCG 59.990 37.037 0.00 0.00 40.83 4.18
203 204 7.221452 GCTACAAAAAGATTTCTACGTATCCGA 59.779 37.037 0.00 0.00 37.88 4.55
204 205 7.287050 ACAAAAAGATTTCTACGTATCCGAC 57.713 36.000 0.00 0.00 37.88 4.79
205 206 6.312180 ACAAAAAGATTTCTACGTATCCGACC 59.688 38.462 0.00 0.00 37.88 4.79
206 207 5.587388 AAAGATTTCTACGTATCCGACCA 57.413 39.130 0.00 0.00 37.88 4.02
207 208 5.587388 AAGATTTCTACGTATCCGACCAA 57.413 39.130 0.00 0.00 37.88 3.67
208 209 5.587388 AGATTTCTACGTATCCGACCAAA 57.413 39.130 0.00 0.00 37.88 3.28
209 210 6.158023 AGATTTCTACGTATCCGACCAAAT 57.842 37.500 0.00 0.00 37.88 2.32
210 211 6.214399 AGATTTCTACGTATCCGACCAAATC 58.786 40.000 0.00 2.86 36.73 2.17
222 223 3.641439 GACCAAATCGATCAAGACACG 57.359 47.619 0.00 0.00 0.00 4.49
223 224 1.732259 ACCAAATCGATCAAGACACGC 59.268 47.619 0.00 0.00 0.00 5.34
224 225 1.267038 CCAAATCGATCAAGACACGCG 60.267 52.381 3.53 3.53 0.00 6.01
225 226 0.370273 AAATCGATCAAGACACGCGC 59.630 50.000 5.73 0.00 0.00 6.86
226 227 0.735978 AATCGATCAAGACACGCGCA 60.736 50.000 5.73 0.00 0.00 6.09
227 228 0.735978 ATCGATCAAGACACGCGCAA 60.736 50.000 5.73 0.00 0.00 4.85
228 229 1.225475 CGATCAAGACACGCGCAAC 60.225 57.895 5.73 0.00 0.00 4.17
229 230 1.132640 GATCAAGACACGCGCAACC 59.867 57.895 5.73 0.00 0.00 3.77
230 231 2.240612 GATCAAGACACGCGCAACCC 62.241 60.000 5.73 0.00 0.00 4.11
231 232 4.025401 CAAGACACGCGCAACCCC 62.025 66.667 5.73 0.00 0.00 4.95
232 233 4.250305 AAGACACGCGCAACCCCT 62.250 61.111 5.73 0.00 0.00 4.79
233 234 4.681978 AGACACGCGCAACCCCTC 62.682 66.667 5.73 0.00 0.00 4.30
294 295 5.686124 GCAGTATTCTAGTTGAAGGCAGGAT 60.686 44.000 0.00 0.00 38.18 3.24
311 318 6.212388 AGGCAGGATGTATAGTATTCAAGGAG 59.788 42.308 0.00 0.00 39.31 3.69
312 319 6.402222 GCAGGATGTATAGTATTCAAGGAGG 58.598 44.000 0.00 0.00 39.31 4.30
340 347 1.275291 GTGACCGAGGACCTGAAATCA 59.725 52.381 0.00 0.00 0.00 2.57
341 348 1.974957 TGACCGAGGACCTGAAATCAA 59.025 47.619 0.00 0.00 0.00 2.57
352 401 4.074970 ACCTGAAATCAATCGCTCTTGTT 58.925 39.130 0.00 0.00 0.00 2.83
365 414 9.385902 CAATCGCTCTTGTTATAATAACAATGG 57.614 33.333 0.00 0.00 39.16 3.16
366 415 8.677148 ATCGCTCTTGTTATAATAACAATGGT 57.323 30.769 0.00 0.00 39.16 3.55
367 416 7.915508 TCGCTCTTGTTATAATAACAATGGTG 58.084 34.615 0.00 2.03 39.16 4.17
368 417 7.766738 TCGCTCTTGTTATAATAACAATGGTGA 59.233 33.333 0.00 4.42 39.16 4.02
369 418 8.559536 CGCTCTTGTTATAATAACAATGGTGAT 58.440 33.333 0.00 0.00 39.16 3.06
414 463 2.031465 GCGGGACAAGGGACGAAA 59.969 61.111 0.00 0.00 0.00 3.46
418 467 0.605589 GGGACAAGGGACGAAACCAG 60.606 60.000 0.00 0.00 0.00 4.00
419 468 1.235281 GGACAAGGGACGAAACCAGC 61.235 60.000 0.00 0.00 0.00 4.85
420 469 1.566018 GACAAGGGACGAAACCAGCG 61.566 60.000 0.00 0.00 0.00 5.18
421 470 1.301401 CAAGGGACGAAACCAGCGA 60.301 57.895 0.00 0.00 0.00 4.93
422 471 1.301479 AAGGGACGAAACCAGCGAC 60.301 57.895 0.00 0.00 0.00 5.19
424 473 2.027625 GGGACGAAACCAGCGACAG 61.028 63.158 0.00 0.00 0.00 3.51
439 488 0.319728 GACAGCAGAGCCACTCTCAA 59.680 55.000 0.00 0.00 44.35 3.02
442 491 2.008329 CAGCAGAGCCACTCTCAAATC 58.992 52.381 0.00 0.00 44.35 2.17
448 497 2.746362 GAGCCACTCTCAAATCCACTTG 59.254 50.000 0.00 0.00 41.51 3.16
453 502 2.290577 ACTCTCAAATCCACTTGGGCTC 60.291 50.000 0.00 0.00 36.21 4.70
454 503 1.089920 CTCAAATCCACTTGGGCTCG 58.910 55.000 0.00 0.00 36.21 5.03
485 544 4.838423 TCCCAATTAAGTCAGTCAGTCAGA 59.162 41.667 0.00 0.00 0.00 3.27
508 567 2.618241 GGTCCATATGCTCGCAATCAAA 59.382 45.455 0.00 0.00 0.00 2.69
509 568 3.304257 GGTCCATATGCTCGCAATCAAAG 60.304 47.826 0.00 0.00 0.00 2.77
510 569 2.291465 TCCATATGCTCGCAATCAAAGC 59.709 45.455 0.00 0.00 36.56 3.51
516 575 0.109597 CTCGCAATCAAAGCCACCAC 60.110 55.000 0.00 0.00 0.00 4.16
518 577 1.659794 GCAATCAAAGCCACCACGT 59.340 52.632 0.00 0.00 0.00 4.49
521 580 0.179004 AATCAAAGCCACCACGTCCA 60.179 50.000 0.00 0.00 0.00 4.02
524 583 0.606401 CAAAGCCACCACGTCCAGAT 60.606 55.000 0.00 0.00 0.00 2.90
540 599 2.337583 CAGATGTGGACGTGTACCAAG 58.662 52.381 0.00 0.00 39.22 3.61
550 609 0.249398 GTGTACCAAGACTCCGGCAT 59.751 55.000 0.00 0.00 0.00 4.40
774 839 4.498520 CTCTGTCACGCGGGCGAT 62.499 66.667 20.98 1.03 42.83 4.58
780 845 4.812476 CACGCGGGCGATTCTCCA 62.812 66.667 20.98 0.00 42.83 3.86
808 874 3.041940 GCGAGGTTGGTCACGTGG 61.042 66.667 17.00 0.00 0.00 4.94
891 961 2.587777 TCCCCTATCTGTCTCCAAGTCT 59.412 50.000 0.00 0.00 0.00 3.24
892 962 2.962421 CCCCTATCTGTCTCCAAGTCTC 59.038 54.545 0.00 0.00 0.00 3.36
896 966 4.653341 CCTATCTGTCTCCAAGTCTCCAAT 59.347 45.833 0.00 0.00 0.00 3.16
900 970 4.339530 TCTGTCTCCAAGTCTCCAATATCG 59.660 45.833 0.00 0.00 0.00 2.92
933 1003 4.925576 CTTCCCCGTCGCCGATCG 62.926 72.222 8.51 8.51 40.15 3.69
945 1015 2.277310 CGATCGAGACGAAGCGCA 60.277 61.111 10.26 0.00 39.99 6.09
1079 1212 1.135460 GCTCCAGTTTGCTCATCTTGC 60.135 52.381 0.00 0.00 0.00 4.01
1080 1213 1.129998 CTCCAGTTTGCTCATCTTGCG 59.870 52.381 0.00 0.00 0.00 4.85
1082 1215 1.267806 CCAGTTTGCTCATCTTGCGTT 59.732 47.619 0.00 0.00 0.00 4.84
1112 1245 1.271597 GGATCCAGGTTGTGCTGAAGT 60.272 52.381 6.95 0.00 0.00 3.01
1188 1330 0.463833 CACGGTAAGAATCCCCTGCC 60.464 60.000 0.00 0.00 0.00 4.85
1195 1337 0.399806 AGAATCCCCTGCCTCTCCTC 60.400 60.000 0.00 0.00 0.00 3.71
1224 1442 1.166531 GGGGATCGCCAGGATTTTCG 61.167 60.000 23.21 0.00 34.82 3.46
1503 1790 1.902918 TGTACACGCCGTGGTACCT 60.903 57.895 22.60 2.03 37.94 3.08
1719 2040 0.098200 GTAAGGATTTTGCGCCGGTC 59.902 55.000 4.18 0.00 0.00 4.79
1771 2093 8.507249 GCTTAGTTTATAAAGTGCAGATATGGG 58.493 37.037 14.62 0.00 0.00 4.00
1785 2112 6.430925 TGCAGATATGGGATTTATTAGTGTGC 59.569 38.462 0.00 0.00 0.00 4.57
1808 2135 9.672086 GTGCAGAATTACTAGTAGTTGATAGAG 57.328 37.037 14.70 1.14 0.00 2.43
1871 2198 3.875727 CTGCTCTCCAATGTGATAACAGG 59.124 47.826 0.00 0.00 0.00 4.00
1906 2233 1.481772 AGATCAAGTGCTCTGCTCTCC 59.518 52.381 0.00 0.00 30.88 3.71
1914 2241 2.203640 TCTGCTCTCCGGTGTGGT 60.204 61.111 0.00 0.00 39.52 4.16
1929 2256 5.470777 CCGGTGTGGTAAGAAAATAGTGAAA 59.529 40.000 0.00 0.00 0.00 2.69
1930 2257 6.150474 CCGGTGTGGTAAGAAAATAGTGAAAT 59.850 38.462 0.00 0.00 0.00 2.17
1931 2258 7.334921 CCGGTGTGGTAAGAAAATAGTGAAATA 59.665 37.037 0.00 0.00 0.00 1.40
1982 2314 1.604185 CGTCAGGCTAGCTAGATTGGC 60.604 57.143 25.15 19.51 0.00 4.52
2019 2351 7.273815 CCTTCACACTTACGAATAGAAACTCTC 59.726 40.741 0.00 0.00 0.00 3.20
2043 2383 1.827969 TCTTAAGCTCTGCTCCACCTC 59.172 52.381 0.00 0.00 38.25 3.85
2051 2391 0.107456 CTGCTCCACCTCACAGTTGT 59.893 55.000 0.00 0.00 0.00 3.32
2071 2411 2.533266 TTTCAGTCAGCCTGTCAGTC 57.467 50.000 0.00 0.00 42.19 3.51
2087 2427 4.130118 GTCAGTCATCTCAACCACAAAGT 58.870 43.478 0.00 0.00 0.00 2.66
2108 2448 7.848223 AAGTGAAAAGGTTTCCAAGATTTTG 57.152 32.000 0.00 0.00 0.00 2.44
2211 2551 6.318648 ACATGATTACGACCTAATGCATTGTT 59.681 34.615 22.27 5.60 0.00 2.83
2232 2572 1.523758 AACTGCCCATCTCACGAAAC 58.476 50.000 0.00 0.00 0.00 2.78
2301 2641 3.814945 GCATGGCGCTTTCAGTAATATC 58.185 45.455 7.64 0.00 37.77 1.63
2302 2642 3.250762 GCATGGCGCTTTCAGTAATATCA 59.749 43.478 7.64 0.00 37.77 2.15
2303 2643 4.083110 GCATGGCGCTTTCAGTAATATCAT 60.083 41.667 7.64 0.00 37.77 2.45
2321 2661 3.750371 TCATCGGTCCAACATCTTTTGT 58.250 40.909 0.00 0.00 41.53 2.83
2329 2669 2.470999 CCAACATCTTTTGTTTTCCGCG 59.529 45.455 0.00 0.00 46.51 6.46
2388 2728 4.281525 TGCTCGACTTTTTGGTGTTTAC 57.718 40.909 0.00 0.00 0.00 2.01
2392 2732 6.261381 TGCTCGACTTTTTGGTGTTTACTAAT 59.739 34.615 0.00 0.00 0.00 1.73
2395 2735 9.807386 CTCGACTTTTTGGTGTTTACTAATAAG 57.193 33.333 0.00 0.00 39.99 1.73
2396 2736 8.776470 TCGACTTTTTGGTGTTTACTAATAAGG 58.224 33.333 9.90 0.00 39.15 2.69
2397 2737 8.019094 CGACTTTTTGGTGTTTACTAATAAGGG 58.981 37.037 9.90 1.51 39.15 3.95
2398 2738 8.771521 ACTTTTTGGTGTTTACTAATAAGGGT 57.228 30.769 9.90 0.00 39.15 4.34
2399 2739 8.853126 ACTTTTTGGTGTTTACTAATAAGGGTC 58.147 33.333 9.90 0.00 39.15 4.46
2400 2740 8.763984 TTTTTGGTGTTTACTAATAAGGGTCA 57.236 30.769 0.00 0.00 0.00 4.02
2401 2741 8.763984 TTTTGGTGTTTACTAATAAGGGTCAA 57.236 30.769 0.00 0.00 0.00 3.18
2402 2742 8.943594 TTTGGTGTTTACTAATAAGGGTCAAT 57.056 30.769 0.00 0.00 0.00 2.57
2405 2745 9.049050 TGGTGTTTACTAATAAGGGTCAATCTA 57.951 33.333 0.00 0.00 0.00 1.98
2408 4591 8.711170 TGTTTACTAATAAGGGTCAATCTAGGG 58.289 37.037 0.00 0.00 0.00 3.53
2415 4598 4.153371 AGGGTCAATCTAGGGCATATCT 57.847 45.455 0.00 0.00 0.00 1.98
2416 4599 5.291100 AGGGTCAATCTAGGGCATATCTA 57.709 43.478 0.00 0.00 0.00 1.98
2433 4616 8.958175 GCATATCTAGATATGGCGTAGTTATC 57.042 38.462 36.73 21.24 46.62 1.75
2439 4622 9.628500 TCTAGATATGGCGTAGTTATCATATGT 57.372 33.333 1.90 0.00 34.22 2.29
2440 4623 9.885934 CTAGATATGGCGTAGTTATCATATGTC 57.114 37.037 1.90 0.00 34.22 3.06
2441 4624 8.526667 AGATATGGCGTAGTTATCATATGTCT 57.473 34.615 1.90 0.98 34.22 3.41
2447 4630 7.229907 TGGCGTAGTTATCATATGTCTAAGTGA 59.770 37.037 1.90 0.00 0.00 3.41
2448 4631 7.537991 GGCGTAGTTATCATATGTCTAAGTGAC 59.462 40.741 1.90 0.00 45.54 3.67
2449 4632 8.291032 GCGTAGTTATCATATGTCTAAGTGACT 58.709 37.037 1.90 0.47 45.54 3.41
2450 4633 9.814507 CGTAGTTATCATATGTCTAAGTGACTC 57.185 37.037 1.90 0.12 45.54 3.36
2459 4642 9.761504 CATATGTCTAAGTGACTCAATCAATCT 57.238 33.333 0.00 0.00 45.54 2.40
2464 5339 8.637986 GTCTAAGTGACTCAATCAATCTAGGAT 58.362 37.037 0.00 0.00 39.72 3.24
2506 5381 9.748708 ATAAAATGCTTACATGAATTATTGCGT 57.251 25.926 0.00 0.00 36.36 5.24
2508 5383 9.579768 AAAATGCTTACATGAATTATTGCGTAA 57.420 25.926 0.00 0.00 36.36 3.18
2509 5384 9.579768 AAATGCTTACATGAATTATTGCGTAAA 57.420 25.926 0.00 0.00 36.36 2.01
2510 5385 9.579768 AATGCTTACATGAATTATTGCGTAAAA 57.420 25.926 0.00 0.00 36.36 1.52
2511 5386 9.748708 ATGCTTACATGAATTATTGCGTAAAAT 57.251 25.926 0.00 0.00 34.35 1.82
2512 5387 9.232082 TGCTTACATGAATTATTGCGTAAAATC 57.768 29.630 0.00 0.00 0.00 2.17
2513 5388 9.232082 GCTTACATGAATTATTGCGTAAAATCA 57.768 29.630 0.00 0.00 31.15 2.57
2517 5392 9.800433 ACATGAATTATTGCGTAAAATCAATGA 57.200 25.926 0.00 0.00 34.95 2.57
2527 5402 8.902540 TGCGTAAAATCAATGATATAGGTCTT 57.097 30.769 0.00 0.00 0.00 3.01
2535 5410 9.664332 AATCAATGATATAGGTCTTAGATGTGC 57.336 33.333 0.00 0.00 0.00 4.57
2537 5412 8.650490 TCAATGATATAGGTCTTAGATGTGCAA 58.350 33.333 0.00 0.00 0.00 4.08
2547 5422 8.624776 AGGTCTTAGATGTGCAATATTTAAAGC 58.375 33.333 0.00 0.00 0.00 3.51
2548 5423 8.405531 GGTCTTAGATGTGCAATATTTAAAGCA 58.594 33.333 0.00 0.00 34.10 3.91
2583 5458 9.781633 TGTGCTTTAGTAAAACTGTATTAGGAA 57.218 29.630 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.812571 GGGAACGATTCAACACTGCAT 59.187 47.619 0.00 0.00 0.00 3.96
1 2 1.234821 GGGAACGATTCAACACTGCA 58.765 50.000 0.00 0.00 0.00 4.41
2 3 0.521735 GGGGAACGATTCAACACTGC 59.478 55.000 0.00 0.00 0.00 4.40
3 4 1.535462 GTGGGGAACGATTCAACACTG 59.465 52.381 0.00 0.00 35.95 3.66
4 5 1.142060 TGTGGGGAACGATTCAACACT 59.858 47.619 16.57 0.00 38.13 3.55
5 6 1.600023 TGTGGGGAACGATTCAACAC 58.400 50.000 0.00 3.63 37.93 3.32
6 7 2.158559 CATGTGGGGAACGATTCAACA 58.841 47.619 0.00 0.00 0.00 3.33
7 8 1.472480 CCATGTGGGGAACGATTCAAC 59.528 52.381 0.00 0.00 0.00 3.18
8 9 1.832883 CCATGTGGGGAACGATTCAA 58.167 50.000 0.00 0.00 0.00 2.69
9 10 0.679640 GCCATGTGGGGAACGATTCA 60.680 55.000 0.54 0.00 37.04 2.57
10 11 2.106844 GCCATGTGGGGAACGATTC 58.893 57.895 0.54 0.00 37.04 2.52
11 12 4.337013 GCCATGTGGGGAACGATT 57.663 55.556 0.54 0.00 37.04 3.34
20 21 4.676951 ACCAACCCCGCCATGTGG 62.677 66.667 0.00 0.00 38.53 4.17
21 22 3.372730 CACCAACCCCGCCATGTG 61.373 66.667 0.00 0.00 0.00 3.21
44 45 2.434185 TTGCGATCCGTCCTGCAC 60.434 61.111 0.00 0.00 37.01 4.57
45 46 2.434185 GTTGCGATCCGTCCTGCA 60.434 61.111 0.00 0.00 35.15 4.41
46 47 3.554692 CGTTGCGATCCGTCCTGC 61.555 66.667 0.00 0.00 0.00 4.85
47 48 1.226974 ATCGTTGCGATCCGTCCTG 60.227 57.895 0.00 0.00 43.45 3.86
48 49 1.226974 CATCGTTGCGATCCGTCCT 60.227 57.895 0.68 0.00 45.19 3.85
49 50 2.871427 GCATCGTTGCGATCCGTCC 61.871 63.158 2.15 0.00 45.19 4.79
50 51 2.621000 GCATCGTTGCGATCCGTC 59.379 61.111 2.15 0.00 45.19 4.79
58 59 2.378945 CTATGGGTGCGCATCGTTGC 62.379 60.000 15.91 8.44 45.78 4.17
59 60 1.643292 CTATGGGTGCGCATCGTTG 59.357 57.895 15.91 8.12 0.00 4.10
60 61 1.523711 CCTATGGGTGCGCATCGTT 60.524 57.895 15.91 6.25 0.00 3.85
61 62 2.108976 CCTATGGGTGCGCATCGT 59.891 61.111 15.91 13.40 0.00 3.73
62 63 3.349006 GCCTATGGGTGCGCATCG 61.349 66.667 15.91 0.00 34.45 3.84
63 64 2.980233 GGCCTATGGGTGCGCATC 60.980 66.667 15.91 14.71 34.45 3.91
64 65 4.935495 CGGCCTATGGGTGCGCAT 62.935 66.667 15.91 0.00 34.45 4.73
67 68 4.856801 AAGCGGCCTATGGGTGCG 62.857 66.667 0.00 0.00 39.75 5.34
68 69 1.604147 AAAAAGCGGCCTATGGGTGC 61.604 55.000 0.00 6.40 36.72 5.01
69 70 0.455815 GAAAAAGCGGCCTATGGGTG 59.544 55.000 0.00 0.00 34.45 4.61
70 71 0.331616 AGAAAAAGCGGCCTATGGGT 59.668 50.000 0.00 0.00 34.45 4.51
71 72 1.134946 CAAGAAAAAGCGGCCTATGGG 59.865 52.381 0.00 0.00 0.00 4.00
72 73 1.818674 ACAAGAAAAAGCGGCCTATGG 59.181 47.619 0.00 0.00 0.00 2.74
73 74 2.867429 CACAAGAAAAAGCGGCCTATG 58.133 47.619 0.00 0.00 0.00 2.23
74 75 1.202348 GCACAAGAAAAAGCGGCCTAT 59.798 47.619 0.00 0.00 0.00 2.57
75 76 0.596082 GCACAAGAAAAAGCGGCCTA 59.404 50.000 0.00 0.00 0.00 3.93
76 77 1.363807 GCACAAGAAAAAGCGGCCT 59.636 52.632 0.00 0.00 0.00 5.19
77 78 2.016165 CGCACAAGAAAAAGCGGCC 61.016 57.895 0.00 0.00 45.83 6.13
78 79 3.526029 CGCACAAGAAAAAGCGGC 58.474 55.556 0.00 0.00 45.83 6.53
81 82 2.401720 CGATCAACGCACAAGAAAAAGC 59.598 45.455 0.00 0.00 34.51 3.51
82 83 3.872354 TCGATCAACGCACAAGAAAAAG 58.128 40.909 0.00 0.00 42.26 2.27
83 84 3.953874 TCGATCAACGCACAAGAAAAA 57.046 38.095 0.00 0.00 42.26 1.94
84 85 3.745975 AGATCGATCAACGCACAAGAAAA 59.254 39.130 26.47 0.00 42.26 2.29
85 86 3.325870 AGATCGATCAACGCACAAGAAA 58.674 40.909 26.47 0.00 42.26 2.52
86 87 2.959516 AGATCGATCAACGCACAAGAA 58.040 42.857 26.47 0.00 42.26 2.52
87 88 2.654749 AGATCGATCAACGCACAAGA 57.345 45.000 26.47 0.00 42.26 3.02
88 89 2.926200 AGAAGATCGATCAACGCACAAG 59.074 45.455 26.47 0.00 42.26 3.16
89 90 2.959516 AGAAGATCGATCAACGCACAA 58.040 42.857 26.47 0.00 42.26 3.33
90 91 2.654749 AGAAGATCGATCAACGCACA 57.345 45.000 26.47 0.00 42.26 4.57
91 92 2.535732 GCAAGAAGATCGATCAACGCAC 60.536 50.000 26.47 8.69 42.26 5.34
92 93 1.660607 GCAAGAAGATCGATCAACGCA 59.339 47.619 26.47 0.00 42.26 5.24
93 94 1.929836 AGCAAGAAGATCGATCAACGC 59.070 47.619 26.47 19.28 42.26 4.84
94 95 2.285486 GCAGCAAGAAGATCGATCAACG 60.285 50.000 26.47 11.24 44.09 4.10
95 96 2.031437 GGCAGCAAGAAGATCGATCAAC 59.969 50.000 26.47 18.49 0.00 3.18
96 97 2.093288 AGGCAGCAAGAAGATCGATCAA 60.093 45.455 26.47 0.00 0.00 2.57
97 98 1.483827 AGGCAGCAAGAAGATCGATCA 59.516 47.619 26.47 0.00 0.00 2.92
98 99 2.237393 AGGCAGCAAGAAGATCGATC 57.763 50.000 17.91 17.91 0.00 3.69
99 100 2.093288 TCAAGGCAGCAAGAAGATCGAT 60.093 45.455 0.00 0.00 0.00 3.59
100 101 1.276138 TCAAGGCAGCAAGAAGATCGA 59.724 47.619 0.00 0.00 0.00 3.59
101 102 1.396301 GTCAAGGCAGCAAGAAGATCG 59.604 52.381 0.00 0.00 0.00 3.69
102 103 1.742268 GGTCAAGGCAGCAAGAAGATC 59.258 52.381 0.00 0.00 0.00 2.75
103 104 1.615384 GGGTCAAGGCAGCAAGAAGAT 60.615 52.381 0.00 0.00 0.00 2.40
104 105 0.250901 GGGTCAAGGCAGCAAGAAGA 60.251 55.000 0.00 0.00 0.00 2.87
105 106 0.251077 AGGGTCAAGGCAGCAAGAAG 60.251 55.000 0.00 0.00 0.00 2.85
106 107 0.250901 GAGGGTCAAGGCAGCAAGAA 60.251 55.000 0.00 0.00 0.00 2.52
107 108 1.376466 GAGGGTCAAGGCAGCAAGA 59.624 57.895 0.00 0.00 0.00 3.02
108 109 2.037136 CGAGGGTCAAGGCAGCAAG 61.037 63.158 0.00 0.00 0.00 4.01
109 110 2.032528 CGAGGGTCAAGGCAGCAA 59.967 61.111 0.00 0.00 0.00 3.91
110 111 2.922503 TCGAGGGTCAAGGCAGCA 60.923 61.111 0.00 0.00 0.00 4.41
111 112 2.125350 CTCGAGGGTCAAGGCAGC 60.125 66.667 3.91 0.00 0.00 5.25
112 113 2.581354 CCTCGAGGGTCAAGGCAG 59.419 66.667 24.62 0.00 0.00 4.85
115 116 2.266055 GTGCCTCGAGGGTCAAGG 59.734 66.667 32.06 6.94 37.43 3.61
116 117 2.125912 CGTGCCTCGAGGGTCAAG 60.126 66.667 32.06 19.93 42.86 3.02
117 118 3.691342 CCGTGCCTCGAGGGTCAA 61.691 66.667 32.06 5.50 42.86 3.18
118 119 4.988716 ACCGTGCCTCGAGGGTCA 62.989 66.667 32.06 19.77 42.86 4.02
119 120 3.692406 AACCGTGCCTCGAGGGTC 61.692 66.667 32.06 17.28 42.86 4.46
120 121 4.003788 CAACCGTGCCTCGAGGGT 62.004 66.667 32.06 18.61 42.86 4.34
134 135 3.066190 GGCCCCCGGTTTAGCAAC 61.066 66.667 0.00 0.00 0.00 4.17
135 136 4.726304 CGGCCCCCGGTTTAGCAA 62.726 66.667 0.00 0.00 44.15 3.91
149 150 4.112341 AGACTGCGTACGACCGGC 62.112 66.667 21.65 9.10 0.00 6.13
150 151 2.202440 CAGACTGCGTACGACCGG 60.202 66.667 21.65 9.88 0.00 5.28
151 152 1.063951 GAACAGACTGCGTACGACCG 61.064 60.000 21.65 9.35 0.00 4.79
152 153 0.240411 AGAACAGACTGCGTACGACC 59.760 55.000 21.65 2.16 0.00 4.79
153 154 1.714460 CAAGAACAGACTGCGTACGAC 59.286 52.381 21.65 11.11 0.00 4.34
154 155 1.335597 CCAAGAACAGACTGCGTACGA 60.336 52.381 21.65 3.19 0.00 3.43
155 156 1.060713 CCAAGAACAGACTGCGTACG 58.939 55.000 11.84 11.84 0.00 3.67
156 157 2.150397 ACCAAGAACAGACTGCGTAC 57.850 50.000 1.25 0.00 0.00 3.67
157 158 2.479837 CAACCAAGAACAGACTGCGTA 58.520 47.619 1.25 0.00 0.00 4.42
158 159 1.299541 CAACCAAGAACAGACTGCGT 58.700 50.000 1.25 0.00 0.00 5.24
159 160 0.040958 GCAACCAAGAACAGACTGCG 60.041 55.000 1.25 0.00 0.00 5.18
160 161 1.312815 AGCAACCAAGAACAGACTGC 58.687 50.000 1.25 0.00 0.00 4.40
161 162 3.466836 TGTAGCAACCAAGAACAGACTG 58.533 45.455 0.00 0.00 0.00 3.51
162 163 3.838244 TGTAGCAACCAAGAACAGACT 57.162 42.857 0.00 0.00 0.00 3.24
163 164 4.893424 TTTGTAGCAACCAAGAACAGAC 57.107 40.909 0.00 0.00 0.00 3.51
164 165 5.650266 TCTTTTTGTAGCAACCAAGAACAGA 59.350 36.000 0.00 0.00 0.00 3.41
165 166 5.890334 TCTTTTTGTAGCAACCAAGAACAG 58.110 37.500 0.00 0.00 0.00 3.16
166 167 5.906113 TCTTTTTGTAGCAACCAAGAACA 57.094 34.783 0.00 0.00 0.00 3.18
167 168 7.706607 AGAAATCTTTTTGTAGCAACCAAGAAC 59.293 33.333 6.72 3.86 0.00 3.01
168 169 7.781056 AGAAATCTTTTTGTAGCAACCAAGAA 58.219 30.769 6.72 0.00 0.00 2.52
169 170 7.346751 AGAAATCTTTTTGTAGCAACCAAGA 57.653 32.000 0.00 5.61 0.00 3.02
170 171 7.323656 CGTAGAAATCTTTTTGTAGCAACCAAG 59.676 37.037 0.00 0.00 0.00 3.61
171 172 7.136119 CGTAGAAATCTTTTTGTAGCAACCAA 58.864 34.615 0.00 0.00 0.00 3.67
172 173 6.261381 ACGTAGAAATCTTTTTGTAGCAACCA 59.739 34.615 0.00 0.00 0.00 3.67
173 174 6.665465 ACGTAGAAATCTTTTTGTAGCAACC 58.335 36.000 0.00 0.00 0.00 3.77
174 175 9.474249 GATACGTAGAAATCTTTTTGTAGCAAC 57.526 33.333 0.08 0.00 0.00 4.17
175 176 8.662141 GGATACGTAGAAATCTTTTTGTAGCAA 58.338 33.333 0.08 0.00 0.00 3.91
176 177 8.193250 GGATACGTAGAAATCTTTTTGTAGCA 57.807 34.615 0.08 0.00 0.00 3.49
202 203 2.222819 GCGTGTCTTGATCGATTTGGTC 60.223 50.000 0.00 0.00 0.00 4.02
203 204 1.732259 GCGTGTCTTGATCGATTTGGT 59.268 47.619 0.00 0.00 0.00 3.67
204 205 1.267038 CGCGTGTCTTGATCGATTTGG 60.267 52.381 0.00 0.00 0.00 3.28
205 206 1.848186 GCGCGTGTCTTGATCGATTTG 60.848 52.381 8.43 0.00 0.00 2.32
206 207 0.370273 GCGCGTGTCTTGATCGATTT 59.630 50.000 8.43 0.00 0.00 2.17
207 208 0.735978 TGCGCGTGTCTTGATCGATT 60.736 50.000 8.43 0.00 0.00 3.34
208 209 0.735978 TTGCGCGTGTCTTGATCGAT 60.736 50.000 8.43 0.00 0.00 3.59
209 210 1.372375 TTGCGCGTGTCTTGATCGA 60.372 52.632 8.43 0.00 0.00 3.59
210 211 1.225475 GTTGCGCGTGTCTTGATCG 60.225 57.895 8.43 0.00 0.00 3.69
211 212 1.132640 GGTTGCGCGTGTCTTGATC 59.867 57.895 8.43 0.00 0.00 2.92
212 213 2.325082 GGGTTGCGCGTGTCTTGAT 61.325 57.895 8.43 0.00 0.00 2.57
213 214 2.970324 GGGTTGCGCGTGTCTTGA 60.970 61.111 8.43 0.00 0.00 3.02
214 215 4.025401 GGGGTTGCGCGTGTCTTG 62.025 66.667 8.43 0.00 0.00 3.02
215 216 4.250305 AGGGGTTGCGCGTGTCTT 62.250 61.111 8.43 0.00 0.00 3.01
216 217 4.681978 GAGGGGTTGCGCGTGTCT 62.682 66.667 8.43 0.00 0.00 3.41
224 225 4.778143 ACGATGCGGAGGGGTTGC 62.778 66.667 0.00 0.00 0.00 4.17
225 226 2.796483 TTCACGATGCGGAGGGGTTG 62.796 60.000 0.00 0.00 0.00 3.77
226 227 2.521958 CTTCACGATGCGGAGGGGTT 62.522 60.000 0.00 0.00 0.00 4.11
227 228 3.000819 TTCACGATGCGGAGGGGT 61.001 61.111 0.00 0.00 0.00 4.95
228 229 2.202932 CTTCACGATGCGGAGGGG 60.203 66.667 0.00 0.00 0.00 4.79
229 230 2.892425 GCTTCACGATGCGGAGGG 60.892 66.667 0.00 0.00 0.00 4.30
230 231 1.493950 GATGCTTCACGATGCGGAGG 61.494 60.000 0.00 0.00 34.59 4.30
231 232 0.529337 AGATGCTTCACGATGCGGAG 60.529 55.000 2.07 0.00 34.59 4.63
232 233 0.108186 AAGATGCTTCACGATGCGGA 60.108 50.000 2.07 0.00 34.59 5.54
233 234 0.302890 GAAGATGCTTCACGATGCGG 59.697 55.000 2.07 0.00 34.59 5.69
234 235 0.302890 GGAAGATGCTTCACGATGCG 59.697 55.000 9.16 0.00 34.59 4.73
235 236 1.329906 CTGGAAGATGCTTCACGATGC 59.670 52.381 9.16 0.00 34.07 3.91
236 237 2.897436 TCTGGAAGATGCTTCACGATG 58.103 47.619 9.16 0.00 38.67 3.84
294 295 5.304614 GCCACTCCTCCTTGAATACTATACA 59.695 44.000 0.00 0.00 0.00 2.29
340 347 9.120538 ACCATTGTTATTATAACAAGAGCGATT 57.879 29.630 27.27 12.30 42.57 3.34
341 348 8.559536 CACCATTGTTATTATAACAAGAGCGAT 58.440 33.333 27.27 12.87 42.57 4.58
361 410 6.540438 AGATGCAAATCTGAAATCACCATT 57.460 33.333 0.00 0.00 0.00 3.16
396 445 3.540367 TTTCGTCCCTTGTCCCGCC 62.540 63.158 0.00 0.00 0.00 6.13
397 446 2.031465 TTTCGTCCCTTGTCCCGC 59.969 61.111 0.00 0.00 0.00 6.13
398 447 1.670083 GGTTTCGTCCCTTGTCCCG 60.670 63.158 0.00 0.00 0.00 5.14
414 463 4.385405 GGCTCTGCTGTCGCTGGT 62.385 66.667 7.33 0.00 35.96 4.00
418 467 2.813042 GAGTGGCTCTGCTGTCGC 60.813 66.667 0.00 0.00 0.00 5.19
419 468 1.153862 GAGAGTGGCTCTGCTGTCG 60.154 63.158 3.12 0.00 41.35 4.35
420 469 0.319728 TTGAGAGTGGCTCTGCTGTC 59.680 55.000 3.12 0.00 41.35 3.51
421 470 0.761187 TTTGAGAGTGGCTCTGCTGT 59.239 50.000 3.12 0.00 41.35 4.40
422 471 2.008329 GATTTGAGAGTGGCTCTGCTG 58.992 52.381 3.12 0.00 41.35 4.41
424 473 1.339438 TGGATTTGAGAGTGGCTCTGC 60.339 52.381 3.12 0.00 41.35 4.26
426 475 2.264455 AGTGGATTTGAGAGTGGCTCT 58.736 47.619 0.00 0.00 44.28 4.09
427 476 2.746362 CAAGTGGATTTGAGAGTGGCTC 59.254 50.000 0.00 0.00 44.21 4.70
428 477 2.553904 CCAAGTGGATTTGAGAGTGGCT 60.554 50.000 0.00 0.00 37.39 4.75
429 478 1.815003 CCAAGTGGATTTGAGAGTGGC 59.185 52.381 0.00 0.00 37.39 5.01
430 479 2.440409 CCCAAGTGGATTTGAGAGTGG 58.560 52.381 0.00 0.00 37.39 4.00
431 480 1.815003 GCCCAAGTGGATTTGAGAGTG 59.185 52.381 0.00 0.00 37.39 3.51
432 481 1.707427 AGCCCAAGTGGATTTGAGAGT 59.293 47.619 0.00 0.00 37.39 3.24
433 482 2.363683 GAGCCCAAGTGGATTTGAGAG 58.636 52.381 0.00 0.00 37.39 3.20
439 488 2.044946 GCCGAGCCCAAGTGGATT 60.045 61.111 0.00 0.00 37.39 3.01
442 491 1.450312 CTAAGCCGAGCCCAAGTGG 60.450 63.158 0.00 0.00 37.09 4.00
448 497 4.243008 GGGAGCTAAGCCGAGCCC 62.243 72.222 3.89 5.39 43.97 5.19
453 502 2.872858 GACTTAATTGGGAGCTAAGCCG 59.127 50.000 0.00 0.00 0.00 5.52
454 503 3.879892 CTGACTTAATTGGGAGCTAAGCC 59.120 47.826 0.00 0.00 0.00 4.35
485 544 0.106708 ATTGCGAGCATATGGACCGT 59.893 50.000 4.56 0.00 0.00 4.83
487 546 1.882912 TGATTGCGAGCATATGGACC 58.117 50.000 4.56 0.00 0.00 4.46
508 567 2.217038 ACATCTGGACGTGGTGGCT 61.217 57.895 0.00 0.00 0.00 4.75
509 568 2.034879 CACATCTGGACGTGGTGGC 61.035 63.158 0.00 0.00 0.00 5.01
510 569 1.375908 CCACATCTGGACGTGGTGG 60.376 63.158 7.57 0.00 46.31 4.61
518 577 0.892755 GGTACACGTCCACATCTGGA 59.107 55.000 0.00 0.00 45.11 3.86
521 580 2.029290 GTCTTGGTACACGTCCACATCT 60.029 50.000 0.00 0.00 39.29 2.90
524 583 1.338973 GAGTCTTGGTACACGTCCACA 59.661 52.381 0.00 0.00 39.29 4.17
532 591 0.249120 CATGCCGGAGTCTTGGTACA 59.751 55.000 5.05 0.00 0.00 2.90
679 739 1.165907 TCTTCTGTGGTTGCTTGCGG 61.166 55.000 0.00 0.00 0.00 5.69
748 813 0.389948 GCGTGACAGAGAAATCCGGT 60.390 55.000 0.00 0.00 0.00 5.28
753 818 1.741770 GCCCGCGTGACAGAGAAAT 60.742 57.895 4.92 0.00 0.00 2.17
754 819 2.357034 GCCCGCGTGACAGAGAAA 60.357 61.111 4.92 0.00 0.00 2.52
774 839 2.126463 CGCGACGCTTCTGGAGAA 60.126 61.111 19.02 0.00 0.00 2.87
827 897 1.607251 CGGGTGGATTTATAGGCCGTC 60.607 57.143 0.00 0.00 0.00 4.79
900 970 2.514505 GAAGGAAGAAAGCGCGGTGC 62.515 60.000 13.41 7.54 46.98 5.01
933 1003 3.832171 CGTGCTGCGCTTCGTCTC 61.832 66.667 9.73 0.00 0.00 3.36
1093 1226 2.191128 ACTTCAGCACAACCTGGATC 57.809 50.000 0.00 0.00 33.64 3.36
1096 1229 0.670162 CCAACTTCAGCACAACCTGG 59.330 55.000 0.00 0.00 33.64 4.45
1112 1245 2.028484 GTCGTCGTGCAGGTCCAA 59.972 61.111 6.26 0.00 0.00 3.53
1211 1386 3.185188 CAGATATGACGAAAATCCTGGCG 59.815 47.826 0.00 0.00 0.00 5.69
1224 1442 7.482654 TCGGAAATGTCAATTCAGATATGAC 57.517 36.000 3.13 8.51 42.90 3.06
1719 2040 1.241990 ACAAGCACAGCAGCTGGATG 61.242 55.000 26.38 16.96 45.89 3.51
1785 2112 9.891828 CAGCTCTATCAACTACTAGTAATTCTG 57.108 37.037 3.76 0.00 0.00 3.02
1799 2126 2.935201 CAACTCCAGCAGCTCTATCAAC 59.065 50.000 0.00 0.00 0.00 3.18
1801 2128 1.483827 CCAACTCCAGCAGCTCTATCA 59.516 52.381 0.00 0.00 0.00 2.15
1808 2135 1.888512 TCAAAATCCAACTCCAGCAGC 59.111 47.619 0.00 0.00 0.00 5.25
1844 2171 1.066358 TCACATTGGAGAGCAGAGCAG 60.066 52.381 0.00 0.00 0.00 4.24
1871 2198 9.331282 AGCACTTGATCTAATTATTTCACTACC 57.669 33.333 0.00 0.00 0.00 3.18
1890 2217 1.447489 CCGGAGAGCAGAGCACTTG 60.447 63.158 0.00 0.00 28.14 3.16
1906 2233 6.548441 TTTCACTATTTTCTTACCACACCG 57.452 37.500 0.00 0.00 0.00 4.94
1929 2256 8.635765 TCTCTTGCACCTTGACTTTATTTTAT 57.364 30.769 0.00 0.00 0.00 1.40
1930 2257 8.635765 ATCTCTTGCACCTTGACTTTATTTTA 57.364 30.769 0.00 0.00 0.00 1.52
1931 2258 6.959639 TCTCTTGCACCTTGACTTTATTTT 57.040 33.333 0.00 0.00 0.00 1.82
1939 2270 2.161211 GCTCAATCTCTTGCACCTTGAC 59.839 50.000 0.00 0.00 32.11 3.18
1941 2272 1.129998 CGCTCAATCTCTTGCACCTTG 59.870 52.381 0.00 0.00 32.11 3.61
1982 2314 1.974236 AGTGTGAAGGTTCAGGAGAGG 59.026 52.381 0.00 0.00 37.98 3.69
2019 2351 2.999355 GTGGAGCAGAGCTTAAGAGTTG 59.001 50.000 6.67 1.56 39.88 3.16
2043 2383 2.684881 AGGCTGACTGAAAACAACTGTG 59.315 45.455 0.00 0.00 0.00 3.66
2071 2411 5.163519 ACCTTTTCACTTTGTGGTTGAGATG 60.164 40.000 0.00 0.00 33.87 2.90
2108 2448 2.961526 TGAGTGATTAGAAGCCGTCC 57.038 50.000 0.00 0.00 0.00 4.79
2112 2452 6.690194 AACATGAATGAGTGATTAGAAGCC 57.310 37.500 0.00 0.00 0.00 4.35
2211 2551 3.071479 GTTTCGTGAGATGGGCAGTTAA 58.929 45.455 0.00 0.00 41.60 2.01
2232 2572 6.199154 TGCGGTTAACATTTTAACAATGTGTG 59.801 34.615 14.68 6.58 46.24 3.82
2343 2683 0.164217 GGTTAACGAAATGCGCACGA 59.836 50.000 23.36 1.29 46.04 4.35
2388 2728 5.825593 TGCCCTAGATTGACCCTTATTAG 57.174 43.478 0.00 0.00 0.00 1.73
2392 2732 5.665701 AGATATGCCCTAGATTGACCCTTA 58.334 41.667 0.00 0.00 0.00 2.69
2395 2735 5.273208 TCTAGATATGCCCTAGATTGACCC 58.727 45.833 0.00 0.00 38.08 4.46
2396 2736 8.584157 CATATCTAGATATGCCCTAGATTGACC 58.416 40.741 30.49 0.00 46.30 4.02
2397 2737 8.584157 CCATATCTAGATATGCCCTAGATTGAC 58.416 40.741 33.74 0.00 46.30 3.18
2398 2738 7.234371 GCCATATCTAGATATGCCCTAGATTGA 59.766 40.741 33.74 5.98 46.30 2.57
2399 2739 7.385267 GCCATATCTAGATATGCCCTAGATTG 58.615 42.308 33.74 22.46 46.30 2.67
2400 2740 6.210385 CGCCATATCTAGATATGCCCTAGATT 59.790 42.308 33.74 7.97 46.30 2.40
2402 2742 5.073428 CGCCATATCTAGATATGCCCTAGA 58.927 45.833 33.74 7.69 45.72 2.43
2405 2745 3.647636 ACGCCATATCTAGATATGCCCT 58.352 45.455 33.74 18.59 45.72 5.19
2408 4591 8.568794 TGATAACTACGCCATATCTAGATATGC 58.431 37.037 33.74 28.10 45.72 3.14
2415 4598 9.628500 AGACATATGATAACTACGCCATATCTA 57.372 33.333 10.38 0.00 31.88 1.98
2416 4599 8.526667 AGACATATGATAACTACGCCATATCT 57.473 34.615 10.38 0.00 31.88 1.98
2420 4603 8.029522 CACTTAGACATATGATAACTACGCCAT 58.970 37.037 10.38 0.00 0.00 4.40
2421 4604 7.229907 TCACTTAGACATATGATAACTACGCCA 59.770 37.037 10.38 0.00 0.00 5.69
2422 4605 7.537991 GTCACTTAGACATATGATAACTACGCC 59.462 40.741 10.38 0.00 46.77 5.68
2439 4622 8.774546 ATCCTAGATTGATTGAGTCACTTAGA 57.225 34.615 0.00 0.00 36.32 2.10
2441 4624 9.868160 TCTATCCTAGATTGATTGAGTCACTTA 57.132 33.333 0.00 0.00 36.32 2.24
2480 5355 9.748708 ACGCAATAATTCATGTAAGCATTTTAT 57.251 25.926 0.00 0.00 31.99 1.40
2482 5357 9.579768 TTACGCAATAATTCATGTAAGCATTTT 57.420 25.926 0.00 0.00 31.99 1.82
2483 5358 9.579768 TTTACGCAATAATTCATGTAAGCATTT 57.420 25.926 0.00 0.00 31.99 2.32
2484 5359 9.579768 TTTTACGCAATAATTCATGTAAGCATT 57.420 25.926 0.00 0.00 31.99 3.56
2486 5361 9.232082 GATTTTACGCAATAATTCATGTAAGCA 57.768 29.630 0.00 0.00 0.00 3.91
2487 5362 9.232082 TGATTTTACGCAATAATTCATGTAAGC 57.768 29.630 0.00 0.00 0.00 3.09
2491 5366 9.800433 TCATTGATTTTACGCAATAATTCATGT 57.200 25.926 0.00 0.00 33.68 3.21
2500 5375 9.507329 AGACCTATATCATTGATTTTACGCAAT 57.493 29.630 4.14 0.00 35.24 3.56
2501 5376 8.902540 AGACCTATATCATTGATTTTACGCAA 57.097 30.769 4.14 0.00 0.00 4.85
2502 5377 8.902540 AAGACCTATATCATTGATTTTACGCA 57.097 30.769 4.14 0.00 0.00 5.24
2509 5384 9.664332 GCACATCTAAGACCTATATCATTGATT 57.336 33.333 4.14 0.00 0.00 2.57
2510 5385 8.819845 TGCACATCTAAGACCTATATCATTGAT 58.180 33.333 4.28 4.28 0.00 2.57
2511 5386 8.193953 TGCACATCTAAGACCTATATCATTGA 57.806 34.615 0.00 0.00 0.00 2.57
2512 5387 8.837788 TTGCACATCTAAGACCTATATCATTG 57.162 34.615 0.00 0.00 0.00 2.82
2521 5396 8.624776 GCTTTAAATATTGCACATCTAAGACCT 58.375 33.333 0.00 0.00 0.00 3.85
2522 5397 8.405531 TGCTTTAAATATTGCACATCTAAGACC 58.594 33.333 0.00 0.00 0.00 3.85
2556 5431 9.953565 TCCTAATACAGTTTTACTAAAGCACAT 57.046 29.630 0.00 0.00 0.00 3.21
2557 5432 9.781633 TTCCTAATACAGTTTTACTAAAGCACA 57.218 29.630 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.