Multiple sequence alignment - TraesCS7D01G380000

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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 TraesCS7D01G380000 chr7D 100.000 4147 0 0 1 4147 492215661 492219807 0.000000e+00 7659.0
1 TraesCS7D01G380000 chr7B 93.540 3901 158 31 284 4147 521611928 521615771 0.000000e+00 5722.0
2 TraesCS7D01G380000 chr7A 93.726 3156 123 32 393 3502 558751192 558754318 0.000000e+00 4662.0
3 TraesCS7D01G380000 chr7A 92.473 558 40 2 3592 4147 558754333 558754890 0.000000e+00 797.0
4 TraesCS7D01G380000 chr7A 91.582 392 29 3 9 399 558746584 558746972 4.720000e-149 538.0
5 TraesCS7D01G380000 chr7A 91.935 62 5 0 3525 3586 87692430 87692491 2.050000e-13 87.9
6 TraesCS7D01G380000 chrUn 85.047 107 7 1 3524 3630 15903920 15904017 2.640000e-17 100.0
7 TraesCS7D01G380000 chr2D 85.047 107 7 1 3524 3630 2476682 2476585 2.640000e-17 100.0
8 TraesCS7D01G380000 chr2D 91.176 68 4 2 3521 3586 290738941 290739008 1.590000e-14 91.6
9 TraesCS7D01G380000 chr1A 83.636 110 6 8 3525 3634 460934476 460934573 4.410000e-15 93.5
10 TraesCS7D01G380000 chr2A 92.308 65 3 2 3524 3586 315038081 315038017 1.590000e-14 91.6
11 TraesCS7D01G380000 chr2A 90.769 65 4 2 3524 3586 724414331 724414395 7.390000e-13 86.1
12 TraesCS7D01G380000 chr4A 81.739 115 9 4 3519 3631 37060104 37060208 7.390000e-13 86.1


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 TraesCS7D01G380000 chr7D 492215661 492219807 4146 False 7659.0 7659 100.0000 1 4147 1 chr7D.!!$F1 4146
1 TraesCS7D01G380000 chr7B 521611928 521615771 3843 False 5722.0 5722 93.5400 284 4147 1 chr7B.!!$F1 3863
2 TraesCS7D01G380000 chr7A 558751192 558754890 3698 False 2729.5 4662 93.0995 393 4147 2 chr7A.!!$F3 3754

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
102 103 0.379669 AAGACCGAGTACCGTATGCG 59.620 55.0 0.00 0.0 36.31 4.73 F
1001 1030 0.036105 TGGATCAGAGCGCACAACAT 60.036 50.0 11.47 0.0 0.00 2.71 F
2250 2298 1.207390 TTTTGCAAATGTGTCTGCGC 58.793 45.0 13.65 0.0 41.63 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1217 1253 3.610669 CGATCTCCTCGGGGGCAG 61.611 72.222 0.00 0.00 43.82 4.85 R
2579 2628 0.535780 CTGCCACAAGAGAAGCACCA 60.536 55.000 0.00 0.00 0.00 4.17 R
3498 3575 1.003580 TCCTAGAAGGCAAGTTGGCAG 59.996 52.381 28.85 17.64 46.46 4.85 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
23 24 6.567687 TGTTGTTGGTGTCCTAAATATGTG 57.432 37.500 0.00 0.00 0.00 3.21
24 25 5.048364 TGTTGTTGGTGTCCTAAATATGTGC 60.048 40.000 0.00 0.00 0.00 4.57
25 26 4.917385 TGTTGGTGTCCTAAATATGTGCT 58.083 39.130 0.00 0.00 0.00 4.40
26 27 4.941263 TGTTGGTGTCCTAAATATGTGCTC 59.059 41.667 0.00 0.00 0.00 4.26
27 28 5.186198 GTTGGTGTCCTAAATATGTGCTCT 58.814 41.667 0.00 0.00 0.00 4.09
28 29 5.023533 TGGTGTCCTAAATATGTGCTCTC 57.976 43.478 0.00 0.00 0.00 3.20
29 30 4.469586 TGGTGTCCTAAATATGTGCTCTCA 59.530 41.667 0.00 0.00 0.00 3.27
30 31 5.130975 TGGTGTCCTAAATATGTGCTCTCAT 59.869 40.000 0.00 0.00 0.00 2.90
31 32 5.468072 GGTGTCCTAAATATGTGCTCTCATG 59.532 44.000 0.00 0.00 0.00 3.07
32 33 5.468072 GTGTCCTAAATATGTGCTCTCATGG 59.532 44.000 0.00 0.00 0.00 3.66
33 34 5.130975 TGTCCTAAATATGTGCTCTCATGGT 59.869 40.000 0.00 0.00 0.00 3.55
34 35 6.058183 GTCCTAAATATGTGCTCTCATGGTT 58.942 40.000 0.00 0.00 0.00 3.67
35 36 7.147567 TGTCCTAAATATGTGCTCTCATGGTTA 60.148 37.037 0.00 0.00 0.00 2.85
36 37 7.386299 GTCCTAAATATGTGCTCTCATGGTTAG 59.614 40.741 0.00 0.00 32.09 2.34
37 38 6.652481 CCTAAATATGTGCTCTCATGGTTAGG 59.348 42.308 14.24 14.24 38.17 2.69
38 39 5.636903 AATATGTGCTCTCATGGTTAGGT 57.363 39.130 0.00 0.00 0.00 3.08
39 40 5.636903 ATATGTGCTCTCATGGTTAGGTT 57.363 39.130 0.00 0.00 0.00 3.50
40 41 3.788227 TGTGCTCTCATGGTTAGGTTT 57.212 42.857 0.00 0.00 0.00 3.27
41 42 3.674997 TGTGCTCTCATGGTTAGGTTTC 58.325 45.455 0.00 0.00 0.00 2.78
42 43 3.010420 GTGCTCTCATGGTTAGGTTTCC 58.990 50.000 0.00 0.00 0.00 3.13
43 44 2.026262 TGCTCTCATGGTTAGGTTTCCC 60.026 50.000 0.00 0.00 0.00 3.97
44 45 2.684038 GCTCTCATGGTTAGGTTTCCCC 60.684 54.545 0.00 0.00 0.00 4.81
45 46 2.576191 CTCTCATGGTTAGGTTTCCCCA 59.424 50.000 0.00 0.00 34.66 4.96
46 47 2.990284 TCTCATGGTTAGGTTTCCCCAA 59.010 45.455 0.00 0.00 34.66 4.12
47 48 3.399644 TCTCATGGTTAGGTTTCCCCAAA 59.600 43.478 0.00 0.00 34.66 3.28
48 49 3.502356 TCATGGTTAGGTTTCCCCAAAC 58.498 45.455 0.00 0.00 41.22 2.93
60 61 5.902681 GTTTCCCCAAACCATCTTTATAGC 58.097 41.667 0.00 0.00 36.62 2.97
61 62 5.466127 TTCCCCAAACCATCTTTATAGCT 57.534 39.130 0.00 0.00 0.00 3.32
62 63 5.048846 TCCCCAAACCATCTTTATAGCTC 57.951 43.478 0.00 0.00 0.00 4.09
63 64 4.141251 TCCCCAAACCATCTTTATAGCTCC 60.141 45.833 0.00 0.00 0.00 4.70
64 65 4.141158 CCCCAAACCATCTTTATAGCTCCT 60.141 45.833 0.00 0.00 0.00 3.69
65 66 5.449553 CCCAAACCATCTTTATAGCTCCTT 58.550 41.667 0.00 0.00 0.00 3.36
66 67 5.300286 CCCAAACCATCTTTATAGCTCCTTG 59.700 44.000 0.00 0.00 0.00 3.61
67 68 5.221126 CCAAACCATCTTTATAGCTCCTTGC 60.221 44.000 0.00 0.00 43.29 4.01
68 69 4.092116 ACCATCTTTATAGCTCCTTGCC 57.908 45.455 0.00 0.00 44.23 4.52
69 70 3.070018 CCATCTTTATAGCTCCTTGCCG 58.930 50.000 0.00 0.00 44.23 5.69
70 71 2.240493 TCTTTATAGCTCCTTGCCGC 57.760 50.000 0.00 0.00 44.23 6.53
71 72 1.762957 TCTTTATAGCTCCTTGCCGCT 59.237 47.619 0.00 0.00 44.23 5.52
72 73 2.963101 TCTTTATAGCTCCTTGCCGCTA 59.037 45.455 0.00 0.00 44.23 4.26
74 75 4.040461 TCTTTATAGCTCCTTGCCGCTATT 59.960 41.667 8.81 0.00 44.63 1.73
75 76 2.938956 ATAGCTCCTTGCCGCTATTT 57.061 45.000 0.00 0.00 44.63 1.40
76 77 2.710096 TAGCTCCTTGCCGCTATTTT 57.290 45.000 0.00 0.00 44.23 1.82
77 78 1.098050 AGCTCCTTGCCGCTATTTTG 58.902 50.000 0.00 0.00 44.23 2.44
78 79 0.811281 GCTCCTTGCCGCTATTTTGT 59.189 50.000 0.00 0.00 35.15 2.83
79 80 1.202188 GCTCCTTGCCGCTATTTTGTC 60.202 52.381 0.00 0.00 35.15 3.18
80 81 2.083774 CTCCTTGCCGCTATTTTGTCA 58.916 47.619 0.00 0.00 0.00 3.58
81 82 2.487762 CTCCTTGCCGCTATTTTGTCAA 59.512 45.455 0.00 0.00 0.00 3.18
82 83 2.887783 TCCTTGCCGCTATTTTGTCAAA 59.112 40.909 0.00 0.00 0.00 2.69
83 84 3.319405 TCCTTGCCGCTATTTTGTCAAAA 59.681 39.130 12.97 12.97 34.41 2.44
84 85 4.054671 CCTTGCCGCTATTTTGTCAAAAA 58.945 39.130 14.47 4.29 39.53 1.94
85 86 4.150451 CCTTGCCGCTATTTTGTCAAAAAG 59.850 41.667 14.47 13.13 38.62 2.27
86 87 4.576216 TGCCGCTATTTTGTCAAAAAGA 57.424 36.364 14.47 5.52 38.62 2.52
97 98 2.747436 GTCAAAAAGACCGAGTACCGT 58.253 47.619 0.00 0.00 41.56 4.83
98 99 3.900941 GTCAAAAAGACCGAGTACCGTA 58.099 45.455 0.00 0.00 41.56 4.02
99 100 4.488879 GTCAAAAAGACCGAGTACCGTAT 58.511 43.478 0.00 0.00 41.56 3.06
100 101 4.325472 GTCAAAAAGACCGAGTACCGTATG 59.675 45.833 0.00 0.00 41.56 2.39
101 102 2.573941 AAAGACCGAGTACCGTATGC 57.426 50.000 0.00 0.00 36.31 3.14
102 103 0.379669 AAGACCGAGTACCGTATGCG 59.620 55.000 0.00 0.00 36.31 4.73
103 104 1.656569 GACCGAGTACCGTATGCGC 60.657 63.158 0.00 0.00 36.67 6.09
104 105 2.327002 GACCGAGTACCGTATGCGCA 62.327 60.000 14.96 14.96 36.67 6.09
105 106 1.226745 CCGAGTACCGTATGCGCAA 60.227 57.895 17.11 0.11 36.67 4.85
106 107 0.802994 CCGAGTACCGTATGCGCAAA 60.803 55.000 17.11 0.00 36.67 3.68
107 108 0.993532 CGAGTACCGTATGCGCAAAA 59.006 50.000 17.11 2.00 36.67 2.44
108 109 1.390803 CGAGTACCGTATGCGCAAAAA 59.609 47.619 17.11 0.00 36.67 1.94
135 136 9.696917 AAAAAGACTGAGCACCATAAAATTTAG 57.303 29.630 0.00 0.00 0.00 1.85
136 137 8.409358 AAAGACTGAGCACCATAAAATTTAGT 57.591 30.769 0.00 0.00 0.00 2.24
137 138 9.515226 AAAGACTGAGCACCATAAAATTTAGTA 57.485 29.630 0.00 0.00 0.00 1.82
138 139 8.494016 AGACTGAGCACCATAAAATTTAGTAC 57.506 34.615 0.00 0.00 0.00 2.73
139 140 7.277981 AGACTGAGCACCATAAAATTTAGTACG 59.722 37.037 0.00 0.00 0.00 3.67
140 141 6.315393 ACTGAGCACCATAAAATTTAGTACGG 59.685 38.462 0.00 0.00 0.00 4.02
141 142 5.065474 TGAGCACCATAAAATTTAGTACGGC 59.935 40.000 0.00 0.00 0.00 5.68
142 143 4.034742 AGCACCATAAAATTTAGTACGGCG 59.965 41.667 4.80 4.80 0.00 6.46
143 144 4.276460 CACCATAAAATTTAGTACGGCGC 58.724 43.478 6.90 0.00 0.00 6.53
144 145 3.940221 ACCATAAAATTTAGTACGGCGCA 59.060 39.130 10.83 0.00 0.00 6.09
145 146 4.395542 ACCATAAAATTTAGTACGGCGCAA 59.604 37.500 10.83 0.00 0.00 4.85
146 147 5.106237 ACCATAAAATTTAGTACGGCGCAAA 60.106 36.000 10.83 0.00 0.00 3.68
147 148 5.228427 CCATAAAATTTAGTACGGCGCAAAC 59.772 40.000 10.83 3.48 0.00 2.93
148 149 3.900388 AAATTTAGTACGGCGCAAACA 57.100 38.095 10.83 0.00 0.00 2.83
149 150 3.900388 AATTTAGTACGGCGCAAACAA 57.100 38.095 10.83 0.00 0.00 2.83
150 151 4.428615 AATTTAGTACGGCGCAAACAAT 57.571 36.364 10.83 0.00 0.00 2.71
151 152 2.884663 TTAGTACGGCGCAAACAATG 57.115 45.000 10.83 0.00 0.00 2.82
152 153 1.798283 TAGTACGGCGCAAACAATGT 58.202 45.000 10.83 0.00 0.00 2.71
153 154 0.948678 AGTACGGCGCAAACAATGTT 59.051 45.000 10.83 0.00 0.00 2.71
154 155 2.144730 AGTACGGCGCAAACAATGTTA 58.855 42.857 10.83 0.00 0.00 2.41
155 156 2.096119 AGTACGGCGCAAACAATGTTAC 60.096 45.455 10.83 0.00 0.00 2.50
156 157 0.948678 ACGGCGCAAACAATGTTACT 59.051 45.000 10.83 0.00 0.00 2.24
157 158 1.326576 CGGCGCAAACAATGTTACTG 58.673 50.000 10.83 0.00 0.00 2.74
158 159 1.696988 GGCGCAAACAATGTTACTGG 58.303 50.000 10.83 0.00 0.00 4.00
159 160 1.268352 GGCGCAAACAATGTTACTGGA 59.732 47.619 10.83 0.00 0.00 3.86
160 161 2.287909 GGCGCAAACAATGTTACTGGAA 60.288 45.455 10.83 0.00 0.00 3.53
161 162 2.979813 GCGCAAACAATGTTACTGGAAG 59.020 45.455 0.30 0.00 42.29 3.46
177 178 2.783135 GGAAGTGTCCAAGCTTCATGA 58.217 47.619 0.00 0.00 44.26 3.07
178 179 3.149196 GGAAGTGTCCAAGCTTCATGAA 58.851 45.455 8.12 8.12 44.26 2.57
179 180 3.569701 GGAAGTGTCCAAGCTTCATGAAA 59.430 43.478 9.88 0.00 44.26 2.69
180 181 4.320788 GGAAGTGTCCAAGCTTCATGAAAG 60.321 45.833 9.88 5.19 44.26 2.62
181 182 3.825328 AGTGTCCAAGCTTCATGAAAGT 58.175 40.909 9.88 0.00 37.31 2.66
182 183 3.817647 AGTGTCCAAGCTTCATGAAAGTC 59.182 43.478 9.88 2.03 37.31 3.01
183 184 3.565482 GTGTCCAAGCTTCATGAAAGTCA 59.435 43.478 9.88 0.24 37.31 3.41
184 185 4.217118 GTGTCCAAGCTTCATGAAAGTCAT 59.783 41.667 9.88 0.00 37.65 3.06
195 196 5.281693 CATGAAAGTCATGCGTTAGTTGA 57.718 39.130 5.36 0.00 46.37 3.18
196 197 5.688823 CATGAAAGTCATGCGTTAGTTGAA 58.311 37.500 5.36 0.00 46.37 2.69
197 198 5.940192 TGAAAGTCATGCGTTAGTTGAAT 57.060 34.783 0.00 0.00 0.00 2.57
198 199 6.312399 TGAAAGTCATGCGTTAGTTGAATT 57.688 33.333 0.00 0.00 29.78 2.17
199 200 6.142139 TGAAAGTCATGCGTTAGTTGAATTG 58.858 36.000 0.00 0.00 29.20 2.32
200 201 5.940192 AAGTCATGCGTTAGTTGAATTGA 57.060 34.783 0.00 0.00 0.00 2.57
201 202 5.536554 AGTCATGCGTTAGTTGAATTGAG 57.463 39.130 0.00 0.00 0.00 3.02
202 203 4.997395 AGTCATGCGTTAGTTGAATTGAGT 59.003 37.500 0.00 0.00 0.00 3.41
203 204 5.470098 AGTCATGCGTTAGTTGAATTGAGTT 59.530 36.000 0.00 0.00 0.00 3.01
204 205 6.017109 AGTCATGCGTTAGTTGAATTGAGTTT 60.017 34.615 0.00 0.00 0.00 2.66
205 206 6.303259 GTCATGCGTTAGTTGAATTGAGTTTC 59.697 38.462 0.00 0.00 0.00 2.78
206 207 5.103290 TGCGTTAGTTGAATTGAGTTTCC 57.897 39.130 0.00 0.00 0.00 3.13
207 208 4.819630 TGCGTTAGTTGAATTGAGTTTCCT 59.180 37.500 0.00 0.00 0.00 3.36
208 209 5.298276 TGCGTTAGTTGAATTGAGTTTCCTT 59.702 36.000 0.00 0.00 0.00 3.36
209 210 5.625311 GCGTTAGTTGAATTGAGTTTCCTTG 59.375 40.000 0.00 0.00 0.00 3.61
210 211 6.725246 CGTTAGTTGAATTGAGTTTCCTTGT 58.275 36.000 0.00 0.00 0.00 3.16
211 212 7.519328 GCGTTAGTTGAATTGAGTTTCCTTGTA 60.519 37.037 0.00 0.00 0.00 2.41
212 213 8.504005 CGTTAGTTGAATTGAGTTTCCTTGTAT 58.496 33.333 0.00 0.00 0.00 2.29
213 214 9.827411 GTTAGTTGAATTGAGTTTCCTTGTATC 57.173 33.333 0.00 0.00 0.00 2.24
214 215 9.567776 TTAGTTGAATTGAGTTTCCTTGTATCA 57.432 29.630 0.00 0.00 0.00 2.15
215 216 8.641498 AGTTGAATTGAGTTTCCTTGTATCAT 57.359 30.769 0.00 0.00 0.00 2.45
216 217 8.734386 AGTTGAATTGAGTTTCCTTGTATCATC 58.266 33.333 0.00 0.00 0.00 2.92
217 218 8.514594 GTTGAATTGAGTTTCCTTGTATCATCA 58.485 33.333 0.00 0.00 0.00 3.07
218 219 8.812513 TGAATTGAGTTTCCTTGTATCATCAT 57.187 30.769 0.00 0.00 0.00 2.45
219 220 9.904198 TGAATTGAGTTTCCTTGTATCATCATA 57.096 29.630 0.00 0.00 0.00 2.15
221 222 9.911788 AATTGAGTTTCCTTGTATCATCATAGT 57.088 29.630 0.00 0.00 0.00 2.12
222 223 8.722480 TTGAGTTTCCTTGTATCATCATAGTG 57.278 34.615 0.00 0.00 0.00 2.74
223 224 7.275183 TGAGTTTCCTTGTATCATCATAGTGG 58.725 38.462 0.00 0.00 0.00 4.00
224 225 7.125659 TGAGTTTCCTTGTATCATCATAGTGGA 59.874 37.037 0.00 0.00 0.00 4.02
225 226 8.038862 AGTTTCCTTGTATCATCATAGTGGAT 57.961 34.615 0.00 0.00 0.00 3.41
226 227 8.153550 AGTTTCCTTGTATCATCATAGTGGATC 58.846 37.037 0.00 0.00 0.00 3.36
227 228 7.862274 TTCCTTGTATCATCATAGTGGATCT 57.138 36.000 0.00 0.00 0.00 2.75
228 229 8.956446 TTCCTTGTATCATCATAGTGGATCTA 57.044 34.615 0.00 0.00 0.00 1.98
229 230 8.354711 TCCTTGTATCATCATAGTGGATCTAC 57.645 38.462 0.00 0.00 0.00 2.59
230 231 7.397476 TCCTTGTATCATCATAGTGGATCTACC 59.603 40.741 5.47 0.00 39.54 3.18
231 232 7.398618 CCTTGTATCATCATAGTGGATCTACCT 59.601 40.741 5.47 0.00 39.86 3.08
232 233 8.727100 TTGTATCATCATAGTGGATCTACCTT 57.273 34.615 5.47 0.00 39.86 3.50
233 234 8.727100 TGTATCATCATAGTGGATCTACCTTT 57.273 34.615 5.47 0.00 39.86 3.11
234 235 9.159254 TGTATCATCATAGTGGATCTACCTTTT 57.841 33.333 5.47 0.00 39.86 2.27
237 238 8.089625 TCATCATAGTGGATCTACCTTTTTCA 57.910 34.615 5.47 0.00 39.86 2.69
238 239 8.548025 TCATCATAGTGGATCTACCTTTTTCAA 58.452 33.333 5.47 0.00 39.86 2.69
239 240 8.616076 CATCATAGTGGATCTACCTTTTTCAAC 58.384 37.037 5.47 0.00 39.86 3.18
240 241 7.685481 TCATAGTGGATCTACCTTTTTCAACA 58.315 34.615 5.47 0.00 39.86 3.33
241 242 8.160765 TCATAGTGGATCTACCTTTTTCAACAA 58.839 33.333 5.47 0.00 39.86 2.83
242 243 6.884280 AGTGGATCTACCTTTTTCAACAAG 57.116 37.500 5.47 0.00 39.86 3.16
243 244 5.770162 AGTGGATCTACCTTTTTCAACAAGG 59.230 40.000 5.47 0.34 45.74 3.61
254 255 8.716646 CCTTTTTCAACAAGGTTTTGACTAAT 57.283 30.769 0.00 0.00 36.74 1.73
255 256 9.161629 CCTTTTTCAACAAGGTTTTGACTAATT 57.838 29.630 0.00 0.00 36.74 1.40
275 276 9.463443 ACTAATTATTTTTCATTGGCTAATCGC 57.537 29.630 0.00 0.00 38.13 4.58
292 293 6.688813 GCTAATCGCCTTTCTCTATTTTTGTG 59.311 38.462 0.00 0.00 0.00 3.33
457 458 9.543783 AACAATATCCCTAACGTAAAGAATCTC 57.456 33.333 0.00 0.00 0.00 2.75
484 485 6.238648 ACCGATTTCTTGATGAGTTTAAGGT 58.761 36.000 0.00 0.00 0.00 3.50
534 535 3.064820 ACTTCAACGGTGTTCATGTTGTC 59.935 43.478 0.00 0.00 42.65 3.18
571 572 5.088026 ACTAAGCTAGGTTGTTCTTCCTCT 58.912 41.667 17.34 0.00 35.51 3.69
572 573 6.254522 ACTAAGCTAGGTTGTTCTTCCTCTA 58.745 40.000 17.34 0.00 35.51 2.43
590 591 3.941483 CTCTAACGGGTTTTGCTCATGAT 59.059 43.478 0.00 0.00 0.00 2.45
629 630 2.492012 CTCTCATGGCTAATGGCTCAC 58.508 52.381 0.00 0.00 41.46 3.51
636 637 0.532196 GCTAATGGCTCACCGTACCC 60.532 60.000 0.00 0.00 39.70 3.69
674 675 4.424061 TGCATGTGTCAAAGTCAATAGC 57.576 40.909 0.00 0.00 0.00 2.97
705 724 2.069273 CACATCGTTCTCTTTCGCCTT 58.931 47.619 0.00 0.00 0.00 4.35
833 859 5.240891 TCTCAACAAATCTCAGCTAGGTTG 58.759 41.667 0.00 0.00 36.42 3.77
834 860 4.973168 TCAACAAATCTCAGCTAGGTTGT 58.027 39.130 0.00 0.00 36.18 3.32
835 861 5.376625 TCAACAAATCTCAGCTAGGTTGTT 58.623 37.500 0.00 0.00 41.02 2.83
840 866 2.977914 TCTCAGCTAGGTTGTTCATGC 58.022 47.619 0.00 0.00 0.00 4.06
902 931 5.960704 TGTGGATGGGCTACTCTTAGTATA 58.039 41.667 0.00 0.00 29.08 1.47
909 938 2.754002 GCTACTCTTAGTATAGGCCGGG 59.246 54.545 2.18 0.00 29.08 5.73
949 978 7.392673 AGCAATTTCTTCTAAGCTTCTTCATCA 59.607 33.333 0.00 0.00 0.00 3.07
993 1022 1.064946 GACCGACTGGATCAGAGCG 59.935 63.158 1.59 5.23 39.21 5.03
1001 1030 0.036105 TGGATCAGAGCGCACAACAT 60.036 50.000 11.47 0.00 0.00 2.71
1383 1422 3.207669 CTGCCCTTCCGCATGCTC 61.208 66.667 17.13 0.00 38.30 4.26
1514 1554 2.312140 ACACTTAGGAGCCTCTAGGTCA 59.688 50.000 0.00 0.00 45.21 4.02
1522 1562 2.417239 GAGCCTCTAGGTCATCGTATCG 59.583 54.545 0.00 0.00 42.81 2.92
1647 1688 8.691661 TTTAAGACTAGCAAGTGGAGAATTTT 57.308 30.769 0.00 0.00 35.56 1.82
1663 1704 9.527157 TGGAGAATTTTTGTTATAACATCCAGA 57.473 29.630 22.31 6.76 38.95 3.86
1748 1789 5.989477 TCCAGTAATTAGCTGTATTGTGCT 58.011 37.500 0.00 0.00 42.67 4.40
1949 1995 6.865834 TTGGGTATGTGCCAATTCTTTATT 57.134 33.333 0.00 0.00 0.00 1.40
2028 2075 9.690913 AGTGGCTCATATATATTTGTTGCATAT 57.309 29.630 17.47 0.00 0.00 1.78
2082 2129 2.353109 CCTCTGATCACTGTCGCTGAAA 60.353 50.000 0.00 0.00 0.00 2.69
2211 2259 3.181471 GCACTAAAGCTGCCTATCTGAGA 60.181 47.826 0.00 0.00 0.00 3.27
2218 2266 3.715834 AGCTGCCTATCTGAGATTTCCTT 59.284 43.478 0.00 0.00 0.00 3.36
2250 2298 1.207390 TTTTGCAAATGTGTCTGCGC 58.793 45.000 13.65 0.00 41.63 6.09
2482 2531 3.550561 TCGTTAAATCGCTTGTGCAAAG 58.449 40.909 0.00 0.00 39.64 2.77
2513 2562 2.240493 ACCTTTGTGTTCCAGTCTCG 57.760 50.000 0.00 0.00 0.00 4.04
2879 2928 1.473434 GGTTTAGACCCGGCTGATCTG 60.473 57.143 0.00 0.00 40.25 2.90
3268 3338 3.191078 TCAGCATTTTTGTTTGTGGGG 57.809 42.857 0.00 0.00 0.00 4.96
3301 3371 5.667466 AGTCGTGGTTCTGTAAAAGAGAAA 58.333 37.500 0.00 0.00 35.91 2.52
3305 3375 6.364165 TCGTGGTTCTGTAAAAGAGAAATACG 59.636 38.462 13.27 13.27 39.70 3.06
3444 3519 9.547753 ACATTATTACGATCTGCTATTGAAGTT 57.452 29.630 0.00 0.00 0.00 2.66
3480 3557 3.126000 GCTGGACTCAACATTGCTAACTC 59.874 47.826 0.00 0.00 0.00 3.01
3484 3561 5.011635 TGGACTCAACATTGCTAACTCTACA 59.988 40.000 0.00 0.00 0.00 2.74
3502 3579 8.045176 ACTCTACAAAATTTAACTGATCTGCC 57.955 34.615 0.00 0.00 0.00 4.85
3513 3590 1.471684 CTGATCTGCCAACTTGCCTTC 59.528 52.381 0.00 0.00 0.00 3.46
3516 3593 2.479566 TCTGCCAACTTGCCTTCTAG 57.520 50.000 0.00 0.00 0.00 2.43
3517 3594 1.003580 TCTGCCAACTTGCCTTCTAGG 59.996 52.381 0.00 0.00 38.80 3.02
3525 3602 5.768164 CCAACTTGCCTTCTAGGAAAAAGTA 59.232 40.000 0.00 0.00 37.67 2.24
3533 3610 5.722441 CCTTCTAGGAAAAAGTACTCCCTCT 59.278 44.000 0.00 0.00 37.67 3.69
3548 3625 8.865090 AGTACTCCCTCTGATTCATAATAAGTG 58.135 37.037 0.00 0.00 0.00 3.16
3551 3628 7.345653 ACTCCCTCTGATTCATAATAAGTGTCA 59.654 37.037 0.00 0.00 0.00 3.58
3553 3630 7.125659 TCCCTCTGATTCATAATAAGTGTCACA 59.874 37.037 5.62 0.00 0.00 3.58
3562 3640 9.944663 TTCATAATAAGTGTCACAGTTTTGAAC 57.055 29.630 2.42 0.00 0.00 3.18
3571 3649 5.034797 GTCACAGTTTTGAACTAAGGTTGC 58.965 41.667 0.00 0.00 40.46 4.17
3572 3650 4.097286 TCACAGTTTTGAACTAAGGTTGCC 59.903 41.667 0.00 0.00 40.46 4.52
3573 3651 4.020543 ACAGTTTTGAACTAAGGTTGCCA 58.979 39.130 0.00 0.00 40.46 4.92
3574 3652 4.464597 ACAGTTTTGAACTAAGGTTGCCAA 59.535 37.500 0.00 0.00 40.46 4.52
3575 3653 4.803613 CAGTTTTGAACTAAGGTTGCCAAC 59.196 41.667 0.00 0.00 40.46 3.77
3576 3654 4.142026 AGTTTTGAACTAAGGTTGCCAACC 60.142 41.667 19.12 19.12 45.61 3.77
3587 3665 2.035449 GGTTGCCAACCTTAGTTCAACC 59.965 50.000 19.45 11.48 45.77 3.77
3588 3666 2.956333 GTTGCCAACCTTAGTTCAACCT 59.044 45.455 0.00 0.00 35.89 3.50
3589 3667 3.306472 TGCCAACCTTAGTTCAACCTT 57.694 42.857 0.00 0.00 32.45 3.50
3590 3668 3.637769 TGCCAACCTTAGTTCAACCTTT 58.362 40.909 0.00 0.00 32.45 3.11
3600 3678 6.533723 CCTTAGTTCAACCTTTGTTCAAAACC 59.466 38.462 0.00 0.00 30.42 3.27
3603 3681 2.231478 TCAACCTTTGTTCAAAACCGCA 59.769 40.909 0.00 0.00 30.42 5.69
3610 3688 3.305398 TGTTCAAAACCGCAACACTTT 57.695 38.095 0.00 0.00 0.00 2.66
3620 3698 3.823873 ACCGCAACACTTTTTATGGATCA 59.176 39.130 0.00 0.00 0.00 2.92
3628 3706 5.251700 ACACTTTTTATGGATCAGAGGGAGT 59.748 40.000 0.00 0.00 0.00 3.85
3662 3740 3.325870 TGACAAACTAATGCTCCACTCG 58.674 45.455 0.00 0.00 0.00 4.18
3705 3783 9.967346 GAGTCTTAGATACATACTGCATTACAA 57.033 33.333 0.00 0.00 0.00 2.41
3722 3800 8.363390 TGCATTACAAAACCATGTCTTATTTGA 58.637 29.630 3.81 0.00 35.52 2.69
3742 3820 5.649782 TGAAGGGTAGTTAGTAAGTTCCG 57.350 43.478 7.16 0.00 0.00 4.30
3775 3853 7.816031 ACATCAATGCTAACCAAAGAAAGAATG 59.184 33.333 0.00 0.00 0.00 2.67
3832 3912 3.838565 TGGAGGGTGAAAATTGCTTGTA 58.161 40.909 0.00 0.00 0.00 2.41
4055 4135 1.313812 ATCCTGTCCACCTCGACGAC 61.314 60.000 0.00 0.00 35.40 4.34
4079 4159 3.716006 CAACACGGCGCACCTGAG 61.716 66.667 10.83 0.00 0.00 3.35
4080 4160 4.988598 AACACGGCGCACCTGAGG 62.989 66.667 10.83 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.183140 AGCACATATTTAGGACACCAACAAC 59.817 40.000 0.00 0.00 0.00 3.32
2 3 5.321102 AGCACATATTTAGGACACCAACAA 58.679 37.500 0.00 0.00 0.00 2.83
4 5 5.186198 AGAGCACATATTTAGGACACCAAC 58.814 41.667 0.00 0.00 0.00 3.77
5 6 5.045942 TGAGAGCACATATTTAGGACACCAA 60.046 40.000 0.00 0.00 0.00 3.67
6 7 4.469586 TGAGAGCACATATTTAGGACACCA 59.530 41.667 0.00 0.00 0.00 4.17
7 8 5.023533 TGAGAGCACATATTTAGGACACC 57.976 43.478 0.00 0.00 0.00 4.16
8 9 5.468072 CCATGAGAGCACATATTTAGGACAC 59.532 44.000 0.00 0.00 0.00 3.67
9 10 5.130975 ACCATGAGAGCACATATTTAGGACA 59.869 40.000 0.00 0.00 0.00 4.02
10 11 5.615289 ACCATGAGAGCACATATTTAGGAC 58.385 41.667 0.00 0.00 0.00 3.85
11 12 5.894298 ACCATGAGAGCACATATTTAGGA 57.106 39.130 0.00 0.00 0.00 2.94
12 13 6.652481 CCTAACCATGAGAGCACATATTTAGG 59.348 42.308 0.00 14.93 37.46 2.69
13 14 7.220030 ACCTAACCATGAGAGCACATATTTAG 58.780 38.462 0.00 0.00 0.00 1.85
14 15 7.136822 ACCTAACCATGAGAGCACATATTTA 57.863 36.000 0.00 0.00 0.00 1.40
15 16 6.006275 ACCTAACCATGAGAGCACATATTT 57.994 37.500 0.00 0.00 0.00 1.40
16 17 5.636903 ACCTAACCATGAGAGCACATATT 57.363 39.130 0.00 0.00 0.00 1.28
17 18 5.636903 AACCTAACCATGAGAGCACATAT 57.363 39.130 0.00 0.00 0.00 1.78
18 19 5.428253 GAAACCTAACCATGAGAGCACATA 58.572 41.667 0.00 0.00 0.00 2.29
19 20 4.265073 GAAACCTAACCATGAGAGCACAT 58.735 43.478 0.00 0.00 0.00 3.21
20 21 3.559171 GGAAACCTAACCATGAGAGCACA 60.559 47.826 0.00 0.00 0.00 4.57
21 22 3.010420 GGAAACCTAACCATGAGAGCAC 58.990 50.000 0.00 0.00 0.00 4.40
22 23 3.350219 GGAAACCTAACCATGAGAGCA 57.650 47.619 0.00 0.00 0.00 4.26
37 38 5.656859 AGCTATAAAGATGGTTTGGGGAAAC 59.343 40.000 0.00 0.00 0.00 2.78
38 39 5.837829 AGCTATAAAGATGGTTTGGGGAAA 58.162 37.500 0.00 0.00 0.00 3.13
39 40 5.445964 GAGCTATAAAGATGGTTTGGGGAA 58.554 41.667 0.00 0.00 0.00 3.97
40 41 4.141251 GGAGCTATAAAGATGGTTTGGGGA 60.141 45.833 0.00 0.00 0.00 4.81
41 42 4.141158 AGGAGCTATAAAGATGGTTTGGGG 60.141 45.833 0.00 0.00 0.00 4.96
42 43 5.053978 AGGAGCTATAAAGATGGTTTGGG 57.946 43.478 0.00 0.00 0.00 4.12
43 44 5.221126 GCAAGGAGCTATAAAGATGGTTTGG 60.221 44.000 0.00 0.00 41.15 3.28
44 45 5.221126 GGCAAGGAGCTATAAAGATGGTTTG 60.221 44.000 0.00 0.00 44.79 2.93
45 46 4.889995 GGCAAGGAGCTATAAAGATGGTTT 59.110 41.667 0.00 0.00 44.79 3.27
46 47 4.464947 GGCAAGGAGCTATAAAGATGGTT 58.535 43.478 0.00 0.00 44.79 3.67
47 48 3.495100 CGGCAAGGAGCTATAAAGATGGT 60.495 47.826 0.00 0.00 44.79 3.55
48 49 3.070018 CGGCAAGGAGCTATAAAGATGG 58.930 50.000 0.00 0.00 44.79 3.51
49 50 2.481952 GCGGCAAGGAGCTATAAAGATG 59.518 50.000 0.00 0.00 44.79 2.90
50 51 2.370189 AGCGGCAAGGAGCTATAAAGAT 59.630 45.455 1.45 0.00 42.60 2.40
51 52 1.762957 AGCGGCAAGGAGCTATAAAGA 59.237 47.619 1.45 0.00 42.60 2.52
52 53 2.246719 AGCGGCAAGGAGCTATAAAG 57.753 50.000 1.45 0.00 42.60 1.85
58 59 1.098050 CAAAATAGCGGCAAGGAGCT 58.902 50.000 1.45 0.00 46.53 4.09
59 60 0.811281 ACAAAATAGCGGCAAGGAGC 59.189 50.000 1.45 0.00 44.65 4.70
60 61 2.083774 TGACAAAATAGCGGCAAGGAG 58.916 47.619 1.45 0.00 0.00 3.69
61 62 2.192664 TGACAAAATAGCGGCAAGGA 57.807 45.000 1.45 0.00 0.00 3.36
62 63 3.296322 TTTGACAAAATAGCGGCAAGG 57.704 42.857 1.45 0.00 0.00 3.61
63 64 4.981674 TCTTTTTGACAAAATAGCGGCAAG 59.018 37.500 13.90 6.33 31.28 4.01
64 65 4.742659 GTCTTTTTGACAAAATAGCGGCAA 59.257 37.500 13.90 0.00 44.73 4.52
65 66 4.295051 GTCTTTTTGACAAAATAGCGGCA 58.705 39.130 13.90 0.00 44.73 5.69
66 67 4.886009 GTCTTTTTGACAAAATAGCGGC 57.114 40.909 13.90 0.00 44.73 6.53
67 68 4.319911 TCGGTCTTTTTGACAAAATAGCGG 60.320 41.667 28.59 19.11 44.10 5.52
77 78 2.747436 ACGGTACTCGGTCTTTTTGAC 58.253 47.619 8.31 0.00 44.45 3.18
78 79 4.487948 CATACGGTACTCGGTCTTTTTGA 58.512 43.478 8.31 0.00 44.45 2.69
79 80 3.061697 GCATACGGTACTCGGTCTTTTTG 59.938 47.826 8.31 0.00 44.45 2.44
80 81 3.256558 GCATACGGTACTCGGTCTTTTT 58.743 45.455 8.31 0.00 44.45 1.94
81 82 2.733227 CGCATACGGTACTCGGTCTTTT 60.733 50.000 8.31 0.00 44.45 2.27
82 83 1.202222 CGCATACGGTACTCGGTCTTT 60.202 52.381 8.31 0.00 44.45 2.52
83 84 0.379669 CGCATACGGTACTCGGTCTT 59.620 55.000 8.31 0.00 44.45 3.01
84 85 2.020131 CGCATACGGTACTCGGTCT 58.980 57.895 8.31 0.00 44.45 3.85
85 86 1.656569 GCGCATACGGTACTCGGTC 60.657 63.158 0.30 0.00 44.45 4.79
86 87 1.936436 TTGCGCATACGGTACTCGGT 61.936 55.000 12.75 0.45 44.45 4.69
87 88 0.802994 TTTGCGCATACGGTACTCGG 60.803 55.000 12.75 0.00 44.45 4.63
88 89 0.993532 TTTTGCGCATACGGTACTCG 59.006 50.000 12.75 6.54 45.88 4.18
109 110 9.696917 CTAAATTTTATGGTGCTCAGTCTTTTT 57.303 29.630 0.00 0.00 0.00 1.94
110 111 8.860088 ACTAAATTTTATGGTGCTCAGTCTTTT 58.140 29.630 0.00 0.00 0.00 2.27
111 112 8.409358 ACTAAATTTTATGGTGCTCAGTCTTT 57.591 30.769 0.00 0.00 0.00 2.52
112 113 8.947115 GTACTAAATTTTATGGTGCTCAGTCTT 58.053 33.333 0.00 0.00 0.00 3.01
113 114 7.277981 CGTACTAAATTTTATGGTGCTCAGTCT 59.722 37.037 0.00 0.00 0.00 3.24
114 115 7.399523 CGTACTAAATTTTATGGTGCTCAGTC 58.600 38.462 0.00 0.00 0.00 3.51
115 116 6.315393 CCGTACTAAATTTTATGGTGCTCAGT 59.685 38.462 0.00 0.00 0.00 3.41
116 117 6.715464 CCGTACTAAATTTTATGGTGCTCAG 58.285 40.000 0.00 0.00 0.00 3.35
117 118 5.065474 GCCGTACTAAATTTTATGGTGCTCA 59.935 40.000 0.00 0.00 0.00 4.26
118 119 5.507974 GCCGTACTAAATTTTATGGTGCTC 58.492 41.667 0.00 0.00 0.00 4.26
119 120 4.034742 CGCCGTACTAAATTTTATGGTGCT 59.965 41.667 8.18 0.00 30.17 4.40
120 121 4.276460 CGCCGTACTAAATTTTATGGTGC 58.724 43.478 8.18 0.84 30.17 5.01
121 122 4.201832 TGCGCCGTACTAAATTTTATGGTG 60.202 41.667 4.18 13.83 37.75 4.17
122 123 3.940221 TGCGCCGTACTAAATTTTATGGT 59.060 39.130 4.18 0.00 0.00 3.55
123 124 4.539509 TGCGCCGTACTAAATTTTATGG 57.460 40.909 4.18 0.00 0.00 2.74
124 125 5.795939 TGTTTGCGCCGTACTAAATTTTATG 59.204 36.000 4.18 0.00 0.00 1.90
125 126 5.940595 TGTTTGCGCCGTACTAAATTTTAT 58.059 33.333 4.18 0.00 0.00 1.40
126 127 5.354054 TGTTTGCGCCGTACTAAATTTTA 57.646 34.783 4.18 0.00 0.00 1.52
127 128 4.226113 TGTTTGCGCCGTACTAAATTTT 57.774 36.364 4.18 0.00 0.00 1.82
128 129 3.900388 TGTTTGCGCCGTACTAAATTT 57.100 38.095 4.18 0.00 0.00 1.82
129 130 3.900388 TTGTTTGCGCCGTACTAAATT 57.100 38.095 4.18 0.00 0.00 1.82
130 131 3.189702 ACATTGTTTGCGCCGTACTAAAT 59.810 39.130 4.18 0.00 0.00 1.40
131 132 2.548904 ACATTGTTTGCGCCGTACTAAA 59.451 40.909 4.18 0.00 0.00 1.85
132 133 2.144730 ACATTGTTTGCGCCGTACTAA 58.855 42.857 4.18 0.00 0.00 2.24
133 134 1.798283 ACATTGTTTGCGCCGTACTA 58.202 45.000 4.18 0.00 0.00 1.82
134 135 0.948678 AACATTGTTTGCGCCGTACT 59.051 45.000 4.18 0.00 0.00 2.73
135 136 2.096119 AGTAACATTGTTTGCGCCGTAC 60.096 45.455 7.45 0.08 0.00 3.67
136 137 2.096169 CAGTAACATTGTTTGCGCCGTA 60.096 45.455 7.45 0.00 0.00 4.02
137 138 0.948678 AGTAACATTGTTTGCGCCGT 59.051 45.000 7.45 0.00 0.00 5.68
138 139 1.326576 CAGTAACATTGTTTGCGCCG 58.673 50.000 7.45 0.00 0.00 6.46
139 140 1.268352 TCCAGTAACATTGTTTGCGCC 59.732 47.619 7.45 0.00 0.00 6.53
140 141 2.697431 TCCAGTAACATTGTTTGCGC 57.303 45.000 7.45 0.00 0.00 6.09
141 142 3.974401 CACTTCCAGTAACATTGTTTGCG 59.026 43.478 7.45 0.00 0.00 4.85
142 143 4.932146 ACACTTCCAGTAACATTGTTTGC 58.068 39.130 7.45 1.85 0.00 3.68
143 144 5.519722 GGACACTTCCAGTAACATTGTTTG 58.480 41.667 7.45 0.84 42.30 2.93
144 145 5.767816 GGACACTTCCAGTAACATTGTTT 57.232 39.130 7.45 0.00 42.30 2.83
157 158 2.783135 TCATGAAGCTTGGACACTTCC 58.217 47.619 2.10 0.00 41.31 3.46
158 159 4.276926 ACTTTCATGAAGCTTGGACACTTC 59.723 41.667 2.10 0.00 42.15 3.01
159 160 4.210331 ACTTTCATGAAGCTTGGACACTT 58.790 39.130 2.10 0.00 39.04 3.16
160 161 3.817647 GACTTTCATGAAGCTTGGACACT 59.182 43.478 2.10 0.00 39.04 3.55
161 162 3.565482 TGACTTTCATGAAGCTTGGACAC 59.435 43.478 2.10 0.00 39.04 3.67
162 163 3.819368 TGACTTTCATGAAGCTTGGACA 58.181 40.909 2.10 0.00 39.04 4.02
174 175 5.940192 TTCAACTAACGCATGACTTTCAT 57.060 34.783 0.00 0.00 37.65 2.57
175 176 5.940192 ATTCAACTAACGCATGACTTTCA 57.060 34.783 0.00 0.00 0.00 2.69
176 177 6.370593 TCAATTCAACTAACGCATGACTTTC 58.629 36.000 0.00 0.00 0.00 2.62
177 178 6.017109 ACTCAATTCAACTAACGCATGACTTT 60.017 34.615 0.00 0.00 0.00 2.66
178 179 5.470098 ACTCAATTCAACTAACGCATGACTT 59.530 36.000 0.00 0.00 0.00 3.01
179 180 4.997395 ACTCAATTCAACTAACGCATGACT 59.003 37.500 0.00 0.00 0.00 3.41
180 181 5.283060 ACTCAATTCAACTAACGCATGAC 57.717 39.130 0.00 0.00 0.00 3.06
181 182 5.940192 AACTCAATTCAACTAACGCATGA 57.060 34.783 0.00 0.00 0.00 3.07
182 183 5.569059 GGAAACTCAATTCAACTAACGCATG 59.431 40.000 0.00 0.00 0.00 4.06
183 184 5.473504 AGGAAACTCAATTCAACTAACGCAT 59.526 36.000 0.00 0.00 32.90 4.73
184 185 4.819630 AGGAAACTCAATTCAACTAACGCA 59.180 37.500 0.00 0.00 32.90 5.24
185 186 5.358298 AGGAAACTCAATTCAACTAACGC 57.642 39.130 0.00 0.00 32.90 4.84
186 187 6.725246 ACAAGGAAACTCAATTCAACTAACG 58.275 36.000 0.00 0.00 42.68 3.18
187 188 9.827411 GATACAAGGAAACTCAATTCAACTAAC 57.173 33.333 0.00 0.00 42.68 2.34
188 189 9.567776 TGATACAAGGAAACTCAATTCAACTAA 57.432 29.630 0.00 0.00 42.68 2.24
189 190 9.739276 ATGATACAAGGAAACTCAATTCAACTA 57.261 29.630 0.00 0.00 42.68 2.24
190 191 8.641498 ATGATACAAGGAAACTCAATTCAACT 57.359 30.769 0.00 0.00 42.68 3.16
191 192 8.514594 TGATGATACAAGGAAACTCAATTCAAC 58.485 33.333 0.00 0.00 42.68 3.18
192 193 8.634335 TGATGATACAAGGAAACTCAATTCAA 57.366 30.769 0.00 0.00 42.68 2.69
193 194 8.812513 ATGATGATACAAGGAAACTCAATTCA 57.187 30.769 0.00 0.00 42.68 2.57
195 196 9.911788 ACTATGATGATACAAGGAAACTCAATT 57.088 29.630 0.00 0.00 42.68 2.32
196 197 9.334947 CACTATGATGATACAAGGAAACTCAAT 57.665 33.333 0.00 0.00 42.68 2.57
197 198 7.770433 CCACTATGATGATACAAGGAAACTCAA 59.230 37.037 0.00 0.00 42.68 3.02
198 199 7.125659 TCCACTATGATGATACAAGGAAACTCA 59.874 37.037 0.00 0.00 42.68 3.41
199 200 7.500992 TCCACTATGATGATACAAGGAAACTC 58.499 38.462 0.00 0.00 42.68 3.01
201 202 8.153550 AGATCCACTATGATGATACAAGGAAAC 58.846 37.037 0.00 0.00 0.00 2.78
202 203 8.267620 AGATCCACTATGATGATACAAGGAAA 57.732 34.615 0.00 0.00 0.00 3.13
203 204 7.862274 AGATCCACTATGATGATACAAGGAA 57.138 36.000 0.00 0.00 0.00 3.36
204 205 7.397476 GGTAGATCCACTATGATGATACAAGGA 59.603 40.741 0.00 0.00 35.97 3.36
205 206 7.398618 AGGTAGATCCACTATGATGATACAAGG 59.601 40.741 0.00 0.00 39.02 3.61
206 207 8.359875 AGGTAGATCCACTATGATGATACAAG 57.640 38.462 0.00 0.00 39.02 3.16
207 208 8.727100 AAGGTAGATCCACTATGATGATACAA 57.273 34.615 0.00 0.00 39.02 2.41
208 209 8.727100 AAAGGTAGATCCACTATGATGATACA 57.273 34.615 0.00 0.00 39.02 2.29
211 212 8.717717 TGAAAAAGGTAGATCCACTATGATGAT 58.282 33.333 0.00 0.00 39.02 2.45
212 213 8.089625 TGAAAAAGGTAGATCCACTATGATGA 57.910 34.615 0.00 0.00 39.02 2.92
213 214 8.616076 GTTGAAAAAGGTAGATCCACTATGATG 58.384 37.037 0.00 0.00 39.02 3.07
214 215 8.328758 TGTTGAAAAAGGTAGATCCACTATGAT 58.671 33.333 0.00 0.00 39.02 2.45
215 216 7.685481 TGTTGAAAAAGGTAGATCCACTATGA 58.315 34.615 0.00 0.00 39.02 2.15
216 217 7.921786 TGTTGAAAAAGGTAGATCCACTATG 57.078 36.000 0.00 0.00 39.02 2.23
217 218 7.611855 CCTTGTTGAAAAAGGTAGATCCACTAT 59.388 37.037 5.96 0.00 39.55 2.12
218 219 6.940298 CCTTGTTGAAAAAGGTAGATCCACTA 59.060 38.462 5.96 0.00 39.55 2.74
219 220 5.770162 CCTTGTTGAAAAAGGTAGATCCACT 59.230 40.000 5.96 0.00 39.55 4.00
220 221 6.013842 CCTTGTTGAAAAAGGTAGATCCAC 57.986 41.667 5.96 0.00 39.55 4.02
249 250 9.463443 GCGATTAGCCAATGAAAAATAATTAGT 57.537 29.630 0.00 0.00 40.81 2.24
268 269 7.148239 ACCACAAAAATAGAGAAAGGCGATTAG 60.148 37.037 0.00 0.00 0.00 1.73
269 270 6.657541 ACCACAAAAATAGAGAAAGGCGATTA 59.342 34.615 0.00 0.00 0.00 1.75
270 271 5.476945 ACCACAAAAATAGAGAAAGGCGATT 59.523 36.000 0.00 0.00 0.00 3.34
271 272 5.010282 ACCACAAAAATAGAGAAAGGCGAT 58.990 37.500 0.00 0.00 0.00 4.58
272 273 4.394729 ACCACAAAAATAGAGAAAGGCGA 58.605 39.130 0.00 0.00 0.00 5.54
273 274 4.766404 ACCACAAAAATAGAGAAAGGCG 57.234 40.909 0.00 0.00 0.00 5.52
274 275 7.786178 AAAAACCACAAAAATAGAGAAAGGC 57.214 32.000 0.00 0.00 0.00 4.35
457 458 7.538678 CCTTAAACTCATCAAGAAATCGGTTTG 59.461 37.037 0.00 0.00 0.00 2.93
484 485 6.714356 CCCAAAAATAAGGCCAATTCTTTTCA 59.286 34.615 5.01 0.00 0.00 2.69
534 535 3.657634 AGCTTAGTCGCATACATGGATG 58.342 45.455 14.05 14.05 0.00 3.51
571 572 3.438781 GTGATCATGAGCAAAACCCGTTA 59.561 43.478 16.53 0.00 0.00 3.18
572 573 2.228822 GTGATCATGAGCAAAACCCGTT 59.771 45.455 16.53 0.00 0.00 4.44
590 591 6.476378 TGAGAGGATGATGATCGTATAGTGA 58.524 40.000 0.00 0.00 0.00 3.41
629 630 2.798499 CGAAGCTGAATGTAGGGTACGG 60.798 54.545 0.00 0.00 0.00 4.02
674 675 1.227999 AACGATGTGGACAAGTGCGG 61.228 55.000 0.00 0.00 0.00 5.69
705 724 5.829924 AGAAAGAATTTGTTGAGAGGCAAGA 59.170 36.000 0.00 0.00 39.27 3.02
773 799 5.463392 GGACAAGTGCCTCAATTTTTCTTTC 59.537 40.000 0.00 0.00 0.00 2.62
802 828 1.625818 AGATTTGTTGAGAGGCCGACT 59.374 47.619 0.00 0.00 0.00 4.18
833 859 0.311790 CACATATGGCCCGCATGAAC 59.688 55.000 13.56 0.00 0.00 3.18
834 860 0.822944 CCACATATGGCCCGCATGAA 60.823 55.000 13.56 0.00 39.82 2.57
835 861 1.228215 CCACATATGGCCCGCATGA 60.228 57.895 13.56 0.00 39.82 3.07
840 866 1.375908 CCGATCCACATATGGCCCG 60.376 63.158 7.80 3.36 46.80 6.13
920 949 6.740411 AGAAGCTTAGAAGAAATTGCTCTG 57.260 37.500 0.00 0.00 0.00 3.35
993 1022 2.837031 ATCGGGGTCCCATGTTGTGC 62.837 60.000 10.98 0.00 35.37 4.57
1216 1252 3.934962 GATCTCCTCGGGGGCAGC 61.935 72.222 0.00 0.00 34.39 5.25
1217 1253 3.610669 CGATCTCCTCGGGGGCAG 61.611 72.222 0.00 0.00 43.82 4.85
1522 1562 6.800892 CGGCTATCCTAGAGTTTAATCGTAAC 59.199 42.308 0.00 0.00 0.00 2.50
1647 1688 7.827236 ACCGAATCTTTCTGGATGTTATAACAA 59.173 33.333 21.57 5.42 43.03 2.83
1655 1696 8.871125 AGTAATATACCGAATCTTTCTGGATGT 58.129 33.333 0.00 0.00 0.00 3.06
1949 1995 9.151471 GAGAACAGCACTTTTCAGTATAACATA 57.849 33.333 0.00 0.00 0.00 2.29
1967 2013 5.119434 GCAGTAAGTGACTAAAGAGAACAGC 59.881 44.000 0.00 0.00 35.64 4.40
2039 2086 8.589338 AGAGGCAGATTATCTTTCGTAATGTAT 58.411 33.333 0.00 0.00 0.00 2.29
2170 2217 6.588348 AGTGCTTTGAAACATTTGCTTAAC 57.412 33.333 0.00 0.00 0.00 2.01
2174 2221 5.234972 GCTTTAGTGCTTTGAAACATTTGCT 59.765 36.000 0.00 0.00 0.00 3.91
2211 2259 2.969821 TGTGCAGTACCCAAGGAAAT 57.030 45.000 0.00 0.00 0.00 2.17
2250 2298 9.350357 GATATAAATTTGCAGACATAATGGCAG 57.650 33.333 0.00 0.00 37.59 4.85
2482 2531 3.798202 ACACAAAGGTTCTCTGACAGAC 58.202 45.455 0.00 0.00 0.00 3.51
2513 2562 2.349817 CGGAAATATGCGGATCTTGCAC 60.350 50.000 13.99 3.27 46.57 4.57
2579 2628 0.535780 CTGCCACAAGAGAAGCACCA 60.536 55.000 0.00 0.00 0.00 4.17
2879 2928 5.163513 CACAGTTTCAAATACTCAATGGCC 58.836 41.667 0.00 0.00 0.00 5.36
3268 3338 2.436646 CCACGACTCATGGTGCCC 60.437 66.667 0.00 0.00 33.44 5.36
3301 3371 5.418676 CAAAATCATTTTTGGCCCTCGTAT 58.581 37.500 0.00 0.00 45.18 3.06
3409 3481 7.275697 CAGATCGTAATAATGTCTGCAGATC 57.724 40.000 21.47 13.93 34.04 2.75
3444 3519 5.016831 TGAGTCCAGCTGTTAGAAGATACA 58.983 41.667 13.81 3.70 0.00 2.29
3480 3557 8.299570 AGTTGGCAGATCAGTTAAATTTTGTAG 58.700 33.333 0.00 0.00 0.00 2.74
3484 3561 6.424812 GCAAGTTGGCAGATCAGTTAAATTTT 59.575 34.615 4.75 0.00 0.00 1.82
3498 3575 1.003580 TCCTAGAAGGCAAGTTGGCAG 59.996 52.381 28.85 17.64 46.46 4.85
3502 3579 5.774498 ACTTTTTCCTAGAAGGCAAGTTG 57.226 39.130 0.00 0.00 34.61 3.16
3513 3590 6.800072 ATCAGAGGGAGTACTTTTTCCTAG 57.200 41.667 0.00 0.14 33.85 3.02
3516 3593 5.805728 TGAATCAGAGGGAGTACTTTTTCC 58.194 41.667 0.00 0.00 0.00 3.13
3517 3594 9.620259 ATTATGAATCAGAGGGAGTACTTTTTC 57.380 33.333 0.00 0.00 0.00 2.29
3525 3602 7.345653 TGACACTTATTATGAATCAGAGGGAGT 59.654 37.037 0.00 0.00 0.00 3.85
3545 3622 5.497474 ACCTTAGTTCAAAACTGTGACACT 58.503 37.500 7.20 0.00 42.84 3.55
3548 3625 5.034797 GCAACCTTAGTTCAAAACTGTGAC 58.965 41.667 2.65 0.00 42.84 3.67
3551 3628 4.020543 TGGCAACCTTAGTTCAAAACTGT 58.979 39.130 2.65 0.00 42.84 3.55
3553 3630 5.006153 GTTGGCAACCTTAGTTCAAAACT 57.994 39.130 19.57 0.00 45.40 2.66
3571 3649 5.126384 TGAACAAAGGTTGAACTAAGGTTGG 59.874 40.000 0.00 0.00 37.36 3.77
3572 3650 6.202516 TGAACAAAGGTTGAACTAAGGTTG 57.797 37.500 0.00 0.00 37.36 3.77
3573 3651 6.844097 TTGAACAAAGGTTGAACTAAGGTT 57.156 33.333 0.00 0.00 37.36 3.50
3574 3652 6.844097 TTTGAACAAAGGTTGAACTAAGGT 57.156 33.333 0.00 0.00 37.36 3.50
3575 3653 6.533723 GGTTTTGAACAAAGGTTGAACTAAGG 59.466 38.462 0.00 0.00 37.36 2.69
3576 3654 6.252655 CGGTTTTGAACAAAGGTTGAACTAAG 59.747 38.462 0.00 0.00 37.36 2.18
3577 3655 6.094061 CGGTTTTGAACAAAGGTTGAACTAA 58.906 36.000 0.00 0.00 37.36 2.24
3578 3656 5.642686 CGGTTTTGAACAAAGGTTGAACTA 58.357 37.500 0.00 0.00 37.36 2.24
3579 3657 4.490743 CGGTTTTGAACAAAGGTTGAACT 58.509 39.130 0.00 0.00 37.36 3.01
3580 3658 3.061563 GCGGTTTTGAACAAAGGTTGAAC 59.938 43.478 0.46 0.00 37.36 3.18
3581 3659 3.254892 GCGGTTTTGAACAAAGGTTGAA 58.745 40.909 0.46 0.00 37.36 2.69
3582 3660 2.231478 TGCGGTTTTGAACAAAGGTTGA 59.769 40.909 0.46 0.00 37.36 3.18
3583 3661 2.611518 TGCGGTTTTGAACAAAGGTTG 58.388 42.857 0.46 0.00 37.36 3.77
3584 3662 2.997303 GTTGCGGTTTTGAACAAAGGTT 59.003 40.909 0.46 0.00 40.76 3.50
3585 3663 2.028930 TGTTGCGGTTTTGAACAAAGGT 60.029 40.909 0.46 0.00 0.00 3.50
3586 3664 2.347150 GTGTTGCGGTTTTGAACAAAGG 59.653 45.455 0.46 0.00 31.62 3.11
3587 3665 3.249917 AGTGTTGCGGTTTTGAACAAAG 58.750 40.909 0.46 0.00 31.62 2.77
3588 3666 3.305398 AGTGTTGCGGTTTTGAACAAA 57.695 38.095 0.00 0.00 31.62 2.83
3589 3667 3.305398 AAGTGTTGCGGTTTTGAACAA 57.695 38.095 0.00 0.00 31.62 2.83
3590 3668 3.305398 AAAGTGTTGCGGTTTTGAACA 57.695 38.095 0.00 0.00 0.00 3.18
3600 3678 5.295431 TCTGATCCATAAAAAGTGTTGCG 57.705 39.130 0.00 0.00 0.00 4.85
3603 3681 6.139679 TCCCTCTGATCCATAAAAAGTGTT 57.860 37.500 0.00 0.00 0.00 3.32
3610 3688 8.798975 AATACTTACTCCCTCTGATCCATAAA 57.201 34.615 0.00 0.00 0.00 1.40
3620 3698 6.497259 TGTCAGTTCAAATACTTACTCCCTCT 59.503 38.462 0.00 0.00 0.00 3.69
3662 3740 5.261209 AGACTCATGCATAGAACTGAGAC 57.739 43.478 17.39 12.03 38.74 3.36
3705 3783 7.238710 ACTACCCTTCAAATAAGACATGGTTT 58.761 34.615 0.00 0.00 0.00 3.27
3722 3800 3.834231 TGCGGAACTTACTAACTACCCTT 59.166 43.478 0.00 0.00 0.00 3.95
3735 3813 4.273480 GCATTGATGTAGTATGCGGAACTT 59.727 41.667 0.00 0.00 35.79 2.66
3736 3814 3.809832 GCATTGATGTAGTATGCGGAACT 59.190 43.478 0.00 0.00 35.79 3.01
3739 3817 3.751479 AGCATTGATGTAGTATGCGGA 57.249 42.857 0.00 0.00 46.97 5.54
3742 3820 6.618287 TTGGTTAGCATTGATGTAGTATGC 57.382 37.500 0.00 0.00 43.78 3.14
3813 3893 6.024552 TGATTACAAGCAATTTTCACCCTC 57.975 37.500 0.00 0.00 0.00 4.30
3814 3894 6.211184 TCATGATTACAAGCAATTTTCACCCT 59.789 34.615 0.00 0.00 0.00 4.34
3832 3912 4.726035 AGCCATCTCCATTCTCATGATT 57.274 40.909 0.00 0.00 31.07 2.57
3918 3998 2.544267 CACCTTCTCCAAGAACGACAAC 59.456 50.000 0.00 0.00 29.89 3.32


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

AutoCloner maintained by Alex Coulton.