Multiple sequence alignment - TraesCS2D01G344200

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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 TraesCS2D01G344200 chr2D 100.000 3945 0 0 1 3945 440329268 440325324 0.000000e+00 7286
1 TraesCS2D01G344200 chr2D 97.683 259 6 0 1 259 43797548 43797806 2.800000e-121 446
2 TraesCS2D01G344200 chr2A 93.390 2602 97 32 462 2993 583845265 583842669 0.000000e+00 3783
3 TraesCS2D01G344200 chr2A 94.006 684 18 17 2985 3651 583842571 583841894 0.000000e+00 1014
4 TraesCS2D01G344200 chr2A 97.154 246 7 0 3700 3945 583841897 583841652 2.190000e-112 416
5 TraesCS2D01G344200 chr2A 90.960 177 13 1 258 431 583845865 583845689 6.590000e-58 235
6 TraesCS2D01G344200 chr2A 84.977 213 29 1 258 467 693415876 693416088 3.090000e-51 213
7 TraesCS2D01G344200 chr2A 89.865 148 12 2 119 264 705552431 705552285 1.870000e-43 187
8 TraesCS2D01G344200 chr2B 94.483 2465 98 19 549 2990 518056057 518053608 0.000000e+00 3764
9 TraesCS2D01G344200 chr2B 87.868 577 19 20 3064 3614 518050934 518050383 7.190000e-177 630
10 TraesCS2D01G344200 chr2B 87.833 263 26 4 3684 3945 518050011 518049754 1.780000e-78 303
11 TraesCS2D01G344200 chr5D 98.054 257 5 0 1 257 36210738 36210994 7.780000e-122 448
12 TraesCS2D01G344200 chr7A 90.204 245 14 3 11 253 130382847 130383083 1.060000e-80 311
13 TraesCS2D01G344200 chr7A 87.500 208 23 3 50 257 39131854 39132058 1.830000e-58 237
14 TraesCS2D01G344200 chr7A 88.690 168 17 2 97 263 49058297 49058131 1.860000e-48 204
15 TraesCS2D01G344200 chr3A 86.667 225 25 3 258 479 640356315 640356093 1.100000e-60 244
16 TraesCS2D01G344200 chr1A 86.538 208 25 3 50 257 481676360 481676156 3.970000e-55 226
17 TraesCS2D01G344200 chr6A 85.377 212 28 3 48 259 498543532 498543740 2.390000e-52 217
18 TraesCS2D01G344200 chr4A 84.762 210 29 3 50 259 489421956 489422162 1.440000e-49 207
19 TraesCS2D01G344200 chr6B 81.000 200 33 5 273 468 25796565 25796367 1.900000e-33 154
20 TraesCS2D01G344200 chr6B 79.397 199 37 3 273 468 523944784 523944587 1.910000e-28 137


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 TraesCS2D01G344200 chr2D 440325324 440329268 3944 True 7286.000000 7286 100.000000 1 3945 1 chr2D.!!$R1 3944
1 TraesCS2D01G344200 chr2A 583841652 583845865 4213 True 1362.000000 3783 93.877500 258 3945 4 chr2A.!!$R2 3687
2 TraesCS2D01G344200 chr2B 518049754 518056057 6303 True 1565.666667 3764 90.061333 549 3945 3 chr2B.!!$R1 3396

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
81 82 0.034059 GCTATGTGGTCCCCTGATCG 59.966 60.0 0.00 0.0 0.0 3.69 F
1415 1838 0.031043 ACGTACGTACAAGTGCAGCA 59.969 50.0 21.41 0.0 0.0 4.41 F
2275 2726 0.597637 ACGGGTGATCGATGCGATTC 60.598 55.0 0.54 0.0 47.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 2244 0.179192 CATCACGAAATGGGCACACG 60.179 55.0 0.00 0.00 0.00 4.49 R
2279 2730 0.250684 TGAGCCGCCTGTCAATTGAA 60.251 50.0 10.35 0.06 0.00 2.69 R
3664 7126 0.320374 ATGGTCGGTATATGTGCCCG 59.680 55.0 0.00 0.00 43.03 6.13 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 2.858745 GTTCTAGCCCTGTTTTGTGGA 58.141 47.619 0.00 0.00 0.00 4.02
21 22 2.814336 GTTCTAGCCCTGTTTTGTGGAG 59.186 50.000 0.00 0.00 0.00 3.86
22 23 1.351017 TCTAGCCCTGTTTTGTGGAGG 59.649 52.381 0.00 0.00 0.00 4.30
24 25 1.908299 GCCCTGTTTTGTGGAGGGG 60.908 63.158 0.00 0.00 46.01 4.79
25 26 1.908299 CCCTGTTTTGTGGAGGGGC 60.908 63.158 0.00 0.00 42.65 5.80
26 27 1.153756 CCTGTTTTGTGGAGGGGCT 59.846 57.895 0.00 0.00 0.00 5.19
27 28 0.469892 CCTGTTTTGTGGAGGGGCTT 60.470 55.000 0.00 0.00 0.00 4.35
28 29 0.675633 CTGTTTTGTGGAGGGGCTTG 59.324 55.000 0.00 0.00 0.00 4.01
29 30 0.758685 TGTTTTGTGGAGGGGCTTGG 60.759 55.000 0.00 0.00 0.00 3.61
30 31 0.759060 GTTTTGTGGAGGGGCTTGGT 60.759 55.000 0.00 0.00 0.00 3.67
31 32 0.469144 TTTTGTGGAGGGGCTTGGTC 60.469 55.000 0.00 0.00 0.00 4.02
32 33 1.360393 TTTGTGGAGGGGCTTGGTCT 61.360 55.000 0.00 0.00 0.00 3.85
33 34 1.360393 TTGTGGAGGGGCTTGGTCTT 61.360 55.000 0.00 0.00 0.00 3.01
34 35 1.360393 TGTGGAGGGGCTTGGTCTTT 61.360 55.000 0.00 0.00 0.00 2.52
35 36 0.895559 GTGGAGGGGCTTGGTCTTTG 60.896 60.000 0.00 0.00 0.00 2.77
36 37 1.979155 GGAGGGGCTTGGTCTTTGC 60.979 63.158 0.00 0.00 0.00 3.68
37 38 1.228552 GAGGGGCTTGGTCTTTGCA 60.229 57.895 0.00 0.00 0.00 4.08
38 39 0.613012 GAGGGGCTTGGTCTTTGCAT 60.613 55.000 0.00 0.00 0.00 3.96
39 40 0.901580 AGGGGCTTGGTCTTTGCATG 60.902 55.000 0.00 0.00 0.00 4.06
40 41 1.079612 GGGCTTGGTCTTTGCATGC 60.080 57.895 11.82 11.82 0.00 4.06
41 42 1.444895 GGCTTGGTCTTTGCATGCG 60.445 57.895 14.09 0.00 0.00 4.73
42 43 1.286880 GCTTGGTCTTTGCATGCGT 59.713 52.632 14.09 0.00 0.00 5.24
43 44 0.318955 GCTTGGTCTTTGCATGCGTT 60.319 50.000 14.09 0.00 0.00 4.84
44 45 1.411394 CTTGGTCTTTGCATGCGTTG 58.589 50.000 14.09 5.25 0.00 4.10
74 75 2.408333 GCATGTGCTATGTGGTCCC 58.592 57.895 0.00 0.00 38.21 4.46
75 76 1.103398 GCATGTGCTATGTGGTCCCC 61.103 60.000 0.00 0.00 38.21 4.81
76 77 0.548031 CATGTGCTATGTGGTCCCCT 59.452 55.000 0.00 0.00 0.00 4.79
77 78 0.548031 ATGTGCTATGTGGTCCCCTG 59.452 55.000 0.00 0.00 0.00 4.45
78 79 0.546507 TGTGCTATGTGGTCCCCTGA 60.547 55.000 0.00 0.00 0.00 3.86
79 80 0.839946 GTGCTATGTGGTCCCCTGAT 59.160 55.000 0.00 0.00 0.00 2.90
80 81 1.131638 TGCTATGTGGTCCCCTGATC 58.868 55.000 0.00 0.00 0.00 2.92
81 82 0.034059 GCTATGTGGTCCCCTGATCG 59.966 60.000 0.00 0.00 0.00 3.69
82 83 0.681733 CTATGTGGTCCCCTGATCGG 59.318 60.000 0.00 0.00 0.00 4.18
104 105 2.436521 GGGGGTTTGTTTGTCCAGG 58.563 57.895 0.00 0.00 0.00 4.45
105 106 0.105913 GGGGGTTTGTTTGTCCAGGA 60.106 55.000 0.00 0.00 0.00 3.86
106 107 1.037493 GGGGTTTGTTTGTCCAGGAC 58.963 55.000 13.35 13.35 0.00 3.85
107 108 0.666374 GGGTTTGTTTGTCCAGGACG 59.334 55.000 15.24 0.00 34.95 4.79
108 109 1.670791 GGTTTGTTTGTCCAGGACGA 58.329 50.000 15.24 10.56 34.95 4.20
109 110 2.018515 GGTTTGTTTGTCCAGGACGAA 58.981 47.619 17.47 17.47 34.95 3.85
112 113 2.231820 GTTTGTCCAGGACGAACCG 58.768 57.895 31.84 0.00 45.86 4.44
113 114 1.595929 TTTGTCCAGGACGAACCGC 60.596 57.895 17.47 0.00 44.74 5.68
123 124 3.856508 CGAACCGCGTGAGATGTT 58.143 55.556 4.92 0.00 34.64 2.71
124 125 2.150424 CGAACCGCGTGAGATGTTT 58.850 52.632 4.92 0.00 34.64 2.83
125 126 1.342555 CGAACCGCGTGAGATGTTTA 58.657 50.000 4.92 0.00 34.64 2.01
126 127 1.058695 CGAACCGCGTGAGATGTTTAC 59.941 52.381 4.92 0.00 34.64 2.01
127 128 1.392510 GAACCGCGTGAGATGTTTACC 59.607 52.381 4.92 0.00 0.00 2.85
128 129 0.390735 ACCGCGTGAGATGTTTACCC 60.391 55.000 4.92 0.00 0.00 3.69
129 130 1.418342 CCGCGTGAGATGTTTACCCG 61.418 60.000 4.92 0.00 0.00 5.28
130 131 0.457166 CGCGTGAGATGTTTACCCGA 60.457 55.000 0.00 0.00 0.00 5.14
131 132 0.997196 GCGTGAGATGTTTACCCGAC 59.003 55.000 0.00 0.00 0.00 4.79
132 133 1.636988 CGTGAGATGTTTACCCGACC 58.363 55.000 0.00 0.00 0.00 4.79
133 134 1.738030 CGTGAGATGTTTACCCGACCC 60.738 57.143 0.00 0.00 0.00 4.46
134 135 0.533491 TGAGATGTTTACCCGACCCG 59.467 55.000 0.00 0.00 0.00 5.28
135 136 0.533951 GAGATGTTTACCCGACCCGT 59.466 55.000 0.00 0.00 0.00 5.28
136 137 0.978907 AGATGTTTACCCGACCCGTT 59.021 50.000 0.00 0.00 0.00 4.44
137 138 1.348696 AGATGTTTACCCGACCCGTTT 59.651 47.619 0.00 0.00 0.00 3.60
138 139 2.566724 AGATGTTTACCCGACCCGTTTA 59.433 45.455 0.00 0.00 0.00 2.01
139 140 2.453983 TGTTTACCCGACCCGTTTAG 57.546 50.000 0.00 0.00 0.00 1.85
140 141 1.001860 TGTTTACCCGACCCGTTTAGG 59.998 52.381 0.00 0.00 40.63 2.69
141 142 1.001974 GTTTACCCGACCCGTTTAGGT 59.998 52.381 0.00 0.00 45.12 3.08
142 143 0.607620 TTACCCGACCCGTTTAGGTG 59.392 55.000 0.00 0.00 41.42 4.00
143 144 0.541764 TACCCGACCCGTTTAGGTGT 60.542 55.000 0.00 0.00 41.42 4.16
144 145 1.372307 CCCGACCCGTTTAGGTGTT 59.628 57.895 0.00 0.00 41.42 3.32
145 146 0.671472 CCCGACCCGTTTAGGTGTTC 60.671 60.000 0.00 0.00 41.42 3.18
146 147 0.319405 CCGACCCGTTTAGGTGTTCT 59.681 55.000 0.00 0.00 41.42 3.01
147 148 1.270465 CCGACCCGTTTAGGTGTTCTT 60.270 52.381 0.00 0.00 41.42 2.52
148 149 2.486918 CGACCCGTTTAGGTGTTCTTT 58.513 47.619 0.00 0.00 41.42 2.52
149 150 2.874086 CGACCCGTTTAGGTGTTCTTTT 59.126 45.455 0.00 0.00 41.42 2.27
150 151 3.059393 CGACCCGTTTAGGTGTTCTTTTC 60.059 47.826 0.00 0.00 41.42 2.29
151 152 4.132336 GACCCGTTTAGGTGTTCTTTTCT 58.868 43.478 0.00 0.00 41.42 2.52
152 153 3.881089 ACCCGTTTAGGTGTTCTTTTCTG 59.119 43.478 0.00 0.00 39.24 3.02
153 154 3.881089 CCCGTTTAGGTGTTCTTTTCTGT 59.119 43.478 0.00 0.00 38.74 3.41
154 155 4.337274 CCCGTTTAGGTGTTCTTTTCTGTT 59.663 41.667 0.00 0.00 38.74 3.16
155 156 5.163591 CCCGTTTAGGTGTTCTTTTCTGTTT 60.164 40.000 0.00 0.00 38.74 2.83
156 157 6.327154 CCGTTTAGGTGTTCTTTTCTGTTTT 58.673 36.000 0.00 0.00 34.51 2.43
157 158 6.809689 CCGTTTAGGTGTTCTTTTCTGTTTTT 59.190 34.615 0.00 0.00 34.51 1.94
180 181 8.692110 TTTTGATGATTTTGCTGCTAATACAG 57.308 30.769 0.00 0.00 40.80 2.74
181 182 7.628769 TTGATGATTTTGCTGCTAATACAGA 57.371 32.000 0.00 0.00 40.25 3.41
182 183 7.812690 TGATGATTTTGCTGCTAATACAGAT 57.187 32.000 0.00 0.00 40.25 2.90
183 184 7.645402 TGATGATTTTGCTGCTAATACAGATG 58.355 34.615 0.00 0.00 40.25 2.90
184 185 7.283807 TGATGATTTTGCTGCTAATACAGATGT 59.716 33.333 0.00 0.00 40.25 3.06
185 186 8.681486 ATGATTTTGCTGCTAATACAGATGTA 57.319 30.769 0.00 0.00 40.25 2.29
186 187 8.681486 TGATTTTGCTGCTAATACAGATGTAT 57.319 30.769 0.00 0.00 42.60 2.29
199 200 8.579850 AATACAGATGTATTGTGTTGATTGGT 57.420 30.769 15.60 0.00 46.20 3.67
200 201 6.500684 ACAGATGTATTGTGTTGATTGGTC 57.499 37.500 0.00 0.00 0.00 4.02
201 202 5.122239 ACAGATGTATTGTGTTGATTGGTCG 59.878 40.000 0.00 0.00 0.00 4.79
202 203 4.635765 AGATGTATTGTGTTGATTGGTCGG 59.364 41.667 0.00 0.00 0.00 4.79
203 204 3.078097 TGTATTGTGTTGATTGGTCGGG 58.922 45.455 0.00 0.00 0.00 5.14
204 205 2.577606 ATTGTGTTGATTGGTCGGGA 57.422 45.000 0.00 0.00 0.00 5.14
205 206 2.350057 TTGTGTTGATTGGTCGGGAA 57.650 45.000 0.00 0.00 0.00 3.97
206 207 2.350057 TGTGTTGATTGGTCGGGAAA 57.650 45.000 0.00 0.00 0.00 3.13
207 208 2.870175 TGTGTTGATTGGTCGGGAAAT 58.130 42.857 0.00 0.00 0.00 2.17
208 209 3.226777 TGTGTTGATTGGTCGGGAAATT 58.773 40.909 0.00 0.00 0.00 1.82
209 210 3.639094 TGTGTTGATTGGTCGGGAAATTT 59.361 39.130 0.00 0.00 0.00 1.82
210 211 3.987220 GTGTTGATTGGTCGGGAAATTTG 59.013 43.478 0.00 0.00 0.00 2.32
211 212 3.891977 TGTTGATTGGTCGGGAAATTTGA 59.108 39.130 0.00 0.00 0.00 2.69
212 213 4.234574 GTTGATTGGTCGGGAAATTTGAC 58.765 43.478 0.00 0.00 0.00 3.18
213 214 3.761897 TGATTGGTCGGGAAATTTGACT 58.238 40.909 0.00 0.00 33.21 3.41
214 215 3.505680 TGATTGGTCGGGAAATTTGACTG 59.494 43.478 0.00 0.00 33.21 3.51
215 216 2.649531 TGGTCGGGAAATTTGACTGT 57.350 45.000 0.00 0.00 33.21 3.55
216 217 2.938838 TGGTCGGGAAATTTGACTGTT 58.061 42.857 0.00 0.00 33.21 3.16
217 218 3.292460 TGGTCGGGAAATTTGACTGTTT 58.708 40.909 0.00 0.00 33.21 2.83
218 219 3.702045 TGGTCGGGAAATTTGACTGTTTT 59.298 39.130 0.00 0.00 33.21 2.43
219 220 4.202070 TGGTCGGGAAATTTGACTGTTTTC 60.202 41.667 0.00 0.00 33.21 2.29
220 221 3.972502 GTCGGGAAATTTGACTGTTTTCG 59.027 43.478 0.00 0.00 31.60 3.46
221 222 3.878103 TCGGGAAATTTGACTGTTTTCGA 59.122 39.130 0.00 0.00 31.60 3.71
222 223 4.335874 TCGGGAAATTTGACTGTTTTCGAA 59.664 37.500 0.00 0.00 31.60 3.71
223 224 5.009210 TCGGGAAATTTGACTGTTTTCGAAT 59.991 36.000 0.00 0.00 31.83 3.34
224 225 5.689961 CGGGAAATTTGACTGTTTTCGAATT 59.310 36.000 0.00 0.00 40.10 2.17
225 226 6.858993 CGGGAAATTTGACTGTTTTCGAATTA 59.141 34.615 0.00 0.00 38.25 1.40
226 227 7.380065 CGGGAAATTTGACTGTTTTCGAATTAA 59.620 33.333 0.00 0.00 38.25 1.40
227 228 9.036671 GGGAAATTTGACTGTTTTCGAATTAAA 57.963 29.630 0.00 0.00 38.25 1.52
271 272 6.944096 AGACAGTCCCAATAAAGTACTTACC 58.056 40.000 8.92 0.00 0.00 2.85
274 275 6.040878 CAGTCCCAATAAAGTACTTACCGAG 58.959 44.000 8.92 0.00 0.00 4.63
281 282 7.816031 CCAATAAAGTACTTACCGAGTCTTCAA 59.184 37.037 8.92 0.00 39.86 2.69
310 311 8.595362 TCTTGTATTACTCTTCTTCCTCATCA 57.405 34.615 0.00 0.00 0.00 3.07
311 312 9.035890 TCTTGTATTACTCTTCTTCCTCATCAA 57.964 33.333 0.00 0.00 0.00 2.57
312 313 9.658799 CTTGTATTACTCTTCTTCCTCATCAAA 57.341 33.333 0.00 0.00 0.00 2.69
323 327 4.882671 TCCTCATCAAAATAAAGCGAGC 57.117 40.909 0.00 0.00 0.00 5.03
339 343 3.058777 AGCGAGCGATAAACTAGCTAGTC 60.059 47.826 26.21 12.92 43.18 2.59
368 372 0.452987 TCGAGGGTCGGACAATTACG 59.547 55.000 10.76 8.02 40.88 3.18
406 410 3.262420 CGGAGGAGATTTTGTCGATTGT 58.738 45.455 0.00 0.00 0.00 2.71
426 430 5.661056 TGTCCGAGATGATTGTAAGAACT 57.339 39.130 0.00 0.00 0.00 3.01
431 435 6.980978 TCCGAGATGATTGTAAGAACTTGATC 59.019 38.462 0.00 0.00 0.00 2.92
432 436 6.983307 CCGAGATGATTGTAAGAACTTGATCT 59.017 38.462 0.00 0.00 0.00 2.75
433 437 7.493971 CCGAGATGATTGTAAGAACTTGATCTT 59.506 37.037 0.00 0.00 42.21 2.40
434 438 8.877779 CGAGATGATTGTAAGAACTTGATCTTT 58.122 33.333 0.00 0.00 40.13 2.52
435 439 9.985318 GAGATGATTGTAAGAACTTGATCTTTG 57.015 33.333 0.00 0.00 40.13 2.77
436 440 9.730705 AGATGATTGTAAGAACTTGATCTTTGA 57.269 29.630 0.00 0.00 40.13 2.69
437 441 9.985318 GATGATTGTAAGAACTTGATCTTTGAG 57.015 33.333 0.00 0.00 40.13 3.02
438 442 8.908786 TGATTGTAAGAACTTGATCTTTGAGT 57.091 30.769 0.00 0.00 40.13 3.41
439 443 9.996554 TGATTGTAAGAACTTGATCTTTGAGTA 57.003 29.630 0.00 0.00 40.13 2.59
458 462 8.597662 TTGAGTAATACAAGTATTATTCCCGC 57.402 34.615 22.13 11.21 40.78 6.13
459 463 7.728148 TGAGTAATACAAGTATTATTCCCGCA 58.272 34.615 22.13 12.88 40.78 5.69
460 464 8.205512 TGAGTAATACAAGTATTATTCCCGCAA 58.794 33.333 22.13 9.16 40.78 4.85
509 906 7.939784 ATAGAGTTCTTTTACCATTTCCCAC 57.060 36.000 0.00 0.00 0.00 4.61
513 910 8.170730 AGAGTTCTTTTACCATTTCCCACTATT 58.829 33.333 0.00 0.00 0.00 1.73
522 919 6.187682 ACCATTTCCCACTATTTTCCTACTG 58.812 40.000 0.00 0.00 0.00 2.74
776 1199 0.935196 ACCACGTTTCTGTTCGAAGC 59.065 50.000 0.00 0.00 32.21 3.86
882 1305 5.399301 CGCCATCGAATACAATTTCAAATCC 59.601 40.000 0.00 0.00 38.10 3.01
933 1356 3.686128 CGTATATATCTGCTCCACTCGC 58.314 50.000 0.00 0.00 0.00 5.03
955 1378 2.969016 CTCGAGCTGCACACTCCT 59.031 61.111 0.00 0.00 0.00 3.69
995 1418 1.563435 CGGTGCTCTGCTCACACAAG 61.563 60.000 0.00 0.00 36.00 3.16
1019 1442 0.390124 ATGCCCAGTTTGCACAACAG 59.610 50.000 12.28 6.06 42.38 3.16
1384 1807 2.369394 CCAAGGTCTTCATGGTAAGCC 58.631 52.381 0.00 0.00 0.00 4.35
1415 1838 0.031043 ACGTACGTACAAGTGCAGCA 59.969 50.000 21.41 0.00 0.00 4.41
1421 1844 1.073025 TACAAGTGCAGCACCAGGG 59.927 57.895 22.41 11.36 34.49 4.45
1422 1845 3.677648 CAAGTGCAGCACCAGGGC 61.678 66.667 22.41 0.00 34.49 5.19
1428 1851 2.993264 CAGCACCAGGGCCCAAAG 60.993 66.667 27.56 14.78 0.00 2.77
1435 1858 1.674322 CAGGGCCCAAAGGTACGTG 60.674 63.158 27.56 5.93 34.57 4.49
1442 1865 2.428491 CCCAAAGGTACGTGCATGTAA 58.572 47.619 20.12 2.46 0.00 2.41
1447 1870 4.742438 AAGGTACGTGCATGTAACAAAG 57.258 40.909 30.63 0.20 34.40 2.77
1815 2239 3.637229 GCACTCCAGGTAAGCTCATACTA 59.363 47.826 0.00 0.00 0.00 1.82
1819 2244 5.595133 ACTCCAGGTAAGCTCATACTAGTTC 59.405 44.000 0.00 0.00 0.00 3.01
1824 2249 5.035443 GGTAAGCTCATACTAGTTCGTGTG 58.965 45.833 0.00 0.86 0.00 3.82
1847 2291 3.181487 CCCATTTCGTGATGGTTCATTCC 60.181 47.826 15.31 0.00 44.17 3.01
1851 2295 1.003003 TCGTGATGGTTCATTCCTGCA 59.997 47.619 0.00 0.00 33.56 4.41
1852 2296 1.811965 CGTGATGGTTCATTCCTGCAA 59.188 47.619 0.00 0.00 33.56 4.08
1855 2299 4.427312 GTGATGGTTCATTCCTGCAAATC 58.573 43.478 0.00 0.00 33.56 2.17
1856 2300 3.129113 TGATGGTTCATTCCTGCAAATCG 59.871 43.478 0.00 0.00 0.00 3.34
1857 2301 2.789213 TGGTTCATTCCTGCAAATCGA 58.211 42.857 0.00 0.00 0.00 3.59
1858 2302 2.749076 TGGTTCATTCCTGCAAATCGAG 59.251 45.455 0.00 0.00 0.00 4.04
1869 2313 0.832030 CAAATCGAGTCGAGCGTACG 59.168 55.000 21.36 11.84 39.91 3.67
1920 2364 1.379977 TGTTCGAGAGGGCGGAGAT 60.380 57.895 0.00 0.00 0.00 2.75
2229 2680 1.652619 GGTAACAACTAAGCGCTCGTC 59.347 52.381 12.06 0.00 0.00 4.20
2233 2684 1.337823 ACAACTAAGCGCTCGTCCATT 60.338 47.619 12.06 0.00 0.00 3.16
2239 2690 2.579201 CGCTCGTCCATTCCCAGT 59.421 61.111 0.00 0.00 0.00 4.00
2240 2691 1.519455 CGCTCGTCCATTCCCAGTC 60.519 63.158 0.00 0.00 0.00 3.51
2241 2692 1.596934 GCTCGTCCATTCCCAGTCA 59.403 57.895 0.00 0.00 0.00 3.41
2245 2696 3.681594 GCTCGTCCATTCCCAGTCAATTA 60.682 47.826 0.00 0.00 0.00 1.40
2271 2722 2.961721 CCACGGGTGATCGATGCG 60.962 66.667 0.54 0.00 0.00 4.73
2274 2725 0.875908 CACGGGTGATCGATGCGATT 60.876 55.000 0.54 0.00 47.00 3.34
2275 2726 0.597637 ACGGGTGATCGATGCGATTC 60.598 55.000 0.54 0.00 47.00 2.52
2277 2728 1.581934 GGGTGATCGATGCGATTCAA 58.418 50.000 0.54 0.00 47.00 2.69
2278 2729 1.939934 GGGTGATCGATGCGATTCAAA 59.060 47.619 0.54 0.00 47.00 2.69
2279 2730 2.549754 GGGTGATCGATGCGATTCAAAT 59.450 45.455 0.54 0.00 47.00 2.32
2280 2731 3.003689 GGGTGATCGATGCGATTCAAATT 59.996 43.478 0.54 0.00 47.00 1.82
2281 2732 4.214437 GGTGATCGATGCGATTCAAATTC 58.786 43.478 0.54 0.00 47.00 2.17
2282 2733 4.260743 GGTGATCGATGCGATTCAAATTCA 60.261 41.667 0.54 0.00 47.00 2.57
2283 2734 5.265477 GTGATCGATGCGATTCAAATTCAA 58.735 37.500 0.54 0.00 47.00 2.69
2377 2842 3.710722 AAGCTGAGGGAGGTGCGG 61.711 66.667 0.00 0.00 30.84 5.69
2575 3040 3.622826 CTCAACACCCGGGTCGGT 61.623 66.667 27.51 18.16 46.80 4.69
2688 3153 2.149383 AGAACTGGCAGTGGCTCCA 61.149 57.895 22.83 2.92 40.87 3.86
2784 3249 2.764128 GATGGCGAGGGTCCAGGA 60.764 66.667 0.00 0.00 36.98 3.86
2839 3304 0.621571 ACAAGGAGGCTGGCAGGATA 60.622 55.000 17.64 0.00 0.00 2.59
3042 6153 7.443302 AACAGAATAATCATCTGGGAGAGAA 57.557 36.000 8.26 0.00 46.81 2.87
3052 6163 2.564947 TCTGGGAGAGAAAGAGCAGAAC 59.435 50.000 0.00 0.00 0.00 3.01
3053 6164 2.566724 CTGGGAGAGAAAGAGCAGAACT 59.433 50.000 0.00 0.00 0.00 3.01
3054 6165 3.766591 CTGGGAGAGAAAGAGCAGAACTA 59.233 47.826 0.00 0.00 0.00 2.24
3093 6205 8.039603 TGCGTTAGATTTTCTGTGTCATATTT 57.960 30.769 0.00 0.00 0.00 1.40
3159 6293 5.400066 AAAAGGCAAATATGTGTACCCAC 57.600 39.130 0.00 0.00 42.19 4.61
3237 6377 7.255312 GCTCTACATATCACTGCTAGTTGTACT 60.255 40.741 0.00 0.00 0.00 2.73
3271 6411 3.066900 ACATGAGGAGGTTCTAATCGACG 59.933 47.826 0.00 0.00 0.00 5.12
3344 6484 5.011090 ACAGCGCAGATCTAAATCAGTTA 57.989 39.130 11.47 0.00 34.07 2.24
3345 6485 5.419542 ACAGCGCAGATCTAAATCAGTTAA 58.580 37.500 11.47 0.00 34.07 2.01
3463 6603 8.975663 ATATCTGATGATCAAATATTGCCGAT 57.024 30.769 0.00 0.00 34.32 4.18
3605 6748 7.693951 GCATATCGGCTAATCATTGTTATCAAC 59.306 37.037 0.00 0.00 36.33 3.18
3645 7107 2.044123 AATGCCCAATCTTCCGAGAC 57.956 50.000 0.00 0.00 33.99 3.36
3648 7110 0.528684 GCCCAATCTTCCGAGACGAG 60.529 60.000 0.00 0.00 33.99 4.18
3649 7111 0.528684 CCCAATCTTCCGAGACGAGC 60.529 60.000 0.00 0.00 33.99 5.03
3657 7119 1.107538 TCCGAGACGAGCATAAGGGG 61.108 60.000 0.00 0.00 0.00 4.79
3658 7120 1.364171 CGAGACGAGCATAAGGGGG 59.636 63.158 0.00 0.00 0.00 5.40
3673 7135 2.678470 GGGGGAAACGGGCACATA 59.322 61.111 0.00 0.00 0.00 2.29
3674 7136 1.229076 GGGGGAAACGGGCACATAT 59.771 57.895 0.00 0.00 0.00 1.78
3675 7137 0.475044 GGGGGAAACGGGCACATATA 59.525 55.000 0.00 0.00 0.00 0.86
3676 7138 1.601166 GGGGAAACGGGCACATATAC 58.399 55.000 0.00 0.00 0.00 1.47
3677 7139 1.601166 GGGAAACGGGCACATATACC 58.399 55.000 0.00 0.00 0.00 2.73
3754 7216 9.793252 GATGTCATTTGCATTCTAAGTATTTGT 57.207 29.630 0.00 0.00 0.00 2.83
3812 7274 7.174107 ACTATTCAATAATTGCAGCTTTGGT 57.826 32.000 0.00 0.00 0.00 3.67
3860 7322 9.967346 TCTTTCGATATGAATTATTCGAGAACT 57.033 29.630 0.23 0.00 36.22 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.814336 CTCCACAAAACAGGGCTAGAAC 59.186 50.000 0.00 0.00 0.00 3.01
1 2 2.224769 CCTCCACAAAACAGGGCTAGAA 60.225 50.000 0.00 0.00 0.00 2.10
2 3 1.351017 CCTCCACAAAACAGGGCTAGA 59.649 52.381 0.00 0.00 0.00 2.43
3 4 1.614317 CCCTCCACAAAACAGGGCTAG 60.614 57.143 0.00 0.00 40.71 3.42
4 5 0.404040 CCCTCCACAAAACAGGGCTA 59.596 55.000 0.00 0.00 40.71 3.93
5 6 1.153756 CCCTCCACAAAACAGGGCT 59.846 57.895 0.00 0.00 40.71 5.19
6 7 1.908299 CCCCTCCACAAAACAGGGC 60.908 63.158 0.00 0.00 45.25 5.19
7 8 1.908299 GCCCCTCCACAAAACAGGG 60.908 63.158 0.00 0.00 46.08 4.45
8 9 0.469892 AAGCCCCTCCACAAAACAGG 60.470 55.000 0.00 0.00 0.00 4.00
9 10 0.675633 CAAGCCCCTCCACAAAACAG 59.324 55.000 0.00 0.00 0.00 3.16
10 11 0.758685 CCAAGCCCCTCCACAAAACA 60.759 55.000 0.00 0.00 0.00 2.83
11 12 0.759060 ACCAAGCCCCTCCACAAAAC 60.759 55.000 0.00 0.00 0.00 2.43
12 13 0.469144 GACCAAGCCCCTCCACAAAA 60.469 55.000 0.00 0.00 0.00 2.44
13 14 1.152830 GACCAAGCCCCTCCACAAA 59.847 57.895 0.00 0.00 0.00 2.83
14 15 1.360393 AAGACCAAGCCCCTCCACAA 61.360 55.000 0.00 0.00 0.00 3.33
15 16 1.360393 AAAGACCAAGCCCCTCCACA 61.360 55.000 0.00 0.00 0.00 4.17
16 17 0.895559 CAAAGACCAAGCCCCTCCAC 60.896 60.000 0.00 0.00 0.00 4.02
17 18 1.460255 CAAAGACCAAGCCCCTCCA 59.540 57.895 0.00 0.00 0.00 3.86
18 19 1.979155 GCAAAGACCAAGCCCCTCC 60.979 63.158 0.00 0.00 0.00 4.30
19 20 0.613012 ATGCAAAGACCAAGCCCCTC 60.613 55.000 0.00 0.00 0.00 4.30
20 21 0.901580 CATGCAAAGACCAAGCCCCT 60.902 55.000 0.00 0.00 0.00 4.79
21 22 1.593265 CATGCAAAGACCAAGCCCC 59.407 57.895 0.00 0.00 0.00 5.80
22 23 1.079612 GCATGCAAAGACCAAGCCC 60.080 57.895 14.21 0.00 0.00 5.19
23 24 1.444895 CGCATGCAAAGACCAAGCC 60.445 57.895 19.57 0.00 0.00 4.35
24 25 0.318955 AACGCATGCAAAGACCAAGC 60.319 50.000 19.57 0.00 0.00 4.01
25 26 1.411394 CAACGCATGCAAAGACCAAG 58.589 50.000 19.57 0.00 0.00 3.61
26 27 3.566273 CAACGCATGCAAAGACCAA 57.434 47.368 19.57 0.00 0.00 3.67
41 42 4.936226 GCACATGCTAGCAAGTTTGCAAC 61.936 47.826 22.26 5.50 46.54 4.17
42 43 2.863312 GCACATGCTAGCAAGTTTGCAA 60.863 45.455 22.26 0.00 46.54 4.08
43 44 1.336148 GCACATGCTAGCAAGTTTGCA 60.336 47.619 22.26 0.00 46.54 4.08
44 45 1.343506 GCACATGCTAGCAAGTTTGC 58.656 50.000 22.26 21.24 45.45 3.68
56 57 2.408333 GGGACCACATAGCACATGC 58.592 57.895 0.00 0.00 42.49 4.06
86 87 0.105913 TCCTGGACAAACAAACCCCC 60.106 55.000 0.00 0.00 0.00 5.40
87 88 1.037493 GTCCTGGACAAACAAACCCC 58.963 55.000 21.70 0.00 32.09 4.95
88 89 0.666374 CGTCCTGGACAAACAAACCC 59.334 55.000 25.42 0.00 32.09 4.11
89 90 1.670791 TCGTCCTGGACAAACAAACC 58.329 50.000 25.42 0.00 32.09 3.27
90 91 2.223409 GGTTCGTCCTGGACAAACAAAC 60.223 50.000 26.87 19.33 31.85 2.93
91 92 2.018515 GGTTCGTCCTGGACAAACAAA 58.981 47.619 26.87 10.97 31.85 2.83
92 93 1.670791 GGTTCGTCCTGGACAAACAA 58.329 50.000 26.87 11.85 31.85 2.83
93 94 0.531090 CGGTTCGTCCTGGACAAACA 60.531 55.000 26.87 6.80 31.85 2.83
94 95 1.838568 GCGGTTCGTCCTGGACAAAC 61.839 60.000 25.42 22.63 29.70 2.93
95 96 1.595929 GCGGTTCGTCCTGGACAAA 60.596 57.895 25.42 12.06 32.09 2.83
96 97 2.029964 GCGGTTCGTCCTGGACAA 59.970 61.111 25.42 15.65 32.09 3.18
97 98 4.351938 CGCGGTTCGTCCTGGACA 62.352 66.667 25.42 10.75 32.09 4.02
106 107 1.058695 GTAAACATCTCACGCGGTTCG 59.941 52.381 12.47 0.00 45.38 3.95
107 108 1.392510 GGTAAACATCTCACGCGGTTC 59.607 52.381 12.47 0.00 0.00 3.62
108 109 1.435577 GGTAAACATCTCACGCGGTT 58.564 50.000 12.47 0.00 0.00 4.44
109 110 0.390735 GGGTAAACATCTCACGCGGT 60.391 55.000 12.47 0.00 0.00 5.68
110 111 1.418342 CGGGTAAACATCTCACGCGG 61.418 60.000 12.47 0.00 42.69 6.46
111 112 0.457166 TCGGGTAAACATCTCACGCG 60.457 55.000 3.53 3.53 46.27 6.01
112 113 0.997196 GTCGGGTAAACATCTCACGC 59.003 55.000 0.00 0.00 0.00 5.34
113 114 1.636988 GGTCGGGTAAACATCTCACG 58.363 55.000 0.00 0.00 0.00 4.35
114 115 1.738030 CGGGTCGGGTAAACATCTCAC 60.738 57.143 0.00 0.00 0.00 3.51
115 116 0.533491 CGGGTCGGGTAAACATCTCA 59.467 55.000 0.00 0.00 0.00 3.27
116 117 0.533951 ACGGGTCGGGTAAACATCTC 59.466 55.000 0.00 0.00 0.00 2.75
117 118 0.978907 AACGGGTCGGGTAAACATCT 59.021 50.000 0.00 0.00 0.00 2.90
118 119 1.812235 AAACGGGTCGGGTAAACATC 58.188 50.000 0.00 0.00 0.00 3.06
119 120 2.355007 CCTAAACGGGTCGGGTAAACAT 60.355 50.000 0.00 0.00 0.00 2.71
120 121 1.001860 CCTAAACGGGTCGGGTAAACA 59.998 52.381 0.00 0.00 0.00 2.83
121 122 1.001974 ACCTAAACGGGTCGGGTAAAC 59.998 52.381 0.00 0.00 33.84 2.01
122 123 1.001860 CACCTAAACGGGTCGGGTAAA 59.998 52.381 0.00 0.00 37.52 2.01
123 124 0.607620 CACCTAAACGGGTCGGGTAA 59.392 55.000 0.00 0.00 37.52 2.85
124 125 0.541764 ACACCTAAACGGGTCGGGTA 60.542 55.000 0.00 0.00 37.52 3.69
125 126 1.410050 AACACCTAAACGGGTCGGGT 61.410 55.000 0.00 0.00 37.52 5.28
126 127 0.671472 GAACACCTAAACGGGTCGGG 60.671 60.000 0.00 0.00 37.52 5.14
127 128 0.319405 AGAACACCTAAACGGGTCGG 59.681 55.000 0.00 0.00 37.52 4.79
128 129 2.159327 AAGAACACCTAAACGGGTCG 57.841 50.000 0.00 0.00 37.52 4.79
129 130 4.024302 CAGAAAAGAACACCTAAACGGGTC 60.024 45.833 0.00 0.00 37.52 4.46
130 131 3.881089 CAGAAAAGAACACCTAAACGGGT 59.119 43.478 0.00 0.00 40.73 5.28
131 132 3.881089 ACAGAAAAGAACACCTAAACGGG 59.119 43.478 0.00 0.00 36.97 5.28
132 133 5.494632 AACAGAAAAGAACACCTAAACGG 57.505 39.130 0.00 0.00 39.35 4.44
133 134 7.806149 AAAAACAGAAAAGAACACCTAAACG 57.194 32.000 0.00 0.00 0.00 3.60
154 155 9.142515 CTGTATTAGCAGCAAAATCATCAAAAA 57.857 29.630 0.00 0.00 0.00 1.94
155 156 8.522003 TCTGTATTAGCAGCAAAATCATCAAAA 58.478 29.630 0.00 0.00 36.49 2.44
156 157 8.054152 TCTGTATTAGCAGCAAAATCATCAAA 57.946 30.769 0.00 0.00 36.49 2.69
157 158 7.628769 TCTGTATTAGCAGCAAAATCATCAA 57.371 32.000 0.00 0.00 36.49 2.57
158 159 7.283807 ACATCTGTATTAGCAGCAAAATCATCA 59.716 33.333 0.00 0.00 36.49 3.07
159 160 7.646314 ACATCTGTATTAGCAGCAAAATCATC 58.354 34.615 0.00 0.00 36.49 2.92
160 161 7.578310 ACATCTGTATTAGCAGCAAAATCAT 57.422 32.000 0.00 0.00 36.49 2.45
161 162 8.681486 ATACATCTGTATTAGCAGCAAAATCA 57.319 30.769 0.00 0.00 37.97 2.57
162 163 9.390795 CAATACATCTGTATTAGCAGCAAAATC 57.609 33.333 13.67 0.00 46.23 2.17
163 164 8.906867 ACAATACATCTGTATTAGCAGCAAAAT 58.093 29.630 13.67 0.00 46.23 1.82
164 165 8.183536 CACAATACATCTGTATTAGCAGCAAAA 58.816 33.333 13.67 0.00 46.23 2.44
165 166 7.336679 ACACAATACATCTGTATTAGCAGCAAA 59.663 33.333 13.67 0.00 46.23 3.68
166 167 6.823182 ACACAATACATCTGTATTAGCAGCAA 59.177 34.615 13.67 0.00 46.23 3.91
167 168 6.348498 ACACAATACATCTGTATTAGCAGCA 58.652 36.000 13.67 0.00 46.23 4.41
168 169 6.851222 ACACAATACATCTGTATTAGCAGC 57.149 37.500 13.67 0.00 46.23 5.25
169 170 8.424274 TCAACACAATACATCTGTATTAGCAG 57.576 34.615 13.67 6.09 46.23 4.24
170 171 8.962884 ATCAACACAATACATCTGTATTAGCA 57.037 30.769 13.67 1.81 46.23 3.49
171 172 9.655769 CAATCAACACAATACATCTGTATTAGC 57.344 33.333 13.67 0.00 46.23 3.09
173 174 9.679661 ACCAATCAACACAATACATCTGTATTA 57.320 29.630 13.67 0.68 46.23 0.98
175 176 7.011389 CGACCAATCAACACAATACATCTGTAT 59.989 37.037 0.00 0.00 42.60 2.29
176 177 6.312672 CGACCAATCAACACAATACATCTGTA 59.687 38.462 0.00 0.00 34.67 2.74
177 178 5.122239 CGACCAATCAACACAATACATCTGT 59.878 40.000 0.00 0.00 0.00 3.41
178 179 5.447683 CCGACCAATCAACACAATACATCTG 60.448 44.000 0.00 0.00 0.00 2.90
179 180 4.635765 CCGACCAATCAACACAATACATCT 59.364 41.667 0.00 0.00 0.00 2.90
180 181 4.201910 CCCGACCAATCAACACAATACATC 60.202 45.833 0.00 0.00 0.00 3.06
181 182 3.694072 CCCGACCAATCAACACAATACAT 59.306 43.478 0.00 0.00 0.00 2.29
182 183 3.078097 CCCGACCAATCAACACAATACA 58.922 45.455 0.00 0.00 0.00 2.29
183 184 3.340034 TCCCGACCAATCAACACAATAC 58.660 45.455 0.00 0.00 0.00 1.89
184 185 3.704800 TCCCGACCAATCAACACAATA 57.295 42.857 0.00 0.00 0.00 1.90
185 186 2.577606 TCCCGACCAATCAACACAAT 57.422 45.000 0.00 0.00 0.00 2.71
186 187 2.350057 TTCCCGACCAATCAACACAA 57.650 45.000 0.00 0.00 0.00 3.33
187 188 2.350057 TTTCCCGACCAATCAACACA 57.650 45.000 0.00 0.00 0.00 3.72
188 189 3.934457 AATTTCCCGACCAATCAACAC 57.066 42.857 0.00 0.00 0.00 3.32
189 190 3.891977 TCAAATTTCCCGACCAATCAACA 59.108 39.130 0.00 0.00 0.00 3.33
190 191 4.022329 AGTCAAATTTCCCGACCAATCAAC 60.022 41.667 4.08 0.00 0.00 3.18
191 192 4.022416 CAGTCAAATTTCCCGACCAATCAA 60.022 41.667 4.08 0.00 0.00 2.57
192 193 3.505680 CAGTCAAATTTCCCGACCAATCA 59.494 43.478 4.08 0.00 0.00 2.57
193 194 3.506067 ACAGTCAAATTTCCCGACCAATC 59.494 43.478 4.08 0.00 0.00 2.67
194 195 3.496331 ACAGTCAAATTTCCCGACCAAT 58.504 40.909 4.08 0.00 0.00 3.16
195 196 2.938838 ACAGTCAAATTTCCCGACCAA 58.061 42.857 4.08 0.00 0.00 3.67
196 197 2.649531 ACAGTCAAATTTCCCGACCA 57.350 45.000 4.08 0.00 0.00 4.02
197 198 4.295870 GAAAACAGTCAAATTTCCCGACC 58.704 43.478 4.08 0.00 0.00 4.79
198 199 3.972502 CGAAAACAGTCAAATTTCCCGAC 59.027 43.478 0.00 0.00 31.03 4.79
199 200 3.878103 TCGAAAACAGTCAAATTTCCCGA 59.122 39.130 0.00 0.00 31.03 5.14
200 201 4.217754 TCGAAAACAGTCAAATTTCCCG 57.782 40.909 0.00 0.00 31.03 5.14
201 202 8.582433 TTAATTCGAAAACAGTCAAATTTCCC 57.418 30.769 0.00 0.00 31.03 3.97
240 241 7.923414 ACTTTATTGGGACTGTCTATTTGAC 57.077 36.000 7.85 0.00 45.54 3.18
241 242 8.822805 AGTACTTTATTGGGACTGTCTATTTGA 58.177 33.333 7.85 0.00 0.00 2.69
242 243 9.449719 AAGTACTTTATTGGGACTGTCTATTTG 57.550 33.333 1.12 0.00 0.00 2.32
245 246 8.702819 GGTAAGTACTTTATTGGGACTGTCTAT 58.297 37.037 14.49 2.37 0.00 1.98
246 247 7.148018 CGGTAAGTACTTTATTGGGACTGTCTA 60.148 40.741 14.49 0.00 0.00 2.59
247 248 6.350780 CGGTAAGTACTTTATTGGGACTGTCT 60.351 42.308 14.49 0.00 0.00 3.41
248 249 5.809051 CGGTAAGTACTTTATTGGGACTGTC 59.191 44.000 14.49 0.00 0.00 3.51
249 250 5.481473 TCGGTAAGTACTTTATTGGGACTGT 59.519 40.000 14.49 0.00 0.00 3.55
250 251 5.969423 TCGGTAAGTACTTTATTGGGACTG 58.031 41.667 14.49 8.99 0.00 3.51
251 252 5.718607 ACTCGGTAAGTACTTTATTGGGACT 59.281 40.000 14.49 0.00 36.07 3.85
252 253 5.970592 ACTCGGTAAGTACTTTATTGGGAC 58.029 41.667 14.49 3.64 36.07 4.46
253 254 5.954150 AGACTCGGTAAGTACTTTATTGGGA 59.046 40.000 14.49 2.88 38.74 4.37
254 255 6.218108 AGACTCGGTAAGTACTTTATTGGG 57.782 41.667 14.49 4.44 38.74 4.12
255 256 7.318141 TGAAGACTCGGTAAGTACTTTATTGG 58.682 38.462 14.49 4.93 38.74 3.16
256 257 8.752766 TTGAAGACTCGGTAAGTACTTTATTG 57.247 34.615 14.49 2.17 38.74 1.90
271 272 9.959775 GAGTAATACAAGAATTTTGAAGACTCG 57.040 33.333 7.18 0.00 0.00 4.18
300 301 5.269313 GCTCGCTTTATTTTGATGAGGAAG 58.731 41.667 0.00 0.00 0.00 3.46
307 308 7.016361 AGTTTATCGCTCGCTTTATTTTGAT 57.984 32.000 0.00 0.00 0.00 2.57
309 310 6.354622 GCTAGTTTATCGCTCGCTTTATTTTG 59.645 38.462 0.00 0.00 0.00 2.44
310 311 6.258068 AGCTAGTTTATCGCTCGCTTTATTTT 59.742 34.615 0.00 0.00 32.14 1.82
311 312 5.753921 AGCTAGTTTATCGCTCGCTTTATTT 59.246 36.000 0.00 0.00 32.14 1.40
312 313 5.290386 AGCTAGTTTATCGCTCGCTTTATT 58.710 37.500 0.00 0.00 32.14 1.40
318 322 3.058777 AGACTAGCTAGTTTATCGCTCGC 60.059 47.826 26.71 10.37 36.50 5.03
339 343 0.378962 CGACCCTCGACTCTAGCAAG 59.621 60.000 0.00 0.00 43.74 4.01
368 372 4.717313 GGGCCTGAACCGACCCAC 62.717 72.222 0.84 0.00 42.33 4.61
393 397 4.503910 TCATCTCGGACAATCGACAAAAT 58.496 39.130 0.00 0.00 35.18 1.82
406 410 6.280855 TCAAGTTCTTACAATCATCTCGGA 57.719 37.500 0.00 0.00 0.00 4.55
432 436 9.048446 GCGGGAATAATACTTGTATTACTCAAA 57.952 33.333 17.81 1.04 0.00 2.69
433 437 8.205512 TGCGGGAATAATACTTGTATTACTCAA 58.794 33.333 17.81 1.59 0.00 3.02
434 438 7.728148 TGCGGGAATAATACTTGTATTACTCA 58.272 34.615 17.81 6.14 0.00 3.41
435 439 8.597662 TTGCGGGAATAATACTTGTATTACTC 57.402 34.615 13.43 12.33 0.00 2.59
436 440 8.967664 TTTGCGGGAATAATACTTGTATTACT 57.032 30.769 13.43 5.09 0.00 2.24
513 910 9.485206 GTTCTTCAAATGTAGTACAGTAGGAAA 57.515 33.333 9.25 3.57 0.00 3.13
522 919 6.183360 GCTACGGTGTTCTTCAAATGTAGTAC 60.183 42.308 0.00 0.00 33.61 2.73
741 1160 2.933906 CGTGGTTGTTACGATAAGGCAT 59.066 45.455 0.00 0.00 43.82 4.40
776 1199 6.145858 GGATGATGAAGATGAATGACGAAGAG 59.854 42.308 0.00 0.00 0.00 2.85
882 1305 0.876342 GGGCGCCGAGATCAGTTTAG 60.876 60.000 22.54 0.00 0.00 1.85
955 1378 1.067974 CGTGTGTAAGCGGGGATGATA 59.932 52.381 0.00 0.00 0.00 2.15
977 1400 1.849976 GCTTGTGTGAGCAGAGCACC 61.850 60.000 0.00 0.00 42.25 5.01
991 1414 1.122227 AAACTGGGCATTGTGCTTGT 58.878 45.000 1.64 0.00 44.28 3.16
995 1418 1.069427 TGCAAACTGGGCATTGTGC 59.931 52.632 0.00 0.00 44.08 4.57
1040 1463 4.849329 CCTCCGGCGTGTCGTAGC 62.849 72.222 6.01 0.00 0.00 3.58
1221 1644 3.308705 GTGGAGGGGTCGAACCGT 61.309 66.667 15.98 15.98 39.83 4.83
1404 1827 2.203394 CCCTGGTGCTGCACTTGT 60.203 61.111 29.54 0.00 34.40 3.16
1415 1838 2.902457 CGTACCTTTGGGCCCTGGT 61.902 63.158 28.53 28.53 35.63 4.00
1421 1844 1.241315 ACATGCACGTACCTTTGGGC 61.241 55.000 0.00 0.00 35.63 5.36
1422 1845 2.102070 TACATGCACGTACCTTTGGG 57.898 50.000 0.00 0.00 38.88 4.12
1428 1851 5.594724 TTACTTTGTTACATGCACGTACC 57.405 39.130 0.00 0.00 0.00 3.34
1435 1858 6.343616 CGTCACGTTTTTACTTTGTTACATGC 60.344 38.462 0.00 0.00 0.00 4.06
1442 1865 3.683822 TCCACGTCACGTTTTTACTTTGT 59.316 39.130 0.00 0.00 38.32 2.83
1447 1870 2.268700 CGTCCACGTCACGTTTTTAC 57.731 50.000 0.00 0.00 38.32 2.01
1805 2229 2.159226 GGCACACGAACTAGTATGAGCT 60.159 50.000 17.46 0.00 0.00 4.09
1815 2239 0.534203 ACGAAATGGGCACACGAACT 60.534 50.000 4.28 0.00 0.00 3.01
1819 2244 0.179192 CATCACGAAATGGGCACACG 60.179 55.000 0.00 0.00 0.00 4.49
1847 2291 1.073216 ACGCTCGACTCGATTTGCAG 61.073 55.000 0.62 2.40 34.61 4.41
1851 2295 0.445436 ACGTACGCTCGACTCGATTT 59.555 50.000 16.72 0.00 34.61 2.17
1852 2296 0.247576 CACGTACGCTCGACTCGATT 60.248 55.000 16.72 0.00 34.61 3.34
1855 2299 2.898087 ATGCACGTACGCTCGACTCG 62.898 60.000 16.72 0.00 34.70 4.18
1856 2300 1.226323 ATGCACGTACGCTCGACTC 60.226 57.895 16.72 0.00 34.70 3.36
1857 2301 1.514228 CATGCACGTACGCTCGACT 60.514 57.895 16.72 0.00 34.70 4.18
1858 2302 2.987593 CATGCACGTACGCTCGAC 59.012 61.111 16.72 0.74 34.70 4.20
1869 2313 4.783621 TCGCCTCCCTGCATGCAC 62.784 66.667 18.46 4.82 0.00 4.57
2229 2680 3.627577 CGGAGTTAATTGACTGGGAATGG 59.372 47.826 7.73 0.00 0.00 3.16
2233 2684 1.906574 AGCGGAGTTAATTGACTGGGA 59.093 47.619 7.73 0.00 0.00 4.37
2239 2690 2.004583 CGTGGAGCGGAGTTAATTGA 57.995 50.000 0.00 0.00 36.85 2.57
2271 2722 4.563976 CCGCCTGTCAATTGAATTTGAATC 59.436 41.667 10.35 0.00 37.36 2.52
2273 2724 3.860378 GCCGCCTGTCAATTGAATTTGAA 60.860 43.478 10.35 0.00 37.36 2.69
2274 2725 2.352617 GCCGCCTGTCAATTGAATTTGA 60.353 45.455 10.35 0.00 33.32 2.69
2275 2726 1.994779 GCCGCCTGTCAATTGAATTTG 59.005 47.619 10.35 0.57 0.00 2.32
2277 2728 1.474077 GAGCCGCCTGTCAATTGAATT 59.526 47.619 10.35 0.00 0.00 2.17
2278 2729 1.098050 GAGCCGCCTGTCAATTGAAT 58.902 50.000 10.35 0.00 0.00 2.57
2279 2730 0.250684 TGAGCCGCCTGTCAATTGAA 60.251 50.000 10.35 0.06 0.00 2.69
2280 2731 0.674581 CTGAGCCGCCTGTCAATTGA 60.675 55.000 3.38 3.38 0.00 2.57
2281 2732 0.674581 TCTGAGCCGCCTGTCAATTG 60.675 55.000 0.00 0.00 0.00 2.32
2282 2733 0.254178 ATCTGAGCCGCCTGTCAATT 59.746 50.000 0.00 0.00 0.00 2.32
2283 2734 0.254178 AATCTGAGCCGCCTGTCAAT 59.746 50.000 0.00 0.00 0.00 2.57
2354 2819 2.674220 CCTCCCTCAGCTTGTCCCC 61.674 68.421 0.00 0.00 0.00 4.81
2751 3216 1.032657 CATCTCCTCCTCCACGACGT 61.033 60.000 0.00 0.00 0.00 4.34
2822 3287 1.423161 GAATATCCTGCCAGCCTCCTT 59.577 52.381 0.00 0.00 0.00 3.36
2823 3288 1.063183 GAATATCCTGCCAGCCTCCT 58.937 55.000 0.00 0.00 0.00 3.69
2839 3304 1.815421 GACGCACTGCCGGATGAAT 60.815 57.895 5.05 0.00 0.00 2.57
2927 3392 2.124983 TCAGAGCTTGGATGCCGC 60.125 61.111 0.00 0.00 0.00 6.53
2930 3395 0.747283 CCCAGTCAGAGCTTGGATGC 60.747 60.000 2.79 0.00 0.00 3.91
3000 6111 4.824537 TCTGTTTAAGCAACACAGCCAATA 59.175 37.500 0.22 0.00 40.71 1.90
3001 6112 3.636300 TCTGTTTAAGCAACACAGCCAAT 59.364 39.130 0.22 0.00 40.71 3.16
3022 6133 6.650390 GCTCTTTCTCTCCCAGATGATTATTC 59.350 42.308 0.00 0.00 0.00 1.75
3159 6293 2.416547 CCACGTCATAAGCTCCACTTTG 59.583 50.000 0.00 0.00 39.97 2.77
3237 6377 3.256383 CCTCCTCATGTTGAATGTTTGCA 59.744 43.478 0.00 0.00 0.00 4.08
3271 6411 4.156556 TGCTGTAAATCTGAGATGTTTGCC 59.843 41.667 0.00 0.00 0.00 4.52
3344 6484 5.336213 CCATGCTGATGCTACAAAGTCTTTT 60.336 40.000 0.00 0.00 40.48 2.27
3345 6485 4.157289 CCATGCTGATGCTACAAAGTCTTT 59.843 41.667 0.00 0.00 40.48 2.52
3463 6603 4.894114 GCTCTGGGGAGTTACACTTAGATA 59.106 45.833 0.00 0.00 41.38 1.98
3657 7119 1.601166 GTATATGTGCCCGTTTCCCC 58.399 55.000 0.00 0.00 0.00 4.81
3658 7120 1.601166 GGTATATGTGCCCGTTTCCC 58.399 55.000 0.00 0.00 0.00 3.97
3659 7121 1.202557 TCGGTATATGTGCCCGTTTCC 60.203 52.381 0.00 0.00 42.30 3.13
3660 7122 1.862827 GTCGGTATATGTGCCCGTTTC 59.137 52.381 0.00 0.00 42.30 2.78
3664 7126 0.320374 ATGGTCGGTATATGTGCCCG 59.680 55.000 0.00 0.00 43.03 6.13
3665 7127 2.093658 CCTATGGTCGGTATATGTGCCC 60.094 54.545 0.00 0.00 0.00 5.36
3666 7128 2.093658 CCCTATGGTCGGTATATGTGCC 60.094 54.545 0.00 0.00 0.00 5.01
3667 7129 2.565834 ACCCTATGGTCGGTATATGTGC 59.434 50.000 0.00 0.00 43.06 4.57
3680 7142 1.341531 CTAGTTGCCTCGACCCTATGG 59.658 57.143 0.00 0.00 37.80 2.74
3681 7143 1.269831 GCTAGTTGCCTCGACCCTATG 60.270 57.143 0.00 0.00 35.15 2.23
3682 7144 1.041437 GCTAGTTGCCTCGACCCTAT 58.959 55.000 0.00 0.00 35.15 2.57
3688 7150 4.941263 ACAAATAATTGCTAGTTGCCTCGA 59.059 37.500 0.00 0.00 38.82 4.04
3693 7155 5.323371 TGGGACAAATAATTGCTAGTTGC 57.677 39.130 0.00 0.00 38.82 4.17
3860 7322 6.671190 CATCATTTTGTGAGCTAGTTCAACA 58.329 36.000 11.19 8.94 40.92 3.33
3867 7329 5.353400 TCAAGAGCATCATTTTGTGAGCTAG 59.647 40.000 0.00 0.00 40.92 3.42


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

AutoCloner maintained by Alex Coulton.