Multiple sequence alignment - TraesCS1D01G120900

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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 TraesCS1D01G120900 chr1D 100.000 2651 0 0 1000 3650 120046349 120043699 0.000000e+00 4896.0
1 TraesCS1D01G120900 chr1D 100.000 803 0 0 1 803 120047348 120046546 0.000000e+00 1483.0
2 TraesCS1D01G120900 chr1B 95.959 1559 45 8 1001 2546 183453550 183451997 0.000000e+00 2514.0
3 TraesCS1D01G120900 chr1B 92.713 247 13 4 2514 2758 183394004 183393761 5.800000e-93 351.0
4 TraesCS1D01G120900 chr1B 92.308 247 14 4 2514 2758 183449350 183449107 2.700000e-91 346.0
5 TraesCS1D01G120900 chr1B 90.310 258 5 2 2755 3009 183449044 183448804 1.640000e-83 320.0
6 TraesCS1D01G120900 chr1B 89.147 258 8 2 2755 3009 183393698 183393458 1.650000e-78 303.0
7 TraesCS1D01G120900 chr1B 100.000 62 0 0 709 770 183453692 183453631 8.280000e-22 115.0
8 TraesCS1D01G120900 chr1A 94.569 939 47 4 1001 1938 132416214 132415279 0.000000e+00 1448.0
9 TraesCS1D01G120900 chr1A 98.113 636 12 0 1934 2569 132415252 132414617 0.000000e+00 1109.0
10 TraesCS1D01G120900 chr1A 95.462 639 26 1 3014 3649 125103385 125102747 0.000000e+00 1016.0
11 TraesCS1D01G120900 chr1A 98.485 132 2 0 2531 2662 132414620 132414489 2.190000e-57 233.0
12 TraesCS1D01G120900 chr1A 90.361 166 7 4 2755 2911 132414007 132414172 3.690000e-50 209.0
13 TraesCS1D01G120900 chr1A 95.699 93 4 0 2917 3009 132413986 132413894 2.270000e-32 150.0
14 TraesCS1D01G120900 chr1A 98.039 51 0 1 720 770 132416340 132416291 1.810000e-13 87.9
15 TraesCS1D01G120900 chr4A 86.158 419 50 6 268 680 609563197 609562781 2.590000e-121 446.0
16 TraesCS1D01G120900 chr7A 85.167 418 55 5 268 680 690045828 690045413 4.360000e-114 422.0
17 TraesCS1D01G120900 chr7A 84.906 424 54 9 264 680 40794454 40794874 1.570000e-113 420.0
18 TraesCS1D01G120900 chr7A 85.075 402 54 4 266 662 663965035 663965435 4.390000e-109 405.0
19 TraesCS1D01G120900 chr6B 85.132 417 55 5 268 680 688289365 688289778 1.570000e-113 420.0
20 TraesCS1D01G120900 chr7B 84.689 418 56 8 267 680 161631607 161631194 9.430000e-111 411.0
21 TraesCS1D01G120900 chr2A 85.075 402 53 5 266 662 709189059 709189458 1.580000e-108 403.0
22 TraesCS1D01G120900 chr2A 100.000 29 0 0 3373 3401 298638862 298638890 2.000000e-03 54.7
23 TraesCS1D01G120900 chr3A 84.248 419 59 5 268 680 221916148 221915731 5.680000e-108 401.0
24 TraesCS1D01G120900 chr5A 84.925 398 54 4 270 662 552329969 552330365 7.340000e-107 398.0
25 TraesCS1D01G120900 chr5B 74.619 394 91 7 3182 3569 434818629 434818239 8.110000e-37 165.0
26 TraesCS1D01G120900 chr3D 83.815 173 22 5 1 171 113617835 113618003 3.770000e-35 159.0
27 TraesCS1D01G120900 chr6A 72.921 469 113 9 3186 3648 48050388 48050848 2.270000e-32 150.0
28 TraesCS1D01G120900 chr4B 73.165 395 92 12 3184 3569 612319555 612319944 2.960000e-26 130.0


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 TraesCS1D01G120900 chr1D 120043699 120047348 3649 True 3189.50 4896 100.00000 1 3650 2 chr1D.!!$R1 3649
1 TraesCS1D01G120900 chr1B 183448804 183453692 4888 True 823.75 2514 94.64425 709 3009 4 chr1B.!!$R2 2300
2 TraesCS1D01G120900 chr1B 183393458 183394004 546 True 327.00 351 90.93000 2514 3009 2 chr1B.!!$R1 495
3 TraesCS1D01G120900 chr1A 125102747 125103385 638 True 1016.00 1016 95.46200 3014 3649 1 chr1A.!!$R1 635
4 TraesCS1D01G120900 chr1A 132413894 132416340 2446 True 605.58 1448 96.98100 720 3009 5 chr1A.!!$R2 2289

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
199 200 0.108615 CGTAGAGGAGCAAGTGGGTG 60.109 60.0 0.00 0.00 0.00 4.61 F
267 268 0.174389 ATATAGCCAGCAGCCGATCG 59.826 55.0 8.51 8.51 45.47 3.69 F
1688 1698 0.039074 GCGTACATCTGCTCGCCTAT 60.039 55.0 7.89 0.00 42.33 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1325 1326 2.747446 CCAAATCAAACTACTCCCCGTG 59.253 50.0 0.00 0.0 0.00 4.94 R
2240 2284 0.036952 CACCGCTCAGGATGTTGAGT 60.037 55.0 5.08 0.0 45.07 3.41 R
3269 6469 0.037975 TTTTGTCCCTCGCTCGGTAC 60.038 55.0 0.00 0.0 0.00 3.34 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
72 73 8.986477 AATTCAAGAACTTTTATGGAATTCGG 57.014 30.769 0.00 0.00 30.16 4.30
73 74 7.519032 TTCAAGAACTTTTATGGAATTCGGT 57.481 32.000 0.00 0.00 0.00 4.69
74 75 8.624367 TTCAAGAACTTTTATGGAATTCGGTA 57.376 30.769 0.00 0.00 0.00 4.02
75 76 8.624367 TCAAGAACTTTTATGGAATTCGGTAA 57.376 30.769 0.00 0.00 0.00 2.85
76 77 9.069082 TCAAGAACTTTTATGGAATTCGGTAAA 57.931 29.630 0.00 4.82 0.00 2.01
77 78 9.124807 CAAGAACTTTTATGGAATTCGGTAAAC 57.875 33.333 11.30 3.86 0.00 2.01
78 79 8.398878 AGAACTTTTATGGAATTCGGTAAACA 57.601 30.769 11.30 0.00 0.00 2.83
79 80 9.020731 AGAACTTTTATGGAATTCGGTAAACAT 57.979 29.630 11.30 5.88 0.00 2.71
80 81 9.634163 GAACTTTTATGGAATTCGGTAAACATT 57.366 29.630 11.30 9.39 0.00 2.71
81 82 9.990360 AACTTTTATGGAATTCGGTAAACATTT 57.010 25.926 11.30 5.21 0.00 2.32
82 83 9.990360 ACTTTTATGGAATTCGGTAAACATTTT 57.010 25.926 11.30 0.00 0.00 1.82
174 175 4.738998 CACATGGGCCGGCCAAGA 62.739 66.667 44.46 28.73 37.98 3.02
175 176 3.978193 ACATGGGCCGGCCAAGAA 61.978 61.111 44.46 27.52 37.98 2.52
176 177 3.142838 CATGGGCCGGCCAAGAAG 61.143 66.667 44.46 25.03 37.98 2.85
177 178 4.447342 ATGGGCCGGCCAAGAAGG 62.447 66.667 44.46 0.00 41.84 3.46
179 180 4.360405 GGGCCGGCCAAGAAGGAA 62.360 66.667 44.46 0.00 41.22 3.36
180 181 3.062466 GGCCGGCCAAGAAGGAAC 61.062 66.667 40.73 8.62 41.22 3.62
181 182 3.431725 GCCGGCCAAGAAGGAACG 61.432 66.667 18.11 0.00 41.22 3.95
182 183 2.032071 CCGGCCAAGAAGGAACGT 59.968 61.111 2.24 0.00 41.22 3.99
183 184 1.294138 CCGGCCAAGAAGGAACGTA 59.706 57.895 2.24 0.00 41.22 3.57
184 185 0.739813 CCGGCCAAGAAGGAACGTAG 60.740 60.000 2.24 0.00 41.22 3.51
185 186 0.245539 CGGCCAAGAAGGAACGTAGA 59.754 55.000 2.24 0.00 41.22 2.59
186 187 1.736032 CGGCCAAGAAGGAACGTAGAG 60.736 57.143 2.24 0.00 41.22 2.43
187 188 1.405661 GGCCAAGAAGGAACGTAGAGG 60.406 57.143 0.00 0.00 41.22 3.69
188 189 1.549170 GCCAAGAAGGAACGTAGAGGA 59.451 52.381 0.00 0.00 41.22 3.71
189 190 2.417515 GCCAAGAAGGAACGTAGAGGAG 60.418 54.545 0.00 0.00 41.22 3.69
190 191 2.417515 CCAAGAAGGAACGTAGAGGAGC 60.418 54.545 0.00 0.00 41.22 4.70
191 192 2.217510 AGAAGGAACGTAGAGGAGCA 57.782 50.000 0.00 0.00 0.00 4.26
192 193 2.526432 AGAAGGAACGTAGAGGAGCAA 58.474 47.619 0.00 0.00 0.00 3.91
193 194 2.494073 AGAAGGAACGTAGAGGAGCAAG 59.506 50.000 0.00 0.00 0.00 4.01
194 195 1.926108 AGGAACGTAGAGGAGCAAGT 58.074 50.000 0.00 0.00 0.00 3.16
195 196 1.546476 AGGAACGTAGAGGAGCAAGTG 59.454 52.381 0.00 0.00 0.00 3.16
196 197 1.404315 GGAACGTAGAGGAGCAAGTGG 60.404 57.143 0.00 0.00 0.00 4.00
197 198 0.608640 AACGTAGAGGAGCAAGTGGG 59.391 55.000 0.00 0.00 0.00 4.61
198 199 0.542232 ACGTAGAGGAGCAAGTGGGT 60.542 55.000 0.00 0.00 0.00 4.51
199 200 0.108615 CGTAGAGGAGCAAGTGGGTG 60.109 60.000 0.00 0.00 0.00 4.61
200 201 0.391793 GTAGAGGAGCAAGTGGGTGC 60.392 60.000 0.00 0.00 45.28 5.01
221 222 4.675029 CGCCTGTTCCCCGACGTT 62.675 66.667 0.00 0.00 0.00 3.99
222 223 2.658422 GCCTGTTCCCCGACGTTA 59.342 61.111 0.00 0.00 0.00 3.18
223 224 1.447314 GCCTGTTCCCCGACGTTAG 60.447 63.158 0.00 0.00 0.00 2.34
224 225 1.217244 CCTGTTCCCCGACGTTAGG 59.783 63.158 4.24 4.24 0.00 2.69
233 234 4.679412 GACGTTAGGGTCGCCAAA 57.321 55.556 0.00 0.00 0.00 3.28
234 235 3.148340 GACGTTAGGGTCGCCAAAT 57.852 52.632 0.00 0.00 0.00 2.32
235 236 1.004595 GACGTTAGGGTCGCCAAATC 58.995 55.000 0.00 0.00 0.00 2.17
236 237 0.322322 ACGTTAGGGTCGCCAAATCA 59.678 50.000 0.00 0.00 0.00 2.57
237 238 1.006832 CGTTAGGGTCGCCAAATCAG 58.993 55.000 0.00 0.00 0.00 2.90
238 239 1.404986 CGTTAGGGTCGCCAAATCAGA 60.405 52.381 0.00 0.00 0.00 3.27
239 240 2.280628 GTTAGGGTCGCCAAATCAGAG 58.719 52.381 0.00 0.00 0.00 3.35
240 241 0.178068 TAGGGTCGCCAAATCAGAGC 59.822 55.000 0.00 0.00 0.00 4.09
241 242 1.377202 GGGTCGCCAAATCAGAGCA 60.377 57.895 0.00 0.00 34.43 4.26
242 243 1.648467 GGGTCGCCAAATCAGAGCAC 61.648 60.000 0.00 0.00 34.43 4.40
243 244 1.648467 GGTCGCCAAATCAGAGCACC 61.648 60.000 0.00 0.00 33.15 5.01
244 245 1.377202 TCGCCAAATCAGAGCACCC 60.377 57.895 0.00 0.00 0.00 4.61
245 246 1.675310 CGCCAAATCAGAGCACCCA 60.675 57.895 0.00 0.00 0.00 4.51
246 247 1.033746 CGCCAAATCAGAGCACCCAT 61.034 55.000 0.00 0.00 0.00 4.00
247 248 0.743097 GCCAAATCAGAGCACCCATC 59.257 55.000 0.00 0.00 0.00 3.51
248 249 1.956636 GCCAAATCAGAGCACCCATCA 60.957 52.381 0.00 0.00 0.00 3.07
249 250 2.662866 CCAAATCAGAGCACCCATCAT 58.337 47.619 0.00 0.00 0.00 2.45
250 251 3.824133 CCAAATCAGAGCACCCATCATA 58.176 45.455 0.00 0.00 0.00 2.15
251 252 4.404640 CCAAATCAGAGCACCCATCATAT 58.595 43.478 0.00 0.00 0.00 1.78
252 253 5.563592 CCAAATCAGAGCACCCATCATATA 58.436 41.667 0.00 0.00 0.00 0.86
253 254 5.646793 CCAAATCAGAGCACCCATCATATAG 59.353 44.000 0.00 0.00 0.00 1.31
254 255 3.969287 TCAGAGCACCCATCATATAGC 57.031 47.619 0.00 0.00 0.00 2.97
255 256 2.568956 TCAGAGCACCCATCATATAGCC 59.431 50.000 0.00 0.00 0.00 3.93
256 257 2.303890 CAGAGCACCCATCATATAGCCA 59.696 50.000 0.00 0.00 0.00 4.75
257 258 2.570752 AGAGCACCCATCATATAGCCAG 59.429 50.000 0.00 0.00 0.00 4.85
258 259 1.004044 AGCACCCATCATATAGCCAGC 59.996 52.381 0.00 0.00 0.00 4.85
259 260 1.271543 GCACCCATCATATAGCCAGCA 60.272 52.381 0.00 0.00 0.00 4.41
260 261 2.708051 CACCCATCATATAGCCAGCAG 58.292 52.381 0.00 0.00 0.00 4.24
261 262 1.004044 ACCCATCATATAGCCAGCAGC 59.996 52.381 0.00 0.00 44.25 5.25
262 263 1.681166 CCCATCATATAGCCAGCAGCC 60.681 57.143 0.00 0.00 45.47 4.85
263 264 1.366679 CATCATATAGCCAGCAGCCG 58.633 55.000 0.00 0.00 45.47 5.52
264 265 1.066645 CATCATATAGCCAGCAGCCGA 60.067 52.381 0.00 0.00 45.47 5.54
265 266 1.269958 TCATATAGCCAGCAGCCGAT 58.730 50.000 0.00 0.00 45.47 4.18
266 267 1.205655 TCATATAGCCAGCAGCCGATC 59.794 52.381 0.00 0.00 45.47 3.69
267 268 0.174389 ATATAGCCAGCAGCCGATCG 59.826 55.000 8.51 8.51 45.47 3.69
268 269 0.893727 TATAGCCAGCAGCCGATCGA 60.894 55.000 18.66 0.00 45.47 3.59
269 270 2.152297 ATAGCCAGCAGCCGATCGAG 62.152 60.000 18.66 8.00 45.47 4.04
270 271 4.212913 GCCAGCAGCCGATCGAGA 62.213 66.667 18.66 0.00 34.35 4.04
271 272 2.027314 CCAGCAGCCGATCGAGAG 59.973 66.667 18.66 6.48 0.00 3.20
272 273 2.780094 CCAGCAGCCGATCGAGAGT 61.780 63.158 18.66 0.00 0.00 3.24
273 274 1.588403 CAGCAGCCGATCGAGAGTG 60.588 63.158 18.66 8.99 0.00 3.51
274 275 2.279120 GCAGCCGATCGAGAGTGG 60.279 66.667 18.66 0.00 0.00 4.00
275 276 2.775856 GCAGCCGATCGAGAGTGGA 61.776 63.158 18.66 0.00 0.00 4.02
276 277 2.037053 CAGCCGATCGAGAGTGGAT 58.963 57.895 18.66 0.00 0.00 3.41
277 278 0.387202 CAGCCGATCGAGAGTGGATT 59.613 55.000 18.66 0.00 0.00 3.01
278 279 1.115467 AGCCGATCGAGAGTGGATTT 58.885 50.000 18.66 0.00 0.00 2.17
279 280 1.482593 AGCCGATCGAGAGTGGATTTT 59.517 47.619 18.66 0.00 0.00 1.82
280 281 2.093447 AGCCGATCGAGAGTGGATTTTT 60.093 45.455 18.66 0.00 0.00 1.94
281 282 2.030946 GCCGATCGAGAGTGGATTTTTG 59.969 50.000 18.66 0.00 0.00 2.44
282 283 2.609459 CCGATCGAGAGTGGATTTTTGG 59.391 50.000 18.66 0.00 0.00 3.28
283 284 3.521560 CGATCGAGAGTGGATTTTTGGA 58.478 45.455 10.26 0.00 0.00 3.53
284 285 3.932710 CGATCGAGAGTGGATTTTTGGAA 59.067 43.478 10.26 0.00 0.00 3.53
285 286 4.201724 CGATCGAGAGTGGATTTTTGGAAC 60.202 45.833 10.26 0.00 0.00 3.62
286 287 3.408634 TCGAGAGTGGATTTTTGGAACC 58.591 45.455 0.00 0.00 0.00 3.62
287 288 2.488153 CGAGAGTGGATTTTTGGAACCC 59.512 50.000 0.00 0.00 0.00 4.11
288 289 3.496331 GAGAGTGGATTTTTGGAACCCA 58.504 45.455 0.00 0.00 0.00 4.51
289 290 3.230976 AGAGTGGATTTTTGGAACCCAC 58.769 45.455 0.00 0.00 45.57 4.61
292 293 3.663025 GTGGATTTTTGGAACCCACATG 58.337 45.455 0.00 0.00 44.83 3.21
293 294 3.070878 GTGGATTTTTGGAACCCACATGT 59.929 43.478 0.00 0.00 44.83 3.21
294 295 4.282195 GTGGATTTTTGGAACCCACATGTA 59.718 41.667 0.00 0.00 44.83 2.29
295 296 5.046663 GTGGATTTTTGGAACCCACATGTAT 60.047 40.000 0.00 0.00 44.83 2.29
296 297 5.545723 TGGATTTTTGGAACCCACATGTATT 59.454 36.000 0.00 0.00 30.78 1.89
297 298 6.726299 TGGATTTTTGGAACCCACATGTATTA 59.274 34.615 0.00 0.00 30.78 0.98
298 299 7.235606 TGGATTTTTGGAACCCACATGTATTAA 59.764 33.333 0.00 0.00 30.78 1.40
299 300 8.097662 GGATTTTTGGAACCCACATGTATTAAA 58.902 33.333 0.00 0.00 30.78 1.52
300 301 9.150348 GATTTTTGGAACCCACATGTATTAAAG 57.850 33.333 0.00 0.00 30.78 1.85
301 302 6.597832 TTTGGAACCCACATGTATTAAAGG 57.402 37.500 0.00 0.00 30.78 3.11
302 303 5.522315 TGGAACCCACATGTATTAAAGGA 57.478 39.130 0.00 0.00 0.00 3.36
303 304 5.258051 TGGAACCCACATGTATTAAAGGAC 58.742 41.667 0.00 0.00 0.00 3.85
304 305 4.643334 GGAACCCACATGTATTAAAGGACC 59.357 45.833 0.00 0.00 0.00 4.46
305 306 5.506708 GAACCCACATGTATTAAAGGACCT 58.493 41.667 0.00 0.00 0.00 3.85
306 307 5.530176 ACCCACATGTATTAAAGGACCTT 57.470 39.130 0.00 0.00 0.00 3.50
307 308 6.645884 ACCCACATGTATTAAAGGACCTTA 57.354 37.500 7.30 0.00 0.00 2.69
308 309 7.220890 ACCCACATGTATTAAAGGACCTTAT 57.779 36.000 7.30 0.60 0.00 1.73
309 310 7.648770 ACCCACATGTATTAAAGGACCTTATT 58.351 34.615 7.30 0.00 0.00 1.40
310 311 8.119891 ACCCACATGTATTAAAGGACCTTATTT 58.880 33.333 7.30 0.00 0.00 1.40
311 312 8.977412 CCCACATGTATTAAAGGACCTTATTTT 58.023 33.333 7.30 0.00 0.00 1.82
456 457 9.883142 ACAAAAAGACAAAATAGTGATTTCCAA 57.117 25.926 0.00 0.00 34.01 3.53
462 463 9.865321 AGACAAAATAGTGATTTCCAAATGATG 57.135 29.630 0.00 0.00 34.01 3.07
463 464 9.859427 GACAAAATAGTGATTTCCAAATGATGA 57.141 29.630 0.00 0.00 34.01 2.92
486 487 8.969260 TGAATAATTCATGCACTACTCATCTT 57.031 30.769 0.00 0.00 34.08 2.40
487 488 9.399797 TGAATAATTCATGCACTACTCATCTTT 57.600 29.630 0.00 0.00 34.08 2.52
488 489 9.875675 GAATAATTCATGCACTACTCATCTTTC 57.124 33.333 0.00 0.00 0.00 2.62
489 490 6.690194 AATTCATGCACTACTCATCTTTCC 57.310 37.500 0.00 0.00 0.00 3.13
490 491 3.785486 TCATGCACTACTCATCTTTCCG 58.215 45.455 0.00 0.00 0.00 4.30
491 492 3.447229 TCATGCACTACTCATCTTTCCGA 59.553 43.478 0.00 0.00 0.00 4.55
492 493 3.953712 TGCACTACTCATCTTTCCGAA 57.046 42.857 0.00 0.00 0.00 4.30
493 494 4.265904 TGCACTACTCATCTTTCCGAAA 57.734 40.909 0.00 0.00 0.00 3.46
494 495 4.637276 TGCACTACTCATCTTTCCGAAAA 58.363 39.130 0.00 0.00 0.00 2.29
495 496 5.245531 TGCACTACTCATCTTTCCGAAAAT 58.754 37.500 0.00 0.00 0.00 1.82
496 497 5.351465 TGCACTACTCATCTTTCCGAAAATC 59.649 40.000 0.00 0.00 0.00 2.17
497 498 5.351465 GCACTACTCATCTTTCCGAAAATCA 59.649 40.000 0.00 0.00 0.00 2.57
498 499 6.037610 GCACTACTCATCTTTCCGAAAATCAT 59.962 38.462 0.00 0.00 0.00 2.45
499 500 7.404985 CACTACTCATCTTTCCGAAAATCATG 58.595 38.462 0.00 0.00 0.00 3.07
500 501 7.278646 CACTACTCATCTTTCCGAAAATCATGA 59.721 37.037 0.00 0.00 0.00 3.07
501 502 7.989741 ACTACTCATCTTTCCGAAAATCATGAT 59.010 33.333 1.18 1.18 29.68 2.45
502 503 7.636150 ACTCATCTTTCCGAAAATCATGATT 57.364 32.000 15.36 15.36 29.68 2.57
503 504 8.059798 ACTCATCTTTCCGAAAATCATGATTT 57.940 30.769 24.83 24.83 42.35 2.17
540 541 9.733556 ATGTAACTCACATGGTTACTTATTTCA 57.266 29.630 18.35 3.85 46.41 2.69
541 542 9.214957 TGTAACTCACATGGTTACTTATTTCAG 57.785 33.333 18.35 0.00 45.19 3.02
542 543 6.743575 ACTCACATGGTTACTTATTTCAGC 57.256 37.500 0.00 0.00 0.00 4.26
543 544 6.237901 ACTCACATGGTTACTTATTTCAGCA 58.762 36.000 0.00 0.00 0.00 4.41
544 545 6.886459 ACTCACATGGTTACTTATTTCAGCAT 59.114 34.615 0.00 0.00 0.00 3.79
545 546 7.066284 ACTCACATGGTTACTTATTTCAGCATC 59.934 37.037 0.00 0.00 0.00 3.91
546 547 6.883756 TCACATGGTTACTTATTTCAGCATCA 59.116 34.615 0.00 0.00 0.00 3.07
547 548 7.066163 TCACATGGTTACTTATTTCAGCATCAG 59.934 37.037 0.00 0.00 0.00 2.90
548 549 7.066163 CACATGGTTACTTATTTCAGCATCAGA 59.934 37.037 0.00 0.00 0.00 3.27
549 550 7.611467 ACATGGTTACTTATTTCAGCATCAGAA 59.389 33.333 0.00 0.00 0.00 3.02
550 551 8.627403 CATGGTTACTTATTTCAGCATCAGAAT 58.373 33.333 0.00 0.00 0.00 2.40
551 552 8.579850 TGGTTACTTATTTCAGCATCAGAATT 57.420 30.769 0.00 0.00 0.00 2.17
552 553 9.023962 TGGTTACTTATTTCAGCATCAGAATTT 57.976 29.630 0.00 0.00 0.00 1.82
557 558 9.013229 ACTTATTTCAGCATCAGAATTTACACA 57.987 29.630 0.00 0.00 0.00 3.72
561 562 9.961265 ATTTCAGCATCAGAATTTACACATATG 57.039 29.630 0.00 0.00 0.00 1.78
562 563 8.510243 TTCAGCATCAGAATTTACACATATGT 57.490 30.769 1.41 1.41 43.30 2.29
563 564 9.612066 TTCAGCATCAGAATTTACACATATGTA 57.388 29.630 8.32 0.00 40.48 2.29
661 662 9.830975 ATTTAAAATATAAGGTTCCAATGCACC 57.169 29.630 0.00 0.00 0.00 5.01
662 663 5.869649 AAATATAAGGTTCCAATGCACCC 57.130 39.130 0.00 0.00 32.92 4.61
663 664 2.917713 ATAAGGTTCCAATGCACCCA 57.082 45.000 0.00 0.00 32.92 4.51
664 665 1.917872 TAAGGTTCCAATGCACCCAC 58.082 50.000 0.00 0.00 32.92 4.61
665 666 0.831711 AAGGTTCCAATGCACCCACC 60.832 55.000 0.00 0.00 32.92 4.61
666 667 2.282783 GGTTCCAATGCACCCACCC 61.283 63.158 0.00 0.00 0.00 4.61
667 668 1.228862 GTTCCAATGCACCCACCCT 60.229 57.895 0.00 0.00 0.00 4.34
668 669 0.831711 GTTCCAATGCACCCACCCTT 60.832 55.000 0.00 0.00 0.00 3.95
669 670 0.541764 TTCCAATGCACCCACCCTTC 60.542 55.000 0.00 0.00 0.00 3.46
670 671 1.228831 CCAATGCACCCACCCTTCA 60.229 57.895 0.00 0.00 0.00 3.02
671 672 0.831288 CCAATGCACCCACCCTTCAA 60.831 55.000 0.00 0.00 0.00 2.69
672 673 1.047002 CAATGCACCCACCCTTCAAA 58.953 50.000 0.00 0.00 0.00 2.69
673 674 1.001181 CAATGCACCCACCCTTCAAAG 59.999 52.381 0.00 0.00 0.00 2.77
674 675 0.188342 ATGCACCCACCCTTCAAAGT 59.812 50.000 0.00 0.00 0.00 2.66
675 676 0.754957 TGCACCCACCCTTCAAAGTG 60.755 55.000 0.00 0.00 0.00 3.16
676 677 0.467290 GCACCCACCCTTCAAAGTGA 60.467 55.000 0.00 0.00 36.01 3.41
677 678 1.318576 CACCCACCCTTCAAAGTGAC 58.681 55.000 0.00 0.00 36.01 3.67
678 679 1.133792 CACCCACCCTTCAAAGTGACT 60.134 52.381 0.00 0.00 36.01 3.41
679 680 1.569072 ACCCACCCTTCAAAGTGACTT 59.431 47.619 0.00 0.00 36.01 3.01
680 681 2.230660 CCCACCCTTCAAAGTGACTTC 58.769 52.381 0.00 0.00 36.01 3.01
681 682 2.158608 CCCACCCTTCAAAGTGACTTCT 60.159 50.000 0.00 0.00 36.01 2.85
682 683 3.142174 CCACCCTTCAAAGTGACTTCTC 58.858 50.000 0.00 0.00 36.01 2.87
683 684 2.802816 CACCCTTCAAAGTGACTTCTCG 59.197 50.000 0.00 0.00 36.01 4.04
684 685 2.698797 ACCCTTCAAAGTGACTTCTCGA 59.301 45.455 0.00 0.00 0.00 4.04
685 686 3.243907 ACCCTTCAAAGTGACTTCTCGAG 60.244 47.826 5.93 5.93 0.00 4.04
686 687 3.005897 CCCTTCAAAGTGACTTCTCGAGA 59.994 47.826 12.08 12.08 0.00 4.04
687 688 4.501571 CCCTTCAAAGTGACTTCTCGAGAA 60.502 45.833 25.57 25.57 0.00 2.87
694 695 2.202810 CTTCTCGAGAAGGCCGGC 60.203 66.667 36.99 21.18 45.79 6.13
695 696 2.994995 TTCTCGAGAAGGCCGGCA 60.995 61.111 30.85 4.11 0.00 5.69
696 697 2.303549 CTTCTCGAGAAGGCCGGCAT 62.304 60.000 36.99 21.35 45.79 4.40
697 698 2.279784 CTCGAGAAGGCCGGCATC 60.280 66.667 30.85 24.94 0.00 3.91
698 699 4.207281 TCGAGAAGGCCGGCATCG 62.207 66.667 30.85 28.29 34.80 3.84
770 771 6.209192 TCTGTCTATGTAAAAGTACCAACGGA 59.791 38.462 0.00 0.00 0.00 4.69
772 773 7.388437 TGTCTATGTAAAAGTACCAACGGATT 58.612 34.615 0.00 0.00 0.00 3.01
774 775 7.763071 GTCTATGTAAAAGTACCAACGGATTCT 59.237 37.037 0.00 0.00 0.00 2.40
775 776 6.980051 ATGTAAAAGTACCAACGGATTCTC 57.020 37.500 0.00 0.00 0.00 2.87
776 777 5.856156 TGTAAAAGTACCAACGGATTCTCA 58.144 37.500 0.00 0.00 0.00 3.27
778 779 6.766944 TGTAAAAGTACCAACGGATTCTCAAA 59.233 34.615 0.00 0.00 0.00 2.69
780 781 4.345859 AGTACCAACGGATTCTCAAACA 57.654 40.909 0.00 0.00 0.00 2.83
781 782 4.710324 AGTACCAACGGATTCTCAAACAA 58.290 39.130 0.00 0.00 0.00 2.83
782 783 5.127491 AGTACCAACGGATTCTCAAACAAA 58.873 37.500 0.00 0.00 0.00 2.83
783 784 4.993029 ACCAACGGATTCTCAAACAAAA 57.007 36.364 0.00 0.00 0.00 2.44
784 785 5.331876 ACCAACGGATTCTCAAACAAAAA 57.668 34.783 0.00 0.00 0.00 1.94
1078 1079 2.202756 GAGGAATTCGCCGACGCT 60.203 61.111 0.00 0.00 39.84 5.07
1168 1169 0.817634 CTCCCGTCTTTGTTGTGGCA 60.818 55.000 0.00 0.00 0.00 4.92
1178 1179 2.124529 TTGTGGCACTTGGTCGCA 60.125 55.556 19.83 0.00 40.47 5.10
1197 1198 2.185608 GCCTCGCTCTCCAGGTTC 59.814 66.667 0.00 0.00 31.65 3.62
1325 1326 5.055812 CAGGACATCCAGCTCTTTTAGATC 58.944 45.833 0.00 0.00 38.89 2.75
1386 1387 2.035704 TGTGGCTCGCATTGTTTGAATT 59.964 40.909 0.00 0.00 0.00 2.17
1433 1434 7.095523 CCTGTTTAGAATTGAAATTTGGTGCTG 60.096 37.037 0.00 0.00 0.00 4.41
1458 1468 5.971763 TCCATTATTTTGTTTCCCCATTCG 58.028 37.500 0.00 0.00 0.00 3.34
1688 1698 0.039074 GCGTACATCTGCTCGCCTAT 60.039 55.000 7.89 0.00 42.33 2.57
1803 1814 6.748132 TCCTCATTCCAATTTTGACACTTTC 58.252 36.000 0.00 0.00 0.00 2.62
1811 1822 5.687285 CCAATTTTGACACTTTCACTACTGC 59.313 40.000 0.00 0.00 32.26 4.40
1904 1916 4.931601 TCAACTCTACTTGATGTGTGATGC 59.068 41.667 0.00 0.00 0.00 3.91
2326 2370 1.889530 AACTGCCCCGCTCTGTAGAC 61.890 60.000 0.00 0.00 0.00 2.59
2392 2436 2.941064 CTCCATATGTGACTGTTGCCAG 59.059 50.000 1.24 0.00 44.68 4.85
2497 2542 7.491696 GCAATAGTAGTACTAGTTTGTTCAGGG 59.508 40.741 15.34 4.46 33.66 4.45
2633 5393 2.603021 ACAGACAGGAGAGCAGAGAAA 58.397 47.619 0.00 0.00 0.00 2.52
2666 5457 7.834068 TCAAAGAGATTATGCTGTTACAGAC 57.166 36.000 17.40 8.10 32.44 3.51
2667 5458 7.386059 TCAAAGAGATTATGCTGTTACAGACA 58.614 34.615 17.40 13.50 36.65 3.41
2687 5478 6.889722 CAGACAGGGTTTTTATAGGGAAATGA 59.110 38.462 0.00 0.00 0.00 2.57
2722 5513 1.841302 TTGCCTCGGCTTCCATCAGT 61.841 55.000 9.65 0.00 42.51 3.41
2867 6067 6.486657 TGTCCAGGCTAATTGTTTGCTATATC 59.513 38.462 0.00 0.00 0.00 1.63
2890 6090 4.082081 CAGCAGGAGTTTATGGCAATTTGA 60.082 41.667 0.00 0.00 0.00 2.69
2906 6106 5.353123 GCAATTTGATGCCATTCTTCACATT 59.647 36.000 0.00 0.00 40.49 2.71
3012 6212 9.720667 TTGCATATTCATAATAATAAGATGCGC 57.279 29.630 0.00 0.00 45.91 6.09
3127 6327 0.323302 TCAGCCTTGGTGCGAATACA 59.677 50.000 0.00 0.00 36.02 2.29
3177 6377 1.135139 CTGTCTATGGACCCACTGACG 59.865 57.143 6.77 8.49 41.47 4.35
3180 6380 2.629050 CTATGGACCCACTGACGCGG 62.629 65.000 12.47 0.00 0.00 6.46
3209 6409 1.004504 GATGCGTTCTTTGCGGAGATC 60.005 52.381 0.00 0.00 32.45 2.75
3218 6418 4.863707 GCGGAGATCATCAGCCAA 57.136 55.556 0.00 0.00 42.63 4.52
3231 6431 2.357396 GCCAAAAGCCTTTGCCGG 60.357 61.111 0.00 0.00 40.61 6.13
3232 6432 2.866726 GCCAAAAGCCTTTGCCGGA 61.867 57.895 5.05 0.00 40.61 5.14
3269 6469 4.202441 CATTAGGGGACTTCAACCAGATG 58.798 47.826 0.00 0.00 43.67 2.90
3294 6494 3.377172 CCGAGCGAGGGACAAAAATAAAT 59.623 43.478 0.00 0.00 0.00 1.40
3296 6496 4.142687 CGAGCGAGGGACAAAAATAAATGT 60.143 41.667 0.00 0.00 0.00 2.71
3304 6504 9.573133 GAGGGACAAAAATAAATGTAATGTGAG 57.427 33.333 0.00 0.00 0.00 3.51
3307 6507 7.009174 GGACAAAAATAAATGTAATGTGAGCCG 59.991 37.037 0.00 0.00 0.00 5.52
3356 6556 2.032204 GCTGCAATCCGATGAGCTTAAG 60.032 50.000 0.00 0.00 0.00 1.85
3408 6608 4.205584 GCAACGAGCGAAACAACC 57.794 55.556 0.00 0.00 0.00 3.77
3491 6694 5.337894 CCATATTCTCCATGCCTTATCGTCT 60.338 44.000 0.00 0.00 0.00 4.18
3506 6709 0.448593 CGTCTTCTCTCTCCGACCAC 59.551 60.000 0.00 0.00 0.00 4.16
3518 6721 2.328099 CGACCACTGCCCTTTGCTC 61.328 63.158 0.00 0.00 42.00 4.26
3620 6823 3.562639 GGTCCAAAAAGCGTGGAAC 57.437 52.632 3.47 2.63 46.66 3.62
3649 6852 1.880675 AGCTCACTACGATCCATACCG 59.119 52.381 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 9.423061 CCGAATTCCATAAAAGTTCTTGAATTT 57.577 29.630 0.00 0.00 32.74 1.82
47 48 8.585018 ACCGAATTCCATAAAAGTTCTTGAATT 58.415 29.630 0.00 0.00 34.62 2.17
48 49 8.122472 ACCGAATTCCATAAAAGTTCTTGAAT 57.878 30.769 0.00 0.00 0.00 2.57
49 50 7.519032 ACCGAATTCCATAAAAGTTCTTGAA 57.481 32.000 0.00 0.00 0.00 2.69
50 51 8.624367 TTACCGAATTCCATAAAAGTTCTTGA 57.376 30.769 0.00 0.00 0.00 3.02
51 52 9.124807 GTTTACCGAATTCCATAAAAGTTCTTG 57.875 33.333 9.32 0.00 0.00 3.02
52 53 8.852135 TGTTTACCGAATTCCATAAAAGTTCTT 58.148 29.630 9.32 0.00 0.00 2.52
53 54 8.398878 TGTTTACCGAATTCCATAAAAGTTCT 57.601 30.769 9.32 0.00 0.00 3.01
54 55 9.634163 AATGTTTACCGAATTCCATAAAAGTTC 57.366 29.630 9.32 1.39 0.00 3.01
55 56 9.990360 AAATGTTTACCGAATTCCATAAAAGTT 57.010 25.926 9.32 6.15 0.00 2.66
56 57 9.990360 AAAATGTTTACCGAATTCCATAAAAGT 57.010 25.926 9.32 1.81 0.00 2.66
134 135 2.200337 GCGAGGTGCCCCAGTTTTT 61.200 57.895 0.00 0.00 37.76 1.94
135 136 2.597510 GCGAGGTGCCCCAGTTTT 60.598 61.111 0.00 0.00 37.76 2.43
157 158 4.738998 TCTTGGCCGGCCCATGTG 62.739 66.667 41.75 25.21 44.89 3.21
158 159 3.944250 CTTCTTGGCCGGCCCATGT 62.944 63.158 41.75 0.00 44.89 3.21
159 160 3.142838 CTTCTTGGCCGGCCCATG 61.143 66.667 41.75 29.43 44.89 3.66
160 161 4.447342 CCTTCTTGGCCGGCCCAT 62.447 66.667 41.75 0.00 44.89 4.00
162 163 4.360405 TTCCTTCTTGGCCGGCCC 62.360 66.667 41.75 24.44 35.26 5.80
163 164 3.062466 GTTCCTTCTTGGCCGGCC 61.062 66.667 39.40 39.40 35.26 6.13
164 165 2.791501 TACGTTCCTTCTTGGCCGGC 62.792 60.000 21.18 21.18 35.27 6.13
165 166 0.739813 CTACGTTCCTTCTTGGCCGG 60.740 60.000 0.00 0.00 35.27 6.13
166 167 0.245539 TCTACGTTCCTTCTTGGCCG 59.754 55.000 0.00 0.00 36.44 6.13
167 168 1.405661 CCTCTACGTTCCTTCTTGGCC 60.406 57.143 0.00 0.00 35.26 5.36
168 169 1.549170 TCCTCTACGTTCCTTCTTGGC 59.451 52.381 0.00 0.00 35.26 4.52
169 170 2.417515 GCTCCTCTACGTTCCTTCTTGG 60.418 54.545 0.00 0.00 37.10 3.61
170 171 2.231478 TGCTCCTCTACGTTCCTTCTTG 59.769 50.000 0.00 0.00 0.00 3.02
171 172 2.526432 TGCTCCTCTACGTTCCTTCTT 58.474 47.619 0.00 0.00 0.00 2.52
172 173 2.217510 TGCTCCTCTACGTTCCTTCT 57.782 50.000 0.00 0.00 0.00 2.85
173 174 2.231721 ACTTGCTCCTCTACGTTCCTTC 59.768 50.000 0.00 0.00 0.00 3.46
174 175 2.028930 CACTTGCTCCTCTACGTTCCTT 60.029 50.000 0.00 0.00 0.00 3.36
175 176 1.546476 CACTTGCTCCTCTACGTTCCT 59.454 52.381 0.00 0.00 0.00 3.36
176 177 1.404315 CCACTTGCTCCTCTACGTTCC 60.404 57.143 0.00 0.00 0.00 3.62
177 178 1.404315 CCCACTTGCTCCTCTACGTTC 60.404 57.143 0.00 0.00 0.00 3.95
178 179 0.608640 CCCACTTGCTCCTCTACGTT 59.391 55.000 0.00 0.00 0.00 3.99
179 180 0.542232 ACCCACTTGCTCCTCTACGT 60.542 55.000 0.00 0.00 0.00 3.57
180 181 0.108615 CACCCACTTGCTCCTCTACG 60.109 60.000 0.00 0.00 0.00 3.51
181 182 0.391793 GCACCCACTTGCTCCTCTAC 60.392 60.000 0.00 0.00 39.59 2.59
182 183 1.888436 CGCACCCACTTGCTCCTCTA 61.888 60.000 0.00 0.00 40.62 2.43
183 184 2.753029 GCACCCACTTGCTCCTCT 59.247 61.111 0.00 0.00 39.59 3.69
184 185 2.743928 CGCACCCACTTGCTCCTC 60.744 66.667 0.00 0.00 40.62 3.71
187 188 4.030452 GTGCGCACCCACTTGCTC 62.030 66.667 30.12 0.00 40.62 4.26
205 206 1.447314 CTAACGTCGGGGAACAGGC 60.447 63.158 0.00 0.00 0.00 4.85
206 207 1.217244 CCTAACGTCGGGGAACAGG 59.783 63.158 0.00 0.00 0.00 4.00
207 208 1.217244 CCCTAACGTCGGGGAACAG 59.783 63.158 17.78 0.00 45.18 3.16
208 209 1.533753 ACCCTAACGTCGGGGAACA 60.534 57.895 26.17 0.00 46.40 3.18
209 210 1.216444 GACCCTAACGTCGGGGAAC 59.784 63.158 26.17 17.19 46.40 3.62
210 211 3.698765 GACCCTAACGTCGGGGAA 58.301 61.111 26.17 0.00 46.40 3.97
216 217 1.004595 GATTTGGCGACCCTAACGTC 58.995 55.000 0.00 0.00 35.87 4.34
217 218 0.322322 TGATTTGGCGACCCTAACGT 59.678 50.000 0.00 0.00 0.00 3.99
218 219 1.006832 CTGATTTGGCGACCCTAACG 58.993 55.000 0.00 0.00 0.00 3.18
219 220 2.280628 CTCTGATTTGGCGACCCTAAC 58.719 52.381 0.00 0.00 0.00 2.34
220 221 1.406887 GCTCTGATTTGGCGACCCTAA 60.407 52.381 0.00 0.00 0.00 2.69
221 222 0.178068 GCTCTGATTTGGCGACCCTA 59.822 55.000 0.00 0.00 0.00 3.53
222 223 1.078143 GCTCTGATTTGGCGACCCT 60.078 57.895 0.00 0.00 0.00 4.34
223 224 1.377202 TGCTCTGATTTGGCGACCC 60.377 57.895 0.00 0.00 0.00 4.46
224 225 1.648467 GGTGCTCTGATTTGGCGACC 61.648 60.000 0.00 0.00 0.00 4.79
225 226 1.648467 GGGTGCTCTGATTTGGCGAC 61.648 60.000 0.00 0.00 0.00 5.19
226 227 1.377202 GGGTGCTCTGATTTGGCGA 60.377 57.895 0.00 0.00 0.00 5.54
227 228 1.033746 ATGGGTGCTCTGATTTGGCG 61.034 55.000 0.00 0.00 0.00 5.69
228 229 0.743097 GATGGGTGCTCTGATTTGGC 59.257 55.000 0.00 0.00 0.00 4.52
229 230 2.133281 TGATGGGTGCTCTGATTTGG 57.867 50.000 0.00 0.00 0.00 3.28
230 231 5.123502 GCTATATGATGGGTGCTCTGATTTG 59.876 44.000 0.00 0.00 0.00 2.32
231 232 5.251764 GCTATATGATGGGTGCTCTGATTT 58.748 41.667 0.00 0.00 0.00 2.17
232 233 4.324099 GGCTATATGATGGGTGCTCTGATT 60.324 45.833 0.00 0.00 0.00 2.57
233 234 3.199508 GGCTATATGATGGGTGCTCTGAT 59.800 47.826 0.00 0.00 0.00 2.90
234 235 2.568956 GGCTATATGATGGGTGCTCTGA 59.431 50.000 0.00 0.00 0.00 3.27
235 236 2.303890 TGGCTATATGATGGGTGCTCTG 59.696 50.000 0.00 0.00 0.00 3.35
236 237 2.570752 CTGGCTATATGATGGGTGCTCT 59.429 50.000 0.00 0.00 0.00 4.09
237 238 2.938756 GCTGGCTATATGATGGGTGCTC 60.939 54.545 0.00 0.00 0.00 4.26
238 239 1.004044 GCTGGCTATATGATGGGTGCT 59.996 52.381 0.00 0.00 0.00 4.40
239 240 1.271543 TGCTGGCTATATGATGGGTGC 60.272 52.381 0.00 0.00 0.00 5.01
240 241 2.708051 CTGCTGGCTATATGATGGGTG 58.292 52.381 0.00 0.00 0.00 4.61
241 242 1.004044 GCTGCTGGCTATATGATGGGT 59.996 52.381 0.00 0.00 38.06 4.51
242 243 1.681166 GGCTGCTGGCTATATGATGGG 60.681 57.143 10.05 0.00 41.46 4.00
243 244 1.747709 GGCTGCTGGCTATATGATGG 58.252 55.000 10.05 0.00 41.46 3.51
244 245 1.066645 TCGGCTGCTGGCTATATGATG 60.067 52.381 15.09 0.00 41.46 3.07
245 246 1.269958 TCGGCTGCTGGCTATATGAT 58.730 50.000 15.09 0.00 41.46 2.45
246 247 1.205655 GATCGGCTGCTGGCTATATGA 59.794 52.381 15.09 5.01 41.46 2.15
247 248 1.649664 GATCGGCTGCTGGCTATATG 58.350 55.000 15.09 0.00 41.46 1.78
248 249 0.174389 CGATCGGCTGCTGGCTATAT 59.826 55.000 15.09 5.99 41.46 0.86
249 250 0.893727 TCGATCGGCTGCTGGCTATA 60.894 55.000 16.41 1.30 41.46 1.31
250 251 2.152297 CTCGATCGGCTGCTGGCTAT 62.152 60.000 16.41 9.62 41.46 2.97
251 252 2.833121 TCGATCGGCTGCTGGCTA 60.833 61.111 16.41 4.66 41.46 3.93
252 253 4.218578 CTCGATCGGCTGCTGGCT 62.219 66.667 16.41 0.00 41.46 4.75
253 254 4.212913 TCTCGATCGGCTGCTGGC 62.213 66.667 16.41 7.12 40.90 4.85
254 255 2.027314 CTCTCGATCGGCTGCTGG 59.973 66.667 16.41 0.00 0.00 4.85
255 256 1.588403 CACTCTCGATCGGCTGCTG 60.588 63.158 16.41 0.95 0.00 4.41
256 257 2.780094 CCACTCTCGATCGGCTGCT 61.780 63.158 16.41 0.00 0.00 4.24
257 258 2.081425 ATCCACTCTCGATCGGCTGC 62.081 60.000 16.41 0.00 0.00 5.25
258 259 0.387202 AATCCACTCTCGATCGGCTG 59.613 55.000 16.41 7.86 0.00 4.85
259 260 1.115467 AAATCCACTCTCGATCGGCT 58.885 50.000 16.41 0.00 0.00 5.52
260 261 1.941325 AAAATCCACTCTCGATCGGC 58.059 50.000 16.41 0.00 0.00 5.54
261 262 2.609459 CCAAAAATCCACTCTCGATCGG 59.391 50.000 16.41 6.26 0.00 4.18
262 263 3.521560 TCCAAAAATCCACTCTCGATCG 58.478 45.455 9.36 9.36 0.00 3.69
263 264 4.095036 GGTTCCAAAAATCCACTCTCGATC 59.905 45.833 0.00 0.00 0.00 3.69
264 265 4.010349 GGTTCCAAAAATCCACTCTCGAT 58.990 43.478 0.00 0.00 0.00 3.59
265 266 3.408634 GGTTCCAAAAATCCACTCTCGA 58.591 45.455 0.00 0.00 0.00 4.04
266 267 2.488153 GGGTTCCAAAAATCCACTCTCG 59.512 50.000 0.00 0.00 0.00 4.04
267 268 3.255888 GTGGGTTCCAAAAATCCACTCTC 59.744 47.826 11.98 0.00 43.14 3.20
268 269 3.230976 GTGGGTTCCAAAAATCCACTCT 58.769 45.455 11.98 0.00 43.14 3.24
269 270 2.962421 TGTGGGTTCCAAAAATCCACTC 59.038 45.455 18.27 0.00 45.74 3.51
270 271 3.039252 TGTGGGTTCCAAAAATCCACT 57.961 42.857 18.27 0.00 45.74 4.00
271 272 3.070878 ACATGTGGGTTCCAAAAATCCAC 59.929 43.478 12.28 12.28 45.75 4.02
272 273 3.312890 ACATGTGGGTTCCAAAAATCCA 58.687 40.909 0.00 0.00 34.18 3.41
273 274 5.675684 ATACATGTGGGTTCCAAAAATCC 57.324 39.130 9.11 0.00 34.18 3.01
274 275 9.150348 CTTTAATACATGTGGGTTCCAAAAATC 57.850 33.333 9.11 0.00 34.18 2.17
275 276 8.100164 CCTTTAATACATGTGGGTTCCAAAAAT 58.900 33.333 9.11 0.00 34.18 1.82
276 277 7.290248 TCCTTTAATACATGTGGGTTCCAAAAA 59.710 33.333 9.11 0.00 34.18 1.94
277 278 6.782988 TCCTTTAATACATGTGGGTTCCAAAA 59.217 34.615 9.11 0.00 34.18 2.44
278 279 6.209788 GTCCTTTAATACATGTGGGTTCCAAA 59.790 38.462 9.11 0.00 34.18 3.28
279 280 5.712917 GTCCTTTAATACATGTGGGTTCCAA 59.287 40.000 9.11 0.00 34.18 3.53
280 281 5.258051 GTCCTTTAATACATGTGGGTTCCA 58.742 41.667 9.11 0.00 0.00 3.53
281 282 4.643334 GGTCCTTTAATACATGTGGGTTCC 59.357 45.833 9.11 0.96 0.00 3.62
282 283 5.506708 AGGTCCTTTAATACATGTGGGTTC 58.493 41.667 9.11 0.00 0.00 3.62
283 284 5.530176 AGGTCCTTTAATACATGTGGGTT 57.470 39.130 9.11 3.49 0.00 4.11
284 285 5.530176 AAGGTCCTTTAATACATGTGGGT 57.470 39.130 9.11 0.00 0.00 4.51
285 286 8.533569 AAATAAGGTCCTTTAATACATGTGGG 57.466 34.615 10.04 1.42 0.00 4.61
430 431 9.883142 TTGGAAATCACTATTTTGTCTTTTTGT 57.117 25.926 0.00 0.00 35.41 2.83
436 437 9.865321 CATCATTTGGAAATCACTATTTTGTCT 57.135 29.630 0.00 0.00 35.41 3.41
437 438 9.859427 TCATCATTTGGAAATCACTATTTTGTC 57.141 29.630 0.00 0.00 35.41 3.18
461 462 8.969260 AAGATGAGTAGTGCATGAATTATTCA 57.031 30.769 10.23 10.23 45.01 2.57
462 463 9.875675 GAAAGATGAGTAGTGCATGAATTATTC 57.124 33.333 0.00 0.00 0.00 1.75
463 464 8.844244 GGAAAGATGAGTAGTGCATGAATTATT 58.156 33.333 0.00 0.00 0.00 1.40
464 465 7.172190 CGGAAAGATGAGTAGTGCATGAATTAT 59.828 37.037 0.00 0.00 0.00 1.28
465 466 6.479990 CGGAAAGATGAGTAGTGCATGAATTA 59.520 38.462 0.00 0.00 0.00 1.40
466 467 5.295292 CGGAAAGATGAGTAGTGCATGAATT 59.705 40.000 0.00 0.00 0.00 2.17
467 468 4.813161 CGGAAAGATGAGTAGTGCATGAAT 59.187 41.667 0.00 0.00 0.00 2.57
468 469 4.081697 TCGGAAAGATGAGTAGTGCATGAA 60.082 41.667 0.00 0.00 0.00 2.57
469 470 3.447229 TCGGAAAGATGAGTAGTGCATGA 59.553 43.478 0.00 0.00 0.00 3.07
470 471 3.785486 TCGGAAAGATGAGTAGTGCATG 58.215 45.455 0.00 0.00 0.00 4.06
471 472 4.471904 TTCGGAAAGATGAGTAGTGCAT 57.528 40.909 0.00 0.00 0.00 3.96
472 473 3.953712 TTCGGAAAGATGAGTAGTGCA 57.046 42.857 0.00 0.00 0.00 4.57
473 474 5.351465 TGATTTTCGGAAAGATGAGTAGTGC 59.649 40.000 3.09 0.00 0.00 4.40
474 475 6.968131 TGATTTTCGGAAAGATGAGTAGTG 57.032 37.500 3.09 0.00 0.00 2.74
475 476 7.331026 TCATGATTTTCGGAAAGATGAGTAGT 58.669 34.615 8.83 0.00 30.24 2.73
476 477 7.776933 TCATGATTTTCGGAAAGATGAGTAG 57.223 36.000 8.83 0.65 30.24 2.57
477 478 8.737168 AATCATGATTTTCGGAAAGATGAGTA 57.263 30.769 15.36 1.41 34.04 2.59
478 479 7.636150 AATCATGATTTTCGGAAAGATGAGT 57.364 32.000 15.36 11.71 34.04 3.41
479 480 8.804743 CAAAATCATGATTTTCGGAAAGATGAG 58.195 33.333 33.48 18.96 46.01 2.90
480 481 8.306038 ACAAAATCATGATTTTCGGAAAGATGA 58.694 29.630 33.48 13.43 46.01 2.92
481 482 8.470040 ACAAAATCATGATTTTCGGAAAGATG 57.530 30.769 33.48 24.44 46.01 2.90
482 483 8.526147 AGACAAAATCATGATTTTCGGAAAGAT 58.474 29.630 33.48 14.73 46.01 2.40
483 484 7.885297 AGACAAAATCATGATTTTCGGAAAGA 58.115 30.769 33.48 0.00 46.01 2.52
484 485 8.524870 AAGACAAAATCATGATTTTCGGAAAG 57.475 30.769 33.48 25.20 46.01 2.62
485 486 8.885494 AAAGACAAAATCATGATTTTCGGAAA 57.115 26.923 33.48 0.00 46.01 3.13
486 487 8.885494 AAAAGACAAAATCATGATTTTCGGAA 57.115 26.923 33.48 0.00 46.01 4.30
487 488 8.885494 AAAAAGACAAAATCATGATTTTCGGA 57.115 26.923 33.48 0.00 46.01 4.55
516 517 8.175716 GCTGAAATAAGTAACCATGTGAGTTAC 58.824 37.037 12.83 12.83 46.45 2.50
517 518 7.880713 TGCTGAAATAAGTAACCATGTGAGTTA 59.119 33.333 0.00 0.00 0.00 2.24
518 519 6.714810 TGCTGAAATAAGTAACCATGTGAGTT 59.285 34.615 0.00 0.00 0.00 3.01
519 520 6.237901 TGCTGAAATAAGTAACCATGTGAGT 58.762 36.000 0.00 0.00 0.00 3.41
520 521 6.741992 TGCTGAAATAAGTAACCATGTGAG 57.258 37.500 0.00 0.00 0.00 3.51
521 522 6.883756 TGATGCTGAAATAAGTAACCATGTGA 59.116 34.615 0.00 0.00 0.00 3.58
522 523 7.066163 TCTGATGCTGAAATAAGTAACCATGTG 59.934 37.037 0.00 0.00 0.00 3.21
523 524 7.112122 TCTGATGCTGAAATAAGTAACCATGT 58.888 34.615 0.00 0.00 0.00 3.21
524 525 7.558161 TCTGATGCTGAAATAAGTAACCATG 57.442 36.000 0.00 0.00 0.00 3.66
525 526 8.757982 ATTCTGATGCTGAAATAAGTAACCAT 57.242 30.769 0.00 0.00 0.00 3.55
526 527 8.579850 AATTCTGATGCTGAAATAAGTAACCA 57.420 30.769 0.00 0.00 0.00 3.67
531 532 9.013229 TGTGTAAATTCTGATGCTGAAATAAGT 57.987 29.630 0.00 0.00 0.00 2.24
535 536 9.961265 CATATGTGTAAATTCTGATGCTGAAAT 57.039 29.630 0.00 0.00 0.00 2.17
536 537 8.959548 ACATATGTGTAAATTCTGATGCTGAAA 58.040 29.630 7.78 0.00 36.63 2.69
537 538 8.510243 ACATATGTGTAAATTCTGATGCTGAA 57.490 30.769 7.78 0.00 36.63 3.02
538 539 9.612066 TTACATATGTGTAAATTCTGATGCTGA 57.388 29.630 18.81 0.00 45.29 4.26
635 636 9.830975 GGTGCATTGGAACCTTATATTTTAAAT 57.169 29.630 0.00 0.00 39.96 1.40
636 637 8.261522 GGGTGCATTGGAACCTTATATTTTAAA 58.738 33.333 4.77 0.00 43.07 1.52
637 638 7.400339 TGGGTGCATTGGAACCTTATATTTTAA 59.600 33.333 13.84 0.00 43.07 1.52
638 639 6.897966 TGGGTGCATTGGAACCTTATATTTTA 59.102 34.615 13.84 0.00 43.07 1.52
639 640 5.723887 TGGGTGCATTGGAACCTTATATTTT 59.276 36.000 13.84 0.00 43.07 1.82
640 641 5.128663 GTGGGTGCATTGGAACCTTATATTT 59.871 40.000 13.84 0.00 43.07 1.40
641 642 4.649218 GTGGGTGCATTGGAACCTTATATT 59.351 41.667 13.84 0.00 43.07 1.28
642 643 4.215109 GTGGGTGCATTGGAACCTTATAT 58.785 43.478 13.84 0.00 43.07 0.86
643 644 3.626222 GGTGGGTGCATTGGAACCTTATA 60.626 47.826 13.84 0.00 43.07 0.98
644 645 2.456577 GTGGGTGCATTGGAACCTTAT 58.543 47.619 13.84 0.00 43.07 1.73
645 646 1.549037 GGTGGGTGCATTGGAACCTTA 60.549 52.381 13.84 0.00 43.07 2.69
646 647 0.831711 GGTGGGTGCATTGGAACCTT 60.832 55.000 13.84 0.00 43.07 3.50
647 648 1.228862 GGTGGGTGCATTGGAACCT 60.229 57.895 13.84 0.00 43.07 3.50
648 649 2.282783 GGGTGGGTGCATTGGAACC 61.283 63.158 5.10 5.10 42.74 3.62
649 650 0.831711 AAGGGTGGGTGCATTGGAAC 60.832 55.000 0.00 0.00 0.00 3.62
650 651 0.541764 GAAGGGTGGGTGCATTGGAA 60.542 55.000 0.00 0.00 0.00 3.53
651 652 1.076549 GAAGGGTGGGTGCATTGGA 59.923 57.895 0.00 0.00 0.00 3.53
652 653 0.831288 TTGAAGGGTGGGTGCATTGG 60.831 55.000 0.00 0.00 0.00 3.16
653 654 1.001181 CTTTGAAGGGTGGGTGCATTG 59.999 52.381 0.00 0.00 0.00 2.82
654 655 1.341080 CTTTGAAGGGTGGGTGCATT 58.659 50.000 0.00 0.00 0.00 3.56
655 656 0.188342 ACTTTGAAGGGTGGGTGCAT 59.812 50.000 0.00 0.00 0.00 3.96
656 657 0.754957 CACTTTGAAGGGTGGGTGCA 60.755 55.000 0.00 0.00 0.00 4.57
657 658 0.467290 TCACTTTGAAGGGTGGGTGC 60.467 55.000 0.00 0.00 34.57 5.01
658 659 1.133792 AGTCACTTTGAAGGGTGGGTG 60.134 52.381 0.00 0.00 34.57 4.61
659 660 1.222567 AGTCACTTTGAAGGGTGGGT 58.777 50.000 0.00 0.00 34.57 4.51
660 661 2.158608 AGAAGTCACTTTGAAGGGTGGG 60.159 50.000 0.00 0.00 34.57 4.61
661 662 3.142174 GAGAAGTCACTTTGAAGGGTGG 58.858 50.000 0.00 0.00 34.57 4.61
662 663 2.802816 CGAGAAGTCACTTTGAAGGGTG 59.197 50.000 0.00 0.00 35.06 4.61
663 664 2.698797 TCGAGAAGTCACTTTGAAGGGT 59.301 45.455 0.00 0.00 0.00 4.34
664 665 3.005897 TCTCGAGAAGTCACTTTGAAGGG 59.994 47.826 14.01 0.00 0.00 3.95
665 666 4.244425 TCTCGAGAAGTCACTTTGAAGG 57.756 45.455 14.01 0.00 0.00 3.46
666 667 5.820926 CTTCTCGAGAAGTCACTTTGAAG 57.179 43.478 36.43 15.62 44.80 3.02
678 679 2.298158 GATGCCGGCCTTCTCGAGAA 62.298 60.000 26.77 25.57 0.00 2.87
679 680 2.759973 ATGCCGGCCTTCTCGAGA 60.760 61.111 26.77 12.08 0.00 4.04
680 681 2.279784 GATGCCGGCCTTCTCGAG 60.280 66.667 26.77 5.93 0.00 4.04
681 682 4.207281 CGATGCCGGCCTTCTCGA 62.207 66.667 26.77 2.60 0.00 4.04
693 694 2.870372 GTGACCAACTGGCGATGC 59.130 61.111 0.00 0.00 39.32 3.91
694 695 1.374125 TCGTGACCAACTGGCGATG 60.374 57.895 0.00 0.00 39.32 3.84
695 696 1.374252 GTCGTGACCAACTGGCGAT 60.374 57.895 0.00 0.00 39.32 4.58
696 697 2.028484 GTCGTGACCAACTGGCGA 59.972 61.111 0.00 0.00 39.32 5.54
697 698 3.403057 CGTCGTGACCAACTGGCG 61.403 66.667 0.00 0.00 39.32 5.69
698 699 0.108992 TATCGTCGTGACCAACTGGC 60.109 55.000 0.00 0.00 39.32 4.85
699 700 1.471287 TCTATCGTCGTGACCAACTGG 59.529 52.381 0.00 0.00 42.17 4.00
700 701 2.478031 CCTCTATCGTCGTGACCAACTG 60.478 54.545 0.00 0.00 0.00 3.16
701 702 1.743958 CCTCTATCGTCGTGACCAACT 59.256 52.381 0.00 0.00 0.00 3.16
702 703 1.798079 GCCTCTATCGTCGTGACCAAC 60.798 57.143 0.00 0.00 0.00 3.77
703 704 0.454600 GCCTCTATCGTCGTGACCAA 59.545 55.000 0.00 0.00 0.00 3.67
704 705 1.381928 GGCCTCTATCGTCGTGACCA 61.382 60.000 0.00 0.00 0.00 4.02
705 706 1.359475 GGCCTCTATCGTCGTGACC 59.641 63.158 0.00 0.00 0.00 4.02
706 707 1.359475 GGGCCTCTATCGTCGTGAC 59.641 63.158 0.84 0.00 0.00 3.67
707 708 1.077285 TGGGCCTCTATCGTCGTGA 60.077 57.895 4.53 0.00 0.00 4.35
999 1000 3.063861 CGAGTGACACATCTCTCTCTCTG 59.936 52.174 8.59 0.00 41.41 3.35
1078 1079 4.697756 CCGCCTTCCTCCGTTGCA 62.698 66.667 0.00 0.00 0.00 4.08
1325 1326 2.747446 CCAAATCAAACTACTCCCCGTG 59.253 50.000 0.00 0.00 0.00 4.94
1369 1370 3.305094 CCATCAATTCAAACAATGCGAGC 59.695 43.478 0.00 0.00 0.00 5.03
1433 1434 6.701400 CGAATGGGGAAACAAAATAATGGATC 59.299 38.462 0.00 0.00 0.00 3.36
1458 1468 5.923733 ACTGGTCTGGATATATCGAATCC 57.076 43.478 7.55 7.55 42.84 3.01
1688 1698 5.344743 TCCAGTATTGGTTTGCAAACAAA 57.655 34.783 35.95 32.78 45.26 2.83
1911 1923 9.838339 CTGGAATCTATCAACCTAACAAGTTAT 57.162 33.333 0.00 0.00 0.00 1.89
2240 2284 0.036952 CACCGCTCAGGATGTTGAGT 60.037 55.000 5.08 0.00 45.07 3.41
2326 2370 1.081242 GCTTGCACATGAACGGTGG 60.081 57.895 0.00 0.00 36.76 4.61
2392 2436 1.209128 CACTGTGACGACCTGACAAC 58.791 55.000 0.32 0.00 0.00 3.32
2400 2444 1.137513 GTGGCTAACACTGTGACGAC 58.862 55.000 15.86 4.81 46.72 4.34
2497 2542 2.358898 TCTGCTTCACTGAAAAAGCCAC 59.641 45.455 4.79 0.00 45.77 5.01
2664 5455 7.898014 ATCATTTCCCTATAAAAACCCTGTC 57.102 36.000 0.00 0.00 0.00 3.51
2666 5457 7.125659 ACCAATCATTTCCCTATAAAAACCCTG 59.874 37.037 0.00 0.00 0.00 4.45
2667 5458 7.125659 CACCAATCATTTCCCTATAAAAACCCT 59.874 37.037 0.00 0.00 0.00 4.34
2669 5460 8.073467 TCACCAATCATTTCCCTATAAAAACC 57.927 34.615 0.00 0.00 0.00 3.27
2670 5461 9.586435 CTTCACCAATCATTTCCCTATAAAAAC 57.414 33.333 0.00 0.00 0.00 2.43
2671 5462 8.257306 GCTTCACCAATCATTTCCCTATAAAAA 58.743 33.333 0.00 0.00 0.00 1.94
2687 5478 1.187567 GCAACCCCAGCTTCACCAAT 61.188 55.000 0.00 0.00 0.00 3.16
2722 5513 3.568007 GGTTCAACAAACATGCCTCACTA 59.432 43.478 0.00 0.00 39.81 2.74
2830 6027 1.750682 GCCTGGACAGTCCACAACTTT 60.751 52.381 19.21 0.00 42.67 2.66
2867 6067 4.082081 TCAAATTGCCATAAACTCCTGCTG 60.082 41.667 0.00 0.00 0.00 4.41
2906 6106 3.571590 AGTGGCCATAGGAAAAACACAA 58.428 40.909 9.72 0.00 0.00 3.33
3025 6225 0.761802 GATGCCCCCTCTAGTTCCTG 59.238 60.000 0.00 0.00 0.00 3.86
3075 6275 2.639347 TGGTGGTGACAATGTCAGAGAT 59.361 45.455 17.28 0.00 43.57 2.75
3127 6327 6.506500 CTTTGAAGCAAATACCAGATGAGT 57.493 37.500 0.00 0.00 32.70 3.41
3194 6394 2.031437 GCTGATGATCTCCGCAAAGAAC 59.969 50.000 0.00 0.00 34.50 3.01
3218 6418 0.967380 CCATCTCCGGCAAAGGCTTT 60.967 55.000 6.68 6.68 40.87 3.51
3269 6469 0.037975 TTTTGTCCCTCGCTCGGTAC 60.038 55.000 0.00 0.00 0.00 3.34
3294 6494 0.108186 CTGCTCCGGCTCACATTACA 60.108 55.000 0.00 0.00 39.59 2.41
3296 6496 0.975556 TCCTGCTCCGGCTCACATTA 60.976 55.000 0.00 0.00 39.59 1.90
3304 6504 2.514824 GGTTGATCCTGCTCCGGC 60.515 66.667 0.00 0.00 39.26 6.13
3307 6507 1.087501 GAAACGGTTGATCCTGCTCC 58.912 55.000 0.00 0.00 0.00 4.70
3345 6545 5.760743 GGAGGTGTATTTCCTTAAGCTCATC 59.239 44.000 0.00 0.00 37.17 2.92
3346 6546 5.191722 TGGAGGTGTATTTCCTTAAGCTCAT 59.808 40.000 0.00 0.00 37.17 2.90
3356 6556 4.390264 GCCTATTCTGGAGGTGTATTTCC 58.610 47.826 0.00 0.00 36.37 3.13
3408 6608 1.172180 TCGAGCTTGCAAAGGGTTGG 61.172 55.000 0.00 0.00 46.35 3.77
3491 6694 1.251527 GGCAGTGGTCGGAGAGAGAA 61.252 60.000 0.00 0.00 36.95 2.87
3518 6721 2.237143 TGGTCCTTTGTCATCTGCTAGG 59.763 50.000 0.00 0.00 0.00 3.02
3524 6727 1.611673 CGCCTTGGTCCTTTGTCATCT 60.612 52.381 0.00 0.00 0.00 2.90
3533 6736 4.003788 CGTGGTCGCCTTGGTCCT 62.004 66.667 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.