Multiple sequence alignment - TraesCS2D01G204400

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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 TraesCS2D01G204400 chr2D 100.000 3294 0 0 1530 4823 156592466 156595759 0.000000e+00 6083.0
1 TraesCS2D01G204400 chr2D 94.214 2264 104 7 1533 3769 156707480 156709743 0.000000e+00 3430.0
2 TraesCS2D01G204400 chr2D 92.973 2149 149 1 1536 3682 182575902 182573754 0.000000e+00 3131.0
3 TraesCS2D01G204400 chr2D 100.000 1147 0 0 1 1147 156590937 156592083 0.000000e+00 2119.0
4 TraesCS2D01G204400 chr2D 84.233 463 55 12 1 451 375578252 375577796 7.410000e-118 435.0
5 TraesCS2D01G204400 chr2D 84.330 351 35 11 775 1120 156707014 156707349 4.660000e-85 326.0
6 TraesCS2D01G204400 chr2D 81.022 411 54 12 4416 4823 156710671 156711060 6.060000e-79 305.0
7 TraesCS2D01G204400 chr2B 95.088 2341 98 4 1533 3873 214281154 214283477 0.000000e+00 3670.0
8 TraesCS2D01G204400 chr2B 94.099 2152 124 1 1533 3684 214312952 214315100 0.000000e+00 3267.0
9 TraesCS2D01G204400 chr2B 82.480 371 37 13 770 1118 214312478 214312842 2.820000e-77 300.0
10 TraesCS2D01G204400 chr2B 88.571 245 21 5 3947 4185 214284434 214284677 1.700000e-74 291.0
11 TraesCS2D01G204400 chr2B 90.551 127 12 0 4697 4823 214284746 214284872 8.300000e-38 169.0
12 TraesCS2D01G204400 chr2B 89.024 82 3 2 3879 3954 214283525 214283606 3.970000e-16 97.1
13 TraesCS2D01G204400 chr1B 92.344 2351 172 6 1536 3881 148416273 148413926 0.000000e+00 3338.0
14 TraesCS2D01G204400 chr1D 92.298 2350 175 4 1536 3881 93105154 93102807 0.000000e+00 3332.0
15 TraesCS2D01G204400 chr1D 85.010 487 48 14 1 464 416453698 416454182 5.650000e-129 472.0
16 TraesCS2D01G204400 chr1A 92.082 2349 176 5 1536 3880 90163485 90161143 0.000000e+00 3299.0
17 TraesCS2D01G204400 chr2A 93.154 2264 128 11 1533 3769 166628108 166630371 0.000000e+00 3297.0
18 TraesCS2D01G204400 chr2A 93.206 2149 144 1 1536 3682 197566162 197564014 0.000000e+00 3158.0
19 TraesCS2D01G204400 chr2A 91.066 1220 66 18 3620 4823 166256549 166257741 0.000000e+00 1609.0
20 TraesCS2D01G204400 chr2A 90.948 696 58 5 1554 2246 197344509 197343816 0.000000e+00 931.0
21 TraesCS2D01G204400 chr2A 94.407 447 17 5 706 1147 166254058 166254501 0.000000e+00 680.0
22 TraesCS2D01G204400 chr2A 87.407 270 26 6 852 1118 166627709 166627973 2.180000e-78 303.0
23 TraesCS2D01G204400 chr2A 79.803 406 56 13 4421 4823 166631294 166631676 6.150000e-69 272.0
24 TraesCS2D01G204400 chr2A 82.562 281 33 12 845 1120 197566576 197566307 2.900000e-57 233.0
25 TraesCS2D01G204400 chr2A 86.740 181 20 3 940 1120 197344832 197344656 1.060000e-46 198.0
26 TraesCS2D01G204400 chr2A 91.852 135 9 2 571 704 166250480 166250613 2.290000e-43 187.0
27 TraesCS2D01G204400 chr2A 97.087 103 3 0 468 570 166249336 166249438 1.780000e-39 174.0
28 TraesCS2D01G204400 chr7D 84.388 474 50 14 1 455 186321974 186321506 1.230000e-120 444.0
29 TraesCS2D01G204400 chr7D 82.922 486 53 20 1 463 164484511 164484989 1.250000e-110 411.0
30 TraesCS2D01G204400 chr5D 83.891 478 46 25 1 456 102028634 102028166 1.240000e-115 427.0
31 TraesCS2D01G204400 chr5D 82.974 417 28 22 1 411 395745737 395745358 2.150000e-88 337.0
32 TraesCS2D01G204400 chr4B 83.297 455 65 10 1 451 386740588 386741035 4.490000e-110 409.0
33 TraesCS2D01G204400 chr6D 84.300 414 54 10 55 463 58219756 58220163 1.260000e-105 394.0
34 TraesCS2D01G204400 chr6D 85.463 227 21 10 242 463 202463883 202463664 4.860000e-55 226.0
35 TraesCS2D01G204400 chr5A 82.618 466 61 8 1 463 587426784 587427232 1.260000e-105 394.0
36 TraesCS2D01G204400 chr5B 84.848 396 42 9 1 379 562796611 562797005 2.720000e-102 383.0
37 TraesCS2D01G204400 chr4A 83.465 381 43 11 28 400 527906610 527906242 2.150000e-88 337.0
38 TraesCS2D01G204400 chr4A 84.444 270 31 10 138 400 527905660 527905395 6.190000e-64 255.0
39 TraesCS2D01G204400 chr3D 83.511 376 30 19 106 452 526970075 526970447 6.020000e-84 322.0
40 TraesCS2D01G204400 chr3A 88.983 236 22 3 1 236 601164998 601165229 6.110000e-74 289.0
41 TraesCS2D01G204400 chr6A 80.992 363 30 27 115 451 266098380 266098729 8.010000e-63 252.0
42 TraesCS2D01G204400 chr3B 88.670 203 21 2 251 452 141810185 141809984 3.730000e-61 246.0


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 TraesCS2D01G204400 chr2D 156590937 156595759 4822 False 4101.000000 6083 100.0000 1 4823 2 chr2D.!!$F1 4822
1 TraesCS2D01G204400 chr2D 182573754 182575902 2148 True 3131.000000 3131 92.9730 1536 3682 1 chr2D.!!$R1 2146
2 TraesCS2D01G204400 chr2D 156707014 156711060 4046 False 1353.666667 3430 86.5220 775 4823 3 chr2D.!!$F2 4048
3 TraesCS2D01G204400 chr2B 214312478 214315100 2622 False 1783.500000 3267 88.2895 770 3684 2 chr2B.!!$F2 2914
4 TraesCS2D01G204400 chr2B 214281154 214284872 3718 False 1056.775000 3670 90.8085 1533 4823 4 chr2B.!!$F1 3290
5 TraesCS2D01G204400 chr1B 148413926 148416273 2347 True 3338.000000 3338 92.3440 1536 3881 1 chr1B.!!$R1 2345
6 TraesCS2D01G204400 chr1D 93102807 93105154 2347 True 3332.000000 3332 92.2980 1536 3881 1 chr1D.!!$R1 2345
7 TraesCS2D01G204400 chr1A 90161143 90163485 2342 True 3299.000000 3299 92.0820 1536 3880 1 chr1A.!!$R1 2344
8 TraesCS2D01G204400 chr2A 197564014 197566576 2562 True 1695.500000 3158 87.8840 845 3682 2 chr2A.!!$R2 2837
9 TraesCS2D01G204400 chr2A 166627709 166631676 3967 False 1290.666667 3297 86.7880 852 4823 3 chr2A.!!$F2 3971
10 TraesCS2D01G204400 chr2A 166249336 166257741 8405 False 662.500000 1609 93.6030 468 4823 4 chr2A.!!$F1 4355
11 TraesCS2D01G204400 chr2A 197343816 197344832 1016 True 564.500000 931 88.8440 940 2246 2 chr2A.!!$R1 1306
12 TraesCS2D01G204400 chr4A 527905395 527906610 1215 True 296.000000 337 83.9545 28 400 2 chr4A.!!$R1 372

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
790 5281 0.033090 TCGCCATCAGCTAGCATCTG 59.967 55.000 18.83 6.82 40.39 2.90 F
837 5336 0.811616 GTTCCCCTCGCATAGCACTG 60.812 60.000 0.00 0.00 0.00 3.66 F
843 5352 1.000171 CCTCGCATAGCACTGCATAGA 60.000 52.381 3.30 0.32 42.40 1.98 F
1552 6100 1.098712 ATGGCAACGACGGTTTGTGT 61.099 50.000 0.00 0.00 42.51 3.72 F
2407 6989 1.615116 CCAGAGTACACCGACCACCTA 60.615 57.143 0.00 0.00 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2266 6848 1.063972 CGCCGTGCCATTAACCATG 59.936 57.895 0.0 0.0 0.00 3.66 R
2330 6912 1.473258 ACTTCAGCAAGCACACCAAA 58.527 45.000 0.0 0.0 32.09 3.28 R
2407 6989 2.094752 GTGGTGCTTCAACTTGTGTGTT 60.095 45.455 0.0 0.0 0.00 3.32 R
3321 7903 0.812412 CACCGAGGTTTCCACGTTGT 60.812 55.000 0.0 0.0 35.94 3.32 R
4340 9970 0.533755 GTTCAGATGATGGCCCTCGG 60.534 60.000 0.0 0.0 0.00 4.63 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
40 41 3.494378 TCGTCGTCCGAGTCCATC 58.506 61.111 0.00 0.00 41.60 3.51
68 69 1.274167 AGACAAATCGCCGAACACCTA 59.726 47.619 0.00 0.00 0.00 3.08
69 70 2.070783 GACAAATCGCCGAACACCTAA 58.929 47.619 0.00 0.00 0.00 2.69
74 75 3.122971 GCCGAACACCTAACGGGC 61.123 66.667 0.00 0.00 45.66 6.13
80 81 2.740826 CACCTAACGGGCGTGGTG 60.741 66.667 0.00 0.00 42.98 4.17
102 103 2.512974 CACAACCGCCGGTATCCC 60.513 66.667 10.30 0.00 33.12 3.85
134 135 2.737376 GAGCGCCGGAAAACTCGT 60.737 61.111 5.05 0.00 0.00 4.18
136 137 2.737376 GCGCCGGAAAACTCGTCT 60.737 61.111 5.05 0.00 0.00 4.18
138 139 1.411493 GCGCCGGAAAACTCGTCTAG 61.411 60.000 5.05 0.00 0.00 2.43
139 140 0.169672 CGCCGGAAAACTCGTCTAGA 59.830 55.000 5.05 0.00 0.00 2.43
142 143 2.666994 GCCGGAAAACTCGTCTAGAAAG 59.333 50.000 5.05 0.00 0.00 2.62
144 145 3.305881 CCGGAAAACTCGTCTAGAAAGGT 60.306 47.826 0.00 0.00 0.00 3.50
148 149 3.662247 AACTCGTCTAGAAAGGTGGTG 57.338 47.619 0.00 0.00 0.00 4.17
176 177 3.839432 CGGCGGAACCCTCTCTCC 61.839 72.222 0.00 0.00 33.26 3.71
180 181 0.108089 GCGGAACCCTCTCTCCTTTC 60.108 60.000 0.00 0.00 0.00 2.62
212 214 1.301009 GCCTATCTAGCGGTGGTGC 60.301 63.158 0.00 0.00 0.00 5.01
214 216 1.617322 CCTATCTAGCGGTGGTGCTA 58.383 55.000 0.00 0.00 45.14 3.49
218 220 3.294750 TAGCGGTGGTGCTAGTGG 58.705 61.111 0.00 0.00 45.14 4.00
219 221 2.355986 TAGCGGTGGTGCTAGTGGG 61.356 63.158 0.00 0.00 45.14 4.61
220 222 4.778143 GCGGTGGTGCTAGTGGGG 62.778 72.222 0.00 0.00 0.00 4.96
221 223 4.096003 CGGTGGTGCTAGTGGGGG 62.096 72.222 0.00 0.00 0.00 5.40
258 260 4.256180 GGGATGGGCGAGGCGAAT 62.256 66.667 0.00 0.00 0.00 3.34
259 261 2.666526 GGATGGGCGAGGCGAATC 60.667 66.667 0.00 3.45 0.00 2.52
260 262 2.423446 GATGGGCGAGGCGAATCT 59.577 61.111 0.00 0.00 0.00 2.40
261 263 1.958205 GATGGGCGAGGCGAATCTG 60.958 63.158 0.00 0.00 0.00 2.90
262 264 3.466791 ATGGGCGAGGCGAATCTGG 62.467 63.158 0.00 0.00 0.00 3.86
263 265 3.849951 GGGCGAGGCGAATCTGGA 61.850 66.667 0.00 0.00 0.00 3.86
264 266 2.586357 GGCGAGGCGAATCTGGAC 60.586 66.667 0.00 0.00 0.00 4.02
265 267 2.956964 GCGAGGCGAATCTGGACG 60.957 66.667 0.00 0.00 0.00 4.79
266 268 2.490217 CGAGGCGAATCTGGACGT 59.510 61.111 0.00 0.00 0.00 4.34
267 269 1.874019 CGAGGCGAATCTGGACGTG 60.874 63.158 0.00 0.00 0.00 4.49
268 270 2.125512 AGGCGAATCTGGACGTGC 60.126 61.111 0.00 0.00 0.00 5.34
269 271 2.434185 GGCGAATCTGGACGTGCA 60.434 61.111 10.11 10.11 0.00 4.57
270 272 2.032634 GGCGAATCTGGACGTGCAA 61.033 57.895 11.97 2.74 0.00 4.08
271 273 1.421485 GCGAATCTGGACGTGCAAG 59.579 57.895 11.97 5.71 0.00 4.01
272 274 1.014044 GCGAATCTGGACGTGCAAGA 61.014 55.000 11.97 11.11 0.00 3.02
273 275 1.645034 CGAATCTGGACGTGCAAGAT 58.355 50.000 11.97 12.88 31.99 2.40
274 276 1.325640 CGAATCTGGACGTGCAAGATG 59.674 52.381 11.97 0.00 31.11 2.90
275 277 2.621338 GAATCTGGACGTGCAAGATGA 58.379 47.619 11.97 5.12 31.11 2.92
276 278 2.015736 ATCTGGACGTGCAAGATGAC 57.984 50.000 11.97 0.00 29.52 3.06
277 279 0.969149 TCTGGACGTGCAAGATGACT 59.031 50.000 11.97 0.00 0.00 3.41
278 280 1.344438 TCTGGACGTGCAAGATGACTT 59.656 47.619 11.97 0.00 36.73 3.01
279 281 2.146342 CTGGACGTGCAAGATGACTTT 58.854 47.619 11.97 0.00 33.70 2.66
280 282 2.549754 CTGGACGTGCAAGATGACTTTT 59.450 45.455 11.97 0.00 33.70 2.27
281 283 2.548057 TGGACGTGCAAGATGACTTTTC 59.452 45.455 7.52 0.00 33.70 2.29
282 284 2.411547 GGACGTGCAAGATGACTTTTCG 60.412 50.000 6.65 0.00 33.70 3.46
283 285 1.069906 ACGTGCAAGATGACTTTTCGC 60.070 47.619 6.65 0.00 33.70 4.70
284 286 1.725931 CGTGCAAGATGACTTTTCGCC 60.726 52.381 0.00 0.00 33.70 5.54
285 287 1.537202 GTGCAAGATGACTTTTCGCCT 59.463 47.619 0.00 0.00 33.70 5.52
286 288 1.536766 TGCAAGATGACTTTTCGCCTG 59.463 47.619 0.00 0.00 33.70 4.85
287 289 1.806542 GCAAGATGACTTTTCGCCTGA 59.193 47.619 0.00 0.00 33.70 3.86
288 290 2.413371 GCAAGATGACTTTTCGCCTGAC 60.413 50.000 0.00 0.00 33.70 3.51
289 291 2.807967 CAAGATGACTTTTCGCCTGACA 59.192 45.455 0.00 0.00 33.70 3.58
290 292 2.693069 AGATGACTTTTCGCCTGACAG 58.307 47.619 0.00 0.00 0.00 3.51
291 293 2.037772 AGATGACTTTTCGCCTGACAGT 59.962 45.455 0.93 0.00 0.00 3.55
292 294 1.581934 TGACTTTTCGCCTGACAGTG 58.418 50.000 0.93 0.00 0.00 3.66
293 295 1.134521 TGACTTTTCGCCTGACAGTGT 60.135 47.619 0.00 0.00 0.00 3.55
294 296 1.261619 GACTTTTCGCCTGACAGTGTG 59.738 52.381 0.00 0.23 0.00 3.82
295 297 0.588252 CTTTTCGCCTGACAGTGTGG 59.412 55.000 0.00 0.00 0.00 4.17
296 298 1.444119 TTTTCGCCTGACAGTGTGGC 61.444 55.000 13.41 13.41 42.94 5.01
297 299 3.825160 TTCGCCTGACAGTGTGGCC 62.825 63.158 16.71 0.00 43.42 5.36
299 301 4.269523 GCCTGACAGTGTGGCCCA 62.270 66.667 12.58 0.00 40.71 5.36
300 302 2.033141 CCTGACAGTGTGGCCCAG 59.967 66.667 0.00 1.11 0.00 4.45
301 303 2.519622 CCTGACAGTGTGGCCCAGA 61.520 63.158 0.00 0.00 0.00 3.86
302 304 1.681666 CTGACAGTGTGGCCCAGAT 59.318 57.895 0.00 0.00 0.00 2.90
303 305 0.675837 CTGACAGTGTGGCCCAGATG 60.676 60.000 0.00 2.72 0.00 2.90
304 306 2.034687 ACAGTGTGGCCCAGATGC 59.965 61.111 0.00 0.00 0.00 3.91
305 307 3.129502 CAGTGTGGCCCAGATGCG 61.130 66.667 0.00 0.00 0.00 4.73
306 308 4.415150 AGTGTGGCCCAGATGCGG 62.415 66.667 0.00 0.00 0.00 5.69
307 309 4.722700 GTGTGGCCCAGATGCGGT 62.723 66.667 0.00 0.00 0.00 5.68
308 310 3.965258 TGTGGCCCAGATGCGGTT 61.965 61.111 0.00 0.00 0.00 4.44
309 311 2.676471 GTGGCCCAGATGCGGTTT 60.676 61.111 0.00 0.00 0.00 3.27
310 312 2.117206 TGGCCCAGATGCGGTTTT 59.883 55.556 0.00 0.00 0.00 2.43
311 313 1.532794 TGGCCCAGATGCGGTTTTT 60.533 52.632 0.00 0.00 0.00 1.94
312 314 1.215382 GGCCCAGATGCGGTTTTTC 59.785 57.895 0.00 0.00 0.00 2.29
313 315 1.215382 GCCCAGATGCGGTTTTTCC 59.785 57.895 0.00 0.00 0.00 3.13
314 316 1.250840 GCCCAGATGCGGTTTTTCCT 61.251 55.000 0.00 0.00 0.00 3.36
315 317 1.256812 CCCAGATGCGGTTTTTCCTT 58.743 50.000 0.00 0.00 0.00 3.36
316 318 1.202348 CCCAGATGCGGTTTTTCCTTC 59.798 52.381 0.00 0.00 0.00 3.46
317 319 1.202348 CCAGATGCGGTTTTTCCTTCC 59.798 52.381 0.00 0.00 0.00 3.46
318 320 1.135689 CAGATGCGGTTTTTCCTTCCG 60.136 52.381 0.00 0.00 45.94 4.30
321 323 2.559330 CGGTTTTTCCTTCCGCCG 59.441 61.111 0.00 0.00 37.90 6.46
322 324 2.959372 GGTTTTTCCTTCCGCCGG 59.041 61.111 0.00 0.00 0.00 6.13
323 325 1.601477 GGTTTTTCCTTCCGCCGGA 60.601 57.895 5.05 0.00 0.00 5.14
324 326 1.583495 GGTTTTTCCTTCCGCCGGAG 61.583 60.000 5.05 0.00 31.21 4.63
325 327 1.969589 TTTTTCCTTCCGCCGGAGC 60.970 57.895 5.05 0.00 31.21 4.70
326 328 3.912745 TTTTCCTTCCGCCGGAGCC 62.913 63.158 5.05 0.00 34.57 4.70
364 366 3.411517 CTGGGTTCGGCCTGGGAT 61.412 66.667 0.00 0.00 37.43 3.85
365 367 3.406595 CTGGGTTCGGCCTGGGATC 62.407 68.421 0.00 0.00 37.43 3.36
366 368 4.547367 GGGTTCGGCCTGGGATCG 62.547 72.222 0.00 0.00 37.43 3.69
379 381 3.822192 GATCGCCGGGCCCAAAAC 61.822 66.667 24.92 6.41 0.00 2.43
388 390 3.373565 GCCCAAAACCAGGCCGAG 61.374 66.667 0.00 0.00 43.76 4.63
389 391 2.115266 CCCAAAACCAGGCCGAGT 59.885 61.111 0.00 0.00 0.00 4.18
390 392 1.971695 CCCAAAACCAGGCCGAGTC 60.972 63.158 0.00 0.00 0.00 3.36
391 393 2.325082 CCAAAACCAGGCCGAGTCG 61.325 63.158 5.29 5.29 0.00 4.18
402 404 2.954868 CGAGTCGGCGGATTTCGG 60.955 66.667 7.21 5.38 39.69 4.30
409 411 2.399611 GCGGATTTCGGCGTCTTG 59.600 61.111 6.85 0.00 39.69 3.02
410 412 3.089784 CGGATTTCGGCGTCTTGG 58.910 61.111 6.85 0.00 34.75 3.61
411 413 1.447140 CGGATTTCGGCGTCTTGGA 60.447 57.895 6.85 0.00 34.75 3.53
412 414 1.421410 CGGATTTCGGCGTCTTGGAG 61.421 60.000 6.85 0.00 34.75 3.86
413 415 1.090052 GGATTTCGGCGTCTTGGAGG 61.090 60.000 6.85 0.00 0.00 4.30
414 416 1.706287 GATTTCGGCGTCTTGGAGGC 61.706 60.000 6.85 3.97 41.88 4.70
418 420 4.373116 GGCGTCTTGGAGGCGTGA 62.373 66.667 3.80 0.00 46.51 4.35
419 421 3.112709 GCGTCTTGGAGGCGTGAC 61.113 66.667 3.80 0.00 46.51 3.67
420 422 2.651361 CGTCTTGGAGGCGTGACT 59.349 61.111 0.00 0.00 38.73 3.41
421 423 1.734477 CGTCTTGGAGGCGTGACTG 60.734 63.158 0.00 0.00 38.73 3.51
422 424 1.666011 GTCTTGGAGGCGTGACTGA 59.334 57.895 0.00 0.00 0.00 3.41
423 425 0.389166 GTCTTGGAGGCGTGACTGAG 60.389 60.000 0.00 0.00 0.00 3.35
424 426 1.079543 CTTGGAGGCGTGACTGAGG 60.080 63.158 0.00 0.00 0.00 3.86
425 427 2.513026 CTTGGAGGCGTGACTGAGGG 62.513 65.000 0.00 0.00 0.00 4.30
426 428 3.775654 GGAGGCGTGACTGAGGGG 61.776 72.222 0.00 0.00 0.00 4.79
427 429 3.775654 GAGGCGTGACTGAGGGGG 61.776 72.222 0.00 0.00 0.00 5.40
428 430 4.640690 AGGCGTGACTGAGGGGGT 62.641 66.667 0.00 0.00 0.00 4.95
429 431 3.637273 GGCGTGACTGAGGGGGTT 61.637 66.667 0.00 0.00 0.00 4.11
430 432 2.430367 GCGTGACTGAGGGGGTTT 59.570 61.111 0.00 0.00 0.00 3.27
431 433 1.228154 GCGTGACTGAGGGGGTTTT 60.228 57.895 0.00 0.00 0.00 2.43
432 434 0.035739 GCGTGACTGAGGGGGTTTTA 59.964 55.000 0.00 0.00 0.00 1.52
433 435 1.804601 CGTGACTGAGGGGGTTTTAC 58.195 55.000 0.00 0.00 0.00 2.01
434 436 1.804601 GTGACTGAGGGGGTTTTACG 58.195 55.000 0.00 0.00 0.00 3.18
435 437 0.688487 TGACTGAGGGGGTTTTACGG 59.312 55.000 0.00 0.00 0.00 4.02
436 438 0.675837 GACTGAGGGGGTTTTACGGC 60.676 60.000 0.00 0.00 0.00 5.68
437 439 1.743995 CTGAGGGGGTTTTACGGCG 60.744 63.158 4.80 4.80 0.00 6.46
438 440 3.129502 GAGGGGGTTTTACGGCGC 61.130 66.667 6.90 0.00 0.00 6.53
439 441 4.728110 AGGGGGTTTTACGGCGCC 62.728 66.667 19.07 19.07 37.03 6.53
479 481 1.109609 GGGTACTCTAACCTGGACGG 58.890 60.000 0.00 0.00 39.65 4.79
480 482 1.109609 GGTACTCTAACCTGGACGGG 58.890 60.000 0.00 0.00 36.53 5.28
557 559 1.900545 AACCTTGCCGCCCTCTAGTC 61.901 60.000 0.00 0.00 0.00 2.59
593 1636 2.077413 GCCATGTCGCCAAAAATTCA 57.923 45.000 0.00 0.00 0.00 2.57
605 1648 4.024977 GCCAAAAATTCACAAGTCGCAAAT 60.025 37.500 0.00 0.00 0.00 2.32
648 1691 1.873591 CGAGAGTTTGTTGGACTTGGG 59.126 52.381 0.00 0.00 0.00 4.12
653 1696 0.820871 TTTGTTGGACTTGGGCACAC 59.179 50.000 0.00 0.00 0.00 3.82
654 1697 0.323816 TTGTTGGACTTGGGCACACA 60.324 50.000 0.00 0.00 0.00 3.72
655 1698 1.034838 TGTTGGACTTGGGCACACAC 61.035 55.000 0.00 0.00 0.00 3.82
656 1699 1.034838 GTTGGACTTGGGCACACACA 61.035 55.000 0.00 0.00 0.00 3.72
658 1701 1.453015 GGACTTGGGCACACACACA 60.453 57.895 0.00 0.00 0.00 3.72
659 1702 1.724582 GGACTTGGGCACACACACAC 61.725 60.000 0.00 0.00 0.00 3.82
662 1705 0.179032 CTTGGGCACACACACACCTA 60.179 55.000 0.00 0.00 0.00 3.08
704 1747 4.232221 GACAATGATGGACAAGTTTGCTG 58.768 43.478 0.00 0.00 0.00 4.41
723 5209 1.663695 GCTAATTAGCTGGGTCGCAA 58.336 50.000 26.79 0.00 45.62 4.85
756 5244 1.289066 CTCGTCGCCAAGTCTCCAA 59.711 57.895 0.00 0.00 0.00 3.53
760 5248 1.305201 GTCGCCAAGTCTCCAAAACA 58.695 50.000 0.00 0.00 0.00 2.83
790 5281 0.033090 TCGCCATCAGCTAGCATCTG 59.967 55.000 18.83 6.82 40.39 2.90
836 5335 1.522569 GTTCCCCTCGCATAGCACT 59.477 57.895 0.00 0.00 0.00 4.40
837 5336 0.811616 GTTCCCCTCGCATAGCACTG 60.812 60.000 0.00 0.00 0.00 3.66
842 5351 1.426423 CCTCGCATAGCACTGCATAG 58.574 55.000 3.30 6.99 42.40 2.23
843 5352 1.000171 CCTCGCATAGCACTGCATAGA 60.000 52.381 3.30 0.32 42.40 1.98
1040 5562 4.359996 ACCTATTTAACTCCTTCCCTCGT 58.640 43.478 0.00 0.00 0.00 4.18
1060 5582 3.624861 CGTCTCCATTTCCATCCAAGAAG 59.375 47.826 0.00 0.00 0.00 2.85
1061 5583 4.623886 CGTCTCCATTTCCATCCAAGAAGA 60.624 45.833 0.00 0.00 0.00 2.87
1062 5584 5.256474 GTCTCCATTTCCATCCAAGAAGAA 58.744 41.667 0.00 0.00 0.00 2.52
1096 5620 2.096248 CTCTCCTACTCCAACGAGCTT 58.904 52.381 0.00 0.00 40.03 3.74
1552 6100 1.098712 ATGGCAACGACGGTTTGTGT 61.099 50.000 0.00 0.00 42.51 3.72
2330 6912 4.999751 GTTCTCTTTGAAGCGAACATCT 57.000 40.909 17.23 0.00 45.39 2.90
2407 6989 1.615116 CCAGAGTACACCGACCACCTA 60.615 57.143 0.00 0.00 0.00 3.08
2839 7421 2.270205 CTCTCTGGTGGCCGCAAT 59.730 61.111 19.98 0.00 0.00 3.56
3253 7835 3.064324 GACCCTTGCAGCGCCAAT 61.064 61.111 2.29 0.00 0.00 3.16
3295 7877 2.616330 CGCGGTGTTGGTTGAGCAT 61.616 57.895 0.00 0.00 0.00 3.79
3392 7974 2.297315 CTCTGTGCAACACTACCTCAGA 59.703 50.000 0.00 0.00 45.67 3.27
3508 8090 2.267324 GAGGAGCTGGGCACAGTC 59.733 66.667 19.18 13.42 46.62 3.51
3652 8234 3.072184 CCCTGCCTATCTGCTAATCAAGT 59.928 47.826 0.00 0.00 0.00 3.16
3769 8380 1.938016 GCAACGTTCTTCCGGAGCTAA 60.938 52.381 3.34 0.00 0.00 3.09
3912 8617 3.404978 TTGCATTGCAAGTCATCGC 57.595 47.368 19.77 1.23 43.99 4.58
3923 8628 4.201841 TGCAAGTCATCGCACAATTAGATG 60.202 41.667 0.00 0.00 42.11 2.90
4024 9622 9.908747 GAGGATATACACAGGAGTAGTACATAT 57.091 37.037 2.52 0.00 0.00 1.78
4038 9636 8.453238 AGTAGTACATATGAACTAGTCACAGG 57.547 38.462 10.38 0.00 39.72 4.00
4051 9649 6.249951 ACTAGTCACAGGAACTAATCAGACT 58.750 40.000 0.00 0.00 36.02 3.24
4054 9652 7.540474 AGTCACAGGAACTAATCAGACTAAA 57.460 36.000 0.00 0.00 36.02 1.85
4270 9900 0.107410 TGTCCGTGAACAGCAAGGTT 60.107 50.000 0.00 0.00 45.18 3.50
4340 9970 1.530293 CTTCACTGAGCTGCTCAACAC 59.470 52.381 30.00 6.08 40.18 3.32
4342 9996 1.301244 ACTGAGCTGCTCAACACCG 60.301 57.895 30.00 20.87 40.18 4.94
4344 9998 1.005748 TGAGCTGCTCAACACCGAG 60.006 57.895 28.72 0.00 37.57 4.63
4366 10020 2.158696 GGCCATCATCTGAACTTAGGCT 60.159 50.000 0.00 0.00 40.61 4.58
4375 10029 1.003718 AACTTAGGCTGCCACCGTC 60.004 57.895 22.65 0.00 33.69 4.79
4417 10236 1.016130 GCACCACTGTGACATCTCCG 61.016 60.000 9.86 0.00 45.76 4.63
4445 10264 5.188751 AGCTGCTAGTAATCTGAGGAAAACT 59.811 40.000 0.00 0.00 0.00 2.66
4496 10317 3.904800 TGAATTAGGATGAACTGCGGA 57.095 42.857 0.00 0.00 0.00 5.54
4511 10332 3.244422 ACTGCGGAAAAGATAGGTTGACA 60.244 43.478 0.00 0.00 0.00 3.58
4550 10387 8.547894 GTTGAAAAGTGTTTTCTCACTGTTTTT 58.452 29.630 12.15 0.00 46.25 1.94
4692 10529 5.433855 CGGAATTGCAGAAAAACAAACATG 58.566 37.500 0.00 0.00 0.00 3.21
4694 10531 6.199908 CGGAATTGCAGAAAAACAAACATGTA 59.800 34.615 0.00 0.00 0.00 2.29
4695 10532 7.254252 CGGAATTGCAGAAAAACAAACATGTAA 60.254 33.333 0.00 0.00 0.00 2.41
4754 10591 4.323028 CCTTGTGTCTTCCAGCTCATTAGA 60.323 45.833 0.00 0.00 0.00 2.10
4771 10608 9.030301 GCTCATTAGACTCTTTATCAACTTCTC 57.970 37.037 0.00 0.00 0.00 2.87
4787 10624 3.823304 ACTTCTCAAATGCCTGAAGGAAC 59.177 43.478 0.00 0.00 39.90 3.62
4799 10638 1.829222 TGAAGGAACCCGTGGAGATAC 59.171 52.381 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.022902 CGATGGACTCGGACGACG 59.977 66.667 0.00 0.00 43.82 5.12
40 41 2.697425 CGATTTGTCTGCTCGGCG 59.303 61.111 0.00 0.00 0.00 6.46
116 117 3.488090 CGAGTTTTCCGGCGCTCC 61.488 66.667 7.64 0.00 0.00 4.70
117 118 2.727684 GACGAGTTTTCCGGCGCTC 61.728 63.158 7.64 0.75 0.00 5.03
118 119 1.870055 TAGACGAGTTTTCCGGCGCT 61.870 55.000 7.64 0.00 40.56 5.92
119 120 1.411493 CTAGACGAGTTTTCCGGCGC 61.411 60.000 0.00 0.00 40.56 6.53
120 121 0.169672 TCTAGACGAGTTTTCCGGCG 59.830 55.000 0.00 0.00 40.56 6.46
134 135 3.107601 CATCCTCCACCACCTTTCTAGA 58.892 50.000 0.00 0.00 0.00 2.43
136 137 1.559682 GCATCCTCCACCACCTTTCTA 59.440 52.381 0.00 0.00 0.00 2.10
138 139 0.681243 GGCATCCTCCACCACCTTTC 60.681 60.000 0.00 0.00 0.00 2.62
139 140 1.384191 GGCATCCTCCACCACCTTT 59.616 57.895 0.00 0.00 0.00 3.11
161 162 0.108089 GAAAGGAGAGAGGGTTCCGC 60.108 60.000 0.00 0.00 38.54 5.54
176 177 2.828549 CATTCCCCCGCCGGAAAG 60.829 66.667 5.05 0.00 44.97 2.62
195 197 1.617322 TAGCACCACCGCTAGATAGG 58.383 55.000 0.00 0.00 43.56 2.57
241 243 4.256180 ATTCGCCTCGCCCATCCC 62.256 66.667 0.00 0.00 0.00 3.85
242 244 2.666526 GATTCGCCTCGCCCATCC 60.667 66.667 0.00 0.00 0.00 3.51
243 245 1.958205 CAGATTCGCCTCGCCCATC 60.958 63.158 0.00 0.00 0.00 3.51
244 246 2.109799 CAGATTCGCCTCGCCCAT 59.890 61.111 0.00 0.00 0.00 4.00
245 247 4.161295 CCAGATTCGCCTCGCCCA 62.161 66.667 0.00 0.00 0.00 5.36
246 248 3.849951 TCCAGATTCGCCTCGCCC 61.850 66.667 0.00 0.00 0.00 6.13
247 249 2.586357 GTCCAGATTCGCCTCGCC 60.586 66.667 0.00 0.00 0.00 5.54
248 250 2.956964 CGTCCAGATTCGCCTCGC 60.957 66.667 0.00 0.00 0.00 5.03
249 251 1.874019 CACGTCCAGATTCGCCTCG 60.874 63.158 0.00 0.00 0.00 4.63
250 252 2.167861 GCACGTCCAGATTCGCCTC 61.168 63.158 0.00 0.00 0.00 4.70
251 253 2.125512 GCACGTCCAGATTCGCCT 60.126 61.111 0.00 0.00 0.00 5.52
252 254 1.970917 CTTGCACGTCCAGATTCGCC 61.971 60.000 0.00 0.00 0.00 5.54
253 255 1.014044 TCTTGCACGTCCAGATTCGC 61.014 55.000 0.00 0.00 0.00 4.70
254 256 1.325640 CATCTTGCACGTCCAGATTCG 59.674 52.381 0.00 0.00 0.00 3.34
255 257 2.349886 GTCATCTTGCACGTCCAGATTC 59.650 50.000 0.00 0.00 0.00 2.52
256 258 2.027745 AGTCATCTTGCACGTCCAGATT 60.028 45.455 0.00 0.00 0.00 2.40
257 259 1.552337 AGTCATCTTGCACGTCCAGAT 59.448 47.619 0.00 0.00 0.00 2.90
258 260 0.969149 AGTCATCTTGCACGTCCAGA 59.031 50.000 0.00 0.00 0.00 3.86
259 261 1.800805 AAGTCATCTTGCACGTCCAG 58.199 50.000 0.00 0.00 32.09 3.86
260 262 2.254546 AAAGTCATCTTGCACGTCCA 57.745 45.000 0.00 0.00 33.79 4.02
261 263 2.411547 CGAAAAGTCATCTTGCACGTCC 60.412 50.000 0.00 0.00 33.79 4.79
262 264 2.827555 CGAAAAGTCATCTTGCACGTC 58.172 47.619 0.00 0.00 33.79 4.34
263 265 1.069906 GCGAAAAGTCATCTTGCACGT 60.070 47.619 0.00 0.00 33.79 4.49
264 266 1.595609 GCGAAAAGTCATCTTGCACG 58.404 50.000 0.00 0.00 33.79 5.34
265 267 1.537202 AGGCGAAAAGTCATCTTGCAC 59.463 47.619 0.00 0.00 33.79 4.57
266 268 1.536766 CAGGCGAAAAGTCATCTTGCA 59.463 47.619 0.00 0.00 33.79 4.08
267 269 1.806542 TCAGGCGAAAAGTCATCTTGC 59.193 47.619 0.00 0.00 33.79 4.01
268 270 2.807967 TGTCAGGCGAAAAGTCATCTTG 59.192 45.455 0.00 0.00 33.79 3.02
269 271 3.070018 CTGTCAGGCGAAAAGTCATCTT 58.930 45.455 0.00 0.00 35.14 2.40
270 272 2.037772 ACTGTCAGGCGAAAAGTCATCT 59.962 45.455 4.53 0.00 0.00 2.90
271 273 2.158449 CACTGTCAGGCGAAAAGTCATC 59.842 50.000 4.53 0.00 0.00 2.92
272 274 2.146342 CACTGTCAGGCGAAAAGTCAT 58.854 47.619 4.53 0.00 0.00 3.06
273 275 1.134521 ACACTGTCAGGCGAAAAGTCA 60.135 47.619 4.53 0.00 0.00 3.41
274 276 1.261619 CACACTGTCAGGCGAAAAGTC 59.738 52.381 4.53 0.00 0.00 3.01
275 277 1.299541 CACACTGTCAGGCGAAAAGT 58.700 50.000 4.53 0.00 0.00 2.66
276 278 0.588252 CCACACTGTCAGGCGAAAAG 59.412 55.000 4.53 0.00 0.00 2.27
277 279 1.444119 GCCACACTGTCAGGCGAAAA 61.444 55.000 4.53 0.00 38.86 2.29
278 280 1.891919 GCCACACTGTCAGGCGAAA 60.892 57.895 4.53 0.00 38.86 3.46
279 281 2.280797 GCCACACTGTCAGGCGAA 60.281 61.111 4.53 0.00 38.86 4.70
283 285 1.845627 ATCTGGGCCACACTGTCAGG 61.846 60.000 0.00 0.00 0.00 3.86
284 286 0.675837 CATCTGGGCCACACTGTCAG 60.676 60.000 0.00 0.00 0.00 3.51
285 287 1.376086 CATCTGGGCCACACTGTCA 59.624 57.895 0.00 0.00 0.00 3.58
286 288 2.042831 GCATCTGGGCCACACTGTC 61.043 63.158 0.00 0.00 0.00 3.51
287 289 2.034687 GCATCTGGGCCACACTGT 59.965 61.111 0.00 0.00 0.00 3.55
288 290 3.129502 CGCATCTGGGCCACACTG 61.130 66.667 0.00 0.96 0.00 3.66
289 291 4.415150 CCGCATCTGGGCCACACT 62.415 66.667 0.00 0.00 0.00 3.55
290 292 4.722700 ACCGCATCTGGGCCACAC 62.723 66.667 0.00 0.00 0.00 3.82
291 293 2.992817 AAAACCGCATCTGGGCCACA 62.993 55.000 0.00 0.00 0.00 4.17
292 294 1.815817 AAAAACCGCATCTGGGCCAC 61.816 55.000 0.00 0.00 0.00 5.01
293 295 1.531739 GAAAAACCGCATCTGGGCCA 61.532 55.000 5.85 5.85 0.00 5.36
294 296 1.215382 GAAAAACCGCATCTGGGCC 59.785 57.895 0.00 0.00 0.00 5.80
295 297 1.215382 GGAAAAACCGCATCTGGGC 59.785 57.895 0.00 0.00 0.00 5.36
296 298 1.202348 GAAGGAAAAACCGCATCTGGG 59.798 52.381 0.00 0.00 44.74 4.45
297 299 1.202348 GGAAGGAAAAACCGCATCTGG 59.798 52.381 0.00 0.00 44.74 3.86
298 300 1.135689 CGGAAGGAAAAACCGCATCTG 60.136 52.381 0.00 0.00 44.74 2.90
299 301 1.165270 CGGAAGGAAAAACCGCATCT 58.835 50.000 0.00 0.00 44.74 2.90
300 302 3.694889 CGGAAGGAAAAACCGCATC 57.305 52.632 0.00 0.00 44.74 3.91
305 307 1.583495 CTCCGGCGGAAGGAAAAACC 61.583 60.000 30.59 0.00 37.32 3.27
306 308 1.873863 CTCCGGCGGAAGGAAAAAC 59.126 57.895 30.59 0.00 37.32 2.43
307 309 1.969589 GCTCCGGCGGAAGGAAAAA 60.970 57.895 30.59 4.61 37.32 1.94
308 310 2.359478 GCTCCGGCGGAAGGAAAA 60.359 61.111 30.59 5.46 37.32 2.29
309 311 4.404098 GGCTCCGGCGGAAGGAAA 62.404 66.667 30.59 6.30 37.32 3.13
347 349 3.406595 GATCCCAGGCCGAACCCAG 62.407 68.421 0.00 0.00 40.58 4.45
348 350 3.407967 GATCCCAGGCCGAACCCA 61.408 66.667 0.00 0.00 40.58 4.51
349 351 4.547367 CGATCCCAGGCCGAACCC 62.547 72.222 0.00 0.00 40.58 4.11
362 364 3.822192 GTTTTGGGCCCGGCGATC 61.822 66.667 19.37 1.20 0.00 3.69
371 373 3.373565 CTCGGCCTGGTTTTGGGC 61.374 66.667 0.00 0.00 46.89 5.36
372 374 1.971695 GACTCGGCCTGGTTTTGGG 60.972 63.158 0.00 0.00 0.00 4.12
373 375 2.325082 CGACTCGGCCTGGTTTTGG 61.325 63.158 0.00 0.00 0.00 3.28
374 376 2.325082 CCGACTCGGCCTGGTTTTG 61.325 63.158 4.10 0.00 41.17 2.44
375 377 2.032071 CCGACTCGGCCTGGTTTT 59.968 61.111 4.10 0.00 41.17 2.43
385 387 2.954868 CCGAAATCCGCCGACTCG 60.955 66.667 0.00 0.00 36.84 4.18
386 388 3.262686 GCCGAAATCCGCCGACTC 61.263 66.667 0.00 0.00 36.84 3.36
391 393 2.818274 AAGACGCCGAAATCCGCC 60.818 61.111 0.00 0.00 36.84 6.13
392 394 2.399611 CAAGACGCCGAAATCCGC 59.600 61.111 0.00 0.00 36.84 5.54
393 395 1.421410 CTCCAAGACGCCGAAATCCG 61.421 60.000 0.00 0.00 38.18 4.18
394 396 1.090052 CCTCCAAGACGCCGAAATCC 61.090 60.000 0.00 0.00 0.00 3.01
395 397 1.706287 GCCTCCAAGACGCCGAAATC 61.706 60.000 0.00 0.00 0.00 2.17
396 398 1.745489 GCCTCCAAGACGCCGAAAT 60.745 57.895 0.00 0.00 0.00 2.17
397 399 2.358247 GCCTCCAAGACGCCGAAA 60.358 61.111 0.00 0.00 0.00 3.46
398 400 4.735132 CGCCTCCAAGACGCCGAA 62.735 66.667 0.00 0.00 0.00 4.30
401 403 4.373116 TCACGCCTCCAAGACGCC 62.373 66.667 0.00 0.00 0.00 5.68
402 404 3.112709 GTCACGCCTCCAAGACGC 61.113 66.667 0.00 0.00 0.00 5.19
403 405 1.734477 CAGTCACGCCTCCAAGACG 60.734 63.158 0.00 0.00 36.18 4.18
404 406 0.389166 CTCAGTCACGCCTCCAAGAC 60.389 60.000 0.00 0.00 0.00 3.01
405 407 1.536073 CCTCAGTCACGCCTCCAAGA 61.536 60.000 0.00 0.00 0.00 3.02
406 408 1.079543 CCTCAGTCACGCCTCCAAG 60.080 63.158 0.00 0.00 0.00 3.61
407 409 2.583441 CCCTCAGTCACGCCTCCAA 61.583 63.158 0.00 0.00 0.00 3.53
408 410 2.997315 CCCTCAGTCACGCCTCCA 60.997 66.667 0.00 0.00 0.00 3.86
409 411 3.775654 CCCCTCAGTCACGCCTCC 61.776 72.222 0.00 0.00 0.00 4.30
410 412 3.775654 CCCCCTCAGTCACGCCTC 61.776 72.222 0.00 0.00 0.00 4.70
411 413 4.640690 ACCCCCTCAGTCACGCCT 62.641 66.667 0.00 0.00 0.00 5.52
412 414 2.692273 AAAACCCCCTCAGTCACGCC 62.692 60.000 0.00 0.00 0.00 5.68
413 415 0.035739 TAAAACCCCCTCAGTCACGC 59.964 55.000 0.00 0.00 0.00 5.34
414 416 1.804601 GTAAAACCCCCTCAGTCACG 58.195 55.000 0.00 0.00 0.00 4.35
415 417 1.609841 CCGTAAAACCCCCTCAGTCAC 60.610 57.143 0.00 0.00 0.00 3.67
416 418 0.688487 CCGTAAAACCCCCTCAGTCA 59.312 55.000 0.00 0.00 0.00 3.41
417 419 0.675837 GCCGTAAAACCCCCTCAGTC 60.676 60.000 0.00 0.00 0.00 3.51
418 420 1.377612 GCCGTAAAACCCCCTCAGT 59.622 57.895 0.00 0.00 0.00 3.41
419 421 1.743995 CGCCGTAAAACCCCCTCAG 60.744 63.158 0.00 0.00 0.00 3.35
420 422 2.348243 CGCCGTAAAACCCCCTCA 59.652 61.111 0.00 0.00 0.00 3.86
421 423 3.129502 GCGCCGTAAAACCCCCTC 61.130 66.667 0.00 0.00 0.00 4.30
422 424 4.728110 GGCGCCGTAAAACCCCCT 62.728 66.667 12.58 0.00 0.00 4.79
448 450 5.936372 GGTTAGAGTACCCAAGACGATTTTT 59.064 40.000 0.00 0.00 31.71 1.94
449 451 5.247792 AGGTTAGAGTACCCAAGACGATTTT 59.752 40.000 0.00 0.00 39.08 1.82
450 452 4.776308 AGGTTAGAGTACCCAAGACGATTT 59.224 41.667 0.00 0.00 39.08 2.17
451 453 4.159879 CAGGTTAGAGTACCCAAGACGATT 59.840 45.833 0.00 0.00 39.08 3.34
452 454 3.700038 CAGGTTAGAGTACCCAAGACGAT 59.300 47.826 0.00 0.00 39.08 3.73
453 455 3.087031 CAGGTTAGAGTACCCAAGACGA 58.913 50.000 0.00 0.00 39.08 4.20
454 456 2.165845 CCAGGTTAGAGTACCCAAGACG 59.834 54.545 0.00 0.00 39.08 4.18
455 457 3.195182 GTCCAGGTTAGAGTACCCAAGAC 59.805 52.174 0.00 0.00 39.08 3.01
456 458 3.438183 GTCCAGGTTAGAGTACCCAAGA 58.562 50.000 0.00 0.00 39.08 3.02
457 459 2.165845 CGTCCAGGTTAGAGTACCCAAG 59.834 54.545 0.00 0.00 39.08 3.61
458 460 2.173519 CGTCCAGGTTAGAGTACCCAA 58.826 52.381 0.00 0.00 39.08 4.12
459 461 1.617804 CCGTCCAGGTTAGAGTACCCA 60.618 57.143 0.00 0.00 39.08 4.51
460 462 1.109609 CCGTCCAGGTTAGAGTACCC 58.890 60.000 0.00 0.00 39.08 3.69
461 463 1.109609 CCCGTCCAGGTTAGAGTACC 58.890 60.000 0.00 0.00 38.74 3.34
462 464 1.844687 ACCCGTCCAGGTTAGAGTAC 58.155 55.000 0.00 0.00 36.44 2.73
463 465 2.357154 GGTACCCGTCCAGGTTAGAGTA 60.357 54.545 0.00 0.00 41.58 2.59
464 466 1.618074 GGTACCCGTCCAGGTTAGAGT 60.618 57.143 0.00 0.00 41.58 3.24
465 467 1.109609 GGTACCCGTCCAGGTTAGAG 58.890 60.000 0.00 0.00 41.58 2.43
466 468 0.409092 TGGTACCCGTCCAGGTTAGA 59.591 55.000 10.07 0.00 41.58 2.10
479 481 6.209788 TCCAACATGTTAATTTCCTTGGTACC 59.790 38.462 11.53 4.43 0.00 3.34
480 482 7.222000 TCCAACATGTTAATTTCCTTGGTAC 57.778 36.000 11.53 0.00 0.00 3.34
557 559 2.328099 GCCTTGAGCCTTGACCGTG 61.328 63.158 0.00 0.00 34.35 4.94
576 1619 4.050553 ACTTGTGAATTTTTGGCGACATG 58.949 39.130 0.00 0.00 42.32 3.21
582 1625 2.468831 TGCGACTTGTGAATTTTTGGC 58.531 42.857 0.00 0.00 0.00 4.52
584 1627 6.346040 GGAGATTTGCGACTTGTGAATTTTTG 60.346 38.462 0.00 0.00 0.00 2.44
593 1636 0.320771 AGCGGAGATTTGCGACTTGT 60.321 50.000 0.07 0.00 41.04 3.16
605 1648 5.816258 CGTATGATTAGGTATAGAGCGGAGA 59.184 44.000 0.00 0.00 0.00 3.71
648 1691 3.980646 TTCAATTAGGTGTGTGTGTGC 57.019 42.857 0.00 0.00 0.00 4.57
653 1696 8.084073 ACTCATTTCATTTCAATTAGGTGTGTG 58.916 33.333 0.00 0.00 0.00 3.82
654 1697 8.084073 CACTCATTTCATTTCAATTAGGTGTGT 58.916 33.333 0.00 0.00 0.00 3.72
655 1698 7.543172 CCACTCATTTCATTTCAATTAGGTGTG 59.457 37.037 0.00 0.00 0.00 3.82
656 1699 7.309990 CCCACTCATTTCATTTCAATTAGGTGT 60.310 37.037 0.00 0.00 0.00 4.16
658 1701 6.953520 TCCCACTCATTTCATTTCAATTAGGT 59.046 34.615 0.00 0.00 0.00 3.08
659 1702 7.093814 TGTCCCACTCATTTCATTTCAATTAGG 60.094 37.037 0.00 0.00 0.00 2.69
662 1705 6.669125 TGTCCCACTCATTTCATTTCAATT 57.331 33.333 0.00 0.00 0.00 2.32
746 5234 3.808728 TCCAGTCTGTTTTGGAGACTTG 58.191 45.455 0.00 0.00 46.57 3.16
756 5244 1.278985 TGGCGATGATCCAGTCTGTTT 59.721 47.619 0.00 0.00 0.00 2.83
760 5248 1.343789 CTGATGGCGATGATCCAGTCT 59.656 52.381 0.00 0.00 36.98 3.24
836 5335 8.435931 ACAATGGGATACTAGTATTCTATGCA 57.564 34.615 18.11 9.76 0.00 3.96
837 5336 7.702772 CGACAATGGGATACTAGTATTCTATGC 59.297 40.741 18.11 11.12 0.00 3.14
842 5351 5.779922 TGCGACAATGGGATACTAGTATTC 58.220 41.667 16.46 14.32 0.00 1.75
843 5352 5.784177 CTGCGACAATGGGATACTAGTATT 58.216 41.667 16.46 0.00 0.00 1.89
1040 5562 5.251468 TCTTCTTCTTGGATGGAAATGGAGA 59.749 40.000 0.00 0.00 0.00 3.71
1060 5582 1.524849 GAGGCGGGGAATGCTCTTC 60.525 63.158 0.00 0.00 0.00 2.87
1061 5583 1.977293 GAGAGGCGGGGAATGCTCTT 61.977 60.000 0.00 0.00 0.00 2.85
1062 5584 2.366167 AGAGGCGGGGAATGCTCT 60.366 61.111 0.00 0.00 0.00 4.09
1096 5620 3.006967 GTGGAGTAGCCTTGTGAGAGAAA 59.993 47.826 0.00 0.00 37.63 2.52
1531 6079 1.264557 CACAAACCGTCGTTGCCATTA 59.735 47.619 0.00 0.00 30.72 1.90
1807 6388 4.063967 CCGTAGCTGTCGGTGCCA 62.064 66.667 19.42 0.00 42.62 4.92
2266 6848 1.063972 CGCCGTGCCATTAACCATG 59.936 57.895 0.00 0.00 0.00 3.66
2330 6912 1.473258 ACTTCAGCAAGCACACCAAA 58.527 45.000 0.00 0.00 32.09 3.28
2407 6989 2.094752 GTGGTGCTTCAACTTGTGTGTT 60.095 45.455 0.00 0.00 0.00 3.32
2839 7421 3.582647 TGAAGCCATAGTCAAGACTTGGA 59.417 43.478 23.48 1.97 42.54 3.53
3253 7835 5.536260 CGCATCTTCTTCATGAGAGGATAA 58.464 41.667 14.77 1.93 46.19 1.75
3321 7903 0.812412 CACCGAGGTTTCCACGTTGT 60.812 55.000 0.00 0.00 35.94 3.32
3392 7974 0.908198 CCTCTAGCAGCCTCAACCTT 59.092 55.000 0.00 0.00 0.00 3.50
3508 8090 3.349022 AGTCTTCTCTCCGGTCAAGTAG 58.651 50.000 0.00 1.21 0.00 2.57
3652 8234 4.718774 ACCAAGGCATCTTCTCTTCATCTA 59.281 41.667 0.00 0.00 0.00 1.98
3923 8628 4.497006 GCTTGTGCCTGAACATGTATGATC 60.497 45.833 0.00 0.00 0.00 2.92
4024 9622 6.719829 TCTGATTAGTTCCTGTGACTAGTTCA 59.280 38.462 0.00 0.00 31.74 3.18
4078 9676 5.914033 TGCTAGTACCAATGGATTGACTAC 58.086 41.667 6.16 0.00 40.14 2.73
4080 9678 4.471386 ACTGCTAGTACCAATGGATTGACT 59.529 41.667 6.16 6.23 40.14 3.41
4081 9679 4.770795 ACTGCTAGTACCAATGGATTGAC 58.229 43.478 6.16 0.00 40.14 3.18
4214 9844 4.571369 TCTACCTATAGATCTCCCGTGG 57.429 50.000 0.00 0.00 32.16 4.94
4229 9859 3.899726 ACCACTACGACATCATCTACCT 58.100 45.455 0.00 0.00 0.00 3.08
4270 9900 6.428083 TTTGGAGTTCTCCATGTTAGTGTA 57.572 37.500 20.26 1.80 39.86 2.90
4299 9929 3.270960 AGGACCTCCTCAAGATGTCTACT 59.729 47.826 0.00 0.00 44.77 2.57
4340 9970 0.533755 GTTCAGATGATGGCCCTCGG 60.534 60.000 0.00 0.00 0.00 4.63
4342 9996 2.725221 AAGTTCAGATGATGGCCCTC 57.275 50.000 0.00 0.00 0.00 4.30
4344 9998 2.856222 CCTAAGTTCAGATGATGGCCC 58.144 52.381 0.00 0.00 0.00 5.80
4366 10020 2.425592 CCTGTTCAGACGGTGGCA 59.574 61.111 1.00 0.00 0.00 4.92
4375 10029 1.016130 CAGCACGCTACCCTGTTCAG 61.016 60.000 0.00 0.00 0.00 3.02
4417 10236 3.257127 CCTCAGATTACTAGCAGCTACCC 59.743 52.174 0.00 0.00 0.00 3.69
4496 10317 6.601332 TCCTTCAGTTGTCAACCTATCTTTT 58.399 36.000 12.17 0.00 0.00 2.27
4511 10332 7.881775 ACACTTTTCAACTTATCCTTCAGTT 57.118 32.000 0.00 0.00 33.29 3.16
4553 10390 8.076178 GCACTTGTTAGAACAGAAAACACATAT 58.924 33.333 0.00 0.00 40.50 1.78
4555 10392 6.095440 AGCACTTGTTAGAACAGAAAACACAT 59.905 34.615 0.00 0.00 40.50 3.21
4557 10394 5.739161 CAGCACTTGTTAGAACAGAAAACAC 59.261 40.000 0.00 0.00 40.50 3.32
4559 10396 6.119144 TCAGCACTTGTTAGAACAGAAAAC 57.881 37.500 0.00 0.00 40.50 2.43
4560 10397 6.597672 TCTTCAGCACTTGTTAGAACAGAAAA 59.402 34.615 0.00 0.00 40.50 2.29
4562 10399 5.670485 TCTTCAGCACTTGTTAGAACAGAA 58.330 37.500 0.00 0.00 40.50 3.02
4563 10400 5.276461 TCTTCAGCACTTGTTAGAACAGA 57.724 39.130 0.00 0.00 40.50 3.41
4564 10401 5.525378 AGTTCTTCAGCACTTGTTAGAACAG 59.475 40.000 13.33 0.00 43.67 3.16
4565 10402 5.428253 AGTTCTTCAGCACTTGTTAGAACA 58.572 37.500 13.33 0.00 43.67 3.18
4566 10403 5.993106 AGTTCTTCAGCACTTGTTAGAAC 57.007 39.130 0.00 0.00 42.76 3.01
4567 10404 6.112734 TCAAGTTCTTCAGCACTTGTTAGAA 58.887 36.000 15.95 0.00 45.25 2.10
4568 10405 5.670485 TCAAGTTCTTCAGCACTTGTTAGA 58.330 37.500 15.95 0.00 45.25 2.10
4569 10406 5.755375 TCTCAAGTTCTTCAGCACTTGTTAG 59.245 40.000 15.95 9.37 45.25 2.34
4570 10407 5.670485 TCTCAAGTTCTTCAGCACTTGTTA 58.330 37.500 15.95 6.00 45.25 2.41
4571 10408 4.517285 TCTCAAGTTCTTCAGCACTTGTT 58.483 39.130 15.95 0.00 45.25 2.83
4572 10409 4.142609 TCTCAAGTTCTTCAGCACTTGT 57.857 40.909 15.95 0.00 45.25 3.16
4573 10410 4.574013 ACTTCTCAAGTTCTTCAGCACTTG 59.426 41.667 11.77 11.77 45.99 3.16
4606 10443 1.008538 GCCAGTTTGTCAGTTGCCG 60.009 57.895 0.00 0.00 0.00 5.69
4695 10532 5.048991 CCGTAGCATCAACTAACAGGTTTTT 60.049 40.000 0.00 0.00 0.00 1.94
4754 10591 6.944862 AGGCATTTGAGAAGTTGATAAAGAGT 59.055 34.615 0.00 0.00 0.00 3.24
4771 10608 0.527565 CGGGTTCCTTCAGGCATTTG 59.472 55.000 0.00 0.00 34.44 2.32
4787 10624 3.475566 AATGTGATGTATCTCCACGGG 57.524 47.619 0.00 0.00 33.78 5.28


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

AutoCloner maintained by Alex Coulton.