Multiple sequence alignment - TraesCS3A01G425400

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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 TraesCS3A01G425400 chr3A 100.000 2237 0 0 1 2237 667705722 667703486 0.000000e+00 4132
1 TraesCS3A01G425400 chr3A 91.116 439 32 4 847 1281 667514136 667513701 2.470000e-164 588
2 TraesCS3A01G425400 chr3A 93.898 295 12 5 1273 1561 667513276 667512982 7.330000e-120 440
3 TraesCS3A01G425400 chr3A 92.965 199 14 0 441 639 434835107 434834909 7.820000e-75 291
4 TraesCS3A01G425400 chr3A 91.667 204 17 0 443 646 466246415 466246618 1.310000e-72 283
5 TraesCS3A01G425400 chr3B 94.295 929 41 6 636 1555 704654339 704653414 0.000000e+00 1411
6 TraesCS3A01G425400 chr3B 92.244 722 49 5 847 1561 704577853 704577132 0.000000e+00 1016
7 TraesCS3A01G425400 chr3B 95.588 204 8 1 1 203 704654644 704654441 2.140000e-85 326
8 TraesCS3A01G425400 chr3B 94.783 115 3 2 340 451 704654445 704654331 2.280000e-40 176
9 TraesCS3A01G425400 chr3D 94.022 920 40 5 636 1551 532584030 532583122 0.000000e+00 1380
10 TraesCS3A01G425400 chr3D 91.226 718 52 6 847 1558 532343845 532343133 0.000000e+00 966
11 TraesCS3A01G425400 chr3D 96.552 203 7 0 1 203 532584333 532584131 9.900000e-89 337
12 TraesCS3A01G425400 chr3D 92.982 114 6 2 340 451 532584135 532584022 4.940000e-37 165
13 TraesCS3A01G425400 chr7D 95.645 574 25 0 1661 2234 634183392 634182819 0.000000e+00 922
14 TraesCS3A01G425400 chr7D 92.919 579 39 1 1661 2237 599904080 599904658 0.000000e+00 841
15 TraesCS3A01G425400 chr7D 92.548 577 43 0 1661 2237 592629466 592630042 0.000000e+00 828
16 TraesCS3A01G425400 chr5D 93.913 575 35 0 1661 2235 542103198 542103772 0.000000e+00 869
17 TraesCS3A01G425400 chr5D 92.870 575 41 0 1661 2235 527725558 527724984 0.000000e+00 835
18 TraesCS3A01G425400 chr5D 92.715 151 9 2 196 345 341197647 341197796 1.350000e-52 217
19 TraesCS3A01G425400 chr2D 93.588 577 37 0 1661 2237 519331252 519331828 0.000000e+00 861
20 TraesCS3A01G425400 chr2D 95.283 106 5 0 236 341 315496369 315496264 3.820000e-38 169
21 TraesCS3A01G425400 chr1A 93.391 575 36 2 1661 2235 29211422 29210850 0.000000e+00 850
22 TraesCS3A01G425400 chr1A 92.965 199 14 0 448 646 330765864 330766062 7.820000e-75 291
23 TraesCS3A01G425400 chr1A 92.929 198 12 2 448 645 398058483 398058678 1.010000e-73 287
24 TraesCS3A01G425400 chr1A 95.283 106 5 0 236 341 38000114 38000219 3.820000e-38 169
25 TraesCS3A01G425400 chr1D 93.217 575 39 0 1661 2235 246704278 246703704 0.000000e+00 846
26 TraesCS3A01G425400 chr6B 92.696 575 42 0 1661 2235 35155175 35154601 0.000000e+00 830
27 TraesCS3A01G425400 chr6B 91.667 144 12 0 199 342 393235166 393235309 1.350000e-47 200
28 TraesCS3A01G425400 chr6A 94.444 198 10 1 448 645 273584435 273584239 1.000000e-78 303
29 TraesCS3A01G425400 chr6A 93.532 201 9 3 446 644 21147834 21147636 1.680000e-76 296
30 TraesCS3A01G425400 chr6A 93.401 197 11 2 449 644 180309155 180309350 7.820000e-75 291
31 TraesCS3A01G425400 chr2A 95.699 186 8 0 451 636 278996441 278996256 1.300000e-77 300
32 TraesCS3A01G425400 chr2A 93.717 191 12 0 448 638 631864933 631865123 1.010000e-73 287
33 TraesCS3A01G425400 chr2A 95.862 145 6 0 200 344 345374826 345374970 3.710000e-58 235
34 TraesCS3A01G425400 chr7A 94.326 141 7 1 202 341 723755769 723755909 4.840000e-52 215
35 TraesCS3A01G425400 chr4D 88.591 149 16 1 194 341 177742137 177742285 1.770000e-41 180
36 TraesCS3A01G425400 chrUn 91.753 97 4 3 1551 1647 131920514 131920606 5.010000e-27 132


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 TraesCS3A01G425400 chr3A 667703486 667705722 2236 True 4132.000000 4132 100.000000 1 2237 1 chr3A.!!$R2 2236
1 TraesCS3A01G425400 chr3A 667512982 667514136 1154 True 514.000000 588 92.507000 847 1561 2 chr3A.!!$R3 714
2 TraesCS3A01G425400 chr3B 704577132 704577853 721 True 1016.000000 1016 92.244000 847 1561 1 chr3B.!!$R1 714
3 TraesCS3A01G425400 chr3B 704653414 704654644 1230 True 637.666667 1411 94.888667 1 1555 3 chr3B.!!$R2 1554
4 TraesCS3A01G425400 chr3D 532343133 532343845 712 True 966.000000 966 91.226000 847 1558 1 chr3D.!!$R1 711
5 TraesCS3A01G425400 chr3D 532583122 532584333 1211 True 627.333333 1380 94.518667 1 1551 3 chr3D.!!$R2 1550
6 TraesCS3A01G425400 chr7D 634182819 634183392 573 True 922.000000 922 95.645000 1661 2234 1 chr7D.!!$R1 573
7 TraesCS3A01G425400 chr7D 599904080 599904658 578 False 841.000000 841 92.919000 1661 2237 1 chr7D.!!$F2 576
8 TraesCS3A01G425400 chr7D 592629466 592630042 576 False 828.000000 828 92.548000 1661 2237 1 chr7D.!!$F1 576
9 TraesCS3A01G425400 chr5D 542103198 542103772 574 False 869.000000 869 93.913000 1661 2235 1 chr5D.!!$F2 574
10 TraesCS3A01G425400 chr5D 527724984 527725558 574 True 835.000000 835 92.870000 1661 2235 1 chr5D.!!$R1 574
11 TraesCS3A01G425400 chr2D 519331252 519331828 576 False 861.000000 861 93.588000 1661 2237 1 chr2D.!!$F1 576
12 TraesCS3A01G425400 chr1A 29210850 29211422 572 True 850.000000 850 93.391000 1661 2235 1 chr1A.!!$R1 574
13 TraesCS3A01G425400 chr1D 246703704 246704278 574 True 846.000000 846 93.217000 1661 2235 1 chr1D.!!$R1 574
14 TraesCS3A01G425400 chr6B 35154601 35155175 574 True 830.000000 830 92.696000 1661 2235 1 chr6B.!!$R1 574

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
342 344 0.03716 GGTTTCCGAACAGCCCCTTA 59.963 55.0 0.0 0.0 37.51 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 2035 0.034574 ATCAACCCATAGCAACCGCA 60.035 50.0 0.0 0.0 42.27 5.69 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
183 185 9.812347 ATGAATTATCCATAGGCATAGTCAAAA 57.188 29.630 0.00 0.00 0.00 2.44
205 207 9.358872 CAAAATTGAAGATCTTTAACTTAGGGC 57.641 33.333 14.28 0.00 0.00 5.19
206 208 7.646548 AATTGAAGATCTTTAACTTAGGGCC 57.353 36.000 14.28 0.00 0.00 5.80
207 209 6.388619 TTGAAGATCTTTAACTTAGGGCCT 57.611 37.500 12.58 12.58 0.00 5.19
208 210 5.745227 TGAAGATCTTTAACTTAGGGCCTG 58.255 41.667 18.53 2.03 0.00 4.85
209 211 5.250774 TGAAGATCTTTAACTTAGGGCCTGT 59.749 40.000 18.53 2.84 0.00 4.00
210 212 5.780958 AGATCTTTAACTTAGGGCCTGTT 57.219 39.130 18.53 15.35 0.00 3.16
211 213 5.746284 AGATCTTTAACTTAGGGCCTGTTC 58.254 41.667 18.53 1.22 0.00 3.18
212 214 3.934068 TCTTTAACTTAGGGCCTGTTCG 58.066 45.455 18.53 3.92 0.00 3.95
213 215 2.773993 TTAACTTAGGGCCTGTTCGG 57.226 50.000 18.53 3.95 0.00 4.30
214 216 1.941377 TAACTTAGGGCCTGTTCGGA 58.059 50.000 18.53 0.00 33.16 4.55
215 217 0.613777 AACTTAGGGCCTGTTCGGAG 59.386 55.000 18.53 6.80 33.16 4.63
216 218 1.265454 ACTTAGGGCCTGTTCGGAGG 61.265 60.000 18.53 0.00 36.03 4.30
222 224 2.269241 CCTGTTCGGAGGCCCTTC 59.731 66.667 0.00 0.00 33.16 3.46
223 225 2.125512 CTGTTCGGAGGCCCTTCG 60.126 66.667 4.61 4.61 33.10 3.79
224 226 4.388499 TGTTCGGAGGCCCTTCGC 62.388 66.667 6.55 0.00 31.67 4.70
225 227 4.083862 GTTCGGAGGCCCTTCGCT 62.084 66.667 6.55 0.00 37.74 4.93
226 228 3.771160 TTCGGAGGCCCTTCGCTC 61.771 66.667 6.55 0.00 37.74 5.03
229 231 4.475135 GGAGGCCCTTCGCTCCAC 62.475 72.222 0.00 0.00 35.81 4.02
230 232 3.706373 GAGGCCCTTCGCTCCACA 61.706 66.667 0.00 0.00 37.74 4.17
231 233 3.959991 GAGGCCCTTCGCTCCACAC 62.960 68.421 0.00 0.00 37.74 3.82
233 235 4.681978 GCCCTTCGCTCCACACGT 62.682 66.667 0.00 0.00 0.00 4.49
234 236 2.432628 CCCTTCGCTCCACACGTC 60.433 66.667 0.00 0.00 0.00 4.34
235 237 2.432628 CCTTCGCTCCACACGTCC 60.433 66.667 0.00 0.00 0.00 4.79
236 238 2.432628 CTTCGCTCCACACGTCCC 60.433 66.667 0.00 0.00 0.00 4.46
237 239 4.351938 TTCGCTCCACACGTCCCG 62.352 66.667 0.00 0.00 0.00 5.14
241 243 4.436998 CTCCACACGTCCCGCTCC 62.437 72.222 0.00 0.00 0.00 4.70
243 245 4.742201 CCACACGTCCCGCTCCAG 62.742 72.222 0.00 0.00 0.00 3.86
244 246 4.742201 CACACGTCCCGCTCCAGG 62.742 72.222 0.00 0.00 0.00 4.45
245 247 4.988716 ACACGTCCCGCTCCAGGA 62.989 66.667 0.00 0.00 0.00 3.86
246 248 4.135153 CACGTCCCGCTCCAGGAG 62.135 72.222 12.81 12.81 32.84 3.69
255 257 3.847602 CTCCAGGAGCAGCCGGAG 61.848 72.222 5.05 16.07 44.83 4.63
266 268 3.981308 GCCGGAGCTGCAGTTTAA 58.019 55.556 16.64 0.00 35.50 1.52
267 269 2.253513 GCCGGAGCTGCAGTTTAAA 58.746 52.632 16.64 0.00 35.50 1.52
268 270 0.596082 GCCGGAGCTGCAGTTTAAAA 59.404 50.000 16.64 0.00 35.50 1.52
269 271 1.666023 GCCGGAGCTGCAGTTTAAAAC 60.666 52.381 16.64 0.00 35.50 2.43
270 272 1.606668 CCGGAGCTGCAGTTTAAAACA 59.393 47.619 16.64 0.00 0.00 2.83
271 273 2.350772 CCGGAGCTGCAGTTTAAAACAG 60.351 50.000 16.64 8.91 0.00 3.16
289 291 4.617875 CGGAGCGAGGAAATTGGT 57.382 55.556 0.00 0.00 0.00 3.67
290 292 3.752796 CGGAGCGAGGAAATTGGTA 57.247 52.632 0.00 0.00 0.00 3.25
291 293 1.287425 CGGAGCGAGGAAATTGGTAC 58.713 55.000 0.00 0.00 0.00 3.34
292 294 1.134788 CGGAGCGAGGAAATTGGTACT 60.135 52.381 0.00 0.00 0.00 2.73
293 295 2.552031 GGAGCGAGGAAATTGGTACTC 58.448 52.381 0.00 0.00 0.00 2.59
294 296 2.552031 GAGCGAGGAAATTGGTACTCC 58.448 52.381 0.00 0.00 0.00 3.85
295 297 1.134788 AGCGAGGAAATTGGTACTCCG 60.135 52.381 0.00 0.00 36.30 4.63
296 298 1.405121 GCGAGGAAATTGGTACTCCGT 60.405 52.381 0.00 0.00 36.30 4.69
297 299 2.159198 GCGAGGAAATTGGTACTCCGTA 60.159 50.000 0.00 0.00 36.30 4.02
298 300 3.703420 CGAGGAAATTGGTACTCCGTAG 58.297 50.000 0.00 0.00 36.30 3.51
299 301 3.379372 CGAGGAAATTGGTACTCCGTAGA 59.621 47.826 0.00 0.00 36.30 2.59
300 302 4.037684 CGAGGAAATTGGTACTCCGTAGAT 59.962 45.833 0.00 0.00 36.30 1.98
301 303 5.451520 CGAGGAAATTGGTACTCCGTAGATT 60.452 44.000 0.00 0.00 36.30 2.40
302 304 5.915175 AGGAAATTGGTACTCCGTAGATTC 58.085 41.667 0.00 0.00 36.30 2.52
303 305 5.661759 AGGAAATTGGTACTCCGTAGATTCT 59.338 40.000 0.00 0.00 36.30 2.40
304 306 5.753921 GGAAATTGGTACTCCGTAGATTCTG 59.246 44.000 0.00 0.00 36.30 3.02
305 307 5.934402 AATTGGTACTCCGTAGATTCTGT 57.066 39.130 0.00 0.00 36.30 3.41
306 308 4.713824 TTGGTACTCCGTAGATTCTGTG 57.286 45.455 0.00 0.00 36.30 3.66
307 309 3.959293 TGGTACTCCGTAGATTCTGTGA 58.041 45.455 0.00 0.00 36.30 3.58
308 310 4.533815 TGGTACTCCGTAGATTCTGTGAT 58.466 43.478 0.00 0.00 36.30 3.06
309 311 4.954202 TGGTACTCCGTAGATTCTGTGATT 59.046 41.667 0.00 0.00 36.30 2.57
310 312 5.421056 TGGTACTCCGTAGATTCTGTGATTT 59.579 40.000 0.00 0.00 36.30 2.17
311 313 5.978322 GGTACTCCGTAGATTCTGTGATTTC 59.022 44.000 0.00 0.00 0.00 2.17
312 314 5.012328 ACTCCGTAGATTCTGTGATTTCC 57.988 43.478 0.00 0.00 0.00 3.13
313 315 4.041740 TCCGTAGATTCTGTGATTTCCG 57.958 45.455 0.00 0.00 0.00 4.30
314 316 3.697542 TCCGTAGATTCTGTGATTTCCGA 59.302 43.478 0.00 0.00 0.00 4.55
315 317 4.158949 TCCGTAGATTCTGTGATTTCCGAA 59.841 41.667 0.00 0.00 0.00 4.30
316 318 4.504461 CCGTAGATTCTGTGATTTCCGAAG 59.496 45.833 0.00 0.00 0.00 3.79
317 319 4.026475 CGTAGATTCTGTGATTTCCGAAGC 60.026 45.833 0.00 0.00 0.00 3.86
318 320 2.932614 AGATTCTGTGATTTCCGAAGCG 59.067 45.455 0.00 0.00 0.00 4.68
328 330 3.053896 CCGAAGCGGGTGGGTTTC 61.054 66.667 0.00 0.00 44.15 2.78
329 331 3.053896 CGAAGCGGGTGGGTTTCC 61.054 66.667 0.00 0.00 36.25 3.13
335 337 4.074647 GGGTGGGTTTCCGAACAG 57.925 61.111 0.00 0.00 37.51 3.16
336 338 2.265904 GGGTGGGTTTCCGAACAGC 61.266 63.158 0.00 0.00 37.51 4.40
337 339 2.265904 GGTGGGTTTCCGAACAGCC 61.266 63.158 0.00 5.21 37.51 4.85
338 340 2.114411 TGGGTTTCCGAACAGCCC 59.886 61.111 7.37 7.37 37.51 5.19
339 341 2.675423 GGGTTTCCGAACAGCCCC 60.675 66.667 4.11 0.00 37.51 5.80
340 342 2.434774 GGTTTCCGAACAGCCCCT 59.565 61.111 0.00 0.00 37.51 4.79
341 343 1.228459 GGTTTCCGAACAGCCCCTT 60.228 57.895 0.00 0.00 37.51 3.95
342 344 0.037160 GGTTTCCGAACAGCCCCTTA 59.963 55.000 0.00 0.00 37.51 2.69
343 345 1.450025 GTTTCCGAACAGCCCCTTAG 58.550 55.000 0.00 0.00 35.79 2.18
347 349 1.485066 TCCGAACAGCCCCTTAGAATC 59.515 52.381 0.00 0.00 0.00 2.52
352 354 0.533755 CAGCCCCTTAGAATCAGCCG 60.534 60.000 0.00 0.00 0.00 5.52
459 464 7.725142 TGCGCTATAATTTAAAACAGTTTTGC 58.275 30.769 19.77 11.30 34.19 3.68
460 465 7.596995 TGCGCTATAATTTAAAACAGTTTTGCT 59.403 29.630 19.77 5.52 34.19 3.91
461 466 9.068008 GCGCTATAATTTAAAACAGTTTTGCTA 57.932 29.630 19.77 6.64 34.19 3.49
492 497 8.822652 CATCTAGATGTGTCATAAGTATTGCA 57.177 34.615 22.42 0.00 34.23 4.08
493 498 8.706936 CATCTAGATGTGTCATAAGTATTGCAC 58.293 37.037 22.42 0.00 34.23 4.57
494 499 7.781056 TCTAGATGTGTCATAAGTATTGCACA 58.219 34.615 0.00 0.00 40.42 4.57
495 500 8.424133 TCTAGATGTGTCATAAGTATTGCACAT 58.576 33.333 13.21 13.21 46.19 3.21
496 501 7.255491 AGATGTGTCATAAGTATTGCACATG 57.745 36.000 16.15 0.00 44.38 3.21
497 502 6.825213 AGATGTGTCATAAGTATTGCACATGT 59.175 34.615 16.15 12.04 44.38 3.21
498 503 7.986889 AGATGTGTCATAAGTATTGCACATGTA 59.013 33.333 16.15 0.00 44.38 2.29
499 504 7.913674 TGTGTCATAAGTATTGCACATGTAA 57.086 32.000 0.00 0.00 32.79 2.41
500 505 8.329203 TGTGTCATAAGTATTGCACATGTAAA 57.671 30.769 0.00 0.00 32.79 2.01
501 506 8.955388 TGTGTCATAAGTATTGCACATGTAAAT 58.045 29.630 0.00 4.60 32.79 1.40
502 507 9.438291 GTGTCATAAGTATTGCACATGTAAATC 57.562 33.333 0.00 0.00 0.00 2.17
503 508 9.171877 TGTCATAAGTATTGCACATGTAAATCA 57.828 29.630 0.00 0.00 0.00 2.57
510 515 9.341078 AGTATTGCACATGTAAATCATATGTCA 57.659 29.630 0.00 0.00 36.90 3.58
513 518 8.859517 TTGCACATGTAAATCATATGTCATTG 57.140 30.769 0.00 0.00 36.90 2.82
514 519 8.223177 TGCACATGTAAATCATATGTCATTGA 57.777 30.769 0.00 0.00 36.90 2.57
515 520 8.852135 TGCACATGTAAATCATATGTCATTGAT 58.148 29.630 0.00 0.00 36.90 2.57
516 521 9.338291 GCACATGTAAATCATATGTCATTGATC 57.662 33.333 0.00 0.00 36.90 2.92
551 556 9.462606 AGATTCGTGTAAATATTTTCTTTCCCT 57.537 29.630 5.91 0.00 0.00 4.20
554 559 9.685828 TTCGTGTAAATATTTTCTTTCCCTTTG 57.314 29.630 5.91 0.00 0.00 2.77
555 560 9.069082 TCGTGTAAATATTTTCTTTCCCTTTGA 57.931 29.630 5.91 0.00 0.00 2.69
556 561 9.855021 CGTGTAAATATTTTCTTTCCCTTTGAT 57.145 29.630 5.91 0.00 0.00 2.57
565 570 9.770097 ATTTTCTTTCCCTTTGATCTTTTTCTC 57.230 29.630 0.00 0.00 0.00 2.87
566 571 8.539117 TTTCTTTCCCTTTGATCTTTTTCTCT 57.461 30.769 0.00 0.00 0.00 3.10
567 572 8.539117 TTCTTTCCCTTTGATCTTTTTCTCTT 57.461 30.769 0.00 0.00 0.00 2.85
568 573 8.539117 TCTTTCCCTTTGATCTTTTTCTCTTT 57.461 30.769 0.00 0.00 0.00 2.52
569 574 9.640952 TCTTTCCCTTTGATCTTTTTCTCTTTA 57.359 29.630 0.00 0.00 0.00 1.85
594 599 8.939201 ATACTTGATTCACTCACTTAGATGTG 57.061 34.615 0.00 0.00 39.15 3.21
595 600 5.641209 ACTTGATTCACTCACTTAGATGTGC 59.359 40.000 0.00 0.00 37.81 4.57
596 601 5.151297 TGATTCACTCACTTAGATGTGCA 57.849 39.130 0.00 0.00 37.81 4.57
597 602 5.550290 TGATTCACTCACTTAGATGTGCAA 58.450 37.500 0.00 0.00 37.81 4.08
598 603 6.175471 TGATTCACTCACTTAGATGTGCAAT 58.825 36.000 0.00 0.00 37.81 3.56
599 604 7.330262 TGATTCACTCACTTAGATGTGCAATA 58.670 34.615 0.00 0.00 37.81 1.90
600 605 7.823799 TGATTCACTCACTTAGATGTGCAATAA 59.176 33.333 0.00 0.00 37.81 1.40
601 606 6.968131 TCACTCACTTAGATGTGCAATAAC 57.032 37.500 0.00 0.00 37.81 1.89
602 607 6.701340 TCACTCACTTAGATGTGCAATAACT 58.299 36.000 0.00 0.00 37.81 2.24
603 608 7.836842 TCACTCACTTAGATGTGCAATAACTA 58.163 34.615 0.00 0.00 37.81 2.24
604 609 7.976175 TCACTCACTTAGATGTGCAATAACTAG 59.024 37.037 0.00 0.00 37.81 2.57
605 610 7.223582 CACTCACTTAGATGTGCAATAACTAGG 59.776 40.741 0.00 0.00 37.81 3.02
606 611 6.582636 TCACTTAGATGTGCAATAACTAGGG 58.417 40.000 0.00 0.00 37.81 3.53
607 612 5.237344 CACTTAGATGTGCAATAACTAGGGC 59.763 44.000 0.00 0.00 0.00 5.19
608 613 3.931907 AGATGTGCAATAACTAGGGCA 57.068 42.857 0.00 0.00 0.00 5.36
613 618 3.931907 TGCAATAACTAGGGCACATCT 57.068 42.857 0.00 0.00 0.00 2.90
615 620 4.960938 TGCAATAACTAGGGCACATCTAG 58.039 43.478 0.00 0.00 39.88 2.43
616 621 4.653801 TGCAATAACTAGGGCACATCTAGA 59.346 41.667 0.00 0.00 38.02 2.43
617 622 5.307976 TGCAATAACTAGGGCACATCTAGAT 59.692 40.000 0.00 0.00 38.02 1.98
618 623 5.641209 GCAATAACTAGGGCACATCTAGATG 59.359 44.000 27.63 27.63 44.15 2.90
630 635 4.250116 CATCTAGATGTGCCCTAGACAC 57.750 50.000 22.42 8.47 43.57 3.67
634 639 3.478780 TGTGCCCTAGACACACCC 58.521 61.111 12.81 0.00 42.88 4.61
635 640 1.460497 TGTGCCCTAGACACACCCA 60.460 57.895 12.81 0.00 42.88 4.51
636 641 1.057275 TGTGCCCTAGACACACCCAA 61.057 55.000 12.81 0.00 42.88 4.12
637 642 0.328258 GTGCCCTAGACACACCCAAT 59.672 55.000 10.07 0.00 37.96 3.16
638 643 1.072266 TGCCCTAGACACACCCAATT 58.928 50.000 0.00 0.00 0.00 2.32
639 644 1.427368 TGCCCTAGACACACCCAATTT 59.573 47.619 0.00 0.00 0.00 1.82
640 645 2.645297 TGCCCTAGACACACCCAATTTA 59.355 45.455 0.00 0.00 0.00 1.40
641 646 3.074687 TGCCCTAGACACACCCAATTTAA 59.925 43.478 0.00 0.00 0.00 1.52
642 647 4.083565 GCCCTAGACACACCCAATTTAAA 58.916 43.478 0.00 0.00 0.00 1.52
643 648 4.525100 GCCCTAGACACACCCAATTTAAAA 59.475 41.667 0.00 0.00 0.00 1.52
777 782 6.430864 TCCAATGGCTTCAACATTAGGAATA 58.569 36.000 0.00 0.00 36.47 1.75
830 835 0.179094 AACCGCAAGAACACGAGACA 60.179 50.000 0.00 0.00 43.02 3.41
854 859 3.246112 TGAACCCACTCCCCACCG 61.246 66.667 0.00 0.00 0.00 4.94
900 907 2.270352 AAATCCTCAAGAACACCGCA 57.730 45.000 0.00 0.00 0.00 5.69
920 927 2.153401 CCTTCCTCCACCCACCACA 61.153 63.158 0.00 0.00 0.00 4.17
930 937 2.345244 CCACCACAAGAGCTCGCT 59.655 61.111 8.37 0.00 0.00 4.93
952 959 4.836125 AATAATCCACCGCAATAAGCAG 57.164 40.909 0.00 0.00 46.13 4.24
959 968 2.942376 CACCGCAATAAGCAGATAACCA 59.058 45.455 0.00 0.00 46.13 3.67
966 975 2.403252 AAGCAGATAACCAACCTCCG 57.597 50.000 0.00 0.00 0.00 4.63
1251 1260 3.471244 CTGATCGACGACCCTCCGC 62.471 68.421 0.00 0.00 0.00 5.54
1511 1972 0.320697 GTGTAAGGGCCGTCTGTTCT 59.679 55.000 0.00 0.00 0.00 3.01
1514 1975 2.074576 GTAAGGGCCGTCTGTTCTTTC 58.925 52.381 0.00 0.00 0.00 2.62
1528 1989 0.892755 TCTTTCGTACGTGGCCTCAT 59.107 50.000 16.05 0.00 0.00 2.90
1572 2036 8.821147 TTATATTACTAGTAAATGTGCCCGTG 57.179 34.615 18.88 0.00 0.00 4.94
1573 2037 1.734163 ACTAGTAAATGTGCCCGTGC 58.266 50.000 0.00 0.00 38.26 5.34
1574 2038 0.650512 CTAGTAAATGTGCCCGTGCG 59.349 55.000 0.00 0.00 41.78 5.34
1575 2039 0.741574 TAGTAAATGTGCCCGTGCGG 60.742 55.000 3.25 3.25 41.78 5.69
1576 2040 2.032834 TAAATGTGCCCGTGCGGT 59.967 55.556 9.90 0.00 41.78 5.68
1577 2041 1.601197 TAAATGTGCCCGTGCGGTT 60.601 52.632 9.90 0.00 41.78 4.44
1578 2042 1.857318 TAAATGTGCCCGTGCGGTTG 61.857 55.000 9.90 0.00 41.78 3.77
1582 2046 4.402528 TGCCCGTGCGGTTGCTAT 62.403 61.111 9.90 0.00 43.34 2.97
1583 2047 3.876198 GCCCGTGCGGTTGCTATG 61.876 66.667 9.90 0.00 43.34 2.23
1584 2048 3.202001 CCCGTGCGGTTGCTATGG 61.202 66.667 9.90 0.00 43.34 2.74
1585 2049 3.202001 CCGTGCGGTTGCTATGGG 61.202 66.667 1.93 0.00 43.34 4.00
1586 2050 2.435938 CGTGCGGTTGCTATGGGT 60.436 61.111 0.00 0.00 43.34 4.51
1587 2051 2.038269 CGTGCGGTTGCTATGGGTT 61.038 57.895 0.00 0.00 43.34 4.11
1588 2052 1.506262 GTGCGGTTGCTATGGGTTG 59.494 57.895 0.00 0.00 43.34 3.77
1589 2053 0.958382 GTGCGGTTGCTATGGGTTGA 60.958 55.000 0.00 0.00 43.34 3.18
1590 2054 0.034574 TGCGGTTGCTATGGGTTGAT 60.035 50.000 0.00 0.00 43.34 2.57
1591 2055 1.102978 GCGGTTGCTATGGGTTGATT 58.897 50.000 0.00 0.00 38.39 2.57
1592 2056 1.202290 GCGGTTGCTATGGGTTGATTG 60.202 52.381 0.00 0.00 38.39 2.67
1593 2057 1.405105 CGGTTGCTATGGGTTGATTGG 59.595 52.381 0.00 0.00 0.00 3.16
1594 2058 1.756538 GGTTGCTATGGGTTGATTGGG 59.243 52.381 0.00 0.00 0.00 4.12
1595 2059 1.756538 GTTGCTATGGGTTGATTGGGG 59.243 52.381 0.00 0.00 0.00 4.96
1596 2060 1.303898 TGCTATGGGTTGATTGGGGA 58.696 50.000 0.00 0.00 0.00 4.81
1597 2061 1.643286 TGCTATGGGTTGATTGGGGAA 59.357 47.619 0.00 0.00 0.00 3.97
1598 2062 2.043664 TGCTATGGGTTGATTGGGGAAA 59.956 45.455 0.00 0.00 0.00 3.13
1599 2063 3.103742 GCTATGGGTTGATTGGGGAAAA 58.896 45.455 0.00 0.00 0.00 2.29
1600 2064 3.517500 GCTATGGGTTGATTGGGGAAAAA 59.482 43.478 0.00 0.00 0.00 1.94
1629 2093 9.611284 TTCTTCAATATCATTTTTGTTCTCGTG 57.389 29.630 0.00 0.00 0.00 4.35
1630 2094 8.998377 TCTTCAATATCATTTTTGTTCTCGTGA 58.002 29.630 0.00 0.00 0.00 4.35
1631 2095 8.948853 TTCAATATCATTTTTGTTCTCGTGAC 57.051 30.769 0.00 0.00 0.00 3.67
1632 2096 8.093659 TCAATATCATTTTTGTTCTCGTGACA 57.906 30.769 0.00 0.00 0.00 3.58
1633 2097 8.729756 TCAATATCATTTTTGTTCTCGTGACAT 58.270 29.630 0.00 0.00 0.00 3.06
1634 2098 9.003112 CAATATCATTTTTGTTCTCGTGACATC 57.997 33.333 0.00 0.00 0.00 3.06
1635 2099 6.558771 ATCATTTTTGTTCTCGTGACATCA 57.441 33.333 0.00 0.00 0.00 3.07
1636 2100 5.747565 TCATTTTTGTTCTCGTGACATCAC 58.252 37.500 1.70 1.70 43.15 3.06
1637 2101 5.527214 TCATTTTTGTTCTCGTGACATCACT 59.473 36.000 10.18 0.00 44.34 3.41
1638 2102 5.403897 TTTTTGTTCTCGTGACATCACTC 57.596 39.130 10.18 0.00 44.34 3.51
1639 2103 3.726291 TTGTTCTCGTGACATCACTCA 57.274 42.857 10.18 0.00 44.34 3.41
1640 2104 3.726291 TGTTCTCGTGACATCACTCAA 57.274 42.857 10.18 0.00 44.34 3.02
1641 2105 3.381045 TGTTCTCGTGACATCACTCAAC 58.619 45.455 10.18 9.58 44.34 3.18
1642 2106 2.724977 TCTCGTGACATCACTCAACC 57.275 50.000 10.18 0.00 44.34 3.77
1643 2107 1.960689 TCTCGTGACATCACTCAACCA 59.039 47.619 10.18 0.00 44.34 3.67
1644 2108 2.562738 TCTCGTGACATCACTCAACCAT 59.437 45.455 10.18 0.00 44.34 3.55
1645 2109 3.006859 TCTCGTGACATCACTCAACCATT 59.993 43.478 10.18 0.00 44.34 3.16
1646 2110 3.738982 TCGTGACATCACTCAACCATTT 58.261 40.909 10.18 0.00 44.34 2.32
1647 2111 4.133820 TCGTGACATCACTCAACCATTTT 58.866 39.130 10.18 0.00 44.34 1.82
1648 2112 4.578516 TCGTGACATCACTCAACCATTTTT 59.421 37.500 10.18 0.00 44.34 1.94
1649 2113 4.676471 CGTGACATCACTCAACCATTTTTG 59.324 41.667 10.18 0.00 44.34 2.44
1650 2114 5.591099 GTGACATCACTCAACCATTTTTGT 58.409 37.500 4.72 0.00 43.25 2.83
1651 2115 6.042143 GTGACATCACTCAACCATTTTTGTT 58.958 36.000 4.72 0.00 43.25 2.83
1652 2116 6.198966 GTGACATCACTCAACCATTTTTGTTC 59.801 38.462 4.72 0.00 43.25 3.18
1653 2117 6.096705 TGACATCACTCAACCATTTTTGTTCT 59.903 34.615 0.00 0.00 0.00 3.01
1654 2118 6.507023 ACATCACTCAACCATTTTTGTTCTC 58.493 36.000 0.00 0.00 0.00 2.87
1655 2119 5.168526 TCACTCAACCATTTTTGTTCTCG 57.831 39.130 0.00 0.00 0.00 4.04
1656 2120 4.638421 TCACTCAACCATTTTTGTTCTCGT 59.362 37.500 0.00 0.00 0.00 4.18
1657 2121 5.818336 TCACTCAACCATTTTTGTTCTCGTA 59.182 36.000 0.00 0.00 0.00 3.43
1658 2122 6.316640 TCACTCAACCATTTTTGTTCTCGTAA 59.683 34.615 0.00 0.00 0.00 3.18
1659 2123 7.012894 TCACTCAACCATTTTTGTTCTCGTAAT 59.987 33.333 0.00 0.00 0.00 1.89
1829 2295 6.674694 ACTCACTGCTGATGAAAATGATAC 57.325 37.500 0.00 0.00 0.00 2.24
1878 2344 2.415893 GGTGTTTGAAGCTATTGCGCAT 60.416 45.455 12.75 3.99 45.42 4.73
1881 2347 4.672413 GTGTTTGAAGCTATTGCGCATATC 59.328 41.667 12.75 4.30 45.42 1.63
1895 2361 5.347342 TGCGCATATCAAAAACAATAAGGG 58.653 37.500 5.66 0.00 0.00 3.95
1904 2370 1.382914 AACAATAAGGGTCCAGGGCT 58.617 50.000 0.00 0.00 0.00 5.19
1966 2432 9.095700 GGCATATTATTAAGGGGGATTTGTTAA 57.904 33.333 0.00 0.00 0.00 2.01
1996 2462 5.462240 TCCATGATCTATTCTCTGGACAGT 58.538 41.667 0.00 0.00 34.15 3.55
2108 2574 5.398416 GCCTCGTCAATGTTAGTTTCAAAAC 59.602 40.000 0.00 0.00 39.17 2.43
2163 2629 2.192187 TGCGCATTCTGTGGTGCAA 61.192 52.632 5.66 0.00 46.38 4.08
2176 2642 1.686052 TGGTGCAACATTCCCAAACTC 59.314 47.619 0.00 0.00 39.98 3.01
2200 2666 1.003003 TCATGCCGGACAGAAACATCA 59.997 47.619 5.05 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 145 6.551975 TGGATAATTCATCTGCACCATCAAAT 59.448 34.615 0.00 0.00 33.78 2.32
151 153 5.005740 TGCCTATGGATAATTCATCTGCAC 58.994 41.667 0.00 0.00 33.78 4.57
183 185 6.830838 CAGGCCCTAAGTTAAAGATCTTCAAT 59.169 38.462 8.78 0.00 0.00 2.57
205 207 2.269241 GAAGGGCCTCCGAACAGG 59.731 66.667 6.46 0.00 42.97 4.00
206 208 2.125512 CGAAGGGCCTCCGAACAG 60.126 66.667 6.33 0.00 38.33 3.16
207 209 4.388499 GCGAAGGGCCTCCGAACA 62.388 66.667 19.21 0.00 38.33 3.18
208 210 4.083862 AGCGAAGGGCCTCCGAAC 62.084 66.667 19.21 0.00 45.17 3.95
209 211 3.771160 GAGCGAAGGGCCTCCGAA 61.771 66.667 19.21 0.00 45.17 4.30
212 214 4.475135 GTGGAGCGAAGGGCCTCC 62.475 72.222 6.46 3.70 45.17 4.30
213 215 3.706373 TGTGGAGCGAAGGGCCTC 61.706 66.667 6.46 0.00 45.17 4.70
214 216 4.021925 GTGTGGAGCGAAGGGCCT 62.022 66.667 0.00 0.00 45.17 5.19
216 218 4.681978 ACGTGTGGAGCGAAGGGC 62.682 66.667 0.00 0.00 44.05 5.19
217 219 2.432628 GACGTGTGGAGCGAAGGG 60.433 66.667 0.00 0.00 0.00 3.95
218 220 2.432628 GGACGTGTGGAGCGAAGG 60.433 66.667 0.00 0.00 0.00 3.46
219 221 2.432628 GGGACGTGTGGAGCGAAG 60.433 66.667 0.00 0.00 0.00 3.79
238 240 3.847602 CTCCGGCTGCTCCTGGAG 61.848 72.222 19.55 19.55 43.74 3.86
249 251 0.596082 TTTTAAACTGCAGCTCCGGC 59.404 50.000 15.27 0.00 39.06 6.13
250 252 1.606668 TGTTTTAAACTGCAGCTCCGG 59.393 47.619 15.27 0.00 0.00 5.14
251 253 2.921126 CTGTTTTAAACTGCAGCTCCG 58.079 47.619 15.27 0.00 0.00 4.63
259 261 1.529438 TCGCTCCGCTGTTTTAAACTG 59.471 47.619 9.33 9.59 0.00 3.16
260 262 1.798813 CTCGCTCCGCTGTTTTAAACT 59.201 47.619 9.33 0.00 0.00 2.66
261 263 1.136057 CCTCGCTCCGCTGTTTTAAAC 60.136 52.381 0.20 0.20 0.00 2.01
262 264 1.153353 CCTCGCTCCGCTGTTTTAAA 58.847 50.000 0.00 0.00 0.00 1.52
263 265 0.319083 TCCTCGCTCCGCTGTTTTAA 59.681 50.000 0.00 0.00 0.00 1.52
264 266 0.319083 TTCCTCGCTCCGCTGTTTTA 59.681 50.000 0.00 0.00 0.00 1.52
265 267 0.534203 TTTCCTCGCTCCGCTGTTTT 60.534 50.000 0.00 0.00 0.00 2.43
266 268 0.321653 ATTTCCTCGCTCCGCTGTTT 60.322 50.000 0.00 0.00 0.00 2.83
267 269 0.321653 AATTTCCTCGCTCCGCTGTT 60.322 50.000 0.00 0.00 0.00 3.16
268 270 1.021390 CAATTTCCTCGCTCCGCTGT 61.021 55.000 0.00 0.00 0.00 4.40
269 271 1.709147 CCAATTTCCTCGCTCCGCTG 61.709 60.000 0.00 0.00 0.00 5.18
270 272 1.450312 CCAATTTCCTCGCTCCGCT 60.450 57.895 0.00 0.00 0.00 5.52
271 273 0.461339 TACCAATTTCCTCGCTCCGC 60.461 55.000 0.00 0.00 0.00 5.54
272 274 1.134788 AGTACCAATTTCCTCGCTCCG 60.135 52.381 0.00 0.00 0.00 4.63
273 275 2.552031 GAGTACCAATTTCCTCGCTCC 58.448 52.381 0.00 0.00 0.00 4.70
274 276 2.552031 GGAGTACCAATTTCCTCGCTC 58.448 52.381 0.00 0.00 35.97 5.03
275 277 1.134788 CGGAGTACCAATTTCCTCGCT 60.135 52.381 0.00 0.00 35.59 4.93
276 278 1.287425 CGGAGTACCAATTTCCTCGC 58.713 55.000 0.00 0.00 35.59 5.03
277 279 2.667473 ACGGAGTACCAATTTCCTCG 57.333 50.000 0.00 0.00 41.94 4.63
278 280 4.996788 TCTACGGAGTACCAATTTCCTC 57.003 45.455 0.00 0.00 45.11 3.71
279 281 5.661759 AGAATCTACGGAGTACCAATTTCCT 59.338 40.000 0.00 0.00 45.11 3.36
280 282 5.753921 CAGAATCTACGGAGTACCAATTTCC 59.246 44.000 0.00 0.00 45.11 3.13
281 283 6.255887 CACAGAATCTACGGAGTACCAATTTC 59.744 42.308 0.00 0.00 45.11 2.17
282 284 6.070995 TCACAGAATCTACGGAGTACCAATTT 60.071 38.462 0.00 0.00 45.11 1.82
283 285 5.421056 TCACAGAATCTACGGAGTACCAATT 59.579 40.000 0.00 0.00 45.11 2.32
284 286 4.954202 TCACAGAATCTACGGAGTACCAAT 59.046 41.667 0.00 0.00 45.11 3.16
285 287 4.338012 TCACAGAATCTACGGAGTACCAA 58.662 43.478 0.00 0.00 45.11 3.67
286 288 3.959293 TCACAGAATCTACGGAGTACCA 58.041 45.455 0.00 0.00 45.11 3.25
287 289 5.517322 AATCACAGAATCTACGGAGTACC 57.483 43.478 0.00 0.00 45.11 3.34
288 290 5.978322 GGAAATCACAGAATCTACGGAGTAC 59.022 44.000 0.00 0.00 45.11 2.73
289 291 5.220989 CGGAAATCACAGAATCTACGGAGTA 60.221 44.000 0.00 0.00 45.11 2.59
291 293 4.045104 CGGAAATCACAGAATCTACGGAG 58.955 47.826 0.00 0.00 0.00 4.63
292 294 3.697542 TCGGAAATCACAGAATCTACGGA 59.302 43.478 0.00 0.00 0.00 4.69
293 295 4.041740 TCGGAAATCACAGAATCTACGG 57.958 45.455 0.00 0.00 0.00 4.02
294 296 4.026475 GCTTCGGAAATCACAGAATCTACG 60.026 45.833 0.00 0.00 0.00 3.51
295 297 4.026475 CGCTTCGGAAATCACAGAATCTAC 60.026 45.833 0.00 0.00 0.00 2.59
296 298 4.112634 CGCTTCGGAAATCACAGAATCTA 58.887 43.478 0.00 0.00 0.00 1.98
297 299 2.932614 CGCTTCGGAAATCACAGAATCT 59.067 45.455 0.00 0.00 0.00 2.40
298 300 3.310303 CGCTTCGGAAATCACAGAATC 57.690 47.619 0.00 0.00 0.00 2.52
312 314 3.053896 GGAAACCCACCCGCTTCG 61.054 66.667 0.00 0.00 0.00 3.79
313 315 3.053896 CGGAAACCCACCCGCTTC 61.054 66.667 0.00 0.00 39.22 3.86
314 316 3.122727 TTCGGAAACCCACCCGCTT 62.123 57.895 0.00 0.00 44.96 4.68
315 317 3.562232 TTCGGAAACCCACCCGCT 61.562 61.111 0.00 0.00 44.96 5.52
316 318 3.359523 GTTCGGAAACCCACCCGC 61.360 66.667 0.00 0.00 44.96 6.13
317 319 1.964373 CTGTTCGGAAACCCACCCG 60.964 63.158 0.00 0.00 46.57 5.28
318 320 2.265904 GCTGTTCGGAAACCCACCC 61.266 63.158 0.00 0.00 34.28 4.61
319 321 2.265904 GGCTGTTCGGAAACCCACC 61.266 63.158 0.00 0.00 34.28 4.61
320 322 2.265904 GGGCTGTTCGGAAACCCAC 61.266 63.158 16.05 0.00 40.52 4.61
321 323 2.114411 GGGCTGTTCGGAAACCCA 59.886 61.111 16.05 0.73 40.52 4.51
322 324 2.675423 GGGGCTGTTCGGAAACCC 60.675 66.667 13.68 13.68 40.05 4.11
323 325 0.037160 TAAGGGGCTGTTCGGAAACC 59.963 55.000 0.00 0.00 34.28 3.27
324 326 1.002773 TCTAAGGGGCTGTTCGGAAAC 59.997 52.381 0.00 0.00 35.85 2.78
325 327 1.354101 TCTAAGGGGCTGTTCGGAAA 58.646 50.000 0.00 0.00 0.00 3.13
326 328 1.354101 TTCTAAGGGGCTGTTCGGAA 58.646 50.000 0.00 0.00 0.00 4.30
327 329 1.485066 GATTCTAAGGGGCTGTTCGGA 59.515 52.381 0.00 0.00 0.00 4.55
328 330 1.209504 TGATTCTAAGGGGCTGTTCGG 59.790 52.381 0.00 0.00 0.00 4.30
329 331 2.555199 CTGATTCTAAGGGGCTGTTCG 58.445 52.381 0.00 0.00 0.00 3.95
330 332 2.293170 GCTGATTCTAAGGGGCTGTTC 58.707 52.381 0.00 0.00 0.00 3.18
331 333 1.064389 GGCTGATTCTAAGGGGCTGTT 60.064 52.381 0.00 0.00 0.00 3.16
332 334 0.548510 GGCTGATTCTAAGGGGCTGT 59.451 55.000 0.00 0.00 0.00 4.40
333 335 0.533755 CGGCTGATTCTAAGGGGCTG 60.534 60.000 0.00 0.00 0.00 4.85
334 336 0.691078 TCGGCTGATTCTAAGGGGCT 60.691 55.000 0.00 0.00 0.00 5.19
335 337 0.180406 TTCGGCTGATTCTAAGGGGC 59.820 55.000 0.00 0.00 0.00 5.80
336 338 2.710096 TTTCGGCTGATTCTAAGGGG 57.290 50.000 0.00 0.00 0.00 4.79
337 339 4.260784 CGAATTTTCGGCTGATTCTAAGGG 60.261 45.833 0.00 0.00 46.30 3.95
338 340 4.837567 CGAATTTTCGGCTGATTCTAAGG 58.162 43.478 0.00 0.00 46.30 2.69
352 354 8.248253 ACTATGTTCCAAAATACCCGAATTTTC 58.752 33.333 0.00 0.00 37.03 2.29
467 472 8.706936 GTGCAATACTTATGACACATCTAGATG 58.293 37.037 27.63 27.63 44.15 2.90
468 473 8.424133 TGTGCAATACTTATGACACATCTAGAT 58.576 33.333 0.00 0.00 33.26 1.98
469 474 7.781056 TGTGCAATACTTATGACACATCTAGA 58.219 34.615 0.00 0.00 33.26 2.43
470 475 8.493547 CATGTGCAATACTTATGACACATCTAG 58.506 37.037 11.67 0.00 40.34 2.43
471 476 7.986889 ACATGTGCAATACTTATGACACATCTA 59.013 33.333 0.00 0.00 40.34 1.98
472 477 6.825213 ACATGTGCAATACTTATGACACATCT 59.175 34.615 0.00 2.59 40.34 2.90
473 478 7.019774 ACATGTGCAATACTTATGACACATC 57.980 36.000 0.00 0.00 40.34 3.06
474 479 8.504812 TTACATGTGCAATACTTATGACACAT 57.495 30.769 9.11 9.84 41.62 3.21
475 480 7.913674 TTACATGTGCAATACTTATGACACA 57.086 32.000 9.11 0.00 38.34 3.72
476 481 9.438291 GATTTACATGTGCAATACTTATGACAC 57.562 33.333 9.11 0.00 0.00 3.67
477 482 9.171877 TGATTTACATGTGCAATACTTATGACA 57.828 29.630 9.11 0.00 0.00 3.58
484 489 9.341078 TGACATATGATTTACATGTGCAATACT 57.659 29.630 10.38 1.06 46.98 2.12
487 492 9.471084 CAATGACATATGATTTACATGTGCAAT 57.529 29.630 10.38 6.70 46.98 3.56
488 493 8.684520 TCAATGACATATGATTTACATGTGCAA 58.315 29.630 10.38 1.32 46.98 4.08
489 494 8.223177 TCAATGACATATGATTTACATGTGCA 57.777 30.769 10.38 1.77 46.98 4.57
490 495 9.338291 GATCAATGACATATGATTTACATGTGC 57.662 33.333 10.38 0.00 46.98 4.57
525 530 9.462606 AGGGAAAGAAAATATTTACACGAATCT 57.537 29.630 0.01 0.00 0.00 2.40
528 533 9.685828 CAAAGGGAAAGAAAATATTTACACGAA 57.314 29.630 0.01 0.00 0.00 3.85
529 534 9.069082 TCAAAGGGAAAGAAAATATTTACACGA 57.931 29.630 0.01 0.00 0.00 4.35
530 535 9.855021 ATCAAAGGGAAAGAAAATATTTACACG 57.145 29.630 0.01 0.00 0.00 4.49
539 544 9.770097 GAGAAAAAGATCAAAGGGAAAGAAAAT 57.230 29.630 0.00 0.00 0.00 1.82
540 545 8.981659 AGAGAAAAAGATCAAAGGGAAAGAAAA 58.018 29.630 0.00 0.00 0.00 2.29
541 546 8.539117 AGAGAAAAAGATCAAAGGGAAAGAAA 57.461 30.769 0.00 0.00 0.00 2.52
542 547 8.539117 AAGAGAAAAAGATCAAAGGGAAAGAA 57.461 30.769 0.00 0.00 0.00 2.52
543 548 8.539117 AAAGAGAAAAAGATCAAAGGGAAAGA 57.461 30.769 0.00 0.00 0.00 2.52
569 574 7.493971 GCACATCTAAGTGAGTGAATCAAGTAT 59.506 37.037 0.00 0.00 42.05 2.12
570 575 6.813649 GCACATCTAAGTGAGTGAATCAAGTA 59.186 38.462 0.00 0.00 42.05 2.24
571 576 5.641209 GCACATCTAAGTGAGTGAATCAAGT 59.359 40.000 0.00 0.00 42.05 3.16
572 577 5.640783 TGCACATCTAAGTGAGTGAATCAAG 59.359 40.000 0.00 0.00 42.05 3.02
573 578 5.550290 TGCACATCTAAGTGAGTGAATCAA 58.450 37.500 0.00 0.00 42.05 2.57
574 579 5.151297 TGCACATCTAAGTGAGTGAATCA 57.849 39.130 0.00 0.00 42.05 2.57
575 580 6.674694 ATTGCACATCTAAGTGAGTGAATC 57.325 37.500 0.00 0.00 42.05 2.52
576 581 7.826252 AGTTATTGCACATCTAAGTGAGTGAAT 59.174 33.333 0.00 0.00 42.05 2.57
577 582 7.161404 AGTTATTGCACATCTAAGTGAGTGAA 58.839 34.615 0.00 0.00 42.05 3.18
578 583 6.701340 AGTTATTGCACATCTAAGTGAGTGA 58.299 36.000 0.00 0.00 42.05 3.41
579 584 6.974932 AGTTATTGCACATCTAAGTGAGTG 57.025 37.500 0.00 0.00 42.05 3.51
580 585 7.268586 CCTAGTTATTGCACATCTAAGTGAGT 58.731 38.462 0.00 0.00 42.05 3.41
581 586 6.703607 CCCTAGTTATTGCACATCTAAGTGAG 59.296 42.308 0.00 0.00 42.05 3.51
582 587 6.582636 CCCTAGTTATTGCACATCTAAGTGA 58.417 40.000 0.00 0.00 42.05 3.41
583 588 5.237344 GCCCTAGTTATTGCACATCTAAGTG 59.763 44.000 0.00 0.00 42.37 3.16
584 589 5.104527 TGCCCTAGTTATTGCACATCTAAGT 60.105 40.000 0.00 0.00 0.00 2.24
585 590 5.368145 TGCCCTAGTTATTGCACATCTAAG 58.632 41.667 0.00 0.00 0.00 2.18
586 591 5.366482 TGCCCTAGTTATTGCACATCTAA 57.634 39.130 0.00 0.00 0.00 2.10
588 593 3.931907 TGCCCTAGTTATTGCACATCT 57.068 42.857 0.00 0.00 0.00 2.90
593 598 3.931907 AGATGTGCCCTAGTTATTGCA 57.068 42.857 0.00 0.00 0.00 4.08
594 599 5.215252 TCTAGATGTGCCCTAGTTATTGC 57.785 43.478 0.00 0.00 36.06 3.56
609 614 3.638627 TGTGTCTAGGGCACATCTAGATG 59.361 47.826 27.63 27.63 43.25 2.90
610 615 3.639094 GTGTGTCTAGGGCACATCTAGAT 59.361 47.826 18.92 0.00 46.66 1.98
611 616 3.024547 GTGTGTCTAGGGCACATCTAGA 58.975 50.000 18.92 0.00 46.66 2.43
612 617 2.101582 GGTGTGTCTAGGGCACATCTAG 59.898 54.545 18.92 0.00 46.66 2.43
613 618 2.108168 GGTGTGTCTAGGGCACATCTA 58.892 52.381 18.92 0.21 46.66 1.98
614 619 0.905357 GGTGTGTCTAGGGCACATCT 59.095 55.000 18.92 0.00 46.66 2.90
615 620 0.107654 GGGTGTGTCTAGGGCACATC 60.108 60.000 18.92 18.25 46.66 3.06
616 621 0.840288 TGGGTGTGTCTAGGGCACAT 60.840 55.000 18.92 0.00 46.66 3.21
617 622 1.057275 TTGGGTGTGTCTAGGGCACA 61.057 55.000 14.22 14.22 43.60 4.57
618 623 0.328258 ATTGGGTGTGTCTAGGGCAC 59.672 55.000 10.20 10.20 37.37 5.01
619 624 1.072266 AATTGGGTGTGTCTAGGGCA 58.928 50.000 0.00 0.00 0.00 5.36
620 625 2.215942 AAATTGGGTGTGTCTAGGGC 57.784 50.000 0.00 0.00 0.00 5.19
621 626 6.452242 GTTTTTAAATTGGGTGTGTCTAGGG 58.548 40.000 0.00 0.00 0.00 3.53
622 627 6.041069 TGGTTTTTAAATTGGGTGTGTCTAGG 59.959 38.462 0.00 0.00 0.00 3.02
623 628 7.045126 TGGTTTTTAAATTGGGTGTGTCTAG 57.955 36.000 0.00 0.00 0.00 2.43
624 629 7.604657 ATGGTTTTTAAATTGGGTGTGTCTA 57.395 32.000 0.00 0.00 0.00 2.59
625 630 5.941555 TGGTTTTTAAATTGGGTGTGTCT 57.058 34.783 0.00 0.00 0.00 3.41
626 631 7.497579 AGAAATGGTTTTTAAATTGGGTGTGTC 59.502 33.333 0.00 0.00 0.00 3.67
627 632 7.342581 AGAAATGGTTTTTAAATTGGGTGTGT 58.657 30.769 0.00 0.00 0.00 3.72
628 633 7.041440 GGAGAAATGGTTTTTAAATTGGGTGTG 60.041 37.037 0.00 0.00 0.00 3.82
629 634 6.995686 GGAGAAATGGTTTTTAAATTGGGTGT 59.004 34.615 0.00 0.00 0.00 4.16
630 635 7.223584 AGGAGAAATGGTTTTTAAATTGGGTG 58.776 34.615 0.00 0.00 0.00 4.61
631 636 7.387265 AGGAGAAATGGTTTTTAAATTGGGT 57.613 32.000 0.00 0.00 0.00 4.51
632 637 8.690203 AAAGGAGAAATGGTTTTTAAATTGGG 57.310 30.769 0.00 0.00 0.00 4.12
633 638 8.495148 CGAAAGGAGAAATGGTTTTTAAATTGG 58.505 33.333 0.00 0.00 0.00 3.16
634 639 9.040939 ACGAAAGGAGAAATGGTTTTTAAATTG 57.959 29.630 0.00 0.00 0.00 2.32
635 640 9.607988 AACGAAAGGAGAAATGGTTTTTAAATT 57.392 25.926 0.00 0.00 0.00 1.82
636 641 9.607988 AAACGAAAGGAGAAATGGTTTTTAAAT 57.392 25.926 0.00 0.00 0.00 1.40
637 642 9.089601 GAAACGAAAGGAGAAATGGTTTTTAAA 57.910 29.630 0.00 0.00 0.00 1.52
638 643 8.471609 AGAAACGAAAGGAGAAATGGTTTTTAA 58.528 29.630 0.00 0.00 0.00 1.52
639 644 8.002984 AGAAACGAAAGGAGAAATGGTTTTTA 57.997 30.769 0.00 0.00 0.00 1.52
640 645 6.873997 AGAAACGAAAGGAGAAATGGTTTTT 58.126 32.000 0.00 0.00 0.00 1.94
641 646 6.465439 AGAAACGAAAGGAGAAATGGTTTT 57.535 33.333 0.00 0.00 0.00 2.43
642 647 5.277828 CGAGAAACGAAAGGAGAAATGGTTT 60.278 40.000 0.00 0.00 45.77 3.27
643 648 4.213482 CGAGAAACGAAAGGAGAAATGGTT 59.787 41.667 0.00 0.00 45.77 3.67
725 730 0.251916 TAGCATGGGACCTTCGGTTG 59.748 55.000 0.00 0.00 35.25 3.77
729 734 2.872038 GCCTATTAGCATGGGACCTTCG 60.872 54.545 0.00 0.00 32.51 3.79
777 782 0.320771 GCGAATGGCGTGGATCCTAT 60.321 55.000 14.23 0.00 43.41 2.57
830 835 1.290134 GGGAGTGGGTTCAGGAGAAT 58.710 55.000 0.00 0.00 35.92 2.40
900 907 1.163309 TGGTGGGTGGAGGAAGGAT 59.837 57.895 0.00 0.00 0.00 3.24
920 927 3.553096 CGGTGGATTATTAGCGAGCTCTT 60.553 47.826 12.85 2.34 39.92 2.85
930 937 5.940192 CTGCTTATTGCGGTGGATTATTA 57.060 39.130 0.00 0.00 46.63 0.98
952 959 0.808847 GCGGACGGAGGTTGGTTATC 60.809 60.000 0.00 0.00 0.00 1.75
959 968 4.388499 ATTGCGCGGACGGAGGTT 62.388 61.111 8.83 0.00 42.06 3.50
966 975 0.579156 GATTGAGAGATTGCGCGGAC 59.421 55.000 8.83 0.00 0.00 4.79
1143 1152 2.031012 CTGTTGAGACTGCGGCCA 59.969 61.111 2.24 0.00 0.00 5.36
1187 1196 4.101448 CCCCCTTGGCGACCTCAG 62.101 72.222 0.00 0.00 0.00 3.35
1363 1816 2.996395 CATGCAGGAGCTCTGGGT 59.004 61.111 14.64 0.00 43.54 4.51
1367 1820 2.125229 CGTGCATGCAGGAGCTCT 60.125 61.111 31.46 0.00 42.74 4.09
1389 1842 1.825090 ATCAAACGAGGCAGCATTCA 58.175 45.000 0.00 0.00 0.00 2.57
1462 1923 2.438975 CGGATGGGTGCAGCACAT 60.439 61.111 26.78 17.54 45.45 3.21
1511 1972 1.001068 TCAATGAGGCCACGTACGAAA 59.999 47.619 24.41 0.00 0.00 3.46
1514 1975 1.209128 GATCAATGAGGCCACGTACG 58.791 55.000 15.01 15.01 0.00 3.67
1561 2025 3.669344 CAACCGCACGGGCACATT 61.669 61.111 11.77 0.00 41.24 2.71
1565 2029 4.402528 ATAGCAACCGCACGGGCA 62.403 61.111 11.77 0.00 42.27 5.36
1566 2030 3.876198 CATAGCAACCGCACGGGC 61.876 66.667 14.51 0.00 42.27 6.13
1567 2031 3.202001 CCATAGCAACCGCACGGG 61.202 66.667 14.51 0.00 42.27 5.28
1568 2032 3.202001 CCCATAGCAACCGCACGG 61.202 66.667 7.71 7.71 42.27 4.94
1569 2033 2.038269 AACCCATAGCAACCGCACG 61.038 57.895 0.00 0.00 42.27 5.34
1570 2034 0.958382 TCAACCCATAGCAACCGCAC 60.958 55.000 0.00 0.00 42.27 5.34
1571 2035 0.034574 ATCAACCCATAGCAACCGCA 60.035 50.000 0.00 0.00 42.27 5.69
1572 2036 1.102978 AATCAACCCATAGCAACCGC 58.897 50.000 0.00 0.00 38.99 5.68
1573 2037 1.405105 CCAATCAACCCATAGCAACCG 59.595 52.381 0.00 0.00 0.00 4.44
1574 2038 1.756538 CCCAATCAACCCATAGCAACC 59.243 52.381 0.00 0.00 0.00 3.77
1575 2039 1.756538 CCCCAATCAACCCATAGCAAC 59.243 52.381 0.00 0.00 0.00 4.17
1576 2040 1.643286 TCCCCAATCAACCCATAGCAA 59.357 47.619 0.00 0.00 0.00 3.91
1577 2041 1.303898 TCCCCAATCAACCCATAGCA 58.696 50.000 0.00 0.00 0.00 3.49
1578 2042 2.452600 TTCCCCAATCAACCCATAGC 57.547 50.000 0.00 0.00 0.00 2.97
1603 2067 9.611284 CACGAGAACAAAAATGATATTGAAGAA 57.389 29.630 0.00 0.00 0.00 2.52
1604 2068 8.998377 TCACGAGAACAAAAATGATATTGAAGA 58.002 29.630 0.00 0.00 0.00 2.87
1605 2069 9.055248 GTCACGAGAACAAAAATGATATTGAAG 57.945 33.333 0.00 0.00 0.00 3.02
1606 2070 8.563732 TGTCACGAGAACAAAAATGATATTGAA 58.436 29.630 0.00 0.00 0.00 2.69
1607 2071 8.093659 TGTCACGAGAACAAAAATGATATTGA 57.906 30.769 0.00 0.00 0.00 2.57
1608 2072 8.900511 ATGTCACGAGAACAAAAATGATATTG 57.099 30.769 0.00 0.00 0.00 1.90
1609 2073 8.729756 TGATGTCACGAGAACAAAAATGATATT 58.270 29.630 0.00 0.00 0.00 1.28
1610 2074 8.177663 GTGATGTCACGAGAACAAAAATGATAT 58.822 33.333 0.00 0.00 37.10 1.63
1611 2075 7.518161 GTGATGTCACGAGAACAAAAATGATA 58.482 34.615 0.00 0.00 37.10 2.15
1612 2076 6.373779 GTGATGTCACGAGAACAAAAATGAT 58.626 36.000 0.00 0.00 37.10 2.45
1613 2077 5.747565 GTGATGTCACGAGAACAAAAATGA 58.252 37.500 0.00 0.00 37.10 2.57
1624 2088 9.529327 ACAAAAATGGTTGAGTGATGTCACGAG 62.529 40.741 7.44 0.00 40.45 4.18
1625 2089 7.845871 ACAAAAATGGTTGAGTGATGTCACGA 61.846 38.462 7.44 0.00 40.45 4.35
1626 2090 5.733091 ACAAAAATGGTTGAGTGATGTCACG 60.733 40.000 7.44 0.00 40.45 4.35
1627 2091 5.591099 ACAAAAATGGTTGAGTGATGTCAC 58.409 37.500 5.01 5.01 38.22 3.67
1628 2092 5.850557 ACAAAAATGGTTGAGTGATGTCA 57.149 34.783 0.00 0.00 32.59 3.58
1629 2093 6.507023 AGAACAAAAATGGTTGAGTGATGTC 58.493 36.000 0.00 0.00 32.59 3.06
1630 2094 6.469782 AGAACAAAAATGGTTGAGTGATGT 57.530 33.333 0.00 0.00 32.59 3.06
1631 2095 5.626543 CGAGAACAAAAATGGTTGAGTGATG 59.373 40.000 0.00 0.00 32.59 3.07
1632 2096 5.299279 ACGAGAACAAAAATGGTTGAGTGAT 59.701 36.000 0.00 0.00 32.59 3.06
1633 2097 4.638421 ACGAGAACAAAAATGGTTGAGTGA 59.362 37.500 0.00 0.00 32.59 3.41
1634 2098 4.920376 ACGAGAACAAAAATGGTTGAGTG 58.080 39.130 0.00 0.00 32.59 3.51
1635 2099 6.687081 TTACGAGAACAAAAATGGTTGAGT 57.313 33.333 0.00 0.00 32.59 3.41
1636 2100 9.490663 GATATTACGAGAACAAAAATGGTTGAG 57.509 33.333 0.00 0.00 32.59 3.02
1637 2101 9.226606 AGATATTACGAGAACAAAAATGGTTGA 57.773 29.630 0.00 0.00 32.59 3.18
1638 2102 9.840427 AAGATATTACGAGAACAAAAATGGTTG 57.160 29.630 0.00 0.00 34.52 3.77
1643 2107 9.774742 GCTGAAAGATATTACGAGAACAAAAAT 57.225 29.630 0.00 0.00 34.07 1.82
1644 2108 8.999431 AGCTGAAAGATATTACGAGAACAAAAA 58.001 29.630 0.00 0.00 34.07 1.94
1645 2109 8.547967 AGCTGAAAGATATTACGAGAACAAAA 57.452 30.769 0.00 0.00 34.07 2.44
1646 2110 8.443160 CAAGCTGAAAGATATTACGAGAACAAA 58.557 33.333 0.00 0.00 34.07 2.83
1647 2111 7.817478 TCAAGCTGAAAGATATTACGAGAACAA 59.183 33.333 0.00 0.00 34.07 2.83
1648 2112 7.320399 TCAAGCTGAAAGATATTACGAGAACA 58.680 34.615 0.00 0.00 34.07 3.18
1649 2113 7.757097 TCAAGCTGAAAGATATTACGAGAAC 57.243 36.000 0.00 0.00 34.07 3.01
1650 2114 7.817478 TGTTCAAGCTGAAAGATATTACGAGAA 59.183 33.333 0.00 0.00 38.22 2.87
1651 2115 7.320399 TGTTCAAGCTGAAAGATATTACGAGA 58.680 34.615 0.00 0.00 38.22 4.04
1652 2116 7.525688 TGTTCAAGCTGAAAGATATTACGAG 57.474 36.000 0.00 0.00 38.22 4.18
1653 2117 7.817478 TCTTGTTCAAGCTGAAAGATATTACGA 59.183 33.333 7.58 0.00 38.22 3.43
1654 2118 7.963981 TCTTGTTCAAGCTGAAAGATATTACG 58.036 34.615 7.58 0.00 38.22 3.18
1655 2119 9.713740 CATCTTGTTCAAGCTGAAAGATATTAC 57.286 33.333 9.82 0.00 38.22 1.89
1656 2120 9.671279 TCATCTTGTTCAAGCTGAAAGATATTA 57.329 29.630 14.09 0.00 38.22 0.98
1657 2121 8.571461 TCATCTTGTTCAAGCTGAAAGATATT 57.429 30.769 14.09 0.00 38.22 1.28
1658 2122 8.571461 TTCATCTTGTTCAAGCTGAAAGATAT 57.429 30.769 21.45 2.13 38.22 1.63
1659 2123 7.879677 TCTTCATCTTGTTCAAGCTGAAAGATA 59.120 33.333 22.84 12.24 38.22 1.98
1829 2295 0.512952 CGAGAACGAGGCAACCAAAG 59.487 55.000 0.00 0.00 42.66 2.77
1878 2344 5.955355 CCCTGGACCCTTATTGTTTTTGATA 59.045 40.000 0.00 0.00 0.00 2.15
1881 2347 3.306710 GCCCTGGACCCTTATTGTTTTTG 60.307 47.826 0.00 0.00 0.00 2.44
1895 2361 2.027385 GAAATCCATTCAGCCCTGGAC 58.973 52.381 0.00 0.00 44.06 4.02
1904 2370 0.463654 CTCCGCCGGAAATCCATTCA 60.464 55.000 7.50 0.00 39.98 2.57
2024 2490 7.283127 CCATTTTCTTAGGAAGCAGTGCTATTA 59.717 37.037 20.09 8.48 38.25 0.98
2029 2495 3.758554 TCCATTTTCTTAGGAAGCAGTGC 59.241 43.478 7.13 7.13 32.61 4.40
2163 2629 3.259123 GCATGAAAGGAGTTTGGGAATGT 59.741 43.478 0.00 0.00 0.00 2.71
2176 2642 1.200020 GTTTCTGTCCGGCATGAAAGG 59.800 52.381 13.22 0.00 30.64 3.11
2200 2666 0.421904 AGGACCACCACCCCTTCTAT 59.578 55.000 0.00 0.00 38.94 1.98


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

AutoCloner maintained by Alex Coulton.