Multiple sequence alignment - TraesCS5A01G046300

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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 TraesCS5A01G046300 chr5A 100.000 2500 0 0 1 2500 41462791 41460292 0.000000e+00 4617.0
1 TraesCS5A01G046300 chr5A 90.693 505 43 4 1699 2202 674211029 674210528 0.000000e+00 669.0
2 TraesCS5A01G046300 chr5A 95.500 200 9 0 263 462 368238764 368238565 1.120000e-83 320.0
3 TraesCS5A01G046300 chr5A 83.333 78 11 2 683 759 34381201 34381277 1.240000e-08 71.3
4 TraesCS5A01G046300 chr5B 89.573 1266 80 27 463 1698 55509521 55508278 0.000000e+00 1559.0
5 TraesCS5A01G046300 chr5B 92.884 267 16 3 1 266 55527753 55527489 3.900000e-103 385.0
6 TraesCS5A01G046300 chr5B 94.378 249 12 2 19 266 55509762 55509515 5.050000e-102 381.0
7 TraesCS5A01G046300 chr5D 90.125 719 51 9 986 1698 52362275 52361571 0.000000e+00 917.0
8 TraesCS5A01G046300 chr5D 91.547 556 25 10 463 999 52362852 52362300 0.000000e+00 747.0
9 TraesCS5A01G046300 chr5D 94.118 204 11 1 261 463 269063728 269063931 2.420000e-80 309.0
10 TraesCS5A01G046300 chr5D 91.558 154 12 1 99 251 52363019 52362866 7.010000e-51 211.0
11 TraesCS5A01G046300 chr6B 90.220 501 39 10 1704 2200 124390823 124390329 0.000000e+00 645.0
12 TraesCS5A01G046300 chr6B 88.477 512 49 8 1699 2207 124390552 124390048 5.910000e-171 610.0
13 TraesCS5A01G046300 chr7B 90.760 487 38 7 1709 2193 652493949 652493468 0.000000e+00 643.0
14 TraesCS5A01G046300 chr7B 92.857 280 18 1 2221 2500 729127473 729127196 2.990000e-109 405.0
15 TraesCS5A01G046300 chr7B 92.500 280 19 1 2221 2500 729195167 729194890 1.390000e-107 399.0
16 TraesCS5A01G046300 chr3A 89.587 509 50 3 1695 2202 56967361 56967867 0.000000e+00 643.0
17 TraesCS5A01G046300 chr3A 89.041 511 49 6 1695 2204 56967090 56967594 5.870000e-176 627.0
18 TraesCS5A01G046300 chr3A 94.608 204 11 0 259 462 82101431 82101634 1.440000e-82 316.0
19 TraesCS5A01G046300 chr7A 89.567 508 45 8 1700 2205 17393224 17392723 2.710000e-179 638.0
20 TraesCS5A01G046300 chr6A 89.505 505 45 7 1699 2200 22288502 22289001 1.260000e-177 632.0
21 TraesCS5A01G046300 chrUn 89.412 510 41 6 1704 2206 288814767 288814264 4.540000e-177 630.0
22 TraesCS5A01G046300 chrUn 93.262 282 17 1 2219 2500 97227749 97228028 4.980000e-112 414.0
23 TraesCS5A01G046300 chrUn 92.171 281 19 2 2220 2500 97329382 97329659 6.480000e-106 394.0
24 TraesCS5A01G046300 chr1A 93.919 296 15 2 2206 2500 579206403 579206110 6.350000e-121 444.0
25 TraesCS5A01G046300 chr1A 92.683 287 14 3 2219 2500 20250429 20250713 8.320000e-110 407.0
26 TraesCS5A01G046300 chr3D 93.594 281 15 2 2220 2500 98565501 98565224 1.380000e-112 416.0
27 TraesCS5A01G046300 chr3D 92.171 281 20 1 2220 2500 581801725 581801447 1.800000e-106 396.0
28 TraesCS5A01G046300 chr3D 94.089 203 11 1 261 462 351838171 351837969 8.690000e-80 307.0
29 TraesCS5A01G046300 chr4D 92.500 280 19 1 2221 2500 440031260 440031537 1.390000e-107 399.0
30 TraesCS5A01G046300 chr2D 94.975 199 10 0 264 462 9924896 9925094 1.870000e-81 313.0
31 TraesCS5A01G046300 chr2D 93.720 207 13 0 261 467 536454342 536454548 6.710000e-81 311.0
32 TraesCS5A01G046300 chr7D 94.500 200 11 0 263 462 528407182 528406983 2.420000e-80 309.0
33 TraesCS5A01G046300 chr1D 93.659 205 13 0 258 462 318729803 318730007 8.690000e-80 307.0
34 TraesCS5A01G046300 chr4A 92.754 207 15 0 259 465 281503851 281503645 1.450000e-77 300.0
35 TraesCS5A01G046300 chr4A 83.333 78 11 2 682 758 577113653 577113729 1.240000e-08 71.3


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 TraesCS5A01G046300 chr5A 41460292 41462791 2499 True 4617.0 4617 100.000000 1 2500 1 chr5A.!!$R1 2499
1 TraesCS5A01G046300 chr5A 674210528 674211029 501 True 669.0 669 90.693000 1699 2202 1 chr5A.!!$R3 503
2 TraesCS5A01G046300 chr5B 55508278 55509762 1484 True 970.0 1559 91.975500 19 1698 2 chr5B.!!$R2 1679
3 TraesCS5A01G046300 chr5D 52361571 52363019 1448 True 625.0 917 91.076667 99 1698 3 chr5D.!!$R1 1599
4 TraesCS5A01G046300 chr6B 124390048 124390823 775 True 627.5 645 89.348500 1699 2207 2 chr6B.!!$R1 508
5 TraesCS5A01G046300 chr3A 56967090 56967867 777 False 635.0 643 89.314000 1695 2204 2 chr3A.!!$F2 509
6 TraesCS5A01G046300 chr7A 17392723 17393224 501 True 638.0 638 89.567000 1700 2205 1 chr7A.!!$R1 505
7 TraesCS5A01G046300 chrUn 288814264 288814767 503 True 630.0 630 89.412000 1704 2206 1 chrUn.!!$R1 502

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
989 1021 0.034896 TTCTTGGTTGAGCGGGAGAC 59.965 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2468 2833 0.606673 GACAAGCCCTCCAACCTGTC 60.607 60.0 0.0 0.0 0.0 3.51 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
55 56 6.653320 AGTTCATAAATACGAACAAGGCTTGA 59.347 34.615 32.50 11.14 43.20 3.02
84 85 4.640201 CAGTCACTGGTTCCTTCTCAAAAA 59.360 41.667 0.00 0.00 0.00 1.94
160 161 4.555348 CAACAATGCTTGGTTTGCAATT 57.445 36.364 0.00 0.00 44.01 2.32
197 198 1.425448 ACTGCTTTAGCCAGGGAAGTT 59.575 47.619 0.00 0.00 41.18 2.66
211 212 5.115480 CAGGGAAGTTTCTAGAGAAGATGC 58.885 45.833 0.00 0.00 35.21 3.91
259 266 1.202177 CGCCACCATTCACATTAGCAC 60.202 52.381 0.00 0.00 0.00 4.40
266 273 4.878397 ACCATTCACATTAGCACTTAGAGC 59.122 41.667 0.00 0.00 0.00 4.09
267 274 4.877823 CCATTCACATTAGCACTTAGAGCA 59.122 41.667 4.27 0.00 0.00 4.26
268 275 5.530171 CCATTCACATTAGCACTTAGAGCAT 59.470 40.000 4.27 0.00 0.00 3.79
269 276 6.707608 CCATTCACATTAGCACTTAGAGCATA 59.292 38.462 4.27 0.00 0.00 3.14
270 277 7.227314 CCATTCACATTAGCACTTAGAGCATAA 59.773 37.037 4.27 1.12 0.00 1.90
271 278 8.781196 CATTCACATTAGCACTTAGAGCATAAT 58.219 33.333 4.27 3.23 0.00 1.28
272 279 8.737168 TTCACATTAGCACTTAGAGCATAATT 57.263 30.769 4.27 0.00 0.00 1.40
273 280 8.146479 TCACATTAGCACTTAGAGCATAATTG 57.854 34.615 4.27 6.90 0.00 2.32
274 281 7.227314 TCACATTAGCACTTAGAGCATAATTGG 59.773 37.037 4.27 1.73 0.00 3.16
275 282 7.012704 CACATTAGCACTTAGAGCATAATTGGT 59.987 37.037 4.27 8.20 35.95 3.67
276 283 7.557719 ACATTAGCACTTAGAGCATAATTGGTT 59.442 33.333 4.27 0.00 32.62 3.67
277 284 7.938140 TTAGCACTTAGAGCATAATTGGTTT 57.062 32.000 4.27 0.00 32.62 3.27
278 285 6.199937 AGCACTTAGAGCATAATTGGTTTG 57.800 37.500 4.27 0.00 32.62 2.93
279 286 5.945784 AGCACTTAGAGCATAATTGGTTTGA 59.054 36.000 4.27 0.00 32.62 2.69
280 287 6.604795 AGCACTTAGAGCATAATTGGTTTGAT 59.395 34.615 4.27 0.00 32.62 2.57
281 288 6.694411 GCACTTAGAGCATAATTGGTTTGATG 59.306 38.462 0.00 0.00 32.62 3.07
282 289 6.694411 CACTTAGAGCATAATTGGTTTGATGC 59.306 38.462 1.15 1.15 44.05 3.91
283 290 4.660789 AGAGCATAATTGGTTTGATGCC 57.339 40.909 5.24 0.00 44.65 4.40
284 291 4.025360 AGAGCATAATTGGTTTGATGCCA 58.975 39.130 5.24 0.00 44.65 4.92
293 300 5.938438 TTGGTTTGATGCCAAAAATAAGC 57.062 34.783 0.00 0.00 43.18 3.09
294 301 4.965814 TGGTTTGATGCCAAAAATAAGCA 58.034 34.783 0.00 0.00 43.18 3.91
296 303 5.411977 TGGTTTGATGCCAAAAATAAGCATG 59.588 36.000 0.77 0.00 46.81 4.06
297 304 5.326292 GTTTGATGCCAAAAATAAGCATGC 58.674 37.500 10.51 10.51 46.81 4.06
298 305 3.533547 TGATGCCAAAAATAAGCATGCC 58.466 40.909 15.66 0.00 46.81 4.40
299 306 3.055312 TGATGCCAAAAATAAGCATGCCA 60.055 39.130 15.66 2.46 46.81 4.92
300 307 3.413846 TGCCAAAAATAAGCATGCCAA 57.586 38.095 15.66 2.47 0.00 4.52
301 308 3.952931 TGCCAAAAATAAGCATGCCAAT 58.047 36.364 15.66 5.19 0.00 3.16
302 309 3.690139 TGCCAAAAATAAGCATGCCAATG 59.310 39.130 15.66 4.27 36.82 2.82
303 310 3.690628 GCCAAAAATAAGCATGCCAATGT 59.309 39.130 15.66 0.00 36.08 2.71
304 311 4.156373 GCCAAAAATAAGCATGCCAATGTT 59.844 37.500 15.66 6.77 36.08 2.71
305 312 5.335819 GCCAAAAATAAGCATGCCAATGTTT 60.336 36.000 15.66 12.60 40.05 2.83
306 313 6.087522 CCAAAAATAAGCATGCCAATGTTTG 58.912 36.000 25.19 25.19 37.72 2.93
307 314 6.072618 CCAAAAATAAGCATGCCAATGTTTGA 60.073 34.615 29.72 4.22 37.72 2.69
308 315 6.484818 AAAATAAGCATGCCAATGTTTGAC 57.515 33.333 15.66 0.00 37.72 3.18
309 316 4.804868 ATAAGCATGCCAATGTTTGACA 57.195 36.364 15.66 0.00 37.72 3.58
310 317 2.736144 AGCATGCCAATGTTTGACAG 57.264 45.000 15.66 0.00 36.08 3.51
311 318 1.965643 AGCATGCCAATGTTTGACAGT 59.034 42.857 15.66 0.00 36.08 3.55
312 319 2.063266 GCATGCCAATGTTTGACAGTG 58.937 47.619 6.36 1.85 43.12 3.66
313 320 2.546373 GCATGCCAATGTTTGACAGTGT 60.546 45.455 6.36 0.00 42.06 3.55
314 321 2.867287 TGCCAATGTTTGACAGTGTG 57.133 45.000 0.00 1.56 42.06 3.82
315 322 1.202394 TGCCAATGTTTGACAGTGTGC 60.202 47.619 0.00 10.09 42.06 4.57
316 323 1.869342 GCCAATGTTTGACAGTGTGCC 60.869 52.381 0.00 0.00 42.06 5.01
317 324 1.408340 CCAATGTTTGACAGTGTGCCA 59.592 47.619 0.00 0.00 42.06 4.92
318 325 2.159128 CCAATGTTTGACAGTGTGCCAA 60.159 45.455 0.00 0.00 42.06 4.52
319 326 3.519579 CAATGTTTGACAGTGTGCCAAA 58.480 40.909 0.00 2.99 39.14 3.28
320 327 4.121317 CAATGTTTGACAGTGTGCCAAAT 58.879 39.130 11.89 0.00 39.14 2.32
321 328 5.288015 CAATGTTTGACAGTGTGCCAAATA 58.712 37.500 11.89 10.21 39.14 1.40
322 329 5.726980 ATGTTTGACAGTGTGCCAAATAT 57.273 34.783 11.89 11.69 33.17 1.28
323 330 5.528043 TGTTTGACAGTGTGCCAAATATT 57.472 34.783 11.89 0.00 33.17 1.28
324 331 5.527951 TGTTTGACAGTGTGCCAAATATTC 58.472 37.500 11.89 2.55 33.17 1.75
325 332 4.418013 TTGACAGTGTGCCAAATATTCG 57.582 40.909 0.00 0.00 0.00 3.34
326 333 2.161410 TGACAGTGTGCCAAATATTCGC 59.839 45.455 0.00 0.00 0.00 4.70
327 334 2.420022 GACAGTGTGCCAAATATTCGCT 59.580 45.455 0.00 0.00 0.00 4.93
328 335 3.605634 ACAGTGTGCCAAATATTCGCTA 58.394 40.909 0.00 0.00 0.00 4.26
329 336 3.374058 ACAGTGTGCCAAATATTCGCTAC 59.626 43.478 0.00 7.67 0.00 3.58
330 337 3.623060 CAGTGTGCCAAATATTCGCTACT 59.377 43.478 8.47 9.25 0.00 2.57
331 338 4.808895 CAGTGTGCCAAATATTCGCTACTA 59.191 41.667 8.47 0.00 0.00 1.82
332 339 4.809426 AGTGTGCCAAATATTCGCTACTAC 59.191 41.667 8.47 0.90 0.00 2.73
333 340 4.809426 GTGTGCCAAATATTCGCTACTACT 59.191 41.667 8.47 0.00 0.00 2.57
334 341 5.293569 GTGTGCCAAATATTCGCTACTACTT 59.706 40.000 8.47 0.00 0.00 2.24
335 342 5.293324 TGTGCCAAATATTCGCTACTACTTG 59.707 40.000 8.47 0.00 0.00 3.16
336 343 5.522460 GTGCCAAATATTCGCTACTACTTGA 59.478 40.000 8.47 0.00 0.00 3.02
337 344 6.202954 GTGCCAAATATTCGCTACTACTTGAT 59.797 38.462 8.47 0.00 0.00 2.57
338 345 6.765989 TGCCAAATATTCGCTACTACTTGATT 59.234 34.615 8.47 0.00 0.00 2.57
339 346 7.072030 GCCAAATATTCGCTACTACTTGATTG 58.928 38.462 0.00 0.00 0.00 2.67
340 347 7.042051 GCCAAATATTCGCTACTACTTGATTGA 60.042 37.037 0.00 0.00 0.00 2.57
341 348 8.993121 CCAAATATTCGCTACTACTTGATTGAT 58.007 33.333 0.00 0.00 0.00 2.57
344 351 8.764524 ATATTCGCTACTACTTGATTGATTCC 57.235 34.615 0.00 0.00 0.00 3.01
345 352 4.945246 TCGCTACTACTTGATTGATTCCC 58.055 43.478 0.00 0.00 0.00 3.97
346 353 3.736252 CGCTACTACTTGATTGATTCCCG 59.264 47.826 0.00 0.00 0.00 5.14
347 354 4.499188 CGCTACTACTTGATTGATTCCCGA 60.499 45.833 0.00 0.00 0.00 5.14
348 355 4.985409 GCTACTACTTGATTGATTCCCGAG 59.015 45.833 0.00 0.00 0.00 4.63
349 356 5.452077 GCTACTACTTGATTGATTCCCGAGT 60.452 44.000 0.00 0.00 0.00 4.18
350 357 5.422214 ACTACTTGATTGATTCCCGAGTT 57.578 39.130 0.00 0.00 0.00 3.01
351 358 5.178797 ACTACTTGATTGATTCCCGAGTTG 58.821 41.667 0.00 0.00 0.00 3.16
352 359 4.021102 ACTTGATTGATTCCCGAGTTGT 57.979 40.909 0.00 0.00 0.00 3.32
353 360 4.003648 ACTTGATTGATTCCCGAGTTGTC 58.996 43.478 0.00 0.00 0.00 3.18
354 361 3.981071 TGATTGATTCCCGAGTTGTCT 57.019 42.857 0.00 0.00 0.00 3.41
355 362 4.286297 TGATTGATTCCCGAGTTGTCTT 57.714 40.909 0.00 0.00 0.00 3.01
356 363 4.002982 TGATTGATTCCCGAGTTGTCTTG 58.997 43.478 0.00 0.00 0.00 3.02
357 364 3.485463 TTGATTCCCGAGTTGTCTTGT 57.515 42.857 0.00 0.00 0.00 3.16
358 365 3.040147 TGATTCCCGAGTTGTCTTGTC 57.960 47.619 0.00 0.00 0.00 3.18
359 366 2.632996 TGATTCCCGAGTTGTCTTGTCT 59.367 45.455 0.00 0.00 0.00 3.41
360 367 3.830178 TGATTCCCGAGTTGTCTTGTCTA 59.170 43.478 0.00 0.00 0.00 2.59
361 368 4.466370 TGATTCCCGAGTTGTCTTGTCTAT 59.534 41.667 0.00 0.00 0.00 1.98
362 369 4.451629 TTCCCGAGTTGTCTTGTCTATC 57.548 45.455 0.00 0.00 0.00 2.08
363 370 3.698289 TCCCGAGTTGTCTTGTCTATCT 58.302 45.455 0.00 0.00 0.00 1.98
364 371 3.695060 TCCCGAGTTGTCTTGTCTATCTC 59.305 47.826 0.00 0.00 0.00 2.75
365 372 3.444034 CCCGAGTTGTCTTGTCTATCTCA 59.556 47.826 0.00 0.00 0.00 3.27
366 373 4.416620 CCGAGTTGTCTTGTCTATCTCAC 58.583 47.826 0.00 0.00 0.00 3.51
367 374 4.082733 CCGAGTTGTCTTGTCTATCTCACA 60.083 45.833 0.00 0.00 0.00 3.58
368 375 5.393569 CCGAGTTGTCTTGTCTATCTCACAT 60.394 44.000 0.00 0.00 0.00 3.21
369 376 6.183360 CCGAGTTGTCTTGTCTATCTCACATA 60.183 42.308 0.00 0.00 0.00 2.29
370 377 7.251281 CGAGTTGTCTTGTCTATCTCACATAA 58.749 38.462 0.00 0.00 0.00 1.90
371 378 7.755373 CGAGTTGTCTTGTCTATCTCACATAAA 59.245 37.037 0.00 0.00 0.00 1.40
372 379 8.994429 AGTTGTCTTGTCTATCTCACATAAAG 57.006 34.615 0.00 0.00 0.00 1.85
373 380 8.589338 AGTTGTCTTGTCTATCTCACATAAAGT 58.411 33.333 0.00 0.00 0.00 2.66
374 381 9.209175 GTTGTCTTGTCTATCTCACATAAAGTT 57.791 33.333 0.00 0.00 0.00 2.66
375 382 8.763049 TGTCTTGTCTATCTCACATAAAGTTG 57.237 34.615 0.00 0.00 0.00 3.16
376 383 7.331934 TGTCTTGTCTATCTCACATAAAGTTGC 59.668 37.037 0.00 0.00 0.00 4.17
377 384 7.547370 GTCTTGTCTATCTCACATAAAGTTGCT 59.453 37.037 0.00 0.00 0.00 3.91
378 385 8.749354 TCTTGTCTATCTCACATAAAGTTGCTA 58.251 33.333 0.00 0.00 0.00 3.49
379 386 9.371136 CTTGTCTATCTCACATAAAGTTGCTAA 57.629 33.333 0.00 0.00 0.00 3.09
380 387 9.890629 TTGTCTATCTCACATAAAGTTGCTAAT 57.109 29.630 0.00 0.00 0.00 1.73
387 394 8.405531 TCTCACATAAAGTTGCTAATATTTGGC 58.594 33.333 0.00 0.00 37.69 4.52
388 395 8.060931 TCACATAAAGTTGCTAATATTTGGCA 57.939 30.769 10.43 10.43 45.81 4.92
395 402 4.389890 TGCTAATATTTGGCAAGCCTTG 57.610 40.909 12.96 0.00 44.47 3.61
396 403 3.132646 TGCTAATATTTGGCAAGCCTTGG 59.867 43.478 12.96 1.09 44.47 3.61
397 404 3.132824 GCTAATATTTGGCAAGCCTTGGT 59.867 43.478 12.96 0.00 37.09 3.67
398 405 4.340950 GCTAATATTTGGCAAGCCTTGGTA 59.659 41.667 12.96 1.16 37.09 3.25
399 406 5.011023 GCTAATATTTGGCAAGCCTTGGTAT 59.989 40.000 12.96 3.37 37.09 2.73
400 407 5.955961 AATATTTGGCAAGCCTTGGTATT 57.044 34.783 12.96 8.67 36.94 1.89
401 408 3.615224 ATTTGGCAAGCCTTGGTATTG 57.385 42.857 12.96 3.47 36.94 1.90
402 409 0.607620 TTGGCAAGCCTTGGTATTGC 59.392 50.000 12.96 17.44 46.67 3.56
453 460 3.331478 CCAAATATTGGCAGCAAACCA 57.669 42.857 0.00 0.00 45.17 3.67
459 466 2.459060 TTGGCAGCAAACCAATCATG 57.541 45.000 0.00 0.00 42.23 3.07
460 467 0.037139 TGGCAGCAAACCAATCATGC 60.037 50.000 0.00 0.00 40.34 4.06
468 475 5.025986 GCAAACCAATCATGCTTTTTGAG 57.974 39.130 9.53 0.50 37.12 3.02
469 476 4.751098 GCAAACCAATCATGCTTTTTGAGA 59.249 37.500 9.53 0.00 37.12 3.27
489 499 5.070981 TGAGACCAAGATAAGGATCATCCAC 59.929 44.000 6.42 0.00 39.61 4.02
506 516 1.767759 CACCCTGTGGAAATGGATCC 58.232 55.000 4.20 4.20 40.10 3.36
516 526 3.643792 TGGAAATGGATCCCGTTGTTTTT 59.356 39.130 9.90 0.00 38.82 1.94
548 560 3.498082 CTGAACACACATCACATGCATG 58.502 45.455 25.09 25.09 0.00 4.06
549 561 2.256174 GAACACACATCACATGCATGC 58.744 47.619 26.53 11.82 0.00 4.06
592 608 5.698741 TTGCTCAGGATCAGAGGAATAAA 57.301 39.130 14.47 0.00 38.32 1.40
600 616 7.453126 TCAGGATCAGAGGAATAAAGTCTATCC 59.547 40.741 0.00 0.00 0.00 2.59
669 696 1.071987 CTGGGACTGCACAAGAGCA 59.928 57.895 0.00 0.00 43.35 4.26
839 866 7.041635 TGCATTATAATCCCACTCACATTTG 57.958 36.000 0.00 0.00 0.00 2.32
843 870 8.562892 CATTATAATCCCACTCACATTTGTCTC 58.437 37.037 0.00 0.00 0.00 3.36
844 871 4.647564 AATCCCACTCACATTTGTCTCT 57.352 40.909 0.00 0.00 0.00 3.10
975 1007 6.054860 TGATCTTCCTTACTCCCTTTCTTG 57.945 41.667 0.00 0.00 0.00 3.02
984 1016 0.250727 TCCCTTTCTTGGTTGAGCGG 60.251 55.000 0.00 0.00 0.00 5.52
989 1021 0.034896 TTCTTGGTTGAGCGGGAGAC 59.965 55.000 0.00 0.00 0.00 3.36
1035 1108 2.360350 AAGCTCATGGTGCCACCG 60.360 61.111 9.78 0.00 42.58 4.94
1106 1179 2.827921 CTGGTAAGCATTTGCCTCCTTT 59.172 45.455 0.00 0.00 43.38 3.11
1117 1190 1.271054 TGCCTCCTTTCTCAGTCTTGC 60.271 52.381 0.00 0.00 0.00 4.01
1131 1204 5.440610 TCAGTCTTGCCTTCTTTCTTTCTT 58.559 37.500 0.00 0.00 0.00 2.52
1133 1206 6.483640 TCAGTCTTGCCTTCTTTCTTTCTTAC 59.516 38.462 0.00 0.00 0.00 2.34
1134 1207 6.260936 CAGTCTTGCCTTCTTTCTTTCTTACA 59.739 38.462 0.00 0.00 0.00 2.41
1150 1223 7.877612 TCTTTCTTACAAATATGACACTCTGCA 59.122 33.333 0.00 0.00 0.00 4.41
1159 1232 1.552337 TGACACTCTGCATCCTTCCTC 59.448 52.381 0.00 0.00 0.00 3.71
1161 1234 0.907486 CACTCTGCATCCTTCCTCCA 59.093 55.000 0.00 0.00 0.00 3.86
1174 1251 7.120432 GCATCCTTCCTCCATGTTCTAATATTC 59.880 40.741 0.00 0.00 0.00 1.75
1202 1279 2.565391 TCCGAGACCAGTTTATTGCTGA 59.435 45.455 0.00 0.00 36.12 4.26
1226 1303 6.867519 TCTGGTATGTGAGTGAAAGGATTA 57.132 37.500 0.00 0.00 0.00 1.75
1227 1304 7.437713 TCTGGTATGTGAGTGAAAGGATTAT 57.562 36.000 0.00 0.00 0.00 1.28
1228 1305 8.547481 TCTGGTATGTGAGTGAAAGGATTATA 57.453 34.615 0.00 0.00 0.00 0.98
1229 1306 8.988060 TCTGGTATGTGAGTGAAAGGATTATAA 58.012 33.333 0.00 0.00 0.00 0.98
1230 1307 9.613428 CTGGTATGTGAGTGAAAGGATTATAAA 57.387 33.333 0.00 0.00 0.00 1.40
1282 1359 5.361427 TGAAAGGTTCATCGAACTAACACA 58.639 37.500 6.80 0.39 41.70 3.72
1364 1441 0.179020 CTGAGGGCAACAACAGGACA 60.179 55.000 0.00 0.00 37.53 4.02
1528 1605 1.136147 GCTGCTTCAGGATGTTGCG 59.864 57.895 0.00 0.00 37.97 4.85
1531 1608 1.300971 TGCTTCAGGATGTTGCGAGC 61.301 55.000 0.00 0.00 37.97 5.03
1546 1623 1.200483 CGAGCGATGCAACGAGTAAT 58.800 50.000 21.39 0.00 34.12 1.89
1547 1624 2.381589 CGAGCGATGCAACGAGTAATA 58.618 47.619 21.39 0.00 34.12 0.98
1549 1626 3.360765 CGAGCGATGCAACGAGTAATAAC 60.361 47.826 21.39 0.00 34.12 1.89
1550 1627 3.782046 AGCGATGCAACGAGTAATAACT 58.218 40.909 21.39 1.74 39.21 2.24
1551 1628 4.928601 AGCGATGCAACGAGTAATAACTA 58.071 39.130 21.39 0.00 35.56 2.24
1552 1629 5.345702 AGCGATGCAACGAGTAATAACTAA 58.654 37.500 21.39 0.00 35.56 2.24
1585 1662 5.904941 TCAAAGTGTTGATGTGCATTTTCT 58.095 33.333 0.00 0.00 38.88 2.52
1591 1668 6.817641 AGTGTTGATGTGCATTTTCTCAAAAA 59.182 30.769 0.00 0.00 38.66 1.94
1642 1721 5.300792 ACCGCAACAAATTTCCTTCTCTAAA 59.699 36.000 0.00 0.00 0.00 1.85
1682 1764 7.157347 CAGTTGCAAGCTATATAATCTGAGGA 58.843 38.462 0.00 0.00 0.00 3.71
1728 1810 9.981460 AACCTGAGTTTAATTCCTAGAATTGAT 57.019 29.630 11.82 0.00 29.61 2.57
1745 1827 0.109342 GATAGGTGATGCACAGGGGG 59.891 60.000 0.00 0.00 35.86 5.40
1781 1863 9.575868 TTTATTAAGGATCAAGTTTGGTGTGTA 57.424 29.630 0.00 0.00 0.00 2.90
1850 2207 6.566079 ATCTGAGGACCATGTTTATCTTGA 57.434 37.500 0.00 0.00 0.00 3.02
1871 2228 8.271458 TCTTGATACTCATACTAAAAATGGCCA 58.729 33.333 8.56 8.56 0.00 5.36
1880 2237 7.670979 TCATACTAAAAATGGCCATATGCATCT 59.329 33.333 21.15 0.00 43.89 2.90
1978 2340 2.258013 GCGGTTGTGCAGCCTAACA 61.258 57.895 10.11 0.00 32.01 2.41
1980 2342 0.881118 CGGTTGTGCAGCCTAACAAT 59.119 50.000 10.11 0.00 38.47 2.71
1982 2344 1.885887 GGTTGTGCAGCCTAACAATCA 59.114 47.619 10.11 0.00 37.36 2.57
2145 2510 5.043737 TGGTACTCATACTAAAATGGCCC 57.956 43.478 0.00 0.00 0.00 5.80
2155 2520 2.781403 AAAATGGCCCTATGCATCCT 57.219 45.000 0.19 0.00 43.89 3.24
2160 2525 1.699634 TGGCCCTATGCATCCTTAGTC 59.300 52.381 0.19 0.00 43.89 2.59
2168 2533 0.108138 GCATCCTTAGTCGGTGCAGT 60.108 55.000 0.00 0.00 33.87 4.40
2179 2544 4.966787 GTGCAGTGGCCGGGGAAA 62.967 66.667 2.18 0.00 40.13 3.13
2181 2546 2.679996 GCAGTGGCCGGGGAAATT 60.680 61.111 2.18 0.00 0.00 1.82
2207 2572 6.620877 ATTCTCCCCAAATTTTTAAGGTCC 57.379 37.500 0.00 0.00 0.00 4.46
2208 2573 5.348259 TCTCCCCAAATTTTTAAGGTCCT 57.652 39.130 0.00 0.00 0.00 3.85
2211 2576 5.468658 TCCCCAAATTTTTAAGGTCCTGAA 58.531 37.500 0.00 0.00 0.00 3.02
2212 2577 5.305902 TCCCCAAATTTTTAAGGTCCTGAAC 59.694 40.000 0.00 0.00 0.00 3.18
2221 2586 1.002011 GGTCCTGAACCTGAAGCCC 60.002 63.158 0.00 0.00 45.45 5.19
2223 2588 2.045926 CCTGAACCTGAAGCCCCG 60.046 66.667 0.00 0.00 0.00 5.73
2224 2589 2.750350 CTGAACCTGAAGCCCCGT 59.250 61.111 0.00 0.00 0.00 5.28
2225 2590 1.376037 CTGAACCTGAAGCCCCGTC 60.376 63.158 0.00 0.00 0.00 4.79
2226 2591 2.046217 GAACCTGAAGCCCCGTCC 60.046 66.667 0.00 0.00 0.00 4.79
2227 2592 3.623703 GAACCTGAAGCCCCGTCCC 62.624 68.421 0.00 0.00 0.00 4.46
2252 2617 2.487428 CCTCTCTGAGGCGACACG 59.513 66.667 4.59 0.00 43.29 4.49
2253 2618 2.487428 CTCTCTGAGGCGACACGG 59.513 66.667 4.59 0.00 0.00 4.94
2254 2619 3.057547 CTCTCTGAGGCGACACGGG 62.058 68.421 4.59 0.00 0.00 5.28
2255 2620 4.135153 CTCTGAGGCGACACGGGG 62.135 72.222 0.00 0.00 0.00 5.73
2259 2624 4.754667 GAGGCGACACGGGGGAAC 62.755 72.222 0.00 0.00 0.00 3.62
2298 2663 4.825679 CCTCCCTCCACCCTCCCC 62.826 77.778 0.00 0.00 0.00 4.81
2299 2664 4.825679 CTCCCTCCACCCTCCCCC 62.826 77.778 0.00 0.00 0.00 5.40
2336 2701 4.927782 AGAGCCACCGTTGCGCAA 62.928 61.111 21.02 21.02 0.00 4.85
2337 2702 3.959975 GAGCCACCGTTGCGCAAA 61.960 61.111 26.87 6.26 0.00 3.68
2338 2703 3.879351 GAGCCACCGTTGCGCAAAG 62.879 63.158 26.87 26.53 0.00 2.77
2349 2714 4.047059 CGCAAAGCCCAGGCAGTG 62.047 66.667 12.03 9.21 44.88 3.66
2350 2715 4.368543 GCAAAGCCCAGGCAGTGC 62.369 66.667 17.48 17.48 44.88 4.40
2382 2747 3.787001 CTTCTCCCCTGGCCCGAC 61.787 72.222 0.00 0.00 0.00 4.79
2392 2757 1.842381 CTGGCCCGACTTCCCTTCTT 61.842 60.000 0.00 0.00 0.00 2.52
2393 2758 1.078356 GGCCCGACTTCCCTTCTTC 60.078 63.158 0.00 0.00 0.00 2.87
2394 2759 1.078356 GCCCGACTTCCCTTCTTCC 60.078 63.158 0.00 0.00 0.00 3.46
2395 2760 1.554583 GCCCGACTTCCCTTCTTCCT 61.555 60.000 0.00 0.00 0.00 3.36
2396 2761 0.537653 CCCGACTTCCCTTCTTCCTC 59.462 60.000 0.00 0.00 0.00 3.71
2397 2762 0.173708 CCGACTTCCCTTCTTCCTCG 59.826 60.000 0.00 0.00 0.00 4.63
2398 2763 0.458716 CGACTTCCCTTCTTCCTCGC 60.459 60.000 0.00 0.00 0.00 5.03
2400 2765 1.153549 CTTCCCTTCTTCCTCGCGG 60.154 63.158 6.13 0.00 0.00 6.46
2408 2773 4.508128 TTCCTCGCGGCGGCTTAG 62.508 66.667 23.46 12.11 36.88 2.18
2413 2778 4.796231 CGCGGCGGCTTAGTCACT 62.796 66.667 15.84 0.00 36.88 3.41
2414 2779 2.886124 GCGGCGGCTTAGTCACTC 60.886 66.667 9.78 0.00 35.83 3.51
2415 2780 2.202756 CGGCGGCTTAGTCACTCC 60.203 66.667 7.61 0.00 0.00 3.85
2416 2781 2.187163 GGCGGCTTAGTCACTCCC 59.813 66.667 0.00 0.00 0.00 4.30
2417 2782 2.202756 GCGGCTTAGTCACTCCCG 60.203 66.667 7.02 7.02 41.72 5.14
2418 2783 2.494918 CGGCTTAGTCACTCCCGG 59.505 66.667 0.00 0.00 35.54 5.73
2419 2784 2.348888 CGGCTTAGTCACTCCCGGT 61.349 63.158 0.00 0.00 35.54 5.28
2420 2785 1.218316 GGCTTAGTCACTCCCGGTG 59.782 63.158 0.00 0.00 46.60 4.94
2421 2786 1.218316 GCTTAGTCACTCCCGGTGG 59.782 63.158 0.00 0.00 45.38 4.61
2422 2787 1.898154 CTTAGTCACTCCCGGTGGG 59.102 63.158 0.00 0.00 45.38 4.61
2423 2788 2.240162 CTTAGTCACTCCCGGTGGGC 62.240 65.000 0.00 0.00 43.94 5.36
2424 2789 2.741878 TTAGTCACTCCCGGTGGGCT 62.742 60.000 0.00 0.00 43.94 5.19
2425 2790 2.741878 TAGTCACTCCCGGTGGGCTT 62.742 60.000 0.00 0.00 43.94 4.35
2426 2791 3.636231 TCACTCCCGGTGGGCTTG 61.636 66.667 0.00 0.00 43.94 4.01
2427 2792 4.722700 CACTCCCGGTGGGCTTGG 62.723 72.222 0.00 0.00 43.94 3.61
2429 2794 4.722700 CTCCCGGTGGGCTTGGTG 62.723 72.222 0.00 0.00 43.94 4.17
2478 2843 3.744559 GCTTTGCGACAGGTTGGA 58.255 55.556 0.00 0.00 0.00 3.53
2482 2847 3.842925 TTGCGACAGGTTGGAGGGC 62.843 63.158 0.00 0.00 0.00 5.19
2485 2850 1.672356 CGACAGGTTGGAGGGCTTG 60.672 63.158 0.00 0.00 0.00 4.01
2499 2864 2.347490 CTTGTCCCCGTCTGGTGG 59.653 66.667 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.665972 TCTTTCAAATTTGCGGGCGC 60.666 50.000 13.54 0.00 42.35 6.53
10 11 1.777101 TTCTTTCAAATTTGCGGGCG 58.223 45.000 13.54 0.67 0.00 6.13
11 12 3.130633 ACTTTCTTTCAAATTTGCGGGC 58.869 40.909 13.54 0.00 0.00 6.13
12 13 4.808364 TGAACTTTCTTTCAAATTTGCGGG 59.192 37.500 13.54 5.68 32.42 6.13
13 14 5.964887 TGAACTTTCTTTCAAATTTGCGG 57.035 34.783 13.54 6.01 32.42 5.69
55 56 2.119495 AGGAACCAGTGACTGTCTTGT 58.881 47.619 12.15 0.00 0.00 3.16
197 198 4.964897 TCTTCATGGGCATCTTCTCTAGAA 59.035 41.667 0.00 0.00 36.22 2.10
211 212 2.019249 ACGCACATCATTCTTCATGGG 58.981 47.619 0.00 0.00 33.07 4.00
241 242 5.185454 TCTAAGTGCTAATGTGAATGGTGG 58.815 41.667 0.00 0.00 0.00 4.61
259 266 6.183360 TGGCATCAAACCAATTATGCTCTAAG 60.183 38.462 8.17 0.00 43.33 2.18
266 273 9.991388 CTTATTTTTGGCATCAAACCAATTATG 57.009 29.630 0.00 0.00 46.25 1.90
267 274 8.676401 GCTTATTTTTGGCATCAAACCAATTAT 58.324 29.630 0.00 0.00 46.25 1.28
268 275 7.663081 TGCTTATTTTTGGCATCAAACCAATTA 59.337 29.630 0.00 0.00 46.25 1.40
269 276 6.489361 TGCTTATTTTTGGCATCAAACCAATT 59.511 30.769 0.00 0.00 46.25 2.32
270 277 6.002704 TGCTTATTTTTGGCATCAAACCAAT 58.997 32.000 0.00 0.00 46.25 3.16
271 278 5.371526 TGCTTATTTTTGGCATCAAACCAA 58.628 33.333 0.00 0.00 45.37 3.67
272 279 4.965814 TGCTTATTTTTGGCATCAAACCA 58.034 34.783 0.00 0.00 41.97 3.67
273 280 5.674318 GCATGCTTATTTTTGGCATCAAACC 60.674 40.000 11.37 0.00 43.62 3.27
274 281 5.326292 GCATGCTTATTTTTGGCATCAAAC 58.674 37.500 11.37 0.00 43.62 2.93
275 282 4.395542 GGCATGCTTATTTTTGGCATCAAA 59.604 37.500 18.92 0.00 43.62 2.69
276 283 3.940221 GGCATGCTTATTTTTGGCATCAA 59.060 39.130 18.92 0.00 43.62 2.57
277 284 3.055312 TGGCATGCTTATTTTTGGCATCA 60.055 39.130 18.92 0.00 43.62 3.07
278 285 3.533547 TGGCATGCTTATTTTTGGCATC 58.466 40.909 18.92 0.00 43.62 3.91
279 286 3.630892 TGGCATGCTTATTTTTGGCAT 57.369 38.095 18.92 0.00 45.91 4.40
280 287 3.413846 TTGGCATGCTTATTTTTGGCA 57.586 38.095 18.92 0.00 40.32 4.92
281 288 3.690628 ACATTGGCATGCTTATTTTTGGC 59.309 39.130 18.92 0.00 33.05 4.52
282 289 5.883503 AACATTGGCATGCTTATTTTTGG 57.116 34.783 18.92 2.09 33.05 3.28
283 290 6.797995 GTCAAACATTGGCATGCTTATTTTTG 59.202 34.615 23.33 23.33 34.79 2.44
284 291 6.485984 TGTCAAACATTGGCATGCTTATTTTT 59.514 30.769 18.92 12.95 40.96 1.94
285 292 5.996513 TGTCAAACATTGGCATGCTTATTTT 59.003 32.000 18.92 7.77 40.96 1.82
286 293 5.549347 TGTCAAACATTGGCATGCTTATTT 58.451 33.333 18.92 8.64 40.96 1.40
287 294 5.149973 TGTCAAACATTGGCATGCTTATT 57.850 34.783 18.92 2.63 40.96 1.40
288 295 4.221262 ACTGTCAAACATTGGCATGCTTAT 59.779 37.500 18.92 8.43 45.37 1.73
289 296 3.573538 ACTGTCAAACATTGGCATGCTTA 59.426 39.130 18.92 6.18 45.37 3.09
290 297 2.366266 ACTGTCAAACATTGGCATGCTT 59.634 40.909 18.92 0.00 45.37 3.91
291 298 1.965643 ACTGTCAAACATTGGCATGCT 59.034 42.857 18.92 0.00 45.37 3.79
292 299 2.063266 CACTGTCAAACATTGGCATGC 58.937 47.619 9.90 9.90 45.37 4.06
293 300 3.054166 CACACTGTCAAACATTGGCATG 58.946 45.455 0.00 2.62 45.37 4.06
294 301 2.546373 GCACACTGTCAAACATTGGCAT 60.546 45.455 0.00 0.00 45.37 4.40
295 302 1.202394 GCACACTGTCAAACATTGGCA 60.202 47.619 0.00 0.00 44.14 4.92
296 303 1.490621 GCACACTGTCAAACATTGGC 58.509 50.000 3.05 0.00 33.65 4.52
297 304 1.408340 TGGCACACTGTCAAACATTGG 59.592 47.619 3.05 0.00 33.65 3.16
298 305 2.867287 TGGCACACTGTCAAACATTG 57.133 45.000 0.00 0.00 35.25 2.82
299 306 3.883830 TTTGGCACACTGTCAAACATT 57.116 38.095 0.00 0.00 45.74 2.71
304 311 3.365868 GCGAATATTTGGCACACTGTCAA 60.366 43.478 4.84 0.00 40.62 3.18
305 312 2.161410 GCGAATATTTGGCACACTGTCA 59.839 45.455 4.84 0.00 39.29 3.58
306 313 2.420022 AGCGAATATTTGGCACACTGTC 59.580 45.455 13.01 0.00 39.29 3.51
307 314 2.436417 AGCGAATATTTGGCACACTGT 58.564 42.857 13.01 0.00 39.29 3.55
308 315 3.623060 AGTAGCGAATATTTGGCACACTG 59.377 43.478 13.01 0.00 39.29 3.66
309 316 3.873910 AGTAGCGAATATTTGGCACACT 58.126 40.909 13.01 11.86 39.29 3.55
310 317 4.809426 AGTAGTAGCGAATATTTGGCACAC 59.191 41.667 13.01 10.32 39.29 3.82
311 318 5.018539 AGTAGTAGCGAATATTTGGCACA 57.981 39.130 13.01 0.00 36.79 4.57
312 319 5.522460 TCAAGTAGTAGCGAATATTTGGCAC 59.478 40.000 9.03 9.53 36.79 5.01
313 320 5.666462 TCAAGTAGTAGCGAATATTTGGCA 58.334 37.500 9.03 0.00 36.79 4.92
314 321 6.787085 ATCAAGTAGTAGCGAATATTTGGC 57.213 37.500 9.03 4.77 34.30 4.52
315 322 8.365399 TCAATCAAGTAGTAGCGAATATTTGG 57.635 34.615 9.03 0.00 0.00 3.28
318 325 9.209175 GGAATCAATCAAGTAGTAGCGAATATT 57.791 33.333 0.00 0.00 0.00 1.28
319 326 7.819900 GGGAATCAATCAAGTAGTAGCGAATAT 59.180 37.037 0.00 0.00 0.00 1.28
320 327 7.152645 GGGAATCAATCAAGTAGTAGCGAATA 58.847 38.462 0.00 0.00 0.00 1.75
321 328 5.992217 GGGAATCAATCAAGTAGTAGCGAAT 59.008 40.000 0.00 0.00 0.00 3.34
322 329 5.357257 GGGAATCAATCAAGTAGTAGCGAA 58.643 41.667 0.00 0.00 0.00 4.70
323 330 4.499188 CGGGAATCAATCAAGTAGTAGCGA 60.499 45.833 0.00 0.00 0.00 4.93
324 331 3.736252 CGGGAATCAATCAAGTAGTAGCG 59.264 47.826 0.00 0.00 0.00 4.26
325 332 4.945246 TCGGGAATCAATCAAGTAGTAGC 58.055 43.478 0.00 0.00 0.00 3.58
326 333 6.150396 ACTCGGGAATCAATCAAGTAGTAG 57.850 41.667 0.00 0.00 0.00 2.57
327 334 6.070995 ACAACTCGGGAATCAATCAAGTAGTA 60.071 38.462 0.00 0.00 0.00 1.82
328 335 5.178797 CAACTCGGGAATCAATCAAGTAGT 58.821 41.667 0.00 0.00 0.00 2.73
329 336 5.178797 ACAACTCGGGAATCAATCAAGTAG 58.821 41.667 0.00 0.00 0.00 2.57
330 337 5.046591 AGACAACTCGGGAATCAATCAAGTA 60.047 40.000 0.00 0.00 0.00 2.24
331 338 4.003648 GACAACTCGGGAATCAATCAAGT 58.996 43.478 0.00 0.00 0.00 3.16
332 339 4.256920 AGACAACTCGGGAATCAATCAAG 58.743 43.478 0.00 0.00 0.00 3.02
333 340 4.286297 AGACAACTCGGGAATCAATCAA 57.714 40.909 0.00 0.00 0.00 2.57
334 341 3.981071 AGACAACTCGGGAATCAATCA 57.019 42.857 0.00 0.00 0.00 2.57
335 342 4.003648 ACAAGACAACTCGGGAATCAATC 58.996 43.478 0.00 0.00 0.00 2.67
336 343 4.003648 GACAAGACAACTCGGGAATCAAT 58.996 43.478 0.00 0.00 0.00 2.57
337 344 3.071023 AGACAAGACAACTCGGGAATCAA 59.929 43.478 0.00 0.00 0.00 2.57
338 345 2.632996 AGACAAGACAACTCGGGAATCA 59.367 45.455 0.00 0.00 0.00 2.57
339 346 3.320673 AGACAAGACAACTCGGGAATC 57.679 47.619 0.00 0.00 0.00 2.52
340 347 4.712337 AGATAGACAAGACAACTCGGGAAT 59.288 41.667 0.00 0.00 0.00 3.01
341 348 4.087182 AGATAGACAAGACAACTCGGGAA 58.913 43.478 0.00 0.00 0.00 3.97
342 349 3.695060 GAGATAGACAAGACAACTCGGGA 59.305 47.826 0.00 0.00 0.00 5.14
343 350 3.444034 TGAGATAGACAAGACAACTCGGG 59.556 47.826 0.00 0.00 0.00 5.14
344 351 4.082733 TGTGAGATAGACAAGACAACTCGG 60.083 45.833 0.00 0.00 0.00 4.63
345 352 5.048153 TGTGAGATAGACAAGACAACTCG 57.952 43.478 0.00 0.00 0.00 4.18
346 353 8.988064 TTTATGTGAGATAGACAAGACAACTC 57.012 34.615 0.00 0.00 0.00 3.01
347 354 8.589338 ACTTTATGTGAGATAGACAAGACAACT 58.411 33.333 0.00 0.00 0.00 3.16
348 355 8.764524 ACTTTATGTGAGATAGACAAGACAAC 57.235 34.615 0.00 0.00 0.00 3.32
349 356 9.208022 CAACTTTATGTGAGATAGACAAGACAA 57.792 33.333 0.00 0.00 0.00 3.18
350 357 7.331934 GCAACTTTATGTGAGATAGACAAGACA 59.668 37.037 0.00 0.00 0.00 3.41
351 358 7.547370 AGCAACTTTATGTGAGATAGACAAGAC 59.453 37.037 0.00 0.00 0.00 3.01
352 359 7.615403 AGCAACTTTATGTGAGATAGACAAGA 58.385 34.615 0.00 0.00 0.00 3.02
353 360 7.840342 AGCAACTTTATGTGAGATAGACAAG 57.160 36.000 0.00 0.00 0.00 3.16
354 361 9.890629 ATTAGCAACTTTATGTGAGATAGACAA 57.109 29.630 0.00 0.00 0.00 3.18
361 368 8.405531 GCCAAATATTAGCAACTTTATGTGAGA 58.594 33.333 5.70 0.00 0.00 3.27
362 369 8.190122 TGCCAAATATTAGCAACTTTATGTGAG 58.810 33.333 9.92 0.00 32.56 3.51
363 370 8.060931 TGCCAAATATTAGCAACTTTATGTGA 57.939 30.769 9.92 0.00 32.56 3.58
364 371 8.700722 TTGCCAAATATTAGCAACTTTATGTG 57.299 30.769 17.45 0.00 41.35 3.21
365 372 7.492344 GCTTGCCAAATATTAGCAACTTTATGT 59.508 33.333 17.45 0.00 41.35 2.29
366 373 7.042523 GGCTTGCCAAATATTAGCAACTTTATG 60.043 37.037 17.45 10.58 41.35 1.90
367 374 6.986231 GGCTTGCCAAATATTAGCAACTTTAT 59.014 34.615 17.45 0.00 41.35 1.40
368 375 6.154363 AGGCTTGCCAAATATTAGCAACTTTA 59.846 34.615 17.45 2.90 41.35 1.85
369 376 5.046376 AGGCTTGCCAAATATTAGCAACTTT 60.046 36.000 17.45 7.01 41.35 2.66
370 377 4.467438 AGGCTTGCCAAATATTAGCAACTT 59.533 37.500 17.45 10.73 41.35 2.66
371 378 4.026052 AGGCTTGCCAAATATTAGCAACT 58.974 39.130 17.45 12.93 41.35 3.16
372 379 4.391405 AGGCTTGCCAAATATTAGCAAC 57.609 40.909 17.45 14.52 41.35 4.17
373 380 4.382901 CCAAGGCTTGCCAAATATTAGCAA 60.383 41.667 21.77 19.27 43.83 3.91
374 381 3.132646 CCAAGGCTTGCCAAATATTAGCA 59.867 43.478 21.77 8.59 33.60 3.49
375 382 3.132824 ACCAAGGCTTGCCAAATATTAGC 59.867 43.478 21.77 3.92 0.00 3.09
376 383 6.655078 ATACCAAGGCTTGCCAAATATTAG 57.345 37.500 21.77 6.50 0.00 1.73
377 384 6.685116 GCAATACCAAGGCTTGCCAAATATTA 60.685 38.462 21.77 2.83 39.42 0.98
378 385 5.673514 CAATACCAAGGCTTGCCAAATATT 58.326 37.500 21.77 14.71 0.00 1.28
379 386 4.443315 GCAATACCAAGGCTTGCCAAATAT 60.443 41.667 21.77 10.20 39.42 1.28
380 387 3.118811 GCAATACCAAGGCTTGCCAAATA 60.119 43.478 21.77 8.46 39.42 1.40
381 388 2.355007 GCAATACCAAGGCTTGCCAAAT 60.355 45.455 21.77 8.58 39.42 2.32
382 389 1.001860 GCAATACCAAGGCTTGCCAAA 59.998 47.619 21.77 6.61 39.42 3.28
383 390 0.607620 GCAATACCAAGGCTTGCCAA 59.392 50.000 21.77 9.09 39.42 4.52
384 391 2.275880 GCAATACCAAGGCTTGCCA 58.724 52.632 21.77 11.28 39.42 4.92
440 447 5.381876 AAGCATGATTGGTTTGCTGCCAA 62.382 43.478 0.00 9.04 45.54 4.52
441 448 0.037139 GCATGATTGGTTTGCTGCCA 60.037 50.000 0.00 0.00 33.61 4.92
442 449 0.248289 AGCATGATTGGTTTGCTGCC 59.752 50.000 0.00 0.00 44.63 4.85
443 450 2.088950 AAGCATGATTGGTTTGCTGC 57.911 45.000 0.00 0.00 45.54 5.25
449 456 4.344679 TGGTCTCAAAAAGCATGATTGGTT 59.655 37.500 0.00 0.00 45.16 3.67
450 457 3.896888 TGGTCTCAAAAAGCATGATTGGT 59.103 39.130 0.00 0.00 34.30 3.67
451 458 4.524316 TGGTCTCAAAAAGCATGATTGG 57.476 40.909 0.00 0.00 0.00 3.16
452 459 5.775686 TCTTGGTCTCAAAAAGCATGATTG 58.224 37.500 0.00 0.00 31.77 2.67
453 460 6.600882 ATCTTGGTCTCAAAAAGCATGATT 57.399 33.333 0.00 0.00 36.30 2.57
454 461 7.147949 CCTTATCTTGGTCTCAAAAAGCATGAT 60.148 37.037 0.00 0.00 40.20 2.45
455 462 6.151648 CCTTATCTTGGTCTCAAAAAGCATGA 59.848 38.462 0.00 0.00 34.26 3.07
456 463 6.151648 TCCTTATCTTGGTCTCAAAAAGCATG 59.848 38.462 0.00 0.00 31.77 4.06
457 464 6.248433 TCCTTATCTTGGTCTCAAAAAGCAT 58.752 36.000 0.00 0.00 31.77 3.79
458 465 5.630121 TCCTTATCTTGGTCTCAAAAAGCA 58.370 37.500 0.00 0.00 31.77 3.91
459 466 6.375455 TGATCCTTATCTTGGTCTCAAAAAGC 59.625 38.462 0.00 0.00 32.93 3.51
460 467 7.928307 TGATCCTTATCTTGGTCTCAAAAAG 57.072 36.000 0.00 0.00 32.93 2.27
461 468 7.557719 GGATGATCCTTATCTTGGTCTCAAAAA 59.442 37.037 3.71 0.00 32.53 1.94
462 469 7.056635 GGATGATCCTTATCTTGGTCTCAAAA 58.943 38.462 3.71 0.00 32.53 2.44
463 470 6.158520 TGGATGATCCTTATCTTGGTCTCAAA 59.841 38.462 13.44 0.00 37.46 2.69
464 471 5.667172 TGGATGATCCTTATCTTGGTCTCAA 59.333 40.000 13.44 0.00 37.46 3.02
465 472 5.070981 GTGGATGATCCTTATCTTGGTCTCA 59.929 44.000 13.44 0.00 37.46 3.27
466 473 5.512232 GGTGGATGATCCTTATCTTGGTCTC 60.512 48.000 13.44 0.00 37.46 3.36
467 474 4.349342 GGTGGATGATCCTTATCTTGGTCT 59.651 45.833 13.44 0.00 37.46 3.85
468 475 4.505742 GGGTGGATGATCCTTATCTTGGTC 60.506 50.000 13.44 0.00 37.46 4.02
469 476 3.395941 GGGTGGATGATCCTTATCTTGGT 59.604 47.826 13.44 0.00 37.46 3.67
489 499 0.466189 CGGGATCCATTTCCACAGGG 60.466 60.000 15.23 0.00 37.53 4.45
506 516 4.500477 CAGCAAAAGAGAGAAAAACAACGG 59.500 41.667 0.00 0.00 0.00 4.44
516 526 3.872696 TGTGTGTTCAGCAAAAGAGAGA 58.127 40.909 0.00 0.00 0.00 3.10
548 560 2.064762 GACACGCAGATGGATAGATGC 58.935 52.381 0.00 0.00 35.32 3.91
549 561 3.375782 TGACACGCAGATGGATAGATG 57.624 47.619 0.00 0.00 0.00 2.90
592 608 6.610830 CCCATAGATAGCAAGATGGATAGACT 59.389 42.308 7.85 0.00 41.23 3.24
600 616 4.011966 TGCACCCATAGATAGCAAGATG 57.988 45.455 0.00 0.00 31.42 2.90
669 696 5.285651 GTTACGATGCTCTGCTATCTTCTT 58.714 41.667 0.00 0.00 0.00 2.52
739 766 4.415150 ATGTGGTGGGAGGCTGCG 62.415 66.667 0.00 0.00 0.00 5.18
856 884 3.416253 CCATGGATGGCTGAGAAGG 57.584 57.895 5.56 0.00 41.75 3.46
975 1007 1.216710 CTCTGTCTCCCGCTCAACC 59.783 63.158 0.00 0.00 0.00 3.77
984 1016 1.408702 GCCATGTCTCTCTCTGTCTCC 59.591 57.143 0.00 0.00 0.00 3.71
989 1021 1.227205 GCCGCCATGTCTCTCTCTG 60.227 63.158 0.00 0.00 0.00 3.35
1035 1108 1.202568 AGAAACAAGCAAAAGCCTGCC 60.203 47.619 0.00 0.00 43.73 4.85
1038 1111 3.243535 GCAGTAGAAACAAGCAAAAGCCT 60.244 43.478 0.00 0.00 0.00 4.58
1039 1112 3.052745 GCAGTAGAAACAAGCAAAAGCC 58.947 45.455 0.00 0.00 0.00 4.35
1040 1113 3.969899 AGCAGTAGAAACAAGCAAAAGC 58.030 40.909 0.00 0.00 32.99 3.51
1041 1114 5.173774 TGAGCAGTAGAAACAAGCAAAAG 57.826 39.130 0.00 0.00 32.99 2.27
1042 1115 5.522456 CATGAGCAGTAGAAACAAGCAAAA 58.478 37.500 0.00 0.00 32.99 2.44
1043 1116 4.557296 GCATGAGCAGTAGAAACAAGCAAA 60.557 41.667 0.00 0.00 41.58 3.68
1044 1117 3.058016 GCATGAGCAGTAGAAACAAGCAA 60.058 43.478 0.00 0.00 41.58 3.91
1051 1124 1.350684 TGGTGGCATGAGCAGTAGAAA 59.649 47.619 0.00 0.00 44.61 2.52
1053 1126 0.250234 GTGGTGGCATGAGCAGTAGA 59.750 55.000 0.00 0.00 44.61 2.59
1056 1129 1.002868 GAGTGGTGGCATGAGCAGT 60.003 57.895 0.00 0.00 44.61 4.40
1106 1179 4.696479 AAGAAAGAAGGCAAGACTGAGA 57.304 40.909 0.00 0.00 0.00 3.27
1131 1204 6.239217 AGGATGCAGAGTGTCATATTTGTA 57.761 37.500 0.00 0.00 0.00 2.41
1133 1206 5.008415 GGAAGGATGCAGAGTGTCATATTTG 59.992 44.000 0.00 0.00 0.00 2.32
1134 1207 5.104193 AGGAAGGATGCAGAGTGTCATATTT 60.104 40.000 0.00 0.00 0.00 1.40
1150 1223 8.517323 AGAATATTAGAACATGGAGGAAGGAT 57.483 34.615 0.00 0.00 0.00 3.24
1159 1232 9.109393 TCGGAAAGAAAGAATATTAGAACATGG 57.891 33.333 0.00 0.00 0.00 3.66
1174 1251 6.603095 CAATAAACTGGTCTCGGAAAGAAAG 58.397 40.000 0.00 0.00 35.21 2.62
1183 1260 4.785669 GATCAGCAATAAACTGGTCTCG 57.214 45.455 0.00 0.00 41.24 4.04
1202 1279 5.965033 ATCCTTTCACTCACATACCAGAT 57.035 39.130 0.00 0.00 0.00 2.90
1234 1311 9.316730 CAACTATTTTGGCATGCAGTTTATTAT 57.683 29.630 21.36 4.08 0.00 1.28
1251 1328 8.166422 AGTTCGATGAACCTTTCAACTATTTT 57.834 30.769 6.09 0.00 42.85 1.82
1364 1441 1.744368 CTTGCTCAGCTCCGTGCAT 60.744 57.895 0.00 0.00 45.94 3.96
1528 1605 3.797256 AGTTATTACTCGTTGCATCGCTC 59.203 43.478 12.30 0.00 0.00 5.03
1531 1608 9.177304 TCTTATTAGTTATTACTCGTTGCATCG 57.823 33.333 10.93 10.93 35.78 3.84
1547 1624 9.013229 TCAACACTTTGATGCATCTTATTAGTT 57.987 29.630 26.32 19.06 36.79 2.24
1597 1674 1.024271 ACAACTTGCGCATCAACACT 58.976 45.000 12.75 0.00 0.00 3.55
1598 1675 2.679355 TACAACTTGCGCATCAACAC 57.321 45.000 12.75 0.00 0.00 3.32
1599 1676 2.287308 GGTTACAACTTGCGCATCAACA 60.287 45.455 12.75 0.00 0.00 3.33
1702 1784 9.981460 ATCAATTCTAGGAATTAAACTCAGGTT 57.019 29.630 5.37 0.00 37.24 3.50
1712 1794 8.659527 TGCATCACCTATCAATTCTAGGAATTA 58.340 33.333 14.77 1.73 38.44 1.40
1728 1810 0.844661 AACCCCCTGTGCATCACCTA 60.845 55.000 0.00 0.00 32.73 3.08
1745 1827 8.758829 ACTTGATCCTTAATAAATGGGGAAAAC 58.241 33.333 0.00 0.00 0.00 2.43
1820 2176 6.484364 AAACATGGTCCTCAGATTGTTTTT 57.516 33.333 0.00 0.00 32.83 1.94
1825 2181 6.825213 TCAAGATAAACATGGTCCTCAGATTG 59.175 38.462 0.00 0.00 0.00 2.67
1850 2207 8.960591 GCATATGGCCATTTTTAGTATGAGTAT 58.039 33.333 26.37 2.43 36.11 2.12
1871 2228 4.346127 TCTGCACCAACTAGAGATGCATAT 59.654 41.667 8.97 0.00 44.73 1.78
1880 2237 1.888436 CGGCCTCTGCACCAACTAGA 61.888 60.000 0.00 0.00 40.13 2.43
1978 2340 9.171877 GTCAATTCTAGGAATTGAACTCTGATT 57.828 33.333 26.66 0.00 45.06 2.57
1980 2342 7.679783 TGTCAATTCTAGGAATTGAACTCTGA 58.320 34.615 26.66 9.63 45.06 3.27
1982 2344 7.108847 CCTGTCAATTCTAGGAATTGAACTCT 58.891 38.462 26.66 0.00 45.06 3.24
2102 2465 9.654663 GTACCAAGATAAATATGGTCCTCATAC 57.345 37.037 0.00 0.00 43.90 2.39
2145 2510 2.224042 TGCACCGACTAAGGATGCATAG 60.224 50.000 0.00 0.00 41.18 2.23
2155 2520 2.345991 GGCCACTGCACCGACTAA 59.654 61.111 0.00 0.00 40.13 2.24
2168 2533 3.028130 GAGAATTTAATTTCCCCGGCCA 58.972 45.455 2.24 0.00 0.00 5.36
2181 2546 8.598916 GGACCTTAAAAATTTGGGGAGAATTTA 58.401 33.333 0.00 0.00 36.09 1.40
2206 2571 2.045926 CGGGGCTTCAGGTTCAGG 60.046 66.667 0.00 0.00 0.00 3.86
2207 2572 1.376037 GACGGGGCTTCAGGTTCAG 60.376 63.158 0.00 0.00 0.00 3.02
2208 2573 2.747686 GACGGGGCTTCAGGTTCA 59.252 61.111 0.00 0.00 0.00 3.18
2227 2592 3.522731 CTCAGAGAGGGACGCGGG 61.523 72.222 12.47 0.00 0.00 6.13
2228 2593 3.522731 CCTCAGAGAGGGACGCGG 61.523 72.222 12.47 0.00 45.43 6.46
2236 2601 2.487428 CCGTGTCGCCTCAGAGAG 59.513 66.667 0.00 0.00 0.00 3.20
2238 2603 4.135153 CCCCGTGTCGCCTCAGAG 62.135 72.222 0.00 0.00 0.00 3.35
2281 2646 4.825679 GGGGAGGGTGGAGGGAGG 62.826 77.778 0.00 0.00 0.00 4.30
2282 2647 4.825679 GGGGGAGGGTGGAGGGAG 62.826 77.778 0.00 0.00 0.00 4.30
2319 2684 4.927782 TTGCGCAACGGTGGCTCT 62.928 61.111 21.02 0.00 0.00 4.09
2320 2685 3.879351 CTTTGCGCAACGGTGGCTC 62.879 63.158 24.99 0.00 0.00 4.70
2321 2686 3.964875 CTTTGCGCAACGGTGGCT 61.965 61.111 24.99 0.00 0.00 4.75
2323 2688 4.999939 GGCTTTGCGCAACGGTGG 63.000 66.667 24.99 11.59 41.67 4.61
2324 2689 4.999939 GGGCTTTGCGCAACGGTG 63.000 66.667 24.99 14.15 41.23 4.94
2332 2697 4.047059 CACTGCCTGGGCTTTGCG 62.047 66.667 13.05 0.00 42.51 4.85
2333 2698 4.368543 GCACTGCCTGGGCTTTGC 62.369 66.667 17.43 17.43 43.01 3.68
2334 2699 3.688159 GGCACTGCCTGGGCTTTG 61.688 66.667 13.28 10.24 46.69 2.77
2365 2730 3.787001 GTCGGGCCAGGGGAGAAG 61.787 72.222 4.39 0.00 0.00 2.85
2366 2731 3.864983 AAGTCGGGCCAGGGGAGAA 62.865 63.158 4.39 0.00 0.00 2.87
2367 2732 4.332543 AAGTCGGGCCAGGGGAGA 62.333 66.667 4.39 0.00 0.00 3.71
2368 2733 3.787001 GAAGTCGGGCCAGGGGAG 61.787 72.222 4.39 0.00 0.00 4.30
2372 2737 3.330720 AAGGGAAGTCGGGCCAGG 61.331 66.667 4.39 0.00 0.00 4.45
2373 2738 1.842381 AAGAAGGGAAGTCGGGCCAG 61.842 60.000 4.39 0.00 0.00 4.85
2374 2739 1.838073 GAAGAAGGGAAGTCGGGCCA 61.838 60.000 4.39 0.00 0.00 5.36
2376 2741 1.078356 GGAAGAAGGGAAGTCGGGC 60.078 63.158 0.00 0.00 0.00 6.13
2382 2747 4.504132 CGCGAGGAAGAAGGGAAG 57.496 61.111 0.00 0.00 0.00 3.46
2394 2759 4.492160 TGACTAAGCCGCCGCGAG 62.492 66.667 15.93 5.96 41.18 5.03
2395 2760 4.789075 GTGACTAAGCCGCCGCGA 62.789 66.667 15.93 0.00 41.18 5.87
2396 2761 4.796231 AGTGACTAAGCCGCCGCG 62.796 66.667 5.59 5.59 41.18 6.46
2397 2762 2.886124 GAGTGACTAAGCCGCCGC 60.886 66.667 0.00 0.00 0.00 6.53
2398 2763 2.202756 GGAGTGACTAAGCCGCCG 60.203 66.667 0.00 0.00 0.00 6.46
2400 2765 2.202756 CGGGAGTGACTAAGCCGC 60.203 66.667 0.00 0.00 0.00 6.53
2402 2767 3.709567 ACCGGGAGTGACTAAGCC 58.290 61.111 6.32 0.00 0.00 4.35
2461 2826 1.576421 CTCCAACCTGTCGCAAAGC 59.424 57.895 0.00 0.00 0.00 3.51
2462 2827 1.237285 CCCTCCAACCTGTCGCAAAG 61.237 60.000 0.00 0.00 0.00 2.77
2463 2828 1.228124 CCCTCCAACCTGTCGCAAA 60.228 57.895 0.00 0.00 0.00 3.68
2464 2829 2.429930 CCCTCCAACCTGTCGCAA 59.570 61.111 0.00 0.00 0.00 4.85
2465 2830 4.329545 GCCCTCCAACCTGTCGCA 62.330 66.667 0.00 0.00 0.00 5.10
2466 2831 3.553095 AAGCCCTCCAACCTGTCGC 62.553 63.158 0.00 0.00 0.00 5.19
2467 2832 1.672356 CAAGCCCTCCAACCTGTCG 60.672 63.158 0.00 0.00 0.00 4.35
2468 2833 0.606673 GACAAGCCCTCCAACCTGTC 60.607 60.000 0.00 0.00 0.00 3.51
2469 2834 1.456287 GACAAGCCCTCCAACCTGT 59.544 57.895 0.00 0.00 0.00 4.00
2470 2835 1.303643 GGACAAGCCCTCCAACCTG 60.304 63.158 0.00 0.00 0.00 4.00
2471 2836 3.171348 GGACAAGCCCTCCAACCT 58.829 61.111 0.00 0.00 0.00 3.50
2482 2847 2.347490 CCACCAGACGGGGACAAG 59.653 66.667 0.00 0.00 38.36 3.16


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

AutoCloner maintained by Alex Coulton.