Multiple sequence alignment - TraesCS2A01G068000

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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 TraesCS2A01G068000 chr2A 100.000 4370 0 0 1 4370 30165882 30161513 0.000000e+00 8070
1 TraesCS2A01G068000 chr2A 84.858 3335 460 26 996 4311 30300995 30304303 0.000000e+00 3319
2 TraesCS2A01G068000 chr2A 84.620 3329 472 20 997 4312 30272083 30268782 0.000000e+00 3275
3 TraesCS2A01G068000 chr2A 84.248 3333 477 28 997 4312 30246833 30243532 0.000000e+00 3203
4 TraesCS2A01G068000 chr2A 84.128 3333 482 27 997 4312 30256436 30253134 0.000000e+00 3181
5 TraesCS2A01G068000 chr2A 91.076 706 48 11 604 1303 30212921 30212225 0.000000e+00 941
6 TraesCS2A01G068000 chr2A 78.932 337 44 18 449 763 22435577 22435908 2.060000e-48 204
7 TraesCS2A01G068000 chr2D 92.844 4290 277 17 44 4316 27955879 27960155 0.000000e+00 6194
8 TraesCS2A01G068000 chr2D 90.089 3814 312 39 598 4370 28002144 27998356 0.000000e+00 4889
9 TraesCS2A01G068000 chr2D 83.698 2196 306 27 2193 4368 28417361 28415198 0.000000e+00 2025
10 TraesCS2A01G068000 chr2D 85.152 1347 160 24 87 1407 28095565 28094233 0.000000e+00 1343
11 TraesCS2A01G068000 chr2D 88.557 201 22 1 4119 4319 27976408 27976209 4.370000e-60 243
12 TraesCS2A01G068000 chr2D 78.541 233 28 11 402 634 28005134 28004924 2.740000e-27 134
13 TraesCS2A01G068000 chr2B 90.892 3700 270 24 635 4319 45033459 45029812 0.000000e+00 4903
14 TraesCS2A01G068000 chr2B 87.739 4127 417 43 280 4370 44755401 44751328 0.000000e+00 4735
15 TraesCS2A01G068000 chr2B 93.715 2466 141 8 1863 4319 45135922 45133462 0.000000e+00 3683
16 TraesCS2A01G068000 chr2B 89.324 2735 285 7 956 3687 45542365 45545095 0.000000e+00 3426
17 TraesCS2A01G068000 chr2B 93.631 2041 91 6 2185 4191 45667347 45669382 0.000000e+00 3013
18 TraesCS2A01G068000 chr2B 88.324 1850 186 14 34 1860 45137800 45135958 0.000000e+00 2193
19 TraesCS2A01G068000 chr2B 85.529 2087 273 17 606 2682 45041694 45039627 0.000000e+00 2154
20 TraesCS2A01G068000 chr2B 89.090 1384 101 21 44 1407 45687852 45689205 0.000000e+00 1674
21 TraesCS2A01G068000 chr2B 83.151 1371 198 19 2948 4309 44926463 44927809 0.000000e+00 1221
22 TraesCS2A01G068000 chr2B 82.990 970 130 22 606 1561 45532978 45533926 0.000000e+00 845
23 TraesCS2A01G068000 chr1A 77.931 290 44 13 426 702 242072675 242072393 3.500000e-36 163


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 TraesCS2A01G068000 chr2A 30161513 30165882 4369 True 8070.0 8070 100.0000 1 4370 1 chr2A.!!$R1 4369
1 TraesCS2A01G068000 chr2A 30300995 30304303 3308 False 3319.0 3319 84.8580 996 4311 1 chr2A.!!$F2 3315
2 TraesCS2A01G068000 chr2A 30268782 30272083 3301 True 3275.0 3275 84.6200 997 4312 1 chr2A.!!$R5 3315
3 TraesCS2A01G068000 chr2A 30243532 30246833 3301 True 3203.0 3203 84.2480 997 4312 1 chr2A.!!$R3 3315
4 TraesCS2A01G068000 chr2A 30253134 30256436 3302 True 3181.0 3181 84.1280 997 4312 1 chr2A.!!$R4 3315
5 TraesCS2A01G068000 chr2A 30212225 30212921 696 True 941.0 941 91.0760 604 1303 1 chr2A.!!$R2 699
6 TraesCS2A01G068000 chr2D 27955879 27960155 4276 False 6194.0 6194 92.8440 44 4316 1 chr2D.!!$F1 4272
7 TraesCS2A01G068000 chr2D 27998356 28005134 6778 True 2511.5 4889 84.3150 402 4370 2 chr2D.!!$R4 3968
8 TraesCS2A01G068000 chr2D 28415198 28417361 2163 True 2025.0 2025 83.6980 2193 4368 1 chr2D.!!$R3 2175
9 TraesCS2A01G068000 chr2D 28094233 28095565 1332 True 1343.0 1343 85.1520 87 1407 1 chr2D.!!$R2 1320
10 TraesCS2A01G068000 chr2B 45029812 45033459 3647 True 4903.0 4903 90.8920 635 4319 1 chr2B.!!$R2 3684
11 TraesCS2A01G068000 chr2B 44751328 44755401 4073 True 4735.0 4735 87.7390 280 4370 1 chr2B.!!$R1 4090
12 TraesCS2A01G068000 chr2B 45542365 45545095 2730 False 3426.0 3426 89.3240 956 3687 1 chr2B.!!$F3 2731
13 TraesCS2A01G068000 chr2B 45667347 45669382 2035 False 3013.0 3013 93.6310 2185 4191 1 chr2B.!!$F4 2006
14 TraesCS2A01G068000 chr2B 45133462 45137800 4338 True 2938.0 3683 91.0195 34 4319 2 chr2B.!!$R4 4285
15 TraesCS2A01G068000 chr2B 45039627 45041694 2067 True 2154.0 2154 85.5290 606 2682 1 chr2B.!!$R3 2076
16 TraesCS2A01G068000 chr2B 45687852 45689205 1353 False 1674.0 1674 89.0900 44 1407 1 chr2B.!!$F5 1363
17 TraesCS2A01G068000 chr2B 44926463 44927809 1346 False 1221.0 1221 83.1510 2948 4309 1 chr2B.!!$F1 1361
18 TraesCS2A01G068000 chr2B 45532978 45533926 948 False 845.0 845 82.9900 606 1561 1 chr2B.!!$F2 955

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
946 3889 0.038166 AAGATCGCCCAAGCTCCAAA 59.962 50.000 0.0 0.0 36.60 3.28 F
1409 4371 0.313043 CTTGCCAGCAACAGTCTTGG 59.687 55.000 0.0 0.0 0.00 3.61 F
1714 4676 1.008327 TCTCTGGAAGCATACCTCCCA 59.992 52.381 0.0 0.0 0.00 4.37 F
2456 5453 0.995024 ATCCCTCCTTCAGTTGGTGG 59.005 55.000 0.0 0.0 37.82 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 5266 1.001158 GCCCGAAATTTGGTTTGACGA 60.001 47.619 0.00 0.0 0.0 4.20 R
2456 5453 1.135286 GCTTGCCCAGTTGAGTAATGC 60.135 52.381 0.00 0.0 0.0 3.56 R
2520 5517 1.348036 AGTCCCTTGCACTGACCTAAC 59.652 52.381 5.97 0.0 0.0 2.34 R
4045 7076 1.183030 TCCGCGACTCTTTCAGGGAA 61.183 55.000 8.23 0.0 0.0 3.97 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
25 26 3.453559 CGGAATCCAGCCGTTACTT 57.546 52.632 0.00 0.00 43.66 2.24
26 27 1.734163 CGGAATCCAGCCGTTACTTT 58.266 50.000 0.00 0.00 43.66 2.66
27 28 2.896168 CGGAATCCAGCCGTTACTTTA 58.104 47.619 0.00 0.00 43.66 1.85
28 29 3.264104 CGGAATCCAGCCGTTACTTTAA 58.736 45.455 0.00 0.00 43.66 1.52
29 30 3.308866 CGGAATCCAGCCGTTACTTTAAG 59.691 47.826 0.00 0.00 43.66 1.85
30 31 4.510571 GGAATCCAGCCGTTACTTTAAGA 58.489 43.478 0.00 0.00 0.00 2.10
31 32 5.123936 GGAATCCAGCCGTTACTTTAAGAT 58.876 41.667 0.00 0.00 0.00 2.40
32 33 5.007724 GGAATCCAGCCGTTACTTTAAGATG 59.992 44.000 0.00 0.00 0.00 2.90
276 294 4.220163 GGTGTGGAACTAGTGTAAGTAGCT 59.780 45.833 0.00 0.00 43.79 3.32
277 295 5.162075 GTGTGGAACTAGTGTAAGTAGCTG 58.838 45.833 0.00 0.00 43.79 4.24
278 296 4.174762 GTGGAACTAGTGTAAGTAGCTGC 58.825 47.826 0.00 0.00 43.79 5.25
279 297 3.119602 TGGAACTAGTGTAAGTAGCTGCG 60.120 47.826 0.00 0.00 43.79 5.18
280 298 2.563471 ACTAGTGTAAGTAGCTGCGC 57.437 50.000 0.00 0.00 43.79 6.09
281 299 1.134560 ACTAGTGTAAGTAGCTGCGCC 59.865 52.381 4.18 0.00 43.79 6.53
282 300 1.405821 CTAGTGTAAGTAGCTGCGCCT 59.594 52.381 4.18 0.00 32.26 5.52
283 301 0.608640 AGTGTAAGTAGCTGCGCCTT 59.391 50.000 4.18 2.57 0.00 4.35
284 302 0.721718 GTGTAAGTAGCTGCGCCTTG 59.278 55.000 4.18 0.00 0.00 3.61
285 303 0.320374 TGTAAGTAGCTGCGCCTTGT 59.680 50.000 4.18 0.00 0.00 3.16
286 304 1.546923 TGTAAGTAGCTGCGCCTTGTA 59.453 47.619 4.18 3.78 0.00 2.41
287 305 2.167693 TGTAAGTAGCTGCGCCTTGTAT 59.832 45.455 4.18 0.00 0.00 2.29
288 306 1.656652 AAGTAGCTGCGCCTTGTATG 58.343 50.000 4.18 0.00 0.00 2.39
289 307 0.824109 AGTAGCTGCGCCTTGTATGA 59.176 50.000 4.18 0.00 0.00 2.15
290 308 1.202463 AGTAGCTGCGCCTTGTATGAG 60.202 52.381 4.18 0.00 0.00 2.90
291 309 0.104855 TAGCTGCGCCTTGTATGAGG 59.895 55.000 4.18 0.00 39.93 3.86
292 310 1.450312 GCTGCGCCTTGTATGAGGT 60.450 57.895 4.18 0.00 39.11 3.85
293 311 0.179084 GCTGCGCCTTGTATGAGGTA 60.179 55.000 4.18 0.00 39.11 3.08
294 312 1.742411 GCTGCGCCTTGTATGAGGTAA 60.742 52.381 4.18 0.00 39.11 2.85
295 313 2.205074 CTGCGCCTTGTATGAGGTAAG 58.795 52.381 4.18 0.00 39.11 2.34
296 314 0.938008 GCGCCTTGTATGAGGTAAGC 59.062 55.000 0.00 0.00 39.11 3.09
297 315 1.583054 CGCCTTGTATGAGGTAAGCC 58.417 55.000 0.00 0.00 39.11 4.35
298 316 1.810412 CGCCTTGTATGAGGTAAGCCC 60.810 57.143 0.00 0.00 39.11 5.19
300 318 2.746472 GCCTTGTATGAGGTAAGCCCTG 60.746 54.545 0.00 0.00 46.51 4.45
301 319 2.565841 CTTGTATGAGGTAAGCCCTGC 58.434 52.381 0.00 0.00 46.51 4.85
302 320 1.578897 TGTATGAGGTAAGCCCTGCA 58.421 50.000 0.00 0.00 46.51 4.41
303 321 1.486310 TGTATGAGGTAAGCCCTGCAG 59.514 52.381 6.78 6.78 46.51 4.41
304 322 1.486726 GTATGAGGTAAGCCCTGCAGT 59.513 52.381 13.81 0.00 46.51 4.40
305 323 0.995024 ATGAGGTAAGCCCTGCAGTT 59.005 50.000 13.81 2.91 46.51 3.16
306 324 0.324943 TGAGGTAAGCCCTGCAGTTC 59.675 55.000 13.81 3.53 46.51 3.01
307 325 0.741221 GAGGTAAGCCCTGCAGTTCG 60.741 60.000 13.81 0.32 46.51 3.95
308 326 1.745489 GGTAAGCCCTGCAGTTCGG 60.745 63.158 13.81 8.10 0.00 4.30
309 327 1.003718 GTAAGCCCTGCAGTTCGGT 60.004 57.895 13.81 2.13 0.00 4.69
310 328 0.605589 GTAAGCCCTGCAGTTCGGTT 60.606 55.000 13.81 13.17 0.00 4.44
311 329 0.321298 TAAGCCCTGCAGTTCGGTTC 60.321 55.000 13.81 0.00 0.00 3.62
312 330 3.056328 GCCCTGCAGTTCGGTTCC 61.056 66.667 13.81 0.00 0.00 3.62
313 331 2.359975 CCCTGCAGTTCGGTTCCC 60.360 66.667 13.81 0.00 0.00 3.97
314 332 2.429930 CCTGCAGTTCGGTTCCCA 59.570 61.111 13.81 0.00 0.00 4.37
315 333 1.228124 CCTGCAGTTCGGTTCCCAA 60.228 57.895 13.81 0.00 0.00 4.12
316 334 0.609131 CCTGCAGTTCGGTTCCCAAT 60.609 55.000 13.81 0.00 0.00 3.16
317 335 1.247567 CTGCAGTTCGGTTCCCAATT 58.752 50.000 5.25 0.00 0.00 2.32
318 336 1.613437 CTGCAGTTCGGTTCCCAATTT 59.387 47.619 5.25 0.00 0.00 1.82
319 337 2.035632 TGCAGTTCGGTTCCCAATTTT 58.964 42.857 0.00 0.00 0.00 1.82
320 338 2.035321 TGCAGTTCGGTTCCCAATTTTC 59.965 45.455 0.00 0.00 0.00 2.29
321 339 2.609491 GCAGTTCGGTTCCCAATTTTCC 60.609 50.000 0.00 0.00 0.00 3.13
322 340 2.625790 CAGTTCGGTTCCCAATTTTCCA 59.374 45.455 0.00 0.00 0.00 3.53
323 341 3.258123 CAGTTCGGTTCCCAATTTTCCAT 59.742 43.478 0.00 0.00 0.00 3.41
324 342 3.258123 AGTTCGGTTCCCAATTTTCCATG 59.742 43.478 0.00 0.00 0.00 3.66
325 343 1.548269 TCGGTTCCCAATTTTCCATGC 59.452 47.619 0.00 0.00 0.00 4.06
326 344 1.550072 CGGTTCCCAATTTTCCATGCT 59.450 47.619 0.00 0.00 0.00 3.79
327 345 2.757868 CGGTTCCCAATTTTCCATGCTA 59.242 45.455 0.00 0.00 0.00 3.49
328 346 3.194542 CGGTTCCCAATTTTCCATGCTAA 59.805 43.478 0.00 0.00 0.00 3.09
329 347 4.322349 CGGTTCCCAATTTTCCATGCTAAA 60.322 41.667 0.00 0.00 0.00 1.85
330 348 5.626578 CGGTTCCCAATTTTCCATGCTAAAT 60.627 40.000 0.00 0.00 0.00 1.40
331 349 6.179756 GGTTCCCAATTTTCCATGCTAAATT 58.820 36.000 9.09 9.09 35.05 1.82
332 350 7.334858 GGTTCCCAATTTTCCATGCTAAATTA 58.665 34.615 12.71 0.67 33.46 1.40
333 351 7.495606 GGTTCCCAATTTTCCATGCTAAATTAG 59.504 37.037 12.71 0.00 33.46 1.73
334 352 7.969690 TCCCAATTTTCCATGCTAAATTAGA 57.030 32.000 3.88 10.76 33.46 2.10
335 353 8.551682 TCCCAATTTTCCATGCTAAATTAGAT 57.448 30.769 3.88 0.00 33.46 1.98
336 354 8.423349 TCCCAATTTTCCATGCTAAATTAGATG 58.577 33.333 3.88 5.13 33.46 2.90
337 355 8.423349 CCCAATTTTCCATGCTAAATTAGATGA 58.577 33.333 3.88 0.00 33.46 2.92
338 356 9.820725 CCAATTTTCCATGCTAAATTAGATGAA 57.179 29.630 3.88 0.00 33.46 2.57
344 362 8.400184 TCCATGCTAAATTAGATGAAATGAGG 57.600 34.615 3.88 0.00 0.00 3.86
345 363 8.000709 TCCATGCTAAATTAGATGAAATGAGGT 58.999 33.333 3.88 0.00 0.00 3.85
346 364 8.636213 CCATGCTAAATTAGATGAAATGAGGTT 58.364 33.333 3.88 0.00 0.00 3.50
356 374 6.987386 AGATGAAATGAGGTTATCTACTCGG 58.013 40.000 0.00 0.00 36.53 4.63
357 375 6.778069 AGATGAAATGAGGTTATCTACTCGGA 59.222 38.462 0.00 0.00 36.53 4.55
358 376 6.785337 TGAAATGAGGTTATCTACTCGGAA 57.215 37.500 0.00 0.00 36.53 4.30
359 377 7.361457 TGAAATGAGGTTATCTACTCGGAAT 57.639 36.000 0.00 0.00 36.53 3.01
360 378 7.792032 TGAAATGAGGTTATCTACTCGGAATT 58.208 34.615 0.00 0.00 36.53 2.17
361 379 7.926555 TGAAATGAGGTTATCTACTCGGAATTC 59.073 37.037 0.00 0.00 36.53 2.17
362 380 5.786264 TGAGGTTATCTACTCGGAATTCC 57.214 43.478 15.01 15.01 36.53 3.01
363 381 5.205821 TGAGGTTATCTACTCGGAATTCCA 58.794 41.667 24.09 10.39 36.53 3.53
364 382 5.839063 TGAGGTTATCTACTCGGAATTCCAT 59.161 40.000 24.09 11.12 36.53 3.41
365 383 6.326583 TGAGGTTATCTACTCGGAATTCCATT 59.673 38.462 24.09 9.70 36.53 3.16
366 384 6.525629 AGGTTATCTACTCGGAATTCCATTG 58.474 40.000 24.09 14.62 35.14 2.82
367 385 6.099845 AGGTTATCTACTCGGAATTCCATTGT 59.900 38.462 24.09 19.04 35.14 2.71
368 386 6.766467 GGTTATCTACTCGGAATTCCATTGTT 59.234 38.462 24.09 5.88 35.14 2.83
369 387 7.041984 GGTTATCTACTCGGAATTCCATTGTTC 60.042 40.741 24.09 4.52 35.14 3.18
370 388 4.766375 TCTACTCGGAATTCCATTGTTCC 58.234 43.478 24.09 0.00 40.37 3.62
371 389 3.433306 ACTCGGAATTCCATTGTTCCA 57.567 42.857 24.09 0.00 43.22 3.53
372 390 3.968265 ACTCGGAATTCCATTGTTCCAT 58.032 40.909 24.09 0.00 43.22 3.41
373 391 3.696051 ACTCGGAATTCCATTGTTCCATG 59.304 43.478 24.09 3.97 43.22 3.66
374 392 2.426738 TCGGAATTCCATTGTTCCATGC 59.573 45.455 24.09 0.00 43.22 4.06
375 393 2.428171 CGGAATTCCATTGTTCCATGCT 59.572 45.455 24.09 0.00 43.22 3.79
376 394 3.631686 CGGAATTCCATTGTTCCATGCTA 59.368 43.478 24.09 0.00 43.22 3.49
377 395 4.498009 CGGAATTCCATTGTTCCATGCTAC 60.498 45.833 24.09 0.00 43.22 3.58
378 396 4.498009 GGAATTCCATTGTTCCATGCTACG 60.498 45.833 20.04 0.00 42.72 3.51
379 397 2.779755 TCCATTGTTCCATGCTACGT 57.220 45.000 0.00 0.00 0.00 3.57
380 398 3.066291 TCCATTGTTCCATGCTACGTT 57.934 42.857 0.00 0.00 0.00 3.99
381 399 3.417101 TCCATTGTTCCATGCTACGTTT 58.583 40.909 0.00 0.00 0.00 3.60
382 400 4.580868 TCCATTGTTCCATGCTACGTTTA 58.419 39.130 0.00 0.00 0.00 2.01
383 401 4.393680 TCCATTGTTCCATGCTACGTTTAC 59.606 41.667 0.00 0.00 0.00 2.01
384 402 4.155099 CCATTGTTCCATGCTACGTTTACA 59.845 41.667 0.00 0.00 0.00 2.41
385 403 4.735662 TTGTTCCATGCTACGTTTACAC 57.264 40.909 0.00 0.00 0.00 2.90
386 404 3.729966 TGTTCCATGCTACGTTTACACA 58.270 40.909 0.00 0.00 0.00 3.72
387 405 4.320023 TGTTCCATGCTACGTTTACACAT 58.680 39.130 0.00 0.00 0.00 3.21
388 406 4.757657 TGTTCCATGCTACGTTTACACATT 59.242 37.500 0.00 0.00 0.00 2.71
389 407 5.106869 TGTTCCATGCTACGTTTACACATTC 60.107 40.000 0.00 0.00 0.00 2.67
390 408 4.570930 TCCATGCTACGTTTACACATTCA 58.429 39.130 0.00 0.00 0.00 2.57
391 409 4.629634 TCCATGCTACGTTTACACATTCAG 59.370 41.667 0.00 0.00 0.00 3.02
392 410 4.201812 CCATGCTACGTTTACACATTCAGG 60.202 45.833 0.00 0.00 0.00 3.86
393 411 3.997762 TGCTACGTTTACACATTCAGGT 58.002 40.909 0.00 0.00 0.00 4.00
394 412 3.991773 TGCTACGTTTACACATTCAGGTC 59.008 43.478 0.00 0.00 0.00 3.85
395 413 3.370061 GCTACGTTTACACATTCAGGTCC 59.630 47.826 0.00 0.00 0.00 4.46
396 414 3.478857 ACGTTTACACATTCAGGTCCA 57.521 42.857 0.00 0.00 0.00 4.02
397 415 3.811083 ACGTTTACACATTCAGGTCCAA 58.189 40.909 0.00 0.00 0.00 3.53
398 416 4.394729 ACGTTTACACATTCAGGTCCAAT 58.605 39.130 0.00 0.00 0.00 3.16
399 417 4.825085 ACGTTTACACATTCAGGTCCAATT 59.175 37.500 0.00 0.00 0.00 2.32
400 418 5.153513 CGTTTACACATTCAGGTCCAATTG 58.846 41.667 0.00 0.00 0.00 2.32
407 425 2.655090 TCAGGTCCAATTGTGAAGCA 57.345 45.000 4.43 0.00 0.00 3.91
412 430 4.218200 CAGGTCCAATTGTGAAGCATGTTA 59.782 41.667 4.43 0.00 0.00 2.41
416 434 3.922240 CCAATTGTGAAGCATGTTAGTGC 59.078 43.478 4.43 0.00 45.38 4.40
425 443 1.869503 CATGTTAGTGCAACGCGAAG 58.130 50.000 15.93 5.50 45.86 3.79
440 458 2.331194 GCGAAGTTGCAATGCAGAATT 58.669 42.857 8.31 5.47 40.61 2.17
441 459 2.343544 GCGAAGTTGCAATGCAGAATTC 59.656 45.455 8.31 12.89 40.61 2.17
446 3317 3.983344 AGTTGCAATGCAGAATTCGTTTC 59.017 39.130 8.31 0.00 40.61 2.78
538 3430 3.498774 AATCTCACAACTTCAGTGGCT 57.501 42.857 0.00 0.00 37.58 4.75
580 3472 3.961414 GTCGCCCCTTGGGGTTGA 61.961 66.667 24.38 19.20 44.57 3.18
582 3474 2.037208 CGCCCCTTGGGGTTGATT 59.963 61.111 24.38 0.00 44.57 2.57
602 3494 5.355071 TGATTATCCTGTCTGTTTGATGTGC 59.645 40.000 0.00 0.00 0.00 4.57
623 3515 4.798288 CCGCAGGTTGCAATCATG 57.202 55.556 13.22 10.45 45.36 3.07
624 3516 1.885157 CCGCAGGTTGCAATCATGT 59.115 52.632 13.22 0.00 45.36 3.21
625 3517 1.093972 CCGCAGGTTGCAATCATGTA 58.906 50.000 13.22 0.00 45.36 2.29
639 3536 5.802465 CAATCATGTAGTATGAGCCAGGAT 58.198 41.667 0.00 0.00 30.39 3.24
674 3572 2.548057 TCCTTGTGTCGCTGTCAAAATC 59.452 45.455 0.00 0.00 0.00 2.17
803 3712 9.503399 TTCATTCTTCTACTTTTCTTTACCCTC 57.497 33.333 0.00 0.00 0.00 4.30
814 3724 0.938713 TTTACCCTCGCAACACGTTG 59.061 50.000 5.53 5.53 44.19 4.10
946 3889 0.038166 AAGATCGCCCAAGCTCCAAA 59.962 50.000 0.00 0.00 36.60 3.28
985 3943 1.457346 CTGGTTCTTCCACATCCTGC 58.543 55.000 0.00 0.00 41.93 4.85
991 3951 1.074405 TCTTCCACATCCTGCAAGCTT 59.926 47.619 0.00 0.00 0.00 3.74
1015 3975 3.255969 ACATCATGCCCTCATTTTTGC 57.744 42.857 0.00 0.00 0.00 3.68
1094 4054 2.348591 CGCAAGAAAACAAGTCCGAGAC 60.349 50.000 0.00 0.00 43.02 3.36
1100 4060 4.039245 AGAAAACAAGTCCGAGACTGATCA 59.961 41.667 7.23 0.00 42.59 2.92
1245 4207 1.497161 CCCGGGTGGTCTCTCTTAAT 58.503 55.000 14.18 0.00 0.00 1.40
1246 4208 1.139058 CCCGGGTGGTCTCTCTTAATG 59.861 57.143 14.18 0.00 0.00 1.90
1325 4287 0.461870 TCATCGATGAACCTTGCCGG 60.462 55.000 25.44 0.00 33.08 6.13
1377 4339 2.963101 GTTGGGTAAGCTTCCAAACCTT 59.037 45.455 18.44 0.00 43.68 3.50
1409 4371 0.313043 CTTGCCAGCAACAGTCTTGG 59.687 55.000 0.00 0.00 0.00 3.61
1429 4391 2.777692 GGAGGTAACATCCCTGATTCCA 59.222 50.000 0.00 0.00 41.41 3.53
1479 4441 4.736793 GTCAATCTTGCAAACAACACTCTG 59.263 41.667 0.00 0.00 0.00 3.35
1537 4499 3.849911 TCACTCAGCACACTTATACTGC 58.150 45.455 0.00 0.00 0.00 4.40
1570 4532 2.899256 CTCTCTGGAATGATCCCCTCTC 59.101 54.545 0.00 0.00 45.95 3.20
1581 4543 3.397618 TGATCCCCTCTCCTTTGTTTGAA 59.602 43.478 0.00 0.00 0.00 2.69
1616 4578 4.813697 GCTTTCTATGGTTGATCTCCAGAC 59.186 45.833 13.70 0.00 38.42 3.51
1628 4590 5.982356 TGATCTCCAGACGAATTCTTTCAT 58.018 37.500 3.52 0.00 28.96 2.57
1629 4591 6.045318 TGATCTCCAGACGAATTCTTTCATC 58.955 40.000 3.52 0.48 28.96 2.92
1635 4597 5.340803 CAGACGAATTCTTTCATCGGTCTA 58.659 41.667 3.52 0.00 40.71 2.59
1644 4606 3.536956 TTCATCGGTCTAATCCCACAC 57.463 47.619 0.00 0.00 0.00 3.82
1653 4615 4.141779 GGTCTAATCCCACACTTCCGTAAT 60.142 45.833 0.00 0.00 0.00 1.89
1656 4618 4.829872 AATCCCACACTTCCGTAATGTA 57.170 40.909 0.00 0.00 0.00 2.29
1713 4675 1.691434 CTCTCTGGAAGCATACCTCCC 59.309 57.143 0.00 0.00 0.00 4.30
1714 4676 1.008327 TCTCTGGAAGCATACCTCCCA 59.992 52.381 0.00 0.00 0.00 4.37
1829 4791 4.934602 ACTGCTTGAGCTTGATCTAAGTTC 59.065 41.667 4.44 11.87 44.25 3.01
1867 4862 2.056577 GTGTCCCGTTGTCTCTTTACG 58.943 52.381 0.00 0.00 35.20 3.18
2124 5120 3.889538 AGTTAGTTTTGGGGAGCAACTTC 59.110 43.478 0.00 0.00 32.88 3.01
2183 5180 3.125316 CAAATTGCACCCAACTGACAAG 58.875 45.455 0.00 0.00 32.95 3.16
2187 5184 1.213182 TGCACCCAACTGACAAGGTTA 59.787 47.619 0.00 0.00 0.00 2.85
2250 5247 5.594317 AGCAGTTGTTAATCTTTCCACAAGT 59.406 36.000 0.00 0.00 33.88 3.16
2331 5328 4.762251 AGCAATCTTGTTAACCTCACTTCC 59.238 41.667 2.48 0.00 0.00 3.46
2456 5453 0.995024 ATCCCTCCTTCAGTTGGTGG 59.005 55.000 0.00 0.00 37.82 4.61
2569 5566 7.981142 TGAACTAAATTTGTCTCGAAACAACT 58.019 30.769 3.23 0.00 38.80 3.16
2985 6011 4.099266 GCATTACCAATTTGTCCTGGCATA 59.901 41.667 0.00 0.00 0.00 3.14
3124 6150 2.427453 TGGAAGAGAGCGGTATTCTCAC 59.573 50.000 4.84 1.64 42.79 3.51
3140 6166 4.503741 TCTCACTTTTACAATTGGCTGC 57.496 40.909 10.83 0.00 0.00 5.25
3223 6250 3.005472 TCCGTTCAACGATGAGAAGAAGT 59.995 43.478 12.68 0.00 46.05 3.01
3693 6721 4.456911 GTGATTTGAAGCCAGAGAACATCA 59.543 41.667 0.00 0.00 0.00 3.07
3842 6873 4.119136 AGTTTTGCTTTTCCATTTCCACG 58.881 39.130 0.00 0.00 0.00 4.94
4045 7076 6.018469 TCCCATTTTCTCTGAATCCATGTTT 58.982 36.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.174845 CGGCTGGATTCCGTCAAGTA 59.825 55.000 0.00 0.00 41.85 2.24
1 2 1.079127 CGGCTGGATTCCGTCAAGT 60.079 57.895 0.00 0.00 41.85 3.16
8 9 4.510571 TCTTAAAGTAACGGCTGGATTCC 58.489 43.478 0.00 0.00 0.00 3.01
9 10 5.504173 GCATCTTAAAGTAACGGCTGGATTC 60.504 44.000 0.00 0.00 0.00 2.52
10 11 4.335594 GCATCTTAAAGTAACGGCTGGATT 59.664 41.667 0.00 0.00 0.00 3.01
11 12 3.877508 GCATCTTAAAGTAACGGCTGGAT 59.122 43.478 0.00 0.00 0.00 3.41
12 13 3.267483 GCATCTTAAAGTAACGGCTGGA 58.733 45.455 0.00 0.00 0.00 3.86
13 14 3.006940 TGCATCTTAAAGTAACGGCTGG 58.993 45.455 0.00 0.00 0.00 4.85
14 15 4.550831 CGATGCATCTTAAAGTAACGGCTG 60.551 45.833 23.73 0.00 0.00 4.85
15 16 3.555956 CGATGCATCTTAAAGTAACGGCT 59.444 43.478 23.73 0.00 0.00 5.52
16 17 3.554324 TCGATGCATCTTAAAGTAACGGC 59.446 43.478 23.73 0.00 0.00 5.68
17 18 5.490213 GTTCGATGCATCTTAAAGTAACGG 58.510 41.667 23.73 4.47 0.00 4.44
18 19 5.181084 CGTTCGATGCATCTTAAAGTAACG 58.819 41.667 23.73 19.76 0.00 3.18
19 20 4.956184 GCGTTCGATGCATCTTAAAGTAAC 59.044 41.667 23.73 13.85 0.00 2.50
20 21 4.033587 GGCGTTCGATGCATCTTAAAGTAA 59.966 41.667 23.73 4.72 0.00 2.24
21 22 3.554324 GGCGTTCGATGCATCTTAAAGTA 59.446 43.478 23.73 0.00 0.00 2.24
22 23 2.351726 GGCGTTCGATGCATCTTAAAGT 59.648 45.455 23.73 0.00 0.00 2.66
23 24 2.609459 AGGCGTTCGATGCATCTTAAAG 59.391 45.455 23.73 18.83 0.00 1.85
24 25 2.607635 GAGGCGTTCGATGCATCTTAAA 59.392 45.455 23.73 12.53 37.87 1.52
25 26 2.201732 GAGGCGTTCGATGCATCTTAA 58.798 47.619 23.73 14.89 37.87 1.85
26 27 1.538204 GGAGGCGTTCGATGCATCTTA 60.538 52.381 23.73 9.64 40.44 2.10
27 28 0.811616 GGAGGCGTTCGATGCATCTT 60.812 55.000 23.73 0.00 40.44 2.40
28 29 1.227380 GGAGGCGTTCGATGCATCT 60.227 57.895 23.73 3.50 40.44 2.90
29 30 1.493950 CTGGAGGCGTTCGATGCATC 61.494 60.000 17.10 17.10 39.93 3.91
30 31 1.522355 CTGGAGGCGTTCGATGCAT 60.522 57.895 0.00 0.00 0.00 3.96
31 32 2.125552 CTGGAGGCGTTCGATGCA 60.126 61.111 11.65 0.00 0.00 3.96
32 33 3.567797 GCTGGAGGCGTTCGATGC 61.568 66.667 1.74 1.74 0.00 3.91
207 217 3.662247 TTTGAGACTCCGAGGTTTCTC 57.338 47.619 0.00 12.66 35.93 2.87
255 273 4.321750 GCAGCTACTTACACTAGTTCCACA 60.322 45.833 0.00 0.00 0.00 4.17
276 294 1.742411 GCTTACCTCATACAAGGCGCA 60.742 52.381 10.83 0.00 40.34 6.09
277 295 0.938008 GCTTACCTCATACAAGGCGC 59.062 55.000 0.00 0.00 40.34 6.53
278 296 1.583054 GGCTTACCTCATACAAGGCG 58.417 55.000 0.00 0.00 40.34 5.52
279 297 1.968704 GGGCTTACCTCATACAAGGC 58.031 55.000 0.00 0.00 40.34 4.35
290 308 1.745489 CCGAACTGCAGGGCTTACC 60.745 63.158 19.93 0.00 40.67 2.85
291 309 0.605589 AACCGAACTGCAGGGCTTAC 60.606 55.000 19.93 1.65 0.00 2.34
292 310 0.321298 GAACCGAACTGCAGGGCTTA 60.321 55.000 19.93 0.00 0.00 3.09
293 311 1.600916 GAACCGAACTGCAGGGCTT 60.601 57.895 19.93 2.73 0.00 4.35
294 312 2.032681 GAACCGAACTGCAGGGCT 59.967 61.111 19.93 0.21 0.00 5.19
295 313 3.056328 GGAACCGAACTGCAGGGC 61.056 66.667 19.93 8.37 0.00 5.19
296 314 2.359975 GGGAACCGAACTGCAGGG 60.360 66.667 19.93 12.37 40.86 4.45
308 326 8.257306 TCTAATTTAGCATGGAAAATTGGGAAC 58.743 33.333 0.00 0.00 36.31 3.62
309 327 8.372877 TCTAATTTAGCATGGAAAATTGGGAA 57.627 30.769 0.00 0.00 36.31 3.97
310 328 7.969690 TCTAATTTAGCATGGAAAATTGGGA 57.030 32.000 0.00 0.82 36.31 4.37
311 329 8.423349 TCATCTAATTTAGCATGGAAAATTGGG 58.577 33.333 0.00 0.00 36.31 4.12
312 330 9.820725 TTCATCTAATTTAGCATGGAAAATTGG 57.179 29.630 0.00 1.58 36.31 3.16
318 336 8.853126 CCTCATTTCATCTAATTTAGCATGGAA 58.147 33.333 0.00 9.85 0.00 3.53
319 337 8.000709 ACCTCATTTCATCTAATTTAGCATGGA 58.999 33.333 0.00 0.00 0.00 3.41
320 338 8.174733 ACCTCATTTCATCTAATTTAGCATGG 57.825 34.615 0.00 0.00 0.00 3.66
330 348 8.577296 CCGAGTAGATAACCTCATTTCATCTAA 58.423 37.037 0.00 0.00 31.78 2.10
331 349 7.942894 TCCGAGTAGATAACCTCATTTCATCTA 59.057 37.037 0.00 0.00 0.00 1.98
332 350 6.778069 TCCGAGTAGATAACCTCATTTCATCT 59.222 38.462 0.00 0.00 0.00 2.90
333 351 6.982852 TCCGAGTAGATAACCTCATTTCATC 58.017 40.000 0.00 0.00 0.00 2.92
334 352 6.978674 TCCGAGTAGATAACCTCATTTCAT 57.021 37.500 0.00 0.00 0.00 2.57
335 353 6.785337 TTCCGAGTAGATAACCTCATTTCA 57.215 37.500 0.00 0.00 0.00 2.69
336 354 7.385478 GGAATTCCGAGTAGATAACCTCATTTC 59.615 40.741 9.17 0.00 0.00 2.17
337 355 7.147549 TGGAATTCCGAGTAGATAACCTCATTT 60.148 37.037 19.57 0.00 39.43 2.32
338 356 6.326583 TGGAATTCCGAGTAGATAACCTCATT 59.673 38.462 19.57 0.00 39.43 2.57
339 357 5.839063 TGGAATTCCGAGTAGATAACCTCAT 59.161 40.000 19.57 0.00 39.43 2.90
340 358 5.205821 TGGAATTCCGAGTAGATAACCTCA 58.794 41.667 19.57 0.00 39.43 3.86
341 359 5.786264 TGGAATTCCGAGTAGATAACCTC 57.214 43.478 19.57 0.00 39.43 3.85
342 360 6.099845 ACAATGGAATTCCGAGTAGATAACCT 59.900 38.462 19.57 0.00 39.43 3.50
343 361 6.289064 ACAATGGAATTCCGAGTAGATAACC 58.711 40.000 19.57 0.00 39.43 2.85
344 362 7.041984 GGAACAATGGAATTCCGAGTAGATAAC 60.042 40.741 19.57 4.33 39.43 1.89
345 363 6.990349 GGAACAATGGAATTCCGAGTAGATAA 59.010 38.462 19.57 0.00 39.43 1.75
346 364 6.099125 TGGAACAATGGAATTCCGAGTAGATA 59.901 38.462 19.57 0.00 46.35 1.98
347 365 5.104527 TGGAACAATGGAATTCCGAGTAGAT 60.105 40.000 19.57 3.50 46.35 1.98
348 366 4.224147 TGGAACAATGGAATTCCGAGTAGA 59.776 41.667 19.57 0.95 46.35 2.59
349 367 4.513442 TGGAACAATGGAATTCCGAGTAG 58.487 43.478 19.57 9.82 46.35 2.57
350 368 4.561500 TGGAACAATGGAATTCCGAGTA 57.438 40.909 19.57 2.13 46.35 2.59
351 369 3.433306 TGGAACAATGGAATTCCGAGT 57.567 42.857 19.57 14.14 46.35 4.18
366 384 4.939509 ATGTGTAAACGTAGCATGGAAC 57.060 40.909 0.00 0.00 0.00 3.62
367 385 4.998033 TGAATGTGTAAACGTAGCATGGAA 59.002 37.500 0.00 0.00 0.00 3.53
368 386 4.570930 TGAATGTGTAAACGTAGCATGGA 58.429 39.130 0.00 0.00 0.00 3.41
369 387 4.201812 CCTGAATGTGTAAACGTAGCATGG 60.202 45.833 0.00 0.00 0.00 3.66
370 388 4.391830 ACCTGAATGTGTAAACGTAGCATG 59.608 41.667 0.00 0.00 0.00 4.06
371 389 4.575885 ACCTGAATGTGTAAACGTAGCAT 58.424 39.130 0.00 0.00 0.00 3.79
372 390 3.991773 GACCTGAATGTGTAAACGTAGCA 59.008 43.478 0.00 0.00 0.00 3.49
373 391 3.370061 GGACCTGAATGTGTAAACGTAGC 59.630 47.826 0.00 0.00 0.00 3.58
374 392 4.562082 TGGACCTGAATGTGTAAACGTAG 58.438 43.478 0.00 0.00 0.00 3.51
375 393 4.603989 TGGACCTGAATGTGTAAACGTA 57.396 40.909 0.00 0.00 0.00 3.57
376 394 3.478857 TGGACCTGAATGTGTAAACGT 57.521 42.857 0.00 0.00 0.00 3.99
377 395 5.153513 CAATTGGACCTGAATGTGTAAACG 58.846 41.667 0.00 0.00 0.00 3.60
378 396 5.920273 CACAATTGGACCTGAATGTGTAAAC 59.080 40.000 10.83 0.00 0.00 2.01
379 397 5.830457 TCACAATTGGACCTGAATGTGTAAA 59.170 36.000 10.83 0.81 0.00 2.01
380 398 5.380900 TCACAATTGGACCTGAATGTGTAA 58.619 37.500 10.83 1.32 0.00 2.41
381 399 4.979335 TCACAATTGGACCTGAATGTGTA 58.021 39.130 10.83 5.13 0.00 2.90
382 400 3.831323 TCACAATTGGACCTGAATGTGT 58.169 40.909 10.83 4.48 0.00 3.72
383 401 4.801891 CTTCACAATTGGACCTGAATGTG 58.198 43.478 10.83 11.59 0.00 3.21
384 402 3.256631 GCTTCACAATTGGACCTGAATGT 59.743 43.478 10.83 0.00 0.00 2.71
385 403 3.256383 TGCTTCACAATTGGACCTGAATG 59.744 43.478 10.83 6.14 0.00 2.67
386 404 3.499338 TGCTTCACAATTGGACCTGAAT 58.501 40.909 10.83 0.00 0.00 2.57
387 405 2.942804 TGCTTCACAATTGGACCTGAA 58.057 42.857 10.83 9.40 0.00 3.02
388 406 2.655090 TGCTTCACAATTGGACCTGA 57.345 45.000 10.83 1.18 0.00 3.86
389 407 2.559668 ACATGCTTCACAATTGGACCTG 59.440 45.455 10.83 0.00 0.00 4.00
390 408 2.880443 ACATGCTTCACAATTGGACCT 58.120 42.857 10.83 0.00 0.00 3.85
391 409 3.665745 AACATGCTTCACAATTGGACC 57.334 42.857 10.83 0.00 0.00 4.46
392 410 5.156355 CACTAACATGCTTCACAATTGGAC 58.844 41.667 10.83 0.00 0.00 4.02
393 411 4.321156 GCACTAACATGCTTCACAATTGGA 60.321 41.667 10.83 1.40 42.62 3.53
394 412 3.922240 GCACTAACATGCTTCACAATTGG 59.078 43.478 10.83 0.00 42.62 3.16
395 413 4.548494 TGCACTAACATGCTTCACAATTG 58.452 39.130 3.24 3.24 46.28 2.32
396 414 4.852134 TGCACTAACATGCTTCACAATT 57.148 36.364 0.00 0.00 46.28 2.32
397 415 4.549458 GTTGCACTAACATGCTTCACAAT 58.451 39.130 0.00 0.00 46.28 2.71
398 416 3.547813 CGTTGCACTAACATGCTTCACAA 60.548 43.478 0.00 0.00 46.28 3.33
399 417 2.032117 CGTTGCACTAACATGCTTCACA 60.032 45.455 0.00 0.00 46.28 3.58
400 418 2.574322 CGTTGCACTAACATGCTTCAC 58.426 47.619 0.00 0.00 46.28 3.18
407 425 1.508632 ACTTCGCGTTGCACTAACAT 58.491 45.000 5.77 0.00 39.30 2.71
420 438 1.986698 ATTCTGCATTGCAACTTCGC 58.013 45.000 13.18 2.93 38.41 4.70
425 443 3.983344 AGAAACGAATTCTGCATTGCAAC 59.017 39.130 13.18 0.00 46.71 4.17
440 458 5.584649 ACACATTTCTTCACAGAAGAAACGA 59.415 36.000 27.52 13.47 45.58 3.85
441 459 5.810525 ACACATTTCTTCACAGAAGAAACG 58.189 37.500 27.52 23.85 45.58 3.60
538 3430 3.984838 GCAAACCAAGCCATTGACA 57.015 47.368 0.00 0.00 38.83 3.58
575 3467 6.375455 ACATCAAACAGACAGGATAATCAACC 59.625 38.462 0.00 0.00 0.00 3.77
576 3468 7.246311 CACATCAAACAGACAGGATAATCAAC 58.754 38.462 0.00 0.00 0.00 3.18
580 3472 4.333649 CGCACATCAAACAGACAGGATAAT 59.666 41.667 0.00 0.00 0.00 1.28
582 3474 3.261580 CGCACATCAAACAGACAGGATA 58.738 45.455 0.00 0.00 0.00 2.59
615 3507 3.750130 CCTGGCTCATACTACATGATTGC 59.250 47.826 0.00 0.00 0.00 3.56
622 3514 5.706447 AGACTAATCCTGGCTCATACTACA 58.294 41.667 0.00 0.00 0.00 2.74
623 3515 6.658188 AAGACTAATCCTGGCTCATACTAC 57.342 41.667 0.00 0.00 0.00 2.73
624 3516 7.295340 TGTAAGACTAATCCTGGCTCATACTA 58.705 38.462 0.00 0.00 0.00 1.82
625 3517 6.136857 TGTAAGACTAATCCTGGCTCATACT 58.863 40.000 0.00 0.00 0.00 2.12
639 3536 5.479306 GACACAAGGATGCTGTAAGACTAA 58.521 41.667 0.00 0.00 34.07 2.24
674 3572 4.026356 ACTGGAAGAGGAAAGGTGAATG 57.974 45.455 0.00 0.00 37.43 2.67
946 3889 4.202472 CCAGGAAGTTGGGAGAACTTTAGT 60.202 45.833 0.00 0.00 40.27 2.24
985 3943 2.232941 AGGGCATGATGTTCAAAGCTTG 59.767 45.455 0.00 0.00 33.69 4.01
991 3951 5.239351 CAAAAATGAGGGCATGATGTTCAA 58.761 37.500 0.00 0.00 34.26 2.69
1015 3975 5.526846 GGATGAGAAAAATACAGAGCAGAGG 59.473 44.000 0.00 0.00 0.00 3.69
1094 4054 0.622665 AAGGAGGGCTTGGTGATCAG 59.377 55.000 0.00 0.00 0.00 2.90
1100 4060 3.265601 AGCAAAGGAGGGCTTGGT 58.734 55.556 0.00 0.00 36.92 3.67
1179 4140 2.546584 CCCTTTCCAGCTGCAAAAGTTC 60.547 50.000 25.65 0.00 0.00 3.01
1245 4207 0.537371 TGAGACGAGCAGAGGTGACA 60.537 55.000 0.00 0.00 0.00 3.58
1246 4208 0.170116 CTGAGACGAGCAGAGGTGAC 59.830 60.000 0.00 0.00 35.39 3.67
1296 4258 3.432252 GGTTCATCGATGACAGAAACGTT 59.568 43.478 27.28 0.00 36.36 3.99
1305 4267 0.652592 CGGCAAGGTTCATCGATGAC 59.347 55.000 27.28 20.29 36.36 3.06
1325 4287 3.536956 TGGTTCCCGACAGATCATTAC 57.463 47.619 0.00 0.00 0.00 1.89
1377 4339 2.554142 CTGGCAAGATTCAGCGTATGA 58.446 47.619 0.00 0.00 35.62 2.15
1409 4371 4.713792 ATGGAATCAGGGATGTTACCTC 57.286 45.455 0.00 0.00 35.78 3.85
1429 4391 4.505742 GCTAAGGGAATTGCTAGTGCCTAT 60.506 45.833 9.24 3.12 39.43 2.57
1446 4408 6.127925 TGTTTGCAAGATTGACATAGCTAAGG 60.128 38.462 0.00 0.00 0.00 2.69
1537 4499 4.730949 TTCCAGAGAGGTTATTACGTGG 57.269 45.455 0.00 0.00 39.02 4.94
1570 4532 7.428826 AGCTTAGATGAGTTTTCAAACAAAGG 58.571 34.615 5.26 0.00 41.30 3.11
1581 4543 8.103305 TCAACCATAGAAAGCTTAGATGAGTTT 58.897 33.333 13.87 4.73 0.00 2.66
1616 4578 5.177696 GGGATTAGACCGATGAAAGAATTCG 59.822 44.000 0.00 0.00 38.46 3.34
1628 4590 1.829222 GGAAGTGTGGGATTAGACCGA 59.171 52.381 0.00 0.00 0.00 4.69
1629 4591 1.470979 CGGAAGTGTGGGATTAGACCG 60.471 57.143 0.00 0.00 0.00 4.79
1644 4606 6.533819 TTGAGTGTTGTTACATTACGGAAG 57.466 37.500 0.00 0.00 36.50 3.46
1653 4615 6.533367 GGCAAAGAAATTTGAGTGTTGTTACA 59.467 34.615 0.00 0.00 33.95 2.41
1656 4618 5.581874 CAGGCAAAGAAATTTGAGTGTTGTT 59.418 36.000 0.00 0.00 33.95 2.83
1713 4675 5.126067 AGGGATGAAACATTTCCTATCGTG 58.874 41.667 2.00 0.00 36.36 4.35
1714 4676 5.104527 TGAGGGATGAAACATTTCCTATCGT 60.105 40.000 2.00 0.00 36.36 3.73
1829 4791 4.003648 GACACTCCCTGATAAACTGTTGG 58.996 47.826 0.00 0.00 0.00 3.77
1867 4862 7.276658 CCTAAAGTACTTGAGTGATGTCATGTC 59.723 40.741 17.29 0.00 36.51 3.06
2124 5120 2.234661 TGACCAGTCATGTGCTTCTAGG 59.765 50.000 0.00 0.00 34.14 3.02
2153 5150 3.282021 TGGGTGCAATTTGCTAGAGATC 58.718 45.455 21.19 1.92 45.31 2.75
2269 5266 1.001158 GCCCGAAATTTGGTTTGACGA 60.001 47.619 0.00 0.00 0.00 4.20
2322 5319 4.778213 TTCCATCATAAGGGAAGTGAGG 57.222 45.455 0.00 0.00 40.32 3.86
2331 5328 8.782339 AAAGAAAATTGCTTTCCATCATAAGG 57.218 30.769 0.00 0.00 43.98 2.69
2456 5453 1.135286 GCTTGCCCAGTTGAGTAATGC 60.135 52.381 0.00 0.00 0.00 3.56
2520 5517 1.348036 AGTCCCTTGCACTGACCTAAC 59.652 52.381 5.97 0.00 0.00 2.34
2587 5584 3.254892 GAGGGTTAGCAAAGAGTTCGAG 58.745 50.000 0.00 0.00 0.00 4.04
2985 6011 6.146673 GCTTTGTTTTATTTGCTGAAGCTGAT 59.853 34.615 3.61 0.67 42.66 2.90
3124 6150 3.981211 ACACAGCAGCCAATTGTAAAAG 58.019 40.909 4.43 0.00 0.00 2.27
3140 6166 3.809832 ACGAAACATCTTCTTGGACACAG 59.190 43.478 0.00 0.00 0.00 3.66
3171 6198 5.802465 TGCATTTCTCTTCTCTTCTGATGT 58.198 37.500 0.00 0.00 0.00 3.06
3223 6250 4.162320 GTCCTGATATGACACCCTCTTCAA 59.838 45.833 0.00 0.00 32.91 2.69
3572 6600 5.279156 CCTCTTGCCAAAGTTTAGCATTCTT 60.279 40.000 9.55 0.00 36.20 2.52
3576 6604 3.766545 TCCTCTTGCCAAAGTTTAGCAT 58.233 40.909 9.55 0.00 36.20 3.79
3693 6721 2.677836 CGGTCATGTCATCGTCCAAAAT 59.322 45.455 0.00 0.00 0.00 1.82
4045 7076 1.183030 TCCGCGACTCTTTCAGGGAA 61.183 55.000 8.23 0.00 0.00 3.97
4096 7127 2.939640 GCGTCCATACACACCCTTGATT 60.940 50.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.