Multiple sequence alignment - TraesCS7D01G040400

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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 TraesCS7D01G040400 chr7D 100.000 4754 0 0 1 4754 20403328 20408081 0.000000e+00 8780
1 TraesCS7D01G040400 chr7D 85.775 2805 390 8 961 3760 89533057 89530257 0.000000e+00 2961
2 TraesCS7D01G040400 chr7D 85.931 2772 382 8 957 3724 555196412 555193645 0.000000e+00 2952
3 TraesCS7D01G040400 chr7D 85.290 2760 392 9 972 3724 20947141 20949893 0.000000e+00 2835
4 TraesCS7D01G040400 chr7D 88.621 290 30 3 522 809 20403528 20403816 2.720000e-92 350
5 TraesCS7D01G040400 chr7D 88.621 290 30 3 201 489 20403849 20404136 2.720000e-92 350
6 TraesCS7D01G040400 chr7A 96.054 4105 143 8 529 4616 20659192 20663294 0.000000e+00 6665
7 TraesCS7D01G040400 chr7A 96.141 2980 90 6 1780 4754 20722274 20725233 0.000000e+00 4843
8 TraesCS7D01G040400 chr7A 84.658 2920 422 17 823 3724 20482640 20485551 0.000000e+00 2887
9 TraesCS7D01G040400 chr7A 86.240 516 36 14 1 489 20720734 20721241 1.170000e-145 527
10 TraesCS7D01G040400 chr7A 82.046 479 42 19 13 489 20659036 20659472 7.520000e-98 368
11 TraesCS7D01G040400 chr7A 90.756 119 11 0 4632 4750 20663374 20663492 4.920000e-35 159
12 TraesCS7D01G040400 chr2A 86.108 2829 377 14 963 3781 733087764 733090586 0.000000e+00 3033
13 TraesCS7D01G040400 chr2D 85.931 2829 389 8 957 3781 598814056 598816879 0.000000e+00 3011
14 TraesCS7D01G040400 chr2D 81.977 172 27 3 4270 4439 598888987 598889156 4.960000e-30 143
15 TraesCS7D01G040400 chr2B 85.482 2831 396 14 957 3781 727686014 727688835 0.000000e+00 2937
16 TraesCS7D01G040400 chr2B 86.861 137 11 4 4313 4448 727736037 727736167 3.830000e-31 147
17 TraesCS7D01G040400 chr2B 82.836 134 9 6 4310 4441 727710642 727710763 1.810000e-19 108
18 TraesCS7D01G040400 chr7B 84.743 2884 417 20 954 3828 601114442 601117311 0.000000e+00 2867
19 TraesCS7D01G040400 chr3A 92.197 346 13 7 578 914 714515014 714514674 1.200000e-130 477
20 TraesCS7D01G040400 chr3A 87.967 241 14 8 259 489 714515014 714514779 2.180000e-68 270
21 TraesCS7D01G040400 chr3A 90.860 186 12 3 4 189 714515197 714515017 1.320000e-60 244
22 TraesCS7D01G040400 chr5B 83.789 512 53 13 879 1365 591515470 591515976 4.340000e-125 459


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 TraesCS7D01G040400 chr7D 20403328 20408081 4753 False 8780.000000 8780 100.000000 1 4754 1 chr7D.!!$F1 4753
1 TraesCS7D01G040400 chr7D 89530257 89533057 2800 True 2961.000000 2961 85.775000 961 3760 1 chr7D.!!$R1 2799
2 TraesCS7D01G040400 chr7D 555193645 555196412 2767 True 2952.000000 2952 85.931000 957 3724 1 chr7D.!!$R2 2767
3 TraesCS7D01G040400 chr7D 20947141 20949893 2752 False 2835.000000 2835 85.290000 972 3724 1 chr7D.!!$F2 2752
4 TraesCS7D01G040400 chr7D 20403528 20404136 608 False 350.000000 350 88.621000 201 809 2 chr7D.!!$F3 608
5 TraesCS7D01G040400 chr7A 20482640 20485551 2911 False 2887.000000 2887 84.658000 823 3724 1 chr7A.!!$F1 2901
6 TraesCS7D01G040400 chr7A 20720734 20725233 4499 False 2685.000000 4843 91.190500 1 4754 2 chr7A.!!$F3 4753
7 TraesCS7D01G040400 chr7A 20659036 20663492 4456 False 2397.333333 6665 89.618667 13 4750 3 chr7A.!!$F2 4737
8 TraesCS7D01G040400 chr2A 733087764 733090586 2822 False 3033.000000 3033 86.108000 963 3781 1 chr2A.!!$F1 2818
9 TraesCS7D01G040400 chr2D 598814056 598816879 2823 False 3011.000000 3011 85.931000 957 3781 1 chr2D.!!$F1 2824
10 TraesCS7D01G040400 chr2B 727686014 727688835 2821 False 2937.000000 2937 85.482000 957 3781 1 chr2B.!!$F1 2824
11 TraesCS7D01G040400 chr7B 601114442 601117311 2869 False 2867.000000 2867 84.743000 954 3828 1 chr7B.!!$F1 2874
12 TraesCS7D01G040400 chr3A 714514674 714515197 523 True 330.333333 477 90.341333 4 914 3 chr3A.!!$R1 910
13 TraesCS7D01G040400 chr5B 591515470 591515976 506 False 459.000000 459 83.789000 879 1365 1 chr5B.!!$F1 486

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
439 464 0.106419 TTTGGTCGAGGGCCACTTTT 60.106 50.000 6.18 0.00 35.46 2.27 F
442 467 0.250770 GGTCGAGGGCCACTTTTCTT 60.251 55.000 6.18 0.00 0.00 2.52 F
482 507 0.467804 TGACACAGTTGGCTACAGCA 59.532 50.000 3.24 0.00 44.36 4.41 F
484 509 0.469917 ACACAGTTGGCTACAGCAGT 59.530 50.000 3.24 0.00 44.36 4.40 F
486 511 0.758734 ACAGTTGGCTACAGCAGTCA 59.241 50.000 3.24 0.00 44.36 3.41 F
488 513 0.758734 AGTTGGCTACAGCAGTCACA 59.241 50.000 3.24 0.00 39.05 3.58 F
489 514 1.349026 AGTTGGCTACAGCAGTCACAT 59.651 47.619 3.24 0.00 39.05 3.21 F
2181 2643 1.350319 GTGTGTGCGCGAGAAAACA 59.650 52.632 12.10 2.54 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 1873 1.827969 AGATCTTGGGACCTCTTGACG 59.172 52.381 0.00 0.00 0.00 4.35 R
1680 2077 3.315142 GATCCAGGCGTGGCACTGA 62.315 63.158 20.76 3.23 44.60 3.41 R
2181 2643 8.331740 TCATTAATTCTTCTCCATTCTTCCACT 58.668 33.333 0.00 0.00 0.00 4.00 R
2652 3115 3.181493 GGTGCATGCTAGAAAATGACTGG 60.181 47.826 20.33 0.00 0.00 4.00 R
3126 3589 5.765182 CCATAACCTCAAACTTCTCACTTGT 59.235 40.000 0.00 0.00 0.00 3.16 R
3130 3593 6.431234 ACATTCCATAACCTCAAACTTCTCAC 59.569 38.462 0.00 0.00 0.00 3.51 R
3215 3678 2.223433 GCACTTGCATTCACATCTAGGC 60.223 50.000 0.00 0.00 41.59 3.93 R
3754 4217 0.482446 TCCAAACCAGTCTGGGCATT 59.518 50.000 23.06 11.73 43.37 3.56 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
73 74 7.094805 GGAATTAATCTGCAGTGTAGTTGTTGA 60.095 37.037 14.67 0.56 0.00 3.18
291 316 0.585357 CGGATACATCTGCTTGCTGC 59.415 55.000 0.00 0.00 43.25 5.25
292 317 1.809271 CGGATACATCTGCTTGCTGCT 60.809 52.381 0.00 0.00 43.37 4.24
293 318 2.295885 GGATACATCTGCTTGCTGCTT 58.704 47.619 0.00 0.00 43.37 3.91
294 319 3.470709 GGATACATCTGCTTGCTGCTTA 58.529 45.455 0.00 0.00 43.37 3.09
295 320 3.879295 GGATACATCTGCTTGCTGCTTAA 59.121 43.478 0.00 0.00 43.37 1.85
296 321 4.518211 GGATACATCTGCTTGCTGCTTAAT 59.482 41.667 0.00 0.00 43.37 1.40
297 322 5.334724 GGATACATCTGCTTGCTGCTTAATC 60.335 44.000 0.00 0.00 43.37 1.75
298 323 3.349927 ACATCTGCTTGCTGCTTAATCA 58.650 40.909 0.00 0.00 43.37 2.57
299 324 3.760151 ACATCTGCTTGCTGCTTAATCAA 59.240 39.130 0.00 0.00 43.37 2.57
300 325 3.837213 TCTGCTTGCTGCTTAATCAAC 57.163 42.857 0.00 0.00 43.37 3.18
301 326 3.148412 TCTGCTTGCTGCTTAATCAACA 58.852 40.909 0.00 0.00 43.37 3.33
302 327 3.189910 TCTGCTTGCTGCTTAATCAACAG 59.810 43.478 0.00 0.00 43.37 3.16
308 333 2.860062 CTGCTTAATCAACAGCACTGC 58.140 47.619 0.00 0.00 41.20 4.40
309 334 1.541147 TGCTTAATCAACAGCACTGCC 59.459 47.619 0.00 0.00 41.20 4.85
310 335 1.815003 GCTTAATCAACAGCACTGCCT 59.185 47.619 0.00 0.00 35.95 4.75
311 336 3.009723 GCTTAATCAACAGCACTGCCTA 58.990 45.455 0.00 0.00 35.95 3.93
312 337 3.629398 GCTTAATCAACAGCACTGCCTAT 59.371 43.478 0.00 0.00 35.95 2.57
313 338 4.260948 GCTTAATCAACAGCACTGCCTATC 60.261 45.833 0.00 0.00 35.95 2.08
314 339 3.641434 AATCAACAGCACTGCCTATCT 57.359 42.857 0.00 0.00 0.00 1.98
315 340 2.391616 TCAACAGCACTGCCTATCTG 57.608 50.000 0.00 0.00 0.00 2.90
316 341 1.625315 TCAACAGCACTGCCTATCTGT 59.375 47.619 0.00 0.00 41.08 3.41
317 342 2.038952 TCAACAGCACTGCCTATCTGTT 59.961 45.455 0.00 0.00 46.88 3.16
318 343 2.816087 CAACAGCACTGCCTATCTGTTT 59.184 45.455 3.99 0.00 44.52 2.83
319 344 2.704572 ACAGCACTGCCTATCTGTTTC 58.295 47.619 0.00 0.00 36.48 2.78
320 345 2.304180 ACAGCACTGCCTATCTGTTTCT 59.696 45.455 0.00 0.00 36.48 2.52
321 346 2.935201 CAGCACTGCCTATCTGTTTCTC 59.065 50.000 0.00 0.00 0.00 2.87
322 347 2.093235 AGCACTGCCTATCTGTTTCTCC 60.093 50.000 0.00 0.00 0.00 3.71
323 348 2.355108 GCACTGCCTATCTGTTTCTCCA 60.355 50.000 0.00 0.00 0.00 3.86
324 349 3.683847 GCACTGCCTATCTGTTTCTCCAT 60.684 47.826 0.00 0.00 0.00 3.41
325 350 4.443457 GCACTGCCTATCTGTTTCTCCATA 60.443 45.833 0.00 0.00 0.00 2.74
326 351 5.053145 CACTGCCTATCTGTTTCTCCATAC 58.947 45.833 0.00 0.00 0.00 2.39
327 352 4.716784 ACTGCCTATCTGTTTCTCCATACA 59.283 41.667 0.00 0.00 0.00 2.29
328 353 5.367937 ACTGCCTATCTGTTTCTCCATACAT 59.632 40.000 0.00 0.00 0.00 2.29
329 354 5.858381 TGCCTATCTGTTTCTCCATACATC 58.142 41.667 0.00 0.00 0.00 3.06
330 355 5.604231 TGCCTATCTGTTTCTCCATACATCT 59.396 40.000 0.00 0.00 0.00 2.90
331 356 5.931146 GCCTATCTGTTTCTCCATACATCTG 59.069 44.000 0.00 0.00 0.00 2.90
332 357 6.462500 CCTATCTGTTTCTCCATACATCTGG 58.538 44.000 0.00 0.00 37.66 3.86
333 358 4.760530 TCTGTTTCTCCATACATCTGGG 57.239 45.455 0.00 0.00 36.89 4.45
334 359 4.361783 TCTGTTTCTCCATACATCTGGGA 58.638 43.478 0.00 0.00 36.89 4.37
335 360 4.971282 TCTGTTTCTCCATACATCTGGGAT 59.029 41.667 0.00 0.00 36.89 3.85
336 361 5.039920 TGTTTCTCCATACATCTGGGATG 57.960 43.478 6.04 6.04 36.89 3.51
337 362 3.777106 TTCTCCATACATCTGGGATGC 57.223 47.619 7.35 0.00 36.89 3.91
338 363 2.693210 TCTCCATACATCTGGGATGCA 58.307 47.619 7.35 0.00 36.89 3.96
339 364 3.047857 TCTCCATACATCTGGGATGCAA 58.952 45.455 7.35 0.00 36.89 4.08
340 365 3.654321 TCTCCATACATCTGGGATGCAAT 59.346 43.478 7.35 0.14 36.89 3.56
341 366 4.105217 TCTCCATACATCTGGGATGCAATT 59.895 41.667 7.35 0.00 36.89 2.32
342 367 5.310331 TCTCCATACATCTGGGATGCAATTA 59.690 40.000 7.35 0.00 36.89 1.40
343 368 5.563592 TCCATACATCTGGGATGCAATTAG 58.436 41.667 7.35 0.00 36.89 1.73
344 369 5.310331 TCCATACATCTGGGATGCAATTAGA 59.690 40.000 7.35 0.00 36.89 2.10
345 370 6.012245 TCCATACATCTGGGATGCAATTAGAT 60.012 38.462 7.35 0.00 36.89 1.98
346 371 6.318144 CCATACATCTGGGATGCAATTAGATC 59.682 42.308 7.35 0.00 32.28 2.75
347 372 4.321718 ACATCTGGGATGCAATTAGATCG 58.678 43.478 7.35 0.00 0.00 3.69
348 373 4.040829 ACATCTGGGATGCAATTAGATCGA 59.959 41.667 7.35 0.00 0.00 3.59
349 374 4.897509 TCTGGGATGCAATTAGATCGAT 57.102 40.909 0.00 0.00 0.00 3.59
350 375 6.070596 ACATCTGGGATGCAATTAGATCGATA 60.071 38.462 0.00 0.00 0.00 2.92
351 376 6.550938 TCTGGGATGCAATTAGATCGATAT 57.449 37.500 0.00 0.00 0.00 1.63
352 377 6.950842 TCTGGGATGCAATTAGATCGATATT 58.049 36.000 0.00 0.00 0.00 1.28
353 378 7.397221 TCTGGGATGCAATTAGATCGATATTT 58.603 34.615 0.00 0.00 0.00 1.40
354 379 7.335171 TCTGGGATGCAATTAGATCGATATTTG 59.665 37.037 0.00 0.00 0.00 2.32
355 380 6.375174 TGGGATGCAATTAGATCGATATTTGG 59.625 38.462 0.00 0.00 0.00 3.28
356 381 6.183360 GGGATGCAATTAGATCGATATTTGGG 60.183 42.308 0.00 0.00 0.00 4.12
357 382 6.599244 GGATGCAATTAGATCGATATTTGGGA 59.401 38.462 0.00 0.00 0.00 4.37
358 383 7.121168 GGATGCAATTAGATCGATATTTGGGAA 59.879 37.037 0.00 0.00 0.00 3.97
359 384 7.815840 TGCAATTAGATCGATATTTGGGAAA 57.184 32.000 0.00 0.00 0.00 3.13
360 385 7.874940 TGCAATTAGATCGATATTTGGGAAAG 58.125 34.615 0.00 0.00 0.00 2.62
361 386 7.502226 TGCAATTAGATCGATATTTGGGAAAGT 59.498 33.333 0.00 0.00 0.00 2.66
362 387 8.352942 GCAATTAGATCGATATTTGGGAAAGTT 58.647 33.333 0.00 0.00 0.00 2.66
365 390 9.726438 ATTAGATCGATATTTGGGAAAGTTAGG 57.274 33.333 0.00 0.00 0.00 2.69
366 391 6.534634 AGATCGATATTTGGGAAAGTTAGGG 58.465 40.000 0.00 0.00 0.00 3.53
367 392 5.703730 TCGATATTTGGGAAAGTTAGGGT 57.296 39.130 0.00 0.00 0.00 4.34
368 393 5.677567 TCGATATTTGGGAAAGTTAGGGTC 58.322 41.667 0.00 0.00 0.00 4.46
369 394 5.190132 TCGATATTTGGGAAAGTTAGGGTCA 59.810 40.000 0.00 0.00 0.00 4.02
370 395 6.062095 CGATATTTGGGAAAGTTAGGGTCAT 58.938 40.000 0.00 0.00 0.00 3.06
371 396 6.546034 CGATATTTGGGAAAGTTAGGGTCATT 59.454 38.462 0.00 0.00 0.00 2.57
372 397 7.068226 CGATATTTGGGAAAGTTAGGGTCATTT 59.932 37.037 0.00 0.00 0.00 2.32
373 398 8.679344 ATATTTGGGAAAGTTAGGGTCATTTT 57.321 30.769 0.00 0.00 0.00 1.82
374 399 6.816616 TTTGGGAAAGTTAGGGTCATTTTT 57.183 33.333 0.00 0.00 0.00 1.94
375 400 6.413783 TTGGGAAAGTTAGGGTCATTTTTC 57.586 37.500 0.00 0.00 0.00 2.29
376 401 4.521256 TGGGAAAGTTAGGGTCATTTTTCG 59.479 41.667 0.00 0.00 0.00 3.46
377 402 4.763279 GGGAAAGTTAGGGTCATTTTTCGA 59.237 41.667 0.00 0.00 0.00 3.71
378 403 5.335426 GGGAAAGTTAGGGTCATTTTTCGAC 60.335 44.000 0.00 0.00 0.00 4.20
385 410 3.053831 GGTCATTTTTCGACCCTCTGA 57.946 47.619 0.00 0.00 46.12 3.27
386 411 3.610911 GGTCATTTTTCGACCCTCTGAT 58.389 45.455 0.00 0.00 46.12 2.90
387 412 4.766375 GGTCATTTTTCGACCCTCTGATA 58.234 43.478 0.00 0.00 46.12 2.15
388 413 4.571176 GGTCATTTTTCGACCCTCTGATAC 59.429 45.833 0.00 0.00 46.12 2.24
389 414 4.571176 GTCATTTTTCGACCCTCTGATACC 59.429 45.833 0.00 0.00 0.00 2.73
390 415 3.622166 TTTTTCGACCCTCTGATACCC 57.378 47.619 0.00 0.00 0.00 3.69
391 416 2.544844 TTTCGACCCTCTGATACCCT 57.455 50.000 0.00 0.00 0.00 4.34
392 417 2.544844 TTCGACCCTCTGATACCCTT 57.455 50.000 0.00 0.00 0.00 3.95
393 418 3.675348 TTCGACCCTCTGATACCCTTA 57.325 47.619 0.00 0.00 0.00 2.69
394 419 3.897657 TCGACCCTCTGATACCCTTAT 57.102 47.619 0.00 0.00 0.00 1.73
395 420 5.329191 TTCGACCCTCTGATACCCTTATA 57.671 43.478 0.00 0.00 0.00 0.98
396 421 4.660168 TCGACCCTCTGATACCCTTATAC 58.340 47.826 0.00 0.00 0.00 1.47
397 422 3.439476 CGACCCTCTGATACCCTTATACG 59.561 52.174 0.00 0.00 0.00 3.06
398 423 3.762823 GACCCTCTGATACCCTTATACGG 59.237 52.174 0.00 0.00 0.00 4.02
399 424 2.496470 CCCTCTGATACCCTTATACGGC 59.504 54.545 0.00 0.00 0.00 5.68
400 425 3.162666 CCTCTGATACCCTTATACGGCA 58.837 50.000 0.00 0.00 0.00 5.69
401 426 3.193691 CCTCTGATACCCTTATACGGCAG 59.806 52.174 0.00 0.00 0.00 4.85
402 427 2.561419 TCTGATACCCTTATACGGCAGC 59.439 50.000 0.00 0.00 0.00 5.25
403 428 2.299013 CTGATACCCTTATACGGCAGCA 59.701 50.000 0.00 0.00 0.00 4.41
404 429 2.299013 TGATACCCTTATACGGCAGCAG 59.701 50.000 0.00 0.00 0.00 4.24
405 430 2.076207 TACCCTTATACGGCAGCAGA 57.924 50.000 0.00 0.00 0.00 4.26
406 431 0.753262 ACCCTTATACGGCAGCAGAG 59.247 55.000 0.00 0.00 0.00 3.35
407 432 0.753262 CCCTTATACGGCAGCAGAGT 59.247 55.000 0.00 0.00 0.00 3.24
408 433 1.961394 CCCTTATACGGCAGCAGAGTA 59.039 52.381 0.00 0.00 0.00 2.59
409 434 2.563179 CCCTTATACGGCAGCAGAGTAT 59.437 50.000 0.00 6.14 35.52 2.12
410 435 3.579709 CCTTATACGGCAGCAGAGTATG 58.420 50.000 14.18 3.99 33.64 2.39
424 449 4.978186 CAGAGTATGCATGTTCAGTTTGG 58.022 43.478 10.16 0.00 0.00 3.28
425 450 4.456911 CAGAGTATGCATGTTCAGTTTGGT 59.543 41.667 10.16 0.00 0.00 3.67
426 451 4.697352 AGAGTATGCATGTTCAGTTTGGTC 59.303 41.667 10.16 0.00 0.00 4.02
427 452 2.995466 ATGCATGTTCAGTTTGGTCG 57.005 45.000 0.00 0.00 0.00 4.79
428 453 1.960417 TGCATGTTCAGTTTGGTCGA 58.040 45.000 0.00 0.00 0.00 4.20
429 454 1.872952 TGCATGTTCAGTTTGGTCGAG 59.127 47.619 0.00 0.00 0.00 4.04
430 455 1.197721 GCATGTTCAGTTTGGTCGAGG 59.802 52.381 0.00 0.00 0.00 4.63
431 456 1.806542 CATGTTCAGTTTGGTCGAGGG 59.193 52.381 0.00 0.00 0.00 4.30
432 457 0.534203 TGTTCAGTTTGGTCGAGGGC 60.534 55.000 0.00 0.00 0.00 5.19
433 458 1.072505 TTCAGTTTGGTCGAGGGCC 59.927 57.895 0.00 0.00 0.00 5.80
434 459 1.701031 TTCAGTTTGGTCGAGGGCCA 61.701 55.000 6.18 0.00 0.00 5.36
435 460 1.966451 CAGTTTGGTCGAGGGCCAC 60.966 63.158 6.18 0.00 35.46 5.01
436 461 2.147387 AGTTTGGTCGAGGGCCACT 61.147 57.895 6.18 0.00 35.46 4.00
437 462 1.228154 GTTTGGTCGAGGGCCACTT 60.228 57.895 6.18 0.00 35.46 3.16
438 463 0.822121 GTTTGGTCGAGGGCCACTTT 60.822 55.000 6.18 0.00 35.46 2.66
439 464 0.106419 TTTGGTCGAGGGCCACTTTT 60.106 50.000 6.18 0.00 35.46 2.27
440 465 0.536460 TTGGTCGAGGGCCACTTTTC 60.536 55.000 6.18 0.00 35.46 2.29
441 466 1.375326 GGTCGAGGGCCACTTTTCT 59.625 57.895 6.18 0.00 0.00 2.52
442 467 0.250770 GGTCGAGGGCCACTTTTCTT 60.251 55.000 6.18 0.00 0.00 2.52
443 468 1.002773 GGTCGAGGGCCACTTTTCTTA 59.997 52.381 6.18 0.00 0.00 2.10
444 469 2.355818 GGTCGAGGGCCACTTTTCTTAT 60.356 50.000 6.18 0.00 0.00 1.73
445 470 2.937149 GTCGAGGGCCACTTTTCTTATC 59.063 50.000 6.18 0.00 0.00 1.75
446 471 2.569853 TCGAGGGCCACTTTTCTTATCA 59.430 45.455 6.18 0.00 0.00 2.15
447 472 2.939103 CGAGGGCCACTTTTCTTATCAG 59.061 50.000 6.18 0.00 0.00 2.90
448 473 3.619979 CGAGGGCCACTTTTCTTATCAGT 60.620 47.826 6.18 0.00 0.00 3.41
449 474 4.336280 GAGGGCCACTTTTCTTATCAGTT 58.664 43.478 6.18 0.00 0.00 3.16
450 475 5.497474 GAGGGCCACTTTTCTTATCAGTTA 58.503 41.667 6.18 0.00 0.00 2.24
451 476 5.887754 AGGGCCACTTTTCTTATCAGTTAA 58.112 37.500 6.18 0.00 0.00 2.01
452 477 6.494059 AGGGCCACTTTTCTTATCAGTTAAT 58.506 36.000 6.18 0.00 0.00 1.40
453 478 7.639378 AGGGCCACTTTTCTTATCAGTTAATA 58.361 34.615 6.18 0.00 0.00 0.98
454 479 8.113462 AGGGCCACTTTTCTTATCAGTTAATAA 58.887 33.333 6.18 0.00 0.00 1.40
455 480 8.188799 GGGCCACTTTTCTTATCAGTTAATAAC 58.811 37.037 4.39 0.00 0.00 1.89
456 481 8.736244 GGCCACTTTTCTTATCAGTTAATAACA 58.264 33.333 5.89 0.00 0.00 2.41
475 500 8.532977 AATAACAAATAATTGACACAGTTGGC 57.467 30.769 0.00 0.00 38.94 4.52
476 501 5.789643 ACAAATAATTGACACAGTTGGCT 57.210 34.783 0.00 0.00 38.94 4.75
477 502 6.892658 ACAAATAATTGACACAGTTGGCTA 57.107 33.333 0.00 0.00 38.94 3.93
478 503 6.677913 ACAAATAATTGACACAGTTGGCTAC 58.322 36.000 0.00 0.00 38.94 3.58
479 504 6.264292 ACAAATAATTGACACAGTTGGCTACA 59.736 34.615 1.24 0.00 38.94 2.74
480 505 6.500684 AATAATTGACACAGTTGGCTACAG 57.499 37.500 1.24 0.00 0.00 2.74
481 506 1.593196 TTGACACAGTTGGCTACAGC 58.407 50.000 1.24 0.00 41.14 4.40
482 507 0.467804 TGACACAGTTGGCTACAGCA 59.532 50.000 3.24 0.00 44.36 4.41
483 508 1.151668 GACACAGTTGGCTACAGCAG 58.848 55.000 3.24 0.00 44.36 4.24
484 509 0.469917 ACACAGTTGGCTACAGCAGT 59.530 50.000 3.24 0.00 44.36 4.40
485 510 1.151668 CACAGTTGGCTACAGCAGTC 58.848 55.000 3.24 0.00 44.36 3.51
486 511 0.758734 ACAGTTGGCTACAGCAGTCA 59.241 50.000 3.24 0.00 44.36 3.41
487 512 1.151668 CAGTTGGCTACAGCAGTCAC 58.848 55.000 3.24 0.00 39.05 3.67
488 513 0.758734 AGTTGGCTACAGCAGTCACA 59.241 50.000 3.24 0.00 39.05 3.58
489 514 1.349026 AGTTGGCTACAGCAGTCACAT 59.651 47.619 3.24 0.00 39.05 3.21
490 515 2.567169 AGTTGGCTACAGCAGTCACATA 59.433 45.455 3.24 0.00 39.05 2.29
491 516 3.198635 AGTTGGCTACAGCAGTCACATAT 59.801 43.478 3.24 0.00 39.05 1.78
492 517 3.183793 TGGCTACAGCAGTCACATATG 57.816 47.619 0.00 0.00 44.36 1.78
493 518 2.765699 TGGCTACAGCAGTCACATATGA 59.234 45.455 10.38 0.00 44.36 2.15
494 519 3.197549 TGGCTACAGCAGTCACATATGAA 59.802 43.478 10.38 0.00 44.36 2.57
495 520 3.557595 GGCTACAGCAGTCACATATGAAC 59.442 47.826 10.38 7.27 44.36 3.18
496 521 4.183865 GCTACAGCAGTCACATATGAACA 58.816 43.478 10.38 0.00 41.59 3.18
497 522 4.631377 GCTACAGCAGTCACATATGAACAA 59.369 41.667 10.38 0.00 41.59 2.83
498 523 5.220548 GCTACAGCAGTCACATATGAACAAG 60.221 44.000 10.38 5.62 41.59 3.16
499 524 4.898320 ACAGCAGTCACATATGAACAAGA 58.102 39.130 10.38 0.00 36.31 3.02
500 525 5.308014 ACAGCAGTCACATATGAACAAGAA 58.692 37.500 10.38 0.00 36.31 2.52
501 526 5.410746 ACAGCAGTCACATATGAACAAGAAG 59.589 40.000 10.38 0.00 36.31 2.85
502 527 4.394300 AGCAGTCACATATGAACAAGAAGC 59.606 41.667 10.38 7.66 36.31 3.86
503 528 4.437930 GCAGTCACATATGAACAAGAAGCC 60.438 45.833 10.38 0.00 36.31 4.35
504 529 4.940046 CAGTCACATATGAACAAGAAGCCT 59.060 41.667 10.38 0.00 36.31 4.58
505 530 5.413833 CAGTCACATATGAACAAGAAGCCTT 59.586 40.000 10.38 0.00 36.31 4.35
506 531 5.645497 AGTCACATATGAACAAGAAGCCTTC 59.355 40.000 10.38 0.00 36.31 3.46
507 532 5.645497 GTCACATATGAACAAGAAGCCTTCT 59.355 40.000 10.38 0.00 37.97 2.85
508 533 6.150140 GTCACATATGAACAAGAAGCCTTCTT 59.850 38.462 13.92 13.92 42.94 2.52
509 534 7.308830 GTCACATATGAACAAGAAGCCTTCTTT 60.309 37.037 16.92 4.01 41.45 2.52
518 543 4.830826 AGAAGCCTTCTTTTTGTTACGG 57.169 40.909 0.00 0.00 36.36 4.02
519 544 3.004419 AGAAGCCTTCTTTTTGTTACGGC 59.996 43.478 0.00 0.00 36.36 5.68
520 545 2.303175 AGCCTTCTTTTTGTTACGGCA 58.697 42.857 0.00 0.00 38.48 5.69
521 546 2.691011 AGCCTTCTTTTTGTTACGGCAA 59.309 40.909 0.00 0.00 38.48 4.52
522 547 3.320826 AGCCTTCTTTTTGTTACGGCAAT 59.679 39.130 0.00 0.00 38.48 3.56
523 548 4.521256 AGCCTTCTTTTTGTTACGGCAATA 59.479 37.500 0.00 0.00 38.48 1.90
524 549 5.010213 AGCCTTCTTTTTGTTACGGCAATAA 59.990 36.000 0.00 0.00 38.48 1.40
525 550 5.867174 GCCTTCTTTTTGTTACGGCAATAAT 59.133 36.000 0.00 0.00 36.16 1.28
526 551 7.030768 GCCTTCTTTTTGTTACGGCAATAATA 58.969 34.615 0.00 0.00 36.16 0.98
527 552 7.704899 GCCTTCTTTTTGTTACGGCAATAATAT 59.295 33.333 0.00 0.00 36.16 1.28
537 562 9.719355 TGTTACGGCAATAATATATTGATGTCT 57.281 29.630 12.93 2.54 0.00 3.41
539 564 7.849804 ACGGCAATAATATATTGATGTCTCC 57.150 36.000 12.93 3.70 0.00 3.71
540 565 7.624549 ACGGCAATAATATATTGATGTCTCCT 58.375 34.615 12.93 0.00 0.00 3.69
541 566 7.550551 ACGGCAATAATATATTGATGTCTCCTG 59.449 37.037 12.93 2.83 0.00 3.86
542 567 7.765819 CGGCAATAATATATTGATGTCTCCTGA 59.234 37.037 12.93 0.00 0.00 3.86
543 568 9.624373 GGCAATAATATATTGATGTCTCCTGAT 57.376 33.333 12.93 0.00 0.00 2.90
550 575 4.655762 TTGATGTCTCCTGATTACTCGG 57.344 45.455 0.00 0.00 0.00 4.63
551 576 3.898482 TGATGTCTCCTGATTACTCGGA 58.102 45.455 0.00 0.00 0.00 4.55
552 577 4.474394 TGATGTCTCCTGATTACTCGGAT 58.526 43.478 0.00 0.00 0.00 4.18
679 706 8.275015 TGCAATTAGATCGACATTTAGGAAAA 57.725 30.769 0.00 0.00 0.00 2.29
686 713 5.652994 TCGACATTTAGGAAAATTTGGGG 57.347 39.130 0.00 0.00 32.87 4.96
687 714 5.081032 TCGACATTTAGGAAAATTTGGGGT 58.919 37.500 0.00 0.00 32.87 4.95
718 746 4.603094 TCCTCTGATACCCTTACACAGA 57.397 45.455 0.00 0.00 36.42 3.41
858 1212 3.945285 TGTGGTTGGAGAGTTTTCAAGTC 59.055 43.478 0.00 0.00 0.00 3.01
953 1307 6.537660 CAGTGCTCATTCTGACAATATTGAGA 59.462 38.462 22.16 12.05 34.00 3.27
1170 1567 5.334337 GCTTCGCATAATGCATGATGTTCTA 60.334 40.000 22.64 7.69 45.36 2.10
1476 1873 5.409826 GGATAGTGGCAGCACTAATTACATC 59.590 44.000 6.88 1.28 40.56 3.06
1542 1939 2.766828 CGAAGAAGATCTAGTGGGGGTT 59.233 50.000 0.00 0.00 0.00 4.11
1680 2077 4.226384 ACAAGAAGGCAAGGGAGAAATTT 58.774 39.130 0.00 0.00 0.00 1.82
2181 2643 1.350319 GTGTGTGCGCGAGAAAACA 59.650 52.632 12.10 2.54 0.00 2.83
3126 3589 5.045942 TGTTAGACATTTATGGGAGCTGACA 60.046 40.000 0.00 0.00 0.00 3.58
3130 3593 4.012374 ACATTTATGGGAGCTGACACAAG 58.988 43.478 0.00 0.00 0.00 3.16
3215 3678 0.583438 CGGATGCGCTATTTGTCCTG 59.417 55.000 9.73 0.57 0.00 3.86
3266 3729 5.010719 ACGAGGTTCTCTTGTTGAATGTCTA 59.989 40.000 0.00 0.00 36.75 2.59
3459 3922 3.117046 GCGTCTACAATTCACTAGAGCC 58.883 50.000 0.00 0.00 0.00 4.70
3559 4022 7.946381 AATCTGAATCGGCTAGAGATACATA 57.054 36.000 0.00 0.00 0.00 2.29
3754 4217 5.769367 CGGTGTATTCTCTCCGATATTGAA 58.231 41.667 0.00 0.00 44.05 2.69
3781 4249 3.243501 CCAGACTGGTTTGGAAATGTGTG 60.244 47.826 13.84 0.00 37.03 3.82
3937 4405 1.858091 ACGAAGATGCTTCGCTATGG 58.142 50.000 24.38 3.42 44.98 2.74
3948 4416 5.368145 TGCTTCGCTATGGAGTTCATTATT 58.632 37.500 0.00 0.00 37.30 1.40
4105 4573 1.081242 CGTGCCATGGTGTGCTTTC 60.081 57.895 14.67 0.00 0.00 2.62
4244 4712 2.802247 TCGTGTGCATTCTTGTTCTGAG 59.198 45.455 0.00 0.00 0.00 3.35
4472 4945 4.332268 GCAGTGAAAATGTTTTGGAAAGCA 59.668 37.500 0.00 0.00 32.28 3.91
4474 4947 4.566360 AGTGAAAATGTTTTGGAAAGCACG 59.434 37.500 0.00 0.00 31.94 5.34
4671 5208 6.039382 GCCCGATTTATGTAAGATTGGTTTCT 59.961 38.462 0.00 0.00 0.00 2.52
4701 5238 2.817258 TCCCTTGGTGCTTATTGTTTCG 59.183 45.455 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 7.452501 AGCATATGCCACCATTAACAAGATTAT 59.547 33.333 23.96 0.00 43.38 1.28
114 137 2.000447 GTTGACTCCCTACATTGTCGC 59.000 52.381 0.00 0.00 32.64 5.19
289 314 1.541147 GGCAGTGCTGTTGATTAAGCA 59.459 47.619 16.11 0.00 46.84 3.91
290 315 1.815003 AGGCAGTGCTGTTGATTAAGC 59.185 47.619 16.11 0.00 39.96 3.09
291 316 5.007430 CAGATAGGCAGTGCTGTTGATTAAG 59.993 44.000 16.11 0.00 0.00 1.85
292 317 4.877823 CAGATAGGCAGTGCTGTTGATTAA 59.122 41.667 16.11 0.00 0.00 1.40
293 318 4.080919 ACAGATAGGCAGTGCTGTTGATTA 60.081 41.667 16.11 0.00 38.34 1.75
294 319 3.276857 CAGATAGGCAGTGCTGTTGATT 58.723 45.455 16.11 0.00 0.00 2.57
295 320 2.238144 ACAGATAGGCAGTGCTGTTGAT 59.762 45.455 16.11 1.40 38.34 2.57
296 321 1.625315 ACAGATAGGCAGTGCTGTTGA 59.375 47.619 16.11 0.00 38.34 3.18
297 322 2.105006 ACAGATAGGCAGTGCTGTTG 57.895 50.000 16.11 9.21 38.34 3.33
298 323 2.867109 AACAGATAGGCAGTGCTGTT 57.133 45.000 16.11 13.99 44.25 3.16
299 324 2.304180 AGAAACAGATAGGCAGTGCTGT 59.696 45.455 16.11 8.15 42.91 4.40
300 325 2.935201 GAGAAACAGATAGGCAGTGCTG 59.065 50.000 16.11 7.44 34.65 4.41
301 326 2.093235 GGAGAAACAGATAGGCAGTGCT 60.093 50.000 16.11 3.64 0.00 4.40
302 327 2.284190 GGAGAAACAGATAGGCAGTGC 58.716 52.381 6.55 6.55 0.00 4.40
303 328 3.616956 TGGAGAAACAGATAGGCAGTG 57.383 47.619 0.00 0.00 0.00 3.66
304 329 4.716784 TGTATGGAGAAACAGATAGGCAGT 59.283 41.667 0.00 0.00 0.00 4.40
305 330 5.282055 TGTATGGAGAAACAGATAGGCAG 57.718 43.478 0.00 0.00 0.00 4.85
306 331 5.604231 AGATGTATGGAGAAACAGATAGGCA 59.396 40.000 0.00 0.00 0.00 4.75
307 332 5.931146 CAGATGTATGGAGAAACAGATAGGC 59.069 44.000 0.00 0.00 0.00 3.93
308 333 6.462500 CCAGATGTATGGAGAAACAGATAGG 58.538 44.000 0.00 0.00 43.57 2.57
309 334 6.268617 TCCCAGATGTATGGAGAAACAGATAG 59.731 42.308 0.00 0.00 43.57 2.08
310 335 6.143206 TCCCAGATGTATGGAGAAACAGATA 58.857 40.000 0.00 0.00 43.57 1.98
311 336 4.971282 TCCCAGATGTATGGAGAAACAGAT 59.029 41.667 0.00 0.00 43.57 2.90
312 337 4.361783 TCCCAGATGTATGGAGAAACAGA 58.638 43.478 0.00 0.00 43.57 3.41
313 338 4.760530 TCCCAGATGTATGGAGAAACAG 57.239 45.455 0.00 0.00 43.57 3.16
314 339 4.686944 GCATCCCAGATGTATGGAGAAACA 60.687 45.833 6.46 0.00 43.57 2.83
315 340 3.817647 GCATCCCAGATGTATGGAGAAAC 59.182 47.826 6.46 0.00 43.57 2.78
316 341 3.459227 TGCATCCCAGATGTATGGAGAAA 59.541 43.478 6.46 0.00 43.57 2.52
317 342 3.047857 TGCATCCCAGATGTATGGAGAA 58.952 45.455 6.46 0.00 43.57 2.87
318 343 2.693210 TGCATCCCAGATGTATGGAGA 58.307 47.619 6.46 0.00 43.57 3.71
319 344 3.497103 TTGCATCCCAGATGTATGGAG 57.503 47.619 6.46 0.00 43.57 3.86
320 345 4.458256 AATTGCATCCCAGATGTATGGA 57.542 40.909 6.46 0.00 43.57 3.41
321 346 5.563592 TCTAATTGCATCCCAGATGTATGG 58.436 41.667 6.46 0.00 40.29 2.74
322 347 6.036844 CGATCTAATTGCATCCCAGATGTATG 59.963 42.308 6.46 0.00 0.00 2.39
323 348 6.070596 TCGATCTAATTGCATCCCAGATGTAT 60.071 38.462 6.46 0.00 0.00 2.29
324 349 5.245977 TCGATCTAATTGCATCCCAGATGTA 59.754 40.000 6.46 0.00 0.00 2.29
325 350 4.040829 TCGATCTAATTGCATCCCAGATGT 59.959 41.667 6.46 0.00 0.00 3.06
326 351 4.572909 TCGATCTAATTGCATCCCAGATG 58.427 43.478 0.09 0.09 0.00 2.90
327 352 4.897509 TCGATCTAATTGCATCCCAGAT 57.102 40.909 0.00 0.00 0.00 2.90
328 353 4.897509 ATCGATCTAATTGCATCCCAGA 57.102 40.909 0.00 0.00 0.00 3.86
329 354 7.414873 CCAAATATCGATCTAATTGCATCCCAG 60.415 40.741 0.00 0.00 0.00 4.45
330 355 6.375174 CCAAATATCGATCTAATTGCATCCCA 59.625 38.462 0.00 0.00 0.00 4.37
331 356 6.183360 CCCAAATATCGATCTAATTGCATCCC 60.183 42.308 0.00 0.00 0.00 3.85
332 357 6.599244 TCCCAAATATCGATCTAATTGCATCC 59.401 38.462 0.00 0.00 0.00 3.51
333 358 7.615582 TCCCAAATATCGATCTAATTGCATC 57.384 36.000 0.00 0.00 0.00 3.91
334 359 8.408043 TTTCCCAAATATCGATCTAATTGCAT 57.592 30.769 0.00 0.00 0.00 3.96
335 360 7.502226 ACTTTCCCAAATATCGATCTAATTGCA 59.498 33.333 0.00 0.00 0.00 4.08
336 361 7.875971 ACTTTCCCAAATATCGATCTAATTGC 58.124 34.615 0.00 0.00 0.00 3.56
339 364 9.726438 CCTAACTTTCCCAAATATCGATCTAAT 57.274 33.333 0.00 0.00 0.00 1.73
340 365 8.154856 CCCTAACTTTCCCAAATATCGATCTAA 58.845 37.037 0.00 0.00 0.00 2.10
341 366 7.291651 ACCCTAACTTTCCCAAATATCGATCTA 59.708 37.037 0.00 0.00 0.00 1.98
342 367 6.101296 ACCCTAACTTTCCCAAATATCGATCT 59.899 38.462 0.00 0.00 0.00 2.75
343 368 6.296803 ACCCTAACTTTCCCAAATATCGATC 58.703 40.000 0.00 0.00 0.00 3.69
344 369 6.126594 TGACCCTAACTTTCCCAAATATCGAT 60.127 38.462 2.16 2.16 0.00 3.59
345 370 5.190132 TGACCCTAACTTTCCCAAATATCGA 59.810 40.000 0.00 0.00 0.00 3.59
346 371 5.433526 TGACCCTAACTTTCCCAAATATCG 58.566 41.667 0.00 0.00 0.00 2.92
347 372 7.898014 AATGACCCTAACTTTCCCAAATATC 57.102 36.000 0.00 0.00 0.00 1.63
348 373 8.679344 AAAATGACCCTAACTTTCCCAAATAT 57.321 30.769 0.00 0.00 0.00 1.28
349 374 8.499288 AAAAATGACCCTAACTTTCCCAAATA 57.501 30.769 0.00 0.00 0.00 1.40
350 375 7.387265 AAAAATGACCCTAACTTTCCCAAAT 57.613 32.000 0.00 0.00 0.00 2.32
351 376 6.461788 CGAAAAATGACCCTAACTTTCCCAAA 60.462 38.462 0.00 0.00 0.00 3.28
352 377 5.010213 CGAAAAATGACCCTAACTTTCCCAA 59.990 40.000 0.00 0.00 0.00 4.12
353 378 4.521256 CGAAAAATGACCCTAACTTTCCCA 59.479 41.667 0.00 0.00 0.00 4.37
354 379 4.763279 TCGAAAAATGACCCTAACTTTCCC 59.237 41.667 0.00 0.00 0.00 3.97
355 380 5.696822 GTCGAAAAATGACCCTAACTTTCC 58.303 41.667 0.00 0.00 0.00 3.13
366 391 4.571176 GGTATCAGAGGGTCGAAAAATGAC 59.429 45.833 0.00 0.00 35.60 3.06
367 392 4.383770 GGGTATCAGAGGGTCGAAAAATGA 60.384 45.833 0.00 0.00 0.00 2.57
368 393 3.877508 GGGTATCAGAGGGTCGAAAAATG 59.122 47.826 0.00 0.00 0.00 2.32
369 394 3.780850 AGGGTATCAGAGGGTCGAAAAAT 59.219 43.478 0.00 0.00 0.00 1.82
370 395 3.178865 AGGGTATCAGAGGGTCGAAAAA 58.821 45.455 0.00 0.00 0.00 1.94
371 396 2.829023 AGGGTATCAGAGGGTCGAAAA 58.171 47.619 0.00 0.00 0.00 2.29
372 397 2.544844 AGGGTATCAGAGGGTCGAAA 57.455 50.000 0.00 0.00 0.00 3.46
373 398 2.544844 AAGGGTATCAGAGGGTCGAA 57.455 50.000 0.00 0.00 0.00 3.71
374 399 3.897657 ATAAGGGTATCAGAGGGTCGA 57.102 47.619 0.00 0.00 0.00 4.20
375 400 3.439476 CGTATAAGGGTATCAGAGGGTCG 59.561 52.174 0.00 0.00 0.00 4.79
376 401 3.762823 CCGTATAAGGGTATCAGAGGGTC 59.237 52.174 0.00 0.00 0.00 4.46
377 402 3.775910 CCGTATAAGGGTATCAGAGGGT 58.224 50.000 0.00 0.00 0.00 4.34
378 403 2.496470 GCCGTATAAGGGTATCAGAGGG 59.504 54.545 6.84 0.00 0.00 4.30
379 404 3.162666 TGCCGTATAAGGGTATCAGAGG 58.837 50.000 6.84 0.00 0.00 3.69
380 405 3.367498 GCTGCCGTATAAGGGTATCAGAG 60.367 52.174 12.10 0.00 0.00 3.35
381 406 2.561419 GCTGCCGTATAAGGGTATCAGA 59.439 50.000 12.10 0.00 0.00 3.27
382 407 2.299013 TGCTGCCGTATAAGGGTATCAG 59.701 50.000 6.84 6.31 0.00 2.90
383 408 2.299013 CTGCTGCCGTATAAGGGTATCA 59.701 50.000 6.84 0.00 0.00 2.15
384 409 2.561419 TCTGCTGCCGTATAAGGGTATC 59.439 50.000 6.84 0.00 0.00 2.24
385 410 2.563179 CTCTGCTGCCGTATAAGGGTAT 59.437 50.000 6.84 0.00 0.00 2.73
386 411 1.961394 CTCTGCTGCCGTATAAGGGTA 59.039 52.381 6.84 0.00 0.00 3.69
387 412 0.753262 CTCTGCTGCCGTATAAGGGT 59.247 55.000 6.84 0.00 0.00 4.34
388 413 0.753262 ACTCTGCTGCCGTATAAGGG 59.247 55.000 6.84 0.00 0.00 3.95
389 414 3.579709 CATACTCTGCTGCCGTATAAGG 58.420 50.000 0.00 0.00 0.00 2.69
402 427 4.456911 ACCAAACTGAACATGCATACTCTG 59.543 41.667 0.00 5.76 0.00 3.35
403 428 4.655963 ACCAAACTGAACATGCATACTCT 58.344 39.130 0.00 0.00 0.00 3.24
404 429 4.436050 CGACCAAACTGAACATGCATACTC 60.436 45.833 0.00 0.00 0.00 2.59
405 430 3.436704 CGACCAAACTGAACATGCATACT 59.563 43.478 0.00 0.00 0.00 2.12
406 431 3.435327 TCGACCAAACTGAACATGCATAC 59.565 43.478 0.00 0.00 0.00 2.39
407 432 3.669536 TCGACCAAACTGAACATGCATA 58.330 40.909 0.00 0.00 0.00 3.14
408 433 2.485426 CTCGACCAAACTGAACATGCAT 59.515 45.455 0.00 0.00 0.00 3.96
409 434 1.872952 CTCGACCAAACTGAACATGCA 59.127 47.619 0.00 0.00 0.00 3.96
410 435 1.197721 CCTCGACCAAACTGAACATGC 59.802 52.381 0.00 0.00 0.00 4.06
411 436 1.806542 CCCTCGACCAAACTGAACATG 59.193 52.381 0.00 0.00 0.00 3.21
412 437 1.882352 GCCCTCGACCAAACTGAACAT 60.882 52.381 0.00 0.00 0.00 2.71
413 438 0.534203 GCCCTCGACCAAACTGAACA 60.534 55.000 0.00 0.00 0.00 3.18
414 439 1.235281 GGCCCTCGACCAAACTGAAC 61.235 60.000 0.00 0.00 0.00 3.18
415 440 1.072505 GGCCCTCGACCAAACTGAA 59.927 57.895 0.00 0.00 0.00 3.02
416 441 2.144078 TGGCCCTCGACCAAACTGA 61.144 57.895 0.00 0.00 33.12 3.41
417 442 1.966451 GTGGCCCTCGACCAAACTG 60.966 63.158 0.00 0.00 39.39 3.16
418 443 1.705997 AAGTGGCCCTCGACCAAACT 61.706 55.000 0.00 0.00 39.39 2.66
419 444 0.822121 AAAGTGGCCCTCGACCAAAC 60.822 55.000 0.00 0.00 39.39 2.93
420 445 0.106419 AAAAGTGGCCCTCGACCAAA 60.106 50.000 0.00 0.00 39.39 3.28
421 446 0.536460 GAAAAGTGGCCCTCGACCAA 60.536 55.000 0.00 0.00 39.39 3.67
422 447 1.072505 GAAAAGTGGCCCTCGACCA 59.927 57.895 0.00 0.00 33.84 4.02
423 448 0.250770 AAGAAAAGTGGCCCTCGACC 60.251 55.000 0.00 0.00 0.00 4.79
424 449 2.467566 TAAGAAAAGTGGCCCTCGAC 57.532 50.000 0.00 0.00 0.00 4.20
425 450 2.569853 TGATAAGAAAAGTGGCCCTCGA 59.430 45.455 0.00 0.00 0.00 4.04
426 451 2.939103 CTGATAAGAAAAGTGGCCCTCG 59.061 50.000 0.00 0.00 0.00 4.63
427 452 3.956744 ACTGATAAGAAAAGTGGCCCTC 58.043 45.455 0.00 0.00 0.00 4.30
428 453 4.388577 AACTGATAAGAAAAGTGGCCCT 57.611 40.909 0.00 0.00 0.00 5.19
429 454 6.775594 ATTAACTGATAAGAAAAGTGGCCC 57.224 37.500 0.00 0.00 0.00 5.80
430 455 8.736244 TGTTATTAACTGATAAGAAAAGTGGCC 58.264 33.333 7.99 0.00 0.00 5.36
449 474 9.632807 GCCAACTGTGTCAATTATTTGTTATTA 57.367 29.630 0.00 0.00 34.32 0.98
450 475 8.367156 AGCCAACTGTGTCAATTATTTGTTATT 58.633 29.630 0.00 0.00 34.32 1.40
451 476 7.895759 AGCCAACTGTGTCAATTATTTGTTAT 58.104 30.769 0.00 0.00 34.32 1.89
452 477 7.283625 AGCCAACTGTGTCAATTATTTGTTA 57.716 32.000 0.00 0.00 34.32 2.41
453 478 6.160576 AGCCAACTGTGTCAATTATTTGTT 57.839 33.333 0.00 0.00 34.32 2.83
454 479 5.789643 AGCCAACTGTGTCAATTATTTGT 57.210 34.783 0.00 0.00 34.32 2.83
455 480 6.676950 TGTAGCCAACTGTGTCAATTATTTG 58.323 36.000 0.00 0.00 0.00 2.32
456 481 6.570378 GCTGTAGCCAACTGTGTCAATTATTT 60.570 38.462 0.00 0.00 34.31 1.40
457 482 5.106157 GCTGTAGCCAACTGTGTCAATTATT 60.106 40.000 0.00 0.00 34.31 1.40
458 483 4.396166 GCTGTAGCCAACTGTGTCAATTAT 59.604 41.667 0.00 0.00 34.31 1.28
459 484 3.751175 GCTGTAGCCAACTGTGTCAATTA 59.249 43.478 0.00 0.00 34.31 1.40
460 485 2.554032 GCTGTAGCCAACTGTGTCAATT 59.446 45.455 0.00 0.00 34.31 2.32
461 486 2.154462 GCTGTAGCCAACTGTGTCAAT 58.846 47.619 0.00 0.00 34.31 2.57
462 487 1.134250 TGCTGTAGCCAACTGTGTCAA 60.134 47.619 0.80 0.00 41.18 3.18
463 488 0.467804 TGCTGTAGCCAACTGTGTCA 59.532 50.000 0.80 0.00 41.18 3.58
464 489 1.151668 CTGCTGTAGCCAACTGTGTC 58.848 55.000 0.80 0.00 41.18 3.67
465 490 0.469917 ACTGCTGTAGCCAACTGTGT 59.530 50.000 0.80 0.00 41.18 3.72
466 491 1.151668 GACTGCTGTAGCCAACTGTG 58.848 55.000 0.80 0.00 41.18 3.66
467 492 0.758734 TGACTGCTGTAGCCAACTGT 59.241 50.000 0.80 0.00 41.18 3.55
468 493 1.151668 GTGACTGCTGTAGCCAACTG 58.848 55.000 0.80 0.00 41.18 3.16
469 494 0.758734 TGTGACTGCTGTAGCCAACT 59.241 50.000 0.80 0.00 41.18 3.16
470 495 1.813513 ATGTGACTGCTGTAGCCAAC 58.186 50.000 0.80 0.00 41.18 3.77
471 496 3.197549 TCATATGTGACTGCTGTAGCCAA 59.802 43.478 1.90 0.00 41.18 4.52
472 497 2.765699 TCATATGTGACTGCTGTAGCCA 59.234 45.455 1.90 0.00 41.18 4.75
473 498 3.459232 TCATATGTGACTGCTGTAGCC 57.541 47.619 1.90 0.00 41.18 3.93
474 499 4.183865 TGTTCATATGTGACTGCTGTAGC 58.816 43.478 1.90 0.00 36.33 3.58
475 500 6.101997 TCTTGTTCATATGTGACTGCTGTAG 58.898 40.000 1.90 0.00 33.11 2.74
476 501 6.036577 TCTTGTTCATATGTGACTGCTGTA 57.963 37.500 1.90 0.00 33.11 2.74
477 502 4.898320 TCTTGTTCATATGTGACTGCTGT 58.102 39.130 1.90 0.00 33.11 4.40
478 503 5.673068 GCTTCTTGTTCATATGTGACTGCTG 60.673 44.000 1.90 0.00 33.11 4.41
479 504 4.394300 GCTTCTTGTTCATATGTGACTGCT 59.606 41.667 1.90 0.00 33.11 4.24
480 505 4.437930 GGCTTCTTGTTCATATGTGACTGC 60.438 45.833 1.90 0.00 33.11 4.40
481 506 4.940046 AGGCTTCTTGTTCATATGTGACTG 59.060 41.667 1.90 2.12 33.11 3.51
482 507 5.171339 AGGCTTCTTGTTCATATGTGACT 57.829 39.130 1.90 0.00 33.11 3.41
483 508 5.645497 AGAAGGCTTCTTGTTCATATGTGAC 59.355 40.000 23.76 4.04 36.36 3.67
484 509 5.809001 AGAAGGCTTCTTGTTCATATGTGA 58.191 37.500 23.76 0.00 36.36 3.58
488 513 8.424133 AACAAAAAGAAGGCTTCTTGTTCATAT 58.576 29.630 35.86 20.81 46.81 1.78
489 514 7.781056 AACAAAAAGAAGGCTTCTTGTTCATA 58.219 30.769 35.86 0.00 46.81 2.15
490 515 6.643388 AACAAAAAGAAGGCTTCTTGTTCAT 58.357 32.000 35.86 24.89 46.81 2.57
491 516 6.036577 AACAAAAAGAAGGCTTCTTGTTCA 57.963 33.333 35.86 0.00 46.81 3.18
492 517 6.196538 CGTAACAAAAAGAAGGCTTCTTGTTC 59.803 38.462 32.92 25.40 46.81 3.18
497 522 3.004419 GCCGTAACAAAAAGAAGGCTTCT 59.996 43.478 23.76 23.76 43.15 2.85
498 523 3.243267 TGCCGTAACAAAAAGAAGGCTTC 60.243 43.478 19.53 19.53 43.15 3.86
499 524 2.691011 TGCCGTAACAAAAAGAAGGCTT 59.309 40.909 0.00 0.00 43.15 4.35
500 525 2.303175 TGCCGTAACAAAAAGAAGGCT 58.697 42.857 5.16 0.00 43.15 4.58
501 526 2.785713 TGCCGTAACAAAAAGAAGGC 57.214 45.000 0.00 0.00 43.05 4.35
511 536 9.719355 AGACATCAATATATTATTGCCGTAACA 57.281 29.630 0.00 0.00 0.00 2.41
513 538 9.378551 GGAGACATCAATATATTATTGCCGTAA 57.621 33.333 0.00 0.00 0.00 3.18
514 539 8.758829 AGGAGACATCAATATATTATTGCCGTA 58.241 33.333 0.00 0.00 0.00 4.02
515 540 7.550551 CAGGAGACATCAATATATTATTGCCGT 59.449 37.037 0.00 2.91 0.00 5.68
516 541 7.765819 TCAGGAGACATCAATATATTATTGCCG 59.234 37.037 0.00 0.28 0.00 5.69
517 542 9.624373 ATCAGGAGACATCAATATATTATTGCC 57.376 33.333 0.00 0.00 0.00 4.52
524 549 8.690884 CCGAGTAATCAGGAGACATCAATATAT 58.309 37.037 0.00 0.00 0.00 0.86
525 550 7.888546 TCCGAGTAATCAGGAGACATCAATATA 59.111 37.037 0.64 0.00 0.00 0.86
526 551 6.721668 TCCGAGTAATCAGGAGACATCAATAT 59.278 38.462 0.64 0.00 0.00 1.28
527 552 6.068670 TCCGAGTAATCAGGAGACATCAATA 58.931 40.000 0.64 0.00 0.00 1.90
528 553 4.895889 TCCGAGTAATCAGGAGACATCAAT 59.104 41.667 0.64 0.00 0.00 2.57
529 554 4.278310 TCCGAGTAATCAGGAGACATCAA 58.722 43.478 0.64 0.00 0.00 2.57
530 555 3.898482 TCCGAGTAATCAGGAGACATCA 58.102 45.455 0.64 0.00 0.00 3.07
531 556 5.945155 GTATCCGAGTAATCAGGAGACATC 58.055 45.833 17.61 0.00 43.52 3.06
532 557 5.968528 GTATCCGAGTAATCAGGAGACAT 57.031 43.478 17.61 3.44 43.52 3.06
534 559 5.968528 ATGTATCCGAGTAATCAGGAGAC 57.031 43.478 16.44 16.44 44.11 3.36
535 560 9.397280 CTATAATGTATCCGAGTAATCAGGAGA 57.603 37.037 9.07 3.03 37.49 3.71
536 561 8.132362 GCTATAATGTATCCGAGTAATCAGGAG 58.868 40.741 9.07 0.00 37.49 3.69
537 562 7.834681 AGCTATAATGTATCCGAGTAATCAGGA 59.165 37.037 6.29 6.29 38.56 3.86
538 563 8.001881 AGCTATAATGTATCCGAGTAATCAGG 57.998 38.462 0.00 0.00 0.00 3.86
539 564 9.862371 AAAGCTATAATGTATCCGAGTAATCAG 57.138 33.333 0.00 0.00 0.00 2.90
540 565 9.639601 CAAAGCTATAATGTATCCGAGTAATCA 57.360 33.333 0.00 0.00 0.00 2.57
541 566 9.640963 ACAAAGCTATAATGTATCCGAGTAATC 57.359 33.333 0.00 0.00 0.00 1.75
542 567 9.998106 AACAAAGCTATAATGTATCCGAGTAAT 57.002 29.630 0.00 0.00 0.00 1.89
543 568 9.826574 AAACAAAGCTATAATGTATCCGAGTAA 57.173 29.630 0.00 0.00 0.00 2.24
544 569 9.826574 AAAACAAAGCTATAATGTATCCGAGTA 57.173 29.630 0.00 0.00 0.00 2.59
545 570 8.732746 AAAACAAAGCTATAATGTATCCGAGT 57.267 30.769 0.00 0.00 0.00 4.18
546 571 9.046296 AGAAAACAAAGCTATAATGTATCCGAG 57.954 33.333 0.00 0.00 0.00 4.63
547 572 8.958119 AGAAAACAAAGCTATAATGTATCCGA 57.042 30.769 0.00 0.00 0.00 4.55
591 616 8.704668 TGATTAAGCTACAAGAAGATGTATCCA 58.295 33.333 0.00 0.00 35.37 3.41
607 632 4.651778 AGGCAGTGTTGTTGATTAAGCTA 58.348 39.130 0.00 0.00 0.00 3.32
679 706 7.882755 TCAGAGGATAGAAAAATACCCCAAAT 58.117 34.615 0.00 0.00 0.00 2.32
682 709 7.017254 GGTATCAGAGGATAGAAAAATACCCCA 59.983 40.741 0.00 0.00 36.69 4.96
695 722 6.275692 TCTGTGTAAGGGTATCAGAGGATA 57.724 41.667 0.00 0.00 34.89 2.59
697 725 4.603094 TCTGTGTAAGGGTATCAGAGGA 57.397 45.455 0.00 0.00 32.49 3.71
713 741 6.101997 TGAACATACATACTCTGCTTCTGTG 58.898 40.000 0.00 0.00 0.00 3.66
718 746 6.372659 CCAAACTGAACATACATACTCTGCTT 59.627 38.462 0.00 0.00 0.00 3.91
858 1212 2.000447 GCAGTAAGCACCTACCGAAAG 59.000 52.381 0.00 0.00 44.79 2.62
953 1307 1.145738 ACTGTTTGATGGTGGCCTCTT 59.854 47.619 3.32 0.00 0.00 2.85
1192 1589 4.180817 CCGTCATATACTTGACTGTTGCA 58.819 43.478 5.23 0.00 43.10 4.08
1476 1873 1.827969 AGATCTTGGGACCTCTTGACG 59.172 52.381 0.00 0.00 0.00 4.35
1542 1939 8.465999 TGCTCAAGTTTTTCTCTGTTTTTATCA 58.534 29.630 0.00 0.00 0.00 2.15
1680 2077 3.315142 GATCCAGGCGTGGCACTGA 62.315 63.158 20.76 3.23 44.60 3.41
2181 2643 8.331740 TCATTAATTCTTCTCCATTCTTCCACT 58.668 33.333 0.00 0.00 0.00 4.00
2652 3115 3.181493 GGTGCATGCTAGAAAATGACTGG 60.181 47.826 20.33 0.00 0.00 4.00
3126 3589 5.765182 CCATAACCTCAAACTTCTCACTTGT 59.235 40.000 0.00 0.00 0.00 3.16
3130 3593 6.431234 ACATTCCATAACCTCAAACTTCTCAC 59.569 38.462 0.00 0.00 0.00 3.51
3215 3678 2.223433 GCACTTGCATTCACATCTAGGC 60.223 50.000 0.00 0.00 41.59 3.93
3266 3729 1.751349 CTTTTGCAGGCTTGGCAGGT 61.751 55.000 0.00 0.00 43.05 4.00
3459 3922 0.528017 TCAGCTGCTCTCCGTTGTAG 59.472 55.000 9.47 0.00 0.00 2.74
3559 4022 3.064324 GCTCGCCATGGCACCTTT 61.064 61.111 34.93 0.00 42.06 3.11
3754 4217 0.482446 TCCAAACCAGTCTGGGCATT 59.518 50.000 23.06 11.73 43.37 3.56
3948 4416 7.565680 GGATACTCCTTTTTCCTTGATCTACA 58.434 38.462 0.00 0.00 32.53 2.74
4244 4712 2.636830 ACAGACACAGCTGGAATATGC 58.363 47.619 19.93 3.46 40.20 3.14
4671 5208 3.306472 AGCACCAAGGGACAGTTTAAA 57.694 42.857 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.