Multiple sequence alignment - TraesCS7D01G087400

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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 TraesCS7D01G087400 chr7D 100.000 3610 0 0 1 3610 53510821 53507212 0.000000e+00 6667
1 TraesCS7D01G087400 chr7D 84.119 2758 361 47 864 3579 53498748 53496026 0.000000e+00 2595
2 TraesCS7D01G087400 chr7D 87.717 1270 137 14 2284 3549 53484058 53482804 0.000000e+00 1463
3 TraesCS7D01G087400 chr7D 87.660 1248 135 14 2303 3546 52696501 52697733 0.000000e+00 1434
4 TraesCS7D01G087400 chr7D 79.819 1551 271 30 606 2145 53427505 53425986 0.000000e+00 1092
5 TraesCS7D01G087400 chr7D 78.788 1683 310 38 547 2199 53434725 53433060 0.000000e+00 1086
6 TraesCS7D01G087400 chr7D 82.777 1109 172 18 769 1869 53485505 53484408 0.000000e+00 972
7 TraesCS7D01G087400 chr7A 92.584 2724 183 8 862 3583 55895510 55892804 0.000000e+00 3893
8 TraesCS7D01G087400 chr7A 83.728 2747 380 48 874 3579 55883566 55880846 0.000000e+00 2534
9 TraesCS7D01G087400 chr7A 87.010 1301 146 19 2247 3543 55427140 55425859 0.000000e+00 1445
10 TraesCS7D01G087400 chr7A 87.293 1149 139 7 2262 3407 55383717 55382573 0.000000e+00 1306
11 TraesCS7D01G087400 chr7A 80.220 1547 269 23 606 2145 55385284 55383768 0.000000e+00 1127
12 TraesCS7D01G087400 chr7A 82.071 1188 192 16 691 1869 55428630 55427455 0.000000e+00 994
13 TraesCS7D01G087400 chr4A 86.055 3105 365 40 515 3596 668163224 668160165 0.000000e+00 3273
14 TraesCS7D01G087400 chr4A 83.635 2762 380 49 864 3579 668148985 668146250 0.000000e+00 2531
15 TraesCS7D01G087400 chr4A 80.284 1547 268 25 606 2145 668086196 668084680 0.000000e+00 1133
16 TraesCS7D01G087400 chr4A 80.989 1415 226 27 691 2101 668110506 668109131 0.000000e+00 1083
17 TraesCS7D01G087400 chr4A 85.886 333 18 14 2 316 668163546 668163225 9.660000e-86 327


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 TraesCS7D01G087400 chr7D 53507212 53510821 3609 True 6667.0 6667 100.0000 1 3610 1 chr7D.!!$R4 3609
1 TraesCS7D01G087400 chr7D 53496026 53498748 2722 True 2595.0 2595 84.1190 864 3579 1 chr7D.!!$R3 2715
2 TraesCS7D01G087400 chr7D 52696501 52697733 1232 False 1434.0 1434 87.6600 2303 3546 1 chr7D.!!$F1 1243
3 TraesCS7D01G087400 chr7D 53482804 53485505 2701 True 1217.5 1463 85.2470 769 3549 2 chr7D.!!$R5 2780
4 TraesCS7D01G087400 chr7D 53425986 53427505 1519 True 1092.0 1092 79.8190 606 2145 1 chr7D.!!$R1 1539
5 TraesCS7D01G087400 chr7D 53433060 53434725 1665 True 1086.0 1086 78.7880 547 2199 1 chr7D.!!$R2 1652
6 TraesCS7D01G087400 chr7A 55892804 55895510 2706 True 3893.0 3893 92.5840 862 3583 1 chr7A.!!$R2 2721
7 TraesCS7D01G087400 chr7A 55880846 55883566 2720 True 2534.0 2534 83.7280 874 3579 1 chr7A.!!$R1 2705
8 TraesCS7D01G087400 chr7A 55425859 55428630 2771 True 1219.5 1445 84.5405 691 3543 2 chr7A.!!$R4 2852
9 TraesCS7D01G087400 chr7A 55382573 55385284 2711 True 1216.5 1306 83.7565 606 3407 2 chr7A.!!$R3 2801
10 TraesCS7D01G087400 chr4A 668146250 668148985 2735 True 2531.0 2531 83.6350 864 3579 1 chr4A.!!$R3 2715
11 TraesCS7D01G087400 chr4A 668160165 668163546 3381 True 1800.0 3273 85.9705 2 3596 2 chr4A.!!$R4 3594
12 TraesCS7D01G087400 chr4A 668084680 668086196 1516 True 1133.0 1133 80.2840 606 2145 1 chr4A.!!$R1 1539
13 TraesCS7D01G087400 chr4A 668109131 668110506 1375 True 1083.0 1083 80.9890 691 2101 1 chr4A.!!$R2 1410

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
337 355 0.035915 GAACCCCAGAGGAGACAAGC 60.036 60.0 0.00 0.00 39.89 4.01 F
1141 1177 0.323957 GGCCTCAACCGAAGTTAGGT 59.676 55.0 1.18 1.18 45.29 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1170 1206 1.208535 TGTGGGTTCTGAACACGAACT 59.791 47.619 21.01 0.0 40.37 3.01 R
3081 3203 0.453793 CATCGCTCTTCTCCGTGAGT 59.546 55.000 1.60 0.0 33.22 3.41 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
66 67 6.038356 CACTTAATTGTTGGGATGAAGATGC 58.962 40.000 0.00 0.00 0.00 3.91
67 68 5.954150 ACTTAATTGTTGGGATGAAGATGCT 59.046 36.000 0.00 0.00 0.00 3.79
109 124 1.623811 ACGAAGTAGTGGCATGGAAGT 59.376 47.619 0.00 0.00 41.94 3.01
120 135 1.266989 GCATGGAAGTAATAAGGCCGC 59.733 52.381 0.00 0.00 0.00 6.53
124 139 1.596260 GGAAGTAATAAGGCCGCGTTC 59.404 52.381 4.92 0.00 0.00 3.95
159 174 7.056635 AGGGATTGGAGTGTTATTCAGTTATG 58.943 38.462 0.00 0.00 0.00 1.90
160 175 6.238759 GGGATTGGAGTGTTATTCAGTTATGC 60.239 42.308 0.00 0.00 0.00 3.14
161 176 6.318648 GGATTGGAGTGTTATTCAGTTATGCA 59.681 38.462 0.00 0.00 0.00 3.96
162 177 6.741992 TTGGAGTGTTATTCAGTTATGCAG 57.258 37.500 0.00 0.00 0.00 4.41
164 179 5.045942 TGGAGTGTTATTCAGTTATGCAGGA 60.046 40.000 0.00 0.00 0.00 3.86
165 180 5.525378 GGAGTGTTATTCAGTTATGCAGGAG 59.475 44.000 0.00 0.00 0.00 3.69
166 181 5.431765 AGTGTTATTCAGTTATGCAGGAGG 58.568 41.667 0.00 0.00 0.00 4.30
169 184 6.821665 GTGTTATTCAGTTATGCAGGAGGTTA 59.178 38.462 0.00 0.00 0.00 2.85
170 185 6.821665 TGTTATTCAGTTATGCAGGAGGTTAC 59.178 38.462 0.00 0.00 0.00 2.50
219 234 8.953990 CAAGATGTAAGTAAAACGGAACAAAAG 58.046 33.333 0.00 0.00 0.00 2.27
238 256 1.926511 GCATGAAAGGTGGTGCTCGG 61.927 60.000 0.00 0.00 34.85 4.63
297 315 0.375803 AAAAACTGTGTGCCGTCGTC 59.624 50.000 0.00 0.00 0.00 4.20
317 335 2.477845 TGTGCTTGAGCTGCATAGAA 57.522 45.000 1.02 0.00 42.69 2.10
318 336 2.353323 TGTGCTTGAGCTGCATAGAAG 58.647 47.619 1.02 0.00 42.69 2.85
319 337 2.027837 TGTGCTTGAGCTGCATAGAAGA 60.028 45.455 1.02 0.00 42.69 2.87
320 338 3.005554 GTGCTTGAGCTGCATAGAAGAA 58.994 45.455 1.02 0.00 42.69 2.52
321 339 3.005554 TGCTTGAGCTGCATAGAAGAAC 58.994 45.455 1.02 0.00 42.66 3.01
322 340 2.354199 GCTTGAGCTGCATAGAAGAACC 59.646 50.000 1.02 0.00 38.21 3.62
323 341 2.698855 TGAGCTGCATAGAAGAACCC 57.301 50.000 1.02 0.00 0.00 4.11
324 342 1.210478 TGAGCTGCATAGAAGAACCCC 59.790 52.381 1.02 0.00 0.00 4.95
325 343 1.210478 GAGCTGCATAGAAGAACCCCA 59.790 52.381 1.02 0.00 0.00 4.96
326 344 1.211457 AGCTGCATAGAAGAACCCCAG 59.789 52.381 1.02 0.00 0.00 4.45
327 345 1.210478 GCTGCATAGAAGAACCCCAGA 59.790 52.381 0.00 0.00 0.00 3.86
328 346 2.744494 GCTGCATAGAAGAACCCCAGAG 60.744 54.545 0.00 0.00 0.00 3.35
329 347 1.839994 TGCATAGAAGAACCCCAGAGG 59.160 52.381 0.00 0.00 43.78 3.69
330 348 2.119495 GCATAGAAGAACCCCAGAGGA 58.881 52.381 0.00 0.00 39.89 3.71
331 349 2.103941 GCATAGAAGAACCCCAGAGGAG 59.896 54.545 0.00 0.00 39.89 3.69
332 350 3.647636 CATAGAAGAACCCCAGAGGAGA 58.352 50.000 0.00 0.00 39.89 3.71
333 351 1.945580 AGAAGAACCCCAGAGGAGAC 58.054 55.000 0.00 0.00 39.89 3.36
334 352 1.150135 AGAAGAACCCCAGAGGAGACA 59.850 52.381 0.00 0.00 39.89 3.41
335 353 1.978580 GAAGAACCCCAGAGGAGACAA 59.021 52.381 0.00 0.00 39.89 3.18
336 354 1.650528 AGAACCCCAGAGGAGACAAG 58.349 55.000 0.00 0.00 39.89 3.16
337 355 0.035915 GAACCCCAGAGGAGACAAGC 60.036 60.000 0.00 0.00 39.89 4.01
338 356 0.474660 AACCCCAGAGGAGACAAGCT 60.475 55.000 0.00 0.00 39.89 3.74
339 357 0.413832 ACCCCAGAGGAGACAAGCTA 59.586 55.000 0.00 0.00 39.89 3.32
340 358 1.118838 CCCCAGAGGAGACAAGCTAG 58.881 60.000 0.00 0.00 38.24 3.42
341 359 1.621072 CCCCAGAGGAGACAAGCTAGT 60.621 57.143 0.00 0.00 38.24 2.57
342 360 2.358300 CCCCAGAGGAGACAAGCTAGTA 60.358 54.545 0.00 0.00 38.24 1.82
343 361 3.366396 CCCAGAGGAGACAAGCTAGTAA 58.634 50.000 0.00 0.00 33.47 2.24
344 362 3.769844 CCCAGAGGAGACAAGCTAGTAAA 59.230 47.826 0.00 0.00 33.47 2.01
345 363 4.407296 CCCAGAGGAGACAAGCTAGTAAAT 59.593 45.833 0.00 0.00 33.47 1.40
346 364 5.452636 CCCAGAGGAGACAAGCTAGTAAATC 60.453 48.000 0.00 0.00 33.47 2.17
347 365 5.362430 CCAGAGGAGACAAGCTAGTAAATCT 59.638 44.000 0.00 0.00 0.00 2.40
348 366 6.127196 CCAGAGGAGACAAGCTAGTAAATCTT 60.127 42.308 0.00 0.00 0.00 2.40
349 367 6.756074 CAGAGGAGACAAGCTAGTAAATCTTG 59.244 42.308 5.74 5.74 41.99 3.02
356 374 7.817418 ACAAGCTAGTAAATCTTGTTTTGGA 57.183 32.000 6.81 0.00 45.55 3.53
357 375 8.409358 ACAAGCTAGTAAATCTTGTTTTGGAT 57.591 30.769 6.81 0.00 45.55 3.41
358 376 8.860088 ACAAGCTAGTAAATCTTGTTTTGGATT 58.140 29.630 6.81 0.00 45.55 3.01
361 379 9.959721 AGCTAGTAAATCTTGTTTTGGATTAGA 57.040 29.630 0.00 0.00 32.65 2.10
365 383 9.588096 AGTAAATCTTGTTTTGGATTAGAGGTT 57.412 29.630 0.00 0.00 32.65 3.50
374 392 9.457436 TGTTTTGGATTAGAGGTTATACTTTCC 57.543 33.333 0.00 0.00 0.00 3.13
375 393 9.682465 GTTTTGGATTAGAGGTTATACTTTCCT 57.318 33.333 0.00 0.00 0.00 3.36
379 397 9.725206 TGGATTAGAGGTTATACTTTCCTAACT 57.275 33.333 0.00 0.00 0.00 2.24
388 406 9.984190 GGTTATACTTTCCTAACTATCTCTTGG 57.016 37.037 0.00 0.00 0.00 3.61
392 410 7.979786 ACTTTCCTAACTATCTCTTGGATGA 57.020 36.000 0.00 0.00 35.98 2.92
393 411 8.560124 ACTTTCCTAACTATCTCTTGGATGAT 57.440 34.615 0.00 0.00 35.98 2.45
394 412 9.661954 ACTTTCCTAACTATCTCTTGGATGATA 57.338 33.333 0.00 0.00 35.98 2.15
397 415 9.434275 TTCCTAACTATCTCTTGGATGATAACA 57.566 33.333 0.00 0.00 35.98 2.41
398 416 9.607333 TCCTAACTATCTCTTGGATGATAACAT 57.393 33.333 0.00 0.00 39.67 2.71
411 429 9.865152 TTGGATGATAACATAAAGAATCATGGA 57.135 29.630 1.63 0.00 38.77 3.41
412 430 9.511272 TGGATGATAACATAAAGAATCATGGAG 57.489 33.333 1.63 0.00 38.77 3.86
413 431 8.457261 GGATGATAACATAAAGAATCATGGAGC 58.543 37.037 1.63 0.00 38.77 4.70
414 432 7.750229 TGATAACATAAAGAATCATGGAGCC 57.250 36.000 0.00 0.00 0.00 4.70
415 433 7.520798 TGATAACATAAAGAATCATGGAGCCT 58.479 34.615 0.00 0.00 0.00 4.58
416 434 7.446319 TGATAACATAAAGAATCATGGAGCCTG 59.554 37.037 0.00 0.00 0.00 4.85
417 435 4.467769 ACATAAAGAATCATGGAGCCTGG 58.532 43.478 0.00 0.00 0.00 4.45
418 436 4.166725 ACATAAAGAATCATGGAGCCTGGA 59.833 41.667 0.00 0.00 0.00 3.86
419 437 3.294038 AAAGAATCATGGAGCCTGGAG 57.706 47.619 0.00 0.00 0.00 3.86
420 438 1.890552 AGAATCATGGAGCCTGGAGT 58.109 50.000 0.00 0.00 0.00 3.85
421 439 3.051940 AGAATCATGGAGCCTGGAGTA 57.948 47.619 0.00 0.00 0.00 2.59
422 440 3.387962 AGAATCATGGAGCCTGGAGTAA 58.612 45.455 0.00 0.00 0.00 2.24
423 441 3.782523 AGAATCATGGAGCCTGGAGTAAA 59.217 43.478 0.00 0.00 0.00 2.01
424 442 4.414846 AGAATCATGGAGCCTGGAGTAAAT 59.585 41.667 0.00 0.00 0.00 1.40
425 443 5.608437 AGAATCATGGAGCCTGGAGTAAATA 59.392 40.000 0.00 0.00 0.00 1.40
426 444 4.689612 TCATGGAGCCTGGAGTAAATAC 57.310 45.455 0.00 0.00 0.00 1.89
427 445 4.298626 TCATGGAGCCTGGAGTAAATACT 58.701 43.478 0.00 0.00 39.71 2.12
428 446 4.101585 TCATGGAGCCTGGAGTAAATACTG 59.898 45.833 0.00 0.00 36.50 2.74
429 447 3.719871 TGGAGCCTGGAGTAAATACTGA 58.280 45.455 0.00 0.00 36.50 3.41
430 448 4.101114 TGGAGCCTGGAGTAAATACTGAA 58.899 43.478 0.00 0.00 36.50 3.02
431 449 4.721776 TGGAGCCTGGAGTAAATACTGAAT 59.278 41.667 0.00 0.00 36.50 2.57
432 450 5.163301 TGGAGCCTGGAGTAAATACTGAATC 60.163 44.000 0.00 0.00 36.50 2.52
433 451 4.950050 AGCCTGGAGTAAATACTGAATCG 58.050 43.478 0.00 0.00 36.50 3.34
434 452 3.495001 GCCTGGAGTAAATACTGAATCGC 59.505 47.826 0.00 0.00 36.50 4.58
435 453 3.736252 CCTGGAGTAAATACTGAATCGCG 59.264 47.826 0.00 0.00 36.50 5.87
436 454 4.499188 CCTGGAGTAAATACTGAATCGCGA 60.499 45.833 13.09 13.09 36.50 5.87
437 455 4.357142 TGGAGTAAATACTGAATCGCGAC 58.643 43.478 12.93 0.00 36.50 5.19
438 456 4.097437 TGGAGTAAATACTGAATCGCGACT 59.903 41.667 12.93 0.00 36.50 4.18
439 457 5.041940 GGAGTAAATACTGAATCGCGACTT 58.958 41.667 12.93 7.28 36.50 3.01
440 458 5.173492 GGAGTAAATACTGAATCGCGACTTC 59.827 44.000 12.93 16.67 36.50 3.01
441 459 5.041940 AGTAAATACTGAATCGCGACTTCC 58.958 41.667 12.93 0.89 34.72 3.46
442 460 3.802948 AATACTGAATCGCGACTTCCT 57.197 42.857 12.93 7.26 0.00 3.36
443 461 3.802948 ATACTGAATCGCGACTTCCTT 57.197 42.857 12.93 0.00 0.00 3.36
444 462 2.457366 ACTGAATCGCGACTTCCTTT 57.543 45.000 12.93 0.00 0.00 3.11
445 463 2.767505 ACTGAATCGCGACTTCCTTTT 58.232 42.857 12.93 0.00 0.00 2.27
446 464 2.480419 ACTGAATCGCGACTTCCTTTTG 59.520 45.455 12.93 1.13 0.00 2.44
447 465 2.480419 CTGAATCGCGACTTCCTTTTGT 59.520 45.455 12.93 0.00 0.00 2.83
448 466 2.875933 TGAATCGCGACTTCCTTTTGTT 59.124 40.909 12.93 0.00 0.00 2.83
449 467 3.059188 TGAATCGCGACTTCCTTTTGTTC 60.059 43.478 12.93 7.94 0.00 3.18
450 468 2.234300 TCGCGACTTCCTTTTGTTCT 57.766 45.000 3.71 0.00 0.00 3.01
451 469 3.374220 TCGCGACTTCCTTTTGTTCTA 57.626 42.857 3.71 0.00 0.00 2.10
452 470 3.054878 TCGCGACTTCCTTTTGTTCTAC 58.945 45.455 3.71 0.00 0.00 2.59
453 471 2.157085 CGCGACTTCCTTTTGTTCTACC 59.843 50.000 0.00 0.00 0.00 3.18
454 472 2.483106 GCGACTTCCTTTTGTTCTACCC 59.517 50.000 0.00 0.00 0.00 3.69
455 473 3.072211 CGACTTCCTTTTGTTCTACCCC 58.928 50.000 0.00 0.00 0.00 4.95
456 474 3.495453 CGACTTCCTTTTGTTCTACCCCA 60.495 47.826 0.00 0.00 0.00 4.96
457 475 4.466827 GACTTCCTTTTGTTCTACCCCAA 58.533 43.478 0.00 0.00 0.00 4.12
458 476 4.212716 ACTTCCTTTTGTTCTACCCCAAC 58.787 43.478 0.00 0.00 0.00 3.77
459 477 2.853705 TCCTTTTGTTCTACCCCAACG 58.146 47.619 0.00 0.00 0.00 4.10
460 478 2.173143 TCCTTTTGTTCTACCCCAACGT 59.827 45.455 0.00 0.00 0.00 3.99
461 479 3.390639 TCCTTTTGTTCTACCCCAACGTA 59.609 43.478 0.00 0.00 0.00 3.57
462 480 3.749609 CCTTTTGTTCTACCCCAACGTAG 59.250 47.826 0.00 0.00 37.63 3.51
463 481 4.503643 CCTTTTGTTCTACCCCAACGTAGA 60.504 45.833 0.00 0.00 42.31 2.59
464 482 4.895668 TTTGTTCTACCCCAACGTAGAT 57.104 40.909 0.00 0.00 43.22 1.98
465 483 3.880047 TGTTCTACCCCAACGTAGATG 57.120 47.619 0.00 0.00 43.22 2.90
466 484 3.167485 TGTTCTACCCCAACGTAGATGT 58.833 45.455 0.00 0.00 43.22 3.06
467 485 4.343231 TGTTCTACCCCAACGTAGATGTA 58.657 43.478 0.00 0.00 43.22 2.29
468 486 4.957954 TGTTCTACCCCAACGTAGATGTAT 59.042 41.667 0.00 0.00 43.22 2.29
469 487 6.128486 TGTTCTACCCCAACGTAGATGTATA 58.872 40.000 0.00 0.00 43.22 1.47
470 488 6.606796 TGTTCTACCCCAACGTAGATGTATAA 59.393 38.462 0.00 0.00 43.22 0.98
471 489 7.288389 TGTTCTACCCCAACGTAGATGTATAAT 59.712 37.037 0.00 0.00 43.22 1.28
472 490 7.844493 TCTACCCCAACGTAGATGTATAATT 57.156 36.000 0.00 0.00 39.81 1.40
473 491 8.253867 TCTACCCCAACGTAGATGTATAATTT 57.746 34.615 0.00 0.00 39.81 1.82
474 492 8.145767 TCTACCCCAACGTAGATGTATAATTTG 58.854 37.037 0.00 0.00 39.81 2.32
475 493 6.891388 ACCCCAACGTAGATGTATAATTTGA 58.109 36.000 0.00 0.00 0.00 2.69
476 494 6.764560 ACCCCAACGTAGATGTATAATTTGAC 59.235 38.462 0.00 0.00 0.00 3.18
477 495 6.764085 CCCCAACGTAGATGTATAATTTGACA 59.236 38.462 0.00 0.00 0.00 3.58
478 496 7.444183 CCCCAACGTAGATGTATAATTTGACAT 59.556 37.037 4.96 4.96 38.99 3.06
479 497 8.282592 CCCAACGTAGATGTATAATTTGACATG 58.717 37.037 9.06 0.00 36.42 3.21
480 498 8.282592 CCAACGTAGATGTATAATTTGACATGG 58.717 37.037 9.06 2.11 36.42 3.66
481 499 8.826710 CAACGTAGATGTATAATTTGACATGGT 58.173 33.333 9.06 1.32 36.42 3.55
482 500 8.958119 ACGTAGATGTATAATTTGACATGGTT 57.042 30.769 9.06 0.33 36.42 3.67
483 501 9.391006 ACGTAGATGTATAATTTGACATGGTTT 57.609 29.630 9.06 0.00 36.42 3.27
493 511 9.829507 ATAATTTGACATGGTTTTGTTTCTTCA 57.170 25.926 0.00 0.00 0.00 3.02
494 512 8.735692 AATTTGACATGGTTTTGTTTCTTCAT 57.264 26.923 0.00 0.00 0.00 2.57
495 513 9.829507 AATTTGACATGGTTTTGTTTCTTCATA 57.170 25.926 0.00 0.00 0.00 2.15
496 514 8.641499 TTTGACATGGTTTTGTTTCTTCATAC 57.359 30.769 0.00 0.00 0.00 2.39
497 515 6.744112 TGACATGGTTTTGTTTCTTCATACC 58.256 36.000 0.00 0.00 0.00 2.73
498 516 6.549364 TGACATGGTTTTGTTTCTTCATACCT 59.451 34.615 0.00 0.00 0.00 3.08
499 517 7.721842 TGACATGGTTTTGTTTCTTCATACCTA 59.278 33.333 0.00 0.00 0.00 3.08
500 518 8.472007 ACATGGTTTTGTTTCTTCATACCTAA 57.528 30.769 0.00 0.00 0.00 2.69
501 519 8.919145 ACATGGTTTTGTTTCTTCATACCTAAA 58.081 29.630 0.00 0.00 0.00 1.85
502 520 9.927668 CATGGTTTTGTTTCTTCATACCTAAAT 57.072 29.630 0.00 0.00 0.00 1.40
504 522 9.137459 TGGTTTTGTTTCTTCATACCTAAATCA 57.863 29.630 0.00 0.00 0.00 2.57
505 523 9.974980 GGTTTTGTTTCTTCATACCTAAATCAA 57.025 29.630 0.00 0.00 0.00 2.57
752 780 4.321230 GGATTGAAGGAATGGTGTTGACAC 60.321 45.833 5.72 5.72 45.72 3.67
854 890 9.453572 CCCATATCAGTTACTATAACATGCATT 57.546 33.333 0.00 0.00 0.00 3.56
860 896 9.612066 TCAGTTACTATAACATGCATTCATTCA 57.388 29.630 0.00 0.00 0.00 2.57
922 958 3.386402 GCCTACAGGTCAGAAGCTCTTAT 59.614 47.826 0.00 0.00 37.57 1.73
933 969 6.034044 GTCAGAAGCTCTTATTACTTGTCGTG 59.966 42.308 0.00 0.00 0.00 4.35
942 978 1.412453 TACTTGTCGTGGCCACCCTT 61.412 55.000 29.95 10.88 0.00 3.95
943 979 1.966451 CTTGTCGTGGCCACCCTTC 60.966 63.158 29.95 17.00 0.00 3.46
945 981 1.990160 TTGTCGTGGCCACCCTTCTT 61.990 55.000 29.95 0.00 0.00 2.52
946 982 1.966451 GTCGTGGCCACCCTTCTTG 60.966 63.158 29.95 14.08 0.00 3.02
948 984 1.966451 CGTGGCCACCCTTCTTGTC 60.966 63.158 29.95 0.98 0.00 3.18
950 986 2.430367 GGCCACCCTTCTTGTCGT 59.570 61.111 0.00 0.00 0.00 4.34
955 991 1.429463 CACCCTTCTTGTCGTACAGC 58.571 55.000 0.00 0.00 0.00 4.40
956 992 1.045407 ACCCTTCTTGTCGTACAGCA 58.955 50.000 0.00 0.00 0.00 4.41
959 995 3.119101 ACCCTTCTTGTCGTACAGCATAG 60.119 47.826 0.00 0.00 0.00 2.23
964 1000 6.037940 CCTTCTTGTCGTACAGCATAGTACTA 59.962 42.308 4.77 4.77 41.65 1.82
1092 1128 2.742589 CTGCTTCCGAGAACCCTTTAAC 59.257 50.000 0.00 0.00 0.00 2.01
1141 1177 0.323957 GGCCTCAACCGAAGTTAGGT 59.676 55.000 1.18 1.18 45.29 3.08
1167 1203 2.436173 GGAGATCAGTCTTACCCTTGGG 59.564 54.545 3.77 3.77 33.97 4.12
1170 1206 5.368578 GAGATCAGTCTTACCCTTGGGGAA 61.369 50.000 9.86 6.93 39.11 3.97
1196 1232 3.554129 CGTGTTCAGAACCCACACATAGA 60.554 47.826 10.93 0.00 40.80 1.98
1197 1233 4.579869 GTGTTCAGAACCCACACATAGAT 58.420 43.478 10.93 0.00 40.53 1.98
1215 1251 2.162208 AGATTGGCAATGCAACTACACG 59.838 45.455 19.07 0.00 0.00 4.49
1223 1259 0.810426 TGCAACTACACGAACGGCAA 60.810 50.000 0.00 0.00 0.00 4.52
1224 1260 0.305313 GCAACTACACGAACGGCAAA 59.695 50.000 0.00 0.00 0.00 3.68
1232 1268 2.241722 CACGAACGGCAAAAATAGCAG 58.758 47.619 0.00 0.00 0.00 4.24
1238 1280 1.733389 CGGCAAAAATAGCAGCAGTGG 60.733 52.381 0.00 0.00 0.00 4.00
1243 1285 4.619973 CAAAAATAGCAGCAGTGGTTTGA 58.380 39.130 0.00 0.00 35.51 2.69
1246 1288 4.708726 AATAGCAGCAGTGGTTTGAATC 57.291 40.909 0.00 0.00 35.51 2.52
1254 1296 3.572255 GCAGTGGTTTGAATCCCTTAACA 59.428 43.478 0.00 0.00 0.00 2.41
1257 1299 4.827284 AGTGGTTTGAATCCCTTAACACTG 59.173 41.667 0.00 0.00 0.00 3.66
1278 1320 7.725844 ACACTGGATTCTTTTCATAAGGTTTCT 59.274 33.333 0.00 0.00 0.00 2.52
1279 1321 8.025445 CACTGGATTCTTTTCATAAGGTTTCTG 58.975 37.037 0.00 0.00 0.00 3.02
1294 1336 3.945285 GGTTTCTGACACCAAGAACAAGA 59.055 43.478 8.09 0.00 34.04 3.02
1330 1372 1.466950 GTGCTACGCTTGCAATGGTTA 59.533 47.619 0.00 0.00 42.41 2.85
1421 1463 3.592898 TGCAAGTAGTGTCGATGATGT 57.407 42.857 0.00 0.00 0.00 3.06
1506 1548 3.053395 TCACCGTATCCTTACCAGTACCT 60.053 47.826 0.00 0.00 0.00 3.08
1510 1552 4.217983 CCGTATCCTTACCAGTACCTGATC 59.782 50.000 0.00 0.00 32.44 2.92
1519 1561 5.818678 ACCAGTACCTGATCTTTACAACA 57.181 39.130 0.00 0.00 32.44 3.33
1830 1873 3.828451 GAGGGTGCCAAGGTACGTATATA 59.172 47.826 0.00 0.00 0.00 0.86
1834 1877 6.097839 AGGGTGCCAAGGTACGTATATATATG 59.902 42.308 9.95 9.95 0.00 1.78
1927 2010 2.890945 TCACGACATTCTCCTCACTTCA 59.109 45.455 0.00 0.00 0.00 3.02
2106 2194 8.934023 ACCCAAACAAAACTCTGAAGATAATA 57.066 30.769 0.00 0.00 0.00 0.98
2160 2252 1.931551 CACACTAGTTGCGCACGTT 59.068 52.632 11.12 0.15 0.00 3.99
2201 2305 7.118971 ACAGAAAGCATTTTTGCACTTTTTACA 59.881 29.630 0.33 0.00 43.28 2.41
2288 2410 6.418141 GGACAACATGTTGCAATTGTTTTAC 58.582 36.000 33.23 15.38 44.03 2.01
2413 2535 1.276989 ACGGGCCGAGTATCAGAAAAA 59.723 47.619 35.78 0.00 33.17 1.94
2445 2567 6.385843 GCAAAAGAGAAGGAAAGATTCTTCC 58.614 40.000 0.00 3.47 44.61 3.46
2522 2644 3.243877 CGTTGAAGATATTCACGCAGGAG 59.756 47.826 1.37 0.00 0.00 3.69
2528 2650 3.509575 AGATATTCACGCAGGAGGATCTC 59.490 47.826 0.00 0.00 33.73 2.75
2571 2693 1.881903 CGAGAGCAGAGAAGTGGGCA 61.882 60.000 0.00 0.00 0.00 5.36
2653 2775 4.514816 TGAAACGCTCAAAGATCATGAACA 59.485 37.500 0.00 0.00 0.00 3.18
2784 2906 5.104527 ACTGGTCTATGAATTCATCCCGAAA 60.105 40.000 23.95 5.24 37.12 3.46
2810 2932 5.485620 CACTCTCTTTCAGTTCATCCATCA 58.514 41.667 0.00 0.00 0.00 3.07
2811 2933 5.581479 CACTCTCTTTCAGTTCATCCATCAG 59.419 44.000 0.00 0.00 0.00 2.90
2868 2990 0.537188 TCAGGGTCGCTCAAGAATCC 59.463 55.000 0.00 0.00 0.00 3.01
2880 3002 2.233676 TCAAGAATCCGCTGAAGCACTA 59.766 45.455 2.79 0.00 42.21 2.74
2881 3003 3.118629 TCAAGAATCCGCTGAAGCACTAT 60.119 43.478 2.79 0.00 42.21 2.12
2934 3056 2.161808 AGTACACGGAGATGTCAAGTCG 59.838 50.000 0.00 0.00 33.85 4.18
2947 3069 4.245660 TGTCAAGTCGATGAACATTCTCC 58.754 43.478 0.00 0.00 0.00 3.71
2952 3074 3.708631 AGTCGATGAACATTCTCCTGGAT 59.291 43.478 0.00 0.00 0.00 3.41
2955 3077 3.806521 CGATGAACATTCTCCTGGATGAC 59.193 47.826 0.00 0.00 0.00 3.06
3081 3203 0.545309 AGTACCTGCAGGAGAGGCAA 60.545 55.000 39.19 11.68 41.39 4.52
3099 3221 1.135257 CAACTCACGGAGAAGAGCGAT 60.135 52.381 7.76 0.00 36.88 4.58
3120 3242 2.164624 TGTTTACAGCTTTGGCGTTGTT 59.835 40.909 0.00 0.00 44.37 2.83
3146 3268 0.391661 GAGCTGATCACGGGCAAGAA 60.392 55.000 8.02 0.00 0.00 2.52
3228 3350 4.272489 CAATGAAGGATGGTAGCCTTGAA 58.728 43.478 2.70 0.00 45.43 2.69
3242 3367 1.064166 CCTTGAAGGCATCCTGGATGT 60.064 52.381 31.40 16.60 41.60 3.06
3592 3717 2.419673 TGCAAAGAAGAGTGTGTGTGTG 59.580 45.455 0.00 0.00 0.00 3.82
3598 3723 3.194755 AGAAGAGTGTGTGTGTGTGTGTA 59.805 43.478 0.00 0.00 0.00 2.90
3599 3724 2.888594 AGAGTGTGTGTGTGTGTGTAC 58.111 47.619 0.00 0.00 0.00 2.90
3600 3725 1.586578 GAGTGTGTGTGTGTGTGTACG 59.413 52.381 0.00 0.00 0.00 3.67
3601 3726 1.067425 AGTGTGTGTGTGTGTGTACGT 60.067 47.619 0.00 0.00 0.00 3.57
3602 3727 1.059979 GTGTGTGTGTGTGTGTACGTG 59.940 52.381 0.00 0.00 0.00 4.49
3603 3728 1.336980 TGTGTGTGTGTGTGTACGTGT 60.337 47.619 0.00 0.00 0.00 4.49
3604 3729 1.727880 GTGTGTGTGTGTGTACGTGTT 59.272 47.619 0.00 0.00 0.00 3.32
3605 3730 2.922387 GTGTGTGTGTGTGTACGTGTTA 59.078 45.455 0.00 0.00 0.00 2.41
3606 3731 3.000476 GTGTGTGTGTGTGTACGTGTTAG 60.000 47.826 0.00 0.00 0.00 2.34
3607 3732 3.119566 TGTGTGTGTGTGTACGTGTTAGA 60.120 43.478 0.00 0.00 0.00 2.10
3608 3733 3.484649 GTGTGTGTGTGTACGTGTTAGAG 59.515 47.826 0.00 0.00 0.00 2.43
3609 3734 3.047796 GTGTGTGTGTACGTGTTAGAGG 58.952 50.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.149308 TGCCACTGATTTCACATGTAAAGTAG 59.851 38.462 0.00 5.57 0.00 2.57
41 42 5.643379 TCTTCATCCCAACAATTAAGTGC 57.357 39.130 2.17 0.00 0.00 4.40
48 49 3.028850 CCAGCATCTTCATCCCAACAAT 58.971 45.455 0.00 0.00 0.00 2.71
50 51 1.956636 GCCAGCATCTTCATCCCAACA 60.957 52.381 0.00 0.00 0.00 3.33
66 67 4.641541 TGAAACTGATTCCATACATGCCAG 59.358 41.667 0.00 0.00 37.22 4.85
67 68 4.398988 GTGAAACTGATTCCATACATGCCA 59.601 41.667 0.00 0.00 37.22 4.92
120 135 0.179056 ATCCCTATTGCCACCGAACG 60.179 55.000 0.00 0.00 0.00 3.95
124 139 0.182537 TCCAATCCCTATTGCCACCG 59.817 55.000 0.00 0.00 41.06 4.94
203 218 6.292114 CCTTTCATGCTTTTGTTCCGTTTTAC 60.292 38.462 0.00 0.00 0.00 2.01
204 219 5.751028 CCTTTCATGCTTTTGTTCCGTTTTA 59.249 36.000 0.00 0.00 0.00 1.52
205 220 4.570369 CCTTTCATGCTTTTGTTCCGTTTT 59.430 37.500 0.00 0.00 0.00 2.43
206 221 4.119136 CCTTTCATGCTTTTGTTCCGTTT 58.881 39.130 0.00 0.00 0.00 3.60
209 224 3.052036 CACCTTTCATGCTTTTGTTCCG 58.948 45.455 0.00 0.00 0.00 4.30
219 234 1.503542 CGAGCACCACCTTTCATGC 59.496 57.895 0.00 0.00 38.39 4.06
288 306 2.661537 CAAGCACAGACGACGGCA 60.662 61.111 2.19 0.00 0.00 5.69
292 310 1.895280 GCAGCTCAAGCACAGACGAC 61.895 60.000 4.59 0.00 45.16 4.34
294 312 1.296755 ATGCAGCTCAAGCACAGACG 61.297 55.000 4.59 0.00 45.95 4.18
295 313 1.664659 CTATGCAGCTCAAGCACAGAC 59.335 52.381 4.59 0.00 45.95 3.51
297 315 2.019948 TCTATGCAGCTCAAGCACAG 57.980 50.000 4.59 0.00 45.95 3.66
316 334 1.981495 CTTGTCTCCTCTGGGGTTCTT 59.019 52.381 0.00 0.00 36.25 2.52
317 335 1.650528 CTTGTCTCCTCTGGGGTTCT 58.349 55.000 0.00 0.00 36.25 3.01
318 336 0.035915 GCTTGTCTCCTCTGGGGTTC 60.036 60.000 0.00 0.00 36.25 3.62
319 337 0.474660 AGCTTGTCTCCTCTGGGGTT 60.475 55.000 0.00 0.00 36.25 4.11
320 338 0.413832 TAGCTTGTCTCCTCTGGGGT 59.586 55.000 0.00 0.00 36.25 4.95
321 339 1.118838 CTAGCTTGTCTCCTCTGGGG 58.881 60.000 0.00 0.00 0.00 4.96
322 340 1.859302 ACTAGCTTGTCTCCTCTGGG 58.141 55.000 0.00 0.00 0.00 4.45
323 341 5.362430 AGATTTACTAGCTTGTCTCCTCTGG 59.638 44.000 3.45 0.00 0.00 3.86
324 342 6.463995 AGATTTACTAGCTTGTCTCCTCTG 57.536 41.667 3.45 0.00 0.00 3.35
325 343 6.439058 ACAAGATTTACTAGCTTGTCTCCTCT 59.561 38.462 3.45 0.94 46.60 3.69
326 344 6.635755 ACAAGATTTACTAGCTTGTCTCCTC 58.364 40.000 3.45 0.00 46.60 3.71
327 345 6.613153 ACAAGATTTACTAGCTTGTCTCCT 57.387 37.500 3.45 0.00 46.60 3.69
335 353 9.959721 TCTAATCCAAAACAAGATTTACTAGCT 57.040 29.630 0.00 0.00 34.60 3.32
339 357 9.588096 AACCTCTAATCCAAAACAAGATTTACT 57.412 29.630 0.00 0.00 34.60 2.24
348 366 9.457436 GGAAAGTATAACCTCTAATCCAAAACA 57.543 33.333 0.00 0.00 0.00 2.83
349 367 9.682465 AGGAAAGTATAACCTCTAATCCAAAAC 57.318 33.333 0.00 0.00 0.00 2.43
353 371 9.725206 AGTTAGGAAAGTATAACCTCTAATCCA 57.275 33.333 0.00 0.00 35.52 3.41
362 380 9.984190 CCAAGAGATAGTTAGGAAAGTATAACC 57.016 37.037 0.00 0.00 32.44 2.85
366 384 9.661954 TCATCCAAGAGATAGTTAGGAAAGTAT 57.338 33.333 0.00 0.00 34.54 2.12
367 385 9.661954 ATCATCCAAGAGATAGTTAGGAAAGTA 57.338 33.333 0.00 0.00 32.37 2.24
368 386 7.979786 TCATCCAAGAGATAGTTAGGAAAGT 57.020 36.000 0.00 0.00 32.37 2.66
371 389 9.434275 TGTTATCATCCAAGAGATAGTTAGGAA 57.566 33.333 0.00 0.00 32.37 3.36
372 390 9.607333 ATGTTATCATCCAAGAGATAGTTAGGA 57.393 33.333 0.00 0.00 32.37 2.94
385 403 9.865152 TCCATGATTCTTTATGTTATCATCCAA 57.135 29.630 0.00 0.00 36.00 3.53
386 404 9.511272 CTCCATGATTCTTTATGTTATCATCCA 57.489 33.333 0.00 0.00 36.00 3.41
387 405 8.457261 GCTCCATGATTCTTTATGTTATCATCC 58.543 37.037 0.00 0.00 36.00 3.51
388 406 8.457261 GGCTCCATGATTCTTTATGTTATCATC 58.543 37.037 0.00 0.00 36.00 2.92
389 407 8.168725 AGGCTCCATGATTCTTTATGTTATCAT 58.831 33.333 0.00 0.00 38.03 2.45
390 408 7.446319 CAGGCTCCATGATTCTTTATGTTATCA 59.554 37.037 0.00 0.00 0.00 2.15
391 409 7.094463 CCAGGCTCCATGATTCTTTATGTTATC 60.094 40.741 0.00 0.00 0.00 1.75
392 410 6.718454 CCAGGCTCCATGATTCTTTATGTTAT 59.282 38.462 0.00 0.00 0.00 1.89
393 411 6.064060 CCAGGCTCCATGATTCTTTATGTTA 58.936 40.000 0.00 0.00 0.00 2.41
394 412 4.891756 CCAGGCTCCATGATTCTTTATGTT 59.108 41.667 0.00 0.00 0.00 2.71
395 413 4.166725 TCCAGGCTCCATGATTCTTTATGT 59.833 41.667 0.00 0.00 0.00 2.29
396 414 4.722220 TCCAGGCTCCATGATTCTTTATG 58.278 43.478 0.00 0.00 0.00 1.90
397 415 4.414846 ACTCCAGGCTCCATGATTCTTTAT 59.585 41.667 0.00 0.00 0.00 1.40
398 416 3.782523 ACTCCAGGCTCCATGATTCTTTA 59.217 43.478 0.00 0.00 0.00 1.85
399 417 2.579860 ACTCCAGGCTCCATGATTCTTT 59.420 45.455 0.00 0.00 0.00 2.52
400 418 2.203584 ACTCCAGGCTCCATGATTCTT 58.796 47.619 0.00 0.00 0.00 2.52
401 419 1.890552 ACTCCAGGCTCCATGATTCT 58.109 50.000 0.00 0.00 0.00 2.40
402 420 3.845781 TTACTCCAGGCTCCATGATTC 57.154 47.619 0.00 0.00 0.00 2.52
403 421 4.803329 ATTTACTCCAGGCTCCATGATT 57.197 40.909 0.00 0.00 0.00 2.57
404 422 4.910304 AGTATTTACTCCAGGCTCCATGAT 59.090 41.667 0.00 0.00 0.00 2.45
405 423 4.101585 CAGTATTTACTCCAGGCTCCATGA 59.898 45.833 0.00 0.00 33.46 3.07
406 424 4.101585 TCAGTATTTACTCCAGGCTCCATG 59.898 45.833 0.00 0.00 33.46 3.66
407 425 4.298626 TCAGTATTTACTCCAGGCTCCAT 58.701 43.478 0.00 0.00 33.46 3.41
408 426 3.719871 TCAGTATTTACTCCAGGCTCCA 58.280 45.455 0.00 0.00 33.46 3.86
409 427 4.755266 TTCAGTATTTACTCCAGGCTCC 57.245 45.455 0.00 0.00 33.46 4.70
410 428 4.985409 CGATTCAGTATTTACTCCAGGCTC 59.015 45.833 0.00 0.00 33.46 4.70
411 429 4.740934 GCGATTCAGTATTTACTCCAGGCT 60.741 45.833 0.00 0.00 33.46 4.58
412 430 3.495001 GCGATTCAGTATTTACTCCAGGC 59.505 47.826 0.00 0.00 33.46 4.85
413 431 3.736252 CGCGATTCAGTATTTACTCCAGG 59.264 47.826 0.00 0.00 33.46 4.45
414 432 4.441415 GTCGCGATTCAGTATTTACTCCAG 59.559 45.833 14.06 0.00 33.46 3.86
415 433 4.097437 AGTCGCGATTCAGTATTTACTCCA 59.903 41.667 14.06 0.00 33.46 3.86
416 434 4.608951 AGTCGCGATTCAGTATTTACTCC 58.391 43.478 14.06 0.00 33.46 3.85
417 435 5.173492 GGAAGTCGCGATTCAGTATTTACTC 59.827 44.000 14.06 0.00 33.46 2.59
418 436 5.041940 GGAAGTCGCGATTCAGTATTTACT 58.958 41.667 14.06 0.00 36.90 2.24
419 437 5.041940 AGGAAGTCGCGATTCAGTATTTAC 58.958 41.667 14.06 0.00 0.00 2.01
420 438 5.258456 AGGAAGTCGCGATTCAGTATTTA 57.742 39.130 14.06 0.00 0.00 1.40
421 439 4.124851 AGGAAGTCGCGATTCAGTATTT 57.875 40.909 14.06 0.00 0.00 1.40
422 440 3.802948 AGGAAGTCGCGATTCAGTATT 57.197 42.857 14.06 0.00 0.00 1.89
423 441 3.802948 AAGGAAGTCGCGATTCAGTAT 57.197 42.857 14.06 0.00 0.00 2.12
424 442 3.587797 AAAGGAAGTCGCGATTCAGTA 57.412 42.857 14.06 0.00 0.00 2.74
425 443 2.457366 AAAGGAAGTCGCGATTCAGT 57.543 45.000 14.06 5.92 0.00 3.41
426 444 2.480419 ACAAAAGGAAGTCGCGATTCAG 59.520 45.455 14.06 8.24 0.00 3.02
427 445 2.489971 ACAAAAGGAAGTCGCGATTCA 58.510 42.857 14.06 0.00 0.00 2.57
428 446 3.186613 AGAACAAAAGGAAGTCGCGATTC 59.813 43.478 14.06 16.36 0.00 2.52
429 447 3.139077 AGAACAAAAGGAAGTCGCGATT 58.861 40.909 14.06 4.67 0.00 3.34
430 448 2.767505 AGAACAAAAGGAAGTCGCGAT 58.232 42.857 14.06 0.00 0.00 4.58
431 449 2.234300 AGAACAAAAGGAAGTCGCGA 57.766 45.000 3.71 3.71 0.00 5.87
432 450 2.157085 GGTAGAACAAAAGGAAGTCGCG 59.843 50.000 0.00 0.00 0.00 5.87
433 451 2.483106 GGGTAGAACAAAAGGAAGTCGC 59.517 50.000 0.00 0.00 0.00 5.19
434 452 3.072211 GGGGTAGAACAAAAGGAAGTCG 58.928 50.000 0.00 0.00 0.00 4.18
435 453 4.094830 TGGGGTAGAACAAAAGGAAGTC 57.905 45.455 0.00 0.00 0.00 3.01
436 454 4.212716 GTTGGGGTAGAACAAAAGGAAGT 58.787 43.478 0.00 0.00 0.00 3.01
437 455 3.252458 CGTTGGGGTAGAACAAAAGGAAG 59.748 47.826 0.00 0.00 0.00 3.46
438 456 3.215975 CGTTGGGGTAGAACAAAAGGAA 58.784 45.455 0.00 0.00 0.00 3.36
439 457 2.173143 ACGTTGGGGTAGAACAAAAGGA 59.827 45.455 0.00 0.00 0.00 3.36
440 458 2.578786 ACGTTGGGGTAGAACAAAAGG 58.421 47.619 0.00 0.00 0.00 3.11
441 459 4.634199 TCTACGTTGGGGTAGAACAAAAG 58.366 43.478 0.00 0.00 44.32 2.27
442 460 4.686191 TCTACGTTGGGGTAGAACAAAA 57.314 40.909 0.00 0.00 44.32 2.44
449 467 8.145767 TCAAATTATACATCTACGTTGGGGTAG 58.854 37.037 0.00 0.00 40.98 3.18
450 468 7.927629 GTCAAATTATACATCTACGTTGGGGTA 59.072 37.037 0.00 0.00 0.00 3.69
451 469 6.764560 GTCAAATTATACATCTACGTTGGGGT 59.235 38.462 0.00 0.00 0.00 4.95
452 470 6.764085 TGTCAAATTATACATCTACGTTGGGG 59.236 38.462 0.00 0.00 0.00 4.96
453 471 7.780008 TGTCAAATTATACATCTACGTTGGG 57.220 36.000 0.00 0.00 0.00 4.12
454 472 8.282592 CCATGTCAAATTATACATCTACGTTGG 58.717 37.037 0.00 0.00 34.12 3.77
455 473 8.826710 ACCATGTCAAATTATACATCTACGTTG 58.173 33.333 0.00 0.00 34.12 4.10
456 474 8.958119 ACCATGTCAAATTATACATCTACGTT 57.042 30.769 0.00 0.00 34.12 3.99
457 475 8.958119 AACCATGTCAAATTATACATCTACGT 57.042 30.769 0.00 0.00 34.12 3.57
467 485 9.829507 TGAAGAAACAAAACCATGTCAAATTAT 57.170 25.926 0.00 0.00 31.81 1.28
468 486 9.829507 ATGAAGAAACAAAACCATGTCAAATTA 57.170 25.926 0.00 0.00 31.81 1.40
469 487 8.735692 ATGAAGAAACAAAACCATGTCAAATT 57.264 26.923 0.00 0.00 31.81 1.82
470 488 9.260002 GTATGAAGAAACAAAACCATGTCAAAT 57.740 29.630 0.00 0.00 31.81 2.32
471 489 7.708752 GGTATGAAGAAACAAAACCATGTCAAA 59.291 33.333 0.00 0.00 33.20 2.69
472 490 7.069331 AGGTATGAAGAAACAAAACCATGTCAA 59.931 33.333 0.00 0.00 34.48 3.18
473 491 6.549364 AGGTATGAAGAAACAAAACCATGTCA 59.451 34.615 0.00 0.00 34.48 3.58
474 492 6.981722 AGGTATGAAGAAACAAAACCATGTC 58.018 36.000 0.00 0.00 34.48 3.06
475 493 6.976934 AGGTATGAAGAAACAAAACCATGT 57.023 33.333 0.00 0.00 34.48 3.21
476 494 9.927668 ATTTAGGTATGAAGAAACAAAACCATG 57.072 29.630 0.00 0.00 34.48 3.66
478 496 9.137459 TGATTTAGGTATGAAGAAACAAAACCA 57.863 29.630 0.00 0.00 34.48 3.67
479 497 9.974980 TTGATTTAGGTATGAAGAAACAAAACC 57.025 29.630 0.00 0.00 33.17 3.27
715 742 6.361433 TCCTTCAATCCAAACACTGTTTAGA 58.639 36.000 6.84 6.07 0.00 2.10
811 847 1.305886 GGGTCCTTTATTCCCCCACT 58.694 55.000 0.00 0.00 35.32 4.00
825 861 7.549488 GCATGTTATAGTAACTGATATGGGTCC 59.451 40.741 0.00 0.00 0.00 4.46
922 958 1.071814 GGGTGGCCACGACAAGTAA 59.928 57.895 29.08 0.00 0.00 2.24
933 969 0.672711 GTACGACAAGAAGGGTGGCC 60.673 60.000 0.00 0.00 0.00 5.36
942 978 7.415229 CAATAGTACTATGCTGTACGACAAGA 58.585 38.462 16.11 0.00 45.23 3.02
943 979 6.142480 GCAATAGTACTATGCTGTACGACAAG 59.858 42.308 16.11 0.00 45.23 3.16
945 981 5.298527 AGCAATAGTACTATGCTGTACGACA 59.701 40.000 25.80 0.00 45.23 4.35
946 982 5.759963 AGCAATAGTACTATGCTGTACGAC 58.240 41.667 25.80 8.85 45.23 4.34
948 984 7.273598 CCATAAGCAATAGTACTATGCTGTACG 59.726 40.741 26.51 18.99 45.23 3.67
950 986 7.234782 ACCCATAAGCAATAGTACTATGCTGTA 59.765 37.037 26.51 21.67 33.49 2.74
955 991 7.099764 CCAGACCCATAAGCAATAGTACTATG 58.900 42.308 16.11 11.07 0.00 2.23
956 992 6.213600 CCCAGACCCATAAGCAATAGTACTAT 59.786 42.308 9.71 9.71 0.00 2.12
959 995 4.347000 TCCCAGACCCATAAGCAATAGTAC 59.653 45.833 0.00 0.00 0.00 2.73
964 1000 1.215423 GGTCCCAGACCCATAAGCAAT 59.785 52.381 2.14 0.00 46.19 3.56
1019 1055 2.620115 CTCATGTTGCCACACTTGTCTT 59.380 45.455 0.00 0.00 35.03 3.01
1092 1128 2.587956 CCAGTTTCATTGCATGTGACG 58.412 47.619 2.10 0.00 0.00 4.35
1107 1143 1.538666 GGCCAGATATGCCCCAGTT 59.461 57.895 0.00 0.00 43.33 3.16
1167 1203 1.871676 GGGTTCTGAACACGAACTTCC 59.128 52.381 21.01 7.52 40.37 3.46
1170 1206 1.208535 TGTGGGTTCTGAACACGAACT 59.791 47.619 21.01 0.00 40.37 3.01
1196 1232 2.158559 TCGTGTAGTTGCATTGCCAAT 58.841 42.857 6.12 0.00 0.00 3.16
1197 1233 1.598882 TCGTGTAGTTGCATTGCCAA 58.401 45.000 6.12 0.00 0.00 4.52
1215 1251 2.253603 CTGCTGCTATTTTTGCCGTTC 58.746 47.619 0.00 0.00 0.00 3.95
1223 1259 4.935352 TTCAAACCACTGCTGCTATTTT 57.065 36.364 0.00 0.00 0.00 1.82
1224 1260 4.082026 GGATTCAAACCACTGCTGCTATTT 60.082 41.667 0.00 0.00 0.00 1.40
1232 1268 3.572255 TGTTAAGGGATTCAAACCACTGC 59.428 43.478 0.00 0.00 0.00 4.40
1238 1280 6.590234 AATCCAGTGTTAAGGGATTCAAAC 57.410 37.500 0.00 0.00 45.82 2.93
1246 1288 6.840780 ATGAAAAGAATCCAGTGTTAAGGG 57.159 37.500 0.00 0.00 0.00 3.95
1254 1296 7.944554 TCAGAAACCTTATGAAAAGAATCCAGT 59.055 33.333 0.00 0.00 0.00 4.00
1257 1299 8.023706 GTGTCAGAAACCTTATGAAAAGAATCC 58.976 37.037 0.00 0.00 0.00 3.01
1261 1303 6.361433 TGGTGTCAGAAACCTTATGAAAAGA 58.639 36.000 11.39 0.00 38.60 2.52
1278 1320 4.149511 TGTCATCTTGTTCTTGGTGTCA 57.850 40.909 0.00 0.00 0.00 3.58
1279 1321 4.756642 TGATGTCATCTTGTTCTTGGTGTC 59.243 41.667 13.90 0.00 0.00 3.67
1294 1336 2.453521 AGCACAGCCAATTGATGTCAT 58.546 42.857 7.12 0.00 0.00 3.06
1330 1372 2.045926 GCTCTTGGTGCGTCCCAT 60.046 61.111 0.00 0.00 33.60 4.00
1506 1548 6.013725 ACTGGATGGTAGTGTTGTAAAGATCA 60.014 38.462 0.00 0.00 0.00 2.92
1510 1552 5.794894 AGACTGGATGGTAGTGTTGTAAAG 58.205 41.667 0.00 0.00 0.00 1.85
1519 1561 3.515901 GGACTGAAAGACTGGATGGTAGT 59.484 47.826 0.00 0.00 37.43 2.73
1830 1873 7.124901 AGAGTACAGGTTGATTCTGTGACATAT 59.875 37.037 6.95 0.00 44.24 1.78
1834 1877 5.140747 AGAGTACAGGTTGATTCTGTGAC 57.859 43.478 6.95 2.64 44.24 3.67
1927 2010 7.176165 ACACTCATTGATGTCTGTCATTTCAAT 59.824 33.333 0.00 0.00 36.68 2.57
2160 2252 8.621532 ATGCTTTCTGTTTACATTGAAGTAGA 57.378 30.769 0.00 0.00 0.00 2.59
2201 2305 4.811969 TGTATTGGACTTGTATGACCGT 57.188 40.909 0.00 0.00 0.00 4.83
2413 2535 2.107204 TCCTTCTCTTTTGCCAGCTTCT 59.893 45.455 0.00 0.00 0.00 2.85
2445 2567 6.060136 ACAATATCTGACCACCATTCTGATG 58.940 40.000 0.00 0.00 34.54 3.07
2522 2644 5.431765 TCATTTGTAGCCTTCTTGAGATCC 58.568 41.667 0.00 0.00 0.00 3.36
2528 2650 6.306356 CGTCAAAATCATTTGTAGCCTTCTTG 59.694 38.462 1.69 0.00 45.02 3.02
2653 2775 1.821216 AATTCGTCAGTTTCGGCCAT 58.179 45.000 2.24 0.00 0.00 4.40
2784 2906 3.307339 GGATGAACTGAAAGAGAGTGCCT 60.307 47.826 0.00 0.00 37.43 4.75
2810 2932 2.753247 GAGGTGGACTCCCATAGTTCT 58.247 52.381 0.00 0.00 45.68 3.01
2868 2990 3.367327 GCAGATATGATAGTGCTTCAGCG 59.633 47.826 0.00 0.00 45.83 5.18
2880 3002 5.757099 TCATGGACAGATGCAGATATGAT 57.243 39.130 0.00 0.00 0.00 2.45
2881 3003 5.303165 GTTCATGGACAGATGCAGATATGA 58.697 41.667 0.00 0.00 0.00 2.15
2934 3056 4.774124 TGTCATCCAGGAGAATGTTCATC 58.226 43.478 0.00 0.00 0.00 2.92
2947 3069 1.935873 CGCCATGTAGTTGTCATCCAG 59.064 52.381 0.00 0.00 0.00 3.86
2952 3074 2.805671 CACTTTCGCCATGTAGTTGTCA 59.194 45.455 0.00 0.00 0.00 3.58
2955 3077 2.159627 GGTCACTTTCGCCATGTAGTTG 59.840 50.000 0.00 0.00 0.00 3.16
3076 3198 0.605589 CTCTTCTCCGTGAGTTGCCT 59.394 55.000 1.60 0.00 0.00 4.75
3081 3203 0.453793 CATCGCTCTTCTCCGTGAGT 59.546 55.000 1.60 0.00 33.22 3.41
3099 3221 1.746220 ACAACGCCAAAGCTGTAAACA 59.254 42.857 0.00 0.00 36.60 2.83
3120 3242 1.514553 CGTGATCAGCTCCAGCAGA 59.485 57.895 0.00 0.00 45.16 4.26
3146 3268 2.041976 CCATCGTGGTAGATCGCCT 58.958 57.895 10.06 0.00 31.35 5.52
3228 3350 1.276859 TGCTCACATCCAGGATGCCT 61.277 55.000 27.17 8.02 43.15 4.75
3242 3367 0.249120 CCCGACACCAACTATGCTCA 59.751 55.000 0.00 0.00 0.00 4.26
3575 3700 3.002791 CACACACACACACACTCTTCTT 58.997 45.455 0.00 0.00 0.00 2.52
3576 3701 2.028112 ACACACACACACACACTCTTCT 60.028 45.455 0.00 0.00 0.00 2.85
3577 3702 2.346803 ACACACACACACACACTCTTC 58.653 47.619 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.