Multiple sequence alignment - TraesCS5D01G248600

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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 TraesCS5D01G248600 chr5D 100.000 3533 0 0 1 3533 355606639 355610171 0.000000e+00 6525.0
1 TraesCS5D01G248600 chr5A 92.963 2970 138 28 582 3533 457567998 457565082 0.000000e+00 4261.0
2 TraesCS5D01G248600 chr5B 91.751 1879 90 28 718 2567 420184501 420186343 0.000000e+00 2551.0
3 TraesCS5D01G248600 chr5B 87.903 124 6 6 2560 2679 420188153 420188271 1.710000e-28 137.0
4 TraesCS5D01G248600 chr5B 97.436 39 1 0 477 515 540048848 540048810 2.280000e-07 67.6
5 TraesCS5D01G248600 chr5B 97.436 39 1 0 1 39 693422368 693422406 2.280000e-07 67.6
6 TraesCS5D01G248600 chr5B 78.788 99 12 4 288 386 603520554 603520465 1.370000e-04 58.4
7 TraesCS5D01G248600 chr7A 78.321 1453 277 26 1069 2511 126367566 126366142 0.000000e+00 904.0
8 TraesCS5D01G248600 chr7A 78.237 1452 272 27 1069 2507 126191383 126192803 0.000000e+00 891.0
9 TraesCS5D01G248600 chr7A 78.162 1447 282 22 1069 2507 126195845 126197265 0.000000e+00 891.0
10 TraesCS5D01G248600 chr7A 85.526 76 10 1 463 538 148533125 148533199 1.050000e-10 78.7
11 TraesCS5D01G248600 chr7D 78.077 1446 285 21 1069 2507 123490624 123489204 0.000000e+00 885.0
12 TraesCS5D01G248600 chr7D 77.548 1452 290 21 1069 2511 123455278 123456702 0.000000e+00 843.0
13 TraesCS5D01G248600 chr7D 77.184 1328 261 30 1075 2391 123462138 123463434 0.000000e+00 736.0
14 TraesCS5D01G248600 chr7D 76.235 972 213 13 1436 2399 123484807 123483846 1.890000e-137 499.0
15 TraesCS5D01G248600 chr7D 79.149 470 82 12 35 494 102959284 102959747 9.520000e-81 311.0
16 TraesCS5D01G248600 chr7D 97.436 39 1 0 1 39 106634440 106634402 2.280000e-07 67.6
17 TraesCS5D01G248600 chr7B 77.908 1453 283 27 1069 2511 84701038 84702462 0.000000e+00 870.0
18 TraesCS5D01G248600 chr7B 78.114 1389 272 21 1069 2450 84765415 84764052 0.000000e+00 852.0
19 TraesCS5D01G248600 chr7B 76.246 341 51 19 72 389 631134236 631133903 1.700000e-33 154.0
20 TraesCS5D01G248600 chr7B 95.238 42 0 2 1 42 225367767 225367728 8.190000e-07 65.8
21 TraesCS5D01G248600 chr7B 95.238 42 0 2 1 42 384588052 384588013 8.190000e-07 65.8
22 TraesCS5D01G248600 chr7B 95.000 40 2 0 277 316 102886621 102886660 2.940000e-06 63.9
23 TraesCS5D01G248600 chr2B 78.937 527 86 14 30 539 775109525 775110043 5.650000e-88 335.0
24 TraesCS5D01G248600 chr2B 75.336 446 89 12 63 496 23003935 23004371 1.000000e-45 195.0
25 TraesCS5D01G248600 chr1B 78.763 485 79 14 59 538 458378428 458377963 1.590000e-78 303.0
26 TraesCS5D01G248600 chr1B 76.892 502 92 11 29 514 354244370 354243877 2.700000e-66 263.0
27 TraesCS5D01G248600 chr1B 83.133 83 14 0 464 546 676604156 676604074 3.780000e-10 76.8
28 TraesCS5D01G248600 chr1B 80.723 83 16 0 464 546 676560277 676560195 8.190000e-07 65.8
29 TraesCS5D01G248600 chr6B 75.681 514 87 23 29 513 692192319 692192823 4.590000e-54 222.0
30 TraesCS5D01G248600 chr6A 75.348 503 89 22 30 515 32896793 32896309 3.570000e-50 209.0
31 TraesCS5D01G248600 chr6A 97.436 39 1 0 1 39 221224357 221224319 2.280000e-07 67.6
32 TraesCS5D01G248600 chr6D 76.010 396 65 17 28 400 455084107 455084495 1.010000e-40 178.0
33 TraesCS5D01G248600 chr1A 86.508 126 12 3 64 189 441941859 441941739 2.210000e-27 134.0
34 TraesCS5D01G248600 chr1D 81.875 160 25 2 22 181 307425530 307425685 7.960000e-27 132.0
35 TraesCS5D01G248600 chr1D 85.577 104 15 0 283 386 134529962 134529859 3.730000e-20 110.0
36 TraesCS5D01G248600 chr3A 84.259 108 16 1 283 389 239387237 239387344 1.730000e-18 104.0
37 TraesCS5D01G248600 chr3A 95.000 40 0 1 1 40 138477548 138477585 1.060000e-05 62.1
38 TraesCS5D01G248600 chr3D 82.692 104 18 0 283 386 82492851 82492748 3.760000e-15 93.5
39 TraesCS5D01G248600 chr2D 97.561 41 1 0 1 41 493823035 493823075 1.760000e-08 71.3
40 TraesCS5D01G248600 chr4D 97.436 39 1 0 1 39 295514837 295514875 2.280000e-07 67.6
41 TraesCS5D01G248600 chr4A 97.500 40 0 1 1 40 72550129 72550167 2.280000e-07 67.6
42 TraesCS5D01G248600 chr4A 85.714 63 8 1 478 539 86324651 86324589 8.190000e-07 65.8
43 TraesCS5D01G248600 chr2A 95.238 42 1 1 478 519 633159346 633159386 8.190000e-07 65.8


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 TraesCS5D01G248600 chr5D 355606639 355610171 3532 False 6525 6525 100.0000 1 3533 1 chr5D.!!$F1 3532
1 TraesCS5D01G248600 chr5A 457565082 457567998 2916 True 4261 4261 92.9630 582 3533 1 chr5A.!!$R1 2951
2 TraesCS5D01G248600 chr5B 420184501 420188271 3770 False 1344 2551 89.8270 718 2679 2 chr5B.!!$F2 1961
3 TraesCS5D01G248600 chr7A 126366142 126367566 1424 True 904 904 78.3210 1069 2511 1 chr7A.!!$R1 1442
4 TraesCS5D01G248600 chr7A 126191383 126197265 5882 False 891 891 78.1995 1069 2507 2 chr7A.!!$F2 1438
5 TraesCS5D01G248600 chr7D 123489204 123490624 1420 True 885 885 78.0770 1069 2507 1 chr7D.!!$R3 1438
6 TraesCS5D01G248600 chr7D 123455278 123456702 1424 False 843 843 77.5480 1069 2511 1 chr7D.!!$F2 1442
7 TraesCS5D01G248600 chr7D 123462138 123463434 1296 False 736 736 77.1840 1075 2391 1 chr7D.!!$F3 1316
8 TraesCS5D01G248600 chr7D 123483846 123484807 961 True 499 499 76.2350 1436 2399 1 chr7D.!!$R2 963
9 TraesCS5D01G248600 chr7B 84701038 84702462 1424 False 870 870 77.9080 1069 2511 1 chr7B.!!$F1 1442
10 TraesCS5D01G248600 chr7B 84764052 84765415 1363 True 852 852 78.1140 1069 2450 1 chr7B.!!$R1 1381
11 TraesCS5D01G248600 chr2B 775109525 775110043 518 False 335 335 78.9370 30 539 1 chr2B.!!$F2 509
12 TraesCS5D01G248600 chr6B 692192319 692192823 504 False 222 222 75.6810 29 513 1 chr6B.!!$F1 484

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
269 295 0.104304 GATGTAGGGCGATGAACCGT 59.896 55.0 0.0 0.0 0.0 4.83 F
1018 1052 0.250640 GATGCCCAGCCTAGTCCATG 60.251 60.0 0.0 0.0 0.0 3.66 F
1026 1060 0.253044 GCCTAGTCCATGTCCAAGCA 59.747 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1770 6291 0.477597 TCCACACCTTCATCCCCCTT 60.478 55.000 0.0 0.0 0.0 3.95 R
2001 6526 1.191535 CGTCCTTGACCACCCAGATA 58.808 55.000 0.0 0.0 0.0 1.98 R
2726 9100 2.036217 ACCAAATACCGTCGAGTCACAA 59.964 45.455 0.0 0.0 0.0 3.33 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
17 18 2.584608 CCCGAGATCTGCCGGTTT 59.415 61.111 18.55 0.00 43.93 3.27
18 19 1.078426 CCCGAGATCTGCCGGTTTT 60.078 57.895 18.55 0.00 43.93 2.43
19 20 1.369091 CCCGAGATCTGCCGGTTTTG 61.369 60.000 18.55 3.10 43.93 2.44
20 21 0.391130 CCGAGATCTGCCGGTTTTGA 60.391 55.000 13.39 0.00 40.78 2.69
21 22 0.721718 CGAGATCTGCCGGTTTTGAC 59.278 55.000 0.00 0.00 0.00 3.18
22 23 1.808411 GAGATCTGCCGGTTTTGACA 58.192 50.000 0.00 0.00 0.00 3.58
23 24 1.464997 GAGATCTGCCGGTTTTGACAC 59.535 52.381 0.00 0.00 0.00 3.67
24 25 0.521735 GATCTGCCGGTTTTGACACC 59.478 55.000 1.90 0.00 0.00 4.16
40 41 0.824109 CACCGACAGCCATCTCCTTA 59.176 55.000 0.00 0.00 0.00 2.69
49 53 2.441001 AGCCATCTCCTTATGGTTGGAG 59.559 50.000 14.08 0.00 46.93 3.86
56 60 2.045885 TCCTTATGGTTGGAGGAGAGGT 59.954 50.000 0.00 0.00 34.74 3.85
61 65 1.353091 GGTTGGAGGAGAGGTTGTCT 58.647 55.000 0.00 0.00 38.71 3.41
77 81 2.408565 TGTCTCAGAGGGTTTTGGAGT 58.591 47.619 0.00 0.00 0.00 3.85
90 94 3.706373 GGAGTGCGAGGAGGCCAA 61.706 66.667 5.01 0.00 0.00 4.52
113 117 2.202932 GCGTGGTGCGGAGATGAT 60.203 61.111 0.00 0.00 41.69 2.45
122 126 2.115427 TGCGGAGATGATAAAGGGACA 58.885 47.619 0.00 0.00 0.00 4.02
123 127 2.503765 TGCGGAGATGATAAAGGGACAA 59.496 45.455 0.00 0.00 0.00 3.18
134 138 1.589414 AAGGGACAAGAGGAGGATGG 58.411 55.000 0.00 0.00 0.00 3.51
136 140 1.144936 GGACAAGAGGAGGATGGCG 59.855 63.158 0.00 0.00 0.00 5.69
137 141 1.617947 GGACAAGAGGAGGATGGCGT 61.618 60.000 0.00 0.00 0.00 5.68
138 142 1.112113 GACAAGAGGAGGATGGCGTA 58.888 55.000 0.00 0.00 0.00 4.42
139 143 0.824759 ACAAGAGGAGGATGGCGTAC 59.175 55.000 0.00 0.00 0.00 3.67
140 144 1.115467 CAAGAGGAGGATGGCGTACT 58.885 55.000 0.00 0.00 0.00 2.73
141 145 1.115467 AAGAGGAGGATGGCGTACTG 58.885 55.000 0.00 0.00 0.00 2.74
142 146 1.068250 GAGGAGGATGGCGTACTGC 59.932 63.158 1.52 1.52 45.38 4.40
186 190 2.046009 TATAGCGGGCGGATGGCAAA 62.046 55.000 0.00 0.00 46.16 3.68
229 255 2.062177 GGGGCGCCAGAGTAGGTTA 61.062 63.158 30.85 0.00 0.00 2.85
250 276 3.460114 CGGCAACCGCATATCATTG 57.540 52.632 0.00 0.00 41.17 2.82
264 290 5.422145 CATATCATTGATGTAGGGCGATGA 58.578 41.667 9.46 0.00 38.79 2.92
269 295 0.104304 GATGTAGGGCGATGAACCGT 59.896 55.000 0.00 0.00 0.00 4.83
274 300 3.186047 GGCGATGAACCGTCGTGG 61.186 66.667 9.82 0.00 43.73 4.94
292 318 1.468340 GGTGTGTTGTTTGAACGCGC 61.468 55.000 5.73 0.00 39.60 6.86
320 346 4.555709 TGCACCGGGAAGCAACGT 62.556 61.111 14.88 0.00 37.90 3.99
321 347 4.025401 GCACCGGGAAGCAACGTG 62.025 66.667 6.32 0.00 0.00 4.49
322 348 3.353836 CACCGGGAAGCAACGTGG 61.354 66.667 6.32 0.00 0.00 4.94
323 349 4.636435 ACCGGGAAGCAACGTGGG 62.636 66.667 6.32 0.00 0.00 4.61
359 385 4.183686 CGCCCCGCTTCAATGCTG 62.184 66.667 0.00 0.00 0.00 4.41
360 386 3.830192 GCCCCGCTTCAATGCTGG 61.830 66.667 0.00 0.00 37.13 4.85
361 387 2.361610 CCCCGCTTCAATGCTGGT 60.362 61.111 0.00 0.00 35.89 4.00
362 388 1.077787 CCCCGCTTCAATGCTGGTA 60.078 57.895 0.00 0.00 35.89 3.25
363 389 1.097547 CCCCGCTTCAATGCTGGTAG 61.098 60.000 0.00 0.00 35.89 3.18
364 390 0.392998 CCCGCTTCAATGCTGGTAGT 60.393 55.000 0.00 0.00 33.50 2.73
365 391 1.134521 CCCGCTTCAATGCTGGTAGTA 60.135 52.381 0.00 0.00 33.50 1.82
366 392 2.205074 CCGCTTCAATGCTGGTAGTAG 58.795 52.381 0.00 0.00 0.00 2.57
367 393 2.418746 CCGCTTCAATGCTGGTAGTAGT 60.419 50.000 0.00 0.00 0.00 2.73
368 394 2.604914 CGCTTCAATGCTGGTAGTAGTG 59.395 50.000 0.00 0.00 0.00 2.74
369 395 3.676049 CGCTTCAATGCTGGTAGTAGTGA 60.676 47.826 0.00 0.00 33.39 3.41
370 396 3.868077 GCTTCAATGCTGGTAGTAGTGAG 59.132 47.826 0.00 0.00 36.40 3.51
371 397 4.382040 GCTTCAATGCTGGTAGTAGTGAGA 60.382 45.833 0.00 0.00 36.40 3.27
372 398 4.991153 TCAATGCTGGTAGTAGTGAGAG 57.009 45.455 0.00 0.00 30.45 3.20
373 399 3.701542 TCAATGCTGGTAGTAGTGAGAGG 59.298 47.826 0.00 0.00 30.45 3.69
374 400 2.901338 TGCTGGTAGTAGTGAGAGGT 57.099 50.000 0.00 0.00 0.00 3.85
375 401 2.724454 TGCTGGTAGTAGTGAGAGGTC 58.276 52.381 0.00 0.00 0.00 3.85
376 402 1.671845 GCTGGTAGTAGTGAGAGGTCG 59.328 57.143 0.00 0.00 0.00 4.79
377 403 1.671845 CTGGTAGTAGTGAGAGGTCGC 59.328 57.143 0.00 0.00 0.00 5.19
378 404 0.656785 GGTAGTAGTGAGAGGTCGCG 59.343 60.000 0.00 0.00 38.32 5.87
379 405 1.367659 GTAGTAGTGAGAGGTCGCGT 58.632 55.000 5.77 0.00 38.32 6.01
380 406 1.327156 GTAGTAGTGAGAGGTCGCGTC 59.673 57.143 5.77 0.00 38.32 5.19
381 407 1.025647 AGTAGTGAGAGGTCGCGTCC 61.026 60.000 14.89 14.89 38.32 4.79
382 408 2.104859 TAGTGAGAGGTCGCGTCCG 61.105 63.158 16.59 0.00 38.32 4.79
385 411 4.539881 GAGAGGTCGCGTCCGCTC 62.540 72.222 31.72 31.72 44.35 5.03
394 420 2.586079 CGTCCGCTCGGCATGAAT 60.586 61.111 2.96 0.00 34.68 2.57
395 421 2.874694 CGTCCGCTCGGCATGAATG 61.875 63.158 2.96 0.00 34.68 2.67
408 434 3.476295 CATGAATGCAACACTAACGCT 57.524 42.857 0.00 0.00 0.00 5.07
409 435 3.419915 CATGAATGCAACACTAACGCTC 58.580 45.455 0.00 0.00 0.00 5.03
410 436 2.766313 TGAATGCAACACTAACGCTCT 58.234 42.857 0.00 0.00 0.00 4.09
411 437 2.480037 TGAATGCAACACTAACGCTCTG 59.520 45.455 0.00 0.00 0.00 3.35
412 438 1.442769 ATGCAACACTAACGCTCTGG 58.557 50.000 0.00 0.00 0.00 3.86
413 439 0.391228 TGCAACACTAACGCTCTGGA 59.609 50.000 0.00 0.00 0.00 3.86
414 440 1.071605 GCAACACTAACGCTCTGGAG 58.928 55.000 0.00 0.00 0.00 3.86
415 441 1.605712 GCAACACTAACGCTCTGGAGT 60.606 52.381 0.00 0.00 0.00 3.85
416 442 2.061773 CAACACTAACGCTCTGGAGTG 58.938 52.381 9.30 9.30 43.97 3.51
417 443 0.603569 ACACTAACGCTCTGGAGTGG 59.396 55.000 14.44 3.40 42.93 4.00
418 444 0.737715 CACTAACGCTCTGGAGTGGC 60.738 60.000 14.44 0.00 42.91 5.01
460 486 4.143333 CACGGGCGAGTAGGGGTG 62.143 72.222 0.00 0.00 0.00 4.61
465 491 3.782443 GCGAGTAGGGGTGGGGTG 61.782 72.222 0.00 0.00 0.00 4.61
466 492 3.081409 CGAGTAGGGGTGGGGTGG 61.081 72.222 0.00 0.00 0.00 4.61
467 493 2.691252 GAGTAGGGGTGGGGTGGG 60.691 72.222 0.00 0.00 0.00 4.61
479 505 4.380945 GGTGGGCCAGGGCAATCA 62.381 66.667 16.36 0.16 44.11 2.57
480 506 2.757099 GTGGGCCAGGGCAATCAG 60.757 66.667 16.36 0.00 44.11 2.90
481 507 2.940467 TGGGCCAGGGCAATCAGA 60.940 61.111 16.36 0.00 44.11 3.27
482 508 2.360191 GGGCCAGGGCAATCAGAA 59.640 61.111 16.36 0.00 44.11 3.02
483 509 1.755783 GGGCCAGGGCAATCAGAAG 60.756 63.158 16.36 0.00 44.11 2.85
484 510 2.421399 GGCCAGGGCAATCAGAAGC 61.421 63.158 13.10 0.00 44.11 3.86
485 511 2.768492 GCCAGGGCAATCAGAAGCG 61.768 63.158 5.20 0.00 41.49 4.68
486 512 2.117156 CCAGGGCAATCAGAAGCGG 61.117 63.158 0.00 0.00 0.00 5.52
487 513 2.439156 AGGGCAATCAGAAGCGGC 60.439 61.111 0.00 0.00 0.00 6.53
488 514 3.521796 GGGCAATCAGAAGCGGCC 61.522 66.667 0.00 0.00 43.86 6.13
489 515 3.880846 GGCAATCAGAAGCGGCCG 61.881 66.667 24.05 24.05 34.56 6.13
490 516 3.127533 GCAATCAGAAGCGGCCGT 61.128 61.111 28.70 7.71 0.00 5.68
491 517 2.787249 CAATCAGAAGCGGCCGTG 59.213 61.111 28.70 17.39 0.00 4.94
492 518 2.436646 AATCAGAAGCGGCCGTGG 60.437 61.111 28.70 11.94 0.00 4.94
519 545 2.178273 GGACGCCCGCAAAACATC 59.822 61.111 0.00 0.00 0.00 3.06
520 546 2.178273 GACGCCCGCAAAACATCC 59.822 61.111 0.00 0.00 0.00 3.51
521 547 3.336715 GACGCCCGCAAAACATCCC 62.337 63.158 0.00 0.00 0.00 3.85
522 548 3.369400 CGCCCGCAAAACATCCCA 61.369 61.111 0.00 0.00 0.00 4.37
523 549 2.261361 GCCCGCAAAACATCCCAC 59.739 61.111 0.00 0.00 0.00 4.61
524 550 2.275380 GCCCGCAAAACATCCCACT 61.275 57.895 0.00 0.00 0.00 4.00
525 551 1.815817 GCCCGCAAAACATCCCACTT 61.816 55.000 0.00 0.00 0.00 3.16
526 552 0.678950 CCCGCAAAACATCCCACTTT 59.321 50.000 0.00 0.00 0.00 2.66
527 553 1.605202 CCCGCAAAACATCCCACTTTG 60.605 52.381 0.00 0.00 33.99 2.77
528 554 1.068434 CCGCAAAACATCCCACTTTGT 59.932 47.619 0.00 0.00 33.51 2.83
529 555 2.393764 CGCAAAACATCCCACTTTGTC 58.606 47.619 0.00 0.00 33.51 3.18
530 556 2.034558 CGCAAAACATCCCACTTTGTCT 59.965 45.455 0.00 0.00 33.51 3.41
531 557 3.490761 CGCAAAACATCCCACTTTGTCTT 60.491 43.478 0.00 0.00 33.51 3.01
532 558 4.051237 GCAAAACATCCCACTTTGTCTTC 58.949 43.478 0.00 0.00 33.51 2.87
533 559 4.290155 CAAAACATCCCACTTTGTCTTCG 58.710 43.478 0.00 0.00 0.00 3.79
534 560 2.185004 ACATCCCACTTTGTCTTCGG 57.815 50.000 0.00 0.00 0.00 4.30
535 561 1.420138 ACATCCCACTTTGTCTTCGGT 59.580 47.619 0.00 0.00 0.00 4.69
536 562 2.158667 ACATCCCACTTTGTCTTCGGTT 60.159 45.455 0.00 0.00 0.00 4.44
537 563 2.721425 TCCCACTTTGTCTTCGGTTT 57.279 45.000 0.00 0.00 0.00 3.27
538 564 2.294074 TCCCACTTTGTCTTCGGTTTG 58.706 47.619 0.00 0.00 0.00 2.93
539 565 2.021457 CCCACTTTGTCTTCGGTTTGT 58.979 47.619 0.00 0.00 0.00 2.83
540 566 2.223479 CCCACTTTGTCTTCGGTTTGTG 60.223 50.000 0.00 0.00 0.00 3.33
541 567 2.223479 CCACTTTGTCTTCGGTTTGTGG 60.223 50.000 0.00 0.00 37.87 4.17
542 568 2.680841 CACTTTGTCTTCGGTTTGTGGA 59.319 45.455 0.00 0.00 0.00 4.02
543 569 3.127895 CACTTTGTCTTCGGTTTGTGGAA 59.872 43.478 0.00 0.00 0.00 3.53
544 570 3.759618 ACTTTGTCTTCGGTTTGTGGAAA 59.240 39.130 0.00 0.00 0.00 3.13
545 571 4.218852 ACTTTGTCTTCGGTTTGTGGAAAA 59.781 37.500 0.00 0.00 0.00 2.29
546 572 3.768468 TGTCTTCGGTTTGTGGAAAAC 57.232 42.857 0.00 0.00 0.00 2.43
547 573 2.424246 TGTCTTCGGTTTGTGGAAAACC 59.576 45.455 9.48 9.48 44.69 3.27
548 574 2.686405 GTCTTCGGTTTGTGGAAAACCT 59.314 45.455 15.83 0.00 45.66 3.50
549 575 3.878699 GTCTTCGGTTTGTGGAAAACCTA 59.121 43.478 15.83 4.60 45.66 3.08
550 576 4.517832 GTCTTCGGTTTGTGGAAAACCTAT 59.482 41.667 15.83 0.00 45.66 2.57
551 577 4.758165 TCTTCGGTTTGTGGAAAACCTATC 59.242 41.667 15.83 0.00 45.66 2.08
552 578 4.360951 TCGGTTTGTGGAAAACCTATCT 57.639 40.909 15.83 0.00 45.66 1.98
553 579 5.486735 TCGGTTTGTGGAAAACCTATCTA 57.513 39.130 15.83 0.00 45.66 1.98
554 580 5.867330 TCGGTTTGTGGAAAACCTATCTAA 58.133 37.500 15.83 0.00 45.66 2.10
555 581 6.478129 TCGGTTTGTGGAAAACCTATCTAAT 58.522 36.000 15.83 0.00 45.66 1.73
556 582 6.373216 TCGGTTTGTGGAAAACCTATCTAATG 59.627 38.462 15.83 1.14 45.66 1.90
557 583 6.373216 CGGTTTGTGGAAAACCTATCTAATGA 59.627 38.462 15.83 0.00 45.66 2.57
558 584 7.094549 CGGTTTGTGGAAAACCTATCTAATGAA 60.095 37.037 15.83 0.00 45.66 2.57
559 585 8.581578 GGTTTGTGGAAAACCTATCTAATGAAA 58.418 33.333 11.80 0.00 44.71 2.69
560 586 9.626045 GTTTGTGGAAAACCTATCTAATGAAAG 57.374 33.333 0.00 0.00 0.00 2.62
561 587 7.391148 TGTGGAAAACCTATCTAATGAAAGC 57.609 36.000 0.00 0.00 0.00 3.51
562 588 6.377146 TGTGGAAAACCTATCTAATGAAAGCC 59.623 38.462 0.00 0.00 0.00 4.35
563 589 6.603599 GTGGAAAACCTATCTAATGAAAGCCT 59.396 38.462 0.00 0.00 0.00 4.58
564 590 7.122799 GTGGAAAACCTATCTAATGAAAGCCTT 59.877 37.037 0.00 0.00 0.00 4.35
565 591 7.673926 TGGAAAACCTATCTAATGAAAGCCTTT 59.326 33.333 0.00 0.00 0.00 3.11
566 592 8.191446 GGAAAACCTATCTAATGAAAGCCTTTC 58.809 37.037 10.29 10.29 40.08 2.62
567 593 8.885693 AAAACCTATCTAATGAAAGCCTTTCT 57.114 30.769 17.51 1.75 40.32 2.52
568 594 8.885693 AAACCTATCTAATGAAAGCCTTTCTT 57.114 30.769 17.51 9.06 40.32 2.52
569 595 8.512966 AACCTATCTAATGAAAGCCTTTCTTC 57.487 34.615 17.51 0.00 40.32 2.87
570 596 7.633789 ACCTATCTAATGAAAGCCTTTCTTCA 58.366 34.615 17.51 0.00 40.32 3.02
571 597 7.772757 ACCTATCTAATGAAAGCCTTTCTTCAG 59.227 37.037 17.51 7.68 40.32 3.02
572 598 7.989741 CCTATCTAATGAAAGCCTTTCTTCAGA 59.010 37.037 17.51 12.50 40.32 3.27
573 599 9.388506 CTATCTAATGAAAGCCTTTCTTCAGAA 57.611 33.333 17.51 0.00 40.32 3.02
574 600 8.641498 ATCTAATGAAAGCCTTTCTTCAGAAA 57.359 30.769 17.51 2.07 41.29 2.52
575 601 8.463930 TCTAATGAAAGCCTTTCTTCAGAAAA 57.536 30.769 17.51 0.00 42.72 2.29
576 602 8.912988 TCTAATGAAAGCCTTTCTTCAGAAAAA 58.087 29.630 17.51 0.00 42.72 1.94
577 603 9.702494 CTAATGAAAGCCTTTCTTCAGAAAAAT 57.298 29.630 17.51 0.00 42.72 1.82
580 606 8.871686 TGAAAGCCTTTCTTCAGAAAAATAAC 57.128 30.769 17.51 0.00 42.72 1.89
673 701 2.410469 GCACATGCGGGCATCTTC 59.590 61.111 2.58 0.00 33.90 2.87
942 971 5.921976 TCGACGTTCTTTAAATCACTTGCTA 59.078 36.000 0.00 0.00 0.00 3.49
1007 1041 4.864334 GGAGCCCACGATGCCCAG 62.864 72.222 0.00 0.00 0.00 4.45
1015 1049 2.423446 CGATGCCCAGCCTAGTCC 59.577 66.667 0.00 0.00 0.00 3.85
1017 1051 1.762522 CGATGCCCAGCCTAGTCCAT 61.763 60.000 0.00 0.00 0.00 3.41
1018 1052 0.250640 GATGCCCAGCCTAGTCCATG 60.251 60.000 0.00 0.00 0.00 3.66
1019 1053 0.990282 ATGCCCAGCCTAGTCCATGT 60.990 55.000 0.00 0.00 0.00 3.21
1020 1054 1.147153 GCCCAGCCTAGTCCATGTC 59.853 63.158 0.00 0.00 0.00 3.06
1021 1055 1.832912 CCCAGCCTAGTCCATGTCC 59.167 63.158 0.00 0.00 0.00 4.02
1022 1056 0.982852 CCCAGCCTAGTCCATGTCCA 60.983 60.000 0.00 0.00 0.00 4.02
1023 1057 0.911769 CCAGCCTAGTCCATGTCCAA 59.088 55.000 0.00 0.00 0.00 3.53
1024 1058 1.134280 CCAGCCTAGTCCATGTCCAAG 60.134 57.143 0.00 0.00 0.00 3.61
1025 1059 0.543749 AGCCTAGTCCATGTCCAAGC 59.456 55.000 0.00 0.00 0.00 4.01
1026 1060 0.253044 GCCTAGTCCATGTCCAAGCA 59.747 55.000 0.00 0.00 0.00 3.91
1027 1061 1.745141 GCCTAGTCCATGTCCAAGCAG 60.745 57.143 0.00 0.00 0.00 4.24
1033 1067 1.672030 CATGTCCAAGCAGCGACCA 60.672 57.895 0.00 0.00 0.00 4.02
1048 1082 2.413371 GCGACCAATGAAGAAGTGAAGC 60.413 50.000 0.00 0.00 0.00 3.86
1086 1120 2.128128 GCGCACTTCGTGTTCGTG 60.128 61.111 0.30 0.00 41.07 4.35
1149 1183 2.746671 CTGCTGCTGGCCACTCAG 60.747 66.667 20.62 20.62 40.92 3.35
1825 6346 2.920384 TCTACCACCAGCACGCCA 60.920 61.111 0.00 0.00 0.00 5.69
2001 6526 2.046604 GCGTCGGGCTACCCTTTT 60.047 61.111 0.32 0.00 42.67 2.27
2229 6754 4.539083 ACGTGGCCGCACTTCACA 62.539 61.111 18.18 0.00 37.70 3.58
2494 7037 0.463295 CATCTGCGATCTGGCCAAGT 60.463 55.000 7.01 0.00 0.00 3.16
2535 7078 1.340248 CAAGGTACCGCCGAGTGATAT 59.660 52.381 6.18 0.00 43.70 1.63
2547 7092 2.800985 CGAGTGATATCTGGGCAGTGTG 60.801 54.545 3.98 0.00 0.00 3.82
2548 7093 2.169352 GAGTGATATCTGGGCAGTGTGT 59.831 50.000 3.98 0.00 0.00 3.72
2549 7094 2.093288 AGTGATATCTGGGCAGTGTGTG 60.093 50.000 3.98 0.00 0.00 3.82
2606 8970 4.815269 CCTAAAATGCCGTTCCAATCAAA 58.185 39.130 0.00 0.00 0.00 2.69
2643 9009 9.214957 TGAAAACTCATAGTACACTACATTTGG 57.785 33.333 0.00 0.00 0.00 3.28
2688 9054 9.527157 TTTTTATCAATGTGGAAGGTCTTATCA 57.473 29.630 0.00 0.00 0.00 2.15
2689 9055 8.737168 TTTATCAATGTGGAAGGTCTTATCAG 57.263 34.615 0.00 0.00 0.00 2.90
2690 9056 6.566079 ATCAATGTGGAAGGTCTTATCAGA 57.434 37.500 0.00 0.00 0.00 3.27
2691 9057 6.373005 TCAATGTGGAAGGTCTTATCAGAA 57.627 37.500 0.00 0.00 0.00 3.02
2692 9058 6.173339 TCAATGTGGAAGGTCTTATCAGAAC 58.827 40.000 0.00 0.00 36.93 3.01
2733 9107 8.049117 TGAGATTATTAGAATTGGCTTGTGACT 58.951 33.333 0.00 0.00 0.00 3.41
2748 9122 1.990563 GTGACTCGACGGTATTTGGTG 59.009 52.381 0.00 0.00 0.00 4.17
2759 9133 4.460034 ACGGTATTTGGTGGTTTGTATTCC 59.540 41.667 0.00 0.00 0.00 3.01
2774 9148 7.539366 GGTTTGTATTCCGAATTCGAATTTTCA 59.461 33.333 28.76 18.62 43.02 2.69
2775 9149 8.907685 GTTTGTATTCCGAATTCGAATTTTCAA 58.092 29.630 28.76 21.77 43.02 2.69
2776 9150 8.442605 TTGTATTCCGAATTCGAATTTTCAAC 57.557 30.769 28.76 17.74 43.02 3.18
2779 9153 6.741448 TTCCGAATTCGAATTTTCAACAAC 57.259 33.333 28.76 8.13 43.02 3.32
2817 9191 3.935203 AGGATGTTCTAATGTTCGTGCAG 59.065 43.478 0.00 0.00 0.00 4.41
2820 9194 3.937814 TGTTCTAATGTTCGTGCAGGAT 58.062 40.909 10.35 0.00 0.00 3.24
2827 9201 7.497595 TCTAATGTTCGTGCAGGATAATTAGT 58.502 34.615 28.56 13.20 30.91 2.24
2862 9236 4.222114 GCAAGTGGTCTGAATTTTTCTCG 58.778 43.478 0.00 0.00 0.00 4.04
2903 9277 9.919348 TTTGTACGAGTAAACAGAAACATAAAC 57.081 29.630 0.00 0.00 0.00 2.01
3073 9447 9.273016 CTTGAAACTTGAGTAGAATTTCCTACA 57.727 33.333 6.98 0.00 41.01 2.74
3080 9454 7.311092 TGAGTAGAATTTCCTACACCTTGAA 57.689 36.000 6.98 0.00 41.01 2.69
3081 9455 7.918076 TGAGTAGAATTTCCTACACCTTGAAT 58.082 34.615 6.98 0.00 41.01 2.57
3197 9576 6.304356 TGTTGTTCAAAGCTTCTGTCATAG 57.696 37.500 0.00 0.00 0.00 2.23
3231 9610 4.756642 TGTGAAACCTGCTCTCATAACAAG 59.243 41.667 0.00 0.00 34.36 3.16
3287 9666 5.914033 TCTCCAAACTAATCTATTGGACGG 58.086 41.667 2.48 0.00 45.71 4.79
3298 9677 0.250124 ATTGGACGGACGCAGAACAA 60.250 50.000 0.00 0.00 0.00 2.83
3307 9686 3.050619 GGACGCAGAACAATAGGTATCG 58.949 50.000 0.00 0.00 0.00 2.92
3310 9689 2.726760 CGCAGAACAATAGGTATCGAGC 59.273 50.000 0.00 0.00 0.00 5.03
3322 9701 4.171754 AGGTATCGAGCACGTTCTTTAAC 58.828 43.478 2.86 0.00 40.69 2.01
3329 9708 2.226437 AGCACGTTCTTTAACCATGCAG 59.774 45.455 12.15 0.00 42.56 4.41
3336 9715 6.035843 CGTTCTTTAACCATGCAGCATTATT 58.964 36.000 4.69 5.64 31.46 1.40
3337 9716 6.531240 CGTTCTTTAACCATGCAGCATTATTT 59.469 34.615 4.69 1.67 31.46 1.40
3401 9780 3.118738 AGAGTGTGGTTATAAAGGGAGCG 60.119 47.826 0.00 0.00 0.00 5.03
3413 9792 1.629043 AGGGAGCGTCTCTACAAACA 58.371 50.000 6.78 0.00 0.00 2.83
3420 9799 4.632153 AGCGTCTCTACAAACATGAACTT 58.368 39.130 0.00 0.00 0.00 2.66
3456 9835 2.232208 TCTCGAGCATGAGAGAGCAAAA 59.768 45.455 7.81 0.00 40.01 2.44
3457 9836 2.341257 TCGAGCATGAGAGAGCAAAAC 58.659 47.619 0.00 0.00 0.00 2.43
3474 9853 4.546570 CAAAACAGTAAGGCCTTTAGTGC 58.453 43.478 26.08 2.00 43.55 4.40
3493 9872 5.424757 AGTGCATAATAAAAGCAGGTACGA 58.575 37.500 0.00 0.00 39.21 3.43
3519 9899 0.907230 GGGTCTCCTTGTCTGAGCCT 60.907 60.000 0.00 0.00 42.92 4.58
3526 9906 1.558756 CCTTGTCTGAGCCTCCTCAAT 59.441 52.381 0.00 0.00 46.84 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.721718 GTCAAAACCGGCAGATCTCG 59.278 55.000 0.00 0.00 0.00 4.04
3 4 1.464997 GTGTCAAAACCGGCAGATCTC 59.535 52.381 0.00 0.00 0.00 2.75
4 5 1.523758 GTGTCAAAACCGGCAGATCT 58.476 50.000 0.00 0.00 0.00 2.75
5 6 0.521735 GGTGTCAAAACCGGCAGATC 59.478 55.000 0.00 0.00 0.00 2.75
6 7 2.641197 GGTGTCAAAACCGGCAGAT 58.359 52.632 0.00 0.00 0.00 2.90
7 8 4.150994 GGTGTCAAAACCGGCAGA 57.849 55.556 0.00 0.00 0.00 4.26
13 14 1.098712 TGGCTGTCGGTGTCAAAACC 61.099 55.000 0.00 0.00 36.82 3.27
14 15 0.951558 ATGGCTGTCGGTGTCAAAAC 59.048 50.000 0.00 0.00 0.00 2.43
15 16 1.202758 AGATGGCTGTCGGTGTCAAAA 60.203 47.619 0.00 0.00 0.00 2.44
16 17 0.396435 AGATGGCTGTCGGTGTCAAA 59.604 50.000 0.00 0.00 0.00 2.69
17 18 0.037326 GAGATGGCTGTCGGTGTCAA 60.037 55.000 0.00 0.00 0.00 3.18
18 19 1.591703 GAGATGGCTGTCGGTGTCA 59.408 57.895 0.00 0.00 0.00 3.58
19 20 1.153549 GGAGATGGCTGTCGGTGTC 60.154 63.158 0.00 0.00 0.00 3.67
20 21 1.194781 AAGGAGATGGCTGTCGGTGT 61.195 55.000 0.00 0.00 0.00 4.16
21 22 0.824109 TAAGGAGATGGCTGTCGGTG 59.176 55.000 0.00 0.00 0.00 4.94
22 23 1.414181 CATAAGGAGATGGCTGTCGGT 59.586 52.381 0.00 0.00 0.00 4.69
23 24 1.270518 CCATAAGGAGATGGCTGTCGG 60.271 57.143 0.00 0.00 40.08 4.79
24 25 2.160822 CCATAAGGAGATGGCTGTCG 57.839 55.000 0.00 0.00 40.08 4.35
40 41 1.630878 GACAACCTCTCCTCCAACCAT 59.369 52.381 0.00 0.00 0.00 3.55
49 53 1.190643 CCCTCTGAGACAACCTCTCC 58.809 60.000 6.17 0.00 44.63 3.71
56 60 2.777692 ACTCCAAAACCCTCTGAGACAA 59.222 45.455 6.17 0.00 0.00 3.18
61 65 0.250295 CGCACTCCAAAACCCTCTGA 60.250 55.000 0.00 0.00 0.00 3.27
77 81 4.020617 CACCTTGGCCTCCTCGCA 62.021 66.667 3.32 0.00 0.00 5.10
98 102 2.213499 CCTTTATCATCTCCGCACCAC 58.787 52.381 0.00 0.00 0.00 4.16
110 114 4.074799 TCCTCCTCTTGTCCCTTTATCA 57.925 45.455 0.00 0.00 0.00 2.15
113 117 3.115390 CCATCCTCCTCTTGTCCCTTTA 58.885 50.000 0.00 0.00 0.00 1.85
122 126 1.115467 CAGTACGCCATCCTCCTCTT 58.885 55.000 0.00 0.00 0.00 2.85
123 127 1.395826 GCAGTACGCCATCCTCCTCT 61.396 60.000 0.00 0.00 32.94 3.69
136 140 1.299926 CCGACCATAGCGGCAGTAC 60.300 63.158 1.45 0.00 42.55 2.73
137 141 3.125607 CCGACCATAGCGGCAGTA 58.874 61.111 1.45 0.00 42.55 2.74
143 147 4.609018 CCAGCCCCGACCATAGCG 62.609 72.222 0.00 0.00 0.00 4.26
212 238 1.143401 GTAACCTACTCTGGCGCCC 59.857 63.158 26.77 6.44 0.00 6.13
250 276 0.104304 ACGGTTCATCGCCCTACATC 59.896 55.000 0.00 0.00 0.00 3.06
269 295 1.128878 CGTTCAAACAACACACCACGA 59.871 47.619 0.00 0.00 0.00 4.35
274 300 0.794981 TGCGCGTTCAAACAACACAC 60.795 50.000 8.43 0.00 0.00 3.82
275 301 0.522286 CTGCGCGTTCAAACAACACA 60.522 50.000 8.43 0.00 0.00 3.72
342 368 4.183686 CAGCATTGAAGCGGGGCG 62.184 66.667 0.00 0.00 40.15 6.13
343 369 3.830192 CCAGCATTGAAGCGGGGC 61.830 66.667 0.00 0.00 44.70 5.80
346 372 2.205074 CTACTACCAGCATTGAAGCGG 58.795 52.381 0.00 0.00 40.15 5.52
347 373 2.604914 CACTACTACCAGCATTGAAGCG 59.395 50.000 0.00 0.00 40.15 4.68
348 374 3.861840 TCACTACTACCAGCATTGAAGC 58.138 45.455 0.00 0.00 0.00 3.86
349 375 5.330455 TCTCACTACTACCAGCATTGAAG 57.670 43.478 0.00 0.00 0.00 3.02
350 376 4.160439 CCTCTCACTACTACCAGCATTGAA 59.840 45.833 0.00 0.00 0.00 2.69
351 377 3.701542 CCTCTCACTACTACCAGCATTGA 59.298 47.826 0.00 0.00 0.00 2.57
352 378 3.449018 ACCTCTCACTACTACCAGCATTG 59.551 47.826 0.00 0.00 0.00 2.82
353 379 3.702045 GACCTCTCACTACTACCAGCATT 59.298 47.826 0.00 0.00 0.00 3.56
354 380 3.292460 GACCTCTCACTACTACCAGCAT 58.708 50.000 0.00 0.00 0.00 3.79
355 381 2.724454 GACCTCTCACTACTACCAGCA 58.276 52.381 0.00 0.00 0.00 4.41
356 382 1.671845 CGACCTCTCACTACTACCAGC 59.328 57.143 0.00 0.00 0.00 4.85
357 383 1.671845 GCGACCTCTCACTACTACCAG 59.328 57.143 0.00 0.00 0.00 4.00
358 384 1.747709 GCGACCTCTCACTACTACCA 58.252 55.000 0.00 0.00 0.00 3.25
359 385 0.656785 CGCGACCTCTCACTACTACC 59.343 60.000 0.00 0.00 0.00 3.18
360 386 1.327156 GACGCGACCTCTCACTACTAC 59.673 57.143 15.93 0.00 0.00 2.73
361 387 1.649664 GACGCGACCTCTCACTACTA 58.350 55.000 15.93 0.00 0.00 1.82
362 388 1.025647 GGACGCGACCTCTCACTACT 61.026 60.000 20.46 0.00 0.00 2.57
363 389 1.428620 GGACGCGACCTCTCACTAC 59.571 63.158 20.46 0.00 0.00 2.73
364 390 2.104859 CGGACGCGACCTCTCACTA 61.105 63.158 24.38 0.00 0.00 2.74
365 391 3.432588 CGGACGCGACCTCTCACT 61.433 66.667 24.38 0.00 0.00 3.41
377 403 2.586079 ATTCATGCCGAGCGGACG 60.586 61.111 13.94 0.00 37.50 4.79
378 404 3.017323 CATTCATGCCGAGCGGAC 58.983 61.111 13.94 4.80 37.50 4.79
388 414 3.125829 AGAGCGTTAGTGTTGCATTCATG 59.874 43.478 0.00 0.00 0.00 3.07
389 415 3.125829 CAGAGCGTTAGTGTTGCATTCAT 59.874 43.478 0.00 0.00 0.00 2.57
390 416 2.480037 CAGAGCGTTAGTGTTGCATTCA 59.520 45.455 0.00 0.00 0.00 2.57
391 417 2.159653 CCAGAGCGTTAGTGTTGCATTC 60.160 50.000 0.00 0.00 0.00 2.67
392 418 1.806542 CCAGAGCGTTAGTGTTGCATT 59.193 47.619 0.00 0.00 0.00 3.56
393 419 1.001974 TCCAGAGCGTTAGTGTTGCAT 59.998 47.619 0.00 0.00 0.00 3.96
394 420 0.391228 TCCAGAGCGTTAGTGTTGCA 59.609 50.000 0.00 0.00 0.00 4.08
395 421 1.071605 CTCCAGAGCGTTAGTGTTGC 58.928 55.000 0.00 0.00 0.00 4.17
396 422 2.061773 CACTCCAGAGCGTTAGTGTTG 58.938 52.381 0.00 0.00 35.66 3.33
397 423 1.000955 CCACTCCAGAGCGTTAGTGTT 59.999 52.381 0.00 0.00 38.10 3.32
398 424 0.603569 CCACTCCAGAGCGTTAGTGT 59.396 55.000 0.00 0.00 38.10 3.55
399 425 0.737715 GCCACTCCAGAGCGTTAGTG 60.738 60.000 0.00 0.00 39.22 2.74
400 426 1.592223 GCCACTCCAGAGCGTTAGT 59.408 57.895 0.00 0.00 0.00 2.24
401 427 1.517257 CGCCACTCCAGAGCGTTAG 60.517 63.158 7.35 0.00 44.65 2.34
402 428 2.571757 CGCCACTCCAGAGCGTTA 59.428 61.111 7.35 0.00 44.65 3.18
423 449 2.097728 CGCTTCGCCTTAAACGGC 59.902 61.111 0.00 0.00 46.68 5.68
443 469 4.143333 CACCCCTACTCGCCCGTG 62.143 72.222 0.00 0.00 0.00 4.94
448 474 3.782443 CACCCCACCCCTACTCGC 61.782 72.222 0.00 0.00 0.00 5.03
449 475 3.081409 CCACCCCACCCCTACTCG 61.081 72.222 0.00 0.00 0.00 4.18
450 476 2.691252 CCCACCCCACCCCTACTC 60.691 72.222 0.00 0.00 0.00 2.59
462 488 4.380945 TGATTGCCCTGGCCCACC 62.381 66.667 5.57 0.00 41.09 4.61
463 489 2.757099 CTGATTGCCCTGGCCCAC 60.757 66.667 5.57 0.00 41.09 4.61
464 490 2.503846 CTTCTGATTGCCCTGGCCCA 62.504 60.000 5.57 0.58 41.09 5.36
465 491 1.755783 CTTCTGATTGCCCTGGCCC 60.756 63.158 5.57 0.00 41.09 5.80
466 492 2.421399 GCTTCTGATTGCCCTGGCC 61.421 63.158 5.57 0.00 41.09 5.36
467 493 2.768492 CGCTTCTGATTGCCCTGGC 61.768 63.158 0.00 0.00 42.35 4.85
468 494 2.117156 CCGCTTCTGATTGCCCTGG 61.117 63.158 0.00 0.00 0.00 4.45
469 495 2.768492 GCCGCTTCTGATTGCCCTG 61.768 63.158 0.00 0.00 0.00 4.45
470 496 2.439156 GCCGCTTCTGATTGCCCT 60.439 61.111 0.00 0.00 0.00 5.19
471 497 3.521796 GGCCGCTTCTGATTGCCC 61.522 66.667 0.00 0.00 36.07 5.36
472 498 3.880846 CGGCCGCTTCTGATTGCC 61.881 66.667 14.67 0.00 38.74 4.52
473 499 3.127533 ACGGCCGCTTCTGATTGC 61.128 61.111 28.58 0.00 0.00 3.56
474 500 2.753966 CCACGGCCGCTTCTGATTG 61.754 63.158 28.58 13.47 0.00 2.67
475 501 2.436646 CCACGGCCGCTTCTGATT 60.437 61.111 28.58 0.00 0.00 2.57
502 528 2.178273 GATGTTTTGCGGGCGTCC 59.822 61.111 0.00 0.00 0.00 4.79
503 529 2.178273 GGATGTTTTGCGGGCGTC 59.822 61.111 0.00 0.00 0.00 5.19
504 530 3.370231 GGGATGTTTTGCGGGCGT 61.370 61.111 0.00 0.00 0.00 5.68
505 531 3.369400 TGGGATGTTTTGCGGGCG 61.369 61.111 0.00 0.00 0.00 6.13
506 532 1.815817 AAGTGGGATGTTTTGCGGGC 61.816 55.000 0.00 0.00 0.00 6.13
507 533 0.678950 AAAGTGGGATGTTTTGCGGG 59.321 50.000 0.00 0.00 0.00 6.13
508 534 1.068434 ACAAAGTGGGATGTTTTGCGG 59.932 47.619 0.00 0.00 35.71 5.69
509 535 2.034558 AGACAAAGTGGGATGTTTTGCG 59.965 45.455 0.00 0.00 35.71 4.85
510 536 3.733443 AGACAAAGTGGGATGTTTTGC 57.267 42.857 0.00 0.00 35.71 3.68
511 537 4.290155 CGAAGACAAAGTGGGATGTTTTG 58.710 43.478 0.00 0.00 37.71 2.44
512 538 3.317993 CCGAAGACAAAGTGGGATGTTTT 59.682 43.478 0.00 0.00 0.00 2.43
513 539 2.884639 CCGAAGACAAAGTGGGATGTTT 59.115 45.455 0.00 0.00 0.00 2.83
514 540 2.158667 ACCGAAGACAAAGTGGGATGTT 60.159 45.455 0.00 0.00 0.00 2.71
515 541 1.420138 ACCGAAGACAAAGTGGGATGT 59.580 47.619 0.00 0.00 0.00 3.06
516 542 2.185004 ACCGAAGACAAAGTGGGATG 57.815 50.000 0.00 0.00 0.00 3.51
517 543 2.884639 CAAACCGAAGACAAAGTGGGAT 59.115 45.455 0.00 0.00 0.00 3.85
518 544 2.294074 CAAACCGAAGACAAAGTGGGA 58.706 47.619 0.00 0.00 0.00 4.37
519 545 2.021457 ACAAACCGAAGACAAAGTGGG 58.979 47.619 0.00 0.00 0.00 4.61
520 546 2.223479 CCACAAACCGAAGACAAAGTGG 60.223 50.000 0.00 0.00 39.25 4.00
521 547 2.680841 TCCACAAACCGAAGACAAAGTG 59.319 45.455 0.00 0.00 0.00 3.16
522 548 2.993937 TCCACAAACCGAAGACAAAGT 58.006 42.857 0.00 0.00 0.00 2.66
523 549 4.364415 TTTCCACAAACCGAAGACAAAG 57.636 40.909 0.00 0.00 0.00 2.77
524 550 4.487019 GTTTTCCACAAACCGAAGACAAA 58.513 39.130 0.00 0.00 0.00 2.83
525 551 3.119424 GGTTTTCCACAAACCGAAGACAA 60.119 43.478 0.82 0.00 40.10 3.18
526 552 2.424246 GGTTTTCCACAAACCGAAGACA 59.576 45.455 0.82 0.00 40.10 3.41
527 553 3.074504 GGTTTTCCACAAACCGAAGAC 57.925 47.619 0.82 0.00 40.10 3.01
534 560 9.626045 CTTTCATTAGATAGGTTTTCCACAAAC 57.374 33.333 0.00 0.00 43.73 2.93
535 561 8.303876 GCTTTCATTAGATAGGTTTTCCACAAA 58.696 33.333 0.00 0.00 43.73 2.83
536 562 7.093945 GGCTTTCATTAGATAGGTTTTCCACAA 60.094 37.037 0.00 0.00 43.73 3.33
537 563 6.377146 GGCTTTCATTAGATAGGTTTTCCACA 59.623 38.462 0.00 0.00 43.73 4.17
538 564 6.603599 AGGCTTTCATTAGATAGGTTTTCCAC 59.396 38.462 0.00 0.00 43.73 4.02
539 565 6.731467 AGGCTTTCATTAGATAGGTTTTCCA 58.269 36.000 0.00 0.00 43.73 3.53
540 566 7.646548 AAGGCTTTCATTAGATAGGTTTTCC 57.353 36.000 0.00 0.00 41.05 3.13
541 567 8.961634 AGAAAGGCTTTCATTAGATAGGTTTTC 58.038 33.333 34.34 8.81 42.10 2.29
542 568 8.885693 AGAAAGGCTTTCATTAGATAGGTTTT 57.114 30.769 34.34 11.75 42.10 2.43
543 569 8.885693 AAGAAAGGCTTTCATTAGATAGGTTT 57.114 30.769 34.34 16.82 42.10 3.27
544 570 8.109634 TGAAGAAAGGCTTTCATTAGATAGGTT 58.890 33.333 34.34 19.33 42.10 3.50
545 571 7.633789 TGAAGAAAGGCTTTCATTAGATAGGT 58.366 34.615 34.34 12.79 42.10 3.08
546 572 7.989741 TCTGAAGAAAGGCTTTCATTAGATAGG 59.010 37.037 34.34 17.17 42.10 2.57
547 573 8.954950 TCTGAAGAAAGGCTTTCATTAGATAG 57.045 34.615 34.34 22.42 42.10 2.08
548 574 9.739276 TTTCTGAAGAAAGGCTTTCATTAGATA 57.261 29.630 34.34 25.76 42.10 1.98
549 575 8.641498 TTTCTGAAGAAAGGCTTTCATTAGAT 57.359 30.769 34.34 15.43 42.10 1.98
550 576 8.463930 TTTTCTGAAGAAAGGCTTTCATTAGA 57.536 30.769 34.34 29.93 43.90 2.10
551 577 9.702494 ATTTTTCTGAAGAAAGGCTTTCATTAG 57.298 29.630 34.34 28.50 43.90 1.73
554 580 9.481340 GTTATTTTTCTGAAGAAAGGCTTTCAT 57.519 29.630 34.34 26.47 43.90 2.57
555 581 8.695456 AGTTATTTTTCTGAAGAAAGGCTTTCA 58.305 29.630 34.34 18.83 43.90 2.69
598 624 6.637254 GTCATTTGACTAAGATCGCTAATCGA 59.363 38.462 3.45 0.00 45.37 3.59
626 654 0.748367 ACCACGAGATCTGCGCTCTA 60.748 55.000 9.73 0.00 0.00 2.43
672 700 2.433970 TGTCCTGTCACTGACAATGTGA 59.566 45.455 12.92 5.12 42.26 3.58
673 701 2.837498 TGTCCTGTCACTGACAATGTG 58.163 47.619 12.92 1.75 42.26 3.21
906 935 0.603569 AACGTCGACAGATCCAAGCT 59.396 50.000 17.16 0.00 0.00 3.74
1003 1037 0.982852 TGGACATGGACTAGGCTGGG 60.983 60.000 2.02 0.00 0.00 4.45
1007 1041 0.253044 TGCTTGGACATGGACTAGGC 59.747 55.000 0.00 1.77 0.00 3.93
1015 1049 1.236616 TTGGTCGCTGCTTGGACATG 61.237 55.000 8.13 0.00 34.87 3.21
1017 1051 1.073025 ATTGGTCGCTGCTTGGACA 59.927 52.632 8.13 0.00 34.87 4.02
1018 1052 0.955428 TCATTGGTCGCTGCTTGGAC 60.955 55.000 0.00 0.00 0.00 4.02
1019 1053 0.250684 TTCATTGGTCGCTGCTTGGA 60.251 50.000 0.00 0.00 0.00 3.53
1020 1054 0.169672 CTTCATTGGTCGCTGCTTGG 59.830 55.000 0.00 0.00 0.00 3.61
1021 1055 1.159285 TCTTCATTGGTCGCTGCTTG 58.841 50.000 0.00 0.00 0.00 4.01
1022 1056 1.808945 CTTCTTCATTGGTCGCTGCTT 59.191 47.619 0.00 0.00 0.00 3.91
1023 1057 1.271054 ACTTCTTCATTGGTCGCTGCT 60.271 47.619 0.00 0.00 0.00 4.24
1024 1058 1.135859 CACTTCTTCATTGGTCGCTGC 60.136 52.381 0.00 0.00 0.00 5.25
1025 1059 2.416747 TCACTTCTTCATTGGTCGCTG 58.583 47.619 0.00 0.00 0.00 5.18
1026 1060 2.839486 TCACTTCTTCATTGGTCGCT 57.161 45.000 0.00 0.00 0.00 4.93
1027 1061 2.413371 GCTTCACTTCTTCATTGGTCGC 60.413 50.000 0.00 0.00 0.00 5.19
1033 1067 2.616510 CCTCCGGCTTCACTTCTTCATT 60.617 50.000 0.00 0.00 0.00 2.57
1414 1448 1.226101 CGGACACGATGCATGTTGC 60.226 57.895 2.46 0.00 43.23 4.17
1479 5975 4.416738 AAGAAGCTGAGCCGGGGC 62.417 66.667 2.18 0.18 42.33 5.80
1590 6111 1.000486 CCTCTTCTCCAGTCCCGGA 60.000 63.158 0.73 0.00 0.00 5.14
1596 6117 1.203075 ACCTCGAACCTCTTCTCCAGT 60.203 52.381 0.00 0.00 0.00 4.00
1770 6291 0.477597 TCCACACCTTCATCCCCCTT 60.478 55.000 0.00 0.00 0.00 3.95
1775 6296 0.673644 CACGGTCCACACCTTCATCC 60.674 60.000 0.00 0.00 41.17 3.51
2001 6526 1.191535 CGTCCTTGACCACCCAGATA 58.808 55.000 0.00 0.00 0.00 1.98
2535 7078 2.884997 AAACGCACACACTGCCCAGA 62.885 55.000 1.69 0.00 43.84 3.86
2541 7084 3.125146 ACATGCTATAAACGCACACACTG 59.875 43.478 0.00 0.00 40.65 3.66
2628 8994 9.569122 ACAAAAATAGACCAAATGTAGTGTACT 57.431 29.630 0.00 0.00 0.00 2.73
2726 9100 2.036217 ACCAAATACCGTCGAGTCACAA 59.964 45.455 0.00 0.00 0.00 3.33
2733 9107 2.144730 CAAACCACCAAATACCGTCGA 58.855 47.619 0.00 0.00 0.00 4.20
2748 9122 7.539366 TGAAAATTCGAATTCGGAATACAAACC 59.461 33.333 26.47 8.10 40.29 3.27
2759 9133 6.968004 TGAGTTGTTGAAAATTCGAATTCG 57.032 33.333 22.93 21.78 41.45 3.34
2774 9148 4.279169 CCTGGATTCAACACATGAGTTGTT 59.721 41.667 27.85 19.47 46.78 2.83
2775 9149 3.822735 CCTGGATTCAACACATGAGTTGT 59.177 43.478 27.85 15.09 46.78 3.32
2779 9153 4.267536 ACATCCTGGATTCAACACATGAG 58.732 43.478 6.42 0.00 39.77 2.90
2817 9191 8.232913 TGCCAATAAAAGGTCACTAATTATCC 57.767 34.615 0.00 0.00 0.00 2.59
2820 9194 8.519526 CACTTGCCAATAAAAGGTCACTAATTA 58.480 33.333 0.00 0.00 0.00 1.40
2827 9201 3.571590 ACCACTTGCCAATAAAAGGTCA 58.428 40.909 0.00 0.00 0.00 4.02
2879 9253 8.876275 AGTTTATGTTTCTGTTTACTCGTACA 57.124 30.769 0.00 0.00 0.00 2.90
2903 9277 8.576936 TGCGGTTAATTGGTTTTTAGTTAAAG 57.423 30.769 0.00 0.00 0.00 1.85
3073 9447 6.478512 TGGCAAGAAAAACTAATTCAAGGT 57.521 33.333 0.00 0.00 0.00 3.50
3080 9454 7.038799 AGTGAATGGATGGCAAGAAAAACTAAT 60.039 33.333 0.00 0.00 0.00 1.73
3081 9455 6.267471 AGTGAATGGATGGCAAGAAAAACTAA 59.733 34.615 0.00 0.00 0.00 2.24
3175 9554 6.305693 ACTATGACAGAAGCTTTGAACAAC 57.694 37.500 0.00 0.00 0.00 3.32
3197 9576 6.150140 AGAGCAGGTTTCACAATTCTTGATAC 59.850 38.462 0.00 0.81 0.00 2.24
3246 9625 6.053632 TGGAGAAGTCAAGCATCTTATTCA 57.946 37.500 0.00 0.00 0.00 2.57
3247 9626 6.992063 TTGGAGAAGTCAAGCATCTTATTC 57.008 37.500 0.00 0.00 0.00 1.75
3284 9663 0.606604 ACCTATTGTTCTGCGTCCGT 59.393 50.000 0.00 0.00 0.00 4.69
3287 9666 3.961182 TCGATACCTATTGTTCTGCGTC 58.039 45.455 0.00 0.00 0.00 5.19
3298 9677 4.650754 AAAGAACGTGCTCGATACCTAT 57.349 40.909 16.04 0.00 40.62 2.57
3307 9686 2.225491 TGCATGGTTAAAGAACGTGCTC 59.775 45.455 0.00 0.00 43.13 4.26
3310 9689 2.031245 TGCTGCATGGTTAAAGAACGTG 60.031 45.455 0.00 0.00 36.32 4.49
3322 9701 3.530265 ACACCAAATAATGCTGCATGG 57.470 42.857 17.00 16.24 0.00 3.66
3329 9708 8.034804 ACTTATGAAGGAAACACCAAATAATGC 58.965 33.333 0.00 0.00 42.04 3.56
3336 9715 7.721842 TGTTGATACTTATGAAGGAAACACCAA 59.278 33.333 0.00 0.00 42.04 3.67
3337 9716 7.227873 TGTTGATACTTATGAAGGAAACACCA 58.772 34.615 0.00 0.00 42.04 4.17
3379 9758 3.118738 CGCTCCCTTTATAACCACACTCT 60.119 47.826 0.00 0.00 0.00 3.24
3384 9763 3.132467 AGAGACGCTCCCTTTATAACCAC 59.868 47.826 3.66 0.00 0.00 4.16
3392 9771 2.367567 TGTTTGTAGAGACGCTCCCTTT 59.632 45.455 3.66 0.00 0.00 3.11
3401 9780 6.650807 TGATGGAAGTTCATGTTTGTAGAGAC 59.349 38.462 5.01 0.00 0.00 3.36
3413 9792 7.146715 AGATAATGGACTGATGGAAGTTCAT 57.853 36.000 5.01 0.00 46.46 2.57
3420 9799 3.256879 GCTCGAGATAATGGACTGATGGA 59.743 47.826 18.75 0.00 0.00 3.41
3456 9835 3.721087 ATGCACTAAAGGCCTTACTGT 57.279 42.857 20.84 14.78 0.00 3.55
3457 9836 7.801716 TTATTATGCACTAAAGGCCTTACTG 57.198 36.000 20.84 14.85 0.00 2.74
3474 9853 7.696453 CCTTTTGTCGTACCTGCTTTTATTATG 59.304 37.037 0.00 0.00 0.00 1.90
3511 9891 1.661463 AACCATTGAGGAGGCTCAGA 58.339 50.000 17.69 0.00 41.22 3.27


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

AutoCloner maintained by Alex Coulton.