Multiple sequence alignment - TraesCS3D01G166200

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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 TraesCS3D01G166200 chr3D 100.000 4946 0 0 1 4946 138091083 138086138 0.000000e+00 9134.0
1 TraesCS3D01G166200 chr3B 96.708 3919 100 15 1001 4900 201322592 201318684 0.000000e+00 6495.0
2 TraesCS3D01G166200 chr3B 92.991 214 12 3 745 956 201323298 201323086 4.810000e-80 309.0
3 TraesCS3D01G166200 chr3B 86.131 274 17 7 46 316 201323721 201323466 4.880000e-70 276.0
4 TraesCS3D01G166200 chr3B 100.000 37 0 0 688 724 201323399 201323363 8.880000e-08 69.4
5 TraesCS3D01G166200 chr3A 96.630 3858 102 20 749 4598 156244448 156240611 0.000000e+00 6379.0
6 TraesCS3D01G166200 chr3A 93.629 361 11 4 4598 4946 156239690 156239330 3.390000e-146 529.0
7 TraesCS3D01G166200 chr3A 91.418 268 20 3 46 312 156244963 156244698 1.010000e-96 364.0
8 TraesCS3D01G166200 chr3A 88.095 84 6 4 520 600 732663403 732663485 4.080000e-16 97.1
9 TraesCS3D01G166200 chr3A 97.917 48 1 0 677 724 156244566 156244519 3.170000e-12 84.2
10 TraesCS3D01G166200 chr3A 92.683 41 2 1 636 675 156244629 156244589 1.920000e-04 58.4
11 TraesCS3D01G166200 chr3A 100.000 31 0 0 621 651 156244674 156244644 1.920000e-04 58.4
12 TraesCS3D01G166200 chr5D 86.261 575 60 10 3527 4085 3241443 3240872 1.520000e-169 606.0
13 TraesCS3D01G166200 chr5D 81.790 648 79 26 967 1608 2585014 2585628 1.590000e-139 507.0
14 TraesCS3D01G166200 chr5D 81.307 658 83 24 959 1607 3250554 3249928 9.560000e-137 497.0
15 TraesCS3D01G166200 chr5D 89.457 313 30 1 2799 3108 3241767 3241455 4.640000e-105 392.0
16 TraesCS3D01G166200 chr5D 81.081 333 38 16 2555 2862 3241830 3242162 4.950000e-60 243.0
17 TraesCS3D01G166200 chr5D 91.667 72 4 2 519 589 291769203 291769273 1.130000e-16 99.0
18 TraesCS3D01G166200 chr7A 86.301 292 33 6 4618 4905 623644360 623644072 1.340000e-80 311.0
19 TraesCS3D01G166200 chr1D 84.899 298 32 6 4618 4905 26222159 26222453 6.260000e-74 289.0
20 TraesCS3D01G166200 chr1D 86.170 94 7 6 526 613 28027692 28027599 4.080000e-16 97.1
21 TraesCS3D01G166200 chr2A 88.940 217 17 5 4686 4899 378007644 378007856 1.370000e-65 261.0
22 TraesCS3D01G166200 chr5A 85.263 190 21 6 316 501 62974418 62974232 6.540000e-44 189.0
23 TraesCS3D01G166200 chr7D 91.000 100 8 1 4807 4905 62214816 62214915 3.110000e-27 134.0
24 TraesCS3D01G166200 chr7D 89.873 79 6 2 523 599 207968809 207968887 3.150000e-17 100.0
25 TraesCS3D01G166200 chr7D 90.278 72 5 1 3920 3989 62214758 62214829 5.270000e-15 93.5
26 TraesCS3D01G166200 chr6B 90.099 101 8 2 4807 4905 17909201 17909101 4.020000e-26 130.0
27 TraesCS3D01G166200 chr6B 89.041 73 5 2 3920 3989 17909260 17909188 2.450000e-13 87.9
28 TraesCS3D01G166200 chr5B 90.000 100 9 1 4807 4905 638277398 638277497 1.450000e-25 128.0
29 TraesCS3D01G166200 chr5B 91.667 72 4 1 3920 3989 638277340 638277411 1.130000e-16 99.0
30 TraesCS3D01G166200 chrUn 93.827 81 5 0 315 395 327756346 327756266 6.720000e-24 122.0
31 TraesCS3D01G166200 chr2D 91.026 78 3 4 520 595 625778328 625778253 8.760000e-18 102.0
32 TraesCS3D01G166200 chr2D 88.235 85 5 5 523 603 28885129 28885212 4.080000e-16 97.1
33 TraesCS3D01G166200 chr2D 88.889 81 4 5 518 595 625776692 625776614 1.470000e-15 95.3
34 TraesCS3D01G166200 chr4A 91.667 72 6 0 462 533 490776282 490776211 3.150000e-17 100.0
35 TraesCS3D01G166200 chr7B 89.873 79 5 3 520 596 715361136 715361059 1.130000e-16 99.0
36 TraesCS3D01G166200 chr4D 83.495 103 11 6 502 600 408395693 408395793 1.900000e-14 91.6
37 TraesCS3D01G166200 chr1B 93.182 44 3 0 4878 4921 63052442 63052485 1.150000e-06 65.8
38 TraesCS3D01G166200 chr1A 97.297 37 1 0 4885 4921 42547725 42547761 4.130000e-06 63.9


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 TraesCS3D01G166200 chr3D 138086138 138091083 4945 True 9134.00 9134 100.0000 1 4946 1 chr3D.!!$R1 4945
1 TraesCS3D01G166200 chr3B 201318684 201323721 5037 True 1787.35 6495 93.9575 46 4900 4 chr3B.!!$R1 4854
2 TraesCS3D01G166200 chr3A 156239330 156244963 5633 True 1245.50 6379 95.3795 46 4946 6 chr3A.!!$R1 4900
3 TraesCS3D01G166200 chr5D 2585014 2585628 614 False 507.00 507 81.7900 967 1608 1 chr5D.!!$F1 641
4 TraesCS3D01G166200 chr5D 3240872 3241767 895 True 499.00 606 87.8590 2799 4085 2 chr5D.!!$R2 1286
5 TraesCS3D01G166200 chr5D 3249928 3250554 626 True 497.00 497 81.3070 959 1607 1 chr5D.!!$R1 648

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
462 465 0.103937 GTGCTAGCCTGCTAGGTGAG 59.896 60.000 23.61 5.1 44.48 3.51 F
530 533 0.391528 TGAGGTATGACGACGGACGA 60.392 55.000 6.90 0.0 45.77 4.20 F
1319 1880 0.681564 CTCCAGCTCCTACTCACCGT 60.682 60.000 0.00 0.0 0.00 4.83 F
2967 3531 1.075659 GGCAAGCCTCTTCCCAGTT 59.924 57.895 3.29 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1326 1887 0.682532 AGAGCTGCGACTGGATGAGA 60.683 55.0 0.00 0.0 0.00 3.27 R
2016 2577 1.288188 TCATTGCATCAGGAGTCCCA 58.712 50.0 5.25 0.0 33.88 4.37 R
3051 3615 1.561643 AATTCTGCGAGAGAGGTGGA 58.438 50.0 0.00 0.0 30.18 4.02 R
4399 4980 1.297968 TGATGCCTCCCATTTCCAGA 58.702 50.0 0.00 0.0 33.29 3.86 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
33 34 6.892691 GGATGTATCTATCCAAGCTTTTTCG 58.107 40.000 0.00 0.00 44.90 3.46
34 35 6.073003 GGATGTATCTATCCAAGCTTTTTCGG 60.073 42.308 0.00 0.00 44.90 4.30
35 36 5.984725 TGTATCTATCCAAGCTTTTTCGGA 58.015 37.500 5.77 5.77 0.00 4.55
36 37 5.815740 TGTATCTATCCAAGCTTTTTCGGAC 59.184 40.000 5.44 0.00 0.00 4.79
37 38 3.259064 TCTATCCAAGCTTTTTCGGACG 58.741 45.455 5.44 1.44 0.00 4.79
38 39 1.165270 ATCCAAGCTTTTTCGGACGG 58.835 50.000 5.44 0.00 0.00 4.79
39 40 0.107081 TCCAAGCTTTTTCGGACGGA 59.893 50.000 0.00 0.00 0.00 4.69
40 41 0.237498 CCAAGCTTTTTCGGACGGAC 59.763 55.000 0.00 0.00 0.00 4.79
41 42 0.110823 CAAGCTTTTTCGGACGGACG 60.111 55.000 0.00 0.00 0.00 4.79
42 43 1.226030 AAGCTTTTTCGGACGGACGG 61.226 55.000 0.00 0.00 0.00 4.79
43 44 1.665599 GCTTTTTCGGACGGACGGA 60.666 57.895 0.00 0.00 0.00 4.69
44 45 1.623973 GCTTTTTCGGACGGACGGAG 61.624 60.000 0.00 0.00 0.00 4.63
117 118 8.689972 ACATTGGATGATCCTCATTAACTTTTC 58.310 33.333 13.44 0.00 37.20 2.29
119 120 5.822519 TGGATGATCCTCATTAACTTTTCCG 59.177 40.000 13.44 0.00 37.20 4.30
124 125 3.008594 TCCTCATTAACTTTTCCGGCTCA 59.991 43.478 0.00 0.00 0.00 4.26
126 127 4.399303 CCTCATTAACTTTTCCGGCTCAAT 59.601 41.667 0.00 0.00 0.00 2.57
172 173 5.939296 CCAACCCTTTAAATGTTGCATGATT 59.061 36.000 18.43 0.00 38.38 2.57
174 175 5.733676 ACCCTTTAAATGTTGCATGATTCC 58.266 37.500 0.00 0.00 0.00 3.01
175 176 5.484998 ACCCTTTAAATGTTGCATGATTCCT 59.515 36.000 0.00 0.00 0.00 3.36
179 180 3.393426 AATGTTGCATGATTCCTCCCT 57.607 42.857 0.00 0.00 0.00 4.20
191 192 0.991920 TCCTCCCTCGAAAATGGCTT 59.008 50.000 0.00 0.00 0.00 4.35
199 200 4.022329 CCCTCGAAAATGGCTTAAACAGTT 60.022 41.667 0.00 0.00 0.00 3.16
211 212 5.225642 GCTTAAACAGTTACTACGGTCTGT 58.774 41.667 0.00 0.00 41.93 3.41
213 214 6.639632 TTAAACAGTTACTACGGTCTGTCT 57.360 37.500 0.61 0.00 39.72 3.41
241 242 5.301805 CCATTGCGGGAAGACCTAAATATTT 59.698 40.000 5.89 5.89 36.97 1.40
258 259 9.354673 CTAAATATTTATCAGAAAGGGCTTGGA 57.645 33.333 8.34 0.00 0.00 3.53
292 293 3.863142 ATGTTGGCAAATCTCAGCTTC 57.137 42.857 0.00 0.00 0.00 3.86
330 333 8.879342 TTTTATAACATCACAACCAAAACCTG 57.121 30.769 0.00 0.00 0.00 4.00
344 347 2.674380 CCTGGTTGAGGTGGCTGC 60.674 66.667 0.00 0.00 37.02 5.25
345 348 3.052082 CTGGTTGAGGTGGCTGCG 61.052 66.667 0.00 0.00 0.00 5.18
346 349 4.641645 TGGTTGAGGTGGCTGCGG 62.642 66.667 0.00 0.00 0.00 5.69
347 350 4.643387 GGTTGAGGTGGCTGCGGT 62.643 66.667 0.00 0.00 0.00 5.68
348 351 3.050275 GTTGAGGTGGCTGCGGTC 61.050 66.667 0.00 0.00 0.00 4.79
349 352 3.241530 TTGAGGTGGCTGCGGTCT 61.242 61.111 0.00 0.00 0.00 3.85
350 353 2.818169 TTGAGGTGGCTGCGGTCTT 61.818 57.895 0.00 0.00 0.00 3.01
351 354 2.435059 GAGGTGGCTGCGGTCTTC 60.435 66.667 0.00 0.00 0.00 2.87
352 355 4.379243 AGGTGGCTGCGGTCTTCG 62.379 66.667 0.00 0.00 42.76 3.79
353 356 4.681978 GGTGGCTGCGGTCTTCGT 62.682 66.667 0.00 0.00 41.72 3.85
354 357 3.414700 GTGGCTGCGGTCTTCGTG 61.415 66.667 0.00 0.00 41.72 4.35
355 358 3.611674 TGGCTGCGGTCTTCGTGA 61.612 61.111 0.00 0.00 41.72 4.35
356 359 3.112709 GGCTGCGGTCTTCGTGAC 61.113 66.667 0.00 3.42 44.63 3.67
357 360 3.470567 GCTGCGGTCTTCGTGACG 61.471 66.667 0.00 0.00 46.24 4.35
358 361 2.805353 CTGCGGTCTTCGTGACGG 60.805 66.667 4.70 11.91 46.24 4.79
359 362 4.351938 TGCGGTCTTCGTGACGGG 62.352 66.667 4.70 0.00 46.24 5.28
360 363 4.047059 GCGGTCTTCGTGACGGGA 62.047 66.667 4.70 0.97 46.24 5.14
361 364 2.178521 CGGTCTTCGTGACGGGAG 59.821 66.667 4.70 3.98 46.24 4.30
362 365 2.572284 GGTCTTCGTGACGGGAGG 59.428 66.667 4.70 0.00 46.24 4.30
363 366 2.273912 GGTCTTCGTGACGGGAGGT 61.274 63.158 4.70 0.00 46.24 3.85
364 367 1.080705 GTCTTCGTGACGGGAGGTG 60.081 63.158 4.70 0.00 35.81 4.00
365 368 1.228337 TCTTCGTGACGGGAGGTGA 60.228 57.895 4.70 0.00 0.00 4.02
366 369 1.213013 CTTCGTGACGGGAGGTGAG 59.787 63.158 4.70 0.00 0.00 3.51
367 370 1.524863 CTTCGTGACGGGAGGTGAGT 61.525 60.000 4.70 0.00 0.00 3.41
368 371 1.521450 TTCGTGACGGGAGGTGAGTC 61.521 60.000 4.70 0.00 35.61 3.36
369 372 2.971452 GTGACGGGAGGTGAGTCC 59.029 66.667 0.00 0.00 34.24 3.85
373 376 3.760035 CGGGAGGTGAGTCCGTGG 61.760 72.222 0.00 0.00 41.99 4.94
374 377 3.391382 GGGAGGTGAGTCCGTGGG 61.391 72.222 0.00 0.00 41.99 4.61
375 378 2.603776 GGAGGTGAGTCCGTGGGT 60.604 66.667 0.00 0.00 41.99 4.51
376 379 2.214920 GGAGGTGAGTCCGTGGGTT 61.215 63.158 0.00 0.00 41.99 4.11
377 380 1.292541 GAGGTGAGTCCGTGGGTTC 59.707 63.158 0.00 0.00 41.99 3.62
378 381 2.048503 GGTGAGTCCGTGGGTTCG 60.049 66.667 0.00 0.00 0.00 3.95
379 382 2.567497 GGTGAGTCCGTGGGTTCGA 61.567 63.158 0.00 0.00 0.00 3.71
380 383 1.364901 GTGAGTCCGTGGGTTCGAA 59.635 57.895 0.00 0.00 0.00 3.71
381 384 0.942884 GTGAGTCCGTGGGTTCGAAC 60.943 60.000 20.14 20.14 0.00 3.95
390 393 3.110178 GGTTCGAACCCTCACGCG 61.110 66.667 33.02 3.53 43.43 6.01
391 394 2.049802 GTTCGAACCCTCACGCGA 60.050 61.111 17.68 0.00 0.00 5.87
392 395 2.087009 GTTCGAACCCTCACGCGAG 61.087 63.158 17.68 4.59 39.16 5.03
393 396 3.909258 TTCGAACCCTCACGCGAGC 62.909 63.158 15.93 0.00 38.00 5.03
394 397 4.717629 CGAACCCTCACGCGAGCA 62.718 66.667 15.93 0.00 38.00 4.26
395 398 2.125512 GAACCCTCACGCGAGCAT 60.126 61.111 15.93 0.00 38.00 3.79
396 399 1.741770 GAACCCTCACGCGAGCATT 60.742 57.895 15.93 0.00 38.00 3.56
397 400 1.298859 GAACCCTCACGCGAGCATTT 61.299 55.000 15.93 0.00 38.00 2.32
398 401 0.889186 AACCCTCACGCGAGCATTTT 60.889 50.000 15.93 0.00 38.00 1.82
399 402 0.889186 ACCCTCACGCGAGCATTTTT 60.889 50.000 15.93 0.00 38.00 1.94
418 421 4.664150 TTTTTCTTTTGGGCTAGTGGTG 57.336 40.909 0.00 0.00 0.00 4.17
419 422 1.616159 TTCTTTTGGGCTAGTGGTGC 58.384 50.000 0.00 0.00 0.00 5.01
420 423 0.476338 TCTTTTGGGCTAGTGGTGCA 59.524 50.000 0.00 0.00 0.00 4.57
421 424 0.598065 CTTTTGGGCTAGTGGTGCAC 59.402 55.000 8.80 8.80 34.10 4.57
423 426 1.060729 TTTGGGCTAGTGGTGCACTA 58.939 50.000 17.98 8.10 43.46 2.74
429 432 1.888018 TAGTGGTGCACTAGGACGC 59.112 57.895 17.98 6.14 43.46 5.19
430 433 0.896479 TAGTGGTGCACTAGGACGCA 60.896 55.000 17.98 0.67 43.46 5.24
431 434 1.079127 GTGGTGCACTAGGACGCAT 60.079 57.895 17.98 0.00 40.89 4.73
432 435 1.079197 TGGTGCACTAGGACGCATG 60.079 57.895 17.98 0.00 40.89 4.06
433 436 2.464459 GGTGCACTAGGACGCATGC 61.464 63.158 17.98 7.91 40.89 4.06
434 437 2.125147 TGCACTAGGACGCATGCC 60.125 61.111 13.15 0.00 37.26 4.40
435 438 2.125147 GCACTAGGACGCATGCCA 60.125 61.111 13.15 0.00 31.71 4.92
436 439 1.524621 GCACTAGGACGCATGCCAT 60.525 57.895 13.15 0.00 31.71 4.40
437 440 1.779025 GCACTAGGACGCATGCCATG 61.779 60.000 13.15 0.00 31.71 3.66
455 458 2.046892 CAACGGTGCTAGCCTGCT 60.047 61.111 13.29 0.00 0.00 4.24
456 459 1.218047 CAACGGTGCTAGCCTGCTA 59.782 57.895 13.29 0.00 0.00 3.49
457 460 0.807667 CAACGGTGCTAGCCTGCTAG 60.808 60.000 19.48 19.48 46.41 3.42
458 461 1.961180 AACGGTGCTAGCCTGCTAGG 61.961 60.000 23.61 11.93 44.48 3.02
459 462 2.427245 CGGTGCTAGCCTGCTAGGT 61.427 63.158 23.61 0.00 44.48 3.08
460 463 1.144936 GGTGCTAGCCTGCTAGGTG 59.855 63.158 23.61 4.28 44.48 4.00
461 464 1.330655 GGTGCTAGCCTGCTAGGTGA 61.331 60.000 23.61 0.00 44.48 4.02
462 465 0.103937 GTGCTAGCCTGCTAGGTGAG 59.896 60.000 23.61 5.10 44.48 3.51
463 466 1.045350 TGCTAGCCTGCTAGGTGAGG 61.045 60.000 23.61 0.00 44.48 3.86
467 470 2.688666 CCTGCTAGGTGAGGCCCA 60.689 66.667 0.00 0.00 38.26 5.36
468 471 2.300967 CCTGCTAGGTGAGGCCCAA 61.301 63.158 0.00 0.00 38.26 4.12
469 472 1.639635 CCTGCTAGGTGAGGCCCAAT 61.640 60.000 0.00 0.00 38.26 3.16
470 473 1.131638 CTGCTAGGTGAGGCCCAATA 58.868 55.000 0.00 0.00 38.26 1.90
471 474 1.701847 CTGCTAGGTGAGGCCCAATAT 59.298 52.381 0.00 0.00 38.26 1.28
472 475 2.906389 CTGCTAGGTGAGGCCCAATATA 59.094 50.000 0.00 0.00 38.26 0.86
473 476 2.906389 TGCTAGGTGAGGCCCAATATAG 59.094 50.000 0.00 0.00 38.26 1.31
474 477 2.355209 GCTAGGTGAGGCCCAATATAGC 60.355 54.545 0.00 5.04 38.26 2.97
481 484 2.029838 GGCCCAATATAGCCTCGATG 57.970 55.000 0.00 0.00 46.14 3.84
482 485 1.407437 GGCCCAATATAGCCTCGATGG 60.407 57.143 0.00 0.00 46.14 3.51
491 494 2.029666 CCTCGATGGCTTAGGCGG 59.970 66.667 0.40 0.00 39.81 6.13
492 495 2.498941 CCTCGATGGCTTAGGCGGA 61.499 63.158 0.40 0.00 39.81 5.54
493 496 1.300233 CTCGATGGCTTAGGCGGAC 60.300 63.158 0.40 0.00 39.81 4.79
494 497 2.658593 CGATGGCTTAGGCGGACG 60.659 66.667 0.40 3.21 39.81 4.79
495 498 2.499685 GATGGCTTAGGCGGACGT 59.500 61.111 0.40 0.00 39.81 4.34
496 499 1.883084 GATGGCTTAGGCGGACGTG 60.883 63.158 0.00 0.00 39.81 4.49
497 500 4.752879 TGGCTTAGGCGGACGTGC 62.753 66.667 0.00 0.00 39.81 5.34
499 502 4.789075 GCTTAGGCGGACGTGCGA 62.789 66.667 33.99 9.77 35.06 5.10
500 503 2.879462 CTTAGGCGGACGTGCGAC 60.879 66.667 33.99 31.74 35.06 5.19
501 504 3.620300 CTTAGGCGGACGTGCGACA 62.620 63.158 36.65 19.92 35.06 4.35
502 505 3.620300 TTAGGCGGACGTGCGACAG 62.620 63.158 36.65 6.71 35.06 3.51
506 509 4.379143 CGGACGTGCGACAGACGA 62.379 66.667 26.18 0.00 45.77 4.20
507 510 2.050714 GGACGTGCGACAGACGAA 60.051 61.111 0.00 0.00 45.77 3.85
508 511 1.659335 GGACGTGCGACAGACGAAA 60.659 57.895 0.00 0.00 45.77 3.46
509 512 1.007336 GGACGTGCGACAGACGAAAT 61.007 55.000 0.00 0.00 45.77 2.17
510 513 0.782384 GACGTGCGACAGACGAAATT 59.218 50.000 0.00 0.00 45.77 1.82
511 514 1.191647 GACGTGCGACAGACGAAATTT 59.808 47.619 0.00 0.00 45.77 1.82
512 515 1.070843 ACGTGCGACAGACGAAATTTG 60.071 47.619 0.00 0.00 45.77 2.32
513 516 1.191425 CGTGCGACAGACGAAATTTGA 59.809 47.619 0.00 0.00 45.77 2.69
514 517 2.718789 CGTGCGACAGACGAAATTTGAG 60.719 50.000 0.00 0.00 45.77 3.02
515 518 1.798223 TGCGACAGACGAAATTTGAGG 59.202 47.619 0.00 0.00 45.77 3.86
516 519 1.798813 GCGACAGACGAAATTTGAGGT 59.201 47.619 0.00 0.00 45.77 3.85
517 520 2.991190 GCGACAGACGAAATTTGAGGTA 59.009 45.455 0.00 0.00 45.77 3.08
518 521 3.617263 GCGACAGACGAAATTTGAGGTAT 59.383 43.478 0.00 0.00 45.77 2.73
519 522 4.492570 GCGACAGACGAAATTTGAGGTATG 60.493 45.833 0.00 1.26 45.77 2.39
520 523 4.862574 CGACAGACGAAATTTGAGGTATGA 59.137 41.667 12.49 0.00 45.77 2.15
521 524 5.220228 CGACAGACGAAATTTGAGGTATGAC 60.220 44.000 12.49 7.49 45.77 3.06
522 525 4.625742 ACAGACGAAATTTGAGGTATGACG 59.374 41.667 12.49 2.95 0.00 4.35
523 526 4.862574 CAGACGAAATTTGAGGTATGACGA 59.137 41.667 0.00 0.00 0.00 4.20
524 527 4.863131 AGACGAAATTTGAGGTATGACGAC 59.137 41.667 0.00 0.00 0.00 4.34
525 528 3.611113 ACGAAATTTGAGGTATGACGACG 59.389 43.478 0.00 0.00 0.00 5.12
526 529 3.000078 CGAAATTTGAGGTATGACGACGG 60.000 47.826 0.00 0.00 0.00 4.79
527 530 3.880047 AATTTGAGGTATGACGACGGA 57.120 42.857 0.00 0.00 0.00 4.69
528 531 2.642139 TTTGAGGTATGACGACGGAC 57.358 50.000 0.00 0.00 0.00 4.79
530 533 0.391528 TGAGGTATGACGACGGACGA 60.392 55.000 6.90 0.00 45.77 4.20
531 534 0.729116 GAGGTATGACGACGGACGAA 59.271 55.000 6.90 0.00 45.77 3.85
532 535 1.131126 GAGGTATGACGACGGACGAAA 59.869 52.381 6.90 0.00 45.77 3.46
533 536 1.541147 AGGTATGACGACGGACGAAAA 59.459 47.619 6.90 0.00 45.77 2.29
534 537 2.030007 AGGTATGACGACGGACGAAAAA 60.030 45.455 6.90 0.00 45.77 1.94
535 538 2.091122 GGTATGACGACGGACGAAAAAC 59.909 50.000 6.90 0.16 45.77 2.43
536 539 1.855513 ATGACGACGGACGAAAAACA 58.144 45.000 6.90 0.06 45.77 2.83
537 540 1.638133 TGACGACGGACGAAAAACAA 58.362 45.000 6.90 0.00 45.77 2.83
538 541 1.998315 TGACGACGGACGAAAAACAAA 59.002 42.857 6.90 0.00 45.77 2.83
539 542 2.222774 TGACGACGGACGAAAAACAAAC 60.223 45.455 6.90 0.00 45.77 2.93
540 543 1.062440 ACGACGGACGAAAAACAAACC 59.938 47.619 6.90 0.00 45.77 3.27
541 544 1.062294 CGACGGACGAAAAACAAACCA 59.938 47.619 0.00 0.00 45.77 3.67
542 545 2.475852 CGACGGACGAAAAACAAACCAA 60.476 45.455 0.00 0.00 45.77 3.67
543 546 3.500014 GACGGACGAAAAACAAACCAAA 58.500 40.909 0.00 0.00 0.00 3.28
544 547 4.106909 GACGGACGAAAAACAAACCAAAT 58.893 39.130 0.00 0.00 0.00 2.32
545 548 4.496360 ACGGACGAAAAACAAACCAAATT 58.504 34.783 0.00 0.00 0.00 1.82
546 549 5.648572 ACGGACGAAAAACAAACCAAATTA 58.351 33.333 0.00 0.00 0.00 1.40
547 550 5.515982 ACGGACGAAAAACAAACCAAATTAC 59.484 36.000 0.00 0.00 0.00 1.89
548 551 5.330939 CGGACGAAAAACAAACCAAATTACG 60.331 40.000 0.00 0.00 0.00 3.18
549 552 5.051574 GGACGAAAAACAAACCAAATTACGG 60.052 40.000 0.00 0.00 0.00 4.02
550 553 5.409211 ACGAAAAACAAACCAAATTACGGT 58.591 33.333 0.00 0.00 38.85 4.83
551 554 5.288952 ACGAAAAACAAACCAAATTACGGTG 59.711 36.000 0.40 0.00 36.67 4.94
552 555 5.276442 CGAAAAACAAACCAAATTACGGTGG 60.276 40.000 0.40 0.00 41.00 4.61
560 563 3.754850 ACCAAATTACGGTGGTAAGAAGC 59.245 43.478 0.00 0.00 46.47 3.86
561 564 3.754323 CCAAATTACGGTGGTAAGAAGCA 59.246 43.478 0.00 0.00 41.64 3.91
562 565 4.216687 CCAAATTACGGTGGTAAGAAGCAA 59.783 41.667 0.00 0.00 41.64 3.91
563 566 5.105917 CCAAATTACGGTGGTAAGAAGCAAT 60.106 40.000 0.00 0.00 41.64 3.56
564 567 6.094325 CCAAATTACGGTGGTAAGAAGCAATA 59.906 38.462 0.00 0.00 41.64 1.90
565 568 6.920569 AATTACGGTGGTAAGAAGCAATAG 57.079 37.500 0.00 0.00 41.64 1.73
566 569 2.629051 ACGGTGGTAAGAAGCAATAGC 58.371 47.619 0.00 0.00 42.56 2.97
567 570 1.940613 CGGTGGTAAGAAGCAATAGCC 59.059 52.381 0.00 0.00 43.56 3.93
568 571 2.298610 GGTGGTAAGAAGCAATAGCCC 58.701 52.381 0.00 0.00 43.56 5.19
569 572 2.298610 GTGGTAAGAAGCAATAGCCCC 58.701 52.381 0.00 0.00 43.56 5.80
570 573 2.092375 GTGGTAAGAAGCAATAGCCCCT 60.092 50.000 0.00 0.00 43.56 4.79
571 574 2.580783 TGGTAAGAAGCAATAGCCCCTT 59.419 45.455 0.00 0.00 43.56 3.95
572 575 3.011257 TGGTAAGAAGCAATAGCCCCTTT 59.989 43.478 0.00 0.00 43.56 3.11
573 576 4.228666 TGGTAAGAAGCAATAGCCCCTTTA 59.771 41.667 0.00 0.00 43.56 1.85
574 577 5.103686 TGGTAAGAAGCAATAGCCCCTTTAT 60.104 40.000 0.00 0.00 43.56 1.40
575 578 5.833667 GGTAAGAAGCAATAGCCCCTTTATT 59.166 40.000 0.00 0.00 43.56 1.40
576 579 7.002276 GGTAAGAAGCAATAGCCCCTTTATTA 58.998 38.462 0.00 0.00 43.56 0.98
577 580 7.670140 GGTAAGAAGCAATAGCCCCTTTATTAT 59.330 37.037 0.00 0.00 43.56 1.28
578 581 9.078990 GTAAGAAGCAATAGCCCCTTTATTATT 57.921 33.333 0.00 0.00 43.56 1.40
580 583 8.870075 AGAAGCAATAGCCCCTTTATTATTAG 57.130 34.615 0.00 0.00 43.56 1.73
581 584 7.890655 AGAAGCAATAGCCCCTTTATTATTAGG 59.109 37.037 0.00 0.00 43.56 2.69
669 709 3.842923 CTCCCATGGCGACGCTCT 61.843 66.667 20.77 4.21 0.00 4.09
672 712 4.457496 CCATGGCGACGCTCTGGT 62.457 66.667 24.11 5.43 0.00 4.00
674 714 2.125512 ATGGCGACGCTCTGGTTC 60.126 61.111 20.77 1.05 0.00 3.62
675 715 3.989698 ATGGCGACGCTCTGGTTCG 62.990 63.158 20.77 0.00 0.00 3.95
724 786 3.898123 TCTAGTCATCTGGGCCAATACTC 59.102 47.826 8.04 0.00 0.00 2.59
885 994 1.213430 CTTCTCTCTCCCCTACCGACT 59.787 57.143 0.00 0.00 0.00 4.18
890 999 2.619484 TCCCCTACCGACTCCCCT 60.619 66.667 0.00 0.00 0.00 4.79
892 1001 1.761271 CCCCTACCGACTCCCCTTC 60.761 68.421 0.00 0.00 0.00 3.46
896 1005 2.239680 CTACCGACTCCCCTTCCCCT 62.240 65.000 0.00 0.00 0.00 4.79
897 1006 2.234246 TACCGACTCCCCTTCCCCTC 62.234 65.000 0.00 0.00 0.00 4.30
898 1007 2.364961 CGACTCCCCTTCCCCTCT 59.635 66.667 0.00 0.00 0.00 3.69
1319 1880 0.681564 CTCCAGCTCCTACTCACCGT 60.682 60.000 0.00 0.00 0.00 4.83
1326 1887 2.754658 CTACTCACCGTCCCGCCT 60.755 66.667 0.00 0.00 0.00 5.52
1959 2520 3.241530 TCCCGTGGTCAGCTTGCT 61.242 61.111 0.00 0.00 0.00 3.91
1992 2553 1.139058 AGGTTCTTGACAACAGTCGCT 59.861 47.619 0.00 0.00 35.00 4.93
2016 2577 3.701040 AGAGTGTTCACCATGCTTTGTTT 59.299 39.130 0.00 0.00 0.00 2.83
2130 2691 1.166531 GGGTGGAATATGTCAGGCGC 61.167 60.000 0.00 0.00 0.00 6.53
2595 3156 5.344743 TCTTTATCGAGAACCTGCTGATT 57.655 39.130 0.00 0.00 0.00 2.57
2675 3236 4.633126 TGTTGCTGCTGATATCAACTCTTC 59.367 41.667 6.90 0.00 39.44 2.87
2853 3414 1.529226 TGGAAGTGTGCAATAACCCG 58.471 50.000 0.00 0.00 0.00 5.28
2967 3531 1.075659 GGCAAGCCTCTTCCCAGTT 59.924 57.895 3.29 0.00 0.00 3.16
3051 3615 1.891150 CAGCTTGTCAATTTGAGCCCT 59.109 47.619 0.00 0.00 35.79 5.19
3246 3810 1.341531 AGTCTAGTTTCACGCAGCAGT 59.658 47.619 0.00 0.00 0.00 4.40
3249 3813 2.295070 TCTAGTTTCACGCAGCAGTACA 59.705 45.455 0.00 0.00 0.00 2.90
3435 3999 0.327924 TCAAGTATGGGCCAGGTGTG 59.672 55.000 13.78 8.04 0.00 3.82
3912 4485 4.864247 GCAAACAAAAGTGCTCTTCTTCAA 59.136 37.500 0.74 0.00 37.78 2.69
3924 4497 2.032054 TCTTCTTCAACTTTGTGCTGCG 59.968 45.455 0.00 0.00 0.00 5.18
3966 4539 9.722184 GTCTAGGTAAATAACTTGTTCCTTTCT 57.278 33.333 0.00 0.00 0.00 2.52
3970 4543 9.856162 AGGTAAATAACTTGTTCCTTTCTGTTA 57.144 29.630 0.00 0.00 0.00 2.41
4022 4596 2.930826 ACGTGTCCTCAAAATCTGGT 57.069 45.000 0.00 0.00 0.00 4.00
4023 4597 3.208747 ACGTGTCCTCAAAATCTGGTT 57.791 42.857 0.00 0.00 0.00 3.67
4027 4603 4.216257 CGTGTCCTCAAAATCTGGTTTGAT 59.784 41.667 1.16 0.00 44.38 2.57
4062 4642 4.926832 GGTACAAGTTTGTTTGCTGTGTTT 59.073 37.500 2.46 0.00 42.35 2.83
4201 4781 3.093057 TGCACCTGTGGTTTAAACACTT 58.907 40.909 19.57 0.00 39.52 3.16
4202 4782 3.129638 TGCACCTGTGGTTTAAACACTTC 59.870 43.478 19.57 3.27 39.52 3.01
4399 4980 5.163602 TGTTTTAATTTCGAGTGCACTTGGT 60.164 36.000 29.69 15.78 0.00 3.67
4414 4995 0.039618 TTGGTCTGGAAATGGGAGGC 59.960 55.000 0.00 0.00 0.00 4.70
4536 5120 7.697691 GCTAGAAGCTGCACATTAGATTTTTA 58.302 34.615 1.02 0.00 38.45 1.52
4679 6187 9.817809 TTCCCGCAGTAAGATAATATGATAATC 57.182 33.333 0.00 0.00 0.00 1.75
4738 6259 5.005586 ACAAACAAAAATGTGTTCAGATGCG 59.994 36.000 0.00 0.00 40.86 4.73
4749 6270 3.259064 GTTCAGATGCGTGCCTTTAGTA 58.741 45.455 0.00 0.00 0.00 1.82
4750 6271 3.603158 TCAGATGCGTGCCTTTAGTAA 57.397 42.857 0.00 0.00 0.00 2.24
4815 6336 5.366477 TGTAATGCACCTATCTCCAGATGAA 59.634 40.000 0.00 0.00 36.05 2.57
4929 6451 8.778358 GTGGTGATGCTAAGGATAGATTTTAAG 58.222 37.037 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.073003 CCGAAAAAGCTTGGATAGATACATCC 60.073 42.308 0.00 0.00 44.21 3.51
10 11 6.706270 TCCGAAAAAGCTTGGATAGATACATC 59.294 38.462 0.00 0.00 0.00 3.06
11 12 6.483640 GTCCGAAAAAGCTTGGATAGATACAT 59.516 38.462 0.00 0.00 32.18 2.29
12 13 5.815740 GTCCGAAAAAGCTTGGATAGATACA 59.184 40.000 0.00 0.00 32.18 2.29
13 14 5.050972 CGTCCGAAAAAGCTTGGATAGATAC 60.051 44.000 0.00 0.00 32.18 2.24
14 15 5.047847 CGTCCGAAAAAGCTTGGATAGATA 58.952 41.667 0.00 0.00 32.18 1.98
15 16 3.871594 CGTCCGAAAAAGCTTGGATAGAT 59.128 43.478 0.00 0.00 32.18 1.98
16 17 3.259064 CGTCCGAAAAAGCTTGGATAGA 58.741 45.455 0.00 0.00 32.18 1.98
17 18 2.351726 CCGTCCGAAAAAGCTTGGATAG 59.648 50.000 0.00 1.23 32.18 2.08
18 19 2.027929 TCCGTCCGAAAAAGCTTGGATA 60.028 45.455 0.00 0.00 32.18 2.59
19 20 1.165270 CCGTCCGAAAAAGCTTGGAT 58.835 50.000 0.00 0.00 32.18 3.41
20 21 0.107081 TCCGTCCGAAAAAGCTTGGA 59.893 50.000 0.00 0.00 0.00 3.53
21 22 0.237498 GTCCGTCCGAAAAAGCTTGG 59.763 55.000 0.00 0.00 0.00 3.61
22 23 0.110823 CGTCCGTCCGAAAAAGCTTG 60.111 55.000 0.00 0.00 0.00 4.01
23 24 1.226030 CCGTCCGTCCGAAAAAGCTT 61.226 55.000 0.00 0.00 0.00 3.74
24 25 1.666872 CCGTCCGTCCGAAAAAGCT 60.667 57.895 0.00 0.00 0.00 3.74
25 26 1.623973 CTCCGTCCGTCCGAAAAAGC 61.624 60.000 0.00 0.00 0.00 3.51
26 27 0.319297 ACTCCGTCCGTCCGAAAAAG 60.319 55.000 0.00 0.00 0.00 2.27
27 28 0.958091 TACTCCGTCCGTCCGAAAAA 59.042 50.000 0.00 0.00 0.00 1.94
28 29 1.176527 ATACTCCGTCCGTCCGAAAA 58.823 50.000 0.00 0.00 0.00 2.29
29 30 2.036958 TATACTCCGTCCGTCCGAAA 57.963 50.000 0.00 0.00 0.00 3.46
30 31 1.670811 GTTATACTCCGTCCGTCCGAA 59.329 52.381 0.00 0.00 0.00 4.30
31 32 1.299541 GTTATACTCCGTCCGTCCGA 58.700 55.000 0.00 0.00 0.00 4.55
32 33 0.308993 GGTTATACTCCGTCCGTCCG 59.691 60.000 0.00 0.00 0.00 4.79
33 34 1.606189 GAGGTTATACTCCGTCCGTCC 59.394 57.143 0.00 0.00 0.00 4.79
34 35 2.570135 AGAGGTTATACTCCGTCCGTC 58.430 52.381 0.00 0.00 38.26 4.79
35 36 2.725221 AGAGGTTATACTCCGTCCGT 57.275 50.000 0.00 0.00 38.26 4.69
36 37 3.072944 CCTAGAGGTTATACTCCGTCCG 58.927 54.545 0.00 0.00 38.26 4.79
37 38 2.819019 GCCTAGAGGTTATACTCCGTCC 59.181 54.545 0.00 0.00 38.26 4.79
38 39 3.752747 GAGCCTAGAGGTTATACTCCGTC 59.247 52.174 0.00 0.00 38.26 4.79
39 40 3.753815 GAGCCTAGAGGTTATACTCCGT 58.246 50.000 0.00 0.00 38.26 4.69
40 41 2.743126 CGAGCCTAGAGGTTATACTCCG 59.257 54.545 0.00 0.00 38.26 4.63
41 42 4.004982 CTCGAGCCTAGAGGTTATACTCC 58.995 52.174 0.00 0.00 38.26 3.85
55 56 2.696526 TACATTATCCCCTCGAGCCT 57.303 50.000 6.99 0.00 0.00 4.58
117 118 2.037772 AGCCTAGATAACATTGAGCCGG 59.962 50.000 0.00 0.00 0.00 6.13
119 120 3.005897 TCGAGCCTAGATAACATTGAGCC 59.994 47.826 0.00 0.00 0.00 4.70
124 125 2.900546 CCCCTCGAGCCTAGATAACATT 59.099 50.000 6.99 0.00 0.00 2.71
126 127 1.497716 TCCCCTCGAGCCTAGATAACA 59.502 52.381 6.99 0.00 0.00 2.41
172 173 0.991920 AAGCCATTTTCGAGGGAGGA 59.008 50.000 0.89 0.00 0.00 3.71
174 175 3.756434 TGTTTAAGCCATTTTCGAGGGAG 59.244 43.478 0.00 0.00 0.00 4.30
175 176 3.756434 CTGTTTAAGCCATTTTCGAGGGA 59.244 43.478 0.00 0.00 0.00 4.20
179 180 6.870971 AGTAACTGTTTAAGCCATTTTCGA 57.129 33.333 0.00 0.00 0.00 3.71
191 192 5.764686 TGAGACAGACCGTAGTAACTGTTTA 59.235 40.000 0.00 0.00 42.45 2.01
199 200 3.144657 TGGTTGAGACAGACCGTAGTA 57.855 47.619 0.00 0.00 38.81 1.82
211 212 0.690192 TCTTCCCGCAATGGTTGAGA 59.310 50.000 0.00 0.00 35.15 3.27
213 214 0.608035 GGTCTTCCCGCAATGGTTGA 60.608 55.000 0.00 0.00 35.15 3.18
241 242 3.290710 GCAATCCAAGCCCTTTCTGATA 58.709 45.455 0.00 0.00 0.00 2.15
328 331 3.052082 CGCAGCCACCTCAACCAG 61.052 66.667 0.00 0.00 0.00 4.00
329 332 4.641645 CCGCAGCCACCTCAACCA 62.642 66.667 0.00 0.00 0.00 3.67
330 333 4.643387 ACCGCAGCCACCTCAACC 62.643 66.667 0.00 0.00 0.00 3.77
331 334 3.050275 GACCGCAGCCACCTCAAC 61.050 66.667 0.00 0.00 0.00 3.18
332 335 2.731691 GAAGACCGCAGCCACCTCAA 62.732 60.000 0.00 0.00 0.00 3.02
333 336 3.240134 GAAGACCGCAGCCACCTCA 62.240 63.158 0.00 0.00 0.00 3.86
334 337 2.435059 GAAGACCGCAGCCACCTC 60.435 66.667 0.00 0.00 0.00 3.85
335 338 4.379243 CGAAGACCGCAGCCACCT 62.379 66.667 0.00 0.00 0.00 4.00
336 339 4.681978 ACGAAGACCGCAGCCACC 62.682 66.667 0.00 0.00 43.32 4.61
337 340 3.414700 CACGAAGACCGCAGCCAC 61.415 66.667 0.00 0.00 43.32 5.01
338 341 3.611674 TCACGAAGACCGCAGCCA 61.612 61.111 0.00 0.00 43.32 4.75
339 342 3.112709 GTCACGAAGACCGCAGCC 61.113 66.667 0.00 0.00 41.56 4.85
340 343 3.470567 CGTCACGAAGACCGCAGC 61.471 66.667 0.00 0.00 44.66 5.25
341 344 2.805353 CCGTCACGAAGACCGCAG 60.805 66.667 0.00 0.00 44.66 5.18
342 345 4.351938 CCCGTCACGAAGACCGCA 62.352 66.667 0.00 0.00 44.66 5.69
343 346 3.966026 CTCCCGTCACGAAGACCGC 62.966 68.421 0.00 0.00 44.66 5.68
344 347 2.178521 CTCCCGTCACGAAGACCG 59.821 66.667 0.00 0.00 44.66 4.79
345 348 2.273912 ACCTCCCGTCACGAAGACC 61.274 63.158 0.00 0.00 44.66 3.85
346 349 1.080705 CACCTCCCGTCACGAAGAC 60.081 63.158 0.00 0.00 44.02 3.01
347 350 1.228337 TCACCTCCCGTCACGAAGA 60.228 57.895 0.00 0.00 0.00 2.87
348 351 1.213013 CTCACCTCCCGTCACGAAG 59.787 63.158 0.00 0.00 0.00 3.79
349 352 1.521450 GACTCACCTCCCGTCACGAA 61.521 60.000 0.00 0.00 0.00 3.85
350 353 1.970114 GACTCACCTCCCGTCACGA 60.970 63.158 0.00 0.00 0.00 4.35
351 354 2.567049 GACTCACCTCCCGTCACG 59.433 66.667 0.00 0.00 0.00 4.35
352 355 2.971452 GGACTCACCTCCCGTCAC 59.029 66.667 0.00 0.00 35.41 3.67
353 356 2.675423 CGGACTCACCTCCCGTCA 60.675 66.667 0.00 0.00 38.55 4.35
357 360 3.391382 CCCACGGACTCACCTCCC 61.391 72.222 0.00 0.00 36.31 4.30
358 361 2.168666 GAACCCACGGACTCACCTCC 62.169 65.000 0.00 0.00 36.31 4.30
359 362 1.292541 GAACCCACGGACTCACCTC 59.707 63.158 0.00 0.00 36.31 3.85
360 363 2.571216 CGAACCCACGGACTCACCT 61.571 63.158 0.00 0.00 36.31 4.00
361 364 2.048503 CGAACCCACGGACTCACC 60.049 66.667 0.00 0.00 0.00 4.02
362 365 0.942884 GTTCGAACCCACGGACTCAC 60.943 60.000 17.68 0.00 38.55 3.51
363 366 1.364901 GTTCGAACCCACGGACTCA 59.635 57.895 17.68 0.00 38.55 3.41
364 367 1.373873 GGTTCGAACCCACGGACTC 60.374 63.158 33.02 7.79 43.43 3.36
365 368 2.739132 GGTTCGAACCCACGGACT 59.261 61.111 33.02 0.00 43.43 3.85
374 377 2.049802 TCGCGTGAGGGTTCGAAC 60.050 61.111 20.14 20.14 45.36 3.95
375 378 2.257371 CTCGCGTGAGGGTTCGAA 59.743 61.111 18.36 0.00 45.36 3.71
376 379 4.415332 GCTCGCGTGAGGGTTCGA 62.415 66.667 26.24 2.69 42.79 3.71
377 380 3.989698 ATGCTCGCGTGAGGGTTCG 62.990 63.158 26.24 2.10 42.79 3.95
378 381 1.298859 AAATGCTCGCGTGAGGGTTC 61.299 55.000 26.24 10.85 42.79 3.62
379 382 0.889186 AAAATGCTCGCGTGAGGGTT 60.889 50.000 26.24 0.00 42.79 4.11
380 383 0.889186 AAAAATGCTCGCGTGAGGGT 60.889 50.000 26.24 0.00 42.79 4.34
381 384 1.875963 AAAAATGCTCGCGTGAGGG 59.124 52.632 26.24 4.42 42.79 4.30
397 400 3.181470 GCACCACTAGCCCAAAAGAAAAA 60.181 43.478 0.00 0.00 0.00 1.94
398 401 2.364002 GCACCACTAGCCCAAAAGAAAA 59.636 45.455 0.00 0.00 0.00 2.29
399 402 1.960689 GCACCACTAGCCCAAAAGAAA 59.039 47.619 0.00 0.00 0.00 2.52
400 403 1.133637 TGCACCACTAGCCCAAAAGAA 60.134 47.619 0.00 0.00 0.00 2.52
401 404 0.476338 TGCACCACTAGCCCAAAAGA 59.524 50.000 0.00 0.00 0.00 2.52
402 405 0.598065 GTGCACCACTAGCCCAAAAG 59.402 55.000 5.22 0.00 0.00 2.27
403 406 0.184933 AGTGCACCACTAGCCCAAAA 59.815 50.000 14.63 0.00 43.46 2.44
404 407 1.060729 TAGTGCACCACTAGCCCAAA 58.939 50.000 14.63 0.00 43.46 3.28
405 408 2.766698 TAGTGCACCACTAGCCCAA 58.233 52.632 14.63 0.00 43.46 4.12
406 409 4.551148 TAGTGCACCACTAGCCCA 57.449 55.556 14.63 0.00 43.46 5.36
411 414 0.896479 TGCGTCCTAGTGCACCACTA 60.896 55.000 14.63 5.13 43.46 2.74
413 416 1.079127 ATGCGTCCTAGTGCACCAC 60.079 57.895 14.63 4.49 45.07 4.16
414 417 1.079197 CATGCGTCCTAGTGCACCA 60.079 57.895 14.63 0.00 45.07 4.17
415 418 2.464459 GCATGCGTCCTAGTGCACC 61.464 63.158 14.63 0.00 45.07 5.01
416 419 2.464459 GGCATGCGTCCTAGTGCAC 61.464 63.158 9.40 9.40 45.07 4.57
417 420 2.125147 GGCATGCGTCCTAGTGCA 60.125 61.111 12.44 4.31 46.51 4.57
418 421 1.524621 ATGGCATGCGTCCTAGTGC 60.525 57.895 12.44 0.00 36.88 4.40
419 422 2.314256 CATGGCATGCGTCCTAGTG 58.686 57.895 15.53 0.00 0.00 2.74
420 423 4.863707 CATGGCATGCGTCCTAGT 57.136 55.556 15.53 0.00 0.00 2.57
438 441 0.807667 CTAGCAGGCTAGCACCGTTG 60.808 60.000 18.24 7.47 39.42 4.10
439 442 1.517832 CTAGCAGGCTAGCACCGTT 59.482 57.895 18.24 4.49 39.42 4.44
440 443 2.427245 CCTAGCAGGCTAGCACCGT 61.427 63.158 20.28 0.31 43.35 4.83
441 444 2.419198 CCTAGCAGGCTAGCACCG 59.581 66.667 20.28 4.93 43.35 4.94
442 445 1.144936 CACCTAGCAGGCTAGCACC 59.855 63.158 20.28 3.64 43.35 5.01
443 446 0.103937 CTCACCTAGCAGGCTAGCAC 59.896 60.000 20.28 6.06 43.35 4.40
444 447 1.045350 CCTCACCTAGCAGGCTAGCA 61.045 60.000 20.28 7.50 43.35 3.49
445 448 1.745264 CCTCACCTAGCAGGCTAGC 59.255 63.158 20.28 6.04 43.35 3.42
450 453 1.639635 ATTGGGCCTCACCTAGCAGG 61.640 60.000 4.53 1.16 42.49 4.85
451 454 1.131638 TATTGGGCCTCACCTAGCAG 58.868 55.000 4.53 0.00 39.10 4.24
452 455 1.819753 ATATTGGGCCTCACCTAGCA 58.180 50.000 4.53 0.00 39.10 3.49
453 456 2.355209 GCTATATTGGGCCTCACCTAGC 60.355 54.545 4.53 7.05 39.10 3.42
454 457 2.237392 GGCTATATTGGGCCTCACCTAG 59.763 54.545 4.53 0.19 44.48 3.02
455 458 2.266279 GGCTATATTGGGCCTCACCTA 58.734 52.381 4.53 0.00 44.48 3.08
456 459 1.068121 GGCTATATTGGGCCTCACCT 58.932 55.000 4.53 0.00 44.48 4.00
457 460 3.652581 GGCTATATTGGGCCTCACC 57.347 57.895 4.53 0.00 44.48 4.02
463 466 2.029838 CCATCGAGGCTATATTGGGC 57.970 55.000 0.00 0.00 0.00 5.36
474 477 2.029666 CCGCCTAAGCCATCGAGG 59.970 66.667 0.00 0.00 41.84 4.63
475 478 1.300233 GTCCGCCTAAGCCATCGAG 60.300 63.158 0.00 0.00 34.57 4.04
476 479 2.812499 GTCCGCCTAAGCCATCGA 59.188 61.111 0.00 0.00 34.57 3.59
477 480 2.658593 CGTCCGCCTAAGCCATCG 60.659 66.667 0.00 0.00 34.57 3.84
478 481 1.883084 CACGTCCGCCTAAGCCATC 60.883 63.158 0.00 0.00 34.57 3.51
479 482 2.186903 CACGTCCGCCTAAGCCAT 59.813 61.111 0.00 0.00 34.57 4.40
480 483 4.752879 GCACGTCCGCCTAAGCCA 62.753 66.667 0.00 0.00 34.57 4.75
482 485 4.789075 TCGCACGTCCGCCTAAGC 62.789 66.667 0.00 0.00 0.00 3.09
483 486 2.879462 GTCGCACGTCCGCCTAAG 60.879 66.667 0.00 0.00 0.00 2.18
484 487 3.620300 CTGTCGCACGTCCGCCTAA 62.620 63.158 0.00 0.00 0.00 2.69
485 488 4.111016 CTGTCGCACGTCCGCCTA 62.111 66.667 0.00 0.00 0.00 3.93
489 492 3.867226 TTCGTCTGTCGCACGTCCG 62.867 63.158 0.00 0.00 38.45 4.79
490 493 1.007336 ATTTCGTCTGTCGCACGTCC 61.007 55.000 0.00 0.00 38.45 4.79
491 494 0.782384 AATTTCGTCTGTCGCACGTC 59.218 50.000 0.00 0.00 38.45 4.34
492 495 1.070843 CAAATTTCGTCTGTCGCACGT 60.071 47.619 0.00 0.00 38.45 4.49
493 496 1.191425 TCAAATTTCGTCTGTCGCACG 59.809 47.619 0.00 0.00 39.67 5.34
494 497 2.411547 CCTCAAATTTCGTCTGTCGCAC 60.412 50.000 0.00 0.00 39.67 5.34
495 498 1.798223 CCTCAAATTTCGTCTGTCGCA 59.202 47.619 0.00 0.00 39.67 5.10
496 499 1.798813 ACCTCAAATTTCGTCTGTCGC 59.201 47.619 0.00 0.00 39.67 5.19
497 500 4.862574 TCATACCTCAAATTTCGTCTGTCG 59.137 41.667 0.00 0.00 41.41 4.35
498 501 5.220228 CGTCATACCTCAAATTTCGTCTGTC 60.220 44.000 0.00 0.00 0.00 3.51
499 502 4.625742 CGTCATACCTCAAATTTCGTCTGT 59.374 41.667 0.00 0.00 0.00 3.41
500 503 4.862574 TCGTCATACCTCAAATTTCGTCTG 59.137 41.667 0.00 0.00 0.00 3.51
501 504 4.863131 GTCGTCATACCTCAAATTTCGTCT 59.137 41.667 0.00 0.00 0.00 4.18
502 505 4.259292 CGTCGTCATACCTCAAATTTCGTC 60.259 45.833 0.00 0.00 0.00 4.20
503 506 3.611113 CGTCGTCATACCTCAAATTTCGT 59.389 43.478 0.00 0.00 0.00 3.85
504 507 3.000078 CCGTCGTCATACCTCAAATTTCG 60.000 47.826 0.00 0.00 0.00 3.46
505 508 4.032558 GTCCGTCGTCATACCTCAAATTTC 59.967 45.833 0.00 0.00 0.00 2.17
506 509 3.930848 GTCCGTCGTCATACCTCAAATTT 59.069 43.478 0.00 0.00 0.00 1.82
507 510 3.518590 GTCCGTCGTCATACCTCAAATT 58.481 45.455 0.00 0.00 0.00 1.82
508 511 2.479049 CGTCCGTCGTCATACCTCAAAT 60.479 50.000 0.00 0.00 34.52 2.32
509 512 1.135603 CGTCCGTCGTCATACCTCAAA 60.136 52.381 0.00 0.00 34.52 2.69
510 513 0.448990 CGTCCGTCGTCATACCTCAA 59.551 55.000 0.00 0.00 34.52 3.02
511 514 0.391528 TCGTCCGTCGTCATACCTCA 60.392 55.000 0.00 0.00 40.80 3.86
512 515 0.729116 TTCGTCCGTCGTCATACCTC 59.271 55.000 0.00 0.00 40.80 3.85
513 516 1.167851 TTTCGTCCGTCGTCATACCT 58.832 50.000 0.00 0.00 40.80 3.08
514 517 1.981254 TTTTCGTCCGTCGTCATACC 58.019 50.000 0.00 0.00 40.80 2.73
515 518 2.725723 TGTTTTTCGTCCGTCGTCATAC 59.274 45.455 0.00 0.00 40.80 2.39
516 519 3.010624 TGTTTTTCGTCCGTCGTCATA 57.989 42.857 0.00 0.00 40.80 2.15
517 520 1.855513 TGTTTTTCGTCCGTCGTCAT 58.144 45.000 0.00 0.00 40.80 3.06
518 521 1.638133 TTGTTTTTCGTCCGTCGTCA 58.362 45.000 0.00 0.00 40.80 4.35
519 522 2.356892 GTTTGTTTTTCGTCCGTCGTC 58.643 47.619 0.00 0.00 40.80 4.20
520 523 1.062440 GGTTTGTTTTTCGTCCGTCGT 59.938 47.619 0.00 0.00 40.80 4.34
521 524 1.062294 TGGTTTGTTTTTCGTCCGTCG 59.938 47.619 0.00 0.00 41.41 5.12
522 525 2.828874 TGGTTTGTTTTTCGTCCGTC 57.171 45.000 0.00 0.00 0.00 4.79
523 526 3.572604 TTTGGTTTGTTTTTCGTCCGT 57.427 38.095 0.00 0.00 0.00 4.69
524 527 5.330939 CGTAATTTGGTTTGTTTTTCGTCCG 60.331 40.000 0.00 0.00 0.00 4.79
525 528 5.051574 CCGTAATTTGGTTTGTTTTTCGTCC 60.052 40.000 0.00 0.00 0.00 4.79
526 529 5.515982 ACCGTAATTTGGTTTGTTTTTCGTC 59.484 36.000 0.00 0.00 35.82 4.20
527 530 5.288952 CACCGTAATTTGGTTTGTTTTTCGT 59.711 36.000 0.00 0.00 37.72 3.85
528 531 5.276442 CCACCGTAATTTGGTTTGTTTTTCG 60.276 40.000 0.00 0.00 37.72 3.46
529 532 5.581479 ACCACCGTAATTTGGTTTGTTTTTC 59.419 36.000 0.00 0.00 44.06 2.29
530 533 5.489249 ACCACCGTAATTTGGTTTGTTTTT 58.511 33.333 0.00 0.00 44.06 1.94
531 534 5.087391 ACCACCGTAATTTGGTTTGTTTT 57.913 34.783 0.00 0.00 44.06 2.43
532 535 4.739587 ACCACCGTAATTTGGTTTGTTT 57.260 36.364 0.00 0.00 44.06 2.83
533 536 5.593502 TCTTACCACCGTAATTTGGTTTGTT 59.406 36.000 4.90 0.00 44.06 2.83
534 537 5.131784 TCTTACCACCGTAATTTGGTTTGT 58.868 37.500 4.90 5.97 44.06 2.83
535 538 5.692613 TCTTACCACCGTAATTTGGTTTG 57.307 39.130 4.90 0.83 44.06 2.93
536 539 5.278610 GCTTCTTACCACCGTAATTTGGTTT 60.279 40.000 4.90 0.00 44.06 3.27
537 540 4.216902 GCTTCTTACCACCGTAATTTGGTT 59.783 41.667 4.90 0.00 44.06 3.67
539 542 3.754323 TGCTTCTTACCACCGTAATTTGG 59.246 43.478 0.00 0.00 39.00 3.28
540 543 5.365403 TTGCTTCTTACCACCGTAATTTG 57.635 39.130 0.00 0.00 33.98 2.32
541 544 6.183360 GCTATTGCTTCTTACCACCGTAATTT 60.183 38.462 0.00 0.00 33.56 1.82
542 545 5.296035 GCTATTGCTTCTTACCACCGTAATT 59.704 40.000 0.00 0.00 33.56 1.40
543 546 4.814771 GCTATTGCTTCTTACCACCGTAAT 59.185 41.667 0.00 0.00 33.56 1.89
544 547 4.186159 GCTATTGCTTCTTACCACCGTAA 58.814 43.478 0.00 0.00 36.03 3.18
545 548 3.431207 GGCTATTGCTTCTTACCACCGTA 60.431 47.826 0.00 0.00 39.59 4.02
546 549 2.629051 GCTATTGCTTCTTACCACCGT 58.371 47.619 0.00 0.00 36.03 4.83
547 550 1.940613 GGCTATTGCTTCTTACCACCG 59.059 52.381 0.00 0.00 39.59 4.94
548 551 2.298610 GGGCTATTGCTTCTTACCACC 58.701 52.381 0.00 0.00 39.59 4.61
549 552 2.092375 AGGGGCTATTGCTTCTTACCAC 60.092 50.000 0.00 0.00 39.59 4.16
550 553 2.205342 AGGGGCTATTGCTTCTTACCA 58.795 47.619 0.00 0.00 39.59 3.25
551 554 3.298686 AAGGGGCTATTGCTTCTTACC 57.701 47.619 0.00 0.00 39.59 2.85
552 555 6.961360 AATAAAGGGGCTATTGCTTCTTAC 57.039 37.500 0.00 0.00 39.59 2.34
554 557 9.301897 CTAATAATAAAGGGGCTATTGCTTCTT 57.698 33.333 0.00 0.96 39.59 2.52
555 558 7.890655 CCTAATAATAAAGGGGCTATTGCTTCT 59.109 37.037 0.00 0.00 39.59 2.85
556 559 8.056407 CCTAATAATAAAGGGGCTATTGCTTC 57.944 38.462 0.00 0.00 39.59 3.86
671 711 0.668535 GCCCAGAATAATGGCCGAAC 59.331 55.000 0.00 0.00 39.17 3.95
672 712 3.109847 GCCCAGAATAATGGCCGAA 57.890 52.632 0.00 0.00 39.17 4.30
731 820 2.028385 GGCCGAGACTGGTTTCTCTAAA 60.028 50.000 0.00 0.00 40.07 1.85
747 855 1.519751 CGGTGTTGAAATTGGGCCGA 61.520 55.000 0.00 0.00 40.04 5.54
779 887 1.628340 GGGGAAAAATGGAAAGTGGGG 59.372 52.381 0.00 0.00 0.00 4.96
783 891 1.618343 CGCAGGGGAAAAATGGAAAGT 59.382 47.619 0.00 0.00 0.00 2.66
865 973 1.213430 AGTCGGTAGGGGAGAGAGAAG 59.787 57.143 0.00 0.00 0.00 2.85
867 975 0.838608 GAGTCGGTAGGGGAGAGAGA 59.161 60.000 0.00 0.00 0.00 3.10
885 994 1.230182 GGGAAAGAGGGGAAGGGGA 60.230 63.158 0.00 0.00 0.00 4.81
890 999 1.151987 TCGTGGGGAAAGAGGGGAA 60.152 57.895 0.00 0.00 0.00 3.97
892 1001 1.612442 TCTCGTGGGGAAAGAGGGG 60.612 63.158 0.00 0.00 35.33 4.79
896 1005 2.534042 ATCTCTCTCGTGGGGAAAGA 57.466 50.000 0.00 0.00 0.00 2.52
897 1006 3.618690 AAATCTCTCTCGTGGGGAAAG 57.381 47.619 0.00 0.00 0.00 2.62
898 1007 3.326588 TGAAAATCTCTCTCGTGGGGAAA 59.673 43.478 0.00 0.00 0.00 3.13
1319 1880 1.758514 GACTGGATGAGAGGCGGGA 60.759 63.158 0.00 0.00 0.00 5.14
1326 1887 0.682532 AGAGCTGCGACTGGATGAGA 60.683 55.000 0.00 0.00 0.00 3.27
1959 2520 3.006430 TCAAGAACCTTATCGCAGTCACA 59.994 43.478 0.00 0.00 0.00 3.58
1992 2553 2.880268 CAAAGCATGGTGAACACTCTCA 59.120 45.455 0.00 0.00 0.00 3.27
2016 2577 1.288188 TCATTGCATCAGGAGTCCCA 58.712 50.000 5.25 0.00 33.88 4.37
2130 2691 2.748605 GTATCACTTCCCTCTGCATCG 58.251 52.381 0.00 0.00 0.00 3.84
2853 3414 8.794335 AGTAATGATTAAAGTCAGGGTTCTTC 57.206 34.615 0.00 0.00 0.00 2.87
2967 3531 6.071984 GTCCTCAACTAATATCCTCTGGAGA 58.928 44.000 0.00 0.00 34.05 3.71
3051 3615 1.561643 AATTCTGCGAGAGAGGTGGA 58.438 50.000 0.00 0.00 30.18 4.02
3249 3813 5.682659 AGCATGTAGAATGCAGAATCTTCT 58.317 37.500 12.44 4.97 46.77 2.85
3435 3999 3.987868 TCGTATCAACAGAACTGACAAGC 59.012 43.478 8.87 0.00 0.00 4.01
3606 4170 2.588620 AGCAATTTACCCCACGTTTGA 58.411 42.857 0.00 0.00 0.00 2.69
3912 4485 2.097466 GGCATTATACGCAGCACAAAGT 59.903 45.455 0.00 0.00 0.00 2.66
3924 4497 8.671384 TTACCTAGACAATGTTGGCATTATAC 57.329 34.615 0.86 0.00 42.91 1.47
4022 4596 8.862325 ACTTGTACCAATGAATGACTATCAAA 57.138 30.769 0.00 0.00 0.00 2.69
4023 4597 8.862325 AACTTGTACCAATGAATGACTATCAA 57.138 30.769 0.00 0.00 0.00 2.57
4027 4603 8.458573 AACAAACTTGTACCAATGAATGACTA 57.541 30.769 0.00 0.00 41.31 2.59
4062 4642 4.403734 GTGTTTTAAATGACAGGGAGGGA 58.596 43.478 0.00 0.00 0.00 4.20
4201 4781 2.543430 GTGCTTAAACCAAACCGTACGA 59.457 45.455 18.76 0.00 0.00 3.43
4202 4782 2.545106 AGTGCTTAAACCAAACCGTACG 59.455 45.455 8.69 8.69 0.00 3.67
4344 4925 9.868277 ACACAGAAGTTTGAAAACAAAATATGA 57.132 25.926 8.53 0.00 41.30 2.15
4351 4932 6.640499 CACTGAACACAGAAGTTTGAAAACAA 59.360 34.615 8.53 0.00 37.12 2.83
4399 4980 1.297968 TGATGCCTCCCATTTCCAGA 58.702 50.000 0.00 0.00 33.29 3.86
4454 5035 9.997482 GAAACTAAAACACAGAACAATGAAGTA 57.003 29.630 0.00 0.00 0.00 2.24
4536 5120 5.940470 GGTAAGATGTTGTCTGAATGGAGTT 59.060 40.000 0.00 0.00 37.23 3.01
4550 5134 5.211973 TCTGCTCCTATCTGGTAAGATGTT 58.788 41.667 0.00 0.00 43.27 2.71
4551 5135 4.809193 TCTGCTCCTATCTGGTAAGATGT 58.191 43.478 0.00 0.00 43.27 3.06
4552 5136 4.321899 GCTCTGCTCCTATCTGGTAAGATG 60.322 50.000 0.00 0.00 43.27 2.90
4678 6186 7.874528 AGCATCTGAACATATATGAACGAATGA 59.125 33.333 19.63 7.97 0.00 2.57
4679 6187 8.026341 AGCATCTGAACATATATGAACGAATG 57.974 34.615 19.63 15.54 0.00 2.67
4682 6190 7.436933 AGAAGCATCTGAACATATATGAACGA 58.563 34.615 19.63 9.75 33.59 3.85
4683 6191 7.649370 AGAAGCATCTGAACATATATGAACG 57.351 36.000 19.63 5.00 33.59 3.95
4684 6192 9.875675 GAAAGAAGCATCTGAACATATATGAAC 57.124 33.333 19.63 12.13 35.59 3.18
4692 6213 5.302568 TGTTTGGAAAGAAGCATCTGAACAT 59.697 36.000 0.00 0.00 35.59 2.71


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

AutoCloner maintained by Alex Coulton.