Multiple sequence alignment - TraesCS2A01G114700

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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 TraesCS2A01G114700 chr2A 100.000 3242 0 0 1 3242 65516163 65519404 0.000000e+00 5987.0
1 TraesCS2A01G114700 chr2A 80.233 172 24 9 1603 1770 313771430 313771265 1.580000e-23 121.0
2 TraesCS2A01G114700 chr2D 91.914 2659 144 29 608 3242 64062888 64065499 0.000000e+00 3653.0
3 TraesCS2A01G114700 chr2D 86.207 116 11 2 2 116 64052413 64052524 1.580000e-23 121.0
4 TraesCS2A01G114700 chr2D 79.651 172 25 9 1603 1770 276932277 276932112 7.350000e-22 115.0
5 TraesCS2A01G114700 chr2D 100.000 30 0 0 3 32 53492563 53492592 4.520000e-04 56.5
6 TraesCS2A01G114700 chr2B 90.906 2771 156 34 518 3242 100075483 100078203 0.000000e+00 3633.0
7 TraesCS2A01G114700 chr2B 85.417 336 28 6 1 335 100075167 100075482 2.410000e-86 329.0
8 TraesCS2A01G114700 chr2B 80.233 172 24 9 1603 1770 329473694 329473529 1.580000e-23 121.0
9 TraesCS2A01G114700 chr5D 88.554 332 36 2 3 332 80359326 80359657 5.040000e-108 401.0
10 TraesCS2A01G114700 chrUn 94.565 184 10 0 334 517 45097000 45096817 5.290000e-73 285.0
11 TraesCS2A01G114700 chr7D 94.565 184 10 0 334 517 626646445 626646262 5.290000e-73 285.0
12 TraesCS2A01G114700 chr6A 94.565 184 10 0 334 517 155842847 155842664 5.290000e-73 285.0
13 TraesCS2A01G114700 chr6A 94.565 184 10 0 334 517 278453545 278453362 5.290000e-73 285.0
14 TraesCS2A01G114700 chr5B 94.565 184 10 0 334 517 130572555 130572738 5.290000e-73 285.0
15 TraesCS2A01G114700 chr5B 94.565 184 10 0 334 517 130606078 130605895 5.290000e-73 285.0
16 TraesCS2A01G114700 chr5A 94.565 184 10 0 334 517 238831823 238832006 5.290000e-73 285.0
17 TraesCS2A01G114700 chr1D 94.565 184 10 0 334 517 493800660 493800477 5.290000e-73 285.0
18 TraesCS2A01G114700 chr1B 94.565 184 10 0 334 517 339054042 339054225 5.290000e-73 285.0
19 TraesCS2A01G114700 chr3B 78.466 339 45 12 1 335 434978728 434979042 2.550000e-46 196.0
20 TraesCS2A01G114700 chr1A 86.335 161 21 1 1 160 538781994 538781834 1.200000e-39 174.0
21 TraesCS2A01G114700 chr4A 89.320 103 10 1 2 103 688699590 688699692 9.440000e-26 128.0
22 TraesCS2A01G114700 chr4A 89.320 103 10 1 2 103 688754599 688754701 9.440000e-26 128.0
23 TraesCS2A01G114700 chr4A 91.111 45 4 0 1610 1654 714838754 714838798 9.710000e-06 62.1


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 TraesCS2A01G114700 chr2A 65516163 65519404 3241 False 5987 5987 100.0000 1 3242 1 chr2A.!!$F1 3241
1 TraesCS2A01G114700 chr2D 64062888 64065499 2611 False 3653 3653 91.9140 608 3242 1 chr2D.!!$F3 2634
2 TraesCS2A01G114700 chr2B 100075167 100078203 3036 False 1981 3633 88.1615 1 3242 2 chr2B.!!$F1 3241

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
509 511 0.036732 TCCTTGAGCGCTTTCACCAT 59.963 50.0 13.26 0.0 0.00 3.55 F
572 574 0.250338 GGTCCGAACAGGTGCTTTCT 60.250 55.0 0.00 0.0 41.99 2.52 F
1810 1858 0.319083 TTTCCGCGGCTCTCTGTTTA 59.681 50.0 23.51 0.0 0.00 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 2144 0.320421 CCGTCTGTTCATCACCGGTT 60.320 55.0 2.97 0.0 33.46 4.44 R
2125 2174 0.604578 AATTTCATGCTTGCACCGCT 59.395 45.0 8.46 0.0 0.00 5.52 R
2676 2726 1.021390 AATGGCAGAAACGAGGCGAG 61.021 55.0 0.00 0.0 0.00 5.03 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
20 21 4.120755 GCAAGGGGAGGAGGCCAG 62.121 72.222 5.01 0.00 0.00 4.85
61 63 2.828868 GGTGATCCCGCAGCCATA 59.171 61.111 0.00 0.00 0.00 2.74
73 75 0.757188 CAGCCATAGAGGACCTCCGT 60.757 60.000 18.32 4.09 41.22 4.69
74 76 0.468400 AGCCATAGAGGACCTCCGTC 60.468 60.000 18.32 3.58 41.22 4.79
75 77 1.797211 GCCATAGAGGACCTCCGTCG 61.797 65.000 18.32 4.98 40.17 5.12
76 78 1.655329 CATAGAGGACCTCCGTCGC 59.345 63.158 18.32 0.00 40.17 5.19
77 79 1.528776 ATAGAGGACCTCCGTCGCC 60.529 63.158 18.32 0.00 40.17 5.54
78 80 2.980105 ATAGAGGACCTCCGTCGCCC 62.980 65.000 18.32 0.00 40.17 6.13
80 82 3.711059 GAGGACCTCCGTCGCCCTA 62.711 68.421 10.74 0.00 40.17 3.53
81 83 3.525545 GGACCTCCGTCGCCCTAC 61.526 72.222 0.00 0.00 40.17 3.18
82 84 2.439883 GACCTCCGTCGCCCTACT 60.440 66.667 0.00 0.00 0.00 2.57
83 85 2.754658 ACCTCCGTCGCCCTACTG 60.755 66.667 0.00 0.00 0.00 2.74
108 110 3.367743 CACGGACGGAAGGGACGA 61.368 66.667 0.00 0.00 34.93 4.20
112 114 2.576832 GGACGGAAGGGACGACCAA 61.577 63.158 6.20 0.00 43.73 3.67
117 119 1.192803 GGAAGGGACGACCAACTCCT 61.193 60.000 6.20 0.00 43.89 3.69
122 124 1.733399 GACGACCAACTCCTGCGAC 60.733 63.158 0.00 0.00 0.00 5.19
123 125 2.338620 CGACCAACTCCTGCGACA 59.661 61.111 0.00 0.00 0.00 4.35
124 126 2.022129 CGACCAACTCCTGCGACAC 61.022 63.158 0.00 0.00 0.00 3.67
133 135 2.347114 CTGCGACACCATCCACCA 59.653 61.111 0.00 0.00 0.00 4.17
221 223 3.461773 GGTAGCAGAGCCTCGCCA 61.462 66.667 5.19 0.00 0.00 5.69
226 228 4.767255 CAGAGCCTCGCCACCACC 62.767 72.222 0.00 0.00 0.00 4.61
233 235 1.811266 CTCGCCACCACCTTCATCG 60.811 63.158 0.00 0.00 0.00 3.84
234 236 2.225791 CTCGCCACCACCTTCATCGA 62.226 60.000 0.00 0.00 0.00 3.59
247 249 0.037326 TCATCGAAGGCCACACAGTC 60.037 55.000 5.01 0.00 0.00 3.51
272 274 3.522731 CGGAGTCCTCAGGCGGAG 61.523 72.222 7.77 7.75 43.65 4.63
336 338 3.437795 GGTCGCCCTCGAGTCGAA 61.438 66.667 22.74 0.00 46.46 3.71
337 339 2.564975 GTCGCCCTCGAGTCGAAA 59.435 61.111 22.74 5.42 46.46 3.46
338 340 1.139095 GTCGCCCTCGAGTCGAAAT 59.861 57.895 22.74 0.00 46.46 2.17
339 341 0.379669 GTCGCCCTCGAGTCGAAATA 59.620 55.000 22.74 4.53 46.46 1.40
340 342 0.661552 TCGCCCTCGAGTCGAAATAG 59.338 55.000 17.27 8.80 40.21 1.73
341 343 0.317938 CGCCCTCGAGTCGAAATAGG 60.318 60.000 17.27 13.62 34.74 2.57
342 344 0.745468 GCCCTCGAGTCGAAATAGGT 59.255 55.000 17.27 0.00 34.74 3.08
343 345 1.952296 GCCCTCGAGTCGAAATAGGTA 59.048 52.381 17.27 0.00 34.74 3.08
344 346 2.030981 GCCCTCGAGTCGAAATAGGTAG 60.031 54.545 17.27 1.91 34.74 3.18
345 347 3.212685 CCCTCGAGTCGAAATAGGTAGT 58.787 50.000 17.27 0.00 34.74 2.73
346 348 4.384056 CCCTCGAGTCGAAATAGGTAGTA 58.616 47.826 17.27 0.00 34.74 1.82
347 349 4.818546 CCCTCGAGTCGAAATAGGTAGTAA 59.181 45.833 17.27 0.00 34.74 2.24
348 350 5.297776 CCCTCGAGTCGAAATAGGTAGTAAA 59.702 44.000 17.27 0.00 34.74 2.01
349 351 6.428799 CCTCGAGTCGAAATAGGTAGTAAAG 58.571 44.000 17.27 0.00 34.74 1.85
350 352 6.038050 CCTCGAGTCGAAATAGGTAGTAAAGT 59.962 42.308 17.27 0.00 34.74 2.66
351 353 7.225538 CCTCGAGTCGAAATAGGTAGTAAAGTA 59.774 40.741 17.27 0.00 34.74 2.24
352 354 8.136057 TCGAGTCGAAATAGGTAGTAAAGTAG 57.864 38.462 13.98 0.00 31.06 2.57
353 355 7.766278 TCGAGTCGAAATAGGTAGTAAAGTAGT 59.234 37.037 13.98 0.00 31.06 2.73
354 356 7.850003 CGAGTCGAAATAGGTAGTAAAGTAGTG 59.150 40.741 6.73 0.00 0.00 2.74
355 357 8.798859 AGTCGAAATAGGTAGTAAAGTAGTGA 57.201 34.615 0.00 0.00 0.00 3.41
356 358 9.406113 AGTCGAAATAGGTAGTAAAGTAGTGAT 57.594 33.333 0.00 0.00 0.00 3.06
362 364 9.901172 AATAGGTAGTAAAGTAGTGATTTTGGG 57.099 33.333 0.00 0.00 0.00 4.12
363 365 6.178324 AGGTAGTAAAGTAGTGATTTTGGGC 58.822 40.000 0.00 0.00 0.00 5.36
364 366 5.356190 GGTAGTAAAGTAGTGATTTTGGGCC 59.644 44.000 0.00 0.00 0.00 5.80
365 367 4.341487 AGTAAAGTAGTGATTTTGGGCCC 58.659 43.478 17.59 17.59 0.00 5.80
366 368 2.990740 AAGTAGTGATTTTGGGCCCA 57.009 45.000 24.45 24.45 0.00 5.36
367 369 2.990740 AGTAGTGATTTTGGGCCCAA 57.009 45.000 34.07 34.07 0.00 4.12
368 370 3.473113 AGTAGTGATTTTGGGCCCAAT 57.527 42.857 37.41 24.48 35.70 3.16
369 371 3.790126 AGTAGTGATTTTGGGCCCAATT 58.210 40.909 37.41 26.97 35.70 2.32
370 372 3.769300 AGTAGTGATTTTGGGCCCAATTC 59.231 43.478 37.41 32.27 35.70 2.17
371 373 2.618794 AGTGATTTTGGGCCCAATTCA 58.381 42.857 37.41 34.19 35.70 2.57
372 374 3.183801 AGTGATTTTGGGCCCAATTCAT 58.816 40.909 35.33 28.27 35.70 2.57
373 375 4.360889 AGTGATTTTGGGCCCAATTCATA 58.639 39.130 35.33 22.99 35.70 2.15
374 376 4.970640 AGTGATTTTGGGCCCAATTCATAT 59.029 37.500 35.33 27.95 35.70 1.78
375 377 6.142498 AGTGATTTTGGGCCCAATTCATATA 58.858 36.000 35.33 21.76 35.70 0.86
376 378 6.788957 AGTGATTTTGGGCCCAATTCATATAT 59.211 34.615 35.33 24.64 35.70 0.86
377 379 7.293062 AGTGATTTTGGGCCCAATTCATATATT 59.707 33.333 35.33 22.71 35.70 1.28
378 380 7.938490 GTGATTTTGGGCCCAATTCATATATTT 59.062 33.333 35.33 15.98 35.70 1.40
379 381 8.501070 TGATTTTGGGCCCAATTCATATATTTT 58.499 29.630 37.41 8.98 35.70 1.82
380 382 9.353431 GATTTTGGGCCCAATTCATATATTTTT 57.647 29.630 37.41 7.47 35.70 1.94
407 409 7.736447 AAATTGGAATTCTTATCCTAGCTCG 57.264 36.000 5.23 0.00 37.85 5.03
408 410 4.873746 TGGAATTCTTATCCTAGCTCGG 57.126 45.455 5.23 0.00 37.85 4.63
409 411 3.006967 TGGAATTCTTATCCTAGCTCGGC 59.993 47.826 5.23 0.00 37.85 5.54
410 412 3.591023 GAATTCTTATCCTAGCTCGGCC 58.409 50.000 0.00 0.00 0.00 6.13
411 413 2.383442 TTCTTATCCTAGCTCGGCCT 57.617 50.000 0.00 0.00 0.00 5.19
412 414 3.520691 TTCTTATCCTAGCTCGGCCTA 57.479 47.619 0.00 0.00 0.00 3.93
413 415 2.792878 TCTTATCCTAGCTCGGCCTAC 58.207 52.381 0.00 0.00 0.00 3.18
414 416 2.375845 TCTTATCCTAGCTCGGCCTACT 59.624 50.000 0.00 0.00 0.00 2.57
415 417 2.493414 TATCCTAGCTCGGCCTACTC 57.507 55.000 0.00 0.00 0.00 2.59
416 418 0.606944 ATCCTAGCTCGGCCTACTCG 60.607 60.000 0.00 0.00 0.00 4.18
417 419 2.640421 CTAGCTCGGCCTACTCGC 59.360 66.667 0.00 0.00 0.00 5.03
418 420 2.124445 TAGCTCGGCCTACTCGCA 60.124 61.111 0.00 0.00 0.00 5.10
419 421 1.725557 CTAGCTCGGCCTACTCGCAA 61.726 60.000 0.00 0.00 0.00 4.85
420 422 1.725557 TAGCTCGGCCTACTCGCAAG 61.726 60.000 0.00 0.00 0.00 4.01
433 435 2.760634 TCGCAAGATGTTAGCCTTCA 57.239 45.000 0.00 0.00 45.01 3.02
434 436 3.052455 TCGCAAGATGTTAGCCTTCAA 57.948 42.857 0.00 0.00 45.01 2.69
435 437 2.742053 TCGCAAGATGTTAGCCTTCAAC 59.258 45.455 0.00 0.00 45.01 3.18
436 438 2.159517 CGCAAGATGTTAGCCTTCAACC 60.160 50.000 0.00 0.00 43.02 3.77
437 439 3.084786 GCAAGATGTTAGCCTTCAACCT 58.915 45.455 0.00 0.00 0.00 3.50
438 440 3.119708 GCAAGATGTTAGCCTTCAACCTG 60.120 47.826 0.00 0.00 0.00 4.00
439 441 4.326826 CAAGATGTTAGCCTTCAACCTGA 58.673 43.478 0.00 0.00 0.00 3.86
440 442 4.851639 AGATGTTAGCCTTCAACCTGAT 57.148 40.909 0.00 0.00 0.00 2.90
441 443 5.184892 AGATGTTAGCCTTCAACCTGATT 57.815 39.130 0.00 0.00 0.00 2.57
442 444 6.313519 AGATGTTAGCCTTCAACCTGATTA 57.686 37.500 0.00 0.00 0.00 1.75
443 445 6.116126 AGATGTTAGCCTTCAACCTGATTAC 58.884 40.000 0.00 0.00 0.00 1.89
444 446 5.235850 TGTTAGCCTTCAACCTGATTACA 57.764 39.130 0.00 0.00 0.00 2.41
445 447 5.815581 TGTTAGCCTTCAACCTGATTACAT 58.184 37.500 0.00 0.00 0.00 2.29
446 448 6.953101 TGTTAGCCTTCAACCTGATTACATA 58.047 36.000 0.00 0.00 0.00 2.29
447 449 7.398829 TGTTAGCCTTCAACCTGATTACATAA 58.601 34.615 0.00 0.00 0.00 1.90
448 450 7.885922 TGTTAGCCTTCAACCTGATTACATAAA 59.114 33.333 0.00 0.00 0.00 1.40
449 451 8.398665 GTTAGCCTTCAACCTGATTACATAAAG 58.601 37.037 0.00 0.00 0.00 1.85
450 452 5.358160 AGCCTTCAACCTGATTACATAAAGC 59.642 40.000 0.00 0.00 0.00 3.51
451 453 5.125417 GCCTTCAACCTGATTACATAAAGCA 59.875 40.000 0.00 0.00 31.38 3.91
452 454 6.183360 GCCTTCAACCTGATTACATAAAGCAT 60.183 38.462 0.00 0.00 31.94 3.79
453 455 7.013274 GCCTTCAACCTGATTACATAAAGCATA 59.987 37.037 0.00 0.00 31.94 3.14
454 456 8.562892 CCTTCAACCTGATTACATAAAGCATAG 58.437 37.037 0.00 0.00 31.94 2.23
455 457 9.113838 CTTCAACCTGATTACATAAAGCATAGT 57.886 33.333 0.00 0.00 31.94 2.12
457 459 9.542462 TCAACCTGATTACATAAAGCATAGTAC 57.458 33.333 0.00 0.00 31.94 2.73
458 460 9.547753 CAACCTGATTACATAAAGCATAGTACT 57.452 33.333 0.00 0.00 31.94 2.73
460 462 9.765795 ACCTGATTACATAAAGCATAGTACTTC 57.234 33.333 0.00 0.00 31.94 3.01
461 463 9.988815 CCTGATTACATAAAGCATAGTACTTCT 57.011 33.333 0.00 0.00 31.94 2.85
472 474 9.453572 AAAGCATAGTACTTCTGATCAATTTGA 57.546 29.630 0.00 0.75 0.00 2.69
473 475 9.453572 AAGCATAGTACTTCTGATCAATTTGAA 57.546 29.630 0.00 0.00 0.00 2.69
474 476 9.624373 AGCATAGTACTTCTGATCAATTTGAAT 57.376 29.630 0.00 0.00 0.00 2.57
485 487 8.863086 TCTGATCAATTTGAATATTCCATTCCC 58.137 33.333 12.90 4.12 0.00 3.97
486 488 8.786710 TGATCAATTTGAATATTCCATTCCCT 57.213 30.769 12.90 0.00 0.00 4.20
487 489 9.880254 TGATCAATTTGAATATTCCATTCCCTA 57.120 29.630 12.90 0.00 0.00 3.53
493 495 9.903190 ATTTGAATATTCCATTCCCTATTTCCT 57.097 29.630 12.90 0.00 0.00 3.36
494 496 9.728100 TTTGAATATTCCATTCCCTATTTCCTT 57.272 29.630 12.90 0.00 0.00 3.36
495 497 8.710749 TGAATATTCCATTCCCTATTTCCTTG 57.289 34.615 12.90 0.00 0.00 3.61
496 498 8.510283 TGAATATTCCATTCCCTATTTCCTTGA 58.490 33.333 12.90 0.00 0.00 3.02
497 499 8.946797 AATATTCCATTCCCTATTTCCTTGAG 57.053 34.615 0.00 0.00 0.00 3.02
498 500 4.170468 TCCATTCCCTATTTCCTTGAGC 57.830 45.455 0.00 0.00 0.00 4.26
499 501 2.880890 CCATTCCCTATTTCCTTGAGCG 59.119 50.000 0.00 0.00 0.00 5.03
500 502 2.038387 TTCCCTATTTCCTTGAGCGC 57.962 50.000 0.00 0.00 0.00 5.92
501 503 1.204146 TCCCTATTTCCTTGAGCGCT 58.796 50.000 11.27 11.27 0.00 5.92
502 504 1.559682 TCCCTATTTCCTTGAGCGCTT 59.440 47.619 13.26 0.00 0.00 4.68
503 505 2.026262 TCCCTATTTCCTTGAGCGCTTT 60.026 45.455 13.26 0.00 0.00 3.51
504 506 2.356069 CCCTATTTCCTTGAGCGCTTTC 59.644 50.000 13.26 0.00 0.00 2.62
505 507 3.009723 CCTATTTCCTTGAGCGCTTTCA 58.990 45.455 13.26 2.44 0.00 2.69
506 508 2.997485 ATTTCCTTGAGCGCTTTCAC 57.003 45.000 13.26 0.00 0.00 3.18
507 509 0.951558 TTTCCTTGAGCGCTTTCACC 59.048 50.000 13.26 0.00 0.00 4.02
508 510 0.179032 TTCCTTGAGCGCTTTCACCA 60.179 50.000 13.26 0.17 0.00 4.17
509 511 0.036732 TCCTTGAGCGCTTTCACCAT 59.963 50.000 13.26 0.00 0.00 3.55
510 512 0.883833 CCTTGAGCGCTTTCACCATT 59.116 50.000 13.26 0.00 0.00 3.16
511 513 2.083774 CCTTGAGCGCTTTCACCATTA 58.916 47.619 13.26 0.00 0.00 1.90
512 514 2.487762 CCTTGAGCGCTTTCACCATTAA 59.512 45.455 13.26 0.00 0.00 1.40
513 515 3.492313 CTTGAGCGCTTTCACCATTAAC 58.508 45.455 13.26 0.00 0.00 2.01
514 516 1.810151 TGAGCGCTTTCACCATTAACC 59.190 47.619 13.26 0.00 0.00 2.85
515 517 1.132453 GAGCGCTTTCACCATTAACCC 59.868 52.381 13.26 0.00 0.00 4.11
516 518 0.885196 GCGCTTTCACCATTAACCCA 59.115 50.000 0.00 0.00 0.00 4.51
517 519 1.402325 GCGCTTTCACCATTAACCCAC 60.402 52.381 0.00 0.00 0.00 4.61
520 522 2.821625 GCTTTCACCATTAACCCACCCT 60.822 50.000 0.00 0.00 0.00 4.34
561 563 1.904865 GGGGGTTTTGGGTCCGAAC 60.905 63.158 0.00 0.00 0.00 3.95
572 574 0.250338 GGTCCGAACAGGTGCTTTCT 60.250 55.000 0.00 0.00 41.99 2.52
583 585 5.079643 ACAGGTGCTTTCTCATACCATTTT 58.920 37.500 0.00 0.00 35.66 1.82
584 586 5.539955 ACAGGTGCTTTCTCATACCATTTTT 59.460 36.000 0.00 0.00 35.66 1.94
585 587 5.865552 CAGGTGCTTTCTCATACCATTTTTG 59.134 40.000 0.00 0.00 35.66 2.44
586 588 5.774690 AGGTGCTTTCTCATACCATTTTTGA 59.225 36.000 0.00 0.00 35.66 2.69
587 589 6.438425 AGGTGCTTTCTCATACCATTTTTGAT 59.562 34.615 0.00 0.00 35.66 2.57
626 628 6.783708 TGTCCAATTTCACTGGTTAAAGTT 57.216 33.333 0.00 0.00 35.30 2.66
675 678 9.793259 TGGAAATGTGTACTTAATTCTTCTTCT 57.207 29.630 0.00 0.00 0.00 2.85
755 769 0.452585 ACAAACAAACCCACCGAACG 59.547 50.000 0.00 0.00 0.00 3.95
775 789 2.478370 CGCGGTCATTTGCATTGATTCT 60.478 45.455 0.00 0.00 0.00 2.40
779 793 4.110482 GGTCATTTGCATTGATTCTCAGC 58.890 43.478 3.47 0.00 0.00 4.26
780 794 4.381185 GGTCATTTGCATTGATTCTCAGCA 60.381 41.667 3.47 0.00 0.00 4.41
784 798 2.014857 TGCATTGATTCTCAGCAGAGC 58.985 47.619 0.32 0.00 41.81 4.09
785 799 1.003759 GCATTGATTCTCAGCAGAGCG 60.004 52.381 0.32 0.00 41.81 5.03
786 800 1.003759 CATTGATTCTCAGCAGAGCGC 60.004 52.381 0.00 0.00 41.81 5.92
803 817 2.475466 GCCGGTGGATCACATGCTG 61.475 63.158 1.90 0.00 35.86 4.41
804 818 2.475466 CCGGTGGATCACATGCTGC 61.475 63.158 0.00 0.00 35.86 5.25
805 819 1.746239 CGGTGGATCACATGCTGCA 60.746 57.895 4.13 4.13 35.86 4.41
806 820 1.099295 CGGTGGATCACATGCTGCAT 61.099 55.000 9.81 9.81 35.86 3.96
808 822 2.511659 GGTGGATCACATGCTGCATAT 58.488 47.619 15.78 0.00 35.86 1.78
809 823 2.889045 GGTGGATCACATGCTGCATATT 59.111 45.455 15.78 2.25 35.86 1.28
810 824 3.057736 GGTGGATCACATGCTGCATATTC 60.058 47.826 15.78 5.04 35.86 1.75
813 827 3.124806 GGATCACATGCTGCATATTCTCG 59.875 47.826 15.78 4.31 0.00 4.04
814 828 3.457610 TCACATGCTGCATATTCTCGA 57.542 42.857 15.78 3.12 0.00 4.04
815 829 3.999046 TCACATGCTGCATATTCTCGAT 58.001 40.909 15.78 0.00 0.00 3.59
816 830 3.992427 TCACATGCTGCATATTCTCGATC 59.008 43.478 15.78 0.00 0.00 3.69
817 831 3.995048 CACATGCTGCATATTCTCGATCT 59.005 43.478 15.78 0.00 0.00 2.75
818 832 4.091655 CACATGCTGCATATTCTCGATCTC 59.908 45.833 15.78 0.00 0.00 2.75
842 856 1.664659 CTGAAAAGCGCTGGAGATCTG 59.335 52.381 12.58 5.72 0.00 2.90
857 871 3.172339 AGATCTGCTTCCTCTTGTCACT 58.828 45.455 0.00 0.00 0.00 3.41
978 992 2.335933 ACACCAGGTACTACAAAGCCT 58.664 47.619 0.00 0.00 36.02 4.58
1006 1020 2.444895 GCTCGATCCACCCTCCCT 60.445 66.667 0.00 0.00 0.00 4.20
1007 1021 2.801631 GCTCGATCCACCCTCCCTG 61.802 68.421 0.00 0.00 0.00 4.45
1008 1022 2.041922 TCGATCCACCCTCCCTGG 60.042 66.667 0.00 0.00 0.00 4.45
1009 1023 3.866582 CGATCCACCCTCCCTGGC 61.867 72.222 0.00 0.00 0.00 4.85
1010 1024 2.367512 GATCCACCCTCCCTGGCT 60.368 66.667 0.00 0.00 0.00 4.75
1130 1144 1.452651 CACGATCCATTGCCAGCCT 60.453 57.895 0.00 0.00 0.00 4.58
1145 1159 2.344950 CAGCCTCTTGAGCAACAGTAG 58.655 52.381 0.00 0.00 0.00 2.57
1149 1163 1.002430 CTCTTGAGCAACAGTAGCCCA 59.998 52.381 0.00 0.00 0.00 5.36
1150 1164 1.002430 TCTTGAGCAACAGTAGCCCAG 59.998 52.381 0.00 0.00 0.00 4.45
1186 1221 3.131933 CGACTCTGACCCATTCTTGATCT 59.868 47.826 0.00 0.00 0.00 2.75
1205 1240 3.059982 CAGAAGCTGTCGGGTGGA 58.940 61.111 0.00 0.00 0.00 4.02
1208 1243 1.374758 GAAGCTGTCGGGTGGACTG 60.375 63.158 0.00 0.00 46.24 3.51
1248 1283 0.890996 CAAGGTCAGGCCACTTCCAC 60.891 60.000 5.01 0.00 40.61 4.02
1268 1303 3.248029 CGCATCATCCGCTTAGCC 58.752 61.111 0.00 0.00 0.00 3.93
1270 1305 1.072159 GCATCATCCGCTTAGCCCT 59.928 57.895 0.00 0.00 0.00 5.19
1277 1312 2.437359 CGCTTAGCCCTGCTTGCT 60.437 61.111 0.00 1.12 40.44 3.91
1278 1313 2.467826 CGCTTAGCCCTGCTTGCTC 61.468 63.158 0.00 0.00 40.44 4.26
1306 1341 1.392589 ATGGCGATCGGCTGATTTTT 58.607 45.000 36.77 13.86 42.94 1.94
1307 1342 0.451383 TGGCGATCGGCTGATTTTTG 59.549 50.000 36.77 1.80 42.94 2.44
1308 1343 0.867329 GGCGATCGGCTGATTTTTGC 60.867 55.000 31.96 11.30 42.94 3.68
1488 1528 3.126879 TGCAGAAATGGCGCTCCG 61.127 61.111 7.64 0.00 34.14 4.63
1538 1578 1.446907 ACGTGAGTACCACTACTCCG 58.553 55.000 11.21 12.95 46.03 4.63
1540 1580 1.808945 CGTGAGTACCACTACTCCGTT 59.191 52.381 11.21 0.00 46.03 4.44
1541 1581 3.002791 CGTGAGTACCACTACTCCGTTA 58.997 50.000 11.21 0.00 46.03 3.18
1562 1602 8.264632 CCGTTACTACTTTTTAGTTCGCATATC 58.735 37.037 0.00 0.00 0.00 1.63
1573 1613 3.127548 AGTTCGCATATCAGGTTTGCTTG 59.872 43.478 0.00 0.00 34.23 4.01
1702 1743 9.601217 AGTTGGTATTGTAGATGTTCATACTTC 57.399 33.333 0.00 0.00 0.00 3.01
1704 1745 9.599866 TTGGTATTGTAGATGTTCATACTTCTG 57.400 33.333 0.00 0.00 38.71 3.02
1777 1825 6.737254 ATATGTGAAGTAAAAAGACACGGG 57.263 37.500 0.00 0.00 34.72 5.28
1778 1826 2.614983 TGTGAAGTAAAAAGACACGGGC 59.385 45.455 0.00 0.00 34.72 6.13
1787 1835 1.477553 AAGACACGGGCGGAGTAATA 58.522 50.000 0.00 0.00 0.00 0.98
1810 1858 0.319083 TTTCCGCGGCTCTCTGTTTA 59.681 50.000 23.51 0.00 0.00 2.01
1881 1929 1.779061 TTGTGGAGGTGAAGGAGGGC 61.779 60.000 0.00 0.00 0.00 5.19
1930 1978 1.068588 CCGTGTGTCCTCTTTCTGTCA 59.931 52.381 0.00 0.00 0.00 3.58
1932 1980 3.194861 CGTGTGTCCTCTTTCTGTCAAA 58.805 45.455 0.00 0.00 0.00 2.69
1942 1990 9.106070 GTCCTCTTTCTGTCAAACTTTTTACTA 57.894 33.333 0.00 0.00 0.00 1.82
1944 1992 9.110502 CCTCTTTCTGTCAAACTTTTTACTACT 57.889 33.333 0.00 0.00 0.00 2.57
1964 2013 3.055530 ACTTTCTGGCTCTGTGTATCCTG 60.056 47.826 0.00 0.00 0.00 3.86
1965 2014 2.238084 TCTGGCTCTGTGTATCCTGT 57.762 50.000 0.00 0.00 0.00 4.00
2024 2073 3.659183 AGGACATCAAGGAAATCAGGG 57.341 47.619 0.00 0.00 0.00 4.45
2053 2102 1.002888 CAGGAAGAGAAGGCAAGCTCA 59.997 52.381 0.00 0.00 33.62 4.26
2069 2118 0.667993 CTCAAAAACGGAGCAAGCCA 59.332 50.000 0.00 0.00 0.00 4.75
2095 2144 3.709653 AGACACAAGACCAGGTACTCAAA 59.290 43.478 0.00 0.00 34.60 2.69
2098 2147 3.564225 CACAAGACCAGGTACTCAAAACC 59.436 47.826 0.00 0.00 34.60 3.27
2125 2174 1.668751 GAACAGACGGAGCAACAAACA 59.331 47.619 0.00 0.00 0.00 2.83
2231 2281 9.054580 ACCCAGAAAAGTAGGTAAATACATAGT 57.945 33.333 0.00 0.00 0.00 2.12
2232 2282 9.326413 CCCAGAAAAGTAGGTAAATACATAGTG 57.674 37.037 0.00 0.00 0.00 2.74
2233 2283 9.326413 CCAGAAAAGTAGGTAAATACATAGTGG 57.674 37.037 0.00 0.00 0.00 4.00
2234 2284 9.886132 CAGAAAAGTAGGTAAATACATAGTGGT 57.114 33.333 0.00 0.00 0.00 4.16
2262 2312 7.062584 ACATTAGATCAGGAGGGGTAGATAT 57.937 40.000 0.00 0.00 0.00 1.63
2274 2324 8.410623 AGGAGGGGTAGATATGTATATGAACTT 58.589 37.037 0.00 0.00 0.00 2.66
2307 2357 1.080093 CTTGCTTGCCACATGCCAG 60.080 57.895 0.00 0.00 40.16 4.85
2353 2403 2.287909 TGCGTATGTTTCAAAACCCTGC 60.288 45.455 3.33 3.54 38.11 4.85
2365 2415 2.435372 AACCCTGCAAGAGTGAAACA 57.565 45.000 0.00 0.00 41.43 2.83
2471 2521 8.737168 TGGTTCCATAAATACTCTGAATCAAG 57.263 34.615 0.00 0.00 0.00 3.02
2483 2533 5.703130 ACTCTGAATCAAGTCCTTTTGTAGC 59.297 40.000 0.00 0.00 0.00 3.58
2504 2554 4.767928 AGCCGATTTTACACACCCATTTTA 59.232 37.500 0.00 0.00 0.00 1.52
2637 2687 5.069251 ACTTCCAGAGAGAAGAACTTTTCGA 59.931 40.000 8.21 0.00 45.08 3.71
2676 2726 1.917872 ATAGACCAGATCTCCGCTCC 58.082 55.000 0.00 0.00 39.04 4.70
2689 2739 2.574399 GCTCCTCGCCTCGTTTCT 59.426 61.111 0.00 0.00 0.00 2.52
2693 2743 2.048222 CTCGCCTCGTTTCTGCCA 60.048 61.111 0.00 0.00 0.00 4.92
2694 2744 1.448540 CTCGCCTCGTTTCTGCCAT 60.449 57.895 0.00 0.00 0.00 4.40
2700 2750 2.426522 CCTCGTTTCTGCCATTTCTCA 58.573 47.619 0.00 0.00 0.00 3.27
2744 2802 6.526674 GTGGTAGAACTTTAAATTGATTGCGG 59.473 38.462 0.00 0.00 0.00 5.69
2890 2948 8.026607 GTGCCACTATAAGCAAACAGAAATTAA 58.973 33.333 0.00 0.00 41.48 1.40
2964 3022 4.182693 AGTTCAATGTGCATGACCAATG 57.817 40.909 0.00 0.00 39.49 2.82
3182 3241 1.227943 GCAAGACCAGCAGACCACA 60.228 57.895 0.00 0.00 0.00 4.17
3189 3248 2.887152 GACCAGCAGACCACAAATCTTT 59.113 45.455 0.00 0.00 0.00 2.52
3196 3255 2.365293 AGACCACAAATCTTTGGCCAAC 59.635 45.455 20.35 1.44 42.34 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.083997 GGGATCACCGGTGGCTCT 61.084 66.667 33.40 16.23 36.97 4.09
60 62 2.124403 GGCGACGGAGGTCCTCTA 60.124 66.667 18.58 0.00 40.17 2.43
76 78 4.778143 GTGTGGGCGGCAGTAGGG 62.778 72.222 12.47 0.00 0.00 3.53
95 97 1.373873 GTTGGTCGTCCCTTCCGTC 60.374 63.158 0.00 0.00 0.00 4.79
96 98 1.813728 GAGTTGGTCGTCCCTTCCGT 61.814 60.000 0.00 0.00 0.00 4.69
108 110 1.768684 ATGGTGTCGCAGGAGTTGGT 61.769 55.000 0.00 0.00 0.00 3.67
112 114 1.913262 TGGATGGTGTCGCAGGAGT 60.913 57.895 0.00 0.00 0.00 3.85
117 119 2.347114 CTGGTGGATGGTGTCGCA 59.653 61.111 0.00 0.00 0.00 5.10
122 124 1.134280 GGATCTCACTGGTGGATGGTG 60.134 57.143 0.70 0.00 0.00 4.17
123 125 1.207791 GGATCTCACTGGTGGATGGT 58.792 55.000 0.70 0.00 0.00 3.55
124 126 0.105593 CGGATCTCACTGGTGGATGG 59.894 60.000 0.70 0.00 0.00 3.51
206 208 3.461773 GGTGGCGAGGCTCTGCTA 61.462 66.667 23.42 18.03 0.00 3.49
226 228 1.081892 CTGTGTGGCCTTCGATGAAG 58.918 55.000 3.32 0.00 39.17 3.02
233 235 2.358737 CCCGACTGTGTGGCCTTC 60.359 66.667 3.32 0.00 0.00 3.46
234 236 4.643387 GCCCGACTGTGTGGCCTT 62.643 66.667 3.32 0.00 39.30 4.35
286 288 2.368011 CGAACCCTCCTTCCCCCTC 61.368 68.421 0.00 0.00 0.00 4.30
287 289 2.285442 CGAACCCTCCTTCCCCCT 60.285 66.667 0.00 0.00 0.00 4.79
288 290 2.285144 TCGAACCCTCCTTCCCCC 60.285 66.667 0.00 0.00 0.00 5.40
289 291 2.368011 CCTCGAACCCTCCTTCCCC 61.368 68.421 0.00 0.00 0.00 4.81
290 292 3.032667 GCCTCGAACCCTCCTTCCC 62.033 68.421 0.00 0.00 0.00 3.97
291 293 2.585153 GCCTCGAACCCTCCTTCC 59.415 66.667 0.00 0.00 0.00 3.46
292 294 2.184579 CGCCTCGAACCCTCCTTC 59.815 66.667 0.00 0.00 0.00 3.46
293 295 4.083862 GCGCCTCGAACCCTCCTT 62.084 66.667 0.00 0.00 0.00 3.36
336 338 9.901172 CCCAAAATCACTACTTTACTACCTATT 57.099 33.333 0.00 0.00 0.00 1.73
337 339 7.991460 GCCCAAAATCACTACTTTACTACCTAT 59.009 37.037 0.00 0.00 0.00 2.57
338 340 7.333323 GCCCAAAATCACTACTTTACTACCTA 58.667 38.462 0.00 0.00 0.00 3.08
339 341 6.178324 GCCCAAAATCACTACTTTACTACCT 58.822 40.000 0.00 0.00 0.00 3.08
340 342 5.356190 GGCCCAAAATCACTACTTTACTACC 59.644 44.000 0.00 0.00 0.00 3.18
341 343 5.356190 GGGCCCAAAATCACTACTTTACTAC 59.644 44.000 19.95 0.00 0.00 2.73
342 344 5.014333 TGGGCCCAAAATCACTACTTTACTA 59.986 40.000 26.33 0.00 0.00 1.82
343 345 4.202631 TGGGCCCAAAATCACTACTTTACT 60.203 41.667 26.33 0.00 0.00 2.24
344 346 4.083565 TGGGCCCAAAATCACTACTTTAC 58.916 43.478 26.33 0.00 0.00 2.01
345 347 4.390129 TGGGCCCAAAATCACTACTTTA 57.610 40.909 26.33 0.00 0.00 1.85
346 348 3.252554 TGGGCCCAAAATCACTACTTT 57.747 42.857 26.33 0.00 0.00 2.66
347 349 2.990740 TGGGCCCAAAATCACTACTT 57.009 45.000 26.33 0.00 0.00 2.24
348 350 2.990740 TTGGGCCCAAAATCACTACT 57.009 45.000 35.47 0.00 32.44 2.57
349 351 3.513515 TGAATTGGGCCCAAAATCACTAC 59.486 43.478 40.00 22.51 39.55 2.73
350 352 3.784178 TGAATTGGGCCCAAAATCACTA 58.216 40.909 40.00 21.29 39.55 2.74
351 353 2.618794 TGAATTGGGCCCAAAATCACT 58.381 42.857 40.00 20.84 39.55 3.41
352 354 3.632643 ATGAATTGGGCCCAAAATCAC 57.367 42.857 38.60 28.06 38.07 3.06
353 355 7.630005 AATATATGAATTGGGCCCAAAATCA 57.370 32.000 38.16 38.16 39.55 2.57
354 356 8.922931 AAAATATATGAATTGGGCCCAAAATC 57.077 30.769 40.00 35.31 39.55 2.17
381 383 9.273016 CGAGCTAGGATAAGAATTCCAATTTAA 57.727 33.333 0.65 0.00 35.59 1.52
382 384 7.878127 CCGAGCTAGGATAAGAATTCCAATTTA 59.122 37.037 7.14 0.00 35.59 1.40
383 385 6.712547 CCGAGCTAGGATAAGAATTCCAATTT 59.287 38.462 7.14 0.00 35.59 1.82
384 386 6.234177 CCGAGCTAGGATAAGAATTCCAATT 58.766 40.000 7.14 0.00 35.59 2.32
385 387 5.799213 CCGAGCTAGGATAAGAATTCCAAT 58.201 41.667 7.14 0.00 35.59 3.16
386 388 4.503296 GCCGAGCTAGGATAAGAATTCCAA 60.503 45.833 18.16 0.00 35.59 3.53
387 389 3.006967 GCCGAGCTAGGATAAGAATTCCA 59.993 47.826 18.16 0.00 35.59 3.53
388 390 3.591023 GCCGAGCTAGGATAAGAATTCC 58.409 50.000 18.16 0.00 0.00 3.01
389 391 3.259625 AGGCCGAGCTAGGATAAGAATTC 59.740 47.826 18.16 0.00 0.00 2.17
390 392 3.243724 AGGCCGAGCTAGGATAAGAATT 58.756 45.455 18.16 0.00 0.00 2.17
391 393 2.896039 AGGCCGAGCTAGGATAAGAAT 58.104 47.619 18.16 0.00 0.00 2.40
392 394 2.383442 AGGCCGAGCTAGGATAAGAA 57.617 50.000 18.16 0.00 0.00 2.52
393 395 2.375845 AGTAGGCCGAGCTAGGATAAGA 59.624 50.000 18.16 0.00 0.00 2.10
394 396 2.750712 GAGTAGGCCGAGCTAGGATAAG 59.249 54.545 18.16 0.00 0.00 1.73
395 397 2.792878 GAGTAGGCCGAGCTAGGATAA 58.207 52.381 18.16 0.00 0.00 1.75
396 398 1.338864 CGAGTAGGCCGAGCTAGGATA 60.339 57.143 18.16 5.61 0.00 2.59
397 399 0.606944 CGAGTAGGCCGAGCTAGGAT 60.607 60.000 18.16 6.66 0.00 3.24
398 400 1.227883 CGAGTAGGCCGAGCTAGGA 60.228 63.158 18.16 0.00 0.00 2.94
399 401 2.910345 GCGAGTAGGCCGAGCTAGG 61.910 68.421 8.78 8.78 0.00 3.02
400 402 1.725557 TTGCGAGTAGGCCGAGCTAG 61.726 60.000 0.00 0.00 0.00 3.42
401 403 1.725557 CTTGCGAGTAGGCCGAGCTA 61.726 60.000 0.00 0.00 0.00 3.32
402 404 3.068691 TTGCGAGTAGGCCGAGCT 61.069 61.111 0.00 0.00 0.00 4.09
403 405 2.356818 ATCTTGCGAGTAGGCCGAGC 62.357 60.000 0.00 0.01 0.00 5.03
404 406 0.596083 CATCTTGCGAGTAGGCCGAG 60.596 60.000 0.00 0.00 0.00 4.63
405 407 1.320344 ACATCTTGCGAGTAGGCCGA 61.320 55.000 0.00 0.00 0.00 5.54
406 408 0.460284 AACATCTTGCGAGTAGGCCG 60.460 55.000 0.00 0.00 0.00 6.13
407 409 2.474816 CTAACATCTTGCGAGTAGGCC 58.525 52.381 0.00 0.00 0.00 5.19
408 410 1.861575 GCTAACATCTTGCGAGTAGGC 59.138 52.381 0.00 0.00 0.00 3.93
409 411 2.101582 AGGCTAACATCTTGCGAGTAGG 59.898 50.000 0.00 0.00 0.00 3.18
410 412 3.444703 AGGCTAACATCTTGCGAGTAG 57.555 47.619 0.00 0.00 0.00 2.57
411 413 3.194755 TGAAGGCTAACATCTTGCGAGTA 59.805 43.478 0.00 0.00 0.00 2.59
412 414 2.028112 TGAAGGCTAACATCTTGCGAGT 60.028 45.455 0.00 0.00 0.00 4.18
413 415 2.621338 TGAAGGCTAACATCTTGCGAG 58.379 47.619 0.00 0.00 0.00 5.03
414 416 2.742053 GTTGAAGGCTAACATCTTGCGA 59.258 45.455 0.00 0.00 0.00 5.10
415 417 2.159517 GGTTGAAGGCTAACATCTTGCG 60.160 50.000 2.82 0.00 0.00 4.85
416 418 3.084786 AGGTTGAAGGCTAACATCTTGC 58.915 45.455 2.82 0.00 0.00 4.01
417 419 4.326826 TCAGGTTGAAGGCTAACATCTTG 58.673 43.478 2.82 5.75 0.00 3.02
418 420 4.640771 TCAGGTTGAAGGCTAACATCTT 57.359 40.909 2.82 0.00 0.00 2.40
419 421 4.851639 ATCAGGTTGAAGGCTAACATCT 57.148 40.909 2.82 0.00 0.00 2.90
420 422 5.880332 TGTAATCAGGTTGAAGGCTAACATC 59.120 40.000 2.82 0.00 0.00 3.06
421 423 5.815581 TGTAATCAGGTTGAAGGCTAACAT 58.184 37.500 2.82 0.00 0.00 2.71
422 424 5.235850 TGTAATCAGGTTGAAGGCTAACA 57.764 39.130 2.82 0.00 0.00 2.41
423 425 7.859325 TTATGTAATCAGGTTGAAGGCTAAC 57.141 36.000 0.00 0.00 0.00 2.34
424 426 7.067008 GCTTTATGTAATCAGGTTGAAGGCTAA 59.933 37.037 0.00 0.00 0.00 3.09
425 427 6.542370 GCTTTATGTAATCAGGTTGAAGGCTA 59.458 38.462 0.00 0.00 0.00 3.93
426 428 5.358160 GCTTTATGTAATCAGGTTGAAGGCT 59.642 40.000 0.00 0.00 0.00 4.58
427 429 5.125417 TGCTTTATGTAATCAGGTTGAAGGC 59.875 40.000 0.00 0.00 0.00 4.35
428 430 6.757897 TGCTTTATGTAATCAGGTTGAAGG 57.242 37.500 0.00 0.00 0.00 3.46
429 431 9.113838 ACTATGCTTTATGTAATCAGGTTGAAG 57.886 33.333 0.00 0.00 0.00 3.02
431 433 9.542462 GTACTATGCTTTATGTAATCAGGTTGA 57.458 33.333 0.00 0.00 0.00 3.18
432 434 9.547753 AGTACTATGCTTTATGTAATCAGGTTG 57.452 33.333 0.00 0.00 0.00 3.77
434 436 9.765795 GAAGTACTATGCTTTATGTAATCAGGT 57.234 33.333 0.00 0.00 0.00 4.00
435 437 9.988815 AGAAGTACTATGCTTTATGTAATCAGG 57.011 33.333 0.00 0.00 0.00 3.86
446 448 9.453572 TCAAATTGATCAGAAGTACTATGCTTT 57.546 29.630 0.00 0.00 0.00 3.51
447 449 9.453572 TTCAAATTGATCAGAAGTACTATGCTT 57.546 29.630 0.00 0.00 0.00 3.91
448 450 9.624373 ATTCAAATTGATCAGAAGTACTATGCT 57.376 29.630 0.00 0.00 0.00 3.79
459 461 8.863086 GGGAATGGAATATTCAAATTGATCAGA 58.137 33.333 17.07 0.00 0.00 3.27
460 462 8.867097 AGGGAATGGAATATTCAAATTGATCAG 58.133 33.333 17.07 0.00 0.00 2.90
461 463 8.786710 AGGGAATGGAATATTCAAATTGATCA 57.213 30.769 17.07 3.82 0.00 2.92
467 469 9.903190 AGGAAATAGGGAATGGAATATTCAAAT 57.097 29.630 17.07 7.33 0.00 2.32
468 470 9.728100 AAGGAAATAGGGAATGGAATATTCAAA 57.272 29.630 17.07 5.26 0.00 2.69
469 471 9.146586 CAAGGAAATAGGGAATGGAATATTCAA 57.853 33.333 17.07 6.38 0.00 2.69
470 472 8.510283 TCAAGGAAATAGGGAATGGAATATTCA 58.490 33.333 17.07 4.18 0.00 2.57
471 473 8.940397 TCAAGGAAATAGGGAATGGAATATTC 57.060 34.615 6.93 6.93 0.00 1.75
472 474 7.452813 GCTCAAGGAAATAGGGAATGGAATATT 59.547 37.037 0.00 0.00 0.00 1.28
473 475 6.950619 GCTCAAGGAAATAGGGAATGGAATAT 59.049 38.462 0.00 0.00 0.00 1.28
474 476 6.306987 GCTCAAGGAAATAGGGAATGGAATA 58.693 40.000 0.00 0.00 0.00 1.75
475 477 5.143369 GCTCAAGGAAATAGGGAATGGAAT 58.857 41.667 0.00 0.00 0.00 3.01
476 478 4.536765 GCTCAAGGAAATAGGGAATGGAA 58.463 43.478 0.00 0.00 0.00 3.53
477 479 3.433598 CGCTCAAGGAAATAGGGAATGGA 60.434 47.826 0.00 0.00 0.00 3.41
478 480 2.880890 CGCTCAAGGAAATAGGGAATGG 59.119 50.000 0.00 0.00 0.00 3.16
479 481 2.291741 GCGCTCAAGGAAATAGGGAATG 59.708 50.000 0.00 0.00 0.00 2.67
480 482 2.173569 AGCGCTCAAGGAAATAGGGAAT 59.826 45.455 2.64 0.00 0.00 3.01
481 483 1.559682 AGCGCTCAAGGAAATAGGGAA 59.440 47.619 2.64 0.00 0.00 3.97
482 484 1.204146 AGCGCTCAAGGAAATAGGGA 58.796 50.000 2.64 0.00 0.00 4.20
483 485 2.044123 AAGCGCTCAAGGAAATAGGG 57.956 50.000 12.06 0.00 0.00 3.53
484 486 3.009723 TGAAAGCGCTCAAGGAAATAGG 58.990 45.455 12.06 0.00 0.00 2.57
485 487 3.181506 GGTGAAAGCGCTCAAGGAAATAG 60.182 47.826 12.06 0.00 0.00 1.73
486 488 2.747446 GGTGAAAGCGCTCAAGGAAATA 59.253 45.455 12.06 0.00 0.00 1.40
487 489 1.541588 GGTGAAAGCGCTCAAGGAAAT 59.458 47.619 12.06 0.00 0.00 2.17
488 490 0.951558 GGTGAAAGCGCTCAAGGAAA 59.048 50.000 12.06 0.00 0.00 3.13
489 491 0.179032 TGGTGAAAGCGCTCAAGGAA 60.179 50.000 12.06 0.00 36.92 3.36
490 492 0.036732 ATGGTGAAAGCGCTCAAGGA 59.963 50.000 12.06 0.00 36.92 3.36
491 493 0.883833 AATGGTGAAAGCGCTCAAGG 59.116 50.000 12.06 0.00 36.92 3.61
492 494 3.492313 GTTAATGGTGAAAGCGCTCAAG 58.508 45.455 12.06 0.00 36.92 3.02
493 495 2.227865 GGTTAATGGTGAAAGCGCTCAA 59.772 45.455 12.06 0.00 36.92 3.02
494 496 1.810151 GGTTAATGGTGAAAGCGCTCA 59.190 47.619 12.06 3.76 36.92 4.26
495 497 1.132453 GGGTTAATGGTGAAAGCGCTC 59.868 52.381 12.06 0.00 36.92 5.03
496 498 1.173913 GGGTTAATGGTGAAAGCGCT 58.826 50.000 2.64 2.64 36.92 5.92
497 499 0.885196 TGGGTTAATGGTGAAAGCGC 59.115 50.000 0.00 0.00 36.92 5.92
498 500 1.201414 GGTGGGTTAATGGTGAAAGCG 59.799 52.381 0.00 0.00 36.92 4.68
499 501 1.548719 GGGTGGGTTAATGGTGAAAGC 59.451 52.381 0.00 0.00 0.00 3.51
500 502 3.169512 AGGGTGGGTTAATGGTGAAAG 57.830 47.619 0.00 0.00 0.00 2.62
501 503 3.559597 CGTAGGGTGGGTTAATGGTGAAA 60.560 47.826 0.00 0.00 0.00 2.69
502 504 2.027007 CGTAGGGTGGGTTAATGGTGAA 60.027 50.000 0.00 0.00 0.00 3.18
503 505 1.555992 CGTAGGGTGGGTTAATGGTGA 59.444 52.381 0.00 0.00 0.00 4.02
504 506 1.555992 TCGTAGGGTGGGTTAATGGTG 59.444 52.381 0.00 0.00 0.00 4.17
505 507 1.835531 CTCGTAGGGTGGGTTAATGGT 59.164 52.381 0.00 0.00 0.00 3.55
506 508 1.140252 CCTCGTAGGGTGGGTTAATGG 59.860 57.143 0.00 0.00 0.00 3.16
507 509 2.614829 CCTCGTAGGGTGGGTTAATG 57.385 55.000 0.00 0.00 0.00 1.90
561 563 5.649782 AAAATGGTATGAGAAAGCACCTG 57.350 39.130 0.00 0.00 32.04 4.00
572 574 6.535150 GTCACTCGAGATCAAAAATGGTATGA 59.465 38.462 21.68 3.87 0.00 2.15
583 585 5.451937 GGACATAATGGTCACTCGAGATCAA 60.452 44.000 21.68 2.59 39.59 2.57
584 586 4.038042 GGACATAATGGTCACTCGAGATCA 59.962 45.833 21.68 4.50 39.59 2.92
585 587 4.038042 TGGACATAATGGTCACTCGAGATC 59.962 45.833 21.68 8.47 39.59 2.75
586 588 3.960755 TGGACATAATGGTCACTCGAGAT 59.039 43.478 21.68 0.00 39.59 2.75
587 589 3.361786 TGGACATAATGGTCACTCGAGA 58.638 45.455 21.68 0.00 39.59 4.04
626 628 2.107552 CTCCCAGTTTGTCACCCCTTTA 59.892 50.000 0.00 0.00 0.00 1.85
683 686 9.408069 AGCAAGCGTAAAGATATAAGTATGTAC 57.592 33.333 0.00 0.00 0.00 2.90
684 687 9.976511 AAGCAAGCGTAAAGATATAAGTATGTA 57.023 29.630 0.00 0.00 0.00 2.29
685 688 8.888579 AAGCAAGCGTAAAGATATAAGTATGT 57.111 30.769 0.00 0.00 0.00 2.29
686 689 9.197694 AGAAGCAAGCGTAAAGATATAAGTATG 57.802 33.333 0.00 0.00 0.00 2.39
687 690 9.413048 GAGAAGCAAGCGTAAAGATATAAGTAT 57.587 33.333 0.00 0.00 0.00 2.12
688 691 7.590322 CGAGAAGCAAGCGTAAAGATATAAGTA 59.410 37.037 0.00 0.00 0.00 2.24
689 692 6.418226 CGAGAAGCAAGCGTAAAGATATAAGT 59.582 38.462 0.00 0.00 0.00 2.24
690 693 6.418226 ACGAGAAGCAAGCGTAAAGATATAAG 59.582 38.462 0.00 0.00 36.37 1.73
691 694 6.270815 ACGAGAAGCAAGCGTAAAGATATAA 58.729 36.000 0.00 0.00 36.37 0.98
755 769 3.111098 GAGAATCAATGCAAATGACCGC 58.889 45.455 7.63 2.54 33.17 5.68
779 793 4.147449 TGATCCACCGGCGCTCTG 62.147 66.667 7.64 0.00 0.00 3.35
780 794 4.148825 GTGATCCACCGGCGCTCT 62.149 66.667 7.64 0.00 0.00 4.09
784 798 3.576356 GCATGTGATCCACCGGCG 61.576 66.667 0.00 0.00 32.73 6.46
785 799 2.124570 AGCATGTGATCCACCGGC 60.125 61.111 0.00 0.00 34.29 6.13
786 800 2.475466 GCAGCATGTGATCCACCGG 61.475 63.158 0.00 0.00 39.31 5.28
813 827 2.218302 CAGCGCTTTTCAGATCGAGATC 59.782 50.000 7.50 5.00 38.09 2.75
814 828 2.200067 CAGCGCTTTTCAGATCGAGAT 58.800 47.619 7.50 0.00 0.00 2.75
815 829 1.633561 CAGCGCTTTTCAGATCGAGA 58.366 50.000 7.50 0.00 0.00 4.04
816 830 0.649475 CCAGCGCTTTTCAGATCGAG 59.351 55.000 7.50 0.00 0.00 4.04
817 831 0.246360 TCCAGCGCTTTTCAGATCGA 59.754 50.000 7.50 0.00 0.00 3.59
818 832 0.649475 CTCCAGCGCTTTTCAGATCG 59.351 55.000 7.50 0.00 0.00 3.69
857 871 2.598589 GAAGGCATGTCACGTACGTAA 58.401 47.619 22.34 2.95 0.00 3.18
1130 1144 1.002430 CTGGGCTACTGTTGCTCAAGA 59.998 52.381 17.02 0.00 40.71 3.02
1145 1159 2.747855 CGTGGAAGGAAGCTGGGC 60.748 66.667 0.00 0.00 0.00 5.36
1149 1163 1.179814 AGTCGTCGTGGAAGGAAGCT 61.180 55.000 0.00 0.00 30.33 3.74
1150 1164 0.733223 GAGTCGTCGTGGAAGGAAGC 60.733 60.000 0.00 0.00 30.33 3.86
1186 1221 2.031012 CACCCGACAGCTTCTGCA 59.969 61.111 0.00 0.00 42.74 4.41
1268 1303 1.243902 TTAAAACCCGAGCAAGCAGG 58.756 50.000 0.00 0.00 0.00 4.85
1270 1305 1.543802 CCATTAAAACCCGAGCAAGCA 59.456 47.619 0.00 0.00 0.00 3.91
1277 1312 1.292061 CGATCGCCATTAAAACCCGA 58.708 50.000 0.26 0.00 0.00 5.14
1278 1313 0.306533 CCGATCGCCATTAAAACCCG 59.693 55.000 10.32 0.00 0.00 5.28
1306 1341 2.594303 CTCCTGCAAACCACCGCA 60.594 61.111 0.00 0.00 36.52 5.69
1307 1342 4.043200 GCTCCTGCAAACCACCGC 62.043 66.667 0.00 0.00 39.41 5.68
1308 1343 2.281761 AGCTCCTGCAAACCACCG 60.282 61.111 0.00 0.00 42.74 4.94
1488 1528 3.112709 GACCTGCGCCTCAACGTC 61.113 66.667 4.18 0.00 34.88 4.34
1540 1580 8.472413 ACCTGATATGCGAACTAAAAAGTAGTA 58.528 33.333 0.00 0.00 0.00 1.82
1541 1581 7.328737 ACCTGATATGCGAACTAAAAAGTAGT 58.671 34.615 0.00 0.00 0.00 2.73
1562 1602 7.595311 AAAAGTTTAACTTCAAGCAAACCTG 57.405 32.000 10.98 0.00 37.47 4.00
1761 1809 1.202675 TCCGCCCGTGTCTTTTTACTT 60.203 47.619 0.00 0.00 0.00 2.24
1772 1820 0.458669 ACTGTATTACTCCGCCCGTG 59.541 55.000 0.00 0.00 0.00 4.94
1787 1835 2.048127 GAGAGCCGCGGAAACTGT 60.048 61.111 33.48 15.78 0.00 3.55
1828 1876 6.332630 GGTAACTTAACCGTCAGCATAAGTA 58.667 40.000 0.00 0.00 37.55 2.24
1829 1877 5.173664 GGTAACTTAACCGTCAGCATAAGT 58.826 41.667 0.00 0.00 39.57 2.24
1830 1878 5.713822 GGTAACTTAACCGTCAGCATAAG 57.286 43.478 0.00 0.00 0.00 1.73
1881 1929 1.633852 GCTGCACTTCAGAAGCGAGG 61.634 60.000 10.33 0.00 45.72 4.63
1930 1978 7.556635 ACAGAGCCAGAAAGTAGTAAAAAGTTT 59.443 33.333 0.00 0.00 0.00 2.66
1932 1980 6.483640 CACAGAGCCAGAAAGTAGTAAAAAGT 59.516 38.462 0.00 0.00 0.00 2.66
1942 1990 3.055530 CAGGATACACAGAGCCAGAAAGT 60.056 47.826 0.00 0.00 41.41 2.66
1944 1992 2.906389 ACAGGATACACAGAGCCAGAAA 59.094 45.455 0.00 0.00 41.41 2.52
1964 2013 6.697019 ACACAATGTGAGCTTGAAATGTTTAC 59.303 34.615 21.34 0.00 36.96 2.01
1965 2014 6.804677 ACACAATGTGAGCTTGAAATGTTTA 58.195 32.000 21.34 0.00 36.96 2.01
2024 2073 0.901124 TTCTCTTCCTGGAGAGCAGC 59.099 55.000 14.57 0.00 42.37 5.25
2053 2102 0.467290 TCCTGGCTTGCTCCGTTTTT 60.467 50.000 0.00 0.00 0.00 1.94
2069 2118 1.807814 ACCTGGTCTTGTGTCTTCCT 58.192 50.000 0.00 0.00 0.00 3.36
2095 2144 0.320421 CCGTCTGTTCATCACCGGTT 60.320 55.000 2.97 0.00 33.46 4.44
2098 2147 1.078759 GCTCCGTCTGTTCATCACCG 61.079 60.000 0.00 0.00 0.00 4.94
2125 2174 0.604578 AATTTCATGCTTGCACCGCT 59.395 45.000 8.46 0.00 0.00 5.52
2231 2281 5.394738 CCCTCCTGATCTAATGTAGTACCA 58.605 45.833 0.00 0.00 0.00 3.25
2232 2282 4.773149 CCCCTCCTGATCTAATGTAGTACC 59.227 50.000 0.00 0.00 0.00 3.34
2233 2283 5.395611 ACCCCTCCTGATCTAATGTAGTAC 58.604 45.833 0.00 0.00 0.00 2.73
2234 2284 5.681494 ACCCCTCCTGATCTAATGTAGTA 57.319 43.478 0.00 0.00 0.00 1.82
2235 2285 4.561254 ACCCCTCCTGATCTAATGTAGT 57.439 45.455 0.00 0.00 0.00 2.73
2236 2286 5.893500 TCTACCCCTCCTGATCTAATGTAG 58.106 45.833 0.00 0.00 0.00 2.74
2262 2312 5.220643 CGATGTGCAAGCAAGTTCATATACA 60.221 40.000 0.00 0.00 0.00 2.29
2274 2324 3.356267 AAGCGCGATGTGCAAGCA 61.356 55.556 12.10 0.00 46.97 3.91
2307 2357 4.191544 TCAGTTTGCTGATGCTGGTATAC 58.808 43.478 0.00 0.00 45.94 1.47
2335 2385 5.195001 TCTTGCAGGGTTTTGAAACATAC 57.805 39.130 8.68 0.00 40.63 2.39
2338 2388 3.096092 ACTCTTGCAGGGTTTTGAAACA 58.904 40.909 8.68 0.00 40.63 2.83
2471 2521 5.049267 TGTGTAAAATCGGCTACAAAAGGAC 60.049 40.000 0.00 0.00 30.11 3.85
2483 2533 7.815068 TGAAATAAAATGGGTGTGTAAAATCGG 59.185 33.333 0.00 0.00 0.00 4.18
2625 2675 9.939802 ATACACTAACCTATTCGAAAAGTTCTT 57.060 29.630 0.00 0.00 0.00 2.52
2676 2726 1.021390 AATGGCAGAAACGAGGCGAG 61.021 55.000 0.00 0.00 0.00 5.03
2689 2739 1.689984 TGTGCAACTGAGAAATGGCA 58.310 45.000 0.00 0.00 38.04 4.92
2693 2743 4.401022 TCTGGATTGTGCAACTGAGAAAT 58.599 39.130 0.00 0.00 38.04 2.17
2694 2744 3.819368 TCTGGATTGTGCAACTGAGAAA 58.181 40.909 0.00 0.00 38.04 2.52
2700 2750 2.559668 CACCATTCTGGATTGTGCAACT 59.440 45.455 0.00 0.00 40.96 3.16
2744 2802 2.854805 GCGTTCTCTGTTCTTGCCAAAC 60.855 50.000 0.00 0.00 0.00 2.93
2890 2948 5.242171 TGGCTTAAATCATGCAATCGATGAT 59.758 36.000 0.00 0.00 41.41 2.45
3182 3241 3.960102 TCAGAAGTGTTGGCCAAAGATTT 59.040 39.130 22.47 12.80 0.00 2.17
3189 3248 2.957402 ATCTTCAGAAGTGTTGGCCA 57.043 45.000 0.00 0.00 0.00 5.36
3196 3255 7.767659 TCATGAATGGTAGAATCTTCAGAAGTG 59.232 37.037 10.09 0.00 31.69 3.16


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

AutoCloner maintained by Alex Coulton.