Multiple sequence alignment - TraesCS7D01G078800

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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 TraesCS7D01G078800 chr7D 100.000 3163 0 0 1 3163 46587761 46584599 0.000000e+00 5842.0
1 TraesCS7D01G078800 chr7D 80.545 1100 88 68 879 1899 46671322 46670270 0.000000e+00 730.0
2 TraesCS7D01G078800 chr7D 96.262 214 7 1 1630 1843 46711925 46711713 1.810000e-92 350.0
3 TraesCS7D01G078800 chr4A 88.181 2166 105 59 563 2615 660653418 660655545 0.000000e+00 2442.0
4 TraesCS7D01G078800 chr4A 81.657 1074 81 63 812 1843 660624184 660625183 0.000000e+00 785.0
5 TraesCS7D01G078800 chr4A 88.250 400 28 8 2776 3163 660655660 660656052 7.990000e-126 460.0
6 TraesCS7D01G078800 chr4A 93.151 219 12 3 1626 1843 660452655 660452871 5.090000e-83 318.0
7 TraesCS7D01G078800 chr7A 86.023 2268 149 72 591 2751 48755168 48757374 0.000000e+00 2278.0
8 TraesCS7D01G078800 chr7A 82.544 1077 89 51 812 1832 48715034 48716067 0.000000e+00 856.0
9 TraesCS7D01G078800 chr7A 80.086 934 101 45 944 1836 48583211 48584100 1.610000e-172 616.0
10 TraesCS7D01G078800 chr7A 90.499 421 29 5 2751 3163 48757337 48757754 2.150000e-151 545.0
11 TraesCS7D01G078800 chr7A 93.953 215 10 3 1630 1843 48526181 48526393 3.940000e-84 322.0
12 TraesCS7D01G078800 chr7A 83.476 351 43 7 18 355 48754120 48754468 2.370000e-81 313.0
13 TraesCS7D01G078800 chr7A 95.000 60 3 0 351 410 185372553 185372494 9.340000e-16 95.3
14 TraesCS7D01G078800 chr3B 89.865 148 13 1 1376 1523 191290488 191290633 4.160000e-44 189.0
15 TraesCS7D01G078800 chr3B 96.774 62 2 0 349 410 780308614 780308553 1.550000e-18 104.0
16 TraesCS7D01G078800 chr3B 95.161 62 3 0 349 410 780333037 780332976 7.220000e-17 99.0
17 TraesCS7D01G078800 chr1A 75.073 341 41 22 1051 1372 71709905 71709590 5.540000e-23 119.0
18 TraesCS7D01G078800 chr6D 95.312 64 2 1 348 410 461324928 461324991 2.010000e-17 100.0
19 TraesCS7D01G078800 chr7B 95.082 61 3 0 350 410 720349768 720349708 2.600000e-16 97.1
20 TraesCS7D01G078800 chr6B 95.082 61 3 0 350 410 178243485 178243425 2.600000e-16 97.1
21 TraesCS7D01G078800 chr3D 95.082 61 3 0 350 410 508189453 508189513 2.600000e-16 97.1
22 TraesCS7D01G078800 chr1B 93.548 62 4 0 349 410 11632729 11632668 3.360000e-15 93.5
23 TraesCS7D01G078800 chr2B 89.706 68 7 0 343 410 184906848 184906781 1.560000e-13 87.9


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 TraesCS7D01G078800 chr7D 46584599 46587761 3162 True 5842.000000 5842 100.0000 1 3163 1 chr7D.!!$R1 3162
1 TraesCS7D01G078800 chr7D 46670270 46671322 1052 True 730.000000 730 80.5450 879 1899 1 chr7D.!!$R2 1020
2 TraesCS7D01G078800 chr4A 660653418 660656052 2634 False 1451.000000 2442 88.2155 563 3163 2 chr4A.!!$F3 2600
3 TraesCS7D01G078800 chr4A 660624184 660625183 999 False 785.000000 785 81.6570 812 1843 1 chr4A.!!$F2 1031
4 TraesCS7D01G078800 chr7A 48754120 48757754 3634 False 1045.333333 2278 86.6660 18 3163 3 chr7A.!!$F4 3145
5 TraesCS7D01G078800 chr7A 48715034 48716067 1033 False 856.000000 856 82.5440 812 1832 1 chr7A.!!$F3 1020
6 TraesCS7D01G078800 chr7A 48583211 48584100 889 False 616.000000 616 80.0860 944 1836 1 chr7A.!!$F2 892

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
291 292 0.036010 AACAAGATCCTCTGTGGCGG 60.036 55.0 0.00 0.00 35.26 6.13 F
340 354 0.165944 GTGTACTTGTGGCGTGCATC 59.834 55.0 0.00 0.00 30.03 3.91 F
353 367 0.168128 GTGCATCGTAGGCGCTTTTT 59.832 50.0 7.64 0.00 38.67 1.94 F
1058 1795 0.183971 ACTCTCAGATCGGATCGGGT 59.816 55.0 16.34 4.92 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 2350 0.034059 GATCTTGCCGGATGGATCGT 59.966 55.0 5.05 0.0 37.49 3.73 R
1552 2372 0.108804 ACGAACACTTGGCGATCGAT 60.109 50.0 21.57 0.0 37.27 3.59 R
1553 2373 0.731514 GACGAACACTTGGCGATCGA 60.732 55.0 21.57 0.0 37.27 3.59 R
2741 3657 0.252421 TCCTGCAGATGGGTCACTCT 60.252 55.0 17.39 0.0 0.00 3.24 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
18 19 3.788672 CCTGCAGACCCAATCCTAC 57.211 57.895 17.39 0.00 0.00 3.18
19 20 0.911769 CCTGCAGACCCAATCCTACA 59.088 55.000 17.39 0.00 0.00 2.74
20 21 1.407437 CCTGCAGACCCAATCCTACAC 60.407 57.143 17.39 0.00 0.00 2.90
21 22 1.556911 CTGCAGACCCAATCCTACACT 59.443 52.381 8.42 0.00 0.00 3.55
22 23 1.278985 TGCAGACCCAATCCTACACTG 59.721 52.381 0.00 0.00 0.00 3.66
38 39 2.840974 CTGGCCACAGTTTAGACGG 58.159 57.895 0.00 0.00 39.92 4.79
56 57 3.353836 GTTCCGCAAGCGCAAGGA 61.354 61.111 11.47 9.76 38.40 3.36
101 102 0.462759 GATCGGTGCAAGGGAAGGAG 60.463 60.000 0.00 0.00 0.00 3.69
111 112 0.912006 AGGGAAGGAGGAAGGCTCAC 60.912 60.000 0.00 0.00 0.00 3.51
114 115 1.283321 GGAAGGAGGAAGGCTCACATT 59.717 52.381 0.00 0.00 0.00 2.71
135 136 2.176273 GCAGGAGCATGCACGGTAG 61.176 63.158 21.98 5.51 45.77 3.18
154 155 1.961180 GCTGGGCACTATGACGAGGT 61.961 60.000 0.00 0.00 31.26 3.85
171 172 0.966875 GGTGAGTGGCATGCAATGGA 60.967 55.000 21.36 0.00 46.86 3.41
186 187 7.359765 GCATGCAATGGAAACTATTTATCATGC 60.360 37.037 14.21 15.51 46.86 4.06
254 255 0.176680 GATTGCCAGCGAGGAGAAGA 59.823 55.000 2.12 0.00 41.22 2.87
255 256 0.177604 ATTGCCAGCGAGGAGAAGAG 59.822 55.000 2.12 0.00 41.22 2.85
256 257 1.188219 TTGCCAGCGAGGAGAAGAGT 61.188 55.000 2.12 0.00 41.22 3.24
267 268 2.175202 GGAGAAGAGTTCCAGCTCTCA 58.825 52.381 3.27 0.00 44.34 3.27
268 269 2.564947 GGAGAAGAGTTCCAGCTCTCAA 59.435 50.000 3.27 0.00 44.34 3.02
270 271 4.323409 GGAGAAGAGTTCCAGCTCTCAATT 60.323 45.833 3.27 0.00 44.34 2.32
284 285 5.045724 AGCTCTCAATTGAACAAGATCCTCT 60.046 40.000 9.88 0.00 0.00 3.69
285 286 5.064962 GCTCTCAATTGAACAAGATCCTCTG 59.935 44.000 9.88 0.00 0.00 3.35
288 289 5.005740 TCAATTGAACAAGATCCTCTGTGG 58.994 41.667 5.45 0.00 37.10 4.17
289 290 2.479566 TGAACAAGATCCTCTGTGGC 57.520 50.000 0.00 0.00 35.26 5.01
290 291 1.338105 TGAACAAGATCCTCTGTGGCG 60.338 52.381 0.00 0.00 35.26 5.69
291 292 0.036010 AACAAGATCCTCTGTGGCGG 60.036 55.000 0.00 0.00 35.26 6.13
292 293 1.194781 ACAAGATCCTCTGTGGCGGT 61.195 55.000 0.00 0.00 35.26 5.68
294 295 2.512515 GATCCTCTGTGGCGGTGC 60.513 66.667 0.00 0.00 35.26 5.01
295 296 3.315142 GATCCTCTGTGGCGGTGCA 62.315 63.158 0.00 0.00 35.26 4.57
296 297 2.803155 GATCCTCTGTGGCGGTGCAA 62.803 60.000 0.00 0.00 35.26 4.08
340 354 0.165944 GTGTACTTGTGGCGTGCATC 59.834 55.000 0.00 0.00 30.03 3.91
343 357 0.244178 TACTTGTGGCGTGCATCGTA 59.756 50.000 9.76 0.00 42.13 3.43
346 360 3.564027 GTGGCGTGCATCGTAGGC 61.564 66.667 9.76 3.82 42.13 3.93
350 364 2.885644 CGTGCATCGTAGGCGCTT 60.886 61.111 7.64 0.52 39.53 4.68
351 365 2.452813 CGTGCATCGTAGGCGCTTT 61.453 57.895 7.64 0.00 39.53 3.51
352 366 1.794222 GTGCATCGTAGGCGCTTTT 59.206 52.632 7.64 0.00 38.67 2.27
353 367 0.168128 GTGCATCGTAGGCGCTTTTT 59.832 50.000 7.64 0.00 38.67 1.94
376 390 6.959671 TTTTTGCAACGAAGTCAAAAGAAT 57.040 29.167 0.00 0.00 45.00 2.40
377 391 6.959671 TTTTGCAACGAAGTCAAAAGAATT 57.040 29.167 0.00 0.00 45.00 2.17
378 392 5.947503 TTGCAACGAAGTCAAAAGAATTG 57.052 34.783 0.00 0.00 45.00 2.32
379 393 3.796178 TGCAACGAAGTCAAAAGAATTGC 59.204 39.130 0.00 0.00 45.00 3.56
380 394 3.182372 GCAACGAAGTCAAAAGAATTGCC 59.818 43.478 0.00 0.00 45.00 4.52
381 395 4.610945 CAACGAAGTCAAAAGAATTGCCT 58.389 39.130 0.00 0.00 45.00 4.75
382 396 4.489679 ACGAAGTCAAAAGAATTGCCTC 57.510 40.909 0.00 0.00 29.74 4.70
383 397 3.882888 ACGAAGTCAAAAGAATTGCCTCA 59.117 39.130 0.00 0.00 29.74 3.86
384 398 4.520492 ACGAAGTCAAAAGAATTGCCTCAT 59.480 37.500 0.00 0.00 29.74 2.90
385 399 5.091431 CGAAGTCAAAAGAATTGCCTCATC 58.909 41.667 0.00 0.00 0.00 2.92
386 400 4.691860 AGTCAAAAGAATTGCCTCATCG 57.308 40.909 0.00 0.00 0.00 3.84
387 401 4.326826 AGTCAAAAGAATTGCCTCATCGA 58.673 39.130 0.00 0.00 0.00 3.59
388 402 4.946157 AGTCAAAAGAATTGCCTCATCGAT 59.054 37.500 0.00 0.00 0.00 3.59
389 403 5.416952 AGTCAAAAGAATTGCCTCATCGATT 59.583 36.000 0.00 0.00 0.00 3.34
390 404 6.599244 AGTCAAAAGAATTGCCTCATCGATTA 59.401 34.615 0.00 0.00 0.00 1.75
391 405 7.121168 AGTCAAAAGAATTGCCTCATCGATTAA 59.879 33.333 0.00 0.00 0.00 1.40
392 406 7.917505 GTCAAAAGAATTGCCTCATCGATTAAT 59.082 33.333 0.00 0.00 0.00 1.40
393 407 8.469200 TCAAAAGAATTGCCTCATCGATTAATT 58.531 29.630 0.00 0.00 0.00 1.40
394 408 9.734620 CAAAAGAATTGCCTCATCGATTAATTA 57.265 29.630 0.00 0.00 0.00 1.40
396 410 9.956720 AAAGAATTGCCTCATCGATTAATTAAG 57.043 29.630 3.94 0.00 0.00 1.85
397 411 8.908786 AGAATTGCCTCATCGATTAATTAAGA 57.091 30.769 3.94 0.00 0.00 2.10
398 412 9.342308 AGAATTGCCTCATCGATTAATTAAGAA 57.658 29.630 3.94 0.00 0.00 2.52
399 413 9.604626 GAATTGCCTCATCGATTAATTAAGAAG 57.395 33.333 3.94 0.00 0.00 2.85
400 414 8.908786 ATTGCCTCATCGATTAATTAAGAAGA 57.091 30.769 3.94 3.72 0.00 2.87
401 415 8.731275 TTGCCTCATCGATTAATTAAGAAGAA 57.269 30.769 3.94 0.00 0.00 2.52
402 416 8.370493 TGCCTCATCGATTAATTAAGAAGAAG 57.630 34.615 3.94 1.26 0.00 2.85
403 417 8.204160 TGCCTCATCGATTAATTAAGAAGAAGA 58.796 33.333 3.94 5.03 0.00 2.87
404 418 8.707839 GCCTCATCGATTAATTAAGAAGAAGAG 58.292 37.037 16.89 16.89 0.00 2.85
405 419 9.973450 CCTCATCGATTAATTAAGAAGAAGAGA 57.027 33.333 21.25 12.30 0.00 3.10
418 432 9.886132 TTAAGAAGAAGAGAATTGTATGTACCC 57.114 33.333 0.00 0.00 0.00 3.69
419 433 6.890293 AGAAGAAGAGAATTGTATGTACCCC 58.110 40.000 0.00 0.00 0.00 4.95
420 434 6.674419 AGAAGAAGAGAATTGTATGTACCCCT 59.326 38.462 0.00 0.00 0.00 4.79
421 435 7.844779 AGAAGAAGAGAATTGTATGTACCCCTA 59.155 37.037 0.00 0.00 0.00 3.53
422 436 8.568617 AAGAAGAGAATTGTATGTACCCCTAT 57.431 34.615 0.00 0.00 0.00 2.57
423 437 7.967908 AGAAGAGAATTGTATGTACCCCTATG 58.032 38.462 0.00 0.00 0.00 2.23
424 438 7.789831 AGAAGAGAATTGTATGTACCCCTATGA 59.210 37.037 0.00 0.00 0.00 2.15
425 439 7.304497 AGAGAATTGTATGTACCCCTATGAC 57.696 40.000 0.00 0.00 0.00 3.06
426 440 6.844388 AGAGAATTGTATGTACCCCTATGACA 59.156 38.462 0.00 0.00 0.00 3.58
427 441 7.514127 AGAGAATTGTATGTACCCCTATGACAT 59.486 37.037 0.00 0.00 37.55 3.06
428 442 8.736097 AGAATTGTATGTACCCCTATGACATA 57.264 34.615 0.00 0.00 35.48 2.29
429 443 9.338968 AGAATTGTATGTACCCCTATGACATAT 57.661 33.333 0.00 0.00 38.11 1.78
430 444 9.601217 GAATTGTATGTACCCCTATGACATATC 57.399 37.037 0.00 0.00 38.11 1.63
431 445 8.917414 ATTGTATGTACCCCTATGACATATCT 57.083 34.615 0.00 0.00 38.11 1.98
432 446 8.736097 TTGTATGTACCCCTATGACATATCTT 57.264 34.615 0.00 0.00 38.11 2.40
433 447 8.362464 TGTATGTACCCCTATGACATATCTTC 57.638 38.462 0.00 0.00 38.11 2.87
434 448 6.875972 ATGTACCCCTATGACATATCTTCC 57.124 41.667 0.00 0.00 32.07 3.46
435 449 5.977533 TGTACCCCTATGACATATCTTCCT 58.022 41.667 0.00 0.00 0.00 3.36
436 450 7.111136 TGTACCCCTATGACATATCTTCCTA 57.889 40.000 0.00 0.00 0.00 2.94
437 451 6.952358 TGTACCCCTATGACATATCTTCCTAC 59.048 42.308 0.00 0.00 0.00 3.18
438 452 5.977533 ACCCCTATGACATATCTTCCTACA 58.022 41.667 0.00 0.00 0.00 2.74
439 453 5.780793 ACCCCTATGACATATCTTCCTACAC 59.219 44.000 0.00 0.00 0.00 2.90
440 454 6.019748 CCCCTATGACATATCTTCCTACACT 58.980 44.000 0.00 0.00 0.00 3.55
441 455 6.498651 CCCCTATGACATATCTTCCTACACTT 59.501 42.308 0.00 0.00 0.00 3.16
442 456 7.382110 CCCTATGACATATCTTCCTACACTTG 58.618 42.308 0.00 0.00 0.00 3.16
443 457 7.015682 CCCTATGACATATCTTCCTACACTTGT 59.984 40.741 0.00 0.00 0.00 3.16
444 458 9.078990 CCTATGACATATCTTCCTACACTTGTA 57.921 37.037 0.00 0.00 0.00 2.41
445 459 9.900710 CTATGACATATCTTCCTACACTTGTAC 57.099 37.037 0.00 0.00 0.00 2.90
446 460 7.956328 TGACATATCTTCCTACACTTGTACT 57.044 36.000 0.00 0.00 0.00 2.73
447 461 9.642343 ATGACATATCTTCCTACACTTGTACTA 57.358 33.333 0.00 0.00 0.00 1.82
448 462 9.642343 TGACATATCTTCCTACACTTGTACTAT 57.358 33.333 0.00 0.00 0.00 2.12
467 481 9.636789 TGTACTATATGTAATGTCTAGTGGTGT 57.363 33.333 0.00 0.00 32.25 4.16
473 487 6.720112 TGTAATGTCTAGTGGTGTATACCC 57.280 41.667 6.15 2.04 46.96 3.69
474 488 5.599656 TGTAATGTCTAGTGGTGTATACCCC 59.400 44.000 6.15 0.00 46.96 4.95
475 489 4.554553 ATGTCTAGTGGTGTATACCCCT 57.445 45.455 6.15 2.24 46.96 4.79
476 490 5.674799 ATGTCTAGTGGTGTATACCCCTA 57.325 43.478 6.15 3.42 46.96 3.53
477 491 5.674799 TGTCTAGTGGTGTATACCCCTAT 57.325 43.478 6.15 0.00 46.96 2.57
478 492 6.034442 TGTCTAGTGGTGTATACCCCTATT 57.966 41.667 6.15 0.00 46.96 1.73
479 493 7.165495 TGTCTAGTGGTGTATACCCCTATTA 57.835 40.000 6.15 0.00 46.96 0.98
480 494 7.594570 TGTCTAGTGGTGTATACCCCTATTAA 58.405 38.462 6.15 0.00 46.96 1.40
481 495 8.236643 TGTCTAGTGGTGTATACCCCTATTAAT 58.763 37.037 6.15 0.00 46.96 1.40
482 496 9.097946 GTCTAGTGGTGTATACCCCTATTAATT 57.902 37.037 6.15 0.00 46.96 1.40
483 497 9.096823 TCTAGTGGTGTATACCCCTATTAATTG 57.903 37.037 6.15 0.00 46.96 2.32
484 498 7.701257 AGTGGTGTATACCCCTATTAATTGT 57.299 36.000 6.15 0.00 46.96 2.71
485 499 8.802057 AGTGGTGTATACCCCTATTAATTGTA 57.198 34.615 6.15 0.00 46.96 2.41
486 500 9.228077 AGTGGTGTATACCCCTATTAATTGTAA 57.772 33.333 6.15 0.00 46.96 2.41
530 544 8.630917 TGTACTAAGAGCATGAGGTTTAGTATC 58.369 37.037 15.95 12.32 38.40 2.24
532 546 8.998277 ACTAAGAGCATGAGGTTTAGTATCTA 57.002 34.615 0.00 0.00 33.96 1.98
554 568 7.363031 TCTACCCCTATGACATATCTAATCCC 58.637 42.308 0.00 0.00 0.00 3.85
555 569 5.927465 ACCCCTATGACATATCTAATCCCA 58.073 41.667 0.00 0.00 0.00 4.37
556 570 5.966935 ACCCCTATGACATATCTAATCCCAG 59.033 44.000 0.00 0.00 0.00 4.45
558 572 5.367937 CCCTATGACATATCTAATCCCAGGG 59.632 48.000 0.00 0.00 32.43 4.45
559 573 5.966935 CCTATGACATATCTAATCCCAGGGT 59.033 44.000 5.01 0.00 0.00 4.34
561 575 5.567037 TGACATATCTAATCCCAGGGTTG 57.433 43.478 5.01 0.00 0.00 3.77
574 588 2.568090 GGTTGCATGGACCAAGCG 59.432 61.111 16.43 1.08 37.14 4.68
621 1252 2.332514 CACGCACCAAAGCCTGTG 59.667 61.111 0.00 0.00 35.58 3.66
629 1260 1.767692 CAAAGCCTGTGGTACCCCT 59.232 57.895 10.07 0.00 0.00 4.79
654 1285 1.738099 CCGCACCGAGAGTTCCAAG 60.738 63.158 0.00 0.00 0.00 3.61
680 1332 2.411290 CCACACGGCCACAACAAC 59.589 61.111 2.24 0.00 0.00 3.32
707 1362 2.437359 CTCCGCCAGCCAAGGAAG 60.437 66.667 0.00 0.00 33.10 3.46
752 1412 1.144936 GGGTCAAGGCTCAGATCGG 59.855 63.158 0.00 0.00 0.00 4.18
828 1495 8.364894 GGGGAAAGTATTTATCGCCATTATTTT 58.635 33.333 3.54 0.00 43.53 1.82
830 1497 9.744468 GGAAAGTATTTATCGCCATTATTTTGT 57.256 29.630 0.00 0.00 39.27 2.83
904 1595 0.394565 GGAGATCCACCTCCCAATCG 59.605 60.000 0.00 0.00 45.44 3.34
1009 1730 0.536724 TCATCACATCTCCACCACCG 59.463 55.000 0.00 0.00 0.00 4.94
1010 1731 0.536724 CATCACATCTCCACCACCGA 59.463 55.000 0.00 0.00 0.00 4.69
1011 1732 0.826715 ATCACATCTCCACCACCGAG 59.173 55.000 0.00 0.00 0.00 4.63
1032 1757 1.990060 CCACCATCGTCCTCCCACT 60.990 63.158 0.00 0.00 0.00 4.00
1034 1759 1.686110 ACCATCGTCCTCCCACTCC 60.686 63.158 0.00 0.00 0.00 3.85
1058 1795 0.183971 ACTCTCAGATCGGATCGGGT 59.816 55.000 16.34 4.92 0.00 5.28
1251 2050 2.514592 CTGCACCAGTATGCCGGG 60.515 66.667 2.18 0.00 45.50 5.73
1254 2053 2.514592 CACCAGTATGCCGGGCAG 60.515 66.667 27.62 15.37 43.65 4.85
1530 2350 0.680280 CCTTCTCCGTCCTTCTCCGA 60.680 60.000 0.00 0.00 0.00 4.55
1542 2362 1.452953 TTCTCCGACGATCCATCCGG 61.453 60.000 0.00 0.00 43.02 5.14
1551 2371 0.318441 GATCCATCCGGCAAGATCGA 59.682 55.000 0.00 0.00 0.00 3.59
1552 2372 0.758734 ATCCATCCGGCAAGATCGAA 59.241 50.000 0.00 0.00 0.00 3.71
1553 2373 0.758734 TCCATCCGGCAAGATCGAAT 59.241 50.000 0.00 0.00 0.00 3.34
1554 2374 1.151668 CCATCCGGCAAGATCGAATC 58.848 55.000 0.00 0.00 0.00 2.52
1555 2375 0.786581 CATCCGGCAAGATCGAATCG 59.213 55.000 0.00 0.00 0.00 3.34
1574 2412 1.683790 GATCGCCAAGTGTTCGTCCG 61.684 60.000 0.00 0.00 0.00 4.79
1585 2423 0.459759 GTTCGTCCGTGGATTCCTCC 60.460 60.000 3.95 0.00 42.45 4.30
1616 2458 2.275318 GAGCTGACCGAGATTTCCTTG 58.725 52.381 0.00 0.00 0.00 3.61
1628 2470 1.102154 TTTCCTTGTGGCTGTGTGTG 58.898 50.000 0.00 0.00 0.00 3.82
1629 2471 0.034574 TTCCTTGTGGCTGTGTGTGT 60.035 50.000 0.00 0.00 0.00 3.72
1632 2474 2.020720 CCTTGTGGCTGTGTGTGTTTA 58.979 47.619 0.00 0.00 0.00 2.01
1656 2498 2.047465 CAGAAGACTGCGCTGGCT 60.047 61.111 18.05 18.05 40.82 4.75
1938 2798 2.908428 CAGCACCAGCACCAGCAA 60.908 61.111 0.00 0.00 45.49 3.91
1940 2800 2.908940 GCACCAGCACCAGCAACT 60.909 61.111 0.00 0.00 45.49 3.16
2013 2879 1.672356 CCACTGCCAGTTCTTCCCG 60.672 63.158 0.00 0.00 0.00 5.14
2224 3100 2.669808 ATCAGTCAGTCGATCGCCGC 62.670 60.000 11.09 3.08 38.37 6.53
2227 3103 2.202610 TCAGTCGATCGCCGCAAG 60.203 61.111 11.09 0.00 38.37 4.01
2266 3147 7.416326 GGTTTGGTTTGGATAGCAGTAATTAGG 60.416 40.741 0.00 0.00 0.00 2.69
2272 3153 2.814280 TAGCAGTAATTAGGAGCGCC 57.186 50.000 2.29 0.00 0.00 6.53
2275 3156 1.473434 GCAGTAATTAGGAGCGCCAGT 60.473 52.381 9.88 0.00 36.29 4.00
2292 3173 2.541346 CCAGTGATCGATCGATGGTTTG 59.459 50.000 33.86 22.99 34.60 2.93
2293 3174 2.541346 CAGTGATCGATCGATGGTTTGG 59.459 50.000 33.86 14.50 34.60 3.28
2294 3175 2.168521 AGTGATCGATCGATGGTTTGGT 59.831 45.455 33.86 9.47 34.60 3.67
2295 3176 2.936498 GTGATCGATCGATGGTTTGGTT 59.064 45.455 33.86 8.66 34.60 3.67
2296 3177 3.374058 GTGATCGATCGATGGTTTGGTTT 59.626 43.478 33.86 7.85 34.60 3.27
2297 3178 3.621268 TGATCGATCGATGGTTTGGTTTC 59.379 43.478 33.86 16.87 34.60 2.78
2304 3185 2.033550 CGATGGTTTGGTTTCGGTTTCA 59.966 45.455 0.00 0.00 0.00 2.69
2337 3224 6.671614 AATTCGGTTTGGGTTTTCTTTTTC 57.328 33.333 0.00 0.00 0.00 2.29
2353 3246 6.743575 TCTTTTTCTCTTTGGGATTCGATC 57.256 37.500 0.00 0.00 0.00 3.69
2454 3351 1.898902 CGTGTACCCATCCACCAAAA 58.101 50.000 0.00 0.00 0.00 2.44
2617 3528 3.013219 GGAGCCATGTCCTTCTCTTTTC 58.987 50.000 0.00 0.00 33.30 2.29
2622 3533 6.430007 AGCCATGTCCTTCTCTTTTCATTAT 58.570 36.000 0.00 0.00 0.00 1.28
2625 3536 8.686334 GCCATGTCCTTCTCTTTTCATTATTAA 58.314 33.333 0.00 0.00 0.00 1.40
2699 3610 1.403780 CGACGAACCCGATCTCCTTTT 60.404 52.381 0.00 0.00 39.50 2.27
2700 3611 2.000447 GACGAACCCGATCTCCTTTTG 59.000 52.381 0.00 0.00 39.50 2.44
2701 3612 1.346722 ACGAACCCGATCTCCTTTTGT 59.653 47.619 0.00 0.00 39.50 2.83
2702 3613 2.564062 ACGAACCCGATCTCCTTTTGTA 59.436 45.455 0.00 0.00 39.50 2.41
2734 3650 5.970592 TCTCATCTGCTGGATATAATTCGG 58.029 41.667 0.00 0.00 32.64 4.30
2735 3651 4.507710 TCATCTGCTGGATATAATTCGGC 58.492 43.478 0.00 0.00 32.64 5.54
2736 3652 2.959516 TCTGCTGGATATAATTCGGCG 58.040 47.619 0.00 0.00 0.00 6.46
2737 3653 2.560981 TCTGCTGGATATAATTCGGCGA 59.439 45.455 4.99 4.99 0.00 5.54
2738 3654 3.006430 TCTGCTGGATATAATTCGGCGAA 59.994 43.478 25.88 25.88 0.00 4.70
2739 3655 3.734463 TGCTGGATATAATTCGGCGAAA 58.266 40.909 27.40 11.80 0.00 3.46
2740 3656 4.130857 TGCTGGATATAATTCGGCGAAAA 58.869 39.130 27.40 17.81 0.00 2.29
2741 3657 4.576873 TGCTGGATATAATTCGGCGAAAAA 59.423 37.500 27.40 17.43 0.00 1.94
2742 3658 5.147162 GCTGGATATAATTCGGCGAAAAAG 58.853 41.667 27.40 14.65 0.00 2.27
2743 3659 5.049680 GCTGGATATAATTCGGCGAAAAAGA 60.050 40.000 27.40 14.82 0.00 2.52
2744 3660 6.539649 TGGATATAATTCGGCGAAAAAGAG 57.460 37.500 27.40 0.00 0.00 2.85
2745 3661 6.053005 TGGATATAATTCGGCGAAAAAGAGT 58.947 36.000 27.40 11.14 0.00 3.24
2746 3662 6.018262 TGGATATAATTCGGCGAAAAAGAGTG 60.018 38.462 27.40 0.00 0.00 3.51
2747 3663 6.202188 GGATATAATTCGGCGAAAAAGAGTGA 59.798 38.462 27.40 1.87 0.00 3.41
2748 3664 3.537793 AATTCGGCGAAAAAGAGTGAC 57.462 42.857 27.40 0.00 0.00 3.67
2749 3665 1.223187 TTCGGCGAAAAAGAGTGACC 58.777 50.000 21.53 0.00 0.00 4.02
2750 3666 0.601841 TCGGCGAAAAAGAGTGACCC 60.602 55.000 7.35 0.00 0.00 4.46
2751 3667 0.882927 CGGCGAAAAAGAGTGACCCA 60.883 55.000 0.00 0.00 0.00 4.51
2752 3668 1.534729 GGCGAAAAAGAGTGACCCAT 58.465 50.000 0.00 0.00 0.00 4.00
2753 3669 1.468914 GGCGAAAAAGAGTGACCCATC 59.531 52.381 0.00 0.00 0.00 3.51
2754 3670 2.427506 GCGAAAAAGAGTGACCCATCT 58.572 47.619 0.00 0.00 0.00 2.90
2755 3671 2.160417 GCGAAAAAGAGTGACCCATCTG 59.840 50.000 0.00 0.00 0.00 2.90
2756 3672 2.160417 CGAAAAAGAGTGACCCATCTGC 59.840 50.000 0.00 0.00 0.00 4.26
2757 3673 2.957402 AAAAGAGTGACCCATCTGCA 57.043 45.000 0.00 0.00 0.00 4.41
2758 3674 2.486472 AAAGAGTGACCCATCTGCAG 57.514 50.000 7.63 7.63 0.00 4.41
2759 3675 0.617413 AAGAGTGACCCATCTGCAGG 59.383 55.000 15.13 0.00 0.00 4.85
2760 3676 0.252421 AGAGTGACCCATCTGCAGGA 60.252 55.000 15.13 0.57 0.00 3.86
2761 3677 0.835941 GAGTGACCCATCTGCAGGAT 59.164 55.000 15.13 3.26 34.51 3.24
2762 3678 2.042464 GAGTGACCCATCTGCAGGATA 58.958 52.381 15.13 0.00 32.64 2.59
2763 3679 2.636893 GAGTGACCCATCTGCAGGATAT 59.363 50.000 15.13 0.00 32.64 1.63
2764 3680 3.834813 GAGTGACCCATCTGCAGGATATA 59.165 47.826 15.13 0.00 32.64 0.86
2765 3681 4.234550 AGTGACCCATCTGCAGGATATAA 58.765 43.478 15.13 0.00 32.64 0.98
2766 3682 4.848660 AGTGACCCATCTGCAGGATATAAT 59.151 41.667 15.13 0.00 32.64 1.28
2767 3683 5.311649 AGTGACCCATCTGCAGGATATAATT 59.688 40.000 15.13 0.00 32.64 1.40
2768 3684 5.413833 GTGACCCATCTGCAGGATATAATTG 59.586 44.000 15.13 0.00 32.64 2.32
2774 3690 7.061054 CCATCTGCAGGATATAATTGGATGAT 58.939 38.462 15.13 0.00 32.64 2.45
2778 3695 9.676861 TCTGCAGGATATAATTGGATGATAAAG 57.323 33.333 15.13 0.00 0.00 1.85
2808 3725 4.443063 CCGGTTCGAAAAGAATGGTTTTTC 59.557 41.667 0.00 1.44 41.49 2.29
2837 3765 7.393234 AGCTACTACTCCTACTCATGATGAATC 59.607 40.741 0.00 0.00 0.00 2.52
2844 3772 4.936411 CCTACTCATGATGAATCTGCATCC 59.064 45.833 0.00 0.00 43.10 3.51
2860 3788 1.000385 CATCCGAGAGCAGACATCTCC 60.000 57.143 0.00 0.00 40.11 3.71
2908 3836 5.248640 CCACCCACACCTCATTATCATATC 58.751 45.833 0.00 0.00 0.00 1.63
2909 3837 5.221904 CCACCCACACCTCATTATCATATCA 60.222 44.000 0.00 0.00 0.00 2.15
2911 3839 7.311234 CCACCCACACCTCATTATCATATCATA 60.311 40.741 0.00 0.00 0.00 2.15
2912 3840 7.550551 CACCCACACCTCATTATCATATCATAC 59.449 40.741 0.00 0.00 0.00 2.39
2943 3872 1.426041 GACAGACAACCGTGCGTGTT 61.426 55.000 0.00 0.00 0.00 3.32
2944 3873 1.275657 CAGACAACCGTGCGTGTTC 59.724 57.895 0.00 0.00 0.00 3.18
2988 3917 1.422179 GCGCCTCGGAGAAGCTTTAC 61.422 60.000 6.58 0.00 42.75 2.01
3022 3951 4.939509 TTAACTATTCCGCAGACAAAGC 57.060 40.909 0.00 0.00 0.00 3.51
3107 4036 0.744414 TCCAGCTTGATTAGTGCGCC 60.744 55.000 4.18 0.00 0.00 6.53
3115 4044 1.429148 GATTAGTGCGCCTTGGACCG 61.429 60.000 4.18 0.00 40.31 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.911769 TGTAGGATTGGGTCTGCAGG 59.088 55.000 15.13 0.00 0.00 4.85
3 4 1.407437 CCAGTGTAGGATTGGGTCTGC 60.407 57.143 0.00 0.00 0.00 4.26
4 5 1.407437 GCCAGTGTAGGATTGGGTCTG 60.407 57.143 0.00 0.00 31.88 3.51
5 6 0.912486 GCCAGTGTAGGATTGGGTCT 59.088 55.000 0.00 0.00 31.88 3.85
7 8 0.844661 TGGCCAGTGTAGGATTGGGT 60.845 55.000 0.00 0.00 31.88 4.51
8 9 0.394352 GTGGCCAGTGTAGGATTGGG 60.394 60.000 5.11 0.00 31.88 4.12
9 10 0.327924 TGTGGCCAGTGTAGGATTGG 59.672 55.000 5.11 0.00 34.46 3.16
10 11 1.742761 CTGTGGCCAGTGTAGGATTG 58.257 55.000 5.11 0.00 33.80 2.67
20 21 0.673644 CCCGTCTAAACTGTGGCCAG 60.674 60.000 5.11 0.00 44.68 4.85
21 22 1.373435 CCCGTCTAAACTGTGGCCA 59.627 57.895 0.00 0.00 0.00 5.36
22 23 0.250597 AACCCGTCTAAACTGTGGCC 60.251 55.000 0.00 0.00 0.00 5.36
37 38 4.404654 CTTGCGCTTGCGGAACCC 62.405 66.667 17.16 0.54 43.34 4.11
38 39 4.404654 CCTTGCGCTTGCGGAACC 62.405 66.667 17.16 0.90 43.34 3.62
75 76 4.467084 TTGCACCGATCCGCCTCC 62.467 66.667 0.00 0.00 0.00 4.30
79 80 3.969250 TTCCCTTGCACCGATCCGC 62.969 63.158 0.00 0.00 0.00 5.54
81 82 1.452108 CCTTCCCTTGCACCGATCC 60.452 63.158 0.00 0.00 0.00 3.36
95 96 2.026822 TCAATGTGAGCCTTCCTCCTTC 60.027 50.000 0.00 0.00 39.98 3.46
111 112 0.100682 GTGCATGCTCCTGCTCAATG 59.899 55.000 20.33 0.00 42.75 2.82
114 115 2.435410 CGTGCATGCTCCTGCTCA 60.435 61.111 20.33 0.00 42.75 4.26
118 119 2.176273 GCTACCGTGCATGCTCCTG 61.176 63.158 20.33 10.50 0.00 3.86
135 136 1.227380 CCTCGTCATAGTGCCCAGC 60.227 63.158 0.00 0.00 0.00 4.85
142 143 0.818296 GCCACTCACCTCGTCATAGT 59.182 55.000 0.00 0.00 0.00 2.12
154 155 1.273048 GTTTCCATTGCATGCCACTCA 59.727 47.619 16.68 0.00 0.00 3.41
225 226 1.267806 CGCTGGCAATCATTGTATCCC 59.732 52.381 0.00 0.00 0.00 3.85
232 233 0.543277 TCTCCTCGCTGGCAATCATT 59.457 50.000 0.00 0.00 35.26 2.57
233 234 0.543277 TTCTCCTCGCTGGCAATCAT 59.457 50.000 0.00 0.00 35.26 2.45
234 235 0.107993 CTTCTCCTCGCTGGCAATCA 60.108 55.000 0.00 0.00 35.26 2.57
237 238 1.188219 ACTCTTCTCCTCGCTGGCAA 61.188 55.000 0.00 0.00 35.26 4.52
254 255 4.090761 TGTTCAATTGAGAGCTGGAACT 57.909 40.909 8.41 0.00 36.50 3.01
255 256 4.516698 TCTTGTTCAATTGAGAGCTGGAAC 59.483 41.667 8.41 2.12 36.18 3.62
256 257 4.717877 TCTTGTTCAATTGAGAGCTGGAA 58.282 39.130 8.41 0.00 0.00 3.53
284 285 4.594854 ATGGGTTGCACCGCCACA 62.595 61.111 0.00 0.00 39.83 4.17
285 286 4.054825 CATGGGTTGCACCGCCAC 62.055 66.667 0.00 0.00 39.83 5.01
288 289 1.876497 ATTGTCATGGGTTGCACCGC 61.876 55.000 0.00 0.00 39.83 5.68
289 290 1.458398 TATTGTCATGGGTTGCACCG 58.542 50.000 0.00 0.00 39.83 4.94
290 291 4.160252 AGAATTATTGTCATGGGTTGCACC 59.840 41.667 0.00 0.00 37.60 5.01
291 292 5.329035 AGAATTATTGTCATGGGTTGCAC 57.671 39.130 0.00 0.00 0.00 4.57
292 293 8.759481 TTATAGAATTATTGTCATGGGTTGCA 57.241 30.769 0.00 0.00 0.00 4.08
296 297 9.920946 ACAACTTATAGAATTATTGTCATGGGT 57.079 29.630 0.00 0.00 0.00 4.51
353 367 6.959671 ATTCTTTTGACTTCGTTGCAAAAA 57.040 29.167 0.00 0.00 39.94 1.94
354 368 6.671879 GCAATTCTTTTGACTTCGTTGCAAAA 60.672 34.615 0.00 0.00 40.13 2.44
355 369 5.220378 GCAATTCTTTTGACTTCGTTGCAAA 60.220 36.000 0.00 0.00 40.13 3.68
356 370 4.267452 GCAATTCTTTTGACTTCGTTGCAA 59.733 37.500 0.00 0.00 40.13 4.08
357 371 3.796178 GCAATTCTTTTGACTTCGTTGCA 59.204 39.130 0.00 0.00 40.13 4.08
358 372 3.182372 GGCAATTCTTTTGACTTCGTTGC 59.818 43.478 0.00 0.00 39.78 4.17
359 373 4.610945 AGGCAATTCTTTTGACTTCGTTG 58.389 39.130 0.00 0.00 33.03 4.10
360 374 4.338118 TGAGGCAATTCTTTTGACTTCGTT 59.662 37.500 0.00 0.00 38.02 3.85
361 375 3.882888 TGAGGCAATTCTTTTGACTTCGT 59.117 39.130 0.00 0.00 38.02 3.85
362 376 4.488126 TGAGGCAATTCTTTTGACTTCG 57.512 40.909 0.00 0.00 38.02 3.79
363 377 5.091431 CGATGAGGCAATTCTTTTGACTTC 58.909 41.667 0.00 0.00 38.02 3.01
364 378 4.761739 TCGATGAGGCAATTCTTTTGACTT 59.238 37.500 0.00 0.00 38.02 3.01
365 379 4.326826 TCGATGAGGCAATTCTTTTGACT 58.673 39.130 0.00 0.00 41.23 3.41
366 380 4.685169 TCGATGAGGCAATTCTTTTGAC 57.315 40.909 0.00 0.00 0.00 3.18
367 381 5.902613 AATCGATGAGGCAATTCTTTTGA 57.097 34.783 0.00 0.00 0.00 2.69
368 382 8.638685 AATTAATCGATGAGGCAATTCTTTTG 57.361 30.769 0.00 0.00 0.00 2.44
370 384 9.956720 CTTAATTAATCGATGAGGCAATTCTTT 57.043 29.630 0.00 0.00 0.00 2.52
371 385 9.342308 TCTTAATTAATCGATGAGGCAATTCTT 57.658 29.630 0.00 0.00 0.00 2.52
372 386 8.908786 TCTTAATTAATCGATGAGGCAATTCT 57.091 30.769 0.00 0.00 0.00 2.40
373 387 9.604626 CTTCTTAATTAATCGATGAGGCAATTC 57.395 33.333 0.00 0.00 0.00 2.17
374 388 9.342308 TCTTCTTAATTAATCGATGAGGCAATT 57.658 29.630 0.00 3.46 0.00 2.32
375 389 8.908786 TCTTCTTAATTAATCGATGAGGCAAT 57.091 30.769 0.00 0.00 0.00 3.56
376 390 8.731275 TTCTTCTTAATTAATCGATGAGGCAA 57.269 30.769 0.00 0.00 0.00 4.52
377 391 8.204160 TCTTCTTCTTAATTAATCGATGAGGCA 58.796 33.333 0.00 0.00 0.00 4.75
378 392 8.594881 TCTTCTTCTTAATTAATCGATGAGGC 57.405 34.615 0.00 0.00 0.00 4.70
379 393 9.973450 TCTCTTCTTCTTAATTAATCGATGAGG 57.027 33.333 19.96 13.97 0.00 3.86
392 406 9.886132 GGGTACATACAATTCTCTTCTTCTTAA 57.114 33.333 0.00 0.00 0.00 1.85
393 407 8.483758 GGGGTACATACAATTCTCTTCTTCTTA 58.516 37.037 0.00 0.00 0.00 2.10
394 408 7.182930 AGGGGTACATACAATTCTCTTCTTCTT 59.817 37.037 0.00 0.00 0.00 2.52
395 409 6.674419 AGGGGTACATACAATTCTCTTCTTCT 59.326 38.462 0.00 0.00 0.00 2.85
396 410 6.890293 AGGGGTACATACAATTCTCTTCTTC 58.110 40.000 0.00 0.00 0.00 2.87
397 411 6.893020 AGGGGTACATACAATTCTCTTCTT 57.107 37.500 0.00 0.00 0.00 2.52
398 412 7.789831 TCATAGGGGTACATACAATTCTCTTCT 59.210 37.037 0.00 0.00 0.00 2.85
399 413 7.873505 GTCATAGGGGTACATACAATTCTCTTC 59.126 40.741 0.00 0.00 0.00 2.87
400 414 7.347222 TGTCATAGGGGTACATACAATTCTCTT 59.653 37.037 0.00 0.00 0.00 2.85
401 415 6.844388 TGTCATAGGGGTACATACAATTCTCT 59.156 38.462 0.00 0.00 0.00 3.10
402 416 7.062749 TGTCATAGGGGTACATACAATTCTC 57.937 40.000 0.00 0.00 0.00 2.87
403 417 7.633018 ATGTCATAGGGGTACATACAATTCT 57.367 36.000 0.00 0.00 32.21 2.40
404 418 9.601217 GATATGTCATAGGGGTACATACAATTC 57.399 37.037 0.00 0.00 38.53 2.17
405 419 9.338968 AGATATGTCATAGGGGTACATACAATT 57.661 33.333 0.00 0.00 38.53 2.32
406 420 8.917414 AGATATGTCATAGGGGTACATACAAT 57.083 34.615 0.00 0.00 38.53 2.71
407 421 8.736097 AAGATATGTCATAGGGGTACATACAA 57.264 34.615 0.00 0.00 38.53 2.41
408 422 7.399191 GGAAGATATGTCATAGGGGTACATACA 59.601 40.741 0.00 0.00 38.53 2.29
409 423 7.620094 AGGAAGATATGTCATAGGGGTACATAC 59.380 40.741 0.00 0.00 38.53 2.39
410 424 7.719424 AGGAAGATATGTCATAGGGGTACATA 58.281 38.462 0.00 0.00 39.64 2.29
411 425 6.575411 AGGAAGATATGTCATAGGGGTACAT 58.425 40.000 0.00 0.00 37.58 2.29
412 426 5.977533 AGGAAGATATGTCATAGGGGTACA 58.022 41.667 0.00 0.00 0.00 2.90
413 427 6.952358 TGTAGGAAGATATGTCATAGGGGTAC 59.048 42.308 0.00 0.00 0.00 3.34
414 428 6.952358 GTGTAGGAAGATATGTCATAGGGGTA 59.048 42.308 0.00 0.00 0.00 3.69
415 429 5.780793 GTGTAGGAAGATATGTCATAGGGGT 59.219 44.000 0.00 0.00 0.00 4.95
416 430 6.019748 AGTGTAGGAAGATATGTCATAGGGG 58.980 44.000 0.00 0.00 0.00 4.79
417 431 7.015682 ACAAGTGTAGGAAGATATGTCATAGGG 59.984 40.741 0.00 0.00 0.00 3.53
418 432 7.957002 ACAAGTGTAGGAAGATATGTCATAGG 58.043 38.462 0.00 0.00 0.00 2.57
419 433 9.900710 GTACAAGTGTAGGAAGATATGTCATAG 57.099 37.037 0.00 0.00 0.00 2.23
420 434 9.642343 AGTACAAGTGTAGGAAGATATGTCATA 57.358 33.333 0.00 0.00 0.00 2.15
421 435 8.540507 AGTACAAGTGTAGGAAGATATGTCAT 57.459 34.615 0.00 0.00 0.00 3.06
422 436 7.956328 AGTACAAGTGTAGGAAGATATGTCA 57.044 36.000 0.00 0.00 0.00 3.58
441 455 9.636789 ACACCACTAGACATTACATATAGTACA 57.363 33.333 0.00 0.00 30.91 2.90
448 462 7.452501 GGGGTATACACCACTAGACATTACATA 59.547 40.741 19.81 0.00 45.73 2.29
449 463 6.269307 GGGGTATACACCACTAGACATTACAT 59.731 42.308 19.81 0.00 45.73 2.29
450 464 5.599656 GGGGTATACACCACTAGACATTACA 59.400 44.000 19.81 0.00 45.73 2.41
451 465 6.094193 GGGGTATACACCACTAGACATTAC 57.906 45.833 19.81 0.00 45.73 1.89
503 517 7.425224 ACTAAACCTCATGCTCTTAGTACAT 57.575 36.000 0.00 0.00 32.44 2.29
507 521 7.906199 AGATACTAAACCTCATGCTCTTAGT 57.094 36.000 11.51 11.51 36.86 2.24
508 522 8.301002 GGTAGATACTAAACCTCATGCTCTTAG 58.699 40.741 0.00 0.00 0.00 2.18
510 524 6.042208 GGGTAGATACTAAACCTCATGCTCTT 59.958 42.308 0.00 0.00 33.59 2.85
511 525 5.540719 GGGTAGATACTAAACCTCATGCTCT 59.459 44.000 0.00 0.00 33.59 4.09
512 526 5.279556 GGGGTAGATACTAAACCTCATGCTC 60.280 48.000 0.00 0.00 33.68 4.26
513 527 4.593634 GGGGTAGATACTAAACCTCATGCT 59.406 45.833 0.00 0.00 33.68 3.79
530 544 7.132805 TGGGATTAGATATGTCATAGGGGTAG 58.867 42.308 0.00 0.00 0.00 3.18
532 546 5.927465 TGGGATTAGATATGTCATAGGGGT 58.073 41.667 0.00 0.00 0.00 4.95
547 561 1.215173 TCCATGCAACCCTGGGATTAG 59.785 52.381 22.23 6.92 33.13 1.73
549 563 0.324645 GTCCATGCAACCCTGGGATT 60.325 55.000 22.23 7.25 33.13 3.01
553 567 1.228831 TTGGTCCATGCAACCCTGG 60.229 57.895 11.70 0.43 35.84 4.45
554 568 1.880819 GCTTGGTCCATGCAACCCTG 61.881 60.000 21.74 6.71 35.84 4.45
555 569 1.607467 GCTTGGTCCATGCAACCCT 60.607 57.895 21.74 0.00 35.84 4.34
556 570 2.973082 GCTTGGTCCATGCAACCC 59.027 61.111 21.74 0.00 35.84 4.11
558 572 1.503542 CTCGCTTGGTCCATGCAAC 59.496 57.895 24.92 1.56 34.78 4.17
559 573 2.334946 GCTCGCTTGGTCCATGCAA 61.335 57.895 24.92 9.99 34.78 4.08
561 575 1.865788 TTTGCTCGCTTGGTCCATGC 61.866 55.000 17.80 17.80 0.00 4.06
574 588 0.233332 GTCTCGTGTGTGCTTTGCTC 59.767 55.000 0.00 0.00 0.00 4.26
643 1274 1.531578 GCGTTGGAACTTGGAACTCTC 59.468 52.381 0.00 0.00 0.00 3.20
644 1275 1.594331 GCGTTGGAACTTGGAACTCT 58.406 50.000 0.00 0.00 0.00 3.24
722 1377 1.895020 CTTGACCCGGTCCGATCCAA 61.895 60.000 14.39 11.74 0.00 3.53
723 1378 2.284039 TTGACCCGGTCCGATCCA 60.284 61.111 14.39 4.05 0.00 3.41
724 1379 2.499685 CTTGACCCGGTCCGATCC 59.500 66.667 14.39 1.16 0.00 3.36
725 1380 2.499685 CCTTGACCCGGTCCGATC 59.500 66.667 14.39 10.65 0.00 3.69
726 1381 3.782443 GCCTTGACCCGGTCCGAT 61.782 66.667 14.39 0.00 0.00 4.18
752 1412 3.818787 CGTGCATGCTGCCTTCCC 61.819 66.667 20.33 0.00 44.23 3.97
798 1465 4.204799 GGCGATAAATACTTTCCCCTTGT 58.795 43.478 0.00 0.00 0.00 3.16
854 1521 6.014925 TCGCTAGGCATCCAATTATTACTGTA 60.015 38.462 0.00 0.00 0.00 2.74
856 1523 5.237815 TCGCTAGGCATCCAATTATTACTG 58.762 41.667 0.00 0.00 0.00 2.74
858 1525 4.631813 CCTCGCTAGGCATCCAATTATTAC 59.368 45.833 0.00 0.00 35.64 1.89
900 1590 2.271800 GATGAGCTGTTCGGTTCGATT 58.728 47.619 0.00 0.00 35.23 3.34
904 1595 3.751621 CAAATGATGAGCTGTTCGGTTC 58.248 45.455 0.00 0.00 0.00 3.62
1009 1730 1.153549 GAGGACGATGGTGGTGCTC 60.154 63.158 0.00 0.00 43.86 4.26
1010 1731 2.660064 GGAGGACGATGGTGGTGCT 61.660 63.158 0.00 0.00 38.88 4.40
1011 1732 2.125106 GGAGGACGATGGTGGTGC 60.125 66.667 0.00 0.00 0.00 5.01
1032 1757 0.752009 CCGATCTGAGAGTTCCCGGA 60.752 60.000 0.73 0.00 37.87 5.14
1034 1759 1.268352 GATCCGATCTGAGAGTTCCCG 59.732 57.143 0.75 0.00 0.00 5.14
1058 1795 0.380733 CATCGTCGATCTCCGGTGAA 59.619 55.000 10.77 0.00 37.37 3.18
1530 2350 0.034059 GATCTTGCCGGATGGATCGT 59.966 55.000 5.05 0.00 37.49 3.73
1551 2371 0.999406 CGAACACTTGGCGATCGATT 59.001 50.000 21.57 0.20 35.65 3.34
1552 2372 0.108804 ACGAACACTTGGCGATCGAT 60.109 50.000 21.57 0.00 37.27 3.59
1553 2373 0.731514 GACGAACACTTGGCGATCGA 60.732 55.000 21.57 0.00 37.27 3.59
1554 2374 1.683790 GGACGAACACTTGGCGATCG 61.684 60.000 11.69 11.69 39.30 3.69
1555 2375 1.683790 CGGACGAACACTTGGCGATC 61.684 60.000 0.00 0.00 0.00 3.69
1574 2412 1.301009 GCGATCGGGAGGAATCCAC 60.301 63.158 18.30 0.00 0.00 4.02
1616 2458 2.285083 TCTGTAAACACACACAGCCAC 58.715 47.619 0.00 0.00 41.58 5.01
1938 2798 4.962836 GGGTGGCACTGCTGCAGT 62.963 66.667 28.49 28.49 46.51 4.40
2109 2978 2.126424 GGCGGCGAGATATCGTCC 60.126 66.667 12.98 10.53 33.73 4.79
2129 3004 2.004583 TTTATCGCCTGAAGTGGACG 57.995 50.000 0.00 0.00 0.00 4.79
2135 3010 7.442364 TCAAATCTCCTAATTTATCGCCTGAAG 59.558 37.037 0.00 0.00 0.00 3.02
2137 3012 6.826668 TCAAATCTCCTAATTTATCGCCTGA 58.173 36.000 0.00 0.00 0.00 3.86
2224 3100 5.857268 ACCAAACCAAATCAAATCTCCTTG 58.143 37.500 0.00 0.00 0.00 3.61
2227 3103 5.469760 CCAAACCAAACCAAATCAAATCTCC 59.530 40.000 0.00 0.00 0.00 3.71
2228 3104 6.287525 TCCAAACCAAACCAAATCAAATCTC 58.712 36.000 0.00 0.00 0.00 2.75
2236 3117 4.592778 ACTGCTATCCAAACCAAACCAAAT 59.407 37.500 0.00 0.00 0.00 2.32
2266 3147 2.013483 CGATCGATCACTGGCGCTC 61.013 63.158 24.40 0.00 0.00 5.03
2272 3153 2.541346 CCAAACCATCGATCGATCACTG 59.459 50.000 27.20 17.50 31.62 3.66
2275 3156 2.979814 ACCAAACCATCGATCGATCA 57.020 45.000 27.20 12.32 31.62 2.92
2292 3173 7.895975 ATTACTACTAACTGAAACCGAAACC 57.104 36.000 0.00 0.00 0.00 3.27
2293 3174 8.158445 CGAATTACTACTAACTGAAACCGAAAC 58.842 37.037 0.00 0.00 0.00 2.78
2294 3175 7.329226 CCGAATTACTACTAACTGAAACCGAAA 59.671 37.037 0.00 0.00 0.00 3.46
2295 3176 6.808212 CCGAATTACTACTAACTGAAACCGAA 59.192 38.462 0.00 0.00 0.00 4.30
2296 3177 6.071952 ACCGAATTACTACTAACTGAAACCGA 60.072 38.462 0.00 0.00 0.00 4.69
2297 3178 6.095377 ACCGAATTACTACTAACTGAAACCG 58.905 40.000 0.00 0.00 0.00 4.44
2304 3185 6.364568 ACCCAAACCGAATTACTACTAACT 57.635 37.500 0.00 0.00 0.00 2.24
2353 3246 1.182363 GTTCGTCGTCGATTCGATTCG 59.818 52.381 20.58 20.58 45.65 3.34
2362 3255 4.739228 TGTTTCTATTTTGTTCGTCGTCGA 59.261 37.500 0.00 0.00 44.66 4.20
2378 3271 6.258727 CCTCCGTACGTACTAATCTGTTTCTA 59.741 42.308 22.55 0.00 0.00 2.10
2394 3291 0.725117 GCCATTTGTTCCTCCGTACG 59.275 55.000 8.69 8.69 0.00 3.67
2396 3293 1.349688 ACAGCCATTTGTTCCTCCGTA 59.650 47.619 0.00 0.00 0.00 4.02
2398 3295 0.804989 GACAGCCATTTGTTCCTCCG 59.195 55.000 0.00 0.00 0.00 4.63
2553 3453 7.013823 AGAGAGGAGAATGTGAATGAAAGAA 57.986 36.000 0.00 0.00 0.00 2.52
2573 3479 6.270000 TCCAAATACTCTTGTTGGAGAAGAGA 59.730 38.462 18.23 5.91 46.44 3.10
2664 3575 1.800315 GTCGACGCGCTAGCTTGAA 60.800 57.895 13.93 0.00 42.32 2.69
2670 3581 2.943034 GGTTCGTCGACGCGCTAG 60.943 66.667 32.19 6.30 39.60 3.42
2717 3633 2.959516 TCGCCGAATTATATCCAGCAG 58.040 47.619 0.00 0.00 0.00 4.24
2725 3641 5.292589 GGTCACTCTTTTTCGCCGAATTATA 59.707 40.000 0.00 0.00 0.00 0.98
2726 3642 4.094442 GGTCACTCTTTTTCGCCGAATTAT 59.906 41.667 0.00 0.00 0.00 1.28
2728 3644 2.225727 GGTCACTCTTTTTCGCCGAATT 59.774 45.455 0.00 0.00 0.00 2.17
2730 3646 1.223187 GGTCACTCTTTTTCGCCGAA 58.777 50.000 0.00 0.00 0.00 4.30
2732 3648 0.882927 TGGGTCACTCTTTTTCGCCG 60.883 55.000 0.00 0.00 0.00 6.46
2733 3649 1.468914 GATGGGTCACTCTTTTTCGCC 59.531 52.381 0.00 0.00 0.00 5.54
2734 3650 2.160417 CAGATGGGTCACTCTTTTTCGC 59.840 50.000 0.00 0.00 0.00 4.70
2735 3651 2.160417 GCAGATGGGTCACTCTTTTTCG 59.840 50.000 0.00 0.00 0.00 3.46
2736 3652 3.149196 TGCAGATGGGTCACTCTTTTTC 58.851 45.455 0.00 0.00 0.00 2.29
2737 3653 3.152341 CTGCAGATGGGTCACTCTTTTT 58.848 45.455 8.42 0.00 0.00 1.94
2738 3654 2.553904 CCTGCAGATGGGTCACTCTTTT 60.554 50.000 17.39 0.00 0.00 2.27
2739 3655 1.004044 CCTGCAGATGGGTCACTCTTT 59.996 52.381 17.39 0.00 0.00 2.52
2740 3656 0.617413 CCTGCAGATGGGTCACTCTT 59.383 55.000 17.39 0.00 0.00 2.85
2741 3657 0.252421 TCCTGCAGATGGGTCACTCT 60.252 55.000 17.39 0.00 0.00 3.24
2742 3658 0.835941 ATCCTGCAGATGGGTCACTC 59.164 55.000 17.39 0.00 32.41 3.51
2743 3659 2.180946 TATCCTGCAGATGGGTCACT 57.819 50.000 17.39 0.00 36.33 3.41
2744 3660 4.623932 TTATATCCTGCAGATGGGTCAC 57.376 45.455 17.39 0.00 36.33 3.67
2745 3661 5.515359 CCAATTATATCCTGCAGATGGGTCA 60.515 44.000 17.39 0.00 36.33 4.02
2746 3662 4.946157 CCAATTATATCCTGCAGATGGGTC 59.054 45.833 17.39 0.00 36.33 4.46
2747 3663 4.603171 TCCAATTATATCCTGCAGATGGGT 59.397 41.667 17.39 0.00 36.33 4.51
2748 3664 5.183530 TCCAATTATATCCTGCAGATGGG 57.816 43.478 17.39 6.60 36.33 4.00
2749 3665 6.420638 TCATCCAATTATATCCTGCAGATGG 58.579 40.000 17.39 9.85 36.33 3.51
2750 3666 9.623000 TTATCATCCAATTATATCCTGCAGATG 57.377 33.333 17.39 6.56 36.33 2.90
2752 3668 9.676861 CTTTATCATCCAATTATATCCTGCAGA 57.323 33.333 17.39 1.21 0.00 4.26
2753 3669 9.676861 TCTTTATCATCCAATTATATCCTGCAG 57.323 33.333 6.78 6.78 0.00 4.41
2754 3670 9.676861 CTCTTTATCATCCAATTATATCCTGCA 57.323 33.333 0.00 0.00 0.00 4.41
2755 3671 9.678260 ACTCTTTATCATCCAATTATATCCTGC 57.322 33.333 0.00 0.00 0.00 4.85
2758 3674 8.897752 GCCACTCTTTATCATCCAATTATATCC 58.102 37.037 0.00 0.00 0.00 2.59
2759 3675 8.897752 GGCCACTCTTTATCATCCAATTATATC 58.102 37.037 0.00 0.00 0.00 1.63
2760 3676 7.836183 GGGCCACTCTTTATCATCCAATTATAT 59.164 37.037 4.39 0.00 0.00 0.86
2761 3677 7.175104 GGGCCACTCTTTATCATCCAATTATA 58.825 38.462 4.39 0.00 0.00 0.98
2762 3678 6.012745 GGGCCACTCTTTATCATCCAATTAT 58.987 40.000 4.39 0.00 0.00 1.28
2763 3679 5.385198 GGGCCACTCTTTATCATCCAATTA 58.615 41.667 4.39 0.00 0.00 1.40
2764 3680 4.218312 GGGCCACTCTTTATCATCCAATT 58.782 43.478 4.39 0.00 0.00 2.32
2765 3681 3.748668 CGGGCCACTCTTTATCATCCAAT 60.749 47.826 4.39 0.00 0.00 3.16
2766 3682 2.421388 CGGGCCACTCTTTATCATCCAA 60.421 50.000 4.39 0.00 0.00 3.53
2767 3683 1.140852 CGGGCCACTCTTTATCATCCA 59.859 52.381 4.39 0.00 0.00 3.41
2768 3684 1.543429 CCGGGCCACTCTTTATCATCC 60.543 57.143 4.39 0.00 0.00 3.51
2774 3690 1.186917 TCGAACCGGGCCACTCTTTA 61.187 55.000 6.32 0.00 0.00 1.85
2778 3695 1.574702 CTTTTCGAACCGGGCCACTC 61.575 60.000 6.32 0.00 0.00 3.51
2808 3725 5.133941 TCATGAGTAGGAGTAGTAGCTTGG 58.866 45.833 0.00 0.00 0.00 3.61
2810 3727 6.606069 TCATCATGAGTAGGAGTAGTAGCTT 58.394 40.000 0.09 0.00 0.00 3.74
2812 3729 6.885952 TTCATCATGAGTAGGAGTAGTAGC 57.114 41.667 0.09 0.00 0.00 3.58
2814 3731 7.175816 GCAGATTCATCATGAGTAGGAGTAGTA 59.824 40.741 0.09 0.00 0.00 1.82
2816 3733 6.015603 TGCAGATTCATCATGAGTAGGAGTAG 60.016 42.308 0.09 0.00 0.00 2.57
2817 3734 5.835280 TGCAGATTCATCATGAGTAGGAGTA 59.165 40.000 0.09 0.00 0.00 2.59
2818 3735 4.652881 TGCAGATTCATCATGAGTAGGAGT 59.347 41.667 0.09 0.00 0.00 3.85
2821 3748 4.936411 GGATGCAGATTCATCATGAGTAGG 59.064 45.833 0.09 0.00 43.44 3.18
2860 3788 2.151172 GCTTTCGCTTAAACAAGTTGCG 59.849 45.455 1.81 9.10 46.71 4.85
2908 3836 6.603237 TGTCTGTCTGAAACTGTTTGTATG 57.397 37.500 11.03 0.00 0.00 2.39
2909 3837 6.038271 GGTTGTCTGTCTGAAACTGTTTGTAT 59.962 38.462 11.03 0.00 0.00 2.29
2911 3839 4.156008 GGTTGTCTGTCTGAAACTGTTTGT 59.844 41.667 11.03 0.00 0.00 2.83
2912 3840 4.662145 GGTTGTCTGTCTGAAACTGTTTG 58.338 43.478 11.03 0.00 0.00 2.93
2963 3892 4.819761 TCTCCGAGGCGCATGTGC 62.820 66.667 23.05 23.05 37.78 4.57
2988 3917 6.253512 GCGGAATAGTTAATTGGCTTTTTGAG 59.746 38.462 0.00 0.00 0.00 3.02
3022 3951 0.815615 GCCATGACTTTAGCCCCTCG 60.816 60.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.