Multiple sequence alignment - TraesCS7B01G024500

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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 TraesCS7B01G024500 chr7B 100.000 4226 0 0 1 4226 23443853 23439628 0.000000e+00 7805
1 TraesCS7B01G024500 chr7B 91.729 532 39 3 1 529 202992970 202992441 0.000000e+00 734
2 TraesCS7B01G024500 chr7B 89.610 539 44 5 2911 3437 23396970 23396432 0.000000e+00 675
3 TraesCS7B01G024500 chr7A 91.796 3425 182 44 621 4002 80854762 80851394 0.000000e+00 4676
4 TraesCS7B01G024500 chr7A 86.905 840 85 19 3071 3895 80839357 80838528 0.000000e+00 918
5 TraesCS7B01G024500 chr7A 86.190 840 90 16 3071 3895 80704057 80703229 0.000000e+00 885
6 TraesCS7B01G024500 chr7A 85.952 840 92 17 3071 3895 80806987 80806159 0.000000e+00 874
7 TraesCS7B01G024500 chr7A 97.248 109 2 1 3999 4107 80851363 80851256 2.600000e-42 183
8 TraesCS7B01G024500 chr7D 91.781 3419 173 53 623 4002 76734340 76730991 0.000000e+00 4658
9 TraesCS7B01G024500 chr7D 95.572 271 12 0 3374 3644 76613424 76613154 6.490000e-118 435
10 TraesCS7B01G024500 chr7D 91.176 238 6 1 3148 3385 76614883 76614661 4.100000e-80 309
11 TraesCS7B01G024500 chr7D 91.803 122 9 1 3997 4117 76730945 76730824 7.270000e-38 169
12 TraesCS7B01G024500 chr7D 90.984 122 11 0 402 523 179629482 179629361 9.400000e-37 165
13 TraesCS7B01G024500 chr7D 92.727 110 8 0 402 511 179631918 179632027 4.370000e-35 159
14 TraesCS7B01G024500 chr7D 84.404 109 10 2 4118 4226 76730177 76730076 2.690000e-17 100
15 TraesCS7B01G024500 chr1A 84.074 1576 216 20 1717 3266 308814417 308812851 0.000000e+00 1487
16 TraesCS7B01G024500 chr1A 83.820 1508 229 11 1714 3207 37480010 37481516 0.000000e+00 1419
17 TraesCS7B01G024500 chr1A 91.964 112 8 1 3999 4109 581584031 581584142 5.660000e-34 156
18 TraesCS7B01G024500 chr1A 80.676 207 20 12 1051 1250 308816021 308815828 4.400000e-30 143
19 TraesCS7B01G024500 chr1A 78.539 219 32 11 1042 1254 37478585 37478794 3.430000e-26 130
20 TraesCS7B01G024500 chr1D 84.315 1511 214 16 1714 3207 38551133 38552637 0.000000e+00 1456
21 TraesCS7B01G024500 chr1D 85.855 1216 162 6 2054 3266 236806078 236807286 0.000000e+00 1284
22 TraesCS7B01G024500 chr1D 91.964 112 8 1 3999 4109 484402366 484402477 5.660000e-34 156
23 TraesCS7B01G024500 chr1D 79.310 232 27 13 1025 1250 236803291 236803507 4.400000e-30 143
24 TraesCS7B01G024500 chr1D 77.132 258 37 17 998 1250 38549726 38549966 3.430000e-26 130
25 TraesCS7B01G024500 chr1B 83.165 1586 235 17 1703 3265 58323210 58324786 0.000000e+00 1421
26 TraesCS7B01G024500 chr1B 86.767 1126 149 0 2082 3207 342116466 342117591 0.000000e+00 1254
27 TraesCS7B01G024500 chr1B 83.987 306 45 4 1714 2015 342116064 342116369 1.490000e-74 291
28 TraesCS7B01G024500 chr1B 93.443 122 7 1 3997 4117 674631438 674631559 3.360000e-41 180
29 TraesCS7B01G024500 chr1B 76.744 258 38 17 998 1250 58321767 58322007 1.600000e-24 124
30 TraesCS7B01G024500 chr5B 92.841 447 27 4 1 446 122836392 122835950 0.000000e+00 643
31 TraesCS7B01G024500 chr5A 84.047 514 73 8 1 510 622383079 622383587 1.770000e-133 486
32 TraesCS7B01G024500 chr5A 90.496 242 20 2 1 239 654092612 654092371 2.450000e-82 316
33 TraesCS7B01G024500 chr5A 82.569 218 35 3 4 221 8090863 8091077 5.580000e-44 189
34 TraesCS7B01G024500 chr4A 84.047 514 59 14 1 511 157873971 157873478 1.380000e-129 473
35 TraesCS7B01G024500 chr6A 82.846 513 78 8 1 511 112264759 112264255 6.440000e-123 451
36 TraesCS7B01G024500 chr6D 88.401 319 30 5 1 315 22188109 22188424 1.110000e-100 377
37 TraesCS7B01G024500 chr3D 87.543 289 34 2 2 290 147472908 147473194 2.440000e-87 333
38 TraesCS7B01G024500 chr4B 91.473 129 5 6 410 535 626070997 626071122 5.620000e-39 172
39 TraesCS7B01G024500 chr3B 89.781 137 11 3 402 535 950618 950754 5.620000e-39 172
40 TraesCS7B01G024500 chr2B 90.698 129 9 3 410 535 708795037 708794909 7.270000e-38 169
41 TraesCS7B01G024500 chr2B 86.986 146 12 5 401 539 554726260 554726115 1.570000e-34 158


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 TraesCS7B01G024500 chr7B 23439628 23443853 4225 True 7805.000000 7805 100.000000 1 4226 1 chr7B.!!$R2 4225
1 TraesCS7B01G024500 chr7B 202992441 202992970 529 True 734.000000 734 91.729000 1 529 1 chr7B.!!$R3 528
2 TraesCS7B01G024500 chr7B 23396432 23396970 538 True 675.000000 675 89.610000 2911 3437 1 chr7B.!!$R1 526
3 TraesCS7B01G024500 chr7A 80851256 80854762 3506 True 2429.500000 4676 94.522000 621 4107 2 chr7A.!!$R4 3486
4 TraesCS7B01G024500 chr7A 80838528 80839357 829 True 918.000000 918 86.905000 3071 3895 1 chr7A.!!$R3 824
5 TraesCS7B01G024500 chr7A 80703229 80704057 828 True 885.000000 885 86.190000 3071 3895 1 chr7A.!!$R1 824
6 TraesCS7B01G024500 chr7A 80806159 80806987 828 True 874.000000 874 85.952000 3071 3895 1 chr7A.!!$R2 824
7 TraesCS7B01G024500 chr7D 76730076 76734340 4264 True 1642.333333 4658 89.329333 623 4226 3 chr7D.!!$R3 3603
8 TraesCS7B01G024500 chr7D 76613154 76614883 1729 True 372.000000 435 93.374000 3148 3644 2 chr7D.!!$R2 496
9 TraesCS7B01G024500 chr1A 308812851 308816021 3170 True 815.000000 1487 82.375000 1051 3266 2 chr1A.!!$R1 2215
10 TraesCS7B01G024500 chr1A 37478585 37481516 2931 False 774.500000 1419 81.179500 1042 3207 2 chr1A.!!$F2 2165
11 TraesCS7B01G024500 chr1D 38549726 38552637 2911 False 793.000000 1456 80.723500 998 3207 2 chr1D.!!$F2 2209
12 TraesCS7B01G024500 chr1D 236803291 236807286 3995 False 713.500000 1284 82.582500 1025 3266 2 chr1D.!!$F3 2241
13 TraesCS7B01G024500 chr1B 58321767 58324786 3019 False 772.500000 1421 79.954500 998 3265 2 chr1B.!!$F2 2267
14 TraesCS7B01G024500 chr1B 342116064 342117591 1527 False 772.500000 1254 85.377000 1714 3207 2 chr1B.!!$F3 1493
15 TraesCS7B01G024500 chr5A 622383079 622383587 508 False 486.000000 486 84.047000 1 510 1 chr5A.!!$F2 509
16 TraesCS7B01G024500 chr6A 112264255 112264759 504 True 451.000000 451 82.846000 1 511 1 chr6A.!!$R1 510

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
494 498 0.029567 GACGGACGATCAGAAGCGAT 59.970 55.000 0.00 0.00 37.81 4.58 F
653 657 0.179000 AAATAGAGCACGAGGGCCTG 59.821 55.000 12.95 6.05 0.00 4.85 F
1526 2640 0.312102 GCGCAGGAAAGCTTGTTTCT 59.688 50.000 0.30 0.00 0.00 2.52 F
2068 4348 1.477295 GGGTAGAAGCTCTAACGCTGT 59.523 52.381 0.00 0.00 37.55 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1398 1449 0.841289 ACCAACTCCCAACTTTCGGA 59.159 50.000 0.0 0.0 0.0 4.55 R
2576 4910 2.831333 CGGCAGCTTCATACATCTCTT 58.169 47.619 0.0 0.0 0.0 2.85 R
2877 5211 0.710588 TAGAGTCCCTCCAAGCCTCA 59.289 55.000 0.0 0.0 0.0 3.86 R
3898 7537 0.465097 CGAGGAGGCCGGTAGTTCTA 60.465 60.000 1.9 0.0 0.0 2.10 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
192 196 5.747197 CGTAATTGTACTGTGTAGACCATCC 59.253 44.000 0.00 0.00 0.00 3.51
270 274 4.898829 AAAAAGCTGCAAAAATTGGGAC 57.101 36.364 1.02 0.00 0.00 4.46
276 280 0.732538 GCAAAAATTGGGACGAGCCG 60.733 55.000 0.00 0.00 37.63 5.52
320 324 2.834113 TGGTAGAGAAAGGCCTAAGCT 58.166 47.619 5.16 3.12 39.73 3.74
322 326 3.961408 TGGTAGAGAAAGGCCTAAGCTAG 59.039 47.826 5.16 0.00 39.73 3.42
344 348 1.073923 AGGCTGGTTTGTCTACTTGGG 59.926 52.381 0.00 0.00 0.00 4.12
349 353 3.547746 TGGTTTGTCTACTTGGGTTGTC 58.452 45.455 0.00 0.00 0.00 3.18
350 354 3.201266 TGGTTTGTCTACTTGGGTTGTCT 59.799 43.478 0.00 0.00 0.00 3.41
362 366 1.743394 GGGTTGTCTAAGGGCATTTCG 59.257 52.381 0.00 0.00 0.00 3.46
396 400 1.065998 AGGTTATCGGCGGCAACTTAA 60.066 47.619 18.96 0.00 0.00 1.85
397 401 1.329599 GGTTATCGGCGGCAACTTAAG 59.670 52.381 18.96 0.00 0.00 1.85
398 402 2.273557 GTTATCGGCGGCAACTTAAGA 58.726 47.619 10.09 0.00 0.00 2.10
438 442 2.179764 CACTTACGGGTGGCATTGG 58.820 57.895 0.00 0.00 33.95 3.16
439 443 0.608035 CACTTACGGGTGGCATTGGT 60.608 55.000 0.00 0.00 33.95 3.67
440 444 0.608035 ACTTACGGGTGGCATTGGTG 60.608 55.000 0.00 0.00 0.00 4.17
441 445 1.303724 TTACGGGTGGCATTGGTGG 60.304 57.895 0.00 0.00 0.00 4.61
442 446 2.773007 TTACGGGTGGCATTGGTGGG 62.773 60.000 0.00 0.00 0.00 4.61
443 447 4.676951 CGGGTGGCATTGGTGGGT 62.677 66.667 0.00 0.00 0.00 4.51
444 448 2.767352 GGGTGGCATTGGTGGGTA 59.233 61.111 0.00 0.00 0.00 3.69
445 449 1.077625 GGGTGGCATTGGTGGGTAA 59.922 57.895 0.00 0.00 0.00 2.85
446 450 0.325203 GGGTGGCATTGGTGGGTAAT 60.325 55.000 0.00 0.00 0.00 1.89
447 451 1.567357 GGTGGCATTGGTGGGTAATT 58.433 50.000 0.00 0.00 0.00 1.40
448 452 1.905894 GGTGGCATTGGTGGGTAATTT 59.094 47.619 0.00 0.00 0.00 1.82
449 453 2.304470 GGTGGCATTGGTGGGTAATTTT 59.696 45.455 0.00 0.00 0.00 1.82
450 454 3.244735 GGTGGCATTGGTGGGTAATTTTT 60.245 43.478 0.00 0.00 0.00 1.94
451 455 4.020128 GGTGGCATTGGTGGGTAATTTTTA 60.020 41.667 0.00 0.00 0.00 1.52
452 456 4.932799 GTGGCATTGGTGGGTAATTTTTAC 59.067 41.667 0.00 0.00 0.00 2.01
453 457 4.020128 TGGCATTGGTGGGTAATTTTTACC 60.020 41.667 7.74 7.74 36.88 2.85
454 458 4.020128 GGCATTGGTGGGTAATTTTTACCA 60.020 41.667 16.13 0.00 39.31 3.25
458 462 6.809976 TTGGTGGGTAATTTTTACCAACTT 57.190 33.333 18.78 0.00 44.08 2.66
459 463 7.909485 TTGGTGGGTAATTTTTACCAACTTA 57.091 32.000 18.78 9.38 44.08 2.24
460 464 7.909485 TGGTGGGTAATTTTTACCAACTTAA 57.091 32.000 18.78 7.01 41.27 1.85
461 465 8.315220 TGGTGGGTAATTTTTACCAACTTAAA 57.685 30.769 18.78 5.17 41.27 1.52
462 466 8.422566 TGGTGGGTAATTTTTACCAACTTAAAG 58.577 33.333 18.78 0.00 41.27 1.85
463 467 8.423349 GGTGGGTAATTTTTACCAACTTAAAGT 58.577 33.333 18.78 0.00 40.55 2.66
464 468 9.251792 GTGGGTAATTTTTACCAACTTAAAGTG 57.748 33.333 16.13 0.00 38.27 3.16
465 469 8.979534 TGGGTAATTTTTACCAACTTAAAGTGT 58.020 29.630 16.13 0.00 39.31 3.55
482 486 9.257865 CTTAAAGTGTAATTTTAATGACGGACG 57.742 33.333 0.00 0.00 37.37 4.79
483 487 7.424227 AAAGTGTAATTTTAATGACGGACGA 57.576 32.000 0.00 0.00 0.00 4.20
484 488 7.605410 AAGTGTAATTTTAATGACGGACGAT 57.395 32.000 0.00 0.00 0.00 3.73
485 489 7.230466 AGTGTAATTTTAATGACGGACGATC 57.770 36.000 0.00 0.00 0.00 3.69
486 490 6.814644 AGTGTAATTTTAATGACGGACGATCA 59.185 34.615 0.00 0.00 0.00 2.92
487 491 7.010183 AGTGTAATTTTAATGACGGACGATCAG 59.990 37.037 0.00 0.00 0.00 2.90
488 492 7.009815 GTGTAATTTTAATGACGGACGATCAGA 59.990 37.037 0.00 0.00 0.00 3.27
489 493 6.978343 AATTTTAATGACGGACGATCAGAA 57.022 33.333 0.00 0.00 0.00 3.02
490 494 6.589830 ATTTTAATGACGGACGATCAGAAG 57.410 37.500 0.00 0.00 0.00 2.85
491 495 1.927895 AATGACGGACGATCAGAAGC 58.072 50.000 0.00 0.00 0.00 3.86
492 496 0.248661 ATGACGGACGATCAGAAGCG 60.249 55.000 0.00 0.00 40.92 4.68
493 497 1.303091 TGACGGACGATCAGAAGCGA 61.303 55.000 0.00 0.00 37.81 4.93
494 498 0.029567 GACGGACGATCAGAAGCGAT 59.970 55.000 0.00 0.00 37.81 4.58
495 499 1.263484 GACGGACGATCAGAAGCGATA 59.737 52.381 0.00 0.00 37.81 2.92
496 500 1.264557 ACGGACGATCAGAAGCGATAG 59.735 52.381 0.00 0.00 37.81 2.08
561 565 8.592105 AGTTTGTTTATTCAAATGATGTGTGG 57.408 30.769 0.00 0.00 39.09 4.17
562 566 7.171337 AGTTTGTTTATTCAAATGATGTGTGGC 59.829 33.333 0.00 0.00 39.09 5.01
563 567 6.094193 TGTTTATTCAAATGATGTGTGGCA 57.906 33.333 0.00 0.00 0.00 4.92
564 568 6.157904 TGTTTATTCAAATGATGTGTGGCAG 58.842 36.000 0.00 0.00 0.00 4.85
565 569 5.981088 TTATTCAAATGATGTGTGGCAGT 57.019 34.783 0.00 0.00 0.00 4.40
566 570 3.921119 TTCAAATGATGTGTGGCAGTC 57.079 42.857 0.00 0.00 0.00 3.51
567 571 2.861274 TCAAATGATGTGTGGCAGTCA 58.139 42.857 0.00 0.00 0.00 3.41
568 572 2.815503 TCAAATGATGTGTGGCAGTCAG 59.184 45.455 0.00 0.00 0.00 3.51
569 573 2.815503 CAAATGATGTGTGGCAGTCAGA 59.184 45.455 0.00 0.00 0.00 3.27
570 574 3.361281 AATGATGTGTGGCAGTCAGAT 57.639 42.857 0.00 0.00 0.00 2.90
571 575 4.492494 AATGATGTGTGGCAGTCAGATA 57.508 40.909 0.00 0.00 0.00 1.98
572 576 3.979101 TGATGTGTGGCAGTCAGATAA 57.021 42.857 0.00 0.00 0.00 1.75
573 577 3.865446 TGATGTGTGGCAGTCAGATAAG 58.135 45.455 0.00 0.00 0.00 1.73
574 578 2.768253 TGTGTGGCAGTCAGATAAGG 57.232 50.000 0.00 0.00 0.00 2.69
575 579 1.339055 TGTGTGGCAGTCAGATAAGGC 60.339 52.381 0.00 0.00 0.00 4.35
576 580 1.065854 GTGTGGCAGTCAGATAAGGCT 60.066 52.381 0.00 0.00 0.00 4.58
577 581 1.630369 TGTGGCAGTCAGATAAGGCTT 59.370 47.619 4.58 4.58 0.00 4.35
578 582 2.040278 TGTGGCAGTCAGATAAGGCTTT 59.960 45.455 4.45 0.00 0.00 3.51
579 583 2.421424 GTGGCAGTCAGATAAGGCTTTG 59.579 50.000 4.45 0.00 0.00 2.77
580 584 2.040278 TGGCAGTCAGATAAGGCTTTGT 59.960 45.455 4.45 0.00 0.00 2.83
581 585 2.680339 GGCAGTCAGATAAGGCTTTGTC 59.320 50.000 4.45 4.58 0.00 3.18
582 586 2.680339 GCAGTCAGATAAGGCTTTGTCC 59.320 50.000 4.45 0.00 0.00 4.02
583 587 3.620966 GCAGTCAGATAAGGCTTTGTCCT 60.621 47.826 4.45 0.00 38.31 3.85
585 589 5.006386 CAGTCAGATAAGGCTTTGTCCTTT 58.994 41.667 4.45 0.00 43.62 3.11
586 590 5.123027 CAGTCAGATAAGGCTTTGTCCTTTC 59.877 44.000 4.45 0.00 43.62 2.62
587 591 5.013599 AGTCAGATAAGGCTTTGTCCTTTCT 59.986 40.000 4.45 2.00 43.62 2.52
588 592 5.352846 GTCAGATAAGGCTTTGTCCTTTCTC 59.647 44.000 4.45 0.00 43.62 2.87
589 593 5.013079 TCAGATAAGGCTTTGTCCTTTCTCA 59.987 40.000 4.45 0.00 43.62 3.27
590 594 5.884792 CAGATAAGGCTTTGTCCTTTCTCAT 59.115 40.000 4.45 0.00 43.62 2.90
591 595 6.038050 CAGATAAGGCTTTGTCCTTTCTCATC 59.962 42.308 4.45 0.00 43.62 2.92
592 596 3.795688 AGGCTTTGTCCTTTCTCATCA 57.204 42.857 0.00 0.00 30.82 3.07
593 597 4.313020 AGGCTTTGTCCTTTCTCATCAT 57.687 40.909 0.00 0.00 30.82 2.45
594 598 4.268359 AGGCTTTGTCCTTTCTCATCATC 58.732 43.478 0.00 0.00 30.82 2.92
595 599 4.018597 AGGCTTTGTCCTTTCTCATCATCT 60.019 41.667 0.00 0.00 30.82 2.90
596 600 5.190528 AGGCTTTGTCCTTTCTCATCATCTA 59.809 40.000 0.00 0.00 30.82 1.98
597 601 5.526846 GGCTTTGTCCTTTCTCATCATCTAG 59.473 44.000 0.00 0.00 0.00 2.43
598 602 6.344500 GCTTTGTCCTTTCTCATCATCTAGA 58.656 40.000 0.00 0.00 0.00 2.43
599 603 6.991531 GCTTTGTCCTTTCTCATCATCTAGAT 59.008 38.462 0.00 0.00 37.48 1.98
618 622 9.838339 ATCTAGATGAGATTTTAACAAATCCGT 57.162 29.630 3.89 0.00 46.80 4.69
653 657 0.179000 AAATAGAGCACGAGGGCCTG 59.821 55.000 12.95 6.05 0.00 4.85
660 664 2.852075 ACGAGGGCCTGGTGGAAA 60.852 61.111 21.21 0.00 34.57 3.13
670 674 4.141801 GGGCCTGGTGGAAATAATAAAACC 60.142 45.833 0.84 0.00 34.57 3.27
676 680 4.082136 GGTGGAAATAATAAAACCGTGCCA 60.082 41.667 0.00 0.00 0.00 4.92
681 685 7.339721 TGGAAATAATAAAACCGTGCCAATAGA 59.660 33.333 0.00 0.00 0.00 1.98
860 878 3.431725 GCCCGAGGCGAAAACCAG 61.432 66.667 0.00 0.00 39.62 4.00
923 941 2.029020 CCAAGAACTCCGAGACACATCA 60.029 50.000 1.33 0.00 0.00 3.07
924 942 3.249091 CAAGAACTCCGAGACACATCAG 58.751 50.000 1.33 0.00 0.00 2.90
925 943 1.203523 AGAACTCCGAGACACATCAGC 59.796 52.381 1.33 0.00 0.00 4.26
927 945 1.226802 CTCCGAGACACATCAGCCG 60.227 63.158 0.00 0.00 0.00 5.52
928 946 2.202797 CCGAGACACATCAGCCGG 60.203 66.667 0.00 0.00 0.00 6.13
944 964 1.792006 CCGGTTATCCACGGCTATTC 58.208 55.000 0.00 0.00 43.96 1.75
965 985 1.442526 CCTGCATCAATCTGGTCCGC 61.443 60.000 0.00 0.00 0.00 5.54
1241 1278 1.977544 CCGACCGTGAGTTCCTCCT 60.978 63.158 0.00 0.00 0.00 3.69
1262 1312 3.157949 CTCTCTTCCTCCCCGCCC 61.158 72.222 0.00 0.00 0.00 6.13
1300 1351 3.733337 GATGCGATTCCTGTAATCCTGT 58.267 45.455 0.00 0.00 40.91 4.00
1306 1357 4.509230 CGATTCCTGTAATCCTGTGATGTG 59.491 45.833 0.00 0.00 40.91 3.21
1308 1359 2.505407 TCCTGTAATCCTGTGATGTGGG 59.495 50.000 0.00 0.00 0.00 4.61
1310 1361 3.137176 CCTGTAATCCTGTGATGTGGGAT 59.863 47.826 0.00 0.00 41.09 3.85
1311 1362 4.384056 CTGTAATCCTGTGATGTGGGATC 58.616 47.826 0.00 0.00 38.73 3.36
1313 1364 3.572632 AATCCTGTGATGTGGGATCTG 57.427 47.619 0.00 0.00 38.73 2.90
1314 1365 0.543277 TCCTGTGATGTGGGATCTGC 59.457 55.000 0.00 0.00 0.00 4.26
1315 1366 0.812811 CCTGTGATGTGGGATCTGCG 60.813 60.000 0.00 0.00 0.00 5.18
1317 1368 0.832626 TGTGATGTGGGATCTGCGAT 59.167 50.000 0.00 0.00 0.00 4.58
1318 1369 1.210234 TGTGATGTGGGATCTGCGATT 59.790 47.619 0.00 0.00 0.00 3.34
1319 1370 2.433970 TGTGATGTGGGATCTGCGATTA 59.566 45.455 0.00 0.00 0.00 1.75
1321 1372 3.434641 GTGATGTGGGATCTGCGATTATG 59.565 47.826 0.00 0.00 0.00 1.90
1322 1373 1.882912 TGTGGGATCTGCGATTATGC 58.117 50.000 0.00 0.00 0.00 3.14
1323 1374 1.160137 GTGGGATCTGCGATTATGCC 58.840 55.000 0.00 0.00 34.40 4.40
1324 1375 0.764271 TGGGATCTGCGATTATGCCA 59.236 50.000 0.00 1.34 40.81 4.92
1325 1376 1.271001 TGGGATCTGCGATTATGCCAG 60.271 52.381 0.00 0.00 38.52 4.85
1326 1377 1.271054 GGGATCTGCGATTATGCCAGT 60.271 52.381 0.00 0.00 34.01 4.00
1327 1378 2.028112 GGGATCTGCGATTATGCCAGTA 60.028 50.000 0.00 0.00 34.01 2.74
1328 1379 3.369892 GGGATCTGCGATTATGCCAGTAT 60.370 47.826 0.00 0.00 34.01 2.12
1329 1380 3.620374 GGATCTGCGATTATGCCAGTATG 59.380 47.826 0.00 0.00 0.00 2.39
1330 1381 4.498241 GATCTGCGATTATGCCAGTATGA 58.502 43.478 0.00 0.00 39.69 2.15
1331 1382 4.541973 TCTGCGATTATGCCAGTATGAT 57.458 40.909 0.00 0.00 39.69 2.45
1332 1383 4.898320 TCTGCGATTATGCCAGTATGATT 58.102 39.130 0.00 0.00 39.69 2.57
1333 1384 5.308014 TCTGCGATTATGCCAGTATGATTT 58.692 37.500 0.00 0.00 39.69 2.17
1334 1385 6.463360 TCTGCGATTATGCCAGTATGATTTA 58.537 36.000 0.00 0.00 39.69 1.40
1335 1386 6.591448 TCTGCGATTATGCCAGTATGATTTAG 59.409 38.462 0.00 0.00 39.69 1.85
1336 1387 5.122239 TGCGATTATGCCAGTATGATTTAGC 59.878 40.000 0.00 0.00 39.69 3.09
1337 1388 5.352569 GCGATTATGCCAGTATGATTTAGCT 59.647 40.000 0.00 0.00 39.69 3.32
1338 1389 6.128172 GCGATTATGCCAGTATGATTTAGCTT 60.128 38.462 0.00 0.00 39.69 3.74
1339 1390 7.239271 CGATTATGCCAGTATGATTTAGCTTG 58.761 38.462 0.00 0.00 39.69 4.01
1340 1391 4.843220 ATGCCAGTATGATTTAGCTTGC 57.157 40.909 0.00 0.00 39.69 4.01
1373 1424 0.583917 GCGCGAATTGAGGGATCTTC 59.416 55.000 12.10 0.00 0.00 2.87
1382 1433 3.467226 GGGATCTTCGCGGTGGGA 61.467 66.667 6.13 0.00 0.00 4.37
1384 1435 2.722201 GGATCTTCGCGGTGGGAGT 61.722 63.158 6.13 0.00 0.00 3.85
1386 1437 1.079127 ATCTTCGCGGTGGGAGTTG 60.079 57.895 6.13 0.00 0.00 3.16
1388 1439 3.530910 CTTCGCGGTGGGAGTTGGT 62.531 63.158 6.13 0.00 0.00 3.67
1389 1440 3.524648 TTCGCGGTGGGAGTTGGTC 62.525 63.158 6.13 0.00 0.00 4.02
1391 1442 2.112297 GCGGTGGGAGTTGGTCAA 59.888 61.111 0.00 0.00 0.00 3.18
1393 1444 1.147376 CGGTGGGAGTTGGTCAACA 59.853 57.895 15.12 0.00 43.47 3.33
1394 1445 0.464735 CGGTGGGAGTTGGTCAACAA 60.465 55.000 15.12 0.00 43.47 2.83
1395 1446 1.770294 GGTGGGAGTTGGTCAACAAA 58.230 50.000 15.12 0.00 43.47 2.83
1396 1447 2.316108 GGTGGGAGTTGGTCAACAAAT 58.684 47.619 15.12 0.00 43.47 2.32
1398 1449 3.133901 GGTGGGAGTTGGTCAACAAATTT 59.866 43.478 15.12 0.00 43.47 1.82
1399 1450 4.368315 GTGGGAGTTGGTCAACAAATTTC 58.632 43.478 15.12 4.52 43.47 2.17
1400 1451 3.386402 TGGGAGTTGGTCAACAAATTTCC 59.614 43.478 15.12 11.91 43.47 3.13
1402 1453 3.316868 GGAGTTGGTCAACAAATTTCCGA 59.683 43.478 15.12 0.00 43.47 4.55
1403 1454 4.202070 GGAGTTGGTCAACAAATTTCCGAA 60.202 41.667 15.12 0.00 43.47 4.30
1404 1455 5.331876 AGTTGGTCAACAAATTTCCGAAA 57.668 34.783 15.12 0.00 43.47 3.46
1405 1456 5.348164 AGTTGGTCAACAAATTTCCGAAAG 58.652 37.500 15.12 0.00 43.47 2.62
1406 1457 4.993029 TGGTCAACAAATTTCCGAAAGT 57.007 36.364 0.00 0.00 0.00 2.66
1449 1500 1.476110 CCGAAAGTTGGGAGTTGGTCA 60.476 52.381 0.00 0.00 0.00 4.02
1509 2623 6.346598 CGGACATTTTCCAAGTGTATATAGCG 60.347 42.308 0.00 0.00 46.29 4.26
1526 2640 0.312102 GCGCAGGAAAGCTTGTTTCT 59.688 50.000 0.30 0.00 0.00 2.52
1638 3859 8.645110 ACATCAGGATCTTCAAAATTTTCAAGT 58.355 29.630 13.39 2.63 0.00 3.16
1737 3971 7.614908 CATCTGACAATGTTTTGTTTTCACTG 58.385 34.615 0.00 0.00 46.01 3.66
1911 4161 4.256920 CTGCTGTTCTTAGTACCTGCAAT 58.743 43.478 7.73 0.00 0.00 3.56
1965 4215 3.070302 GGAACCGAGGCATTAGAGAGATT 59.930 47.826 0.00 0.00 0.00 2.40
1990 4240 5.779241 AGATTGGATGTCAAAGGTAAGGA 57.221 39.130 0.00 0.00 39.05 3.36
1994 4246 4.513442 TGGATGTCAAAGGTAAGGATTCG 58.487 43.478 0.00 0.00 0.00 3.34
2068 4348 1.477295 GGGTAGAAGCTCTAACGCTGT 59.523 52.381 0.00 0.00 37.55 4.40
2217 4509 3.686016 TGGAGAAGGACAAATACTTGCC 58.314 45.455 0.00 0.00 35.84 4.52
2568 4902 5.644977 AAGACATCGAGATTGTGTACAGA 57.355 39.130 0.00 0.00 0.00 3.41
2576 4910 4.082733 CGAGATTGTGTACAGACCTCTCAA 60.083 45.833 21.89 11.82 0.00 3.02
2683 5017 3.137360 AGAAGCACTTCCTCCTGTTTCTT 59.863 43.478 6.77 0.00 35.19 2.52
3011 5353 5.319453 AGATGCTCTGACCAAGAAAATGAA 58.681 37.500 0.00 0.00 33.37 2.57
3036 5378 0.743688 CCATCGAGCAGCTCAGTACT 59.256 55.000 22.49 0.00 0.00 2.73
3354 5715 7.277760 TGAGTTCGTCCATTGTATAGTGAATTG 59.722 37.037 0.00 0.00 0.00 2.32
3410 7019 5.359576 AGACAGCAAAATGTTTGTACTCCAA 59.640 36.000 2.92 0.00 32.25 3.53
3581 7213 6.345298 TGGATTTTTCCTTTGGTTTGAGTTC 58.655 36.000 0.00 0.00 0.00 3.01
3594 7226 4.868171 GGTTTGAGTTCCAAAGAAACAACC 59.132 41.667 0.00 0.00 44.64 3.77
3600 7232 3.799281 TCCAAAGAAACAACCAAGCAG 57.201 42.857 0.00 0.00 0.00 4.24
3778 7417 2.154462 CACTCAATCCCGCAAAGTTCT 58.846 47.619 0.00 0.00 0.00 3.01
3787 7426 3.886505 TCCCGCAAAGTTCTTGTGTTTAT 59.113 39.130 0.00 0.00 0.00 1.40
3900 7539 9.930693 AACTCTTAAAACCTGAGATACTGTTAG 57.069 33.333 0.00 0.00 0.00 2.34
3901 7540 9.310449 ACTCTTAAAACCTGAGATACTGTTAGA 57.690 33.333 0.00 0.00 0.00 2.10
3903 7542 9.924650 TCTTAAAACCTGAGATACTGTTAGAAC 57.075 33.333 0.00 0.00 0.00 3.01
3904 7543 9.930693 CTTAAAACCTGAGATACTGTTAGAACT 57.069 33.333 0.00 0.00 0.00 3.01
3923 7565 4.697756 CCGGCCTCCTCGTTGCAA 62.698 66.667 0.00 0.00 0.00 4.08
3925 7567 3.056328 GGCCTCCTCGTTGCAACC 61.056 66.667 23.42 7.55 0.00 3.77
3957 7601 6.992123 TGAAATTATTCATGGATAGCGACTGT 59.008 34.615 0.00 0.00 40.59 3.55
3961 7605 1.206849 TCATGGATAGCGACTGTTGCA 59.793 47.619 21.37 8.45 33.85 4.08
3975 7620 1.404748 TGTTGCACAGTGTGGTCATTG 59.595 47.619 24.24 0.00 37.33 2.82
4108 7805 8.594550 AGGTTTGAACAACTCATAGTATGTAGT 58.405 33.333 9.94 9.13 32.78 2.73
4112 7809 9.529325 TTGAACAACTCATAGTATGTAGTATGC 57.471 33.333 9.94 4.73 38.74 3.14
4120 8463 7.975750 TCATAGTATGTAGTATGCTTAGCTCG 58.024 38.462 9.94 0.00 38.74 5.03
4126 8469 4.643334 TGTAGTATGCTTAGCTCGAAGGAA 59.357 41.667 5.60 0.00 29.93 3.36
4143 8486 6.092670 TCGAAGGAAGATGCAAATTCAGTTAG 59.907 38.462 14.16 8.52 0.00 2.34
4150 8493 3.609853 TGCAAATTCAGTTAGCGGAGAT 58.390 40.909 0.00 0.00 0.00 2.75
4151 8494 3.374988 TGCAAATTCAGTTAGCGGAGATG 59.625 43.478 0.00 0.00 0.00 2.90
4152 8495 3.790123 GCAAATTCAGTTAGCGGAGATGC 60.790 47.826 0.00 0.00 0.00 3.91
4153 8496 2.988010 ATTCAGTTAGCGGAGATGCA 57.012 45.000 0.00 0.00 37.31 3.96
4154 8497 2.760634 TTCAGTTAGCGGAGATGCAA 57.239 45.000 0.00 0.00 37.31 4.08
4155 8498 2.010145 TCAGTTAGCGGAGATGCAAC 57.990 50.000 0.00 0.00 37.31 4.17
4156 8499 0.647410 CAGTTAGCGGAGATGCAACG 59.353 55.000 0.00 0.00 37.31 4.10
4157 8500 0.530744 AGTTAGCGGAGATGCAACGA 59.469 50.000 7.50 0.00 37.31 3.85
4158 8501 0.924090 GTTAGCGGAGATGCAACGAG 59.076 55.000 7.50 0.00 37.31 4.18
4162 8505 1.424493 GCGGAGATGCAACGAGGAAG 61.424 60.000 7.50 0.00 34.15 3.46
4196 8539 2.210013 TGCAGTCAGTCTCGGGCTT 61.210 57.895 0.00 0.00 0.00 4.35
4198 8541 1.079543 CAGTCAGTCTCGGGCTTGG 60.080 63.158 0.00 0.00 0.00 3.61
4209 8552 1.667722 GGGCTTGGGCTTGTCTTTG 59.332 57.895 0.00 0.00 38.73 2.77
4211 8554 0.600057 GGCTTGGGCTTGTCTTTGAG 59.400 55.000 0.00 0.00 38.73 3.02
4213 8556 1.268079 GCTTGGGCTTGTCTTTGAGAC 59.732 52.381 1.21 1.21 39.38 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 8.325787 AGTATGTTATATATGGAAATCGCCCAA 58.674 33.333 0.00 0.00 37.22 4.12
192 196 0.793861 TTGCTAAGTGCCGCTTAACG 59.206 50.000 0.00 0.00 39.01 3.18
210 214 7.069085 TCAGTTGGCGTAATATAGAGTTACCTT 59.931 37.037 0.00 0.00 0.00 3.50
216 220 7.169308 CGAATTTCAGTTGGCGTAATATAGAGT 59.831 37.037 0.00 0.00 0.00 3.24
253 257 1.270550 CTCGTCCCAATTTTTGCAGCT 59.729 47.619 0.00 0.00 0.00 4.24
320 324 4.222145 CCAAGTAGACAAACCAGCCTACTA 59.778 45.833 0.00 0.00 40.42 1.82
322 326 3.335579 CCAAGTAGACAAACCAGCCTAC 58.664 50.000 0.00 0.00 33.55 3.18
328 332 3.201266 AGACAACCCAAGTAGACAAACCA 59.799 43.478 0.00 0.00 0.00 3.67
340 344 2.990740 AATGCCCTTAGACAACCCAA 57.009 45.000 0.00 0.00 0.00 4.12
342 346 1.743394 CGAAATGCCCTTAGACAACCC 59.257 52.381 0.00 0.00 0.00 4.11
344 348 2.544480 GCGAAATGCCCTTAGACAAC 57.456 50.000 0.00 0.00 37.76 3.32
362 366 4.051922 CGATAACCTCTGGTTCATGTAGC 58.948 47.826 5.16 0.00 43.05 3.58
407 411 3.332034 CCGTAAGTGGGAAAACGATTCT 58.668 45.455 0.00 0.00 37.53 2.40
432 436 5.153950 TGGTAAAAATTACCCACCAATGC 57.846 39.130 14.88 0.00 36.36 3.56
435 439 6.809976 AAGTTGGTAAAAATTACCCACCAA 57.190 33.333 15.85 8.85 44.76 3.67
436 440 7.909485 TTAAGTTGGTAAAAATTACCCACCA 57.091 32.000 15.85 5.91 34.75 4.17
437 441 8.423349 ACTTTAAGTTGGTAAAAATTACCCACC 58.577 33.333 15.85 6.08 34.75 4.61
438 442 9.251792 CACTTTAAGTTGGTAAAAATTACCCAC 57.748 33.333 14.88 13.90 36.79 4.61
439 443 8.979534 ACACTTTAAGTTGGTAAAAATTACCCA 58.020 29.630 14.88 3.34 36.79 4.51
456 460 9.257865 CGTCCGTCATTAAAATTACACTTTAAG 57.742 33.333 0.00 0.00 33.10 1.85
457 461 8.986847 TCGTCCGTCATTAAAATTACACTTTAA 58.013 29.630 0.00 0.00 33.87 1.52
458 462 8.531622 TCGTCCGTCATTAAAATTACACTTTA 57.468 30.769 0.00 0.00 0.00 1.85
459 463 7.424227 TCGTCCGTCATTAAAATTACACTTT 57.576 32.000 0.00 0.00 0.00 2.66
460 464 7.332430 TGATCGTCCGTCATTAAAATTACACTT 59.668 33.333 0.00 0.00 0.00 3.16
461 465 6.814644 TGATCGTCCGTCATTAAAATTACACT 59.185 34.615 0.00 0.00 0.00 3.55
462 466 6.996106 TGATCGTCCGTCATTAAAATTACAC 58.004 36.000 0.00 0.00 0.00 2.90
463 467 7.036829 TCTGATCGTCCGTCATTAAAATTACA 58.963 34.615 0.00 0.00 0.00 2.41
464 468 7.459394 TCTGATCGTCCGTCATTAAAATTAC 57.541 36.000 0.00 0.00 0.00 1.89
465 469 7.254319 GCTTCTGATCGTCCGTCATTAAAATTA 60.254 37.037 0.00 0.00 0.00 1.40
466 470 6.456988 GCTTCTGATCGTCCGTCATTAAAATT 60.457 38.462 0.00 0.00 0.00 1.82
467 471 5.006746 GCTTCTGATCGTCCGTCATTAAAAT 59.993 40.000 0.00 0.00 0.00 1.82
468 472 4.328983 GCTTCTGATCGTCCGTCATTAAAA 59.671 41.667 0.00 0.00 0.00 1.52
469 473 3.863424 GCTTCTGATCGTCCGTCATTAAA 59.137 43.478 0.00 0.00 0.00 1.52
470 474 3.444916 GCTTCTGATCGTCCGTCATTAA 58.555 45.455 0.00 0.00 0.00 1.40
471 475 2.540973 CGCTTCTGATCGTCCGTCATTA 60.541 50.000 0.00 0.00 0.00 1.90
472 476 1.799181 CGCTTCTGATCGTCCGTCATT 60.799 52.381 0.00 0.00 0.00 2.57
473 477 0.248661 CGCTTCTGATCGTCCGTCAT 60.249 55.000 0.00 0.00 0.00 3.06
474 478 1.136774 CGCTTCTGATCGTCCGTCA 59.863 57.895 0.00 0.00 0.00 4.35
475 479 0.029567 ATCGCTTCTGATCGTCCGTC 59.970 55.000 0.00 0.00 0.00 4.79
476 480 1.264557 CTATCGCTTCTGATCGTCCGT 59.735 52.381 0.00 0.00 0.00 4.69
477 481 1.957089 CTATCGCTTCTGATCGTCCG 58.043 55.000 0.00 0.00 0.00 4.79
478 482 1.667467 GGCTATCGCTTCTGATCGTCC 60.667 57.143 0.00 0.00 36.09 4.79
479 483 1.692296 GGCTATCGCTTCTGATCGTC 58.308 55.000 0.00 0.00 36.09 4.20
480 484 0.039978 CGGCTATCGCTTCTGATCGT 60.040 55.000 0.00 0.00 36.09 3.73
481 485 2.718220 CGGCTATCGCTTCTGATCG 58.282 57.895 0.00 0.00 36.09 3.69
535 539 9.689976 CCACACATCATTTGAATAAACAAACTA 57.310 29.630 0.00 0.00 41.49 2.24
536 540 7.171337 GCCACACATCATTTGAATAAACAAACT 59.829 33.333 0.00 0.00 41.49 2.66
537 541 7.042187 TGCCACACATCATTTGAATAAACAAAC 60.042 33.333 0.00 0.00 41.49 2.93
538 542 6.988580 TGCCACACATCATTTGAATAAACAAA 59.011 30.769 0.00 0.00 42.58 2.83
539 543 6.519382 TGCCACACATCATTTGAATAAACAA 58.481 32.000 0.00 0.00 0.00 2.83
540 544 6.094193 TGCCACACATCATTTGAATAAACA 57.906 33.333 0.00 0.00 0.00 2.83
541 545 6.158598 ACTGCCACACATCATTTGAATAAAC 58.841 36.000 0.00 0.00 0.00 2.01
542 546 6.015603 TGACTGCCACACATCATTTGAATAAA 60.016 34.615 0.00 0.00 0.00 1.40
543 547 5.476254 TGACTGCCACACATCATTTGAATAA 59.524 36.000 0.00 0.00 0.00 1.40
544 548 5.008980 TGACTGCCACACATCATTTGAATA 58.991 37.500 0.00 0.00 0.00 1.75
545 549 3.827876 TGACTGCCACACATCATTTGAAT 59.172 39.130 0.00 0.00 0.00 2.57
546 550 3.220940 TGACTGCCACACATCATTTGAA 58.779 40.909 0.00 0.00 0.00 2.69
547 551 2.815503 CTGACTGCCACACATCATTTGA 59.184 45.455 0.00 0.00 0.00 2.69
548 552 2.815503 TCTGACTGCCACACATCATTTG 59.184 45.455 0.00 0.00 0.00 2.32
549 553 3.144657 TCTGACTGCCACACATCATTT 57.855 42.857 0.00 0.00 0.00 2.32
550 554 2.865119 TCTGACTGCCACACATCATT 57.135 45.000 0.00 0.00 0.00 2.57
551 555 4.449131 CTTATCTGACTGCCACACATCAT 58.551 43.478 0.00 0.00 0.00 2.45
552 556 3.369787 CCTTATCTGACTGCCACACATCA 60.370 47.826 0.00 0.00 0.00 3.07
553 557 3.201290 CCTTATCTGACTGCCACACATC 58.799 50.000 0.00 0.00 0.00 3.06
554 558 2.681976 GCCTTATCTGACTGCCACACAT 60.682 50.000 0.00 0.00 0.00 3.21
555 559 1.339055 GCCTTATCTGACTGCCACACA 60.339 52.381 0.00 0.00 0.00 3.72
556 560 1.065854 AGCCTTATCTGACTGCCACAC 60.066 52.381 0.00 0.00 0.00 3.82
557 561 1.279496 AGCCTTATCTGACTGCCACA 58.721 50.000 0.00 0.00 0.00 4.17
558 562 2.409948 AAGCCTTATCTGACTGCCAC 57.590 50.000 0.00 0.00 0.00 5.01
559 563 2.040278 ACAAAGCCTTATCTGACTGCCA 59.960 45.455 0.00 0.00 0.00 4.92
560 564 2.680339 GACAAAGCCTTATCTGACTGCC 59.320 50.000 0.00 0.00 0.00 4.85
561 565 2.680339 GGACAAAGCCTTATCTGACTGC 59.320 50.000 0.00 0.00 0.00 4.40
562 566 4.213564 AGGACAAAGCCTTATCTGACTG 57.786 45.455 0.00 0.00 33.46 3.51
563 567 4.917906 AAGGACAAAGCCTTATCTGACT 57.082 40.909 0.00 0.00 46.18 3.41
572 576 3.795688 TGATGAGAAAGGACAAAGCCT 57.204 42.857 0.00 0.00 40.93 4.58
573 577 4.268359 AGATGATGAGAAAGGACAAAGCC 58.732 43.478 0.00 0.00 0.00 4.35
574 578 6.344500 TCTAGATGATGAGAAAGGACAAAGC 58.656 40.000 0.00 0.00 0.00 3.51
626 630 4.358851 CCTCGTGCTCTATTTCTTCTCTG 58.641 47.826 0.00 0.00 0.00 3.35
653 657 4.082136 TGGCACGGTTTTATTATTTCCACC 60.082 41.667 0.00 0.00 0.00 4.61
660 664 9.361315 GTTTTTCTATTGGCACGGTTTTATTAT 57.639 29.630 0.00 0.00 0.00 1.28
670 674 1.135517 CCCCGTTTTTCTATTGGCACG 60.136 52.381 0.00 0.00 0.00 5.34
676 680 3.263425 TCAGCTCTCCCCGTTTTTCTATT 59.737 43.478 0.00 0.00 0.00 1.73
681 685 0.250770 GGTCAGCTCTCCCCGTTTTT 60.251 55.000 0.00 0.00 0.00 1.94
860 878 2.346365 GTGGAGGGGACGTGGAAC 59.654 66.667 0.00 0.00 0.00 3.62
925 943 1.792006 GAATAGCCGTGGATAACCGG 58.208 55.000 0.00 0.00 46.90 5.28
927 945 1.145803 GCGAATAGCCGTGGATAACC 58.854 55.000 0.00 0.00 40.81 2.85
943 963 0.462581 GACCAGATTGATGCAGGCGA 60.463 55.000 0.00 0.00 0.00 5.54
944 964 1.442526 GGACCAGATTGATGCAGGCG 61.443 60.000 0.00 0.00 0.00 5.52
965 985 0.461135 GCAGGCTTCTCCTCTCTCTG 59.539 60.000 0.00 0.00 45.52 3.35
1241 1278 1.615814 CGGGGAGGAAGAGAGAGGA 59.384 63.158 0.00 0.00 0.00 3.71
1262 1312 1.091771 ATCGACAGCAGCCAATTCGG 61.092 55.000 0.00 0.00 38.11 4.30
1300 1351 3.667360 CATAATCGCAGATCCCACATCA 58.333 45.455 0.00 0.00 45.12 3.07
1306 1357 1.271054 ACTGGCATAATCGCAGATCCC 60.271 52.381 0.00 0.00 45.12 3.85
1308 1359 4.498241 TCATACTGGCATAATCGCAGATC 58.502 43.478 0.00 0.00 45.12 2.75
1310 1361 4.541973 ATCATACTGGCATAATCGCAGA 57.458 40.909 0.00 0.00 45.75 4.26
1311 1362 5.618056 AAATCATACTGGCATAATCGCAG 57.382 39.130 0.00 0.00 0.00 5.18
1313 1364 5.352569 AGCTAAATCATACTGGCATAATCGC 59.647 40.000 0.00 0.00 0.00 4.58
1314 1365 6.974932 AGCTAAATCATACTGGCATAATCG 57.025 37.500 0.00 0.00 0.00 3.34
1315 1366 7.025963 GCAAGCTAAATCATACTGGCATAATC 58.974 38.462 0.00 0.00 0.00 1.75
1317 1368 5.241506 GGCAAGCTAAATCATACTGGCATAA 59.758 40.000 0.00 0.00 30.26 1.90
1318 1369 4.761739 GGCAAGCTAAATCATACTGGCATA 59.238 41.667 0.00 0.00 30.26 3.14
1319 1370 3.571401 GGCAAGCTAAATCATACTGGCAT 59.429 43.478 0.00 0.00 30.26 4.40
1321 1372 3.217626 AGGCAAGCTAAATCATACTGGC 58.782 45.455 0.00 0.00 0.00 4.85
1322 1373 3.496130 CGAGGCAAGCTAAATCATACTGG 59.504 47.826 0.00 0.00 0.00 4.00
1323 1374 4.122776 ACGAGGCAAGCTAAATCATACTG 58.877 43.478 0.00 0.00 0.00 2.74
1324 1375 4.408182 ACGAGGCAAGCTAAATCATACT 57.592 40.909 0.00 0.00 0.00 2.12
1325 1376 5.266242 CAAACGAGGCAAGCTAAATCATAC 58.734 41.667 0.00 0.00 0.00 2.39
1326 1377 4.335315 CCAAACGAGGCAAGCTAAATCATA 59.665 41.667 0.00 0.00 0.00 2.15
1327 1378 3.129287 CCAAACGAGGCAAGCTAAATCAT 59.871 43.478 0.00 0.00 0.00 2.45
1328 1379 2.487762 CCAAACGAGGCAAGCTAAATCA 59.512 45.455 0.00 0.00 0.00 2.57
1329 1380 3.136808 CCAAACGAGGCAAGCTAAATC 57.863 47.619 0.00 0.00 0.00 2.17
1373 1424 3.818121 TTGACCAACTCCCACCGCG 62.818 63.158 0.00 0.00 0.00 6.46
1382 1433 4.993029 TTCGGAAATTTGTTGACCAACT 57.007 36.364 13.26 0.00 41.67 3.16
1384 1435 5.331876 ACTTTCGGAAATTTGTTGACCAA 57.668 34.783 3.24 0.00 0.00 3.67
1386 1437 4.506288 CCAACTTTCGGAAATTTGTTGACC 59.494 41.667 24.21 1.57 37.53 4.02
1388 1439 4.402793 TCCCAACTTTCGGAAATTTGTTGA 59.597 37.500 24.21 18.92 37.53 3.18
1389 1440 4.688021 TCCCAACTTTCGGAAATTTGTTG 58.312 39.130 23.44 21.32 35.82 3.33
1391 1442 3.958147 ACTCCCAACTTTCGGAAATTTGT 59.042 39.130 23.44 9.52 31.39 2.83
1393 1444 4.202212 CCAACTCCCAACTTTCGGAAATTT 60.202 41.667 3.24 1.86 0.00 1.82
1394 1445 3.320826 CCAACTCCCAACTTTCGGAAATT 59.679 43.478 3.24 0.00 0.00 1.82
1395 1446 2.890945 CCAACTCCCAACTTTCGGAAAT 59.109 45.455 3.24 0.00 0.00 2.17
1396 1447 2.303175 CCAACTCCCAACTTTCGGAAA 58.697 47.619 2.78 2.78 0.00 3.13
1398 1449 0.841289 ACCAACTCCCAACTTTCGGA 59.159 50.000 0.00 0.00 0.00 4.55
1399 1450 1.235724 GACCAACTCCCAACTTTCGG 58.764 55.000 0.00 0.00 0.00 4.30
1400 1451 1.961793 TGACCAACTCCCAACTTTCG 58.038 50.000 0.00 0.00 0.00 3.46
1402 1453 3.094484 TGTTGACCAACTCCCAACTTT 57.906 42.857 13.26 0.00 41.67 2.66
1403 1454 2.818751 TGTTGACCAACTCCCAACTT 57.181 45.000 13.26 0.00 41.67 2.66
1404 1455 2.818751 TTGTTGACCAACTCCCAACT 57.181 45.000 13.26 0.00 41.67 3.16
1424 1475 3.243401 CCAACTCCCAACTTTCGGAAAAG 60.243 47.826 4.53 0.79 46.11 2.27
1441 1492 3.445805 ACACCGAAAATGTTTGACCAACT 59.554 39.130 0.00 0.00 36.21 3.16
1449 1500 4.200874 TGGTCAGTACACCGAAAATGTTT 58.799 39.130 0.00 0.00 39.62 2.83
1509 2623 3.067320 ACAAGAGAAACAAGCTTTCCTGC 59.933 43.478 0.00 0.00 0.00 4.85
1526 2640 4.439057 ACTGCAGAGTAAAAACGACAAGA 58.561 39.130 23.35 0.00 0.00 3.02
1737 3971 3.758554 TCTTTTCTTTCATGTAGCCTGGC 59.241 43.478 11.65 11.65 0.00 4.85
1911 4161 4.201871 GCGACCACATAAATTTCCATTCGA 60.202 41.667 0.00 0.00 0.00 3.71
1965 4215 6.214615 TCCTTACCTTTGACATCCAATCTACA 59.785 38.462 0.00 0.00 34.23 2.74
2020 4297 6.928492 ACTGTGTTCTTGAACAACAACAAAAT 59.072 30.769 16.46 0.00 35.53 1.82
2217 4509 3.815809 TCTGACAACCTGTTTAACCTGG 58.184 45.455 0.00 0.00 0.00 4.45
2576 4910 2.831333 CGGCAGCTTCATACATCTCTT 58.169 47.619 0.00 0.00 0.00 2.85
2877 5211 0.710588 TAGAGTCCCTCCAAGCCTCA 59.289 55.000 0.00 0.00 0.00 3.86
3011 5353 2.681848 CTGAGCTGCTCGATGGATTTTT 59.318 45.455 23.35 0.00 32.35 1.94
3036 5378 3.055819 GGAGAAGTCTGTTCACTATGCCA 60.056 47.826 0.00 0.00 0.00 4.92
3410 7019 5.640357 CCATGATAATGCACAAAAGCTGTTT 59.360 36.000 0.00 0.00 35.47 2.83
3502 7125 7.500720 TCACATGAATGAATATTGCCACTAG 57.499 36.000 0.00 0.00 0.00 2.57
3581 7213 3.525268 ACTGCTTGGTTGTTTCTTTGG 57.475 42.857 0.00 0.00 0.00 3.28
3594 7226 4.067896 AGTGTGGATTGTAGAACTGCTTG 58.932 43.478 0.00 0.00 0.00 4.01
3600 7232 8.779354 AAAGAGATTAGTGTGGATTGTAGAAC 57.221 34.615 0.00 0.00 0.00 3.01
3749 7388 2.945008 GCGGGATTGAGTGATTGATTCA 59.055 45.455 0.00 0.00 0.00 2.57
3787 7426 9.802039 ACTTGGTTTGTAAAACAGAGGATTATA 57.198 29.630 5.33 0.00 36.87 0.98
3834 7473 2.915349 TGTAGTGGCACGTAAAAACCA 58.085 42.857 12.71 0.00 0.00 3.67
3892 7531 3.019564 GAGGCCGGTAGTTCTAACAGTA 58.980 50.000 1.90 0.00 0.00 2.74
3893 7532 1.823610 GAGGCCGGTAGTTCTAACAGT 59.176 52.381 1.90 0.00 0.00 3.55
3894 7533 1.136500 GGAGGCCGGTAGTTCTAACAG 59.864 57.143 1.90 0.00 0.00 3.16
3895 7534 1.188863 GGAGGCCGGTAGTTCTAACA 58.811 55.000 1.90 0.00 0.00 2.41
3896 7535 1.408340 GAGGAGGCCGGTAGTTCTAAC 59.592 57.143 1.90 0.00 0.00 2.34
3897 7536 1.772836 GAGGAGGCCGGTAGTTCTAA 58.227 55.000 1.90 0.00 0.00 2.10
3898 7537 0.465097 CGAGGAGGCCGGTAGTTCTA 60.465 60.000 1.90 0.00 0.00 2.10
3899 7538 1.753463 CGAGGAGGCCGGTAGTTCT 60.753 63.158 1.90 0.00 0.00 3.01
3900 7539 1.602327 AACGAGGAGGCCGGTAGTTC 61.602 60.000 1.90 0.00 0.00 3.01
3901 7540 1.608627 AACGAGGAGGCCGGTAGTT 60.609 57.895 1.90 0.00 0.00 2.24
3902 7541 2.036890 AACGAGGAGGCCGGTAGT 59.963 61.111 1.90 0.00 0.00 2.73
3903 7542 2.494918 CAACGAGGAGGCCGGTAG 59.505 66.667 1.90 0.00 0.00 3.18
3904 7543 3.766691 GCAACGAGGAGGCCGGTA 61.767 66.667 1.90 0.00 0.00 4.02
3923 7565 6.411376 TCCATGAATAATTTCAGTGTACGGT 58.589 36.000 0.00 0.00 44.75 4.83
3925 7567 8.223769 GCTATCCATGAATAATTTCAGTGTACG 58.776 37.037 0.00 0.00 44.75 3.67
3957 7601 1.761449 ACAATGACCACACTGTGCAA 58.239 45.000 7.90 0.00 35.13 4.08
3961 7605 3.620488 ACTGAAACAATGACCACACTGT 58.380 40.909 0.00 0.00 38.12 3.55
3964 7608 4.096382 ACAAGACTGAAACAATGACCACAC 59.904 41.667 0.00 0.00 0.00 3.82
3975 7620 9.788960 AAAGAGATTTAACAACAAGACTGAAAC 57.211 29.630 0.00 0.00 0.00 2.78
4108 7805 4.797604 GCATCTTCCTTCGAGCTAAGCATA 60.798 45.833 0.00 0.00 0.00 3.14
4112 7809 3.170791 TGCATCTTCCTTCGAGCTAAG 57.829 47.619 0.00 0.00 0.00 2.18
4120 8463 6.032717 GCTAACTGAATTTGCATCTTCCTTC 58.967 40.000 6.37 0.00 38.71 3.46
4126 8469 3.609853 TCCGCTAACTGAATTTGCATCT 58.390 40.909 0.00 0.00 38.78 2.90
4143 8486 1.424493 CTTCCTCGTTGCATCTCCGC 61.424 60.000 0.00 0.00 0.00 5.54
4150 8493 2.416747 CTGTTCATCTTCCTCGTTGCA 58.583 47.619 0.00 0.00 0.00 4.08
4151 8494 1.734465 CCTGTTCATCTTCCTCGTTGC 59.266 52.381 0.00 0.00 0.00 4.17
4152 8495 3.319137 TCCTGTTCATCTTCCTCGTTG 57.681 47.619 0.00 0.00 0.00 4.10
4153 8496 4.559862 ATTCCTGTTCATCTTCCTCGTT 57.440 40.909 0.00 0.00 0.00 3.85
4154 8497 5.187967 ACTTATTCCTGTTCATCTTCCTCGT 59.812 40.000 0.00 0.00 0.00 4.18
4155 8498 5.521735 CACTTATTCCTGTTCATCTTCCTCG 59.478 44.000 0.00 0.00 0.00 4.63
4156 8499 5.295540 GCACTTATTCCTGTTCATCTTCCTC 59.704 44.000 0.00 0.00 0.00 3.71
4157 8500 5.189180 GCACTTATTCCTGTTCATCTTCCT 58.811 41.667 0.00 0.00 0.00 3.36
4158 8501 4.943705 TGCACTTATTCCTGTTCATCTTCC 59.056 41.667 0.00 0.00 0.00 3.46
4162 8505 4.937620 TGACTGCACTTATTCCTGTTCATC 59.062 41.667 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.