Multiple sequence alignment - TraesCS5D01G424600

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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 TraesCS5D01G424600 chr5D 100.000 2726 0 0 1 2726 483718304 483715579 0.000000e+00 5035
1 TraesCS5D01G424600 chr5A 86.603 2202 189 48 453 2604 605233448 605231303 0.000000e+00 2335
2 TraesCS5D01G424600 chr5A 82.398 392 38 11 10 378 605233845 605233462 2.040000e-81 313
3 TraesCS5D01G424600 chr5A 91.935 124 9 1 2603 2725 605231144 605231021 3.610000e-39 172
4 TraesCS5D01G424600 chr5B 86.540 1679 136 38 458 2101 594922754 594921131 0.000000e+00 1766
5 TraesCS5D01G424600 chr5B 91.304 598 34 9 2144 2726 594921132 594920538 0.000000e+00 800
6 TraesCS5D01G424600 chr5B 79.500 400 32 18 10 378 594923130 594922750 3.510000e-59 239
7 TraesCS5D01G424600 chr4D 79.471 794 118 24 958 1731 201184888 201184120 3.110000e-144 521
8 TraesCS5D01G424600 chr1A 81.034 638 87 19 961 1578 67133961 67133338 6.830000e-131 477
9 TraesCS5D01G424600 chr7D 82.118 576 77 18 968 1529 289882463 289881900 1.140000e-128 470
10 TraesCS5D01G424600 chr6A 80.187 641 93 19 958 1578 497674290 497674916 1.490000e-122 449
11 TraesCS5D01G424600 chr1B 80.094 638 91 20 961 1578 525926110 525925489 2.490000e-120 442
12 TraesCS5D01G424600 chr2A 80.420 286 44 4 1322 1606 34883143 34883417 9.890000e-50 207
13 TraesCS5D01G424600 chr4B 83.453 139 20 2 1440 1578 536481936 536481801 2.850000e-25 126


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 TraesCS5D01G424600 chr5D 483715579 483718304 2725 True 5035 5035 100.000000 1 2726 1 chr5D.!!$R1 2725
1 TraesCS5D01G424600 chr5A 605231021 605233845 2824 True 940 2335 86.978667 10 2725 3 chr5A.!!$R1 2715
2 TraesCS5D01G424600 chr5B 594920538 594923130 2592 True 935 1766 85.781333 10 2726 3 chr5B.!!$R1 2716
3 TraesCS5D01G424600 chr4D 201184120 201184888 768 True 521 521 79.471000 958 1731 1 chr4D.!!$R1 773
4 TraesCS5D01G424600 chr1A 67133338 67133961 623 True 477 477 81.034000 961 1578 1 chr1A.!!$R1 617
5 TraesCS5D01G424600 chr7D 289881900 289882463 563 True 470 470 82.118000 968 1529 1 chr7D.!!$R1 561
6 TraesCS5D01G424600 chr6A 497674290 497674916 626 False 449 449 80.187000 958 1578 1 chr6A.!!$F1 620
7 TraesCS5D01G424600 chr1B 525925489 525926110 621 True 442 442 80.094000 961 1578 1 chr1B.!!$R1 617

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
446 478 0.035820 CCAGCGGGCCAAGTAAAGTA 60.036 55.0 4.39 0.00 0.00 2.24 F
694 733 0.108329 ATTACTTGGTCCGCGGACTG 60.108 55.0 46.25 37.08 44.04 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1462 1564 0.627451 AGCCATCCTCCAGAAATGCA 59.373 50.0 0.0 0.00 0.00 3.96 R
2356 2477 1.331214 ACAGGCCTGTCAAAACCATG 58.669 50.0 33.2 5.54 40.24 3.66 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
23 24 0.307760 GTGGTTACACAGTGCAGTGC 59.692 55.000 21.57 8.58 46.90 4.40
30 31 1.151668 CACAGTGCAGTGCCTAAGAC 58.848 55.000 21.57 3.27 32.04 3.01
34 35 2.161012 CAGTGCAGTGCCTAAGACATTG 59.839 50.000 13.72 0.00 0.00 2.82
44 45 4.082625 TGCCTAAGACATTGCAATCTGTTG 60.083 41.667 9.53 1.72 38.39 3.33
64 65 1.524621 ATGCAGGCCGTATGCTGTC 60.525 57.895 15.70 0.00 44.17 3.51
67 68 1.502163 GCAGGCCGTATGCTGTCATC 61.502 60.000 8.16 0.00 40.59 2.92
129 130 6.315144 TCATCGGTGATACCAAACACATAAAG 59.685 38.462 0.00 0.00 38.47 1.85
162 163 1.074405 TGCAGAGCAACCATTTCTCCT 59.926 47.619 0.00 0.00 34.76 3.69
173 174 2.749076 CCATTTCTCCTGCATTTCGACA 59.251 45.455 0.00 0.00 0.00 4.35
183 184 3.264947 TGCATTTCGACAGGAGAATCTG 58.735 45.455 0.00 0.00 40.40 2.90
184 185 2.031437 GCATTTCGACAGGAGAATCTGC 59.969 50.000 0.00 0.00 38.26 4.26
192 193 0.540923 AGGAGAATCTGCTGCTGGTC 59.459 55.000 2.74 5.11 35.09 4.02
203 210 0.883833 CTGCTGGTCGGCTGAAAAAT 59.116 50.000 0.00 0.00 33.89 1.82
204 211 0.597568 TGCTGGTCGGCTGAAAAATG 59.402 50.000 0.00 0.00 0.00 2.32
205 212 0.733909 GCTGGTCGGCTGAAAAATGC 60.734 55.000 0.00 0.00 0.00 3.56
206 213 0.597568 CTGGTCGGCTGAAAAATGCA 59.402 50.000 0.00 0.00 0.00 3.96
208 215 1.269517 TGGTCGGCTGAAAAATGCAAC 60.270 47.619 0.00 0.00 0.00 4.17
209 216 1.418373 GTCGGCTGAAAAATGCAACC 58.582 50.000 0.00 0.00 0.00 3.77
212 219 1.601663 CGGCTGAAAAATGCAACCGAA 60.602 47.619 0.00 0.00 45.20 4.30
217 224 4.376311 GCTGAAAAATGCAACCGAATCAAC 60.376 41.667 0.00 0.00 0.00 3.18
220 228 0.109319 AATGCAACCGAATCAACCGC 60.109 50.000 0.00 0.00 0.00 5.68
225 233 3.483665 CCGAATCAACCGCGCGAA 61.484 61.111 34.63 14.18 0.00 4.70
275 298 3.837893 TGGCATGTCCAAACTCCAA 57.162 47.368 6.42 0.00 43.21 3.53
276 299 2.079170 TGGCATGTCCAAACTCCAAA 57.921 45.000 6.42 0.00 43.21 3.28
296 319 1.558294 AGTTTTCCCCTCCGGATGTAC 59.442 52.381 3.57 0.00 41.63 2.90
299 322 0.754217 TTCCCCTCCGGATGTACGAG 60.754 60.000 3.57 0.00 41.63 4.18
303 326 2.290514 CCCCTCCGGATGTACGAGTATA 60.291 54.545 3.57 0.00 35.47 1.47
304 327 3.618351 CCCTCCGGATGTACGAGTATAT 58.382 50.000 3.57 0.00 35.47 0.86
305 328 3.626670 CCCTCCGGATGTACGAGTATATC 59.373 52.174 3.57 10.34 34.27 1.63
312 335 6.761099 GGATGTACGAGTATATCCACAGAT 57.239 41.667 24.74 0.00 46.69 2.90
313 336 6.556212 GGATGTACGAGTATATCCACAGATG 58.444 44.000 24.74 0.00 46.69 2.90
314 337 6.151312 GGATGTACGAGTATATCCACAGATGT 59.849 42.308 24.74 0.00 46.69 3.06
315 338 6.313744 TGTACGAGTATATCCACAGATGTG 57.686 41.667 5.97 5.97 45.23 3.21
316 339 4.244425 ACGAGTATATCCACAGATGTGC 57.756 45.455 7.46 0.00 44.34 4.57
317 340 3.636764 ACGAGTATATCCACAGATGTGCA 59.363 43.478 7.46 0.00 44.34 4.57
336 368 1.673665 GACTCTGCAAGCACCCTGG 60.674 63.158 0.00 0.00 0.00 4.45
344 376 1.210478 GCAAGCACCCTGGAGAATCTA 59.790 52.381 0.00 0.00 33.73 1.98
378 410 3.431673 TGTAAGTTGGCCATGTGATGA 57.568 42.857 6.09 0.00 0.00 2.92
379 411 3.346315 TGTAAGTTGGCCATGTGATGAG 58.654 45.455 6.09 0.00 0.00 2.90
380 412 2.885135 AAGTTGGCCATGTGATGAGA 57.115 45.000 6.09 0.00 0.00 3.27
381 413 2.414994 AGTTGGCCATGTGATGAGAG 57.585 50.000 6.09 0.00 0.00 3.20
382 414 1.632409 AGTTGGCCATGTGATGAGAGT 59.368 47.619 6.09 0.00 0.00 3.24
383 415 2.040813 AGTTGGCCATGTGATGAGAGTT 59.959 45.455 6.09 0.00 0.00 3.01
384 416 2.821969 GTTGGCCATGTGATGAGAGTTT 59.178 45.455 6.09 0.00 0.00 2.66
385 417 3.159213 TGGCCATGTGATGAGAGTTTT 57.841 42.857 0.00 0.00 0.00 2.43
386 418 2.821378 TGGCCATGTGATGAGAGTTTTG 59.179 45.455 0.00 0.00 0.00 2.44
387 419 2.821969 GGCCATGTGATGAGAGTTTTGT 59.178 45.455 0.00 0.00 0.00 2.83
388 420 3.366679 GGCCATGTGATGAGAGTTTTGTG 60.367 47.826 0.00 0.00 0.00 3.33
389 421 3.503363 GCCATGTGATGAGAGTTTTGTGA 59.497 43.478 0.00 0.00 0.00 3.58
390 422 4.379186 GCCATGTGATGAGAGTTTTGTGAG 60.379 45.833 0.00 0.00 0.00 3.51
391 423 4.155462 CCATGTGATGAGAGTTTTGTGAGG 59.845 45.833 0.00 0.00 0.00 3.86
405 437 1.003580 TGTGAGGGCATCTTCCAGTTC 59.996 52.381 0.00 0.00 0.00 3.01
406 438 0.620556 TGAGGGCATCTTCCAGTTCC 59.379 55.000 0.00 0.00 0.00 3.62
407 439 0.620556 GAGGGCATCTTCCAGTTCCA 59.379 55.000 0.00 0.00 0.00 3.53
408 440 1.004745 GAGGGCATCTTCCAGTTCCAA 59.995 52.381 0.00 0.00 0.00 3.53
409 441 1.005215 AGGGCATCTTCCAGTTCCAAG 59.995 52.381 0.00 0.00 0.00 3.61
410 442 1.004745 GGGCATCTTCCAGTTCCAAGA 59.995 52.381 0.00 0.00 33.18 3.02
411 443 2.363683 GGCATCTTCCAGTTCCAAGAG 58.636 52.381 0.00 0.00 32.16 2.85
412 444 2.026822 GGCATCTTCCAGTTCCAAGAGA 60.027 50.000 0.00 0.00 32.16 3.10
413 445 3.560025 GGCATCTTCCAGTTCCAAGAGAA 60.560 47.826 0.00 0.00 32.16 2.87
414 446 3.688673 GCATCTTCCAGTTCCAAGAGAAG 59.311 47.826 0.00 0.00 34.29 2.85
415 447 3.409026 TCTTCCAGTTCCAAGAGAAGC 57.591 47.619 0.00 0.00 34.29 3.86
416 448 2.072298 CTTCCAGTTCCAAGAGAAGCG 58.928 52.381 0.00 0.00 34.29 4.68
417 449 0.321671 TCCAGTTCCAAGAGAAGCGG 59.678 55.000 0.00 0.00 34.29 5.52
418 450 1.301677 CCAGTTCCAAGAGAAGCGGC 61.302 60.000 0.00 0.00 34.29 6.53
419 451 0.321122 CAGTTCCAAGAGAAGCGGCT 60.321 55.000 0.00 0.00 34.29 5.52
420 452 0.321122 AGTTCCAAGAGAAGCGGCTG 60.321 55.000 1.81 0.00 34.29 4.85
421 453 1.003355 TTCCAAGAGAAGCGGCTGG 60.003 57.895 1.81 0.00 0.00 4.85
422 454 3.130160 CCAAGAGAAGCGGCTGGC 61.130 66.667 1.81 0.00 44.05 4.85
423 455 3.130160 CAAGAGAAGCGGCTGGCC 61.130 66.667 1.81 0.00 45.17 5.36
424 456 3.325753 AAGAGAAGCGGCTGGCCT 61.326 61.111 1.81 0.90 45.17 5.19
425 457 3.618780 AAGAGAAGCGGCTGGCCTG 62.619 63.158 1.81 4.26 45.17 4.85
444 476 3.590824 CCAGCGGGCCAAGTAAAG 58.409 61.111 4.39 0.00 0.00 1.85
445 477 1.303317 CCAGCGGGCCAAGTAAAGT 60.303 57.895 4.39 0.00 0.00 2.66
446 478 0.035820 CCAGCGGGCCAAGTAAAGTA 60.036 55.000 4.39 0.00 0.00 2.24
447 479 1.408266 CCAGCGGGCCAAGTAAAGTAT 60.408 52.381 4.39 0.00 0.00 2.12
448 480 1.670811 CAGCGGGCCAAGTAAAGTATG 59.329 52.381 4.39 0.00 0.00 2.39
449 481 1.021968 GCGGGCCAAGTAAAGTATGG 58.978 55.000 4.39 0.00 37.29 2.74
456 488 0.916809 AAGTAAAGTATGGCCCGGCT 59.083 50.000 9.86 0.00 0.00 5.52
470 502 0.890683 CCGGCTTGAGGCATCTTTTT 59.109 50.000 0.00 0.00 44.01 1.94
508 547 3.898529 ACGCTTTCACTACTACTGTGAC 58.101 45.455 0.00 0.00 43.13 3.67
528 567 4.996113 GCGTATTGCAATGGACCG 57.004 55.556 22.27 17.51 45.45 4.79
603 642 4.630505 GCTAACTAAGCCTGTGGACTTAAC 59.369 45.833 0.00 0.00 46.25 2.01
604 643 4.976540 AACTAAGCCTGTGGACTTAACT 57.023 40.909 0.00 0.00 0.00 2.24
605 644 4.976540 ACTAAGCCTGTGGACTTAACTT 57.023 40.909 0.00 0.00 0.00 2.66
606 645 4.642429 ACTAAGCCTGTGGACTTAACTTG 58.358 43.478 0.00 0.00 0.00 3.16
607 646 2.568623 AGCCTGTGGACTTAACTTGG 57.431 50.000 0.00 0.00 0.00 3.61
608 647 2.054799 AGCCTGTGGACTTAACTTGGA 58.945 47.619 0.00 0.00 0.00 3.53
615 654 5.070001 TGTGGACTTAACTTGGATTGGAAG 58.930 41.667 0.00 0.00 0.00 3.46
633 672 2.604046 AGCCACGCTTAATCCTACTG 57.396 50.000 0.00 0.00 33.89 2.74
634 673 1.831736 AGCCACGCTTAATCCTACTGT 59.168 47.619 0.00 0.00 33.89 3.55
635 674 3.028850 AGCCACGCTTAATCCTACTGTA 58.971 45.455 0.00 0.00 33.89 2.74
636 675 3.068307 AGCCACGCTTAATCCTACTGTAG 59.932 47.826 7.87 7.87 33.89 2.74
637 676 3.067742 GCCACGCTTAATCCTACTGTAGA 59.932 47.826 16.22 3.27 0.00 2.59
638 677 4.262079 GCCACGCTTAATCCTACTGTAGAT 60.262 45.833 16.22 5.38 0.00 1.98
639 678 5.223382 CCACGCTTAATCCTACTGTAGATG 58.777 45.833 16.22 0.80 0.00 2.90
640 679 5.223382 CACGCTTAATCCTACTGTAGATGG 58.777 45.833 16.22 0.87 0.00 3.51
641 680 4.894114 ACGCTTAATCCTACTGTAGATGGT 59.106 41.667 16.22 1.70 0.00 3.55
642 681 5.009811 ACGCTTAATCCTACTGTAGATGGTC 59.990 44.000 16.22 0.00 0.00 4.02
643 682 5.462405 GCTTAATCCTACTGTAGATGGTCG 58.538 45.833 16.22 0.00 0.00 4.79
644 683 5.449107 TTAATCCTACTGTAGATGGTCGC 57.551 43.478 16.22 0.00 0.00 5.19
648 687 2.553172 CCTACTGTAGATGGTCGCTACC 59.447 54.545 16.22 0.00 46.98 3.18
650 689 2.299521 ACTGTAGATGGTCGCTACCTC 58.700 52.381 9.09 4.14 46.91 3.85
651 690 1.264557 CTGTAGATGGTCGCTACCTCG 59.735 57.143 9.09 0.00 46.91 4.63
652 691 1.307097 GTAGATGGTCGCTACCTCGT 58.693 55.000 9.09 0.00 46.91 4.18
654 693 1.183549 AGATGGTCGCTACCTCGTTT 58.816 50.000 9.09 0.00 46.91 3.60
655 694 1.549170 AGATGGTCGCTACCTCGTTTT 59.451 47.619 9.09 0.00 46.91 2.43
657 696 0.387622 TGGTCGCTACCTCGTTTTCG 60.388 55.000 9.09 0.00 46.91 3.46
658 697 1.681025 GGTCGCTACCTCGTTTTCGC 61.681 60.000 0.00 0.00 43.08 4.70
660 699 2.450345 CGCTACCTCGTTTTCGCCC 61.450 63.158 0.00 0.00 43.73 6.13
661 700 1.375013 GCTACCTCGTTTTCGCCCA 60.375 57.895 0.00 0.00 43.73 5.36
664 703 0.393820 TACCTCGTTTTCGCCCAAGT 59.606 50.000 0.00 0.00 43.73 3.16
665 704 0.393820 ACCTCGTTTTCGCCCAAGTA 59.606 50.000 0.00 0.00 43.73 2.24
666 705 1.202675 ACCTCGTTTTCGCCCAAGTAA 60.203 47.619 0.00 0.00 43.73 2.24
667 706 1.463444 CCTCGTTTTCGCCCAAGTAAG 59.537 52.381 0.00 0.00 43.73 2.34
668 707 2.409975 CTCGTTTTCGCCCAAGTAAGA 58.590 47.619 0.00 0.00 43.73 2.10
669 708 2.409975 TCGTTTTCGCCCAAGTAAGAG 58.590 47.619 0.00 0.00 43.73 2.85
670 709 1.136057 CGTTTTCGCCCAAGTAAGAGC 60.136 52.381 0.00 0.00 36.22 4.09
672 711 0.322187 TTTCGCCCAAGTAAGAGCCC 60.322 55.000 0.00 0.00 0.00 5.19
673 712 1.198759 TTCGCCCAAGTAAGAGCCCT 61.199 55.000 0.00 0.00 0.00 5.19
674 713 1.450312 CGCCCAAGTAAGAGCCCTG 60.450 63.158 0.00 0.00 0.00 4.45
675 714 1.899437 CGCCCAAGTAAGAGCCCTGA 61.899 60.000 0.00 0.00 0.00 3.86
676 715 0.548510 GCCCAAGTAAGAGCCCTGAT 59.451 55.000 0.00 0.00 0.00 2.90
677 716 1.064389 GCCCAAGTAAGAGCCCTGATT 60.064 52.381 0.00 0.00 0.00 2.57
678 717 2.172717 GCCCAAGTAAGAGCCCTGATTA 59.827 50.000 0.00 0.00 0.00 1.75
679 718 3.809905 CCCAAGTAAGAGCCCTGATTAC 58.190 50.000 0.00 0.00 0.00 1.89
680 719 3.456277 CCCAAGTAAGAGCCCTGATTACT 59.544 47.826 0.00 0.00 40.55 2.24
681 720 4.080299 CCCAAGTAAGAGCCCTGATTACTT 60.080 45.833 4.23 4.23 45.80 2.24
683 722 4.762289 AGTAAGAGCCCTGATTACTTGG 57.238 45.455 0.00 0.00 36.58 3.61
684 723 4.104831 AGTAAGAGCCCTGATTACTTGGT 58.895 43.478 0.00 0.00 36.58 3.67
685 724 3.636153 AAGAGCCCTGATTACTTGGTC 57.364 47.619 0.00 0.00 0.00 4.02
686 725 1.840635 AGAGCCCTGATTACTTGGTCC 59.159 52.381 0.00 0.00 0.00 4.46
687 726 0.541863 AGCCCTGATTACTTGGTCCG 59.458 55.000 0.00 0.00 0.00 4.79
688 727 1.095807 GCCCTGATTACTTGGTCCGC 61.096 60.000 0.00 0.00 0.00 5.54
689 728 0.810031 CCCTGATTACTTGGTCCGCG 60.810 60.000 0.00 0.00 0.00 6.46
690 729 0.810031 CCTGATTACTTGGTCCGCGG 60.810 60.000 22.12 22.12 0.00 6.46
691 730 0.174845 CTGATTACTTGGTCCGCGGA 59.825 55.000 27.28 27.28 0.00 5.54
692 731 0.108520 TGATTACTTGGTCCGCGGAC 60.109 55.000 43.30 43.30 43.87 4.79
693 732 0.175073 GATTACTTGGTCCGCGGACT 59.825 55.000 46.25 33.48 44.04 3.85
694 733 0.108329 ATTACTTGGTCCGCGGACTG 60.108 55.000 46.25 37.08 44.04 3.51
695 734 2.162338 TTACTTGGTCCGCGGACTGG 62.162 60.000 46.25 36.63 44.04 4.00
708 747 2.293399 GCGGACTGGAAACAAAAGTGAT 59.707 45.455 0.00 0.00 42.06 3.06
719 758 3.070018 ACAAAAGTGATCAGCGAAGAGG 58.930 45.455 0.00 0.00 0.00 3.69
760 799 6.994221 TCCACCTAAGTTTCAACTCTTCTAG 58.006 40.000 0.00 0.00 38.57 2.43
761 800 6.781014 TCCACCTAAGTTTCAACTCTTCTAGA 59.219 38.462 0.00 0.00 38.57 2.43
762 801 7.289317 TCCACCTAAGTTTCAACTCTTCTAGAA 59.711 37.037 4.81 4.81 38.57 2.10
763 802 7.931948 CCACCTAAGTTTCAACTCTTCTAGAAA 59.068 37.037 6.63 0.00 38.57 2.52
764 803 9.326413 CACCTAAGTTTCAACTCTTCTAGAAAA 57.674 33.333 6.63 0.00 38.57 2.29
765 804 9.901172 ACCTAAGTTTCAACTCTTCTAGAAAAA 57.099 29.630 6.63 0.33 38.57 1.94
888 938 2.125552 CGCGACCAGCCAAGATGA 60.126 61.111 0.00 0.00 44.76 2.92
889 939 1.522355 CGCGACCAGCCAAGATGAT 60.522 57.895 0.00 0.00 44.76 2.45
890 940 1.769098 CGCGACCAGCCAAGATGATG 61.769 60.000 0.00 0.00 44.76 3.07
908 958 0.179121 TGCGATACCTTGCGTACTGG 60.179 55.000 0.00 0.00 34.16 4.00
923 976 0.534412 ACTGGTGCTGCTGCTACTAG 59.466 55.000 17.00 19.16 40.48 2.57
930 983 1.751924 GCTGCTGCTACTAGTACACCT 59.248 52.381 8.53 0.00 36.03 4.00
1348 1446 3.751518 GGCTGAAGGTTTTCTTGGTCTA 58.248 45.455 0.00 0.00 35.50 2.59
1349 1447 3.502595 GGCTGAAGGTTTTCTTGGTCTAC 59.497 47.826 0.00 0.00 35.50 2.59
1393 1492 7.081976 GCTCGGTGTTTTATTACAGTTTCAAT 58.918 34.615 0.00 0.00 0.00 2.57
1395 1494 9.458374 CTCGGTGTTTTATTACAGTTTCAATTT 57.542 29.630 0.00 0.00 0.00 1.82
1405 1504 8.728088 ATTACAGTTTCAATTTGAACGATGAC 57.272 30.769 11.30 7.00 35.89 3.06
1406 1505 6.130298 ACAGTTTCAATTTGAACGATGACA 57.870 33.333 11.30 0.00 35.89 3.58
1418 1517 4.940654 TGAACGATGACATAGCCATGAAAA 59.059 37.500 0.00 0.00 35.96 2.29
1419 1518 5.414144 TGAACGATGACATAGCCATGAAAAA 59.586 36.000 0.00 0.00 35.96 1.94
1450 1549 3.005554 CCTGTGCATACCTCTGAACAAG 58.994 50.000 0.00 0.00 34.25 3.16
1460 1562 3.877508 ACCTCTGAACAAGTAAACAGCAC 59.122 43.478 0.00 0.00 0.00 4.40
1461 1563 4.130118 CCTCTGAACAAGTAAACAGCACT 58.870 43.478 0.00 0.00 0.00 4.40
1462 1564 4.576463 CCTCTGAACAAGTAAACAGCACTT 59.424 41.667 0.00 0.00 36.68 3.16
1480 1583 1.407979 CTTGCATTTCTGGAGGATGGC 59.592 52.381 0.00 0.00 0.00 4.40
1488 1591 1.573857 TCTGGAGGATGGCTAGTACCA 59.426 52.381 0.00 0.00 45.82 3.25
1505 1608 1.603802 ACCAATGTGTCTGTTGCTTCG 59.396 47.619 0.00 0.00 0.00 3.79
1506 1609 1.069022 CCAATGTGTCTGTTGCTTCGG 60.069 52.381 0.00 0.00 0.00 4.30
1515 1618 0.756294 TGTTGCTTCGGTTGGAGAGA 59.244 50.000 0.00 0.00 0.00 3.10
1516 1619 1.149148 GTTGCTTCGGTTGGAGAGAC 58.851 55.000 0.00 0.00 0.00 3.36
1732 1835 7.607615 TTGGATGATGAGATATGAGTTCAGA 57.392 36.000 0.00 0.00 0.00 3.27
1748 1851 9.956640 ATGAGTTCAGATTCTCTTACAAGAATT 57.043 29.630 1.05 0.00 44.16 2.17
1770 1874 5.917541 TTGTAAGAGTTAAGAAAGCGTGG 57.082 39.130 0.00 0.00 0.00 4.94
1776 1880 7.506328 AAGAGTTAAGAAAGCGTGGTTTATT 57.494 32.000 9.06 9.06 0.00 1.40
1778 1882 8.788325 AGAGTTAAGAAAGCGTGGTTTATTAT 57.212 30.769 11.07 0.31 0.00 1.28
1819 1923 0.681175 AACCATGCCAAACTTGAGCC 59.319 50.000 0.00 0.00 0.00 4.70
1822 1926 0.389426 CATGCCAAACTTGAGCCTGC 60.389 55.000 0.00 0.00 0.00 4.85
1823 1927 0.828762 ATGCCAAACTTGAGCCTGCA 60.829 50.000 0.00 0.00 0.00 4.41
1942 2047 9.703892 ATATCAGCTATGAAGTATGAACTCAAC 57.296 33.333 0.00 0.00 39.39 3.18
1944 2049 7.386059 TCAGCTATGAAGTATGAACTCAACAA 58.614 34.615 0.00 0.00 33.75 2.83
1945 2050 7.331934 TCAGCTATGAAGTATGAACTCAACAAC 59.668 37.037 0.00 0.00 33.75 3.32
1946 2051 6.595716 AGCTATGAAGTATGAACTCAACAACC 59.404 38.462 0.00 0.00 33.75 3.77
1947 2052 6.183360 GCTATGAAGTATGAACTCAACAACCC 60.183 42.308 0.00 0.00 33.75 4.11
1948 2053 5.042463 TGAAGTATGAACTCAACAACCCA 57.958 39.130 0.00 0.00 33.75 4.51
1949 2054 5.630121 TGAAGTATGAACTCAACAACCCAT 58.370 37.500 0.00 0.00 33.75 4.00
1950 2055 6.774673 TGAAGTATGAACTCAACAACCCATA 58.225 36.000 0.00 0.00 33.75 2.74
1990 2100 5.531287 ACGAACCAATTAGCTTCCATATTCC 59.469 40.000 0.00 0.00 0.00 3.01
2024 2134 7.088905 ACATCTGAAGAGCAAATGTGAATTTC 58.911 34.615 0.00 0.00 0.00 2.17
2125 2246 4.438148 GTCCTCTGTTCTAGATCCAAAGC 58.562 47.826 0.00 0.00 34.21 3.51
2135 2256 1.637553 AGATCCAAAGCCCTGTGACAT 59.362 47.619 0.00 0.00 0.00 3.06
2199 2320 7.988599 AGACTTGTTTGTAAGGTGTACACATAA 59.011 33.333 26.51 9.16 31.94 1.90
2277 2398 2.229792 ACAGGTCACGCACATTTCATT 58.770 42.857 0.00 0.00 0.00 2.57
2347 2468 4.786507 TGCTGTGAAAATGTTGAATCTCG 58.213 39.130 0.00 0.00 0.00 4.04
2356 2477 2.058798 TGTTGAATCTCGCGTGTTCTC 58.941 47.619 5.77 3.16 0.00 2.87
2365 2486 1.262950 TCGCGTGTTCTCATGGTTTTG 59.737 47.619 5.77 0.00 0.00 2.44
2460 2588 7.524912 CAACTCAGAACCAACAGAATTAGATG 58.475 38.462 0.00 0.00 0.00 2.90
2461 2601 5.645497 ACTCAGAACCAACAGAATTAGATGC 59.355 40.000 0.00 0.00 0.00 3.91
2463 2603 6.240894 TCAGAACCAACAGAATTAGATGCTT 58.759 36.000 0.00 0.00 0.00 3.91
2592 2736 7.762159 GGACAAAACTTTCCAAGAAATTACACA 59.238 33.333 0.00 0.00 0.00 3.72
2615 2919 9.113838 CACAAATAGCTTCTAGAACATTATGGT 57.886 33.333 0.00 0.00 0.00 3.55
2619 2923 5.121811 AGCTTCTAGAACATTATGGTGCAG 58.878 41.667 0.00 0.00 0.00 4.41
2689 2993 4.336889 AGCTTGCAGAACTTACACAGTA 57.663 40.909 0.00 0.00 32.94 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.307760 GCACTGCACTGTGTAACCAC 59.692 55.000 9.86 0.00 42.19 4.16
5 6 0.817634 GGCACTGCACTGTGTAACCA 60.818 55.000 9.86 0.00 39.89 3.67
6 7 0.535102 AGGCACTGCACTGTGTAACC 60.535 55.000 9.86 6.87 39.89 2.85
7 8 2.163818 TAGGCACTGCACTGTGTAAC 57.836 50.000 9.86 0.00 41.52 2.50
8 9 2.367241 TCTTAGGCACTGCACTGTGTAA 59.633 45.455 9.86 0.00 41.52 2.41
14 15 2.430465 CAATGTCTTAGGCACTGCACT 58.570 47.619 2.82 0.50 41.52 4.40
15 16 1.135575 GCAATGTCTTAGGCACTGCAC 60.136 52.381 15.48 0.00 41.52 4.57
44 45 2.903855 AGCATACGGCCTGCATGC 60.904 61.111 19.77 19.77 46.50 4.06
61 62 1.445410 CCCTTTCGACGCGATGACA 60.445 57.895 15.93 1.65 35.23 3.58
64 65 1.421410 CTTCCCCTTTCGACGCGATG 61.421 60.000 15.93 4.17 35.23 3.84
67 68 1.623973 GAACTTCCCCTTTCGACGCG 61.624 60.000 3.53 3.53 0.00 6.01
162 163 3.264947 CAGATTCTCCTGTCGAAATGCA 58.735 45.455 0.00 0.00 0.00 3.96
173 174 0.540923 GACCAGCAGCAGATTCTCCT 59.459 55.000 0.00 0.00 0.00 3.69
183 184 1.795170 TTTTTCAGCCGACCAGCAGC 61.795 55.000 0.00 0.00 34.23 5.25
184 185 0.883833 ATTTTTCAGCCGACCAGCAG 59.116 50.000 0.00 0.00 34.23 4.24
188 189 1.035923 TTGCATTTTTCAGCCGACCA 58.964 45.000 0.00 0.00 0.00 4.02
189 190 1.418373 GTTGCATTTTTCAGCCGACC 58.582 50.000 0.00 0.00 0.00 4.79
203 210 2.950673 GCGGTTGATTCGGTTGCA 59.049 55.556 0.00 0.00 0.00 4.08
204 211 2.202298 CGCGGTTGATTCGGTTGC 60.202 61.111 0.00 0.00 0.00 4.17
205 212 2.202298 GCGCGGTTGATTCGGTTG 60.202 61.111 8.83 0.00 0.00 3.77
206 213 3.784412 CGCGCGGTTGATTCGGTT 61.784 61.111 24.84 0.00 0.00 4.44
208 215 2.879942 CTTTCGCGCGGTTGATTCGG 62.880 60.000 31.69 6.28 0.00 4.30
209 216 1.577616 CTTTCGCGCGGTTGATTCG 60.578 57.895 31.69 6.17 0.00 3.34
212 219 1.852067 AAAGCTTTCGCGCGGTTGAT 61.852 50.000 31.69 15.63 42.32 2.57
237 245 4.062293 CCACACAGAATTTTACCGACAGA 58.938 43.478 0.00 0.00 0.00 3.41
270 293 1.534729 CGGAGGGGAAAACTTTGGAG 58.465 55.000 0.00 0.00 0.00 3.86
271 294 3.737702 CGGAGGGGAAAACTTTGGA 57.262 52.632 0.00 0.00 0.00 3.53
287 310 3.754850 TGTGGATATACTCGTACATCCGG 59.245 47.826 9.20 0.00 41.00 5.14
296 319 4.022849 TCTGCACATCTGTGGATATACTCG 60.023 45.833 11.98 0.00 45.17 4.18
299 322 5.010516 AGAGTCTGCACATCTGTGGATATAC 59.989 44.000 11.98 7.87 45.17 1.47
303 326 2.093606 CAGAGTCTGCACATCTGTGGAT 60.094 50.000 7.33 0.00 45.17 3.41
304 327 1.274447 CAGAGTCTGCACATCTGTGGA 59.726 52.381 7.33 8.30 45.72 4.02
305 328 1.723220 CAGAGTCTGCACATCTGTGG 58.277 55.000 7.33 0.00 45.72 4.17
316 339 0.954449 CAGGGTGCTTGCAGAGTCTG 60.954 60.000 16.21 16.21 34.12 3.51
317 340 1.374190 CAGGGTGCTTGCAGAGTCT 59.626 57.895 0.00 0.00 0.00 3.24
326 358 4.228210 TGATTTAGATTCTCCAGGGTGCTT 59.772 41.667 0.00 0.00 0.00 3.91
332 364 7.636150 AAACATGTGATTTAGATTCTCCAGG 57.364 36.000 0.00 0.00 0.00 4.45
344 376 7.096551 GGCCAACTTACATAAACATGTGATTT 58.903 34.615 0.00 0.00 36.08 2.17
359 391 3.609853 TCTCATCACATGGCCAACTTAC 58.390 45.455 10.96 0.00 0.00 2.34
378 410 3.416156 GAAGATGCCCTCACAAAACTCT 58.584 45.455 0.00 0.00 0.00 3.24
379 411 2.489722 GGAAGATGCCCTCACAAAACTC 59.510 50.000 0.00 0.00 0.00 3.01
380 412 2.158475 TGGAAGATGCCCTCACAAAACT 60.158 45.455 0.00 0.00 0.00 2.66
381 413 2.229784 CTGGAAGATGCCCTCACAAAAC 59.770 50.000 0.00 0.00 34.07 2.43
382 414 2.158475 ACTGGAAGATGCCCTCACAAAA 60.158 45.455 0.00 0.00 37.43 2.44
383 415 1.425066 ACTGGAAGATGCCCTCACAAA 59.575 47.619 0.00 0.00 37.43 2.83
384 416 1.067295 ACTGGAAGATGCCCTCACAA 58.933 50.000 0.00 0.00 37.43 3.33
385 417 1.003580 GAACTGGAAGATGCCCTCACA 59.996 52.381 0.00 0.00 37.43 3.58
386 418 1.680249 GGAACTGGAAGATGCCCTCAC 60.680 57.143 0.00 0.00 37.43 3.51
387 419 0.620556 GGAACTGGAAGATGCCCTCA 59.379 55.000 0.00 0.00 37.43 3.86
388 420 0.620556 TGGAACTGGAAGATGCCCTC 59.379 55.000 0.00 0.00 37.43 4.30
389 421 1.005215 CTTGGAACTGGAAGATGCCCT 59.995 52.381 0.00 0.00 37.43 5.19
390 422 1.004745 TCTTGGAACTGGAAGATGCCC 59.995 52.381 0.00 0.00 37.43 5.36
391 423 2.026822 TCTCTTGGAACTGGAAGATGCC 60.027 50.000 0.00 0.00 37.43 4.40
405 437 3.130160 GCCAGCCGCTTCTCTTGG 61.130 66.667 0.00 0.00 0.00 3.61
406 438 3.130160 GGCCAGCCGCTTCTCTTG 61.130 66.667 0.00 0.00 37.74 3.02
407 439 3.325753 AGGCCAGCCGCTTCTCTT 61.326 61.111 5.01 0.00 41.95 2.85
408 440 4.093291 CAGGCCAGCCGCTTCTCT 62.093 66.667 5.01 0.00 41.95 3.10
427 459 0.035820 TACTTTACTTGGCCCGCTGG 60.036 55.000 0.00 0.00 0.00 4.85
428 460 1.670811 CATACTTTACTTGGCCCGCTG 59.329 52.381 0.00 0.00 0.00 5.18
429 461 1.408266 CCATACTTTACTTGGCCCGCT 60.408 52.381 0.00 0.00 0.00 5.52
430 462 1.021968 CCATACTTTACTTGGCCCGC 58.978 55.000 0.00 0.00 0.00 6.13
435 467 1.675552 CCGGGCCATACTTTACTTGG 58.324 55.000 4.39 0.00 0.00 3.61
436 468 1.021968 GCCGGGCCATACTTTACTTG 58.978 55.000 8.12 0.00 0.00 3.16
437 469 0.916809 AGCCGGGCCATACTTTACTT 59.083 50.000 17.02 0.00 0.00 2.24
438 470 0.916809 AAGCCGGGCCATACTTTACT 59.083 50.000 17.02 0.00 0.00 2.24
439 471 1.021968 CAAGCCGGGCCATACTTTAC 58.978 55.000 17.02 0.00 0.00 2.01
440 472 0.913205 TCAAGCCGGGCCATACTTTA 59.087 50.000 17.02 0.00 0.00 1.85
441 473 0.394352 CTCAAGCCGGGCCATACTTT 60.394 55.000 17.02 0.00 0.00 2.66
442 474 1.224592 CTCAAGCCGGGCCATACTT 59.775 57.895 17.02 0.51 0.00 2.24
443 475 2.746375 CCTCAAGCCGGGCCATACT 61.746 63.158 17.02 0.00 0.00 2.12
444 476 2.203209 CCTCAAGCCGGGCCATAC 60.203 66.667 17.02 0.00 0.00 2.39
445 477 4.189580 GCCTCAAGCCGGGCCATA 62.190 66.667 17.02 0.00 42.30 2.74
450 482 0.967380 AAAAGATGCCTCAAGCCGGG 60.967 55.000 2.18 0.00 42.71 5.73
451 483 0.890683 AAAAAGATGCCTCAAGCCGG 59.109 50.000 0.00 0.00 42.71 6.13
470 502 2.565834 AGCGTAGAGGTTTTAGCTGGAA 59.434 45.455 0.00 0.00 33.31 3.53
471 503 2.176889 AGCGTAGAGGTTTTAGCTGGA 58.823 47.619 0.00 0.00 33.31 3.86
472 504 2.674796 AGCGTAGAGGTTTTAGCTGG 57.325 50.000 0.00 0.00 33.31 4.85
528 567 2.262915 CACGGCTGGGTCAGAGAC 59.737 66.667 0.00 0.00 32.44 3.36
594 633 4.079253 GCTTCCAATCCAAGTTAAGTCCA 58.921 43.478 0.00 0.00 0.00 4.02
603 642 0.962356 AGCGTGGCTTCCAATCCAAG 60.962 55.000 0.00 0.00 33.89 3.61
604 643 0.539438 AAGCGTGGCTTCCAATCCAA 60.539 50.000 0.00 0.00 46.77 3.53
605 644 0.326595 TAAGCGTGGCTTCCAATCCA 59.673 50.000 6.07 0.00 46.77 3.41
606 645 1.459450 TTAAGCGTGGCTTCCAATCC 58.541 50.000 6.07 0.00 46.77 3.01
607 646 2.033424 GGATTAAGCGTGGCTTCCAATC 59.967 50.000 6.07 10.81 46.77 2.67
608 647 2.024414 GGATTAAGCGTGGCTTCCAAT 58.976 47.619 6.07 2.31 46.77 3.16
615 654 2.311124 ACAGTAGGATTAAGCGTGGC 57.689 50.000 0.00 0.00 0.00 5.01
625 664 3.231207 AGCGACCATCTACAGTAGGAT 57.769 47.619 7.79 0.00 0.00 3.24
640 679 1.681025 GGCGAAAACGAGGTAGCGAC 61.681 60.000 0.00 0.00 34.83 5.19
641 680 1.444895 GGCGAAAACGAGGTAGCGA 60.445 57.895 0.00 0.00 34.83 4.93
642 681 2.450345 GGGCGAAAACGAGGTAGCG 61.450 63.158 0.00 0.00 37.29 4.26
643 682 0.952010 TTGGGCGAAAACGAGGTAGC 60.952 55.000 0.00 0.00 0.00 3.58
644 683 1.076332 CTTGGGCGAAAACGAGGTAG 58.924 55.000 0.00 0.00 0.00 3.18
648 687 2.409975 TCTTACTTGGGCGAAAACGAG 58.590 47.619 0.00 0.00 0.00 4.18
650 689 1.136057 GCTCTTACTTGGGCGAAAACG 60.136 52.381 0.00 0.00 0.00 3.60
651 690 1.199327 GGCTCTTACTTGGGCGAAAAC 59.801 52.381 0.00 0.00 0.00 2.43
652 691 1.530323 GGCTCTTACTTGGGCGAAAA 58.470 50.000 0.00 0.00 0.00 2.29
654 693 1.198759 AGGGCTCTTACTTGGGCGAA 61.199 55.000 0.00 0.00 0.00 4.70
655 694 1.612442 AGGGCTCTTACTTGGGCGA 60.612 57.895 0.00 0.00 0.00 5.54
657 696 0.548510 ATCAGGGCTCTTACTTGGGC 59.451 55.000 0.00 0.00 0.00 5.36
658 697 3.456277 AGTAATCAGGGCTCTTACTTGGG 59.544 47.826 0.00 0.00 33.10 4.12
661 700 4.536489 ACCAAGTAATCAGGGCTCTTACTT 59.464 41.667 3.72 3.72 43.12 2.24
664 703 3.454812 GGACCAAGTAATCAGGGCTCTTA 59.545 47.826 0.00 0.00 0.00 2.10
665 704 2.239907 GGACCAAGTAATCAGGGCTCTT 59.760 50.000 0.00 0.00 0.00 2.85
666 705 1.840635 GGACCAAGTAATCAGGGCTCT 59.159 52.381 0.00 0.00 0.00 4.09
667 706 1.473434 CGGACCAAGTAATCAGGGCTC 60.473 57.143 0.00 0.00 0.00 4.70
668 707 0.541863 CGGACCAAGTAATCAGGGCT 59.458 55.000 0.00 0.00 0.00 5.19
669 708 1.095807 GCGGACCAAGTAATCAGGGC 61.096 60.000 0.00 0.00 0.00 5.19
670 709 0.810031 CGCGGACCAAGTAATCAGGG 60.810 60.000 0.00 0.00 0.00 4.45
672 711 0.174845 TCCGCGGACCAAGTAATCAG 59.825 55.000 27.28 0.00 0.00 2.90
673 712 0.108520 GTCCGCGGACCAAGTAATCA 60.109 55.000 41.88 9.02 39.08 2.57
674 713 0.175073 AGTCCGCGGACCAAGTAATC 59.825 55.000 45.66 24.27 45.59 1.75
675 714 0.108329 CAGTCCGCGGACCAAGTAAT 60.108 55.000 45.66 28.13 45.59 1.89
676 715 1.290955 CAGTCCGCGGACCAAGTAA 59.709 57.895 45.66 15.08 45.59 2.24
677 716 2.642254 CCAGTCCGCGGACCAAGTA 61.642 63.158 45.66 15.91 45.59 2.24
678 717 4.003788 CCAGTCCGCGGACCAAGT 62.004 66.667 45.66 29.93 45.59 3.16
679 718 2.725203 TTTCCAGTCCGCGGACCAAG 62.725 60.000 45.66 35.49 45.59 3.61
680 719 2.809307 TTTCCAGTCCGCGGACCAA 61.809 57.895 45.66 34.08 45.59 3.67
681 720 3.235481 TTTCCAGTCCGCGGACCA 61.235 61.111 45.66 31.04 45.59 4.02
683 722 1.161563 TTTGTTTCCAGTCCGCGGAC 61.162 55.000 43.92 43.92 44.86 4.79
684 723 0.464013 TTTTGTTTCCAGTCCGCGGA 60.464 50.000 27.28 27.28 0.00 5.54
685 724 0.040425 CTTTTGTTTCCAGTCCGCGG 60.040 55.000 22.12 22.12 0.00 6.46
686 725 0.661020 ACTTTTGTTTCCAGTCCGCG 59.339 50.000 0.00 0.00 0.00 6.46
687 726 1.673920 TCACTTTTGTTTCCAGTCCGC 59.326 47.619 0.00 0.00 0.00 5.54
688 727 3.563808 TGATCACTTTTGTTTCCAGTCCG 59.436 43.478 0.00 0.00 0.00 4.79
689 728 4.557496 GCTGATCACTTTTGTTTCCAGTCC 60.557 45.833 0.00 0.00 0.00 3.85
690 729 4.540824 GCTGATCACTTTTGTTTCCAGTC 58.459 43.478 0.00 0.00 0.00 3.51
691 730 3.003689 CGCTGATCACTTTTGTTTCCAGT 59.996 43.478 0.00 0.00 0.00 4.00
692 731 3.250762 TCGCTGATCACTTTTGTTTCCAG 59.749 43.478 0.00 0.00 0.00 3.86
693 732 3.210227 TCGCTGATCACTTTTGTTTCCA 58.790 40.909 0.00 0.00 0.00 3.53
694 733 3.896648 TCGCTGATCACTTTTGTTTCC 57.103 42.857 0.00 0.00 0.00 3.13
695 734 5.095691 TCTTCGCTGATCACTTTTGTTTC 57.904 39.130 0.00 0.00 0.00 2.78
708 747 1.667830 CGTTTGGCCTCTTCGCTGA 60.668 57.895 3.32 0.00 0.00 4.26
798 838 3.146066 TGACCGGTAGTACAACGTTAGT 58.854 45.455 7.34 4.52 0.00 2.24
888 938 1.538204 CCAGTACGCAAGGTATCGCAT 60.538 52.381 0.00 0.00 46.39 4.73
889 939 0.179121 CCAGTACGCAAGGTATCGCA 60.179 55.000 0.00 0.00 46.39 5.10
890 940 0.179119 ACCAGTACGCAAGGTATCGC 60.179 55.000 1.32 0.00 46.39 4.58
908 958 2.531206 GTGTACTAGTAGCAGCAGCAC 58.469 52.381 1.87 2.47 45.49 4.40
923 976 1.180029 TAGAGCCGTCCAAGGTGTAC 58.820 55.000 0.00 0.00 0.00 2.90
930 983 2.093658 GGAACAGAATAGAGCCGTCCAA 60.094 50.000 0.00 0.00 0.00 3.53
1095 1156 2.087009 CGGAGAAACCAGACGACGC 61.087 63.158 0.00 0.00 38.90 5.19
1321 1419 4.698304 CCAAGAAAACCTTCAGCCGTTATA 59.302 41.667 0.00 0.00 33.64 0.98
1393 1492 4.512484 TCATGGCTATGTCATCGTTCAAA 58.488 39.130 10.12 0.00 35.73 2.69
1395 1494 3.817709 TCATGGCTATGTCATCGTTCA 57.182 42.857 10.12 0.00 35.73 3.18
1419 1518 3.089284 GGTATGCACAGGCTAGGTTTTT 58.911 45.455 0.00 0.00 41.91 1.94
1428 1527 1.339055 TGTTCAGAGGTATGCACAGGC 60.339 52.381 0.00 0.00 41.68 4.85
1450 1549 3.983344 CCAGAAATGCAAGTGCTGTTTAC 59.017 43.478 4.69 2.04 42.66 2.01
1460 1562 1.407979 GCCATCCTCCAGAAATGCAAG 59.592 52.381 0.00 0.00 0.00 4.01
1461 1563 1.006281 AGCCATCCTCCAGAAATGCAA 59.994 47.619 0.00 0.00 0.00 4.08
1462 1564 0.627451 AGCCATCCTCCAGAAATGCA 59.373 50.000 0.00 0.00 0.00 3.96
1464 1566 3.853355 ACTAGCCATCCTCCAGAAATG 57.147 47.619 0.00 0.00 0.00 2.32
1480 1583 4.569943 AGCAACAGACACATTGGTACTAG 58.430 43.478 0.00 0.00 34.88 2.57
1488 1591 1.967319 ACCGAAGCAACAGACACATT 58.033 45.000 0.00 0.00 0.00 2.71
1505 1608 3.889520 AAATAGACGGTCTCTCCAACC 57.110 47.619 15.05 0.00 35.57 3.77
1506 1609 5.008415 TCGATAAATAGACGGTCTCTCCAAC 59.992 44.000 15.05 3.44 35.57 3.77
1515 1618 6.715464 CAAAAAGCATCGATAAATAGACGGT 58.285 36.000 0.00 0.00 0.00 4.83
1516 1619 5.621228 GCAAAAAGCATCGATAAATAGACGG 59.379 40.000 0.00 0.00 44.79 4.79
1743 1846 8.283291 CACGCTTTCTTAACTCTTACAAATTCT 58.717 33.333 0.00 0.00 0.00 2.40
1748 1851 5.362263 ACCACGCTTTCTTAACTCTTACAA 58.638 37.500 0.00 0.00 0.00 2.41
1750 1853 5.919272 AACCACGCTTTCTTAACTCTTAC 57.081 39.130 0.00 0.00 0.00 2.34
1762 1866 9.997482 CACTTTACATATAATAAACCACGCTTT 57.003 29.630 0.00 0.00 0.00 3.51
1778 1882 8.598916 TGGTTAATCTCAAGGTCACTTTACATA 58.401 33.333 0.00 0.00 33.81 2.29
1822 1926 9.683069 AACTAGAACTTTGCAATAACAATCTTG 57.317 29.630 0.00 3.07 0.00 3.02
1836 1940 7.936584 TGTTTTGGTCCATAACTAGAACTTTG 58.063 34.615 21.35 0.00 35.34 2.77
1837 1941 8.706322 ATGTTTTGGTCCATAACTAGAACTTT 57.294 30.769 21.35 0.00 35.34 2.66
1846 1951 2.752903 AGCCGATGTTTTGGTCCATAAC 59.247 45.455 16.00 16.00 0.00 1.89
1922 2027 6.183360 GGGTTGTTGAGTTCATACTTCATAGC 60.183 42.308 0.00 0.00 33.84 2.97
1923 2028 6.878923 TGGGTTGTTGAGTTCATACTTCATAG 59.121 38.462 0.00 0.00 33.84 2.23
1978 2083 3.194005 TCCTGAACGGAATATGGAAGC 57.806 47.619 0.00 0.00 39.40 3.86
1990 2100 2.670414 GCTCTTCAGATGTTCCTGAACG 59.330 50.000 5.62 0.00 45.25 3.95
2049 2170 8.352201 CAATAGGTCTGTTCAAATCTTGACAAA 58.648 33.333 0.00 0.00 39.87 2.83
2125 2246 2.821378 TGCTTGAATTCATGTCACAGGG 59.179 45.455 19.25 1.25 0.00 4.45
2135 2256 5.939296 TGATCGCCATATATGCTTGAATTCA 59.061 36.000 3.38 3.38 0.00 2.57
2171 2292 7.329499 TGTGTACACCTTACAAACAAGTCTTA 58.671 34.615 22.91 0.00 0.00 2.10
2199 2320 7.767659 GGTAATTTTATCGTTTCTCCCTACTGT 59.232 37.037 0.00 0.00 0.00 3.55
2277 2398 2.095461 TGCAGCACAACAAGGTTAACA 58.905 42.857 8.10 0.00 0.00 2.41
2347 2468 2.032799 TGTCAAAACCATGAGAACACGC 59.967 45.455 0.00 0.00 0.00 5.34
2356 2477 1.331214 ACAGGCCTGTCAAAACCATG 58.669 50.000 33.20 5.54 40.24 3.66
2472 2612 8.084073 AGTTAATCACTTTTGTCCAATGACATG 58.916 33.333 0.00 0.00 41.41 3.21
2473 2613 8.181904 AGTTAATCACTTTTGTCCAATGACAT 57.818 30.769 0.00 0.00 41.41 3.06
2474 2614 7.581213 AGTTAATCACTTTTGTCCAATGACA 57.419 32.000 0.00 0.00 40.56 3.58
2592 2736 7.775093 TGCACCATAATGTTCTAGAAGCTATTT 59.225 33.333 5.12 0.00 0.00 1.40
2615 2919 7.067372 CCTGGACAACATTATTCTATTTCTGCA 59.933 37.037 0.00 0.00 0.00 4.41
2619 2923 8.956426 TGAACCTGGACAACATTATTCTATTTC 58.044 33.333 0.00 0.00 0.00 2.17
2689 2993 5.769662 TCAATGCTGACAGTTTATTCCTTGT 59.230 36.000 3.99 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.