Multiple sequence alignment - TraesCS3B01G378500

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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 TraesCS3B01G378500 chr3B 100.000 3994 0 0 1 3994 596601968 596597975 0.000000e+00 7376
1 TraesCS3B01G378500 chr3D 92.530 2798 133 39 509 3277 454152975 454150225 0.000000e+00 3940
2 TraesCS3B01G378500 chr3D 87.789 303 30 2 3 304 454153347 454153051 8.220000e-92 348
3 TraesCS3B01G378500 chr3A 91.504 2719 128 40 613 3277 595964156 595961487 0.000000e+00 3646
4 TraesCS3B01G378500 chr3A 88.028 710 80 3 3280 3989 674283908 674284612 0.000000e+00 835
5 TraesCS3B01G378500 chr3A 87.500 712 65 9 3279 3989 46969153 46969841 0.000000e+00 800
6 TraesCS3B01G378500 chr3A 89.151 212 20 2 63 274 595964766 595964558 1.100000e-65 261
7 TraesCS3B01G378500 chr1A 92.525 709 49 2 3279 3987 520843834 520843130 0.000000e+00 1013
8 TraesCS3B01G378500 chr7A 91.408 710 56 3 3280 3989 672864369 672865073 0.000000e+00 968
9 TraesCS3B01G378500 chr6A 90.113 708 61 4 3280 3987 103769857 103769159 0.000000e+00 911
10 TraesCS3B01G378500 chr5A 87.744 718 77 9 3279 3992 703395485 703394775 0.000000e+00 828
11 TraesCS3B01G378500 chr2A 90.973 565 48 3 3273 3836 705777088 705777650 0.000000e+00 758
12 TraesCS3B01G378500 chr2A 90.600 500 37 4 3283 3781 36703445 36702955 0.000000e+00 654
13 TraesCS3B01G378500 chrUn 90.600 500 37 4 3283 3781 319045154 319044664 0.000000e+00 654


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 TraesCS3B01G378500 chr3B 596597975 596601968 3993 True 7376.0 7376 100.0000 1 3994 1 chr3B.!!$R1 3993
1 TraesCS3B01G378500 chr3D 454150225 454153347 3122 True 2144.0 3940 90.1595 3 3277 2 chr3D.!!$R1 3274
2 TraesCS3B01G378500 chr3A 595961487 595964766 3279 True 1953.5 3646 90.3275 63 3277 2 chr3A.!!$R1 3214
3 TraesCS3B01G378500 chr3A 674283908 674284612 704 False 835.0 835 88.0280 3280 3989 1 chr3A.!!$F2 709
4 TraesCS3B01G378500 chr3A 46969153 46969841 688 False 800.0 800 87.5000 3279 3989 1 chr3A.!!$F1 710
5 TraesCS3B01G378500 chr1A 520843130 520843834 704 True 1013.0 1013 92.5250 3279 3987 1 chr1A.!!$R1 708
6 TraesCS3B01G378500 chr7A 672864369 672865073 704 False 968.0 968 91.4080 3280 3989 1 chr7A.!!$F1 709
7 TraesCS3B01G378500 chr6A 103769159 103769857 698 True 911.0 911 90.1130 3280 3987 1 chr6A.!!$R1 707
8 TraesCS3B01G378500 chr5A 703394775 703395485 710 True 828.0 828 87.7440 3279 3992 1 chr5A.!!$R1 713
9 TraesCS3B01G378500 chr2A 705777088 705777650 562 False 758.0 758 90.9730 3273 3836 1 chr2A.!!$F1 563

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
701 942 0.323629 TGAACGGGAAAGTAGGCCAG 59.676 55.0 5.01 0.0 0.00 4.85 F
702 943 0.392595 GAACGGGAAAGTAGGCCAGG 60.393 60.0 5.01 0.0 0.00 4.45 F
1809 2081 0.176449 CCATGTCGAGGATGAGCACA 59.824 55.0 6.01 0.0 0.00 4.57 F
1812 2084 0.176449 TGTCGAGGATGAGCACATGG 59.824 55.0 0.00 0.0 36.82 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 2057 0.977627 TCATCCTCGACATGGCTGGT 60.978 55.000 0.0 0.0 0.00 4.00 R
1988 2265 1.482182 TGTACCTCAGCGAATCTGCAT 59.518 47.619 0.0 0.0 42.56 3.96 R
2751 3036 0.322816 AAGCAGGTGATCAATGGCGT 60.323 50.000 0.0 0.0 0.00 5.68 R
3800 4107 0.470766 TCCGCCAAGGTACAACAAGT 59.529 50.000 0.0 0.0 41.99 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.624364 TCACCGCTGCCACACCTG 62.624 66.667 0.00 0.00 0.00 4.00
39 40 1.779025 CGCTGCCACACCTGCATATC 61.779 60.000 0.00 0.00 38.22 1.63
76 77 2.093500 AGTGCATGCTAGATTCCGTGAA 60.093 45.455 20.33 0.00 0.00 3.18
91 92 2.405805 TGAAATCCCCATGCACGCG 61.406 57.895 3.53 3.53 0.00 6.01
184 186 1.157870 AGTGTTGTTCGGTTGCCTCG 61.158 55.000 0.00 0.00 0.00 4.63
187 189 1.952133 TTGTTCGGTTGCCTCGACG 60.952 57.895 0.00 0.00 36.30 5.12
224 226 3.655211 CCCCCTTCACCAGCAGCT 61.655 66.667 0.00 0.00 0.00 4.24
289 496 3.376234 GCCGTGGAAATACTAGGGTTTTC 59.624 47.826 0.00 0.52 37.35 2.29
314 521 3.361158 CGCCCAATGTTGACGCCA 61.361 61.111 0.00 0.00 0.00 5.69
315 522 2.913765 CGCCCAATGTTGACGCCAA 61.914 57.895 0.00 0.00 0.00 4.52
316 523 1.591183 GCCCAATGTTGACGCCAAT 59.409 52.632 0.00 0.00 34.39 3.16
317 524 0.737019 GCCCAATGTTGACGCCAATG 60.737 55.000 0.00 0.00 34.39 2.82
321 528 2.339418 CAATGTTGACGCCAATGCAAT 58.661 42.857 0.00 0.00 37.32 3.56
322 529 2.282701 ATGTTGACGCCAATGCAATC 57.717 45.000 0.00 0.00 37.32 2.67
323 530 1.246649 TGTTGACGCCAATGCAATCT 58.753 45.000 0.00 0.00 37.32 2.40
324 531 1.068402 TGTTGACGCCAATGCAATCTG 60.068 47.619 0.00 0.00 37.32 2.90
331 538 2.518949 GCCAATGCAATCTGTAACGTG 58.481 47.619 0.00 0.00 37.47 4.49
333 540 3.491356 CCAATGCAATCTGTAACGTGTG 58.509 45.455 0.00 0.00 0.00 3.82
335 542 4.397382 CAATGCAATCTGTAACGTGTGAG 58.603 43.478 0.00 0.00 0.00 3.51
336 543 1.798223 TGCAATCTGTAACGTGTGAGC 59.202 47.619 0.00 0.00 0.00 4.26
337 544 2.069273 GCAATCTGTAACGTGTGAGCT 58.931 47.619 0.00 0.00 0.00 4.09
338 545 3.250744 GCAATCTGTAACGTGTGAGCTA 58.749 45.455 0.00 0.00 0.00 3.32
339 546 3.865745 GCAATCTGTAACGTGTGAGCTAT 59.134 43.478 0.00 0.00 0.00 2.97
340 547 5.041287 GCAATCTGTAACGTGTGAGCTATA 58.959 41.667 0.00 0.00 0.00 1.31
341 548 5.692204 GCAATCTGTAACGTGTGAGCTATAT 59.308 40.000 0.00 0.00 0.00 0.86
342 549 6.129062 GCAATCTGTAACGTGTGAGCTATATC 60.129 42.308 0.00 0.00 0.00 1.63
343 550 6.885952 ATCTGTAACGTGTGAGCTATATCT 57.114 37.500 0.00 0.00 0.00 1.98
344 551 6.694877 TCTGTAACGTGTGAGCTATATCTT 57.305 37.500 0.00 0.00 0.00 2.40
345 552 6.495706 TCTGTAACGTGTGAGCTATATCTTG 58.504 40.000 0.00 0.00 0.00 3.02
346 553 6.317893 TCTGTAACGTGTGAGCTATATCTTGA 59.682 38.462 0.00 0.00 0.00 3.02
347 554 7.013369 TCTGTAACGTGTGAGCTATATCTTGAT 59.987 37.037 0.00 0.00 0.00 2.57
348 555 7.489160 TGTAACGTGTGAGCTATATCTTGATT 58.511 34.615 0.00 0.00 0.00 2.57
349 556 6.834959 AACGTGTGAGCTATATCTTGATTG 57.165 37.500 0.00 0.00 0.00 2.67
350 557 5.907207 ACGTGTGAGCTATATCTTGATTGT 58.093 37.500 0.00 0.00 0.00 2.71
351 558 5.750547 ACGTGTGAGCTATATCTTGATTGTG 59.249 40.000 0.00 0.00 0.00 3.33
352 559 5.750547 CGTGTGAGCTATATCTTGATTGTGT 59.249 40.000 0.00 0.00 0.00 3.72
353 560 6.918022 CGTGTGAGCTATATCTTGATTGTGTA 59.082 38.462 0.00 0.00 0.00 2.90
354 561 7.596621 CGTGTGAGCTATATCTTGATTGTGTAT 59.403 37.037 0.00 0.00 0.00 2.29
355 562 9.265901 GTGTGAGCTATATCTTGATTGTGTATT 57.734 33.333 0.00 0.00 0.00 1.89
356 563 9.264719 TGTGAGCTATATCTTGATTGTGTATTG 57.735 33.333 0.00 0.00 0.00 1.90
357 564 9.265901 GTGAGCTATATCTTGATTGTGTATTGT 57.734 33.333 0.00 0.00 0.00 2.71
361 568 9.979270 GCTATATCTTGATTGTGTATTGTATGC 57.021 33.333 0.00 0.00 0.00 3.14
365 572 8.743085 ATCTTGATTGTGTATTGTATGCTCTT 57.257 30.769 0.00 0.00 0.00 2.85
366 573 9.836864 ATCTTGATTGTGTATTGTATGCTCTTA 57.163 29.630 0.00 0.00 0.00 2.10
367 574 9.836864 TCTTGATTGTGTATTGTATGCTCTTAT 57.163 29.630 0.00 0.00 0.00 1.73
368 575 9.874215 CTTGATTGTGTATTGTATGCTCTTATG 57.126 33.333 0.00 0.00 0.00 1.90
369 576 8.962884 TGATTGTGTATTGTATGCTCTTATGT 57.037 30.769 0.00 0.00 0.00 2.29
370 577 8.829612 TGATTGTGTATTGTATGCTCTTATGTG 58.170 33.333 0.00 0.00 0.00 3.21
371 578 7.552458 TTGTGTATTGTATGCTCTTATGTGG 57.448 36.000 0.00 0.00 0.00 4.17
372 579 6.054941 TGTGTATTGTATGCTCTTATGTGGG 58.945 40.000 0.00 0.00 0.00 4.61
373 580 6.055588 GTGTATTGTATGCTCTTATGTGGGT 58.944 40.000 0.00 0.00 0.00 4.51
374 581 6.017934 GTGTATTGTATGCTCTTATGTGGGTG 60.018 42.308 0.00 0.00 0.00 4.61
375 582 2.917933 TGTATGCTCTTATGTGGGTGC 58.082 47.619 0.00 0.00 0.00 5.01
376 583 2.238395 TGTATGCTCTTATGTGGGTGCA 59.762 45.455 0.00 0.00 36.60 4.57
377 584 2.742428 ATGCTCTTATGTGGGTGCAT 57.258 45.000 0.00 0.00 37.68 3.96
378 585 2.512692 TGCTCTTATGTGGGTGCATT 57.487 45.000 0.00 0.00 0.00 3.56
379 586 2.806434 TGCTCTTATGTGGGTGCATTT 58.194 42.857 0.00 0.00 0.00 2.32
380 587 3.164268 TGCTCTTATGTGGGTGCATTTT 58.836 40.909 0.00 0.00 0.00 1.82
381 588 3.577848 TGCTCTTATGTGGGTGCATTTTT 59.422 39.130 0.00 0.00 0.00 1.94
382 589 4.176271 GCTCTTATGTGGGTGCATTTTTC 58.824 43.478 0.00 0.00 0.00 2.29
383 590 4.082026 GCTCTTATGTGGGTGCATTTTTCT 60.082 41.667 0.00 0.00 0.00 2.52
384 591 5.389859 TCTTATGTGGGTGCATTTTTCTG 57.610 39.130 0.00 0.00 0.00 3.02
385 592 4.832266 TCTTATGTGGGTGCATTTTTCTGT 59.168 37.500 0.00 0.00 0.00 3.41
386 593 6.007076 TCTTATGTGGGTGCATTTTTCTGTA 58.993 36.000 0.00 0.00 0.00 2.74
387 594 4.789012 ATGTGGGTGCATTTTTCTGTAG 57.211 40.909 0.00 0.00 0.00 2.74
388 595 2.295909 TGTGGGTGCATTTTTCTGTAGC 59.704 45.455 0.00 0.00 0.00 3.58
389 596 2.295909 GTGGGTGCATTTTTCTGTAGCA 59.704 45.455 0.00 0.00 31.85 3.49
390 597 2.961741 TGGGTGCATTTTTCTGTAGCAA 59.038 40.909 0.00 0.00 36.91 3.91
391 598 3.386078 TGGGTGCATTTTTCTGTAGCAAA 59.614 39.130 0.00 0.00 36.91 3.68
392 599 4.040217 TGGGTGCATTTTTCTGTAGCAAAT 59.960 37.500 0.00 0.00 36.91 2.32
393 600 4.389687 GGGTGCATTTTTCTGTAGCAAATG 59.610 41.667 0.00 9.96 39.78 2.32
394 601 5.229423 GGTGCATTTTTCTGTAGCAAATGA 58.771 37.500 15.09 4.16 39.34 2.57
395 602 5.870978 GGTGCATTTTTCTGTAGCAAATGAT 59.129 36.000 15.09 0.00 39.34 2.45
396 603 7.035004 GGTGCATTTTTCTGTAGCAAATGATA 58.965 34.615 15.09 5.71 39.34 2.15
397 604 7.545265 GGTGCATTTTTCTGTAGCAAATGATAA 59.455 33.333 15.09 3.63 39.34 1.75
398 605 8.924691 GTGCATTTTTCTGTAGCAAATGATAAA 58.075 29.630 15.09 0.00 39.34 1.40
399 606 9.656040 TGCATTTTTCTGTAGCAAATGATAAAT 57.344 25.926 15.09 1.73 39.34 1.40
402 609 8.909708 TTTTTCTGTAGCAAATGATAAATCGG 57.090 30.769 0.00 0.00 0.00 4.18
403 610 7.624360 TTTCTGTAGCAAATGATAAATCGGT 57.376 32.000 0.00 0.00 0.00 4.69
404 611 6.603237 TCTGTAGCAAATGATAAATCGGTG 57.397 37.500 0.00 0.00 0.00 4.94
405 612 6.345298 TCTGTAGCAAATGATAAATCGGTGA 58.655 36.000 0.00 0.00 0.00 4.02
406 613 6.992123 TCTGTAGCAAATGATAAATCGGTGAT 59.008 34.615 0.00 0.00 0.00 3.06
407 614 8.147704 TCTGTAGCAAATGATAAATCGGTGATA 58.852 33.333 0.00 0.00 0.00 2.15
408 615 8.846943 TGTAGCAAATGATAAATCGGTGATAT 57.153 30.769 0.00 0.00 0.00 1.63
409 616 9.936759 TGTAGCAAATGATAAATCGGTGATATA 57.063 29.630 0.00 0.00 0.00 0.86
412 619 9.507329 AGCAAATGATAAATCGGTGATATAGTT 57.493 29.630 0.00 0.00 0.00 2.24
413 620 9.546909 GCAAATGATAAATCGGTGATATAGTTG 57.453 33.333 0.00 0.00 0.00 3.16
416 623 9.778741 AATGATAAATCGGTGATATAGTTGTGT 57.221 29.630 0.00 0.00 0.00 3.72
417 624 8.587952 TGATAAATCGGTGATATAGTTGTGTG 57.412 34.615 0.00 0.00 0.00 3.82
418 625 5.734855 AAATCGGTGATATAGTTGTGTGC 57.265 39.130 0.00 0.00 0.00 4.57
419 626 3.878160 TCGGTGATATAGTTGTGTGCA 57.122 42.857 0.00 0.00 0.00 4.57
420 627 4.400529 TCGGTGATATAGTTGTGTGCAT 57.599 40.909 0.00 0.00 0.00 3.96
421 628 4.368315 TCGGTGATATAGTTGTGTGCATC 58.632 43.478 0.00 0.00 0.00 3.91
422 629 3.182372 CGGTGATATAGTTGTGTGCATCG 59.818 47.826 0.00 0.00 0.00 3.84
423 630 4.368315 GGTGATATAGTTGTGTGCATCGA 58.632 43.478 0.00 0.00 0.00 3.59
424 631 4.808895 GGTGATATAGTTGTGTGCATCGAA 59.191 41.667 0.00 0.00 0.00 3.71
425 632 5.050769 GGTGATATAGTTGTGTGCATCGAAG 60.051 44.000 0.00 0.00 0.00 3.79
426 633 4.507756 TGATATAGTTGTGTGCATCGAAGC 59.492 41.667 5.52 5.52 0.00 3.86
427 634 2.162319 TAGTTGTGTGCATCGAAGCA 57.838 45.000 11.93 11.93 43.35 3.91
444 651 2.877043 GCATCAATTGCCAGGTTAGG 57.123 50.000 0.00 0.00 46.15 2.69
448 655 3.756082 TCAATTGCCAGGTTAGGGATT 57.244 42.857 0.00 0.00 0.00 3.01
461 668 5.321927 GGTTAGGGATTTGAACCTTCTTCA 58.678 41.667 0.00 0.00 39.67 3.02
502 709 3.871594 CGTAGAAGGATTGGAGCGAAAAT 59.128 43.478 0.00 0.00 0.00 1.82
505 712 6.036735 CGTAGAAGGATTGGAGCGAAAATAAA 59.963 38.462 0.00 0.00 0.00 1.40
506 713 6.442513 AGAAGGATTGGAGCGAAAATAAAG 57.557 37.500 0.00 0.00 0.00 1.85
511 718 6.318900 AGGATTGGAGCGAAAATAAAGGTTAG 59.681 38.462 0.00 0.00 0.00 2.34
512 719 6.317893 GGATTGGAGCGAAAATAAAGGTTAGA 59.682 38.462 0.00 0.00 0.00 2.10
513 720 6.737254 TTGGAGCGAAAATAAAGGTTAGAG 57.263 37.500 0.00 0.00 0.00 2.43
514 721 5.183228 TGGAGCGAAAATAAAGGTTAGAGG 58.817 41.667 0.00 0.00 0.00 3.69
515 722 5.046159 TGGAGCGAAAATAAAGGTTAGAGGA 60.046 40.000 0.00 0.00 0.00 3.71
516 723 5.878669 GGAGCGAAAATAAAGGTTAGAGGAA 59.121 40.000 0.00 0.00 0.00 3.36
517 724 6.373495 GGAGCGAAAATAAAGGTTAGAGGAAA 59.627 38.462 0.00 0.00 0.00 3.13
518 725 7.094506 GGAGCGAAAATAAAGGTTAGAGGAAAA 60.095 37.037 0.00 0.00 0.00 2.29
519 726 8.173542 AGCGAAAATAAAGGTTAGAGGAAAAA 57.826 30.769 0.00 0.00 0.00 1.94
567 801 3.774066 TCATGATCTGCACGTCACTAAG 58.226 45.455 0.00 0.00 0.00 2.18
575 809 3.527533 TGCACGTCACTAAGTCACTTTT 58.472 40.909 0.00 0.00 0.00 2.27
580 814 6.207213 CACGTCACTAAGTCACTTTTACTCT 58.793 40.000 0.00 0.00 0.00 3.24
602 837 9.482627 ACTCTAATAGTTTAGTGATGCTAATGC 57.517 33.333 2.78 0.00 39.23 3.56
663 904 2.151202 GCGAAACACATTCCAGAAGGA 58.849 47.619 0.00 0.00 43.93 3.36
701 942 0.323629 TGAACGGGAAAGTAGGCCAG 59.676 55.000 5.01 0.00 0.00 4.85
702 943 0.392595 GAACGGGAAAGTAGGCCAGG 60.393 60.000 5.01 0.00 0.00 4.45
912 1154 1.981495 CCCTTTCTCACCACTCCTTCT 59.019 52.381 0.00 0.00 0.00 2.85
940 1182 1.209275 CTCGAGCCGCCGATTACAAG 61.209 60.000 0.00 0.00 37.96 3.16
982 1224 1.232792 CTCTCTCCCTCCCCCTCTG 59.767 68.421 0.00 0.00 0.00 3.35
983 1225 2.445654 CTCTCCCTCCCCCTCTGC 60.446 72.222 0.00 0.00 0.00 4.26
984 1226 2.955246 TCTCCCTCCCCCTCTGCT 60.955 66.667 0.00 0.00 0.00 4.24
985 1227 2.445654 CTCCCTCCCCCTCTGCTC 60.446 72.222 0.00 0.00 0.00 4.26
988 1230 2.373707 CCCTCCCCCTCTGCTCTTG 61.374 68.421 0.00 0.00 0.00 3.02
989 1231 2.588989 CTCCCCCTCTGCTCTTGC 59.411 66.667 0.00 0.00 40.20 4.01
991 1233 1.539869 TCCCCCTCTGCTCTTGCTT 60.540 57.895 0.00 0.00 40.48 3.91
992 1234 1.136329 TCCCCCTCTGCTCTTGCTTT 61.136 55.000 0.00 0.00 40.48 3.51
993 1235 0.964358 CCCCCTCTGCTCTTGCTTTG 60.964 60.000 0.00 0.00 40.48 2.77
994 1236 1.593296 CCCCTCTGCTCTTGCTTTGC 61.593 60.000 0.00 0.00 40.48 3.68
996 1238 1.245732 CCTCTGCTCTTGCTTTGCTT 58.754 50.000 0.00 0.00 40.48 3.91
998 1240 3.015327 CCTCTGCTCTTGCTTTGCTTAT 58.985 45.455 0.00 0.00 40.48 1.73
1411 1657 7.313646 CGTCTACCTCATAATCATCGGTAATT 58.686 38.462 0.00 0.00 30.51 1.40
1412 1658 7.273598 CGTCTACCTCATAATCATCGGTAATTG 59.726 40.741 0.00 0.00 30.51 2.32
1414 1660 8.866093 TCTACCTCATAATCATCGGTAATTGAA 58.134 33.333 0.00 0.00 30.51 2.69
1425 1696 0.453782 GTAATTGAACCGCGGTGCAC 60.454 55.000 38.63 27.22 32.55 4.57
1688 1959 1.001268 TCGAATCGAGCACAGCTATCC 60.001 52.381 0.00 0.00 39.88 2.59
1690 1961 0.598680 AATCGAGCACAGCTATCCGC 60.599 55.000 0.00 0.00 39.88 5.54
1706 1977 3.621394 GCTGCGCGACCGAGAATC 61.621 66.667 12.10 0.00 36.29 2.52
1772 2044 6.483974 TCCAAAAACTCAAGCTAATAACACGA 59.516 34.615 0.00 0.00 0.00 4.35
1809 2081 0.176449 CCATGTCGAGGATGAGCACA 59.824 55.000 6.01 0.00 0.00 4.57
1810 2082 1.202615 CCATGTCGAGGATGAGCACAT 60.203 52.381 0.00 0.00 39.67 3.21
1811 2083 1.865340 CATGTCGAGGATGAGCACATG 59.135 52.381 0.00 0.00 38.69 3.21
1812 2084 0.176449 TGTCGAGGATGAGCACATGG 59.824 55.000 0.00 0.00 36.82 3.66
1813 2085 1.144716 TCGAGGATGAGCACATGGC 59.855 57.895 0.00 0.00 45.30 4.40
1931 2204 2.351276 GCCGACAGTGGGGAATGT 59.649 61.111 3.43 0.00 0.00 2.71
1932 2205 1.195442 TGCCGACAGTGGGGAATGTA 61.195 55.000 3.43 0.00 0.00 2.29
1966 2239 4.067896 CCAGTAGAGTTGCAGTGACAAAT 58.932 43.478 0.00 0.00 0.00 2.32
1967 2240 4.083643 CCAGTAGAGTTGCAGTGACAAATG 60.084 45.833 0.00 0.00 0.00 2.32
1977 2254 5.049167 TGCAGTGACAAATGAAAAATGGTC 58.951 37.500 0.00 0.00 0.00 4.02
1981 2258 6.753897 GTGACAAATGAAAAATGGTCACTC 57.246 37.500 13.67 0.00 46.95 3.51
1983 2260 6.418819 GTGACAAATGAAAAATGGTCACTCTG 59.581 38.462 13.67 0.00 46.95 3.35
1988 2265 9.695526 CAAATGAAAAATGGTCACTCTGAATTA 57.304 29.630 0.00 0.00 0.00 1.40
2076 2353 2.183300 GGGATCGCGCTGTACACA 59.817 61.111 5.56 0.00 0.00 3.72
2163 2440 4.452733 CTCTTCACCGCCGTCCCC 62.453 72.222 0.00 0.00 0.00 4.81
2256 2536 4.095483 AGCTTTCAAATATTCGAGGCTGTG 59.905 41.667 0.00 0.00 0.00 3.66
2692 2977 1.174783 GGACGCTCTTCCAGTACTCA 58.825 55.000 0.00 0.00 35.49 3.41
2740 3025 1.454479 CATCTTCCCTGGCGCCATT 60.454 57.895 32.87 6.05 0.00 3.16
2751 3036 0.392461 GGCGCCATTGTTCTCAGGTA 60.392 55.000 24.80 0.00 0.00 3.08
2765 3050 1.134521 TCAGGTACGCCATTGATCACC 60.135 52.381 0.00 0.00 37.19 4.02
2797 3082 6.630071 ACAACAAGCACATAAAACTTTCAGT 58.370 32.000 0.00 0.00 0.00 3.41
2821 3107 3.825908 AAAGTTTCCTGGCCTAATCCA 57.174 42.857 3.32 0.00 34.42 3.41
2827 3113 0.748005 CCTGGCCTAATCCAACACCG 60.748 60.000 3.32 0.00 35.36 4.94
2829 3115 0.402504 TGGCCTAATCCAACACCGTT 59.597 50.000 3.32 0.00 32.18 4.44
2830 3116 1.092348 GGCCTAATCCAACACCGTTC 58.908 55.000 0.00 0.00 0.00 3.95
2833 3119 2.752903 GCCTAATCCAACACCGTTCAAT 59.247 45.455 0.00 0.00 0.00 2.57
2834 3120 3.192633 GCCTAATCCAACACCGTTCAATT 59.807 43.478 0.00 0.00 0.00 2.32
2861 3147 3.824133 CAGGGATGTTCATGGAATAGCA 58.176 45.455 0.00 0.00 0.00 3.49
2870 3156 5.649395 TGTTCATGGAATAGCAAAGAGGAAG 59.351 40.000 0.00 0.00 0.00 3.46
2885 3171 1.508088 GAAGGACAAGGCAATGGCG 59.492 57.895 0.00 0.00 42.47 5.69
2888 3174 3.372730 GACAAGGCAATGGCGGCA 61.373 61.111 16.34 16.34 42.47 5.69
2975 3261 1.053424 AGGGCGAAGTGAAAGGTGTA 58.947 50.000 0.00 0.00 0.00 2.90
3046 3341 5.976458 TCAAAATTCTTTCACCTGCAAAGT 58.024 33.333 0.00 0.00 33.32 2.66
3062 3358 2.875933 CAAAGTTTGTAGCGTTCCTCCA 59.124 45.455 7.48 0.00 0.00 3.86
3111 3407 4.808895 TGATACGAGGCATTGTGTATGTTC 59.191 41.667 0.35 0.00 36.57 3.18
3119 3415 5.181245 AGGCATTGTGTATGTTCTGTGTAAC 59.819 40.000 0.00 0.00 36.57 2.50
3120 3416 5.079406 GCATTGTGTATGTTCTGTGTAACG 58.921 41.667 0.00 0.00 36.62 3.18
3121 3417 5.894763 GCATTGTGTATGTTCTGTGTAACGG 60.895 44.000 0.00 0.00 39.57 4.44
3192 3497 7.389607 ACATTTACCGTGTATAAATATCAGGCC 59.610 37.037 0.00 0.00 32.27 5.19
3200 3505 8.567948 CGTGTATAAATATCAGGCCAAGAAAAT 58.432 33.333 5.01 0.00 0.00 1.82
3216 3521 2.422276 AAATGAGCGCCTTTTGTCAC 57.578 45.000 2.29 0.00 0.00 3.67
3247 3552 3.546815 GCTGTGGATACGATGTTTCATGC 60.547 47.826 0.00 0.00 42.51 4.06
3277 3582 3.054948 TCAAATCGAACGGGGGATTAGTT 60.055 43.478 0.00 0.00 32.80 2.24
3370 3676 1.080569 GCCAAGCCAAACATGACGG 60.081 57.895 0.00 0.00 0.00 4.79
3399 3705 9.914131 AAAAGCTAACCTTAAAGCAAATCTAAG 57.086 29.630 0.04 0.00 41.32 2.18
3501 3807 3.829026 TCAGAGATGATCGAACCATAGGG 59.171 47.826 4.00 0.00 41.29 3.53
3502 3808 3.829026 CAGAGATGATCGAACCATAGGGA 59.171 47.826 0.00 0.00 38.05 4.20
3510 3817 1.280998 CGAACCATAGGGACCCTTGTT 59.719 52.381 20.96 19.05 38.05 2.83
3586 3893 4.060900 GCTGAATATGAAGATCTTCCGCA 58.939 43.478 28.40 18.15 38.77 5.69
3626 3933 3.367703 GCATGCAATAGCCTCAAGTGTTT 60.368 43.478 14.21 0.00 41.13 2.83
3641 3948 2.158385 AGTGTTTGCTGGGTCCCAAATA 60.158 45.455 12.96 0.00 33.96 1.40
3682 3989 2.378547 AGCTCCCCAAGAAAACACCATA 59.621 45.455 0.00 0.00 0.00 2.74
3683 3990 3.161866 GCTCCCCAAGAAAACACCATAA 58.838 45.455 0.00 0.00 0.00 1.90
3706 4013 1.138266 GTCCCTGCAAATAGCTACCGA 59.862 52.381 0.00 0.00 45.94 4.69
3800 4107 2.034878 CTCTGCCTGACCATGCTAGTA 58.965 52.381 0.00 0.00 0.00 1.82
3851 4158 2.042464 ACTCTCACTGCTTCCAAGTCA 58.958 47.619 0.00 0.00 0.00 3.41
3875 4182 2.192664 TGAAGCGGGTAATGAAAGCA 57.807 45.000 0.00 0.00 0.00 3.91
3950 4258 3.118075 TCGATGTCCATATTGCCCAAAGA 60.118 43.478 0.00 0.00 0.00 2.52
3968 4276 5.157781 CAAAGAGTTACTGAGAGGAGAACG 58.842 45.833 0.00 0.00 0.00 3.95
3989 4297 2.997485 ACTTTTCATGAGAAAGCGCC 57.003 45.000 20.72 0.00 44.03 6.53
3992 4300 2.239341 TTTCATGAGAAAGCGCCGCG 62.239 55.000 8.83 8.83 38.76 6.46
3993 4301 3.188100 CATGAGAAAGCGCCGCGA 61.188 61.111 18.91 0.00 0.00 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.651701 GGTGACACGAGATATGCTACG 58.348 52.381 0.00 0.00 0.00 3.51
1 2 2.651701 CGGTGACACGAGATATGCTAC 58.348 52.381 0.00 0.00 35.47 3.58
3 4 0.249073 GCGGTGACACGAGATATGCT 60.249 55.000 0.00 0.00 35.47 3.79
4 5 0.249073 AGCGGTGACACGAGATATGC 60.249 55.000 0.00 0.00 35.47 3.14
5 6 1.481240 CAGCGGTGACACGAGATATG 58.519 55.000 9.50 0.00 35.47 1.78
7 8 1.138883 GCAGCGGTGACACGAGATA 59.861 57.895 20.69 0.00 35.47 1.98
8 9 2.125912 GCAGCGGTGACACGAGAT 60.126 61.111 20.69 0.00 35.47 2.75
9 10 4.357947 GGCAGCGGTGACACGAGA 62.358 66.667 20.69 0.00 35.47 4.04
33 34 1.471684 GCCTAAGCCATGCAGATATGC 59.528 52.381 5.09 5.09 0.00 3.14
55 56 1.482182 TCACGGAATCTAGCATGCACT 59.518 47.619 21.98 1.90 0.00 4.40
56 57 1.939974 TCACGGAATCTAGCATGCAC 58.060 50.000 21.98 3.65 0.00 4.57
57 58 2.689553 TTCACGGAATCTAGCATGCA 57.310 45.000 21.98 5.01 0.00 3.96
60 61 3.496870 GGGGATTTCACGGAATCTAGCAT 60.497 47.826 0.00 0.00 36.50 3.79
61 62 2.158813 GGGGATTTCACGGAATCTAGCA 60.159 50.000 0.00 0.00 36.50 3.49
184 186 0.448593 CAGGTCTCTTCCTCGTCGTC 59.551 60.000 0.00 0.00 35.37 4.20
187 189 1.513622 GGCAGGTCTCTTCCTCGTC 59.486 63.158 0.00 0.00 35.37 4.20
243 245 2.178984 CCCTACTCCTCTCATCCCTCTT 59.821 54.545 0.00 0.00 0.00 2.85
296 503 4.776647 GGCGTCAACATTGGGCGC 62.777 66.667 18.95 18.95 45.04 6.53
307 514 2.106477 TACAGATTGCATTGGCGTCA 57.894 45.000 0.00 0.00 45.35 4.35
308 515 2.785679 GTTACAGATTGCATTGGCGTC 58.214 47.619 0.00 0.00 45.35 5.19
309 516 1.130373 CGTTACAGATTGCATTGGCGT 59.870 47.619 0.00 0.00 45.35 5.68
314 521 3.120199 GCTCACACGTTACAGATTGCATT 60.120 43.478 0.00 0.00 0.00 3.56
315 522 2.416547 GCTCACACGTTACAGATTGCAT 59.583 45.455 0.00 0.00 0.00 3.96
316 523 1.798223 GCTCACACGTTACAGATTGCA 59.202 47.619 0.00 0.00 0.00 4.08
317 524 2.069273 AGCTCACACGTTACAGATTGC 58.931 47.619 0.00 0.00 0.00 3.56
321 528 6.317893 TCAAGATATAGCTCACACGTTACAGA 59.682 38.462 0.00 0.00 0.00 3.41
322 529 6.495706 TCAAGATATAGCTCACACGTTACAG 58.504 40.000 0.00 0.00 0.00 2.74
323 530 6.445357 TCAAGATATAGCTCACACGTTACA 57.555 37.500 0.00 0.00 0.00 2.41
324 531 7.435488 ACAATCAAGATATAGCTCACACGTTAC 59.565 37.037 0.00 0.00 0.00 2.50
331 538 9.265901 ACAATACACAATCAAGATATAGCTCAC 57.734 33.333 0.00 0.00 0.00 3.51
335 542 9.979270 GCATACAATACACAATCAAGATATAGC 57.021 33.333 0.00 0.00 0.00 2.97
339 546 9.836864 AAGAGCATACAATACACAATCAAGATA 57.163 29.630 0.00 0.00 0.00 1.98
340 547 8.743085 AAGAGCATACAATACACAATCAAGAT 57.257 30.769 0.00 0.00 0.00 2.40
341 548 9.836864 ATAAGAGCATACAATACACAATCAAGA 57.163 29.630 0.00 0.00 0.00 3.02
342 549 9.874215 CATAAGAGCATACAATACACAATCAAG 57.126 33.333 0.00 0.00 0.00 3.02
343 550 9.394767 ACATAAGAGCATACAATACACAATCAA 57.605 29.630 0.00 0.00 0.00 2.57
344 551 8.829612 CACATAAGAGCATACAATACACAATCA 58.170 33.333 0.00 0.00 0.00 2.57
345 552 8.285394 CCACATAAGAGCATACAATACACAATC 58.715 37.037 0.00 0.00 0.00 2.67
346 553 7.229306 CCCACATAAGAGCATACAATACACAAT 59.771 37.037 0.00 0.00 0.00 2.71
347 554 6.542005 CCCACATAAGAGCATACAATACACAA 59.458 38.462 0.00 0.00 0.00 3.33
348 555 6.054941 CCCACATAAGAGCATACAATACACA 58.945 40.000 0.00 0.00 0.00 3.72
349 556 6.017934 CACCCACATAAGAGCATACAATACAC 60.018 42.308 0.00 0.00 0.00 2.90
350 557 6.054941 CACCCACATAAGAGCATACAATACA 58.945 40.000 0.00 0.00 0.00 2.29
351 558 5.049405 GCACCCACATAAGAGCATACAATAC 60.049 44.000 0.00 0.00 0.00 1.89
352 559 5.063204 GCACCCACATAAGAGCATACAATA 58.937 41.667 0.00 0.00 0.00 1.90
353 560 3.885297 GCACCCACATAAGAGCATACAAT 59.115 43.478 0.00 0.00 0.00 2.71
354 561 3.278574 GCACCCACATAAGAGCATACAA 58.721 45.455 0.00 0.00 0.00 2.41
355 562 2.238395 TGCACCCACATAAGAGCATACA 59.762 45.455 0.00 0.00 0.00 2.29
356 563 2.917933 TGCACCCACATAAGAGCATAC 58.082 47.619 0.00 0.00 0.00 2.39
357 564 3.862877 ATGCACCCACATAAGAGCATA 57.137 42.857 0.00 0.00 40.54 3.14
358 565 2.742428 ATGCACCCACATAAGAGCAT 57.258 45.000 0.00 0.00 37.83 3.79
359 566 2.512692 AATGCACCCACATAAGAGCA 57.487 45.000 0.00 0.00 36.34 4.26
360 567 3.874392 AAAATGCACCCACATAAGAGC 57.126 42.857 0.00 0.00 0.00 4.09
361 568 5.047802 ACAGAAAAATGCACCCACATAAGAG 60.048 40.000 0.00 0.00 0.00 2.85
362 569 4.832266 ACAGAAAAATGCACCCACATAAGA 59.168 37.500 0.00 0.00 0.00 2.10
363 570 5.138125 ACAGAAAAATGCACCCACATAAG 57.862 39.130 0.00 0.00 0.00 1.73
364 571 5.336372 GCTACAGAAAAATGCACCCACATAA 60.336 40.000 0.00 0.00 0.00 1.90
365 572 4.157656 GCTACAGAAAAATGCACCCACATA 59.842 41.667 0.00 0.00 0.00 2.29
366 573 3.056607 GCTACAGAAAAATGCACCCACAT 60.057 43.478 0.00 0.00 0.00 3.21
367 574 2.295909 GCTACAGAAAAATGCACCCACA 59.704 45.455 0.00 0.00 0.00 4.17
368 575 2.295909 TGCTACAGAAAAATGCACCCAC 59.704 45.455 0.00 0.00 0.00 4.61
369 576 2.591923 TGCTACAGAAAAATGCACCCA 58.408 42.857 0.00 0.00 0.00 4.51
370 577 3.658757 TTGCTACAGAAAAATGCACCC 57.341 42.857 0.00 0.00 33.13 4.61
371 578 5.229423 TCATTTGCTACAGAAAAATGCACC 58.771 37.500 0.00 0.00 39.85 5.01
372 579 6.956299 ATCATTTGCTACAGAAAAATGCAC 57.044 33.333 0.00 0.00 39.85 4.57
373 580 9.656040 ATTTATCATTTGCTACAGAAAAATGCA 57.344 25.926 0.00 0.00 39.85 3.96
376 583 9.520204 CCGATTTATCATTTGCTACAGAAAAAT 57.480 29.630 0.00 0.00 0.00 1.82
377 584 8.519526 ACCGATTTATCATTTGCTACAGAAAAA 58.480 29.630 0.00 0.00 0.00 1.94
378 585 7.967854 CACCGATTTATCATTTGCTACAGAAAA 59.032 33.333 0.00 0.00 0.00 2.29
379 586 7.335673 TCACCGATTTATCATTTGCTACAGAAA 59.664 33.333 0.00 0.00 0.00 2.52
380 587 6.821160 TCACCGATTTATCATTTGCTACAGAA 59.179 34.615 0.00 0.00 0.00 3.02
381 588 6.345298 TCACCGATTTATCATTTGCTACAGA 58.655 36.000 0.00 0.00 0.00 3.41
382 589 6.603237 TCACCGATTTATCATTTGCTACAG 57.397 37.500 0.00 0.00 0.00 2.74
383 590 8.846943 ATATCACCGATTTATCATTTGCTACA 57.153 30.769 0.00 0.00 0.00 2.74
386 593 9.507329 AACTATATCACCGATTTATCATTTGCT 57.493 29.630 0.00 0.00 0.00 3.91
387 594 9.546909 CAACTATATCACCGATTTATCATTTGC 57.453 33.333 0.00 0.00 0.00 3.68
390 597 9.778741 ACACAACTATATCACCGATTTATCATT 57.221 29.630 0.00 0.00 0.00 2.57
391 598 9.208022 CACACAACTATATCACCGATTTATCAT 57.792 33.333 0.00 0.00 0.00 2.45
392 599 7.170828 GCACACAACTATATCACCGATTTATCA 59.829 37.037 0.00 0.00 0.00 2.15
393 600 7.170828 TGCACACAACTATATCACCGATTTATC 59.829 37.037 0.00 0.00 0.00 1.75
394 601 6.989759 TGCACACAACTATATCACCGATTTAT 59.010 34.615 0.00 0.00 0.00 1.40
395 602 6.342111 TGCACACAACTATATCACCGATTTA 58.658 36.000 0.00 0.00 0.00 1.40
396 603 5.182487 TGCACACAACTATATCACCGATTT 58.818 37.500 0.00 0.00 0.00 2.17
397 604 4.765273 TGCACACAACTATATCACCGATT 58.235 39.130 0.00 0.00 0.00 3.34
398 605 4.400529 TGCACACAACTATATCACCGAT 57.599 40.909 0.00 0.00 0.00 4.18
399 606 3.878160 TGCACACAACTATATCACCGA 57.122 42.857 0.00 0.00 0.00 4.69
400 607 3.182372 CGATGCACACAACTATATCACCG 59.818 47.826 0.00 0.00 0.00 4.94
401 608 4.368315 TCGATGCACACAACTATATCACC 58.632 43.478 0.00 0.00 0.00 4.02
402 609 5.557136 GCTTCGATGCACACAACTATATCAC 60.557 44.000 17.62 0.00 0.00 3.06
403 610 4.507756 GCTTCGATGCACACAACTATATCA 59.492 41.667 17.62 0.00 0.00 2.15
404 611 4.507756 TGCTTCGATGCACACAACTATATC 59.492 41.667 20.86 0.00 38.12 1.63
405 612 4.441792 TGCTTCGATGCACACAACTATAT 58.558 39.130 20.86 0.00 38.12 0.86
406 613 3.855858 TGCTTCGATGCACACAACTATA 58.144 40.909 20.86 0.00 38.12 1.31
407 614 2.698803 TGCTTCGATGCACACAACTAT 58.301 42.857 20.86 0.00 38.12 2.12
408 615 2.162319 TGCTTCGATGCACACAACTA 57.838 45.000 20.86 0.00 38.12 2.24
409 616 1.466167 GATGCTTCGATGCACACAACT 59.534 47.619 26.10 10.95 46.33 3.16
410 617 1.197492 TGATGCTTCGATGCACACAAC 59.803 47.619 26.10 15.47 46.33 3.32
411 618 1.521580 TGATGCTTCGATGCACACAA 58.478 45.000 26.10 10.71 46.33 3.33
412 619 1.521580 TTGATGCTTCGATGCACACA 58.478 45.000 26.10 23.59 46.33 3.72
413 620 2.838386 ATTGATGCTTCGATGCACAC 57.162 45.000 26.10 21.66 46.33 3.82
414 621 3.139603 CAATTGATGCTTCGATGCACA 57.860 42.857 26.10 21.31 46.33 4.57
426 633 3.017048 TCCCTAACCTGGCAATTGATG 57.983 47.619 10.34 0.00 0.00 3.07
427 634 3.979501 ATCCCTAACCTGGCAATTGAT 57.020 42.857 10.34 0.00 0.00 2.57
428 635 3.756082 AATCCCTAACCTGGCAATTGA 57.244 42.857 10.34 0.00 0.00 2.57
429 636 3.768757 TCAAATCCCTAACCTGGCAATTG 59.231 43.478 0.00 0.00 0.00 2.32
430 637 4.059773 TCAAATCCCTAACCTGGCAATT 57.940 40.909 0.00 0.00 0.00 2.32
431 638 3.756082 TCAAATCCCTAACCTGGCAAT 57.244 42.857 0.00 0.00 0.00 3.56
432 639 3.161866 GTTCAAATCCCTAACCTGGCAA 58.838 45.455 0.00 0.00 0.00 4.52
433 640 2.556559 GGTTCAAATCCCTAACCTGGCA 60.557 50.000 0.00 0.00 39.66 4.92
434 641 2.100197 GGTTCAAATCCCTAACCTGGC 58.900 52.381 0.00 0.00 39.66 4.85
438 645 5.321927 TGAAGAAGGTTCAAATCCCTAACC 58.678 41.667 0.00 0.00 42.48 2.85
439 646 6.004574 ACTGAAGAAGGTTCAAATCCCTAAC 58.995 40.000 0.00 0.00 0.00 2.34
440 647 6.003950 CACTGAAGAAGGTTCAAATCCCTAA 58.996 40.000 0.00 0.00 0.00 2.69
441 648 5.514834 CCACTGAAGAAGGTTCAAATCCCTA 60.515 44.000 0.00 0.00 0.00 3.53
442 649 4.401925 CACTGAAGAAGGTTCAAATCCCT 58.598 43.478 0.00 0.00 0.00 4.20
443 650 3.507622 CCACTGAAGAAGGTTCAAATCCC 59.492 47.826 0.00 0.00 0.00 3.85
444 651 4.398319 TCCACTGAAGAAGGTTCAAATCC 58.602 43.478 0.00 0.00 0.00 3.01
470 677 8.406297 GCTCCAATCCTTCTACGATTTTATTTT 58.594 33.333 0.00 0.00 0.00 1.82
474 681 5.047847 CGCTCCAATCCTTCTACGATTTTA 58.952 41.667 0.00 0.00 0.00 1.52
492 699 5.425630 TCCTCTAACCTTTATTTTCGCTCC 58.574 41.667 0.00 0.00 0.00 4.70
531 738 9.882996 TGCAGATCATGATACGATTTATTTTTC 57.117 29.630 8.54 0.00 0.00 2.29
532 739 9.669353 GTGCAGATCATGATACGATTTATTTTT 57.331 29.630 8.54 0.00 0.00 1.94
537 744 5.528870 ACGTGCAGATCATGATACGATTTA 58.471 37.500 27.09 3.35 41.01 1.40
580 814 9.481340 CAGAGCATTAGCATCACTAAACTATTA 57.519 33.333 0.00 0.00 43.99 0.98
602 837 1.670087 CCGTGCAAGTGACCTACAGAG 60.670 57.143 0.00 0.00 0.00 3.35
671 912 5.492895 ACTTTCCCGTTCAAAACCATTTTT 58.507 33.333 0.00 0.00 35.15 1.94
701 942 1.469423 GCGCTACAGACAACTAGACCC 60.469 57.143 0.00 0.00 0.00 4.46
702 943 1.473278 AGCGCTACAGACAACTAGACC 59.527 52.381 8.99 0.00 0.00 3.85
806 1048 0.392461 TCCACGGCTTGATTACTGCC 60.392 55.000 0.00 0.00 42.94 4.85
807 1049 1.009829 CTCCACGGCTTGATTACTGC 58.990 55.000 0.00 0.00 0.00 4.40
982 1224 3.129988 ACCATGATAAGCAAAGCAAGAGC 59.870 43.478 0.00 0.00 42.56 4.09
983 1225 4.157289 ACACCATGATAAGCAAAGCAAGAG 59.843 41.667 0.00 0.00 0.00 2.85
984 1226 4.081406 ACACCATGATAAGCAAAGCAAGA 58.919 39.130 0.00 0.00 0.00 3.02
985 1227 4.418392 GACACCATGATAAGCAAAGCAAG 58.582 43.478 0.00 0.00 0.00 4.01
988 1230 2.754552 TGGACACCATGATAAGCAAAGC 59.245 45.455 0.00 0.00 0.00 3.51
989 1231 4.701651 TCTTGGACACCATGATAAGCAAAG 59.298 41.667 0.00 0.00 33.63 2.77
991 1233 4.264253 CTCTTGGACACCATGATAAGCAA 58.736 43.478 0.00 0.00 37.13 3.91
992 1234 3.877559 CTCTTGGACACCATGATAAGCA 58.122 45.455 0.00 0.00 37.13 3.91
993 1235 2.615912 GCTCTTGGACACCATGATAAGC 59.384 50.000 0.00 4.48 37.13 3.09
994 1236 4.125703 GAGCTCTTGGACACCATGATAAG 58.874 47.826 6.43 0.00 37.13 1.73
996 1238 2.101415 CGAGCTCTTGGACACCATGATA 59.899 50.000 12.85 0.00 37.13 2.15
998 1240 0.247460 CGAGCTCTTGGACACCATGA 59.753 55.000 12.85 0.00 36.48 3.07
1463 1734 3.197333 CCAACACTCAGGATCTCTCACAT 59.803 47.826 0.00 0.00 0.00 3.21
1464 1735 2.564504 CCAACACTCAGGATCTCTCACA 59.435 50.000 0.00 0.00 0.00 3.58
1690 1961 3.315521 CGATTCTCGGTCGCGCAG 61.316 66.667 8.75 0.00 36.00 5.18
1702 1973 7.838498 ACACGTTGAATATTACTAAGCGATTC 58.162 34.615 0.00 0.00 0.00 2.52
1703 1974 7.766219 ACACGTTGAATATTACTAAGCGATT 57.234 32.000 0.00 0.00 0.00 3.34
1704 1975 7.490079 TCAACACGTTGAATATTACTAAGCGAT 59.510 33.333 10.11 0.00 45.56 4.58
1705 1976 6.807720 TCAACACGTTGAATATTACTAAGCGA 59.192 34.615 10.11 0.00 45.56 4.93
1706 1977 6.985013 TCAACACGTTGAATATTACTAAGCG 58.015 36.000 10.11 0.00 45.56 4.68
1749 2021 7.352739 ACTCGTGTTATTAGCTTGAGTTTTTG 58.647 34.615 0.00 0.00 31.61 2.44
1755 2027 6.575572 CGATCTACTCGTGTTATTAGCTTGAG 59.424 42.308 0.00 0.00 42.56 3.02
1756 2028 6.427974 CGATCTACTCGTGTTATTAGCTTGA 58.572 40.000 0.00 0.00 42.56 3.02
1772 2044 1.341089 TGGCTGGTCTCACGATCTACT 60.341 52.381 0.00 0.00 0.00 2.57
1785 2057 0.977627 TCATCCTCGACATGGCTGGT 60.978 55.000 0.00 0.00 0.00 4.00
1872 2144 6.244654 TCATTGGTGGTACAATCAAAGATGA 58.755 36.000 0.00 0.00 44.16 2.92
1931 2204 5.722172 ACTCTACTGGTGGTAGTGGTATA 57.278 43.478 8.87 0.00 45.86 1.47
1932 2205 4.604784 ACTCTACTGGTGGTAGTGGTAT 57.395 45.455 8.87 0.00 45.86 2.73
1966 2239 7.039853 TGCATAATTCAGAGTGACCATTTTTCA 60.040 33.333 0.00 0.00 0.00 2.69
1967 2240 7.315142 TGCATAATTCAGAGTGACCATTTTTC 58.685 34.615 0.00 0.00 0.00 2.29
1977 2254 4.510711 AGCGAATCTGCATAATTCAGAGTG 59.489 41.667 17.37 6.27 43.02 3.51
1981 2258 4.083961 CCTCAGCGAATCTGCATAATTCAG 60.084 45.833 17.37 12.49 42.56 3.02
1983 2260 3.812053 ACCTCAGCGAATCTGCATAATTC 59.188 43.478 10.49 10.49 42.56 2.17
1988 2265 1.482182 TGTACCTCAGCGAATCTGCAT 59.518 47.619 0.00 0.00 42.56 3.96
2076 2353 4.681978 GCGGTGCCGGTGAAGACT 62.682 66.667 12.82 0.00 40.19 3.24
2163 2440 2.202440 AAGGCGACGACGATGACG 60.202 61.111 12.29 3.09 42.66 4.35
2256 2536 2.323580 GCAGACACAGGTGAGCTGC 61.324 63.158 24.23 24.23 46.06 5.25
2740 3025 1.621317 TCAATGGCGTACCTGAGAACA 59.379 47.619 0.00 0.00 36.63 3.18
2751 3036 0.322816 AAGCAGGTGATCAATGGCGT 60.323 50.000 0.00 0.00 0.00 5.68
2797 3082 6.975949 TGGATTAGGCCAGGAAACTTTATTA 58.024 36.000 5.01 0.00 40.21 0.98
2803 3089 2.378547 TGTTGGATTAGGCCAGGAAACT 59.621 45.455 5.01 0.00 46.44 2.66
2804 3090 2.492088 GTGTTGGATTAGGCCAGGAAAC 59.508 50.000 5.01 2.18 39.52 2.78
2834 3120 3.237746 TCCATGAACATCCCTGCAAAAA 58.762 40.909 0.00 0.00 0.00 1.94
2861 3147 3.160269 CATTGCCTTGTCCTTCCTCTTT 58.840 45.455 0.00 0.00 0.00 2.52
2870 3156 4.133796 GCCGCCATTGCCTTGTCC 62.134 66.667 0.00 0.00 0.00 4.02
2885 3171 1.607628 GCCAGAGTGATCATCATTGCC 59.392 52.381 0.00 0.00 0.00 4.52
2888 3174 1.487976 ACCGCCAGAGTGATCATCATT 59.512 47.619 0.00 0.00 0.00 2.57
2975 3261 1.954927 GCTAACTAGCTCCGGCATTT 58.045 50.000 0.00 0.00 45.62 2.32
3046 3341 2.922740 AAGTGGAGGAACGCTACAAA 57.077 45.000 0.00 0.00 42.74 2.83
3062 3358 3.482436 TGCCACGATCAAAACCTAAAGT 58.518 40.909 0.00 0.00 0.00 2.66
3111 3407 2.095853 CCATTTGCTAGCCGTTACACAG 59.904 50.000 13.29 0.00 0.00 3.66
3119 3415 1.723870 GACTGCCATTTGCTAGCCG 59.276 57.895 13.29 0.00 42.00 5.52
3120 3416 1.718757 CCGACTGCCATTTGCTAGCC 61.719 60.000 13.29 0.00 42.00 3.93
3121 3417 1.723870 CCGACTGCCATTTGCTAGC 59.276 57.895 8.10 8.10 42.00 3.42
3192 3497 3.383761 ACAAAAGGCGCTCATTTTCTTG 58.616 40.909 7.64 4.86 0.00 3.02
3200 3505 1.771073 CGTGTGACAAAAGGCGCTCA 61.771 55.000 7.64 0.00 0.00 4.26
3216 3521 2.670905 TCGTATCCACAGCAAATTCGTG 59.329 45.455 0.00 0.00 0.00 4.35
3247 3552 1.726791 CCGTTCGATTTGAGTGTCAGG 59.273 52.381 0.00 0.00 0.00 3.86
3327 3633 5.245751 CAGCCTCATGACCAGACTTATATCT 59.754 44.000 0.00 0.00 0.00 1.98
3332 3638 1.833630 CCAGCCTCATGACCAGACTTA 59.166 52.381 0.00 0.00 0.00 2.24
3337 3643 2.124403 GGCCAGCCTCATGACCAG 60.124 66.667 0.00 0.00 0.00 4.00
3370 3676 4.251543 TGCTTTAAGGTTAGCTTTTGGC 57.748 40.909 0.92 5.19 38.22 4.52
3454 3760 8.488651 AAATAAAGTCGAGATCATTACCGTTT 57.511 30.769 0.00 0.00 0.00 3.60
3469 3775 7.306283 GGTTCGATCATCTCTGAAATAAAGTCG 60.306 40.741 0.00 0.00 34.37 4.18
3501 3807 5.070685 ACATAACAAGAGGAAACAAGGGTC 58.929 41.667 0.00 0.00 0.00 4.46
3502 3808 5.061721 ACATAACAAGAGGAAACAAGGGT 57.938 39.130 0.00 0.00 0.00 4.34
3510 3817 6.657541 GGTTATTGGTGACATAACAAGAGGAA 59.342 38.462 7.74 0.00 42.32 3.36
3641 3948 2.746277 GCTTTGGTCATCGCGGGT 60.746 61.111 6.13 0.00 0.00 5.28
3682 3989 3.954258 GGTAGCTATTTGCAGGGACAATT 59.046 43.478 0.00 0.00 45.94 2.32
3683 3990 3.555966 GGTAGCTATTTGCAGGGACAAT 58.444 45.455 0.00 0.00 45.94 2.71
3706 4013 1.192428 GACACATAGAGGGGGAACGT 58.808 55.000 0.00 0.00 0.00 3.99
3800 4107 0.470766 TCCGCCAAGGTACAACAAGT 59.529 50.000 0.00 0.00 41.99 3.16
3811 4118 2.178912 TCTAAAACCTGTCCGCCAAG 57.821 50.000 0.00 0.00 0.00 3.61
3851 4158 4.757149 GCTTTCATTACCCGCTTCATATCT 59.243 41.667 0.00 0.00 0.00 1.98
3892 4199 3.337358 CATGAGGCAATTTTTCAACCCC 58.663 45.455 0.00 0.00 0.00 4.95
3893 4200 3.007831 TCCATGAGGCAATTTTTCAACCC 59.992 43.478 0.00 0.00 33.74 4.11
3894 4201 4.270245 TCCATGAGGCAATTTTTCAACC 57.730 40.909 0.00 0.00 33.74 3.77
3895 4202 5.521372 GCTATCCATGAGGCAATTTTTCAAC 59.479 40.000 0.00 0.00 33.74 3.18
3950 4258 4.400120 AGTTCGTTCTCCTCTCAGTAACT 58.600 43.478 0.00 0.00 0.00 2.24
3968 4276 3.237628 GGCGCTTTCTCATGAAAAGTTC 58.762 45.455 21.15 15.82 41.09 3.01


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

AutoCloner maintained by Alex Coulton.