Multiple sequence alignment - TraesCS3D01G180000

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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 TraesCS3D01G180000 chr3D 100.000 1307 0 0 1 1307 161929980 161928674 0.000000e+00 2414
1 TraesCS3D01G180000 chr3D 100.000 529 0 0 1655 2183 161928326 161927798 0.000000e+00 977
2 TraesCS3D01G180000 chr3A 92.263 517 26 6 1673 2183 191836965 191836457 0.000000e+00 721
3 TraesCS3D01G180000 chr3A 94.382 356 18 2 949 1303 191837574 191837220 1.470000e-151 545
4 TraesCS3D01G180000 chr3A 88.618 246 22 3 1 240 191838588 191838343 5.890000e-76 294
5 TraesCS3D01G180000 chr3A 75.649 308 44 18 354 659 191838124 191837846 8.180000e-25 124
6 TraesCS3D01G180000 chr3B 92.517 441 23 3 877 1307 238496472 238496032 6.620000e-175 623
7 TraesCS3D01G180000 chr3B 92.732 399 24 3 1790 2183 238495687 238495289 2.430000e-159 571
8 TraesCS3D01G180000 chr3B 79.295 681 83 31 1 653 238497348 238496698 7.200000e-115 424


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 TraesCS3D01G180000 chr3D 161927798 161929980 2182 True 1695.500000 2414 100.000000 1 2183 2 chr3D.!!$R1 2182
1 TraesCS3D01G180000 chr3A 191836457 191838588 2131 True 421.000000 721 87.728000 1 2183 4 chr3A.!!$R1 2182
2 TraesCS3D01G180000 chr3B 238495289 238497348 2059 True 539.333333 623 88.181333 1 2183 3 chr3B.!!$R1 2182

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
801 923 0.03392 CCAGCCCAACCTTTTGCTTC 59.966 55.0 0.0 0.0 30.08 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 2527 2.229543 GCAGCAACATTGATCAGTTCCA 59.77 45.455 0.0 0.0 0.0 3.53 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
61 62 0.815734 GAGGAACCGTGGATCTCGAA 59.184 55.000 11.16 0.00 0.00 3.71
84 85 2.271800 GATTGTTTCGAGATCACGCCT 58.728 47.619 7.75 0.00 0.00 5.52
90 91 1.066587 CGAGATCACGCCTCCCTTC 59.933 63.158 0.00 0.00 0.00 3.46
179 184 4.991056 AGTGTTGTACTGTTGCTGTAGATG 59.009 41.667 0.00 0.00 38.49 2.90
205 210 3.385577 AGTTCTTCAGACAACGAAGCTC 58.614 45.455 0.00 0.00 39.80 4.09
207 212 1.607148 TCTTCAGACAACGAAGCTCGA 59.393 47.619 11.64 0.00 43.74 4.04
210 215 3.026630 TCAGACAACGAAGCTCGAAAT 57.973 42.857 11.64 0.00 43.74 2.17
214 221 5.073478 CAGACAACGAAGCTCGAAATAAAC 58.927 41.667 11.64 0.00 43.74 2.01
220 227 5.168569 ACGAAGCTCGAAATAAACAGATGA 58.831 37.500 11.64 0.00 43.74 2.92
223 230 6.183360 CGAAGCTCGAAATAAACAGATGAACT 60.183 38.462 0.00 0.00 43.74 3.01
225 232 5.289675 AGCTCGAAATAAACAGATGAACTCG 59.710 40.000 0.00 0.00 0.00 4.18
231 238 8.592155 CGAAATAAACAGATGAACTCGTCAATA 58.408 33.333 1.94 0.00 40.50 1.90
243 250 3.254903 ACTCGTCAATATGCGCCAGTATA 59.745 43.478 4.18 0.00 0.00 1.47
244 251 3.833442 TCGTCAATATGCGCCAGTATAG 58.167 45.455 4.18 0.00 0.00 1.31
246 253 4.456566 TCGTCAATATGCGCCAGTATAGTA 59.543 41.667 4.18 0.00 0.00 1.82
247 254 4.557690 CGTCAATATGCGCCAGTATAGTAC 59.442 45.833 4.18 0.00 0.00 2.73
248 255 4.557690 GTCAATATGCGCCAGTATAGTACG 59.442 45.833 4.18 0.00 0.00 3.67
251 258 0.949397 TGCGCCAGTATAGTACGGAG 59.051 55.000 4.18 0.00 0.00 4.63
253 260 2.146342 GCGCCAGTATAGTACGGAGTA 58.854 52.381 0.00 0.00 45.11 2.59
269 298 3.741388 CGGAGTACTAGCTTCCATTTGGG 60.741 52.174 0.00 0.00 35.41 4.12
275 304 1.188863 AGCTTCCATTTGGGCATGTC 58.811 50.000 0.00 0.00 36.21 3.06
284 313 4.353737 CATTTGGGCATGTCGTAATGAAG 58.646 43.478 14.43 0.00 0.00 3.02
285 314 1.378531 TGGGCATGTCGTAATGAAGC 58.621 50.000 0.00 0.00 0.00 3.86
286 315 1.339535 TGGGCATGTCGTAATGAAGCA 60.340 47.619 0.00 0.00 0.00 3.91
287 316 1.742831 GGGCATGTCGTAATGAAGCAA 59.257 47.619 0.00 0.00 0.00 3.91
291 320 4.091424 GCATGTCGTAATGAAGCAACTTC 58.909 43.478 0.32 0.32 40.54 3.01
296 325 4.391830 GTCGTAATGAAGCAACTTCCATGA 59.608 41.667 4.96 0.00 39.51 3.07
305 334 2.424956 GCAACTTCCATGACCCTTGATC 59.575 50.000 0.00 0.00 0.00 2.92
307 336 3.922171 ACTTCCATGACCCTTGATCTC 57.078 47.619 0.00 0.00 0.00 2.75
308 337 3.184628 ACTTCCATGACCCTTGATCTCA 58.815 45.455 0.00 0.00 0.00 3.27
309 338 3.784763 ACTTCCATGACCCTTGATCTCAT 59.215 43.478 0.00 0.00 0.00 2.90
311 340 5.429762 ACTTCCATGACCCTTGATCTCATTA 59.570 40.000 0.00 0.00 0.00 1.90
312 341 6.102321 ACTTCCATGACCCTTGATCTCATTAT 59.898 38.462 0.00 0.00 0.00 1.28
314 343 7.631510 TCCATGACCCTTGATCTCATTATTA 57.368 36.000 0.00 0.00 0.00 0.98
360 415 1.791204 CACCTGCAATCGATCGATCTG 59.209 52.381 29.48 26.11 33.08 2.90
362 417 2.101415 ACCTGCAATCGATCGATCTGAA 59.899 45.455 29.48 21.23 33.08 3.02
382 437 6.149973 TCTGAAAACATCATTTCCTGCAGTAG 59.850 38.462 13.81 0.00 38.30 2.57
396 514 4.929808 CCTGCAGTAGTTAGTTCATCGTTT 59.070 41.667 13.81 0.00 0.00 3.60
400 518 6.649141 TGCAGTAGTTAGTTCATCGTTTCATT 59.351 34.615 0.00 0.00 0.00 2.57
404 522 9.367444 AGTAGTTAGTTCATCGTTTCATTTAGG 57.633 33.333 0.00 0.00 0.00 2.69
405 523 7.611213 AGTTAGTTCATCGTTTCATTTAGGG 57.389 36.000 0.00 0.00 0.00 3.53
406 524 7.391620 AGTTAGTTCATCGTTTCATTTAGGGA 58.608 34.615 0.00 0.00 0.00 4.20
407 525 8.047310 AGTTAGTTCATCGTTTCATTTAGGGAT 58.953 33.333 0.00 0.00 0.00 3.85
409 527 7.321745 AGTTCATCGTTTCATTTAGGGATTC 57.678 36.000 0.00 0.00 0.00 2.52
410 528 6.884295 AGTTCATCGTTTCATTTAGGGATTCA 59.116 34.615 0.00 0.00 0.00 2.57
411 529 7.557719 AGTTCATCGTTTCATTTAGGGATTCAT 59.442 33.333 0.00 0.00 0.00 2.57
412 530 7.496529 TCATCGTTTCATTTAGGGATTCATC 57.503 36.000 0.00 0.00 0.00 2.92
413 531 7.282585 TCATCGTTTCATTTAGGGATTCATCT 58.717 34.615 0.00 0.00 0.00 2.90
414 532 8.428852 TCATCGTTTCATTTAGGGATTCATCTA 58.571 33.333 0.00 0.00 0.00 1.98
415 533 9.224267 CATCGTTTCATTTAGGGATTCATCTAT 57.776 33.333 0.00 0.00 0.00 1.98
416 534 8.607441 TCGTTTCATTTAGGGATTCATCTATG 57.393 34.615 0.00 0.00 0.00 2.23
417 535 8.210946 TCGTTTCATTTAGGGATTCATCTATGT 58.789 33.333 0.00 0.00 0.00 2.29
418 536 8.840321 CGTTTCATTTAGGGATTCATCTATGTT 58.160 33.333 0.00 0.00 0.00 2.71
428 550 7.071698 AGGGATTCATCTATGTTATGTCACTGT 59.928 37.037 0.00 0.00 0.00 3.55
445 567 3.192001 CACTGTGCATGCCTCTTTTATGT 59.808 43.478 16.68 0.00 0.00 2.29
454 576 3.785887 TGCCTCTTTTATGTGGTCCCTAT 59.214 43.478 0.00 0.00 0.00 2.57
455 577 4.137543 GCCTCTTTTATGTGGTCCCTATG 58.862 47.826 0.00 0.00 0.00 2.23
457 579 5.755849 CCTCTTTTATGTGGTCCCTATGTT 58.244 41.667 0.00 0.00 0.00 2.71
459 581 6.766467 CCTCTTTTATGTGGTCCCTATGTTAC 59.234 42.308 0.00 0.00 0.00 2.50
470 592 5.445964 GTCCCTATGTTACAACCATTGGAT 58.554 41.667 10.37 0.00 34.12 3.41
479 601 4.806640 ACAACCATTGGATTGGATTCAC 57.193 40.909 10.37 0.00 39.25 3.18
480 602 4.158786 ACAACCATTGGATTGGATTCACA 58.841 39.130 10.37 0.00 39.25 3.58
486 608 6.669154 ACCATTGGATTGGATTCACAAGTTAT 59.331 34.615 10.37 0.00 39.25 1.89
489 611 7.395190 TTGGATTGGATTCACAAGTTATCAG 57.605 36.000 0.00 0.00 33.23 2.90
490 612 6.484288 TGGATTGGATTCACAAGTTATCAGT 58.516 36.000 0.00 0.00 33.23 3.41
491 613 6.599244 TGGATTGGATTCACAAGTTATCAGTC 59.401 38.462 0.00 0.00 33.23 3.51
492 614 6.238211 GGATTGGATTCACAAGTTATCAGTCG 60.238 42.308 0.00 0.00 33.23 4.18
493 615 5.147330 TGGATTCACAAGTTATCAGTCGT 57.853 39.130 0.00 0.00 0.00 4.34
494 616 5.547465 TGGATTCACAAGTTATCAGTCGTT 58.453 37.500 0.00 0.00 0.00 3.85
495 617 5.995282 TGGATTCACAAGTTATCAGTCGTTT 59.005 36.000 0.00 0.00 0.00 3.60
496 618 6.147164 TGGATTCACAAGTTATCAGTCGTTTC 59.853 38.462 0.00 0.00 0.00 2.78
497 619 6.147164 GGATTCACAAGTTATCAGTCGTTTCA 59.853 38.462 0.00 0.00 0.00 2.69
499 621 6.525121 TCACAAGTTATCAGTCGTTTCAAG 57.475 37.500 0.00 0.00 0.00 3.02
500 622 6.277605 TCACAAGTTATCAGTCGTTTCAAGA 58.722 36.000 0.00 0.00 0.00 3.02
501 623 6.420903 TCACAAGTTATCAGTCGTTTCAAGAG 59.579 38.462 0.00 0.00 0.00 2.85
502 624 6.201044 CACAAGTTATCAGTCGTTTCAAGAGT 59.799 38.462 0.00 0.00 0.00 3.24
503 625 6.421202 ACAAGTTATCAGTCGTTTCAAGAGTC 59.579 38.462 0.00 0.00 0.00 3.36
504 626 6.334102 AGTTATCAGTCGTTTCAAGAGTCT 57.666 37.500 0.00 0.00 0.00 3.24
505 627 6.750148 AGTTATCAGTCGTTTCAAGAGTCTT 58.250 36.000 0.00 0.00 0.00 3.01
506 628 6.864165 AGTTATCAGTCGTTTCAAGAGTCTTC 59.136 38.462 1.26 0.00 0.00 2.87
507 629 4.920640 TCAGTCGTTTCAAGAGTCTTCT 57.079 40.909 1.26 0.00 34.29 2.85
508 630 6.576662 ATCAGTCGTTTCAAGAGTCTTCTA 57.423 37.500 1.26 0.00 31.96 2.10
509 631 6.576662 TCAGTCGTTTCAAGAGTCTTCTAT 57.423 37.500 1.26 0.00 31.96 1.98
510 632 6.982852 TCAGTCGTTTCAAGAGTCTTCTATT 58.017 36.000 1.26 0.00 31.96 1.73
511 633 7.434492 TCAGTCGTTTCAAGAGTCTTCTATTT 58.566 34.615 1.26 0.00 31.96 1.40
512 634 8.573885 TCAGTCGTTTCAAGAGTCTTCTATTTA 58.426 33.333 1.26 0.00 31.96 1.40
513 635 8.855279 CAGTCGTTTCAAGAGTCTTCTATTTAG 58.145 37.037 1.26 0.00 31.96 1.85
514 636 8.794553 AGTCGTTTCAAGAGTCTTCTATTTAGA 58.205 33.333 1.26 0.00 31.96 2.10
515 637 9.408069 GTCGTTTCAAGAGTCTTCTATTTAGAA 57.592 33.333 1.26 0.00 39.82 2.10
516 638 9.408069 TCGTTTCAAGAGTCTTCTATTTAGAAC 57.592 33.333 1.26 0.00 37.40 3.01
517 639 8.648968 CGTTTCAAGAGTCTTCTATTTAGAACC 58.351 37.037 1.26 0.00 37.40 3.62
518 640 9.490379 GTTTCAAGAGTCTTCTATTTAGAACCA 57.510 33.333 1.26 0.00 37.40 3.67
568 690 7.137490 TGAATTGTGTATTCTGCTTCTTCAG 57.863 36.000 0.00 0.00 42.63 3.02
574 696 6.531594 TGTGTATTCTGCTTCTTCAGTTATCG 59.468 38.462 0.00 0.00 35.63 2.92
575 697 6.531948 GTGTATTCTGCTTCTTCAGTTATCGT 59.468 38.462 0.00 0.00 35.63 3.73
586 708 5.545658 TTCAGTTATCGTTGAAGATTGGC 57.454 39.130 0.00 0.00 32.39 4.52
600 722 5.010922 TGAAGATTGGCAGTACATTGCTTTT 59.989 36.000 7.01 0.00 43.57 2.27
601 723 5.064441 AGATTGGCAGTACATTGCTTTTC 57.936 39.130 7.01 2.61 43.57 2.29
616 738 3.256383 TGCTTTTCACACATGGAAGATGG 59.744 43.478 0.00 0.00 0.00 3.51
617 739 3.367703 GCTTTTCACACATGGAAGATGGG 60.368 47.826 0.00 0.00 0.00 4.00
626 748 1.728323 TGGAAGATGGGATATCGCCA 58.272 50.000 16.42 14.74 0.00 5.69
637 759 5.368145 TGGGATATCGCCATAATTAGATGC 58.632 41.667 16.42 0.00 0.00 3.91
639 761 5.698545 GGGATATCGCCATAATTAGATGCTC 59.301 44.000 8.56 0.00 0.00 4.26
649 771 8.786898 GCCATAATTAGATGCTCATTTCTACAA 58.213 33.333 0.00 0.00 0.00 2.41
659 781 3.531538 TCATTTCTACAACCCGATGAGC 58.468 45.455 0.00 0.00 0.00 4.26
660 782 3.055458 TCATTTCTACAACCCGATGAGCA 60.055 43.478 0.00 0.00 0.00 4.26
661 783 2.672961 TTCTACAACCCGATGAGCAG 57.327 50.000 0.00 0.00 0.00 4.24
662 784 0.824109 TCTACAACCCGATGAGCAGG 59.176 55.000 0.00 0.00 0.00 4.85
682 804 2.202623 CGGAGCTACGTGAGGTGC 60.203 66.667 11.15 2.07 40.39 5.01
683 805 2.701780 CGGAGCTACGTGAGGTGCT 61.702 63.158 11.15 0.00 41.53 4.40
684 806 4.796225 GAGCTACGTGAGGTGCTC 57.204 61.111 0.00 11.65 46.79 4.26
685 807 1.139947 GAGCTACGTGAGGTGCTCC 59.860 63.158 14.40 0.00 46.92 4.70
686 808 2.202623 GCTACGTGAGGTGCTCCG 60.203 66.667 0.00 0.00 39.05 4.63
687 809 2.490217 CTACGTGAGGTGCTCCGG 59.510 66.667 0.00 0.00 39.05 5.14
688 810 3.701604 CTACGTGAGGTGCTCCGGC 62.702 68.421 0.00 0.00 39.05 6.13
711 833 3.793144 CAGCGCGGCAGGAGTTTC 61.793 66.667 8.83 0.00 0.00 2.78
712 834 4.008933 AGCGCGGCAGGAGTTTCT 62.009 61.111 8.83 0.00 0.00 2.52
713 835 3.050275 GCGCGGCAGGAGTTTCTT 61.050 61.111 8.83 0.00 0.00 2.52
714 836 3.028366 GCGCGGCAGGAGTTTCTTC 62.028 63.158 8.83 0.00 0.00 2.87
715 837 1.667830 CGCGGCAGGAGTTTCTTCA 60.668 57.895 0.00 0.00 0.00 3.02
716 838 1.021390 CGCGGCAGGAGTTTCTTCAT 61.021 55.000 0.00 0.00 0.00 2.57
717 839 1.168714 GCGGCAGGAGTTTCTTCATT 58.831 50.000 0.00 0.00 0.00 2.57
718 840 1.135575 GCGGCAGGAGTTTCTTCATTG 60.136 52.381 0.00 0.00 0.00 2.82
719 841 1.135575 CGGCAGGAGTTTCTTCATTGC 60.136 52.381 0.00 0.00 0.00 3.56
720 842 1.888512 GGCAGGAGTTTCTTCATTGCA 59.111 47.619 0.00 0.00 33.49 4.08
721 843 2.352127 GGCAGGAGTTTCTTCATTGCAC 60.352 50.000 0.00 0.00 33.49 4.57
722 844 2.294233 GCAGGAGTTTCTTCATTGCACA 59.706 45.455 0.00 0.00 32.66 4.57
723 845 3.854784 GCAGGAGTTTCTTCATTGCACAC 60.855 47.826 0.00 0.00 32.66 3.82
724 846 3.567164 CAGGAGTTTCTTCATTGCACACT 59.433 43.478 0.00 0.00 0.00 3.55
725 847 4.037208 CAGGAGTTTCTTCATTGCACACTT 59.963 41.667 0.00 0.00 0.00 3.16
726 848 5.239306 CAGGAGTTTCTTCATTGCACACTTA 59.761 40.000 0.00 0.00 0.00 2.24
727 849 5.471456 AGGAGTTTCTTCATTGCACACTTAG 59.529 40.000 0.00 0.00 0.00 2.18
728 850 5.239525 GGAGTTTCTTCATTGCACACTTAGT 59.760 40.000 0.00 0.00 0.00 2.24
729 851 6.238759 GGAGTTTCTTCATTGCACACTTAGTT 60.239 38.462 0.00 0.00 0.00 2.24
730 852 7.100458 AGTTTCTTCATTGCACACTTAGTTT 57.900 32.000 0.00 0.00 0.00 2.66
731 853 6.974622 AGTTTCTTCATTGCACACTTAGTTTG 59.025 34.615 0.00 0.00 0.00 2.93
732 854 6.449635 TTCTTCATTGCACACTTAGTTTGT 57.550 33.333 0.37 0.00 0.00 2.83
733 855 5.820131 TCTTCATTGCACACTTAGTTTGTG 58.180 37.500 0.37 0.00 46.05 3.33
741 863 5.940192 CACACTTAGTTTGTGCTATGGAA 57.060 39.130 0.00 0.00 38.11 3.53
742 864 5.689819 CACACTTAGTTTGTGCTATGGAAC 58.310 41.667 0.00 0.00 38.11 3.62
743 865 4.451096 ACACTTAGTTTGTGCTATGGAACG 59.549 41.667 0.00 0.00 38.86 3.95
744 866 4.000988 ACTTAGTTTGTGCTATGGAACGG 58.999 43.478 0.00 0.00 0.00 4.44
745 867 1.165270 AGTTTGTGCTATGGAACGGC 58.835 50.000 0.00 0.00 0.00 5.68
746 868 0.878416 GTTTGTGCTATGGAACGGCA 59.122 50.000 0.00 0.00 0.00 5.69
747 869 1.268352 GTTTGTGCTATGGAACGGCAA 59.732 47.619 0.00 0.00 37.73 4.52
748 870 1.832883 TTGTGCTATGGAACGGCAAT 58.167 45.000 0.00 0.00 37.73 3.56
749 871 1.378531 TGTGCTATGGAACGGCAATC 58.621 50.000 0.00 0.00 37.73 2.67
750 872 1.339535 TGTGCTATGGAACGGCAATCA 60.340 47.619 0.00 0.00 37.73 2.57
751 873 1.742831 GTGCTATGGAACGGCAATCAA 59.257 47.619 0.00 0.00 37.73 2.57
752 874 2.163412 GTGCTATGGAACGGCAATCAAA 59.837 45.455 0.00 0.00 37.73 2.69
753 875 2.423185 TGCTATGGAACGGCAATCAAAG 59.577 45.455 0.00 0.00 32.79 2.77
754 876 2.682856 GCTATGGAACGGCAATCAAAGA 59.317 45.455 0.00 0.00 0.00 2.52
755 877 3.242870 GCTATGGAACGGCAATCAAAGAG 60.243 47.826 0.00 0.00 0.00 2.85
756 878 2.270352 TGGAACGGCAATCAAAGAGT 57.730 45.000 0.00 0.00 0.00 3.24
757 879 3.410631 TGGAACGGCAATCAAAGAGTA 57.589 42.857 0.00 0.00 0.00 2.59
758 880 3.745799 TGGAACGGCAATCAAAGAGTAA 58.254 40.909 0.00 0.00 0.00 2.24
759 881 4.331968 TGGAACGGCAATCAAAGAGTAAT 58.668 39.130 0.00 0.00 0.00 1.89
760 882 4.394920 TGGAACGGCAATCAAAGAGTAATC 59.605 41.667 0.00 0.00 0.00 1.75
761 883 4.636206 GGAACGGCAATCAAAGAGTAATCT 59.364 41.667 0.00 0.00 0.00 2.40
762 884 5.220681 GGAACGGCAATCAAAGAGTAATCTC 60.221 44.000 0.00 0.00 40.70 2.75
780 902 3.357203 TCTCTATAGATTAGCCAGCCCG 58.643 50.000 2.11 0.00 0.00 6.13
781 903 2.428890 CTCTATAGATTAGCCAGCCCGG 59.571 54.545 2.11 0.00 38.11 5.73
795 917 4.994756 CCGGCCAGCCCAACCTTT 62.995 66.667 2.24 0.00 0.00 3.11
796 918 2.917227 CGGCCAGCCCAACCTTTT 60.917 61.111 2.24 0.00 0.00 2.27
797 919 2.743060 GGCCAGCCCAACCTTTTG 59.257 61.111 0.00 0.00 0.00 2.44
798 920 2.031012 GCCAGCCCAACCTTTTGC 59.969 61.111 0.00 0.00 0.00 3.68
799 921 2.510551 GCCAGCCCAACCTTTTGCT 61.511 57.895 0.00 0.00 33.52 3.91
800 922 2.043604 GCCAGCCCAACCTTTTGCTT 62.044 55.000 0.00 0.00 30.08 3.91
801 923 0.033920 CCAGCCCAACCTTTTGCTTC 59.966 55.000 0.00 0.00 30.08 3.86
802 924 0.752054 CAGCCCAACCTTTTGCTTCA 59.248 50.000 0.00 0.00 30.08 3.02
803 925 1.138661 CAGCCCAACCTTTTGCTTCAA 59.861 47.619 0.00 0.00 30.08 2.69
804 926 1.413812 AGCCCAACCTTTTGCTTCAAG 59.586 47.619 0.00 0.00 0.00 3.02
805 927 1.869774 CCCAACCTTTTGCTTCAAGC 58.130 50.000 1.04 1.04 42.82 4.01
806 928 1.413812 CCCAACCTTTTGCTTCAAGCT 59.586 47.619 11.57 0.00 42.97 3.74
807 929 2.546584 CCCAACCTTTTGCTTCAAGCTC 60.547 50.000 11.57 0.00 42.97 4.09
808 930 2.546584 CCAACCTTTTGCTTCAAGCTCC 60.547 50.000 11.57 0.00 42.97 4.70
809 931 0.954452 ACCTTTTGCTTCAAGCTCCG 59.046 50.000 11.57 0.00 42.97 4.63
810 932 0.387750 CCTTTTGCTTCAAGCTCCGC 60.388 55.000 11.57 0.00 42.97 5.54
811 933 0.387750 CTTTTGCTTCAAGCTCCGCC 60.388 55.000 11.57 0.00 42.97 6.13
812 934 1.106351 TTTTGCTTCAAGCTCCGCCA 61.106 50.000 11.57 0.00 42.97 5.69
813 935 1.795170 TTTGCTTCAAGCTCCGCCAC 61.795 55.000 11.57 0.00 42.97 5.01
814 936 2.359230 GCTTCAAGCTCCGCCACT 60.359 61.111 0.71 0.00 38.45 4.00
815 937 2.684843 GCTTCAAGCTCCGCCACTG 61.685 63.158 0.71 0.00 38.45 3.66
816 938 2.669569 TTCAAGCTCCGCCACTGC 60.670 61.111 0.00 0.00 0.00 4.40
817 939 4.704833 TCAAGCTCCGCCACTGCC 62.705 66.667 0.00 0.00 0.00 4.85
822 944 4.147449 CTCCGCCACTGCCGATGA 62.147 66.667 0.00 0.00 0.00 2.92
823 945 4.147449 TCCGCCACTGCCGATGAG 62.147 66.667 0.00 0.00 0.00 2.90
824 946 4.457496 CCGCCACTGCCGATGAGT 62.457 66.667 0.00 0.00 0.00 3.41
825 947 3.190849 CGCCACTGCCGATGAGTG 61.191 66.667 0.00 0.00 40.55 3.51
826 948 3.503363 GCCACTGCCGATGAGTGC 61.503 66.667 0.00 0.00 39.69 4.40
827 949 2.046988 CCACTGCCGATGAGTGCA 60.047 61.111 0.00 0.00 39.69 4.57
828 950 1.450848 CCACTGCCGATGAGTGCAT 60.451 57.895 0.00 0.00 39.69 3.96
829 951 1.028330 CCACTGCCGATGAGTGCATT 61.028 55.000 0.00 0.00 39.69 3.56
830 952 0.806868 CACTGCCGATGAGTGCATTT 59.193 50.000 0.00 0.00 36.79 2.32
831 953 1.200716 CACTGCCGATGAGTGCATTTT 59.799 47.619 0.00 0.00 36.79 1.82
832 954 1.200716 ACTGCCGATGAGTGCATTTTG 59.799 47.619 0.00 0.00 36.79 2.44
833 955 1.200716 CTGCCGATGAGTGCATTTTGT 59.799 47.619 0.00 0.00 36.79 2.83
834 956 1.612950 TGCCGATGAGTGCATTTTGTT 59.387 42.857 0.00 0.00 34.11 2.83
835 957 2.816672 TGCCGATGAGTGCATTTTGTTA 59.183 40.909 0.00 0.00 34.11 2.41
836 958 3.171277 GCCGATGAGTGCATTTTGTTAC 58.829 45.455 0.00 0.00 34.11 2.50
837 959 3.119849 GCCGATGAGTGCATTTTGTTACT 60.120 43.478 0.00 0.00 34.11 2.24
838 960 4.406069 CCGATGAGTGCATTTTGTTACTG 58.594 43.478 0.00 0.00 34.11 2.74
839 961 4.154015 CCGATGAGTGCATTTTGTTACTGA 59.846 41.667 0.00 0.00 34.11 3.41
840 962 5.163723 CCGATGAGTGCATTTTGTTACTGAT 60.164 40.000 0.00 0.00 34.11 2.90
843 965 5.771469 TGAGTGCATTTTGTTACTGATTGG 58.229 37.500 0.00 0.00 0.00 3.16
849 971 8.028938 GTGCATTTTGTTACTGATTGGTCTTAT 58.971 33.333 0.00 0.00 0.00 1.73
859 981 6.064717 ACTGATTGGTCTTATAAATCTGGCC 58.935 40.000 0.00 0.00 35.04 5.36
870 992 2.717639 AATCTGGCCGTTCATAAGCT 57.282 45.000 0.00 0.00 0.00 3.74
912 1208 8.576442 CAGTTAATGGTCTTCTTGTGGTTTATT 58.424 33.333 0.00 0.00 0.00 1.40
964 1264 6.426937 TCTTTACACAACTTCCTTATGCTGAC 59.573 38.462 0.00 0.00 0.00 3.51
972 1272 2.111384 TCCTTATGCTGACTCCAGTCC 58.889 52.381 4.25 0.00 44.15 3.85
984 1284 0.687354 TCCAGTCCTTCTCTTGGCAC 59.313 55.000 0.00 0.00 0.00 5.01
1049 1349 0.797542 GCACAGAGCAAGCAGAAGAG 59.202 55.000 0.00 0.00 44.79 2.85
1067 1367 2.365941 AGAGGAGCCCTACTAAAATCGC 59.634 50.000 0.00 0.00 31.76 4.58
1193 1493 0.322187 GGGAACTAAGCCCGAGCAAA 60.322 55.000 0.00 0.00 43.56 3.68
1206 1506 3.631686 CCCGAGCAAATGTGGAATGATTA 59.368 43.478 0.00 0.00 0.00 1.75
1210 1510 6.418819 CCGAGCAAATGTGGAATGATTAATTC 59.581 38.462 0.00 0.00 43.52 2.17
1245 1546 7.936496 TGTATCATCTTGTTGGCTAATTTCA 57.064 32.000 0.00 0.00 0.00 2.69
1260 1561 6.151144 GGCTAATTTCAGTTGTTGTACTCCAT 59.849 38.462 0.00 0.00 0.00 3.41
1303 1612 8.084684 AGATTCTTTTGCCATGTTTAGTTCTTC 58.915 33.333 0.00 0.00 0.00 2.87
1304 1613 6.959639 TCTTTTGCCATGTTTAGTTCTTCT 57.040 33.333 0.00 0.00 0.00 2.85
1305 1614 7.346751 TCTTTTGCCATGTTTAGTTCTTCTT 57.653 32.000 0.00 0.00 0.00 2.52
1306 1615 8.458573 TCTTTTGCCATGTTTAGTTCTTCTTA 57.541 30.769 0.00 0.00 0.00 2.10
1717 2251 9.182214 CTTGATATTTTTCTCTTCTGGGATGAA 57.818 33.333 0.00 0.00 0.00 2.57
1718 2252 8.511604 TGATATTTTTCTCTTCTGGGATGAAC 57.488 34.615 0.00 0.00 0.00 3.18
1788 2525 5.975693 TTTATGGTTTACTGGCTTGGAAG 57.024 39.130 0.00 0.00 0.00 3.46
1790 2527 3.306472 TGGTTTACTGGCTTGGAAGTT 57.694 42.857 0.00 0.00 0.00 2.66
1791 2528 2.955660 TGGTTTACTGGCTTGGAAGTTG 59.044 45.455 0.00 0.00 0.00 3.16
1792 2529 2.296190 GGTTTACTGGCTTGGAAGTTGG 59.704 50.000 0.00 0.00 0.00 3.77
1793 2530 3.219281 GTTTACTGGCTTGGAAGTTGGA 58.781 45.455 0.00 0.00 0.00 3.53
1794 2531 3.586470 TTACTGGCTTGGAAGTTGGAA 57.414 42.857 0.00 0.00 0.00 3.53
1795 2532 1.692411 ACTGGCTTGGAAGTTGGAAC 58.308 50.000 0.00 0.00 0.00 3.62
1796 2533 1.215423 ACTGGCTTGGAAGTTGGAACT 59.785 47.619 0.00 0.00 42.04 3.01
1797 2534 1.610522 CTGGCTTGGAAGTTGGAACTG 59.389 52.381 0.00 0.00 39.66 3.16
1798 2535 1.214175 TGGCTTGGAAGTTGGAACTGA 59.786 47.619 0.00 0.00 39.66 3.41
1799 2536 2.158475 TGGCTTGGAAGTTGGAACTGAT 60.158 45.455 0.00 0.00 39.66 2.90
1802 2539 3.569701 GCTTGGAAGTTGGAACTGATCAA 59.430 43.478 0.00 0.00 39.66 2.57
1831 2568 3.189285 GCTCAAGCAAAGCAAAAGTTGA 58.811 40.909 0.00 0.00 41.59 3.18
1838 2575 7.710044 TCAAGCAAAGCAAAAGTTGATTATGAA 59.290 29.630 0.00 0.00 38.50 2.57
1847 2584 8.497554 GCAAAAGTTGATTATGAATTGCTTCAA 58.502 29.630 0.00 0.00 44.29 2.69
2099 2839 3.963129 TGGGACCTTTTCAATCGCTATT 58.037 40.909 0.00 0.00 0.00 1.73
2104 2844 3.758554 ACCTTTTCAATCGCTATTGCAGT 59.241 39.130 6.09 0.00 41.96 4.40
2112 2857 2.463876 TCGCTATTGCAGTCGAGAATG 58.536 47.619 0.00 0.00 39.64 2.67
2170 2915 5.686159 AATCTACTCGTATTACTGACCGG 57.314 43.478 0.00 0.00 0.00 5.28
2179 2924 5.105635 TCGTATTACTGACCGGACTGAAATT 60.106 40.000 9.46 0.17 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.080300 ACCGAAATTAATCACCTGGCA 57.920 42.857 0.00 0.00 0.00 4.92
58 59 2.921121 TGATCTCGAAACAATCCGTTCG 59.079 45.455 0.00 0.00 36.59 3.95
61 62 2.259618 CGTGATCTCGAAACAATCCGT 58.740 47.619 11.64 0.00 0.00 4.69
84 85 2.044793 ACCAAGGACAGATGAAGGGA 57.955 50.000 0.00 0.00 0.00 4.20
90 91 2.036475 CGGGATCTACCAAGGACAGATG 59.964 54.545 11.04 0.00 41.20 2.90
173 178 4.402793 TGTCTGAAGAACTAGGCCATCTAC 59.597 45.833 5.01 0.00 0.00 2.59
179 184 2.029290 TCGTTGTCTGAAGAACTAGGCC 60.029 50.000 0.00 0.00 0.00 5.19
205 210 6.389622 TGACGAGTTCATCTGTTTATTTCG 57.610 37.500 0.00 0.00 0.00 3.46
210 215 6.019881 CGCATATTGACGAGTTCATCTGTTTA 60.020 38.462 0.00 0.00 32.84 2.01
214 221 3.362401 GCGCATATTGACGAGTTCATCTG 60.362 47.826 0.30 0.00 32.84 2.90
220 227 1.290203 CTGGCGCATATTGACGAGTT 58.710 50.000 10.83 0.00 0.00 3.01
223 230 2.812358 ATACTGGCGCATATTGACGA 57.188 45.000 10.83 0.00 0.00 4.20
225 232 4.557690 CGTACTATACTGGCGCATATTGAC 59.442 45.833 10.83 5.08 0.00 3.18
231 238 1.540267 CTCCGTACTATACTGGCGCAT 59.460 52.381 10.83 0.00 0.00 4.73
243 250 8.078250 CCAAATGGAAGCTAGTACTCCGTACT 62.078 46.154 0.00 11.02 43.74 2.73
244 251 4.915158 AATGGAAGCTAGTACTCCGTAC 57.085 45.455 0.00 0.00 39.10 3.67
246 253 3.118738 CCAAATGGAAGCTAGTACTCCGT 60.119 47.826 0.00 0.00 37.39 4.69
247 254 3.458189 CCAAATGGAAGCTAGTACTCCG 58.542 50.000 0.00 0.00 37.39 4.63
248 255 3.809905 CCCAAATGGAAGCTAGTACTCC 58.190 50.000 0.00 0.00 37.39 3.85
251 258 2.999331 TGCCCAAATGGAAGCTAGTAC 58.001 47.619 0.00 0.00 37.39 2.73
252 259 3.053693 ACATGCCCAAATGGAAGCTAGTA 60.054 43.478 0.00 0.00 37.39 1.82
253 260 2.291800 ACATGCCCAAATGGAAGCTAGT 60.292 45.455 0.00 0.00 37.39 2.57
254 261 2.360165 GACATGCCCAAATGGAAGCTAG 59.640 50.000 0.00 0.00 37.39 3.42
259 288 2.498644 TACGACATGCCCAAATGGAA 57.501 45.000 0.00 0.00 37.39 3.53
269 298 3.747099 AGTTGCTTCATTACGACATGC 57.253 42.857 0.00 0.00 0.00 4.06
275 304 4.437390 GGTCATGGAAGTTGCTTCATTACG 60.437 45.833 10.51 0.00 41.77 3.18
284 313 1.909700 TCAAGGGTCATGGAAGTTGC 58.090 50.000 0.00 0.00 0.00 4.17
285 314 3.944015 GAGATCAAGGGTCATGGAAGTTG 59.056 47.826 0.00 0.00 0.00 3.16
286 315 3.588842 TGAGATCAAGGGTCATGGAAGTT 59.411 43.478 0.00 0.00 0.00 2.66
287 316 3.184628 TGAGATCAAGGGTCATGGAAGT 58.815 45.455 0.00 0.00 0.00 3.01
291 320 9.964354 TTATAATAATGAGATCAAGGGTCATGG 57.036 33.333 0.00 0.00 31.21 3.66
314 343 7.440255 GCCATCTGCTGCTTGAAATTAAATTAT 59.560 33.333 0.00 0.00 36.87 1.28
347 402 7.488187 AATGATGTTTTCAGATCGATCGATT 57.512 32.000 29.89 17.33 37.89 3.34
350 405 6.018425 AGGAAATGATGTTTTCAGATCGATCG 60.018 38.462 19.33 9.36 37.89 3.69
360 415 6.259550 ACTACTGCAGGAAATGATGTTTTC 57.740 37.500 19.93 0.00 35.34 2.29
362 417 6.942576 ACTAACTACTGCAGGAAATGATGTTT 59.057 34.615 19.93 0.00 0.00 2.83
382 437 7.605410 TCCCTAAATGAAACGATGAACTAAC 57.395 36.000 0.00 0.00 0.00 2.34
400 518 9.159254 AGTGACATAACATAGATGAATCCCTAA 57.841 33.333 0.00 0.00 0.00 2.69
403 521 7.172190 CACAGTGACATAACATAGATGAATCCC 59.828 40.741 0.00 0.00 0.00 3.85
404 522 7.307632 GCACAGTGACATAACATAGATGAATCC 60.308 40.741 4.15 0.00 0.00 3.01
405 523 7.225341 TGCACAGTGACATAACATAGATGAATC 59.775 37.037 4.15 0.00 0.00 2.52
406 524 7.049754 TGCACAGTGACATAACATAGATGAAT 58.950 34.615 4.15 0.00 0.00 2.57
407 525 6.405538 TGCACAGTGACATAACATAGATGAA 58.594 36.000 4.15 0.00 0.00 2.57
409 527 6.656003 CATGCACAGTGACATAACATAGATG 58.344 40.000 4.15 0.00 0.00 2.90
410 528 5.237996 GCATGCACAGTGACATAACATAGAT 59.762 40.000 14.21 0.00 0.00 1.98
411 529 4.571984 GCATGCACAGTGACATAACATAGA 59.428 41.667 14.21 0.00 0.00 1.98
412 530 4.260907 GGCATGCACAGTGACATAACATAG 60.261 45.833 21.36 0.00 0.00 2.23
413 531 3.627123 GGCATGCACAGTGACATAACATA 59.373 43.478 21.36 0.00 0.00 2.29
414 532 2.424601 GGCATGCACAGTGACATAACAT 59.575 45.455 21.36 0.00 0.00 2.71
415 533 1.811965 GGCATGCACAGTGACATAACA 59.188 47.619 21.36 0.00 0.00 2.41
416 534 2.086869 AGGCATGCACAGTGACATAAC 58.913 47.619 21.36 4.31 0.00 1.89
417 535 2.026915 AGAGGCATGCACAGTGACATAA 60.027 45.455 21.36 0.00 0.00 1.90
418 536 1.556451 AGAGGCATGCACAGTGACATA 59.444 47.619 21.36 0.00 0.00 2.29
419 537 0.327259 AGAGGCATGCACAGTGACAT 59.673 50.000 21.36 4.70 0.00 3.06
420 538 0.109153 AAGAGGCATGCACAGTGACA 59.891 50.000 21.36 2.20 0.00 3.58
421 539 1.242076 AAAGAGGCATGCACAGTGAC 58.758 50.000 21.36 0.00 0.00 3.67
428 550 2.754552 GACCACATAAAAGAGGCATGCA 59.245 45.455 21.36 0.00 0.00 3.96
445 567 4.568804 CCAATGGTTGTAACATAGGGACCA 60.569 45.833 0.00 0.00 40.99 4.02
454 576 5.777223 TGAATCCAATCCAATGGTTGTAACA 59.223 36.000 0.00 0.00 41.46 2.41
455 577 6.099341 GTGAATCCAATCCAATGGTTGTAAC 58.901 40.000 0.00 0.00 41.46 2.50
457 579 5.328565 TGTGAATCCAATCCAATGGTTGTA 58.671 37.500 0.00 0.00 41.46 2.41
459 581 4.804868 TGTGAATCCAATCCAATGGTTG 57.195 40.909 0.00 3.52 41.46 3.77
470 592 5.547465 ACGACTGATAACTTGTGAATCCAA 58.453 37.500 0.00 0.00 0.00 3.53
479 601 6.642950 AGACTCTTGAAACGACTGATAACTTG 59.357 38.462 0.00 0.00 0.00 3.16
480 602 6.750148 AGACTCTTGAAACGACTGATAACTT 58.250 36.000 0.00 0.00 0.00 2.66
486 608 4.920640 AGAAGACTCTTGAAACGACTGA 57.079 40.909 0.00 0.00 0.00 3.41
489 611 8.967552 TCTAAATAGAAGACTCTTGAAACGAC 57.032 34.615 0.00 0.00 32.70 4.34
490 612 9.408069 GTTCTAAATAGAAGACTCTTGAAACGA 57.592 33.333 3.17 0.00 42.48 3.85
491 613 8.648968 GGTTCTAAATAGAAGACTCTTGAAACG 58.351 37.037 3.17 0.00 42.48 3.60
492 614 9.490379 TGGTTCTAAATAGAAGACTCTTGAAAC 57.510 33.333 3.17 0.00 42.48 2.78
550 672 6.531948 ACGATAACTGAAGAAGCAGAATACAC 59.468 38.462 0.00 0.00 39.20 2.90
553 675 7.320399 TCAACGATAACTGAAGAAGCAGAATA 58.680 34.615 0.00 0.00 39.20 1.75
554 676 6.166279 TCAACGATAACTGAAGAAGCAGAAT 58.834 36.000 0.00 0.00 39.20 2.40
557 679 5.845985 TTCAACGATAACTGAAGAAGCAG 57.154 39.130 0.00 0.00 41.63 4.24
568 690 4.946784 ACTGCCAATCTTCAACGATAAC 57.053 40.909 0.00 0.00 0.00 1.89
574 696 4.082571 AGCAATGTACTGCCAATCTTCAAC 60.083 41.667 3.63 0.00 43.73 3.18
575 697 4.081406 AGCAATGTACTGCCAATCTTCAA 58.919 39.130 3.63 0.00 43.73 2.69
581 703 4.039004 TGTGAAAAGCAATGTACTGCCAAT 59.961 37.500 3.63 0.00 43.73 3.16
586 708 4.919168 CCATGTGTGAAAAGCAATGTACTG 59.081 41.667 0.00 0.00 0.00 2.74
600 722 4.262592 CGATATCCCATCTTCCATGTGTGA 60.263 45.833 0.00 0.00 0.00 3.58
601 723 3.999001 CGATATCCCATCTTCCATGTGTG 59.001 47.826 0.00 0.00 0.00 3.82
616 738 6.283694 TGAGCATCTAATTATGGCGATATCC 58.716 40.000 0.00 0.00 34.92 2.59
617 739 7.959689 ATGAGCATCTAATTATGGCGATATC 57.040 36.000 0.00 0.00 34.92 1.63
626 748 9.289782 GGGTTGTAGAAATGAGCATCTAATTAT 57.710 33.333 0.00 0.00 34.92 1.28
637 759 3.557595 GCTCATCGGGTTGTAGAAATGAG 59.442 47.826 7.37 7.37 41.80 2.90
639 761 3.270027 TGCTCATCGGGTTGTAGAAATG 58.730 45.455 0.00 0.00 0.00 2.32
659 781 4.514577 CACGTAGCTCCGCCCCTG 62.515 72.222 0.00 0.00 0.00 4.45
660 782 4.753662 TCACGTAGCTCCGCCCCT 62.754 66.667 0.00 0.00 0.00 4.79
661 783 4.208686 CTCACGTAGCTCCGCCCC 62.209 72.222 0.00 0.00 0.00 5.80
662 784 4.208686 CCTCACGTAGCTCCGCCC 62.209 72.222 0.00 0.00 0.00 6.13
664 786 2.202623 CACCTCACGTAGCTCCGC 60.203 66.667 0.00 0.00 0.00 5.54
665 787 2.202623 GCACCTCACGTAGCTCCG 60.203 66.667 0.00 0.00 0.00 4.63
666 788 1.139947 GAGCACCTCACGTAGCTCC 59.860 63.158 12.33 0.00 45.79 4.70
667 789 4.796225 GAGCACCTCACGTAGCTC 57.204 61.111 0.00 9.33 45.50 4.09
668 790 2.701780 CGGAGCACCTCACGTAGCT 61.702 63.158 0.00 0.00 40.60 3.32
669 791 2.202623 CGGAGCACCTCACGTAGC 60.203 66.667 0.00 0.00 31.08 3.58
694 816 3.793144 GAAACTCCTGCCGCGCTG 61.793 66.667 5.56 0.00 0.00 5.18
695 817 3.537206 AAGAAACTCCTGCCGCGCT 62.537 57.895 5.56 0.00 0.00 5.92
696 818 3.028366 GAAGAAACTCCTGCCGCGC 62.028 63.158 0.00 0.00 0.00 6.86
697 819 1.021390 ATGAAGAAACTCCTGCCGCG 61.021 55.000 0.00 0.00 0.00 6.46
698 820 1.135575 CAATGAAGAAACTCCTGCCGC 60.136 52.381 0.00 0.00 0.00 6.53
699 821 1.135575 GCAATGAAGAAACTCCTGCCG 60.136 52.381 0.00 0.00 0.00 5.69
700 822 1.888512 TGCAATGAAGAAACTCCTGCC 59.111 47.619 0.00 0.00 0.00 4.85
701 823 2.294233 TGTGCAATGAAGAAACTCCTGC 59.706 45.455 0.00 0.00 0.00 4.85
702 824 3.567164 AGTGTGCAATGAAGAAACTCCTG 59.433 43.478 0.00 0.00 0.00 3.86
703 825 3.825328 AGTGTGCAATGAAGAAACTCCT 58.175 40.909 0.00 0.00 0.00 3.69
704 826 4.574599 AAGTGTGCAATGAAGAAACTCC 57.425 40.909 0.00 0.00 0.00 3.85
705 827 6.305693 ACTAAGTGTGCAATGAAGAAACTC 57.694 37.500 0.00 0.00 0.00 3.01
706 828 6.699575 AACTAAGTGTGCAATGAAGAAACT 57.300 33.333 0.00 0.00 0.00 2.66
707 829 6.751888 ACAAACTAAGTGTGCAATGAAGAAAC 59.248 34.615 0.00 0.00 0.00 2.78
708 830 6.751425 CACAAACTAAGTGTGCAATGAAGAAA 59.249 34.615 0.00 0.00 39.93 2.52
709 831 6.264832 CACAAACTAAGTGTGCAATGAAGAA 58.735 36.000 0.00 0.00 39.93 2.52
710 832 5.820131 CACAAACTAAGTGTGCAATGAAGA 58.180 37.500 0.00 0.00 39.93 2.87
720 842 4.451096 CGTTCCATAGCACAAACTAAGTGT 59.549 41.667 0.00 0.00 39.17 3.55
721 843 4.142902 CCGTTCCATAGCACAAACTAAGTG 60.143 45.833 0.00 0.00 39.92 3.16
722 844 4.000988 CCGTTCCATAGCACAAACTAAGT 58.999 43.478 0.00 0.00 0.00 2.24
723 845 3.181510 GCCGTTCCATAGCACAAACTAAG 60.182 47.826 0.00 0.00 0.00 2.18
724 846 2.745281 GCCGTTCCATAGCACAAACTAA 59.255 45.455 0.00 0.00 0.00 2.24
725 847 2.289756 TGCCGTTCCATAGCACAAACTA 60.290 45.455 0.00 0.00 0.00 2.24
726 848 1.165270 GCCGTTCCATAGCACAAACT 58.835 50.000 0.00 0.00 0.00 2.66
727 849 0.878416 TGCCGTTCCATAGCACAAAC 59.122 50.000 0.00 0.00 0.00 2.93
728 850 1.610363 TTGCCGTTCCATAGCACAAA 58.390 45.000 0.00 0.00 35.96 2.83
729 851 1.742831 GATTGCCGTTCCATAGCACAA 59.257 47.619 0.00 0.00 35.96 3.33
730 852 1.339535 TGATTGCCGTTCCATAGCACA 60.340 47.619 0.00 0.00 35.96 4.57
731 853 1.378531 TGATTGCCGTTCCATAGCAC 58.621 50.000 0.00 0.00 35.96 4.40
732 854 2.121291 TTGATTGCCGTTCCATAGCA 57.879 45.000 0.00 0.00 33.97 3.49
733 855 2.682856 TCTTTGATTGCCGTTCCATAGC 59.317 45.455 0.00 0.00 0.00 2.97
734 856 3.941483 ACTCTTTGATTGCCGTTCCATAG 59.059 43.478 0.00 0.00 0.00 2.23
735 857 3.950397 ACTCTTTGATTGCCGTTCCATA 58.050 40.909 0.00 0.00 0.00 2.74
736 858 2.795329 ACTCTTTGATTGCCGTTCCAT 58.205 42.857 0.00 0.00 0.00 3.41
737 859 2.270352 ACTCTTTGATTGCCGTTCCA 57.730 45.000 0.00 0.00 0.00 3.53
738 860 4.636206 AGATTACTCTTTGATTGCCGTTCC 59.364 41.667 0.00 0.00 0.00 3.62
739 861 5.801012 GAGATTACTCTTTGATTGCCGTTC 58.199 41.667 0.00 0.00 39.78 3.95
740 862 5.803020 GAGATTACTCTTTGATTGCCGTT 57.197 39.130 0.00 0.00 39.78 4.44
758 880 3.957497 CGGGCTGGCTAATCTATAGAGAT 59.043 47.826 8.70 0.00 44.79 2.75
759 881 3.357203 CGGGCTGGCTAATCTATAGAGA 58.643 50.000 8.70 0.00 35.71 3.10
760 882 2.428890 CCGGGCTGGCTAATCTATAGAG 59.571 54.545 8.70 0.00 0.00 2.43
761 883 2.457598 CCGGGCTGGCTAATCTATAGA 58.542 52.381 4.57 4.57 0.00 1.98
762 884 2.969628 CCGGGCTGGCTAATCTATAG 57.030 55.000 0.00 0.00 0.00 1.31
778 900 4.994756 AAAGGTTGGGCTGGCCGG 62.995 66.667 16.08 7.41 36.85 6.13
779 901 2.917227 AAAAGGTTGGGCTGGCCG 60.917 61.111 16.08 0.00 36.85 6.13
780 902 2.743060 CAAAAGGTTGGGCTGGCC 59.257 61.111 14.23 14.23 0.00 5.36
781 903 2.031012 GCAAAAGGTTGGGCTGGC 59.969 61.111 0.00 0.00 35.10 4.85
782 904 0.033920 GAAGCAAAAGGTTGGGCTGG 59.966 55.000 0.00 0.00 36.58 4.85
783 905 0.752054 TGAAGCAAAAGGTTGGGCTG 59.248 50.000 0.00 0.00 36.58 4.85
784 906 1.413812 CTTGAAGCAAAAGGTTGGGCT 59.586 47.619 0.00 0.00 38.45 5.19
785 907 1.869774 CTTGAAGCAAAAGGTTGGGC 58.130 50.000 0.00 0.00 35.10 5.36
786 908 1.413812 AGCTTGAAGCAAAAGGTTGGG 59.586 47.619 20.45 0.00 45.56 4.12
787 909 2.546584 GGAGCTTGAAGCAAAAGGTTGG 60.547 50.000 20.45 0.00 45.56 3.77
788 910 2.747436 GGAGCTTGAAGCAAAAGGTTG 58.253 47.619 20.45 0.00 45.56 3.77
789 911 1.338020 CGGAGCTTGAAGCAAAAGGTT 59.662 47.619 20.45 0.00 45.56 3.50
790 912 0.954452 CGGAGCTTGAAGCAAAAGGT 59.046 50.000 20.45 0.00 45.56 3.50
791 913 3.780925 CGGAGCTTGAAGCAAAAGG 57.219 52.632 20.45 0.00 45.56 3.11
809 931 3.503363 GCACTCATCGGCAGTGGC 61.503 66.667 6.62 6.62 41.49 5.01
810 932 1.028330 AATGCACTCATCGGCAGTGG 61.028 55.000 10.18 0.00 44.24 4.00
811 933 0.806868 AAATGCACTCATCGGCAGTG 59.193 50.000 0.00 5.29 44.24 3.66
812 934 1.200716 CAAAATGCACTCATCGGCAGT 59.799 47.619 0.00 0.00 44.24 4.40
813 935 1.200716 ACAAAATGCACTCATCGGCAG 59.799 47.619 0.00 0.00 44.24 4.85
814 936 1.246649 ACAAAATGCACTCATCGGCA 58.753 45.000 0.00 0.00 45.23 5.69
815 937 2.352503 AACAAAATGCACTCATCGGC 57.647 45.000 0.00 0.00 31.27 5.54
816 938 4.154015 TCAGTAACAAAATGCACTCATCGG 59.846 41.667 0.00 0.00 31.27 4.18
817 939 5.281693 TCAGTAACAAAATGCACTCATCG 57.718 39.130 0.00 0.00 31.27 3.84
818 940 6.529125 CCAATCAGTAACAAAATGCACTCATC 59.471 38.462 0.00 0.00 31.27 2.92
819 941 6.015180 ACCAATCAGTAACAAAATGCACTCAT 60.015 34.615 0.00 0.00 33.53 2.90
820 942 5.301551 ACCAATCAGTAACAAAATGCACTCA 59.698 36.000 0.00 0.00 0.00 3.41
821 943 5.772521 ACCAATCAGTAACAAAATGCACTC 58.227 37.500 0.00 0.00 0.00 3.51
822 944 5.536161 AGACCAATCAGTAACAAAATGCACT 59.464 36.000 0.00 0.00 0.00 4.40
823 945 5.772521 AGACCAATCAGTAACAAAATGCAC 58.227 37.500 0.00 0.00 0.00 4.57
824 946 6.403866 AAGACCAATCAGTAACAAAATGCA 57.596 33.333 0.00 0.00 0.00 3.96
831 953 9.613428 CCAGATTTATAAGACCAATCAGTAACA 57.387 33.333 0.00 0.00 30.51 2.41
832 954 8.560374 GCCAGATTTATAAGACCAATCAGTAAC 58.440 37.037 0.00 0.00 30.51 2.50
833 955 7.719633 GGCCAGATTTATAAGACCAATCAGTAA 59.280 37.037 0.00 0.00 30.51 2.24
834 956 7.224297 GGCCAGATTTATAAGACCAATCAGTA 58.776 38.462 0.00 0.00 30.51 2.74
835 957 6.064717 GGCCAGATTTATAAGACCAATCAGT 58.935 40.000 0.00 0.00 30.51 3.41
836 958 5.180117 CGGCCAGATTTATAAGACCAATCAG 59.820 44.000 2.24 0.00 30.51 2.90
837 959 5.063204 CGGCCAGATTTATAAGACCAATCA 58.937 41.667 2.24 0.00 30.51 2.57
838 960 5.063880 ACGGCCAGATTTATAAGACCAATC 58.936 41.667 2.24 0.00 0.00 2.67
839 961 5.048846 ACGGCCAGATTTATAAGACCAAT 57.951 39.130 2.24 0.00 0.00 3.16
840 962 4.497291 ACGGCCAGATTTATAAGACCAA 57.503 40.909 2.24 0.00 0.00 3.67
843 965 7.571428 GCTTATGAACGGCCAGATTTATAAGAC 60.571 40.741 25.09 17.54 31.74 3.01
849 971 4.150897 AGCTTATGAACGGCCAGATTTA 57.849 40.909 2.24 0.00 0.00 1.40
855 977 4.215399 GCATTATAAGCTTATGAACGGCCA 59.785 41.667 25.99 3.42 0.00 5.36
936 1236 6.770785 AGCATAAGGAAGTTGTGTAAAGAACA 59.229 34.615 0.00 0.00 35.06 3.18
941 1241 6.296026 AGTCAGCATAAGGAAGTTGTGTAAA 58.704 36.000 0.00 0.00 30.10 2.01
964 1264 0.979665 TGCCAAGAGAAGGACTGGAG 59.020 55.000 0.00 0.00 0.00 3.86
972 1272 2.827800 TCTGACAGTGCCAAGAGAAG 57.172 50.000 1.59 0.00 0.00 2.85
984 1284 1.735386 CCATGGCTCACTTCTGACAG 58.265 55.000 0.00 0.00 0.00 3.51
1049 1349 1.542767 GGGCGATTTTAGTAGGGCTCC 60.543 57.143 0.00 0.00 0.00 4.70
1067 1367 1.415659 TGAAGGCAAACATTGTTGGGG 59.584 47.619 2.13 0.00 0.00 4.96
1161 1461 1.692411 AGTTCCCAGCAACACTTTCC 58.308 50.000 0.00 0.00 0.00 3.13
1210 1510 9.345517 CCAACAAGATGATACATACAACAAAAG 57.654 33.333 0.00 0.00 0.00 2.27
1271 1572 7.472334 AAACATGGCAAAAGAATCTGTCTAT 57.528 32.000 0.00 0.00 34.56 1.98
1686 1997 8.457261 CCCAGAAGAGAAAAATATCAAGTCAAG 58.543 37.037 0.00 0.00 0.00 3.02
1717 2251 5.698104 TGGATATCAATCATTCCAGCAAGT 58.302 37.500 4.83 0.00 33.40 3.16
1718 2252 6.350194 CCATGGATATCAATCATTCCAGCAAG 60.350 42.308 5.56 0.00 41.33 4.01
1788 2525 4.232221 CAGCAACATTGATCAGTTCCAAC 58.768 43.478 0.00 0.00 0.00 3.77
1790 2527 2.229543 GCAGCAACATTGATCAGTTCCA 59.770 45.455 0.00 0.00 0.00 3.53
1791 2528 2.490903 AGCAGCAACATTGATCAGTTCC 59.509 45.455 0.00 0.00 0.00 3.62
1792 2529 3.189910 TGAGCAGCAACATTGATCAGTTC 59.810 43.478 0.00 0.00 36.18 3.01
1793 2530 3.151554 TGAGCAGCAACATTGATCAGTT 58.848 40.909 0.00 0.00 36.18 3.16
1794 2531 2.786777 TGAGCAGCAACATTGATCAGT 58.213 42.857 0.00 0.00 36.18 3.41
1795 2532 3.759418 CTTGAGCAGCAACATTGATCAG 58.241 45.455 0.00 0.00 41.39 2.90
1796 2533 3.842732 CTTGAGCAGCAACATTGATCA 57.157 42.857 0.00 0.00 39.01 2.92
1831 2568 7.778083 TGCAGAATCTTGAAGCAATTCATAAT 58.222 30.769 8.68 0.00 32.92 1.28
1838 2575 4.440250 GCAGATGCAGAATCTTGAAGCAAT 60.440 41.667 0.00 0.00 43.52 3.56
2112 2857 3.489785 AGAACTGTCATGAACGTTTCGAC 59.510 43.478 0.46 10.21 0.00 4.20


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

AutoCloner maintained by Alex Coulton.