Multiple sequence alignment - TraesCS5B01G242900

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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 TraesCS5B01G242900 chr5B 100.000 1869 0 0 2178 4046 422939851 422941719 0.000000e+00 3452
1 TraesCS5B01G242900 chr5B 100.000 1714 0 0 1 1714 422937674 422939387 0.000000e+00 3166
2 TraesCS5B01G242900 chr5B 90.210 143 13 1 2223 2365 422939851 422939992 6.910000e-43 185
3 TraesCS5B01G242900 chr5B 90.210 143 13 1 2178 2319 422939896 422940038 6.910000e-43 185
4 TraesCS5B01G242900 chr5B 85.143 175 26 0 1540 1714 422939168 422939342 3.210000e-41 180
5 TraesCS5B01G242900 chr5B 85.143 175 26 0 1495 1669 422939213 422939387 3.210000e-41 180
6 TraesCS5B01G242900 chr5B 78.088 251 47 6 442 688 299912189 299912435 7.000000e-33 152
7 TraesCS5B01G242900 chr5B 78.243 239 48 4 448 683 391158691 391158928 2.520000e-32 150
8 TraesCS5B01G242900 chr5D 94.007 1919 52 19 2178 4039 357898472 357900384 0.000000e+00 2848
9 TraesCS5B01G242900 chr5D 95.464 948 31 6 778 1714 357897524 357898470 0.000000e+00 1502
10 TraesCS5B01G242900 chr5D 84.867 641 74 17 21 653 357896858 357897483 3.430000e-175 625
11 TraesCS5B01G242900 chr5D 87.500 184 22 1 2182 2365 357898431 357898613 1.140000e-50 211
12 TraesCS5B01G242900 chr5D 83.410 217 36 0 1495 1711 357898296 357898512 6.860000e-48 202
13 TraesCS5B01G242900 chr5D 86.857 175 23 0 1540 1714 357898251 357898425 3.190000e-46 196
14 TraesCS5B01G242900 chr5D 79.545 264 49 5 448 707 533002794 533003056 2.480000e-42 183
15 TraesCS5B01G242900 chr5A 93.438 1920 50 19 2178 4039 458909606 458911507 0.000000e+00 2778
16 TraesCS5B01G242900 chr5A 93.692 967 34 10 773 1714 458908640 458909604 0.000000e+00 1423
17 TraesCS5B01G242900 chr5A 83.410 217 36 0 1495 1711 458909430 458909646 6.860000e-48 202
18 TraesCS5B01G242900 chr5A 85.143 175 26 0 1540 1714 458909385 458909559 3.210000e-41 180
19 TraesCS5B01G242900 chr5A 91.304 115 9 1 2206 2319 458909667 458909781 5.410000e-34 156
20 TraesCS5B01G242900 chr3A 81.550 271 43 6 448 715 552303227 552303493 2.450000e-52 217
21 TraesCS5B01G242900 chr2D 81.933 238 34 8 441 673 565153440 565153673 4.130000e-45 193
22 TraesCS5B01G242900 chr2D 79.630 270 48 6 450 715 306315781 306316047 1.920000e-43 187
23 TraesCS5B01G242900 chr2D 78.512 242 41 10 448 683 74135679 74135915 9.060000e-32 148
24 TraesCS5B01G242900 chr1D 80.176 227 40 5 461 683 489752093 489752318 9.000000e-37 165
25 TraesCS5B01G242900 chr7A 78.776 245 46 4 448 688 501033617 501033375 4.190000e-35 159


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 TraesCS5B01G242900 chr5B 422937674 422941719 4045 False 1224.666667 3452 91.784333 1 4046 6 chr5B.!!$F3 4045
1 TraesCS5B01G242900 chr5D 357896858 357900384 3526 False 930.666667 2848 88.684167 21 4039 6 chr5D.!!$F2 4018
2 TraesCS5B01G242900 chr5A 458908640 458911507 2867 False 947.800000 2778 89.397400 773 4039 5 chr5A.!!$F1 3266

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
697 704 0.029300 GTGTGCATGCAAGTGTTCGT 59.971 50.000 24.58 0.0 0.0 3.85 F
700 707 0.030504 TGCATGCAAGTGTTCGTTGG 59.969 50.000 20.30 0.0 0.0 3.77 F
702 709 0.039256 CATGCAAGTGTTCGTTGGGG 60.039 55.000 0.00 0.0 0.0 4.96 F
847 854 0.247460 GTCCAAGGCCCATGAAAAGC 59.753 55.000 0.00 0.0 0.0 3.51 F
2249 2283 1.071471 CTCCACAGCCAAGTCCGTT 59.929 57.895 0.00 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2601 2635 0.403271 GATCCACATAGCCAGGGCAT 59.597 55.000 13.63 1.37 44.88 4.40 R
2613 2647 1.991813 TGGGAATTGACCAGATCCACA 59.008 47.619 0.00 0.00 33.48 4.17 R
2801 2835 2.281484 GTTCTGGCGCAGGTTCCA 60.281 61.111 10.83 0.00 31.51 3.53 R
2851 2885 1.750399 GCATCACAGGTTCCGGCAT 60.750 57.895 0.00 0.00 0.00 4.40 R
3357 3391 1.492176 GAGCAATCCCCAGGAATCTCA 59.508 52.381 0.00 0.00 34.34 3.27 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
29 30 3.374220 TGTACCTTGAGTAACACCACG 57.626 47.619 0.00 0.00 31.05 4.94
31 32 2.234300 ACCTTGAGTAACACCACGTG 57.766 50.000 9.08 9.08 39.75 4.49
52 53 5.064962 CGTGGTACAAACAGTAAAGTGGAAA 59.935 40.000 0.00 0.00 44.16 3.13
55 56 4.649088 ACAAACAGTAAAGTGGAAAGGC 57.351 40.909 0.00 0.00 0.00 4.35
56 57 3.383505 ACAAACAGTAAAGTGGAAAGGCC 59.616 43.478 0.00 0.00 37.10 5.19
72 73 3.454573 CCGCGTACCTACCTGGCA 61.455 66.667 4.92 0.00 40.22 4.92
75 76 2.652095 GCGTACCTACCTGGCACCA 61.652 63.158 0.00 0.00 40.22 4.17
80 81 2.579201 CTACCTGGCACCACGGAG 59.421 66.667 10.87 0.00 0.00 4.63
97 98 0.176680 GAGATTCCTCTCAAGCGGCA 59.823 55.000 1.45 0.00 46.13 5.69
98 99 0.835941 AGATTCCTCTCAAGCGGCAT 59.164 50.000 1.45 0.00 0.00 4.40
99 100 1.211457 AGATTCCTCTCAAGCGGCATT 59.789 47.619 1.45 0.00 0.00 3.56
100 101 1.601430 GATTCCTCTCAAGCGGCATTC 59.399 52.381 1.45 0.00 0.00 2.67
107 108 1.517694 CAAGCGGCATTCCATGTGC 60.518 57.895 1.45 0.00 41.78 4.57
134 135 5.129980 GCCCCAACCAGTAGTAAGTTACTAT 59.870 44.000 22.45 11.12 42.68 2.12
139 140 7.924947 CCAACCAGTAGTAAGTTACTATTAGGC 59.075 40.741 22.45 11.44 42.68 3.93
142 143 8.057623 ACCAGTAGTAAGTTACTATTAGGCTGA 58.942 37.037 25.08 5.96 42.68 4.26
161 163 4.326548 GCTGAAGTACGGTTAGTTCACATC 59.673 45.833 0.46 0.00 41.04 3.06
167 169 6.666417 AGTACGGTTAGTTCACATCGATATC 58.334 40.000 0.00 0.00 0.00 1.63
168 170 5.509716 ACGGTTAGTTCACATCGATATCA 57.490 39.130 0.00 0.00 0.00 2.15
201 203 7.101652 TGTAGTTGGAAGCACAAATTTTGTA 57.898 32.000 14.13 0.00 43.23 2.41
205 207 6.925165 AGTTGGAAGCACAAATTTTGTATGAG 59.075 34.615 14.13 4.03 43.23 2.90
206 208 6.647334 TGGAAGCACAAATTTTGTATGAGA 57.353 33.333 14.13 0.00 43.23 3.27
213 215 9.382275 AGCACAAATTTTGTATGAGAAAAGTTT 57.618 25.926 14.13 0.00 43.23 2.66
214 216 9.424659 GCACAAATTTTGTATGAGAAAAGTTTG 57.575 29.630 14.13 11.94 43.23 2.93
279 281 9.340695 TGATGCAAGAAATACAACGATAAAAAG 57.659 29.630 0.00 0.00 0.00 2.27
301 303 5.243207 AGGGTTTGTAATTTAGACTCACGG 58.757 41.667 0.00 0.00 0.00 4.94
350 353 7.823745 AACAAATCCAGAAAAGAGTACACAT 57.176 32.000 0.00 0.00 0.00 3.21
351 354 8.918202 AACAAATCCAGAAAAGAGTACACATA 57.082 30.769 0.00 0.00 0.00 2.29
352 355 8.324163 ACAAATCCAGAAAAGAGTACACATAC 57.676 34.615 0.00 0.00 0.00 2.39
353 356 8.157476 ACAAATCCAGAAAAGAGTACACATACT 58.843 33.333 0.00 0.00 44.74 2.12
390 394 3.111853 TGCGTGAATGTGAAACTCTCT 57.888 42.857 0.00 0.00 38.04 3.10
399 404 2.037121 TGTGAAACTCTCTGATGCCGAA 59.963 45.455 0.00 0.00 38.04 4.30
429 434 2.498481 CCCATGTGCTCCATCATTTGTT 59.502 45.455 0.00 0.00 0.00 2.83
434 439 6.406065 CCATGTGCTCCATCATTTGTTATCAA 60.406 38.462 0.00 0.00 0.00 2.57
457 462 9.311916 TCAACAAAGAATTTATGAACCAACTTG 57.688 29.630 0.00 0.00 35.03 3.16
458 463 9.097257 CAACAAAGAATTTATGAACCAACTTGT 57.903 29.630 0.00 0.00 35.03 3.16
459 464 9.665719 AACAAAGAATTTATGAACCAACTTGTT 57.334 25.926 0.00 0.00 35.03 2.83
460 465 9.097257 ACAAAGAATTTATGAACCAACTTGTTG 57.903 29.630 6.52 6.52 35.03 3.33
461 466 9.097257 CAAAGAATTTATGAACCAACTTGTTGT 57.903 29.630 11.82 0.00 35.03 3.32
462 467 9.665719 AAAGAATTTATGAACCAACTTGTTGTT 57.334 25.926 11.82 6.82 35.86 2.83
483 488 2.225522 TGGATGGTTAGGAGGACAGTGA 60.226 50.000 0.00 0.00 0.00 3.41
495 500 4.892934 GGAGGACAGTGATATCTTCAGTCT 59.107 45.833 16.52 5.47 35.76 3.24
501 506 7.446931 GGACAGTGATATCTTCAGTCTATCAGA 59.553 40.741 16.52 0.00 35.76 3.27
511 516 6.945435 TCTTCAGTCTATCAGAGTTCAAGTCT 59.055 38.462 0.00 0.00 0.00 3.24
514 519 8.637196 TCAGTCTATCAGAGTTCAAGTCTTAA 57.363 34.615 0.00 0.00 0.00 1.85
534 539 0.534877 ACTTGACAATGGTGCTCGCA 60.535 50.000 0.00 0.00 0.00 5.10
562 567 8.696410 TTTTTGGATTTATTTCATACTTCGGC 57.304 30.769 0.00 0.00 0.00 5.54
564 569 5.361427 TGGATTTATTTCATACTTCGGCGA 58.639 37.500 4.99 4.99 0.00 5.54
565 570 5.235616 TGGATTTATTTCATACTTCGGCGAC 59.764 40.000 10.16 0.00 0.00 5.19
578 585 3.028019 GCGACGTGCGTTCAGTGA 61.028 61.111 0.00 0.00 43.41 3.41
580 587 1.370051 CGACGTGCGTTCAGTGAGA 60.370 57.895 0.00 0.00 34.64 3.27
585 592 1.423395 GTGCGTTCAGTGAGAGAAGG 58.577 55.000 0.00 0.00 34.84 3.46
587 594 3.894257 CGTTCAGTGAGAGAAGGCA 57.106 52.632 0.00 0.00 0.00 4.75
595 602 0.537188 TGAGAGAAGGCATTCCCGTC 59.463 55.000 7.63 2.90 41.81 4.79
625 632 2.094659 CGTCTGCGGCGACTTCATT 61.095 57.895 12.98 0.00 0.00 2.57
629 636 2.033662 GTCTGCGGCGACTTCATTAATC 60.034 50.000 12.98 0.00 0.00 1.75
634 641 3.302740 GCGGCGACTTCATTAATCTCAAG 60.303 47.826 12.98 0.00 0.00 3.02
637 644 5.332883 CGGCGACTTCATTAATCTCAAGATG 60.333 44.000 0.00 0.00 34.49 2.90
642 649 9.468532 CGACTTCATTAATCTCAAGATGATGTA 57.531 33.333 12.59 6.32 37.16 2.29
645 652 9.551734 CTTCATTAATCTCAAGATGATGTACCA 57.448 33.333 12.59 0.00 34.49 3.25
653 660 4.118410 CAAGATGATGTACCAGCTCAGTC 58.882 47.826 0.00 0.00 30.67 3.51
655 662 3.636300 AGATGATGTACCAGCTCAGTCTC 59.364 47.826 0.00 0.00 0.00 3.36
656 663 3.093057 TGATGTACCAGCTCAGTCTCT 57.907 47.619 0.00 0.00 0.00 3.10
657 664 4.236527 TGATGTACCAGCTCAGTCTCTA 57.763 45.455 0.00 0.00 0.00 2.43
658 665 4.600062 TGATGTACCAGCTCAGTCTCTAA 58.400 43.478 0.00 0.00 0.00 2.10
659 666 4.642437 TGATGTACCAGCTCAGTCTCTAAG 59.358 45.833 0.00 0.00 0.00 2.18
662 669 3.730215 ACCAGCTCAGTCTCTAAGAGA 57.270 47.619 0.00 0.00 36.22 3.10
663 670 4.249638 ACCAGCTCAGTCTCTAAGAGAT 57.750 45.455 0.00 0.00 40.98 2.75
664 671 3.953612 ACCAGCTCAGTCTCTAAGAGATG 59.046 47.826 0.00 0.00 43.37 2.90
665 672 3.243501 CCAGCTCAGTCTCTAAGAGATGC 60.244 52.174 0.00 0.00 42.65 3.91
666 673 3.633525 CAGCTCAGTCTCTAAGAGATGCT 59.366 47.826 0.00 0.00 40.98 3.79
667 674 4.098349 CAGCTCAGTCTCTAAGAGATGCTT 59.902 45.833 0.00 0.00 40.98 3.91
668 675 5.299028 CAGCTCAGTCTCTAAGAGATGCTTA 59.701 44.000 0.00 0.00 40.98 3.09
669 676 6.016024 CAGCTCAGTCTCTAAGAGATGCTTAT 60.016 42.308 0.00 0.00 40.98 1.73
670 677 7.174772 CAGCTCAGTCTCTAAGAGATGCTTATA 59.825 40.741 0.00 0.00 40.98 0.98
671 678 7.391554 AGCTCAGTCTCTAAGAGATGCTTATAG 59.608 40.741 0.00 0.00 40.98 1.31
672 679 7.362056 GCTCAGTCTCTAAGAGATGCTTATAGG 60.362 44.444 0.00 0.00 40.98 2.57
673 680 6.945435 TCAGTCTCTAAGAGATGCTTATAGGG 59.055 42.308 0.00 0.00 40.98 3.53
674 681 6.719370 CAGTCTCTAAGAGATGCTTATAGGGT 59.281 42.308 0.00 0.00 40.98 4.34
675 682 7.885922 CAGTCTCTAAGAGATGCTTATAGGGTA 59.114 40.741 0.00 0.00 40.98 3.69
676 683 8.107095 AGTCTCTAAGAGATGCTTATAGGGTAG 58.893 40.741 0.00 0.00 40.98 3.18
677 684 8.104566 GTCTCTAAGAGATGCTTATAGGGTAGA 58.895 40.741 0.00 0.00 40.98 2.59
678 685 8.325787 TCTCTAAGAGATGCTTATAGGGTAGAG 58.674 40.741 0.00 0.00 38.36 2.43
679 686 7.991174 TCTAAGAGATGCTTATAGGGTAGAGT 58.009 38.462 0.00 0.00 38.36 3.24
680 687 6.909550 AAGAGATGCTTATAGGGTAGAGTG 57.090 41.667 0.00 0.00 34.31 3.51
681 688 5.959512 AGAGATGCTTATAGGGTAGAGTGT 58.040 41.667 0.00 0.00 0.00 3.55
682 689 5.772672 AGAGATGCTTATAGGGTAGAGTGTG 59.227 44.000 0.00 0.00 0.00 3.82
683 690 4.282195 AGATGCTTATAGGGTAGAGTGTGC 59.718 45.833 0.00 0.00 0.00 4.57
684 691 3.371034 TGCTTATAGGGTAGAGTGTGCA 58.629 45.455 0.00 0.00 0.00 4.57
685 692 3.967326 TGCTTATAGGGTAGAGTGTGCAT 59.033 43.478 0.00 0.00 0.00 3.96
686 693 4.202253 TGCTTATAGGGTAGAGTGTGCATG 60.202 45.833 0.00 0.00 0.00 4.06
687 694 2.918712 ATAGGGTAGAGTGTGCATGC 57.081 50.000 11.82 11.82 0.00 4.06
688 695 1.567357 TAGGGTAGAGTGTGCATGCA 58.433 50.000 18.46 18.46 0.00 3.96
689 696 0.692476 AGGGTAGAGTGTGCATGCAA 59.308 50.000 24.58 10.26 0.00 4.08
690 697 1.089920 GGGTAGAGTGTGCATGCAAG 58.910 55.000 24.58 0.00 0.00 4.01
691 698 1.611673 GGGTAGAGTGTGCATGCAAGT 60.612 52.381 24.58 15.27 0.00 3.16
692 699 1.466167 GGTAGAGTGTGCATGCAAGTG 59.534 52.381 24.58 0.00 0.00 3.16
693 700 2.146342 GTAGAGTGTGCATGCAAGTGT 58.854 47.619 24.58 15.63 0.00 3.55
694 701 1.683943 AGAGTGTGCATGCAAGTGTT 58.316 45.000 24.58 6.55 0.00 3.32
695 702 1.605710 AGAGTGTGCATGCAAGTGTTC 59.394 47.619 24.58 15.22 0.00 3.18
696 703 0.308684 AGTGTGCATGCAAGTGTTCG 59.691 50.000 24.58 0.00 0.00 3.95
697 704 0.029300 GTGTGCATGCAAGTGTTCGT 59.971 50.000 24.58 0.00 0.00 3.85
698 705 0.737804 TGTGCATGCAAGTGTTCGTT 59.262 45.000 24.58 0.00 0.00 3.85
699 706 1.122849 GTGCATGCAAGTGTTCGTTG 58.877 50.000 24.58 0.00 0.00 4.10
700 707 0.030504 TGCATGCAAGTGTTCGTTGG 59.969 50.000 20.30 0.00 0.00 3.77
701 708 0.664166 GCATGCAAGTGTTCGTTGGG 60.664 55.000 14.21 0.00 0.00 4.12
702 709 0.039256 CATGCAAGTGTTCGTTGGGG 60.039 55.000 0.00 0.00 0.00 4.96
703 710 1.178534 ATGCAAGTGTTCGTTGGGGG 61.179 55.000 0.00 0.00 0.00 5.40
704 711 1.826487 GCAAGTGTTCGTTGGGGGT 60.826 57.895 0.00 0.00 0.00 4.95
705 712 2.029743 CAAGTGTTCGTTGGGGGTG 58.970 57.895 0.00 0.00 0.00 4.61
706 713 0.464735 CAAGTGTTCGTTGGGGGTGA 60.465 55.000 0.00 0.00 0.00 4.02
707 714 0.256464 AAGTGTTCGTTGGGGGTGAA 59.744 50.000 0.00 0.00 0.00 3.18
708 715 0.256464 AGTGTTCGTTGGGGGTGAAA 59.744 50.000 0.00 0.00 0.00 2.69
709 716 0.666374 GTGTTCGTTGGGGGTGAAAG 59.334 55.000 0.00 0.00 0.00 2.62
710 717 0.256464 TGTTCGTTGGGGGTGAAAGT 59.744 50.000 0.00 0.00 0.00 2.66
711 718 1.489649 TGTTCGTTGGGGGTGAAAGTA 59.510 47.619 0.00 0.00 0.00 2.24
712 719 2.106857 TGTTCGTTGGGGGTGAAAGTAT 59.893 45.455 0.00 0.00 0.00 2.12
713 720 2.483014 TCGTTGGGGGTGAAAGTATG 57.517 50.000 0.00 0.00 0.00 2.39
714 721 1.700739 TCGTTGGGGGTGAAAGTATGT 59.299 47.619 0.00 0.00 0.00 2.29
715 722 2.081462 CGTTGGGGGTGAAAGTATGTC 58.919 52.381 0.00 0.00 0.00 3.06
716 723 2.290071 CGTTGGGGGTGAAAGTATGTCT 60.290 50.000 0.00 0.00 0.00 3.41
722 729 6.007703 TGGGGGTGAAAGTATGTCTTTTTAG 58.992 40.000 0.00 0.00 45.15 1.85
724 731 5.417894 GGGGTGAAAGTATGTCTTTTTAGGG 59.582 44.000 0.00 0.00 45.15 3.53
729 736 9.010029 GTGAAAGTATGTCTTTTTAGGGATGAA 57.990 33.333 0.00 0.00 45.15 2.57
733 740 7.844009 AGTATGTCTTTTTAGGGATGAACGTA 58.156 34.615 0.00 0.00 0.00 3.57
736 743 6.469410 TGTCTTTTTAGGGATGAACGTATGT 58.531 36.000 0.00 0.00 0.00 2.29
737 744 6.370442 TGTCTTTTTAGGGATGAACGTATGTG 59.630 38.462 0.00 0.00 0.00 3.21
738 745 6.370718 GTCTTTTTAGGGATGAACGTATGTGT 59.629 38.462 0.00 0.00 0.00 3.72
741 748 5.918426 TTAGGGATGAACGTATGTGTGTA 57.082 39.130 0.00 0.00 0.00 2.90
745 752 5.361571 AGGGATGAACGTATGTGTGTATGTA 59.638 40.000 0.00 0.00 0.00 2.29
747 754 6.145534 GGGATGAACGTATGTGTGTATGTATG 59.854 42.308 0.00 0.00 0.00 2.39
749 756 7.598869 GGATGAACGTATGTGTGTATGTATGAT 59.401 37.037 0.00 0.00 0.00 2.45
750 757 7.924103 TGAACGTATGTGTGTATGTATGATC 57.076 36.000 0.00 0.00 0.00 2.92
751 758 7.712797 TGAACGTATGTGTGTATGTATGATCT 58.287 34.615 0.00 0.00 0.00 2.75
752 759 7.860872 TGAACGTATGTGTGTATGTATGATCTC 59.139 37.037 0.00 0.00 0.00 2.75
753 760 6.371389 ACGTATGTGTGTATGTATGATCTCG 58.629 40.000 0.00 0.00 0.00 4.04
754 761 6.017357 ACGTATGTGTGTATGTATGATCTCGT 60.017 38.462 0.00 0.00 0.00 4.18
755 762 6.520104 CGTATGTGTGTATGTATGATCTCGTC 59.480 42.308 0.00 0.00 0.00 4.20
756 763 5.183014 TGTGTGTATGTATGATCTCGTCC 57.817 43.478 0.00 0.00 0.00 4.79
757 764 4.219802 GTGTGTATGTATGATCTCGTCCG 58.780 47.826 0.00 0.00 0.00 4.79
758 765 3.881089 TGTGTATGTATGATCTCGTCCGT 59.119 43.478 0.00 0.00 0.00 4.69
759 766 5.049886 GTGTGTATGTATGATCTCGTCCGTA 60.050 44.000 0.00 0.00 0.00 4.02
760 767 5.049886 TGTGTATGTATGATCTCGTCCGTAC 60.050 44.000 0.00 0.00 0.00 3.67
761 768 5.049886 GTGTATGTATGATCTCGTCCGTACA 60.050 44.000 0.00 0.00 33.93 2.90
762 769 4.750952 ATGTATGATCTCGTCCGTACAG 57.249 45.455 0.00 0.00 33.34 2.74
763 770 3.538591 TGTATGATCTCGTCCGTACAGT 58.461 45.455 0.00 0.00 0.00 3.55
764 771 3.311596 TGTATGATCTCGTCCGTACAGTG 59.688 47.826 0.00 0.00 0.00 3.66
765 772 1.817357 TGATCTCGTCCGTACAGTGT 58.183 50.000 0.00 0.00 0.00 3.55
766 773 2.156917 TGATCTCGTCCGTACAGTGTT 58.843 47.619 0.00 0.00 0.00 3.32
767 774 2.555325 TGATCTCGTCCGTACAGTGTTT 59.445 45.455 0.00 0.00 0.00 2.83
768 775 3.005050 TGATCTCGTCCGTACAGTGTTTT 59.995 43.478 0.00 0.00 0.00 2.43
769 776 4.216042 TGATCTCGTCCGTACAGTGTTTTA 59.784 41.667 0.00 0.00 0.00 1.52
770 777 4.566545 TCTCGTCCGTACAGTGTTTTAA 57.433 40.909 0.00 0.00 0.00 1.52
771 778 4.930963 TCTCGTCCGTACAGTGTTTTAAA 58.069 39.130 0.00 0.00 0.00 1.52
772 779 5.347342 TCTCGTCCGTACAGTGTTTTAAAA 58.653 37.500 0.00 0.00 0.00 1.52
773 780 5.809562 TCTCGTCCGTACAGTGTTTTAAAAA 59.190 36.000 0.00 0.00 0.00 1.94
797 804 4.156739 AGAAATCACCCGAGAATTTTGAGC 59.843 41.667 0.00 0.00 0.00 4.26
818 825 4.427312 GCAATGAGCAAAATTCGGATTCT 58.573 39.130 0.00 0.00 44.79 2.40
847 854 0.247460 GTCCAAGGCCCATGAAAAGC 59.753 55.000 0.00 0.00 0.00 3.51
879 886 3.927854 TGTCGGAATCGTCCATGTTAAA 58.072 40.909 0.00 0.00 45.26 1.52
894 901 6.367695 TCCATGTTAAACATCGCTATTATCGG 59.632 38.462 0.00 0.00 36.53 4.18
985 998 2.606826 ACCTCCACCGAACCCTCC 60.607 66.667 0.00 0.00 0.00 4.30
986 999 2.284699 CCTCCACCGAACCCTCCT 60.285 66.667 0.00 0.00 0.00 3.69
1098 1117 2.665000 CTCGAGGGCTGCAAGGAA 59.335 61.111 3.91 0.00 0.00 3.36
1488 1522 4.459089 GTGGAGAGGAGGCCGCAC 62.459 72.222 9.31 1.44 34.84 5.34
1671 1705 3.006756 GCGAGCAGCTACCCAGACA 62.007 63.158 0.00 0.00 44.04 3.41
1693 1727 4.379243 CGCCTCCACAGCCGAGTT 62.379 66.667 0.00 0.00 0.00 3.01
1695 1729 3.059982 CCTCCACAGCCGAGTTCA 58.940 61.111 0.00 0.00 0.00 3.18
1700 1734 2.356313 ACAGCCGAGTTCACTGCG 60.356 61.111 0.00 0.00 34.72 5.18
2201 2235 4.459089 GTCTCCACAGCCGAGCCC 62.459 72.222 0.00 0.00 0.00 5.19
2249 2283 1.071471 CTCCACAGCCAAGTCCGTT 59.929 57.895 0.00 0.00 0.00 4.44
2301 2335 2.594303 CCAAGTCCGCTGCAACCA 60.594 61.111 0.00 0.00 0.00 3.67
2613 2647 3.252284 CCCGGATGCCCTGGCTAT 61.252 66.667 0.73 1.40 42.51 2.97
2615 2649 2.822637 CCGGATGCCCTGGCTATGT 61.823 63.158 9.97 0.00 42.51 2.29
2801 2835 1.152118 TGGAGGTGCCACTGGTACT 60.152 57.895 15.16 2.57 43.33 2.73
3099 3133 0.971386 GGTCAGACCGGGTTAGTTCA 59.029 55.000 6.32 0.00 0.00 3.18
3153 3187 1.606224 GCATTTGCTCTGTTGGTTGGG 60.606 52.381 0.00 0.00 38.21 4.12
3353 3387 2.899900 TCTCCTTGAGCTAGCTTTGTGA 59.100 45.455 20.42 12.49 0.00 3.58
3357 3391 4.019860 TCCTTGAGCTAGCTTTGTGAATCT 60.020 41.667 20.42 0.00 0.00 2.40
3404 3438 7.132694 TGTTAACTGAGCAATGTACATTCAG 57.867 36.000 24.76 24.76 0.00 3.02
3435 3469 4.201950 GCTGCAATAATCGGACAGTTGATT 60.202 41.667 0.00 7.05 38.34 2.57
3551 3585 1.272425 CCTGGTGAGGGCCAATGTTTA 60.272 52.381 6.18 0.00 38.18 2.01
3709 3765 4.214971 GCTCTGATTCAGTTTCAGCTTGAA 59.785 41.667 13.23 0.47 40.35 2.69
3757 3813 4.526262 TGGAAGAGGACTCTGAAAAGAGAG 59.474 45.833 9.65 1.04 44.50 3.20
3805 3876 2.636893 AGCCTGATTGTCTCTGAACTGT 59.363 45.455 0.00 0.00 0.00 3.55
3807 3878 3.929610 GCCTGATTGTCTCTGAACTGTAC 59.070 47.826 0.00 0.00 0.00 2.90
3808 3879 4.561530 GCCTGATTGTCTCTGAACTGTACA 60.562 45.833 0.00 0.00 0.00 2.90
3889 3979 7.174599 CCCTGAAAAGAGAATCATTGGCTATAG 59.825 40.741 0.00 0.00 37.82 1.31
3890 3980 7.718753 CCTGAAAAGAGAATCATTGGCTATAGT 59.281 37.037 0.84 0.00 37.82 2.12
3891 3981 9.770097 CTGAAAAGAGAATCATTGGCTATAGTA 57.230 33.333 0.84 0.00 37.82 1.82
3892 3982 9.547753 TGAAAAGAGAATCATTGGCTATAGTAC 57.452 33.333 0.84 0.00 37.82 2.73
3893 3983 8.594881 AAAAGAGAATCATTGGCTATAGTACG 57.405 34.615 0.84 0.00 37.82 3.67
3971 4063 6.179756 TGTATGGTGCTGTCAAATATGAAGT 58.820 36.000 0.00 0.00 37.30 3.01
4039 4131 1.145945 AGATGTATCGGAGGCTGAGGA 59.854 52.381 0.00 0.00 0.00 3.71
4040 4132 1.271102 GATGTATCGGAGGCTGAGGAC 59.729 57.143 0.00 0.00 0.00 3.85
4041 4133 0.755698 TGTATCGGAGGCTGAGGACC 60.756 60.000 0.00 0.00 0.00 4.46
4042 4134 0.468400 GTATCGGAGGCTGAGGACCT 60.468 60.000 0.00 0.00 41.41 3.85
4043 4135 0.468214 TATCGGAGGCTGAGGACCTG 60.468 60.000 0.00 0.00 37.77 4.00
4044 4136 2.230189 ATCGGAGGCTGAGGACCTGA 62.230 60.000 0.00 0.00 37.77 3.86
4045 4137 2.422231 CGGAGGCTGAGGACCTGAG 61.422 68.421 3.15 3.15 37.77 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.704493 GTGTTACTCAAGGTACAAGAACATGA 59.296 38.462 0.00 0.00 0.00 3.07
1 2 6.073222 GGTGTTACTCAAGGTACAAGAACATG 60.073 42.308 0.00 0.00 0.00 3.21
3 4 5.104859 TGGTGTTACTCAAGGTACAAGAACA 60.105 40.000 0.00 0.00 0.00 3.18
4 5 5.235831 GTGGTGTTACTCAAGGTACAAGAAC 59.764 44.000 0.00 0.00 0.00 3.01
5 6 5.362263 GTGGTGTTACTCAAGGTACAAGAA 58.638 41.667 0.00 0.00 0.00 2.52
6 7 4.500205 CGTGGTGTTACTCAAGGTACAAGA 60.500 45.833 0.00 0.00 0.00 3.02
7 8 3.739300 CGTGGTGTTACTCAAGGTACAAG 59.261 47.826 0.00 0.00 0.00 3.16
8 9 3.132646 ACGTGGTGTTACTCAAGGTACAA 59.867 43.478 0.00 0.00 0.00 2.41
9 10 2.694628 ACGTGGTGTTACTCAAGGTACA 59.305 45.455 0.00 0.00 0.00 2.90
10 11 3.054878 CACGTGGTGTTACTCAAGGTAC 58.945 50.000 7.95 0.00 0.00 3.34
11 12 2.036217 CCACGTGGTGTTACTCAAGGTA 59.964 50.000 26.95 0.00 0.00 3.08
12 13 1.202604 CCACGTGGTGTTACTCAAGGT 60.203 52.381 26.95 0.00 0.00 3.50
13 14 1.508632 CCACGTGGTGTTACTCAAGG 58.491 55.000 26.95 0.00 0.00 3.61
29 30 6.439675 TTTCCACTTTACTGTTTGTACCAC 57.560 37.500 0.00 0.00 0.00 4.16
31 32 5.506815 GCCTTTCCACTTTACTGTTTGTACC 60.507 44.000 0.00 0.00 0.00 3.34
52 53 3.145551 CAGGTAGGTACGCGGCCT 61.146 66.667 24.09 24.09 40.00 5.19
55 56 3.454573 TGCCAGGTAGGTACGCGG 61.455 66.667 12.47 0.00 40.61 6.46
56 57 2.202703 GTGCCAGGTAGGTACGCG 60.203 66.667 3.53 3.53 43.29 6.01
62 63 3.000819 TCCGTGGTGCCAGGTAGG 61.001 66.667 9.65 3.60 41.84 3.18
72 73 1.827969 CTTGAGAGGAATCTCCGTGGT 59.172 52.381 2.97 0.00 42.75 4.16
75 76 0.457851 CGCTTGAGAGGAATCTCCGT 59.542 55.000 2.97 0.00 42.75 4.69
80 81 1.601430 GAATGCCGCTTGAGAGGAATC 59.399 52.381 4.87 0.00 31.45 2.52
107 108 2.510064 TTACTACTGGTTGGGGCGCG 62.510 60.000 0.00 0.00 0.00 6.86
134 135 4.523943 TGAACTAACCGTACTTCAGCCTAA 59.476 41.667 0.00 0.00 0.00 2.69
139 140 4.557690 CGATGTGAACTAACCGTACTTCAG 59.442 45.833 0.00 0.00 0.00 3.02
142 143 4.771590 TCGATGTGAACTAACCGTACTT 57.228 40.909 0.00 0.00 0.00 2.24
161 163 9.923143 TTCCAACTACAATAACCTATGATATCG 57.077 33.333 0.00 0.00 0.00 2.92
167 169 6.597672 TGTGCTTCCAACTACAATAACCTATG 59.402 38.462 0.00 0.00 0.00 2.23
168 170 6.717289 TGTGCTTCCAACTACAATAACCTAT 58.283 36.000 0.00 0.00 0.00 2.57
176 178 6.402222 ACAAAATTTGTGCTTCCAACTACAA 58.598 32.000 10.91 0.00 43.48 2.41
201 203 8.257306 TGAAAGGCTTTTACAAACTTTTCTCAT 58.743 29.630 14.66 0.00 32.07 2.90
205 207 8.024146 TGTTGAAAGGCTTTTACAAACTTTTC 57.976 30.769 19.90 7.86 32.07 2.29
206 208 7.971183 TGTTGAAAGGCTTTTACAAACTTTT 57.029 28.000 19.90 0.00 32.07 2.27
213 215 5.843673 TCACATGTTGAAAGGCTTTTACA 57.156 34.783 22.62 22.62 0.00 2.41
214 216 6.681777 AGATCACATGTTGAAAGGCTTTTAC 58.318 36.000 14.66 15.04 37.92 2.01
279 281 4.999311 ACCGTGAGTCTAAATTACAAACCC 59.001 41.667 0.00 0.00 0.00 4.11
350 353 6.873605 CACGCATGAGGGATATCAAATTAGTA 59.126 38.462 4.83 0.00 31.76 1.82
351 354 5.702670 CACGCATGAGGGATATCAAATTAGT 59.297 40.000 4.83 0.00 31.76 2.24
352 355 5.934043 TCACGCATGAGGGATATCAAATTAG 59.066 40.000 0.00 0.00 31.76 1.73
353 356 5.863965 TCACGCATGAGGGATATCAAATTA 58.136 37.500 0.00 0.00 31.76 1.40
361 365 2.433970 TCACATTCACGCATGAGGGATA 59.566 45.455 0.98 0.00 35.83 2.59
369 373 3.434641 CAGAGAGTTTCACATTCACGCAT 59.565 43.478 0.00 0.00 0.00 4.73
370 374 2.802247 CAGAGAGTTTCACATTCACGCA 59.198 45.455 0.00 0.00 0.00 5.24
390 394 0.810648 GGCATCACTTTTCGGCATCA 59.189 50.000 0.00 0.00 0.00 3.07
399 404 1.180029 GAGCACATGGGCATCACTTT 58.820 50.000 24.51 0.00 35.83 2.66
434 439 9.097257 CAACAAGTTGGTTCATAAATTCTTTGT 57.903 29.630 7.96 0.00 36.95 2.83
452 457 4.798882 TCCTAACCATCCAACAACAAGTT 58.201 39.130 0.00 0.00 42.42 2.66
453 458 4.398319 CTCCTAACCATCCAACAACAAGT 58.602 43.478 0.00 0.00 0.00 3.16
454 459 3.758554 CCTCCTAACCATCCAACAACAAG 59.241 47.826 0.00 0.00 0.00 3.16
455 460 3.396276 TCCTCCTAACCATCCAACAACAA 59.604 43.478 0.00 0.00 0.00 2.83
456 461 2.983192 TCCTCCTAACCATCCAACAACA 59.017 45.455 0.00 0.00 0.00 3.33
457 462 3.244770 TGTCCTCCTAACCATCCAACAAC 60.245 47.826 0.00 0.00 0.00 3.32
458 463 2.983192 TGTCCTCCTAACCATCCAACAA 59.017 45.455 0.00 0.00 0.00 2.83
459 464 2.571653 CTGTCCTCCTAACCATCCAACA 59.428 50.000 0.00 0.00 0.00 3.33
460 465 2.572104 ACTGTCCTCCTAACCATCCAAC 59.428 50.000 0.00 0.00 0.00 3.77
461 466 2.571653 CACTGTCCTCCTAACCATCCAA 59.428 50.000 0.00 0.00 0.00 3.53
462 467 2.187958 CACTGTCCTCCTAACCATCCA 58.812 52.381 0.00 0.00 0.00 3.41
463 468 2.467880 TCACTGTCCTCCTAACCATCC 58.532 52.381 0.00 0.00 0.00 3.51
473 478 7.446931 TGATAGACTGAAGATATCACTGTCCTC 59.553 40.741 22.81 20.55 35.07 3.71
483 488 9.420118 ACTTGAACTCTGATAGACTGAAGATAT 57.580 33.333 0.00 0.00 0.00 1.63
511 516 3.304391 GCGAGCACCATTGTCAAGTTTAA 60.304 43.478 0.00 0.00 0.00 1.52
514 519 0.593128 GCGAGCACCATTGTCAAGTT 59.407 50.000 0.00 0.00 0.00 2.66
540 545 5.818336 TCGCCGAAGTATGAAATAAATCCAA 59.182 36.000 0.00 0.00 0.00 3.53
543 548 5.051240 ACGTCGCCGAAGTATGAAATAAATC 60.051 40.000 3.28 0.00 37.88 2.17
555 560 4.936823 AACGCACGTCGCCGAAGT 62.937 61.111 12.06 0.00 43.23 3.01
557 562 4.927444 TGAACGCACGTCGCCGAA 62.927 61.111 12.06 0.00 43.23 4.30
560 565 4.059459 CACTGAACGCACGTCGCC 62.059 66.667 0.00 1.82 43.23 5.54
561 566 2.988549 CTCACTGAACGCACGTCGC 61.989 63.158 0.00 3.99 43.23 5.19
562 567 1.330779 CTCTCACTGAACGCACGTCG 61.331 60.000 0.00 5.97 45.38 5.12
564 569 0.384309 TTCTCTCACTGAACGCACGT 59.616 50.000 0.00 0.00 0.00 4.49
565 570 1.056103 CTTCTCTCACTGAACGCACG 58.944 55.000 0.00 0.00 0.00 5.34
578 585 0.970937 TCGACGGGAATGCCTTCTCT 60.971 55.000 0.00 0.00 28.89 3.10
580 587 1.218316 GTCGACGGGAATGCCTTCT 59.782 57.895 0.00 0.00 0.00 2.85
607 614 0.800683 TAATGAAGTCGCCGCAGACG 60.801 55.000 8.89 0.00 45.26 4.18
610 617 2.205074 AGATTAATGAAGTCGCCGCAG 58.795 47.619 0.00 0.00 0.00 5.18
612 619 2.201732 TGAGATTAATGAAGTCGCCGC 58.798 47.619 0.00 0.00 0.00 6.53
613 620 4.112634 TCTTGAGATTAATGAAGTCGCCG 58.887 43.478 0.00 0.00 0.00 6.46
614 621 5.755375 TCATCTTGAGATTAATGAAGTCGCC 59.245 40.000 0.00 0.00 31.21 5.54
615 622 6.834959 TCATCTTGAGATTAATGAAGTCGC 57.165 37.500 0.00 0.00 31.21 5.19
625 632 6.324770 TGAGCTGGTACATCATCTTGAGATTA 59.675 38.462 0.00 0.00 38.20 1.75
629 636 4.141981 ACTGAGCTGGTACATCATCTTGAG 60.142 45.833 0.00 0.00 38.20 3.02
634 641 3.636300 AGAGACTGAGCTGGTACATCATC 59.364 47.826 0.00 0.00 38.20 2.92
637 644 4.884744 TCTTAGAGACTGAGCTGGTACATC 59.115 45.833 0.00 0.00 38.20 3.06
642 649 3.730215 TCTCTTAGAGACTGAGCTGGT 57.270 47.619 8.00 0.00 33.35 4.00
643 650 3.243501 GCATCTCTTAGAGACTGAGCTGG 60.244 52.174 14.73 0.00 41.76 4.85
645 652 3.902218 AGCATCTCTTAGAGACTGAGCT 58.098 45.455 14.73 16.89 41.76 4.09
653 660 8.107095 ACTCTACCCTATAAGCATCTCTTAGAG 58.893 40.741 2.23 2.23 43.05 2.43
655 662 7.668052 ACACTCTACCCTATAAGCATCTCTTAG 59.332 40.741 0.00 0.00 40.34 2.18
656 663 7.448777 CACACTCTACCCTATAAGCATCTCTTA 59.551 40.741 0.00 0.00 41.17 2.10
657 664 6.266558 CACACTCTACCCTATAAGCATCTCTT 59.733 42.308 0.00 0.00 38.79 2.85
658 665 5.772672 CACACTCTACCCTATAAGCATCTCT 59.227 44.000 0.00 0.00 0.00 3.10
659 666 5.565834 GCACACTCTACCCTATAAGCATCTC 60.566 48.000 0.00 0.00 0.00 2.75
662 669 3.967326 TGCACACTCTACCCTATAAGCAT 59.033 43.478 0.00 0.00 0.00 3.79
663 670 3.371034 TGCACACTCTACCCTATAAGCA 58.629 45.455 0.00 0.00 0.00 3.91
664 671 4.310769 CATGCACACTCTACCCTATAAGC 58.689 47.826 0.00 0.00 0.00 3.09
665 672 4.202253 TGCATGCACACTCTACCCTATAAG 60.202 45.833 18.46 0.00 0.00 1.73
666 673 3.709141 TGCATGCACACTCTACCCTATAA 59.291 43.478 18.46 0.00 0.00 0.98
667 674 3.304829 TGCATGCACACTCTACCCTATA 58.695 45.455 18.46 0.00 0.00 1.31
668 675 2.118679 TGCATGCACACTCTACCCTAT 58.881 47.619 18.46 0.00 0.00 2.57
669 676 1.567357 TGCATGCACACTCTACCCTA 58.433 50.000 18.46 0.00 0.00 3.53
670 677 0.692476 TTGCATGCACACTCTACCCT 59.308 50.000 22.58 0.00 0.00 4.34
671 678 1.089920 CTTGCATGCACACTCTACCC 58.910 55.000 22.58 0.00 0.00 3.69
672 679 1.466167 CACTTGCATGCACACTCTACC 59.534 52.381 22.58 0.00 0.00 3.18
673 680 2.146342 ACACTTGCATGCACACTCTAC 58.854 47.619 22.58 0.00 0.00 2.59
674 681 2.549064 ACACTTGCATGCACACTCTA 57.451 45.000 22.58 3.16 0.00 2.43
675 682 1.605710 GAACACTTGCATGCACACTCT 59.394 47.619 22.58 5.06 0.00 3.24
676 683 1.661178 CGAACACTTGCATGCACACTC 60.661 52.381 22.58 11.62 0.00 3.51
677 684 0.308684 CGAACACTTGCATGCACACT 59.691 50.000 22.58 2.02 0.00 3.55
678 685 0.029300 ACGAACACTTGCATGCACAC 59.971 50.000 22.58 7.32 0.00 3.82
679 686 0.737804 AACGAACACTTGCATGCACA 59.262 45.000 22.58 11.00 0.00 4.57
680 687 1.122849 CAACGAACACTTGCATGCAC 58.877 50.000 22.58 6.78 0.00 4.57
681 688 0.030504 CCAACGAACACTTGCATGCA 59.969 50.000 18.46 18.46 0.00 3.96
682 689 0.664166 CCCAACGAACACTTGCATGC 60.664 55.000 11.82 11.82 0.00 4.06
683 690 0.039256 CCCCAACGAACACTTGCATG 60.039 55.000 0.00 0.00 0.00 4.06
684 691 1.178534 CCCCCAACGAACACTTGCAT 61.179 55.000 0.00 0.00 0.00 3.96
685 692 1.826054 CCCCCAACGAACACTTGCA 60.826 57.895 0.00 0.00 0.00 4.08
686 693 1.826487 ACCCCCAACGAACACTTGC 60.826 57.895 0.00 0.00 0.00 4.01
687 694 0.464735 TCACCCCCAACGAACACTTG 60.465 55.000 0.00 0.00 0.00 3.16
688 695 0.256464 TTCACCCCCAACGAACACTT 59.744 50.000 0.00 0.00 0.00 3.16
689 696 0.256464 TTTCACCCCCAACGAACACT 59.744 50.000 0.00 0.00 0.00 3.55
690 697 0.666374 CTTTCACCCCCAACGAACAC 59.334 55.000 0.00 0.00 0.00 3.32
691 698 0.256464 ACTTTCACCCCCAACGAACA 59.744 50.000 0.00 0.00 0.00 3.18
692 699 2.259266 TACTTTCACCCCCAACGAAC 57.741 50.000 0.00 0.00 0.00 3.95
693 700 2.106857 ACATACTTTCACCCCCAACGAA 59.893 45.455 0.00 0.00 0.00 3.85
694 701 1.700739 ACATACTTTCACCCCCAACGA 59.299 47.619 0.00 0.00 0.00 3.85
695 702 2.081462 GACATACTTTCACCCCCAACG 58.919 52.381 0.00 0.00 0.00 4.10
696 703 3.434940 AGACATACTTTCACCCCCAAC 57.565 47.619 0.00 0.00 0.00 3.77
697 704 4.463050 AAAGACATACTTTCACCCCCAA 57.537 40.909 0.00 0.00 44.36 4.12
698 705 4.463050 AAAAGACATACTTTCACCCCCA 57.537 40.909 0.00 0.00 46.55 4.96
699 706 5.417894 CCTAAAAAGACATACTTTCACCCCC 59.582 44.000 0.00 0.00 46.55 5.40
700 707 5.417894 CCCTAAAAAGACATACTTTCACCCC 59.582 44.000 0.00 0.00 46.55 4.95
701 708 6.243148 TCCCTAAAAAGACATACTTTCACCC 58.757 40.000 0.00 0.00 46.55 4.61
702 709 7.610305 TCATCCCTAAAAAGACATACTTTCACC 59.390 37.037 0.00 0.00 46.55 4.02
703 710 8.561738 TCATCCCTAAAAAGACATACTTTCAC 57.438 34.615 0.00 0.00 46.55 3.18
704 711 9.010029 GTTCATCCCTAAAAAGACATACTTTCA 57.990 33.333 0.00 0.00 46.55 2.69
705 712 8.175716 CGTTCATCCCTAAAAAGACATACTTTC 58.824 37.037 0.00 0.00 46.55 2.62
707 714 7.166167 ACGTTCATCCCTAAAAAGACATACTT 58.834 34.615 0.00 0.00 40.98 2.24
708 715 6.708285 ACGTTCATCCCTAAAAAGACATACT 58.292 36.000 0.00 0.00 0.00 2.12
709 716 6.980051 ACGTTCATCCCTAAAAAGACATAC 57.020 37.500 0.00 0.00 0.00 2.39
710 717 8.262227 ACATACGTTCATCCCTAAAAAGACATA 58.738 33.333 0.00 0.00 0.00 2.29
711 718 7.065803 CACATACGTTCATCCCTAAAAAGACAT 59.934 37.037 0.00 0.00 0.00 3.06
712 719 6.370442 CACATACGTTCATCCCTAAAAAGACA 59.630 38.462 0.00 0.00 0.00 3.41
713 720 6.370718 ACACATACGTTCATCCCTAAAAAGAC 59.629 38.462 0.00 0.00 0.00 3.01
714 721 6.370442 CACACATACGTTCATCCCTAAAAAGA 59.630 38.462 0.00 0.00 0.00 2.52
715 722 6.148811 ACACACATACGTTCATCCCTAAAAAG 59.851 38.462 0.00 0.00 0.00 2.27
716 723 5.998981 ACACACATACGTTCATCCCTAAAAA 59.001 36.000 0.00 0.00 0.00 1.94
718 725 5.155278 ACACACATACGTTCATCCCTAAA 57.845 39.130 0.00 0.00 0.00 1.85
722 729 4.439057 ACATACACACATACGTTCATCCC 58.561 43.478 0.00 0.00 0.00 3.85
724 731 7.924103 TCATACATACACACATACGTTCATC 57.076 36.000 0.00 0.00 0.00 2.92
729 736 6.017357 ACGAGATCATACATACACACATACGT 60.017 38.462 0.00 0.00 0.00 3.57
733 740 5.562890 CGGACGAGATCATACATACACACAT 60.563 44.000 0.00 0.00 0.00 3.21
736 743 3.881089 ACGGACGAGATCATACATACACA 59.119 43.478 0.00 0.00 0.00 3.72
737 744 4.485024 ACGGACGAGATCATACATACAC 57.515 45.455 0.00 0.00 0.00 2.90
738 745 5.058490 TGTACGGACGAGATCATACATACA 58.942 41.667 0.00 0.00 29.72 2.29
741 748 4.023963 CACTGTACGGACGAGATCATACAT 60.024 45.833 9.17 0.00 32.72 2.29
745 752 2.366533 ACACTGTACGGACGAGATCAT 58.633 47.619 9.17 0.00 0.00 2.45
747 754 2.915738 AACACTGTACGGACGAGATC 57.084 50.000 9.17 0.00 0.00 2.75
749 756 4.566545 TTAAAACACTGTACGGACGAGA 57.433 40.909 9.17 0.00 0.00 4.04
750 757 5.640218 TTTTAAAACACTGTACGGACGAG 57.360 39.130 9.17 0.00 0.00 4.18
770 777 7.496747 TCAAAATTCTCGGGTGATTTCTTTTT 58.503 30.769 1.03 0.00 0.00 1.94
771 778 7.049799 TCAAAATTCTCGGGTGATTTCTTTT 57.950 32.000 1.03 0.00 0.00 2.27
772 779 6.648879 TCAAAATTCTCGGGTGATTTCTTT 57.351 33.333 1.03 0.00 0.00 2.52
773 780 5.335976 GCTCAAAATTCTCGGGTGATTTCTT 60.336 40.000 1.03 0.00 0.00 2.52
774 781 4.156739 GCTCAAAATTCTCGGGTGATTTCT 59.843 41.667 1.03 0.00 0.00 2.52
775 782 4.082787 TGCTCAAAATTCTCGGGTGATTTC 60.083 41.667 1.03 0.00 0.00 2.17
776 783 3.826157 TGCTCAAAATTCTCGGGTGATTT 59.174 39.130 0.00 0.00 0.00 2.17
777 784 3.420893 TGCTCAAAATTCTCGGGTGATT 58.579 40.909 0.00 0.00 0.00 2.57
783 790 3.119743 TGCTCATTGCTCAAAATTCTCGG 60.120 43.478 0.00 0.00 43.37 4.63
784 791 4.087510 TGCTCATTGCTCAAAATTCTCG 57.912 40.909 0.00 0.00 43.37 4.04
797 804 8.537223 CAATAAGAATCCGAATTTTGCTCATTG 58.463 33.333 0.00 0.00 0.00 2.82
842 849 2.030628 CCGACATAAACCAACGGCTTTT 60.031 45.455 0.00 0.00 37.32 2.27
847 854 2.029970 CGATTCCGACATAAACCAACGG 59.970 50.000 0.00 0.00 44.09 4.44
879 886 1.698165 CGTGCCGATAATAGCGATGT 58.302 50.000 0.00 0.00 0.00 3.06
985 998 0.698238 TCCATTGTTGGGTGGAGGAG 59.302 55.000 0.00 0.00 43.81 3.69
986 999 1.284785 GATCCATTGTTGGGTGGAGGA 59.715 52.381 0.37 0.00 46.87 3.71
1098 1117 1.414061 CGATGGCCTGGGAGGAGAAT 61.414 60.000 3.32 0.00 37.67 2.40
1202 1221 2.439960 TATGGATCGGGCTTGCCGT 61.440 57.895 5.49 0.00 0.00 5.68
1207 1226 1.069765 CAGCGTATGGATCGGGCTT 59.930 57.895 0.00 0.00 0.00 4.35
1450 1469 3.803082 CGGCTGTTGCATCGGTGG 61.803 66.667 0.00 0.00 41.91 4.61
1592 1626 2.126071 GCAGCGAACTCGGCTGTA 60.126 61.111 14.41 0.00 41.75 2.74
1642 1676 3.953444 CTGCTCGCAGCGAACTCGA 62.953 63.158 20.04 0.00 46.26 4.04
1692 1726 1.079819 GGTAGCTGCTCGCAGTGAA 60.080 57.895 19.00 3.77 45.24 3.18
1693 1727 2.573869 GGTAGCTGCTCGCAGTGA 59.426 61.111 19.00 5.88 45.24 3.41
1695 1729 2.997315 TGGGTAGCTGCTCGCAGT 60.997 61.111 19.00 9.35 45.24 4.40
2201 2235 0.520404 CTTGGTAGCTGCTTGCAGTG 59.480 55.000 21.55 1.31 45.94 3.66
2202 2236 1.239968 GCTTGGTAGCTGCTTGCAGT 61.240 55.000 21.55 12.12 44.27 4.40
2249 2283 1.973281 GGCTTGGTAGCTGCTTGCA 60.973 57.895 7.79 0.00 46.90 4.08
2601 2635 0.403271 GATCCACATAGCCAGGGCAT 59.597 55.000 13.63 1.37 44.88 4.40
2613 2647 1.991813 TGGGAATTGACCAGATCCACA 59.008 47.619 0.00 0.00 33.48 4.17
2801 2835 2.281484 GTTCTGGCGCAGGTTCCA 60.281 61.111 10.83 0.00 31.51 3.53
2851 2885 1.750399 GCATCACAGGTTCCGGCAT 60.750 57.895 0.00 0.00 0.00 4.40
3099 3133 6.823689 ACGACAACAGGATGAAATTAATAGCT 59.176 34.615 0.00 0.00 39.69 3.32
3153 3187 4.245660 TGTCAGCAGCAAATGAGTAGTAC 58.754 43.478 0.00 0.00 0.00 2.73
3237 3271 6.209986 TCATCAACTAAGAAAAGACTACCCGA 59.790 38.462 0.00 0.00 0.00 5.14
3353 3387 3.436180 GCAATCCCCAGGAATCTCAGATT 60.436 47.826 0.00 0.00 34.34 2.40
3357 3391 1.492176 GAGCAATCCCCAGGAATCTCA 59.508 52.381 0.00 0.00 34.34 3.27
3404 3438 5.049474 TGTCCGATTATTGCAGCACATTATC 60.049 40.000 0.00 1.08 0.00 1.75
3435 3469 8.974060 ACTAAACTGGAGAAGAAACACATAAA 57.026 30.769 0.00 0.00 0.00 1.40
3551 3585 6.587560 TCTAGGTAAGTAGGTACCATGTCT 57.412 41.667 15.94 3.57 45.27 3.41
3709 3765 8.622157 CAGAGAGAATCATAGTCAAATTGCATT 58.378 33.333 0.00 0.00 37.82 3.56
3768 3839 1.532604 GGCTACAGTTTGGCCAACCC 61.533 60.000 20.35 12.17 44.69 4.11
3805 3876 5.114764 TCAAGCTGATTGAATCCCATGTA 57.885 39.130 5.78 0.00 45.00 2.29
3889 3979 5.975344 TCAGATTCGAATTCACCATACGTAC 59.025 40.000 12.81 0.00 0.00 3.67
3890 3980 5.975344 GTCAGATTCGAATTCACCATACGTA 59.025 40.000 12.81 0.00 0.00 3.57
3891 3981 4.804139 GTCAGATTCGAATTCACCATACGT 59.196 41.667 12.81 0.00 0.00 3.57
3892 3982 5.043903 AGTCAGATTCGAATTCACCATACG 58.956 41.667 12.81 0.00 0.00 3.06
3893 3983 6.042777 TCAGTCAGATTCGAATTCACCATAC 58.957 40.000 12.81 4.68 0.00 2.39
3971 4063 4.594854 ATGGTGTTGCCGTGCCCA 62.595 61.111 0.00 0.00 41.21 5.36


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

AutoCloner maintained by Alex Coulton.