Multiple sequence alignment - TraesCS2A01G224500

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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 TraesCS2A01G224500 chr2A 100.000 6491 0 0 1 6491 224919495 224913005 0.000000e+00 11987.0
1 TraesCS2A01G224500 chr2A 96.693 514 14 1 2 512 224944588 224944075 0.000000e+00 852.0
2 TraesCS2A01G224500 chr2A 94.406 143 7 1 691 833 43140042 43139901 1.100000e-52 219.0
3 TraesCS2A01G224500 chr2A 94.203 138 8 0 692 829 71626092 71626229 1.830000e-50 211.0
4 TraesCS2A01G224500 chr2D 96.805 4695 126 15 842 5527 201837410 201832731 0.000000e+00 7817.0
5 TraesCS2A01G224500 chr2D 88.261 920 61 20 5590 6491 201832722 201831832 0.000000e+00 1057.0
6 TraesCS2A01G224500 chr2D 89.759 166 15 2 692 855 67303382 67303547 1.830000e-50 211.0
7 TraesCS2A01G224500 chr2D 94.805 77 1 2 606 682 201837485 201837412 4.110000e-22 117.0
8 TraesCS2A01G224500 chr2B 95.582 2173 87 7 1787 3953 378438899 378436730 0.000000e+00 3472.0
9 TraesCS2A01G224500 chr2B 95.325 1647 65 5 3952 5594 378436648 378435010 0.000000e+00 2604.0
10 TraesCS2A01G224500 chr2B 94.193 861 40 5 884 1742 378439755 378438903 0.000000e+00 1304.0
11 TraesCS2A01G224500 chr2B 89.531 640 37 5 5861 6491 378434718 378434100 0.000000e+00 784.0
12 TraesCS2A01G224500 chr2B 88.824 170 16 3 692 859 9033431 9033599 8.530000e-49 206.0
13 TraesCS2A01G224500 chr2B 82.178 101 14 2 1729 1829 622914010 622914106 4.170000e-12 84.2
14 TraesCS2A01G224500 chr4A 97.456 511 12 1 2 512 561136972 561136463 0.000000e+00 870.0
15 TraesCS2A01G224500 chr4A 96.686 513 15 2 2 513 561124822 561124311 0.000000e+00 852.0
16 TraesCS2A01G224500 chr1A 96.869 511 14 2 2 512 145991275 145991783 0.000000e+00 854.0
17 TraesCS2A01G224500 chr1A 96.673 511 15 2 2 512 4458617 4459125 0.000000e+00 848.0
18 TraesCS2A01G224500 chr1A 87.879 99 9 3 1733 1829 385895958 385896055 5.320000e-21 113.0
19 TraesCS2A01G224500 chr7A 96.673 511 17 0 2 512 633255378 633254868 0.000000e+00 850.0
20 TraesCS2A01G224500 chr7A 96.673 511 16 1 2 512 105109922 105110431 0.000000e+00 848.0
21 TraesCS2A01G224500 chr5A 96.673 511 15 2 2 512 111051750 111052258 0.000000e+00 848.0
22 TraesCS2A01G224500 chr5A 96.673 511 15 2 2 512 601267683 601267175 0.000000e+00 848.0
23 TraesCS2A01G224500 chr5A 93.038 158 9 2 691 847 24199770 24199614 5.060000e-56 230.0
24 TraesCS2A01G224500 chr3B 81.994 311 33 8 5613 5904 685388926 685389232 6.500000e-60 243.0
25 TraesCS2A01G224500 chr5D 89.349 169 17 1 688 855 211860010 211859842 1.830000e-50 211.0
26 TraesCS2A01G224500 chr3A 89.286 168 18 0 678 845 641466145 641466312 1.830000e-50 211.0
27 TraesCS2A01G224500 chr3A 78.605 215 35 10 5588 5794 19764418 19764207 1.470000e-26 132.0
28 TraesCS2A01G224500 chr3A 84.000 100 15 1 1733 1831 7126837 7126936 1.930000e-15 95.3
29 TraesCS2A01G224500 chr7D 88.623 167 17 2 691 855 228456874 228456708 1.100000e-47 202.0
30 TraesCS2A01G224500 chr7D 86.076 158 17 3 5752 5904 461090624 461090781 1.450000e-36 165.0
31 TraesCS2A01G224500 chr7D 87.755 98 9 3 1733 1828 29877480 29877576 1.910000e-20 111.0
32 TraesCS2A01G224500 chr6A 89.024 164 16 1 691 854 604588010 604587849 1.100000e-47 202.0
33 TraesCS2A01G224500 chr7B 87.500 144 14 2 5765 5904 483533083 483533226 5.210000e-36 163.0
34 TraesCS2A01G224500 chr7B 90.196 102 9 1 5494 5594 675838941 675838840 1.470000e-26 132.0
35 TraesCS2A01G224500 chr1B 79.070 258 19 7 5493 5715 460580168 460580425 1.890000e-30 145.0
36 TraesCS2A01G224500 chr1B 85.859 99 11 3 1733 1829 415226989 415227086 1.150000e-17 102.0
37 TraesCS2A01G224500 chr1B 89.552 67 7 0 5709 5775 669910808 669910742 1.160000e-12 86.1
38 TraesCS2A01G224500 chr1D 88.235 102 9 3 1733 1832 31154861 31154761 1.140000e-22 119.0
39 TraesCS2A01G224500 chr1D 94.915 59 3 0 5493 5551 343363458 343363516 6.930000e-15 93.5
40 TraesCS2A01G224500 chr3D 84.694 98 12 3 1733 1828 1887680 1887584 1.930000e-15 95.3
41 TraesCS2A01G224500 chr3D 84.694 98 12 3 1733 1828 414906883 414906979 1.930000e-15 95.3


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 TraesCS2A01G224500 chr2A 224913005 224919495 6490 True 11987 11987 100.000000 1 6491 1 chr2A.!!$R2 6490
1 TraesCS2A01G224500 chr2A 224944075 224944588 513 True 852 852 96.693000 2 512 1 chr2A.!!$R3 510
2 TraesCS2A01G224500 chr2D 201831832 201837485 5653 True 2997 7817 93.290333 606 6491 3 chr2D.!!$R1 5885
3 TraesCS2A01G224500 chr2B 378434100 378439755 5655 True 2041 3472 93.657750 884 6491 4 chr2B.!!$R1 5607
4 TraesCS2A01G224500 chr4A 561136463 561136972 509 True 870 870 97.456000 2 512 1 chr4A.!!$R2 510
5 TraesCS2A01G224500 chr4A 561124311 561124822 511 True 852 852 96.686000 2 513 1 chr4A.!!$R1 511
6 TraesCS2A01G224500 chr1A 145991275 145991783 508 False 854 854 96.869000 2 512 1 chr1A.!!$F2 510
7 TraesCS2A01G224500 chr1A 4458617 4459125 508 False 848 848 96.673000 2 512 1 chr1A.!!$F1 510
8 TraesCS2A01G224500 chr7A 633254868 633255378 510 True 850 850 96.673000 2 512 1 chr7A.!!$R1 510
9 TraesCS2A01G224500 chr7A 105109922 105110431 509 False 848 848 96.673000 2 512 1 chr7A.!!$F1 510
10 TraesCS2A01G224500 chr5A 111051750 111052258 508 False 848 848 96.673000 2 512 1 chr5A.!!$F1 510
11 TraesCS2A01G224500 chr5A 601267175 601267683 508 True 848 848 96.673000 2 512 1 chr5A.!!$R2 510

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
544 549 0.036388 CGGTCTGGTGCACTGGTTAT 60.036 55.000 17.98 0.0 0.00 1.89 F
598 603 0.106918 AAAGAGGCACGAACAACCCA 60.107 50.000 0.00 0.0 0.00 4.51 F
1401 1409 0.250038 CCGCCTGATGAGGTACATGG 60.250 60.000 0.00 0.0 42.15 3.66 F
2069 2080 0.465824 GAGCTCCTGCCATGCATTCT 60.466 55.000 0.87 0.0 38.13 2.40 F
2104 2115 1.068127 AGCTTGGCTTGTTTTGCTCAG 59.932 47.619 0.00 0.0 33.89 3.35 F
3485 3503 0.033781 TTGCTGCATTGCCAGGAAAC 59.966 50.000 1.84 0.0 39.69 2.78 F
4421 4523 0.183731 CCCTTCCCTATGGTTGCTCC 59.816 60.000 0.00 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 2214 0.173481 ATACACATCAGTCGCACGCT 59.827 50.000 0.00 0.0 0.00 5.07 R
2241 2252 5.420739 GGCCTTTTAGGTGGATTAAACATCA 59.579 40.000 0.00 0.0 37.80 3.07 R
2976 2992 0.179020 CTGGGGCACACTGACTTTCA 60.179 55.000 0.00 0.0 0.00 2.69 R
3418 3436 1.981256 AACAGCAATTCAAGTCCGGT 58.019 45.000 0.00 0.0 0.00 5.28 R
3642 3660 2.026262 AGTGTTAAGTTCCCGGATGCAT 60.026 45.455 0.73 0.0 0.00 3.96 R
5165 5267 0.315251 CACGCTTCCACAGAGACTGA 59.685 55.000 5.76 0.0 35.18 3.41 R
5583 5689 0.105142 TCACCCTAGGATAGTGGGGC 60.105 60.000 11.48 0.0 42.12 5.80 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
302 303 3.895656 TGGCGAACTCTATATAAGCCACT 59.104 43.478 1.80 0.00 46.73 4.00
501 506 5.839063 CCCCCTATATCACTGTCAGAGTTAA 59.161 44.000 6.91 0.00 29.75 2.01
513 518 3.866910 GTCAGAGTTAAAACCACGACACA 59.133 43.478 0.00 0.00 0.00 3.72
514 519 4.330620 GTCAGAGTTAAAACCACGACACAA 59.669 41.667 0.00 0.00 0.00 3.33
515 520 4.330620 TCAGAGTTAAAACCACGACACAAC 59.669 41.667 0.00 0.00 0.00 3.32
516 521 4.331717 CAGAGTTAAAACCACGACACAACT 59.668 41.667 0.00 0.00 0.00 3.16
517 522 4.569564 AGAGTTAAAACCACGACACAACTC 59.430 41.667 0.00 0.00 40.28 3.01
518 523 4.255301 AGTTAAAACCACGACACAACTCA 58.745 39.130 0.00 0.00 0.00 3.41
519 524 4.696402 AGTTAAAACCACGACACAACTCAA 59.304 37.500 0.00 0.00 0.00 3.02
520 525 3.481112 AAAACCACGACACAACTCAAC 57.519 42.857 0.00 0.00 0.00 3.18
521 526 2.102070 AACCACGACACAACTCAACA 57.898 45.000 0.00 0.00 0.00 3.33
522 527 2.102070 ACCACGACACAACTCAACAA 57.898 45.000 0.00 0.00 0.00 2.83
523 528 1.735571 ACCACGACACAACTCAACAAC 59.264 47.619 0.00 0.00 0.00 3.32
524 529 1.267334 CCACGACACAACTCAACAACG 60.267 52.381 0.00 0.00 0.00 4.10
525 530 0.372334 ACGACACAACTCAACAACGC 59.628 50.000 0.00 0.00 0.00 4.84
526 531 0.650476 CGACACAACTCAACAACGCG 60.650 55.000 3.53 3.53 0.00 6.01
527 532 0.315869 GACACAACTCAACAACGCGG 60.316 55.000 12.47 0.00 0.00 6.46
528 533 1.022451 ACACAACTCAACAACGCGGT 61.022 50.000 12.47 0.00 0.00 5.68
529 534 0.315869 CACAACTCAACAACGCGGTC 60.316 55.000 12.47 0.00 0.00 4.79
530 535 0.461339 ACAACTCAACAACGCGGTCT 60.461 50.000 12.47 0.00 0.00 3.85
531 536 0.042188 CAACTCAACAACGCGGTCTG 60.042 55.000 12.47 7.36 0.00 3.51
532 537 1.157870 AACTCAACAACGCGGTCTGG 61.158 55.000 12.47 0.00 0.00 3.86
533 538 1.594293 CTCAACAACGCGGTCTGGT 60.594 57.895 12.47 0.00 0.00 4.00
534 539 1.831389 CTCAACAACGCGGTCTGGTG 61.831 60.000 12.47 13.88 0.00 4.17
535 540 3.276846 AACAACGCGGTCTGGTGC 61.277 61.111 12.47 0.00 0.00 5.01
536 541 4.539083 ACAACGCGGTCTGGTGCA 62.539 61.111 12.47 0.00 0.00 4.57
537 542 4.012895 CAACGCGGTCTGGTGCAC 62.013 66.667 12.47 8.80 0.00 4.57
538 543 4.235762 AACGCGGTCTGGTGCACT 62.236 61.111 17.98 0.00 0.00 4.40
539 544 4.969196 ACGCGGTCTGGTGCACTG 62.969 66.667 17.98 10.30 0.00 3.66
541 546 4.626081 GCGGTCTGGTGCACTGGT 62.626 66.667 17.98 0.00 0.00 4.00
542 547 2.111043 CGGTCTGGTGCACTGGTT 59.889 61.111 17.98 0.00 0.00 3.67
543 548 1.369692 CGGTCTGGTGCACTGGTTA 59.630 57.895 17.98 0.00 0.00 2.85
544 549 0.036388 CGGTCTGGTGCACTGGTTAT 60.036 55.000 17.98 0.00 0.00 1.89
545 550 1.610624 CGGTCTGGTGCACTGGTTATT 60.611 52.381 17.98 0.00 0.00 1.40
546 551 2.514803 GGTCTGGTGCACTGGTTATTT 58.485 47.619 17.98 0.00 0.00 1.40
547 552 2.890945 GGTCTGGTGCACTGGTTATTTT 59.109 45.455 17.98 0.00 0.00 1.82
548 553 4.076394 GGTCTGGTGCACTGGTTATTTTA 58.924 43.478 17.98 0.00 0.00 1.52
549 554 4.521256 GGTCTGGTGCACTGGTTATTTTAA 59.479 41.667 17.98 0.00 0.00 1.52
550 555 5.458015 GTCTGGTGCACTGGTTATTTTAAC 58.542 41.667 17.98 0.00 0.00 2.01
551 556 5.009210 GTCTGGTGCACTGGTTATTTTAACA 59.991 40.000 17.98 0.00 0.00 2.41
552 557 5.772672 TCTGGTGCACTGGTTATTTTAACAT 59.227 36.000 17.98 0.00 0.00 2.71
553 558 6.266558 TCTGGTGCACTGGTTATTTTAACATT 59.733 34.615 17.98 0.00 0.00 2.71
554 559 6.219473 TGGTGCACTGGTTATTTTAACATTG 58.781 36.000 17.98 0.00 0.00 2.82
555 560 6.183360 TGGTGCACTGGTTATTTTAACATTGT 60.183 34.615 17.98 0.00 0.00 2.71
556 561 6.704050 GGTGCACTGGTTATTTTAACATTGTT 59.296 34.615 17.98 7.30 0.00 2.83
557 562 7.225734 GGTGCACTGGTTATTTTAACATTGTTT 59.774 33.333 17.98 0.00 0.00 2.83
558 563 9.250624 GTGCACTGGTTATTTTAACATTGTTTA 57.749 29.630 10.32 0.00 0.00 2.01
559 564 9.817809 TGCACTGGTTATTTTAACATTGTTTAA 57.182 25.926 7.45 1.90 0.00 1.52
593 598 5.570234 AAAAACTAAAAGAGGCACGAACA 57.430 34.783 0.00 0.00 0.00 3.18
594 599 5.570234 AAAACTAAAAGAGGCACGAACAA 57.430 34.783 0.00 0.00 0.00 2.83
595 600 4.547406 AACTAAAAGAGGCACGAACAAC 57.453 40.909 0.00 0.00 0.00 3.32
596 601 2.876550 ACTAAAAGAGGCACGAACAACC 59.123 45.455 0.00 0.00 0.00 3.77
597 602 1.029681 AAAAGAGGCACGAACAACCC 58.970 50.000 0.00 0.00 0.00 4.11
598 603 0.106918 AAAGAGGCACGAACAACCCA 60.107 50.000 0.00 0.00 0.00 4.51
599 604 0.818040 AAGAGGCACGAACAACCCAC 60.818 55.000 0.00 0.00 0.00 4.61
600 605 2.590575 AGGCACGAACAACCCACG 60.591 61.111 0.00 0.00 0.00 4.94
601 606 3.656045 GGCACGAACAACCCACGG 61.656 66.667 0.00 0.00 0.00 4.94
602 607 2.589442 GCACGAACAACCCACGGA 60.589 61.111 0.00 0.00 0.00 4.69
603 608 2.888998 GCACGAACAACCCACGGAC 61.889 63.158 0.00 0.00 0.00 4.79
604 609 1.521906 CACGAACAACCCACGGACA 60.522 57.895 0.00 0.00 0.00 4.02
695 700 9.965902 AGTATCACATCTAATCTTTTTGTTCCT 57.034 29.630 0.00 0.00 0.00 3.36
731 736 9.567776 TCTTTCTAGACATTTCAAATGGTTACA 57.432 29.630 14.70 0.00 0.00 2.41
733 738 9.959749 TTTCTAGACATTTCAAATGGTTACAAC 57.040 29.630 14.70 0.00 0.00 3.32
734 739 8.684386 TCTAGACATTTCAAATGGTTACAACA 57.316 30.769 14.70 0.00 0.00 3.33
735 740 9.295825 TCTAGACATTTCAAATGGTTACAACAT 57.704 29.630 14.70 0.00 0.00 2.71
738 743 8.020819 AGACATTTCAAATGGTTACAACATACG 58.979 33.333 14.70 0.00 0.00 3.06
739 744 7.087639 ACATTTCAAATGGTTACAACATACGG 58.912 34.615 14.70 0.00 0.00 4.02
740 745 6.879276 TTTCAAATGGTTACAACATACGGA 57.121 33.333 0.00 0.00 0.00 4.69
741 746 7.455641 TTTCAAATGGTTACAACATACGGAT 57.544 32.000 0.00 0.00 0.00 4.18
742 747 6.429791 TCAAATGGTTACAACATACGGATG 57.570 37.500 5.94 5.94 39.16 3.51
744 749 7.104290 TCAAATGGTTACAACATACGGATGTA 58.896 34.615 15.10 0.00 45.93 2.29
745 750 7.771361 TCAAATGGTTACAACATACGGATGTAT 59.229 33.333 15.10 8.21 45.93 2.29
760 765 7.202016 ACGGATGTATGTAGCCATATTTTTG 57.798 36.000 0.00 0.00 36.02 2.44
761 766 6.995686 ACGGATGTATGTAGCCATATTTTTGA 59.004 34.615 0.00 0.00 36.02 2.69
762 767 7.173218 ACGGATGTATGTAGCCATATTTTTGAG 59.827 37.037 0.00 0.00 36.02 3.02
763 768 7.173218 CGGATGTATGTAGCCATATTTTTGAGT 59.827 37.037 0.00 0.00 36.02 3.41
764 769 8.292448 GGATGTATGTAGCCATATTTTTGAGTG 58.708 37.037 0.00 0.00 36.02 3.51
765 770 8.752005 ATGTATGTAGCCATATTTTTGAGTGT 57.248 30.769 0.00 0.00 36.02 3.55
766 771 9.845740 ATGTATGTAGCCATATTTTTGAGTGTA 57.154 29.630 0.00 0.00 36.02 2.90
767 772 9.325198 TGTATGTAGCCATATTTTTGAGTGTAG 57.675 33.333 0.00 0.00 36.02 2.74
768 773 9.542462 GTATGTAGCCATATTTTTGAGTGTAGA 57.458 33.333 0.00 0.00 36.02 2.59
770 775 9.632638 ATGTAGCCATATTTTTGAGTGTAGATT 57.367 29.630 0.00 0.00 0.00 2.40
771 776 9.109393 TGTAGCCATATTTTTGAGTGTAGATTC 57.891 33.333 0.00 0.00 0.00 2.52
772 777 9.109393 GTAGCCATATTTTTGAGTGTAGATTCA 57.891 33.333 0.00 0.00 0.00 2.57
773 778 7.989826 AGCCATATTTTTGAGTGTAGATTCAC 58.010 34.615 0.00 0.00 38.46 3.18
775 780 8.462016 GCCATATTTTTGAGTGTAGATTCACTT 58.538 33.333 0.98 0.00 46.81 3.16
782 787 9.677567 TTTTGAGTGTAGATTCACTTATTTTGC 57.322 29.630 0.98 0.00 46.81 3.68
783 788 8.621532 TTGAGTGTAGATTCACTTATTTTGCT 57.378 30.769 0.98 0.00 46.81 3.91
784 789 8.621532 TGAGTGTAGATTCACTTATTTTGCTT 57.378 30.769 0.98 0.00 46.81 3.91
785 790 9.066892 TGAGTGTAGATTCACTTATTTTGCTTT 57.933 29.630 0.98 0.00 46.81 3.51
786 791 9.334693 GAGTGTAGATTCACTTATTTTGCTTTG 57.665 33.333 0.98 0.00 46.81 2.77
787 792 8.850156 AGTGTAGATTCACTTATTTTGCTTTGT 58.150 29.630 0.00 0.00 44.92 2.83
803 808 9.891828 TTTTGCTTTGTATATAGTCACTTGTTG 57.108 29.630 0.00 0.00 0.00 3.33
804 809 8.840833 TTGCTTTGTATATAGTCACTTGTTGA 57.159 30.769 0.00 0.00 0.00 3.18
805 810 8.840833 TGCTTTGTATATAGTCACTTGTTGAA 57.159 30.769 0.00 0.00 35.39 2.69
806 811 9.278978 TGCTTTGTATATAGTCACTTGTTGAAA 57.721 29.630 0.00 0.00 35.39 2.69
818 823 8.902806 AGTCACTTGTTGAAATGTCTAAAATGA 58.097 29.630 0.00 0.00 35.39 2.57
819 824 8.958043 GTCACTTGTTGAAATGTCTAAAATGAC 58.042 33.333 0.00 0.00 35.39 3.06
939 944 2.685017 TGCGCTCAGTCTCCCCAT 60.685 61.111 9.73 0.00 0.00 4.00
940 945 2.107953 GCGCTCAGTCTCCCCATC 59.892 66.667 0.00 0.00 0.00 3.51
941 946 2.818132 CGCTCAGTCTCCCCATCC 59.182 66.667 0.00 0.00 0.00 3.51
942 947 2.801631 CGCTCAGTCTCCCCATCCC 61.802 68.421 0.00 0.00 0.00 3.85
943 948 1.690633 GCTCAGTCTCCCCATCCCA 60.691 63.158 0.00 0.00 0.00 4.37
944 949 1.274703 GCTCAGTCTCCCCATCCCAA 61.275 60.000 0.00 0.00 0.00 4.12
945 950 1.289160 CTCAGTCTCCCCATCCCAAA 58.711 55.000 0.00 0.00 0.00 3.28
946 951 1.849039 CTCAGTCTCCCCATCCCAAAT 59.151 52.381 0.00 0.00 0.00 2.32
1401 1409 0.250038 CCGCCTGATGAGGTACATGG 60.250 60.000 0.00 0.00 42.15 3.66
1407 1415 1.486310 TGATGAGGTACATGGTCCTGC 59.514 52.381 14.24 7.82 39.56 4.85
1526 1534 1.134521 TGGTGCTGAATCGGTGATACC 60.135 52.381 0.00 0.00 34.05 2.73
1533 1541 2.167693 TGAATCGGTGATACCTGGTGTC 59.832 50.000 15.85 15.85 35.66 3.67
1723 1731 3.229276 AGAGATCAGACGTTTCAGCTG 57.771 47.619 7.63 7.63 0.00 4.24
1747 1755 0.468214 CAGCTACTCCCTCCGATCCA 60.468 60.000 0.00 0.00 0.00 3.41
1801 1809 7.282224 TCTCTACAAATTTGTACAAAGTGTGCT 59.718 33.333 31.46 18.27 42.35 4.40
1815 1823 7.322664 ACAAAGTGTGCTTCAATTAATATGGG 58.677 34.615 0.00 0.00 33.04 4.00
1820 1828 3.568007 TGCTTCAATTAATATGGGTCGGC 59.432 43.478 0.00 0.00 0.00 5.54
1944 1952 4.692228 TCTTTTGAAGTTTTGTGATGGCC 58.308 39.130 0.00 0.00 0.00 5.36
2003 2013 6.567687 TTGGTGGTCAACTTTGTACATATG 57.432 37.500 0.00 0.00 0.00 1.78
2069 2080 0.465824 GAGCTCCTGCCATGCATTCT 60.466 55.000 0.87 0.00 38.13 2.40
2104 2115 1.068127 AGCTTGGCTTGTTTTGCTCAG 59.932 47.619 0.00 0.00 33.89 3.35
2241 2252 7.564793 TGTGTATGCTTCTATAATTGACACCT 58.435 34.615 0.00 0.00 35.03 4.00
2281 2292 2.165998 AGGCCTCTTTGTTGAATGCTC 58.834 47.619 0.00 0.00 0.00 4.26
2535 2546 8.504005 CATTGAGTAAGTTTGTTTTCCGTCTAT 58.496 33.333 0.00 0.00 0.00 1.98
2536 2547 7.647907 TGAGTAAGTTTGTTTTCCGTCTATC 57.352 36.000 0.00 0.00 0.00 2.08
2976 2992 1.299976 GGAAGAGTTGCCCCACGAT 59.700 57.895 0.00 0.00 0.00 3.73
3082 3098 2.874701 CACTTGGGAGAGATTATTGGCG 59.125 50.000 0.00 0.00 0.00 5.69
3171 3188 4.887071 GTGATATGTGCCCCTATTGTTTGA 59.113 41.667 0.00 0.00 0.00 2.69
3195 3212 3.374220 TGCTGCTTTGAAATTCACCTG 57.626 42.857 0.00 0.00 0.00 4.00
3418 3436 4.201940 CCTCGAATGTCATTAAATGCTGCA 60.202 41.667 4.13 4.13 0.00 4.41
3485 3503 0.033781 TTGCTGCATTGCCAGGAAAC 59.966 50.000 1.84 0.00 39.69 2.78
3490 3508 0.667184 GCATTGCCAGGAAACAACGG 60.667 55.000 0.00 0.00 0.00 4.44
3536 3554 6.323739 ACTTGATTCCTTGCTAAAACAGGAAA 59.676 34.615 4.04 0.00 41.29 3.13
3641 3659 0.534203 TCTTCGGCTTGGTGTTGACC 60.534 55.000 0.00 0.00 43.48 4.02
3709 3727 2.457598 TCTCCGATTCTGCAGGTAAGT 58.542 47.619 15.13 0.00 0.00 2.24
3715 3733 3.667960 CGATTCTGCAGGTAAGTTGTTGC 60.668 47.826 15.13 2.28 37.09 4.17
3886 3904 9.959721 AATCTTTCATTTGTACTACCATACTGT 57.040 29.630 0.00 0.00 0.00 3.55
3893 3911 3.450817 TGTACTACCATACTGTGCATGCT 59.549 43.478 20.33 0.00 0.00 3.79
3946 3965 9.956720 GACATAAGTTTTGCATAGCATTCTTAT 57.043 29.630 13.01 13.01 38.76 1.73
3979 4081 9.603921 TTTATTATTTCCTTCTACCGTTACCAG 57.396 33.333 0.00 0.00 0.00 4.00
3988 4090 1.971481 ACCGTTACCAGTTTGTTCCC 58.029 50.000 0.00 0.00 0.00 3.97
4421 4523 0.183731 CCCTTCCCTATGGTTGCTCC 59.816 60.000 0.00 0.00 0.00 4.70
4690 4792 3.193479 GCCTTGGAAGTTATTGAACCAGG 59.807 47.826 0.00 0.00 36.08 4.45
4795 4897 6.461509 CCATGTCATTATTTCAAGGCCTTACC 60.462 42.308 20.00 0.00 39.61 2.85
4935 5037 5.954296 ACCAAGATGACATGTCAAAAGAG 57.046 39.130 31.00 21.06 43.58 2.85
4983 5085 7.256756 ACTCTGCTATTGTTTATTCATCTGC 57.743 36.000 0.00 0.00 0.00 4.26
4984 5086 7.052873 ACTCTGCTATTGTTTATTCATCTGCT 58.947 34.615 0.00 0.00 0.00 4.24
5165 5267 3.820467 TGAATTTCACTGGCAAAGATCGT 59.180 39.130 0.00 0.00 0.00 3.73
5303 5405 4.676986 GCCGCCCTATTTTCGAAAAAGAAT 60.677 41.667 25.77 12.80 0.00 2.40
5310 5412 8.555361 CCCTATTTTCGAAAAAGAATGCAAAAA 58.445 29.630 25.77 0.00 0.00 1.94
5513 5619 7.961326 AATGGTTTTGCTATTTCTCAGGTAT 57.039 32.000 0.00 0.00 0.00 2.73
5514 5620 7.961326 ATGGTTTTGCTATTTCTCAGGTATT 57.039 32.000 0.00 0.00 0.00 1.89
5538 5644 5.538118 TGAAAATTTCTCTAGCGTCAGTCA 58.462 37.500 7.29 0.00 0.00 3.41
5539 5645 5.405571 TGAAAATTTCTCTAGCGTCAGTCAC 59.594 40.000 7.29 0.00 0.00 3.67
5540 5646 3.512033 ATTTCTCTAGCGTCAGTCACC 57.488 47.619 0.00 0.00 0.00 4.02
5541 5647 2.201921 TTCTCTAGCGTCAGTCACCT 57.798 50.000 0.00 0.00 0.00 4.00
5546 5652 2.891580 TCTAGCGTCAGTCACCTTCTTT 59.108 45.455 0.00 0.00 0.00 2.52
5569 5675 0.955919 CCTTCTGGCACCGAAACCTC 60.956 60.000 0.00 0.00 0.00 3.85
5571 5677 3.423154 CTGGCACCGAAACCTCGC 61.423 66.667 0.00 0.00 44.04 5.03
5585 5691 3.609703 TCGCCAGAGAAGAGAGCC 58.390 61.111 0.00 0.00 0.00 4.70
5586 5692 2.055042 TCGCCAGAGAAGAGAGCCC 61.055 63.158 0.00 0.00 0.00 5.19
5587 5693 2.907236 GCCAGAGAAGAGAGCCCC 59.093 66.667 0.00 0.00 0.00 5.80
5588 5694 1.992277 GCCAGAGAAGAGAGCCCCA 60.992 63.158 0.00 0.00 0.00 4.96
5598 5704 1.431243 AGAGAGCCCCACTATCCTAGG 59.569 57.143 0.82 0.82 37.33 3.02
5627 5733 7.951347 ATTCATTGCCCCATTATCTATCTTC 57.049 36.000 0.00 0.00 0.00 2.87
5636 5742 3.339713 TTATCTATCTTCGGGTGGGGT 57.660 47.619 0.00 0.00 0.00 4.95
5639 5746 0.463833 CTATCTTCGGGTGGGGTTGC 60.464 60.000 0.00 0.00 0.00 4.17
5652 5759 4.467084 GTTGCAGGGGATCGCCGA 62.467 66.667 21.98 8.46 33.83 5.54
5668 5777 0.875059 CCGAAAGTCTTCCTTGGTGC 59.125 55.000 0.00 0.00 32.32 5.01
5671 5780 1.172812 AAAGTCTTCCTTGGTGCGGC 61.173 55.000 0.00 0.00 32.32 6.53
5776 5986 4.892291 GGGCGGGGTAGGATGGGA 62.892 72.222 0.00 0.00 0.00 4.37
5795 6007 0.820871 AGCATCGTGAGGAGGAAGAC 59.179 55.000 0.00 0.00 0.00 3.01
5796 6008 0.179097 GCATCGTGAGGAGGAAGACC 60.179 60.000 0.00 0.00 0.00 3.85
5797 6009 1.186200 CATCGTGAGGAGGAAGACCA 58.814 55.000 0.00 0.00 38.94 4.02
5798 6010 1.759445 CATCGTGAGGAGGAAGACCAT 59.241 52.381 0.00 0.00 38.94 3.55
5799 6011 1.186200 TCGTGAGGAGGAAGACCATG 58.814 55.000 0.00 0.00 38.94 3.66
5800 6012 1.186200 CGTGAGGAGGAAGACCATGA 58.814 55.000 0.00 0.00 38.94 3.07
5801 6013 1.550524 CGTGAGGAGGAAGACCATGAA 59.449 52.381 0.00 0.00 38.94 2.57
5802 6014 2.675317 CGTGAGGAGGAAGACCATGAAC 60.675 54.545 0.00 0.00 38.94 3.18
5805 6017 2.569404 GAGGAGGAAGACCATGAACAGT 59.431 50.000 0.00 0.00 38.94 3.55
5824 6036 4.070716 CAGTTCATGGATCTATTCTGGGC 58.929 47.826 0.00 0.00 0.00 5.36
5831 6043 1.416401 GATCTATTCTGGGCGGTTGGA 59.584 52.381 0.00 0.00 0.00 3.53
5843 6055 2.564771 GCGGTTGGATGATGATCTGAA 58.435 47.619 0.00 0.00 0.00 3.02
5857 6069 7.371159 TGATGATCTGAACGTCCATATTAGAC 58.629 38.462 4.91 0.00 0.00 2.59
5859 6071 6.504398 TGATCTGAACGTCCATATTAGACAC 58.496 40.000 0.00 0.00 33.70 3.67
5871 6083 1.996292 TTAGACACTGATGCACTCGC 58.004 50.000 0.00 0.00 39.24 5.03
5904 6116 1.482593 ACTGACAAATAGAGGCTCCCG 59.517 52.381 11.71 0.00 0.00 5.14
5907 6119 3.101437 TGACAAATAGAGGCTCCCGTTA 58.899 45.455 11.71 0.00 0.00 3.18
5916 6128 0.179153 GGCTCCCGTTACAGTACGTC 60.179 60.000 0.00 0.00 39.81 4.34
6012 6230 0.734253 GCAGATCACGACTGAAGCGT 60.734 55.000 0.00 0.00 43.67 5.07
6017 6243 2.327081 TCACGACTGAAGCGTAGTTC 57.673 50.000 0.00 0.00 40.44 3.01
6096 6322 0.252057 TACAGTACCTGCCAGGCTGA 60.252 55.000 20.99 1.28 39.63 4.26
6108 6334 0.533531 CAGGCTGACACTGCACTTGA 60.534 55.000 9.42 0.00 0.00 3.02
6215 6441 3.300388 TCAATCTTATCCTCCGACAGCT 58.700 45.455 0.00 0.00 0.00 4.24
6216 6442 4.470602 TCAATCTTATCCTCCGACAGCTA 58.529 43.478 0.00 0.00 0.00 3.32
6217 6443 4.278669 TCAATCTTATCCTCCGACAGCTAC 59.721 45.833 0.00 0.00 0.00 3.58
6218 6444 2.219458 TCTTATCCTCCGACAGCTACG 58.781 52.381 5.65 5.65 0.00 3.51
6219 6445 1.948145 CTTATCCTCCGACAGCTACGT 59.052 52.381 10.67 0.00 0.00 3.57
6220 6446 2.916702 TATCCTCCGACAGCTACGTA 57.083 50.000 10.67 0.00 0.00 3.57
6221 6447 1.307097 ATCCTCCGACAGCTACGTAC 58.693 55.000 10.67 0.00 0.00 3.67
6222 6448 0.251354 TCCTCCGACAGCTACGTACT 59.749 55.000 10.67 0.00 0.00 2.73
6223 6449 1.093159 CCTCCGACAGCTACGTACTT 58.907 55.000 10.67 0.00 0.00 2.24
6249 6475 3.625314 ACTCCCATCTCCAGAGTCC 57.375 57.895 0.00 0.00 36.06 3.85
6268 6494 4.017958 AGTCCACTCTCATCTCCTCAACTA 60.018 45.833 0.00 0.00 0.00 2.24
6269 6495 4.097286 GTCCACTCTCATCTCCTCAACTAC 59.903 50.000 0.00 0.00 0.00 2.73
6270 6496 4.017958 TCCACTCTCATCTCCTCAACTACT 60.018 45.833 0.00 0.00 0.00 2.57
6271 6497 4.709397 CCACTCTCATCTCCTCAACTACTT 59.291 45.833 0.00 0.00 0.00 2.24
6298 6524 1.014044 CGCGGCAGCTCTTCAGTTAA 61.014 55.000 7.38 0.00 42.32 2.01
6303 6529 2.489329 GGCAGCTCTTCAGTTAATGCAA 59.511 45.455 0.00 0.00 33.94 4.08
6333 6559 0.608035 ACCCGCCAACCAACTACATG 60.608 55.000 0.00 0.00 0.00 3.21
6335 6561 1.506262 CGCCAACCAACTACATGCC 59.494 57.895 0.00 0.00 0.00 4.40
6476 6702 1.152984 CCATGGCCGCCACTATCAA 60.153 57.895 16.16 0.00 35.80 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.850917 TGGGTAGGGTACTTAGGACAA 57.149 47.619 0.00 0.00 0.00 3.18
302 303 1.062121 CCCTTGATACTGAGGAGGGGA 60.062 57.143 0.00 0.00 42.73 4.81
484 489 5.924254 CGTGGTTTTAACTCTGACAGTGATA 59.076 40.000 11.37 1.21 34.56 2.15
501 506 2.428491 TGTTGAGTTGTGTCGTGGTTT 58.572 42.857 0.00 0.00 0.00 3.27
513 518 1.157870 CCAGACCGCGTTGTTGAGTT 61.158 55.000 4.92 0.00 0.00 3.01
514 519 1.594293 CCAGACCGCGTTGTTGAGT 60.594 57.895 4.92 0.00 0.00 3.41
515 520 1.594293 ACCAGACCGCGTTGTTGAG 60.594 57.895 4.92 0.00 0.00 3.02
516 521 1.885388 CACCAGACCGCGTTGTTGA 60.885 57.895 4.92 0.00 0.00 3.18
517 522 2.631428 CACCAGACCGCGTTGTTG 59.369 61.111 4.92 0.00 0.00 3.33
518 523 3.276846 GCACCAGACCGCGTTGTT 61.277 61.111 4.92 0.00 0.00 2.83
519 524 4.539083 TGCACCAGACCGCGTTGT 62.539 61.111 4.92 0.00 0.00 3.32
520 525 4.012895 GTGCACCAGACCGCGTTG 62.013 66.667 5.22 0.00 0.00 4.10
521 526 4.235762 AGTGCACCAGACCGCGTT 62.236 61.111 14.63 0.00 0.00 4.84
522 527 4.969196 CAGTGCACCAGACCGCGT 62.969 66.667 14.63 0.00 0.00 6.01
524 529 2.725203 TAACCAGTGCACCAGACCGC 62.725 60.000 14.63 0.00 0.00 5.68
525 530 0.036388 ATAACCAGTGCACCAGACCG 60.036 55.000 14.63 0.00 0.00 4.79
526 531 2.200373 AATAACCAGTGCACCAGACC 57.800 50.000 14.63 0.00 0.00 3.85
527 532 5.009210 TGTTAAAATAACCAGTGCACCAGAC 59.991 40.000 14.63 0.00 0.00 3.51
528 533 5.133941 TGTTAAAATAACCAGTGCACCAGA 58.866 37.500 14.63 0.00 0.00 3.86
529 534 5.446143 TGTTAAAATAACCAGTGCACCAG 57.554 39.130 14.63 7.78 0.00 4.00
530 535 6.183360 ACAATGTTAAAATAACCAGTGCACCA 60.183 34.615 14.63 0.00 0.00 4.17
531 536 6.220201 ACAATGTTAAAATAACCAGTGCACC 58.780 36.000 14.63 0.00 0.00 5.01
532 537 7.707774 AACAATGTTAAAATAACCAGTGCAC 57.292 32.000 9.40 9.40 0.00 4.57
533 538 9.817809 TTAAACAATGTTAAAATAACCAGTGCA 57.182 25.926 0.00 0.00 0.00 4.57
571 576 5.570234 TGTTCGTGCCTCTTTTAGTTTTT 57.430 34.783 0.00 0.00 0.00 1.94
572 577 5.337554 GTTGTTCGTGCCTCTTTTAGTTTT 58.662 37.500 0.00 0.00 0.00 2.43
573 578 4.201980 GGTTGTTCGTGCCTCTTTTAGTTT 60.202 41.667 0.00 0.00 0.00 2.66
574 579 3.314357 GGTTGTTCGTGCCTCTTTTAGTT 59.686 43.478 0.00 0.00 0.00 2.24
575 580 2.876550 GGTTGTTCGTGCCTCTTTTAGT 59.123 45.455 0.00 0.00 0.00 2.24
576 581 2.225727 GGGTTGTTCGTGCCTCTTTTAG 59.774 50.000 0.00 0.00 0.00 1.85
577 582 2.223745 GGGTTGTTCGTGCCTCTTTTA 58.776 47.619 0.00 0.00 0.00 1.52
578 583 1.029681 GGGTTGTTCGTGCCTCTTTT 58.970 50.000 0.00 0.00 0.00 2.27
579 584 0.106918 TGGGTTGTTCGTGCCTCTTT 60.107 50.000 0.00 0.00 0.00 2.52
580 585 0.818040 GTGGGTTGTTCGTGCCTCTT 60.818 55.000 0.00 0.00 0.00 2.85
581 586 1.227853 GTGGGTTGTTCGTGCCTCT 60.228 57.895 0.00 0.00 0.00 3.69
582 587 2.604174 CGTGGGTTGTTCGTGCCTC 61.604 63.158 0.00 0.00 0.00 4.70
583 588 2.590575 CGTGGGTTGTTCGTGCCT 60.591 61.111 0.00 0.00 0.00 4.75
584 589 3.656045 CCGTGGGTTGTTCGTGCC 61.656 66.667 0.00 0.00 0.00 5.01
585 590 2.589442 TCCGTGGGTTGTTCGTGC 60.589 61.111 0.00 0.00 0.00 5.34
586 591 1.090625 TTGTCCGTGGGTTGTTCGTG 61.091 55.000 0.00 0.00 0.00 4.35
587 592 0.392729 TTTGTCCGTGGGTTGTTCGT 60.393 50.000 0.00 0.00 0.00 3.85
588 593 0.733729 TTTTGTCCGTGGGTTGTTCG 59.266 50.000 0.00 0.00 0.00 3.95
589 594 2.943449 TTTTTGTCCGTGGGTTGTTC 57.057 45.000 0.00 0.00 0.00 3.18
638 643 6.582636 TCTCACATCTAACATCATTACCACC 58.417 40.000 0.00 0.00 0.00 4.61
639 644 9.935241 ATATCTCACATCTAACATCATTACCAC 57.065 33.333 0.00 0.00 0.00 4.16
705 710 9.567776 TGTAACCATTTGAAATGTCTAGAAAGA 57.432 29.630 15.93 0.00 0.00 2.52
707 712 9.959749 GTTGTAACCATTTGAAATGTCTAGAAA 57.040 29.630 15.93 0.00 0.00 2.52
708 713 9.126151 TGTTGTAACCATTTGAAATGTCTAGAA 57.874 29.630 15.93 8.86 0.00 2.10
709 714 8.684386 TGTTGTAACCATTTGAAATGTCTAGA 57.316 30.769 15.93 3.81 0.00 2.43
712 717 8.020819 CGTATGTTGTAACCATTTGAAATGTCT 58.979 33.333 15.93 5.83 0.00 3.41
713 718 7.272515 CCGTATGTTGTAACCATTTGAAATGTC 59.727 37.037 15.93 5.28 0.00 3.06
714 719 7.040340 TCCGTATGTTGTAACCATTTGAAATGT 60.040 33.333 15.93 2.12 0.00 2.71
715 720 7.309177 TCCGTATGTTGTAACCATTTGAAATG 58.691 34.615 10.84 10.84 0.00 2.32
716 721 7.455641 TCCGTATGTTGTAACCATTTGAAAT 57.544 32.000 0.00 0.00 0.00 2.17
717 722 6.879276 TCCGTATGTTGTAACCATTTGAAA 57.121 33.333 0.00 0.00 0.00 2.69
718 723 6.431543 ACATCCGTATGTTGTAACCATTTGAA 59.568 34.615 0.00 0.00 44.07 2.69
719 724 5.941058 ACATCCGTATGTTGTAACCATTTGA 59.059 36.000 0.00 0.00 44.07 2.69
720 725 6.189677 ACATCCGTATGTTGTAACCATTTG 57.810 37.500 0.00 0.00 44.07 2.32
721 726 7.925993 CATACATCCGTATGTTGTAACCATTT 58.074 34.615 0.00 0.00 46.70 2.32
722 727 7.490962 CATACATCCGTATGTTGTAACCATT 57.509 36.000 0.00 0.00 46.70 3.16
734 739 8.946085 CAAAAATATGGCTACATACATCCGTAT 58.054 33.333 0.00 0.00 42.05 3.06
735 740 8.151596 TCAAAAATATGGCTACATACATCCGTA 58.848 33.333 0.00 0.00 42.05 4.02
736 741 6.995686 TCAAAAATATGGCTACATACATCCGT 59.004 34.615 0.00 0.00 42.05 4.69
737 742 7.173218 ACTCAAAAATATGGCTACATACATCCG 59.827 37.037 0.00 0.00 42.05 4.18
738 743 8.292448 CACTCAAAAATATGGCTACATACATCC 58.708 37.037 0.00 0.00 42.05 3.51
739 744 8.840321 ACACTCAAAAATATGGCTACATACATC 58.160 33.333 0.00 0.00 42.05 3.06
740 745 8.752005 ACACTCAAAAATATGGCTACATACAT 57.248 30.769 0.00 0.00 42.05 2.29
741 746 9.325198 CTACACTCAAAAATATGGCTACATACA 57.675 33.333 0.00 0.00 42.05 2.29
742 747 9.542462 TCTACACTCAAAAATATGGCTACATAC 57.458 33.333 0.00 0.00 42.05 2.39
744 749 9.632638 AATCTACACTCAAAAATATGGCTACAT 57.367 29.630 0.00 0.00 41.13 2.29
745 750 9.109393 GAATCTACACTCAAAAATATGGCTACA 57.891 33.333 0.00 0.00 0.00 2.74
746 751 9.109393 TGAATCTACACTCAAAAATATGGCTAC 57.891 33.333 0.00 0.00 0.00 3.58
747 752 9.109393 GTGAATCTACACTCAAAAATATGGCTA 57.891 33.333 0.00 0.00 37.73 3.93
748 753 7.831193 AGTGAATCTACACTCAAAAATATGGCT 59.169 33.333 0.00 0.00 46.36 4.75
749 754 7.989826 AGTGAATCTACACTCAAAAATATGGC 58.010 34.615 0.00 0.00 46.36 4.40
777 782 9.891828 CAACAAGTGACTATATACAAAGCAAAA 57.108 29.630 0.00 0.00 0.00 2.44
778 783 9.278978 TCAACAAGTGACTATATACAAAGCAAA 57.721 29.630 0.00 0.00 0.00 3.68
779 784 8.840833 TCAACAAGTGACTATATACAAAGCAA 57.159 30.769 0.00 0.00 0.00 3.91
780 785 8.840833 TTCAACAAGTGACTATATACAAAGCA 57.159 30.769 0.00 0.00 35.39 3.91
792 797 8.902806 TCATTTTAGACATTTCAACAAGTGACT 58.097 29.630 0.00 0.00 35.39 3.41
793 798 8.958043 GTCATTTTAGACATTTCAACAAGTGAC 58.042 33.333 0.00 0.00 38.40 3.67
794 799 8.681806 TGTCATTTTAGACATTTCAACAAGTGA 58.318 29.630 0.00 0.00 43.18 3.41
795 800 8.854979 TGTCATTTTAGACATTTCAACAAGTG 57.145 30.769 0.00 0.00 43.18 3.16
796 801 9.868277 TTTGTCATTTTAGACATTTCAACAAGT 57.132 25.926 0.00 0.00 46.90 3.16
829 834 9.877178 CTATTTCACATCTACTACCTTTGTTCT 57.123 33.333 0.00 0.00 0.00 3.01
830 835 8.604890 GCTATTTCACATCTACTACCTTTGTTC 58.395 37.037 0.00 0.00 0.00 3.18
831 836 8.100791 TGCTATTTCACATCTACTACCTTTGTT 58.899 33.333 0.00 0.00 0.00 2.83
832 837 7.620880 TGCTATTTCACATCTACTACCTTTGT 58.379 34.615 0.00 0.00 0.00 2.83
833 838 8.492673 TTGCTATTTCACATCTACTACCTTTG 57.507 34.615 0.00 0.00 0.00 2.77
834 839 9.686683 AATTGCTATTTCACATCTACTACCTTT 57.313 29.630 0.00 0.00 0.00 3.11
835 840 9.331282 GAATTGCTATTTCACATCTACTACCTT 57.669 33.333 0.00 0.00 0.00 3.50
836 841 7.934120 GGAATTGCTATTTCACATCTACTACCT 59.066 37.037 0.00 0.00 0.00 3.08
837 842 7.095607 CGGAATTGCTATTTCACATCTACTACC 60.096 40.741 0.05 0.00 0.00 3.18
838 843 7.438459 ACGGAATTGCTATTTCACATCTACTAC 59.562 37.037 0.05 0.00 0.00 2.73
839 844 7.497595 ACGGAATTGCTATTTCACATCTACTA 58.502 34.615 0.05 0.00 0.00 1.82
840 845 6.349300 ACGGAATTGCTATTTCACATCTACT 58.651 36.000 0.05 0.00 0.00 2.57
939 944 1.856920 GGAGGTATGGGGAATTTGGGA 59.143 52.381 0.00 0.00 0.00 4.37
940 945 1.859574 AGGAGGTATGGGGAATTTGGG 59.140 52.381 0.00 0.00 0.00 4.12
941 946 2.158460 GGAGGAGGTATGGGGAATTTGG 60.158 54.545 0.00 0.00 0.00 3.28
942 947 2.513738 TGGAGGAGGTATGGGGAATTTG 59.486 50.000 0.00 0.00 0.00 2.32
943 948 2.785857 CTGGAGGAGGTATGGGGAATTT 59.214 50.000 0.00 0.00 0.00 1.82
944 949 2.422746 CTGGAGGAGGTATGGGGAATT 58.577 52.381 0.00 0.00 0.00 2.17
945 950 2.047742 GCTGGAGGAGGTATGGGGAAT 61.048 57.143 0.00 0.00 0.00 3.01
946 951 0.694444 GCTGGAGGAGGTATGGGGAA 60.694 60.000 0.00 0.00 0.00 3.97
1221 1229 2.392821 CGAAGCTCATCAGATTCCGAG 58.607 52.381 0.00 0.00 41.31 4.63
1224 1232 2.611225 ACCGAAGCTCATCAGATTCC 57.389 50.000 0.00 0.00 41.31 3.01
1401 1409 3.499737 CGACGGCAATGGCAGGAC 61.500 66.667 7.75 0.00 43.71 3.85
1407 1415 3.014036 CCGATTCGACGGCAATGG 58.986 61.111 7.83 0.00 46.20 3.16
1424 1432 1.492319 TACACACACGAAGCGGCAAC 61.492 55.000 1.45 0.00 0.00 4.17
1425 1433 1.218875 CTACACACACGAAGCGGCAA 61.219 55.000 1.45 0.00 0.00 4.52
1477 1485 1.510383 CTCTCACAGCCTCACCTCG 59.490 63.158 0.00 0.00 0.00 4.63
1605 1613 1.261619 GAACAACTTCACAGTCGCTGG 59.738 52.381 10.80 1.86 35.51 4.85
1723 1731 1.457009 CGGAGGGAGTAGCTGCTACC 61.457 65.000 30.49 24.85 39.83 3.18
1801 1809 3.142951 CCGCCGACCCATATTAATTGAA 58.857 45.455 0.00 0.00 0.00 2.69
1815 1823 1.027357 TATCAAGTACTCCCGCCGAC 58.973 55.000 0.00 0.00 0.00 4.79
1820 1828 8.582437 TCAATATAAGGTTATCAAGTACTCCCG 58.418 37.037 0.00 0.00 0.00 5.14
2002 2012 2.806244 GCGGAAAAAGCTAGAGAACACA 59.194 45.455 0.00 0.00 0.00 3.72
2003 2013 2.159827 CGCGGAAAAAGCTAGAGAACAC 60.160 50.000 0.00 0.00 0.00 3.32
2104 2115 2.104963 AGGACTTCCAGTTCCACTCAAC 59.895 50.000 0.00 0.00 38.89 3.18
2189 2200 1.822186 ACGCTGCCCACGTTCTTTT 60.822 52.632 0.00 0.00 41.93 2.27
2203 2214 0.173481 ATACACATCAGTCGCACGCT 59.827 50.000 0.00 0.00 0.00 5.07
2241 2252 5.420739 GGCCTTTTAGGTGGATTAAACATCA 59.579 40.000 0.00 0.00 37.80 3.07
2281 2292 7.337689 TGAGAAAGATCACAAAATGGATAGGTG 59.662 37.037 0.00 0.00 0.00 4.00
2593 2607 6.985645 AGCACTTCAGAAATGTAAAATGCAAA 59.014 30.769 0.00 0.00 0.00 3.68
2942 2958 6.670077 ACTCTTCCGCTGAAAAGATAATTC 57.330 37.500 0.00 0.00 31.45 2.17
2976 2992 0.179020 CTGGGGCACACTGACTTTCA 60.179 55.000 0.00 0.00 0.00 2.69
3082 3098 2.813754 TCTTGTGCACAGAACTAATGCC 59.186 45.455 20.59 0.00 38.63 4.40
3171 3188 4.060205 GGTGAATTTCAAAGCAGCATGTT 58.940 39.130 0.00 0.00 39.31 2.71
3195 3212 5.682862 CCGCTTAGCAATTTGTATGATCAAC 59.317 40.000 4.70 0.12 0.00 3.18
3418 3436 1.981256 AACAGCAATTCAAGTCCGGT 58.019 45.000 0.00 0.00 0.00 5.28
3485 3503 2.388121 CTTTGCTGCTTTTCTCCGTTG 58.612 47.619 0.00 0.00 0.00 4.10
3490 3508 2.880890 TGTCTCCTTTGCTGCTTTTCTC 59.119 45.455 0.00 0.00 0.00 2.87
3536 3554 7.213178 ACCTGGGATTTGAGTTATCAATACT 57.787 36.000 0.00 0.00 44.75 2.12
3641 3659 2.097466 GTGTTAAGTTCCCGGATGCATG 59.903 50.000 2.46 0.00 0.00 4.06
3642 3660 2.026262 AGTGTTAAGTTCCCGGATGCAT 60.026 45.455 0.73 0.00 0.00 3.96
3709 3727 7.264221 AGATGAAGTAACAAACAATGCAACAA 58.736 30.769 0.00 0.00 0.00 2.83
3715 3733 9.778993 CCATAGAAGATGAAGTAACAAACAATG 57.221 33.333 0.00 0.00 0.00 2.82
3886 3904 5.355071 CCTCAGATTTAACTTGTAGCATGCA 59.645 40.000 21.98 2.77 0.00 3.96
3893 3911 9.753674 AAATCATTCCCTCAGATTTAACTTGTA 57.246 29.630 0.00 0.00 39.46 2.41
3973 4075 3.673543 AAGTGGGGAACAAACTGGTAA 57.326 42.857 0.00 0.00 0.00 2.85
4421 4523 7.696992 TTTAGGTTAGAGTTGGCAAATAAGG 57.303 36.000 0.00 0.00 0.00 2.69
4690 4792 4.513318 AGAGTAGCTGCTGAAACAGTTTTC 59.487 41.667 9.82 0.00 41.49 2.29
4935 5037 2.616634 TGCAGATCTCATCCAGCTTC 57.383 50.000 0.00 0.00 33.52 3.86
5016 5118 8.410673 TCATAAACCTGGCAAAGTATGTTAAA 57.589 30.769 0.00 0.00 0.00 1.52
5089 5191 0.318441 CTTCTCGTCAGGTTGCTCCA 59.682 55.000 1.79 0.00 39.02 3.86
5153 5255 1.895798 AGAGACTGACGATCTTTGCCA 59.104 47.619 0.00 0.00 0.00 4.92
5165 5267 0.315251 CACGCTTCCACAGAGACTGA 59.685 55.000 5.76 0.00 35.18 3.41
5270 5372 2.605535 ATAGGGCGGCCTTCCTCTCA 62.606 60.000 37.40 17.02 34.75 3.27
5303 5405 2.495270 TGGCAACTCTGAAGTTTTTGCA 59.505 40.909 6.91 0.00 43.28 4.08
5310 5412 3.540211 CCGATGGCAACTCTGAAGT 57.460 52.632 0.00 0.00 37.32 3.01
5345 5447 1.550524 CTCTCGTCAAATGGACCCAGA 59.449 52.381 0.00 0.00 43.95 3.86
5513 5619 6.481976 TGACTGACGCTAGAGAAATTTTCAAA 59.518 34.615 11.53 0.00 0.00 2.69
5514 5620 5.989168 TGACTGACGCTAGAGAAATTTTCAA 59.011 36.000 11.53 0.00 0.00 2.69
5538 5644 2.443255 TGCCAGAAGGAAGAAAGAAGGT 59.557 45.455 0.00 0.00 36.89 3.50
5539 5645 2.816672 GTGCCAGAAGGAAGAAAGAAGG 59.183 50.000 0.00 0.00 36.89 3.46
5540 5646 2.816672 GGTGCCAGAAGGAAGAAAGAAG 59.183 50.000 0.00 0.00 36.89 2.85
5541 5647 2.810400 CGGTGCCAGAAGGAAGAAAGAA 60.810 50.000 0.00 0.00 36.89 2.52
5546 5652 0.762418 TTTCGGTGCCAGAAGGAAGA 59.238 50.000 0.00 0.00 36.89 2.87
5569 5675 2.498726 GGGCTCTCTTCTCTGGCG 59.501 66.667 0.00 0.00 0.00 5.69
5571 5677 0.617249 AGTGGGGCTCTCTTCTCTGG 60.617 60.000 0.00 0.00 0.00 3.86
5572 5678 2.151502 TAGTGGGGCTCTCTTCTCTG 57.848 55.000 0.00 0.00 0.00 3.35
5573 5679 2.425683 GGATAGTGGGGCTCTCTTCTCT 60.426 54.545 0.00 0.00 0.00 3.10
5577 5683 2.158234 CCTAGGATAGTGGGGCTCTCTT 60.158 54.545 1.05 0.00 36.82 2.85
5583 5689 0.105142 TCACCCTAGGATAGTGGGGC 60.105 60.000 11.48 0.00 42.12 5.80
5584 5690 2.489528 TTCACCCTAGGATAGTGGGG 57.510 55.000 11.48 0.00 44.97 4.96
5585 5691 3.973973 TGAATTCACCCTAGGATAGTGGG 59.026 47.826 11.48 0.00 46.07 4.61
5586 5692 5.832539 ATGAATTCACCCTAGGATAGTGG 57.167 43.478 11.48 0.00 36.82 4.00
5587 5693 5.471456 GCAATGAATTCACCCTAGGATAGTG 59.529 44.000 11.48 10.38 36.82 2.74
5588 5694 5.456763 GGCAATGAATTCACCCTAGGATAGT 60.457 44.000 11.48 0.00 36.82 2.12
5598 5704 4.590222 AGATAATGGGGCAATGAATTCACC 59.410 41.667 11.07 7.67 0.00 4.02
5636 5742 3.261039 TTTCGGCGATCCCCTGCAA 62.261 57.895 11.76 0.00 0.00 4.08
5639 5746 1.521681 GACTTTCGGCGATCCCCTG 60.522 63.158 11.76 0.08 0.00 4.45
5652 5759 1.172812 GCCGCACCAAGGAAGACTTT 61.173 55.000 0.00 0.00 37.29 2.66
5671 5780 1.831652 GACCATCCCTCTATGCCCCG 61.832 65.000 0.00 0.00 0.00 5.73
5776 5986 0.820871 GTCTTCCTCCTCACGATGCT 59.179 55.000 0.00 0.00 0.00 3.79
5798 6010 6.351711 CCAGAATAGATCCATGAACTGTTCA 58.648 40.000 23.94 23.94 45.01 3.18
5799 6011 5.762218 CCCAGAATAGATCCATGAACTGTTC 59.238 44.000 13.49 13.49 34.58 3.18
5800 6012 5.688807 CCCAGAATAGATCCATGAACTGTT 58.311 41.667 0.00 0.00 0.00 3.16
5801 6013 4.445448 GCCCAGAATAGATCCATGAACTGT 60.445 45.833 0.00 0.00 0.00 3.55
5802 6014 4.070716 GCCCAGAATAGATCCATGAACTG 58.929 47.826 0.00 0.00 0.00 3.16
5805 6017 2.038952 CCGCCCAGAATAGATCCATGAA 59.961 50.000 0.00 0.00 0.00 2.57
5821 6033 0.109342 AGATCATCATCCAACCGCCC 59.891 55.000 0.00 0.00 0.00 6.13
5824 6036 2.541346 CGTTCAGATCATCATCCAACCG 59.459 50.000 0.00 0.00 0.00 4.44
5831 6043 8.031864 GTCTAATATGGACGTTCAGATCATCAT 58.968 37.037 4.04 0.00 0.00 2.45
5843 6055 4.099419 TGCATCAGTGTCTAATATGGACGT 59.901 41.667 0.00 0.00 36.58 4.34
5857 6069 2.693797 AAAAAGCGAGTGCATCAGTG 57.306 45.000 0.00 0.00 46.23 3.66
5916 6128 0.389948 AACCGAGCCTTGACGCTTAG 60.390 55.000 0.00 0.00 39.87 2.18
6012 6230 4.159693 ACGGCACTGTATCTCAATGAACTA 59.840 41.667 0.00 0.00 0.00 2.24
6017 6243 1.854743 CGACGGCACTGTATCTCAATG 59.145 52.381 0.00 0.00 0.00 2.82
6108 6334 1.447317 GCGGACGAAATGGATGGCAT 61.447 55.000 0.00 0.00 0.00 4.40
6189 6415 6.294361 TGTCGGAGGATAAGATTGAAAAGA 57.706 37.500 0.00 0.00 0.00 2.52
6215 6441 6.435277 AGATGGGAGTCAAACTAAAGTACGTA 59.565 38.462 0.00 0.00 0.00 3.57
6216 6442 4.942761 TGGGAGTCAAACTAAAGTACGT 57.057 40.909 0.00 0.00 0.00 3.57
6217 6443 5.721232 AGATGGGAGTCAAACTAAAGTACG 58.279 41.667 0.00 0.00 0.00 3.67
6218 6444 6.107343 GGAGATGGGAGTCAAACTAAAGTAC 58.893 44.000 0.00 0.00 0.00 2.73
6219 6445 5.783360 TGGAGATGGGAGTCAAACTAAAGTA 59.217 40.000 0.00 0.00 0.00 2.24
6220 6446 4.597507 TGGAGATGGGAGTCAAACTAAAGT 59.402 41.667 0.00 0.00 0.00 2.66
6221 6447 5.046304 TCTGGAGATGGGAGTCAAACTAAAG 60.046 44.000 0.00 0.00 0.00 1.85
6222 6448 4.844085 TCTGGAGATGGGAGTCAAACTAAA 59.156 41.667 0.00 0.00 0.00 1.85
6223 6449 4.425772 TCTGGAGATGGGAGTCAAACTAA 58.574 43.478 0.00 0.00 0.00 2.24
6249 6475 5.913137 AAGTAGTTGAGGAGATGAGAGTG 57.087 43.478 0.00 0.00 0.00 3.51
6298 6524 4.383602 GTGGCGCGAACGTTGCAT 62.384 61.111 12.10 0.00 42.83 3.96


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

AutoCloner maintained by Alex Coulton.