Multiple sequence alignment - TraesCS4D01G173500

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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 TraesCS4D01G173500 chr4D 100.000 6683 0 0 1 6683 301510292 301516974 0.000000e+00 12342.0
1 TraesCS4D01G173500 chr4D 100.000 48 0 0 4397 4444 301514640 301514687 9.230000e-14 89.8
2 TraesCS4D01G173500 chr4D 100.000 48 0 0 4349 4396 301514688 301514735 9.230000e-14 89.8
3 TraesCS4D01G173500 chr4B 97.120 3507 48 9 899 4396 375391651 375395113 0.000000e+00 5867.0
4 TraesCS4D01G173500 chr4B 97.717 657 13 1 5493 6149 375396245 375396899 0.000000e+00 1129.0
5 TraesCS4D01G173500 chr4B 97.966 639 9 4 4859 5495 375395497 375396133 0.000000e+00 1105.0
6 TraesCS4D01G173500 chr4B 97.732 529 10 2 6157 6683 375410703 375411231 0.000000e+00 909.0
7 TraesCS4D01G173500 chr4B 97.691 433 9 1 4397 4829 375395066 375395497 0.000000e+00 743.0
8 TraesCS4D01G173500 chr4B 95.062 81 4 0 768 848 375391557 375391637 1.960000e-25 128.0
9 TraesCS4D01G173500 chr4A 96.296 2241 72 10 2160 4396 179550106 179547873 0.000000e+00 3668.0
10 TraesCS4D01G173500 chr4A 95.118 2294 59 11 4397 6683 179547920 179545673 0.000000e+00 3567.0
11 TraesCS4D01G173500 chr4A 93.173 1084 37 12 819 1884 179551798 179550734 0.000000e+00 1557.0
12 TraesCS4D01G173500 chr4A 90.391 281 15 5 1882 2162 179550631 179550363 6.370000e-95 359.0
13 TraesCS4D01G173500 chr3D 78.490 702 85 39 102 750 533681072 533680384 3.750000e-107 399.0
14 TraesCS4D01G173500 chr3D 83.750 320 43 9 444 757 513611794 513612110 1.820000e-75 294.0
15 TraesCS4D01G173500 chr3D 83.699 319 43 9 444 757 7067959 7067645 6.560000e-75 292.0
16 TraesCS4D01G173500 chr3D 78.774 212 36 4 100 310 450240967 450241170 4.200000e-27 134.0
17 TraesCS4D01G173500 chr3D 93.103 87 4 2 319 404 28325070 28325155 7.040000e-25 126.0
18 TraesCS4D01G173500 chr3D 91.209 91 5 3 319 407 179463784 179463695 3.270000e-23 121.0
19 TraesCS4D01G173500 chr2A 80.786 458 59 25 319 754 729181439 729180989 1.390000e-86 331.0
20 TraesCS4D01G173500 chr2A 94.737 38 0 2 5142 5179 31013856 31013821 2.600000e-04 58.4
21 TraesCS4D01G173500 chr6A 84.494 316 40 9 444 754 61190877 61191188 3.030000e-78 303.0
22 TraesCS4D01G173500 chr6A 84.566 311 41 7 444 750 539166916 539167223 1.090000e-77 302.0
23 TraesCS4D01G173500 chr7D 84.615 312 38 9 445 750 64511324 64511631 1.090000e-77 302.0
24 TraesCS4D01G173500 chr7D 82.629 213 32 3 100 310 92760529 92760738 4.120000e-42 183.0
25 TraesCS4D01G173500 chr7D 81.132 212 37 3 100 310 618173668 618173459 4.150000e-37 167.0
26 TraesCS4D01G173500 chr1B 79.443 467 58 22 319 777 16922964 16923400 5.070000e-76 296.0
27 TraesCS4D01G173500 chr6B 75.664 715 106 32 111 767 498865406 498864702 1.820000e-75 294.0
28 TraesCS4D01G173500 chr6B 80.573 314 52 9 410 716 626881641 626881330 4.030000e-57 233.0
29 TraesCS4D01G173500 chr5D 82.698 341 48 10 432 766 544788440 544788775 6.560000e-75 292.0
30 TraesCS4D01G173500 chr5D 82.583 333 49 8 438 766 454029867 454029540 1.100000e-72 285.0
31 TraesCS4D01G173500 chr3B 74.702 755 116 44 1 710 631516842 631517566 3.970000e-67 267.0
32 TraesCS4D01G173500 chr3B 85.714 133 14 4 100 231 512805167 512805039 1.170000e-27 135.0
33 TraesCS4D01G173500 chr2D 79.739 306 41 14 319 605 61007394 61007091 1.140000e-47 202.0
34 TraesCS4D01G173500 chr2D 90.000 80 6 2 409 487 629376755 629376833 1.190000e-17 102.0
35 TraesCS4D01G173500 chrUn 81.944 216 29 7 97 308 86806387 86806596 2.480000e-39 174.0
36 TraesCS4D01G173500 chrUn 80.952 168 20 9 319 476 98199917 98200082 9.100000e-24 122.0
37 TraesCS4D01G173500 chr1D 83.000 200 27 4 111 310 466476805 466476997 2.480000e-39 174.0
38 TraesCS4D01G173500 chr1D 79.888 179 13 16 319 476 391235604 391235780 7.090000e-20 110.0
39 TraesCS4D01G173500 chr7A 78.648 281 41 14 319 582 156271883 156272161 1.150000e-37 169.0
40 TraesCS4D01G173500 chr7A 76.875 320 56 14 1 310 716249451 716249762 1.490000e-36 165.0
41 TraesCS4D01G173500 chr7A 81.609 174 12 13 319 474 205182549 205182378 7.040000e-25 126.0
42 TraesCS4D01G173500 chr6D 84.146 164 10 13 319 471 461506802 461506960 1.940000e-30 145.0
43 TraesCS4D01G173500 chr5A 75.385 325 62 12 1 310 637616586 637616265 2.510000e-29 141.0
44 TraesCS4D01G173500 chr1A 82.036 167 22 4 319 477 50961341 50961175 1.170000e-27 135.0
45 TraesCS4D01G173500 chr2B 77.489 231 42 10 86 310 449954808 449954582 5.440000e-26 130.0
46 TraesCS4D01G173500 chr3A 92.135 89 6 1 319 407 130834054 130833967 2.530000e-24 124.0


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 TraesCS4D01G173500 chr4D 301510292 301516974 6682 False 4173.866667 12342 100.0000 1 6683 3 chr4D.!!$F1 6682
1 TraesCS4D01G173500 chr4B 375391557 375396899 5342 False 1794.400000 5867 97.1112 768 6149 5 chr4B.!!$F2 5381
2 TraesCS4D01G173500 chr4B 375410703 375411231 528 False 909.000000 909 97.7320 6157 6683 1 chr4B.!!$F1 526
3 TraesCS4D01G173500 chr4A 179545673 179551798 6125 True 2287.750000 3668 93.7445 819 6683 4 chr4A.!!$R1 5864
4 TraesCS4D01G173500 chr3D 533680384 533681072 688 True 399.000000 399 78.4900 102 750 1 chr3D.!!$R3 648
5 TraesCS4D01G173500 chr6B 498864702 498865406 704 True 294.000000 294 75.6640 111 767 1 chr6B.!!$R1 656
6 TraesCS4D01G173500 chr3B 631516842 631517566 724 False 267.000000 267 74.7020 1 710 1 chr3B.!!$F1 709

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
600 671 0.026027 GCTTTGAAGATCTCTGCGCG 59.974 55.000 0.00 0.00 0.00 6.86 F
738 809 0.034756 ATGTAGTGCGCCACTTGTCA 59.965 50.000 15.81 13.05 42.59 3.58 F
1059 1138 0.105709 CCCCTCTCTTCTCCTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30 F
2790 3332 0.404040 CCCTTGTAAGTTCAGGCCCA 59.596 55.000 0.00 0.00 0.00 5.36 F
3023 3565 0.250295 TTGACCTTGTTCCTGGCTCG 60.250 55.000 0.00 0.00 0.00 5.03 F
4122 4667 0.380378 TCTTTGCTGCAACGAACCAC 59.620 50.000 17.78 0.00 0.00 4.16 F
4387 4932 1.471119 CAGCATGCCAATCTCCTTGT 58.529 50.000 15.66 0.00 32.61 3.16 F
4388 4933 1.822990 CAGCATGCCAATCTCCTTGTT 59.177 47.619 15.66 0.00 32.61 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 2350 1.135199 CAAGTGATTGGTGGATGCTGC 60.135 52.381 0.00 0.00 0.00 5.25 R
2364 2901 1.340889 GCAACAGGGAACATTGCTGAA 59.659 47.619 1.06 0.00 45.86 3.02 R
2983 3525 1.361793 TACGCACGGTTTAATCAGGC 58.638 50.000 0.00 0.00 0.00 4.85 R
4367 4912 0.102481 CAAGGAGATTGGCATGCTGC 59.898 55.000 18.92 2.02 44.08 5.25 R
4368 4913 1.471119 ACAAGGAGATTGGCATGCTG 58.529 50.000 18.92 6.95 43.68 4.41 R
5061 5607 0.601057 CGGGGCCAAACGAAATCTTT 59.399 50.000 4.39 0.00 0.00 2.52 R
5281 5828 1.202687 TCAGTCACCTCTTTGGCAGTG 60.203 52.381 0.00 0.00 40.22 3.66 R
6049 6714 2.177594 CTCCAGTGCTCCACCTCCAC 62.178 65.000 0.00 0.00 34.49 4.02 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 9.541724 GCTTTTTCTAACTTTTTGGTTTTTCAG 57.458 29.630 0.00 0.00 0.00 3.02
36 37 6.197364 TCTAACTTTTTGGTTTTTCAGCGA 57.803 33.333 0.00 0.00 0.00 4.93
47 48 4.437524 GGTTTTTCAGCGATCTTCCTTAGC 60.438 45.833 0.00 0.00 0.00 3.09
48 49 2.604046 TTCAGCGATCTTCCTTAGCC 57.396 50.000 0.00 0.00 0.00 3.93
55 56 3.745797 GCGATCTTCCTTAGCCTTTGGAT 60.746 47.826 0.00 0.00 0.00 3.41
59 61 4.589908 TCTTCCTTAGCCTTTGGATCAAC 58.410 43.478 0.00 0.00 0.00 3.18
61 63 4.657814 TCCTTAGCCTTTGGATCAACTT 57.342 40.909 0.00 0.00 0.00 2.66
139 142 0.110192 GGTTTTGCTTTCGCGAGAGG 60.110 55.000 25.84 13.55 43.69 3.69
142 145 0.955428 TTTGCTTTCGCGAGAGGCAT 60.955 50.000 25.84 0.00 45.05 4.40
144 147 1.811266 GCTTTCGCGAGAGGCATGA 60.811 57.895 25.84 0.00 43.84 3.07
147 150 2.166130 TTTCGCGAGAGGCATGACCA 62.166 55.000 9.59 0.00 43.84 4.02
196 222 9.701355 AACGCATTTTCTGTTTTATTTTTCTTG 57.299 25.926 0.00 0.00 0.00 3.02
200 226 5.898630 TTCTGTTTTATTTTTCTTGCGCC 57.101 34.783 4.18 0.00 0.00 6.53
201 227 3.978217 TCTGTTTTATTTTTCTTGCGCCG 59.022 39.130 4.18 0.00 0.00 6.46
203 229 2.355717 TTTATTTTTCTTGCGCCGGG 57.644 45.000 4.18 0.00 0.00 5.73
227 253 1.626654 CGGTTGTGCTTTCGCGAGAT 61.627 55.000 9.59 0.00 41.60 2.75
228 254 0.179215 GGTTGTGCTTTCGCGAGATG 60.179 55.000 9.59 4.76 41.60 2.90
232 258 1.667510 TGCTTTCGCGAGATGCACA 60.668 52.632 22.30 9.61 46.97 4.57
255 281 1.439679 GTGCCTCTCGAAAACGGAAT 58.560 50.000 0.00 0.00 0.00 3.01
267 297 4.656262 CGAAAACGGAATAAACGCGTTTTG 60.656 41.667 38.53 24.64 41.48 2.44
271 301 2.648431 CGGAATAAACGCGTTTTGTGTC 59.352 45.455 38.53 27.34 41.44 3.67
310 340 2.594962 CGGTTGTGCTTTCGCGAGT 61.595 57.895 9.59 0.00 39.65 4.18
312 342 1.722507 GTTGTGCTTTCGCGAGTGC 60.723 57.895 22.64 22.64 39.65 4.40
314 344 3.044305 GTGCTTTCGCGAGTGCCT 61.044 61.111 25.08 0.00 39.65 4.75
317 365 2.448705 GCTTTCGCGAGTGCCTCTC 61.449 63.158 20.00 0.00 38.08 3.20
361 416 1.215647 CTTTCGCTAGAGGCACGGT 59.784 57.895 0.00 0.00 41.91 4.83
495 566 2.225491 CGACCATGCCTCTTTCGAAAAA 59.775 45.455 12.41 0.00 0.00 1.94
522 593 3.662247 AAAACGTCCTCTCGATTCAGT 57.338 42.857 0.00 0.00 34.70 3.41
523 594 3.662247 AAACGTCCTCTCGATTCAGTT 57.338 42.857 0.00 0.00 34.70 3.16
524 595 3.662247 AACGTCCTCTCGATTCAGTTT 57.338 42.857 0.00 0.00 34.70 2.66
525 596 3.662247 ACGTCCTCTCGATTCAGTTTT 57.338 42.857 0.00 0.00 34.70 2.43
526 597 3.991367 ACGTCCTCTCGATTCAGTTTTT 58.009 40.909 0.00 0.00 34.70 1.94
544 615 3.936902 TTTTCGTCCTGTTTCTTCGTG 57.063 42.857 0.00 0.00 0.00 4.35
545 616 2.875087 TTCGTCCTGTTTCTTCGTGA 57.125 45.000 0.00 0.00 0.00 4.35
546 617 2.875087 TCGTCCTGTTTCTTCGTGAA 57.125 45.000 0.00 0.00 0.00 3.18
547 618 3.167921 TCGTCCTGTTTCTTCGTGAAA 57.832 42.857 3.10 3.10 41.85 2.69
548 619 3.523547 TCGTCCTGTTTCTTCGTGAAAA 58.476 40.909 7.64 0.00 45.10 2.29
549 620 3.933955 TCGTCCTGTTTCTTCGTGAAAAA 59.066 39.130 7.64 3.16 45.10 1.94
573 644 8.519492 AAAATTCGTCAAAACCTATCAACATG 57.481 30.769 0.00 0.00 0.00 3.21
574 645 5.621197 TTCGTCAAAACCTATCAACATGG 57.379 39.130 0.00 0.00 0.00 3.66
575 646 4.006989 TCGTCAAAACCTATCAACATGGG 58.993 43.478 0.00 0.00 36.68 4.00
576 647 4.006989 CGTCAAAACCTATCAACATGGGA 58.993 43.478 0.00 0.00 34.16 4.37
577 648 4.640201 CGTCAAAACCTATCAACATGGGAT 59.360 41.667 0.00 2.37 34.16 3.85
578 649 5.220854 CGTCAAAACCTATCAACATGGGATC 60.221 44.000 5.52 0.00 34.16 3.36
579 650 5.888161 GTCAAAACCTATCAACATGGGATCT 59.112 40.000 5.52 0.00 34.16 2.75
580 651 7.054124 GTCAAAACCTATCAACATGGGATCTA 58.946 38.462 5.52 0.00 34.16 1.98
581 652 7.227512 GTCAAAACCTATCAACATGGGATCTAG 59.772 40.741 5.52 0.40 34.16 2.43
582 653 4.899352 ACCTATCAACATGGGATCTAGC 57.101 45.455 5.52 0.00 34.16 3.42
583 654 4.497516 ACCTATCAACATGGGATCTAGCT 58.502 43.478 5.52 0.00 34.16 3.32
584 655 4.910304 ACCTATCAACATGGGATCTAGCTT 59.090 41.667 5.52 0.00 34.16 3.74
585 656 5.370880 ACCTATCAACATGGGATCTAGCTTT 59.629 40.000 5.52 0.00 34.16 3.51
586 657 5.704515 CCTATCAACATGGGATCTAGCTTTG 59.295 44.000 5.52 0.00 32.06 2.77
587 658 4.842531 TCAACATGGGATCTAGCTTTGA 57.157 40.909 0.00 0.00 0.00 2.69
588 659 5.178096 TCAACATGGGATCTAGCTTTGAA 57.822 39.130 0.00 0.00 0.00 2.69
589 660 5.188434 TCAACATGGGATCTAGCTTTGAAG 58.812 41.667 0.00 0.00 0.00 3.02
590 661 5.045651 TCAACATGGGATCTAGCTTTGAAGA 60.046 40.000 0.00 0.00 0.00 2.87
591 662 5.643421 ACATGGGATCTAGCTTTGAAGAT 57.357 39.130 0.00 0.00 35.15 2.40
592 663 5.619220 ACATGGGATCTAGCTTTGAAGATC 58.381 41.667 13.66 13.66 44.88 2.75
593 664 5.369110 ACATGGGATCTAGCTTTGAAGATCT 59.631 40.000 19.05 0.00 44.94 2.75
594 665 5.543507 TGGGATCTAGCTTTGAAGATCTC 57.456 43.478 19.05 16.99 45.96 2.75
595 666 5.215069 TGGGATCTAGCTTTGAAGATCTCT 58.785 41.667 20.00 0.00 45.94 3.10
596 667 5.070180 TGGGATCTAGCTTTGAAGATCTCTG 59.930 44.000 20.00 0.00 45.94 3.35
597 668 4.990426 GGATCTAGCTTTGAAGATCTCTGC 59.010 45.833 19.05 4.16 44.94 4.26
598 669 4.039151 TCTAGCTTTGAAGATCTCTGCG 57.961 45.455 0.00 0.00 0.00 5.18
599 670 1.367659 AGCTTTGAAGATCTCTGCGC 58.632 50.000 0.00 0.00 0.00 6.09
600 671 0.026027 GCTTTGAAGATCTCTGCGCG 59.974 55.000 0.00 0.00 0.00 6.86
601 672 1.633561 CTTTGAAGATCTCTGCGCGA 58.366 50.000 12.10 1.90 0.00 5.87
602 673 1.587490 CTTTGAAGATCTCTGCGCGAG 59.413 52.381 12.10 18.94 41.30 5.03
603 674 0.179127 TTGAAGATCTCTGCGCGAGG 60.179 55.000 22.70 0.20 40.30 4.63
604 675 1.032114 TGAAGATCTCTGCGCGAGGA 61.032 55.000 22.70 12.51 40.30 3.71
605 676 0.101399 GAAGATCTCTGCGCGAGGAA 59.899 55.000 22.70 10.08 40.30 3.36
606 677 0.749649 AAGATCTCTGCGCGAGGAAT 59.250 50.000 22.70 13.50 40.30 3.01
607 678 0.313672 AGATCTCTGCGCGAGGAATC 59.686 55.000 22.70 19.07 40.30 2.52
608 679 0.665972 GATCTCTGCGCGAGGAATCC 60.666 60.000 22.70 0.00 40.30 3.01
609 680 1.395045 ATCTCTGCGCGAGGAATCCA 61.395 55.000 22.70 8.36 40.30 3.41
610 681 1.153568 CTCTGCGCGAGGAATCCAA 60.154 57.895 12.10 0.00 36.06 3.53
611 682 0.531532 CTCTGCGCGAGGAATCCAAT 60.532 55.000 12.10 0.00 36.06 3.16
612 683 0.811219 TCTGCGCGAGGAATCCAATG 60.811 55.000 12.10 0.00 0.00 2.82
613 684 0.811219 CTGCGCGAGGAATCCAATGA 60.811 55.000 12.10 0.00 0.00 2.57
614 685 0.179048 TGCGCGAGGAATCCAATGAT 60.179 50.000 12.10 0.00 0.00 2.45
615 686 0.236711 GCGCGAGGAATCCAATGATG 59.763 55.000 12.10 0.00 0.00 3.07
616 687 1.869774 CGCGAGGAATCCAATGATGA 58.130 50.000 0.00 0.00 0.00 2.92
617 688 2.212652 CGCGAGGAATCCAATGATGAA 58.787 47.619 0.00 0.00 0.00 2.57
618 689 2.613595 CGCGAGGAATCCAATGATGAAA 59.386 45.455 0.00 0.00 0.00 2.69
619 690 3.065233 CGCGAGGAATCCAATGATGAAAA 59.935 43.478 0.00 0.00 0.00 2.29
620 691 4.354587 GCGAGGAATCCAATGATGAAAAC 58.645 43.478 0.61 0.00 0.00 2.43
621 692 4.591202 CGAGGAATCCAATGATGAAAACG 58.409 43.478 0.61 0.00 0.00 3.60
622 693 4.496341 CGAGGAATCCAATGATGAAAACGG 60.496 45.833 0.61 0.00 0.00 4.44
623 694 4.344104 AGGAATCCAATGATGAAAACGGT 58.656 39.130 0.61 0.00 0.00 4.83
624 695 4.772100 AGGAATCCAATGATGAAAACGGTT 59.228 37.500 0.61 0.00 0.00 4.44
625 696 5.102313 GGAATCCAATGATGAAAACGGTTC 58.898 41.667 0.00 0.00 0.00 3.62
626 697 5.336372 GGAATCCAATGATGAAAACGGTTCA 60.336 40.000 6.30 6.30 0.00 3.18
627 698 5.720371 ATCCAATGATGAAAACGGTTCAA 57.280 34.783 7.74 0.00 31.55 2.69
628 699 5.119931 TCCAATGATGAAAACGGTTCAAG 57.880 39.130 7.74 0.00 31.55 3.02
629 700 4.824537 TCCAATGATGAAAACGGTTCAAGA 59.175 37.500 7.74 0.00 31.55 3.02
630 701 5.476599 TCCAATGATGAAAACGGTTCAAGAT 59.523 36.000 7.74 1.56 31.55 2.40
631 702 5.801947 CCAATGATGAAAACGGTTCAAGATC 59.198 40.000 7.74 3.02 31.55 2.75
632 703 6.349611 CCAATGATGAAAACGGTTCAAGATCT 60.350 38.462 7.74 0.00 31.55 2.75
633 704 5.611796 TGATGAAAACGGTTCAAGATCTG 57.388 39.130 7.74 0.00 31.55 2.90
634 705 5.304778 TGATGAAAACGGTTCAAGATCTGA 58.695 37.500 7.74 0.00 31.55 3.27
635 706 5.762711 TGATGAAAACGGTTCAAGATCTGAA 59.237 36.000 7.74 0.00 41.93 3.02
647 718 7.815840 TTCAAGATCTGAACACATGGTTTAA 57.184 32.000 0.00 0.00 40.63 1.52
648 719 7.815840 TCAAGATCTGAACACATGGTTTAAA 57.184 32.000 0.00 0.00 40.63 1.52
649 720 8.231692 TCAAGATCTGAACACATGGTTTAAAA 57.768 30.769 0.00 0.00 40.63 1.52
650 721 8.352201 TCAAGATCTGAACACATGGTTTAAAAG 58.648 33.333 0.00 0.00 40.63 2.27
651 722 8.352201 CAAGATCTGAACACATGGTTTAAAAGA 58.648 33.333 0.00 2.45 40.63 2.52
652 723 8.641498 AGATCTGAACACATGGTTTAAAAGAT 57.359 30.769 0.00 6.47 40.63 2.40
653 724 9.739276 AGATCTGAACACATGGTTTAAAAGATA 57.261 29.630 0.00 0.00 40.63 1.98
682 753 8.739193 CATTCTGAATAAACGAATGTACGAAG 57.261 34.615 1.98 0.00 39.25 3.79
683 754 8.592155 CATTCTGAATAAACGAATGTACGAAGA 58.408 33.333 1.98 0.00 39.25 2.87
684 755 8.523523 TTCTGAATAAACGAATGTACGAAGAA 57.476 30.769 0.00 0.00 37.03 2.52
685 756 8.523523 TCTGAATAAACGAATGTACGAAGAAA 57.476 30.769 0.00 0.00 37.03 2.52
686 757 8.980610 TCTGAATAAACGAATGTACGAAGAAAA 58.019 29.630 0.00 0.00 37.03 2.29
687 758 9.588774 CTGAATAAACGAATGTACGAAGAAAAA 57.411 29.630 0.00 0.00 37.03 1.94
688 759 9.588774 TGAATAAACGAATGTACGAAGAAAAAG 57.411 29.630 0.00 0.00 37.03 2.27
689 760 9.801714 GAATAAACGAATGTACGAAGAAAAAGA 57.198 29.630 0.00 0.00 37.03 2.52
692 763 8.898983 AAACGAATGTACGAAGAAAAAGAAAA 57.101 26.923 0.00 0.00 37.03 2.29
693 764 8.898983 AACGAATGTACGAAGAAAAAGAAAAA 57.101 26.923 0.00 0.00 37.03 1.94
694 765 8.543071 ACGAATGTACGAAGAAAAAGAAAAAG 57.457 30.769 0.00 0.00 37.03 2.27
695 766 8.179615 ACGAATGTACGAAGAAAAAGAAAAAGT 58.820 29.630 0.00 0.00 37.03 2.66
696 767 8.670668 CGAATGTACGAAGAAAAAGAAAAAGTC 58.329 33.333 0.00 0.00 35.09 3.01
697 768 9.717892 GAATGTACGAAGAAAAAGAAAAAGTCT 57.282 29.630 0.00 0.00 38.69 3.24
698 769 9.717892 AATGTACGAAGAAAAAGAAAAAGTCTC 57.282 29.630 0.00 0.00 34.56 3.36
699 770 8.259049 TGTACGAAGAAAAAGAAAAAGTCTCA 57.741 30.769 0.00 0.00 34.56 3.27
700 771 8.388103 TGTACGAAGAAAAAGAAAAAGTCTCAG 58.612 33.333 0.00 0.00 34.56 3.35
701 772 6.786207 ACGAAGAAAAAGAAAAAGTCTCAGG 58.214 36.000 0.00 0.00 34.56 3.86
702 773 6.374613 ACGAAGAAAAAGAAAAAGTCTCAGGT 59.625 34.615 0.00 0.00 34.56 4.00
703 774 7.094334 ACGAAGAAAAAGAAAAAGTCTCAGGTT 60.094 33.333 0.00 0.00 34.56 3.50
704 775 7.218963 CGAAGAAAAAGAAAAAGTCTCAGGTTG 59.781 37.037 0.00 0.00 34.56 3.77
705 776 6.333416 AGAAAAAGAAAAAGTCTCAGGTTGC 58.667 36.000 0.00 0.00 34.56 4.17
706 777 3.971032 AAGAAAAAGTCTCAGGTTGCG 57.029 42.857 0.00 0.00 34.56 4.85
707 778 3.194005 AGAAAAAGTCTCAGGTTGCGA 57.806 42.857 0.00 0.00 0.00 5.10
708 779 2.872858 AGAAAAAGTCTCAGGTTGCGAC 59.127 45.455 0.00 0.00 32.62 5.19
709 780 2.325583 AAAAGTCTCAGGTTGCGACA 57.674 45.000 6.39 0.00 34.75 4.35
710 781 1.871080 AAAGTCTCAGGTTGCGACAG 58.129 50.000 6.39 0.00 34.75 3.51
711 782 0.601311 AAGTCTCAGGTTGCGACAGC 60.601 55.000 6.39 0.00 45.41 4.40
734 805 3.578456 GCATGTAGTGCGCCACTT 58.422 55.556 15.81 2.77 42.59 3.16
735 806 1.135315 GCATGTAGTGCGCCACTTG 59.865 57.895 15.81 14.00 42.59 3.16
736 807 1.577328 GCATGTAGTGCGCCACTTGT 61.577 55.000 15.81 2.90 42.59 3.16
737 808 0.443869 CATGTAGTGCGCCACTTGTC 59.556 55.000 15.81 9.08 42.59 3.18
738 809 0.034756 ATGTAGTGCGCCACTTGTCA 59.965 50.000 15.81 13.05 42.59 3.58
739 810 0.878523 TGTAGTGCGCCACTTGTCAC 60.879 55.000 15.81 9.67 42.59 3.67
740 811 0.878523 GTAGTGCGCCACTTGTCACA 60.879 55.000 15.81 0.00 42.59 3.58
741 812 0.179070 TAGTGCGCCACTTGTCACAA 60.179 50.000 15.81 0.00 42.59 3.33
742 813 1.298339 GTGCGCCACTTGTCACAAC 60.298 57.895 4.18 0.00 0.00 3.32
743 814 2.331451 GCGCCACTTGTCACAACC 59.669 61.111 0.00 0.00 0.00 3.77
744 815 2.186826 GCGCCACTTGTCACAACCT 61.187 57.895 0.00 0.00 0.00 3.50
745 816 1.648720 CGCCACTTGTCACAACCTG 59.351 57.895 0.00 0.00 0.00 4.00
746 817 0.813610 CGCCACTTGTCACAACCTGA 60.814 55.000 0.00 0.00 0.00 3.86
747 818 0.947244 GCCACTTGTCACAACCTGAG 59.053 55.000 0.00 0.00 0.00 3.35
748 819 1.597742 CCACTTGTCACAACCTGAGG 58.402 55.000 0.00 0.00 0.00 3.86
749 820 1.140852 CCACTTGTCACAACCTGAGGA 59.859 52.381 4.99 0.00 0.00 3.71
750 821 2.487934 CACTTGTCACAACCTGAGGAG 58.512 52.381 4.99 0.00 0.00 3.69
751 822 1.417890 ACTTGTCACAACCTGAGGAGG 59.582 52.381 4.99 0.00 46.21 4.30
769 840 3.795688 AGGTGAGCCTGATCTTTTGAA 57.204 42.857 0.00 0.00 45.05 2.69
791 862 7.663827 TGAAAGAAGTAGTGATTTCGACCTAA 58.336 34.615 0.00 0.00 35.01 2.69
832 903 1.136828 TGTTAGGGTGTGAACAGGCT 58.863 50.000 0.00 0.00 31.98 4.58
864 936 1.935300 GCCCGTGGATAATAGCACTCG 60.935 57.143 0.00 0.00 0.00 4.18
1059 1138 0.105709 CCCCTCTCTTCTCCTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
1067 1146 0.266152 TTCTCCTCCTCCTCATCCCC 59.734 60.000 0.00 0.00 0.00 4.81
1068 1147 0.631998 TCTCCTCCTCCTCATCCCCT 60.632 60.000 0.00 0.00 0.00 4.79
1069 1148 0.178935 CTCCTCCTCCTCATCCCCTC 60.179 65.000 0.00 0.00 0.00 4.30
1070 1149 0.631998 TCCTCCTCCTCATCCCCTCT 60.632 60.000 0.00 0.00 0.00 3.69
1071 1150 0.178935 CCTCCTCCTCATCCCCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
1072 1151 0.859760 CTCCTCCTCATCCCCTCTCT 59.140 60.000 0.00 0.00 0.00 3.10
1073 1152 1.220236 CTCCTCCTCATCCCCTCTCTT 59.780 57.143 0.00 0.00 0.00 2.85
1074 1153 1.219213 TCCTCCTCATCCCCTCTCTTC 59.781 57.143 0.00 0.00 0.00 2.87
1075 1154 1.220236 CCTCCTCATCCCCTCTCTTCT 59.780 57.143 0.00 0.00 0.00 2.85
1076 1155 2.597455 CTCCTCATCCCCTCTCTTCTC 58.403 57.143 0.00 0.00 0.00 2.87
1077 1156 1.219213 TCCTCATCCCCTCTCTTCTCC 59.781 57.143 0.00 0.00 0.00 3.71
1078 1157 1.220236 CCTCATCCCCTCTCTTCTCCT 59.780 57.143 0.00 0.00 0.00 3.69
1079 1158 2.597455 CTCATCCCCTCTCTTCTCCTC 58.403 57.143 0.00 0.00 0.00 3.71
1080 1159 1.219213 TCATCCCCTCTCTTCTCCTCC 59.781 57.143 0.00 0.00 0.00 4.30
1081 1160 1.220236 CATCCCCTCTCTTCTCCTCCT 59.780 57.143 0.00 0.00 0.00 3.69
1082 1161 0.930726 TCCCCTCTCTTCTCCTCCTC 59.069 60.000 0.00 0.00 0.00 3.71
1083 1162 0.105709 CCCCTCTCTTCTCCTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
1084 1163 0.933700 CCCTCTCTTCTCCTCCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
1085 1164 1.133482 CCCTCTCTTCTCCTCCTCCTC 60.133 61.905 0.00 0.00 0.00 3.71
1086 1165 1.568597 CCTCTCTTCTCCTCCTCCTCA 59.431 57.143 0.00 0.00 0.00 3.86
1087 1166 2.177669 CCTCTCTTCTCCTCCTCCTCAT 59.822 54.545 0.00 0.00 0.00 2.90
1088 1167 3.490348 CTCTCTTCTCCTCCTCCTCATC 58.510 54.545 0.00 0.00 0.00 2.92
1089 1168 2.176798 TCTCTTCTCCTCCTCCTCATCC 59.823 54.545 0.00 0.00 0.00 3.51
1090 1169 1.219213 TCTTCTCCTCCTCCTCATCCC 59.781 57.143 0.00 0.00 0.00 3.85
1765 1934 6.558394 TGGTGAATGATCCATACAATCCTAGA 59.442 38.462 0.00 0.00 0.00 2.43
1842 2015 5.358298 AAGCCAAGTACGAAATGAAGAAC 57.642 39.130 0.00 0.00 0.00 3.01
1979 2257 4.511454 GCATACATGAGCCTATTTTCGTGA 59.489 41.667 0.00 0.00 35.00 4.35
2025 2303 7.826744 CCAGAAGAAATTAAGGCTAGAAAGAGT 59.173 37.037 0.00 0.00 0.00 3.24
2072 2350 5.251764 CAATCAGAGCCCCTCCATATAAAG 58.748 45.833 0.00 0.00 0.00 1.85
2290 2827 6.037391 TGGTTAACTTGTTTTCTGTTAGGACG 59.963 38.462 5.42 0.00 0.00 4.79
2361 2898 2.197465 CCCTAACAGCCTAACTCCCTT 58.803 52.381 0.00 0.00 0.00 3.95
2362 2899 2.170817 CCCTAACAGCCTAACTCCCTTC 59.829 54.545 0.00 0.00 0.00 3.46
2363 2900 2.170817 CCTAACAGCCTAACTCCCTTCC 59.829 54.545 0.00 0.00 0.00 3.46
2364 2901 2.046280 AACAGCCTAACTCCCTTCCT 57.954 50.000 0.00 0.00 0.00 3.36
2486 3027 5.869649 AGGCCATAAAGACAAAAACACTT 57.130 34.783 5.01 0.00 0.00 3.16
2711 3252 4.599047 TTGTTAAAGGAAATGCTGGTGG 57.401 40.909 0.00 0.00 0.00 4.61
2790 3332 0.404040 CCCTTGTAAGTTCAGGCCCA 59.596 55.000 0.00 0.00 0.00 5.36
2906 3448 6.435430 TTTCTTATGTAATGCGAGCATTGT 57.565 33.333 27.59 17.48 45.15 2.71
2983 3525 1.619654 TGTTTGCATCTCCAAGGTGG 58.380 50.000 0.00 0.00 39.43 4.61
2996 3538 1.472480 CAAGGTGGCCTGATTAAACCG 59.528 52.381 3.32 0.00 35.99 4.44
3023 3565 0.250295 TTGACCTTGTTCCTGGCTCG 60.250 55.000 0.00 0.00 0.00 5.03
3052 3594 6.682746 TCTAGACATTCAGTTGAGTGTTCTC 58.317 40.000 10.94 0.64 43.62 2.87
3303 3845 7.255277 GGACCTCTTGAGGTTTGAATATTATGC 60.255 40.741 21.61 5.91 43.24 3.14
3972 4517 7.442364 CCATAATACCAGTTCATAGTTCCACAG 59.558 40.741 0.00 0.00 0.00 3.66
4047 4592 7.389884 CAGGCATAATATCTCAAAGCTGTATGT 59.610 37.037 0.00 0.00 0.00 2.29
4122 4667 0.380378 TCTTTGCTGCAACGAACCAC 59.620 50.000 17.78 0.00 0.00 4.16
4387 4932 1.471119 CAGCATGCCAATCTCCTTGT 58.529 50.000 15.66 0.00 32.61 3.16
4388 4933 1.822990 CAGCATGCCAATCTCCTTGTT 59.177 47.619 15.66 0.00 32.61 2.83
4389 4934 2.232941 CAGCATGCCAATCTCCTTGTTT 59.767 45.455 15.66 0.00 32.61 2.83
4390 4935 2.901839 AGCATGCCAATCTCCTTGTTTT 59.098 40.909 15.66 0.00 32.61 2.43
4391 4936 2.997986 GCATGCCAATCTCCTTGTTTTG 59.002 45.455 6.36 0.00 32.61 2.44
4392 4937 3.555586 GCATGCCAATCTCCTTGTTTTGT 60.556 43.478 6.36 0.00 32.61 2.83
4393 4938 4.634199 CATGCCAATCTCCTTGTTTTGTT 58.366 39.130 0.00 0.00 32.61 2.83
4394 4939 4.057406 TGCCAATCTCCTTGTTTTGTTG 57.943 40.909 0.00 0.00 32.61 3.33
4395 4940 3.703556 TGCCAATCTCCTTGTTTTGTTGA 59.296 39.130 0.00 0.00 32.61 3.18
4396 4941 4.344679 TGCCAATCTCCTTGTTTTGTTGAT 59.655 37.500 0.00 0.00 32.61 2.57
4397 4942 5.538053 TGCCAATCTCCTTGTTTTGTTGATA 59.462 36.000 0.00 0.00 32.61 2.15
4398 4943 6.211184 TGCCAATCTCCTTGTTTTGTTGATAT 59.789 34.615 0.00 0.00 32.61 1.63
4399 4944 7.395772 TGCCAATCTCCTTGTTTTGTTGATATA 59.604 33.333 0.00 0.00 32.61 0.86
4400 4945 8.416329 GCCAATCTCCTTGTTTTGTTGATATAT 58.584 33.333 0.00 0.00 32.61 0.86
4454 4999 5.743872 CCTTGTTTTGTTGAGACTTGTTAGC 59.256 40.000 0.00 0.00 0.00 3.09
4456 5001 6.509418 TGTTTTGTTGAGACTTGTTAGCTT 57.491 33.333 0.00 0.00 0.00 3.74
4469 5014 8.280497 AGACTTGTTAGCTTTATGTTTGTTACG 58.720 33.333 0.00 0.00 0.00 3.18
4967 5512 2.871633 ACAAAATTTTGCCTGCTTTCGG 59.128 40.909 26.94 3.30 41.79 4.30
4978 5523 2.978018 GCTTTCGGGGCTGTTTCCG 61.978 63.158 0.00 0.00 46.89 4.30
5061 5607 6.715280 AGCATTCCTCTATCTTGTTTCAAGA 58.285 36.000 13.34 13.34 0.00 3.02
5128 5675 2.555325 CAACTCTTGCCTGCTTTCATGA 59.445 45.455 0.00 0.00 0.00 3.07
5281 5828 5.362556 TCTGTTTTGTGCATCTTTAGAGC 57.637 39.130 0.00 0.00 0.00 4.09
5308 5855 4.703897 CCAAAGAGGTGACTGAACTTGTA 58.296 43.478 0.00 0.00 44.43 2.41
5725 6387 7.852971 TTCGTTCACTCTTCTTTTTCCTAAA 57.147 32.000 0.00 0.00 0.00 1.85
5726 6388 7.852971 TCGTTCACTCTTCTTTTTCCTAAAA 57.147 32.000 0.00 0.00 0.00 1.52
6049 6714 1.779221 TTTGGCCAGGCATATCCTTG 58.221 50.000 15.19 0.00 44.75 3.61
6071 6736 0.321122 GAGGTGGAGCACTGGAGTTG 60.321 60.000 0.00 0.00 34.40 3.16
6124 6790 5.175859 TCGTCCTGTAAGATTTGTTGGATC 58.824 41.667 0.00 0.00 34.07 3.36
6614 7284 2.574006 ATCTTTCTGAGTTGCTGCCA 57.426 45.000 0.00 0.00 0.00 4.92
6641 7311 0.040058 TCCTGGCCATGCAAGTTGAT 59.960 50.000 5.51 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.057089 TGAAAAACCAAAAAGTTAGAAAAAGCA 57.943 25.926 0.00 0.00 0.00 3.91
15 16 6.801575 AGATCGCTGAAAAACCAAAAAGTTA 58.198 32.000 0.00 0.00 0.00 2.24
19 20 5.047188 GGAAGATCGCTGAAAAACCAAAAA 58.953 37.500 0.00 0.00 0.00 1.94
24 25 4.437524 GCTAAGGAAGATCGCTGAAAAACC 60.438 45.833 0.00 0.00 0.00 3.27
33 34 1.943340 CCAAAGGCTAAGGAAGATCGC 59.057 52.381 0.00 0.00 0.00 4.58
36 37 5.044550 AGTTGATCCAAAGGCTAAGGAAGAT 60.045 40.000 11.33 0.00 34.62 2.40
79 81 1.997669 ACCTGTTTTTCGCGCAAAAA 58.002 40.000 17.85 18.31 40.93 1.94
82 84 1.997669 AAAACCTGTTTTTCGCGCAA 58.002 40.000 8.75 0.00 39.52 4.85
83 85 1.997669 AAAAACCTGTTTTTCGCGCA 58.002 40.000 8.75 0.00 46.30 6.09
109 112 2.257353 GCAAAACCATGCCTCTCGT 58.743 52.632 0.00 0.00 40.49 4.18
187 191 2.645192 CCCCCGGCGCAAGAAAAAT 61.645 57.895 10.83 0.00 43.02 1.82
232 258 2.613390 GTTTTCGAGAGGCACGGTT 58.387 52.632 0.00 0.00 0.00 4.44
255 281 5.392286 AGAAAAAGACACAAAACGCGTTTA 58.608 33.333 34.89 0.00 31.63 2.01
267 297 3.495001 CCTCTCACGGAAGAAAAAGACAC 59.505 47.826 0.00 0.00 0.00 3.67
271 301 2.224314 GTGCCTCTCACGGAAGAAAAAG 59.776 50.000 0.00 0.00 35.76 2.27
350 405 1.877443 GAAGCAAAAACCGTGCCTCTA 59.123 47.619 0.00 0.00 43.27 2.43
384 439 1.657538 CGACTCTCGCAAAAGCACAAC 60.658 52.381 0.00 0.00 31.14 3.32
441 504 3.164028 GCAAAACCGTGCTTCTCAC 57.836 52.632 0.00 0.00 41.51 3.51
501 572 3.991367 ACTGAATCGAGAGGACGTTTTT 58.009 40.909 0.00 0.00 34.70 1.94
502 573 3.662247 ACTGAATCGAGAGGACGTTTT 57.338 42.857 0.00 0.00 34.70 2.43
503 574 3.662247 AACTGAATCGAGAGGACGTTT 57.338 42.857 0.00 0.00 34.70 3.60
504 575 3.662247 AAACTGAATCGAGAGGACGTT 57.338 42.857 0.00 0.00 34.70 3.99
505 576 3.662247 AAAACTGAATCGAGAGGACGT 57.338 42.857 0.00 0.00 34.70 4.34
523 594 3.933955 TCACGAAGAAACAGGACGAAAAA 59.066 39.130 0.00 0.00 0.00 1.94
524 595 3.523547 TCACGAAGAAACAGGACGAAAA 58.476 40.909 0.00 0.00 0.00 2.29
525 596 3.167921 TCACGAAGAAACAGGACGAAA 57.832 42.857 0.00 0.00 0.00 3.46
526 597 2.875087 TCACGAAGAAACAGGACGAA 57.125 45.000 0.00 0.00 0.00 3.85
527 598 2.875087 TTCACGAAGAAACAGGACGA 57.125 45.000 0.00 0.00 32.05 4.20
528 599 3.936902 TTTTCACGAAGAAACAGGACG 57.063 42.857 7.18 0.00 45.48 4.79
547 618 8.977505 CATGTTGATAGGTTTTGACGAATTTTT 58.022 29.630 0.00 0.00 0.00 1.94
548 619 7.598493 CCATGTTGATAGGTTTTGACGAATTTT 59.402 33.333 0.00 0.00 0.00 1.82
549 620 7.090173 CCATGTTGATAGGTTTTGACGAATTT 58.910 34.615 0.00 0.00 0.00 1.82
550 621 6.350110 CCCATGTTGATAGGTTTTGACGAATT 60.350 38.462 0.00 0.00 0.00 2.17
551 622 5.125417 CCCATGTTGATAGGTTTTGACGAAT 59.875 40.000 0.00 0.00 0.00 3.34
552 623 4.457603 CCCATGTTGATAGGTTTTGACGAA 59.542 41.667 0.00 0.00 0.00 3.85
553 624 4.006989 CCCATGTTGATAGGTTTTGACGA 58.993 43.478 0.00 0.00 0.00 4.20
554 625 4.006989 TCCCATGTTGATAGGTTTTGACG 58.993 43.478 0.00 0.00 0.00 4.35
555 626 5.888161 AGATCCCATGTTGATAGGTTTTGAC 59.112 40.000 0.00 0.00 0.00 3.18
556 627 6.078456 AGATCCCATGTTGATAGGTTTTGA 57.922 37.500 0.00 0.00 0.00 2.69
557 628 6.016777 GCTAGATCCCATGTTGATAGGTTTTG 60.017 42.308 0.00 0.00 0.00 2.44
558 629 6.064717 GCTAGATCCCATGTTGATAGGTTTT 58.935 40.000 0.00 0.00 0.00 2.43
559 630 5.370880 AGCTAGATCCCATGTTGATAGGTTT 59.629 40.000 0.00 0.00 0.00 3.27
560 631 4.910304 AGCTAGATCCCATGTTGATAGGTT 59.090 41.667 0.00 0.00 0.00 3.50
561 632 4.497516 AGCTAGATCCCATGTTGATAGGT 58.502 43.478 0.00 0.00 0.00 3.08
562 633 5.495926 AAGCTAGATCCCATGTTGATAGG 57.504 43.478 0.00 0.00 0.00 2.57
563 634 6.528321 TCAAAGCTAGATCCCATGTTGATAG 58.472 40.000 0.00 0.00 0.00 2.08
564 635 6.499106 TCAAAGCTAGATCCCATGTTGATA 57.501 37.500 0.00 0.00 0.00 2.15
565 636 5.378230 TCAAAGCTAGATCCCATGTTGAT 57.622 39.130 0.00 0.00 0.00 2.57
566 637 4.842531 TCAAAGCTAGATCCCATGTTGA 57.157 40.909 0.00 0.00 0.00 3.18
567 638 5.188434 TCTTCAAAGCTAGATCCCATGTTG 58.812 41.667 0.00 0.00 0.00 3.33
568 639 5.441718 TCTTCAAAGCTAGATCCCATGTT 57.558 39.130 0.00 0.00 0.00 2.71
569 640 5.369110 AGATCTTCAAAGCTAGATCCCATGT 59.631 40.000 17.05 0.43 45.05 3.21
570 641 5.867330 AGATCTTCAAAGCTAGATCCCATG 58.133 41.667 17.05 0.00 45.05 3.66
571 642 5.845614 AGAGATCTTCAAAGCTAGATCCCAT 59.154 40.000 17.05 3.25 45.05 4.00
572 643 5.070180 CAGAGATCTTCAAAGCTAGATCCCA 59.930 44.000 17.05 0.00 45.05 4.37
573 644 5.540911 CAGAGATCTTCAAAGCTAGATCCC 58.459 45.833 17.05 8.61 45.05 3.85
574 645 4.990426 GCAGAGATCTTCAAAGCTAGATCC 59.010 45.833 17.05 10.74 45.05 3.36
575 646 4.681025 CGCAGAGATCTTCAAAGCTAGATC 59.319 45.833 14.05 14.05 44.54 2.75
576 647 4.619973 CGCAGAGATCTTCAAAGCTAGAT 58.380 43.478 0.00 0.00 33.92 1.98
577 648 3.736433 GCGCAGAGATCTTCAAAGCTAGA 60.736 47.826 0.30 0.00 0.00 2.43
578 649 2.539274 GCGCAGAGATCTTCAAAGCTAG 59.461 50.000 0.30 0.00 0.00 3.42
579 650 2.544685 GCGCAGAGATCTTCAAAGCTA 58.455 47.619 0.30 0.00 0.00 3.32
580 651 1.367659 GCGCAGAGATCTTCAAAGCT 58.632 50.000 0.30 0.00 0.00 3.74
581 652 0.026027 CGCGCAGAGATCTTCAAAGC 59.974 55.000 8.75 0.00 0.00 3.51
582 653 1.633561 TCGCGCAGAGATCTTCAAAG 58.366 50.000 8.75 0.00 0.00 2.77
583 654 3.812577 TCGCGCAGAGATCTTCAAA 57.187 47.368 8.75 0.00 0.00 2.69
592 663 0.531532 ATTGGATTCCTCGCGCAGAG 60.532 55.000 18.33 18.33 46.44 3.35
593 664 0.811219 CATTGGATTCCTCGCGCAGA 60.811 55.000 8.75 4.86 0.00 4.26
594 665 0.811219 TCATTGGATTCCTCGCGCAG 60.811 55.000 8.75 3.84 0.00 5.18
595 666 0.179048 ATCATTGGATTCCTCGCGCA 60.179 50.000 8.75 0.00 0.00 6.09
596 667 0.236711 CATCATTGGATTCCTCGCGC 59.763 55.000 0.00 0.00 0.00 6.86
597 668 1.869774 TCATCATTGGATTCCTCGCG 58.130 50.000 0.00 0.00 0.00 5.87
598 669 4.354587 GTTTTCATCATTGGATTCCTCGC 58.645 43.478 3.95 0.00 0.00 5.03
599 670 4.496341 CCGTTTTCATCATTGGATTCCTCG 60.496 45.833 3.95 0.00 0.00 4.63
600 671 4.399303 ACCGTTTTCATCATTGGATTCCTC 59.601 41.667 3.95 0.00 0.00 3.71
601 672 4.344104 ACCGTTTTCATCATTGGATTCCT 58.656 39.130 3.95 0.00 0.00 3.36
602 673 4.718940 ACCGTTTTCATCATTGGATTCC 57.281 40.909 0.00 0.00 0.00 3.01
603 674 5.708948 TGAACCGTTTTCATCATTGGATTC 58.291 37.500 0.00 0.00 0.00 2.52
604 675 5.720371 TGAACCGTTTTCATCATTGGATT 57.280 34.783 0.00 0.00 0.00 3.01
605 676 5.476599 TCTTGAACCGTTTTCATCATTGGAT 59.523 36.000 0.00 0.00 0.00 3.41
606 677 4.824537 TCTTGAACCGTTTTCATCATTGGA 59.175 37.500 0.00 0.00 0.00 3.53
607 678 5.119931 TCTTGAACCGTTTTCATCATTGG 57.880 39.130 0.00 0.00 0.00 3.16
608 679 6.525628 CAGATCTTGAACCGTTTTCATCATTG 59.474 38.462 0.00 0.00 0.00 2.82
609 680 6.430925 TCAGATCTTGAACCGTTTTCATCATT 59.569 34.615 0.00 0.00 31.34 2.57
610 681 5.939883 TCAGATCTTGAACCGTTTTCATCAT 59.060 36.000 0.00 0.00 31.34 2.45
611 682 5.304778 TCAGATCTTGAACCGTTTTCATCA 58.695 37.500 0.00 0.00 31.34 3.07
612 683 5.862924 TCAGATCTTGAACCGTTTTCATC 57.137 39.130 0.00 0.00 31.34 2.92
623 694 7.815840 TTAAACCATGTGTTCAGATCTTGAA 57.184 32.000 0.00 0.00 43.40 2.69
624 695 7.815840 TTTAAACCATGTGTTCAGATCTTGA 57.184 32.000 0.00 0.00 35.67 3.02
625 696 8.352201 TCTTTTAAACCATGTGTTCAGATCTTG 58.648 33.333 0.00 0.00 35.67 3.02
626 697 8.463930 TCTTTTAAACCATGTGTTCAGATCTT 57.536 30.769 0.00 0.00 35.67 2.40
627 698 8.641498 ATCTTTTAAACCATGTGTTCAGATCT 57.359 30.769 0.00 0.00 35.67 2.75
658 729 8.697846 TCTTCGTACATTCGTTTATTCAGAAT 57.302 30.769 0.20 0.20 35.24 2.40
659 730 8.523523 TTCTTCGTACATTCGTTTATTCAGAA 57.476 30.769 0.00 0.00 0.00 3.02
660 731 8.523523 TTTCTTCGTACATTCGTTTATTCAGA 57.476 30.769 0.00 0.00 0.00 3.27
661 732 9.588774 TTTTTCTTCGTACATTCGTTTATTCAG 57.411 29.630 0.00 0.00 0.00 3.02
662 733 9.588774 CTTTTTCTTCGTACATTCGTTTATTCA 57.411 29.630 0.00 0.00 0.00 2.57
663 734 9.801714 TCTTTTTCTTCGTACATTCGTTTATTC 57.198 29.630 0.00 0.00 0.00 1.75
666 737 9.985318 TTTTCTTTTTCTTCGTACATTCGTTTA 57.015 25.926 0.00 0.00 0.00 2.01
667 738 8.898983 TTTTCTTTTTCTTCGTACATTCGTTT 57.101 26.923 0.00 0.00 0.00 3.60
668 739 8.898983 TTTTTCTTTTTCTTCGTACATTCGTT 57.101 26.923 0.00 0.00 0.00 3.85
669 740 8.179615 ACTTTTTCTTTTTCTTCGTACATTCGT 58.820 29.630 0.00 0.00 0.00 3.85
670 741 8.543071 ACTTTTTCTTTTTCTTCGTACATTCG 57.457 30.769 0.00 0.00 0.00 3.34
671 742 9.717892 AGACTTTTTCTTTTTCTTCGTACATTC 57.282 29.630 0.00 0.00 0.00 2.67
672 743 9.717892 GAGACTTTTTCTTTTTCTTCGTACATT 57.282 29.630 0.00 0.00 33.22 2.71
673 744 8.889717 TGAGACTTTTTCTTTTTCTTCGTACAT 58.110 29.630 0.00 0.00 33.22 2.29
674 745 8.259049 TGAGACTTTTTCTTTTTCTTCGTACA 57.741 30.769 0.00 0.00 33.22 2.90
675 746 7.851472 CCTGAGACTTTTTCTTTTTCTTCGTAC 59.149 37.037 0.00 0.00 33.22 3.67
676 747 7.551617 ACCTGAGACTTTTTCTTTTTCTTCGTA 59.448 33.333 0.00 0.00 33.22 3.43
677 748 6.374613 ACCTGAGACTTTTTCTTTTTCTTCGT 59.625 34.615 0.00 0.00 33.22 3.85
678 749 6.786207 ACCTGAGACTTTTTCTTTTTCTTCG 58.214 36.000 0.00 0.00 33.22 3.79
679 750 7.009631 GCAACCTGAGACTTTTTCTTTTTCTTC 59.990 37.037 0.00 0.00 33.22 2.87
680 751 6.813649 GCAACCTGAGACTTTTTCTTTTTCTT 59.186 34.615 0.00 0.00 33.22 2.52
681 752 6.333416 GCAACCTGAGACTTTTTCTTTTTCT 58.667 36.000 0.00 0.00 33.22 2.52
682 753 5.230097 CGCAACCTGAGACTTTTTCTTTTTC 59.770 40.000 0.00 0.00 33.22 2.29
683 754 5.102313 CGCAACCTGAGACTTTTTCTTTTT 58.898 37.500 0.00 0.00 33.22 1.94
684 755 4.398044 TCGCAACCTGAGACTTTTTCTTTT 59.602 37.500 0.00 0.00 33.22 2.27
685 756 3.945285 TCGCAACCTGAGACTTTTTCTTT 59.055 39.130 0.00 0.00 33.22 2.52
686 757 3.312697 GTCGCAACCTGAGACTTTTTCTT 59.687 43.478 3.62 0.00 42.66 2.52
687 758 2.872858 GTCGCAACCTGAGACTTTTTCT 59.127 45.455 3.62 0.00 42.66 2.52
688 759 2.612212 TGTCGCAACCTGAGACTTTTTC 59.388 45.455 11.06 0.00 45.51 2.29
689 760 2.614057 CTGTCGCAACCTGAGACTTTTT 59.386 45.455 11.06 0.00 45.51 1.94
690 761 2.213499 CTGTCGCAACCTGAGACTTTT 58.787 47.619 11.06 0.00 45.51 2.27
691 762 1.871080 CTGTCGCAACCTGAGACTTT 58.129 50.000 11.06 0.00 45.51 2.66
692 763 0.601311 GCTGTCGCAACCTGAGACTT 60.601 55.000 11.06 0.00 45.51 3.01
693 764 1.005630 GCTGTCGCAACCTGAGACT 60.006 57.895 11.06 0.00 45.51 3.24
694 765 2.375766 CGCTGTCGCAACCTGAGAC 61.376 63.158 3.87 3.87 45.51 3.36
695 766 2.049156 CGCTGTCGCAACCTGAGA 60.049 61.111 0.00 0.00 35.30 3.27
696 767 3.114616 CCGCTGTCGCAACCTGAG 61.115 66.667 0.00 0.00 35.30 3.35
718 789 0.443869 GACAAGTGGCGCACTACATG 59.556 55.000 10.83 10.83 44.62 3.21
719 790 0.034756 TGACAAGTGGCGCACTACAT 59.965 50.000 10.83 0.00 44.62 2.29
720 791 0.878523 GTGACAAGTGGCGCACTACA 60.879 55.000 10.83 9.42 44.62 2.74
721 792 0.878523 TGTGACAAGTGGCGCACTAC 60.879 55.000 10.83 5.01 44.62 2.73
722 793 0.179070 TTGTGACAAGTGGCGCACTA 60.179 50.000 10.83 0.00 44.62 2.74
724 795 1.298339 GTTGTGACAAGTGGCGCAC 60.298 57.895 10.83 5.73 44.28 5.34
725 796 2.477176 GGTTGTGACAAGTGGCGCA 61.477 57.895 10.83 0.00 42.66 6.09
726 797 2.186826 AGGTTGTGACAAGTGGCGC 61.187 57.895 0.00 0.00 0.00 6.53
727 798 0.813610 TCAGGTTGTGACAAGTGGCG 60.814 55.000 0.00 0.00 0.00 5.69
728 799 0.947244 CTCAGGTTGTGACAAGTGGC 59.053 55.000 0.00 0.00 0.00 5.01
729 800 1.140852 TCCTCAGGTTGTGACAAGTGG 59.859 52.381 0.00 0.00 0.00 4.00
730 801 2.487934 CTCCTCAGGTTGTGACAAGTG 58.512 52.381 0.00 0.00 0.00 3.16
731 802 1.417890 CCTCCTCAGGTTGTGACAAGT 59.582 52.381 0.00 0.00 34.60 3.16
732 803 2.175878 CCTCCTCAGGTTGTGACAAG 57.824 55.000 0.00 0.00 34.60 3.16
742 813 0.690411 ATCAGGCTCACCTCCTCAGG 60.690 60.000 0.00 0.00 46.34 3.86
743 814 0.752054 GATCAGGCTCACCTCCTCAG 59.248 60.000 0.00 0.00 46.34 3.35
744 815 0.337773 AGATCAGGCTCACCTCCTCA 59.662 55.000 0.00 0.00 46.34 3.86
745 816 1.494960 AAGATCAGGCTCACCTCCTC 58.505 55.000 0.00 0.00 46.34 3.71
746 817 1.963985 AAAGATCAGGCTCACCTCCT 58.036 50.000 0.00 0.00 46.34 3.69
747 818 2.026822 TCAAAAGATCAGGCTCACCTCC 60.027 50.000 0.00 0.00 46.34 4.30
748 819 3.340814 TCAAAAGATCAGGCTCACCTC 57.659 47.619 0.00 0.00 46.34 3.85
749 820 4.077822 CTTTCAAAAGATCAGGCTCACCT 58.922 43.478 0.00 0.00 42.33 4.00
750 821 4.074970 TCTTTCAAAAGATCAGGCTCACC 58.925 43.478 1.06 0.00 39.95 4.02
751 822 5.240403 ACTTCTTTCAAAAGATCAGGCTCAC 59.760 40.000 6.05 0.00 43.92 3.51
752 823 5.380043 ACTTCTTTCAAAAGATCAGGCTCA 58.620 37.500 6.05 0.00 43.92 4.26
753 824 5.956068 ACTTCTTTCAAAAGATCAGGCTC 57.044 39.130 6.05 0.00 43.92 4.70
754 825 6.429385 CACTACTTCTTTCAAAAGATCAGGCT 59.571 38.462 6.05 0.00 43.92 4.58
755 826 6.428159 TCACTACTTCTTTCAAAAGATCAGGC 59.572 38.462 6.05 0.00 43.92 4.85
756 827 7.969536 TCACTACTTCTTTCAAAAGATCAGG 57.030 36.000 6.05 1.72 43.92 3.86
759 830 9.535270 CGAAATCACTACTTCTTTCAAAAGATC 57.465 33.333 6.05 0.00 43.92 2.75
760 831 9.273016 TCGAAATCACTACTTCTTTCAAAAGAT 57.727 29.630 6.05 0.00 43.92 2.40
761 832 8.548721 GTCGAAATCACTACTTCTTTCAAAAGA 58.451 33.333 1.06 1.06 42.91 2.52
762 833 7.798982 GGTCGAAATCACTACTTCTTTCAAAAG 59.201 37.037 0.00 0.00 37.36 2.27
763 834 7.497909 AGGTCGAAATCACTACTTCTTTCAAAA 59.502 33.333 0.00 0.00 0.00 2.44
764 835 6.990349 AGGTCGAAATCACTACTTCTTTCAAA 59.010 34.615 0.00 0.00 0.00 2.69
765 836 6.522054 AGGTCGAAATCACTACTTCTTTCAA 58.478 36.000 0.00 0.00 0.00 2.69
766 837 6.097915 AGGTCGAAATCACTACTTCTTTCA 57.902 37.500 0.00 0.00 0.00 2.69
767 838 8.705048 ATTAGGTCGAAATCACTACTTCTTTC 57.295 34.615 0.00 0.00 0.00 2.62
768 839 9.152595 GAATTAGGTCGAAATCACTACTTCTTT 57.847 33.333 0.00 0.00 0.00 2.52
769 840 7.488471 CGAATTAGGTCGAAATCACTACTTCTT 59.512 37.037 0.00 0.00 43.86 2.52
778 849 3.899052 ACCCGAATTAGGTCGAAATCA 57.101 42.857 3.75 0.00 43.86 2.57
874 947 1.022451 TTGCGTATTTGCCGTCCTCC 61.022 55.000 0.00 0.00 0.00 4.30
1059 1138 2.597455 GAGGAGAAGAGAGGGGATGAG 58.403 57.143 0.00 0.00 0.00 2.90
1067 1146 3.490348 GATGAGGAGGAGGAGAAGAGAG 58.510 54.545 0.00 0.00 0.00 3.20
1068 1147 2.176798 GGATGAGGAGGAGGAGAAGAGA 59.823 54.545 0.00 0.00 0.00 3.10
1069 1148 2.597455 GGATGAGGAGGAGGAGAAGAG 58.403 57.143 0.00 0.00 0.00 2.85
1070 1149 1.219213 GGGATGAGGAGGAGGAGAAGA 59.781 57.143 0.00 0.00 0.00 2.87
1071 1150 1.715785 GGGATGAGGAGGAGGAGAAG 58.284 60.000 0.00 0.00 0.00 2.85
1072 1151 0.105964 CGGGATGAGGAGGAGGAGAA 60.106 60.000 0.00 0.00 0.00 2.87
1073 1152 1.539165 CGGGATGAGGAGGAGGAGA 59.461 63.158 0.00 0.00 0.00 3.71
1074 1153 2.206536 GCGGGATGAGGAGGAGGAG 61.207 68.421 0.00 0.00 0.00 3.69
1075 1154 2.123251 GCGGGATGAGGAGGAGGA 60.123 66.667 0.00 0.00 0.00 3.71
1076 1155 3.237741 GGCGGGATGAGGAGGAGG 61.238 72.222 0.00 0.00 0.00 4.30
1077 1156 3.237741 GGGCGGGATGAGGAGGAG 61.238 72.222 0.00 0.00 0.00 3.69
1078 1157 4.880426 GGGGCGGGATGAGGAGGA 62.880 72.222 0.00 0.00 0.00 3.71
1080 1159 2.851102 ATGGGGCGGGATGAGGAG 60.851 66.667 0.00 0.00 0.00 3.69
1081 1160 2.849162 GATGGGGCGGGATGAGGA 60.849 66.667 0.00 0.00 0.00 3.71
1082 1161 3.958860 GGATGGGGCGGGATGAGG 61.959 72.222 0.00 0.00 0.00 3.86
1083 1162 2.851102 AGGATGGGGCGGGATGAG 60.851 66.667 0.00 0.00 0.00 2.90
1084 1163 2.849162 GAGGATGGGGCGGGATGA 60.849 66.667 0.00 0.00 0.00 2.92
1085 1164 3.958860 GGAGGATGGGGCGGGATG 61.959 72.222 0.00 0.00 0.00 3.51
1114 1193 1.611977 CACGGAGATATAACCCAGCGA 59.388 52.381 0.00 0.00 0.00 4.93
1765 1934 7.339212 TCCATTCGATTCATTAAACCAAGTGAT 59.661 33.333 0.00 0.00 0.00 3.06
1842 2015 5.212532 TCAAATTTGGTTGAATGACCCAG 57.787 39.130 17.90 0.00 39.01 4.45
1979 2257 4.317530 GGATTTGGTCCCTAAGAGGTTT 57.682 45.455 0.00 0.00 41.50 3.27
2025 2303 3.833650 TCACTGTTAACTGGAATACCCGA 59.166 43.478 15.84 0.00 37.93 5.14
2072 2350 1.135199 CAAGTGATTGGTGGATGCTGC 60.135 52.381 0.00 0.00 0.00 5.25
2290 2827 3.065925 GCAGAATCAAGTGATAGCCCAAC 59.934 47.826 0.00 0.00 33.73 3.77
2361 2898 1.425066 ACAGGGAACATTGCTGAAGGA 59.575 47.619 0.00 0.00 0.00 3.36
2362 2899 1.915141 ACAGGGAACATTGCTGAAGG 58.085 50.000 0.00 0.00 0.00 3.46
2363 2900 2.608752 GCAACAGGGAACATTGCTGAAG 60.609 50.000 1.06 0.00 45.86 3.02
2364 2901 1.340889 GCAACAGGGAACATTGCTGAA 59.659 47.619 1.06 0.00 45.86 3.02
2486 3027 4.943705 GGTCAAATGGATCTGCTTTACTGA 59.056 41.667 0.00 0.00 0.00 3.41
2906 3448 3.149196 GCTGAACTTCCCACAGAATTCA 58.851 45.455 8.44 0.00 34.12 2.57
2983 3525 1.361793 TACGCACGGTTTAATCAGGC 58.638 50.000 0.00 0.00 0.00 4.85
2996 3538 2.812011 AGGAACAAGGTCAATTACGCAC 59.188 45.455 0.00 0.00 0.00 5.34
3023 3565 6.983307 ACACTCAACTGAATGTCTAGATATGC 59.017 38.462 2.35 1.35 26.80 3.14
3679 4224 8.598924 CATACTGTATTGAATATCGCAATCTCC 58.401 37.037 0.00 0.51 37.22 3.71
4080 4625 1.352352 AGACTGCAGGTAAGCCAACAT 59.648 47.619 19.93 0.00 37.19 2.71
4367 4912 0.102481 CAAGGAGATTGGCATGCTGC 59.898 55.000 18.92 2.02 44.08 5.25
4368 4913 1.471119 ACAAGGAGATTGGCATGCTG 58.529 50.000 18.92 6.95 43.68 4.41
4369 4914 2.226962 AACAAGGAGATTGGCATGCT 57.773 45.000 18.92 0.00 43.68 3.79
4370 4915 2.997986 CAAAACAAGGAGATTGGCATGC 59.002 45.455 9.90 9.90 43.68 4.06
4371 4916 4.261578 ACAAAACAAGGAGATTGGCATG 57.738 40.909 0.00 0.00 43.68 4.06
4372 4917 4.344679 TCAACAAAACAAGGAGATTGGCAT 59.655 37.500 0.00 0.00 43.68 4.40
4373 4918 3.703556 TCAACAAAACAAGGAGATTGGCA 59.296 39.130 0.00 0.00 43.68 4.92
4374 4919 4.320608 TCAACAAAACAAGGAGATTGGC 57.679 40.909 0.00 0.00 43.68 4.52
4813 5358 7.916450 GTGCTATCAAGTACCTAAACTCTACAG 59.084 40.741 0.00 0.00 32.62 2.74
4978 5523 8.612619 TGCTTAACTTACTTTATAATCTGCTGC 58.387 33.333 0.00 0.00 0.00 5.25
5061 5607 0.601057 CGGGGCCAAACGAAATCTTT 59.399 50.000 4.39 0.00 0.00 2.52
5281 5828 1.202687 TCAGTCACCTCTTTGGCAGTG 60.203 52.381 0.00 0.00 40.22 3.66
5308 5855 6.946009 ACACTACACATAAAAAGTTAGGCCAT 59.054 34.615 5.01 0.00 0.00 4.40
5703 6365 9.516314 AAATTTTAGGAAAAAGAAGAGTGAACG 57.484 29.630 0.00 0.00 37.97 3.95
6049 6714 2.177594 CTCCAGTGCTCCACCTCCAC 62.178 65.000 0.00 0.00 34.49 4.02
6614 7284 2.128226 ATGGCCAGGAAGGGAGGT 59.872 61.111 13.05 0.00 38.09 3.85
6641 7311 7.361286 CCGAGTATCATATTGATGAAGTCGAGA 60.361 40.741 14.55 0.00 45.23 4.04


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

AutoCloner maintained by Alex Coulton.