Multiple sequence alignment - TraesCS5D01G491400

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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 TraesCS5D01G491400 chr5D 100.000 2507 0 0 1 2507 525304959 525307465 0.000000e+00 4630.0
1 TraesCS5D01G491400 chr5D 84.035 689 77 17 857 1524 525253568 525254244 1.270000e-177 632.0
2 TraesCS5D01G491400 chr5D 79.773 880 126 25 713 1549 525378287 525379157 2.150000e-165 592.0
3 TraesCS5D01G491400 chr5D 82.484 628 89 7 938 1548 525321798 525322421 4.750000e-147 531.0
4 TraesCS5D01G491400 chr5D 78.596 883 124 28 713 1549 23863269 23864132 7.950000e-145 523.0
5 TraesCS5D01G491400 chr3D 95.217 690 19 3 2 678 231894855 231894167 0.000000e+00 1079.0
6 TraesCS5D01G491400 chr3D 89.286 224 22 2 1787 2010 544820618 544820397 1.900000e-71 279.0
7 TraesCS5D01G491400 chr3D 100.000 33 0 0 1741 1773 394577205 394577173 7.490000e-06 62.1
8 TraesCS5D01G491400 chr5A 88.282 879 69 20 680 1537 651748677 651749542 0.000000e+00 1022.0
9 TraesCS5D01G491400 chr5A 84.957 811 97 17 734 1524 651734017 651734822 0.000000e+00 798.0
10 TraesCS5D01G491400 chr5A 86.547 446 46 9 2072 2507 593100447 593100888 1.740000e-131 479.0
11 TraesCS5D01G491400 chr5A 87.500 336 23 12 1 336 691835835 691836151 1.100000e-98 370.0
12 TraesCS5D01G491400 chr5A 95.135 185 9 0 1366 1550 651638898 651639082 2.440000e-75 292.0
13 TraesCS5D01G491400 chr5A 94.444 72 4 0 807 878 651637879 651637950 7.330000e-21 111.0
14 TraesCS5D01G491400 chr5A 96.970 33 1 0 687 719 651733955 651733987 3.480000e-04 56.5
15 TraesCS5D01G491400 chr5B 87.868 882 85 14 680 1551 659625406 659626275 0.000000e+00 1016.0
16 TraesCS5D01G491400 chr5B 79.551 890 118 32 713 1548 659739218 659740097 6.010000e-161 577.0
17 TraesCS5D01G491400 chr5B 79.651 860 118 26 713 1523 659743300 659744151 1.300000e-157 566.0
18 TraesCS5D01G491400 chr5B 79.584 769 92 25 997 1739 659704427 659705156 8.060000e-135 490.0
19 TraesCS5D01G491400 chr5B 91.195 318 24 4 365 679 586866953 586866637 1.780000e-116 429.0
20 TraesCS5D01G491400 chr1D 92.319 703 21 8 1 678 27849883 27850577 0.000000e+00 968.0
21 TraesCS5D01G491400 chr1D 98.765 81 1 0 1 81 453605910 453605990 7.230000e-31 145.0
22 TraesCS5D01G491400 chr1D 95.349 43 2 0 1741 1783 486160998 486160956 4.470000e-08 69.4
23 TraesCS5D01G491400 chrUn 81.579 988 122 35 805 1741 67240538 67241516 0.000000e+00 761.0
24 TraesCS5D01G491400 chrUn 80.435 92 5 5 687 778 67240452 67240530 9.690000e-05 58.4
25 TraesCS5D01G491400 chr4A 91.781 438 29 4 2072 2507 122255971 122256403 9.920000e-169 603.0
26 TraesCS5D01G491400 chr4A 92.188 320 22 3 362 678 680564757 680565076 1.370000e-122 449.0
27 TraesCS5D01G491400 chr4A 91.039 279 23 2 1796 2074 122255146 122255422 2.350000e-100 375.0
28 TraesCS5D01G491400 chr4D 94.051 353 4 1 1 336 507272029 507271677 1.030000e-143 520.0
29 TraesCS5D01G491400 chr4D 94.389 303 16 1 376 678 417466814 417466513 4.880000e-127 464.0
30 TraesCS5D01G491400 chr4D 89.796 245 21 3 2072 2314 32413177 32413419 6.730000e-81 311.0
31 TraesCS5D01G491400 chr4D 88.444 225 25 1 1785 2009 108628806 108629029 1.140000e-68 270.0
32 TraesCS5D01G491400 chr4D 97.531 81 2 0 1 81 475746481 475746401 3.360000e-29 139.0
33 TraesCS5D01G491400 chr2D 94.516 310 14 2 369 678 166314017 166314323 2.260000e-130 475.0
34 TraesCS5D01G491400 chr2D 93.831 308 17 2 376 682 75642170 75641864 1.760000e-126 462.0
35 TraesCS5D01G491400 chr2D 94.079 304 17 1 376 679 629186976 629186674 6.320000e-126 460.0
36 TraesCS5D01G491400 chr2D 94.040 302 17 1 376 677 127257592 127257292 8.170000e-125 457.0
37 TraesCS5D01G491400 chr4B 90.202 347 20 7 1 336 654275510 654275853 8.230000e-120 440.0
38 TraesCS5D01G491400 chr1B 90.462 325 25 3 2183 2507 432445808 432445490 8.290000e-115 424.0
39 TraesCS5D01G491400 chr1B 90.909 275 21 2 1805 2076 432461898 432461625 1.420000e-97 366.0
40 TraesCS5D01G491400 chr1B 76.271 354 59 19 2073 2406 348068569 348068221 5.550000e-37 165.0
41 TraesCS5D01G491400 chr3B 90.000 290 25 4 1787 2076 666684651 666684936 3.050000e-99 372.0
42 TraesCS5D01G491400 chr3B 93.000 200 9 4 2309 2507 666685688 666685883 1.130000e-73 287.0
43 TraesCS5D01G491400 chr3B 91.500 200 11 5 2309 2507 666686563 666686757 1.140000e-68 270.0
44 TraesCS5D01G491400 chr3B 90.640 203 16 2 2073 2273 666685488 666685689 1.480000e-67 267.0
45 TraesCS5D01G491400 chr3B 88.182 220 25 1 1794 2013 538816059 538815841 6.880000e-66 261.0
46 TraesCS5D01G491400 chr3B 90.404 198 16 2 2073 2268 666686363 666686559 8.900000e-65 257.0
47 TraesCS5D01G491400 chr3B 94.828 58 2 1 1 57 815307852 815307909 3.430000e-14 89.8
48 TraesCS5D01G491400 chr3B 95.745 47 2 0 1734 1780 572839018 572839064 2.670000e-10 76.8
49 TraesCS5D01G491400 chr3B 94.595 37 2 0 1743 1779 775485515 775485479 9.690000e-05 58.4
50 TraesCS5D01G491400 chr1A 88.839 224 24 1 1791 2014 490778112 490778334 8.830000e-70 274.0
51 TraesCS5D01G491400 chr7D 87.444 223 27 1 1787 2009 42220980 42220759 3.200000e-64 255.0
52 TraesCS5D01G491400 chr7D 88.482 191 18 3 2072 2259 38641665 38641854 6.980000e-56 228.0
53 TraesCS5D01G491400 chr3A 87.054 224 27 2 1787 2010 538857642 538857863 4.140000e-63 252.0
54 TraesCS5D01G491400 chr3A 100.000 33 0 0 1739 1771 726205216 726205248 7.490000e-06 62.1
55 TraesCS5D01G491400 chr2B 95.652 92 4 0 2286 2377 152708533 152708624 5.590000e-32 148.0
56 TraesCS5D01G491400 chr2B 78.673 211 38 6 2201 2406 211171361 211171153 1.560000e-27 134.0
57 TraesCS5D01G491400 chr2B 97.368 38 0 1 1734 1771 773922906 773922870 2.080000e-06 63.9
58 TraesCS5D01G491400 chr2A 93.878 49 3 0 1740 1788 429123697 429123745 9.620000e-10 75.0
59 TraesCS5D01G491400 chr6D 100.000 33 0 0 1739 1771 431054175 431054143 7.490000e-06 62.1
60 TraesCS5D01G491400 chr7B 92.683 41 3 0 1730 1770 652495761 652495801 2.690000e-05 60.2


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 TraesCS5D01G491400 chr5D 525304959 525307465 2506 False 4630.00 4630 100.0000 1 2507 1 chr5D.!!$F3 2506
1 TraesCS5D01G491400 chr5D 525253568 525254244 676 False 632.00 632 84.0350 857 1524 1 chr5D.!!$F2 667
2 TraesCS5D01G491400 chr5D 525378287 525379157 870 False 592.00 592 79.7730 713 1549 1 chr5D.!!$F5 836
3 TraesCS5D01G491400 chr5D 525321798 525322421 623 False 531.00 531 82.4840 938 1548 1 chr5D.!!$F4 610
4 TraesCS5D01G491400 chr5D 23863269 23864132 863 False 523.00 523 78.5960 713 1549 1 chr5D.!!$F1 836
5 TraesCS5D01G491400 chr3D 231894167 231894855 688 True 1079.00 1079 95.2170 2 678 1 chr3D.!!$R1 676
6 TraesCS5D01G491400 chr5A 651748677 651749542 865 False 1022.00 1022 88.2820 680 1537 1 chr5A.!!$F2 857
7 TraesCS5D01G491400 chr5A 651733955 651734822 867 False 427.25 798 90.9635 687 1524 2 chr5A.!!$F5 837
8 TraesCS5D01G491400 chr5A 651637879 651639082 1203 False 201.50 292 94.7895 807 1550 2 chr5A.!!$F4 743
9 TraesCS5D01G491400 chr5B 659625406 659626275 869 False 1016.00 1016 87.8680 680 1551 1 chr5B.!!$F1 871
10 TraesCS5D01G491400 chr5B 659739218 659744151 4933 False 571.50 577 79.6010 713 1548 2 chr5B.!!$F3 835
11 TraesCS5D01G491400 chr5B 659704427 659705156 729 False 490.00 490 79.5840 997 1739 1 chr5B.!!$F2 742
12 TraesCS5D01G491400 chr1D 27849883 27850577 694 False 968.00 968 92.3190 1 678 1 chr1D.!!$F1 677
13 TraesCS5D01G491400 chrUn 67240452 67241516 1064 False 409.70 761 81.0070 687 1741 2 chrUn.!!$F1 1054
14 TraesCS5D01G491400 chr4A 122255146 122256403 1257 False 489.00 603 91.4100 1796 2507 2 chr4A.!!$F2 711
15 TraesCS5D01G491400 chr3B 666684651 666686757 2106 False 290.60 372 91.1088 1787 2507 5 chr3B.!!$F3 720

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
604 630 0.036294 GCCCCAGACTTGGTACTGAC 60.036 60.0 0.0 0.0 43.4 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 6580 0.09473 GCAACGCACGGACATTCTAC 59.905 55.0 0.0 0.0 0.0 2.59 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
354 380 3.541713 GCCGGCTGAGGTAGGAGG 61.542 72.222 22.15 0.00 0.00 4.30
355 381 3.541713 CCGGCTGAGGTAGGAGGC 61.542 72.222 0.00 0.00 0.00 4.70
356 382 3.541713 CGGCTGAGGTAGGAGGCC 61.542 72.222 0.00 0.00 39.43 5.19
357 383 3.541713 GGCTGAGGTAGGAGGCCG 61.542 72.222 0.00 0.00 33.30 6.13
358 384 4.228567 GCTGAGGTAGGAGGCCGC 62.229 72.222 0.00 0.00 0.00 6.53
359 385 3.541713 CTGAGGTAGGAGGCCGCC 61.542 72.222 19.43 19.43 0.00 6.13
360 386 4.392166 TGAGGTAGGAGGCCGCCA 62.392 66.667 28.68 10.95 0.00 5.69
361 387 3.851128 GAGGTAGGAGGCCGCCAC 61.851 72.222 28.68 21.43 0.00 5.01
389 415 3.464494 CGAGGGGACGGGGGTTAC 61.464 72.222 0.00 0.00 0.00 2.50
390 416 3.464494 GAGGGGACGGGGGTTACG 61.464 72.222 0.00 0.00 37.36 3.18
394 420 3.464494 GGACGGGGGTTACGGGAG 61.464 72.222 0.00 0.00 35.23 4.30
395 421 3.464494 GACGGGGGTTACGGGAGG 61.464 72.222 0.00 0.00 35.23 4.30
399 425 3.393106 GGGGTTACGGGAGGCGAA 61.393 66.667 0.00 0.00 0.00 4.70
400 426 2.186125 GGGTTACGGGAGGCGAAG 59.814 66.667 0.00 0.00 0.00 3.79
401 427 2.186125 GGTTACGGGAGGCGAAGG 59.814 66.667 0.00 0.00 0.00 3.46
402 428 2.353610 GGTTACGGGAGGCGAAGGA 61.354 63.158 0.00 0.00 0.00 3.36
403 429 1.141234 GTTACGGGAGGCGAAGGAG 59.859 63.158 0.00 0.00 0.00 3.69
404 430 2.718073 TTACGGGAGGCGAAGGAGC 61.718 63.158 0.00 0.00 0.00 4.70
405 431 3.949885 TACGGGAGGCGAAGGAGCA 62.950 63.158 0.00 0.00 39.27 4.26
406 432 4.821589 CGGGAGGCGAAGGAGCAC 62.822 72.222 0.00 0.00 39.27 4.40
407 433 4.821589 GGGAGGCGAAGGAGCACG 62.822 72.222 0.00 0.00 39.27 5.34
408 434 4.821589 GGAGGCGAAGGAGCACGG 62.822 72.222 0.00 0.00 39.27 4.94
409 435 4.821589 GAGGCGAAGGAGCACGGG 62.822 72.222 0.00 0.00 39.27 5.28
434 460 2.920384 GGCTCCTCCCCTCGATCC 60.920 72.222 0.00 0.00 0.00 3.36
435 461 2.123251 GCTCCTCCCCTCGATCCA 60.123 66.667 0.00 0.00 0.00 3.41
436 462 2.206536 GCTCCTCCCCTCGATCCAG 61.207 68.421 0.00 0.00 0.00 3.86
437 463 1.539165 CTCCTCCCCTCGATCCAGA 59.461 63.158 0.00 0.00 0.00 3.86
438 464 0.114168 CTCCTCCCCTCGATCCAGAT 59.886 60.000 0.00 0.00 0.00 2.90
439 465 0.113385 TCCTCCCCTCGATCCAGATC 59.887 60.000 0.00 0.00 34.56 2.75
472 498 1.079750 GTGAGGACGAAGGAGGTGC 60.080 63.158 0.00 0.00 0.00 5.01
473 499 2.182030 GAGGACGAAGGAGGTGCG 59.818 66.667 0.00 0.00 0.00 5.34
474 500 3.358076 GAGGACGAAGGAGGTGCGG 62.358 68.421 0.00 0.00 0.00 5.69
475 501 4.452733 GGACGAAGGAGGTGCGGG 62.453 72.222 0.00 0.00 0.00 6.13
476 502 4.452733 GACGAAGGAGGTGCGGGG 62.453 72.222 0.00 0.00 0.00 5.73
507 533 3.871775 AAAAATGCCACGTCAGCAG 57.128 47.368 14.50 0.00 44.90 4.24
508 534 0.318955 AAAAATGCCACGTCAGCAGC 60.319 50.000 14.50 0.67 44.90 5.25
509 535 1.174712 AAAATGCCACGTCAGCAGCT 61.175 50.000 14.50 0.00 44.90 4.24
510 536 1.859427 AAATGCCACGTCAGCAGCTG 61.859 55.000 17.10 17.10 44.90 4.24
511 537 2.736579 AATGCCACGTCAGCAGCTGA 62.737 55.000 21.85 21.85 44.90 4.26
518 544 4.383861 TCAGCAGCTGACAGGCGG 62.384 66.667 21.85 1.77 35.39 6.13
535 561 3.161450 GGCCCTGCCGGTCAGATA 61.161 66.667 22.49 0.00 45.72 1.98
536 562 2.109181 GCCCTGCCGGTCAGATAC 59.891 66.667 22.49 10.65 45.72 2.24
537 563 2.731571 GCCCTGCCGGTCAGATACA 61.732 63.158 22.49 1.81 45.72 2.29
538 564 1.144057 CCCTGCCGGTCAGATACAC 59.856 63.158 22.49 0.00 45.72 2.90
539 565 1.330655 CCCTGCCGGTCAGATACACT 61.331 60.000 22.49 0.00 45.72 3.55
540 566 0.179100 CCTGCCGGTCAGATACACTG 60.179 60.000 22.49 5.03 45.72 3.66
541 567 0.532573 CTGCCGGTCAGATACACTGT 59.467 55.000 17.75 0.00 45.72 3.55
542 568 0.530744 TGCCGGTCAGATACACTGTC 59.469 55.000 1.90 0.00 45.86 3.51
543 569 0.530744 GCCGGTCAGATACACTGTCA 59.469 55.000 1.90 0.00 45.86 3.58
544 570 1.067142 GCCGGTCAGATACACTGTCAA 60.067 52.381 1.90 0.00 45.86 3.18
545 571 2.418746 GCCGGTCAGATACACTGTCAAT 60.419 50.000 1.90 0.00 45.86 2.57
546 572 3.181479 GCCGGTCAGATACACTGTCAATA 60.181 47.826 1.90 0.00 45.86 1.90
547 573 4.679639 GCCGGTCAGATACACTGTCAATAA 60.680 45.833 1.90 0.00 45.86 1.40
548 574 5.043903 CCGGTCAGATACACTGTCAATAAG 58.956 45.833 0.00 0.00 45.86 1.73
549 575 4.504461 CGGTCAGATACACTGTCAATAAGC 59.496 45.833 0.00 0.00 45.86 3.09
550 576 4.504461 GGTCAGATACACTGTCAATAAGCG 59.496 45.833 0.00 0.00 45.86 4.68
551 577 5.103000 GTCAGATACACTGTCAATAAGCGT 58.897 41.667 0.00 0.00 45.86 5.07
552 578 5.577164 GTCAGATACACTGTCAATAAGCGTT 59.423 40.000 0.00 0.00 45.86 4.84
553 579 6.090898 GTCAGATACACTGTCAATAAGCGTTT 59.909 38.462 0.00 0.00 45.86 3.60
554 580 7.274904 GTCAGATACACTGTCAATAAGCGTTTA 59.725 37.037 0.00 0.00 45.86 2.01
555 581 7.979537 TCAGATACACTGTCAATAAGCGTTTAT 59.020 33.333 0.00 0.00 45.86 1.40
556 582 9.244799 CAGATACACTGTCAATAAGCGTTTATA 57.755 33.333 4.86 0.00 41.30 0.98
557 583 9.245962 AGATACACTGTCAATAAGCGTTTATAC 57.754 33.333 4.86 1.90 0.00 1.47
571 597 5.878261 CGTTTATACGCGATTTAGACCTT 57.122 39.130 15.93 0.00 41.41 3.50
572 598 6.264909 CGTTTATACGCGATTTAGACCTTT 57.735 37.500 15.93 0.00 41.41 3.11
573 599 6.699063 CGTTTATACGCGATTTAGACCTTTT 58.301 36.000 15.93 0.00 41.41 2.27
574 600 7.175410 CGTTTATACGCGATTTAGACCTTTTT 58.825 34.615 15.93 0.00 41.41 1.94
575 601 7.161418 CGTTTATACGCGATTTAGACCTTTTTG 59.839 37.037 15.93 0.00 41.41 2.44
576 602 7.599630 TTATACGCGATTTAGACCTTTTTGT 57.400 32.000 15.93 0.00 0.00 2.83
577 603 8.700722 TTATACGCGATTTAGACCTTTTTGTA 57.299 30.769 15.93 0.00 0.00 2.41
578 604 5.927954 ACGCGATTTAGACCTTTTTGTAA 57.072 34.783 15.93 0.00 0.00 2.41
579 605 5.682869 ACGCGATTTAGACCTTTTTGTAAC 58.317 37.500 15.93 0.00 0.00 2.50
580 606 4.779523 CGCGATTTAGACCTTTTTGTAACG 59.220 41.667 0.00 0.00 0.00 3.18
581 607 5.613142 CGCGATTTAGACCTTTTTGTAACGT 60.613 40.000 0.00 0.00 0.00 3.99
582 608 5.787062 GCGATTTAGACCTTTTTGTAACGTC 59.213 40.000 0.00 0.00 0.00 4.34
583 609 6.347160 GCGATTTAGACCTTTTTGTAACGTCT 60.347 38.462 0.00 0.00 37.54 4.18
584 610 7.148755 GCGATTTAGACCTTTTTGTAACGTCTA 60.149 37.037 0.00 0.00 35.50 2.59
585 611 8.371053 CGATTTAGACCTTTTTGTAACGTCTAG 58.629 37.037 0.00 0.00 37.36 2.43
586 612 7.412137 TTTAGACCTTTTTGTAACGTCTAGC 57.588 36.000 0.00 0.00 37.36 3.42
587 613 4.313282 AGACCTTTTTGTAACGTCTAGCC 58.687 43.478 0.00 0.00 32.15 3.93
588 614 3.405831 ACCTTTTTGTAACGTCTAGCCC 58.594 45.455 0.00 0.00 0.00 5.19
589 615 2.745821 CCTTTTTGTAACGTCTAGCCCC 59.254 50.000 0.00 0.00 0.00 5.80
590 616 3.404899 CTTTTTGTAACGTCTAGCCCCA 58.595 45.455 0.00 0.00 0.00 4.96
591 617 2.754946 TTTGTAACGTCTAGCCCCAG 57.245 50.000 0.00 0.00 0.00 4.45
592 618 1.927487 TTGTAACGTCTAGCCCCAGA 58.073 50.000 0.00 0.00 0.00 3.86
593 619 1.180029 TGTAACGTCTAGCCCCAGAC 58.820 55.000 0.00 1.55 41.33 3.51
594 620 1.272313 TGTAACGTCTAGCCCCAGACT 60.272 52.381 8.56 0.00 42.36 3.24
595 621 1.823610 GTAACGTCTAGCCCCAGACTT 59.176 52.381 8.56 5.46 42.36 3.01
596 622 0.608640 AACGTCTAGCCCCAGACTTG 59.391 55.000 8.56 0.00 42.36 3.16
597 623 1.258445 ACGTCTAGCCCCAGACTTGG 61.258 60.000 8.56 0.00 42.36 3.61
598 624 1.258445 CGTCTAGCCCCAGACTTGGT 61.258 60.000 8.56 0.00 43.40 3.67
599 625 1.861982 GTCTAGCCCCAGACTTGGTA 58.138 55.000 4.00 0.00 43.40 3.25
600 626 1.481363 GTCTAGCCCCAGACTTGGTAC 59.519 57.143 4.00 0.00 43.40 3.34
601 627 1.361543 TCTAGCCCCAGACTTGGTACT 59.638 52.381 0.00 0.00 43.40 2.73
602 628 1.482593 CTAGCCCCAGACTTGGTACTG 59.517 57.143 0.00 0.00 43.40 2.74
603 629 0.178903 AGCCCCAGACTTGGTACTGA 60.179 55.000 0.00 0.00 43.40 3.41
604 630 0.036294 GCCCCAGACTTGGTACTGAC 60.036 60.000 0.00 0.00 43.40 3.51
605 631 1.348064 CCCCAGACTTGGTACTGACA 58.652 55.000 0.00 0.00 43.40 3.58
606 632 1.909302 CCCCAGACTTGGTACTGACAT 59.091 52.381 0.00 0.00 43.40 3.06
607 633 2.355108 CCCCAGACTTGGTACTGACATG 60.355 54.545 0.00 0.00 43.40 3.21
608 634 2.303022 CCCAGACTTGGTACTGACATGT 59.697 50.000 0.00 0.00 43.40 3.21
609 635 3.513912 CCCAGACTTGGTACTGACATGTA 59.486 47.826 0.00 0.00 43.40 2.29
610 636 4.020573 CCCAGACTTGGTACTGACATGTAA 60.021 45.833 0.00 0.00 43.40 2.41
611 637 5.512404 CCCAGACTTGGTACTGACATGTAAA 60.512 44.000 0.00 0.00 43.40 2.01
612 638 5.995282 CCAGACTTGGTACTGACATGTAAAA 59.005 40.000 0.00 0.00 39.79 1.52
613 639 6.485313 CCAGACTTGGTACTGACATGTAAAAA 59.515 38.462 0.00 0.00 39.79 1.94
614 640 7.174946 CCAGACTTGGTACTGACATGTAAAAAT 59.825 37.037 0.00 0.00 39.79 1.82
615 641 8.567948 CAGACTTGGTACTGACATGTAAAAATT 58.432 33.333 0.00 0.00 36.38 1.82
616 642 9.787435 AGACTTGGTACTGACATGTAAAAATTA 57.213 29.630 0.00 0.00 0.00 1.40
617 643 9.821662 GACTTGGTACTGACATGTAAAAATTAC 57.178 33.333 0.00 0.00 0.00 1.89
618 644 8.789762 ACTTGGTACTGACATGTAAAAATTACC 58.210 33.333 0.00 5.12 0.00 2.85
619 645 8.693120 TTGGTACTGACATGTAAAAATTACCA 57.307 30.769 0.00 7.63 35.72 3.25
620 646 8.693120 TGGTACTGACATGTAAAAATTACCAA 57.307 30.769 14.30 4.21 34.82 3.67
621 647 9.132923 TGGTACTGACATGTAAAAATTACCAAA 57.867 29.630 14.30 0.00 34.82 3.28
622 648 9.401873 GGTACTGACATGTAAAAATTACCAAAC 57.598 33.333 0.00 0.00 0.00 2.93
636 662 9.705290 AAAATTACCAAACTTAATACCAAGCTG 57.295 29.630 0.00 0.00 0.00 4.24
637 663 4.783764 ACCAAACTTAATACCAAGCTGC 57.216 40.909 0.00 0.00 0.00 5.25
638 664 4.407365 ACCAAACTTAATACCAAGCTGCT 58.593 39.130 0.00 0.00 0.00 4.24
639 665 4.832823 ACCAAACTTAATACCAAGCTGCTT 59.167 37.500 9.53 9.53 0.00 3.91
640 666 5.048013 ACCAAACTTAATACCAAGCTGCTTC 60.048 40.000 12.82 0.00 0.00 3.86
641 667 5.402398 CAAACTTAATACCAAGCTGCTTCC 58.598 41.667 12.82 0.00 0.00 3.46
642 668 4.301072 ACTTAATACCAAGCTGCTTCCA 57.699 40.909 12.82 0.59 0.00 3.53
643 669 4.662278 ACTTAATACCAAGCTGCTTCCAA 58.338 39.130 12.82 0.60 0.00 3.53
644 670 5.264395 ACTTAATACCAAGCTGCTTCCAAT 58.736 37.500 12.82 3.11 0.00 3.16
645 671 5.126061 ACTTAATACCAAGCTGCTTCCAATG 59.874 40.000 12.82 1.21 0.00 2.82
646 672 1.176527 TACCAAGCTGCTTCCAATGC 58.823 50.000 12.82 0.00 0.00 3.56
647 673 1.217244 CCAAGCTGCTTCCAATGCC 59.783 57.895 12.82 0.00 0.00 4.40
648 674 1.255667 CCAAGCTGCTTCCAATGCCT 61.256 55.000 12.82 0.00 0.00 4.75
649 675 0.172803 CAAGCTGCTTCCAATGCCTC 59.827 55.000 12.82 0.00 0.00 4.70
650 676 1.310933 AAGCTGCTTCCAATGCCTCG 61.311 55.000 9.53 0.00 0.00 4.63
651 677 1.746615 GCTGCTTCCAATGCCTCGA 60.747 57.895 0.00 0.00 0.00 4.04
652 678 1.099879 GCTGCTTCCAATGCCTCGAT 61.100 55.000 0.00 0.00 0.00 3.59
653 679 0.661552 CTGCTTCCAATGCCTCGATG 59.338 55.000 0.00 0.00 0.00 3.84
654 680 0.749091 TGCTTCCAATGCCTCGATGG 60.749 55.000 0.00 0.00 39.35 3.51
655 681 0.749454 GCTTCCAATGCCTCGATGGT 60.749 55.000 2.09 0.00 38.35 3.55
656 682 1.019673 CTTCCAATGCCTCGATGGTG 58.980 55.000 2.09 0.00 38.35 4.17
657 683 0.394216 TTCCAATGCCTCGATGGTGG 60.394 55.000 2.09 3.15 38.35 4.61
658 684 1.077501 CCAATGCCTCGATGGTGGT 60.078 57.895 0.00 0.00 38.35 4.16
659 685 0.180171 CCAATGCCTCGATGGTGGTA 59.820 55.000 0.00 0.00 38.35 3.25
660 686 1.299541 CAATGCCTCGATGGTGGTAC 58.700 55.000 0.00 0.00 38.35 3.34
661 687 1.134401 CAATGCCTCGATGGTGGTACT 60.134 52.381 0.00 0.00 38.35 2.73
662 688 1.204146 ATGCCTCGATGGTGGTACTT 58.796 50.000 0.00 0.00 38.35 2.24
663 689 0.535335 TGCCTCGATGGTGGTACTTC 59.465 55.000 0.00 0.00 38.35 3.01
664 690 0.824759 GCCTCGATGGTGGTACTTCT 59.175 55.000 0.00 0.00 38.35 2.85
665 691 1.471676 GCCTCGATGGTGGTACTTCTG 60.472 57.143 0.00 0.00 38.35 3.02
666 692 1.825474 CCTCGATGGTGGTACTTCTGT 59.175 52.381 0.00 0.00 0.00 3.41
667 693 2.417379 CCTCGATGGTGGTACTTCTGTG 60.417 54.545 0.00 0.00 0.00 3.66
668 694 1.067142 TCGATGGTGGTACTTCTGTGC 60.067 52.381 0.00 0.00 0.00 4.57
669 695 1.337728 CGATGGTGGTACTTCTGTGCA 60.338 52.381 0.00 0.00 0.00 4.57
670 696 2.778299 GATGGTGGTACTTCTGTGCAA 58.222 47.619 0.00 0.00 0.00 4.08
671 697 2.949177 TGGTGGTACTTCTGTGCAAT 57.051 45.000 0.00 0.00 0.00 3.56
672 698 3.222173 TGGTGGTACTTCTGTGCAATT 57.778 42.857 0.00 0.00 0.00 2.32
673 699 3.561143 TGGTGGTACTTCTGTGCAATTT 58.439 40.909 0.00 0.00 0.00 1.82
674 700 4.720046 TGGTGGTACTTCTGTGCAATTTA 58.280 39.130 0.00 0.00 0.00 1.40
675 701 4.517453 TGGTGGTACTTCTGTGCAATTTAC 59.483 41.667 0.00 0.00 0.00 2.01
676 702 4.760204 GGTGGTACTTCTGTGCAATTTACT 59.240 41.667 0.00 0.00 0.00 2.24
677 703 5.106673 GGTGGTACTTCTGTGCAATTTACTC 60.107 44.000 0.00 0.00 0.00 2.59
678 704 5.468746 GTGGTACTTCTGTGCAATTTACTCA 59.531 40.000 0.00 0.00 0.00 3.41
688 714 2.546368 GCAATTTACTCACACCACACGA 59.454 45.455 0.00 0.00 0.00 4.35
720 748 1.133598 ACGCACGACTGAAATATCCGA 59.866 47.619 0.00 0.00 0.00 4.55
747 803 1.099295 ATCCTATCCGTCACGTCGCA 61.099 55.000 0.00 0.00 0.00 5.10
899 982 4.414956 TCTCCCCTGCCGACCCAT 62.415 66.667 0.00 0.00 0.00 4.00
900 983 3.866582 CTCCCCTGCCGACCCATC 61.867 72.222 0.00 0.00 0.00 3.51
901 984 4.414956 TCCCCTGCCGACCCATCT 62.415 66.667 0.00 0.00 0.00 2.90
950 1051 3.006323 ACAACTCCACAACAGCACAAAAA 59.994 39.130 0.00 0.00 0.00 1.94
967 1068 3.795561 AAAAAGCTTCGATCACAGACG 57.204 42.857 0.00 0.00 0.00 4.18
969 1070 2.270275 AAGCTTCGATCACAGACGAG 57.730 50.000 0.00 0.00 39.59 4.18
975 5205 0.733909 CGATCACAGACGAGCAGCAA 60.734 55.000 0.00 0.00 0.00 3.91
982 5212 2.816087 ACAGACGAGCAGCAAATCATTT 59.184 40.909 0.00 0.00 0.00 2.32
1007 5243 1.964223 GAGTAGCGAATCCATGGGAGA 59.036 52.381 13.02 0.00 34.05 3.71
1023 5259 4.838152 GAGGGGATGAAGCGCGCA 62.838 66.667 35.10 13.97 0.00 6.09
1041 5277 1.539869 AAGGGAGAAGGAGCCAGCA 60.540 57.895 0.00 0.00 0.00 4.41
1043 5279 2.124778 GGAGAAGGAGCCAGCAGC 60.125 66.667 0.00 0.00 44.25 5.25
1064 5300 2.186384 GCTGGCGCTGTCTCTCAT 59.814 61.111 7.64 0.00 0.00 2.90
1074 5310 2.491298 GCTGTCTCTCATCACAGACTCA 59.509 50.000 3.24 0.00 42.37 3.41
1089 5331 1.176619 ACTCATCGACGTCCACCACA 61.177 55.000 10.58 0.00 0.00 4.17
1368 5636 1.367471 CACACTGGGCTTCGAGACA 59.633 57.895 0.00 0.00 0.00 3.41
1554 6374 5.941058 TGTTAGTTCAGGACTTGTTTGTTCA 59.059 36.000 0.00 0.00 39.86 3.18
1557 6377 4.095610 GTTCAGGACTTGTTTGTTCAACG 58.904 43.478 0.00 0.00 38.36 4.10
1559 6379 3.372822 TCAGGACTTGTTTGTTCAACGTC 59.627 43.478 0.00 0.00 38.36 4.34
1573 6393 5.575218 TGTTCAACGTCGTATAGAGTACGTA 59.425 40.000 0.00 0.00 46.89 3.57
1645 6469 5.642063 GTCCATTTTCTAACCGATTGACTGA 59.358 40.000 0.00 0.00 0.00 3.41
1662 6495 4.275689 TGACTGAAGGTTTACATGCACTTG 59.724 41.667 0.00 0.00 0.00 3.16
1663 6496 4.207165 ACTGAAGGTTTACATGCACTTGT 58.793 39.130 0.00 0.00 0.00 3.16
1664 6497 5.373222 ACTGAAGGTTTACATGCACTTGTA 58.627 37.500 0.00 0.00 0.00 2.41
1665 6498 6.003950 ACTGAAGGTTTACATGCACTTGTAT 58.996 36.000 1.13 0.00 32.39 2.29
1666 6499 7.165485 ACTGAAGGTTTACATGCACTTGTATA 58.835 34.615 1.13 0.00 32.39 1.47
1667 6500 7.119262 ACTGAAGGTTTACATGCACTTGTATAC 59.881 37.037 10.74 10.74 34.94 1.47
1668 6501 6.937465 TGAAGGTTTACATGCACTTGTATACA 59.063 34.615 17.32 0.08 36.40 2.29
1680 6515 8.196802 TGCACTTGTATACATAATGAAGACAC 57.803 34.615 6.36 0.00 0.00 3.67
1693 6529 4.545823 TGAAGACACATTCGTTTGTTCC 57.454 40.909 0.00 0.00 26.92 3.62
1700 6536 4.050553 CACATTCGTTTGTTCCAAATGCT 58.949 39.130 4.44 0.00 31.96 3.79
1718 6554 6.710597 AATGCTATTGACAGATTCTTGCAT 57.289 33.333 0.00 0.00 39.81 3.96
1741 6577 9.455847 GCATCCAGATTGTTTTTCTATGAATAC 57.544 33.333 0.00 0.00 0.00 1.89
1756 6592 9.570468 TTCTATGAATACTAGTAGAATGTCCGT 57.430 33.333 8.85 0.00 30.53 4.69
1757 6593 9.000486 TCTATGAATACTAGTAGAATGTCCGTG 58.000 37.037 8.85 0.00 0.00 4.94
1758 6594 5.828747 TGAATACTAGTAGAATGTCCGTGC 58.171 41.667 8.85 0.00 0.00 5.34
1759 6595 2.846039 ACTAGTAGAATGTCCGTGCG 57.154 50.000 3.59 0.00 0.00 5.34
1760 6596 2.089980 ACTAGTAGAATGTCCGTGCGT 58.910 47.619 3.59 0.00 0.00 5.24
1761 6597 2.490903 ACTAGTAGAATGTCCGTGCGTT 59.509 45.455 3.59 0.00 0.00 4.84
1762 6598 1.710013 AGTAGAATGTCCGTGCGTTG 58.290 50.000 0.00 0.00 0.00 4.10
1763 6599 0.094730 GTAGAATGTCCGTGCGTTGC 59.905 55.000 0.00 0.00 0.00 4.17
1764 6600 1.017177 TAGAATGTCCGTGCGTTGCC 61.017 55.000 0.00 0.00 0.00 4.52
1765 6601 2.593148 AATGTCCGTGCGTTGCCA 60.593 55.556 0.00 0.00 0.00 4.92
1766 6602 2.780149 GAATGTCCGTGCGTTGCCAC 62.780 60.000 0.00 0.00 0.00 5.01
1994 6830 9.262472 CACAAATCTTATACGCAGAGTAAAAAC 57.738 33.333 0.00 0.00 39.04 2.43
2017 6853 3.949113 GACTGGAGGGAGTACTTCACTAG 59.051 52.174 2.92 6.48 40.54 2.57
2044 6880 3.307691 CCACTCCACTCAAAATCTGGCTA 60.308 47.826 0.00 0.00 0.00 3.93
2062 6898 1.900486 CTAGTGTTTCCTCCGGGTCTT 59.100 52.381 0.00 0.00 0.00 3.01
2063 6899 2.019807 AGTGTTTCCTCCGGGTCTTA 57.980 50.000 0.00 0.00 0.00 2.10
2064 6900 2.547990 AGTGTTTCCTCCGGGTCTTAT 58.452 47.619 0.00 0.00 0.00 1.73
2065 6901 2.500504 AGTGTTTCCTCCGGGTCTTATC 59.499 50.000 0.00 0.00 0.00 1.75
2068 6904 3.328343 TGTTTCCTCCGGGTCTTATCAAA 59.672 43.478 0.00 0.00 0.00 2.69
2070 6906 4.855298 TTCCTCCGGGTCTTATCAAATT 57.145 40.909 0.00 0.00 0.00 1.82
2100 7490 4.850386 ACCACAACTTTCCCTAAGTAGGAT 59.150 41.667 5.91 0.00 46.34 3.24
2194 7586 3.283751 ACCTCGAGTGATTCTCCTACTG 58.716 50.000 12.31 0.00 39.84 2.74
2209 7601 2.159366 CCTACTGCTACAACCTCAGTCG 60.159 54.545 0.00 0.00 40.96 4.18
2261 7653 3.502191 TGCTTGTTTCTTTGACACACC 57.498 42.857 0.00 0.00 0.00 4.16
2268 7660 4.082463 TGTTTCTTTGACACACCCTCAAAC 60.082 41.667 0.00 0.00 34.60 2.93
2280 7672 4.160814 ACACCCTCAAACCAGTTAAAAACC 59.839 41.667 0.00 0.00 0.00 3.27
2282 7674 3.070446 CCCTCAAACCAGTTAAAAACCCC 59.930 47.826 0.00 0.00 0.00 4.95
2283 7675 3.707102 CCTCAAACCAGTTAAAAACCCCA 59.293 43.478 0.00 0.00 0.00 4.96
2300 7692 4.939255 ACCCCATTGATGAGATTCTTTGT 58.061 39.130 0.00 0.00 0.00 2.83
2490 7882 5.560724 TCCTTTTTCAACCATCTCGATCTT 58.439 37.500 0.00 0.00 0.00 2.40
2491 7883 6.003950 TCCTTTTTCAACCATCTCGATCTTT 58.996 36.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 284 4.941713 AGCTCTTCTTCTTCTTCCTCCTA 58.058 43.478 0.00 0.00 0.00 2.94
372 398 3.464494 GTAACCCCCGTCCCCTCG 61.464 72.222 0.00 0.00 0.00 4.63
373 399 3.464494 CGTAACCCCCGTCCCCTC 61.464 72.222 0.00 0.00 0.00 4.30
377 403 3.464494 CTCCCGTAACCCCCGTCC 61.464 72.222 0.00 0.00 0.00 4.79
378 404 3.464494 CCTCCCGTAACCCCCGTC 61.464 72.222 0.00 0.00 0.00 4.79
382 408 3.381333 CTTCGCCTCCCGTAACCCC 62.381 68.421 0.00 0.00 38.35 4.95
383 409 2.186125 CTTCGCCTCCCGTAACCC 59.814 66.667 0.00 0.00 38.35 4.11
384 410 2.186125 CCTTCGCCTCCCGTAACC 59.814 66.667 0.00 0.00 38.35 2.85
385 411 1.141234 CTCCTTCGCCTCCCGTAAC 59.859 63.158 0.00 0.00 38.35 2.50
386 412 2.718073 GCTCCTTCGCCTCCCGTAA 61.718 63.158 0.00 0.00 38.35 3.18
387 413 3.145551 GCTCCTTCGCCTCCCGTA 61.146 66.667 0.00 0.00 38.35 4.02
389 415 4.821589 GTGCTCCTTCGCCTCCCG 62.822 72.222 0.00 0.00 38.61 5.14
390 416 4.821589 CGTGCTCCTTCGCCTCCC 62.822 72.222 0.00 0.00 0.00 4.30
391 417 4.821589 CCGTGCTCCTTCGCCTCC 62.822 72.222 0.00 0.00 0.00 4.30
392 418 4.821589 CCCGTGCTCCTTCGCCTC 62.822 72.222 0.00 0.00 0.00 4.70
417 443 2.920384 GGATCGAGGGGAGGAGCC 60.920 72.222 0.00 0.00 0.00 4.70
418 444 2.123251 TGGATCGAGGGGAGGAGC 60.123 66.667 0.00 0.00 0.00 4.70
419 445 0.114168 ATCTGGATCGAGGGGAGGAG 59.886 60.000 4.78 0.00 0.00 3.69
420 446 0.113385 GATCTGGATCGAGGGGAGGA 59.887 60.000 4.78 0.00 0.00 3.71
421 447 2.664825 GATCTGGATCGAGGGGAGG 58.335 63.158 4.78 0.00 0.00 4.30
448 474 4.753877 CTTCGTCCTCACGCGCGA 62.754 66.667 39.36 14.99 46.28 5.87
450 476 4.415332 TCCTTCGTCCTCACGCGC 62.415 66.667 5.73 0.00 46.28 6.86
451 477 2.202492 CTCCTTCGTCCTCACGCG 60.202 66.667 3.53 3.53 46.28 6.01
452 478 2.182030 CCTCCTTCGTCCTCACGC 59.818 66.667 0.00 0.00 46.28 5.34
454 480 1.079750 GCACCTCCTTCGTCCTCAC 60.080 63.158 0.00 0.00 0.00 3.51
455 481 2.636412 CGCACCTCCTTCGTCCTCA 61.636 63.158 0.00 0.00 0.00 3.86
456 482 2.182030 CGCACCTCCTTCGTCCTC 59.818 66.667 0.00 0.00 0.00 3.71
457 483 3.382832 CCGCACCTCCTTCGTCCT 61.383 66.667 0.00 0.00 0.00 3.85
458 484 4.452733 CCCGCACCTCCTTCGTCC 62.453 72.222 0.00 0.00 0.00 4.79
459 485 4.452733 CCCCGCACCTCCTTCGTC 62.453 72.222 0.00 0.00 0.00 4.20
489 515 0.318955 GCTGCTGACGTGGCATTTTT 60.319 50.000 12.25 0.00 39.07 1.94
490 516 1.174712 AGCTGCTGACGTGGCATTTT 61.175 50.000 12.25 0.88 39.07 1.82
491 517 1.601759 AGCTGCTGACGTGGCATTT 60.602 52.632 12.25 2.94 39.07 2.32
492 518 2.033141 AGCTGCTGACGTGGCATT 59.967 55.556 12.25 3.24 39.07 3.56
493 519 2.745100 CAGCTGCTGACGTGGCAT 60.745 61.111 24.88 0.00 39.07 4.40
494 520 3.927548 TCAGCTGCTGACGTGGCA 61.928 61.111 27.35 11.48 35.39 4.92
501 527 4.383861 CCGCCTGTCAGCTGCTGA 62.384 66.667 27.35 27.35 38.25 4.26
520 546 1.144057 GTGTATCTGACCGGCAGGG 59.856 63.158 20.90 0.00 44.98 4.45
521 547 0.179100 CAGTGTATCTGACCGGCAGG 60.179 60.000 20.90 0.00 46.27 4.85
522 548 0.532573 ACAGTGTATCTGACCGGCAG 59.467 55.000 16.84 16.84 46.27 4.85
523 549 0.530744 GACAGTGTATCTGACCGGCA 59.469 55.000 0.00 0.00 46.27 5.69
524 550 0.530744 TGACAGTGTATCTGACCGGC 59.469 55.000 0.00 0.00 46.27 6.13
525 551 3.526931 ATTGACAGTGTATCTGACCGG 57.473 47.619 0.00 0.00 46.27 5.28
526 552 4.504461 GCTTATTGACAGTGTATCTGACCG 59.496 45.833 0.00 0.00 46.27 4.79
527 553 4.504461 CGCTTATTGACAGTGTATCTGACC 59.496 45.833 0.00 0.00 46.27 4.02
528 554 5.103000 ACGCTTATTGACAGTGTATCTGAC 58.897 41.667 0.00 0.00 46.27 3.51
529 555 5.324784 ACGCTTATTGACAGTGTATCTGA 57.675 39.130 0.00 0.00 46.27 3.27
531 557 9.245962 GTATAAACGCTTATTGACAGTGTATCT 57.754 33.333 0.00 0.00 33.77 1.98
532 558 8.205948 CGTATAAACGCTTATTGACAGTGTATC 58.794 37.037 0.00 0.00 43.12 2.24
533 559 8.057812 CGTATAAACGCTTATTGACAGTGTAT 57.942 34.615 0.00 0.00 43.12 2.29
534 560 7.440541 CGTATAAACGCTTATTGACAGTGTA 57.559 36.000 0.00 0.00 43.12 2.90
535 561 6.327177 CGTATAAACGCTTATTGACAGTGT 57.673 37.500 0.00 0.00 43.12 3.55
550 576 7.959109 ACAAAAAGGTCTAAATCGCGTATAAAC 59.041 33.333 5.77 0.00 0.00 2.01
551 577 8.031848 ACAAAAAGGTCTAAATCGCGTATAAA 57.968 30.769 5.77 0.00 0.00 1.40
552 578 7.599630 ACAAAAAGGTCTAAATCGCGTATAA 57.400 32.000 5.77 0.00 0.00 0.98
553 579 8.594687 GTTACAAAAAGGTCTAAATCGCGTATA 58.405 33.333 5.77 0.00 0.00 1.47
554 580 7.458677 GTTACAAAAAGGTCTAAATCGCGTAT 58.541 34.615 5.77 0.00 0.00 3.06
555 581 6.399880 CGTTACAAAAAGGTCTAAATCGCGTA 60.400 38.462 5.77 0.00 0.00 4.42
556 582 5.613142 CGTTACAAAAAGGTCTAAATCGCGT 60.613 40.000 5.77 0.00 0.00 6.01
557 583 4.779523 CGTTACAAAAAGGTCTAAATCGCG 59.220 41.667 0.00 0.00 0.00 5.87
558 584 5.682869 ACGTTACAAAAAGGTCTAAATCGC 58.317 37.500 0.00 0.00 0.00 4.58
559 585 7.113704 AGACGTTACAAAAAGGTCTAAATCG 57.886 36.000 10.43 0.00 41.76 3.34
560 586 8.167345 GCTAGACGTTACAAAAAGGTCTAAATC 58.833 37.037 16.52 8.74 43.01 2.17
561 587 7.118825 GGCTAGACGTTACAAAAAGGTCTAAAT 59.881 37.037 16.52 0.78 43.01 1.40
562 588 6.424812 GGCTAGACGTTACAAAAAGGTCTAAA 59.575 38.462 16.52 3.58 43.01 1.85
563 589 5.928264 GGCTAGACGTTACAAAAAGGTCTAA 59.072 40.000 16.52 6.02 43.01 2.10
564 590 5.473039 GGCTAGACGTTACAAAAAGGTCTA 58.527 41.667 15.51 15.51 42.91 2.59
565 591 4.313282 GGCTAGACGTTACAAAAAGGTCT 58.687 43.478 15.02 15.02 44.50 3.85
566 592 3.434641 GGGCTAGACGTTACAAAAAGGTC 59.565 47.826 0.00 3.11 35.84 3.85
567 593 3.405831 GGGCTAGACGTTACAAAAAGGT 58.594 45.455 0.00 0.00 0.00 3.50
568 594 2.745821 GGGGCTAGACGTTACAAAAAGG 59.254 50.000 0.00 0.00 0.00 3.11
569 595 3.404899 TGGGGCTAGACGTTACAAAAAG 58.595 45.455 0.00 0.00 0.00 2.27
570 596 3.071312 TCTGGGGCTAGACGTTACAAAAA 59.929 43.478 0.00 0.00 0.00 1.94
571 597 2.633967 TCTGGGGCTAGACGTTACAAAA 59.366 45.455 0.00 0.00 0.00 2.44
572 598 2.028748 GTCTGGGGCTAGACGTTACAAA 60.029 50.000 0.00 0.00 37.88 2.83
573 599 1.547372 GTCTGGGGCTAGACGTTACAA 59.453 52.381 0.00 0.00 37.88 2.41
574 600 1.180029 GTCTGGGGCTAGACGTTACA 58.820 55.000 0.00 0.00 37.88 2.41
589 615 7.490962 TTTTTACATGTCAGTACCAAGTCTG 57.509 36.000 0.00 0.00 0.00 3.51
590 616 8.691661 AATTTTTACATGTCAGTACCAAGTCT 57.308 30.769 0.00 0.00 0.00 3.24
591 617 9.821662 GTAATTTTTACATGTCAGTACCAAGTC 57.178 33.333 0.00 0.00 0.00 3.01
592 618 8.789762 GGTAATTTTTACATGTCAGTACCAAGT 58.210 33.333 0.00 0.00 0.00 3.16
593 619 8.788806 TGGTAATTTTTACATGTCAGTACCAAG 58.211 33.333 17.47 0.00 36.44 3.61
594 620 8.693120 TGGTAATTTTTACATGTCAGTACCAA 57.307 30.769 17.47 0.00 36.44 3.67
595 621 8.693120 TTGGTAATTTTTACATGTCAGTACCA 57.307 30.769 16.52 16.52 37.33 3.25
596 622 9.401873 GTTTGGTAATTTTTACATGTCAGTACC 57.598 33.333 0.00 9.02 0.00 3.34
610 636 9.705290 CAGCTTGGTATTAAGTTTGGTAATTTT 57.295 29.630 0.00 0.00 0.00 1.82
611 637 7.817478 GCAGCTTGGTATTAAGTTTGGTAATTT 59.183 33.333 0.00 0.00 0.00 1.82
612 638 7.178451 AGCAGCTTGGTATTAAGTTTGGTAATT 59.822 33.333 0.00 0.00 0.00 1.40
613 639 6.663523 AGCAGCTTGGTATTAAGTTTGGTAAT 59.336 34.615 0.00 0.00 0.00 1.89
614 640 6.007703 AGCAGCTTGGTATTAAGTTTGGTAA 58.992 36.000 0.00 0.00 0.00 2.85
615 641 5.566469 AGCAGCTTGGTATTAAGTTTGGTA 58.434 37.500 0.00 0.00 0.00 3.25
616 642 4.407365 AGCAGCTTGGTATTAAGTTTGGT 58.593 39.130 0.00 0.00 0.00 3.67
617 643 5.391312 AAGCAGCTTGGTATTAAGTTTGG 57.609 39.130 6.93 0.00 0.00 3.28
618 644 5.048083 TGGAAGCAGCTTGGTATTAAGTTTG 60.048 40.000 13.91 0.00 0.00 2.93
619 645 5.076873 TGGAAGCAGCTTGGTATTAAGTTT 58.923 37.500 13.91 0.00 0.00 2.66
620 646 4.662278 TGGAAGCAGCTTGGTATTAAGTT 58.338 39.130 13.91 0.00 0.00 2.66
621 647 4.301072 TGGAAGCAGCTTGGTATTAAGT 57.699 40.909 13.91 0.00 0.00 2.24
622 648 5.585390 CATTGGAAGCAGCTTGGTATTAAG 58.415 41.667 13.91 0.00 0.00 1.85
623 649 4.142182 GCATTGGAAGCAGCTTGGTATTAA 60.142 41.667 13.91 0.00 0.00 1.40
624 650 3.381272 GCATTGGAAGCAGCTTGGTATTA 59.619 43.478 13.91 0.00 0.00 0.98
625 651 2.167075 GCATTGGAAGCAGCTTGGTATT 59.833 45.455 13.91 0.00 0.00 1.89
626 652 1.753073 GCATTGGAAGCAGCTTGGTAT 59.247 47.619 13.91 0.00 0.00 2.73
627 653 1.176527 GCATTGGAAGCAGCTTGGTA 58.823 50.000 13.91 0.00 0.00 3.25
628 654 1.538687 GGCATTGGAAGCAGCTTGGT 61.539 55.000 13.91 0.00 0.00 3.67
629 655 1.217244 GGCATTGGAAGCAGCTTGG 59.783 57.895 13.91 0.00 0.00 3.61
630 656 0.172803 GAGGCATTGGAAGCAGCTTG 59.827 55.000 13.91 0.00 0.00 4.01
631 657 1.310933 CGAGGCATTGGAAGCAGCTT 61.311 55.000 7.60 7.60 0.00 3.74
632 658 1.748122 CGAGGCATTGGAAGCAGCT 60.748 57.895 0.00 0.00 0.00 4.24
633 659 1.099879 ATCGAGGCATTGGAAGCAGC 61.100 55.000 0.00 0.00 0.00 5.25
634 660 0.661552 CATCGAGGCATTGGAAGCAG 59.338 55.000 0.00 0.00 0.00 4.24
635 661 0.749091 CCATCGAGGCATTGGAAGCA 60.749 55.000 0.00 0.00 31.94 3.91
636 662 0.749454 ACCATCGAGGCATTGGAAGC 60.749 55.000 8.96 0.00 43.14 3.86
637 663 1.019673 CACCATCGAGGCATTGGAAG 58.980 55.000 8.96 0.00 43.14 3.46
638 664 0.394216 CCACCATCGAGGCATTGGAA 60.394 55.000 8.96 0.00 43.14 3.53
639 665 1.224315 CCACCATCGAGGCATTGGA 59.776 57.895 8.96 0.00 43.14 3.53
640 666 0.180171 TACCACCATCGAGGCATTGG 59.820 55.000 8.53 8.53 43.14 3.16
641 667 1.134401 AGTACCACCATCGAGGCATTG 60.134 52.381 0.00 0.00 43.14 2.82
642 668 1.204146 AGTACCACCATCGAGGCATT 58.796 50.000 0.00 0.00 43.14 3.56
643 669 1.139058 GAAGTACCACCATCGAGGCAT 59.861 52.381 0.00 0.00 43.14 4.40
644 670 0.535335 GAAGTACCACCATCGAGGCA 59.465 55.000 0.00 0.00 43.14 4.75
645 671 0.824759 AGAAGTACCACCATCGAGGC 59.175 55.000 0.00 0.00 43.14 4.70
646 672 1.825474 ACAGAAGTACCACCATCGAGG 59.175 52.381 0.00 0.00 45.67 4.63
647 673 2.881074 CACAGAAGTACCACCATCGAG 58.119 52.381 0.00 0.00 0.00 4.04
648 674 1.067142 GCACAGAAGTACCACCATCGA 60.067 52.381 0.00 0.00 0.00 3.59
649 675 1.337728 TGCACAGAAGTACCACCATCG 60.338 52.381 0.00 0.00 0.00 3.84
650 676 2.472695 TGCACAGAAGTACCACCATC 57.527 50.000 0.00 0.00 0.00 3.51
651 677 2.949177 TTGCACAGAAGTACCACCAT 57.051 45.000 0.00 0.00 0.00 3.55
652 678 2.949177 ATTGCACAGAAGTACCACCA 57.051 45.000 0.00 0.00 0.00 4.17
653 679 4.760204 AGTAAATTGCACAGAAGTACCACC 59.240 41.667 0.00 0.00 0.00 4.61
654 680 5.468746 TGAGTAAATTGCACAGAAGTACCAC 59.531 40.000 0.00 0.00 0.00 4.16
655 681 5.468746 GTGAGTAAATTGCACAGAAGTACCA 59.531 40.000 0.00 0.00 32.96 3.25
656 682 5.468746 TGTGAGTAAATTGCACAGAAGTACC 59.531 40.000 0.00 0.00 37.60 3.34
657 683 6.363473 GTGTGAGTAAATTGCACAGAAGTAC 58.637 40.000 0.00 0.00 42.53 2.73
658 684 5.468746 GGTGTGAGTAAATTGCACAGAAGTA 59.531 40.000 0.00 0.00 42.53 2.24
659 685 4.275936 GGTGTGAGTAAATTGCACAGAAGT 59.724 41.667 0.00 0.00 42.53 3.01
660 686 4.275689 TGGTGTGAGTAAATTGCACAGAAG 59.724 41.667 0.00 0.00 42.53 2.85
661 687 4.036262 GTGGTGTGAGTAAATTGCACAGAA 59.964 41.667 0.00 0.00 42.53 3.02
662 688 3.563808 GTGGTGTGAGTAAATTGCACAGA 59.436 43.478 0.00 0.00 42.53 3.41
663 689 3.314913 TGTGGTGTGAGTAAATTGCACAG 59.685 43.478 0.00 0.00 42.53 3.66
664 690 3.066064 GTGTGGTGTGAGTAAATTGCACA 59.934 43.478 0.00 0.00 39.95 4.57
665 691 3.628017 GTGTGGTGTGAGTAAATTGCAC 58.372 45.455 0.00 0.00 0.00 4.57
666 692 2.289274 CGTGTGGTGTGAGTAAATTGCA 59.711 45.455 0.00 0.00 0.00 4.08
667 693 2.546368 TCGTGTGGTGTGAGTAAATTGC 59.454 45.455 0.00 0.00 0.00 3.56
668 694 4.434198 CGATCGTGTGGTGTGAGTAAATTG 60.434 45.833 7.03 0.00 0.00 2.32
669 695 3.678072 CGATCGTGTGGTGTGAGTAAATT 59.322 43.478 7.03 0.00 0.00 1.82
670 696 3.250744 CGATCGTGTGGTGTGAGTAAAT 58.749 45.455 7.03 0.00 0.00 1.40
671 697 2.608506 CCGATCGTGTGGTGTGAGTAAA 60.609 50.000 15.09 0.00 0.00 2.01
672 698 1.068125 CCGATCGTGTGGTGTGAGTAA 60.068 52.381 15.09 0.00 0.00 2.24
673 699 0.524414 CCGATCGTGTGGTGTGAGTA 59.476 55.000 15.09 0.00 0.00 2.59
674 700 1.289066 CCGATCGTGTGGTGTGAGT 59.711 57.895 15.09 0.00 0.00 3.41
675 701 2.094659 GCCGATCGTGTGGTGTGAG 61.095 63.158 15.09 0.00 0.00 3.51
676 702 2.048597 GCCGATCGTGTGGTGTGA 60.049 61.111 15.09 0.00 0.00 3.58
677 703 3.118454 GGCCGATCGTGTGGTGTG 61.118 66.667 15.09 0.00 0.00 3.82
678 704 4.735132 CGGCCGATCGTGTGGTGT 62.735 66.667 24.07 0.00 0.00 4.16
720 748 0.609681 GACGGATAGGATCGGGCTCT 60.610 60.000 0.00 0.00 35.00 4.09
747 803 3.343421 GAAGCCACCGCGACGTTT 61.343 61.111 8.23 0.00 41.18 3.60
898 981 6.215227 GGAGAAGGAAGAATGGATGGATAGAT 59.785 42.308 0.00 0.00 0.00 1.98
899 982 5.545723 GGAGAAGGAAGAATGGATGGATAGA 59.454 44.000 0.00 0.00 0.00 1.98
900 983 5.309020 TGGAGAAGGAAGAATGGATGGATAG 59.691 44.000 0.00 0.00 0.00 2.08
901 984 5.226803 TGGAGAAGGAAGAATGGATGGATA 58.773 41.667 0.00 0.00 0.00 2.59
950 1051 1.734047 GCTCGTCTGTGATCGAAGCTT 60.734 52.381 0.00 0.00 35.69 3.74
961 1062 2.105006 ATGATTTGCTGCTCGTCTGT 57.895 45.000 0.00 0.00 0.00 3.41
962 1063 3.482722 AAATGATTTGCTGCTCGTCTG 57.517 42.857 0.00 0.00 0.00 3.51
963 1064 4.331168 GTCTAAATGATTTGCTGCTCGTCT 59.669 41.667 0.00 0.00 0.00 4.18
964 1065 4.582459 GTCTAAATGATTTGCTGCTCGTC 58.418 43.478 0.00 0.00 0.00 4.20
965 1066 3.062639 CGTCTAAATGATTTGCTGCTCGT 59.937 43.478 0.00 0.00 0.00 4.18
967 1068 4.331168 ACTCGTCTAAATGATTTGCTGCTC 59.669 41.667 0.00 0.00 0.00 4.26
969 1070 4.606457 ACTCGTCTAAATGATTTGCTGC 57.394 40.909 0.00 0.00 0.00 5.25
975 5205 5.921408 GGATTCGCTACTCGTCTAAATGATT 59.079 40.000 0.00 0.00 39.67 2.57
982 5212 2.552743 CCATGGATTCGCTACTCGTCTA 59.447 50.000 5.56 0.00 39.67 2.59
1007 5243 4.408821 TTGCGCGCTTCATCCCCT 62.409 61.111 33.29 0.00 0.00 4.79
1023 5259 1.539869 TGCTGGCTCCTTCTCCCTT 60.540 57.895 0.00 0.00 0.00 3.95
1030 5266 4.749310 CGACGCTGCTGGCTCCTT 62.749 66.667 0.00 0.00 39.13 3.36
1064 5300 0.803117 GGACGTCGATGAGTCTGTGA 59.197 55.000 12.58 0.00 37.52 3.58
1074 5310 1.005394 GGTTGTGGTGGACGTCGAT 60.005 57.895 9.92 0.00 0.00 3.59
1146 5406 2.285442 GTGGCCACTACCCTCCCT 60.285 66.667 29.12 0.00 0.00 4.20
1344 5612 1.364626 CGAAGCCCAGTGTGCAGATC 61.365 60.000 0.00 0.00 0.00 2.75
1554 6374 5.904080 GCAAATACGTACTCTATACGACGTT 59.096 40.000 5.50 0.00 45.63 3.99
1557 6377 6.653183 TCAGCAAATACGTACTCTATACGAC 58.347 40.000 13.00 0.00 42.94 4.34
1559 6379 9.263626 CTAATCAGCAAATACGTACTCTATACG 57.736 37.037 0.00 5.00 45.44 3.06
1590 6410 1.330521 CAAATATCCAGCACGAACGGG 59.669 52.381 0.00 0.00 0.00 5.28
1625 6448 6.238648 ACCTTCAGTCAATCGGTTAGAAAAT 58.761 36.000 0.00 0.00 0.00 1.82
1645 6469 7.938140 ATGTATACAAGTGCATGTAAACCTT 57.062 32.000 10.14 0.00 39.12 3.50
1664 6497 8.946085 ACAAACGAATGTGTCTTCATTATGTAT 58.054 29.630 0.00 0.00 38.03 2.29
1665 6498 8.317891 ACAAACGAATGTGTCTTCATTATGTA 57.682 30.769 0.00 0.00 38.03 2.29
1666 6499 7.202016 ACAAACGAATGTGTCTTCATTATGT 57.798 32.000 0.00 0.00 38.03 2.29
1667 6500 7.271223 GGAACAAACGAATGTGTCTTCATTATG 59.729 37.037 0.00 0.00 38.03 1.90
1668 6501 7.040755 TGGAACAAACGAATGTGTCTTCATTAT 60.041 33.333 0.00 0.00 34.98 1.28
1693 6529 6.327154 TGCAAGAATCTGTCAATAGCATTTG 58.673 36.000 0.00 0.00 0.00 2.32
1700 6536 5.993055 TCTGGATGCAAGAATCTGTCAATA 58.007 37.500 0.00 0.00 0.00 1.90
1741 6577 2.846039 ACGCACGGACATTCTACTAG 57.154 50.000 0.00 0.00 0.00 2.57
1742 6578 2.871133 CAACGCACGGACATTCTACTA 58.129 47.619 0.00 0.00 0.00 1.82
1743 6579 1.710013 CAACGCACGGACATTCTACT 58.290 50.000 0.00 0.00 0.00 2.57
1744 6580 0.094730 GCAACGCACGGACATTCTAC 59.905 55.000 0.00 0.00 0.00 2.59
1745 6581 1.017177 GGCAACGCACGGACATTCTA 61.017 55.000 0.00 0.00 0.00 2.10
1746 6582 2.325082 GGCAACGCACGGACATTCT 61.325 57.895 0.00 0.00 0.00 2.40
1747 6583 2.175811 GGCAACGCACGGACATTC 59.824 61.111 0.00 0.00 0.00 2.67
1748 6584 2.593148 TGGCAACGCACGGACATT 60.593 55.556 0.00 0.00 42.51 2.71
1763 6599 1.613437 GATCCATTTATTGGCCCGTGG 59.387 52.381 0.00 0.00 46.01 4.94
1764 6600 2.586425 AGATCCATTTATTGGCCCGTG 58.414 47.619 0.00 0.00 46.01 4.94
1765 6601 4.289672 AGATAGATCCATTTATTGGCCCGT 59.710 41.667 0.00 0.00 46.01 5.28
1766 6602 4.848357 AGATAGATCCATTTATTGGCCCG 58.152 43.478 0.00 0.00 46.01 6.13
1767 6603 8.829373 ATTTAGATAGATCCATTTATTGGCCC 57.171 34.615 0.00 0.00 46.01 5.80
1994 6830 1.473278 GTGAAGTACTCCCTCCAGTCG 59.527 57.143 0.00 0.00 0.00 4.18
2017 6853 1.398692 TTTTGAGTGGAGTGGCAACC 58.601 50.000 5.21 5.21 0.00 3.77
2062 6898 6.707440 AGTTGTGGTGTCAACAATTTGATA 57.293 33.333 2.79 0.00 46.78 2.15
2063 6899 5.596836 AGTTGTGGTGTCAACAATTTGAT 57.403 34.783 2.79 0.00 46.78 2.57
2064 6900 5.398603 AAGTTGTGGTGTCAACAATTTGA 57.601 34.783 2.79 0.00 46.78 2.69
2065 6901 5.063312 GGAAAGTTGTGGTGTCAACAATTTG 59.937 40.000 11.22 0.00 46.78 2.32
2068 6904 3.132111 GGGAAAGTTGTGGTGTCAACAAT 59.868 43.478 11.22 0.93 46.78 2.71
2070 6906 2.096248 GGGAAAGTTGTGGTGTCAACA 58.904 47.619 11.22 0.00 46.78 3.33
2167 7559 5.446860 AGGAGAATCACTCGAGGTATTGTA 58.553 41.667 18.41 0.00 45.76 2.41
2168 7560 4.282496 AGGAGAATCACTCGAGGTATTGT 58.718 43.478 18.41 13.60 45.76 2.71
2169 7561 4.927978 AGGAGAATCACTCGAGGTATTG 57.072 45.455 18.41 5.87 45.76 1.90
2171 7563 5.067273 CAGTAGGAGAATCACTCGAGGTAT 58.933 45.833 18.41 6.67 45.76 2.73
2172 7564 4.452825 CAGTAGGAGAATCACTCGAGGTA 58.547 47.826 18.41 4.22 45.76 3.08
2173 7565 3.283751 CAGTAGGAGAATCACTCGAGGT 58.716 50.000 18.41 0.00 45.76 3.85
2174 7566 2.034053 GCAGTAGGAGAATCACTCGAGG 59.966 54.545 18.41 5.96 45.76 4.63
2194 7586 0.320421 TTGGCGACTGAGGTTGTAGC 60.320 55.000 0.00 0.00 35.76 3.58
2209 7601 3.451141 TGAACCATGACAAAGTTTGGC 57.549 42.857 19.45 17.34 39.85 4.52
2261 7653 3.707102 TGGGGTTTTTAACTGGTTTGAGG 59.293 43.478 0.00 0.00 0.00 3.86
2268 7660 5.480073 TCTCATCAATGGGGTTTTTAACTGG 59.520 40.000 0.00 0.00 0.00 4.00
2307 7699 9.569167 TCTTCTATTTTGAGTATCTGTGTTACG 57.431 33.333 0.00 0.00 34.92 3.18


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

AutoCloner maintained by Alex Coulton.