Multiple sequence alignment - TraesCS3A01G326100

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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 TraesCS3A01G326100 chr3A 100.000 4543 0 0 1 4543 571404985 571400443 0.000000e+00 8390.0
1 TraesCS3A01G326100 chr3A 84.157 789 114 10 787 1568 571410459 571409675 0.000000e+00 754.0
2 TraesCS3A01G326100 chr3A 89.712 243 23 2 472 713 731213507 731213266 4.410000e-80 309.0
3 TraesCS3A01G326100 chr3D 95.011 3047 117 17 706 3723 433310913 433307873 0.000000e+00 4752.0
4 TraesCS3A01G326100 chr3D 83.523 789 119 9 787 1568 433317627 433316843 0.000000e+00 726.0
5 TraesCS3A01G326100 chr3D 95.787 451 16 1 25 475 433311356 433310909 0.000000e+00 725.0
6 TraesCS3A01G326100 chr3D 90.625 320 23 5 4224 4543 433297317 433297005 7.030000e-113 418.0
7 TraesCS3A01G326100 chr3D 87.938 257 17 4 3982 4238 433297979 433297737 1.600000e-74 291.0
8 TraesCS3A01G326100 chr3B 92.980 2792 128 30 1322 4078 565639647 565636889 0.000000e+00 4008.0
9 TraesCS3A01G326100 chr3B 94.451 1694 73 14 1563 3244 565438410 565436726 0.000000e+00 2588.0
10 TraesCS3A01G326100 chr3B 97.949 585 10 1 706 1288 565640231 565639647 0.000000e+00 1013.0
11 TraesCS3A01G326100 chr3B 95.368 475 17 3 1 475 565640696 565640227 0.000000e+00 750.0
12 TraesCS3A01G326100 chr3B 92.077 467 28 7 4078 4543 565573934 565573476 0.000000e+00 649.0
13 TraesCS3A01G326100 chr3B 94.444 234 9 4 4042 4275 565436582 565436353 1.550000e-94 357.0
14 TraesCS3A01G326100 chr3B 96.552 174 5 1 4370 4543 565436316 565436144 2.070000e-73 287.0
15 TraesCS3A01G326100 chr3B 93.706 143 8 1 3760 3902 565436724 565436583 3.560000e-51 213.0
16 TraesCS3A01G326100 chr5A 99.574 235 0 1 475 709 52287437 52287670 1.170000e-115 427.0
17 TraesCS3A01G326100 chr5A 93.506 231 14 1 475 705 289366107 289365878 4.350000e-90 342.0
18 TraesCS3A01G326100 chr5A 85.401 137 15 3 4237 4370 623374511 623374377 2.200000e-28 137.0
19 TraesCS3A01G326100 chr5A 86.076 79 9 2 4160 4238 415163706 415163782 2.910000e-12 84.2
20 TraesCS3A01G326100 chr2A 99.149 235 2 0 475 709 124658116 124657882 1.510000e-114 424.0
21 TraesCS3A01G326100 chr2A 89.787 235 24 0 470 704 516313027 516312793 7.390000e-78 302.0
22 TraesCS3A01G326100 chr2A 92.982 114 5 1 4241 4351 761454486 761454373 3.640000e-36 163.0
23 TraesCS3A01G326100 chr2A 86.364 132 11 4 4237 4364 197486496 197486368 2.200000e-28 137.0
24 TraesCS3A01G326100 chr7A 92.437 238 16 2 472 708 106961566 106961802 5.630000e-89 339.0
25 TraesCS3A01G326100 chrUn 90.987 233 21 0 473 705 52973873 52973641 9.490000e-82 315.0
26 TraesCS3A01G326100 chr5D 90.948 232 21 0 474 705 285454737 285454968 3.410000e-81 313.0
27 TraesCS3A01G326100 chr5D 90.000 80 6 2 4160 4238 451168286 451168208 8.040000e-18 102.0
28 TraesCS3A01G326100 chr5B 86.638 232 31 0 474 705 327085399 327085630 1.620000e-64 257.0
29 TraesCS3A01G326100 chr5B 75.333 450 105 6 1126 1572 704887027 704886581 1.280000e-50 211.0
30 TraesCS3A01G326100 chr5B 84.962 133 16 2 4237 4365 659103849 659103981 1.030000e-26 132.0
31 TraesCS3A01G326100 chr5B 85.227 88 10 3 4146 4232 372162157 372162242 2.250000e-13 87.9
32 TraesCS3A01G326100 chr4A 88.722 133 11 2 4237 4365 603722547 603722679 4.700000e-35 159.0
33 TraesCS3A01G326100 chr7D 88.722 133 10 2 4236 4365 47234835 47234705 1.690000e-34 158.0
34 TraesCS3A01G326100 chr2D 86.029 136 14 3 4237 4369 638155642 638155509 1.700000e-29 141.0
35 TraesCS3A01G326100 chr6B 85.870 92 7 5 4151 4238 695791689 695791778 4.840000e-15 93.5
36 TraesCS3A01G326100 chr1A 87.013 77 8 2 4163 4238 19873115 19873040 8.100000e-13 86.1
37 TraesCS3A01G326100 chr4D 91.837 49 1 3 4183 4229 67324671 67324624 1.050000e-06 65.8


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 TraesCS3A01G326100 chr3A 571400443 571404985 4542 True 8390.000000 8390 100.000000 1 4543 1 chr3A.!!$R1 4542
1 TraesCS3A01G326100 chr3A 571409675 571410459 784 True 754.000000 754 84.157000 787 1568 1 chr3A.!!$R2 781
2 TraesCS3A01G326100 chr3D 433307873 433311356 3483 True 2738.500000 4752 95.399000 25 3723 2 chr3D.!!$R3 3698
3 TraesCS3A01G326100 chr3D 433316843 433317627 784 True 726.000000 726 83.523000 787 1568 1 chr3D.!!$R1 781
4 TraesCS3A01G326100 chr3D 433297005 433297979 974 True 354.500000 418 89.281500 3982 4543 2 chr3D.!!$R2 561
5 TraesCS3A01G326100 chr3B 565636889 565640696 3807 True 1923.666667 4008 95.432333 1 4078 3 chr3B.!!$R3 4077
6 TraesCS3A01G326100 chr3B 565436144 565438410 2266 True 861.250000 2588 94.788250 1563 4543 4 chr3B.!!$R2 2980

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
479 480 0.030092 TGGCAGGTTATCTAGGGGCT 60.030 55.000 0.00 0.00 0.00 5.19 F
601 602 0.110486 TCCCACTTCCCAAGTTCAGC 59.890 55.000 0.00 0.00 40.46 4.26 F
602 603 0.111253 CCCACTTCCCAAGTTCAGCT 59.889 55.000 0.00 0.00 40.46 4.24 F
685 686 0.179048 CGATTGGCAGGGCTCACATA 60.179 55.000 0.00 0.00 0.00 2.29 F
687 688 0.184451 ATTGGCAGGGCTCACATAGG 59.816 55.000 0.00 0.00 0.00 2.57 F
917 920 0.959553 CTGCATTGGGATCCTCATGC 59.040 55.000 28.39 28.39 39.61 4.06 F
1949 1958 2.128771 TAGGGAAATGCCTGCAAGAC 57.871 50.000 3.43 0.00 34.07 3.01 F
2862 2876 2.314246 TGTGTGGCAATGGTCATTTGA 58.686 42.857 0.00 0.00 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 1932 1.779221 TGCAGGCATTTCCCTAATGG 58.221 50.000 0.00 0.0 43.20 3.16 R
2007 2016 2.986479 GCACTTTGAAAATGTAAGGGCG 59.014 45.455 0.00 0.0 38.40 6.13 R
2273 2285 3.818210 CACACAACATTAAGCCTACCACA 59.182 43.478 0.00 0.0 0.00 4.17 R
2617 2631 0.385029 ACGCACAGCAAATCAGCAAA 59.615 45.000 0.00 0.0 36.85 3.68 R
2620 2634 1.887320 CTTACGCACAGCAAATCAGC 58.113 50.000 0.00 0.0 0.00 4.26 R
2712 2726 3.559242 ACAAACAAATGAAACATTGCCCG 59.441 39.130 0.00 0.0 0.00 6.13 R
3100 3114 0.103208 GCTGCGTACCTGTCTATGCT 59.897 55.000 0.00 0.0 30.97 3.79 R
3756 3809 0.322546 ATCAAACCCGGAGCCAAGAC 60.323 55.000 0.73 0.0 0.00 3.01 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
30 31 5.615289 ACCTATGATTGACCAGACATTAGC 58.385 41.667 0.00 0.00 0.00 3.09
48 49 1.002087 AGCGACGGTCTCCTTTTTCAT 59.998 47.619 6.57 0.00 0.00 2.57
180 181 9.334693 CAAGCAAGATTTCTTACTTGTCAATAC 57.665 33.333 18.85 0.00 45.51 1.89
405 406 7.939039 TGGACACTCTTGAGATAATTGAACTTT 59.061 33.333 4.49 0.00 0.00 2.66
419 420 2.091885 TGAACTTTTTCTCTGCTGGGGT 60.092 45.455 0.00 0.00 32.36 4.95
425 426 1.198713 TTCTCTGCTGGGGTCTCATC 58.801 55.000 0.00 0.00 0.00 2.92
469 470 7.165485 GGAATGTGTATATACATGGCAGGTTA 58.835 38.462 18.27 3.41 40.24 2.85
470 471 7.829211 GGAATGTGTATATACATGGCAGGTTAT 59.171 37.037 18.27 10.56 40.24 1.89
471 472 8.792830 AATGTGTATATACATGGCAGGTTATC 57.207 34.615 18.27 2.36 40.24 1.75
472 473 7.553504 TGTGTATATACATGGCAGGTTATCT 57.446 36.000 18.27 0.00 38.63 1.98
473 474 8.658840 TGTGTATATACATGGCAGGTTATCTA 57.341 34.615 18.27 0.00 38.63 1.98
474 475 8.749354 TGTGTATATACATGGCAGGTTATCTAG 58.251 37.037 18.27 0.00 38.63 2.43
475 476 8.198109 GTGTATATACATGGCAGGTTATCTAGG 58.802 40.741 18.27 0.00 38.63 3.02
476 477 6.814954 ATATACATGGCAGGTTATCTAGGG 57.185 41.667 11.12 0.00 0.00 3.53
477 478 2.057922 ACATGGCAGGTTATCTAGGGG 58.942 52.381 0.00 0.00 0.00 4.79
478 479 1.068121 ATGGCAGGTTATCTAGGGGC 58.932 55.000 0.00 0.00 0.00 5.80
479 480 0.030092 TGGCAGGTTATCTAGGGGCT 60.030 55.000 0.00 0.00 0.00 5.19
480 481 0.398318 GGCAGGTTATCTAGGGGCTG 59.602 60.000 0.00 0.00 0.00 4.85
481 482 1.132500 GCAGGTTATCTAGGGGCTGT 58.868 55.000 0.00 0.00 0.00 4.40
482 483 1.490910 GCAGGTTATCTAGGGGCTGTT 59.509 52.381 0.00 0.00 0.00 3.16
483 484 2.092375 GCAGGTTATCTAGGGGCTGTTT 60.092 50.000 0.00 0.00 0.00 2.83
484 485 3.545703 CAGGTTATCTAGGGGCTGTTTG 58.454 50.000 0.00 0.00 0.00 2.93
485 486 2.509964 AGGTTATCTAGGGGCTGTTTGG 59.490 50.000 0.00 0.00 0.00 3.28
486 487 2.508300 GGTTATCTAGGGGCTGTTTGGA 59.492 50.000 0.00 0.00 0.00 3.53
487 488 3.138468 GGTTATCTAGGGGCTGTTTGGAT 59.862 47.826 0.00 0.00 0.00 3.41
488 489 4.386424 GGTTATCTAGGGGCTGTTTGGATT 60.386 45.833 0.00 0.00 0.00 3.01
489 490 2.806945 TCTAGGGGCTGTTTGGATTG 57.193 50.000 0.00 0.00 0.00 2.67
490 491 1.106285 CTAGGGGCTGTTTGGATTGC 58.894 55.000 0.00 0.00 0.00 3.56
491 492 0.407528 TAGGGGCTGTTTGGATTGCA 59.592 50.000 0.00 0.00 0.00 4.08
492 493 0.901580 AGGGGCTGTTTGGATTGCAG 60.902 55.000 0.00 0.00 0.00 4.41
494 495 4.584688 GCTGTTTGGATTGCAGCC 57.415 55.556 4.60 0.97 46.93 4.85
495 496 1.079612 GCTGTTTGGATTGCAGCCC 60.080 57.895 4.60 2.70 46.93 5.19
496 497 1.538687 GCTGTTTGGATTGCAGCCCT 61.539 55.000 4.60 0.00 46.93 5.19
497 498 0.529378 CTGTTTGGATTGCAGCCCTC 59.471 55.000 7.78 0.00 0.00 4.30
498 499 0.178967 TGTTTGGATTGCAGCCCTCA 60.179 50.000 7.78 3.03 0.00 3.86
499 500 0.968405 GTTTGGATTGCAGCCCTCAA 59.032 50.000 7.78 0.00 0.00 3.02
500 501 0.968405 TTTGGATTGCAGCCCTCAAC 59.032 50.000 7.78 0.00 0.00 3.18
501 502 0.112995 TTGGATTGCAGCCCTCAACT 59.887 50.000 7.78 0.00 0.00 3.16
502 503 0.609957 TGGATTGCAGCCCTCAACTG 60.610 55.000 7.78 0.00 38.22 3.16
507 508 4.179361 CAGCCCTCAACTGCCAAA 57.821 55.556 0.00 0.00 0.00 3.28
508 509 1.662044 CAGCCCTCAACTGCCAAAC 59.338 57.895 0.00 0.00 0.00 2.93
509 510 1.531602 AGCCCTCAACTGCCAAACC 60.532 57.895 0.00 0.00 0.00 3.27
510 511 1.832167 GCCCTCAACTGCCAAACCA 60.832 57.895 0.00 0.00 0.00 3.67
511 512 1.398958 GCCCTCAACTGCCAAACCAA 61.399 55.000 0.00 0.00 0.00 3.67
512 513 1.118838 CCCTCAACTGCCAAACCAAA 58.881 50.000 0.00 0.00 0.00 3.28
513 514 1.484240 CCCTCAACTGCCAAACCAAAA 59.516 47.619 0.00 0.00 0.00 2.44
514 515 2.093235 CCCTCAACTGCCAAACCAAAAA 60.093 45.455 0.00 0.00 0.00 1.94
540 541 0.529378 CATTGACCAAGCCTGGCTTC 59.471 55.000 30.24 20.10 46.77 3.86
541 542 0.613012 ATTGACCAAGCCTGGCTTCC 60.613 55.000 30.24 21.08 46.77 3.46
542 543 2.747855 GACCAAGCCTGGCTTCCG 60.748 66.667 30.24 23.72 46.77 4.30
543 544 4.351054 ACCAAGCCTGGCTTCCGG 62.351 66.667 30.24 28.61 46.77 5.14
544 545 4.351054 CCAAGCCTGGCTTCCGGT 62.351 66.667 30.24 7.56 46.77 5.28
545 546 2.282462 CAAGCCTGGCTTCCGGTT 60.282 61.111 30.24 6.73 46.77 4.44
546 547 1.903404 CAAGCCTGGCTTCCGGTTT 60.903 57.895 30.24 5.91 46.77 3.27
547 548 1.903404 AAGCCTGGCTTCCGGTTTG 60.903 57.895 27.70 0.00 46.77 2.93
548 549 3.373565 GCCTGGCTTCCGGTTTGG 61.374 66.667 12.43 0.00 40.09 3.28
576 577 3.249986 CCAATATTTTGGTGCACCCAG 57.750 47.619 32.62 8.96 46.31 4.45
577 578 2.620242 CAATATTTTGGTGCACCCAGC 58.380 47.619 32.62 8.74 46.31 4.85
578 579 1.194218 ATATTTTGGTGCACCCAGCC 58.806 50.000 32.62 8.54 46.31 4.85
579 580 0.178950 TATTTTGGTGCACCCAGCCA 60.179 50.000 32.62 11.49 46.31 4.75
580 581 1.053264 ATTTTGGTGCACCCAGCCAA 61.053 50.000 32.62 17.22 46.31 4.52
581 582 1.965754 TTTTGGTGCACCCAGCCAAC 61.966 55.000 32.62 5.95 46.31 3.77
582 583 2.870035 TTTGGTGCACCCAGCCAACT 62.870 55.000 32.62 0.00 46.31 3.16
583 584 2.985847 GGTGCACCCAGCCAACTC 60.986 66.667 26.31 0.00 44.83 3.01
584 585 2.985847 GTGCACCCAGCCAACTCC 60.986 66.667 5.22 0.00 44.83 3.85
585 586 4.284550 TGCACCCAGCCAACTCCC 62.285 66.667 0.00 0.00 44.83 4.30
586 587 4.284550 GCACCCAGCCAACTCCCA 62.285 66.667 0.00 0.00 37.23 4.37
587 588 2.282462 CACCCAGCCAACTCCCAC 60.282 66.667 0.00 0.00 0.00 4.61
588 589 2.450502 ACCCAGCCAACTCCCACT 60.451 61.111 0.00 0.00 0.00 4.00
589 590 2.084930 ACCCAGCCAACTCCCACTT 61.085 57.895 0.00 0.00 0.00 3.16
590 591 1.303643 CCCAGCCAACTCCCACTTC 60.304 63.158 0.00 0.00 0.00 3.01
591 592 1.303643 CCAGCCAACTCCCACTTCC 60.304 63.158 0.00 0.00 0.00 3.46
592 593 1.303643 CAGCCAACTCCCACTTCCC 60.304 63.158 0.00 0.00 0.00 3.97
593 594 1.774217 AGCCAACTCCCACTTCCCA 60.774 57.895 0.00 0.00 0.00 4.37
594 595 1.152830 GCCAACTCCCACTTCCCAA 59.847 57.895 0.00 0.00 0.00 4.12
595 596 0.895559 GCCAACTCCCACTTCCCAAG 60.896 60.000 0.00 0.00 0.00 3.61
596 597 0.478507 CCAACTCCCACTTCCCAAGT 59.521 55.000 0.00 0.00 44.06 3.16
597 598 1.133482 CCAACTCCCACTTCCCAAGTT 60.133 52.381 0.00 0.00 40.46 2.66
598 599 2.230660 CAACTCCCACTTCCCAAGTTC 58.769 52.381 0.00 0.00 40.46 3.01
599 600 1.518367 ACTCCCACTTCCCAAGTTCA 58.482 50.000 0.00 0.00 40.46 3.18
600 601 1.421646 ACTCCCACTTCCCAAGTTCAG 59.578 52.381 0.00 0.00 40.46 3.02
601 602 0.110486 TCCCACTTCCCAAGTTCAGC 59.890 55.000 0.00 0.00 40.46 4.26
602 603 0.111253 CCCACTTCCCAAGTTCAGCT 59.889 55.000 0.00 0.00 40.46 4.24
603 604 1.528129 CCACTTCCCAAGTTCAGCTC 58.472 55.000 0.00 0.00 40.46 4.09
604 605 1.151668 CACTTCCCAAGTTCAGCTCG 58.848 55.000 0.00 0.00 40.46 5.03
605 606 1.048601 ACTTCCCAAGTTCAGCTCGA 58.951 50.000 0.00 0.00 39.04 4.04
606 607 1.270358 ACTTCCCAAGTTCAGCTCGAC 60.270 52.381 0.00 0.00 39.04 4.20
607 608 0.319555 TTCCCAAGTTCAGCTCGACG 60.320 55.000 0.00 0.00 0.00 5.12
608 609 2.383527 CCCAAGTTCAGCTCGACGC 61.384 63.158 0.00 0.00 39.57 5.19
609 610 2.383527 CCAAGTTCAGCTCGACGCC 61.384 63.158 3.66 0.00 40.39 5.68
610 611 1.664649 CAAGTTCAGCTCGACGCCA 60.665 57.895 3.66 0.00 40.39 5.69
611 612 1.069090 AAGTTCAGCTCGACGCCAA 59.931 52.632 3.66 0.00 40.39 4.52
612 613 0.531974 AAGTTCAGCTCGACGCCAAA 60.532 50.000 3.66 0.00 40.39 3.28
613 614 0.531974 AGTTCAGCTCGACGCCAAAA 60.532 50.000 3.66 0.00 40.39 2.44
614 615 0.306533 GTTCAGCTCGACGCCAAAAA 59.693 50.000 3.66 0.00 40.39 1.94
615 616 0.586319 TTCAGCTCGACGCCAAAAAG 59.414 50.000 3.66 0.00 40.39 2.27
616 617 0.531974 TCAGCTCGACGCCAAAAAGT 60.532 50.000 3.66 0.00 40.39 2.66
617 618 0.307760 CAGCTCGACGCCAAAAAGTT 59.692 50.000 3.66 0.00 40.39 2.66
618 619 0.307760 AGCTCGACGCCAAAAAGTTG 59.692 50.000 3.66 0.00 40.39 3.16
629 630 2.825205 CAAAAAGTTGGCAAGTCTGGG 58.175 47.619 8.24 0.00 0.00 4.45
630 631 1.413118 AAAAGTTGGCAAGTCTGGGG 58.587 50.000 8.24 0.00 0.00 4.96
631 632 1.115326 AAAGTTGGCAAGTCTGGGGC 61.115 55.000 8.24 0.00 0.00 5.80
632 633 3.365265 GTTGGCAAGTCTGGGGCG 61.365 66.667 0.00 0.00 0.00 6.13
650 651 2.516930 CCCGAATCCTGCGCCAAT 60.517 61.111 4.18 0.00 0.00 3.16
651 652 1.227823 CCCGAATCCTGCGCCAATA 60.228 57.895 4.18 0.00 0.00 1.90
652 653 0.817634 CCCGAATCCTGCGCCAATAA 60.818 55.000 4.18 0.00 0.00 1.40
653 654 1.021202 CCGAATCCTGCGCCAATAAA 58.979 50.000 4.18 0.00 0.00 1.40
654 655 1.608590 CCGAATCCTGCGCCAATAAAT 59.391 47.619 4.18 0.00 0.00 1.40
655 656 2.034558 CCGAATCCTGCGCCAATAAATT 59.965 45.455 4.18 0.00 0.00 1.82
656 657 3.044986 CGAATCCTGCGCCAATAAATTG 58.955 45.455 4.18 0.00 37.52 2.32
679 680 2.361610 CCAACGATTGGCAGGGCT 60.362 61.111 4.23 0.00 45.17 5.19
680 681 2.409870 CCAACGATTGGCAGGGCTC 61.410 63.158 4.23 0.00 45.17 4.70
681 682 1.675310 CAACGATTGGCAGGGCTCA 60.675 57.895 0.00 0.00 0.00 4.26
682 683 1.675641 AACGATTGGCAGGGCTCAC 60.676 57.895 0.00 0.00 0.00 3.51
683 684 2.046023 CGATTGGCAGGGCTCACA 60.046 61.111 0.00 0.00 0.00 3.58
684 685 1.452651 CGATTGGCAGGGCTCACAT 60.453 57.895 0.00 0.00 0.00 3.21
685 686 0.179048 CGATTGGCAGGGCTCACATA 60.179 55.000 0.00 0.00 0.00 2.29
686 687 1.602311 GATTGGCAGGGCTCACATAG 58.398 55.000 0.00 0.00 0.00 2.23
687 688 0.184451 ATTGGCAGGGCTCACATAGG 59.816 55.000 0.00 0.00 0.00 2.57
696 697 2.113860 GCTCACATAGGCAAGAACCA 57.886 50.000 0.00 0.00 0.00 3.67
697 698 2.436417 GCTCACATAGGCAAGAACCAA 58.564 47.619 0.00 0.00 0.00 3.67
698 699 2.819608 GCTCACATAGGCAAGAACCAAA 59.180 45.455 0.00 0.00 0.00 3.28
699 700 3.366374 GCTCACATAGGCAAGAACCAAAC 60.366 47.826 0.00 0.00 0.00 2.93
700 701 3.820467 CTCACATAGGCAAGAACCAAACA 59.180 43.478 0.00 0.00 0.00 2.83
701 702 3.820467 TCACATAGGCAAGAACCAAACAG 59.180 43.478 0.00 0.00 0.00 3.16
702 703 2.558359 ACATAGGCAAGAACCAAACAGC 59.442 45.455 0.00 0.00 0.00 4.40
703 704 1.616159 TAGGCAAGAACCAAACAGCC 58.384 50.000 0.00 0.00 42.31 4.85
704 705 1.115326 AGGCAAGAACCAAACAGCCC 61.115 55.000 0.00 0.00 42.97 5.19
715 716 2.519013 CAAACAGCCCTCTAGCCTTTT 58.481 47.619 0.00 0.00 0.00 2.27
917 920 0.959553 CTGCATTGGGATCCTCATGC 59.040 55.000 28.39 28.39 39.61 4.06
1421 1424 3.251043 GCTAGAGAGCGCACGCAC 61.251 66.667 18.24 11.29 44.88 5.34
1512 1515 4.502171 TGCACTATTTGGTTGTGACATG 57.498 40.909 0.00 0.00 35.89 3.21
1623 1627 7.893302 TGTCATAAATTCTGTATGGAAAAGGGT 59.107 33.333 0.00 0.00 31.13 4.34
1670 1674 2.428530 CTGTATCTAGAGCTGTGGTGCA 59.571 50.000 0.00 0.00 34.99 4.57
1702 1706 4.499758 GTCGCTTGTAGTTGATAGTAGCAC 59.500 45.833 0.00 0.00 0.00 4.40
1710 1714 3.131223 AGTTGATAGTAGCACGTCAGCAT 59.869 43.478 0.36 0.00 36.85 3.79
1872 1878 7.681939 TGCTTAATTTACCTCCTGTAAGTTG 57.318 36.000 3.89 0.00 39.07 3.16
1949 1958 2.128771 TAGGGAAATGCCTGCAAGAC 57.871 50.000 3.43 0.00 34.07 3.01
1955 1964 3.311966 GAAATGCCTGCAAGACAAACTC 58.688 45.455 0.00 0.00 34.07 3.01
2007 2016 4.154942 ACCCTGATGGATTGAATATTGGC 58.845 43.478 0.00 0.00 38.00 4.52
2033 2042 4.682860 CCTTACATTTTCAAAGTGCAGCAG 59.317 41.667 0.00 0.00 0.00 4.24
2035 2044 4.916983 ACATTTTCAAAGTGCAGCAGTA 57.083 36.364 2.23 0.00 0.00 2.74
2051 2060 5.394553 GCAGCAGTAGATTTTGCCCTATTTT 60.395 40.000 0.00 0.00 41.17 1.82
2073 2082 5.811399 TCAAGGCGTATTTGTCTATTTGG 57.189 39.130 0.00 0.00 0.00 3.28
2132 2141 7.639039 TCTTCATGTGTTATGTTTGTTGAGAC 58.361 34.615 0.00 0.00 0.00 3.36
2137 2146 4.751098 GTGTTATGTTTGTTGAGACCGGTA 59.249 41.667 7.34 0.00 0.00 4.02
2150 2159 7.441157 TGTTGAGACCGGTAATGATTGAATATC 59.559 37.037 7.34 0.00 0.00 1.63
2161 2170 5.247507 TGATTGAATATCGGTTGCCTTTG 57.752 39.130 0.00 0.00 0.00 2.77
2255 2267 5.108385 AGGTTCTTCGCAAGTTATGTTTG 57.892 39.130 0.00 0.00 39.48 2.93
2302 2314 3.818773 GGCTTAATGTTGTGTGTGTACCT 59.181 43.478 0.00 0.00 0.00 3.08
2351 2363 4.414852 GACGTGAATGTGCAAAGCAATAT 58.585 39.130 0.00 0.00 41.47 1.28
2352 2364 5.448496 GGACGTGAATGTGCAAAGCAATATA 60.448 40.000 0.00 0.00 41.47 0.86
2357 2369 9.992910 CGTGAATGTGCAAAGCAATATATATAT 57.007 29.630 0.00 0.00 41.47 0.86
2391 2403 9.679661 TGAGTTTATCCATTAATGCTGAACTAA 57.320 29.630 18.22 12.68 0.00 2.24
2397 2409 7.572523 TCCATTAATGCTGAACTAATTCTGG 57.427 36.000 10.11 0.00 35.69 3.86
2595 2609 6.703607 AGCTAAGATATCAAACGTCATTCTGG 59.296 38.462 5.32 0.00 0.00 3.86
2617 2631 9.812347 TCTGGTTGATATGGATATTTTAAGCAT 57.188 29.630 0.00 0.00 0.00 3.79
2712 2726 4.878397 AGGTGCAGCTATTGTAGAAACATC 59.122 41.667 18.63 0.00 34.97 3.06
2862 2876 2.314246 TGTGTGGCAATGGTCATTTGA 58.686 42.857 0.00 0.00 0.00 2.69
2883 2897 8.436046 TTTGATCTTTTCCCATTTTTGTTCAG 57.564 30.769 0.00 0.00 0.00 3.02
2938 2952 4.143597 CGGAATAGTTATAACTCGCTTGCG 60.144 45.833 21.25 22.03 40.37 4.85
2945 2959 2.933495 TAACTCGCTTGCGTACTCAT 57.067 45.000 14.70 0.44 0.00 2.90
2960 2974 8.500753 TGCGTACTCATTTAATCAAGGTTATT 57.499 30.769 0.00 0.00 0.00 1.40
3093 3107 2.750166 TCACCAAGACTAGAAGAGCTCG 59.250 50.000 8.37 0.00 0.00 5.03
3117 3131 1.822371 TGAAGCATAGACAGGTACGCA 59.178 47.619 0.00 0.00 0.00 5.24
3121 3135 1.539065 GCATAGACAGGTACGCAGCAT 60.539 52.381 0.00 0.00 0.00 3.79
3140 3154 9.396938 CGCAGCATGTAATATTATTGAATTGAA 57.603 29.630 10.82 0.00 39.31 2.69
3178 3192 4.501071 TCGCTAACATGTAGGACCTTTTC 58.499 43.478 0.00 0.00 0.00 2.29
3302 3319 6.784473 TCATCATACAGTATTCAGAGGGTGAT 59.216 38.462 0.00 0.00 34.17 3.06
3345 3362 0.249120 TGTCCTGGTAGCGAATGGTG 59.751 55.000 0.00 0.00 0.00 4.17
3401 3418 5.008118 CGAAGATATCAAAAAGAGGGCCTTC 59.992 44.000 7.89 6.80 33.02 3.46
3408 3425 1.194781 AAAGAGGGCCTTCGCTGAGA 61.195 55.000 7.89 0.00 35.44 3.27
3410 3427 0.980231 AGAGGGCCTTCGCTGAGAAT 60.980 55.000 7.89 0.00 38.34 2.40
3417 3434 1.357258 CTTCGCTGAGAATGCACGCT 61.357 55.000 0.00 0.00 38.34 5.07
3438 3455 2.047179 AAGAGGAACGCCCGAAGC 60.047 61.111 0.00 0.00 40.87 3.86
3513 3530 3.898123 GAGTAACCCTGATGATCCTAGCA 59.102 47.826 0.00 0.00 0.00 3.49
3547 3564 3.340814 TCCTGATGACTTTTGAGGAGC 57.659 47.619 0.00 0.00 0.00 4.70
3549 3566 2.354103 CCTGATGACTTTTGAGGAGCGA 60.354 50.000 0.00 0.00 0.00 4.93
3550 3567 3.329386 CTGATGACTTTTGAGGAGCGAA 58.671 45.455 0.00 0.00 0.00 4.70
3573 3596 2.112380 TTGGCAGCGATGAATCTGAA 57.888 45.000 4.02 0.00 32.26 3.02
3583 3606 5.763698 AGCGATGAATCTGAACATGATGATT 59.236 36.000 0.00 3.49 32.59 2.57
3595 3618 7.208777 TGAACATGATGATTTCTAGAGCTCTC 58.791 38.462 22.17 5.38 0.00 3.20
3610 3633 4.464597 AGAGCTCTCTAGGGTTAAGTTGTG 59.535 45.833 11.45 0.00 38.35 3.33
3687 3738 1.962807 TGAAACTTGGTGAATGCTGGG 59.037 47.619 0.00 0.00 0.00 4.45
3690 3741 2.086610 ACTTGGTGAATGCTGGGTTT 57.913 45.000 0.00 0.00 0.00 3.27
3691 3742 2.397597 ACTTGGTGAATGCTGGGTTTT 58.602 42.857 0.00 0.00 0.00 2.43
3705 3756 1.338105 GGGTTTTGGAGCAGCAAATCC 60.338 52.381 0.00 0.00 36.05 3.01
3710 3761 2.645838 TGGAGCAGCAAATCCTATCC 57.354 50.000 0.00 0.00 36.50 2.59
3745 3798 2.416296 GCATTTGCACTGCTTGAGCATA 60.416 45.455 12.15 0.79 45.17 3.14
3755 3808 1.596727 GCTTGAGCATAGCTGTGTAGC 59.403 52.381 12.41 11.58 44.91 3.58
3767 3820 1.805945 GTGTAGCGTCTTGGCTCCG 60.806 63.158 0.00 0.00 43.54 4.63
3768 3821 2.202756 GTAGCGTCTTGGCTCCGG 60.203 66.667 0.00 0.00 43.54 5.14
3789 3842 0.675208 TTTGATTTCCGCGCCTGCTA 60.675 50.000 0.00 0.00 39.65 3.49
3802 3855 2.735126 CGCCTGCTATTTTGCCGAAATT 60.735 45.455 0.00 0.00 38.80 1.82
3803 3856 2.604462 GCCTGCTATTTTGCCGAAATTG 59.396 45.455 0.00 0.00 38.80 2.32
3810 3863 3.363341 TTTTGCCGAAATTGTCTGGAC 57.637 42.857 0.00 0.00 0.00 4.02
3871 3924 3.961480 ACTGATGGTTCTTCGATGTGA 57.039 42.857 0.00 0.00 0.00 3.58
3876 3929 1.344438 TGGTTCTTCGATGTGAGCTGT 59.656 47.619 0.00 0.00 0.00 4.40
3897 3950 4.814234 TGTAAATAGATGCGTGGATGTTCC 59.186 41.667 0.00 0.00 36.96 3.62
3944 4000 8.992835 TGCTAGATGATATGCAGTTGTATTAG 57.007 34.615 0.00 0.00 0.00 1.73
3961 4017 6.432581 TGTATTAGAGATGTGTAGTGGAGGT 58.567 40.000 0.00 0.00 0.00 3.85
3973 4029 0.393820 GTGGAGGTGGACGTTTGGTA 59.606 55.000 0.00 0.00 0.00 3.25
4004 4060 6.884832 TGTATCTACACCCTACATGAAAAGG 58.115 40.000 0.00 3.01 0.00 3.11
4008 4064 6.472887 TCTACACCCTACATGAAAAGGAAAG 58.527 40.000 0.00 0.00 34.58 2.62
4107 4163 3.834610 TCCGTCTCGAAATTCTTGTCTC 58.165 45.455 0.00 0.00 0.00 3.36
4184 4240 7.562088 ACCCTTGACTGGTTTTAAAAAGATACA 59.438 33.333 1.31 0.00 29.75 2.29
4275 4784 3.648339 TGTAGTTGTCGTTAGGTGGTC 57.352 47.619 0.00 0.00 0.00 4.02
4276 4785 3.225104 TGTAGTTGTCGTTAGGTGGTCT 58.775 45.455 0.00 0.00 0.00 3.85
4277 4786 4.397420 TGTAGTTGTCGTTAGGTGGTCTA 58.603 43.478 0.00 0.00 0.00 2.59
4278 4787 3.930634 AGTTGTCGTTAGGTGGTCTAC 57.069 47.619 0.00 0.00 0.00 2.59
4279 4788 2.227388 AGTTGTCGTTAGGTGGTCTACG 59.773 50.000 0.00 0.00 0.00 3.51
4280 4789 1.167851 TGTCGTTAGGTGGTCTACGG 58.832 55.000 0.00 0.00 0.00 4.02
4281 4790 1.271325 TGTCGTTAGGTGGTCTACGGA 60.271 52.381 0.00 0.00 0.00 4.69
4282 4791 1.399791 GTCGTTAGGTGGTCTACGGAG 59.600 57.143 0.00 0.00 0.00 4.63
4283 4792 0.100146 CGTTAGGTGGTCTACGGAGC 59.900 60.000 0.00 0.00 40.08 4.70
4284 4793 1.472188 GTTAGGTGGTCTACGGAGCT 58.528 55.000 0.00 0.00 40.29 4.09
4285 4794 1.134560 GTTAGGTGGTCTACGGAGCTG 59.865 57.143 0.00 0.00 40.29 4.24
4286 4795 0.395311 TAGGTGGTCTACGGAGCTGG 60.395 60.000 0.00 0.00 40.29 4.85
4287 4796 1.681327 GGTGGTCTACGGAGCTGGA 60.681 63.158 0.00 0.00 40.29 3.86
4288 4797 1.043673 GGTGGTCTACGGAGCTGGAT 61.044 60.000 0.00 0.00 40.29 3.41
4289 4798 0.103208 GTGGTCTACGGAGCTGGATG 59.897 60.000 0.00 0.00 40.29 3.51
4290 4799 0.324368 TGGTCTACGGAGCTGGATGT 60.324 55.000 0.00 0.00 40.29 3.06
4291 4800 1.064240 TGGTCTACGGAGCTGGATGTA 60.064 52.381 0.00 0.00 40.29 2.29
4292 4801 2.029623 GGTCTACGGAGCTGGATGTAA 58.970 52.381 0.00 0.00 37.05 2.41
4293 4802 2.628657 GGTCTACGGAGCTGGATGTAAT 59.371 50.000 0.00 0.00 37.05 1.89
4322 4831 9.478768 TCATTATTTCTTGTGTTCGTTGTACTA 57.521 29.630 0.00 0.00 0.00 1.82
4330 4839 5.358090 TGTGTTCGTTGTACTACCATTGAA 58.642 37.500 1.76 0.00 0.00 2.69
4331 4840 5.992829 TGTGTTCGTTGTACTACCATTGAAT 59.007 36.000 1.76 0.00 0.00 2.57
4332 4841 7.153315 TGTGTTCGTTGTACTACCATTGAATA 58.847 34.615 1.76 0.00 0.00 1.75
4333 4842 7.820386 TGTGTTCGTTGTACTACCATTGAATAT 59.180 33.333 1.76 0.00 0.00 1.28
4334 4843 8.114290 GTGTTCGTTGTACTACCATTGAATATG 58.886 37.037 1.76 0.00 0.00 1.78
4335 4844 8.035984 TGTTCGTTGTACTACCATTGAATATGA 58.964 33.333 1.76 0.00 0.00 2.15
4336 4845 8.875803 GTTCGTTGTACTACCATTGAATATGAA 58.124 33.333 1.76 0.00 0.00 2.57
4337 4846 9.607988 TTCGTTGTACTACCATTGAATATGAAT 57.392 29.630 1.76 0.00 0.00 2.57
4345 4854 9.035890 ACTACCATTGAATATGAATAGATCGGA 57.964 33.333 0.00 0.00 0.00 4.55
4346 4855 9.875691 CTACCATTGAATATGAATAGATCGGAA 57.124 33.333 0.00 0.00 0.00 4.30
4347 4856 8.783833 ACCATTGAATATGAATAGATCGGAAG 57.216 34.615 0.00 0.00 0.00 3.46
4348 4857 8.378565 ACCATTGAATATGAATAGATCGGAAGT 58.621 33.333 0.00 0.00 0.00 3.01
4349 4858 9.224267 CCATTGAATATGAATAGATCGGAAGTT 57.776 33.333 0.00 0.00 0.00 2.66
4353 4862 9.273016 TGAATATGAATAGATCGGAAGTTTTCC 57.727 33.333 0.00 0.00 46.62 3.13
4426 4973 6.269769 ACTCTGGGCTTATTTTCCATGAAAAA 59.730 34.615 6.14 0.00 43.32 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.449743 TGTAAATGAAAAAGGAGACCGTCG 59.550 41.667 0.00 0.00 0.00 5.12
180 181 6.409524 ACCACAATAGGGCATCAAAATATG 57.590 37.500 0.00 0.00 0.00 1.78
405 406 1.556911 GATGAGACCCCAGCAGAGAAA 59.443 52.381 0.00 0.00 0.00 2.52
425 426 7.852454 CACATTCCACGATTAATACATCAAGTG 59.148 37.037 0.00 0.00 0.00 3.16
458 459 1.271597 GCCCCTAGATAACCTGCCATG 60.272 57.143 0.00 0.00 0.00 3.66
469 470 2.687914 GCAATCCAAACAGCCCCTAGAT 60.688 50.000 0.00 0.00 0.00 1.98
470 471 1.340991 GCAATCCAAACAGCCCCTAGA 60.341 52.381 0.00 0.00 0.00 2.43
471 472 1.106285 GCAATCCAAACAGCCCCTAG 58.894 55.000 0.00 0.00 0.00 3.02
472 473 0.407528 TGCAATCCAAACAGCCCCTA 59.592 50.000 0.00 0.00 0.00 3.53
473 474 0.901580 CTGCAATCCAAACAGCCCCT 60.902 55.000 0.00 0.00 0.00 4.79
474 475 1.593265 CTGCAATCCAAACAGCCCC 59.407 57.895 0.00 0.00 0.00 5.80
478 479 0.529378 GAGGGCTGCAATCCAAACAG 59.471 55.000 0.50 0.00 34.48 3.16
479 480 0.178967 TGAGGGCTGCAATCCAAACA 60.179 50.000 0.50 2.79 0.00 2.83
480 481 0.968405 TTGAGGGCTGCAATCCAAAC 59.032 50.000 0.50 0.62 0.00 2.93
481 482 0.968405 GTTGAGGGCTGCAATCCAAA 59.032 50.000 0.50 0.00 0.00 3.28
482 483 0.112995 AGTTGAGGGCTGCAATCCAA 59.887 50.000 0.50 0.00 0.00 3.53
483 484 0.609957 CAGTTGAGGGCTGCAATCCA 60.610 55.000 0.50 0.00 0.00 3.41
484 485 2.187073 CAGTTGAGGGCTGCAATCC 58.813 57.895 0.50 0.00 0.00 3.01
490 491 1.662044 GTTTGGCAGTTGAGGGCTG 59.338 57.895 0.00 0.00 37.06 4.85
491 492 1.531602 GGTTTGGCAGTTGAGGGCT 60.532 57.895 0.00 0.00 0.00 5.19
492 493 1.398958 TTGGTTTGGCAGTTGAGGGC 61.399 55.000 0.00 0.00 0.00 5.19
493 494 1.118838 TTTGGTTTGGCAGTTGAGGG 58.881 50.000 0.00 0.00 0.00 4.30
494 495 2.977772 TTTTGGTTTGGCAGTTGAGG 57.022 45.000 0.00 0.00 0.00 3.86
519 520 0.610232 AGCCAGGCTTGGTCAATGAC 60.610 55.000 17.25 4.51 46.80 3.06
520 521 1.769665 AGCCAGGCTTGGTCAATGA 59.230 52.632 17.25 0.00 46.80 2.57
521 522 4.428845 AGCCAGGCTTGGTCAATG 57.571 55.556 17.25 0.00 46.80 2.82
530 531 2.282462 CAAACCGGAAGCCAGGCT 60.282 61.111 8.70 8.70 42.56 4.58
531 532 3.373565 CCAAACCGGAAGCCAGGC 61.374 66.667 9.46 1.84 36.56 4.85
532 533 2.434331 TCCAAACCGGAAGCCAGG 59.566 61.111 9.46 0.61 42.52 4.45
540 541 0.540830 TTGGTTCCCATCCAAACCGG 60.541 55.000 0.00 0.00 46.49 5.28
541 542 1.555967 ATTGGTTCCCATCCAAACCG 58.444 50.000 1.55 0.00 46.49 4.44
542 543 5.692115 AAATATTGGTTCCCATCCAAACC 57.308 39.130 1.55 0.00 46.07 3.27
543 544 6.983474 CAAAATATTGGTTCCCATCCAAAC 57.017 37.500 1.55 0.00 46.07 2.93
566 567 2.985847 GAGTTGGCTGGGTGCACC 60.986 66.667 28.57 28.57 45.15 5.01
567 568 2.985847 GGAGTTGGCTGGGTGCAC 60.986 66.667 8.80 8.80 45.15 4.57
568 569 4.284550 GGGAGTTGGCTGGGTGCA 62.285 66.667 0.00 0.00 45.15 4.57
569 570 4.284550 TGGGAGTTGGCTGGGTGC 62.285 66.667 0.00 0.00 41.94 5.01
570 571 2.282462 GTGGGAGTTGGCTGGGTG 60.282 66.667 0.00 0.00 0.00 4.61
571 572 2.069165 GAAGTGGGAGTTGGCTGGGT 62.069 60.000 0.00 0.00 0.00 4.51
572 573 1.303643 GAAGTGGGAGTTGGCTGGG 60.304 63.158 0.00 0.00 0.00 4.45
573 574 1.303643 GGAAGTGGGAGTTGGCTGG 60.304 63.158 0.00 0.00 0.00 4.85
574 575 1.303643 GGGAAGTGGGAGTTGGCTG 60.304 63.158 0.00 0.00 0.00 4.85
575 576 1.360393 TTGGGAAGTGGGAGTTGGCT 61.360 55.000 0.00 0.00 0.00 4.75
576 577 0.895559 CTTGGGAAGTGGGAGTTGGC 60.896 60.000 0.00 0.00 0.00 4.52
577 578 0.478507 ACTTGGGAAGTGGGAGTTGG 59.521 55.000 0.00 0.00 41.01 3.77
578 579 2.230660 GAACTTGGGAAGTGGGAGTTG 58.769 52.381 0.00 0.00 41.91 3.16
579 580 1.850345 TGAACTTGGGAAGTGGGAGTT 59.150 47.619 0.00 0.00 41.91 3.01
580 581 1.421646 CTGAACTTGGGAAGTGGGAGT 59.578 52.381 0.00 0.00 41.91 3.85
581 582 1.884067 GCTGAACTTGGGAAGTGGGAG 60.884 57.143 0.00 0.00 41.91 4.30
582 583 0.110486 GCTGAACTTGGGAAGTGGGA 59.890 55.000 0.00 0.00 41.91 4.37
583 584 0.111253 AGCTGAACTTGGGAAGTGGG 59.889 55.000 0.00 0.00 41.91 4.61
584 585 1.528129 GAGCTGAACTTGGGAAGTGG 58.472 55.000 0.00 0.00 41.91 4.00
585 586 1.151668 CGAGCTGAACTTGGGAAGTG 58.848 55.000 0.00 0.00 41.91 3.16
586 587 1.048601 TCGAGCTGAACTTGGGAAGT 58.951 50.000 0.00 0.00 45.46 3.01
587 588 1.433534 GTCGAGCTGAACTTGGGAAG 58.566 55.000 0.00 0.00 0.00 3.46
588 589 0.319555 CGTCGAGCTGAACTTGGGAA 60.320 55.000 0.00 0.00 0.00 3.97
589 590 1.289066 CGTCGAGCTGAACTTGGGA 59.711 57.895 0.00 0.00 0.00 4.37
590 591 2.383527 GCGTCGAGCTGAACTTGGG 61.384 63.158 0.00 0.00 44.04 4.12
591 592 3.159984 GCGTCGAGCTGAACTTGG 58.840 61.111 0.00 0.00 44.04 3.61
599 600 3.003056 CCAACTTTTTGGCGTCGAGCT 62.003 52.381 0.00 0.00 46.09 4.09
600 601 0.660300 CCAACTTTTTGGCGTCGAGC 60.660 55.000 0.00 0.00 46.09 5.03
601 602 3.454941 CCAACTTTTTGGCGTCGAG 57.545 52.632 0.00 0.00 46.09 4.04
609 610 2.483538 CCCCAGACTTGCCAACTTTTTG 60.484 50.000 0.00 0.00 0.00 2.44
610 611 1.762370 CCCCAGACTTGCCAACTTTTT 59.238 47.619 0.00 0.00 0.00 1.94
611 612 1.413118 CCCCAGACTTGCCAACTTTT 58.587 50.000 0.00 0.00 0.00 2.27
612 613 1.115326 GCCCCAGACTTGCCAACTTT 61.115 55.000 0.00 0.00 0.00 2.66
613 614 1.531602 GCCCCAGACTTGCCAACTT 60.532 57.895 0.00 0.00 0.00 2.66
614 615 2.116125 GCCCCAGACTTGCCAACT 59.884 61.111 0.00 0.00 0.00 3.16
615 616 3.365265 CGCCCCAGACTTGCCAAC 61.365 66.667 0.00 0.00 0.00 3.77
633 634 0.817634 TTATTGGCGCAGGATTCGGG 60.818 55.000 10.83 0.00 0.00 5.14
634 635 1.021202 TTTATTGGCGCAGGATTCGG 58.979 50.000 10.83 0.00 0.00 4.30
635 636 3.044986 CAATTTATTGGCGCAGGATTCG 58.955 45.455 10.83 0.00 34.22 3.34
655 656 4.635769 CCAATCGTTGGCTAGCCA 57.364 55.556 32.88 32.88 45.17 4.75
663 664 1.675310 TGAGCCCTGCCAATCGTTG 60.675 57.895 0.00 0.00 0.00 4.10
664 665 1.675641 GTGAGCCCTGCCAATCGTT 60.676 57.895 0.00 0.00 0.00 3.85
665 666 2.045926 GTGAGCCCTGCCAATCGT 60.046 61.111 0.00 0.00 0.00 3.73
666 667 0.179048 TATGTGAGCCCTGCCAATCG 60.179 55.000 0.00 0.00 0.00 3.34
667 668 1.602311 CTATGTGAGCCCTGCCAATC 58.398 55.000 0.00 0.00 0.00 2.67
668 669 0.184451 CCTATGTGAGCCCTGCCAAT 59.816 55.000 0.00 0.00 0.00 3.16
669 670 1.609239 CCTATGTGAGCCCTGCCAA 59.391 57.895 0.00 0.00 0.00 4.52
670 671 3.047807 GCCTATGTGAGCCCTGCCA 62.048 63.158 0.00 0.00 0.00 4.92
671 672 2.203266 GCCTATGTGAGCCCTGCC 60.203 66.667 0.00 0.00 0.00 4.85
672 673 1.077501 TTGCCTATGTGAGCCCTGC 60.078 57.895 0.00 0.00 0.00 4.85
673 674 0.543277 TCTTGCCTATGTGAGCCCTG 59.457 55.000 0.00 0.00 0.00 4.45
674 675 1.065126 GTTCTTGCCTATGTGAGCCCT 60.065 52.381 0.00 0.00 0.00 5.19
675 676 1.383523 GTTCTTGCCTATGTGAGCCC 58.616 55.000 0.00 0.00 0.00 5.19
676 677 1.340017 TGGTTCTTGCCTATGTGAGCC 60.340 52.381 0.00 0.00 0.00 4.70
677 678 2.113860 TGGTTCTTGCCTATGTGAGC 57.886 50.000 0.00 0.00 0.00 4.26
678 679 3.820467 TGTTTGGTTCTTGCCTATGTGAG 59.180 43.478 0.00 0.00 0.00 3.51
679 680 3.820467 CTGTTTGGTTCTTGCCTATGTGA 59.180 43.478 0.00 0.00 0.00 3.58
680 681 3.612479 GCTGTTTGGTTCTTGCCTATGTG 60.612 47.826 0.00 0.00 0.00 3.21
681 682 2.558359 GCTGTTTGGTTCTTGCCTATGT 59.442 45.455 0.00 0.00 0.00 2.29
682 683 2.094545 GGCTGTTTGGTTCTTGCCTATG 60.095 50.000 0.00 0.00 37.58 2.23
683 684 2.171003 GGCTGTTTGGTTCTTGCCTAT 58.829 47.619 0.00 0.00 37.58 2.57
684 685 1.616159 GGCTGTTTGGTTCTTGCCTA 58.384 50.000 0.00 0.00 37.58 3.93
685 686 1.115326 GGGCTGTTTGGTTCTTGCCT 61.115 55.000 0.00 0.00 40.15 4.75
686 687 1.115326 AGGGCTGTTTGGTTCTTGCC 61.115 55.000 0.00 0.00 39.61 4.52
687 688 0.315251 GAGGGCTGTTTGGTTCTTGC 59.685 55.000 0.00 0.00 0.00 4.01
688 689 1.986882 AGAGGGCTGTTTGGTTCTTG 58.013 50.000 0.00 0.00 0.00 3.02
689 690 2.553247 GCTAGAGGGCTGTTTGGTTCTT 60.553 50.000 0.00 0.00 0.00 2.52
690 691 1.003696 GCTAGAGGGCTGTTTGGTTCT 59.996 52.381 0.00 0.00 0.00 3.01
691 692 1.454201 GCTAGAGGGCTGTTTGGTTC 58.546 55.000 0.00 0.00 0.00 3.62
692 693 0.038310 GGCTAGAGGGCTGTTTGGTT 59.962 55.000 0.00 0.00 37.53 3.67
693 694 1.685820 GGCTAGAGGGCTGTTTGGT 59.314 57.895 0.00 0.00 37.53 3.67
694 695 4.645809 GGCTAGAGGGCTGTTTGG 57.354 61.111 0.00 0.00 37.53 3.28
701 702 1.924731 AACCAAAAAGGCTAGAGGGC 58.075 50.000 0.00 0.00 43.14 5.19
702 703 4.017126 CCTTAACCAAAAAGGCTAGAGGG 58.983 47.826 0.00 0.00 43.14 4.30
703 704 4.918588 TCCTTAACCAAAAAGGCTAGAGG 58.081 43.478 0.00 0.00 42.79 3.69
704 705 6.887002 AGATTCCTTAACCAAAAAGGCTAGAG 59.113 38.462 0.00 0.00 42.79 2.43
715 716 3.308402 CCTGCCTCAGATTCCTTAACCAA 60.308 47.826 0.00 0.00 32.44 3.67
917 920 2.022195 CATCATTGCAGTTCAGGGGAG 58.978 52.381 0.00 0.00 0.00 4.30
1314 1317 6.897986 AGGAGCAGAAATTGTCATTCTATCT 58.102 36.000 0.00 0.00 35.43 1.98
1421 1424 4.695217 AATGTACGCCCACAAGTATTTG 57.305 40.909 0.00 0.00 40.24 2.32
1512 1515 5.988561 CCTGTCTTCTGATAAGCATACCTTC 59.011 44.000 0.00 0.00 34.95 3.46
1681 1685 3.482472 CGTGCTACTATCAACTACAAGCG 59.518 47.826 0.00 0.00 0.00 4.68
1710 1714 7.496263 TGCTTTCGGTAAATATAGCAATACACA 59.504 33.333 0.00 0.00 0.00 3.72
1720 1724 8.962679 ACTTCCATTTTGCTTTCGGTAAATATA 58.037 29.630 0.00 0.00 30.20 0.86
1727 1731 2.955660 TGACTTCCATTTTGCTTTCGGT 59.044 40.909 0.00 0.00 0.00 4.69
1729 1733 7.382218 ACTTTATTGACTTCCATTTTGCTTTCG 59.618 33.333 0.00 0.00 0.00 3.46
1781 1785 3.749665 TTTGCCTTTTAGTTGCAGCAT 57.250 38.095 2.55 0.00 36.21 3.79
1839 1845 6.036470 GGAGGTAAATTAAGCAAAGCATGAC 58.964 40.000 0.00 0.00 0.00 3.06
1926 1932 1.779221 TGCAGGCATTTCCCTAATGG 58.221 50.000 0.00 0.00 43.20 3.16
1927 1933 3.025978 TCTTGCAGGCATTTCCCTAATG 58.974 45.455 0.00 0.00 45.30 1.90
1949 1958 5.959527 GCAATACATGTGATACACGAGTTTG 59.040 40.000 9.11 0.00 37.14 2.93
1955 1964 9.502145 AAAATTAAGCAATACATGTGATACACG 57.498 29.630 9.11 0.00 37.14 4.49
2007 2016 2.986479 GCACTTTGAAAATGTAAGGGCG 59.014 45.455 0.00 0.00 38.40 6.13
2033 2042 6.042777 GCCTTGAAAATAGGGCAAAATCTAC 58.957 40.000 0.00 0.00 43.59 2.59
2035 2044 4.381932 CGCCTTGAAAATAGGGCAAAATCT 60.382 41.667 0.00 0.00 44.27 2.40
2051 2060 4.638421 CCCAAATAGACAAATACGCCTTGA 59.362 41.667 0.00 0.00 0.00 3.02
2132 2141 5.616866 GCAACCGATATTCAATCATTACCGG 60.617 44.000 0.00 0.00 40.15 5.28
2137 2146 6.275335 CAAAGGCAACCGATATTCAATCATT 58.725 36.000 0.00 0.00 37.17 2.57
2183 2192 9.567776 TCTGATTTCAAATACACCTCAGTAAAA 57.432 29.630 0.00 0.00 32.49 1.52
2255 2267 8.718734 CCTACCACACTAGAATTAAACTTCAAC 58.281 37.037 0.00 0.00 0.00 3.18
2273 2285 3.818210 CACACAACATTAAGCCTACCACA 59.182 43.478 0.00 0.00 0.00 4.17
2331 2343 9.992910 ATATATATATTGCTTTGCACATTCACG 57.007 29.630 0.00 0.00 38.71 4.35
2357 2369 7.229306 GCATTAATGGATAAACTCATGGTCTCA 59.771 37.037 17.02 0.00 0.00 3.27
2391 2403 8.109634 ACTTAGACCAACATGAATTACCAGAAT 58.890 33.333 0.00 0.00 0.00 2.40
2469 2482 6.973474 CGACTGATAGAAGGAAAGTAAATCGT 59.027 38.462 0.00 0.00 0.00 3.73
2470 2483 6.973474 ACGACTGATAGAAGGAAAGTAAATCG 59.027 38.462 0.00 0.00 0.00 3.34
2481 2495 7.317842 TCTAGTGTAAACGACTGATAGAAGG 57.682 40.000 0.00 0.00 0.00 3.46
2488 2502 5.562307 GCTCTGTTCTAGTGTAAACGACTGA 60.562 44.000 0.00 0.00 0.00 3.41
2584 2598 4.753516 TCCATATCAACCAGAATGACGT 57.246 40.909 0.00 0.00 39.69 4.34
2617 2631 0.385029 ACGCACAGCAAATCAGCAAA 59.615 45.000 0.00 0.00 36.85 3.68
2620 2634 1.887320 CTTACGCACAGCAAATCAGC 58.113 50.000 0.00 0.00 0.00 4.26
2712 2726 3.559242 ACAAACAAATGAAACATTGCCCG 59.441 39.130 0.00 0.00 0.00 6.13
2960 2974 3.495331 TGTAGGCAGCTCATTTTCCAAA 58.505 40.909 0.00 0.00 0.00 3.28
3100 3114 0.103208 GCTGCGTACCTGTCTATGCT 59.897 55.000 0.00 0.00 30.97 3.79
3106 3120 2.004583 TTACATGCTGCGTACCTGTC 57.995 50.000 0.00 0.00 0.00 3.51
3140 3154 9.139174 CATGTTAGCGAACCTTTTCAAAATATT 57.861 29.630 7.26 0.00 34.38 1.28
3141 3155 8.303876 ACATGTTAGCGAACCTTTTCAAAATAT 58.696 29.630 7.26 0.00 34.38 1.28
3143 3157 6.512297 ACATGTTAGCGAACCTTTTCAAAAT 58.488 32.000 7.26 0.00 34.38 1.82
3178 3192 4.766891 AGAGACAAACAGGAAGAGAGAGAG 59.233 45.833 0.00 0.00 0.00 3.20
3302 3319 2.821378 CACCAGCTTGTCAATTCCATCA 59.179 45.455 0.00 0.00 0.00 3.07
3345 3362 4.557205 ACACTTATCTTGTCCGAACTGAC 58.443 43.478 0.00 0.00 35.77 3.51
3401 3418 2.699809 GAGCGTGCATTCTCAGCG 59.300 61.111 11.77 0.35 33.85 5.18
3408 3425 1.448540 CCTCTTCGGAGCGTGCATT 60.449 57.895 0.00 0.00 40.56 3.56
3410 3427 2.570284 TTCCTCTTCGGAGCGTGCA 61.570 57.895 0.00 0.00 44.28 4.57
3417 3434 3.755628 CGGGCGTTCCTCTTCGGA 61.756 66.667 0.00 0.00 41.06 4.55
3428 3445 2.262915 CTCTTCTGCTTCGGGCGT 59.737 61.111 0.00 0.00 45.43 5.68
3431 3448 2.124942 GCCCTCTTCTGCTTCGGG 60.125 66.667 0.00 0.00 37.97 5.14
3434 3451 0.247736 TCTTCGCCCTCTTCTGCTTC 59.752 55.000 0.00 0.00 0.00 3.86
3438 3455 3.127721 GGATTTTTCTTCGCCCTCTTCTG 59.872 47.826 0.00 0.00 0.00 3.02
3513 3530 4.277174 GTCATCAGGATCATACTCGTCACT 59.723 45.833 0.00 0.00 0.00 3.41
3573 3596 6.982160 AGAGAGCTCTAGAAATCATCATGT 57.018 37.500 18.25 0.00 38.35 3.21
3595 3618 2.871096 TGGGCACAACTTAACCCTAG 57.129 50.000 0.00 0.00 43.25 3.02
3606 3629 2.630580 GGAAACTAATGGTTGGGCACAA 59.369 45.455 0.00 0.00 38.29 3.33
3608 3631 1.548719 GGGAAACTAATGGTTGGGCAC 59.451 52.381 0.00 0.00 38.29 5.01
3610 3633 2.231716 AGGGAAACTAATGGTTGGGC 57.768 50.000 0.00 0.00 38.29 5.36
3687 3738 4.440663 GGATAGGATTTGCTGCTCCAAAAC 60.441 45.833 8.85 4.52 38.12 2.43
3690 3741 2.241941 TGGATAGGATTTGCTGCTCCAA 59.758 45.455 8.85 0.00 33.75 3.53
3691 3742 1.845791 TGGATAGGATTTGCTGCTCCA 59.154 47.619 8.85 4.31 33.75 3.86
3745 3798 1.374758 GCCAAGACGCTACACAGCT 60.375 57.895 0.00 0.00 46.26 4.24
3754 3807 4.699522 AACCCGGAGCCAAGACGC 62.700 66.667 0.73 0.00 0.00 5.19
3755 3808 2.032071 AAACCCGGAGCCAAGACG 59.968 61.111 0.73 0.00 0.00 4.18
3756 3809 0.322546 ATCAAACCCGGAGCCAAGAC 60.323 55.000 0.73 0.00 0.00 3.01
3757 3810 0.404040 AATCAAACCCGGAGCCAAGA 59.596 50.000 0.73 0.00 0.00 3.02
3758 3811 1.202348 GAAATCAAACCCGGAGCCAAG 59.798 52.381 0.73 0.00 0.00 3.61
3767 3820 2.180769 GGCGCGGAAATCAAACCC 59.819 61.111 8.83 0.00 0.00 4.11
3768 3821 1.154035 CAGGCGCGGAAATCAAACC 60.154 57.895 8.83 0.00 0.00 3.27
3789 3842 3.306019 GGTCCAGACAATTTCGGCAAAAT 60.306 43.478 0.00 0.00 39.30 1.82
3802 3855 1.140852 CAAACACCTCTGGTCCAGACA 59.859 52.381 18.15 0.00 35.39 3.41
3803 3856 1.884235 CAAACACCTCTGGTCCAGAC 58.116 55.000 18.15 0.00 35.39 3.51
3810 3863 1.342174 AGCAATTGCAAACACCTCTGG 59.658 47.619 30.89 0.00 45.16 3.86
3871 3924 3.819564 TCCACGCATCTATTTACAGCT 57.180 42.857 0.00 0.00 0.00 4.24
3876 3929 5.056480 CAGGAACATCCACGCATCTATTTA 58.944 41.667 0.00 0.00 39.61 1.40
3897 3950 4.393062 CAGTAGTAACAGCCCAAATCACAG 59.607 45.833 0.00 0.00 0.00 3.66
3944 4000 2.166664 GTCCACCTCCACTACACATCTC 59.833 54.545 0.00 0.00 0.00 2.75
3961 4017 2.572556 ACACCCATATACCAAACGTCCA 59.427 45.455 0.00 0.00 0.00 4.02
4159 4215 7.947282 TGTATCTTTTTAAAACCAGTCAAGGG 58.053 34.615 0.00 0.00 0.00 3.95
4275 4784 5.116180 TGAAAATTACATCCAGCTCCGTAG 58.884 41.667 0.00 0.00 0.00 3.51
4276 4785 5.092554 TGAAAATTACATCCAGCTCCGTA 57.907 39.130 0.00 0.00 0.00 4.02
4277 4786 3.950397 TGAAAATTACATCCAGCTCCGT 58.050 40.909 0.00 0.00 0.00 4.69
4278 4787 5.505173 AATGAAAATTACATCCAGCTCCG 57.495 39.130 0.00 0.00 0.00 4.63
4279 4788 9.468532 GAAATAATGAAAATTACATCCAGCTCC 57.531 33.333 0.00 0.00 0.00 4.70
4292 4801 9.528018 ACAACGAACACAAGAAATAATGAAAAT 57.472 25.926 0.00 0.00 0.00 1.82
4293 4802 8.918961 ACAACGAACACAAGAAATAATGAAAA 57.081 26.923 0.00 0.00 0.00 2.29
4322 4831 8.378565 ACTTCCGATCTATTCATATTCAATGGT 58.621 33.333 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.