Multiple sequence alignment - TraesCS1A01G351800

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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 TraesCS1A01G351800 chr1A 100.000 4667 0 0 1 4667 536350206 536345540 0.000000e+00 8619.0
1 TraesCS1A01G351800 chr1B 97.154 3549 98 2 768 4316 600969887 600973432 0.000000e+00 5991.0
2 TraesCS1A01G351800 chr1B 96.409 362 8 2 4306 4667 600973517 600973873 4.020000e-165 592.0
3 TraesCS1A01G351800 chr1B 84.755 551 61 15 1 546 600969291 600969823 8.890000e-147 531.0
4 TraesCS1A01G351800 chr1B 75.615 447 83 17 2 436 365673684 365674116 1.020000e-46 198.0
5 TraesCS1A01G351800 chr1B 83.099 142 18 6 565 703 588805733 588805595 1.760000e-24 124.0
6 TraesCS1A01G351800 chr1D 95.847 3251 118 8 768 4017 442370548 442373782 0.000000e+00 5240.0
7 TraesCS1A01G351800 chr1D 96.382 304 4 2 4020 4316 442373866 442374169 1.170000e-135 494.0
8 TraesCS1A01G351800 chr1D 92.308 338 19 4 4322 4655 442374238 442374572 1.520000e-129 473.0
9 TraesCS1A01G351800 chr1D 77.009 448 75 19 1 436 480321551 480321982 1.010000e-56 231.0
10 TraesCS1A01G351800 chr1D 79.615 260 49 4 179 436 111857873 111857616 2.870000e-42 183.0
11 TraesCS1A01G351800 chr1D 88.785 107 10 2 590 696 474378752 474378856 3.790000e-26 130.0
12 TraesCS1A01G351800 chr3D 79.394 330 51 11 1 326 24867890 24868206 2.830000e-52 217.0
13 TraesCS1A01G351800 chr3B 76.364 440 83 12 5 436 123451930 123452356 2.830000e-52 217.0
14 TraesCS1A01G351800 chr3B 85.057 87 6 1 1 87 573289621 573289700 1.080000e-11 82.4
15 TraesCS1A01G351800 chr6A 76.845 393 72 11 1 385 442022822 442022441 2.200000e-48 204.0
16 TraesCS1A01G351800 chr3A 78.229 271 48 5 1 269 588146443 588146704 3.740000e-36 163.0
17 TraesCS1A01G351800 chr2B 92.105 114 7 1 585 696 23889153 23889040 4.830000e-35 159.0
18 TraesCS1A01G351800 chr2B 87.736 106 3 3 581 677 667413147 667413251 1.060000e-21 115.0
19 TraesCS1A01G351800 chr5A 89.147 129 5 1 578 697 668160079 668159951 8.090000e-33 152.0
20 TraesCS1A01G351800 chr5A 87.970 133 7 1 577 700 645121794 645121662 1.050000e-31 148.0
21 TraesCS1A01G351800 chr5A 86.598 97 12 1 155 251 338933089 338933184 6.390000e-19 106.0
22 TraesCS1A01G351800 chr5A 82.075 106 14 5 577 680 651579782 651579884 8.320000e-13 86.1
23 TraesCS1A01G351800 chr5A 76.613 124 25 4 575 696 85783345 85783224 1.080000e-06 65.8
24 TraesCS1A01G351800 chr5A 76.033 121 24 5 578 696 91852684 91852801 1.810000e-04 58.4
25 TraesCS1A01G351800 chr4A 88.550 131 6 1 576 697 36799615 36799745 2.910000e-32 150.0
26 TraesCS1A01G351800 chr2A 88.550 131 6 1 577 698 51499881 51499751 2.910000e-32 150.0
27 TraesCS1A01G351800 chr2A 88.618 123 13 1 577 699 53434464 53434585 1.050000e-31 148.0
28 TraesCS1A01G351800 chr2A 97.590 83 2 0 618 700 43500300 43500218 4.870000e-30 143.0
29 TraesCS1A01G351800 chr6D 97.826 46 1 0 1 46 458473442 458473487 3.870000e-11 80.5
30 TraesCS1A01G351800 chr5B 76.761 142 30 3 147 288 563514986 563514848 5.010000e-10 76.8
31 TraesCS1A01G351800 chr6B 90.385 52 5 0 3 54 696893123 696893174 8.380000e-08 69.4
32 TraesCS1A01G351800 chr2D 76.613 124 26 3 574 696 233429645 233429766 1.080000e-06 65.8
33 TraesCS1A01G351800 chr7B 76.667 120 25 3 578 696 42026941 42026824 3.900000e-06 63.9


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 TraesCS1A01G351800 chr1A 536345540 536350206 4666 True 8619.000000 8619 100.000000 1 4667 1 chr1A.!!$R1 4666
1 TraesCS1A01G351800 chr1B 600969291 600973873 4582 False 2371.333333 5991 92.772667 1 4667 3 chr1B.!!$F2 4666
2 TraesCS1A01G351800 chr1D 442370548 442374572 4024 False 2069.000000 5240 94.845667 768 4655 3 chr1D.!!$F3 3887

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
212 213 0.107654 GATTCCTCCTTGGTGGTCCG 60.108 60.000 7.53 0.0 37.07 4.79 F
1080 1086 0.112412 CTAGGCTCCTCTCCTCCTCC 59.888 65.000 0.00 0.0 35.21 4.30 F
1081 1087 0.329039 TAGGCTCCTCTCCTCCTCCT 60.329 60.000 0.00 0.0 35.21 3.69 F
1849 1855 0.601576 TGGCGTCGCTGCTTTTCTTA 60.602 50.000 18.11 0.0 34.52 2.10 F
1962 1968 2.338381 CGGGAGGGTAGGTGATACG 58.662 63.158 0.00 0.0 34.99 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1170 1176 1.227497 CAAGAGGAGCTCGATGGGC 60.227 63.158 7.83 0.0 35.36 5.36 R
3033 3039 1.199789 TCAGCACATCCACGCAAAATC 59.800 47.619 0.00 0.0 0.00 2.17 R
3097 3103 6.825721 ACATCAGAGATCAAACCCATCTTTAC 59.174 38.462 0.00 0.0 30.30 2.01 R
3535 3541 0.322648 TGGTCAGATCCAGTGCTGTG 59.677 55.000 0.00 0.0 33.90 3.66 R
3684 3690 3.393278 ACAGGGCCAGTAAGTAGTTTTCA 59.607 43.478 6.18 0.0 0.00 2.69 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
37 38 6.480651 ACGACATTCAACTGTATGTTACAACA 59.519 34.615 3.82 0.00 44.06 3.33
60 61 2.104963 GGTAATGGCTTAGGACTCAGGG 59.895 54.545 0.00 0.00 0.00 4.45
63 64 0.617820 TGGCTTAGGACTCAGGGGAC 60.618 60.000 0.00 0.00 0.00 4.46
71 72 1.566231 GGACTCAGGGGACATTGGATT 59.434 52.381 0.00 0.00 0.00 3.01
119 120 2.283529 CGGCACACACCTCCTACCT 61.284 63.158 0.00 0.00 0.00 3.08
120 121 1.296715 GGCACACACCTCCTACCTG 59.703 63.158 0.00 0.00 0.00 4.00
127 128 3.769844 ACACACCTCCTACCTGTTGATAG 59.230 47.826 0.00 0.00 0.00 2.08
152 153 1.087202 GCATATCGGCACCAACACGA 61.087 55.000 0.00 0.00 41.20 4.35
156 157 3.430862 CGGCACCAACACGATGGG 61.431 66.667 10.50 0.00 45.18 4.00
169 170 2.451294 ATGGGAGGGGATCAGGGC 60.451 66.667 0.00 0.00 0.00 5.19
171 172 4.880426 GGGAGGGGATCAGGGCGA 62.880 72.222 0.00 0.00 0.00 5.54
212 213 0.107654 GATTCCTCCTTGGTGGTCCG 60.108 60.000 7.53 0.00 37.07 4.79
217 218 0.320771 CTCCTTGGTGGTCCGTGAAG 60.321 60.000 0.00 0.00 37.07 3.02
222 223 1.707106 TGGTGGTCCGTGAAGAAGTA 58.293 50.000 0.00 0.00 36.30 2.24
233 234 4.478699 CGTGAAGAAGTACGGTGTGAATA 58.521 43.478 0.00 0.00 36.71 1.75
242 243 1.207329 ACGGTGTGAATAAGAGAGGGC 59.793 52.381 0.00 0.00 0.00 5.19
247 248 0.178068 TGAATAAGAGAGGGCGCCAC 59.822 55.000 30.85 21.36 0.00 5.01
269 270 1.787847 GAAGGTGATGTTGGCGTCG 59.212 57.895 0.00 0.00 33.44 5.12
270 271 2.240612 GAAGGTGATGTTGGCGTCGC 62.241 60.000 9.22 9.22 39.67 5.19
292 293 1.816835 CGGTTTTAAAAGGAGAGGGCC 59.183 52.381 0.00 0.00 0.00 5.80
293 294 2.176889 GGTTTTAAAAGGAGAGGGCCC 58.823 52.381 16.46 16.46 0.00 5.80
295 296 1.462426 TTTAAAAGGAGAGGGCCCCA 58.538 50.000 21.43 0.00 0.00 4.96
296 297 1.462426 TTAAAAGGAGAGGGCCCCAA 58.538 50.000 21.43 0.00 0.00 4.12
308 309 1.313091 GGCCCCAACGAGAAATGTCC 61.313 60.000 0.00 0.00 0.00 4.02
309 310 1.313091 GCCCCAACGAGAAATGTCCC 61.313 60.000 0.00 0.00 0.00 4.46
317 318 1.068588 CGAGAAATGTCCCGCTATGGA 59.931 52.381 0.00 0.00 42.00 3.41
318 319 2.760374 GAGAAATGTCCCGCTATGGAG 58.240 52.381 0.00 0.00 42.00 3.86
352 353 2.284405 GGGAAGGGTCCGACAGGA 60.284 66.667 0.00 0.00 46.04 3.86
367 369 2.159382 ACAGGAAAGGTAAATGGTGCG 58.841 47.619 0.00 0.00 0.00 5.34
370 372 2.156098 GGAAAGGTAAATGGTGCGTCA 58.844 47.619 0.00 0.00 0.00 4.35
378 380 3.643595 ATGGTGCGTCATGGGGTGG 62.644 63.158 0.00 0.00 0.00 4.61
407 413 3.721575 TGGGCCCATGTACTGAAGATAAT 59.278 43.478 24.45 0.00 0.00 1.28
438 444 2.289547 AGTTCGGACAACCACATTTTCG 59.710 45.455 0.00 0.00 35.59 3.46
439 445 1.231221 TCGGACAACCACATTTTCGG 58.769 50.000 0.00 0.00 35.59 4.30
441 447 0.671251 GGACAACCACATTTTCGGCA 59.329 50.000 0.00 0.00 35.97 5.69
446 452 0.178975 ACCACATTTTCGGCAAGGGA 60.179 50.000 0.00 0.00 0.00 4.20
449 455 1.067635 CACATTTTCGGCAAGGGAAGG 60.068 52.381 0.00 0.00 0.00 3.46
450 456 1.203001 ACATTTTCGGCAAGGGAAGGA 60.203 47.619 0.00 0.00 0.00 3.36
451 457 1.474077 CATTTTCGGCAAGGGAAGGAG 59.526 52.381 0.00 0.00 0.00 3.69
452 458 0.768622 TTTTCGGCAAGGGAAGGAGA 59.231 50.000 0.00 0.00 0.00 3.71
453 459 0.324943 TTTCGGCAAGGGAAGGAGAG 59.675 55.000 0.00 0.00 0.00 3.20
454 460 2.124942 CGGCAAGGGAAGGAGAGC 60.125 66.667 0.00 0.00 0.00 4.09
455 461 2.959484 CGGCAAGGGAAGGAGAGCA 61.959 63.158 0.00 0.00 0.00 4.26
456 462 1.380302 GGCAAGGGAAGGAGAGCAA 59.620 57.895 0.00 0.00 0.00 3.91
457 463 0.679321 GGCAAGGGAAGGAGAGCAAG 60.679 60.000 0.00 0.00 0.00 4.01
458 464 0.679321 GCAAGGGAAGGAGAGCAAGG 60.679 60.000 0.00 0.00 0.00 3.61
459 465 0.679321 CAAGGGAAGGAGAGCAAGGC 60.679 60.000 0.00 0.00 0.00 4.35
460 466 2.124942 GGGAAGGAGAGCAAGGCG 60.125 66.667 0.00 0.00 0.00 5.52
461 467 2.124942 GGAAGGAGAGCAAGGCGG 60.125 66.667 0.00 0.00 0.00 6.13
462 468 2.660064 GGAAGGAGAGCAAGGCGGA 61.660 63.158 0.00 0.00 0.00 5.54
463 469 1.153469 GAAGGAGAGCAAGGCGGAG 60.153 63.158 0.00 0.00 0.00 4.63
464 470 1.608717 GAAGGAGAGCAAGGCGGAGA 61.609 60.000 0.00 0.00 0.00 3.71
465 471 1.612395 AAGGAGAGCAAGGCGGAGAG 61.612 60.000 0.00 0.00 0.00 3.20
466 472 2.355193 GGAGAGCAAGGCGGAGAGT 61.355 63.158 0.00 0.00 0.00 3.24
481 487 2.840651 GGAGAGTGGGGATGAGAAAGAA 59.159 50.000 0.00 0.00 0.00 2.52
486 492 5.014544 AGAGTGGGGATGAGAAAGAAATGAA 59.985 40.000 0.00 0.00 0.00 2.57
491 497 5.163713 GGGGATGAGAAAGAAATGAACTTCG 60.164 44.000 0.00 0.00 0.00 3.79
512 518 7.661847 ACTTCGACTTTGAAGATCAACCTAATT 59.338 33.333 12.40 0.00 46.64 1.40
540 546 9.926158 TTTGTTTGATGCAATTATGTCTATTGT 57.074 25.926 0.00 0.00 35.82 2.71
546 552 4.754618 TGCAATTATGTCTATTGTAGCCCG 59.245 41.667 0.00 0.00 35.82 6.13
547 553 4.755123 GCAATTATGTCTATTGTAGCCCGT 59.245 41.667 0.00 0.00 35.82 5.28
548 554 5.929992 GCAATTATGTCTATTGTAGCCCGTA 59.070 40.000 0.00 0.00 35.82 4.02
549 555 6.090898 GCAATTATGTCTATTGTAGCCCGTAG 59.909 42.308 0.00 0.00 35.82 3.51
550 556 3.662247 ATGTCTATTGTAGCCCGTAGC 57.338 47.619 0.00 0.00 44.25 3.58
559 565 2.633657 GCCCGTAGCAATCGCATG 59.366 61.111 0.00 0.00 42.97 4.06
560 566 1.887242 GCCCGTAGCAATCGCATGA 60.887 57.895 0.00 0.00 42.97 3.07
561 567 1.436195 GCCCGTAGCAATCGCATGAA 61.436 55.000 0.00 0.00 42.97 2.57
569 575 1.529826 GCAATCGCATGAACGTTCTCC 60.530 52.381 27.32 14.74 38.36 3.71
579 585 6.327934 GCATGAACGTTCTCCTAGTAAACTA 58.672 40.000 27.32 4.30 0.00 2.24
580 586 6.979238 GCATGAACGTTCTCCTAGTAAACTAT 59.021 38.462 27.32 6.48 0.00 2.12
581 587 7.491696 GCATGAACGTTCTCCTAGTAAACTATT 59.508 37.037 27.32 0.00 0.00 1.73
582 588 9.021863 CATGAACGTTCTCCTAGTAAACTATTC 57.978 37.037 27.32 0.00 0.00 1.75
583 589 8.345724 TGAACGTTCTCCTAGTAAACTATTCT 57.654 34.615 27.32 0.00 0.00 2.40
584 590 8.457261 TGAACGTTCTCCTAGTAAACTATTCTC 58.543 37.037 27.32 0.00 0.00 2.87
585 591 8.578448 AACGTTCTCCTAGTAAACTATTCTCT 57.422 34.615 0.00 0.00 0.00 3.10
586 592 8.212317 ACGTTCTCCTAGTAAACTATTCTCTC 57.788 38.462 0.00 0.00 0.00 3.20
587 593 7.282901 ACGTTCTCCTAGTAAACTATTCTCTCC 59.717 40.741 0.00 0.00 0.00 3.71
588 594 7.518689 CGTTCTCCTAGTAAACTATTCTCTCCG 60.519 44.444 0.00 0.00 0.00 4.63
589 595 6.897986 TCTCCTAGTAAACTATTCTCTCCGT 58.102 40.000 0.00 0.00 0.00 4.69
590 596 7.344913 TCTCCTAGTAAACTATTCTCTCCGTT 58.655 38.462 0.00 0.00 0.00 4.44
591 597 7.498570 TCTCCTAGTAAACTATTCTCTCCGTTC 59.501 40.741 0.00 0.00 0.00 3.95
592 598 6.545298 TCCTAGTAAACTATTCTCTCCGTTCC 59.455 42.308 0.00 0.00 0.00 3.62
593 599 5.246145 AGTAAACTATTCTCTCCGTTCCG 57.754 43.478 0.00 0.00 0.00 4.30
594 600 4.946157 AGTAAACTATTCTCTCCGTTCCGA 59.054 41.667 0.00 0.00 0.00 4.55
595 601 4.796038 AAACTATTCTCTCCGTTCCGAA 57.204 40.909 0.00 0.00 0.00 4.30
596 602 5.340439 AAACTATTCTCTCCGTTCCGAAT 57.660 39.130 0.00 0.00 0.00 3.34
597 603 5.340439 AACTATTCTCTCCGTTCCGAATT 57.660 39.130 0.00 0.00 0.00 2.17
598 604 6.461110 AACTATTCTCTCCGTTCCGAATTA 57.539 37.500 0.00 0.00 0.00 1.40
599 605 5.829829 ACTATTCTCTCCGTTCCGAATTAC 58.170 41.667 0.00 0.00 0.00 1.89
600 606 5.593502 ACTATTCTCTCCGTTCCGAATTACT 59.406 40.000 0.00 0.00 0.00 2.24
601 607 4.796038 TTCTCTCCGTTCCGAATTACTT 57.204 40.909 0.00 0.00 0.00 2.24
602 608 4.106029 TCTCTCCGTTCCGAATTACTTG 57.894 45.455 0.00 0.00 0.00 3.16
603 609 3.508793 TCTCTCCGTTCCGAATTACTTGT 59.491 43.478 0.00 0.00 0.00 3.16
604 610 4.021719 TCTCTCCGTTCCGAATTACTTGTT 60.022 41.667 0.00 0.00 0.00 2.83
605 611 4.634199 TCTCCGTTCCGAATTACTTGTTT 58.366 39.130 0.00 0.00 0.00 2.83
606 612 5.058490 TCTCCGTTCCGAATTACTTGTTTT 58.942 37.500 0.00 0.00 0.00 2.43
607 613 6.222389 TCTCCGTTCCGAATTACTTGTTTTA 58.778 36.000 0.00 0.00 0.00 1.52
608 614 6.705381 TCTCCGTTCCGAATTACTTGTTTTAA 59.295 34.615 0.00 0.00 0.00 1.52
609 615 7.226325 TCTCCGTTCCGAATTACTTGTTTTAAA 59.774 33.333 0.00 0.00 0.00 1.52
610 616 7.873910 TCCGTTCCGAATTACTTGTTTTAAAT 58.126 30.769 0.00 0.00 0.00 1.40
611 617 8.351461 TCCGTTCCGAATTACTTGTTTTAAATT 58.649 29.630 0.00 0.00 0.00 1.82
612 618 8.970293 CCGTTCCGAATTACTTGTTTTAAATTT 58.030 29.630 0.00 0.00 0.00 1.82
613 619 9.772282 CGTTCCGAATTACTTGTTTTAAATTTG 57.228 29.630 0.00 0.00 0.00 2.32
627 633 9.290988 TGTTTTAAATTTGTCTGGTATCTAGCA 57.709 29.630 0.00 0.00 0.00 3.49
628 634 9.556030 GTTTTAAATTTGTCTGGTATCTAGCAC 57.444 33.333 0.00 0.00 0.00 4.40
629 635 9.515226 TTTTAAATTTGTCTGGTATCTAGCACT 57.485 29.630 0.00 0.00 0.00 4.40
633 639 9.515226 AAATTTGTCTGGTATCTAGCACTAAAA 57.485 29.630 0.00 0.00 0.00 1.52
634 640 9.686683 AATTTGTCTGGTATCTAGCACTAAAAT 57.313 29.630 0.00 0.00 0.00 1.82
635 641 8.492673 TTTGTCTGGTATCTAGCACTAAAATG 57.507 34.615 0.00 0.00 0.00 2.32
636 642 7.418337 TGTCTGGTATCTAGCACTAAAATGA 57.582 36.000 0.00 0.00 0.00 2.57
637 643 7.492524 TGTCTGGTATCTAGCACTAAAATGAG 58.507 38.462 0.00 0.00 0.00 2.90
638 644 7.124298 TGTCTGGTATCTAGCACTAAAATGAGT 59.876 37.037 0.00 0.00 0.00 3.41
639 645 7.982354 GTCTGGTATCTAGCACTAAAATGAGTT 59.018 37.037 0.00 0.00 0.00 3.01
640 646 8.540388 TCTGGTATCTAGCACTAAAATGAGTTT 58.460 33.333 0.00 0.00 0.00 2.66
641 647 9.817809 CTGGTATCTAGCACTAAAATGAGTTTA 57.182 33.333 0.00 0.00 0.00 2.01
667 673 7.776618 ATACATCCGTATCTAGACAAATCCA 57.223 36.000 0.00 0.00 32.66 3.41
668 674 6.479972 ACATCCGTATCTAGACAAATCCAA 57.520 37.500 0.00 0.00 0.00 3.53
669 675 6.516718 ACATCCGTATCTAGACAAATCCAAG 58.483 40.000 0.00 0.00 0.00 3.61
670 676 6.323996 ACATCCGTATCTAGACAAATCCAAGA 59.676 38.462 0.00 0.00 0.00 3.02
671 677 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
672 678 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
673 679 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
674 680 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
675 681 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
676 682 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
677 683 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
679 685 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
680 686 9.793259 TCTAGACAAATCCAAGACAAGTAATTT 57.207 29.630 0.00 0.00 0.00 1.82
681 687 9.831737 CTAGACAAATCCAAGACAAGTAATTTG 57.168 33.333 0.00 0.00 42.68 2.32
682 688 7.661040 AGACAAATCCAAGACAAGTAATTTGG 58.339 34.615 9.60 0.00 41.25 3.28
686 692 5.682943 TCCAAGACAAGTAATTTGGAACG 57.317 39.130 2.52 0.00 44.38 3.95
687 693 4.517453 TCCAAGACAAGTAATTTGGAACGG 59.483 41.667 2.52 0.00 44.38 4.44
688 694 4.517453 CCAAGACAAGTAATTTGGAACGGA 59.483 41.667 0.00 0.00 42.05 4.69
689 695 5.334879 CCAAGACAAGTAATTTGGAACGGAG 60.335 44.000 0.00 0.00 42.05 4.63
690 696 4.324267 AGACAAGTAATTTGGAACGGAGG 58.676 43.478 0.00 0.00 41.25 4.30
691 697 3.418047 ACAAGTAATTTGGAACGGAGGG 58.582 45.455 0.00 0.00 41.25 4.30
692 698 3.073356 ACAAGTAATTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 41.25 4.20
693 699 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
694 700 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
707 713 3.631227 CGGAGGGAGTAGTAAGATCGTTT 59.369 47.826 0.00 0.00 0.00 3.60
712 718 4.202131 GGGAGTAGTAAGATCGTTTGAGGG 60.202 50.000 0.00 0.00 0.00 4.30
714 720 2.693267 AGTAAGATCGTTTGAGGGCC 57.307 50.000 0.00 0.00 0.00 5.80
715 721 2.188817 AGTAAGATCGTTTGAGGGCCT 58.811 47.619 5.25 5.25 0.00 5.19
716 722 2.572104 AGTAAGATCGTTTGAGGGCCTT 59.428 45.455 7.89 0.00 0.00 4.35
730 736 1.895798 GGGCCTTCTTTTTCCCTCTTG 59.104 52.381 0.84 0.00 35.87 3.02
735 741 4.464947 CCTTCTTTTTCCCTCTTGAGTGT 58.535 43.478 0.00 0.00 0.00 3.55
736 742 4.517075 CCTTCTTTTTCCCTCTTGAGTGTC 59.483 45.833 0.00 0.00 0.00 3.67
737 743 5.372373 CTTCTTTTTCCCTCTTGAGTGTCT 58.628 41.667 0.00 0.00 0.00 3.41
738 744 5.373812 TCTTTTTCCCTCTTGAGTGTCTT 57.626 39.130 0.00 0.00 0.00 3.01
739 745 6.494666 TCTTTTTCCCTCTTGAGTGTCTTA 57.505 37.500 0.00 0.00 0.00 2.10
740 746 6.525629 TCTTTTTCCCTCTTGAGTGTCTTAG 58.474 40.000 0.00 0.00 0.00 2.18
741 747 6.326583 TCTTTTTCCCTCTTGAGTGTCTTAGA 59.673 38.462 0.00 0.00 0.00 2.10
742 748 6.688073 TTTTCCCTCTTGAGTGTCTTAGAT 57.312 37.500 0.00 0.00 0.00 1.98
743 749 6.688073 TTTCCCTCTTGAGTGTCTTAGATT 57.312 37.500 0.00 0.00 0.00 2.40
744 750 6.688073 TTCCCTCTTGAGTGTCTTAGATTT 57.312 37.500 0.00 0.00 0.00 2.17
745 751 6.042638 TCCCTCTTGAGTGTCTTAGATTTG 57.957 41.667 0.00 0.00 0.00 2.32
746 752 5.544176 TCCCTCTTGAGTGTCTTAGATTTGT 59.456 40.000 0.00 0.00 0.00 2.83
747 753 5.872070 CCCTCTTGAGTGTCTTAGATTTGTC 59.128 44.000 0.00 0.00 0.00 3.18
748 754 6.295575 CCCTCTTGAGTGTCTTAGATTTGTCT 60.296 42.308 0.00 0.00 0.00 3.41
749 755 7.093727 CCCTCTTGAGTGTCTTAGATTTGTCTA 60.094 40.741 0.00 0.00 0.00 2.59
750 756 8.307483 CCTCTTGAGTGTCTTAGATTTGTCTAA 58.693 37.037 0.00 0.00 0.00 2.10
751 757 9.698309 CTCTTGAGTGTCTTAGATTTGTCTAAA 57.302 33.333 0.26 0.00 32.51 1.85
756 762 9.535878 GAGTGTCTTAGATTTGTCTAAATAGGG 57.464 37.037 0.26 0.00 36.66 3.53
757 763 9.268282 AGTGTCTTAGATTTGTCTAAATAGGGA 57.732 33.333 0.26 0.00 36.66 4.20
758 764 9.535878 GTGTCTTAGATTTGTCTAAATAGGGAG 57.464 37.037 0.26 0.00 36.66 4.30
759 765 8.705594 TGTCTTAGATTTGTCTAAATAGGGAGG 58.294 37.037 0.26 0.00 36.66 4.30
760 766 8.706521 GTCTTAGATTTGTCTAAATAGGGAGGT 58.293 37.037 0.26 0.00 36.66 3.85
761 767 9.947189 TCTTAGATTTGTCTAAATAGGGAGGTA 57.053 33.333 0.26 0.00 36.66 3.08
764 770 8.568617 AGATTTGTCTAAATAGGGAGGTATGT 57.431 34.615 0.00 0.00 36.66 2.29
765 771 9.670442 AGATTTGTCTAAATAGGGAGGTATGTA 57.330 33.333 0.00 0.00 36.66 2.29
766 772 9.930693 GATTTGTCTAAATAGGGAGGTATGTAG 57.069 37.037 0.00 0.00 36.66 2.74
805 811 2.991540 GCCAGGCCCTCCAAACAC 60.992 66.667 0.00 0.00 33.74 3.32
1008 1014 1.470285 GCCACCTCGCTTATGTTACGA 60.470 52.381 0.00 0.00 0.00 3.43
1046 1052 4.504916 CCACTCCGCGCTCTCCTG 62.505 72.222 5.56 0.00 0.00 3.86
1074 1080 0.544120 CCCCATCTAGGCTCCTCTCC 60.544 65.000 0.00 0.00 35.39 3.71
1078 1084 1.428912 CATCTAGGCTCCTCTCCTCCT 59.571 57.143 0.00 0.00 35.21 3.69
1080 1086 0.112412 CTAGGCTCCTCTCCTCCTCC 59.888 65.000 0.00 0.00 35.21 4.30
1081 1087 0.329039 TAGGCTCCTCTCCTCCTCCT 60.329 60.000 0.00 0.00 35.21 3.69
1082 1088 1.228215 AGGCTCCTCTCCTCCTCCTT 61.228 60.000 0.00 0.00 0.00 3.36
1161 1167 4.803426 GTCTCGGCCGTGCTGGAG 62.803 72.222 27.15 14.34 42.00 3.86
1164 1170 3.781770 CTCGGCCGTGCTGGAGATC 62.782 68.421 27.15 0.00 42.00 2.75
1170 1176 2.187946 GTGCTGGAGATCGTGGGG 59.812 66.667 0.00 0.00 0.00 4.96
1290 1296 4.681978 GGGCACGTCCTCAAGCGT 62.682 66.667 0.00 0.00 42.45 5.07
1329 1335 3.330766 CGTCTCCAACGTCCTGATC 57.669 57.895 0.00 0.00 46.42 2.92
1422 1428 1.741770 GTCCTGGTGCACCGTCATC 60.742 63.158 30.07 15.40 39.43 2.92
1488 1494 0.768221 TCAAGGGGCTGTTGTCCTCT 60.768 55.000 0.00 0.00 38.23 3.69
1537 1543 1.135315 GCGACGCTGAATGCATGTT 59.865 52.632 13.73 0.00 43.06 2.71
1596 1602 2.912295 TGGATTGGTGATCAAGTCTGGA 59.088 45.455 0.00 0.00 38.95 3.86
1629 1635 2.876581 AGGTTTGTGGAGGTTGGATTC 58.123 47.619 0.00 0.00 0.00 2.52
1775 1781 1.521450 GAGGCTGCTGAGCTTTGCAA 61.521 55.000 5.83 0.00 45.44 4.08
1849 1855 0.601576 TGGCGTCGCTGCTTTTCTTA 60.602 50.000 18.11 0.00 34.52 2.10
1962 1968 2.338381 CGGGAGGGTAGGTGATACG 58.662 63.158 0.00 0.00 34.99 3.06
2194 2200 7.231925 TGCATGCTTATACATTGAAATCTGGAT 59.768 33.333 20.33 0.00 0.00 3.41
2253 2259 9.922477 ATATCGGTATACTCTGAAATAGGATCA 57.078 33.333 2.25 0.00 0.00 2.92
2254 2260 8.830915 ATCGGTATACTCTGAAATAGGATCAT 57.169 34.615 2.25 0.00 0.00 2.45
2262 2268 7.232188 ACTCTGAAATAGGATCATTGATGCAT 58.768 34.615 18.79 0.00 32.78 3.96
2649 2655 3.456644 TCTCGGGGTATTGCTGGAATTTA 59.543 43.478 0.00 0.00 0.00 1.40
2650 2656 4.080243 TCTCGGGGTATTGCTGGAATTTAA 60.080 41.667 0.00 0.00 0.00 1.52
2702 2708 3.195610 AGTGAATATCGTTCTGGTCTGCA 59.804 43.478 0.00 0.00 0.00 4.41
2703 2709 3.307242 GTGAATATCGTTCTGGTCTGCAC 59.693 47.826 0.00 0.00 0.00 4.57
2940 2946 2.607631 ATGCAATGCTAATGTTGGGC 57.392 45.000 6.82 0.00 0.00 5.36
2943 2949 2.426738 TGCAATGCTAATGTTGGGCTAC 59.573 45.455 6.82 0.00 0.00 3.58
3097 3103 4.201891 GGAGACAAGTGCATGCTTCTATTG 60.202 45.833 20.33 16.83 0.00 1.90
3239 3245 7.147828 TGGTCCAGAACAGAATACTGAAGATAG 60.148 40.741 0.00 0.00 46.03 2.08
3322 3328 7.536622 CGTTGGAAGAAGAGAAAAATCATGAAG 59.463 37.037 0.00 0.00 0.00 3.02
3482 3488 8.845227 TGAAAGCAATGTTTTTCTAGATACACA 58.155 29.630 4.90 4.90 35.02 3.72
3521 3527 4.935885 GTGGATCTCACAAGCTGTTTAG 57.064 45.455 8.84 0.00 45.39 1.85
3535 3541 3.541711 CTGTTTAGCTTGTTACACGTGC 58.458 45.455 17.22 0.00 0.00 5.34
4004 4011 5.769662 TCAAGAATGTTGAACAGGTTAGCAT 59.230 36.000 3.74 0.00 0.00 3.79
4011 4018 7.517614 TGTTGAACAGGTTAGCATGAAATAA 57.482 32.000 0.00 0.00 0.00 1.40
4017 4105 6.959361 ACAGGTTAGCATGAAATAATTAGCG 58.041 36.000 0.00 0.00 0.00 4.26
4316 4411 7.592885 ATTGCTTTACTAATACTACCTCCGA 57.407 36.000 0.00 0.00 0.00 4.55
4317 4412 6.630444 TGCTTTACTAATACTACCTCCGAG 57.370 41.667 0.00 0.00 0.00 4.63
4318 4413 5.533903 TGCTTTACTAATACTACCTCCGAGG 59.466 44.000 13.31 13.31 42.49 4.63
4333 4520 5.802465 CCTCCGAGGTAGTACTACATCATA 58.198 45.833 34.36 24.41 44.39 2.15
4511 4701 2.873649 GCAACTCCTCAAGCTGCTACTT 60.874 50.000 0.90 0.00 42.63 2.24
4539 4729 6.490721 CACCGTCTCCTAATCTCCTATAGTTT 59.509 42.308 0.00 0.00 0.00 2.66
4561 4751 7.664318 AGTTTATTCAACTTCACCGGTAAGATT 59.336 33.333 22.58 13.71 43.89 2.40
4562 4752 5.880054 ATTCAACTTCACCGGTAAGATTG 57.120 39.130 22.58 20.44 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 3.392616 CCTGAGTCCTAAGCCATTACCAT 59.607 47.826 0.00 0.00 0.00 3.55
60 61 3.368739 CCAAGAAGGCAAATCCAATGTCC 60.369 47.826 0.00 0.00 37.29 4.02
119 120 2.038426 CGATATGCCACCCCTATCAACA 59.962 50.000 0.00 0.00 0.00 3.33
120 121 2.615493 CCGATATGCCACCCCTATCAAC 60.615 54.545 0.00 0.00 0.00 3.18
127 128 2.594592 GTGCCGATATGCCACCCC 60.595 66.667 0.00 0.00 0.00 4.95
145 146 0.179045 GATCCCCTCCCATCGTGTTG 60.179 60.000 0.00 0.00 0.00 3.33
152 153 2.451294 GCCCTGATCCCCTCCCAT 60.451 66.667 0.00 0.00 0.00 4.00
156 157 1.753368 CTCTTCGCCCTGATCCCCTC 61.753 65.000 0.00 0.00 0.00 4.30
189 190 1.615262 CACCAAGGAGGAATCCCCC 59.385 63.158 0.00 0.00 41.22 5.40
195 196 1.460689 ACGGACCACCAAGGAGGAA 60.461 57.895 9.67 0.00 41.22 3.36
212 213 6.154445 TCTTATTCACACCGTACTTCTTCAC 58.846 40.000 0.00 0.00 0.00 3.18
217 218 5.341617 CCTCTCTTATTCACACCGTACTTC 58.658 45.833 0.00 0.00 0.00 3.01
222 223 1.207329 GCCCTCTCTTATTCACACCGT 59.793 52.381 0.00 0.00 0.00 4.83
247 248 3.039202 GCCAACATCACCTTCGCCG 62.039 63.158 0.00 0.00 0.00 6.46
269 270 1.816835 CCTCTCCTTTTAAAACCGGGC 59.183 52.381 6.32 0.00 0.00 6.13
270 271 2.443416 CCCTCTCCTTTTAAAACCGGG 58.557 52.381 6.32 0.00 0.00 5.73
273 274 2.176889 GGGCCCTCTCCTTTTAAAACC 58.823 52.381 17.04 0.00 0.00 3.27
274 275 2.176889 GGGGCCCTCTCCTTTTAAAAC 58.823 52.381 24.38 0.00 0.00 2.43
277 278 1.076513 GTTGGGGCCCTCTCCTTTTAA 59.923 52.381 25.93 2.64 0.00 1.52
279 280 1.465172 GTTGGGGCCCTCTCCTTTT 59.535 57.895 25.93 0.00 0.00 2.27
292 293 2.466867 CGGGACATTTCTCGTTGGG 58.533 57.895 0.00 0.00 41.19 4.12
308 309 1.227556 CGGTTTCCCTCCATAGCGG 60.228 63.158 0.00 0.00 0.00 5.52
309 310 0.249489 CTCGGTTTCCCTCCATAGCG 60.249 60.000 0.00 0.00 0.00 4.26
317 318 0.036875 CCTTCTTGCTCGGTTTCCCT 59.963 55.000 0.00 0.00 0.00 4.20
318 319 0.960861 CCCTTCTTGCTCGGTTTCCC 60.961 60.000 0.00 0.00 0.00 3.97
331 332 0.905337 CTGTCGGACCCTTCCCTTCT 60.905 60.000 5.55 0.00 38.99 2.85
352 353 2.491693 CCATGACGCACCATTTACCTTT 59.508 45.455 0.00 0.00 0.00 3.11
356 358 0.738389 CCCCATGACGCACCATTTAC 59.262 55.000 0.00 0.00 0.00 2.01
357 359 0.329931 ACCCCATGACGCACCATTTA 59.670 50.000 0.00 0.00 0.00 1.40
361 363 4.343323 CCACCCCATGACGCACCA 62.343 66.667 0.00 0.00 0.00 4.17
407 413 6.153170 TGTGGTTGTCCGAACTATCTGTAATA 59.847 38.462 0.00 0.00 36.30 0.98
418 424 2.603652 CCGAAAATGTGGTTGTCCGAAC 60.604 50.000 0.00 0.00 36.30 3.95
420 426 1.231221 CCGAAAATGTGGTTGTCCGA 58.769 50.000 0.00 0.00 36.30 4.55
421 427 0.386731 GCCGAAAATGTGGTTGTCCG 60.387 55.000 0.00 0.00 36.30 4.79
422 428 0.671251 TGCCGAAAATGTGGTTGTCC 59.329 50.000 0.00 0.00 0.00 4.02
438 444 0.679321 CTTGCTCTCCTTCCCTTGCC 60.679 60.000 0.00 0.00 0.00 4.52
439 445 0.679321 CCTTGCTCTCCTTCCCTTGC 60.679 60.000 0.00 0.00 0.00 4.01
441 447 1.688211 GCCTTGCTCTCCTTCCCTT 59.312 57.895 0.00 0.00 0.00 3.95
446 452 1.610673 TCTCCGCCTTGCTCTCCTT 60.611 57.895 0.00 0.00 0.00 3.36
449 455 1.153667 CACTCTCCGCCTTGCTCTC 60.154 63.158 0.00 0.00 0.00 3.20
450 456 2.654079 CCACTCTCCGCCTTGCTCT 61.654 63.158 0.00 0.00 0.00 4.09
451 457 2.125350 CCACTCTCCGCCTTGCTC 60.125 66.667 0.00 0.00 0.00 4.26
452 458 3.710722 CCCACTCTCCGCCTTGCT 61.711 66.667 0.00 0.00 0.00 3.91
453 459 4.785453 CCCCACTCTCCGCCTTGC 62.785 72.222 0.00 0.00 0.00 4.01
454 460 2.370445 ATCCCCACTCTCCGCCTTG 61.370 63.158 0.00 0.00 0.00 3.61
455 461 2.041265 ATCCCCACTCTCCGCCTT 59.959 61.111 0.00 0.00 0.00 4.35
456 462 2.765807 CATCCCCACTCTCCGCCT 60.766 66.667 0.00 0.00 0.00 5.52
457 463 2.764128 TCATCCCCACTCTCCGCC 60.764 66.667 0.00 0.00 0.00 6.13
458 464 1.330655 TTCTCATCCCCACTCTCCGC 61.331 60.000 0.00 0.00 0.00 5.54
459 465 1.137872 CTTTCTCATCCCCACTCTCCG 59.862 57.143 0.00 0.00 0.00 4.63
460 466 2.472029 TCTTTCTCATCCCCACTCTCC 58.528 52.381 0.00 0.00 0.00 3.71
461 467 4.559862 TTTCTTTCTCATCCCCACTCTC 57.440 45.455 0.00 0.00 0.00 3.20
462 468 4.537688 TCATTTCTTTCTCATCCCCACTCT 59.462 41.667 0.00 0.00 0.00 3.24
463 469 4.848357 TCATTTCTTTCTCATCCCCACTC 58.152 43.478 0.00 0.00 0.00 3.51
464 470 4.934797 TCATTTCTTTCTCATCCCCACT 57.065 40.909 0.00 0.00 0.00 4.00
465 471 5.012893 AGTTCATTTCTTTCTCATCCCCAC 58.987 41.667 0.00 0.00 0.00 4.61
466 472 5.261040 AGTTCATTTCTTTCTCATCCCCA 57.739 39.130 0.00 0.00 0.00 4.96
481 487 7.355778 GTTGATCTTCAAAGTCGAAGTTCATT 58.644 34.615 12.67 0.00 44.86 2.57
486 492 4.962155 AGGTTGATCTTCAAAGTCGAAGT 58.038 39.130 0.00 0.00 42.53 3.01
519 525 7.040478 GGGCTACAATAGACATAATTGCATCAA 60.040 37.037 0.00 0.00 37.77 2.57
521 527 6.402550 CGGGCTACAATAGACATAATTGCATC 60.403 42.308 0.00 0.00 37.77 3.91
524 530 4.755123 ACGGGCTACAATAGACATAATTGC 59.245 41.667 0.00 0.00 37.77 3.56
532 538 3.447918 TTGCTACGGGCTACAATAGAC 57.552 47.619 4.43 0.00 42.39 2.59
535 541 2.864882 GCGATTGCTACGGGCTACAATA 60.865 50.000 0.00 0.00 42.39 1.90
540 546 0.599991 CATGCGATTGCTACGGGCTA 60.600 55.000 6.47 0.00 43.34 3.93
546 552 2.348666 AGAACGTTCATGCGATTGCTAC 59.651 45.455 28.78 0.00 43.34 3.58
547 553 2.603110 GAGAACGTTCATGCGATTGCTA 59.397 45.455 28.78 0.00 43.34 3.49
548 554 1.394917 GAGAACGTTCATGCGATTGCT 59.605 47.619 28.78 5.07 43.34 3.91
549 555 1.529826 GGAGAACGTTCATGCGATTGC 60.530 52.381 28.78 8.97 43.20 3.56
550 556 2.002586 AGGAGAACGTTCATGCGATTG 58.997 47.619 28.78 0.00 35.59 2.67
551 557 2.386661 AGGAGAACGTTCATGCGATT 57.613 45.000 28.78 7.37 35.59 3.34
552 558 2.427453 ACTAGGAGAACGTTCATGCGAT 59.573 45.455 28.78 8.14 35.59 4.58
553 559 1.816835 ACTAGGAGAACGTTCATGCGA 59.183 47.619 28.78 14.36 35.59 5.10
554 560 2.279582 ACTAGGAGAACGTTCATGCG 57.720 50.000 28.78 15.13 37.94 4.73
555 561 5.169295 AGTTTACTAGGAGAACGTTCATGC 58.831 41.667 28.78 18.36 0.00 4.06
556 562 8.928270 AATAGTTTACTAGGAGAACGTTCATG 57.072 34.615 28.78 15.48 0.00 3.07
557 563 8.968969 AGAATAGTTTACTAGGAGAACGTTCAT 58.031 33.333 28.78 16.71 31.43 2.57
558 564 8.345724 AGAATAGTTTACTAGGAGAACGTTCA 57.654 34.615 28.78 8.41 31.43 3.18
559 565 8.676401 AGAGAATAGTTTACTAGGAGAACGTTC 58.324 37.037 20.71 20.71 0.00 3.95
560 566 8.578448 AGAGAATAGTTTACTAGGAGAACGTT 57.422 34.615 0.00 0.00 0.00 3.99
561 567 7.282901 GGAGAGAATAGTTTACTAGGAGAACGT 59.717 40.741 0.00 0.00 0.00 3.99
601 607 9.290988 TGCTAGATACCAGACAAATTTAAAACA 57.709 29.630 0.00 0.00 0.00 2.83
602 608 9.556030 GTGCTAGATACCAGACAAATTTAAAAC 57.444 33.333 0.00 0.00 0.00 2.43
603 609 9.515226 AGTGCTAGATACCAGACAAATTTAAAA 57.485 29.630 0.00 0.00 0.00 1.52
607 613 9.515226 TTTTAGTGCTAGATACCAGACAAATTT 57.485 29.630 0.00 0.00 0.00 1.82
608 614 9.686683 ATTTTAGTGCTAGATACCAGACAAATT 57.313 29.630 0.00 0.00 0.00 1.82
609 615 9.113838 CATTTTAGTGCTAGATACCAGACAAAT 57.886 33.333 0.00 0.00 0.00 2.32
610 616 8.318412 TCATTTTAGTGCTAGATACCAGACAAA 58.682 33.333 0.00 0.00 0.00 2.83
611 617 7.847096 TCATTTTAGTGCTAGATACCAGACAA 58.153 34.615 0.00 0.00 0.00 3.18
612 618 7.124298 ACTCATTTTAGTGCTAGATACCAGACA 59.876 37.037 0.00 0.00 0.00 3.41
613 619 7.493367 ACTCATTTTAGTGCTAGATACCAGAC 58.507 38.462 0.00 0.00 0.00 3.51
614 620 7.661536 ACTCATTTTAGTGCTAGATACCAGA 57.338 36.000 0.00 0.00 0.00 3.86
615 621 8.723942 AAACTCATTTTAGTGCTAGATACCAG 57.276 34.615 0.00 0.00 0.00 4.00
616 622 9.817809 CTAAACTCATTTTAGTGCTAGATACCA 57.182 33.333 0.00 0.00 41.30 3.25
624 630 9.331282 GGATGTATCTAAACTCATTTTAGTGCT 57.669 33.333 4.20 0.00 44.99 4.40
625 631 8.276325 CGGATGTATCTAAACTCATTTTAGTGC 58.724 37.037 4.20 0.00 44.99 4.40
626 632 9.314321 ACGGATGTATCTAAACTCATTTTAGTG 57.686 33.333 4.20 0.00 44.99 2.74
643 649 7.776618 TGGATTTGTCTAGATACGGATGTAT 57.223 36.000 0.00 0.00 43.97 2.29
644 650 7.504574 TCTTGGATTTGTCTAGATACGGATGTA 59.495 37.037 0.00 0.00 34.45 2.29
645 651 6.323996 TCTTGGATTTGTCTAGATACGGATGT 59.676 38.462 0.00 0.00 0.00 3.06
646 652 6.642950 GTCTTGGATTTGTCTAGATACGGATG 59.357 42.308 0.00 0.00 0.00 3.51
647 653 6.323996 TGTCTTGGATTTGTCTAGATACGGAT 59.676 38.462 0.00 0.00 0.00 4.18
648 654 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
649 655 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
650 656 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
651 657 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
653 659 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
654 660 9.793259 AAATTACTTGTCTTGGATTTGTCTAGA 57.207 29.630 0.00 0.00 0.00 2.43
655 661 9.831737 CAAATTACTTGTCTTGGATTTGTCTAG 57.168 33.333 0.00 0.00 32.62 2.43
656 662 8.792633 CCAAATTACTTGTCTTGGATTTGTCTA 58.207 33.333 0.00 0.00 40.72 2.59
657 663 7.505585 TCCAAATTACTTGTCTTGGATTTGTCT 59.494 33.333 0.00 0.00 41.83 3.41
658 664 7.657336 TCCAAATTACTTGTCTTGGATTTGTC 58.343 34.615 0.00 0.00 41.83 3.18
659 665 7.595819 TCCAAATTACTTGTCTTGGATTTGT 57.404 32.000 0.00 0.00 41.83 2.83
660 666 7.114811 CGTTCCAAATTACTTGTCTTGGATTTG 59.885 37.037 3.38 0.00 45.10 2.32
661 667 7.145323 CGTTCCAAATTACTTGTCTTGGATTT 58.855 34.615 3.38 0.00 45.10 2.17
662 668 6.294508 CCGTTCCAAATTACTTGTCTTGGATT 60.295 38.462 3.38 0.00 45.10 3.01
663 669 5.183140 CCGTTCCAAATTACTTGTCTTGGAT 59.817 40.000 3.38 0.00 45.10 3.41
664 670 4.517453 CCGTTCCAAATTACTTGTCTTGGA 59.483 41.667 0.00 0.00 44.32 3.53
665 671 4.517453 TCCGTTCCAAATTACTTGTCTTGG 59.483 41.667 0.00 0.00 39.80 3.61
666 672 5.334879 CCTCCGTTCCAAATTACTTGTCTTG 60.335 44.000 0.00 0.00 32.65 3.02
667 673 4.760204 CCTCCGTTCCAAATTACTTGTCTT 59.240 41.667 0.00 0.00 32.65 3.01
668 674 4.324267 CCTCCGTTCCAAATTACTTGTCT 58.676 43.478 0.00 0.00 32.65 3.41
669 675 3.439129 CCCTCCGTTCCAAATTACTTGTC 59.561 47.826 0.00 0.00 32.65 3.18
670 676 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.00 32.65 3.16
671 677 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
672 678 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
673 679 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
674 680 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
675 681 4.098894 ACTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
676 682 2.910977 ACTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
677 683 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
678 684 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
679 685 2.905415 TACTACTCCCTCCGTTCCAA 57.095 50.000 0.00 0.00 0.00 3.53
680 686 2.309755 TCTTACTACTCCCTCCGTTCCA 59.690 50.000 0.00 0.00 0.00 3.53
681 687 3.010200 TCTTACTACTCCCTCCGTTCC 57.990 52.381 0.00 0.00 0.00 3.62
682 688 3.250521 CGATCTTACTACTCCCTCCGTTC 59.749 52.174 0.00 0.00 0.00 3.95
683 689 3.212685 CGATCTTACTACTCCCTCCGTT 58.787 50.000 0.00 0.00 0.00 4.44
684 690 2.172293 ACGATCTTACTACTCCCTCCGT 59.828 50.000 0.00 0.00 0.00 4.69
685 691 2.848691 ACGATCTTACTACTCCCTCCG 58.151 52.381 0.00 0.00 0.00 4.63
686 692 4.643784 TCAAACGATCTTACTACTCCCTCC 59.356 45.833 0.00 0.00 0.00 4.30
687 693 5.221087 CCTCAAACGATCTTACTACTCCCTC 60.221 48.000 0.00 0.00 0.00 4.30
688 694 4.645588 CCTCAAACGATCTTACTACTCCCT 59.354 45.833 0.00 0.00 0.00 4.20
689 695 4.202131 CCCTCAAACGATCTTACTACTCCC 60.202 50.000 0.00 0.00 0.00 4.30
690 696 4.737055 GCCCTCAAACGATCTTACTACTCC 60.737 50.000 0.00 0.00 0.00 3.85
691 697 4.361420 GCCCTCAAACGATCTTACTACTC 58.639 47.826 0.00 0.00 0.00 2.59
692 698 3.132467 GGCCCTCAAACGATCTTACTACT 59.868 47.826 0.00 0.00 0.00 2.57
693 699 3.132467 AGGCCCTCAAACGATCTTACTAC 59.868 47.826 0.00 0.00 0.00 2.73
694 700 3.371965 AGGCCCTCAAACGATCTTACTA 58.628 45.455 0.00 0.00 0.00 1.82
707 713 3.765968 GGGAAAAAGAAGGCCCTCA 57.234 52.632 3.68 0.00 37.59 3.86
712 718 3.254411 CACTCAAGAGGGAAAAAGAAGGC 59.746 47.826 1.73 0.00 32.29 4.35
714 720 5.372373 AGACACTCAAGAGGGAAAAAGAAG 58.628 41.667 6.30 0.00 35.36 2.85
715 721 5.373812 AGACACTCAAGAGGGAAAAAGAA 57.626 39.130 6.30 0.00 35.36 2.52
716 722 5.373812 AAGACACTCAAGAGGGAAAAAGA 57.626 39.130 6.30 0.00 35.36 2.52
730 736 9.535878 CCCTATTTAGACAAATCTAAGACACTC 57.464 37.037 0.00 0.00 45.93 3.51
735 741 8.855804 ACCTCCCTATTTAGACAAATCTAAGA 57.144 34.615 0.00 0.00 45.93 2.10
738 744 9.670442 ACATACCTCCCTATTTAGACAAATCTA 57.330 33.333 0.00 0.00 35.88 1.98
739 745 8.568617 ACATACCTCCCTATTTAGACAAATCT 57.431 34.615 0.00 0.00 35.88 2.40
740 746 9.930693 CTACATACCTCCCTATTTAGACAAATC 57.069 37.037 0.00 0.00 35.88 2.17
741 747 8.376270 GCTACATACCTCCCTATTTAGACAAAT 58.624 37.037 0.00 0.00 38.02 2.32
742 748 7.346175 TGCTACATACCTCCCTATTTAGACAAA 59.654 37.037 0.00 0.00 0.00 2.83
743 749 6.842280 TGCTACATACCTCCCTATTTAGACAA 59.158 38.462 0.00 0.00 0.00 3.18
744 750 6.267014 GTGCTACATACCTCCCTATTTAGACA 59.733 42.308 0.00 0.00 0.00 3.41
745 751 6.295180 GGTGCTACATACCTCCCTATTTAGAC 60.295 46.154 0.00 0.00 35.30 2.59
746 752 5.778750 GGTGCTACATACCTCCCTATTTAGA 59.221 44.000 0.00 0.00 35.30 2.10
747 753 5.542635 TGGTGCTACATACCTCCCTATTTAG 59.457 44.000 0.00 0.00 39.01 1.85
748 754 5.469579 TGGTGCTACATACCTCCCTATTTA 58.530 41.667 0.00 0.00 39.01 1.40
749 755 4.303794 TGGTGCTACATACCTCCCTATTT 58.696 43.478 0.00 0.00 39.01 1.40
750 756 3.904339 CTGGTGCTACATACCTCCCTATT 59.096 47.826 0.00 0.00 39.01 1.73
751 757 3.142217 TCTGGTGCTACATACCTCCCTAT 59.858 47.826 0.00 0.00 39.01 2.57
752 758 2.516702 TCTGGTGCTACATACCTCCCTA 59.483 50.000 0.00 0.00 39.01 3.53
753 759 1.291033 TCTGGTGCTACATACCTCCCT 59.709 52.381 0.00 0.00 39.01 4.20
754 760 1.789523 TCTGGTGCTACATACCTCCC 58.210 55.000 0.00 0.00 39.01 4.30
755 761 3.388024 TGAATCTGGTGCTACATACCTCC 59.612 47.826 0.00 0.00 39.01 4.30
756 762 4.672587 TGAATCTGGTGCTACATACCTC 57.327 45.455 0.00 0.00 39.01 3.85
757 763 4.040952 GGATGAATCTGGTGCTACATACCT 59.959 45.833 0.00 0.00 39.01 3.08
758 764 4.319177 GGATGAATCTGGTGCTACATACC 58.681 47.826 0.00 0.00 38.71 2.73
759 765 3.990469 CGGATGAATCTGGTGCTACATAC 59.010 47.826 0.00 0.00 0.00 2.39
760 766 3.641436 ACGGATGAATCTGGTGCTACATA 59.359 43.478 4.23 0.00 37.50 2.29
761 767 2.435805 ACGGATGAATCTGGTGCTACAT 59.564 45.455 4.23 0.00 37.50 2.29
762 768 1.831106 ACGGATGAATCTGGTGCTACA 59.169 47.619 4.23 0.00 37.50 2.74
763 769 2.604046 ACGGATGAATCTGGTGCTAC 57.396 50.000 4.23 0.00 37.50 3.58
764 770 3.055458 TGAAACGGATGAATCTGGTGCTA 60.055 43.478 4.23 0.00 37.50 3.49
765 771 2.290260 TGAAACGGATGAATCTGGTGCT 60.290 45.455 4.23 0.00 37.50 4.40
766 772 2.083774 TGAAACGGATGAATCTGGTGC 58.916 47.619 4.23 0.00 37.50 5.01
805 811 1.756430 TCTCCTGACCGTCTGATCAG 58.244 55.000 17.07 17.07 41.75 2.90
1008 1014 3.181412 GGAGGAGTAGAATGGGGAGAGAT 60.181 52.174 0.00 0.00 0.00 2.75
1046 1052 1.227674 CTAGATGGGGTCGGCTTGC 60.228 63.158 0.00 0.00 0.00 4.01
1146 1152 3.781770 GATCTCCAGCACGGCCGAG 62.782 68.421 35.90 27.15 33.14 4.63
1155 1161 4.554036 GGCCCCACGATCTCCAGC 62.554 72.222 0.00 0.00 0.00 4.85
1160 1166 3.550431 CGATGGGCCCCACGATCT 61.550 66.667 26.60 0.00 35.80 2.75
1161 1167 3.521529 CTCGATGGGCCCCACGATC 62.522 68.421 30.74 21.23 36.83 3.69
1170 1176 1.227497 CAAGAGGAGCTCGATGGGC 60.227 63.158 7.83 0.00 35.36 5.36
1329 1335 2.125673 CCCTTGGCGTAGGTGTCG 60.126 66.667 4.96 0.00 33.17 4.35
1488 1494 1.228124 CCGGTTTGGCTTCACCTCA 60.228 57.895 0.00 0.00 40.22 3.86
1596 1602 3.831911 CCACAAACCTATCAACACCCAAT 59.168 43.478 0.00 0.00 0.00 3.16
1629 1635 4.432892 CCACATTTCGCATACATATCGACG 60.433 45.833 0.00 0.00 31.48 5.12
1720 1726 7.276438 GCCATTCTCAATAAAACCTGAAATCAC 59.724 37.037 0.00 0.00 0.00 3.06
1775 1781 4.923516 ATGCCAACTCTATGCATATCCT 57.076 40.909 6.92 0.00 43.51 3.24
1849 1855 3.225104 TCCTGCAAAGCTCAAACATTCT 58.775 40.909 0.00 0.00 0.00 2.40
1962 1968 2.154462 ACAAGCTGTCCAATGTACTGC 58.846 47.619 0.00 0.00 40.80 4.40
2681 2687 3.307242 GTGCAGACCAGAACGATATTCAC 59.693 47.826 0.00 0.00 0.00 3.18
2702 2708 3.245016 TGAGCAAGTGAAATGATCAGGGT 60.245 43.478 0.09 0.00 38.20 4.34
2703 2709 3.349927 TGAGCAAGTGAAATGATCAGGG 58.650 45.455 0.09 0.00 38.20 4.45
2743 2749 3.326297 GCCTCCTTTGCTCCTATATCAGT 59.674 47.826 0.00 0.00 0.00 3.41
2940 2946 8.193438 TCATCACTACATCTGTTCTGAATGTAG 58.807 37.037 19.69 19.69 45.94 2.74
2943 2949 7.465647 GCTTCATCACTACATCTGTTCTGAATG 60.466 40.741 0.00 0.00 0.00 2.67
3033 3039 1.199789 TCAGCACATCCACGCAAAATC 59.800 47.619 0.00 0.00 0.00 2.17
3097 3103 6.825721 ACATCAGAGATCAAACCCATCTTTAC 59.174 38.462 0.00 0.00 30.30 2.01
3239 3245 3.347216 TCCCTTTGTTCTGAATAGCAGC 58.653 45.455 0.00 0.00 44.52 5.25
3322 3328 1.016627 TTCCGCACATCAGCATAAGC 58.983 50.000 0.00 0.00 42.56 3.09
3482 3488 4.111577 TCCACCTCTGTTTCCCTGATATT 58.888 43.478 0.00 0.00 0.00 1.28
3521 3527 0.657368 GCTGTGCACGTGTAACAAGC 60.657 55.000 18.38 17.61 35.74 4.01
3535 3541 0.322648 TGGTCAGATCCAGTGCTGTG 59.677 55.000 0.00 0.00 33.90 3.66
3684 3690 3.393278 ACAGGGCCAGTAAGTAGTTTTCA 59.607 43.478 6.18 0.00 0.00 2.69
4011 4018 9.702494 GTACCAAGTAAATAAGGTATCGCTAAT 57.298 33.333 0.00 0.00 38.73 1.73
4208 4296 7.425224 AGAGGTATTAGTAAGAATGTGTGCT 57.575 36.000 0.00 0.00 0.00 4.40
4316 4411 7.899648 AGCAAGTTATGATGTAGTACTACCT 57.100 36.000 26.41 18.77 35.26 3.08
4317 4412 8.195436 TCAAGCAAGTTATGATGTAGTACTACC 58.805 37.037 26.41 14.68 35.26 3.18
4318 4413 9.239002 CTCAAGCAAGTTATGATGTAGTACTAC 57.761 37.037 23.58 23.58 36.63 2.73
4319 4414 7.921214 GCTCAAGCAAGTTATGATGTAGTACTA 59.079 37.037 0.00 0.00 41.59 1.82
4324 4511 6.457934 CCAAGCTCAAGCAAGTTATGATGTAG 60.458 42.308 4.59 0.00 45.16 2.74
4333 4520 1.271656 GCATCCAAGCTCAAGCAAGTT 59.728 47.619 4.59 0.00 45.16 2.66
4440 4627 2.821969 ACGTACTGGTGTTAGTGTAGGG 59.178 50.000 0.00 0.00 32.19 3.53
4511 4701 1.480954 GGAGATTAGGAGACGGTGCAA 59.519 52.381 0.00 0.00 0.00 4.08
4539 4729 6.370442 CACAATCTTACCGGTGAAGTTGAATA 59.630 38.462 19.93 0.00 33.16 1.75
4632 4822 6.744112 TGAACCACATTTCTAATGTTCAACC 58.256 36.000 2.45 0.00 39.12 3.77


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

AutoCloner maintained by Alex Coulton.