Multiple sequence alignment - TraesCS2A01G512700

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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 TraesCS2A01G512700 chr2A 100.000 2849 0 0 1 2849 737736145 737733297 0.000000e+00 5262.0
1 TraesCS2A01G512700 chr2A 93.337 1681 80 10 678 2332 737880627 737878953 0.000000e+00 2455.0
2 TraesCS2A01G512700 chr2A 87.995 1566 139 26 787 2332 738007000 738005464 0.000000e+00 1805.0
3 TraesCS2A01G512700 chr2A 97.683 518 12 0 2332 2849 737836881 737836364 0.000000e+00 891.0
4 TraesCS2A01G512700 chr2A 94.634 410 12 2 1933 2332 737837322 737836913 6.700000e-176 627.0
5 TraesCS2A01G512700 chr2A 84.762 525 68 8 2335 2849 738003102 738002580 1.510000e-142 516.0
6 TraesCS2A01G512700 chr2A 97.153 281 8 0 2332 2612 737878921 737878641 2.570000e-130 475.0
7 TraesCS2A01G512700 chr2A 87.059 85 10 1 492 575 707659895 707659979 8.400000e-16 95.3
8 TraesCS2A01G512700 chr2D 89.110 2057 146 31 834 2848 606188757 606186737 0.000000e+00 2486.0
9 TraesCS2A01G512700 chr2D 87.233 2248 192 49 678 2849 606156651 606154423 0.000000e+00 2473.0
10 TraesCS2A01G512700 chr2D 86.256 2110 203 39 788 2848 606214859 606212788 0.000000e+00 2209.0
11 TraesCS2A01G512700 chr2D 91.760 983 37 11 678 1650 606164505 606163557 0.000000e+00 1327.0
12 TraesCS2A01G512700 chr2D 84.437 1163 120 38 1739 2849 606162004 606160851 0.000000e+00 1088.0
13 TraesCS2A01G512700 chr2D 89.884 346 35 0 2504 2849 606136533 606136188 2.010000e-121 446.0
14 TraesCS2A01G512700 chr2D 83.231 489 73 8 6 491 606189651 606189169 9.370000e-120 440.0
15 TraesCS2A01G512700 chr2D 89.865 148 8 4 678 822 606189109 606188966 1.740000e-42 183.0
16 TraesCS2A01G512700 chr2D 86.905 84 11 0 491 574 7657752 7657835 8.400000e-16 95.3
17 TraesCS2A01G512700 chr2D 88.889 54 3 2 491 541 10307292 10307239 2.370000e-06 63.9
18 TraesCS2A01G512700 chr2B 93.317 1631 82 13 573 2197 737097485 737095876 0.000000e+00 2383.0
19 TraesCS2A01G512700 chr2B 90.281 1780 108 23 572 2332 737108746 737107013 0.000000e+00 2268.0
20 TraesCS2A01G512700 chr2B 89.870 1619 89 27 679 2264 737160815 737159239 0.000000e+00 2012.0
21 TraesCS2A01G512700 chr2B 94.239 1215 57 7 657 1862 737227205 737225995 0.000000e+00 1844.0
22 TraesCS2A01G512700 chr2B 94.239 1215 56 7 657 1862 737246260 737245051 0.000000e+00 1844.0
23 TraesCS2A01G512700 chr2B 84.375 352 47 5 2506 2849 737219181 737218830 3.520000e-89 339.0
24 TraesCS2A01G512700 chr2B 84.375 352 47 5 2506 2849 737238565 737238214 3.520000e-89 339.0
25 TraesCS2A01G512700 chr2B 78.862 492 76 6 1 491 737248244 737247780 9.910000e-80 307.0
26 TraesCS2A01G512700 chr2B 89.655 87 7 2 491 575 2897168 2897254 3.000000e-20 110.0
27 TraesCS2A01G512700 chr2B 100.000 29 0 0 787 815 737272459 737272431 1.000000e-03 54.7
28 TraesCS2A01G512700 chrUn 94.696 1301 55 4 1046 2332 386125594 386124294 0.000000e+00 2008.0
29 TraesCS2A01G512700 chrUn 98.106 264 5 0 2332 2595 386124262 386123999 7.190000e-126 460.0
30 TraesCS2A01G512700 chrUn 84.375 352 47 5 2506 2849 334698582 334698231 3.520000e-89 339.0
31 TraesCS2A01G512700 chrUn 86.250 240 15 11 678 905 30267131 30266898 7.880000e-61 244.0
32 TraesCS2A01G512700 chr7B 80.523 344 57 8 6 342 79317675 79317335 3.640000e-64 255.0
33 TraesCS2A01G512700 chr7D 88.506 87 9 1 491 576 461627925 461628011 1.400000e-18 104.0
34 TraesCS2A01G512700 chr5A 87.356 87 9 2 491 575 625759397 625759483 6.500000e-17 99.0
35 TraesCS2A01G512700 chr5A 89.062 64 7 0 34 97 631860601 631860664 2.350000e-11 80.5
36 TraesCS2A01G512700 chr4D 94.828 58 3 0 34 91 6763510 6763567 1.090000e-14 91.6
37 TraesCS2A01G512700 chr3B 86.047 86 9 3 492 575 784068646 784068730 3.910000e-14 89.8
38 TraesCS2A01G512700 chr3B 86.111 72 9 1 34 105 752000794 752000724 3.040000e-10 76.8
39 TraesCS2A01G512700 chr1A 90.625 64 6 0 34 97 455049146 455049209 5.060000e-13 86.1


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 TraesCS2A01G512700 chr2A 737733297 737736145 2848 True 5262.000000 5262 100.0000 1 2849 1 chr2A.!!$R1 2848
1 TraesCS2A01G512700 chr2A 737878641 737880627 1986 True 1465.000000 2455 95.2450 678 2612 2 chr2A.!!$R3 1934
2 TraesCS2A01G512700 chr2A 738002580 738007000 4420 True 1160.500000 1805 86.3785 787 2849 2 chr2A.!!$R4 2062
3 TraesCS2A01G512700 chr2A 737836364 737837322 958 True 759.000000 891 96.1585 1933 2849 2 chr2A.!!$R2 916
4 TraesCS2A01G512700 chr2D 606154423 606156651 2228 True 2473.000000 2473 87.2330 678 2849 1 chr2D.!!$R3 2171
5 TraesCS2A01G512700 chr2D 606212788 606214859 2071 True 2209.000000 2209 86.2560 788 2848 1 chr2D.!!$R4 2060
6 TraesCS2A01G512700 chr2D 606160851 606164505 3654 True 1207.500000 1327 88.0985 678 2849 2 chr2D.!!$R5 2171
7 TraesCS2A01G512700 chr2D 606186737 606189651 2914 True 1036.333333 2486 87.4020 6 2848 3 chr2D.!!$R6 2842
8 TraesCS2A01G512700 chr2B 737095876 737097485 1609 True 2383.000000 2383 93.3170 573 2197 1 chr2B.!!$R1 1624
9 TraesCS2A01G512700 chr2B 737107013 737108746 1733 True 2268.000000 2268 90.2810 572 2332 1 chr2B.!!$R2 1760
10 TraesCS2A01G512700 chr2B 737159239 737160815 1576 True 2012.000000 2012 89.8700 679 2264 1 chr2B.!!$R3 1585
11 TraesCS2A01G512700 chr2B 737225995 737227205 1210 True 1844.000000 1844 94.2390 657 1862 1 chr2B.!!$R5 1205
12 TraesCS2A01G512700 chr2B 737245051 737248244 3193 True 1075.500000 1844 86.5505 1 1862 2 chr2B.!!$R8 1861
13 TraesCS2A01G512700 chrUn 386123999 386125594 1595 True 1234.000000 2008 96.4010 1046 2595 2 chrUn.!!$R3 1549

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
565 588 0.111266 GCGTTTGCGTCTGTACAGTG 60.111 55.0 21.99 16.32 40.81 3.66 F
566 589 1.205657 CGTTTGCGTCTGTACAGTGT 58.794 50.0 21.99 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 3374 0.250295 CCACGTCACCCACACTGAAT 60.250 55.000 0.0 0.0 0.0 2.57 R
2395 7997 3.615536 GACCGTCGTACACACCCCG 62.616 68.421 0.0 0.0 0.0 5.73 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
99 100 4.323477 CGGTTGAAGCACCCCCGA 62.323 66.667 0.00 0.00 41.08 5.14
100 101 2.671963 GGTTGAAGCACCCCCGAC 60.672 66.667 0.00 0.00 0.00 4.79
101 102 3.047877 GTTGAAGCACCCCCGACG 61.048 66.667 0.00 0.00 0.00 5.12
124 147 0.788391 CGGTTGTAACACCTTCGAGC 59.212 55.000 0.00 0.00 34.22 5.03
170 193 0.177836 CGCACCCACACAGATGGATA 59.822 55.000 0.00 0.00 43.02 2.59
173 196 1.839994 CACCCACACAGATGGATAGGT 59.160 52.381 0.00 0.00 43.02 3.08
181 204 1.056700 AGATGGATAGGTGGCCGCTT 61.057 55.000 17.49 11.93 0.00 4.68
182 205 0.603975 GATGGATAGGTGGCCGCTTC 60.604 60.000 17.49 10.72 0.00 3.86
183 206 1.056700 ATGGATAGGTGGCCGCTTCT 61.057 55.000 17.49 8.34 0.00 2.85
186 209 1.735376 GATAGGTGGCCGCTTCTCGA 61.735 60.000 17.49 0.00 41.67 4.04
248 271 0.745486 CGCTGGCAAGTGGATGATGA 60.745 55.000 0.00 0.00 0.00 2.92
249 272 1.466856 GCTGGCAAGTGGATGATGAA 58.533 50.000 0.00 0.00 0.00 2.57
250 273 1.404391 GCTGGCAAGTGGATGATGAAG 59.596 52.381 0.00 0.00 0.00 3.02
258 281 1.146930 GGATGATGAAGGCTCGCCA 59.853 57.895 11.02 0.00 38.92 5.69
259 282 0.464373 GGATGATGAAGGCTCGCCAA 60.464 55.000 11.02 0.00 38.92 4.52
281 304 1.842381 GAGCAGTAGGGGGTGTGCTT 61.842 60.000 0.00 0.00 46.21 3.91
290 313 0.321346 GGGGTGTGCTTTGATTTGGG 59.679 55.000 0.00 0.00 0.00 4.12
296 319 1.821136 GTGCTTTGATTTGGGGGAGAG 59.179 52.381 0.00 0.00 0.00 3.20
297 320 1.710244 TGCTTTGATTTGGGGGAGAGA 59.290 47.619 0.00 0.00 0.00 3.10
300 323 3.056536 GCTTTGATTTGGGGGAGAGAAAC 60.057 47.826 0.00 0.00 0.00 2.78
302 325 1.004277 TGATTTGGGGGAGAGAAACCG 59.996 52.381 0.00 0.00 0.00 4.44
342 365 0.595310 GATAAGGGAGACGCTGCGAC 60.595 60.000 30.47 23.06 0.00 5.19
366 389 1.888436 TTGCTGGCCTACGAGGTGAG 61.888 60.000 3.32 0.00 37.80 3.51
384 407 2.652530 GCGTGGTGGGAAGACGTA 59.347 61.111 0.00 0.00 35.52 3.57
385 408 1.005867 GCGTGGTGGGAAGACGTAA 60.006 57.895 0.00 0.00 35.52 3.18
390 413 1.069513 TGGTGGGAAGACGTAACACAG 59.930 52.381 0.00 0.00 33.91 3.66
421 444 1.188138 GAAGATTGTGCGCGATCGTAG 59.812 52.381 19.44 12.35 39.84 3.51
423 446 0.870307 GATTGTGCGCGATCGTAGGT 60.870 55.000 17.81 0.00 38.14 3.08
425 448 1.348538 TTGTGCGCGATCGTAGGTTG 61.349 55.000 17.81 1.44 38.14 3.77
429 452 1.803922 CGCGATCGTAGGTTGTGCA 60.804 57.895 17.81 0.00 0.00 4.57
431 454 1.011968 GCGATCGTAGGTTGTGCACA 61.012 55.000 17.42 17.42 0.00 4.57
439 462 1.666553 GGTTGTGCACATCGTCCGA 60.667 57.895 22.39 0.00 0.00 4.55
440 463 1.019278 GGTTGTGCACATCGTCCGAT 61.019 55.000 22.39 0.00 34.81 4.18
451 474 1.129809 CGTCCGATGCAACGTTCAC 59.870 57.895 15.54 7.78 34.30 3.18
467 490 1.038681 TCACCCGGCGCACTAGATAA 61.039 55.000 10.83 0.00 0.00 1.75
502 525 3.512219 TTTTAAGTGGGGTAGGGTGTG 57.488 47.619 0.00 0.00 0.00 3.82
503 526 0.694196 TTAAGTGGGGTAGGGTGTGC 59.306 55.000 0.00 0.00 0.00 4.57
504 527 1.546589 TAAGTGGGGTAGGGTGTGCG 61.547 60.000 0.00 0.00 0.00 5.34
505 528 3.633116 GTGGGGTAGGGTGTGCGT 61.633 66.667 0.00 0.00 0.00 5.24
506 529 3.632080 TGGGGTAGGGTGTGCGTG 61.632 66.667 0.00 0.00 0.00 5.34
507 530 3.633116 GGGGTAGGGTGTGCGTGT 61.633 66.667 0.00 0.00 0.00 4.49
508 531 2.358247 GGGTAGGGTGTGCGTGTG 60.358 66.667 0.00 0.00 0.00 3.82
509 532 2.424302 GGTAGGGTGTGCGTGTGT 59.576 61.111 0.00 0.00 0.00 3.72
510 533 1.959226 GGTAGGGTGTGCGTGTGTG 60.959 63.158 0.00 0.00 0.00 3.82
511 534 1.227438 GTAGGGTGTGCGTGTGTGT 60.227 57.895 0.00 0.00 0.00 3.72
512 535 1.227409 TAGGGTGTGCGTGTGTGTG 60.227 57.895 0.00 0.00 0.00 3.82
513 536 1.962321 TAGGGTGTGCGTGTGTGTGT 61.962 55.000 0.00 0.00 0.00 3.72
514 537 2.403378 GGGTGTGCGTGTGTGTGTT 61.403 57.895 0.00 0.00 0.00 3.32
515 538 1.504446 GGTGTGCGTGTGTGTGTTT 59.496 52.632 0.00 0.00 0.00 2.83
516 539 0.727970 GGTGTGCGTGTGTGTGTTTA 59.272 50.000 0.00 0.00 0.00 2.01
517 540 1.332375 GGTGTGCGTGTGTGTGTTTAT 59.668 47.619 0.00 0.00 0.00 1.40
518 541 2.544686 GGTGTGCGTGTGTGTGTTTATA 59.455 45.455 0.00 0.00 0.00 0.98
519 542 3.187637 GGTGTGCGTGTGTGTGTTTATAT 59.812 43.478 0.00 0.00 0.00 0.86
520 543 4.148166 GTGTGCGTGTGTGTGTTTATATG 58.852 43.478 0.00 0.00 0.00 1.78
521 544 4.058817 TGTGCGTGTGTGTGTTTATATGA 58.941 39.130 0.00 0.00 0.00 2.15
522 545 4.151512 TGTGCGTGTGTGTGTTTATATGAG 59.848 41.667 0.00 0.00 0.00 2.90
523 546 4.151689 GTGCGTGTGTGTGTTTATATGAGT 59.848 41.667 0.00 0.00 0.00 3.41
524 547 4.151512 TGCGTGTGTGTGTTTATATGAGTG 59.848 41.667 0.00 0.00 0.00 3.51
525 548 4.387559 GCGTGTGTGTGTTTATATGAGTGA 59.612 41.667 0.00 0.00 0.00 3.41
526 549 5.444613 GCGTGTGTGTGTTTATATGAGTGAG 60.445 44.000 0.00 0.00 0.00 3.51
527 550 5.633601 CGTGTGTGTGTTTATATGAGTGAGT 59.366 40.000 0.00 0.00 0.00 3.41
528 551 6.399986 CGTGTGTGTGTTTATATGAGTGAGTG 60.400 42.308 0.00 0.00 0.00 3.51
529 552 6.423905 GTGTGTGTGTTTATATGAGTGAGTGT 59.576 38.462 0.00 0.00 0.00 3.55
530 553 7.597369 GTGTGTGTGTTTATATGAGTGAGTGTA 59.403 37.037 0.00 0.00 0.00 2.90
531 554 8.311109 TGTGTGTGTTTATATGAGTGAGTGTAT 58.689 33.333 0.00 0.00 0.00 2.29
532 555 8.595533 GTGTGTGTTTATATGAGTGAGTGTATG 58.404 37.037 0.00 0.00 0.00 2.39
533 556 7.277760 TGTGTGTTTATATGAGTGAGTGTATGC 59.722 37.037 0.00 0.00 0.00 3.14
534 557 6.475402 TGTGTTTATATGAGTGAGTGTATGCG 59.525 38.462 0.00 0.00 0.00 4.73
535 558 5.462068 TGTTTATATGAGTGAGTGTATGCGC 59.538 40.000 0.00 0.00 0.00 6.09
536 559 2.119671 TATGAGTGAGTGTATGCGCG 57.880 50.000 0.00 0.00 0.00 6.86
537 560 0.173481 ATGAGTGAGTGTATGCGCGT 59.827 50.000 8.43 7.55 0.00 6.01
538 561 0.456142 TGAGTGAGTGTATGCGCGTC 60.456 55.000 4.79 0.00 0.00 5.19
539 562 0.179161 GAGTGAGTGTATGCGCGTCT 60.179 55.000 4.79 0.00 0.00 4.18
540 563 1.063616 GAGTGAGTGTATGCGCGTCTA 59.936 52.381 4.79 0.00 0.00 2.59
541 564 1.676529 AGTGAGTGTATGCGCGTCTAT 59.323 47.619 4.79 2.74 0.00 1.98
542 565 2.876550 AGTGAGTGTATGCGCGTCTATA 59.123 45.455 4.79 1.67 0.00 1.31
543 566 3.502595 AGTGAGTGTATGCGCGTCTATAT 59.497 43.478 4.79 0.00 0.00 0.86
544 567 4.694037 AGTGAGTGTATGCGCGTCTATATA 59.306 41.667 4.79 0.28 0.00 0.86
545 568 5.180680 AGTGAGTGTATGCGCGTCTATATAA 59.819 40.000 4.79 0.00 0.00 0.98
546 569 5.508573 GTGAGTGTATGCGCGTCTATATAAG 59.491 44.000 4.79 0.00 0.00 1.73
547 570 4.413087 AGTGTATGCGCGTCTATATAAGC 58.587 43.478 4.79 0.00 0.00 3.09
553 576 3.073022 CGCGTCTATATAAGCGTTTGC 57.927 47.619 14.81 0.00 46.48 3.68
564 587 2.222592 GCGTTTGCGTCTGTACAGT 58.777 52.632 21.99 0.00 40.81 3.55
565 588 0.111266 GCGTTTGCGTCTGTACAGTG 60.111 55.000 21.99 16.32 40.81 3.66
566 589 1.205657 CGTTTGCGTCTGTACAGTGT 58.794 50.000 21.99 0.00 0.00 3.55
567 590 1.591158 CGTTTGCGTCTGTACAGTGTT 59.409 47.619 21.99 0.00 0.00 3.32
568 591 2.790448 CGTTTGCGTCTGTACAGTGTTA 59.210 45.455 21.99 0.00 0.00 2.41
569 592 3.243410 CGTTTGCGTCTGTACAGTGTTAA 59.757 43.478 21.99 11.05 0.00 2.01
570 593 4.259890 CGTTTGCGTCTGTACAGTGTTAAA 60.260 41.667 21.99 15.56 0.00 1.52
604 627 6.204688 CCTTTAAAATTTTGGCTCCAAGGTTC 59.795 38.462 13.76 0.00 37.24 3.62
608 2084 4.607293 ATTTTGGCTCCAAGGTTCTTTC 57.393 40.909 1.26 0.00 37.24 2.62
658 2135 5.487153 TCGACCATCGAAAAACAAAAGAA 57.513 34.783 0.00 0.00 46.90 2.52
659 2136 5.881447 TCGACCATCGAAAAACAAAAGAAA 58.119 33.333 0.00 0.00 46.90 2.52
660 2137 6.500041 TCGACCATCGAAAAACAAAAGAAAT 58.500 32.000 0.00 0.00 46.90 2.17
661 2138 7.640852 TCGACCATCGAAAAACAAAAGAAATA 58.359 30.769 0.00 0.00 46.90 1.40
662 2139 7.588488 TCGACCATCGAAAAACAAAAGAAATAC 59.412 33.333 0.00 0.00 46.90 1.89
663 2140 7.377397 CGACCATCGAAAAACAAAAGAAATACA 59.623 33.333 0.00 0.00 43.74 2.29
664 2141 9.191995 GACCATCGAAAAACAAAAGAAATACAT 57.808 29.630 0.00 0.00 0.00 2.29
886 2585 1.424302 CCTCCTCTGCATCCATCCATT 59.576 52.381 0.00 0.00 0.00 3.16
919 2636 2.351447 CCGAGACAACCGCATACGATAT 60.351 50.000 0.00 0.00 43.93 1.63
966 2683 1.675552 ACCAGCGTAAACTGTTTGCT 58.324 45.000 15.69 13.18 35.83 3.91
973 2690 1.264288 GTAAACTGTTTGCTGCGAGCT 59.736 47.619 15.69 0.00 42.97 4.09
1647 3374 2.143122 GACTTCATCAACAACTGCGGA 58.857 47.619 0.00 0.00 0.00 5.54
1771 4962 9.650539 CTCTCTACATTCTCTTCATCAAGAAAA 57.349 33.333 0.00 0.00 38.23 2.29
1915 5113 2.928116 GTTCTATGGTAGTGTTGCGACC 59.072 50.000 0.45 0.00 42.35 4.79
1917 5115 2.426024 TCTATGGTAGTGTTGCGACCTC 59.574 50.000 0.45 0.00 42.47 3.85
1965 5171 6.993308 TGGTGTTAAGACTTGCATGTAACTTA 59.007 34.615 5.05 7.38 0.00 2.24
1966 5172 7.499563 TGGTGTTAAGACTTGCATGTAACTTAA 59.500 33.333 16.36 16.36 0.00 1.85
2156 5374 3.639561 ACATTCCCTACACCAAACAAACC 59.360 43.478 0.00 0.00 0.00 3.27
2372 7974 4.904253 AGGCGACATCTCTAGTTTAGTC 57.096 45.455 0.00 0.00 0.00 2.59
2395 7997 7.438459 AGTCTTGTTGTGATACAAAGTCAGTAC 59.562 37.037 0.00 0.00 40.15 2.73
2629 8234 1.202722 GGAAACCTCAAACTCGACCCA 60.203 52.381 0.00 0.00 0.00 4.51
2721 8332 5.013495 ACATGCACATGGTAGATTAGGCTAT 59.987 40.000 14.73 0.00 42.91 2.97
2737 8348 7.775053 TTAGGCTATTGGACTTGACAAATTT 57.225 32.000 0.00 0.00 33.70 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 4.125097 GTTACAACCGCGGCGTCG 62.125 66.667 28.58 13.85 39.81 5.12
98 99 3.037249 TGTTACAACCGCGGCGTC 61.037 61.111 28.58 12.31 0.00 5.19
99 100 3.340253 GTGTTACAACCGCGGCGT 61.340 61.111 28.58 25.08 0.00 5.68
100 101 4.079748 GGTGTTACAACCGCGGCG 62.080 66.667 28.58 20.08 0.00 6.46
101 102 2.178892 GAAGGTGTTACAACCGCGGC 62.179 60.000 28.58 8.37 45.53 6.53
102 103 1.864176 GAAGGTGTTACAACCGCGG 59.136 57.895 26.86 26.86 45.53 6.46
103 104 0.940519 TCGAAGGTGTTACAACCGCG 60.941 55.000 0.00 0.00 45.53 6.46
104 105 0.788391 CTCGAAGGTGTTACAACCGC 59.212 55.000 0.00 0.00 45.53 5.68
105 106 0.788391 GCTCGAAGGTGTTACAACCG 59.212 55.000 0.00 0.00 45.53 4.44
106 107 1.798813 CAGCTCGAAGGTGTTACAACC 59.201 52.381 0.00 0.00 38.80 3.77
107 108 1.194772 GCAGCTCGAAGGTGTTACAAC 59.805 52.381 13.13 0.00 44.96 3.32
108 109 1.508632 GCAGCTCGAAGGTGTTACAA 58.491 50.000 13.13 0.00 44.96 2.41
109 110 0.666274 CGCAGCTCGAAGGTGTTACA 60.666 55.000 13.13 0.00 44.96 2.41
124 147 1.442526 CCAGCTTGCTATTCCCGCAG 61.443 60.000 0.00 0.00 38.80 5.18
152 175 1.475751 CCTATCCATCTGTGTGGGTGC 60.476 57.143 0.00 0.00 39.80 5.01
154 177 1.839994 CACCTATCCATCTGTGTGGGT 59.160 52.381 0.00 0.00 39.80 4.51
155 178 1.141657 CCACCTATCCATCTGTGTGGG 59.858 57.143 0.00 0.00 39.60 4.61
158 181 0.839946 GGCCACCTATCCATCTGTGT 59.160 55.000 0.00 0.00 0.00 3.72
160 183 2.044806 GCGGCCACCTATCCATCTGT 62.045 60.000 2.24 0.00 0.00 3.41
170 193 3.302347 CTTCGAGAAGCGGCCACCT 62.302 63.158 2.24 0.00 41.33 4.00
181 204 4.069232 CCCCGTGCTGCTTCGAGA 62.069 66.667 16.24 0.00 0.00 4.04
207 230 2.847234 TCCGGCAAGTGGACACCT 60.847 61.111 0.00 0.00 0.00 4.00
210 233 3.555324 TGCTCCGGCAAGTGGACA 61.555 61.111 0.00 0.00 46.36 4.02
228 251 1.028330 CATCATCCACTTGCCAGCGT 61.028 55.000 0.00 0.00 0.00 5.07
232 255 1.956636 GCCTTCATCATCCACTTGCCA 60.957 52.381 0.00 0.00 0.00 4.92
237 260 0.179062 GCGAGCCTTCATCATCCACT 60.179 55.000 0.00 0.00 0.00 4.00
248 271 2.360475 GCTCCTTTGGCGAGCCTT 60.360 61.111 15.75 0.00 45.76 4.35
258 281 0.475828 ACACCCCCTACTGCTCCTTT 60.476 55.000 0.00 0.00 0.00 3.11
259 282 1.161113 ACACCCCCTACTGCTCCTT 59.839 57.895 0.00 0.00 0.00 3.36
268 291 2.524306 CAAATCAAAGCACACCCCCTA 58.476 47.619 0.00 0.00 0.00 3.53
281 304 2.554344 CGGTTTCTCTCCCCCAAATCAA 60.554 50.000 0.00 0.00 0.00 2.57
290 313 0.250338 AACACAGCGGTTTCTCTCCC 60.250 55.000 0.00 0.00 0.00 4.30
296 319 1.261619 CTCAGTCAACACAGCGGTTTC 59.738 52.381 0.00 0.00 0.00 2.78
297 320 1.299541 CTCAGTCAACACAGCGGTTT 58.700 50.000 0.00 0.00 0.00 3.27
300 323 3.248029 GCTCAGTCAACACAGCGG 58.752 61.111 0.00 0.00 0.00 5.52
302 325 0.510359 CTTCGCTCAGTCAACACAGC 59.490 55.000 0.00 0.00 0.00 4.40
342 365 3.124921 CGTAGGCCAGCAAACCGG 61.125 66.667 5.01 0.00 0.00 5.28
356 379 2.282674 ACCACGCCTCACCTCGTA 60.283 61.111 0.00 0.00 37.14 3.43
366 389 2.438951 TTACGTCTTCCCACCACGCC 62.439 60.000 0.00 0.00 37.02 5.68
399 422 1.148157 CGATCGCGCACAATCTTCCT 61.148 55.000 8.75 0.00 0.00 3.36
409 432 1.803922 CACAACCTACGATCGCGCA 60.804 57.895 16.60 0.00 42.48 6.09
421 444 1.019278 ATCGGACGATGTGCACAACC 61.019 55.000 25.72 21.41 32.98 3.77
423 446 2.454921 CATCGGACGATGTGCACAA 58.545 52.632 25.72 5.47 44.93 3.33
431 454 0.389296 TGAACGTTGCATCGGACGAT 60.389 50.000 20.39 6.63 41.53 3.73
439 462 3.361977 GCCGGGTGAACGTTGCAT 61.362 61.111 5.00 0.00 0.00 3.96
451 474 1.217882 CTTTTATCTAGTGCGCCGGG 58.782 55.000 4.18 0.00 0.00 5.73
486 509 2.890766 CGCACACCCTACCCCACTT 61.891 63.158 0.00 0.00 0.00 3.16
487 510 3.319198 CGCACACCCTACCCCACT 61.319 66.667 0.00 0.00 0.00 4.00
488 511 3.633116 ACGCACACCCTACCCCAC 61.633 66.667 0.00 0.00 0.00 4.61
489 512 3.632080 CACGCACACCCTACCCCA 61.632 66.667 0.00 0.00 0.00 4.96
490 513 3.633116 ACACGCACACCCTACCCC 61.633 66.667 0.00 0.00 0.00 4.95
491 514 2.358247 CACACGCACACCCTACCC 60.358 66.667 0.00 0.00 0.00 3.69
492 515 1.959226 CACACACGCACACCCTACC 60.959 63.158 0.00 0.00 0.00 3.18
493 516 1.227438 ACACACACGCACACCCTAC 60.227 57.895 0.00 0.00 0.00 3.18
494 517 1.227409 CACACACACGCACACCCTA 60.227 57.895 0.00 0.00 0.00 3.53
495 518 2.513666 CACACACACGCACACCCT 60.514 61.111 0.00 0.00 0.00 4.34
496 519 1.928706 AAACACACACACGCACACCC 61.929 55.000 0.00 0.00 0.00 4.61
497 520 0.727970 TAAACACACACACGCACACC 59.272 50.000 0.00 0.00 0.00 4.16
498 521 2.748461 ATAAACACACACACGCACAC 57.252 45.000 0.00 0.00 0.00 3.82
499 522 4.058817 TCATATAAACACACACACGCACA 58.941 39.130 0.00 0.00 0.00 4.57
500 523 4.151689 ACTCATATAAACACACACACGCAC 59.848 41.667 0.00 0.00 0.00 5.34
501 524 4.151512 CACTCATATAAACACACACACGCA 59.848 41.667 0.00 0.00 0.00 5.24
502 525 4.387559 TCACTCATATAAACACACACACGC 59.612 41.667 0.00 0.00 0.00 5.34
503 526 5.633601 ACTCACTCATATAAACACACACACG 59.366 40.000 0.00 0.00 0.00 4.49
504 527 6.423905 ACACTCACTCATATAAACACACACAC 59.576 38.462 0.00 0.00 0.00 3.82
505 528 6.521162 ACACTCACTCATATAAACACACACA 58.479 36.000 0.00 0.00 0.00 3.72
506 529 8.595533 CATACACTCACTCATATAAACACACAC 58.404 37.037 0.00 0.00 0.00 3.82
507 530 7.277760 GCATACACTCACTCATATAAACACACA 59.722 37.037 0.00 0.00 0.00 3.72
508 531 7.515215 CGCATACACTCACTCATATAAACACAC 60.515 40.741 0.00 0.00 0.00 3.82
509 532 6.475402 CGCATACACTCACTCATATAAACACA 59.525 38.462 0.00 0.00 0.00 3.72
510 533 6.562270 GCGCATACACTCACTCATATAAACAC 60.562 42.308 0.30 0.00 0.00 3.32
511 534 5.462068 GCGCATACACTCACTCATATAAACA 59.538 40.000 0.30 0.00 0.00 2.83
512 535 5.387444 CGCGCATACACTCACTCATATAAAC 60.387 44.000 8.75 0.00 0.00 2.01
513 536 4.679654 CGCGCATACACTCACTCATATAAA 59.320 41.667 8.75 0.00 0.00 1.40
514 537 4.226761 CGCGCATACACTCACTCATATAA 58.773 43.478 8.75 0.00 0.00 0.98
515 538 3.252458 ACGCGCATACACTCACTCATATA 59.748 43.478 5.73 0.00 0.00 0.86
516 539 2.034685 ACGCGCATACACTCACTCATAT 59.965 45.455 5.73 0.00 0.00 1.78
517 540 1.404035 ACGCGCATACACTCACTCATA 59.596 47.619 5.73 0.00 0.00 2.15
518 541 0.173481 ACGCGCATACACTCACTCAT 59.827 50.000 5.73 0.00 0.00 2.90
519 542 0.456142 GACGCGCATACACTCACTCA 60.456 55.000 5.73 0.00 0.00 3.41
520 543 0.179161 AGACGCGCATACACTCACTC 60.179 55.000 5.73 0.00 0.00 3.51
521 544 1.092348 TAGACGCGCATACACTCACT 58.908 50.000 5.73 0.00 0.00 3.41
522 545 2.121116 ATAGACGCGCATACACTCAC 57.879 50.000 5.73 0.00 0.00 3.51
523 546 5.616488 TTATATAGACGCGCATACACTCA 57.384 39.130 5.73 0.00 0.00 3.41
524 547 4.496183 GCTTATATAGACGCGCATACACTC 59.504 45.833 5.73 0.00 0.00 3.51
525 548 4.413087 GCTTATATAGACGCGCATACACT 58.587 43.478 5.73 0.97 0.00 3.55
526 549 3.237660 CGCTTATATAGACGCGCATACAC 59.762 47.826 5.73 0.00 39.11 2.90
527 550 3.422655 CGCTTATATAGACGCGCATACA 58.577 45.455 5.73 0.00 39.11 2.29
534 557 2.470257 ACGCAAACGCTTATATAGACGC 59.530 45.455 6.44 0.12 45.53 5.19
535 558 3.973135 AGACGCAAACGCTTATATAGACG 59.027 43.478 5.27 5.27 45.53 4.18
536 559 4.738740 ACAGACGCAAACGCTTATATAGAC 59.261 41.667 0.00 0.00 45.53 2.59
537 560 4.928601 ACAGACGCAAACGCTTATATAGA 58.071 39.130 0.00 0.00 45.53 1.98
538 561 5.684184 TGTACAGACGCAAACGCTTATATAG 59.316 40.000 0.00 0.00 45.53 1.31
539 562 5.580661 TGTACAGACGCAAACGCTTATATA 58.419 37.500 0.00 0.00 45.53 0.86
540 563 4.426416 TGTACAGACGCAAACGCTTATAT 58.574 39.130 0.00 0.00 45.53 0.86
541 564 3.835779 TGTACAGACGCAAACGCTTATA 58.164 40.909 0.00 0.00 45.53 0.98
542 565 2.666508 CTGTACAGACGCAAACGCTTAT 59.333 45.455 18.45 0.00 45.53 1.73
543 566 2.055838 CTGTACAGACGCAAACGCTTA 58.944 47.619 18.45 0.00 45.53 3.09
544 567 0.859232 CTGTACAGACGCAAACGCTT 59.141 50.000 18.45 0.00 45.53 4.68
545 568 0.249322 ACTGTACAGACGCAAACGCT 60.249 50.000 29.30 0.00 45.53 5.07
546 569 0.111266 CACTGTACAGACGCAAACGC 60.111 55.000 29.30 0.00 45.53 4.84
548 571 4.782252 TTAACACTGTACAGACGCAAAC 57.218 40.909 29.30 0.00 0.00 2.93
549 572 5.798015 TTTTAACACTGTACAGACGCAAA 57.202 34.783 29.30 18.25 0.00 3.68
550 573 5.798015 TTTTTAACACTGTACAGACGCAA 57.202 34.783 29.30 13.86 0.00 4.85
570 593 8.574251 AGCCAAAATTTTAAAGGACACTTTTT 57.426 26.923 2.44 0.00 44.26 1.94
581 604 6.894682 AGAACCTTGGAGCCAAAATTTTAAA 58.105 32.000 2.44 0.00 35.33 1.52
584 607 5.372343 AAGAACCTTGGAGCCAAAATTTT 57.628 34.783 3.24 0.00 35.33 1.82
604 627 1.227999 TTCTTGCGCCCGACAGAAAG 61.228 55.000 4.18 0.00 0.00 2.62
608 2084 0.652592 CTTATTCTTGCGCCCGACAG 59.347 55.000 4.18 0.00 0.00 3.51
671 2148 4.713792 ATGTATTTGGATGGTCTCCCTC 57.286 45.455 0.00 0.00 44.23 4.30
827 2333 4.765339 CCGTATATATGGATCCATCGGCTA 59.235 45.833 30.61 17.24 37.82 3.93
828 2334 3.574396 CCGTATATATGGATCCATCGGCT 59.426 47.826 30.61 15.73 37.82 5.52
886 2585 3.959478 GTCTCGGCGACAATGGATA 57.041 52.632 4.99 0.00 42.37 2.59
966 2683 4.056125 CTGTGTCCCGAGCTCGCA 62.056 66.667 30.49 19.84 38.18 5.10
973 2690 1.829096 TGTTCGTCCTGTGTCCCGA 60.829 57.895 0.00 0.00 0.00 5.14
1113 2835 1.683707 AGAGAGTCTGGCCGCATCA 60.684 57.895 0.00 0.00 0.00 3.07
1341 3063 2.342279 CGGAACCGGTTCTGCTGA 59.658 61.111 38.59 0.00 38.89 4.26
1647 3374 0.250295 CCACGTCACCCACACTGAAT 60.250 55.000 0.00 0.00 0.00 2.57
2296 5533 3.651803 AGAGTCCAGAACACGAGAAAG 57.348 47.619 0.00 0.00 0.00 2.62
2297 5534 4.119862 CAAAGAGTCCAGAACACGAGAAA 58.880 43.478 0.00 0.00 0.00 2.52
2372 7974 6.346598 CCGTACTGACTTTGTATCACAACAAG 60.347 42.308 0.00 0.00 40.29 3.16
2395 7997 3.615536 GACCGTCGTACACACCCCG 62.616 68.421 0.00 0.00 0.00 5.73
2629 8234 5.503002 GTCCTAGACTAGTCTGAGAACCTT 58.497 45.833 31.47 8.06 40.71 3.50
2721 8332 8.558973 AAACATTGAAAATTTGTCAAGTCCAA 57.441 26.923 7.98 0.00 38.34 3.53
2737 8348 4.810345 ACCACCTTAAGGGAAACATTGAA 58.190 39.130 25.31 0.00 40.27 2.69


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

AutoCloner maintained by Alex Coulton.