Multiple sequence alignment - TraesCS6B01G368200

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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 TraesCS6B01G368200 chr6B 100.000 2552 0 0 1 2552 642385876 642383325 0.000000e+00 4713.0
1 TraesCS6B01G368200 chr6A 96.213 977 31 2 704 1680 571651409 571650439 0.000000e+00 1594.0
2 TraesCS6B01G368200 chr6A 90.753 584 42 8 1 572 571652294 571651711 0.000000e+00 769.0
3 TraesCS6B01G368200 chr6A 97.297 37 1 0 2516 2552 571650447 571650411 2.120000e-06 63.9
4 TraesCS6B01G368200 chr1B 93.050 518 36 0 1999 2516 399001534 399002051 0.000000e+00 758.0
5 TraesCS6B01G368200 chr1B 90.935 353 15 9 1680 2016 399001136 399001487 2.310000e-125 459.0
6 TraesCS6B01G368200 chr1B 90.625 64 5 1 1680 1743 633778731 633778669 1.630000e-12 84.2
7 TraesCS6B01G368200 chr6D 90.414 532 44 7 1 527 426923407 426922878 0.000000e+00 693.0
8 TraesCS6B01G368200 chr6D 97.704 392 9 0 1289 1680 426893132 426892741 0.000000e+00 675.0
9 TraesCS6B01G368200 chr6D 96.073 331 13 0 668 998 426895500 426895170 8.030000e-150 540.0
10 TraesCS6B01G368200 chr6D 97.333 300 8 0 990 1289 426893511 426893212 6.300000e-141 510.0
11 TraesCS6B01G368200 chr6D 84.500 200 28 3 423 621 398731562 398731759 7.200000e-46 195.0
12 TraesCS6B01G368200 chr6D 97.297 37 1 0 2516 2552 426892749 426892713 2.120000e-06 63.9
13 TraesCS6B01G368200 chr7A 78.723 893 134 24 811 1679 661828122 661827262 1.730000e-151 545.0
14 TraesCS6B01G368200 chr7A 74.667 525 74 36 1999 2516 639295081 639294609 7.260000e-41 178.0
15 TraesCS6B01G368200 chr7A 79.894 189 17 10 1999 2184 69714269 69714439 4.460000e-23 119.0
16 TraesCS6B01G368200 chr7A 84.167 120 18 1 68 187 157232815 157232933 5.770000e-22 115.0
17 TraesCS6B01G368200 chr7B 78.149 897 140 27 808 1679 629411991 629412856 1.050000e-143 520.0
18 TraesCS6B01G368200 chr5D 88.127 379 22 14 1682 2042 50817795 50817422 1.810000e-116 429.0
19 TraesCS6B01G368200 chr5D 87.863 379 23 14 1682 2042 515105577 515105204 8.440000e-115 424.0
20 TraesCS6B01G368200 chr5D 95.570 158 7 0 2291 2448 21007549 21007392 1.170000e-63 254.0
21 TraesCS6B01G368200 chr5D 91.608 143 11 1 2000 2141 515105163 515105021 2.000000e-46 196.0
22 TraesCS6B01G368200 chr5D 83.981 206 29 4 423 627 509680913 509681115 7.200000e-46 195.0
23 TraesCS6B01G368200 chr5D 84.021 194 29 2 442 635 495195490 495195681 4.340000e-43 185.0
24 TraesCS6B01G368200 chr5D 100.000 31 0 0 2251 2281 21007605 21007575 9.860000e-05 58.4
25 TraesCS6B01G368200 chr2D 87.335 379 25 14 1682 2042 85760027 85759654 1.830000e-111 412.0
26 TraesCS6B01G368200 chr2D 90.909 143 12 1 2000 2141 85759613 85759471 9.320000e-45 191.0
27 TraesCS6B01G368200 chr3D 76.832 505 87 20 1167 1653 436180070 436179578 9.060000e-65 257.0
28 TraesCS6B01G368200 chr3D 84.236 203 28 3 423 624 125294917 125294718 7.200000e-46 195.0
29 TraesCS6B01G368200 chr3D 84.896 192 24 5 423 613 100768735 100768548 3.350000e-44 189.0
30 TraesCS6B01G368200 chr3D 79.200 250 42 7 423 670 546203727 546203486 5.650000e-37 165.0
31 TraesCS6B01G368200 chr3D 73.743 537 69 42 2005 2531 577026911 577026437 7.360000e-31 145.0
32 TraesCS6B01G368200 chr2B 85.427 199 27 2 1679 1876 414613926 414614123 3.330000e-49 206.0
33 TraesCS6B01G368200 chr5B 75.712 527 59 42 1999 2515 555955779 555955312 1.550000e-47 200.0
34 TraesCS6B01G368200 chr3B 81.405 242 40 5 431 670 263518702 263518464 2.590000e-45 193.0
35 TraesCS6B01G368200 chr3A 81.818 231 36 6 442 670 243860229 243860003 3.350000e-44 189.0
36 TraesCS6B01G368200 chr1A 83.523 176 24 5 48 221 246694398 246694570 2.630000e-35 159.0
37 TraesCS6B01G368200 chr1A 77.670 206 24 17 1999 2201 360402939 360403125 3.470000e-19 106.0
38 TraesCS6B01G368200 chr7D 82.456 171 23 4 952 1118 572657671 572657504 2.650000e-30 143.0
39 TraesCS6B01G368200 chr4D 91.045 67 3 3 1681 1746 5588563 5588499 1.260000e-13 87.9
40 TraesCS6B01G368200 chrUn 83.516 91 14 1 1679 1769 89796554 89796465 1.630000e-12 84.2
41 TraesCS6B01G368200 chr1D 90.323 62 4 2 1686 1746 428879991 428880051 2.100000e-11 80.5


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 TraesCS6B01G368200 chr6B 642383325 642385876 2551 True 4713.000000 4713 100.000000 1 2552 1 chr6B.!!$R1 2551
1 TraesCS6B01G368200 chr6A 571650411 571652294 1883 True 808.966667 1594 94.754333 1 2552 3 chr6A.!!$R1 2551
2 TraesCS6B01G368200 chr1B 399001136 399002051 915 False 608.500000 758 91.992500 1680 2516 2 chr1B.!!$F1 836
3 TraesCS6B01G368200 chr6D 426922878 426923407 529 True 693.000000 693 90.414000 1 527 1 chr6D.!!$R1 526
4 TraesCS6B01G368200 chr6D 426892713 426895500 2787 True 447.225000 675 97.101750 668 2552 4 chr6D.!!$R2 1884
5 TraesCS6B01G368200 chr7A 661827262 661828122 860 True 545.000000 545 78.723000 811 1679 1 chr7A.!!$R2 868
6 TraesCS6B01G368200 chr7B 629411991 629412856 865 False 520.000000 520 78.149000 808 1679 1 chr7B.!!$F1 871
7 TraesCS6B01G368200 chr5D 515105021 515105577 556 True 310.000000 424 89.735500 1682 2141 2 chr5D.!!$R3 459
8 TraesCS6B01G368200 chr2D 85759471 85760027 556 True 301.500000 412 89.122000 1682 2141 2 chr2D.!!$R1 459

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
711 894 0.032403 CGTGACCGGGTGTTTCTACA 59.968 55.0 3.3 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2301 4356 0.116143 ACCACAGAGGAGAGAGGCTT 59.884 55.0 0.0 0.0 41.22 4.35 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
17 18 4.740822 GCCCGGATGCCACCTTGT 62.741 66.667 0.73 0.00 0.00 3.16
27 28 0.887387 GCCACCTTGTTACGCTCCAA 60.887 55.000 0.00 0.00 0.00 3.53
37 38 2.105006 TACGCTCCAACTACTCTCGT 57.895 50.000 0.00 0.00 0.00 4.18
66 67 3.303990 CCTTGTCTTTGACACATTGTCCG 60.304 47.826 3.91 0.00 46.40 4.79
71 72 2.333688 TTGACACATTGTCCGACCAA 57.666 45.000 3.91 0.00 46.40 3.67
97 98 3.932545 TGCGATTGTTTTGTAGGCAAT 57.067 38.095 0.00 0.00 35.78 3.56
144 145 4.927267 AATGAGGAGTATGGAACCACAA 57.073 40.909 0.00 0.00 0.00 3.33
158 159 4.687483 GGAACCACAAAGCTTGATGAATTG 59.313 41.667 0.00 0.00 0.00 2.32
184 185 7.510549 TTCAAAAGGAGTTCTTCGATTCATT 57.489 32.000 0.00 0.00 33.94 2.57
213 214 2.636830 ACGAAGAAGCCAAGATGATGG 58.363 47.619 0.00 0.00 43.70 3.51
273 274 0.605589 GCATCGGGATAGGGTCTCTG 59.394 60.000 0.00 0.00 0.00 3.35
281 282 2.111384 GATAGGGTCTCTGGAGCACAA 58.889 52.381 0.00 0.00 41.29 3.33
314 315 5.584551 AGGACTACTTTGATCCAAAACCT 57.415 39.130 0.00 0.00 32.75 3.50
374 375 1.001815 CGGAAACCATTGTTCTTGCGT 60.002 47.619 0.00 0.00 32.15 5.24
377 378 0.743688 AACCATTGTTCTTGCGTGCA 59.256 45.000 0.00 0.00 0.00 4.57
404 405 1.748403 GGAGTGGAGGCGCATGATA 59.252 57.895 10.83 0.00 0.00 2.15
405 406 0.322975 GGAGTGGAGGCGCATGATAT 59.677 55.000 10.83 0.00 0.00 1.63
406 407 1.271054 GGAGTGGAGGCGCATGATATT 60.271 52.381 10.83 0.00 0.00 1.28
407 408 2.072298 GAGTGGAGGCGCATGATATTC 58.928 52.381 10.83 0.00 0.00 1.75
408 409 1.417517 AGTGGAGGCGCATGATATTCA 59.582 47.619 10.83 0.00 0.00 2.57
410 411 0.792640 GGAGGCGCATGATATTCACG 59.207 55.000 10.83 0.00 0.00 4.35
411 412 1.502231 GAGGCGCATGATATTCACGT 58.498 50.000 10.83 0.00 0.00 4.49
412 413 1.193203 GAGGCGCATGATATTCACGTG 59.807 52.381 10.83 9.94 0.00 4.49
413 414 0.937304 GGCGCATGATATTCACGTGT 59.063 50.000 16.51 0.00 0.00 4.49
414 415 1.330521 GGCGCATGATATTCACGTGTT 59.669 47.619 16.51 7.21 0.00 3.32
416 417 3.186409 GGCGCATGATATTCACGTGTTAT 59.814 43.478 16.51 13.63 0.00 1.89
418 419 5.305812 GCGCATGATATTCACGTGTTATAC 58.694 41.667 16.51 6.65 0.00 1.47
419 420 5.667888 GCGCATGATATTCACGTGTTATACC 60.668 44.000 16.51 6.65 0.00 2.73
420 421 5.633601 CGCATGATATTCACGTGTTATACCT 59.366 40.000 16.51 1.43 0.00 3.08
421 422 6.145534 CGCATGATATTCACGTGTTATACCTT 59.854 38.462 16.51 1.96 0.00 3.50
426 439 9.908152 TGATATTCACGTGTTATACCTTAGATG 57.092 33.333 16.51 0.00 0.00 2.90
487 500 4.058797 GTGGACCCACAACGGAAG 57.941 61.111 13.92 0.00 45.53 3.46
505 518 5.163652 ACGGAAGCCAAATAGCTAATGTTTC 60.164 40.000 0.00 6.67 44.11 2.78
559 572 7.623770 TCGAACATATATTTTTCGCTACCAAC 58.376 34.615 16.47 0.00 41.48 3.77
572 585 9.745880 TTTTCGCTACCAACAAATGTTTATTTA 57.254 25.926 0.00 0.00 35.83 1.40
573 586 8.730970 TTCGCTACCAACAAATGTTTATTTAC 57.269 30.769 0.00 0.00 35.83 2.01
574 587 7.872881 TCGCTACCAACAAATGTTTATTTACA 58.127 30.769 0.00 0.00 35.83 2.41
577 590 9.418045 GCTACCAACAAATGTTTATTTACATGT 57.582 29.630 2.69 2.69 38.69 3.21
599 635 6.453643 GTGATATTCACGTGTATGATGGAC 57.546 41.667 16.51 2.75 37.67 4.02
600 636 5.117135 GTGATATTCACGTGTATGATGGACG 59.883 44.000 16.51 0.00 37.67 4.79
601 637 3.520290 ATTCACGTGTATGATGGACGT 57.480 42.857 16.51 0.00 46.78 4.34
604 640 0.245266 ACGTGTATGATGGACGTGCA 59.755 50.000 13.59 13.59 44.27 4.57
605 641 1.134818 ACGTGTATGATGGACGTGCAT 60.135 47.619 23.41 23.41 44.27 3.96
606 642 1.258720 CGTGTATGATGGACGTGCATG 59.741 52.381 28.10 7.09 33.20 4.06
609 645 2.104622 TGTATGATGGACGTGCATGGAT 59.895 45.455 28.10 19.43 0.00 3.41
610 646 2.353357 ATGATGGACGTGCATGGATT 57.647 45.000 28.10 3.00 0.00 3.01
611 647 2.127271 TGATGGACGTGCATGGATTT 57.873 45.000 28.10 2.12 0.00 2.17
612 648 1.744522 TGATGGACGTGCATGGATTTG 59.255 47.619 28.10 0.00 0.00 2.32
613 649 1.745087 GATGGACGTGCATGGATTTGT 59.255 47.619 28.10 0.36 0.00 2.83
614 650 2.481289 TGGACGTGCATGGATTTGTA 57.519 45.000 5.33 0.00 0.00 2.41
615 651 2.997980 TGGACGTGCATGGATTTGTAT 58.002 42.857 5.33 0.00 0.00 2.29
616 652 2.682352 TGGACGTGCATGGATTTGTATG 59.318 45.455 5.33 0.00 0.00 2.39
617 653 2.033299 GGACGTGCATGGATTTGTATGG 59.967 50.000 11.36 0.00 0.00 2.74
618 654 2.942376 GACGTGCATGGATTTGTATGGA 59.058 45.455 11.36 0.00 0.00 3.41
619 655 3.554934 ACGTGCATGGATTTGTATGGAT 58.445 40.909 11.36 0.00 0.00 3.41
620 656 3.953612 ACGTGCATGGATTTGTATGGATT 59.046 39.130 11.36 0.00 0.00 3.01
621 657 4.402155 ACGTGCATGGATTTGTATGGATTT 59.598 37.500 11.36 0.00 0.00 2.17
622 658 4.741185 CGTGCATGGATTTGTATGGATTTG 59.259 41.667 0.00 0.00 0.00 2.32
624 660 6.339730 GTGCATGGATTTGTATGGATTTGAA 58.660 36.000 0.00 0.00 0.00 2.69
625 661 6.477688 GTGCATGGATTTGTATGGATTTGAAG 59.522 38.462 0.00 0.00 0.00 3.02
626 662 6.380560 TGCATGGATTTGTATGGATTTGAAGA 59.619 34.615 0.00 0.00 0.00 2.87
628 664 7.929785 GCATGGATTTGTATGGATTTGAAGATT 59.070 33.333 0.00 0.00 0.00 2.40
629 665 9.826574 CATGGATTTGTATGGATTTGAAGATTT 57.173 29.630 0.00 0.00 0.00 2.17
640 676 8.827832 TGGATTTGAAGATTTAGATTCCATGT 57.172 30.769 0.00 0.00 0.00 3.21
641 677 9.258629 TGGATTTGAAGATTTAGATTCCATGTT 57.741 29.630 0.00 0.00 0.00 2.71
645 681 9.695526 TTTGAAGATTTAGATTCCATGTTTGTG 57.304 29.630 0.00 0.00 0.00 3.33
646 682 8.634335 TGAAGATTTAGATTCCATGTTTGTGA 57.366 30.769 0.00 0.00 0.00 3.58
647 683 8.514594 TGAAGATTTAGATTCCATGTTTGTGAC 58.485 33.333 0.00 0.00 0.00 3.67
648 684 8.641498 AAGATTTAGATTCCATGTTTGTGACT 57.359 30.769 0.00 0.00 0.00 3.41
649 685 8.048534 AGATTTAGATTCCATGTTTGTGACTG 57.951 34.615 0.00 0.00 0.00 3.51
650 686 7.667219 AGATTTAGATTCCATGTTTGTGACTGT 59.333 33.333 0.00 0.00 0.00 3.55
651 687 6.558771 TTAGATTCCATGTTTGTGACTGTG 57.441 37.500 0.00 0.00 0.00 3.66
652 688 4.464008 AGATTCCATGTTTGTGACTGTGT 58.536 39.130 0.00 0.00 0.00 3.72
653 689 4.276678 AGATTCCATGTTTGTGACTGTGTG 59.723 41.667 0.00 0.00 0.00 3.82
655 691 2.023673 CCATGTTTGTGACTGTGTGGT 58.976 47.619 0.00 0.00 0.00 4.16
656 692 3.118223 TCCATGTTTGTGACTGTGTGGTA 60.118 43.478 0.00 0.00 0.00 3.25
657 693 3.820467 CCATGTTTGTGACTGTGTGGTAT 59.180 43.478 0.00 0.00 0.00 2.73
658 694 4.320421 CCATGTTTGTGACTGTGTGGTATG 60.320 45.833 0.00 0.00 0.00 2.39
659 695 2.616376 TGTTTGTGACTGTGTGGTATGC 59.384 45.455 0.00 0.00 0.00 3.14
660 696 1.890876 TTGTGACTGTGTGGTATGCC 58.109 50.000 0.00 0.00 0.00 4.40
661 697 0.761802 TGTGACTGTGTGGTATGCCA 59.238 50.000 0.00 0.00 43.73 4.92
672 708 0.324943 GGTATGCCATATGCGGGTCT 59.675 55.000 0.00 0.00 45.60 3.85
711 894 0.032403 CGTGACCGGGTGTTTCTACA 59.968 55.000 3.30 0.00 0.00 2.74
733 916 1.679153 ACGTTTGAAGTGCCGGATTTT 59.321 42.857 5.05 0.00 0.00 1.82
742 925 2.088423 GTGCCGGATTTTGTGTATCCA 58.912 47.619 5.05 0.00 41.38 3.41
1271 3130 2.741612 TGTGTATTTGTTTGCTGCTGC 58.258 42.857 8.89 8.89 40.20 5.25
1285 3144 3.256383 TGCTGCTGCATCAATTACTTGTT 59.744 39.130 14.93 0.00 45.31 2.83
1286 3145 4.458642 TGCTGCTGCATCAATTACTTGTTA 59.541 37.500 14.93 0.00 45.31 2.41
1287 3146 4.795278 GCTGCTGCATCAATTACTTGTTAC 59.205 41.667 11.11 0.00 39.41 2.50
1775 3728 3.876198 GCCGTTCAATCGCCGCAT 61.876 61.111 0.00 0.00 0.00 4.73
1818 3771 0.681243 GTTCTTCCATCCTGCACCCC 60.681 60.000 0.00 0.00 0.00 4.95
1913 3878 3.365265 GCTTCACTGCAACCCCGG 61.365 66.667 0.00 0.00 0.00 5.73
1929 3894 4.211502 GGCGATGCCCCAATGCAC 62.212 66.667 0.00 0.00 45.48 4.57
1986 3976 1.373435 CCCCAACGGTGCTTCACTA 59.627 57.895 0.00 0.00 34.40 2.74
1987 3977 0.035439 CCCCAACGGTGCTTCACTAT 60.035 55.000 0.00 0.00 34.40 2.12
2016 4006 2.101770 GCTTCATTGCAGCTCCGC 59.898 61.111 0.73 0.00 34.15 5.54
2091 4146 1.066430 GTGGACATGGGCGAGTTTCTA 60.066 52.381 0.00 0.00 0.00 2.10
2184 4239 4.335647 CCTCGGGGTTGCAGCACT 62.336 66.667 1.81 0.00 0.00 4.40
2185 4240 3.052082 CTCGGGGTTGCAGCACTG 61.052 66.667 5.05 5.05 0.00 3.66
2186 4241 3.832237 CTCGGGGTTGCAGCACTGT 62.832 63.158 11.74 0.00 0.00 3.55
2283 4338 2.262915 GCACCGTGGAGTGAGAGG 59.737 66.667 0.00 0.00 40.34 3.69
2288 4343 2.680352 GTGGAGTGAGAGGGGCGA 60.680 66.667 0.00 0.00 0.00 5.54
2289 4344 2.060980 GTGGAGTGAGAGGGGCGAT 61.061 63.158 0.00 0.00 0.00 4.58
2316 4371 1.413445 CATGGAAGCCTCTCTCCTCTG 59.587 57.143 0.00 0.00 0.00 3.35
2338 4393 2.072298 GGTGTGTGAAGATGCAGAGAC 58.928 52.381 0.00 0.00 0.00 3.36
2383 4438 2.447443 GGGAAAATGAGTGGGGAGAAC 58.553 52.381 0.00 0.00 0.00 3.01
2385 4440 2.290071 GGAAAATGAGTGGGGAGAACGA 60.290 50.000 0.00 0.00 0.00 3.85
2393 4448 1.305046 GGGGAGAACGAGTGGAGGA 60.305 63.158 0.00 0.00 0.00 3.71
2447 4502 3.338250 GTGGATGGGCCCAGTGGA 61.338 66.667 31.97 11.20 36.78 4.02
2450 4505 2.044946 GATGGGCCCAGTGGACAC 60.045 66.667 31.97 0.00 44.10 3.67
2475 4530 2.511600 GTCCTGCGTGCGGCTTAT 60.512 61.111 0.00 0.00 44.05 1.73
2476 4531 2.511373 TCCTGCGTGCGGCTTATG 60.511 61.111 0.00 0.00 44.05 1.90
2492 4547 7.007117 GCGGCTTATGTTTGTTTGTTTTAATC 58.993 34.615 0.00 0.00 0.00 1.75
2495 4550 7.382759 GGCTTATGTTTGTTTGTTTTAATCCGA 59.617 33.333 0.00 0.00 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.302192 GGAGCGTAACAAGGTGGCA 60.302 57.895 0.00 0.00 0.00 4.92
11 12 2.631545 AGTAGTTGGAGCGTAACAAGGT 59.368 45.455 4.14 0.00 0.00 3.50
14 15 3.365666 CGAGAGTAGTTGGAGCGTAACAA 60.366 47.826 4.14 0.00 0.00 2.83
17 18 2.430465 ACGAGAGTAGTTGGAGCGTAA 58.570 47.619 0.00 0.00 46.88 3.18
37 38 3.202906 GTGTCAAAGACAAGGTGCAGTA 58.797 45.455 0.82 0.00 44.49 2.74
97 98 3.909430 GAACCATTCGTATCCATCGCTA 58.091 45.455 0.00 0.00 0.00 4.26
144 145 7.673180 TCCTTTTGAATCAATTCATCAAGCTT 58.327 30.769 6.27 0.00 45.30 3.74
158 159 7.133891 TGAATCGAAGAACTCCTTTTGAATC 57.866 36.000 0.00 0.00 43.58 2.52
184 185 1.001520 TGGCTTCTTCGTTCGAATCCA 59.998 47.619 0.00 10.03 35.11 3.41
213 214 1.202222 CGAAGCCAATTGGATGCTCAC 60.202 52.381 29.02 13.47 37.39 3.51
257 258 0.478942 CTCCAGAGACCCTATCCCGA 59.521 60.000 0.00 0.00 0.00 5.14
273 274 6.174049 AGTCCTTTTAGAGTATTTGTGCTCC 58.826 40.000 0.00 0.00 32.47 4.70
308 309 1.063266 TCACCAGGGAAAGCAGGTTTT 60.063 47.619 0.00 0.00 30.44 2.43
314 315 0.482446 ACCATTCACCAGGGAAAGCA 59.518 50.000 0.00 0.00 0.00 3.91
374 375 2.605607 CCACTCCCTCCACCATGCA 61.606 63.158 0.00 0.00 0.00 3.96
377 378 1.307343 CCTCCACTCCCTCCACCAT 60.307 63.158 0.00 0.00 0.00 3.55
405 406 9.961265 CTAATCATCTAAGGTATAACACGTGAA 57.039 33.333 25.01 10.36 0.00 3.18
406 407 8.573885 CCTAATCATCTAAGGTATAACACGTGA 58.426 37.037 25.01 0.00 0.00 4.35
407 408 8.358148 ACCTAATCATCTAAGGTATAACACGTG 58.642 37.037 15.48 15.48 41.86 4.49
408 409 8.474710 ACCTAATCATCTAAGGTATAACACGT 57.525 34.615 0.00 0.00 41.86 4.49
412 413 9.837525 CGTGTACCTAATCATCTAAGGTATAAC 57.162 37.037 3.93 5.48 45.22 1.89
413 414 8.517878 GCGTGTACCTAATCATCTAAGGTATAA 58.482 37.037 3.93 0.00 45.22 0.98
414 415 7.666804 TGCGTGTACCTAATCATCTAAGGTATA 59.333 37.037 3.93 0.00 45.22 1.47
416 417 5.829391 TGCGTGTACCTAATCATCTAAGGTA 59.171 40.000 0.00 0.00 41.86 3.08
418 419 4.982916 GTGCGTGTACCTAATCATCTAAGG 59.017 45.833 0.00 0.00 36.42 2.69
419 420 5.588240 TGTGCGTGTACCTAATCATCTAAG 58.412 41.667 0.00 0.00 0.00 2.18
420 421 5.585820 TGTGCGTGTACCTAATCATCTAA 57.414 39.130 0.00 0.00 0.00 2.10
421 422 5.126545 AGTTGTGCGTGTACCTAATCATCTA 59.873 40.000 0.00 0.00 0.00 1.98
426 439 4.741342 AGTAGTTGTGCGTGTACCTAATC 58.259 43.478 0.00 0.00 0.00 1.75
487 500 7.201548 CCACAATTGAAACATTAGCTATTTGGC 60.202 37.037 13.59 0.00 0.00 4.52
577 590 5.219633 CGTCCATCATACACGTGAATATCA 58.780 41.667 25.01 0.00 0.00 2.15
578 591 5.220381 ACGTCCATCATACACGTGAATATC 58.780 41.667 25.01 2.57 44.78 1.63
590 626 3.490439 AATCCATGCACGTCCATCATA 57.510 42.857 0.00 0.00 0.00 2.15
593 629 1.745087 ACAAATCCATGCACGTCCATC 59.255 47.619 0.00 0.00 0.00 3.51
594 630 1.838112 ACAAATCCATGCACGTCCAT 58.162 45.000 0.00 0.00 0.00 3.41
595 631 2.481289 TACAAATCCATGCACGTCCA 57.519 45.000 0.00 0.00 0.00 4.02
596 632 2.033299 CCATACAAATCCATGCACGTCC 59.967 50.000 0.00 0.00 0.00 4.79
597 633 2.942376 TCCATACAAATCCATGCACGTC 59.058 45.455 0.00 0.00 0.00 4.34
598 634 2.997980 TCCATACAAATCCATGCACGT 58.002 42.857 0.00 0.00 0.00 4.49
599 635 4.572985 AATCCATACAAATCCATGCACG 57.427 40.909 0.00 0.00 0.00 5.34
600 636 5.904941 TCAAATCCATACAAATCCATGCAC 58.095 37.500 0.00 0.00 0.00 4.57
601 637 6.380560 TCTTCAAATCCATACAAATCCATGCA 59.619 34.615 0.00 0.00 0.00 3.96
602 638 6.808829 TCTTCAAATCCATACAAATCCATGC 58.191 36.000 0.00 0.00 0.00 4.06
611 647 9.919416 TGGAATCTAAATCTTCAAATCCATACA 57.081 29.630 0.00 0.00 29.93 2.29
614 650 9.430399 ACATGGAATCTAAATCTTCAAATCCAT 57.570 29.630 0.00 0.00 43.88 3.41
615 651 8.827832 ACATGGAATCTAAATCTTCAAATCCA 57.172 30.769 0.00 0.00 38.66 3.41
619 655 9.695526 CACAAACATGGAATCTAAATCTTCAAA 57.304 29.630 0.00 0.00 0.00 2.69
620 656 9.076781 TCACAAACATGGAATCTAAATCTTCAA 57.923 29.630 0.00 0.00 0.00 2.69
621 657 8.514594 GTCACAAACATGGAATCTAAATCTTCA 58.485 33.333 0.00 0.00 0.00 3.02
622 658 8.734386 AGTCACAAACATGGAATCTAAATCTTC 58.266 33.333 0.00 0.00 0.00 2.87
624 660 7.667219 ACAGTCACAAACATGGAATCTAAATCT 59.333 33.333 0.00 0.00 0.00 2.40
625 661 7.752239 CACAGTCACAAACATGGAATCTAAATC 59.248 37.037 0.00 0.00 0.00 2.17
626 662 7.231317 ACACAGTCACAAACATGGAATCTAAAT 59.769 33.333 0.00 0.00 0.00 1.40
628 664 6.017192 CACACAGTCACAAACATGGAATCTAA 60.017 38.462 0.00 0.00 0.00 2.10
629 665 5.469760 CACACAGTCACAAACATGGAATCTA 59.530 40.000 0.00 0.00 0.00 1.98
630 666 4.276678 CACACAGTCACAAACATGGAATCT 59.723 41.667 0.00 0.00 0.00 2.40
631 667 4.539870 CACACAGTCACAAACATGGAATC 58.460 43.478 0.00 0.00 0.00 2.52
632 668 3.318839 CCACACAGTCACAAACATGGAAT 59.681 43.478 0.00 0.00 0.00 3.01
634 670 2.296792 CCACACAGTCACAAACATGGA 58.703 47.619 0.00 0.00 0.00 3.41
635 671 2.023673 ACCACACAGTCACAAACATGG 58.976 47.619 0.00 0.00 0.00 3.66
636 672 4.786507 CATACCACACAGTCACAAACATG 58.213 43.478 0.00 0.00 0.00 3.21
638 674 2.616376 GCATACCACACAGTCACAAACA 59.384 45.455 0.00 0.00 0.00 2.83
639 675 2.031157 GGCATACCACACAGTCACAAAC 60.031 50.000 0.00 0.00 35.26 2.93
640 676 2.226330 GGCATACCACACAGTCACAAA 58.774 47.619 0.00 0.00 35.26 2.83
641 677 1.141858 TGGCATACCACACAGTCACAA 59.858 47.619 0.00 0.00 42.67 3.33
642 678 0.761802 TGGCATACCACACAGTCACA 59.238 50.000 0.00 0.00 42.67 3.58
643 679 3.623848 TGGCATACCACACAGTCAC 57.376 52.632 0.00 0.00 42.67 3.67
653 689 0.324943 AGACCCGCATATGGCATACC 59.675 55.000 9.83 3.22 45.17 2.73
655 691 1.055849 ACAGACCCGCATATGGCATA 58.944 50.000 10.07 10.07 45.17 3.14
656 692 0.183492 AACAGACCCGCATATGGCAT 59.817 50.000 4.88 4.88 45.17 4.40
657 693 0.034574 AAACAGACCCGCATATGGCA 60.035 50.000 4.56 0.00 45.17 4.92
658 694 0.381801 CAAACAGACCCGCATATGGC 59.618 55.000 4.56 0.00 39.90 4.40
659 695 1.024271 CCAAACAGACCCGCATATGG 58.976 55.000 4.56 0.00 0.00 2.74
660 696 0.381801 GCCAAACAGACCCGCATATG 59.618 55.000 0.00 0.00 0.00 1.78
661 697 1.095228 CGCCAAACAGACCCGCATAT 61.095 55.000 0.00 0.00 0.00 1.78
662 698 1.743623 CGCCAAACAGACCCGCATA 60.744 57.895 0.00 0.00 0.00 3.14
663 699 2.819984 ATCGCCAAACAGACCCGCAT 62.820 55.000 0.00 0.00 0.00 4.73
664 700 3.545124 ATCGCCAAACAGACCCGCA 62.545 57.895 0.00 0.00 0.00 5.69
665 701 2.746277 ATCGCCAAACAGACCCGC 60.746 61.111 0.00 0.00 0.00 6.13
694 730 1.342174 GTCTGTAGAAACACCCGGTCA 59.658 52.381 0.00 0.00 0.00 4.02
711 894 0.034896 ATCCGGCACTTCAAACGTCT 59.965 50.000 0.00 0.00 0.00 4.18
742 925 6.600882 AGTGAAATGAGAGCATCCAAAATT 57.399 33.333 0.00 0.00 33.66 1.82
1223 3082 6.018262 CACTCAGAAAAACCGTATGAACTTCA 60.018 38.462 0.00 0.00 0.00 3.02
1231 3090 4.024048 CACAAGCACTCAGAAAAACCGTAT 60.024 41.667 0.00 0.00 0.00 3.06
1285 3144 8.900781 ACGTTAATCTCTGCTTATCAACTAGTA 58.099 33.333 0.00 0.00 0.00 1.82
1286 3145 7.702772 CACGTTAATCTCTGCTTATCAACTAGT 59.297 37.037 0.00 0.00 0.00 2.57
1287 3146 7.915923 TCACGTTAATCTCTGCTTATCAACTAG 59.084 37.037 0.00 0.00 0.00 2.57
1663 3616 4.634443 AGCCGCCAACTAATTAACTTGTAG 59.366 41.667 0.00 0.00 0.00 2.74
1667 3620 2.163613 GCAGCCGCCAACTAATTAACTT 59.836 45.455 0.00 0.00 0.00 2.66
1671 3624 2.093394 TGTAGCAGCCGCCAACTAATTA 60.093 45.455 0.00 0.00 39.83 1.40
1672 3625 1.339631 TGTAGCAGCCGCCAACTAATT 60.340 47.619 0.00 0.00 39.83 1.40
1673 3626 0.251916 TGTAGCAGCCGCCAACTAAT 59.748 50.000 0.00 0.00 39.83 1.73
1674 3627 0.391130 CTGTAGCAGCCGCCAACTAA 60.391 55.000 0.00 0.00 39.83 2.24
1675 3628 1.218047 CTGTAGCAGCCGCCAACTA 59.782 57.895 0.00 0.00 39.83 2.24
1676 3629 1.903877 ATCTGTAGCAGCCGCCAACT 61.904 55.000 0.00 0.00 39.83 3.16
1677 3630 0.179084 TATCTGTAGCAGCCGCCAAC 60.179 55.000 0.00 0.00 39.83 3.77
1678 3631 0.539518 TTATCTGTAGCAGCCGCCAA 59.460 50.000 0.00 0.00 39.83 4.52
1765 3718 2.244651 GGCTTCGTATGCGGCGATT 61.245 57.895 12.98 0.00 38.21 3.34
1818 3771 2.617250 TTTTTGCTGCAGATGCTACG 57.383 45.000 20.43 0.00 42.66 3.51
1913 3878 4.211502 GGTGCATTGGGGCATCGC 62.212 66.667 0.00 0.00 46.92 4.58
1929 3894 2.274645 TTGCATTGAAGCACCGGGG 61.275 57.895 6.32 0.84 45.61 5.73
2022 4012 3.678717 CTGCTGGTGCTGCAATCGC 62.679 63.158 2.77 7.62 37.82 4.58
2023 4013 2.483745 CTGCTGGTGCTGCAATCG 59.516 61.111 2.77 0.00 37.82 3.34
2091 4146 1.282248 CGAACTCGGTGTTGCGACAT 61.282 55.000 10.68 0.00 39.30 3.06
2099 4154 2.246739 TCGTCGACGAACTCGGTGT 61.247 57.895 36.25 0.00 46.30 4.16
2288 4343 2.124151 GGCTTCCATGGCGGACAT 60.124 61.111 6.96 0.00 46.36 3.06
2289 4344 3.329542 GAGGCTTCCATGGCGGACA 62.330 63.158 6.96 0.00 46.36 4.02
2301 4356 0.116143 ACCACAGAGGAGAGAGGCTT 59.884 55.000 0.00 0.00 41.22 4.35
2316 4371 1.802960 CTCTGCATCTTCACACACCAC 59.197 52.381 0.00 0.00 0.00 4.16
2338 4393 2.581409 CGTCGGATTCGTTCCCCG 60.581 66.667 0.00 0.00 42.06 5.73
2383 4438 2.621055 CACCTCTATTCTCCTCCACTCG 59.379 54.545 0.00 0.00 0.00 4.18
2385 4440 2.587777 TCCACCTCTATTCTCCTCCACT 59.412 50.000 0.00 0.00 0.00 4.00
2393 4448 5.542251 GCCTTATCTCTTCCACCTCTATTCT 59.458 44.000 0.00 0.00 0.00 2.40
2443 4498 4.223514 GACTCGACACGTGTCCAC 57.776 61.111 36.01 22.64 42.17 4.02
2447 4502 2.335369 GCAGGACTCGACACGTGT 59.665 61.111 23.64 23.64 36.30 4.49
2450 4505 2.801162 CACGCAGGACTCGACACG 60.801 66.667 0.00 0.00 0.00 4.49
2475 4530 8.703604 TTCAATCGGATTAAAACAAACAAACA 57.296 26.923 2.35 0.00 0.00 2.83
2476 4531 9.974750 TTTTCAATCGGATTAAAACAAACAAAC 57.025 25.926 2.35 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.