Multiple sequence alignment - TraesCS6B01G038000

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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 TraesCS6B01G038000 chr6B 100.000 2603 0 0 1 2603 22426484 22429086 0.000000e+00 4807
1 TraesCS6B01G038000 chr3B 97.970 1527 19 4 940 2459 201488914 201487393 0.000000e+00 2638
2 TraesCS6B01G038000 chr3B 97.382 1528 31 6 940 2459 201485641 201484115 0.000000e+00 2591
3 TraesCS6B01G038000 chr7B 97.772 1526 28 3 940 2459 662741829 662743354 0.000000e+00 2625
4 TraesCS6B01G038000 chr7B 99.320 147 1 0 2457 2603 137679351 137679497 1.540000e-67 267
5 TraesCS6B01G038000 chr2B 97.510 1526 31 5 940 2459 683741638 683740114 0.000000e+00 2601
6 TraesCS6B01G038000 chr3A 97.051 1526 28 6 940 2459 524024374 524022860 0.000000e+00 2553
7 TraesCS6B01G038000 chr3D 96.859 1528 25 6 940 2459 24161354 24159842 0.000000e+00 2534
8 TraesCS6B01G038000 chr3D 99.320 147 1 0 2457 2603 596659311 596659457 1.540000e-67 267
9 TraesCS6B01G038000 chr1D 96.219 1534 35 8 933 2459 254472606 254471089 0.000000e+00 2490
10 TraesCS6B01G038000 chr1D 96.493 941 31 2 1 940 254498538 254499477 0.000000e+00 1554
11 TraesCS6B01G038000 chr1D 92.242 941 61 8 1 940 244483509 244482580 0.000000e+00 1323
12 TraesCS6B01G038000 chr1D 97.959 147 3 0 2457 2603 254449506 254449652 3.320000e-64 255
13 TraesCS6B01G038000 chr5D 96.330 1526 33 8 940 2459 6240104 6241612 0.000000e+00 2486
14 TraesCS6B01G038000 chr5D 96.204 1528 32 11 940 2459 503326691 503325182 0.000000e+00 2477
15 TraesCS6B01G038000 chr5D 96.918 941 27 2 1 940 560873008 560873947 0.000000e+00 1576
16 TraesCS6B01G038000 chr5D 96.603 942 28 4 1 940 6200742 6199803 0.000000e+00 1559
17 TraesCS6B01G038000 chr5D 95.957 940 34 4 1 938 329162717 329163654 0.000000e+00 1522
18 TraesCS6B01G038000 chr5D 99.320 147 1 0 2457 2603 6162421 6162275 1.540000e-67 267
19 TraesCS6B01G038000 chr5D 99.320 147 1 0 2457 2603 6260414 6260268 1.540000e-67 267
20 TraesCS6B01G038000 chr5D 99.320 147 1 0 2457 2603 503306361 503306507 1.540000e-67 267
21 TraesCS6B01G038000 chr5D 99.320 147 1 0 2457 2603 512405402 512405548 1.540000e-67 267
22 TraesCS6B01G038000 chrUn 97.872 940 20 0 1 940 445812523 445811584 0.000000e+00 1626
23 TraesCS6B01G038000 chr4D 95.324 941 40 4 1 940 19917035 19917972 0.000000e+00 1491
24 TraesCS6B01G038000 chr4D 99.306 144 1 0 2457 2600 19882924 19883067 7.150000e-66 261
25 TraesCS6B01G038000 chr1A 95.324 941 39 4 1 940 168450027 168449091 0.000000e+00 1489
26 TraesCS6B01G038000 chr1A 99.320 147 1 0 2457 2603 241517539 241517685 1.540000e-67 267
27 TraesCS6B01G038000 chr7A 94.681 940 48 2 1 940 352193484 352192547 0.000000e+00 1458
28 TraesCS6B01G038000 chr2A 97.826 92 2 0 849 940 677892869 677892960 2.680000e-35 159


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 TraesCS6B01G038000 chr6B 22426484 22429086 2602 False 4807.0 4807 100.000 1 2603 1 chr6B.!!$F1 2602
1 TraesCS6B01G038000 chr3B 201484115 201488914 4799 True 2614.5 2638 97.676 940 2459 2 chr3B.!!$R1 1519
2 TraesCS6B01G038000 chr7B 662741829 662743354 1525 False 2625.0 2625 97.772 940 2459 1 chr7B.!!$F2 1519
3 TraesCS6B01G038000 chr2B 683740114 683741638 1524 True 2601.0 2601 97.510 940 2459 1 chr2B.!!$R1 1519
4 TraesCS6B01G038000 chr3A 524022860 524024374 1514 True 2553.0 2553 97.051 940 2459 1 chr3A.!!$R1 1519
5 TraesCS6B01G038000 chr3D 24159842 24161354 1512 True 2534.0 2534 96.859 940 2459 1 chr3D.!!$R1 1519
6 TraesCS6B01G038000 chr1D 254471089 254472606 1517 True 2490.0 2490 96.219 933 2459 1 chr1D.!!$R2 1526
7 TraesCS6B01G038000 chr1D 254498538 254499477 939 False 1554.0 1554 96.493 1 940 1 chr1D.!!$F2 939
8 TraesCS6B01G038000 chr1D 244482580 244483509 929 True 1323.0 1323 92.242 1 940 1 chr1D.!!$R1 939
9 TraesCS6B01G038000 chr5D 6240104 6241612 1508 False 2486.0 2486 96.330 940 2459 1 chr5D.!!$F1 1519
10 TraesCS6B01G038000 chr5D 503325182 503326691 1509 True 2477.0 2477 96.204 940 2459 1 chr5D.!!$R4 1519
11 TraesCS6B01G038000 chr5D 560873008 560873947 939 False 1576.0 1576 96.918 1 940 1 chr5D.!!$F5 939
12 TraesCS6B01G038000 chr5D 6199803 6200742 939 True 1559.0 1559 96.603 1 940 1 chr5D.!!$R2 939
13 TraesCS6B01G038000 chr5D 329162717 329163654 937 False 1522.0 1522 95.957 1 938 1 chr5D.!!$F2 937
14 TraesCS6B01G038000 chrUn 445811584 445812523 939 True 1626.0 1626 97.872 1 940 1 chrUn.!!$R1 939
15 TraesCS6B01G038000 chr4D 19917035 19917972 937 False 1491.0 1491 95.324 1 940 1 chr4D.!!$F2 939
16 TraesCS6B01G038000 chr1A 168449091 168450027 936 True 1489.0 1489 95.324 1 940 1 chr1A.!!$R1 939
17 TraesCS6B01G038000 chr7A 352192547 352193484 937 True 1458.0 1458 94.681 1 940 1 chr7A.!!$R1 939

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
805 809 1.612676 AACCTAGGCCAAAACGAACC 58.387 50.0 9.3 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 1936 0.388294 CGTATCCCCCTCTTTCCGTC 59.612 60.0 0.0 0.0 0.0 4.79 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
58 59 4.630894 TTGCTTTGCTCTTCTTTTTCGA 57.369 36.364 0.00 0.00 0.00 3.71
113 114 5.088739 CGAGATGTTTTTGCTGGTATTGAC 58.911 41.667 0.00 0.00 0.00 3.18
273 274 6.040842 TCCCATCCTTTCTTTGACTCTTTTTG 59.959 38.462 0.00 0.00 0.00 2.44
277 278 9.154847 CATCCTTTCTTTGACTCTTTTTGTTTT 57.845 29.630 0.00 0.00 0.00 2.43
325 326 8.780846 ATTACAAATGAATACGTGTGGAAGTA 57.219 30.769 0.00 0.00 27.91 2.24
377 378 5.751243 ATGGAAGCATTGGTTTATACGTC 57.249 39.130 2.14 0.00 0.00 4.34
519 521 6.042208 CCAGATAGGGGGACTTCTTACTTAAG 59.958 46.154 0.00 0.00 34.65 1.85
693 695 9.838339 AGATTACAATGGATCTACGAAAAGATT 57.162 29.630 0.00 0.00 36.33 2.40
805 809 1.612676 AACCTAGGCCAAAACGAACC 58.387 50.000 9.30 0.00 0.00 3.62
1476 1490 0.470766 CATCGGACCCGGGGAAATTA 59.529 55.000 27.92 5.09 40.25 1.40
1595 1609 9.367717 GTTAGTTGTAGAATATTACTCTCGTCG 57.632 37.037 0.00 0.00 0.00 5.12
1923 1947 9.109393 TGATGAATTAATAAAGACGGAAAGAGG 57.891 33.333 0.00 0.00 0.00 3.69
1929 1953 2.563039 AAGACGGAAAGAGGGGGATA 57.437 50.000 0.00 0.00 0.00 2.59
2459 5773 3.829026 GTCCAAGCAGAAGGAAAAGGATT 59.171 43.478 0.00 0.00 35.29 3.01
2460 5774 5.010282 GTCCAAGCAGAAGGAAAAGGATTA 58.990 41.667 0.00 0.00 35.29 1.75
2461 5775 5.476945 GTCCAAGCAGAAGGAAAAGGATTAA 59.523 40.000 0.00 0.00 35.29 1.40
2462 5776 6.153510 GTCCAAGCAGAAGGAAAAGGATTAAT 59.846 38.462 0.00 0.00 35.29 1.40
2463 5777 7.339466 GTCCAAGCAGAAGGAAAAGGATTAATA 59.661 37.037 0.00 0.00 35.29 0.98
2464 5778 7.557719 TCCAAGCAGAAGGAAAAGGATTAATAG 59.442 37.037 0.00 0.00 0.00 1.73
2465 5779 7.557719 CCAAGCAGAAGGAAAAGGATTAATAGA 59.442 37.037 0.00 0.00 0.00 1.98
2466 5780 9.129532 CAAGCAGAAGGAAAAGGATTAATAGAT 57.870 33.333 0.00 0.00 0.00 1.98
2467 5781 8.916628 AGCAGAAGGAAAAGGATTAATAGATC 57.083 34.615 0.00 0.00 0.00 2.75
2468 5782 8.497745 AGCAGAAGGAAAAGGATTAATAGATCA 58.502 33.333 0.00 0.00 0.00 2.92
2469 5783 9.294614 GCAGAAGGAAAAGGATTAATAGATCAT 57.705 33.333 0.00 0.00 0.00 2.45
2480 5794 9.317827 AGGATTAATAGATCATTTTGGAATGGG 57.682 33.333 0.00 0.00 42.36 4.00
2481 5795 9.312904 GGATTAATAGATCATTTTGGAATGGGA 57.687 33.333 0.00 0.00 42.36 4.37
2489 5803 9.471702 AGATCATTTTGGAATGGGATATACATC 57.528 33.333 0.00 0.00 42.36 3.06
2517 5831 9.689976 CATATACTGGATCAACTAAAGACTCTG 57.310 37.037 0.00 0.00 0.00 3.35
2518 5832 5.413309 ACTGGATCAACTAAAGACTCTGG 57.587 43.478 0.00 0.00 0.00 3.86
2519 5833 4.223923 ACTGGATCAACTAAAGACTCTGGG 59.776 45.833 0.00 0.00 0.00 4.45
2520 5834 3.055094 TGGATCAACTAAAGACTCTGGGC 60.055 47.826 0.00 0.00 0.00 5.36
2521 5835 3.198853 GGATCAACTAAAGACTCTGGGCT 59.801 47.826 0.00 0.00 0.00 5.19
2522 5836 4.323868 GGATCAACTAAAGACTCTGGGCTT 60.324 45.833 0.00 0.00 0.00 4.35
2523 5837 4.273148 TCAACTAAAGACTCTGGGCTTC 57.727 45.455 0.00 0.00 0.00 3.86
2524 5838 3.008049 TCAACTAAAGACTCTGGGCTTCC 59.992 47.826 0.00 0.00 0.00 3.46
2525 5839 2.621070 ACTAAAGACTCTGGGCTTCCA 58.379 47.619 0.00 0.00 39.08 3.53
2526 5840 3.185455 ACTAAAGACTCTGGGCTTCCAT 58.815 45.455 0.00 0.00 40.27 3.41
2527 5841 2.797177 AAAGACTCTGGGCTTCCATC 57.203 50.000 0.00 0.00 40.27 3.51
2528 5842 1.661463 AAGACTCTGGGCTTCCATCA 58.339 50.000 0.00 0.00 40.27 3.07
2529 5843 1.661463 AGACTCTGGGCTTCCATCAA 58.339 50.000 0.00 0.00 40.27 2.57
2530 5844 1.558756 AGACTCTGGGCTTCCATCAAG 59.441 52.381 0.00 0.00 40.27 3.02
2541 5855 4.471904 CTTCCATCAAGCCACTACTACA 57.528 45.455 0.00 0.00 0.00 2.74
2542 5856 5.028549 CTTCCATCAAGCCACTACTACAT 57.971 43.478 0.00 0.00 0.00 2.29
2543 5857 4.672587 TCCATCAAGCCACTACTACATC 57.327 45.455 0.00 0.00 0.00 3.06
2544 5858 3.068165 TCCATCAAGCCACTACTACATCG 59.932 47.826 0.00 0.00 0.00 3.84
2545 5859 3.068165 CCATCAAGCCACTACTACATCGA 59.932 47.826 0.00 0.00 0.00 3.59
2546 5860 4.262207 CCATCAAGCCACTACTACATCGAT 60.262 45.833 0.00 0.00 0.00 3.59
2547 5861 5.292765 CATCAAGCCACTACTACATCGATT 58.707 41.667 0.00 0.00 0.00 3.34
2548 5862 5.339008 TCAAGCCACTACTACATCGATTT 57.661 39.130 0.00 0.00 0.00 2.17
2549 5863 5.348986 TCAAGCCACTACTACATCGATTTC 58.651 41.667 0.00 0.00 0.00 2.17
2550 5864 3.966154 AGCCACTACTACATCGATTTCG 58.034 45.455 0.00 0.00 41.45 3.46
2551 5865 3.380637 AGCCACTACTACATCGATTTCGT 59.619 43.478 0.00 0.00 40.80 3.85
2552 5866 4.110482 GCCACTACTACATCGATTTCGTT 58.890 43.478 0.00 0.00 40.80 3.85
2553 5867 5.066893 AGCCACTACTACATCGATTTCGTTA 59.933 40.000 0.00 0.00 40.80 3.18
2554 5868 5.398711 GCCACTACTACATCGATTTCGTTAG 59.601 44.000 0.00 0.00 40.80 2.34
2555 5869 5.913514 CCACTACTACATCGATTTCGTTAGG 59.086 44.000 0.00 0.00 40.80 2.69
2556 5870 6.238566 CCACTACTACATCGATTTCGTTAGGA 60.239 42.308 0.00 0.00 40.80 2.94
2557 5871 7.191551 CACTACTACATCGATTTCGTTAGGAA 58.808 38.462 0.00 0.00 40.80 3.36
2558 5872 7.861372 CACTACTACATCGATTTCGTTAGGAAT 59.139 37.037 0.00 0.00 40.80 3.01
2559 5873 8.074972 ACTACTACATCGATTTCGTTAGGAATC 58.925 37.037 0.00 0.00 40.80 2.52
2560 5874 5.913514 ACTACATCGATTTCGTTAGGAATCG 59.086 40.000 13.88 13.88 40.80 3.34
2561 5875 4.928601 ACATCGATTTCGTTAGGAATCGA 58.071 39.130 21.87 21.87 42.78 3.59
2562 5876 4.976731 ACATCGATTTCGTTAGGAATCGAG 59.023 41.667 23.25 18.20 42.35 4.04
2563 5877 4.888038 TCGATTTCGTTAGGAATCGAGA 57.112 40.909 17.51 0.96 38.52 4.04
2564 5878 5.239359 TCGATTTCGTTAGGAATCGAGAA 57.761 39.130 17.51 0.34 38.52 2.87
2565 5879 5.828747 TCGATTTCGTTAGGAATCGAGAAT 58.171 37.500 17.51 2.44 38.52 2.40
2566 5880 5.913514 TCGATTTCGTTAGGAATCGAGAATC 59.086 40.000 17.51 8.49 38.52 2.52
2567 5881 5.915758 CGATTTCGTTAGGAATCGAGAATCT 59.084 40.000 14.67 0.00 37.61 2.40
2568 5882 6.418226 CGATTTCGTTAGGAATCGAGAATCTT 59.582 38.462 14.67 0.00 37.61 2.40
2569 5883 7.043325 CGATTTCGTTAGGAATCGAGAATCTTT 60.043 37.037 14.67 0.00 37.61 2.52
2570 5884 7.900782 TTTCGTTAGGAATCGAGAATCTTTT 57.099 32.000 0.00 0.00 37.38 2.27
2571 5885 8.991243 TTTCGTTAGGAATCGAGAATCTTTTA 57.009 30.769 0.00 0.00 37.38 1.52
2572 5886 8.991243 TTCGTTAGGAATCGAGAATCTTTTAA 57.009 30.769 0.00 0.00 37.38 1.52
2573 5887 8.403606 TCGTTAGGAATCGAGAATCTTTTAAC 57.596 34.615 0.00 1.22 0.00 2.01
2574 5888 8.030692 TCGTTAGGAATCGAGAATCTTTTAACA 58.969 33.333 0.00 0.00 0.00 2.41
2575 5889 8.653338 CGTTAGGAATCGAGAATCTTTTAACAA 58.347 33.333 0.00 0.00 0.00 2.83
2579 5893 9.110502 AGGAATCGAGAATCTTTTAACAATACC 57.889 33.333 0.00 0.00 0.00 2.73
2580 5894 8.343366 GGAATCGAGAATCTTTTAACAATACCC 58.657 37.037 0.00 0.00 0.00 3.69
2581 5895 9.110502 GAATCGAGAATCTTTTAACAATACCCT 57.889 33.333 0.00 0.00 0.00 4.34
2582 5896 8.664211 ATCGAGAATCTTTTAACAATACCCTC 57.336 34.615 0.00 0.00 0.00 4.30
2583 5897 7.848128 TCGAGAATCTTTTAACAATACCCTCT 58.152 34.615 0.00 0.00 0.00 3.69
2584 5898 8.974238 TCGAGAATCTTTTAACAATACCCTCTA 58.026 33.333 0.00 0.00 0.00 2.43
2585 5899 9.595823 CGAGAATCTTTTAACAATACCCTCTAA 57.404 33.333 0.00 0.00 0.00 2.10
2587 5901 9.907229 AGAATCTTTTAACAATACCCTCTAAGG 57.093 33.333 0.00 0.00 34.30 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 1.374505 GCGCCATGCCAAATGTGTT 60.375 52.632 0.00 0.00 37.76 3.32
113 114 2.426024 CACTTGAGCATCCAAATCTGGG 59.574 50.000 0.00 0.00 43.71 4.45
302 303 8.780846 ATTACTTCCACACGTATTCATTTGTA 57.219 30.769 0.00 0.00 0.00 2.41
377 378 5.554070 TCCCTAAAGTCGAAACTAAAAGGG 58.446 41.667 11.07 11.07 43.71 3.95
405 407 7.362142 GGTTCTTGGAAGAAGATAGCGAAAAAT 60.362 37.037 1.96 0.00 45.01 1.82
519 521 3.549299 TCGAAGAACACGGAGACTAAC 57.451 47.619 0.00 0.00 0.00 2.34
693 695 9.524106 CTATTCCGTTGTAGATGTAAATACACA 57.476 33.333 0.00 0.00 39.30 3.72
705 709 8.959548 TGACTTTGTATACTATTCCGTTGTAGA 58.040 33.333 4.17 0.00 0.00 2.59
805 809 2.736144 TCAGTAAACTACCTGCACCG 57.264 50.000 0.00 0.00 0.00 4.94
1231 1245 4.650972 ATTGTAGTAAAACCTGGCCTGA 57.349 40.909 11.88 0.00 0.00 3.86
1409 1423 8.477419 ACCTTTTGATCTTTGGTTATCTTTCA 57.523 30.769 0.00 0.00 0.00 2.69
1912 1936 0.388294 CGTATCCCCCTCTTTCCGTC 59.612 60.000 0.00 0.00 0.00 4.79
1923 1947 0.468029 TACCGAGGGTTCGTATCCCC 60.468 60.000 8.25 0.00 45.64 4.81
1929 1953 2.618442 TTTGTTTACCGAGGGTTCGT 57.382 45.000 0.00 0.00 45.28 3.85
2110 2134 5.179452 TCCTTCCACTTAGATCAAAAGGG 57.821 43.478 11.28 7.67 34.04 3.95
2255 2285 5.523438 TGCAAACGGAATTCTAAGGTTTT 57.477 34.783 5.23 0.00 0.00 2.43
2434 5748 1.981256 TTTCCTTCTGCTTGGACACC 58.019 50.000 0.00 0.00 31.24 4.16
2463 5777 9.471702 GATGTATATCCCATTCCAAAATGATCT 57.528 33.333 0.00 0.00 44.25 2.75
2464 5778 8.689972 GGATGTATATCCCATTCCAAAATGATC 58.310 37.037 7.26 0.00 46.03 2.92
2465 5779 8.599624 GGATGTATATCCCATTCCAAAATGAT 57.400 34.615 7.26 0.00 46.03 2.45
2491 5805 9.689976 CAGAGTCTTTAGTTGATCCAGTATATG 57.310 37.037 0.00 0.00 0.00 1.78
2492 5806 8.865090 CCAGAGTCTTTAGTTGATCCAGTATAT 58.135 37.037 0.00 0.00 0.00 0.86
2493 5807 7.287927 CCCAGAGTCTTTAGTTGATCCAGTATA 59.712 40.741 0.00 0.00 0.00 1.47
2494 5808 6.098982 CCCAGAGTCTTTAGTTGATCCAGTAT 59.901 42.308 0.00 0.00 0.00 2.12
2495 5809 5.422331 CCCAGAGTCTTTAGTTGATCCAGTA 59.578 44.000 0.00 0.00 0.00 2.74
2496 5810 4.223923 CCCAGAGTCTTTAGTTGATCCAGT 59.776 45.833 0.00 0.00 0.00 4.00
2497 5811 4.764172 CCCAGAGTCTTTAGTTGATCCAG 58.236 47.826 0.00 0.00 0.00 3.86
2498 5812 3.055094 GCCCAGAGTCTTTAGTTGATCCA 60.055 47.826 0.00 0.00 0.00 3.41
2499 5813 3.198853 AGCCCAGAGTCTTTAGTTGATCC 59.801 47.826 0.00 0.00 0.00 3.36
2500 5814 4.479786 AGCCCAGAGTCTTTAGTTGATC 57.520 45.455 0.00 0.00 0.00 2.92
2501 5815 4.323868 GGAAGCCCAGAGTCTTTAGTTGAT 60.324 45.833 0.00 0.00 0.00 2.57
2502 5816 3.008049 GGAAGCCCAGAGTCTTTAGTTGA 59.992 47.826 0.00 0.00 0.00 3.18
2503 5817 3.244561 TGGAAGCCCAGAGTCTTTAGTTG 60.245 47.826 0.00 0.00 37.58 3.16
2504 5818 2.979678 TGGAAGCCCAGAGTCTTTAGTT 59.020 45.455 0.00 0.00 37.58 2.24
2505 5819 2.621070 TGGAAGCCCAGAGTCTTTAGT 58.379 47.619 0.00 0.00 37.58 2.24
2520 5834 4.471904 TGTAGTAGTGGCTTGATGGAAG 57.528 45.455 0.00 0.00 34.41 3.46
2521 5835 4.441495 CGATGTAGTAGTGGCTTGATGGAA 60.441 45.833 0.00 0.00 0.00 3.53
2522 5836 3.068165 CGATGTAGTAGTGGCTTGATGGA 59.932 47.826 0.00 0.00 0.00 3.41
2523 5837 3.068165 TCGATGTAGTAGTGGCTTGATGG 59.932 47.826 0.00 0.00 0.00 3.51
2524 5838 4.307443 TCGATGTAGTAGTGGCTTGATG 57.693 45.455 0.00 0.00 0.00 3.07
2525 5839 5.537300 AATCGATGTAGTAGTGGCTTGAT 57.463 39.130 0.00 0.00 0.00 2.57
2526 5840 5.339008 AAATCGATGTAGTAGTGGCTTGA 57.661 39.130 0.00 0.00 0.00 3.02
2527 5841 4.207224 CGAAATCGATGTAGTAGTGGCTTG 59.793 45.833 0.00 0.00 43.02 4.01
2528 5842 4.142227 ACGAAATCGATGTAGTAGTGGCTT 60.142 41.667 10.16 0.00 43.02 4.35
2529 5843 3.380637 ACGAAATCGATGTAGTAGTGGCT 59.619 43.478 10.16 0.00 43.02 4.75
2530 5844 3.703420 ACGAAATCGATGTAGTAGTGGC 58.297 45.455 10.16 0.00 43.02 5.01
2531 5845 5.913514 CCTAACGAAATCGATGTAGTAGTGG 59.086 44.000 10.16 1.89 43.02 4.00
2532 5846 6.722301 TCCTAACGAAATCGATGTAGTAGTG 58.278 40.000 10.16 0.00 43.02 2.74
2533 5847 6.932356 TCCTAACGAAATCGATGTAGTAGT 57.068 37.500 10.16 0.00 43.02 2.73
2534 5848 7.268659 CGATTCCTAACGAAATCGATGTAGTAG 59.731 40.741 10.16 1.27 43.02 2.57
2535 5849 7.041848 TCGATTCCTAACGAAATCGATGTAGTA 60.042 37.037 14.17 0.00 43.02 1.82
2536 5850 5.913514 CGATTCCTAACGAAATCGATGTAGT 59.086 40.000 10.16 0.00 43.02 2.73
2537 5851 6.140786 TCGATTCCTAACGAAATCGATGTAG 58.859 40.000 14.17 0.00 43.02 2.74
2538 5852 6.017687 TCTCGATTCCTAACGAAATCGATGTA 60.018 38.462 17.35 6.84 43.02 2.29
2539 5853 4.928601 TCGATTCCTAACGAAATCGATGT 58.071 39.130 14.17 0.00 43.02 3.06
2540 5854 5.212934 TCTCGATTCCTAACGAAATCGATG 58.787 41.667 17.35 12.61 43.02 3.84
2541 5855 5.434352 TCTCGATTCCTAACGAAATCGAT 57.566 39.130 17.35 0.00 43.02 3.59
2542 5856 4.888038 TCTCGATTCCTAACGAAATCGA 57.112 40.909 16.44 16.44 43.02 3.59
2543 5857 5.915758 AGATTCTCGATTCCTAACGAAATCG 59.084 40.000 10.36 10.36 46.33 3.34
2544 5858 7.701809 AAGATTCTCGATTCCTAACGAAATC 57.298 36.000 0.57 0.57 38.05 2.17
2545 5859 8.494016 AAAAGATTCTCGATTCCTAACGAAAT 57.506 30.769 0.00 0.00 38.05 2.17
2546 5860 7.900782 AAAAGATTCTCGATTCCTAACGAAA 57.099 32.000 0.00 0.00 38.05 3.46
2547 5861 8.866956 GTTAAAAGATTCTCGATTCCTAACGAA 58.133 33.333 0.00 0.00 38.05 3.85
2548 5862 8.030692 TGTTAAAAGATTCTCGATTCCTAACGA 58.969 33.333 0.00 0.00 37.03 3.85
2549 5863 8.181487 TGTTAAAAGATTCTCGATTCCTAACG 57.819 34.615 0.00 0.00 0.00 3.18
2553 5867 9.110502 GGTATTGTTAAAAGATTCTCGATTCCT 57.889 33.333 0.00 0.00 0.00 3.36
2554 5868 8.343366 GGGTATTGTTAAAAGATTCTCGATTCC 58.657 37.037 0.00 0.00 0.00 3.01
2555 5869 9.110502 AGGGTATTGTTAAAAGATTCTCGATTC 57.889 33.333 0.00 0.00 0.00 2.52
2556 5870 9.110502 GAGGGTATTGTTAAAAGATTCTCGATT 57.889 33.333 0.00 0.00 0.00 3.34
2557 5871 8.487028 AGAGGGTATTGTTAAAAGATTCTCGAT 58.513 33.333 0.00 0.00 0.00 3.59
2558 5872 7.848128 AGAGGGTATTGTTAAAAGATTCTCGA 58.152 34.615 0.00 0.00 0.00 4.04
2559 5873 9.595823 TTAGAGGGTATTGTTAAAAGATTCTCG 57.404 33.333 0.00 0.00 0.00 4.04
2561 5875 9.907229 CCTTAGAGGGTATTGTTAAAAGATTCT 57.093 33.333 0.00 0.00 0.00 2.40
2579 5893 3.654273 TGGACTAACCATCCCTTAGAGG 58.346 50.000 0.00 0.00 44.64 3.69


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

AutoCloner maintained by Alex Coulton.