Multiple sequence alignment - TraesCS2D01G406000

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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 TraesCS2D01G406000 chr2D 100.000 4406 0 0 1 4406 521409786 521414191 0.000000e+00 8137.0
1 TraesCS2D01G406000 chr2D 91.788 755 44 6 3653 4399 135510918 135510174 0.000000e+00 1035.0
2 TraesCS2D01G406000 chr2D 89.189 629 58 6 3775 4399 94717614 94718236 0.000000e+00 776.0
3 TraesCS2D01G406000 chr2D 70.495 444 122 9 1493 1933 521587751 521587314 7.850000e-13 86.1
4 TraesCS2D01G406000 chr2A 96.292 3182 107 10 479 3653 666293526 666290349 0.000000e+00 5212.0
5 TraesCS2D01G406000 chr2A 89.389 622 62 3 3775 4396 653863481 653862864 0.000000e+00 780.0
6 TraesCS2D01G406000 chr2A 86.542 483 49 8 1 476 666294069 666293596 6.530000e-143 518.0
7 TraesCS2D01G406000 chr2B 96.160 3177 104 10 479 3653 614399460 614396300 0.000000e+00 5175.0
8 TraesCS2D01G406000 chr2B 94.589 1497 66 7 479 1974 614504418 614502936 0.000000e+00 2302.0
9 TraesCS2D01G406000 chr2B 97.502 1121 25 2 2534 3653 614502852 614501734 0.000000e+00 1912.0
10 TraesCS2D01G406000 chr2B 92.905 451 30 2 1 450 614504938 614504489 0.000000e+00 654.0
11 TraesCS2D01G406000 chr2B 91.667 372 29 2 80 450 614399901 614399531 8.450000e-142 514.0
12 TraesCS2D01G406000 chr2B 77.622 143 32 0 1497 1639 613902327 613902469 2.180000e-13 87.9
13 TraesCS2D01G406000 chr2B 76.074 163 39 0 1487 1649 613205851 613206013 7.850000e-13 86.1
14 TraesCS2D01G406000 chr7A 90.924 617 54 2 3780 4396 602042442 602041828 0.000000e+00 828.0
15 TraesCS2D01G406000 chr7A 80.702 114 20 2 2676 2788 556299719 556299831 2.180000e-13 87.9
16 TraesCS2D01G406000 chr3A 90.096 626 59 3 3775 4399 579648251 579647628 0.000000e+00 809.0
17 TraesCS2D01G406000 chr6D 89.748 634 60 4 3775 4406 372351589 372350959 0.000000e+00 806.0
18 TraesCS2D01G406000 chr6D 77.686 968 189 19 1126 2081 319053022 319052070 2.300000e-157 566.0
19 TraesCS2D01G406000 chr6D 84.058 138 14 7 3647 3780 346979980 346979847 4.630000e-25 126.0
20 TraesCS2D01G406000 chr1B 89.727 623 60 4 3775 4397 5035591 5034973 0.000000e+00 793.0
21 TraesCS2D01G406000 chr7D 89.694 621 59 3 3775 4395 638315056 638315671 0.000000e+00 787.0
22 TraesCS2D01G406000 chr7D 80.702 114 20 2 2676 2788 489114593 489114705 2.180000e-13 87.9
23 TraesCS2D01G406000 chr1D 88.784 633 64 7 3775 4406 430064452 430063826 0.000000e+00 769.0
24 TraesCS2D01G406000 chr1D 87.302 126 12 3 3652 3775 386708642 386708765 1.650000e-29 141.0
25 TraesCS2D01G406000 chr6A 78.099 968 185 19 1126 2081 457020067 457019115 4.910000e-164 588.0
26 TraesCS2D01G406000 chr6B 77.446 971 189 20 1126 2081 504158251 504159206 1.790000e-153 553.0
27 TraesCS2D01G406000 chr1A 91.200 125 11 0 3653 3777 593039121 593038997 2.110000e-38 171.0
28 TraesCS2D01G406000 chr3D 85.496 131 13 4 3651 3779 172019136 172019010 9.940000e-27 132.0
29 TraesCS2D01G406000 chr3D 85.271 129 18 1 3652 3780 604299476 604299349 9.940000e-27 132.0
30 TraesCS2D01G406000 chr3D 81.046 153 27 2 311 461 380566273 380566425 2.150000e-23 121.0
31 TraesCS2D01G406000 chr3D 82.857 140 17 6 3643 3780 430314232 430314098 7.740000e-23 119.0
32 TraesCS2D01G406000 chr3D 80.392 153 28 2 311 461 380584843 380584995 1.000000e-21 115.0
33 TraesCS2D01G406000 chr3B 81.410 156 27 2 308 461 495812492 495812647 4.630000e-25 126.0
34 TraesCS2D01G406000 chr5B 84.375 128 16 2 3653 3779 250538971 250538847 5.980000e-24 122.0
35 TraesCS2D01G406000 chr7B 83.846 130 16 3 3652 3779 604945876 604945750 7.740000e-23 119.0
36 TraesCS2D01G406000 chr7B 80.702 114 20 2 2676 2788 517394238 517394350 2.180000e-13 87.9
37 TraesCS2D01G406000 chrUn 83.206 131 18 3 3652 3780 300542900 300543028 2.780000e-22 117.0


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 TraesCS2D01G406000 chr2D 521409786 521414191 4405 False 8137.000000 8137 100.000000 1 4406 1 chr2D.!!$F2 4405
1 TraesCS2D01G406000 chr2D 135510174 135510918 744 True 1035.000000 1035 91.788000 3653 4399 1 chr2D.!!$R1 746
2 TraesCS2D01G406000 chr2D 94717614 94718236 622 False 776.000000 776 89.189000 3775 4399 1 chr2D.!!$F1 624
3 TraesCS2D01G406000 chr2A 666290349 666294069 3720 True 2865.000000 5212 91.417000 1 3653 2 chr2A.!!$R2 3652
4 TraesCS2D01G406000 chr2A 653862864 653863481 617 True 780.000000 780 89.389000 3775 4396 1 chr2A.!!$R1 621
5 TraesCS2D01G406000 chr2B 614396300 614399901 3601 True 2844.500000 5175 93.913500 80 3653 2 chr2B.!!$R1 3573
6 TraesCS2D01G406000 chr2B 614501734 614504938 3204 True 1622.666667 2302 94.998667 1 3653 3 chr2B.!!$R2 3652
7 TraesCS2D01G406000 chr7A 602041828 602042442 614 True 828.000000 828 90.924000 3780 4396 1 chr7A.!!$R1 616
8 TraesCS2D01G406000 chr3A 579647628 579648251 623 True 809.000000 809 90.096000 3775 4399 1 chr3A.!!$R1 624
9 TraesCS2D01G406000 chr6D 372350959 372351589 630 True 806.000000 806 89.748000 3775 4406 1 chr6D.!!$R3 631
10 TraesCS2D01G406000 chr6D 319052070 319053022 952 True 566.000000 566 77.686000 1126 2081 1 chr6D.!!$R1 955
11 TraesCS2D01G406000 chr1B 5034973 5035591 618 True 793.000000 793 89.727000 3775 4397 1 chr1B.!!$R1 622
12 TraesCS2D01G406000 chr7D 638315056 638315671 615 False 787.000000 787 89.694000 3775 4395 1 chr7D.!!$F2 620
13 TraesCS2D01G406000 chr1D 430063826 430064452 626 True 769.000000 769 88.784000 3775 4406 1 chr1D.!!$R1 631
14 TraesCS2D01G406000 chr6A 457019115 457020067 952 True 588.000000 588 78.099000 1126 2081 1 chr6A.!!$R1 955
15 TraesCS2D01G406000 chr6B 504158251 504159206 955 False 553.000000 553 77.446000 1126 2081 1 chr6B.!!$F1 955

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
535 609 0.678048 GCTTTCTGATGACCGGCCTT 60.678 55.000 0.00 0.0 0.00 4.35 F
656 732 0.946221 CCTCTGTCTTGCACGGACAC 60.946 60.000 15.17 0.0 38.57 3.67 F
768 846 1.144708 TCATTTCAAGGCACCTGGTCA 59.855 47.619 0.00 0.0 0.00 4.02 F
860 939 1.345415 GCCTCCCCAATTATTGCATGG 59.655 52.381 0.00 0.0 0.00 3.66 F
1013 1092 1.957877 GACCCAAATGGACAACCGAAA 59.042 47.619 0.00 0.0 39.42 3.46 F
2790 2872 2.125912 GCGCTGATGACGACCACT 60.126 61.111 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2241 0.886563 CCCGTAGTCCTTGACTTCGT 59.113 55.000 17.78 0.00 46.57 3.85 R
2655 2737 1.084370 CGTCGAACTTGGGCATCTCC 61.084 60.000 0.00 0.00 0.00 3.71 R
2715 2797 2.125872 TTCATTAGCGCGGCGACA 60.126 55.556 28.54 9.62 0.00 4.35 R
2790 2872 3.256383 TCTTCTCGTTATCGGTGGTTTCA 59.744 43.478 0.00 0.00 37.69 2.69 R
3011 3093 3.857052 TCGGCGATCTTTGTTATCTTGT 58.143 40.909 4.99 0.00 0.00 3.16 R
3659 3743 0.102663 TTGCAACGCATGGGCATATG 59.897 50.000 10.10 0.00 38.76 1.78 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
27 28 6.902771 ACTAGCACTATACATCTAGGTTGG 57.097 41.667 0.00 0.00 34.39 3.77
50 51 3.261580 CATACACCTGCACGAATCTCAA 58.738 45.455 0.00 0.00 0.00 3.02
114 115 4.090354 CCATGTAAAATGACTTTTGCGCTG 59.910 41.667 9.73 0.00 39.11 5.18
322 328 3.697166 ACCTGAAACCTTTTCACTGTGT 58.303 40.909 7.79 0.00 0.00 3.72
378 385 5.029807 TCGCATGTATAATGGAGGTGAAA 57.970 39.130 0.00 0.00 0.00 2.69
380 387 6.764379 TCGCATGTATAATGGAGGTGAAATA 58.236 36.000 0.00 0.00 0.00 1.40
407 414 5.163602 TGGAATTGGTGACACTTTGTAACAC 60.164 40.000 5.39 0.00 42.67 3.32
411 418 3.192466 GGTGACACTTTGTAACACTCGT 58.808 45.455 5.39 0.00 33.26 4.18
415 422 3.852286 ACACTTTGTAACACTCGTCACA 58.148 40.909 0.00 0.00 0.00 3.58
421 428 5.651172 TTGTAACACTCGTCACAATTCTG 57.349 39.130 0.00 0.00 0.00 3.02
444 451 4.141482 GGTTCAATTGTGGCTCCTATCCTA 60.141 45.833 5.13 0.00 0.00 2.94
476 483 4.006319 GGAGAGCATGCTAGTGTTTTCTT 58.994 43.478 22.74 0.00 0.00 2.52
502 576 4.160439 TGAATGTGACCGAGAGCTATCTTT 59.840 41.667 6.80 0.00 35.30 2.52
515 589 4.786425 AGCTATCTTTGATGAAACTCCCC 58.214 43.478 0.00 0.00 0.00 4.81
523 597 1.740025 GATGAAACTCCCCGCTTTCTG 59.260 52.381 0.00 0.00 0.00 3.02
535 609 0.678048 GCTTTCTGATGACCGGCCTT 60.678 55.000 0.00 0.00 0.00 4.35
536 610 1.373570 CTTTCTGATGACCGGCCTTC 58.626 55.000 0.00 0.00 0.00 3.46
541 615 1.519455 GATGACCGGCCTTCTGACG 60.519 63.158 0.00 0.00 0.00 4.35
564 638 9.110502 GACGGATTGTCCTAAGAATTCTTTTAT 57.889 33.333 25.02 4.29 42.04 1.40
588 662 7.316544 TCTGAATAAAGCTTTCCGATTTACC 57.683 36.000 16.57 0.00 36.42 2.85
589 663 6.317893 TCTGAATAAAGCTTTCCGATTTACCC 59.682 38.462 16.57 0.00 36.42 3.69
591 665 2.773993 AAGCTTTCCGATTTACCCGA 57.226 45.000 0.00 0.00 0.00 5.14
615 691 5.573337 AAAAGAAAGATGATGGTGCTAGC 57.427 39.130 8.10 8.10 0.00 3.42
656 732 0.946221 CCTCTGTCTTGCACGGACAC 60.946 60.000 15.17 0.00 38.57 3.67
667 743 1.948104 CACGGACACCAAAACAGAGA 58.052 50.000 0.00 0.00 0.00 3.10
668 744 2.494059 CACGGACACCAAAACAGAGAT 58.506 47.619 0.00 0.00 0.00 2.75
761 837 3.648339 TTCAGCTTCATTTCAAGGCAC 57.352 42.857 0.00 0.00 0.00 5.01
764 840 1.891150 AGCTTCATTTCAAGGCACCTG 59.109 47.619 0.00 0.00 0.00 4.00
768 846 1.144708 TCATTTCAAGGCACCTGGTCA 59.855 47.619 0.00 0.00 0.00 4.02
784 862 4.164988 CCTGGTCACCTTCATTTCCTCTAT 59.835 45.833 0.00 0.00 0.00 1.98
818 897 3.928992 TGAAATGAAAGCGCAGAGTCTAG 59.071 43.478 11.47 0.00 0.00 2.43
860 939 1.345415 GCCTCCCCAATTATTGCATGG 59.655 52.381 0.00 0.00 0.00 3.66
925 1004 3.385111 AGGCTACGTTCCATCTTTAGAGG 59.615 47.826 0.00 0.00 0.00 3.69
955 1034 2.420967 GCCAACTCCCCATATGTAACGT 60.421 50.000 1.24 0.00 0.00 3.99
962 1041 3.642848 TCCCCATATGTAACGTTACCTCC 59.357 47.826 30.20 10.79 32.72 4.30
1008 1087 4.010349 CTCCTTAGACCCAAATGGACAAC 58.990 47.826 0.00 0.00 37.39 3.32
1013 1092 1.957877 GACCCAAATGGACAACCGAAA 59.042 47.619 0.00 0.00 39.42 3.46
2037 2119 2.828549 GGCAACATCGGCCCGAAT 60.829 61.111 11.19 0.00 45.87 3.34
2288 2370 3.434319 CATTTGCGAGGCTGGCGT 61.434 61.111 16.81 2.63 0.00 5.68
2376 2458 4.754667 GAGGTGTTCGGCCCGGTC 62.755 72.222 1.90 0.00 0.00 4.79
2571 2653 2.830370 CTGCAAAGCCGGGGGATC 60.830 66.667 2.18 0.00 0.00 3.36
2790 2872 2.125912 GCGCTGATGACGACCACT 60.126 61.111 0.00 0.00 0.00 4.00
3597 3680 5.067023 GGATCACTTTGCCCTCAATTAGAAG 59.933 44.000 0.00 0.00 31.33 2.85
3632 3716 8.999431 TGCTAATTCTAGTTTCTTTGAAATCGT 58.001 29.630 0.00 0.00 0.00 3.73
3659 3743 3.491792 GCCTCATGAGTTCCTACTAGCAC 60.492 52.174 21.11 0.00 33.84 4.40
3662 3746 5.536538 CCTCATGAGTTCCTACTAGCACATA 59.463 44.000 21.11 0.00 33.84 2.29
3668 3752 6.967896 GAGTTCCTACTAGCACATATGCCCA 61.968 48.000 1.58 0.00 43.52 5.36
3709 3793 9.075678 AGAGATATTATTTTGAGAAGCAATGGG 57.924 33.333 0.00 0.00 36.15 4.00
3731 3815 5.121811 GGAGAGATAATTGATGTGTGCACT 58.878 41.667 19.41 0.00 0.00 4.40
3738 3822 8.575589 AGATAATTGATGTGTGCACTAAAAACA 58.424 29.630 19.41 13.78 0.00 2.83
3747 3831 2.031560 TGCACTAAAAACAGTCTGCACG 59.968 45.455 0.00 0.00 0.00 5.34
3844 3930 1.375523 CCTTTGGGTTCGTCCTCGG 60.376 63.158 0.30 0.00 37.69 4.63
3884 3970 1.851021 CTCATTTGGTGGTTGCGCGA 61.851 55.000 12.10 0.00 0.00 5.87
3925 4013 1.403679 CTTCGCCACTCTCTCCTACTG 59.596 57.143 0.00 0.00 0.00 2.74
4009 4097 2.754552 GCATAACCAGGCAGTCATTTCA 59.245 45.455 0.00 0.00 0.00 2.69
4018 4106 5.128205 CAGGCAGTCATTTCATTATCAGGA 58.872 41.667 0.00 0.00 0.00 3.86
4168 4264 6.917477 TCTTTTATCGTCAAATAATGCATGGC 59.083 34.615 0.00 0.00 0.00 4.40
4229 4325 2.757868 CACCAAAAGGACCTGTGTTTGA 59.242 45.455 15.78 0.00 33.70 2.69
4375 4473 3.245284 CGTTTAAGGACATACCGCATCAG 59.755 47.826 0.00 0.00 44.74 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.657840 GATTCGTGCAGGTGTATGGC 59.342 55.000 6.26 0.00 0.00 4.40
50 51 4.400884 ACATCTGAGAGCACTCGTTTCTAT 59.599 41.667 6.67 0.00 45.25 1.98
92 93 4.090354 CCAGCGCAAAAGTCATTTTACATG 59.910 41.667 11.47 0.00 36.47 3.21
378 385 4.657814 AAGTGTCACCAATTCCAGGTAT 57.342 40.909 0.00 0.00 37.23 2.73
380 387 2.958355 CAAAGTGTCACCAATTCCAGGT 59.042 45.455 0.00 0.00 40.85 4.00
383 390 4.950475 TGTTACAAAGTGTCACCAATTCCA 59.050 37.500 0.00 0.00 0.00 3.53
387 394 4.272504 CGAGTGTTACAAAGTGTCACCAAT 59.727 41.667 0.00 0.00 0.00 3.16
392 399 3.861113 GTGACGAGTGTTACAAAGTGTCA 59.139 43.478 6.80 6.80 34.88 3.58
407 414 5.149273 CAATTGAACCAGAATTGTGACGAG 58.851 41.667 3.74 0.00 36.47 4.18
415 422 3.259123 GGAGCCACAATTGAACCAGAATT 59.741 43.478 13.59 0.00 0.00 2.17
421 428 2.952310 GGATAGGAGCCACAATTGAACC 59.048 50.000 13.59 7.59 0.00 3.62
444 451 7.016072 ACACTAGCATGCTCTCCTATTTCTAAT 59.984 37.037 26.57 0.00 0.00 1.73
461 468 8.196771 TCACATTCAAAAAGAAAACACTAGCAT 58.803 29.630 0.00 0.00 40.22 3.79
476 483 3.126001 AGCTCTCGGTCACATTCAAAA 57.874 42.857 0.00 0.00 0.00 2.44
502 576 1.351017 AGAAAGCGGGGAGTTTCATCA 59.649 47.619 0.00 0.00 35.49 3.07
515 589 2.464459 GGCCGGTCATCAGAAAGCG 61.464 63.158 0.00 1.75 36.23 4.68
523 597 1.519455 CGTCAGAAGGCCGGTCATC 60.519 63.158 9.71 5.81 0.00 2.92
535 609 6.070767 AAGAATTCTTAGGACAATCCGTCAGA 60.071 38.462 19.17 0.00 42.75 3.27
536 610 6.109359 AAGAATTCTTAGGACAATCCGTCAG 58.891 40.000 19.17 0.00 42.75 3.51
557 631 8.786826 TCGGAAAGCTTTATTCAGATAAAAGA 57.213 30.769 12.68 0.00 37.30 2.52
564 638 6.317893 GGGTAAATCGGAAAGCTTTATTCAGA 59.682 38.462 12.68 6.81 35.88 3.27
571 645 3.062122 TCGGGTAAATCGGAAAGCTTT 57.938 42.857 12.53 12.53 0.00 3.51
615 691 7.555554 AGAGGAAATCAAAACTAGATCACATGG 59.444 37.037 0.00 0.00 0.00 3.66
656 732 4.944962 TGCGTTGATATCTCTGTTTTGG 57.055 40.909 3.98 0.00 0.00 3.28
699 775 3.992999 TCCCCATGATTTGGCTAAATGT 58.007 40.909 13.28 0.00 44.97 2.71
761 837 2.307098 AGAGGAAATGAAGGTGACCAGG 59.693 50.000 3.63 0.00 0.00 4.45
764 840 7.125792 TCTTATAGAGGAAATGAAGGTGACC 57.874 40.000 0.00 0.00 0.00 4.02
768 846 7.558081 GGCTTTTCTTATAGAGGAAATGAAGGT 59.442 37.037 10.71 0.00 32.40 3.50
784 862 5.564651 CGCTTTCATTTCAGGGCTTTTCTTA 60.565 40.000 0.00 0.00 0.00 2.10
818 897 2.533266 TGCTCTGACCAGAAGTTCAC 57.467 50.000 5.50 0.00 36.94 3.18
860 939 7.880105 AGATGGCTTAATAAAGATAGCAAAGC 58.120 34.615 0.00 0.00 37.67 3.51
925 1004 0.606673 GGGGAGTTGGCTCTTGTGAC 60.607 60.000 0.00 0.00 41.38 3.67
955 1034 1.229400 AGGGAGTTGCGGGAGGTAA 60.229 57.895 0.00 0.00 0.00 2.85
962 1041 1.333636 ATCAGAGGAGGGAGTTGCGG 61.334 60.000 0.00 0.00 0.00 5.69
1008 1087 3.100545 CCATCCTCCATGGTTTCGG 57.899 57.895 12.58 8.56 46.72 4.30
1056 1135 0.907230 ACAGGAAGAGGAGGGCAGAC 60.907 60.000 0.00 0.00 0.00 3.51
1059 1138 2.596851 GCACAGGAAGAGGAGGGCA 61.597 63.158 0.00 0.00 0.00 5.36
1061 1140 0.970937 TACGCACAGGAAGAGGAGGG 60.971 60.000 0.00 0.00 0.00 4.30
1117 1196 4.088762 GTGCACGCCGGTGTCATG 62.089 66.667 20.00 8.87 46.13 3.07
1223 1302 3.490759 CCATGTCGCACACCTCGC 61.491 66.667 0.00 0.00 0.00 5.03
1539 1621 4.189188 CCCTCGCCGTCGAACGAT 62.189 66.667 10.12 0.00 46.05 3.73
2159 2241 0.886563 CCCGTAGTCCTTGACTTCGT 59.113 55.000 17.78 0.00 46.57 3.85
2288 2370 1.462432 TTGGTGGTGCTAGGGGTGA 60.462 57.895 0.00 0.00 0.00 4.02
2376 2458 3.170672 TGGGGCCTCGGGATGATG 61.171 66.667 0.84 0.00 0.00 3.07
2571 2653 2.487934 CCGATGATGTCAGGCTTTAGG 58.512 52.381 0.00 0.00 0.00 2.69
2634 2716 2.759973 TTGGGCGGCAACACCAAA 60.760 55.556 12.47 0.00 46.55 3.28
2655 2737 1.084370 CGTCGAACTTGGGCATCTCC 61.084 60.000 0.00 0.00 0.00 3.71
2715 2797 2.125872 TTCATTAGCGCGGCGACA 60.126 55.556 28.54 9.62 0.00 4.35
2790 2872 3.256383 TCTTCTCGTTATCGGTGGTTTCA 59.744 43.478 0.00 0.00 37.69 2.69
3011 3093 3.857052 TCGGCGATCTTTGTTATCTTGT 58.143 40.909 4.99 0.00 0.00 3.16
3180 3262 3.916392 CTCCAGCTTCGTCGGCGTT 62.916 63.158 10.18 0.00 39.49 4.84
3597 3680 8.512966 AGAAACTAGAATTAGCAGGAAATTCC 57.487 34.615 3.29 3.29 41.99 3.01
3624 3708 6.101650 ACTCATGAGGCATATACGATTTCA 57.898 37.500 26.08 0.00 0.00 2.69
3632 3716 6.378564 GCTAGTAGGAACTCATGAGGCATATA 59.621 42.308 26.08 9.72 41.75 0.86
3633 3717 5.186797 GCTAGTAGGAACTCATGAGGCATAT 59.813 44.000 26.08 10.65 41.75 1.78
3659 3743 0.102663 TTGCAACGCATGGGCATATG 59.897 50.000 10.10 0.00 38.76 1.78
3662 3746 2.262292 GTTGCAACGCATGGGCAT 59.738 55.556 14.90 0.00 38.76 4.40
3684 3768 9.071276 TCCCATTGCTTCTCAAAATAATATCTC 57.929 33.333 0.00 0.00 38.34 2.75
3692 3776 4.927049 TCTCTCCCATTGCTTCTCAAAAT 58.073 39.130 0.00 0.00 38.34 1.82
3709 3793 7.776933 TTAGTGCACACATCAATTATCTCTC 57.223 36.000 21.04 0.00 0.00 3.20
3731 3815 1.669604 TGCCGTGCAGACTGTTTTTA 58.330 45.000 3.99 0.00 33.32 1.52
3747 3831 4.767255 CTCTGTCGCCCCACTGCC 62.767 72.222 0.00 0.00 0.00 4.85
3826 3912 1.375523 CCGAGGACGAACCCAAAGG 60.376 63.158 0.00 0.00 42.66 3.11
3827 3913 1.375523 CCCGAGGACGAACCCAAAG 60.376 63.158 0.00 0.00 42.66 2.77
3828 3914 2.103339 GACCCGAGGACGAACCCAAA 62.103 60.000 0.00 0.00 42.66 3.28
3884 3970 4.003788 CCGTGCCCTGAAGGTCGT 62.004 66.667 0.00 0.00 38.26 4.34
3925 4013 2.038387 AATCCACCCAGTTACATCGC 57.962 50.000 0.00 0.00 0.00 4.58
4046 4134 2.633967 TGAAAAGAACGGTAGGCAGGTA 59.366 45.455 0.00 0.00 0.00 3.08
4160 4256 1.345089 ACAATTGTGTGTGCCATGCAT 59.655 42.857 11.07 0.00 41.91 3.96
4161 4257 0.751452 ACAATTGTGTGTGCCATGCA 59.249 45.000 11.07 0.00 36.31 3.96
4168 4264 1.003972 AGACGCGAACAATTGTGTGTG 60.004 47.619 15.93 17.30 38.27 3.82
4178 4274 2.571757 CTGGCCTAGACGCGAACA 59.428 61.111 15.93 0.00 0.00 3.18
4229 4325 6.827586 TTTTGGATTTATACTCGTGCCTTT 57.172 33.333 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.