Multiple sequence alignment - TraesCS3D01G259900

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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 TraesCS3D01G259900 chr3D 100.000 2816 0 0 1 2816 361775499 361778314 0.000000e+00 5201.0
1 TraesCS3D01G259900 chr3D 92.262 168 13 0 1649 1816 531680024 531679857 3.630000e-59 239.0
2 TraesCS3D01G259900 chr3B 92.035 1695 39 21 409 2057 471484517 471486161 0.000000e+00 2294.0
3 TraesCS3D01G259900 chr3B 94.286 385 20 2 20 404 471483739 471484121 3.120000e-164 588.0
4 TraesCS3D01G259900 chr3B 90.270 185 15 3 1635 1816 703296622 703296438 3.630000e-59 239.0
5 TraesCS3D01G259900 chr3A 92.266 1487 79 24 401 1868 482092062 482093531 0.000000e+00 2076.0
6 TraesCS3D01G259900 chr3A 93.229 384 22 2 21 404 482090083 482090462 1.890000e-156 562.0
7 TraesCS3D01G259900 chr3A 94.652 187 10 0 1868 2054 482093574 482093760 9.870000e-75 291.0
8 TraesCS3D01G259900 chr3A 91.071 168 15 0 1649 1816 666222077 666221910 7.850000e-56 228.0
9 TraesCS3D01G259900 chr3A 90.476 42 4 0 1503 1544 666222217 666222176 3.920000e-04 56.5
10 TraesCS3D01G259900 chr2B 90.690 580 44 6 2081 2652 298160731 298160154 0.000000e+00 763.0
11 TraesCS3D01G259900 chr5D 84.055 577 85 5 2097 2669 88502285 88502858 1.470000e-152 549.0
12 TraesCS3D01G259900 chr5D 97.333 75 2 0 2742 2816 514578834 514578908 8.190000e-26 128.0
13 TraesCS3D01G259900 chr7D 75.852 352 63 19 1482 1816 234348327 234347981 2.900000e-35 159.0
14 TraesCS3D01G259900 chr7D 98.630 73 1 0 2744 2816 412718585 412718513 2.280000e-26 130.0
15 TraesCS3D01G259900 chr7A 85.333 150 22 0 1667 1816 247251714 247251565 3.760000e-34 156.0
16 TraesCS3D01G259900 chr7B 75.504 347 67 17 1482 1816 206337267 206336927 1.350000e-33 154.0
17 TraesCS3D01G259900 chr2D 98.649 74 1 0 2743 2816 24763426 24763353 6.330000e-27 132.0
18 TraesCS3D01G259900 chr2D 95.062 81 3 1 2736 2816 645624213 645624292 2.940000e-25 126.0
19 TraesCS3D01G259900 chr2A 83.803 142 20 3 2072 2213 417102888 417103026 6.330000e-27 132.0
20 TraesCS3D01G259900 chr2A 95.000 80 3 1 2737 2816 235533042 235533120 1.060000e-24 124.0
21 TraesCS3D01G259900 chr6A 92.553 94 2 5 2726 2816 33372101 33372010 2.280000e-26 130.0
22 TraesCS3D01G259900 chr4D 96.203 79 2 1 2738 2816 467720420 467720343 8.190000e-26 128.0
23 TraesCS3D01G259900 chr4D 94.048 84 2 2 2733 2816 320298303 320298223 1.060000e-24 124.0
24 TraesCS3D01G259900 chr5A 98.571 70 1 0 2747 2816 403382192 403382123 1.060000e-24 124.0
25 TraesCS3D01G259900 chr1A 96.875 32 1 0 399 430 23615807 23615776 1.000000e-03 54.7


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 TraesCS3D01G259900 chr3D 361775499 361778314 2815 False 5201.000000 5201 100.000000 1 2816 1 chr3D.!!$F1 2815
1 TraesCS3D01G259900 chr3B 471483739 471486161 2422 False 1441.000000 2294 93.160500 20 2057 2 chr3B.!!$F1 2037
2 TraesCS3D01G259900 chr3A 482090083 482093760 3677 False 976.333333 2076 93.382333 21 2054 3 chr3A.!!$F1 2033
3 TraesCS3D01G259900 chr2B 298160154 298160731 577 True 763.000000 763 90.690000 2081 2652 1 chr2B.!!$R1 571
4 TraesCS3D01G259900 chr5D 88502285 88502858 573 False 549.000000 549 84.055000 2097 2669 1 chr5D.!!$F1 572

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
234 235 0.031994 GTGAAAGGCGCAAACCACAT 59.968 50.0 10.83 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1901 3633 0.318441 CGGGTCTCAGTTTCAGAGCA 59.682 55.0 1.69 0.0 39.69 4.26 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
53 54 2.032681 GAAAGTGCCTCCAGCCGT 59.967 61.111 0.00 0.00 42.71 5.68
93 94 0.529119 GTTGTCGCATACCCCTACGG 60.529 60.000 0.00 0.00 37.81 4.02
110 111 1.520666 GGTATCCACCACCACCTCG 59.479 63.158 0.00 0.00 45.04 4.63
234 235 0.031994 GTGAAAGGCGCAAACCACAT 59.968 50.000 10.83 0.00 0.00 3.21
277 278 1.080705 GGTACGCGCTCTCACTTGT 60.081 57.895 5.73 0.00 0.00 3.16
280 281 1.241990 TACGCGCTCTCACTTGTCCT 61.242 55.000 5.73 0.00 0.00 3.85
295 296 3.126879 CCTCATTGCGCTCGCCAA 61.127 61.111 9.73 6.69 41.09 4.52
504 2136 9.206870 AGTTAATTTGGATTGTTTATGCACAAG 57.793 29.630 0.00 0.00 40.01 3.16
510 2142 5.954752 TGGATTGTTTATGCACAAGGGAATA 59.045 36.000 0.00 0.00 40.01 1.75
664 2317 1.739035 CGTTCTCGGCTAAGCATGGAA 60.739 52.381 0.00 0.00 0.00 3.53
866 2524 1.001145 ACCCGCTCTACGTCCTCTT 60.001 57.895 0.00 0.00 41.42 2.85
884 2542 2.846827 TCTTCTCTTCCCCCATTCCTTC 59.153 50.000 0.00 0.00 0.00 3.46
885 2543 1.596496 TCTCTTCCCCCATTCCTTCC 58.404 55.000 0.00 0.00 0.00 3.46
899 2557 0.543749 CCTTCCACCACCATCTCTCC 59.456 60.000 0.00 0.00 0.00 3.71
1455 3129 1.098712 GCTCCGAGGACGAGTCAGAT 61.099 60.000 5.55 0.00 42.66 2.90
1494 3168 0.620121 AAGGCAAGGAGGAGGAGGAG 60.620 60.000 0.00 0.00 0.00 3.69
1734 3423 2.693762 CCACACATTCTGCCGCCTG 61.694 63.158 0.00 0.00 0.00 4.85
1991 3723 7.272244 TCTGTCTGCGATTTATTTCTGGAATA 58.728 34.615 0.00 0.00 0.00 1.75
2057 3790 5.311649 AGAATGGGATGCCTACAATGATACT 59.688 40.000 4.35 0.00 0.00 2.12
2058 3791 4.623932 TGGGATGCCTACAATGATACTC 57.376 45.455 4.35 0.00 0.00 2.59
2059 3792 3.327757 TGGGATGCCTACAATGATACTCC 59.672 47.826 4.35 0.00 0.00 3.85
2060 3793 3.307762 GGGATGCCTACAATGATACTCCC 60.308 52.174 0.00 0.00 33.56 4.30
2061 3794 3.584848 GGATGCCTACAATGATACTCCCT 59.415 47.826 0.00 0.00 0.00 4.20
2062 3795 4.777896 GGATGCCTACAATGATACTCCCTA 59.222 45.833 0.00 0.00 0.00 3.53
2063 3796 5.337652 GGATGCCTACAATGATACTCCCTAC 60.338 48.000 0.00 0.00 0.00 3.18
2064 3797 3.901844 TGCCTACAATGATACTCCCTACC 59.098 47.826 0.00 0.00 0.00 3.18
2065 3798 4.161102 GCCTACAATGATACTCCCTACCT 58.839 47.826 0.00 0.00 0.00 3.08
2066 3799 4.593634 GCCTACAATGATACTCCCTACCTT 59.406 45.833 0.00 0.00 0.00 3.50
2067 3800 5.279556 GCCTACAATGATACTCCCTACCTTC 60.280 48.000 0.00 0.00 0.00 3.46
2068 3801 4.939052 ACAATGATACTCCCTACCTTCG 57.061 45.455 0.00 0.00 0.00 3.79
2069 3802 3.069729 ACAATGATACTCCCTACCTTCGC 59.930 47.826 0.00 0.00 0.00 4.70
2070 3803 1.315690 TGATACTCCCTACCTTCGCG 58.684 55.000 0.00 0.00 0.00 5.87
2071 3804 0.039346 GATACTCCCTACCTTCGCGC 60.039 60.000 0.00 0.00 0.00 6.86
2072 3805 1.461911 ATACTCCCTACCTTCGCGCC 61.462 60.000 0.00 0.00 0.00 6.53
2073 3806 4.222847 CTCCCTACCTTCGCGCCC 62.223 72.222 0.00 0.00 0.00 6.13
2074 3807 4.772231 TCCCTACCTTCGCGCCCT 62.772 66.667 0.00 0.00 0.00 5.19
2075 3808 4.222847 CCCTACCTTCGCGCCCTC 62.223 72.222 0.00 0.00 0.00 4.30
2076 3809 4.222847 CCTACCTTCGCGCCCTCC 62.223 72.222 0.00 0.00 0.00 4.30
2077 3810 4.222847 CTACCTTCGCGCCCTCCC 62.223 72.222 0.00 0.00 0.00 4.30
2427 4166 2.359230 GCTTCGAACAGGCAGCCT 60.359 61.111 8.70 8.70 0.00 4.58
2446 4185 1.679305 GTCTGGCTCCTCTCGTCCA 60.679 63.158 0.00 0.00 0.00 4.02
2473 4214 2.674380 GTCCAACCCTGCCTGCTG 60.674 66.667 0.00 0.00 0.00 4.41
2541 4282 2.111043 CGTCACTGCACCAACCCT 59.889 61.111 0.00 0.00 0.00 4.34
2657 4398 4.537433 GCTTCGCCCTCGCCATCT 62.537 66.667 0.00 0.00 35.26 2.90
2659 4400 3.074369 TTCGCCCTCGCCATCTGA 61.074 61.111 0.00 0.00 35.26 3.27
2662 4403 4.899239 GCCCTCGCCATCTGACGG 62.899 72.222 0.00 0.00 0.00 4.79
2745 4486 1.790387 GCATCTGCGTCACACTTCC 59.210 57.895 0.00 0.00 0.00 3.46
2746 4487 1.639298 GCATCTGCGTCACACTTCCC 61.639 60.000 0.00 0.00 0.00 3.97
2747 4488 1.021390 CATCTGCGTCACACTTCCCC 61.021 60.000 0.00 0.00 0.00 4.81
2748 4489 1.194781 ATCTGCGTCACACTTCCCCT 61.195 55.000 0.00 0.00 0.00 4.79
2749 4490 1.669115 CTGCGTCACACTTCCCCTG 60.669 63.158 0.00 0.00 0.00 4.45
2750 4491 2.383245 CTGCGTCACACTTCCCCTGT 62.383 60.000 0.00 0.00 0.00 4.00
2751 4492 1.227853 GCGTCACACTTCCCCTGTT 60.228 57.895 0.00 0.00 0.00 3.16
2752 4493 1.507141 GCGTCACACTTCCCCTGTTG 61.507 60.000 0.00 0.00 0.00 3.33
2753 4494 0.884704 CGTCACACTTCCCCTGTTGG 60.885 60.000 0.00 0.00 0.00 3.77
2763 4504 4.296265 CCTGTTGGGGAACGTAGC 57.704 61.111 0.00 0.00 0.00 3.58
2764 4505 1.373435 CCTGTTGGGGAACGTAGCA 59.627 57.895 0.00 0.00 0.00 3.49
2765 4506 0.673644 CCTGTTGGGGAACGTAGCAG 60.674 60.000 0.00 0.00 0.00 4.24
2766 4507 0.320374 CTGTTGGGGAACGTAGCAGA 59.680 55.000 0.00 0.00 31.30 4.26
2767 4508 0.759959 TGTTGGGGAACGTAGCAGAA 59.240 50.000 0.00 0.00 0.00 3.02
2768 4509 1.141254 TGTTGGGGAACGTAGCAGAAA 59.859 47.619 0.00 0.00 0.00 2.52
2769 4510 2.224670 TGTTGGGGAACGTAGCAGAAAT 60.225 45.455 0.00 0.00 0.00 2.17
2770 4511 2.817844 GTTGGGGAACGTAGCAGAAATT 59.182 45.455 0.00 0.00 0.00 1.82
2771 4512 2.706890 TGGGGAACGTAGCAGAAATTC 58.293 47.619 0.00 0.00 0.00 2.17
2772 4513 2.039216 TGGGGAACGTAGCAGAAATTCA 59.961 45.455 0.00 0.00 0.00 2.57
2773 4514 3.078837 GGGGAACGTAGCAGAAATTCAA 58.921 45.455 0.00 0.00 0.00 2.69
2774 4515 3.504520 GGGGAACGTAGCAGAAATTCAAA 59.495 43.478 0.00 0.00 0.00 2.69
2775 4516 4.022676 GGGGAACGTAGCAGAAATTCAAAA 60.023 41.667 0.00 0.00 0.00 2.44
2776 4517 5.336451 GGGGAACGTAGCAGAAATTCAAAAT 60.336 40.000 0.00 0.00 0.00 1.82
2777 4518 6.156519 GGGAACGTAGCAGAAATTCAAAATT 58.843 36.000 0.00 0.00 0.00 1.82
2778 4519 6.645003 GGGAACGTAGCAGAAATTCAAAATTT 59.355 34.615 0.00 0.00 0.00 1.82
2779 4520 7.170828 GGGAACGTAGCAGAAATTCAAAATTTT 59.829 33.333 0.00 0.00 0.00 1.82
2780 4521 8.214472 GGAACGTAGCAGAAATTCAAAATTTTC 58.786 33.333 0.00 0.00 33.08 2.29
2781 4522 8.871686 AACGTAGCAGAAATTCAAAATTTTCT 57.128 26.923 0.00 0.00 41.61 2.52
2782 4523 9.959749 AACGTAGCAGAAATTCAAAATTTTCTA 57.040 25.926 0.00 0.00 39.53 2.10
2783 4524 9.394477 ACGTAGCAGAAATTCAAAATTTTCTAC 57.606 29.630 0.00 5.68 39.53 2.59
2784 4525 8.567221 CGTAGCAGAAATTCAAAATTTTCTACG 58.433 33.333 19.51 19.51 39.53 3.51
2785 4526 7.338440 AGCAGAAATTCAAAATTTTCTACGC 57.662 32.000 0.00 0.00 39.53 4.42
2786 4527 6.922957 AGCAGAAATTCAAAATTTTCTACGCA 59.077 30.769 0.00 0.00 39.53 5.24
2787 4528 7.599998 AGCAGAAATTCAAAATTTTCTACGCAT 59.400 29.630 0.00 0.00 39.53 4.73
2788 4529 7.894753 GCAGAAATTCAAAATTTTCTACGCATC 59.105 33.333 0.00 0.00 39.53 3.91
2789 4530 8.914654 CAGAAATTCAAAATTTTCTACGCATCA 58.085 29.630 0.00 0.00 39.53 3.07
2790 4531 8.915654 AGAAATTCAAAATTTTCTACGCATCAC 58.084 29.630 0.00 0.00 39.70 3.06
2791 4532 7.581011 AATTCAAAATTTTCTACGCATCACC 57.419 32.000 0.00 0.00 0.00 4.02
2792 4533 5.697473 TCAAAATTTTCTACGCATCACCA 57.303 34.783 0.00 0.00 0.00 4.17
2793 4534 6.078202 TCAAAATTTTCTACGCATCACCAA 57.922 33.333 0.00 0.00 0.00 3.67
2794 4535 6.148948 TCAAAATTTTCTACGCATCACCAAG 58.851 36.000 0.00 0.00 0.00 3.61
2795 4536 5.957842 AAATTTTCTACGCATCACCAAGA 57.042 34.783 0.00 0.00 0.00 3.02
2796 4537 6.515272 AAATTTTCTACGCATCACCAAGAT 57.485 33.333 0.00 0.00 37.48 2.40
2797 4538 5.741388 ATTTTCTACGCATCACCAAGATC 57.259 39.130 0.00 0.00 33.72 2.75
2798 4539 3.885724 TTCTACGCATCACCAAGATCA 57.114 42.857 0.00 0.00 33.72 2.92
2799 4540 3.885724 TCTACGCATCACCAAGATCAA 57.114 42.857 0.00 0.00 33.72 2.57
2800 4541 4.406648 TCTACGCATCACCAAGATCAAT 57.593 40.909 0.00 0.00 33.72 2.57
2801 4542 4.371786 TCTACGCATCACCAAGATCAATC 58.628 43.478 0.00 0.00 33.72 2.67
2802 4543 3.272574 ACGCATCACCAAGATCAATCT 57.727 42.857 0.00 0.00 39.22 2.40
2803 4544 4.406648 ACGCATCACCAAGATCAATCTA 57.593 40.909 0.00 0.00 35.76 1.98
2804 4545 4.965814 ACGCATCACCAAGATCAATCTAT 58.034 39.130 0.00 0.00 35.76 1.98
2805 4546 4.753610 ACGCATCACCAAGATCAATCTATG 59.246 41.667 0.00 0.00 35.76 2.23
2806 4547 4.153655 CGCATCACCAAGATCAATCTATGG 59.846 45.833 14.46 14.46 39.18 2.74
2807 4548 5.311265 GCATCACCAAGATCAATCTATGGA 58.689 41.667 19.34 6.96 37.92 3.41
2808 4549 5.411977 GCATCACCAAGATCAATCTATGGAG 59.588 44.000 19.34 14.57 37.92 3.86
2809 4550 6.531923 CATCACCAAGATCAATCTATGGAGT 58.468 40.000 19.34 8.56 37.92 3.85
2810 4551 6.166984 TCACCAAGATCAATCTATGGAGTC 57.833 41.667 19.34 0.00 37.92 3.36
2811 4552 5.662657 TCACCAAGATCAATCTATGGAGTCA 59.337 40.000 19.34 3.88 37.92 3.41
2812 4553 6.328410 TCACCAAGATCAATCTATGGAGTCAT 59.672 38.462 19.34 0.00 37.92 3.06
2813 4554 6.649973 CACCAAGATCAATCTATGGAGTCATC 59.350 42.308 19.34 0.00 37.92 2.92
2814 4555 6.558014 ACCAAGATCAATCTATGGAGTCATCT 59.442 38.462 19.34 0.00 37.92 2.90
2815 4556 7.732140 ACCAAGATCAATCTATGGAGTCATCTA 59.268 37.037 19.34 0.00 37.92 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.649023 ACGGGTATTTATGGACCATGCTA 59.351 43.478 17.73 2.48 37.47 3.49
1 2 2.441750 ACGGGTATTTATGGACCATGCT 59.558 45.455 17.73 4.05 37.47 3.79
2 3 2.552315 CACGGGTATTTATGGACCATGC 59.448 50.000 17.73 0.00 37.47 4.06
4 5 2.488347 GGCACGGGTATTTATGGACCAT 60.488 50.000 12.67 12.67 37.47 3.55
5 6 1.134037 GGCACGGGTATTTATGGACCA 60.134 52.381 0.00 0.00 37.47 4.02
7 8 2.632987 AGGCACGGGTATTTATGGAC 57.367 50.000 0.00 0.00 0.00 4.02
93 94 1.153429 GCGAGGTGGTGGTGGATAC 60.153 63.158 0.00 0.00 0.00 2.24
159 160 0.541863 CAGTTTAGGGCCTCGATGGT 59.458 55.000 10.74 0.00 38.35 3.55
246 247 1.567537 CGTACCAACTGTTGTGGCG 59.432 57.895 18.38 14.36 0.00 5.69
277 278 3.604129 TTGGCGAGCGCAATGAGGA 62.604 57.895 17.16 0.00 44.11 3.71
280 281 1.137194 CATTTGGCGAGCGCAATGA 59.863 52.632 17.16 0.00 44.11 2.57
295 296 5.414454 ACACCAAAAGCACGACATATACATT 59.586 36.000 0.00 0.00 0.00 2.71
504 2136 8.603242 TCGTTTTGCTTATATCTCTTATTCCC 57.397 34.615 0.00 0.00 0.00 3.97
602 2239 7.662897 TGCTATATTTGGATGTACGTACATGA 58.337 34.615 38.47 24.35 46.20 3.07
664 2317 0.179029 CGTGTGGTGGGGAGAAAAGT 60.179 55.000 0.00 0.00 0.00 2.66
722 2375 0.716108 CAATGGACGAGTCGAGTTGC 59.284 55.000 21.50 2.49 0.00 4.17
848 2506 1.001145 AAGAGGACGTAGAGCGGGT 60.001 57.895 0.00 0.00 46.52 5.28
857 2515 0.615261 GGGGGAAGAGAAGAGGACGT 60.615 60.000 0.00 0.00 0.00 4.34
859 2517 1.886422 ATGGGGGAAGAGAAGAGGAC 58.114 55.000 0.00 0.00 0.00 3.85
866 2524 1.203557 TGGAAGGAATGGGGGAAGAGA 60.204 52.381 0.00 0.00 0.00 3.10
884 2542 1.685765 TCGGGAGAGATGGTGGTGG 60.686 63.158 0.00 0.00 0.00 4.61
885 2543 1.517832 GTCGGGAGAGATGGTGGTG 59.482 63.158 0.00 0.00 41.26 4.17
899 2557 0.393077 AGATTCCGCCTTATGGTCGG 59.607 55.000 18.32 18.32 46.73 4.79
913 2571 1.762957 TGGTGGAAGGGATCGAGATTC 59.237 52.381 0.00 0.00 0.00 2.52
1122 2796 2.284921 CTGCCTCCACCTCCTCCA 60.285 66.667 0.00 0.00 0.00 3.86
1148 2822 1.448540 AGCGGCTTCCAGTTGATCG 60.449 57.895 0.00 0.00 0.00 3.69
1383 3057 2.517402 GTGGCGTTGGAACCCACA 60.517 61.111 18.05 0.41 43.60 4.17
1386 3060 2.359478 ATCGTGGCGTTGGAACCC 60.359 61.111 0.00 0.00 0.00 4.11
1455 3129 1.078356 CTCCTCGTCCTCGTCCTGA 60.078 63.158 0.00 0.00 38.33 3.86
1641 3321 3.532155 ACCATCTCCTCCTCGCGC 61.532 66.667 0.00 0.00 0.00 6.86
1642 3322 2.415010 CACCATCTCCTCCTCGCG 59.585 66.667 0.00 0.00 0.00 5.87
1643 3323 2.107953 GCACCATCTCCTCCTCGC 59.892 66.667 0.00 0.00 0.00 5.03
1644 3324 1.142748 GTGCACCATCTCCTCCTCG 59.857 63.158 5.22 0.00 0.00 4.63
1645 3325 1.142748 CGTGCACCATCTCCTCCTC 59.857 63.158 12.15 0.00 0.00 3.71
1646 3326 1.610673 ACGTGCACCATCTCCTCCT 60.611 57.895 12.15 0.00 0.00 3.69
1647 3327 1.448540 CACGTGCACCATCTCCTCC 60.449 63.158 12.15 0.00 0.00 4.30
1648 3328 1.016130 CACACGTGCACCATCTCCTC 61.016 60.000 17.22 0.00 0.00 3.71
1649 3329 1.004560 CACACGTGCACCATCTCCT 60.005 57.895 17.22 0.00 0.00 3.69
1901 3633 0.318441 CGGGTCTCAGTTTCAGAGCA 59.682 55.000 1.69 0.00 39.69 4.26
2057 3790 4.772231 AGGGCGCGAAGGTAGGGA 62.772 66.667 12.10 0.00 0.00 4.20
2058 3791 4.222847 GAGGGCGCGAAGGTAGGG 62.223 72.222 12.10 0.00 0.00 3.53
2059 3792 4.222847 GGAGGGCGCGAAGGTAGG 62.223 72.222 12.10 0.00 0.00 3.18
2060 3793 4.222847 GGGAGGGCGCGAAGGTAG 62.223 72.222 12.10 0.00 0.00 3.18
2080 3813 3.160748 GGAGAGAGAGCTGGGGGC 61.161 72.222 0.00 0.00 42.19 5.80
2081 3814 2.445654 GGGAGAGAGAGCTGGGGG 60.446 72.222 0.00 0.00 0.00 5.40
2082 3815 2.445654 GGGGAGAGAGAGCTGGGG 60.446 72.222 0.00 0.00 0.00 4.96
2083 3816 2.445654 GGGGGAGAGAGAGCTGGG 60.446 72.222 0.00 0.00 0.00 4.45
2084 3817 2.837291 CGGGGGAGAGAGAGCTGG 60.837 72.222 0.00 0.00 0.00 4.85
2085 3818 3.535962 GCGGGGGAGAGAGAGCTG 61.536 72.222 0.00 0.00 0.00 4.24
2427 4166 1.679305 GGACGAGAGGAGCCAGACA 60.679 63.158 0.00 0.00 0.00 3.41
2481 4222 1.717937 GCAGTTGTAGCAGCATCCG 59.282 57.895 0.00 0.00 0.00 4.18
2526 4267 1.116536 TCGTAGGGTTGGTGCAGTGA 61.117 55.000 0.00 0.00 0.00 3.41
2541 4282 0.732538 CACAGCGCACACATCTCGTA 60.733 55.000 11.47 0.00 0.00 3.43
2727 4468 1.639298 GGGAAGTGTGACGCAGATGC 61.639 60.000 0.00 0.00 37.78 3.91
2728 4469 1.021390 GGGGAAGTGTGACGCAGATG 61.021 60.000 0.00 0.00 0.00 2.90
2729 4470 1.194781 AGGGGAAGTGTGACGCAGAT 61.195 55.000 0.00 0.00 0.00 2.90
2730 4471 1.837051 AGGGGAAGTGTGACGCAGA 60.837 57.895 0.00 0.00 0.00 4.26
2731 4472 1.669115 CAGGGGAAGTGTGACGCAG 60.669 63.158 0.00 0.00 0.00 5.18
2732 4473 1.978455 AACAGGGGAAGTGTGACGCA 61.978 55.000 0.00 0.00 0.00 5.24
2733 4474 1.227853 AACAGGGGAAGTGTGACGC 60.228 57.895 0.00 0.00 0.00 5.19
2734 4475 0.884704 CCAACAGGGGAAGTGTGACG 60.885 60.000 0.00 0.00 0.00 4.35
2735 4476 3.021451 CCAACAGGGGAAGTGTGAC 57.979 57.895 0.00 0.00 0.00 3.67
2746 4487 0.673644 CTGCTACGTTCCCCAACAGG 60.674 60.000 0.00 0.00 32.14 4.00
2747 4488 0.320374 TCTGCTACGTTCCCCAACAG 59.680 55.000 0.00 0.00 32.14 3.16
2748 4489 0.759959 TTCTGCTACGTTCCCCAACA 59.240 50.000 0.00 0.00 32.14 3.33
2749 4490 1.886886 TTTCTGCTACGTTCCCCAAC 58.113 50.000 0.00 0.00 0.00 3.77
2750 4491 2.871096 ATTTCTGCTACGTTCCCCAA 57.129 45.000 0.00 0.00 0.00 4.12
2751 4492 2.039216 TGAATTTCTGCTACGTTCCCCA 59.961 45.455 0.00 0.00 0.00 4.96
2752 4493 2.706890 TGAATTTCTGCTACGTTCCCC 58.293 47.619 0.00 0.00 0.00 4.81
2753 4494 4.759516 TTTGAATTTCTGCTACGTTCCC 57.240 40.909 0.00 0.00 0.00 3.97
2754 4495 7.637709 AAATTTTGAATTTCTGCTACGTTCC 57.362 32.000 0.00 0.00 0.00 3.62
2755 4496 8.968242 AGAAAATTTTGAATTTCTGCTACGTTC 58.032 29.630 8.47 0.00 42.62 3.95
2756 4497 8.871686 AGAAAATTTTGAATTTCTGCTACGTT 57.128 26.923 8.47 0.00 42.62 3.99
2757 4498 9.394477 GTAGAAAATTTTGAATTTCTGCTACGT 57.606 29.630 8.47 0.00 43.67 3.57
2758 4499 8.567221 CGTAGAAAATTTTGAATTTCTGCTACG 58.433 33.333 22.91 22.91 43.67 3.51
2759 4500 8.365938 GCGTAGAAAATTTTGAATTTCTGCTAC 58.634 33.333 8.47 8.90 43.67 3.58
2760 4501 8.079203 TGCGTAGAAAATTTTGAATTTCTGCTA 58.921 29.630 8.47 0.00 43.67 3.49
2761 4502 6.922957 TGCGTAGAAAATTTTGAATTTCTGCT 59.077 30.769 8.47 0.00 43.67 4.24
2762 4503 7.104326 TGCGTAGAAAATTTTGAATTTCTGC 57.896 32.000 8.47 8.21 43.67 4.26
2763 4504 8.914654 TGATGCGTAGAAAATTTTGAATTTCTG 58.085 29.630 8.47 0.00 43.67 3.02
2764 4505 8.915654 GTGATGCGTAGAAAATTTTGAATTTCT 58.084 29.630 8.47 0.48 45.29 2.52
2765 4506 8.162245 GGTGATGCGTAGAAAATTTTGAATTTC 58.838 33.333 8.47 0.00 36.11 2.17
2766 4507 7.655328 TGGTGATGCGTAGAAAATTTTGAATTT 59.345 29.630 8.47 0.00 0.00 1.82
2767 4508 7.151308 TGGTGATGCGTAGAAAATTTTGAATT 58.849 30.769 8.47 0.00 0.00 2.17
2768 4509 6.686630 TGGTGATGCGTAGAAAATTTTGAAT 58.313 32.000 8.47 0.00 0.00 2.57
2769 4510 6.078202 TGGTGATGCGTAGAAAATTTTGAA 57.922 33.333 8.47 0.00 0.00 2.69
2770 4511 5.697473 TGGTGATGCGTAGAAAATTTTGA 57.303 34.783 8.47 0.00 0.00 2.69
2771 4512 6.148948 TCTTGGTGATGCGTAGAAAATTTTG 58.851 36.000 8.47 0.00 0.00 2.44
2772 4513 6.325919 TCTTGGTGATGCGTAGAAAATTTT 57.674 33.333 2.28 2.28 0.00 1.82
2773 4514 5.957842 TCTTGGTGATGCGTAGAAAATTT 57.042 34.783 0.00 0.00 0.00 1.82
2774 4515 5.647658 TGATCTTGGTGATGCGTAGAAAATT 59.352 36.000 0.00 0.00 35.14 1.82
2775 4516 5.185454 TGATCTTGGTGATGCGTAGAAAAT 58.815 37.500 0.00 0.00 35.14 1.82
2776 4517 4.574892 TGATCTTGGTGATGCGTAGAAAA 58.425 39.130 0.00 0.00 35.14 2.29
2777 4518 4.200838 TGATCTTGGTGATGCGTAGAAA 57.799 40.909 0.00 0.00 35.14 2.52
2778 4519 3.885724 TGATCTTGGTGATGCGTAGAA 57.114 42.857 0.00 0.00 35.14 2.10
2779 4520 3.885724 TTGATCTTGGTGATGCGTAGA 57.114 42.857 0.00 0.00 35.14 2.59
2780 4521 4.375272 AGATTGATCTTGGTGATGCGTAG 58.625 43.478 0.00 0.00 35.14 3.51
2781 4522 4.406648 AGATTGATCTTGGTGATGCGTA 57.593 40.909 0.00 0.00 35.14 4.42
2782 4523 3.272574 AGATTGATCTTGGTGATGCGT 57.727 42.857 0.00 0.00 35.14 5.24
2783 4524 4.153655 CCATAGATTGATCTTGGTGATGCG 59.846 45.833 0.00 0.00 38.32 4.73
2784 4525 5.311265 TCCATAGATTGATCTTGGTGATGC 58.689 41.667 15.48 0.00 38.32 3.91
2785 4526 6.531923 ACTCCATAGATTGATCTTGGTGATG 58.468 40.000 19.38 10.22 38.32 3.07
2786 4527 6.328410 TGACTCCATAGATTGATCTTGGTGAT 59.672 38.462 19.38 10.95 38.32 3.06
2787 4528 5.662657 TGACTCCATAGATTGATCTTGGTGA 59.337 40.000 19.38 6.63 38.32 4.02
2788 4529 5.922053 TGACTCCATAGATTGATCTTGGTG 58.078 41.667 15.48 15.28 38.32 4.17
2789 4530 6.558014 AGATGACTCCATAGATTGATCTTGGT 59.442 38.462 15.48 4.75 38.32 3.67
2790 4531 7.006865 AGATGACTCCATAGATTGATCTTGG 57.993 40.000 0.00 7.19 38.32 3.61


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

AutoCloner maintained by Alex Coulton.