Multiple sequence alignment - TraesCS6B01G439200

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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 TraesCS6B01G439200 chr6B 100.000 3695 0 0 1 3695 704863092 704859398 0.000000e+00 6824.0
1 TraesCS6B01G439200 chr6B 79.937 638 81 17 2178 2778 681929511 681928884 3.410000e-115 425.0
2 TraesCS6B01G439200 chr6B 76.362 863 156 29 1089 1920 681930661 681929816 1.590000e-113 420.0
3 TraesCS6B01G439200 chr6B 79.039 458 77 11 2241 2685 682707560 682707109 2.790000e-76 296.0
4 TraesCS6B01G439200 chr6B 85.542 249 25 8 1835 2074 681929809 681929563 2.200000e-62 250.0
5 TraesCS6B01G439200 chr6B 75.118 422 68 22 1 397 636972745 636972336 2.950000e-36 163.0
6 TraesCS6B01G439200 chr6B 77.731 238 40 10 963 1189 679752733 679752968 2.320000e-27 134.0
7 TraesCS6B01G439200 chr6B 87.000 100 9 2 473 571 616426254 616426350 3.900000e-20 110.0
8 TraesCS6B01G439200 chr6B 85.047 107 11 2 465 570 36810720 36810822 1.820000e-18 104.0
9 TraesCS6B01G439200 chr6B 84.615 104 14 1 2241 2342 682741501 682741398 6.530000e-18 102.0
10 TraesCS6B01G439200 chr6B 86.957 69 9 0 1116 1184 69719958 69719890 1.100000e-10 78.7
11 TraesCS6B01G439200 chr6B 80.612 98 15 3 1089 1184 70564528 70564433 5.120000e-09 73.1
12 TraesCS6B01G439200 chr6D 93.101 3131 153 27 597 3695 452083209 452080110 0.000000e+00 4527.0
13 TraesCS6B01G439200 chr6D 93.541 2090 92 13 1622 3695 462409647 462407585 0.000000e+00 3072.0
14 TraesCS6B01G439200 chr6D 80.220 637 76 19 2178 2778 449817224 449816602 2.040000e-117 433.0
15 TraesCS6B01G439200 chr6D 83.010 412 40 16 2 391 61008521 61008924 2.730000e-91 346.0
16 TraesCS6B01G439200 chr6D 77.729 458 83 12 2241 2685 450211269 450210818 2.830000e-66 263.0
17 TraesCS6B01G439200 chr6A 92.539 3123 147 32 604 3695 609163835 609160768 0.000000e+00 4397.0
18 TraesCS6B01G439200 chr6A 86.992 123 13 2 1 120 585578350 585578228 6.440000e-28 135.0
19 TraesCS6B01G439200 chr6A 100.000 63 0 0 512 574 68503240 68503302 2.330000e-22 117.0
20 TraesCS6B01G439200 chr6A 79.592 98 16 3 1089 1184 38104990 38104895 2.380000e-07 67.6
21 TraesCS6B01G439200 chr7B 94.965 576 15 9 2 571 616897902 616897335 0.000000e+00 891.0
22 TraesCS6B01G439200 chr7B 77.123 424 48 27 2 389 746624327 746624737 2.250000e-47 200.0
23 TraesCS6B01G439200 chr7B 76.259 278 50 12 129 397 705729604 705729334 2.320000e-27 134.0
24 TraesCS6B01G439200 chr5D 90.787 597 30 16 1 579 480809799 480810388 0.000000e+00 774.0
25 TraesCS6B01G439200 chr4D 89.562 594 38 14 1 575 322225817 322226405 0.000000e+00 732.0
26 TraesCS6B01G439200 chr4D 89.552 67 5 2 1118 1183 441639152 441639087 2.360000e-12 84.2
27 TraesCS6B01G439200 chr1A 88.553 463 23 19 44 486 39654009 39653557 5.430000e-148 534.0
28 TraesCS6B01G439200 chr7D 88.060 335 11 9 251 570 60129940 60130260 1.620000e-98 370.0
29 TraesCS6B01G439200 chr7D 93.023 215 11 3 3 213 60117497 60117711 9.960000e-81 311.0
30 TraesCS6B01G439200 chr7D 76.087 276 52 12 129 398 122524152 122523885 8.330000e-27 132.0
31 TraesCS6B01G439200 chr7A 76.140 285 51 10 110 388 704843476 704843749 2.320000e-27 134.0
32 TraesCS6B01G439200 chr2A 97.143 70 2 0 502 571 19572695 19572764 6.480000e-23 119.0
33 TraesCS6B01G439200 chr1D 86.486 111 9 3 468 576 391861524 391861418 2.330000e-22 117.0
34 TraesCS6B01G439200 chr4A 90.625 64 4 2 1118 1180 25803040 25803102 2.360000e-12 84.2
35 TraesCS6B01G439200 chr4A 89.062 64 5 2 1118 1180 26012707 26012769 1.100000e-10 78.7


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 TraesCS6B01G439200 chr6B 704859398 704863092 3694 True 6824 6824 100.000000 1 3695 1 chr6B.!!$R6 3694
1 TraesCS6B01G439200 chr6B 681928884 681930661 1777 True 365 425 80.613667 1089 2778 3 chr6B.!!$R7 1689
2 TraesCS6B01G439200 chr6D 452080110 452083209 3099 True 4527 4527 93.101000 597 3695 1 chr6D.!!$R3 3098
3 TraesCS6B01G439200 chr6D 462407585 462409647 2062 True 3072 3072 93.541000 1622 3695 1 chr6D.!!$R4 2073
4 TraesCS6B01G439200 chr6D 449816602 449817224 622 True 433 433 80.220000 2178 2778 1 chr6D.!!$R1 600
5 TraesCS6B01G439200 chr6A 609160768 609163835 3067 True 4397 4397 92.539000 604 3695 1 chr6A.!!$R3 3091
6 TraesCS6B01G439200 chr7B 616897335 616897902 567 True 891 891 94.965000 2 571 1 chr7B.!!$R1 569
7 TraesCS6B01G439200 chr5D 480809799 480810388 589 False 774 774 90.787000 1 579 1 chr5D.!!$F1 578
8 TraesCS6B01G439200 chr4D 322225817 322226405 588 False 732 732 89.562000 1 575 1 chr4D.!!$F1 574

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
412 421 0.035458 ACGCTTGTTAGGCTTCAGCT 59.965 50.0 0.00 0.00 41.7 4.24 F
413 422 0.445436 CGCTTGTTAGGCTTCAGCTG 59.555 55.0 7.63 7.63 41.7 4.24 F
845 880 0.526662 CCCTCGCTTAGTTGACTCGT 59.473 55.0 0.00 0.00 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2396 2582 0.319383 AGCAGAAGTGTCAGCGTCTG 60.319 55.000 11.27 11.27 44.13 3.51 R
2527 2717 3.890756 TCATATGTTTCCATCACATGCCC 59.109 43.478 1.90 0.00 35.57 5.36 R
2803 3006 1.457346 AACTAGGTCGGTCGGTACTG 58.543 55.000 0.00 0.00 0.00 2.74 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
231 235 2.486918 CATTCATAGCATCGCAGTGGA 58.513 47.619 0.00 0.00 0.00 4.02
411 420 0.166814 CACGCTTGTTAGGCTTCAGC 59.833 55.000 0.00 0.00 41.14 4.26
412 421 0.035458 ACGCTTGTTAGGCTTCAGCT 59.965 50.000 0.00 0.00 41.70 4.24
413 422 0.445436 CGCTTGTTAGGCTTCAGCTG 59.555 55.000 7.63 7.63 41.70 4.24
414 423 1.813513 GCTTGTTAGGCTTCAGCTGA 58.186 50.000 13.74 13.74 41.70 4.26
571 594 5.437060 TCTAGATGTGAAATAGCAAACCCC 58.563 41.667 0.00 0.00 0.00 4.95
575 598 6.252995 AGATGTGAAATAGCAAACCCCTAAA 58.747 36.000 0.00 0.00 0.00 1.85
578 601 7.309770 TGTGAAATAGCAAACCCCTAAATTT 57.690 32.000 0.00 0.00 0.00 1.82
579 602 8.423906 TGTGAAATAGCAAACCCCTAAATTTA 57.576 30.769 0.00 0.00 0.00 1.40
580 603 8.871125 TGTGAAATAGCAAACCCCTAAATTTAA 58.129 29.630 0.00 0.00 0.00 1.52
581 604 9.713713 GTGAAATAGCAAACCCCTAAATTTAAA 57.286 29.630 0.00 0.00 0.00 1.52
584 607 9.733556 AAATAGCAAACCCCTAAATTTAAAAGG 57.266 29.630 0.00 0.00 0.00 3.11
585 608 8.673456 ATAGCAAACCCCTAAATTTAAAAGGA 57.327 30.769 7.01 0.00 31.64 3.36
586 609 7.381789 AGCAAACCCCTAAATTTAAAAGGAA 57.618 32.000 7.01 0.00 31.64 3.36
587 610 7.807198 AGCAAACCCCTAAATTTAAAAGGAAA 58.193 30.769 7.01 0.00 31.64 3.13
588 611 8.275758 AGCAAACCCCTAAATTTAAAAGGAAAA 58.724 29.630 7.01 0.00 31.64 2.29
589 612 8.904834 GCAAACCCCTAAATTTAAAAGGAAAAA 58.095 29.630 7.01 0.00 31.64 1.94
795 826 1.506907 AAGCCCCCTACCCCAAGAAC 61.507 60.000 0.00 0.00 0.00 3.01
833 868 1.304879 ACTTCTGCTCTCCCTCGCT 60.305 57.895 0.00 0.00 0.00 4.93
844 879 0.809385 TCCCTCGCTTAGTTGACTCG 59.191 55.000 0.00 0.00 0.00 4.18
845 880 0.526662 CCCTCGCTTAGTTGACTCGT 59.473 55.000 0.00 0.00 0.00 4.18
846 881 1.467713 CCCTCGCTTAGTTGACTCGTC 60.468 57.143 0.00 0.00 0.00 4.20
847 882 1.525596 CTCGCTTAGTTGACTCGTCG 58.474 55.000 0.00 0.00 0.00 5.12
848 883 0.870393 TCGCTTAGTTGACTCGTCGT 59.130 50.000 0.00 0.00 0.00 4.34
958 995 1.152204 TCCCTTCCCTGGACGTCAA 60.152 57.895 18.91 4.84 0.00 3.18
959 996 0.765135 TCCCTTCCCTGGACGTCAAA 60.765 55.000 18.91 3.79 0.00 2.69
967 1004 2.076863 CCTGGACGTCAAATGAACTCC 58.923 52.381 18.91 0.00 0.00 3.85
975 1012 2.030805 GTCAAATGAACTCCGCAGCTTT 60.031 45.455 0.00 0.00 0.00 3.51
976 1013 2.622942 TCAAATGAACTCCGCAGCTTTT 59.377 40.909 0.00 0.00 0.00 2.27
1022 1059 2.757508 CAGGAGGCTGAGCGAGGA 60.758 66.667 0.00 0.00 0.00 3.71
1027 1064 3.535962 GGCTGAGCGAGGAGGGAG 61.536 72.222 0.00 0.00 0.00 4.30
1078 1115 3.933048 GACCTCCCGGACGACCTGA 62.933 68.421 0.73 0.00 0.00 3.86
1240 1277 3.295273 TCGTGGACGAGCTGCTGT 61.295 61.111 7.01 5.60 44.22 4.40
1395 1453 1.947146 CGTCGCTGGTTCGTTGACA 60.947 57.895 0.00 0.00 0.00 3.58
1443 1501 2.626840 CTGAAGAGGGTAGAGCTTTGC 58.373 52.381 0.00 0.00 0.00 3.68
1491 1549 4.008933 ACGGGCTGTCAGGTGCTC 62.009 66.667 1.14 0.00 0.00 4.26
1603 1661 1.357907 TAAAACCCGCCGTCGTATTG 58.642 50.000 0.00 0.00 0.00 1.90
1769 1833 2.542411 GCGATAGGCAAGCAGGATTTTG 60.542 50.000 0.00 0.00 42.87 2.44
1793 1857 2.306847 GGTTTTGGAAGGCTTGTCTGA 58.693 47.619 3.46 0.00 0.00 3.27
1834 1898 4.492494 ACAACTGATGATCAGGTATGCA 57.508 40.909 24.79 0.00 43.78 3.96
1835 1899 5.045012 ACAACTGATGATCAGGTATGCAT 57.955 39.130 24.79 3.79 43.78 3.96
1836 1900 4.820173 ACAACTGATGATCAGGTATGCATG 59.180 41.667 24.79 9.24 43.78 4.06
1837 1901 3.819337 AACTGATGATCAGGTATGCATGC 59.181 43.478 24.79 11.82 43.79 4.06
2002 2159 7.251281 TCTTGATGTTTCTATGTACTCGTCTG 58.749 38.462 0.00 0.00 0.00 3.51
2025 2183 5.869753 GCAATATGCATACCTCTACTTGG 57.130 43.478 8.99 0.00 44.26 3.61
2031 2189 5.339008 TGCATACCTCTACTTGGTACTTG 57.661 43.478 0.00 0.00 42.12 3.16
2342 2528 3.435105 TGTTGCTGAACAAATGGTGTC 57.565 42.857 0.00 0.00 40.60 3.67
2366 2552 3.084039 GCTGGTGATTTCACTGGATTGA 58.916 45.455 10.32 0.00 45.73 2.57
2396 2582 3.265791 CTCCAGCACTCACCAATTCTAC 58.734 50.000 0.00 0.00 0.00 2.59
2694 2893 4.576053 TCCGAGCAAATTGACATCCAATAG 59.424 41.667 0.00 0.00 44.28 1.73
2695 2894 4.576053 CCGAGCAAATTGACATCCAATAGA 59.424 41.667 0.00 0.00 44.28 1.98
2696 2895 5.066375 CCGAGCAAATTGACATCCAATAGAA 59.934 40.000 0.00 0.00 44.28 2.10
2697 2896 6.197276 CGAGCAAATTGACATCCAATAGAAG 58.803 40.000 0.00 0.00 44.28 2.85
2698 2897 6.183360 CGAGCAAATTGACATCCAATAGAAGT 60.183 38.462 0.00 0.00 44.28 3.01
2699 2898 7.011389 CGAGCAAATTGACATCCAATAGAAGTA 59.989 37.037 0.00 0.00 44.28 2.24
2700 2899 8.757982 AGCAAATTGACATCCAATAGAAGTAT 57.242 30.769 0.00 0.00 44.28 2.12
2701 2900 9.851686 AGCAAATTGACATCCAATAGAAGTATA 57.148 29.630 0.00 0.00 44.28 1.47
2803 3006 7.982224 TGTACATAGTGTGCTCGGATATATAC 58.018 38.462 0.00 0.00 33.97 1.47
3035 3242 2.457366 AGTGTCTGTCCATTTCGTCC 57.543 50.000 0.00 0.00 0.00 4.79
3037 3244 2.368875 AGTGTCTGTCCATTTCGTCCTT 59.631 45.455 0.00 0.00 0.00 3.36
3042 3249 4.151867 GTCTGTCCATTTCGTCCTTGTAAC 59.848 45.833 0.00 0.00 0.00 2.50
3051 3258 2.901192 TCGTCCTTGTAACAGGATTGGA 59.099 45.455 0.00 0.00 45.14 3.53
3056 3263 4.044065 TCCTTGTAACAGGATTGGATTGGT 59.956 41.667 0.00 0.00 38.11 3.67
3109 3316 6.338146 CCTGTAGATCGAGTAAATGGTCAAA 58.662 40.000 0.00 0.00 0.00 2.69
3110 3317 6.255887 CCTGTAGATCGAGTAAATGGTCAAAC 59.744 42.308 0.00 0.00 0.00 2.93
3140 3347 5.335661 GCTACCCTATGAACCAACAAAGTTG 60.336 44.000 3.00 3.00 0.00 3.16
3154 3361 5.461032 ACAAAGTTGAACCTTGTGTTGAA 57.539 34.783 11.19 0.00 37.29 2.69
3158 3365 7.443879 ACAAAGTTGAACCTTGTGTTGAATTTT 59.556 29.630 11.19 0.00 39.37 1.82
3165 3372 9.743057 TGAACCTTGTGTTGAATTTTATGTTAG 57.257 29.630 0.00 0.00 37.29 2.34
3174 3381 9.685828 TGTTGAATTTTATGTTAGTAGCAAACC 57.314 29.630 0.00 0.00 0.00 3.27
3191 3398 3.833559 AACCATCCTTCCAACATTCCT 57.166 42.857 0.00 0.00 0.00 3.36
3196 3403 5.135020 ACCATCCTTCCAACATTCCTATGAT 59.865 40.000 0.00 0.00 35.65 2.45
3211 3418 6.499106 TCCTATGATTAGATCAAGTGGCAA 57.501 37.500 0.00 0.00 43.50 4.52
3212 3419 7.083062 TCCTATGATTAGATCAAGTGGCAAT 57.917 36.000 0.00 0.00 43.50 3.56
3213 3420 6.938596 TCCTATGATTAGATCAAGTGGCAATG 59.061 38.462 0.00 0.00 43.50 2.82
3214 3421 6.713903 CCTATGATTAGATCAAGTGGCAATGT 59.286 38.462 0.00 0.00 43.50 2.71
3215 3422 5.823209 TGATTAGATCAAGTGGCAATGTG 57.177 39.130 0.00 0.00 36.11 3.21
3216 3423 4.641541 TGATTAGATCAAGTGGCAATGTGG 59.358 41.667 0.00 0.00 36.11 4.17
3217 3424 1.180029 AGATCAAGTGGCAATGTGGC 58.820 50.000 0.00 0.00 44.03 5.01
3280 3495 3.287867 ACAGTTTCCCCTGCATCTATG 57.712 47.619 0.00 0.00 35.83 2.23
3542 3757 2.989824 CACCGTGGTCCTCCTCGT 60.990 66.667 7.69 0.00 45.58 4.18
3587 3802 2.980233 GCGGCAAGCCTGAACTGT 60.980 61.111 9.73 0.00 40.81 3.55
3657 3872 2.678190 GCGCTAGGTTGATTCCAGAACT 60.678 50.000 0.00 0.00 0.00 3.01
3658 3873 3.430374 GCGCTAGGTTGATTCCAGAACTA 60.430 47.826 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.492881 TGACCCGTCGCTATTAACTTCA 59.507 45.455 0.00 0.00 0.00 3.02
16 17 3.001939 CCATTTGACCCGTCGCTATTAAC 59.998 47.826 0.00 0.00 0.00 2.01
248 252 9.533831 TTCTGAGGCCTTTTATCTTTTCTTTAT 57.466 29.630 6.77 0.00 0.00 1.40
249 253 8.934023 TTCTGAGGCCTTTTATCTTTTCTTTA 57.066 30.769 6.77 0.00 0.00 1.85
250 254 7.839680 TTCTGAGGCCTTTTATCTTTTCTTT 57.160 32.000 6.77 0.00 0.00 2.52
586 609 7.014702 GCGTGCAAATGCTAAATATTGTTTTT 58.985 30.769 6.97 0.00 42.66 1.94
587 610 6.402011 GGCGTGCAAATGCTAAATATTGTTTT 60.402 34.615 6.97 0.00 42.66 2.43
588 611 5.063312 GGCGTGCAAATGCTAAATATTGTTT 59.937 36.000 6.97 0.00 42.66 2.83
589 612 4.566360 GGCGTGCAAATGCTAAATATTGTT 59.434 37.500 6.97 0.00 42.66 2.83
590 613 4.111916 GGCGTGCAAATGCTAAATATTGT 58.888 39.130 6.97 0.00 42.66 2.71
591 614 4.207635 CAGGCGTGCAAATGCTAAATATTG 59.792 41.667 6.97 0.00 42.66 1.90
592 615 4.362279 CAGGCGTGCAAATGCTAAATATT 58.638 39.130 6.97 0.00 42.66 1.28
593 616 3.968649 CAGGCGTGCAAATGCTAAATAT 58.031 40.909 6.97 0.00 42.66 1.28
594 617 3.419264 CAGGCGTGCAAATGCTAAATA 57.581 42.857 6.97 0.00 42.66 1.40
595 618 2.282701 CAGGCGTGCAAATGCTAAAT 57.717 45.000 6.97 0.00 42.66 1.40
775 806 1.506028 TTCTTGGGGTAGGGGGCTTG 61.506 60.000 0.00 0.00 0.00 4.01
777 808 1.929088 GTTCTTGGGGTAGGGGGCT 60.929 63.158 0.00 0.00 0.00 5.19
778 809 2.681591 GTTCTTGGGGTAGGGGGC 59.318 66.667 0.00 0.00 0.00 5.80
844 879 1.004440 AAGAAGCCTGCCTGACGAC 60.004 57.895 0.00 0.00 0.00 4.34
845 880 1.004560 CAAGAAGCCTGCCTGACGA 60.005 57.895 0.00 0.00 0.00 4.20
846 881 2.684843 GCAAGAAGCCTGCCTGACG 61.685 63.158 0.00 0.00 37.23 4.35
847 882 2.684843 CGCAAGAAGCCTGCCTGAC 61.685 63.158 0.00 0.00 41.38 3.51
848 883 2.359107 CGCAAGAAGCCTGCCTGA 60.359 61.111 0.00 0.00 41.38 3.86
890 925 2.931969 TGTGCTGCAAGAATATCTGTCG 59.068 45.455 2.77 0.00 34.07 4.35
937 974 3.787001 CGTCCAGGGAAGGGAGCC 61.787 72.222 0.00 0.00 34.44 4.70
958 995 1.336240 GCAAAAGCTGCGGAGTTCATT 60.336 47.619 5.62 0.00 42.37 2.57
959 996 0.242017 GCAAAAGCTGCGGAGTTCAT 59.758 50.000 5.62 0.00 42.37 2.57
989 1026 0.713883 CCTGGACATTTCGTCGAACG 59.286 55.000 7.29 4.62 46.42 3.95
1078 1115 0.535335 AACGACATCAGGTACGCCAT 59.465 50.000 0.00 0.00 37.19 4.40
1209 1246 1.672356 CACGAACTTGCTCCTGGGG 60.672 63.158 0.00 0.00 0.00 4.96
1443 1501 4.153986 CAGAGCGTTTAAACTGCATGAAG 58.846 43.478 25.76 0.00 33.20 3.02
1459 1517 1.361668 CCCGTGAAATCCACAGAGCG 61.362 60.000 0.00 0.00 45.98 5.03
1491 1549 4.269603 CAGCCTTTCATCTCTAACACATCG 59.730 45.833 0.00 0.00 0.00 3.84
1603 1661 1.030457 CTGATGAGATTTGGGGCAGC 58.970 55.000 0.00 0.00 0.00 5.25
1762 1826 4.126437 CCTTCCAAAACCACACAAAATCC 58.874 43.478 0.00 0.00 0.00 3.01
1769 1833 1.480545 ACAAGCCTTCCAAAACCACAC 59.519 47.619 0.00 0.00 0.00 3.82
1793 1857 7.867403 CAGTTGTTAACTCCAAATTTGTAGCAT 59.133 33.333 16.73 6.23 40.46 3.79
1834 1898 4.718276 AGGAATTAGCAAAAATGGGAGCAT 59.282 37.500 0.00 0.00 0.00 3.79
1835 1899 4.095946 AGGAATTAGCAAAAATGGGAGCA 58.904 39.130 0.00 0.00 0.00 4.26
1836 1900 4.743057 AGGAATTAGCAAAAATGGGAGC 57.257 40.909 0.00 0.00 0.00 4.70
1837 1901 6.466812 ACAAAGGAATTAGCAAAAATGGGAG 58.533 36.000 0.00 0.00 0.00 4.30
1869 2024 6.573434 ACATAAACGAGATCTAGCACATGAA 58.427 36.000 0.00 0.00 0.00 2.57
1874 2029 6.648725 ACAAACATAAACGAGATCTAGCAC 57.351 37.500 2.33 0.00 0.00 4.40
2002 2159 4.697352 CCAAGTAGAGGTATGCATATTGCC 59.303 45.833 10.16 6.71 44.23 4.52
2155 2321 9.137459 TGGTGGTTCTTATTTTTCATAGAAACA 57.863 29.630 0.00 0.00 40.84 2.83
2156 2322 9.626045 CTGGTGGTTCTTATTTTTCATAGAAAC 57.374 33.333 0.00 0.00 35.42 2.78
2186 2352 7.831193 AGATACAGAAGTACATGCTTTGGAAAT 59.169 33.333 0.00 0.00 31.96 2.17
2366 2552 3.307762 GGTGAGTGCTGGAGGAAGTAAAT 60.308 47.826 0.00 0.00 0.00 1.40
2396 2582 0.319383 AGCAGAAGTGTCAGCGTCTG 60.319 55.000 11.27 11.27 44.13 3.51
2527 2717 3.890756 TCATATGTTTCCATCACATGCCC 59.109 43.478 1.90 0.00 35.57 5.36
2694 2893 8.541133 AACAGCAGAAGAAAGTTCTATACTTC 57.459 34.615 0.00 0.00 46.34 3.01
2696 2895 6.809196 CGAACAGCAGAAGAAAGTTCTATACT 59.191 38.462 0.00 0.00 36.28 2.12
2697 2896 6.807230 TCGAACAGCAGAAGAAAGTTCTATAC 59.193 38.462 0.00 0.00 36.28 1.47
2698 2897 6.807230 GTCGAACAGCAGAAGAAAGTTCTATA 59.193 38.462 0.00 0.00 36.28 1.31
2699 2898 5.635700 GTCGAACAGCAGAAGAAAGTTCTAT 59.364 40.000 0.00 0.00 36.28 1.98
2700 2899 4.982916 GTCGAACAGCAGAAGAAAGTTCTA 59.017 41.667 0.00 0.00 36.28 2.10
2701 2900 3.804873 GTCGAACAGCAGAAGAAAGTTCT 59.195 43.478 0.00 0.00 39.74 3.01
2803 3006 1.457346 AACTAGGTCGGTCGGTACTG 58.543 55.000 0.00 0.00 0.00 2.74
3006 3213 4.044336 TGGACAGACACTTGCAAAATTG 57.956 40.909 0.00 0.47 0.00 2.32
3007 3214 4.942761 ATGGACAGACACTTGCAAAATT 57.057 36.364 0.00 0.00 0.00 1.82
3009 3216 4.681744 GAAATGGACAGACACTTGCAAAA 58.318 39.130 0.00 0.00 0.00 2.44
3023 3230 3.435671 CCTGTTACAAGGACGAAATGGAC 59.564 47.826 0.00 0.00 40.02 4.02
3035 3242 4.380867 GCACCAATCCAATCCTGTTACAAG 60.381 45.833 0.00 0.00 0.00 3.16
3037 3244 3.088532 GCACCAATCCAATCCTGTTACA 58.911 45.455 0.00 0.00 0.00 2.41
3042 3249 1.843368 ACTGCACCAATCCAATCCTG 58.157 50.000 0.00 0.00 0.00 3.86
3051 3258 2.504367 ACTCGCTAAAACTGCACCAAT 58.496 42.857 0.00 0.00 0.00 3.16
3140 3347 9.744468 ACTAACATAAAATTCAACACAAGGTTC 57.256 29.630 0.00 0.00 37.72 3.62
3154 3361 8.823220 AGGATGGTTTGCTACTAACATAAAAT 57.177 30.769 0.00 0.00 0.00 1.82
3158 3365 6.069905 TGGAAGGATGGTTTGCTACTAACATA 60.070 38.462 0.00 0.00 0.00 2.29
3165 3372 3.153919 TGTTGGAAGGATGGTTTGCTAC 58.846 45.455 0.00 0.00 0.00 3.58
3174 3381 8.159447 TCTAATCATAGGAATGTTGGAAGGATG 58.841 37.037 0.00 0.00 34.50 3.51
3191 3398 6.487668 CCACATTGCCACTTGATCTAATCATA 59.512 38.462 0.00 0.00 39.39 2.15
3196 3403 2.754552 GCCACATTGCCACTTGATCTAA 59.245 45.455 0.00 0.00 0.00 2.10
3211 3418 0.324923 ATTGGACCAGCATGCCACAT 60.325 50.000 15.66 0.00 31.97 3.21
3212 3419 0.330941 TATTGGACCAGCATGCCACA 59.669 50.000 15.66 3.59 31.97 4.17
3213 3420 1.134946 GTTATTGGACCAGCATGCCAC 59.865 52.381 15.66 3.23 31.97 5.01
3214 3421 1.473258 GTTATTGGACCAGCATGCCA 58.527 50.000 15.66 1.05 31.97 4.92
3215 3422 0.746659 GGTTATTGGACCAGCATGCC 59.253 55.000 15.66 0.00 39.57 4.40
3216 3423 1.473258 TGGTTATTGGACCAGCATGC 58.527 50.000 10.51 10.51 44.53 4.06
3280 3495 0.595095 CAGGTTGGAAGAAGCAGTGC 59.405 55.000 7.13 7.13 0.00 4.40
3281 3496 1.202806 TCCAGGTTGGAAGAAGCAGTG 60.203 52.381 0.00 0.00 45.00 3.66
3396 3611 4.400120 GGGTGGTATGGTAGACAAAAACA 58.600 43.478 0.00 0.00 0.00 2.83
3473 3688 4.319046 GCATCCAAGCAAGACATACATACG 60.319 45.833 0.00 0.00 0.00 3.06
3587 3802 3.308402 GGGTCCCTGAAACATCATCTTGA 60.308 47.826 0.00 0.00 0.00 3.02
3657 3872 5.364446 TCCTAGCCACAAGACGGAATTTATA 59.636 40.000 0.00 0.00 0.00 0.98
3658 3873 4.163458 TCCTAGCCACAAGACGGAATTTAT 59.837 41.667 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.