Multiple sequence alignment - TraesCS6A01G321400

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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 TraesCS6A01G321400 chr6A 100.000 3934 0 0 1 3934 555754628 555750695 0.000000e+00 7265
1 TraesCS6A01G321400 chr6D 87.466 3295 170 95 239 3430 410829623 410826469 0.000000e+00 3572
2 TraesCS6A01G321400 chr6D 85.366 492 43 8 3451 3934 410826483 410826013 2.130000e-132 483
3 TraesCS6A01G321400 chr6D 86.700 203 7 5 1 183 410829972 410829770 1.430000e-49 207
4 TraesCS6A01G321400 chr6B 89.043 2747 166 66 754 3430 617646463 617643782 0.000000e+00 3280
5 TraesCS6A01G321400 chr6B 86.905 504 32 18 3451 3934 617643796 617643307 5.790000e-148 534
6 TraesCS6A01G321400 chr6B 86.214 515 24 14 240 741 617646989 617646509 7.540000e-142 514
7 TraesCS6A01G321400 chr6B 85.981 214 4 6 17 209 617647303 617647095 5.150000e-49 206
8 TraesCS6A01G321400 chr2B 94.690 113 6 0 1282 1394 682194110 682194222 4.040000e-40 176


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 TraesCS6A01G321400 chr6A 555750695 555754628 3933 True 7265.000000 7265 100.000000 1 3934 1 chr6A.!!$R1 3933
1 TraesCS6A01G321400 chr6D 410826013 410829972 3959 True 1420.666667 3572 86.510667 1 3934 3 chr6D.!!$R1 3933
2 TraesCS6A01G321400 chr6B 617643307 617647303 3996 True 1133.500000 3280 87.035750 17 3934 4 chr6B.!!$R1 3917

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
383 518 0.034059 GTGTGGAGTGGAGTGGAGTG 59.966 60.0 0.00 0.0 0.00 3.51 F
390 525 0.036732 GTGGAGTGGAGTGGATTGCA 59.963 55.0 0.00 0.0 0.00 4.08 F
1748 1967 0.249073 AGGTGCGAGATCGAATTCCG 60.249 55.0 6.39 0.0 43.02 4.30 F
2423 2659 0.098905 TCACTCGCTCGCTCACATAC 59.901 55.0 0.00 0.0 0.00 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 2354 0.034337 TCGAAGTTGTACCTGGCCAC 59.966 55.0 0.0 0.0 0.00 5.01 R
2122 2356 1.012486 CGTCGAAGTTGTACCTGGCC 61.012 60.0 0.0 0.0 0.00 5.36 R
2754 3018 0.035317 TCTCGCAGGAACAGTGCAAT 59.965 50.0 0.0 0.0 41.26 3.56 R
3456 3765 0.318445 GCGTGTGGTGTAGTTCGTCT 60.318 55.0 0.0 0.0 0.00 4.18 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
32 33 3.186047 CCCGCGACGATCAACCAC 61.186 66.667 8.23 0.00 0.00 4.16
209 234 2.680913 GCGCTGGTCGATGCAGTTT 61.681 57.895 0.00 0.00 41.67 2.66
235 260 3.419759 CGTTACACGGCTGGCCAC 61.420 66.667 0.00 0.00 38.08 5.01
282 416 5.761234 ACTTAACTGAATTAACCACTTCGCA 59.239 36.000 0.00 0.00 0.00 5.10
283 417 4.749245 AACTGAATTAACCACTTCGCAG 57.251 40.909 0.00 0.00 0.00 5.18
290 424 1.388547 AACCACTTCGCAGAAAGCAA 58.611 45.000 0.00 0.00 45.90 3.91
299 434 0.670162 GCAGAAAGCAAGCCTGACAA 59.330 50.000 0.00 0.00 44.79 3.18
328 463 2.167808 CTACCGGCGATCCTCGTACG 62.168 65.000 9.30 9.53 42.81 3.67
337 472 2.337749 ATCCTCGTACGCAGCCTTCG 62.338 60.000 11.24 0.00 0.00 3.79
381 516 1.290324 CGTGTGGAGTGGAGTGGAG 59.710 63.158 0.00 0.00 0.00 3.86
383 518 0.034059 GTGTGGAGTGGAGTGGAGTG 59.966 60.000 0.00 0.00 0.00 3.51
384 519 1.121407 TGTGGAGTGGAGTGGAGTGG 61.121 60.000 0.00 0.00 0.00 4.00
385 520 0.832135 GTGGAGTGGAGTGGAGTGGA 60.832 60.000 0.00 0.00 0.00 4.02
386 521 0.117140 TGGAGTGGAGTGGAGTGGAT 59.883 55.000 0.00 0.00 0.00 3.41
387 522 1.280457 GGAGTGGAGTGGAGTGGATT 58.720 55.000 0.00 0.00 0.00 3.01
388 523 1.065854 GGAGTGGAGTGGAGTGGATTG 60.066 57.143 0.00 0.00 0.00 2.67
389 524 0.326264 AGTGGAGTGGAGTGGATTGC 59.674 55.000 0.00 0.00 0.00 3.56
390 525 0.036732 GTGGAGTGGAGTGGATTGCA 59.963 55.000 0.00 0.00 0.00 4.08
391 526 0.325933 TGGAGTGGAGTGGATTGCAG 59.674 55.000 0.00 0.00 0.00 4.41
402 537 2.362120 ATTGCAGGCAGACCCAGC 60.362 61.111 0.00 0.00 45.70 4.85
741 892 2.671396 CTCCAAATCCGAACGTCGAATT 59.329 45.455 0.00 0.00 43.74 2.17
742 893 3.847542 TCCAAATCCGAACGTCGAATTA 58.152 40.909 0.00 0.00 43.74 1.40
780 968 5.023452 AGTTTCAAATCCATCTTAACCCCC 58.977 41.667 0.00 0.00 0.00 5.40
861 1049 2.202892 GGGGCAATCTCGTCCGTC 60.203 66.667 0.00 0.00 0.00 4.79
862 1050 2.202892 GGGCAATCTCGTCCGTCC 60.203 66.667 0.00 0.00 0.00 4.79
863 1051 2.582498 GGCAATCTCGTCCGTCCG 60.582 66.667 0.00 0.00 0.00 4.79
864 1052 2.181021 GCAATCTCGTCCGTCCGT 59.819 61.111 0.00 0.00 0.00 4.69
865 1053 2.158959 GCAATCTCGTCCGTCCGTG 61.159 63.158 0.00 0.00 0.00 4.94
910 1098 2.787723 GTGATGATCACGTTCCGTTG 57.212 50.000 10.11 0.00 38.32 4.10
916 1104 2.459202 ATCACGTTCCGTTGGGGGTC 62.459 60.000 0.00 0.00 38.32 4.46
918 1106 2.358247 CGTTCCGTTGGGGGTCTG 60.358 66.667 0.00 0.00 36.01 3.51
926 1114 3.190738 TTGGGGGTCTGCAGAACGG 62.191 63.158 24.99 0.00 30.99 4.44
933 1121 1.731613 TCTGCAGAACGGCGTTACG 60.732 57.895 26.87 19.77 40.31 3.18
1036 1228 0.951558 CCCCTTGGCGTGTTATATGC 59.048 55.000 0.00 0.00 40.71 3.14
1116 1317 2.750350 CGGCATCATACCCCTCCC 59.250 66.667 0.00 0.00 0.00 4.30
1124 1325 3.049231 ATACCCCTCCCTCCCACCC 62.049 68.421 0.00 0.00 0.00 4.61
1550 1767 4.106925 CAGGACAGGAGCCTGCCC 62.107 72.222 16.20 14.77 45.66 5.36
1668 1887 0.734253 CCGTGTCTTTCTCCGCTCTG 60.734 60.000 0.00 0.00 0.00 3.35
1748 1967 0.249073 AGGTGCGAGATCGAATTCCG 60.249 55.000 6.39 0.00 43.02 4.30
1751 1970 0.738975 TGCGAGATCGAATTCCGTCT 59.261 50.000 6.39 6.89 43.02 4.18
1753 1972 1.781998 GCGAGATCGAATTCCGTCTTC 59.218 52.381 6.39 0.00 43.02 2.87
1755 1974 3.696898 CGAGATCGAATTCCGTCTTCTT 58.303 45.455 0.00 0.00 43.02 2.52
1759 1978 3.671008 TCGAATTCCGTCTTCTTTCCA 57.329 42.857 0.00 0.00 39.75 3.53
1762 1981 1.726853 ATTCCGTCTTCTTTCCAGCG 58.273 50.000 0.00 0.00 0.00 5.18
1787 2006 3.282021 TCTTGTGAATTATGCCTCCTGC 58.718 45.455 0.00 0.00 41.77 4.85
1897 2116 3.917760 GAGTCGGATCTGGCGGGG 61.918 72.222 0.00 0.00 0.00 5.73
2047 2266 1.398451 CGGTTCGCTTGCAAGTAAGTG 60.398 52.381 26.55 9.29 39.04 3.16
2071 2295 4.598257 GCAGCAGCGGAAACTCTA 57.402 55.556 0.00 0.00 0.00 2.43
2072 2296 2.840974 GCAGCAGCGGAAACTCTAA 58.159 52.632 0.00 0.00 0.00 2.10
2074 2298 1.740025 GCAGCAGCGGAAACTCTAATT 59.260 47.619 0.00 0.00 0.00 1.40
2075 2299 2.223135 GCAGCAGCGGAAACTCTAATTC 60.223 50.000 0.00 0.00 0.00 2.17
2076 2300 3.265791 CAGCAGCGGAAACTCTAATTCT 58.734 45.455 0.00 0.00 0.00 2.40
2077 2301 3.308323 CAGCAGCGGAAACTCTAATTCTC 59.692 47.826 0.00 0.00 0.00 2.87
2078 2302 2.609916 GCAGCGGAAACTCTAATTCTCC 59.390 50.000 0.00 0.00 0.00 3.71
2079 2303 3.861840 CAGCGGAAACTCTAATTCTCCA 58.138 45.455 0.00 0.00 0.00 3.86
2081 2305 3.515901 AGCGGAAACTCTAATTCTCCACT 59.484 43.478 0.00 0.00 0.00 4.00
2082 2306 4.020128 AGCGGAAACTCTAATTCTCCACTT 60.020 41.667 0.00 0.00 0.00 3.16
2093 2327 3.685214 CTCCACTTCGTCGCCGGAG 62.685 68.421 5.05 0.00 45.66 4.63
2104 2338 1.210931 CGCCGGAGTTCTAACGTGA 59.789 57.895 5.05 0.00 0.00 4.35
2110 2344 2.095161 CGGAGTTCTAACGTGAGAGCTT 60.095 50.000 19.27 4.83 37.17 3.74
2114 2348 4.800784 AGTTCTAACGTGAGAGCTTTCTC 58.199 43.478 13.25 0.76 33.65 2.87
2390 2626 2.158559 CCAACCACCGATTCATCAACA 58.841 47.619 0.00 0.00 0.00 3.33
2391 2627 2.556189 CCAACCACCGATTCATCAACAA 59.444 45.455 0.00 0.00 0.00 2.83
2410 2646 6.580791 TCAACAACAACTTTTTCTTTCACTCG 59.419 34.615 0.00 0.00 0.00 4.18
2423 2659 0.098905 TCACTCGCTCGCTCACATAC 59.901 55.000 0.00 0.00 0.00 2.39
2445 2683 1.846439 CCCACCATTATCACCTCACCT 59.154 52.381 0.00 0.00 0.00 4.00
2474 2719 1.203994 CTGATTTTTCCCAGCAGCAGG 59.796 52.381 0.00 0.00 0.00 4.85
2521 2777 5.745988 TCCCCTACTGGTACTTATCTTCT 57.254 43.478 0.00 0.00 0.00 2.85
2540 2796 0.323629 TTGGTTGACAGGACGGATCC 59.676 55.000 0.00 0.00 46.69 3.36
2587 2843 5.757099 AATTGCCACCTAGTAGTAGTTGT 57.243 39.130 3.91 0.00 0.00 3.32
2588 2844 6.862469 AATTGCCACCTAGTAGTAGTTGTA 57.138 37.500 3.91 0.00 0.00 2.41
2589 2845 5.909621 TTGCCACCTAGTAGTAGTTGTAG 57.090 43.478 3.91 0.00 0.00 2.74
2590 2846 4.927049 TGCCACCTAGTAGTAGTTGTAGT 58.073 43.478 3.91 0.00 0.00 2.73
2591 2847 5.327732 TGCCACCTAGTAGTAGTTGTAGTT 58.672 41.667 3.91 0.00 0.00 2.24
2592 2848 5.184479 TGCCACCTAGTAGTAGTTGTAGTTG 59.816 44.000 3.91 0.00 0.00 3.16
2593 2849 5.416952 GCCACCTAGTAGTAGTTGTAGTTGA 59.583 44.000 3.91 0.00 0.00 3.18
2595 2851 7.363617 GCCACCTAGTAGTAGTTGTAGTTGATT 60.364 40.741 3.91 0.00 0.00 2.57
2596 2852 7.974501 CCACCTAGTAGTAGTTGTAGTTGATTG 59.025 40.741 3.91 0.00 0.00 2.67
2597 2853 7.488471 CACCTAGTAGTAGTTGTAGTTGATTGC 59.512 40.741 3.91 0.00 0.00 3.56
2598 2854 6.979238 CCTAGTAGTAGTTGTAGTTGATTGCC 59.021 42.308 3.91 0.00 0.00 4.52
2644 2900 1.135660 ACTGTACATCGTCGTCAGCAG 60.136 52.381 0.00 0.00 0.00 4.24
2646 2902 0.456142 GTACATCGTCGTCAGCAGCA 60.456 55.000 0.00 0.00 0.00 4.41
2647 2903 0.455815 TACATCGTCGTCAGCAGCAT 59.544 50.000 0.00 0.00 0.00 3.79
2649 2905 1.080435 CATCGTCGTCAGCAGCATGT 61.080 55.000 0.00 0.00 39.31 3.21
2736 3000 1.226379 CGTTTCCGTCCATGCATGC 60.226 57.895 21.69 11.82 0.00 4.06
2737 3001 1.882311 GTTTCCGTCCATGCATGCA 59.118 52.632 25.04 25.04 0.00 3.96
2738 3002 0.457035 GTTTCCGTCCATGCATGCAT 59.543 50.000 27.46 27.46 37.08 3.96
2754 3018 4.461431 GCATGCATGATTCCATCTTATCCA 59.539 41.667 30.64 0.00 0.00 3.41
2763 3027 4.508551 TCCATCTTATCCATTGCACTGT 57.491 40.909 3.14 0.00 0.00 3.55
2770 3034 1.210931 CCATTGCACTGTTCCTGCG 59.789 57.895 3.14 0.00 37.46 5.18
2810 3074 0.316196 GCGGTTATGCAGATCGTTGC 60.316 55.000 7.28 0.09 44.33 4.17
2858 3125 2.336945 CAGACATGCAGGCTATGGAA 57.663 50.000 0.00 0.00 29.36 3.53
2860 3127 3.018856 CAGACATGCAGGCTATGGAAAA 58.981 45.455 0.00 0.00 29.36 2.29
2861 3128 3.444742 CAGACATGCAGGCTATGGAAAAA 59.555 43.478 0.00 0.00 29.36 1.94
2862 3129 4.098960 CAGACATGCAGGCTATGGAAAAAT 59.901 41.667 0.00 0.00 29.36 1.82
2863 3130 4.340381 AGACATGCAGGCTATGGAAAAATC 59.660 41.667 0.00 0.00 29.36 2.17
2864 3131 4.284178 ACATGCAGGCTATGGAAAAATCT 58.716 39.130 0.00 0.00 30.55 2.40
2865 3132 4.340381 ACATGCAGGCTATGGAAAAATCTC 59.660 41.667 0.00 0.00 30.55 2.75
2874 3141 3.507162 TGGAAAAATCTCCAGTGCTCA 57.493 42.857 0.00 0.00 40.71 4.26
2875 3142 3.415212 TGGAAAAATCTCCAGTGCTCAG 58.585 45.455 0.00 0.00 40.71 3.35
2876 3143 2.163211 GGAAAAATCTCCAGTGCTCAGC 59.837 50.000 0.00 0.00 35.36 4.26
2877 3144 1.446907 AAAATCTCCAGTGCTCAGCG 58.553 50.000 0.00 0.00 0.00 5.18
2933 3213 0.033090 CAGAGTGCAGTGCAGACAGA 59.967 55.000 20.42 0.00 40.08 3.41
2935 3215 1.280886 GAGTGCAGTGCAGACAGACG 61.281 60.000 20.42 0.00 40.08 4.18
2950 3230 2.923035 ACGGTACAGGCAGGCAGT 60.923 61.111 0.00 0.00 0.00 4.40
3012 3294 1.581447 GCCGTGGAAAGAAGGCTTG 59.419 57.895 3.46 0.00 45.67 4.01
3109 3395 0.108281 GAAGTTACCGCTGTCTCCCC 60.108 60.000 0.00 0.00 0.00 4.81
3136 3422 0.179268 CCGTCGTCGCGGTTAAAAAG 60.179 55.000 6.13 0.00 46.11 2.27
3147 3433 3.129813 GCGGTTAAAAAGGGGGTTAGATG 59.870 47.826 0.00 0.00 0.00 2.90
3169 3455 0.179163 GCAAGTGGCGATTAACCTGC 60.179 55.000 0.00 0.00 0.00 4.85
3363 3672 1.124477 GGAGTAGGATGGGAGCAGGG 61.124 65.000 0.00 0.00 0.00 4.45
3364 3673 0.105453 GAGTAGGATGGGAGCAGGGA 60.105 60.000 0.00 0.00 0.00 4.20
3365 3674 0.105246 AGTAGGATGGGAGCAGGGAG 60.105 60.000 0.00 0.00 0.00 4.30
3366 3675 1.124477 GTAGGATGGGAGCAGGGAGG 61.124 65.000 0.00 0.00 0.00 4.30
3384 3693 2.439104 GGAGGGAGAGATGCCGCTT 61.439 63.158 0.00 0.00 0.00 4.68
3430 3739 1.370064 CGGGAACTGGGACGAACTT 59.630 57.895 0.00 0.00 0.00 2.66
3431 3740 0.250166 CGGGAACTGGGACGAACTTT 60.250 55.000 0.00 0.00 0.00 2.66
3432 3741 1.812708 CGGGAACTGGGACGAACTTTT 60.813 52.381 0.00 0.00 0.00 2.27
3433 3742 2.304092 GGGAACTGGGACGAACTTTTT 58.696 47.619 0.00 0.00 0.00 1.94
3462 3771 6.489127 TTTTTGAAACAGAACTGAGACGAA 57.511 33.333 8.87 3.14 0.00 3.85
3463 3772 5.464965 TTTGAAACAGAACTGAGACGAAC 57.535 39.130 8.87 0.00 0.00 3.95
3464 3773 4.386867 TGAAACAGAACTGAGACGAACT 57.613 40.909 8.87 0.00 0.00 3.01
3465 3774 5.509716 TGAAACAGAACTGAGACGAACTA 57.490 39.130 8.87 0.00 0.00 2.24
3466 3775 5.279384 TGAAACAGAACTGAGACGAACTAC 58.721 41.667 8.87 0.00 0.00 2.73
3467 3776 4.913335 AACAGAACTGAGACGAACTACA 57.087 40.909 8.87 0.00 0.00 2.74
3468 3777 4.226113 ACAGAACTGAGACGAACTACAC 57.774 45.455 8.87 0.00 0.00 2.90
3469 3778 3.004524 ACAGAACTGAGACGAACTACACC 59.995 47.826 8.87 0.00 0.00 4.16
3470 3779 3.004419 CAGAACTGAGACGAACTACACCA 59.996 47.826 0.00 0.00 0.00 4.17
3471 3780 3.004524 AGAACTGAGACGAACTACACCAC 59.995 47.826 0.00 0.00 0.00 4.16
3472 3781 2.304092 ACTGAGACGAACTACACCACA 58.696 47.619 0.00 0.00 0.00 4.17
3473 3782 2.034305 ACTGAGACGAACTACACCACAC 59.966 50.000 0.00 0.00 0.00 3.82
3474 3783 1.002142 TGAGACGAACTACACCACACG 60.002 52.381 0.00 0.00 0.00 4.49
3522 3831 5.752955 TGGCTTTAATTTTGCACTGAAACTC 59.247 36.000 0.00 0.00 0.00 3.01
3563 3872 2.627737 GGCTCTCGTGTGACCTCGT 61.628 63.158 0.00 0.00 0.00 4.18
3650 3969 1.268845 GCTCGTTGTAGGCTCTAGCTC 60.269 57.143 1.39 0.00 41.70 4.09
3686 4005 6.205784 TGGAAAATACTGAACTTTTCTTGCG 58.794 36.000 7.46 0.00 39.92 4.85
3687 4006 5.117135 GGAAAATACTGAACTTTTCTTGCGC 59.883 40.000 0.00 0.00 39.92 6.09
3689 4008 2.763249 ACTGAACTTTTCTTGCGCTG 57.237 45.000 9.73 1.08 0.00 5.18
3706 4028 3.674423 CGCTGCTAGAACTGTATTTTGC 58.326 45.455 0.00 0.00 0.00 3.68
3729 4051 4.927782 TGACGCTTTGCCGGTGCT 62.928 61.111 1.90 0.00 38.71 4.40
3747 4069 2.076863 GCTAACGGCAATCTGAACTGT 58.923 47.619 0.00 0.00 41.35 3.55
3748 4070 3.259064 GCTAACGGCAATCTGAACTGTA 58.741 45.455 0.00 0.00 41.35 2.74
3752 4074 5.705609 AACGGCAATCTGAACTGTATTTT 57.294 34.783 0.00 0.00 0.00 1.82
3766 4088 4.618489 ACTGTATTTTCTTACGTTCGTCCG 59.382 41.667 0.00 0.00 0.00 4.79
3768 4090 1.850377 TTTTCTTACGTTCGTCCGCA 58.150 45.000 0.00 0.00 0.00 5.69
3769 4091 1.130955 TTTCTTACGTTCGTCCGCAC 58.869 50.000 0.00 0.00 0.00 5.34
3774 4102 1.784036 TACGTTCGTCCGCACTGTGA 61.784 55.000 12.86 0.00 0.00 3.58
3776 4104 2.355837 TTCGTCCGCACTGTGAGC 60.356 61.111 12.86 0.00 0.00 4.26
3881 4216 4.614535 GCTGTTGGAGCTGAAATAACACTG 60.615 45.833 0.00 0.00 45.21 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.444838 TGGTTGATCGTCGCGGGG 62.445 66.667 6.13 0.00 0.00 5.73
69 70 4.980805 TGGCGTGAGTTCGGTGGC 62.981 66.667 0.00 0.00 0.00 5.01
104 125 2.923568 GGAGCCCCCGGATCTACC 60.924 72.222 0.73 0.00 38.31 3.18
235 260 5.119588 GTGAAATGGCAAATGTGTTCAGATG 59.880 40.000 0.00 0.00 0.00 2.90
282 416 3.084786 GGTATTGTCAGGCTTGCTTTCT 58.915 45.455 0.00 0.00 0.00 2.52
283 417 3.084786 AGGTATTGTCAGGCTTGCTTTC 58.915 45.455 0.00 0.00 0.00 2.62
290 424 1.221840 CGGCAGGTATTGTCAGGCT 59.778 57.895 0.00 0.00 0.00 4.58
354 489 0.723414 CACTCCACACGTGATGATGC 59.277 55.000 25.01 0.00 34.35 3.91
381 516 2.048603 GGGTCTGCCTGCAATCCAC 61.049 63.158 12.18 0.10 34.45 4.02
383 518 1.751927 CTGGGTCTGCCTGCAATCC 60.752 63.158 0.00 0.00 34.45 3.01
384 519 2.413142 GCTGGGTCTGCCTGCAATC 61.413 63.158 0.00 0.00 35.49 2.67
385 520 2.362120 GCTGGGTCTGCCTGCAAT 60.362 61.111 0.00 0.00 35.49 3.56
386 521 4.666253 GGCTGGGTCTGCCTGCAA 62.666 66.667 8.29 0.00 43.62 4.08
389 524 4.767255 GTCGGCTGGGTCTGCCTG 62.767 72.222 12.66 7.47 44.56 4.85
424 559 1.821332 CCTGATCTGCTTTCGGCCC 60.821 63.158 0.00 0.00 40.92 5.80
427 562 1.153086 CCCCCTGATCTGCTTTCGG 60.153 63.158 0.00 0.00 0.00 4.30
581 724 4.217210 TGGGTGCTGGGTGGGTTG 62.217 66.667 0.00 0.00 0.00 3.77
839 1027 3.735037 GACGAGATTGCCCCCGGTC 62.735 68.421 0.00 0.00 0.00 4.79
843 1031 3.735037 GACGGACGAGATTGCCCCC 62.735 68.421 0.00 0.00 0.00 5.40
916 1104 2.726691 CCGTAACGCCGTTCTGCAG 61.727 63.158 5.42 7.63 0.00 4.41
918 1106 4.143363 GCCGTAACGCCGTTCTGC 62.143 66.667 5.42 4.02 0.00 4.26
926 1114 4.867599 CCCCTCGAGCCGTAACGC 62.868 72.222 6.99 0.00 0.00 4.84
1016 1205 1.604604 CATATAACACGCCAAGGGGG 58.395 55.000 8.11 1.60 41.67 5.40
1017 1206 0.951558 GCATATAACACGCCAAGGGG 59.048 55.000 1.12 1.12 37.18 4.79
1018 1207 0.586319 CGCATATAACACGCCAAGGG 59.414 55.000 0.00 0.00 0.00 3.95
1183 1387 1.402787 CATGTACTTCCCCATTGCCC 58.597 55.000 0.00 0.00 0.00 5.36
1187 1391 0.034574 TGCGCATGTACTTCCCCATT 60.035 50.000 5.66 0.00 0.00 3.16
1579 1796 1.075536 GACCCAATTCCCTCACCTTGT 59.924 52.381 0.00 0.00 0.00 3.16
1641 1859 2.484947 GGAGAAAGACACGGGTTTCAGT 60.485 50.000 5.11 0.00 35.49 3.41
1648 1867 1.446272 GAGCGGAGAAAGACACGGG 60.446 63.158 0.00 0.00 0.00 5.28
1654 1873 1.593787 CCTGCAGAGCGGAGAAAGA 59.406 57.895 17.39 0.00 37.02 2.52
1748 1967 4.214332 ACAAGAATTCGCTGGAAAGAAGAC 59.786 41.667 13.18 0.00 35.40 3.01
1751 1970 4.133820 TCACAAGAATTCGCTGGAAAGAA 58.866 39.130 13.18 0.00 35.40 2.52
1753 1972 4.488126 TTCACAAGAATTCGCTGGAAAG 57.512 40.909 13.18 3.36 35.40 2.62
1762 1981 6.954073 GCAGGAGGCATAATTCACAAGAATTC 60.954 42.308 6.71 0.00 45.27 2.17
1816 2035 5.519722 GTCTCTCGCCTGAATTTTCAAAAA 58.480 37.500 0.00 0.00 36.64 1.94
2029 2248 1.264288 AGCACTTACTTGCAAGCGAAC 59.736 47.619 26.27 11.03 45.62 3.95
2047 2266 0.240945 TTTCCGCTGCTGCTAAAAGC 59.759 50.000 14.03 0.00 43.82 3.51
2110 2344 1.984570 CCTGGCCACGGAGAGAGAA 60.985 63.158 14.21 0.00 0.00 2.87
2114 2348 1.541310 TTGTACCTGGCCACGGAGAG 61.541 60.000 23.24 4.45 0.00 3.20
2116 2350 1.375523 GTTGTACCTGGCCACGGAG 60.376 63.158 23.24 5.54 0.00 4.63
2117 2351 1.412453 AAGTTGTACCTGGCCACGGA 61.412 55.000 23.24 5.38 0.00 4.69
2118 2352 0.953960 GAAGTTGTACCTGGCCACGG 60.954 60.000 16.92 16.92 0.00 4.94
2119 2353 1.289109 CGAAGTTGTACCTGGCCACG 61.289 60.000 0.00 0.00 0.00 4.94
2120 2354 0.034337 TCGAAGTTGTACCTGGCCAC 59.966 55.000 0.00 0.00 0.00 5.01
2121 2355 0.034337 GTCGAAGTTGTACCTGGCCA 59.966 55.000 4.71 4.71 0.00 5.36
2122 2356 1.012486 CGTCGAAGTTGTACCTGGCC 61.012 60.000 0.00 0.00 0.00 5.36
2254 2489 4.854291 CAGCTCTACAGTGAGTAACTTTCG 59.146 45.833 0.00 0.00 36.83 3.46
2313 2548 1.474077 CCGGAGCATCTTTTTCCCTTG 59.526 52.381 0.00 0.00 33.73 3.61
2390 2626 5.310720 AGCGAGTGAAAGAAAAAGTTGTT 57.689 34.783 0.00 0.00 0.00 2.83
2391 2627 4.494199 CGAGCGAGTGAAAGAAAAAGTTGT 60.494 41.667 0.00 0.00 0.00 3.32
2410 2646 0.528684 GTGGGAGTATGTGAGCGAGC 60.529 60.000 0.00 0.00 0.00 5.03
2423 2659 2.158755 GGTGAGGTGATAATGGTGGGAG 60.159 54.545 0.00 0.00 0.00 4.30
2445 2683 4.956075 GCTGGGAAAAATCAGGATTAAGGA 59.044 41.667 0.00 0.00 0.00 3.36
2474 2719 0.673022 AACTGCTACTGCTGCTGCTC 60.673 55.000 17.00 2.00 41.07 4.26
2521 2777 0.323629 GGATCCGTCCTGTCAACCAA 59.676 55.000 0.00 0.00 41.60 3.67
2540 2796 1.323412 AAGGGACTGATCGATCGAGG 58.677 55.000 23.84 17.03 40.86 4.63
2542 2798 3.210232 AGTAAGGGACTGATCGATCGA 57.790 47.619 21.86 21.86 40.86 3.59
2570 2826 7.642082 ATCAACTACAACTACTACTAGGTGG 57.358 40.000 0.00 0.00 41.50 4.61
2587 2843 6.094881 GCAAATACAGGTAAGGCAATCAACTA 59.905 38.462 0.00 0.00 0.00 2.24
2588 2844 5.105756 GCAAATACAGGTAAGGCAATCAACT 60.106 40.000 0.00 0.00 0.00 3.16
2589 2845 5.102313 GCAAATACAGGTAAGGCAATCAAC 58.898 41.667 0.00 0.00 0.00 3.18
2590 2846 4.159506 GGCAAATACAGGTAAGGCAATCAA 59.840 41.667 0.00 0.00 0.00 2.57
2591 2847 3.699038 GGCAAATACAGGTAAGGCAATCA 59.301 43.478 0.00 0.00 0.00 2.57
2592 2848 3.954258 AGGCAAATACAGGTAAGGCAATC 59.046 43.478 0.00 0.00 0.00 2.67
2593 2849 3.701040 CAGGCAAATACAGGTAAGGCAAT 59.299 43.478 0.00 0.00 0.00 3.56
2595 2851 2.620367 CCAGGCAAATACAGGTAAGGCA 60.620 50.000 0.00 0.00 0.00 4.75
2596 2852 2.024414 CCAGGCAAATACAGGTAAGGC 58.976 52.381 0.00 0.00 0.00 4.35
2597 2853 3.644966 TCCAGGCAAATACAGGTAAGG 57.355 47.619 0.00 0.00 0.00 2.69
2598 2854 6.530019 AAAATCCAGGCAAATACAGGTAAG 57.470 37.500 0.00 0.00 0.00 2.34
2644 2900 2.324332 CTGCTGCTGCTGCTACATGC 62.324 60.000 27.67 12.50 40.48 4.06
2646 2902 4.220413 CTGCTGCTGCTGCTACAT 57.780 55.556 27.67 0.00 40.48 2.29
2739 3003 5.533903 ACAGTGCAATGGATAAGATGGAATC 59.466 40.000 19.57 0.00 46.04 2.52
2745 3009 4.885907 CAGGAACAGTGCAATGGATAAGAT 59.114 41.667 19.57 0.00 0.00 2.40
2746 3010 4.264253 CAGGAACAGTGCAATGGATAAGA 58.736 43.478 19.57 0.00 0.00 2.10
2754 3018 0.035317 TCTCGCAGGAACAGTGCAAT 59.965 50.000 0.00 0.00 41.26 3.56
2763 3027 1.806542 GTGCATTTCTTCTCGCAGGAA 59.193 47.619 0.00 0.00 34.49 3.36
2770 3034 4.091424 GCATAACGTGTGCATTTCTTCTC 58.909 43.478 18.18 0.00 42.08 2.87
2810 3074 3.875727 TGCAGAACTACCTAGTAGCTACG 59.124 47.826 17.99 6.96 39.51 3.51
2842 3109 4.284178 AGATTTTTCCATAGCCTGCATGT 58.716 39.130 0.00 0.00 0.00 3.21
2850 3117 3.950395 AGCACTGGAGATTTTTCCATAGC 59.050 43.478 9.49 9.49 45.80 2.97
2851 3118 5.188434 TGAGCACTGGAGATTTTTCCATAG 58.812 41.667 0.00 0.00 45.80 2.23
2852 3119 5.178096 TGAGCACTGGAGATTTTTCCATA 57.822 39.130 0.00 0.00 45.80 2.74
2853 3120 4.015084 CTGAGCACTGGAGATTTTTCCAT 58.985 43.478 0.00 0.00 45.80 3.41
2855 3122 2.163211 GCTGAGCACTGGAGATTTTTCC 59.837 50.000 0.00 0.00 37.77 3.13
2856 3123 2.159599 CGCTGAGCACTGGAGATTTTTC 60.160 50.000 4.88 0.00 0.00 2.29
2857 3124 1.808945 CGCTGAGCACTGGAGATTTTT 59.191 47.619 4.88 0.00 0.00 1.94
2858 3125 1.446907 CGCTGAGCACTGGAGATTTT 58.553 50.000 4.88 0.00 0.00 1.82
2860 3127 4.928398 CGCTGAGCACTGGAGATT 57.072 55.556 4.88 0.00 0.00 2.40
2870 3137 4.266070 CATGCATGGGCGCTGAGC 62.266 66.667 19.40 7.56 45.35 4.26
2871 3138 3.592814 CCATGCATGGGCGCTGAG 61.593 66.667 34.31 9.25 44.31 3.35
2933 3213 2.923035 ACTGCCTGCCTGTACCGT 60.923 61.111 0.00 0.00 0.00 4.83
2935 3215 1.078848 CAGACTGCCTGCCTGTACC 60.079 63.158 0.00 0.00 35.89 3.34
2950 3230 3.072476 GGAAGCCTCCACTGCAGA 58.928 61.111 23.35 0.00 41.96 4.26
3012 3294 3.493303 GTCCCCCATCTCCCAGCC 61.493 72.222 0.00 0.00 0.00 4.85
3070 3356 2.614013 TCCCCTTCTTCCCTGGGC 60.614 66.667 8.22 0.00 39.61 5.36
3136 3422 0.919710 ACTTGCTCCATCTAACCCCC 59.080 55.000 0.00 0.00 0.00 5.40
3147 3433 0.733150 GGTTAATCGCCACTTGCTCC 59.267 55.000 0.00 0.00 38.05 4.70
3169 3455 4.044426 TCTGATCACTAATCATTCACGCG 58.956 43.478 3.53 3.53 43.44 6.01
3196 3486 2.291190 AGCGGCGCTTTGTTTAGTTTAA 59.709 40.909 31.35 0.00 33.89 1.52
3363 3672 2.206536 CGGCATCTCTCCCTCCCTC 61.207 68.421 0.00 0.00 0.00 4.30
3364 3673 2.123077 CGGCATCTCTCCCTCCCT 60.123 66.667 0.00 0.00 0.00 4.20
3365 3674 3.934962 GCGGCATCTCTCCCTCCC 61.935 72.222 0.00 0.00 0.00 4.30
3366 3675 2.439104 AAGCGGCATCTCTCCCTCC 61.439 63.158 1.45 0.00 0.00 4.30
3384 3693 4.776322 CGCCTGGCACCGAATCCA 62.776 66.667 20.29 0.00 0.00 3.41
3439 3748 6.148811 AGTTCGTCTCAGTTCTGTTTCAAAAA 59.851 34.615 0.00 0.00 0.00 1.94
3440 3749 5.642063 AGTTCGTCTCAGTTCTGTTTCAAAA 59.358 36.000 0.00 0.00 0.00 2.44
3441 3750 5.175859 AGTTCGTCTCAGTTCTGTTTCAAA 58.824 37.500 0.00 0.00 0.00 2.69
3442 3751 4.755411 AGTTCGTCTCAGTTCTGTTTCAA 58.245 39.130 0.00 0.00 0.00 2.69
3443 3752 4.386867 AGTTCGTCTCAGTTCTGTTTCA 57.613 40.909 0.00 0.00 0.00 2.69
3444 3753 5.173492 GTGTAGTTCGTCTCAGTTCTGTTTC 59.827 44.000 0.00 0.00 0.00 2.78
3445 3754 5.041940 GTGTAGTTCGTCTCAGTTCTGTTT 58.958 41.667 0.00 0.00 0.00 2.83
3446 3755 4.499357 GGTGTAGTTCGTCTCAGTTCTGTT 60.499 45.833 0.00 0.00 0.00 3.16
3447 3756 3.004524 GGTGTAGTTCGTCTCAGTTCTGT 59.995 47.826 0.00 0.00 0.00 3.41
3448 3757 3.004419 TGGTGTAGTTCGTCTCAGTTCTG 59.996 47.826 0.00 0.00 0.00 3.02
3449 3758 3.004524 GTGGTGTAGTTCGTCTCAGTTCT 59.995 47.826 0.00 0.00 0.00 3.01
3450 3759 3.243301 TGTGGTGTAGTTCGTCTCAGTTC 60.243 47.826 0.00 0.00 0.00 3.01
3451 3760 2.691526 TGTGGTGTAGTTCGTCTCAGTT 59.308 45.455 0.00 0.00 0.00 3.16
3452 3761 2.034305 GTGTGGTGTAGTTCGTCTCAGT 59.966 50.000 0.00 0.00 0.00 3.41
3453 3762 2.662700 GTGTGGTGTAGTTCGTCTCAG 58.337 52.381 0.00 0.00 0.00 3.35
3454 3763 1.002142 CGTGTGGTGTAGTTCGTCTCA 60.002 52.381 0.00 0.00 0.00 3.27
3455 3764 1.682982 CGTGTGGTGTAGTTCGTCTC 58.317 55.000 0.00 0.00 0.00 3.36
3456 3765 0.318445 GCGTGTGGTGTAGTTCGTCT 60.318 55.000 0.00 0.00 0.00 4.18
3457 3766 0.595567 TGCGTGTGGTGTAGTTCGTC 60.596 55.000 0.00 0.00 0.00 4.20
3458 3767 0.872881 GTGCGTGTGGTGTAGTTCGT 60.873 55.000 0.00 0.00 0.00 3.85
3459 3768 1.850640 GTGCGTGTGGTGTAGTTCG 59.149 57.895 0.00 0.00 0.00 3.95
3460 3769 1.850640 CGTGCGTGTGGTGTAGTTC 59.149 57.895 0.00 0.00 0.00 3.01
3461 3770 2.241880 GCGTGCGTGTGGTGTAGTT 61.242 57.895 0.00 0.00 0.00 2.24
3462 3771 2.660552 GCGTGCGTGTGGTGTAGT 60.661 61.111 0.00 0.00 0.00 2.73
3463 3772 2.660224 TGCGTGCGTGTGGTGTAG 60.660 61.111 0.00 0.00 0.00 2.74
3464 3773 2.962786 GTGCGTGCGTGTGGTGTA 60.963 61.111 0.00 0.00 0.00 2.90
3563 3872 3.559171 GGGTGCAGAAGTTACCAATGAGA 60.559 47.826 0.00 0.00 36.19 3.27
3591 3900 2.275547 CTACACGTACGAGCCCCCAC 62.276 65.000 24.41 0.00 0.00 4.61
3650 3969 5.009210 TCAGTATTTTCCAAAACTGAACCCG 59.991 40.000 1.73 0.00 31.88 5.28
3686 4005 4.954092 AGCAAAATACAGTTCTAGCAGC 57.046 40.909 0.00 0.00 0.00 5.25
3687 4006 5.007136 GGCTAGCAAAATACAGTTCTAGCAG 59.993 44.000 18.24 0.00 46.34 4.24
3689 4008 5.007136 CAGGCTAGCAAAATACAGTTCTAGC 59.993 44.000 18.24 9.77 44.78 3.42
3729 4051 6.653320 AGAAAATACAGTTCAGATTGCCGTTA 59.347 34.615 0.00 0.00 0.00 3.18
3739 4061 7.101993 ACGAACGTAAGAAAATACAGTTCAG 57.898 36.000 0.00 12.19 38.15 3.02
3741 4063 6.520175 GGACGAACGTAAGAAAATACAGTTC 58.480 40.000 0.00 0.00 43.62 3.01
3743 4065 4.618489 CGGACGAACGTAAGAAAATACAGT 59.382 41.667 0.00 0.00 43.62 3.55
3747 4069 3.364621 GTGCGGACGAACGTAAGAAAATA 59.635 43.478 0.00 0.00 43.62 1.40
3748 4070 2.156310 GTGCGGACGAACGTAAGAAAAT 59.844 45.455 0.00 0.00 43.62 1.82
3752 4074 0.386352 CAGTGCGGACGAACGTAAGA 60.386 55.000 0.00 0.00 43.62 2.10
3766 4088 2.173669 ACACACACGCTCACAGTGC 61.174 57.895 0.00 0.00 42.94 4.40
3768 4090 1.083806 CACACACACACGCTCACAGT 61.084 55.000 0.00 0.00 0.00 3.55
3769 4091 1.083806 ACACACACACACGCTCACAG 61.084 55.000 0.00 0.00 0.00 3.66
3774 4102 1.089481 CCTTCACACACACACACGCT 61.089 55.000 0.00 0.00 0.00 5.07
3776 4104 1.581934 ATCCTTCACACACACACACG 58.418 50.000 0.00 0.00 0.00 4.49
3818 4153 2.148916 TCTTCGTTAGCACACCACTG 57.851 50.000 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.