Multiple sequence alignment - TraesCS6A01G252700

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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 TraesCS6A01G252700 chr6A 100.000 3038 0 0 1 3038 467056464 467053427 0.000000e+00 5611.0
1 TraesCS6A01G252700 chr6A 94.872 78 2 2 2296 2372 467054096 467054020 1.480000e-23 121.0
2 TraesCS6A01G252700 chr6A 94.872 78 2 2 2369 2445 467054169 467054093 1.480000e-23 121.0
3 TraesCS6A01G252700 chr6B 95.522 1898 56 9 787 2656 492219732 492217836 0.000000e+00 3007.0
4 TraesCS6A01G252700 chr6B 86.767 801 88 13 1 800 492221715 492220932 0.000000e+00 876.0
5 TraesCS6A01G252700 chr6B 89.583 240 12 6 2808 3038 492212557 492212322 2.960000e-75 292.0
6 TraesCS6A01G252700 chr6B 96.053 152 5 1 2646 2796 492212762 492212611 2.340000e-61 246.0
7 TraesCS6A01G252700 chr6B 96.154 78 2 1 2296 2372 492218129 492218052 3.180000e-25 126.0
8 TraesCS6A01G252700 chr6D 95.067 1642 47 13 753 2375 328342162 328340536 0.000000e+00 2553.0
9 TraesCS6A01G252700 chr6D 88.116 690 74 5 1 689 328354116 328353434 0.000000e+00 813.0
10 TraesCS6A01G252700 chr6D 88.981 481 20 14 2369 2845 328340613 328340162 5.690000e-157 564.0
11 TraesCS6A01G252700 chr6D 92.199 141 3 1 2906 3038 328340158 328340018 3.090000e-45 193.0
12 TraesCS6A01G252700 chr7A 83.582 67 10 1 271 337 152934172 152934107 9.090000e-06 62.1
13 TraesCS6A01G252700 chr7D 83.077 65 10 1 271 335 152639902 152639839 1.180000e-04 58.4


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 TraesCS6A01G252700 chr6A 467053427 467056464 3037 True 1951.000000 5611 96.581333 1 3038 3 chr6A.!!$R1 3037
1 TraesCS6A01G252700 chr6B 492217836 492221715 3879 True 1336.333333 3007 92.814333 1 2656 3 chr6B.!!$R2 2655
2 TraesCS6A01G252700 chr6D 328340018 328342162 2144 True 1103.333333 2553 92.082333 753 3038 3 chr6D.!!$R2 2285
3 TraesCS6A01G252700 chr6D 328353434 328354116 682 True 813.000000 813 88.116000 1 689 1 chr6D.!!$R1 688

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
610 611 0.24691 TGACGTGGCGCCAGTAATTA 59.753 50.0 33.73 11.86 0.0 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2315 3569 1.061421 TCAAACGACGAACAAGCACAC 59.939 47.619 0.0 0.0 0.0 3.82 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
82 83 5.107989 CCACGTCGTCATGTTACTATTATGC 60.108 44.000 0.00 0.00 0.00 3.14
90 91 7.382218 CGTCATGTTACTATTATGCAGATCACA 59.618 37.037 0.00 0.00 0.00 3.58
148 149 2.716217 GGTTCACCATAGAAGCTTGCT 58.284 47.619 2.10 3.53 41.48 3.91
168 169 1.382522 AGGCGCCAATCAACACTATG 58.617 50.000 31.54 0.00 0.00 2.23
172 173 1.327460 CGCCAATCAACACTATGTCCG 59.673 52.381 0.00 0.00 0.00 4.79
225 226 5.646215 AGTACCCCAACACCATTTCATTAA 58.354 37.500 0.00 0.00 0.00 1.40
229 230 6.078664 ACCCCAACACCATTTCATTAAACTA 58.921 36.000 0.00 0.00 0.00 2.24
255 256 4.396478 TGTCAAAACGAACAAGATCACCAA 59.604 37.500 0.00 0.00 0.00 3.67
332 333 3.328931 AGATAAATCACATCCGCTCCCAT 59.671 43.478 0.00 0.00 0.00 4.00
338 339 3.620785 ATCCGCTCCCATCCGCTC 61.621 66.667 0.00 0.00 0.00 5.03
364 365 4.167268 GAGATCCAACAACTCACGTACTC 58.833 47.826 0.00 0.00 0.00 2.59
366 367 1.342174 TCCAACAACTCACGTACTCCC 59.658 52.381 0.00 0.00 0.00 4.30
367 368 1.069513 CCAACAACTCACGTACTCCCA 59.930 52.381 0.00 0.00 0.00 4.37
400 401 4.394920 GCATGTCGGGATAGTTTCAGAAAA 59.605 41.667 0.00 0.00 0.00 2.29
401 402 5.106317 GCATGTCGGGATAGTTTCAGAAAAA 60.106 40.000 0.00 0.00 0.00 1.94
421 422 3.594603 AAGACTTTCATCATCGTCGGT 57.405 42.857 0.00 0.00 0.00 4.69
442 443 1.237285 GCCAGTGCAACGAGGAACAT 61.237 55.000 0.00 0.00 45.86 2.71
448 449 0.721718 GCAACGAGGAACATCGAAGG 59.278 55.000 15.25 5.59 45.56 3.46
449 450 1.671850 GCAACGAGGAACATCGAAGGA 60.672 52.381 15.25 0.00 45.56 3.36
473 474 1.061546 AAACTCTCAGGGGCCGTTTA 58.938 50.000 0.00 0.00 0.00 2.01
474 475 0.323957 AACTCTCAGGGGCCGTTTAC 59.676 55.000 0.00 0.00 0.00 2.01
508 509 2.998097 CCTCGCCAAATCAGGGGA 59.002 61.111 0.00 0.00 46.95 4.81
512 513 1.153168 CGCCAAATCAGGGGATCGT 60.153 57.895 0.00 0.00 43.81 3.73
523 524 6.874278 ATCAGGGGATCGTCAATATATTGA 57.126 37.500 21.67 21.67 43.94 2.57
535 536 4.216902 TCAATATATTGACGGACGGATCGT 59.783 41.667 21.67 0.00 41.46 3.73
536 537 4.778534 ATATATTGACGGACGGATCGTT 57.221 40.909 0.00 0.00 41.37 3.85
537 538 2.945447 TATTGACGGACGGATCGTTT 57.055 45.000 0.00 0.00 41.37 3.60
542 543 2.822701 GGACGGATCGTTTGCCCC 60.823 66.667 0.00 0.00 41.37 5.80
543 544 2.822701 GACGGATCGTTTGCCCCC 60.823 66.667 0.00 0.00 41.37 5.40
578 579 3.124466 CGTGGATGTAGAATCAAACGCAA 59.876 43.478 0.00 0.00 0.00 4.85
610 611 0.246910 TGACGTGGCGCCAGTAATTA 59.753 50.000 33.73 11.86 0.00 1.40
641 642 1.227999 AAACGGTGTCATGTGGCTCG 61.228 55.000 0.00 0.00 0.00 5.03
644 645 1.293498 GGTGTCATGTGGCTCGAGT 59.707 57.895 15.13 0.00 0.00 4.18
655 656 1.298859 GGCTCGAGTGAACGCCAAAT 61.299 55.000 15.13 0.00 42.06 2.32
660 661 4.671766 GCTCGAGTGAACGCCAAATATTTT 60.672 41.667 15.13 0.00 0.00 1.82
676 677 1.448119 TTTTGCATGACAACCGCCGA 61.448 50.000 0.00 0.00 38.23 5.54
692 693 1.635663 CCGACCACGATCCAAACAGC 61.636 60.000 0.00 0.00 42.66 4.40
694 695 1.303317 ACCACGATCCAAACAGCCC 60.303 57.895 0.00 0.00 0.00 5.19
820 2035 4.174411 AGATTGATTCTCACGTGACGAA 57.826 40.909 23.37 23.37 0.00 3.85
840 2055 0.313987 TTGACGACACTGCGTGATCT 59.686 50.000 14.18 0.00 45.72 2.75
915 2131 1.366111 CGGATTAGTGGCACAACGGG 61.366 60.000 21.41 0.19 44.16 5.28
946 2162 2.893398 GTCACCTAGCCGGGTCAG 59.107 66.667 10.79 5.15 37.52 3.51
949 2166 4.400251 ACCTAGCCGGGTCAGCCT 62.400 66.667 10.79 0.00 33.84 4.58
952 2169 2.443390 TAGCCGGGTCAGCCTACC 60.443 66.667 10.79 0.00 38.94 3.18
989 2206 2.885113 GAACCCAAATCTGCGCCC 59.115 61.111 4.18 0.00 0.00 6.13
1401 2621 3.112709 GACGACCTGCCGTGCTTC 61.113 66.667 0.00 0.00 43.49 3.86
1704 2924 2.780094 CGAGATGGCGGAGTGCTCT 61.780 63.158 0.00 0.00 45.43 4.09
2085 3320 5.182001 AGTTATGTGGTGCTGAAATTCTGTC 59.818 40.000 2.00 0.00 0.00 3.51
2166 3401 5.751243 TTCTGTCCAAAACTTAGCAAGTC 57.249 39.130 2.65 0.00 41.91 3.01
2315 3569 6.607735 TCGTTTGTAAGAAAGTTTACCTGG 57.392 37.500 0.00 0.00 33.56 4.45
2335 3589 1.061421 GTGTGCTTGTTCGTCGTTTGA 59.939 47.619 0.00 0.00 0.00 2.69
2547 3802 2.159599 AGCACGCGTCAACTAGTACTAC 60.160 50.000 9.86 0.00 0.00 2.73
2548 3803 2.159599 GCACGCGTCAACTAGTACTACT 60.160 50.000 9.86 0.00 0.00 2.57
2614 3874 7.406031 TCTTGTCTAGGGAGTTAACACTATG 57.594 40.000 8.61 2.88 31.22 2.23
2665 3925 8.541899 TCACTCAAATTTTAGGGGTTAAGTTT 57.458 30.769 1.87 0.00 0.00 2.66
2712 3972 4.608170 TTGATTAGAATTTGCCCCCTCT 57.392 40.909 0.00 0.00 0.00 3.69
2713 3973 4.170468 TGATTAGAATTTGCCCCCTCTC 57.830 45.455 0.00 0.00 0.00 3.20
2714 3974 3.788142 TGATTAGAATTTGCCCCCTCTCT 59.212 43.478 0.00 0.00 0.00 3.10
2715 3975 4.975147 TGATTAGAATTTGCCCCCTCTCTA 59.025 41.667 0.00 0.00 0.00 2.43
2716 3976 5.612688 TGATTAGAATTTGCCCCCTCTCTAT 59.387 40.000 0.00 0.00 0.00 1.98
2717 3977 5.568620 TTAGAATTTGCCCCCTCTCTATC 57.431 43.478 0.00 0.00 0.00 2.08
2718 3978 2.713708 AGAATTTGCCCCCTCTCTATCC 59.286 50.000 0.00 0.00 0.00 2.59
2719 3979 1.450360 ATTTGCCCCCTCTCTATCCC 58.550 55.000 0.00 0.00 0.00 3.85
2720 3980 0.045623 TTTGCCCCCTCTCTATCCCA 59.954 55.000 0.00 0.00 0.00 4.37
2721 3981 0.271927 TTGCCCCCTCTCTATCCCAT 59.728 55.000 0.00 0.00 0.00 4.00
2722 3982 1.176182 TGCCCCCTCTCTATCCCATA 58.824 55.000 0.00 0.00 0.00 2.74
2723 3983 1.512194 TGCCCCCTCTCTATCCCATAA 59.488 52.381 0.00 0.00 0.00 1.90
2724 3984 2.089638 TGCCCCCTCTCTATCCCATAAA 60.090 50.000 0.00 0.00 0.00 1.40
2725 3985 2.986728 GCCCCCTCTCTATCCCATAAAA 59.013 50.000 0.00 0.00 0.00 1.52
2726 3986 3.397955 GCCCCCTCTCTATCCCATAAAAA 59.602 47.826 0.00 0.00 0.00 1.94
2727 3987 4.507512 GCCCCCTCTCTATCCCATAAAAAG 60.508 50.000 0.00 0.00 0.00 2.27
2728 3988 4.665483 CCCCCTCTCTATCCCATAAAAAGT 59.335 45.833 0.00 0.00 0.00 2.66
2762 4022 0.883833 CTTTTGCAATCACCGCCTCT 59.116 50.000 0.00 0.00 0.00 3.69
2769 4029 2.257409 AATCACCGCCTCTCGCCATT 62.257 55.000 0.00 0.00 36.73 3.16
2804 4064 2.202797 CTCCGGCCATGTCACTCG 60.203 66.667 2.24 0.00 0.00 4.18
2807 4067 2.501128 CGGCCATGTCACTCGGAT 59.499 61.111 2.24 0.00 0.00 4.18
2815 4075 0.678950 TGTCACTCGGATGCTCACAA 59.321 50.000 0.00 0.00 0.00 3.33
2816 4076 1.276138 TGTCACTCGGATGCTCACAAT 59.724 47.619 0.00 0.00 0.00 2.71
2820 4080 0.533755 CTCGGATGCTCACAATCCCC 60.534 60.000 0.00 0.00 0.00 4.81
2821 4081 1.224315 CGGATGCTCACAATCCCCA 59.776 57.895 0.00 0.00 0.00 4.96
2824 4084 0.753111 GATGCTCACAATCCCCACCC 60.753 60.000 0.00 0.00 0.00 4.61
2836 4096 2.268076 CCCACCCTTCCAAGTTGCG 61.268 63.158 0.00 0.00 0.00 4.85
2837 4097 2.268076 CCACCCTTCCAAGTTGCGG 61.268 63.158 0.00 0.00 0.00 5.69
2841 4101 0.958876 CCCTTCCAAGTTGCGGTACC 60.959 60.000 0.16 0.16 0.00 3.34
2852 4112 2.502093 CGGTACCGCCTATTGCCA 59.498 61.111 23.44 0.00 36.24 4.92
2853 4113 1.885850 CGGTACCGCCTATTGCCAC 60.886 63.158 23.44 0.00 36.24 5.01
2854 4114 1.525306 GGTACCGCCTATTGCCACC 60.525 63.158 0.00 0.00 36.24 4.61
2855 4115 1.222387 GTACCGCCTATTGCCACCA 59.778 57.895 0.00 0.00 36.24 4.17
2856 4116 1.093496 GTACCGCCTATTGCCACCAC 61.093 60.000 0.00 0.00 36.24 4.16
2857 4117 1.268992 TACCGCCTATTGCCACCACT 61.269 55.000 0.00 0.00 36.24 4.00
2858 4118 1.819632 CCGCCTATTGCCACCACTC 60.820 63.158 0.00 0.00 36.24 3.51
2859 4119 1.221840 CGCCTATTGCCACCACTCT 59.778 57.895 0.00 0.00 36.24 3.24
2860 4120 0.392998 CGCCTATTGCCACCACTCTT 60.393 55.000 0.00 0.00 36.24 2.85
2861 4121 1.098050 GCCTATTGCCACCACTCTTG 58.902 55.000 0.00 0.00 0.00 3.02
2862 4122 1.098050 CCTATTGCCACCACTCTTGC 58.902 55.000 0.00 0.00 0.00 4.01
2863 4123 1.614051 CCTATTGCCACCACTCTTGCA 60.614 52.381 0.00 0.00 0.00 4.08
2864 4124 2.161855 CTATTGCCACCACTCTTGCAA 58.838 47.619 0.00 0.00 46.51 4.08
2865 4125 0.675633 ATTGCCACCACTCTTGCAAC 59.324 50.000 0.00 0.00 45.44 4.17
2866 4126 0.682532 TTGCCACCACTCTTGCAACA 60.683 50.000 0.00 0.00 38.68 3.33
2867 4127 0.682532 TGCCACCACTCTTGCAACAA 60.683 50.000 0.00 0.00 0.00 2.83
2868 4128 0.249031 GCCACCACTCTTGCAACAAC 60.249 55.000 0.00 0.00 0.00 3.32
2869 4129 0.385390 CCACCACTCTTGCAACAACC 59.615 55.000 0.00 0.00 0.00 3.77
2870 4130 1.102154 CACCACTCTTGCAACAACCA 58.898 50.000 0.00 0.00 0.00 3.67
2871 4131 1.102978 ACCACTCTTGCAACAACCAC 58.897 50.000 0.00 0.00 0.00 4.16
2872 4132 0.385390 CCACTCTTGCAACAACCACC 59.615 55.000 0.00 0.00 0.00 4.61
2873 4133 1.392589 CACTCTTGCAACAACCACCT 58.607 50.000 0.00 0.00 0.00 4.00
2874 4134 1.334869 CACTCTTGCAACAACCACCTC 59.665 52.381 0.00 0.00 0.00 3.85
2875 4135 1.212935 ACTCTTGCAACAACCACCTCT 59.787 47.619 0.00 0.00 0.00 3.69
2876 4136 2.301346 CTCTTGCAACAACCACCTCTT 58.699 47.619 0.00 0.00 0.00 2.85
2877 4137 2.023673 TCTTGCAACAACCACCTCTTG 58.976 47.619 0.00 0.00 0.00 3.02
2878 4138 0.459489 TTGCAACAACCACCTCTTGC 59.541 50.000 0.00 0.00 39.60 4.01
2879 4139 0.395586 TGCAACAACCACCTCTTGCT 60.396 50.000 0.00 0.00 39.81 3.91
2880 4140 1.133945 TGCAACAACCACCTCTTGCTA 60.134 47.619 0.00 0.00 39.81 3.49
2881 4141 1.266989 GCAACAACCACCTCTTGCTAC 59.733 52.381 0.00 0.00 36.81 3.58
2882 4142 2.851195 CAACAACCACCTCTTGCTACT 58.149 47.619 0.00 0.00 0.00 2.57
2883 4143 3.805807 GCAACAACCACCTCTTGCTACTA 60.806 47.826 0.00 0.00 36.81 1.82
2884 4144 4.385825 CAACAACCACCTCTTGCTACTAA 58.614 43.478 0.00 0.00 0.00 2.24
2885 4145 4.273148 ACAACCACCTCTTGCTACTAAG 57.727 45.455 0.00 0.00 0.00 2.18
2902 4162 2.105128 GCTGTAGCTCGCGGTCAT 59.895 61.111 6.13 0.00 38.21 3.06
2903 4163 1.946650 GCTGTAGCTCGCGGTCATC 60.947 63.158 6.13 0.00 38.21 2.92
2904 4164 1.433471 CTGTAGCTCGCGGTCATCA 59.567 57.895 6.13 0.00 0.00 3.07
2924 4184 1.739562 CACTGTGCCGGAAGAGCTC 60.740 63.158 6.48 5.27 0.00 4.09
2968 4236 2.503382 GCCTCCTAAGCCTCCTCCG 61.503 68.421 0.00 0.00 0.00 4.63
2982 4250 2.428530 CTCCTCCGACACATCTTCATCA 59.571 50.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 2.342910 AGTAACATGACGACGTGGTC 57.657 50.000 22.17 22.17 37.35 4.02
82 83 5.491070 TCTTGGTCCTATTTGTGTGATCTG 58.509 41.667 0.00 0.00 0.00 2.90
121 122 4.225942 AGCTTCTATGGTGAACCTGATTGA 59.774 41.667 0.37 0.00 36.82 2.57
148 149 2.093181 ACATAGTGTTGATTGGCGCCTA 60.093 45.455 29.70 22.36 0.00 3.93
168 169 5.783100 TTTATTGATGGTTAACGACGGAC 57.217 39.130 0.00 0.00 0.00 4.79
172 173 9.931210 CCTCTAATTTTATTGATGGTTAACGAC 57.069 33.333 0.00 0.00 0.00 4.34
206 207 5.482163 AGTTTAATGAAATGGTGTTGGGG 57.518 39.130 0.00 0.00 0.00 4.96
225 226 8.402472 TGATCTTGTTCGTTTTGACAATTAGTT 58.598 29.630 0.00 0.00 0.00 2.24
229 230 5.977129 GGTGATCTTGTTCGTTTTGACAATT 59.023 36.000 0.00 0.00 0.00 2.32
255 256 5.705609 ATTGAGTTCAACATTAACCGCTT 57.294 34.783 0.00 0.00 38.86 4.68
332 333 4.785575 TGGATCTCCAAGAGCGGA 57.214 55.556 0.00 0.00 44.35 5.54
364 365 1.293924 GACATGCTCTCAACGATGGG 58.706 55.000 0.00 0.00 0.00 4.00
366 367 0.926155 CCGACATGCTCTCAACGATG 59.074 55.000 0.00 0.00 0.00 3.84
367 368 0.179100 CCCGACATGCTCTCAACGAT 60.179 55.000 0.00 0.00 0.00 3.73
400 401 3.926616 ACCGACGATGATGAAAGTCTTT 58.073 40.909 0.00 0.00 0.00 2.52
401 402 3.594603 ACCGACGATGATGAAAGTCTT 57.405 42.857 0.00 0.00 0.00 3.01
412 413 1.878522 GCACTGGCTACCGACGATG 60.879 63.158 0.00 0.00 36.96 3.84
413 414 1.884075 TTGCACTGGCTACCGACGAT 61.884 55.000 0.00 0.00 41.91 3.73
421 422 0.320421 GTTCCTCGTTGCACTGGCTA 60.320 55.000 0.00 0.00 41.91 3.93
461 462 1.094785 CATGAAGTAAACGGCCCCTG 58.905 55.000 0.00 0.00 0.00 4.45
462 463 0.679960 GCATGAAGTAAACGGCCCCT 60.680 55.000 0.00 0.00 0.00 4.79
512 513 4.216902 ACGATCCGTCCGTCAATATATTGA 59.783 41.667 21.67 21.67 39.04 2.57
523 524 2.433664 GGCAAACGATCCGTCCGT 60.434 61.111 0.00 0.00 39.99 4.69
528 529 4.770874 ACGGGGGCAAACGATCCG 62.771 66.667 0.00 0.00 45.42 4.18
530 531 1.504900 GAAACGGGGGCAAACGATC 59.495 57.895 0.00 0.00 0.00 3.69
531 532 2.329614 CGAAACGGGGGCAAACGAT 61.330 57.895 0.00 0.00 0.00 3.73
553 554 3.309682 CGTTTGATTCTACATCCACGCAT 59.690 43.478 0.00 0.00 0.00 4.73
559 560 3.369756 TCGTTGCGTTTGATTCTACATCC 59.630 43.478 0.00 0.00 0.00 3.51
561 562 3.124636 GGTCGTTGCGTTTGATTCTACAT 59.875 43.478 0.00 0.00 0.00 2.29
564 565 1.722464 CGGTCGTTGCGTTTGATTCTA 59.278 47.619 0.00 0.00 0.00 2.10
570 571 1.749153 AAAATCGGTCGTTGCGTTTG 58.251 45.000 0.00 0.00 0.00 2.93
603 604 6.433093 ACCGTTTGAATCAAAGCCTAATTACT 59.567 34.615 8.88 0.00 33.82 2.24
610 611 2.293399 GACACCGTTTGAATCAAAGCCT 59.707 45.455 8.88 0.00 33.82 4.58
615 616 3.004210 CCACATGACACCGTTTGAATCAA 59.996 43.478 0.00 0.00 0.00 2.57
616 617 2.551887 CCACATGACACCGTTTGAATCA 59.448 45.455 0.00 0.00 0.00 2.57
619 620 0.665835 GCCACATGACACCGTTTGAA 59.334 50.000 0.00 0.00 0.00 2.69
620 621 0.179032 AGCCACATGACACCGTTTGA 60.179 50.000 0.00 0.00 0.00 2.69
641 642 4.233789 TGCAAAATATTTGGCGTTCACTC 58.766 39.130 20.14 0.00 40.01 3.51
644 645 4.624882 GTCATGCAAAATATTTGGCGTTCA 59.375 37.500 17.97 6.78 40.01 3.18
655 656 1.135546 CGGCGGTTGTCATGCAAAATA 60.136 47.619 0.00 0.00 39.03 1.40
660 661 3.047280 GTCGGCGGTTGTCATGCA 61.047 61.111 7.21 0.00 0.00 3.96
676 677 1.303317 GGGCTGTTTGGATCGTGGT 60.303 57.895 0.00 0.00 0.00 4.16
706 707 4.459089 GCTCTTCTCCGGCGGCTT 62.459 66.667 23.83 0.00 0.00 4.35
709 710 2.176273 CATTGCTCTTCTCCGGCGG 61.176 63.158 22.51 22.51 0.00 6.13
717 718 1.808133 CGTCCCCTAGCATTGCTCTTC 60.808 57.143 15.81 0.89 40.44 2.87
718 719 0.179000 CGTCCCCTAGCATTGCTCTT 59.821 55.000 15.81 0.00 40.44 2.85
746 747 1.074566 CCTGGCCAAGGTTTTCTCTCT 59.925 52.381 7.01 0.00 41.74 3.10
772 774 3.157087 CCAACATTGGTAAAGCCTCACT 58.843 45.455 2.22 0.00 43.43 3.41
773 775 3.575965 CCAACATTGGTAAAGCCTCAC 57.424 47.619 2.22 0.00 43.43 3.51
915 2131 2.087009 GTGACGCTGTACCGCACTC 61.087 63.158 10.03 3.89 34.66 3.51
921 2137 1.141234 GGCTAGGTGACGCTGTACC 59.859 63.158 0.00 0.00 37.23 3.34
923 2139 3.193757 CGGCTAGGTGACGCTGTA 58.806 61.111 0.00 0.00 41.83 2.74
946 2162 1.254026 GGTTTCTTGGGTTGGTAGGC 58.746 55.000 0.00 0.00 0.00 3.93
949 2166 3.492337 GATGTGGTTTCTTGGGTTGGTA 58.508 45.455 0.00 0.00 0.00 3.25
952 2169 1.269448 CGGATGTGGTTTCTTGGGTTG 59.731 52.381 0.00 0.00 0.00 3.77
1107 2327 1.032114 CAAAAGATGGGGAGGCGGTC 61.032 60.000 0.00 0.00 0.00 4.79
2166 3401 8.236585 TCATTTGATACCATGTTATTTCAGGG 57.763 34.615 0.00 0.00 43.73 4.45
2219 3459 6.152661 CCCATGCAGTAGGAACTCAAAAATTA 59.847 38.462 4.33 0.00 41.75 1.40
2315 3569 1.061421 TCAAACGACGAACAAGCACAC 59.939 47.619 0.00 0.00 0.00 3.82
2426 3681 6.780522 AGTACCTGAAATGTTTTACCACCATT 59.219 34.615 0.00 0.00 0.00 3.16
2548 3803 3.543665 GGAAAGACCTAGAGACGCTCTA 58.456 50.000 13.54 13.54 41.50 2.43
2665 3925 9.839185 AATATAGGCAGAATTTACTACTCCCTA 57.161 33.333 0.00 0.00 0.00 3.53
2712 3972 8.575736 TTCCTCCATACTTTTTATGGGATAGA 57.424 34.615 9.87 1.19 43.50 1.98
2713 3973 8.440771 ACTTCCTCCATACTTTTTATGGGATAG 58.559 37.037 9.87 1.73 43.50 2.08
2714 3974 8.344939 ACTTCCTCCATACTTTTTATGGGATA 57.655 34.615 9.87 0.00 43.50 2.59
2715 3975 7.226059 ACTTCCTCCATACTTTTTATGGGAT 57.774 36.000 9.87 0.00 43.50 3.85
2716 3976 6.652205 ACTTCCTCCATACTTTTTATGGGA 57.348 37.500 9.87 0.00 43.50 4.37
2717 3977 7.147897 GGAAACTTCCTCCATACTTTTTATGGG 60.148 40.741 9.87 2.36 44.11 4.00
2718 3978 7.772166 GGAAACTTCCTCCATACTTTTTATGG 58.228 38.462 4.19 4.19 44.11 2.74
2747 4007 2.125552 CGAGAGGCGGTGATTGCA 60.126 61.111 0.00 0.00 36.03 4.08
2772 4032 2.815647 GAGAGGTTGCCGGCTTCG 60.816 66.667 29.70 0.00 0.00 3.79
2804 4064 0.753111 GGTGGGGATTGTGAGCATCC 60.753 60.000 0.00 0.00 0.00 3.51
2807 4067 1.434513 AAGGGTGGGGATTGTGAGCA 61.435 55.000 0.00 0.00 0.00 4.26
2815 4075 0.409484 CAACTTGGAAGGGTGGGGAT 59.591 55.000 0.00 0.00 0.00 3.85
2816 4076 1.850549 CAACTTGGAAGGGTGGGGA 59.149 57.895 0.00 0.00 0.00 4.81
2820 4080 0.250553 TACCGCAACTTGGAAGGGTG 60.251 55.000 0.00 0.00 0.00 4.61
2821 4081 0.250597 GTACCGCAACTTGGAAGGGT 60.251 55.000 0.00 0.00 0.00 4.34
2824 4084 2.159181 CGGTACCGCAACTTGGAAG 58.841 57.895 23.44 0.00 0.00 3.46
2836 4096 1.525306 GGTGGCAATAGGCGGTACC 60.525 63.158 0.16 0.16 46.16 3.34
2837 4097 1.093496 GTGGTGGCAATAGGCGGTAC 61.093 60.000 0.00 0.00 46.16 3.34
2841 4101 0.392998 AAGAGTGGTGGCAATAGGCG 60.393 55.000 0.00 0.00 46.16 5.52
2845 4105 1.885887 GTTGCAAGAGTGGTGGCAATA 59.114 47.619 0.00 0.00 46.52 1.90
2846 4106 0.675633 GTTGCAAGAGTGGTGGCAAT 59.324 50.000 0.00 0.00 46.52 3.56
2847 4107 0.682532 TGTTGCAAGAGTGGTGGCAA 60.683 50.000 0.00 0.00 43.32 4.52
2848 4108 0.682532 TTGTTGCAAGAGTGGTGGCA 60.683 50.000 0.00 0.00 0.00 4.92
2849 4109 0.249031 GTTGTTGCAAGAGTGGTGGC 60.249 55.000 0.00 0.00 0.00 5.01
2850 4110 0.385390 GGTTGTTGCAAGAGTGGTGG 59.615 55.000 0.00 0.00 0.00 4.61
2851 4111 1.102154 TGGTTGTTGCAAGAGTGGTG 58.898 50.000 0.00 0.00 0.00 4.17
2852 4112 1.102978 GTGGTTGTTGCAAGAGTGGT 58.897 50.000 0.00 0.00 0.00 4.16
2853 4113 0.385390 GGTGGTTGTTGCAAGAGTGG 59.615 55.000 0.00 0.00 0.00 4.00
2854 4114 1.334869 GAGGTGGTTGTTGCAAGAGTG 59.665 52.381 0.00 0.00 0.00 3.51
2855 4115 1.212935 AGAGGTGGTTGTTGCAAGAGT 59.787 47.619 0.00 0.00 0.00 3.24
2856 4116 1.972872 AGAGGTGGTTGTTGCAAGAG 58.027 50.000 0.00 0.00 0.00 2.85
2857 4117 2.023673 CAAGAGGTGGTTGTTGCAAGA 58.976 47.619 0.00 0.00 0.00 3.02
2858 4118 1.536709 GCAAGAGGTGGTTGTTGCAAG 60.537 52.381 0.00 0.00 44.22 4.01
2859 4119 0.459489 GCAAGAGGTGGTTGTTGCAA 59.541 50.000 0.00 0.00 44.22 4.08
2860 4120 0.395586 AGCAAGAGGTGGTTGTTGCA 60.396 50.000 9.95 0.00 46.41 4.08
2861 4121 1.266989 GTAGCAAGAGGTGGTTGTTGC 59.733 52.381 0.21 0.21 44.90 4.17
2862 4122 2.851195 AGTAGCAAGAGGTGGTTGTTG 58.149 47.619 0.00 0.00 39.22 3.33
2863 4123 4.642429 CTTAGTAGCAAGAGGTGGTTGTT 58.358 43.478 0.00 0.00 39.22 2.83
2864 4124 3.557264 GCTTAGTAGCAAGAGGTGGTTGT 60.557 47.826 0.00 0.00 46.95 3.32
2865 4125 3.003480 GCTTAGTAGCAAGAGGTGGTTG 58.997 50.000 0.00 0.00 46.95 3.77
2866 4126 3.336138 GCTTAGTAGCAAGAGGTGGTT 57.664 47.619 0.00 0.00 46.95 3.67
2885 4145 1.946650 GATGACCGCGAGCTACAGC 60.947 63.158 8.23 0.00 42.49 4.40
2886 4146 0.031314 ATGATGACCGCGAGCTACAG 59.969 55.000 8.23 0.00 0.00 2.74
2887 4147 0.030773 GATGATGACCGCGAGCTACA 59.969 55.000 8.23 2.34 0.00 2.74
2888 4148 0.030773 TGATGATGACCGCGAGCTAC 59.969 55.000 8.23 0.00 0.00 3.58
2889 4149 0.030773 GTGATGATGACCGCGAGCTA 59.969 55.000 8.23 0.00 0.00 3.32
2890 4150 1.227089 GTGATGATGACCGCGAGCT 60.227 57.895 8.23 0.00 0.00 4.09
2891 4151 1.227089 AGTGATGATGACCGCGAGC 60.227 57.895 8.23 0.00 0.00 5.03
2892 4152 0.179127 ACAGTGATGATGACCGCGAG 60.179 55.000 8.23 0.00 0.00 5.03
2893 4153 0.458370 CACAGTGATGATGACCGCGA 60.458 55.000 8.23 0.00 0.00 5.87
2894 4154 2.001357 CACAGTGATGATGACCGCG 58.999 57.895 0.00 0.00 0.00 6.46
2895 4155 1.709147 GGCACAGTGATGATGACCGC 61.709 60.000 4.15 0.00 0.00 5.68
2896 4156 1.423721 CGGCACAGTGATGATGACCG 61.424 60.000 4.15 1.65 35.67 4.79
2897 4157 1.091771 CCGGCACAGTGATGATGACC 61.092 60.000 4.15 0.00 0.00 4.02
2898 4158 0.108186 TCCGGCACAGTGATGATGAC 60.108 55.000 4.15 0.00 0.00 3.06
2899 4159 0.612744 TTCCGGCACAGTGATGATGA 59.387 50.000 4.15 0.00 0.00 2.92
2900 4160 1.012086 CTTCCGGCACAGTGATGATG 58.988 55.000 4.15 0.00 0.00 3.07
2901 4161 0.904649 TCTTCCGGCACAGTGATGAT 59.095 50.000 4.15 0.00 0.00 2.45
2902 4162 0.247460 CTCTTCCGGCACAGTGATGA 59.753 55.000 4.15 0.00 0.00 2.92
2903 4163 1.364626 GCTCTTCCGGCACAGTGATG 61.365 60.000 4.15 0.00 0.00 3.07
2904 4164 1.078848 GCTCTTCCGGCACAGTGAT 60.079 57.895 4.15 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.