Multiple sequence alignment - TraesCS6D01G086900

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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 TraesCS6D01G086900 chr6D 100.000 4255 0 0 1 4255 52348894 52344640 0.000000e+00 7858.0
1 TraesCS6D01G086900 chr6D 84.694 686 91 11 174 849 163352290 163351609 0.000000e+00 673.0
2 TraesCS6D01G086900 chr6D 90.909 55 5 0 3892 3946 159799714 159799768 1.640000e-09 75.0
3 TraesCS6D01G086900 chr6A 92.257 2725 123 42 915 3595 63172944 63170264 0.000000e+00 3783.0
4 TraesCS6D01G086900 chr6A 89.194 583 58 4 265 845 63174011 63173432 0.000000e+00 723.0
5 TraesCS6D01G086900 chr6A 88.215 297 16 6 3962 4241 63128936 63128642 1.900000e-88 337.0
6 TraesCS6D01G086900 chr6A 94.009 217 13 0 3628 3844 63170272 63170056 3.170000e-86 329.0
7 TraesCS6D01G086900 chr6A 91.667 120 9 1 1 119 63174159 63174040 9.470000e-37 165.0
8 TraesCS6D01G086900 chr6A 100.000 32 0 0 3860 3891 63170055 63170024 4.590000e-05 60.2
9 TraesCS6D01G086900 chr6B 92.446 2383 132 26 910 3279 119136652 119134305 0.000000e+00 3360.0
10 TraesCS6D01G086900 chr6B 92.466 876 47 9 3398 4255 119133979 119133105 0.000000e+00 1234.0
11 TraesCS6D01G086900 chr6B 89.932 586 48 3 265 849 119137758 119137183 0.000000e+00 745.0
12 TraesCS6D01G086900 chr6B 96.721 122 3 1 3276 3397 119134191 119134071 7.210000e-48 202.0
13 TraesCS6D01G086900 chr6B 91.667 120 8 2 1 119 119137905 119137787 9.470000e-37 165.0
14 TraesCS6D01G086900 chr2B 85.836 819 100 11 40 849 417251889 417251078 0.000000e+00 856.0
15 TraesCS6D01G086900 chr3D 84.499 858 116 9 1 850 431224584 431225432 0.000000e+00 832.0
16 TraesCS6D01G086900 chr2D 85.972 777 90 13 7 773 351064765 351063998 0.000000e+00 813.0
17 TraesCS6D01G086900 chr2A 83.721 860 121 12 1 849 468596013 468595162 0.000000e+00 795.0
18 TraesCS6D01G086900 chr5B 94.828 58 2 1 1646 1702 575975679 575975736 5.860000e-14 89.8
19 TraesCS6D01G086900 chr4A 75.904 166 29 10 4004 4163 49979153 49979313 1.640000e-09 75.0
20 TraesCS6D01G086900 chr5D 95.122 41 2 0 1662 1702 310496650 310496610 9.880000e-07 65.8
21 TraesCS6D01G086900 chr7B 88.000 50 3 3 3897 3945 92324930 92324977 5.940000e-04 56.5
22 TraesCS6D01G086900 chr1B 92.308 39 3 0 4120 4158 202629753 202629791 5.940000e-04 56.5


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 TraesCS6D01G086900 chr6D 52344640 52348894 4254 True 7858.00 7858 100.0000 1 4255 1 chr6D.!!$R1 4254
1 TraesCS6D01G086900 chr6D 163351609 163352290 681 True 673.00 673 84.6940 174 849 1 chr6D.!!$R2 675
2 TraesCS6D01G086900 chr6A 63170024 63174159 4135 True 1012.04 3783 93.4254 1 3891 5 chr6A.!!$R2 3890
3 TraesCS6D01G086900 chr6B 119133105 119137905 4800 True 1141.20 3360 92.6464 1 4255 5 chr6B.!!$R1 4254
4 TraesCS6D01G086900 chr2B 417251078 417251889 811 True 856.00 856 85.8360 40 849 1 chr2B.!!$R1 809
5 TraesCS6D01G086900 chr3D 431224584 431225432 848 False 832.00 832 84.4990 1 850 1 chr3D.!!$F1 849
6 TraesCS6D01G086900 chr2D 351063998 351064765 767 True 813.00 813 85.9720 7 773 1 chr2D.!!$R1 766
7 TraesCS6D01G086900 chr2A 468595162 468596013 851 True 795.00 795 83.7210 1 849 1 chr2A.!!$R1 848

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
909 941 0.034059 CTCGTGCTGGACTTGGACTT 59.966 55.0 0.00 0.0 0.00 3.01 F
1229 1745 0.031585 TCCGAGTATCCAAATCGCGG 59.968 55.0 6.13 0.0 43.61 6.46 F
2995 3541 0.615850 GGCCTGTAAAGCTCTCCAGT 59.384 55.0 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
2840 3386 0.605589 GGGTCAACACTGGTGGTAGC 60.606 60.000 5.7 0.0 34.19 3.58 R
3149 3710 3.202906 GCTCACCAAGTAACACAAGACA 58.797 45.455 0.0 0.0 0.00 3.41 R
3925 4699 3.862124 CGGAGCTGACTTGTTCGG 58.138 61.111 0.0 0.0 0.00 4.30 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
66 67 2.401351 GTACTGTGTTCTCACCGGTTC 58.599 52.381 2.97 0.00 43.26 3.62
118 125 5.013079 TCCAAGCTCTAGAAGATTTTGTGGA 59.987 40.000 0.00 0.00 28.98 4.02
122 129 6.715280 AGCTCTAGAAGATTTTGTGGATTGA 58.285 36.000 0.00 0.00 0.00 2.57
138 145 8.094798 TGTGGATTGACAATTTACTAAGTCAC 57.905 34.615 1.39 0.00 40.37 3.67
157 164 5.236478 AGTCACGAACATTTTCAGTTAGGTG 59.764 40.000 0.00 0.00 36.04 4.00
158 165 5.235616 GTCACGAACATTTTCAGTTAGGTGA 59.764 40.000 0.00 0.00 38.79 4.02
159 166 5.818336 TCACGAACATTTTCAGTTAGGTGAA 59.182 36.000 0.00 0.00 38.47 3.18
237 248 9.784376 ATAGCCCTGGTAAGTCTCATATAAATA 57.216 33.333 0.00 0.00 0.00 1.40
238 249 8.506196 AGCCCTGGTAAGTCTCATATAAATAA 57.494 34.615 0.00 0.00 0.00 1.40
312 323 2.247358 GATGGAAGGTTTTGAAGGGCA 58.753 47.619 0.00 0.00 0.00 5.36
386 398 5.338219 CCCAATGCCCATTTTGTAAGATTGA 60.338 40.000 0.00 0.00 0.00 2.57
452 465 6.292919 GCGAATGAGATATGGACCAAACTAAC 60.293 42.308 0.00 0.00 0.00 2.34
509 522 0.105039 CACTCGGGCTCTATCAACCC 59.895 60.000 0.00 0.00 40.51 4.11
533 546 4.338379 AAGCTCTTCTCCAACTACGTTT 57.662 40.909 0.00 0.00 0.00 3.60
538 551 3.385433 TCTTCTCCAACTACGTTTGGTGA 59.615 43.478 16.62 16.37 45.60 4.02
559 572 4.466015 TGATGCATGAACTACCAGTAGTGA 59.534 41.667 2.46 2.35 44.96 3.41
563 576 3.570926 TGAACTACCAGTAGTGAAGCG 57.429 47.619 11.09 0.00 44.96 4.68
654 672 6.544197 AGAACTCAGAGAGAATAGCGATAACA 59.456 38.462 3.79 0.00 33.32 2.41
657 675 7.144661 ACTCAGAGAGAATAGCGATAACAATG 58.855 38.462 3.79 0.00 33.32 2.82
675 693 6.787085 ACAATGTGAGTTCTAGCTACAAAC 57.213 37.500 6.25 6.25 0.00 2.93
694 712 6.646267 ACAAACTTTATCCGGAGCTATACAA 58.354 36.000 11.34 0.00 0.00 2.41
707 727 5.992217 GGAGCTATACAATGAACCAACCTAG 59.008 44.000 0.00 0.00 0.00 3.02
708 728 6.183360 GGAGCTATACAATGAACCAACCTAGA 60.183 42.308 0.00 0.00 0.00 2.43
731 754 3.079578 CAGGAAATCTGAGCATGTGTGT 58.920 45.455 0.00 0.00 46.18 3.72
745 769 3.617540 TGTGTGTAGAAACCAAATGCG 57.382 42.857 0.00 0.00 0.00 4.73
759 783 4.283722 ACCAAATGCGGGGTATGTTAAAAA 59.716 37.500 0.00 0.00 35.09 1.94
760 784 4.627900 CCAAATGCGGGGTATGTTAAAAAC 59.372 41.667 0.00 0.00 0.00 2.43
773 804 4.744570 TGTTAAAAACCAATGTTGACGCA 58.255 34.783 0.00 0.00 34.13 5.24
850 882 2.094894 CAGTAACTTCATTGCAGCGGAG 59.905 50.000 0.00 0.00 0.00 4.63
852 884 1.446907 AACTTCATTGCAGCGGAGAG 58.553 50.000 0.00 0.00 0.00 3.20
862 894 3.927501 GCGGAGAGCTAGACTGGT 58.072 61.111 0.00 0.00 44.04 4.00
864 896 0.750182 GCGGAGAGCTAGACTGGTCT 60.750 60.000 8.36 8.36 45.97 3.85
869 901 3.211045 GAGAGCTAGACTGGTCTCGATT 58.789 50.000 6.52 0.00 46.78 3.34
870 902 2.948979 AGAGCTAGACTGGTCTCGATTG 59.051 50.000 6.52 0.00 40.28 2.67
871 903 2.028130 AGCTAGACTGGTCTCGATTGG 58.972 52.381 6.52 0.00 40.93 3.16
872 904 2.025155 GCTAGACTGGTCTCGATTGGA 58.975 52.381 6.52 0.00 40.93 3.53
874 906 2.223803 AGACTGGTCTCGATTGGACT 57.776 50.000 3.63 0.00 34.17 3.85
875 907 2.530701 AGACTGGTCTCGATTGGACTT 58.469 47.619 3.63 0.00 34.17 3.01
876 908 2.232452 AGACTGGTCTCGATTGGACTTG 59.768 50.000 3.63 0.65 34.17 3.16
877 909 1.276421 ACTGGTCTCGATTGGACTTGG 59.724 52.381 3.63 0.00 34.47 3.61
878 910 1.550524 CTGGTCTCGATTGGACTTGGA 59.449 52.381 3.63 0.00 34.47 3.53
879 911 1.275291 TGGTCTCGATTGGACTTGGAC 59.725 52.381 3.63 0.00 34.47 4.02
883 915 1.202582 CTCGATTGGACTTGGACTCGT 59.797 52.381 0.00 0.00 0.00 4.18
884 916 1.067846 TCGATTGGACTTGGACTCGTG 60.068 52.381 0.00 0.00 0.00 4.35
885 917 1.079503 GATTGGACTTGGACTCGTGC 58.920 55.000 0.00 0.00 0.00 5.34
886 918 0.687354 ATTGGACTTGGACTCGTGCT 59.313 50.000 0.00 0.00 0.00 4.40
887 919 0.249868 TTGGACTTGGACTCGTGCTG 60.250 55.000 0.00 0.00 0.00 4.41
890 922 0.667792 GACTTGGACTCGTGCTGGTC 60.668 60.000 0.00 0.00 0.00 4.02
891 923 1.115930 ACTTGGACTCGTGCTGGTCT 61.116 55.000 0.00 0.00 33.46 3.85
892 924 0.389166 CTTGGACTCGTGCTGGTCTC 60.389 60.000 0.00 0.00 33.46 3.36
894 926 2.627737 GGACTCGTGCTGGTCTCGT 61.628 63.158 0.00 0.00 33.77 4.18
895 927 1.442857 GACTCGTGCTGGTCTCGTG 60.443 63.158 0.00 0.00 33.77 4.35
897 929 3.274455 CTCGTGCTGGTCTCGTGCT 62.274 63.158 0.00 0.00 33.77 4.40
898 930 3.108289 CGTGCTGGTCTCGTGCTG 61.108 66.667 0.00 0.00 0.00 4.41
899 931 2.740055 GTGCTGGTCTCGTGCTGG 60.740 66.667 0.00 0.00 0.00 4.85
902 934 2.936912 GCTGGTCTCGTGCTGGACT 61.937 63.158 0.00 0.00 33.46 3.85
903 935 1.668294 CTGGTCTCGTGCTGGACTT 59.332 57.895 0.00 0.00 33.46 3.01
904 936 0.668706 CTGGTCTCGTGCTGGACTTG 60.669 60.000 0.00 0.00 33.46 3.16
905 937 1.374758 GGTCTCGTGCTGGACTTGG 60.375 63.158 0.00 0.00 33.46 3.61
906 938 1.666011 GTCTCGTGCTGGACTTGGA 59.334 57.895 0.00 0.00 0.00 3.53
907 939 0.667792 GTCTCGTGCTGGACTTGGAC 60.668 60.000 0.00 0.00 0.00 4.02
908 940 0.827925 TCTCGTGCTGGACTTGGACT 60.828 55.000 0.00 0.00 0.00 3.85
909 941 0.034059 CTCGTGCTGGACTTGGACTT 59.966 55.000 0.00 0.00 0.00 3.01
910 942 0.249868 TCGTGCTGGACTTGGACTTG 60.250 55.000 0.00 0.00 0.00 3.16
911 943 1.230635 CGTGCTGGACTTGGACTTGG 61.231 60.000 0.00 0.00 0.00 3.61
913 945 0.108585 TGCTGGACTTGGACTTGGAC 59.891 55.000 0.00 0.00 0.00 4.02
963 1479 7.864882 GCTTTGTCTCAAAAAGAAAAGCTAGAT 59.135 33.333 17.59 0.00 44.30 1.98
1137 1653 3.090532 GAGGGCGAGTGGGGGATT 61.091 66.667 0.00 0.00 0.00 3.01
1181 1697 1.152989 GAGCAGCAGATGGAGCTTCG 61.153 60.000 0.00 0.00 41.14 3.79
1229 1745 0.031585 TCCGAGTATCCAAATCGCGG 59.968 55.000 6.13 0.00 43.61 6.46
1283 1801 1.328439 CTCGTTTTCCTCTCGTCGTG 58.672 55.000 0.00 0.00 0.00 4.35
1320 1838 1.405391 CGATTCCCCATTGTTTTGGCC 60.405 52.381 0.00 0.00 35.29 5.36
1350 1868 2.151202 CCTTCTTTAGTCGGCTTGCAA 58.849 47.619 0.00 0.00 0.00 4.08
1496 2014 1.731969 CGTTTCGGTCAGGGACGAC 60.732 63.158 0.00 0.00 39.04 4.34
1702 2221 8.114102 TCAGTTAATATGGATCGTAGGGAGTAT 58.886 37.037 0.00 0.00 0.00 2.12
1760 2279 6.866480 TGCAGTTTTTCTCACAGAATCTTTT 58.134 32.000 0.00 0.00 33.67 2.27
1791 2318 9.752961 TTTTTATGCCTGATGAACATTGATATG 57.247 29.630 0.00 0.00 37.79 1.78
1896 2433 2.048603 GGCAGAGCGGAGGCAAAAT 61.049 57.895 0.00 0.00 43.41 1.82
1899 2436 1.001641 AGAGCGGAGGCAAAATGCT 60.002 52.632 2.00 0.00 44.28 3.79
1904 2441 1.138247 GGAGGCAAAATGCTCGCTG 59.862 57.895 2.00 0.00 44.28 5.18
2020 2563 0.718343 CTGCTGAAGCGTTAGTGCTC 59.282 55.000 0.00 0.00 46.60 4.26
2026 2569 0.875059 AAGCGTTAGTGCTCTTTGCC 59.125 50.000 0.00 0.00 46.60 4.52
2467 3013 1.007238 TGCCTAGAGGACAAGGTAGCT 59.993 52.381 0.00 0.00 37.39 3.32
2501 3047 5.013704 TCCAAAGTGATTAGAAGCAGGGTTA 59.986 40.000 0.00 0.00 0.00 2.85
2583 3129 6.090493 GCCACCTTTAAGTTTACTCTTAGTCG 59.910 42.308 0.00 0.00 32.55 4.18
2595 3141 5.923733 ACTCTTAGTCGGATCAAGACAAT 57.076 39.130 18.66 5.75 40.84 2.71
2608 3154 5.309323 TCAAGACAATCATAAAAAGGCCG 57.691 39.130 0.00 0.00 0.00 6.13
2695 3241 1.133790 GGCAAGATCACTGTTGGCATC 59.866 52.381 12.37 0.00 46.63 3.91
2719 3265 1.272147 GGAATTGCTGAGGGTGTCCTT 60.272 52.381 0.00 0.00 45.05 3.36
2821 3367 5.293079 GCTTCCTCTATCAATCAACACAGTC 59.707 44.000 0.00 0.00 0.00 3.51
2840 3386 5.039984 CAGTCTCTCGTGATGGTAAGAATG 58.960 45.833 0.00 0.00 0.00 2.67
2855 3401 2.783135 AGAATGCTACCACCAGTGTTG 58.217 47.619 0.00 0.00 0.00 3.33
2897 3443 1.139058 AGACCTTCGTTGTGACAGCTT 59.861 47.619 0.00 0.00 0.00 3.74
2995 3541 0.615850 GGCCTGTAAAGCTCTCCAGT 59.384 55.000 0.00 0.00 0.00 4.00
3119 3680 7.439356 TGATCAGACTTGTAGCACTAATTATGC 59.561 37.037 10.22 10.22 43.74 3.14
3138 3699 4.782019 TGCGGAAAGAAGCAACAATATT 57.218 36.364 0.00 0.00 40.78 1.28
3139 3700 5.132897 TGCGGAAAGAAGCAACAATATTT 57.867 34.783 0.00 0.00 40.78 1.40
3140 3701 5.537188 TGCGGAAAGAAGCAACAATATTTT 58.463 33.333 0.00 0.00 40.78 1.82
3141 3702 5.633182 TGCGGAAAGAAGCAACAATATTTTC 59.367 36.000 0.00 0.00 40.78 2.29
3142 3703 5.062183 GCGGAAAGAAGCAACAATATTTTCC 59.938 40.000 3.61 3.61 38.96 3.13
3143 3704 6.155827 CGGAAAGAAGCAACAATATTTTCCA 58.844 36.000 12.06 0.00 41.16 3.53
3144 3705 6.813152 CGGAAAGAAGCAACAATATTTTCCAT 59.187 34.615 12.06 0.00 41.16 3.41
3145 3706 7.009540 CGGAAAGAAGCAACAATATTTTCCATC 59.990 37.037 12.06 2.65 41.16 3.51
3146 3707 8.037166 GGAAAGAAGCAACAATATTTTCCATCT 58.963 33.333 7.91 0.00 40.92 2.90
3147 3708 9.428097 GAAAGAAGCAACAATATTTTCCATCTT 57.572 29.630 0.00 0.00 0.00 2.40
3230 3791 6.602803 ACACATGGTAGCATTGTAATCAATCA 59.397 34.615 16.09 0.00 41.66 2.57
3362 4040 5.467063 CAGTAGGAAGAACAAGAACAAGTCC 59.533 44.000 0.00 0.00 0.00 3.85
3496 4265 1.005097 TGCTGATGGAACCTCTGCAAT 59.995 47.619 15.81 0.00 42.32 3.56
3521 4290 6.777580 TGAGAGGGCAAAACTAAAATCTCTTT 59.222 34.615 0.00 0.00 34.44 2.52
3599 4373 7.316640 GTCGAGTACATTATTCATGCCTCTAT 58.683 38.462 0.00 0.00 36.14 1.98
3656 4430 7.499321 TTCCGTTCTCTGTTTGCTTAATAAA 57.501 32.000 0.00 0.00 0.00 1.40
3738 4512 1.497722 CGAAGGCGTTCTTGCTTCC 59.502 57.895 16.45 0.00 35.50 3.46
3751 4525 1.254975 TGCTTCCGCCACTACTAGCA 61.255 55.000 0.00 0.00 36.38 3.49
3944 4718 2.720758 CGAACAAGTCAGCTCCGCG 61.721 63.158 0.00 0.00 0.00 6.46
3960 4734 3.359033 TCCGCGCTACAATAGGGTATAT 58.641 45.455 5.56 0.00 40.50 0.86
3961 4735 3.765511 TCCGCGCTACAATAGGGTATATT 59.234 43.478 5.56 0.00 40.50 1.28
3963 4737 5.595542 TCCGCGCTACAATAGGGTATATTAT 59.404 40.000 5.56 0.00 40.50 1.28
3965 4739 6.460537 CCGCGCTACAATAGGGTATATTATGA 60.461 42.308 5.56 0.00 40.50 2.15
4004 4790 9.807921 AAAAACAAGAAAGATCACTATCCCTAA 57.192 29.630 0.00 0.00 31.98 2.69
4054 4840 7.665690 ACACATCTTTTGTTATGTTAATGGCA 58.334 30.769 0.00 0.00 36.00 4.92
4055 4841 8.313292 ACACATCTTTTGTTATGTTAATGGCAT 58.687 29.630 0.00 0.00 36.00 4.40
4056 4842 9.800433 CACATCTTTTGTTATGTTAATGGCATA 57.200 29.630 0.00 0.00 36.00 3.14
4057 4843 9.801873 ACATCTTTTGTTATGTTAATGGCATAC 57.198 29.630 0.00 0.00 33.74 2.39
4058 4844 9.800433 CATCTTTTGTTATGTTAATGGCATACA 57.200 29.630 0.00 2.44 0.00 2.29
4097 4884 7.363031 ACAAGTGTATCCTAGAGATTAAGGGA 58.637 38.462 0.00 0.00 36.33 4.20
4128 4916 6.884836 ACTTTTACATGTATCCTTGGACCTTC 59.115 38.462 6.36 0.00 0.00 3.46
4141 4929 5.163258 CCTTGGACCTTCTGCTTATAGACAT 60.163 44.000 0.00 0.00 0.00 3.06
4145 4933 6.839134 TGGACCTTCTGCTTATAGACATAAGA 59.161 38.462 8.27 0.00 44.40 2.10
4231 5019 5.221165 GCTATTTTTGTGTACAAGTGGTGGT 60.221 40.000 0.00 0.00 37.15 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.195115 GCACCTCATCCCACTGTCTA 58.805 55.000 0.00 0.00 0.00 2.59
66 67 8.361889 TGGGATTTGCATAATTCTATGAACATG 58.638 33.333 0.00 0.00 37.68 3.21
118 125 8.373048 TGTTCGTGACTTAGTAAATTGTCAAT 57.627 30.769 5.34 0.00 40.47 2.57
122 129 9.659830 GAAAATGTTCGTGACTTAGTAAATTGT 57.340 29.630 0.00 0.00 0.00 2.71
138 145 5.238650 AGGTTCACCTAACTGAAAATGTTCG 59.761 40.000 0.00 0.00 46.48 3.95
157 164 5.119694 GGTTGAACTCCATCTGATAGGTTC 58.880 45.833 15.93 15.93 35.20 3.62
158 165 4.536090 TGGTTGAACTCCATCTGATAGGTT 59.464 41.667 0.00 0.00 0.00 3.50
159 166 4.104086 TGGTTGAACTCCATCTGATAGGT 58.896 43.478 0.00 0.00 0.00 3.08
168 175 3.828451 CCAAACTGATGGTTGAACTCCAT 59.172 43.478 0.00 0.00 46.78 3.41
185 192 4.023963 GCTCTAGAAAAGTGGTGTCCAAAC 60.024 45.833 0.00 0.00 34.18 2.93
237 248 3.960102 TGCCACAAATCTTTCCAGACTTT 59.040 39.130 0.00 0.00 0.00 2.66
238 249 3.565307 TGCCACAAATCTTTCCAGACTT 58.435 40.909 0.00 0.00 0.00 3.01
242 253 1.891150 AGCTGCCACAAATCTTTCCAG 59.109 47.619 0.00 0.00 0.00 3.86
328 340 1.343142 TGTGTCGTCCAGCTAACACAT 59.657 47.619 11.73 0.00 45.05 3.21
452 465 5.334957 GCATGATGGATTGCATCAACTAGAG 60.335 44.000 22.35 10.75 41.66 2.43
509 522 2.917971 CGTAGTTGGAGAAGAGCTTTCG 59.082 50.000 0.00 0.00 0.00 3.46
533 546 2.305635 ACTGGTAGTTCATGCATCACCA 59.694 45.455 0.00 4.94 34.95 4.17
538 551 5.420725 TTCACTACTGGTAGTTCATGCAT 57.579 39.130 10.31 0.00 43.35 3.96
559 572 4.122776 CACATAGCTACAAGAATCCGCTT 58.877 43.478 0.00 0.00 32.49 4.68
563 576 9.726438 AAATATACCACATAGCTACAAGAATCC 57.274 33.333 0.00 0.00 0.00 3.01
654 672 9.726438 ATAAAGTTTGTAGCTAGAACTCACATT 57.274 29.630 18.01 12.83 32.79 2.71
657 675 7.009357 CGGATAAAGTTTGTAGCTAGAACTCAC 59.991 40.741 18.01 8.74 32.79 3.51
675 693 6.369065 GGTTCATTGTATAGCTCCGGATAAAG 59.631 42.308 3.57 0.00 0.00 1.85
731 754 3.283751 CATACCCCGCATTTGGTTTCTA 58.716 45.455 0.00 0.00 36.04 2.10
745 769 6.647481 GTCAACATTGGTTTTTAACATACCCC 59.353 38.462 0.00 0.00 34.21 4.95
759 783 3.940209 AAATGATGCGTCAACATTGGT 57.060 38.095 13.65 0.00 37.05 3.67
760 784 5.276489 GCATAAAATGATGCGTCAACATTGG 60.276 40.000 13.65 3.36 42.63 3.16
773 804 5.938710 TGCCAATGTTTGTGCATAAAATGAT 59.061 32.000 10.43 0.92 33.81 2.45
850 882 2.034053 CCAATCGAGACCAGTCTAGCTC 59.966 54.545 0.00 0.00 40.61 4.09
852 884 2.025155 TCCAATCGAGACCAGTCTAGC 58.975 52.381 0.00 0.00 40.61 3.42
853 885 3.283751 AGTCCAATCGAGACCAGTCTAG 58.716 50.000 0.00 0.61 40.61 2.43
855 887 2.223803 AGTCCAATCGAGACCAGTCT 57.776 50.000 0.00 0.00 43.78 3.24
859 891 1.275291 GTCCAAGTCCAATCGAGACCA 59.725 52.381 0.00 0.00 34.67 4.02
860 892 1.550976 AGTCCAAGTCCAATCGAGACC 59.449 52.381 0.00 0.00 34.67 3.85
861 893 2.732597 CGAGTCCAAGTCCAATCGAGAC 60.733 54.545 0.00 0.00 32.13 3.36
862 894 1.472878 CGAGTCCAAGTCCAATCGAGA 59.527 52.381 0.00 0.00 32.13 4.04
864 896 1.067846 CACGAGTCCAAGTCCAATCGA 60.068 52.381 0.00 0.00 34.46 3.59
865 897 1.350193 CACGAGTCCAAGTCCAATCG 58.650 55.000 0.00 0.00 36.32 3.34
866 898 1.079503 GCACGAGTCCAAGTCCAATC 58.920 55.000 0.00 0.00 0.00 2.67
869 901 1.367471 CAGCACGAGTCCAAGTCCA 59.633 57.895 0.00 0.00 0.00 4.02
870 902 1.374758 CCAGCACGAGTCCAAGTCC 60.375 63.158 0.00 0.00 0.00 3.85
871 903 0.667792 GACCAGCACGAGTCCAAGTC 60.668 60.000 0.00 0.00 0.00 3.01
872 904 1.115930 AGACCAGCACGAGTCCAAGT 61.116 55.000 0.00 0.00 33.29 3.16
874 906 1.666011 GAGACCAGCACGAGTCCAA 59.334 57.895 0.00 0.00 33.29 3.53
875 907 2.626780 CGAGACCAGCACGAGTCCA 61.627 63.158 0.00 0.00 33.29 4.02
876 908 2.179517 CGAGACCAGCACGAGTCC 59.820 66.667 0.00 0.00 33.29 3.85
877 909 1.442857 CACGAGACCAGCACGAGTC 60.443 63.158 0.00 0.00 34.56 3.36
878 910 2.645567 CACGAGACCAGCACGAGT 59.354 61.111 0.00 0.00 34.56 4.18
879 911 2.807045 GCACGAGACCAGCACGAG 60.807 66.667 0.00 0.00 34.56 4.18
883 915 2.917227 TCCAGCACGAGACCAGCA 60.917 61.111 0.00 0.00 0.00 4.41
884 916 2.433318 GTCCAGCACGAGACCAGC 60.433 66.667 0.00 0.00 0.00 4.85
885 917 0.668706 CAAGTCCAGCACGAGACCAG 60.669 60.000 0.00 0.00 33.29 4.00
886 918 1.367471 CAAGTCCAGCACGAGACCA 59.633 57.895 0.00 0.00 33.29 4.02
887 919 1.374758 CCAAGTCCAGCACGAGACC 60.375 63.158 0.00 0.00 33.29 3.85
890 922 0.034059 AAGTCCAAGTCCAGCACGAG 59.966 55.000 0.00 0.00 0.00 4.18
891 923 0.249868 CAAGTCCAAGTCCAGCACGA 60.250 55.000 0.00 0.00 0.00 4.35
892 924 1.230635 CCAAGTCCAAGTCCAGCACG 61.231 60.000 0.00 0.00 0.00 5.34
894 926 0.108585 GTCCAAGTCCAAGTCCAGCA 59.891 55.000 0.00 0.00 0.00 4.41
895 927 0.398318 AGTCCAAGTCCAAGTCCAGC 59.602 55.000 0.00 0.00 0.00 4.85
897 929 0.764890 CCAGTCCAAGTCCAAGTCCA 59.235 55.000 0.00 0.00 0.00 4.02
898 930 1.056660 TCCAGTCCAAGTCCAAGTCC 58.943 55.000 0.00 0.00 0.00 3.85
899 931 1.694696 AGTCCAGTCCAAGTCCAAGTC 59.305 52.381 0.00 0.00 0.00 3.01
902 934 0.679505 CGAGTCCAGTCCAAGTCCAA 59.320 55.000 0.00 0.00 0.00 3.53
903 935 0.469331 ACGAGTCCAGTCCAAGTCCA 60.469 55.000 0.00 0.00 0.00 4.02
904 936 0.038159 CACGAGTCCAGTCCAAGTCC 60.038 60.000 0.00 0.00 0.00 3.85
905 937 0.667792 GCACGAGTCCAGTCCAAGTC 60.668 60.000 0.00 0.00 0.00 3.01
906 938 1.115930 AGCACGAGTCCAGTCCAAGT 61.116 55.000 0.00 0.00 0.00 3.16
907 939 0.034059 AAGCACGAGTCCAGTCCAAG 59.966 55.000 0.00 0.00 0.00 3.61
908 940 0.033504 GAAGCACGAGTCCAGTCCAA 59.966 55.000 0.00 0.00 0.00 3.53
909 941 1.112916 TGAAGCACGAGTCCAGTCCA 61.113 55.000 0.00 0.00 0.00 4.02
910 942 0.389166 CTGAAGCACGAGTCCAGTCC 60.389 60.000 0.00 0.00 0.00 3.85
911 943 0.598562 TCTGAAGCACGAGTCCAGTC 59.401 55.000 0.00 0.00 0.00 3.51
913 945 0.315251 TGTCTGAAGCACGAGTCCAG 59.685 55.000 0.00 0.00 0.00 3.86
963 1479 2.815684 TAGCTCTCCGGGGCTTTGGA 62.816 60.000 19.05 2.88 39.65 3.53
1038 1554 3.811083 TGTGTAAGAGCCGAAAAGGAAA 58.189 40.909 0.00 0.00 45.00 3.13
1137 1653 1.824852 TGCTTCGCTATGACCTTCTCA 59.175 47.619 0.00 0.00 0.00 3.27
1181 1697 1.000717 GGCTCTCGAGATACTTCAGCC 60.001 57.143 19.86 19.86 0.00 4.85
1185 1701 4.640789 TTTGAGGCTCTCGAGATACTTC 57.359 45.455 17.03 16.59 32.35 3.01
1229 1745 1.289800 GGACGGACTTTTCCTGTCGC 61.290 60.000 0.00 0.00 42.06 5.19
1294 1812 1.762708 ACAATGGGGAATCGCGAAAT 58.237 45.000 15.24 4.87 0.00 2.17
1320 1838 5.673818 GCCGACTAAAGAAGGTAAATTGCAG 60.674 44.000 0.00 0.00 0.00 4.41
1350 1868 1.153628 GCATCGGCGACTTGGTAGT 60.154 57.895 13.76 0.00 37.31 2.73
1496 2014 0.241749 ACACACGCTTGGCATCAATG 59.758 50.000 0.00 0.00 31.75 2.82
1625 2143 4.561500 TGTAGTACTTTGCTGGCCAATA 57.438 40.909 7.01 0.00 32.49 1.90
1791 2318 1.666189 GAGCGCCTAGGAACAATCAAC 59.334 52.381 14.75 0.00 0.00 3.18
1796 2323 2.125673 GCGAGCGCCTAGGAACAA 60.126 61.111 14.75 0.00 34.56 2.83
1882 2419 1.431036 GAGCATTTTGCCTCCGCTC 59.569 57.895 0.00 0.00 46.52 5.03
2020 2563 4.404073 AGATAGTGAGGTAGACAGGCAAAG 59.596 45.833 0.00 0.00 0.00 2.77
2026 2569 4.066490 CGGGTAGATAGTGAGGTAGACAG 58.934 52.174 0.00 0.00 0.00 3.51
2292 2838 4.790962 AGCACATCAGGCCGGCTG 62.791 66.667 28.56 21.71 32.76 4.85
2390 2936 6.936900 TCCAAACTCCTAATCTTCAAGTCAAG 59.063 38.462 0.00 0.00 0.00 3.02
2467 3013 8.660295 TTCTAATCACTTTGGAGTAAGAGGTA 57.340 34.615 0.00 0.00 33.90 3.08
2501 3047 3.925630 CTGAGCACAATGGGCCGGT 62.926 63.158 2.80 0.00 0.00 5.28
2583 3129 6.276091 GGCCTTTTTATGATTGTCTTGATCC 58.724 40.000 0.00 0.00 0.00 3.36
2595 3141 4.580167 CAGATCCATTCGGCCTTTTTATGA 59.420 41.667 0.00 0.00 0.00 2.15
2608 3154 0.659957 GCCGAGCAACAGATCCATTC 59.340 55.000 0.00 0.00 0.00 2.67
2642 3188 3.065371 CAGTGTTCCTTGTTGTCCTTGTC 59.935 47.826 0.00 0.00 0.00 3.18
2695 3241 1.004044 ACACCCTCAGCAATTCCAGAG 59.996 52.381 0.00 0.00 0.00 3.35
2719 3265 5.815581 ACCAAACTACTGCCATCATAAAGA 58.184 37.500 0.00 0.00 0.00 2.52
2821 3367 4.052159 AGCATTCTTACCATCACGAGAG 57.948 45.455 0.00 0.00 0.00 3.20
2840 3386 0.605589 GGGTCAACACTGGTGGTAGC 60.606 60.000 5.70 0.00 34.19 3.58
2995 3541 3.552132 TCACCACACAGTTAAAGCTGA 57.448 42.857 0.49 0.00 39.62 4.26
3119 3680 6.155827 TGGAAAATATTGTTGCTTCTTTCCG 58.844 36.000 0.00 0.00 42.03 4.30
3136 3697 9.520515 AGTAACACAAGACATAAGATGGAAAAT 57.479 29.630 0.00 0.00 33.60 1.82
3137 3698 8.918202 AGTAACACAAGACATAAGATGGAAAA 57.082 30.769 0.00 0.00 33.60 2.29
3138 3699 8.783093 CAAGTAACACAAGACATAAGATGGAAA 58.217 33.333 0.00 0.00 33.60 3.13
3139 3700 7.390440 CCAAGTAACACAAGACATAAGATGGAA 59.610 37.037 0.00 0.00 33.60 3.53
3140 3701 6.878923 CCAAGTAACACAAGACATAAGATGGA 59.121 38.462 0.00 0.00 33.60 3.41
3141 3702 6.655003 ACCAAGTAACACAAGACATAAGATGG 59.345 38.462 0.00 0.00 33.60 3.51
3142 3703 7.387673 TCACCAAGTAACACAAGACATAAGATG 59.612 37.037 0.00 0.00 0.00 2.90
3143 3704 7.450074 TCACCAAGTAACACAAGACATAAGAT 58.550 34.615 0.00 0.00 0.00 2.40
3144 3705 6.822442 TCACCAAGTAACACAAGACATAAGA 58.178 36.000 0.00 0.00 0.00 2.10
3145 3706 6.347725 GCTCACCAAGTAACACAAGACATAAG 60.348 42.308 0.00 0.00 0.00 1.73
3146 3707 5.468746 GCTCACCAAGTAACACAAGACATAA 59.531 40.000 0.00 0.00 0.00 1.90
3147 3708 4.994852 GCTCACCAAGTAACACAAGACATA 59.005 41.667 0.00 0.00 0.00 2.29
3148 3709 3.815401 GCTCACCAAGTAACACAAGACAT 59.185 43.478 0.00 0.00 0.00 3.06
3149 3710 3.202906 GCTCACCAAGTAACACAAGACA 58.797 45.455 0.00 0.00 0.00 3.41
3242 3803 7.868906 AAGTAGAGGTCATCAACTAGACTAC 57.131 40.000 0.00 0.00 35.18 2.73
3284 3845 4.801330 CTTCCATGGAAGGGGTTTAAAC 57.199 45.455 37.26 9.98 45.60 2.01
3489 4258 1.888512 GTTTTGCCCTCTCATTGCAGA 59.111 47.619 0.00 0.00 36.21 4.26
3496 4265 5.880901 AGAGATTTTAGTTTTGCCCTCTCA 58.119 37.500 0.00 0.00 32.29 3.27
3529 4298 4.913924 CGTCTCAATTCTTGCCTTTCTTTG 59.086 41.667 0.00 0.00 0.00 2.77
3537 4311 1.523758 ACACCGTCTCAATTCTTGCC 58.476 50.000 0.00 0.00 0.00 4.52
3599 4373 3.368635 GGTGAATCAATGCCTTTCATGCA 60.369 43.478 0.00 0.00 43.97 3.96
3656 4430 6.150641 CACTCATGACTTCTTCATTGTTCCAT 59.849 38.462 0.00 0.00 42.87 3.41
3705 4479 2.440385 CTTCGCCACTGTCAGCCTCA 62.440 60.000 0.00 0.00 0.00 3.86
3735 4509 1.956629 GCCTGCTAGTAGTGGCGGAA 61.957 60.000 15.85 0.00 38.85 4.30
3925 4699 3.862124 CGGAGCTGACTTGTTCGG 58.138 61.111 0.00 0.00 0.00 4.30
4062 4849 9.667107 CTCTAGGATACACTTGTATTCCAAAAA 57.333 33.333 14.84 3.62 40.99 1.94
4070 4857 9.315363 CCCTTAATCTCTAGGATACACTTGTAT 57.685 37.037 1.36 1.36 43.38 2.29
4075 4862 8.855804 TTTTCCCTTAATCTCTAGGATACACT 57.144 34.615 0.00 0.00 41.41 3.55
4128 4916 8.723942 ACCAAAAGTCTTATGTCTATAAGCAG 57.276 34.615 0.00 0.00 43.52 4.24


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

AutoCloner maintained by Alex Coulton.