Multiple sequence alignment - TraesCS6D01G343200

Loading Multiple Alignment...

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 TraesCS6D01G343200 chr6D 100.000 3952 0 0 1 3952 441919230 441915279 0.000000e+00 7299.0
1 TraesCS6D01G343200 chr6D 88.325 788 71 14 1 777 359558554 359557777 0.000000e+00 926.0
2 TraesCS6D01G343200 chr6D 98.058 103 2 0 1642 1744 441917494 441917392 3.140000e-41 180.0
3 TraesCS6D01G343200 chr6D 98.058 103 2 0 1737 1839 441917589 441917487 3.140000e-41 180.0
4 TraesCS6D01G343200 chr6A 94.378 2490 96 15 862 3339 591343264 591340807 0.000000e+00 3783.0
5 TraesCS6D01G343200 chr6A 79.346 581 43 25 3413 3952 591339774 591339230 1.760000e-88 337.0
6 TraesCS6D01G343200 chr6A 97.087 103 3 0 1737 1839 591342476 591342374 1.460000e-39 174.0
7 TraesCS6D01G343200 chr6A 96.117 103 4 0 1642 1744 591342381 591342279 6.790000e-38 169.0
8 TraesCS6D01G343200 chr6B 92.652 1810 82 22 1934 3703 667963967 667962169 0.000000e+00 2558.0
9 TraesCS6D01G343200 chr6B 86.239 545 38 12 862 1370 667964814 667964271 1.240000e-154 556.0
10 TraesCS6D01G343200 chr6B 91.257 183 8 4 1565 1744 667964206 667964029 3.950000e-60 243.0
11 TraesCS6D01G343200 chr6B 90.426 188 10 4 3718 3902 667962186 667962004 1.420000e-59 241.0
12 TraesCS6D01G343200 chr6B 90.789 152 12 1 1744 1893 667964124 667963973 6.700000e-48 202.0
13 TraesCS6D01G343200 chr6B 96.000 50 1 1 3902 3951 667961982 667961934 3.270000e-11 80.5
14 TraesCS6D01G343200 chr3D 89.721 788 59 16 1 777 475866534 475867310 0.000000e+00 987.0
15 TraesCS6D01G343200 chr7A 89.286 784 69 14 1 777 37286425 37287200 0.000000e+00 968.0
16 TraesCS6D01G343200 chr7A 88.369 791 70 17 2 777 628357717 628356934 0.000000e+00 931.0
17 TraesCS6D01G343200 chr7D 89.150 765 64 14 2 758 25329026 25329779 0.000000e+00 935.0
18 TraesCS6D01G343200 chr7D 88.168 786 75 15 1 777 14554924 14555700 0.000000e+00 920.0
19 TraesCS6D01G343200 chr7D 88.146 793 68 20 1 778 119561739 119560958 0.000000e+00 920.0
20 TraesCS6D01G343200 chr2D 88.354 790 73 14 1 778 489573862 489573080 0.000000e+00 931.0
21 TraesCS6D01G343200 chr2D 88.506 783 72 16 1 776 576459405 576460176 0.000000e+00 931.0


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 TraesCS6D01G343200 chr6D 441915279 441919230 3951 True 2553.00 7299 98.705333 1 3952 3 chr6D.!!$R2 3951
1 TraesCS6D01G343200 chr6D 359557777 359558554 777 True 926.00 926 88.325000 1 777 1 chr6D.!!$R1 776
2 TraesCS6D01G343200 chr6A 591339230 591343264 4034 True 1115.75 3783 91.732000 862 3952 4 chr6A.!!$R1 3090
3 TraesCS6D01G343200 chr6B 667961934 667964814 2880 True 646.75 2558 91.227167 862 3951 6 chr6B.!!$R1 3089
4 TraesCS6D01G343200 chr3D 475866534 475867310 776 False 987.00 987 89.721000 1 777 1 chr3D.!!$F1 776
5 TraesCS6D01G343200 chr7A 37286425 37287200 775 False 968.00 968 89.286000 1 777 1 chr7A.!!$F1 776
6 TraesCS6D01G343200 chr7A 628356934 628357717 783 True 931.00 931 88.369000 2 777 1 chr7A.!!$R1 775
7 TraesCS6D01G343200 chr7D 25329026 25329779 753 False 935.00 935 89.150000 2 758 1 chr7D.!!$F2 756
8 TraesCS6D01G343200 chr7D 14554924 14555700 776 False 920.00 920 88.168000 1 777 1 chr7D.!!$F1 776
9 TraesCS6D01G343200 chr7D 119560958 119561739 781 True 920.00 920 88.146000 1 778 1 chr7D.!!$R1 777
10 TraesCS6D01G343200 chr2D 489573080 489573862 782 True 931.00 931 88.354000 1 778 1 chr2D.!!$R1 777
11 TraesCS6D01G343200 chr2D 576459405 576460176 771 False 931.00 931 88.506000 1 776 1 chr2D.!!$F1 775

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
808 849 0.041663 GCGTTGTGCATGTACGTGTT 60.042 50.0 16.28 0.00 45.45 3.32 F
1318 1396 0.602905 GCCGTACTGCAGTTCTTGGT 60.603 55.0 27.06 0.33 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2238 2321 0.179215 GCTCGCGAAACCTTGTCATG 60.179 55.0 11.33 0.0 0.0 3.07 R
2997 3087 0.037303 CCTTGAGCCAGTGGATGTGT 59.963 55.0 15.20 0.0 0.0 3.72 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
109 121 4.421479 CTTCCGCGAGAGGCACGT 62.421 66.667 8.23 0.00 43.84 4.49
308 340 1.880027 GAGTCACGGTTTTGCTTCCAT 59.120 47.619 0.00 0.00 0.00 3.41
419 454 2.400399 CGAGAGTCACGGTTTTGCTTA 58.600 47.619 1.62 0.00 0.00 3.09
476 511 0.949105 GCGTGCCTCTTTCGGAAAGA 60.949 55.000 26.61 26.61 44.82 2.52
675 715 6.812879 ACGAATCTACGAAAAAGGGAAAAT 57.187 33.333 0.00 0.00 37.03 1.82
678 718 7.040961 ACGAATCTACGAAAAAGGGAAAATTCA 60.041 33.333 0.00 0.00 37.03 2.57
743 784 0.409484 CCAGGGGAATTGGAGTGGTT 59.591 55.000 0.00 0.00 37.96 3.67
758 799 2.356695 AGTGGTTTTTGCAACGAGTACC 59.643 45.455 0.00 3.22 0.00 3.34
778 819 3.265995 ACCCCTCAATTAGTGATTTCGGT 59.734 43.478 0.00 0.00 35.07 4.69
779 820 3.627577 CCCCTCAATTAGTGATTTCGGTG 59.372 47.826 0.00 0.00 35.07 4.94
780 821 4.261801 CCCTCAATTAGTGATTTCGGTGT 58.738 43.478 0.00 0.00 35.07 4.16
781 822 4.094887 CCCTCAATTAGTGATTTCGGTGTG 59.905 45.833 0.00 0.00 35.07 3.82
782 823 4.695455 CCTCAATTAGTGATTTCGGTGTGT 59.305 41.667 0.00 0.00 35.07 3.72
783 824 5.872617 CCTCAATTAGTGATTTCGGTGTGTA 59.127 40.000 0.00 0.00 35.07 2.90
784 825 6.538742 CCTCAATTAGTGATTTCGGTGTGTAT 59.461 38.462 0.00 0.00 35.07 2.29
785 826 7.065803 CCTCAATTAGTGATTTCGGTGTGTATT 59.934 37.037 0.00 0.00 35.07 1.89
786 827 8.330466 TCAATTAGTGATTTCGGTGTGTATTT 57.670 30.769 0.00 0.00 0.00 1.40
787 828 8.233868 TCAATTAGTGATTTCGGTGTGTATTTG 58.766 33.333 0.00 0.00 0.00 2.32
788 829 7.915293 ATTAGTGATTTCGGTGTGTATTTGA 57.085 32.000 0.00 0.00 0.00 2.69
789 830 5.862924 AGTGATTTCGGTGTGTATTTGAG 57.137 39.130 0.00 0.00 0.00 3.02
790 831 4.154195 AGTGATTTCGGTGTGTATTTGAGC 59.846 41.667 0.00 0.00 0.00 4.26
791 832 3.124466 TGATTTCGGTGTGTATTTGAGCG 59.876 43.478 0.00 0.00 0.00 5.03
792 833 2.157834 TTCGGTGTGTATTTGAGCGT 57.842 45.000 0.00 0.00 32.60 5.07
793 834 2.157834 TCGGTGTGTATTTGAGCGTT 57.842 45.000 0.00 0.00 32.60 4.84
794 835 1.795872 TCGGTGTGTATTTGAGCGTTG 59.204 47.619 0.00 0.00 32.60 4.10
795 836 1.529438 CGGTGTGTATTTGAGCGTTGT 59.471 47.619 0.00 0.00 0.00 3.32
796 837 2.661709 CGGTGTGTATTTGAGCGTTGTG 60.662 50.000 0.00 0.00 0.00 3.33
797 838 2.307049 GTGTGTATTTGAGCGTTGTGC 58.693 47.619 0.00 0.00 46.98 4.57
806 847 4.415490 GCGTTGTGCATGTACGTG 57.585 55.556 10.89 10.89 45.45 4.49
807 848 1.567537 GCGTTGTGCATGTACGTGT 59.432 52.632 16.28 0.00 45.45 4.49
808 849 0.041663 GCGTTGTGCATGTACGTGTT 60.042 50.000 16.28 0.00 45.45 3.32
809 850 1.595976 GCGTTGTGCATGTACGTGTTT 60.596 47.619 16.28 0.00 45.45 2.83
810 851 2.348685 GCGTTGTGCATGTACGTGTTTA 60.349 45.455 16.28 1.34 45.45 2.01
811 852 3.845303 GCGTTGTGCATGTACGTGTTTAA 60.845 43.478 16.28 6.46 45.45 1.52
812 853 4.272480 CGTTGTGCATGTACGTGTTTAAA 58.728 39.130 16.28 4.18 0.00 1.52
813 854 4.729086 CGTTGTGCATGTACGTGTTTAAAA 59.271 37.500 16.28 2.93 0.00 1.52
814 855 5.227391 CGTTGTGCATGTACGTGTTTAAAAA 59.773 36.000 16.28 0.00 0.00 1.94
857 898 2.495866 GCATTGGTTGCCATCCGG 59.504 61.111 0.00 0.00 46.15 5.14
867 908 3.530260 CCATCCGGCAACATGGGC 61.530 66.667 11.30 0.00 36.68 5.36
868 909 2.440796 CATCCGGCAACATGGGCT 60.441 61.111 10.84 0.00 0.00 5.19
871 912 2.898920 ATCCGGCAACATGGGCTCTG 62.899 60.000 10.84 2.92 0.00 3.35
885 926 2.961062 GGGCTCTGATGGCAATACAATT 59.039 45.455 0.00 0.00 0.00 2.32
902 944 5.852282 ACAATTCCCAAATAAATCCCTCG 57.148 39.130 0.00 0.00 0.00 4.63
904 946 5.359860 ACAATTCCCAAATAAATCCCTCGTC 59.640 40.000 0.00 0.00 0.00 4.20
905 947 3.570912 TCCCAAATAAATCCCTCGTCC 57.429 47.619 0.00 0.00 0.00 4.79
979 1029 2.828549 CCAAATCCGCCCTTCCCG 60.829 66.667 0.00 0.00 0.00 5.14
992 1054 2.725203 CTTCCCGTTCCCGTCAAGCA 62.725 60.000 0.00 0.00 0.00 3.91
1303 1381 4.247612 GTCGTATCTCGCCGCCGT 62.248 66.667 0.00 0.00 39.67 5.68
1318 1396 0.602905 GCCGTACTGCAGTTCTTGGT 60.603 55.000 27.06 0.33 0.00 3.67
1319 1397 1.148310 CCGTACTGCAGTTCTTGGTG 58.852 55.000 27.06 6.51 0.00 4.17
1323 1401 1.529010 CTGCAGTTCTTGGTGCCCA 60.529 57.895 5.25 0.00 39.04 5.36
1383 1461 4.563061 GTTGGAAGAAGGTAAAGCGTAGA 58.437 43.478 0.00 0.00 0.00 2.59
1446 1524 5.088739 CACAAGCCGATTTTACTGCTTTAG 58.911 41.667 0.00 0.00 41.83 1.85
1470 1548 2.960819 TCTTCTCTGCTTAAAGCGTCC 58.039 47.619 0.00 0.00 46.26 4.79
1471 1549 2.299013 TCTTCTCTGCTTAAAGCGTCCA 59.701 45.455 0.00 0.00 46.26 4.02
1477 1555 4.765273 TCTGCTTAAAGCGTCCATGAATA 58.235 39.130 0.00 0.00 46.26 1.75
1490 1568 9.337396 AGCGTCCATGAATAAATCTATGTAAAA 57.663 29.630 0.00 0.00 0.00 1.52
1765 1846 8.324306 TCTCAAATCTAATGTCAATGAGAAGGT 58.676 33.333 0.00 0.00 38.94 3.50
2061 2144 0.899253 AGCAGCAGAGACTGAGAGCA 60.899 55.000 2.81 0.00 40.25 4.26
2078 2161 1.227380 CATACTCTCCCGGCTGCAC 60.227 63.158 0.50 0.00 0.00 4.57
2079 2162 1.381872 ATACTCTCCCGGCTGCACT 60.382 57.895 0.50 0.00 0.00 4.40
2238 2321 3.389329 TCTCATAAATGGAGACCAGAGGC 59.611 47.826 0.00 0.00 36.75 4.70
2283 2366 0.110056 CACGTCATTGGCAACTGCTC 60.110 55.000 0.00 0.00 41.70 4.26
2337 2420 6.611381 TCAAATGCTATCTACTTGTTGTTGC 58.389 36.000 0.00 0.00 0.00 4.17
2343 2426 5.063564 GCTATCTACTTGTTGTTGCTGTACC 59.936 44.000 0.00 0.00 0.00 3.34
2393 2479 9.521841 ACTCGAATGATCTTCTCACCTTATATA 57.478 33.333 0.00 0.00 36.48 0.86
2663 2750 5.163683 CTCCTTTTGAGCTCACATATTGTGG 60.164 44.000 18.03 10.13 40.46 4.17
2680 2767 2.038426 TGTGGTGTGACATAACCCTGAG 59.962 50.000 7.58 0.00 35.44 3.35
2829 2916 1.365699 ATTACCGGTACTTGCTTGCG 58.634 50.000 15.53 0.00 0.00 4.85
2871 2958 6.772716 TCTCTTATTGCTGTTGTTTCCTTTCT 59.227 34.615 0.00 0.00 0.00 2.52
2872 2959 6.738114 TCTTATTGCTGTTGTTTCCTTTCTG 58.262 36.000 0.00 0.00 0.00 3.02
2873 2960 6.545666 TCTTATTGCTGTTGTTTCCTTTCTGA 59.454 34.615 0.00 0.00 0.00 3.27
2885 2972 2.500098 TCCTTTCTGATGACTAACGGGG 59.500 50.000 0.00 0.00 0.00 5.73
2954 3044 2.498167 GCCAGTGGCCATCAATAGTAG 58.502 52.381 24.53 0.00 44.06 2.57
2955 3045 2.158755 GCCAGTGGCCATCAATAGTAGT 60.159 50.000 24.53 0.00 44.06 2.73
2956 3046 3.071023 GCCAGTGGCCATCAATAGTAGTA 59.929 47.826 24.53 0.00 44.06 1.82
2997 3087 4.202631 TGCTTAAGCCCCTCTTTTCCTTTA 60.203 41.667 24.30 0.00 41.18 1.85
3008 3098 5.182001 CCTCTTTTCCTTTACACATCCACTG 59.818 44.000 0.00 0.00 0.00 3.66
3014 3104 3.411446 CTTTACACATCCACTGGCTCAA 58.589 45.455 0.00 0.00 0.00 3.02
3057 3147 2.666098 GGAGCTTAACCGGCCCTCA 61.666 63.158 0.00 0.00 0.00 3.86
3140 3230 2.238521 GAAGCTCCAACCACCAATTCA 58.761 47.619 0.00 0.00 0.00 2.57
3145 3235 2.294233 CTCCAACCACCAATTCAGTGTG 59.706 50.000 4.81 0.00 33.20 3.82
3195 3286 1.169577 GCTGAGAGTCTCCGACAAGA 58.830 55.000 17.57 0.00 34.60 3.02
3203 3294 0.390340 TCTCCGACAAGATGCAGTGC 60.390 55.000 8.58 8.58 0.00 4.40
3272 3364 3.696782 GCAAGTGCAAGCATCTGAG 57.303 52.632 0.00 0.00 41.59 3.35
3289 3381 5.581126 TCTGAGTCATGTTTTTGTTTGCT 57.419 34.783 0.00 0.00 0.00 3.91
3290 3382 6.691754 TCTGAGTCATGTTTTTGTTTGCTA 57.308 33.333 0.00 0.00 0.00 3.49
3324 3416 5.450965 CCATGGAGAACAATGGTGAATTAGC 60.451 44.000 5.56 0.00 0.00 3.09
3335 3427 4.069304 TGGTGAATTAGCAGCGTTTACTT 58.931 39.130 0.00 0.00 39.04 2.24
3336 3428 4.517453 TGGTGAATTAGCAGCGTTTACTTT 59.483 37.500 0.00 0.00 39.04 2.66
3337 3429 4.851558 GGTGAATTAGCAGCGTTTACTTTG 59.148 41.667 0.00 0.00 0.00 2.77
3338 3430 4.320953 GTGAATTAGCAGCGTTTACTTTGC 59.679 41.667 0.00 0.00 36.83 3.68
3339 3431 2.587612 TTAGCAGCGTTTACTTTGCG 57.412 45.000 0.00 0.00 41.27 4.85
3340 3432 0.793861 TAGCAGCGTTTACTTTGCGG 59.206 50.000 0.00 0.00 41.27 5.69
3386 4412 0.589708 CGCATGTGCATGTATCCCTG 59.410 55.000 12.96 0.00 42.21 4.45
3399 4425 1.583556 ATCCCTGTGATGTACTGCCA 58.416 50.000 0.00 0.00 30.54 4.92
3411 4437 1.952102 TACTGCCACCGTCCCGAATC 61.952 60.000 0.00 0.00 0.00 2.52
3416 4473 1.474498 GCCACCGTCCCGAATCTAAAT 60.474 52.381 0.00 0.00 0.00 1.40
3420 4477 4.202182 CCACCGTCCCGAATCTAAATCTAA 60.202 45.833 0.00 0.00 0.00 2.10
3426 4483 6.924060 CGTCCCGAATCTAAATCTAAGACAAT 59.076 38.462 0.00 0.00 0.00 2.71
3539 4603 1.830477 GACACTGCATCTTCCTCCTCT 59.170 52.381 0.00 0.00 0.00 3.69
3551 4615 2.125233 TCCTCCTCTAGCCGAGTCTTA 58.875 52.381 5.50 0.00 38.11 2.10
3563 4627 3.803021 GCCGAGTCTTATCCTCTAGTCGA 60.803 52.174 0.00 0.00 37.03 4.20
3570 4634 6.099269 AGTCTTATCCTCTAGTCGAGTTCTCT 59.901 42.308 0.00 0.00 38.11 3.10
3597 4661 2.787866 CCCTCCCTCTCCTCCCAA 59.212 66.667 0.00 0.00 0.00 4.12
3703 4801 9.167311 GACAAATCTGAATACTTCTACACCATT 57.833 33.333 0.00 0.00 0.00 3.16
3704 4802 9.520515 ACAAATCTGAATACTTCTACACCATTT 57.479 29.630 0.00 0.00 0.00 2.32
3729 4827 6.790285 TTTTTGACGGGTGAATACTTCTAC 57.210 37.500 0.00 0.00 0.00 2.59
3730 4828 5.471556 TTTGACGGGTGAATACTTCTACA 57.528 39.130 0.00 0.00 0.00 2.74
3731 4829 4.445452 TGACGGGTGAATACTTCTACAC 57.555 45.455 0.00 0.00 0.00 2.90
3754 4852 7.083858 CACCATAGTACCACATTGTTTTTGAG 58.916 38.462 0.00 0.00 0.00 3.02
3812 4912 5.390779 CGGTACTAATGGTTTTGTAAACCGG 60.391 44.000 14.62 0.00 43.15 5.28
3877 4978 1.749063 GGGTTGGATTGGTTTCCGATC 59.251 52.381 7.32 7.32 42.25 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.213013 GCACGACCATGACTCTCGT 59.787 57.895 0.00 0.00 41.23 4.18
75 87 2.210116 GAAGCAAAACCGTGACTCTCA 58.790 47.619 0.00 0.00 0.00 3.27
279 311 1.325355 AACCGTGACTCGAGAAAGGA 58.675 50.000 21.68 0.00 42.86 3.36
280 312 2.150397 AAACCGTGACTCGAGAAAGG 57.850 50.000 21.68 19.33 42.86 3.11
281 313 2.348591 GCAAAACCGTGACTCGAGAAAG 60.349 50.000 21.68 9.01 42.86 2.62
283 315 1.202486 AGCAAAACCGTGACTCGAGAA 60.202 47.619 21.68 3.67 42.86 2.87
286 318 1.214367 GAAGCAAAACCGTGACTCGA 58.786 50.000 0.00 0.00 42.86 4.04
287 319 0.234884 GGAAGCAAAACCGTGACTCG 59.765 55.000 0.00 0.00 39.52 4.18
431 466 2.413453 GCCTCTCACGAAATCACAACTC 59.587 50.000 0.00 0.00 0.00 3.01
432 467 2.224281 TGCCTCTCACGAAATCACAACT 60.224 45.455 0.00 0.00 0.00 3.16
553 590 9.794719 TCGAGATCTTCAAAACTAGATCCTATA 57.205 33.333 0.00 0.00 38.24 1.31
556 593 6.459024 CGTCGAGATCTTCAAAACTAGATCCT 60.459 42.308 0.00 0.00 38.24 3.24
607 644 2.649331 ATCGTTCGTCCAATTCTCGT 57.351 45.000 0.00 0.00 0.00 4.18
613 650 8.712285 TTTATCTCTTAAATCGTTCGTCCAAT 57.288 30.769 0.00 0.00 0.00 3.16
650 690 5.851047 TTCCCTTTTTCGTAGATTCGTTC 57.149 39.130 0.00 0.00 35.04 3.95
675 715 1.013596 CACTTGTCGCAACCTGTGAA 58.986 50.000 0.00 0.00 38.76 3.18
678 718 2.186826 GCCACTTGTCGCAACCTGT 61.187 57.895 0.00 0.00 0.00 4.00
714 755 0.178975 ATTCCCCTGGTTGCGACAAA 60.179 50.000 6.39 0.00 0.00 2.83
743 784 1.886886 GAGGGGTACTCGTTGCAAAA 58.113 50.000 0.00 0.00 36.29 2.44
758 799 4.094887 CACACCGAAATCACTAATTGAGGG 59.905 45.833 0.00 0.00 37.77 4.30
778 819 1.943340 TGCACAACGCTCAAATACACA 59.057 42.857 0.00 0.00 43.06 3.72
779 820 2.679355 TGCACAACGCTCAAATACAC 57.321 45.000 0.00 0.00 43.06 2.90
780 821 2.551887 ACATGCACAACGCTCAAATACA 59.448 40.909 0.00 0.00 43.06 2.29
781 822 3.201726 ACATGCACAACGCTCAAATAC 57.798 42.857 0.00 0.00 43.06 1.89
782 823 3.181525 CGTACATGCACAACGCTCAAATA 60.182 43.478 4.62 0.00 43.06 1.40
783 824 2.412716 CGTACATGCACAACGCTCAAAT 60.413 45.455 4.62 0.00 43.06 2.32
784 825 1.070242 CGTACATGCACAACGCTCAAA 60.070 47.619 4.62 0.00 43.06 2.69
785 826 0.510790 CGTACATGCACAACGCTCAA 59.489 50.000 4.62 0.00 43.06 3.02
786 827 0.598942 ACGTACATGCACAACGCTCA 60.599 50.000 14.98 0.00 43.06 4.26
787 828 0.179250 CACGTACATGCACAACGCTC 60.179 55.000 14.98 0.00 43.06 5.03
788 829 0.878523 ACACGTACATGCACAACGCT 60.879 50.000 14.98 3.04 43.06 5.07
789 830 0.041663 AACACGTACATGCACAACGC 60.042 50.000 14.98 0.00 40.18 4.84
790 831 2.376915 AAACACGTACATGCACAACG 57.623 45.000 13.84 13.84 42.17 4.10
791 832 6.556146 TTTTTAAACACGTACATGCACAAC 57.444 33.333 0.00 0.00 0.00 3.32
850 891 3.530260 GCCCATGTTGCCGGATGG 61.530 66.667 5.05 9.60 39.18 3.51
851 892 2.440796 AGCCCATGTTGCCGGATG 60.441 61.111 5.05 0.00 0.00 3.51
852 893 2.124151 GAGCCCATGTTGCCGGAT 60.124 61.111 5.05 0.00 0.00 4.18
853 894 3.329889 AGAGCCCATGTTGCCGGA 61.330 61.111 5.05 0.00 0.00 5.14
854 895 2.898920 ATCAGAGCCCATGTTGCCGG 62.899 60.000 0.00 0.00 0.00 6.13
855 896 1.452651 ATCAGAGCCCATGTTGCCG 60.453 57.895 1.17 0.00 0.00 5.69
856 897 1.389609 CCATCAGAGCCCATGTTGCC 61.390 60.000 1.17 0.00 0.00 4.52
857 898 2.012902 GCCATCAGAGCCCATGTTGC 62.013 60.000 0.00 0.00 0.00 4.17
858 899 0.681887 TGCCATCAGAGCCCATGTTG 60.682 55.000 0.00 0.00 0.00 3.33
859 900 0.040058 TTGCCATCAGAGCCCATGTT 59.960 50.000 0.00 0.00 0.00 2.71
860 901 0.260816 ATTGCCATCAGAGCCCATGT 59.739 50.000 0.00 0.00 0.00 3.21
861 902 1.884579 GTATTGCCATCAGAGCCCATG 59.115 52.381 0.00 0.00 0.00 3.66
862 903 1.496001 TGTATTGCCATCAGAGCCCAT 59.504 47.619 0.00 0.00 0.00 4.00
863 904 0.918258 TGTATTGCCATCAGAGCCCA 59.082 50.000 0.00 0.00 0.00 5.36
864 905 2.057137 TTGTATTGCCATCAGAGCCC 57.943 50.000 0.00 0.00 0.00 5.19
865 906 3.005155 GGAATTGTATTGCCATCAGAGCC 59.995 47.826 0.00 0.00 0.00 4.70
866 907 3.005155 GGGAATTGTATTGCCATCAGAGC 59.995 47.826 5.23 0.00 0.00 4.09
867 908 4.209538 TGGGAATTGTATTGCCATCAGAG 58.790 43.478 8.35 0.00 34.89 3.35
868 909 4.248174 TGGGAATTGTATTGCCATCAGA 57.752 40.909 8.35 0.00 34.89 3.27
871 912 8.907222 ATTTATTTGGGAATTGTATTGCCATC 57.093 30.769 12.50 0.00 39.66 3.51
885 926 2.173996 GGGACGAGGGATTTATTTGGGA 59.826 50.000 0.00 0.00 0.00 4.37
905 947 0.266152 AGAGTGGGATCTGTAGGGGG 59.734 60.000 0.00 0.00 0.00 5.40
910 952 0.264955 GGGGGAGAGTGGGATCTGTA 59.735 60.000 0.00 0.00 0.00 2.74
1163 1235 0.250989 AAAACTGATTTCGGGCGGGA 60.251 50.000 0.00 0.00 0.00 5.14
1214 1292 0.037734 ATCTTTTCTTTCCCCCGCGT 59.962 50.000 4.92 0.00 0.00 6.01
1280 1358 2.328235 GGCGAGATACGACCTGCTA 58.672 57.895 0.00 0.00 45.37 3.49
1281 1359 3.121019 GGCGAGATACGACCTGCT 58.879 61.111 0.00 0.00 45.37 4.24
1303 1381 3.322514 GGCACCAAGAACTGCAGTA 57.677 52.632 22.01 0.00 34.90 2.74
1323 1401 2.620115 CGAAAGTTCATATGGCAGCCAT 59.380 45.455 30.05 30.05 46.99 4.40
1383 1461 4.225942 TCTTGGGAGTCAATCACATAGCTT 59.774 41.667 0.00 0.00 42.28 3.74
1446 1524 5.005875 GGACGCTTTAAGCAGAGAAGAATAC 59.994 44.000 17.51 0.00 42.58 1.89
1490 1568 8.974060 TTCCTAAAGATAATTTAAGCCGTCAT 57.026 30.769 0.00 0.00 0.00 3.06
1510 1588 5.248477 ACTGAAGAAGGTATGTTGCTTCCTA 59.752 40.000 0.00 0.00 35.34 2.94
1765 1846 8.198778 TGTCGGTATATTTGCACTAGATTACAA 58.801 33.333 0.00 0.00 0.00 2.41
2061 2144 0.978146 AAGTGCAGCCGGGAGAGTAT 60.978 55.000 2.18 0.00 0.00 2.12
2078 2161 2.614057 GGAAATGTAGGATCGCACCAAG 59.386 50.000 0.00 0.00 0.00 3.61
2079 2162 2.026729 TGGAAATGTAGGATCGCACCAA 60.027 45.455 0.00 0.00 0.00 3.67
2238 2321 0.179215 GCTCGCGAAACCTTGTCATG 60.179 55.000 11.33 0.00 0.00 3.07
2283 2366 4.655963 TCTCCTGAGAAATGAAAACCAGG 58.344 43.478 0.00 0.00 41.74 4.45
2343 2426 3.019564 AGCTGCTTTGGTGCCTATAAAG 58.980 45.455 0.00 0.00 35.18 1.85
2393 2479 0.886043 TCTTCTGCACTGCACGCATT 60.886 50.000 6.52 0.00 39.02 3.56
2468 2554 8.951614 ACAGAAAAATCATCCCATATCATCAT 57.048 30.769 0.00 0.00 0.00 2.45
2663 2750 2.350522 CTGCTCAGGGTTATGTCACAC 58.649 52.381 0.00 0.00 0.00 3.82
2871 2958 3.008594 ACATGTTTCCCCGTTAGTCATCA 59.991 43.478 0.00 0.00 0.00 3.07
2872 2959 3.606687 ACATGTTTCCCCGTTAGTCATC 58.393 45.455 0.00 0.00 0.00 2.92
2873 2960 3.713826 ACATGTTTCCCCGTTAGTCAT 57.286 42.857 0.00 0.00 0.00 3.06
2885 2972 4.771590 TCCAGATTCTGCAACATGTTTC 57.228 40.909 8.77 4.54 0.00 2.78
2954 3044 9.595823 TTAAGCATGTGGAATTCTTACTACTAC 57.404 33.333 5.23 0.00 0.00 2.73
2955 3045 9.817809 CTTAAGCATGTGGAATTCTTACTACTA 57.182 33.333 5.23 0.00 0.00 1.82
2956 3046 7.281100 GCTTAAGCATGTGGAATTCTTACTACT 59.719 37.037 22.59 2.55 41.59 2.57
2997 3087 0.037303 CCTTGAGCCAGTGGATGTGT 59.963 55.000 15.20 0.00 0.00 3.72
3008 3098 3.950395 ACATGAAAGATTAGCCTTGAGCC 59.050 43.478 0.00 0.00 45.47 4.70
3014 3104 6.662755 TGTAATGGACATGAAAGATTAGCCT 58.337 36.000 0.00 0.00 31.20 4.58
3057 3147 7.124750 AGCATCAAATTCCTAGCCTTTTATGTT 59.875 33.333 0.00 0.00 0.00 2.71
3195 3286 2.034879 GCCTACACACGCACTGCAT 61.035 57.895 1.11 0.00 0.00 3.96
3203 3294 4.180817 TCAAACATGATAGCCTACACACG 58.819 43.478 0.00 0.00 0.00 4.49
3289 3381 9.519191 CCATTGTTCTCCATGGTATGATTTATA 57.481 33.333 12.58 0.00 0.00 0.98
3290 3382 8.006564 ACCATTGTTCTCCATGGTATGATTTAT 58.993 33.333 12.58 0.00 44.78 1.40
3324 3416 1.394697 CAACCGCAAAGTAAACGCTG 58.605 50.000 0.00 0.00 0.00 5.18
3335 3427 2.163412 GAGTTATGATTGGCAACCGCAA 59.837 45.455 0.00 0.00 41.24 4.85
3336 3428 1.742831 GAGTTATGATTGGCAACCGCA 59.257 47.619 0.00 1.48 41.24 5.69
3337 3429 1.268032 CGAGTTATGATTGGCAACCGC 60.268 52.381 0.00 0.00 37.44 5.68
3338 3430 2.276201 TCGAGTTATGATTGGCAACCG 58.724 47.619 0.00 0.00 0.00 4.44
3339 3431 3.270877 ACTCGAGTTATGATTGGCAACC 58.729 45.455 13.58 0.00 0.00 3.77
3340 3432 6.604735 AATACTCGAGTTATGATTGGCAAC 57.395 37.500 25.44 0.00 0.00 4.17
3386 4412 0.739813 GGACGGTGGCAGTACATCAC 60.740 60.000 0.00 0.14 0.00 3.06
3416 4473 7.834181 CCTCCTTCCCAAATTAATTGTCTTAGA 59.166 37.037 0.39 0.00 37.32 2.10
3420 4477 5.903923 ACCTCCTTCCCAAATTAATTGTCT 58.096 37.500 0.39 0.00 37.32 3.41
3426 4483 9.603189 TTTTGTATTACCTCCTTCCCAAATTAA 57.397 29.630 0.00 0.00 0.00 1.40
3539 4603 4.561123 CGACTAGAGGATAAGACTCGGCTA 60.561 50.000 0.00 0.00 39.90 3.93
3563 4627 3.334054 GGGGCTGGGCAGAGAACT 61.334 66.667 0.00 0.00 0.00 3.01
3719 4817 7.966339 TGTGGTACTATGGTGTAGAAGTATT 57.034 36.000 0.00 0.00 0.00 1.89
3720 4818 8.421784 CAATGTGGTACTATGGTGTAGAAGTAT 58.578 37.037 0.00 0.00 0.00 2.12
3721 4819 7.398047 ACAATGTGGTACTATGGTGTAGAAGTA 59.602 37.037 0.00 0.00 0.00 2.24
3722 4820 6.212791 ACAATGTGGTACTATGGTGTAGAAGT 59.787 38.462 0.00 0.00 0.00 3.01
3723 4821 6.640518 ACAATGTGGTACTATGGTGTAGAAG 58.359 40.000 0.00 0.00 0.00 2.85
3724 4822 6.614694 ACAATGTGGTACTATGGTGTAGAA 57.385 37.500 0.00 0.00 0.00 2.10
3725 4823 6.614694 AACAATGTGGTACTATGGTGTAGA 57.385 37.500 0.00 0.00 0.00 2.59
3726 4824 7.681939 AAAACAATGTGGTACTATGGTGTAG 57.318 36.000 0.00 0.00 0.00 2.74
3727 4825 7.720074 TCAAAAACAATGTGGTACTATGGTGTA 59.280 33.333 0.00 0.00 0.00 2.90
3728 4826 6.547880 TCAAAAACAATGTGGTACTATGGTGT 59.452 34.615 0.00 0.00 0.00 4.16
3729 4827 6.976088 TCAAAAACAATGTGGTACTATGGTG 58.024 36.000 0.00 0.00 0.00 4.17
3730 4828 7.001674 TCTCAAAAACAATGTGGTACTATGGT 58.998 34.615 0.00 0.00 0.00 3.55
3731 4829 7.447374 TCTCAAAAACAATGTGGTACTATGG 57.553 36.000 0.00 0.00 0.00 2.74
3732 4830 9.743057 TTTTCTCAAAAACAATGTGGTACTATG 57.257 29.630 0.00 0.00 29.44 2.23
3776 4876 8.907222 AACCATTAGTACCGACTTTTTCTTTA 57.093 30.769 0.00 0.00 37.10 1.85
3780 4880 7.420002 ACAAAACCATTAGTACCGACTTTTTC 58.580 34.615 0.00 0.00 37.10 2.29
3877 4978 2.022129 GTGTCGTGTTGGGCTCTCG 61.022 63.158 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.