Multiple sequence alignment - TraesCS2B01G130100

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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 TraesCS2B01G130100 chr2B 100.000 2742 0 0 1 2742 97423432 97426173 0.000000e+00 5064.0
1 TraesCS2B01G130100 chr2B 87.594 1201 94 31 943 2104 97414676 97415860 0.000000e+00 1341.0
2 TraesCS2B01G130100 chr2B 92.453 53 3 1 2145 2196 197590575 197590523 1.050000e-09 75.0
3 TraesCS2B01G130100 chr7D 93.018 888 54 6 61 945 10101076 10101958 0.000000e+00 1290.0
4 TraesCS2B01G130100 chr7D 90.719 862 59 12 61 918 629660846 629661690 0.000000e+00 1129.0
5 TraesCS2B01G130100 chr7D 89.078 879 79 9 61 936 503924723 503923859 0.000000e+00 1075.0
6 TraesCS2B01G130100 chr7D 88.843 484 48 5 473 952 4428757 4428276 8.460000e-165 590.0
7 TraesCS2B01G130100 chr2D 86.422 1090 83 35 944 1993 62052129 62053193 0.000000e+00 1133.0
8 TraesCS2B01G130100 chr2D 89.433 899 52 13 62 941 7239544 7240418 0.000000e+00 1094.0
9 TraesCS2B01G130100 chr2D 90.741 54 4 1 2143 2196 384489625 384489677 1.360000e-08 71.3
10 TraesCS2B01G130100 chr2D 90.566 53 3 2 2143 2194 248186023 248186074 4.900000e-08 69.4
11 TraesCS2B01G130100 chr2D 91.837 49 3 1 2149 2197 248579756 248579709 1.760000e-07 67.6
12 TraesCS2B01G130100 chr2A 92.793 777 49 5 944 1720 62380509 62381278 0.000000e+00 1118.0
13 TraesCS2B01G130100 chr2A 87.363 910 82 12 61 942 678532290 678533194 0.000000e+00 1013.0
14 TraesCS2B01G130100 chr2A 86.800 500 48 10 1653 2139 62381504 62381998 2.400000e-150 542.0
15 TraesCS2B01G130100 chr5D 89.907 862 67 11 61 917 565842145 565841299 0.000000e+00 1092.0
16 TraesCS2B01G130100 chr5D 88.354 893 71 15 61 936 435155486 435154610 0.000000e+00 1042.0
17 TraesCS2B01G130100 chr5D 93.092 304 17 3 61 363 379246159 379246459 2.510000e-120 442.0
18 TraesCS2B01G130100 chr1D 88.813 876 66 13 61 918 22593515 22594376 0.000000e+00 1046.0
19 TraesCS2B01G130100 chr1D 94.276 594 25 8 2155 2742 26415526 26416116 0.000000e+00 900.0
20 TraesCS2B01G130100 chr1D 91.332 473 28 4 61 532 476788389 476788849 3.850000e-178 634.0
21 TraesCS2B01G130100 chr3D 88.137 902 73 14 61 943 70094855 70093969 0.000000e+00 1042.0
22 TraesCS2B01G130100 chr3D 89.542 698 52 12 226 918 590029517 590028836 0.000000e+00 865.0
23 TraesCS2B01G130100 chr3A 87.569 901 78 13 61 942 699109644 699108759 0.000000e+00 1013.0
24 TraesCS2B01G130100 chr7A 86.780 885 90 17 61 942 695379801 695378941 0.000000e+00 961.0
25 TraesCS2B01G130100 chr5A 88.727 754 57 6 216 942 48885137 48885889 0.000000e+00 896.0
26 TraesCS2B01G130100 chr5A 93.878 49 2 1 2149 2197 297079401 297079448 3.790000e-09 73.1
27 TraesCS2B01G130100 chr6D 94.708 548 24 3 2166 2711 38451029 38450485 0.000000e+00 846.0
28 TraesCS2B01G130100 chr6D 94.526 548 25 4 2166 2711 38437785 38437241 0.000000e+00 841.0
29 TraesCS2B01G130100 chr5B 83.165 695 82 18 61 739 557256269 557255594 1.090000e-168 603.0
30 TraesCS2B01G130100 chr4A 88.172 465 47 5 480 937 626920489 626920026 5.160000e-152 547.0
31 TraesCS2B01G130100 chr1A 87.931 58 5 2 2143 2199 297095424 297095480 1.760000e-07 67.6


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 TraesCS2B01G130100 chr2B 97423432 97426173 2741 False 5064 5064 100.0000 1 2742 1 chr2B.!!$F2 2741
1 TraesCS2B01G130100 chr2B 97414676 97415860 1184 False 1341 1341 87.5940 943 2104 1 chr2B.!!$F1 1161
2 TraesCS2B01G130100 chr7D 10101076 10101958 882 False 1290 1290 93.0180 61 945 1 chr7D.!!$F1 884
3 TraesCS2B01G130100 chr7D 629660846 629661690 844 False 1129 1129 90.7190 61 918 1 chr7D.!!$F2 857
4 TraesCS2B01G130100 chr7D 503923859 503924723 864 True 1075 1075 89.0780 61 936 1 chr7D.!!$R2 875
5 TraesCS2B01G130100 chr2D 62052129 62053193 1064 False 1133 1133 86.4220 944 1993 1 chr2D.!!$F2 1049
6 TraesCS2B01G130100 chr2D 7239544 7240418 874 False 1094 1094 89.4330 62 941 1 chr2D.!!$F1 879
7 TraesCS2B01G130100 chr2A 678532290 678533194 904 False 1013 1013 87.3630 61 942 1 chr2A.!!$F1 881
8 TraesCS2B01G130100 chr2A 62380509 62381998 1489 False 830 1118 89.7965 944 2139 2 chr2A.!!$F2 1195
9 TraesCS2B01G130100 chr5D 565841299 565842145 846 True 1092 1092 89.9070 61 917 1 chr5D.!!$R2 856
10 TraesCS2B01G130100 chr5D 435154610 435155486 876 True 1042 1042 88.3540 61 936 1 chr5D.!!$R1 875
11 TraesCS2B01G130100 chr1D 22593515 22594376 861 False 1046 1046 88.8130 61 918 1 chr1D.!!$F1 857
12 TraesCS2B01G130100 chr1D 26415526 26416116 590 False 900 900 94.2760 2155 2742 1 chr1D.!!$F2 587
13 TraesCS2B01G130100 chr3D 70093969 70094855 886 True 1042 1042 88.1370 61 943 1 chr3D.!!$R1 882
14 TraesCS2B01G130100 chr3D 590028836 590029517 681 True 865 865 89.5420 226 918 1 chr3D.!!$R2 692
15 TraesCS2B01G130100 chr3A 699108759 699109644 885 True 1013 1013 87.5690 61 942 1 chr3A.!!$R1 881
16 TraesCS2B01G130100 chr7A 695378941 695379801 860 True 961 961 86.7800 61 942 1 chr7A.!!$R1 881
17 TraesCS2B01G130100 chr5A 48885137 48885889 752 False 896 896 88.7270 216 942 1 chr5A.!!$F1 726
18 TraesCS2B01G130100 chr6D 38450485 38451029 544 True 846 846 94.7080 2166 2711 1 chr6D.!!$R2 545
19 TraesCS2B01G130100 chr6D 38437241 38437785 544 True 841 841 94.5260 2166 2711 1 chr6D.!!$R1 545
20 TraesCS2B01G130100 chr5B 557255594 557256269 675 True 603 603 83.1650 61 739 1 chr5B.!!$R1 678

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
769 885 0.468226 GATAACTGATGGGTCCCGCA 59.532 55.0 2.65 3.14 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 2348 0.111061 TGGCCTCTTTGATGTGCACT 59.889 50.0 19.41 3.19 0.0 4.4 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
27 28 8.937634 AATGATTTTTGAGGCTTTCATACATC 57.062 30.769 0.00 0.00 35.27 3.06
28 29 6.866480 TGATTTTTGAGGCTTTCATACATCC 58.134 36.000 0.00 0.00 35.27 3.51
29 30 5.659440 TTTTTGAGGCTTTCATACATCCC 57.341 39.130 0.00 0.00 35.27 3.85
30 31 3.297134 TTGAGGCTTTCATACATCCCC 57.703 47.619 0.00 0.00 35.27 4.81
31 32 2.204463 TGAGGCTTTCATACATCCCCA 58.796 47.619 0.00 0.00 0.00 4.96
32 33 2.785269 TGAGGCTTTCATACATCCCCAT 59.215 45.455 0.00 0.00 0.00 4.00
33 34 3.205056 TGAGGCTTTCATACATCCCCATT 59.795 43.478 0.00 0.00 0.00 3.16
34 35 4.218312 GAGGCTTTCATACATCCCCATTT 58.782 43.478 0.00 0.00 0.00 2.32
35 36 4.623863 AGGCTTTCATACATCCCCATTTT 58.376 39.130 0.00 0.00 0.00 1.82
36 37 5.032170 AGGCTTTCATACATCCCCATTTTT 58.968 37.500 0.00 0.00 0.00 1.94
37 38 6.201591 AGGCTTTCATACATCCCCATTTTTA 58.798 36.000 0.00 0.00 0.00 1.52
38 39 6.845975 AGGCTTTCATACATCCCCATTTTTAT 59.154 34.615 0.00 0.00 0.00 1.40
39 40 6.930722 GGCTTTCATACATCCCCATTTTTATG 59.069 38.462 0.00 0.00 0.00 1.90
40 41 6.424812 GCTTTCATACATCCCCATTTTTATGC 59.575 38.462 0.00 0.00 0.00 3.14
41 42 7.429374 TTTCATACATCCCCATTTTTATGCA 57.571 32.000 0.00 0.00 0.00 3.96
42 43 7.615039 TTCATACATCCCCATTTTTATGCAT 57.385 32.000 3.79 3.79 0.00 3.96
43 44 6.995364 TCATACATCCCCATTTTTATGCATG 58.005 36.000 10.16 0.00 0.00 4.06
44 45 6.781507 TCATACATCCCCATTTTTATGCATGA 59.218 34.615 10.16 0.00 32.37 3.07
45 46 5.954153 ACATCCCCATTTTTATGCATGAA 57.046 34.783 10.16 4.23 0.00 2.57
46 47 5.673514 ACATCCCCATTTTTATGCATGAAC 58.326 37.500 10.16 0.00 0.00 3.18
47 48 5.426185 ACATCCCCATTTTTATGCATGAACT 59.574 36.000 10.16 0.00 0.00 3.01
48 49 6.070078 ACATCCCCATTTTTATGCATGAACTT 60.070 34.615 10.16 0.00 0.00 2.66
49 50 6.371595 TCCCCATTTTTATGCATGAACTTT 57.628 33.333 10.16 0.00 0.00 2.66
50 51 6.777782 TCCCCATTTTTATGCATGAACTTTT 58.222 32.000 10.16 0.00 0.00 2.27
51 52 6.878389 TCCCCATTTTTATGCATGAACTTTTC 59.122 34.615 10.16 0.00 0.00 2.29
52 53 6.093909 CCCCATTTTTATGCATGAACTTTTCC 59.906 38.462 10.16 0.00 0.00 3.13
53 54 6.654161 CCCATTTTTATGCATGAACTTTTCCA 59.346 34.615 10.16 0.00 0.00 3.53
54 55 7.361116 CCCATTTTTATGCATGAACTTTTCCAC 60.361 37.037 10.16 0.00 0.00 4.02
55 56 7.388500 CCATTTTTATGCATGAACTTTTCCACT 59.612 33.333 10.16 0.00 0.00 4.00
56 57 9.421806 CATTTTTATGCATGAACTTTTCCACTA 57.578 29.630 10.16 0.00 0.00 2.74
58 59 9.995003 TTTTTATGCATGAACTTTTCCACTATT 57.005 25.926 10.16 0.00 0.00 1.73
59 60 8.984891 TTTATGCATGAACTTTTCCACTATTG 57.015 30.769 10.16 0.00 0.00 1.90
108 109 0.668706 CTGTCCATCATCGGATCGGC 60.669 60.000 0.00 0.00 37.41 5.54
109 110 1.115326 TGTCCATCATCGGATCGGCT 61.115 55.000 0.00 0.00 37.41 5.52
137 138 1.745264 CCAAATGTGGGGCGTGTTT 59.255 52.632 0.00 0.00 41.77 2.83
154 158 2.580155 TTTCACACAAGCTGCCCCCA 62.580 55.000 0.00 0.00 0.00 4.96
250 254 4.792068 TGTCCACATTTCTTCAGAACCTT 58.208 39.130 0.00 0.00 33.13 3.50
265 269 7.576861 TCAGAACCTTAAAAACAGGGTAAAG 57.423 36.000 0.00 0.00 35.46 1.85
272 276 3.985553 AAAACAGGGTAAAGAGGGGTT 57.014 42.857 0.00 0.00 0.00 4.11
276 280 1.702957 CAGGGTAAAGAGGGGTTGACA 59.297 52.381 0.00 0.00 0.00 3.58
339 352 4.765339 ACGGAAAAAGAAAGAAATCGGGAT 59.235 37.500 0.00 0.00 0.00 3.85
387 400 2.131709 CGGATCTAACCTGCCCCGA 61.132 63.158 0.00 0.00 39.31 5.14
533 548 1.678728 CGTACTGTGGCCATGATTGGT 60.679 52.381 9.72 4.63 45.57 3.67
549 564 2.359975 GTGGGAGGCCGAAGTTGG 60.360 66.667 0.00 0.00 0.00 3.77
568 598 1.725557 GGCTAGACATCACTCGCCGA 61.726 60.000 0.00 0.00 38.57 5.54
606 668 2.094442 CGGAGAGAGGAAGAACAAGGTC 60.094 54.545 0.00 0.00 0.00 3.85
611 673 1.002502 GGAAGAACAAGGTCGGGGG 60.003 63.158 0.00 0.00 0.00 5.40
627 689 1.228920 GGGGAAGGGGAAAGGGGAAT 61.229 60.000 0.00 0.00 0.00 3.01
676 756 4.457496 CGGGGCACGCTGATGAGT 62.457 66.667 0.00 0.00 40.02 3.41
769 885 0.468226 GATAACTGATGGGTCCCGCA 59.532 55.000 2.65 3.14 0.00 5.69
833 949 1.530323 GTTAAACAGGGCCATGTCGT 58.470 50.000 25.45 17.18 31.50 4.34
840 956 0.916086 AGGGCCATGTCGTATTGGAA 59.084 50.000 6.18 0.00 34.81 3.53
850 966 6.984474 CCATGTCGTATTGGAACTATAGTTGT 59.016 38.462 22.68 8.40 38.56 3.32
866 982 2.729882 AGTTGTCTGCAAATACGTCGTC 59.270 45.455 0.00 0.00 36.22 4.20
923 1039 5.246981 TCCAATTCATCTCAAAGGTGTCT 57.753 39.130 0.00 0.00 0.00 3.41
948 1064 3.007635 CGGAACTATTGACCCTCCAAAC 58.992 50.000 0.00 0.00 0.00 2.93
1144 1274 1.382009 GAGGAGAGGGGAGTGGGAC 60.382 68.421 0.00 0.00 0.00 4.46
1497 1630 2.178521 CGACGAGTAGCTGCCGTT 59.821 61.111 16.51 4.41 36.60 4.44
1555 1688 0.172578 GCATGTGTGATGCATGTGCT 59.827 50.000 2.46 0.00 43.93 4.40
1556 1689 1.797713 GCATGTGTGATGCATGTGCTC 60.798 52.381 2.46 0.00 43.93 4.26
1564 1697 3.993234 GCATGTGCTCGATCGGCG 61.993 66.667 16.41 0.00 42.69 6.46
1585 1718 2.095212 GGCCTGCTGCTTAGTTGTAAAC 60.095 50.000 0.00 0.00 43.84 2.01
1606 1739 9.483916 GTAAACTTGTAATTGGCCAAAATAACT 57.516 29.630 24.71 0.66 0.00 2.24
1607 1740 8.601845 AAACTTGTAATTGGCCAAAATAACTC 57.398 30.769 24.71 9.39 0.00 3.01
1625 2008 3.594134 ACTCTTGAGCCTCTTTGATTCG 58.406 45.455 0.00 0.00 0.00 3.34
1646 2029 7.435068 TTCGAAGAATTTTTAGAGGGTTCTG 57.565 36.000 0.00 0.00 45.90 3.02
1651 2034 6.116126 AGAATTTTTAGAGGGTTCTGATCCG 58.884 40.000 0.00 0.00 34.79 4.18
1654 2037 4.996788 TTTAGAGGGTTCTGATCCGTAC 57.003 45.455 0.25 0.00 34.79 3.67
1662 2087 2.203800 TCTGATCCGTACGCATGTTC 57.796 50.000 10.49 2.12 0.00 3.18
1669 2094 2.159476 TCCGTACGCATGTTCTCTACAC 60.159 50.000 10.49 0.00 40.19 2.90
1705 2130 7.658525 TTCATAGGATTGCAAACCATACAAT 57.341 32.000 25.68 8.16 36.74 2.71
1731 2157 3.212685 TCCGGTTGTTTTATTTGTCGGT 58.787 40.909 0.00 0.00 37.72 4.69
1740 2166 8.641155 GTTGTTTTATTTGTCGGTTTTATAGCC 58.359 33.333 0.00 0.00 0.00 3.93
1745 2171 9.760077 TTTATTTGTCGGTTTTATAGCCAAAAA 57.240 25.926 0.00 0.00 0.00 1.94
1790 2276 9.796120 TTTTATTTATAGCAAAACTTCCATCCG 57.204 29.630 0.00 0.00 0.00 4.18
1797 2283 3.673323 GCAAAACTTCCATCCGCCTTAAG 60.673 47.826 0.00 0.00 0.00 1.85
1821 2307 5.118817 GCTCTTGAAAACGAATTCTACGTCT 59.881 40.000 3.52 0.00 43.16 4.18
1832 2318 5.735892 CGAATTCTACGTCTTTCATGTACGA 59.264 40.000 15.63 0.00 39.80 3.43
1862 2348 2.890311 AGCCATTCATTTCGGTGTTTGA 59.110 40.909 0.00 0.00 0.00 2.69
1972 2478 6.509418 TGTTCCAGCTAAACATGTATTTCC 57.491 37.500 0.00 0.00 31.90 3.13
1987 2493 8.119891 ACATGTATTTCCTGGTTTATTTACCCT 58.880 33.333 0.00 0.00 37.39 4.34
2008 2514 1.339610 TGGAACGAAAGCAATGTTGGG 59.660 47.619 0.00 0.00 0.00 4.12
2057 2570 8.500753 TTTTCTTTTCTTACTGACTGCTTGTA 57.499 30.769 0.00 0.00 0.00 2.41
2118 2631 1.137086 TCAGCTAGCCTCTTAAAGCCG 59.863 52.381 12.13 0.00 35.54 5.52
2123 2636 1.198759 AGCCTCTTAAAGCCGTCCCA 61.199 55.000 0.00 0.00 0.00 4.37
2124 2637 1.025113 GCCTCTTAAAGCCGTCCCAC 61.025 60.000 0.00 0.00 0.00 4.61
2139 2652 4.277423 CCGTCCCACAAACTCTTGTATTTT 59.723 41.667 0.00 0.00 44.15 1.82
2140 2653 5.470777 CCGTCCCACAAACTCTTGTATTTTA 59.529 40.000 0.00 0.00 44.15 1.52
2141 2654 6.016943 CCGTCCCACAAACTCTTGTATTTTAA 60.017 38.462 0.00 0.00 44.15 1.52
2142 2655 6.854381 CGTCCCACAAACTCTTGTATTTTAAC 59.146 38.462 0.00 0.00 44.15 2.01
2143 2656 7.255001 CGTCCCACAAACTCTTGTATTTTAACT 60.255 37.037 0.00 0.00 44.15 2.24
2144 2657 8.410912 GTCCCACAAACTCTTGTATTTTAACTT 58.589 33.333 0.00 0.00 44.15 2.66
2145 2658 9.629878 TCCCACAAACTCTTGTATTTTAACTTA 57.370 29.630 0.00 0.00 44.15 2.24
2227 2740 0.249322 CTTCAACACGACGTCCCACT 60.249 55.000 10.58 0.00 0.00 4.00
2258 2771 2.131709 CATCCTCCTTCCCGCCGTA 61.132 63.158 0.00 0.00 0.00 4.02
2273 2786 2.875485 GTAGCCTCGACGTGCTCA 59.125 61.111 15.81 3.62 39.00 4.26
2285 2798 4.022849 TCGACGTGCTCATGATCATAATCT 60.023 41.667 8.15 0.00 32.75 2.40
2318 2831 3.192922 GCCACCGCACGATACACC 61.193 66.667 0.00 0.00 34.03 4.16
2323 2836 1.872234 CCGCACGATACACCTGTCG 60.872 63.158 0.00 0.00 43.13 4.35
2376 2889 2.295349 CCAATGCTGCTCCATGAATACC 59.705 50.000 0.00 0.00 0.00 2.73
2471 2984 5.860941 TTTAACAGGGTGCAATTTTCAGA 57.139 34.783 0.00 0.00 0.00 3.27
2512 3025 4.677378 CGCAACAATTGAAACGACCAATAA 59.323 37.500 13.59 0.00 33.51 1.40
2698 3216 2.610433 GCAAAAGCATAAACCAGAGGC 58.390 47.619 0.00 0.00 0.00 4.70
2722 3240 1.001248 TGGTCTTACCTCCCCCTCG 59.999 63.158 0.00 0.00 39.58 4.63
2729 3247 0.917333 TACCTCCCCCTCGGCAAATT 60.917 55.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.983484 GGATGTATGAAAGCCTCAAAAATCATT 59.017 33.333 0.00 0.00 37.67 2.57
3 4 7.418254 GGGATGTATGAAAGCCTCAAAAATCAT 60.418 37.037 0.00 0.00 37.67 2.45
4 5 6.127366 GGGATGTATGAAAGCCTCAAAAATCA 60.127 38.462 0.00 0.00 37.67 2.57
5 6 6.276091 GGGATGTATGAAAGCCTCAAAAATC 58.724 40.000 0.00 0.00 37.67 2.17
6 7 5.129320 GGGGATGTATGAAAGCCTCAAAAAT 59.871 40.000 0.00 0.00 37.67 1.82
7 8 4.466015 GGGGATGTATGAAAGCCTCAAAAA 59.534 41.667 0.00 0.00 37.67 1.94
8 9 4.023291 GGGGATGTATGAAAGCCTCAAAA 58.977 43.478 0.00 0.00 37.67 2.44
9 10 3.011144 TGGGGATGTATGAAAGCCTCAAA 59.989 43.478 0.00 0.00 37.67 2.69
10 11 2.580322 TGGGGATGTATGAAAGCCTCAA 59.420 45.455 0.00 0.00 37.67 3.02
11 12 2.204463 TGGGGATGTATGAAAGCCTCA 58.796 47.619 0.00 0.00 38.81 3.86
12 13 3.515602 ATGGGGATGTATGAAAGCCTC 57.484 47.619 0.00 0.00 0.00 4.70
13 14 3.979501 AATGGGGATGTATGAAAGCCT 57.020 42.857 0.00 0.00 0.00 4.58
14 15 5.357742 AAAAATGGGGATGTATGAAAGCC 57.642 39.130 0.00 0.00 0.00 4.35
15 16 6.424812 GCATAAAAATGGGGATGTATGAAAGC 59.575 38.462 0.00 0.00 0.00 3.51
16 17 7.499292 TGCATAAAAATGGGGATGTATGAAAG 58.501 34.615 0.00 0.00 0.00 2.62
17 18 7.429374 TGCATAAAAATGGGGATGTATGAAA 57.571 32.000 0.00 0.00 0.00 2.69
18 19 7.289549 TCATGCATAAAAATGGGGATGTATGAA 59.710 33.333 0.00 0.00 43.71 2.57
19 20 6.781507 TCATGCATAAAAATGGGGATGTATGA 59.218 34.615 0.00 9.49 44.14 2.15
20 21 6.995364 TCATGCATAAAAATGGGGATGTATG 58.005 36.000 0.00 5.70 41.20 2.39
21 22 7.290714 AGTTCATGCATAAAAATGGGGATGTAT 59.709 33.333 0.00 0.00 31.92 2.29
22 23 6.610830 AGTTCATGCATAAAAATGGGGATGTA 59.389 34.615 0.00 0.00 31.92 2.29
23 24 5.426185 AGTTCATGCATAAAAATGGGGATGT 59.574 36.000 0.00 0.00 31.92 3.06
24 25 5.920903 AGTTCATGCATAAAAATGGGGATG 58.079 37.500 0.00 0.00 0.00 3.51
25 26 6.564557 AAGTTCATGCATAAAAATGGGGAT 57.435 33.333 0.00 0.00 0.00 3.85
26 27 6.371595 AAAGTTCATGCATAAAAATGGGGA 57.628 33.333 0.00 0.00 0.00 4.81
27 28 6.093909 GGAAAAGTTCATGCATAAAAATGGGG 59.906 38.462 0.00 0.00 0.00 4.96
28 29 6.654161 TGGAAAAGTTCATGCATAAAAATGGG 59.346 34.615 0.00 0.00 0.00 4.00
29 30 7.388500 AGTGGAAAAGTTCATGCATAAAAATGG 59.612 33.333 0.00 0.00 0.00 3.16
30 31 8.314143 AGTGGAAAAGTTCATGCATAAAAATG 57.686 30.769 0.00 0.00 0.00 2.32
32 33 9.995003 AATAGTGGAAAAGTTCATGCATAAAAA 57.005 25.926 0.00 0.00 0.00 1.94
33 34 9.421806 CAATAGTGGAAAAGTTCATGCATAAAA 57.578 29.630 0.00 0.00 0.00 1.52
34 35 8.584157 ACAATAGTGGAAAAGTTCATGCATAAA 58.416 29.630 0.00 0.00 0.00 1.40
35 36 8.121305 ACAATAGTGGAAAAGTTCATGCATAA 57.879 30.769 0.00 0.00 0.00 1.90
36 37 7.701539 ACAATAGTGGAAAAGTTCATGCATA 57.298 32.000 0.00 0.00 0.00 3.14
37 38 6.594788 ACAATAGTGGAAAAGTTCATGCAT 57.405 33.333 0.00 0.00 0.00 3.96
38 39 6.403866 AACAATAGTGGAAAAGTTCATGCA 57.596 33.333 0.00 0.00 0.00 3.96
39 40 7.653311 AGAAAACAATAGTGGAAAAGTTCATGC 59.347 33.333 0.00 0.00 0.00 4.06
40 41 9.533253 AAGAAAACAATAGTGGAAAAGTTCATG 57.467 29.630 0.00 0.00 0.00 3.07
41 42 9.750125 GAAGAAAACAATAGTGGAAAAGTTCAT 57.250 29.630 0.00 0.00 0.00 2.57
42 43 8.744652 TGAAGAAAACAATAGTGGAAAAGTTCA 58.255 29.630 0.00 0.00 0.00 3.18
43 44 9.581099 TTGAAGAAAACAATAGTGGAAAAGTTC 57.419 29.630 0.00 0.00 0.00 3.01
48 49 9.528018 GTGAATTGAAGAAAACAATAGTGGAAA 57.472 29.630 0.00 0.00 37.04 3.13
49 50 8.690884 TGTGAATTGAAGAAAACAATAGTGGAA 58.309 29.630 0.00 0.00 37.04 3.53
50 51 8.134895 GTGTGAATTGAAGAAAACAATAGTGGA 58.865 33.333 0.00 0.00 37.04 4.02
51 52 8.137437 AGTGTGAATTGAAGAAAACAATAGTGG 58.863 33.333 0.00 0.00 37.04 4.00
52 53 9.520204 AAGTGTGAATTGAAGAAAACAATAGTG 57.480 29.630 0.00 0.00 37.04 2.74
53 54 9.736023 GAAGTGTGAATTGAAGAAAACAATAGT 57.264 29.630 0.00 0.00 37.04 2.12
54 55 9.734620 TGAAGTGTGAATTGAAGAAAACAATAG 57.265 29.630 0.00 0.00 37.04 1.73
55 56 9.515020 GTGAAGTGTGAATTGAAGAAAACAATA 57.485 29.630 0.00 0.00 37.04 1.90
56 57 8.253113 AGTGAAGTGTGAATTGAAGAAAACAAT 58.747 29.630 0.00 0.00 39.25 2.71
57 58 7.601856 AGTGAAGTGTGAATTGAAGAAAACAA 58.398 30.769 0.00 0.00 0.00 2.83
58 59 7.156876 AGTGAAGTGTGAATTGAAGAAAACA 57.843 32.000 0.00 0.00 0.00 2.83
59 60 7.754924 TGAAGTGAAGTGTGAATTGAAGAAAAC 59.245 33.333 0.00 0.00 0.00 2.43
137 138 2.580155 TTTGGGGGCAGCTTGTGTGA 62.580 55.000 0.00 0.00 0.00 3.58
154 158 8.392612 CAACACAAGAGCTCAATTTCAATTTTT 58.607 29.630 17.77 0.00 0.00 1.94
250 254 5.103601 TCAACCCCTCTTTACCCTGTTTTTA 60.104 40.000 0.00 0.00 0.00 1.52
265 269 3.628646 ATGCCGCTGTCAACCCCTC 62.629 63.158 0.00 0.00 0.00 4.30
272 276 1.549243 TAGGGTTCATGCCGCTGTCA 61.549 55.000 10.66 0.00 0.00 3.58
276 280 0.394565 GATCTAGGGTTCATGCCGCT 59.605 55.000 6.92 6.92 0.00 5.52
339 352 5.007626 CGCACCAAGCAGCTTATCTAAATTA 59.992 40.000 7.52 0.00 46.13 1.40
533 548 3.646715 CCCAACTTCGGCCTCCCA 61.647 66.667 0.00 0.00 0.00 4.37
549 564 4.740235 GGCGAGTGATGTCTAGCC 57.260 61.111 2.54 2.54 45.59 3.93
606 668 3.739613 CCCTTTCCCCTTCCCCCG 61.740 72.222 0.00 0.00 0.00 5.73
611 673 0.687757 GCCATTCCCCTTTCCCCTTC 60.688 60.000 0.00 0.00 0.00 3.46
676 756 0.833949 TCCACATAAGCATGCCCGTA 59.166 50.000 15.66 4.86 35.39 4.02
769 885 5.944007 GGGTTAGTGGTTTGAGTTATGACAT 59.056 40.000 0.00 0.00 0.00 3.06
840 956 5.742453 CGACGTATTTGCAGACAACTATAGT 59.258 40.000 0.00 0.00 34.87 2.12
850 966 3.011818 TCTAGGACGACGTATTTGCAGA 58.988 45.455 0.00 0.00 0.00 4.26
923 1039 1.829222 GAGGGTCAATAGTTCCGGTGA 59.171 52.381 0.00 0.00 0.00 4.02
927 1043 3.007635 GTTTGGAGGGTCAATAGTTCCG 58.992 50.000 0.00 0.00 0.00 4.30
931 1047 5.772393 TGTATGTTTGGAGGGTCAATAGT 57.228 39.130 0.00 0.00 0.00 2.12
948 1064 1.651132 GTTCGGCGCGCATTGTATG 60.651 57.895 34.42 12.59 0.00 2.39
1102 1232 3.219928 ATCATCGCTCGCTCCGGT 61.220 61.111 0.00 0.00 0.00 5.28
1166 1296 2.482796 ATCACCACCGCCATCAGCAA 62.483 55.000 0.00 0.00 44.04 3.91
1358 1488 2.486042 GTCGAGCGACTCTCCCAC 59.514 66.667 15.13 0.00 41.57 4.61
1423 1553 1.649664 CGAGCAGGAAGAACATCAGG 58.350 55.000 0.00 0.00 0.00 3.86
1564 1697 1.821216 TTACAACTAAGCAGCAGGCC 58.179 50.000 0.00 0.00 46.50 5.19
1585 1718 8.087750 TCAAGAGTTATTTTGGCCAATTACAAG 58.912 33.333 21.26 3.16 0.00 3.16
1593 1726 2.825532 GGCTCAAGAGTTATTTTGGCCA 59.174 45.455 0.00 0.00 38.94 5.36
1597 1730 7.206981 TCAAAGAGGCTCAAGAGTTATTTTG 57.793 36.000 18.26 14.20 0.00 2.44
1606 1739 3.961480 TCGAATCAAAGAGGCTCAAGA 57.039 42.857 18.26 11.38 0.00 3.02
1607 1740 4.248859 TCTTCGAATCAAAGAGGCTCAAG 58.751 43.478 18.26 8.09 0.00 3.02
1625 2008 7.201652 CGGATCAGAACCCTCTAAAAATTCTTC 60.202 40.741 0.00 0.00 0.00 2.87
1646 2029 2.493713 AGAGAACATGCGTACGGATC 57.506 50.000 20.08 10.02 0.00 3.36
1651 2034 3.127081 TCGTGTAGAGAACATGCGTAC 57.873 47.619 0.00 0.00 43.65 3.67
1669 2094 5.049818 GCAATCCTATGAATCCAAGAACTCG 60.050 44.000 0.00 0.00 0.00 4.18
1711 2136 3.629438 ACCGACAAATAAAACAACCGG 57.371 42.857 0.00 0.00 41.24 5.28
1713 2138 8.641155 GCTATAAAACCGACAAATAAAACAACC 58.359 33.333 0.00 0.00 0.00 3.77
1714 2139 8.641155 GGCTATAAAACCGACAAATAAAACAAC 58.359 33.333 0.00 0.00 0.00 3.32
1715 2140 8.358148 TGGCTATAAAACCGACAAATAAAACAA 58.642 29.630 0.00 0.00 0.00 2.83
1716 2141 7.883217 TGGCTATAAAACCGACAAATAAAACA 58.117 30.769 0.00 0.00 0.00 2.83
1717 2142 8.745464 TTGGCTATAAAACCGACAAATAAAAC 57.255 30.769 0.00 0.00 0.00 2.43
1751 2177 9.828852 TGCTATAAATAAAACTTACAACAACCG 57.171 29.630 0.00 0.00 0.00 4.44
1764 2190 9.796120 CGGATGGAAGTTTTGCTATAAATAAAA 57.204 29.630 0.00 0.00 0.00 1.52
1772 2198 2.024414 GGCGGATGGAAGTTTTGCTAT 58.976 47.619 0.00 0.00 0.00 2.97
1790 2276 4.483476 TTCGTTTTCAAGAGCTTAAGGC 57.517 40.909 4.29 0.00 42.19 4.35
1797 2283 5.118817 AGACGTAGAATTCGTTTTCAAGAGC 59.881 40.000 0.00 0.00 41.64 4.09
1821 2307 5.009110 TGGCTGTTTGATTTCGTACATGAAA 59.991 36.000 0.00 0.00 41.69 2.69
1832 2318 4.931002 CCGAAATGAATGGCTGTTTGATTT 59.069 37.500 0.00 0.00 0.00 2.17
1862 2348 0.111061 TGGCCTCTTTGATGTGCACT 59.889 50.000 19.41 3.19 0.00 4.40
1972 2478 5.005094 TCGTTCCAAGGGTAAATAAACCAG 58.995 41.667 0.00 0.00 41.67 4.00
1987 2493 2.223923 CCCAACATTGCTTTCGTTCCAA 60.224 45.455 0.00 0.00 0.00 3.53
2008 2514 5.712152 AATGGTGTCTGTTTGGATTCTTC 57.288 39.130 0.00 0.00 0.00 2.87
2035 2541 7.769044 AGTTTACAAGCAGTCAGTAAGAAAAGA 59.231 33.333 0.00 0.00 0.00 2.52
2036 2542 7.920738 AGTTTACAAGCAGTCAGTAAGAAAAG 58.079 34.615 0.00 0.00 0.00 2.27
2037 2543 7.769044 AGAGTTTACAAGCAGTCAGTAAGAAAA 59.231 33.333 0.00 0.00 0.00 2.29
2038 2544 7.224753 CAGAGTTTACAAGCAGTCAGTAAGAAA 59.775 37.037 0.00 0.00 0.00 2.52
2039 2545 6.701841 CAGAGTTTACAAGCAGTCAGTAAGAA 59.298 38.462 0.00 0.00 0.00 2.52
2118 2631 7.937649 AGTTAAAATACAAGAGTTTGTGGGAC 58.062 34.615 3.33 0.00 46.63 4.46
2197 2710 1.620822 GTGTTGAAGGGCAAGGACAT 58.379 50.000 0.00 0.00 37.12 3.06
2198 2711 0.817634 CGTGTTGAAGGGCAAGGACA 60.818 55.000 0.00 0.00 37.12 4.02
2227 2740 1.134220 GGAGGATGCCCGACAATACAA 60.134 52.381 0.00 0.00 37.58 2.41
2258 2771 1.670949 ATCATGAGCACGTCGAGGCT 61.671 55.000 14.25 14.25 44.48 4.58
2285 2798 1.487976 GTGGCTGAGATCATCCCTTCA 59.512 52.381 0.00 0.00 31.39 3.02
2318 2831 3.193691 AGTCCCATTAGAGTCAACGACAG 59.806 47.826 0.00 0.00 34.60 3.51
2323 2836 4.894784 TGTTCAGTCCCATTAGAGTCAAC 58.105 43.478 0.00 0.00 0.00 3.18
2471 2984 6.280643 TGTTGCGTAGTTGATAGCATCTAAT 58.719 36.000 0.46 0.00 39.50 1.73
2512 3025 4.022935 CCATAATGGATAAATGCACGCTGT 60.023 41.667 0.00 0.00 40.96 4.40
2655 3172 5.519722 CGAAAACAGTTTACCAAGCTCAAT 58.480 37.500 0.00 0.00 0.00 2.57
2698 3216 1.962100 GGGGAGGTAAGACCAGATACG 59.038 57.143 0.00 0.00 41.95 3.06


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

AutoCloner maintained by Alex Coulton.