Multiple sequence alignment - TraesCS1D01G062200

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 TraesCS1D01G062200 chr1D 100.000 2623 0 0 1 2623 41913705 41916327 0.000000e+00 4844.0
1 TraesCS1D01G062200 chr1D 91.814 794 39 8 63 830 203875108 203875901 0.000000e+00 1083.0
2 TraesCS1D01G062200 chr1A 91.642 1675 91 23 835 2498 41918958 41920594 0.000000e+00 2272.0
3 TraesCS1D01G062200 chr1A 89.523 859 58 6 3 830 583657266 583658123 0.000000e+00 1059.0
4 TraesCS1D01G062200 chr1B 92.087 1289 60 17 845 2127 62284286 62285538 0.000000e+00 1777.0
5 TraesCS1D01G062200 chr1B 91.325 415 33 1 2125 2539 62285699 62286110 4.900000e-157 564.0
6 TraesCS1D01G062200 chr1B 86.250 160 19 2 2331 2489 62003027 62003184 1.250000e-38 171.0
7 TraesCS1D01G062200 chr1B 81.208 149 19 8 2306 2451 62059400 62059542 7.670000e-21 111.0
8 TraesCS1D01G062200 chr1B 83.333 90 14 1 1861 1950 62199130 62199218 6.020000e-12 82.4
9 TraesCS1D01G062200 chr1B 77.165 127 12 6 2415 2536 61965312 61965426 1.010000e-04 58.4
10 TraesCS1D01G062200 chr6D 91.162 826 42 14 34 830 402357712 402358535 0.000000e+00 1092.0
11 TraesCS1D01G062200 chr6D 87.530 834 63 18 34 831 397351843 397352671 0.000000e+00 926.0
12 TraesCS1D01G062200 chr6D 87.668 819 70 16 3 808 447921114 447921914 0.000000e+00 924.0
13 TraesCS1D01G062200 chr3A 89.884 860 57 5 1 830 708007933 708008792 0.000000e+00 1079.0
14 TraesCS1D01G062200 chr3A 89.437 871 61 6 1 840 401459333 401460203 0.000000e+00 1070.0
15 TraesCS1D01G062200 chr2D 90.920 815 46 7 51 837 637908775 637907961 0.000000e+00 1070.0
16 TraesCS1D01G062200 chr5B 89.639 859 60 3 1 830 54203883 54204741 0.000000e+00 1066.0
17 TraesCS1D01G062200 chr5B 100.000 80 0 0 2542 2621 74026181 74026260 5.850000e-32 148.0
18 TraesCS1D01G062200 chr5B 97.590 83 2 0 2539 2621 652853265 652853183 2.720000e-30 143.0
19 TraesCS1D01G062200 chr4A 89.639 859 60 3 1 830 533199107 533199965 0.000000e+00 1066.0
20 TraesCS1D01G062200 chr5D 89.406 859 51 6 1 831 27849149 27848303 0.000000e+00 1046.0
21 TraesCS1D01G062200 chr7B 88.953 860 64 19 1 830 423255683 423254825 0.000000e+00 1033.0
22 TraesCS1D01G062200 chr7B 98.765 81 1 0 2543 2623 137215051 137214971 7.570000e-31 145.0
23 TraesCS1D01G062200 chr5A 89.346 826 58 9 34 830 618468367 618469191 0.000000e+00 1011.0
24 TraesCS1D01G062200 chr7A 88.815 751 56 12 107 830 38697606 38696857 0.000000e+00 896.0
25 TraesCS1D01G062200 chr7A 88.682 751 57 7 107 830 38728202 38727453 0.000000e+00 891.0
26 TraesCS1D01G062200 chr6A 87.373 491 34 7 367 830 100323591 100323102 2.970000e-149 538.0
27 TraesCS1D01G062200 chr6A 100.000 80 0 0 2542 2621 606389748 606389827 5.850000e-32 148.0
28 TraesCS1D01G062200 chr6A 98.780 82 1 0 2542 2623 132428551 132428632 2.100000e-31 147.0
29 TraesCS1D01G062200 chr3B 100.000 80 0 0 2542 2621 100665676 100665597 5.850000e-32 148.0
30 TraesCS1D01G062200 chr4B 98.780 82 1 0 2542 2623 334046159 334046078 2.100000e-31 147.0
31 TraesCS1D01G062200 chrUn 97.590 83 1 1 2539 2621 60463828 60463747 9.790000e-30 141.0
32 TraesCS1D01G062200 chr2B 95.455 88 3 1 2535 2621 588601497 588601584 3.520000e-29 139.0


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 TraesCS1D01G062200 chr1D 41913705 41916327 2622 False 4844.0 4844 100.000 1 2623 1 chr1D.!!$F1 2622
1 TraesCS1D01G062200 chr1D 203875108 203875901 793 False 1083.0 1083 91.814 63 830 1 chr1D.!!$F2 767
2 TraesCS1D01G062200 chr1A 41918958 41920594 1636 False 2272.0 2272 91.642 835 2498 1 chr1A.!!$F1 1663
3 TraesCS1D01G062200 chr1A 583657266 583658123 857 False 1059.0 1059 89.523 3 830 1 chr1A.!!$F2 827
4 TraesCS1D01G062200 chr1B 62284286 62286110 1824 False 1170.5 1777 91.706 845 2539 2 chr1B.!!$F5 1694
5 TraesCS1D01G062200 chr6D 402357712 402358535 823 False 1092.0 1092 91.162 34 830 1 chr6D.!!$F2 796
6 TraesCS1D01G062200 chr6D 397351843 397352671 828 False 926.0 926 87.530 34 831 1 chr6D.!!$F1 797
7 TraesCS1D01G062200 chr6D 447921114 447921914 800 False 924.0 924 87.668 3 808 1 chr6D.!!$F3 805
8 TraesCS1D01G062200 chr3A 708007933 708008792 859 False 1079.0 1079 89.884 1 830 1 chr3A.!!$F2 829
9 TraesCS1D01G062200 chr3A 401459333 401460203 870 False 1070.0 1070 89.437 1 840 1 chr3A.!!$F1 839
10 TraesCS1D01G062200 chr2D 637907961 637908775 814 True 1070.0 1070 90.920 51 837 1 chr2D.!!$R1 786
11 TraesCS1D01G062200 chr5B 54203883 54204741 858 False 1066.0 1066 89.639 1 830 1 chr5B.!!$F1 829
12 TraesCS1D01G062200 chr4A 533199107 533199965 858 False 1066.0 1066 89.639 1 830 1 chr4A.!!$F1 829
13 TraesCS1D01G062200 chr5D 27848303 27849149 846 True 1046.0 1046 89.406 1 831 1 chr5D.!!$R1 830
14 TraesCS1D01G062200 chr7B 423254825 423255683 858 True 1033.0 1033 88.953 1 830 1 chr7B.!!$R2 829
15 TraesCS1D01G062200 chr5A 618468367 618469191 824 False 1011.0 1011 89.346 34 830 1 chr5A.!!$F1 796
16 TraesCS1D01G062200 chr7A 38696857 38697606 749 True 896.0 896 88.815 107 830 1 chr7A.!!$R1 723
17 TraesCS1D01G062200 chr7A 38727453 38728202 749 True 891.0 891 88.682 107 830 1 chr7A.!!$R2 723

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
550 563 0.685097 CCTTCTTGAAGGGTGTCGGA 59.315 55.0 18.9 0.0 36.29 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2548 2760 0.232046 CACGGTGATGTGTTCGTGTG 59.768 55.0 0.74 0.0 45.15 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
456 465 2.908015 GGCTCCGATTGGCTGGTA 59.092 61.111 0.00 0.00 34.14 3.25
459 468 1.686325 GCTCCGATTGGCTGGTAGGA 61.686 60.000 0.00 0.00 34.14 2.94
465 474 2.683742 CGATTGGCTGGTAGGATTTGGT 60.684 50.000 0.00 0.00 0.00 3.67
550 563 0.685097 CCTTCTTGAAGGGTGTCGGA 59.315 55.000 18.90 0.00 36.29 4.55
575 588 1.950000 TATCCCCCACCTCCCTCCA 60.950 63.158 0.00 0.00 0.00 3.86
715 754 1.146041 ACACTTTGTCGAGCTGCCA 59.854 52.632 0.00 0.00 0.00 4.92
809 850 6.949715 ACAATGATGGTTTGCTTTGGAATAT 58.050 32.000 0.00 0.00 0.00 1.28
830 871 3.452755 AAAGCGAGGAAACCCTTTTTG 57.547 42.857 0.00 0.00 33.25 2.44
831 872 2.358322 AGCGAGGAAACCCTTTTTGA 57.642 45.000 0.00 0.00 33.25 2.69
832 873 2.661718 AGCGAGGAAACCCTTTTTGAA 58.338 42.857 0.00 0.00 33.25 2.69
833 874 3.230976 AGCGAGGAAACCCTTTTTGAAT 58.769 40.909 0.00 0.00 33.25 2.57
834 875 4.403734 AGCGAGGAAACCCTTTTTGAATA 58.596 39.130 0.00 0.00 33.25 1.75
835 876 4.830600 AGCGAGGAAACCCTTTTTGAATAA 59.169 37.500 0.00 0.00 33.25 1.40
836 877 5.303333 AGCGAGGAAACCCTTTTTGAATAAA 59.697 36.000 0.00 0.00 33.25 1.40
837 878 5.986741 GCGAGGAAACCCTTTTTGAATAAAA 59.013 36.000 0.00 0.00 33.25 1.52
838 879 6.649141 GCGAGGAAACCCTTTTTGAATAAAAT 59.351 34.615 0.00 0.00 35.82 1.82
839 880 7.172532 GCGAGGAAACCCTTTTTGAATAAAATT 59.827 33.333 0.00 0.00 35.82 1.82
840 881 9.699703 CGAGGAAACCCTTTTTGAATAAAATTA 57.300 29.630 0.00 0.00 35.82 1.40
869 910 1.268539 CCAACACGGCTTGTTCAACTC 60.269 52.381 6.37 0.00 46.05 3.01
873 914 1.798813 CACGGCTTGTTCAACTCTACC 59.201 52.381 0.00 0.00 0.00 3.18
877 918 1.461127 GCTTGTTCAACTCTACCAGCG 59.539 52.381 0.00 0.00 0.00 5.18
906 947 1.135915 CTAAGAGCTGCACCATCGTCT 59.864 52.381 1.02 0.00 0.00 4.18
910 951 2.294791 AGAGCTGCACCATCGTCTATAC 59.705 50.000 1.02 0.00 0.00 1.47
911 952 2.031870 AGCTGCACCATCGTCTATACA 58.968 47.619 1.02 0.00 0.00 2.29
912 953 2.128035 GCTGCACCATCGTCTATACAC 58.872 52.381 0.00 0.00 0.00 2.90
919 960 4.909880 CACCATCGTCTATACACATACACG 59.090 45.833 0.00 0.00 32.28 4.49
923 964 3.561310 TCGTCTATACACATACACGTCCC 59.439 47.826 0.00 0.00 32.70 4.46
981 1022 1.904852 AACAGCACAGCGCAAGATCG 61.905 55.000 11.47 0.00 46.13 3.69
1033 1074 1.899437 GCTGTCCTTCGTCCCCATCA 61.899 60.000 0.00 0.00 0.00 3.07
1038 1079 1.562672 CCTTCGTCCCCATCACCCTT 61.563 60.000 0.00 0.00 0.00 3.95
1041 1082 1.221840 CGTCCCCATCACCCTTCTG 59.778 63.158 0.00 0.00 0.00 3.02
1348 1389 6.349280 CCGTCATGTCCACATACTGAATTTTT 60.349 38.462 0.00 0.00 34.26 1.94
1354 1395 6.072508 TGTCCACATACTGAATTTTTCTCTGC 60.073 38.462 0.00 0.00 0.00 4.26
1360 1401 5.526506 ACTGAATTTTTCTCTGCTTGCTT 57.473 34.783 0.00 0.00 0.00 3.91
1514 1555 4.044825 AGAAGAAGAACCTGGAGGAGTCTA 59.955 45.833 0.00 0.00 38.94 2.59
1558 1599 2.813179 CGACCGGCACTGCATTAGC 61.813 63.158 0.00 0.00 42.57 3.09
1709 1750 6.566187 CGAGGAGTTCGTATCGTCTATCATTT 60.566 42.308 0.00 0.00 44.27 2.32
1779 1820 3.881688 AGCAGTAATTCTGGCTTATGCTG 59.118 43.478 0.13 0.00 43.78 4.41
1792 1833 0.321564 TATGCTGCTGTGTGGTGGTC 60.322 55.000 0.00 0.00 0.00 4.02
1793 1834 2.060567 ATGCTGCTGTGTGGTGGTCT 62.061 55.000 0.00 0.00 0.00 3.85
1794 1835 2.256591 GCTGCTGTGTGGTGGTCTG 61.257 63.158 0.00 0.00 0.00 3.51
1795 1836 1.598962 CTGCTGTGTGGTGGTCTGG 60.599 63.158 0.00 0.00 0.00 3.86
1796 1837 2.329539 CTGCTGTGTGGTGGTCTGGT 62.330 60.000 0.00 0.00 0.00 4.00
1811 1852 4.210331 GGTCTGGTCTCCATTTGCAATAT 58.790 43.478 0.00 0.00 30.82 1.28
1829 1870 6.602803 TGCAATATTATCTCTGTTTCTTGCCA 59.397 34.615 0.00 0.00 36.52 4.92
1887 1928 8.974238 TCCTTCTACAATCTAAATCTCGGTAAA 58.026 33.333 0.00 0.00 0.00 2.01
1888 1929 9.595823 CCTTCTACAATCTAAATCTCGGTAAAA 57.404 33.333 0.00 0.00 0.00 1.52
1914 1955 5.336744 ACCGTAAAATCATGTAAAATGCGG 58.663 37.500 12.88 12.88 40.03 5.69
1918 1959 7.646130 CCGTAAAATCATGTAAAATGCGGTAAT 59.354 33.333 0.00 0.00 0.00 1.89
1921 1962 4.300189 TCATGTAAAATGCGGTAATGGC 57.700 40.909 0.00 0.00 0.00 4.40
1922 1963 3.951037 TCATGTAAAATGCGGTAATGGCT 59.049 39.130 0.00 0.00 0.00 4.75
1926 1967 4.944930 TGTAAAATGCGGTAATGGCTAACT 59.055 37.500 0.00 0.00 0.00 2.24
1930 1971 0.529992 GCGGTAATGGCTAACTCGCT 60.530 55.000 0.00 0.00 38.82 4.93
1932 1973 2.609737 GCGGTAATGGCTAACTCGCTAT 60.610 50.000 0.00 0.00 38.82 2.97
1963 2005 7.466746 AAATGAATCTTCGAATTTTCTGGGA 57.533 32.000 16.54 2.75 0.00 4.37
1964 2006 5.880054 TGAATCTTCGAATTTTCTGGGAC 57.120 39.130 16.54 0.00 0.00 4.46
1968 2010 1.803334 TCGAATTTTCTGGGACGGTG 58.197 50.000 0.00 0.00 35.30 4.94
1972 2014 2.781681 ATTTTCTGGGACGGTGGTAG 57.218 50.000 0.00 0.00 35.30 3.18
1973 2015 1.426751 TTTTCTGGGACGGTGGTAGT 58.573 50.000 0.00 0.00 35.30 2.73
2007 2052 3.243501 ACAACTGTACATGCAGCAAAAGG 60.244 43.478 0.00 0.00 39.96 3.11
2137 2348 8.762645 TCCAGCAAATATATACAAGCTAGCTAT 58.237 33.333 19.70 12.18 0.00 2.97
2160 2371 2.757314 TGCATTCAACACACACTTTGGA 59.243 40.909 0.00 0.00 0.00 3.53
2169 2380 2.813754 CACACACTTTGGATGGTGGTAG 59.186 50.000 0.00 0.00 37.72 3.18
2170 2381 2.441750 ACACACTTTGGATGGTGGTAGT 59.558 45.455 0.00 0.00 37.72 2.73
2171 2382 3.649023 ACACACTTTGGATGGTGGTAGTA 59.351 43.478 0.00 0.00 37.72 1.82
2181 2392 4.141914 GGATGGTGGTAGTACTTCTCTTGG 60.142 50.000 0.00 0.00 0.00 3.61
2192 2403 3.309296 ACTTCTCTTGGGACAGTTGAGA 58.691 45.455 0.00 0.00 42.39 3.27
2218 2429 2.604914 CCCAAAGAGTTGATCGATCACG 59.395 50.000 27.28 9.78 36.83 4.35
2242 2453 0.963962 AGTTGAAGCAGCACCATTGG 59.036 50.000 0.00 0.00 0.00 3.16
2244 2455 1.818959 TTGAAGCAGCACCATTGGCC 61.819 55.000 1.54 0.00 0.00 5.36
2254 2465 2.491152 CATTGGCCCGTGCATGAC 59.509 61.111 7.72 0.00 40.13 3.06
2276 2487 1.000843 GCCCACCAAAAGGACATGAAC 59.999 52.381 0.00 0.00 0.00 3.18
2298 2509 4.082625 ACCGTAAACGATGTACAGATCACA 60.083 41.667 3.65 0.00 43.02 3.58
2301 2512 4.928661 AAACGATGTACAGATCACAAGC 57.071 40.909 0.33 0.00 0.00 4.01
2304 2515 3.679980 ACGATGTACAGATCACAAGCAAC 59.320 43.478 0.33 0.00 0.00 4.17
2318 2529 8.951787 ATCACAAGCAACGTACCTATAAAATA 57.048 30.769 0.00 0.00 0.00 1.40
2407 2618 4.022464 ACGTCAAAAGCGACAATGAAAA 57.978 36.364 0.00 0.00 35.54 2.29
2500 2712 4.079096 ACAATACAGGTAGCTAGGAGAGGT 60.079 45.833 0.00 0.00 39.82 3.85
2510 2722 3.519913 AGCTAGGAGAGGTTTGGTTTAGG 59.480 47.826 0.00 0.00 29.01 2.69
2517 2729 5.538813 GGAGAGGTTTGGTTTAGGTCAAATT 59.461 40.000 0.00 0.00 35.66 1.82
2547 2759 7.552848 AATGAGAAATCATTTTTCGTGTTCG 57.447 32.000 0.00 0.00 37.03 3.95
2548 2760 4.909305 TGAGAAATCATTTTTCGTGTTCGC 59.091 37.500 0.00 0.00 36.96 4.70
2549 2761 4.854399 AGAAATCATTTTTCGTGTTCGCA 58.146 34.783 0.00 0.00 36.96 5.10
2550 2762 4.675114 AGAAATCATTTTTCGTGTTCGCAC 59.325 37.500 0.00 0.00 44.33 5.34
2563 2775 4.798152 CGCACACGAACACATCAC 57.202 55.556 0.00 0.00 43.93 3.06
2564 2776 1.204062 CGCACACGAACACATCACC 59.796 57.895 0.00 0.00 43.93 4.02
2565 2777 1.204062 GCACACGAACACATCACCG 59.796 57.895 0.00 0.00 0.00 4.94
2566 2778 1.495584 GCACACGAACACATCACCGT 61.496 55.000 0.00 0.00 35.46 4.83
2574 2786 3.436001 CACATCACCGTGTACCCTC 57.564 57.895 0.00 0.00 32.00 4.30
2575 2787 0.457853 CACATCACCGTGTACCCTCG 60.458 60.000 0.00 0.00 32.00 4.63
2576 2788 0.609957 ACATCACCGTGTACCCTCGA 60.610 55.000 0.00 0.00 0.00 4.04
2577 2789 0.179145 CATCACCGTGTACCCTCGAC 60.179 60.000 0.00 0.00 0.00 4.20
2578 2790 1.651240 ATCACCGTGTACCCTCGACG 61.651 60.000 0.00 0.00 0.00 5.12
2579 2791 3.741476 ACCGTGTACCCTCGACGC 61.741 66.667 0.00 0.00 0.00 5.19
2580 2792 4.487412 CCGTGTACCCTCGACGCC 62.487 72.222 0.00 0.00 0.00 5.68
2581 2793 4.824166 CGTGTACCCTCGACGCCG 62.824 72.222 0.00 0.00 37.07 6.46
2582 2794 4.487412 GTGTACCCTCGACGCCGG 62.487 72.222 0.00 0.00 36.24 6.13
2601 2813 3.503363 GGTGATGCACCGCAGCTC 61.503 66.667 5.76 1.79 45.80 4.09
2602 2814 2.743538 GTGATGCACCGCAGCTCA 60.744 61.111 5.76 0.00 45.80 4.26
2603 2815 2.743538 TGATGCACCGCAGCTCAC 60.744 61.111 5.76 0.00 45.80 3.51
2604 2816 3.857854 GATGCACCGCAGCTCACG 61.858 66.667 0.00 0.00 43.65 4.35
2605 2817 4.687215 ATGCACCGCAGCTCACGT 62.687 61.111 5.06 0.00 43.65 4.49
2608 2820 4.700365 CACCGCAGCTCACGTCGA 62.700 66.667 0.00 0.00 0.00 4.20
2609 2821 3.973516 ACCGCAGCTCACGTCGAA 61.974 61.111 0.00 0.00 0.00 3.71
2610 2822 3.175240 CCGCAGCTCACGTCGAAG 61.175 66.667 0.00 0.00 0.00 3.79
2611 2823 3.175240 CGCAGCTCACGTCGAAGG 61.175 66.667 0.00 0.00 0.00 3.46
2612 2824 2.258591 GCAGCTCACGTCGAAGGA 59.741 61.111 0.00 0.00 0.00 3.36
2613 2825 1.803519 GCAGCTCACGTCGAAGGAG 60.804 63.158 0.00 7.74 0.00 3.69
2614 2826 1.876664 CAGCTCACGTCGAAGGAGA 59.123 57.895 16.63 7.92 0.00 3.71
2615 2827 0.455295 CAGCTCACGTCGAAGGAGAC 60.455 60.000 16.63 10.11 37.76 3.36
2616 2828 1.153997 GCTCACGTCGAAGGAGACC 60.154 63.158 16.63 0.00 37.85 3.85
2617 2829 1.507174 CTCACGTCGAAGGAGACCC 59.493 63.158 0.00 0.00 37.85 4.46
2618 2830 2.178521 CACGTCGAAGGAGACCCG 59.821 66.667 0.00 0.00 37.85 5.28
2619 2831 3.745803 ACGTCGAAGGAGACCCGC 61.746 66.667 0.00 0.00 37.85 6.13
2620 2832 4.493747 CGTCGAAGGAGACCCGCC 62.494 72.222 0.00 0.00 37.85 6.13
2621 2833 3.379445 GTCGAAGGAGACCCGCCA 61.379 66.667 0.00 0.00 37.58 5.69
2622 2834 3.068691 TCGAAGGAGACCCGCCAG 61.069 66.667 0.00 0.00 37.58 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
456 465 1.002134 CTCCCGCACACCAAATCCT 60.002 57.895 0.00 0.00 0.00 3.24
459 468 1.818674 GATTTCTCCCGCACACCAAAT 59.181 47.619 0.00 0.00 0.00 2.32
465 474 0.960364 GCAAGGATTTCTCCCGCACA 60.960 55.000 0.00 0.00 43.21 4.57
550 563 1.414685 GGAGGTGGGGGATAGCTACTT 60.415 57.143 0.00 0.00 0.00 2.24
575 588 2.176055 CGACGCTGCTCAGTACGT 59.824 61.111 0.00 0.00 42.27 3.57
601 640 0.329596 GCACCTCCAAGAAGGGATGT 59.670 55.000 0.00 0.00 41.04 3.06
715 754 8.962884 AAGAAAAAGAAATAAATGCCAACAGT 57.037 26.923 0.00 0.00 0.00 3.55
809 850 4.208746 TCAAAAAGGGTTTCCTCGCTTTA 58.791 39.130 8.63 0.00 45.26 1.85
832 873 9.361315 GCCGTGTTGGTAAGATTTTAATTTTAT 57.639 29.630 0.00 0.00 41.21 1.40
833 874 8.578151 AGCCGTGTTGGTAAGATTTTAATTTTA 58.422 29.630 0.00 0.00 41.21 1.52
834 875 7.438564 AGCCGTGTTGGTAAGATTTTAATTTT 58.561 30.769 0.00 0.00 41.21 1.82
835 876 6.988522 AGCCGTGTTGGTAAGATTTTAATTT 58.011 32.000 0.00 0.00 41.21 1.82
836 877 6.584185 AGCCGTGTTGGTAAGATTTTAATT 57.416 33.333 0.00 0.00 41.21 1.40
837 878 6.015772 ACAAGCCGTGTTGGTAAGATTTTAAT 60.016 34.615 0.00 0.00 37.01 1.40
838 879 5.299782 ACAAGCCGTGTTGGTAAGATTTTAA 59.700 36.000 0.00 0.00 37.01 1.52
839 880 4.822896 ACAAGCCGTGTTGGTAAGATTTTA 59.177 37.500 0.00 0.00 37.01 1.52
840 881 3.634910 ACAAGCCGTGTTGGTAAGATTTT 59.365 39.130 0.00 0.00 37.01 1.82
857 898 1.461127 CGCTGGTAGAGTTGAACAAGC 59.539 52.381 0.00 0.00 38.97 4.01
869 910 2.225791 TAGTGCTGCACCGCTGGTAG 62.226 60.000 27.74 0.00 34.49 3.18
873 914 1.357258 CTCTTAGTGCTGCACCGCTG 61.357 60.000 27.74 15.84 34.49 5.18
948 989 2.687935 GTGCTGTTTCTTCAACCAAGGA 59.312 45.455 0.00 0.00 33.97 3.36
949 990 2.426738 TGTGCTGTTTCTTCAACCAAGG 59.573 45.455 0.00 0.00 33.97 3.61
950 991 3.699067 CTGTGCTGTTTCTTCAACCAAG 58.301 45.455 0.00 0.00 33.97 3.61
951 992 2.159254 GCTGTGCTGTTTCTTCAACCAA 60.159 45.455 0.00 0.00 33.97 3.67
952 993 1.405105 GCTGTGCTGTTTCTTCAACCA 59.595 47.619 0.00 0.00 33.97 3.67
953 994 1.597937 CGCTGTGCTGTTTCTTCAACC 60.598 52.381 0.00 0.00 33.97 3.77
981 1022 1.609208 TCTTGCTTCTTTGGCAGACC 58.391 50.000 0.00 0.00 40.90 3.85
1013 1054 1.613630 ATGGGGACGAAGGACAGCT 60.614 57.895 0.00 0.00 0.00 4.24
1033 1074 1.908340 CTGGCTAGCAGCAGAAGGGT 61.908 60.000 18.24 0.00 44.75 4.34
1076 1117 0.875040 CTCTGTATCCGCAGCTGCTG 60.875 60.000 34.22 28.58 39.32 4.41
1077 1118 1.440893 CTCTGTATCCGCAGCTGCT 59.559 57.895 34.22 19.82 39.32 4.24
1090 1131 4.899243 GAGGTCCCCTTCCTCTGT 57.101 61.111 4.91 0.00 45.56 3.41
1348 1389 0.313043 GCAAGCAAAGCAAGCAGAGA 59.687 50.000 0.00 0.00 32.47 3.10
1354 1395 1.610522 AGTGGTAGCAAGCAAAGCAAG 59.389 47.619 0.00 0.00 34.25 4.01
1360 1401 0.472044 TGGTGAGTGGTAGCAAGCAA 59.528 50.000 0.00 0.00 34.25 3.91
1696 1737 4.679373 AGACAGGCAAATGATAGACGAT 57.321 40.909 0.00 0.00 0.00 3.73
1709 1750 4.098960 CCGAGGTACTAAATAAGACAGGCA 59.901 45.833 0.00 0.00 41.55 4.75
1779 1820 1.598130 GACCAGACCACCACACAGC 60.598 63.158 0.00 0.00 0.00 4.40
1792 1833 7.664731 AGAGATAATATTGCAAATGGAGACCAG 59.335 37.037 1.71 0.00 36.75 4.00
1793 1834 7.446319 CAGAGATAATATTGCAAATGGAGACCA 59.554 37.037 1.71 0.00 38.19 4.02
1794 1835 7.446625 ACAGAGATAATATTGCAAATGGAGACC 59.553 37.037 1.71 0.00 0.00 3.85
1795 1836 8.388484 ACAGAGATAATATTGCAAATGGAGAC 57.612 34.615 1.71 0.00 0.00 3.36
1796 1837 8.985315 AACAGAGATAATATTGCAAATGGAGA 57.015 30.769 1.71 0.00 0.00 3.71
1811 1852 4.985538 AGGTTGGCAAGAAACAGAGATAA 58.014 39.130 0.00 0.00 0.00 1.75
1887 1928 7.148885 CGCATTTTACATGATTTTACGGTTGTT 60.149 33.333 0.00 0.00 0.00 2.83
1888 1929 6.306837 CGCATTTTACATGATTTTACGGTTGT 59.693 34.615 0.00 0.00 0.00 3.32
1894 1935 8.751335 CCATTACCGCATTTTACATGATTTTAC 58.249 33.333 0.00 0.00 0.00 2.01
1896 1937 6.257630 GCCATTACCGCATTTTACATGATTTT 59.742 34.615 0.00 0.00 0.00 1.82
1914 1955 4.252971 TCCATAGCGAGTTAGCCATTAC 57.747 45.455 0.00 0.00 38.01 1.89
1918 1959 3.620427 TTTTCCATAGCGAGTTAGCCA 57.380 42.857 0.00 0.00 38.01 4.75
1941 1983 5.065218 CGTCCCAGAAAATTCGAAGATTCAT 59.935 40.000 21.05 8.95 35.04 2.57
1951 1993 1.905637 ACCACCGTCCCAGAAAATTC 58.094 50.000 0.00 0.00 0.00 2.17
1953 1995 1.982958 ACTACCACCGTCCCAGAAAAT 59.017 47.619 0.00 0.00 0.00 1.82
1958 2000 0.529378 GTGTACTACCACCGTCCCAG 59.471 60.000 0.00 0.00 0.00 4.45
1961 2003 1.340889 TGTTGTGTACTACCACCGTCC 59.659 52.381 0.00 0.00 34.35 4.79
1963 2005 2.224113 CCTTGTTGTGTACTACCACCGT 60.224 50.000 0.00 0.00 34.35 4.83
1964 2006 2.036217 TCCTTGTTGTGTACTACCACCG 59.964 50.000 0.00 0.00 34.35 4.94
1968 2010 4.510340 CAGTTGTCCTTGTTGTGTACTACC 59.490 45.833 0.00 0.00 0.00 3.18
1972 2014 4.871557 TGTACAGTTGTCCTTGTTGTGTAC 59.128 41.667 0.00 0.00 39.36 2.90
1973 2015 5.087391 TGTACAGTTGTCCTTGTTGTGTA 57.913 39.130 0.00 0.00 0.00 2.90
2007 2052 6.169557 ACCTAAACCATGTTTCCCTTTTTC 57.830 37.500 0.00 0.00 0.00 2.29
2137 2348 4.582240 TCCAAAGTGTGTGTTGAATGCATA 59.418 37.500 0.00 0.00 0.00 3.14
2160 2371 3.775316 CCCAAGAGAAGTACTACCACCAT 59.225 47.826 0.00 0.00 0.00 3.55
2169 2380 4.281182 TCTCAACTGTCCCAAGAGAAGTAC 59.719 45.833 0.00 0.00 32.83 2.73
2170 2381 4.281182 GTCTCAACTGTCCCAAGAGAAGTA 59.719 45.833 0.00 0.00 37.13 2.24
2171 2382 3.070302 GTCTCAACTGTCCCAAGAGAAGT 59.930 47.826 0.00 0.00 37.13 3.01
2181 2392 1.668151 GGGCGTGTCTCAACTGTCC 60.668 63.158 0.00 0.00 0.00 4.02
2192 2403 1.523758 GATCAACTCTTTGGGCGTGT 58.476 50.000 0.00 0.00 33.06 4.49
2218 2429 0.598419 GGTGCTGCTTCAACTTTGGC 60.598 55.000 0.00 0.00 0.00 4.52
2254 2465 1.606313 ATGTCCTTTTGGTGGGCGG 60.606 57.895 0.00 0.00 41.38 6.13
2258 2469 1.269448 CGGTTCATGTCCTTTTGGTGG 59.731 52.381 0.00 0.00 41.38 4.61
2276 2487 4.417506 TGTGATCTGTACATCGTTTACGG 58.582 43.478 0.00 0.00 40.29 4.02
2383 2594 2.154198 TCATTGTCGCTTTTGACGTACG 59.846 45.455 15.01 15.01 41.87 3.67
2407 2618 9.754382 GTATGCATTTCATATTTCTTTCATGGT 57.246 29.630 3.54 0.00 39.63 3.55
2465 2676 4.398319 ACCTGTATTGTCTCCCTTTGTTG 58.602 43.478 0.00 0.00 0.00 3.33
2472 2683 3.574826 CCTAGCTACCTGTATTGTCTCCC 59.425 52.174 0.00 0.00 0.00 4.30
2473 2684 4.471548 TCCTAGCTACCTGTATTGTCTCC 58.528 47.826 0.00 0.00 0.00 3.71
2545 2757 1.218875 GGTGATGTGTTCGTGTGCGA 61.219 55.000 0.00 0.00 46.36 5.10
2546 2758 1.204062 GGTGATGTGTTCGTGTGCG 59.796 57.895 0.00 0.00 39.92 5.34
2547 2759 1.204062 CGGTGATGTGTTCGTGTGC 59.796 57.895 0.00 0.00 0.00 4.57
2548 2760 0.232046 CACGGTGATGTGTTCGTGTG 59.768 55.000 0.74 0.00 45.15 3.82
2549 2761 2.600388 CACGGTGATGTGTTCGTGT 58.400 52.632 0.74 0.00 45.15 4.49
2556 2768 0.457853 CGAGGGTACACGGTGATGTG 60.458 60.000 16.29 0.00 45.41 3.21
2557 2769 0.609957 TCGAGGGTACACGGTGATGT 60.610 55.000 16.29 0.00 36.56 3.06
2558 2770 0.179145 GTCGAGGGTACACGGTGATG 60.179 60.000 16.29 0.00 0.00 3.07
2559 2771 1.651240 CGTCGAGGGTACACGGTGAT 61.651 60.000 16.29 1.80 0.00 3.06
2560 2772 2.327343 CGTCGAGGGTACACGGTGA 61.327 63.158 16.29 0.00 0.00 4.02
2561 2773 2.177531 CGTCGAGGGTACACGGTG 59.822 66.667 6.58 6.58 0.00 4.94
2562 2774 3.741476 GCGTCGAGGGTACACGGT 61.741 66.667 7.31 0.00 34.04 4.83
2563 2775 4.487412 GGCGTCGAGGGTACACGG 62.487 72.222 7.31 0.00 34.04 4.94
2564 2776 4.824166 CGGCGTCGAGGGTACACG 62.824 72.222 1.44 0.00 39.00 4.49
2565 2777 4.487412 CCGGCGTCGAGGGTACAC 62.487 72.222 12.93 0.00 39.00 2.90
2585 2797 2.743538 TGAGCTGCGGTGCATCAC 60.744 61.111 0.00 0.00 38.13 3.06
2586 2798 2.743538 GTGAGCTGCGGTGCATCA 60.744 61.111 0.00 0.00 38.13 3.07
2587 2799 3.857854 CGTGAGCTGCGGTGCATC 61.858 66.667 0.00 0.00 38.13 3.91
2588 2800 4.687215 ACGTGAGCTGCGGTGCAT 62.687 61.111 11.28 0.00 38.13 3.96
2591 2803 4.700365 TCGACGTGAGCTGCGGTG 62.700 66.667 11.28 4.12 0.00 4.94
2592 2804 3.898627 CTTCGACGTGAGCTGCGGT 62.899 63.158 11.28 0.00 0.00 5.68
2593 2805 3.175240 CTTCGACGTGAGCTGCGG 61.175 66.667 11.28 0.00 0.00 5.69
2594 2806 3.175240 CCTTCGACGTGAGCTGCG 61.175 66.667 0.00 0.00 0.00 5.18
2595 2807 1.803519 CTCCTTCGACGTGAGCTGC 60.804 63.158 0.00 0.00 0.00 5.25
2596 2808 0.455295 GTCTCCTTCGACGTGAGCTG 60.455 60.000 0.00 0.00 0.00 4.24
2597 2809 1.587933 GGTCTCCTTCGACGTGAGCT 61.588 60.000 0.00 0.00 34.75 4.09
2598 2810 1.153997 GGTCTCCTTCGACGTGAGC 60.154 63.158 0.00 0.00 34.75 4.26
2599 2811 1.507174 GGGTCTCCTTCGACGTGAG 59.493 63.158 0.00 0.00 34.75 3.51
2600 2812 2.330372 CGGGTCTCCTTCGACGTGA 61.330 63.158 0.00 0.00 34.75 4.35
2601 2813 2.178521 CGGGTCTCCTTCGACGTG 59.821 66.667 0.00 0.00 34.75 4.49
2602 2814 3.745803 GCGGGTCTCCTTCGACGT 61.746 66.667 0.00 0.00 34.75 4.34
2603 2815 4.493747 GGCGGGTCTCCTTCGACG 62.494 72.222 0.00 0.00 34.75 5.12
2604 2816 3.358076 CTGGCGGGTCTCCTTCGAC 62.358 68.421 0.00 0.00 0.00 4.20
2605 2817 3.068691 CTGGCGGGTCTCCTTCGA 61.069 66.667 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.