Multiple sequence alignment - TraesCS3A01G474000

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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 TraesCS3A01G474000 chr3A 100.000 2710 0 0 1 2710 705231976 705229267 0.000000e+00 5005
1 TraesCS3A01G474000 chr3A 97.758 669 14 1 2043 2710 713220900 713221568 0.000000e+00 1151
2 TraesCS3A01G474000 chrUn 92.324 1850 86 22 68 1889 132261665 132263486 0.000000e+00 2579
3 TraesCS3A01G474000 chrUn 86.111 108 3 1 1934 2041 132263463 132263558 3.690000e-19 106
4 TraesCS3A01G474000 chr3B 93.192 1366 62 16 406 1758 760373988 760372641 0.000000e+00 1978
5 TraesCS3A01G474000 chr3B 92.113 672 40 6 2037 2708 479987001 479987659 0.000000e+00 935
6 TraesCS3A01G474000 chr3B 88.095 336 13 11 71 397 760381840 760381523 9.160000e-100 374
7 TraesCS3A01G474000 chr3B 88.732 213 17 3 1760 1971 760372552 760372346 1.250000e-63 254
8 TraesCS3A01G474000 chr3B 91.667 120 8 1 1656 1773 760372691 760372572 6.000000e-37 165
9 TraesCS3A01G474000 chr3B 94.667 75 4 0 72 146 760386280 760386206 1.700000e-22 117
10 TraesCS3A01G474000 chr4D 95.659 668 21 3 2044 2710 446899412 446898752 0.000000e+00 1066
11 TraesCS3A01G474000 chr2B 93.433 670 34 7 2043 2710 788226465 788225804 0.000000e+00 985
12 TraesCS3A01G474000 chr2D 92.825 669 36 8 2043 2710 413951217 413950560 0.000000e+00 959
13 TraesCS3A01G474000 chr5B 92.537 670 39 8 2043 2710 418552029 418551369 0.000000e+00 950
14 TraesCS3A01G474000 chr1A 92.433 674 35 14 2042 2710 587671976 587671314 0.000000e+00 948
15 TraesCS3A01G474000 chr1A 92.204 667 41 7 2043 2708 423988402 423987746 0.000000e+00 933
16 TraesCS3A01G474000 chr1D 91.826 575 37 7 2096 2669 462295892 462296457 0.000000e+00 793
17 TraesCS3A01G474000 chr2A 88.350 103 9 3 2044 2145 350707248 350707148 1.320000e-23 121


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 TraesCS3A01G474000 chr3A 705229267 705231976 2709 True 5005.0 5005 100.0000 1 2710 1 chr3A.!!$R1 2709
1 TraesCS3A01G474000 chr3A 713220900 713221568 668 False 1151.0 1151 97.7580 2043 2710 1 chr3A.!!$F1 667
2 TraesCS3A01G474000 chrUn 132261665 132263558 1893 False 1342.5 2579 89.2175 68 2041 2 chrUn.!!$F1 1973
3 TraesCS3A01G474000 chr3B 479987001 479987659 658 False 935.0 935 92.1130 2037 2708 1 chr3B.!!$F1 671
4 TraesCS3A01G474000 chr3B 760372346 760373988 1642 True 799.0 1978 91.1970 406 1971 3 chr3B.!!$R3 1565
5 TraesCS3A01G474000 chr4D 446898752 446899412 660 True 1066.0 1066 95.6590 2044 2710 1 chr4D.!!$R1 666
6 TraesCS3A01G474000 chr2B 788225804 788226465 661 True 985.0 985 93.4330 2043 2710 1 chr2B.!!$R1 667
7 TraesCS3A01G474000 chr2D 413950560 413951217 657 True 959.0 959 92.8250 2043 2710 1 chr2D.!!$R1 667
8 TraesCS3A01G474000 chr5B 418551369 418552029 660 True 950.0 950 92.5370 2043 2710 1 chr5B.!!$R1 667
9 TraesCS3A01G474000 chr1A 587671314 587671976 662 True 948.0 948 92.4330 2042 2710 1 chr1A.!!$R2 668
10 TraesCS3A01G474000 chr1A 423987746 423988402 656 True 933.0 933 92.2040 2043 2708 1 chr1A.!!$R1 665
11 TraesCS3A01G474000 chr1D 462295892 462296457 565 False 793.0 793 91.8260 2096 2669 1 chr1D.!!$F1 573

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
891 917 0.04087 CGCGACATCAGATACGAGCT 60.041 55.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2348 2484 0.603975 GCTCAAGTGTCGCTCCCTTT 60.604 55.0 0.0 0.0 0.0 3.11 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
21 22 4.629251 GAGAATTCTGGACCAGCAAATC 57.371 45.455 17.33 13.41 0.00 2.17
22 23 3.012518 AGAATTCTGGACCAGCAAATCG 58.987 45.455 17.33 0.00 0.00 3.34
23 24 2.496899 ATTCTGGACCAGCAAATCGT 57.503 45.000 17.33 0.00 0.00 3.73
24 25 1.808411 TTCTGGACCAGCAAATCGTC 58.192 50.000 17.33 0.00 0.00 4.20
25 26 0.684535 TCTGGACCAGCAAATCGTCA 59.315 50.000 17.33 0.00 0.00 4.35
26 27 1.278985 TCTGGACCAGCAAATCGTCAT 59.721 47.619 17.33 0.00 0.00 3.06
27 28 2.499693 TCTGGACCAGCAAATCGTCATA 59.500 45.455 17.33 0.00 0.00 2.15
28 29 2.868583 CTGGACCAGCAAATCGTCATAG 59.131 50.000 8.99 0.00 0.00 2.23
29 30 2.236146 TGGACCAGCAAATCGTCATAGT 59.764 45.455 0.00 0.00 0.00 2.12
30 31 3.270877 GGACCAGCAAATCGTCATAGTT 58.729 45.455 0.00 0.00 0.00 2.24
31 32 3.689649 GGACCAGCAAATCGTCATAGTTT 59.310 43.478 0.00 0.00 0.00 2.66
32 33 4.201822 GGACCAGCAAATCGTCATAGTTTC 60.202 45.833 0.00 0.00 0.00 2.78
33 34 4.579869 ACCAGCAAATCGTCATAGTTTCT 58.420 39.130 0.00 0.00 0.00 2.52
34 35 4.393062 ACCAGCAAATCGTCATAGTTTCTG 59.607 41.667 0.00 0.00 0.00 3.02
35 36 4.337763 CAGCAAATCGTCATAGTTTCTGC 58.662 43.478 0.00 0.00 0.00 4.26
36 37 4.002982 AGCAAATCGTCATAGTTTCTGCA 58.997 39.130 0.00 0.00 0.00 4.41
37 38 4.455533 AGCAAATCGTCATAGTTTCTGCAA 59.544 37.500 0.00 0.00 0.00 4.08
38 39 5.124457 AGCAAATCGTCATAGTTTCTGCAAT 59.876 36.000 0.00 0.00 0.00 3.56
39 40 5.801947 GCAAATCGTCATAGTTTCTGCAATT 59.198 36.000 0.00 0.00 0.00 2.32
40 41 6.237384 GCAAATCGTCATAGTTTCTGCAATTG 60.237 38.462 0.00 0.00 0.00 2.32
41 42 4.944962 TCGTCATAGTTTCTGCAATTGG 57.055 40.909 7.72 0.00 0.00 3.16
42 43 3.689161 TCGTCATAGTTTCTGCAATTGGG 59.311 43.478 7.72 0.00 0.00 4.12
43 44 3.440173 CGTCATAGTTTCTGCAATTGGGT 59.560 43.478 7.72 0.00 0.00 4.51
44 45 4.437390 CGTCATAGTTTCTGCAATTGGGTC 60.437 45.833 7.72 0.00 0.00 4.46
45 46 4.458989 GTCATAGTTTCTGCAATTGGGTCA 59.541 41.667 7.72 0.00 0.00 4.02
46 47 4.458989 TCATAGTTTCTGCAATTGGGTCAC 59.541 41.667 7.72 0.00 0.00 3.67
47 48 2.949447 AGTTTCTGCAATTGGGTCACT 58.051 42.857 7.72 0.00 0.00 3.41
48 49 2.887152 AGTTTCTGCAATTGGGTCACTC 59.113 45.455 7.72 0.00 0.00 3.51
49 50 2.887152 GTTTCTGCAATTGGGTCACTCT 59.113 45.455 7.72 0.00 0.00 3.24
50 51 2.189594 TCTGCAATTGGGTCACTCTG 57.810 50.000 7.72 0.00 0.00 3.35
51 52 0.524862 CTGCAATTGGGTCACTCTGC 59.475 55.000 7.72 0.00 0.00 4.26
52 53 0.111061 TGCAATTGGGTCACTCTGCT 59.889 50.000 7.72 0.00 0.00 4.24
53 54 0.807496 GCAATTGGGTCACTCTGCTC 59.193 55.000 7.72 0.00 0.00 4.26
54 55 1.457346 CAATTGGGTCACTCTGCTCC 58.543 55.000 0.00 0.00 0.00 4.70
55 56 0.329596 AATTGGGTCACTCTGCTCCC 59.670 55.000 0.00 0.00 40.26 4.30
56 57 0.842030 ATTGGGTCACTCTGCTCCCA 60.842 55.000 0.00 0.00 46.77 4.37
57 58 1.915266 TGGGTCACTCTGCTCCCAG 60.915 63.158 0.00 0.00 44.07 4.45
58 59 2.664081 GGGTCACTCTGCTCCCAGG 61.664 68.421 0.00 0.00 39.61 4.45
59 60 2.267324 GTCACTCTGCTCCCAGGC 59.733 66.667 0.00 0.00 39.61 4.85
60 61 3.005539 TCACTCTGCTCCCAGGCC 61.006 66.667 0.00 0.00 39.61 5.19
61 62 4.106925 CACTCTGCTCCCAGGCCC 62.107 72.222 0.00 0.00 39.61 5.80
62 63 4.664267 ACTCTGCTCCCAGGCCCA 62.664 66.667 0.00 0.00 39.61 5.36
63 64 4.106925 CTCTGCTCCCAGGCCCAC 62.107 72.222 0.00 0.00 39.61 4.61
64 65 4.980592 TCTGCTCCCAGGCCCACA 62.981 66.667 0.00 0.00 39.61 4.17
65 66 3.736224 CTGCTCCCAGGCCCACAT 61.736 66.667 0.00 0.00 35.38 3.21
66 67 4.051167 TGCTCCCAGGCCCACATG 62.051 66.667 0.00 0.00 0.00 3.21
69 70 2.531428 TCCCAGGCCCACATGTCA 60.531 61.111 0.00 0.00 0.00 3.58
82 83 3.158537 ATGTCACGACGTGCACCCA 62.159 57.895 22.99 15.62 32.98 4.51
84 85 4.595538 TCACGACGTGCACCCACC 62.596 66.667 22.99 0.00 38.79 4.61
88 89 4.344865 GACGTGCACCCACCCCAT 62.345 66.667 12.15 0.00 38.79 4.00
89 90 4.659172 ACGTGCACCCACCCCATG 62.659 66.667 12.15 0.00 38.79 3.66
91 92 4.684134 GTGCACCCACCCCATGCT 62.684 66.667 5.22 0.00 40.13 3.79
92 93 4.682334 TGCACCCACCCCATGCTG 62.682 66.667 0.00 0.00 40.13 4.41
95 96 4.371417 ACCCACCCCATGCTGCAG 62.371 66.667 10.11 10.11 0.00 4.41
138 139 4.733542 CCGCCACCCAACCCGATT 62.734 66.667 0.00 0.00 0.00 3.34
139 140 3.439540 CGCCACCCAACCCGATTG 61.440 66.667 0.00 0.00 38.12 2.67
304 316 1.721489 CGAAACGATGCCTCAACAACG 60.721 52.381 0.00 0.00 41.10 4.10
486 508 1.921049 CCTGCCTATCCATCCATCCAT 59.079 52.381 0.00 0.00 0.00 3.41
503 525 0.756442 CATTCCATCGCCCCAACCAT 60.756 55.000 0.00 0.00 0.00 3.55
561 583 2.656069 CGTCCCGATCACCAACCCT 61.656 63.158 0.00 0.00 0.00 4.34
605 627 1.589993 CAGCCGATCCGTAGCACTG 60.590 63.158 0.00 0.00 0.00 3.66
657 679 1.862147 CGTTCACGCTCGAGTACGG 60.862 63.158 15.13 3.94 40.21 4.02
673 695 1.032114 ACGGGCTGAATTTAGCTGGC 61.032 55.000 20.25 5.44 43.22 4.85
713 735 2.587241 CGAGTTCGTTTCACGTAGCTAC 59.413 50.000 14.19 14.19 43.14 3.58
722 744 2.403987 CGTAGCTACGCTCGCTGT 59.596 61.111 31.24 0.00 43.14 4.40
726 748 2.324332 TAGCTACGCTCGCTGTCTGC 62.324 60.000 4.21 0.00 40.44 4.26
728 750 3.057547 CTACGCTCGCTGTCTGCCT 62.058 63.158 0.00 0.00 38.78 4.75
730 752 4.731612 CGCTCGCTGTCTGCCTGT 62.732 66.667 0.00 0.00 38.78 4.00
731 753 2.813042 GCTCGCTGTCTGCCTGTC 60.813 66.667 0.00 0.00 38.78 3.51
732 754 2.125753 CTCGCTGTCTGCCTGTCC 60.126 66.667 0.00 0.00 38.78 4.02
733 755 3.978723 CTCGCTGTCTGCCTGTCCG 62.979 68.421 0.00 0.00 38.78 4.79
735 757 4.008933 GCTGTCTGCCTGTCCGGT 62.009 66.667 0.00 0.00 35.15 5.28
736 758 2.646175 GCTGTCTGCCTGTCCGGTA 61.646 63.158 0.00 0.00 35.15 4.02
737 759 1.215647 CTGTCTGCCTGTCCGGTAC 59.784 63.158 0.00 0.00 34.25 3.34
885 911 1.399744 AAGGCCCGCGACATCAGATA 61.400 55.000 8.23 0.00 0.00 1.98
886 912 1.664965 GGCCCGCGACATCAGATAC 60.665 63.158 8.23 0.00 0.00 2.24
888 914 1.652563 CCCGCGACATCAGATACGA 59.347 57.895 8.23 0.00 0.00 3.43
890 916 0.999228 CCGCGACATCAGATACGAGC 60.999 60.000 8.23 2.43 0.00 5.03
891 917 0.040870 CGCGACATCAGATACGAGCT 60.041 55.000 0.00 0.00 0.00 4.09
892 918 1.194772 CGCGACATCAGATACGAGCTA 59.805 52.381 0.00 0.00 0.00 3.32
899 925 6.183360 CGACATCAGATACGAGCTACTACTAC 60.183 46.154 0.00 0.00 0.00 2.73
1019 1048 2.634940 TCACTTCTTCTTCCACCCTCTG 59.365 50.000 0.00 0.00 0.00 3.35
1072 1101 2.816958 ACCATGAGCAGCTTCGCG 60.817 61.111 0.00 0.00 36.85 5.87
1076 1105 1.874019 ATGAGCAGCTTCGCGTACG 60.874 57.895 11.84 11.84 42.01 3.67
1177 1206 2.569657 CACTACTACCGCCACGCA 59.430 61.111 0.00 0.00 0.00 5.24
1180 1209 4.137872 TACTACCGCCACGCAGCC 62.138 66.667 0.00 0.00 0.00 4.85
1207 1236 3.695606 GTCGCCAGCAGGAGGACA 61.696 66.667 12.80 0.00 38.80 4.02
1768 1855 9.565213 CTAGTGCTTAGTATAAGTTTGTACGTT 57.435 33.333 0.00 0.00 31.09 3.99
1824 1950 5.925506 TTGAATGAATGGTTGATGCTGAT 57.074 34.783 0.00 0.00 0.00 2.90
1825 1951 5.257082 TGAATGAATGGTTGATGCTGATG 57.743 39.130 0.00 0.00 0.00 3.07
1826 1952 4.098807 TGAATGAATGGTTGATGCTGATGG 59.901 41.667 0.00 0.00 0.00 3.51
1865 1991 1.799544 TGAGCTATGTATGCATGCGG 58.200 50.000 14.09 3.74 36.58 5.69
1874 2000 3.061231 TGCATGCGGGCATTTCGT 61.061 55.556 14.09 0.00 39.25 3.85
1893 2020 2.418197 CGTACTTGGTAGGTCACATGGG 60.418 54.545 0.00 0.00 0.00 4.00
1902 2029 0.681175 GGTCACATGGGCTTGCTTTT 59.319 50.000 0.00 0.00 0.00 2.27
1904 2031 0.597568 TCACATGGGCTTGCTTTTCG 59.402 50.000 0.00 0.00 0.00 3.46
1966 2093 2.171840 TGGTAGGTCACTCAGAAGCTC 58.828 52.381 0.00 0.00 0.00 4.09
1971 2098 3.096092 AGGTCACTCAGAAGCTCTTAGG 58.904 50.000 0.00 0.00 0.00 2.69
1972 2099 2.829120 GGTCACTCAGAAGCTCTTAGGT 59.171 50.000 0.00 0.00 0.00 3.08
1973 2100 3.367910 GGTCACTCAGAAGCTCTTAGGTG 60.368 52.174 0.00 0.00 0.00 4.00
1974 2101 2.828520 TCACTCAGAAGCTCTTAGGTGG 59.171 50.000 0.00 0.00 0.00 4.61
1975 2102 2.564947 CACTCAGAAGCTCTTAGGTGGT 59.435 50.000 0.00 0.00 0.00 4.16
1976 2103 2.829120 ACTCAGAAGCTCTTAGGTGGTC 59.171 50.000 0.00 0.00 0.00 4.02
1977 2104 2.167487 CTCAGAAGCTCTTAGGTGGTCC 59.833 54.545 0.00 0.00 0.00 4.46
1978 2105 1.902508 CAGAAGCTCTTAGGTGGTCCA 59.097 52.381 0.00 0.00 35.89 4.02
1979 2106 2.503356 CAGAAGCTCTTAGGTGGTCCAT 59.497 50.000 0.00 0.00 35.89 3.41
1980 2107 3.054802 CAGAAGCTCTTAGGTGGTCCATT 60.055 47.826 0.00 0.00 35.89 3.16
1981 2108 4.162320 CAGAAGCTCTTAGGTGGTCCATTA 59.838 45.833 0.00 0.00 35.89 1.90
1982 2109 4.407296 AGAAGCTCTTAGGTGGTCCATTAG 59.593 45.833 0.00 0.00 35.89 1.73
2030 2157 2.352651 CGTACGTAGCTGTACCTGCTTA 59.647 50.000 14.28 1.08 41.30 3.09
2131 2260 2.109799 CCCGGCCTCTGCATAGTG 59.890 66.667 0.00 0.00 40.13 2.74
2155 2284 0.822811 TGCACACAGCCAACACAAAT 59.177 45.000 0.00 0.00 44.83 2.32
2348 2484 6.823689 GGTTCTTCAATAGTAATGCCTTCAGA 59.176 38.462 0.00 0.00 0.00 3.27
2630 2766 0.806102 GCTACATGCGATGTGACCGT 60.806 55.000 10.77 0.00 44.60 4.83
2695 2831 4.134563 GTTCATAGTTTGCATATCCCCGT 58.865 43.478 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.064545 CGATTTGCTGGTCCAGAATTCTC 59.935 47.826 23.77 8.22 32.44 2.87
1 2 3.012518 CGATTTGCTGGTCCAGAATTCT 58.987 45.455 23.77 0.88 32.44 2.40
2 3 2.749621 ACGATTTGCTGGTCCAGAATTC 59.250 45.455 23.77 15.98 32.44 2.17
3 4 2.749621 GACGATTTGCTGGTCCAGAATT 59.250 45.455 23.77 9.94 32.44 2.17
4 5 2.290260 TGACGATTTGCTGGTCCAGAAT 60.290 45.455 23.77 13.86 32.00 2.40
5 6 1.071542 TGACGATTTGCTGGTCCAGAA 59.928 47.619 23.77 9.81 32.00 3.02
6 7 0.684535 TGACGATTTGCTGGTCCAGA 59.315 50.000 23.77 1.66 32.00 3.86
7 8 1.742761 ATGACGATTTGCTGGTCCAG 58.257 50.000 15.15 15.15 32.00 3.86
8 9 2.236146 ACTATGACGATTTGCTGGTCCA 59.764 45.455 0.00 0.00 32.00 4.02
9 10 2.906354 ACTATGACGATTTGCTGGTCC 58.094 47.619 0.00 0.00 32.00 4.46
10 11 4.631813 AGAAACTATGACGATTTGCTGGTC 59.368 41.667 0.00 0.00 33.51 4.02
11 12 4.393062 CAGAAACTATGACGATTTGCTGGT 59.607 41.667 0.00 0.00 0.00 4.00
12 13 4.728882 GCAGAAACTATGACGATTTGCTGG 60.729 45.833 0.00 0.00 0.00 4.85
13 14 4.142838 TGCAGAAACTATGACGATTTGCTG 60.143 41.667 0.00 0.00 0.00 4.41
14 15 4.002982 TGCAGAAACTATGACGATTTGCT 58.997 39.130 0.00 0.00 0.00 3.91
15 16 4.340894 TGCAGAAACTATGACGATTTGC 57.659 40.909 0.00 0.00 0.00 3.68
16 17 6.252015 CCAATTGCAGAAACTATGACGATTTG 59.748 38.462 0.00 0.00 0.00 2.32
17 18 6.324819 CCAATTGCAGAAACTATGACGATTT 58.675 36.000 0.00 0.00 0.00 2.17
18 19 5.163622 CCCAATTGCAGAAACTATGACGATT 60.164 40.000 0.00 0.00 0.00 3.34
19 20 4.336433 CCCAATTGCAGAAACTATGACGAT 59.664 41.667 0.00 0.00 0.00 3.73
20 21 3.689161 CCCAATTGCAGAAACTATGACGA 59.311 43.478 0.00 0.00 0.00 4.20
21 22 3.440173 ACCCAATTGCAGAAACTATGACG 59.560 43.478 0.00 0.00 0.00 4.35
22 23 4.458989 TGACCCAATTGCAGAAACTATGAC 59.541 41.667 0.00 0.00 0.00 3.06
23 24 4.458989 GTGACCCAATTGCAGAAACTATGA 59.541 41.667 0.00 0.00 0.00 2.15
24 25 4.460382 AGTGACCCAATTGCAGAAACTATG 59.540 41.667 0.00 0.00 0.00 2.23
25 26 4.666512 AGTGACCCAATTGCAGAAACTAT 58.333 39.130 0.00 0.00 0.00 2.12
26 27 4.072131 GAGTGACCCAATTGCAGAAACTA 58.928 43.478 0.00 0.00 0.00 2.24
27 28 2.887152 GAGTGACCCAATTGCAGAAACT 59.113 45.455 0.00 0.00 0.00 2.66
28 29 2.887152 AGAGTGACCCAATTGCAGAAAC 59.113 45.455 0.00 0.00 0.00 2.78
29 30 2.886523 CAGAGTGACCCAATTGCAGAAA 59.113 45.455 0.00 0.00 0.00 2.52
30 31 2.507484 CAGAGTGACCCAATTGCAGAA 58.493 47.619 0.00 0.00 0.00 3.02
31 32 1.883638 GCAGAGTGACCCAATTGCAGA 60.884 52.381 0.00 0.00 0.00 4.26
32 33 0.524862 GCAGAGTGACCCAATTGCAG 59.475 55.000 0.00 0.00 0.00 4.41
33 34 0.111061 AGCAGAGTGACCCAATTGCA 59.889 50.000 0.00 0.00 34.17 4.08
34 35 0.807496 GAGCAGAGTGACCCAATTGC 59.193 55.000 0.00 0.00 0.00 3.56
35 36 1.457346 GGAGCAGAGTGACCCAATTG 58.543 55.000 0.00 0.00 0.00 2.32
36 37 0.329596 GGGAGCAGAGTGACCCAATT 59.670 55.000 0.00 0.00 41.72 2.32
37 38 1.994463 GGGAGCAGAGTGACCCAAT 59.006 57.895 0.00 0.00 41.72 3.16
38 39 3.483587 GGGAGCAGAGTGACCCAA 58.516 61.111 0.00 0.00 41.72 4.12
40 41 2.664081 CCTGGGAGCAGAGTGACCC 61.664 68.421 0.00 0.00 42.37 4.46
41 42 2.985456 CCTGGGAGCAGAGTGACC 59.015 66.667 0.00 0.00 0.00 4.02
42 43 2.267324 GCCTGGGAGCAGAGTGAC 59.733 66.667 0.00 0.00 0.00 3.67
43 44 3.005539 GGCCTGGGAGCAGAGTGA 61.006 66.667 0.00 0.00 0.00 3.41
44 45 4.106925 GGGCCTGGGAGCAGAGTG 62.107 72.222 0.84 0.00 0.00 3.51
45 46 4.664267 TGGGCCTGGGAGCAGAGT 62.664 66.667 4.53 0.00 0.00 3.24
46 47 4.106925 GTGGGCCTGGGAGCAGAG 62.107 72.222 4.53 0.00 0.00 3.35
47 48 4.980592 TGTGGGCCTGGGAGCAGA 62.981 66.667 4.53 0.00 0.00 4.26
48 49 3.736224 ATGTGGGCCTGGGAGCAG 61.736 66.667 4.53 0.00 0.00 4.24
49 50 4.051167 CATGTGGGCCTGGGAGCA 62.051 66.667 4.53 0.00 0.00 4.26
50 51 4.052518 ACATGTGGGCCTGGGAGC 62.053 66.667 4.53 0.00 0.00 4.70
51 52 2.273449 GACATGTGGGCCTGGGAG 59.727 66.667 1.15 0.00 0.00 4.30
52 53 2.531428 TGACATGTGGGCCTGGGA 60.531 61.111 1.15 0.00 0.00 4.37
53 54 2.361610 GTGACATGTGGGCCTGGG 60.362 66.667 1.15 0.00 0.00 4.45
54 55 2.747460 CGTGACATGTGGGCCTGG 60.747 66.667 1.15 0.00 0.00 4.45
55 56 2.034879 GTCGTGACATGTGGGCCTG 61.035 63.158 1.15 0.00 0.00 4.85
56 57 2.347490 GTCGTGACATGTGGGCCT 59.653 61.111 1.15 0.00 0.00 5.19
57 58 3.118454 CGTCGTGACATGTGGGCC 61.118 66.667 1.15 0.00 0.00 5.80
58 59 2.357034 ACGTCGTGACATGTGGGC 60.357 61.111 1.15 0.00 0.00 5.36
59 60 2.667318 GCACGTCGTGACATGTGGG 61.667 63.158 28.83 0.00 35.23 4.61
60 61 1.953642 TGCACGTCGTGACATGTGG 60.954 57.895 28.83 0.00 35.23 4.17
61 62 1.201578 GTGCACGTCGTGACATGTG 59.798 57.895 28.83 2.61 35.23 3.21
62 63 1.954146 GGTGCACGTCGTGACATGT 60.954 57.895 28.83 0.00 35.23 3.21
63 64 2.667318 GGGTGCACGTCGTGACATG 61.667 63.158 28.83 2.21 35.23 3.21
64 65 2.357034 GGGTGCACGTCGTGACAT 60.357 61.111 28.83 0.00 35.23 3.06
65 66 3.839432 TGGGTGCACGTCGTGACA 61.839 61.111 28.83 21.24 35.23 3.58
66 67 3.335534 GTGGGTGCACGTCGTGAC 61.336 66.667 28.83 20.88 35.23 3.67
136 137 0.937304 CGCGACGAATCCAATCCAAT 59.063 50.000 0.00 0.00 0.00 3.16
137 138 1.701545 GCGCGACGAATCCAATCCAA 61.702 55.000 12.10 0.00 0.00 3.53
138 139 2.171079 GCGCGACGAATCCAATCCA 61.171 57.895 12.10 0.00 0.00 3.41
139 140 2.626455 GCGCGACGAATCCAATCC 59.374 61.111 12.10 0.00 0.00 3.01
204 205 4.790861 GCGGAAGGACGTCGGACC 62.791 72.222 9.92 10.98 35.98 4.46
252 264 3.047877 CGTGCGTCCAAAGGGGTC 61.048 66.667 0.00 0.00 38.11 4.46
401 413 3.922893 GACTGCTGCGCGATGCTC 61.923 66.667 12.10 3.73 46.63 4.26
420 432 1.005630 GTTGGCTGCTGACTCGACT 60.006 57.895 0.00 0.00 0.00 4.18
421 433 0.880278 TTGTTGGCTGCTGACTCGAC 60.880 55.000 0.00 0.00 0.00 4.20
486 508 0.850100 ATATGGTTGGGGCGATGGAA 59.150 50.000 0.00 0.00 0.00 3.53
503 525 2.420967 GGAGTTAAGGAGGGCGCAAATA 60.421 50.000 10.83 0.00 0.00 1.40
561 583 0.459585 CGGCTAAGCTCGGTAAAGCA 60.460 55.000 0.00 0.00 45.00 3.91
605 627 3.869473 TACCGGAGTTGCGTGTGCC 62.869 63.158 9.46 0.00 41.78 5.01
657 679 1.403323 GTGAGCCAGCTAAATTCAGCC 59.597 52.381 0.00 0.00 42.84 4.85
673 695 2.169663 GCACATGATCTTTGCGTGAG 57.830 50.000 0.00 0.00 0.00 3.51
722 744 1.002257 TACGTACCGGACAGGCAGA 60.002 57.895 9.46 0.00 46.52 4.26
730 752 0.171679 CTGTGCATGTACGTACCGGA 59.828 55.000 22.43 12.25 0.00 5.14
731 753 0.171679 TCTGTGCATGTACGTACCGG 59.828 55.000 22.43 15.06 0.00 5.28
732 754 1.652124 GTTCTGTGCATGTACGTACCG 59.348 52.381 22.43 14.53 0.00 4.02
733 755 2.666508 CAGTTCTGTGCATGTACGTACC 59.333 50.000 22.43 8.27 0.00 3.34
734 756 2.666508 CCAGTTCTGTGCATGTACGTAC 59.333 50.000 18.90 18.90 0.00 3.67
735 757 2.929161 GCCAGTTCTGTGCATGTACGTA 60.929 50.000 9.48 0.00 0.00 3.57
736 758 1.795768 CCAGTTCTGTGCATGTACGT 58.204 50.000 9.48 0.00 0.00 3.57
737 759 0.443869 GCCAGTTCTGTGCATGTACG 59.556 55.000 9.48 4.65 0.00 3.67
767 789 1.522355 ATGGCTGGCAAGATCGACG 60.522 57.895 8.35 0.00 0.00 5.12
885 911 4.405358 ACCACTCTAGTAGTAGTAGCTCGT 59.595 45.833 7.10 2.50 35.76 4.18
886 912 4.947645 ACCACTCTAGTAGTAGTAGCTCG 58.052 47.826 7.10 1.98 35.76 5.03
891 917 7.339721 ACGTGTACTACCACTCTAGTAGTAGTA 59.660 40.741 18.58 18.58 46.38 1.82
899 925 4.217118 ACCAAACGTGTACTACCACTCTAG 59.783 45.833 0.00 0.00 33.07 2.43
1019 1048 1.589196 GCGGTATGGCGAGACAGAC 60.589 63.158 0.00 0.00 32.06 3.51
1153 1182 0.682209 GGCGGTAGTAGTGGTCCTGA 60.682 60.000 0.00 0.00 0.00 3.86
1255 1284 2.790791 CGAGATCCTCAGCGGCCTT 61.791 63.158 0.00 0.00 0.00 4.35
1261 1290 1.363443 CAGGCTCGAGATCCTCAGC 59.637 63.158 18.75 0.00 35.51 4.26
1383 1412 3.014085 TAGTTGCCGGCGAAGAGGG 62.014 63.158 20.60 0.00 0.00 4.30
1768 1855 6.943146 TGTAATTAACACAGGGTAATCAAGCA 59.057 34.615 0.00 0.00 31.43 3.91
1824 1950 3.698289 ACTGCTAGTAGTTACTCAGCCA 58.302 45.455 7.78 0.91 37.73 4.75
1825 1951 4.158025 TCAACTGCTAGTAGTTACTCAGCC 59.842 45.833 23.49 0.00 38.78 4.85
1826 1952 5.312120 TCAACTGCTAGTAGTTACTCAGC 57.688 43.478 23.49 6.59 38.78 4.26
1865 1991 2.934553 GACCTACCAAGTACGAAATGCC 59.065 50.000 0.00 0.00 0.00 4.40
1874 2000 1.557832 GCCCATGTGACCTACCAAGTA 59.442 52.381 0.00 0.00 0.00 2.24
1912 2039 9.618890 AATGCAGTCAATTATATGTACTCAAGT 57.381 29.630 0.00 0.00 0.00 3.16
1927 2054 4.151883 ACCAAGTACCAAATGCAGTCAAT 58.848 39.130 0.00 0.00 0.00 2.57
2030 2157 5.828299 TTGTCGAAAAATTCAAGGACAGT 57.172 34.783 0.00 0.00 36.00 3.55
2131 2260 0.953727 TGTTGGCTGTGTGCATCTTC 59.046 50.000 0.00 0.00 45.15 2.87
2155 2284 1.607713 CGTGTTTTTGTGTGCGTGAA 58.392 45.000 0.00 0.00 0.00 3.18
2233 2369 3.389002 GGATATGATTGCTTTGGGGCTTT 59.611 43.478 0.00 0.00 0.00 3.51
2246 2382 3.507162 TTGCCCATCGTGGATATGATT 57.493 42.857 5.71 0.00 40.96 2.57
2348 2484 0.603975 GCTCAAGTGTCGCTCCCTTT 60.604 55.000 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.