Multiple sequence alignment - TraesCS4A01G247400

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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 TraesCS4A01G247400 chr4A 100.000 2460 0 0 600 3059 558548475 558546016 0.000000e+00 4543.0
1 TraesCS4A01G247400 chr4A 100.000 140 0 0 1 140 558549074 558548935 3.030000e-65 259.0
2 TraesCS4A01G247400 chr4B 89.379 2495 146 49 600 3059 60176297 60178707 0.000000e+00 3029.0
3 TraesCS4A01G247400 chr4B 94.667 75 2 1 68 140 60176107 60176181 6.930000e-22 115.0
4 TraesCS4A01G247400 chr4D 92.265 1823 78 26 600 2406 41073943 41075718 0.000000e+00 2527.0
5 TraesCS4A01G247400 chr4D 91.353 266 22 1 2453 2717 41077095 41077360 2.240000e-96 363.0
6 TraesCS4A01G247400 chr4D 97.500 80 1 1 44 122 41073748 41073827 5.320000e-28 135.0
7 TraesCS4A01G247400 chr3D 85.714 77 10 1 2926 3001 179917015 179917091 2.530000e-11 80.5
8 TraesCS4A01G247400 chr3A 83.696 92 8 6 2933 3020 177717275 177717187 2.530000e-11 80.5
9 TraesCS4A01G247400 chr3A 85.915 71 5 4 2933 3000 177718116 177718048 1.520000e-08 71.3
10 TraesCS4A01G247400 chr3A 83.582 67 7 4 2926 2990 568243808 568243872 3.290000e-05 60.2
11 TraesCS4A01G247400 chr7D 85.507 69 9 1 2926 2993 619671215 619671283 1.520000e-08 71.3
12 TraesCS4A01G247400 chr5D 84.127 63 9 1 2939 3001 493132913 493132852 3.290000e-05 60.2
13 TraesCS4A01G247400 chr5A 94.872 39 1 1 2926 2963 26811345 26811307 3.290000e-05 60.2
14 TraesCS4A01G247400 chr5A 87.500 48 6 0 2939 2986 7355160 7355113 4.260000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G247400 chr4A 558546016 558549074 3058 True 2401.000000 4543 100.000 1 3059 2 chr4A.!!$R1 3058
1 TraesCS4A01G247400 chr4B 60176107 60178707 2600 False 1572.000000 3029 92.023 68 3059 2 chr4B.!!$F1 2991
2 TraesCS4A01G247400 chr4D 41073748 41077360 3612 False 1008.333333 2527 93.706 44 2717 3 chr4D.!!$F1 2673

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
672 692 0.536233 CCACACCAAACACCGATCCA 60.536 55.0 0.0 0.0 0.00 3.41 F
684 704 0.749091 CCGATCCAAGCCAATCAGCA 60.749 55.0 0.0 0.0 34.23 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1838 0.108520 GGCAGTTGCATCAATGGTGG 60.109 55.0 6.43 0.0 44.36 4.61 R
2077 2114 0.179067 TCGCACCGAACCAAGAAACT 60.179 50.0 0.00 0.0 31.06 2.66 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
39 40 3.345808 GAGCACGTCCGCAAGCAA 61.346 61.111 0.36 0.00 0.00 3.91
40 41 3.300667 GAGCACGTCCGCAAGCAAG 62.301 63.158 0.36 0.00 0.00 4.01
41 42 4.389576 GCACGTCCGCAAGCAAGG 62.390 66.667 0.00 0.00 0.00 3.61
42 43 2.664851 CACGTCCGCAAGCAAGGA 60.665 61.111 0.00 0.00 0.00 3.36
119 139 3.000819 CACCGACCTACCAGGCCA 61.001 66.667 5.01 0.00 39.63 5.36
120 140 3.001406 ACCGACCTACCAGGCCAC 61.001 66.667 5.01 0.00 39.63 5.01
121 141 4.143333 CCGACCTACCAGGCCACG 62.143 72.222 5.01 0.00 39.63 4.94
122 142 4.814294 CGACCTACCAGGCCACGC 62.814 72.222 5.01 0.00 39.63 5.34
672 692 0.536233 CCACACCAAACACCGATCCA 60.536 55.000 0.00 0.00 0.00 3.41
683 703 0.749454 ACCGATCCAAGCCAATCAGC 60.749 55.000 0.00 0.00 0.00 4.26
684 704 0.749091 CCGATCCAAGCCAATCAGCA 60.749 55.000 0.00 0.00 34.23 4.41
688 708 0.899717 TCCAAGCCAATCAGCAACCC 60.900 55.000 0.00 0.00 34.23 4.11
694 714 0.937304 CCAATCAGCAACCCGTATCG 59.063 55.000 0.00 0.00 0.00 2.92
756 776 2.428902 CGAAACGGCGTCCACGTA 60.429 61.111 15.17 0.00 44.83 3.57
803 823 2.435059 GGAGGCAGGCAAGTCGTC 60.435 66.667 0.00 0.00 0.00 4.20
925 945 3.418068 GTCGAGTGCAGCTGCCAC 61.418 66.667 34.64 28.89 41.18 5.01
926 946 4.687215 TCGAGTGCAGCTGCCACC 62.687 66.667 34.64 22.02 41.18 4.61
927 947 4.994471 CGAGTGCAGCTGCCACCA 62.994 66.667 34.64 14.66 41.18 4.17
928 948 2.360852 GAGTGCAGCTGCCACCAT 60.361 61.111 34.64 17.26 41.18 3.55
929 949 2.360852 AGTGCAGCTGCCACCATC 60.361 61.111 34.64 17.28 41.18 3.51
936 956 1.450134 GCTGCCACCATCATCGTCA 60.450 57.895 0.00 0.00 0.00 4.35
1295 1318 3.462678 GGACGAGGTGGAGGAGGC 61.463 72.222 0.00 0.00 0.00 4.70
1578 1601 4.660938 GTGTGGGGCCTGGTGGTC 62.661 72.222 0.84 0.00 37.19 4.02
1811 1834 3.310193 ACTAGCATAGAAGAACCTCCCC 58.690 50.000 0.00 0.00 42.77 4.81
1828 1851 2.755064 CCCGCCACCATTGATGCA 60.755 61.111 0.00 0.00 0.00 3.96
1830 1853 1.153784 CCGCCACCATTGATGCAAC 60.154 57.895 0.00 0.00 0.00 4.17
1910 1944 4.823989 ACCCCATTGATCGATGATTCTTTC 59.176 41.667 22.50 0.00 0.00 2.62
1911 1945 5.068636 CCCCATTGATCGATGATTCTTTCT 58.931 41.667 22.50 0.00 0.00 2.52
1913 1947 6.436261 CCCATTGATCGATGATTCTTTCTTG 58.564 40.000 22.50 3.54 0.00 3.02
1914 1948 5.913514 CCATTGATCGATGATTCTTTCTTGC 59.086 40.000 22.50 0.00 0.00 4.01
1918 1952 5.295292 TGATCGATGATTCTTTCTTGCCTTC 59.705 40.000 0.54 0.00 0.00 3.46
1919 1953 4.578871 TCGATGATTCTTTCTTGCCTTCA 58.421 39.130 0.00 0.00 0.00 3.02
1983 2017 6.201044 GTGATCGAGTAATTGGAATCACGAAT 59.799 38.462 0.00 0.00 32.69 3.34
2050 2084 8.437742 GCTTGATTATGAATTGAAAACCAACTG 58.562 33.333 0.00 0.00 37.63 3.16
2068 2105 5.704515 CCAACTGTTGATCATGAAGTTCTCT 59.295 40.000 21.49 0.00 0.00 3.10
2070 2107 6.798315 ACTGTTGATCATGAAGTTCTCTTG 57.202 37.500 0.00 0.05 33.64 3.02
2071 2108 6.294473 ACTGTTGATCATGAAGTTCTCTTGT 58.706 36.000 0.00 0.00 33.64 3.16
2072 2109 6.769822 ACTGTTGATCATGAAGTTCTCTTGTT 59.230 34.615 0.00 0.00 33.64 2.83
2073 2110 7.041508 ACTGTTGATCATGAAGTTCTCTTGTTC 60.042 37.037 0.00 5.18 33.64 3.18
2074 2111 6.994496 TGTTGATCATGAAGTTCTCTTGTTCT 59.006 34.615 0.00 0.00 32.73 3.01
2075 2112 7.172190 TGTTGATCATGAAGTTCTCTTGTTCTC 59.828 37.037 0.00 0.00 32.73 2.87
2076 2113 5.866092 TGATCATGAAGTTCTCTTGTTCTCG 59.134 40.000 0.00 0.00 32.73 4.04
2077 2114 5.453567 TCATGAAGTTCTCTTGTTCTCGA 57.546 39.130 4.17 0.00 33.64 4.04
2078 2115 5.465051 TCATGAAGTTCTCTTGTTCTCGAG 58.535 41.667 5.93 5.93 33.64 4.04
2079 2116 4.920640 TGAAGTTCTCTTGTTCTCGAGT 57.079 40.909 13.13 0.00 33.64 4.18
2141 2182 1.583054 GTCTCGGTTATGCCATGGAC 58.417 55.000 18.40 7.64 36.97 4.02
2179 2220 3.902063 CGACGGCAATGCGTCTCG 61.902 66.667 20.93 13.46 32.91 4.04
2202 2243 2.815503 TGACGGCTCGAATATTCCGATA 59.184 45.455 17.44 5.59 44.23 2.92
2283 2324 5.636123 AGTAGAGTAGGATTCGGTGATGAT 58.364 41.667 0.00 0.00 0.00 2.45
2287 2328 5.541868 AGAGTAGGATTCGGTGATGATTGAT 59.458 40.000 0.00 0.00 0.00 2.57
2322 2364 2.812011 AGTTAATGGCAAGAACGTGGAC 59.188 45.455 8.65 0.00 0.00 4.02
2391 2433 3.186047 CGTCCGGTCCAATGACGC 61.186 66.667 0.00 0.00 44.29 5.19
2424 3789 8.777413 CATGATTAGTGGTGGTATAATCTTGTG 58.223 37.037 9.91 3.20 36.87 3.33
2438 3803 2.256391 TTGTGGCCAAGATCGCAAG 58.744 52.632 7.24 0.00 0.00 4.01
2446 3823 1.328680 CCAAGATCGCAAGTTCATCCG 59.671 52.381 0.00 0.00 38.53 4.18
2449 3826 2.094126 GATCGCAAGTTCATCCGCCG 62.094 60.000 0.00 0.00 36.11 6.46
2451 3828 2.677003 CGCAAGTTCATCCGCCGTT 61.677 57.895 0.00 0.00 0.00 4.44
2456 3833 1.935933 AGTTCATCCGCCGTTCATAC 58.064 50.000 0.00 0.00 0.00 2.39
2462 3839 0.742505 TCCGCCGTTCATACCAGTAG 59.257 55.000 0.00 0.00 0.00 2.57
2465 3842 1.404391 CGCCGTTCATACCAGTAGAGT 59.596 52.381 0.00 0.00 0.00 3.24
2499 3876 6.526674 GGTAGTAATTTGCTTCCAATTTGACG 59.473 38.462 5.48 0.00 0.00 4.35
2538 3915 5.753921 AGCGAGCAAACAAGACTATATAACC 59.246 40.000 0.00 0.00 0.00 2.85
2540 3917 6.202954 GCGAGCAAACAAGACTATATAACCAT 59.797 38.462 0.00 0.00 0.00 3.55
2581 3958 4.327982 CACCATCCATAGTAGACTGGTG 57.672 50.000 5.24 5.24 45.27 4.17
2621 3998 3.149196 GAGACAGTCAATTTGGGAGCAA 58.851 45.455 2.66 0.00 0.00 3.91
2721 4100 5.960202 AGGGTGCTTCCAATTATCTCATTTT 59.040 36.000 1.43 0.00 38.11 1.82
2745 4127 9.442047 TTTTTGTTAAAAAGAAAATCCTGCTCA 57.558 25.926 0.00 0.00 36.65 4.26
2748 4130 8.458573 TGTTAAAAAGAAAATCCTGCTCACTA 57.541 30.769 0.00 0.00 0.00 2.74
2749 4131 8.349983 TGTTAAAAAGAAAATCCTGCTCACTAC 58.650 33.333 0.00 0.00 0.00 2.73
2756 4138 1.589993 CCTGCTCACTACGGCATCG 60.590 63.158 0.00 0.00 37.83 3.84
2796 4178 7.969536 ATCTGATAAGTATTGAATGTTCGGG 57.030 36.000 0.00 0.00 0.00 5.14
2820 4202 3.980775 CGAAAAACGTGGCAATTCAGAAT 59.019 39.130 0.00 0.00 37.22 2.40
2827 4209 4.202101 ACGTGGCAATTCAGAATGTTTTCA 60.202 37.500 0.00 0.00 37.40 2.69
2830 4212 5.523188 GTGGCAATTCAGAATGTTTTCAACA 59.477 36.000 0.00 0.00 46.94 3.33
2832 4214 5.754890 GGCAATTCAGAATGTTTTCAACAGT 59.245 36.000 0.00 0.00 45.95 3.55
2835 4217 8.482429 GCAATTCAGAATGTTTTCAACAGTAAG 58.518 33.333 0.00 0.00 45.95 2.34
2845 4227 7.457868 TGTTTTCAACAGTAAGTTTAGTGACG 58.542 34.615 12.41 4.51 38.74 4.35
2846 4228 7.118101 TGTTTTCAACAGTAAGTTTAGTGACGT 59.882 33.333 12.41 0.00 38.74 4.34
2854 4236 2.960819 AGTTTAGTGACGTGAGGATGC 58.039 47.619 0.00 0.00 0.00 3.91
2924 4306 4.574599 TTTTTGGCAGAAAGCTTCTCTC 57.425 40.909 0.00 0.00 44.79 3.20
2925 4307 2.191128 TTGGCAGAAAGCTTCTCTCC 57.809 50.000 0.00 9.07 44.79 3.71
2926 4308 1.356124 TGGCAGAAAGCTTCTCTCCT 58.644 50.000 0.00 0.00 44.79 3.69
2927 4309 1.701847 TGGCAGAAAGCTTCTCTCCTT 59.298 47.619 0.00 0.00 44.79 3.36
2928 4310 2.083002 GGCAGAAAGCTTCTCTCCTTG 58.917 52.381 0.00 0.00 44.79 3.61
2929 4311 2.551938 GGCAGAAAGCTTCTCTCCTTGT 60.552 50.000 0.00 0.00 44.79 3.16
2930 4312 2.741517 GCAGAAAGCTTCTCTCCTTGTC 59.258 50.000 0.00 0.00 38.11 3.18
2931 4313 3.805108 GCAGAAAGCTTCTCTCCTTGTCA 60.805 47.826 0.00 0.00 38.11 3.58
2932 4314 4.384056 CAGAAAGCTTCTCTCCTTGTCAA 58.616 43.478 0.00 0.00 38.11 3.18
2933 4315 4.213059 CAGAAAGCTTCTCTCCTTGTCAAC 59.787 45.833 0.00 0.00 38.11 3.18
2934 4316 4.102367 AGAAAGCTTCTCTCCTTGTCAACT 59.898 41.667 0.00 0.00 34.07 3.16
2935 4317 5.305644 AGAAAGCTTCTCTCCTTGTCAACTA 59.694 40.000 0.00 0.00 34.07 2.24
2936 4318 5.552870 AAGCTTCTCTCCTTGTCAACTAA 57.447 39.130 0.00 0.00 0.00 2.24
2937 4319 4.888917 AGCTTCTCTCCTTGTCAACTAAC 58.111 43.478 0.00 0.00 0.00 2.34
2941 4323 5.871396 TCTCTCCTTGTCAACTAACTTGT 57.129 39.130 0.00 0.00 0.00 3.16
2949 4331 4.556233 TGTCAACTAACTTGTCATCCTCG 58.444 43.478 0.00 0.00 0.00 4.63
2951 4333 2.279582 ACTAACTTGTCATCCTCGCG 57.720 50.000 0.00 0.00 0.00 5.87
2955 4337 0.388649 ACTTGTCATCCTCGCGTCAC 60.389 55.000 5.77 0.00 0.00 3.67
2967 4349 0.179282 CGCGTCACTAAACTTGTCGC 60.179 55.000 0.00 4.28 44.56 5.19
2968 4350 0.179282 GCGTCACTAAACTTGTCGCG 60.179 55.000 0.00 0.00 40.60 5.87
2969 4351 1.401530 CGTCACTAAACTTGTCGCGA 58.598 50.000 3.71 3.71 0.00 5.87
2974 4356 4.432345 GTCACTAAACTTGTCGCGAAAAAC 59.568 41.667 12.06 0.00 0.00 2.43
2978 4360 6.020995 CACTAAACTTGTCGCGAAAAACATTT 60.021 34.615 12.06 14.61 0.00 2.32
3004 4386 1.441729 CCATGTGCTCGTACCCGAT 59.558 57.895 0.00 0.00 43.27 4.18
3008 4390 0.319083 TGTGCTCGTACCCGATGTTT 59.681 50.000 0.00 0.00 43.27 2.83
3024 4406 9.106070 ACCCGATGTTTAGTACTTATCATTTTC 57.894 33.333 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.680237 TTGCGGACGTGCTCCAGG 62.680 66.667 5.27 0.00 39.39 4.45
19 20 3.114616 CTTGCGGACGTGCTCCAG 61.115 66.667 5.27 0.00 39.39 3.86
22 23 3.300667 CTTGCTTGCGGACGTGCTC 62.301 63.158 5.27 0.00 35.36 4.26
23 24 3.349006 CTTGCTTGCGGACGTGCT 61.349 61.111 5.27 0.00 35.36 4.40
24 25 4.389576 CCTTGCTTGCGGACGTGC 62.390 66.667 0.00 0.00 0.00 5.34
25 26 2.664851 TCCTTGCTTGCGGACGTG 60.665 61.111 0.00 0.00 0.00 4.49
26 27 2.357517 CTCCTTGCTTGCGGACGT 60.358 61.111 0.00 0.00 0.00 4.34
27 28 2.048222 TCTCCTTGCTTGCGGACG 60.048 61.111 0.00 0.00 0.00 4.79
28 29 0.739112 CTCTCTCCTTGCTTGCGGAC 60.739 60.000 0.00 0.00 0.00 4.79
29 30 0.900182 TCTCTCTCCTTGCTTGCGGA 60.900 55.000 0.00 0.00 0.00 5.54
30 31 0.459934 CTCTCTCTCCTTGCTTGCGG 60.460 60.000 0.00 0.00 0.00 5.69
31 32 1.083242 GCTCTCTCTCCTTGCTTGCG 61.083 60.000 0.00 0.00 0.00 4.85
32 33 0.036577 TGCTCTCTCTCCTTGCTTGC 60.037 55.000 0.00 0.00 0.00 4.01
33 34 1.724429 GTGCTCTCTCTCCTTGCTTG 58.276 55.000 0.00 0.00 0.00 4.01
34 35 0.246086 CGTGCTCTCTCTCCTTGCTT 59.754 55.000 0.00 0.00 0.00 3.91
35 36 0.610509 TCGTGCTCTCTCTCCTTGCT 60.611 55.000 0.00 0.00 0.00 3.91
36 37 0.457681 GTCGTGCTCTCTCTCCTTGC 60.458 60.000 0.00 0.00 0.00 4.01
37 38 0.179176 CGTCGTGCTCTCTCTCCTTG 60.179 60.000 0.00 0.00 0.00 3.61
38 39 1.928706 GCGTCGTGCTCTCTCTCCTT 61.929 60.000 0.00 0.00 41.73 3.36
39 40 2.403378 GCGTCGTGCTCTCTCTCCT 61.403 63.158 0.00 0.00 41.73 3.69
40 41 2.101380 GCGTCGTGCTCTCTCTCC 59.899 66.667 0.00 0.00 41.73 3.71
41 42 2.276994 CGCGTCGTGCTCTCTCTC 60.277 66.667 0.00 0.00 43.27 3.20
42 43 3.805307 CCGCGTCGTGCTCTCTCT 61.805 66.667 4.92 0.00 43.27 3.10
122 142 4.722700 CGTGGGCCTTGGGTGAGG 62.723 72.222 4.53 0.00 39.93 3.86
672 692 0.037590 TACGGGTTGCTGATTGGCTT 59.962 50.000 0.00 0.00 0.00 4.35
706 726 3.316573 GAGAAGGGACCTGTGGGCG 62.317 68.421 0.00 0.00 35.63 6.13
719 739 4.880537 ATCCGCTGCGCCGAGAAG 62.881 66.667 18.00 0.70 0.00 2.85
720 740 4.873129 GATCCGCTGCGCCGAGAA 62.873 66.667 18.00 0.00 0.00 2.87
786 806 2.435059 GACGACTTGCCTGCCTCC 60.435 66.667 0.00 0.00 0.00 4.30
803 823 0.030908 GTAGAGGATTCCGAGCCGTG 59.969 60.000 0.00 0.00 36.12 4.94
924 944 7.099764 GGTAAATAGATGATGACGATGATGGT 58.900 38.462 0.00 0.00 0.00 3.55
925 945 7.063898 GTGGTAAATAGATGATGACGATGATGG 59.936 40.741 0.00 0.00 0.00 3.51
926 946 7.063898 GGTGGTAAATAGATGATGACGATGATG 59.936 40.741 0.00 0.00 0.00 3.07
927 947 7.099764 GGTGGTAAATAGATGATGACGATGAT 58.900 38.462 0.00 0.00 0.00 2.45
928 948 6.455647 GGTGGTAAATAGATGATGACGATGA 58.544 40.000 0.00 0.00 0.00 2.92
929 949 5.346011 CGGTGGTAAATAGATGATGACGATG 59.654 44.000 0.00 0.00 0.00 3.84
936 956 3.893200 TCGGTCGGTGGTAAATAGATGAT 59.107 43.478 0.00 0.00 0.00 2.45
1002 1025 3.068691 TCCCTCCTCTTCACGCGG 61.069 66.667 12.47 0.00 0.00 6.46
1007 1030 1.682684 GCGACCTCCCTCCTCTTCA 60.683 63.158 0.00 0.00 0.00 3.02
1277 1300 2.760385 CCTCCTCCACCTCGTCCC 60.760 72.222 0.00 0.00 0.00 4.46
1279 1302 3.827898 CGCCTCCTCCACCTCGTC 61.828 72.222 0.00 0.00 0.00 4.20
1309 1332 3.797353 CATCCACCCCTCCACCCG 61.797 72.222 0.00 0.00 0.00 5.28
1741 1764 2.278596 CGGCTATCGTCGGTGGTG 60.279 66.667 0.00 0.00 33.88 4.17
1774 1797 1.266175 CTAGTAGTGGTACATCGGCGG 59.734 57.143 7.21 0.00 44.52 6.13
1775 1798 1.334779 GCTAGTAGTGGTACATCGGCG 60.335 57.143 0.00 0.00 44.52 6.46
1776 1799 1.679680 TGCTAGTAGTGGTACATCGGC 59.320 52.381 0.00 0.00 44.52 5.54
1777 1800 5.001874 TCTATGCTAGTAGTGGTACATCGG 58.998 45.833 0.00 0.00 44.52 4.18
1778 1801 6.427242 TCTTCTATGCTAGTAGTGGTACATCG 59.573 42.308 0.00 0.00 44.52 3.84
1779 1802 7.747155 TCTTCTATGCTAGTAGTGGTACATC 57.253 40.000 0.00 0.00 44.52 3.06
1811 1834 2.349672 TTGCATCAATGGTGGCGGG 61.350 57.895 0.00 0.00 0.00 6.13
1815 1838 0.108520 GGCAGTTGCATCAATGGTGG 60.109 55.000 6.43 0.00 44.36 4.61
1816 1839 0.892755 AGGCAGTTGCATCAATGGTG 59.107 50.000 6.43 0.00 44.36 4.17
1817 1840 3.369042 AGGCAGTTGCATCAATGGT 57.631 47.368 6.43 0.00 44.36 3.55
1910 1944 2.378028 GCTAGAGCGTGAAGGCAAG 58.622 57.895 0.00 0.00 34.64 4.01
1911 1945 4.598257 GCTAGAGCGTGAAGGCAA 57.402 55.556 0.00 0.00 34.64 4.52
2044 2078 5.704515 AGAGAACTTCATGATCAACAGTTGG 59.295 40.000 17.67 0.00 0.00 3.77
2050 2084 7.432350 AGAACAAGAGAACTTCATGATCAAC 57.568 36.000 0.00 0.00 31.17 3.18
2068 2105 3.554324 CGAACCAAGAAACTCGAGAACAA 59.446 43.478 21.68 0.00 33.13 2.83
2070 2107 2.475487 CCGAACCAAGAAACTCGAGAAC 59.525 50.000 21.68 9.63 33.13 3.01
2071 2108 2.101917 ACCGAACCAAGAAACTCGAGAA 59.898 45.455 21.68 0.00 33.13 2.87
2072 2109 1.684983 ACCGAACCAAGAAACTCGAGA 59.315 47.619 21.68 0.00 33.13 4.04
2073 2110 1.792949 CACCGAACCAAGAAACTCGAG 59.207 52.381 11.84 11.84 33.13 4.04
2074 2111 1.860676 CACCGAACCAAGAAACTCGA 58.139 50.000 0.00 0.00 33.13 4.04
2075 2112 0.234884 GCACCGAACCAAGAAACTCG 59.765 55.000 0.00 0.00 0.00 4.18
2076 2113 0.234884 CGCACCGAACCAAGAAACTC 59.765 55.000 0.00 0.00 0.00 3.01
2077 2114 0.179067 TCGCACCGAACCAAGAAACT 60.179 50.000 0.00 0.00 31.06 2.66
2078 2115 0.234884 CTCGCACCGAACCAAGAAAC 59.765 55.000 0.00 0.00 34.74 2.78
2079 2116 0.179067 ACTCGCACCGAACCAAGAAA 60.179 50.000 0.00 0.00 34.74 2.52
2179 2220 1.499049 GGAATATTCGAGCCGTCACC 58.501 55.000 9.32 0.00 0.00 4.02
2202 2243 3.812019 CGACGGCAGCCTACTCGT 61.812 66.667 10.54 0.87 38.62 4.18
2283 2324 7.765819 CCATTAACTATGTCTCACACTCATCAA 59.234 37.037 0.00 0.00 31.99 2.57
2287 2328 5.046663 TGCCATTAACTATGTCTCACACTCA 60.047 40.000 0.00 0.00 31.99 3.41
2391 2433 0.179084 ACCACTAATCATGCCGTCGG 60.179 55.000 6.99 6.99 0.00 4.79
2424 3789 1.064654 GATGAACTTGCGATCTTGGCC 59.935 52.381 0.00 0.00 0.00 5.36
2431 3796 2.173669 CGGCGGATGAACTTGCGAT 61.174 57.895 0.00 0.00 31.44 4.58
2438 3803 0.935196 GGTATGAACGGCGGATGAAC 59.065 55.000 13.24 3.50 0.00 3.18
2446 3823 4.547532 CATACTCTACTGGTATGAACGGC 58.452 47.826 7.77 0.00 45.31 5.68
2449 3826 5.363005 ACCACCATACTCTACTGGTATGAAC 59.637 44.000 13.34 0.00 43.91 3.18
2451 3828 4.893524 CACCACCATACTCTACTGGTATGA 59.106 45.833 13.34 0.00 43.91 2.15
2456 3833 2.467880 ACCACCACCATACTCTACTGG 58.532 52.381 0.00 0.00 38.55 4.00
2462 3839 5.296035 GCAAATTACTACCACCACCATACTC 59.704 44.000 0.00 0.00 0.00 2.59
2465 3842 5.444744 AGCAAATTACTACCACCACCATA 57.555 39.130 0.00 0.00 0.00 2.74
2499 3876 1.264288 CTCGCTTGTGACAAAGAACCC 59.736 52.381 0.00 0.00 0.00 4.11
2538 3915 2.455674 TGAAGACGACTTGGTCCATG 57.544 50.000 4.51 3.21 37.66 3.66
2540 3917 1.275291 GGATGAAGACGACTTGGTCCA 59.725 52.381 17.13 6.23 37.66 4.02
2581 3958 6.688578 TGTCTCTTTGTCACAATAGACTACC 58.311 40.000 23.83 7.83 39.27 3.18
2621 3998 3.373226 CAGCAGCCTGGTGCAATT 58.627 55.556 21.79 0.09 46.60 2.32
2664 4041 3.821033 AGTCTTGTACTCCAACCAAATGC 59.179 43.478 0.00 0.00 30.33 3.56
2721 4100 8.257306 AGTGAGCAGGATTTTCTTTTTAACAAA 58.743 29.630 0.00 0.00 0.00 2.83
2727 4106 5.048713 CCGTAGTGAGCAGGATTTTCTTTTT 60.049 40.000 0.00 0.00 0.00 1.94
2734 4113 0.613260 TGCCGTAGTGAGCAGGATTT 59.387 50.000 0.00 0.00 33.08 2.17
2742 4124 1.306148 TCTACCGATGCCGTAGTGAG 58.694 55.000 0.00 0.00 0.00 3.51
2745 4127 4.924305 TTTAATCTACCGATGCCGTAGT 57.076 40.909 0.00 0.00 0.00 2.73
2769 4151 9.265901 CCGAACATTCAATACTTATCAGATTCT 57.734 33.333 0.00 0.00 0.00 2.40
2784 4166 3.546417 CGTTTTTCGTCCCGAACATTCAA 60.546 43.478 0.00 0.00 45.64 2.69
2801 4183 4.320608 ACATTCTGAATTGCCACGTTTT 57.679 36.364 0.00 0.00 0.00 2.43
2804 4186 4.202101 TGAAAACATTCTGAATTGCCACGT 60.202 37.500 0.00 0.00 0.00 4.49
2805 4187 4.297510 TGAAAACATTCTGAATTGCCACG 58.702 39.130 0.00 0.00 0.00 4.94
2827 4209 5.068198 TCCTCACGTCACTAAACTTACTGTT 59.932 40.000 0.00 0.00 41.29 3.16
2830 4212 5.710984 CATCCTCACGTCACTAAACTTACT 58.289 41.667 0.00 0.00 0.00 2.24
2832 4214 4.491676 GCATCCTCACGTCACTAAACTTA 58.508 43.478 0.00 0.00 0.00 2.24
2835 4217 2.000447 GGCATCCTCACGTCACTAAAC 59.000 52.381 0.00 0.00 0.00 2.01
2838 4220 1.067142 GTTGGCATCCTCACGTCACTA 60.067 52.381 0.00 0.00 0.00 2.74
2870 4252 2.097142 GCAGAAAGGCTGTCATGCTTAG 59.903 50.000 16.89 0.00 46.62 2.18
2871 4253 2.086869 GCAGAAAGGCTGTCATGCTTA 58.913 47.619 16.89 0.00 46.62 3.09
2872 4254 0.886563 GCAGAAAGGCTGTCATGCTT 59.113 50.000 16.89 0.00 46.62 3.91
2879 4261 6.901081 AATAAACTAAAGCAGAAAGGCTGT 57.099 33.333 0.00 0.00 45.07 4.40
2907 4289 1.356124 AGGAGAGAAGCTTTCTGCCA 58.644 50.000 19.08 0.00 44.23 4.92
2908 4290 2.083002 CAAGGAGAGAAGCTTTCTGCC 58.917 52.381 19.08 15.85 44.23 4.85
2909 4291 2.741517 GACAAGGAGAGAAGCTTTCTGC 59.258 50.000 16.67 16.67 40.87 4.26
2910 4292 4.000331 TGACAAGGAGAGAAGCTTTCTG 58.000 45.455 13.60 1.46 40.87 3.02
2911 4293 4.102367 AGTTGACAAGGAGAGAAGCTTTCT 59.898 41.667 0.00 5.63 44.21 2.52
2912 4294 4.384940 AGTTGACAAGGAGAGAAGCTTTC 58.615 43.478 0.00 0.24 0.00 2.62
2915 4297 4.591072 AGTTAGTTGACAAGGAGAGAAGCT 59.409 41.667 0.00 0.00 0.00 3.74
2916 4298 4.888917 AGTTAGTTGACAAGGAGAGAAGC 58.111 43.478 0.00 0.00 0.00 3.86
2917 4299 6.284459 ACAAGTTAGTTGACAAGGAGAGAAG 58.716 40.000 6.80 0.00 38.60 2.85
2918 4300 6.127168 TGACAAGTTAGTTGACAAGGAGAGAA 60.127 38.462 6.80 0.00 37.79 2.87
2919 4301 5.362717 TGACAAGTTAGTTGACAAGGAGAGA 59.637 40.000 6.80 0.00 37.79 3.10
2920 4302 5.601662 TGACAAGTTAGTTGACAAGGAGAG 58.398 41.667 6.80 0.00 37.79 3.20
2921 4303 5.607939 TGACAAGTTAGTTGACAAGGAGA 57.392 39.130 6.80 0.00 37.79 3.71
2922 4304 5.409826 GGATGACAAGTTAGTTGACAAGGAG 59.590 44.000 6.80 0.00 42.78 3.69
2923 4305 5.071788 AGGATGACAAGTTAGTTGACAAGGA 59.928 40.000 6.80 0.00 42.78 3.36
2924 4306 5.308825 AGGATGACAAGTTAGTTGACAAGG 58.691 41.667 6.80 0.00 42.78 3.61
2925 4307 5.119279 CGAGGATGACAAGTTAGTTGACAAG 59.881 44.000 6.80 0.00 42.78 3.16
2926 4308 4.988540 CGAGGATGACAAGTTAGTTGACAA 59.011 41.667 6.80 0.00 42.78 3.18
2927 4309 4.556233 CGAGGATGACAAGTTAGTTGACA 58.444 43.478 6.80 7.09 43.50 3.58
2928 4310 3.368236 GCGAGGATGACAAGTTAGTTGAC 59.632 47.826 6.80 0.96 38.60 3.18
2929 4311 3.585862 GCGAGGATGACAAGTTAGTTGA 58.414 45.455 6.80 0.00 38.60 3.18
2930 4312 2.345641 CGCGAGGATGACAAGTTAGTTG 59.654 50.000 0.00 0.00 42.48 3.16
2931 4313 2.029290 ACGCGAGGATGACAAGTTAGTT 60.029 45.455 15.93 0.00 0.00 2.24
2932 4314 1.544691 ACGCGAGGATGACAAGTTAGT 59.455 47.619 15.93 0.00 0.00 2.24
2933 4315 2.186076 GACGCGAGGATGACAAGTTAG 58.814 52.381 15.93 0.00 0.00 2.34
2934 4316 1.542472 TGACGCGAGGATGACAAGTTA 59.458 47.619 15.93 0.00 0.00 2.24
2935 4317 0.317160 TGACGCGAGGATGACAAGTT 59.683 50.000 15.93 0.00 0.00 2.66
2936 4318 0.388649 GTGACGCGAGGATGACAAGT 60.389 55.000 15.93 0.00 0.00 3.16
2937 4319 0.109086 AGTGACGCGAGGATGACAAG 60.109 55.000 15.93 0.00 0.00 3.16
2941 4323 1.816835 AGTTTAGTGACGCGAGGATGA 59.183 47.619 15.93 0.00 0.00 2.92
2951 4333 3.847037 TTTCGCGACAAGTTTAGTGAC 57.153 42.857 9.15 0.00 0.00 3.67
2955 4337 6.490877 AAATGTTTTTCGCGACAAGTTTAG 57.509 33.333 9.15 0.00 0.00 1.85
2967 4349 5.920273 ACATGGCAACTCTAAATGTTTTTCG 59.080 36.000 0.00 0.00 37.61 3.46
2968 4350 6.346838 GCACATGGCAACTCTAAATGTTTTTC 60.347 38.462 0.00 0.00 43.97 2.29
2969 4351 5.466393 GCACATGGCAACTCTAAATGTTTTT 59.534 36.000 0.00 0.00 43.97 1.94


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

AutoCloner maintained by Alex Coulton.