Multiple sequence alignment - TraesCS6A01G331100

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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 TraesCS6A01G331100 chr6A 100.000 3457 0 0 1 3457 563383178 563386634 0.000000e+00 6384
1 TraesCS6A01G331100 chr6A 91.503 2589 207 10 774 3357 61567978 61565398 0.000000e+00 3550
2 TraesCS6A01G331100 chr6A 80.224 536 95 8 136 663 61568500 61567968 3.230000e-105 392
3 TraesCS6A01G331100 chr6A 96.791 187 5 1 134 320 563397242 563397427 9.320000e-81 311
4 TraesCS6A01G331100 chr6A 82.996 247 28 5 398 631 582232532 582232287 9.720000e-51 211
5 TraesCS6A01G331100 chrUn 97.634 3254 76 1 136 3388 290086751 290090004 0.000000e+00 5581
6 TraesCS6A01G331100 chrUn 95.745 188 8 0 134 321 442211637 442211824 1.560000e-78 303
7 TraesCS6A01G331100 chr5A 97.244 3266 88 2 133 3397 547174007 547170743 0.000000e+00 5531
8 TraesCS6A01G331100 chr4B 94.001 2967 157 10 496 3457 74326420 74323470 0.000000e+00 4473
9 TraesCS6A01G331100 chr4B 91.826 367 30 0 136 502 74328291 74327925 2.380000e-141 512
10 TraesCS6A01G331100 chr4B 90.811 185 17 0 136 320 74305041 74304857 7.410000e-62 248
11 TraesCS6A01G331100 chr6B 92.244 2527 190 6 928 3451 712152580 712155103 0.000000e+00 3576
12 TraesCS6A01G331100 chr4A 90.902 2671 224 14 795 3451 58508201 58510866 0.000000e+00 3568
13 TraesCS6A01G331100 chr2D 90.851 2678 216 17 804 3457 46693231 46690559 0.000000e+00 3561
14 TraesCS6A01G331100 chr7D 90.733 2687 217 19 795 3457 615779007 615781685 0.000000e+00 3554
15 TraesCS6A01G331100 chr3B 90.034 2679 234 19 795 3457 465858371 465861032 0.000000e+00 3437


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 TraesCS6A01G331100 chr6A 563383178 563386634 3456 False 6384.0 6384 100.0000 1 3457 1 chr6A.!!$F1 3456
1 TraesCS6A01G331100 chr6A 61565398 61568500 3102 True 1971.0 3550 85.8635 136 3357 2 chr6A.!!$R2 3221
2 TraesCS6A01G331100 chrUn 290086751 290090004 3253 False 5581.0 5581 97.6340 136 3388 1 chrUn.!!$F1 3252
3 TraesCS6A01G331100 chr5A 547170743 547174007 3264 True 5531.0 5531 97.2440 133 3397 1 chr5A.!!$R1 3264
4 TraesCS6A01G331100 chr4B 74323470 74328291 4821 True 2492.5 4473 92.9135 136 3457 2 chr4B.!!$R2 3321
5 TraesCS6A01G331100 chr6B 712152580 712155103 2523 False 3576.0 3576 92.2440 928 3451 1 chr6B.!!$F1 2523
6 TraesCS6A01G331100 chr4A 58508201 58510866 2665 False 3568.0 3568 90.9020 795 3451 1 chr4A.!!$F1 2656
7 TraesCS6A01G331100 chr2D 46690559 46693231 2672 True 3561.0 3561 90.8510 804 3457 1 chr2D.!!$R1 2653
8 TraesCS6A01G331100 chr7D 615779007 615781685 2678 False 3554.0 3554 90.7330 795 3457 1 chr7D.!!$F1 2662
9 TraesCS6A01G331100 chr3B 465858371 465861032 2661 False 3437.0 3437 90.0340 795 3457 1 chr3B.!!$F1 2662

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
240 241 0.179000 ACTGGATCGGTGAGGAATGC 59.821 55.0 0.0 0.0 0.00 3.56 F
840 2360 0.324943 AAGCTCGTATTGCTGGGTGT 59.675 50.0 0.0 0.0 41.03 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1866 3413 2.372264 CAAGTTGGATAGCCATGCAGT 58.628 47.619 0.0 0.0 45.46 4.40 R
2567 4123 3.502979 GGGGTAAATACGAAACAGTGCAA 59.497 43.478 0.0 0.0 0.00 4.08 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
23 24 5.741388 AGATCAAACCTTCGTATTCATGC 57.259 39.130 0.00 0.00 0.00 4.06
24 25 5.185454 AGATCAAACCTTCGTATTCATGCA 58.815 37.500 0.00 0.00 0.00 3.96
25 26 5.647658 AGATCAAACCTTCGTATTCATGCAA 59.352 36.000 0.00 0.00 0.00 4.08
26 27 5.697473 TCAAACCTTCGTATTCATGCAAA 57.303 34.783 0.00 0.00 0.00 3.68
27 28 6.078202 TCAAACCTTCGTATTCATGCAAAA 57.922 33.333 0.00 0.00 0.00 2.44
28 29 6.686630 TCAAACCTTCGTATTCATGCAAAAT 58.313 32.000 0.00 0.00 0.00 1.82
29 30 7.151308 TCAAACCTTCGTATTCATGCAAAATT 58.849 30.769 0.00 0.00 0.00 1.82
30 31 7.655328 TCAAACCTTCGTATTCATGCAAAATTT 59.345 29.630 0.00 0.00 0.00 1.82
31 32 7.961325 AACCTTCGTATTCATGCAAAATTTT 57.039 28.000 0.00 0.00 0.00 1.82
32 33 7.581011 ACCTTCGTATTCATGCAAAATTTTC 57.419 32.000 0.00 0.00 0.00 2.29
33 34 7.378181 ACCTTCGTATTCATGCAAAATTTTCT 58.622 30.769 0.00 0.00 0.00 2.52
34 35 7.872483 ACCTTCGTATTCATGCAAAATTTTCTT 59.128 29.630 0.00 0.00 0.00 2.52
35 36 8.711457 CCTTCGTATTCATGCAAAATTTTCTTT 58.289 29.630 0.00 0.00 0.00 2.52
71 72 9.483916 TTTCTTTCTTTCTTACATGATACGTCA 57.516 29.630 0.00 0.00 39.04 4.35
72 73 9.653287 TTCTTTCTTTCTTACATGATACGTCAT 57.347 29.630 0.00 0.00 45.87 3.06
73 74 9.653287 TCTTTCTTTCTTACATGATACGTCATT 57.347 29.630 0.00 0.00 42.37 2.57
76 77 8.996024 TCTTTCTTACATGATACGTCATTTGA 57.004 30.769 0.00 0.00 42.37 2.69
77 78 8.869897 TCTTTCTTACATGATACGTCATTTGAC 58.130 33.333 0.00 0.46 42.37 3.18
78 79 7.534085 TTCTTACATGATACGTCATTTGACC 57.466 36.000 0.00 0.00 42.37 4.02
79 80 5.746721 TCTTACATGATACGTCATTTGACCG 59.253 40.000 0.00 3.65 42.37 4.79
80 81 4.118093 ACATGATACGTCATTTGACCGA 57.882 40.909 0.00 0.00 42.37 4.69
81 82 4.112634 ACATGATACGTCATTTGACCGAG 58.887 43.478 0.00 0.00 42.37 4.63
82 83 4.142249 ACATGATACGTCATTTGACCGAGA 60.142 41.667 0.00 0.00 42.37 4.04
83 84 3.766151 TGATACGTCATTTGACCGAGAC 58.234 45.455 5.17 0.00 41.86 3.36
84 85 3.442625 TGATACGTCATTTGACCGAGACT 59.557 43.478 5.17 0.00 41.86 3.24
85 86 2.814280 ACGTCATTTGACCGAGACTT 57.186 45.000 5.17 0.00 41.86 3.01
86 87 2.404215 ACGTCATTTGACCGAGACTTG 58.596 47.619 5.17 0.00 41.86 3.16
87 88 1.726791 CGTCATTTGACCGAGACTTGG 59.273 52.381 7.25 7.25 41.86 3.61
88 89 2.767505 GTCATTTGACCGAGACTTGGT 58.232 47.619 14.73 14.73 44.10 3.67
89 90 3.139077 GTCATTTGACCGAGACTTGGTT 58.861 45.455 15.92 0.00 40.63 3.67
90 91 4.312443 GTCATTTGACCGAGACTTGGTTA 58.688 43.478 15.92 9.09 40.63 2.85
91 92 4.151867 GTCATTTGACCGAGACTTGGTTAC 59.848 45.833 15.92 4.82 40.63 2.50
92 93 3.823281 TTTGACCGAGACTTGGTTACA 57.177 42.857 15.92 7.45 40.63 2.41
93 94 4.345859 TTTGACCGAGACTTGGTTACAT 57.654 40.909 15.92 0.00 40.63 2.29
94 95 3.587797 TGACCGAGACTTGGTTACATC 57.412 47.619 15.92 3.38 40.63 3.06
95 96 3.162666 TGACCGAGACTTGGTTACATCT 58.837 45.455 15.92 0.00 40.63 2.90
96 97 3.192844 TGACCGAGACTTGGTTACATCTC 59.807 47.826 15.92 1.97 40.63 2.75
97 98 3.432378 ACCGAGACTTGGTTACATCTCT 58.568 45.455 8.76 0.00 35.82 3.10
98 99 3.193691 ACCGAGACTTGGTTACATCTCTG 59.806 47.826 8.76 0.00 35.82 3.35
99 100 3.193691 CCGAGACTTGGTTACATCTCTGT 59.806 47.826 0.00 0.00 36.29 3.41
100 101 4.416620 CGAGACTTGGTTACATCTCTGTC 58.583 47.826 0.00 0.00 36.29 3.51
101 102 4.416620 GAGACTTGGTTACATCTCTGTCG 58.583 47.826 0.00 0.00 36.79 4.35
102 103 4.079970 AGACTTGGTTACATCTCTGTCGA 58.920 43.478 0.00 0.00 36.79 4.20
103 104 4.082679 AGACTTGGTTACATCTCTGTCGAC 60.083 45.833 9.11 9.11 36.79 4.20
104 105 3.827302 ACTTGGTTACATCTCTGTCGACT 59.173 43.478 17.92 0.00 36.79 4.18
105 106 3.850122 TGGTTACATCTCTGTCGACTG 57.150 47.619 17.92 16.72 36.79 3.51
106 107 2.492088 TGGTTACATCTCTGTCGACTGG 59.508 50.000 20.57 11.84 36.79 4.00
107 108 2.159226 GGTTACATCTCTGTCGACTGGG 60.159 54.545 20.57 18.24 36.79 4.45
108 109 2.753452 GTTACATCTCTGTCGACTGGGA 59.247 50.000 24.87 24.87 36.79 4.37
109 110 1.178276 ACATCTCTGTCGACTGGGAC 58.822 55.000 25.11 0.00 37.45 4.46
110 111 0.457851 CATCTCTGTCGACTGGGACC 59.542 60.000 25.11 0.00 36.07 4.46
111 112 0.333312 ATCTCTGTCGACTGGGACCT 59.667 55.000 25.11 9.65 36.07 3.85
112 113 0.989602 TCTCTGTCGACTGGGACCTA 59.010 55.000 19.88 0.00 36.07 3.08
113 114 1.065345 TCTCTGTCGACTGGGACCTAG 60.065 57.143 19.88 9.98 36.07 3.02
114 115 0.680280 TCTGTCGACTGGGACCTAGC 60.680 60.000 20.57 0.00 36.07 3.42
115 116 1.668101 CTGTCGACTGGGACCTAGCC 61.668 65.000 17.92 0.00 36.07 3.93
116 117 2.439701 TCGACTGGGACCTAGCCG 60.440 66.667 7.26 7.26 0.00 5.52
117 118 4.208686 CGACTGGGACCTAGCCGC 62.209 72.222 4.46 0.00 0.00 6.53
118 119 3.075005 GACTGGGACCTAGCCGCA 61.075 66.667 4.46 0.00 0.00 5.69
119 120 3.372554 GACTGGGACCTAGCCGCAC 62.373 68.421 4.46 0.00 0.00 5.34
120 121 4.162690 CTGGGACCTAGCCGCACC 62.163 72.222 0.00 0.00 0.00 5.01
123 124 3.400054 GGACCTAGCCGCACCCTT 61.400 66.667 0.00 0.00 0.00 3.95
124 125 2.187163 GACCTAGCCGCACCCTTC 59.813 66.667 0.00 0.00 0.00 3.46
125 126 2.606519 ACCTAGCCGCACCCTTCA 60.607 61.111 0.00 0.00 0.00 3.02
126 127 2.125106 CCTAGCCGCACCCTTCAC 60.125 66.667 0.00 0.00 0.00 3.18
127 128 2.662596 CTAGCCGCACCCTTCACA 59.337 61.111 0.00 0.00 0.00 3.58
128 129 1.221840 CTAGCCGCACCCTTCACAT 59.778 57.895 0.00 0.00 0.00 3.21
129 130 0.392998 CTAGCCGCACCCTTCACATT 60.393 55.000 0.00 0.00 0.00 2.71
130 131 0.906066 TAGCCGCACCCTTCACATTA 59.094 50.000 0.00 0.00 0.00 1.90
131 132 0.255890 AGCCGCACCCTTCACATTAT 59.744 50.000 0.00 0.00 0.00 1.28
238 239 2.035632 GAGACTGGATCGGTGAGGAAT 58.964 52.381 0.00 0.00 0.00 3.01
240 241 0.179000 ACTGGATCGGTGAGGAATGC 59.821 55.000 0.00 0.00 0.00 3.56
817 2336 2.420022 GACAATTGTGATTAGTGCCGCT 59.580 45.455 17.58 0.00 0.00 5.52
840 2360 0.324943 AAGCTCGTATTGCTGGGTGT 59.675 50.000 0.00 0.00 41.03 4.16
932 2475 7.094975 TGCCATCAACATTTTGTACTAGTGTAC 60.095 37.037 5.39 0.00 46.74 2.90
982 2529 1.827344 TCATGTGTGACTAGCTCCTGG 59.173 52.381 0.00 0.00 0.00 4.45
1004 2551 2.615391 TGGGTTGTAGTGAGTCATGGA 58.385 47.619 0.00 0.00 0.00 3.41
1151 2698 4.200092 GAGCCTAATCCAGTAAAGTTGGG 58.800 47.826 0.00 0.00 36.34 4.12
1272 2819 2.374184 AGTGGCACTAGCACAAAACAA 58.626 42.857 20.61 0.00 44.61 2.83
1492 3039 3.540314 ATGCAGGTGAGATGAAGAGAC 57.460 47.619 0.00 0.00 0.00 3.36
1536 3083 2.242043 CACCCTTTTGAGCCTGTTGAT 58.758 47.619 0.00 0.00 0.00 2.57
1549 3096 5.748402 AGCCTGTTGATAAGAATGACATGA 58.252 37.500 0.00 0.00 0.00 3.07
1792 3339 2.608268 GTCGTGCTCCTAAGTCCTTTC 58.392 52.381 0.00 0.00 0.00 2.62
1860 3407 1.888512 GGACACACAAAGGATGCATGT 59.111 47.619 2.46 0.00 34.14 3.21
1866 3413 4.809958 CACACAAAGGATGCATGTTTTGAA 59.190 37.500 26.86 0.00 35.21 2.69
1988 3535 2.979058 TACCGGTGGTAGATGTGCA 58.021 52.632 19.93 0.00 37.09 4.57
2019 3566 3.589288 AGGATTTCACCTCCAAGCTTAGT 59.411 43.478 0.00 0.00 34.98 2.24
2057 3604 2.777459 TCCTCCCAGGATTCCTCTAC 57.223 55.000 0.98 0.00 40.06 2.59
2112 3659 0.460284 GTATGACACCTCACCAGGCG 60.460 60.000 0.00 0.00 45.05 5.52
2119 3672 2.693762 CCTCACCAGGCGCACAATG 61.694 63.158 10.83 1.65 30.98 2.82
2336 3889 8.579850 TTGCATGTTCCTAATTTTCTAGTCAT 57.420 30.769 0.00 0.00 0.00 3.06
2360 3913 8.584157 CATCCTCTTGTCAGTTAGCTCTATTAT 58.416 37.037 0.00 0.00 0.00 1.28
2567 4123 2.165998 GCTTGGGCATCTCTCTTTTGT 58.834 47.619 0.00 0.00 38.54 2.83
2847 4406 4.024048 AGTGATGTGTGCTCGGTTTTTAAG 60.024 41.667 0.00 0.00 0.00 1.85
2943 4502 9.403583 GAATATATTAACCAGGAGTTTGGACAA 57.596 33.333 0.00 0.00 40.87 3.18
2975 4534 4.297510 TCAAACGGCATTGAACATCAAAG 58.702 39.130 0.65 0.00 40.12 2.77
3080 4639 4.955925 TTACCATGAACGTGCCTAAATG 57.044 40.909 0.00 0.00 0.00 2.32
3430 4993 2.041620 GGCATTGCCTTATCCCCATCTA 59.958 50.000 20.66 0.00 46.69 1.98
3440 5003 0.107703 TCCCCATCTAAAGTGCAGCG 60.108 55.000 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.647658 TGCATGAATACGAAGGTTTGATCTT 59.352 36.000 0.00 0.00 0.00 2.40
1 2 5.185454 TGCATGAATACGAAGGTTTGATCT 58.815 37.500 0.00 0.00 0.00 2.75
2 3 5.484173 TGCATGAATACGAAGGTTTGATC 57.516 39.130 0.00 0.00 0.00 2.92
3 4 5.895636 TTGCATGAATACGAAGGTTTGAT 57.104 34.783 0.00 0.00 0.00 2.57
4 5 5.697473 TTTGCATGAATACGAAGGTTTGA 57.303 34.783 0.00 0.00 0.00 2.69
5 6 6.949578 ATTTTGCATGAATACGAAGGTTTG 57.050 33.333 0.00 0.00 0.00 2.93
6 7 7.961325 AAATTTTGCATGAATACGAAGGTTT 57.039 28.000 0.00 0.00 0.00 3.27
7 8 7.872483 AGAAAATTTTGCATGAATACGAAGGTT 59.128 29.630 8.47 0.00 0.00 3.50
8 9 7.378181 AGAAAATTTTGCATGAATACGAAGGT 58.622 30.769 8.47 0.00 0.00 3.50
9 10 7.816945 AGAAAATTTTGCATGAATACGAAGG 57.183 32.000 8.47 0.00 0.00 3.46
45 46 9.483916 TGACGTATCATGTAAGAAAGAAAGAAA 57.516 29.630 0.00 0.00 0.00 2.52
46 47 9.653287 ATGACGTATCATGTAAGAAAGAAAGAA 57.347 29.630 0.00 0.00 44.26 2.52
47 48 9.653287 AATGACGTATCATGTAAGAAAGAAAGA 57.347 29.630 0.00 0.00 45.26 2.52
50 51 9.430623 TCAAATGACGTATCATGTAAGAAAGAA 57.569 29.630 0.00 0.00 45.26 2.52
51 52 8.869897 GTCAAATGACGTATCATGTAAGAAAGA 58.130 33.333 0.00 0.00 45.26 2.52
52 53 8.116753 GGTCAAATGACGTATCATGTAAGAAAG 58.883 37.037 7.42 0.00 45.26 2.62
53 54 7.201487 CGGTCAAATGACGTATCATGTAAGAAA 60.201 37.037 7.42 0.00 45.26 2.52
54 55 6.254804 CGGTCAAATGACGTATCATGTAAGAA 59.745 38.462 7.42 0.00 45.26 2.52
55 56 5.746721 CGGTCAAATGACGTATCATGTAAGA 59.253 40.000 7.42 0.00 45.26 2.10
56 57 5.746721 TCGGTCAAATGACGTATCATGTAAG 59.253 40.000 7.42 0.00 45.26 2.34
57 58 5.652518 TCGGTCAAATGACGTATCATGTAA 58.347 37.500 7.42 0.00 45.26 2.41
58 59 5.066764 TCTCGGTCAAATGACGTATCATGTA 59.933 40.000 7.42 0.00 45.26 2.29
59 60 4.112634 CTCGGTCAAATGACGTATCATGT 58.887 43.478 7.42 0.00 45.26 3.21
60 61 4.207224 GTCTCGGTCAAATGACGTATCATG 59.793 45.833 7.42 0.00 45.26 3.07
62 63 3.442625 AGTCTCGGTCAAATGACGTATCA 59.557 43.478 7.42 0.00 45.65 2.15
63 64 4.030134 AGTCTCGGTCAAATGACGTATC 57.970 45.455 7.42 0.00 45.65 2.24
64 65 4.174009 CAAGTCTCGGTCAAATGACGTAT 58.826 43.478 7.42 0.00 45.65 3.06
65 66 3.571571 CAAGTCTCGGTCAAATGACGTA 58.428 45.455 7.42 0.00 45.65 3.57
66 67 2.404215 CAAGTCTCGGTCAAATGACGT 58.596 47.619 7.42 0.00 45.65 4.34
67 68 1.726791 CCAAGTCTCGGTCAAATGACG 59.273 52.381 7.42 3.80 45.65 4.35
68 69 2.767505 ACCAAGTCTCGGTCAAATGAC 58.232 47.619 4.96 4.96 44.04 3.06
69 70 3.485463 AACCAAGTCTCGGTCAAATGA 57.515 42.857 0.00 0.00 34.99 2.57
70 71 4.062293 TGTAACCAAGTCTCGGTCAAATG 58.938 43.478 0.00 0.00 34.99 2.32
71 72 4.345859 TGTAACCAAGTCTCGGTCAAAT 57.654 40.909 0.00 0.00 34.99 2.32
72 73 3.823281 TGTAACCAAGTCTCGGTCAAA 57.177 42.857 0.00 0.00 34.99 2.69
73 74 3.576982 AGATGTAACCAAGTCTCGGTCAA 59.423 43.478 0.00 0.00 34.99 3.18
74 75 3.162666 AGATGTAACCAAGTCTCGGTCA 58.837 45.455 0.00 0.00 34.99 4.02
75 76 3.444388 AGAGATGTAACCAAGTCTCGGTC 59.556 47.826 0.00 0.00 41.43 4.79
76 77 3.193691 CAGAGATGTAACCAAGTCTCGGT 59.806 47.826 0.00 0.00 41.43 4.69
77 78 3.193691 ACAGAGATGTAACCAAGTCTCGG 59.806 47.826 0.00 0.00 41.43 4.63
78 79 4.416620 GACAGAGATGTAACCAAGTCTCG 58.583 47.826 0.00 0.00 41.43 4.04
79 80 4.156190 TCGACAGAGATGTAACCAAGTCTC 59.844 45.833 0.00 0.00 37.86 3.36
80 81 4.079970 TCGACAGAGATGTAACCAAGTCT 58.920 43.478 0.00 0.00 0.00 3.24
81 82 4.082679 AGTCGACAGAGATGTAACCAAGTC 60.083 45.833 19.50 0.00 0.00 3.01
82 83 3.827302 AGTCGACAGAGATGTAACCAAGT 59.173 43.478 19.50 0.00 0.00 3.16
83 84 4.169508 CAGTCGACAGAGATGTAACCAAG 58.830 47.826 19.50 0.00 0.00 3.61
84 85 3.056821 CCAGTCGACAGAGATGTAACCAA 60.057 47.826 19.50 0.00 0.00 3.67
85 86 2.492088 CCAGTCGACAGAGATGTAACCA 59.508 50.000 19.50 0.00 0.00 3.67
86 87 2.159226 CCCAGTCGACAGAGATGTAACC 60.159 54.545 19.50 0.00 0.00 2.85
87 88 2.753452 TCCCAGTCGACAGAGATGTAAC 59.247 50.000 19.50 0.00 0.00 2.50
88 89 2.753452 GTCCCAGTCGACAGAGATGTAA 59.247 50.000 19.50 0.00 32.74 2.41
89 90 2.366533 GTCCCAGTCGACAGAGATGTA 58.633 52.381 19.50 0.00 32.74 2.29
90 91 1.178276 GTCCCAGTCGACAGAGATGT 58.822 55.000 19.50 0.00 32.74 3.06
91 92 0.457851 GGTCCCAGTCGACAGAGATG 59.542 60.000 19.50 6.55 34.24 2.90
92 93 0.333312 AGGTCCCAGTCGACAGAGAT 59.667 55.000 19.50 0.00 34.24 2.75
93 94 0.989602 TAGGTCCCAGTCGACAGAGA 59.010 55.000 19.50 2.59 34.24 3.10
94 95 1.384525 CTAGGTCCCAGTCGACAGAG 58.615 60.000 19.50 7.01 34.24 3.35
95 96 0.680280 GCTAGGTCCCAGTCGACAGA 60.680 60.000 19.50 8.60 34.24 3.41
96 97 1.668101 GGCTAGGTCCCAGTCGACAG 61.668 65.000 19.50 10.04 34.24 3.51
97 98 1.681327 GGCTAGGTCCCAGTCGACA 60.681 63.158 19.50 0.00 34.24 4.35
98 99 2.772691 CGGCTAGGTCCCAGTCGAC 61.773 68.421 5.26 7.70 43.67 4.20
99 100 2.439701 CGGCTAGGTCCCAGTCGA 60.440 66.667 5.26 0.00 43.67 4.20
100 101 4.208686 GCGGCTAGGTCCCAGTCG 62.209 72.222 6.98 6.98 43.80 4.18
101 102 3.075005 TGCGGCTAGGTCCCAGTC 61.075 66.667 0.00 0.00 0.00 3.51
102 103 3.391382 GTGCGGCTAGGTCCCAGT 61.391 66.667 0.00 0.00 0.00 4.00
103 104 4.162690 GGTGCGGCTAGGTCCCAG 62.163 72.222 0.00 0.00 0.00 4.45
106 107 3.387225 GAAGGGTGCGGCTAGGTCC 62.387 68.421 0.00 0.00 0.00 4.46
107 108 2.187163 GAAGGGTGCGGCTAGGTC 59.813 66.667 0.00 0.00 0.00 3.85
108 109 2.606519 TGAAGGGTGCGGCTAGGT 60.607 61.111 0.00 0.00 0.00 3.08
109 110 2.125106 GTGAAGGGTGCGGCTAGG 60.125 66.667 0.00 0.00 0.00 3.02
110 111 0.392998 AATGTGAAGGGTGCGGCTAG 60.393 55.000 0.00 0.00 0.00 3.42
111 112 0.906066 TAATGTGAAGGGTGCGGCTA 59.094 50.000 0.00 0.00 0.00 3.93
112 113 0.255890 ATAATGTGAAGGGTGCGGCT 59.744 50.000 0.00 0.00 0.00 5.52
113 114 1.102978 AATAATGTGAAGGGTGCGGC 58.897 50.000 0.00 0.00 0.00 6.53
114 115 3.312421 CACTAATAATGTGAAGGGTGCGG 59.688 47.826 0.00 0.00 37.60 5.69
115 116 3.938963 ACACTAATAATGTGAAGGGTGCG 59.061 43.478 0.00 0.00 38.65 5.34
116 117 5.393027 CCAACACTAATAATGTGAAGGGTGC 60.393 44.000 0.00 0.00 38.65 5.01
117 118 5.710099 ACCAACACTAATAATGTGAAGGGTG 59.290 40.000 0.00 0.00 38.65 4.61
118 119 5.710099 CACCAACACTAATAATGTGAAGGGT 59.290 40.000 0.00 0.00 38.65 4.34
119 120 5.710099 ACACCAACACTAATAATGTGAAGGG 59.290 40.000 0.00 0.00 38.65 3.95
120 121 6.817765 ACACCAACACTAATAATGTGAAGG 57.182 37.500 0.00 0.00 38.65 3.46
163 164 8.657712 ACTTTACATTTTAGACCCTACAGAGTT 58.342 33.333 0.00 0.00 0.00 3.01
238 239 0.783206 TTTGGGGGAATTCTGGAGCA 59.217 50.000 5.23 0.00 0.00 4.26
240 241 2.245806 AGGATTTGGGGGAATTCTGGAG 59.754 50.000 5.23 0.00 0.00 3.86
360 362 2.517875 GCCTCAATCAGCCGCCAT 60.518 61.111 0.00 0.00 0.00 4.40
545 2064 0.183492 GATGGACCAGCCCAAGCATA 59.817 55.000 0.00 0.00 43.56 3.14
817 2336 1.678728 CCCAGCAATACGAGCTTTCCA 60.679 52.381 0.00 0.00 41.14 3.53
840 2360 4.098960 ACGAGCAGAGTATTTTAATCCGGA 59.901 41.667 6.61 6.61 0.00 5.14
932 2475 3.479370 GCACTCCGCTAGCAACAG 58.521 61.111 16.45 9.16 37.77 3.16
982 2529 3.074412 CCATGACTCACTACAACCCAAC 58.926 50.000 0.00 0.00 0.00 3.77
1004 2551 5.259632 CTGATTTCTCCTTGGTTGGATCTT 58.740 41.667 0.00 0.00 35.30 2.40
1151 2698 2.609459 CTGATGTAATTGCTCGGTCCAC 59.391 50.000 0.00 0.00 0.00 4.02
1272 2819 7.633789 ACCAGACCAACACTCTATCATTAATT 58.366 34.615 0.00 0.00 0.00 1.40
1492 3039 5.527582 GGTAATAATGCAACTCCCTGTACAG 59.472 44.000 16.34 16.34 0.00 2.74
1536 3083 5.863965 TGGTGAACAGTCATGTCATTCTTA 58.136 37.500 0.00 0.00 39.29 2.10
1860 3407 3.429492 TGGATAGCCATGCAGTTCAAAA 58.571 40.909 0.00 0.00 39.92 2.44
1866 3413 2.372264 CAAGTTGGATAGCCATGCAGT 58.628 47.619 0.00 0.00 45.46 4.40
2057 3604 6.820656 AGTAGCATGGAAACTAGATTCAACTG 59.179 38.462 13.98 8.86 0.00 3.16
2112 3659 6.580963 TTTGATTGTGTTGTAACATTGTGC 57.419 33.333 0.26 0.00 41.59 4.57
2119 3672 8.816640 ATCCAAGATTTTGATTGTGTTGTAAC 57.183 30.769 0.00 0.00 36.36 2.50
2336 3889 8.540507 AATAATAGAGCTAACTGACAAGAGGA 57.459 34.615 0.00 0.00 0.00 3.71
2360 3913 8.383175 ACCAACCTCTACAATTGAGAGATTTAA 58.617 33.333 24.58 4.40 42.69 1.52
2567 4123 3.502979 GGGGTAAATACGAAACAGTGCAA 59.497 43.478 0.00 0.00 0.00 4.08
2730 4288 5.105752 CCAAAAATTGAACGAACCTCACAA 58.894 37.500 0.00 0.00 0.00 3.33
3418 4981 3.744214 CGCTGCACTTTAGATGGGGATAA 60.744 47.826 0.00 0.00 0.00 1.75
3430 4993 2.282462 CCCTTCCCGCTGCACTTT 60.282 61.111 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.