Multiple sequence alignment - TraesCS2A01G346500

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 TraesCS2A01G346500 chr2A 100.000 5323 0 0 1 5323 585135287 585140609 0.000000e+00 9830
1 TraesCS2A01G346500 chr2A 100.000 72 0 0 66 137 585135423 585135352 3.340000e-27 134
2 TraesCS2A01G346500 chr2D 96.616 5231 123 30 132 5323 441525172 441530387 0.000000e+00 8630
3 TraesCS2A01G346500 chr2D 95.833 72 2 1 1 71 441525102 441525173 1.210000e-21 115
4 TraesCS2A01G346500 chr2D 93.243 74 2 2 70 140 233379753 233379680 7.290000e-19 106
5 TraesCS2A01G346500 chr2B 95.589 4217 121 21 510 4675 519014172 519018374 0.000000e+00 6697
6 TraesCS2A01G346500 chr2B 94.973 557 24 4 4769 5323 519018621 519019175 0.000000e+00 870
7 TraesCS2A01G346500 chr2B 88.281 256 17 9 260 509 519013867 519014115 1.450000e-75 294
8 TraesCS2A01G346500 chr2B 94.958 119 6 0 4642 4760 519018377 519018495 2.530000e-43 187
9 TraesCS2A01G346500 chr3B 91.675 1057 59 11 769 1815 75589826 75588789 0.000000e+00 1437
10 TraesCS2A01G346500 chr3B 90.000 80 3 4 70 144 771798776 771798697 1.220000e-16 99
11 TraesCS2A01G346500 chr6B 79.732 671 111 20 2205 2867 435305938 435306591 3.760000e-126 462
12 TraesCS2A01G346500 chr6B 94.286 70 0 1 70 135 113712215 113712284 2.620000e-18 104
13 TraesCS2A01G346500 chr6B 94.286 70 0 1 68 133 113712284 113712215 2.620000e-18 104
14 TraesCS2A01G346500 chr6A 79.701 670 113 18 2205 2867 390732440 390733093 3.760000e-126 462
15 TraesCS2A01G346500 chr6D 79.583 671 112 20 2205 2867 273089087 273089740 1.750000e-124 457
16 TraesCS2A01G346500 chr3D 92.308 78 3 1 65 139 567708631 567708554 2.030000e-19 108
17 TraesCS2A01G346500 chr3D 93.151 73 2 1 68 137 567708558 567708630 2.620000e-18 104
18 TraesCS2A01G346500 chr1D 90.909 77 4 3 65 138 246070304 246070228 3.390000e-17 100
19 TraesCS2A01G346500 chr1B 91.892 74 3 2 69 140 112863356 112863284 3.390000e-17 100


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 TraesCS2A01G346500 chr2A 585135287 585140609 5322 False 9830.0 9830 100.00000 1 5323 1 chr2A.!!$F1 5322
1 TraesCS2A01G346500 chr2D 441525102 441530387 5285 False 4372.5 8630 96.22450 1 5323 2 chr2D.!!$F1 5322
2 TraesCS2A01G346500 chr2B 519013867 519019175 5308 False 2012.0 6697 93.45025 260 5323 4 chr2B.!!$F1 5063
3 TraesCS2A01G346500 chr3B 75588789 75589826 1037 True 1437.0 1437 91.67500 769 1815 1 chr3B.!!$R1 1046
4 TraesCS2A01G346500 chr6B 435305938 435306591 653 False 462.0 462 79.73200 2205 2867 1 chr6B.!!$F2 662
5 TraesCS2A01G346500 chr6A 390732440 390733093 653 False 462.0 462 79.70100 2205 2867 1 chr6A.!!$F1 662
6 TraesCS2A01G346500 chr6D 273089087 273089740 653 False 457.0 457 79.58300 2205 2867 1 chr6D.!!$F1 662

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
436 439 0.390124 AGAAACCCGACGTTGCAGTA 59.610 50.000 0.00 0.00 31.49 2.74 F
1687 1817 0.038159 CAGAGAGGTTGGTCGTGGAC 60.038 60.000 0.00 0.00 0.00 4.02 F
1746 1876 0.744414 AACACTGAGCAGTTGCACGT 60.744 50.000 6.90 0.79 45.16 4.49 F
2056 2186 2.759355 TCAGGGAGAATGGGTAACGAT 58.241 47.619 0.00 0.00 36.07 3.73 F
3744 3877 3.318017 CTCTAAACGAACTGGACAGGTG 58.682 50.000 4.14 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 2099 0.478507 CAACCTCCCCAAGTTCTGGT 59.521 55.000 0.00 0.00 44.76 4.00 R
2934 3065 3.604582 CCAAGGAGGAGAAACAGACATC 58.395 50.000 0.00 0.00 41.22 3.06 R
3070 3201 6.037172 TGTCTAGCTGTTCAAACTCTGTTTTC 59.963 38.462 0.00 0.00 0.00 2.29 R
3969 4103 3.392616 ACCTCACTGATTCAGGTTGAAGT 59.607 43.478 17.66 9.91 40.05 3.01 R
5018 5307 1.895131 CATGGGCAAGTAACCAGCTTT 59.105 47.619 0.00 0.00 40.67 3.51 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
77 79 9.577222 AGAGTGATAGTTTTATACTACTCCCTC 57.423 37.037 0.00 0.00 41.99 4.30
78 80 8.709272 AGTGATAGTTTTATACTACTCCCTCC 57.291 38.462 0.00 0.00 41.99 4.30
79 81 7.447853 AGTGATAGTTTTATACTACTCCCTCCG 59.552 40.741 0.00 0.00 41.99 4.63
80 82 7.230309 GTGATAGTTTTATACTACTCCCTCCGT 59.770 40.741 0.00 0.00 41.99 4.69
81 83 7.446625 TGATAGTTTTATACTACTCCCTCCGTC 59.553 40.741 0.00 0.00 41.99 4.79
82 84 4.892345 AGTTTTATACTACTCCCTCCGTCC 59.108 45.833 0.00 0.00 34.56 4.79
83 85 3.515602 TTATACTACTCCCTCCGTCCC 57.484 52.381 0.00 0.00 0.00 4.46
84 86 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
85 87 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
86 88 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
87 89 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
88 90 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
89 91 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
90 92 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
91 93 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
92 94 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
93 95 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
94 96 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
95 97 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
96 98 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
97 99 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
98 100 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
99 101 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
100 102 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
101 103 7.950512 TCCGTCCCATAATATAAGAACGTTTA 58.049 34.615 0.46 0.00 0.00 2.01
102 104 8.420222 TCCGTCCCATAATATAAGAACGTTTAA 58.580 33.333 0.46 0.00 0.00 1.52
103 105 9.044150 CCGTCCCATAATATAAGAACGTTTAAA 57.956 33.333 0.46 0.00 0.00 1.52
104 106 9.853921 CGTCCCATAATATAAGAACGTTTAAAC 57.146 33.333 8.35 8.35 0.00 2.01
122 124 9.853921 CGTTTAAACGTTCTTATATTATGGGAC 57.146 33.333 28.24 0.00 46.63 4.46
123 125 9.853921 GTTTAAACGTTCTTATATTATGGGACG 57.146 33.333 0.00 9.33 0.00 4.79
124 126 8.592105 TTAAACGTTCTTATATTATGGGACGG 57.408 34.615 0.00 1.76 0.00 4.79
125 127 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
126 128 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
127 129 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
128 130 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
129 131 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
130 132 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
131 133 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
132 134 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
154 156 5.599999 AGTATTTACTCGTGCTCCTTCAT 57.400 39.130 0.00 0.00 0.00 2.57
194 196 1.412079 ACTTTTGCACATTGCCCTCA 58.588 45.000 0.00 0.00 44.23 3.86
196 198 3.164268 ACTTTTGCACATTGCCCTCATA 58.836 40.909 0.00 0.00 44.23 2.15
200 202 2.101783 TGCACATTGCCCTCATAAAGG 58.898 47.619 0.00 0.00 44.23 3.11
312 315 8.875803 CATATGCTTGTAACCGACTTACTTTTA 58.124 33.333 0.00 0.00 36.43 1.52
313 316 7.916914 ATGCTTGTAACCGACTTACTTTTAT 57.083 32.000 5.04 0.00 36.43 1.40
315 318 7.156673 TGCTTGTAACCGACTTACTTTTATCT 58.843 34.615 5.04 0.00 36.43 1.98
316 319 7.117236 TGCTTGTAACCGACTTACTTTTATCTG 59.883 37.037 5.04 0.00 36.43 2.90
427 430 8.512138 CCCATAATAAATGATAAGAAACCCGAC 58.488 37.037 0.00 0.00 0.00 4.79
436 439 0.390124 AGAAACCCGACGTTGCAGTA 59.610 50.000 0.00 0.00 31.49 2.74
485 492 4.083855 GCAGTGTCAATCATTTCTTGTCGA 60.084 41.667 0.00 0.00 0.00 4.20
514 576 8.647256 AAGAAGAAGAAGATGTCAATGGAAAT 57.353 30.769 0.00 0.00 0.00 2.17
625 703 4.789012 TCCTTTGATGAAGCATGTTTCC 57.211 40.909 18.27 5.83 33.84 3.13
639 717 3.320673 TGTTTCCAACAAAACCACCAC 57.679 42.857 0.00 0.00 38.72 4.16
641 719 2.235155 GTTTCCAACAAAACCACCACCT 59.765 45.455 0.00 0.00 33.86 4.00
683 763 4.416738 GCCTCTGTCCCCACCTGC 62.417 72.222 0.00 0.00 0.00 4.85
692 772 4.447342 CCCACCTGCCATCCACCC 62.447 72.222 0.00 0.00 0.00 4.61
701 781 3.131478 CATCCACCCGCGAAACCC 61.131 66.667 8.23 0.00 0.00 4.11
886 980 2.482333 CCTCGCGGAATCCTCTCGT 61.482 63.158 6.13 0.00 0.00 4.18
990 1084 4.060667 ATCCAAACCCCAGCCCCG 62.061 66.667 0.00 0.00 0.00 5.73
1046 1140 2.111251 GGATCTAGGGTTGGCCGC 59.889 66.667 0.00 0.00 34.97 6.53
1267 1397 1.299648 CGGTGGCAGGGAATTCTCA 59.700 57.895 8.33 0.00 0.00 3.27
1435 1565 0.618968 CCAGTTCTAGCAGGGAGGGT 60.619 60.000 0.00 0.00 0.00 4.34
1495 1625 3.121025 GCAAAAAGAGGAAATTTTCGCCG 60.121 43.478 3.17 0.00 0.00 6.46
1529 1659 4.109675 ATAGCCCAAAGCCGCCGT 62.110 61.111 0.00 0.00 45.47 5.68
1544 1674 1.467883 CGCCGTCGTTACATTCTGGTA 60.468 52.381 0.00 0.00 0.00 3.25
1570 1700 1.203364 ACTCTGAAGGGAGTGGTGGAT 60.203 52.381 0.00 0.00 43.89 3.41
1687 1817 0.038159 CAGAGAGGTTGGTCGTGGAC 60.038 60.000 0.00 0.00 0.00 4.02
1720 1850 0.889186 ATGTGGACCTTGCCGTTGAC 60.889 55.000 0.00 0.00 0.00 3.18
1746 1876 0.744414 AACACTGAGCAGTTGCACGT 60.744 50.000 6.90 0.79 45.16 4.49
1789 1919 5.393678 GCTTGAGGTAGAGGAGAGTAAAGTG 60.394 48.000 0.00 0.00 0.00 3.16
1841 1971 2.789409 AGAGGAGTACCCAACAATGC 57.211 50.000 3.60 0.00 37.41 3.56
1917 2047 6.049790 GTGTAACACTGAGGAAGAAGAAAGT 58.950 40.000 0.00 0.00 36.32 2.66
1969 2099 3.097614 GCAGGGTAAGAAGACTCCTACA 58.902 50.000 0.00 0.00 0.00 2.74
2056 2186 2.759355 TCAGGGAGAATGGGTAACGAT 58.241 47.619 0.00 0.00 36.07 3.73
2698 2828 8.533569 TCCTGTTGACTATGTACTGATGATAA 57.466 34.615 0.00 0.00 0.00 1.75
3744 3877 3.318017 CTCTAAACGAACTGGACAGGTG 58.682 50.000 4.14 0.00 0.00 4.00
3969 4103 5.865552 GGTTTTGTTCGTACTGACTGCTATA 59.134 40.000 0.00 0.00 0.00 1.31
4119 4253 3.824133 TGTGGCCCATCATAGAATTCTG 58.176 45.455 18.47 3.21 0.00 3.02
4161 4295 4.260661 CGACCAGATTGATCATGAAAGCAG 60.261 45.833 0.00 0.00 0.00 4.24
4218 4352 4.148838 TGGCTTTATTGGCTACACACTTT 58.851 39.130 0.00 0.00 0.00 2.66
4243 4377 3.203487 ACCTGTTTCACCTTTGGAACCTA 59.797 43.478 0.00 0.00 40.21 3.08
4366 4500 9.171877 CTCCTATAGTGCTCTTTTCTTTTGATT 57.828 33.333 0.00 0.00 0.00 2.57
5018 5307 9.410556 GTAGTTAGTCTAAATGTCCGTTTTACA 57.589 33.333 2.83 0.00 0.00 2.41
5047 5336 2.885135 ACTTGCCCATGACAAGATCA 57.115 45.000 25.88 0.00 45.99 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 73 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
72 74 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
73 75 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
74 76 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
75 77 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
76 78 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
77 79 8.592105 TTAAACGTTCTTATATTATGGGACGG 57.408 34.615 0.00 1.76 0.00 4.79
78 80 9.853921 GTTTAAACGTTCTTATATTATGGGACG 57.146 33.333 0.00 9.33 0.00 4.79
79 81 9.853921 CGTTTAAACGTTCTTATATTATGGGAC 57.146 33.333 28.24 0.00 46.63 4.46
97 99 9.853921 CGTCCCATAATATAAGAACGTTTAAAC 57.146 33.333 8.35 8.35 0.00 2.01
98 100 9.044150 CCGTCCCATAATATAAGAACGTTTAAA 57.956 33.333 0.46 0.00 0.00 1.52
99 101 8.420222 TCCGTCCCATAATATAAGAACGTTTAA 58.580 33.333 0.46 0.00 0.00 1.52
100 102 7.950512 TCCGTCCCATAATATAAGAACGTTTA 58.049 34.615 0.46 0.00 0.00 2.01
101 103 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
102 104 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
103 105 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
104 106 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
105 107 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
106 108 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
107 109 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
108 110 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
109 111 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
110 112 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
111 113 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
112 114 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
113 115 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
114 116 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
115 117 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
116 118 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
117 119 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
118 120 2.378378 AATACTACTCCCTCCGTCCC 57.622 55.000 0.00 0.00 0.00 4.46
119 121 4.468713 AGTAAATACTACTCCCTCCGTCC 58.531 47.826 0.00 0.00 34.13 4.79
120 122 4.213059 CGAGTAAATACTACTCCCTCCGTC 59.787 50.000 6.39 0.00 40.48 4.79
121 123 4.133078 CGAGTAAATACTACTCCCTCCGT 58.867 47.826 6.39 0.00 40.48 4.69
122 124 4.024218 CACGAGTAAATACTACTCCCTCCG 60.024 50.000 6.39 0.00 40.48 4.63
123 125 4.261530 GCACGAGTAAATACTACTCCCTCC 60.262 50.000 6.39 0.00 40.48 4.30
124 126 4.579753 AGCACGAGTAAATACTACTCCCTC 59.420 45.833 6.39 0.00 40.48 4.30
125 127 4.534797 AGCACGAGTAAATACTACTCCCT 58.465 43.478 6.39 0.00 40.48 4.20
126 128 4.261530 GGAGCACGAGTAAATACTACTCCC 60.262 50.000 14.52 0.00 40.48 4.30
127 129 4.579753 AGGAGCACGAGTAAATACTACTCC 59.420 45.833 16.24 16.24 40.48 3.85
128 130 5.754543 AGGAGCACGAGTAAATACTACTC 57.245 43.478 0.00 2.44 40.26 2.59
129 131 5.651139 TGAAGGAGCACGAGTAAATACTACT 59.349 40.000 0.00 0.00 36.50 2.57
130 132 5.888105 TGAAGGAGCACGAGTAAATACTAC 58.112 41.667 0.00 0.00 36.50 2.73
131 133 6.710597 ATGAAGGAGCACGAGTAAATACTA 57.289 37.500 0.00 0.00 36.50 1.82
132 134 5.599999 ATGAAGGAGCACGAGTAAATACT 57.400 39.130 0.00 0.00 39.71 2.12
154 156 5.925509 AGTTACTTTTGAGTGCTCCTTGTA 58.074 37.500 0.00 0.00 0.00 2.41
194 196 5.597182 TGATCTAGCACCTCGTTACCTTTAT 59.403 40.000 0.00 0.00 0.00 1.40
196 198 3.767673 TGATCTAGCACCTCGTTACCTTT 59.232 43.478 0.00 0.00 0.00 3.11
200 202 4.839668 AGATGATCTAGCACCTCGTTAC 57.160 45.455 0.00 0.00 0.00 2.50
287 290 7.916914 AAAAGTAAGTCGGTTACAAGCATAT 57.083 32.000 10.13 0.00 43.26 1.78
418 421 1.219646 TTACTGCAACGTCGGGTTTC 58.780 50.000 0.00 0.00 36.49 2.78
422 425 2.977169 CAAAATTTACTGCAACGTCGGG 59.023 45.455 0.00 0.00 0.00 5.14
423 426 3.879427 TCAAAATTTACTGCAACGTCGG 58.121 40.909 0.00 0.00 0.00 4.79
427 430 6.559810 TGGGATATCAAAATTTACTGCAACG 58.440 36.000 4.83 0.00 0.00 4.10
436 439 8.378115 TCCAGTTTCATGGGATATCAAAATTT 57.622 30.769 4.83 0.00 41.01 1.82
533 595 3.306780 GGTGGTTTCTTGGATTCTCTCGA 60.307 47.826 0.00 0.00 0.00 4.04
534 596 3.003480 GGTGGTTTCTTGGATTCTCTCG 58.997 50.000 0.00 0.00 0.00 4.04
541 603 1.823250 GCTGGTGGTGGTTTCTTGGAT 60.823 52.381 0.00 0.00 0.00 3.41
544 606 1.463553 GGGCTGGTGGTGGTTTCTTG 61.464 60.000 0.00 0.00 0.00 3.02
625 703 0.179086 GGCAGGTGGTGGTTTTGTTG 60.179 55.000 0.00 0.00 0.00 3.33
669 749 2.204136 ATGGCAGGTGGGGACAGA 60.204 61.111 0.00 0.00 44.46 3.41
683 763 3.131478 GGTTTCGCGGGTGGATGG 61.131 66.667 6.13 0.00 0.00 3.51
872 966 1.360911 GGAGACGAGAGGATTCCGC 59.639 63.158 0.00 0.00 0.00 5.54
1009 1103 6.429078 AGATCCGTACCAAAACCTAGAAAAAC 59.571 38.462 0.00 0.00 0.00 2.43
1133 1235 3.528370 CCTGGCCTCGTAGTCCCG 61.528 72.222 3.32 0.00 0.00 5.14
1399 1529 2.293856 ACTGGACATGGTATTCTCCCCT 60.294 50.000 0.00 0.00 0.00 4.79
1495 1625 4.336280 GGCTATCCCTGTCCCAAATTATC 58.664 47.826 0.00 0.00 0.00 1.75
1529 1659 4.521639 AGTCACTGTACCAGAATGTAACGA 59.478 41.667 0.00 0.00 35.18 3.85
1544 1674 1.967066 CACTCCCTTCAGAGTCACTGT 59.033 52.381 0.00 0.00 45.38 3.55
1553 1683 1.065126 GGAATCCACCACTCCCTTCAG 60.065 57.143 0.00 0.00 0.00 3.02
1618 1748 1.621672 GGGGAGGGAGTTGAGCAGAG 61.622 65.000 0.00 0.00 0.00 3.35
1687 1817 3.119029 GGTCCACATCCATTGGTGAATTG 60.119 47.826 1.86 0.00 37.18 2.32
1720 1850 1.945387 ACTGCTCAGTGTTGTCAGTG 58.055 50.000 1.15 0.00 43.96 3.66
1746 1876 2.237143 AGCACTTTACTATCCTGCAGCA 59.763 45.455 8.66 0.00 0.00 4.41
1751 1881 5.091261 ACCTCAAGCACTTTACTATCCTG 57.909 43.478 0.00 0.00 0.00 3.86
1789 1919 5.020795 ACTTTACTCTCCTCTTCCTCCTTC 58.979 45.833 0.00 0.00 0.00 3.46
1841 1971 4.094887 CCACCTTGAAGTTGATATGTTCCG 59.905 45.833 0.00 0.00 0.00 4.30
1917 2047 2.036475 GCGGAATCTGCAGGAGATAAGA 59.964 50.000 15.13 0.00 40.89 2.10
1969 2099 0.478507 CAACCTCCCCAAGTTCTGGT 59.521 55.000 0.00 0.00 44.76 4.00
2056 2186 7.032598 ACCTAATTCCAAATCTTCCTTCTCA 57.967 36.000 0.00 0.00 0.00 3.27
2698 2828 7.562454 TCAAATCCCTGAAATAAATGAGATGCT 59.438 33.333 0.00 0.00 0.00 3.79
2934 3065 3.604582 CCAAGGAGGAGAAACAGACATC 58.395 50.000 0.00 0.00 41.22 3.06
3070 3201 6.037172 TGTCTAGCTGTTCAAACTCTGTTTTC 59.963 38.462 0.00 0.00 0.00 2.29
3399 3531 6.595716 CCCTTAATCTGTTGTACCTGAAGAAG 59.404 42.308 0.00 0.00 0.00 2.85
3819 3952 6.527023 CGTCTGGTACGCCTGATATTTTATAG 59.473 42.308 0.00 0.00 46.10 1.31
3969 4103 3.392616 ACCTCACTGATTCAGGTTGAAGT 59.607 43.478 17.66 9.91 40.05 3.01
4119 4253 2.094182 TCGGAGTGCTAATCCTGTGAAC 60.094 50.000 0.00 0.00 34.45 3.18
4161 4295 1.689273 ACGATGGAGGCAGGTTAGATC 59.311 52.381 0.00 0.00 0.00 2.75
4218 4352 3.935818 TCCAAAGGTGAAACAGGTGTA 57.064 42.857 0.00 0.00 39.98 2.90
4331 4465 4.141274 AGAGCACTATAGGAGCAGAGAGAA 60.141 45.833 18.07 0.00 0.00 2.87
4656 4826 4.955925 TTTGCACTTTTCTTCGTTCTCA 57.044 36.364 0.00 0.00 0.00 3.27
5018 5307 1.895131 CATGGGCAAGTAACCAGCTTT 59.105 47.619 0.00 0.00 40.67 3.51
5047 5336 7.927683 TCAAGAAGAGATATCCCTGATCTTT 57.072 36.000 0.00 0.00 33.71 2.52
5174 5463 8.816640 AAAAGTAGTTATCACCAAATGCAAAG 57.183 30.769 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.