Multiple sequence alignment - TraesCS5D01G376500

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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 TraesCS5D01G376500 chr5D 100.000 4499 0 0 1 4499 449024783 449029281 0.000000e+00 8309.0
1 TraesCS5D01G376500 chr5A 94.281 4354 126 45 199 4490 567910989 567915281 0.000000e+00 6547.0
2 TraesCS5D01G376500 chr5A 84.545 1417 126 57 3114 4484 567990092 567991461 0.000000e+00 1317.0
3 TraesCS5D01G376500 chr5A 89.206 945 66 16 2201 3124 567964131 567965060 0.000000e+00 1147.0
4 TraesCS5D01G376500 chr5A 83.761 585 70 18 1149 1711 567963034 567963615 8.570000e-147 531.0
5 TraesCS5D01G376500 chr5B 90.386 3547 183 62 611 4027 548998031 548994513 0.000000e+00 4516.0
6 TraesCS5D01G376500 chr5B 87.931 58 5 2 309 366 395712653 395712598 2.900000e-07 67.6
7 TraesCS5D01G376500 chrUn 100.000 421 0 0 2339 2759 476814555 476814135 0.000000e+00 778.0
8 TraesCS5D01G376500 chr1B 80.612 98 15 4 272 366 13256397 13256493 6.240000e-09 73.1
9 TraesCS5D01G376500 chr3B 85.246 61 8 1 306 366 245374687 245374746 1.350000e-05 62.1
10 TraesCS5D01G376500 chr4D 100.000 29 0 0 338 366 88083666 88083638 2.000000e-03 54.7


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 TraesCS5D01G376500 chr5D 449024783 449029281 4498 False 8309 8309 100.0000 1 4499 1 chr5D.!!$F1 4498
1 TraesCS5D01G376500 chr5A 567910989 567915281 4292 False 6547 6547 94.2810 199 4490 1 chr5A.!!$F1 4291
2 TraesCS5D01G376500 chr5A 567990092 567991461 1369 False 1317 1317 84.5450 3114 4484 1 chr5A.!!$F2 1370
3 TraesCS5D01G376500 chr5A 567963034 567965060 2026 False 839 1147 86.4835 1149 3124 2 chr5A.!!$F3 1975
4 TraesCS5D01G376500 chr5B 548994513 548998031 3518 True 4516 4516 90.3860 611 4027 1 chr5B.!!$R2 3416

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
235 236 0.179015 TGCTTCGGGTTGCTGGTTTA 60.179 50.000 0.0 0.0 0.0 2.01 F
236 237 0.240145 GCTTCGGGTTGCTGGTTTAC 59.760 55.000 0.0 0.0 0.0 2.01 F
788 817 0.252103 TCTAGGCCCTGTTCGACCTT 60.252 55.000 0.0 0.0 33.6 3.50 F
1466 1529 0.037326 TTCTCCGGTGTCATCAGTGC 60.037 55.000 0.0 0.0 0.0 4.40 F
2063 2179 1.745653 CTCACCACTATCACTCGCTGA 59.254 52.381 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1132 1189 0.685097 TTCTGGGAGAAACTGGACCG 59.315 55.000 0.0 0.0 29.99 4.79 R
1216 1277 1.067295 TCCCAGCATCTGTTTCAGGT 58.933 50.000 0.0 0.0 31.51 4.00 R
2188 2305 6.825284 TGTAACAGCATTGAACATTTGTTG 57.175 33.333 0.0 0.0 38.56 3.33 R
3068 3244 6.364165 CAGAGTTGCATGGAAATTACAAACAG 59.636 38.462 0.0 0.0 0.00 3.16 R
3637 3851 8.375506 ACTATCTTCTGTCATGGTGTTTCTTTA 58.624 33.333 0.0 0.0 0.00 1.85 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
22 23 5.481200 CACATATTTGCTCCTGTGAGAAG 57.519 43.478 0.00 0.00 41.11 2.85
23 24 3.944015 ACATATTTGCTCCTGTGAGAAGC 59.056 43.478 0.00 0.00 41.42 3.86
24 25 2.574006 ATTTGCTCCTGTGAGAAGCA 57.426 45.000 0.00 0.00 41.42 3.91
32 33 4.456806 GTGAGAAGCACAACCGGT 57.543 55.556 0.00 0.00 46.91 5.28
47 48 2.435059 GGTGCTTCCGTCTGAGGC 60.435 66.667 0.00 0.00 45.81 4.70
50 51 2.343758 GCTTCCGTCTGAGGCACA 59.656 61.111 0.00 0.00 45.00 4.57
51 52 2.029844 GCTTCCGTCTGAGGCACAC 61.030 63.158 0.00 0.00 45.00 3.82
52 53 1.734477 CTTCCGTCTGAGGCACACG 60.734 63.158 0.00 0.00 0.00 4.49
53 54 2.421877 CTTCCGTCTGAGGCACACGT 62.422 60.000 0.00 0.00 0.00 4.49
54 55 2.023414 TTCCGTCTGAGGCACACGTT 62.023 55.000 0.00 0.00 0.00 3.99
55 56 2.310233 CCGTCTGAGGCACACGTTG 61.310 63.158 0.00 0.00 0.00 4.10
56 57 1.591594 CGTCTGAGGCACACGTTGT 60.592 57.895 0.00 0.00 0.00 3.32
64 65 4.996113 CACACGTTGTGCTTCCAC 57.004 55.556 5.42 0.00 41.89 4.02
65 66 1.011242 CACACGTTGTGCTTCCACG 60.011 57.895 5.42 5.05 45.04 4.94
66 67 1.153529 ACACGTTGTGCTTCCACGA 60.154 52.632 11.40 0.00 45.04 4.35
67 68 1.151777 ACACGTTGTGCTTCCACGAG 61.152 55.000 11.40 7.27 45.04 4.18
68 69 0.874175 CACGTTGTGCTTCCACGAGA 60.874 55.000 11.40 0.00 45.04 4.04
69 70 0.179094 ACGTTGTGCTTCCACGAGAA 60.179 50.000 11.40 0.00 45.04 2.87
76 77 2.157421 CTTCCACGAGAAGCACAGC 58.843 57.895 6.95 0.00 45.38 4.40
77 78 0.320247 CTTCCACGAGAAGCACAGCT 60.320 55.000 6.95 0.00 45.38 4.24
78 79 0.966179 TTCCACGAGAAGCACAGCTA 59.034 50.000 0.00 0.00 38.25 3.32
79 80 1.186200 TCCACGAGAAGCACAGCTAT 58.814 50.000 0.00 0.00 38.25 2.97
80 81 2.375146 TCCACGAGAAGCACAGCTATA 58.625 47.619 0.00 0.00 38.25 1.31
81 82 2.758423 TCCACGAGAAGCACAGCTATAA 59.242 45.455 0.00 0.00 38.25 0.98
82 83 3.119291 CCACGAGAAGCACAGCTATAAG 58.881 50.000 0.00 0.00 38.25 1.73
83 84 3.181486 CCACGAGAAGCACAGCTATAAGA 60.181 47.826 0.00 0.00 38.25 2.10
84 85 4.424626 CACGAGAAGCACAGCTATAAGAA 58.575 43.478 0.00 0.00 38.25 2.52
85 86 4.864806 CACGAGAAGCACAGCTATAAGAAA 59.135 41.667 0.00 0.00 38.25 2.52
86 87 5.348724 CACGAGAAGCACAGCTATAAGAAAA 59.651 40.000 0.00 0.00 38.25 2.29
87 88 5.932303 ACGAGAAGCACAGCTATAAGAAAAA 59.068 36.000 0.00 0.00 38.25 1.94
108 109 4.500603 AAGACACAGTTGTACTCCTACG 57.499 45.455 0.00 0.00 35.47 3.51
109 110 3.748083 AGACACAGTTGTACTCCTACGA 58.252 45.455 0.00 0.00 35.47 3.43
110 111 4.139786 AGACACAGTTGTACTCCTACGAA 58.860 43.478 0.00 0.00 35.47 3.85
111 112 4.581824 AGACACAGTTGTACTCCTACGAAA 59.418 41.667 0.00 0.00 35.47 3.46
112 113 5.068198 AGACACAGTTGTACTCCTACGAAAA 59.932 40.000 0.00 0.00 35.47 2.29
113 114 5.663456 ACACAGTTGTACTCCTACGAAAAA 58.337 37.500 0.00 0.00 32.60 1.94
133 134 5.582689 AAAAGGAAAGGCATAGTATGTGC 57.417 39.130 11.73 0.00 41.78 4.57
134 135 4.510167 AAGGAAAGGCATAGTATGTGCT 57.490 40.909 11.73 0.00 42.16 4.40
135 136 4.510167 AGGAAAGGCATAGTATGTGCTT 57.490 40.909 11.73 2.83 42.16 3.91
136 137 4.860022 AGGAAAGGCATAGTATGTGCTTT 58.140 39.130 11.73 0.00 42.68 3.51
137 138 4.884164 AGGAAAGGCATAGTATGTGCTTTC 59.116 41.667 11.73 10.44 40.42 2.62
138 139 4.260784 GGAAAGGCATAGTATGTGCTTTCG 60.261 45.833 11.73 0.00 40.42 3.46
139 140 3.543680 AGGCATAGTATGTGCTTTCGT 57.456 42.857 11.73 0.00 42.16 3.85
140 141 3.198068 AGGCATAGTATGTGCTTTCGTG 58.802 45.455 11.73 0.00 42.16 4.35
141 142 3.118775 AGGCATAGTATGTGCTTTCGTGA 60.119 43.478 11.73 0.00 42.16 4.35
142 143 3.246226 GGCATAGTATGTGCTTTCGTGAG 59.754 47.826 11.73 0.00 42.16 3.51
143 144 4.112634 GCATAGTATGTGCTTTCGTGAGA 58.887 43.478 11.73 0.00 39.45 3.27
144 145 4.566759 GCATAGTATGTGCTTTCGTGAGAA 59.433 41.667 11.73 0.00 42.68 2.87
145 146 5.276584 GCATAGTATGTGCTTTCGTGAGAAG 60.277 44.000 11.73 0.00 41.17 2.85
146 147 8.612903 GCATAGTATGTGCTTTCGTGAGAAGC 62.613 46.154 11.73 2.09 41.17 3.86
155 156 4.456806 GTGAGAAGCACAACCCGT 57.543 55.556 0.00 0.00 46.91 5.28
163 164 4.025401 CACAACCCGTGCTTCCGC 62.025 66.667 0.00 0.00 39.19 5.54
235 236 0.179015 TGCTTCGGGTTGCTGGTTTA 60.179 50.000 0.00 0.00 0.00 2.01
236 237 0.240145 GCTTCGGGTTGCTGGTTTAC 59.760 55.000 0.00 0.00 0.00 2.01
237 238 0.515564 CTTCGGGTTGCTGGTTTACG 59.484 55.000 0.00 0.00 0.00 3.18
238 239 0.885596 TTCGGGTTGCTGGTTTACGG 60.886 55.000 0.00 0.00 0.00 4.02
239 240 1.598685 CGGGTTGCTGGTTTACGGT 60.599 57.895 0.00 0.00 0.00 4.83
240 241 0.320596 CGGGTTGCTGGTTTACGGTA 60.321 55.000 0.00 0.00 0.00 4.02
241 242 1.676615 CGGGTTGCTGGTTTACGGTAT 60.677 52.381 0.00 0.00 0.00 2.73
243 244 2.421073 GGGTTGCTGGTTTACGGTATTC 59.579 50.000 0.00 0.00 0.00 1.75
244 245 3.340928 GGTTGCTGGTTTACGGTATTCT 58.659 45.455 0.00 0.00 0.00 2.40
245 246 3.754850 GGTTGCTGGTTTACGGTATTCTT 59.245 43.478 0.00 0.00 0.00 2.52
368 381 5.595952 ACATGGGATCTAATTTTGAAGAGCC 59.404 40.000 2.20 2.20 45.58 4.70
371 384 4.200092 GGATCTAATTTTGAAGAGCCCGT 58.800 43.478 0.00 0.00 41.48 5.28
387 400 1.667724 CCCGTCATGAGATGCAGTTTC 59.332 52.381 0.00 0.00 0.00 2.78
397 419 8.358895 TCATGAGATGCAGTTTCAAAATGTTTA 58.641 29.630 0.00 0.00 0.00 2.01
401 423 9.853921 GAGATGCAGTTTCAAAATGTTTAAAAG 57.146 29.630 0.00 0.00 0.00 2.27
775 804 2.030262 CGCTCATGGGCTCTAGGC 59.970 66.667 17.16 0.00 40.90 3.93
784 813 3.617368 GCTCTAGGCCCTGTTCGA 58.383 61.111 0.00 0.00 34.27 3.71
787 816 0.684805 CTCTAGGCCCTGTTCGACCT 60.685 60.000 0.00 0.00 36.27 3.85
788 817 0.252103 TCTAGGCCCTGTTCGACCTT 60.252 55.000 0.00 0.00 33.60 3.50
789 818 1.006281 TCTAGGCCCTGTTCGACCTTA 59.994 52.381 0.00 0.00 33.60 2.69
791 820 0.544595 AGGCCCTGTTCGACCTTAGT 60.545 55.000 0.00 0.00 0.00 2.24
793 822 1.136500 GGCCCTGTTCGACCTTAGTAG 59.864 57.143 0.00 0.00 0.00 2.57
795 824 3.019564 GCCCTGTTCGACCTTAGTAGTA 58.980 50.000 0.00 0.00 0.00 1.82
800 837 3.065786 TGTTCGACCTTAGTAGTATGCGG 59.934 47.826 0.00 0.00 0.00 5.69
847 884 2.055042 CCAGTCACCTCCTCCTCCG 61.055 68.421 0.00 0.00 0.00 4.63
918 960 0.456312 CTCTGCCACCGAAGTCGTAC 60.456 60.000 0.00 0.00 37.74 3.67
1077 1131 4.735132 CTCGCGCGGTTCCTTGGA 62.735 66.667 31.69 5.83 0.00 3.53
1172 1229 6.166982 AGAAATGTTTCTGCTGTACTACTCC 58.833 40.000 7.18 0.00 45.27 3.85
1181 1238 5.104485 TCTGCTGTACTACTCCTGTGAGATA 60.104 44.000 0.00 0.00 41.42 1.98
1216 1277 1.272092 CCCTGTTGGCTTCCTGAATGA 60.272 52.381 0.00 0.00 0.00 2.57
1223 1284 2.108075 TGGCTTCCTGAATGACCTGAAA 59.892 45.455 0.00 0.00 0.00 2.69
1466 1529 0.037326 TTCTCCGGTGTCATCAGTGC 60.037 55.000 0.00 0.00 0.00 4.40
1908 2018 4.955450 TGGTAGCTGAATGGCAAATATTGT 59.045 37.500 0.00 0.00 34.17 2.71
2026 2142 3.423539 CAGGATGGACAGGTCAAGAAA 57.576 47.619 1.41 0.00 0.00 2.52
2063 2179 1.745653 CTCACCACTATCACTCGCTGA 59.254 52.381 0.00 0.00 0.00 4.26
2288 2443 6.309737 ACCGACTGACTGTATTTCGTAATTTC 59.690 38.462 0.00 0.00 0.00 2.17
3068 3244 6.745116 ACCTTGCTTTATTTTTACTCCACAC 58.255 36.000 0.00 0.00 0.00 3.82
3274 3461 6.191657 TCATATCCAGTGGTGATAGCAAAT 57.808 37.500 9.54 0.00 0.00 2.32
3637 3851 4.932146 ACTGTGAACTTGCGCTTATTTTT 58.068 34.783 9.73 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.943381 TGCTTCTCACAGGAGCAAATATG 59.057 43.478 3.87 0.00 41.13 1.78
5 6 2.157738 GTGCTTCTCACAGGAGCAAAT 58.842 47.619 8.12 0.00 44.98 2.32
6 7 1.597742 GTGCTTCTCACAGGAGCAAA 58.402 50.000 8.12 0.00 44.98 3.68
7 8 3.312404 GTGCTTCTCACAGGAGCAA 57.688 52.632 8.12 0.00 44.98 3.91
15 16 1.941812 CACCGGTTGTGCTTCTCAC 59.058 57.895 2.97 0.00 45.82 3.51
16 17 4.454948 CACCGGTTGTGCTTCTCA 57.545 55.556 2.97 0.00 38.34 3.27
30 31 2.435059 GCCTCAGACGGAAGCACC 60.435 66.667 0.00 0.00 32.98 5.01
31 32 2.343758 TGCCTCAGACGGAAGCAC 59.656 61.111 0.00 0.00 38.03 4.40
32 33 2.343758 GTGCCTCAGACGGAAGCA 59.656 61.111 0.00 0.00 40.60 3.91
33 34 2.029844 GTGTGCCTCAGACGGAAGC 61.030 63.158 0.00 0.00 33.37 3.86
34 35 1.734477 CGTGTGCCTCAGACGGAAG 60.734 63.158 8.37 0.00 45.21 3.46
35 36 2.338620 CGTGTGCCTCAGACGGAA 59.661 61.111 8.37 0.00 45.21 4.30
39 40 1.934463 CACAACGTGTGCCTCAGAC 59.066 57.895 5.42 0.00 41.89 3.51
40 41 4.436515 CACAACGTGTGCCTCAGA 57.563 55.556 5.42 0.00 41.89 3.27
48 49 1.151777 CTCGTGGAAGCACAACGTGT 61.152 55.000 9.87 0.00 35.75 4.49
49 50 0.874175 TCTCGTGGAAGCACAACGTG 60.874 55.000 9.87 8.16 36.51 4.49
50 51 0.179094 TTCTCGTGGAAGCACAACGT 60.179 50.000 9.87 0.00 0.00 3.99
51 52 0.508641 CTTCTCGTGGAAGCACAACG 59.491 55.000 4.78 4.78 43.88 4.10
59 60 0.966179 TAGCTGTGCTTCTCGTGGAA 59.034 50.000 0.00 0.00 40.44 3.53
60 61 1.186200 ATAGCTGTGCTTCTCGTGGA 58.814 50.000 0.00 0.00 40.44 4.02
61 62 2.871182 TATAGCTGTGCTTCTCGTGG 57.129 50.000 0.00 0.00 40.44 4.94
62 63 4.033990 TCTTATAGCTGTGCTTCTCGTG 57.966 45.455 0.00 0.00 40.44 4.35
63 64 4.720649 TTCTTATAGCTGTGCTTCTCGT 57.279 40.909 0.00 0.00 40.44 4.18
64 65 6.408858 TTTTTCTTATAGCTGTGCTTCTCG 57.591 37.500 0.00 0.00 40.44 4.04
84 85 5.751990 CGTAGGAGTACAACTGTGTCTTTTT 59.248 40.000 0.00 0.00 39.30 1.94
85 86 5.068198 TCGTAGGAGTACAACTGTGTCTTTT 59.932 40.000 0.00 0.00 39.30 2.27
86 87 4.581824 TCGTAGGAGTACAACTGTGTCTTT 59.418 41.667 0.00 0.00 39.30 2.52
87 88 4.139786 TCGTAGGAGTACAACTGTGTCTT 58.860 43.478 0.00 0.00 39.30 3.01
88 89 3.748083 TCGTAGGAGTACAACTGTGTCT 58.252 45.455 0.00 0.00 39.30 3.41
89 90 4.494350 TTCGTAGGAGTACAACTGTGTC 57.506 45.455 0.00 0.00 39.30 3.67
90 91 4.924305 TTTCGTAGGAGTACAACTGTGT 57.076 40.909 0.00 0.00 42.09 3.72
110 111 5.716703 AGCACATACTATGCCTTTCCTTTTT 59.283 36.000 0.00 0.00 44.53 1.94
111 112 5.264395 AGCACATACTATGCCTTTCCTTTT 58.736 37.500 0.00 0.00 44.53 2.27
112 113 4.860022 AGCACATACTATGCCTTTCCTTT 58.140 39.130 0.00 0.00 44.53 3.11
113 114 4.510167 AGCACATACTATGCCTTTCCTT 57.490 40.909 0.00 0.00 44.53 3.36
114 115 4.510167 AAGCACATACTATGCCTTTCCT 57.490 40.909 0.00 0.00 44.53 3.36
115 116 4.260784 CGAAAGCACATACTATGCCTTTCC 60.261 45.833 22.22 13.20 44.53 3.13
116 117 4.332819 ACGAAAGCACATACTATGCCTTTC 59.667 41.667 20.37 20.37 44.53 2.62
117 118 4.094887 CACGAAAGCACATACTATGCCTTT 59.905 41.667 12.00 12.00 44.53 3.11
118 119 3.623060 CACGAAAGCACATACTATGCCTT 59.377 43.478 0.00 0.00 44.53 4.35
119 120 3.118775 TCACGAAAGCACATACTATGCCT 60.119 43.478 0.00 0.00 44.53 4.75
120 121 3.194861 TCACGAAAGCACATACTATGCC 58.805 45.455 0.00 0.00 44.53 4.40
121 122 4.112634 TCTCACGAAAGCACATACTATGC 58.887 43.478 0.00 0.00 43.74 3.14
122 123 5.276584 GCTTCTCACGAAAGCACATACTATG 60.277 44.000 3.12 0.00 0.00 2.23
123 124 4.806247 GCTTCTCACGAAAGCACATACTAT 59.194 41.667 3.12 0.00 0.00 2.12
124 125 4.174009 GCTTCTCACGAAAGCACATACTA 58.826 43.478 3.12 0.00 0.00 1.82
125 126 2.996621 GCTTCTCACGAAAGCACATACT 59.003 45.455 3.12 0.00 0.00 2.12
126 127 2.736721 TGCTTCTCACGAAAGCACATAC 59.263 45.455 6.45 0.00 32.35 2.39
127 128 2.736721 GTGCTTCTCACGAAAGCACATA 59.263 45.455 27.15 0.00 44.47 2.29
128 129 1.532868 GTGCTTCTCACGAAAGCACAT 59.467 47.619 27.15 0.00 44.47 3.21
129 130 0.937304 GTGCTTCTCACGAAAGCACA 59.063 50.000 27.15 0.83 44.47 4.57
130 131 3.736581 GTGCTTCTCACGAAAGCAC 57.263 52.632 20.97 20.97 41.88 4.40
138 139 1.941812 CACGGGTTGTGCTTCTCAC 59.058 57.895 0.00 0.00 42.70 3.51
139 140 4.454948 CACGGGTTGTGCTTCTCA 57.545 55.556 0.00 0.00 42.70 3.27
200 201 2.830285 GCACGGTTGCGGTCACTTT 61.830 57.895 0.00 0.00 39.50 2.66
215 216 1.734388 AAACCAGCAACCCGAAGCAC 61.734 55.000 0.00 0.00 0.00 4.40
225 226 6.394025 AAAAAGAATACCGTAAACCAGCAA 57.606 33.333 0.00 0.00 0.00 3.91
324 337 8.512138 CCCATGTTAATAAGTTTCGAAGAACTT 58.488 33.333 16.99 16.99 45.90 2.66
330 343 9.893634 TTAGATCCCATGTTAATAAGTTTCGAA 57.106 29.630 0.00 0.00 0.00 3.71
345 358 5.010415 GGGCTCTTCAAAATTAGATCCCATG 59.990 44.000 9.19 0.00 43.34 3.66
368 381 2.349590 TGAAACTGCATCTCATGACGG 58.650 47.619 0.00 0.00 0.00 4.79
371 384 6.335471 ACATTTTGAAACTGCATCTCATGA 57.665 33.333 0.00 0.00 0.00 3.07
387 400 9.932699 TGATGTGAATTGCTTTTAAACATTTTG 57.067 25.926 0.00 0.00 0.00 2.44
698 724 6.182507 ACTACTCGGATCAAGATAGAGAGT 57.817 41.667 16.75 15.57 40.16 3.24
775 804 4.499357 GCATACTACTAAGGTCGAACAGGG 60.499 50.000 1.87 0.00 0.00 4.45
778 807 3.065786 CCGCATACTACTAAGGTCGAACA 59.934 47.826 1.87 0.00 0.00 3.18
779 808 3.065925 ACCGCATACTACTAAGGTCGAAC 59.934 47.826 0.00 0.00 0.00 3.95
781 810 2.923121 ACCGCATACTACTAAGGTCGA 58.077 47.619 0.00 0.00 0.00 4.20
782 811 3.369385 CAACCGCATACTACTAAGGTCG 58.631 50.000 0.00 0.00 0.00 4.79
784 813 2.480759 CGCAACCGCATACTACTAAGGT 60.481 50.000 0.00 0.00 38.40 3.50
835 872 3.641925 GACGGACGGAGGAGGAGGT 62.642 68.421 0.00 0.00 0.00 3.85
838 875 4.790962 CGGACGGACGGAGGAGGA 62.791 72.222 0.00 0.00 0.00 3.71
1090 1144 1.270147 GCTATTACCGGATGAAGCGGT 60.270 52.381 9.46 0.00 39.54 5.68
1127 1184 1.446272 GAGAAACTGGACCGAGCCG 60.446 63.158 0.00 0.00 0.00 5.52
1128 1185 1.079057 GGAGAAACTGGACCGAGCC 60.079 63.158 0.00 0.00 0.00 4.70
1132 1189 0.685097 TTCTGGGAGAAACTGGACCG 59.315 55.000 0.00 0.00 29.99 4.79
1136 1193 4.829492 AGAAACATTTCTGGGAGAAACTGG 59.171 41.667 6.07 0.00 45.83 4.00
1172 1229 7.142021 GGTCATACACACTACATATCTCACAG 58.858 42.308 0.00 0.00 0.00 3.66
1181 1238 4.323485 CCAACAGGGTCATACACACTACAT 60.323 45.833 0.00 0.00 36.13 2.29
1216 1277 1.067295 TCCCAGCATCTGTTTCAGGT 58.933 50.000 0.00 0.00 31.51 4.00
1223 1284 4.457496 CGCCGTCCCAGCATCTGT 62.457 66.667 0.00 0.00 0.00 3.41
1418 1479 2.187946 GATCCTGGTGGACTGCCG 59.812 66.667 0.00 0.00 46.51 5.69
1908 2018 9.906660 CCTATTGTTTGACAGCTGTTTATAAAA 57.093 29.630 22.65 13.42 0.00 1.52
2063 2179 8.090214 CCAACAGTTCACCATGAATTTAATCTT 58.910 33.333 0.00 0.00 38.79 2.40
2188 2305 6.825284 TGTAACAGCATTGAACATTTGTTG 57.175 33.333 0.00 0.00 38.56 3.33
3068 3244 6.364165 CAGAGTTGCATGGAAATTACAAACAG 59.636 38.462 0.00 0.00 0.00 3.16
3637 3851 8.375506 ACTATCTTCTGTCATGGTGTTTCTTTA 58.624 33.333 0.00 0.00 0.00 1.85
3955 4208 9.772973 CCACACTAAATAATTAGCTACATGGTA 57.227 33.333 0.00 0.00 41.92 3.25
4091 4363 6.993902 TCCAAAACGGTTTCTTACATAAGACT 59.006 34.615 6.57 0.00 37.80 3.24


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

AutoCloner maintained by Alex Coulton.