Multiple sequence alignment - TraesCS5A01G314700

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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 TraesCS5A01G314700 chr5A 100.000 3322 0 0 1 3322 525080362 525077041 0.000000e+00 6135.0
1 TraesCS5A01G314700 chr5A 82.222 225 37 2 1082 1303 453877138 453876914 1.220000e-44 191.0
2 TraesCS5A01G314700 chr5D 92.789 3162 111 40 201 3322 413059872 413056788 0.000000e+00 4468.0
3 TraesCS5A01G314700 chr5D 81.897 232 39 2 1082 1310 352219222 352219453 3.380000e-45 193.0
4 TraesCS5A01G314700 chr5D 78.281 221 41 7 1094 1312 558247775 558247560 5.780000e-28 135.0
5 TraesCS5A01G314700 chr5B 92.783 3090 150 40 102 3148 497758970 497755911 0.000000e+00 4403.0
6 TraesCS5A01G314700 chr5B 82.222 225 37 2 1082 1303 416851158 416850934 1.220000e-44 191.0
7 TraesCS5A01G314700 chr2B 83.590 195 30 2 1113 1306 146442441 146442248 7.320000e-42 182.0
8 TraesCS5A01G314700 chr2A 83.590 195 30 2 1113 1306 92318255 92318062 7.320000e-42 182.0
9 TraesCS5A01G314700 chr1B 82.812 192 27 6 1114 1302 595176892 595177080 2.050000e-37 167.0
10 TraesCS5A01G314700 chr1B 85.484 62 8 1 24 84 538430286 538430225 2.770000e-06 63.9
11 TraesCS5A01G314700 chr1A 82.812 192 27 6 1114 1302 535312154 535312342 2.050000e-37 167.0
12 TraesCS5A01G314700 chr1D 81.152 191 32 4 1114 1302 439022280 439022468 2.060000e-32 150.0
13 TraesCS5A01G314700 chr4A 91.579 95 4 4 1 92 430224294 430224387 9.670000e-26 128.0
14 TraesCS5A01G314700 chr4A 91.489 94 5 3 1 92 430260501 430260593 3.480000e-25 126.0
15 TraesCS5A01G314700 chr7D 89.109 101 11 0 1430 1530 256444267 256444167 3.480000e-25 126.0
16 TraesCS5A01G314700 chr7B 89.109 101 11 0 1430 1530 235449833 235449733 3.480000e-25 126.0
17 TraesCS5A01G314700 chr7A 89.109 101 11 0 1430 1530 276185855 276185755 3.480000e-25 126.0
18 TraesCS5A01G314700 chr4B 88.235 51 5 1 34 83 150741099 150741049 3.580000e-05 60.2


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 TraesCS5A01G314700 chr5A 525077041 525080362 3321 True 6135 6135 100.000 1 3322 1 chr5A.!!$R2 3321
1 TraesCS5A01G314700 chr5D 413056788 413059872 3084 True 4468 4468 92.789 201 3322 1 chr5D.!!$R1 3121
2 TraesCS5A01G314700 chr5B 497755911 497758970 3059 True 4403 4403 92.783 102 3148 1 chr5B.!!$R2 3046

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
78 79 0.238289 CAACGCACGAGCATTTTCCT 59.762 50.0 5.50 0.00 42.27 3.36 F
871 882 0.389391 AGTCTCATAATCCCGCGTGG 59.611 55.0 8.42 8.42 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 1949 1.006102 CGACTCACCCGAGCAGTTT 60.006 57.895 0.0 0.0 43.66 2.66 R
2862 2911 0.040204 ATCCAAACCAAGCCCCTGAG 59.960 55.000 0.0 0.0 0.00 3.35 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
50 51 7.867445 GGTGTTGACCACTAAAATTTGTATG 57.133 36.000 0.00 0.00 43.94 2.39
51 52 6.364976 GGTGTTGACCACTAAAATTTGTATGC 59.635 38.462 0.00 0.00 43.94 3.14
52 53 6.364976 GTGTTGACCACTAAAATTTGTATGCC 59.635 38.462 0.00 0.00 41.11 4.40
53 54 5.652994 TGACCACTAAAATTTGTATGCCC 57.347 39.130 0.00 0.00 0.00 5.36
54 55 4.464597 TGACCACTAAAATTTGTATGCCCC 59.535 41.667 0.00 0.00 0.00 5.80
55 56 3.445805 ACCACTAAAATTTGTATGCCCCG 59.554 43.478 0.00 0.00 0.00 5.73
56 57 3.445805 CCACTAAAATTTGTATGCCCCGT 59.554 43.478 0.00 0.00 0.00 5.28
57 58 4.081917 CCACTAAAATTTGTATGCCCCGTT 60.082 41.667 0.00 0.00 0.00 4.44
58 59 4.862018 CACTAAAATTTGTATGCCCCGTTG 59.138 41.667 0.00 0.00 0.00 4.10
59 60 2.378445 AAATTTGTATGCCCCGTTGC 57.622 45.000 0.00 0.00 0.00 4.17
60 61 1.261480 AATTTGTATGCCCCGTTGCA 58.739 45.000 0.00 0.00 46.94 4.08
61 62 1.261480 ATTTGTATGCCCCGTTGCAA 58.739 45.000 0.00 0.00 45.84 4.08
62 63 0.315568 TTTGTATGCCCCGTTGCAAC 59.684 50.000 19.89 19.89 45.84 4.17
71 72 4.292208 CGTTGCAACGCACGAGCA 62.292 61.111 35.89 9.96 46.06 4.26
72 73 2.252260 GTTGCAACGCACGAGCAT 59.748 55.556 14.90 0.00 38.71 3.79
73 74 1.370414 GTTGCAACGCACGAGCATT 60.370 52.632 14.90 0.00 38.71 3.56
74 75 0.934436 GTTGCAACGCACGAGCATTT 60.934 50.000 14.90 0.00 38.71 2.32
75 76 0.248825 TTGCAACGCACGAGCATTTT 60.249 45.000 13.57 0.00 38.71 1.82
76 77 0.660005 TGCAACGCACGAGCATTTTC 60.660 50.000 5.50 0.00 42.27 2.29
77 78 1.337110 GCAACGCACGAGCATTTTCC 61.337 55.000 5.50 0.00 42.27 3.13
78 79 0.238289 CAACGCACGAGCATTTTCCT 59.762 50.000 5.50 0.00 42.27 3.36
79 80 1.463056 CAACGCACGAGCATTTTCCTA 59.537 47.619 5.50 0.00 42.27 2.94
80 81 1.359848 ACGCACGAGCATTTTCCTAG 58.640 50.000 5.50 0.00 42.27 3.02
81 82 1.337823 ACGCACGAGCATTTTCCTAGT 60.338 47.619 5.50 0.00 42.27 2.57
82 83 2.094390 ACGCACGAGCATTTTCCTAGTA 60.094 45.455 5.50 0.00 42.27 1.82
83 84 2.927477 CGCACGAGCATTTTCCTAGTAA 59.073 45.455 5.50 0.00 42.27 2.24
84 85 3.369756 CGCACGAGCATTTTCCTAGTAAA 59.630 43.478 5.50 0.00 42.27 2.01
85 86 4.142988 CGCACGAGCATTTTCCTAGTAAAA 60.143 41.667 5.50 0.00 42.27 1.52
86 87 5.447279 CGCACGAGCATTTTCCTAGTAAAAT 60.447 40.000 5.50 0.45 42.27 1.82
87 88 5.965918 GCACGAGCATTTTCCTAGTAAAATC 59.034 40.000 3.22 0.57 37.03 2.17
88 89 6.183360 GCACGAGCATTTTCCTAGTAAAATCT 60.183 38.462 3.22 4.68 37.03 2.40
89 90 7.011109 GCACGAGCATTTTCCTAGTAAAATCTA 59.989 37.037 3.22 0.00 37.03 1.98
90 91 9.046296 CACGAGCATTTTCCTAGTAAAATCTAT 57.954 33.333 3.22 0.00 37.03 1.98
154 155 9.114952 TCATTTATTTTACATAATCCGCACTGA 57.885 29.630 0.00 0.00 0.00 3.41
160 161 6.603237 TTACATAATCCGCACTGAAATCTG 57.397 37.500 0.00 0.00 0.00 2.90
161 162 3.313526 ACATAATCCGCACTGAAATCTGC 59.686 43.478 0.00 0.00 0.00 4.26
166 167 2.030893 TCCGCACTGAAATCTGCAAAAG 60.031 45.455 0.00 0.00 32.57 2.27
169 170 3.311966 GCACTGAAATCTGCAAAAGGAC 58.688 45.455 0.00 0.00 33.31 3.85
183 186 5.596361 TGCAAAAGGACTTGTATTCAGGAAA 59.404 36.000 0.00 0.00 0.00 3.13
184 187 6.097554 TGCAAAAGGACTTGTATTCAGGAAAA 59.902 34.615 0.00 0.00 0.00 2.29
197 200 6.704056 ATTCAGGAAAAGAAGGGAGTAGAA 57.296 37.500 0.00 0.00 0.00 2.10
202 205 6.428465 CAGGAAAAGAAGGGAGTAGAACTTTC 59.572 42.308 0.00 0.00 0.00 2.62
237 240 7.895759 ACTGACAAAAATAGCACAAATACCAT 58.104 30.769 0.00 0.00 0.00 3.55
244 247 9.638239 AAAAATAGCACAAATACCATGTACAAG 57.362 29.630 0.00 0.00 0.00 3.16
256 259 9.770097 AATACCATGTACAAGTATCAGAAGATG 57.230 33.333 17.54 1.01 35.67 2.90
287 290 2.565391 TCTTTCGAATGGTAGGCTGACA 59.435 45.455 10.78 0.00 0.00 3.58
353 363 5.578005 TCTTCGAATAGTAGGGTGACAAG 57.422 43.478 0.00 0.00 0.00 3.16
358 368 6.761312 TCGAATAGTAGGGTGACAAGAAAAA 58.239 36.000 0.00 0.00 0.00 1.94
384 394 0.810031 ATACCAAGCATCCGACGCAC 60.810 55.000 0.00 0.00 0.00 5.34
501 511 1.539157 CTGAACCTTCCAGAAAGCCC 58.461 55.000 0.00 0.00 33.65 5.19
735 746 2.027024 GAGTGGTGTGCGTCGTGA 59.973 61.111 0.00 0.00 0.00 4.35
746 757 4.081030 GTCGTGACGCGGTCGAGA 62.081 66.667 18.98 10.72 41.72 4.04
753 764 2.409378 GTGACGCGGTCGAGAAAAATTA 59.591 45.455 12.47 0.00 39.41 1.40
754 765 3.061697 GTGACGCGGTCGAGAAAAATTAT 59.938 43.478 12.47 0.00 39.41 1.28
805 816 3.127721 CCTCGCCTTTCTCTCCATTTTTC 59.872 47.826 0.00 0.00 0.00 2.29
812 823 6.401394 CCTTTCTCTCCATTTTTCCATTTCC 58.599 40.000 0.00 0.00 0.00 3.13
869 880 4.082354 GGTATAAGTCTCATAATCCCGCGT 60.082 45.833 4.92 0.00 0.00 6.01
871 882 0.389391 AGTCTCATAATCCCGCGTGG 59.611 55.000 8.42 8.42 0.00 4.94
1149 1166 0.732880 CCAAGACGTACCAGCTCGTG 60.733 60.000 2.59 0.00 40.39 4.35
1371 1389 1.148867 TGGGATTTGGCCTTTCTGGAA 59.851 47.619 3.32 0.00 38.35 3.53
1841 1859 1.078214 CGAGCTGGGGCAGATGAAA 60.078 57.895 0.00 0.00 41.70 2.69
1928 1946 3.434319 GGGTCGCTGTCGTCCGTA 61.434 66.667 0.00 0.00 43.29 4.02
1931 1949 1.361668 GGTCGCTGTCGTCCGTAGTA 61.362 60.000 0.00 0.00 34.54 1.82
1943 1961 0.529378 CCGTAGTAAACTGCTCGGGT 59.471 55.000 12.21 0.00 34.79 5.28
2003 2021 1.131638 TACTGGACCTGATGCCATCC 58.868 55.000 5.22 0.00 32.89 3.51
2090 2108 4.899239 GGCGTCTCCATCGGGCTG 62.899 72.222 0.00 0.00 34.01 4.85
2116 2134 4.796225 GCGAGACGAGGAAGAAGG 57.204 61.111 0.00 0.00 0.00 3.46
2149 2167 1.337823 GGAGCTTCCTAACAGCAACGA 60.338 52.381 0.00 0.00 39.99 3.85
2504 2536 9.494271 TCCTGTTTCATTTGATCTATACTATGC 57.506 33.333 0.00 0.00 0.00 3.14
2553 2586 4.389890 ACTGCAGAAATGAAAAGTGCAA 57.610 36.364 23.35 0.00 43.24 4.08
2563 2596 2.039216 TGAAAAGTGCAATCCCGGTAGA 59.961 45.455 0.00 0.00 0.00 2.59
2570 2603 2.256117 CAATCCCGGTAGATTGGTCC 57.744 55.000 20.00 0.00 46.18 4.46
2572 2605 0.105862 ATCCCGGTAGATTGGTCCGA 60.106 55.000 0.00 0.00 46.05 4.55
2578 2611 2.607635 CGGTAGATTGGTCCGACATTTG 59.392 50.000 0.00 0.00 46.05 2.32
2583 2616 6.710744 GGTAGATTGGTCCGACATTTGATATT 59.289 38.462 0.00 0.00 0.00 1.28
2631 2664 5.675071 GCTTGTGCTAGAGACAGTAGTAGTG 60.675 48.000 3.30 3.30 36.03 2.74
2633 2666 4.263374 TGTGCTAGAGACAGTAGTAGTGGT 60.263 45.833 9.78 0.00 0.00 4.16
2638 2671 6.183360 GCTAGAGACAGTAGTAGTGGTAGAGA 60.183 46.154 9.78 0.00 0.00 3.10
2739 2783 1.872313 GATAGCTGTAGACGGTAGCGT 59.128 52.381 21.51 21.51 42.10 5.07
2880 2929 1.360393 ACTCAGGGGCTTGGTTTGGA 61.360 55.000 0.00 0.00 0.00 3.53
2922 2996 2.948323 CGGGGCACGTAACCAAAC 59.052 61.111 0.00 0.00 37.93 2.93
2923 2997 2.619165 CGGGGCACGTAACCAAACC 61.619 63.158 0.00 0.82 37.93 3.27
2924 2998 2.619165 GGGGCACGTAACCAAACCG 61.619 63.158 8.88 0.00 0.00 4.44
2925 2999 1.597578 GGGCACGTAACCAAACCGA 60.598 57.895 8.88 0.00 0.00 4.69
2926 3000 1.570967 GGCACGTAACCAAACCGAC 59.429 57.895 1.99 0.00 0.00 4.79
2927 3001 1.570967 GCACGTAACCAAACCGACC 59.429 57.895 0.00 0.00 0.00 4.79
2928 3002 1.844771 GCACGTAACCAAACCGACCC 61.845 60.000 0.00 0.00 0.00 4.46
2929 3003 1.071299 ACGTAACCAAACCGACCCC 59.929 57.895 0.00 0.00 0.00 4.95
2930 3004 2.028733 CGTAACCAAACCGACCCCG 61.029 63.158 0.00 0.00 0.00 5.73
2931 3005 1.071299 GTAACCAAACCGACCCCGT 59.929 57.895 0.00 0.00 0.00 5.28
2932 3006 1.071128 TAACCAAACCGACCCCGTG 59.929 57.895 0.00 0.00 0.00 4.94
2933 3007 1.694133 TAACCAAACCGACCCCGTGT 61.694 55.000 0.00 0.00 0.00 4.49
2934 3008 2.975799 CCAAACCGACCCCGTGTG 60.976 66.667 0.00 0.00 0.00 3.82
2935 3009 2.109387 CAAACCGACCCCGTGTGA 59.891 61.111 0.00 0.00 0.00 3.58
2936 3010 1.524165 CAAACCGACCCCGTGTGAA 60.524 57.895 0.00 0.00 0.00 3.18
2937 3011 1.524393 AAACCGACCCCGTGTGAAC 60.524 57.895 0.00 0.00 0.00 3.18
2938 3012 3.795499 AACCGACCCCGTGTGAACG 62.795 63.158 0.00 0.00 0.00 3.95
2939 3013 4.289245 CCGACCCCGTGTGAACGT 62.289 66.667 0.00 0.00 0.00 3.99
2940 3014 2.732094 CGACCCCGTGTGAACGTC 60.732 66.667 0.00 0.00 0.00 4.34
2941 3015 2.732094 GACCCCGTGTGAACGTCG 60.732 66.667 0.00 0.00 0.00 5.12
2942 3016 4.955774 ACCCCGTGTGAACGTCGC 62.956 66.667 0.00 0.00 0.00 5.19
2984 3058 4.193334 GCGGAATGCGCCCCTTTC 62.193 66.667 8.22 2.82 0.00 2.62
3143 3218 4.453480 TTCTTTGGGATGAGAAGGTGTT 57.547 40.909 0.00 0.00 0.00 3.32
3147 3222 3.695830 TGGGATGAGAAGGTGTTGTAC 57.304 47.619 0.00 0.00 0.00 2.90
3149 3224 3.007940 TGGGATGAGAAGGTGTTGTACTG 59.992 47.826 0.00 0.00 0.00 2.74
3150 3225 3.600388 GGATGAGAAGGTGTTGTACTGG 58.400 50.000 0.00 0.00 0.00 4.00
3228 3308 1.369625 CGTCCCGGATCTCCAAAAAG 58.630 55.000 0.73 0.00 35.14 2.27
3229 3309 1.751437 GTCCCGGATCTCCAAAAAGG 58.249 55.000 0.73 0.00 39.47 3.11
3230 3310 1.280998 GTCCCGGATCTCCAAAAAGGA 59.719 52.381 0.73 0.00 46.75 3.36
3241 3321 3.172339 TCCAAAAAGGATCCCATGTTGG 58.828 45.455 23.00 23.00 43.07 3.77
3265 3350 1.584724 CCTGGGTTCTGGTAGACCAT 58.415 55.000 0.89 0.00 46.46 3.55
3274 3359 1.146041 GGTAGACCATGGCGCATCA 59.854 57.895 13.04 0.00 35.64 3.07
3301 3386 3.399330 TGGGTTCTTGCTAGAAACTTCG 58.601 45.455 22.37 0.00 45.59 3.79
3302 3387 2.742589 GGGTTCTTGCTAGAAACTTCGG 59.257 50.000 22.37 0.00 45.59 4.30
3305 3390 1.975680 TCTTGCTAGAAACTTCGGGGT 59.024 47.619 0.00 0.00 0.00 4.95
3309 3394 1.610886 GCTAGAAACTTCGGGGTGCTT 60.611 52.381 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.451393 GGCATACAAATTTTAGTGGTCAACA 58.549 36.000 0.00 0.00 0.00 3.33
29 30 5.867174 GGGCATACAAATTTTAGTGGTCAAC 59.133 40.000 0.00 0.00 0.00 3.18
30 31 5.046950 GGGGCATACAAATTTTAGTGGTCAA 60.047 40.000 0.00 0.00 0.00 3.18
31 32 4.464597 GGGGCATACAAATTTTAGTGGTCA 59.535 41.667 0.00 0.00 0.00 4.02
32 33 4.439563 CGGGGCATACAAATTTTAGTGGTC 60.440 45.833 0.00 0.00 0.00 4.02
33 34 3.445805 CGGGGCATACAAATTTTAGTGGT 59.554 43.478 0.00 0.00 0.00 4.16
34 35 3.445805 ACGGGGCATACAAATTTTAGTGG 59.554 43.478 0.00 0.00 0.00 4.00
35 36 4.712122 ACGGGGCATACAAATTTTAGTG 57.288 40.909 0.00 0.00 0.00 2.74
36 37 4.619628 GCAACGGGGCATACAAATTTTAGT 60.620 41.667 0.00 0.00 0.00 2.24
37 38 3.862845 GCAACGGGGCATACAAATTTTAG 59.137 43.478 0.00 0.00 0.00 1.85
38 39 3.258372 TGCAACGGGGCATACAAATTTTA 59.742 39.130 0.00 0.00 39.25 1.52
39 40 2.037772 TGCAACGGGGCATACAAATTTT 59.962 40.909 0.00 0.00 39.25 1.82
40 41 1.620819 TGCAACGGGGCATACAAATTT 59.379 42.857 0.00 0.00 39.25 1.82
41 42 1.261480 TGCAACGGGGCATACAAATT 58.739 45.000 0.00 0.00 39.25 1.82
42 43 1.067213 GTTGCAACGGGGCATACAAAT 60.067 47.619 14.90 0.00 44.48 2.32
43 44 0.315568 GTTGCAACGGGGCATACAAA 59.684 50.000 14.90 0.00 44.48 2.83
44 45 1.960612 GTTGCAACGGGGCATACAA 59.039 52.632 14.90 0.00 44.48 2.41
45 46 3.674906 GTTGCAACGGGGCATACA 58.325 55.556 14.90 0.00 44.48 2.29
55 56 0.934436 AAATGCTCGTGCGTTGCAAC 60.934 50.000 19.89 19.89 46.57 4.17
56 57 0.248825 AAAATGCTCGTGCGTTGCAA 60.249 45.000 16.88 0.00 46.57 4.08
57 58 0.660005 GAAAATGCTCGTGCGTTGCA 60.660 50.000 16.88 14.15 46.57 4.08
58 59 1.337110 GGAAAATGCTCGTGCGTTGC 61.337 55.000 16.88 11.99 46.57 4.17
59 60 0.238289 AGGAAAATGCTCGTGCGTTG 59.762 50.000 16.88 0.00 46.57 4.10
61 62 1.337823 ACTAGGAAAATGCTCGTGCGT 60.338 47.619 4.84 0.99 43.34 5.24
62 63 1.359848 ACTAGGAAAATGCTCGTGCG 58.640 50.000 4.84 0.00 43.34 5.34
63 64 4.939509 TTTACTAGGAAAATGCTCGTGC 57.060 40.909 0.00 1.71 40.20 5.34
64 65 7.308782 AGATTTTACTAGGAAAATGCTCGTG 57.691 36.000 26.91 0.00 38.76 4.35
132 133 9.944663 GATTTCAGTGCGGATTATGTAAAATAA 57.055 29.630 0.00 0.00 0.00 1.40
133 134 9.337396 AGATTTCAGTGCGGATTATGTAAAATA 57.663 29.630 0.00 0.00 0.00 1.40
136 137 6.458206 GCAGATTTCAGTGCGGATTATGTAAA 60.458 38.462 0.00 0.00 0.00 2.01
139 140 3.313526 GCAGATTTCAGTGCGGATTATGT 59.686 43.478 0.00 0.00 0.00 2.29
144 145 1.825090 TTGCAGATTTCAGTGCGGAT 58.175 45.000 0.00 0.00 42.96 4.18
151 152 5.192327 ACAAGTCCTTTTGCAGATTTCAG 57.808 39.130 0.00 0.00 0.00 3.02
154 155 7.288810 TGAATACAAGTCCTTTTGCAGATTT 57.711 32.000 0.00 0.00 0.00 2.17
160 161 5.705609 TTCCTGAATACAAGTCCTTTTGC 57.294 39.130 0.00 0.00 0.00 3.68
161 162 7.940850 TCTTTTCCTGAATACAAGTCCTTTTG 58.059 34.615 0.00 0.00 0.00 2.44
166 167 5.416013 CCCTTCTTTTCCTGAATACAAGTCC 59.584 44.000 0.00 0.00 0.00 3.85
169 170 6.241645 ACTCCCTTCTTTTCCTGAATACAAG 58.758 40.000 0.00 0.00 0.00 3.16
183 186 5.803237 TTCGAAAGTTCTACTCCCTTCTT 57.197 39.130 0.00 0.00 0.00 2.52
184 187 6.664384 ACTATTCGAAAGTTCTACTCCCTTCT 59.336 38.462 0.00 0.00 0.00 2.85
197 200 4.866508 TGTCAGTCCACTATTCGAAAGT 57.133 40.909 0.00 4.56 0.00 2.66
202 205 6.092122 TGCTATTTTTGTCAGTCCACTATTCG 59.908 38.462 0.00 0.00 0.00 3.34
237 240 8.462811 GTTCTCTCATCTTCTGATACTTGTACA 58.537 37.037 0.00 0.00 32.10 2.90
244 247 6.791303 AGAACGTTCTCTCATCTTCTGATAC 58.209 40.000 24.93 0.00 32.10 2.24
353 363 5.120674 GGATGCTTGGTATTTGTGCTTTTTC 59.879 40.000 0.00 0.00 0.00 2.29
358 368 1.745087 CGGATGCTTGGTATTTGTGCT 59.255 47.619 0.00 0.00 0.00 4.40
435 445 3.097728 CGAGCACGTGTCGACCAC 61.098 66.667 25.89 10.30 39.92 4.16
735 746 4.673534 AAATAATTTTTCTCGACCGCGT 57.326 36.364 4.92 0.00 38.98 6.01
805 816 7.582667 ACGAGGATAAAAATAAGGGAAATGG 57.417 36.000 0.00 0.00 0.00 3.16
812 823 6.706716 GGAGGAGAACGAGGATAAAAATAAGG 59.293 42.308 0.00 0.00 0.00 2.69
825 836 0.966370 AACGGGAGGAGGAGAACGAG 60.966 60.000 0.00 0.00 0.00 4.18
871 882 1.004161 AGAAGCCTTCTGGAAGCTTCC 59.996 52.381 34.48 34.48 43.88 3.46
1316 1333 1.544724 ATCAACCAACCGAACCCATG 58.455 50.000 0.00 0.00 0.00 3.66
1399 1417 3.259064 CAGCAAGCAAAATCCAAGGATG 58.741 45.455 1.66 0.00 34.70 3.51
1598 1616 2.919856 AGCGCCATAGGGATCGCT 60.920 61.111 17.27 17.27 46.70 4.93
1772 1790 1.519455 GTCGTTCTCCTCGCCCATG 60.519 63.158 0.00 0.00 0.00 3.66
1841 1859 1.405105 ACGATGTTGTTGCACAGCTTT 59.595 42.857 0.00 0.00 30.50 3.51
1928 1946 1.272769 GACTCACCCGAGCAGTTTACT 59.727 52.381 0.00 0.00 43.66 2.24
1931 1949 1.006102 CGACTCACCCGAGCAGTTT 60.006 57.895 0.00 0.00 43.66 2.66
2054 2072 3.332493 GAACAGCCTCGCGTCCGTA 62.332 63.158 5.77 0.00 35.54 4.02
2090 2108 4.813526 TCGTCTCGCGCTCGCTTC 62.814 66.667 5.56 0.00 41.07 3.86
2126 2144 1.224870 GCTGTTAGGAAGCTCCCCC 59.775 63.158 0.00 0.00 37.19 5.40
2128 2146 1.454201 GTTGCTGTTAGGAAGCTCCC 58.546 55.000 0.00 0.00 41.42 4.30
2285 2315 2.037367 TCCTGGTCTGACCCGGAG 59.963 66.667 29.44 18.04 45.19 4.63
2499 2531 4.781026 CACGACAAATTACACAACGCATAG 59.219 41.667 0.00 0.00 0.00 2.23
2504 2536 3.595709 ACCACGACAAATTACACAACG 57.404 42.857 0.00 0.00 0.00 4.10
2547 2580 1.134098 CCAATCTACCGGGATTGCACT 60.134 52.381 21.55 0.00 46.45 4.40
2553 2586 0.105862 TCGGACCAATCTACCGGGAT 60.106 55.000 6.32 0.00 45.61 3.85
2563 2596 6.122277 ACAGAATATCAAATGTCGGACCAAT 58.878 36.000 5.55 0.00 0.00 3.16
2567 2600 7.715265 ACATACAGAATATCAAATGTCGGAC 57.285 36.000 0.00 0.00 0.00 4.79
2583 2616 6.463049 GCAGGAAGGAGCTATTTACATACAGA 60.463 42.308 0.00 0.00 0.00 3.41
2631 2664 7.220491 GCAAATCGTAGTTACTCTTTCTCTACC 59.780 40.741 0.00 0.00 0.00 3.18
2633 2666 8.053026 AGCAAATCGTAGTTACTCTTTCTCTA 57.947 34.615 0.00 0.00 0.00 2.43
2638 2671 4.863131 CGGAGCAAATCGTAGTTACTCTTT 59.137 41.667 0.00 0.00 0.00 2.52
2739 2783 0.840617 TATATCTGGCCGCCAAACCA 59.159 50.000 14.45 0.00 30.80 3.67
2821 2870 0.999712 AGTTGGAACCATACCCCTGG 59.000 55.000 0.00 0.00 42.35 4.45
2862 2911 0.040204 ATCCAAACCAAGCCCCTGAG 59.960 55.000 0.00 0.00 0.00 3.35
2863 2912 0.486879 AATCCAAACCAAGCCCCTGA 59.513 50.000 0.00 0.00 0.00 3.86
2880 2929 0.251165 CCAGACCAAACCGACCCAAT 60.251 55.000 0.00 0.00 0.00 3.16
2915 2989 2.203238 CACGGGGTCGGTTTGGTT 60.203 61.111 0.00 0.00 41.39 3.67
2920 2994 2.109593 GTTCACACGGGGTCGGTT 59.890 61.111 0.00 0.00 41.39 4.44
2945 3019 2.583593 GCCTTCTAGCGAGTGCCG 60.584 66.667 0.00 0.00 44.31 5.69
3128 3203 3.600388 CAGTACAACACCTTCTCATCCC 58.400 50.000 0.00 0.00 0.00 3.85
3129 3204 3.008049 ACCAGTACAACACCTTCTCATCC 59.992 47.826 0.00 0.00 0.00 3.51
3233 3313 2.751436 CCAGGCGACCCAACATGG 60.751 66.667 0.00 0.00 37.25 3.66
3234 3314 2.751436 CCCAGGCGACCCAACATG 60.751 66.667 0.00 0.00 0.00 3.21
3235 3315 2.764637 GAACCCAGGCGACCCAACAT 62.765 60.000 0.00 0.00 0.00 2.71
3236 3316 3.485346 GAACCCAGGCGACCCAACA 62.485 63.158 0.00 0.00 0.00 3.33
3237 3317 2.671963 GAACCCAGGCGACCCAAC 60.672 66.667 0.00 0.00 0.00 3.77
3238 3318 2.852075 AGAACCCAGGCGACCCAA 60.852 61.111 0.00 0.00 0.00 4.12
3239 3319 3.636231 CAGAACCCAGGCGACCCA 61.636 66.667 0.00 0.00 0.00 4.51
3240 3320 4.410400 CCAGAACCCAGGCGACCC 62.410 72.222 0.00 0.00 0.00 4.46
3241 3321 2.240162 CTACCAGAACCCAGGCGACC 62.240 65.000 0.00 0.00 0.00 4.79
3242 3322 1.218316 CTACCAGAACCCAGGCGAC 59.782 63.158 0.00 0.00 0.00 5.19
3243 3323 1.077805 TCTACCAGAACCCAGGCGA 59.922 57.895 0.00 0.00 0.00 5.54
3274 3359 2.108168 TCTAGCAAGAACCCATACGCT 58.892 47.619 0.00 0.00 0.00 5.07


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

AutoCloner maintained by Alex Coulton.