Multiple sequence alignment - TraesCS5B01G144300

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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 TraesCS5B01G144300 chr5B 100.000 2684 0 0 1 2684 271663872 271666555 0.000000e+00 4957
1 TraesCS5B01G144300 chr5A 89.425 2468 113 58 261 2661 321329773 321327387 0.000000e+00 2976
2 TraesCS5B01G144300 chr5A 93.852 244 12 2 31 274 321330709 321330469 5.460000e-97 364
3 TraesCS5B01G144300 chr5D 91.159 1674 66 35 626 2240 233414183 233412533 0.000000e+00 2196
4 TraesCS5B01G144300 chr5D 91.820 599 26 6 54 644 233414780 233414197 0.000000e+00 813
5 TraesCS5B01G144300 chr5D 91.892 444 22 8 2248 2684 233412552 233412116 2.280000e-170 608
6 TraesCS5B01G144300 chr7B 79.377 514 83 13 1174 1686 212419021 212418530 9.200000e-90 340
7 TraesCS5B01G144300 chr7A 79.377 514 83 12 1174 1686 251253960 251253469 9.200000e-90 340
8 TraesCS5B01G144300 chr7D 78.794 514 86 14 1174 1686 236010587 236010096 9.270000e-85 324
9 TraesCS5B01G144300 chr2A 84.270 178 21 1 1461 1631 629998528 629998351 1.650000e-37 167
10 TraesCS5B01G144300 chr4A 83.708 178 22 1 1461 1631 610111068 610110891 7.690000e-36 161
11 TraesCS5B01G144300 chrUn 83.146 178 22 2 1461 1631 74705359 74705535 3.580000e-34 156
12 TraesCS5B01G144300 chr2B 94.186 86 5 0 1594 1679 159331294 159331209 6.030000e-27 132


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 TraesCS5B01G144300 chr5B 271663872 271666555 2683 False 4957.000000 4957 100.000000 1 2684 1 chr5B.!!$F1 2683
1 TraesCS5B01G144300 chr5A 321327387 321330709 3322 True 1670.000000 2976 91.638500 31 2661 2 chr5A.!!$R1 2630
2 TraesCS5B01G144300 chr5D 233412116 233414780 2664 True 1205.666667 2196 91.623667 54 2684 3 chr5D.!!$R1 2630

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
881 1652 0.266453 TATCCTTCCATCCCCACCGA 59.734 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2432 3266 0.108585 GCCTCGATTTATCCCTGGCA 59.891 55.0 2.01 0.0 38.79 4.92 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
20 21 3.810310 GCACTATGGCTAGTCTCAGTT 57.190 47.619 0.00 0.00 35.99 3.16
21 22 3.712187 GCACTATGGCTAGTCTCAGTTC 58.288 50.000 0.00 0.00 35.99 3.01
22 23 3.383185 GCACTATGGCTAGTCTCAGTTCT 59.617 47.826 0.00 0.00 35.99 3.01
23 24 4.580995 GCACTATGGCTAGTCTCAGTTCTA 59.419 45.833 0.00 0.00 35.99 2.10
24 25 5.067936 GCACTATGGCTAGTCTCAGTTCTAA 59.932 44.000 0.00 0.00 35.99 2.10
25 26 6.405953 GCACTATGGCTAGTCTCAGTTCTAAA 60.406 42.308 0.00 0.00 35.99 1.85
26 27 7.685641 GCACTATGGCTAGTCTCAGTTCTAAAT 60.686 40.741 0.00 0.00 35.99 1.40
27 28 7.651304 CACTATGGCTAGTCTCAGTTCTAAATG 59.349 40.741 0.00 0.00 35.99 2.32
28 29 4.759782 TGGCTAGTCTCAGTTCTAAATGC 58.240 43.478 0.00 0.00 0.00 3.56
29 30 4.467795 TGGCTAGTCTCAGTTCTAAATGCT 59.532 41.667 0.00 0.00 0.00 3.79
38 39 9.036671 GTCTCAGTTCTAAATGCTCTAATAACC 57.963 37.037 0.00 0.00 0.00 2.85
46 47 8.428852 TCTAAATGCTCTAATAACCAGTGCATA 58.571 33.333 11.06 0.00 46.80 3.14
176 177 2.482333 CGGTTGGGCGTGGAAACAA 61.482 57.895 0.00 0.00 46.06 2.83
307 1017 0.676466 CTGTGGGACTAATTGGCGCA 60.676 55.000 10.83 0.00 44.91 6.09
379 1090 3.699538 GGCTTCCCAATTTAATTCGTCCT 59.300 43.478 0.00 0.00 0.00 3.85
428 1139 0.731514 CAGTTCGTTTCGCGCTCCTA 60.732 55.000 5.56 0.00 41.07 2.94
536 1252 1.074248 ACCCAACCGTCCAACCATC 59.926 57.895 0.00 0.00 0.00 3.51
539 1255 2.359478 AACCGTCCAACCATCGGC 60.359 61.111 2.72 0.00 46.92 5.54
680 1440 2.674177 GCTGTGTACTATCGGTGTGCTT 60.674 50.000 0.00 0.00 0.00 3.91
686 1446 1.139058 ACTATCGGTGTGCTTGATCCC 59.861 52.381 0.00 0.00 0.00 3.85
700 1462 1.308746 ATCCCCCTCCCCGTTTCAT 60.309 57.895 0.00 0.00 0.00 2.57
861 1632 2.180204 GTCGTCATCCGGGCATTGG 61.180 63.158 0.00 0.00 37.11 3.16
881 1652 0.266453 TATCCTTCCATCCCCACCGA 59.734 55.000 0.00 0.00 0.00 4.69
966 1737 2.049435 CAAGTTTGCAACCCCCTCC 58.951 57.895 0.00 0.00 0.00 4.30
977 1748 0.719015 ACCCCCTCCATCTCTCTCAA 59.281 55.000 0.00 0.00 0.00 3.02
1765 2548 0.541764 GAGATGGAGGCGAGGAGGAT 60.542 60.000 0.00 0.00 0.00 3.24
1766 2549 0.541764 AGATGGAGGCGAGGAGGATC 60.542 60.000 0.00 0.00 0.00 3.36
1779 2563 1.923356 GAGGATCCCTTTTTGTGCCA 58.077 50.000 8.55 0.00 31.76 4.92
1856 2640 4.585162 TCACGGAGAGAAGAGAAAAGAGTT 59.415 41.667 0.00 0.00 0.00 3.01
1857 2641 4.920927 CACGGAGAGAAGAGAAAAGAGTTC 59.079 45.833 0.00 0.00 0.00 3.01
1858 2642 4.830600 ACGGAGAGAAGAGAAAAGAGTTCT 59.169 41.667 0.00 0.00 31.85 3.01
1859 2643 6.005198 ACGGAGAGAAGAGAAAAGAGTTCTA 58.995 40.000 0.00 0.00 29.28 2.10
1860 2644 6.150474 ACGGAGAGAAGAGAAAAGAGTTCTAG 59.850 42.308 0.00 0.00 29.28 2.43
1861 2645 6.373216 CGGAGAGAAGAGAAAAGAGTTCTAGA 59.627 42.308 0.00 0.00 29.28 2.43
1862 2646 7.094549 CGGAGAGAAGAGAAAAGAGTTCTAGAA 60.095 40.741 0.00 0.00 29.28 2.10
1866 2650 8.980143 AGAAGAGAAAAGAGTTCTAGAATTCG 57.020 34.615 18.93 0.00 33.02 3.34
1867 2651 8.581578 AGAAGAGAAAAGAGTTCTAGAATTCGT 58.418 33.333 18.93 14.63 33.02 3.85
1868 2652 9.198837 GAAGAGAAAAGAGTTCTAGAATTCGTT 57.801 33.333 18.77 18.77 32.26 3.85
1869 2653 8.751302 AGAGAAAAGAGTTCTAGAATTCGTTC 57.249 34.615 22.65 23.60 30.43 3.95
1870 2654 7.815549 AGAGAAAAGAGTTCTAGAATTCGTTCC 59.184 37.037 26.12 17.88 30.43 3.62
1872 2656 7.600752 AGAAAAGAGTTCTAGAATTCGTTCCTG 59.399 37.037 26.12 0.00 30.43 3.86
1873 2657 6.591750 AAGAGTTCTAGAATTCGTTCCTGA 57.408 37.500 18.93 0.00 33.02 3.86
1898 2686 5.859114 CGGTGCTTCATCATCAGTATAGTAC 59.141 44.000 0.00 0.00 0.00 2.73
1899 2687 6.515035 CGGTGCTTCATCATCAGTATAGTACA 60.515 42.308 0.00 0.00 0.00 2.90
1900 2688 6.865726 GGTGCTTCATCATCAGTATAGTACAG 59.134 42.308 0.00 0.00 0.00 2.74
1944 2743 5.449999 GGCCTTGGGTAGAATTAATTTGTCG 60.450 44.000 1.43 0.00 0.00 4.35
1948 2747 7.753580 CCTTGGGTAGAATTAATTTGTCGTTTC 59.246 37.037 1.43 0.00 0.00 2.78
1965 2764 4.576873 TCGTTTCAGTTGTTTCCATTGCTA 59.423 37.500 0.00 0.00 0.00 3.49
1968 2767 2.819608 TCAGTTGTTTCCATTGCTAGGC 59.180 45.455 0.00 0.00 0.00 3.93
1972 2771 3.153369 TGTTTCCATTGCTAGGCTTGA 57.847 42.857 0.00 0.00 0.00 3.02
2011 2815 5.997746 TGGAATTTTCTTGTACAGAGACAGG 59.002 40.000 0.00 0.00 31.12 4.00
2012 2816 5.412904 GGAATTTTCTTGTACAGAGACAGGG 59.587 44.000 0.00 0.00 31.12 4.45
2013 2817 5.568620 ATTTTCTTGTACAGAGACAGGGT 57.431 39.130 0.00 0.00 31.12 4.34
2016 2820 2.158370 TCTTGTACAGAGACAGGGTGGA 60.158 50.000 0.00 0.00 0.00 4.02
2017 2821 1.629043 TGTACAGAGACAGGGTGGAC 58.371 55.000 0.00 0.00 0.00 4.02
2034 2846 5.713861 GGGTGGACTAGTATACACGGATATT 59.286 44.000 5.50 0.00 34.78 1.28
2086 2906 8.791327 TCATCATGTGTTTAGATTCTTGCTTA 57.209 30.769 0.00 0.00 0.00 3.09
2117 2937 0.687757 TCCTAAGCACGGCCTCATCT 60.688 55.000 0.00 0.00 0.00 2.90
2130 2950 7.041721 CACGGCCTCATCTTATATTATGCTTA 58.958 38.462 0.00 0.00 0.00 3.09
2176 3006 0.677098 TCGGAGACCTTCCTCGAGTG 60.677 60.000 12.31 3.02 44.41 3.51
2221 3054 2.725221 ATCCTCTAAAGCCAAGCCAG 57.275 50.000 0.00 0.00 0.00 4.85
2222 3055 1.656587 TCCTCTAAAGCCAAGCCAGA 58.343 50.000 0.00 0.00 0.00 3.86
2223 3056 1.279271 TCCTCTAAAGCCAAGCCAGAC 59.721 52.381 0.00 0.00 0.00 3.51
2224 3057 1.680249 CCTCTAAAGCCAAGCCAGACC 60.680 57.143 0.00 0.00 0.00 3.85
2225 3058 1.003580 CTCTAAAGCCAAGCCAGACCA 59.996 52.381 0.00 0.00 0.00 4.02
2226 3059 1.168714 CTAAAGCCAAGCCAGACCAC 58.831 55.000 0.00 0.00 0.00 4.16
2227 3060 0.251165 TAAAGCCAAGCCAGACCACC 60.251 55.000 0.00 0.00 0.00 4.61
2228 3061 2.011617 AAAGCCAAGCCAGACCACCT 62.012 55.000 0.00 0.00 0.00 4.00
2229 3062 2.674380 GCCAAGCCAGACCACCTG 60.674 66.667 0.00 0.00 42.55 4.00
2230 3063 2.839098 CCAAGCCAGACCACCTGT 59.161 61.111 0.00 0.00 41.33 4.00
2231 3064 1.601759 CCAAGCCAGACCACCTGTG 60.602 63.158 0.00 0.00 41.33 3.66
2232 3065 2.113986 AAGCCAGACCACCTGTGC 59.886 61.111 0.00 0.00 41.33 4.57
2233 3066 2.455565 AAGCCAGACCACCTGTGCT 61.456 57.895 0.00 0.00 45.18 4.40
2234 3067 2.670934 GCCAGACCACCTGTGCTG 60.671 66.667 0.00 0.00 41.33 4.41
2235 3068 3.150949 CCAGACCACCTGTGCTGA 58.849 61.111 6.51 0.00 41.33 4.26
2236 3069 1.451504 CCAGACCACCTGTGCTGAA 59.548 57.895 6.51 0.00 41.33 3.02
2237 3070 0.179020 CCAGACCACCTGTGCTGAAA 60.179 55.000 6.51 0.00 41.33 2.69
2238 3071 1.233019 CAGACCACCTGTGCTGAAAG 58.767 55.000 0.00 0.00 38.10 2.62
2239 3072 0.839946 AGACCACCTGTGCTGAAAGT 59.160 50.000 0.00 0.00 35.30 2.66
2240 3073 1.212935 AGACCACCTGTGCTGAAAGTT 59.787 47.619 0.00 0.00 35.30 2.66
2241 3074 1.604278 GACCACCTGTGCTGAAAGTTC 59.396 52.381 0.00 0.00 35.30 3.01
2242 3075 1.064758 ACCACCTGTGCTGAAAGTTCA 60.065 47.619 0.00 0.00 35.30 3.18
2243 3076 2.023673 CCACCTGTGCTGAAAGTTCAA 58.976 47.619 0.00 0.00 36.64 2.69
2244 3077 2.426738 CCACCTGTGCTGAAAGTTCAAA 59.573 45.455 0.00 0.00 36.64 2.69
2245 3078 3.119173 CCACCTGTGCTGAAAGTTCAAAA 60.119 43.478 0.00 0.00 36.64 2.44
2246 3079 4.493547 CACCTGTGCTGAAAGTTCAAAAA 58.506 39.130 0.00 0.00 36.64 1.94
2273 3106 5.600696 CCACCTGTGCTGAAAGTAATTTTT 58.399 37.500 0.00 0.00 35.30 1.94
2333 3167 5.250235 TGTCGGCAAATAAAGTCAAACAA 57.750 34.783 0.00 0.00 0.00 2.83
2336 3170 5.517054 GTCGGCAAATAAAGTCAAACAAACA 59.483 36.000 0.00 0.00 0.00 2.83
2337 3171 6.200097 GTCGGCAAATAAAGTCAAACAAACAT 59.800 34.615 0.00 0.00 0.00 2.71
2428 3262 4.077108 ACAAAGGGGACGAAAAAGGATAC 58.923 43.478 0.00 0.00 0.00 2.24
2429 3263 4.076394 CAAAGGGGACGAAAAAGGATACA 58.924 43.478 0.00 0.00 41.41 2.29
2432 3266 4.930696 AGGGGACGAAAAAGGATACAAAT 58.069 39.130 0.00 0.00 41.41 2.32
2441 3275 3.979501 AAGGATACAAATGCCAGGGAT 57.020 42.857 0.00 0.00 41.41 3.85
2520 3354 3.211865 GAAGAGCAGCCATCAATCATCA 58.788 45.455 0.00 0.00 0.00 3.07
2535 3369 1.004595 CATCATGACAGACCAGCACG 58.995 55.000 0.00 0.00 0.00 5.34
2563 3397 2.831333 AGGCAGATGAATTACAGCTCG 58.169 47.619 0.00 0.00 43.79 5.03
2578 3412 3.000041 CAGCTCGGCACAATTAACACTA 59.000 45.455 0.00 0.00 0.00 2.74
2579 3413 3.000727 AGCTCGGCACAATTAACACTAC 58.999 45.455 0.00 0.00 0.00 2.73
2580 3414 3.000727 GCTCGGCACAATTAACACTACT 58.999 45.455 0.00 0.00 0.00 2.57
2626 3465 1.154225 GTCGCATCAAACCAAGCCG 60.154 57.895 0.00 0.00 0.00 5.52
2662 3501 0.530870 TGCGTCATTTCGGTGTCACA 60.531 50.000 5.12 0.00 0.00 3.58
2667 3506 3.390135 GTCATTTCGGTGTCACAAGAGA 58.610 45.455 5.12 0.00 0.00 3.10
2668 3507 3.430218 GTCATTTCGGTGTCACAAGAGAG 59.570 47.826 5.12 0.00 0.00 3.20
2669 3508 3.069586 TCATTTCGGTGTCACAAGAGAGT 59.930 43.478 5.12 0.00 0.00 3.24
2670 3509 4.279922 TCATTTCGGTGTCACAAGAGAGTA 59.720 41.667 5.12 0.00 0.00 2.59
2671 3510 4.866508 TTTCGGTGTCACAAGAGAGTAT 57.133 40.909 5.12 0.00 0.00 2.12
2672 3511 4.866508 TTCGGTGTCACAAGAGAGTATT 57.133 40.909 5.12 0.00 0.00 1.89
2674 3513 5.306532 TCGGTGTCACAAGAGAGTATTAC 57.693 43.478 5.12 0.00 0.00 1.89
2675 3514 4.763279 TCGGTGTCACAAGAGAGTATTACA 59.237 41.667 5.12 0.00 0.00 2.41
2676 3515 5.417894 TCGGTGTCACAAGAGAGTATTACAT 59.582 40.000 5.12 0.00 0.00 2.29
2677 3516 5.744345 CGGTGTCACAAGAGAGTATTACATC 59.256 44.000 5.12 0.00 0.00 3.06
2678 3517 6.043411 GGTGTCACAAGAGAGTATTACATCC 58.957 44.000 5.12 0.00 0.00 3.51
2679 3518 6.351033 GGTGTCACAAGAGAGTATTACATCCA 60.351 42.308 5.12 0.00 0.00 3.41
2680 3519 7.097192 GTGTCACAAGAGAGTATTACATCCAA 58.903 38.462 0.00 0.00 0.00 3.53
2681 3520 7.276658 GTGTCACAAGAGAGTATTACATCCAAG 59.723 40.741 0.00 0.00 0.00 3.61
2682 3521 7.039011 TGTCACAAGAGAGTATTACATCCAAGT 60.039 37.037 0.00 0.00 0.00 3.16
2683 3522 7.276658 GTCACAAGAGAGTATTACATCCAAGTG 59.723 40.741 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.383185 AGAACTGAGACTAGCCATAGTGC 59.617 47.826 0.00 0.00 42.46 4.40
1 2 6.701145 TTAGAACTGAGACTAGCCATAGTG 57.299 41.667 0.00 0.00 42.46 2.74
2 3 7.685641 GCATTTAGAACTGAGACTAGCCATAGT 60.686 40.741 0.00 0.00 45.16 2.12
3 4 6.644592 GCATTTAGAACTGAGACTAGCCATAG 59.355 42.308 0.00 0.00 34.96 2.23
4 5 6.325028 AGCATTTAGAACTGAGACTAGCCATA 59.675 38.462 0.00 0.00 0.00 2.74
5 6 5.130145 AGCATTTAGAACTGAGACTAGCCAT 59.870 40.000 0.00 0.00 0.00 4.40
6 7 4.467795 AGCATTTAGAACTGAGACTAGCCA 59.532 41.667 0.00 0.00 0.00 4.75
7 8 5.017294 AGCATTTAGAACTGAGACTAGCC 57.983 43.478 0.00 0.00 0.00 3.93
8 9 5.901552 AGAGCATTTAGAACTGAGACTAGC 58.098 41.667 0.00 0.00 0.00 3.42
11 12 9.810545 GTTATTAGAGCATTTAGAACTGAGACT 57.189 33.333 0.00 0.00 0.00 3.24
12 13 9.036671 GGTTATTAGAGCATTTAGAACTGAGAC 57.963 37.037 0.00 0.00 0.00 3.36
13 14 8.758829 TGGTTATTAGAGCATTTAGAACTGAGA 58.241 33.333 0.00 0.00 0.00 3.27
14 15 8.948631 TGGTTATTAGAGCATTTAGAACTGAG 57.051 34.615 0.00 0.00 0.00 3.35
15 16 8.540388 ACTGGTTATTAGAGCATTTAGAACTGA 58.460 33.333 0.00 0.00 0.00 3.41
16 17 8.607459 CACTGGTTATTAGAGCATTTAGAACTG 58.393 37.037 0.00 0.00 0.00 3.16
17 18 7.281100 GCACTGGTTATTAGAGCATTTAGAACT 59.719 37.037 0.00 0.00 32.92 3.01
18 19 7.065803 TGCACTGGTTATTAGAGCATTTAGAAC 59.934 37.037 0.00 0.00 36.95 3.01
19 20 7.109501 TGCACTGGTTATTAGAGCATTTAGAA 58.890 34.615 0.00 0.00 36.95 2.10
20 21 6.649155 TGCACTGGTTATTAGAGCATTTAGA 58.351 36.000 0.00 0.00 36.95 2.10
21 22 6.925610 TGCACTGGTTATTAGAGCATTTAG 57.074 37.500 0.00 0.00 36.95 1.85
22 23 9.573166 AATATGCACTGGTTATTAGAGCATTTA 57.427 29.630 13.43 0.28 45.77 1.40
23 24 8.469309 AATATGCACTGGTTATTAGAGCATTT 57.531 30.769 13.43 5.25 45.77 2.32
24 25 7.175641 GGAATATGCACTGGTTATTAGAGCATT 59.824 37.037 13.43 0.45 45.77 3.56
26 27 5.997746 GGAATATGCACTGGTTATTAGAGCA 59.002 40.000 0.00 0.00 43.84 4.26
27 28 5.997746 TGGAATATGCACTGGTTATTAGAGC 59.002 40.000 0.00 0.00 33.23 4.09
28 29 8.450578 TTTGGAATATGCACTGGTTATTAGAG 57.549 34.615 0.00 0.00 0.00 2.43
29 30 8.815565 TTTTGGAATATGCACTGGTTATTAGA 57.184 30.769 0.00 0.00 0.00 2.10
38 39 4.142315 CCCTGTCTTTTGGAATATGCACTG 60.142 45.833 0.00 0.00 0.00 3.66
46 47 3.973425 CAGGATCCCTGTCTTTTGGAAT 58.027 45.455 8.55 0.00 45.82 3.01
103 104 1.669115 CAGCTCCAAGTCCACCGTG 60.669 63.158 0.00 0.00 0.00 4.94
176 177 0.821517 TTGGTATCGCGGTGTCATCT 59.178 50.000 6.13 0.00 0.00 2.90
291 1001 1.377987 GGTGCGCCAATTAGTCCCA 60.378 57.895 12.58 0.00 34.09 4.37
292 1002 2.119029 GGGTGCGCCAATTAGTCCC 61.119 63.158 19.98 0.06 36.17 4.46
360 1071 3.375922 GCGAGGACGAATTAAATTGGGAA 59.624 43.478 0.00 0.00 42.66 3.97
361 1072 2.940410 GCGAGGACGAATTAAATTGGGA 59.060 45.455 0.00 0.00 42.66 4.37
362 1073 2.032924 GGCGAGGACGAATTAAATTGGG 59.967 50.000 0.00 0.00 42.66 4.12
363 1074 2.032924 GGGCGAGGACGAATTAAATTGG 59.967 50.000 0.00 0.00 42.66 3.16
364 1075 2.680841 TGGGCGAGGACGAATTAAATTG 59.319 45.455 0.00 0.00 42.66 2.32
365 1076 2.943033 CTGGGCGAGGACGAATTAAATT 59.057 45.455 0.00 0.00 42.66 1.82
403 1114 1.200839 GCGAAACGAACTGACACGG 59.799 57.895 0.00 0.00 0.00 4.94
416 1127 2.202570 GCGACTAGGAGCGCGAAA 60.203 61.111 12.10 0.00 43.96 3.46
428 1139 4.003788 CCAACCAGACCGGCGACT 62.004 66.667 9.30 4.35 39.03 4.18
606 1330 5.398416 CGATCCCAACGAAAGAAAAGAAAAC 59.602 40.000 0.00 0.00 0.00 2.43
680 1440 1.999002 GAAACGGGGAGGGGGATCA 60.999 63.158 0.00 0.00 0.00 2.92
686 1446 2.824041 CGCATGAAACGGGGAGGG 60.824 66.667 0.00 0.00 0.00 4.30
700 1462 3.316588 TCATTTTCCTTTTACAGCACGCA 59.683 39.130 0.00 0.00 0.00 5.24
815 1583 1.661112 CTGCTTCTAAACACGGCTAGC 59.339 52.381 6.04 6.04 0.00 3.42
861 1632 0.396811 CGGTGGGGATGGAAGGATAC 59.603 60.000 0.00 0.00 0.00 2.24
881 1652 4.586841 TGGAGGTGGTTTGATTCGATTTTT 59.413 37.500 0.00 0.00 0.00 1.94
966 1737 2.545532 GCTCGGGATGTTGAGAGAGATG 60.546 54.545 0.00 0.00 34.04 2.90
1050 1821 4.263572 TTGGAGGTGGCGGTGTGG 62.264 66.667 0.00 0.00 0.00 4.17
1368 2139 4.189188 CCGCGGTAGGTGAGGTCG 62.189 72.222 19.50 0.00 0.00 4.79
1866 2650 1.079503 GATGAAGCACCGTCAGGAAC 58.920 55.000 0.00 0.00 41.02 3.62
1867 2651 0.684535 TGATGAAGCACCGTCAGGAA 59.315 50.000 0.00 0.00 41.02 3.36
1868 2652 0.904649 ATGATGAAGCACCGTCAGGA 59.095 50.000 6.46 0.00 41.02 3.86
1869 2653 1.293924 GATGATGAAGCACCGTCAGG 58.706 55.000 6.46 0.00 45.13 3.86
1870 2654 1.931841 CTGATGATGAAGCACCGTCAG 59.068 52.381 0.00 0.00 37.53 3.51
1872 2656 2.015736 ACTGATGATGAAGCACCGTC 57.984 50.000 0.00 0.00 0.00 4.79
1873 2657 3.827008 ATACTGATGATGAAGCACCGT 57.173 42.857 0.00 0.00 0.00 4.83
1875 2659 6.749139 TGTACTATACTGATGATGAAGCACC 58.251 40.000 0.00 0.00 0.00 5.01
1899 2687 3.940221 CCGAGACTAACTACAGCAGTACT 59.060 47.826 0.00 0.00 36.04 2.73
1900 2688 3.487209 GCCGAGACTAACTACAGCAGTAC 60.487 52.174 0.00 0.00 36.04 2.73
2011 2815 6.618811 CAATATCCGTGTATACTAGTCCACC 58.381 44.000 0.00 0.00 0.00 4.61
2012 2816 6.072064 AGCAATATCCGTGTATACTAGTCCAC 60.072 42.308 0.00 4.44 0.00 4.02
2013 2817 6.008331 AGCAATATCCGTGTATACTAGTCCA 58.992 40.000 0.00 0.00 0.00 4.02
2016 2820 6.015350 AGCAAGCAATATCCGTGTATACTAGT 60.015 38.462 0.00 0.00 0.00 2.57
2017 2821 6.390721 AGCAAGCAATATCCGTGTATACTAG 58.609 40.000 4.17 0.00 0.00 2.57
2034 2846 4.761227 TGTGATGAACAATAAGAGCAAGCA 59.239 37.500 0.00 0.00 35.24 3.91
2072 2892 3.370978 GTGCGCACTAAGCAAGAATCTAA 59.629 43.478 32.55 0.00 46.97 2.10
2086 2906 1.084370 GCTTAGGATTCGTGCGCACT 61.084 55.000 35.27 19.61 0.00 4.40
2130 2950 4.530946 ACCCCGTAACAGCAAGCTATATAT 59.469 41.667 0.00 0.00 0.00 0.86
2176 3006 9.534565 TTATGTAGAGTAATCAGAACATCAAGC 57.465 33.333 8.48 0.00 0.00 4.01
2203 3033 1.279271 GTCTGGCTTGGCTTTAGAGGA 59.721 52.381 0.00 0.00 0.00 3.71
2207 3037 1.168714 GTGGTCTGGCTTGGCTTTAG 58.831 55.000 0.00 0.00 0.00 1.85
2221 3054 1.604278 GAACTTTCAGCACAGGTGGTC 59.396 52.381 0.38 0.00 39.58 4.02
2222 3055 1.064758 TGAACTTTCAGCACAGGTGGT 60.065 47.619 0.00 0.00 42.74 4.16
2223 3056 1.679139 TGAACTTTCAGCACAGGTGG 58.321 50.000 1.10 0.00 32.50 4.61
2224 3057 3.781079 TTTGAACTTTCAGCACAGGTG 57.219 42.857 0.00 0.00 38.61 4.00
2225 3058 4.799564 TTTTTGAACTTTCAGCACAGGT 57.200 36.364 0.00 0.00 38.61 4.00
2244 3077 1.484038 TTCAGCACAGGTGGCTTTTT 58.516 45.000 1.10 0.00 40.23 1.94
2245 3078 1.410153 CTTTCAGCACAGGTGGCTTTT 59.590 47.619 1.10 0.00 40.23 2.27
2246 3079 1.035139 CTTTCAGCACAGGTGGCTTT 58.965 50.000 1.10 0.00 40.23 3.51
2273 3106 6.098552 TCACGAATCCACCATATTGTAACCTA 59.901 38.462 0.00 0.00 0.00 3.08
2283 3116 1.488393 TGGCATCACGAATCCACCATA 59.512 47.619 0.00 0.00 0.00 2.74
2286 3119 2.098293 GTGGCATCACGAATCCACC 58.902 57.895 8.91 0.00 42.25 4.61
2333 3167 7.872483 CAGGGTTTATTTTTCACTGCTTATGTT 59.128 33.333 0.00 0.00 0.00 2.71
2336 3170 7.539034 ACAGGGTTTATTTTTCACTGCTTAT 57.461 32.000 0.00 0.00 36.22 1.73
2337 3171 6.969993 ACAGGGTTTATTTTTCACTGCTTA 57.030 33.333 0.00 0.00 36.22 3.09
2428 3262 3.254166 CCTCGATTTATCCCTGGCATTTG 59.746 47.826 0.00 0.00 0.00 2.32
2429 3263 3.490348 CCTCGATTTATCCCTGGCATTT 58.510 45.455 0.00 0.00 0.00 2.32
2432 3266 0.108585 GCCTCGATTTATCCCTGGCA 59.891 55.000 2.01 0.00 38.79 4.92
2441 3275 4.827481 GCTGACGGCCTCGATTTA 57.173 55.556 0.00 0.00 40.11 1.40
2520 3354 3.610040 TTAATCGTGCTGGTCTGTCAT 57.390 42.857 0.00 0.00 0.00 3.06
2535 3369 9.007901 AGCTGTAATTCATCTGCCTTATTAATC 57.992 33.333 0.00 0.00 0.00 1.75
2563 3397 5.005107 GCGTACTAGTAGTGTTAATTGTGCC 59.995 44.000 13.29 0.00 0.00 5.01
2626 3465 0.452784 GCAGTGGCGAATTCGAACAC 60.453 55.000 31.54 31.54 43.79 3.32
2646 3485 3.390135 TCTCTTGTGACACCGAAATGAC 58.610 45.455 2.45 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.