Multiple sequence alignment - TraesCS3B01G477400

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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 TraesCS3B01G477400 chr3B 100.000 3756 0 0 1 3756 725711668 725707913 0.000000e+00 6937
1 TraesCS3B01G477400 chr3A 91.058 2080 122 28 156 2195 685124086 685122031 0.000000e+00 2752
2 TraesCS3B01G477400 chr3A 94.185 1565 62 5 2195 3756 685121934 685120396 0.000000e+00 2359
3 TraesCS3B01G477400 chr3A 88.281 128 13 2 4 129 685124364 685124237 6.500000e-33 152
4 TraesCS3B01G477400 chr3D 95.730 1569 59 3 2195 3756 548249322 548247755 0.000000e+00 2519
5 TraesCS3B01G477400 chr3D 92.839 1536 90 14 666 2195 548250940 548249419 0.000000e+00 2209
6 TraesCS3B01G477400 chr3D 86.486 518 42 16 162 661 548251483 548250976 9.180000e-151 544
7 TraesCS3B01G477400 chr3D 96.078 153 6 0 1426 1578 54716778 54716930 2.240000e-62 250
8 TraesCS3B01G477400 chr3D 94.969 159 8 0 1426 1584 520650537 520650379 2.240000e-62 250
9 TraesCS3B01G477400 chr3D 93.130 131 7 2 1 129 548251774 548251644 1.380000e-44 191
10 TraesCS3B01G477400 chr2D 94.272 419 23 1 960 1377 352630722 352631140 1.140000e-179 640
11 TraesCS3B01G477400 chr2D 94.170 223 13 0 1362 1584 352631371 352631593 1.290000e-89 340
12 TraesCS3B01G477400 chr2D 94.969 159 8 0 1426 1584 577120815 577120657 2.240000e-62 250
13 TraesCS3B01G477400 chr6D 94.969 159 8 0 1426 1584 469922874 469922716 2.240000e-62 250
14 TraesCS3B01G477400 chr6D 94.969 159 8 0 1426 1584 469924304 469924146 2.240000e-62 250
15 TraesCS3B01G477400 chr2B 94.969 159 8 0 1426 1584 766560150 766559992 2.240000e-62 250


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 TraesCS3B01G477400 chr3B 725707913 725711668 3755 True 6937.000000 6937 100.000000 1 3756 1 chr3B.!!$R1 3755
1 TraesCS3B01G477400 chr3A 685120396 685124364 3968 True 1754.333333 2752 91.174667 4 3756 3 chr3A.!!$R1 3752
2 TraesCS3B01G477400 chr3D 548247755 548251774 4019 True 1365.750000 2519 92.046250 1 3756 4 chr3D.!!$R2 3755
3 TraesCS3B01G477400 chr2D 352630722 352631593 871 False 490.000000 640 94.221000 960 1584 2 chr2D.!!$F1 624
4 TraesCS3B01G477400 chr6D 469922716 469924304 1588 True 250.000000 250 94.969000 1426 1584 2 chr6D.!!$R1 158

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
734 918 0.039346 TACGTCGTTGTCGGAATGCA 60.039 50.0 1.78 0.0 37.69 3.96 F
1546 1999 0.178961 GTTGGTGGCCTTTTCTCCCT 60.179 55.0 3.32 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1855 2308 0.687920 TGGAGTTGGTGCCGATGTAA 59.312 50.0 0.00 0.00 0.0 2.41 R
2880 3431 0.309922 CACTTGAGTTGCACAGCTGG 59.690 55.0 19.93 8.27 0.0 4.85 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
44 45 9.748708 TGGAATTTGTTGATATAGCTTATTTGC 57.251 29.630 0.00 0.00 0.00 3.68
112 114 5.106442 CACGTATACATGGAGCAACAGTTA 58.894 41.667 3.32 0.00 0.00 2.24
114 116 6.921307 CACGTATACATGGAGCAACAGTTATA 59.079 38.462 3.32 0.00 0.00 0.98
118 120 9.326413 GTATACATGGAGCAACAGTTATACTTT 57.674 33.333 0.00 0.00 29.93 2.66
120 122 7.524717 ACATGGAGCAACAGTTATACTTTTT 57.475 32.000 0.00 0.00 0.00 1.94
148 150 2.694213 TGCGCATAGAGCAACAGTTAA 58.306 42.857 5.66 0.00 46.13 2.01
150 152 4.438148 TGCGCATAGAGCAACAGTTAATA 58.562 39.130 5.66 0.00 46.13 0.98
151 153 4.270084 TGCGCATAGAGCAACAGTTAATAC 59.730 41.667 5.66 0.00 46.13 1.89
153 155 5.006746 GCGCATAGAGCAACAGTTAATACTT 59.993 40.000 0.30 0.00 46.13 2.24
154 156 6.641062 CGCATAGAGCAACAGTTAATACTTC 58.359 40.000 0.00 0.00 46.13 3.01
155 157 6.477033 CGCATAGAGCAACAGTTAATACTTCT 59.523 38.462 0.00 0.00 46.13 2.85
160 162 8.779354 AGAGCAACAGTTAATACTTCTAAAGG 57.221 34.615 0.00 0.00 30.26 3.11
166 301 7.762382 ACAGTTAATACTTCTAAAGGCATTGC 58.238 34.615 0.00 0.00 30.26 3.56
185 320 1.335324 GCTGGTTTGCAAGCACTACTG 60.335 52.381 15.54 3.17 41.32 2.74
218 353 3.916359 TCGCATACCCCTTTTGTATGA 57.084 42.857 13.09 0.00 45.38 2.15
278 413 3.637432 ACAGTTTTTGTGTGTGTGTGTG 58.363 40.909 0.00 0.00 38.99 3.82
279 414 3.067461 ACAGTTTTTGTGTGTGTGTGTGT 59.933 39.130 0.00 0.00 38.99 3.72
280 415 3.424861 CAGTTTTTGTGTGTGTGTGTGTG 59.575 43.478 0.00 0.00 0.00 3.82
282 417 2.695613 TTTGTGTGTGTGTGTGTGTG 57.304 45.000 0.00 0.00 0.00 3.82
283 418 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
388 523 7.502561 GGGAATTTTATTAGTGCTAGTCATGGT 59.497 37.037 0.00 0.00 0.00 3.55
414 549 6.571588 CGAAATATTTGAATATTGCAACGGC 58.428 36.000 5.17 0.00 39.89 5.68
416 551 2.270275 TTTGAATATTGCAACGGCCG 57.730 45.000 26.86 26.86 40.13 6.13
417 552 1.454201 TTGAATATTGCAACGGCCGA 58.546 45.000 35.90 9.64 40.13 5.54
522 657 1.065102 AGTACGTGTCATAGCGCGAAT 59.935 47.619 12.10 0.00 44.10 3.34
526 661 2.158841 ACGTGTCATAGCGCGAATTTTT 59.841 40.909 12.10 0.00 44.10 1.94
560 712 0.601576 TGGTTGTGCGCGTTATCTGT 60.602 50.000 8.43 0.00 0.00 3.41
561 713 0.515564 GGTTGTGCGCGTTATCTGTT 59.484 50.000 8.43 0.00 0.00 3.16
562 714 1.463528 GGTTGTGCGCGTTATCTGTTC 60.464 52.381 8.43 0.00 0.00 3.18
570 722 5.566016 GTGCGCGTTATCTGTTCAATAAAAA 59.434 36.000 8.43 0.00 0.00 1.94
575 727 7.535940 CGCGTTATCTGTTCAATAAAAAGGAAA 59.464 33.333 0.00 0.00 0.00 3.13
576 728 8.635983 GCGTTATCTGTTCAATAAAAAGGAAAC 58.364 33.333 0.00 0.00 0.00 2.78
706 890 7.880160 TTATGTGCTAATAATTGCTTGGTCT 57.120 32.000 0.00 0.00 0.00 3.85
721 905 1.344942 GGTCTGTGCTGCTTACGTCG 61.345 60.000 0.00 0.00 0.00 5.12
734 918 0.039346 TACGTCGTTGTCGGAATGCA 60.039 50.000 1.78 0.00 37.69 3.96
739 923 1.944024 TCGTTGTCGGAATGCACTTTT 59.056 42.857 0.00 0.00 37.69 2.27
772 956 6.930164 ACAACTGCTCATATTCATCTCTCATC 59.070 38.462 0.00 0.00 0.00 2.92
790 974 3.576982 TCATCTAACCGGTCCATCCATAC 59.423 47.826 8.04 0.00 35.57 2.39
794 978 1.801242 ACCGGTCCATCCATACATGA 58.199 50.000 0.00 0.00 35.57 3.07
853 1037 1.715519 CACTTTGTATTGTTGCGCTGC 59.284 47.619 9.73 1.25 0.00 5.25
1147 1337 0.391597 TTCGTCGGGTCAAGCTCTTT 59.608 50.000 0.00 0.00 0.00 2.52
1162 1352 2.611518 CTCTTTCAGGTACCGCTCAAG 58.388 52.381 6.18 7.91 0.00 3.02
1223 1413 6.308766 CAGCTGGTGTCAAATTAGCATTTTAC 59.691 38.462 5.57 0.00 36.87 2.01
1229 1419 9.699703 GGTGTCAAATTAGCATTTTACCTTAAA 57.300 29.630 0.00 0.00 31.47 1.52
1257 1447 7.137426 ACTACTTTTGTTGTGTACTCTAGACG 58.863 38.462 0.00 0.00 37.04 4.18
1370 1560 5.047164 TGGAGAAGTATACAACGGTTTGCTA 60.047 40.000 5.50 0.00 36.00 3.49
1546 1999 0.178961 GTTGGTGGCCTTTTCTCCCT 60.179 55.000 3.32 0.00 0.00 4.20
1712 2165 9.757227 TTTCATTGTGTGTTTCCTATTTTTAGG 57.243 29.630 0.00 0.00 38.58 2.69
1796 2249 0.729140 GCAACGGCAATTCTCCAACG 60.729 55.000 0.00 0.00 40.72 4.10
1855 2308 1.980036 TGGAACCGCTAAGGGTAAGTT 59.020 47.619 0.00 0.00 42.60 2.66
1874 2327 0.687920 TTACATCGGCACCAACTCCA 59.312 50.000 0.00 0.00 0.00 3.86
1885 2338 3.861886 GCACCAACTCCACATTTCCATTG 60.862 47.826 0.00 0.00 0.00 2.82
1907 2360 3.084536 TGGCAGAGGCATGTTTTCATA 57.915 42.857 0.00 0.00 43.71 2.15
1948 2402 7.446931 TGCCTCATTTTCAGTCACAAAGTTATA 59.553 33.333 0.00 0.00 0.00 0.98
2079 2533 1.439353 CCTGGTGGATGCGGATTTCG 61.439 60.000 0.00 0.00 37.46 3.46
2138 2592 0.107456 ATCGACTAGGCAATGCTGGG 59.893 55.000 4.82 0.00 0.00 4.45
2147 2601 4.365111 AATGCTGGGCCGCCTTCA 62.365 61.111 9.86 5.35 0.00 3.02
2171 2625 8.724229 TCAATGATATTCAATGATCCATTCGTC 58.276 33.333 0.00 0.00 31.87 4.20
2174 2628 6.366061 TGATATTCAATGATCCATTCGTCGAC 59.634 38.462 5.18 5.18 31.05 4.20
2177 2631 0.393077 ATGATCCATTCGTCGACCCC 59.607 55.000 10.58 0.00 0.00 4.95
2191 2645 1.129058 GACCCCCGGTAATGACTGAT 58.871 55.000 0.00 0.00 35.25 2.90
2220 2771 1.846007 AGCAAATTTACCGGCATCCA 58.154 45.000 0.00 0.00 0.00 3.41
2221 2772 2.387757 AGCAAATTTACCGGCATCCAT 58.612 42.857 0.00 0.00 0.00 3.41
2238 2789 6.854496 CATCCATTGCTTGATTTTAATGGG 57.146 37.500 13.16 0.00 46.00 4.00
2406 2957 8.130671 ACTGATTCCTGATGATTGTTCAATTT 57.869 30.769 0.00 0.00 34.96 1.82
2407 2958 8.591072 ACTGATTCCTGATGATTGTTCAATTTT 58.409 29.630 0.00 0.00 34.96 1.82
2496 3047 3.969312 TCCATCTCTGATATGCAGGTTCA 59.031 43.478 0.00 0.00 44.98 3.18
2497 3048 4.409901 TCCATCTCTGATATGCAGGTTCAA 59.590 41.667 0.00 0.00 44.98 2.69
2518 3069 9.305925 GTTCAAAACTTTCAAGAATCAAGTGAT 57.694 29.630 0.00 0.00 36.07 3.06
2621 3172 1.006571 GTGAACCCGACAAGCGAGA 60.007 57.895 0.00 0.00 44.57 4.04
2650 3201 1.606531 GATGAGCCTGGTGGAAGCT 59.393 57.895 0.00 0.00 40.24 3.74
2694 3245 1.028905 GAGATCAGGAGGACGACAGG 58.971 60.000 0.00 0.00 0.00 4.00
2796 3347 3.950395 AGCATTTCAAAGGCTAAGCTAGG 59.050 43.478 7.70 0.00 35.82 3.02
2864 3415 6.266131 TGCCCCATTAGTTTCTTCTCATAT 57.734 37.500 0.00 0.00 0.00 1.78
3032 3585 4.931661 AGACTTTTGTAACACCGAGAGA 57.068 40.909 0.00 0.00 0.00 3.10
3048 3601 0.037232 GAGAGTAGCGCCAAACTGGT 60.037 55.000 11.88 0.31 40.46 4.00
3102 3658 6.677781 TTGCCATTAGTAGCATAGTGTTTC 57.322 37.500 0.00 0.00 39.11 2.78
3111 3667 6.109359 AGTAGCATAGTGTTTCCTGACAATC 58.891 40.000 0.00 0.00 0.00 2.67
3172 3728 4.165950 TCCTTTTCTTGGAGCTATGCCATA 59.834 41.667 0.00 0.00 34.90 2.74
3258 3814 2.158769 TGAATCTAGCCAATGCGACCAT 60.159 45.455 0.00 0.00 44.33 3.55
3260 3816 0.249447 TCTAGCCAATGCGACCATCG 60.249 55.000 0.00 0.00 44.33 3.84
3466 4022 2.467838 CATCTCGATGACGCAGAACAT 58.532 47.619 0.59 0.00 41.20 2.71
3579 4139 6.835174 ACAGATGATGCATGTAAATAGGAGT 58.165 36.000 2.46 0.00 0.00 3.85
3683 4243 3.940221 GAGATGAGTGCTGCAAGAGATTT 59.060 43.478 2.77 0.00 34.07 2.17
3687 4247 2.157738 AGTGCTGCAAGAGATTTCCAC 58.842 47.619 2.77 0.00 34.07 4.02
3705 4265 4.774124 TCCACTGATGCTAATGAGAAAGG 58.226 43.478 0.00 0.00 0.00 3.11
3739 4300 7.712639 ACATGTATACTGTTTCCAGATAGCAAG 59.287 37.037 0.00 0.00 41.50 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 7.413475 AAAAAGCACGCAGTATGATCTATAG 57.587 36.000 0.00 0.00 41.61 1.31
129 131 3.951979 ATTAACTGTTGCTCTATGCGC 57.048 42.857 0.00 0.00 46.63 6.09
131 133 7.778470 AGAAGTATTAACTGTTGCTCTATGC 57.222 36.000 2.69 0.00 37.94 3.14
134 136 9.871238 CCTTTAGAAGTATTAACTGTTGCTCTA 57.129 33.333 2.69 0.00 35.62 2.43
135 137 7.334671 GCCTTTAGAAGTATTAACTGTTGCTCT 59.665 37.037 2.69 0.00 35.62 4.09
136 138 7.119262 TGCCTTTAGAAGTATTAACTGTTGCTC 59.881 37.037 2.69 0.00 35.62 4.26
138 140 7.141100 TGCCTTTAGAAGTATTAACTGTTGC 57.859 36.000 2.69 0.00 35.62 4.17
142 144 7.912250 CAGCAATGCCTTTAGAAGTATTAACTG 59.088 37.037 0.00 0.00 35.62 3.16
145 147 6.889722 ACCAGCAATGCCTTTAGAAGTATTAA 59.110 34.615 0.00 0.00 0.00 1.40
148 150 4.860022 ACCAGCAATGCCTTTAGAAGTAT 58.140 39.130 0.00 0.00 0.00 2.12
150 152 3.160679 ACCAGCAATGCCTTTAGAAGT 57.839 42.857 0.00 0.00 0.00 3.01
151 153 4.240096 CAAACCAGCAATGCCTTTAGAAG 58.760 43.478 0.00 0.00 0.00 2.85
153 155 2.029110 GCAAACCAGCAATGCCTTTAGA 60.029 45.455 0.00 0.00 34.03 2.10
154 156 2.288948 TGCAAACCAGCAATGCCTTTAG 60.289 45.455 0.00 0.00 42.46 1.85
155 157 1.690893 TGCAAACCAGCAATGCCTTTA 59.309 42.857 0.00 0.00 42.46 1.85
166 301 2.693797 CAGTAGTGCTTGCAAACCAG 57.306 50.000 0.00 0.00 0.00 4.00
218 353 2.430921 CAGGAACGCTTCGTCGCT 60.431 61.111 0.00 0.00 39.99 4.93
278 413 7.193377 TGACAATGCATGATCATATACACAC 57.807 36.000 8.15 0.00 0.00 3.82
279 414 7.255208 GGTTGACAATGCATGATCATATACACA 60.255 37.037 8.15 2.71 0.00 3.72
280 415 7.080099 GGTTGACAATGCATGATCATATACAC 58.920 38.462 8.15 8.23 0.00 2.90
282 417 7.205737 TGGTTGACAATGCATGATCATATAC 57.794 36.000 8.15 8.79 0.00 1.47
283 418 7.820578 TTGGTTGACAATGCATGATCATATA 57.179 32.000 8.15 0.44 33.18 0.86
388 523 6.198029 CCGTTGCAATATTCAAATATTTCGCA 59.802 34.615 0.59 12.73 39.03 5.10
414 549 4.494484 CCTTTTGCCTTTTATTTCCTCGG 58.506 43.478 0.00 0.00 0.00 4.63
416 551 3.926527 CGCCTTTTGCCTTTTATTTCCTC 59.073 43.478 0.00 0.00 36.24 3.71
417 552 3.864540 GCGCCTTTTGCCTTTTATTTCCT 60.865 43.478 0.00 0.00 36.24 3.36
443 578 1.511043 CAATTACGTGGCGTTGCGG 60.511 57.895 0.00 0.00 41.54 5.69
526 661 4.624882 GCACAACCATTGCGATAATTCAAA 59.375 37.500 0.00 0.00 0.00 2.69
528 663 3.768406 GCACAACCATTGCGATAATTCA 58.232 40.909 0.00 0.00 0.00 2.57
541 693 0.601576 ACAGATAACGCGCACAACCA 60.602 50.000 5.73 0.00 0.00 3.67
545 697 1.503294 TTGAACAGATAACGCGCACA 58.497 45.000 5.73 0.00 0.00 4.57
560 712 9.699703 CCTTTTATCGGTTTCCTTTTTATTGAA 57.300 29.630 0.00 0.00 0.00 2.69
561 713 7.815549 GCCTTTTATCGGTTTCCTTTTTATTGA 59.184 33.333 0.00 0.00 0.00 2.57
562 714 7.600752 TGCCTTTTATCGGTTTCCTTTTTATTG 59.399 33.333 0.00 0.00 0.00 1.90
570 722 4.021456 CCTTTTGCCTTTTATCGGTTTCCT 60.021 41.667 0.00 0.00 0.00 3.36
575 727 1.201414 CGCCTTTTGCCTTTTATCGGT 59.799 47.619 0.00 0.00 36.24 4.69
576 728 1.908065 CGCCTTTTGCCTTTTATCGG 58.092 50.000 0.00 0.00 36.24 4.18
706 890 0.528901 ACAACGACGTAAGCAGCACA 60.529 50.000 0.00 0.00 45.62 4.57
721 905 3.626028 AGAAAAGTGCATTCCGACAAC 57.374 42.857 0.00 0.00 0.00 3.32
734 918 6.942532 TGAGCAGTTGTGAAATAGAAAAGT 57.057 33.333 0.00 0.00 0.00 2.66
739 923 8.969260 ATGAATATGAGCAGTTGTGAAATAGA 57.031 30.769 0.00 0.00 0.00 1.98
772 956 3.323691 TCATGTATGGATGGACCGGTTAG 59.676 47.826 9.42 0.00 42.61 2.34
866 1050 6.509418 ACAAGCAATAACAATAACCGACAT 57.491 33.333 0.00 0.00 0.00 3.06
917 1101 5.817816 AGATGCAACCTAAATAGTGTAGTGC 59.182 40.000 0.00 0.00 0.00 4.40
918 1102 6.238211 GCAGATGCAACCTAAATAGTGTAGTG 60.238 42.308 0.00 0.00 41.59 2.74
920 1104 6.292389 GCAGATGCAACCTAAATAGTGTAG 57.708 41.667 0.00 0.00 41.59 2.74
936 1120 4.309347 CAGCGGCGATGCAGATGC 62.309 66.667 13.77 0.00 33.32 3.91
1147 1337 2.522185 ACTAACTTGAGCGGTACCTGA 58.478 47.619 10.90 0.00 0.00 3.86
1162 1352 8.671384 AAATTAAAAGCCCCTCAAAAACTAAC 57.329 30.769 0.00 0.00 0.00 2.34
1229 1419 8.910944 TCTAGAGTACACAACAAAAGTAGTCTT 58.089 33.333 12.67 1.28 42.74 3.01
1235 1425 5.747197 CACGTCTAGAGTACACAACAAAAGT 59.253 40.000 0.00 0.00 0.00 2.66
1346 1536 3.998341 GCAAACCGTTGTATACTTCTCCA 59.002 43.478 4.17 0.00 37.06 3.86
1352 1542 4.221262 TCCTGTAGCAAACCGTTGTATACT 59.779 41.667 4.17 0.00 37.06 2.12
1370 1560 3.141398 CGCTATAATTGTGCCATCCTGT 58.859 45.455 0.00 0.00 0.00 4.00
1424 1861 4.320608 TTTTGGCACCTCATGAAGAAAC 57.679 40.909 0.00 0.00 0.00 2.78
1546 1999 8.159645 CGGATCGACGACAGGTAATTAACCTA 62.160 46.154 0.00 0.00 46.83 3.08
1566 2019 1.447314 GTTGGGGTGACGACGGATC 60.447 63.158 0.00 0.00 0.00 3.36
1578 2031 3.763897 CCAAGAGATTTACAAGGTTGGGG 59.236 47.826 0.00 0.00 31.21 4.96
1688 2141 8.472007 ACCTAAAAATAGGAAACACACAATGA 57.528 30.769 8.83 0.00 39.60 2.57
1708 2161 5.480422 TGCTCTTCTTGTACATCAGACCTAA 59.520 40.000 0.00 0.00 0.00 2.69
1712 2165 5.414360 TGATGCTCTTCTTGTACATCAGAC 58.586 41.667 0.00 0.00 41.49 3.51
1796 2249 2.941720 CTGCTTGAATTCTAGCCTCACC 59.058 50.000 30.36 10.17 42.61 4.02
1855 2308 0.687920 TGGAGTTGGTGCCGATGTAA 59.312 50.000 0.00 0.00 0.00 2.41
1885 2338 1.340889 TGAAAACATGCCTCTGCCAAC 59.659 47.619 0.00 0.00 36.33 3.77
1907 2360 9.807649 GAAAATGAGGCAATTCATAATGTAGTT 57.192 29.630 0.00 0.00 36.81 2.24
1962 2416 9.263446 ACAGTAACAGGAAAGGTCATTATACTA 57.737 33.333 0.00 0.00 0.00 1.82
1963 2417 8.147244 ACAGTAACAGGAAAGGTCATTATACT 57.853 34.615 0.00 0.00 0.00 2.12
1964 2418 8.788325 AACAGTAACAGGAAAGGTCATTATAC 57.212 34.615 0.00 0.00 0.00 1.47
1997 2451 1.896220 TGGAATGCAGGTGACTCAAC 58.104 50.000 0.00 0.00 40.21 3.18
1998 2452 2.040145 TCATGGAATGCAGGTGACTCAA 59.960 45.455 0.00 0.00 46.21 3.02
2079 2533 4.379499 GCCAGTATCAGCAACTTTTGGTAC 60.379 45.833 0.00 0.00 39.79 3.34
2138 2592 3.988379 TTGAATATCATTGAAGGCGGC 57.012 42.857 0.00 0.00 0.00 6.53
2147 2601 7.603784 TCGACGAATGGATCATTGAATATCATT 59.396 33.333 0.00 0.00 33.90 2.57
2171 2625 1.143183 CAGTCATTACCGGGGGTCG 59.857 63.158 6.32 0.00 37.09 4.79
2174 2628 1.424638 AGATCAGTCATTACCGGGGG 58.575 55.000 6.32 0.00 0.00 5.40
2177 2631 6.090483 ACTATCAAGATCAGTCATTACCGG 57.910 41.667 0.00 0.00 0.00 5.28
2191 2645 5.526111 GCCGGTAAATTTGCTACTATCAAGA 59.474 40.000 1.90 0.00 0.00 3.02
2220 2771 7.404481 ACAAATCCCCATTAAAATCAAGCAAT 58.596 30.769 0.00 0.00 0.00 3.56
2221 2772 6.777782 ACAAATCCCCATTAAAATCAAGCAA 58.222 32.000 0.00 0.00 0.00 3.91
2224 2775 6.654161 TGCAACAAATCCCCATTAAAATCAAG 59.346 34.615 0.00 0.00 0.00 3.02
2225 2776 6.537355 TGCAACAAATCCCCATTAAAATCAA 58.463 32.000 0.00 0.00 0.00 2.57
2228 2779 6.598850 GTCATGCAACAAATCCCCATTAAAAT 59.401 34.615 0.00 0.00 0.00 1.82
2238 2789 1.205417 CCCTGGTCATGCAACAAATCC 59.795 52.381 0.00 0.00 0.00 3.01
2287 2838 5.050091 CACACCAAAACTGTAGACATCACTC 60.050 44.000 0.00 0.00 0.00 3.51
2296 2847 4.398044 ACAAGGAACACACCAAAACTGTAG 59.602 41.667 0.00 0.00 0.00 2.74
2525 3076 5.604231 TGGTCATTCTCCTATCTGCTATTGT 59.396 40.000 0.00 0.00 0.00 2.71
2650 3201 1.682740 TGCGTATCCGGTGTATCTCA 58.317 50.000 0.00 0.00 33.68 3.27
2669 3220 1.494960 GTCCTCCTGATCTCCTGCTT 58.505 55.000 0.00 0.00 0.00 3.91
2761 3312 7.223387 GCCTTTGAAATGCTATAACTTTCCATG 59.777 37.037 0.00 0.00 0.00 3.66
2796 3347 9.549078 CTAATCTATAACCCTGAAAGAGGAAAC 57.451 37.037 0.00 0.00 46.33 2.78
2880 3431 0.309922 CACTTGAGTTGCACAGCTGG 59.690 55.000 19.93 8.27 0.00 4.85
3025 3578 0.802607 GTTTGGCGCTACTCTCTCGG 60.803 60.000 7.64 0.00 0.00 4.63
3032 3585 1.346722 AGTTACCAGTTTGGCGCTACT 59.653 47.619 7.64 5.92 42.67 2.57
3102 3658 2.039818 ATGCAGAGCAGATTGTCAGG 57.960 50.000 0.00 0.00 43.65 3.86
3133 3689 6.877236 AGAAAAGGATCTTCAAACAAAGCAA 58.123 32.000 0.00 0.00 0.00 3.91
3140 3696 5.242615 AGCTCCAAGAAAAGGATCTTCAAAC 59.757 40.000 0.00 0.00 37.56 2.93
3172 3728 4.100373 AGCACTCTCTAAGGAAATCAGGT 58.900 43.478 0.00 0.00 0.00 4.00
3258 3814 3.270027 CATAGGTGCCATTCAGAAACGA 58.730 45.455 0.00 0.00 0.00 3.85
3260 3816 3.356290 ACCATAGGTGCCATTCAGAAAC 58.644 45.455 0.00 0.00 32.98 2.78
3466 4022 1.069204 GGGCAGCTATCTTCATCGTCA 59.931 52.381 0.00 0.00 0.00 4.35
3683 4243 4.225942 ACCTTTCTCATTAGCATCAGTGGA 59.774 41.667 0.00 0.00 0.00 4.02
3687 4247 6.183360 CCTTGAACCTTTCTCATTAGCATCAG 60.183 42.308 0.00 0.00 0.00 2.90
3705 4265 6.653320 TGGAAACAGTATACATGTCCTTGAAC 59.347 38.462 0.00 0.00 35.01 3.18


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

AutoCloner maintained by Alex Coulton.