Multiple sequence alignment - TraesCS4B01G123000

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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 TraesCS4B01G123000 chr4B 100.000 2666 0 0 1 2666 146494503 146491838 0.000000e+00 4924
1 TraesCS4B01G123000 chr4B 77.079 493 83 20 2027 2490 272070803 272070312 9.470000e-65 257
2 TraesCS4B01G123000 chr4B 78.961 385 69 8 2229 2607 25961113 25960735 4.410000e-63 252
3 TraesCS4B01G123000 chr4A 87.778 2021 145 50 2 1967 472921671 472923644 0.000000e+00 2270
4 TraesCS4B01G123000 chr4A 86.152 686 87 5 1982 2666 472931363 472932041 0.000000e+00 734
5 TraesCS4B01G123000 chr4D 87.399 1484 93 45 477 1905 102164233 102162789 0.000000e+00 1618
6 TraesCS4B01G123000 chr4D 87.802 787 72 12 1887 2666 102162109 102161340 0.000000e+00 900
7 TraesCS4B01G123000 chr7A 76.758 697 118 21 1935 2607 249586538 249585862 1.520000e-92 350
8 TraesCS4B01G123000 chr3D 77.677 551 96 14 1980 2508 475782349 475782894 7.170000e-81 311
9 TraesCS4B01G123000 chr3D 77.170 311 62 8 2181 2485 155720493 155720800 3.530000e-39 172
10 TraesCS4B01G123000 chr2A 79.303 459 82 12 2176 2626 320186832 320187285 2.580000e-80 309
11 TraesCS4B01G123000 chr7B 78.986 414 71 9 2176 2585 2956703 2956302 4.370000e-68 268
12 TraesCS4B01G123000 chr7B 79.412 306 49 12 2176 2478 478838252 478838546 1.250000e-48 204


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 TraesCS4B01G123000 chr4B 146491838 146494503 2665 True 4924 4924 100.0000 1 2666 1 chr4B.!!$R2 2665
1 TraesCS4B01G123000 chr4A 472921671 472923644 1973 False 2270 2270 87.7780 2 1967 1 chr4A.!!$F1 1965
2 TraesCS4B01G123000 chr4A 472931363 472932041 678 False 734 734 86.1520 1982 2666 1 chr4A.!!$F2 684
3 TraesCS4B01G123000 chr4D 102161340 102164233 2893 True 1259 1618 87.6005 477 2666 2 chr4D.!!$R1 2189
4 TraesCS4B01G123000 chr7A 249585862 249586538 676 True 350 350 76.7580 1935 2607 1 chr7A.!!$R1 672
5 TraesCS4B01G123000 chr3D 475782349 475782894 545 False 311 311 77.6770 1980 2508 1 chr3D.!!$F2 528


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
711 721 0.031585 CATTGATCCTGGCCGCATTG 59.968 55.0 0.0 0.0 0.0 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 1826 0.182537 TAGCTGCACACACCAAACCT 59.817 50.0 1.02 0.0 0.0 3.5 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
28 29 1.133790 GCCAGCTCATGACCAAATGTC 59.866 52.381 0.00 0.00 44.72 3.06
42 43 3.238497 TGTCTGTGGACACCCCGG 61.238 66.667 0.00 0.00 46.19 5.73
49 51 0.106149 GTGGACACCCCGGACATATC 59.894 60.000 0.73 0.00 37.93 1.63
63 65 3.433031 GGACATATCCGTGGACATTTGGA 60.433 47.826 0.00 0.00 34.48 3.53
81 83 2.025793 TGGAGTCTTGTTTGGTGAACCA 60.026 45.455 0.00 0.00 45.94 3.67
85 87 4.398319 AGTCTTGTTTGGTGAACCATAGG 58.602 43.478 2.34 0.00 46.97 2.57
87 89 5.010282 GTCTTGTTTGGTGAACCATAGGAT 58.990 41.667 2.34 0.00 46.97 3.24
100 102 6.906901 TGAACCATAGGATAAGTCTTAAGGGT 59.093 38.462 1.85 0.00 31.25 4.34
113 115 3.262405 TCTTAAGGGTAACTCCAACGCAT 59.738 43.478 1.85 0.00 38.11 4.73
125 127 1.791785 CCAACGCATGAACGCATTTTT 59.208 42.857 0.00 0.00 36.19 1.94
157 159 0.363512 CGCGTCGACAGAAATCACAG 59.636 55.000 17.16 0.00 0.00 3.66
166 168 1.546923 CAGAAATCACAGCCCAATGCA 59.453 47.619 0.00 0.00 44.83 3.96
168 170 0.244450 AAATCACAGCCCAATGCACG 59.756 50.000 0.00 0.00 44.83 5.34
177 179 1.408702 GCCCAATGCACGGACATAAAT 59.591 47.619 5.55 0.00 40.77 1.40
178 180 2.543653 GCCCAATGCACGGACATAAATC 60.544 50.000 5.55 0.00 40.77 2.17
179 181 2.951642 CCCAATGCACGGACATAAATCT 59.048 45.455 5.55 0.00 0.00 2.40
197 199 2.305928 TCTGTTTTGTGTCCATGTGGG 58.694 47.619 0.00 0.00 35.41 4.61
204 206 1.606025 TGTCCATGTGGGCGCAAAT 60.606 52.632 10.83 1.76 44.44 2.32
221 223 1.937191 AATCCGCCTCAAATTTGGGT 58.063 45.000 16.75 0.00 0.00 4.51
222 224 1.474330 ATCCGCCTCAAATTTGGGTC 58.526 50.000 16.75 2.86 0.00 4.46
236 238 1.379843 GGGTCGGGTTTGCATCCAT 60.380 57.895 10.02 0.00 0.00 3.41
244 246 2.687935 GGGTTTGCATCCATACGAACAT 59.312 45.455 10.02 0.00 32.72 2.71
249 251 3.457234 TGCATCCATACGAACATGAGAC 58.543 45.455 0.00 0.00 0.00 3.36
250 252 2.472861 GCATCCATACGAACATGAGACG 59.527 50.000 0.00 4.55 0.00 4.18
251 253 3.795488 GCATCCATACGAACATGAGACGA 60.795 47.826 0.00 0.00 0.00 4.20
252 254 3.416119 TCCATACGAACATGAGACGAC 57.584 47.619 0.00 0.00 0.00 4.34
254 256 2.109463 CATACGAACATGAGACGACCG 58.891 52.381 0.00 0.00 0.00 4.79
256 258 2.497092 CGAACATGAGACGACCGCG 61.497 63.158 0.00 0.00 44.79 6.46
299 301 3.741388 CGCCCTACAGTCCTTTTAGATGG 60.741 52.174 0.00 0.00 0.00 3.51
302 304 3.199946 CCTACAGTCCTTTTAGATGGGCA 59.800 47.826 0.00 0.00 0.00 5.36
303 305 3.356529 ACAGTCCTTTTAGATGGGCAG 57.643 47.619 0.00 0.00 0.00 4.85
305 307 1.566231 AGTCCTTTTAGATGGGCAGGG 59.434 52.381 0.00 0.00 0.00 4.45
307 309 0.756815 CCTTTTAGATGGGCAGGGGC 60.757 60.000 0.00 0.00 40.13 5.80
335 341 1.899438 GCCCACTCTTCTCCCTCTCTT 60.899 57.143 0.00 0.00 0.00 2.85
345 351 0.850883 TCCCTCTCTTTGCCCCCAAT 60.851 55.000 0.00 0.00 0.00 3.16
377 383 1.185315 CCCAACCCTAGCCATTGTTG 58.815 55.000 0.00 0.00 38.20 3.33
379 385 1.549203 CAACCCTAGCCATTGTTGCT 58.451 50.000 0.00 0.00 42.81 3.91
381 387 0.405585 ACCCTAGCCATTGTTGCTGT 59.594 50.000 0.00 0.00 39.91 4.40
382 388 1.203050 ACCCTAGCCATTGTTGCTGTT 60.203 47.619 0.00 0.00 39.91 3.16
385 391 3.955775 GCCATTGTTGCTGTTGGC 58.044 55.556 0.00 0.00 46.94 4.52
403 409 2.434359 CGGAGAGGGTTTCGGTGC 60.434 66.667 0.00 0.00 0.00 5.01
405 411 2.747686 GAGAGGGTTTCGGTGCCA 59.252 61.111 0.00 0.00 0.00 4.92
412 418 2.361104 TTTCGGTGCCAGCCATCC 60.361 61.111 0.00 0.00 0.00 3.51
449 455 1.534175 CGACGAGCTCAAGATACACCC 60.534 57.143 15.40 0.00 0.00 4.61
453 459 1.523938 GCTCAAGATACACCCCCGC 60.524 63.158 0.00 0.00 0.00 6.13
454 460 1.227263 CTCAAGATACACCCCCGCG 60.227 63.158 0.00 0.00 0.00 6.46
472 481 0.106918 CGGAGCTCTCCCTGTAGACT 60.107 60.000 14.64 0.00 46.96 3.24
503 512 1.432251 CGGCATAGGACGTCGACTT 59.568 57.895 14.70 3.52 41.88 3.01
506 515 0.179134 GCATAGGACGTCGACTTGCT 60.179 55.000 19.46 19.46 0.00 3.91
510 519 0.603569 AGGACGTCGACTTGCTGAAT 59.396 50.000 15.23 0.00 0.00 2.57
525 534 2.162681 CTGAATTGGGACACCTGGTTC 58.837 52.381 0.00 0.00 39.29 3.62
541 550 4.034258 TCGTGGACGAGCACGACC 62.034 66.667 16.99 16.99 46.91 4.79
586 595 1.372997 CGTGTGCGTGCTCCTAGTT 60.373 57.895 0.00 0.00 0.00 2.24
622 631 2.760385 GGGAGACCGGTGAGGAGG 60.760 72.222 14.63 0.00 45.00 4.30
707 717 3.599704 GGCATTGATCCTGGCCGC 61.600 66.667 0.00 0.00 36.58 6.53
708 718 2.829914 GCATTGATCCTGGCCGCA 60.830 61.111 0.00 0.00 0.00 5.69
709 719 2.198287 GCATTGATCCTGGCCGCAT 61.198 57.895 0.00 0.00 0.00 4.73
710 720 1.741327 GCATTGATCCTGGCCGCATT 61.741 55.000 0.00 0.00 0.00 3.56
711 721 0.031585 CATTGATCCTGGCCGCATTG 59.968 55.000 0.00 0.00 0.00 2.82
712 722 1.111116 ATTGATCCTGGCCGCATTGG 61.111 55.000 0.00 0.00 42.50 3.16
739 749 1.374252 GATGTCGTCGTGCCCAAGT 60.374 57.895 0.00 0.00 0.00 3.16
758 768 3.112709 GGAGCACGCGTTGGAGTC 61.113 66.667 10.22 1.38 0.00 3.36
815 830 5.486775 TGGATGATAATCAAAAGGCCCAAAA 59.513 36.000 0.00 0.00 0.00 2.44
843 868 1.536766 TGAGATTTGAAGCAGGCAACG 59.463 47.619 0.00 0.00 46.39 4.10
851 876 0.804989 AAGCAGGCAACGTATGAAGC 59.195 50.000 0.00 0.00 46.39 3.86
854 879 1.200020 GCAGGCAACGTATGAAGCTTT 59.800 47.619 0.00 0.00 46.39 3.51
1017 1069 0.555769 GCATGGGGTCCCCTAAATCA 59.444 55.000 28.11 6.69 45.70 2.57
1331 1383 2.050350 CCTCCTTCACCTACGCCGA 61.050 63.158 0.00 0.00 0.00 5.54
1669 1721 2.360475 GCACCAAGCTCTGACCCC 60.360 66.667 0.00 0.00 41.15 4.95
1670 1722 2.046892 CACCAAGCTCTGACCCCG 60.047 66.667 0.00 0.00 0.00 5.73
1671 1723 2.203788 ACCAAGCTCTGACCCCGA 60.204 61.111 0.00 0.00 0.00 5.14
1672 1724 1.613630 ACCAAGCTCTGACCCCGAT 60.614 57.895 0.00 0.00 0.00 4.18
1673 1725 1.153289 CCAAGCTCTGACCCCGATG 60.153 63.158 0.00 0.00 0.00 3.84
1674 1726 1.617018 CCAAGCTCTGACCCCGATGA 61.617 60.000 0.00 0.00 0.00 2.92
1675 1727 0.467384 CAAGCTCTGACCCCGATGAT 59.533 55.000 0.00 0.00 0.00 2.45
1676 1728 0.755686 AAGCTCTGACCCCGATGATC 59.244 55.000 0.00 0.00 0.00 2.92
1677 1729 1.006805 GCTCTGACCCCGATGATCG 60.007 63.158 8.05 8.05 40.07 3.69
1678 1730 1.456196 GCTCTGACCCCGATGATCGA 61.456 60.000 17.52 0.00 43.74 3.59
1771 1847 1.454847 GGGAGGTTTGGTGTGTGCA 60.455 57.895 0.00 0.00 0.00 4.57
1773 1849 1.360192 GAGGTTTGGTGTGTGCAGC 59.640 57.895 0.00 0.00 42.95 5.25
1785 1861 0.249114 TGTGCAGCTACACGTTCGAA 60.249 50.000 12.39 0.00 43.74 3.71
1786 1862 0.161024 GTGCAGCTACACGTTCGAAC 59.839 55.000 18.47 18.47 0.00 3.95
1795 1871 2.427905 CGTTCGAACGTCCGCTCA 60.428 61.111 35.92 0.00 46.63 4.26
1796 1872 2.704193 CGTTCGAACGTCCGCTCAC 61.704 63.158 35.92 4.53 46.63 3.51
1797 1873 2.049802 TTCGAACGTCCGCTCACC 60.050 61.111 0.00 0.00 0.00 4.02
1798 1874 3.884581 TTCGAACGTCCGCTCACCG 62.885 63.158 0.00 0.00 0.00 4.94
1861 1938 4.336532 AAATCGATGCGTTTGTTCTACC 57.663 40.909 0.00 0.00 0.00 3.18
1880 1957 1.138036 CGTACGTGCGAGATTGGGA 59.862 57.895 21.98 0.00 0.00 4.37
1890 1967 3.882888 TGCGAGATTGGGAATTTGTATCC 59.117 43.478 0.00 0.00 36.16 2.59
2027 2806 8.121305 AGCACATAGTTATTTCATGGTTTTGA 57.879 30.769 0.00 0.00 0.00 2.69
2036 2815 9.921637 GTTATTTCATGGTTTTGACTAATCCAA 57.078 29.630 3.96 0.00 38.70 3.53
2065 2844 4.620982 AGAAAAATCGGCTCAAAAACCTG 58.379 39.130 0.00 0.00 0.00 4.00
2089 2868 9.219603 CTGAACAAGTTGGTCTTATTTATGAGA 57.780 33.333 21.18 0.00 34.53 3.27
2124 2903 2.348411 ATCGGACAAATAGCAAGGGG 57.652 50.000 0.00 0.00 0.00 4.79
2128 2907 2.823154 CGGACAAATAGCAAGGGGAAAA 59.177 45.455 0.00 0.00 0.00 2.29
2211 3008 3.487372 AGATGTGGAATATCGTCGAGGA 58.513 45.455 10.66 10.66 39.70 3.71
2222 3019 3.431922 TCGTCGAGGAATCACAATACC 57.568 47.619 5.12 0.00 0.00 2.73
2274 3073 0.953471 GCGTGTGTATCAAGCCCACA 60.953 55.000 0.00 0.00 43.69 4.17
2323 3122 3.243636 ACGAGTACCATTGAACACGAACT 60.244 43.478 12.94 0.00 34.45 3.01
2327 3126 5.816919 AGTACCATTGAACACGAACTTTTG 58.183 37.500 0.00 0.00 0.00 2.44
2409 3209 3.192422 CGTCAATGGGCAAAGATAAACCA 59.808 43.478 0.00 0.00 35.39 3.67
2452 3252 1.209898 CGCCGCAACACAATGACAT 59.790 52.632 0.00 0.00 0.00 3.06
2467 3267 0.741915 GACATCCACGAGAGGGTCTC 59.258 60.000 0.00 0.00 40.06 3.36
2518 3319 4.575885 CCTTCACAAGGGAAAATAGACGA 58.424 43.478 0.00 0.00 45.27 4.20
2592 3394 1.302949 CCACCATCGACCCCAATGT 59.697 57.895 0.00 0.00 0.00 2.71
2647 3449 2.250031 ACATGCACCACACCAATCAAT 58.750 42.857 0.00 0.00 0.00 2.57
2655 3457 2.019249 CACACCAATCAATCGAGCCAT 58.981 47.619 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.394762 TCATGAGCTGGCATCCAACC 60.395 55.000 0.00 0.00 30.80 3.77
28 29 1.261938 TATGTCCGGGGTGTCCACAG 61.262 60.000 0.00 0.00 34.36 3.66
41 42 2.878406 CCAAATGTCCACGGATATGTCC 59.122 50.000 0.00 0.00 41.40 4.02
42 43 3.804036 TCCAAATGTCCACGGATATGTC 58.196 45.455 0.00 0.00 0.00 3.06
49 51 1.806542 CAAGACTCCAAATGTCCACGG 59.193 52.381 0.00 0.00 35.21 4.94
51 53 4.499696 CCAAACAAGACTCCAAATGTCCAC 60.500 45.833 0.00 0.00 35.21 4.02
81 83 8.294690 TGGAGTTACCCTTAAGACTTATCCTAT 58.705 37.037 3.36 0.00 38.00 2.57
85 87 6.755607 CGTTGGAGTTACCCTTAAGACTTATC 59.244 42.308 3.36 0.00 38.00 1.75
87 89 5.567423 GCGTTGGAGTTACCCTTAAGACTTA 60.567 44.000 3.36 0.00 38.00 2.24
100 102 0.793861 GCGTTCATGCGTTGGAGTTA 59.206 50.000 0.00 0.00 0.00 2.24
125 127 1.469703 TCGACGCGGATCTAAACAGAA 59.530 47.619 12.47 0.00 0.00 3.02
138 140 0.363512 CTGTGATTTCTGTCGACGCG 59.636 55.000 11.62 3.53 0.00 6.01
140 142 0.716108 GGCTGTGATTTCTGTCGACG 59.284 55.000 11.62 6.07 0.00 5.12
157 159 0.814457 TTTATGTCCGTGCATTGGGC 59.186 50.000 5.65 5.65 45.13 5.36
166 168 5.048991 GGACACAAAACAGATTTATGTCCGT 60.049 40.000 15.58 0.00 45.29 4.69
177 179 2.305928 CCCACATGGACACAAAACAGA 58.694 47.619 0.00 0.00 37.39 3.41
178 180 1.269726 GCCCACATGGACACAAAACAG 60.270 52.381 0.00 0.00 37.39 3.16
179 181 0.749649 GCCCACATGGACACAAAACA 59.250 50.000 0.00 0.00 37.39 2.83
197 199 0.458370 AATTTGAGGCGGATTTGCGC 60.458 50.000 8.00 8.00 35.06 6.09
204 206 0.958382 CGACCCAAATTTGAGGCGGA 60.958 55.000 19.28 0.00 0.00 5.54
221 223 0.537653 TCGTATGGATGCAAACCCGA 59.462 50.000 10.15 9.11 0.00 5.14
222 224 1.063469 GTTCGTATGGATGCAAACCCG 59.937 52.381 10.15 7.27 0.00 5.28
236 238 0.179181 GCGGTCGTCTCATGTTCGTA 60.179 55.000 0.00 0.00 0.00 3.43
263 265 3.255379 GGCGGACATCGAGCGAAC 61.255 66.667 0.00 0.00 42.43 3.95
271 273 1.043673 AGGACTGTAGGGCGGACATC 61.044 60.000 0.00 0.00 0.00 3.06
272 274 0.617820 AAGGACTGTAGGGCGGACAT 60.618 55.000 0.00 0.00 0.00 3.06
312 314 1.950973 GAGGGAGAAGAGTGGGCGTC 61.951 65.000 0.00 0.00 0.00 5.19
313 315 1.985116 GAGGGAGAAGAGTGGGCGT 60.985 63.158 0.00 0.00 0.00 5.68
335 341 1.691195 TATCGAGCGATTGGGGGCAA 61.691 55.000 10.89 0.00 36.17 4.52
345 351 1.141019 GTTGGGCACTATCGAGCGA 59.859 57.895 0.00 0.00 0.00 4.93
377 383 4.785453 CCCTCTCCGGCCAACAGC 62.785 72.222 2.24 0.00 42.60 4.40
379 385 2.406002 GAAACCCTCTCCGGCCAACA 62.406 60.000 2.24 0.00 0.00 3.33
381 387 2.754375 GAAACCCTCTCCGGCCAA 59.246 61.111 2.24 0.00 0.00 4.52
382 388 3.702048 CGAAACCCTCTCCGGCCA 61.702 66.667 2.24 0.00 0.00 5.36
385 391 2.264794 CACCGAAACCCTCTCCGG 59.735 66.667 0.00 0.00 46.65 5.14
427 433 0.100682 TGTATCTTGAGCTCGTCGGC 59.899 55.000 9.64 0.00 0.00 5.54
428 434 1.534175 GGTGTATCTTGAGCTCGTCGG 60.534 57.143 9.64 0.00 0.00 4.79
429 435 1.534175 GGGTGTATCTTGAGCTCGTCG 60.534 57.143 9.64 0.00 0.00 5.12
430 436 1.202428 GGGGTGTATCTTGAGCTCGTC 60.202 57.143 9.64 0.00 0.00 4.20
431 437 0.824759 GGGGTGTATCTTGAGCTCGT 59.175 55.000 9.64 0.00 0.00 4.18
439 445 2.364579 TCCGCGGGGGTGTATCTT 60.365 61.111 27.83 0.00 37.00 2.40
465 474 1.542492 GGTCGTGGAGGAAGTCTACA 58.458 55.000 0.00 0.00 36.44 2.74
467 476 0.679002 CGGGTCGTGGAGGAAGTCTA 60.679 60.000 0.00 0.00 0.00 2.59
503 512 0.251297 CCAGGTGTCCCAATTCAGCA 60.251 55.000 0.00 0.00 34.97 4.41
506 515 1.544537 CGAACCAGGTGTCCCAATTCA 60.545 52.381 0.00 0.00 0.00 2.57
510 519 1.147376 CACGAACCAGGTGTCCCAA 59.853 57.895 0.00 0.00 0.00 4.12
551 560 2.352032 CGGGAGGCGAAGAAGGACT 61.352 63.158 0.00 0.00 0.00 3.85
586 595 2.809174 CTCAATCGCCGCACGTGA 60.809 61.111 22.23 0.00 44.19 4.35
597 606 1.689582 ACCGGTCTCCCCCTCAATC 60.690 63.158 0.00 0.00 0.00 2.67
634 643 0.609957 TCCTCGACGGCCTTCTTGTA 60.610 55.000 7.75 0.00 0.00 2.41
721 731 1.352156 GACTTGGGCACGACGACATC 61.352 60.000 0.00 0.00 0.00 3.06
722 732 1.374252 GACTTGGGCACGACGACAT 60.374 57.895 0.00 0.00 0.00 3.06
723 733 2.028484 GACTTGGGCACGACGACA 59.972 61.111 0.00 0.00 0.00 4.35
724 734 3.103911 CGACTTGGGCACGACGAC 61.104 66.667 0.00 0.00 0.00 4.34
725 735 4.351938 CCGACTTGGGCACGACGA 62.352 66.667 0.00 0.00 0.00 4.20
726 736 4.351938 TCCGACTTGGGCACGACG 62.352 66.667 0.00 0.00 38.76 5.12
727 737 2.432628 CTCCGACTTGGGCACGAC 60.433 66.667 0.00 0.00 38.76 4.34
728 738 4.373116 GCTCCGACTTGGGCACGA 62.373 66.667 0.00 0.00 38.76 4.35
729 739 4.680237 TGCTCCGACTTGGGCACG 62.680 66.667 0.00 0.00 38.50 5.34
731 741 4.680237 CGTGCTCCGACTTGGGCA 62.680 66.667 0.00 0.00 40.31 5.36
735 745 3.036084 AACGCGTGCTCCGACTTG 61.036 61.111 14.98 0.00 39.56 3.16
736 746 3.036084 CAACGCGTGCTCCGACTT 61.036 61.111 14.98 0.00 39.56 3.01
739 749 4.717629 CTCCAACGCGTGCTCCGA 62.718 66.667 14.98 3.01 39.56 4.55
758 768 1.956477 CTTATCTTGGGGGCAAATCCG 59.044 52.381 0.00 0.00 34.94 4.18
815 830 5.873164 GCCTGCTTCAAATCTCAATCATTTT 59.127 36.000 0.00 0.00 0.00 1.82
821 836 3.366679 CGTTGCCTGCTTCAAATCTCAAT 60.367 43.478 0.00 0.00 0.00 2.57
826 851 3.126858 TCATACGTTGCCTGCTTCAAATC 59.873 43.478 0.00 0.00 0.00 2.17
831 856 1.202076 GCTTCATACGTTGCCTGCTTC 60.202 52.381 0.00 0.00 0.00 3.86
1017 1069 0.106519 CCATGGGGGAGCTCGATTTT 60.107 55.000 7.83 0.00 40.01 1.82
1342 1394 2.187163 GCGGTAGGAGAGGTTGGC 59.813 66.667 0.00 0.00 0.00 4.52
1518 1570 4.404098 ACGGTGGTGGCGGATTCC 62.404 66.667 0.00 0.00 0.00 3.01
1604 1656 1.758514 ATCTCCATGACGGCGACCT 60.759 57.895 16.62 0.00 29.06 3.85
1669 1721 0.791238 GCGAGATCCGTCGATCATCG 60.791 60.000 0.00 0.00 46.42 3.84
1670 1722 0.455295 GGCGAGATCCGTCGATCATC 60.455 60.000 8.43 0.00 46.42 2.92
1671 1723 1.581954 GGCGAGATCCGTCGATCAT 59.418 57.895 8.43 0.00 46.42 2.45
1672 1724 3.031495 GGCGAGATCCGTCGATCA 58.969 61.111 8.43 0.00 46.42 2.92
1756 1826 0.182537 TAGCTGCACACACCAAACCT 59.817 50.000 1.02 0.00 0.00 3.50
1757 1827 0.310854 GTAGCTGCACACACCAAACC 59.689 55.000 1.02 0.00 0.00 3.27
1798 1874 0.248289 TTCAATCCTCGGTCGAACCC 59.752 55.000 0.00 0.00 33.75 4.11
1799 1875 2.088950 TTTCAATCCTCGGTCGAACC 57.911 50.000 0.00 0.00 34.05 3.62
1800 1876 4.680171 AAATTTCAATCCTCGGTCGAAC 57.320 40.909 0.00 0.00 0.00 3.95
1801 1877 6.205076 TGTTTAAATTTCAATCCTCGGTCGAA 59.795 34.615 0.00 0.00 0.00 3.71
1802 1878 5.701750 TGTTTAAATTTCAATCCTCGGTCGA 59.298 36.000 0.00 0.00 0.00 4.20
1803 1879 5.933790 TGTTTAAATTTCAATCCTCGGTCG 58.066 37.500 0.00 0.00 0.00 4.79
1804 1880 5.800438 GCTGTTTAAATTTCAATCCTCGGTC 59.200 40.000 0.00 0.00 0.00 4.79
1805 1881 5.619086 CGCTGTTTAAATTTCAATCCTCGGT 60.619 40.000 0.00 0.00 0.00 4.69
1806 1882 4.793216 CGCTGTTTAAATTTCAATCCTCGG 59.207 41.667 0.00 0.00 0.00 4.63
1807 1883 4.793216 CCGCTGTTTAAATTTCAATCCTCG 59.207 41.667 0.00 0.00 0.00 4.63
1852 1928 0.387112 CGCACGTACGGGTAGAACAA 60.387 55.000 20.35 0.00 0.00 2.83
1861 1938 1.876714 CCCAATCTCGCACGTACGG 60.877 63.158 21.06 9.73 0.00 4.02
1880 1957 6.366332 GCTTATCGTCAGATCGGATACAAATT 59.634 38.462 0.00 0.00 38.26 1.82
1890 1967 5.289917 AGTCATAGCTTATCGTCAGATCG 57.710 43.478 0.00 0.00 38.26 3.69
2030 2809 9.750125 GAGCCGATTTTTCTTATAAATTGGATT 57.250 29.630 15.48 5.65 42.39 3.01
2050 2829 2.045561 TGTTCAGGTTTTTGAGCCGA 57.954 45.000 0.00 0.00 0.00 5.54
2106 2885 1.281419 TCCCCTTGCTATTTGTCCGA 58.719 50.000 0.00 0.00 0.00 4.55
2199 2996 5.243060 TGGTATTGTGATTCCTCGACGATAT 59.757 40.000 0.00 0.00 0.00 1.63
2201 2998 3.383505 TGGTATTGTGATTCCTCGACGAT 59.616 43.478 0.00 0.00 0.00 3.73
2264 3062 1.340502 TGAGTTGTGTTGTGGGCTTGA 60.341 47.619 0.00 0.00 0.00 3.02
2266 3064 1.846007 TTGAGTTGTGTTGTGGGCTT 58.154 45.000 0.00 0.00 0.00 4.35
2274 3073 3.446873 TGTGGATGCTTTTGAGTTGTGTT 59.553 39.130 0.00 0.00 0.00 3.32
2409 3209 4.437239 CTTCGTGCTCTTGGTGATATCTT 58.563 43.478 3.98 0.00 0.00 2.40
2467 3267 1.122849 GTTGTTGTTGTGCATGCTCG 58.877 50.000 20.33 0.00 0.00 5.03
2512 3313 3.050703 GTCGTAGGACGGTCGTCTA 57.949 57.895 20.55 9.98 42.81 2.59
2555 3357 2.093075 TGGTTGTTCGGTGGTGTTCTTA 60.093 45.455 0.00 0.00 0.00 2.10
2608 3410 2.095161 TGTTTGTTGTGGGTTTGACGAC 60.095 45.455 0.00 0.00 0.00 4.34
2609 3411 2.160205 TGTTTGTTGTGGGTTTGACGA 58.840 42.857 0.00 0.00 0.00 4.20
2647 3449 2.764128 GTCTGGGGGATGGCTCGA 60.764 66.667 0.00 0.00 0.00 4.04



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

AutoCloner maintained by Alex Coulton.