Multiple sequence alignment - TraesCS6D01G030400

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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 TraesCS6D01G030400 chr6D 100.000 4022 0 0 773 4794 11894030 11890009 0.000000e+00 7428.0
1 TraesCS6D01G030400 chr6D 100.000 413 0 0 1 413 11894802 11894390 0.000000e+00 763.0
2 TraesCS6D01G030400 chr6B 92.948 3290 168 31 796 4068 21788731 21785489 0.000000e+00 4732.0
3 TraesCS6D01G030400 chr6B 92.048 415 17 8 1 413 21789507 21789107 1.940000e-158 569.0
4 TraesCS6D01G030400 chr6B 88.366 361 26 8 4445 4794 21785300 21784945 2.060000e-113 420.0
5 TraesCS6D01G030400 chr6B 79.195 149 23 7 4225 4371 171809551 171809693 3.950000e-16 97.1
6 TraesCS6D01G030400 chr6B 96.429 56 2 0 4304 4359 21785384 21785329 5.110000e-15 93.5
7 TraesCS6D01G030400 chr6A 94.897 2763 102 10 773 3513 13386250 13383505 0.000000e+00 4285.0
8 TraesCS6D01G030400 chr6A 88.601 965 38 21 3508 4451 13383300 13382387 0.000000e+00 1107.0
9 TraesCS6D01G030400 chr6A 90.000 430 24 6 1 413 13386684 13386257 5.460000e-149 538.0
10 TraesCS6D01G030400 chr6A 87.822 427 26 11 4381 4794 13382416 13382003 1.210000e-130 477.0


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 TraesCS6D01G030400 chr6D 11890009 11894802 4793 True 4095.500 7428 100.00000 1 4794 2 chr6D.!!$R1 4793
1 TraesCS6D01G030400 chr6B 21784945 21789507 4562 True 1453.625 4732 92.44775 1 4794 4 chr6B.!!$R1 4793
2 TraesCS6D01G030400 chr6A 13382003 13386684 4681 True 1601.750 4285 90.33000 1 4794 4 chr6A.!!$R1 4793

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
245 270 0.257616 AGCTCGCCTCCTCTTCTAGT 59.742 55.0 0.00 0.00 0.00 2.57 F
1384 1420 0.322008 GTTGCTTCCACCTCCTCCAG 60.322 60.0 0.00 0.00 0.00 3.86 F
1871 1910 0.398318 ACCAGAAGGCCTTGACTGTC 59.602 55.0 26.25 7.35 39.06 3.51 F
3079 3129 0.376152 GTGATCTTGGCATCAGCACG 59.624 55.0 0.00 0.00 44.61 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 1736 0.249120 CGTCATAGTCACCCTTGGCA 59.751 55.0 0.0 0.0 0.00 4.92 R
2432 2471 0.393820 TGGCATCATAGATCGCAGCA 59.606 50.0 0.0 0.0 0.00 4.41 R
3700 3962 0.396811 CGGACCCAAACAGGTTCTCT 59.603 55.0 0.0 0.0 41.42 3.10 R
4220 4528 0.030101 CAACCGACCGCAACAACATT 59.970 50.0 0.0 0.0 0.00 2.71 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
32 34 9.674068 AGATGAGAATTTCCAGATCATCATATG 57.326 33.333 20.00 0.00 45.56 1.78
89 91 1.262417 CGTCGCTTGATCATGGATTGG 59.738 52.381 10.35 0.00 0.00 3.16
96 98 1.227943 ATCATGGATTGGACGGCGG 60.228 57.895 13.24 0.00 0.00 6.13
189 205 2.550180 GTCTTCCCTGTCAAGCAAGAAC 59.450 50.000 0.00 0.00 0.00 3.01
196 212 1.024271 GTCAAGCAAGAACCAGCACA 58.976 50.000 0.00 0.00 0.00 4.57
197 213 1.002033 GTCAAGCAAGAACCAGCACAG 60.002 52.381 0.00 0.00 0.00 3.66
198 214 0.318445 CAAGCAAGAACCAGCACAGC 60.318 55.000 0.00 0.00 0.00 4.40
199 215 0.466922 AAGCAAGAACCAGCACAGCT 60.467 50.000 0.00 0.00 40.77 4.24
200 216 0.397941 AGCAAGAACCAGCACAGCTA 59.602 50.000 0.00 0.00 36.40 3.32
201 217 0.801251 GCAAGAACCAGCACAGCTAG 59.199 55.000 0.00 0.00 36.40 3.42
202 218 0.801251 CAAGAACCAGCACAGCTAGC 59.199 55.000 6.62 6.62 36.40 3.42
203 219 0.671781 AAGAACCAGCACAGCTAGCG 60.672 55.000 9.55 7.05 36.40 4.26
204 220 2.743928 AACCAGCACAGCTAGCGC 60.744 61.111 9.55 7.05 36.40 5.92
245 270 0.257616 AGCTCGCCTCCTCTTCTAGT 59.742 55.000 0.00 0.00 0.00 2.57
1384 1420 0.322008 GTTGCTTCCACCTCCTCCAG 60.322 60.000 0.00 0.00 0.00 3.86
1619 1658 3.297620 CTGTGCCGCAAAGCCCTT 61.298 61.111 0.00 0.00 0.00 3.95
1676 1715 4.208686 GAAGCCTCCGATCGCCGT 62.209 66.667 10.32 0.00 36.31 5.68
1697 1736 1.991070 CTGATGGCCCTTATCCTGGAT 59.009 52.381 14.66 14.66 0.00 3.41
1772 1811 2.406616 GGTTGCCAATGGACGCGAT 61.407 57.895 15.93 0.00 0.00 4.58
1850 1889 1.440708 TCGACGAGTCTGTCTTCTCC 58.559 55.000 0.00 0.00 36.71 3.71
1862 1901 1.483004 GTCTTCTCCTACCAGAAGGCC 59.517 57.143 9.74 0.00 45.70 5.19
1871 1910 0.398318 ACCAGAAGGCCTTGACTGTC 59.602 55.000 26.25 7.35 39.06 3.51
1889 1928 2.743718 CTCAAGTCTGCCCGTGGT 59.256 61.111 0.00 0.00 0.00 4.16
2030 2069 4.729918 CCTGGTGCTGCCCCTGAC 62.730 72.222 9.49 0.00 36.04 3.51
2084 2123 1.709578 TCTATGAGGCGCTTGGAGAT 58.290 50.000 7.64 0.00 0.00 2.75
2097 2136 2.187239 TGGAGATCTTGATGAGGCCT 57.813 50.000 3.86 3.86 0.00 5.19
2111 2150 3.679389 TGAGGCCTTAAAGCTTCTTCAG 58.321 45.455 6.77 0.00 39.46 3.02
2129 2168 0.475906 AGAGGGCACTGAAGTTGCTT 59.524 50.000 0.00 0.00 0.00 3.91
2213 2252 5.017093 ACTACATGATAGGGAGGTATGCT 57.983 43.478 0.00 0.00 0.00 3.79
2276 2315 1.374947 CAGCGGGGAAAGGAAGTCA 59.625 57.895 0.00 0.00 0.00 3.41
2279 2318 1.377333 CGGGGAAAGGAAGTCAGCC 60.377 63.158 0.00 0.00 0.00 4.85
2432 2471 0.464735 TTGGCGTGTACAGCAACCTT 60.465 50.000 15.90 0.00 36.08 3.50
2470 2509 3.813443 CCATGGGAAGGTATGTCTTGAG 58.187 50.000 2.85 0.00 0.00 3.02
2502 2541 0.613012 ATTCTTCTGCAACCCCCAGC 60.613 55.000 0.00 0.00 0.00 4.85
2513 2552 1.775385 ACCCCCAGCCATTTTATTCG 58.225 50.000 0.00 0.00 0.00 3.34
2739 2778 8.678199 GGTGGCTAGATTTAATTATTCTATGCC 58.322 37.037 21.44 21.44 37.11 4.40
2917 2956 2.537633 AATGGCAAGTGACCCATGAT 57.462 45.000 0.00 0.00 40.84 2.45
2953 3000 1.271871 TGCAGTGGACCTGTTATTGGG 60.272 52.381 0.00 0.00 43.55 4.12
2954 3001 1.004277 GCAGTGGACCTGTTATTGGGA 59.996 52.381 0.00 0.00 43.55 4.37
3006 3056 7.364200 TCTACATTTGTGGTTTTGTTATTCCG 58.636 34.615 0.00 0.00 0.00 4.30
3040 3090 4.469657 TGACCCAGCTTTGTCACTTTAAT 58.530 39.130 10.32 0.00 36.62 1.40
3046 3096 6.373779 CCAGCTTTGTCACTTTAATACACAG 58.626 40.000 0.00 0.00 0.00 3.66
3079 3129 0.376152 GTGATCTTGGCATCAGCACG 59.624 55.000 0.00 0.00 44.61 5.34
3082 3132 0.745845 ATCTTGGCATCAGCACGACC 60.746 55.000 0.00 0.00 44.61 4.79
3097 3147 1.274167 ACGACCGCCTCTGTTGAATTA 59.726 47.619 0.00 0.00 0.00 1.40
3108 3158 3.628032 TCTGTTGAATTAACGGTGTGCAA 59.372 39.130 0.00 0.00 44.42 4.08
3112 3162 6.504398 TGTTGAATTAACGGTGTGCAAAATA 58.496 32.000 0.00 0.00 42.34 1.40
3121 3171 3.333804 GGTGTGCAAAATACATTTGGGG 58.666 45.455 0.00 0.00 46.93 4.96
3245 3295 2.627771 TGGGGTTCCACTTGTGTCT 58.372 52.632 0.00 0.00 38.32 3.41
3428 3478 1.596260 CCACATGTCGCTTCATGCTAG 59.404 52.381 14.80 7.74 46.15 3.42
3491 3541 6.143206 TGTCCTTCCTGTTAGATGATCCATA 58.857 40.000 0.00 0.00 0.00 2.74
3494 3544 6.441924 TCCTTCCTGTTAGATGATCCATATCC 59.558 42.308 0.00 0.00 0.00 2.59
3667 3929 2.668120 GGAGCTGCTGAAGGAGGCT 61.668 63.158 7.01 0.00 33.79 4.58
3700 3962 1.248785 ACCGGAAGCAGAAGTCGCTA 61.249 55.000 9.46 0.00 39.29 4.26
3712 3974 3.574826 AGAAGTCGCTAGAGAACCTGTTT 59.425 43.478 0.00 0.00 0.00 2.83
3721 3983 1.149854 GAACCTGTTTGGGTCCGGT 59.850 57.895 0.00 0.00 46.80 5.28
3751 4013 4.699522 GGCGCCAAGAAGGACGGT 62.700 66.667 24.80 0.00 41.22 4.83
3811 4073 3.864243 CTGAGCTGAGCTGAGAAGAAAT 58.136 45.455 16.12 0.00 42.26 2.17
3846 4108 5.119694 GCCTTTGTAACATAAGAGGAGAGG 58.880 45.833 0.00 0.00 0.00 3.69
3965 4254 7.151999 TGCAGTTTGTTTTGAGTTTCTTCTA 57.848 32.000 0.00 0.00 0.00 2.10
3966 4255 7.027161 TGCAGTTTGTTTTGAGTTTCTTCTAC 58.973 34.615 0.00 0.00 0.00 2.59
3967 4256 7.027161 GCAGTTTGTTTTGAGTTTCTTCTACA 58.973 34.615 0.00 0.00 0.00 2.74
3968 4257 7.702348 GCAGTTTGTTTTGAGTTTCTTCTACAT 59.298 33.333 0.00 0.00 0.00 2.29
3969 4258 9.013490 CAGTTTGTTTTGAGTTTCTTCTACATG 57.987 33.333 0.00 0.00 0.00 3.21
3970 4259 8.739972 AGTTTGTTTTGAGTTTCTTCTACATGT 58.260 29.630 2.69 2.69 0.00 3.21
3971 4260 9.353999 GTTTGTTTTGAGTTTCTTCTACATGTT 57.646 29.630 2.30 0.00 0.00 2.71
3972 4261 9.567848 TTTGTTTTGAGTTTCTTCTACATGTTC 57.432 29.630 2.30 0.00 0.00 3.18
3973 4262 8.506168 TGTTTTGAGTTTCTTCTACATGTTCT 57.494 30.769 2.30 0.00 0.00 3.01
3974 4263 8.397906 TGTTTTGAGTTTCTTCTACATGTTCTG 58.602 33.333 2.30 0.00 0.00 3.02
3975 4264 6.545504 TTGAGTTTCTTCTACATGTTCTGC 57.454 37.500 2.30 0.00 0.00 4.26
3976 4265 5.610398 TGAGTTTCTTCTACATGTTCTGCA 58.390 37.500 2.30 0.00 0.00 4.41
3977 4266 6.233434 TGAGTTTCTTCTACATGTTCTGCAT 58.767 36.000 2.30 0.00 38.60 3.96
4012 4301 3.628487 GCTGTTGTGTACCCACTTGTTTA 59.372 43.478 0.00 0.00 42.34 2.01
4081 4386 2.092753 ACTGGGCTGTTGTATCTGGATG 60.093 50.000 0.00 0.00 0.00 3.51
4140 4448 2.364970 TGGTGGTTCCTTGATTTGCTTG 59.635 45.455 0.00 0.00 37.07 4.01
4153 4461 2.169832 TTGCTTGCTACTCACTCCAC 57.830 50.000 0.00 0.00 0.00 4.02
4155 4463 1.270305 TGCTTGCTACTCACTCCACAC 60.270 52.381 0.00 0.00 0.00 3.82
4158 4466 3.674682 GCTTGCTACTCACTCCACACTAG 60.675 52.174 0.00 0.00 0.00 2.57
4165 4473 3.283751 CTCACTCCACACTAGTAGAGGG 58.716 54.545 16.75 14.09 38.13 4.30
4176 4484 1.517913 GTAGAGGGTAACGCGTGCC 60.518 63.158 14.98 18.70 37.60 5.01
4208 4516 8.584063 TTTCACTAGTGGGTTTAACTTCTTTT 57.416 30.769 22.48 0.00 0.00 2.27
4209 4517 8.584063 TTCACTAGTGGGTTTAACTTCTTTTT 57.416 30.769 22.48 0.00 0.00 1.94
4210 4518 7.992008 TCACTAGTGGGTTTAACTTCTTTTTG 58.008 34.615 22.48 0.00 0.00 2.44
4211 4519 7.612633 TCACTAGTGGGTTTAACTTCTTTTTGT 59.387 33.333 22.48 0.00 0.00 2.83
4212 4520 8.248253 CACTAGTGGGTTTAACTTCTTTTTGTT 58.752 33.333 15.49 0.00 0.00 2.83
4213 4521 8.809066 ACTAGTGGGTTTAACTTCTTTTTGTTT 58.191 29.630 0.00 0.00 0.00 2.83
4214 4522 9.297586 CTAGTGGGTTTAACTTCTTTTTGTTTC 57.702 33.333 0.00 0.00 0.00 2.78
4215 4523 7.903145 AGTGGGTTTAACTTCTTTTTGTTTCT 58.097 30.769 0.00 0.00 0.00 2.52
4216 4524 8.033038 AGTGGGTTTAACTTCTTTTTGTTTCTC 58.967 33.333 0.00 0.00 0.00 2.87
4217 4525 8.033038 GTGGGTTTAACTTCTTTTTGTTTCTCT 58.967 33.333 0.00 0.00 0.00 3.10
4218 4526 9.245481 TGGGTTTAACTTCTTTTTGTTTCTCTA 57.755 29.630 0.00 0.00 0.00 2.43
4231 4539 8.500837 TTTTGTTTCTCTATAATGTTGTTGCG 57.499 30.769 0.00 0.00 0.00 4.85
4232 4540 6.176975 TGTTTCTCTATAATGTTGTTGCGG 57.823 37.500 0.00 0.00 0.00 5.69
4233 4541 5.703592 TGTTTCTCTATAATGTTGTTGCGGT 59.296 36.000 0.00 0.00 0.00 5.68
4234 4542 6.128391 TGTTTCTCTATAATGTTGTTGCGGTC 60.128 38.462 0.00 0.00 0.00 4.79
4247 4555 1.009335 GCGGTCGGTTGTTTGGTTC 60.009 57.895 0.00 0.00 0.00 3.62
4277 4585 1.231958 TGCGTCGGCTTGGGTTTTAG 61.232 55.000 0.00 0.00 40.82 1.85
4285 4593 4.456566 TCGGCTTGGGTTTTAGTTATGTTC 59.543 41.667 0.00 0.00 0.00 3.18
4295 4603 2.074547 AGTTATGTTCCGACGGTGTG 57.925 50.000 14.79 0.00 0.00 3.82
4332 4641 9.793252 ATTTGTATATCATTTTGAACTGCTGTC 57.207 29.630 0.00 0.00 0.00 3.51
4363 4672 6.231211 GGTATTTGTTTTGAGAGGAGAGTGA 58.769 40.000 0.00 0.00 0.00 3.41
4381 4690 3.055094 AGTGAAGTTGTTCAGTGAGTGGT 60.055 43.478 0.00 0.00 43.51 4.16
4382 4691 3.689649 GTGAAGTTGTTCAGTGAGTGGTT 59.310 43.478 0.00 0.00 43.55 3.67
4399 4708 1.539496 GGTTGTAGTGTCCTTGCACGA 60.539 52.381 0.00 0.00 43.61 4.35
4403 4712 1.654105 GTAGTGTCCTTGCACGATTCG 59.346 52.381 4.14 4.14 43.61 3.34
4409 4718 3.367051 CTTGCACGATTCGGCCACG 62.367 63.158 11.29 5.26 42.74 4.94
4416 4725 2.358247 ATTCGGCCACGGTGTCAC 60.358 61.111 2.24 0.00 41.39 3.67
4444 4757 3.814625 TGTAGTGTCCTTGCATGTTTCA 58.185 40.909 0.00 0.00 0.00 2.69
4550 4892 4.602340 TCCACTCTCTCGCTTAGTTTTT 57.398 40.909 0.00 0.00 0.00 1.94
4702 5057 8.568732 ACATAAATGTTTAAAAGTGTTCACGG 57.431 30.769 0.00 0.00 37.90 4.94
4730 5085 6.484364 AGAAAACATTTGTGGGTCTGAAAT 57.516 33.333 0.00 0.00 0.00 2.17
4733 5088 9.308000 AGAAAACATTTGTGGGTCTGAAATATA 57.692 29.630 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 9 9.451002 ACATATGATGATCTGGAAATTCTCATC 57.549 33.333 10.38 13.00 41.53 2.92
32 34 5.219226 TCGATCGAAACTCTAACTCTGAC 57.781 43.478 16.99 0.00 0.00 3.51
70 72 2.289002 GTCCAATCCATGATCAAGCGAC 59.711 50.000 0.00 0.00 0.00 5.19
96 98 1.070445 CGTCATGATGGCTCCTCCC 59.930 63.158 7.06 0.00 0.00 4.30
196 212 2.801631 GGTGGGATCTGCGCTAGCT 61.802 63.158 13.93 0.00 45.42 3.32
197 213 2.280457 GGTGGGATCTGCGCTAGC 60.280 66.667 9.73 4.06 45.41 3.42
198 214 2.423446 GGGTGGGATCTGCGCTAG 59.577 66.667 9.73 4.58 0.00 3.42
199 215 3.161450 GGGGTGGGATCTGCGCTA 61.161 66.667 9.73 0.00 0.00 4.26
203 219 3.936772 TTTGCGGGGTGGGATCTGC 62.937 63.158 0.00 0.00 35.93 4.26
204 220 1.076777 ATTTGCGGGGTGGGATCTG 60.077 57.895 0.00 0.00 0.00 2.90
1384 1420 9.498307 TGAGATTTTTCTTTTGACGAGTAAAAC 57.502 29.630 0.00 0.00 29.98 2.43
1619 1658 2.038813 TGCTCCCGGTGGATCTCA 59.961 61.111 0.00 0.00 40.80 3.27
1676 1715 1.061424 TCCAGGATAAGGGCCATCAGA 60.061 52.381 6.18 0.00 0.00 3.27
1697 1736 0.249120 CGTCATAGTCACCCTTGGCA 59.751 55.000 0.00 0.00 0.00 4.92
1850 1889 1.625818 ACAGTCAAGGCCTTCTGGTAG 59.374 52.381 28.55 13.88 35.27 3.18
1871 1910 2.046892 CCACGGGCAGACTTGAGG 60.047 66.667 0.00 0.00 0.00 3.86
1889 1928 1.745890 CACTGAAGGGTGGTCGTCA 59.254 57.895 0.00 0.00 33.95 4.35
2030 2069 1.899437 TTAGGCCTCCAGCAACCTCG 61.899 60.000 9.68 0.00 46.50 4.63
2084 2123 4.018960 AGAAGCTTTAAGGCCTCATCAAGA 60.019 41.667 5.23 0.00 0.00 3.02
2097 2136 3.073062 AGTGCCCTCTGAAGAAGCTTTAA 59.927 43.478 0.00 0.00 0.00 1.52
2111 2150 0.595095 CAAGCAACTTCAGTGCCCTC 59.405 55.000 0.00 0.00 0.00 4.30
2129 2168 1.915266 CTGCCCTGGTGAGTCCTCA 60.915 63.158 0.00 0.00 37.24 3.86
2213 2252 3.254903 TCTCGAACGAGTTCCTTGAATCA 59.745 43.478 20.76 0.00 42.49 2.57
2276 2315 0.668535 GCAGAACACCGAAAAAGGCT 59.331 50.000 0.00 0.00 33.69 4.58
2279 2318 3.691049 TTCAGCAGAACACCGAAAAAG 57.309 42.857 0.00 0.00 0.00 2.27
2432 2471 0.393820 TGGCATCATAGATCGCAGCA 59.606 50.000 0.00 0.00 0.00 4.41
2470 2509 4.036734 TGCAGAAGAATCCAGTTTGTGTTC 59.963 41.667 0.00 0.00 0.00 3.18
2560 2599 3.137728 ACCCTTACAGGCATATGGTAACC 59.862 47.826 4.56 0.00 32.73 2.85
2697 2736 4.473444 AGCCACCCACCATATTAAAGATG 58.527 43.478 0.00 0.00 0.00 2.90
2739 2778 7.859598 TGTTTGCAATTAAATTAAGCAACCTG 58.140 30.769 10.60 0.00 43.94 4.00
2881 2920 7.823799 ACTTGCCATTAATTTAGACCAATTTGG 59.176 33.333 14.02 14.02 45.02 3.28
2917 2956 6.007076 TCCACTGCATATGTTAGTTTGGAAA 58.993 36.000 4.29 0.00 0.00 3.13
2953 3000 7.916914 TTACTTAGGCCTAAATTCAACAGTC 57.083 36.000 25.14 0.00 0.00 3.51
2954 3001 7.722285 TGTTTACTTAGGCCTAAATTCAACAGT 59.278 33.333 25.14 18.37 0.00 3.55
3006 3056 3.235200 AGCTGGGTCATATAGGACTGAC 58.765 50.000 16.45 6.57 40.82 3.51
3040 3090 2.158534 ACAGGGGAAATGCAACTGTGTA 60.159 45.455 0.00 0.00 0.00 2.90
3046 3096 2.450476 AGATCACAGGGGAAATGCAAC 58.550 47.619 0.00 0.00 0.00 4.17
3079 3129 2.093783 CGTTAATTCAACAGAGGCGGTC 59.906 50.000 0.00 0.00 36.92 4.79
3082 3132 2.073816 ACCGTTAATTCAACAGAGGCG 58.926 47.619 0.00 0.00 36.92 5.52
3097 3147 4.054671 CCAAATGTATTTTGCACACCGTT 58.945 39.130 0.00 0.00 42.85 4.44
3108 3158 3.881713 GCCTGGAGACCCCAAATGTATTT 60.882 47.826 0.00 0.00 46.07 1.40
3112 3162 1.142688 AGCCTGGAGACCCCAAATGT 61.143 55.000 0.00 0.00 46.07 2.71
3118 3168 1.198759 TGTGTAAGCCTGGAGACCCC 61.199 60.000 0.00 0.00 0.00 4.95
3121 3171 3.134458 GCATATGTGTAAGCCTGGAGAC 58.866 50.000 4.29 0.00 0.00 3.36
3128 3178 4.474226 GCTACAAGCATATGTGTAAGCC 57.526 45.455 4.29 0.00 41.89 4.35
3164 3214 6.092259 CCATTACTCCTACAGCTGTAAACAAC 59.908 42.308 25.95 0.00 0.00 3.32
3239 3289 7.228507 ACAAAGCATCATAACTTACAAGACACA 59.771 33.333 0.00 0.00 0.00 3.72
3240 3290 7.584987 ACAAAGCATCATAACTTACAAGACAC 58.415 34.615 0.00 0.00 0.00 3.67
3241 3291 7.744087 ACAAAGCATCATAACTTACAAGACA 57.256 32.000 0.00 0.00 0.00 3.41
3491 3541 5.160607 TGGAAAAGATACAAGTGACGGAT 57.839 39.130 0.00 0.00 0.00 4.18
3494 3544 5.163854 GGTCATGGAAAAGATACAAGTGACG 60.164 44.000 0.00 0.00 35.52 4.35
3553 3815 1.511318 CCAGGATCTCGATCGCGTCT 61.511 60.000 11.09 1.59 38.69 4.18
3700 3962 0.396811 CGGACCCAAACAGGTTCTCT 59.603 55.000 0.00 0.00 41.42 3.10
3811 4073 1.529010 CAAAGGCCCACAGCACTGA 60.529 57.895 0.00 0.00 46.50 3.41
3846 4108 4.566697 CCTCCCTTCCTTTTCTCTCTTTCC 60.567 50.000 0.00 0.00 0.00 3.13
3967 4256 5.163683 GCAATCAAGAGTACATGCAGAACAT 60.164 40.000 0.00 0.00 40.66 2.71
3968 4257 4.154737 GCAATCAAGAGTACATGCAGAACA 59.845 41.667 0.00 0.00 34.10 3.18
3969 4258 4.394300 AGCAATCAAGAGTACATGCAGAAC 59.606 41.667 0.00 0.00 36.30 3.01
3970 4259 4.393990 CAGCAATCAAGAGTACATGCAGAA 59.606 41.667 0.00 0.00 36.30 3.02
3971 4260 3.937079 CAGCAATCAAGAGTACATGCAGA 59.063 43.478 0.00 0.00 36.30 4.26
3972 4261 3.688185 ACAGCAATCAAGAGTACATGCAG 59.312 43.478 0.00 0.00 36.30 4.41
3973 4262 3.678289 ACAGCAATCAAGAGTACATGCA 58.322 40.909 0.00 0.00 36.30 3.96
3974 4263 4.083110 ACAACAGCAATCAAGAGTACATGC 60.083 41.667 0.00 0.00 0.00 4.06
3975 4264 5.049198 ACACAACAGCAATCAAGAGTACATG 60.049 40.000 0.00 0.00 0.00 3.21
3976 4265 5.065914 ACACAACAGCAATCAAGAGTACAT 58.934 37.500 0.00 0.00 0.00 2.29
3977 4266 4.450976 ACACAACAGCAATCAAGAGTACA 58.549 39.130 0.00 0.00 0.00 2.90
3978 4267 5.107065 GGTACACAACAGCAATCAAGAGTAC 60.107 44.000 0.00 0.00 0.00 2.73
3979 4268 4.994852 GGTACACAACAGCAATCAAGAGTA 59.005 41.667 0.00 0.00 0.00 2.59
4012 4301 4.536090 TCCCATCATAACACTTCTTCAGGT 59.464 41.667 0.00 0.00 0.00 4.00
4140 4448 4.515361 TCTACTAGTGTGGAGTGAGTAGC 58.485 47.826 5.39 0.00 39.52 3.58
4153 4461 2.012673 ACGCGTTACCCTCTACTAGTG 58.987 52.381 5.58 0.00 0.00 2.74
4155 4463 1.268437 GCACGCGTTACCCTCTACTAG 60.268 57.143 10.22 0.00 0.00 2.57
4158 4466 1.517913 GGCACGCGTTACCCTCTAC 60.518 63.158 10.22 0.00 0.00 2.59
4208 4516 6.205853 ACCGCAACAACATTATAGAGAAACAA 59.794 34.615 0.00 0.00 0.00 2.83
4209 4517 5.703592 ACCGCAACAACATTATAGAGAAACA 59.296 36.000 0.00 0.00 0.00 2.83
4210 4518 6.178239 ACCGCAACAACATTATAGAGAAAC 57.822 37.500 0.00 0.00 0.00 2.78
4211 4519 5.062934 CGACCGCAACAACATTATAGAGAAA 59.937 40.000 0.00 0.00 0.00 2.52
4212 4520 4.565166 CGACCGCAACAACATTATAGAGAA 59.435 41.667 0.00 0.00 0.00 2.87
4213 4521 4.109766 CGACCGCAACAACATTATAGAGA 58.890 43.478 0.00 0.00 0.00 3.10
4214 4522 3.245284 CCGACCGCAACAACATTATAGAG 59.755 47.826 0.00 0.00 0.00 2.43
4215 4523 3.191669 CCGACCGCAACAACATTATAGA 58.808 45.455 0.00 0.00 0.00 1.98
4216 4524 2.933906 ACCGACCGCAACAACATTATAG 59.066 45.455 0.00 0.00 0.00 1.31
4217 4525 2.975266 ACCGACCGCAACAACATTATA 58.025 42.857 0.00 0.00 0.00 0.98
4218 4526 1.816074 ACCGACCGCAACAACATTAT 58.184 45.000 0.00 0.00 0.00 1.28
4219 4527 1.264557 CAACCGACCGCAACAACATTA 59.735 47.619 0.00 0.00 0.00 1.90
4220 4528 0.030101 CAACCGACCGCAACAACATT 59.970 50.000 0.00 0.00 0.00 2.71
4221 4529 1.098712 ACAACCGACCGCAACAACAT 61.099 50.000 0.00 0.00 0.00 2.71
4222 4530 1.306642 AACAACCGACCGCAACAACA 61.307 50.000 0.00 0.00 0.00 3.33
4223 4531 0.179158 AAACAACCGACCGCAACAAC 60.179 50.000 0.00 0.00 0.00 3.32
4224 4532 0.179161 CAAACAACCGACCGCAACAA 60.179 50.000 0.00 0.00 0.00 2.83
4225 4533 1.429825 CAAACAACCGACCGCAACA 59.570 52.632 0.00 0.00 0.00 3.33
4226 4534 1.298788 CCAAACAACCGACCGCAAC 60.299 57.895 0.00 0.00 0.00 4.17
4227 4535 1.313812 AACCAAACAACCGACCGCAA 61.314 50.000 0.00 0.00 0.00 4.85
4228 4536 1.716826 GAACCAAACAACCGACCGCA 61.717 55.000 0.00 0.00 0.00 5.69
4229 4537 1.009335 GAACCAAACAACCGACCGC 60.009 57.895 0.00 0.00 0.00 5.68
4230 4538 1.796459 CTAGAACCAAACAACCGACCG 59.204 52.381 0.00 0.00 0.00 4.79
4231 4539 2.842457 ACTAGAACCAAACAACCGACC 58.158 47.619 0.00 0.00 0.00 4.79
4232 4540 4.888038 AAACTAGAACCAAACAACCGAC 57.112 40.909 0.00 0.00 0.00 4.79
4233 4541 6.993902 AGATAAAACTAGAACCAAACAACCGA 59.006 34.615 0.00 0.00 0.00 4.69
4234 4542 7.075741 CAGATAAAACTAGAACCAAACAACCG 58.924 38.462 0.00 0.00 0.00 4.44
4247 4555 2.810650 AGCCGACGCAGATAAAACTAG 58.189 47.619 0.00 0.00 37.52 2.57
4277 4585 1.787012 ACACACCGTCGGAACATAAC 58.213 50.000 20.51 0.00 0.00 1.89
4285 4593 2.178783 GAAAACAAAACACACCGTCGG 58.821 47.619 10.48 10.48 0.00 4.79
4332 4641 5.389516 CCTCTCAAAACAAATACCGTCTTCG 60.390 44.000 0.00 0.00 0.00 3.79
4363 4672 3.686016 ACAACCACTCACTGAACAACTT 58.314 40.909 0.00 0.00 0.00 2.66
4381 4690 2.831685 ATCGTGCAAGGACACTACAA 57.168 45.000 0.00 0.00 38.45 2.41
4382 4691 2.683968 GAATCGTGCAAGGACACTACA 58.316 47.619 0.00 0.00 38.45 2.74
4399 4708 2.358247 GTGACACCGTGGCCGAAT 60.358 61.111 0.75 0.00 35.63 3.34
4403 4712 2.282180 ATTGGTGACACCGTGGCC 60.282 61.111 19.67 0.00 42.58 5.36
4409 4718 3.211045 ACACTACAACATTGGTGACACC 58.789 45.455 18.28 18.28 42.67 4.16
4416 4725 2.884012 TGCAAGGACACTACAACATTGG 59.116 45.455 0.00 0.00 0.00 3.16
4550 4892 8.385111 CGGAAAACAATATAAGAGAGCGTTAAA 58.615 33.333 0.00 0.00 0.00 1.52
4553 4895 5.220605 GCGGAAAACAATATAAGAGAGCGTT 60.221 40.000 0.00 0.00 0.00 4.84
4554 4896 4.270325 GCGGAAAACAATATAAGAGAGCGT 59.730 41.667 0.00 0.00 0.00 5.07
4565 4907 3.244422 ACTGGAGTGAGCGGAAAACAATA 60.244 43.478 0.00 0.00 0.00 1.90
4693 5048 7.434013 ACAAATGTTTTCTAAATCCGTGAACAC 59.566 33.333 0.00 0.00 0.00 3.32
4702 5057 7.657336 TCAGACCCACAAATGTTTTCTAAATC 58.343 34.615 0.00 0.00 0.00 2.17
4753 5108 9.683069 CTATGACCATTTTTACATTTGCTATCC 57.317 33.333 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.