Multiple sequence alignment - TraesCS1B01G146100

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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 TraesCS1B01G146100 chr1B 100.000 3905 0 0 1 3905 201774247 201778151 0.000000e+00 7212.0
1 TraesCS1B01G146100 chr1B 97.826 184 3 1 149 331 201760916 201761099 2.260000e-82 316.0
2 TraesCS1B01G146100 chr1D 92.456 2744 86 39 755 3463 134681990 134684647 0.000000e+00 3808.0
3 TraesCS1B01G146100 chr1D 93.447 412 25 1 330 741 134681511 134681920 9.280000e-171 610.0
4 TraesCS1B01G146100 chr1D 83.392 283 33 7 3566 3840 134684673 134684949 2.330000e-62 250.0
5 TraesCS1B01G146100 chr1A 94.368 2184 73 15 758 2915 163384207 163382048 0.000000e+00 3306.0
6 TraesCS1B01G146100 chr1A 93.072 433 28 1 330 762 163384681 163384251 1.980000e-177 632.0
7 TraesCS1B01G146100 chr1A 95.821 335 13 1 1 334 466283474 466283140 1.230000e-149 540.0
8 TraesCS1B01G146100 chr1A 80.960 625 56 20 3278 3840 163377897 163377274 1.670000e-118 436.0
9 TraesCS1B01G146100 chr1A 91.589 321 15 3 2913 3222 163378214 163377895 2.160000e-117 433.0
10 TraesCS1B01G146100 chr1A 95.628 183 7 1 149 330 466335318 466335136 3.820000e-75 292.0
11 TraesCS1B01G146100 chr2D 97.289 332 8 1 1 331 109768931 109769262 2.630000e-156 562.0
12 TraesCS1B01G146100 chr2D 96.552 87 3 0 149 235 109765288 109765374 1.130000e-30 145.0
13 TraesCS1B01G146100 chr4B 87.766 188 23 0 2203 2390 412778110 412777923 1.830000e-53 220.0
14 TraesCS1B01G146100 chr4D 87.234 188 24 0 2203 2390 334962735 334962548 8.500000e-52 215.0
15 TraesCS1B01G146100 chr4A 87.234 188 24 0 2203 2390 138418992 138419179 8.500000e-52 215.0
16 TraesCS1B01G146100 chr3A 83.133 166 23 3 3647 3809 637123891 637124054 3.140000e-31 147.0
17 TraesCS1B01G146100 chr5A 83.030 165 19 3 3679 3840 520241335 520241493 1.460000e-29 141.0
18 TraesCS1B01G146100 chr5B 84.211 95 12 2 3713 3804 223980931 223981025 5.370000e-14 89.8
19 TraesCS1B01G146100 chr5D 87.692 65 4 3 3685 3747 487597484 487597422 5.410000e-09 73.1


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 TraesCS1B01G146100 chr1B 201774247 201778151 3904 False 7212.00 7212 100.00000 1 3905 1 chr1B.!!$F2 3904
1 TraesCS1B01G146100 chr1D 134681511 134684949 3438 False 1556.00 3808 89.76500 330 3840 3 chr1D.!!$F1 3510
2 TraesCS1B01G146100 chr1A 163377274 163384681 7407 True 1201.75 3306 89.99725 330 3840 4 chr1A.!!$R3 3510
3 TraesCS1B01G146100 chr2D 109765288 109769262 3974 False 353.50 562 96.92050 1 331 2 chr2D.!!$F1 330

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
946 4677 0.108396 GCCCAGCCCACAAACATTTT 59.892 50.0 0.0 0.0 0.00 1.82 F
1227 4958 0.812412 CTCCGTGTTTCACCACCGTT 60.812 55.0 0.0 0.0 31.47 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 5909 1.813178 TCAACAAGCACGGAACAAACA 59.187 42.857 0.0 0.0 0.00 2.83 R
3015 10619 0.886490 GTCAGAGGCAACCACCACAG 60.886 60.000 0.0 0.0 37.17 3.66 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 3672 1.700186 GGGGTTGGAGAAGAAGTCACT 59.300 52.381 0.00 0.00 0.00 3.41
64 3708 1.913951 ATGGCGGCTGATGAGGACAA 61.914 55.000 11.43 0.00 0.00 3.18
65 3709 1.153086 GGCGGCTGATGAGGACAAT 60.153 57.895 0.00 0.00 0.00 2.71
125 3769 1.738099 CAGCGGAAAGAGGTCACGG 60.738 63.158 0.00 0.00 0.00 4.94
147 3791 5.648092 CGGGAAAGAGAAAACTGATACCATT 59.352 40.000 0.00 0.00 0.00 3.16
301 3945 4.813027 TGGAAGTAAACATCCTACGTGAC 58.187 43.478 0.00 0.00 34.96 3.67
348 3993 7.264503 TTCCTACAAGGATGATCTCCACTTCA 61.265 42.308 12.08 0.00 45.34 3.02
389 4034 0.108585 TGCCTTCTTCCAAGCTCGTT 59.891 50.000 0.00 0.00 0.00 3.85
517 4162 0.750850 GCGTTAGCTACATCCTCCCA 59.249 55.000 0.00 0.00 41.01 4.37
539 4184 2.644798 AGTGGTCATACTGGCTTCCTTT 59.355 45.455 0.00 0.00 0.00 3.11
546 4191 4.288626 TCATACTGGCTTCCTTTACCACTT 59.711 41.667 0.00 0.00 0.00 3.16
568 4213 0.323999 TCAATGGCAGCAGCTTCCAT 60.324 50.000 19.98 19.98 42.01 3.41
607 4252 4.135153 CGTGCCTGCCGCTACTCT 62.135 66.667 0.00 0.00 38.78 3.24
631 4276 1.439228 CGTCCTCATCTGGCGACAT 59.561 57.895 0.00 0.00 41.51 3.06
641 4286 1.078709 CTGGCGACATTGACATCGTT 58.921 50.000 0.00 0.00 41.51 3.85
656 4301 0.179094 TCGTTATTAGCCTGCCCGTG 60.179 55.000 0.00 0.00 0.00 4.94
741 4386 1.135527 AGCAAATCAATCATGGGCACG 59.864 47.619 0.00 0.00 0.00 5.34
760 4470 5.335035 GGCACGTACCTATTTTGCTTGTTTA 60.335 40.000 0.00 0.00 33.55 2.01
764 4474 9.828852 CACGTACCTATTTTGCTTGTTTAATTA 57.171 29.630 0.00 0.00 0.00 1.40
943 4674 2.604382 GGCCCAGCCCACAAACAT 60.604 61.111 0.00 0.00 44.06 2.71
944 4675 2.216331 GGCCCAGCCCACAAACATT 61.216 57.895 0.00 0.00 44.06 2.71
945 4676 1.754107 GCCCAGCCCACAAACATTT 59.246 52.632 0.00 0.00 0.00 2.32
946 4677 0.108396 GCCCAGCCCACAAACATTTT 59.892 50.000 0.00 0.00 0.00 1.82
947 4678 1.881591 CCCAGCCCACAAACATTTTG 58.118 50.000 0.00 0.00 0.00 2.44
948 4679 1.542987 CCCAGCCCACAAACATTTTGG 60.543 52.381 3.82 1.32 0.00 3.28
952 4683 2.302733 AGCCCACAAACATTTTGGGATC 59.697 45.455 16.55 2.09 46.59 3.36
953 4684 4.891813 AGCCCACAAACATTTTGGGATCC 61.892 47.826 16.55 1.92 46.59 3.36
954 4685 3.333029 CCACAAACATTTTGGGATCCC 57.667 47.619 25.22 25.22 0.00 3.85
955 4686 2.027285 CCACAAACATTTTGGGATCCCC 60.027 50.000 28.58 10.76 45.71 4.81
956 4687 2.905736 CACAAACATTTTGGGATCCCCT 59.094 45.455 28.58 7.38 45.70 4.79
957 4688 3.327464 CACAAACATTTTGGGATCCCCTT 59.673 43.478 28.58 7.19 45.70 3.95
958 4689 4.530161 CACAAACATTTTGGGATCCCCTTA 59.470 41.667 28.58 13.07 45.70 2.69
1032 4763 3.723922 GGCCGCCTCCAAACCCTA 61.724 66.667 0.71 0.00 0.00 3.53
1033 4764 2.437895 GCCGCCTCCAAACCCTAC 60.438 66.667 0.00 0.00 0.00 3.18
1034 4765 2.271173 CCGCCTCCAAACCCTACC 59.729 66.667 0.00 0.00 0.00 3.18
1035 4766 2.125269 CGCCTCCAAACCCTACCG 60.125 66.667 0.00 0.00 0.00 4.02
1036 4767 2.437895 GCCTCCAAACCCTACCGC 60.438 66.667 0.00 0.00 0.00 5.68
1037 4768 2.271173 CCTCCAAACCCTACCGCC 59.729 66.667 0.00 0.00 0.00 6.13
1184 4915 1.797441 CCCTCTCGTCTCACGTCAG 59.203 63.158 0.00 0.00 43.14 3.51
1226 4957 1.227438 CTCCGTGTTTCACCACCGT 60.227 57.895 0.00 0.00 31.47 4.83
1227 4958 0.812412 CTCCGTGTTTCACCACCGTT 60.812 55.000 0.00 0.00 31.47 4.44
1240 4971 0.911184 CACCGTTGTTTCGTGTTTGC 59.089 50.000 0.00 0.00 0.00 3.68
1400 5131 1.168714 GAGGTGTGATGGTTTCTGGC 58.831 55.000 0.00 0.00 0.00 4.85
1415 5146 2.047274 GGCTTGTGCTGCCTCGTA 60.047 61.111 0.00 0.00 46.38 3.43
1563 5294 5.323371 GCAAGGTTAGTGAATTGCCATTA 57.677 39.130 0.00 0.00 41.65 1.90
1575 5306 7.029563 GTGAATTGCCATTAACCTTGTTAGAG 58.970 38.462 0.00 0.00 0.00 2.43
1592 5323 7.079451 TGTTAGAGTCCTTTCCTTTGAGAAT 57.921 36.000 0.00 0.00 0.00 2.40
1642 5379 7.453752 TCACATAGGAGTAAGTGGAGTAAGTTT 59.546 37.037 0.00 0.00 30.29 2.66
1650 5387 5.546621 AAGTGGAGTAAGTTTGCTAGTCA 57.453 39.130 0.00 0.00 0.00 3.41
1654 5391 6.014156 AGTGGAGTAAGTTTGCTAGTCAGAAT 60.014 38.462 0.00 0.00 0.00 2.40
1829 5581 3.838317 TGTTCACCAGTATGCTTCCTAGT 59.162 43.478 0.00 0.00 31.97 2.57
2096 5851 9.136323 AGAAATTTCTTCATAGTTGTGTCCTTT 57.864 29.630 15.11 0.00 32.55 3.11
2154 5909 3.434309 AGCAAATGTTAGCCATTGTCCT 58.566 40.909 0.00 0.00 43.04 3.85
2197 5952 3.297830 TGTGTGGTTGACTATGACTCG 57.702 47.619 0.00 0.00 0.00 4.18
2383 6138 4.108699 CCTAGATGGCTCGAAGATCATC 57.891 50.000 0.00 8.14 42.89 2.92
2399 6154 7.515841 CGAAGATCATCAAGGTAAGATTTGACG 60.516 40.741 0.00 0.00 36.26 4.35
2421 6176 5.636965 ACGACTGCATTGATATAGCTGATTC 59.363 40.000 0.00 0.00 0.00 2.52
2604 6360 3.004171 ACGCAACAACACAGAGTACAAA 58.996 40.909 0.00 0.00 0.00 2.83
2697 6453 5.582269 CGAAACTGCTTGAAGATCCATCTTA 59.418 40.000 1.66 0.00 46.47 2.10
2774 6530 1.061131 CGTTGTTGCTCGGATCATGTC 59.939 52.381 0.00 0.00 0.00 3.06
2849 6605 4.870426 TCGAGATGGTAATGAGTGAAAAGC 59.130 41.667 0.00 0.00 0.00 3.51
2870 6626 7.532682 AAGCGTTGAATTTTGAGCTTTAAAA 57.467 28.000 10.89 10.89 41.45 1.52
2981 10585 3.173953 TGAAATGTCCCAGCCTCAAAT 57.826 42.857 0.00 0.00 0.00 2.32
3233 10837 1.760480 GGTGGTGTTGGGCAAGGTT 60.760 57.895 0.00 0.00 0.00 3.50
3271 10875 4.021631 CTGCGCTGTGTGGTGCTG 62.022 66.667 9.73 0.00 42.46 4.41
3276 10880 4.935495 CTGTGTGGTGCTGGGCGT 62.935 66.667 0.00 0.00 0.00 5.68
3277 10881 4.927782 TGTGTGGTGCTGGGCGTC 62.928 66.667 0.00 0.00 0.00 5.19
3278 10882 4.626081 GTGTGGTGCTGGGCGTCT 62.626 66.667 0.00 0.00 0.00 4.18
3279 10883 4.624364 TGTGGTGCTGGGCGTCTG 62.624 66.667 0.00 0.00 0.00 3.51
3435 11065 2.571202 AGGAGAGGAAGAGAGGCTTTTG 59.429 50.000 0.00 0.00 36.83 2.44
3470 11108 3.068732 TGTCTCTAGGGATTTGAGCATCG 59.931 47.826 0.00 0.00 38.61 3.84
3478 11116 1.732259 GATTTGAGCATCGACAACCGT 59.268 47.619 0.00 0.00 38.61 4.83
3483 11121 1.654105 GAGCATCGACAACCGTGTAAG 59.346 52.381 0.00 0.00 38.41 2.34
3484 11122 1.000506 AGCATCGACAACCGTGTAAGT 59.999 47.619 0.00 0.00 38.41 2.24
3509 11157 1.202371 TCTGACTTTGCGAACGTGTCT 60.202 47.619 0.00 0.00 0.00 3.41
3520 11168 3.663493 GCGAACGTGTCTGGTCAAATAAC 60.663 47.826 0.00 0.00 0.00 1.89
3532 11180 8.312564 GTCTGGTCAAATAACCTATACTATCCC 58.687 40.741 0.00 0.00 40.20 3.85
3544 11192 6.381420 ACCTATACTATCCCAATCTTGATCGG 59.619 42.308 0.00 0.00 0.00 4.18
3549 11197 4.510167 ATCCCAATCTTGATCGGAGTTT 57.490 40.909 5.86 0.00 0.00 2.66
3554 11202 5.393962 CCAATCTTGATCGGAGTTTTTCAC 58.606 41.667 0.00 0.00 0.00 3.18
3578 11232 4.155733 CGTGCCCGGCTACATGGA 62.156 66.667 11.61 0.00 0.00 3.41
3579 11233 2.510906 GTGCCCGGCTACATGGAT 59.489 61.111 11.61 0.00 0.00 3.41
3582 11236 2.818169 GCCCGGCTACATGGATGGA 61.818 63.158 0.71 0.00 0.00 3.41
3614 11268 1.617947 GGTTCCTGCGACTCCTCCAT 61.618 60.000 0.00 0.00 0.00 3.41
3616 11270 2.202987 CCTGCGACTCCTCCATGC 60.203 66.667 0.00 0.00 0.00 4.06
3650 11304 1.994507 ATCTCCGCTTCGACCTCGTG 61.995 60.000 0.00 0.00 40.80 4.35
3651 11305 2.670592 TCCGCTTCGACCTCGTGA 60.671 61.111 0.00 0.00 40.80 4.35
3663 11317 1.729484 CTCGTGAAAGAGCGCGTCA 60.729 57.895 8.43 0.00 42.03 4.35
3683 11337 4.680237 CGCCACTCGTTCCTGCCA 62.680 66.667 0.00 0.00 0.00 4.92
3709 11375 2.787994 CCTCCATACATGCCTCATTCC 58.212 52.381 0.00 0.00 0.00 3.01
3720 11386 2.243810 GCCTCATTCCGGATAGACTCT 58.756 52.381 4.15 0.00 0.00 3.24
3737 11403 0.984961 TCTAGGATGGCCTGCTGCTT 60.985 55.000 3.32 0.00 46.45 3.91
3759 11425 3.390521 ATCTCGGTCGCTTGGGCA 61.391 61.111 0.00 0.00 38.60 5.36
3776 11442 1.597027 CAACCACGAACTCCGCCTT 60.597 57.895 0.00 0.00 43.32 4.35
3825 11491 1.313812 CCGACGCCAACTACTCCTCT 61.314 60.000 0.00 0.00 0.00 3.69
3840 11506 2.604686 TCTGGTTGCTCCGCCTCT 60.605 61.111 0.00 0.00 39.52 3.69
3841 11507 2.435586 CTGGTTGCTCCGCCTCTG 60.436 66.667 0.00 0.00 39.52 3.35
3842 11508 4.704833 TGGTTGCTCCGCCTCTGC 62.705 66.667 0.00 0.00 39.52 4.26
3843 11509 4.704833 GGTTGCTCCGCCTCTGCA 62.705 66.667 0.00 0.00 37.32 4.41
3844 11510 2.437359 GTTGCTCCGCCTCTGCAT 60.437 61.111 0.00 0.00 36.55 3.96
3845 11511 2.042831 GTTGCTCCGCCTCTGCATT 61.043 57.895 0.00 0.00 36.55 3.56
3846 11512 1.746615 TTGCTCCGCCTCTGCATTC 60.747 57.895 0.00 0.00 36.55 2.67
3847 11513 2.899339 GCTCCGCCTCTGCATTCC 60.899 66.667 0.00 0.00 37.32 3.01
3848 11514 2.203126 CTCCGCCTCTGCATTCCC 60.203 66.667 0.00 0.00 37.32 3.97
3849 11515 3.008517 TCCGCCTCTGCATTCCCA 61.009 61.111 0.00 0.00 37.32 4.37
3850 11516 2.045045 CCGCCTCTGCATTCCCAA 60.045 61.111 0.00 0.00 37.32 4.12
3851 11517 2.409870 CCGCCTCTGCATTCCCAAC 61.410 63.158 0.00 0.00 37.32 3.77
3852 11518 2.409870 CGCCTCTGCATTCCCAACC 61.410 63.158 0.00 0.00 37.32 3.77
3853 11519 2.054453 GCCTCTGCATTCCCAACCC 61.054 63.158 0.00 0.00 37.47 4.11
3854 11520 1.380380 CCTCTGCATTCCCAACCCC 60.380 63.158 0.00 0.00 0.00 4.95
3855 11521 1.750399 CTCTGCATTCCCAACCCCG 60.750 63.158 0.00 0.00 0.00 5.73
3856 11522 2.196997 CTCTGCATTCCCAACCCCGA 62.197 60.000 0.00 0.00 0.00 5.14
3857 11523 1.750399 CTGCATTCCCAACCCCGAG 60.750 63.158 0.00 0.00 0.00 4.63
3858 11524 2.440247 GCATTCCCAACCCCGAGG 60.440 66.667 0.00 0.00 40.04 4.63
3859 11525 2.440247 CATTCCCAACCCCGAGGC 60.440 66.667 0.00 0.00 36.11 4.70
3860 11526 2.614013 ATTCCCAACCCCGAGGCT 60.614 61.111 0.00 0.00 36.11 4.58
3861 11527 2.680370 ATTCCCAACCCCGAGGCTC 61.680 63.158 3.87 3.87 36.11 4.70
3864 11530 3.787001 CCAACCCCGAGGCTCCTC 61.787 72.222 9.32 5.85 39.55 3.71
3865 11531 2.685380 CAACCCCGAGGCTCCTCT 60.685 66.667 9.32 0.00 40.69 3.69
3866 11532 2.685380 AACCCCGAGGCTCCTCTG 60.685 66.667 9.32 7.29 40.69 3.35
3867 11533 3.547787 AACCCCGAGGCTCCTCTGT 62.548 63.158 9.32 5.76 40.69 3.41
3868 11534 2.685380 CCCCGAGGCTCCTCTGTT 60.685 66.667 9.32 0.00 40.69 3.16
3869 11535 2.294078 CCCCGAGGCTCCTCTGTTT 61.294 63.158 9.32 0.00 40.69 2.83
3870 11536 1.679898 CCCGAGGCTCCTCTGTTTT 59.320 57.895 9.32 0.00 40.69 2.43
3871 11537 0.036875 CCCGAGGCTCCTCTGTTTTT 59.963 55.000 9.32 0.00 40.69 1.94
3891 11557 2.829741 TTTGCAAAATACAGTGGCCC 57.170 45.000 10.02 0.00 0.00 5.80
3892 11558 0.600557 TTGCAAAATACAGTGGCCCG 59.399 50.000 0.00 0.00 0.00 6.13
3893 11559 0.538516 TGCAAAATACAGTGGCCCGT 60.539 50.000 0.00 0.00 0.00 5.28
3894 11560 0.170339 GCAAAATACAGTGGCCCGTC 59.830 55.000 0.00 0.00 0.00 4.79
3895 11561 0.808755 CAAAATACAGTGGCCCGTCC 59.191 55.000 0.00 0.00 0.00 4.79
3896 11562 0.675522 AAAATACAGTGGCCCGTCCG 60.676 55.000 0.00 0.00 37.80 4.79
3897 11563 2.530958 AAATACAGTGGCCCGTCCGG 62.531 60.000 0.00 0.00 37.80 5.14
3902 11568 4.006357 GTGGCCCGTCCGGTGTTA 62.006 66.667 0.00 0.00 37.80 2.41
3903 11569 3.004354 TGGCCCGTCCGGTGTTAT 61.004 61.111 0.00 0.00 37.80 1.89
3904 11570 2.512974 GGCCCGTCCGGTGTTATG 60.513 66.667 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.649705 TCTCCAACCCCGGCTCCA 62.650 66.667 0.00 0.00 0.00 3.86
64 3708 1.467678 CCTGACGCCCTAGCTGCTAT 61.468 60.000 10.23 0.00 36.60 2.97
65 3709 2.127869 CCTGACGCCCTAGCTGCTA 61.128 63.158 9.34 9.34 36.60 3.49
125 3769 8.678199 CCTAAATGGTATCAGTTTTCTCTTTCC 58.322 37.037 0.00 0.00 33.03 3.13
147 3791 9.206690 TGCATATTCCCAATTATTCAAACCTAA 57.793 29.630 0.00 0.00 0.00 2.69
152 3796 6.215121 CGCTGCATATTCCCAATTATTCAAA 58.785 36.000 0.00 0.00 0.00 2.69
301 3945 2.238942 TAGGCATTGTATCACAGCGG 57.761 50.000 0.00 0.00 0.00 5.52
389 4034 1.758440 GAGGGAGCACAGTGGACACA 61.758 60.000 1.84 0.00 0.00 3.72
517 4162 2.269940 AGGAAGCCAGTATGACCACTT 58.730 47.619 0.00 0.00 39.69 3.16
539 4184 1.825090 CTGCCATTGAGCAAGTGGTA 58.175 50.000 10.93 7.44 43.52 3.25
546 4191 1.592400 GAAGCTGCTGCCATTGAGCA 61.592 55.000 12.44 0.00 44.22 4.26
561 4206 4.712476 ACCTTAGATGTCATCATGGAAGC 58.288 43.478 15.20 0.00 34.06 3.86
607 4252 2.669133 CCAGATGAGGACGGGCCAA 61.669 63.158 4.39 0.00 40.02 4.52
611 4256 3.147595 TCGCCAGATGAGGACGGG 61.148 66.667 0.00 0.00 0.00 5.28
631 4276 3.202906 GGCAGGCTAATAACGATGTCAA 58.797 45.455 0.00 0.00 0.00 3.18
641 4286 1.692173 GGGTCACGGGCAGGCTAATA 61.692 60.000 0.00 0.00 0.00 0.98
656 4301 1.611519 TTTTTCATGGGTGACGGGTC 58.388 50.000 0.00 0.00 33.11 4.46
776 4486 8.701895 GGAGGACATACGGGATAAATTATGATA 58.298 37.037 0.00 0.00 0.00 2.15
877 4588 5.530915 CACTGGCCCAATTTCGATCTTTATA 59.469 40.000 0.00 0.00 0.00 0.98
910 4624 0.179045 GGCCATGCTCGGTACAGAAT 60.179 55.000 0.00 0.00 0.00 2.40
947 4678 8.640033 ATTTTATAGGTCTATAAGGGGATCCC 57.360 38.462 23.95 23.95 45.90 3.85
948 4679 8.422566 CGATTTTATAGGTCTATAAGGGGATCC 58.577 40.741 1.92 1.92 38.70 3.36
949 4680 8.979534 ACGATTTTATAGGTCTATAAGGGGATC 58.020 37.037 9.53 10.35 38.70 3.36
950 4681 8.912614 ACGATTTTATAGGTCTATAAGGGGAT 57.087 34.615 9.53 4.99 38.70 3.85
957 4688 9.986157 AGTGGGATACGATTTTATAGGTCTATA 57.014 33.333 0.00 0.00 37.60 1.31
958 4689 8.896722 AGTGGGATACGATTTTATAGGTCTAT 57.103 34.615 0.00 0.00 37.60 1.98
1022 4753 2.751688 GTGGCGGTAGGGTTTGGA 59.248 61.111 0.00 0.00 0.00 3.53
1023 4754 2.360726 GGTGGCGGTAGGGTTTGG 60.361 66.667 0.00 0.00 0.00 3.28
1024 4755 2.360726 GGGTGGCGGTAGGGTTTG 60.361 66.667 0.00 0.00 0.00 2.93
1025 4756 3.654143 GGGGTGGCGGTAGGGTTT 61.654 66.667 0.00 0.00 0.00 3.27
1026 4757 4.669773 AGGGGTGGCGGTAGGGTT 62.670 66.667 0.00 0.00 0.00 4.11
1030 4761 3.834799 GTCGAGGGGTGGCGGTAG 61.835 72.222 0.00 0.00 0.00 3.18
1036 4767 4.400251 AGGGAGGTCGAGGGGTGG 62.400 72.222 0.00 0.00 0.00 4.61
1037 4768 2.760385 GAGGGAGGTCGAGGGGTG 60.760 72.222 0.00 0.00 0.00 4.61
1159 4890 0.967887 TGAGACGAGAGGGCTTCCAG 60.968 60.000 0.00 0.00 0.00 3.86
1160 4891 1.076727 TGAGACGAGAGGGCTTCCA 59.923 57.895 0.00 0.00 0.00 3.53
1184 4915 4.666532 GACCACGCGCAACAGCAC 62.667 66.667 5.73 0.00 36.85 4.40
1226 4957 0.528017 TGCCTGCAAACACGAAACAA 59.472 45.000 0.00 0.00 0.00 2.83
1227 4958 0.743688 ATGCCTGCAAACACGAAACA 59.256 45.000 0.00 0.00 0.00 2.83
1240 4971 0.250234 TCCAGGTCGAAGAATGCCTG 59.750 55.000 9.88 9.88 45.86 4.85
1400 5131 0.097674 GCAATACGAGGCAGCACAAG 59.902 55.000 0.00 0.00 0.00 3.16
1415 5146 1.754803 CAACATCCATCTGGCTGCAAT 59.245 47.619 0.50 0.00 34.82 3.56
1563 5294 5.648330 AAGGAAAGGACTCTAACAAGGTT 57.352 39.130 0.00 0.00 0.00 3.50
1575 5306 6.231211 TCACACTATTCTCAAAGGAAAGGAC 58.769 40.000 0.00 0.00 0.00 3.85
1642 5379 6.259387 CACATAAGCAATCATTCTGACTAGCA 59.741 38.462 0.00 0.00 0.00 3.49
1650 5387 8.743085 ATCTACAACACATAAGCAATCATTCT 57.257 30.769 0.00 0.00 0.00 2.40
1654 5391 7.119116 ACGAAATCTACAACACATAAGCAATCA 59.881 33.333 0.00 0.00 0.00 2.57
1829 5581 5.756918 AGAGTACAGCATCCTAGTTGTAGA 58.243 41.667 0.00 0.00 36.16 2.59
1966 5720 7.377662 CCAAATTCGACTTTAAACCAGTAACAC 59.622 37.037 0.00 0.00 0.00 3.32
2096 5851 2.549778 GGTTTTGGCATTTTGCTAGGCA 60.550 45.455 0.00 0.00 44.28 4.75
2154 5909 1.813178 TCAACAAGCACGGAACAAACA 59.187 42.857 0.00 0.00 0.00 2.83
2197 5952 6.851609 TGCAACAATAACAACATCCTACATC 58.148 36.000 0.00 0.00 0.00 3.06
2383 6138 3.745975 TGCAGTCGTCAAATCTTACCTTG 59.254 43.478 0.00 0.00 0.00 3.61
2399 6154 7.172875 ACAAGAATCAGCTATATCAATGCAGTC 59.827 37.037 0.00 0.00 0.00 3.51
2697 6453 3.776417 ACAAGAGGGCCAATATGCAAATT 59.224 39.130 6.18 0.00 0.00 1.82
2895 6652 6.867293 GGAGAATAACTCAGTGTTTACTCGTT 59.133 38.462 0.00 0.00 46.54 3.85
2915 10508 3.165071 GGGCCTGAATTTTCAAGGAGAA 58.835 45.455 0.84 0.00 36.64 2.87
2981 10585 2.038863 TCCCCTACAAGCTTTCCAGA 57.961 50.000 0.00 0.00 0.00 3.86
3009 10613 1.360192 GCAACCACCACAGCAAGAC 59.640 57.895 0.00 0.00 0.00 3.01
3015 10619 0.886490 GTCAGAGGCAACCACCACAG 60.886 60.000 0.00 0.00 37.17 3.66
3182 10786 1.301244 CACCTCGCTCAGTGTTGCT 60.301 57.895 8.65 0.00 0.00 3.91
3233 10837 2.934570 GCCTACCACCGTCGTCCAA 61.935 63.158 0.00 0.00 0.00 3.53
3275 10879 1.991099 GCCTACCTCGTCGTCCAGAC 61.991 65.000 0.00 0.00 46.16 3.51
3276 10880 1.748122 GCCTACCTCGTCGTCCAGA 60.748 63.158 0.00 0.00 0.00 3.86
3277 10881 2.799371 GCCTACCTCGTCGTCCAG 59.201 66.667 0.00 0.00 0.00 3.86
3278 10882 3.129502 CGCCTACCTCGTCGTCCA 61.130 66.667 0.00 0.00 0.00 4.02
3279 10883 2.694760 AACGCCTACCTCGTCGTCC 61.695 63.158 0.00 0.00 39.48 4.79
3435 11065 1.004440 GAGACACAGTCCAGGCCAC 60.004 63.158 5.01 0.00 32.18 5.01
3441 11071 3.474798 AATCCCTAGAGACACAGTCCA 57.525 47.619 0.00 0.00 32.18 4.02
3470 11108 4.748102 TCAGATTTGACTTACACGGTTGTC 59.252 41.667 0.00 0.00 37.15 3.18
3484 11122 2.869801 ACGTTCGCAAAGTCAGATTTGA 59.130 40.909 3.49 0.00 41.71 2.69
3495 11133 0.460459 TGACCAGACACGTTCGCAAA 60.460 50.000 0.00 0.00 0.00 3.68
3496 11134 0.460459 TTGACCAGACACGTTCGCAA 60.460 50.000 0.00 0.00 0.00 4.85
3499 11147 3.120786 GGTTATTTGACCAGACACGTTCG 60.121 47.826 0.00 0.00 39.57 3.95
3509 11157 8.570038 TTGGGATAGTATAGGTTATTTGACCA 57.430 34.615 0.00 0.00 42.35 4.02
3520 11168 6.607600 TCCGATCAAGATTGGGATAGTATAGG 59.392 42.308 14.82 0.00 41.74 2.57
3532 11180 6.246420 AGTGAAAAACTCCGATCAAGATTG 57.754 37.500 0.00 0.00 31.64 2.67
3537 11185 6.106673 GGAGATAGTGAAAAACTCCGATCAA 58.893 40.000 0.00 0.00 40.56 2.57
3544 11192 3.371285 GGCACGGAGATAGTGAAAAACTC 59.629 47.826 0.07 0.00 41.83 3.01
3549 11197 0.174845 CGGGCACGGAGATAGTGAAA 59.825 55.000 0.00 0.00 41.83 2.69
3578 11232 2.436646 CGGAGTTGCGGCTTCCAT 60.437 61.111 15.43 0.00 0.00 3.41
3579 11233 4.697756 CCGGAGTTGCGGCTTCCA 62.698 66.667 0.00 0.00 0.00 3.53
3582 11236 2.668550 GAACCGGAGTTGCGGCTT 60.669 61.111 9.46 5.88 35.94 4.35
3597 11251 1.900351 CATGGAGGAGTCGCAGGAA 59.100 57.895 0.00 0.00 0.00 3.36
3629 11283 1.590259 GAGGTCGAAGCGGAGATGC 60.590 63.158 0.00 0.00 0.00 3.91
3650 11304 3.065015 CGACTGACGCGCTCTTTC 58.935 61.111 5.73 0.00 34.51 2.62
3663 11317 2.651361 CAGGAACGAGTGGCGACT 59.349 61.111 0.00 0.00 44.57 4.18
3683 11337 0.106519 GGCATGTATGGAGGCCAACT 60.107 55.000 5.01 0.00 45.70 3.16
3695 11361 3.258372 GTCTATCCGGAATGAGGCATGTA 59.742 47.826 9.01 0.00 0.00 2.29
3697 11363 2.301296 AGTCTATCCGGAATGAGGCATG 59.699 50.000 9.01 0.00 0.00 4.06
3699 11365 1.964223 GAGTCTATCCGGAATGAGGCA 59.036 52.381 9.01 0.00 0.00 4.75
3709 11375 2.096248 GGCCATCCTAGAGTCTATCCG 58.904 57.143 0.00 0.00 0.00 4.18
3720 11386 1.528824 GAAGCAGCAGGCCATCCTA 59.471 57.895 5.01 0.00 46.50 2.94
3737 11403 3.449227 AAGCGACCGAGATGGCGA 61.449 61.111 0.00 0.00 43.94 5.54
3759 11425 1.597027 CAAGGCGGAGTTCGTGGTT 60.597 57.895 0.00 0.00 41.72 3.67
3763 11429 1.755393 AAGGACAAGGCGGAGTTCGT 61.755 55.000 0.00 0.00 41.72 3.85
3809 11475 0.542232 ACCAGAGGAGTAGTTGGCGT 60.542 55.000 0.00 0.00 33.98 5.68
3840 11506 2.354729 CTCGGGGTTGGGAATGCA 59.645 61.111 0.00 0.00 0.00 3.96
3841 11507 2.440247 CCTCGGGGTTGGGAATGC 60.440 66.667 0.00 0.00 0.00 3.56
3842 11508 2.440247 GCCTCGGGGTTGGGAATG 60.440 66.667 1.62 0.00 34.45 2.67
3843 11509 2.614013 AGCCTCGGGGTTGGGAAT 60.614 61.111 1.62 0.00 34.45 3.01
3844 11510 3.327404 GAGCCTCGGGGTTGGGAA 61.327 66.667 1.62 0.00 31.55 3.97
3847 11513 3.787001 GAGGAGCCTCGGGGTTGG 61.787 72.222 1.62 0.00 31.55 3.77
3848 11514 2.685380 AGAGGAGCCTCGGGGTTG 60.685 66.667 1.62 0.00 46.90 3.77
3849 11515 2.685380 CAGAGGAGCCTCGGGGTT 60.685 66.667 1.62 0.00 46.90 4.11
3850 11516 3.547787 AACAGAGGAGCCTCGGGGT 62.548 63.158 18.61 12.05 46.90 4.95
3851 11517 1.842381 AAAACAGAGGAGCCTCGGGG 61.842 60.000 18.61 0.00 46.90 5.73
3852 11518 0.036875 AAAAACAGAGGAGCCTCGGG 59.963 55.000 18.61 13.61 46.90 5.14
3853 11519 3.633361 AAAAACAGAGGAGCCTCGG 57.367 52.632 13.97 13.97 46.90 4.63
3870 11536 3.471680 GGGCCACTGTATTTTGCAAAAA 58.528 40.909 27.10 14.23 0.00 1.94
3871 11537 2.546795 CGGGCCACTGTATTTTGCAAAA 60.547 45.455 25.76 25.76 0.00 2.44
3872 11538 1.000283 CGGGCCACTGTATTTTGCAAA 60.000 47.619 8.05 8.05 0.00 3.68
3873 11539 0.600557 CGGGCCACTGTATTTTGCAA 59.399 50.000 4.39 0.00 0.00 4.08
3874 11540 0.538516 ACGGGCCACTGTATTTTGCA 60.539 50.000 4.39 0.00 33.46 4.08
3875 11541 0.170339 GACGGGCCACTGTATTTTGC 59.830 55.000 4.39 0.00 36.00 3.68
3876 11542 0.808755 GGACGGGCCACTGTATTTTG 59.191 55.000 4.39 0.00 36.00 2.44
3877 11543 0.675522 CGGACGGGCCACTGTATTTT 60.676 55.000 4.39 0.00 36.00 1.82
3878 11544 1.078708 CGGACGGGCCACTGTATTT 60.079 57.895 4.39 0.00 36.00 1.40
3879 11545 2.582436 CGGACGGGCCACTGTATT 59.418 61.111 4.39 0.00 36.00 1.89
3880 11546 3.467226 CCGGACGGGCCACTGTAT 61.467 66.667 4.39 0.00 36.00 2.29
3885 11551 3.319441 ATAACACCGGACGGGCCAC 62.319 63.158 9.46 0.00 40.62 5.01
3886 11552 3.004354 ATAACACCGGACGGGCCA 61.004 61.111 9.46 0.00 40.62 5.36
3887 11553 2.512974 CATAACACCGGACGGGCC 60.513 66.667 9.46 0.00 40.62 5.80


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

AutoCloner maintained by Alex Coulton.