Multiple sequence alignment - TraesCS4B01G171100

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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 TraesCS4B01G171100 chr4B 100.000 4682 0 0 1 4682 374630847 374626166 0.000000e+00 8647.0
1 TraesCS4B01G171100 chr4D 96.287 4067 104 16 54 4100 301009957 301005918 0.000000e+00 6630.0
2 TraesCS4B01G171100 chr4D 91.260 492 27 10 4148 4625 301005919 301005430 0.000000e+00 656.0
3 TraesCS4B01G171100 chr4D 100.000 54 0 0 4625 4678 301005403 301005350 2.980000e-17 100.0
4 TraesCS4B01G171100 chr4A 95.938 3791 94 21 340 4101 181707259 181711018 0.000000e+00 6093.0
5 TraesCS4B01G171100 chr4A 84.872 390 18 13 4269 4628 181711072 181711450 5.760000e-94 355.0
6 TraesCS4B01G171100 chr4A 92.040 201 11 2 130 330 181706808 181707003 1.280000e-70 278.0
7 TraesCS4B01G171100 chr4A 93.407 91 5 1 50 139 181706595 181706685 2.940000e-27 134.0
8 TraesCS4B01G171100 chr4A 100.000 51 0 0 4625 4675 181711468 181711518 1.390000e-15 95.3
9 TraesCS4B01G171100 chr1D 89.375 3266 258 56 799 4034 316856524 316859730 0.000000e+00 4026.0
10 TraesCS4B01G171100 chr1D 90.164 61 2 3 4099 4158 100460908 100460851 5.020000e-10 76.8
11 TraesCS4B01G171100 chr1B 90.083 3126 243 38 760 3853 429001921 429005011 0.000000e+00 3993.0
12 TraesCS4B01G171100 chr1A 89.006 3229 282 39 833 4034 398050442 398053624 0.000000e+00 3928.0
13 TraesCS4B01G171100 chrUn 100.000 419 0 0 2222 2640 476932637 476932219 0.000000e+00 774.0
14 TraesCS4B01G171100 chr6B 100.000 42 0 0 4111 4152 238158190 238158149 1.400000e-10 78.7
15 TraesCS4B01G171100 chr6B 93.878 49 3 0 4111 4159 336181255 336181207 1.810000e-09 75.0
16 TraesCS4B01G171100 chr6B 92.308 52 2 2 4111 4162 185258999 185258950 6.500000e-09 73.1
17 TraesCS4B01G171100 chr3B 94.000 50 2 1 4111 4159 449738690 449738739 1.810000e-09 75.0
18 TraesCS4B01G171100 chr3B 92.453 53 1 3 4111 4161 766128238 766128289 6.500000e-09 73.1
19 TraesCS4B01G171100 chr3B 90.741 54 4 1 4111 4164 822536338 822536390 2.340000e-08 71.3
20 TraesCS4B01G171100 chr2B 90.566 53 5 0 4111 4163 372955359 372955411 2.340000e-08 71.3
21 TraesCS4B01G171100 chr2B 90.741 54 3 1 4096 4149 446112699 446112750 2.340000e-08 71.3


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 TraesCS4B01G171100 chr4B 374626166 374630847 4681 True 8647.00 8647 100.0000 1 4682 1 chr4B.!!$R1 4681
1 TraesCS4B01G171100 chr4D 301005350 301009957 4607 True 2462.00 6630 95.8490 54 4678 3 chr4D.!!$R1 4624
2 TraesCS4B01G171100 chr4A 181706595 181711518 4923 False 1391.06 6093 93.2514 50 4675 5 chr4A.!!$F1 4625
3 TraesCS4B01G171100 chr1D 316856524 316859730 3206 False 4026.00 4026 89.3750 799 4034 1 chr1D.!!$F1 3235
4 TraesCS4B01G171100 chr1B 429001921 429005011 3090 False 3993.00 3993 90.0830 760 3853 1 chr1B.!!$F1 3093
5 TraesCS4B01G171100 chr1A 398050442 398053624 3182 False 3928.00 3928 89.0060 833 4034 1 chr1A.!!$F1 3201

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
25 26 0.103937 TGAAAAGGTTTGGCGCCTTG 59.896 50.0 29.70 0.00 44.84 3.61 F
26 27 0.104120 GAAAAGGTTTGGCGCCTTGT 59.896 50.0 29.70 8.05 44.84 3.16 F
27 28 0.179086 AAAAGGTTTGGCGCCTTGTG 60.179 50.0 29.70 0.00 44.84 3.33 F
41 42 0.381801 CTTGTGCGCCTTCTGTTGTT 59.618 50.0 4.18 0.00 0.00 2.83 F
183 319 0.457337 GTCGAACGGCACCGAATACT 60.457 55.0 17.40 0.00 42.83 2.12 F
733 1134 0.677098 TCGTAGAGCTGAGCGGAGTT 60.677 55.0 0.00 0.00 0.00 3.01 F
2220 2665 0.537188 CAGGGACGAAGCCACAGTAT 59.463 55.0 0.00 0.00 0.00 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1786 1.004560 CAGCCTGAGGAACTTGCGA 60.005 57.895 0.65 0.0 41.55 5.10 R
2034 2479 0.606401 AGATGTTGAACACCCGCTGG 60.606 55.000 0.00 0.0 37.80 4.85 R
2130 2575 3.774766 TGCTCACCACATAGTCCTTGTAT 59.225 43.478 0.00 0.0 0.00 2.29 R
2157 2602 5.448654 CAGAAATCCATAATCCCAGAACCA 58.551 41.667 0.00 0.0 0.00 3.67 R
2220 2665 6.888088 CCATCCCATTGAGAATAGCATCATAA 59.112 38.462 0.00 0.0 0.00 1.90 R
2796 3241 2.166459 CTCCTCGCAGTAACCAATCAGA 59.834 50.000 0.00 0.0 0.00 3.27 R
4132 4616 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.0 0.00 4.12 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
21 22 2.476241 CTGAAATGAAAAGGTTTGGCGC 59.524 45.455 0.00 0.00 0.00 6.53
22 23 1.798223 GAAATGAAAAGGTTTGGCGCC 59.202 47.619 22.73 22.73 0.00 6.53
23 24 1.047801 AATGAAAAGGTTTGGCGCCT 58.952 45.000 29.70 3.54 38.11 5.52
25 26 0.103937 TGAAAAGGTTTGGCGCCTTG 59.896 50.000 29.70 0.00 44.84 3.61
26 27 0.104120 GAAAAGGTTTGGCGCCTTGT 59.896 50.000 29.70 8.05 44.84 3.16
27 28 0.179086 AAAAGGTTTGGCGCCTTGTG 60.179 50.000 29.70 0.00 44.84 3.33
28 29 2.642996 AAAGGTTTGGCGCCTTGTGC 62.643 55.000 29.70 12.84 44.84 4.57
37 38 2.980233 GCCTTGTGCGCCTTCTGT 60.980 61.111 4.18 0.00 0.00 3.41
38 39 2.555547 GCCTTGTGCGCCTTCTGTT 61.556 57.895 4.18 0.00 0.00 3.16
39 40 1.283793 CCTTGTGCGCCTTCTGTTG 59.716 57.895 4.18 0.00 0.00 3.33
40 41 1.447317 CCTTGTGCGCCTTCTGTTGT 61.447 55.000 4.18 0.00 0.00 3.32
41 42 0.381801 CTTGTGCGCCTTCTGTTGTT 59.618 50.000 4.18 0.00 0.00 2.83
42 43 1.601903 CTTGTGCGCCTTCTGTTGTTA 59.398 47.619 4.18 0.00 0.00 2.41
43 44 1.669604 TGTGCGCCTTCTGTTGTTAA 58.330 45.000 4.18 0.00 0.00 2.01
44 45 2.017782 TGTGCGCCTTCTGTTGTTAAA 58.982 42.857 4.18 0.00 0.00 1.52
45 46 2.423892 TGTGCGCCTTCTGTTGTTAAAA 59.576 40.909 4.18 0.00 0.00 1.52
46 47 3.119459 TGTGCGCCTTCTGTTGTTAAAAA 60.119 39.130 4.18 0.00 0.00 1.94
183 319 0.457337 GTCGAACGGCACCGAATACT 60.457 55.000 17.40 0.00 42.83 2.12
184 320 1.093972 TCGAACGGCACCGAATACTA 58.906 50.000 17.40 0.00 42.83 1.82
190 326 1.263217 CGGCACCGAATACTAATTGCC 59.737 52.381 2.01 0.11 42.83 4.52
287 424 1.810532 GGCCACGGTCTCTGACTAG 59.189 63.158 0.00 0.00 32.47 2.57
350 733 5.069251 GCTGTCCACATTATACTACCTGACT 59.931 44.000 0.00 0.00 0.00 3.41
356 739 4.826183 ACATTATACTACCTGACTCGACCC 59.174 45.833 0.00 0.00 0.00 4.46
395 778 1.817447 GTCGTCTTAGGTACCAGCACT 59.183 52.381 15.94 0.00 0.00 4.40
418 801 1.686587 TGTCAACAGTCCATGACGAGT 59.313 47.619 0.00 0.00 46.99 4.18
476 860 2.102420 CCCACCACAGGAAAACCTTTTC 59.898 50.000 2.39 2.39 44.38 2.29
477 861 3.031013 CCACCACAGGAAAACCTTTTCT 58.969 45.455 9.75 0.00 44.49 2.52
478 862 3.450817 CCACCACAGGAAAACCTTTTCTT 59.549 43.478 9.75 0.62 44.49 2.52
490 874 9.089601 GGAAAACCTTTTCTTTTATTTTGACGA 57.910 29.630 9.75 0.00 44.49 4.20
590 984 3.116531 GCCGTACCGTTCCACTGC 61.117 66.667 0.00 0.00 0.00 4.40
694 1095 1.081175 GGCGGTGAAAAGAAGCAGC 60.081 57.895 0.00 0.00 0.00 5.25
733 1134 0.677098 TCGTAGAGCTGAGCGGAGTT 60.677 55.000 0.00 0.00 0.00 3.01
739 1140 2.125912 CTGAGCGGAGTTGGTCGG 60.126 66.667 0.00 0.00 39.19 4.79
922 1346 3.430862 GCCAGCACGCAAATCCGA 61.431 61.111 0.00 0.00 0.00 4.55
1044 1483 4.869440 CTGCTCCTCGCGGCTCTG 62.869 72.222 6.13 0.00 43.27 3.35
1323 1768 2.656069 GGCGCCCTTCACCTACTCA 61.656 63.158 18.11 0.00 0.00 3.41
1386 1831 1.205460 ACCCGGCCAACTACTCCAAT 61.205 55.000 2.24 0.00 0.00 3.16
2034 2479 5.482526 ACAATCCCCATTTACTAAACCCAAC 59.517 40.000 0.00 0.00 0.00 3.77
2157 2602 2.289694 GGACTATGTGGTGAGCACTGTT 60.290 50.000 16.26 3.79 0.00 3.16
2220 2665 0.537188 CAGGGACGAAGCCACAGTAT 59.463 55.000 0.00 0.00 0.00 2.12
2796 3241 0.320771 GGCACCGTCATCTTGTGTCT 60.321 55.000 0.00 0.00 32.06 3.41
3234 3679 2.283173 CCTGCCTTGAACCCCACC 60.283 66.667 0.00 0.00 0.00 4.61
3537 3988 2.489938 TGGTTGGAAAGAAGGATCCG 57.510 50.000 5.98 0.00 38.63 4.18
3586 4037 2.433239 ACTACGACCACAACAACTTCCT 59.567 45.455 0.00 0.00 0.00 3.36
3618 4069 0.884704 ACCAAAGTGTCGCGAGCATT 60.885 50.000 10.24 4.88 0.00 3.56
3776 4228 1.672363 TGAGTTTGTGCTCTTGCTGTG 59.328 47.619 0.00 0.00 40.48 3.66
3934 4402 1.806542 CCACCACTGCTATGTGTTGTC 59.193 52.381 0.00 0.00 36.30 3.18
4106 4590 7.754851 TTTTGACCTAAACAAATACTCCCTC 57.245 36.000 0.00 0.00 37.15 4.30
4107 4591 5.431179 TGACCTAAACAAATACTCCCTCC 57.569 43.478 0.00 0.00 0.00 4.30
4108 4592 4.081309 TGACCTAAACAAATACTCCCTCCG 60.081 45.833 0.00 0.00 0.00 4.63
4109 4593 3.842436 ACCTAAACAAATACTCCCTCCGT 59.158 43.478 0.00 0.00 0.00 4.69
4110 4594 4.287845 ACCTAAACAAATACTCCCTCCGTT 59.712 41.667 0.00 0.00 0.00 4.44
4111 4595 5.484998 ACCTAAACAAATACTCCCTCCGTTA 59.515 40.000 0.00 0.00 0.00 3.18
4112 4596 5.814188 CCTAAACAAATACTCCCTCCGTTAC 59.186 44.000 0.00 0.00 0.00 2.50
4113 4597 5.494390 AAACAAATACTCCCTCCGTTACT 57.506 39.130 0.00 0.00 0.00 2.24
4114 4598 6.610075 AAACAAATACTCCCTCCGTTACTA 57.390 37.500 0.00 0.00 0.00 1.82
4115 4599 6.610075 AACAAATACTCCCTCCGTTACTAA 57.390 37.500 0.00 0.00 0.00 2.24
4116 4600 6.218108 ACAAATACTCCCTCCGTTACTAAG 57.782 41.667 0.00 0.00 0.00 2.18
4117 4601 5.128335 ACAAATACTCCCTCCGTTACTAAGG 59.872 44.000 0.00 0.00 0.00 2.69
4118 4602 2.915657 ACTCCCTCCGTTACTAAGGT 57.084 50.000 0.48 0.00 0.00 3.50
4119 4603 2.732763 ACTCCCTCCGTTACTAAGGTC 58.267 52.381 0.48 0.00 0.00 3.85
4120 4604 2.042162 ACTCCCTCCGTTACTAAGGTCA 59.958 50.000 0.48 0.00 0.00 4.02
4121 4605 3.094572 CTCCCTCCGTTACTAAGGTCAA 58.905 50.000 0.48 0.00 0.00 3.18
4122 4606 3.094572 TCCCTCCGTTACTAAGGTCAAG 58.905 50.000 0.48 0.00 0.00 3.02
4123 4607 3.094572 CCCTCCGTTACTAAGGTCAAGA 58.905 50.000 0.48 0.00 0.00 3.02
4124 4608 3.119209 CCCTCCGTTACTAAGGTCAAGAC 60.119 52.174 0.00 0.00 0.00 3.01
4125 4609 3.508793 CCTCCGTTACTAAGGTCAAGACA 59.491 47.826 2.29 0.00 0.00 3.41
4126 4610 4.483311 CTCCGTTACTAAGGTCAAGACAC 58.517 47.826 2.29 0.00 0.00 3.67
4127 4611 4.147321 TCCGTTACTAAGGTCAAGACACT 58.853 43.478 2.29 0.00 0.00 3.55
4128 4612 4.586001 TCCGTTACTAAGGTCAAGACACTT 59.414 41.667 2.29 5.99 0.00 3.16
4129 4613 5.769662 TCCGTTACTAAGGTCAAGACACTTA 59.230 40.000 2.29 6.73 0.00 2.24
4130 4614 6.435277 TCCGTTACTAAGGTCAAGACACTTAT 59.565 38.462 2.29 2.45 0.00 1.73
4131 4615 7.039504 TCCGTTACTAAGGTCAAGACACTTATT 60.040 37.037 2.29 5.06 0.00 1.40
4132 4616 7.601508 CCGTTACTAAGGTCAAGACACTTATTT 59.398 37.037 2.29 2.03 0.00 1.40
4133 4617 8.985805 CGTTACTAAGGTCAAGACACTTATTTT 58.014 33.333 2.29 0.15 0.00 1.82
4135 4619 7.745620 ACTAAGGTCAAGACACTTATTTTGG 57.254 36.000 2.29 0.05 0.00 3.28
4136 4620 6.715264 ACTAAGGTCAAGACACTTATTTTGGG 59.285 38.462 2.29 0.00 0.00 4.12
4137 4621 5.319043 AGGTCAAGACACTTATTTTGGGA 57.681 39.130 2.29 0.00 0.00 4.37
4138 4622 5.070685 AGGTCAAGACACTTATTTTGGGAC 58.929 41.667 2.29 0.00 0.00 4.46
4139 4623 4.083484 GGTCAAGACACTTATTTTGGGACG 60.083 45.833 2.29 0.00 0.00 4.79
4140 4624 4.069304 TCAAGACACTTATTTTGGGACGG 58.931 43.478 0.00 0.00 0.00 4.79
4141 4625 4.069304 CAAGACACTTATTTTGGGACGGA 58.931 43.478 0.00 0.00 0.00 4.69
4142 4626 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
4143 4627 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4144 4628 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
4145 4629 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
4146 4630 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
4163 4647 7.147479 ACGGAGGGAGTATGTACTACTAGTAAA 60.147 40.741 3.76 0.00 40.88 2.01
4164 4648 7.172361 CGGAGGGAGTATGTACTACTAGTAAAC 59.828 44.444 3.76 6.13 40.88 2.01
4165 4649 8.217111 GGAGGGAGTATGTACTACTAGTAAACT 58.783 40.741 3.76 3.01 40.88 2.66
4166 4650 8.977267 AGGGAGTATGTACTACTAGTAAACTG 57.023 38.462 3.76 0.00 40.88 3.16
4167 4651 7.501892 AGGGAGTATGTACTACTAGTAAACTGC 59.498 40.741 3.76 12.85 40.88 4.40
4175 4659 1.002773 ACTAGTAAACTGCCCCCAACG 59.997 52.381 0.00 0.00 0.00 4.10
4208 4693 3.527665 AGGAATGGGGTAGTATGTGCTTT 59.472 43.478 0.00 0.00 0.00 3.51
4290 4775 2.798283 ACGTTGATTGTTACACCAGTCG 59.202 45.455 0.00 0.00 0.00 4.18
4343 4829 5.849510 TCCATGTCGTCTTGTCTTTTCTTA 58.150 37.500 0.00 0.00 0.00 2.10
4344 4830 6.285224 TCCATGTCGTCTTGTCTTTTCTTAA 58.715 36.000 0.00 0.00 0.00 1.85
4345 4831 6.934645 TCCATGTCGTCTTGTCTTTTCTTAAT 59.065 34.615 0.00 0.00 0.00 1.40
4346 4832 8.092068 TCCATGTCGTCTTGTCTTTTCTTAATA 58.908 33.333 0.00 0.00 0.00 0.98
4347 4833 8.717821 CCATGTCGTCTTGTCTTTTCTTAATAA 58.282 33.333 0.00 0.00 0.00 1.40
4395 4909 7.436673 TGTTTGTGAGTTGTATTTAATTGCCAC 59.563 33.333 0.00 0.00 0.00 5.01
4408 4922 1.195442 TTGCCACTATCCGGACACCA 61.195 55.000 6.12 0.00 0.00 4.17
4471 4985 4.614475 TCTTGATCCAGAGTAGTGTCCAT 58.386 43.478 0.00 0.00 0.00 3.41
4519 5033 7.011482 CGTTATTTGATTGCTTTACCTAGAGCT 59.989 37.037 3.15 0.00 39.60 4.09
4535 5049 2.177531 CTGTGCAGCGCATGAACC 59.822 61.111 11.47 0.00 41.91 3.62
4589 5103 1.523258 AGCTGTGCGCATCTGATCC 60.523 57.895 15.91 0.00 42.61 3.36
4616 5130 7.041712 GGAGAAAGAGTGGAATCGAATAAATCC 60.042 40.741 0.00 0.00 0.00 3.01
4678 5219 2.567169 TGAAGATTCGACAGATGGGTGT 59.433 45.455 0.00 0.00 0.00 4.16
4679 5220 3.007940 TGAAGATTCGACAGATGGGTGTT 59.992 43.478 0.00 0.00 0.00 3.32
4680 5221 2.977914 AGATTCGACAGATGGGTGTTG 58.022 47.619 0.00 0.00 33.61 3.33
4681 5222 2.567169 AGATTCGACAGATGGGTGTTGA 59.433 45.455 0.00 0.00 38.80 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.478831 GCGCCAAACCTTTTCATTTCA 58.521 42.857 0.00 0.00 0.00 2.69
3 4 1.416030 AGGCGCCAAACCTTTTCATTT 59.584 42.857 31.54 0.00 31.87 2.32
4 5 1.047801 AGGCGCCAAACCTTTTCATT 58.952 45.000 31.54 0.00 31.87 2.57
5 6 1.047801 AAGGCGCCAAACCTTTTCAT 58.952 45.000 31.54 0.00 45.39 2.57
6 7 0.103937 CAAGGCGCCAAACCTTTTCA 59.896 50.000 31.54 0.00 45.39 2.69
7 8 0.104120 ACAAGGCGCCAAACCTTTTC 59.896 50.000 31.54 0.00 45.39 2.29
8 9 0.179086 CACAAGGCGCCAAACCTTTT 60.179 50.000 31.54 9.43 45.39 2.27
9 10 1.441311 CACAAGGCGCCAAACCTTT 59.559 52.632 31.54 10.30 45.39 3.11
11 12 3.605664 GCACAAGGCGCCAAACCT 61.606 61.111 31.54 3.61 40.02 3.50
20 21 2.555547 AACAGAAGGCGCACAAGGC 61.556 57.895 10.83 0.00 39.90 4.35
21 22 1.283793 CAACAGAAGGCGCACAAGG 59.716 57.895 10.83 0.00 0.00 3.61
22 23 0.381801 AACAACAGAAGGCGCACAAG 59.618 50.000 10.83 0.00 0.00 3.16
23 24 1.669604 TAACAACAGAAGGCGCACAA 58.330 45.000 10.83 0.00 0.00 3.33
24 25 1.669604 TTAACAACAGAAGGCGCACA 58.330 45.000 10.83 0.00 0.00 4.57
25 26 2.766970 TTTAACAACAGAAGGCGCAC 57.233 45.000 10.83 0.00 0.00 5.34
26 27 3.784701 TTTTTAACAACAGAAGGCGCA 57.215 38.095 10.83 0.00 0.00 6.09
49 50 9.545105 TGTATTCAAATCACAAAATGAGCTTTT 57.455 25.926 0.00 0.00 41.91 2.27
50 51 9.545105 TTGTATTCAAATCACAAAATGAGCTTT 57.455 25.926 0.00 0.00 41.91 3.51
51 52 9.199982 CTTGTATTCAAATCACAAAATGAGCTT 57.800 29.630 0.00 0.00 41.91 3.74
52 53 8.362639 ACTTGTATTCAAATCACAAAATGAGCT 58.637 29.630 0.00 0.00 41.91 4.09
162 298 0.038435 TATTCGGTGCCGTTCGACAA 60.038 50.000 10.60 0.00 40.74 3.18
273 410 0.697079 TCCCACTAGTCAGAGACCGT 59.303 55.000 0.00 0.00 32.18 4.83
287 424 1.073199 CACCAGAACAGGGTCCCAC 59.927 63.158 11.55 0.00 36.19 4.61
356 739 2.834505 CGGGATTGCATGGGGTGG 60.835 66.667 0.00 0.00 0.00 4.61
476 860 8.363029 GCTTTTTCGGTATCGTCAAAATAAAAG 58.637 33.333 8.15 0.00 37.69 2.27
477 861 8.077386 AGCTTTTTCGGTATCGTCAAAATAAAA 58.923 29.630 8.15 0.00 37.69 1.52
478 862 7.586747 AGCTTTTTCGGTATCGTCAAAATAAA 58.413 30.769 8.15 0.00 37.69 1.40
751 1152 1.077716 ATTAAGTGGGGCTCGCCAC 60.078 57.895 23.52 23.52 40.69 5.01
995 1434 1.225704 GGGCCTCCTCTCATGGTTG 59.774 63.158 0.84 0.00 0.00 3.77
996 1435 2.370445 CGGGCCTCCTCTCATGGTT 61.370 63.158 0.84 0.00 0.00 3.67
1341 1786 1.004560 CAGCCTGAGGAACTTGCGA 60.005 57.895 0.65 0.00 41.55 5.10
2034 2479 0.606401 AGATGTTGAACACCCGCTGG 60.606 55.000 0.00 0.00 37.80 4.85
2130 2575 3.774766 TGCTCACCACATAGTCCTTGTAT 59.225 43.478 0.00 0.00 0.00 2.29
2157 2602 5.448654 CAGAAATCCATAATCCCAGAACCA 58.551 41.667 0.00 0.00 0.00 3.67
2220 2665 6.888088 CCATCCCATTGAGAATAGCATCATAA 59.112 38.462 0.00 0.00 0.00 1.90
2796 3241 2.166459 CTCCTCGCAGTAACCAATCAGA 59.834 50.000 0.00 0.00 0.00 3.27
3234 3679 5.791681 CAAGCTAACTTCTTCCTTTGCAAGG 60.792 44.000 0.68 0.68 41.51 3.61
3339 3784 2.544486 GGCAAACTTCTTGAAGCACTGG 60.544 50.000 9.98 0.00 0.00 4.00
3537 3988 5.738208 GCTGGAATCAATTGATGGGTCATTC 60.738 44.000 21.39 13.28 34.49 2.67
3586 4037 2.890311 CACTTTGGTCACCCATGCTTAA 59.110 45.455 0.00 0.00 41.49 1.85
3618 4069 2.710902 CGTCAGCCCATCCGAGTCA 61.711 63.158 0.00 0.00 0.00 3.41
3934 4402 6.277605 TCATACAGTATTACATGTTGGGTCG 58.722 40.000 2.30 0.00 0.00 4.79
4002 4474 1.677576 GATTCGGAAATGAGCATGGCA 59.322 47.619 0.00 0.00 0.00 4.92
4086 4570 4.081254 ACGGAGGGAGTATTTGTTTAGGTC 60.081 45.833 0.00 0.00 0.00 3.85
4101 4585 2.905415 TGACCTTAGTAACGGAGGGA 57.095 50.000 5.66 0.00 34.81 4.20
4102 4586 3.094572 TCTTGACCTTAGTAACGGAGGG 58.905 50.000 5.66 0.00 34.81 4.30
4103 4587 3.508793 TGTCTTGACCTTAGTAACGGAGG 59.491 47.826 5.66 0.00 36.62 4.30
4104 4588 4.217983 AGTGTCTTGACCTTAGTAACGGAG 59.782 45.833 5.66 0.00 0.00 4.63
4105 4589 4.147321 AGTGTCTTGACCTTAGTAACGGA 58.853 43.478 5.66 0.00 0.00 4.69
4106 4590 4.516365 AGTGTCTTGACCTTAGTAACGG 57.484 45.455 0.00 0.00 0.00 4.44
4107 4591 8.530269 AAATAAGTGTCTTGACCTTAGTAACG 57.470 34.615 13.13 0.00 0.00 3.18
4109 4593 9.280174 CCAAAATAAGTGTCTTGACCTTAGTAA 57.720 33.333 13.13 0.00 0.00 2.24
4110 4594 7.881232 CCCAAAATAAGTGTCTTGACCTTAGTA 59.119 37.037 13.13 0.23 0.00 1.82
4111 4595 6.715264 CCCAAAATAAGTGTCTTGACCTTAGT 59.285 38.462 13.13 9.86 0.00 2.24
4112 4596 6.940298 TCCCAAAATAAGTGTCTTGACCTTAG 59.060 38.462 13.13 0.00 0.00 2.18
4113 4597 6.713450 GTCCCAAAATAAGTGTCTTGACCTTA 59.287 38.462 11.29 11.29 0.00 2.69
4114 4598 5.535030 GTCCCAAAATAAGTGTCTTGACCTT 59.465 40.000 0.00 4.52 0.00 3.50
4115 4599 5.070685 GTCCCAAAATAAGTGTCTTGACCT 58.929 41.667 0.00 0.00 0.00 3.85
4116 4600 4.083484 CGTCCCAAAATAAGTGTCTTGACC 60.083 45.833 0.00 0.00 0.00 4.02
4117 4601 4.083484 CCGTCCCAAAATAAGTGTCTTGAC 60.083 45.833 0.00 0.00 0.00 3.18
4118 4602 4.069304 CCGTCCCAAAATAAGTGTCTTGA 58.931 43.478 0.00 0.00 0.00 3.02
4119 4603 4.069304 TCCGTCCCAAAATAAGTGTCTTG 58.931 43.478 0.00 0.00 0.00 3.02
4120 4604 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
4121 4605 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
4122 4606 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
4123 4607 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
4124 4608 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
4125 4609 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
4126 4610 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
4127 4611 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
4128 4612 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
4129 4613 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4130 4614 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
4131 4615 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
4132 4616 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
4133 4617 0.928505 TACATACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
4134 4618 1.133544 AGTACATACTCCCTCCGTCCC 60.134 57.143 0.00 0.00 0.00 4.46
4135 4619 2.361643 AGTACATACTCCCTCCGTCC 57.638 55.000 0.00 0.00 0.00 4.79
4136 4620 4.084011 AGTAGTACATACTCCCTCCGTC 57.916 50.000 2.52 0.00 40.99 4.79
4137 4621 4.657969 ACTAGTAGTACATACTCCCTCCGT 59.342 45.833 0.00 0.00 43.90 4.69
4138 4622 5.226194 ACTAGTAGTACATACTCCCTCCG 57.774 47.826 0.00 0.00 43.90 4.63
4139 4623 8.217111 AGTTTACTAGTAGTACATACTCCCTCC 58.783 40.741 9.62 0.00 43.90 4.30
4140 4624 9.054922 CAGTTTACTAGTAGTACATACTCCCTC 57.945 40.741 9.62 0.00 43.90 4.30
4141 4625 7.501892 GCAGTTTACTAGTAGTACATACTCCCT 59.498 40.741 9.62 0.00 43.90 4.20
4142 4626 7.255416 GGCAGTTTACTAGTAGTACATACTCCC 60.255 44.444 9.62 9.35 43.90 4.30
4143 4627 7.255416 GGGCAGTTTACTAGTAGTACATACTCC 60.255 44.444 9.62 13.83 43.90 3.85
4144 4628 7.255416 GGGGCAGTTTACTAGTAGTACATACTC 60.255 44.444 9.62 7.84 43.90 2.59
4145 4629 6.548993 GGGGCAGTTTACTAGTAGTACATACT 59.451 42.308 9.62 10.36 46.70 2.12
4146 4630 6.239148 GGGGGCAGTTTACTAGTAGTACATAC 60.239 46.154 9.62 8.48 28.93 2.39
4163 4647 1.575419 TATAAGACGTTGGGGGCAGT 58.425 50.000 0.00 0.00 0.00 4.40
4164 4648 2.930826 ATATAAGACGTTGGGGGCAG 57.069 50.000 0.00 0.00 0.00 4.85
4165 4649 3.655615 AAATATAAGACGTTGGGGGCA 57.344 42.857 0.00 0.00 0.00 5.36
4166 4650 4.070009 CCTAAATATAAGACGTTGGGGGC 58.930 47.826 0.00 0.00 0.00 5.80
4167 4651 5.556006 TCCTAAATATAAGACGTTGGGGG 57.444 43.478 0.00 0.00 0.00 5.40
4208 4693 3.088532 GGATGCCACACCTCAATAACAA 58.911 45.455 0.00 0.00 0.00 2.83
4290 4775 2.775890 AGCACCAGCATATATGAGCAC 58.224 47.619 17.10 0.00 45.49 4.40
4351 4837 8.461222 TCACAAACAATTGATGCTTTATAGGAG 58.539 33.333 13.59 0.00 38.94 3.69
4352 4838 8.347004 TCACAAACAATTGATGCTTTATAGGA 57.653 30.769 13.59 0.00 38.94 2.94
4353 4839 8.246180 ACTCACAAACAATTGATGCTTTATAGG 58.754 33.333 13.59 0.00 38.94 2.57
4355 4841 9.409312 CAACTCACAAACAATTGATGCTTTATA 57.591 29.630 13.59 0.00 38.94 0.98
4356 4842 7.927629 ACAACTCACAAACAATTGATGCTTTAT 59.072 29.630 13.59 0.00 38.94 1.40
4357 4843 7.264221 ACAACTCACAAACAATTGATGCTTTA 58.736 30.769 13.59 0.00 38.94 1.85
4360 4846 5.266733 ACAACTCACAAACAATTGATGCT 57.733 34.783 13.59 0.00 38.94 3.79
4361 4847 7.642071 AATACAACTCACAAACAATTGATGC 57.358 32.000 13.59 0.00 38.94 3.91
4408 4922 3.313526 CAGCTGCAAGTAAACAGACAACT 59.686 43.478 0.00 0.00 35.90 3.16
4471 4985 4.342378 CGGATCAAGATAACAGAGGGAGAA 59.658 45.833 0.00 0.00 0.00 2.87
4519 5033 2.594013 TGGTTCATGCGCTGCACA 60.594 55.556 9.73 0.00 43.04 4.57
4535 5049 1.714794 CTTAGCCTCACAACGTCCTG 58.285 55.000 0.00 0.00 0.00 3.86
4589 5103 2.941453 TCGATTCCACTCTTTCTCCG 57.059 50.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.