Multiple sequence alignment - TraesCS3D01G231500

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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 TraesCS3D01G231500 chr3D 100.000 3818 0 0 1 3818 316814321 316818138 0.000000e+00 7051.0
1 TraesCS3D01G231500 chr3A 95.700 3209 94 25 563 3757 411264725 411261547 0.000000e+00 5121.0
2 TraesCS3D01G231500 chr3A 90.096 313 20 8 1 311 411265261 411264958 2.760000e-106 396.0
3 TraesCS3D01G231500 chr3B 95.033 2839 92 15 443 3255 402452941 402450126 0.000000e+00 4416.0
4 TraesCS3D01G231500 chr3B 95.189 291 5 4 1 285 402453620 402453333 5.820000e-123 451.0
5 TraesCS3D01G231500 chr3B 91.824 159 11 2 3262 3419 402450063 402449906 1.790000e-53 220.0
6 TraesCS3D01G231500 chr3B 87.435 191 11 4 3552 3741 402156592 402156414 1.390000e-49 207.0
7 TraesCS3D01G231500 chr7B 96.591 352 12 0 1583 1934 736624032 736623681 5.500000e-163 584.0
8 TraesCS3D01G231500 chr7B 95.890 73 3 0 1988 2060 736623684 736623612 6.700000e-23 119.0
9 TraesCS3D01G231500 chr7A 94.737 38 2 0 1590 1627 553996624 553996661 4.120000e-05 60.2


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 TraesCS3D01G231500 chr3D 316814321 316818138 3817 False 7051.000000 7051 100.000000 1 3818 1 chr3D.!!$F1 3817
1 TraesCS3D01G231500 chr3A 411261547 411265261 3714 True 2758.500000 5121 92.898000 1 3757 2 chr3A.!!$R1 3756
2 TraesCS3D01G231500 chr3B 402449906 402453620 3714 True 1695.666667 4416 94.015333 1 3419 3 chr3B.!!$R2 3418

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
428 462 0.395312 AACTGGTCAAACGACGGGAT 59.605 50.0 0.0 0.0 33.96 3.85 F
429 463 0.395312 ACTGGTCAAACGACGGGATT 59.605 50.0 0.0 0.0 33.96 3.01 F
922 1174 0.607489 CTTCTCACCACCCCTTGCTG 60.607 60.0 0.0 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2352 1.384191 GGTGGTGCCCAGGAAGATT 59.616 57.895 0.00 0.0 32.34 2.40 R
2253 2505 2.188161 GGAGGCGACGTAGGAGGAG 61.188 68.421 0.00 0.0 0.00 3.69 R
2868 3138 0.249784 ACAATTTGCATGCACGCCAA 60.250 45.000 22.58 12.8 0.00 4.52 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
285 289 9.923143 TCTGAATTCGTTCGTTCCATATATAAT 57.077 29.630 0.04 0.00 0.00 1.28
286 290 9.958285 CTGAATTCGTTCGTTCCATATATAATG 57.042 33.333 0.04 0.00 0.00 1.90
307 339 7.466746 AATGTGTGCATTTGGACTAAGTTAT 57.533 32.000 3.85 0.00 42.19 1.89
315 347 7.611467 TGCATTTGGACTAAGTTATGAGTCAAT 59.389 33.333 0.00 0.00 43.28 2.57
378 412 6.170506 TCACAAGATAGTGATTTGTACACCC 58.829 40.000 0.00 0.00 43.18 4.61
379 413 5.063438 CACAAGATAGTGATTTGTACACCCG 59.937 44.000 0.00 0.00 42.05 5.28
380 414 3.793559 AGATAGTGATTTGTACACCCGC 58.206 45.455 0.00 0.00 38.82 6.13
381 415 3.196901 AGATAGTGATTTGTACACCCGCA 59.803 43.478 0.00 0.00 38.82 5.69
382 416 2.264005 AGTGATTTGTACACCCGCAA 57.736 45.000 0.00 0.00 38.82 4.85
383 417 2.577700 AGTGATTTGTACACCCGCAAA 58.422 42.857 0.00 0.00 38.82 3.68
384 418 2.952978 AGTGATTTGTACACCCGCAAAA 59.047 40.909 0.00 0.00 37.98 2.44
385 419 3.381908 AGTGATTTGTACACCCGCAAAAA 59.618 39.130 0.00 0.00 37.98 1.94
424 458 3.552699 TGTAGAAAACTGGTCAAACGACG 59.447 43.478 0.00 0.00 33.96 5.12
425 459 1.937899 AGAAAACTGGTCAAACGACGG 59.062 47.619 0.00 0.00 33.96 4.79
426 460 1.003223 GAAAACTGGTCAAACGACGGG 60.003 52.381 0.00 0.00 33.96 5.28
428 462 0.395312 AACTGGTCAAACGACGGGAT 59.605 50.000 0.00 0.00 33.96 3.85
429 463 0.395312 ACTGGTCAAACGACGGGATT 59.605 50.000 0.00 0.00 33.96 3.01
435 546 3.437741 GGTCAAACGACGGGATTAAATGT 59.562 43.478 0.00 0.00 33.96 2.71
437 548 3.120130 TCAAACGACGGGATTAAATGTGC 60.120 43.478 0.00 0.00 0.00 4.57
453 691 1.153329 TGCGTAACCATTAGCCCCG 60.153 57.895 0.00 0.00 0.00 5.73
545 786 0.817654 GCAATCCAACTAACTGCCCC 59.182 55.000 0.00 0.00 0.00 5.80
615 857 9.651913 GAAACAGAGAGAGAAAAATAGTGAGAT 57.348 33.333 0.00 0.00 0.00 2.75
625 867 9.598517 GAGAAAAATAGTGAGATGAGTTGATCT 57.401 33.333 0.00 0.00 35.27 2.75
709 951 0.743345 GTATCCACAAGCCACCGGAC 60.743 60.000 9.46 0.00 0.00 4.79
922 1174 0.607489 CTTCTCACCACCCCTTGCTG 60.607 60.000 0.00 0.00 0.00 4.41
923 1175 2.034687 CTCACCACCCCTTGCTGG 59.965 66.667 0.00 0.00 0.00 4.85
1028 1280 1.599606 CCGAGGGAGACAGTGGTGAG 61.600 65.000 0.00 0.00 0.00 3.51
1110 1362 1.313812 CGAGGGCTCTGTCCTACGTT 61.314 60.000 0.00 0.00 38.01 3.99
1119 1371 1.153686 GTCCTACGTTCTTCCGGCC 60.154 63.158 0.00 0.00 0.00 6.13
1257 1509 3.730761 GGCAAGACCACGCTGCTG 61.731 66.667 0.00 0.00 38.86 4.41
1566 1818 1.677552 GAGGGTGTCCATCGGTGTT 59.322 57.895 0.00 0.00 34.83 3.32
1704 1956 1.153568 CGTCGTGCTCACCATCCAT 60.154 57.895 0.00 0.00 0.00 3.41
1872 2124 1.368950 CGCCATGGAGACCATCGAT 59.631 57.895 18.40 0.00 43.15 3.59
2481 2733 2.363795 AACTCCCTCATCGCCGGA 60.364 61.111 5.05 0.00 0.00 5.14
2821 3073 0.250234 CCGCATGAGGAGGTGAAGAA 59.750 55.000 10.41 0.00 0.00 2.52
2862 3132 1.125093 CATGCCATCCCCATTGCCAT 61.125 55.000 0.00 0.00 0.00 4.40
2863 3133 0.400815 ATGCCATCCCCATTGCCATT 60.401 50.000 0.00 0.00 0.00 3.16
2864 3134 1.338890 TGCCATCCCCATTGCCATTG 61.339 55.000 0.00 0.00 0.00 2.82
2865 3135 1.448497 CCATCCCCATTGCCATTGC 59.552 57.895 0.00 0.00 38.26 3.56
2866 3136 1.448497 CATCCCCATTGCCATTGCC 59.552 57.895 0.00 0.00 36.33 4.52
2867 3137 1.003182 ATCCCCATTGCCATTGCCA 59.997 52.632 0.00 0.00 36.33 4.92
2868 3138 0.400815 ATCCCCATTGCCATTGCCAT 60.401 50.000 0.00 0.00 36.33 4.40
2869 3139 0.620990 TCCCCATTGCCATTGCCATT 60.621 50.000 0.00 0.00 36.33 3.16
2870 3140 0.464735 CCCCATTGCCATTGCCATTG 60.465 55.000 0.00 0.00 36.33 2.82
2871 3141 0.464735 CCCATTGCCATTGCCATTGG 60.465 55.000 0.00 0.00 36.33 3.16
2919 3189 8.063038 GTCATCATCTGAATTTGATCTCTTTCG 58.937 37.037 0.00 0.00 35.07 3.46
2920 3190 7.983484 TCATCATCTGAATTTGATCTCTTTCGA 59.017 33.333 0.00 0.00 30.24 3.71
2956 3226 9.630098 TTTGCTGTGATTTTTCTGAAGATATTC 57.370 29.630 0.00 0.00 0.00 1.75
3071 3343 7.425577 TGTTCTTCTGTATCAACATCAACAG 57.574 36.000 0.00 0.00 40.54 3.16
3203 3487 1.843421 TGGGTGTGTTCCTTCCCAG 59.157 57.895 0.00 0.00 44.07 4.45
3223 3508 1.897560 CTCCAAGGGAAAGTGTCACC 58.102 55.000 0.00 0.00 0.00 4.02
3248 3533 6.360844 TCTTGTTGGATTTTGCAATTTGTG 57.639 33.333 0.00 0.00 28.47 3.33
3252 3542 6.344500 TGTTGGATTTTGCAATTTGTGTAGT 58.656 32.000 0.00 0.00 28.47 2.73
3291 3633 2.716217 CAAGGGGTAGCTGAGAAAAGG 58.284 52.381 0.00 0.00 0.00 3.11
3312 3654 0.032678 AGACCAAGTGAGCAGTCGTG 59.967 55.000 0.00 0.00 34.41 4.35
3372 3714 6.266786 TCGGAAACATGCCTAATCTGTATCTA 59.733 38.462 0.00 0.00 0.00 1.98
3409 3751 3.967326 CTGGTGTATCCAAGATCCAGGTA 59.033 47.826 0.00 0.00 46.59 3.08
3426 3768 4.141914 CCAGGTATTAACTGACAGGAGTCC 60.142 50.000 10.39 0.00 44.33 3.85
3427 3769 4.712337 CAGGTATTAACTGACAGGAGTCCT 59.288 45.833 5.62 5.62 44.33 3.85
3428 3770 5.187967 CAGGTATTAACTGACAGGAGTCCTT 59.812 44.000 9.68 0.78 44.33 3.36
3432 3774 1.638529 ACTGACAGGAGTCCTTCTGG 58.361 55.000 9.68 0.02 44.33 3.86
3479 3821 3.461061 ACAGATCCACGCAATATGACTG 58.539 45.455 0.00 0.00 0.00 3.51
3483 3825 3.610040 TCCACGCAATATGACTGACTT 57.390 42.857 0.00 0.00 0.00 3.01
3491 3833 6.036470 CGCAATATGACTGACTTGTCTCTTA 58.964 40.000 2.35 0.00 37.79 2.10
3535 3877 0.617535 TTTCCCTCCGGCTGAGATGA 60.618 55.000 7.57 1.13 44.42 2.92
3581 3923 9.566432 GATGGATTCTGATAGATAACCTGTTTT 57.434 33.333 0.00 0.00 0.00 2.43
3635 3977 2.616960 CAGCAAGCTGGTCGTTATACA 58.383 47.619 14.10 0.00 40.17 2.29
3726 4068 2.161410 TGAATGCCGTATTTGAGCACAC 59.839 45.455 0.00 0.00 39.77 3.82
3757 4099 5.507817 CCATAGGCGAATATTGTTGCACATT 60.508 40.000 0.00 0.00 0.00 2.71
3758 4100 4.454728 AGGCGAATATTGTTGCACATTT 57.545 36.364 0.00 0.00 0.00 2.32
3759 4101 4.819769 AGGCGAATATTGTTGCACATTTT 58.180 34.783 0.00 0.00 0.00 1.82
3760 4102 5.237048 AGGCGAATATTGTTGCACATTTTT 58.763 33.333 0.00 0.00 0.00 1.94
3780 4122 2.994186 TTTGAGGGGTATAACCGAGC 57.006 50.000 0.00 0.00 39.83 5.03
3781 4123 2.170012 TTGAGGGGTATAACCGAGCT 57.830 50.000 0.00 0.00 39.83 4.09
3782 4124 2.170012 TGAGGGGTATAACCGAGCTT 57.830 50.000 0.00 0.00 39.83 3.74
3783 4125 2.474112 TGAGGGGTATAACCGAGCTTT 58.526 47.619 0.00 0.00 39.83 3.51
3784 4126 3.645434 TGAGGGGTATAACCGAGCTTTA 58.355 45.455 0.00 0.00 39.83 1.85
3785 4127 4.228824 TGAGGGGTATAACCGAGCTTTAT 58.771 43.478 0.00 0.00 39.83 1.40
3786 4128 4.657039 TGAGGGGTATAACCGAGCTTTATT 59.343 41.667 0.00 0.00 39.83 1.40
3787 4129 4.969484 AGGGGTATAACCGAGCTTTATTG 58.031 43.478 0.00 0.00 39.83 1.90
3788 4130 3.501062 GGGGTATAACCGAGCTTTATTGC 59.499 47.826 0.00 0.00 39.83 3.56
3789 4131 4.386711 GGGTATAACCGAGCTTTATTGCT 58.613 43.478 0.00 0.00 39.83 3.91
3799 4141 4.773323 AGCTTTATTGCTCAAAGTCCAC 57.227 40.909 6.97 0.00 39.34 4.02
3800 4142 4.144297 AGCTTTATTGCTCAAAGTCCACA 58.856 39.130 6.97 0.00 39.34 4.17
3801 4143 4.768968 AGCTTTATTGCTCAAAGTCCACAT 59.231 37.500 6.97 0.00 39.34 3.21
3802 4144 5.945784 AGCTTTATTGCTCAAAGTCCACATA 59.054 36.000 6.97 0.00 39.34 2.29
3803 4145 6.434028 AGCTTTATTGCTCAAAGTCCACATAA 59.566 34.615 6.97 0.00 39.34 1.90
3804 4146 7.039784 AGCTTTATTGCTCAAAGTCCACATAAA 60.040 33.333 6.97 0.00 39.34 1.40
3805 4147 7.598493 GCTTTATTGCTCAAAGTCCACATAAAA 59.402 33.333 6.97 0.00 35.78 1.52
3806 4148 9.643693 CTTTATTGCTCAAAGTCCACATAAAAT 57.356 29.630 0.00 0.00 0.00 1.82
3807 4149 8.984891 TTATTGCTCAAAGTCCACATAAAATG 57.015 30.769 0.00 0.00 0.00 2.32
3808 4150 5.389859 TGCTCAAAGTCCACATAAAATGG 57.610 39.130 0.00 0.00 38.71 3.16
3809 4151 4.176271 GCTCAAAGTCCACATAAAATGGC 58.824 43.478 0.00 0.00 37.13 4.40
3810 4152 4.321899 GCTCAAAGTCCACATAAAATGGCA 60.322 41.667 0.00 0.00 37.13 4.92
3811 4153 5.625197 GCTCAAAGTCCACATAAAATGGCAT 60.625 40.000 0.00 0.00 37.13 4.40
3812 4154 6.357579 TCAAAGTCCACATAAAATGGCATT 57.642 33.333 6.96 6.96 37.13 3.56
3813 4155 7.473735 TCAAAGTCCACATAAAATGGCATTA 57.526 32.000 14.05 0.00 37.13 1.90
3814 4156 7.319646 TCAAAGTCCACATAAAATGGCATTAC 58.680 34.615 14.05 5.29 37.13 1.89
3815 4157 6.849085 AAGTCCACATAAAATGGCATTACA 57.151 33.333 14.05 4.62 37.13 2.41
3816 4158 6.849085 AGTCCACATAAAATGGCATTACAA 57.151 33.333 14.05 2.34 37.13 2.41
3817 4159 7.238486 AGTCCACATAAAATGGCATTACAAA 57.762 32.000 14.05 0.00 37.13 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.213564 AGAGATTTTCTGATGAGCGGTT 57.786 40.909 0.00 0.00 33.93 4.44
222 226 1.502231 CTTGGTCGGCAATAGGATCG 58.498 55.000 0.00 0.00 0.00 3.69
285 289 6.000840 TCATAACTTAGTCCAAATGCACACA 58.999 36.000 0.00 0.00 0.00 3.72
286 290 6.149474 ACTCATAACTTAGTCCAAATGCACAC 59.851 38.462 0.00 0.00 0.00 3.82
307 339 7.955324 CGATAAAGAACGCTTTTTATTGACTCA 59.045 33.333 3.96 0.00 41.43 3.41
341 375 3.777106 TCTTGTGATGCTCCTGAACTT 57.223 42.857 0.00 0.00 0.00 2.66
356 390 5.175859 CGGGTGTACAAATCACTATCTTGT 58.824 41.667 0.00 0.00 37.13 3.16
387 421 9.612620 CAGTTTTCTACAAATCGCTATCTTTTT 57.387 29.630 0.00 0.00 0.00 1.94
388 422 8.237267 CCAGTTTTCTACAAATCGCTATCTTTT 58.763 33.333 0.00 0.00 0.00 2.27
389 423 7.390718 ACCAGTTTTCTACAAATCGCTATCTTT 59.609 33.333 0.00 0.00 0.00 2.52
390 424 6.879458 ACCAGTTTTCTACAAATCGCTATCTT 59.121 34.615 0.00 0.00 0.00 2.40
391 425 6.407202 ACCAGTTTTCTACAAATCGCTATCT 58.593 36.000 0.00 0.00 0.00 1.98
392 426 6.312918 TGACCAGTTTTCTACAAATCGCTATC 59.687 38.462 0.00 0.00 0.00 2.08
393 427 6.170506 TGACCAGTTTTCTACAAATCGCTAT 58.829 36.000 0.00 0.00 0.00 2.97
394 428 5.543714 TGACCAGTTTTCTACAAATCGCTA 58.456 37.500 0.00 0.00 0.00 4.26
395 429 4.385825 TGACCAGTTTTCTACAAATCGCT 58.614 39.130 0.00 0.00 0.00 4.93
396 430 4.742438 TGACCAGTTTTCTACAAATCGC 57.258 40.909 0.00 0.00 0.00 4.58
397 431 5.619607 CGTTTGACCAGTTTTCTACAAATCG 59.380 40.000 0.00 0.00 33.37 3.34
398 432 6.631636 GTCGTTTGACCAGTTTTCTACAAATC 59.368 38.462 0.00 0.00 39.30 2.17
399 433 6.492254 GTCGTTTGACCAGTTTTCTACAAAT 58.508 36.000 0.00 0.00 39.30 2.32
400 434 5.446206 CGTCGTTTGACCAGTTTTCTACAAA 60.446 40.000 0.00 0.00 42.37 2.83
401 435 4.033129 CGTCGTTTGACCAGTTTTCTACAA 59.967 41.667 0.00 0.00 42.37 2.41
402 436 3.552699 CGTCGTTTGACCAGTTTTCTACA 59.447 43.478 0.00 0.00 42.37 2.74
403 437 3.060070 CCGTCGTTTGACCAGTTTTCTAC 60.060 47.826 0.00 0.00 42.37 2.59
407 441 1.018910 CCCGTCGTTTGACCAGTTTT 58.981 50.000 0.00 0.00 42.37 2.43
424 458 4.911514 ATGGTTACGCACATTTAATCCC 57.088 40.909 0.00 0.00 0.00 3.85
425 459 5.912955 GCTAATGGTTACGCACATTTAATCC 59.087 40.000 0.00 0.00 38.24 3.01
426 460 5.912955 GGCTAATGGTTACGCACATTTAATC 59.087 40.000 0.00 0.00 38.24 1.75
428 462 4.096682 GGGCTAATGGTTACGCACATTTAA 59.903 41.667 0.00 0.00 38.24 1.52
429 463 3.628487 GGGCTAATGGTTACGCACATTTA 59.372 43.478 0.00 0.00 38.24 1.40
435 546 1.153329 CGGGGCTAATGGTTACGCA 60.153 57.895 0.00 0.00 0.00 5.24
437 548 2.249844 ATTCGGGGCTAATGGTTACG 57.750 50.000 0.00 0.00 0.00 3.18
453 691 8.497554 CAGAGTATAGACACGGTAAGAGTATTC 58.502 40.741 0.00 0.00 0.00 1.75
511 752 6.775629 AGTTGGATTGCTGAACCTAGTTTAAA 59.224 34.615 0.00 0.00 0.00 1.52
512 753 6.303839 AGTTGGATTGCTGAACCTAGTTTAA 58.696 36.000 0.00 0.00 0.00 1.52
519 760 4.074970 CAGTTAGTTGGATTGCTGAACCT 58.925 43.478 0.00 0.00 0.00 3.50
524 765 1.474077 GGGCAGTTAGTTGGATTGCTG 59.526 52.381 0.00 0.00 35.23 4.41
592 834 8.359875 TCATCTCACTATTTTTCTCTCTCTGT 57.640 34.615 0.00 0.00 0.00 3.41
615 857 0.608130 CACCGGGACAGATCAACTCA 59.392 55.000 6.32 0.00 0.00 3.41
625 867 4.947147 GCTTGGTGCACCGGGACA 62.947 66.667 30.07 10.28 42.31 4.02
687 929 1.600107 GGTGGCTTGTGGATACGGA 59.400 57.895 0.00 0.00 42.51 4.69
691 933 1.195442 TGTCCGGTGGCTTGTGGATA 61.195 55.000 0.00 0.00 32.18 2.59
709 951 1.529214 CGTCTCGTCTATCCGTGTGTG 60.529 57.143 0.00 0.00 0.00 3.82
807 1059 2.894126 GAGGTCTGAAGTCTGAACCTGA 59.106 50.000 1.36 0.00 32.71 3.86
922 1174 2.418976 GAGATTGTTACAAAGGCGTCCC 59.581 50.000 0.66 0.00 0.00 4.46
923 1175 3.335579 AGAGATTGTTACAAAGGCGTCC 58.664 45.455 0.66 0.00 0.00 4.79
924 1176 3.060895 CGAGAGATTGTTACAAAGGCGTC 59.939 47.826 0.66 0.00 0.00 5.19
925 1177 2.993899 CGAGAGATTGTTACAAAGGCGT 59.006 45.455 0.66 0.00 0.00 5.68
926 1178 2.222819 GCGAGAGATTGTTACAAAGGCG 60.223 50.000 0.66 3.71 0.00 5.52
1563 1815 2.809010 TCGTGCACGAGGTCAACA 59.191 55.556 36.40 13.53 44.22 3.33
1872 2124 2.283388 ACGTCCGGCTTGAGGGTA 60.283 61.111 0.00 0.00 0.00 3.69
1986 2238 4.722700 ATGCAAACCTCCGCCGCT 62.723 61.111 0.00 0.00 0.00 5.52
2100 2352 1.384191 GGTGGTGCCCAGGAAGATT 59.616 57.895 0.00 0.00 32.34 2.40
2253 2505 2.188161 GGAGGCGACGTAGGAGGAG 61.188 68.421 0.00 0.00 0.00 3.69
2481 2733 1.211457 AGGAAGAAGCAGCCGATGAAT 59.789 47.619 0.00 0.00 0.00 2.57
2760 3012 0.459237 CGAAGCAGAGCACCCTGTAG 60.459 60.000 0.00 0.00 36.57 2.74
2851 3103 0.464735 CAATGGCAATGGCAATGGGG 60.465 55.000 14.81 0.00 42.43 4.96
2852 3104 3.088259 CAATGGCAATGGCAATGGG 57.912 52.632 14.81 0.00 42.43 4.00
2864 3134 3.936204 TTGCATGCACGCCAATGGC 62.936 57.895 22.58 15.52 46.75 4.40
2865 3135 0.741574 ATTTGCATGCACGCCAATGG 60.742 50.000 22.58 0.00 0.00 3.16
2866 3136 1.080298 AATTTGCATGCACGCCAATG 58.920 45.000 22.58 0.00 28.54 2.82
2867 3137 1.080298 CAATTTGCATGCACGCCAAT 58.920 45.000 22.58 14.71 0.00 3.16
2868 3138 0.249784 ACAATTTGCATGCACGCCAA 60.250 45.000 22.58 12.80 0.00 4.52
2869 3139 0.600057 TACAATTTGCATGCACGCCA 59.400 45.000 22.58 1.91 0.00 5.69
2870 3140 1.707632 TTACAATTTGCATGCACGCC 58.292 45.000 22.58 0.00 0.00 5.68
2871 3141 3.483901 CCAATTACAATTTGCATGCACGC 60.484 43.478 22.58 0.00 0.00 5.34
2872 3142 3.679025 ACCAATTACAATTTGCATGCACG 59.321 39.130 22.58 11.82 0.00 5.34
2873 3143 4.689812 TGACCAATTACAATTTGCATGCAC 59.310 37.500 22.58 3.91 0.00 4.57
2929 3199 9.635520 AATATCTTCAGAAAAATCACAGCAAAG 57.364 29.630 0.00 0.00 0.00 2.77
3001 3272 1.455822 TCAACCTCTTCCCCCAACAT 58.544 50.000 0.00 0.00 0.00 2.71
3005 3276 1.635487 CTTGATCAACCTCTTCCCCCA 59.365 52.381 3.38 0.00 0.00 4.96
3065 3337 6.566141 CATCATCCATAAATTGCACTGTTGA 58.434 36.000 0.00 0.00 0.00 3.18
3071 3343 4.227512 TCGCATCATCCATAAATTGCAC 57.772 40.909 0.00 0.00 0.00 4.57
3203 3487 1.239347 GTGACACTTTCCCTTGGAGC 58.761 55.000 0.00 0.00 31.21 4.70
3223 3508 6.908284 CACAAATTGCAAAATCCAACAAGAAG 59.092 34.615 1.71 0.00 0.00 2.85
3248 3533 2.609737 CCACAAACACGGGAGAGACTAC 60.610 54.545 0.00 0.00 0.00 2.73
3252 3542 1.752198 CCCACAAACACGGGAGAGA 59.248 57.895 0.00 0.00 46.34 3.10
3291 3633 1.269831 ACGACTGCTCACTTGGTCTTC 60.270 52.381 0.00 0.00 0.00 2.87
3312 3654 3.071479 TGCCCGTACTTTTTCATCACTC 58.929 45.455 0.00 0.00 0.00 3.51
3409 3751 4.223923 CCAGAAGGACTCCTGTCAGTTAAT 59.776 45.833 0.00 0.00 44.61 1.40
3426 3768 1.676006 AGCGAACAAAACCACCAGAAG 59.324 47.619 0.00 0.00 0.00 2.85
3427 3769 1.673920 GAGCGAACAAAACCACCAGAA 59.326 47.619 0.00 0.00 0.00 3.02
3428 3770 1.305201 GAGCGAACAAAACCACCAGA 58.695 50.000 0.00 0.00 0.00 3.86
3432 3774 3.164028 GCTGAGCGAACAAAACCAC 57.836 52.632 0.00 0.00 0.00 4.16
3479 3821 9.604626 CTCATCACAAAAATTAAGAGACAAGTC 57.395 33.333 0.00 0.00 0.00 3.01
3497 3839 7.861629 AGGGAAAATGTTAGTATCTCATCACA 58.138 34.615 0.00 0.00 0.00 3.58
3650 3992 2.105006 ATCTGCCTACTTGTGCTGTG 57.895 50.000 0.00 0.00 0.00 3.66
3652 3994 4.274459 GGAATTATCTGCCTACTTGTGCTG 59.726 45.833 0.00 0.00 0.00 4.41
3759 4101 3.264964 AGCTCGGTTATACCCCTCAAAAA 59.735 43.478 0.00 0.00 33.75 1.94
3760 4102 2.841881 AGCTCGGTTATACCCCTCAAAA 59.158 45.455 0.00 0.00 33.75 2.44
3761 4103 2.474112 AGCTCGGTTATACCCCTCAAA 58.526 47.619 0.00 0.00 33.75 2.69
3762 4104 2.170012 AGCTCGGTTATACCCCTCAA 57.830 50.000 0.00 0.00 33.75 3.02
3763 4105 2.170012 AAGCTCGGTTATACCCCTCA 57.830 50.000 0.00 0.00 33.75 3.86
3764 4106 4.886496 ATAAAGCTCGGTTATACCCCTC 57.114 45.455 0.00 0.00 33.75 4.30
3765 4107 4.745783 GCAATAAAGCTCGGTTATACCCCT 60.746 45.833 0.00 0.00 33.75 4.79
3766 4108 3.501062 GCAATAAAGCTCGGTTATACCCC 59.499 47.826 0.00 0.00 33.75 4.95
3767 4109 4.386711 AGCAATAAAGCTCGGTTATACCC 58.613 43.478 0.00 0.00 42.18 3.69
3779 4121 4.503741 TGTGGACTTTGAGCAATAAAGC 57.496 40.909 7.11 0.00 38.41 3.51
3780 4122 9.643693 ATTTTATGTGGACTTTGAGCAATAAAG 57.356 29.630 5.99 5.99 40.19 1.85
3781 4123 9.421806 CATTTTATGTGGACTTTGAGCAATAAA 57.578 29.630 0.00 0.00 0.00 1.40
3782 4124 8.034215 CCATTTTATGTGGACTTTGAGCAATAA 58.966 33.333 0.00 0.00 39.12 1.40
3783 4125 7.546358 CCATTTTATGTGGACTTTGAGCAATA 58.454 34.615 0.00 0.00 39.12 1.90
3784 4126 6.400568 CCATTTTATGTGGACTTTGAGCAAT 58.599 36.000 0.00 0.00 39.12 3.56
3785 4127 5.782047 CCATTTTATGTGGACTTTGAGCAA 58.218 37.500 0.00 0.00 39.12 3.91
3786 4128 4.321899 GCCATTTTATGTGGACTTTGAGCA 60.322 41.667 0.00 0.00 39.12 4.26
3787 4129 4.176271 GCCATTTTATGTGGACTTTGAGC 58.824 43.478 0.00 0.00 39.12 4.26
3788 4130 5.389859 TGCCATTTTATGTGGACTTTGAG 57.610 39.130 0.00 0.00 39.12 3.02
3789 4131 5.999205 ATGCCATTTTATGTGGACTTTGA 57.001 34.783 0.00 0.00 39.12 2.69
3790 4132 7.095910 TGTAATGCCATTTTATGTGGACTTTG 58.904 34.615 0.00 0.00 39.12 2.77
3791 4133 7.238486 TGTAATGCCATTTTATGTGGACTTT 57.762 32.000 0.00 0.00 39.12 2.66
3792 4134 6.849085 TGTAATGCCATTTTATGTGGACTT 57.151 33.333 0.00 0.00 39.12 3.01
3793 4135 6.849085 TTGTAATGCCATTTTATGTGGACT 57.151 33.333 0.00 0.00 39.12 3.85


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

AutoCloner maintained by Alex Coulton.