Multiple sequence alignment - TraesCS1B01G244100

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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 TraesCS1B01G244100 chr1B 100.000 4156 0 0 1 4156 433433538 433429383 0.000000e+00 7675.0
1 TraesCS1B01G244100 chr1D 96.016 3640 122 12 1 3635 320397285 320393664 0.000000e+00 5897.0
2 TraesCS1B01G244100 chr1D 90.945 254 12 4 3800 4051 320393493 320393249 8.610000e-87 331.0
3 TraesCS1B01G244100 chr1D 96.815 157 4 1 3619 3775 320393646 320393491 1.150000e-65 261.0
4 TraesCS1B01G244100 chr1D 93.939 99 4 1 4058 4156 320393097 320393001 9.310000e-32 148.0
5 TraesCS1B01G244100 chr1A 95.464 2315 85 9 1 2308 402805737 402808038 0.000000e+00 3675.0
6 TraesCS1B01G244100 chr1A 93.333 1035 59 4 2306 3330 402808344 402809378 0.000000e+00 1520.0
7 TraesCS1B01G244100 chr1A 95.833 48 2 0 3302 3349 402809379 402809426 1.240000e-10 78.7
8 TraesCS1B01G244100 chrUn 88.649 185 16 4 3649 3829 87008492 87008675 1.940000e-53 220.0
9 TraesCS1B01G244100 chr3A 88.108 185 17 4 3649 3829 836968 837151 9.050000e-52 215.0
10 TraesCS1B01G244100 chr5B 87.634 186 16 5 3649 3829 513781434 513781617 4.210000e-50 209.0


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 TraesCS1B01G244100 chr1B 433429383 433433538 4155 True 7675.00 7675 100.000000 1 4156 1 chr1B.!!$R1 4155
1 TraesCS1B01G244100 chr1D 320393001 320397285 4284 True 1659.25 5897 94.428750 1 4156 4 chr1D.!!$R1 4155
2 TraesCS1B01G244100 chr1A 402805737 402809426 3689 False 1757.90 3675 94.876667 1 3349 3 chr1A.!!$F1 3348

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
598 604 1.067060 GTTCCTTCCACCAGTTTGTGC 59.933 52.381 0.0 0.0 34.85 4.57 F
1796 1803 0.611200 TACAGGGTGGGTCGTTCATG 59.389 55.000 0.0 0.0 0.00 3.07 F
2837 3156 0.394899 GGCTTTGATGGCTGGCTAGT 60.395 55.000 2.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2107 1.201647 GCTCCGTAGCTTGTCACAGTA 59.798 52.381 0.00 0.00 45.85 2.74 R
2954 3281 0.104855 TCAGCAACTATAGGCAGGCG 59.895 55.000 4.43 0.24 0.00 5.52 R
3742 4132 0.604780 AGAGCTTGCGCACTTCACAT 60.605 50.000 11.12 0.00 39.10 3.21 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
20 21 1.226030 ACGCGTGGGTCTTGTTTAGC 61.226 55.000 12.93 0.00 0.00 3.09
40 41 4.013050 AGCCAGGATCTTGCTTTTTCTAC 58.987 43.478 0.00 0.00 27.56 2.59
143 144 4.583871 AGAGCAGACAGAATTTAAGTGGG 58.416 43.478 0.00 0.00 0.00 4.61
152 153 5.010012 ACAGAATTTAAGTGGGTCTTGCTTG 59.990 40.000 0.00 0.00 37.56 4.01
281 282 3.808728 CCTATTTTCGATGGAAGGCTCA 58.191 45.455 0.00 0.00 32.80 4.26
319 324 3.551846 AGATTAATAAAGCCACACCGGG 58.448 45.455 6.32 0.00 34.06 5.73
406 411 1.345415 CAGGCCCAAAGCAGAACAAAT 59.655 47.619 0.00 0.00 46.50 2.32
443 448 3.681311 AGGGGGCTAAAAGTAGATGGAT 58.319 45.455 0.00 0.00 0.00 3.41
471 476 5.897250 AGGAAAACATTTCCCTAACACAACT 59.103 36.000 16.23 0.00 39.39 3.16
476 481 3.935818 TTTCCCTAACACAACTCCACA 57.064 42.857 0.00 0.00 0.00 4.17
598 604 1.067060 GTTCCTTCCACCAGTTTGTGC 59.933 52.381 0.00 0.00 34.85 4.57
612 618 2.554032 GTTTGTGCAGGTCAGTGCTATT 59.446 45.455 0.00 0.00 44.32 1.73
632 638 3.296322 TTTGGAATGGCGATGTTTGAC 57.704 42.857 0.00 0.00 0.00 3.18
637 643 3.368323 GGAATGGCGATGTTTGACCAATT 60.368 43.478 0.00 0.00 35.41 2.32
665 672 9.824534 GTTTTTCCATGCTAAATTTGTTTATGG 57.175 29.630 14.43 14.43 0.00 2.74
694 701 6.091123 AGAAAATTCGCTCAACGTATGTAC 57.909 37.500 0.00 0.00 44.19 2.90
709 716 8.888025 CAACGTATGTACTTTGTTTGTGTAATG 58.112 33.333 0.00 0.00 32.68 1.90
715 722 8.226819 TGTACTTTGTTTGTGTAATGGATGAA 57.773 30.769 0.00 0.00 0.00 2.57
721 728 2.899976 TGTGTAATGGATGAACGCGAT 58.100 42.857 15.93 0.00 0.00 4.58
740 747 5.957796 CGCGATAATCTGTTTAGTTTTGGTC 59.042 40.000 0.00 0.00 0.00 4.02
744 751 9.968743 CGATAATCTGTTTAGTTTTGGTCTTAC 57.031 33.333 0.00 0.00 0.00 2.34
749 756 9.856162 ATCTGTTTAGTTTTGGTCTTACCTAAA 57.144 29.630 2.24 2.24 39.88 1.85
1014 1021 4.810720 GCCCTGCCTATATTTAATCCAGCA 60.811 45.833 0.00 0.00 0.00 4.41
1112 1119 1.336702 GCATCTGGAGATAGACAGCGG 60.337 57.143 0.00 0.00 34.76 5.52
1237 1244 4.898607 TTGCCAGGACAAGACCAC 57.101 55.556 0.00 0.00 0.00 4.16
1376 1383 4.922206 ACTATGCAATTCTTGGAGTGGAA 58.078 39.130 0.00 0.00 33.40 3.53
1547 1554 2.432146 GACCTATGATCAGACAGGCACA 59.568 50.000 16.81 0.00 0.00 4.57
1563 1570 0.679002 CACACTTGAGGGGCATGAGG 60.679 60.000 0.00 0.00 0.00 3.86
1796 1803 0.611200 TACAGGGTGGGTCGTTCATG 59.389 55.000 0.00 0.00 0.00 3.07
2003 2010 5.149239 GGAAGCCCTACTAGAGATAACCTT 58.851 45.833 0.00 0.00 0.00 3.50
2100 2107 1.485066 CCAATGACTACCCTACGCCTT 59.515 52.381 0.00 0.00 0.00 4.35
2146 2153 2.912771 TGTGGCATAATAGTTCCCACG 58.087 47.619 0.00 0.00 46.81 4.94
2173 2180 6.206634 GGTGATTAGTTTGTTGTCTCCATTGA 59.793 38.462 0.00 0.00 0.00 2.57
2251 2259 3.836229 GAACTGTATGGTCGCGTAATG 57.164 47.619 5.77 0.00 0.00 1.90
2314 2632 5.946377 TCTCAGTAAGAGCATTCAGTGTCTA 59.054 40.000 0.00 0.00 44.35 2.59
2340 2658 7.111139 CACGACATACAGAATCGTAAAATGTC 58.889 38.462 0.00 0.00 46.76 3.06
2463 2781 7.664731 TGTATCGGTAAATTTTGGGTGAACTAA 59.335 33.333 0.00 0.00 0.00 2.24
2484 2802 0.608130 TGGTGCATATAGCTAGGGCG 59.392 55.000 0.00 0.00 45.94 6.13
2818 3137 7.201591 CCAGTAAATTGTCTGCTACATGAAGAG 60.202 40.741 0.00 0.00 38.10 2.85
2837 3156 0.394899 GGCTTTGATGGCTGGCTAGT 60.395 55.000 2.00 0.00 0.00 2.57
2881 3208 0.652592 GCGTGATCTTGGGTTCATCG 59.347 55.000 0.00 0.00 0.00 3.84
2917 3244 5.674525 TCTGGAGCAATTACCATTCTACAG 58.325 41.667 0.00 0.00 33.73 2.74
2954 3281 8.638685 AAATTTTGTGCAGATTATCATGCTAC 57.361 30.769 14.27 11.68 42.98 3.58
2956 3283 2.802247 TGTGCAGATTATCATGCTACGC 59.198 45.455 14.27 0.00 42.98 4.42
2958 3285 2.037641 TGCAGATTATCATGCTACGCCT 59.962 45.455 14.27 0.00 42.98 5.52
3006 3333 9.647797 AATTGTGTACATATACGACTCTGAAAA 57.352 29.630 0.00 0.00 33.60 2.29
3057 3384 1.334869 CTGCCTGAAACCACTGTTGAC 59.665 52.381 0.00 0.00 34.13 3.18
3067 3394 6.152661 TGAAACCACTGTTGACTTGAAATTCT 59.847 34.615 0.00 0.00 34.13 2.40
3083 3410 4.724279 AATTCTCTGGGTTGGTTGTAGT 57.276 40.909 0.00 0.00 0.00 2.73
3193 3520 0.822121 GAAACCCCTGGTGTCGCTTT 60.822 55.000 0.00 0.00 35.34 3.51
3221 3548 3.358707 TTGATGCTTGTGCTGTTGAAG 57.641 42.857 0.00 0.00 40.48 3.02
3245 3573 6.151817 AGTTGATTTCTTTAATCTGGACAGCC 59.848 38.462 0.00 0.00 42.63 4.85
3285 3613 3.091545 GTGCATTTCCTCAGGATTTGGA 58.908 45.455 0.00 0.00 0.00 3.53
3306 3634 4.879545 GGATATCCAGAAGCCGTAAAACAA 59.120 41.667 17.34 0.00 35.64 2.83
3349 3706 2.154139 TCATGGTTGACTGCCAGGT 58.846 52.632 0.00 0.00 39.65 4.00
3350 3707 0.478072 TCATGGTTGACTGCCAGGTT 59.522 50.000 0.00 0.00 39.65 3.50
3351 3708 1.702401 TCATGGTTGACTGCCAGGTTA 59.298 47.619 0.00 0.00 39.65 2.85
3352 3709 2.107378 TCATGGTTGACTGCCAGGTTAA 59.893 45.455 0.00 0.00 39.65 2.01
3353 3710 2.738587 TGGTTGACTGCCAGGTTAAA 57.261 45.000 0.00 0.00 0.00 1.52
3354 3711 3.237268 TGGTTGACTGCCAGGTTAAAT 57.763 42.857 0.00 0.00 0.00 1.40
3355 3712 3.153919 TGGTTGACTGCCAGGTTAAATC 58.846 45.455 0.00 0.00 0.00 2.17
3356 3713 3.181434 TGGTTGACTGCCAGGTTAAATCT 60.181 43.478 0.00 0.00 0.00 2.40
3357 3714 3.191371 GGTTGACTGCCAGGTTAAATCTG 59.809 47.826 0.00 1.30 0.00 2.90
3358 3715 4.072131 GTTGACTGCCAGGTTAAATCTGA 58.928 43.478 0.00 0.00 34.36 3.27
3359 3716 3.674997 TGACTGCCAGGTTAAATCTGAC 58.325 45.455 0.00 0.00 34.36 3.51
3360 3717 3.010420 GACTGCCAGGTTAAATCTGACC 58.990 50.000 0.00 0.00 34.36 4.02
3361 3718 2.290960 ACTGCCAGGTTAAATCTGACCC 60.291 50.000 0.00 0.00 36.57 4.46
3408 3765 9.727859 TTTACTCAACATAAACAACCTATAGCA 57.272 29.630 0.00 0.00 0.00 3.49
3410 3767 8.268850 ACTCAACATAAACAACCTATAGCAAG 57.731 34.615 0.00 0.00 0.00 4.01
3485 3842 5.356190 AGAATGATGCCAGTACACTGAATTG 59.644 40.000 10.96 0.00 46.59 2.32
3497 3854 7.730226 CAGTACACTGAATTGACAAGTTCAAGG 60.730 40.741 3.14 9.67 45.75 3.61
3514 3871 5.241403 TCAAGGCATAACTGAAAGAAGGA 57.759 39.130 0.00 0.00 37.43 3.36
3522 3879 6.484643 GCATAACTGAAAGAAGGATGCATCTA 59.515 38.462 25.28 6.51 39.04 1.98
3523 3880 7.519649 GCATAACTGAAAGAAGGATGCATCTAC 60.520 40.741 25.28 16.13 39.04 2.59
3524 3881 5.690464 ACTGAAAGAAGGATGCATCTACT 57.310 39.130 25.28 17.88 37.43 2.57
3525 3882 6.798427 ACTGAAAGAAGGATGCATCTACTA 57.202 37.500 25.28 7.58 37.43 1.82
3538 3895 9.547753 GGATGCATCTACTAAAGAATTGTCTTA 57.452 33.333 25.28 0.00 43.59 2.10
3617 3976 0.895559 GGGGTTTGCTGCTGCTACTT 60.896 55.000 17.00 0.00 40.48 2.24
3619 3978 2.159382 GGGTTTGCTGCTGCTACTTAA 58.841 47.619 17.00 0.00 40.48 1.85
3620 3979 2.095212 GGGTTTGCTGCTGCTACTTAAC 60.095 50.000 17.00 11.71 40.48 2.01
3746 4136 9.518906 TGAAAACATGCAGCTAATATTTATGTG 57.481 29.630 0.00 0.00 0.00 3.21
3752 4142 6.728200 TGCAGCTAATATTTATGTGAAGTGC 58.272 36.000 0.00 0.00 0.00 4.40
3772 4162 2.133553 CGCAAGCTCTTCGATGATGAT 58.866 47.619 0.95 0.00 0.00 2.45
3773 4163 2.096860 CGCAAGCTCTTCGATGATGATG 60.097 50.000 0.95 2.94 0.00 3.07
3774 4164 2.871022 GCAAGCTCTTCGATGATGATGT 59.129 45.455 0.95 0.00 0.00 3.06
3775 4165 3.303197 GCAAGCTCTTCGATGATGATGTG 60.303 47.826 0.95 0.00 0.00 3.21
3776 4166 4.117685 CAAGCTCTTCGATGATGATGTGA 58.882 43.478 0.95 0.00 0.00 3.58
3777 4167 3.979948 AGCTCTTCGATGATGATGTGAG 58.020 45.455 0.95 0.00 0.00 3.51
3778 4168 3.384146 AGCTCTTCGATGATGATGTGAGT 59.616 43.478 0.95 0.00 0.00 3.41
3779 4169 4.582240 AGCTCTTCGATGATGATGTGAGTA 59.418 41.667 0.95 0.00 0.00 2.59
3780 4170 4.916831 GCTCTTCGATGATGATGTGAGTAG 59.083 45.833 0.95 0.00 0.00 2.57
3781 4171 5.444663 TCTTCGATGATGATGTGAGTAGG 57.555 43.478 0.00 0.00 0.00 3.18
3782 4172 5.133221 TCTTCGATGATGATGTGAGTAGGA 58.867 41.667 0.00 0.00 0.00 2.94
3783 4173 5.240403 TCTTCGATGATGATGTGAGTAGGAG 59.760 44.000 0.00 0.00 0.00 3.69
3784 4174 4.464947 TCGATGATGATGTGAGTAGGAGT 58.535 43.478 0.00 0.00 0.00 3.85
3785 4175 4.889995 TCGATGATGATGTGAGTAGGAGTT 59.110 41.667 0.00 0.00 0.00 3.01
3786 4176 5.360999 TCGATGATGATGTGAGTAGGAGTTT 59.639 40.000 0.00 0.00 0.00 2.66
3787 4177 6.546034 TCGATGATGATGTGAGTAGGAGTTTA 59.454 38.462 0.00 0.00 0.00 2.01
3788 4178 6.638873 CGATGATGATGTGAGTAGGAGTTTAC 59.361 42.308 0.00 0.00 0.00 2.01
3789 4179 5.891451 TGATGATGTGAGTAGGAGTTTACG 58.109 41.667 0.00 0.00 0.00 3.18
3790 4180 5.417894 TGATGATGTGAGTAGGAGTTTACGT 59.582 40.000 0.00 0.00 0.00 3.57
3791 4181 5.717078 TGATGTGAGTAGGAGTTTACGTT 57.283 39.130 0.00 0.00 0.00 3.99
3792 4182 6.092955 TGATGTGAGTAGGAGTTTACGTTT 57.907 37.500 0.00 0.00 0.00 3.60
3793 4183 6.518493 TGATGTGAGTAGGAGTTTACGTTTT 58.482 36.000 0.00 0.00 0.00 2.43
3794 4184 6.987992 TGATGTGAGTAGGAGTTTACGTTTTT 59.012 34.615 0.00 0.00 0.00 1.94
3795 4185 6.592798 TGTGAGTAGGAGTTTACGTTTTTG 57.407 37.500 0.00 0.00 0.00 2.44
3796 4186 5.524646 TGTGAGTAGGAGTTTACGTTTTTGG 59.475 40.000 0.00 0.00 0.00 3.28
3797 4187 5.049886 GTGAGTAGGAGTTTACGTTTTTGGG 60.050 44.000 0.00 0.00 0.00 4.12
3798 4188 3.817084 AGTAGGAGTTTACGTTTTTGGGC 59.183 43.478 0.00 0.00 0.00 5.36
3834 4224 2.172505 TGAACAGGGCATATGTAGGTGG 59.827 50.000 4.29 0.00 0.00 4.61
3866 4256 5.065914 TGCTAAGACTGAGCTTTGTGATTT 58.934 37.500 13.21 0.00 40.76 2.17
3877 4267 4.276926 AGCTTTGTGATTTCAGGTCTCAAC 59.723 41.667 0.00 0.00 31.23 3.18
3888 4278 7.770366 TTTCAGGTCTCAACACAGTAGTATA 57.230 36.000 0.00 0.00 0.00 1.47
3898 4288 8.716646 TCAACACAGTAGTATAATTGTCATGG 57.283 34.615 0.00 0.00 0.00 3.66
3925 4315 8.532186 TGTGGAATATGTAGGTATGCAATTTT 57.468 30.769 0.00 0.00 0.00 1.82
3929 4319 8.860088 GGAATATGTAGGTATGCAATTTTTCCT 58.140 33.333 0.00 0.00 0.00 3.36
3939 4329 9.382275 GGTATGCAATTTTTCCTTGTGATAATT 57.618 29.630 0.00 0.00 0.00 1.40
3963 4353 2.996155 CGTGTCGGACTATGTATGGAC 58.004 52.381 9.88 0.00 0.00 4.02
3964 4354 2.287427 CGTGTCGGACTATGTATGGACC 60.287 54.545 9.88 0.00 0.00 4.46
3965 4355 2.957006 GTGTCGGACTATGTATGGACCT 59.043 50.000 9.88 0.00 0.00 3.85
3966 4356 3.004524 GTGTCGGACTATGTATGGACCTC 59.995 52.174 9.88 0.00 0.00 3.85
3967 4357 3.117625 TGTCGGACTATGTATGGACCTCT 60.118 47.826 9.88 0.00 0.00 3.69
3996 4386 7.102993 AACAATTTGTTTTACTGGAAGTTGCT 58.897 30.769 8.97 0.00 40.85 3.91
4031 4421 9.533831 AATTTGTTCTACTGGAATTTGTATCCT 57.466 29.630 0.00 0.00 37.85 3.24
4032 4422 8.934023 TTTGTTCTACTGGAATTTGTATCCTT 57.066 30.769 0.00 0.00 37.85 3.36
4051 4441 5.016173 TCCTTATCTTTGTGGAATTGGTGG 58.984 41.667 0.00 0.00 0.00 4.61
4052 4442 4.160252 CCTTATCTTTGTGGAATTGGTGGG 59.840 45.833 0.00 0.00 0.00 4.61
4053 4443 2.765689 TCTTTGTGGAATTGGTGGGT 57.234 45.000 0.00 0.00 0.00 4.51
4054 4444 3.039252 TCTTTGTGGAATTGGTGGGTT 57.961 42.857 0.00 0.00 0.00 4.11
4055 4445 2.697751 TCTTTGTGGAATTGGTGGGTTG 59.302 45.455 0.00 0.00 0.00 3.77
4056 4446 0.755686 TTGTGGAATTGGTGGGTTGC 59.244 50.000 0.00 0.00 0.00 4.17
4070 4605 1.686052 GGGTTGCACAGACATTTTCCA 59.314 47.619 0.00 0.00 0.00 3.53
4073 4608 3.989817 GGTTGCACAGACATTTTCCATTC 59.010 43.478 0.00 0.00 0.00 2.67
4084 4619 5.316167 ACATTTTCCATTCTGTAGCTCACA 58.684 37.500 0.00 0.00 35.30 3.58
4085 4620 5.948162 ACATTTTCCATTCTGTAGCTCACAT 59.052 36.000 0.00 0.00 36.29 3.21
4120 4655 8.328758 TCTCATGTATTTCCCTCACATTAGTTT 58.671 33.333 0.00 0.00 30.59 2.66
4133 4668 8.465999 CCTCACATTAGTTTTATTAATGCACCA 58.534 33.333 0.00 0.00 40.50 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.127721 GCAAGATCCTGGCTAAACAAGAC 59.872 47.826 0.00 0.00 0.00 3.01
20 21 4.331168 CGAGTAGAAAAAGCAAGATCCTGG 59.669 45.833 0.00 0.00 0.00 4.45
40 41 0.868406 GATCCAAATTAGCCGCCGAG 59.132 55.000 0.00 0.00 0.00 4.63
124 125 4.327680 AGACCCACTTAAATTCTGTCTGC 58.672 43.478 0.00 0.00 30.91 4.26
152 153 3.066814 CTGCTGGCCAAAGCTCCC 61.067 66.667 17.08 0.00 43.90 4.30
163 164 2.671370 ATACATGGCCGCTCTGCTGG 62.671 60.000 0.00 0.00 0.00 4.85
271 272 2.665000 CTCCGCTTGAGCCTTCCA 59.335 61.111 0.00 0.00 37.91 3.53
319 324 0.742990 TGTAGGGCTGTTATGCGTGC 60.743 55.000 0.00 0.00 0.00 5.34
361 366 4.705507 AGTAATCGTAAACTGAGAGCCTCA 59.294 41.667 0.00 5.03 38.25 3.86
406 411 3.070302 GCCCCCTTGATTTGTTGTTTGTA 59.930 43.478 0.00 0.00 0.00 2.41
443 448 5.768164 GTGTTAGGGAAATGTTTTCCTGAGA 59.232 40.000 14.36 3.35 45.80 3.27
471 476 2.076100 CTTTAGCGCAGTTCATGTGGA 58.924 47.619 11.47 0.00 39.94 4.02
476 481 2.028112 TCTGGTCTTTAGCGCAGTTCAT 60.028 45.455 11.47 0.00 0.00 2.57
598 604 4.142315 CCATTCCAAAATAGCACTGACCTG 60.142 45.833 0.00 0.00 0.00 4.00
612 618 2.029470 GGTCAAACATCGCCATTCCAAA 60.029 45.455 0.00 0.00 0.00 3.28
637 643 9.566432 ATAAACAAATTTAGCATGGAAAAACCA 57.434 25.926 0.00 0.00 42.12 3.67
665 672 3.299020 CGTTGAGCGAATTTTCTTGATGC 59.701 43.478 0.00 0.00 44.77 3.91
694 701 5.116983 GCGTTCATCCATTACACAAACAAAG 59.883 40.000 0.00 0.00 0.00 2.77
709 716 4.795970 AAACAGATTATCGCGTTCATCC 57.204 40.909 5.77 0.00 0.00 3.51
715 722 5.410439 ACCAAAACTAAACAGATTATCGCGT 59.590 36.000 5.77 0.00 0.00 6.01
740 747 9.499479 ACATCATTATGAGCAGATTTAGGTAAG 57.501 33.333 0.29 0.00 36.54 2.34
744 751 8.162878 ACAACATCATTATGAGCAGATTTAGG 57.837 34.615 0.29 0.00 36.54 2.69
749 756 6.709397 CCTGTACAACATCATTATGAGCAGAT 59.291 38.462 0.29 0.00 36.54 2.90
908 915 9.166126 GTTTTTAGTGTGACTAACAAACTATGC 57.834 33.333 16.65 0.00 45.35 3.14
1014 1021 3.294816 GACTTAAGTCGGTCGTTTCCT 57.705 47.619 19.39 0.00 35.12 3.36
1112 1119 5.005682 GGCAATTCGAATAAATTTGTCTGCC 59.994 40.000 22.05 22.05 35.85 4.85
1187 1194 5.261040 TCAGATTCAGGGGATCAAACTTT 57.739 39.130 0.00 0.00 0.00 2.66
1237 1244 5.467035 TTTTAGGTTTTCATGGCCTCTTG 57.533 39.130 3.32 0.00 34.07 3.02
1547 1554 1.668826 TAACCTCATGCCCCTCAAGT 58.331 50.000 0.00 0.00 0.00 3.16
1563 1570 7.079182 TGACATTGGAATATTGGTCGTTAAC 57.921 36.000 0.00 0.00 0.00 2.01
1796 1803 6.149474 ACAGGTGCATCAATACTGTTAAGTTC 59.851 38.462 0.00 0.00 39.16 3.01
1985 1992 5.954757 TCCTCAAGGTTATCTCTAGTAGGG 58.045 45.833 0.00 0.00 36.34 3.53
1989 1996 7.072562 ACATGATCCTCAAGGTTATCTCTAGT 58.927 38.462 0.00 0.00 36.34 2.57
2100 2107 1.201647 GCTCCGTAGCTTGTCACAGTA 59.798 52.381 0.00 0.00 45.85 2.74
2140 2147 2.105134 ACAAACTAATCACCACGTGGGA 59.895 45.455 36.47 28.88 41.15 4.37
2146 2153 4.819630 TGGAGACAACAAACTAATCACCAC 59.180 41.667 0.00 0.00 37.44 4.16
2314 2632 6.588756 ACATTTTACGATTCTGTATGTCGTGT 59.411 34.615 9.59 0.00 46.70 4.49
2340 2658 9.941664 GACTGAAACATCATGTCATAAAATAGG 57.058 33.333 0.00 0.00 0.00 2.57
2463 2781 2.355108 CGCCCTAGCTATATGCACCAAT 60.355 50.000 0.00 0.00 45.94 3.16
2484 2802 3.503748 ACTGCTAAGCTTTCATGTTCCAC 59.496 43.478 3.20 0.00 0.00 4.02
2706 3025 8.821686 TGCTCATCCTTTTCCATAAAATCTTA 57.178 30.769 0.00 0.00 34.18 2.10
2790 3109 5.874810 TCATGTAGCAGACAATTTACTGGTC 59.125 40.000 14.01 1.51 42.78 4.02
2818 3137 0.394899 ACTAGCCAGCCATCAAAGCC 60.395 55.000 0.00 0.00 0.00 4.35
2837 3156 3.847671 TTGAACTCCACCATGTACACA 57.152 42.857 0.00 0.00 0.00 3.72
2881 3208 2.016096 GCTCCAGAAGAATGACAGGCC 61.016 57.143 0.00 0.00 0.00 5.19
2954 3281 0.104855 TCAGCAACTATAGGCAGGCG 59.895 55.000 4.43 0.24 0.00 5.52
2956 3283 2.831333 CACTCAGCAACTATAGGCAGG 58.169 52.381 4.43 0.00 0.00 4.85
2958 3285 2.315925 GCACTCAGCAACTATAGGCA 57.684 50.000 4.43 0.00 44.79 4.75
3006 3333 3.859443 GATCTCATGATCGCTAGCCATT 58.141 45.455 9.66 0.00 39.56 3.16
3057 3384 4.342092 ACAACCAACCCAGAGAATTTCAAG 59.658 41.667 0.00 0.00 0.00 3.02
3067 3394 1.493022 AGCAACTACAACCAACCCAGA 59.507 47.619 0.00 0.00 0.00 3.86
3172 3499 1.303317 GCGACACCAGGGGTTTCAT 60.303 57.895 0.00 0.00 32.45 2.57
3193 3520 0.592637 CACAAGCATCAAACTCGCCA 59.407 50.000 0.00 0.00 0.00 5.69
3221 3548 6.325596 GGCTGTCCAGATTAAAGAAATCAAC 58.674 40.000 0.00 0.00 45.58 3.18
3245 3573 1.064296 AACGCTAGCTCGACATCCG 59.936 57.895 13.93 0.00 40.25 4.18
3285 3613 4.881850 CCTTGTTTTACGGCTTCTGGATAT 59.118 41.667 0.00 0.00 0.00 1.63
3299 3627 5.442391 AGTTCAAGTAGTGCCCTTGTTTTA 58.558 37.500 0.00 0.00 40.15 1.52
3306 3634 4.373156 AATCAAGTTCAAGTAGTGCCCT 57.627 40.909 0.00 0.00 0.00 5.19
3344 3701 1.065418 AGCGGGTCAGATTTAACCTGG 60.065 52.381 2.77 0.00 41.45 4.45
3349 3706 3.838244 ATAGCAGCGGGTCAGATTTAA 57.162 42.857 0.00 0.00 0.00 1.52
3350 3707 5.221641 ACAATATAGCAGCGGGTCAGATTTA 60.222 40.000 0.00 0.00 0.00 1.40
3351 3708 4.067896 CAATATAGCAGCGGGTCAGATTT 58.932 43.478 0.00 0.00 0.00 2.17
3352 3709 3.071602 ACAATATAGCAGCGGGTCAGATT 59.928 43.478 0.00 0.00 0.00 2.40
3353 3710 2.634940 ACAATATAGCAGCGGGTCAGAT 59.365 45.455 0.00 0.00 0.00 2.90
3354 3711 2.039418 ACAATATAGCAGCGGGTCAGA 58.961 47.619 0.00 0.00 0.00 3.27
3355 3712 2.533266 ACAATATAGCAGCGGGTCAG 57.467 50.000 0.00 0.00 0.00 3.51
3356 3713 2.963101 AGTACAATATAGCAGCGGGTCA 59.037 45.455 0.00 0.00 0.00 4.02
3357 3714 3.662247 AGTACAATATAGCAGCGGGTC 57.338 47.619 0.00 0.00 0.00 4.46
3358 3715 4.527038 ACATAGTACAATATAGCAGCGGGT 59.473 41.667 0.00 0.00 0.00 5.28
3359 3716 5.073311 ACATAGTACAATATAGCAGCGGG 57.927 43.478 0.00 0.00 0.00 6.13
3360 3717 7.421530 AAAACATAGTACAATATAGCAGCGG 57.578 36.000 0.00 0.00 0.00 5.52
3361 3718 9.193133 AGTAAAACATAGTACAATATAGCAGCG 57.807 33.333 0.00 0.00 0.00 5.18
3485 3842 5.689383 TTCAGTTATGCCTTGAACTTGTC 57.311 39.130 0.00 0.00 33.60 3.18
3497 3854 4.970662 TGCATCCTTCTTTCAGTTATGC 57.029 40.909 0.00 0.00 38.90 3.14
3565 3924 8.150945 ACCTATCGTTGATTTAGTTATCAGCAT 58.849 33.333 0.00 0.00 36.04 3.79
3585 3944 2.941064 GCAAACCCCGTCTAAACCTATC 59.059 50.000 0.00 0.00 0.00 2.08
3663 4053 4.451629 AATATAGGGCGTCCTTGTATCG 57.548 45.455 17.04 0.00 41.56 2.92
3742 4132 0.604780 AGAGCTTGCGCACTTCACAT 60.605 50.000 11.12 0.00 39.10 3.21
3752 4142 1.564207 TCATCATCGAAGAGCTTGCG 58.436 50.000 0.00 0.00 43.63 4.85
3772 4162 5.524646 CCAAAAACGTAAACTCCTACTCACA 59.475 40.000 0.00 0.00 0.00 3.58
3773 4163 5.049886 CCCAAAAACGTAAACTCCTACTCAC 60.050 44.000 0.00 0.00 0.00 3.51
3774 4164 5.058490 CCCAAAAACGTAAACTCCTACTCA 58.942 41.667 0.00 0.00 0.00 3.41
3775 4165 4.083643 GCCCAAAAACGTAAACTCCTACTC 60.084 45.833 0.00 0.00 0.00 2.59
3776 4166 3.817084 GCCCAAAAACGTAAACTCCTACT 59.183 43.478 0.00 0.00 0.00 2.57
3777 4167 3.817084 AGCCCAAAAACGTAAACTCCTAC 59.183 43.478 0.00 0.00 0.00 3.18
3778 4168 3.816523 CAGCCCAAAAACGTAAACTCCTA 59.183 43.478 0.00 0.00 0.00 2.94
3779 4169 2.621526 CAGCCCAAAAACGTAAACTCCT 59.378 45.455 0.00 0.00 0.00 3.69
3780 4170 2.359848 ACAGCCCAAAAACGTAAACTCC 59.640 45.455 0.00 0.00 0.00 3.85
3781 4171 3.703286 ACAGCCCAAAAACGTAAACTC 57.297 42.857 0.00 0.00 0.00 3.01
3782 4172 4.459390 AAACAGCCCAAAAACGTAAACT 57.541 36.364 0.00 0.00 0.00 2.66
3783 4173 4.389382 ACAAAACAGCCCAAAAACGTAAAC 59.611 37.500 0.00 0.00 0.00 2.01
3784 4174 4.566987 ACAAAACAGCCCAAAAACGTAAA 58.433 34.783 0.00 0.00 0.00 2.01
3785 4175 4.082136 AGACAAAACAGCCCAAAAACGTAA 60.082 37.500 0.00 0.00 0.00 3.18
3786 4176 3.444388 AGACAAAACAGCCCAAAAACGTA 59.556 39.130 0.00 0.00 0.00 3.57
3787 4177 2.232696 AGACAAAACAGCCCAAAAACGT 59.767 40.909 0.00 0.00 0.00 3.99
3788 4178 2.887337 AGACAAAACAGCCCAAAAACG 58.113 42.857 0.00 0.00 0.00 3.60
3789 4179 5.006153 AGTAGACAAAACAGCCCAAAAAC 57.994 39.130 0.00 0.00 0.00 2.43
3790 4180 5.669164 AAGTAGACAAAACAGCCCAAAAA 57.331 34.783 0.00 0.00 0.00 1.94
3791 4181 5.186021 TCAAAGTAGACAAAACAGCCCAAAA 59.814 36.000 0.00 0.00 0.00 2.44
3792 4182 4.707448 TCAAAGTAGACAAAACAGCCCAAA 59.293 37.500 0.00 0.00 0.00 3.28
3793 4183 4.274147 TCAAAGTAGACAAAACAGCCCAA 58.726 39.130 0.00 0.00 0.00 4.12
3794 4184 3.892284 TCAAAGTAGACAAAACAGCCCA 58.108 40.909 0.00 0.00 0.00 5.36
3795 4185 4.097286 TGTTCAAAGTAGACAAAACAGCCC 59.903 41.667 0.00 0.00 0.00 5.19
3796 4186 5.243426 TGTTCAAAGTAGACAAAACAGCC 57.757 39.130 0.00 0.00 0.00 4.85
3797 4187 5.273944 CCTGTTCAAAGTAGACAAAACAGC 58.726 41.667 7.38 0.00 41.25 4.40
3798 4188 5.733373 GCCCTGTTCAAAGTAGACAAAACAG 60.733 44.000 6.16 6.16 41.89 3.16
3834 4224 3.397482 CTCAGTCTTAGCATGGGCATAC 58.603 50.000 0.00 0.00 44.61 2.39
3866 4256 7.956328 ATTATACTACTGTGTTGAGACCTGA 57.044 36.000 0.00 0.00 0.00 3.86
3877 4267 8.390354 CACAACCATGACAATTATACTACTGTG 58.610 37.037 0.00 0.00 0.00 3.66
3888 4278 6.855763 ACATATTCCACAACCATGACAATT 57.144 33.333 0.00 0.00 0.00 2.32
3898 4288 6.935741 TTGCATACCTACATATTCCACAAC 57.064 37.500 0.00 0.00 0.00 3.32
3925 4315 4.658063 ACACGGGAAATTATCACAAGGAA 58.342 39.130 0.00 0.00 0.00 3.36
3929 4319 3.004171 CCGACACGGGAAATTATCACAA 58.996 45.455 0.00 0.00 44.15 3.33
3950 4340 5.594725 TGTTCAGAGAGGTCCATACATAGTC 59.405 44.000 0.00 0.00 0.00 2.59
3954 4344 5.965033 ATTGTTCAGAGAGGTCCATACAT 57.035 39.130 0.00 0.00 0.00 2.29
3956 4346 5.940470 ACAAATTGTTCAGAGAGGTCCATAC 59.060 40.000 0.00 0.00 0.00 2.39
3958 4348 4.990526 ACAAATTGTTCAGAGAGGTCCAT 58.009 39.130 0.00 0.00 0.00 3.41
3960 4350 5.774498 AAACAAATTGTTCAGAGAGGTCC 57.226 39.130 12.11 0.00 40.14 4.46
3961 4351 7.857885 CAGTAAAACAAATTGTTCAGAGAGGTC 59.142 37.037 12.11 0.00 40.14 3.85
3962 4352 7.201821 CCAGTAAAACAAATTGTTCAGAGAGGT 60.202 37.037 12.11 0.00 40.14 3.85
3963 4353 7.013274 TCCAGTAAAACAAATTGTTCAGAGAGG 59.987 37.037 12.11 10.05 40.14 3.69
3964 4354 7.930217 TCCAGTAAAACAAATTGTTCAGAGAG 58.070 34.615 12.11 1.32 40.14 3.20
3965 4355 7.873719 TCCAGTAAAACAAATTGTTCAGAGA 57.126 32.000 12.11 2.59 40.14 3.10
3966 4356 8.190784 ACTTCCAGTAAAACAAATTGTTCAGAG 58.809 33.333 12.11 5.03 40.14 3.35
3967 4357 8.062065 ACTTCCAGTAAAACAAATTGTTCAGA 57.938 30.769 12.11 0.00 40.14 3.27
4022 4412 8.748412 CCAATTCCACAAAGATAAGGATACAAA 58.252 33.333 0.00 0.00 41.41 2.83
4031 4421 4.746466 ACCCACCAATTCCACAAAGATAA 58.254 39.130 0.00 0.00 0.00 1.75
4032 4422 4.396357 ACCCACCAATTCCACAAAGATA 57.604 40.909 0.00 0.00 0.00 1.98
4033 4423 3.258722 ACCCACCAATTCCACAAAGAT 57.741 42.857 0.00 0.00 0.00 2.40
4034 4424 2.697751 CAACCCACCAATTCCACAAAGA 59.302 45.455 0.00 0.00 0.00 2.52
4051 4441 3.665745 ATGGAAAATGTCTGTGCAACC 57.334 42.857 0.00 0.00 34.36 3.77
4052 4442 4.682860 CAGAATGGAAAATGTCTGTGCAAC 59.317 41.667 0.00 0.00 34.15 4.17
4053 4443 4.341806 ACAGAATGGAAAATGTCTGTGCAA 59.658 37.500 4.45 0.00 46.80 4.08
4054 4444 3.890756 ACAGAATGGAAAATGTCTGTGCA 59.109 39.130 4.45 0.00 46.80 4.57
4055 4445 4.510038 ACAGAATGGAAAATGTCTGTGC 57.490 40.909 4.45 0.00 46.80 4.57
4073 4608 8.877808 TGAGATTTTGTATATGTGAGCTACAG 57.122 34.615 0.00 0.00 43.80 2.74
4120 4655 4.928615 GCTTGTGCTTTGGTGCATTAATAA 59.071 37.500 0.00 0.00 45.23 1.40


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

AutoCloner maintained by Alex Coulton.