Multiple sequence alignment - TraesCS1D01G287400

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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 TraesCS1D01G287400 chr1D 100.000 5031 0 0 771 5801 385802967 385807997 0.000000e+00 9291
1 TraesCS1D01G287400 chr1D 100.000 439 0 0 1 439 385802197 385802635 0.000000e+00 811
2 TraesCS1D01G287400 chr1A 96.028 5010 146 26 775 5763 485353191 485358168 0.000000e+00 8100
3 TraesCS1D01G287400 chr1A 93.750 224 12 2 209 431 485352716 485352938 9.310000e-88 335
4 TraesCS1D01G287400 chr1A 79.720 143 29 0 4581 4723 485357047 485357189 2.860000e-18 104
5 TraesCS1D01G287400 chr1B 96.358 3020 89 11 771 3777 518176321 518179332 0.000000e+00 4948
6 TraesCS1D01G287400 chr1B 93.917 1792 95 9 3804 5584 518179326 518181114 0.000000e+00 2693
7 TraesCS1D01G287400 chr1B 78.374 615 129 3 1674 2286 517905337 517905949 4.210000e-106 396
8 TraesCS1D01G287400 chr1B 82.018 456 26 20 1 437 518175865 518176283 2.590000e-88 337


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 TraesCS1D01G287400 chr1D 385802197 385807997 5800 False 5051.000000 9291 100.000000 1 5801 2 chr1D.!!$F1 5800
1 TraesCS1D01G287400 chr1A 485352716 485358168 5452 False 2846.333333 8100 89.832667 209 5763 3 chr1A.!!$F1 5554
2 TraesCS1D01G287400 chr1B 518175865 518181114 5249 False 2659.333333 4948 90.764333 1 5584 3 chr1B.!!$F2 5583
3 TraesCS1D01G287400 chr1B 517905337 517905949 612 False 396.000000 396 78.374000 1674 2286 1 chr1B.!!$F1 612

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
159 175 0.387565 TTTTGAAACGCAGAAGGCCC 59.612 50.000 0.00 0.00 40.31 5.80 F
207 223 0.665835 CCTTGTTAAGTGGCGTGCAA 59.334 50.000 0.00 0.00 0.00 4.08 F
1380 1416 0.462047 CTTTTACCGGCGAGCCTGAT 60.462 55.000 9.30 0.11 0.00 2.90 F
1504 1540 3.877559 TGATGATGCCACTGTTTCTAGG 58.122 45.455 0.00 0.00 0.00 3.02 F
1526 1562 4.676924 GGCTGCAGCGTTGAATAATATTTC 59.323 41.667 31.19 8.58 43.26 2.17 F
3140 3176 5.352569 CCTAAGAAACAGATACAAGTGGCTG 59.647 44.000 0.00 0.00 34.65 4.85 F
3790 3862 0.034059 AGTTGAGACCGTCCAGCAAG 59.966 55.000 0.00 0.00 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1077 1101 0.103026 TCACATCAGAATCTCCCGCG 59.897 55.000 0.00 0.0 0.00 6.46 R
1400 1436 1.199327 CAGAAGCACCAGCAACATCTG 59.801 52.381 0.00 0.0 45.49 2.90 R
2885 2921 4.285775 CCTCTTCTTTCTCCTCCTCTTTGT 59.714 45.833 0.00 0.0 0.00 2.83 R
3327 3363 9.855021 ACACAATTTTAATAGTATTTGTGCTCC 57.145 29.630 18.30 0.0 0.00 4.70 R
3664 3703 5.904362 ACTTCAGCTTTCTCAGTTTTGTT 57.096 34.783 0.00 0.0 0.00 2.83 R
4176 4248 0.034059 CGGGACAGCTGACTTGTTCT 59.966 55.000 23.35 0.0 0.00 3.01 R
5771 5854 0.106268 TGGCCAATTGTGTCTGGTGT 60.106 50.000 0.61 0.0 34.97 4.16 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
60 61 7.013274 GCCATATGACACTTTGCCTCTTTTATA 59.987 37.037 3.65 0.00 0.00 0.98
61 62 8.902806 CCATATGACACTTTGCCTCTTTTATAA 58.097 33.333 3.65 0.00 0.00 0.98
156 172 7.692908 TTTAGAATTTTTGAAACGCAGAAGG 57.307 32.000 0.00 0.00 0.00 3.46
159 175 0.387565 TTTTGAAACGCAGAAGGCCC 59.612 50.000 0.00 0.00 40.31 5.80
160 176 0.753479 TTTGAAACGCAGAAGGCCCA 60.753 50.000 0.00 0.00 40.31 5.36
185 201 2.202427 GAAAATGAACGCGGGCCG 60.202 61.111 24.35 24.35 44.21 6.13
186 202 3.677099 GAAAATGAACGCGGGCCGG 62.677 63.158 29.48 19.86 42.52 6.13
198 214 2.035155 GGCCGGCCCTTGTTAAGT 59.965 61.111 36.64 0.00 0.00 2.24
199 215 2.340328 GGCCGGCCCTTGTTAAGTG 61.340 63.158 36.64 0.00 0.00 3.16
200 216 2.340328 GCCGGCCCTTGTTAAGTGG 61.340 63.158 18.11 0.00 0.00 4.00
201 217 2.340328 CCGGCCCTTGTTAAGTGGC 61.340 63.158 0.00 10.63 41.37 5.01
202 218 2.686816 CGGCCCTTGTTAAGTGGCG 61.687 63.158 0.00 5.73 46.65 5.69
203 219 1.602605 GGCCCTTGTTAAGTGGCGT 60.603 57.895 0.00 0.00 42.34 5.68
204 220 1.579429 GCCCTTGTTAAGTGGCGTG 59.421 57.895 0.00 0.00 35.92 5.34
205 221 1.579429 CCCTTGTTAAGTGGCGTGC 59.421 57.895 0.00 0.00 0.00 5.34
206 222 1.169661 CCCTTGTTAAGTGGCGTGCA 61.170 55.000 0.00 0.00 0.00 4.57
207 223 0.665835 CCTTGTTAAGTGGCGTGCAA 59.334 50.000 0.00 0.00 0.00 4.08
246 262 1.978617 CCGTGCCAGGCCTTTTCAT 60.979 57.895 9.64 0.00 0.00 2.57
247 263 0.679640 CCGTGCCAGGCCTTTTCATA 60.680 55.000 9.64 0.00 0.00 2.15
248 264 1.392589 CGTGCCAGGCCTTTTCATAT 58.607 50.000 9.64 0.00 0.00 1.78
252 268 1.481772 GCCAGGCCTTTTCATATGCAA 59.518 47.619 0.00 0.00 0.00 4.08
836 854 0.906775 TAAATTCCCGAGCTCCCGTT 59.093 50.000 8.47 0.00 0.00 4.44
891 913 2.786495 GCGGCCTTCCAGATCGAGA 61.786 63.158 0.00 0.00 0.00 4.04
892 914 1.361993 CGGCCTTCCAGATCGAGAG 59.638 63.158 0.00 0.00 0.00 3.20
893 915 1.068921 GGCCTTCCAGATCGAGAGC 59.931 63.158 0.00 0.00 0.00 4.09
896 918 1.361993 CTTCCAGATCGAGAGCGGG 59.638 63.158 1.15 1.15 38.28 6.13
898 920 4.292178 CCAGATCGAGAGCGGGGC 62.292 72.222 0.00 0.00 38.28 5.80
923 945 4.803426 CCGAGCTCCGTGGCTGAC 62.803 72.222 8.47 0.00 43.20 3.51
933 957 1.599576 GTGGCTGACCTTCTCTCCC 59.400 63.158 0.00 0.00 36.63 4.30
1005 1029 1.109323 GGGATTTTGCTCCGATGGGG 61.109 60.000 0.00 0.00 36.05 4.96
1077 1101 3.207669 CAGGATTCTGCTGCCGCC 61.208 66.667 0.00 0.00 33.86 6.13
1146 1176 2.125350 GCCGCTGAGGTCAAGGAG 60.125 66.667 0.00 0.00 43.70 3.69
1231 1267 4.845580 AAGAGGCAGATGCGGCGG 62.846 66.667 9.78 0.00 43.26 6.13
1365 1401 1.683385 GACAACAAGGCTGGAGCTTTT 59.317 47.619 0.00 0.00 38.33 2.27
1380 1416 0.462047 CTTTTACCGGCGAGCCTGAT 60.462 55.000 9.30 0.11 0.00 2.90
1483 1519 5.178809 GTCACTTTTCCGTGTACTGCTTATT 59.821 40.000 0.00 0.00 36.33 1.40
1485 1521 5.178623 CACTTTTCCGTGTACTGCTTATTGA 59.821 40.000 0.00 0.00 0.00 2.57
1486 1522 5.938125 ACTTTTCCGTGTACTGCTTATTGAT 59.062 36.000 0.00 0.00 0.00 2.57
1504 1540 3.877559 TGATGATGCCACTGTTTCTAGG 58.122 45.455 0.00 0.00 0.00 3.02
1526 1562 4.676924 GGCTGCAGCGTTGAATAATATTTC 59.323 41.667 31.19 8.58 43.26 2.17
1528 1564 5.506317 GCTGCAGCGTTGAATAATATTTCCT 60.506 40.000 25.23 0.00 0.00 3.36
1571 1607 5.465935 GTGAACTCGGAGGAGAATATCATC 58.534 45.833 10.23 0.00 43.27 2.92
1939 1975 7.074653 ACAGAGTAGTTTGGATTCCTTTGTA 57.925 36.000 3.95 0.00 0.00 2.41
3140 3176 5.352569 CCTAAGAAACAGATACAAGTGGCTG 59.647 44.000 0.00 0.00 34.65 4.85
3327 3363 6.069684 AGAATCTGAAACTGAAGTGCAAAG 57.930 37.500 0.00 0.00 0.00 2.77
3664 3703 3.072330 TGCTGTGAAAGATAACCAGGTCA 59.928 43.478 0.00 0.00 0.00 4.02
3686 3725 5.415701 TCAACAAAACTGAGAAAGCTGAAGT 59.584 36.000 0.00 0.00 0.00 3.01
3773 3845 1.542915 GCAATCATCAGGTGCACAAGT 59.457 47.619 20.43 0.00 38.19 3.16
3774 3846 2.029649 GCAATCATCAGGTGCACAAGTT 60.030 45.455 20.43 2.29 38.19 2.66
3775 3847 3.571571 CAATCATCAGGTGCACAAGTTG 58.428 45.455 20.43 14.56 0.00 3.16
3776 3848 2.636647 TCATCAGGTGCACAAGTTGA 57.363 45.000 20.43 16.50 0.00 3.18
3777 3849 2.497138 TCATCAGGTGCACAAGTTGAG 58.503 47.619 20.43 2.31 0.00 3.02
3778 3850 2.104622 TCATCAGGTGCACAAGTTGAGA 59.895 45.455 20.43 11.76 0.00 3.27
3779 3851 1.953559 TCAGGTGCACAAGTTGAGAC 58.046 50.000 20.43 2.71 0.00 3.36
3780 3852 0.947244 CAGGTGCACAAGTTGAGACC 59.053 55.000 20.43 11.56 31.88 3.85
3781 3853 0.532862 AGGTGCACAAGTTGAGACCG 60.533 55.000 20.43 0.00 35.36 4.79
3782 3854 0.814010 GGTGCACAAGTTGAGACCGT 60.814 55.000 20.43 0.00 0.00 4.83
3783 3855 0.582005 GTGCACAAGTTGAGACCGTC 59.418 55.000 13.17 0.00 0.00 4.79
3784 3856 0.531974 TGCACAAGTTGAGACCGTCC 60.532 55.000 10.54 0.00 0.00 4.79
3785 3857 0.531974 GCACAAGTTGAGACCGTCCA 60.532 55.000 10.54 0.00 0.00 4.02
3786 3858 1.502231 CACAAGTTGAGACCGTCCAG 58.498 55.000 10.54 0.00 0.00 3.86
3787 3859 0.249911 ACAAGTTGAGACCGTCCAGC 60.250 55.000 10.54 0.00 0.00 4.85
3788 3860 0.249868 CAAGTTGAGACCGTCCAGCA 60.250 55.000 0.00 0.00 0.00 4.41
3789 3861 0.468226 AAGTTGAGACCGTCCAGCAA 59.532 50.000 0.00 0.00 0.00 3.91
3790 3862 0.034059 AGTTGAGACCGTCCAGCAAG 59.966 55.000 0.00 0.00 0.00 4.01
3791 3863 1.301716 TTGAGACCGTCCAGCAAGC 60.302 57.895 0.00 0.00 0.00 4.01
3792 3864 2.038814 TTGAGACCGTCCAGCAAGCA 62.039 55.000 0.00 0.00 0.00 3.91
3793 3865 1.078848 GAGACCGTCCAGCAAGCAT 60.079 57.895 0.00 0.00 0.00 3.79
3794 3866 1.364626 GAGACCGTCCAGCAAGCATG 61.365 60.000 0.00 0.00 0.00 4.06
3805 3877 3.806591 CAAGCATGCCAACCTGAAG 57.193 52.632 15.66 0.00 0.00 3.02
3826 3898 2.663063 GCTGACGCTGTTAAGAAAGCAC 60.663 50.000 5.78 0.98 39.47 4.40
3852 3924 0.686789 TTGCTGCTGAGCTAACTGGA 59.313 50.000 5.83 0.00 46.39 3.86
3896 3968 4.023707 AGCTGATGTAACTGAGCAAACAAC 60.024 41.667 0.00 0.00 33.67 3.32
4060 4132 3.013921 GTTCAACCAGAAACACCAGTCA 58.986 45.455 0.00 0.00 38.13 3.41
4086 4158 1.003355 GGGTACAGCAGCAGAAGCA 60.003 57.895 0.00 0.00 45.49 3.91
4145 4217 2.905075 AGCTGGGTTGAAAAAGCAAAC 58.095 42.857 0.00 0.00 38.14 2.93
4176 4248 4.280677 CCCAAAACTGCTGAAATAGAACCA 59.719 41.667 0.00 0.00 0.00 3.67
4338 4413 1.798813 GTAGCACCAGTTGAGGAAACG 59.201 52.381 0.00 0.00 44.04 3.60
4345 4420 3.135167 ACCAGTTGAGGAAACGGTAGAAA 59.865 43.478 0.00 0.00 44.04 2.52
4579 4654 1.668151 GCAGAGGGTGTCGGTGTTC 60.668 63.158 0.00 0.00 0.00 3.18
4663 4738 3.587506 ACCAGGTAAGAAGGCTACAACAT 59.412 43.478 0.00 0.00 0.00 2.71
4698 4773 2.434185 GATGCCACGGTCGAAGCA 60.434 61.111 12.43 12.43 40.00 3.91
4754 4829 2.203294 GGGTGCCACGGTTGAAGT 60.203 61.111 0.00 0.00 0.00 3.01
4842 4917 3.142174 GCAACTGAACAGAAAGGCTAGT 58.858 45.455 8.87 0.00 0.00 2.57
4876 4951 5.550981 CGAATTCTTGTTTCTGTCGGTATG 58.449 41.667 3.52 0.00 0.00 2.39
4895 4970 4.543590 ATGAAGGTAATCTATCTGCCCG 57.456 45.455 0.00 0.00 0.00 6.13
4943 5018 5.616488 TGTTTTGTATAGGAAAAGACGGC 57.384 39.130 0.00 0.00 0.00 5.68
5257 5332 1.212935 ACTGGTTGTGTTCTGGAGCTT 59.787 47.619 0.00 0.00 0.00 3.74
5328 5404 0.780002 CTGCTTGCGTGTTGATTTGC 59.220 50.000 0.00 0.00 0.00 3.68
5590 5672 8.894768 ATAGTAATGGCTGAGTTTGAAGATAC 57.105 34.615 0.00 0.00 0.00 2.24
5591 5673 6.116126 AGTAATGGCTGAGTTTGAAGATACC 58.884 40.000 0.00 0.00 0.00 2.73
5592 5674 4.851639 ATGGCTGAGTTTGAAGATACCT 57.148 40.909 0.00 0.00 0.00 3.08
5695 5778 1.475403 TTCTTTTGGGTGGCGAAACA 58.525 45.000 0.00 0.00 0.00 2.83
5696 5779 1.698506 TCTTTTGGGTGGCGAAACAT 58.301 45.000 0.00 0.00 0.00 2.71
5744 5827 2.114616 ACAATTGGCCTGTGGAAAACA 58.885 42.857 10.83 0.00 37.22 2.83
5763 5846 1.730064 CAGGGTGAAATCCGTTACACG 59.270 52.381 0.00 0.00 42.11 4.49
5764 5847 0.445043 GGGTGAAATCCGTTACACGC 59.555 55.000 0.00 0.00 40.91 5.34
5765 5848 0.445043 GGTGAAATCCGTTACACGCC 59.555 55.000 0.00 0.00 40.91 5.68
5766 5849 1.435577 GTGAAATCCGTTACACGCCT 58.564 50.000 0.00 0.00 40.91 5.52
5767 5850 1.392510 GTGAAATCCGTTACACGCCTC 59.607 52.381 0.00 0.00 40.91 4.70
5768 5851 1.001068 TGAAATCCGTTACACGCCTCA 59.999 47.619 0.00 0.00 40.91 3.86
5769 5852 2.070783 GAAATCCGTTACACGCCTCAA 58.929 47.619 0.00 0.00 40.91 3.02
5770 5853 2.172851 AATCCGTTACACGCCTCAAA 57.827 45.000 0.00 0.00 40.91 2.69
5771 5854 2.172851 ATCCGTTACACGCCTCAAAA 57.827 45.000 0.00 0.00 40.91 2.44
5772 5855 1.219646 TCCGTTACACGCCTCAAAAC 58.780 50.000 0.00 0.00 40.91 2.43
5773 5856 0.938713 CCGTTACACGCCTCAAAACA 59.061 50.000 0.00 0.00 40.91 2.83
5774 5857 1.333435 CCGTTACACGCCTCAAAACAC 60.333 52.381 0.00 0.00 40.91 3.32
5775 5858 1.333435 CGTTACACGCCTCAAAACACC 60.333 52.381 0.00 0.00 33.65 4.16
5776 5859 1.671845 GTTACACGCCTCAAAACACCA 59.328 47.619 0.00 0.00 0.00 4.17
5777 5860 1.588674 TACACGCCTCAAAACACCAG 58.411 50.000 0.00 0.00 0.00 4.00
5778 5861 0.107410 ACACGCCTCAAAACACCAGA 60.107 50.000 0.00 0.00 0.00 3.86
5779 5862 0.307760 CACGCCTCAAAACACCAGAC 59.692 55.000 0.00 0.00 0.00 3.51
5780 5863 0.107410 ACGCCTCAAAACACCAGACA 60.107 50.000 0.00 0.00 0.00 3.41
5781 5864 0.307760 CGCCTCAAAACACCAGACAC 59.692 55.000 0.00 0.00 0.00 3.67
5782 5865 1.388547 GCCTCAAAACACCAGACACA 58.611 50.000 0.00 0.00 0.00 3.72
5783 5866 1.748493 GCCTCAAAACACCAGACACAA 59.252 47.619 0.00 0.00 0.00 3.33
5784 5867 2.362077 GCCTCAAAACACCAGACACAAT 59.638 45.455 0.00 0.00 0.00 2.71
5785 5868 3.181476 GCCTCAAAACACCAGACACAATT 60.181 43.478 0.00 0.00 0.00 2.32
5786 5869 4.362279 CCTCAAAACACCAGACACAATTG 58.638 43.478 3.24 3.24 0.00 2.32
5787 5870 4.362279 CTCAAAACACCAGACACAATTGG 58.638 43.478 10.83 1.35 40.38 3.16
5788 5871 2.865551 CAAAACACCAGACACAATTGGC 59.134 45.455 10.83 0.00 38.03 4.52
5789 5872 1.039856 AACACCAGACACAATTGGCC 58.960 50.000 10.83 0.00 38.03 5.36
5790 5873 0.106268 ACACCAGACACAATTGGCCA 60.106 50.000 0.00 0.00 38.03 5.36
5791 5874 1.039068 CACCAGACACAATTGGCCAA 58.961 50.000 23.00 23.00 38.03 4.52
5792 5875 1.411977 CACCAGACACAATTGGCCAAA 59.588 47.619 24.71 6.13 38.03 3.28
5793 5876 1.412343 ACCAGACACAATTGGCCAAAC 59.588 47.619 24.71 9.79 38.03 2.93
5794 5877 1.688197 CCAGACACAATTGGCCAAACT 59.312 47.619 24.71 10.20 0.00 2.66
5795 5878 2.102925 CCAGACACAATTGGCCAAACTT 59.897 45.455 24.71 10.76 0.00 2.66
5796 5879 3.125316 CAGACACAATTGGCCAAACTTG 58.875 45.455 24.71 24.33 0.00 3.16
5797 5880 2.765699 AGACACAATTGGCCAAACTTGT 59.234 40.909 25.20 25.20 32.27 3.16
5798 5881 3.197549 AGACACAATTGGCCAAACTTGTT 59.802 39.130 27.34 20.14 29.74 2.83
5799 5882 4.404073 AGACACAATTGGCCAAACTTGTTA 59.596 37.500 27.34 3.36 29.74 2.41
5800 5883 4.438148 ACACAATTGGCCAAACTTGTTAC 58.562 39.130 27.34 0.00 29.74 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.203195 TGTCATATGGCCCAGCGC 60.203 61.111 4.54 0.00 0.00 5.92
28 29 0.464373 AAGTGTCATATGGCCCAGCG 60.464 55.000 4.54 0.00 0.00 5.18
30 31 1.406539 GCAAAGTGTCATATGGCCCAG 59.593 52.381 4.54 0.00 0.00 4.45
127 143 9.092876 TCTGCGTTTCAAAAATTCTAAAACAAT 57.907 25.926 0.00 0.00 31.72 2.71
128 144 8.467402 TCTGCGTTTCAAAAATTCTAAAACAA 57.533 26.923 0.00 0.00 31.72 2.83
130 146 8.055986 CCTTCTGCGTTTCAAAAATTCTAAAAC 58.944 33.333 0.00 0.00 0.00 2.43
144 160 0.889186 TTCTGGGCCTTCTGCGTTTC 60.889 55.000 4.53 0.00 42.61 2.78
148 164 2.437359 CCTTCTGGGCCTTCTGCG 60.437 66.667 4.53 0.00 42.61 5.18
159 175 1.729149 GCGTTCATTTTCGGCCTTCTG 60.729 52.381 0.00 0.00 0.00 3.02
160 176 0.521735 GCGTTCATTTTCGGCCTTCT 59.478 50.000 0.00 0.00 0.00 2.85
168 184 2.202427 CGGCCCGCGTTCATTTTC 60.202 61.111 4.92 0.00 0.00 2.29
185 201 1.602605 ACGCCACTTAACAAGGGCC 60.603 57.895 0.00 0.00 39.94 5.80
186 202 1.579429 CACGCCACTTAACAAGGGC 59.421 57.895 0.00 0.00 39.79 5.19
187 203 1.169661 TGCACGCCACTTAACAAGGG 61.170 55.000 0.00 0.00 0.00 3.95
188 204 0.665835 TTGCACGCCACTTAACAAGG 59.334 50.000 0.00 0.00 0.00 3.61
189 205 1.334960 CCTTGCACGCCACTTAACAAG 60.335 52.381 0.00 0.00 35.43 3.16
190 206 0.665835 CCTTGCACGCCACTTAACAA 59.334 50.000 0.00 0.00 0.00 2.83
191 207 1.791103 GCCTTGCACGCCACTTAACA 61.791 55.000 0.00 0.00 0.00 2.41
192 208 1.081442 GCCTTGCACGCCACTTAAC 60.081 57.895 0.00 0.00 0.00 2.01
193 209 2.265182 GGCCTTGCACGCCACTTAA 61.265 57.895 17.33 0.00 46.27 1.85
194 210 2.671619 GGCCTTGCACGCCACTTA 60.672 61.111 17.33 0.00 46.27 2.24
200 216 4.166011 GTGATCGGCCTTGCACGC 62.166 66.667 0.00 0.00 0.00 5.34
201 217 2.741985 TGTGATCGGCCTTGCACG 60.742 61.111 0.00 0.00 34.12 5.34
202 218 2.690778 GGTGTGATCGGCCTTGCAC 61.691 63.158 0.00 6.48 0.00 4.57
203 219 2.359850 GGTGTGATCGGCCTTGCA 60.360 61.111 0.00 0.00 0.00 4.08
204 220 3.499737 CGGTGTGATCGGCCTTGC 61.500 66.667 0.00 0.00 0.00 4.01
205 221 2.819595 CCGGTGTGATCGGCCTTG 60.820 66.667 0.00 0.00 41.07 3.61
230 246 1.202452 GCATATGAAAAGGCCTGGCAC 60.202 52.381 22.05 10.03 0.00 5.01
298 314 1.597854 CAGAGTTGTTGGGCGAGCA 60.598 57.895 0.00 0.00 0.00 4.26
811 829 0.546598 AGCTCGGGAATTTACCTGGG 59.453 55.000 0.00 0.00 39.63 4.45
878 896 1.361993 CCCGCTCTCGATCTGGAAG 59.638 63.158 0.00 0.00 38.10 3.46
879 897 2.127869 CCCCGCTCTCGATCTGGAA 61.128 63.158 0.00 0.00 38.10 3.53
901 923 2.174319 GCCACGGAGCTCGGAAATC 61.174 63.158 26.25 9.40 44.45 2.17
923 945 2.042435 AGCGGAGGGGAGAGAAGG 60.042 66.667 0.00 0.00 0.00 3.46
933 957 1.821332 GGAGGATTTGCAGCGGAGG 60.821 63.158 0.00 0.00 0.00 4.30
978 1002 3.460868 GCAAAATCCCCCTGCCGG 61.461 66.667 0.00 0.00 0.00 6.13
987 1011 0.395724 ACCCCATCGGAGCAAAATCC 60.396 55.000 0.00 0.00 35.88 3.01
1077 1101 0.103026 TCACATCAGAATCTCCCGCG 59.897 55.000 0.00 0.00 0.00 6.46
1089 1119 1.221566 CTCCGCCATGGTCACATCA 59.778 57.895 14.67 0.00 39.52 3.07
1349 1385 1.882352 CGGTAAAAGCTCCAGCCTTGT 60.882 52.381 0.00 0.00 43.38 3.16
1365 1401 2.499205 CAATCAGGCTCGCCGGTA 59.501 61.111 1.90 0.00 41.95 4.02
1400 1436 1.199327 CAGAAGCACCAGCAACATCTG 59.801 52.381 0.00 0.00 45.49 2.90
1457 1493 2.828877 CAGTACACGGAAAAGTGACCA 58.171 47.619 4.00 0.00 44.43 4.02
1483 1519 3.877559 CCTAGAAACAGTGGCATCATCA 58.122 45.455 0.00 0.00 0.00 3.07
1485 1521 2.648059 GCCTAGAAACAGTGGCATCAT 58.352 47.619 0.00 0.00 44.34 2.45
1486 1522 2.113860 GCCTAGAAACAGTGGCATCA 57.886 50.000 0.00 0.00 44.34 3.07
1504 1540 4.676924 GGAAATATTATTCAACGCTGCAGC 59.323 41.667 29.12 29.12 37.78 5.25
1526 1562 2.668457 CGGATTCTGAAACGAAGTGAGG 59.332 50.000 10.99 0.00 45.00 3.86
1528 1564 2.036733 ACCGGATTCTGAAACGAAGTGA 59.963 45.455 9.46 0.00 45.00 3.41
1558 1594 6.002704 GGTTGCATTGAGATGATATTCTCCT 58.997 40.000 2.63 0.00 41.24 3.69
1559 1595 5.182760 GGGTTGCATTGAGATGATATTCTCC 59.817 44.000 2.63 0.00 41.24 3.71
1560 1596 5.182760 GGGGTTGCATTGAGATGATATTCTC 59.817 44.000 0.00 0.00 42.10 2.87
1571 1607 1.880819 GCCACAGGGGTTGCATTGAG 61.881 60.000 0.00 0.00 39.65 3.02
1939 1975 5.316167 TCAAGTGCATAATTGACAGAACCT 58.684 37.500 7.61 0.00 36.12 3.50
2596 2632 5.549742 TTTCATTCTGGGACTTTGCAATT 57.450 34.783 0.00 0.00 0.00 2.32
2885 2921 4.285775 CCTCTTCTTTCTCCTCCTCTTTGT 59.714 45.833 0.00 0.00 0.00 2.83
3327 3363 9.855021 ACACAATTTTAATAGTATTTGTGCTCC 57.145 29.630 18.30 0.00 0.00 4.70
3664 3703 5.904362 ACTTCAGCTTTCTCAGTTTTGTT 57.096 34.783 0.00 0.00 0.00 2.83
3686 3725 2.571202 TCACCTGATGATGGCTGTACAA 59.429 45.455 0.00 0.00 29.99 2.41
3773 3845 1.301716 GCTTGCTGGACGGTCTCAA 60.302 57.895 8.23 8.94 0.00 3.02
3774 3846 1.830587 ATGCTTGCTGGACGGTCTCA 61.831 55.000 8.23 3.83 0.00 3.27
3775 3847 1.078848 ATGCTTGCTGGACGGTCTC 60.079 57.895 8.23 0.00 0.00 3.36
3776 3848 1.376424 CATGCTTGCTGGACGGTCT 60.376 57.895 8.23 0.00 0.00 3.85
3777 3849 3.044059 GCATGCTTGCTGGACGGTC 62.044 63.158 16.80 0.00 45.77 4.79
3778 3850 3.058160 GCATGCTTGCTGGACGGT 61.058 61.111 16.80 0.00 45.77 4.83
3787 3859 0.389426 GCTTCAGGTTGGCATGCTTG 60.389 55.000 18.92 8.73 0.00 4.01
3788 3860 0.541296 AGCTTCAGGTTGGCATGCTT 60.541 50.000 18.92 0.00 0.00 3.91
3789 3861 1.076192 AGCTTCAGGTTGGCATGCT 59.924 52.632 18.92 0.00 0.00 3.79
3790 3862 1.214589 CAGCTTCAGGTTGGCATGC 59.785 57.895 9.90 9.90 0.00 4.06
3791 3863 0.524862 GTCAGCTTCAGGTTGGCATG 59.475 55.000 0.00 0.00 31.01 4.06
3792 3864 0.957395 CGTCAGCTTCAGGTTGGCAT 60.957 55.000 0.00 0.00 29.98 4.40
3793 3865 1.597854 CGTCAGCTTCAGGTTGGCA 60.598 57.895 0.00 0.00 29.98 4.92
3794 3866 2.970974 GCGTCAGCTTCAGGTTGGC 61.971 63.158 0.00 0.00 41.01 4.52
3795 3867 3.257933 GCGTCAGCTTCAGGTTGG 58.742 61.111 0.00 0.00 41.01 3.77
3805 3877 1.531149 TGCTTTCTTAACAGCGTCAGC 59.469 47.619 0.00 0.00 45.58 4.26
3852 3924 2.964464 TGTTGCAATTTGGTCAGATGGT 59.036 40.909 0.59 0.00 0.00 3.55
3896 3968 4.503741 TCTTTTGGAGCTTGATTTTCCG 57.496 40.909 0.00 0.00 33.60 4.30
4060 4132 1.164041 GCTGCTGTACCCACGTGTTT 61.164 55.000 15.65 2.89 0.00 2.83
4086 4158 4.833380 TCAGTTAGGTCTTTAGCAGTGTCT 59.167 41.667 0.00 0.00 0.00 3.41
4145 4217 1.106944 AGCAGTTTTGGGTTCCACGG 61.107 55.000 0.00 0.00 30.78 4.94
4176 4248 0.034059 CGGGACAGCTGACTTGTTCT 59.966 55.000 23.35 0.00 0.00 3.01
4338 4413 5.297029 CCCTGCAGTAGCTTTATTTTCTACC 59.703 44.000 13.81 0.00 42.74 3.18
4345 4420 3.264450 AGTGTCCCTGCAGTAGCTTTATT 59.736 43.478 13.81 0.00 42.74 1.40
4579 4654 2.767505 AGCCTTCTTACCTCGTGTTTG 58.232 47.619 0.00 0.00 0.00 2.93
4663 4738 1.814429 TCCTCCACTGGTTTCTTGGA 58.186 50.000 0.00 0.00 37.07 3.53
4698 4773 1.448540 CGCAGCTTTCTCATCCCGT 60.449 57.895 0.00 0.00 0.00 5.28
4734 4809 3.485346 TTCAACCGTGGCACCCTCC 62.485 63.158 12.86 0.00 0.00 4.30
4749 4824 2.039480 AGCTTTCTCATCTGGCACTTCA 59.961 45.455 0.00 0.00 0.00 3.02
4754 4829 3.198417 TGTCATAGCTTTCTCATCTGGCA 59.802 43.478 0.00 0.00 0.00 4.92
4779 4854 3.785859 GCCATGGCGTCCTCCTCA 61.786 66.667 23.48 0.00 0.00 3.86
4842 4917 1.999735 CAAGAATTCGCCGTGAGCTAA 59.000 47.619 0.00 0.00 40.39 3.09
4876 4951 3.306156 GGTCGGGCAGATAGATTACCTTC 60.306 52.174 0.00 0.00 0.00 3.46
4895 4970 1.522569 CTGATGGGGAGAACCGGTC 59.477 63.158 8.04 0.95 41.60 4.79
4943 5018 1.550327 TGCTAGGGTCAGACAGACTG 58.450 55.000 2.17 0.00 46.72 3.51
5181 5256 2.115427 TCCCAGCAGATTCAACCGATA 58.885 47.619 0.00 0.00 0.00 2.92
5182 5257 0.911769 TCCCAGCAGATTCAACCGAT 59.088 50.000 0.00 0.00 0.00 4.18
5501 5582 4.225942 ACTGAAGTCCAGCCATAGATTTCA 59.774 41.667 0.00 0.00 46.81 2.69
5527 5608 1.308998 GGCCACAATATGAAGTCCGG 58.691 55.000 0.00 0.00 0.00 5.14
5528 5609 2.036958 TGGCCACAATATGAAGTCCG 57.963 50.000 0.00 0.00 0.00 4.79
5535 5616 3.181473 CCTGACCAATTGGCCACAATATG 60.181 47.826 24.79 6.44 46.25 1.78
5537 5618 2.225242 ACCTGACCAATTGGCCACAATA 60.225 45.455 24.79 0.00 46.25 1.90
5590 5672 9.844257 AAATTCTATGAATCAAAGAGGTCTAGG 57.156 33.333 0.00 0.00 0.00 3.02
5678 5761 1.068434 ACATGTTTCGCCACCCAAAAG 59.932 47.619 0.00 0.00 0.00 2.27
5681 5764 1.609555 GTAACATGTTTCGCCACCCAA 59.390 47.619 17.78 0.00 0.00 4.12
5683 5766 1.240256 TGTAACATGTTTCGCCACCC 58.760 50.000 17.78 0.00 0.00 4.61
5696 5779 4.158579 TGTGTTTTGAGGCATGTTGTAACA 59.841 37.500 0.00 0.00 44.06 2.41
5712 5795 2.287769 GCCAATTGTGCCTTGTGTTTT 58.712 42.857 4.43 0.00 0.00 2.43
5737 5820 2.235891 ACGGATTTCACCCTGTTTTCC 58.764 47.619 0.00 0.00 0.00 3.13
5763 5846 1.388547 TGTGTCTGGTGTTTTGAGGC 58.611 50.000 0.00 0.00 0.00 4.70
5764 5847 4.362279 CAATTGTGTCTGGTGTTTTGAGG 58.638 43.478 0.00 0.00 0.00 3.86
5765 5848 4.362279 CCAATTGTGTCTGGTGTTTTGAG 58.638 43.478 4.43 0.00 0.00 3.02
5766 5849 3.430098 GCCAATTGTGTCTGGTGTTTTGA 60.430 43.478 4.43 0.00 34.97 2.69
5767 5850 2.865551 GCCAATTGTGTCTGGTGTTTTG 59.134 45.455 4.43 0.00 34.97 2.44
5768 5851 2.158971 GGCCAATTGTGTCTGGTGTTTT 60.159 45.455 4.43 0.00 34.97 2.43
5769 5852 1.412343 GGCCAATTGTGTCTGGTGTTT 59.588 47.619 4.43 0.00 34.97 2.83
5770 5853 1.039856 GGCCAATTGTGTCTGGTGTT 58.960 50.000 4.43 0.00 34.97 3.32
5771 5854 0.106268 TGGCCAATTGTGTCTGGTGT 60.106 50.000 0.61 0.00 34.97 4.16
5772 5855 1.039068 TTGGCCAATTGTGTCTGGTG 58.961 50.000 16.05 0.00 34.97 4.17
5773 5856 1.412343 GTTTGGCCAATTGTGTCTGGT 59.588 47.619 21.26 0.00 34.97 4.00
5774 5857 1.688197 AGTTTGGCCAATTGTGTCTGG 59.312 47.619 21.26 0.00 35.67 3.86
5775 5858 3.125316 CAAGTTTGGCCAATTGTGTCTG 58.875 45.455 21.26 6.43 0.00 3.51
5776 5859 2.765699 ACAAGTTTGGCCAATTGTGTCT 59.234 40.909 28.44 14.38 34.71 3.41
5777 5860 3.177997 ACAAGTTTGGCCAATTGTGTC 57.822 42.857 28.44 12.73 34.71 3.67
5778 5861 3.625649 AACAAGTTTGGCCAATTGTGT 57.374 38.095 29.27 23.63 36.09 3.72


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

AutoCloner maintained by Alex Coulton.