Multiple sequence alignment - TraesCS1B01G142000

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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 TraesCS1B01G142000 chr1B 100.000 5160 0 0 1 5160 189719772 189714613 0.000000e+00 9529.0
1 TraesCS1B01G142000 chr1D 93.844 4873 146 40 2 4784 125868964 125864156 0.000000e+00 7195.0
2 TraesCS1B01G142000 chr1D 98.788 165 2 0 4996 5160 125864155 125863991 1.410000e-75 294.0
3 TraesCS1B01G142000 chr1A 95.428 2034 69 9 2496 4518 139638723 139636703 0.000000e+00 3219.0
4 TraesCS1B01G142000 chr1A 91.566 2146 80 28 423 2491 139641682 139639561 0.000000e+00 2867.0
5 TraesCS1B01G142000 chr1A 88.503 461 27 10 5 448 139642156 139641705 7.610000e-148 534.0
6 TraesCS1B01G142000 chr1A 86.799 303 23 13 4616 4908 139636583 139636288 6.450000e-84 322.0
7 TraesCS1B01G142000 chr2D 96.403 139 4 1 205 342 168153938 168153800 1.450000e-55 228.0
8 TraesCS1B01G142000 chr7A 94.964 139 6 1 205 342 462450620 462450758 3.130000e-52 217.0
9 TraesCS1B01G142000 chr7A 86.154 65 8 1 4554 4618 107598316 107598253 9.270000e-08 69.4
10 TraesCS1B01G142000 chr7D 93.478 138 8 1 206 342 403929711 403929848 2.440000e-48 204.0


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 TraesCS1B01G142000 chr1B 189714613 189719772 5159 True 9529.0 9529 100.000 1 5160 1 chr1B.!!$R1 5159
1 TraesCS1B01G142000 chr1D 125863991 125868964 4973 True 3744.5 7195 96.316 2 5160 2 chr1D.!!$R1 5158
2 TraesCS1B01G142000 chr1A 139636288 139642156 5868 True 1735.5 3219 90.574 5 4908 4 chr1A.!!$R1 4903

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
487 552 0.036875 AAACTCCCTTCTCGCCAAGG 59.963 55.0 5.45 5.45 42.57 3.61 F
932 1030 0.329596 ATCAGCGGCCTTCTTTTCCT 59.670 50.0 0.00 0.00 0.00 3.36 F
933 1031 0.606401 TCAGCGGCCTTCTTTTCCTG 60.606 55.0 0.00 0.00 0.00 3.86 F
2562 3542 0.602638 TGTTTGGCTTCATCGCGTCT 60.603 50.0 5.77 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 1735 1.154225 GGACACGCGGATGCAAAAG 60.154 57.895 12.47 0.00 42.97 2.27 R
2562 3542 0.310543 CAACAAACTTGGCTAGCGCA 59.689 50.000 11.47 5.17 38.10 6.09 R
2836 3816 2.351726 GCAATTCCGCGACTACATCTTT 59.648 45.455 8.23 0.00 0.00 2.52 R
4402 5408 1.380524 TTTCAGCCGTTCGGAAAACA 58.619 45.000 15.69 0.00 36.25 2.83 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
145 146 8.712363 CAGATTTTCTTCGAAGTCTTGTAATGA 58.288 33.333 23.85 0.00 0.00 2.57
161 162 9.856488 TCTTGTAATGACTGATTGTAACTCTAC 57.144 33.333 0.00 0.00 0.00 2.59
162 163 9.862371 CTTGTAATGACTGATTGTAACTCTACT 57.138 33.333 0.00 0.00 0.00 2.57
370 385 3.773560 TCCAAACAACCCCTTATCCAAG 58.226 45.455 0.00 0.00 0.00 3.61
446 511 3.495753 ACACGTGTTTTAGGATCGAAACC 59.504 43.478 17.22 0.00 35.44 3.27
453 518 1.200519 TAGGATCGAAACCACCCCTG 58.799 55.000 13.17 0.00 0.00 4.45
485 550 2.358322 AAAAACTCCCTTCTCGCCAA 57.642 45.000 0.00 0.00 0.00 4.52
486 551 1.897560 AAAACTCCCTTCTCGCCAAG 58.102 50.000 0.00 0.00 0.00 3.61
487 552 0.036875 AAACTCCCTTCTCGCCAAGG 59.963 55.000 5.45 5.45 42.57 3.61
518 584 1.135024 CCTGATTCCCCGCATGTTTTG 60.135 52.381 0.00 0.00 0.00 2.44
709 779 4.853924 AAACAACAAGATAAGCACCAGG 57.146 40.909 0.00 0.00 0.00 4.45
884 962 3.638627 ACAGCCCAAGAAAGAAAAGAAGG 59.361 43.478 0.00 0.00 0.00 3.46
932 1030 0.329596 ATCAGCGGCCTTCTTTTCCT 59.670 50.000 0.00 0.00 0.00 3.36
933 1031 0.606401 TCAGCGGCCTTCTTTTCCTG 60.606 55.000 0.00 0.00 0.00 3.86
934 1032 1.973812 AGCGGCCTTCTTTTCCTGC 60.974 57.895 0.00 0.00 0.00 4.85
935 1033 2.870372 CGGCCTTCTTTTCCTGCG 59.130 61.111 0.00 0.00 0.00 5.18
936 1034 2.690778 CGGCCTTCTTTTCCTGCGG 61.691 63.158 0.00 0.00 0.00 5.69
1240 1362 7.940688 TCAATCTGCTCATGGTAATACATCAAT 59.059 33.333 0.00 0.00 0.00 2.57
1363 1485 4.383173 CAGGAAGCAGCACACATATGATA 58.617 43.478 10.38 0.00 0.00 2.15
1364 1486 4.212847 CAGGAAGCAGCACACATATGATAC 59.787 45.833 10.38 0.00 0.00 2.24
1512 1653 1.195115 GCTGACAGATGGTGGGAGTA 58.805 55.000 6.65 0.00 0.00 2.59
1575 1716 3.618698 CATGTGACGGATCGTAGTACTG 58.381 50.000 5.39 0.00 41.37 2.74
1785 1930 6.693978 GTGGAACGTTTGCTGTTTAATAACTT 59.306 34.615 0.46 0.00 35.24 2.66
1832 1977 9.390795 CAGCGAATTCCATTTGAATATTCTTAG 57.609 33.333 16.24 4.35 42.97 2.18
1916 2063 9.592196 TTCTAAAAGAACTTAGTACTACCTCCA 57.408 33.333 0.91 0.00 31.86 3.86
2426 2573 1.196766 TCACCTCATGTCAGGCAGCT 61.197 55.000 0.33 0.00 36.98 4.24
2562 3542 0.602638 TGTTTGGCTTCATCGCGTCT 60.603 50.000 5.77 0.00 0.00 4.18
2762 3742 5.105635 TGGAGATGCATTCAAGAAAATCCAC 60.106 40.000 0.00 0.00 0.00 4.02
2796 3776 2.512485 TGTGCCATTTGCTTGACAAG 57.488 45.000 11.02 11.02 40.06 3.16
2881 3861 0.255890 GGCCATGGAGAAGCAAGGTA 59.744 55.000 18.40 0.00 0.00 3.08
2917 3897 2.029290 TCTGCGTTGGTAGGTTCTCTTC 60.029 50.000 0.00 0.00 0.00 2.87
3022 4003 8.100164 TGACATTACTTGTTCATGGTTCAGATA 58.900 33.333 0.00 0.00 39.18 1.98
3116 4097 3.780925 GGCTCAAATGCCGCATATC 57.219 52.632 6.22 0.00 43.74 1.63
3401 4382 3.813166 GCAAGCTTGTAGGACTTACACAA 59.187 43.478 26.55 0.00 41.86 3.33
3404 4385 6.373779 CAAGCTTGTAGGACTTACACAATTG 58.626 40.000 18.65 3.24 41.86 2.32
3411 4399 5.862924 AGGACTTACACAATTGTCATTCG 57.137 39.130 8.48 0.00 37.15 3.34
3425 4413 7.972832 ATTGTCATTCGTGTTAAACCTTAGA 57.027 32.000 0.00 0.00 0.00 2.10
3454 4442 7.555087 CAATGCCCTAACATTCATTTCCTTTA 58.445 34.615 0.00 0.00 38.19 1.85
3537 4525 0.953960 AAAATCGCCTCGCGGTCTTT 60.954 50.000 6.13 1.93 44.10 2.52
3625 4613 4.669728 GCTAACTGTGTTATACGTAGCGAG 59.330 45.833 0.08 0.00 0.00 5.03
3766 4754 2.398588 AGGACTCCTGATATTTCCGCA 58.601 47.619 0.00 0.00 29.57 5.69
3871 4859 0.663688 CTCGGAAGATGGTCGTCGAT 59.336 55.000 0.00 0.00 40.84 3.59
4205 5193 4.036734 ACAGTGGCTGTTGTTATTTGACTG 59.963 41.667 0.00 0.00 42.59 3.51
4258 5246 6.375455 CCTTATGTGCCTCTGTCAAACTAATT 59.625 38.462 0.00 0.00 0.00 1.40
4317 5314 1.650645 GCGTCTTAAGTTCGTAACCGG 59.349 52.381 18.10 0.00 33.95 5.28
4353 5358 6.491745 TGTTGCATAGAAACCAATTTAGGACA 59.508 34.615 0.00 0.00 0.00 4.02
4356 5361 7.546358 TGCATAGAAACCAATTTAGGACATTG 58.454 34.615 0.00 0.00 0.00 2.82
4359 5364 5.086621 AGAAACCAATTTAGGACATTGCCT 58.913 37.500 5.23 5.23 42.15 4.75
4402 5408 3.032265 AGTGGAACAGGGCTTTTCTTT 57.968 42.857 0.00 0.00 41.80 2.52
4414 5420 3.242016 GGCTTTTCTTTGTTTTCCGAACG 59.758 43.478 0.00 0.00 0.00 3.95
4446 5452 8.738645 AATAGAGCTGGTTACTAAATTTCTGG 57.261 34.615 0.00 0.00 0.00 3.86
4543 5549 6.906157 ATTGTCATTGGATGTTGAACTTCT 57.094 33.333 10.46 0.00 0.00 2.85
4587 5593 0.104487 CATCACTCGATGCAGAGGCT 59.896 55.000 7.77 0.00 42.54 4.58
4595 5601 1.003442 ATGCAGAGGCTGAGGGGTA 59.997 57.895 0.00 0.00 41.91 3.69
4672 5701 7.920151 TGAATAAATGGAAATGTTATCAAGGCG 59.080 33.333 0.00 0.00 0.00 5.52
4719 5749 6.378582 ACGTTGGCAATGTAAATTAACAGAG 58.621 36.000 22.90 0.00 31.70 3.35
4786 5821 6.403200 CGAACAAATACCGAATTCTTGGTCAT 60.403 38.462 17.57 4.52 39.70 3.06
4834 5871 7.962918 ACATTTTAGACGCAAACACATATCTTC 59.037 33.333 0.00 0.00 0.00 2.87
4855 5892 6.816640 TCTTCGTTGGAGTTGGTAGAATAATG 59.183 38.462 0.00 0.00 0.00 1.90
4867 5904 9.895138 GTTGGTAGAATAATGTAGGGTAAGAAA 57.105 33.333 0.00 0.00 0.00 2.52
4893 5930 8.624701 ACATTCATTTCTCAAATATTGCTTCG 57.375 30.769 0.00 0.00 0.00 3.79
4894 5931 8.461222 ACATTCATTTCTCAAATATTGCTTCGA 58.539 29.630 0.00 0.00 0.00 3.71
4895 5932 8.740369 CATTCATTTCTCAAATATTGCTTCGAC 58.260 33.333 0.00 0.00 0.00 4.20
4896 5933 7.615582 TCATTTCTCAAATATTGCTTCGACT 57.384 32.000 0.00 0.00 0.00 4.18
4897 5934 7.688372 TCATTTCTCAAATATTGCTTCGACTC 58.312 34.615 0.00 0.00 0.00 3.36
4898 5935 7.550551 TCATTTCTCAAATATTGCTTCGACTCT 59.449 33.333 0.00 0.00 0.00 3.24
4899 5936 8.820933 CATTTCTCAAATATTGCTTCGACTCTA 58.179 33.333 0.00 0.00 0.00 2.43
4901 5938 8.771920 TTCTCAAATATTGCTTCGACTCTAAA 57.228 30.769 0.00 0.00 0.00 1.85
4902 5939 8.771920 TCTCAAATATTGCTTCGACTCTAAAA 57.228 30.769 0.00 0.00 0.00 1.52
4903 5940 8.656849 TCTCAAATATTGCTTCGACTCTAAAAC 58.343 33.333 0.00 0.00 0.00 2.43
4904 5941 8.547967 TCAAATATTGCTTCGACTCTAAAACT 57.452 30.769 0.00 0.00 0.00 2.66
4905 5942 9.647797 TCAAATATTGCTTCGACTCTAAAACTA 57.352 29.630 0.00 0.00 0.00 2.24
4906 5943 9.690434 CAAATATTGCTTCGACTCTAAAACTAC 57.310 33.333 0.00 0.00 0.00 2.73
4907 5944 7.681125 ATATTGCTTCGACTCTAAAACTACG 57.319 36.000 0.00 0.00 0.00 3.51
4908 5945 3.240069 TGCTTCGACTCTAAAACTACGC 58.760 45.455 0.00 0.00 0.00 4.42
4909 5946 3.240069 GCTTCGACTCTAAAACTACGCA 58.760 45.455 0.00 0.00 0.00 5.24
4910 5947 3.671928 GCTTCGACTCTAAAACTACGCAA 59.328 43.478 0.00 0.00 0.00 4.85
4911 5948 4.149396 GCTTCGACTCTAAAACTACGCAAA 59.851 41.667 0.00 0.00 0.00 3.68
4912 5949 5.163982 GCTTCGACTCTAAAACTACGCAAAT 60.164 40.000 0.00 0.00 0.00 2.32
4913 5950 6.034256 GCTTCGACTCTAAAACTACGCAAATA 59.966 38.462 0.00 0.00 0.00 1.40
4914 5951 7.411157 GCTTCGACTCTAAAACTACGCAAATAA 60.411 37.037 0.00 0.00 0.00 1.40
4915 5952 8.470040 TTCGACTCTAAAACTACGCAAATAAT 57.530 30.769 0.00 0.00 0.00 1.28
4916 5953 8.112099 TCGACTCTAAAACTACGCAAATAATC 57.888 34.615 0.00 0.00 0.00 1.75
4917 5954 7.044510 TCGACTCTAAAACTACGCAAATAATCG 60.045 37.037 0.00 0.00 0.00 3.34
4918 5955 6.702897 ACTCTAAAACTACGCAAATAATCGC 58.297 36.000 0.00 0.00 0.00 4.58
4919 5956 6.039781 TCTAAAACTACGCAAATAATCGCC 57.960 37.500 0.00 0.00 0.00 5.54
4920 5957 4.688511 AAAACTACGCAAATAATCGCCA 57.311 36.364 0.00 0.00 0.00 5.69
4921 5958 4.688511 AAACTACGCAAATAATCGCCAA 57.311 36.364 0.00 0.00 0.00 4.52
4922 5959 4.688511 AACTACGCAAATAATCGCCAAA 57.311 36.364 0.00 0.00 0.00 3.28
4923 5960 4.011058 ACTACGCAAATAATCGCCAAAC 57.989 40.909 0.00 0.00 0.00 2.93
4924 5961 2.271821 ACGCAAATAATCGCCAAACC 57.728 45.000 0.00 0.00 0.00 3.27
4925 5962 1.816224 ACGCAAATAATCGCCAAACCT 59.184 42.857 0.00 0.00 0.00 3.50
4926 5963 2.159435 ACGCAAATAATCGCCAAACCTC 60.159 45.455 0.00 0.00 0.00 3.85
4927 5964 2.159448 CGCAAATAATCGCCAAACCTCA 60.159 45.455 0.00 0.00 0.00 3.86
4928 5965 3.671971 CGCAAATAATCGCCAAACCTCAA 60.672 43.478 0.00 0.00 0.00 3.02
4929 5966 4.241681 GCAAATAATCGCCAAACCTCAAA 58.758 39.130 0.00 0.00 0.00 2.69
4930 5967 4.688413 GCAAATAATCGCCAAACCTCAAAA 59.312 37.500 0.00 0.00 0.00 2.44
4931 5968 5.389411 GCAAATAATCGCCAAACCTCAAAAC 60.389 40.000 0.00 0.00 0.00 2.43
4932 5969 5.722021 AATAATCGCCAAACCTCAAAACT 57.278 34.783 0.00 0.00 0.00 2.66
4933 5970 6.827586 AATAATCGCCAAACCTCAAAACTA 57.172 33.333 0.00 0.00 0.00 2.24
4934 5971 4.766404 AATCGCCAAACCTCAAAACTAG 57.234 40.909 0.00 0.00 0.00 2.57
4935 5972 3.202829 TCGCCAAACCTCAAAACTAGT 57.797 42.857 0.00 0.00 0.00 2.57
4936 5973 3.547746 TCGCCAAACCTCAAAACTAGTT 58.452 40.909 1.12 1.12 0.00 2.24
4937 5974 4.706035 TCGCCAAACCTCAAAACTAGTTA 58.294 39.130 8.92 0.00 0.00 2.24
4938 5975 5.124645 TCGCCAAACCTCAAAACTAGTTAA 58.875 37.500 8.92 0.00 0.00 2.01
4939 5976 5.589452 TCGCCAAACCTCAAAACTAGTTAAA 59.411 36.000 8.92 0.00 0.00 1.52
4940 5977 6.095160 TCGCCAAACCTCAAAACTAGTTAAAA 59.905 34.615 8.92 0.00 0.00 1.52
4941 5978 6.752815 CGCCAAACCTCAAAACTAGTTAAAAA 59.247 34.615 8.92 0.00 0.00 1.94
4959 5996 1.168714 AAAAATGCGCTCCTCAGACC 58.831 50.000 9.73 0.00 0.00 3.85
4960 5997 0.036732 AAAATGCGCTCCTCAGACCA 59.963 50.000 9.73 0.00 0.00 4.02
4961 5998 0.254178 AAATGCGCTCCTCAGACCAT 59.746 50.000 9.73 0.00 0.00 3.55
4962 5999 0.254178 AATGCGCTCCTCAGACCATT 59.746 50.000 9.73 0.00 0.00 3.16
4963 6000 1.123077 ATGCGCTCCTCAGACCATTA 58.877 50.000 9.73 0.00 0.00 1.90
4964 6001 0.175760 TGCGCTCCTCAGACCATTAC 59.824 55.000 9.73 0.00 0.00 1.89
4965 6002 0.175760 GCGCTCCTCAGACCATTACA 59.824 55.000 0.00 0.00 0.00 2.41
4966 6003 1.405526 GCGCTCCTCAGACCATTACAA 60.406 52.381 0.00 0.00 0.00 2.41
4967 6004 2.935238 GCGCTCCTCAGACCATTACAAA 60.935 50.000 0.00 0.00 0.00 2.83
4968 6005 3.334691 CGCTCCTCAGACCATTACAAAA 58.665 45.455 0.00 0.00 0.00 2.44
4969 6006 3.372206 CGCTCCTCAGACCATTACAAAAG 59.628 47.826 0.00 0.00 0.00 2.27
4970 6007 3.127721 GCTCCTCAGACCATTACAAAAGC 59.872 47.826 0.00 0.00 0.00 3.51
4971 6008 3.334691 TCCTCAGACCATTACAAAAGCG 58.665 45.455 0.00 0.00 0.00 4.68
4972 6009 2.420022 CCTCAGACCATTACAAAAGCGG 59.580 50.000 0.00 0.00 0.00 5.52
4973 6010 3.074412 CTCAGACCATTACAAAAGCGGT 58.926 45.455 0.00 0.00 0.00 5.68
4974 6011 3.482436 TCAGACCATTACAAAAGCGGTT 58.518 40.909 0.00 0.00 0.00 4.44
4975 6012 3.886505 TCAGACCATTACAAAAGCGGTTT 59.113 39.130 6.80 6.80 0.00 3.27
4976 6013 4.339814 TCAGACCATTACAAAAGCGGTTTT 59.660 37.500 19.03 19.03 36.22 2.43
4988 6025 6.385649 AAAAGCGGTTTTGAGACTATTTCA 57.614 33.333 23.38 0.00 34.44 2.69
4989 6026 6.385649 AAAGCGGTTTTGAGACTATTTCAA 57.614 33.333 6.80 0.00 33.00 2.69
4990 6027 6.385649 AAGCGGTTTTGAGACTATTTCAAA 57.614 33.333 0.00 0.00 41.40 2.69
4991 6028 6.002062 AGCGGTTTTGAGACTATTTCAAAG 57.998 37.500 1.37 0.00 43.22 2.77
4992 6029 5.531287 AGCGGTTTTGAGACTATTTCAAAGT 59.469 36.000 1.37 0.00 43.22 2.66
4993 6030 6.708949 AGCGGTTTTGAGACTATTTCAAAGTA 59.291 34.615 1.37 0.00 43.22 2.24
4994 6031 7.015877 GCGGTTTTGAGACTATTTCAAAGTAG 58.984 38.462 1.37 0.00 43.22 2.57
5012 6049 3.511934 AGTAGTCTGACTTGATGTGGTCC 59.488 47.826 16.53 0.00 0.00 4.46
5153 6190 7.595819 AATAGACAAACCCAAAATCAGAACA 57.404 32.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.405823 TTAAACTCCCGTTCGTCCAAT 57.594 42.857 0.00 0.00 31.66 3.16
97 98 0.532115 GCCTTATGCAACCAACAGGG 59.468 55.000 0.00 0.00 40.96 4.45
113 114 4.646572 ACTTCGAAGAAAATCTGAAGCCT 58.353 39.130 31.08 0.52 45.90 4.58
161 162 9.778741 ACTGTATCCAAACAACCACATATATAG 57.221 33.333 0.00 0.00 0.00 1.31
163 164 9.120538 GAACTGTATCCAAACAACCACATATAT 57.879 33.333 0.00 0.00 0.00 0.86
164 165 8.103935 TGAACTGTATCCAAACAACCACATATA 58.896 33.333 0.00 0.00 0.00 0.86
165 166 6.945435 TGAACTGTATCCAAACAACCACATAT 59.055 34.615 0.00 0.00 0.00 1.78
167 168 5.136828 TGAACTGTATCCAAACAACCACAT 58.863 37.500 0.00 0.00 0.00 3.21
168 169 4.527944 TGAACTGTATCCAAACAACCACA 58.472 39.130 0.00 0.00 0.00 4.17
169 170 4.578928 ACTGAACTGTATCCAAACAACCAC 59.421 41.667 0.00 0.00 0.00 4.16
170 171 4.787551 ACTGAACTGTATCCAAACAACCA 58.212 39.130 0.00 0.00 0.00 3.67
171 172 5.767816 AACTGAACTGTATCCAAACAACC 57.232 39.130 0.00 0.00 0.00 3.77
172 173 9.233232 CTAAAAACTGAACTGTATCCAAACAAC 57.767 33.333 0.00 0.00 0.00 3.32
173 174 9.179909 TCTAAAAACTGAACTGTATCCAAACAA 57.820 29.630 0.00 0.00 0.00 2.83
174 175 8.740123 TCTAAAAACTGAACTGTATCCAAACA 57.260 30.769 0.00 0.00 0.00 2.83
305 320 6.576662 TTCAGATCGATGGGTCTAATCTAC 57.423 41.667 0.54 0.00 0.00 2.59
320 335 6.360947 CGTACTTATCCAGTTCATTCAGATCG 59.639 42.308 0.00 0.00 36.88 3.69
441 506 3.217321 AACCAACAGGGGTGGTTTC 57.783 52.632 12.72 0.00 42.65 2.78
446 511 1.715785 ATTCCAAACCAACAGGGGTG 58.284 50.000 0.00 0.00 41.32 4.61
453 518 6.169557 AGGGAGTTTTTATTCCAAACCAAC 57.830 37.500 0.00 0.00 35.10 3.77
518 584 4.154015 GCCATGGCAAAATAAGGTTTGTTC 59.846 41.667 32.08 0.00 40.06 3.18
709 779 3.011760 CTGCGTCGGCTTCGGAAAC 62.012 63.158 0.00 0.00 40.82 2.78
833 911 2.457366 ACAAGATTCAGTCGTGGGAC 57.543 50.000 0.00 0.00 40.16 4.46
839 917 1.336877 TCGCGAACAAGATTCAGTCG 58.663 50.000 6.20 0.00 0.00 4.18
884 962 2.618053 GTGAGCCGTATATATGGTGGC 58.382 52.381 19.99 14.17 46.07 5.01
934 1032 3.181967 CGAGAACCAAGCGAGCCG 61.182 66.667 0.00 0.00 0.00 5.52
935 1033 2.815647 CCGAGAACCAAGCGAGCC 60.816 66.667 0.00 0.00 0.00 4.70
936 1034 1.668151 AACCGAGAACCAAGCGAGC 60.668 57.895 0.00 0.00 0.00 5.03
1136 1258 0.661552 CATCTTGATCTTGCTGCCGG 59.338 55.000 0.00 0.00 0.00 6.13
1254 1376 5.639082 GTCCGAGAAATTTGCCATGAAAAAT 59.361 36.000 0.00 0.00 0.00 1.82
1363 1485 1.964552 GCAGAGCCATCAATGCTAGT 58.035 50.000 0.00 0.00 39.69 2.57
1590 1735 1.154225 GGACACGCGGATGCAAAAG 60.154 57.895 12.47 0.00 42.97 2.27
1785 1930 4.314440 AGAAGGCGTTCGCAGGCA 62.314 61.111 18.46 0.00 37.79 4.75
1832 1977 7.784633 ATAACTTCAAGCTCTAGAAAGCATC 57.215 36.000 6.73 0.00 45.00 3.91
1861 2006 4.036262 CCCACTTCGTTGAAATTCAAGTCA 59.964 41.667 8.88 0.00 37.00 3.41
2006 2153 6.472016 TGAAGAATATTTGGTGCTGTAGACA 58.528 36.000 0.00 0.00 0.00 3.41
2426 2573 1.548719 AGCATGTGTACTAACCGCAGA 59.451 47.619 0.00 0.00 0.00 4.26
2562 3542 0.310543 CAACAAACTTGGCTAGCGCA 59.689 50.000 11.47 5.17 38.10 6.09
2836 3816 2.351726 GCAATTCCGCGACTACATCTTT 59.648 45.455 8.23 0.00 0.00 2.52
2917 3897 3.186119 GCATCGGTTCAGAAGAGAAGAG 58.814 50.000 0.00 0.00 0.00 2.85
3082 4063 3.568443 TGAGCCGGTACCTAATATCACA 58.432 45.455 10.90 0.00 0.00 3.58
3188 4169 7.531857 TTAGTTATTTGGAATTGAACAGGCA 57.468 32.000 0.00 0.00 0.00 4.75
3401 4382 7.972832 TCTAAGGTTTAACACGAATGACAAT 57.027 32.000 0.00 0.00 0.00 2.71
3404 4385 6.741358 GCAATCTAAGGTTTAACACGAATGAC 59.259 38.462 0.00 0.00 0.00 3.06
3411 4399 5.576774 GGCATTGCAATCTAAGGTTTAACAC 59.423 40.000 9.53 0.00 0.00 3.32
3425 4413 5.362105 AATGAATGTTAGGGCATTGCAAT 57.638 34.783 5.99 5.99 38.98 3.56
3454 4442 7.438459 CCGGATATTAACTTTTCGAAGATCTGT 59.562 37.037 0.00 0.00 35.04 3.41
3537 4525 5.460419 GTGCGTTTAATGTGACCAAAAATCA 59.540 36.000 0.00 0.00 0.00 2.57
3625 4613 8.983724 GGATTATCTGTTCTCTAACATTACTGC 58.016 37.037 0.00 0.00 44.43 4.40
3682 4670 2.508867 GCGTCGAGTCGTATGTTACAA 58.491 47.619 13.12 0.00 0.00 2.41
3766 4754 1.832998 GGGGTTTCATCATGGTGCATT 59.167 47.619 0.00 0.00 0.00 3.56
3871 4859 2.892374 CTGGTCACAATGTCGCAGATA 58.108 47.619 0.00 0.00 40.67 1.98
4013 5001 2.594592 GCACTGCCGGAACTTGGT 60.595 61.111 5.05 0.00 0.00 3.67
4192 5180 8.952278 ACAAAGAACACTACAGTCAAATAACAA 58.048 29.630 0.00 0.00 0.00 2.83
4236 5224 7.168219 AGAAATTAGTTTGACAGAGGCACATA 58.832 34.615 0.00 0.00 0.00 2.29
4258 5246 9.767684 CAGCAAACGTATGTATTTTGATAAGAA 57.232 29.630 2.77 0.00 32.91 2.52
4353 5358 2.979678 ACCTTCCGGATATGTAGGCAAT 59.020 45.455 17.46 0.00 0.00 3.56
4356 5361 3.139077 CAAACCTTCCGGATATGTAGGC 58.861 50.000 17.46 0.00 0.00 3.93
4359 5364 5.423704 TTCACAAACCTTCCGGATATGTA 57.576 39.130 4.15 0.00 0.00 2.29
4402 5408 1.380524 TTTCAGCCGTTCGGAAAACA 58.619 45.000 15.69 0.00 36.25 2.83
4414 5420 4.518249 AGTAACCAGCTCTATTTTCAGCC 58.482 43.478 0.00 0.00 36.17 4.85
4446 5452 4.918810 ACACAAGGTCTTCCACAAAATC 57.081 40.909 0.00 0.00 35.89 2.17
4595 5601 3.529216 TTTTGTTCGGAAATAGGGGGT 57.471 42.857 0.00 0.00 0.00 4.95
4619 5625 8.469200 CAAGAAAATAACAGAATATGAGGGCAA 58.531 33.333 0.00 0.00 0.00 4.52
4743 5773 4.116238 GTTCGAACCCATTGCAAAAGAAA 58.884 39.130 17.68 0.00 0.00 2.52
4795 5830 8.394877 TGCGTCTAAAATGTATTCTACCATTTG 58.605 33.333 0.00 0.00 0.00 2.32
4803 5838 7.197071 TGTGTTTGCGTCTAAAATGTATTCT 57.803 32.000 0.00 0.00 0.00 2.40
4804 5839 9.716507 ATATGTGTTTGCGTCTAAAATGTATTC 57.283 29.630 0.00 0.00 0.00 1.75
4810 5845 7.148474 ACGAAGATATGTGTTTGCGTCTAAAAT 60.148 33.333 0.00 0.00 0.00 1.82
4819 5854 4.154195 ACTCCAACGAAGATATGTGTTTGC 59.846 41.667 0.00 0.00 0.00 3.68
4834 5871 6.479001 CCTACATTATTCTACCAACTCCAACG 59.521 42.308 0.00 0.00 0.00 4.10
4855 5892 9.010029 TGAGAAATGAATGTTTTCTTACCCTAC 57.990 33.333 0.70 0.00 42.08 3.18
4867 5904 9.079833 CGAAGCAATATTTGAGAAATGAATGTT 57.920 29.630 0.00 0.00 32.38 2.71
4874 5911 7.856145 AGAGTCGAAGCAATATTTGAGAAAT 57.144 32.000 0.00 0.00 34.90 2.17
4892 5929 7.049620 CGATTATTTGCGTAGTTTTAGAGTCG 58.950 38.462 0.00 0.00 0.00 4.18
4893 5930 6.839796 GCGATTATTTGCGTAGTTTTAGAGTC 59.160 38.462 0.00 0.00 0.00 3.36
4894 5931 6.238022 GGCGATTATTTGCGTAGTTTTAGAGT 60.238 38.462 0.00 0.00 32.51 3.24
4895 5932 6.127403 GGCGATTATTTGCGTAGTTTTAGAG 58.873 40.000 0.00 0.00 32.51 2.43
4896 5933 5.581479 TGGCGATTATTTGCGTAGTTTTAGA 59.419 36.000 0.00 0.00 32.51 2.10
4897 5934 5.802064 TGGCGATTATTTGCGTAGTTTTAG 58.198 37.500 0.00 0.00 32.51 1.85
4898 5935 5.798015 TGGCGATTATTTGCGTAGTTTTA 57.202 34.783 0.00 0.00 32.51 1.52
4899 5936 4.688511 TGGCGATTATTTGCGTAGTTTT 57.311 36.364 0.00 0.00 32.51 2.43
4901 5938 4.408694 GTTTGGCGATTATTTGCGTAGTT 58.591 39.130 0.00 0.00 32.51 2.24
4902 5939 3.181504 GGTTTGGCGATTATTTGCGTAGT 60.182 43.478 0.00 0.00 32.51 2.73
4903 5940 3.064820 AGGTTTGGCGATTATTTGCGTAG 59.935 43.478 0.00 0.00 32.51 3.51
4904 5941 3.011119 AGGTTTGGCGATTATTTGCGTA 58.989 40.909 0.00 0.00 32.51 4.42
4905 5942 1.816224 AGGTTTGGCGATTATTTGCGT 59.184 42.857 0.00 0.00 32.51 5.24
4906 5943 2.159448 TGAGGTTTGGCGATTATTTGCG 60.159 45.455 0.00 0.00 32.51 4.85
4907 5944 3.502191 TGAGGTTTGGCGATTATTTGC 57.498 42.857 0.00 0.00 0.00 3.68
4908 5945 5.925969 AGTTTTGAGGTTTGGCGATTATTTG 59.074 36.000 0.00 0.00 0.00 2.32
4909 5946 6.096673 AGTTTTGAGGTTTGGCGATTATTT 57.903 33.333 0.00 0.00 0.00 1.40
4910 5947 5.722021 AGTTTTGAGGTTTGGCGATTATT 57.278 34.783 0.00 0.00 0.00 1.40
4911 5948 5.944007 ACTAGTTTTGAGGTTTGGCGATTAT 59.056 36.000 0.00 0.00 0.00 1.28
4912 5949 5.310451 ACTAGTTTTGAGGTTTGGCGATTA 58.690 37.500 0.00 0.00 0.00 1.75
4913 5950 4.142038 ACTAGTTTTGAGGTTTGGCGATT 58.858 39.130 0.00 0.00 0.00 3.34
4914 5951 3.751518 ACTAGTTTTGAGGTTTGGCGAT 58.248 40.909 0.00 0.00 0.00 4.58
4915 5952 3.202829 ACTAGTTTTGAGGTTTGGCGA 57.797 42.857 0.00 0.00 0.00 5.54
4916 5953 3.982576 AACTAGTTTTGAGGTTTGGCG 57.017 42.857 1.12 0.00 0.00 5.69
4940 5977 1.168714 GGTCTGAGGAGCGCATTTTT 58.831 50.000 11.47 0.00 0.00 1.94
4941 5978 0.036732 TGGTCTGAGGAGCGCATTTT 59.963 50.000 11.47 0.00 42.30 1.82
4942 5979 0.254178 ATGGTCTGAGGAGCGCATTT 59.746 50.000 11.47 0.00 42.30 2.32
4943 5980 0.254178 AATGGTCTGAGGAGCGCATT 59.746 50.000 11.47 0.00 42.30 3.56
4944 5981 1.123077 TAATGGTCTGAGGAGCGCAT 58.877 50.000 11.47 0.00 42.30 4.73
4945 5982 0.175760 GTAATGGTCTGAGGAGCGCA 59.824 55.000 11.47 0.00 42.30 6.09
4946 5983 0.175760 TGTAATGGTCTGAGGAGCGC 59.824 55.000 0.00 0.00 42.30 5.92
4947 5984 2.672961 TTGTAATGGTCTGAGGAGCG 57.327 50.000 0.00 0.00 42.30 5.03
4948 5985 3.127721 GCTTTTGTAATGGTCTGAGGAGC 59.872 47.826 0.00 0.00 40.08 4.70
4949 5986 3.372206 CGCTTTTGTAATGGTCTGAGGAG 59.628 47.826 0.00 0.00 0.00 3.69
4950 5987 3.334691 CGCTTTTGTAATGGTCTGAGGA 58.665 45.455 0.00 0.00 0.00 3.71
4951 5988 2.420022 CCGCTTTTGTAATGGTCTGAGG 59.580 50.000 0.00 0.00 0.00 3.86
4952 5989 3.074412 ACCGCTTTTGTAATGGTCTGAG 58.926 45.455 0.00 0.00 0.00 3.35
4953 5990 3.134574 ACCGCTTTTGTAATGGTCTGA 57.865 42.857 0.00 0.00 0.00 3.27
4954 5991 3.915437 AACCGCTTTTGTAATGGTCTG 57.085 42.857 0.00 0.00 31.17 3.51
4955 5992 4.339814 TCAAAACCGCTTTTGTAATGGTCT 59.660 37.500 14.01 0.00 44.60 3.85
4956 5993 4.612943 TCAAAACCGCTTTTGTAATGGTC 58.387 39.130 14.01 0.00 44.60 4.02
4957 5994 4.339814 TCTCAAAACCGCTTTTGTAATGGT 59.660 37.500 14.01 0.00 44.60 3.55
4958 5995 4.679654 GTCTCAAAACCGCTTTTGTAATGG 59.320 41.667 14.01 3.79 44.60 3.16
4959 5996 5.519722 AGTCTCAAAACCGCTTTTGTAATG 58.480 37.500 14.01 5.65 44.60 1.90
4960 5997 5.767816 AGTCTCAAAACCGCTTTTGTAAT 57.232 34.783 14.01 3.07 44.60 1.89
4961 5998 6.870971 ATAGTCTCAAAACCGCTTTTGTAA 57.129 33.333 14.01 3.31 44.60 2.41
4962 5999 6.870971 AATAGTCTCAAAACCGCTTTTGTA 57.129 33.333 14.01 2.26 44.60 2.41
4963 6000 5.767816 AATAGTCTCAAAACCGCTTTTGT 57.232 34.783 14.01 0.29 44.60 2.83
4964 6001 6.205784 TGAAATAGTCTCAAAACCGCTTTTG 58.794 36.000 9.24 9.24 45.34 2.44
4965 6002 6.385649 TGAAATAGTCTCAAAACCGCTTTT 57.614 33.333 0.00 0.00 0.00 2.27
4966 6003 6.385649 TTGAAATAGTCTCAAAACCGCTTT 57.614 33.333 0.00 0.00 29.93 3.51
4967 6004 6.039382 ACTTTGAAATAGTCTCAAAACCGCTT 59.961 34.615 0.26 0.00 41.10 4.68
4968 6005 5.531287 ACTTTGAAATAGTCTCAAAACCGCT 59.469 36.000 0.26 0.00 41.10 5.52
4969 6006 5.758924 ACTTTGAAATAGTCTCAAAACCGC 58.241 37.500 0.26 0.00 41.10 5.68
4970 6007 8.084590 ACTACTTTGAAATAGTCTCAAAACCG 57.915 34.615 0.26 0.00 41.10 4.44
4979 6016 9.646427 ATCAAGTCAGACTACTTTGAAATAGTC 57.354 33.333 2.64 14.29 45.15 2.59
4980 6017 9.429359 CATCAAGTCAGACTACTTTGAAATAGT 57.571 33.333 2.64 1.50 37.61 2.12
4981 6018 9.429359 ACATCAAGTCAGACTACTTTGAAATAG 57.571 33.333 2.64 0.00 37.61 1.73
4982 6019 9.208022 CACATCAAGTCAGACTACTTTGAAATA 57.792 33.333 2.64 0.00 37.61 1.40
4983 6020 7.173907 CCACATCAAGTCAGACTACTTTGAAAT 59.826 37.037 2.64 0.00 37.61 2.17
4984 6021 6.483307 CCACATCAAGTCAGACTACTTTGAAA 59.517 38.462 2.64 0.00 37.61 2.69
4985 6022 5.991606 CCACATCAAGTCAGACTACTTTGAA 59.008 40.000 2.64 0.00 37.61 2.69
4986 6023 5.070446 ACCACATCAAGTCAGACTACTTTGA 59.930 40.000 2.64 4.25 37.61 2.69
4987 6024 5.300752 ACCACATCAAGTCAGACTACTTTG 58.699 41.667 2.64 0.00 37.61 2.77
4988 6025 5.511545 GGACCACATCAAGTCAGACTACTTT 60.512 44.000 2.64 0.00 37.61 2.66
4989 6026 4.021016 GGACCACATCAAGTCAGACTACTT 60.021 45.833 2.64 0.00 40.33 2.24
4990 6027 3.511934 GGACCACATCAAGTCAGACTACT 59.488 47.826 2.64 0.00 34.58 2.57
4991 6028 3.368531 GGGACCACATCAAGTCAGACTAC 60.369 52.174 2.64 0.00 34.58 2.73
4992 6029 2.832129 GGGACCACATCAAGTCAGACTA 59.168 50.000 2.64 0.00 34.58 2.59
4993 6030 1.625818 GGGACCACATCAAGTCAGACT 59.374 52.381 0.00 0.00 34.58 3.24
4994 6031 2.100605 GGGACCACATCAAGTCAGAC 57.899 55.000 0.00 0.00 34.58 3.51
5012 6049 2.123589 TGTGTGGTGGAGGTATATGGG 58.876 52.381 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.