Multiple sequence alignment - TraesCS6D01G088500

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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 TraesCS6D01G088500 chr6D 100.000 2991 0 0 1 2991 53675413 53672423 0.000000e+00 5524
1 TraesCS6D01G088500 chr6D 88.199 161 12 5 732 890 53682258 53682103 5.090000e-43 185
2 TraesCS6D01G088500 chr6A 86.994 2422 149 59 674 2990 61425145 61427505 0.000000e+00 2575
3 TraesCS6D01G088500 chr6A 86.772 189 15 7 705 890 61421470 61421651 5.060000e-48 202
4 TraesCS6D01G088500 chr6B 88.505 2201 128 45 889 2989 117843272 117845447 0.000000e+00 2547
5 TraesCS6D01G088500 chr6B 94.030 134 8 0 674 807 117843081 117843214 1.410000e-48 204
6 TraesCS6D01G088500 chr4D 92.456 676 42 7 1 674 348415322 348414654 0.000000e+00 957
7 TraesCS6D01G088500 chr4B 91.888 678 46 9 1 674 2010962 2011634 0.000000e+00 939
8 TraesCS6D01G088500 chr4B 91.876 677 44 8 1 674 5025662 5024994 0.000000e+00 935
9 TraesCS6D01G088500 chr1B 91.888 678 42 11 1 674 12600012 12600680 0.000000e+00 935
10 TraesCS6D01G088500 chr1B 91.124 676 50 7 1 674 40950784 40950117 0.000000e+00 907
11 TraesCS6D01G088500 chr3D 91.298 678 46 11 1 674 320758407 320757739 0.000000e+00 913
12 TraesCS6D01G088500 chr1D 91.163 679 47 11 1 674 300706544 300707214 0.000000e+00 909
13 TraesCS6D01G088500 chr7A 91.085 673 48 10 1 670 89759979 89759316 0.000000e+00 900
14 TraesCS6D01G088500 chr2D 90.602 681 56 8 3 678 42704951 42704274 0.000000e+00 896


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 TraesCS6D01G088500 chr6D 53672423 53675413 2990 True 5524.0 5524 100.0000 1 2991 1 chr6D.!!$R1 2990
1 TraesCS6D01G088500 chr6A 61421470 61427505 6035 False 1388.5 2575 86.8830 674 2990 2 chr6A.!!$F1 2316
2 TraesCS6D01G088500 chr6B 117843081 117845447 2366 False 1375.5 2547 91.2675 674 2989 2 chr6B.!!$F1 2315
3 TraesCS6D01G088500 chr4D 348414654 348415322 668 True 957.0 957 92.4560 1 674 1 chr4D.!!$R1 673
4 TraesCS6D01G088500 chr4B 2010962 2011634 672 False 939.0 939 91.8880 1 674 1 chr4B.!!$F1 673
5 TraesCS6D01G088500 chr4B 5024994 5025662 668 True 935.0 935 91.8760 1 674 1 chr4B.!!$R1 673
6 TraesCS6D01G088500 chr1B 12600012 12600680 668 False 935.0 935 91.8880 1 674 1 chr1B.!!$F1 673
7 TraesCS6D01G088500 chr1B 40950117 40950784 667 True 907.0 907 91.1240 1 674 1 chr1B.!!$R1 673
8 TraesCS6D01G088500 chr3D 320757739 320758407 668 True 913.0 913 91.2980 1 674 1 chr3D.!!$R1 673
9 TraesCS6D01G088500 chr1D 300706544 300707214 670 False 909.0 909 91.1630 1 674 1 chr1D.!!$F1 673
10 TraesCS6D01G088500 chr7A 89759316 89759979 663 True 900.0 900 91.0850 1 670 1 chr7A.!!$R1 669
11 TraesCS6D01G088500 chr2D 42704274 42704951 677 True 896.0 896 90.6020 3 678 1 chr2D.!!$R1 675

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
175 176 0.254178 ACATCTTCTTCCAGGCGCAT 59.746 50.0 10.83 0.0 0.0 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 5077 0.179116 CAGATGCACTCCTCGACCTG 60.179 60.0 0.0 0.0 0.0 4.0 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
103 104 1.243902 CAACACCGGTGCATACCTTT 58.756 50.000 34.26 16.25 45.22 3.11
168 169 3.807622 GTCGTCAACAACATCTTCTTCCA 59.192 43.478 0.00 0.00 0.00 3.53
175 176 0.254178 ACATCTTCTTCCAGGCGCAT 59.746 50.000 10.83 0.00 0.00 4.73
387 390 1.738099 CTTGAGCAACCTCGTCGGG 60.738 63.158 0.00 0.00 41.13 5.14
398 401 1.812686 CTCGTCGGGTTCCACTCCAA 61.813 60.000 0.00 0.00 0.00 3.53
416 420 2.885644 CCACGACTTCCGCGATGG 60.886 66.667 8.23 0.00 43.32 3.51
560 567 9.756571 GGAAGTATAGGATAGACTAGGATTTGA 57.243 37.037 0.00 0.00 43.33 2.69
582 589 0.608640 CCGCCTTGTCTTGTACTCCT 59.391 55.000 0.00 0.00 0.00 3.69
640 652 4.332819 AGGCTCAAGCAATACAACGAATAC 59.667 41.667 4.13 0.00 44.36 1.89
685 3688 3.065371 CCCTTCTAACATTGACAATCCGC 59.935 47.826 0.00 0.00 0.00 5.54
707 3710 4.310672 CGCTAGCACGGACATCTC 57.689 61.111 16.45 0.00 0.00 2.75
715 3718 1.866063 GCACGGACATCTCGGAAGATC 60.866 57.143 0.00 0.00 40.38 2.75
729 3732 1.933853 GAAGATCGGTGGTTCCATTCG 59.066 52.381 9.84 9.84 35.57 3.34
770 3773 2.539476 CAAGCGCAAAGGTTTCAACTT 58.461 42.857 11.47 0.00 38.72 2.66
807 3810 1.350684 TGCTGGTGTCTATGGAAGCAA 59.649 47.619 1.09 0.00 37.69 3.91
808 3811 2.224744 TGCTGGTGTCTATGGAAGCAAA 60.225 45.455 1.09 0.00 37.69 3.68
809 3812 2.421424 GCTGGTGTCTATGGAAGCAAAG 59.579 50.000 0.00 0.00 0.00 2.77
810 3813 3.012518 CTGGTGTCTATGGAAGCAAAGG 58.987 50.000 0.00 0.00 0.00 3.11
812 3815 2.026262 GGTGTCTATGGAAGCAAAGGGA 60.026 50.000 0.00 0.00 0.00 4.20
813 3816 3.010420 GTGTCTATGGAAGCAAAGGGAC 58.990 50.000 0.00 0.00 0.00 4.46
814 3817 2.280628 GTCTATGGAAGCAAAGGGACG 58.719 52.381 0.00 0.00 0.00 4.79
815 3818 1.017387 CTATGGAAGCAAAGGGACGC 58.983 55.000 0.00 0.00 0.00 5.19
816 3819 0.618458 TATGGAAGCAAAGGGACGCT 59.382 50.000 0.00 0.00 41.20 5.07
818 3825 0.321298 TGGAAGCAAAGGGACGCTAC 60.321 55.000 0.00 0.00 37.54 3.58
824 3831 0.527817 CAAAGGGACGCTACGCTAGG 60.528 60.000 0.00 0.00 32.90 3.02
836 3843 1.170290 ACGCTAGGGTGTTTGCCAAC 61.170 55.000 12.26 0.00 31.43 3.77
846 3853 2.580962 TGTTTGCCAACACTATCAGCA 58.419 42.857 0.00 0.00 38.03 4.41
847 3854 2.293122 TGTTTGCCAACACTATCAGCAC 59.707 45.455 0.00 0.00 38.03 4.40
880 3888 3.575687 CTGAACTTTGCCCCTTCATCTTT 59.424 43.478 0.00 0.00 0.00 2.52
893 3917 3.627395 TCATCTTTATGAACTGCGGGT 57.373 42.857 0.00 0.00 39.20 5.28
909 3933 0.983378 GGGTGGGAGTGGAGTAGCAT 60.983 60.000 0.00 0.00 0.00 3.79
920 3944 1.415659 GGAGTAGCATCCATCTGCAGT 59.584 52.381 14.67 0.00 44.77 4.40
924 3948 5.102953 AGTAGCATCCATCTGCAGTTTTA 57.897 39.130 14.67 0.00 44.77 1.52
944 3968 3.627395 ACTGTGTCTTTCAGGTGTTGA 57.373 42.857 0.00 0.00 37.25 3.18
945 3969 3.535561 ACTGTGTCTTTCAGGTGTTGAG 58.464 45.455 0.00 0.00 37.07 3.02
995 4019 2.729882 GGTACACAGTTTGCGTACTCTG 59.270 50.000 7.17 3.37 36.45 3.35
997 4021 1.138266 ACACAGTTTGCGTACTCTGGT 59.862 47.619 8.45 2.51 32.92 4.00
1007 4031 5.662211 TGCGTACTCTGGTAAAGAAAAAC 57.338 39.130 0.00 0.00 33.37 2.43
1012 4036 6.346678 CGTACTCTGGTAAAGAAAAACTCAGC 60.347 42.308 0.00 0.00 33.37 4.26
1026 4050 2.778299 ACTCAGCGCTTGAACCATTTA 58.222 42.857 7.50 0.00 34.81 1.40
1034 4058 5.863935 AGCGCTTGAACCATTTATTTTTCTC 59.136 36.000 2.64 0.00 0.00 2.87
1035 4059 5.863935 GCGCTTGAACCATTTATTTTTCTCT 59.136 36.000 0.00 0.00 0.00 3.10
1036 4060 6.366061 GCGCTTGAACCATTTATTTTTCTCTT 59.634 34.615 0.00 0.00 0.00 2.85
1037 4061 7.619982 GCGCTTGAACCATTTATTTTTCTCTTG 60.620 37.037 0.00 0.00 0.00 3.02
1067 4091 9.857656 AATTATCACCACATGACTGATAAATCT 57.142 29.630 19.17 10.43 41.24 2.40
1158 4184 2.143419 AGCTAATCGCCCTCCCAGG 61.143 63.158 0.00 0.00 40.39 4.45
1230 4256 9.175312 CTCCATTATATATTTCATCAAGCAGCT 57.825 33.333 0.00 0.00 0.00 4.24
1306 4345 2.698855 TCTGCTGCTATTTCTCCACC 57.301 50.000 0.00 0.00 0.00 4.61
1323 4362 0.036010 ACCCCATTGCTGTCTTCTCG 60.036 55.000 0.00 0.00 0.00 4.04
1363 4402 1.867233 ACACTCAAACACAAGCTAGCG 59.133 47.619 9.55 0.00 0.00 4.26
1385 4424 1.430632 CCAGCCAGCTGCATTTACG 59.569 57.895 14.26 0.00 44.83 3.18
1387 4426 1.002134 AGCCAGCTGCATTTACGGT 60.002 52.632 8.66 0.00 44.83 4.83
1456 4495 2.270205 CATGCGAGTGGAAGCCCT 59.730 61.111 0.00 0.00 0.00 5.19
1461 4500 4.821589 GAGTGGAAGCCCTCGCCG 62.822 72.222 0.00 0.00 34.57 6.46
1579 4651 4.057428 GCACGGCGGAGAGACAGT 62.057 66.667 13.24 0.00 0.00 3.55
1867 4948 1.059994 CAAGTGCGAGCGATCAAGC 59.940 57.895 0.00 0.00 37.41 4.01
1882 4963 3.011566 TCAAGCCCAGTTTGAAAGACA 57.988 42.857 0.00 0.00 30.40 3.41
1883 4964 2.951642 TCAAGCCCAGTTTGAAAGACAG 59.048 45.455 0.00 0.00 30.40 3.51
1935 5016 5.401972 CAGCTGTAAAAATTTCGCATTGTCA 59.598 36.000 5.25 0.00 0.00 3.58
2184 5274 5.397534 CGCTGTGAAATTTTTGTGAGAGAAG 59.602 40.000 0.00 0.00 0.00 2.85
2195 5285 5.551305 TTGTGAGAGAAGATGGAAGACAA 57.449 39.130 0.00 0.00 0.00 3.18
2207 5297 6.176183 AGATGGAAGACAACCACATCTTTAG 58.824 40.000 0.00 0.00 44.08 1.85
2240 5338 9.599866 CTTGATAGTGTCTACATATTTTCCACA 57.400 33.333 0.00 0.00 0.00 4.17
2242 5340 7.704899 TGATAGTGTCTACATATTTTCCACACG 59.295 37.037 0.00 0.00 38.14 4.49
2267 5365 9.483916 CGGTAATAATCTGGACATTATGTGTTA 57.516 33.333 1.24 0.00 42.36 2.41
2284 5382 4.202253 TGTGTTATGAGACTGTTGTCAGCT 60.202 41.667 0.00 0.00 45.20 4.24
2285 5383 5.010617 TGTGTTATGAGACTGTTGTCAGCTA 59.989 40.000 0.00 0.00 45.20 3.32
2286 5384 5.574830 GTGTTATGAGACTGTTGTCAGCTAG 59.425 44.000 0.00 0.00 45.20 3.42
2287 5385 5.476945 TGTTATGAGACTGTTGTCAGCTAGA 59.523 40.000 0.00 0.00 45.20 2.43
2288 5386 4.717233 ATGAGACTGTTGTCAGCTAGAG 57.283 45.455 0.00 0.00 45.20 2.43
2319 5447 6.601741 TTTCAAACAAAATCCATCAAGTGC 57.398 33.333 0.00 0.00 0.00 4.40
2341 5469 7.912383 GTGCTTACACTTTAGTTCAACACTTA 58.088 34.615 0.00 0.00 43.85 2.24
2342 5470 7.849515 GTGCTTACACTTTAGTTCAACACTTAC 59.150 37.037 0.00 0.00 43.85 2.34
2370 5498 9.784680 CTATGGAAAATCTCAAGAAAATCACAG 57.215 33.333 0.00 0.00 0.00 3.66
2449 5577 0.613260 ATTGTTCGCTCCTGGTGCTA 59.387 50.000 17.64 5.06 0.00 3.49
2459 5587 0.400213 CCTGGTGCTACCTCAACCAA 59.600 55.000 6.83 0.00 39.58 3.67
2471 5599 0.109723 TCAACCAACCTTTCTCCCCG 59.890 55.000 0.00 0.00 0.00 5.73
2475 5603 1.002502 CAACCTTTCTCCCCGGGAC 60.003 63.158 26.32 0.00 0.00 4.46
2496 5626 3.323979 ACTCTTTCTCGCCACTCCTTAAA 59.676 43.478 0.00 0.00 0.00 1.52
2546 5676 1.234821 TGAAAATTCAACGCGCCTCT 58.765 45.000 5.73 0.00 33.55 3.69
2553 5683 3.684990 AACGCGCCTCTGAGCTCA 61.685 61.111 17.19 17.19 34.82 4.26
2570 5700 2.182827 CTCAGAGAAGATGGTGGGTGA 58.817 52.381 0.00 0.00 0.00 4.02
2595 5725 2.734720 GGTGGGATGCATTTGGGCC 61.735 63.158 0.00 0.00 0.00 5.80
2612 5742 1.958205 CCTGCCCGATCAGATTCGC 60.958 63.158 5.61 0.00 37.80 4.70
2634 5764 2.437359 GGCGAGTCCAATGCAGCT 60.437 61.111 0.00 0.00 34.01 4.24
2676 5820 3.562182 ACCGACTTGAATCCCAAACTTT 58.438 40.909 0.00 0.00 33.76 2.66
2691 5835 4.549458 CAAACTTTGAATGGATGAACGCT 58.451 39.130 0.00 0.00 0.00 5.07
2727 5871 1.134521 TGGCCGTCCATATCTGTTGTC 60.135 52.381 0.00 0.00 37.47 3.18
2803 5951 2.588877 GCCATATGGTGCTCGCGT 60.589 61.111 22.79 0.00 37.57 6.01
2817 5965 2.906153 CTCGCGTCTAGAAAGTATCCG 58.094 52.381 5.77 0.00 0.00 4.18
2820 5968 1.925068 GCGTCTAGAAAGTATCCGGCG 60.925 57.143 0.00 0.00 32.27 6.46
2974 6123 4.264253 CTCAAACTCATGCTCATTGGGTA 58.736 43.478 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 2.717044 CGGGGCCACATCGTAGACA 61.717 63.158 5.46 0.00 42.51 3.41
168 169 0.179134 GTCGAAGTAGTGATGCGCCT 60.179 55.000 4.18 0.00 0.00 5.52
175 176 2.683968 GCATTGGTGTCGAAGTAGTGA 58.316 47.619 0.00 0.00 0.00 3.41
200 201 2.583593 GAGGCGCCGAGTTAGCAG 60.584 66.667 23.20 0.00 0.00 4.24
339 341 1.362355 CCCTTTGTGCCGTTTGTCC 59.638 57.895 0.00 0.00 0.00 4.02
387 390 0.106149 AGTCGTGGTTGGAGTGGAAC 59.894 55.000 0.00 0.00 0.00 3.62
416 420 1.531912 CACAGTCGTAACGGTCGATC 58.468 55.000 0.00 0.00 39.45 3.69
560 567 1.207329 GAGTACAAGACAAGGCGGGAT 59.793 52.381 0.00 0.00 0.00 3.85
640 652 2.781681 AAGGGACGGTGGAATAGTTG 57.218 50.000 0.00 0.00 0.00 3.16
707 3710 0.178068 ATGGAACCACCGATCTTCCG 59.822 55.000 6.28 0.00 42.61 4.30
715 3718 0.036765 TTCCTCGAATGGAACCACCG 60.037 55.000 2.13 9.91 40.80 4.94
729 3732 1.408969 CCTCTGGGAGTAGCTTCCTC 58.591 60.000 4.45 4.67 37.40 3.71
770 3773 4.269183 CCAGCAGGTTAACATGACCATTA 58.731 43.478 23.53 0.00 39.71 1.90
799 3802 0.321298 GTAGCGTCCCTTTGCTTCCA 60.321 55.000 0.00 0.00 42.48 3.53
815 3818 0.036765 TGGCAAACACCCTAGCGTAG 60.037 55.000 0.00 0.00 0.00 3.51
816 3819 0.397187 TTGGCAAACACCCTAGCGTA 59.603 50.000 0.00 0.00 0.00 4.42
818 3825 1.169661 TGTTGGCAAACACCCTAGCG 61.170 55.000 1.39 0.00 41.41 4.26
828 3835 1.885887 GGTGCTGATAGTGTTGGCAAA 59.114 47.619 0.00 0.00 34.65 3.68
829 3836 1.073763 AGGTGCTGATAGTGTTGGCAA 59.926 47.619 0.00 0.00 34.65 4.52
836 3843 1.827344 TCCACTGAGGTGCTGATAGTG 59.173 52.381 0.00 0.00 41.75 2.74
841 3848 2.840199 AGTTCCACTGAGGTGCTGA 58.160 52.632 0.00 0.00 41.75 4.26
880 3888 0.907704 ACTCCCACCCGCAGTTCATA 60.908 55.000 0.00 0.00 0.00 2.15
893 3917 0.042581 TGGATGCTACTCCACTCCCA 59.957 55.000 0.00 0.00 40.43 4.37
920 3944 5.941058 TCAACACCTGAAAGACACAGTAAAA 59.059 36.000 0.00 0.00 34.07 1.52
924 3948 3.535561 CTCAACACCTGAAAGACACAGT 58.464 45.455 0.00 0.00 34.07 3.55
956 3980 9.877178 CTGTGTACCATTTCTTTATAGAAGAGT 57.123 33.333 0.00 0.00 41.25 3.24
995 4019 3.898517 AGCGCTGAGTTTTTCTTTACC 57.101 42.857 10.39 0.00 0.00 2.85
997 4021 5.270853 GTTCAAGCGCTGAGTTTTTCTTTA 58.729 37.500 12.58 0.00 34.81 1.85
1007 4031 4.361451 AATAAATGGTTCAAGCGCTGAG 57.639 40.909 12.58 7.34 34.81 3.35
1012 4036 7.619982 GCAAGAGAAAAATAAATGGTTCAAGCG 60.620 37.037 0.00 0.00 0.00 4.68
1026 4050 6.213195 TGGTGATAATTGGGCAAGAGAAAAAT 59.787 34.615 0.00 0.00 0.00 1.82
1034 4058 3.700539 TCATGTGGTGATAATTGGGCAAG 59.299 43.478 0.00 0.00 0.00 4.01
1035 4059 3.446873 GTCATGTGGTGATAATTGGGCAA 59.553 43.478 0.00 0.00 39.48 4.52
1036 4060 3.023119 GTCATGTGGTGATAATTGGGCA 58.977 45.455 0.00 0.00 39.48 5.36
1037 4061 3.067180 CAGTCATGTGGTGATAATTGGGC 59.933 47.826 0.00 0.00 39.48 5.36
1164 4190 2.939353 GTAGGGGGTGGTTGGGCT 60.939 66.667 0.00 0.00 0.00 5.19
1165 4191 4.056584 GGTAGGGGGTGGTTGGGC 62.057 72.222 0.00 0.00 0.00 5.36
1166 4192 2.533232 TGGTAGGGGGTGGTTGGG 60.533 66.667 0.00 0.00 0.00 4.12
1167 4193 2.137177 CTGTGGTAGGGGGTGGTTGG 62.137 65.000 0.00 0.00 0.00 3.77
1168 4194 1.378762 CTGTGGTAGGGGGTGGTTG 59.621 63.158 0.00 0.00 0.00 3.77
1169 4195 2.535331 GCTGTGGTAGGGGGTGGTT 61.535 63.158 0.00 0.00 0.00 3.67
1170 4196 2.933834 GCTGTGGTAGGGGGTGGT 60.934 66.667 0.00 0.00 0.00 4.16
1171 4197 3.728373 GGCTGTGGTAGGGGGTGG 61.728 72.222 0.00 0.00 0.00 4.61
1172 4198 2.198304 GAAGGCTGTGGTAGGGGGTG 62.198 65.000 0.00 0.00 0.00 4.61
1173 4199 1.923909 GAAGGCTGTGGTAGGGGGT 60.924 63.158 0.00 0.00 0.00 4.95
1174 4200 1.923395 TGAAGGCTGTGGTAGGGGG 60.923 63.158 0.00 0.00 0.00 5.40
1230 4256 2.494059 CTTTTGTGAAAGCGAGGAGGA 58.506 47.619 0.00 0.00 36.19 3.71
1306 4345 1.372087 GCCGAGAAGACAGCAATGGG 61.372 60.000 0.00 0.00 0.00 4.00
1323 4362 1.475280 TGATGAGCAAATTGAGCTGCC 59.525 47.619 10.10 0.00 43.58 4.85
1363 4402 1.885163 AAATGCAGCTGGCTGGCTTC 61.885 55.000 21.76 7.65 45.15 3.86
1385 4424 1.880819 CTTGCAACCCCATGAGCACC 61.881 60.000 0.00 0.00 36.62 5.01
1387 4426 0.609957 CTCTTGCAACCCCATGAGCA 60.610 55.000 0.00 0.00 32.53 4.26
1562 4616 4.057428 ACTGTCTCTCCGCCGTGC 62.057 66.667 0.00 0.00 0.00 5.34
1579 4651 1.566211 CTCTTCCTTCTGCTCCTCCA 58.434 55.000 0.00 0.00 0.00 3.86
1867 4948 4.061596 GTCTCTCTGTCTTTCAAACTGGG 58.938 47.826 0.00 0.00 0.00 4.45
1882 4963 3.462954 TGGATCATCTCCTCTGTCTCTCT 59.537 47.826 0.00 0.00 45.21 3.10
1883 4964 3.831323 TGGATCATCTCCTCTGTCTCTC 58.169 50.000 0.00 0.00 45.21 3.20
1962 5043 9.899226 AATTTACATTTACACTGAAAGAGAAGC 57.101 29.630 0.00 0.00 37.43 3.86
1993 5077 0.179116 CAGATGCACTCCTCGACCTG 60.179 60.000 0.00 0.00 0.00 4.00
2184 5274 5.940470 ACTAAAGATGTGGTTGTCTTCCATC 59.060 40.000 0.00 0.00 37.30 3.51
2195 5285 9.442047 CTATCAAGAGAAAACTAAAGATGTGGT 57.558 33.333 0.00 0.00 0.00 4.16
2232 5330 5.644636 GTCCAGATTATTACCGTGTGGAAAA 59.355 40.000 0.00 0.00 37.10 2.29
2236 5334 4.131649 TGTCCAGATTATTACCGTGTGG 57.868 45.455 0.00 0.00 42.84 4.17
2240 5338 7.506114 ACACATAATGTCCAGATTATTACCGT 58.494 34.615 0.00 0.00 36.54 4.83
2251 5349 7.044181 ACAGTCTCATAACACATAATGTCCAG 58.956 38.462 0.00 0.00 42.31 3.86
2267 5365 4.085733 ACTCTAGCTGACAACAGTCTCAT 58.914 43.478 0.00 0.00 45.04 2.90
2319 5447 9.095065 AGTGTAAGTGTTGAACTAAAGTGTAAG 57.905 33.333 0.00 0.00 38.56 2.34
2328 5456 9.787435 ATTTTCCATAGTGTAAGTGTTGAACTA 57.213 29.630 0.00 0.00 38.56 2.24
2341 5469 9.300681 TGATTTTCTTGAGATTTTCCATAGTGT 57.699 29.630 0.00 0.00 0.00 3.55
2342 5470 9.565213 GTGATTTTCTTGAGATTTTCCATAGTG 57.435 33.333 0.00 0.00 0.00 2.74
2370 5498 5.308237 AGTTTCCCAGATACATATGGAGGTC 59.692 44.000 7.80 0.00 41.61 3.85
2449 5577 1.145119 GGGAGAAAGGTTGGTTGAGGT 59.855 52.381 0.00 0.00 0.00 3.85
2459 5587 1.612739 GAGTCCCGGGGAGAAAGGT 60.613 63.158 23.50 0.00 29.39 3.50
2471 5599 0.108567 GAGTGGCGAGAAAGAGTCCC 60.109 60.000 0.00 0.00 0.00 4.46
2475 5603 3.594603 TTAAGGAGTGGCGAGAAAGAG 57.405 47.619 0.00 0.00 0.00 2.85
2496 5626 1.760086 CTCTGAGCTCCATCCGGGT 60.760 63.158 12.15 0.00 38.11 5.28
2546 5676 1.829849 CCACCATCTTCTCTGAGCTCA 59.170 52.381 17.19 17.19 0.00 4.26
2553 5683 0.908198 GCTCACCCACCATCTTCTCT 59.092 55.000 0.00 0.00 0.00 3.10
2595 5725 0.315251 TAGCGAATCTGATCGGGCAG 59.685 55.000 0.62 0.00 42.93 4.85
2612 5742 2.240500 GCATTGGACTCGCCGCTAG 61.241 63.158 0.00 0.00 40.66 3.42
2656 5786 3.568007 TCAAAGTTTGGGATTCAAGTCGG 59.432 43.478 15.47 0.00 36.62 4.79
2657 5787 4.829064 TCAAAGTTTGGGATTCAAGTCG 57.171 40.909 15.47 0.00 36.62 4.18
2676 5820 2.183478 ACACAGCGTTCATCCATTCA 57.817 45.000 0.00 0.00 0.00 2.57
2691 5835 1.297664 GCCAAAAGCATTGCAACACA 58.702 45.000 11.91 0.00 42.97 3.72
2727 5871 5.233957 TCACAAGATGAACACAACACTTG 57.766 39.130 0.00 0.00 39.98 3.16
2767 5911 5.991933 TGGCAACATAACCAACAATACAT 57.008 34.783 0.00 0.00 46.17 2.29
2803 5951 2.353357 TCCGCCGGATACTTTCTAGA 57.647 50.000 5.05 0.00 0.00 2.43
2817 5965 4.630894 TGTTTGAAATGTGATATCCGCC 57.369 40.909 0.00 0.00 0.00 6.13
2820 5968 9.288576 TGGATAGATGTTTGAAATGTGATATCC 57.711 33.333 0.00 0.00 36.86 2.59
2891 6040 4.617253 TGGACTTCCATTTCTCGAGAAA 57.383 40.909 35.54 35.54 46.60 2.52
2910 6059 1.496429 AGGCCATCACCCTTCTAATGG 59.504 52.381 5.01 0.00 41.34 3.16


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

AutoCloner maintained by Alex Coulton.