Multiple sequence alignment - TraesCS6D01G372300

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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 TraesCS6D01G372300 chr6D 100.000 2799 0 0 1 2799 457591848 457589050 0.000000e+00 5169
1 TraesCS6D01G372300 chr6D 85.358 2083 239 32 653 2682 457636819 457634750 0.000000e+00 2097
2 TraesCS6D01G372300 chr6A 94.853 2720 116 16 1 2700 604456912 604454197 0.000000e+00 4226
3 TraesCS6D01G372300 chr6A 85.818 1932 219 30 655 2539 604574051 604572128 0.000000e+00 1999
4 TraesCS6D01G372300 chr6B 92.143 2291 145 15 433 2700 696021567 696019289 0.000000e+00 3201
5 TraesCS6D01G372300 chr6B 84.644 1908 224 36 655 2507 696100307 696098414 0.000000e+00 1836
6 TraesCS6D01G372300 chr6B 86.314 643 80 6 2043 2682 696096879 696096242 0.000000e+00 693
7 TraesCS6D01G372300 chr6B 86.609 463 30 15 1 441 696022134 696021682 1.510000e-132 483
8 TraesCS6D01G372300 chr2A 80.853 1290 178 41 695 1943 23878559 23879820 0.000000e+00 950
9 TraesCS6D01G372300 chr2A 81.198 1202 169 34 782 1943 23828232 23829416 0.000000e+00 915
10 TraesCS6D01G372300 chr2D 80.603 1294 183 41 691 1943 21681021 21682287 0.000000e+00 937
11 TraesCS6D01G372300 chr2B 79.861 1291 193 43 694 1943 34864746 34863482 0.000000e+00 881
12 TraesCS6D01G372300 chr2B 79.209 1289 197 45 694 1943 34890068 34888812 0.000000e+00 830


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 TraesCS6D01G372300 chr6D 457589050 457591848 2798 True 5169.0 5169 100.000 1 2799 1 chr6D.!!$R1 2798
1 TraesCS6D01G372300 chr6D 457634750 457636819 2069 True 2097.0 2097 85.358 653 2682 1 chr6D.!!$R2 2029
2 TraesCS6D01G372300 chr6A 604454197 604456912 2715 True 4226.0 4226 94.853 1 2700 1 chr6A.!!$R1 2699
3 TraesCS6D01G372300 chr6A 604572128 604574051 1923 True 1999.0 1999 85.818 655 2539 1 chr6A.!!$R2 1884
4 TraesCS6D01G372300 chr6B 696019289 696022134 2845 True 1842.0 3201 89.376 1 2700 2 chr6B.!!$R1 2699
5 TraesCS6D01G372300 chr6B 696096242 696100307 4065 True 1264.5 1836 85.479 655 2682 2 chr6B.!!$R2 2027
6 TraesCS6D01G372300 chr2A 23878559 23879820 1261 False 950.0 950 80.853 695 1943 1 chr2A.!!$F2 1248
7 TraesCS6D01G372300 chr2A 23828232 23829416 1184 False 915.0 915 81.198 782 1943 1 chr2A.!!$F1 1161
8 TraesCS6D01G372300 chr2D 21681021 21682287 1266 False 937.0 937 80.603 691 1943 1 chr2D.!!$F1 1252
9 TraesCS6D01G372300 chr2B 34863482 34864746 1264 True 881.0 881 79.861 694 1943 1 chr2B.!!$R1 1249
10 TraesCS6D01G372300 chr2B 34888812 34890068 1256 True 830.0 830 79.209 694 1943 1 chr2B.!!$R2 1249

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
509 655 0.249073 ACATGGAGCACGCTCGATAC 60.249 55.0 15.01 1.7 43.59 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2253 4520 0.037326 CCACTCCGCTTCTTACAGCA 60.037 55.0 0.0 0.0 40.09 4.41 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
31 32 5.269554 TCTTCCATACCCCACTTCATTTT 57.730 39.130 0.00 0.00 0.00 1.82
32 33 6.395780 TCTTCCATACCCCACTTCATTTTA 57.604 37.500 0.00 0.00 0.00 1.52
33 34 6.795590 TCTTCCATACCCCACTTCATTTTAA 58.204 36.000 0.00 0.00 0.00 1.52
341 347 5.024555 GCTTTGATTTCTCATTAGTGCGAC 58.975 41.667 0.00 0.00 0.00 5.19
357 363 3.684788 GTGCGACTATTCTTCACATGGTT 59.315 43.478 0.00 0.00 0.00 3.67
386 406 1.685224 GTGCTGTGGGGATGGAAGA 59.315 57.895 0.00 0.00 0.00 2.87
447 593 7.072454 GGCCCATGATAGGAGATAACCAATATA 59.928 40.741 0.00 0.00 0.00 0.86
466 612 7.322260 CAATATAAAAACTCTGAATTTGCGCG 58.678 34.615 0.00 0.00 0.00 6.86
509 655 0.249073 ACATGGAGCACGCTCGATAC 60.249 55.000 15.01 1.70 43.59 2.24
561 707 7.695820 ACTATGCTAGAGTTGTTCTTAGTACG 58.304 38.462 0.00 0.00 37.36 3.67
569 715 5.702865 AGTTGTTCTTAGTACGCGTTATGA 58.297 37.500 20.78 9.80 0.00 2.15
574 720 5.550232 TCTTAGTACGCGTTATGAAGACA 57.450 39.130 20.78 0.00 0.00 3.41
575 721 5.327091 TCTTAGTACGCGTTATGAAGACAC 58.673 41.667 20.78 5.89 0.00 3.67
581 727 4.463209 ACGCGTTATGAAGACACAAAATG 58.537 39.130 5.58 0.00 0.00 2.32
626 772 6.600246 TCTTAGTACATAGCGTGAGTACAG 57.400 41.667 12.11 4.64 40.32 2.74
662 812 6.439375 TCCTGCACAAACTTATAGTTCTCCTA 59.561 38.462 0.00 0.00 37.47 2.94
884 1073 3.749609 ACTAATCAACACGGCAAACCTAC 59.250 43.478 0.00 0.00 0.00 3.18
948 1144 4.023707 ACAGCAACTTGTAGATCTGTTTGC 60.024 41.667 5.18 11.97 31.51 3.68
1102 1323 2.699768 GCGCCAATGCCTAGCACAA 61.700 57.895 0.00 0.00 43.04 3.33
1230 1454 0.674895 GCAAGTGCGAGACCTCCAAT 60.675 55.000 0.00 0.00 0.00 3.16
1278 1502 0.975556 TCCTCGCCATCTTGTGCCTA 60.976 55.000 0.00 0.00 0.00 3.93
1453 1680 2.356313 CGCTGGACTTCGTGCACT 60.356 61.111 16.19 0.00 29.42 4.40
1561 1788 1.406614 CCGAGGAGCTGCTCAAGAATT 60.407 52.381 31.26 8.55 31.08 2.17
1623 1850 3.116939 TCATCTTCCCCACCAAAAGGAAA 60.117 43.478 0.00 0.00 39.14 3.13
1871 2123 1.444119 ATGTTCGGTGTGTGTGCCAC 61.444 55.000 0.00 0.00 44.78 5.01
1937 2192 4.471747 TGTACAATTATGTAGGTGCCCTGA 59.528 41.667 0.00 0.00 42.54 3.86
2094 4357 8.592998 CACATACGTTACACTTCTTTCTTATCC 58.407 37.037 0.00 0.00 0.00 2.59
2192 4455 9.357652 CACTTGAATTTATTGGATAAACACCTG 57.642 33.333 0.00 0.00 37.53 4.00
2225 4488 6.377146 TGGATAGGAGCCATTTCACTAAAAAC 59.623 38.462 0.00 0.00 0.00 2.43
2253 4520 5.806654 ATGTGGGCAAATCTAAAACTTGT 57.193 34.783 0.00 0.00 0.00 3.16
2255 4522 3.740832 GTGGGCAAATCTAAAACTTGTGC 59.259 43.478 0.00 0.00 0.00 4.57
2351 4618 1.312371 GGCACTAGCAATTTCCGCCA 61.312 55.000 0.00 0.00 44.61 5.69
2354 4621 2.357637 GCACTAGCAATTTCCGCCATTA 59.642 45.455 0.00 0.00 41.58 1.90
2371 4638 5.304778 GCCATTAGATTTGTTGTTTTGGGT 58.695 37.500 0.00 0.00 0.00 4.51
2412 4679 2.755469 GTCAATGCGCCCATGGGT 60.755 61.111 31.58 9.46 37.65 4.51
2414 4681 2.755064 CAATGCGCCCATGGGTCA 60.755 61.111 31.58 27.24 37.65 4.02
2428 4695 3.513909 TGGGTCATGGATCATCATTCC 57.486 47.619 0.00 0.00 0.00 3.01
2520 4787 1.439679 GTTGATTCAGGTCCGTGGAC 58.560 55.000 10.65 10.65 43.87 4.02
2585 4860 4.380867 CCTCGCCAGAGCATTTACAAAAAT 60.381 41.667 0.00 0.00 43.05 1.82
2617 4898 4.153986 CAACGTGTGAATCAAGAATGAGC 58.846 43.478 0.00 0.00 39.39 4.26
2622 4903 4.639310 GTGTGAATCAAGAATGAGCTCCAT 59.361 41.667 12.15 0.00 39.39 3.41
2634 4915 6.319152 AGAATGAGCTCCATGAAAAATCTGAG 59.681 38.462 12.15 0.00 35.24 3.35
2682 4963 7.813852 ACTTCGCAACATCTTAACTAACTAG 57.186 36.000 0.00 0.00 0.00 2.57
2700 4982 5.208294 ACTAGACTTAACATCCTCCCTCA 57.792 43.478 0.00 0.00 0.00 3.86
2701 4983 5.782925 ACTAGACTTAACATCCTCCCTCAT 58.217 41.667 0.00 0.00 0.00 2.90
2702 4984 6.206042 ACTAGACTTAACATCCTCCCTCATT 58.794 40.000 0.00 0.00 0.00 2.57
2703 4985 5.622346 AGACTTAACATCCTCCCTCATTC 57.378 43.478 0.00 0.00 0.00 2.67
2704 4986 4.410555 AGACTTAACATCCTCCCTCATTCC 59.589 45.833 0.00 0.00 0.00 3.01
2705 4987 4.375313 ACTTAACATCCTCCCTCATTCCT 58.625 43.478 0.00 0.00 0.00 3.36
2706 4988 5.538877 ACTTAACATCCTCCCTCATTCCTA 58.461 41.667 0.00 0.00 0.00 2.94
2707 4989 5.970640 ACTTAACATCCTCCCTCATTCCTAA 59.029 40.000 0.00 0.00 0.00 2.69
2708 4990 4.779993 AACATCCTCCCTCATTCCTAAC 57.220 45.455 0.00 0.00 0.00 2.34
2709 4991 4.014273 ACATCCTCCCTCATTCCTAACT 57.986 45.455 0.00 0.00 0.00 2.24
2710 4992 4.375313 ACATCCTCCCTCATTCCTAACTT 58.625 43.478 0.00 0.00 0.00 2.66
2711 4993 4.164988 ACATCCTCCCTCATTCCTAACTTG 59.835 45.833 0.00 0.00 0.00 3.16
2712 4994 3.803340 TCCTCCCTCATTCCTAACTTGT 58.197 45.455 0.00 0.00 0.00 3.16
2713 4995 3.775316 TCCTCCCTCATTCCTAACTTGTC 59.225 47.826 0.00 0.00 0.00 3.18
2714 4996 3.777522 CCTCCCTCATTCCTAACTTGTCT 59.222 47.826 0.00 0.00 0.00 3.41
2715 4997 4.141824 CCTCCCTCATTCCTAACTTGTCTC 60.142 50.000 0.00 0.00 0.00 3.36
2716 4998 4.689062 TCCCTCATTCCTAACTTGTCTCT 58.311 43.478 0.00 0.00 0.00 3.10
2717 4999 4.467795 TCCCTCATTCCTAACTTGTCTCTG 59.532 45.833 0.00 0.00 0.00 3.35
2718 5000 4.223923 CCCTCATTCCTAACTTGTCTCTGT 59.776 45.833 0.00 0.00 0.00 3.41
2719 5001 5.174395 CCTCATTCCTAACTTGTCTCTGTG 58.826 45.833 0.00 0.00 0.00 3.66
2720 5002 5.152623 TCATTCCTAACTTGTCTCTGTGG 57.847 43.478 0.00 0.00 0.00 4.17
2721 5003 4.838423 TCATTCCTAACTTGTCTCTGTGGA 59.162 41.667 0.00 0.00 0.00 4.02
2722 5004 4.873746 TTCCTAACTTGTCTCTGTGGAG 57.126 45.455 0.00 0.00 40.73 3.86
2723 5005 3.165875 TCCTAACTTGTCTCTGTGGAGG 58.834 50.000 0.00 0.00 39.86 4.30
2724 5006 2.900546 CCTAACTTGTCTCTGTGGAGGT 59.099 50.000 0.00 0.00 39.86 3.85
2725 5007 3.325135 CCTAACTTGTCTCTGTGGAGGTT 59.675 47.826 0.00 0.00 39.86 3.50
2726 5008 3.933861 AACTTGTCTCTGTGGAGGTTT 57.066 42.857 0.00 0.00 39.86 3.27
2727 5009 3.933861 ACTTGTCTCTGTGGAGGTTTT 57.066 42.857 0.00 0.00 39.86 2.43
2728 5010 4.236527 ACTTGTCTCTGTGGAGGTTTTT 57.763 40.909 0.00 0.00 39.86 1.94
2729 5011 3.947834 ACTTGTCTCTGTGGAGGTTTTTG 59.052 43.478 0.00 0.00 39.86 2.44
2730 5012 3.644966 TGTCTCTGTGGAGGTTTTTGT 57.355 42.857 0.00 0.00 39.86 2.83
2731 5013 4.764050 TGTCTCTGTGGAGGTTTTTGTA 57.236 40.909 0.00 0.00 39.86 2.41
2732 5014 5.105567 TGTCTCTGTGGAGGTTTTTGTAA 57.894 39.130 0.00 0.00 39.86 2.41
2733 5015 5.502079 TGTCTCTGTGGAGGTTTTTGTAAA 58.498 37.500 0.00 0.00 39.86 2.01
2734 5016 5.946972 TGTCTCTGTGGAGGTTTTTGTAAAA 59.053 36.000 0.00 0.00 39.86 1.52
2735 5017 6.605594 TGTCTCTGTGGAGGTTTTTGTAAAAT 59.394 34.615 0.00 0.00 39.86 1.82
2736 5018 7.139392 GTCTCTGTGGAGGTTTTTGTAAAATC 58.861 38.462 0.00 0.00 39.86 2.17
2737 5019 6.264518 TCTCTGTGGAGGTTTTTGTAAAATCC 59.735 38.462 8.47 8.47 39.86 3.01
2738 5020 5.894393 TCTGTGGAGGTTTTTGTAAAATCCA 59.106 36.000 15.71 11.37 39.24 3.41
2739 5021 6.553100 TCTGTGGAGGTTTTTGTAAAATCCAT 59.447 34.615 15.71 5.12 40.60 3.41
2740 5022 7.070571 TCTGTGGAGGTTTTTGTAAAATCCATT 59.929 33.333 15.71 1.18 40.60 3.16
2741 5023 8.251383 TGTGGAGGTTTTTGTAAAATCCATTA 57.749 30.769 15.71 6.86 40.60 1.90
2742 5024 8.705594 TGTGGAGGTTTTTGTAAAATCCATTAA 58.294 29.630 15.71 4.62 40.60 1.40
2743 5025 9.203421 GTGGAGGTTTTTGTAAAATCCATTAAG 57.797 33.333 15.71 0.00 40.60 1.85
2744 5026 7.875554 TGGAGGTTTTTGTAAAATCCATTAAGC 59.124 33.333 15.71 0.41 39.24 3.09
2745 5027 8.094548 GGAGGTTTTTGTAAAATCCATTAAGCT 58.905 33.333 15.71 4.34 39.24 3.74
2746 5028 8.831715 AGGTTTTTGTAAAATCCATTAAGCTG 57.168 30.769 15.71 0.00 39.24 4.24
2747 5029 8.428852 AGGTTTTTGTAAAATCCATTAAGCTGT 58.571 29.630 15.71 0.00 39.24 4.40
2748 5030 9.051679 GGTTTTTGTAAAATCCATTAAGCTGTT 57.948 29.630 10.74 0.00 37.58 3.16
2749 5031 9.862585 GTTTTTGTAAAATCCATTAAGCTGTTG 57.137 29.630 0.00 0.00 0.00 3.33
2750 5032 7.650834 TTTGTAAAATCCATTAAGCTGTTGC 57.349 32.000 0.00 0.00 40.05 4.17
2751 5033 6.338214 TGTAAAATCCATTAAGCTGTTGCA 57.662 33.333 0.00 0.00 42.74 4.08
2752 5034 6.389091 TGTAAAATCCATTAAGCTGTTGCAG 58.611 36.000 0.00 0.00 42.74 4.41
2753 5035 5.726980 AAAATCCATTAAGCTGTTGCAGA 57.273 34.783 0.00 0.00 42.74 4.26
2754 5036 4.708726 AATCCATTAAGCTGTTGCAGAC 57.291 40.909 0.00 0.00 42.74 3.51
2755 5037 3.138884 TCCATTAAGCTGTTGCAGACA 57.861 42.857 0.00 0.00 42.74 3.41
2756 5038 3.689347 TCCATTAAGCTGTTGCAGACAT 58.311 40.909 0.00 0.00 42.74 3.06
2757 5039 4.081406 TCCATTAAGCTGTTGCAGACATT 58.919 39.130 0.00 0.00 42.74 2.71
2758 5040 4.523943 TCCATTAAGCTGTTGCAGACATTT 59.476 37.500 0.00 4.22 42.74 2.32
2759 5041 4.860907 CCATTAAGCTGTTGCAGACATTTC 59.139 41.667 0.00 0.00 42.74 2.17
2760 5042 5.336213 CCATTAAGCTGTTGCAGACATTTCT 60.336 40.000 0.00 0.00 42.74 2.52
2773 5055 6.145807 CAGACATTTCTGTAAACTCGTCTG 57.854 41.667 0.40 0.00 43.95 3.51
2774 5056 4.686554 AGACATTTCTGTAAACTCGTCTGC 59.313 41.667 0.00 0.00 35.14 4.26
2775 5057 4.377021 ACATTTCTGTAAACTCGTCTGCA 58.623 39.130 0.00 0.00 32.49 4.41
2776 5058 4.814234 ACATTTCTGTAAACTCGTCTGCAA 59.186 37.500 0.00 0.00 32.49 4.08
2777 5059 4.789095 TTTCTGTAAACTCGTCTGCAAC 57.211 40.909 0.00 0.00 0.00 4.17
2778 5060 3.728076 TCTGTAAACTCGTCTGCAACT 57.272 42.857 0.00 0.00 0.00 3.16
2779 5061 4.054780 TCTGTAAACTCGTCTGCAACTT 57.945 40.909 0.00 0.00 0.00 2.66
2780 5062 5.190992 TCTGTAAACTCGTCTGCAACTTA 57.809 39.130 0.00 0.00 0.00 2.24
2781 5063 4.980434 TCTGTAAACTCGTCTGCAACTTAC 59.020 41.667 0.00 0.00 0.00 2.34
2782 5064 4.053295 TGTAAACTCGTCTGCAACTTACC 58.947 43.478 0.00 0.00 0.00 2.85
2783 5065 2.902705 AACTCGTCTGCAACTTACCA 57.097 45.000 0.00 0.00 0.00 3.25
2784 5066 2.150397 ACTCGTCTGCAACTTACCAC 57.850 50.000 0.00 0.00 0.00 4.16
2785 5067 1.270147 ACTCGTCTGCAACTTACCACC 60.270 52.381 0.00 0.00 0.00 4.61
2786 5068 1.000955 CTCGTCTGCAACTTACCACCT 59.999 52.381 0.00 0.00 0.00 4.00
2787 5069 1.414919 TCGTCTGCAACTTACCACCTT 59.585 47.619 0.00 0.00 0.00 3.50
2788 5070 2.158871 TCGTCTGCAACTTACCACCTTT 60.159 45.455 0.00 0.00 0.00 3.11
2789 5071 2.032030 CGTCTGCAACTTACCACCTTTG 60.032 50.000 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
223 225 9.342308 CTTGGTGGTTGATTCTTACATATGTAT 57.658 33.333 16.16 2.43 0.00 2.29
447 593 3.078594 ACGCGCAAATTCAGAGTTTTT 57.921 38.095 5.73 0.00 0.00 1.94
466 612 4.757149 GCATATGGAGGATGTTGAGGTAAC 59.243 45.833 4.56 0.00 39.80 2.50
509 655 2.073816 GTTGTCCACCTCCATAACACG 58.926 52.381 0.00 0.00 0.00 4.49
561 707 6.031003 CGTTACATTTTGTGTCTTCATAACGC 59.969 38.462 0.00 0.00 42.29 4.84
569 715 6.426937 AGCATAGTCGTTACATTTTGTGTCTT 59.573 34.615 0.00 0.00 42.29 3.01
574 720 7.321153 ACTCTAGCATAGTCGTTACATTTTGT 58.679 34.615 0.00 0.00 40.38 2.83
575 721 7.757097 ACTCTAGCATAGTCGTTACATTTTG 57.243 36.000 0.00 0.00 40.38 2.44
581 727 4.922719 AGCAACTCTAGCATAGTCGTTAC 58.077 43.478 0.00 0.00 40.38 2.50
626 772 2.363788 TGTGCAGGAGTACGTCATTC 57.636 50.000 0.00 0.00 32.48 2.67
884 1073 5.166398 GCTGAATGATTCCAAAGTCCAAAG 58.834 41.667 2.26 0.00 0.00 2.77
948 1144 1.402456 GCTCAGAAAGGTGCAATGCTG 60.402 52.381 6.82 0.00 0.00 4.41
999 1205 2.482839 CGGAGAAGAAGAAGAGGCCATC 60.483 54.545 5.01 0.00 0.00 3.51
1128 1352 2.506438 GCTAGGTTCGCGACGCTT 60.506 61.111 19.02 3.75 0.00 4.68
1170 1394 2.038269 CAACGCCTGGTACGCCAAT 61.038 57.895 0.00 0.00 45.51 3.16
1230 1454 2.122413 ACCCCTGTGAGCCACTGA 60.122 61.111 11.83 0.00 35.76 3.41
1278 1502 2.354203 GCTGTCGGTGAAGGAGAAGAAT 60.354 50.000 0.00 0.00 0.00 2.40
1314 1538 6.573289 CGAAGCCATAGTATAGCTTTCCATCT 60.573 42.308 15.62 0.00 46.44 2.90
1453 1680 2.048222 CACCGCTGCGAAGAAGGA 60.048 61.111 25.45 0.00 0.00 3.36
1623 1850 2.440409 GTGTCACTGAATCCAATGCCT 58.560 47.619 0.00 0.00 0.00 4.75
1871 2123 9.471084 AATATTTCCTTGTTTACAAAAGAACCG 57.529 29.630 7.05 0.00 35.15 4.44
1945 2200 1.696884 AGCTCTAATAAGCCTGGGAGC 59.303 52.381 9.87 9.87 43.56 4.70
2094 4357 9.090692 GTCATTGTAAAATGAATGGAGAATTGG 57.909 33.333 9.98 0.00 40.49 3.16
2134 4397 9.723299 CGTAAACTTCTAGACTAATTTGTTTCG 57.277 33.333 0.00 0.00 0.00 3.46
2192 4455 6.266103 TGAAATGGCTCCTATCCAATTGATTC 59.734 38.462 7.12 0.00 37.13 2.52
2237 4504 7.138736 TCTTACAGCACAAGTTTTAGATTTGC 58.861 34.615 0.00 0.00 0.00 3.68
2253 4520 0.037326 CCACTCCGCTTCTTACAGCA 60.037 55.000 0.00 0.00 40.09 4.41
2255 4522 0.108138 CCCCACTCCGCTTCTTACAG 60.108 60.000 0.00 0.00 0.00 2.74
2310 4577 6.012745 GCCCTAAGATGGATGGATTAATGTT 58.987 40.000 0.00 0.00 0.00 2.71
2371 4638 2.176889 GGCATCTAACGGCTAGGGATA 58.823 52.381 0.00 0.00 0.00 2.59
2412 4679 1.271543 GCGGGGAATGATGATCCATGA 60.272 52.381 0.00 0.00 38.80 3.07
2414 4681 0.773014 TGCGGGGAATGATGATCCAT 59.227 50.000 0.00 0.00 38.80 3.41
2585 4860 4.807834 TGATTCACACGTTGTAACCGTTTA 59.192 37.500 0.00 0.00 36.17 2.01
2617 4898 8.759641 CGTCTATAACTCAGATTTTTCATGGAG 58.240 37.037 0.00 0.00 0.00 3.86
2622 4903 9.569167 CAGTACGTCTATAACTCAGATTTTTCA 57.431 33.333 0.00 0.00 0.00 2.69
2682 4963 4.410555 AGGAATGAGGGAGGATGTTAAGTC 59.589 45.833 0.00 0.00 0.00 3.01
2700 4982 4.223923 CCTCCACAGAGACAAGTTAGGAAT 59.776 45.833 0.00 0.00 43.39 3.01
2701 4983 3.578716 CCTCCACAGAGACAAGTTAGGAA 59.421 47.826 0.00 0.00 43.39 3.36
2702 4984 3.165875 CCTCCACAGAGACAAGTTAGGA 58.834 50.000 0.00 0.00 43.39 2.94
2703 4985 2.900546 ACCTCCACAGAGACAAGTTAGG 59.099 50.000 0.00 0.00 43.39 2.69
2704 4986 4.608948 AACCTCCACAGAGACAAGTTAG 57.391 45.455 0.00 0.00 43.39 2.34
2705 4987 5.367945 AAAACCTCCACAGAGACAAGTTA 57.632 39.130 0.00 0.00 43.39 2.24
2706 4988 3.933861 AAACCTCCACAGAGACAAGTT 57.066 42.857 0.00 0.00 43.39 2.66
2707 4989 3.933861 AAAACCTCCACAGAGACAAGT 57.066 42.857 0.00 0.00 43.39 3.16
2708 4990 3.947834 ACAAAAACCTCCACAGAGACAAG 59.052 43.478 0.00 0.00 43.39 3.16
2709 4991 3.963129 ACAAAAACCTCCACAGAGACAA 58.037 40.909 0.00 0.00 43.39 3.18
2710 4992 3.644966 ACAAAAACCTCCACAGAGACA 57.355 42.857 0.00 0.00 43.39 3.41
2711 4993 6.445357 TTTTACAAAAACCTCCACAGAGAC 57.555 37.500 0.00 0.00 43.39 3.36
2712 4994 6.264518 GGATTTTACAAAAACCTCCACAGAGA 59.735 38.462 6.51 0.00 43.39 3.10
2713 4995 6.040391 TGGATTTTACAAAAACCTCCACAGAG 59.960 38.462 13.03 0.00 40.36 3.35
2714 4996 5.894393 TGGATTTTACAAAAACCTCCACAGA 59.106 36.000 13.03 0.00 40.36 3.41
2715 4997 6.155475 TGGATTTTACAAAAACCTCCACAG 57.845 37.500 13.03 0.00 40.36 3.66
2716 4998 6.739331 ATGGATTTTACAAAAACCTCCACA 57.261 33.333 13.03 0.00 40.36 4.17
2717 4999 9.203421 CTTAATGGATTTTACAAAAACCTCCAC 57.797 33.333 13.03 0.00 40.36 4.02
2718 5000 7.875554 GCTTAATGGATTTTACAAAAACCTCCA 59.124 33.333 13.03 11.24 40.36 3.86
2719 5001 8.094548 AGCTTAATGGATTTTACAAAAACCTCC 58.905 33.333 13.03 6.87 40.36 4.30
2720 5002 8.925700 CAGCTTAATGGATTTTACAAAAACCTC 58.074 33.333 13.03 0.00 40.36 3.85
2721 5003 8.428852 ACAGCTTAATGGATTTTACAAAAACCT 58.571 29.630 13.03 0.00 40.36 3.50
2722 5004 8.601845 ACAGCTTAATGGATTTTACAAAAACC 57.398 30.769 6.75 6.75 40.19 3.27
2723 5005 9.862585 CAACAGCTTAATGGATTTTACAAAAAC 57.137 29.630 0.00 0.00 0.00 2.43
2724 5006 8.555361 GCAACAGCTTAATGGATTTTACAAAAA 58.445 29.630 0.00 0.00 0.00 1.94
2725 5007 7.712639 TGCAACAGCTTAATGGATTTTACAAAA 59.287 29.630 0.00 0.00 0.00 2.44
2726 5008 7.212976 TGCAACAGCTTAATGGATTTTACAAA 58.787 30.769 0.00 0.00 0.00 2.83
2727 5009 6.753180 TGCAACAGCTTAATGGATTTTACAA 58.247 32.000 0.00 0.00 0.00 2.41
2728 5010 6.208402 TCTGCAACAGCTTAATGGATTTTACA 59.792 34.615 0.00 0.00 0.00 2.41
2729 5011 6.528072 GTCTGCAACAGCTTAATGGATTTTAC 59.472 38.462 0.00 0.00 0.00 2.01
2730 5012 6.208402 TGTCTGCAACAGCTTAATGGATTTTA 59.792 34.615 0.00 0.00 32.81 1.52
2731 5013 5.010922 TGTCTGCAACAGCTTAATGGATTTT 59.989 36.000 0.00 0.00 32.81 1.82
2732 5014 4.523943 TGTCTGCAACAGCTTAATGGATTT 59.476 37.500 0.00 0.00 32.81 2.17
2733 5015 4.081406 TGTCTGCAACAGCTTAATGGATT 58.919 39.130 0.00 0.00 32.81 3.01
2734 5016 3.689347 TGTCTGCAACAGCTTAATGGAT 58.311 40.909 0.00 0.00 32.81 3.41
2735 5017 3.138884 TGTCTGCAACAGCTTAATGGA 57.861 42.857 0.00 0.00 32.81 3.41
2736 5018 4.445452 AATGTCTGCAACAGCTTAATGG 57.555 40.909 7.58 0.00 42.37 3.16
2737 5019 5.571741 CAGAAATGTCTGCAACAGCTTAATG 59.428 40.000 0.00 0.00 44.74 1.90
2738 5020 5.706916 CAGAAATGTCTGCAACAGCTTAAT 58.293 37.500 0.00 0.00 44.74 1.40
2739 5021 5.112220 CAGAAATGTCTGCAACAGCTTAA 57.888 39.130 0.00 0.00 44.74 1.85
2740 5022 4.754372 CAGAAATGTCTGCAACAGCTTA 57.246 40.909 0.00 0.00 44.74 3.09
2741 5023 3.637998 CAGAAATGTCTGCAACAGCTT 57.362 42.857 0.00 4.29 44.74 3.74
2751 5033 4.686554 GCAGACGAGTTTACAGAAATGTCT 59.313 41.667 0.00 0.00 36.03 3.41
2752 5034 4.447724 TGCAGACGAGTTTACAGAAATGTC 59.552 41.667 0.00 0.00 0.00 3.06
2753 5035 4.377021 TGCAGACGAGTTTACAGAAATGT 58.623 39.130 0.00 0.00 0.00 2.71
2754 5036 4.990543 TGCAGACGAGTTTACAGAAATG 57.009 40.909 0.00 0.00 0.00 2.32
2755 5037 5.057149 AGTTGCAGACGAGTTTACAGAAAT 58.943 37.500 0.00 0.00 0.00 2.17
2756 5038 4.439057 AGTTGCAGACGAGTTTACAGAAA 58.561 39.130 0.00 0.00 0.00 2.52
2757 5039 4.054780 AGTTGCAGACGAGTTTACAGAA 57.945 40.909 0.00 0.00 0.00 3.02
2758 5040 3.728076 AGTTGCAGACGAGTTTACAGA 57.272 42.857 0.00 0.00 0.00 3.41
2759 5041 4.150098 GGTAAGTTGCAGACGAGTTTACAG 59.850 45.833 0.00 0.00 0.00 2.74
2760 5042 4.053295 GGTAAGTTGCAGACGAGTTTACA 58.947 43.478 0.00 0.00 0.00 2.41
2761 5043 4.053295 TGGTAAGTTGCAGACGAGTTTAC 58.947 43.478 0.00 0.00 0.00 2.01
2762 5044 4.053295 GTGGTAAGTTGCAGACGAGTTTA 58.947 43.478 0.00 0.00 0.00 2.01
2763 5045 2.870411 GTGGTAAGTTGCAGACGAGTTT 59.130 45.455 0.00 0.00 0.00 2.66
2764 5046 2.480845 GTGGTAAGTTGCAGACGAGTT 58.519 47.619 0.00 0.00 0.00 3.01
2765 5047 1.270147 GGTGGTAAGTTGCAGACGAGT 60.270 52.381 0.00 0.00 0.00 4.18
2766 5048 1.000955 AGGTGGTAAGTTGCAGACGAG 59.999 52.381 0.00 0.00 0.00 4.18
2767 5049 1.045407 AGGTGGTAAGTTGCAGACGA 58.955 50.000 0.00 0.00 0.00 4.20
2768 5050 1.878953 AAGGTGGTAAGTTGCAGACG 58.121 50.000 0.00 0.00 0.00 4.18
2769 5051 2.293399 CCAAAGGTGGTAAGTTGCAGAC 59.707 50.000 0.00 0.00 40.42 3.51
2770 5052 2.582052 CCAAAGGTGGTAAGTTGCAGA 58.418 47.619 0.00 0.00 40.42 4.26
2771 5053 1.613437 CCCAAAGGTGGTAAGTTGCAG 59.387 52.381 0.00 0.00 44.30 4.41
2772 5054 1.698506 CCCAAAGGTGGTAAGTTGCA 58.301 50.000 0.00 0.00 44.30 4.08


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

AutoCloner maintained by Alex Coulton.