Multiple sequence alignment - TraesCS3D01G341300

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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 TraesCS3D01G341300 chr3D 100.000 2800 0 0 1 2800 454678681 454675882 0.000000e+00 5171
1 TraesCS3D01G341300 chr3D 85.424 590 78 5 1 585 49569030 49568444 8.580000e-170 606
2 TraesCS3D01G341300 chr3A 92.814 2171 86 36 605 2753 596753168 596751046 0.000000e+00 3081
3 TraesCS3D01G341300 chr3B 94.604 1946 61 17 819 2753 597462174 597460262 0.000000e+00 2972
4 TraesCS3D01G341300 chrUn 86.847 593 73 3 1 589 67009324 67008733 0.000000e+00 658
5 TraesCS3D01G341300 chrUn 86.678 593 74 3 1 589 171278614 171279205 0.000000e+00 652
6 TraesCS3D01G341300 chrUn 86.509 593 75 3 1 589 171267941 171268532 0.000000e+00 647
7 TraesCS3D01G341300 chr1D 86.757 589 71 4 1 584 474298888 474299474 0.000000e+00 649
8 TraesCS3D01G341300 chr5B 86.195 594 73 6 1 587 584866237 584865646 3.930000e-178 634
9 TraesCS3D01G341300 chr4D 86.003 593 75 5 1 588 73308190 73308779 1.830000e-176 628
10 TraesCS3D01G341300 chr4D 83.108 148 25 0 1112 1259 334110129 334109982 4.860000e-28 135
11 TraesCS3D01G341300 chr1A 85.835 593 75 6 1 587 307447885 307448474 3.060000e-174 621
12 TraesCS3D01G341300 chr2D 85.448 591 79 5 1 586 32523740 32523152 2.380000e-170 608
13 TraesCS3D01G341300 chr1B 81.712 257 35 5 1113 1369 530610290 530610534 1.310000e-48 204
14 TraesCS3D01G341300 chr4A 85.333 150 18 3 1112 1259 139613127 139613274 4.830000e-33 152
15 TraesCS3D01G341300 chr4B 83.108 148 25 0 1112 1259 412084720 412084573 4.860000e-28 135


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 TraesCS3D01G341300 chr3D 454675882 454678681 2799 True 5171 5171 100.000 1 2800 1 chr3D.!!$R2 2799
1 TraesCS3D01G341300 chr3D 49568444 49569030 586 True 606 606 85.424 1 585 1 chr3D.!!$R1 584
2 TraesCS3D01G341300 chr3A 596751046 596753168 2122 True 3081 3081 92.814 605 2753 1 chr3A.!!$R1 2148
3 TraesCS3D01G341300 chr3B 597460262 597462174 1912 True 2972 2972 94.604 819 2753 1 chr3B.!!$R1 1934
4 TraesCS3D01G341300 chrUn 67008733 67009324 591 True 658 658 86.847 1 589 1 chrUn.!!$R1 588
5 TraesCS3D01G341300 chrUn 171278614 171279205 591 False 652 652 86.678 1 589 1 chrUn.!!$F2 588
6 TraesCS3D01G341300 chrUn 171267941 171268532 591 False 647 647 86.509 1 589 1 chrUn.!!$F1 588
7 TraesCS3D01G341300 chr1D 474298888 474299474 586 False 649 649 86.757 1 584 1 chr1D.!!$F1 583
8 TraesCS3D01G341300 chr5B 584865646 584866237 591 True 634 634 86.195 1 587 1 chr5B.!!$R1 586
9 TraesCS3D01G341300 chr4D 73308190 73308779 589 False 628 628 86.003 1 588 1 chr4D.!!$F1 587
10 TraesCS3D01G341300 chr1A 307447885 307448474 589 False 621 621 85.835 1 587 1 chr1A.!!$F1 586
11 TraesCS3D01G341300 chr2D 32523152 32523740 588 True 608 608 85.448 1 586 1 chr2D.!!$R1 585

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
86 87 0.322187 GTATCCGCCCACCAGTGTTT 60.322 55.0 0.00 0.00 0.0 2.83 F
378 383 0.394565 AGCATAACCTCCGGATCAGC 59.605 55.0 3.57 3.88 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 1310 0.368227 CACGATGACGAGCTTCTTGC 59.632 55.0 0.0 0.0 42.66 4.01 R
2057 2071 0.791422 TTGTCGAAAACCCGCATACG 59.209 50.0 0.0 0.0 39.67 3.06 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 3.560902 TTCCAATGTAAATTTGCGCGA 57.439 38.095 12.10 0.00 0.00 5.87
45 46 1.719709 CGCGATCTACGTGGTCAGA 59.280 57.895 0.00 0.00 46.86 3.27
49 50 2.479730 GCGATCTACGTGGTCAGACATT 60.480 50.000 2.17 0.00 44.60 2.71
79 80 2.096248 TCAAATTTGTATCCGCCCACC 58.904 47.619 17.47 0.00 0.00 4.61
86 87 0.322187 GTATCCGCCCACCAGTGTTT 60.322 55.000 0.00 0.00 0.00 2.83
95 96 3.119137 GCCCACCAGTGTTTCCAATATTC 60.119 47.826 0.00 0.00 0.00 1.75
98 99 5.245977 CCCACCAGTGTTTCCAATATTCTTT 59.754 40.000 0.00 0.00 0.00 2.52
110 111 5.951148 TCCAATATTCTTTGTCATTGGCTGA 59.049 36.000 7.21 0.00 44.64 4.26
114 115 2.844946 TCTTTGTCATTGGCTGAACGA 58.155 42.857 0.00 0.00 35.07 3.85
124 125 6.251376 GTCATTGGCTGAACGATATTTCAAAC 59.749 38.462 0.00 0.00 35.07 2.93
129 130 5.335661 GGCTGAACGATATTTCAAACAGGTT 60.336 40.000 0.00 0.00 35.07 3.50
153 154 1.875488 ACGCTAATAAGGGTGGGAGT 58.125 50.000 0.00 0.00 46.31 3.85
165 166 1.134189 GGTGGGAGTGTATGCCTTACC 60.134 57.143 0.00 0.00 40.89 2.85
170 171 2.438021 GGAGTGTATGCCTTACCATGGA 59.562 50.000 21.47 0.00 0.00 3.41
178 179 1.821216 CCTTACCATGGACGCTTTGT 58.179 50.000 21.47 0.00 0.00 2.83
193 195 7.470289 GACGCTTTGTCTATGTAGAATGATT 57.530 36.000 0.00 0.00 44.58 2.57
221 223 9.376075 TGTTTTTAATGACAAAAATGCTTCTCA 57.624 25.926 0.00 0.00 39.04 3.27
253 258 2.710220 TTTCTGTACGCACTCGCTTA 57.290 45.000 0.00 0.00 39.84 3.09
263 268 2.194271 GCACTCGCTTAGTACATGGTC 58.806 52.381 0.00 0.00 35.76 4.02
275 280 3.760151 AGTACATGGTCTACGCTACAACA 59.240 43.478 0.00 0.00 0.00 3.33
301 306 4.560716 CGGAGTATCAACCACTGTTCAAGA 60.561 45.833 0.00 0.00 36.25 3.02
314 319 2.198406 GTTCAAGACAGTGTGTACGCA 58.802 47.619 4.65 4.65 0.00 5.24
319 324 1.407618 AGACAGTGTGTACGCAGTTGA 59.592 47.619 21.35 0.00 37.78 3.18
324 329 1.329292 GTGTGTACGCAGTTGAAGCAA 59.671 47.619 9.91 0.00 37.78 3.91
366 371 4.836125 CCAACATGGGTATCAGCATAAC 57.164 45.455 0.00 0.00 32.67 1.89
378 383 0.394565 AGCATAACCTCCGGATCAGC 59.605 55.000 3.57 3.88 0.00 4.26
414 419 2.361119 GACATAGGCATAGTGTCGGTCA 59.639 50.000 5.60 0.00 33.73 4.02
418 423 5.246203 ACATAGGCATAGTGTCGGTCAATAT 59.754 40.000 0.00 0.00 37.74 1.28
458 463 5.784578 ATTGTCGGCTTTTTACCTTTCTT 57.215 34.783 0.00 0.00 0.00 2.52
462 467 5.808030 TGTCGGCTTTTTACCTTTCTTTTTG 59.192 36.000 0.00 0.00 0.00 2.44
470 475 8.980143 TTTTTACCTTTCTTTTTGTCAGACTG 57.020 30.769 1.31 0.00 0.00 3.51
471 476 7.696992 TTTACCTTTCTTTTTGTCAGACTGT 57.303 32.000 1.59 0.00 0.00 3.55
483 488 3.251571 GTCAGACTGTCGGTATTTGGTC 58.748 50.000 7.78 0.00 0.00 4.02
537 542 7.095607 GGTGATACTCTTAATGCTTTGTATCCG 60.096 40.741 13.45 0.00 36.89 4.18
554 559 7.151999 TGTATCCGTTTGATGCTACATTTTT 57.848 32.000 0.00 0.00 37.04 1.94
666 671 6.910191 TGAATATGTAAACCAGTCCATCCAT 58.090 36.000 0.00 0.00 0.00 3.41
669 674 5.975988 ATGTAAACCAGTCCATCCATACT 57.024 39.130 0.00 0.00 0.00 2.12
675 680 3.451178 ACCAGTCCATCCATACTGTGTAC 59.549 47.826 0.00 0.00 41.25 2.90
679 684 4.890581 AGTCCATCCATACTGTGTACTCTC 59.109 45.833 0.00 0.00 0.00 3.20
686 691 6.299922 TCCATACTGTGTACTCTCCTGATAG 58.700 44.000 0.00 0.00 0.00 2.08
689 694 2.292016 CTGTGTACTCTCCTGATAGCGG 59.708 54.545 0.00 0.00 0.00 5.52
692 697 3.250521 GTGTACTCTCCTGATAGCGGTAC 59.749 52.174 0.00 0.00 0.00 3.34
710 715 5.511088 GGTACGTGAAGTGTACTTTGATG 57.489 43.478 0.00 0.00 41.47 3.07
712 717 4.067972 ACGTGAAGTGTACTTTGATGGT 57.932 40.909 0.00 0.00 36.11 3.55
714 719 5.603596 ACGTGAAGTGTACTTTGATGGTTA 58.396 37.500 0.00 0.00 36.11 2.85
716 721 6.202188 ACGTGAAGTGTACTTTGATGGTTAAG 59.798 38.462 0.00 0.00 36.11 1.85
717 722 6.347402 CGTGAAGTGTACTTTGATGGTTAAGG 60.347 42.308 0.00 0.00 36.11 2.69
718 723 5.472137 TGAAGTGTACTTTGATGGTTAAGGC 59.528 40.000 0.00 0.00 36.11 4.35
726 731 6.012745 ACTTTGATGGTTAAGGCAAGATTCT 58.987 36.000 0.00 0.00 0.00 2.40
727 732 6.151817 ACTTTGATGGTTAAGGCAAGATTCTC 59.848 38.462 0.00 0.00 0.00 2.87
737 742 5.831702 AGGCAAGATTCTCATCAACAATC 57.168 39.130 0.00 0.00 0.00 2.67
754 761 8.109705 TCAACAATCACTATTATTGTGCACTT 57.890 30.769 19.41 8.24 44.66 3.16
756 763 8.853345 CAACAATCACTATTATTGTGCACTTTC 58.147 33.333 19.41 0.00 44.66 2.62
1225 1233 2.109126 GTTCAGCTGCCCGATCACC 61.109 63.158 9.47 0.00 0.00 4.02
1648 1662 5.788014 AGTTCTCTCATCTTTCTTTACCCCT 59.212 40.000 0.00 0.00 0.00 4.79
1882 1896 5.402398 GGAAAATCTTTCATAGTGTGTGCC 58.598 41.667 1.88 0.00 0.00 5.01
1948 1962 9.527157 TCTACAAAAATCTTTCATAACATGGGA 57.473 29.630 0.00 0.00 0.00 4.37
1949 1963 9.793252 CTACAAAAATCTTTCATAACATGGGAG 57.207 33.333 0.00 0.00 0.00 4.30
1950 1964 8.193953 ACAAAAATCTTTCATAACATGGGAGT 57.806 30.769 0.00 0.00 0.00 3.85
1951 1965 8.090214 ACAAAAATCTTTCATAACATGGGAGTG 58.910 33.333 0.00 0.00 0.00 3.51
1993 2007 6.487668 ACAGAAGACAATGTGTGATTCAATGA 59.512 34.615 0.00 0.00 32.37 2.57
2024 2038 6.283694 TCTTTATATTAGTCACCTGCTGCAG 58.716 40.000 22.44 22.44 0.00 4.41
2057 2071 3.928375 CCACTTGGCACATTTAATTCAGC 59.072 43.478 0.00 0.00 39.30 4.26
2073 2087 3.477085 GCGTATGCGGGTTTTCGA 58.523 55.556 5.09 0.00 38.78 3.71
2074 2088 1.059838 GCGTATGCGGGTTTTCGAC 59.940 57.895 5.09 0.00 38.78 4.20
2093 2109 4.585162 TCGACAAATCCCTAGGAGAATCTC 59.415 45.833 11.48 0.71 34.05 2.75
2109 2125 1.804601 TCTCACAAGCACTGCTCATG 58.195 50.000 3.40 6.10 38.25 3.07
2200 2216 3.454375 TCGGCAAATCGACTTAAGATCC 58.546 45.455 10.09 0.00 33.92 3.36
2219 2235 1.750399 CCCCATTGCCGAGGAACTG 60.750 63.158 0.00 0.00 41.55 3.16
2281 2305 2.224548 ACGAAAGGAAAGGGAAGTGGAG 60.225 50.000 0.00 0.00 0.00 3.86
2333 2357 8.692710 TCCGAAATGCTTAGAGAAGTTCTAATA 58.307 33.333 5.09 0.00 45.07 0.98
2334 2358 9.314321 CCGAAATGCTTAGAGAAGTTCTAATAA 57.686 33.333 5.09 7.50 45.07 1.40
2507 2534 9.880157 AATCCAAAATTCAAAACATATCTCCAG 57.120 29.630 0.00 0.00 0.00 3.86
2552 2579 6.506500 AATTCCAGTTGAGAATACAAGCTG 57.493 37.500 0.00 0.00 32.80 4.24
2580 2610 2.649531 TGGGTTGTTAACTGGTCCTG 57.350 50.000 7.22 0.00 0.00 3.86
2649 2679 3.068732 TGGAATTTCGGCAAATTGTGTGA 59.931 39.130 10.82 0.00 41.47 3.58
2753 2791 2.244695 CCCCGGTGCTGTAGATACATA 58.755 52.381 0.00 0.00 35.36 2.29
2754 2792 2.832129 CCCCGGTGCTGTAGATACATAT 59.168 50.000 0.00 0.00 35.36 1.78
2755 2793 4.021229 CCCCGGTGCTGTAGATACATATA 58.979 47.826 0.00 0.00 35.36 0.86
2756 2794 4.464951 CCCCGGTGCTGTAGATACATATAA 59.535 45.833 0.00 0.00 35.36 0.98
2757 2795 5.128827 CCCCGGTGCTGTAGATACATATAAT 59.871 44.000 0.00 0.00 35.36 1.28
2758 2796 6.351881 CCCCGGTGCTGTAGATACATATAATT 60.352 42.308 0.00 0.00 35.36 1.40
2759 2797 7.103641 CCCGGTGCTGTAGATACATATAATTT 58.896 38.462 0.00 0.00 35.36 1.82
2760 2798 7.064609 CCCGGTGCTGTAGATACATATAATTTG 59.935 40.741 0.00 0.00 35.36 2.32
2761 2799 7.602644 CCGGTGCTGTAGATACATATAATTTGT 59.397 37.037 0.00 0.00 35.36 2.83
2762 2800 8.435430 CGGTGCTGTAGATACATATAATTTGTG 58.565 37.037 0.00 0.00 35.36 3.33
2763 2801 8.230486 GGTGCTGTAGATACATATAATTTGTGC 58.770 37.037 0.00 0.00 35.36 4.57
2764 2802 8.993121 GTGCTGTAGATACATATAATTTGTGCT 58.007 33.333 0.00 0.00 35.36 4.40
2765 2803 9.208022 TGCTGTAGATACATATAATTTGTGCTC 57.792 33.333 0.00 0.00 35.36 4.26
2766 2804 9.208022 GCTGTAGATACATATAATTTGTGCTCA 57.792 33.333 0.00 0.00 35.36 4.26
2773 2811 9.882996 ATACATATAATTTGTGCTCAATCAACG 57.117 29.630 1.43 0.00 33.32 4.10
2774 2812 7.761409 ACATATAATTTGTGCTCAATCAACGT 58.239 30.769 1.43 0.00 33.32 3.99
2775 2813 7.910162 ACATATAATTTGTGCTCAATCAACGTC 59.090 33.333 1.43 0.00 33.32 4.34
2776 2814 4.566545 AATTTGTGCTCAATCAACGTCA 57.433 36.364 1.43 0.00 33.32 4.35
2777 2815 4.566545 ATTTGTGCTCAATCAACGTCAA 57.433 36.364 1.43 0.00 33.32 3.18
2778 2816 3.332761 TTGTGCTCAATCAACGTCAAC 57.667 42.857 0.00 0.00 0.00 3.18
2779 2817 2.284190 TGTGCTCAATCAACGTCAACA 58.716 42.857 0.00 0.00 0.00 3.33
2780 2818 2.680339 TGTGCTCAATCAACGTCAACAA 59.320 40.909 0.00 0.00 0.00 2.83
2781 2819 3.314913 TGTGCTCAATCAACGTCAACAAT 59.685 39.130 0.00 0.00 0.00 2.71
2782 2820 3.908382 GTGCTCAATCAACGTCAACAATC 59.092 43.478 0.00 0.00 0.00 2.67
2783 2821 3.814842 TGCTCAATCAACGTCAACAATCT 59.185 39.130 0.00 0.00 0.00 2.40
2784 2822 4.153986 GCTCAATCAACGTCAACAATCTG 58.846 43.478 0.00 0.00 0.00 2.90
2785 2823 4.083855 GCTCAATCAACGTCAACAATCTGA 60.084 41.667 0.00 0.00 0.00 3.27
2786 2824 5.342806 TCAATCAACGTCAACAATCTGAC 57.657 39.130 0.00 0.00 41.98 3.51
2787 2825 4.813697 TCAATCAACGTCAACAATCTGACA 59.186 37.500 4.75 0.00 45.03 3.58
2788 2826 5.295540 TCAATCAACGTCAACAATCTGACAA 59.704 36.000 4.75 0.00 45.03 3.18
2789 2827 5.947228 ATCAACGTCAACAATCTGACAAT 57.053 34.783 4.75 0.00 45.03 2.71
2790 2828 5.094429 TCAACGTCAACAATCTGACAATG 57.906 39.130 4.75 2.90 45.03 2.82
2791 2829 3.542712 ACGTCAACAATCTGACAATGC 57.457 42.857 4.75 0.00 45.03 3.56
2792 2830 2.877786 ACGTCAACAATCTGACAATGCA 59.122 40.909 4.75 0.00 45.03 3.96
2793 2831 3.228749 CGTCAACAATCTGACAATGCAC 58.771 45.455 0.00 0.00 45.03 4.57
2794 2832 3.568538 GTCAACAATCTGACAATGCACC 58.431 45.455 0.00 0.00 44.32 5.01
2795 2833 3.004629 GTCAACAATCTGACAATGCACCA 59.995 43.478 0.00 0.00 44.32 4.17
2796 2834 3.827876 TCAACAATCTGACAATGCACCAT 59.172 39.130 0.00 0.00 0.00 3.55
2797 2835 5.008980 TCAACAATCTGACAATGCACCATA 58.991 37.500 0.00 0.00 0.00 2.74
2798 2836 5.476254 TCAACAATCTGACAATGCACCATAA 59.524 36.000 0.00 0.00 0.00 1.90
2799 2837 5.981088 ACAATCTGACAATGCACCATAAA 57.019 34.783 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 0.459585 ACCACGTAGATCGCGCAAAT 60.460 50.000 8.75 0.00 44.19 2.32
31 32 7.438459 GCTATTTAAATGTCTGACCACGTAGAT 59.562 37.037 11.05 0.00 0.00 1.98
49 50 6.908284 GCGGATACAAATTTGACGCTATTTAA 59.092 34.615 28.43 7.19 37.48 1.52
79 80 8.918658 CAATGACAAAGAATATTGGAAACACTG 58.081 33.333 0.00 0.00 42.67 3.66
95 96 3.837213 ATCGTTCAGCCAATGACAAAG 57.163 42.857 0.00 0.00 37.77 2.77
98 99 4.940654 TGAAATATCGTTCAGCCAATGACA 59.059 37.500 0.00 0.00 37.77 3.58
110 111 7.166804 CGTTTTGAACCTGTTTGAAATATCGTT 59.833 33.333 0.00 0.00 0.00 3.85
114 115 6.512297 AGCGTTTTGAACCTGTTTGAAATAT 58.488 32.000 0.00 0.00 0.00 1.28
124 125 4.457949 ACCCTTATTAGCGTTTTGAACCTG 59.542 41.667 0.00 0.00 0.00 4.00
129 130 3.009253 TCCCACCCTTATTAGCGTTTTGA 59.991 43.478 0.00 0.00 0.00 2.69
153 154 1.474320 GCGTCCATGGTAAGGCATACA 60.474 52.381 12.58 0.00 36.14 2.29
165 166 4.682787 TCTACATAGACAAAGCGTCCATG 58.317 43.478 0.00 0.00 45.88 3.66
170 171 7.849804 AAATCATTCTACATAGACAAAGCGT 57.150 32.000 0.00 0.00 30.81 5.07
229 231 4.516092 GCGAGTGCGTACAGAAAATAAT 57.484 40.909 6.38 0.00 40.36 1.28
253 258 3.760151 TGTTGTAGCGTAGACCATGTACT 59.240 43.478 0.00 0.00 0.00 2.73
275 280 1.623811 ACAGTGGTTGATACTCCGCTT 59.376 47.619 0.00 0.00 41.81 4.68
301 306 2.201732 CTTCAACTGCGTACACACTGT 58.798 47.619 0.00 0.00 0.00 3.55
324 329 6.335781 TGGGTAAAATCCTTTATAGCCACT 57.664 37.500 0.00 0.00 29.62 4.00
378 383 4.518211 GCCTATGTCAAAAGAGATGATGGG 59.482 45.833 0.00 0.00 0.00 4.00
414 419 5.818678 TTCGGCAATAGTAGGGTCATATT 57.181 39.130 0.00 0.00 0.00 1.28
418 423 3.199071 ACAATTCGGCAATAGTAGGGTCA 59.801 43.478 0.00 0.00 0.00 4.02
444 449 9.076596 CAGTCTGACAAAAAGAAAGGTAAAAAG 57.923 33.333 10.88 0.00 0.00 2.27
445 450 8.581578 ACAGTCTGACAAAAAGAAAGGTAAAAA 58.418 29.630 10.88 0.00 0.00 1.94
451 456 4.260784 CCGACAGTCTGACAAAAAGAAAGG 60.261 45.833 10.88 0.00 0.00 3.11
458 463 4.513692 CCAAATACCGACAGTCTGACAAAA 59.486 41.667 10.88 0.00 0.00 2.44
462 467 3.251571 GACCAAATACCGACAGTCTGAC 58.748 50.000 6.91 0.00 0.00 3.51
470 475 0.441145 GCACACGACCAAATACCGAC 59.559 55.000 0.00 0.00 0.00 4.79
471 476 0.033642 TGCACACGACCAAATACCGA 59.966 50.000 0.00 0.00 0.00 4.69
508 513 4.755266 AAGCATTAAGAGTATCACCCGT 57.245 40.909 0.00 0.00 37.82 5.28
657 662 4.038162 GGAGAGTACACAGTATGGATGGAC 59.962 50.000 0.00 0.00 43.62 4.02
666 671 4.127907 CGCTATCAGGAGAGTACACAGTA 58.872 47.826 0.00 0.00 0.00 2.74
669 674 2.298610 CCGCTATCAGGAGAGTACACA 58.701 52.381 0.00 0.00 0.00 3.72
675 680 1.264557 CACGTACCGCTATCAGGAGAG 59.735 57.143 0.00 0.00 0.00 3.20
679 684 1.404391 ACTTCACGTACCGCTATCAGG 59.596 52.381 0.00 0.00 0.00 3.86
686 691 2.056094 AAGTACACTTCACGTACCGC 57.944 50.000 0.00 0.00 40.10 5.68
689 694 4.986659 ACCATCAAAGTACACTTCACGTAC 59.013 41.667 0.00 0.00 39.64 3.67
692 697 6.347402 CCTTAACCATCAAAGTACACTTCACG 60.347 42.308 0.00 0.00 34.61 4.35
695 700 5.472137 TGCCTTAACCATCAAAGTACACTTC 59.528 40.000 0.00 0.00 34.61 3.01
707 712 5.824624 TGATGAGAATCTTGCCTTAACCATC 59.175 40.000 0.00 0.00 34.92 3.51
710 715 5.415701 TGTTGATGAGAATCTTGCCTTAACC 59.584 40.000 0.00 0.00 34.92 2.85
712 717 7.394077 TGATTGTTGATGAGAATCTTGCCTTAA 59.606 33.333 0.00 0.00 38.50 1.85
714 719 5.713389 TGATTGTTGATGAGAATCTTGCCTT 59.287 36.000 0.00 0.00 38.50 4.35
716 721 5.125097 AGTGATTGTTGATGAGAATCTTGCC 59.875 40.000 0.00 0.00 38.50 4.52
717 722 6.192234 AGTGATTGTTGATGAGAATCTTGC 57.808 37.500 0.00 0.00 38.50 4.01
726 731 8.183536 GTGCACAATAATAGTGATTGTTGATGA 58.816 33.333 13.17 0.00 43.38 2.92
727 732 8.186163 AGTGCACAATAATAGTGATTGTTGATG 58.814 33.333 21.04 8.65 43.38 3.07
835 842 7.123355 TCCTTTTTAGGCCATATTTGATTGG 57.877 36.000 5.01 0.00 36.03 3.16
1100 1108 1.225376 TTGCCCATGTTGTCGTCGTC 61.225 55.000 0.00 0.00 0.00 4.20
1101 1109 1.227704 TTGCCCATGTTGTCGTCGT 60.228 52.632 0.00 0.00 0.00 4.34
1302 1310 0.368227 CACGATGACGAGCTTCTTGC 59.632 55.000 0.00 0.00 42.66 4.01
1418 1426 2.694760 GCCGCTTGCTCTTCTTGGG 61.695 63.158 0.00 0.00 36.87 4.12
1648 1662 4.832492 AGCAAGAATAATAGGAGGAGGGA 58.168 43.478 0.00 0.00 0.00 4.20
1882 1896 8.306038 TCAACCATATCTTTCTTTTTGGTGATG 58.694 33.333 0.00 0.00 37.52 3.07
1947 1961 4.331717 TGTTTTGAACGAGAGGAAACACTC 59.668 41.667 0.00 0.00 43.68 3.51
1948 1962 4.258543 TGTTTTGAACGAGAGGAAACACT 58.741 39.130 0.00 0.00 35.86 3.55
1949 1963 4.331717 TCTGTTTTGAACGAGAGGAAACAC 59.668 41.667 0.00 0.00 35.86 3.32
1950 1964 4.509616 TCTGTTTTGAACGAGAGGAAACA 58.490 39.130 0.00 0.00 37.73 2.83
1951 1965 5.293569 TCTTCTGTTTTGAACGAGAGGAAAC 59.706 40.000 0.00 0.00 29.16 2.78
2024 2038 0.881796 GCCAAGTGGAGTTTAGTGCC 59.118 55.000 0.18 0.00 37.39 5.01
2057 2071 0.791422 TTGTCGAAAACCCGCATACG 59.209 50.000 0.00 0.00 39.67 3.06
2067 2081 5.492855 TTCTCCTAGGGATTTGTCGAAAA 57.507 39.130 9.46 0.00 0.00 2.29
2071 2085 4.342378 TGAGATTCTCCTAGGGATTTGTCG 59.658 45.833 9.46 0.00 0.00 4.35
2072 2086 5.129485 TGTGAGATTCTCCTAGGGATTTGTC 59.871 44.000 9.46 5.26 0.00 3.18
2073 2087 5.032846 TGTGAGATTCTCCTAGGGATTTGT 58.967 41.667 9.46 0.00 0.00 2.83
2074 2088 5.620738 TGTGAGATTCTCCTAGGGATTTG 57.379 43.478 9.46 0.00 0.00 2.32
2093 2109 2.292569 ACTTTCATGAGCAGTGCTTGTG 59.707 45.455 20.80 19.80 39.88 3.33
2109 2125 7.062956 CACTTTGGTTGTGTTCCTTTTACTTTC 59.937 37.037 0.00 0.00 0.00 2.62
2200 2216 2.440247 GTTCCTCGGCAATGGGGG 60.440 66.667 0.00 0.00 0.00 5.40
2219 2235 8.106247 TGTTGGTACTTATCATTTCCTTCAAC 57.894 34.615 0.00 0.00 0.00 3.18
2490 2517 9.567776 TTTCTGTTACTGGAGATATGTTTTGAA 57.432 29.630 0.00 0.00 0.00 2.69
2507 2534 9.464714 GAATTTCCCTTCTTCTTTTTCTGTTAC 57.535 33.333 0.00 0.00 0.00 2.50
2552 2579 7.362660 GGACCAGTTAACAACCCAAATTAGATC 60.363 40.741 8.61 0.00 0.00 2.75
2598 2628 6.183359 GCAGCTCAAGAACAAAATAAATCACG 60.183 38.462 0.00 0.00 0.00 4.35
2753 2791 6.252967 TGACGTTGATTGAGCACAAATTAT 57.747 33.333 0.00 0.00 39.54 1.28
2754 2792 5.681337 TGACGTTGATTGAGCACAAATTA 57.319 34.783 0.00 0.00 39.54 1.40
2755 2793 4.566545 TGACGTTGATTGAGCACAAATT 57.433 36.364 0.00 0.00 39.54 1.82
2756 2794 4.202000 TGTTGACGTTGATTGAGCACAAAT 60.202 37.500 0.00 0.00 39.54 2.32
2757 2795 3.127721 TGTTGACGTTGATTGAGCACAAA 59.872 39.130 0.00 0.00 39.54 2.83
2758 2796 2.680339 TGTTGACGTTGATTGAGCACAA 59.320 40.909 0.00 0.00 40.42 3.33
2759 2797 2.284190 TGTTGACGTTGATTGAGCACA 58.716 42.857 0.00 0.00 0.00 4.57
2760 2798 3.332761 TTGTTGACGTTGATTGAGCAC 57.667 42.857 0.00 0.00 0.00 4.40
2761 2799 3.814842 AGATTGTTGACGTTGATTGAGCA 59.185 39.130 0.00 0.00 0.00 4.26
2762 2800 4.083855 TCAGATTGTTGACGTTGATTGAGC 60.084 41.667 0.00 0.00 0.00 4.26
2763 2801 5.377358 GTCAGATTGTTGACGTTGATTGAG 58.623 41.667 0.00 0.00 38.23 3.02
2764 2802 5.342806 GTCAGATTGTTGACGTTGATTGA 57.657 39.130 0.00 0.00 38.23 2.57
2773 2811 3.004629 TGGTGCATTGTCAGATTGTTGAC 59.995 43.478 0.00 0.00 46.02 3.18
2774 2812 3.220940 TGGTGCATTGTCAGATTGTTGA 58.779 40.909 0.00 0.00 0.00 3.18
2775 2813 3.646611 TGGTGCATTGTCAGATTGTTG 57.353 42.857 0.00 0.00 0.00 3.33
2776 2814 5.981088 TTATGGTGCATTGTCAGATTGTT 57.019 34.783 0.00 0.00 0.00 2.83
2777 2815 5.981088 TTTATGGTGCATTGTCAGATTGT 57.019 34.783 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.