Multiple sequence alignment - TraesCS3D01G264800

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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 TraesCS3D01G264800 chr3D 100.000 3934 0 0 1 3934 366457669 366453736 0.000000e+00 7265.0
1 TraesCS3D01G264800 chr3D 100.000 1847 0 0 4240 6086 366453430 366451584 0.000000e+00 3411.0
2 TraesCS3D01G264800 chr3D 93.878 49 3 0 5771 5819 471583899 471583947 2.350000e-09 75.0
3 TraesCS3D01G264800 chr3B 97.458 3265 54 9 692 3934 477888515 477885258 0.000000e+00 5542.0
4 TraesCS3D01G264800 chr3B 95.489 1330 47 3 4769 6086 477884470 477883142 0.000000e+00 2111.0
5 TraesCS3D01G264800 chr3B 92.971 441 29 2 4240 4679 477885214 477884775 5.140000e-180 641.0
6 TraesCS3D01G264800 chr3B 93.684 95 6 0 4677 4771 477884591 477884497 6.360000e-30 143.0
7 TraesCS3D01G264800 chr3A 98.143 3069 39 5 880 3934 488725032 488721968 0.000000e+00 5336.0
8 TraesCS3D01G264800 chr3A 94.307 1089 46 6 4769 5844 488721095 488720010 0.000000e+00 1653.0
9 TraesCS3D01G264800 chr3A 90.159 630 39 11 1 610 552491993 552492619 0.000000e+00 798.0
10 TraesCS3D01G264800 chr3A 92.412 514 33 5 4259 4771 488721630 488721122 0.000000e+00 728.0
11 TraesCS3D01G264800 chr3A 97.619 84 2 0 801 884 488725386 488725303 1.770000e-30 145.0
12 TraesCS3D01G264800 chr7A 90.735 626 39 9 1 610 471006506 471005884 0.000000e+00 817.0
13 TraesCS3D01G264800 chr7A 86.813 91 12 0 5737 5827 729061355 729061265 1.080000e-17 102.0
14 TraesCS3D01G264800 chr7A 88.750 80 8 1 5732 5811 495541623 495541545 5.020000e-16 97.1
15 TraesCS3D01G264800 chr2B 90.156 640 45 13 1 626 20670662 20670027 0.000000e+00 817.0
16 TraesCS3D01G264800 chr6D 90.446 628 37 9 1 609 447471350 447471973 0.000000e+00 806.0
17 TraesCS3D01G264800 chr6D 89.157 83 8 1 5737 5819 420014028 420013947 1.080000e-17 102.0
18 TraesCS3D01G264800 chr6D 87.500 88 10 1 5732 5819 460278819 460278733 3.880000e-17 100.0
19 TraesCS3D01G264800 chr6A 90.224 624 45 8 1 610 609486326 609485705 0.000000e+00 800.0
20 TraesCS3D01G264800 chr5A 89.612 645 43 12 1 625 547998596 547999236 0.000000e+00 798.0
21 TraesCS3D01G264800 chr5A 89.812 638 44 15 1 619 681493355 681493990 0.000000e+00 798.0
22 TraesCS3D01G264800 chr1A 89.606 635 51 10 1 623 9211055 9211686 0.000000e+00 793.0
23 TraesCS3D01G264800 chr1A 82.803 628 94 11 3314 3934 551321505 551320885 3.210000e-152 549.0
24 TraesCS3D01G264800 chr1A 80.560 571 85 25 2623 3181 551322198 551321642 3.390000e-112 416.0
25 TraesCS3D01G264800 chr2A 89.936 626 42 16 1 614 493371011 493370395 0.000000e+00 787.0
26 TraesCS3D01G264800 chr2A 84.848 99 9 5 5737 5832 741239512 741239607 1.810000e-15 95.3
27 TraesCS3D01G264800 chr1D 83.121 628 92 12 3314 3934 458888535 458887915 1.480000e-155 560.0
28 TraesCS3D01G264800 chr1D 93.478 46 3 0 5773 5818 487690339 487690384 1.090000e-07 69.4
29 TraesCS3D01G264800 chr1B 82.830 629 92 12 3314 3934 630832731 630832111 3.210000e-152 549.0
30 TraesCS3D01G264800 chr1B 85.915 71 6 3 5750 5820 666254928 666254994 8.460000e-09 73.1
31 TraesCS3D01G264800 chr1B 97.297 37 0 1 5732 5768 3708761 3708726 1.830000e-05 62.1
32 TraesCS3D01G264800 chr5D 86.813 91 9 3 5732 5821 242627018 242626930 1.400000e-16 99.0
33 TraesCS3D01G264800 chr5D 89.655 58 4 2 5770 5826 255376138 255376194 8.460000e-09 73.1
34 TraesCS3D01G264800 chr5D 100.000 31 0 0 5788 5818 298290716 298290746 2.370000e-04 58.4
35 TraesCS3D01G264800 chr5B 85.870 92 9 4 5732 5821 101895065 101894976 1.810000e-15 95.3
36 TraesCS3D01G264800 chr4D 97.143 35 1 0 5784 5818 21145855 21145821 6.590000e-05 60.2
37 TraesCS3D01G264800 chr4A 90.698 43 4 0 5777 5819 257758435 257758477 2.370000e-04 58.4


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 TraesCS3D01G264800 chr3D 366451584 366457669 6085 True 5338.00 7265 100.00000 1 6086 2 chr3D.!!$R1 6085
1 TraesCS3D01G264800 chr3B 477883142 477888515 5373 True 2109.25 5542 94.90050 692 6086 4 chr3B.!!$R1 5394
2 TraesCS3D01G264800 chr3A 488720010 488725386 5376 True 1965.50 5336 95.62025 801 5844 4 chr3A.!!$R1 5043
3 TraesCS3D01G264800 chr3A 552491993 552492619 626 False 798.00 798 90.15900 1 610 1 chr3A.!!$F1 609
4 TraesCS3D01G264800 chr7A 471005884 471006506 622 True 817.00 817 90.73500 1 610 1 chr7A.!!$R1 609
5 TraesCS3D01G264800 chr2B 20670027 20670662 635 True 817.00 817 90.15600 1 626 1 chr2B.!!$R1 625
6 TraesCS3D01G264800 chr6D 447471350 447471973 623 False 806.00 806 90.44600 1 609 1 chr6D.!!$F1 608
7 TraesCS3D01G264800 chr6A 609485705 609486326 621 True 800.00 800 90.22400 1 610 1 chr6A.!!$R1 609
8 TraesCS3D01G264800 chr5A 547998596 547999236 640 False 798.00 798 89.61200 1 625 1 chr5A.!!$F1 624
9 TraesCS3D01G264800 chr5A 681493355 681493990 635 False 798.00 798 89.81200 1 619 1 chr5A.!!$F2 618
10 TraesCS3D01G264800 chr1A 9211055 9211686 631 False 793.00 793 89.60600 1 623 1 chr1A.!!$F1 622
11 TraesCS3D01G264800 chr1A 551320885 551322198 1313 True 482.50 549 81.68150 2623 3934 2 chr1A.!!$R1 1311
12 TraesCS3D01G264800 chr2A 493370395 493371011 616 True 787.00 787 89.93600 1 614 1 chr2A.!!$R1 613
13 TraesCS3D01G264800 chr1D 458887915 458888535 620 True 560.00 560 83.12100 3314 3934 1 chr1D.!!$R1 620
14 TraesCS3D01G264800 chr1B 630832111 630832731 620 True 549.00 549 82.83000 3314 3934 1 chr1B.!!$R2 620

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
491 530 1.876156 GAAGGAGGATAAGCGGCAATG 59.124 52.381 1.45 0.00 0.00 2.82 F
1481 1809 1.065926 CACTGTAATGCTGCCCTCTCA 60.066 52.381 0.00 0.00 0.00 3.27 F
1593 1921 3.436700 TGTATGTGCCGATCTGTGTAG 57.563 47.619 0.00 0.00 0.00 2.74 F
2516 2867 4.086706 AGGTGTCCCTTCTAAAGTGTTG 57.913 45.455 0.00 0.00 38.13 3.33 F
3308 3672 5.010012 CCTGAAAAAGCTGTATGTCTGGTTT 59.990 40.000 0.00 0.00 43.68 3.27 F
4435 4815 0.884704 ATGACCGTGGTCTGCAACAC 60.885 55.000 19.17 5.93 44.80 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1873 0.037139 CCAACACCCACCGATTCGTA 60.037 55.000 5.20 0.0 0.00 3.43 R
3195 3559 4.823989 ACTACCAAAGATATCATTGCTGGC 59.176 41.667 13.93 0.0 0.00 4.85 R
3308 3672 5.227569 TCAGAGTTTGCCTGACATAGAAA 57.772 39.130 0.00 0.0 35.89 2.52 R
3829 4195 0.028110 GCTGAATTTTCCTAGCGCGG 59.972 55.000 8.83 0.0 0.00 6.46 R
4800 5395 0.240945 CCTGAATTTGACCGGTGCAC 59.759 55.000 14.63 8.8 0.00 4.57 R
6002 6610 1.132453 GTTAGGGCGTGGATTTTCTGC 59.868 52.381 0.00 0.0 0.00 4.26 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
419 451 7.724061 ACGCCTTAGGATTAACCATATTCAAAT 59.276 33.333 0.69 0.00 42.04 2.32
491 530 1.876156 GAAGGAGGATAAGCGGCAATG 59.124 52.381 1.45 0.00 0.00 2.82
518 557 4.462483 TGCCTCGCAAAAATAAAGGAGATT 59.538 37.500 0.00 0.00 34.76 2.40
614 654 6.921857 GCACGGACTCTTTTGCTAGTATATAA 59.078 38.462 0.00 0.00 32.00 0.98
615 655 7.437267 GCACGGACTCTTTTGCTAGTATATAAA 59.563 37.037 0.00 0.00 32.00 1.40
616 656 9.309516 CACGGACTCTTTTGCTAGTATATAAAA 57.690 33.333 0.00 0.00 0.00 1.52
617 657 9.880157 ACGGACTCTTTTGCTAGTATATAAAAA 57.120 29.630 0.00 0.00 0.00 1.94
664 704 8.831715 AAAACAATGGGATAAAACAGATGAAC 57.168 30.769 0.00 0.00 0.00 3.18
665 705 7.781324 AACAATGGGATAAAACAGATGAACT 57.219 32.000 0.00 0.00 0.00 3.01
685 725 9.860898 ATGAACTGTTTATTTTATTTGGAGAGC 57.139 29.630 0.00 0.00 0.00 4.09
686 726 8.303876 TGAACTGTTTATTTTATTTGGAGAGCC 58.696 33.333 0.00 0.00 0.00 4.70
687 727 7.775053 ACTGTTTATTTTATTTGGAGAGCCA 57.225 32.000 0.00 0.00 44.17 4.75
688 728 7.830739 ACTGTTTATTTTATTTGGAGAGCCAG 58.169 34.615 0.00 0.00 46.91 4.85
689 729 7.451566 ACTGTTTATTTTATTTGGAGAGCCAGT 59.548 33.333 0.00 0.00 46.91 4.00
690 730 8.189119 TGTTTATTTTATTTGGAGAGCCAGTT 57.811 30.769 0.00 0.00 46.91 3.16
744 784 8.628882 AAAAGAAAACTAAGACGAACAAATGG 57.371 30.769 0.00 0.00 0.00 3.16
789 836 2.797156 CTGACGATACATAGGCAAGCAC 59.203 50.000 0.00 0.00 0.00 4.40
850 897 3.009714 GAAACCCTCCCGCTCCCT 61.010 66.667 0.00 0.00 0.00 4.20
898 1220 3.726595 CTTATTCCGCGCCCCGACA 62.727 63.158 0.00 0.00 40.02 4.35
1203 1531 1.227527 CACCTCCGACAAGCACACA 60.228 57.895 0.00 0.00 0.00 3.72
1290 1618 2.898343 GTGGTGGACGTGCGGTTT 60.898 61.111 1.60 0.00 0.00 3.27
1365 1693 3.114616 CTTGTGCTCGAGGTGGCG 61.115 66.667 15.58 0.00 0.00 5.69
1481 1809 1.065926 CACTGTAATGCTGCCCTCTCA 60.066 52.381 0.00 0.00 0.00 3.27
1593 1921 3.436700 TGTATGTGCCGATCTGTGTAG 57.563 47.619 0.00 0.00 0.00 2.74
2215 2552 9.971922 ACTATATTTGAGCATAATTTTTCTGCC 57.028 29.630 0.00 0.00 36.56 4.85
2516 2867 4.086706 AGGTGTCCCTTCTAAAGTGTTG 57.913 45.455 0.00 0.00 38.13 3.33
2800 3151 7.425606 AGCTGTTTGTTTATTCTAGGTGTTTG 58.574 34.615 0.00 0.00 0.00 2.93
3195 3559 5.586243 CACTCAGGTACCCTTATGTCAATTG 59.414 44.000 8.74 0.00 0.00 2.32
3308 3672 5.010012 CCTGAAAAAGCTGTATGTCTGGTTT 59.990 40.000 0.00 0.00 43.68 3.27
3892 4258 3.351740 TGTTGCTGAAGTTTTCACAGGA 58.648 40.909 0.00 0.00 35.46 3.86
4346 4725 4.917415 GGTGACAAAATGAACACTGCATAC 59.083 41.667 0.00 0.00 32.55 2.39
4347 4726 5.507149 GGTGACAAAATGAACACTGCATACA 60.507 40.000 0.00 0.00 32.55 2.29
4399 4779 9.905713 TTAGAAAACCTAGATAATGCACATTCT 57.094 29.630 0.00 0.00 32.50 2.40
4420 4800 1.601903 TGCGTTGTCTGTTTCCATGAC 59.398 47.619 0.00 0.00 0.00 3.06
4435 4815 0.884704 ATGACCGTGGTCTGCAACAC 60.885 55.000 19.17 5.93 44.80 3.32
4444 4824 1.543208 GGTCTGCAACACCTGATCACA 60.543 52.381 7.17 0.00 0.00 3.58
4446 4826 2.417933 GTCTGCAACACCTGATCACATC 59.582 50.000 0.00 0.00 0.00 3.06
4617 4997 4.517453 TGTTTCTACGGATTTTGGTTGGAG 59.483 41.667 0.00 0.00 0.00 3.86
4633 5013 4.319549 GGTTGGAGTTTCACTAGAAAAGCG 60.320 45.833 0.00 0.00 44.75 4.68
4636 5016 3.813724 GGAGTTTCACTAGAAAAGCGGTT 59.186 43.478 0.00 0.00 44.75 4.44
4637 5017 4.083961 GGAGTTTCACTAGAAAAGCGGTTC 60.084 45.833 0.00 0.00 44.75 3.62
4638 5018 4.448210 AGTTTCACTAGAAAAGCGGTTCA 58.552 39.130 0.00 0.00 44.75 3.18
4639 5019 4.511826 AGTTTCACTAGAAAAGCGGTTCAG 59.488 41.667 0.00 0.00 44.75 3.02
4640 5020 4.330944 TTCACTAGAAAAGCGGTTCAGA 57.669 40.909 0.00 0.00 0.00 3.27
4729 5295 5.049612 CAGAGGAAATAGCTATGCATGTGTG 60.050 44.000 10.16 0.00 0.00 3.82
4734 5300 6.652481 GGAAATAGCTATGCATGTGTGTCTAT 59.348 38.462 10.16 4.29 0.00 1.98
4736 5302 8.455903 AAATAGCTATGCATGTGTGTCTATTT 57.544 30.769 10.16 14.02 33.32 1.40
4761 5327 5.965033 ACTCCAGATATGTGTTTGGATCT 57.035 39.130 0.00 0.00 38.91 2.75
4766 5332 5.303971 CAGATATGTGTTTGGATCTCCTCC 58.696 45.833 0.00 0.00 45.19 4.30
4782 5377 3.456277 CTCCTCCTTTATGTGCCCTAGTT 59.544 47.826 0.00 0.00 0.00 2.24
4789 5384 5.944007 CCTTTATGTGCCCTAGTTTTACTGT 59.056 40.000 0.00 0.00 0.00 3.55
4800 5395 3.149196 AGTTTTACTGTGCTGGTGGATG 58.851 45.455 0.00 0.00 0.00 3.51
4813 5408 1.149401 TGGATGTGCACCGGTCAAA 59.851 52.632 15.69 1.06 0.00 2.69
4828 5423 3.188460 CGGTCAAATTCAGGAACGAACAT 59.812 43.478 6.37 0.00 46.67 2.71
4925 5520 6.092748 GCATCGTTTCTTTGGTGAAATATGT 58.907 36.000 0.00 0.00 38.09 2.29
4947 5552 5.064198 TGTCAATATTACTTGCTGTTACCGC 59.936 40.000 0.00 0.00 0.00 5.68
5191 5796 6.157645 CCAGGATATGTATTTAGAGGCAGGAT 59.842 42.308 0.00 0.00 0.00 3.24
5215 5820 1.105759 GGCCCTGCTGATGGATGTTC 61.106 60.000 0.00 0.00 0.00 3.18
5474 6080 8.765219 CATTTTTACTCCATACCTACTTCGATG 58.235 37.037 0.00 0.00 0.00 3.84
5677 6285 8.731275 TCGTAGATTATTCATTTTCATGTGGT 57.269 30.769 0.00 0.00 0.00 4.16
5702 6310 7.522555 GTCAATTAACTTGAAATTCGCAAAACG 59.477 33.333 3.03 0.00 45.27 3.60
5806 6414 6.405278 AAAGTTGAGTCACTTATTTTGGGG 57.595 37.500 0.00 0.00 35.87 4.96
5880 6488 7.036996 TGTACAGATAATCTCTCAGCTCTTG 57.963 40.000 0.00 0.00 29.16 3.02
5901 6509 6.377146 TCTTGGGGCTATTCTTTTACATTCAC 59.623 38.462 0.00 0.00 0.00 3.18
5903 6511 4.879545 GGGGCTATTCTTTTACATTCACGA 59.120 41.667 0.00 0.00 0.00 4.35
5916 6524 7.534085 TTACATTCACGACCATATTTCAGAC 57.466 36.000 0.00 0.00 0.00 3.51
6002 6610 1.538512 CACATCTCCCACAACTGCTTG 59.461 52.381 0.00 0.00 0.00 4.01
6016 6624 0.039256 TGCTTGCAGAAAATCCACGC 60.039 50.000 0.00 0.00 0.00 5.34
6062 6670 6.868339 CACTGCAAATACGATATCATACCTCA 59.132 38.462 3.12 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 99 9.921637 AGATTCCACGCATTTTTCTAATAAAAA 57.078 25.926 0.00 0.00 34.15 1.94
158 160 8.560355 AAGTTTGCTTCCAAAACAGTATTTTT 57.440 26.923 2.28 0.00 42.19 1.94
284 293 8.834465 ACATTTTTCAGAGATATGCATGTCTAC 58.166 33.333 24.04 17.09 33.18 2.59
287 296 6.849811 CGACATTTTTCAGAGATATGCATGTC 59.150 38.462 15.09 15.09 36.30 3.06
297 306 2.426522 CCCTGCGACATTTTTCAGAGA 58.573 47.619 0.00 0.00 0.00 3.10
491 530 3.859386 CCTTTATTTTTGCGAGGCATCAC 59.141 43.478 0.00 0.00 38.76 3.06
638 678 9.271828 GTTCATCTGTTTTATCCCATTGTTTTT 57.728 29.630 0.00 0.00 0.00 1.94
639 679 8.650490 AGTTCATCTGTTTTATCCCATTGTTTT 58.350 29.630 0.00 0.00 0.00 2.43
640 680 8.090214 CAGTTCATCTGTTTTATCCCATTGTTT 58.910 33.333 0.00 0.00 39.17 2.83
641 681 7.605449 CAGTTCATCTGTTTTATCCCATTGTT 58.395 34.615 0.00 0.00 39.17 2.83
642 682 7.161773 CAGTTCATCTGTTTTATCCCATTGT 57.838 36.000 0.00 0.00 39.17 2.71
661 701 8.303876 TGGCTCTCCAAATAAAATAAACAGTTC 58.696 33.333 0.00 0.00 39.99 3.01
662 702 8.189119 TGGCTCTCCAAATAAAATAAACAGTT 57.811 30.769 0.00 0.00 39.99 3.16
663 703 7.451566 ACTGGCTCTCCAAATAAAATAAACAGT 59.548 33.333 0.00 0.00 42.91 3.55
664 704 7.830739 ACTGGCTCTCCAAATAAAATAAACAG 58.169 34.615 0.00 0.00 42.91 3.16
665 705 7.775053 ACTGGCTCTCCAAATAAAATAAACA 57.225 32.000 0.00 0.00 42.91 2.83
666 706 9.569167 GTAACTGGCTCTCCAAATAAAATAAAC 57.431 33.333 0.00 0.00 42.91 2.01
667 707 9.528489 AGTAACTGGCTCTCCAAATAAAATAAA 57.472 29.630 0.00 0.00 42.91 1.40
669 709 9.832445 CTAGTAACTGGCTCTCCAAATAAAATA 57.168 33.333 0.00 0.00 42.91 1.40
670 710 7.775561 CCTAGTAACTGGCTCTCCAAATAAAAT 59.224 37.037 0.00 0.00 42.91 1.82
671 711 7.037873 TCCTAGTAACTGGCTCTCCAAATAAAA 60.038 37.037 0.00 0.00 42.91 1.52
672 712 6.442564 TCCTAGTAACTGGCTCTCCAAATAAA 59.557 38.462 0.00 0.00 42.91 1.40
673 713 5.962031 TCCTAGTAACTGGCTCTCCAAATAA 59.038 40.000 0.00 0.00 42.91 1.40
674 714 5.525484 TCCTAGTAACTGGCTCTCCAAATA 58.475 41.667 0.00 0.00 42.91 1.40
675 715 4.362677 TCCTAGTAACTGGCTCTCCAAAT 58.637 43.478 0.00 0.00 42.91 2.32
676 716 3.786553 TCCTAGTAACTGGCTCTCCAAA 58.213 45.455 0.00 0.00 42.91 3.28
677 717 3.468071 TCCTAGTAACTGGCTCTCCAA 57.532 47.619 0.00 0.00 42.91 3.53
678 718 3.052869 TCATCCTAGTAACTGGCTCTCCA 60.053 47.826 0.00 0.00 40.85 3.86
679 719 3.567397 TCATCCTAGTAACTGGCTCTCC 58.433 50.000 0.00 0.00 0.00 3.71
680 720 3.572255 CCTCATCCTAGTAACTGGCTCTC 59.428 52.174 0.00 0.00 0.00 3.20
681 721 3.205507 TCCTCATCCTAGTAACTGGCTCT 59.794 47.826 0.00 0.00 0.00 4.09
682 722 3.567397 TCCTCATCCTAGTAACTGGCTC 58.433 50.000 0.00 0.00 0.00 4.70
683 723 3.689872 TCCTCATCCTAGTAACTGGCT 57.310 47.619 0.00 0.00 0.00 4.75
684 724 3.451178 TGTTCCTCATCCTAGTAACTGGC 59.549 47.826 0.00 0.00 0.00 4.85
685 725 5.677319 TTGTTCCTCATCCTAGTAACTGG 57.323 43.478 0.00 0.00 0.00 4.00
686 726 6.477033 CGATTTGTTCCTCATCCTAGTAACTG 59.523 42.308 0.00 0.00 0.00 3.16
687 727 6.574350 CGATTTGTTCCTCATCCTAGTAACT 58.426 40.000 0.00 0.00 0.00 2.24
688 728 5.234543 GCGATTTGTTCCTCATCCTAGTAAC 59.765 44.000 0.00 0.00 0.00 2.50
689 729 5.357257 GCGATTTGTTCCTCATCCTAGTAA 58.643 41.667 0.00 0.00 0.00 2.24
690 730 4.202223 GGCGATTTGTTCCTCATCCTAGTA 60.202 45.833 0.00 0.00 0.00 1.82
723 763 5.398416 GTGCCATTTGTTCGTCTTAGTTTTC 59.602 40.000 0.00 0.00 0.00 2.29
724 764 5.163602 TGTGCCATTTGTTCGTCTTAGTTTT 60.164 36.000 0.00 0.00 0.00 2.43
731 771 2.226437 GTGATGTGCCATTTGTTCGTCT 59.774 45.455 0.00 0.00 0.00 4.18
734 774 2.485426 AGAGTGATGTGCCATTTGTTCG 59.515 45.455 0.00 0.00 0.00 3.95
744 784 7.536622 CAGTTTTTATCTTGAAGAGTGATGTGC 59.463 37.037 0.00 0.00 0.00 4.57
751 798 9.141400 GTATCGTCAGTTTTTATCTTGAAGAGT 57.859 33.333 0.00 0.00 0.00 3.24
789 836 0.456221 ACCGAGATTACTGGAGCGTG 59.544 55.000 0.00 0.00 0.00 5.34
850 897 2.686106 GGGGACTGGGGCGTTCTA 60.686 66.667 0.00 0.00 0.00 2.10
898 1220 1.276859 GGTAGGGGTTTGGGATCGGT 61.277 60.000 0.00 0.00 0.00 4.69
1203 1531 3.961408 AGTCATCGGTAATCTTAGTGCCT 59.039 43.478 0.00 0.00 0.00 4.75
1365 1693 1.522580 GTTCTCCCCGAGATGCTGC 60.523 63.158 0.00 0.00 38.56 5.25
1481 1809 0.904865 TGACCGAGGTTGAGAGGCAT 60.905 55.000 0.00 0.00 0.00 4.40
1545 1873 0.037139 CCAACACCCACCGATTCGTA 60.037 55.000 5.20 0.00 0.00 3.43
1593 1921 6.683974 AGCCATATATGATTCGCCATTTAC 57.316 37.500 14.54 0.00 0.00 2.01
1815 2151 8.457238 TCTGGTGATAGGAATCGATATATGAG 57.543 38.462 0.00 0.00 34.60 2.90
1903 2239 8.613060 CATAGAGATGCTAAGCCAGAAATTTA 57.387 34.615 0.00 0.00 31.66 1.40
2215 2552 6.201234 TGAACATCACAAATGCATCAACAAAG 59.799 34.615 0.00 0.00 0.00 2.77
2800 3151 7.302350 ACAAGTGAAACAAATAAGCCAAAAC 57.698 32.000 0.00 0.00 41.43 2.43
3195 3559 4.823989 ACTACCAAAGATATCATTGCTGGC 59.176 41.667 13.93 0.00 0.00 4.85
3308 3672 5.227569 TCAGAGTTTGCCTGACATAGAAA 57.772 39.130 0.00 0.00 35.89 2.52
3829 4195 0.028110 GCTGAATTTTCCTAGCGCGG 59.972 55.000 8.83 0.00 0.00 6.46
3892 4258 3.679389 CTCAACATACTTTCCAGGTGCT 58.321 45.455 0.00 0.00 0.00 4.40
4381 4761 4.512944 ACGCAAGAATGTGCATTATCTAGG 59.487 41.667 0.00 0.00 45.19 3.02
4420 4800 2.111043 AGGTGTTGCAGACCACGG 59.889 61.111 16.93 0.00 35.76 4.94
4504 4884 2.722094 TGGGGTGACAATCTAATGTGC 58.278 47.619 0.00 0.00 32.57 4.57
4576 4956 7.409465 AGAAACACAACTCTATCGAGAAAAC 57.591 36.000 0.47 0.00 39.74 2.43
4583 4963 4.978186 TCCGTAGAAACACAACTCTATCG 58.022 43.478 0.00 0.00 0.00 2.92
4602 4982 3.638484 GTGAAACTCCAACCAAAATCCG 58.362 45.455 0.00 0.00 0.00 4.18
4617 4997 4.510340 TCTGAACCGCTTTTCTAGTGAAAC 59.490 41.667 0.00 0.00 41.34 2.78
4654 5034 4.380531 ACCATTATCCTGTCAATGTAGCG 58.619 43.478 0.00 0.00 31.52 4.26
4734 5300 8.877864 ATCCAAACACATATCTGGAGTTAAAA 57.122 30.769 0.00 0.00 41.17 1.52
4736 5302 7.861629 AGATCCAAACACATATCTGGAGTTAA 58.138 34.615 0.00 0.00 41.17 2.01
4761 5327 3.130734 ACTAGGGCACATAAAGGAGGA 57.869 47.619 0.00 0.00 0.00 3.71
4766 5332 6.622896 GCACAGTAAAACTAGGGCACATAAAG 60.623 42.308 0.00 0.00 29.93 1.85
4782 5377 2.503331 CACATCCACCAGCACAGTAAA 58.497 47.619 0.00 0.00 0.00 2.01
4800 5395 0.240945 CCTGAATTTGACCGGTGCAC 59.759 55.000 14.63 8.80 0.00 4.57
4813 5408 4.184629 GAGCTGTATGTTCGTTCCTGAAT 58.815 43.478 0.00 0.00 0.00 2.57
4828 5423 4.103469 TGTTCCTAAAACTTGGGAGCTGTA 59.897 41.667 0.00 0.00 41.63 2.74
4925 5520 5.293324 CAGCGGTAACAGCAAGTAATATTGA 59.707 40.000 0.00 0.00 38.34 2.57
4947 5552 7.095102 TGTGACATGTTGACAAGATTCATACAG 60.095 37.037 0.00 0.00 0.00 2.74
5058 5663 3.618507 CGTTCTCCTTGGCAATCTTCTCT 60.619 47.826 0.00 0.00 0.00 3.10
5474 6080 6.055588 TGTATTGCAGGCTTTTATCTAGTCC 58.944 40.000 0.00 0.00 0.00 3.85
5677 6285 7.551340 CGTTTTGCGAATTTCAAGTTAATTGA 58.449 30.769 0.00 0.00 44.11 2.57
5768 6376 9.502091 TGACTCAACTTTATGCTAACTTTGTAT 57.498 29.630 0.00 0.00 0.00 2.29
5782 6390 6.015772 GCCCCAAAATAAGTGACTCAACTTTA 60.016 38.462 0.00 0.00 40.77 1.85
5806 6414 5.599999 ACCATATCTTATACTCCATCCGC 57.400 43.478 0.00 0.00 0.00 5.54
5880 6488 4.879545 TCGTGAATGTAAAAGAATAGCCCC 59.120 41.667 0.00 0.00 0.00 5.80
5901 6509 7.456253 CAAACTAACTGTCTGAAATATGGTCG 58.544 38.462 0.00 0.00 0.00 4.79
5903 6511 6.151144 GGCAAACTAACTGTCTGAAATATGGT 59.849 38.462 0.00 0.00 0.00 3.55
5912 6520 5.215160 GTCATTTGGCAAACTAACTGTCTG 58.785 41.667 16.00 6.45 0.00 3.51
5916 6524 7.144661 TGTAATGTCATTTGGCAAACTAACTG 58.855 34.615 16.00 9.43 31.21 3.16
5964 6572 4.852134 TGTGATGTGGAAAAGTTGATGG 57.148 40.909 0.00 0.00 0.00 3.51
6002 6610 1.132453 GTTAGGGCGTGGATTTTCTGC 59.868 52.381 0.00 0.00 0.00 4.26
6016 6624 1.560505 ATGGCTGCTTTTGGTTAGGG 58.439 50.000 0.00 0.00 0.00 3.53
6043 6651 8.846943 TTTGCATGAGGTATGATATCGTATTT 57.153 30.769 7.90 0.18 39.21 1.40
6048 6656 6.025896 GCAATTTGCATGAGGTATGATATCG 58.974 40.000 16.35 0.00 44.26 2.92


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

AutoCloner maintained by Alex Coulton.