Multiple sequence alignment - TraesCS3A01G334600

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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 TraesCS3A01G334600 chr3A 100.000 4524 0 0 1 4524 581255959 581260482 0.000000e+00 8355.0
1 TraesCS3A01G334600 chr3D 92.667 2973 130 36 665 3595 441128146 441131072 0.000000e+00 4202.0
2 TraesCS3A01G334600 chr3D 93.005 629 35 2 3899 4523 441132494 441133117 0.000000e+00 909.0
3 TraesCS3A01G334600 chr3D 89.655 58 5 1 597 653 441128048 441128105 6.280000e-09 73.1
4 TraesCS3A01G334600 chr3B 91.996 2686 150 39 928 3578 578279800 578282455 0.000000e+00 3709.0
5 TraesCS3A01G334600 chr3B 88.117 993 71 16 3546 4523 578282461 578283421 0.000000e+00 1136.0
6 TraesCS3A01G334600 chr3B 86.940 268 12 8 598 846 578279063 578279326 3.450000e-71 279.0
7 TraesCS3A01G334600 chr1A 96.975 595 17 1 1 595 90805829 90806422 0.000000e+00 998.0
8 TraesCS3A01G334600 chr5A 97.292 554 14 1 42 595 540035391 540034839 0.000000e+00 939.0
9 TraesCS3A01G334600 chr5A 96.948 557 17 0 42 598 619720692 619720136 0.000000e+00 935.0
10 TraesCS3A01G334600 chr7A 97.112 554 16 0 42 595 677724988 677724435 0.000000e+00 935.0
11 TraesCS3A01G334600 chr2D 96.209 554 20 1 42 594 33912152 33912705 0.000000e+00 905.0
12 TraesCS3A01G334600 chrUn 92.809 598 35 8 1 595 100334299 100333707 0.000000e+00 859.0
13 TraesCS3A01G334600 chr7D 92.346 601 41 5 1 598 46561909 46562507 0.000000e+00 850.0
14 TraesCS3A01G334600 chr2B 91.820 599 42 6 1 595 695927166 695927761 0.000000e+00 828.0
15 TraesCS3A01G334600 chr7B 91.333 600 44 7 1 595 71341678 71342274 0.000000e+00 813.0
16 TraesCS3A01G334600 chr6D 97.297 111 2 1 2649 2758 7513387 7513277 2.150000e-43 187.0


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 TraesCS3A01G334600 chr3A 581255959 581260482 4523 False 8355.000000 8355 100.000000 1 4524 1 chr3A.!!$F1 4523
1 TraesCS3A01G334600 chr3D 441128048 441133117 5069 False 1728.033333 4202 91.775667 597 4523 3 chr3D.!!$F1 3926
2 TraesCS3A01G334600 chr3B 578279063 578283421 4358 False 1708.000000 3709 89.017667 598 4523 3 chr3B.!!$F1 3925
3 TraesCS3A01G334600 chr1A 90805829 90806422 593 False 998.000000 998 96.975000 1 595 1 chr1A.!!$F1 594
4 TraesCS3A01G334600 chr5A 540034839 540035391 552 True 939.000000 939 97.292000 42 595 1 chr5A.!!$R1 553
5 TraesCS3A01G334600 chr5A 619720136 619720692 556 True 935.000000 935 96.948000 42 598 1 chr5A.!!$R2 556
6 TraesCS3A01G334600 chr7A 677724435 677724988 553 True 935.000000 935 97.112000 42 595 1 chr7A.!!$R1 553
7 TraesCS3A01G334600 chr2D 33912152 33912705 553 False 905.000000 905 96.209000 42 594 1 chr2D.!!$F1 552
8 TraesCS3A01G334600 chrUn 100333707 100334299 592 True 859.000000 859 92.809000 1 595 1 chrUn.!!$R1 594
9 TraesCS3A01G334600 chr7D 46561909 46562507 598 False 850.000000 850 92.346000 1 598 1 chr7D.!!$F1 597
10 TraesCS3A01G334600 chr2B 695927166 695927761 595 False 828.000000 828 91.820000 1 595 1 chr2B.!!$F1 594
11 TraesCS3A01G334600 chr7B 71341678 71342274 596 False 813.000000 813 91.333000 1 595 1 chr7B.!!$F1 594

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
942 1415 0.028770 CTCGCTGAGAGTGATCGACC 59.971 60.0 0.0 0.0 41.99 4.79 F
1969 2455 0.462759 GATGGAAGGTTCTCAGGCCG 60.463 60.0 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2349 2835 0.251916 TACAGGAAAGACGCATGGGG 59.748 55.0 14.94 0.00 0.0 4.96 R
3940 5693 0.321653 AGTCCCGGCAGCTGTTTAAG 60.322 55.0 16.64 1.03 0.0 1.85 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
34 35 4.329545 GAGCCGGCCACAACCTGA 62.330 66.667 26.15 0.00 0.00 3.86
314 316 4.011517 GGTTTCGGAGGGCACGGA 62.012 66.667 0.00 0.00 0.00 4.69
512 517 4.999311 GGGTTGAGTTGTATCGGTTTTAGT 59.001 41.667 0.00 0.00 0.00 2.24
575 582 9.590451 TCTTAATCAATGAAAATGGCAAATCTC 57.410 29.630 0.00 0.00 0.00 2.75
650 661 3.303395 GCTGTCGCTGGCATTTTATACTC 60.303 47.826 0.00 0.00 0.00 2.59
654 685 3.644265 TCGCTGGCATTTTATACTCCCTA 59.356 43.478 0.00 0.00 0.00 3.53
679 717 1.423584 TTGGAGTTGACCTCTGCTGA 58.576 50.000 0.00 0.00 40.30 4.26
682 720 2.762887 TGGAGTTGACCTCTGCTGATAG 59.237 50.000 0.00 0.00 40.30 2.08
737 775 9.658475 TTAAAAATCATGTGTAAGTTTGTCTCG 57.342 29.630 0.00 0.00 0.00 4.04
764 806 5.120830 AGCATCTTCAATGTACGAGTGAAAC 59.879 40.000 8.68 2.15 38.16 2.78
839 882 2.136298 TGCTGGGGCAATTATTTCGA 57.864 45.000 0.00 0.00 46.36 3.71
840 883 2.665165 TGCTGGGGCAATTATTTCGAT 58.335 42.857 0.00 0.00 46.36 3.59
841 884 3.826524 TGCTGGGGCAATTATTTCGATA 58.173 40.909 0.00 0.00 46.36 2.92
842 885 4.406456 TGCTGGGGCAATTATTTCGATAT 58.594 39.130 0.00 0.00 46.36 1.63
843 886 4.218200 TGCTGGGGCAATTATTTCGATATG 59.782 41.667 0.00 0.00 46.36 1.78
844 887 4.458989 GCTGGGGCAATTATTTCGATATGA 59.541 41.667 0.00 0.00 38.54 2.15
845 888 5.392380 GCTGGGGCAATTATTTCGATATGAG 60.392 44.000 0.00 0.00 38.54 2.90
846 889 5.630121 TGGGGCAATTATTTCGATATGAGT 58.370 37.500 0.00 0.00 0.00 3.41
847 890 6.068010 TGGGGCAATTATTTCGATATGAGTT 58.932 36.000 0.00 0.00 0.00 3.01
848 891 6.549364 TGGGGCAATTATTTCGATATGAGTTT 59.451 34.615 0.00 0.00 0.00 2.66
849 892 7.069331 TGGGGCAATTATTTCGATATGAGTTTT 59.931 33.333 0.00 0.00 0.00 2.43
850 893 7.926018 GGGGCAATTATTTCGATATGAGTTTTT 59.074 33.333 0.00 0.00 0.00 1.94
881 924 6.823182 ACACCATTTCGATATGAGATGAAACA 59.177 34.615 16.31 0.00 40.71 2.83
883 926 6.484643 ACCATTTCGATATGAGATGAAACAGG 59.515 38.462 16.31 0.00 40.71 4.00
904 956 2.442272 ACACGATCGGGCTAGGCT 60.442 61.111 19.30 0.00 0.00 4.58
916 968 1.728490 GCTAGGCTTTGGGCGATTGG 61.728 60.000 0.00 0.00 42.94 3.16
942 1415 0.028770 CTCGCTGAGAGTGATCGACC 59.971 60.000 0.00 0.00 41.99 4.79
1265 1738 3.429141 CAGCCTCAAGGTGCGCTG 61.429 66.667 9.73 0.00 42.42 5.18
1317 1790 3.326747 AGTTCGTGCACAAGGATTCTAC 58.673 45.455 18.64 1.50 0.00 2.59
1364 1845 3.126831 GTTCAGTCAGTTCTCACCAGTG 58.873 50.000 0.00 0.00 0.00 3.66
1381 1862 4.952262 CAGTGACCACATTGGAGTATTG 57.048 45.455 0.00 0.00 40.96 1.90
1382 1863 3.691118 CAGTGACCACATTGGAGTATTGG 59.309 47.826 0.00 0.00 40.96 3.16
1383 1864 3.587061 AGTGACCACATTGGAGTATTGGA 59.413 43.478 0.00 0.00 40.96 3.53
1397 1878 6.013725 TGGAGTATTGGACAGTTGACATTAGT 60.014 38.462 0.00 0.00 0.00 2.24
1408 1889 9.922305 GACAGTTGACATTAGTATTTTAGCATC 57.078 33.333 0.00 0.00 0.00 3.91
1684 2168 9.905713 TGGCATTCTTAATAGTATAATGATCCC 57.094 33.333 7.32 1.70 30.77 3.85
1749 2233 9.321562 CTTTCTTGCCATGCTGAAATTAATTAT 57.678 29.630 0.01 0.00 34.01 1.28
1936 2422 1.948611 GCGCTAAAGACAATGGGGTGA 60.949 52.381 0.00 0.00 0.00 4.02
1969 2455 0.462759 GATGGAAGGTTCTCAGGCCG 60.463 60.000 0.00 0.00 0.00 6.13
1989 2475 2.704572 GTGGAGATGGAACCTGAACTG 58.295 52.381 0.00 0.00 0.00 3.16
2007 2493 4.364415 ACTGCGTTGTTTGAAAGCTTTA 57.636 36.364 12.68 0.00 0.00 1.85
2037 2523 3.594603 AGTACTGGGATTGTTGACTCG 57.405 47.619 0.00 0.00 0.00 4.18
2086 2572 6.599638 GGTACTTGGCTAATCTGTTCTTGATT 59.400 38.462 0.00 0.00 37.78 2.57
2127 2613 5.732633 TGCATTGTTTATTTTGCCTGCTAT 58.267 33.333 0.00 0.00 34.20 2.97
2144 2630 7.826252 TGCCTGCTATAATCCTCTAAATGATTC 59.174 37.037 0.00 0.00 33.46 2.52
2219 2705 4.976731 AGATAACTGAAATAGCGCTACGTG 59.023 41.667 21.49 10.81 0.00 4.49
2325 2811 2.137523 GCAGCAATGTTTGGAAGGTTG 58.862 47.619 0.00 0.00 0.00 3.77
2331 2817 0.555769 TGTTTGGAAGGTTGAGGCCT 59.444 50.000 3.86 3.86 41.41 5.19
2349 2835 8.181904 TGAGGCCTGATAATCCAAAAATATTC 57.818 34.615 12.00 0.00 0.00 1.75
2374 2860 0.790814 GCGTCTTTCCTGTACACAGC 59.209 55.000 3.75 0.00 42.47 4.40
2535 3021 1.002990 CAGCAGTCATCAGTGGGCA 60.003 57.895 0.00 0.00 0.00 5.36
2613 3099 4.076394 CAGTCTATAGGCTCTCCTGTACC 58.924 52.174 3.19 0.00 44.08 3.34
2749 3235 1.338769 GCCCGTGGATGTTACTTCACT 60.339 52.381 0.84 0.00 0.00 3.41
2848 3334 5.122396 CACACTAGACTTAAATGGCCTTGTC 59.878 44.000 3.32 1.24 0.00 3.18
2991 3479 7.377766 ACTTGTTATACACATCGCTGAAATT 57.622 32.000 0.00 0.00 34.43 1.82
3006 3494 5.569059 CGCTGAAATTGATGGAGTTACAAAC 59.431 40.000 0.00 0.00 0.00 2.93
3059 3570 3.081804 GTTACCACAGTTGCTGCCTAAT 58.918 45.455 0.00 0.00 34.37 1.73
3063 3574 5.110814 ACCACAGTTGCTGCCTAATATTA 57.889 39.130 0.00 0.00 34.37 0.98
3068 3579 5.590259 ACAGTTGCTGCCTAATATTAACTGG 59.410 40.000 21.43 10.77 44.56 4.00
3071 3582 7.282224 CAGTTGCTGCCTAATATTAACTGGTTA 59.718 37.037 14.02 0.00 39.63 2.85
3111 3622 6.656693 TCCTCTTCTTGAAAAAGCTAAGATGG 59.343 38.462 8.44 6.63 31.21 3.51
3115 3626 6.317789 TCTTGAAAAAGCTAAGATGGTGTG 57.682 37.500 0.00 0.00 0.00 3.82
3131 3642 3.814842 TGGTGTGTGACTTTTAGCATCTG 59.185 43.478 0.00 0.00 0.00 2.90
3154 3665 6.764379 TGTGTACATCAGGTTTGATTACTCA 58.236 36.000 0.00 1.04 42.12 3.41
3167 3678 1.809133 TTACTCAGTGAACCCCACCA 58.191 50.000 0.00 0.00 46.87 4.17
3359 3886 7.250569 TCAGCTTGAAAGTTTACTTTTCACTG 58.749 34.615 9.08 12.90 45.37 3.66
3497 4028 1.411394 CTTGGCAATTGCAGAACACG 58.589 50.000 30.32 13.53 44.36 4.49
3499 4030 0.310543 TGGCAATTGCAGAACACGTC 59.689 50.000 30.32 11.20 44.36 4.34
3579 4152 3.692406 GAACCGGACGGCTGGAGT 61.692 66.667 27.08 10.50 43.76 3.85
3640 4213 9.785982 CTTGTTTATTTCCTTTTATTTTGGGGA 57.214 29.630 0.00 0.00 0.00 4.81
3653 4226 2.978156 TTGGGGAAGAACAAGATGCT 57.022 45.000 0.00 0.00 0.00 3.79
3667 4240 1.815003 AGATGCTGCTTGTAAAGGTGC 59.185 47.619 0.00 0.00 46.35 5.01
3694 4269 7.224297 ACTCTCCAGCTTAGTTGAATAAACAA 58.776 34.615 0.00 0.00 41.61 2.83
3739 4318 5.577164 GTGTATTATGTGGATCCTCGCATAC 59.423 44.000 14.23 15.42 39.10 2.39
3740 4319 4.890158 ATTATGTGGATCCTCGCATACA 57.110 40.909 14.23 8.09 39.10 2.29
3742 4321 2.820059 TGTGGATCCTCGCATACATC 57.180 50.000 14.23 0.00 0.00 3.06
3749 4328 0.940126 CCTCGCATACATCTTGTGGC 59.060 55.000 0.00 0.00 0.00 5.01
3772 4351 3.845781 GAGGATCCTCTGCATTACCAA 57.154 47.619 31.11 0.00 39.80 3.67
3782 4361 3.814842 TCTGCATTACCAACTTGTGTCTG 59.185 43.478 0.00 0.00 0.00 3.51
3787 4368 2.418368 ACCAACTTGTGTCTGAGCAA 57.582 45.000 0.00 0.00 0.00 3.91
3790 4371 3.129287 ACCAACTTGTGTCTGAGCAAAAG 59.871 43.478 5.60 5.60 39.10 2.27
3791 4372 3.129287 CCAACTTGTGTCTGAGCAAAAGT 59.871 43.478 6.62 6.62 45.82 2.66
3802 4383 7.852945 GTGTCTGAGCAAAAGTATATGCATTAC 59.147 37.037 3.54 7.66 44.95 1.89
3806 4387 8.449251 TGAGCAAAAGTATATGCATTACATCA 57.551 30.769 3.54 4.47 44.95 3.07
3812 4393 8.752005 AAAGTATATGCATTACATCACCTGTT 57.248 30.769 3.54 0.00 40.38 3.16
3845 4427 3.845398 TGAAAATTGGATGGCCAGGATTT 59.155 39.130 13.05 11.56 46.91 2.17
3859 4441 4.502950 GCCAGGATTTGAATGGAAAACACA 60.503 41.667 0.00 0.00 36.09 3.72
3919 5672 3.498774 ACTCTGACAATTTGCCTCTGT 57.501 42.857 0.00 0.00 0.00 3.41
3924 5677 3.963665 TGACAATTTGCCTCTGTTTTCG 58.036 40.909 0.00 0.00 0.00 3.46
3940 5693 2.892373 TTCGAATCGTGGAATGCAAC 57.108 45.000 1.52 0.00 0.00 4.17
3945 5698 4.452795 TCGAATCGTGGAATGCAACTTAAA 59.547 37.500 1.52 0.00 0.00 1.52
3954 5707 0.310543 TGCAACTTAAACAGCTGCCG 59.689 50.000 15.27 0.00 43.10 5.69
4154 5912 7.915923 GCAAAGGTTATAAAGGTATCTGAAAGC 59.084 37.037 0.00 0.00 0.00 3.51
4171 5931 0.114954 AGCAATGGATGGGGTTGTGT 59.885 50.000 0.00 0.00 0.00 3.72
4387 6148 0.040425 GCACGCCACTTGTAAACAGG 60.040 55.000 0.00 0.00 0.00 4.00
4396 6157 3.565482 CACTTGTAAACAGGCTGTGATGT 59.435 43.478 22.83 11.39 0.00 3.06
4405 6166 6.403866 AACAGGCTGTGATGTTGAATTTAA 57.596 33.333 22.83 0.00 38.19 1.52
4464 6225 5.466819 GTTTCTGCCCCAGTATTAAACAAC 58.533 41.667 0.00 0.00 30.25 3.32
4500 6261 6.864165 TCAAACTTGACAACAAAAACAGTACC 59.136 34.615 0.00 0.00 35.49 3.34
4504 6265 5.704888 TTGACAACAAAAACAGTACCACTG 58.295 37.500 4.79 4.79 41.28 3.66
4523 6284 3.693085 ACTGTACTATCGACGTGACCATT 59.307 43.478 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
325 328 5.114764 TCATCACAAGGGAAATATGCAGA 57.885 39.130 0.00 0.00 0.00 4.26
595 602 4.575645 ACTTCAATTGTTTTGGTTGGCATG 59.424 37.500 5.13 0.00 0.00 4.06
650 661 3.267031 AGGTCAACTCCAAAAGGATAGGG 59.733 47.826 0.00 0.00 0.00 3.53
666 697 5.893824 TCAAGATACTATCAGCAGAGGTCAA 59.106 40.000 0.00 0.00 0.00 3.18
669 700 6.798427 TTTCAAGATACTATCAGCAGAGGT 57.202 37.500 0.00 0.00 0.00 3.85
670 701 8.674263 ATTTTTCAAGATACTATCAGCAGAGG 57.326 34.615 0.00 0.00 0.00 3.69
701 739 7.346751 ACACATGATTTTTAACTGTCCAACT 57.653 32.000 0.00 0.00 0.00 3.16
737 775 5.348724 TCACTCGTACATTGAAGATGCTTTC 59.651 40.000 0.00 0.00 0.00 2.62
769 811 6.272558 ACTGGTACTTCTTTCCCTGTAAAGAT 59.727 38.462 0.00 0.00 43.21 2.40
821 864 4.458989 TCATATCGAAATAATTGCCCCAGC 59.541 41.667 0.00 0.00 40.48 4.85
849 892 9.613428 ATCTCATATCGAAATGGTGTCTAAAAA 57.387 29.630 0.00 0.00 0.00 1.94
850 893 9.045223 CATCTCATATCGAAATGGTGTCTAAAA 57.955 33.333 0.00 0.00 0.00 1.52
851 894 8.421002 TCATCTCATATCGAAATGGTGTCTAAA 58.579 33.333 0.00 0.00 0.00 1.85
852 895 7.951591 TCATCTCATATCGAAATGGTGTCTAA 58.048 34.615 0.00 0.00 0.00 2.10
853 896 7.524717 TCATCTCATATCGAAATGGTGTCTA 57.475 36.000 0.00 0.00 0.00 2.59
854 897 6.410942 TCATCTCATATCGAAATGGTGTCT 57.589 37.500 0.00 0.00 0.00 3.41
855 898 7.011389 TGTTTCATCTCATATCGAAATGGTGTC 59.989 37.037 0.00 0.00 30.68 3.67
856 899 6.823182 TGTTTCATCTCATATCGAAATGGTGT 59.177 34.615 0.00 0.00 30.68 4.16
857 900 7.250445 TGTTTCATCTCATATCGAAATGGTG 57.750 36.000 0.00 0.00 30.68 4.17
858 901 6.484643 CCTGTTTCATCTCATATCGAAATGGT 59.515 38.462 0.00 0.00 30.68 3.55
859 902 6.567321 GCCTGTTTCATCTCATATCGAAATGG 60.567 42.308 0.00 0.00 30.68 3.16
860 903 6.017687 TGCCTGTTTCATCTCATATCGAAATG 60.018 38.462 0.00 0.00 30.68 2.32
881 924 4.148825 GCCCGATCGTGTCTGCCT 62.149 66.667 15.09 0.00 0.00 4.75
883 926 1.299468 CTAGCCCGATCGTGTCTGC 60.299 63.158 15.09 8.36 0.00 4.26
904 956 2.749839 CCGCTCCAATCGCCCAAA 60.750 61.111 0.00 0.00 0.00 3.28
1275 1748 2.029649 TCGTAGATTATACGGCTTGGCC 60.030 50.000 10.63 0.00 46.75 5.36
1279 1752 4.781071 CGAACTCGTAGATTATACGGCTT 58.219 43.478 10.63 3.03 40.90 4.35
1306 1779 6.634805 TCACAGAAAGCTAGTAGAATCCTTG 58.365 40.000 0.00 0.00 0.00 3.61
1317 1790 8.484641 TGAACTGAAATATCACAGAAAGCTAG 57.515 34.615 13.58 0.00 37.54 3.42
1364 1845 3.941483 CTGTCCAATACTCCAATGTGGTC 59.059 47.826 0.00 0.00 39.03 4.02
1379 1860 8.726988 GCTAAAATACTAATGTCAACTGTCCAA 58.273 33.333 0.00 0.00 0.00 3.53
1380 1861 7.880713 TGCTAAAATACTAATGTCAACTGTCCA 59.119 33.333 0.00 0.00 0.00 4.02
1381 1862 8.263940 TGCTAAAATACTAATGTCAACTGTCC 57.736 34.615 0.00 0.00 0.00 4.02
1382 1863 9.922305 GATGCTAAAATACTAATGTCAACTGTC 57.078 33.333 0.00 0.00 0.00 3.51
1383 1864 9.672673 AGATGCTAAAATACTAATGTCAACTGT 57.327 29.630 0.00 0.00 0.00 3.55
1397 1878 8.417106 CACCTAAGAGACTGAGATGCTAAAATA 58.583 37.037 0.00 0.00 0.00 1.40
1408 1889 3.823873 ACACAGACACCTAAGAGACTGAG 59.176 47.826 0.00 0.00 0.00 3.35
1669 2153 9.041354 GGACAGAAGAAGGGATCATTATACTAT 57.959 37.037 0.00 0.00 0.00 2.12
1672 2156 7.309770 AGGACAGAAGAAGGGATCATTATAC 57.690 40.000 0.00 0.00 0.00 1.47
1766 2251 8.915654 CACAAAGATTAGCCTACAAAAACATTC 58.084 33.333 0.00 0.00 0.00 2.67
1917 2403 2.107950 TCACCCCATTGTCTTTAGCG 57.892 50.000 0.00 0.00 0.00 4.26
1936 2422 6.263412 ACCTTCCATCATCTGAAGATCATT 57.737 37.500 0.00 0.00 40.30 2.57
1969 2455 2.704572 CAGTTCAGGTTCCATCTCCAC 58.295 52.381 0.00 0.00 0.00 4.02
1989 2475 6.086371 GTGATAGTAAAGCTTTCAAACAACGC 59.914 38.462 16.57 7.11 37.02 4.84
2007 2493 5.778542 ACAATCCCAGTACTAGGTGATAGT 58.221 41.667 7.26 0.00 46.70 2.12
2086 2572 9.995003 AACAATGCAAAGATAAAAATGGTAAGA 57.005 25.926 0.00 0.00 0.00 2.10
2099 2585 6.348704 GCAGGCAAAATAAACAATGCAAAGAT 60.349 34.615 0.00 0.00 40.51 2.40
2144 2630 7.930865 TGTGAAAAGGGACCTTTCAAATAATTG 59.069 33.333 16.12 0.00 44.50 2.32
2219 2705 1.751563 GATAGTGCAGAGGCCCTCC 59.248 63.158 7.26 0.00 40.13 4.30
2325 2811 7.310052 GGGAATATTTTTGGATTATCAGGCCTC 60.310 40.741 0.00 0.00 0.00 4.70
2331 2817 7.525194 CGCATGGGGAATATTTTTGGATTATCA 60.525 37.037 0.89 0.00 0.00 2.15
2349 2835 0.251916 TACAGGAAAGACGCATGGGG 59.748 55.000 14.94 0.00 0.00 4.96
2535 3021 3.041211 TCGATCCCTTCATCTCCAACAT 58.959 45.455 0.00 0.00 0.00 2.71
2590 3076 4.202482 GGTACAGGAGAGCCTATAGACTGA 60.202 50.000 0.00 0.00 44.80 3.41
2593 3079 3.423749 GGGTACAGGAGAGCCTATAGAC 58.576 54.545 0.00 0.00 44.80 2.59
2613 3099 2.289010 GGAAGCAAAACAATCTGTGGGG 60.289 50.000 0.00 0.00 0.00 4.96
2749 3235 3.309296 AGGACTCTTGGTTTGTGAGAGA 58.691 45.455 6.61 0.00 39.36 3.10
2848 3334 5.640357 CCATTCAACATCTGGTCCAAATTTG 59.360 40.000 11.40 11.40 0.00 2.32
2991 3479 5.924254 CACTAGAACGTTTGTAACTCCATCA 59.076 40.000 0.46 0.00 0.00 3.07
3006 3494 7.837202 TTAAATATTGGACACCACTAGAACG 57.163 36.000 0.00 0.00 30.78 3.95
3043 3554 6.458751 CCAGTTAATATTAGGCAGCAACTGTG 60.459 42.308 17.50 9.68 39.65 3.66
3088 3599 7.040823 ACACCATCTTAGCTTTTTCAAGAAGAG 60.041 37.037 0.00 0.00 30.35 2.85
3111 3622 4.273480 ACACAGATGCTAAAAGTCACACAC 59.727 41.667 0.00 0.00 0.00 3.82
3115 3626 6.368791 TGATGTACACAGATGCTAAAAGTCAC 59.631 38.462 0.00 0.00 0.00 3.67
3131 3642 6.874134 ACTGAGTAATCAAACCTGATGTACAC 59.126 38.462 0.00 0.00 41.66 2.90
3154 3665 1.073923 GAACATCTGGTGGGGTTCACT 59.926 52.381 0.00 0.00 45.38 3.41
3167 3678 7.009179 TCACAGAGTAAAATCCAGAACATCT 57.991 36.000 0.00 0.00 0.00 2.90
3359 3886 3.810941 TCACGGGTTTGTTGATACTTGAC 59.189 43.478 0.00 0.00 0.00 3.18
3497 4028 4.689345 AGTGCTGTTATACCTTGAAACGAC 59.311 41.667 0.00 0.00 0.00 4.34
3499 4030 5.178623 TCAAGTGCTGTTATACCTTGAAACG 59.821 40.000 0.00 0.00 0.00 3.60
3635 4208 1.887956 GCAGCATCTTGTTCTTCCCCA 60.888 52.381 0.00 0.00 0.00 4.96
3653 4226 1.070134 AGAGTCGCACCTTTACAAGCA 59.930 47.619 0.00 0.00 0.00 3.91
3667 4240 3.577649 TTCAACTAAGCTGGAGAGTCG 57.422 47.619 2.97 0.00 0.00 4.18
3694 4269 6.126409 ACACCAACCCACAATCGATATATTT 58.874 36.000 0.00 0.00 0.00 1.40
3739 4318 2.092538 AGGATCCTCTTGCCACAAGATG 60.093 50.000 9.02 8.14 0.00 2.90
3740 4319 2.172293 GAGGATCCTCTTGCCACAAGAT 59.828 50.000 31.11 0.00 39.80 2.40
3742 4321 2.035530 GAGGATCCTCTTGCCACAAG 57.964 55.000 31.11 0.81 39.80 3.16
3772 4351 6.128172 GCATATACTTTTGCTCAGACACAAGT 60.128 38.462 6.09 6.09 41.91 3.16
3782 4361 7.805071 GGTGATGTAATGCATATACTTTTGCTC 59.195 37.037 0.00 0.00 39.60 4.26
3787 4368 8.623903 CAACAGGTGATGTAATGCATATACTTT 58.376 33.333 0.00 0.00 43.00 2.66
3790 4371 7.307989 GGTCAACAGGTGATGTAATGCATATAC 60.308 40.741 0.00 5.90 43.00 1.47
3791 4372 6.710295 GGTCAACAGGTGATGTAATGCATATA 59.290 38.462 0.00 0.00 43.00 0.86
3802 4383 4.460034 TCATCAAATGGTCAACAGGTGATG 59.540 41.667 10.83 10.83 46.03 3.07
3806 4387 5.867903 TTTTCATCAAATGGTCAACAGGT 57.132 34.783 0.00 0.00 0.00 4.00
3812 4393 6.408035 CCATCCAATTTTCATCAAATGGTCA 58.592 36.000 0.00 0.00 35.09 4.02
3865 4447 3.096489 TGCTGCAAGAAAATGGACAAC 57.904 42.857 0.00 0.00 34.07 3.32
3866 4448 3.815856 TTGCTGCAAGAAAATGGACAA 57.184 38.095 11.69 0.00 34.07 3.18
3870 4452 5.404968 TCGTATTTTTGCTGCAAGAAAATGG 59.595 36.000 24.61 18.68 42.19 3.16
3913 5666 2.683968 TCCACGATTCGAAAACAGAGG 58.316 47.619 13.95 2.53 0.00 3.69
3919 5672 3.252215 AGTTGCATTCCACGATTCGAAAA 59.748 39.130 13.95 4.21 0.00 2.29
3924 5677 5.457140 TGTTTAAGTTGCATTCCACGATTC 58.543 37.500 0.00 0.00 0.00 2.52
3940 5693 0.321653 AGTCCCGGCAGCTGTTTAAG 60.322 55.000 16.64 1.03 0.00 1.85
3945 5698 2.129555 ATTTCAGTCCCGGCAGCTGT 62.130 55.000 16.64 0.00 0.00 4.40
3954 5707 9.566432 AGATATTTGTGATAGAATTTCAGTCCC 57.434 33.333 0.00 0.00 0.00 4.46
4154 5912 2.760092 CCTTACACAACCCCATCCATTG 59.240 50.000 0.00 0.00 0.00 2.82
4171 5931 0.407528 TGACATTGCCCTTGCCCTTA 59.592 50.000 0.00 0.00 36.33 2.69
4331 6092 7.476492 CGGTGAGACGCTTTTAGTTTTTATTAC 59.524 37.037 0.00 0.00 0.00 1.89
4349 6110 1.869690 GCAAAGGAAGCGGTGAGAC 59.130 57.895 0.00 0.00 0.00 3.36
4387 6148 8.976986 AGAGATTTTAAATTCAACATCACAGC 57.023 30.769 11.56 0.00 0.00 4.40
4396 6157 9.062524 TCCGTGAAGAAGAGATTTTAAATTCAA 57.937 29.630 11.56 0.00 0.00 2.69
4405 6166 3.971245 AGCTCCGTGAAGAAGAGATTT 57.029 42.857 0.00 0.00 0.00 2.17
4464 6225 7.526608 TGTTGTCAAGTTTGAAGTTACTGAAG 58.473 34.615 0.00 0.00 39.21 3.02
4500 6261 2.417586 TGGTCACGTCGATAGTACAGTG 59.582 50.000 0.00 0.00 37.40 3.66


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

AutoCloner maintained by Alex Coulton.