Multiple sequence alignment - TraesCS3A01G212100

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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 TraesCS3A01G212100 chr3A 100.000 5177 0 0 1 5177 381298850 381293674 0 9561
1 TraesCS3A01G212100 chr3D 97.666 4242 89 4 943 5177 290020196 290015958 0 7276
2 TraesCS3A01G212100 chr3B 97.492 4186 91 4 999 5177 382323087 382318909 0 7136
3 TraesCS3A01G212100 chr4B 84.755 879 128 4 63 940 192694484 192693611 0 876
4 TraesCS3A01G212100 chr4A 84.528 879 126 5 63 940 628933457 628934326 0 861
5 TraesCS3A01G212100 chr5D 84.471 850 125 5 92 940 437601584 437602427 0 832
6 TraesCS3A01G212100 chr6A 83.466 877 138 7 67 940 590211707 590210835 0 809
7 TraesCS3A01G212100 chr5A 83.314 875 141 4 69 940 552639947 552640819 0 802
8 TraesCS3A01G212100 chr5A 82.559 883 132 15 63 940 429002261 429001396 0 758
9 TraesCS3A01G212100 chr5B 83.295 862 139 4 80 940 531630277 531631134 0 789
10 TraesCS3A01G212100 chr1A 82.306 876 136 13 73 940 476900354 476899490 0 741
11 TraesCS3A01G212100 chr6D 81.561 884 147 11 63 940 97920724 97921597 0 715


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 TraesCS3A01G212100 chr3A 381293674 381298850 5176 True 9561 9561 100.000 1 5177 1 chr3A.!!$R1 5176
1 TraesCS3A01G212100 chr3D 290015958 290020196 4238 True 7276 7276 97.666 943 5177 1 chr3D.!!$R1 4234
2 TraesCS3A01G212100 chr3B 382318909 382323087 4178 True 7136 7136 97.492 999 5177 1 chr3B.!!$R1 4178
3 TraesCS3A01G212100 chr4B 192693611 192694484 873 True 876 876 84.755 63 940 1 chr4B.!!$R1 877
4 TraesCS3A01G212100 chr4A 628933457 628934326 869 False 861 861 84.528 63 940 1 chr4A.!!$F1 877
5 TraesCS3A01G212100 chr5D 437601584 437602427 843 False 832 832 84.471 92 940 1 chr5D.!!$F1 848
6 TraesCS3A01G212100 chr6A 590210835 590211707 872 True 809 809 83.466 67 940 1 chr6A.!!$R1 873
7 TraesCS3A01G212100 chr5A 552639947 552640819 872 False 802 802 83.314 69 940 1 chr5A.!!$F1 871
8 TraesCS3A01G212100 chr5A 429001396 429002261 865 True 758 758 82.559 63 940 1 chr5A.!!$R1 877
9 TraesCS3A01G212100 chr5B 531630277 531631134 857 False 789 789 83.295 80 940 1 chr5B.!!$F1 860
10 TraesCS3A01G212100 chr1A 476899490 476900354 864 True 741 741 82.306 73 940 1 chr1A.!!$R1 867
11 TraesCS3A01G212100 chr6D 97920724 97921597 873 False 715 715 81.561 63 940 1 chr6D.!!$F1 877

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
56 57 0.793104 GCGTTTGGATAGCACGTTGC 60.793 55.000 2.28 2.28 45.46 4.17 F
676 688 0.827507 AAGCCTTGCAAACACCGGAT 60.828 50.000 9.46 0.00 0.00 4.18 F
1500 1527 1.074889 AGGCCCACGTCATTTACCTTT 59.925 47.619 0.00 0.00 0.00 3.11 F
1918 1945 1.308069 GCTCAATTCGGGCAGCTCAA 61.308 55.000 0.00 0.00 0.00 3.02 F
2594 2621 2.111384 TGGAGAATGTGGAGCTAGGTC 58.889 52.381 13.67 13.67 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 1622 1.261885 CGTTGCACACCGTTGTATTCA 59.738 47.619 0.00 0.00 33.3 2.57 R
2315 2342 1.006832 CCGATCCCTTGTACAAAGCG 58.993 55.000 10.03 9.42 0.0 4.68 R
2783 2810 2.064434 TCCCAATTCAAGCACACACA 57.936 45.000 0.00 0.00 0.0 3.72 R
3120 3147 3.181510 GCTGTGACCTAATACCAAAAGCG 60.182 47.826 0.00 0.00 0.0 4.68 R
4440 4469 0.833287 AGCCGCATAGGAGTGTTCAT 59.167 50.000 0.00 0.00 45.0 2.57 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
26 27 9.503427 GATGGTTTAAAATTCTATCGTGGAAAG 57.497 33.333 0.00 0.00 0.00 2.62
27 28 7.822658 TGGTTTAAAATTCTATCGTGGAAAGG 58.177 34.615 0.00 0.00 0.00 3.11
28 29 7.094118 TGGTTTAAAATTCTATCGTGGAAAGGG 60.094 37.037 0.00 0.00 0.00 3.95
29 30 7.255569 GTTTAAAATTCTATCGTGGAAAGGGG 58.744 38.462 0.00 0.00 0.00 4.79
30 31 4.586306 AAATTCTATCGTGGAAAGGGGT 57.414 40.909 0.00 0.00 0.00 4.95
31 32 4.586306 AATTCTATCGTGGAAAGGGGTT 57.414 40.909 0.00 0.00 0.00 4.11
32 33 5.703730 AATTCTATCGTGGAAAGGGGTTA 57.296 39.130 0.00 0.00 0.00 2.85
33 34 4.748277 TTCTATCGTGGAAAGGGGTTAG 57.252 45.455 0.00 0.00 0.00 2.34
34 35 3.985127 TCTATCGTGGAAAGGGGTTAGA 58.015 45.455 0.00 0.00 0.00 2.10
35 36 4.355549 TCTATCGTGGAAAGGGGTTAGAA 58.644 43.478 0.00 0.00 0.00 2.10
36 37 4.778958 TCTATCGTGGAAAGGGGTTAGAAA 59.221 41.667 0.00 0.00 0.00 2.52
37 38 3.412237 TCGTGGAAAGGGGTTAGAAAG 57.588 47.619 0.00 0.00 0.00 2.62
38 39 1.810755 CGTGGAAAGGGGTTAGAAAGC 59.189 52.381 0.00 0.00 0.00 3.51
39 40 1.810755 GTGGAAAGGGGTTAGAAAGCG 59.189 52.381 0.00 0.00 0.00 4.68
40 41 1.422402 TGGAAAGGGGTTAGAAAGCGT 59.578 47.619 0.00 0.00 0.00 5.07
41 42 2.158579 TGGAAAGGGGTTAGAAAGCGTT 60.159 45.455 0.00 0.00 0.00 4.84
42 43 2.889045 GGAAAGGGGTTAGAAAGCGTTT 59.111 45.455 0.00 0.00 0.00 3.60
43 44 3.305131 GGAAAGGGGTTAGAAAGCGTTTG 60.305 47.826 0.00 0.00 0.00 2.93
44 45 1.905637 AGGGGTTAGAAAGCGTTTGG 58.094 50.000 0.00 0.00 0.00 3.28
45 46 1.422402 AGGGGTTAGAAAGCGTTTGGA 59.578 47.619 0.00 0.00 0.00 3.53
46 47 2.041216 AGGGGTTAGAAAGCGTTTGGAT 59.959 45.455 0.00 0.00 0.00 3.41
47 48 3.264964 AGGGGTTAGAAAGCGTTTGGATA 59.735 43.478 0.00 0.00 0.00 2.59
48 49 3.626217 GGGGTTAGAAAGCGTTTGGATAG 59.374 47.826 0.00 0.00 0.00 2.08
49 50 3.064958 GGGTTAGAAAGCGTTTGGATAGC 59.935 47.826 0.00 0.00 0.00 2.97
50 51 3.687698 GGTTAGAAAGCGTTTGGATAGCA 59.312 43.478 0.00 0.00 0.00 3.49
51 52 4.436986 GGTTAGAAAGCGTTTGGATAGCAC 60.437 45.833 0.00 0.00 0.00 4.40
52 53 1.732259 AGAAAGCGTTTGGATAGCACG 59.268 47.619 0.00 0.00 36.98 5.34
53 54 1.463444 GAAAGCGTTTGGATAGCACGT 59.537 47.619 0.00 0.00 36.29 4.49
54 55 1.519408 AAGCGTTTGGATAGCACGTT 58.481 45.000 0.00 0.00 36.29 3.99
55 56 0.796312 AGCGTTTGGATAGCACGTTG 59.204 50.000 0.00 0.00 36.29 4.10
56 57 0.793104 GCGTTTGGATAGCACGTTGC 60.793 55.000 2.28 2.28 45.46 4.17
84 85 7.619161 GCACCATCGTTTCACAATCAAATAAAC 60.619 37.037 0.00 0.00 0.00 2.01
179 189 2.637382 TCTACTGGTTGCCAACATGAGA 59.363 45.455 10.18 3.56 30.80 3.27
183 194 2.821378 CTGGTTGCCAACATGAGATCAA 59.179 45.455 10.18 0.00 30.80 2.57
193 204 6.669278 CCAACATGAGATCAAATATGCTCAG 58.331 40.000 0.00 0.00 40.34 3.35
196 207 4.701651 TGAGATCAAATATGCTCAGCCT 57.298 40.909 0.00 0.00 32.85 4.58
212 223 7.109501 TGCTCAGCCTAATCATTTTGTAGTTA 58.890 34.615 0.00 0.00 0.00 2.24
264 275 5.185454 TGATGAAATTCGGTGAACTATGCT 58.815 37.500 0.00 0.00 0.00 3.79
289 300 2.827423 CCGCTCCTCCATGCTCAT 59.173 61.111 0.00 0.00 0.00 2.90
354 366 2.540515 TCATTCGAACGCTCATTCTCC 58.459 47.619 0.00 0.00 0.00 3.71
358 370 0.994995 CGAACGCTCATTCTCCACAG 59.005 55.000 0.00 0.00 0.00 3.66
392 404 6.319405 TGCATAATTACACAAGCAGTCATCAT 59.681 34.615 0.00 0.00 0.00 2.45
417 429 2.165437 TCACAACTTTTTGGTGCTCCAC 59.835 45.455 7.09 0.00 44.22 4.02
426 438 1.279496 TGGTGCTCCACATTCTAGCT 58.721 50.000 2.64 0.00 39.03 3.32
487 499 1.021390 GGCACACTCCACATCCTTCG 61.021 60.000 0.00 0.00 0.00 3.79
503 515 2.029828 CCTTCGTAGCACTCTCTTGTGT 60.030 50.000 0.00 0.00 39.89 3.72
509 521 3.281727 AGCACTCTCTTGTGTTTGGAA 57.718 42.857 0.00 0.00 39.89 3.53
586 598 5.938279 TCCACTTAGGATAGATACTGTCGT 58.062 41.667 0.00 0.00 43.07 4.34
624 636 7.773224 CCTTTATTGTAGTGGTGACCATTGATA 59.227 37.037 7.94 1.88 35.28 2.15
640 652 6.891361 ACCATTGATATCAACATTGACCTTCA 59.109 34.615 20.19 0.00 40.49 3.02
676 688 0.827507 AAGCCTTGCAAACACCGGAT 60.828 50.000 9.46 0.00 0.00 4.18
701 713 2.475187 GCTGAAGCATGTTGATGTCGTC 60.475 50.000 0.00 0.00 41.59 4.20
702 714 2.738314 CTGAAGCATGTTGATGTCGTCA 59.262 45.455 0.00 0.00 34.25 4.35
759 771 2.902486 TCAGAGATCTTGTGAAGCCACT 59.098 45.455 0.00 0.00 43.55 4.00
792 805 4.325972 TGATAGTGCAAGCTTTCACATGA 58.674 39.130 27.21 14.52 35.76 3.07
831 844 4.141482 TGCCAAGTAGAAGGACAGTTCTTT 60.141 41.667 0.00 0.00 37.89 2.52
847 860 5.873712 CAGTTCTTTCACTCTCAGTGCATAT 59.126 40.000 0.00 0.00 45.54 1.78
940 961 5.234466 ACAATTGGCTCTCTCAAGTACTT 57.766 39.130 10.83 1.12 0.00 2.24
941 962 4.999950 ACAATTGGCTCTCTCAAGTACTTG 59.000 41.667 26.60 26.60 41.71 3.16
963 984 1.906574 AGAGCGGGAGTCATTTTACCA 59.093 47.619 0.00 0.00 0.00 3.25
964 985 2.505819 AGAGCGGGAGTCATTTTACCAT 59.494 45.455 0.00 0.00 0.00 3.55
992 1013 1.298859 ATTCTGCCGGAAACAGACGC 61.299 55.000 5.05 0.00 43.64 5.19
997 1018 1.281656 CCGGAAACAGACGCCAAAC 59.718 57.895 0.00 0.00 0.00 2.93
1116 1143 1.533273 ACCTCCAGTGCCACTACGT 60.533 57.895 0.00 0.00 0.00 3.57
1281 1308 1.153086 GCGAGGGCTCACCAATGAT 60.153 57.895 0.00 0.00 43.89 2.45
1308 1335 5.677319 TCCTCTCAAACCATCTCGTTAAT 57.323 39.130 0.00 0.00 0.00 1.40
1500 1527 1.074889 AGGCCCACGTCATTTACCTTT 59.925 47.619 0.00 0.00 0.00 3.11
1595 1622 6.179756 TGGTATCAAAGACTGTGTATGCATT 58.820 36.000 3.54 0.00 0.00 3.56
1686 1713 1.955778 CAGCAGGTGTTTGATTCCACA 59.044 47.619 0.00 0.00 33.19 4.17
1764 1791 3.498082 GCATGTGGTTTCGACATTTACC 58.502 45.455 0.00 0.00 31.46 2.85
1766 1793 4.671766 GCATGTGGTTTCGACATTTACCTC 60.672 45.833 0.00 0.00 31.46 3.85
1918 1945 1.308069 GCTCAATTCGGGCAGCTCAA 61.308 55.000 0.00 0.00 0.00 3.02
1998 2025 9.339492 CTTGATGAAGCTAAGAACATTTTTCTC 57.661 33.333 0.00 0.00 0.00 2.87
2315 2342 3.686916 AGCCTGTAGAGTTTTCCAGTC 57.313 47.619 0.00 0.00 0.00 3.51
2505 2532 2.113774 TCTGTGGGCCAGCAAGTG 59.886 61.111 6.40 0.00 41.25 3.16
2562 2589 4.460263 ACACCTCTGTTTCAAATGCACTA 58.540 39.130 0.00 0.00 0.00 2.74
2594 2621 2.111384 TGGAGAATGTGGAGCTAGGTC 58.889 52.381 13.67 13.67 0.00 3.85
2626 2653 4.396478 GGGAAGTTTTCAACTCTATGGCTC 59.604 45.833 0.00 0.00 41.91 4.70
2649 2676 5.705441 TCAACATGATGTAGTTTCCTGGAAC 59.295 40.000 9.04 4.86 0.00 3.62
2783 2810 3.568000 TGGCTACATTGTCGCCATT 57.432 47.368 26.19 0.00 46.82 3.16
2857 2884 8.919777 TGTAGCTATAGAAGATACTGCAGTTA 57.080 34.615 27.06 10.57 45.50 2.24
3120 3147 0.745845 AGCGTGGAATGGAGATGCAC 60.746 55.000 0.00 0.00 35.98 4.57
3236 3263 4.136796 TCAAAGGTGTTCAGTTCCATGAG 58.863 43.478 0.00 0.00 0.00 2.90
3366 3393 7.201812 GCAAATCCAGACCATGTCACATTTATA 60.202 37.037 0.00 0.00 34.60 0.98
3593 3620 6.128553 ACTGTATTAGTTGCTTGTCGACAATG 60.129 38.462 29.79 22.87 35.67 2.82
3740 3767 1.898574 CAGCCAAAACCCGAGCTGT 60.899 57.895 0.00 0.00 46.00 4.40
3890 3917 8.558973 AGTGTTTTGATTCAGAAGATAAGGAG 57.441 34.615 0.00 0.00 0.00 3.69
3894 3921 5.946942 TGATTCAGAAGATAAGGAGTGCT 57.053 39.130 0.00 0.00 0.00 4.40
4077 4104 3.009723 AGATTGTCACACGGCATTTAGG 58.990 45.455 0.00 0.00 0.00 2.69
4101 4128 0.317160 TATCTCACGCTATTGGCCGG 59.683 55.000 0.00 0.00 37.74 6.13
4183 4210 3.054655 TGGGGATTACTGGTAGCTTGTTC 60.055 47.826 0.00 0.00 0.00 3.18
4187 4214 6.354130 GGGATTACTGGTAGCTTGTTCATAA 58.646 40.000 0.00 0.00 0.00 1.90
4189 4216 7.272978 GGATTACTGGTAGCTTGTTCATAAGA 58.727 38.462 0.00 0.00 0.00 2.10
4286 4314 8.703604 TTAACTTATCTCGAATTTGAGGTCAG 57.296 34.615 20.44 16.82 36.61 3.51
4323 4351 9.173021 CAAAGGTACATGTAATCTGTTCCATTA 57.827 33.333 7.25 0.00 36.74 1.90
4427 4456 7.105588 ACATGAATACTGACTTAGTTGATGCA 58.894 34.615 0.00 0.00 40.89 3.96
4440 4469 4.588899 AGTTGATGCAGTTTGGTGCTATA 58.411 39.130 0.00 0.00 44.32 1.31
4445 4474 4.963276 TGCAGTTTGGTGCTATATGAAC 57.037 40.909 0.00 0.00 44.32 3.18
4480 4509 5.278218 GGCTTAGAATTAGCAATCTGGAAGC 60.278 44.000 1.35 0.00 40.42 3.86
4511 4540 4.199432 CTGTAGGCATTCTTCAGTGAGT 57.801 45.455 0.00 0.00 36.51 3.41
4627 4656 4.831107 AGTTCACTTTTTGCACAAACCAT 58.169 34.783 0.00 0.00 0.00 3.55
4662 4691 8.317891 AGTCTCACTATATCTTCAGTACATCG 57.682 38.462 0.00 0.00 0.00 3.84
4669 4698 6.954487 ATATCTTCAGTACATCGTGGTGTA 57.046 37.500 0.00 0.00 33.62 2.90
4687 4716 8.731605 CGTGGTGTAGACATGATATTATACTCT 58.268 37.037 0.00 0.00 0.00 3.24
4724 4753 6.988329 TCTTTGATCGCAAAAACAAGAAAAC 58.012 32.000 0.00 0.00 42.96 2.43
4725 4754 5.710613 TTGATCGCAAAAACAAGAAAACC 57.289 34.783 0.00 0.00 0.00 3.27
4818 4847 5.873164 ACTCAAACTACGTGACTTGTTCTTT 59.127 36.000 0.00 0.00 0.00 2.52
4836 4865 6.266558 TGTTCTTTGGCCAGAAAGCTAATTTA 59.733 34.615 5.11 0.00 34.50 1.40
4886 4915 7.850193 AGATAACCCTTTACCATGTACGTTAA 58.150 34.615 0.00 0.00 0.00 2.01
4952 4981 9.394477 GTATTAACAAACAAGTAAGCTGGAAAG 57.606 33.333 0.00 0.00 0.00 2.62
4955 4984 4.947388 ACAAACAAGTAAGCTGGAAAGTGA 59.053 37.500 0.00 0.00 0.00 3.41
4985 5014 7.041635 ACATTCATCAAAACTGACATGACAA 57.958 32.000 0.00 0.00 0.00 3.18
5088 5123 5.010314 TCAGACTTATACAGAACAACACCGT 59.990 40.000 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.503427 CTTTCCACGATAGAATTTTAAACCATC 57.497 33.333 0.00 0.00 41.38 3.51
1 2 8.466798 CCTTTCCACGATAGAATTTTAAACCAT 58.533 33.333 0.00 0.00 41.38 3.55
2 3 7.094118 CCCTTTCCACGATAGAATTTTAAACCA 60.094 37.037 0.00 0.00 41.38 3.67
3 4 7.255569 CCCTTTCCACGATAGAATTTTAAACC 58.744 38.462 0.00 0.00 41.38 3.27
4 5 7.094075 ACCCCTTTCCACGATAGAATTTTAAAC 60.094 37.037 0.00 0.00 41.38 2.01
5 6 6.949463 ACCCCTTTCCACGATAGAATTTTAAA 59.051 34.615 0.00 0.00 41.38 1.52
7 8 6.069705 ACCCCTTTCCACGATAGAATTTTA 57.930 37.500 0.00 0.00 41.38 1.52
11 12 4.966805 TCTAACCCCTTTCCACGATAGAAT 59.033 41.667 0.00 0.00 41.38 2.40
12 13 4.355549 TCTAACCCCTTTCCACGATAGAA 58.644 43.478 0.00 0.00 41.38 2.10
13 14 3.985127 TCTAACCCCTTTCCACGATAGA 58.015 45.455 0.00 0.00 41.38 1.98
14 15 4.748277 TTCTAACCCCTTTCCACGATAG 57.252 45.455 0.00 0.00 46.19 2.08
15 16 4.624604 GCTTTCTAACCCCTTTCCACGATA 60.625 45.833 0.00 0.00 0.00 2.92
16 17 3.872630 GCTTTCTAACCCCTTTCCACGAT 60.873 47.826 0.00 0.00 0.00 3.73
17 18 2.551504 GCTTTCTAACCCCTTTCCACGA 60.552 50.000 0.00 0.00 0.00 4.35
18 19 1.810755 GCTTTCTAACCCCTTTCCACG 59.189 52.381 0.00 0.00 0.00 4.94
19 20 1.810755 CGCTTTCTAACCCCTTTCCAC 59.189 52.381 0.00 0.00 0.00 4.02
20 21 1.422402 ACGCTTTCTAACCCCTTTCCA 59.578 47.619 0.00 0.00 0.00 3.53
21 22 2.195741 ACGCTTTCTAACCCCTTTCC 57.804 50.000 0.00 0.00 0.00 3.13
22 23 3.305131 CCAAACGCTTTCTAACCCCTTTC 60.305 47.826 0.00 0.00 0.00 2.62
23 24 2.626266 CCAAACGCTTTCTAACCCCTTT 59.374 45.455 0.00 0.00 0.00 3.11
24 25 2.158579 TCCAAACGCTTTCTAACCCCTT 60.159 45.455 0.00 0.00 0.00 3.95
25 26 1.422402 TCCAAACGCTTTCTAACCCCT 59.578 47.619 0.00 0.00 0.00 4.79
26 27 1.900245 TCCAAACGCTTTCTAACCCC 58.100 50.000 0.00 0.00 0.00 4.95
27 28 3.064958 GCTATCCAAACGCTTTCTAACCC 59.935 47.826 0.00 0.00 0.00 4.11
28 29 3.687698 TGCTATCCAAACGCTTTCTAACC 59.312 43.478 0.00 0.00 0.00 2.85
29 30 4.648970 GTGCTATCCAAACGCTTTCTAAC 58.351 43.478 0.00 0.00 0.00 2.34
30 31 3.369756 CGTGCTATCCAAACGCTTTCTAA 59.630 43.478 0.00 0.00 0.00 2.10
31 32 2.927477 CGTGCTATCCAAACGCTTTCTA 59.073 45.455 0.00 0.00 0.00 2.10
32 33 1.732259 CGTGCTATCCAAACGCTTTCT 59.268 47.619 0.00 0.00 0.00 2.52
33 34 1.463444 ACGTGCTATCCAAACGCTTTC 59.537 47.619 0.00 0.00 40.90 2.62
34 35 1.519408 ACGTGCTATCCAAACGCTTT 58.481 45.000 0.00 0.00 40.90 3.51
35 36 1.196808 CAACGTGCTATCCAAACGCTT 59.803 47.619 0.00 0.00 40.90 4.68
36 37 0.796312 CAACGTGCTATCCAAACGCT 59.204 50.000 0.00 0.00 40.90 5.07
37 38 0.793104 GCAACGTGCTATCCAAACGC 60.793 55.000 0.00 0.00 40.96 4.84
38 39 3.290098 GCAACGTGCTATCCAAACG 57.710 52.632 0.00 0.00 40.96 3.60
48 49 2.126734 GATGGTGCAGCAACGTGC 60.127 61.111 24.18 6.51 45.46 5.34
49 50 2.116736 AACGATGGTGCAGCAACGTG 62.117 55.000 41.25 25.05 34.36 4.49
50 51 1.444119 AAACGATGGTGCAGCAACGT 61.444 50.000 37.62 37.62 35.56 3.99
51 52 0.725784 GAAACGATGGTGCAGCAACG 60.726 55.000 36.43 36.43 0.00 4.10
52 53 0.310543 TGAAACGATGGTGCAGCAAC 59.689 50.000 24.18 19.46 0.00 4.17
53 54 0.310543 GTGAAACGATGGTGCAGCAA 59.689 50.000 24.18 6.59 0.00 3.91
54 55 0.817229 TGTGAAACGATGGTGCAGCA 60.817 50.000 22.56 22.56 42.39 4.41
55 56 0.310543 TTGTGAAACGATGGTGCAGC 59.689 50.000 9.47 9.47 42.39 5.25
56 57 2.226200 TGATTGTGAAACGATGGTGCAG 59.774 45.455 0.00 0.00 42.24 4.41
57 58 2.225467 TGATTGTGAAACGATGGTGCA 58.775 42.857 0.00 0.00 42.24 4.57
58 59 2.987413 TGATTGTGAAACGATGGTGC 57.013 45.000 0.00 0.00 42.24 5.01
59 60 7.380870 TGTTTATTTGATTGTGAAACGATGGTG 59.619 33.333 0.00 0.00 42.24 4.17
60 61 7.429633 TGTTTATTTGATTGTGAAACGATGGT 58.570 30.769 0.00 0.00 42.24 3.55
61 62 7.865875 TGTTTATTTGATTGTGAAACGATGG 57.134 32.000 0.00 0.00 42.24 3.51
179 189 8.418597 AAATGATTAGGCTGAGCATATTTGAT 57.581 30.769 10.58 0.00 0.00 2.57
183 194 7.592885 ACAAAATGATTAGGCTGAGCATATT 57.407 32.000 10.58 0.00 0.00 1.28
212 223 5.845103 TGCATGATTGACAAACTCACATTT 58.155 33.333 0.00 0.00 0.00 2.32
224 235 7.764695 TTTCATCATCAAATGCATGATTGAC 57.235 32.000 14.49 0.00 38.67 3.18
264 275 2.875672 GCATGGAGGAGCGGCAATATTA 60.876 50.000 1.45 0.00 0.00 0.98
289 300 2.373224 TCAAGGTGACAATGTTGTGCA 58.627 42.857 2.65 0.00 42.43 4.57
354 366 6.524239 GTGTAATTATGCACAACATGACTGTG 59.476 38.462 21.08 21.08 45.71 3.66
392 404 3.620488 AGCACCAAAAAGTTGTGAGAGA 58.380 40.909 0.00 0.00 32.40 3.10
417 429 4.693283 TCGTTTGGTATCCAGCTAGAATG 58.307 43.478 0.00 0.00 33.81 2.67
426 438 0.106918 GGGGCATCGTTTGGTATCCA 60.107 55.000 0.00 0.00 0.00 3.41
487 499 3.728845 TCCAAACACAAGAGAGTGCTAC 58.271 45.455 0.00 0.00 43.23 3.58
503 515 7.521669 AGAGAAGAGGAAGAGATTTTTCCAAA 58.478 34.615 6.77 0.00 45.28 3.28
509 521 6.957020 TGTAGGAGAGAAGAGGAAGAGATTTT 59.043 38.462 0.00 0.00 0.00 1.82
581 593 7.776969 ACAATAAAGGGTACTATCTAGACGACA 59.223 37.037 0.00 0.00 0.00 4.35
586 598 9.584008 CCACTACAATAAAGGGTACTATCTAGA 57.416 37.037 0.00 0.00 0.00 2.43
597 609 4.295141 TGGTCACCACTACAATAAAGGG 57.705 45.455 0.00 0.00 0.00 3.95
603 615 6.899089 TGATATCAATGGTCACCACTACAAT 58.101 36.000 0.00 0.00 35.80 2.71
624 636 3.087031 CTGCCTGAAGGTCAATGTTGAT 58.913 45.455 0.00 0.00 39.73 2.57
676 688 3.073678 ACATCAACATGCTTCAGCGTTA 58.926 40.909 0.00 0.00 45.83 3.18
701 713 1.970114 GGCATGGCCGGATCTCATG 60.970 63.158 5.05 13.84 39.62 3.07
702 714 2.433446 GGCATGGCCGGATCTCAT 59.567 61.111 5.05 0.00 39.62 2.90
722 734 3.748048 TCTCTGAATTTGGCACTCTTTCG 59.252 43.478 0.00 0.00 0.00 3.46
759 771 4.445453 CTTGCACTATCATACTTGAGGCA 58.555 43.478 0.00 0.00 34.73 4.75
792 805 1.770518 GCAGGGGCAGTATAGGGGT 60.771 63.158 0.00 0.00 40.72 4.95
868 885 7.828717 TGATCAATGCAAGTAGAGGTTTTATGA 59.171 33.333 0.00 0.00 0.00 2.15
871 889 6.374333 GGTGATCAATGCAAGTAGAGGTTTTA 59.626 38.462 0.00 0.00 0.00 1.52
875 893 3.264193 TGGTGATCAATGCAAGTAGAGGT 59.736 43.478 0.00 0.00 0.00 3.85
940 961 0.984230 AAAATGACTCCCGCTCTCCA 59.016 50.000 0.00 0.00 0.00 3.86
941 962 2.552031 GTAAAATGACTCCCGCTCTCC 58.448 52.381 0.00 0.00 0.00 3.71
963 984 2.980568 TCCGGCAGAATTTCACGTTAT 58.019 42.857 0.00 0.00 0.00 1.89
964 985 2.459060 TCCGGCAGAATTTCACGTTA 57.541 45.000 0.00 0.00 0.00 3.18
992 1013 1.857837 GTTTGCGGTTCATGTGTTTGG 59.142 47.619 0.00 0.00 0.00 3.28
997 1018 0.240945 GGGAGTTTGCGGTTCATGTG 59.759 55.000 0.00 0.00 0.00 3.21
1276 1303 5.768980 TGGTTTGAGAGGAAGAGATCATT 57.231 39.130 0.00 0.00 0.00 2.57
1281 1308 3.445450 CGAGATGGTTTGAGAGGAAGAGA 59.555 47.826 0.00 0.00 0.00 3.10
1595 1622 1.261885 CGTTGCACACCGTTGTATTCA 59.738 47.619 0.00 0.00 33.30 2.57
1686 1713 1.556911 GTGATGATGTCCCTGACTGGT 59.443 52.381 0.00 0.00 33.15 4.00
1764 1791 3.366392 CAACATTGCCGTGAACGAG 57.634 52.632 4.03 0.00 43.02 4.18
1918 1945 1.362932 ACTCCCCACATAGAGGTCACT 59.637 52.381 0.00 0.00 34.27 3.41
1998 2025 6.069684 ACTGCATTTCTCTCTTTCAAACTG 57.930 37.500 0.00 0.00 0.00 3.16
2069 2096 6.122277 CCCATGAAAATCCTAACTGCTTCTA 58.878 40.000 0.00 0.00 0.00 2.10
2079 2106 3.980698 CCCTAGTCCCCATGAAAATCCTA 59.019 47.826 0.00 0.00 0.00 2.94
2080 2107 2.785857 CCCTAGTCCCCATGAAAATCCT 59.214 50.000 0.00 0.00 0.00 3.24
2315 2342 1.006832 CCGATCCCTTGTACAAAGCG 58.993 55.000 10.03 9.42 0.00 4.68
2492 2519 2.203669 AATGCACTTGCTGGCCCA 60.204 55.556 0.00 0.00 42.66 5.36
2493 2520 2.263540 CAATGCACTTGCTGGCCC 59.736 61.111 0.00 0.00 42.66 5.80
2562 2589 7.067494 GCTCCACATTCTCCATACATTTTAACT 59.933 37.037 0.00 0.00 0.00 2.24
2594 2621 2.575532 TGAAAACTTCCCAGCACTCAG 58.424 47.619 0.00 0.00 0.00 3.35
2626 2653 5.707298 AGTTCCAGGAAACTACATCATGTTG 59.293 40.000 2.45 0.00 40.21 3.33
2783 2810 2.064434 TCCCAATTCAAGCACACACA 57.936 45.000 0.00 0.00 0.00 3.72
2857 2884 7.941238 AGCATAACAGGACATTAGAGCATTATT 59.059 33.333 0.00 0.00 0.00 1.40
3120 3147 3.181510 GCTGTGACCTAATACCAAAAGCG 60.182 47.826 0.00 0.00 0.00 4.68
3366 3393 4.772624 TGACTACAGGCAGATAGAACACTT 59.227 41.667 0.00 0.00 0.00 3.16
3510 3537 9.689976 ATTCTTCTGATGTATTCTCGTATCTTG 57.310 33.333 0.00 0.00 0.00 3.02
3593 3620 3.375699 TCTATCTTGTCCCTGTCCTTCC 58.624 50.000 0.00 0.00 0.00 3.46
3804 3831 7.855784 TCTATCTCCAGCAATAAAGGTATGA 57.144 36.000 0.00 0.00 0.00 2.15
3890 3917 3.505680 TGTCATTGGAACATAACCAGCAC 59.494 43.478 0.00 0.00 39.30 4.40
3894 3921 5.241403 ACTCTGTCATTGGAACATAACCA 57.759 39.130 0.00 0.00 39.30 3.67
4077 4104 3.927142 GGCCAATAGCGTGAGATATGTAC 59.073 47.826 0.00 0.00 42.75 2.90
4101 4128 4.768583 TGGCATCCCTTAAAATGATTTGC 58.231 39.130 0.00 0.00 0.00 3.68
4149 4176 5.514136 CCAGTAATCCCCACAAGAACACTTA 60.514 44.000 0.00 0.00 0.00 2.24
4183 4210 5.877012 AGCTTGTCACTGTTACCATCTTATG 59.123 40.000 0.00 0.00 0.00 1.90
4187 4214 5.683876 ATAGCTTGTCACTGTTACCATCT 57.316 39.130 0.00 0.00 0.00 2.90
4189 4216 5.560724 ACAATAGCTTGTCACTGTTACCAT 58.439 37.500 0.00 0.00 41.86 3.55
4262 4290 7.837863 ACTGACCTCAAATTCGAGATAAGTTA 58.162 34.615 0.00 0.00 34.79 2.24
4286 4314 9.855021 ATTACATGTACCTTTGAATAGCAAAAC 57.145 29.630 4.68 0.00 45.26 2.43
4318 4346 3.304391 CGGCCATAAATTCACGGTAATGG 60.304 47.826 2.24 0.00 37.52 3.16
4323 4351 1.381165 GGCGGCCATAAATTCACGGT 61.381 55.000 15.62 0.00 0.00 4.83
4427 4456 5.045578 AGGAGTGTTCATATAGCACCAAACT 60.046 40.000 0.00 0.00 39.98 2.66
4440 4469 0.833287 AGCCGCATAGGAGTGTTCAT 59.167 50.000 0.00 0.00 45.00 2.57
4445 4474 2.890808 TTCTAAGCCGCATAGGAGTG 57.109 50.000 2.93 0.00 45.00 3.51
4480 4509 4.764172 AGAATGCCTACAGTTAAGCAGAG 58.236 43.478 0.00 0.00 38.89 3.35
4489 4518 3.580458 ACTCACTGAAGAATGCCTACAGT 59.420 43.478 0.00 0.00 41.52 3.55
4511 4540 6.184789 TCGTGGAGTATGCTATACATGGATA 58.815 40.000 0.00 0.00 40.06 2.59
4818 4847 4.584638 TCCTAAATTAGCTTTCTGGCCA 57.415 40.909 4.71 4.71 0.00 5.36
4836 4865 5.960202 AGAATAATTGCAGGGTTTCAATCCT 59.040 36.000 0.00 0.00 41.23 3.24
4941 4970 8.855110 TGAATGTAAAATTCACTTTCCAGCTTA 58.145 29.630 12.44 0.00 33.55 3.09
4980 5009 5.417266 TCCTTGAGTTTCATTTGTGTTGTCA 59.583 36.000 0.00 0.00 0.00 3.58
5088 5123 3.699413 TGGATTGATGGCTCATGTTTGA 58.301 40.909 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.