Multiple sequence alignment - TraesCS6D01G237900

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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 TraesCS6D01G237900 chr6D 100.000 3546 0 0 1 3546 337843411 337839866 0.000000e+00 6549.0
1 TraesCS6D01G237900 chr6D 94.118 51 2 1 93 143 307783669 307783620 3.800000e-10 76.8
2 TraesCS6D01G237900 chr6A 95.593 3426 101 23 148 3546 478310926 478307524 0.000000e+00 5445.0
3 TraesCS6D01G237900 chr6B 95.322 3420 97 26 148 3546 482470183 482473560 0.000000e+00 5371.0
4 TraesCS6D01G237900 chr4D 97.203 143 3 1 1 142 442616549 442616691 1.270000e-59 241.0
5 TraesCS6D01G237900 chr7D 95.804 143 5 1 1 142 45657676 45657534 2.750000e-56 230.0
6 TraesCS6D01G237900 chr7A 93.103 145 5 4 1 142 579839434 579839576 1.290000e-49 207.0
7 TraesCS6D01G237900 chr5A 93.007 143 9 1 1 142 625908189 625908047 1.290000e-49 207.0
8 TraesCS6D01G237900 chr3B 91.608 143 11 1 1 142 631965859 631966001 2.790000e-46 196.0
9 TraesCS6D01G237900 chr2B 91.608 143 11 1 1 142 105806400 105806258 2.790000e-46 196.0
10 TraesCS6D01G237900 chr1D 96.078 51 2 0 570 620 275139161 275139111 2.270000e-12 84.2
11 TraesCS6D01G237900 chr1D 96.000 50 2 0 87 136 307338266 307338315 8.160000e-12 82.4
12 TraesCS6D01G237900 chr1B 96.078 51 2 0 570 620 374329919 374329869 2.270000e-12 84.2
13 TraesCS6D01G237900 chr1B 95.833 48 1 1 95 142 430612760 430612806 3.800000e-10 76.8
14 TraesCS6D01G237900 chr1A 96.078 51 2 0 570 620 347635421 347635371 2.270000e-12 84.2
15 TraesCS6D01G237900 chr7B 93.750 48 2 1 660 706 675380180 675380227 1.770000e-08 71.3


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 TraesCS6D01G237900 chr6D 337839866 337843411 3545 True 6549 6549 100.000 1 3546 1 chr6D.!!$R2 3545
1 TraesCS6D01G237900 chr6A 478307524 478310926 3402 True 5445 5445 95.593 148 3546 1 chr6A.!!$R1 3398
2 TraesCS6D01G237900 chr6B 482470183 482473560 3377 False 5371 5371 95.322 148 3546 1 chr6B.!!$F1 3398

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
136 137 0.108520 CCATACGTGTGGGCGTTAGT 60.109 55.0 22.66 0.00 43.04 2.24 F
211 213 0.162507 CAACTCGACGAAAGCAGCTG 59.837 55.0 10.11 10.11 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 2000 2.233654 GCACTAGCGCGATCACCAG 61.234 63.158 12.10 0.0 0.00 4.00 R
2547 2587 5.185635 ACCAAATAGCAATGCAGCTCTTTTA 59.814 36.000 8.35 0.0 45.26 1.52 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
19 20 2.450609 TCGGTCAGGTTAGTTTCAGC 57.549 50.000 0.00 0.00 0.00 4.26
20 21 1.001633 TCGGTCAGGTTAGTTTCAGCC 59.998 52.381 0.00 0.00 0.00 4.85
21 22 1.822506 GGTCAGGTTAGTTTCAGCCC 58.177 55.000 0.00 0.00 0.00 5.19
22 23 1.439679 GTCAGGTTAGTTTCAGCCCG 58.560 55.000 0.00 0.00 0.00 6.13
23 24 0.321298 TCAGGTTAGTTTCAGCCCGC 60.321 55.000 0.00 0.00 0.00 6.13
24 25 0.605319 CAGGTTAGTTTCAGCCCGCA 60.605 55.000 0.00 0.00 0.00 5.69
25 26 0.605589 AGGTTAGTTTCAGCCCGCAC 60.606 55.000 0.00 0.00 0.00 5.34
26 27 1.495951 GTTAGTTTCAGCCCGCACG 59.504 57.895 0.00 0.00 0.00 5.34
27 28 0.947180 GTTAGTTTCAGCCCGCACGA 60.947 55.000 0.00 0.00 0.00 4.35
28 29 0.669318 TTAGTTTCAGCCCGCACGAG 60.669 55.000 0.00 0.00 0.00 4.18
29 30 1.812686 TAGTTTCAGCCCGCACGAGT 61.813 55.000 0.00 0.00 0.00 4.18
30 31 2.357034 TTTCAGCCCGCACGAGTC 60.357 61.111 0.00 0.00 0.00 3.36
31 32 3.876589 TTTCAGCCCGCACGAGTCC 62.877 63.158 0.00 0.00 0.00 3.85
42 43 4.778415 CGAGTCCGTGGGCTGACG 62.778 72.222 0.00 0.00 39.13 4.35
43 44 3.681835 GAGTCCGTGGGCTGACGT 61.682 66.667 0.00 0.00 37.66 4.34
44 45 3.916392 GAGTCCGTGGGCTGACGTG 62.916 68.421 0.00 0.00 37.66 4.49
49 50 2.672996 GTGGGCTGACGTGGCAAT 60.673 61.111 11.40 0.00 0.00 3.56
50 51 2.115052 TGGGCTGACGTGGCAATT 59.885 55.556 11.40 0.00 0.00 2.32
51 52 1.530419 TGGGCTGACGTGGCAATTT 60.530 52.632 11.40 0.00 0.00 1.82
52 53 1.112315 TGGGCTGACGTGGCAATTTT 61.112 50.000 11.40 0.00 0.00 1.82
53 54 0.388520 GGGCTGACGTGGCAATTTTC 60.389 55.000 11.40 0.00 0.00 2.29
54 55 0.313672 GGCTGACGTGGCAATTTTCA 59.686 50.000 11.40 0.00 0.00 2.69
55 56 1.666888 GGCTGACGTGGCAATTTTCAG 60.667 52.381 11.40 10.13 37.37 3.02
56 57 1.001378 GCTGACGTGGCAATTTTCAGT 60.001 47.619 14.00 0.00 36.79 3.41
57 58 2.653890 CTGACGTGGCAATTTTCAGTG 58.346 47.619 0.00 0.00 30.97 3.66
58 59 1.268999 TGACGTGGCAATTTTCAGTGC 60.269 47.619 0.00 0.00 43.56 4.40
59 60 1.001378 GACGTGGCAATTTTCAGTGCT 60.001 47.619 0.00 0.00 43.78 4.40
60 61 1.001378 ACGTGGCAATTTTCAGTGCTC 60.001 47.619 0.00 0.00 43.78 4.26
61 62 1.666888 CGTGGCAATTTTCAGTGCTCC 60.667 52.381 0.00 0.00 43.78 4.70
62 63 1.340889 GTGGCAATTTTCAGTGCTCCA 59.659 47.619 0.00 0.00 43.78 3.86
63 64 2.037901 TGGCAATTTTCAGTGCTCCAA 58.962 42.857 0.00 0.00 43.78 3.53
64 65 2.433604 TGGCAATTTTCAGTGCTCCAAA 59.566 40.909 0.00 0.00 43.78 3.28
65 66 3.118482 TGGCAATTTTCAGTGCTCCAAAA 60.118 39.130 0.00 0.00 43.78 2.44
66 67 3.876320 GGCAATTTTCAGTGCTCCAAAAA 59.124 39.130 0.00 0.00 43.78 1.94
67 68 4.516321 GGCAATTTTCAGTGCTCCAAAAAT 59.484 37.500 0.00 3.96 43.78 1.82
68 69 5.008911 GGCAATTTTCAGTGCTCCAAAAATT 59.991 36.000 12.23 12.23 43.78 1.82
70 71 7.018635 CAATTTTCAGTGCTCCAAAAATTGT 57.981 32.000 23.94 7.24 45.31 2.71
71 72 6.607735 ATTTTCAGTGCTCCAAAAATTGTG 57.392 33.333 3.96 0.00 29.42 3.33
72 73 3.096489 TCAGTGCTCCAAAAATTGTGC 57.904 42.857 0.00 0.00 0.00 4.57
73 74 2.429971 TCAGTGCTCCAAAAATTGTGCA 59.570 40.909 4.63 4.63 36.41 4.57
74 75 2.798283 CAGTGCTCCAAAAATTGTGCAG 59.202 45.455 7.81 0.00 38.32 4.41
75 76 1.528161 GTGCTCCAAAAATTGTGCAGC 59.472 47.619 0.00 0.00 38.32 5.25
76 77 1.413445 TGCTCCAAAAATTGTGCAGCT 59.587 42.857 0.33 0.00 34.78 4.24
77 78 1.796459 GCTCCAAAAATTGTGCAGCTG 59.204 47.619 10.11 10.11 0.00 4.24
78 79 2.546373 GCTCCAAAAATTGTGCAGCTGA 60.546 45.455 20.43 0.00 0.00 4.26
79 80 3.863400 GCTCCAAAAATTGTGCAGCTGAT 60.863 43.478 20.43 0.00 0.00 2.90
80 81 3.655486 TCCAAAAATTGTGCAGCTGATG 58.345 40.909 20.43 0.00 0.00 3.07
81 82 2.739913 CCAAAAATTGTGCAGCTGATGG 59.260 45.455 20.43 6.71 0.00 3.51
82 83 3.555377 CCAAAAATTGTGCAGCTGATGGA 60.555 43.478 20.43 0.00 0.00 3.41
92 93 4.333095 CTGATGGACGGCATCGAG 57.667 61.111 0.00 0.00 40.11 4.04
93 94 1.439228 CTGATGGACGGCATCGAGT 59.561 57.895 0.00 0.00 40.11 4.18
94 95 0.873312 CTGATGGACGGCATCGAGTG 60.873 60.000 0.00 0.00 40.11 3.51
102 103 3.490759 GCATCGAGTGCGTGTGGG 61.491 66.667 4.48 0.00 45.23 4.61
103 104 3.490759 CATCGAGTGCGTGTGGGC 61.491 66.667 0.00 0.00 38.98 5.36
107 108 4.357947 GAGTGCGTGTGGGCGAGA 62.358 66.667 0.00 0.00 35.06 4.04
108 109 3.649277 GAGTGCGTGTGGGCGAGAT 62.649 63.158 0.00 0.00 35.06 2.75
109 110 3.490759 GTGCGTGTGGGCGAGATG 61.491 66.667 0.00 0.00 35.06 2.90
119 120 3.430862 GCGAGATGCAAACGCCCA 61.431 61.111 19.47 0.00 45.35 5.36
120 121 2.764314 GCGAGATGCAAACGCCCAT 61.764 57.895 19.47 0.00 45.35 4.00
121 122 1.436195 GCGAGATGCAAACGCCCATA 61.436 55.000 19.47 0.00 45.35 2.74
122 123 0.304705 CGAGATGCAAACGCCCATAC 59.695 55.000 0.00 0.00 0.00 2.39
123 124 0.304705 GAGATGCAAACGCCCATACG 59.695 55.000 0.00 0.00 39.50 3.06
134 135 4.915298 CCATACGTGTGGGCGTTA 57.085 55.556 22.66 0.00 43.04 3.18
135 136 2.673074 CCATACGTGTGGGCGTTAG 58.327 57.895 22.66 0.00 43.04 2.34
136 137 0.108520 CCATACGTGTGGGCGTTAGT 60.109 55.000 22.66 0.00 43.04 2.24
137 138 1.134753 CCATACGTGTGGGCGTTAGTA 59.865 52.381 22.66 0.00 43.04 1.82
138 139 2.223876 CCATACGTGTGGGCGTTAGTAT 60.224 50.000 22.66 0.00 43.04 2.12
139 140 3.450578 CATACGTGTGGGCGTTAGTATT 58.549 45.455 4.09 0.00 43.04 1.89
140 141 2.460757 ACGTGTGGGCGTTAGTATTT 57.539 45.000 0.00 0.00 43.04 1.40
141 142 2.769893 ACGTGTGGGCGTTAGTATTTT 58.230 42.857 0.00 0.00 43.04 1.82
142 143 3.140623 ACGTGTGGGCGTTAGTATTTTT 58.859 40.909 0.00 0.00 43.04 1.94
190 191 7.657761 TCGAAAATAGAGAAAGAAAAGAGTGCT 59.342 33.333 0.00 0.00 0.00 4.40
211 213 0.162507 CAACTCGACGAAAGCAGCTG 59.837 55.000 10.11 10.11 0.00 4.24
276 278 2.683211 AAAGTGACAGCTTTCCCCAT 57.317 45.000 0.00 0.00 33.87 4.00
527 530 3.157252 GCAGATCCTCCTCCGCCA 61.157 66.667 0.00 0.00 0.00 5.69
1500 1540 4.554036 GAGGCCATGGCGGTCCTC 62.554 72.222 29.90 24.62 42.15 3.71
1765 1805 2.974698 GCATTGGGATCCGAGGCG 60.975 66.667 5.45 0.00 34.96 5.52
2313 2353 0.743097 AACGGCGGTAGTAGGATCAC 59.257 55.000 13.24 0.00 0.00 3.06
2581 2621 2.368439 TGCTATTTGGTCATGGTCAGC 58.632 47.619 0.00 0.00 0.00 4.26
2750 2790 8.320617 TGGCTGCTCCTCAAAATTTATATTTTT 58.679 29.630 0.00 0.00 37.51 1.94
2808 2848 5.709631 TGCAAGTCACATCTTAAGGCAATTA 59.290 36.000 1.85 0.00 0.00 1.40
2810 2850 7.555914 TGCAAGTCACATCTTAAGGCAATTATA 59.444 33.333 1.85 0.00 0.00 0.98
3019 3059 3.257127 TGGCAATTTTAGTTAGGGCACAC 59.743 43.478 0.00 0.00 0.00 3.82
3068 3109 5.995565 AGCCCTTAAATTGTTTCTTACCC 57.004 39.130 0.00 0.00 0.00 3.69
3168 3210 7.452880 TTCCATTCTCTTGGTTTGATAAGTG 57.547 36.000 0.00 0.00 38.01 3.16
3171 3213 6.430925 CCATTCTCTTGGTTTGATAAGTGACA 59.569 38.462 0.00 0.00 31.74 3.58
3287 3329 5.106555 CCACGAAATCTTTGTGCTCTATTGT 60.107 40.000 0.00 0.00 32.32 2.71
3292 3334 6.492007 AATCTTTGTGCTCTATTGTCACTG 57.508 37.500 0.00 0.00 0.00 3.66
3382 3425 7.177878 ACATCTCATATGGTTCTTGTCCTTTT 58.822 34.615 2.13 0.00 0.00 2.27
3519 3564 6.942532 AATTTCTGAAGTCTTGCACTGTTA 57.057 33.333 0.00 0.00 34.56 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.001633 GGCTGAAACTAACCTGACCGA 59.998 52.381 0.00 0.00 0.00 4.69
1 2 1.439679 GGCTGAAACTAACCTGACCG 58.560 55.000 0.00 0.00 0.00 4.79
2 3 1.822506 GGGCTGAAACTAACCTGACC 58.177 55.000 0.00 0.00 0.00 4.02
3 4 1.439679 CGGGCTGAAACTAACCTGAC 58.560 55.000 0.00 0.00 0.00 3.51
4 5 0.321298 GCGGGCTGAAACTAACCTGA 60.321 55.000 0.00 0.00 0.00 3.86
5 6 0.605319 TGCGGGCTGAAACTAACCTG 60.605 55.000 0.00 0.00 0.00 4.00
6 7 0.605589 GTGCGGGCTGAAACTAACCT 60.606 55.000 0.00 0.00 0.00 3.50
7 8 1.873863 GTGCGGGCTGAAACTAACC 59.126 57.895 0.00 0.00 0.00 2.85
8 9 0.947180 TCGTGCGGGCTGAAACTAAC 60.947 55.000 0.00 0.00 0.00 2.34
9 10 0.669318 CTCGTGCGGGCTGAAACTAA 60.669 55.000 0.00 0.00 0.00 2.24
10 11 1.080093 CTCGTGCGGGCTGAAACTA 60.080 57.895 0.00 0.00 0.00 2.24
11 12 2.357517 CTCGTGCGGGCTGAAACT 60.358 61.111 0.00 0.00 0.00 2.66
12 13 2.665185 ACTCGTGCGGGCTGAAAC 60.665 61.111 0.00 0.00 0.00 2.78
13 14 2.357034 GACTCGTGCGGGCTGAAA 60.357 61.111 0.00 0.00 0.00 2.69
14 15 4.373116 GGACTCGTGCGGGCTGAA 62.373 66.667 0.00 0.00 0.00 3.02
25 26 4.778415 CGTCAGCCCACGGACTCG 62.778 72.222 0.00 0.00 38.67 4.18
26 27 3.681835 ACGTCAGCCCACGGACTC 61.682 66.667 9.62 0.00 44.41 3.36
27 28 3.991051 CACGTCAGCCCACGGACT 61.991 66.667 9.62 0.00 44.41 3.85
32 33 1.805428 AAATTGCCACGTCAGCCCAC 61.805 55.000 4.72 0.00 0.00 4.61
33 34 1.112315 AAAATTGCCACGTCAGCCCA 61.112 50.000 4.72 0.00 0.00 5.36
34 35 0.388520 GAAAATTGCCACGTCAGCCC 60.389 55.000 4.72 0.00 0.00 5.19
35 36 0.313672 TGAAAATTGCCACGTCAGCC 59.686 50.000 4.72 0.00 0.00 4.85
36 37 1.001378 ACTGAAAATTGCCACGTCAGC 60.001 47.619 0.04 0.04 39.46 4.26
37 38 2.653890 CACTGAAAATTGCCACGTCAG 58.346 47.619 0.00 0.00 41.21 3.51
38 39 1.268999 GCACTGAAAATTGCCACGTCA 60.269 47.619 0.00 0.00 32.21 4.35
39 40 1.001378 AGCACTGAAAATTGCCACGTC 60.001 47.619 0.00 0.00 39.75 4.34
40 41 1.001378 GAGCACTGAAAATTGCCACGT 60.001 47.619 0.00 0.00 39.75 4.49
41 42 1.666888 GGAGCACTGAAAATTGCCACG 60.667 52.381 0.00 0.00 39.75 4.94
42 43 1.340889 TGGAGCACTGAAAATTGCCAC 59.659 47.619 0.00 0.00 39.75 5.01
43 44 1.702182 TGGAGCACTGAAAATTGCCA 58.298 45.000 0.00 0.00 39.75 4.92
44 45 2.818130 TTGGAGCACTGAAAATTGCC 57.182 45.000 0.00 0.00 39.75 4.52
45 46 5.678132 ATTTTTGGAGCACTGAAAATTGC 57.322 34.783 0.00 0.00 39.16 3.56
47 48 6.458615 GCACAATTTTTGGAGCACTGAAAATT 60.459 34.615 11.65 11.65 40.41 1.82
48 49 5.007921 GCACAATTTTTGGAGCACTGAAAAT 59.992 36.000 0.00 0.00 36.32 1.82
49 50 4.332268 GCACAATTTTTGGAGCACTGAAAA 59.668 37.500 0.00 0.00 36.32 2.29
50 51 3.870419 GCACAATTTTTGGAGCACTGAAA 59.130 39.130 0.00 0.00 36.32 2.69
51 52 3.118847 TGCACAATTTTTGGAGCACTGAA 60.119 39.130 5.80 0.00 39.65 3.02
52 53 2.429971 TGCACAATTTTTGGAGCACTGA 59.570 40.909 5.80 0.00 39.65 3.41
53 54 2.798283 CTGCACAATTTTTGGAGCACTG 59.202 45.455 5.80 0.00 39.65 3.66
54 55 3.102052 CTGCACAATTTTTGGAGCACT 57.898 42.857 5.80 0.00 39.65 4.40
58 59 3.374220 TCAGCTGCACAATTTTTGGAG 57.626 42.857 9.47 0.17 35.62 3.86
59 60 3.555377 CCATCAGCTGCACAATTTTTGGA 60.555 43.478 9.47 0.00 34.12 3.53
60 61 2.739913 CCATCAGCTGCACAATTTTTGG 59.260 45.455 9.47 1.00 34.12 3.28
61 62 3.430895 GTCCATCAGCTGCACAATTTTTG 59.569 43.478 9.47 0.00 0.00 2.44
62 63 3.656559 GTCCATCAGCTGCACAATTTTT 58.343 40.909 9.47 0.00 0.00 1.94
63 64 2.352030 CGTCCATCAGCTGCACAATTTT 60.352 45.455 9.47 0.00 0.00 1.82
64 65 1.200716 CGTCCATCAGCTGCACAATTT 59.799 47.619 9.47 0.00 0.00 1.82
65 66 0.806868 CGTCCATCAGCTGCACAATT 59.193 50.000 9.47 0.00 0.00 2.32
66 67 1.028330 CCGTCCATCAGCTGCACAAT 61.028 55.000 9.47 0.00 0.00 2.71
67 68 1.672030 CCGTCCATCAGCTGCACAA 60.672 57.895 9.47 0.00 0.00 3.33
68 69 2.046988 CCGTCCATCAGCTGCACA 60.047 61.111 9.47 0.00 0.00 4.57
69 70 3.503363 GCCGTCCATCAGCTGCAC 61.503 66.667 9.47 1.87 0.00 4.57
70 71 3.333899 ATGCCGTCCATCAGCTGCA 62.334 57.895 9.47 0.31 0.00 4.41
71 72 2.515523 ATGCCGTCCATCAGCTGC 60.516 61.111 9.47 0.00 0.00 5.25
77 78 4.018609 CACTCGATGCCGTCCATC 57.981 61.111 3.85 3.85 45.58 3.51
86 87 3.490759 GCCCACACGCACTCGATG 61.491 66.667 0.00 0.00 39.41 3.84
90 91 3.649277 ATCTCGCCCACACGCACTC 62.649 63.158 0.00 0.00 0.00 3.51
91 92 3.695606 ATCTCGCCCACACGCACT 61.696 61.111 0.00 0.00 0.00 4.40
92 93 3.490759 CATCTCGCCCACACGCAC 61.491 66.667 0.00 0.00 0.00 5.34
95 96 2.324330 TTTGCATCTCGCCCACACG 61.324 57.895 0.00 0.00 41.33 4.49
96 97 1.210155 GTTTGCATCTCGCCCACAC 59.790 57.895 0.00 0.00 41.33 3.82
97 98 2.324330 CGTTTGCATCTCGCCCACA 61.324 57.895 0.00 0.00 41.33 4.17
98 99 2.480555 CGTTTGCATCTCGCCCAC 59.519 61.111 0.00 0.00 41.33 4.61
99 100 3.430862 GCGTTTGCATCTCGCCCA 61.431 61.111 16.09 0.00 43.41 5.36
103 104 0.304705 GTATGGGCGTTTGCATCTCG 59.695 55.000 0.00 0.00 45.35 4.04
104 105 0.304705 CGTATGGGCGTTTGCATCTC 59.695 55.000 0.00 0.00 45.35 2.75
105 106 0.392461 ACGTATGGGCGTTTGCATCT 60.392 50.000 0.00 0.00 43.04 2.90
106 107 0.248054 CACGTATGGGCGTTTGCATC 60.248 55.000 0.00 0.00 43.83 3.91
107 108 0.958382 ACACGTATGGGCGTTTGCAT 60.958 50.000 0.00 0.00 43.83 3.96
108 109 1.598407 ACACGTATGGGCGTTTGCA 60.598 52.632 0.00 0.00 43.83 4.08
109 110 1.154301 CACACGTATGGGCGTTTGC 60.154 57.895 0.00 0.00 43.83 3.68
110 111 1.499949 CCACACGTATGGGCGTTTG 59.500 57.895 4.49 0.00 43.83 2.93
111 112 3.975246 CCACACGTATGGGCGTTT 58.025 55.556 4.49 0.00 43.83 3.60
122 123 3.817148 AAAAATACTAACGCCCACACG 57.183 42.857 0.00 0.00 39.50 4.49
167 168 9.561069 TGTAGCACTCTTTTCTTTCTCTATTTT 57.439 29.630 0.00 0.00 0.00 1.82
190 191 1.000607 AGCTGCTTTCGTCGAGTTGTA 60.001 47.619 0.00 0.00 0.00 2.41
211 213 0.820871 ACTCTCGATTGACCAGGAGC 59.179 55.000 0.00 0.00 0.00 4.70
214 216 2.428530 TGATCACTCTCGATTGACCAGG 59.571 50.000 0.00 0.00 0.00 4.45
254 256 4.919774 TGGGGAAAGCTGTCACTTTATA 57.080 40.909 6.01 0.00 39.93 0.98
1960 2000 2.233654 GCACTAGCGCGATCACCAG 61.234 63.158 12.10 0.00 0.00 4.00
2547 2587 5.185635 ACCAAATAGCAATGCAGCTCTTTTA 59.814 36.000 8.35 0.00 45.26 1.52
2581 2621 3.321682 ACATATGAAATTCCAATGGGGCG 59.678 43.478 10.38 0.00 36.21 6.13
2750 2790 7.731054 ACATCACACCAAAAATTAAAGCCTAA 58.269 30.769 0.00 0.00 0.00 2.69
2808 2848 8.801882 TTCGTGATTCCAGGTAAAAGAAATAT 57.198 30.769 0.00 0.00 0.00 1.28
2810 2850 6.940298 TCTTCGTGATTCCAGGTAAAAGAAAT 59.060 34.615 0.00 0.00 0.00 2.17
2884 2924 8.779354 AGATTCTGTAGGAACATAAACAGTTC 57.221 34.615 0.00 0.00 43.49 3.01
2889 2929 7.923414 ACCAAGATTCTGTAGGAACATAAAC 57.077 36.000 6.98 0.00 36.70 2.01
2991 3031 5.418676 CCCTAACTAAAATTGCCAACCATG 58.581 41.667 0.00 0.00 0.00 3.66
3101 3142 8.134895 TCACTTGAAAGCCACAAAAACTATAAG 58.865 33.333 0.00 0.00 0.00 1.73
3168 3210 8.336801 ACCAAGAAGATTAACCTTGTAATGTC 57.663 34.615 0.00 0.00 36.47 3.06
3287 3329 7.719193 TCTTTCCTGTAAATTGATCAACAGTGA 59.281 33.333 19.14 14.34 38.10 3.41
3317 3359 9.901172 GTCAAATTAGGGTATCTCTCCTTTAAA 57.099 33.333 0.00 0.00 34.75 1.52
3336 3379 6.899393 TGTTTATCTTGAGGCAGTCAAATT 57.101 33.333 2.70 0.00 44.83 1.82
3382 3425 8.621532 ATTCTTGCATTAAAGTAGACTTGTCA 57.378 30.769 3.49 0.00 36.12 3.58
3519 3564 9.185680 GAGGTGAACCCATAATGTAACTTTAAT 57.814 33.333 0.00 0.00 36.42 1.40


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

AutoCloner maintained by Alex Coulton.