Multiple sequence alignment - TraesCS2A01G148000

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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 TraesCS2A01G148000 chr2A 100.000 2249 0 0 1 2249 94221812 94224060 0.000000e+00 4154
1 TraesCS2A01G148000 chr2A 95.730 1569 67 0 141 1709 65084661 65086229 0.000000e+00 2527
2 TraesCS2A01G148000 chr2A 97.241 145 4 0 1 145 386647614 386647758 1.730000e-61 246
3 TraesCS2A01G148000 chr2A 95.270 148 5 2 1 147 566188185 566188039 1.340000e-57 233
4 TraesCS2A01G148000 chr6A 96.398 2110 74 2 141 2249 508000707 508002815 0.000000e+00 3474
5 TraesCS2A01G148000 chr6A 96.387 941 30 3 141 1080 349779674 349780611 0.000000e+00 1546
6 TraesCS2A01G148000 chr3A 95.827 2109 78 5 141 2249 50435365 50437463 0.000000e+00 3398
7 TraesCS2A01G148000 chr3A 96.699 939 29 2 141 1079 657439544 657440480 0.000000e+00 1561
8 TraesCS2A01G148000 chr1A 95.685 2109 76 6 141 2249 527084169 527082076 0.000000e+00 3376
9 TraesCS2A01G148000 chr1A 96.503 143 5 0 1 143 303645880 303645738 1.040000e-58 237
10 TraesCS2A01G148000 chr5A 96.209 1820 68 1 431 2249 554347665 554349484 0.000000e+00 2977
11 TraesCS2A01G148000 chr5A 96.160 1354 52 0 896 2249 560882915 560881562 0.000000e+00 2213
12 TraesCS2A01G148000 chr5A 95.364 151 5 2 1 150 491990655 491990804 2.890000e-59 239
13 TraesCS2A01G148000 chr5A 97.143 140 4 0 1 140 199360220 199360081 1.040000e-58 237
14 TraesCS2A01G148000 chr5A 96.503 143 5 0 1 143 199373422 199373280 1.040000e-58 237
15 TraesCS2A01G148000 chr7A 94.783 1591 81 2 379 1968 724636562 724638151 0.000000e+00 2477
16 TraesCS2A01G148000 chr7A 97.857 140 3 0 1 140 226012681 226012820 2.230000e-60 243
17 TraesCS2A01G148000 chr7A 96.528 144 4 1 1 144 164673823 164673681 1.040000e-58 237
18 TraesCS2A01G148000 chr7A 97.143 140 4 0 1 140 548133893 548134032 1.040000e-58 237
19 TraesCS2A01G148000 chr6D 96.218 1507 51 3 141 1646 196357755 196359256 0.000000e+00 2462
20 TraesCS2A01G148000 chr6B 94.305 1352 73 3 901 2249 131761702 131760352 0.000000e+00 2067
21 TraesCS2A01G148000 chr6B 97.849 93 2 0 141 233 70513257 70513349 6.430000e-36 161
22 TraesCS2A01G148000 chr1B 94.444 1044 56 2 1206 2249 552389896 552388855 0.000000e+00 1605
23 TraesCS2A01G148000 chr2D 95.281 890 42 0 1360 2249 464801694 464800805 0.000000e+00 1411


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 TraesCS2A01G148000 chr2A 94221812 94224060 2248 False 4154 4154 100.000 1 2249 1 chr2A.!!$F2 2248
1 TraesCS2A01G148000 chr2A 65084661 65086229 1568 False 2527 2527 95.730 141 1709 1 chr2A.!!$F1 1568
2 TraesCS2A01G148000 chr6A 508000707 508002815 2108 False 3474 3474 96.398 141 2249 1 chr6A.!!$F2 2108
3 TraesCS2A01G148000 chr6A 349779674 349780611 937 False 1546 1546 96.387 141 1080 1 chr6A.!!$F1 939
4 TraesCS2A01G148000 chr3A 50435365 50437463 2098 False 3398 3398 95.827 141 2249 1 chr3A.!!$F1 2108
5 TraesCS2A01G148000 chr3A 657439544 657440480 936 False 1561 1561 96.699 141 1079 1 chr3A.!!$F2 938
6 TraesCS2A01G148000 chr1A 527082076 527084169 2093 True 3376 3376 95.685 141 2249 1 chr1A.!!$R2 2108
7 TraesCS2A01G148000 chr5A 554347665 554349484 1819 False 2977 2977 96.209 431 2249 1 chr5A.!!$F2 1818
8 TraesCS2A01G148000 chr5A 560881562 560882915 1353 True 2213 2213 96.160 896 2249 1 chr5A.!!$R3 1353
9 TraesCS2A01G148000 chr7A 724636562 724638151 1589 False 2477 2477 94.783 379 1968 1 chr7A.!!$F3 1589
10 TraesCS2A01G148000 chr6D 196357755 196359256 1501 False 2462 2462 96.218 141 1646 1 chr6D.!!$F1 1505
11 TraesCS2A01G148000 chr6B 131760352 131761702 1350 True 2067 2067 94.305 901 2249 1 chr6B.!!$R1 1348
12 TraesCS2A01G148000 chr1B 552388855 552389896 1041 True 1605 1605 94.444 1206 2249 1 chr1B.!!$R1 1043
13 TraesCS2A01G148000 chr2D 464800805 464801694 889 True 1411 1411 95.281 1360 2249 1 chr2D.!!$R1 889

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
31 32 0.455295 CGAGTGTCTTCGAGTCTGCC 60.455 60.0 0.0 0.0 43.03 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1457 1464 0.965439 GGTTGGTAATGGTGCAGCAA 59.035 50.0 24.18 4.09 0.0 3.91 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 1.865865 TTGCTTCTTGGTCGAGTGTC 58.134 50.000 0.00 0.00 0.00 3.67
20 21 1.040646 TGCTTCTTGGTCGAGTGTCT 58.959 50.000 0.00 0.00 0.00 3.41
21 22 1.412710 TGCTTCTTGGTCGAGTGTCTT 59.587 47.619 0.00 0.00 0.00 3.01
22 23 2.062519 GCTTCTTGGTCGAGTGTCTTC 58.937 52.381 0.00 0.00 0.00 2.87
23 24 2.320367 CTTCTTGGTCGAGTGTCTTCG 58.680 52.381 0.00 0.00 41.79 3.79
24 25 1.601166 TCTTGGTCGAGTGTCTTCGA 58.399 50.000 0.00 0.00 46.41 3.71
30 31 0.517755 TCGAGTGTCTTCGAGTCTGC 59.482 55.000 0.00 0.00 44.00 4.26
31 32 0.455295 CGAGTGTCTTCGAGTCTGCC 60.455 60.000 0.00 0.00 43.03 4.85
32 33 0.455295 GAGTGTCTTCGAGTCTGCCG 60.455 60.000 0.00 0.00 0.00 5.69
33 34 0.889638 AGTGTCTTCGAGTCTGCCGA 60.890 55.000 0.00 0.00 0.00 5.54
34 35 0.455295 GTGTCTTCGAGTCTGCCGAG 60.455 60.000 0.00 0.00 37.35 4.63
35 36 0.889638 TGTCTTCGAGTCTGCCGAGT 60.890 55.000 0.00 0.00 37.35 4.18
36 37 0.455295 GTCTTCGAGTCTGCCGAGTG 60.455 60.000 0.00 0.00 37.35 3.51
37 38 1.153939 CTTCGAGTCTGCCGAGTGG 60.154 63.158 0.00 0.00 37.35 4.00
38 39 1.587043 CTTCGAGTCTGCCGAGTGGA 61.587 60.000 0.00 0.00 37.35 4.02
39 40 1.176619 TTCGAGTCTGCCGAGTGGAA 61.177 55.000 6.36 6.36 35.70 3.53
40 41 1.444553 CGAGTCTGCCGAGTGGAAC 60.445 63.158 0.00 0.00 37.49 3.62
41 42 1.666011 GAGTCTGCCGAGTGGAACA 59.334 57.895 0.00 0.00 41.43 3.18
56 57 3.923017 GGAACACCTCCAAGTCAATTG 57.077 47.619 0.00 0.00 44.67 2.32
67 68 4.670896 CAAGTCAATTGGAAGGTGGTTT 57.329 40.909 5.42 0.00 35.08 3.27
68 69 4.620982 CAAGTCAATTGGAAGGTGGTTTC 58.379 43.478 5.42 0.00 35.08 2.78
69 70 4.184649 AGTCAATTGGAAGGTGGTTTCT 57.815 40.909 5.42 0.00 0.00 2.52
70 71 4.546674 AGTCAATTGGAAGGTGGTTTCTT 58.453 39.130 5.42 0.00 0.00 2.52
71 72 4.584743 AGTCAATTGGAAGGTGGTTTCTTC 59.415 41.667 5.42 0.00 39.73 2.87
72 73 4.584743 GTCAATTGGAAGGTGGTTTCTTCT 59.415 41.667 5.42 0.00 40.17 2.85
73 74 5.768164 GTCAATTGGAAGGTGGTTTCTTCTA 59.232 40.000 5.42 0.00 40.17 2.10
74 75 6.003950 TCAATTGGAAGGTGGTTTCTTCTAG 58.996 40.000 5.42 0.00 40.17 2.43
75 76 5.843019 ATTGGAAGGTGGTTTCTTCTAGA 57.157 39.130 0.00 0.00 40.17 2.43
76 77 4.891992 TGGAAGGTGGTTTCTTCTAGAG 57.108 45.455 0.00 0.00 40.17 2.43
77 78 4.489737 TGGAAGGTGGTTTCTTCTAGAGA 58.510 43.478 0.00 0.00 40.17 3.10
78 79 5.094387 TGGAAGGTGGTTTCTTCTAGAGAT 58.906 41.667 0.00 0.00 40.17 2.75
79 80 5.046304 TGGAAGGTGGTTTCTTCTAGAGATG 60.046 44.000 0.00 0.00 40.17 2.90
80 81 5.046231 GGAAGGTGGTTTCTTCTAGAGATGT 60.046 44.000 0.00 0.00 40.17 3.06
81 82 5.669164 AGGTGGTTTCTTCTAGAGATGTC 57.331 43.478 0.00 0.00 33.49 3.06
82 83 4.468153 AGGTGGTTTCTTCTAGAGATGTCC 59.532 45.833 0.00 0.00 33.49 4.02
83 84 4.468153 GGTGGTTTCTTCTAGAGATGTCCT 59.532 45.833 0.00 0.00 33.49 3.85
84 85 5.046231 GGTGGTTTCTTCTAGAGATGTCCTT 60.046 44.000 0.00 0.00 33.49 3.36
85 86 5.872070 GTGGTTTCTTCTAGAGATGTCCTTG 59.128 44.000 0.00 0.00 33.49 3.61
86 87 5.046304 TGGTTTCTTCTAGAGATGTCCTTGG 60.046 44.000 0.00 0.00 33.49 3.61
87 88 5.423886 GTTTCTTCTAGAGATGTCCTTGGG 58.576 45.833 0.00 0.00 33.49 4.12
88 89 4.338795 TCTTCTAGAGATGTCCTTGGGT 57.661 45.455 0.00 0.00 0.00 4.51
89 90 5.467668 TCTTCTAGAGATGTCCTTGGGTA 57.532 43.478 0.00 0.00 0.00 3.69
90 91 5.450453 TCTTCTAGAGATGTCCTTGGGTAG 58.550 45.833 0.00 0.00 0.00 3.18
91 92 4.186077 TCTAGAGATGTCCTTGGGTAGG 57.814 50.000 0.00 0.00 46.27 3.18
92 93 2.182516 AGAGATGTCCTTGGGTAGGG 57.817 55.000 0.00 0.00 44.86 3.53
97 98 4.681624 TCCTTGGGTAGGGCAGTT 57.318 55.556 0.00 0.00 44.86 3.16
98 99 3.819939 TCCTTGGGTAGGGCAGTTA 57.180 52.632 0.00 0.00 44.86 2.24
99 100 1.580059 TCCTTGGGTAGGGCAGTTAG 58.420 55.000 0.00 0.00 44.86 2.34
100 101 0.546598 CCTTGGGTAGGGCAGTTAGG 59.453 60.000 0.00 0.00 40.67 2.69
101 102 1.580059 CTTGGGTAGGGCAGTTAGGA 58.420 55.000 0.00 0.00 0.00 2.94
102 103 2.127708 CTTGGGTAGGGCAGTTAGGAT 58.872 52.381 0.00 0.00 0.00 3.24
103 104 3.314693 CTTGGGTAGGGCAGTTAGGATA 58.685 50.000 0.00 0.00 0.00 2.59
104 105 2.972348 TGGGTAGGGCAGTTAGGATAG 58.028 52.381 0.00 0.00 0.00 2.08
105 106 2.258109 GGGTAGGGCAGTTAGGATAGG 58.742 57.143 0.00 0.00 0.00 2.57
106 107 2.427445 GGGTAGGGCAGTTAGGATAGGT 60.427 54.545 0.00 0.00 0.00 3.08
107 108 2.898612 GGTAGGGCAGTTAGGATAGGTC 59.101 54.545 0.00 0.00 0.00 3.85
108 109 2.104669 AGGGCAGTTAGGATAGGTCC 57.895 55.000 0.00 0.00 45.45 4.46
117 118 6.256819 CAGTTAGGATAGGTCCATGATCCTA 58.743 44.000 17.36 17.36 46.20 2.94
119 120 4.067944 AGGATAGGTCCATGATCCTACC 57.932 50.000 15.17 14.40 46.20 3.18
120 121 3.108376 GGATAGGTCCATGATCCTACCC 58.892 54.545 14.85 12.33 44.42 3.69
121 122 3.246167 GGATAGGTCCATGATCCTACCCT 60.246 52.174 15.24 4.32 44.42 4.34
122 123 4.016479 GGATAGGTCCATGATCCTACCCTA 60.016 50.000 15.24 5.73 44.42 3.53
123 124 3.551635 AGGTCCATGATCCTACCCTAG 57.448 52.381 6.83 0.00 32.10 3.02
124 125 8.800864 GGATAGGTCCATGATCCTACCCTAGG 62.801 53.846 15.24 0.06 44.67 3.02
125 126 2.158143 GGTCCATGATCCTACCCTAGGT 60.158 54.545 8.29 0.00 46.32 3.08
126 127 3.077088 GGTCCATGATCCTACCCTAGGTA 59.923 52.174 8.29 0.00 46.32 3.08
127 128 4.087907 GTCCATGATCCTACCCTAGGTAC 58.912 52.174 8.29 0.00 46.32 3.34
128 129 3.730594 TCCATGATCCTACCCTAGGTACA 59.269 47.826 8.29 0.00 46.32 2.90
129 130 4.360140 TCCATGATCCTACCCTAGGTACAT 59.640 45.833 8.29 0.00 46.32 2.29
130 131 5.558339 TCCATGATCCTACCCTAGGTACATA 59.442 44.000 8.29 0.00 46.32 2.29
131 132 5.894393 CCATGATCCTACCCTAGGTACATAG 59.106 48.000 8.29 7.59 46.32 2.23
132 133 4.931914 TGATCCTACCCTAGGTACATAGC 58.068 47.826 9.07 0.00 46.32 2.97
133 134 4.606697 TGATCCTACCCTAGGTACATAGCT 59.393 45.833 9.07 0.00 46.32 3.32
134 135 5.076039 TGATCCTACCCTAGGTACATAGCTT 59.924 44.000 9.07 0.75 46.32 3.74
135 136 4.995536 TCCTACCCTAGGTACATAGCTTC 58.004 47.826 9.07 0.00 46.32 3.86
136 137 4.417854 TCCTACCCTAGGTACATAGCTTCA 59.582 45.833 9.07 0.00 46.32 3.02
137 138 5.076039 TCCTACCCTAGGTACATAGCTTCAT 59.924 44.000 9.07 0.00 46.32 2.57
138 139 5.419471 CCTACCCTAGGTACATAGCTTCATC 59.581 48.000 9.07 0.00 41.18 2.92
139 140 4.816126 ACCCTAGGTACATAGCTTCATCA 58.184 43.478 9.07 0.00 32.11 3.07
522 525 5.699097 AAAACCGTACTGCACAATTATGT 57.301 34.783 0.00 0.00 41.61 2.29
729 732 8.433421 TTTTTGTTCGAAGACTGAACTTATCT 57.567 30.769 0.00 0.00 44.67 1.98
730 733 7.408132 TTTGTTCGAAGACTGAACTTATCTG 57.592 36.000 0.00 0.00 44.67 2.90
918 922 5.579511 CCAGTTCTATTTCGTATTTGGTCGT 59.420 40.000 0.00 0.00 0.00 4.34
1035 1042 3.575351 GAGCTGTCCGTCCGTTGCT 62.575 63.158 0.00 0.00 0.00 3.91
1080 1087 2.680352 GAGAGTCCGCCCTGGTCA 60.680 66.667 0.00 0.00 39.52 4.02
1200 1207 5.306394 TCTCTTCTCGACTTACTCTGTTCA 58.694 41.667 0.00 0.00 0.00 3.18
1437 1444 3.367703 CCACCACCATTCTTTCTGCAATC 60.368 47.826 0.00 0.00 0.00 2.67
1450 1457 6.650807 TCTTTCTGCAATCGTATATGAATCCC 59.349 38.462 0.00 0.00 0.00 3.85
1457 1464 2.631062 TCGTATATGAATCCCGCCACTT 59.369 45.455 0.00 0.00 0.00 3.16
1484 1491 5.632118 TGCACCATTACCAACCTTACTTAA 58.368 37.500 0.00 0.00 0.00 1.85
1553 1560 4.839668 TGAAGTGGGTTTACGAATTTGG 57.160 40.909 0.00 0.00 0.00 3.28
1717 1724 9.745018 ATGGGTTTGTAGGATAATAAGATCATG 57.255 33.333 0.00 0.00 0.00 3.07
1824 1831 2.572191 AATCATGCGCCAATTGACAG 57.428 45.000 7.12 0.00 0.00 3.51
2207 2214 3.386078 GGCAGAGTGAATCCATGAGACTA 59.614 47.826 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.062519 GAAGACACTCGACCAAGAAGC 58.937 52.381 0.00 0.00 0.00 3.86
4 5 1.951602 TCGAAGACACTCGACCAAGAA 59.048 47.619 0.00 0.00 42.69 2.52
6 7 1.267261 ACTCGAAGACACTCGACCAAG 59.733 52.381 0.00 0.00 42.69 3.61
7 8 1.266175 GACTCGAAGACACTCGACCAA 59.734 52.381 0.00 0.00 42.69 3.67
8 9 0.873054 GACTCGAAGACACTCGACCA 59.127 55.000 0.00 0.00 42.69 4.02
9 10 1.135916 CAGACTCGAAGACACTCGACC 60.136 57.143 0.00 0.00 42.69 4.79
10 11 1.726571 GCAGACTCGAAGACACTCGAC 60.727 57.143 0.00 0.00 42.69 4.20
11 12 0.517755 GCAGACTCGAAGACACTCGA 59.482 55.000 0.00 0.00 45.22 4.04
12 13 0.455295 GGCAGACTCGAAGACACTCG 60.455 60.000 0.00 0.00 40.25 4.18
13 14 0.455295 CGGCAGACTCGAAGACACTC 60.455 60.000 0.00 0.00 0.00 3.51
14 15 0.889638 TCGGCAGACTCGAAGACACT 60.890 55.000 0.00 0.00 33.42 3.55
15 16 0.455295 CTCGGCAGACTCGAAGACAC 60.455 60.000 0.00 0.00 36.15 3.67
16 17 0.889638 ACTCGGCAGACTCGAAGACA 60.890 55.000 0.00 0.00 36.15 3.41
17 18 0.455295 CACTCGGCAGACTCGAAGAC 60.455 60.000 0.00 0.00 36.15 3.01
18 19 1.587043 CCACTCGGCAGACTCGAAGA 61.587 60.000 0.00 0.00 36.15 2.87
19 20 1.153939 CCACTCGGCAGACTCGAAG 60.154 63.158 0.00 0.00 36.15 3.79
20 21 1.176619 TTCCACTCGGCAGACTCGAA 61.177 55.000 0.00 0.00 36.15 3.71
21 22 1.602605 TTCCACTCGGCAGACTCGA 60.603 57.895 0.00 0.00 35.24 4.04
22 23 1.444553 GTTCCACTCGGCAGACTCG 60.445 63.158 0.00 0.00 0.00 4.18
23 24 0.667792 GTGTTCCACTCGGCAGACTC 60.668 60.000 0.00 0.00 0.00 3.36
24 25 1.367840 GTGTTCCACTCGGCAGACT 59.632 57.895 0.00 0.00 0.00 3.24
25 26 1.668151 GGTGTTCCACTCGGCAGAC 60.668 63.158 0.00 0.00 34.40 3.51
26 27 1.816863 GAGGTGTTCCACTCGGCAGA 61.817 60.000 0.00 0.00 34.40 4.26
27 28 1.374758 GAGGTGTTCCACTCGGCAG 60.375 63.158 0.00 0.00 34.40 4.85
28 29 2.741092 GAGGTGTTCCACTCGGCA 59.259 61.111 0.00 0.00 34.40 5.69
29 30 2.047179 GGAGGTGTTCCACTCGGC 60.047 66.667 0.00 0.00 46.01 5.54
36 37 3.923017 CAATTGACTTGGAGGTGTTCC 57.077 47.619 0.00 0.00 46.98 3.62
46 47 4.342092 AGAAACCACCTTCCAATTGACTTG 59.658 41.667 7.12 0.00 34.42 3.16
47 48 4.546674 AGAAACCACCTTCCAATTGACTT 58.453 39.130 7.12 0.00 0.00 3.01
48 49 4.184649 AGAAACCACCTTCCAATTGACT 57.815 40.909 7.12 0.00 0.00 3.41
49 50 4.584743 AGAAGAAACCACCTTCCAATTGAC 59.415 41.667 7.12 0.00 40.54 3.18
50 51 4.803452 AGAAGAAACCACCTTCCAATTGA 58.197 39.130 7.12 0.00 40.54 2.57
51 52 6.003950 TCTAGAAGAAACCACCTTCCAATTG 58.996 40.000 0.00 0.00 40.54 2.32
52 53 6.044404 TCTCTAGAAGAAACCACCTTCCAATT 59.956 38.462 0.00 0.00 40.54 2.32
53 54 5.548056 TCTCTAGAAGAAACCACCTTCCAAT 59.452 40.000 0.00 0.00 40.54 3.16
54 55 4.905456 TCTCTAGAAGAAACCACCTTCCAA 59.095 41.667 0.00 0.00 40.54 3.53
55 56 4.489737 TCTCTAGAAGAAACCACCTTCCA 58.510 43.478 0.00 0.00 40.54 3.53
56 57 5.046231 ACATCTCTAGAAGAAACCACCTTCC 60.046 44.000 0.00 0.00 40.54 3.46
57 58 6.043854 ACATCTCTAGAAGAAACCACCTTC 57.956 41.667 0.00 0.00 37.61 3.46
58 59 5.046231 GGACATCTCTAGAAGAAACCACCTT 60.046 44.000 0.00 0.00 37.61 3.50
59 60 4.468153 GGACATCTCTAGAAGAAACCACCT 59.532 45.833 0.00 0.00 37.61 4.00
60 61 4.468153 AGGACATCTCTAGAAGAAACCACC 59.532 45.833 0.00 0.00 37.61 4.61
61 62 5.669164 AGGACATCTCTAGAAGAAACCAC 57.331 43.478 0.00 0.00 37.61 4.16
62 63 5.046304 CCAAGGACATCTCTAGAAGAAACCA 60.046 44.000 0.00 0.00 37.61 3.67
63 64 5.423886 CCAAGGACATCTCTAGAAGAAACC 58.576 45.833 0.00 0.00 37.61 3.27
64 65 5.046231 ACCCAAGGACATCTCTAGAAGAAAC 60.046 44.000 0.00 0.00 37.61 2.78
65 66 5.094387 ACCCAAGGACATCTCTAGAAGAAA 58.906 41.667 0.00 0.00 37.61 2.52
66 67 4.689062 ACCCAAGGACATCTCTAGAAGAA 58.311 43.478 0.00 0.00 37.61 2.52
67 68 4.338795 ACCCAAGGACATCTCTAGAAGA 57.661 45.455 0.00 0.00 38.72 2.87
68 69 5.782893 CTACCCAAGGACATCTCTAGAAG 57.217 47.826 0.00 0.00 0.00 2.85
81 82 0.546598 CCTAACTGCCCTACCCAAGG 59.453 60.000 0.00 0.00 46.09 3.61
82 83 1.580059 TCCTAACTGCCCTACCCAAG 58.420 55.000 0.00 0.00 0.00 3.61
83 84 2.280308 ATCCTAACTGCCCTACCCAA 57.720 50.000 0.00 0.00 0.00 4.12
84 85 2.427297 CCTATCCTAACTGCCCTACCCA 60.427 54.545 0.00 0.00 0.00 4.51
85 86 2.258109 CCTATCCTAACTGCCCTACCC 58.742 57.143 0.00 0.00 0.00 3.69
86 87 2.898612 GACCTATCCTAACTGCCCTACC 59.101 54.545 0.00 0.00 0.00 3.18
87 88 2.898612 GGACCTATCCTAACTGCCCTAC 59.101 54.545 0.00 0.00 42.45 3.18
88 89 2.520980 TGGACCTATCCTAACTGCCCTA 59.479 50.000 0.00 0.00 46.43 3.53
89 90 1.294068 TGGACCTATCCTAACTGCCCT 59.706 52.381 0.00 0.00 46.43 5.19
90 91 1.802553 TGGACCTATCCTAACTGCCC 58.197 55.000 0.00 0.00 46.43 5.36
91 92 2.972713 TCATGGACCTATCCTAACTGCC 59.027 50.000 0.00 0.00 46.43 4.85
92 93 4.323104 GGATCATGGACCTATCCTAACTGC 60.323 50.000 11.67 0.00 46.43 4.40
93 94 5.090139 AGGATCATGGACCTATCCTAACTG 58.910 45.833 17.22 0.00 46.10 3.16
94 95 5.361630 AGGATCATGGACCTATCCTAACT 57.638 43.478 17.22 0.46 46.10 2.24
97 98 5.208294 GGTAGGATCATGGACCTATCCTA 57.792 47.826 19.08 19.08 46.10 2.94
100 101 4.067944 AGGGTAGGATCATGGACCTATC 57.932 50.000 17.22 16.59 40.27 2.08
101 102 5.213868 CTAGGGTAGGATCATGGACCTAT 57.786 47.826 17.22 8.23 40.27 2.57
102 103 4.676799 CTAGGGTAGGATCATGGACCTA 57.323 50.000 12.49 12.49 37.68 3.08
103 104 3.551635 CTAGGGTAGGATCATGGACCT 57.448 52.381 14.12 14.12 39.95 3.85
115 116 6.010850 TGATGAAGCTATGTACCTAGGGTAG 58.989 44.000 14.81 10.48 39.02 3.18
116 117 5.773680 GTGATGAAGCTATGTACCTAGGGTA 59.226 44.000 14.81 0.12 37.09 3.69
117 118 4.589374 GTGATGAAGCTATGTACCTAGGGT 59.411 45.833 14.81 1.17 40.16 4.34
118 119 4.835615 AGTGATGAAGCTATGTACCTAGGG 59.164 45.833 14.81 0.00 0.00 3.53
119 120 7.613801 AGATAGTGATGAAGCTATGTACCTAGG 59.386 40.741 7.41 7.41 0.00 3.02
120 121 8.458052 CAGATAGTGATGAAGCTATGTACCTAG 58.542 40.741 1.10 1.10 0.00 3.02
121 122 7.945109 ACAGATAGTGATGAAGCTATGTACCTA 59.055 37.037 0.00 0.00 0.00 3.08
122 123 6.780031 ACAGATAGTGATGAAGCTATGTACCT 59.220 38.462 0.00 0.00 0.00 3.08
123 124 6.987386 ACAGATAGTGATGAAGCTATGTACC 58.013 40.000 0.00 0.00 0.00 3.34
124 125 8.024285 GGTACAGATAGTGATGAAGCTATGTAC 58.976 40.741 0.00 0.00 35.30 2.90
125 126 7.945109 AGGTACAGATAGTGATGAAGCTATGTA 59.055 37.037 0.00 0.00 0.00 2.29
126 127 6.780031 AGGTACAGATAGTGATGAAGCTATGT 59.220 38.462 0.00 0.00 0.00 2.29
127 128 7.225784 AGGTACAGATAGTGATGAAGCTATG 57.774 40.000 0.00 0.00 0.00 2.23
128 129 9.540538 AATAGGTACAGATAGTGATGAAGCTAT 57.459 33.333 0.00 0.00 0.00 2.97
129 130 8.941995 AATAGGTACAGATAGTGATGAAGCTA 57.058 34.615 0.00 0.00 0.00 3.32
130 131 7.847711 AATAGGTACAGATAGTGATGAAGCT 57.152 36.000 0.00 0.00 0.00 3.74
131 132 8.364142 AGAAATAGGTACAGATAGTGATGAAGC 58.636 37.037 0.00 0.00 0.00 3.86
132 133 9.906660 GAGAAATAGGTACAGATAGTGATGAAG 57.093 37.037 0.00 0.00 0.00 3.02
133 134 8.568794 CGAGAAATAGGTACAGATAGTGATGAA 58.431 37.037 0.00 0.00 0.00 2.57
134 135 7.937394 TCGAGAAATAGGTACAGATAGTGATGA 59.063 37.037 0.00 0.00 0.00 2.92
135 136 8.018520 GTCGAGAAATAGGTACAGATAGTGATG 58.981 40.741 0.00 0.00 0.00 3.07
136 137 7.720074 TGTCGAGAAATAGGTACAGATAGTGAT 59.280 37.037 0.00 0.00 0.00 3.06
137 138 7.052248 TGTCGAGAAATAGGTACAGATAGTGA 58.948 38.462 0.00 0.00 0.00 3.41
138 139 7.260558 TGTCGAGAAATAGGTACAGATAGTG 57.739 40.000 0.00 0.00 0.00 2.74
139 140 9.221933 CTATGTCGAGAAATAGGTACAGATAGT 57.778 37.037 2.98 0.00 0.00 2.12
219 220 8.208903 GGTAAGCATTCTAGTATCTGGGTTTAA 58.791 37.037 0.00 0.00 0.00 1.52
522 525 6.655003 GGTGTTCTTCTCATGTCAGGAAATAA 59.345 38.462 0.00 0.00 0.00 1.40
573 576 7.015445 GAAATTGTCAGAATTTCCATGGCACA 61.015 38.462 6.96 0.00 40.43 4.57
749 752 6.840527 TCCATGGCAATCTAACTTATGATGA 58.159 36.000 6.96 0.00 0.00 2.92
918 922 2.101415 CAGTAGCAATCCATCAGACCGA 59.899 50.000 0.00 0.00 0.00 4.69
1080 1087 1.165270 CAAAGGAAAAGGCGACGGAT 58.835 50.000 0.00 0.00 0.00 4.18
1156 1163 1.229529 ACCCACCTCTGTTCCCGAT 60.230 57.895 0.00 0.00 0.00 4.18
1157 1164 2.203182 ACCCACCTCTGTTCCCGA 59.797 61.111 0.00 0.00 0.00 5.14
1200 1207 1.280421 GAGAGAATCAACACCCTGGCT 59.720 52.381 0.00 0.00 37.82 4.75
1437 1444 2.743636 AGTGGCGGGATTCATATACG 57.256 50.000 0.00 0.00 0.00 3.06
1450 1457 2.424705 AATGGTGCAGCAAAGTGGCG 62.425 55.000 24.18 0.00 39.27 5.69
1457 1464 0.965439 GGTTGGTAATGGTGCAGCAA 59.035 50.000 24.18 4.09 0.00 3.91
1484 1491 5.240623 TGGCGACTGAATTTGTTTTAGACAT 59.759 36.000 0.00 0.00 38.26 3.06
1553 1560 4.775236 ACCAAAGCTAGTGAGAATGATCC 58.225 43.478 0.00 0.00 0.00 3.36
1650 1657 5.927281 ACAGTAGTAACCATCAACGGTAT 57.073 39.130 0.00 0.00 38.76 2.73
1654 1661 8.804743 CATAACTAACAGTAGTAACCATCAACG 58.195 37.037 0.00 0.00 39.79 4.10
1797 1804 6.256321 GTCAATTGGCGCATGATTTTTCTTAT 59.744 34.615 10.83 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.