Multiple sequence alignment - TraesCS7B01G182900

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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 TraesCS7B01G182900 chr7B 100.000 2771 0 0 1 2771 287116022 287118792 0.000000e+00 5118
1 TraesCS7B01G182900 chr7B 95.857 2607 102 5 167 2769 286689793 286687189 0.000000e+00 4211
2 TraesCS7B01G182900 chr7B 95.101 2613 119 6 164 2771 169350407 169353015 0.000000e+00 4108
3 TraesCS7B01G182900 chr7B 94.872 2613 128 5 164 2771 56694804 56697415 0.000000e+00 4078
4 TraesCS7B01G182900 chr7B 98.315 178 1 2 1 177 91149018 91149194 7.450000e-81 311
5 TraesCS7B01G182900 chr3B 95.130 2608 120 6 167 2769 133839714 133837109 0.000000e+00 4106
6 TraesCS7B01G182900 chr3B 95.063 2613 120 5 164 2771 661296416 661299024 0.000000e+00 4102
7 TraesCS7B01G182900 chr3B 94.870 2612 126 6 167 2771 50671151 50668541 0.000000e+00 4074
8 TraesCS7B01G182900 chr1B 95.023 2612 125 4 164 2771 674404763 674407373 0.000000e+00 4098
9 TraesCS7B01G182900 chr1B 94.941 2609 121 7 167 2769 642308843 642306240 0.000000e+00 4076
10 TraesCS7B01G182900 chr1B 99.419 172 0 1 1 171 252321822 252321993 7.450000e-81 311
11 TraesCS7B01G182900 chr6B 94.866 2610 127 6 167 2771 685089527 685086920 0.000000e+00 4071
12 TraesCS7B01G182900 chr6B 98.851 174 2 0 1 174 324908019 324907846 7.450000e-81 311
13 TraesCS7B01G182900 chr3A 99.425 174 0 1 1 173 314974835 314975008 5.760000e-82 315
14 TraesCS7B01G182900 chrUn 99.419 172 1 0 1 172 348095658 348095487 2.070000e-81 313
15 TraesCS7B01G182900 chrUn 99.419 172 1 0 1 172 418868872 418868701 2.070000e-81 313
16 TraesCS7B01G182900 chr6A 99.419 172 0 1 1 171 285081912 285082083 7.450000e-81 311
17 TraesCS7B01G182900 chr1A 99.415 171 1 0 1 171 209173032 209173202 7.450000e-81 311
18 TraesCS7B01G182900 chr1A 99.415 171 1 0 1 171 233016844 233016674 7.450000e-81 311


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 TraesCS7B01G182900 chr7B 287116022 287118792 2770 False 5118 5118 100.000 1 2771 1 chr7B.!!$F4 2770
1 TraesCS7B01G182900 chr7B 286687189 286689793 2604 True 4211 4211 95.857 167 2769 1 chr7B.!!$R1 2602
2 TraesCS7B01G182900 chr7B 169350407 169353015 2608 False 4108 4108 95.101 164 2771 1 chr7B.!!$F3 2607
3 TraesCS7B01G182900 chr7B 56694804 56697415 2611 False 4078 4078 94.872 164 2771 1 chr7B.!!$F1 2607
4 TraesCS7B01G182900 chr3B 133837109 133839714 2605 True 4106 4106 95.130 167 2769 1 chr3B.!!$R2 2602
5 TraesCS7B01G182900 chr3B 661296416 661299024 2608 False 4102 4102 95.063 164 2771 1 chr3B.!!$F1 2607
6 TraesCS7B01G182900 chr3B 50668541 50671151 2610 True 4074 4074 94.870 167 2771 1 chr3B.!!$R1 2604
7 TraesCS7B01G182900 chr1B 674404763 674407373 2610 False 4098 4098 95.023 164 2771 1 chr1B.!!$F2 2607
8 TraesCS7B01G182900 chr1B 642306240 642308843 2603 True 4076 4076 94.941 167 2769 1 chr1B.!!$R1 2602
9 TraesCS7B01G182900 chr6B 685086920 685089527 2607 True 4071 4071 94.866 167 2771 1 chr6B.!!$R2 2604

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
143 144 0.035725 GTAGGGGCTGTGGGTGTAAC 60.036 60.0 0.0 0.0 0.0 2.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 1930 0.103208 AGAGCGCTCAGGTTTATCCG 59.897 55.0 36.87 0.0 41.99 4.18 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
23 24 6.736110 AAATGTATCCAATTTAGGCAGCAT 57.264 33.333 0.00 0.00 0.00 3.79
24 25 5.972107 ATGTATCCAATTTAGGCAGCATC 57.028 39.130 0.00 0.00 0.00 3.91
25 26 4.790937 TGTATCCAATTTAGGCAGCATCA 58.209 39.130 0.00 0.00 0.00 3.07
26 27 5.387788 TGTATCCAATTTAGGCAGCATCAT 58.612 37.500 0.00 0.00 0.00 2.45
27 28 6.541907 TGTATCCAATTTAGGCAGCATCATA 58.458 36.000 0.00 0.00 0.00 2.15
28 29 7.177184 TGTATCCAATTTAGGCAGCATCATAT 58.823 34.615 0.00 0.00 0.00 1.78
29 30 7.670979 TGTATCCAATTTAGGCAGCATCATATT 59.329 33.333 0.00 0.00 0.00 1.28
30 31 6.579666 TCCAATTTAGGCAGCATCATATTC 57.420 37.500 0.00 0.00 0.00 1.75
31 32 6.309357 TCCAATTTAGGCAGCATCATATTCT 58.691 36.000 0.00 0.00 0.00 2.40
32 33 6.432162 TCCAATTTAGGCAGCATCATATTCTC 59.568 38.462 0.00 0.00 0.00 2.87
33 34 6.208007 CCAATTTAGGCAGCATCATATTCTCA 59.792 38.462 0.00 0.00 0.00 3.27
34 35 7.093902 CCAATTTAGGCAGCATCATATTCTCAT 60.094 37.037 0.00 0.00 0.00 2.90
35 36 6.812879 TTTAGGCAGCATCATATTCTCATG 57.187 37.500 0.00 0.00 0.00 3.07
36 37 4.635699 AGGCAGCATCATATTCTCATGA 57.364 40.909 0.00 0.00 39.20 3.07
37 38 4.981812 AGGCAGCATCATATTCTCATGAA 58.018 39.130 0.00 0.00 38.39 2.57
38 39 4.760715 AGGCAGCATCATATTCTCATGAAC 59.239 41.667 0.00 0.00 38.39 3.18
39 40 4.517832 GGCAGCATCATATTCTCATGAACA 59.482 41.667 0.00 0.00 38.39 3.18
40 41 5.183331 GGCAGCATCATATTCTCATGAACAT 59.817 40.000 0.00 0.00 38.39 2.71
41 42 6.294564 GGCAGCATCATATTCTCATGAACATT 60.295 38.462 0.00 0.00 38.39 2.71
42 43 7.094506 GGCAGCATCATATTCTCATGAACATTA 60.095 37.037 0.00 0.00 38.39 1.90
43 44 7.963465 GCAGCATCATATTCTCATGAACATTAG 59.037 37.037 0.00 0.00 38.39 1.73
44 45 9.216117 CAGCATCATATTCTCATGAACATTAGA 57.784 33.333 0.00 0.00 38.39 2.10
45 46 9.788889 AGCATCATATTCTCATGAACATTAGAA 57.211 29.630 11.93 11.93 38.39 2.10
54 55 9.904198 TTCTCATGAACATTAGAATCATTACCA 57.096 29.630 0.00 0.00 31.65 3.25
55 56 9.904198 TCTCATGAACATTAGAATCATTACCAA 57.096 29.630 0.00 0.00 31.65 3.67
57 58 9.904198 TCATGAACATTAGAATCATTACCAAGA 57.096 29.630 0.00 0.00 31.65 3.02
61 62 9.490663 GAACATTAGAATCATTACCAAGAAACG 57.509 33.333 0.00 0.00 0.00 3.60
62 63 8.786826 ACATTAGAATCATTACCAAGAAACGA 57.213 30.769 0.00 0.00 0.00 3.85
63 64 9.226606 ACATTAGAATCATTACCAAGAAACGAA 57.773 29.630 0.00 0.00 0.00 3.85
85 86 8.403236 ACGAAAGTACCTGATAATTTAATTGGC 58.597 33.333 0.00 0.00 46.88 4.52
86 87 7.586300 CGAAAGTACCTGATAATTTAATTGGCG 59.414 37.037 0.00 0.00 31.35 5.69
87 88 7.875327 AAGTACCTGATAATTTAATTGGCGT 57.125 32.000 0.00 0.00 0.00 5.68
88 89 7.259290 AGTACCTGATAATTTAATTGGCGTG 57.741 36.000 0.00 0.00 0.00 5.34
89 90 4.932146 ACCTGATAATTTAATTGGCGTGC 58.068 39.130 0.00 0.00 0.00 5.34
90 91 3.974401 CCTGATAATTTAATTGGCGTGCG 59.026 43.478 0.00 0.00 0.00 5.34
91 92 3.367607 TGATAATTTAATTGGCGTGCGC 58.632 40.909 8.17 8.17 41.06 6.09
92 93 1.816370 TAATTTAATTGGCGTGCGCG 58.184 45.000 16.86 16.86 43.06 6.86
93 94 0.169230 AATTTAATTGGCGTGCGCGA 59.831 45.000 26.19 2.13 43.06 5.87
94 95 0.248054 ATTTAATTGGCGTGCGCGAG 60.248 50.000 26.19 0.19 43.06 5.03
108 109 2.493713 CGCGAGCTCTAGTAATTGGT 57.506 50.000 12.85 0.00 0.00 3.67
109 110 2.386249 CGCGAGCTCTAGTAATTGGTC 58.614 52.381 12.85 0.00 0.00 4.02
110 111 2.745102 GCGAGCTCTAGTAATTGGTCC 58.255 52.381 12.85 0.00 0.00 4.46
111 112 2.546162 GCGAGCTCTAGTAATTGGTCCC 60.546 54.545 12.85 0.00 0.00 4.46
112 113 2.287668 CGAGCTCTAGTAATTGGTCCCG 60.288 54.545 12.85 0.00 0.00 5.14
113 114 2.694109 GAGCTCTAGTAATTGGTCCCGT 59.306 50.000 6.43 0.00 0.00 5.28
114 115 3.887716 GAGCTCTAGTAATTGGTCCCGTA 59.112 47.826 6.43 0.00 0.00 4.02
115 116 4.481072 AGCTCTAGTAATTGGTCCCGTAT 58.519 43.478 0.00 0.00 0.00 3.06
116 117 5.638133 AGCTCTAGTAATTGGTCCCGTATA 58.362 41.667 0.00 0.00 0.00 1.47
117 118 6.254522 AGCTCTAGTAATTGGTCCCGTATAT 58.745 40.000 0.00 0.00 0.00 0.86
118 119 6.153000 AGCTCTAGTAATTGGTCCCGTATATG 59.847 42.308 0.00 0.00 0.00 1.78
119 120 6.071503 GCTCTAGTAATTGGTCCCGTATATGT 60.072 42.308 0.00 0.00 0.00 2.29
120 121 7.121759 GCTCTAGTAATTGGTCCCGTATATGTA 59.878 40.741 0.00 0.00 0.00 2.29
121 122 8.571461 TCTAGTAATTGGTCCCGTATATGTAG 57.429 38.462 0.00 0.00 0.00 2.74
122 123 6.034161 AGTAATTGGTCCCGTATATGTAGC 57.966 41.667 0.00 0.00 0.00 3.58
123 124 4.967084 AATTGGTCCCGTATATGTAGCA 57.033 40.909 0.00 0.00 0.00 3.49
124 125 4.537135 ATTGGTCCCGTATATGTAGCAG 57.463 45.455 0.00 0.00 0.00 4.24
125 126 2.953453 TGGTCCCGTATATGTAGCAGT 58.047 47.619 0.00 0.00 0.00 4.40
126 127 4.103013 TGGTCCCGTATATGTAGCAGTA 57.897 45.455 0.00 0.00 0.00 2.74
127 128 4.077108 TGGTCCCGTATATGTAGCAGTAG 58.923 47.826 0.00 0.00 0.00 2.57
128 129 3.442977 GGTCCCGTATATGTAGCAGTAGG 59.557 52.174 0.00 0.00 0.00 3.18
129 130 3.442977 GTCCCGTATATGTAGCAGTAGGG 59.557 52.174 0.00 0.00 37.72 3.53
130 131 2.758979 CCCGTATATGTAGCAGTAGGGG 59.241 54.545 0.00 0.00 36.32 4.79
131 132 2.165845 CCGTATATGTAGCAGTAGGGGC 59.834 54.545 0.00 0.00 0.00 5.80
132 133 3.090037 CGTATATGTAGCAGTAGGGGCT 58.910 50.000 0.00 0.00 45.18 5.19
133 134 3.119459 CGTATATGTAGCAGTAGGGGCTG 60.119 52.174 0.00 0.00 42.62 4.85
134 135 2.471815 TATGTAGCAGTAGGGGCTGT 57.528 50.000 0.00 0.00 42.62 4.40
135 136 0.833287 ATGTAGCAGTAGGGGCTGTG 59.167 55.000 0.00 0.00 42.62 3.66
136 137 1.264749 TGTAGCAGTAGGGGCTGTGG 61.265 60.000 0.00 0.00 42.62 4.17
137 138 1.689233 TAGCAGTAGGGGCTGTGGG 60.689 63.158 0.00 0.00 42.62 4.61
138 139 2.471084 TAGCAGTAGGGGCTGTGGGT 62.471 60.000 0.00 0.00 42.62 4.51
139 140 2.671070 CAGTAGGGGCTGTGGGTG 59.329 66.667 0.00 0.00 0.00 4.61
140 141 2.207189 AGTAGGGGCTGTGGGTGT 59.793 61.111 0.00 0.00 0.00 4.16
141 142 0.907704 CAGTAGGGGCTGTGGGTGTA 60.908 60.000 0.00 0.00 0.00 2.90
142 143 0.178885 AGTAGGGGCTGTGGGTGTAA 60.179 55.000 0.00 0.00 0.00 2.41
143 144 0.035725 GTAGGGGCTGTGGGTGTAAC 60.036 60.000 0.00 0.00 0.00 2.50
144 145 0.474079 TAGGGGCTGTGGGTGTAACA 60.474 55.000 0.00 0.00 39.98 2.41
145 146 1.151908 GGGGCTGTGGGTGTAACAA 59.848 57.895 0.00 0.00 39.98 2.83
146 147 0.251608 GGGGCTGTGGGTGTAACAAT 60.252 55.000 0.00 0.00 39.98 2.71
147 148 0.887933 GGGCTGTGGGTGTAACAATG 59.112 55.000 0.00 0.00 39.98 2.82
148 149 0.887933 GGCTGTGGGTGTAACAATGG 59.112 55.000 0.00 0.00 39.98 3.16
149 150 1.616159 GCTGTGGGTGTAACAATGGT 58.384 50.000 0.00 0.00 39.98 3.55
150 151 2.553466 GGCTGTGGGTGTAACAATGGTA 60.553 50.000 0.00 0.00 39.98 3.25
151 152 3.352648 GCTGTGGGTGTAACAATGGTAT 58.647 45.455 0.00 0.00 39.98 2.73
152 153 3.761752 GCTGTGGGTGTAACAATGGTATT 59.238 43.478 0.00 0.00 39.98 1.89
153 154 4.380444 GCTGTGGGTGTAACAATGGTATTG 60.380 45.833 0.28 0.28 39.98 1.90
154 155 4.986783 TGTGGGTGTAACAATGGTATTGA 58.013 39.130 8.41 0.00 39.98 2.57
155 156 5.575157 TGTGGGTGTAACAATGGTATTGAT 58.425 37.500 8.41 0.00 39.98 2.57
156 157 5.417266 TGTGGGTGTAACAATGGTATTGATG 59.583 40.000 8.41 0.00 39.98 3.07
157 158 5.417580 GTGGGTGTAACAATGGTATTGATGT 59.582 40.000 8.41 0.00 39.98 3.06
158 159 5.650266 TGGGTGTAACAATGGTATTGATGTC 59.350 40.000 8.41 0.00 39.98 3.06
159 160 5.067283 GGGTGTAACAATGGTATTGATGTCC 59.933 44.000 8.41 4.55 39.98 4.02
160 161 5.885912 GGTGTAACAATGGTATTGATGTCCT 59.114 40.000 8.41 0.00 39.98 3.85
161 162 6.038271 GGTGTAACAATGGTATTGATGTCCTC 59.962 42.308 8.41 0.00 39.98 3.71
162 163 6.597672 GTGTAACAATGGTATTGATGTCCTCA 59.402 38.462 8.41 0.00 36.32 3.86
309 310 2.363147 GGCGACCTCCAGGACTCT 60.363 66.667 0.00 0.00 38.94 3.24
436 437 2.180276 AGAAAGGCACTCCTATGACGT 58.820 47.619 0.00 0.00 43.40 4.34
440 441 1.664321 GGCACTCCTATGACGTCGGT 61.664 60.000 11.62 4.73 0.00 4.69
769 771 1.375098 GCGCTACTGACCTCTACCGT 61.375 60.000 0.00 0.00 0.00 4.83
786 788 1.583495 CGTACTGACTGCGGAGGTCA 61.583 60.000 9.36 8.79 40.78 4.02
1207 1209 2.083774 AGGCGATGAAAAAGATTGCGA 58.916 42.857 0.00 0.00 31.75 5.10
1282 1284 2.160721 TACCCGAATCTGGAGCTCTT 57.839 50.000 14.64 0.00 0.00 2.85
1399 1401 1.685765 TATGCTGAGGCCGGACACT 60.686 57.895 11.69 0.55 37.74 3.55
1520 1522 3.815401 GTCTTGCCTTTGAGCTACTTTGA 59.185 43.478 0.00 0.00 0.00 2.69
1582 1584 3.436704 AGTTATCAAGCATTCCGTGTGTG 59.563 43.478 0.00 0.00 0.00 3.82
1888 1891 5.156608 TGAAATCTGAGAGATGCAAGTCA 57.843 39.130 0.00 0.00 34.65 3.41
1909 1912 2.203209 GCTTCTACCCCCATGCCG 60.203 66.667 0.00 0.00 0.00 5.69
1927 1930 2.358737 CGAGTGCTGGGGTGTTCC 60.359 66.667 0.00 0.00 0.00 3.62
1994 1998 2.168621 CGCTCAGCACAACGAACG 59.831 61.111 0.00 0.00 0.00 3.95
2166 2171 3.492829 GGCATAAGTCTTTAGGGACTCGG 60.493 52.174 0.00 0.00 44.67 4.63
2271 2277 0.464373 CTGGGGCACAATCGCAGTAT 60.464 55.000 0.00 0.00 39.41 2.12
2279 2286 2.752354 CACAATCGCAGTATTTCCCCAA 59.248 45.455 0.00 0.00 0.00 4.12
2515 2525 7.899178 TGTCACGACTGAACATATTTGTATT 57.101 32.000 0.00 0.00 34.06 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.972107 ATGATGCTGCCTAAATTGGATAC 57.028 39.130 0.00 0.00 0.00 2.24
5 6 8.111545 AGAATATGATGCTGCCTAAATTGGATA 58.888 33.333 0.00 0.00 0.00 2.59
6 7 6.952358 AGAATATGATGCTGCCTAAATTGGAT 59.048 34.615 0.00 0.00 0.00 3.41
7 8 6.309357 AGAATATGATGCTGCCTAAATTGGA 58.691 36.000 0.00 0.00 0.00 3.53
8 9 6.208007 TGAGAATATGATGCTGCCTAAATTGG 59.792 38.462 0.00 0.00 0.00 3.16
9 10 7.210718 TGAGAATATGATGCTGCCTAAATTG 57.789 36.000 0.00 0.00 0.00 2.32
10 11 7.668469 TCATGAGAATATGATGCTGCCTAAATT 59.332 33.333 0.00 0.00 32.39 1.82
11 12 7.173032 TCATGAGAATATGATGCTGCCTAAAT 58.827 34.615 0.00 0.00 32.39 1.40
12 13 6.536447 TCATGAGAATATGATGCTGCCTAAA 58.464 36.000 0.00 0.00 32.39 1.85
13 14 6.117975 TCATGAGAATATGATGCTGCCTAA 57.882 37.500 0.00 0.00 32.39 2.69
14 15 5.750352 TCATGAGAATATGATGCTGCCTA 57.250 39.130 0.00 0.00 32.39 3.93
15 16 4.635699 TCATGAGAATATGATGCTGCCT 57.364 40.909 0.00 0.00 32.39 4.75
16 17 4.517832 TGTTCATGAGAATATGATGCTGCC 59.482 41.667 0.00 0.00 36.97 4.85
17 18 5.684550 TGTTCATGAGAATATGATGCTGC 57.315 39.130 0.00 0.00 36.97 5.25
18 19 9.216117 TCTAATGTTCATGAGAATATGATGCTG 57.784 33.333 0.00 0.00 35.97 4.41
19 20 9.788889 TTCTAATGTTCATGAGAATATGATGCT 57.211 29.630 8.14 0.00 35.97 3.79
28 29 9.904198 TGGTAATGATTCTAATGTTCATGAGAA 57.096 29.630 13.11 13.11 30.76 2.87
29 30 9.904198 TTGGTAATGATTCTAATGTTCATGAGA 57.096 29.630 0.00 0.00 30.76 3.27
31 32 9.904198 TCTTGGTAATGATTCTAATGTTCATGA 57.096 29.630 0.00 0.00 30.76 3.07
35 36 9.490663 CGTTTCTTGGTAATGATTCTAATGTTC 57.509 33.333 0.00 0.00 0.00 3.18
36 37 9.226606 TCGTTTCTTGGTAATGATTCTAATGTT 57.773 29.630 0.00 0.00 0.00 2.71
37 38 8.786826 TCGTTTCTTGGTAATGATTCTAATGT 57.213 30.769 0.00 0.00 0.00 2.71
40 41 9.280174 ACTTTCGTTTCTTGGTAATGATTCTAA 57.720 29.630 0.00 0.00 0.00 2.10
41 42 8.842358 ACTTTCGTTTCTTGGTAATGATTCTA 57.158 30.769 0.00 0.00 0.00 2.10
42 43 7.745620 ACTTTCGTTTCTTGGTAATGATTCT 57.254 32.000 0.00 0.00 0.00 2.40
43 44 7.961283 GGTACTTTCGTTTCTTGGTAATGATTC 59.039 37.037 0.00 0.00 0.00 2.52
44 45 7.664318 AGGTACTTTCGTTTCTTGGTAATGATT 59.336 33.333 0.00 0.00 27.25 2.57
45 46 7.119262 CAGGTACTTTCGTTTCTTGGTAATGAT 59.881 37.037 0.00 0.00 34.60 2.45
46 47 6.425721 CAGGTACTTTCGTTTCTTGGTAATGA 59.574 38.462 0.00 0.00 34.60 2.57
47 48 6.425721 TCAGGTACTTTCGTTTCTTGGTAATG 59.574 38.462 0.00 0.00 34.60 1.90
48 49 6.527423 TCAGGTACTTTCGTTTCTTGGTAAT 58.473 36.000 0.00 0.00 34.60 1.89
49 50 5.916318 TCAGGTACTTTCGTTTCTTGGTAA 58.084 37.500 0.00 0.00 34.60 2.85
50 51 5.534207 TCAGGTACTTTCGTTTCTTGGTA 57.466 39.130 0.00 0.00 34.60 3.25
51 52 4.411256 TCAGGTACTTTCGTTTCTTGGT 57.589 40.909 0.00 0.00 34.60 3.67
52 53 7.611213 ATTATCAGGTACTTTCGTTTCTTGG 57.389 36.000 0.00 0.00 34.60 3.61
59 60 8.403236 GCCAATTAAATTATCAGGTACTTTCGT 58.597 33.333 0.00 0.00 34.60 3.85
60 61 7.586300 CGCCAATTAAATTATCAGGTACTTTCG 59.414 37.037 0.00 0.00 34.60 3.46
61 62 8.403236 ACGCCAATTAAATTATCAGGTACTTTC 58.597 33.333 0.00 0.00 34.60 2.62
62 63 8.188139 CACGCCAATTAAATTATCAGGTACTTT 58.812 33.333 0.00 0.00 34.60 2.66
63 64 7.681065 GCACGCCAATTAAATTATCAGGTACTT 60.681 37.037 0.00 0.00 34.60 2.24
64 65 6.238648 GCACGCCAATTAAATTATCAGGTACT 60.239 38.462 0.00 0.00 43.88 2.73
65 66 5.912955 GCACGCCAATTAAATTATCAGGTAC 59.087 40.000 0.00 0.00 0.00 3.34
66 67 5.277586 CGCACGCCAATTAAATTATCAGGTA 60.278 40.000 0.00 0.00 0.00 3.08
67 68 4.497340 CGCACGCCAATTAAATTATCAGGT 60.497 41.667 0.00 0.00 0.00 4.00
68 69 3.974401 CGCACGCCAATTAAATTATCAGG 59.026 43.478 0.00 0.00 0.00 3.86
69 70 3.421888 GCGCACGCCAATTAAATTATCAG 59.578 43.478 0.30 0.00 34.56 2.90
70 71 3.367607 GCGCACGCCAATTAAATTATCA 58.632 40.909 0.30 0.00 34.56 2.15
71 72 2.400408 CGCGCACGCCAATTAAATTATC 59.600 45.455 8.75 0.00 37.98 1.75
72 73 2.032302 TCGCGCACGCCAATTAAATTAT 59.968 40.909 8.75 0.00 39.84 1.28
73 74 1.397343 TCGCGCACGCCAATTAAATTA 59.603 42.857 8.75 0.00 39.84 1.40
74 75 0.169230 TCGCGCACGCCAATTAAATT 59.831 45.000 8.75 0.00 39.84 1.82
75 76 0.248054 CTCGCGCACGCCAATTAAAT 60.248 50.000 8.75 0.00 39.84 1.40
76 77 1.133664 CTCGCGCACGCCAATTAAA 59.866 52.632 8.75 0.00 39.84 1.52
77 78 2.781957 CTCGCGCACGCCAATTAA 59.218 55.556 8.75 0.00 39.84 1.40
78 79 3.860125 GCTCGCGCACGCCAATTA 61.860 61.111 8.75 0.00 39.84 1.40
84 85 2.914797 TTACTAGAGCTCGCGCACGC 62.915 60.000 8.75 9.28 39.84 5.34
85 86 0.317103 ATTACTAGAGCTCGCGCACG 60.317 55.000 8.75 0.00 39.10 5.34
86 87 1.518929 CAATTACTAGAGCTCGCGCAC 59.481 52.381 8.75 0.00 39.10 5.34
87 88 1.536072 CCAATTACTAGAGCTCGCGCA 60.536 52.381 8.75 0.00 39.10 6.09
88 89 1.132588 CCAATTACTAGAGCTCGCGC 58.867 55.000 8.37 0.00 0.00 6.86
89 90 2.386249 GACCAATTACTAGAGCTCGCG 58.614 52.381 8.37 0.00 0.00 5.87
90 91 2.546162 GGGACCAATTACTAGAGCTCGC 60.546 54.545 8.37 0.00 0.00 5.03
91 92 2.287668 CGGGACCAATTACTAGAGCTCG 60.288 54.545 8.37 0.00 0.00 5.03
92 93 2.694109 ACGGGACCAATTACTAGAGCTC 59.306 50.000 5.27 5.27 0.00 4.09
93 94 2.748388 ACGGGACCAATTACTAGAGCT 58.252 47.619 0.00 0.00 0.00 4.09
94 95 4.868314 ATACGGGACCAATTACTAGAGC 57.132 45.455 0.00 0.00 0.00 4.09
95 96 7.463961 ACATATACGGGACCAATTACTAGAG 57.536 40.000 0.00 0.00 0.00 2.43
96 97 7.121759 GCTACATATACGGGACCAATTACTAGA 59.878 40.741 0.00 0.00 0.00 2.43
97 98 7.094075 TGCTACATATACGGGACCAATTACTAG 60.094 40.741 0.00 0.00 0.00 2.57
98 99 6.720748 TGCTACATATACGGGACCAATTACTA 59.279 38.462 0.00 0.00 0.00 1.82
99 100 5.541101 TGCTACATATACGGGACCAATTACT 59.459 40.000 0.00 0.00 0.00 2.24
100 101 5.786311 TGCTACATATACGGGACCAATTAC 58.214 41.667 0.00 0.00 0.00 1.89
101 102 5.541101 ACTGCTACATATACGGGACCAATTA 59.459 40.000 0.00 0.00 0.00 1.40
102 103 4.347000 ACTGCTACATATACGGGACCAATT 59.653 41.667 0.00 0.00 0.00 2.32
103 104 3.901844 ACTGCTACATATACGGGACCAAT 59.098 43.478 0.00 0.00 0.00 3.16
104 105 3.302161 ACTGCTACATATACGGGACCAA 58.698 45.455 0.00 0.00 0.00 3.67
105 106 2.953453 ACTGCTACATATACGGGACCA 58.047 47.619 0.00 0.00 0.00 4.02
106 107 3.442977 CCTACTGCTACATATACGGGACC 59.557 52.174 0.00 0.00 0.00 4.46
107 108 3.442977 CCCTACTGCTACATATACGGGAC 59.557 52.174 0.00 0.00 0.00 4.46
108 109 3.562826 CCCCTACTGCTACATATACGGGA 60.563 52.174 0.00 0.00 0.00 5.14
109 110 2.758979 CCCCTACTGCTACATATACGGG 59.241 54.545 0.00 0.00 0.00 5.28
110 111 2.165845 GCCCCTACTGCTACATATACGG 59.834 54.545 0.00 0.00 0.00 4.02
111 112 3.090037 AGCCCCTACTGCTACATATACG 58.910 50.000 0.00 0.00 37.28 3.06
112 113 3.833070 ACAGCCCCTACTGCTACATATAC 59.167 47.826 0.00 0.00 41.60 1.47
113 114 3.832490 CACAGCCCCTACTGCTACATATA 59.168 47.826 0.00 0.00 41.60 0.86
114 115 2.634940 CACAGCCCCTACTGCTACATAT 59.365 50.000 0.00 0.00 41.60 1.78
115 116 2.039418 CACAGCCCCTACTGCTACATA 58.961 52.381 0.00 0.00 41.60 2.29
116 117 0.833287 CACAGCCCCTACTGCTACAT 59.167 55.000 0.00 0.00 41.60 2.29
117 118 1.264749 CCACAGCCCCTACTGCTACA 61.265 60.000 0.00 0.00 41.60 2.74
118 119 1.522569 CCACAGCCCCTACTGCTAC 59.477 63.158 0.00 0.00 41.60 3.58
119 120 1.689233 CCCACAGCCCCTACTGCTA 60.689 63.158 0.00 0.00 41.60 3.49
120 121 3.011517 CCCACAGCCCCTACTGCT 61.012 66.667 0.00 0.00 41.60 4.24
121 122 3.330720 ACCCACAGCCCCTACTGC 61.331 66.667 0.00 0.00 41.60 4.40
122 123 0.907704 TACACCCACAGCCCCTACTG 60.908 60.000 0.00 0.00 43.59 2.74
123 124 0.178885 TTACACCCACAGCCCCTACT 60.179 55.000 0.00 0.00 0.00 2.57
124 125 0.035725 GTTACACCCACAGCCCCTAC 60.036 60.000 0.00 0.00 0.00 3.18
125 126 0.474079 TGTTACACCCACAGCCCCTA 60.474 55.000 0.00 0.00 0.00 3.53
126 127 1.357272 TTGTTACACCCACAGCCCCT 61.357 55.000 0.00 0.00 0.00 4.79
127 128 0.251608 ATTGTTACACCCACAGCCCC 60.252 55.000 0.00 0.00 0.00 5.80
128 129 0.887933 CATTGTTACACCCACAGCCC 59.112 55.000 0.00 0.00 0.00 5.19
129 130 0.887933 CCATTGTTACACCCACAGCC 59.112 55.000 0.00 0.00 0.00 4.85
130 131 1.616159 ACCATTGTTACACCCACAGC 58.384 50.000 0.00 0.00 0.00 4.40
131 132 5.007034 TCAATACCATTGTTACACCCACAG 58.993 41.667 0.00 0.00 0.00 3.66
132 133 4.986783 TCAATACCATTGTTACACCCACA 58.013 39.130 0.00 0.00 0.00 4.17
133 134 5.417580 ACATCAATACCATTGTTACACCCAC 59.582 40.000 0.00 0.00 0.00 4.61
134 135 5.575157 ACATCAATACCATTGTTACACCCA 58.425 37.500 0.00 0.00 0.00 4.51
135 136 5.067283 GGACATCAATACCATTGTTACACCC 59.933 44.000 0.00 0.00 0.00 4.61
136 137 5.885912 AGGACATCAATACCATTGTTACACC 59.114 40.000 0.00 0.00 0.00 4.16
137 138 6.597672 TGAGGACATCAATACCATTGTTACAC 59.402 38.462 0.00 0.00 34.02 2.90
138 139 6.716284 TGAGGACATCAATACCATTGTTACA 58.284 36.000 0.00 0.00 34.02 2.41
139 140 7.807977 ATGAGGACATCAATACCATTGTTAC 57.192 36.000 0.00 0.00 42.53 2.50
154 155 2.768527 ACGAATCCAGTGATGAGGACAT 59.231 45.455 0.00 0.00 36.60 3.06
155 156 2.166459 GACGAATCCAGTGATGAGGACA 59.834 50.000 0.00 0.00 36.60 4.02
156 157 2.796383 CGACGAATCCAGTGATGAGGAC 60.796 54.545 0.00 0.00 36.60 3.85
157 158 1.405463 CGACGAATCCAGTGATGAGGA 59.595 52.381 0.00 0.00 38.50 3.71
158 159 1.536922 CCGACGAATCCAGTGATGAGG 60.537 57.143 0.00 0.00 0.00 3.86
159 160 1.405463 TCCGACGAATCCAGTGATGAG 59.595 52.381 0.00 0.00 0.00 2.90
160 161 1.134367 GTCCGACGAATCCAGTGATGA 59.866 52.381 0.00 0.00 0.00 2.92
161 162 1.560923 GTCCGACGAATCCAGTGATG 58.439 55.000 0.00 0.00 0.00 3.07
162 163 0.100682 CGTCCGACGAATCCAGTGAT 59.899 55.000 16.03 0.00 46.05 3.06
165 166 1.211969 CACGTCCGACGAATCCAGT 59.788 57.895 27.03 0.00 46.05 4.00
302 303 0.621862 CCCTTTGGGCCTAGAGTCCT 60.622 60.000 4.53 0.00 35.35 3.85
426 427 2.420568 GGCCACCGACGTCATAGGA 61.421 63.158 17.16 0.00 0.00 2.94
628 630 2.299297 GGGCTACTGTCTATGCGGTAAT 59.701 50.000 0.00 0.00 30.72 1.89
681 683 7.841282 ATATCTTTTTAGATCCTCAGTCCGA 57.159 36.000 0.00 0.00 0.00 4.55
769 771 0.601558 GTTGACCTCCGCAGTCAGTA 59.398 55.000 0.00 0.00 44.60 2.74
786 788 1.537202 GAGGTTCTGCTTCAATGCGTT 59.463 47.619 0.00 0.00 35.36 4.84
1282 1284 3.103447 CAGATCTGCGAATGCTCCTAA 57.897 47.619 10.38 0.00 43.34 2.69
1481 1483 3.644606 CCTCACCAGGCCACAGCT 61.645 66.667 5.01 0.00 39.73 4.24
1642 1644 1.681166 CCCATCCTTCACCAGCTTCTG 60.681 57.143 0.00 0.00 0.00 3.02
1888 1891 2.056906 GCATGGGGGTAGAAGCCGAT 62.057 60.000 0.00 0.00 36.39 4.18
1909 1912 3.050275 GAACACCCCAGCACTCGC 61.050 66.667 0.00 0.00 38.99 5.03
1927 1930 0.103208 AGAGCGCTCAGGTTTATCCG 59.897 55.000 36.87 0.00 41.99 4.18
1994 1998 3.003480 GCATTATAAGTCCGATGGCCTC 58.997 50.000 3.32 0.00 0.00 4.70
2064 2068 3.134262 GTCTTCCGAATACTAGGGGCTTT 59.866 47.826 0.00 0.00 0.00 3.51
2271 2277 1.339342 GCTAAGGTAGCGTTGGGGAAA 60.339 52.381 0.00 0.00 42.62 3.13
2306 2313 4.278310 GCTCCCATGTTTTGGTACCTTAT 58.722 43.478 14.36 0.00 44.83 1.73


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

AutoCloner maintained by Alex Coulton.