Multiple sequence alignment - TraesCS2B01G264700

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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 TraesCS2B01G264700 chr2B 100.000 2192 0 0 1 2192 357307679 357309870 0 4048
1 TraesCS2B01G264700 chr2B 96.841 1298 41 0 191 1488 234540969 234539672 0 2170
2 TraesCS2B01G264700 chr3B 96.923 1300 37 2 191 1488 92296543 92295245 0 2176
3 TraesCS2B01G264700 chr3B 96.764 1298 41 1 191 1488 6010575 6009279 0 2163
4 TraesCS2B01G264700 chr6A 96.918 1298 37 1 191 1488 597252802 597251508 0 2172
5 TraesCS2B01G264700 chr6A 98.442 706 10 1 1488 2192 289145315 289144610 0 1242
6 TraesCS2B01G264700 chr3A 96.841 1298 41 0 191 1488 495104569 495103272 0 2170
7 TraesCS2B01G264700 chr1A 96.772 1301 41 1 188 1488 278521382 278522681 0 2169
8 TraesCS2B01G264700 chrUn 96.695 1301 42 1 188 1488 217907856 217909155 0 2163
9 TraesCS2B01G264700 chrUn 98.584 706 9 1 1488 2192 45124282 45123577 0 1247
10 TraesCS2B01G264700 chrUn 98.442 706 9 2 1488 2192 186177988 186178692 0 1242
11 TraesCS2B01G264700 chrUn 98.442 706 10 1 1488 2192 258926553 258925848 0 1242
12 TraesCS2B01G264700 chr1B 96.610 1298 44 0 191 1488 619195140 619193843 0 2154
13 TraesCS2B01G264700 chr7A 96.533 1298 45 0 191 1488 563521907 563520610 0 2148
14 TraesCS2B01G264700 chr2A 98.725 706 8 1 1488 2192 755489915 755489210 0 1253
15 TraesCS2B01G264700 chr2A 98.442 706 9 2 1488 2192 714308046 714308750 0 1242
16 TraesCS2B01G264700 chr2D 98.584 706 9 1 1488 2192 635053410 635052705 0 1247
17 TraesCS2B01G264700 chr1D 98.584 706 9 1 1488 2192 493808027 493808732 0 1247
18 TraesCS2B01G264700 chr7D 98.442 706 10 1 1488 2192 626664401 626665106 0 1242


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 TraesCS2B01G264700 chr2B 357307679 357309870 2191 False 4048 4048 100.000 1 2192 1 chr2B.!!$F1 2191
1 TraesCS2B01G264700 chr2B 234539672 234540969 1297 True 2170 2170 96.841 191 1488 1 chr2B.!!$R1 1297
2 TraesCS2B01G264700 chr3B 92295245 92296543 1298 True 2176 2176 96.923 191 1488 1 chr3B.!!$R2 1297
3 TraesCS2B01G264700 chr3B 6009279 6010575 1296 True 2163 2163 96.764 191 1488 1 chr3B.!!$R1 1297
4 TraesCS2B01G264700 chr6A 597251508 597252802 1294 True 2172 2172 96.918 191 1488 1 chr6A.!!$R2 1297
5 TraesCS2B01G264700 chr6A 289144610 289145315 705 True 1242 1242 98.442 1488 2192 1 chr6A.!!$R1 704
6 TraesCS2B01G264700 chr3A 495103272 495104569 1297 True 2170 2170 96.841 191 1488 1 chr3A.!!$R1 1297
7 TraesCS2B01G264700 chr1A 278521382 278522681 1299 False 2169 2169 96.772 188 1488 1 chr1A.!!$F1 1300
8 TraesCS2B01G264700 chrUn 217907856 217909155 1299 False 2163 2163 96.695 188 1488 1 chrUn.!!$F2 1300
9 TraesCS2B01G264700 chrUn 45123577 45124282 705 True 1247 1247 98.584 1488 2192 1 chrUn.!!$R1 704
10 TraesCS2B01G264700 chrUn 186177988 186178692 704 False 1242 1242 98.442 1488 2192 1 chrUn.!!$F1 704
11 TraesCS2B01G264700 chrUn 258925848 258926553 705 True 1242 1242 98.442 1488 2192 1 chrUn.!!$R2 704
12 TraesCS2B01G264700 chr1B 619193843 619195140 1297 True 2154 2154 96.610 191 1488 1 chr1B.!!$R1 1297
13 TraesCS2B01G264700 chr7A 563520610 563521907 1297 True 2148 2148 96.533 191 1488 1 chr7A.!!$R1 1297
14 TraesCS2B01G264700 chr2A 755489210 755489915 705 True 1253 1253 98.725 1488 2192 1 chr2A.!!$R1 704
15 TraesCS2B01G264700 chr2A 714308046 714308750 704 False 1242 1242 98.442 1488 2192 1 chr2A.!!$F1 704
16 TraesCS2B01G264700 chr2D 635052705 635053410 705 True 1247 1247 98.584 1488 2192 1 chr2D.!!$R1 704
17 TraesCS2B01G264700 chr1D 493808027 493808732 705 False 1247 1247 98.584 1488 2192 1 chr1D.!!$F1 704
18 TraesCS2B01G264700 chr7D 626664401 626665106 705 False 1242 1242 98.442 1488 2192 1 chr7D.!!$F1 704

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
821 822 0.534203 TCAAAAAGCGAAGGCCGAGT 60.534 50.0 0.0 0.0 41.76 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 1808 0.327924 TCAATCAACCCATCGCACCT 59.672 50.0 0.0 0.0 0.0 4.0 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
55 56 8.446599 AAGTACAACCTATTATGTAATGCCAC 57.553 34.615 0.00 0.00 34.08 5.01
56 57 7.570132 AGTACAACCTATTATGTAATGCCACA 58.430 34.615 0.00 0.00 34.08 4.17
57 58 8.217799 AGTACAACCTATTATGTAATGCCACAT 58.782 33.333 0.00 1.89 41.88 3.21
58 59 9.496873 GTACAACCTATTATGTAATGCCACATA 57.503 33.333 0.00 0.22 39.77 2.29
68 69 5.645624 TGTAATGCCACATAAAATTCACCG 58.354 37.500 0.00 0.00 0.00 4.94
69 70 4.799564 AATGCCACATAAAATTCACCGT 57.200 36.364 0.00 0.00 0.00 4.83
70 71 4.799564 ATGCCACATAAAATTCACCGTT 57.200 36.364 0.00 0.00 0.00 4.44
71 72 3.906998 TGCCACATAAAATTCACCGTTG 58.093 40.909 0.00 0.00 0.00 4.10
72 73 3.570125 TGCCACATAAAATTCACCGTTGA 59.430 39.130 0.00 0.00 0.00 3.18
73 74 4.165779 GCCACATAAAATTCACCGTTGAG 58.834 43.478 0.00 0.00 31.71 3.02
74 75 4.320935 GCCACATAAAATTCACCGTTGAGT 60.321 41.667 0.00 0.00 31.71 3.41
75 76 5.768317 CCACATAAAATTCACCGTTGAGTT 58.232 37.500 0.00 0.00 33.29 3.01
76 77 5.629020 CCACATAAAATTCACCGTTGAGTTG 59.371 40.000 0.00 0.00 32.32 3.16
77 78 6.434596 CACATAAAATTCACCGTTGAGTTGA 58.565 36.000 0.00 0.00 32.32 3.18
78 79 6.359617 CACATAAAATTCACCGTTGAGTTGAC 59.640 38.462 0.00 0.00 32.32 3.18
79 80 4.974368 AAAATTCACCGTTGAGTTGACA 57.026 36.364 0.00 0.00 32.32 3.58
80 81 3.963383 AATTCACCGTTGAGTTGACAC 57.037 42.857 0.00 0.00 30.85 3.67
81 82 2.388310 TTCACCGTTGAGTTGACACA 57.612 45.000 0.00 0.00 31.71 3.72
82 83 1.647346 TCACCGTTGAGTTGACACAC 58.353 50.000 0.00 0.00 0.00 3.82
83 84 1.066787 TCACCGTTGAGTTGACACACA 60.067 47.619 0.00 0.00 0.00 3.72
84 85 1.939934 CACCGTTGAGTTGACACACAT 59.060 47.619 0.00 0.00 0.00 3.21
85 86 2.354510 CACCGTTGAGTTGACACACATT 59.645 45.455 0.00 0.00 0.00 2.71
86 87 3.558006 CACCGTTGAGTTGACACACATTA 59.442 43.478 0.00 0.00 0.00 1.90
87 88 3.558418 ACCGTTGAGTTGACACACATTAC 59.442 43.478 0.00 0.00 0.00 1.89
88 89 3.558006 CCGTTGAGTTGACACACATTACA 59.442 43.478 0.00 0.00 0.00 2.41
89 90 4.318760 CCGTTGAGTTGACACACATTACAG 60.319 45.833 0.00 0.00 0.00 2.74
90 91 4.270084 CGTTGAGTTGACACACATTACAGT 59.730 41.667 0.00 0.00 0.00 3.55
91 92 5.460748 CGTTGAGTTGACACACATTACAGTA 59.539 40.000 0.00 0.00 0.00 2.74
92 93 6.019398 CGTTGAGTTGACACACATTACAGTAA 60.019 38.462 0.00 0.00 0.00 2.24
93 94 7.345192 GTTGAGTTGACACACATTACAGTAAG 58.655 38.462 0.00 0.00 0.00 2.34
94 95 6.811954 TGAGTTGACACACATTACAGTAAGA 58.188 36.000 0.00 0.00 0.00 2.10
95 96 7.441836 TGAGTTGACACACATTACAGTAAGAT 58.558 34.615 0.00 0.00 0.00 2.40
96 97 8.581578 TGAGTTGACACACATTACAGTAAGATA 58.418 33.333 0.00 0.00 0.00 1.98
97 98 8.988064 AGTTGACACACATTACAGTAAGATAG 57.012 34.615 0.00 0.00 0.00 2.08
98 99 8.035394 AGTTGACACACATTACAGTAAGATAGG 58.965 37.037 0.00 0.00 0.00 2.57
99 100 7.712204 TGACACACATTACAGTAAGATAGGA 57.288 36.000 0.00 0.00 0.00 2.94
100 101 8.306313 TGACACACATTACAGTAAGATAGGAT 57.694 34.615 0.00 0.00 0.00 3.24
101 102 9.416284 TGACACACATTACAGTAAGATAGGATA 57.584 33.333 0.00 0.00 0.00 2.59
112 113 9.139734 ACAGTAAGATAGGATATAAAACCGACA 57.860 33.333 0.00 0.00 0.00 4.35
113 114 9.627395 CAGTAAGATAGGATATAAAACCGACAG 57.373 37.037 0.00 0.00 0.00 3.51
114 115 9.584008 AGTAAGATAGGATATAAAACCGACAGA 57.416 33.333 0.00 0.00 0.00 3.41
117 118 8.480133 AGATAGGATATAAAACCGACAGAACT 57.520 34.615 0.00 0.00 0.00 3.01
118 119 8.361139 AGATAGGATATAAAACCGACAGAACTG 58.639 37.037 0.00 0.00 0.00 3.16
120 121 7.414222 AGGATATAAAACCGACAGAACTGTA 57.586 36.000 7.46 0.00 45.05 2.74
121 122 8.019656 AGGATATAAAACCGACAGAACTGTAT 57.980 34.615 7.46 0.00 45.05 2.29
122 123 8.483758 AGGATATAAAACCGACAGAACTGTATT 58.516 33.333 7.46 0.96 45.05 1.89
123 124 9.754382 GGATATAAAACCGACAGAACTGTATTA 57.246 33.333 7.46 4.06 45.05 0.98
126 127 8.836268 ATAAAACCGACAGAACTGTATTACAA 57.164 30.769 7.46 0.00 45.05 2.41
127 128 7.739498 AAAACCGACAGAACTGTATTACAAT 57.261 32.000 7.46 0.00 45.05 2.71
128 129 6.721571 AACCGACAGAACTGTATTACAATG 57.278 37.500 7.46 0.00 45.05 2.82
129 130 6.032956 ACCGACAGAACTGTATTACAATGA 57.967 37.500 7.46 0.00 45.05 2.57
130 131 5.867716 ACCGACAGAACTGTATTACAATGAC 59.132 40.000 7.46 0.00 45.05 3.06
131 132 6.100004 CCGACAGAACTGTATTACAATGACT 58.900 40.000 7.46 0.00 45.05 3.41
132 133 7.094075 ACCGACAGAACTGTATTACAATGACTA 60.094 37.037 7.46 0.00 45.05 2.59
133 134 7.758076 CCGACAGAACTGTATTACAATGACTAA 59.242 37.037 7.46 0.00 45.05 2.24
134 135 9.302345 CGACAGAACTGTATTACAATGACTAAT 57.698 33.333 7.46 0.00 45.05 1.73
155 156 9.802039 ACTAATTAACATAAAACCACTCAAGGA 57.198 29.630 0.00 0.00 0.00 3.36
158 159 9.758651 AATTAACATAAAACCACTCAAGGAAAC 57.241 29.630 0.00 0.00 0.00 2.78
160 161 6.635030 ACATAAAACCACTCAAGGAAACTC 57.365 37.500 0.00 0.00 42.68 3.01
161 162 6.126409 ACATAAAACCACTCAAGGAAACTCA 58.874 36.000 0.00 0.00 42.68 3.41
162 163 6.263168 ACATAAAACCACTCAAGGAAACTCAG 59.737 38.462 0.00 0.00 42.68 3.35
163 164 2.938956 ACCACTCAAGGAAACTCAGG 57.061 50.000 0.00 0.00 42.68 3.86
164 165 1.421646 ACCACTCAAGGAAACTCAGGG 59.578 52.381 0.00 0.00 42.68 4.45
165 166 1.271597 CCACTCAAGGAAACTCAGGGG 60.272 57.143 0.00 0.00 42.68 4.79
166 167 1.699634 CACTCAAGGAAACTCAGGGGA 59.300 52.381 0.00 0.00 42.68 4.81
167 168 2.106511 CACTCAAGGAAACTCAGGGGAA 59.893 50.000 0.00 0.00 42.68 3.97
168 169 2.783510 ACTCAAGGAAACTCAGGGGAAA 59.216 45.455 0.00 0.00 42.68 3.13
169 170 3.399305 ACTCAAGGAAACTCAGGGGAAAT 59.601 43.478 0.00 0.00 42.68 2.17
170 171 4.013050 CTCAAGGAAACTCAGGGGAAATC 58.987 47.826 0.00 0.00 42.68 2.17
171 172 3.397618 TCAAGGAAACTCAGGGGAAATCA 59.602 43.478 0.00 0.00 42.68 2.57
172 173 4.044571 TCAAGGAAACTCAGGGGAAATCAT 59.955 41.667 0.00 0.00 42.68 2.45
173 174 3.973425 AGGAAACTCAGGGGAAATCATG 58.027 45.455 0.00 0.00 32.90 3.07
174 175 2.428530 GGAAACTCAGGGGAAATCATGC 59.571 50.000 0.00 0.00 0.00 4.06
175 176 2.905415 AACTCAGGGGAAATCATGCA 57.095 45.000 0.00 0.00 0.00 3.96
176 177 3.393426 AACTCAGGGGAAATCATGCAT 57.607 42.857 0.00 0.00 0.00 3.96
177 178 4.524802 AACTCAGGGGAAATCATGCATA 57.475 40.909 0.00 0.00 0.00 3.14
178 179 3.825328 ACTCAGGGGAAATCATGCATAC 58.175 45.455 0.00 0.00 0.00 2.39
179 180 3.152341 CTCAGGGGAAATCATGCATACC 58.848 50.000 0.00 0.00 0.00 2.73
180 181 2.158475 TCAGGGGAAATCATGCATACCC 60.158 50.000 0.00 7.63 36.93 3.69
181 182 1.858910 AGGGGAAATCATGCATACCCA 59.141 47.619 19.29 0.01 39.15 4.51
182 183 2.452047 AGGGGAAATCATGCATACCCAT 59.548 45.455 19.29 13.40 39.15 4.00
183 184 2.564062 GGGGAAATCATGCATACCCATG 59.436 50.000 19.29 2.68 43.04 3.66
189 190 2.921821 TCATGCATACCCATGACACAG 58.078 47.619 0.00 0.00 44.79 3.66
233 234 5.709966 TGTCGATATATTGATTCCTCCACG 58.290 41.667 5.94 0.00 0.00 4.94
280 281 6.280855 TGAATTAGAAGAGATGTCAACCGA 57.719 37.500 0.00 0.00 0.00 4.69
291 292 2.068837 GTCAACCGACAACCGTATCA 57.931 50.000 0.00 0.00 42.13 2.15
321 322 8.241497 ACAACGATTAGTGGATATTGGTACTA 57.759 34.615 0.00 0.00 0.00 1.82
431 432 1.151679 TTCCCATCCGGCAACAACA 59.848 52.632 0.00 0.00 0.00 3.33
528 529 1.381872 GGCTAGGGTGAGCTGAGGA 60.382 63.158 0.00 0.00 42.43 3.71
533 534 1.383803 GGGTGAGCTGAGGAGGGAT 60.384 63.158 0.00 0.00 0.00 3.85
546 547 2.091775 AGGAGGGATAGCGTAAGTGAGT 60.092 50.000 0.00 0.00 41.68 3.41
590 591 2.111972 AGATTCCTATTCTAGGCGGGGA 59.888 50.000 0.00 0.00 45.82 4.81
768 769 6.125029 CCCATCTTTCTCCATATGAAAGTGT 58.875 40.000 3.65 0.00 46.08 3.55
821 822 0.534203 TCAAAAAGCGAAGGCCGAGT 60.534 50.000 0.00 0.00 41.76 4.18
1034 1035 1.480954 GATCTGCCCAAGAACGACCTA 59.519 52.381 0.00 0.00 38.79 3.08
1131 1132 2.949451 AGAAGTATGACGCTCTGTGG 57.051 50.000 0.00 0.00 0.00 4.17
1151 1152 4.342378 GTGGCTGACTCTATTGGTCATAGA 59.658 45.833 0.00 0.00 41.54 1.98
1241 1242 3.675348 TGGGGCATCTGAGAATGATTT 57.325 42.857 0.00 0.00 0.00 2.17
1389 1393 2.316586 AACCTGGGGTATGCTGGGG 61.317 63.158 0.00 0.00 33.12 4.96
1428 1432 5.123820 CACCTTACGATGTTCATGACCAATT 59.876 40.000 0.00 0.00 0.00 2.32
1552 1556 8.098912 CACTAACCAACCAACTTAACCTATAGT 58.901 37.037 0.00 0.00 0.00 2.12
1618 1622 5.513094 GCTACCTTCAATCCATAGTGCCATA 60.513 44.000 0.00 0.00 0.00 2.74
1749 1753 8.271458 TCCACCTACTTTGATAGCATAAAATCA 58.729 33.333 0.00 0.00 0.00 2.57
1804 1808 0.607112 CTTGGAGAGCAGAGCACTCA 59.393 55.000 16.13 2.73 45.46 3.41
2022 2026 5.181433 GGATATAAAAGGGCGAAGGTCAATC 59.819 44.000 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 8.899771 GTGGCATTACATAATAGGTTGTACTTT 58.100 33.333 0.00 0.00 0.00 2.66
30 31 8.050325 TGTGGCATTACATAATAGGTTGTACTT 58.950 33.333 0.00 0.00 0.00 2.24
31 32 7.570132 TGTGGCATTACATAATAGGTTGTACT 58.430 34.615 0.00 0.00 0.00 2.73
32 33 7.795482 TGTGGCATTACATAATAGGTTGTAC 57.205 36.000 0.00 0.00 0.00 2.90
34 35 8.988546 TTATGTGGCATTACATAATAGGTTGT 57.011 30.769 13.24 0.00 44.35 3.32
41 42 9.762933 GGTGAATTTTATGTGGCATTACATAAT 57.237 29.630 16.23 6.64 46.84 1.28
42 43 7.918033 CGGTGAATTTTATGTGGCATTACATAA 59.082 33.333 13.24 13.24 46.31 1.90
43 44 7.067615 ACGGTGAATTTTATGTGGCATTACATA 59.932 33.333 0.00 4.25 41.31 2.29
44 45 6.127479 ACGGTGAATTTTATGTGGCATTACAT 60.127 34.615 0.00 5.90 43.34 2.29
45 46 5.184096 ACGGTGAATTTTATGTGGCATTACA 59.816 36.000 0.00 0.00 34.63 2.41
46 47 5.646606 ACGGTGAATTTTATGTGGCATTAC 58.353 37.500 0.00 0.00 0.00 1.89
47 48 5.906113 ACGGTGAATTTTATGTGGCATTA 57.094 34.783 0.00 0.00 0.00 1.90
48 49 4.799564 ACGGTGAATTTTATGTGGCATT 57.200 36.364 0.00 0.00 0.00 3.56
49 50 4.219507 TCAACGGTGAATTTTATGTGGCAT 59.780 37.500 0.00 0.00 0.00 4.40
50 51 3.570125 TCAACGGTGAATTTTATGTGGCA 59.430 39.130 0.00 0.00 0.00 4.92
51 52 4.165779 CTCAACGGTGAATTTTATGTGGC 58.834 43.478 3.93 0.00 31.88 5.01
52 53 5.371115 ACTCAACGGTGAATTTTATGTGG 57.629 39.130 3.93 0.00 31.88 4.17
53 54 6.359617 GTCAACTCAACGGTGAATTTTATGTG 59.640 38.462 3.93 0.00 31.88 3.21
54 55 6.038825 TGTCAACTCAACGGTGAATTTTATGT 59.961 34.615 3.93 0.00 31.88 2.29
55 56 6.359617 GTGTCAACTCAACGGTGAATTTTATG 59.640 38.462 3.93 0.00 31.88 1.90
56 57 6.038825 TGTGTCAACTCAACGGTGAATTTTAT 59.961 34.615 3.93 0.00 31.88 1.40
57 58 5.354513 TGTGTCAACTCAACGGTGAATTTTA 59.645 36.000 3.93 0.00 31.88 1.52
58 59 4.156922 TGTGTCAACTCAACGGTGAATTTT 59.843 37.500 3.93 0.00 31.88 1.82
59 60 3.692101 TGTGTCAACTCAACGGTGAATTT 59.308 39.130 3.93 0.00 31.88 1.82
60 61 3.064820 GTGTGTCAACTCAACGGTGAATT 59.935 43.478 3.93 0.00 31.88 2.17
61 62 2.612212 GTGTGTCAACTCAACGGTGAAT 59.388 45.455 3.93 0.00 31.88 2.57
62 63 2.004017 GTGTGTCAACTCAACGGTGAA 58.996 47.619 3.93 0.00 31.88 3.18
63 64 1.066787 TGTGTGTCAACTCAACGGTGA 60.067 47.619 1.69 1.69 0.00 4.02
64 65 1.364721 TGTGTGTCAACTCAACGGTG 58.635 50.000 0.00 0.00 0.00 4.94
65 66 2.325583 ATGTGTGTCAACTCAACGGT 57.674 45.000 0.00 0.00 33.76 4.83
66 67 3.558006 TGTAATGTGTGTCAACTCAACGG 59.442 43.478 0.00 0.00 33.76 4.44
67 68 4.270084 ACTGTAATGTGTGTCAACTCAACG 59.730 41.667 0.00 0.00 33.76 4.10
68 69 5.734855 ACTGTAATGTGTGTCAACTCAAC 57.265 39.130 0.00 0.00 33.76 3.18
69 70 7.269316 TCTTACTGTAATGTGTGTCAACTCAA 58.731 34.615 0.00 0.00 33.76 3.02
70 71 6.811954 TCTTACTGTAATGTGTGTCAACTCA 58.188 36.000 0.00 0.00 34.50 3.41
71 72 7.891183 ATCTTACTGTAATGTGTGTCAACTC 57.109 36.000 0.00 0.00 0.00 3.01
72 73 8.035394 CCTATCTTACTGTAATGTGTGTCAACT 58.965 37.037 0.00 0.00 0.00 3.16
73 74 8.033038 TCCTATCTTACTGTAATGTGTGTCAAC 58.967 37.037 0.00 0.00 0.00 3.18
74 75 8.129496 TCCTATCTTACTGTAATGTGTGTCAA 57.871 34.615 0.00 0.00 0.00 3.18
75 76 7.712204 TCCTATCTTACTGTAATGTGTGTCA 57.288 36.000 0.00 0.00 0.00 3.58
86 87 9.139734 TGTCGGTTTTATATCCTATCTTACTGT 57.860 33.333 0.00 0.00 0.00 3.55
87 88 9.627395 CTGTCGGTTTTATATCCTATCTTACTG 57.373 37.037 0.00 0.00 0.00 2.74
88 89 9.584008 TCTGTCGGTTTTATATCCTATCTTACT 57.416 33.333 0.00 0.00 0.00 2.24
91 92 8.925338 AGTTCTGTCGGTTTTATATCCTATCTT 58.075 33.333 0.00 0.00 0.00 2.40
92 93 8.361139 CAGTTCTGTCGGTTTTATATCCTATCT 58.639 37.037 0.00 0.00 0.00 1.98
93 94 8.142551 ACAGTTCTGTCGGTTTTATATCCTATC 58.857 37.037 0.00 0.00 0.00 2.08
94 95 8.019656 ACAGTTCTGTCGGTTTTATATCCTAT 57.980 34.615 0.00 0.00 0.00 2.57
95 96 7.414222 ACAGTTCTGTCGGTTTTATATCCTA 57.586 36.000 0.00 0.00 0.00 2.94
96 97 6.295719 ACAGTTCTGTCGGTTTTATATCCT 57.704 37.500 0.00 0.00 0.00 3.24
97 98 8.658499 AATACAGTTCTGTCGGTTTTATATCC 57.342 34.615 8.80 0.00 0.00 2.59
100 101 9.926158 TTGTAATACAGTTCTGTCGGTTTTATA 57.074 29.630 8.80 0.00 0.00 0.98
101 102 8.836268 TTGTAATACAGTTCTGTCGGTTTTAT 57.164 30.769 8.80 0.00 0.00 1.40
102 103 8.714179 CATTGTAATACAGTTCTGTCGGTTTTA 58.286 33.333 8.80 0.18 0.00 1.52
103 104 7.442969 TCATTGTAATACAGTTCTGTCGGTTTT 59.557 33.333 8.80 0.98 0.00 2.43
104 105 6.932400 TCATTGTAATACAGTTCTGTCGGTTT 59.068 34.615 8.80 3.07 0.00 3.27
105 106 6.367969 GTCATTGTAATACAGTTCTGTCGGTT 59.632 38.462 8.80 6.17 0.00 4.44
106 107 5.867716 GTCATTGTAATACAGTTCTGTCGGT 59.132 40.000 8.80 0.00 0.00 4.69
107 108 6.100004 AGTCATTGTAATACAGTTCTGTCGG 58.900 40.000 8.80 0.00 0.00 4.79
108 109 8.683550 TTAGTCATTGTAATACAGTTCTGTCG 57.316 34.615 8.80 0.00 0.00 4.35
129 130 9.802039 TCCTTGAGTGGTTTTATGTTAATTAGT 57.198 29.630 0.00 0.00 0.00 2.24
132 133 9.758651 GTTTCCTTGAGTGGTTTTATGTTAATT 57.241 29.630 0.00 0.00 0.00 1.40
133 134 9.143155 AGTTTCCTTGAGTGGTTTTATGTTAAT 57.857 29.630 0.00 0.00 0.00 1.40
134 135 8.528044 AGTTTCCTTGAGTGGTTTTATGTTAA 57.472 30.769 0.00 0.00 0.00 2.01
135 136 7.776030 TGAGTTTCCTTGAGTGGTTTTATGTTA 59.224 33.333 0.00 0.00 0.00 2.41
136 137 6.605594 TGAGTTTCCTTGAGTGGTTTTATGTT 59.394 34.615 0.00 0.00 0.00 2.71
137 138 6.126409 TGAGTTTCCTTGAGTGGTTTTATGT 58.874 36.000 0.00 0.00 0.00 2.29
138 139 6.294176 CCTGAGTTTCCTTGAGTGGTTTTATG 60.294 42.308 0.00 0.00 0.00 1.90
139 140 5.770162 CCTGAGTTTCCTTGAGTGGTTTTAT 59.230 40.000 0.00 0.00 0.00 1.40
140 141 5.130350 CCTGAGTTTCCTTGAGTGGTTTTA 58.870 41.667 0.00 0.00 0.00 1.52
141 142 3.954258 CCTGAGTTTCCTTGAGTGGTTTT 59.046 43.478 0.00 0.00 0.00 2.43
142 143 3.555966 CCTGAGTTTCCTTGAGTGGTTT 58.444 45.455 0.00 0.00 0.00 3.27
143 144 2.158608 CCCTGAGTTTCCTTGAGTGGTT 60.159 50.000 0.00 0.00 0.00 3.67
144 145 1.421646 CCCTGAGTTTCCTTGAGTGGT 59.578 52.381 0.00 0.00 0.00 4.16
145 146 1.271597 CCCCTGAGTTTCCTTGAGTGG 60.272 57.143 0.00 0.00 0.00 4.00
146 147 1.699634 TCCCCTGAGTTTCCTTGAGTG 59.300 52.381 0.00 0.00 0.00 3.51
147 148 2.118403 TCCCCTGAGTTTCCTTGAGT 57.882 50.000 0.00 0.00 0.00 3.41
148 149 3.508845 TTTCCCCTGAGTTTCCTTGAG 57.491 47.619 0.00 0.00 0.00 3.02
149 150 3.397618 TGATTTCCCCTGAGTTTCCTTGA 59.602 43.478 0.00 0.00 0.00 3.02
150 151 3.766545 TGATTTCCCCTGAGTTTCCTTG 58.233 45.455 0.00 0.00 0.00 3.61
151 152 4.347607 CATGATTTCCCCTGAGTTTCCTT 58.652 43.478 0.00 0.00 0.00 3.36
152 153 3.879321 GCATGATTTCCCCTGAGTTTCCT 60.879 47.826 0.00 0.00 0.00 3.36
153 154 2.428530 GCATGATTTCCCCTGAGTTTCC 59.571 50.000 0.00 0.00 0.00 3.13
154 155 3.091545 TGCATGATTTCCCCTGAGTTTC 58.908 45.455 0.00 0.00 0.00 2.78
155 156 3.173953 TGCATGATTTCCCCTGAGTTT 57.826 42.857 0.00 0.00 0.00 2.66
156 157 2.905415 TGCATGATTTCCCCTGAGTT 57.095 45.000 0.00 0.00 0.00 3.01
157 158 3.435601 GGTATGCATGATTTCCCCTGAGT 60.436 47.826 10.16 0.00 0.00 3.41
158 159 3.152341 GGTATGCATGATTTCCCCTGAG 58.848 50.000 10.16 0.00 0.00 3.35
159 160 2.158475 GGGTATGCATGATTTCCCCTGA 60.158 50.000 10.16 0.00 0.00 3.86
160 161 2.242043 GGGTATGCATGATTTCCCCTG 58.758 52.381 10.16 0.00 0.00 4.45
161 162 1.858910 TGGGTATGCATGATTTCCCCT 59.141 47.619 10.16 0.00 34.54 4.79
162 163 2.380064 TGGGTATGCATGATTTCCCC 57.620 50.000 10.16 9.12 34.54 4.81
163 164 3.256631 GTCATGGGTATGCATGATTTCCC 59.743 47.826 10.16 12.99 39.61 3.97
164 165 3.890756 TGTCATGGGTATGCATGATTTCC 59.109 43.478 10.16 4.22 39.61 3.13
165 166 4.338964 TGTGTCATGGGTATGCATGATTTC 59.661 41.667 10.16 0.00 39.61 2.17
166 167 4.279982 TGTGTCATGGGTATGCATGATTT 58.720 39.130 10.16 0.00 39.61 2.17
167 168 3.887110 CTGTGTCATGGGTATGCATGATT 59.113 43.478 10.16 0.00 39.61 2.57
168 169 3.136992 TCTGTGTCATGGGTATGCATGAT 59.863 43.478 10.16 0.00 39.61 2.45
169 170 2.504996 TCTGTGTCATGGGTATGCATGA 59.495 45.455 10.16 0.00 35.69 3.07
170 171 2.921821 TCTGTGTCATGGGTATGCATG 58.078 47.619 10.16 0.00 34.21 4.06
171 172 3.200605 TCTTCTGTGTCATGGGTATGCAT 59.799 43.478 3.79 3.79 34.21 3.96
172 173 2.571202 TCTTCTGTGTCATGGGTATGCA 59.429 45.455 0.00 0.00 34.21 3.96
173 174 3.266510 TCTTCTGTGTCATGGGTATGC 57.733 47.619 0.00 0.00 34.21 3.14
174 175 5.055144 CAGATCTTCTGTGTCATGGGTATG 58.945 45.833 0.00 0.00 39.58 2.39
175 176 4.444022 GCAGATCTTCTGTGTCATGGGTAT 60.444 45.833 6.40 0.00 45.94 2.73
176 177 3.118629 GCAGATCTTCTGTGTCATGGGTA 60.119 47.826 6.40 0.00 45.94 3.69
177 178 2.355513 GCAGATCTTCTGTGTCATGGGT 60.356 50.000 6.40 0.00 45.94 4.51
178 179 2.286872 GCAGATCTTCTGTGTCATGGG 58.713 52.381 6.40 0.00 45.94 4.00
179 180 2.093075 AGGCAGATCTTCTGTGTCATGG 60.093 50.000 6.40 0.00 45.94 3.66
180 181 3.118702 AGAGGCAGATCTTCTGTGTCATG 60.119 47.826 6.40 0.00 45.94 3.07
181 182 3.106054 AGAGGCAGATCTTCTGTGTCAT 58.894 45.455 6.40 0.00 45.94 3.06
182 183 2.533916 AGAGGCAGATCTTCTGTGTCA 58.466 47.619 6.40 0.00 45.94 3.58
183 184 3.260740 CAAGAGGCAGATCTTCTGTGTC 58.739 50.000 6.40 3.94 45.94 3.67
184 185 2.027377 CCAAGAGGCAGATCTTCTGTGT 60.027 50.000 6.40 0.00 45.94 3.72
185 186 2.630158 CCAAGAGGCAGATCTTCTGTG 58.370 52.381 6.40 0.00 45.94 3.66
216 217 5.029807 TGTTGCGTGGAGGAATCAATATA 57.970 39.130 0.00 0.00 31.33 0.86
280 281 2.803956 CGTTGTTTCCTGATACGGTTGT 59.196 45.455 0.00 0.00 0.00 3.32
291 292 6.542370 CCAATATCCACTAATCGTTGTTTCCT 59.458 38.462 0.00 0.00 0.00 3.36
321 322 1.000607 CTTTGCTTGCTGTGCAGTGAT 60.001 47.619 0.00 0.00 40.61 3.06
421 422 1.008538 GGCAGAACTGTTGTTGCCG 60.009 57.895 22.28 0.38 36.15 5.69
431 432 1.729586 TTGTAGGGTCAGGCAGAACT 58.270 50.000 0.00 0.00 33.21 3.01
528 529 3.014304 TCACTCACTTACGCTATCCCT 57.986 47.619 0.00 0.00 0.00 4.20
533 534 4.234574 CACACATTCACTCACTTACGCTA 58.765 43.478 0.00 0.00 0.00 4.26
546 547 2.105649 TGACTGGGCTTACACACATTCA 59.894 45.455 0.00 0.00 0.00 2.57
590 591 0.625849 ATTCGAAGGTTGATGGCCCT 59.374 50.000 3.35 0.00 0.00 5.19
768 769 0.541392 ACATCTCTATGTGCCCGCAA 59.459 50.000 0.00 0.00 44.79 4.85
918 919 1.293267 TTTCATTCGACGTTCCGGGC 61.293 55.000 0.00 0.00 0.00 6.13
975 976 1.778803 GGGATAGGGGGAAAGGGGG 60.779 68.421 0.00 0.00 0.00 5.40
1034 1035 1.298667 GTGCCTTCCGTACCACCAT 59.701 57.895 0.00 0.00 0.00 3.55
1151 1152 3.064324 GGCCGCAACAGCAAGGAT 61.064 61.111 0.00 0.00 0.00 3.24
1175 1176 3.865830 TTCACACGCGCGCAAACA 61.866 55.556 32.58 8.84 0.00 2.83
1241 1242 1.906574 AGTTTCCCTTCATACGGCTCA 59.093 47.619 0.00 0.00 0.00 4.26
1329 1333 5.634859 CACTTCACTTTTGCACTTTCACTTT 59.365 36.000 0.00 0.00 0.00 2.66
1389 1393 2.472049 GTGCTGCTCTTCGCGAAC 59.528 61.111 19.38 9.35 43.27 3.95
1428 1432 3.021695 CCTACTGGTACGTCAAGATCCA 58.978 50.000 0.00 0.00 0.00 3.41
1682 1686 1.213296 ACCTGCTATTGGACGGGATT 58.787 50.000 0.00 0.00 36.12 3.01
1749 1753 7.820386 GGTGTTTTTACATTAAAATCCCCGAAT 59.180 33.333 0.00 0.00 37.48 3.34
1804 1808 0.327924 TCAATCAACCCATCGCACCT 59.672 50.000 0.00 0.00 0.00 4.00
2022 2026 6.476378 CAGATACCTATAAGGACCCCATTTG 58.524 44.000 0.00 0.00 37.67 2.32


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

AutoCloner maintained by Alex Coulton.