Multiple sequence alignment - TraesCS2B01G605500

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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 TraesCS2B01G605500 chr2B 100.000 2378 0 0 1 2378 786676892 786679269 0.000000e+00 4392
1 TraesCS2B01G605500 chr2B 97.235 1808 40 5 577 2378 786733005 786734808 0.000000e+00 3053
2 TraesCS2B01G605500 chr2B 96.444 1800 48 2 265 2060 786626880 786628667 0.000000e+00 2955
3 TraesCS2B01G605500 chr2B 80.046 872 101 40 289 1130 786467154 786467982 1.580000e-161 579
4 TraesCS2B01G605500 chr2B 97.161 317 8 1 265 581 786718754 786719069 3.480000e-148 534
5 TraesCS2B01G605500 chr2B 97.701 261 5 1 6 266 786699172 786699431 4.660000e-122 448
6 TraesCS2B01G605500 chr2B 79.866 298 43 8 1804 2096 786626036 786626321 4.010000e-48 202
7 TraesCS2B01G605500 chr2B 85.405 185 22 2 1565 1749 786270804 786270983 1.120000e-43 187
8 TraesCS2B01G605500 chr2B 85.405 185 22 2 1565 1749 786277547 786277726 1.120000e-43 187
9 TraesCS2B01G605500 chr2B 84.865 185 23 2 1565 1749 786263318 786263497 5.220000e-42 182
10 TraesCS2B01G605500 chr2B 77.341 331 44 17 1968 2269 786265763 786266091 1.460000e-37 167
11 TraesCS2B01G605500 chr2B 77.341 331 44 17 1968 2269 786285148 786285476 1.460000e-37 167
12 TraesCS2B01G605500 chr2B 94.286 70 4 0 2309 2378 786266087 786266156 8.990000e-20 108
13 TraesCS2B01G605500 chr2B 94.286 70 4 0 2309 2378 786285472 786285541 8.990000e-20 108
14 TraesCS2B01G605500 chr2D 82.203 1180 125 40 265 1429 650362480 650363589 0.000000e+00 937
15 TraesCS2B01G605500 chr2D 85.782 211 18 6 1570 1777 650363705 650363906 1.850000e-51 213
16 TraesCS2B01G605500 chr2D 80.567 247 25 16 1560 1795 650359009 650359243 4.070000e-38 169
17 TraesCS2B01G605500 chr2D 79.771 262 30 9 1831 2092 650364007 650364245 4.070000e-38 169
18 TraesCS2B01G605500 chr2A 85.803 641 57 17 265 892 774430450 774429831 0.000000e+00 649
19 TraesCS2B01G605500 chr2A 83.619 641 54 21 265 892 774311508 774310906 2.670000e-154 555
20 TraesCS2B01G605500 chr2A 80.048 832 94 25 748 1560 774370475 774369697 3.450000e-153 551
21 TraesCS2B01G605500 chr2A 80.048 832 94 25 748 1560 774432376 774431598 3.450000e-153 551
22 TraesCS2B01G605500 chr2A 80.597 469 52 17 963 1429 774310296 774309865 2.280000e-85 326
23 TraesCS2B01G605500 chr2A 86.294 197 18 5 1564 1758 774429500 774429311 3.100000e-49 206
24 TraesCS2B01G605500 chr2A 85.222 203 21 5 1564 1764 774309749 774309554 1.440000e-47 200
25 TraesCS2B01G605500 chrUn 92.950 383 23 4 265 646 337609907 337609528 2.670000e-154 555
26 TraesCS2B01G605500 chrUn 92.428 383 25 4 265 646 337607281 337606902 5.780000e-151 544
27 TraesCS2B01G605500 chrUn 93.029 373 22 4 265 636 468027233 468027602 2.080000e-150 542
28 TraesCS2B01G605500 chr7D 94.208 259 14 1 8 266 166669488 166669745 6.160000e-106 394
29 TraesCS2B01G605500 chr7D 97.351 151 4 0 116 266 13460165 13460315 8.430000e-65 257
30 TraesCS2B01G605500 chr4D 80.998 421 56 6 982 1390 293860786 293860378 1.770000e-81 313
31 TraesCS2B01G605500 chr4A 79.733 449 64 8 982 1418 323789068 323788635 1.380000e-77 300
32 TraesCS2B01G605500 chr4B 79.810 421 61 6 982 1390 291847968 291847560 3.870000e-73 285


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 TraesCS2B01G605500 chr2B 786676892 786679269 2377 False 4392.000000 4392 100.000000 1 2378 1 chr2B.!!$F4 2377
1 TraesCS2B01G605500 chr2B 786733005 786734808 1803 False 3053.000000 3053 97.235000 577 2378 1 chr2B.!!$F7 1801
2 TraesCS2B01G605500 chr2B 786626036 786628667 2631 False 1578.500000 2955 88.155000 265 2096 2 chr2B.!!$F10 1831
3 TraesCS2B01G605500 chr2B 786467154 786467982 828 False 579.000000 579 80.046000 289 1130 1 chr2B.!!$F3 841
4 TraesCS2B01G605500 chr2D 650359009 650364245 5236 False 372.000000 937 82.080750 265 2092 4 chr2D.!!$F1 1827
5 TraesCS2B01G605500 chr2A 774369697 774370475 778 True 551.000000 551 80.048000 748 1560 1 chr2A.!!$R1 812
6 TraesCS2B01G605500 chr2A 774429311 774432376 3065 True 468.666667 649 84.048333 265 1758 3 chr2A.!!$R3 1493
7 TraesCS2B01G605500 chr2A 774309554 774311508 1954 True 360.333333 555 83.146000 265 1764 3 chr2A.!!$R2 1499
8 TraesCS2B01G605500 chrUn 337606902 337609907 3005 True 549.500000 555 92.689000 265 646 2 chrUn.!!$R1 381

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
174 175 0.110192 GCGTCGGCCAGAAAAGAAAG 60.11 55.0 2.24 0.0 0.0 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 9222 0.468214 TTGGTCCGCAAAACATCCCA 60.468 50.0 0.0 0.0 0.0 4.37 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
32 33 4.361827 CGTCACTACGGAGCGAAG 57.638 61.111 0.00 0.00 45.50 3.79
46 47 3.741029 CGAAGCTGAATCTTCCCGA 57.259 52.632 0.00 0.00 39.33 5.14
47 48 2.231215 CGAAGCTGAATCTTCCCGAT 57.769 50.000 0.00 0.00 39.33 4.18
60 61 7.938140 AATCTTCCCGATTCACAAATAGAAA 57.062 32.000 0.00 0.00 37.85 2.52
61 62 7.938140 ATCTTCCCGATTCACAAATAGAAAA 57.062 32.000 0.00 0.00 0.00 2.29
63 64 7.590279 TCTTCCCGATTCACAAATAGAAAAAC 58.410 34.615 0.00 0.00 0.00 2.43
64 65 5.933790 TCCCGATTCACAAATAGAAAAACG 58.066 37.500 0.00 0.00 0.00 3.60
65 66 5.701750 TCCCGATTCACAAATAGAAAAACGA 59.298 36.000 0.00 0.00 0.00 3.85
67 68 6.523201 CCCGATTCACAAATAGAAAAACGAAG 59.477 38.462 0.00 0.00 0.00 3.79
68 69 6.032460 CCGATTCACAAATAGAAAAACGAAGC 59.968 38.462 0.00 0.00 0.00 3.86
69 70 6.032460 CGATTCACAAATAGAAAAACGAAGCC 59.968 38.462 0.00 0.00 0.00 4.35
70 71 5.116069 TCACAAATAGAAAAACGAAGCCC 57.884 39.130 0.00 0.00 0.00 5.19
71 72 4.580995 TCACAAATAGAAAAACGAAGCCCA 59.419 37.500 0.00 0.00 0.00 5.36
73 74 5.925969 CACAAATAGAAAAACGAAGCCCAAT 59.074 36.000 0.00 0.00 0.00 3.16
74 75 6.089417 CACAAATAGAAAAACGAAGCCCAATC 59.911 38.462 0.00 0.00 0.00 2.67
75 76 2.989422 AGAAAAACGAAGCCCAATCG 57.011 45.000 0.00 0.00 45.47 3.34
80 81 4.910956 CGAAGCCCAATCGTCTCA 57.089 55.556 0.00 0.00 35.64 3.27
81 82 3.369381 CGAAGCCCAATCGTCTCAT 57.631 52.632 0.00 0.00 35.64 2.90
82 83 1.656652 CGAAGCCCAATCGTCTCATT 58.343 50.000 0.00 0.00 35.64 2.57
85 86 3.490933 CGAAGCCCAATCGTCTCATTCTA 60.491 47.826 0.00 0.00 35.64 2.10
86 87 4.442706 GAAGCCCAATCGTCTCATTCTAA 58.557 43.478 0.00 0.00 0.00 2.10
88 89 4.446371 AGCCCAATCGTCTCATTCTAAAG 58.554 43.478 0.00 0.00 0.00 1.85
89 90 4.162320 AGCCCAATCGTCTCATTCTAAAGA 59.838 41.667 0.00 0.00 0.00 2.52
90 91 4.876107 GCCCAATCGTCTCATTCTAAAGAA 59.124 41.667 0.00 0.00 38.56 2.52
91 92 5.354234 GCCCAATCGTCTCATTCTAAAGAAA 59.646 40.000 0.00 0.00 37.61 2.52
92 93 6.128007 GCCCAATCGTCTCATTCTAAAGAAAA 60.128 38.462 0.00 0.00 37.61 2.29
93 94 7.467623 CCCAATCGTCTCATTCTAAAGAAAAG 58.532 38.462 0.00 0.00 37.61 2.27
94 95 7.334421 CCCAATCGTCTCATTCTAAAGAAAAGA 59.666 37.037 0.00 1.04 37.61 2.52
95 96 8.721478 CCAATCGTCTCATTCTAAAGAAAAGAA 58.279 33.333 8.80 0.00 37.61 2.52
99 100 6.402658 CGTCTCATTCTAAAGAAAAGAAGCCC 60.403 42.308 8.80 0.10 36.46 5.19
100 101 6.431234 GTCTCATTCTAAAGAAAAGAAGCCCA 59.569 38.462 8.80 0.00 36.46 5.36
101 102 7.004086 TCTCATTCTAAAGAAAAGAAGCCCAA 58.996 34.615 0.00 0.00 36.46 4.12
102 103 6.981722 TCATTCTAAAGAAAAGAAGCCCAAC 58.018 36.000 0.00 0.00 36.46 3.77
103 104 5.784578 TTCTAAAGAAAAGAAGCCCAACC 57.215 39.130 0.00 0.00 0.00 3.77
104 105 4.798882 TCTAAAGAAAAGAAGCCCAACCA 58.201 39.130 0.00 0.00 0.00 3.67
106 107 4.607293 AAAGAAAAGAAGCCCAACCATC 57.393 40.909 0.00 0.00 0.00 3.51
108 109 3.849527 AGAAAAGAAGCCCAACCATCTT 58.150 40.909 0.00 0.00 33.73 2.40
110 111 2.222227 AAGAAGCCCAACCATCTTCC 57.778 50.000 0.00 0.00 37.51 3.46
112 113 1.642762 AGAAGCCCAACCATCTTCCAT 59.357 47.619 0.00 0.00 37.51 3.41
113 114 2.027385 GAAGCCCAACCATCTTCCATC 58.973 52.381 0.00 0.00 32.31 3.51
114 115 1.302907 AGCCCAACCATCTTCCATCT 58.697 50.000 0.00 0.00 0.00 2.90
116 117 1.213926 GCCCAACCATCTTCCATCTCT 59.786 52.381 0.00 0.00 0.00 3.10
117 118 2.747799 GCCCAACCATCTTCCATCTCTC 60.748 54.545 0.00 0.00 0.00 3.20
119 120 3.137913 CCCAACCATCTTCCATCTCTCAT 59.862 47.826 0.00 0.00 0.00 2.90
121 122 5.163163 CCCAACCATCTTCCATCTCTCATAA 60.163 44.000 0.00 0.00 0.00 1.90
122 123 6.359804 CCAACCATCTTCCATCTCTCATAAA 58.640 40.000 0.00 0.00 0.00 1.40
123 124 6.485984 CCAACCATCTTCCATCTCTCATAAAG 59.514 42.308 0.00 0.00 0.00 1.85
124 125 6.185114 ACCATCTTCCATCTCTCATAAAGG 57.815 41.667 0.00 0.00 0.00 3.11
126 127 6.183361 ACCATCTTCCATCTCTCATAAAGGAC 60.183 42.308 0.00 0.00 0.00 3.85
127 128 5.878406 TCTTCCATCTCTCATAAAGGACC 57.122 43.478 0.00 0.00 0.00 4.46
128 129 5.280499 TCTTCCATCTCTCATAAAGGACCA 58.720 41.667 0.00 0.00 0.00 4.02
129 130 5.726308 TCTTCCATCTCTCATAAAGGACCAA 59.274 40.000 0.00 0.00 0.00 3.67
130 131 5.359194 TCCATCTCTCATAAAGGACCAAC 57.641 43.478 0.00 0.00 0.00 3.77
131 132 4.164221 TCCATCTCTCATAAAGGACCAACC 59.836 45.833 0.00 0.00 39.35 3.77
141 142 3.191182 GGACCAACCTATGCCCTTG 57.809 57.895 0.00 0.00 35.41 3.61
153 154 3.981308 CCCTTGGCAACCGTACAG 58.019 61.111 0.00 0.00 0.00 2.74
154 155 2.332654 CCCTTGGCAACCGTACAGC 61.333 63.158 0.00 0.00 0.00 4.40
155 156 2.677003 CCTTGGCAACCGTACAGCG 61.677 63.158 0.00 0.00 40.95 5.18
156 157 3.308878 CTTGGCAACCGTACAGCGC 62.309 63.158 0.00 0.00 39.71 5.92
159 160 4.130281 GCAACCGTACAGCGCGTC 62.130 66.667 8.43 0.00 39.71 5.19
160 161 3.823421 CAACCGTACAGCGCGTCG 61.823 66.667 8.43 5.67 39.71 5.12
169 170 4.980805 AGCGCGTCGGCCAGAAAA 62.981 61.111 8.43 0.00 35.02 2.29
170 171 4.445545 GCGCGTCGGCCAGAAAAG 62.446 66.667 8.43 0.00 35.02 2.27
171 172 2.736995 CGCGTCGGCCAGAAAAGA 60.737 61.111 2.24 0.00 35.02 2.52
172 173 2.314647 CGCGTCGGCCAGAAAAGAA 61.315 57.895 2.24 0.00 35.02 2.52
174 175 0.110192 GCGTCGGCCAGAAAAGAAAG 60.110 55.000 2.24 0.00 0.00 2.62
175 176 0.517316 CGTCGGCCAGAAAAGAAAGG 59.483 55.000 2.24 0.00 0.00 3.11
176 177 1.876416 CGTCGGCCAGAAAAGAAAGGA 60.876 52.381 2.24 0.00 0.00 3.36
177 178 2.227194 GTCGGCCAGAAAAGAAAGGAA 58.773 47.619 2.24 0.00 0.00 3.36
178 179 2.226674 GTCGGCCAGAAAAGAAAGGAAG 59.773 50.000 2.24 0.00 0.00 3.46
180 181 1.068264 GGCCAGAAAAGAAAGGAAGCG 60.068 52.381 0.00 0.00 0.00 4.68
182 183 2.489722 GCCAGAAAAGAAAGGAAGCGAT 59.510 45.455 0.00 0.00 0.00 4.58
183 184 3.426829 GCCAGAAAAGAAAGGAAGCGATC 60.427 47.826 0.00 0.00 0.00 3.69
184 185 4.006319 CCAGAAAAGAAAGGAAGCGATCT 58.994 43.478 0.00 0.00 0.00 2.75
185 186 4.094146 CCAGAAAAGAAAGGAAGCGATCTC 59.906 45.833 0.00 0.00 0.00 2.75
186 187 4.094146 CAGAAAAGAAAGGAAGCGATCTCC 59.906 45.833 0.00 0.00 0.00 3.71
187 188 2.301577 AAGAAAGGAAGCGATCTCCG 57.698 50.000 0.00 0.00 42.21 4.63
196 197 3.909312 CGATCTCCGCGTGTGATC 58.091 61.111 20.27 20.27 39.51 2.92
197 198 1.356979 CGATCTCCGCGTGTGATCT 59.643 57.895 24.02 5.70 40.33 2.75
199 200 0.596083 GATCTCCGCGTGTGATCTGG 60.596 60.000 21.72 0.89 39.69 3.86
200 201 1.323271 ATCTCCGCGTGTGATCTGGT 61.323 55.000 4.92 0.00 0.00 4.00
201 202 1.517257 CTCCGCGTGTGATCTGGTC 60.517 63.158 4.92 0.00 0.00 4.02
202 203 2.509336 CCGCGTGTGATCTGGTCC 60.509 66.667 4.92 0.00 0.00 4.46
204 205 1.517257 CGCGTGTGATCTGGTCCTC 60.517 63.158 0.00 0.00 0.00 3.71
205 206 1.893786 GCGTGTGATCTGGTCCTCT 59.106 57.895 0.00 0.00 0.00 3.69
206 207 0.459237 GCGTGTGATCTGGTCCTCTG 60.459 60.000 0.00 0.00 0.00 3.35
207 208 0.459237 CGTGTGATCTGGTCCTCTGC 60.459 60.000 0.00 0.00 0.00 4.26
208 209 0.901124 GTGTGATCTGGTCCTCTGCT 59.099 55.000 0.00 0.00 0.00 4.24
210 211 1.552337 TGTGATCTGGTCCTCTGCTTC 59.448 52.381 0.00 0.00 0.00 3.86
212 213 1.107114 GATCTGGTCCTCTGCTTCGA 58.893 55.000 0.00 0.00 0.00 3.71
213 214 0.820871 ATCTGGTCCTCTGCTTCGAC 59.179 55.000 0.00 0.00 0.00 4.20
214 215 1.216710 CTGGTCCTCTGCTTCGACC 59.783 63.158 0.00 0.00 45.30 4.79
215 216 1.228894 TGGTCCTCTGCTTCGACCT 60.229 57.895 6.98 0.00 45.31 3.85
216 217 1.251527 TGGTCCTCTGCTTCGACCTC 61.252 60.000 6.98 0.00 45.31 3.85
218 219 2.046864 TCCTCTGCTTCGACCTCCG 61.047 63.158 0.00 0.00 40.25 4.63
229 230 4.070552 ACCTCCGGTCTTCAGCGC 62.071 66.667 0.00 0.00 42.39 5.92
231 232 4.421479 CTCCGGTCTTCAGCGCGT 62.421 66.667 8.43 0.00 42.39 6.01
232 233 4.415332 TCCGGTCTTCAGCGCGTC 62.415 66.667 8.43 0.00 42.39 5.19
233 234 4.717629 CCGGTCTTCAGCGCGTCA 62.718 66.667 8.43 0.00 42.39 4.35
234 235 3.175240 CGGTCTTCAGCGCGTCAG 61.175 66.667 8.43 0.00 36.57 3.51
235 236 3.482783 GGTCTTCAGCGCGTCAGC 61.483 66.667 8.43 0.00 40.74 4.26
236 237 3.482783 GTCTTCAGCGCGTCAGCC 61.483 66.667 8.43 0.00 41.18 4.85
246 247 3.449227 CGTCAGCCGGGCTCTGTA 61.449 66.667 20.97 1.84 36.40 2.74
247 248 2.496817 GTCAGCCGGGCTCTGTAG 59.503 66.667 20.97 7.86 36.40 2.74
248 249 2.759973 TCAGCCGGGCTCTGTAGG 60.760 66.667 20.97 7.04 36.40 3.18
256 257 2.425562 GGCTCTGTAGGCTCTCTCC 58.574 63.158 0.00 0.00 44.73 3.71
257 258 1.452145 GGCTCTGTAGGCTCTCTCCG 61.452 65.000 0.00 0.00 44.73 4.63
259 260 1.305201 CTCTGTAGGCTCTCTCCGAC 58.695 60.000 0.00 0.00 33.12 4.79
260 261 0.913205 TCTGTAGGCTCTCTCCGACT 59.087 55.000 0.00 0.00 33.58 4.18
261 262 1.021202 CTGTAGGCTCTCTCCGACTG 58.979 60.000 0.00 0.00 33.58 3.51
262 263 0.328592 TGTAGGCTCTCTCCGACTGT 59.671 55.000 0.00 0.00 33.58 3.55
263 264 0.736053 GTAGGCTCTCTCCGACTGTG 59.264 60.000 0.00 0.00 0.00 3.66
274 3989 1.153489 CGACTGTGGCCCTCATCTG 60.153 63.158 0.00 0.00 0.00 2.90
312 4028 6.197096 CAGTGTTCAAAGTTTATGTGCACTTC 59.803 38.462 19.41 0.00 34.40 3.01
425 4160 4.609301 TCCCCCAGAAGTTCCATATTTTG 58.391 43.478 0.00 0.00 0.00 2.44
544 4284 6.682423 TGCTTGAACCTTCATACATATGTG 57.318 37.500 18.81 2.70 37.00 3.21
746 5000 6.307558 GCTAGAGTTGACCTAAACGTTCTAAC 59.692 42.308 0.00 1.62 35.13 2.34
1104 5915 2.548295 GCCGCTTTTCGTGGGTCAA 61.548 57.895 0.00 0.00 43.73 3.18
1242 6065 3.799755 GGCCATGACGTGTTCGCC 61.800 66.667 0.00 0.00 41.18 5.54
1527 6642 3.758554 AGGCAGCAGTAATAACAAAGTGG 59.241 43.478 0.00 0.00 0.00 4.00
1570 6725 2.427410 GTGTTGCGCGCCAAAGAG 60.427 61.111 30.77 0.00 34.68 2.85
1785 9222 6.655078 ATGGCAGTTTTGAAGTCAGTTTAT 57.345 33.333 0.00 0.00 0.00 1.40
1896 9380 1.338136 ACCAGGTCGGGGCTGATAAG 61.338 60.000 0.00 0.00 40.22 1.73
1924 9408 0.984230 GAGTGACATGGTGGGGAAGA 59.016 55.000 0.00 0.00 0.00 2.87
2112 9596 4.887071 GCACAATGTATTCATCCCCTTACA 59.113 41.667 0.00 0.00 32.56 2.41
2115 9599 7.394359 GCACAATGTATTCATCCCCTTACATAT 59.606 37.037 0.00 0.00 34.94 1.78
2193 9677 7.979444 ATCGTTGGATTTAACTTTCAAGAGA 57.021 32.000 0.00 0.00 0.00 3.10
2194 9678 7.795482 TCGTTGGATTTAACTTTCAAGAGAA 57.205 32.000 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.798771 CAGCTTCGCTCCGTAGTGAC 60.799 60.000 0.00 0.00 41.89 3.67
17 18 0.958876 TCAGCTTCGCTCCGTAGTGA 60.959 55.000 0.00 0.00 40.48 3.41
18 19 0.109272 TTCAGCTTCGCTCCGTAGTG 60.109 55.000 0.00 0.00 36.40 2.74
21 22 1.103803 AGATTCAGCTTCGCTCCGTA 58.896 50.000 0.00 0.00 36.40 4.02
23 24 0.926846 GAAGATTCAGCTTCGCTCCG 59.073 55.000 0.00 0.00 36.40 4.63
24 25 1.294857 GGAAGATTCAGCTTCGCTCC 58.705 55.000 0.00 0.00 44.04 4.70
26 27 5.558388 AATCGGGAAGATTCAGCTTCGCT 62.558 47.826 16.82 0.37 45.95 4.93
27 28 3.317318 AATCGGGAAGATTCAGCTTCGC 61.317 50.000 10.89 10.89 45.95 4.70
28 29 2.231215 ATCGGGAAGATTCAGCTTCG 57.769 50.000 0.00 0.00 44.04 3.79
39 40 6.523201 CGTTTTTCTATTTGTGAATCGGGAAG 59.477 38.462 0.00 0.00 0.00 3.46
41 42 5.701750 TCGTTTTTCTATTTGTGAATCGGGA 59.298 36.000 0.00 0.00 0.00 5.14
42 43 5.933790 TCGTTTTTCTATTTGTGAATCGGG 58.066 37.500 0.00 0.00 0.00 5.14
44 45 6.032460 GGCTTCGTTTTTCTATTTGTGAATCG 59.968 38.462 0.00 0.00 0.00 3.34
45 46 6.308041 GGGCTTCGTTTTTCTATTTGTGAATC 59.692 38.462 0.00 0.00 0.00 2.52
46 47 6.156519 GGGCTTCGTTTTTCTATTTGTGAAT 58.843 36.000 0.00 0.00 0.00 2.57
47 48 5.067936 TGGGCTTCGTTTTTCTATTTGTGAA 59.932 36.000 0.00 0.00 0.00 3.18
50 51 5.523438 TTGGGCTTCGTTTTTCTATTTGT 57.477 34.783 0.00 0.00 0.00 2.83
51 52 5.286082 CGATTGGGCTTCGTTTTTCTATTTG 59.714 40.000 0.00 0.00 32.08 2.32
52 53 5.048294 ACGATTGGGCTTCGTTTTTCTATTT 60.048 36.000 0.00 0.00 46.96 1.40
53 54 4.457949 ACGATTGGGCTTCGTTTTTCTATT 59.542 37.500 0.00 0.00 46.96 1.73
54 55 4.007659 ACGATTGGGCTTCGTTTTTCTAT 58.992 39.130 0.00 0.00 46.96 1.98
55 56 3.404899 ACGATTGGGCTTCGTTTTTCTA 58.595 40.909 0.00 0.00 46.96 2.10
56 57 2.227194 ACGATTGGGCTTCGTTTTTCT 58.773 42.857 0.00 0.00 46.96 2.52
57 58 2.699251 ACGATTGGGCTTCGTTTTTC 57.301 45.000 0.00 0.00 46.96 2.29
63 64 1.594862 GAATGAGACGATTGGGCTTCG 59.405 52.381 0.00 4.06 42.20 3.79
64 65 2.911484 AGAATGAGACGATTGGGCTTC 58.089 47.619 0.00 0.00 0.00 3.86
65 66 4.487714 TTAGAATGAGACGATTGGGCTT 57.512 40.909 0.00 0.00 0.00 4.35
67 68 4.442706 TCTTTAGAATGAGACGATTGGGC 58.557 43.478 0.00 0.00 0.00 5.36
68 69 6.985188 TTTCTTTAGAATGAGACGATTGGG 57.015 37.500 0.00 0.00 33.54 4.12
69 70 8.256611 TCTTTTCTTTAGAATGAGACGATTGG 57.743 34.615 0.00 0.00 33.54 3.16
70 71 9.752274 CTTCTTTTCTTTAGAATGAGACGATTG 57.248 33.333 0.00 0.00 33.54 2.67
71 72 8.447053 GCTTCTTTTCTTTAGAATGAGACGATT 58.553 33.333 0.00 0.00 33.54 3.34
73 74 6.369065 GGCTTCTTTTCTTTAGAATGAGACGA 59.631 38.462 0.00 0.00 33.54 4.20
74 75 6.402658 GGGCTTCTTTTCTTTAGAATGAGACG 60.403 42.308 5.90 5.93 33.54 4.18
75 76 6.431234 TGGGCTTCTTTTCTTTAGAATGAGAC 59.569 38.462 5.90 0.19 33.54 3.36
76 77 6.542821 TGGGCTTCTTTTCTTTAGAATGAGA 58.457 36.000 0.00 0.00 33.54 3.27
79 80 6.159293 GGTTGGGCTTCTTTTCTTTAGAATG 58.841 40.000 0.00 0.00 33.54 2.67
80 81 5.838521 TGGTTGGGCTTCTTTTCTTTAGAAT 59.161 36.000 0.00 0.00 33.54 2.40
81 82 5.205056 TGGTTGGGCTTCTTTTCTTTAGAA 58.795 37.500 0.00 0.00 0.00 2.10
82 83 4.798882 TGGTTGGGCTTCTTTTCTTTAGA 58.201 39.130 0.00 0.00 0.00 2.10
85 86 4.226384 AGATGGTTGGGCTTCTTTTCTTT 58.774 39.130 0.00 0.00 0.00 2.52
86 87 3.849527 AGATGGTTGGGCTTCTTTTCTT 58.150 40.909 0.00 0.00 0.00 2.52
88 89 3.056536 GGAAGATGGTTGGGCTTCTTTTC 60.057 47.826 0.00 0.00 38.41 2.29
89 90 2.899900 GGAAGATGGTTGGGCTTCTTTT 59.100 45.455 0.00 0.00 38.41 2.27
90 91 2.158325 TGGAAGATGGTTGGGCTTCTTT 60.158 45.455 0.00 0.00 38.41 2.52
91 92 1.428912 TGGAAGATGGTTGGGCTTCTT 59.571 47.619 0.00 0.00 38.41 2.52
92 93 1.075601 TGGAAGATGGTTGGGCTTCT 58.924 50.000 0.00 0.00 38.41 2.85
93 94 2.027385 GATGGAAGATGGTTGGGCTTC 58.973 52.381 0.00 0.00 37.80 3.86
94 95 1.642762 AGATGGAAGATGGTTGGGCTT 59.357 47.619 0.00 0.00 0.00 4.35
95 96 1.213926 GAGATGGAAGATGGTTGGGCT 59.786 52.381 0.00 0.00 0.00 5.19
99 100 6.485984 CCTTTATGAGAGATGGAAGATGGTTG 59.514 42.308 0.00 0.00 0.00 3.77
100 101 6.388100 TCCTTTATGAGAGATGGAAGATGGTT 59.612 38.462 0.00 0.00 0.00 3.67
101 102 5.907662 TCCTTTATGAGAGATGGAAGATGGT 59.092 40.000 0.00 0.00 0.00 3.55
102 103 6.229733 GTCCTTTATGAGAGATGGAAGATGG 58.770 44.000 0.00 0.00 0.00 3.51
103 104 6.183361 TGGTCCTTTATGAGAGATGGAAGATG 60.183 42.308 0.00 0.00 0.00 2.90
104 105 5.907662 TGGTCCTTTATGAGAGATGGAAGAT 59.092 40.000 0.00 0.00 0.00 2.40
106 107 5.620738 TGGTCCTTTATGAGAGATGGAAG 57.379 43.478 0.00 0.00 0.00 3.46
108 109 4.164221 GGTTGGTCCTTTATGAGAGATGGA 59.836 45.833 0.00 0.00 0.00 3.41
110 111 5.365021 AGGTTGGTCCTTTATGAGAGATG 57.635 43.478 0.00 0.00 45.67 2.90
112 113 5.163301 GCATAGGTTGGTCCTTTATGAGAGA 60.163 44.000 0.00 0.00 45.67 3.10
113 114 5.059833 GCATAGGTTGGTCCTTTATGAGAG 58.940 45.833 0.00 0.00 45.67 3.20
114 115 4.141482 GGCATAGGTTGGTCCTTTATGAGA 60.141 45.833 0.00 0.00 45.67 3.27
116 117 3.117663 GGGCATAGGTTGGTCCTTTATGA 60.118 47.826 0.00 0.00 45.67 2.15
117 118 3.117512 AGGGCATAGGTTGGTCCTTTATG 60.118 47.826 0.00 0.00 45.67 1.90
119 120 2.568979 AGGGCATAGGTTGGTCCTTTA 58.431 47.619 0.00 0.00 45.67 1.85
121 122 1.005924 CAAGGGCATAGGTTGGTCCTT 59.994 52.381 0.00 0.00 45.67 3.36
123 124 0.395724 CCAAGGGCATAGGTTGGTCC 60.396 60.000 0.00 0.00 36.70 4.46
124 125 3.191182 CCAAGGGCATAGGTTGGTC 57.809 57.895 0.00 0.00 36.70 4.02
136 137 2.332654 GCTGTACGGTTGCCAAGGG 61.333 63.158 3.10 0.00 0.00 3.95
137 138 2.677003 CGCTGTACGGTTGCCAAGG 61.677 63.158 3.10 0.00 38.44 3.61
138 139 2.860293 CGCTGTACGGTTGCCAAG 59.140 61.111 3.10 0.00 38.44 3.61
139 140 3.350612 GCGCTGTACGGTTGCCAA 61.351 61.111 0.00 0.00 43.93 4.52
143 144 3.823421 CGACGCGCTGTACGGTTG 61.823 66.667 5.73 0.00 43.93 3.77
152 153 4.980805 TTTTCTGGCCGACGCGCT 62.981 61.111 5.73 0.00 35.02 5.92
153 154 4.445545 CTTTTCTGGCCGACGCGC 62.446 66.667 5.73 0.00 35.02 6.86
154 155 1.837538 TTTCTTTTCTGGCCGACGCG 61.838 55.000 3.53 3.53 35.02 6.01
155 156 0.110192 CTTTCTTTTCTGGCCGACGC 60.110 55.000 0.00 0.00 0.00 5.19
156 157 0.517316 CCTTTCTTTTCTGGCCGACG 59.483 55.000 0.00 0.00 0.00 5.12
157 158 1.892209 TCCTTTCTTTTCTGGCCGAC 58.108 50.000 0.00 0.00 0.00 4.79
158 159 2.504367 CTTCCTTTCTTTTCTGGCCGA 58.496 47.619 0.00 0.00 0.00 5.54
159 160 1.068264 GCTTCCTTTCTTTTCTGGCCG 60.068 52.381 0.00 0.00 0.00 6.13
160 161 1.068264 CGCTTCCTTTCTTTTCTGGCC 60.068 52.381 0.00 0.00 0.00 5.36
161 162 1.880027 TCGCTTCCTTTCTTTTCTGGC 59.120 47.619 0.00 0.00 0.00 4.85
162 163 4.006319 AGATCGCTTCCTTTCTTTTCTGG 58.994 43.478 0.00 0.00 0.00 3.86
165 166 3.062774 CGGAGATCGCTTCCTTTCTTTTC 59.937 47.826 0.00 0.00 0.00 2.29
168 169 2.301577 CGGAGATCGCTTCCTTTCTT 57.698 50.000 0.00 0.00 0.00 2.52
180 181 0.596083 CCAGATCACACGCGGAGATC 60.596 60.000 22.13 22.13 38.70 2.75
182 183 1.934220 GACCAGATCACACGCGGAGA 61.934 60.000 12.47 5.33 0.00 3.71
183 184 1.517257 GACCAGATCACACGCGGAG 60.517 63.158 12.47 4.93 0.00 4.63
184 185 2.571757 GACCAGATCACACGCGGA 59.428 61.111 12.47 0.00 0.00 5.54
185 186 2.509336 GGACCAGATCACACGCGG 60.509 66.667 12.47 1.27 0.00 6.46
186 187 1.517257 GAGGACCAGATCACACGCG 60.517 63.158 3.53 3.53 0.00 6.01
187 188 0.459237 CAGAGGACCAGATCACACGC 60.459 60.000 0.00 0.00 0.00 5.34
188 189 0.459237 GCAGAGGACCAGATCACACG 60.459 60.000 0.00 0.00 0.00 4.49
189 190 0.901124 AGCAGAGGACCAGATCACAC 59.099 55.000 0.00 0.00 0.00 3.82
190 191 1.552337 GAAGCAGAGGACCAGATCACA 59.448 52.381 0.00 0.00 0.00 3.58
191 192 1.470632 CGAAGCAGAGGACCAGATCAC 60.471 57.143 0.00 0.00 0.00 3.06
195 196 2.268022 GTCGAAGCAGAGGACCAGA 58.732 57.895 0.00 0.00 0.00 3.86
196 197 4.900154 GTCGAAGCAGAGGACCAG 57.100 61.111 0.00 0.00 0.00 4.00
199 200 1.513622 GGAGGTCGAAGCAGAGGAC 59.486 63.158 0.00 0.00 0.00 3.85
200 201 2.046864 CGGAGGTCGAAGCAGAGGA 61.047 63.158 0.00 0.00 42.43 3.71
201 202 2.492090 CGGAGGTCGAAGCAGAGG 59.508 66.667 0.00 0.00 42.43 3.69
214 215 4.421479 ACGCGCTGAAGACCGGAG 62.421 66.667 9.46 0.00 0.00 4.63
215 216 4.415332 GACGCGCTGAAGACCGGA 62.415 66.667 9.46 0.00 0.00 5.14
216 217 4.717629 TGACGCGCTGAAGACCGG 62.718 66.667 5.73 0.00 0.00 5.28
218 219 3.482783 GCTGACGCGCTGAAGACC 61.483 66.667 5.73 0.00 0.00 3.85
229 230 3.417275 CTACAGAGCCCGGCTGACG 62.417 68.421 19.21 7.23 39.88 4.35
230 231 2.496817 CTACAGAGCCCGGCTGAC 59.503 66.667 19.21 2.80 39.88 3.51
231 232 2.759973 CCTACAGAGCCCGGCTGA 60.760 66.667 19.21 0.00 39.88 4.26
232 233 4.537433 GCCTACAGAGCCCGGCTG 62.537 72.222 19.21 6.91 39.88 4.85
234 235 4.228567 GAGCCTACAGAGCCCGGC 62.229 72.222 0.00 0.00 42.79 6.13
235 236 2.443016 AGAGCCTACAGAGCCCGG 60.443 66.667 0.00 0.00 0.00 5.73
236 237 1.452145 GAGAGAGCCTACAGAGCCCG 61.452 65.000 0.00 0.00 0.00 6.13
237 238 1.112916 GGAGAGAGCCTACAGAGCCC 61.113 65.000 0.00 0.00 0.00 5.19
238 239 1.452145 CGGAGAGAGCCTACAGAGCC 61.452 65.000 0.00 0.00 0.00 4.70
240 241 1.134220 AGTCGGAGAGAGCCTACAGAG 60.134 57.143 0.00 0.00 36.95 3.35
241 242 0.913205 AGTCGGAGAGAGCCTACAGA 59.087 55.000 0.00 0.00 36.95 3.41
242 243 1.021202 CAGTCGGAGAGAGCCTACAG 58.979 60.000 0.00 0.00 36.95 2.74
243 244 0.328592 ACAGTCGGAGAGAGCCTACA 59.671 55.000 0.00 0.00 36.95 2.74
244 245 0.736053 CACAGTCGGAGAGAGCCTAC 59.264 60.000 0.00 0.00 36.95 3.18
246 247 1.680651 CCACAGTCGGAGAGAGCCT 60.681 63.158 0.00 0.00 36.95 4.58
247 248 2.888863 CCACAGTCGGAGAGAGCC 59.111 66.667 0.00 0.00 36.95 4.70
248 249 2.183046 GCCACAGTCGGAGAGAGC 59.817 66.667 0.00 0.00 36.95 4.09
249 250 2.716017 GGGCCACAGTCGGAGAGAG 61.716 68.421 4.39 0.00 36.95 3.20
250 251 2.680352 GGGCCACAGTCGGAGAGA 60.680 66.667 4.39 0.00 36.95 3.10
251 252 2.681778 AGGGCCACAGTCGGAGAG 60.682 66.667 6.18 0.00 36.95 3.20
252 253 2.680352 GAGGGCCACAGTCGGAGA 60.680 66.667 6.18 0.00 0.00 3.71
255 256 2.187946 GATGAGGGCCACAGTCGG 59.812 66.667 10.06 0.00 0.00 4.79
256 257 1.153489 CAGATGAGGGCCACAGTCG 60.153 63.158 10.06 0.00 0.00 4.18
257 258 0.615331 TTCAGATGAGGGCCACAGTC 59.385 55.000 10.06 7.42 0.00 3.51
259 260 2.205022 TTTTCAGATGAGGGCCACAG 57.795 50.000 10.06 0.00 0.00 3.66
260 261 2.673775 TTTTTCAGATGAGGGCCACA 57.326 45.000 6.01 6.01 0.00 4.17
335 4062 6.258727 CACATATATAACAATCGAGGATGCCC 59.741 42.308 0.00 0.00 0.00 5.36
459 4194 2.367567 GAGCCCGTATACCCTCATGAAA 59.632 50.000 0.00 0.00 0.00 2.69
592 4334 8.389586 AGTTTTGTTTTCTTTAACTTACGCAG 57.610 30.769 0.00 0.00 0.00 5.18
624 4366 5.424252 CCTAGCCGATCCCCTAAATATAACA 59.576 44.000 0.00 0.00 0.00 2.41
693 4935 6.850234 TCCCCTATAGAAGTTTCTAGTCGAT 58.150 40.000 0.00 0.00 42.55 3.59
746 5000 5.522460 TCCACGAAAGTTCAGACTAGTTTTG 59.478 40.000 0.00 0.00 46.40 2.44
1273 6096 1.228245 CGATGGCGGATTCCCCAAT 60.228 57.895 14.54 0.00 34.25 3.16
1474 6571 3.195825 GTGGTGTAGGATGCAAGACTACT 59.804 47.826 19.78 1.90 38.27 2.57
1785 9222 0.468214 TTGGTCCGCAAAACATCCCA 60.468 50.000 0.00 0.00 0.00 4.37
1924 9408 1.207089 CACATCAGTACACCCACGGAT 59.793 52.381 0.00 0.00 34.25 4.18


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

AutoCloner maintained by Alex Coulton.