Multiple sequence alignment - TraesCS3D01G212000

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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 TraesCS3D01G212000 chr3D 100.000 3643 0 0 1 3643 283674806 283678448 0.000000e+00 6728
1 TraesCS3D01G212000 chr3B 95.501 3401 72 20 288 3643 377709864 377713228 0.000000e+00 5358
2 TraesCS3D01G212000 chr3B 80.460 174 34 0 1667 1840 650071776 650071949 2.280000e-27 134
3 TraesCS3D01G212000 chr3A 95.041 2823 62 24 292 3059 371321223 371324022 0.000000e+00 4366
4 TraesCS3D01G212000 chr3A 79.385 553 73 24 3115 3643 371325773 371326308 5.790000e-93 351
5 TraesCS3D01G212000 chr3A 76.923 299 61 5 1546 1840 630807069 630807363 2.910000e-36 163
6 TraesCS3D01G212000 chr1A 81.468 1063 179 14 1536 2586 589791469 589792525 0.000000e+00 856
7 TraesCS3D01G212000 chr1D 81.144 1066 177 20 1536 2586 491794953 491796009 0.000000e+00 833
8 TraesCS3D01G212000 chr1B 80.316 1077 194 15 1536 2600 684098148 684097078 0.000000e+00 798


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 TraesCS3D01G212000 chr3D 283674806 283678448 3642 False 6728.0 6728 100.000 1 3643 1 chr3D.!!$F1 3642
1 TraesCS3D01G212000 chr3B 377709864 377713228 3364 False 5358.0 5358 95.501 288 3643 1 chr3B.!!$F1 3355
2 TraesCS3D01G212000 chr3A 371321223 371326308 5085 False 2358.5 4366 87.213 292 3643 2 chr3A.!!$F2 3351
3 TraesCS3D01G212000 chr1A 589791469 589792525 1056 False 856.0 856 81.468 1536 2586 1 chr1A.!!$F1 1050
4 TraesCS3D01G212000 chr1D 491794953 491796009 1056 False 833.0 833 81.144 1536 2586 1 chr1D.!!$F1 1050
5 TraesCS3D01G212000 chr1B 684097078 684098148 1070 True 798.0 798 80.316 1536 2600 1 chr1B.!!$R1 1064

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
58 59 0.036306 GACAGAAGGAAAAGCCGGGA 59.964 55.0 2.18 0.0 43.43 5.14 F
93 94 0.036875 ACAAAAGGAGAGGAAGCCGG 59.963 55.0 0.00 0.0 0.00 6.13 F
267 268 0.324091 GTCCGGGTAGTCTGAAGGGA 60.324 60.0 0.00 0.0 0.00 4.20 F
428 429 0.546598 GCTGTAGGCCTACCACCAAT 59.453 55.0 34.76 0.0 39.06 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1397 0.323302 TCATGGCCTGCGACTTGTTA 59.677 50.000 3.32 0.0 0.00 2.41 R
1605 1661 2.262915 CGCCGAAACTCTGCCTCT 59.737 61.111 0.00 0.0 0.00 3.69 R
2626 2688 8.682710 GCATGTTTAATTTATCTGTACCCAAGA 58.317 33.333 0.00 0.0 0.00 3.02 R
2754 2818 1.201647 GTAACCGACAGCAGCTACTGA 59.798 52.381 21.00 0.0 40.25 3.41 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
21 22 2.496899 TCCAGAAGCCATGGAGAAAC 57.503 50.000 18.40 0.00 41.96 2.78
22 23 1.704628 TCCAGAAGCCATGGAGAAACA 59.295 47.619 18.40 0.00 41.96 2.83
23 24 1.815003 CCAGAAGCCATGGAGAAACAC 59.185 52.381 18.40 0.00 40.51 3.32
24 25 1.466167 CAGAAGCCATGGAGAAACACG 59.534 52.381 18.40 0.00 0.00 4.49
25 26 0.169009 GAAGCCATGGAGAAACACGC 59.831 55.000 18.40 0.00 0.00 5.34
26 27 1.244019 AAGCCATGGAGAAACACGCC 61.244 55.000 18.40 0.00 38.95 5.68
27 28 2.700773 GCCATGGAGAAACACGCCC 61.701 63.158 18.40 0.00 37.67 6.13
28 29 2.046285 CCATGGAGAAACACGCCCC 61.046 63.158 5.56 0.00 37.67 5.80
29 30 2.046314 ATGGAGAAACACGCCCCG 60.046 61.111 0.00 0.00 37.67 5.73
30 31 2.589157 ATGGAGAAACACGCCCCGA 61.589 57.895 0.00 0.00 37.67 5.14
31 32 2.434359 GGAGAAACACGCCCCGAG 60.434 66.667 0.00 0.00 32.23 4.63
32 33 3.119096 GAGAAACACGCCCCGAGC 61.119 66.667 0.00 0.00 38.52 5.03
45 46 4.753877 CGAGCGACGCCGACAGAA 62.754 66.667 17.79 0.00 38.22 3.02
46 47 2.876645 GAGCGACGCCGACAGAAG 60.877 66.667 17.79 0.00 38.22 2.85
47 48 4.421479 AGCGACGCCGACAGAAGG 62.421 66.667 17.79 0.00 38.22 3.46
48 49 4.415332 GCGACGCCGACAGAAGGA 62.415 66.667 9.14 0.00 38.22 3.36
49 50 2.257371 CGACGCCGACAGAAGGAA 59.743 61.111 0.00 0.00 38.22 3.36
50 51 1.372499 CGACGCCGACAGAAGGAAA 60.372 57.895 0.00 0.00 38.22 3.13
51 52 0.942410 CGACGCCGACAGAAGGAAAA 60.942 55.000 0.00 0.00 38.22 2.29
52 53 0.790814 GACGCCGACAGAAGGAAAAG 59.209 55.000 0.00 0.00 0.00 2.27
53 54 1.228657 ACGCCGACAGAAGGAAAAGC 61.229 55.000 0.00 0.00 0.00 3.51
54 55 1.876664 GCCGACAGAAGGAAAAGCC 59.123 57.895 0.00 0.00 0.00 4.35
55 56 1.912371 GCCGACAGAAGGAAAAGCCG 61.912 60.000 0.00 0.00 43.43 5.52
56 57 1.298859 CCGACAGAAGGAAAAGCCGG 61.299 60.000 0.00 0.00 43.43 6.13
57 58 1.298859 CGACAGAAGGAAAAGCCGGG 61.299 60.000 2.18 0.00 43.43 5.73
58 59 0.036306 GACAGAAGGAAAAGCCGGGA 59.964 55.000 2.18 0.00 43.43 5.14
59 60 0.250770 ACAGAAGGAAAAGCCGGGAC 60.251 55.000 2.18 0.00 43.43 4.46
60 61 0.960861 CAGAAGGAAAAGCCGGGACC 60.961 60.000 2.18 0.00 43.43 4.46
61 62 1.677966 GAAGGAAAAGCCGGGACCC 60.678 63.158 2.18 0.00 43.43 4.46
80 81 4.383602 CGTGGCCGCCGACAAAAG 62.384 66.667 11.56 0.00 0.00 2.27
81 82 4.038080 GTGGCCGCCGACAAAAGG 62.038 66.667 4.45 0.00 0.00 3.11
82 83 4.257654 TGGCCGCCGACAAAAGGA 62.258 61.111 4.58 0.00 0.00 3.36
83 84 3.431725 GGCCGCCGACAAAAGGAG 61.432 66.667 0.00 0.00 0.00 3.69
84 85 2.358247 GCCGCCGACAAAAGGAGA 60.358 61.111 0.00 0.00 0.00 3.71
85 86 2.391389 GCCGCCGACAAAAGGAGAG 61.391 63.158 0.00 0.00 0.00 3.20
86 87 1.741770 CCGCCGACAAAAGGAGAGG 60.742 63.158 0.00 0.00 0.00 3.69
87 88 1.292223 CGCCGACAAAAGGAGAGGA 59.708 57.895 0.00 0.00 0.00 3.71
88 89 0.320421 CGCCGACAAAAGGAGAGGAA 60.320 55.000 0.00 0.00 0.00 3.36
89 90 1.443802 GCCGACAAAAGGAGAGGAAG 58.556 55.000 0.00 0.00 0.00 3.46
90 91 1.443802 CCGACAAAAGGAGAGGAAGC 58.556 55.000 0.00 0.00 0.00 3.86
91 92 1.443802 CGACAAAAGGAGAGGAAGCC 58.556 55.000 0.00 0.00 0.00 4.35
92 93 1.443802 GACAAAAGGAGAGGAAGCCG 58.556 55.000 0.00 0.00 0.00 5.52
93 94 0.036875 ACAAAAGGAGAGGAAGCCGG 59.963 55.000 0.00 0.00 0.00 6.13
94 95 0.678048 CAAAAGGAGAGGAAGCCGGG 60.678 60.000 2.18 0.00 0.00 5.73
95 96 1.853250 AAAAGGAGAGGAAGCCGGGG 61.853 60.000 2.18 0.00 0.00 5.73
173 174 3.291383 CGAGGCTCGCTAGGGGAG 61.291 72.222 25.31 7.15 43.96 4.30
174 175 2.915137 GAGGCTCGCTAGGGGAGG 60.915 72.222 6.99 0.00 41.88 4.30
175 176 4.548513 AGGCTCGCTAGGGGAGGG 62.549 72.222 6.99 0.00 41.88 4.30
178 179 4.548513 CTCGCTAGGGGAGGGGCT 62.549 72.222 6.99 0.00 38.66 5.19
179 180 4.541648 TCGCTAGGGGAGGGGCTC 62.542 72.222 6.99 0.00 38.64 4.70
182 183 4.548513 CTAGGGGAGGGGCTCGCT 62.549 72.222 0.00 0.00 42.06 4.93
183 184 4.860881 TAGGGGAGGGGCTCGCTG 62.861 72.222 0.00 0.00 42.06 5.18
206 207 5.648330 GGGGGATAAACCAAGAATAGTCT 57.352 43.478 0.00 0.00 41.20 3.24
207 208 5.622180 GGGGGATAAACCAAGAATAGTCTC 58.378 45.833 0.00 0.00 41.20 3.36
208 209 5.456330 GGGGGATAAACCAAGAATAGTCTCC 60.456 48.000 0.00 0.00 41.20 3.71
209 210 5.369993 GGGGATAAACCAAGAATAGTCTCCT 59.630 44.000 0.00 0.00 41.20 3.69
210 211 6.292150 GGGATAAACCAAGAATAGTCTCCTG 58.708 44.000 0.00 0.00 41.20 3.86
211 212 6.292150 GGATAAACCAAGAATAGTCTCCTGG 58.708 44.000 8.95 8.95 37.66 4.45
212 213 3.636153 AACCAAGAATAGTCTCCTGGC 57.364 47.619 10.19 0.00 35.81 4.85
213 214 1.482593 ACCAAGAATAGTCTCCTGGCG 59.517 52.381 10.19 0.00 35.81 5.69
214 215 1.757118 CCAAGAATAGTCTCCTGGCGA 59.243 52.381 0.00 0.00 30.70 5.54
215 216 2.168521 CCAAGAATAGTCTCCTGGCGAA 59.831 50.000 0.00 0.00 30.70 4.70
216 217 3.369471 CCAAGAATAGTCTCCTGGCGAAA 60.369 47.826 0.00 0.00 30.70 3.46
217 218 4.253685 CAAGAATAGTCTCCTGGCGAAAA 58.746 43.478 0.00 0.00 30.70 2.29
218 219 4.553330 AGAATAGTCTCCTGGCGAAAAA 57.447 40.909 0.00 0.00 0.00 1.94
258 259 3.303049 CCTATGTTAAGGTCCGGGTAGT 58.697 50.000 0.00 0.00 31.46 2.73
259 260 3.320256 CCTATGTTAAGGTCCGGGTAGTC 59.680 52.174 0.00 0.00 31.46 2.59
260 261 2.610438 TGTTAAGGTCCGGGTAGTCT 57.390 50.000 0.00 0.00 0.00 3.24
261 262 2.173519 TGTTAAGGTCCGGGTAGTCTG 58.826 52.381 0.00 0.00 0.00 3.51
262 263 2.225091 TGTTAAGGTCCGGGTAGTCTGA 60.225 50.000 0.00 0.00 0.00 3.27
263 264 2.827921 GTTAAGGTCCGGGTAGTCTGAA 59.172 50.000 0.00 0.00 0.00 3.02
264 265 1.558233 AAGGTCCGGGTAGTCTGAAG 58.442 55.000 0.00 0.00 0.00 3.02
265 266 0.324460 AGGTCCGGGTAGTCTGAAGG 60.324 60.000 0.00 0.00 0.00 3.46
266 267 1.328430 GGTCCGGGTAGTCTGAAGGG 61.328 65.000 0.00 0.00 0.00 3.95
267 268 0.324091 GTCCGGGTAGTCTGAAGGGA 60.324 60.000 0.00 0.00 0.00 4.20
268 269 0.635009 TCCGGGTAGTCTGAAGGGAT 59.365 55.000 0.00 0.00 0.00 3.85
269 270 0.753262 CCGGGTAGTCTGAAGGGATG 59.247 60.000 0.00 0.00 0.00 3.51
270 271 1.688311 CCGGGTAGTCTGAAGGGATGA 60.688 57.143 0.00 0.00 0.00 2.92
271 272 2.320781 CGGGTAGTCTGAAGGGATGAT 58.679 52.381 0.00 0.00 0.00 2.45
272 273 2.297597 CGGGTAGTCTGAAGGGATGATC 59.702 54.545 0.00 0.00 0.00 2.92
273 274 2.297597 GGGTAGTCTGAAGGGATGATCG 59.702 54.545 0.00 0.00 0.00 3.69
274 275 2.297597 GGTAGTCTGAAGGGATGATCGG 59.702 54.545 0.00 0.00 0.00 4.18
275 276 2.461300 AGTCTGAAGGGATGATCGGA 57.539 50.000 0.00 0.00 0.00 4.55
276 277 2.752030 AGTCTGAAGGGATGATCGGAA 58.248 47.619 0.00 0.00 0.00 4.30
277 278 2.432510 AGTCTGAAGGGATGATCGGAAC 59.567 50.000 0.00 0.00 0.00 3.62
278 279 2.168521 GTCTGAAGGGATGATCGGAACA 59.831 50.000 0.00 0.00 0.00 3.18
279 280 2.432146 TCTGAAGGGATGATCGGAACAG 59.568 50.000 0.00 0.00 0.00 3.16
280 281 2.432146 CTGAAGGGATGATCGGAACAGA 59.568 50.000 0.00 0.00 0.00 3.41
281 282 3.041211 TGAAGGGATGATCGGAACAGAT 58.959 45.455 0.00 0.00 0.00 2.90
282 283 3.181462 TGAAGGGATGATCGGAACAGATG 60.181 47.826 0.00 0.00 0.00 2.90
283 284 2.682594 AGGGATGATCGGAACAGATGA 58.317 47.619 0.00 0.00 0.00 2.92
284 285 2.366916 AGGGATGATCGGAACAGATGAC 59.633 50.000 0.00 0.00 0.00 3.06
285 286 2.103094 GGGATGATCGGAACAGATGACA 59.897 50.000 0.00 0.00 0.00 3.58
286 287 3.388308 GGATGATCGGAACAGATGACAG 58.612 50.000 0.00 0.00 0.00 3.51
385 386 4.764896 GTTTCTCGAACCCCGTGT 57.235 55.556 0.00 0.00 39.75 4.49
428 429 0.546598 GCTGTAGGCCTACCACCAAT 59.453 55.000 34.76 0.00 39.06 3.16
461 485 8.579863 AGTTTGTACGTATTACTCCAGTTTACT 58.420 33.333 0.00 0.00 0.00 2.24
517 547 1.628340 TCATCCCATTGACCACGTTCT 59.372 47.619 0.00 0.00 0.00 3.01
749 785 2.815647 CGGTCTCGCTTTCCTGCC 60.816 66.667 0.00 0.00 0.00 4.85
750 786 2.665603 GGTCTCGCTTTCCTGCCT 59.334 61.111 0.00 0.00 0.00 4.75
914 953 4.684703 TCTCGTTTCGTTTCCTCTTCAATC 59.315 41.667 0.00 0.00 0.00 2.67
915 954 3.427528 TCGTTTCGTTTCCTCTTCAATCG 59.572 43.478 0.00 0.00 0.00 3.34
916 955 3.479949 GTTTCGTTTCCTCTTCAATCGC 58.520 45.455 0.00 0.00 0.00 4.58
917 956 2.743636 TCGTTTCCTCTTCAATCGCT 57.256 45.000 0.00 0.00 0.00 4.93
918 957 3.040147 TCGTTTCCTCTTCAATCGCTT 57.960 42.857 0.00 0.00 0.00 4.68
1341 1397 2.490217 CTCGAGTCCAACGCCGAT 59.510 61.111 3.62 0.00 30.67 4.18
1392 1448 0.750911 CCAAGATGGAGGGCAGCTTC 60.751 60.000 0.00 0.00 40.96 3.86
1398 1454 2.124983 GAGGGCAGCTTCGATGCA 60.125 61.111 23.42 0.00 45.68 3.96
1605 1661 1.912220 CAATAGCCCCGACTTCCCA 59.088 57.895 0.00 0.00 0.00 4.37
2626 2688 1.614824 CTCCTGGCCCTCTCCTTGT 60.615 63.158 0.00 0.00 0.00 3.16
2754 2818 7.484975 TGTAAACATTCTGTGGAAAATTTCGT 58.515 30.769 0.00 0.00 34.90 3.85
3041 3125 0.392998 AAGGTATGCGGCTGTTCTGG 60.393 55.000 0.00 0.00 0.00 3.86
3045 3129 0.613260 TATGCGGCTGTTCTGGTTCT 59.387 50.000 0.00 0.00 0.00 3.01
3080 3164 5.757320 TGACCTTTTTGTGTGCCAAATATTG 59.243 36.000 0.00 0.00 42.45 1.90
3081 3165 5.923204 ACCTTTTTGTGTGCCAAATATTGA 58.077 33.333 0.00 0.00 42.45 2.57
3082 3166 5.757808 ACCTTTTTGTGTGCCAAATATTGAC 59.242 36.000 0.00 0.00 42.45 3.18
3083 3167 5.757320 CCTTTTTGTGTGCCAAATATTGACA 59.243 36.000 0.00 0.00 42.45 3.58
3084 3168 6.259608 CCTTTTTGTGTGCCAAATATTGACAA 59.740 34.615 0.00 0.00 42.45 3.18
3085 3169 7.201679 CCTTTTTGTGTGCCAAATATTGACAAA 60.202 33.333 0.00 0.00 42.45 2.83
3086 3170 7.798596 TTTTGTGTGCCAAATATTGACAAAT 57.201 28.000 0.00 0.00 42.45 2.32
3087 3171 8.893219 TTTTGTGTGCCAAATATTGACAAATA 57.107 26.923 0.00 0.00 42.45 1.40
3088 3172 9.499479 TTTTGTGTGCCAAATATTGACAAATAT 57.501 25.926 0.00 0.00 42.45 1.28
3089 3173 9.499479 TTTGTGTGCCAAATATTGACAAATATT 57.501 25.926 0.00 0.00 46.39 1.28
3132 4929 8.906867 CATTACCAGATGACATTAGTGGAAAAT 58.093 33.333 15.69 12.10 32.26 1.82
3157 4954 3.492313 GCGAAAACAAAATCGATGCTCT 58.508 40.909 0.00 0.00 41.43 4.09
3293 5092 1.102154 CCTCAAATTGCCCGCATACA 58.898 50.000 0.00 0.00 0.00 2.29
3344 5155 5.537300 GACAGGTATATGTCCATGTCTGT 57.463 43.478 15.36 0.00 43.12 3.41
3345 5156 5.918608 GACAGGTATATGTCCATGTCTGTT 58.081 41.667 15.36 0.00 43.12 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.948315 GTTTCTCCATGGCTTCTGGATC 59.052 50.000 6.96 0.00 41.83 3.36
1 2 2.309755 TGTTTCTCCATGGCTTCTGGAT 59.690 45.455 6.96 0.00 41.83 3.41
2 3 1.704628 TGTTTCTCCATGGCTTCTGGA 59.295 47.619 6.96 4.40 40.49 3.86
3 4 1.815003 GTGTTTCTCCATGGCTTCTGG 59.185 52.381 6.96 0.00 34.93 3.86
4 5 1.466167 CGTGTTTCTCCATGGCTTCTG 59.534 52.381 6.96 0.00 0.00 3.02
5 6 1.813513 CGTGTTTCTCCATGGCTTCT 58.186 50.000 6.96 0.00 0.00 2.85
6 7 0.169009 GCGTGTTTCTCCATGGCTTC 59.831 55.000 6.96 0.00 0.00 3.86
7 8 1.244019 GGCGTGTTTCTCCATGGCTT 61.244 55.000 6.96 0.00 42.07 4.35
8 9 1.675641 GGCGTGTTTCTCCATGGCT 60.676 57.895 6.96 0.00 42.07 4.75
9 10 2.700773 GGGCGTGTTTCTCCATGGC 61.701 63.158 6.96 0.00 43.95 4.40
10 11 2.046285 GGGGCGTGTTTCTCCATGG 61.046 63.158 4.97 4.97 0.00 3.66
11 12 2.398554 CGGGGCGTGTTTCTCCATG 61.399 63.158 0.00 0.00 0.00 3.66
12 13 2.046314 CGGGGCGTGTTTCTCCAT 60.046 61.111 0.00 0.00 0.00 3.41
13 14 3.234630 CTCGGGGCGTGTTTCTCCA 62.235 63.158 0.00 0.00 0.00 3.86
14 15 2.434359 CTCGGGGCGTGTTTCTCC 60.434 66.667 0.00 0.00 0.00 3.71
15 16 3.119096 GCTCGGGGCGTGTTTCTC 61.119 66.667 0.00 0.00 0.00 2.87
28 29 4.753877 TTCTGTCGGCGTCGCTCG 62.754 66.667 18.11 18.14 43.12 5.03
29 30 2.876645 CTTCTGTCGGCGTCGCTC 60.877 66.667 18.11 6.41 36.13 5.03
30 31 4.421479 CCTTCTGTCGGCGTCGCT 62.421 66.667 18.11 0.00 36.13 4.93
31 32 3.909258 TTCCTTCTGTCGGCGTCGC 62.909 63.158 9.22 9.22 36.13 5.19
32 33 0.942410 TTTTCCTTCTGTCGGCGTCG 60.942 55.000 1.15 1.15 37.82 5.12
33 34 0.790814 CTTTTCCTTCTGTCGGCGTC 59.209 55.000 6.85 0.72 0.00 5.19
34 35 1.228657 GCTTTTCCTTCTGTCGGCGT 61.229 55.000 6.85 0.00 0.00 5.68
35 36 1.497722 GCTTTTCCTTCTGTCGGCG 59.502 57.895 0.00 0.00 0.00 6.46
36 37 1.876664 GGCTTTTCCTTCTGTCGGC 59.123 57.895 0.00 0.00 0.00 5.54
37 38 1.298859 CCGGCTTTTCCTTCTGTCGG 61.299 60.000 0.00 0.00 0.00 4.79
38 39 1.298859 CCCGGCTTTTCCTTCTGTCG 61.299 60.000 0.00 0.00 0.00 4.35
39 40 0.036306 TCCCGGCTTTTCCTTCTGTC 59.964 55.000 0.00 0.00 0.00 3.51
40 41 0.250770 GTCCCGGCTTTTCCTTCTGT 60.251 55.000 0.00 0.00 0.00 3.41
41 42 0.960861 GGTCCCGGCTTTTCCTTCTG 60.961 60.000 0.00 0.00 0.00 3.02
42 43 1.379146 GGTCCCGGCTTTTCCTTCT 59.621 57.895 0.00 0.00 0.00 2.85
43 44 1.677966 GGGTCCCGGCTTTTCCTTC 60.678 63.158 0.00 0.00 0.00 3.46
44 45 2.439245 GGGTCCCGGCTTTTCCTT 59.561 61.111 0.00 0.00 0.00 3.36
45 46 4.029809 CGGGTCCCGGCTTTTCCT 62.030 66.667 23.59 0.00 44.15 3.36
63 64 4.383602 CTTTTGTCGGCGGCCACG 62.384 66.667 20.71 10.37 44.63 4.94
64 65 4.038080 CCTTTTGTCGGCGGCCAC 62.038 66.667 20.71 16.04 0.00 5.01
65 66 4.257654 TCCTTTTGTCGGCGGCCA 62.258 61.111 20.71 1.96 0.00 5.36
66 67 3.431725 CTCCTTTTGTCGGCGGCC 61.432 66.667 9.84 9.54 0.00 6.13
67 68 2.358247 TCTCCTTTTGTCGGCGGC 60.358 61.111 3.62 3.62 0.00 6.53
68 69 1.741770 CCTCTCCTTTTGTCGGCGG 60.742 63.158 7.21 0.00 0.00 6.13
69 70 0.320421 TTCCTCTCCTTTTGTCGGCG 60.320 55.000 0.00 0.00 0.00 6.46
70 71 1.443802 CTTCCTCTCCTTTTGTCGGC 58.556 55.000 0.00 0.00 0.00 5.54
71 72 1.443802 GCTTCCTCTCCTTTTGTCGG 58.556 55.000 0.00 0.00 0.00 4.79
72 73 1.443802 GGCTTCCTCTCCTTTTGTCG 58.556 55.000 0.00 0.00 0.00 4.35
73 74 1.443802 CGGCTTCCTCTCCTTTTGTC 58.556 55.000 0.00 0.00 0.00 3.18
74 75 0.036875 CCGGCTTCCTCTCCTTTTGT 59.963 55.000 0.00 0.00 0.00 2.83
75 76 0.678048 CCCGGCTTCCTCTCCTTTTG 60.678 60.000 0.00 0.00 0.00 2.44
76 77 1.685820 CCCGGCTTCCTCTCCTTTT 59.314 57.895 0.00 0.00 0.00 2.27
77 78 2.301738 CCCCGGCTTCCTCTCCTTT 61.302 63.158 0.00 0.00 0.00 3.11
78 79 2.689034 CCCCGGCTTCCTCTCCTT 60.689 66.667 0.00 0.00 0.00 3.36
114 115 4.767255 CAGCGTCCACCCTGCCTC 62.767 72.222 0.00 0.00 0.00 4.70
156 157 3.291383 CTCCCCTAGCGAGCCTCG 61.291 72.222 10.36 10.36 43.89 4.63
157 158 2.915137 CCTCCCCTAGCGAGCCTC 60.915 72.222 0.00 0.00 0.00 4.70
158 159 4.548513 CCCTCCCCTAGCGAGCCT 62.549 72.222 0.00 0.00 0.00 4.58
161 162 4.548513 AGCCCCTCCCCTAGCGAG 62.549 72.222 0.00 0.00 0.00 5.03
162 163 4.541648 GAGCCCCTCCCCTAGCGA 62.542 72.222 0.00 0.00 0.00 4.93
165 166 4.548513 AGCGAGCCCCTCCCCTAG 62.549 72.222 0.00 0.00 0.00 3.02
166 167 4.860881 CAGCGAGCCCCTCCCCTA 62.861 72.222 0.00 0.00 0.00 3.53
184 185 5.456330 GGAGACTATTCTTGGTTTATCCCCC 60.456 48.000 0.00 0.00 30.52 5.40
185 186 5.369993 AGGAGACTATTCTTGGTTTATCCCC 59.630 44.000 0.00 0.00 40.61 4.81
186 187 6.292150 CAGGAGACTATTCTTGGTTTATCCC 58.708 44.000 0.00 0.00 40.21 3.85
187 188 6.292150 CCAGGAGACTATTCTTGGTTTATCC 58.708 44.000 0.00 0.00 38.97 2.59
188 189 5.760743 GCCAGGAGACTATTCTTGGTTTATC 59.239 44.000 6.12 0.00 43.99 1.75
189 190 5.685075 CGCCAGGAGACTATTCTTGGTTTAT 60.685 44.000 6.12 0.00 43.99 1.40
190 191 4.382685 CGCCAGGAGACTATTCTTGGTTTA 60.383 45.833 6.12 0.00 43.99 2.01
191 192 3.619979 CGCCAGGAGACTATTCTTGGTTT 60.620 47.826 6.12 0.00 43.99 3.27
192 193 2.093447 CGCCAGGAGACTATTCTTGGTT 60.093 50.000 6.12 0.00 43.99 3.67
193 194 1.482593 CGCCAGGAGACTATTCTTGGT 59.517 52.381 6.12 0.00 43.99 3.67
194 195 1.757118 TCGCCAGGAGACTATTCTTGG 59.243 52.381 0.00 0.28 44.70 3.61
195 196 3.526931 TTCGCCAGGAGACTATTCTTG 57.473 47.619 0.00 0.00 40.21 3.02
196 197 4.553330 TTTTCGCCAGGAGACTATTCTT 57.447 40.909 0.00 0.00 40.21 2.52
197 198 4.553330 TTTTTCGCCAGGAGACTATTCT 57.447 40.909 0.00 0.00 40.21 2.40
237 238 3.303049 ACTACCCGGACCTTAACATAGG 58.697 50.000 0.73 0.00 41.31 2.57
238 239 4.037684 CAGACTACCCGGACCTTAACATAG 59.962 50.000 0.73 0.00 0.00 2.23
239 240 3.956199 CAGACTACCCGGACCTTAACATA 59.044 47.826 0.73 0.00 0.00 2.29
240 241 2.764572 CAGACTACCCGGACCTTAACAT 59.235 50.000 0.73 0.00 0.00 2.71
241 242 2.173519 CAGACTACCCGGACCTTAACA 58.826 52.381 0.73 0.00 0.00 2.41
242 243 2.450476 TCAGACTACCCGGACCTTAAC 58.550 52.381 0.73 0.00 0.00 2.01
243 244 2.905415 TCAGACTACCCGGACCTTAA 57.095 50.000 0.73 0.00 0.00 1.85
244 245 2.622452 CCTTCAGACTACCCGGACCTTA 60.622 54.545 0.73 0.00 0.00 2.69
245 246 1.558233 CTTCAGACTACCCGGACCTT 58.442 55.000 0.73 0.00 0.00 3.50
246 247 0.324460 CCTTCAGACTACCCGGACCT 60.324 60.000 0.73 0.00 0.00 3.85
247 248 1.328430 CCCTTCAGACTACCCGGACC 61.328 65.000 0.73 0.00 0.00 4.46
248 249 0.324091 TCCCTTCAGACTACCCGGAC 60.324 60.000 0.73 0.00 0.00 4.79
249 250 0.635009 ATCCCTTCAGACTACCCGGA 59.365 55.000 0.73 0.00 0.00 5.14
250 251 0.753262 CATCCCTTCAGACTACCCGG 59.247 60.000 0.00 0.00 0.00 5.73
251 252 1.776662 TCATCCCTTCAGACTACCCG 58.223 55.000 0.00 0.00 0.00 5.28
252 253 2.297597 CGATCATCCCTTCAGACTACCC 59.702 54.545 0.00 0.00 0.00 3.69
253 254 2.297597 CCGATCATCCCTTCAGACTACC 59.702 54.545 0.00 0.00 0.00 3.18
254 255 3.223435 TCCGATCATCCCTTCAGACTAC 58.777 50.000 0.00 0.00 0.00 2.73
255 256 3.595190 TCCGATCATCCCTTCAGACTA 57.405 47.619 0.00 0.00 0.00 2.59
256 257 2.432510 GTTCCGATCATCCCTTCAGACT 59.567 50.000 0.00 0.00 0.00 3.24
257 258 2.168521 TGTTCCGATCATCCCTTCAGAC 59.831 50.000 0.00 0.00 0.00 3.51
258 259 2.432146 CTGTTCCGATCATCCCTTCAGA 59.568 50.000 0.00 0.00 0.00 3.27
259 260 2.432146 TCTGTTCCGATCATCCCTTCAG 59.568 50.000 0.00 0.00 0.00 3.02
260 261 2.466846 TCTGTTCCGATCATCCCTTCA 58.533 47.619 0.00 0.00 0.00 3.02
261 262 3.070159 TCATCTGTTCCGATCATCCCTTC 59.930 47.826 0.00 0.00 0.00 3.46
262 263 3.041211 TCATCTGTTCCGATCATCCCTT 58.959 45.455 0.00 0.00 0.00 3.95
263 264 2.366916 GTCATCTGTTCCGATCATCCCT 59.633 50.000 0.00 0.00 0.00 4.20
264 265 2.103094 TGTCATCTGTTCCGATCATCCC 59.897 50.000 0.00 0.00 0.00 3.85
265 266 3.181471 ACTGTCATCTGTTCCGATCATCC 60.181 47.826 0.00 0.00 0.00 3.51
266 267 3.801050 CACTGTCATCTGTTCCGATCATC 59.199 47.826 0.00 0.00 0.00 2.92
267 268 3.431346 CCACTGTCATCTGTTCCGATCAT 60.431 47.826 0.00 0.00 0.00 2.45
268 269 2.094026 CCACTGTCATCTGTTCCGATCA 60.094 50.000 0.00 0.00 0.00 2.92
269 270 2.544685 CCACTGTCATCTGTTCCGATC 58.455 52.381 0.00 0.00 0.00 3.69
270 271 1.208052 CCCACTGTCATCTGTTCCGAT 59.792 52.381 0.00 0.00 0.00 4.18
271 272 0.608130 CCCACTGTCATCTGTTCCGA 59.392 55.000 0.00 0.00 0.00 4.55
272 273 0.321671 ACCCACTGTCATCTGTTCCG 59.678 55.000 0.00 0.00 0.00 4.30
273 274 1.339151 GGACCCACTGTCATCTGTTCC 60.339 57.143 0.00 0.00 46.38 3.62
274 275 1.339151 GGGACCCACTGTCATCTGTTC 60.339 57.143 5.33 0.00 46.38 3.18
275 276 0.693049 GGGACCCACTGTCATCTGTT 59.307 55.000 5.33 0.00 46.38 3.16
276 277 0.178891 AGGGACCCACTGTCATCTGT 60.179 55.000 14.60 0.00 46.38 3.41
277 278 0.987294 AAGGGACCCACTGTCATCTG 59.013 55.000 14.60 0.00 46.38 2.90
278 279 0.987294 CAAGGGACCCACTGTCATCT 59.013 55.000 14.60 0.00 46.38 2.90
279 280 0.984230 TCAAGGGACCCACTGTCATC 59.016 55.000 14.60 0.00 46.38 2.92
280 281 0.987294 CTCAAGGGACCCACTGTCAT 59.013 55.000 14.60 0.00 46.38 3.06
281 282 1.127567 CCTCAAGGGACCCACTGTCA 61.128 60.000 14.60 0.00 46.38 3.58
282 283 1.679898 CCTCAAGGGACCCACTGTC 59.320 63.158 14.60 0.00 43.67 3.51
283 284 2.529744 GCCTCAAGGGACCCACTGT 61.530 63.158 14.60 0.00 37.23 3.55
284 285 1.783250 AAGCCTCAAGGGACCCACTG 61.783 60.000 14.60 9.85 37.23 3.66
285 286 1.464198 AAGCCTCAAGGGACCCACT 60.464 57.895 14.60 0.00 37.23 4.00
286 287 1.303643 CAAGCCTCAAGGGACCCAC 60.304 63.158 14.60 0.00 37.23 4.61
385 386 4.841617 ATCGAGAGCTGGGCCGGA 62.842 66.667 18.84 0.00 0.00 5.14
428 429 7.710044 TGGAGTAATACGTACAAACTGTCAAAA 59.290 33.333 10.14 0.00 34.88 2.44
517 547 1.342672 GGGAATGGGGACTAGCGGAA 61.343 60.000 0.00 0.00 0.00 4.30
749 785 3.254411 GCTTTTTGGACAAGGAAGAGGAG 59.746 47.826 11.81 0.00 0.00 3.69
750 786 3.222603 GCTTTTTGGACAAGGAAGAGGA 58.777 45.455 11.81 0.00 0.00 3.71
1341 1397 0.323302 TCATGGCCTGCGACTTGTTA 59.677 50.000 3.32 0.00 0.00 2.41
1392 1448 2.951745 GAGTCGGCGTCTGCATCG 60.952 66.667 12.12 7.00 45.35 3.84
1605 1661 2.262915 CGCCGAAACTCTGCCTCT 59.737 61.111 0.00 0.00 0.00 3.69
2626 2688 8.682710 GCATGTTTAATTTATCTGTACCCAAGA 58.317 33.333 0.00 0.00 0.00 3.02
2754 2818 1.201647 GTAACCGACAGCAGCTACTGA 59.798 52.381 21.00 0.00 40.25 3.41
3026 3110 0.613260 AGAACCAGAACAGCCGCATA 59.387 50.000 0.00 0.00 0.00 3.14
3028 3112 1.597854 CAGAACCAGAACAGCCGCA 60.598 57.895 0.00 0.00 0.00 5.69
3081 3165 9.775854 TGAATTGTGACCAATCAAAATATTTGT 57.224 25.926 0.39 0.00 41.23 2.83
3086 3170 9.868277 GGTAATGAATTGTGACCAATCAAAATA 57.132 29.630 0.00 0.00 41.23 1.40
3087 3171 8.373981 TGGTAATGAATTGTGACCAATCAAAAT 58.626 29.630 0.00 0.00 43.53 1.82
3088 3172 7.730084 TGGTAATGAATTGTGACCAATCAAAA 58.270 30.769 0.00 0.00 40.42 2.44
3089 3173 7.232330 TCTGGTAATGAATTGTGACCAATCAAA 59.768 33.333 0.00 0.00 40.42 2.69
3132 4929 3.304257 CATCGATTTTGTTTTCGCCACA 58.696 40.909 0.00 0.00 35.39 4.17
3210 5009 0.764271 TCCAAGCTCATGTGTGGTCA 59.236 50.000 0.00 0.00 32.68 4.02
3215 5014 4.341806 TGTTTTGATTCCAAGCTCATGTGT 59.658 37.500 0.00 0.00 33.23 3.72


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

AutoCloner maintained by Alex Coulton.