Multiple sequence alignment - TraesCS5D01G409700

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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 TraesCS5D01G409700 chr5D 100.000 2771 0 0 1 2771 473119326 473122096 0.000000e+00 5118
1 TraesCS5D01G409700 chr3D 98.154 1300 22 2 469 1768 532182016 532183313 0.000000e+00 2266
2 TraesCS5D01G409700 chr3D 95.780 1327 28 13 469 1768 2881832 2883157 0.000000e+00 2115
3 TraesCS5D01G409700 chr3D 99.106 1007 9 0 1765 2771 2883869 2884875 0.000000e+00 1810
4 TraesCS5D01G409700 chr3D 98.610 1007 14 0 1765 2771 532184026 532185032 0.000000e+00 1783
5 TraesCS5D01G409700 chr6D 98.077 1300 24 1 469 1768 83069336 83070634 0.000000e+00 2261
6 TraesCS5D01G409700 chrUn 98.002 1301 24 2 468 1768 11302898 11304196 0.000000e+00 2257
7 TraesCS5D01G409700 chr7D 97.925 1301 26 1 468 1768 28219008 28220307 0.000000e+00 2252
8 TraesCS5D01G409700 chr7D 99.006 1006 9 1 1765 2770 28221017 28222021 0.000000e+00 1801
9 TraesCS5D01G409700 chr1D 97.158 1302 35 2 467 1768 395423754 395422455 0.000000e+00 2198
10 TraesCS5D01G409700 chr1D 95.705 1327 28 14 469 1768 429508479 429509803 0.000000e+00 2108
11 TraesCS5D01G409700 chr1D 98.808 1007 12 0 1765 2771 429510515 429511521 0.000000e+00 1794
12 TraesCS5D01G409700 chr1D 98.606 1004 13 1 1768 2771 395421739 395420737 0.000000e+00 1775
13 TraesCS5D01G409700 chr4A 95.772 1301 52 3 469 1768 544955351 544956649 0.000000e+00 2095
14 TraesCS5D01G409700 chr5A 94.462 1300 69 3 469 1768 382981932 382983228 0.000000e+00 1999
15 TraesCS5D01G409700 chr5A 96.723 1007 32 1 1765 2771 382983941 382984946 0.000000e+00 1676
16 TraesCS5D01G409700 chr5A 80.084 477 49 31 14 459 593098686 593099147 2.070000e-81 313
17 TraesCS5D01G409700 chr2A 97.709 1004 23 0 1768 2771 732962150 732961147 0.000000e+00 1727
18 TraesCS5D01G409700 chr2A 98.273 579 10 0 1190 1768 732963444 732962866 0.000000e+00 1014
19 TraesCS5D01G409700 chr1B 97.012 1004 30 0 1768 2771 392744878 392743875 0.000000e+00 1688
20 TraesCS5D01G409700 chr2B 96.624 1007 34 0 1765 2771 563846936 563847942 0.000000e+00 1672
21 TraesCS5D01G409700 chr2B 93.548 434 20 5 1336 1768 529836211 529836637 8.370000e-180 640
22 TraesCS5D01G409700 chr5B 81.760 466 38 28 13 459 580518702 580519139 2.040000e-91 346


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 TraesCS5D01G409700 chr5D 473119326 473122096 2770 False 5118.0 5118 100.0000 1 2771 1 chr5D.!!$F1 2770
1 TraesCS5D01G409700 chr3D 532182016 532185032 3016 False 2024.5 2266 98.3820 469 2771 2 chr3D.!!$F2 2302
2 TraesCS5D01G409700 chr3D 2881832 2884875 3043 False 1962.5 2115 97.4430 469 2771 2 chr3D.!!$F1 2302
3 TraesCS5D01G409700 chr6D 83069336 83070634 1298 False 2261.0 2261 98.0770 469 1768 1 chr6D.!!$F1 1299
4 TraesCS5D01G409700 chrUn 11302898 11304196 1298 False 2257.0 2257 98.0020 468 1768 1 chrUn.!!$F1 1300
5 TraesCS5D01G409700 chr7D 28219008 28222021 3013 False 2026.5 2252 98.4655 468 2770 2 chr7D.!!$F1 2302
6 TraesCS5D01G409700 chr1D 395420737 395423754 3017 True 1986.5 2198 97.8820 467 2771 2 chr1D.!!$R1 2304
7 TraesCS5D01G409700 chr1D 429508479 429511521 3042 False 1951.0 2108 97.2565 469 2771 2 chr1D.!!$F1 2302
8 TraesCS5D01G409700 chr4A 544955351 544956649 1298 False 2095.0 2095 95.7720 469 1768 1 chr4A.!!$F1 1299
9 TraesCS5D01G409700 chr5A 382981932 382984946 3014 False 1837.5 1999 95.5925 469 2771 2 chr5A.!!$F2 2302
10 TraesCS5D01G409700 chr2A 732961147 732963444 2297 True 1370.5 1727 97.9910 1190 2771 2 chr2A.!!$R1 1581
11 TraesCS5D01G409700 chr1B 392743875 392744878 1003 True 1688.0 1688 97.0120 1768 2771 1 chr1B.!!$R1 1003
12 TraesCS5D01G409700 chr2B 563846936 563847942 1006 False 1672.0 1672 96.6240 1765 2771 1 chr2B.!!$F2 1006

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
172 173 0.030908 GGACGAGTCGGATCCATCAC 59.969 60.0 18.3 4.94 32.35 3.06 F
173 174 0.030908 GACGAGTCGGATCCATCACC 59.969 60.0 18.3 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1500 1529 3.329386 AGTGATCACACCAGTTTCATCG 58.671 45.455 27.02 0.0 46.99 3.84 R
2282 3744 9.640952 AAGCTTGGCCTTATAATAGTTGAAATA 57.359 29.630 3.32 0.0 0.00 1.40 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 2.805671 TGCGGTTAATGATAATGGCTCG 59.194 45.455 0.00 0.00 0.00 5.03
22 23 3.064207 GCGGTTAATGATAATGGCTCGA 58.936 45.455 0.00 0.00 0.00 4.04
23 24 3.120649 GCGGTTAATGATAATGGCTCGAC 60.121 47.826 0.00 0.00 0.00 4.20
24 25 3.121279 CGGTTAATGATAATGGCTCGACG 59.879 47.826 0.00 0.00 0.00 5.12
25 26 3.120649 GGTTAATGATAATGGCTCGACGC 60.121 47.826 0.00 0.00 38.13 5.19
26 27 1.139989 AATGATAATGGCTCGACGCG 58.860 50.000 3.53 3.53 40.44 6.01
27 28 0.667487 ATGATAATGGCTCGACGCGG 60.667 55.000 12.47 0.00 40.44 6.46
28 29 1.007734 GATAATGGCTCGACGCGGA 60.008 57.895 12.47 0.00 40.44 5.54
29 30 1.276145 GATAATGGCTCGACGCGGAC 61.276 60.000 12.47 2.84 40.44 4.79
43 44 4.856801 GGACGGCCGTGGATGCAT 62.857 66.667 39.65 8.28 0.00 3.96
44 45 3.576356 GACGGCCGTGGATGCATG 61.576 66.667 39.65 0.00 0.00 4.06
47 48 3.896133 GGCCGTGGATGCATGCAG 61.896 66.667 26.69 12.01 0.00 4.41
48 49 3.896133 GCCGTGGATGCATGCAGG 61.896 66.667 27.79 27.79 34.43 4.85
49 50 3.896133 CCGTGGATGCATGCAGGC 61.896 66.667 28.90 18.05 33.51 4.85
64 65 3.590824 GGCATGCAGGCGTAAAGT 58.409 55.556 21.36 0.00 33.57 2.66
65 66 1.429423 GGCATGCAGGCGTAAAGTC 59.571 57.895 21.36 0.00 33.57 3.01
66 67 1.060937 GCATGCAGGCGTAAAGTCG 59.939 57.895 14.21 0.00 0.00 4.18
74 75 3.782042 CGTAAAGTCGCCAGCTCC 58.218 61.111 0.00 0.00 0.00 4.70
75 76 1.810030 CGTAAAGTCGCCAGCTCCC 60.810 63.158 0.00 0.00 0.00 4.30
76 77 1.810030 GTAAAGTCGCCAGCTCCCG 60.810 63.158 0.00 0.00 0.00 5.14
77 78 2.280552 TAAAGTCGCCAGCTCCCGT 61.281 57.895 2.85 0.00 0.00 5.28
78 79 2.501223 TAAAGTCGCCAGCTCCCGTG 62.501 60.000 2.85 0.00 0.00 4.94
84 85 4.680237 CCAGCTCCCGTGCGAACA 62.680 66.667 0.00 0.00 38.13 3.18
85 86 3.414700 CAGCTCCCGTGCGAACAC 61.415 66.667 0.00 0.00 43.76 3.32
151 152 4.955774 GCCAACGGACACGGTCGT 62.956 66.667 0.00 0.00 46.48 4.34
152 153 2.732094 CCAACGGACACGGTCGTC 60.732 66.667 0.00 0.00 46.48 4.20
153 154 3.095278 CAACGGACACGGTCGTCG 61.095 66.667 0.00 0.00 46.48 5.12
154 155 4.332637 AACGGACACGGTCGTCGG 62.333 66.667 12.89 12.89 46.48 4.79
156 157 4.748679 CGGACACGGTCGTCGGAC 62.749 72.222 0.00 0.00 44.45 4.79
157 158 4.748679 GGACACGGTCGTCGGACG 62.749 72.222 23.73 23.73 44.39 4.79
165 166 2.125391 TCGTCGGACGAGTCGGAT 60.125 61.111 27.66 0.00 46.73 4.18
166 167 2.169789 TCGTCGGACGAGTCGGATC 61.170 63.158 27.66 6.03 46.73 3.36
167 168 2.714387 GTCGGACGAGTCGGATCC 59.286 66.667 18.30 14.35 40.29 3.36
168 169 2.110967 GTCGGACGAGTCGGATCCA 61.111 63.158 18.30 4.18 40.29 3.41
169 170 1.153025 TCGGACGAGTCGGATCCAT 60.153 57.895 18.30 0.00 34.61 3.41
170 171 1.164662 TCGGACGAGTCGGATCCATC 61.165 60.000 18.30 5.56 34.61 3.51
171 172 1.444917 CGGACGAGTCGGATCCATCA 61.445 60.000 18.30 0.00 32.35 3.07
172 173 0.030908 GGACGAGTCGGATCCATCAC 59.969 60.000 18.30 4.94 32.35 3.06
173 174 0.030908 GACGAGTCGGATCCATCACC 59.969 60.000 18.30 0.00 0.00 4.02
174 175 0.683179 ACGAGTCGGATCCATCACCA 60.683 55.000 18.30 0.00 0.00 4.17
175 176 0.031314 CGAGTCGGATCCATCACCAG 59.969 60.000 13.41 0.00 0.00 4.00
176 177 1.403814 GAGTCGGATCCATCACCAGA 58.596 55.000 13.41 0.00 0.00 3.86
177 178 1.339610 GAGTCGGATCCATCACCAGAG 59.660 57.143 13.41 0.00 0.00 3.35
178 179 1.115467 GTCGGATCCATCACCAGAGT 58.885 55.000 13.41 0.00 0.00 3.24
179 180 1.114627 TCGGATCCATCACCAGAGTG 58.885 55.000 13.41 0.00 46.00 3.51
180 181 0.105593 CGGATCCATCACCAGAGTGG 59.894 60.000 13.41 0.00 44.64 4.00
181 182 1.500474 GGATCCATCACCAGAGTGGA 58.500 55.000 6.95 0.00 45.37 4.02
182 183 1.139853 GGATCCATCACCAGAGTGGAC 59.860 57.143 6.95 0.00 44.21 4.02
183 184 0.826715 ATCCATCACCAGAGTGGACG 59.173 55.000 0.00 0.00 44.21 4.79
184 185 1.448540 CCATCACCAGAGTGGACGC 60.449 63.158 0.00 0.00 44.64 5.19
185 186 1.448540 CATCACCAGAGTGGACGCC 60.449 63.158 0.00 0.00 44.64 5.68
186 187 1.913262 ATCACCAGAGTGGACGCCA 60.913 57.895 0.00 0.00 44.64 5.69
204 205 3.598273 ACTATGGAGTGGAGCTCGT 57.402 52.632 7.83 0.00 45.03 4.18
205 206 1.107114 ACTATGGAGTGGAGCTCGTG 58.893 55.000 7.83 0.00 45.03 4.35
206 207 1.341089 ACTATGGAGTGGAGCTCGTGA 60.341 52.381 7.83 0.00 45.03 4.35
207 208 1.336440 CTATGGAGTGGAGCTCGTGAG 59.664 57.143 7.83 0.00 45.03 3.51
265 266 3.705638 CTGCGTGCGTGGACACTG 61.706 66.667 0.56 0.00 38.45 3.66
267 268 4.961511 GCGTGCGTGGACACTGGA 62.962 66.667 0.56 0.00 38.45 3.86
268 269 3.036084 CGTGCGTGGACACTGGAC 61.036 66.667 0.56 5.18 38.45 4.02
269 270 2.108157 GTGCGTGGACACTGGACA 59.892 61.111 11.55 0.00 37.58 4.02
270 271 1.956170 GTGCGTGGACACTGGACAG 60.956 63.158 11.55 0.00 37.58 3.51
271 272 2.421739 GCGTGGACACTGGACAGT 59.578 61.111 0.00 0.00 43.61 3.55
279 280 3.170672 ACTGGACAGTGCAGGGCA 61.171 61.111 24.49 0.00 40.38 5.36
280 281 2.353958 CTGGACAGTGCAGGGCAT 59.646 61.111 14.20 0.00 41.91 4.40
281 282 2.034532 TGGACAGTGCAGGGCATG 59.965 61.111 0.00 0.00 41.91 4.06
282 283 2.753043 GGACAGTGCAGGGCATGG 60.753 66.667 0.00 0.00 41.91 3.66
283 284 2.753043 GACAGTGCAGGGCATGGG 60.753 66.667 0.00 0.00 41.91 4.00
302 303 4.700365 CGCGACAGGCACGAGTCA 62.700 66.667 0.00 0.00 43.84 3.41
303 304 3.106407 GCGACAGGCACGAGTCAC 61.106 66.667 0.00 0.00 42.87 3.67
305 306 3.106407 GACAGGCACGAGTCACGC 61.106 66.667 0.00 0.00 46.94 5.34
330 331 4.717629 CAGTGGCTCGCCGTTCGA 62.718 66.667 3.14 0.00 46.29 3.71
342 343 4.814294 GTTCGATGGAGCGGCCGT 62.814 66.667 28.70 13.92 40.66 5.68
343 344 4.812476 TTCGATGGAGCGGCCGTG 62.812 66.667 28.70 8.17 40.66 4.94
389 390 2.523168 CCAACCCCGTGCCCTTTT 60.523 61.111 0.00 0.00 0.00 2.27
390 391 2.570284 CCAACCCCGTGCCCTTTTC 61.570 63.158 0.00 0.00 0.00 2.29
391 392 2.203582 AACCCCGTGCCCTTTTCC 60.204 61.111 0.00 0.00 0.00 3.13
392 393 2.774633 AACCCCGTGCCCTTTTCCT 61.775 57.895 0.00 0.00 0.00 3.36
393 394 2.676471 CCCCGTGCCCTTTTCCTG 60.676 66.667 0.00 0.00 0.00 3.86
394 395 3.373565 CCCGTGCCCTTTTCCTGC 61.374 66.667 0.00 0.00 0.00 4.85
395 396 2.282462 CCGTGCCCTTTTCCTGCT 60.282 61.111 0.00 0.00 0.00 4.24
396 397 2.629656 CCGTGCCCTTTTCCTGCTG 61.630 63.158 0.00 0.00 0.00 4.41
397 398 1.898574 CGTGCCCTTTTCCTGCTGT 60.899 57.895 0.00 0.00 0.00 4.40
398 399 1.455383 CGTGCCCTTTTCCTGCTGTT 61.455 55.000 0.00 0.00 0.00 3.16
399 400 0.315251 GTGCCCTTTTCCTGCTGTTC 59.685 55.000 0.00 0.00 0.00 3.18
400 401 0.827507 TGCCCTTTTCCTGCTGTTCC 60.828 55.000 0.00 0.00 0.00 3.62
401 402 1.866853 GCCCTTTTCCTGCTGTTCCG 61.867 60.000 0.00 0.00 0.00 4.30
402 403 1.244019 CCCTTTTCCTGCTGTTCCGG 61.244 60.000 0.00 0.00 0.00 5.14
403 404 0.537371 CCTTTTCCTGCTGTTCCGGT 60.537 55.000 0.00 0.00 0.00 5.28
404 405 0.875059 CTTTTCCTGCTGTTCCGGTC 59.125 55.000 0.00 0.00 0.00 4.79
405 406 0.882927 TTTTCCTGCTGTTCCGGTCG 60.883 55.000 0.00 0.00 0.00 4.79
406 407 2.035237 TTTCCTGCTGTTCCGGTCGT 62.035 55.000 0.00 0.00 0.00 4.34
407 408 2.030562 CCTGCTGTTCCGGTCGTT 59.969 61.111 0.00 0.00 0.00 3.85
408 409 1.597027 CCTGCTGTTCCGGTCGTTT 60.597 57.895 0.00 0.00 0.00 3.60
409 410 1.164041 CCTGCTGTTCCGGTCGTTTT 61.164 55.000 0.00 0.00 0.00 2.43
410 411 0.661020 CTGCTGTTCCGGTCGTTTTT 59.339 50.000 0.00 0.00 0.00 1.94
598 599 3.782656 AACCTTAGTGTCGTTTCCCAT 57.217 42.857 0.00 0.00 0.00 4.00
743 745 2.744494 GCATTCTTCCTTCTCTGGCGAT 60.744 50.000 0.00 0.00 0.00 4.58
766 768 3.927163 ATGGCGACCGACGGTTGAC 62.927 63.158 33.81 32.08 45.23 3.18
889 891 2.294979 GGCATTAGGGTTAGGGTTTCG 58.705 52.381 0.00 0.00 0.00 3.46
1071 1073 4.019858 TCATCCGCATTGGTCCAAATTTA 58.980 39.130 8.75 0.00 39.52 1.40
2282 3744 2.232208 GCTAAGGCTTCCAACAAGCAAT 59.768 45.455 1.30 0.00 44.71 3.56
2561 4023 7.416777 CCAACTTTAGAGGAAAAATATGCCCTC 60.417 40.741 0.00 0.00 44.14 4.30
2671 4133 2.087646 GTGAATGGAAGAGGAAGGCAC 58.912 52.381 0.00 0.00 0.00 5.01
2694 4157 5.891551 ACTACACTGTTGACCTGGAAAAATT 59.108 36.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.121279 CGTCGAGCCATTATCATTAACCG 59.879 47.826 0.00 0.00 0.00 4.44
3 4 3.120649 GCGTCGAGCCATTATCATTAACC 60.121 47.826 0.00 0.00 40.81 2.85
4 5 3.421826 CGCGTCGAGCCATTATCATTAAC 60.422 47.826 0.00 0.00 44.76 2.01
5 6 2.729360 CGCGTCGAGCCATTATCATTAA 59.271 45.455 0.00 0.00 44.76 1.40
6 7 2.324860 CGCGTCGAGCCATTATCATTA 58.675 47.619 0.00 0.00 44.76 1.90
7 8 1.139989 CGCGTCGAGCCATTATCATT 58.860 50.000 0.00 0.00 44.76 2.57
8 9 0.667487 CCGCGTCGAGCCATTATCAT 60.667 55.000 4.92 0.00 44.76 2.45
9 10 1.299850 CCGCGTCGAGCCATTATCA 60.300 57.895 4.92 0.00 44.76 2.15
10 11 1.007734 TCCGCGTCGAGCCATTATC 60.008 57.895 4.92 0.00 44.76 1.75
11 12 1.299926 GTCCGCGTCGAGCCATTAT 60.300 57.895 4.92 0.00 44.76 1.28
12 13 2.103538 GTCCGCGTCGAGCCATTA 59.896 61.111 4.92 0.00 44.76 1.90
26 27 4.856801 ATGCATCCACGGCCGTCC 62.857 66.667 31.80 14.70 0.00 4.79
27 28 3.576356 CATGCATCCACGGCCGTC 61.576 66.667 31.80 18.05 0.00 4.79
30 31 3.896133 CTGCATGCATCCACGGCC 61.896 66.667 22.97 0.00 0.00 6.13
31 32 3.896133 CCTGCATGCATCCACGGC 61.896 66.667 22.97 0.00 0.00 5.68
32 33 3.896133 GCCTGCATGCATCCACGG 61.896 66.667 22.97 19.22 0.00 4.94
33 34 3.135457 TGCCTGCATGCATCCACG 61.135 61.111 22.97 9.00 36.04 4.94
45 46 1.308069 ACTTTACGCCTGCATGCCTG 61.308 55.000 16.68 7.25 0.00 4.85
46 47 1.002134 ACTTTACGCCTGCATGCCT 60.002 52.632 16.68 0.00 0.00 4.75
47 48 1.429423 GACTTTACGCCTGCATGCC 59.571 57.895 16.68 0.00 0.00 4.40
48 49 1.060937 CGACTTTACGCCTGCATGC 59.939 57.895 11.82 11.82 0.00 4.06
57 58 1.810030 GGGAGCTGGCGACTTTACG 60.810 63.158 0.00 0.00 0.00 3.18
58 59 1.810030 CGGGAGCTGGCGACTTTAC 60.810 63.158 0.00 0.00 0.00 2.01
59 60 2.280552 ACGGGAGCTGGCGACTTTA 61.281 57.895 0.00 0.00 0.00 1.85
60 61 3.626924 ACGGGAGCTGGCGACTTT 61.627 61.111 0.00 0.00 0.00 2.66
61 62 4.379243 CACGGGAGCTGGCGACTT 62.379 66.667 0.00 0.00 0.00 3.01
67 68 4.680237 TGTTCGCACGGGAGCTGG 62.680 66.667 0.00 0.00 0.00 4.85
68 69 3.414700 GTGTTCGCACGGGAGCTG 61.415 66.667 0.00 0.00 38.46 4.24
134 135 4.955774 ACGACCGTGTCCGTTGGC 62.956 66.667 0.00 0.00 35.21 4.52
135 136 2.732094 GACGACCGTGTCCGTTGG 60.732 66.667 0.00 0.00 39.30 3.77
136 137 3.095278 CGACGACCGTGTCCGTTG 61.095 66.667 0.00 0.00 39.30 4.10
137 138 4.332637 CCGACGACCGTGTCCGTT 62.333 66.667 0.00 0.00 39.30 4.44
139 140 4.748679 GTCCGACGACCGTGTCCG 62.749 72.222 0.00 0.00 35.40 4.79
140 141 4.748679 CGTCCGACGACCGTGTCC 62.749 72.222 16.03 0.00 46.05 4.02
141 142 3.642008 CTCGTCCGACGACCGTGTC 62.642 68.421 19.51 0.00 46.73 3.67
142 143 3.720193 CTCGTCCGACGACCGTGT 61.720 66.667 19.51 0.00 46.73 4.49
143 144 3.642008 GACTCGTCCGACGACCGTG 62.642 68.421 19.51 12.26 46.73 4.94
144 145 3.418068 GACTCGTCCGACGACCGT 61.418 66.667 19.51 16.37 46.73 4.83
145 146 4.495939 CGACTCGTCCGACGACCG 62.496 72.222 19.51 19.66 46.73 4.79
146 147 4.157958 CCGACTCGTCCGACGACC 62.158 72.222 19.51 12.82 46.73 4.79
147 148 2.358756 GATCCGACTCGTCCGACGAC 62.359 65.000 19.51 10.17 46.73 4.34
149 150 2.323790 GATCCGACTCGTCCGACG 59.676 66.667 14.94 14.94 44.19 5.12
150 151 1.445716 ATGGATCCGACTCGTCCGAC 61.446 60.000 7.39 0.00 34.72 4.79
151 152 1.153025 ATGGATCCGACTCGTCCGA 60.153 57.895 7.39 0.00 34.72 4.55
152 153 1.283181 GATGGATCCGACTCGTCCG 59.717 63.158 7.39 0.00 34.72 4.79
153 154 0.030908 GTGATGGATCCGACTCGTCC 59.969 60.000 7.39 0.00 0.00 4.79
154 155 0.030908 GGTGATGGATCCGACTCGTC 59.969 60.000 7.39 0.00 0.00 4.20
155 156 0.683179 TGGTGATGGATCCGACTCGT 60.683 55.000 7.39 0.00 0.00 4.18
156 157 0.031314 CTGGTGATGGATCCGACTCG 59.969 60.000 7.39 0.00 0.00 4.18
157 158 1.339610 CTCTGGTGATGGATCCGACTC 59.660 57.143 7.39 4.59 0.00 3.36
158 159 1.342474 ACTCTGGTGATGGATCCGACT 60.342 52.381 7.39 0.00 0.00 4.18
159 160 1.115467 ACTCTGGTGATGGATCCGAC 58.885 55.000 7.39 4.10 0.00 4.79
160 161 1.114627 CACTCTGGTGATGGATCCGA 58.885 55.000 7.39 0.00 45.61 4.55
161 162 0.105593 CCACTCTGGTGATGGATCCG 59.894 60.000 7.39 0.00 45.61 4.18
162 163 1.139853 GTCCACTCTGGTGATGGATCC 59.860 57.143 4.20 4.20 44.21 3.36
163 164 1.202463 CGTCCACTCTGGTGATGGATC 60.202 57.143 0.00 0.00 44.21 3.36
164 165 0.826715 CGTCCACTCTGGTGATGGAT 59.173 55.000 0.00 0.00 44.21 3.41
165 166 1.888436 GCGTCCACTCTGGTGATGGA 61.888 60.000 0.00 0.00 45.61 3.41
166 167 1.448540 GCGTCCACTCTGGTGATGG 60.449 63.158 0.00 0.00 45.61 3.51
167 168 1.448540 GGCGTCCACTCTGGTGATG 60.449 63.158 0.00 0.00 45.61 3.07
168 169 1.913262 TGGCGTCCACTCTGGTGAT 60.913 57.895 0.00 0.00 45.61 3.06
169 170 2.523168 TGGCGTCCACTCTGGTGA 60.523 61.111 0.00 0.00 45.61 4.02
178 179 4.453454 ACTCCATAGTGGCGTCCA 57.547 55.556 0.00 0.00 37.47 4.02
186 187 1.107114 CACGAGCTCCACTCCATAGT 58.893 55.000 8.47 0.00 43.01 2.12
187 188 1.336440 CTCACGAGCTCCACTCCATAG 59.664 57.143 8.47 0.00 43.01 2.23
188 189 1.393603 CTCACGAGCTCCACTCCATA 58.606 55.000 8.47 0.00 43.01 2.74
189 190 2.197250 CTCACGAGCTCCACTCCAT 58.803 57.895 8.47 0.00 43.01 3.41
190 191 3.686760 CTCACGAGCTCCACTCCA 58.313 61.111 8.47 0.00 43.01 3.86
248 249 3.705638 CAGTGTCCACGCACGCAG 61.706 66.667 0.00 0.00 43.61 5.18
250 251 4.961511 TCCAGTGTCCACGCACGC 62.962 66.667 0.00 0.00 43.61 5.34
251 252 3.036084 GTCCAGTGTCCACGCACG 61.036 66.667 0.00 0.00 43.61 5.34
252 253 1.956170 CTGTCCAGTGTCCACGCAC 60.956 63.158 0.00 0.00 39.51 5.34
253 254 2.421314 CTGTCCAGTGTCCACGCA 59.579 61.111 0.00 0.00 36.20 5.24
254 255 2.421739 ACTGTCCAGTGTCCACGC 59.578 61.111 0.00 0.00 40.75 5.34
262 263 2.532532 ATGCCCTGCACTGTCCAGT 61.533 57.895 0.00 0.00 43.04 4.00
263 264 2.044555 CATGCCCTGCACTGTCCAG 61.045 63.158 0.00 0.00 43.04 3.86
264 265 2.034532 CATGCCCTGCACTGTCCA 59.965 61.111 0.00 0.00 43.04 4.02
265 266 2.753043 CCATGCCCTGCACTGTCC 60.753 66.667 0.00 0.00 43.04 4.02
266 267 2.753043 CCCATGCCCTGCACTGTC 60.753 66.667 0.00 0.00 43.04 3.51
286 287 3.106407 GTGACTCGTGCCTGTCGC 61.106 66.667 0.00 0.00 36.10 5.19
287 288 2.801162 CGTGACTCGTGCCTGTCG 60.801 66.667 0.00 0.00 36.10 4.35
288 289 3.106407 GCGTGACTCGTGCCTGTC 61.106 66.667 0.00 0.00 42.13 3.51
313 314 4.717629 TCGAACGGCGAGCCACTG 62.718 66.667 16.62 0.34 45.59 3.66
325 326 4.814294 ACGGCCGCTCCATCGAAC 62.814 66.667 28.58 0.00 34.01 3.95
326 327 4.812476 CACGGCCGCTCCATCGAA 62.812 66.667 28.58 0.00 34.01 3.71
372 373 2.523168 AAAAGGGCACGGGGTTGG 60.523 61.111 0.00 0.00 0.00 3.77
373 374 2.570284 GGAAAAGGGCACGGGGTTG 61.570 63.158 0.00 0.00 0.00 3.77
374 375 2.203582 GGAAAAGGGCACGGGGTT 60.204 61.111 0.00 0.00 0.00 4.11
375 376 3.182996 AGGAAAAGGGCACGGGGT 61.183 61.111 0.00 0.00 0.00 4.95
376 377 2.676471 CAGGAAAAGGGCACGGGG 60.676 66.667 0.00 0.00 0.00 5.73
377 378 3.373565 GCAGGAAAAGGGCACGGG 61.374 66.667 0.00 0.00 0.00 5.28
378 379 2.282462 AGCAGGAAAAGGGCACGG 60.282 61.111 0.00 0.00 0.00 4.94
379 380 1.455383 AACAGCAGGAAAAGGGCACG 61.455 55.000 0.00 0.00 0.00 5.34
380 381 0.315251 GAACAGCAGGAAAAGGGCAC 59.685 55.000 0.00 0.00 0.00 5.01
381 382 0.827507 GGAACAGCAGGAAAAGGGCA 60.828 55.000 0.00 0.00 0.00 5.36
382 383 1.866853 CGGAACAGCAGGAAAAGGGC 61.867 60.000 0.00 0.00 0.00 5.19
383 384 1.244019 CCGGAACAGCAGGAAAAGGG 61.244 60.000 0.00 0.00 33.08 3.95
384 385 0.537371 ACCGGAACAGCAGGAAAAGG 60.537 55.000 9.46 0.00 35.60 3.11
385 386 0.875059 GACCGGAACAGCAGGAAAAG 59.125 55.000 9.46 0.00 35.60 2.27
386 387 0.882927 CGACCGGAACAGCAGGAAAA 60.883 55.000 9.46 0.00 35.60 2.29
387 388 1.301401 CGACCGGAACAGCAGGAAA 60.301 57.895 9.46 0.00 35.60 3.13
388 389 2.035237 AACGACCGGAACAGCAGGAA 62.035 55.000 9.46 0.00 35.60 3.36
389 390 2.035237 AAACGACCGGAACAGCAGGA 62.035 55.000 9.46 0.00 35.60 3.86
390 391 1.164041 AAAACGACCGGAACAGCAGG 61.164 55.000 9.46 0.00 37.91 4.85
391 392 0.661020 AAAAACGACCGGAACAGCAG 59.339 50.000 9.46 0.00 0.00 4.24
392 393 2.783228 AAAAACGACCGGAACAGCA 58.217 47.368 9.46 0.00 0.00 4.41
455 456 4.659172 TTTCCCAGCCCCGCACTG 62.659 66.667 0.00 0.00 34.82 3.66
456 457 3.444818 TTTTTCCCAGCCCCGCACT 62.445 57.895 0.00 0.00 0.00 4.40
457 458 2.915137 TTTTTCCCAGCCCCGCAC 60.915 61.111 0.00 0.00 0.00 5.34
458 459 2.600173 CTTTTTCCCAGCCCCGCA 60.600 61.111 0.00 0.00 0.00 5.69
459 460 2.600470 ACTTTTTCCCAGCCCCGC 60.600 61.111 0.00 0.00 0.00 6.13
460 461 1.977009 GGACTTTTTCCCAGCCCCG 60.977 63.158 0.00 0.00 38.70 5.73
461 462 0.252239 ATGGACTTTTTCCCAGCCCC 60.252 55.000 0.00 0.00 45.17 5.80
462 463 1.644509 AATGGACTTTTTCCCAGCCC 58.355 50.000 0.00 0.00 45.17 5.19
463 464 3.769739 AAAATGGACTTTTTCCCAGCC 57.230 42.857 0.00 0.00 45.17 4.85
464 465 6.017440 GGTTTAAAAATGGACTTTTTCCCAGC 60.017 38.462 0.00 0.00 44.10 4.85
465 466 7.279615 AGGTTTAAAAATGGACTTTTTCCCAG 58.720 34.615 0.00 0.00 44.10 4.45
484 485 5.343058 CGAACGTCTACGAATTCAAGGTTTA 59.657 40.000 9.86 0.00 43.02 2.01
654 656 1.608283 GGCCCACTAATATCGCCTCAC 60.608 57.143 0.00 0.00 36.65 3.51
798 800 1.733041 CTTCTTCTTCGACGCGCCA 60.733 57.895 5.73 0.00 0.00 5.69
889 891 2.264480 GTCCCCAAATTTGCCGCC 59.736 61.111 12.92 0.00 0.00 6.13
942 944 7.823745 ATAAAGCATAACAACCTATTCCCTG 57.176 36.000 0.00 0.00 0.00 4.45
1071 1073 3.421394 TGATCTCCCCCAACATAGTCT 57.579 47.619 0.00 0.00 0.00 3.24
1500 1529 3.329386 AGTGATCACACCAGTTTCATCG 58.671 45.455 27.02 0.00 46.99 3.84
2282 3744 9.640952 AAGCTTGGCCTTATAATAGTTGAAATA 57.359 29.630 3.32 0.00 0.00 1.40
2561 4023 6.966435 TTTCTTGAGCTTTTTGAAAACAGG 57.034 33.333 0.00 0.00 0.00 4.00
2671 4133 6.039270 TCAATTTTTCCAGGTCAACAGTGTAG 59.961 38.462 0.00 0.00 0.00 2.74
2694 4157 1.977854 AGTACCCACAAGAGCATGTCA 59.022 47.619 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.