Multiple sequence alignment - TraesCS4A01G166700

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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 TraesCS4A01G166700 chr4A 100.000 2539 0 0 1 2539 407463127 407465665 0.000000e+00 4689.0
1 TraesCS4A01G166700 chr4A 80.147 136 9 11 2120 2239 547297264 547297131 4.500000e-13 86.1
2 TraesCS4A01G166700 chr5D 89.773 2073 104 43 1 1995 81344794 81342752 0.000000e+00 2555.0
3 TraesCS4A01G166700 chr5D 90.541 296 19 4 2244 2539 81342177 81341891 1.430000e-102 383.0
4 TraesCS4A01G166700 chr5D 97.778 45 1 0 2236 2280 81342231 81342187 7.530000e-11 78.7
5 TraesCS4A01G166700 chr5D 94.118 51 3 0 2174 2224 81342381 81342331 7.530000e-11 78.7
6 TraesCS4A01G166700 chr5A 87.582 2142 139 51 266 2327 77367414 77365320 0.000000e+00 2364.0
7 TraesCS4A01G166700 chr5A 97.333 75 2 0 2465 2539 77365209 77365135 7.370000e-26 128.0
8 TraesCS4A01G166700 chr4D 79.389 131 16 4 2120 2239 301245114 301245244 5.820000e-12 82.4
9 TraesCS4A01G166700 chr4D 93.182 44 3 0 2187 2230 426412354 426412397 5.860000e-07 65.8
10 TraesCS4A01G166700 chr2A 92.857 56 4 0 2184 2239 721255760 721255705 5.820000e-12 82.4
11 TraesCS4A01G166700 chr2A 90.741 54 5 0 2186 2239 420682755 420682702 3.500000e-09 73.1
12 TraesCS4A01G166700 chr2D 77.778 135 14 8 2120 2239 590365029 590364896 4.530000e-08 69.4
13 TraesCS4A01G166700 chr2D 96.970 33 0 1 603 635 470211143 470211174 1.000000e-03 54.7
14 TraesCS4A01G166700 chr2D 100.000 28 0 0 2187 2214 356895440 356895413 5.000000e-03 52.8
15 TraesCS4A01G166700 chr2B 88.889 54 6 0 2186 2239 690584304 690584251 1.630000e-07 67.6


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 TraesCS4A01G166700 chr4A 407463127 407465665 2538 False 4689.00 4689 100.0000 1 2539 1 chr4A.!!$F1 2538
1 TraesCS4A01G166700 chr5D 81341891 81344794 2903 True 773.85 2555 93.0525 1 2539 4 chr5D.!!$R1 2538
2 TraesCS4A01G166700 chr5A 77365135 77367414 2279 True 1246.00 2364 92.4575 266 2539 2 chr5A.!!$R1 2273

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
583 629 0.102481 CCCTCACGATTCGATCCGTT 59.898 55.0 13.95 0.0 36.83 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2230 2552 0.097499 CGCACAACACATGATCGCAT 59.903 50.0 0.0 0.0 34.29 4.73 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 23 1.320555 CATTGCCGAGACTCGTTAACG 59.679 52.381 21.85 21.85 38.40 3.18
40 42 4.322080 ACGAATGTGTGAAGAGAAGTCA 57.678 40.909 0.00 0.00 0.00 3.41
46 48 4.060900 TGTGTGAAGAGAAGTCAGATTGC 58.939 43.478 0.00 0.00 0.00 3.56
69 78 2.197324 GAGGTGGGGGTTGTTGCA 59.803 61.111 0.00 0.00 0.00 4.08
88 97 2.570135 CATTCTTAAGGCAGAGGGAGC 58.430 52.381 1.85 0.00 0.00 4.70
89 98 1.656587 TTCTTAAGGCAGAGGGAGCA 58.343 50.000 1.85 0.00 0.00 4.26
98 107 1.079987 AGAGGGAGCAAGAGGAGCA 59.920 57.895 0.00 0.00 0.00 4.26
101 110 2.297129 GGGAGCAAGAGGAGCAGGT 61.297 63.158 0.00 0.00 0.00 4.00
113 122 4.664677 GCAGGTCGCGAGGTGTGT 62.665 66.667 10.24 0.00 0.00 3.72
118 127 3.066190 TCGCGAGGTGTGTAGGGG 61.066 66.667 3.71 0.00 0.00 4.79
122 131 2.423898 CGAGGTGTGTAGGGGCGAT 61.424 63.158 0.00 0.00 0.00 4.58
146 157 5.978934 CAATGTGCTTGCTCTTTTTCTTT 57.021 34.783 0.00 0.00 0.00 2.52
187 199 1.338769 GGAGGCAAAGACTAGGCGAAA 60.339 52.381 0.00 0.00 35.18 3.46
188 200 2.633488 GAGGCAAAGACTAGGCGAAAT 58.367 47.619 0.00 0.00 35.18 2.17
189 201 3.431766 GGAGGCAAAGACTAGGCGAAATA 60.432 47.826 0.00 0.00 35.18 1.40
190 202 3.532542 AGGCAAAGACTAGGCGAAATAC 58.467 45.455 0.00 0.00 35.18 1.89
191 203 3.197983 AGGCAAAGACTAGGCGAAATACT 59.802 43.478 0.00 0.00 35.18 2.12
192 204 4.404715 AGGCAAAGACTAGGCGAAATACTA 59.595 41.667 0.00 0.00 35.18 1.82
193 205 4.745620 GGCAAAGACTAGGCGAAATACTAG 59.254 45.833 0.00 0.00 41.83 2.57
194 206 4.745620 GCAAAGACTAGGCGAAATACTAGG 59.254 45.833 0.00 0.00 40.71 3.02
195 207 5.451520 GCAAAGACTAGGCGAAATACTAGGA 60.452 44.000 0.00 0.00 40.71 2.94
196 208 5.771153 AAGACTAGGCGAAATACTAGGAC 57.229 43.478 0.00 0.00 40.71 3.85
197 209 4.789807 AGACTAGGCGAAATACTAGGACA 58.210 43.478 0.00 0.00 40.71 4.02
209 236 1.212441 ACTAGGACACGAGGGACTAGG 59.788 57.143 11.28 0.00 41.55 3.02
210 237 0.106819 TAGGACACGAGGGACTAGGC 60.107 60.000 0.00 0.00 41.55 3.93
211 238 1.380112 GGACACGAGGGACTAGGCT 60.380 63.158 0.00 0.00 41.55 4.58
219 246 3.263261 CGAGGGACTAGGCTTTCTTTTC 58.737 50.000 0.00 0.00 41.55 2.29
220 247 3.611970 GAGGGACTAGGCTTTCTTTTCC 58.388 50.000 0.00 0.00 41.55 3.13
221 248 3.261083 AGGGACTAGGCTTTCTTTTCCT 58.739 45.455 0.00 0.00 36.02 3.36
230 257 3.379688 GGCTTTCTTTTCCTAGCATCAGG 59.620 47.826 0.00 0.00 35.36 3.86
234 261 2.019984 CTTTTCCTAGCATCAGGTGGC 58.980 52.381 0.00 0.00 36.99 5.01
237 264 0.471191 TCCTAGCATCAGGTGGCATG 59.529 55.000 0.00 0.00 36.99 4.06
238 265 0.471191 CCTAGCATCAGGTGGCATGA 59.529 55.000 0.00 0.00 0.00 3.07
239 266 1.073444 CCTAGCATCAGGTGGCATGAT 59.927 52.381 0.00 0.00 37.90 2.45
288 315 0.452784 GAAGCGCTAGCCAACAAACG 60.453 55.000 12.05 0.00 46.67 3.60
292 319 0.584396 CGCTAGCCAACAAACGTTCA 59.416 50.000 9.66 0.00 0.00 3.18
295 322 2.979813 GCTAGCCAACAAACGTTCATTG 59.020 45.455 2.29 14.51 0.00 2.82
301 328 3.252215 CCAACAAACGTTCATTGGCTAGA 59.748 43.478 23.18 0.00 35.52 2.43
318 345 8.556213 TTGGCTAGACGTGTCTTTATTTTATT 57.444 30.769 7.97 0.00 40.93 1.40
359 389 1.588674 TTAAATGCGCCGGTATCCAG 58.411 50.000 4.18 0.00 0.00 3.86
360 390 0.753867 TAAATGCGCCGGTATCCAGA 59.246 50.000 4.18 0.00 0.00 3.86
361 391 0.107410 AAATGCGCCGGTATCCAGAA 60.107 50.000 4.18 0.00 0.00 3.02
362 392 0.107410 AATGCGCCGGTATCCAGAAA 60.107 50.000 4.18 0.00 0.00 2.52
363 393 0.532862 ATGCGCCGGTATCCAGAAAG 60.533 55.000 4.18 0.00 0.00 2.62
491 528 0.388649 GACGCGCTCTCTTCTGGAAA 60.389 55.000 5.73 0.00 0.00 3.13
583 629 0.102481 CCCTCACGATTCGATCCGTT 59.898 55.000 13.95 0.00 36.83 4.44
584 630 1.478137 CCTCACGATTCGATCCGTTC 58.522 55.000 13.95 0.00 36.83 3.95
850 903 4.671590 TCCCTCCGTCAGCGACCA 62.672 66.667 0.00 0.00 41.33 4.02
908 971 8.923270 TGGTTATTTTGATCTTGAGTTTTTCCT 58.077 29.630 0.00 0.00 0.00 3.36
912 975 4.488126 TGATCTTGAGTTTTTCCTTGCG 57.512 40.909 0.00 0.00 0.00 4.85
913 976 3.253188 TGATCTTGAGTTTTTCCTTGCGG 59.747 43.478 0.00 0.00 0.00 5.69
1056 1125 0.249398 TTAGGAAGGTTGAGCTCCGC 59.751 55.000 12.15 3.52 34.22 5.54
1168 1237 4.719106 ACGAGGGCGAGTCGGTCT 62.719 66.667 15.52 0.00 41.88 3.85
1260 1329 1.623811 GCCAACTTCCTCCTCTACACA 59.376 52.381 0.00 0.00 0.00 3.72
1266 1335 1.267121 TCCTCCTCTACACAGCCAAC 58.733 55.000 0.00 0.00 0.00 3.77
1288 1357 2.277084 GCAGATCCGACGGTAAACATT 58.723 47.619 14.79 0.00 0.00 2.71
1294 1363 2.475864 TCCGACGGTAAACATTGTTTCG 59.524 45.455 17.64 17.28 0.00 3.46
1300 1372 6.542574 ACGGTAAACATTGTTTCGTCATAA 57.457 33.333 17.64 0.00 0.00 1.90
1331 1403 7.484035 AATTTACTCTATTTCTTGGCTAGCG 57.516 36.000 9.00 0.00 0.00 4.26
1376 1448 2.817396 GCAGCTCTCAAGGCCGAC 60.817 66.667 0.00 0.00 0.00 4.79
1461 1551 4.721776 ACAATGGGTCTGAGCCTAATTCTA 59.278 41.667 24.79 4.96 36.53 2.10
1601 1691 2.349817 CGAATCATTGCTGTAATCGGCC 60.350 50.000 0.00 0.00 44.62 6.13
1637 1727 0.250295 TGGGAAGTCTGTTGCTTCGG 60.250 55.000 0.00 0.00 42.23 4.30
1724 1814 6.446781 AAGCATACATTCAGAATTGTCCAG 57.553 37.500 0.00 0.00 0.00 3.86
1752 1842 9.503427 GTGAAACTTATATGCATTGAAGTTACC 57.497 33.333 26.40 22.22 40.36 2.85
1811 1901 7.585936 TGTGCATCGAATATAAAAATTGCGTAG 59.414 33.333 0.00 0.00 0.00 3.51
1832 1922 2.603173 GCGAACAAAGAAACCTGCTCAG 60.603 50.000 0.00 0.00 0.00 3.35
1986 2115 3.625649 TTACATGCTGCCATCTGTGTA 57.374 42.857 0.00 0.00 0.00 2.90
1987 2116 2.495155 ACATGCTGCCATCTGTGTAA 57.505 45.000 0.00 0.00 0.00 2.41
2046 2222 0.034756 TGCCACGCATCACTTGTACT 59.965 50.000 0.00 0.00 31.71 2.73
2049 2225 2.688507 CCACGCATCACTTGTACTCTT 58.311 47.619 0.00 0.00 0.00 2.85
2051 2227 3.579709 CACGCATCACTTGTACTCTTCT 58.420 45.455 0.00 0.00 0.00 2.85
2053 2229 4.559251 CACGCATCACTTGTACTCTTCTAC 59.441 45.833 0.00 0.00 0.00 2.59
2116 2400 7.912778 ATGTTTGGCATACATATTAGGGTTT 57.087 32.000 19.89 0.00 35.74 3.27
2123 2407 6.549736 GGCATACATATTAGGGTTTCTTTGGT 59.450 38.462 0.00 0.00 0.00 3.67
2124 2408 7.069455 GGCATACATATTAGGGTTTCTTTGGTT 59.931 37.037 0.00 0.00 0.00 3.67
2125 2409 7.920682 GCATACATATTAGGGTTTCTTTGGTTG 59.079 37.037 0.00 0.00 0.00 3.77
2128 2412 7.892609 ACATATTAGGGTTTCTTTGGTTGTTC 58.107 34.615 0.00 0.00 0.00 3.18
2130 2414 3.007473 AGGGTTTCTTTGGTTGTTCGA 57.993 42.857 0.00 0.00 0.00 3.71
2131 2415 3.562182 AGGGTTTCTTTGGTTGTTCGAT 58.438 40.909 0.00 0.00 0.00 3.59
2132 2416 3.958147 AGGGTTTCTTTGGTTGTTCGATT 59.042 39.130 0.00 0.00 0.00 3.34
2133 2417 4.037565 AGGGTTTCTTTGGTTGTTCGATTC 59.962 41.667 0.00 0.00 0.00 2.52
2138 2422 6.494893 TTCTTTGGTTGTTCGATTCATAGG 57.505 37.500 0.00 0.00 0.00 2.57
2139 2423 5.800296 TCTTTGGTTGTTCGATTCATAGGA 58.200 37.500 0.00 0.00 0.00 2.94
2141 2425 6.884295 TCTTTGGTTGTTCGATTCATAGGATT 59.116 34.615 0.00 0.00 0.00 3.01
2143 2427 5.739959 TGGTTGTTCGATTCATAGGATTGA 58.260 37.500 0.00 0.00 0.00 2.57
2147 2431 7.645340 GGTTGTTCGATTCATAGGATTGAATTG 59.355 37.037 7.73 7.73 44.35 2.32
2148 2432 7.864108 TGTTCGATTCATAGGATTGAATTGT 57.136 32.000 12.02 0.00 44.35 2.71
2151 2435 7.719778 TCGATTCATAGGATTGAATTGTCAG 57.280 36.000 12.02 0.62 44.35 3.51
2155 2439 9.075678 GATTCATAGGATTGAATTGTCAGGAAT 57.924 33.333 1.60 0.00 44.35 3.01
2214 2536 7.287466 TCCAATCAAACCTCTTTGAAAGAATCA 59.713 33.333 9.15 0.00 46.99 2.57
2216 2538 9.485206 CAATCAAACCTCTTTGAAAGAATCATT 57.515 29.630 9.15 0.00 46.99 2.57
2224 2546 9.925268 CCTCTTTGAAAGAATCATTTGTTTTTG 57.075 29.630 9.15 0.00 38.03 2.44
2225 2547 9.429600 CTCTTTGAAAGAATCATTTGTTTTTGC 57.570 29.630 9.15 0.00 38.03 3.68
2226 2548 9.165035 TCTTTGAAAGAATCATTTGTTTTTGCT 57.835 25.926 4.94 0.00 38.03 3.91
2230 2552 9.761504 TGAAAGAATCATTTGTTTTTGCTATGA 57.238 25.926 0.00 0.00 29.21 2.15
2233 2555 8.193250 AGAATCATTTGTTTTTGCTATGATGC 57.807 30.769 0.00 0.00 36.40 3.91
2267 2693 1.504359 CGTTAAGGTCGTGGCTTCAA 58.496 50.000 0.00 0.00 0.00 2.69
2316 2788 1.082756 CGCCAGAAGTTGACGCAAC 60.083 57.895 12.81 12.81 43.83 4.17
2364 2836 2.812011 ACGTAAAAGGAGAACATGTGCC 59.188 45.455 0.00 1.40 0.00 5.01
2366 2838 1.981256 AAAAGGAGAACATGTGCCGT 58.019 45.000 0.00 0.00 0.00 5.68
2380 2852 2.745884 CCGTTCATCTTGGCGGCA 60.746 61.111 7.97 7.97 37.69 5.69
2381 2853 2.753966 CCGTTCATCTTGGCGGCAG 61.754 63.158 12.87 6.93 37.69 4.85
2382 2854 2.753966 CGTTCATCTTGGCGGCAGG 61.754 63.158 15.41 15.41 0.00 4.85
2383 2855 2.751436 TTCATCTTGGCGGCAGGC 60.751 61.111 16.75 2.73 44.11 4.85
2458 2930 0.936691 AGCTGGATAATGGCCCCTTT 59.063 50.000 0.00 0.00 0.00 3.11
2486 2985 2.797156 GTGGCTGTCATCTGTAATAGCG 59.203 50.000 0.00 0.00 32.22 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.592637 TCGTTAACGAGTCTCGGCAA 59.407 50.000 26.00 15.39 45.59 4.52
15 16 6.200286 TGACTTCTCTTCACACATTCGTTAAC 59.800 38.462 0.00 0.00 0.00 2.01
21 23 6.620303 GCAATCTGACTTCTCTTCACACATTC 60.620 42.308 0.00 0.00 0.00 2.67
23 25 4.694509 GCAATCTGACTTCTCTTCACACAT 59.305 41.667 0.00 0.00 0.00 3.21
32 34 2.094494 TCCTCACGCAATCTGACTTCTC 60.094 50.000 0.00 0.00 0.00 2.87
40 42 1.599047 CCACCTCCTCACGCAATCT 59.401 57.895 0.00 0.00 0.00 2.40
46 48 2.928396 AACCCCCACCTCCTCACG 60.928 66.667 0.00 0.00 0.00 4.35
69 78 2.200081 TGCTCCCTCTGCCTTAAGAAT 58.800 47.619 3.36 0.00 0.00 2.40
80 89 0.977108 CTGCTCCTCTTGCTCCCTCT 60.977 60.000 0.00 0.00 0.00 3.69
88 97 2.507992 CGCGACCTGCTCCTCTTG 60.508 66.667 0.00 0.00 43.27 3.02
89 98 2.676822 TCGCGACCTGCTCCTCTT 60.677 61.111 3.71 0.00 43.27 2.85
98 107 2.341101 CCTACACACCTCGCGACCT 61.341 63.158 3.71 0.00 0.00 3.85
101 110 3.066190 CCCCTACACACCTCGCGA 61.066 66.667 9.26 9.26 0.00 5.87
106 115 3.031417 GCATCGCCCCTACACACCT 62.031 63.158 0.00 0.00 0.00 4.00
113 122 1.823470 GCACATTGCATCGCCCCTA 60.823 57.895 0.00 0.00 44.26 3.53
146 157 0.375454 CGTGTGTCGTCAGGCAAAAA 59.625 50.000 0.00 0.00 31.56 1.94
150 161 4.293648 CCCGTGTGTCGTCAGGCA 62.294 66.667 0.00 0.00 37.94 4.75
162 173 0.108138 CTAGTCTTTGCCTCCCCGTG 60.108 60.000 0.00 0.00 0.00 4.94
163 174 1.265454 CCTAGTCTTTGCCTCCCCGT 61.265 60.000 0.00 0.00 0.00 5.28
173 185 5.655532 TGTCCTAGTATTTCGCCTAGTCTTT 59.344 40.000 0.00 0.00 30.79 2.52
187 199 3.072768 CCTAGTCCCTCGTGTCCTAGTAT 59.927 52.174 0.00 0.00 0.00 2.12
188 200 2.437281 CCTAGTCCCTCGTGTCCTAGTA 59.563 54.545 0.00 0.00 0.00 1.82
189 201 1.212441 CCTAGTCCCTCGTGTCCTAGT 59.788 57.143 0.00 0.00 0.00 2.57
190 202 1.970092 CCTAGTCCCTCGTGTCCTAG 58.030 60.000 0.00 0.00 0.00 3.02
191 203 0.106819 GCCTAGTCCCTCGTGTCCTA 60.107 60.000 0.00 0.00 0.00 2.94
192 204 1.380112 GCCTAGTCCCTCGTGTCCT 60.380 63.158 0.00 0.00 0.00 3.85
193 205 0.971447 AAGCCTAGTCCCTCGTGTCC 60.971 60.000 0.00 0.00 0.00 4.02
194 206 0.896226 AAAGCCTAGTCCCTCGTGTC 59.104 55.000 0.00 0.00 0.00 3.67
195 207 0.896226 GAAAGCCTAGTCCCTCGTGT 59.104 55.000 0.00 0.00 0.00 4.49
196 208 1.187087 AGAAAGCCTAGTCCCTCGTG 58.813 55.000 0.00 0.00 0.00 4.35
197 209 1.939980 AAGAAAGCCTAGTCCCTCGT 58.060 50.000 0.00 0.00 0.00 4.18
209 236 4.013050 ACCTGATGCTAGGAAAAGAAAGC 58.987 43.478 8.85 0.00 40.42 3.51
210 237 4.397417 CCACCTGATGCTAGGAAAAGAAAG 59.603 45.833 8.85 0.00 40.42 2.62
211 238 4.335416 CCACCTGATGCTAGGAAAAGAAA 58.665 43.478 8.85 0.00 40.42 2.52
219 246 0.471191 TCATGCCACCTGATGCTAGG 59.529 55.000 0.00 0.00 43.71 3.02
220 247 2.563261 ATCATGCCACCTGATGCTAG 57.437 50.000 0.00 0.00 32.20 3.42
221 248 3.301794 AAATCATGCCACCTGATGCTA 57.698 42.857 0.00 0.00 33.69 3.49
246 273 2.480419 CGGTGCACACTCTAAAAGGAAG 59.520 50.000 20.43 0.00 0.00 3.46
248 275 1.414919 ACGGTGCACACTCTAAAAGGA 59.585 47.619 20.43 0.00 0.00 3.36
257 284 2.967076 CGCTTCACGGTGCACACT 60.967 61.111 20.43 0.00 38.44 3.55
288 315 2.960819 AGACACGTCTAGCCAATGAAC 58.039 47.619 0.00 0.00 38.35 3.18
292 319 8.732746 ATAAAATAAAGACACGTCTAGCCAAT 57.267 30.769 0.00 0.00 39.39 3.16
295 322 8.193250 TCAATAAAATAAAGACACGTCTAGCC 57.807 34.615 0.00 0.00 39.39 3.93
322 349 7.169476 CGCATTTAATTGGATGTGCAATTATCA 59.831 33.333 16.81 9.77 34.48 2.15
337 367 2.292016 TGGATACCGGCGCATTTAATTG 59.708 45.455 10.83 0.00 0.00 2.32
363 393 0.249280 CCCAACACGCAAGGTTTTCC 60.249 55.000 0.00 0.00 46.39 3.13
491 528 1.148273 TTGCGCTGGTCTTCCTTGT 59.852 52.632 9.73 0.00 34.23 3.16
583 629 2.557317 GGGTCTGTTTCGTTTGTGAGA 58.443 47.619 0.00 0.00 0.00 3.27
584 630 1.602377 GGGGTCTGTTTCGTTTGTGAG 59.398 52.381 0.00 0.00 0.00 3.51
877 940 6.735556 ACTCAAGATCAAAATAACCAGGGAT 58.264 36.000 0.00 0.00 0.00 3.85
908 971 4.081476 TCTGATGAATTCTCTTCTCCGCAA 60.081 41.667 7.05 0.00 0.00 4.85
912 975 8.558973 TTCTTTTCTGATGAATTCTCTTCTCC 57.441 34.615 7.05 0.00 31.56 3.71
939 1002 4.008074 TCAAAATCGCTTGTTCCTCTCT 57.992 40.909 0.00 0.00 0.00 3.10
940 1003 4.954092 ATCAAAATCGCTTGTTCCTCTC 57.046 40.909 0.00 0.00 0.00 3.20
1122 1191 4.148825 CGTAGAGGGCCAGCGCTT 62.149 66.667 7.50 0.00 39.38 4.68
1128 1197 1.550130 CCAAGAACCGTAGAGGGCCA 61.550 60.000 6.18 0.00 46.96 5.36
1134 1203 0.518636 CGTCGACCAAGAACCGTAGA 59.481 55.000 10.58 0.00 0.00 2.59
1318 1390 1.740296 GGACGCGCTAGCCAAGAAA 60.740 57.895 5.73 0.00 41.18 2.52
1331 1403 1.943340 GAAGATGGAATTCAGGGACGC 59.057 52.381 7.93 0.00 0.00 5.19
1376 1448 2.102084 TCCATTGAAGCTGATCCTCTCG 59.898 50.000 0.00 0.00 0.00 4.04
1415 1487 2.029844 GGCGACAGTCTTCTGCCAC 61.030 63.158 11.27 0.00 45.06 5.01
1427 1499 1.963855 CCCATTGTTGTCGGCGACA 60.964 57.895 36.29 36.29 41.09 4.35
1461 1551 3.665971 CCCCTTTCTGCCTGGGCT 61.666 66.667 13.05 0.00 42.51 5.19
1557 1647 1.852895 GAATCGAGCGCACTTATTCGT 59.147 47.619 11.47 0.00 34.83 3.85
1601 1691 4.433186 TCCCAATGCAGTAAAATTGACG 57.567 40.909 0.00 0.00 36.13 4.35
1703 1793 5.124457 ACACTGGACAATTCTGAATGTATGC 59.876 40.000 3.22 0.00 0.00 3.14
1724 1814 8.970691 AACTTCAATGCATATAAGTTTCACAC 57.029 30.769 23.65 0.00 38.65 3.82
1752 1842 5.277058 GCATAAGCATCGAACCAGAGTAAAG 60.277 44.000 0.00 0.00 41.58 1.85
1811 1901 1.333619 TGAGCAGGTTTCTTTGTTCGC 59.666 47.619 0.00 0.00 0.00 4.70
1892 2011 4.971939 TGGCAGCATATTATTAGCACTGA 58.028 39.130 0.00 0.00 0.00 3.41
2049 2225 9.671279 TTGCTTATTGATGATTTGAGAAGTAGA 57.329 29.630 0.00 0.00 0.00 2.59
2053 2229 9.234384 GTCATTGCTTATTGATGATTTGAGAAG 57.766 33.333 0.00 0.00 32.92 2.85
2116 2400 5.800296 TCCTATGAATCGAACAACCAAAGA 58.200 37.500 0.00 0.00 0.00 2.52
2123 2407 8.279970 ACAATTCAATCCTATGAATCGAACAA 57.720 30.769 3.26 0.00 46.57 2.83
2124 2408 7.552330 TGACAATTCAATCCTATGAATCGAACA 59.448 33.333 3.26 0.00 46.57 3.18
2125 2409 7.919690 TGACAATTCAATCCTATGAATCGAAC 58.080 34.615 3.26 0.00 46.57 3.95
2128 2412 6.707608 TCCTGACAATTCAATCCTATGAATCG 59.292 38.462 3.26 0.00 46.57 3.34
2131 2415 8.827832 AATTCCTGACAATTCAATCCTATGAA 57.172 30.769 0.00 0.00 43.03 2.57
2132 2416 8.827832 AAATTCCTGACAATTCAATCCTATGA 57.172 30.769 0.00 0.00 0.00 2.15
2133 2417 9.880157 AAAAATTCCTGACAATTCAATCCTATG 57.120 29.630 0.00 0.00 0.00 2.23
2172 2456 9.066892 GTTTGATTGGATGCAGGATATAGTAAA 57.933 33.333 0.00 0.00 0.00 2.01
2181 2503 2.309755 AGAGGTTTGATTGGATGCAGGA 59.690 45.455 0.00 0.00 0.00 3.86
2214 2536 6.331845 TGATCGCATCATAGCAAAAACAAAT 58.668 32.000 0.00 0.00 33.59 2.32
2216 2538 5.307926 TGATCGCATCATAGCAAAAACAA 57.692 34.783 0.00 0.00 33.59 2.83
2229 2551 1.818850 GCACAACACATGATCGCATC 58.181 50.000 0.00 0.00 30.68 3.91
2230 2552 0.097499 CGCACAACACATGATCGCAT 59.903 50.000 0.00 0.00 34.29 4.73
2232 2554 0.110238 AACGCACAACACATGATCGC 60.110 50.000 0.00 0.00 33.16 4.58
2233 2555 3.407252 CTTAACGCACAACACATGATCG 58.593 45.455 0.00 0.00 34.95 3.69
2267 2693 8.006298 TGTCACTATCTGAATTTGTGGTTTTT 57.994 30.769 0.00 0.00 0.00 1.94
2316 2788 1.966451 GAACCAGCACAACTCCGGG 60.966 63.158 0.00 0.00 0.00 5.73
2327 2799 0.321653 ACGTCCCAATCAGAACCAGC 60.322 55.000 0.00 0.00 0.00 4.85
2364 2836 2.753966 CCTGCCGCCAAGATGAACG 61.754 63.158 0.00 0.00 0.00 3.95
2366 2838 2.751436 GCCTGCCGCCAAGATGAA 60.751 61.111 0.00 0.00 0.00 2.57
2382 2854 2.127232 ATTTGTATGGCCGGCCTGC 61.127 57.895 43.34 31.39 36.94 4.85
2383 2855 1.735360 CATTTGTATGGCCGGCCTG 59.265 57.895 43.34 28.42 36.94 4.85
2407 2879 0.934496 GCAACAGCTACACGTTGTCA 59.066 50.000 14.12 0.00 43.52 3.58
2408 2880 1.070577 CAGCAACAGCTACACGTTGTC 60.071 52.381 14.12 8.12 43.52 3.18
2431 2903 3.415212 GCCATTATCCAGCTGATAGCAA 58.585 45.455 17.39 1.95 45.56 3.91
2434 2906 2.356535 GGGGCCATTATCCAGCTGATAG 60.357 54.545 17.39 0.00 37.26 2.08
2436 2908 0.407139 GGGGCCATTATCCAGCTGAT 59.593 55.000 17.39 9.50 37.49 2.90
2458 2930 2.158769 ACAGATGACAGCCACAGTTCAA 60.159 45.455 0.00 0.00 0.00 2.69
2486 2985 1.199097 CCCGTTTATATGCATTCGCCC 59.801 52.381 3.54 0.00 37.32 6.13


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

AutoCloner maintained by Alex Coulton.