Multiple sequence alignment - TraesCS1B01G138000

Loading Multiple Alignment...

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 TraesCS1B01G138000 chr1B 100.000 3126 0 0 1 3126 177003175 177000050 0.000000e+00 5773.0
1 TraesCS1B01G138000 chr1B 100.000 1088 0 0 3426 4513 176999750 176998663 0.000000e+00 2010.0
2 TraesCS1B01G138000 chr1A 95.229 2180 74 12 1 2175 126859493 126857339 0.000000e+00 3422.0
3 TraesCS1B01G138000 chr1A 94.747 1066 35 2 3467 4513 126856146 126855083 0.000000e+00 1639.0
4 TraesCS1B01G138000 chr1A 95.128 862 30 6 2265 3126 126857329 126856480 0.000000e+00 1349.0
5 TraesCS1B01G138000 chr1A 100.000 45 0 0 3426 3470 126856213 126856169 2.890000e-12 84.2
6 TraesCS1B01G138000 chr1D 96.489 1823 51 10 359 2175 115578811 115576996 0.000000e+00 3000.0
7 TraesCS1B01G138000 chr1D 95.028 1066 34 1 3467 4513 115575662 115574597 0.000000e+00 1657.0
8 TraesCS1B01G138000 chr1D 95.991 873 33 1 2254 3126 115576997 115576127 0.000000e+00 1417.0
9 TraesCS1B01G138000 chr1D 89.691 97 6 3 2162 2255 106843197 106843292 2.210000e-23 121.0
10 TraesCS1B01G138000 chr1D 100.000 45 0 0 3426 3470 115575729 115575685 2.890000e-12 84.2
11 TraesCS1B01G138000 chr5D 86.648 352 30 10 1 337 360408873 360408524 1.530000e-99 374.0
12 TraesCS1B01G138000 chr5D 85.593 118 10 6 2142 2256 267846569 267846682 2.850000e-22 117.0
13 TraesCS1B01G138000 chr7D 93.258 89 3 2 2174 2259 79628344 79628432 1.320000e-25 128.0
14 TraesCS1B01G138000 chr7D 89.899 99 3 6 2163 2256 441864130 441864034 2.210000e-23 121.0
15 TraesCS1B01G138000 chr6D 94.118 85 2 2 2174 2255 146072823 146072907 4.740000e-25 126.0
16 TraesCS1B01G138000 chr6D 86.364 110 9 5 2174 2277 146072907 146072798 1.030000e-21 115.0
17 TraesCS1B01G138000 chr7A 93.103 87 3 2 2172 2255 501073965 501073879 1.700000e-24 124.0
18 TraesCS1B01G138000 chr3D 92.045 88 5 1 2173 2258 26654212 26654125 6.130000e-24 122.0
19 TraesCS1B01G138000 chr3D 90.526 95 6 2 2171 2262 54370500 54370406 6.130000e-24 122.0
20 TraesCS1B01G138000 chr5B 85.586 111 13 2 2151 2258 531365138 531365248 3.690000e-21 113.0


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 TraesCS1B01G138000 chr1B 176998663 177003175 4512 True 3891.50 5773 100.000 1 4513 2 chr1B.!!$R1 4512
1 TraesCS1B01G138000 chr1A 126855083 126859493 4410 True 1623.55 3422 96.276 1 4513 4 chr1A.!!$R1 4512
2 TraesCS1B01G138000 chr1D 115574597 115578811 4214 True 1539.55 3000 96.877 359 4513 4 chr1D.!!$R1 4154

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
126 129 0.253894 CCATGCCAGATCAGGTGACA 59.746 55.0 5.98 0.00 0.0 3.58 F
247 250 0.320697 GTGGTGCCGACTAGTCCTTT 59.679 55.0 17.23 0.00 0.0 3.11 F
248 251 0.606604 TGGTGCCGACTAGTCCTTTC 59.393 55.0 17.23 5.88 0.0 2.62 F
249 252 0.896226 GGTGCCGACTAGTCCTTTCT 59.104 55.0 17.23 0.00 0.0 2.52 F
2187 2197 0.967662 GCTTATACTCCCTCCGTCCC 59.032 60.0 0.00 0.00 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 1760 0.902531 ACCCACTAATCACACTCCCG 59.097 55.000 0.0 0.0 0.0 5.14 R
2237 2247 0.178970 GCTACTCCCTCCGTCCCATA 60.179 60.000 0.0 0.0 0.0 2.74 R
2241 2251 0.396001 AAGAGCTACTCCCTCCGTCC 60.396 60.000 0.0 0.0 0.0 4.79 R
2248 2258 1.136500 CCAACGGTAAGAGCTACTCCC 59.864 57.143 0.0 0.0 0.0 4.30 R
3935 4069 0.524862 CACTGCTGACAATGAAGGGC 59.475 55.000 0.0 0.0 0.0 5.19 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
31 32 1.248101 TGCGGATGTCGTCTTCCTCA 61.248 55.000 11.66 7.81 41.72 3.86
54 55 1.593296 GAGGTACCGTCGTGGAGCTT 61.593 60.000 6.18 0.00 42.00 3.74
90 91 2.370445 ATGGCTTGAGGTCTCCGGG 61.370 63.158 0.00 0.00 0.00 5.73
109 112 1.691434 GGTGAAAACCAAATCAGGCCA 59.309 47.619 5.01 0.00 0.00 5.36
126 129 0.253894 CCATGCCAGATCAGGTGACA 59.746 55.000 5.98 0.00 0.00 3.58
151 154 3.430042 TGTCCTCGACACTAGTACCTT 57.570 47.619 0.00 0.00 37.67 3.50
190 193 1.806496 AGACCCGATGATGGATTCCA 58.194 50.000 8.08 8.08 38.19 3.53
194 197 2.165167 CCCGATGATGGATTCCAATGG 58.835 52.381 9.98 7.19 36.95 3.16
203 206 2.224646 TGGATTCCAATGGTGTTCACGA 60.225 45.455 1.94 0.00 0.00 4.35
212 215 0.665835 GGTGTTCACGATTGTTGGCA 59.334 50.000 0.00 0.00 0.00 4.92
229 232 1.448540 CAGAGCTTCGGATTGCGGT 60.449 57.895 0.00 0.00 0.00 5.68
244 247 2.577593 GGTGGTGCCGACTAGTCC 59.422 66.667 17.23 3.93 0.00 3.85
245 248 1.982938 GGTGGTGCCGACTAGTCCT 60.983 63.158 17.23 0.00 0.00 3.85
246 249 1.542187 GGTGGTGCCGACTAGTCCTT 61.542 60.000 17.23 0.00 0.00 3.36
247 250 0.320697 GTGGTGCCGACTAGTCCTTT 59.679 55.000 17.23 0.00 0.00 3.11
248 251 0.606604 TGGTGCCGACTAGTCCTTTC 59.393 55.000 17.23 5.88 0.00 2.62
249 252 0.896226 GGTGCCGACTAGTCCTTTCT 59.104 55.000 17.23 0.00 0.00 2.52
250 253 1.275573 GGTGCCGACTAGTCCTTTCTT 59.724 52.381 17.23 0.00 0.00 2.52
251 254 2.289506 GGTGCCGACTAGTCCTTTCTTT 60.290 50.000 17.23 0.00 0.00 2.52
278 281 8.702163 TTTCTTTCTTTTCTTTTTGCACTAGG 57.298 30.769 0.00 0.00 0.00 3.02
279 282 6.273071 TCTTTCTTTTCTTTTTGCACTAGGC 58.727 36.000 0.00 0.00 45.13 3.93
281 284 3.320826 TCTTTTCTTTTTGCACTAGGCCC 59.679 43.478 0.00 0.00 43.89 5.80
309 312 4.520492 AGGTGTTCTTGTAATGCCTCTTTG 59.480 41.667 0.00 0.00 0.00 2.77
332 335 8.408043 TTGTGATCAATGAATTTGGTAACTCT 57.592 30.769 0.00 0.00 31.71 3.24
333 336 8.408043 TGTGATCAATGAATTTGGTAACTCTT 57.592 30.769 0.00 0.00 31.71 2.85
342 345 9.668497 ATGAATTTGGTAACTCTTCTACTAACC 57.332 33.333 0.00 0.00 37.61 2.85
347 350 7.001099 TGGTAACTCTTCTACTAACCTTTGG 57.999 40.000 0.00 0.00 37.61 3.28
377 380 7.552458 ACAATTATATCTCATTGTTCGTGCA 57.448 32.000 3.18 0.00 40.05 4.57
385 388 3.872696 TCATTGTTCGTGCATAGACCAT 58.127 40.909 0.00 0.00 0.00 3.55
393 396 3.009723 CGTGCATAGACCATTTCCTTGT 58.990 45.455 0.00 0.00 0.00 3.16
399 402 5.450965 GCATAGACCATTTCCTTGTGAATGG 60.451 44.000 12.27 12.27 37.51 3.16
405 409 6.054941 ACCATTTCCTTGTGAATGGTTTTTC 58.945 36.000 13.42 0.00 39.64 2.29
780 788 4.752514 CGCCTCCGGATCTAAACC 57.247 61.111 3.57 0.00 0.00 3.27
896 904 4.063967 CGCTGCGTGTCCTGGGTA 62.064 66.667 14.93 0.00 0.00 3.69
902 910 1.911766 CGTGTCCTGGGTAGGTGGT 60.912 63.158 0.00 0.00 44.88 4.16
906 914 3.728373 CCTGGGTAGGTGGTGGGC 61.728 72.222 0.00 0.00 39.39 5.36
933 941 2.019807 TTACTTCTCCCTGGTCCGTT 57.980 50.000 0.00 0.00 0.00 4.44
938 946 1.450312 CTCCCTGGTCCGTTCATGC 60.450 63.158 0.00 0.00 0.00 4.06
1085 1093 3.682292 GATCTCCGCCGCCCAAGTT 62.682 63.158 0.00 0.00 0.00 2.66
1512 1520 2.178521 CGGTTCGTCACCTCTCCG 59.821 66.667 5.23 0.00 44.69 4.63
1516 1524 1.228337 TTCGTCACCTCTCCGGTCA 60.228 57.895 0.00 0.00 44.93 4.02
1612 1620 4.302067 TGATCCTAGAGAAAGGGATTGCT 58.698 43.478 0.00 0.00 39.63 3.91
1638 1646 9.929180 TTGAAGACAGTATTGCATAGGATATAC 57.071 33.333 0.00 0.00 0.00 1.47
1734 1742 2.292267 GATCGTCACAATGGGATTGCT 58.708 47.619 0.00 0.00 43.98 3.91
1752 1760 2.147150 GCTGAACTCTTGGAGGTGTTC 58.853 52.381 0.00 0.00 39.18 3.18
2022 2030 2.417787 GCTGGAATTGACAGAAATGCCC 60.418 50.000 10.16 0.00 34.62 5.36
2025 2033 2.098117 GGAATTGACAGAAATGCCCGAG 59.902 50.000 0.00 0.00 29.73 4.63
2150 2160 5.105146 TCCTATTGCCAGTGTTTGTTGTTTT 60.105 36.000 0.00 0.00 0.00 2.43
2181 2191 8.916062 AGTTTCTTTACTAGCTTATACTCCCTC 58.084 37.037 0.00 0.00 0.00 4.30
2182 2192 7.836479 TTCTTTACTAGCTTATACTCCCTCC 57.164 40.000 0.00 0.00 0.00 4.30
2183 2193 6.002704 TCTTTACTAGCTTATACTCCCTCCG 58.997 44.000 0.00 0.00 0.00 4.63
2184 2194 3.880168 ACTAGCTTATACTCCCTCCGT 57.120 47.619 0.00 0.00 0.00 4.69
2185 2195 3.753815 ACTAGCTTATACTCCCTCCGTC 58.246 50.000 0.00 0.00 0.00 4.79
2186 2196 1.998222 AGCTTATACTCCCTCCGTCC 58.002 55.000 0.00 0.00 0.00 4.79
2187 2197 0.967662 GCTTATACTCCCTCCGTCCC 59.032 60.000 0.00 0.00 0.00 4.46
2188 2198 1.756690 GCTTATACTCCCTCCGTCCCA 60.757 57.143 0.00 0.00 0.00 4.37
2189 2199 2.890814 CTTATACTCCCTCCGTCCCAT 58.109 52.381 0.00 0.00 0.00 4.00
2190 2200 3.816842 GCTTATACTCCCTCCGTCCCATA 60.817 52.174 0.00 0.00 0.00 2.74
2191 2201 4.413760 CTTATACTCCCTCCGTCCCATAA 58.586 47.826 0.00 0.00 0.00 1.90
2192 2202 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
2193 2203 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
2194 2204 2.606378 ACTCCCTCCGTCCCATAATAC 58.394 52.381 0.00 0.00 0.00 1.89
2195 2205 1.544691 CTCCCTCCGTCCCATAATACG 59.455 57.143 0.00 0.00 38.80 3.06
2196 2206 1.145531 TCCCTCCGTCCCATAATACGA 59.854 52.381 0.00 0.00 41.55 3.43
2197 2207 1.544691 CCCTCCGTCCCATAATACGAG 59.455 57.143 0.00 0.00 41.55 4.18
2198 2208 2.236766 CCTCCGTCCCATAATACGAGT 58.763 52.381 0.00 0.00 41.55 4.18
2199 2209 2.030185 CCTCCGTCCCATAATACGAGTG 60.030 54.545 0.00 0.00 41.55 3.51
2200 2210 2.621998 CTCCGTCCCATAATACGAGTGT 59.378 50.000 0.00 0.00 41.55 3.55
2201 2211 3.025978 TCCGTCCCATAATACGAGTGTT 58.974 45.455 0.00 0.00 41.55 3.32
2202 2212 3.448301 TCCGTCCCATAATACGAGTGTTT 59.552 43.478 0.00 0.00 41.55 2.83
2203 2213 4.081531 TCCGTCCCATAATACGAGTGTTTT 60.082 41.667 0.00 0.00 41.55 2.43
2204 2214 4.033587 CCGTCCCATAATACGAGTGTTTTG 59.966 45.833 0.00 0.00 41.55 2.44
2205 2215 4.865925 CGTCCCATAATACGAGTGTTTTGA 59.134 41.667 0.00 0.00 41.55 2.69
2206 2216 5.220340 CGTCCCATAATACGAGTGTTTTGAC 60.220 44.000 0.00 0.00 41.55 3.18
2207 2217 5.640357 GTCCCATAATACGAGTGTTTTGACA 59.360 40.000 0.00 0.00 0.00 3.58
2208 2218 5.640357 TCCCATAATACGAGTGTTTTGACAC 59.360 40.000 1.58 1.58 40.69 3.67
2243 2253 9.967451 TGTCAAAAACACTCTTATATTATGGGA 57.033 29.630 0.00 0.00 31.20 4.37
2245 2255 9.104965 TCAAAAACACTCTTATATTATGGGACG 57.895 33.333 0.00 0.00 0.00 4.79
2246 2256 8.342634 CAAAAACACTCTTATATTATGGGACGG 58.657 37.037 0.00 0.00 0.00 4.79
2247 2257 6.989155 AACACTCTTATATTATGGGACGGA 57.011 37.500 0.00 0.00 0.00 4.69
2248 2258 6.591750 ACACTCTTATATTATGGGACGGAG 57.408 41.667 0.00 0.00 0.00 4.63
2249 2259 5.480772 ACACTCTTATATTATGGGACGGAGG 59.519 44.000 0.00 0.00 0.00 4.30
2250 2260 5.024118 ACTCTTATATTATGGGACGGAGGG 58.976 45.833 0.00 0.00 0.00 4.30
2251 2261 5.222484 ACTCTTATATTATGGGACGGAGGGA 60.222 44.000 0.00 0.00 0.00 4.20
2252 2262 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2253 2263 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2254 2264 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2255 2265 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
2256 2266 0.178970 TATGGGACGGAGGGAGTAGC 60.179 60.000 0.00 0.00 0.00 3.58
2257 2267 1.950748 ATGGGACGGAGGGAGTAGCT 61.951 60.000 0.00 0.00 0.00 3.32
2258 2268 1.829096 GGGACGGAGGGAGTAGCTC 60.829 68.421 0.00 0.00 0.00 4.09
2259 2269 1.227946 GGACGGAGGGAGTAGCTCT 59.772 63.158 0.00 0.00 0.00 4.09
2260 2270 0.396001 GGACGGAGGGAGTAGCTCTT 60.396 60.000 0.00 0.00 0.00 2.85
2261 2271 1.133853 GGACGGAGGGAGTAGCTCTTA 60.134 57.143 0.00 0.00 0.00 2.10
2262 2272 1.948834 GACGGAGGGAGTAGCTCTTAC 59.051 57.143 0.00 0.00 0.00 2.34
2263 2273 1.320507 CGGAGGGAGTAGCTCTTACC 58.679 60.000 0.00 0.00 32.37 2.85
2295 2305 4.997395 TCAGAACACTCATTTAGTTCAGGC 59.003 41.667 0.00 0.00 43.00 4.85
2317 2327 8.896744 CAGGCAGTTATTTCAATTGAGAATCTA 58.103 33.333 8.41 2.40 34.92 1.98
2347 2357 8.744652 CATTCTTGTGGGTGGTATTTGTATTTA 58.255 33.333 0.00 0.00 0.00 1.40
2423 2433 9.844790 CAAATTATACTTTGCTCACAGAATTCA 57.155 29.630 8.44 0.00 30.06 2.57
2449 2459 6.997239 TCAGAGATTCTTCACATTTGGATG 57.003 37.500 0.00 0.00 39.25 3.51
2506 2516 5.622914 GCTGAGTAATCACACCAATGCAAAT 60.623 40.000 0.00 0.00 0.00 2.32
2544 2554 5.690865 TCTCCTTATGTTGTTTGTTGGAGT 58.309 37.500 0.00 0.00 40.30 3.85
2686 2696 7.055667 TCATACAATCCTAGCCTAGAAACTG 57.944 40.000 0.00 0.00 0.00 3.16
2879 2889 7.869429 ACAATGAATGTCAGGAAAATGTTCTTC 59.131 33.333 0.00 0.00 37.96 2.87
2910 2920 0.318445 GAAGCTGCTGTTGGCTTGTG 60.318 55.000 1.35 0.00 46.91 3.33
2949 2959 1.028868 GGAAGAGAAGCAAGCCGCAT 61.029 55.000 0.00 0.00 46.13 4.73
3047 3057 3.243873 GCTTTGCTGCTTTTCCTAAACCT 60.244 43.478 0.00 0.00 0.00 3.50
3065 3075 1.381872 TGCTCCTCTGGTAGCTCCC 60.382 63.158 0.00 0.00 39.53 4.30
3510 3644 7.118723 TGACAAGATAATGCCCAATTCTAGTT 58.881 34.615 0.00 0.00 0.00 2.24
3548 3682 1.141053 ACTTTGGATATGGGAGGTCGC 59.859 52.381 0.00 0.00 0.00 5.19
3648 3782 3.347958 TTTGATGGACGAGCAAACAAC 57.652 42.857 0.00 0.00 35.02 3.32
3678 3812 2.694628 TCCACAGTGCTTTTCATGCTTT 59.305 40.909 0.00 0.00 0.00 3.51
3759 3893 5.352293 CAGTAAGCATTGCTACATGTTCTGA 59.648 40.000 12.39 0.00 39.72 3.27
3765 3899 6.544931 AGCATTGCTACATGTTCTGATATTGT 59.455 34.615 10.00 0.00 36.99 2.71
3767 3901 8.509690 GCATTGCTACATGTTCTGATATTGTAT 58.490 33.333 2.30 0.00 0.00 2.29
3829 3963 3.449737 AGGATGATTTGCCTTTGACATGG 59.550 43.478 0.00 0.00 0.00 3.66
3836 3970 7.319646 TGATTTGCCTTTGACATGGTAAATAC 58.680 34.615 17.46 13.42 44.53 1.89
4105 4239 9.696917 CCTAATTTCACCTAAATATTCAATGGC 57.303 33.333 0.00 0.00 36.76 4.40
4150 4284 2.407090 TCAGTGCACATTTCTCAGTCG 58.593 47.619 21.04 0.00 0.00 4.18
4264 4398 7.563724 AAAGATACTCTTACAGGGTTTGGTA 57.436 36.000 0.00 0.00 35.27 3.25
4265 4399 7.563724 AAGATACTCTTACAGGGTTTGGTAA 57.436 36.000 0.00 0.00 34.42 2.85
4281 4415 6.038714 GGTTTGGTAAGATAAGCTTGATGGAG 59.961 42.308 9.86 0.00 37.42 3.86
4508 4661 4.165372 AGTCCTTTTTGTTCCTACTGGTGA 59.835 41.667 0.00 0.00 34.23 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.134530 GAAGACGACATCCGCAGACG 61.135 60.000 0.00 0.00 43.32 4.18
13 14 0.103208 ATGAGGAAGACGACATCCGC 59.897 55.000 6.01 6.01 43.32 5.54
31 32 0.612732 TCCACGACGGTACCTCCAAT 60.613 55.000 10.90 0.00 35.57 3.16
54 55 1.065199 CATGGGGTAAGAAGAGCAGCA 60.065 52.381 0.00 0.00 0.00 4.41
90 91 3.328505 CATGGCCTGATTTGGTTTTCAC 58.671 45.455 3.32 0.00 0.00 3.18
109 112 1.065636 CACTGTCACCTGATCTGGCAT 60.066 52.381 17.94 0.00 0.00 4.40
190 193 2.288152 GCCAACAATCGTGAACACCATT 60.288 45.455 0.00 0.00 0.00 3.16
194 197 1.601903 TCTGCCAACAATCGTGAACAC 59.398 47.619 0.00 0.00 0.00 3.32
203 206 0.036732 TCCGAAGCTCTGCCAACAAT 59.963 50.000 0.00 0.00 0.00 2.71
212 215 1.448540 CACCGCAATCCGAAGCTCT 60.449 57.895 0.00 0.00 40.02 4.09
229 232 0.606604 GAAAGGACTAGTCGGCACCA 59.393 55.000 16.56 0.00 0.00 4.17
256 259 5.463392 GGCCTAGTGCAAAAAGAAAAGAAAG 59.537 40.000 0.00 0.00 43.89 2.62
266 269 0.608035 CCGAGGGCCTAGTGCAAAAA 60.608 55.000 5.73 0.00 43.89 1.94
278 281 1.376037 CAAGAACACCTCCGAGGGC 60.376 63.158 18.99 5.24 40.58 5.19
279 282 1.263356 TACAAGAACACCTCCGAGGG 58.737 55.000 18.99 9.96 40.58 4.30
281 284 2.673368 GCATTACAAGAACACCTCCGAG 59.327 50.000 0.00 0.00 0.00 4.63
309 312 8.734386 AGAAGAGTTACCAAATTCATTGATCAC 58.266 33.333 0.00 0.00 41.85 3.06
354 357 9.750882 CTATGCACGAACAATGAGATATAATTG 57.249 33.333 0.00 0.00 39.26 2.32
377 380 5.831103 ACCATTCACAAGGAAATGGTCTAT 58.169 37.500 12.73 0.00 40.38 1.98
385 388 6.538021 CACATGAAAAACCATTCACAAGGAAA 59.462 34.615 0.00 0.00 41.78 3.13
393 396 4.989797 GCATGTCACATGAAAAACCATTCA 59.010 37.500 22.56 0.00 43.03 2.57
399 402 4.118410 TGGTTGCATGTCACATGAAAAAC 58.882 39.130 22.56 19.16 0.00 2.43
405 409 3.374220 AAGTTGGTTGCATGTCACATG 57.626 42.857 13.93 13.93 0.00 3.21
851 859 1.317613 AATCTTGCAAGGCAACGACA 58.682 45.000 25.73 4.61 43.99 4.35
852 860 2.053627 CAAATCTTGCAAGGCAACGAC 58.946 47.619 25.73 0.00 43.99 4.34
902 910 1.073284 GAGAAGTAAACCCACTGCCCA 59.927 52.381 0.00 0.00 0.00 5.36
906 914 2.290323 CCAGGGAGAAGTAAACCCACTG 60.290 54.545 0.00 0.00 45.43 3.66
933 941 2.827322 CACCCATTTCAAGGAAGCATGA 59.173 45.455 0.00 0.00 0.00 3.07
938 946 3.503748 GTCAGACACCCATTTCAAGGAAG 59.496 47.826 0.00 0.00 0.00 3.46
1512 1520 1.474077 GCCACCTTCACATCAATGACC 59.526 52.381 0.00 0.00 0.00 4.02
1516 1524 1.742761 CGAGCCACCTTCACATCAAT 58.257 50.000 0.00 0.00 0.00 2.57
1612 1620 9.929180 GTATATCCTATGCAATACTGTCTTCAA 57.071 33.333 0.00 0.00 0.00 2.69
1638 1646 3.550030 GCCGATTACCCATGAATTTTCCG 60.550 47.826 0.00 0.00 0.00 4.30
1734 1742 1.070134 CCGAACACCTCCAAGAGTTCA 59.930 52.381 0.00 0.00 40.14 3.18
1752 1760 0.902531 ACCCACTAATCACACTCCCG 59.097 55.000 0.00 0.00 0.00 5.14
1968 1976 2.776536 CTCCCCCAAGAACATCATCTCT 59.223 50.000 0.00 0.00 0.00 3.10
2022 2030 1.081892 CCATGCACTTCTGGAACTCG 58.918 55.000 0.00 0.00 34.24 4.18
2025 2033 1.168714 GGACCATGCACTTCTGGAAC 58.831 55.000 11.04 4.67 36.35 3.62
2175 2185 1.544691 CGTATTATGGGACGGAGGGAG 59.455 57.143 0.00 0.00 35.43 4.30
2176 2186 1.145531 TCGTATTATGGGACGGAGGGA 59.854 52.381 0.00 0.00 39.53 4.20
2177 2187 1.544691 CTCGTATTATGGGACGGAGGG 59.455 57.143 0.00 0.00 39.53 4.30
2179 2189 2.621998 ACACTCGTATTATGGGACGGAG 59.378 50.000 0.00 0.00 39.53 4.63
2181 2191 3.447918 AACACTCGTATTATGGGACGG 57.552 47.619 0.00 0.00 39.53 4.79
2182 2192 4.865925 TCAAAACACTCGTATTATGGGACG 59.134 41.667 0.00 0.00 40.43 4.79
2183 2193 5.640357 TGTCAAAACACTCGTATTATGGGAC 59.360 40.000 0.00 0.00 0.00 4.46
2184 2194 5.795972 TGTCAAAACACTCGTATTATGGGA 58.204 37.500 0.00 0.00 0.00 4.37
2217 2227 9.967451 TCCCATAATATAAGAGTGTTTTTGACA 57.033 29.630 0.00 0.00 35.42 3.58
2219 2229 9.104965 CGTCCCATAATATAAGAGTGTTTTTGA 57.895 33.333 0.00 0.00 0.00 2.69
2220 2230 8.342634 CCGTCCCATAATATAAGAGTGTTTTTG 58.657 37.037 0.00 0.00 0.00 2.44
2221 2231 8.269317 TCCGTCCCATAATATAAGAGTGTTTTT 58.731 33.333 0.00 0.00 0.00 1.94
2222 2232 7.798071 TCCGTCCCATAATATAAGAGTGTTTT 58.202 34.615 0.00 0.00 0.00 2.43
2223 2233 7.369551 TCCGTCCCATAATATAAGAGTGTTT 57.630 36.000 0.00 0.00 0.00 2.83
2224 2234 6.014499 CCTCCGTCCCATAATATAAGAGTGTT 60.014 42.308 0.00 0.00 0.00 3.32
2225 2235 5.480772 CCTCCGTCCCATAATATAAGAGTGT 59.519 44.000 0.00 0.00 0.00 3.55
2226 2236 5.105310 CCCTCCGTCCCATAATATAAGAGTG 60.105 48.000 0.00 0.00 0.00 3.51
2227 2237 5.024118 CCCTCCGTCCCATAATATAAGAGT 58.976 45.833 0.00 0.00 0.00 3.24
2228 2238 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2229 2239 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2230 2240 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2231 2241 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2232 2242 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2233 2243 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2234 2244 3.816842 GCTACTCCCTCCGTCCCATAATA 60.817 52.174 0.00 0.00 0.00 0.98
2235 2245 2.890814 CTACTCCCTCCGTCCCATAAT 58.109 52.381 0.00 0.00 0.00 1.28
2236 2246 1.756690 GCTACTCCCTCCGTCCCATAA 60.757 57.143 0.00 0.00 0.00 1.90
2237 2247 0.178970 GCTACTCCCTCCGTCCCATA 60.179 60.000 0.00 0.00 0.00 2.74
2238 2248 1.457831 GCTACTCCCTCCGTCCCAT 60.458 63.158 0.00 0.00 0.00 4.00
2239 2249 2.043248 GCTACTCCCTCCGTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
2240 2250 1.829096 GAGCTACTCCCTCCGTCCC 60.829 68.421 0.00 0.00 0.00 4.46
2241 2251 0.396001 AAGAGCTACTCCCTCCGTCC 60.396 60.000 0.00 0.00 0.00 4.79
2242 2252 1.948834 GTAAGAGCTACTCCCTCCGTC 59.051 57.143 0.00 0.00 0.00 4.79
2243 2253 1.409942 GGTAAGAGCTACTCCCTCCGT 60.410 57.143 0.00 0.00 0.00 4.69
2244 2254 1.320507 GGTAAGAGCTACTCCCTCCG 58.679 60.000 0.00 0.00 0.00 4.63
2245 2255 1.320507 CGGTAAGAGCTACTCCCTCC 58.679 60.000 0.00 0.00 0.00 4.30
2246 2256 2.055684 ACGGTAAGAGCTACTCCCTC 57.944 55.000 0.00 0.00 0.00 4.30
2247 2257 2.100989 CAACGGTAAGAGCTACTCCCT 58.899 52.381 0.00 0.00 0.00 4.20
2248 2258 1.136500 CCAACGGTAAGAGCTACTCCC 59.864 57.143 0.00 0.00 0.00 4.30
2249 2259 1.823610 ACCAACGGTAAGAGCTACTCC 59.176 52.381 0.00 0.00 32.11 3.85
2250 2260 3.251571 CAACCAACGGTAAGAGCTACTC 58.748 50.000 0.00 0.00 33.12 2.59
2251 2261 2.631545 ACAACCAACGGTAAGAGCTACT 59.368 45.455 0.00 0.00 33.12 2.57
2252 2262 2.991866 GACAACCAACGGTAAGAGCTAC 59.008 50.000 0.00 0.00 33.12 3.58
2253 2263 2.629137 TGACAACCAACGGTAAGAGCTA 59.371 45.455 0.00 0.00 33.12 3.32
2254 2264 1.414919 TGACAACCAACGGTAAGAGCT 59.585 47.619 0.00 0.00 33.12 4.09
2255 2265 1.798813 CTGACAACCAACGGTAAGAGC 59.201 52.381 0.00 0.00 33.12 4.09
2256 2266 3.380479 TCTGACAACCAACGGTAAGAG 57.620 47.619 0.00 0.00 33.12 2.85
2257 2267 3.118702 TGTTCTGACAACCAACGGTAAGA 60.119 43.478 0.00 0.00 33.12 2.10
2258 2268 3.001939 GTGTTCTGACAACCAACGGTAAG 59.998 47.826 0.00 0.00 37.57 2.34
2259 2269 2.937799 GTGTTCTGACAACCAACGGTAA 59.062 45.455 0.00 0.00 37.57 2.85
2260 2270 2.168936 AGTGTTCTGACAACCAACGGTA 59.831 45.455 0.00 0.00 37.57 4.02
2261 2271 1.065709 AGTGTTCTGACAACCAACGGT 60.066 47.619 0.00 0.00 37.57 4.83
2262 2272 1.597663 GAGTGTTCTGACAACCAACGG 59.402 52.381 0.00 0.00 37.57 4.44
2263 2273 2.276201 TGAGTGTTCTGACAACCAACG 58.724 47.619 0.00 0.00 37.57 4.10
2317 2327 2.014010 ACCACCCACAAGAATGCAAT 57.986 45.000 0.00 0.00 0.00 3.56
2347 2357 3.009723 CGGTAAATGTGATGCTGGTTCT 58.990 45.455 0.00 0.00 0.00 3.01
2406 2416 5.237996 TCTGAAGTGAATTCTGTGAGCAAAG 59.762 40.000 7.05 0.00 38.83 2.77
2415 2425 7.387122 TGTGAAGAATCTCTGAAGTGAATTCTG 59.613 37.037 7.05 0.00 38.83 3.02
2423 2433 6.537355 TCCAAATGTGAAGAATCTCTGAAGT 58.463 36.000 0.00 0.00 0.00 3.01
2449 2459 4.338118 TGTGGCCAATTAAATAGCAGCTAC 59.662 41.667 7.24 0.00 0.00 3.58
2474 2484 4.191544 GTGTGATTACTCAGCATTAGCCA 58.808 43.478 0.00 0.00 43.56 4.75
2506 2516 9.807921 AACATAAGGAGAAAGGAAAGAATGTAA 57.192 29.630 0.00 0.00 0.00 2.41
2610 2620 3.424703 ACAACAGGTTTCTCCATCCATG 58.575 45.455 0.00 0.00 39.02 3.66
2669 2679 8.734593 AATATTCTCAGTTTCTAGGCTAGGAT 57.265 34.615 20.92 0.00 0.00 3.24
2879 2889 0.935898 GCAGCTTCTGATCCATGTCG 59.064 55.000 0.00 0.00 32.44 4.35
2910 2920 6.717084 TCTTCCTCCTCTTGGAAATTTTTCTC 59.283 38.462 3.28 0.00 42.29 2.87
2949 2959 2.055042 GCCTTCTCCGCTCCTCAGA 61.055 63.158 0.00 0.00 0.00 3.27
3047 3057 1.381872 GGGAGCTACCAGAGGAGCA 60.382 63.158 11.24 0.00 41.36 4.26
3648 3782 0.603569 AGCACTGTGGACTTACCTCG 59.396 55.000 10.21 0.00 39.86 4.63
3678 3812 6.627243 AGCGACACAATGTAGTTGAGTTATA 58.373 36.000 7.18 0.00 40.92 0.98
3935 4069 0.524862 CACTGCTGACAATGAAGGGC 59.475 55.000 0.00 0.00 0.00 5.19
4105 4239 4.929819 TGCAGATGGATGGAATTGATTG 57.070 40.909 0.00 0.00 0.00 2.67
4150 4284 7.953005 TCAGATCTCTTATGAGTATCCATCC 57.047 40.000 5.60 0.00 40.98 3.51
4221 4355 6.945636 TCTTTTCTGGGGATAACTAGACAA 57.054 37.500 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.