Multiple sequence alignment - TraesCS1D01G198200

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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 TraesCS1D01G198200 chr1D 100.000 1912 0 0 938 2849 279933197 279935108 0.000000e+00 3531
1 TraesCS1D01G198200 chr1D 100.000 438 0 0 1 438 279932260 279932697 0.000000e+00 809
2 TraesCS1D01G198200 chr1D 88.435 147 15 2 2083 2228 119340726 119340581 2.920000e-40 176
3 TraesCS1D01G198200 chr1A 96.954 1149 34 1 938 2085 351856558 351857706 0.000000e+00 1927
4 TraesCS1D01G198200 chr1A 95.355 409 14 5 2188 2593 351857704 351858110 0.000000e+00 645
5 TraesCS1D01G198200 chr1A 92.236 322 12 3 2529 2849 351858102 351858411 7.240000e-121 444
6 TraesCS1D01G198200 chr1A 89.306 346 14 7 3 348 351855935 351856257 2.040000e-111 412
7 TraesCS1D01G198200 chr1B 96.911 1133 33 1 955 2085 380432930 380434062 0.000000e+00 1897
8 TraesCS1D01G198200 chr1B 90.942 552 17 16 2324 2849 380434166 380434710 0.000000e+00 712
9 TraesCS1D01G198200 chr1B 91.324 438 16 8 3 434 380432071 380432492 1.900000e-161 579
10 TraesCS1D01G198200 chr6B 95.349 129 3 2 2079 2206 548122216 548122342 4.810000e-48 202
11 TraesCS1D01G198200 chr7D 99.099 111 1 0 2079 2189 42694857 42694747 1.730000e-47 200
12 TraesCS1D01G198200 chr3B 98.214 112 2 0 2082 2193 22055098 22054987 2.240000e-46 196
13 TraesCS1D01G198200 chr5B 95.161 124 5 1 2066 2189 666201977 666202099 8.050000e-46 195
14 TraesCS1D01G198200 chr5B 95.082 122 5 1 2068 2189 145479133 145479253 1.040000e-44 191
15 TraesCS1D01G198200 chr7B 95.122 123 4 1 2082 2204 261055919 261056039 2.900000e-45 193
16 TraesCS1D01G198200 chr7B 93.750 128 4 4 2072 2198 295202649 295202773 3.750000e-44 189
17 TraesCS1D01G198200 chr5A 95.041 121 6 0 2079 2199 170093761 170093641 1.040000e-44 191


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 TraesCS1D01G198200 chr1D 279932260 279935108 2848 False 2170.000000 3531 100.00000 1 2849 2 chr1D.!!$F1 2848
1 TraesCS1D01G198200 chr1A 351855935 351858411 2476 False 857.000000 1927 93.46275 3 2849 4 chr1A.!!$F1 2846
2 TraesCS1D01G198200 chr1B 380432071 380434710 2639 False 1062.666667 1897 93.05900 3 2849 3 chr1B.!!$F1 2846

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
970 977 1.073125 CACAACCACCACCAGATACCA 59.927 52.381 0.0 0.0 0.0 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2182 0.033796 ATGTACTCCCTCCGTTCCGA 60.034 55.0 0.0 0.0 0.0 4.55 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
57 58 3.397613 GACAGCTAGGGCAGGCAGG 62.398 68.421 0.00 0.00 41.70 4.85
58 59 4.871910 CAGCTAGGGCAGGCAGGC 62.872 72.222 0.00 0.00 41.70 4.85
61 62 4.871910 CTAGGGCAGGCAGGCAGC 62.872 72.222 5.69 2.25 46.44 5.25
109 110 2.433604 TGGTGTACCCACGAGTAAACAA 59.566 45.455 0.00 0.00 42.80 2.83
110 111 3.118482 TGGTGTACCCACGAGTAAACAAA 60.118 43.478 0.00 0.00 42.80 2.83
168 169 1.078214 CGGCCTGCTTCTCCATTCA 60.078 57.895 0.00 0.00 0.00 2.57
171 172 1.538047 GCCTGCTTCTCCATTCACAA 58.462 50.000 0.00 0.00 0.00 3.33
172 173 2.097825 GCCTGCTTCTCCATTCACAAT 58.902 47.619 0.00 0.00 0.00 2.71
173 174 2.494870 GCCTGCTTCTCCATTCACAATT 59.505 45.455 0.00 0.00 0.00 2.32
174 175 3.056322 GCCTGCTTCTCCATTCACAATTT 60.056 43.478 0.00 0.00 0.00 1.82
175 176 4.741342 CCTGCTTCTCCATTCACAATTTC 58.259 43.478 0.00 0.00 0.00 2.17
176 177 4.219070 CCTGCTTCTCCATTCACAATTTCA 59.781 41.667 0.00 0.00 0.00 2.69
177 178 5.125100 TGCTTCTCCATTCACAATTTCAC 57.875 39.130 0.00 0.00 0.00 3.18
178 179 4.583907 TGCTTCTCCATTCACAATTTCACA 59.416 37.500 0.00 0.00 0.00 3.58
179 180 5.244402 TGCTTCTCCATTCACAATTTCACAT 59.756 36.000 0.00 0.00 0.00 3.21
257 258 2.440501 CTAACGAATTCCATTGCGTGC 58.559 47.619 0.00 0.00 37.03 5.34
415 422 2.357517 CCTCGGCGTCAACAAGCT 60.358 61.111 6.85 0.00 0.00 3.74
970 977 1.073125 CACAACCACCACCAGATACCA 59.927 52.381 0.00 0.00 0.00 3.25
1360 1367 0.796312 CGAACTTCCCCATGTTGTCG 59.204 55.000 0.00 0.00 0.00 4.35
1616 1623 1.669211 GGTTGTAGCTCTCGACACCAC 60.669 57.143 0.00 0.00 0.00 4.16
1669 1676 5.358160 GGTTAGCATCATTCTGTAAGGCTTT 59.642 40.000 4.45 0.00 0.00 3.51
1856 1864 6.497785 AAGATGAGCTCTTTCTGACAAATG 57.502 37.500 16.19 0.00 41.60 2.32
1903 1911 7.451566 GGTATGCCTATTCAGGGAACATAAATT 59.548 37.037 0.00 0.00 46.62 1.82
2045 2055 3.861840 TGTCTATTTCTTCTTGGGAGCG 58.138 45.455 0.00 0.00 0.00 5.03
2051 2061 0.976641 TCTTCTTGGGAGCGTCATGT 59.023 50.000 0.00 0.00 0.00 3.21
2082 2092 4.558296 CGCTAGACATGCTCATACAGTCAT 60.558 45.833 0.00 0.00 0.00 3.06
2083 2093 5.335191 CGCTAGACATGCTCATACAGTCATA 60.335 44.000 0.00 0.00 0.00 2.15
2084 2094 5.861251 GCTAGACATGCTCATACAGTCATAC 59.139 44.000 0.00 0.00 0.00 2.39
2085 2095 6.294453 GCTAGACATGCTCATACAGTCATACT 60.294 42.308 0.00 0.00 0.00 2.12
2086 2096 6.083098 AGACATGCTCATACAGTCATACTC 57.917 41.667 0.00 0.00 0.00 2.59
2087 2097 5.010516 AGACATGCTCATACAGTCATACTCC 59.989 44.000 0.00 0.00 0.00 3.85
2088 2098 4.039730 ACATGCTCATACAGTCATACTCCC 59.960 45.833 0.00 0.00 0.00 4.30
2089 2099 3.916035 TGCTCATACAGTCATACTCCCT 58.084 45.455 0.00 0.00 0.00 4.20
2090 2100 3.891977 TGCTCATACAGTCATACTCCCTC 59.108 47.826 0.00 0.00 0.00 4.30
2091 2101 3.257127 GCTCATACAGTCATACTCCCTCC 59.743 52.174 0.00 0.00 0.00 4.30
2092 2102 3.487372 TCATACAGTCATACTCCCTCCG 58.513 50.000 0.00 0.00 0.00 4.63
2093 2103 3.117625 TCATACAGTCATACTCCCTCCGT 60.118 47.826 0.00 0.00 0.00 4.69
2094 2104 1.765230 ACAGTCATACTCCCTCCGTC 58.235 55.000 0.00 0.00 0.00 4.79
2095 2105 1.033574 CAGTCATACTCCCTCCGTCC 58.966 60.000 0.00 0.00 0.00 4.79
2096 2106 0.106116 AGTCATACTCCCTCCGTCCC 60.106 60.000 0.00 0.00 0.00 4.46
2097 2107 0.396695 GTCATACTCCCTCCGTCCCA 60.397 60.000 0.00 0.00 0.00 4.37
2098 2108 0.337082 TCATACTCCCTCCGTCCCAA 59.663 55.000 0.00 0.00 0.00 4.12
2099 2109 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
2100 2110 1.768870 CATACTCCCTCCGTCCCAAAT 59.231 52.381 0.00 0.00 0.00 2.32
2101 2111 1.961133 TACTCCCTCCGTCCCAAATT 58.039 50.000 0.00 0.00 0.00 1.82
2102 2112 1.961133 ACTCCCTCCGTCCCAAATTA 58.039 50.000 0.00 0.00 0.00 1.40
2103 2113 1.558294 ACTCCCTCCGTCCCAAATTAC 59.442 52.381 0.00 0.00 0.00 1.89
2104 2114 1.838077 CTCCCTCCGTCCCAAATTACT 59.162 52.381 0.00 0.00 0.00 2.24
2105 2115 1.835531 TCCCTCCGTCCCAAATTACTC 59.164 52.381 0.00 0.00 0.00 2.59
2106 2116 1.472728 CCCTCCGTCCCAAATTACTCG 60.473 57.143 0.00 0.00 0.00 4.18
2107 2117 1.206371 CCTCCGTCCCAAATTACTCGT 59.794 52.381 0.00 0.00 0.00 4.18
2108 2118 2.537401 CTCCGTCCCAAATTACTCGTC 58.463 52.381 0.00 0.00 0.00 4.20
2109 2119 1.135315 TCCGTCCCAAATTACTCGTCG 60.135 52.381 0.00 0.00 0.00 5.12
2110 2120 0.643820 CGTCCCAAATTACTCGTCGC 59.356 55.000 0.00 0.00 0.00 5.19
2111 2121 1.734707 CGTCCCAAATTACTCGTCGCT 60.735 52.381 0.00 0.00 0.00 4.93
2112 2122 1.659098 GTCCCAAATTACTCGTCGCTG 59.341 52.381 0.00 0.00 0.00 5.18
2113 2123 1.546923 TCCCAAATTACTCGTCGCTGA 59.453 47.619 0.00 0.00 0.00 4.26
2114 2124 2.028839 TCCCAAATTACTCGTCGCTGAA 60.029 45.455 0.00 0.00 0.00 3.02
2115 2125 2.739913 CCCAAATTACTCGTCGCTGAAA 59.260 45.455 0.00 0.00 0.00 2.69
2116 2126 3.374058 CCCAAATTACTCGTCGCTGAAAT 59.626 43.478 0.00 0.00 0.00 2.17
2117 2127 4.334443 CCAAATTACTCGTCGCTGAAATG 58.666 43.478 0.00 0.00 0.00 2.32
2118 2128 4.334443 CAAATTACTCGTCGCTGAAATGG 58.666 43.478 0.00 0.00 0.00 3.16
2119 2129 3.520290 ATTACTCGTCGCTGAAATGGA 57.480 42.857 0.00 0.00 0.00 3.41
2120 2130 3.520290 TTACTCGTCGCTGAAATGGAT 57.480 42.857 0.00 0.00 0.00 3.41
2121 2131 1.645034 ACTCGTCGCTGAAATGGATG 58.355 50.000 0.00 0.00 0.00 3.51
2122 2132 1.066858 ACTCGTCGCTGAAATGGATGT 60.067 47.619 0.00 0.00 0.00 3.06
2123 2133 2.165641 ACTCGTCGCTGAAATGGATGTA 59.834 45.455 0.00 0.00 0.00 2.29
2124 2134 3.181475 ACTCGTCGCTGAAATGGATGTAT 60.181 43.478 0.00 0.00 0.00 2.29
2125 2135 3.381045 TCGTCGCTGAAATGGATGTATC 58.619 45.455 0.00 0.00 0.00 2.24
2126 2136 3.068165 TCGTCGCTGAAATGGATGTATCT 59.932 43.478 0.00 0.00 0.00 1.98
2127 2137 4.277423 TCGTCGCTGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 0.00 1.98
2128 2138 4.618912 CGTCGCTGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 0.00 2.43
2129 2139 5.562890 CGTCGCTGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 0.00 2.43
2130 2140 6.216569 GTCGCTGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 0.00 2.10
2131 2141 6.144724 GTCGCTGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 0.00 3.01
2132 2142 6.040955 TCGCTGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
2133 2143 7.230712 TCGCTGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
2134 2144 7.867909 CGCTGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
2135 2145 9.547753 GCTGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
2161 2171 5.955488 ACATCTAGATACATCCATACGTGC 58.045 41.667 4.54 0.00 0.00 5.34
2162 2172 4.680171 TCTAGATACATCCATACGTGCG 57.320 45.455 0.00 0.00 0.00 5.34
2163 2173 4.320870 TCTAGATACATCCATACGTGCGA 58.679 43.478 0.00 0.00 0.00 5.10
2164 2174 3.284323 AGATACATCCATACGTGCGAC 57.716 47.619 0.00 0.00 0.00 5.19
2165 2175 2.621526 AGATACATCCATACGTGCGACA 59.378 45.455 0.00 0.00 0.00 4.35
2166 2176 2.943449 TACATCCATACGTGCGACAA 57.057 45.000 0.00 0.00 0.00 3.18
2167 2177 1.640428 ACATCCATACGTGCGACAAG 58.360 50.000 0.00 0.00 0.00 3.16
2168 2178 1.067142 ACATCCATACGTGCGACAAGT 60.067 47.619 0.00 0.00 0.00 3.16
2169 2179 2.164827 ACATCCATACGTGCGACAAGTA 59.835 45.455 0.00 7.72 33.49 2.24
2170 2180 3.183754 CATCCATACGTGCGACAAGTAA 58.816 45.455 0.00 0.00 32.82 2.24
2171 2181 3.513680 TCCATACGTGCGACAAGTAAT 57.486 42.857 0.00 0.00 32.82 1.89
2172 2182 3.852286 TCCATACGTGCGACAAGTAATT 58.148 40.909 0.00 0.00 32.82 1.40
2173 2183 3.861113 TCCATACGTGCGACAAGTAATTC 59.139 43.478 0.00 0.00 32.82 2.17
2174 2184 3.301579 CCATACGTGCGACAAGTAATTCG 60.302 47.826 0.00 0.00 32.82 3.34
2175 2185 1.065358 ACGTGCGACAAGTAATTCGG 58.935 50.000 0.00 0.00 35.73 4.30
2176 2186 1.336148 ACGTGCGACAAGTAATTCGGA 60.336 47.619 0.00 0.00 35.73 4.55
2177 2187 1.722464 CGTGCGACAAGTAATTCGGAA 59.278 47.619 0.00 0.00 37.32 4.30
2178 2188 2.471749 CGTGCGACAAGTAATTCGGAAC 60.472 50.000 0.00 0.00 37.32 3.62
2227 2238 5.240623 TGTTAGTGTGGCCTGAAGTTTATTG 59.759 40.000 3.32 0.00 0.00 1.90
2275 2286 9.060347 CAATTTAACATCATGATAGGCAGTAGT 57.940 33.333 8.15 0.00 0.00 2.73
2560 2596 5.049828 GCTTTTGTAATTTGGTTGCAGACT 58.950 37.500 0.00 0.00 33.85 3.24
2561 2597 5.175673 GCTTTTGTAATTTGGTTGCAGACTC 59.824 40.000 0.00 0.00 33.85 3.36
2562 2598 5.843673 TTTGTAATTTGGTTGCAGACTCA 57.156 34.783 0.00 0.00 33.85 3.41
2629 2722 2.679336 GCCCATTGGAATGTGAAATTGC 59.321 45.455 3.62 0.00 34.60 3.56
2733 2826 7.380870 CAGGACTCTATAATCAACAATCTGTCG 59.619 40.741 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.601057 TCGCTCGTTGGACAATCAGA 59.399 50.000 0.00 0.00 0.00 3.27
1 2 0.716108 GTCGCTCGTTGGACAATCAG 59.284 55.000 0.00 0.00 33.41 2.90
109 110 2.182014 GCTGAGTGCGTTTTCGTTTTT 58.818 42.857 0.00 0.00 46.03 1.94
110 111 1.533129 GGCTGAGTGCGTTTTCGTTTT 60.533 47.619 0.00 0.00 46.03 2.43
168 169 1.007118 GGGAGGGGGATGTGAAATTGT 59.993 52.381 0.00 0.00 0.00 2.71
171 172 0.919289 ACGGGAGGGGGATGTGAAAT 60.919 55.000 0.00 0.00 0.00 2.17
172 173 1.540367 ACGGGAGGGGGATGTGAAA 60.540 57.895 0.00 0.00 0.00 2.69
173 174 1.993391 GACGGGAGGGGGATGTGAA 60.993 63.158 0.00 0.00 0.00 3.18
174 175 2.365105 GACGGGAGGGGGATGTGA 60.365 66.667 0.00 0.00 0.00 3.58
175 176 2.365635 AGACGGGAGGGGGATGTG 60.366 66.667 0.00 0.00 0.00 3.21
176 177 2.041819 GAGACGGGAGGGGGATGT 60.042 66.667 0.00 0.00 0.00 3.06
177 178 2.844839 GGAGACGGGAGGGGGATG 60.845 72.222 0.00 0.00 0.00 3.51
204 205 3.129638 CGTGGTTTTCTTTGACTTTGGGA 59.870 43.478 0.00 0.00 0.00 4.37
257 258 3.447025 GATGGGAGGACGGGAAGCG 62.447 68.421 0.00 0.00 0.00 4.68
348 349 3.200593 GCTGCTGCGGTCCATCTG 61.201 66.667 10.62 0.00 0.00 2.90
940 947 2.122769 TGGTTGTGGACGGGAGGA 60.123 61.111 0.00 0.00 0.00 3.71
970 977 0.178984 CGGGGTTGTGGTTAGGGTTT 60.179 55.000 0.00 0.00 0.00 3.27
1616 1623 5.865552 AGCAGCAATTAACAGCAACAAATAG 59.134 36.000 0.00 0.00 0.00 1.73
1656 1663 3.824443 GCCTTTACCAAAGCCTTACAGAA 59.176 43.478 0.00 0.00 37.18 3.02
1669 1676 3.579534 TGTAACCAACAGCCTTTACCA 57.420 42.857 0.00 0.00 33.01 3.25
1856 1864 2.907910 ACAGCAATCATGAGCGAAAC 57.092 45.000 0.09 0.00 35.48 2.78
1903 1911 9.429109 AATACAAGTAGAAGAAAAGGGGAAAAA 57.571 29.630 0.00 0.00 0.00 1.94
2045 2055 4.112634 TGTCTAGCGCAAGATAACATGAC 58.887 43.478 11.47 3.07 38.02 3.06
2051 2061 3.181476 TGAGCATGTCTAGCGCAAGATAA 60.181 43.478 11.47 0.00 38.83 1.75
2082 2092 1.961133 AATTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2083 2093 1.558294 GTAATTTGGGACGGAGGGAGT 59.442 52.381 0.00 0.00 0.00 3.85
2084 2094 1.838077 AGTAATTTGGGACGGAGGGAG 59.162 52.381 0.00 0.00 0.00 4.30
2085 2095 1.835531 GAGTAATTTGGGACGGAGGGA 59.164 52.381 0.00 0.00 0.00 4.20
2086 2096 1.472728 CGAGTAATTTGGGACGGAGGG 60.473 57.143 0.00 0.00 0.00 4.30
2087 2097 1.206371 ACGAGTAATTTGGGACGGAGG 59.794 52.381 0.00 0.00 0.00 4.30
2088 2098 2.537401 GACGAGTAATTTGGGACGGAG 58.463 52.381 0.00 0.00 0.00 4.63
2089 2099 1.135315 CGACGAGTAATTTGGGACGGA 60.135 52.381 0.00 0.00 0.00 4.69
2090 2100 1.274596 CGACGAGTAATTTGGGACGG 58.725 55.000 0.00 0.00 0.00 4.79
2091 2101 0.643820 GCGACGAGTAATTTGGGACG 59.356 55.000 0.00 0.00 0.00 4.79
2092 2102 1.659098 CAGCGACGAGTAATTTGGGAC 59.341 52.381 0.00 0.00 0.00 4.46
2093 2103 1.546923 TCAGCGACGAGTAATTTGGGA 59.453 47.619 0.00 0.00 0.00 4.37
2094 2104 2.004583 TCAGCGACGAGTAATTTGGG 57.995 50.000 0.00 0.00 0.00 4.12
2095 2105 4.334443 CATTTCAGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
2096 2106 4.092821 TCCATTTCAGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
2097 2107 4.250464 TCCATTTCAGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
2098 2108 3.857052 TCCATTTCAGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
2099 2109 3.520290 TCCATTTCAGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
2100 2110 3.186909 CATCCATTTCAGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
2101 2111 2.165641 ACATCCATTTCAGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
2102 2112 1.066858 ACATCCATTTCAGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
2103 2113 1.645034 ACATCCATTTCAGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
2104 2114 2.951457 TACATCCATTTCAGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
2105 2115 3.384668 AGATACATCCATTTCAGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
2106 2116 5.773575 TCTAGATACATCCATTTCAGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
2107 2117 6.040955 AGTTCTAGATACATCCATTTCAGCGA 59.959 38.462 0.00 0.00 0.00 4.93
2108 2118 6.219473 AGTTCTAGATACATCCATTTCAGCG 58.781 40.000 0.00 0.00 0.00 5.18
2109 2119 9.547753 TTTAGTTCTAGATACATCCATTTCAGC 57.452 33.333 0.00 0.00 0.00 4.26
2135 2145 8.191446 GCACGTATGGATGTATCTAGATGTATT 58.809 37.037 15.79 0.00 29.44 1.89
2136 2146 7.467403 CGCACGTATGGATGTATCTAGATGTAT 60.467 40.741 15.79 9.11 29.44 2.29
2137 2147 6.183360 CGCACGTATGGATGTATCTAGATGTA 60.183 42.308 15.79 4.44 29.44 2.29
2138 2148 5.392057 CGCACGTATGGATGTATCTAGATGT 60.392 44.000 15.79 1.25 30.36 3.06
2139 2149 5.030936 CGCACGTATGGATGTATCTAGATG 58.969 45.833 15.79 0.00 0.00 2.90
2140 2150 4.941873 TCGCACGTATGGATGTATCTAGAT 59.058 41.667 10.73 10.73 0.00 1.98
2141 2151 4.153655 GTCGCACGTATGGATGTATCTAGA 59.846 45.833 0.00 0.00 0.00 2.43
2142 2152 4.083484 TGTCGCACGTATGGATGTATCTAG 60.083 45.833 0.00 0.00 0.00 2.43
2143 2153 3.816523 TGTCGCACGTATGGATGTATCTA 59.183 43.478 0.00 0.00 0.00 1.98
2144 2154 2.621526 TGTCGCACGTATGGATGTATCT 59.378 45.455 0.00 0.00 0.00 1.98
2145 2155 3.007979 TGTCGCACGTATGGATGTATC 57.992 47.619 0.00 0.00 0.00 2.24
2146 2156 3.181479 ACTTGTCGCACGTATGGATGTAT 60.181 43.478 0.00 0.00 0.00 2.29
2147 2157 2.164827 ACTTGTCGCACGTATGGATGTA 59.835 45.455 0.00 0.00 0.00 2.29
2148 2158 1.067142 ACTTGTCGCACGTATGGATGT 60.067 47.619 0.00 0.00 0.00 3.06
2149 2159 1.640428 ACTTGTCGCACGTATGGATG 58.360 50.000 0.00 0.00 0.00 3.51
2150 2160 3.513680 TTACTTGTCGCACGTATGGAT 57.486 42.857 0.00 0.00 0.00 3.41
2151 2161 3.513680 ATTACTTGTCGCACGTATGGA 57.486 42.857 0.00 0.00 0.00 3.41
2152 2162 3.301579 CGAATTACTTGTCGCACGTATGG 60.302 47.826 0.00 0.00 0.00 2.74
2153 2163 3.301579 CCGAATTACTTGTCGCACGTATG 60.302 47.826 0.00 0.00 35.93 2.39
2154 2164 2.855963 CCGAATTACTTGTCGCACGTAT 59.144 45.455 0.00 0.00 35.93 3.06
2155 2165 2.095314 TCCGAATTACTTGTCGCACGTA 60.095 45.455 0.00 0.00 35.93 3.57
2156 2166 1.065358 CCGAATTACTTGTCGCACGT 58.935 50.000 0.00 0.00 35.93 4.49
2157 2167 1.342555 TCCGAATTACTTGTCGCACG 58.657 50.000 0.00 0.00 35.93 5.34
2158 2168 2.471749 CGTTCCGAATTACTTGTCGCAC 60.472 50.000 0.00 0.00 35.93 5.34
2159 2169 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
2160 2170 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
2161 2171 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
2162 2172 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2163 2173 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2164 2174 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2165 2175 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2166 2176 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2167 2177 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2168 2178 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2169 2179 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
2170 2180 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
2171 2181 0.251297 TGTACTCCCTCCGTTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
2172 2182 0.033796 ATGTACTCCCTCCGTTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
2173 2183 0.102481 CATGTACTCCCTCCGTTCCG 59.898 60.000 0.00 0.00 0.00 4.30
2174 2184 1.409427 CTCATGTACTCCCTCCGTTCC 59.591 57.143 0.00 0.00 0.00 3.62
2175 2185 2.376109 TCTCATGTACTCCCTCCGTTC 58.624 52.381 0.00 0.00 0.00 3.95
2176 2186 2.526888 TCTCATGTACTCCCTCCGTT 57.473 50.000 0.00 0.00 0.00 4.44
2177 2187 2.757894 ATCTCATGTACTCCCTCCGT 57.242 50.000 0.00 0.00 0.00 4.69
2178 2188 4.585162 ACTTTATCTCATGTACTCCCTCCG 59.415 45.833 0.00 0.00 0.00 4.63
2179 2189 6.487299 AACTTTATCTCATGTACTCCCTCC 57.513 41.667 0.00 0.00 0.00 4.30
2180 2190 7.331791 ACAAACTTTATCTCATGTACTCCCTC 58.668 38.462 0.00 0.00 0.00 4.30
2181 2191 7.259088 ACAAACTTTATCTCATGTACTCCCT 57.741 36.000 0.00 0.00 0.00 4.20
2182 2192 7.923414 AACAAACTTTATCTCATGTACTCCC 57.077 36.000 0.00 0.00 0.00 4.30
2183 2193 9.654663 ACTAACAAACTTTATCTCATGTACTCC 57.345 33.333 0.00 0.00 0.00 3.85
2185 2195 9.998106 ACACTAACAAACTTTATCTCATGTACT 57.002 29.630 0.00 0.00 0.00 2.73
2258 2269 7.603180 TGACTAAACTACTGCCTATCATGAT 57.397 36.000 13.81 13.81 0.00 2.45
2560 2596 8.149647 ACCAAACATTGCATCTTTAAGATTTGA 58.850 29.630 4.51 0.00 31.32 2.69
2561 2597 8.225107 CACCAAACATTGCATCTTTAAGATTTG 58.775 33.333 4.51 6.39 31.32 2.32
2562 2598 7.933033 ACACCAAACATTGCATCTTTAAGATTT 59.067 29.630 4.51 0.00 31.32 2.17
2595 2688 1.244019 AATGGGCAGAACGGTCAAGC 61.244 55.000 1.87 6.26 0.00 4.01
2716 2809 6.406370 TCAGAACCGACAGATTGTTGATTAT 58.594 36.000 0.00 0.00 33.58 1.28
2718 2811 4.641396 TCAGAACCGACAGATTGTTGATT 58.359 39.130 0.00 0.00 33.58 2.57
2733 2826 8.200792 ACTTGAAGATATGTACAGATCAGAACC 58.799 37.037 27.43 13.96 31.80 3.62


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

AutoCloner maintained by Alex Coulton.