Multiple sequence alignment - TraesCS4A01G015200

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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 TraesCS4A01G015200 chr4A 100.000 2363 0 0 1 2363 9549215 9551577 0.000000e+00 4364
1 TraesCS4A01G015200 chr4A 90.756 119 11 0 127 245 732350161 732350279 2.430000e-35 159
2 TraesCS4A01G015200 chr4A 90.833 120 10 1 128 246 738312088 738312207 2.430000e-35 159
3 TraesCS4A01G015200 chr4D 89.253 1433 91 32 316 1721 459269161 459267765 0.000000e+00 1735
4 TraesCS4A01G015200 chr4B 91.718 809 49 13 852 1645 573503253 573502448 0.000000e+00 1107
5 TraesCS4A01G015200 chr4B 86.053 717 76 13 1662 2363 573500110 573499403 0.000000e+00 749
6 TraesCS4A01G015200 chr4B 86.772 635 30 20 241 855 573506410 573505810 0.000000e+00 658
7 TraesCS4A01G015200 chr4B 83.004 253 39 4 1931 2179 423363791 423364043 2.360000e-55 226
8 TraesCS4A01G015200 chr4B 80.328 244 41 6 1942 2179 652400965 652400723 6.710000e-41 178
9 TraesCS4A01G015200 chr4B 92.000 125 6 2 1 121 573506792 573506668 3.120000e-39 172
10 TraesCS4A01G015200 chr1A 82.400 250 39 4 1935 2179 438651569 438651320 1.840000e-51 213
11 TraesCS4A01G015200 chr6D 81.641 256 42 4 1929 2179 422194157 422194412 8.560000e-50 207
12 TraesCS4A01G015200 chr6D 87.023 131 15 2 118 247 437418354 437418483 1.890000e-31 147
13 TraesCS4A01G015200 chr5D 80.315 254 46 3 1929 2178 543833072 543833325 3.100000e-44 189
14 TraesCS4A01G015200 chr5A 80.000 255 45 5 1929 2179 653926722 653926470 1.440000e-42 183
15 TraesCS4A01G015200 chr7B 80.804 224 39 3 1961 2181 374772735 374772513 3.120000e-39 172
16 TraesCS4A01G015200 chr7D 80.519 231 36 4 1963 2186 186793548 186793776 4.040000e-38 169
17 TraesCS4A01G015200 chr7A 91.525 118 10 0 129 246 632588268 632588151 1.880000e-36 163
18 TraesCS4A01G015200 chr3B 90.083 121 12 0 126 246 481619629 481619509 8.740000e-35 158
19 TraesCS4A01G015200 chr5B 88.372 129 13 2 122 249 485568827 485568954 1.130000e-33 154
20 TraesCS4A01G015200 chr6B 89.344 122 12 1 124 245 522062523 522062403 4.070000e-33 152
21 TraesCS4A01G015200 chr2B 88.800 125 12 2 123 246 432137459 432137336 4.070000e-33 152
22 TraesCS4A01G015200 chr2D 88.618 123 14 0 123 245 7396591 7396469 1.460000e-32 150


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 TraesCS4A01G015200 chr4A 9549215 9551577 2362 False 4364.0 4364 100.00000 1 2363 1 chr4A.!!$F1 2362
1 TraesCS4A01G015200 chr4D 459267765 459269161 1396 True 1735.0 1735 89.25300 316 1721 1 chr4D.!!$R1 1405
2 TraesCS4A01G015200 chr4B 573499403 573506792 7389 True 671.5 1107 89.13575 1 2363 4 chr4B.!!$R2 2362

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
719 879 0.403271 AGAAATGCACCTGCTGACCT 59.597 50.0 0.0 0.0 42.66 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 7162 0.036164 CAAGGTCCATGGACAACCGA 59.964 55.0 38.83 4.99 46.2 4.69 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
30 31 5.934625 CACTGAGGTATGCCCTAACAATATC 59.065 44.000 0.00 0.00 46.51 1.63
34 35 4.913968 AGGTATGCCCTAACAATATCTGGT 59.086 41.667 0.00 0.00 43.87 4.00
60 61 4.595762 TTACTCGTGGTGCTACTCTTTT 57.404 40.909 0.00 0.00 0.00 2.27
82 83 3.408634 TGGTCGGAAGGAGAACAATTTC 58.591 45.455 0.00 0.00 31.60 2.17
83 84 3.181449 TGGTCGGAAGGAGAACAATTTCA 60.181 43.478 0.00 0.00 31.60 2.69
89 90 5.281727 GGAAGGAGAACAATTTCACACAAC 58.718 41.667 0.00 0.00 33.72 3.32
117 121 9.589111 TTTTCTATACGCATGAGTGTGTTTATA 57.411 29.630 12.80 0.20 46.41 0.98
118 122 9.758651 TTTCTATACGCATGAGTGTGTTTATAT 57.241 29.630 12.80 0.00 46.41 0.86
123 127 9.875691 ATACGCATGAGTGTGTTTATATATCAT 57.124 29.630 12.80 0.00 46.41 2.45
125 129 9.875691 ACGCATGAGTGTGTTTATATATCATAT 57.124 29.630 0.00 0.00 46.41 1.78
142 146 3.007723 TCATATAGTACTCGCTCCGTCCT 59.992 47.826 0.00 0.00 0.00 3.85
143 147 1.595466 ATAGTACTCGCTCCGTCCTG 58.405 55.000 0.00 0.00 0.00 3.86
144 148 0.538584 TAGTACTCGCTCCGTCCTGA 59.461 55.000 0.00 0.00 0.00 3.86
149 153 2.032620 ACTCGCTCCGTCCTGAAATAT 58.967 47.619 0.00 0.00 0.00 1.28
150 154 2.431057 ACTCGCTCCGTCCTGAAATATT 59.569 45.455 0.00 0.00 0.00 1.28
151 155 3.118738 ACTCGCTCCGTCCTGAAATATTT 60.119 43.478 0.00 0.00 0.00 1.40
152 156 3.194861 TCGCTCCGTCCTGAAATATTTG 58.805 45.455 5.17 0.00 0.00 2.32
153 157 2.936498 CGCTCCGTCCTGAAATATTTGT 59.064 45.455 5.17 0.00 0.00 2.83
154 158 3.001330 CGCTCCGTCCTGAAATATTTGTC 59.999 47.826 5.17 0.00 0.00 3.18
155 159 3.001330 GCTCCGTCCTGAAATATTTGTCG 59.999 47.826 5.17 1.51 0.00 4.35
156 160 4.430007 CTCCGTCCTGAAATATTTGTCGA 58.570 43.478 5.17 0.00 0.00 4.20
157 161 4.823157 TCCGTCCTGAAATATTTGTCGAA 58.177 39.130 5.17 0.00 0.00 3.71
158 162 4.868171 TCCGTCCTGAAATATTTGTCGAAG 59.132 41.667 5.17 0.55 0.00 3.79
159 163 4.868171 CCGTCCTGAAATATTTGTCGAAGA 59.132 41.667 5.17 0.00 0.00 2.87
160 164 5.350365 CCGTCCTGAAATATTTGTCGAAGAA 59.650 40.000 5.17 0.00 39.69 2.52
161 165 6.128391 CCGTCCTGAAATATTTGTCGAAGAAA 60.128 38.462 5.17 0.00 39.69 2.52
164 168 9.922305 GTCCTGAAATATTTGTCGAAGAAATAG 57.078 33.333 5.17 4.85 39.69 1.73
235 239 4.735662 TTTTGACAAGTATTTCCGGACG 57.264 40.909 1.83 0.00 0.00 4.79
236 240 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
239 389 2.165030 GACAAGTATTTCCGGACGGAGA 59.835 50.000 13.64 10.06 46.06 3.71
257 407 7.255001 GGACGGAGAGAGTATTAAAGAAGAGAG 60.255 44.444 0.00 0.00 0.00 3.20
280 430 1.383386 GAGAAGAGTCCCCCTCCCC 60.383 68.421 0.00 0.00 41.47 4.81
298 448 4.722700 CCCACCCCCACTTCGCAG 62.723 72.222 0.00 0.00 0.00 5.18
304 454 1.376609 CCCCCACTTCGCAGCATTAC 61.377 60.000 0.00 0.00 0.00 1.89
342 492 4.898861 ACACTGGTCCACCAACAATTTTAT 59.101 37.500 0.00 0.00 46.97 1.40
345 495 5.182380 ACTGGTCCACCAACAATTTTATACG 59.818 40.000 0.00 0.00 46.97 3.06
401 551 1.611977 GCCCGAAACAAAGCTACCTTT 59.388 47.619 0.00 0.00 41.86 3.11
515 665 2.190398 TGGGATTAGAAGCCTGGCTA 57.810 50.000 23.69 6.47 38.25 3.93
660 820 5.105834 ACGGATTATGTAGCGTAGACTTC 57.894 43.478 0.00 0.00 0.00 3.01
719 879 0.403271 AGAAATGCACCTGCTGACCT 59.597 50.000 0.00 0.00 42.66 3.85
720 880 0.524862 GAAATGCACCTGCTGACCTG 59.475 55.000 0.00 0.00 42.66 4.00
721 881 1.530013 AAATGCACCTGCTGACCTGC 61.530 55.000 0.00 0.00 42.66 4.85
722 882 2.702040 AATGCACCTGCTGACCTGCA 62.702 55.000 11.15 11.15 43.50 4.41
723 883 2.360852 GCACCTGCTGACCTGCAT 60.361 61.111 2.15 0.00 42.48 3.96
724 884 2.697761 GCACCTGCTGACCTGCATG 61.698 63.158 2.15 2.88 42.48 4.06
725 885 2.360852 ACCTGCTGACCTGCATGC 60.361 61.111 11.82 11.82 42.48 4.06
907 3638 1.339711 CATTGCTTTCGCCTTTTCCG 58.660 50.000 0.00 0.00 34.43 4.30
917 3649 2.674357 TCGCCTTTTCCGCACTATAAAC 59.326 45.455 0.00 0.00 0.00 2.01
939 3671 2.417651 CGGGCCAAAGTCTCACGTAATA 60.418 50.000 4.39 0.00 0.00 0.98
941 3673 3.621715 GGGCCAAAGTCTCACGTAATAAG 59.378 47.826 4.39 0.00 0.00 1.73
1388 4124 2.093658 CAGGGCAAGTATCAACCGTACT 60.094 50.000 0.00 0.00 33.98 2.73
1389 4125 2.093658 AGGGCAAGTATCAACCGTACTG 60.094 50.000 0.00 0.00 32.94 2.74
1390 4126 2.277084 GGCAAGTATCAACCGTACTGG 58.723 52.381 2.71 2.71 46.41 4.00
1407 4160 3.958018 ACTGGTACTTTGTTGGTTCACA 58.042 40.909 0.00 0.00 0.00 3.58
1408 4161 4.337145 ACTGGTACTTTGTTGGTTCACAA 58.663 39.130 0.00 0.00 34.76 3.33
1441 4194 4.674362 GCAAGTTTGTTTCTGTCGTCCTTT 60.674 41.667 0.00 0.00 0.00 3.11
1482 4236 2.200373 TTTTTAGAGGGAGTGCCAGC 57.800 50.000 2.50 0.00 35.15 4.85
1509 4263 1.132453 GGCCGTGCAATAAGGTTTCTC 59.868 52.381 0.00 0.00 0.00 2.87
1517 4272 3.635591 CAATAAGGTTTCTCCCCAGCAT 58.364 45.455 0.00 0.00 36.75 3.79
1583 4338 1.760273 CGAATAAACGATTTCACGCGC 59.240 47.619 5.73 0.00 36.70 6.86
1597 4353 2.091588 TCACGCGCGTTTATCTCTTTTC 59.908 45.455 35.90 0.00 0.00 2.29
1598 4354 2.092211 CACGCGCGTTTATCTCTTTTCT 59.908 45.455 35.90 2.64 0.00 2.52
1603 4359 4.323751 CGCGTTTATCTCTTTTCTTTCCG 58.676 43.478 0.00 0.00 0.00 4.30
1613 4369 5.051409 TCTTTTCTTTCCGGGGAGTTTAA 57.949 39.130 0.00 0.00 0.00 1.52
1718 6793 7.029563 AGTGAATCACAAACAGACAAGAAAAC 58.970 34.615 16.38 0.00 36.74 2.43
1729 6804 4.457257 CAGACAAGAAAACCTCCATTCTCC 59.543 45.833 0.00 0.00 34.90 3.71
1731 6806 5.003096 ACAAGAAAACCTCCATTCTCCAT 57.997 39.130 0.00 0.00 34.90 3.41
1769 6844 7.990917 TGAACACACAAAGCTAACATAAGAAA 58.009 30.769 0.00 0.00 0.00 2.52
1843 6918 4.036380 CCGAATTGGCTACTAATTGGAACC 59.964 45.833 0.00 0.00 0.00 3.62
1850 6925 4.636206 GGCTACTAATTGGAACCAGTGAAG 59.364 45.833 0.00 0.00 0.00 3.02
1867 6942 1.804748 GAAGACACGGGCGAGAAAAAT 59.195 47.619 0.00 0.00 0.00 1.82
1876 6951 4.234574 CGGGCGAGAAAAATAAAGCTTTT 58.765 39.130 18.47 0.00 0.00 2.27
1880 6955 7.258441 GGGCGAGAAAAATAAAGCTTTTATCT 58.742 34.615 18.47 13.13 33.74 1.98
1883 6958 7.253783 GCGAGAAAAATAAAGCTTTTATCTGGC 60.254 37.037 18.47 19.25 33.74 4.85
1904 6980 2.483583 TTTGCGTTGTTGCGAAGAAT 57.516 40.000 0.00 0.00 37.81 2.40
1938 7015 0.959553 GCATGAGGCAGGATCCAATG 59.040 55.000 15.82 5.48 43.97 2.82
1955 7032 2.324330 TGGCGACAAATGTGGCTCG 61.324 57.895 17.94 4.56 46.81 5.03
1974 7052 3.101437 TCGTAATGCTGGTTCTTAGGGA 58.899 45.455 0.00 0.00 0.00 4.20
1975 7053 3.132289 TCGTAATGCTGGTTCTTAGGGAG 59.868 47.826 0.00 0.00 0.00 4.30
1983 7061 1.672145 GGTTCTTAGGGAGACGTGCAC 60.672 57.143 6.82 6.82 33.02 4.57
1984 7062 0.242825 TTCTTAGGGAGACGTGCACG 59.757 55.000 35.99 35.99 46.33 5.34
1993 7071 0.318784 AGACGTGCACGAAGACTTCC 60.319 55.000 42.94 19.94 43.02 3.46
1996 7074 2.027625 GTGCACGAAGACTTCCCGG 61.028 63.158 9.63 0.00 0.00 5.73
1997 7075 2.342648 GCACGAAGACTTCCCGGT 59.657 61.111 9.63 0.00 0.00 5.28
2001 7079 2.933928 GCACGAAGACTTCCCGGTTATT 60.934 50.000 9.63 0.00 0.00 1.40
2007 7085 4.581077 AGACTTCCCGGTTATTATCGAC 57.419 45.455 0.00 0.00 0.00 4.20
2013 7091 3.451902 TCCCGGTTATTATCGACAAGGTT 59.548 43.478 0.00 0.00 0.00 3.50
2023 7101 1.002502 GACAAGGTTAGGCCGGCTT 60.003 57.895 28.56 23.35 43.70 4.35
2025 7103 2.106683 CAAGGTTAGGCCGGCTTCG 61.107 63.158 28.56 2.52 43.70 3.79
2043 7121 0.739462 CGGTATGAGAGCGGCAACAA 60.739 55.000 1.45 0.00 45.37 2.83
2046 7124 0.739462 TATGAGAGCGGCAACAACGG 60.739 55.000 1.45 0.00 0.00 4.44
2080 7159 1.145377 CCTAGCGGCGGTAATGGTT 59.855 57.895 20.03 0.00 0.00 3.67
2083 7162 0.036199 TAGCGGCGGTAATGGTTGTT 60.036 50.000 17.34 0.00 0.00 2.83
2085 7164 1.422269 CGGCGGTAATGGTTGTTCG 59.578 57.895 0.00 0.00 0.00 3.95
2099 7178 0.250553 TGTTCGGTTGTCCATGGACC 60.251 55.000 36.27 23.74 43.97 4.46
2102 7181 0.036164 TCGGTTGTCCATGGACCTTG 59.964 55.000 36.27 24.37 43.97 3.61
2105 7184 2.093181 CGGTTGTCCATGGACCTTGATA 60.093 50.000 36.27 18.07 43.97 2.15
2143 7222 2.224670 TGGGGTGCTTTGTACTTTCGAT 60.225 45.455 0.00 0.00 0.00 3.59
2222 7304 4.098914 TGGCCACTCTGTTTTAGTCAAT 57.901 40.909 0.00 0.00 0.00 2.57
2226 7308 5.691754 GGCCACTCTGTTTTAGTCAATTTTG 59.308 40.000 0.00 0.00 0.00 2.44
2250 7332 8.287439 TGATGTCTTTTTGTTGGTTTCTTCTA 57.713 30.769 0.00 0.00 0.00 2.10
2282 7364 9.840427 CAATAAGTGTTTTCGATTTATTCTGGT 57.160 29.630 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.000988 AGCACCACGAGTAAAATTACCAG 58.999 43.478 0.00 0.00 34.19 4.00
34 35 6.276832 AGAGTAGCACCACGAGTAAAATTA 57.723 37.500 0.00 0.00 0.00 1.40
60 61 3.502123 AATTGTTCTCCTTCCGACCAA 57.498 42.857 0.00 0.00 0.00 3.67
82 83 6.598525 TCATGCGTATAGAAAAAGTTGTGTG 58.401 36.000 0.00 0.00 0.00 3.82
83 84 6.426937 ACTCATGCGTATAGAAAAAGTTGTGT 59.573 34.615 0.00 0.00 0.00 3.72
89 90 6.408858 ACACACTCATGCGTATAGAAAAAG 57.591 37.500 0.00 0.00 0.00 2.27
117 121 5.759273 GGACGGAGCGAGTACTATATGATAT 59.241 44.000 0.00 0.00 0.00 1.63
118 122 5.105023 AGGACGGAGCGAGTACTATATGATA 60.105 44.000 0.00 0.00 29.47 2.15
119 123 3.940221 GGACGGAGCGAGTACTATATGAT 59.060 47.826 0.00 0.00 0.00 2.45
120 124 3.007723 AGGACGGAGCGAGTACTATATGA 59.992 47.826 0.00 0.00 29.47 2.15
121 125 3.125487 CAGGACGGAGCGAGTACTATATG 59.875 52.174 0.00 0.00 30.29 1.78
122 126 3.007723 TCAGGACGGAGCGAGTACTATAT 59.992 47.826 0.00 0.00 30.29 0.86
123 127 2.366590 TCAGGACGGAGCGAGTACTATA 59.633 50.000 0.00 0.00 30.29 1.31
124 128 1.140452 TCAGGACGGAGCGAGTACTAT 59.860 52.381 0.00 0.00 30.29 2.12
125 129 0.538584 TCAGGACGGAGCGAGTACTA 59.461 55.000 0.00 0.00 30.29 1.82
126 130 0.322277 TTCAGGACGGAGCGAGTACT 60.322 55.000 0.00 0.00 31.85 2.73
127 131 0.524862 TTTCAGGACGGAGCGAGTAC 59.475 55.000 0.00 0.00 0.00 2.73
133 137 3.001330 CGACAAATATTTCAGGACGGAGC 59.999 47.826 0.00 0.00 0.00 4.70
134 138 4.430007 TCGACAAATATTTCAGGACGGAG 58.570 43.478 0.00 0.00 0.00 4.63
213 217 4.023878 CCGTCCGGAAATACTTGTCAAAAA 60.024 41.667 5.23 0.00 37.50 1.94
214 218 3.499157 CCGTCCGGAAATACTTGTCAAAA 59.501 43.478 5.23 0.00 37.50 2.44
215 219 3.068560 CCGTCCGGAAATACTTGTCAAA 58.931 45.455 5.23 0.00 37.50 2.69
216 220 2.299582 TCCGTCCGGAAATACTTGTCAA 59.700 45.455 5.23 0.00 42.05 3.18
217 221 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
218 222 2.165030 TCTCCGTCCGGAAATACTTGTC 59.835 50.000 5.23 0.00 44.66 3.18
219 223 2.165845 CTCTCCGTCCGGAAATACTTGT 59.834 50.000 5.23 0.00 44.66 3.16
220 224 2.426024 TCTCTCCGTCCGGAAATACTTG 59.574 50.000 5.23 0.00 44.66 3.16
221 225 2.688958 CTCTCTCCGTCCGGAAATACTT 59.311 50.000 5.23 0.00 44.66 2.24
222 226 2.299521 CTCTCTCCGTCCGGAAATACT 58.700 52.381 5.23 0.00 44.66 2.12
223 227 2.022934 ACTCTCTCCGTCCGGAAATAC 58.977 52.381 5.23 0.00 44.66 1.89
224 228 2.431954 ACTCTCTCCGTCCGGAAATA 57.568 50.000 5.23 0.00 44.66 1.40
225 229 2.431954 TACTCTCTCCGTCCGGAAAT 57.568 50.000 5.23 0.00 44.66 2.17
226 230 2.431954 ATACTCTCTCCGTCCGGAAA 57.568 50.000 5.23 0.00 44.66 3.13
227 231 2.431954 AATACTCTCTCCGTCCGGAA 57.568 50.000 5.23 0.00 44.66 4.30
228 232 3.565764 TTAATACTCTCTCCGTCCGGA 57.434 47.619 0.00 0.00 42.90 5.14
229 233 3.881688 TCTTTAATACTCTCTCCGTCCGG 59.118 47.826 0.00 0.00 0.00 5.14
230 234 5.296283 TCTTCTTTAATACTCTCTCCGTCCG 59.704 44.000 0.00 0.00 0.00 4.79
231 235 6.543100 TCTCTTCTTTAATACTCTCTCCGTCC 59.457 42.308 0.00 0.00 0.00 4.79
232 236 7.281549 ACTCTCTTCTTTAATACTCTCTCCGTC 59.718 40.741 0.00 0.00 0.00 4.79
233 237 7.066525 CACTCTCTTCTTTAATACTCTCTCCGT 59.933 40.741 0.00 0.00 0.00 4.69
234 238 7.414436 CACTCTCTTCTTTAATACTCTCTCCG 58.586 42.308 0.00 0.00 0.00 4.63
235 239 7.201875 CCCACTCTCTTCTTTAATACTCTCTCC 60.202 44.444 0.00 0.00 0.00 3.71
236 240 7.201875 CCCCACTCTCTTCTTTAATACTCTCTC 60.202 44.444 0.00 0.00 0.00 3.20
239 389 6.503944 TCCCCACTCTCTTCTTTAATACTCT 58.496 40.000 0.00 0.00 0.00 3.24
286 436 0.676466 TGTAATGCTGCGAAGTGGGG 60.676 55.000 0.00 0.00 0.00 4.96
288 438 2.162208 ACAATGTAATGCTGCGAAGTGG 59.838 45.455 0.00 0.00 0.00 4.00
295 445 4.422840 TGCATGTAACAATGTAATGCTGC 58.577 39.130 21.20 12.65 43.17 5.25
298 448 6.365789 AGTGTTTGCATGTAACAATGTAATGC 59.634 34.615 16.73 16.73 43.08 3.56
304 454 4.619973 ACCAGTGTTTGCATGTAACAATG 58.380 39.130 23.93 23.93 45.82 2.82
342 492 2.658373 TCGCAGCTAAACCAATCGTA 57.342 45.000 0.00 0.00 0.00 3.43
345 495 2.288666 TGGATCGCAGCTAAACCAATC 58.711 47.619 0.00 0.00 0.00 2.67
406 556 4.215613 GGCTAACAGTTCGGATCAGTTTTT 59.784 41.667 0.00 0.00 0.00 1.94
436 586 5.877012 ACTGATTAACTCAATCTGATTGCGT 59.123 36.000 22.46 20.04 43.10 5.24
552 703 7.994851 CAAAAGAGCTTTGTAACGAAGATAC 57.005 36.000 0.00 0.00 39.75 2.24
704 864 2.360852 GCAGGTCAGCAGGTGCAT 60.361 61.111 4.48 0.00 45.16 3.96
721 881 2.029739 TGGAACTTGTTGATGCAGCATG 60.030 45.455 14.22 0.00 40.87 4.06
722 882 2.241160 TGGAACTTGTTGATGCAGCAT 58.759 42.857 7.91 7.91 0.00 3.79
723 883 1.689984 TGGAACTTGTTGATGCAGCA 58.310 45.000 0.00 0.00 0.00 4.41
724 884 2.223782 TGTTGGAACTTGTTGATGCAGC 60.224 45.455 0.00 0.00 0.00 5.25
725 885 3.181488 TGTGTTGGAACTTGTTGATGCAG 60.181 43.478 0.00 0.00 0.00 4.41
907 3638 1.404035 CTTTGGCCCGGTTTATAGTGC 59.596 52.381 0.00 0.00 0.00 4.40
917 3649 2.162338 TACGTGAGACTTTGGCCCGG 62.162 60.000 0.00 0.00 0.00 5.73
939 3671 1.746615 ACCGATGCGAGCAATGCTT 60.747 52.632 9.91 0.00 39.88 3.91
941 3673 2.023741 CACCGATGCGAGCAATGC 59.976 61.111 0.57 0.00 0.00 3.56
1106 3842 3.569210 CCTGCTGGACCACCACCA 61.569 66.667 2.92 0.00 41.77 4.17
1107 3843 3.570212 ACCTGCTGGACCACCACC 61.570 66.667 17.64 0.00 41.77 4.61
1388 4124 4.337145 ACTTGTGAACCAACAAAGTACCA 58.663 39.130 0.00 0.00 39.47 3.25
1389 4125 4.976224 ACTTGTGAACCAACAAAGTACC 57.024 40.909 0.00 0.00 39.47 3.34
1390 4126 5.912955 GCATACTTGTGAACCAACAAAGTAC 59.087 40.000 0.00 0.00 39.47 2.73
1391 4127 5.825679 AGCATACTTGTGAACCAACAAAGTA 59.174 36.000 0.00 0.00 39.47 2.24
1441 4194 3.678056 AATACACTGGCACTCGAAAGA 57.322 42.857 0.00 0.00 39.12 2.52
1465 4218 1.192146 ACGCTGGCACTCCCTCTAAA 61.192 55.000 0.00 0.00 0.00 1.85
1482 4236 1.062002 CTTATTGCACGGCCACTTACG 59.938 52.381 2.24 0.00 0.00 3.18
1509 4263 1.342174 GGCAATCACATTATGCTGGGG 59.658 52.381 0.00 0.00 39.94 4.96
1546 4301 8.110612 CGTTTATTCGATTCAGGCATATATGAC 58.889 37.037 17.10 14.12 35.53 3.06
1547 4302 8.032451 TCGTTTATTCGATTCAGGCATATATGA 58.968 33.333 17.10 0.00 34.85 2.15
1548 4303 8.185003 TCGTTTATTCGATTCAGGCATATATG 57.815 34.615 8.45 8.45 34.85 1.78
1583 4338 4.094442 CCCCGGAAAGAAAAGAGATAAACG 59.906 45.833 0.73 0.00 0.00 3.60
1597 4353 8.515695 AAATAATAGTTAAACTCCCCGGAAAG 57.484 34.615 0.73 1.46 0.00 2.62
1598 4354 9.394767 GTAAATAATAGTTAAACTCCCCGGAAA 57.605 33.333 0.73 0.00 0.00 3.13
1603 4359 8.618677 GCAGTGTAAATAATAGTTAAACTCCCC 58.381 37.037 0.75 0.00 28.35 4.81
1695 6770 6.152661 AGGTTTTCTTGTCTGTTTGTGATTCA 59.847 34.615 0.00 0.00 0.00 2.57
1718 6793 4.970860 AGTGACATATGGAGAATGGAGG 57.029 45.455 7.80 0.00 0.00 4.30
1731 6806 8.664798 GCTTTGTGTGTTCATAATAGTGACATA 58.335 33.333 0.00 0.00 0.00 2.29
1837 6912 0.105964 CCGTGTCTTCACTGGTTCCA 59.894 55.000 0.00 0.00 41.89 3.53
1843 6918 1.734477 CTCGCCCGTGTCTTCACTG 60.734 63.158 0.00 0.00 41.89 3.66
1850 6925 3.743886 CTTTATTTTTCTCGCCCGTGTC 58.256 45.455 0.00 0.00 0.00 3.67
1855 6930 7.220875 CAGATAAAAGCTTTATTTTTCTCGCCC 59.779 37.037 13.10 0.00 34.35 6.13
1876 6951 2.606795 GCAACAACGCAAAAGCCAGATA 60.607 45.455 0.00 0.00 0.00 1.98
1880 6955 1.875813 CGCAACAACGCAAAAGCCA 60.876 52.632 0.00 0.00 0.00 4.75
1883 6958 1.821336 TCTTCGCAACAACGCAAAAG 58.179 45.000 0.00 0.00 0.00 2.27
1898 6974 6.441093 TGCATGATTTGTGTCCTATTCTTC 57.559 37.500 0.00 0.00 0.00 2.87
1904 6980 4.201657 CCTCATGCATGATTTGTGTCCTA 58.798 43.478 28.81 3.03 36.02 2.94
1933 7010 0.737019 GCCACATTTGTCGCCATTGG 60.737 55.000 0.00 0.00 0.00 3.16
1934 7011 0.244450 AGCCACATTTGTCGCCATTG 59.756 50.000 0.00 0.00 32.43 2.82
1938 7015 1.017177 TACGAGCCACATTTGTCGCC 61.017 55.000 0.00 0.00 35.83 5.54
1944 7021 1.745087 CCAGCATTACGAGCCACATTT 59.255 47.619 0.00 0.00 0.00 2.32
1946 7023 0.253044 ACCAGCATTACGAGCCACAT 59.747 50.000 0.00 0.00 0.00 3.21
1948 7025 0.727398 GAACCAGCATTACGAGCCAC 59.273 55.000 0.00 0.00 0.00 5.01
1949 7026 0.613260 AGAACCAGCATTACGAGCCA 59.387 50.000 0.00 0.00 0.00 4.75
1950 7027 1.739067 AAGAACCAGCATTACGAGCC 58.261 50.000 0.00 0.00 0.00 4.70
1955 7032 4.443621 GTCTCCCTAAGAACCAGCATTAC 58.556 47.826 0.00 0.00 35.21 1.89
1974 7052 0.318784 GGAAGTCTTCGTGCACGTCT 60.319 55.000 35.74 25.11 40.80 4.18
1975 7053 1.282930 GGGAAGTCTTCGTGCACGTC 61.283 60.000 35.74 24.69 40.80 4.34
1983 7061 3.979495 CGATAATAACCGGGAAGTCTTCG 59.021 47.826 6.32 2.26 0.00 3.79
1984 7062 4.981054 GTCGATAATAACCGGGAAGTCTTC 59.019 45.833 6.32 3.80 0.00 2.87
1993 7071 4.986659 CCTAACCTTGTCGATAATAACCGG 59.013 45.833 0.00 0.00 0.00 5.28
1996 7074 4.446719 CGGCCTAACCTTGTCGATAATAAC 59.553 45.833 0.00 0.00 35.61 1.89
1997 7075 4.501915 CCGGCCTAACCTTGTCGATAATAA 60.502 45.833 0.00 0.00 35.61 1.40
2001 7079 0.748450 CCGGCCTAACCTTGTCGATA 59.252 55.000 0.00 0.00 35.61 2.92
2007 7085 2.106683 CGAAGCCGGCCTAACCTTG 61.107 63.158 26.15 0.14 35.61 3.61
2023 7101 1.141019 GTTGCCGCTCTCATACCGA 59.859 57.895 0.00 0.00 0.00 4.69
2025 7103 0.727398 GTTGTTGCCGCTCTCATACC 59.273 55.000 0.00 0.00 0.00 2.73
2039 7117 2.604174 GCTGCTACACGCCGTTGTT 61.604 57.895 0.00 0.00 38.05 2.83
2043 7121 4.778415 CGAGCTGCTACACGCCGT 62.778 66.667 0.15 0.00 38.05 5.68
2046 7124 1.989966 TAGGACGAGCTGCTACACGC 61.990 60.000 0.15 0.00 39.77 5.34
2049 7127 1.715862 CGCTAGGACGAGCTGCTACA 61.716 60.000 0.15 0.00 40.51 2.74
2052 7130 3.522731 CCGCTAGGACGAGCTGCT 61.523 66.667 0.00 0.00 40.51 4.24
2054 7132 4.914420 CGCCGCTAGGACGAGCTG 62.914 72.222 0.00 0.00 40.51 4.24
2057 7135 1.793134 ATTACCGCCGCTAGGACGAG 61.793 60.000 0.00 0.00 41.02 4.18
2058 7136 1.825191 ATTACCGCCGCTAGGACGA 60.825 57.895 0.00 0.00 41.02 4.20
2059 7137 1.660575 CATTACCGCCGCTAGGACG 60.661 63.158 0.00 0.00 41.02 4.79
2062 7141 1.145377 AACCATTACCGCCGCTAGG 59.855 57.895 0.00 0.00 41.62 3.02
2072 7151 2.879646 TGGACAACCGAACAACCATTAC 59.120 45.455 0.00 0.00 39.42 1.89
2073 7152 3.210232 TGGACAACCGAACAACCATTA 57.790 42.857 0.00 0.00 39.42 1.90
2080 7159 0.250553 GGTCCATGGACAACCGAACA 60.251 55.000 38.83 2.59 46.20 3.18
2083 7162 0.036164 CAAGGTCCATGGACAACCGA 59.964 55.000 38.83 4.99 46.20 4.69
2085 7164 2.514458 ATCAAGGTCCATGGACAACC 57.486 50.000 38.83 26.31 46.20 3.77
2125 7204 4.742438 TTCATCGAAAGTACAAAGCACC 57.258 40.909 0.00 0.00 0.00 5.01
2127 7206 9.594478 TTATAGATTCATCGAAAGTACAAAGCA 57.406 29.630 0.00 0.00 0.00 3.91
2186 7268 2.809706 CCATGCCCATTTGCCTCG 59.190 61.111 0.00 0.00 0.00 4.63
2222 7304 8.614469 AAGAAACCAACAAAAAGACATCAAAA 57.386 26.923 0.00 0.00 0.00 2.44
2226 7308 8.406297 ACTAGAAGAAACCAACAAAAAGACATC 58.594 33.333 0.00 0.00 0.00 3.06
2264 7346 6.443792 ACCAACACCAGAATAAATCGAAAAC 58.556 36.000 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.