Multiple sequence alignment - TraesCS5A01G480700

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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 TraesCS5A01G480700 chr5A 100.000 2945 0 0 1 2945 653476313 653473369 0.000000e+00 5439
1 TraesCS5A01G480700 chr5A 90.950 1116 74 12 913 2004 653563304 653564416 0.000000e+00 1476
2 TraesCS5A01G480700 chr5A 79.087 416 47 18 446 846 653562793 653563183 1.750000e-62 250
3 TraesCS5A01G480700 chr5B 92.101 1114 68 11 910 2004 661525035 661523923 0.000000e+00 1552
4 TraesCS5A01G480700 chr5B 89.081 1099 93 5 914 1985 661612073 661613171 0.000000e+00 1339
5 TraesCS5A01G480700 chr5B 93.139 481 12 2 2465 2945 661520204 661519745 0.000000e+00 686
6 TraesCS5A01G480700 chr5B 86.553 409 27 16 292 699 661525638 661525257 2.710000e-115 425
7 TraesCS5A01G480700 chr5B 93.421 152 6 3 2326 2473 661523672 661523521 3.820000e-54 222
8 TraesCS5A01G480700 chr5B 81.333 225 29 9 624 846 661611731 661611944 1.400000e-38 171
9 TraesCS5A01G480700 chr5D 91.554 1113 70 15 914 2004 526411353 526410243 0.000000e+00 1513
10 TraesCS5A01G480700 chr5D 91.471 1020 73 8 996 2004 526432434 526433450 0.000000e+00 1389
11 TraesCS5A01G480700 chr5D 93.808 646 17 2 2302 2945 526410011 526409387 0.000000e+00 950
12 TraesCS5A01G480700 chr5D 94.977 438 19 1 1501 1935 526422496 526422933 0.000000e+00 684
13 TraesCS5A01G480700 chr5D 87.258 620 48 12 321 918 526411989 526411379 0.000000e+00 678
14 TraesCS5A01G480700 chr5D 86.364 418 26 18 66 470 526413490 526413091 7.540000e-116 427
15 TraesCS5A01G480700 chr5D 93.233 133 7 1 1998 2130 526410205 526410075 8.330000e-46 195
16 TraesCS5A01G480700 chr3D 88.382 964 77 16 990 1949 496768453 496767521 0.000000e+00 1127
17 TraesCS5A01G480700 chr3D 73.729 472 65 28 244 688 496769594 496769155 2.380000e-26 130
18 TraesCS5A01G480700 chr3A 87.694 967 87 16 987 1949 638016496 638015558 0.000000e+00 1098
19 TraesCS5A01G480700 chr3B 86.880 968 93 15 987 1949 656066835 656065897 0.000000e+00 1053
20 TraesCS5A01G480700 chr2D 79.072 927 145 32 1019 1943 376356683 376355804 2.530000e-165 592
21 TraesCS5A01G480700 chr2A 78.341 928 143 36 1019 1944 509992504 509991633 5.550000e-152 547


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 TraesCS5A01G480700 chr5A 653473369 653476313 2944 True 5439.00 5439 100.0000 1 2945 1 chr5A.!!$R1 2944
1 TraesCS5A01G480700 chr5A 653562793 653564416 1623 False 863.00 1476 85.0185 446 2004 2 chr5A.!!$F1 1558
2 TraesCS5A01G480700 chr5B 661611731 661613171 1440 False 755.00 1339 85.2070 624 1985 2 chr5B.!!$F1 1361
3 TraesCS5A01G480700 chr5B 661519745 661525638 5893 True 721.25 1552 91.3035 292 2945 4 chr5B.!!$R1 2653
4 TraesCS5A01G480700 chr5D 526432434 526433450 1016 False 1389.00 1389 91.4710 996 2004 1 chr5D.!!$F2 1008
5 TraesCS5A01G480700 chr5D 526409387 526413490 4103 True 752.60 1513 90.4434 66 2945 5 chr5D.!!$R1 2879
6 TraesCS5A01G480700 chr3D 496767521 496769594 2073 True 628.50 1127 81.0555 244 1949 2 chr3D.!!$R1 1705
7 TraesCS5A01G480700 chr3A 638015558 638016496 938 True 1098.00 1098 87.6940 987 1949 1 chr3A.!!$R1 962
8 TraesCS5A01G480700 chr3B 656065897 656066835 938 True 1053.00 1053 86.8800 987 1949 1 chr3B.!!$R1 962
9 TraesCS5A01G480700 chr2D 376355804 376356683 879 True 592.00 592 79.0720 1019 1943 1 chr2D.!!$R1 924
10 TraesCS5A01G480700 chr2A 509991633 509992504 871 True 547.00 547 78.3410 1019 1944 1 chr2A.!!$R1 925

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
162 169 0.1023 CTCGGTGTGTCAGTGTGTGA 59.898 55.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2134 4066 0.031585 GAAAGCCCACCAAACCGAAC 59.968 55.0 0.0 0.0 0.0 3.95 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
26 27 9.762933 ACACAATTTTGCACTAAAATATCACTT 57.237 25.926 0.00 0.00 45.74 3.16
96 97 6.174720 AGTATAATTCACACGATGGATGGT 57.825 37.500 0.00 0.00 0.00 3.55
102 103 0.252761 ACACGATGGATGGTGATGCA 59.747 50.000 8.57 0.00 38.58 3.96
103 104 1.134007 ACACGATGGATGGTGATGCAT 60.134 47.619 0.00 0.00 42.91 3.96
104 105 1.265905 CACGATGGATGGTGATGCATG 59.734 52.381 2.46 0.00 40.49 4.06
105 106 0.240145 CGATGGATGGTGATGCATGC 59.760 55.000 11.82 11.82 40.49 4.06
106 107 0.601558 GATGGATGGTGATGCATGCC 59.398 55.000 16.68 6.96 40.49 4.40
108 109 1.152610 GGATGGTGATGCATGCCCT 60.153 57.895 16.68 1.69 0.00 5.19
109 110 1.177256 GGATGGTGATGCATGCCCTC 61.177 60.000 16.68 12.62 0.00 4.30
110 111 0.178998 GATGGTGATGCATGCCCTCT 60.179 55.000 16.68 0.81 0.00 3.69
111 112 1.072806 GATGGTGATGCATGCCCTCTA 59.927 52.381 16.68 6.51 0.00 2.43
112 113 1.142936 TGGTGATGCATGCCCTCTAT 58.857 50.000 16.68 0.26 0.00 1.98
121 128 2.616510 GCATGCCCTCTATACCATGGAC 60.617 54.545 21.47 0.00 36.47 4.02
162 169 0.102300 CTCGGTGTGTCAGTGTGTGA 59.898 55.000 0.00 0.00 0.00 3.58
165 172 1.066454 CGGTGTGTCAGTGTGTGAGTA 59.934 52.381 0.00 0.00 35.13 2.59
166 173 2.480587 CGGTGTGTCAGTGTGTGAGTAA 60.481 50.000 0.00 0.00 35.13 2.24
173 180 2.364324 TCAGTGTGTGAGTAAGTGGTCC 59.636 50.000 0.00 0.00 0.00 4.46
192 199 4.877251 GGTCCGTGGTATAAATAAAGCACA 59.123 41.667 5.63 0.00 42.72 4.57
205 212 7.938140 AAATAAAGCACAGCCTACTCAATAA 57.062 32.000 0.00 0.00 0.00 1.40
228 235 9.737427 ATAAATACACGATTGTAGTCTCTCAAG 57.263 33.333 0.00 0.00 41.62 3.02
264 272 4.856115 GCTGAAGAGCATAACTGAGAAC 57.144 45.455 0.00 0.00 45.46 3.01
274 282 4.748892 CATAACTGAGAACGACTGGTGAT 58.251 43.478 0.00 0.00 0.00 3.06
275 283 3.305398 AACTGAGAACGACTGGTGATC 57.695 47.619 0.00 0.00 0.00 2.92
276 284 2.239400 ACTGAGAACGACTGGTGATCA 58.761 47.619 0.00 0.00 0.00 2.92
324 1547 3.243267 GGGCGTGCTTTCAGACTTAAAAA 60.243 43.478 0.00 0.00 0.00 1.94
346 1599 2.477845 TGTTAGGCCGGTTTTCCTAC 57.522 50.000 1.90 1.49 34.87 3.18
368 1621 2.474032 GCTAACGTAAGAAAAGCGCAGG 60.474 50.000 11.47 0.00 43.62 4.85
382 1635 1.158484 CGCAGGACATCATGAGGCAG 61.158 60.000 7.40 0.00 0.00 4.85
427 1681 4.588278 GAGACCATAAACATAAAGTGCGC 58.412 43.478 0.00 0.00 0.00 6.09
437 1692 0.108520 TAAAGTGCGCGGGAGGTAAG 60.109 55.000 8.83 0.00 0.00 2.34
438 1693 3.952628 AAGTGCGCGGGAGGTAAGC 62.953 63.158 8.83 0.00 0.00 3.09
439 1694 4.752879 GTGCGCGGGAGGTAAGCA 62.753 66.667 8.83 0.00 35.27 3.91
440 1695 3.781307 TGCGCGGGAGGTAAGCAT 61.781 61.111 8.83 0.00 32.43 3.79
441 1696 2.420043 GCGCGGGAGGTAAGCATA 59.580 61.111 8.83 0.00 0.00 3.14
442 1697 1.004918 GCGCGGGAGGTAAGCATAT 60.005 57.895 8.83 0.00 0.00 1.78
510 1782 1.444119 GCGCAAGGCCAATCCGATTA 61.444 55.000 5.01 0.00 40.77 1.75
550 1835 1.593750 CGGCCTGAGCTGCAGTATC 60.594 63.158 16.64 14.25 43.33 2.24
563 1848 0.772926 CAGTATCGCTCATTCGACGC 59.227 55.000 0.00 0.00 41.62 5.19
646 1935 5.374071 GGATGTGGTATTTTAGTCGGGATT 58.626 41.667 0.00 0.00 0.00 3.01
688 1977 1.613437 CAACCGGCTCTTTCCATTTGT 59.387 47.619 0.00 0.00 0.00 2.83
730 2439 2.647158 AACTCTCCCTTCGGCCGAC 61.647 63.158 31.19 0.00 0.00 4.79
861 2615 5.123344 ACGACAAGGTGCCAAGTAAATAATC 59.877 40.000 0.00 0.00 0.00 1.75
884 2638 1.687563 CCTGGAAACGAAACAGGGTT 58.312 50.000 10.76 0.00 46.24 4.11
938 2746 0.250467 TGGAGCTTGGAGAGTGTTGC 60.250 55.000 0.00 0.00 0.00 4.17
1268 3106 1.296715 CCTTCCCGTCCACTTCCAG 59.703 63.158 0.00 0.00 0.00 3.86
1270 3108 0.037232 CTTCCCGTCCACTTCCAGTC 60.037 60.000 0.00 0.00 0.00 3.51
1272 3110 2.214216 CCCGTCCACTTCCAGTCCA 61.214 63.158 0.00 0.00 0.00 4.02
1274 3112 0.320771 CCGTCCACTTCCAGTCCAAG 60.321 60.000 0.00 0.00 0.00 3.61
1464 3329 3.537874 GTACGGATGGCCTCGGCT 61.538 66.667 3.32 0.00 41.60 5.52
2022 3954 3.211045 GAAGCGGGCAATCCTATTTGTA 58.789 45.455 0.00 0.00 0.00 2.41
2023 3955 2.572290 AGCGGGCAATCCTATTTGTAC 58.428 47.619 0.00 0.00 0.00 2.90
2115 4047 2.234414 GTGACAAATCCCACATTGGCAT 59.766 45.455 0.00 0.00 45.64 4.40
2125 4057 2.658285 CACATTGGCATATGTGTCCCT 58.342 47.619 23.13 0.96 46.53 4.20
2126 4058 2.620115 CACATTGGCATATGTGTCCCTC 59.380 50.000 23.13 0.00 46.53 4.30
2127 4059 2.233271 CATTGGCATATGTGTCCCTCC 58.767 52.381 4.29 0.00 0.00 4.30
2128 4060 0.180171 TTGGCATATGTGTCCCTCCG 59.820 55.000 4.29 0.00 0.00 4.63
2129 4061 1.071471 GGCATATGTGTCCCTCCGG 59.929 63.158 4.29 0.00 0.00 5.14
2130 4062 1.071471 GCATATGTGTCCCTCCGGG 59.929 63.158 0.00 0.00 46.11 5.73
2131 4063 1.071471 CATATGTGTCCCTCCGGGC 59.929 63.158 0.00 0.00 43.94 6.13
2132 4064 1.074471 ATATGTGTCCCTCCGGGCT 60.074 57.895 0.00 0.00 43.94 5.19
2133 4065 0.694444 ATATGTGTCCCTCCGGGCTT 60.694 55.000 0.00 0.00 43.94 4.35
2134 4066 1.622607 TATGTGTCCCTCCGGGCTTG 61.623 60.000 0.00 0.00 43.94 4.01
2135 4067 3.637273 GTGTCCCTCCGGGCTTGT 61.637 66.667 0.00 0.00 43.94 3.16
2136 4068 2.852075 TGTCCCTCCGGGCTTGTT 60.852 61.111 0.00 0.00 43.94 2.83
2137 4069 2.046217 GTCCCTCCGGGCTTGTTC 60.046 66.667 0.00 0.00 43.94 3.18
2138 4070 3.702048 TCCCTCCGGGCTTGTTCG 61.702 66.667 0.00 0.00 43.94 3.95
2139 4071 4.778143 CCCTCCGGGCTTGTTCGG 62.778 72.222 0.00 0.00 46.89 4.30
2140 4072 4.016706 CCTCCGGGCTTGTTCGGT 62.017 66.667 0.00 0.00 45.79 4.69
2141 4073 2.032071 CTCCGGGCTTGTTCGGTT 59.968 61.111 0.00 0.00 45.79 4.44
2142 4074 1.599797 CTCCGGGCTTGTTCGGTTT 60.600 57.895 0.00 0.00 45.79 3.27
2143 4075 1.852067 CTCCGGGCTTGTTCGGTTTG 61.852 60.000 0.00 0.00 45.79 2.93
2144 4076 2.642700 CGGGCTTGTTCGGTTTGG 59.357 61.111 0.00 0.00 0.00 3.28
2145 4077 2.190841 CGGGCTTGTTCGGTTTGGT 61.191 57.895 0.00 0.00 0.00 3.67
2146 4078 1.362355 GGGCTTGTTCGGTTTGGTG 59.638 57.895 0.00 0.00 0.00 4.17
2147 4079 1.362355 GGCTTGTTCGGTTTGGTGG 59.638 57.895 0.00 0.00 0.00 4.61
2148 4080 1.362355 GCTTGTTCGGTTTGGTGGG 59.638 57.895 0.00 0.00 0.00 4.61
2149 4081 1.362355 CTTGTTCGGTTTGGTGGGC 59.638 57.895 0.00 0.00 0.00 5.36
2150 4082 1.076632 TTGTTCGGTTTGGTGGGCT 60.077 52.632 0.00 0.00 0.00 5.19
2151 4083 0.684805 TTGTTCGGTTTGGTGGGCTT 60.685 50.000 0.00 0.00 0.00 4.35
2152 4084 0.684805 TGTTCGGTTTGGTGGGCTTT 60.685 50.000 0.00 0.00 0.00 3.51
2153 4085 0.031585 GTTCGGTTTGGTGGGCTTTC 59.968 55.000 0.00 0.00 0.00 2.62
2154 4086 0.395862 TTCGGTTTGGTGGGCTTTCA 60.396 50.000 0.00 0.00 0.00 2.69
2155 4087 0.395862 TCGGTTTGGTGGGCTTTCAA 60.396 50.000 0.00 0.00 0.00 2.69
2156 4088 0.678950 CGGTTTGGTGGGCTTTCAAT 59.321 50.000 0.00 0.00 0.00 2.57
2157 4089 1.336795 CGGTTTGGTGGGCTTTCAATC 60.337 52.381 0.00 0.00 0.00 2.67
2158 4090 1.001974 GGTTTGGTGGGCTTTCAATCC 59.998 52.381 0.00 0.00 0.00 3.01
2159 4091 1.001974 GTTTGGTGGGCTTTCAATCCC 59.998 52.381 0.00 0.00 42.93 3.85
2160 4092 0.544120 TTGGTGGGCTTTCAATCCCC 60.544 55.000 0.00 0.00 41.92 4.81
2161 4093 1.388133 GGTGGGCTTTCAATCCCCT 59.612 57.895 0.00 0.00 41.92 4.79
2162 4094 0.629058 GGTGGGCTTTCAATCCCCTA 59.371 55.000 0.00 0.00 41.92 3.53
2163 4095 1.685180 GGTGGGCTTTCAATCCCCTAC 60.685 57.143 0.00 0.00 41.92 3.18
2164 4096 1.005450 GTGGGCTTTCAATCCCCTACA 59.995 52.381 0.00 0.00 41.92 2.74
2165 4097 1.929494 TGGGCTTTCAATCCCCTACAT 59.071 47.619 0.00 0.00 41.92 2.29
2166 4098 2.091885 TGGGCTTTCAATCCCCTACATC 60.092 50.000 0.00 0.00 41.92 3.06
2167 4099 2.587522 GGCTTTCAATCCCCTACATCC 58.412 52.381 0.00 0.00 0.00 3.51
2168 4100 2.587522 GCTTTCAATCCCCTACATCCC 58.412 52.381 0.00 0.00 0.00 3.85
2180 4112 1.895020 TACATCCCACCGGCACTCAC 61.895 60.000 0.00 0.00 0.00 3.51
2203 4135 2.820037 GTGCTAAGCTGACGCCCC 60.820 66.667 0.00 0.00 36.60 5.80
2204 4136 4.096003 TGCTAAGCTGACGCCCCC 62.096 66.667 0.00 0.00 36.60 5.40
2205 4137 4.096003 GCTAAGCTGACGCCCCCA 62.096 66.667 0.00 0.00 36.60 4.96
2206 4138 2.668632 CTAAGCTGACGCCCCCAA 59.331 61.111 0.00 0.00 36.60 4.12
2207 4139 1.002624 CTAAGCTGACGCCCCCAAA 60.003 57.895 0.00 0.00 36.60 3.28
2208 4140 0.608035 CTAAGCTGACGCCCCCAAAA 60.608 55.000 0.00 0.00 36.60 2.44
2209 4141 0.178987 TAAGCTGACGCCCCCAAAAA 60.179 50.000 0.00 0.00 36.60 1.94
2247 4179 8.670521 TCACCAGAATCATACCACTGATATAT 57.329 34.615 0.00 0.00 34.79 0.86
2255 4187 9.730705 AATCATACCACTGATATATTTCACTGG 57.269 33.333 15.45 15.45 34.79 4.00
2256 4188 8.491045 TCATACCACTGATATATTTCACTGGA 57.509 34.615 20.68 10.28 34.82 3.86
2272 4204 5.580998 TCACTGGATATATGGTACTCCCTC 58.419 45.833 0.00 0.00 0.00 4.30
2273 4205 4.712337 CACTGGATATATGGTACTCCCTCC 59.288 50.000 0.00 0.00 0.00 4.30
2274 4206 3.954904 CTGGATATATGGTACTCCCTCCG 59.045 52.174 0.00 0.00 0.00 4.63
2275 4207 3.335786 TGGATATATGGTACTCCCTCCGT 59.664 47.826 0.00 0.00 0.00 4.69
2276 4208 3.952967 GGATATATGGTACTCCCTCCGTC 59.047 52.174 0.00 0.00 0.00 4.79
2277 4209 2.305858 ATATGGTACTCCCTCCGTCC 57.694 55.000 0.00 0.00 0.00 4.79
2278 4210 0.186873 TATGGTACTCCCTCCGTCCC 59.813 60.000 0.00 0.00 0.00 4.46
2279 4211 1.882189 ATGGTACTCCCTCCGTCCCA 61.882 60.000 0.00 0.00 0.00 4.37
2280 4212 1.075450 GGTACTCCCTCCGTCCCAT 60.075 63.158 0.00 0.00 0.00 4.00
2281 4213 0.186873 GGTACTCCCTCCGTCCCATA 59.813 60.000 0.00 0.00 0.00 2.74
2282 4214 1.203149 GGTACTCCCTCCGTCCCATAT 60.203 57.143 0.00 0.00 0.00 1.78
2283 4215 2.606378 GTACTCCCTCCGTCCCATATT 58.394 52.381 0.00 0.00 0.00 1.28
2284 4216 3.501019 GGTACTCCCTCCGTCCCATATTA 60.501 52.174 0.00 0.00 0.00 0.98
2285 4217 3.562108 ACTCCCTCCGTCCCATATTAT 57.438 47.619 0.00 0.00 0.00 1.28
2286 4218 3.173965 ACTCCCTCCGTCCCATATTATG 58.826 50.000 0.00 0.00 0.00 1.90
2346 4278 2.334946 GGCACGAGCTTGGATGCAA 61.335 57.895 16.16 0.00 39.92 4.08
2347 4279 1.154150 GCACGAGCTTGGATGCAAC 60.154 57.895 10.86 0.00 38.00 4.17
2361 4293 1.852942 TGCAACACGAACTCAGACTC 58.147 50.000 0.00 0.00 0.00 3.36
2501 7762 0.970937 TAACAGGCTCAGACTCGGGG 60.971 60.000 0.00 0.00 0.00 5.73
2502 7763 2.681778 CAGGCTCAGACTCGGGGT 60.682 66.667 0.00 0.00 0.00 4.95
2688 7949 2.266055 CGGTCTTCTGGCTGGGTC 59.734 66.667 0.00 0.00 0.00 4.46
2689 7950 2.286523 CGGTCTTCTGGCTGGGTCT 61.287 63.158 0.00 0.00 0.00 3.85
2690 7951 1.298014 GGTCTTCTGGCTGGGTCTG 59.702 63.158 0.00 0.00 0.00 3.51
2691 7952 1.376553 GTCTTCTGGCTGGGTCTGC 60.377 63.158 0.00 0.00 0.00 4.26
2692 7953 2.045536 CTTCTGGCTGGGTCTGCC 60.046 66.667 8.57 8.57 46.46 4.85
2698 7959 4.021925 GCTGGGTCTGCCGGTCTT 62.022 66.667 1.90 0.00 34.97 3.01
2699 7960 2.266055 CTGGGTCTGCCGGTCTTC 59.734 66.667 1.90 0.00 34.97 2.87
2700 7961 2.203788 TGGGTCTGCCGGTCTTCT 60.204 61.111 1.90 0.00 34.97 2.85
2701 7962 2.266055 GGGTCTGCCGGTCTTCTG 59.734 66.667 1.90 0.00 34.97 3.02
2702 7963 2.266055 GGTCTGCCGGTCTTCTGG 59.734 66.667 1.90 0.00 42.72 3.86
2708 7969 3.322466 CCGGTCTTCTGGCTGGGT 61.322 66.667 0.00 0.00 32.93 4.51
2806 8067 3.586461 CTCGACAGCCAGTGCAGCT 62.586 63.158 0.00 0.00 42.70 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.762933 AAGTGATATTTTAGTGCAAAATTGTGT 57.237 25.926 0.43 0.00 42.93 3.72
62 63 9.647797 TCGTGTGAATTATACTAGTGTGAAAAT 57.352 29.630 5.39 0.00 0.00 1.82
63 64 9.647797 ATCGTGTGAATTATACTAGTGTGAAAA 57.352 29.630 5.39 0.00 0.00 2.29
64 65 9.083080 CATCGTGTGAATTATACTAGTGTGAAA 57.917 33.333 5.39 0.00 0.00 2.69
77 78 4.479786 TCACCATCCATCGTGTGAATTA 57.520 40.909 0.00 0.00 34.98 1.40
96 97 2.337849 TGGTATAGAGGGCATGCATCA 58.662 47.619 21.36 0.00 0.00 3.07
102 103 1.902508 CGTCCATGGTATAGAGGGCAT 59.097 52.381 12.58 0.00 0.00 4.40
103 104 1.338107 CGTCCATGGTATAGAGGGCA 58.662 55.000 12.58 0.00 0.00 5.36
104 105 0.608640 CCGTCCATGGTATAGAGGGC 59.391 60.000 12.58 0.00 0.00 5.19
105 106 1.618837 CACCGTCCATGGTATAGAGGG 59.381 57.143 12.58 9.53 41.38 4.30
106 107 2.594131 TCACCGTCCATGGTATAGAGG 58.406 52.381 12.58 9.58 41.38 3.69
108 109 2.299013 GCATCACCGTCCATGGTATAGA 59.701 50.000 12.58 5.44 41.38 1.98
109 110 2.037121 TGCATCACCGTCCATGGTATAG 59.963 50.000 12.58 1.95 41.38 1.31
110 111 2.043227 TGCATCACCGTCCATGGTATA 58.957 47.619 12.58 0.00 41.38 1.47
111 112 0.836606 TGCATCACCGTCCATGGTAT 59.163 50.000 12.58 0.00 41.38 2.73
112 113 0.836606 ATGCATCACCGTCCATGGTA 59.163 50.000 12.58 0.00 41.38 3.25
121 128 0.378257 GTTGTAGGCATGCATCACCG 59.622 55.000 21.36 0.00 0.00 4.94
148 155 3.430236 CCACTTACTCACACACTGACACA 60.430 47.826 0.00 0.00 0.00 3.72
153 160 2.755650 GGACCACTTACTCACACACTG 58.244 52.381 0.00 0.00 0.00 3.66
154 161 1.340248 CGGACCACTTACTCACACACT 59.660 52.381 0.00 0.00 0.00 3.55
162 169 5.945144 ATTTATACCACGGACCACTTACT 57.055 39.130 0.00 0.00 0.00 2.24
165 172 5.587443 GCTTTATTTATACCACGGACCACTT 59.413 40.000 0.00 0.00 0.00 3.16
166 173 5.121105 GCTTTATTTATACCACGGACCACT 58.879 41.667 0.00 0.00 0.00 4.00
173 180 4.574828 AGGCTGTGCTTTATTTATACCACG 59.425 41.667 0.00 0.00 0.00 4.94
192 199 7.272978 ACAATCGTGTATTTATTGAGTAGGCT 58.727 34.615 0.00 0.00 35.72 4.58
205 212 6.037098 GCTTGAGAGACTACAATCGTGTATT 58.963 40.000 0.00 0.00 39.51 1.89
258 266 2.890945 TCTTGATCACCAGTCGTTCTCA 59.109 45.455 0.00 0.00 0.00 3.27
264 272 3.748048 ACACATTTCTTGATCACCAGTCG 59.252 43.478 0.00 0.00 0.00 4.18
274 282 8.541133 TTCGTCATATGTTACACATTTCTTGA 57.459 30.769 1.90 0.00 39.88 3.02
275 283 9.773328 ATTTCGTCATATGTTACACATTTCTTG 57.227 29.630 1.90 0.00 39.88 3.02
276 284 9.773328 CATTTCGTCATATGTTACACATTTCTT 57.227 29.630 1.90 0.00 39.88 2.52
324 1547 2.884320 AGGAAAACCGGCCTAACATTT 58.116 42.857 0.00 0.00 31.31 2.32
330 1553 1.218854 GCGTAGGAAAACCGGCCTA 59.781 57.895 0.00 0.37 35.73 3.93
368 1621 3.540314 AGTTCTCTGCCTCATGATGTC 57.460 47.619 0.00 0.00 0.00 3.06
382 1635 1.440145 GCATTGGCCGGCTAGTTCTC 61.440 60.000 28.56 8.18 0.00 2.87
427 1681 2.079158 CATGCATATGCTTACCTCCCG 58.921 52.381 27.13 5.03 42.66 5.14
510 1782 2.607134 AGCTGGAGCAGGCTCTGT 60.607 61.111 19.67 1.10 45.16 3.41
545 1830 0.663688 AGCGTCGAATGAGCGATACT 59.336 50.000 0.00 0.00 42.82 2.12
550 1835 1.142185 ATGTCAGCGTCGAATGAGCG 61.142 55.000 0.00 0.00 35.78 5.03
563 1848 2.513204 CTGCGAGCCCCATGTCAG 60.513 66.667 0.00 0.00 0.00 3.51
646 1935 1.941072 CAGTTGCGTTGCTGCTGTA 59.059 52.632 0.00 0.00 35.36 2.74
799 2521 0.179129 GGCCATGGCGAAAATGACAG 60.179 55.000 29.90 0.00 43.06 3.51
884 2638 4.069304 AGAGTTGTTTTATAGGCGTGCAA 58.931 39.130 0.00 0.00 0.00 4.08
924 2719 2.266554 GATCGAGCAACACTCTCCAAG 58.733 52.381 0.00 0.00 43.85 3.61
968 2776 4.409218 GCCGGTGCGTCGACTACA 62.409 66.667 14.70 9.03 0.00 2.74
1187 3022 2.604174 CCGAGGACGTTGTGTTGCC 61.604 63.158 0.00 0.00 37.88 4.52
1464 3329 2.674033 TCCGCCGGAGAGAACGAA 60.674 61.111 5.05 0.00 0.00 3.85
1560 3425 1.733041 CGTGTACCAGTGCCTGTCG 60.733 63.158 0.00 0.00 0.00 4.35
1758 3626 2.347490 GCTTTGCTCCTCGGTCCA 59.653 61.111 0.00 0.00 0.00 4.02
1921 3789 4.194720 GAGCACGACGGAGGCGAT 62.195 66.667 1.02 0.00 0.00 4.58
2084 4016 2.354821 GGGATTTGTCACCAATAGTCGC 59.645 50.000 0.00 0.00 0.00 5.19
2127 4059 2.190841 ACCAAACCGAACAAGCCCG 61.191 57.895 0.00 0.00 0.00 6.13
2128 4060 1.362355 CACCAAACCGAACAAGCCC 59.638 57.895 0.00 0.00 0.00 5.19
2129 4061 1.362355 CCACCAAACCGAACAAGCC 59.638 57.895 0.00 0.00 0.00 4.35
2130 4062 1.362355 CCCACCAAACCGAACAAGC 59.638 57.895 0.00 0.00 0.00 4.01
2131 4063 1.106944 AGCCCACCAAACCGAACAAG 61.107 55.000 0.00 0.00 0.00 3.16
2132 4064 0.684805 AAGCCCACCAAACCGAACAA 60.685 50.000 0.00 0.00 0.00 2.83
2133 4065 0.684805 AAAGCCCACCAAACCGAACA 60.685 50.000 0.00 0.00 0.00 3.18
2134 4066 0.031585 GAAAGCCCACCAAACCGAAC 59.968 55.000 0.00 0.00 0.00 3.95
2135 4067 0.395862 TGAAAGCCCACCAAACCGAA 60.396 50.000 0.00 0.00 0.00 4.30
2136 4068 0.395862 TTGAAAGCCCACCAAACCGA 60.396 50.000 0.00 0.00 0.00 4.69
2137 4069 0.678950 ATTGAAAGCCCACCAAACCG 59.321 50.000 0.00 0.00 0.00 4.44
2138 4070 1.001974 GGATTGAAAGCCCACCAAACC 59.998 52.381 0.00 0.00 0.00 3.27
2139 4071 2.455674 GGATTGAAAGCCCACCAAAC 57.544 50.000 0.00 0.00 0.00 2.93
2147 4079 2.587522 GGATGTAGGGGATTGAAAGCC 58.412 52.381 0.00 0.00 0.00 4.35
2148 4080 2.091885 TGGGATGTAGGGGATTGAAAGC 60.092 50.000 0.00 0.00 0.00 3.51
2149 4081 3.555966 GTGGGATGTAGGGGATTGAAAG 58.444 50.000 0.00 0.00 0.00 2.62
2150 4082 2.243736 GGTGGGATGTAGGGGATTGAAA 59.756 50.000 0.00 0.00 0.00 2.69
2151 4083 1.850345 GGTGGGATGTAGGGGATTGAA 59.150 52.381 0.00 0.00 0.00 2.69
2152 4084 1.518367 GGTGGGATGTAGGGGATTGA 58.482 55.000 0.00 0.00 0.00 2.57
2153 4085 0.108585 CGGTGGGATGTAGGGGATTG 59.891 60.000 0.00 0.00 0.00 2.67
2154 4086 1.060163 CCGGTGGGATGTAGGGGATT 61.060 60.000 0.00 0.00 34.06 3.01
2155 4087 1.461461 CCGGTGGGATGTAGGGGAT 60.461 63.158 0.00 0.00 34.06 3.85
2156 4088 2.041301 CCGGTGGGATGTAGGGGA 60.041 66.667 0.00 0.00 34.06 4.81
2157 4089 3.873812 GCCGGTGGGATGTAGGGG 61.874 72.222 1.90 0.00 34.06 4.79
2158 4090 3.087253 TGCCGGTGGGATGTAGGG 61.087 66.667 1.90 0.00 34.06 3.53
2159 4091 2.189521 GTGCCGGTGGGATGTAGG 59.810 66.667 1.90 0.00 34.06 3.18
2160 4092 1.144057 GAGTGCCGGTGGGATGTAG 59.856 63.158 1.90 0.00 34.06 2.74
2161 4093 1.610967 TGAGTGCCGGTGGGATGTA 60.611 57.895 1.90 0.00 34.06 2.29
2162 4094 2.927856 TGAGTGCCGGTGGGATGT 60.928 61.111 1.90 0.00 34.06 3.06
2163 4095 2.436646 GTGAGTGCCGGTGGGATG 60.437 66.667 1.90 0.00 34.06 3.51
2164 4096 2.607750 AGTGAGTGCCGGTGGGAT 60.608 61.111 1.90 0.00 34.06 3.85
2165 4097 3.625897 CAGTGAGTGCCGGTGGGA 61.626 66.667 1.90 0.00 34.06 4.37
2180 4112 1.357258 CGTCAGCTTAGCACCAGCAG 61.357 60.000 7.07 0.00 45.49 4.24
2185 4117 2.820037 GGGCGTCAGCTTAGCACC 60.820 66.667 7.07 0.00 44.37 5.01
2187 4119 4.096003 GGGGGCGTCAGCTTAGCA 62.096 66.667 7.07 0.00 44.37 3.49
2210 4142 2.325583 TCTGGTGAGCGTCAGTTTTT 57.674 45.000 0.00 0.00 33.13 1.94
2211 4143 2.325583 TTCTGGTGAGCGTCAGTTTT 57.674 45.000 0.00 0.00 33.13 2.43
2212 4144 2.224281 TGATTCTGGTGAGCGTCAGTTT 60.224 45.455 0.00 0.00 33.13 2.66
2213 4145 1.344438 TGATTCTGGTGAGCGTCAGTT 59.656 47.619 0.00 0.00 33.13 3.16
2214 4146 0.969149 TGATTCTGGTGAGCGTCAGT 59.031 50.000 0.00 0.00 33.13 3.41
2215 4147 2.306341 ATGATTCTGGTGAGCGTCAG 57.694 50.000 0.00 0.00 0.00 3.51
2216 4148 2.159099 GGTATGATTCTGGTGAGCGTCA 60.159 50.000 0.00 0.00 0.00 4.35
2217 4149 2.159099 TGGTATGATTCTGGTGAGCGTC 60.159 50.000 0.00 0.00 0.00 5.19
2218 4150 1.831106 TGGTATGATTCTGGTGAGCGT 59.169 47.619 0.00 0.00 0.00 5.07
2219 4151 2.159043 AGTGGTATGATTCTGGTGAGCG 60.159 50.000 0.00 0.00 0.00 5.03
2220 4152 3.118629 TCAGTGGTATGATTCTGGTGAGC 60.119 47.826 0.00 0.00 0.00 4.26
2221 4153 4.743057 TCAGTGGTATGATTCTGGTGAG 57.257 45.455 0.00 0.00 0.00 3.51
2222 4154 8.670521 ATATATCAGTGGTATGATTCTGGTGA 57.329 34.615 6.14 0.00 40.40 4.02
2223 4155 9.730705 AAATATATCAGTGGTATGATTCTGGTG 57.269 33.333 6.14 0.00 40.40 4.17
2247 4179 6.390504 AGGGAGTACCATATATCCAGTGAAA 58.609 40.000 0.00 0.00 43.89 2.69
2255 4187 3.952967 GGACGGAGGGAGTACCATATATC 59.047 52.174 0.00 0.00 43.89 1.63
2256 4188 3.309701 GGGACGGAGGGAGTACCATATAT 60.310 52.174 0.00 0.00 42.20 0.86
2266 4198 2.501723 CCATAATATGGGACGGAGGGAG 59.498 54.545 11.41 0.00 46.86 4.30
2267 4199 2.546899 CCATAATATGGGACGGAGGGA 58.453 52.381 11.41 0.00 46.86 4.20
2278 4210 7.564793 TCATAATCCCTCCGTTCCATAATATG 58.435 38.462 0.00 0.00 0.00 1.78
2279 4211 7.749377 TCATAATCCCTCCGTTCCATAATAT 57.251 36.000 0.00 0.00 0.00 1.28
2280 4212 7.147549 GGATCATAATCCCTCCGTTCCATAATA 60.148 40.741 0.00 0.00 45.11 0.98
2281 4213 6.353082 GGATCATAATCCCTCCGTTCCATAAT 60.353 42.308 0.00 0.00 45.11 1.28
2282 4214 5.045869 GGATCATAATCCCTCCGTTCCATAA 60.046 44.000 0.00 0.00 45.11 1.90
2283 4215 4.469945 GGATCATAATCCCTCCGTTCCATA 59.530 45.833 0.00 0.00 45.11 2.74
2284 4216 3.264450 GGATCATAATCCCTCCGTTCCAT 59.736 47.826 0.00 0.00 45.11 3.41
2285 4217 2.637872 GGATCATAATCCCTCCGTTCCA 59.362 50.000 0.00 0.00 45.11 3.53
2286 4218 3.336138 GGATCATAATCCCTCCGTTCC 57.664 52.381 0.00 0.00 45.11 3.62
2296 4228 7.117523 GTGCATAGTCTTCACTGGATCATAATC 59.882 40.741 0.00 0.00 33.62 1.75
2297 4229 6.933521 GTGCATAGTCTTCACTGGATCATAAT 59.066 38.462 0.00 0.00 33.62 1.28
2298 4230 6.127083 TGTGCATAGTCTTCACTGGATCATAA 60.127 38.462 0.00 0.00 33.62 1.90
2299 4231 5.363580 TGTGCATAGTCTTCACTGGATCATA 59.636 40.000 0.00 0.00 33.62 2.15
2300 4232 4.162888 TGTGCATAGTCTTCACTGGATCAT 59.837 41.667 0.00 0.00 33.62 2.45
2346 4278 2.868044 GCATTGGAGTCTGAGTTCGTGT 60.868 50.000 0.00 0.00 0.00 4.49
2347 4279 1.728971 GCATTGGAGTCTGAGTTCGTG 59.271 52.381 0.00 0.00 0.00 4.35
2361 4293 5.981315 GTCATCATTGAACTATTGGCATTGG 59.019 40.000 0.00 0.00 32.48 3.16
2501 7762 0.588482 GCCTACTCGTCGTAGCGAAC 60.588 60.000 8.49 0.00 43.48 3.95
2502 7763 1.709147 GGCCTACTCGTCGTAGCGAA 61.709 60.000 0.00 0.00 43.48 4.70
2647 7908 2.521958 ATCCAACCAGAAGACCGGCG 62.522 60.000 0.00 0.00 0.00 6.46
2691 7952 3.316573 GACCCAGCCAGAAGACCGG 62.317 68.421 0.00 0.00 0.00 5.28
2692 7953 2.266055 GACCCAGCCAGAAGACCG 59.734 66.667 0.00 0.00 0.00 4.79
2693 7954 2.266055 CGACCCAGCCAGAAGACC 59.734 66.667 0.00 0.00 0.00 3.85
2694 7955 2.435059 GCGACCCAGCCAGAAGAC 60.435 66.667 0.00 0.00 0.00 3.01
2695 7956 2.604686 AGCGACCCAGCCAGAAGA 60.605 61.111 0.00 0.00 38.01 2.87
2696 7957 2.435586 CAGCGACCCAGCCAGAAG 60.436 66.667 0.00 0.00 38.01 2.85
2697 7958 4.020617 CCAGCGACCCAGCCAGAA 62.021 66.667 0.00 0.00 38.01 3.02
2699 7960 4.463879 CTCCAGCGACCCAGCCAG 62.464 72.222 0.00 0.00 38.01 4.85
2701 7962 4.459089 GACTCCAGCGACCCAGCC 62.459 72.222 0.00 0.00 38.01 4.85
2702 7963 2.948720 AAGACTCCAGCGACCCAGC 61.949 63.158 0.00 0.00 37.41 4.85
2703 7964 1.079543 CAAGACTCCAGCGACCCAG 60.080 63.158 0.00 0.00 0.00 4.45
2704 7965 0.541063 TACAAGACTCCAGCGACCCA 60.541 55.000 0.00 0.00 0.00 4.51
2705 7966 0.824759 ATACAAGACTCCAGCGACCC 59.175 55.000 0.00 0.00 0.00 4.46
2706 7967 1.202428 GGATACAAGACTCCAGCGACC 60.202 57.143 0.00 0.00 0.00 4.79
2707 7968 1.202428 GGGATACAAGACTCCAGCGAC 60.202 57.143 0.00 0.00 39.74 5.19
2708 7969 1.112113 GGGATACAAGACTCCAGCGA 58.888 55.000 0.00 0.00 39.74 4.93
2806 8067 1.207089 CTGAACGGAGCCCAGACAATA 59.793 52.381 0.00 0.00 33.14 1.90


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

AutoCloner maintained by Alex Coulton.