Multiple sequence alignment - TraesCS2A01G312200

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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 TraesCS2A01G312200 chr2A 100.000 2459 0 0 1 2459 536314400 536311942 0.000000e+00 4542.0
1 TraesCS2A01G312200 chr2B 95.876 1455 32 10 275 1722 472251914 472250481 0.000000e+00 2329.0
2 TraesCS2A01G312200 chr2B 92.202 218 16 1 1732 1949 472250382 472250166 8.540000e-80 307.0
3 TraesCS2A01G312200 chr2D 93.523 1266 42 12 792 2055 398693027 398691800 0.000000e+00 1847.0
4 TraesCS2A01G312200 chr2D 91.166 815 41 18 6 797 398695645 398694839 0.000000e+00 1077.0
5 TraesCS2A01G312200 chr2D 76.923 338 33 19 2156 2453 398691792 398691460 1.520000e-32 150.0
6 TraesCS2A01G312200 chr4B 81.868 182 26 5 1045 1226 638307904 638307730 1.970000e-31 147.0
7 TraesCS2A01G312200 chr4D 88.298 94 9 2 1104 1196 509798567 509798659 7.190000e-21 111.0
8 TraesCS2A01G312200 chr4D 87.719 57 4 2 1549 1602 497273488 497273432 2.040000e-06 63.9
9 TraesCS2A01G312200 chr5D 84.906 106 16 0 1127 1232 445062753 445062648 9.300000e-20 108.0
10 TraesCS2A01G312200 chr5B 84.906 106 16 0 1127 1232 542295573 542295468 9.300000e-20 108.0
11 TraesCS2A01G312200 chr5B 83.962 106 17 0 1127 1232 542320023 542319918 4.330000e-18 102.0
12 TraesCS2A01G312200 chr5B 85.567 97 14 0 1138 1234 542694750 542694654 4.330000e-18 102.0
13 TraesCS2A01G312200 chr5A 83.962 106 17 0 1127 1232 562108418 562108313 4.330000e-18 102.0
14 TraesCS2A01G312200 chr1A 87.179 78 5 5 2090 2165 9957200 9957274 1.570000e-12 84.2
15 TraesCS2A01G312200 chr6A 89.655 58 6 0 2104 2161 397487722 397487779 9.430000e-10 75.0
16 TraesCS2A01G312200 chr7A 96.875 32 1 0 2129 2160 108944553 108944522 1.000000e-03 54.7


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 TraesCS2A01G312200 chr2A 536311942 536314400 2458 True 4542.000000 4542 100.000 1 2459 1 chr2A.!!$R1 2458
1 TraesCS2A01G312200 chr2B 472250166 472251914 1748 True 1318.000000 2329 94.039 275 1949 2 chr2B.!!$R1 1674
2 TraesCS2A01G312200 chr2D 398691460 398695645 4185 True 1024.666667 1847 87.204 6 2453 3 chr2D.!!$R1 2447

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
305 328 2.633481 GGAGACAGGGACCATACATACC 59.367 54.545 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 4000 0.037232 GACTCAACTTGGGACGAGGG 60.037 60.0 0.0 0.0 0.0 4.3 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
41 42 5.713861 GCCTTCTCTAAATGGCATGGAATAT 59.286 40.000 0.00 0.00 44.34 1.28
57 58 9.542462 GCATGGAATATATATAAAGCCGTCTTA 57.458 33.333 0.00 0.00 31.02 2.10
72 73 9.694137 AAAGCCGTCTTATAAACTAGATGTATC 57.306 33.333 0.00 0.00 31.02 2.24
106 107 7.921041 TGGTGAGAGATACCATTTCTAAGAT 57.079 36.000 0.00 0.00 43.00 2.40
108 109 9.607333 TGGTGAGAGATACCATTTCTAAGATAT 57.393 33.333 0.00 0.00 43.00 1.63
159 160 9.719355 ACAAAACAAAAATCTCAAGGTAAAACT 57.281 25.926 0.00 0.00 0.00 2.66
193 216 7.497595 TCTAGTTTATTTATCCTGCGTGACAT 58.502 34.615 0.00 0.00 0.00 3.06
199 222 8.981724 TTATTTATCCTGCGTGACATACTATC 57.018 34.615 0.00 0.00 0.00 2.08
208 231 4.558697 GCGTGACATACTATCACATGCCTA 60.559 45.833 6.01 0.00 45.64 3.93
273 296 8.566260 ACATGCATAATGATCTCTTAGAAAAGC 58.434 33.333 0.00 0.00 38.72 3.51
279 302 5.808042 TGATCTCTTAGAAAAGCACATGC 57.192 39.130 0.00 0.00 42.49 4.06
305 328 2.633481 GGAGACAGGGACCATACATACC 59.367 54.545 0.00 0.00 0.00 2.73
545 568 2.743636 ACACATCGAACAGTTCCGAT 57.256 45.000 7.76 10.45 45.17 4.18
1035 2888 2.455122 ATGGGGATGGGGATGGGG 60.455 66.667 0.00 0.00 0.00 4.96
1036 2889 3.078909 ATGGGGATGGGGATGGGGA 62.079 63.158 0.00 0.00 0.00 4.81
1037 2890 2.120854 GGGGATGGGGATGGGGAT 60.121 66.667 0.00 0.00 0.00 3.85
1038 2891 2.551413 GGGGATGGGGATGGGGATG 61.551 68.421 0.00 0.00 0.00 3.51
1039 2892 2.551413 GGGATGGGGATGGGGATGG 61.551 68.421 0.00 0.00 0.00 3.51
1040 2893 2.551413 GGATGGGGATGGGGATGGG 61.551 68.421 0.00 0.00 0.00 4.00
1062 2915 2.073101 GGGGATGGACAGGGAGGAC 61.073 68.421 0.00 0.00 0.00 3.85
1465 3318 1.668337 CCCTGAAGCTATGATCGCTCG 60.668 57.143 0.00 0.00 36.56 5.03
1466 3319 1.268079 CCTGAAGCTATGATCGCTCGA 59.732 52.381 0.00 0.00 36.56 4.04
1467 3320 2.094803 CCTGAAGCTATGATCGCTCGAT 60.095 50.000 4.26 4.26 36.56 3.59
1468 3321 3.573598 CTGAAGCTATGATCGCTCGATT 58.426 45.455 6.22 0.00 36.56 3.34
1469 3322 3.569548 TGAAGCTATGATCGCTCGATTC 58.430 45.455 6.22 0.19 36.56 2.52
1470 3323 3.004734 TGAAGCTATGATCGCTCGATTCA 59.995 43.478 6.22 6.56 36.56 2.57
1613 3466 0.459489 GTTGTTGGCTGGTTTCTGCA 59.541 50.000 0.00 0.00 39.25 4.41
1687 3540 7.661536 TGTTAACTATACTGATCAGAAGCCT 57.338 36.000 29.27 8.86 0.00 4.58
1688 3541 8.079211 TGTTAACTATACTGATCAGAAGCCTT 57.921 34.615 29.27 15.18 0.00 4.35
1689 3542 8.540388 TGTTAACTATACTGATCAGAAGCCTTT 58.460 33.333 29.27 15.32 0.00 3.11
1690 3543 9.384764 GTTAACTATACTGATCAGAAGCCTTTT 57.615 33.333 29.27 13.90 0.00 2.27
1741 3683 5.865085 ACTAGTTCTTGCCTGTAAATGACA 58.135 37.500 0.00 0.00 36.35 3.58
1829 3771 7.393515 ACATTCCCAGTTCTGGTTAACTAATTC 59.606 37.037 16.33 0.00 37.61 2.17
1906 3848 5.505780 TCTTCCGGATTTACATGACCAATT 58.494 37.500 4.15 0.00 0.00 2.32
1952 3894 5.844601 AGGGAACTCCTGTTTAGATAGAGT 58.155 41.667 0.00 0.00 46.07 3.24
1953 3895 5.659079 AGGGAACTCCTGTTTAGATAGAGTG 59.341 44.000 0.00 0.00 46.07 3.51
1954 3896 5.657302 GGGAACTCCTGTTTAGATAGAGTGA 59.343 44.000 0.00 0.00 36.39 3.41
1956 3898 7.310485 GGGAACTCCTGTTTAGATAGAGTGAAA 60.310 40.741 0.00 0.00 36.39 2.69
1974 3916 5.180117 AGTGAAAATTACTAGCACAGCACAG 59.820 40.000 0.00 0.00 32.16 3.66
1975 3917 4.083324 TGAAAATTACTAGCACAGCACAGC 60.083 41.667 0.00 0.00 0.00 4.40
1976 3918 2.768253 ATTACTAGCACAGCACAGCA 57.232 45.000 0.00 0.00 0.00 4.41
1980 3922 1.067283 ACTAGCACAGCACAGCACTAG 60.067 52.381 0.00 0.00 34.61 2.57
2002 3944 7.876068 ACTAGCTAGTATACTGATGAGAGACAC 59.124 40.741 24.97 0.00 34.13 3.67
2003 3945 6.001460 AGCTAGTATACTGATGAGAGACACC 58.999 44.000 15.90 0.00 0.00 4.16
2004 3946 6.001460 GCTAGTATACTGATGAGAGACACCT 58.999 44.000 15.90 0.00 0.00 4.00
2005 3947 6.148811 GCTAGTATACTGATGAGAGACACCTC 59.851 46.154 15.90 0.00 39.72 3.85
2030 3972 3.806521 CCTCAGATCAGACGCCTTAATTG 59.193 47.826 0.00 0.00 0.00 2.32
2034 3976 4.631377 CAGATCAGACGCCTTAATTGTTGA 59.369 41.667 0.00 0.00 0.00 3.18
2050 3992 4.944962 TGTTGAGATTTACATCCTTGCG 57.055 40.909 0.00 0.00 0.00 4.85
2055 3997 5.185454 TGAGATTTACATCCTTGCGTGATT 58.815 37.500 0.00 0.00 0.00 2.57
2056 3998 5.294306 TGAGATTTACATCCTTGCGTGATTC 59.706 40.000 0.00 0.00 0.00 2.52
2057 3999 5.431765 AGATTTACATCCTTGCGTGATTCT 58.568 37.500 0.00 0.00 0.00 2.40
2058 4000 5.525378 AGATTTACATCCTTGCGTGATTCTC 59.475 40.000 0.00 0.00 0.00 2.87
2059 4001 2.029838 ACATCCTTGCGTGATTCTCC 57.970 50.000 0.00 0.00 0.00 3.71
2060 4002 1.303309 CATCCTTGCGTGATTCTCCC 58.697 55.000 0.00 0.00 0.00 4.30
2061 4003 1.134280 CATCCTTGCGTGATTCTCCCT 60.134 52.381 0.00 0.00 0.00 4.20
2062 4004 0.537188 TCCTTGCGTGATTCTCCCTC 59.463 55.000 0.00 0.00 0.00 4.30
2063 4005 0.807667 CCTTGCGTGATTCTCCCTCG 60.808 60.000 0.00 0.00 0.00 4.63
2065 4007 0.108804 TTGCGTGATTCTCCCTCGTC 60.109 55.000 0.00 0.00 0.00 4.20
2066 4008 1.227002 GCGTGATTCTCCCTCGTCC 60.227 63.158 0.00 0.00 0.00 4.79
2067 4009 1.437986 CGTGATTCTCCCTCGTCCC 59.562 63.158 0.00 0.00 0.00 4.46
2068 4010 1.320344 CGTGATTCTCCCTCGTCCCA 61.320 60.000 0.00 0.00 0.00 4.37
2069 4011 0.902531 GTGATTCTCCCTCGTCCCAA 59.097 55.000 0.00 0.00 0.00 4.12
2070 4012 1.134670 GTGATTCTCCCTCGTCCCAAG 60.135 57.143 0.00 0.00 0.00 3.61
2071 4013 1.196012 GATTCTCCCTCGTCCCAAGT 58.804 55.000 0.00 0.00 0.00 3.16
2072 4014 1.555533 GATTCTCCCTCGTCCCAAGTT 59.444 52.381 0.00 0.00 0.00 2.66
2073 4015 0.685097 TTCTCCCTCGTCCCAAGTTG 59.315 55.000 0.00 0.00 0.00 3.16
2074 4016 0.178944 TCTCCCTCGTCCCAAGTTGA 60.179 55.000 3.87 0.00 0.00 3.18
2075 4017 0.247736 CTCCCTCGTCCCAAGTTGAG 59.752 60.000 3.87 0.00 0.00 3.02
2076 4018 0.471211 TCCCTCGTCCCAAGTTGAGT 60.471 55.000 3.87 0.00 0.00 3.41
2077 4019 0.037232 CCCTCGTCCCAAGTTGAGTC 60.037 60.000 3.87 0.00 0.00 3.36
2078 4020 0.679505 CCTCGTCCCAAGTTGAGTCA 59.320 55.000 3.87 0.00 0.00 3.41
2079 4021 1.276421 CCTCGTCCCAAGTTGAGTCAT 59.724 52.381 3.87 0.00 0.00 3.06
2080 4022 2.289694 CCTCGTCCCAAGTTGAGTCATT 60.290 50.000 3.87 0.00 0.00 2.57
2081 4023 3.403038 CTCGTCCCAAGTTGAGTCATTT 58.597 45.455 3.87 0.00 0.00 2.32
2082 4024 4.562757 CCTCGTCCCAAGTTGAGTCATTTA 60.563 45.833 3.87 0.00 0.00 1.40
2083 4025 5.160607 TCGTCCCAAGTTGAGTCATTTAT 57.839 39.130 3.87 0.00 0.00 1.40
2084 4026 5.556915 TCGTCCCAAGTTGAGTCATTTATT 58.443 37.500 3.87 0.00 0.00 1.40
2085 4027 6.001460 TCGTCCCAAGTTGAGTCATTTATTT 58.999 36.000 3.87 0.00 0.00 1.40
2086 4028 6.488683 TCGTCCCAAGTTGAGTCATTTATTTT 59.511 34.615 3.87 0.00 0.00 1.82
2087 4029 7.662258 TCGTCCCAAGTTGAGTCATTTATTTTA 59.338 33.333 3.87 0.00 0.00 1.52
2088 4030 7.962918 CGTCCCAAGTTGAGTCATTTATTTTAG 59.037 37.037 3.87 0.00 0.00 1.85
2089 4031 9.010029 GTCCCAAGTTGAGTCATTTATTTTAGA 57.990 33.333 3.87 0.00 0.00 2.10
2090 4032 9.581289 TCCCAAGTTGAGTCATTTATTTTAGAA 57.419 29.630 3.87 0.00 0.00 2.10
2135 4077 9.052759 ACAAAGTTAATACAAATTCGAGTCACT 57.947 29.630 0.00 0.00 0.00 3.41
2136 4078 9.878599 CAAAGTTAATACAAATTCGAGTCACTT 57.121 29.630 0.00 0.00 0.00 3.16
2147 4089 9.250986 CAAATTCGAGTCACTTATTTTAGAACG 57.749 33.333 0.00 0.00 0.00 3.95
2148 4090 6.939551 TTCGAGTCACTTATTTTAGAACGG 57.060 37.500 0.00 0.00 0.00 4.44
2149 4091 6.258230 TCGAGTCACTTATTTTAGAACGGA 57.742 37.500 0.00 0.00 0.00 4.69
2150 4092 6.680810 TCGAGTCACTTATTTTAGAACGGAA 58.319 36.000 0.00 0.00 0.00 4.30
2151 4093 6.805271 TCGAGTCACTTATTTTAGAACGGAAG 59.195 38.462 0.00 0.00 0.00 3.46
2152 4094 6.034683 CGAGTCACTTATTTTAGAACGGAAGG 59.965 42.308 0.00 0.00 0.00 3.46
2153 4095 7.001099 AGTCACTTATTTTAGAACGGAAGGA 57.999 36.000 0.00 0.00 0.00 3.36
2154 4096 7.097834 AGTCACTTATTTTAGAACGGAAGGAG 58.902 38.462 0.00 0.00 0.00 3.69
2155 4097 6.872547 GTCACTTATTTTAGAACGGAAGGAGT 59.127 38.462 0.00 0.00 0.00 3.85
2156 4098 8.031277 GTCACTTATTTTAGAACGGAAGGAGTA 58.969 37.037 0.00 0.00 0.00 2.59
2157 4099 8.755977 TCACTTATTTTAGAACGGAAGGAGTAT 58.244 33.333 0.00 0.00 0.00 2.12
2183 4125 5.608449 ACTACTTCATTATAGGGGAAACGC 58.392 41.667 0.00 0.00 45.13 4.84
2202 4144 3.095016 CGCGCGCATTCTTATGTTTTTA 58.905 40.909 32.61 0.00 34.12 1.52
2205 4147 5.237705 GCGCGCATTCTTATGTTTTTAAAC 58.762 37.500 29.10 0.00 39.33 2.01
2217 4163 3.799420 TGTTTTTAAACAGGCAATGCGTC 59.201 39.130 0.00 0.00 43.45 5.19
2221 4167 0.823356 AAACAGGCAATGCGTCTGGT 60.823 50.000 14.28 6.36 33.19 4.00
2226 4172 2.325082 GCAATGCGTCTGGTCGGTT 61.325 57.895 0.00 0.00 0.00 4.44
2227 4173 1.852067 GCAATGCGTCTGGTCGGTTT 61.852 55.000 0.00 0.00 0.00 3.27
2302 4256 6.304788 CGGAACTATTCGCATTTTCTTTTG 57.695 37.500 0.00 0.00 0.00 2.44
2303 4257 5.856455 CGGAACTATTCGCATTTTCTTTTGT 59.144 36.000 0.00 0.00 0.00 2.83
2304 4258 6.362283 CGGAACTATTCGCATTTTCTTTTGTT 59.638 34.615 0.00 0.00 0.00 2.83
2305 4259 7.096230 CGGAACTATTCGCATTTTCTTTTGTTT 60.096 33.333 0.00 0.00 0.00 2.83
2349 4327 2.588620 TGGCCGGTGTTTTCAGTAATT 58.411 42.857 1.90 0.00 0.00 1.40
2351 4329 4.142790 TGGCCGGTGTTTTCAGTAATTAA 58.857 39.130 1.90 0.00 0.00 1.40
2362 4340 9.991906 TGTTTTCAGTAATTAACTAGTACTGCT 57.008 29.630 15.14 0.00 42.86 4.24
2367 4345 7.912250 TCAGTAATTAACTAGTACTGCTAACGC 59.088 37.037 15.14 0.00 42.86 4.84
2371 4349 3.761311 ACTAGTACTGCTAACGCTGAC 57.239 47.619 5.39 0.00 38.34 3.51
2406 4384 2.680577 GCTTTTGCTGTTTCCCATCTG 58.319 47.619 0.00 0.00 43.35 2.90
2407 4385 2.611224 GCTTTTGCTGTTTCCCATCTGG 60.611 50.000 0.00 0.00 43.35 3.86
2423 4405 4.429505 CATCTGGGATTCTGGGTATAGGA 58.570 47.826 0.00 0.00 0.00 2.94
2425 4407 4.429505 TCTGGGATTCTGGGTATAGGATG 58.570 47.826 0.00 0.00 0.00 3.51
2429 4411 4.322801 GGGATTCTGGGTATAGGATGAACG 60.323 50.000 0.00 0.00 0.00 3.95
2449 4431 3.259876 ACGGGAACACACTAGAATGCTAA 59.740 43.478 0.00 0.00 0.00 3.09
2453 4435 6.379386 GGGAACACACTAGAATGCTAAAAAC 58.621 40.000 0.00 0.00 0.00 2.43
2454 4436 6.016610 GGGAACACACTAGAATGCTAAAAACA 60.017 38.462 0.00 0.00 0.00 2.83
2455 4437 7.309194 GGGAACACACTAGAATGCTAAAAACAT 60.309 37.037 0.00 0.00 0.00 2.71
2456 4438 8.726988 GGAACACACTAGAATGCTAAAAACATA 58.273 33.333 0.00 0.00 0.00 2.29
2457 4439 9.760660 GAACACACTAGAATGCTAAAAACATAG 57.239 33.333 0.00 0.00 0.00 2.23
2458 4440 9.502091 AACACACTAGAATGCTAAAAACATAGA 57.498 29.630 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 8.632679 CGGCTTTATATATATTCCATGCCATTT 58.367 33.333 17.45 0.00 36.75 2.32
28 29 7.290061 ACGGCTTTATATATATTCCATGCCAT 58.710 34.615 17.45 7.42 36.75 4.40
29 30 6.658849 ACGGCTTTATATATATTCCATGCCA 58.341 36.000 17.45 0.00 36.75 4.92
30 31 6.992715 AGACGGCTTTATATATATTCCATGCC 59.007 38.462 0.00 7.94 0.00 4.40
31 32 8.438676 AAGACGGCTTTATATATATTCCATGC 57.561 34.615 0.00 0.72 0.00 4.06
72 73 7.303182 TGGTATCTCTCACCACATAATTAGG 57.697 40.000 0.00 0.00 41.17 2.69
185 208 2.476619 GGCATGTGATAGTATGTCACGC 59.523 50.000 0.00 1.45 46.89 5.34
208 231 3.390003 TTTTTCGGGTCTCAGCGTT 57.610 47.368 0.00 0.00 0.00 4.84
256 279 5.298777 GGCATGTGCTTTTCTAAGAGATCAT 59.701 40.000 4.84 0.00 41.70 2.45
266 289 0.962356 CCTCGGGCATGTGCTTTTCT 60.962 55.000 4.84 0.00 41.70 2.52
267 290 0.960364 TCCTCGGGCATGTGCTTTTC 60.960 55.000 4.84 0.00 41.70 2.29
271 294 2.685017 TCTCCTCGGGCATGTGCT 60.685 61.111 4.84 0.00 41.70 4.40
272 295 2.512515 GTCTCCTCGGGCATGTGC 60.513 66.667 0.00 0.00 41.14 4.57
273 296 1.153489 CTGTCTCCTCGGGCATGTG 60.153 63.158 0.00 0.00 0.00 3.21
279 302 2.760385 GGTCCCTGTCTCCTCGGG 60.760 72.222 0.00 0.00 39.41 5.14
379 402 8.484214 AGATCAATCTACCTAGCTAACATTGA 57.516 34.615 11.74 11.74 34.85 2.57
442 465 1.468520 CAACACGGGTAGGCTTTCATG 59.531 52.381 0.00 0.00 0.00 3.07
466 489 2.904866 GTGCAGCACGGGTCCAAA 60.905 61.111 10.47 0.00 0.00 3.28
545 568 3.492656 CCGCCTTATAGCTAGCTTTCACA 60.493 47.826 24.88 4.23 0.00 3.58
575 598 2.454336 ACTGATCTACATGTCCCCGA 57.546 50.000 0.00 0.00 0.00 5.14
694 717 3.695606 GCGTCCTGCACTCCTGGA 61.696 66.667 0.00 0.00 45.45 3.86
1035 2888 2.156774 GTCCATCCCCCTCCCCATC 61.157 68.421 0.00 0.00 0.00 3.51
1036 2889 2.038330 GTCCATCCCCCTCCCCAT 60.038 66.667 0.00 0.00 0.00 4.00
1037 2890 3.632049 TGTCCATCCCCCTCCCCA 61.632 66.667 0.00 0.00 0.00 4.96
1038 2891 2.774351 CTGTCCATCCCCCTCCCC 60.774 72.222 0.00 0.00 0.00 4.81
1039 2892 2.774351 CCTGTCCATCCCCCTCCC 60.774 72.222 0.00 0.00 0.00 4.30
1040 2893 2.774351 CCCTGTCCATCCCCCTCC 60.774 72.222 0.00 0.00 0.00 4.30
1062 2915 2.037136 CAAGCTGAGGTTGAGCCCG 61.037 63.158 18.81 0.00 42.72 6.13
1134 2987 1.133809 ACTTCCTGGGGCAGTAGCAA 61.134 55.000 0.00 0.00 44.61 3.91
1613 3466 3.074412 CGAGTACAGTTTCAAGCCCATT 58.926 45.455 0.00 0.00 0.00 3.16
1661 3514 8.709308 AGGCTTCTGATCAGTATAGTTAACAAT 58.291 33.333 21.92 0.00 0.00 2.71
1662 3515 8.079211 AGGCTTCTGATCAGTATAGTTAACAA 57.921 34.615 21.92 4.51 0.00 2.83
1741 3683 5.497474 AGTTATTCTAGGACCGCACATTTT 58.503 37.500 0.00 0.00 0.00 1.82
1791 3733 6.486993 AGAACTGGGAATGTAAAGAGTTCAAC 59.513 38.462 0.00 0.00 41.06 3.18
1829 3771 1.490574 AGGAGGCAGCTAGGTAGTTG 58.509 55.000 0.00 0.00 37.55 3.16
1866 3808 5.521735 CCGGAAGAGTTAAACTGATCATGAG 59.478 44.000 0.00 0.00 0.00 2.90
1918 3860 0.542333 GAGTTCCCTAGGACAAGGCC 59.458 60.000 11.48 0.00 35.09 5.19
1945 3887 7.492669 TGCTGTGCTAGTAATTTTCACTCTATC 59.507 37.037 0.00 0.00 0.00 2.08
1950 3892 5.063204 TGTGCTGTGCTAGTAATTTTCACT 58.937 37.500 0.00 0.00 0.00 3.41
1952 3894 4.083324 GCTGTGCTGTGCTAGTAATTTTCA 60.083 41.667 0.00 0.00 0.00 2.69
1953 3895 4.083324 TGCTGTGCTGTGCTAGTAATTTTC 60.083 41.667 0.00 0.00 0.00 2.29
1954 3896 3.820467 TGCTGTGCTGTGCTAGTAATTTT 59.180 39.130 0.00 0.00 0.00 1.82
1956 3898 2.744202 GTGCTGTGCTGTGCTAGTAATT 59.256 45.455 0.00 0.00 0.00 1.40
1974 3916 6.876789 TCTCTCATCAGTATACTAGCTAGTGC 59.123 42.308 32.21 21.88 37.10 4.40
1975 3917 7.875554 TGTCTCTCATCAGTATACTAGCTAGTG 59.124 40.741 32.21 17.47 37.10 2.74
1976 3918 7.876068 GTGTCTCTCATCAGTATACTAGCTAGT 59.124 40.741 28.50 28.50 40.24 2.57
1980 3922 6.001460 AGGTGTCTCTCATCAGTATACTAGC 58.999 44.000 4.74 0.00 0.00 3.42
1983 3925 6.061441 CAGAGGTGTCTCTCATCAGTATACT 58.939 44.000 0.00 0.00 46.79 2.12
1991 3933 1.484038 AGGCAGAGGTGTCTCTCATC 58.516 55.000 0.00 0.00 46.79 2.92
2002 3944 0.385029 CGTCTGATCTGAGGCAGAGG 59.615 60.000 11.78 13.20 44.08 3.69
2003 3945 0.248990 GCGTCTGATCTGAGGCAGAG 60.249 60.000 30.55 4.54 44.08 3.35
2004 3946 1.670949 GGCGTCTGATCTGAGGCAGA 61.671 60.000 33.69 11.51 46.04 4.26
2005 3947 1.227205 GGCGTCTGATCTGAGGCAG 60.227 63.158 33.69 15.62 46.04 4.85
2006 3948 1.260538 AAGGCGTCTGATCTGAGGCA 61.261 55.000 33.69 2.70 46.04 4.75
2007 3949 0.747255 TAAGGCGTCTGATCTGAGGC 59.253 55.000 28.79 28.79 44.25 4.70
2008 3950 3.742433 ATTAAGGCGTCTGATCTGAGG 57.258 47.619 15.58 15.58 0.00 3.86
2030 3972 4.391830 TCACGCAAGGATGTAAATCTCAAC 59.608 41.667 0.00 0.00 46.39 3.18
2034 3976 5.431765 AGAATCACGCAAGGATGTAAATCT 58.568 37.500 0.00 0.00 46.39 2.40
2050 3992 0.902531 TTGGGACGAGGGAGAATCAC 59.097 55.000 0.00 0.00 40.51 3.06
2055 3997 0.178944 TCAACTTGGGACGAGGGAGA 60.179 55.000 0.00 0.00 0.00 3.71
2056 3998 0.247736 CTCAACTTGGGACGAGGGAG 59.752 60.000 0.00 0.00 0.00 4.30
2057 3999 0.471211 ACTCAACTTGGGACGAGGGA 60.471 55.000 0.00 0.00 0.00 4.20
2058 4000 0.037232 GACTCAACTTGGGACGAGGG 60.037 60.000 0.00 0.00 0.00 4.30
2059 4001 0.679505 TGACTCAACTTGGGACGAGG 59.320 55.000 0.00 0.00 0.00 4.63
2060 4002 2.751166 ATGACTCAACTTGGGACGAG 57.249 50.000 0.00 0.00 0.00 4.18
2061 4003 3.485463 AAATGACTCAACTTGGGACGA 57.515 42.857 0.00 0.00 0.00 4.20
2062 4004 5.880054 AATAAATGACTCAACTTGGGACG 57.120 39.130 0.00 0.00 0.00 4.79
2063 4005 9.010029 TCTAAAATAAATGACTCAACTTGGGAC 57.990 33.333 0.00 0.00 0.00 4.46
2109 4051 9.052759 AGTGACTCGAATTTGTATTAACTTTGT 57.947 29.630 0.00 0.00 0.00 2.83
2110 4052 9.878599 AAGTGACTCGAATTTGTATTAACTTTG 57.121 29.630 0.00 0.00 0.00 2.77
2121 4063 9.250986 CGTTCTAAAATAAGTGACTCGAATTTG 57.749 33.333 0.00 0.00 0.00 2.32
2122 4064 8.440833 CCGTTCTAAAATAAGTGACTCGAATTT 58.559 33.333 0.00 0.00 0.00 1.82
2123 4065 7.816031 TCCGTTCTAAAATAAGTGACTCGAATT 59.184 33.333 0.00 0.00 0.00 2.17
2124 4066 7.318141 TCCGTTCTAAAATAAGTGACTCGAAT 58.682 34.615 0.00 0.00 0.00 3.34
2125 4067 6.680810 TCCGTTCTAAAATAAGTGACTCGAA 58.319 36.000 0.00 0.00 0.00 3.71
2126 4068 6.258230 TCCGTTCTAAAATAAGTGACTCGA 57.742 37.500 0.00 0.00 0.00 4.04
2127 4069 6.034683 CCTTCCGTTCTAAAATAAGTGACTCG 59.965 42.308 0.00 0.00 0.00 4.18
2128 4070 7.095270 TCCTTCCGTTCTAAAATAAGTGACTC 58.905 38.462 0.00 0.00 0.00 3.36
2129 4071 7.001099 TCCTTCCGTTCTAAAATAAGTGACT 57.999 36.000 0.00 0.00 0.00 3.41
2130 4072 6.872547 ACTCCTTCCGTTCTAAAATAAGTGAC 59.127 38.462 0.00 0.00 0.00 3.67
2131 4073 7.001099 ACTCCTTCCGTTCTAAAATAAGTGA 57.999 36.000 0.00 0.00 0.00 3.41
2132 4074 8.943909 ATACTCCTTCCGTTCTAAAATAAGTG 57.056 34.615 0.00 0.00 0.00 3.16
2141 4083 9.717942 GAAGTAGTATATACTCCTTCCGTTCTA 57.282 37.037 26.40 3.89 40.98 2.10
2142 4084 8.216423 TGAAGTAGTATATACTCCTTCCGTTCT 58.784 37.037 30.33 8.78 44.10 3.01
2143 4085 8.388484 TGAAGTAGTATATACTCCTTCCGTTC 57.612 38.462 30.33 16.43 44.10 3.95
2144 4086 8.937207 ATGAAGTAGTATATACTCCTTCCGTT 57.063 34.615 30.33 19.36 44.10 4.44
2145 4087 8.937207 AATGAAGTAGTATATACTCCTTCCGT 57.063 34.615 30.33 21.69 44.10 4.69
2157 4099 8.526147 GCGTTTCCCCTATAATGAAGTAGTATA 58.474 37.037 0.00 0.00 0.00 1.47
2158 4100 7.384477 GCGTTTCCCCTATAATGAAGTAGTAT 58.616 38.462 0.00 0.00 0.00 2.12
2159 4101 6.515531 CGCGTTTCCCCTATAATGAAGTAGTA 60.516 42.308 0.00 0.00 0.00 1.82
2160 4102 5.608449 GCGTTTCCCCTATAATGAAGTAGT 58.392 41.667 0.00 0.00 0.00 2.73
2161 4103 4.684703 CGCGTTTCCCCTATAATGAAGTAG 59.315 45.833 0.00 0.00 0.00 2.57
2162 4104 4.624015 CGCGTTTCCCCTATAATGAAGTA 58.376 43.478 0.00 0.00 0.00 2.24
2163 4105 3.463944 CGCGTTTCCCCTATAATGAAGT 58.536 45.455 0.00 0.00 0.00 3.01
2167 4109 0.511221 CGCGCGTTTCCCCTATAATG 59.489 55.000 24.19 0.00 0.00 1.90
2183 4125 6.369326 TGTTTAAAAACATAAGAATGCGCG 57.631 33.333 0.00 0.00 43.45 6.86
2186 4128 7.650834 TGCCTGTTTAAAAACATAAGAATGC 57.349 32.000 8.62 4.83 46.71 3.56
2202 4144 0.823356 ACCAGACGCATTGCCTGTTT 60.823 50.000 12.14 0.00 0.00 2.83
2205 4147 2.743752 CGACCAGACGCATTGCCTG 61.744 63.158 2.41 5.55 0.00 4.85
2231 4177 9.908152 CACACGAGGATGTAAATCAATATACTA 57.092 33.333 0.00 0.00 0.00 1.82
2266 4212 6.962678 GCGAATAGTTCCGCTAAAATTAAACA 59.037 34.615 0.00 0.00 46.96 2.83
2267 4213 7.359733 GCGAATAGTTCCGCTAAAATTAAAC 57.640 36.000 0.00 0.00 46.96 2.01
2314 4268 1.202336 CGGCCAAATGAATTGCCTCTC 60.202 52.381 2.24 0.00 37.73 3.20
2319 4273 0.037419 ACACCGGCCAAATGAATTGC 60.037 50.000 0.00 0.00 37.73 3.56
2332 4286 7.662604 ACTAGTTAATTACTGAAAACACCGG 57.337 36.000 0.00 0.00 37.73 5.28
2362 4340 0.036765 AAGAATGGCCGTCAGCGTTA 60.037 50.000 0.00 0.00 45.17 3.18
2364 4342 0.889186 AAAAGAATGGCCGTCAGCGT 60.889 50.000 0.00 0.00 45.17 5.07
2404 4382 4.429505 TCATCCTATACCCAGAATCCCAG 58.570 47.826 0.00 0.00 0.00 4.45
2405 4383 4.502036 TCATCCTATACCCAGAATCCCA 57.498 45.455 0.00 0.00 0.00 4.37
2406 4384 4.322801 CGTTCATCCTATACCCAGAATCCC 60.323 50.000 0.00 0.00 0.00 3.85
2407 4385 4.322801 CCGTTCATCCTATACCCAGAATCC 60.323 50.000 0.00 0.00 0.00 3.01
2408 4386 4.322801 CCCGTTCATCCTATACCCAGAATC 60.323 50.000 0.00 0.00 0.00 2.52
2409 4387 3.583086 CCCGTTCATCCTATACCCAGAAT 59.417 47.826 0.00 0.00 0.00 2.40
2410 4388 2.969950 CCCGTTCATCCTATACCCAGAA 59.030 50.000 0.00 0.00 0.00 3.02
2414 4396 2.701951 TGTTCCCGTTCATCCTATACCC 59.298 50.000 0.00 0.00 0.00 3.69
2423 4405 4.253685 CATTCTAGTGTGTTCCCGTTCAT 58.746 43.478 0.00 0.00 0.00 2.57
2425 4407 2.415512 GCATTCTAGTGTGTTCCCGTTC 59.584 50.000 0.00 0.00 0.00 3.95
2429 4411 6.016610 TGTTTTTAGCATTCTAGTGTGTTCCC 60.017 38.462 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.