Multiple sequence alignment - TraesCS3B01G239200

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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 TraesCS3B01G239200 chr3B 100.000 4580 0 0 1 4580 377422224 377426803 0.000000e+00 8458.0
1 TraesCS3B01G239200 chr3D 94.628 2569 76 35 1492 4042 283315502 283318026 0.000000e+00 3923.0
2 TraesCS3B01G239200 chr3D 94.564 1490 40 19 1 1484 283313773 283315227 0.000000e+00 2265.0
3 TraesCS3B01G239200 chr3D 81.475 610 25 34 4039 4580 283318261 283318850 1.970000e-113 420.0
4 TraesCS3B01G239200 chr3A 94.894 2507 51 42 1274 3759 370238499 370240949 0.000000e+00 3849.0
5 TraesCS3B01G239200 chr3A 93.937 1270 52 10 1 1261 370237262 370238515 0.000000e+00 1895.0
6 TraesCS3B01G239200 chr3A 89.916 357 17 11 4147 4493 370242673 370243020 4.210000e-120 442.0
7 TraesCS3B01G239200 chr3A 97.222 36 0 1 266 300 44444020 44443985 4.950000e-05 60.2
8 TraesCS3B01G239200 chr6D 78.684 1201 208 35 2247 3438 433477548 433476387 0.000000e+00 756.0
9 TraesCS3B01G239200 chr6B 78.565 1199 213 32 2247 3438 654734416 654733255 0.000000e+00 750.0
10 TraesCS3B01G239200 chr6A 78.518 1201 213 32 2247 3438 579438864 579437700 0.000000e+00 747.0
11 TraesCS3B01G239200 chr7A 77.403 1217 244 25 2242 3438 108237641 108236436 0.000000e+00 695.0
12 TraesCS3B01G239200 chr7A 73.333 285 65 10 2789 3066 49047997 49047717 1.360000e-15 95.3
13 TraesCS3B01G239200 chr7A 75.758 132 24 5 2753 2877 522798993 522799123 4.950000e-05 60.2
14 TraesCS3B01G239200 chr7D 77.157 1217 250 21 2242 3438 104091826 104090618 0.000000e+00 682.0
15 TraesCS3B01G239200 chr7D 75.758 132 24 5 2753 2877 473093932 473093802 4.950000e-05 60.2
16 TraesCS3B01G239200 chr7B 77.138 1216 243 28 2242 3435 61910141 61908939 0.000000e+00 673.0
17 TraesCS3B01G239200 chr7B 95.000 40 1 1 2838 2877 497024959 497024921 1.380000e-05 62.1
18 TraesCS3B01G239200 chr7B 97.222 36 0 1 266 300 458563443 458563408 4.950000e-05 60.2
19 TraesCS3B01G239200 chr5B 97.222 36 0 1 266 300 126610023 126610058 4.950000e-05 60.2
20 TraesCS3B01G239200 chr5A 97.222 36 0 1 266 300 688610379 688610414 4.950000e-05 60.2
21 TraesCS3B01G239200 chr4D 97.222 36 0 1 266 300 27292543 27292508 4.950000e-05 60.2
22 TraesCS3B01G239200 chr2D 97.222 36 0 1 266 300 520639814 520639779 4.950000e-05 60.2
23 TraesCS3B01G239200 chr2D 96.875 32 1 0 2843 2874 209510270 209510301 2.000000e-03 54.7
24 TraesCS3B01G239200 chr1B 97.222 36 0 1 266 300 432109165 432109200 4.950000e-05 60.2


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 TraesCS3B01G239200 chr3B 377422224 377426803 4579 False 8458.000000 8458 100.000000 1 4580 1 chr3B.!!$F1 4579
1 TraesCS3B01G239200 chr3D 283313773 283318850 5077 False 2202.666667 3923 90.222333 1 4580 3 chr3D.!!$F1 4579
2 TraesCS3B01G239200 chr3A 370237262 370243020 5758 False 2062.000000 3849 92.915667 1 4493 3 chr3A.!!$F1 4492
3 TraesCS3B01G239200 chr6D 433476387 433477548 1161 True 756.000000 756 78.684000 2247 3438 1 chr6D.!!$R1 1191
4 TraesCS3B01G239200 chr6B 654733255 654734416 1161 True 750.000000 750 78.565000 2247 3438 1 chr6B.!!$R1 1191
5 TraesCS3B01G239200 chr6A 579437700 579438864 1164 True 747.000000 747 78.518000 2247 3438 1 chr6A.!!$R1 1191
6 TraesCS3B01G239200 chr7A 108236436 108237641 1205 True 695.000000 695 77.403000 2242 3438 1 chr7A.!!$R2 1196
7 TraesCS3B01G239200 chr7D 104090618 104091826 1208 True 682.000000 682 77.157000 2242 3438 1 chr7D.!!$R1 1196
8 TraesCS3B01G239200 chr7B 61908939 61910141 1202 True 673.000000 673 77.138000 2242 3435 1 chr7B.!!$R1 1193

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
762 771 1.468520 GAGCGTGCAAGAATAGCCAAA 59.531 47.619 2.99 0.00 0.00 3.28 F
1956 2248 0.622665 ACCTCCTCTTGGCAAGGATG 59.377 55.000 25.92 16.46 42.01 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2129 2433 1.172175 GAAGGAAGCAAGCAGGAAGG 58.828 55.0 0.0 0.0 0.0 3.46 R
3893 4237 0.107508 AAGCAGATGATGTGACGGGG 60.108 55.0 0.0 0.0 0.0 5.73 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
42 43 4.701765 CAGAAGTATCTGCTGCTAACCAT 58.298 43.478 0.00 0.00 46.11 3.55
257 258 6.946009 CCCTGGACTAAGTATTTCCTTTTTCA 59.054 38.462 0.00 0.00 0.00 2.69
258 259 7.450323 CCCTGGACTAAGTATTTCCTTTTTCAA 59.550 37.037 0.00 0.00 0.00 2.69
335 337 4.574828 AGTAAATATTTCCTTGCGCGTGAT 59.425 37.500 8.43 0.00 0.00 3.06
354 356 5.333645 CGTGATTTTTGATGGATCGATCTCC 60.334 44.000 23.96 11.68 35.74 3.71
730 739 2.593956 GGGTCAAGCTTCTCCGGGT 61.594 63.158 0.00 0.00 0.00 5.28
762 771 1.468520 GAGCGTGCAAGAATAGCCAAA 59.531 47.619 2.99 0.00 0.00 3.28
763 772 2.094675 AGCGTGCAAGAATAGCCAAAT 58.905 42.857 2.99 0.00 0.00 2.32
790 799 1.962100 GTCTAATCTGGTACCCCCTCG 59.038 57.143 10.07 0.00 0.00 4.63
1254 1268 6.982160 TCATTCTTAATGATTTCCCCCATG 57.018 37.500 0.00 0.00 42.69 3.66
1255 1269 6.681538 TCATTCTTAATGATTTCCCCCATGA 58.318 36.000 0.00 0.00 42.69 3.07
1256 1270 7.131451 TCATTCTTAATGATTTCCCCCATGAA 58.869 34.615 0.00 0.00 42.69 2.57
1257 1271 7.622878 TCATTCTTAATGATTTCCCCCATGAAA 59.377 33.333 0.00 0.00 42.69 2.69
1258 1272 7.422465 TTCTTAATGATTTCCCCCATGAAAG 57.578 36.000 0.00 0.00 37.63 2.62
1259 1273 5.363580 TCTTAATGATTTCCCCCATGAAAGC 59.636 40.000 0.00 0.00 40.21 3.51
1260 1274 2.925966 TGATTTCCCCCATGAAAGCT 57.074 45.000 0.00 0.00 40.39 3.74
1261 1275 3.188880 TGATTTCCCCCATGAAAGCTT 57.811 42.857 0.00 0.00 40.39 3.74
1262 1276 3.519667 TGATTTCCCCCATGAAAGCTTT 58.480 40.909 12.53 12.53 40.39 3.51
1263 1277 3.909364 TGATTTCCCCCATGAAAGCTTTT 59.091 39.130 14.05 0.00 40.39 2.27
1264 1278 4.350520 TGATTTCCCCCATGAAAGCTTTTT 59.649 37.500 14.05 1.23 40.39 1.94
1301 1315 3.701040 CCCCATAAAGCTAGTGCAACAAT 59.299 43.478 0.00 0.00 41.43 2.71
1316 1330 2.380084 ACAATCGTAGCGATGGTGTT 57.620 45.000 10.32 0.00 46.94 3.32
1317 1331 1.999735 ACAATCGTAGCGATGGTGTTG 59.000 47.619 10.32 5.71 46.94 3.33
1318 1332 1.999735 CAATCGTAGCGATGGTGTTGT 59.000 47.619 4.75 0.00 46.30 3.32
1319 1333 1.922570 ATCGTAGCGATGGTGTTGTC 58.077 50.000 3.08 0.00 45.24 3.18
1503 1790 7.678947 AGCATGCATATATAGGTTTCTGAAC 57.321 36.000 21.98 0.00 34.96 3.18
1505 1792 6.147821 GCATGCATATATAGGTTTCTGAACGT 59.852 38.462 14.21 0.00 36.61 3.99
1946 2238 2.234296 CCAAGCCCCACCTCCTCTT 61.234 63.158 0.00 0.00 0.00 2.85
1956 2248 0.622665 ACCTCCTCTTGGCAAGGATG 59.377 55.000 25.92 16.46 42.01 3.51
2032 2324 2.568090 CACAGGCCGTGCATTTCC 59.432 61.111 13.44 0.00 39.19 3.13
2129 2433 3.196039 GTGAGTTCCTCCTACCTTCCTTC 59.804 52.174 0.00 0.00 0.00 3.46
2133 2437 3.117552 TCCTCCTACCTTCCTTCCTTC 57.882 52.381 0.00 0.00 0.00 3.46
2136 2440 2.769095 CTCCTACCTTCCTTCCTTCCTG 59.231 54.545 0.00 0.00 0.00 3.86
2137 2441 1.210722 CCTACCTTCCTTCCTTCCTGC 59.789 57.143 0.00 0.00 0.00 4.85
2138 2442 2.192263 CTACCTTCCTTCCTTCCTGCT 58.808 52.381 0.00 0.00 0.00 4.24
2141 2445 1.172175 CTTCCTTCCTTCCTGCTTGC 58.828 55.000 0.00 0.00 0.00 4.01
2154 2458 0.773644 TGCTTGCTTCCTTCCTTCCT 59.226 50.000 0.00 0.00 0.00 3.36
2155 2459 1.145738 TGCTTGCTTCCTTCCTTCCTT 59.854 47.619 0.00 0.00 0.00 3.36
2156 2460 2.242926 GCTTGCTTCCTTCCTTCCTTT 58.757 47.619 0.00 0.00 0.00 3.11
2157 2461 2.230025 GCTTGCTTCCTTCCTTCCTTTC 59.770 50.000 0.00 0.00 0.00 2.62
2158 2462 2.586648 TGCTTCCTTCCTTCCTTTCC 57.413 50.000 0.00 0.00 0.00 3.13
2159 2463 1.075536 TGCTTCCTTCCTTCCTTTCCC 59.924 52.381 0.00 0.00 0.00 3.97
2160 2464 1.950954 GCTTCCTTCCTTCCTTTCCCG 60.951 57.143 0.00 0.00 0.00 5.14
2161 2465 1.351350 CTTCCTTCCTTCCTTTCCCGT 59.649 52.381 0.00 0.00 0.00 5.28
2162 2466 0.981943 TCCTTCCTTCCTTTCCCGTC 59.018 55.000 0.00 0.00 0.00 4.79
2163 2467 0.391263 CCTTCCTTCCTTTCCCGTCG 60.391 60.000 0.00 0.00 0.00 5.12
2164 2468 0.606604 CTTCCTTCCTTTCCCGTCGA 59.393 55.000 0.00 0.00 0.00 4.20
2165 2469 0.606604 TTCCTTCCTTTCCCGTCGAG 59.393 55.000 0.00 0.00 0.00 4.04
2166 2470 0.251474 TCCTTCCTTTCCCGTCGAGA 60.251 55.000 0.00 0.00 0.00 4.04
2167 2471 0.824759 CCTTCCTTTCCCGTCGAGAT 59.175 55.000 0.00 0.00 0.00 2.75
2168 2472 1.202428 CCTTCCTTTCCCGTCGAGATC 60.202 57.143 0.00 0.00 0.00 2.75
2169 2473 0.454600 TTCCTTTCCCGTCGAGATCG 59.545 55.000 0.00 0.00 41.45 3.69
2180 2484 2.358939 TCGAGATCGATCCATGCATG 57.641 50.000 21.66 20.19 44.22 4.06
2208 2512 1.067060 CATGCATGCATGTGCTTAGCT 59.933 47.619 40.30 14.19 46.20 3.32
2209 2513 1.179152 TGCATGCATGTGCTTAGCTT 58.821 45.000 26.79 0.00 45.27 3.74
2210 2514 2.367486 TGCATGCATGTGCTTAGCTTA 58.633 42.857 26.79 0.00 45.27 3.09
2227 2531 7.489113 GCTTAGCTTATTAGTTGGTACGTGTAA 59.511 37.037 0.00 0.00 0.00 2.41
2228 2532 9.357652 CTTAGCTTATTAGTTGGTACGTGTAAA 57.642 33.333 0.00 0.00 0.00 2.01
2229 2533 9.703892 TTAGCTTATTAGTTGGTACGTGTAAAA 57.296 29.630 0.00 0.00 0.00 1.52
2451 2758 2.035442 GGAGAAGGTCAAGTGCCGC 61.035 63.158 0.00 0.00 0.00 6.53
2785 3116 3.322318 GAGGTGGAGGTGCTCAGCC 62.322 68.421 0.00 0.00 31.08 4.85
3506 3846 2.780643 CGACAGCAGTTCGCATGG 59.219 61.111 0.00 0.00 46.13 3.66
3507 3847 2.743752 CGACAGCAGTTCGCATGGG 61.744 63.158 2.76 2.76 46.13 4.00
3508 3848 2.360350 ACAGCAGTTCGCATGGGG 60.360 61.111 10.21 0.00 46.13 4.96
3509 3849 2.046023 CAGCAGTTCGCATGGGGA 60.046 61.111 10.21 0.00 46.13 4.81
3510 3850 2.045926 AGCAGTTCGCATGGGGAC 60.046 61.111 13.24 13.24 46.13 4.46
3511 3851 3.499737 GCAGTTCGCATGGGGACG 61.500 66.667 15.01 11.16 41.79 4.79
3512 3852 2.819595 CAGTTCGCATGGGGACGG 60.820 66.667 15.01 11.04 0.00 4.79
3513 3853 4.096003 AGTTCGCATGGGGACGGG 62.096 66.667 15.01 0.00 0.00 5.28
3514 3854 4.090588 GTTCGCATGGGGACGGGA 62.091 66.667 10.21 0.00 0.00 5.14
3592 3936 1.843368 AAGCTAGCATTGGCACACAT 58.157 45.000 18.83 0.00 44.61 3.21
3770 4114 0.824595 ATGTTTGCAGTGCTGGCTCA 60.825 50.000 17.60 8.80 0.00 4.26
3816 4160 6.823182 TGTACATCCATCGATTCAGAATGTTT 59.177 34.615 0.00 0.00 37.40 2.83
3817 4161 6.369059 ACATCCATCGATTCAGAATGTTTC 57.631 37.500 0.00 0.00 37.40 2.78
3818 4162 6.118170 ACATCCATCGATTCAGAATGTTTCT 58.882 36.000 0.00 0.00 41.70 2.52
3819 4163 6.259608 ACATCCATCGATTCAGAATGTTTCTC 59.740 38.462 0.00 0.00 38.11 2.87
3820 4164 5.982356 TCCATCGATTCAGAATGTTTCTCT 58.018 37.500 0.00 0.00 38.11 3.10
3821 4165 6.409704 TCCATCGATTCAGAATGTTTCTCTT 58.590 36.000 0.00 0.00 38.11 2.85
3822 4166 6.881065 TCCATCGATTCAGAATGTTTCTCTTT 59.119 34.615 0.00 0.00 38.11 2.52
3851 4195 6.061441 TGGGCCTGTATACTGAATTTACATG 58.939 40.000 4.53 0.00 0.00 3.21
3858 4202 6.542005 TGTATACTGAATTTACATGCCACTGG 59.458 38.462 4.17 0.00 0.00 4.00
3878 4222 0.321653 TGCTCTTTTCCTTCCCGAGC 60.322 55.000 0.00 0.00 45.39 5.03
3884 4228 2.668185 TTTCCTTCCCGAGCAACGCA 62.668 55.000 0.00 0.00 41.07 5.24
3886 4230 2.464459 CCTTCCCGAGCAACGCATC 61.464 63.158 0.00 0.00 41.07 3.91
3893 4237 1.638467 GAGCAACGCATCATCCGAC 59.362 57.895 0.00 0.00 0.00 4.79
3901 4245 1.227263 CATCATCCGACCCCGTCAC 60.227 63.158 0.00 0.00 32.09 3.67
3905 4249 1.684391 ATCCGACCCCGTCACATCA 60.684 57.895 0.00 0.00 32.09 3.07
3914 4258 2.086869 CCCGTCACATCATCTGCTTTT 58.913 47.619 0.00 0.00 0.00 2.27
3917 4261 3.438087 CCGTCACATCATCTGCTTTTTCT 59.562 43.478 0.00 0.00 0.00 2.52
3918 4262 4.436584 CCGTCACATCATCTGCTTTTTCTC 60.437 45.833 0.00 0.00 0.00 2.87
3919 4263 4.436584 CGTCACATCATCTGCTTTTTCTCC 60.437 45.833 0.00 0.00 0.00 3.71
3923 4267 5.182570 CACATCATCTGCTTTTTCTCCAAGA 59.817 40.000 0.00 0.00 0.00 3.02
3933 4482 1.518367 TTCTCCAAGACAACCAGGGT 58.482 50.000 0.00 0.00 0.00 4.34
3960 4509 0.685785 TGTTGGAAAGGTGCTGCCAA 60.686 50.000 0.00 0.00 40.61 4.52
4046 5056 3.036577 CTGCAACCACAGGTGCTG 58.963 61.111 4.54 0.00 35.34 4.41
4072 5082 2.184020 TTGCTGGGACCGATGGACAG 62.184 60.000 0.00 0.00 0.00 3.51
4080 5090 0.324368 ACCGATGGACAGAGGTGCTA 60.324 55.000 1.46 0.00 36.16 3.49
4248 5973 2.031012 TGCAGCAACGAGACCAGG 59.969 61.111 0.00 0.00 0.00 4.45
4251 5976 1.374758 CAGCAACGAGACCAGGGAC 60.375 63.158 0.00 0.00 0.00 4.46
4252 5977 1.837051 AGCAACGAGACCAGGGACA 60.837 57.895 0.00 0.00 0.00 4.02
4254 5979 1.374758 CAACGAGACCAGGGACAGC 60.375 63.158 0.00 0.00 0.00 4.40
4256 5981 3.062466 CGAGACCAGGGACAGCGA 61.062 66.667 0.00 0.00 0.00 4.93
4257 5982 2.888863 GAGACCAGGGACAGCGAG 59.111 66.667 0.00 0.00 0.00 5.03
4258 5983 1.979693 GAGACCAGGGACAGCGAGT 60.980 63.158 0.00 0.00 0.00 4.18
4259 5984 2.219325 GAGACCAGGGACAGCGAGTG 62.219 65.000 0.00 0.00 0.00 3.51
4260 5985 3.941657 GACCAGGGACAGCGAGTGC 62.942 68.421 0.00 0.00 43.24 4.40
4273 5998 1.079543 GAGTGCGCTGATGAGTGGT 60.080 57.895 3.44 0.00 0.00 4.16
4367 6115 4.394920 TGTGGGATTATTTCTCGTTTGCTC 59.605 41.667 0.00 0.00 0.00 4.26
4390 6138 4.439305 TTTTTGCCGATCAAATCTGAGG 57.561 40.909 0.00 0.00 43.53 3.86
4456 6227 1.267574 GGTGACCCATCTGAGCTCCA 61.268 60.000 12.15 0.00 0.00 3.86
4493 6265 3.005155 GCCTAGCATTGGCCATTTTAGAG 59.995 47.826 6.09 0.00 44.32 2.43
4495 6267 5.376625 CCTAGCATTGGCCATTTTAGAGTA 58.623 41.667 6.09 0.00 42.56 2.59
4544 6316 4.526770 TGCGACAGGATGCATCTG 57.473 55.556 25.28 21.45 42.53 2.90
4547 6319 0.935898 GCGACAGGATGCATCTGAAG 59.064 55.000 25.28 18.32 42.53 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
257 258 5.424121 GCATCCTTGCGTATTGTATTCTT 57.576 39.130 0.00 0.00 39.49 2.52
335 337 5.357742 TCAGGAGATCGATCCATCAAAAA 57.642 39.130 21.66 0.00 42.26 1.94
354 356 0.742281 CCTCGCCACATCCTGTTCAG 60.742 60.000 0.00 0.00 0.00 3.02
730 739 2.192861 CACGCTCCCACTTTTGGCA 61.193 57.895 0.00 0.00 42.35 4.92
762 771 3.134804 GGTACCAGATTAGACCAGCACAT 59.865 47.826 7.15 0.00 31.89 3.21
763 772 2.500098 GGTACCAGATTAGACCAGCACA 59.500 50.000 7.15 0.00 31.89 4.57
790 799 1.476291 CCGTTAAATGACCTAGGGGGC 60.476 57.143 14.81 2.51 42.24 5.80
1083 1093 4.444838 TCCCGGTCGATGGCAACG 62.445 66.667 11.21 11.21 42.51 4.10
1278 1292 2.024414 GTTGCACTAGCTTTATGGGGG 58.976 52.381 0.00 0.00 42.74 5.40
1279 1293 2.722094 TGTTGCACTAGCTTTATGGGG 58.278 47.619 0.00 0.00 42.74 4.96
1301 1315 0.455464 CGACAACACCATCGCTACGA 60.455 55.000 0.00 0.00 41.13 3.43
1316 1330 0.673333 AATCCATCTGCGCAACGACA 60.673 50.000 13.05 0.00 0.00 4.35
1317 1331 0.447801 AAATCCATCTGCGCAACGAC 59.552 50.000 13.05 0.00 0.00 4.34
1318 1332 0.447406 CAAATCCATCTGCGCAACGA 59.553 50.000 13.05 6.69 0.00 3.85
1319 1333 1.135699 GCAAATCCATCTGCGCAACG 61.136 55.000 13.05 0.00 0.00 4.10
1512 1799 1.503542 CGATTCTTGCACCTGCCAC 59.496 57.895 0.00 0.00 41.18 5.01
1513 1800 1.675310 CCGATTCTTGCACCTGCCA 60.675 57.895 0.00 0.00 41.18 4.92
1514 1801 1.372087 CTCCGATTCTTGCACCTGCC 61.372 60.000 0.00 0.00 41.18 4.85
1946 2238 1.303561 GTGCTGTCCATCCTTGCCA 60.304 57.895 0.00 0.00 0.00 4.92
2032 2324 1.750399 CGCCAAAGTCCATGGAGGG 60.750 63.158 16.81 15.32 40.56 4.30
2129 2433 1.172175 GAAGGAAGCAAGCAGGAAGG 58.828 55.000 0.00 0.00 0.00 3.46
2133 2437 1.172175 GAAGGAAGGAAGCAAGCAGG 58.828 55.000 0.00 0.00 0.00 4.85
2136 2440 1.916506 AAGGAAGGAAGGAAGCAAGC 58.083 50.000 0.00 0.00 0.00 4.01
2137 2441 2.822561 GGAAAGGAAGGAAGGAAGCAAG 59.177 50.000 0.00 0.00 0.00 4.01
2138 2442 2.490902 GGGAAAGGAAGGAAGGAAGCAA 60.491 50.000 0.00 0.00 0.00 3.91
2141 2445 1.351350 ACGGGAAAGGAAGGAAGGAAG 59.649 52.381 0.00 0.00 0.00 3.46
2162 2466 2.358939 TCATGCATGGATCGATCTCG 57.641 50.000 25.97 13.73 41.45 4.04
2169 2473 2.981898 TGGATCGATCATGCATGGATC 58.018 47.619 25.97 25.28 43.02 3.36
2170 2474 3.646736 ATGGATCGATCATGCATGGAT 57.353 42.857 25.97 19.65 41.78 3.41
2177 2481 1.810151 TGCATGCATGGATCGATCATG 59.190 47.619 27.34 24.01 43.39 3.07
2178 2482 2.194201 TGCATGCATGGATCGATCAT 57.806 45.000 27.34 14.60 0.00 2.45
2179 2483 2.194201 ATGCATGCATGGATCGATCA 57.806 45.000 31.74 14.60 33.26 2.92
2227 2531 3.365265 CTCGCGCTGGGCCTTTTT 61.365 61.111 11.31 0.00 38.94 1.94
3033 3373 0.312729 TCTTGCTCACGTAGTTGCGA 59.687 50.000 0.00 0.00 41.61 5.10
3498 3838 3.323286 TTCCCGTCCCCATGCGAA 61.323 61.111 0.00 0.00 0.00 4.70
3508 3848 3.952628 CTTCCTGCCCGTTCCCGTC 62.953 68.421 0.00 0.00 0.00 4.79
3509 3849 4.016706 CTTCCTGCCCGTTCCCGT 62.017 66.667 0.00 0.00 0.00 5.28
3510 3850 4.778143 CCTTCCTGCCCGTTCCCG 62.778 72.222 0.00 0.00 0.00 5.14
3511 3851 4.426313 CCCTTCCTGCCCGTTCCC 62.426 72.222 0.00 0.00 0.00 3.97
3512 3852 4.426313 CCCCTTCCTGCCCGTTCC 62.426 72.222 0.00 0.00 0.00 3.62
3513 3853 3.623703 GACCCCTTCCTGCCCGTTC 62.624 68.421 0.00 0.00 0.00 3.95
3514 3854 3.647771 GACCCCTTCCTGCCCGTT 61.648 66.667 0.00 0.00 0.00 4.44
3526 3866 4.436998 CGTCGGTGAGCTGACCCC 62.437 72.222 17.36 6.69 45.75 4.95
3592 3936 6.610020 AGCTAATATACAGACAACCCTGTGTA 59.390 38.462 6.79 5.12 46.00 2.90
3653 3997 1.501582 ATGCCCCTCTCCTCTTGTAC 58.498 55.000 0.00 0.00 0.00 2.90
3843 4187 2.094675 GAGCACCAGTGGCATGTAAAT 58.905 47.619 9.78 0.00 0.00 1.40
3851 4195 0.538287 AGGAAAAGAGCACCAGTGGC 60.538 55.000 9.78 0.00 0.00 5.01
3858 4202 1.443802 CTCGGGAAGGAAAAGAGCAC 58.556 55.000 0.00 0.00 0.00 4.40
3878 4222 2.180204 GGGGTCGGATGATGCGTTG 61.180 63.158 6.18 0.00 31.47 4.10
3884 4228 1.048724 ATGTGACGGGGTCGGATGAT 61.049 55.000 0.00 0.00 41.39 2.45
3886 4230 1.227263 GATGTGACGGGGTCGGATG 60.227 63.158 0.00 0.00 41.39 3.51
3893 4237 0.107508 AAGCAGATGATGTGACGGGG 60.108 55.000 0.00 0.00 0.00 5.73
3901 4245 5.182570 TGTCTTGGAGAAAAAGCAGATGATG 59.817 40.000 0.00 0.00 0.00 3.07
3905 4249 4.279420 GGTTGTCTTGGAGAAAAAGCAGAT 59.721 41.667 0.00 0.00 0.00 2.90
3914 4258 1.518367 ACCCTGGTTGTCTTGGAGAA 58.482 50.000 0.00 0.00 0.00 2.87
3917 4261 2.781174 AGTTTACCCTGGTTGTCTTGGA 59.219 45.455 0.00 0.00 0.00 3.53
3918 4262 3.223674 AGTTTACCCTGGTTGTCTTGG 57.776 47.619 0.00 0.00 0.00 3.61
3919 4263 5.768164 ACAATAGTTTACCCTGGTTGTCTTG 59.232 40.000 0.00 0.00 0.00 3.02
3923 4267 4.830600 CCAACAATAGTTTACCCTGGTTGT 59.169 41.667 0.00 0.00 35.28 3.32
3933 4482 5.278758 GCAGCACCTTTCCAACAATAGTTTA 60.279 40.000 0.00 0.00 35.28 2.01
3973 4732 2.812178 CGTCGCCCCGTTTACAGG 60.812 66.667 0.00 0.00 0.00 4.00
4046 5056 2.514824 GGTCCCAGCAATCCTCGC 60.515 66.667 0.00 0.00 0.00 5.03
4072 5082 0.798771 CTCGCTCGTTGTAGCACCTC 60.799 60.000 0.00 0.00 42.91 3.85
4130 5154 2.887568 CAGCATCAGGTCGCCGTC 60.888 66.667 0.00 0.00 0.00 4.79
4225 5950 0.601311 GTCTCGTTGCTGCAGACCTT 60.601 55.000 20.43 0.00 31.93 3.50
4226 5951 1.005630 GTCTCGTTGCTGCAGACCT 60.006 57.895 20.43 0.00 31.93 3.85
4254 5979 2.163390 CCACTCATCAGCGCACTCG 61.163 63.158 11.47 0.00 39.07 4.18
4256 5981 0.952497 CAACCACTCATCAGCGCACT 60.952 55.000 11.47 0.00 0.00 4.40
4257 5982 1.499056 CAACCACTCATCAGCGCAC 59.501 57.895 11.47 0.00 0.00 5.34
4258 5983 1.672030 CCAACCACTCATCAGCGCA 60.672 57.895 11.47 0.00 0.00 6.09
4259 5984 3.044059 GCCAACCACTCATCAGCGC 62.044 63.158 0.00 0.00 0.00 5.92
4260 5985 1.236616 TTGCCAACCACTCATCAGCG 61.237 55.000 0.00 0.00 0.00 5.18
4261 5986 0.242017 GTTGCCAACCACTCATCAGC 59.758 55.000 0.00 0.00 0.00 4.26
4262 5987 0.518636 CGTTGCCAACCACTCATCAG 59.481 55.000 1.21 0.00 0.00 2.90
4263 5988 0.888736 CCGTTGCCAACCACTCATCA 60.889 55.000 1.21 0.00 0.00 3.07
4264 5989 1.875963 CCGTTGCCAACCACTCATC 59.124 57.895 1.21 0.00 0.00 2.92
4273 5998 4.283403 GCAGCTTGCCGTTGCCAA 62.283 61.111 1.29 0.00 43.22 4.52
4390 6138 2.045926 AGCCGTTGGATCCTGCAC 60.046 61.111 14.23 6.28 0.00 4.57
4493 6265 6.367422 GCATTAGCCTATCATGTCAACTCTAC 59.633 42.308 0.00 0.00 33.58 2.59
4495 6267 5.303971 GCATTAGCCTATCATGTCAACTCT 58.696 41.667 0.00 0.00 33.58 3.24
4544 6316 3.226347 GCAACGTTACTGCAACATCTTC 58.774 45.455 0.00 0.00 39.69 2.87
4547 6319 1.535462 AGGCAACGTTACTGCAACATC 59.465 47.619 12.42 0.00 41.78 3.06
4553 6325 3.612472 TTAACAAGGCAACGTTACTGC 57.388 42.857 0.00 0.17 46.39 4.40


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

AutoCloner maintained by Alex Coulton.