Multiple sequence alignment - TraesCS5B01G384600

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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 TraesCS5B01G384600 chr5B 100.000 3140 0 0 1 3140 563331987 563335126 0.000000e+00 5799.0
1 TraesCS5B01G384600 chr5B 100.000 322 0 0 3592 3913 563335578 563335899 2.600000e-166 595.0
2 TraesCS5B01G384600 chr5B 91.667 72 6 0 1189 1260 563349256 563349327 2.490000e-17 100.0
3 TraesCS5B01G384600 chr5D 92.087 3172 143 51 2 3140 459207405 459210501 0.000000e+00 4368.0
4 TraesCS5B01G384600 chr5D 88.372 258 6 6 3592 3825 459210566 459210823 4.950000e-74 289.0
5 TraesCS5B01G384600 chr5A 90.835 3186 171 60 2 3140 578446384 578449495 0.000000e+00 4154.0
6 TraesCS5B01G384600 chr5A 91.022 323 5 4 3592 3901 578449562 578449873 7.820000e-112 414.0
7 TraesCS5B01G384600 chr3D 90.909 66 6 0 2759 2824 296430408 296430473 5.390000e-14 89.8
8 TraesCS5B01G384600 chr3D 90.909 66 6 0 2759 2824 511068347 511068412 5.390000e-14 89.8
9 TraesCS5B01G384600 chr3D 90.909 66 6 0 2759 2824 571451319 571451254 5.390000e-14 89.8
10 TraesCS5B01G384600 chr3D 89.394 66 7 0 2759 2824 568577579 568577514 2.510000e-12 84.2
11 TraesCS5B01G384600 chr1D 90.909 66 6 0 2759 2824 321329538 321329603 5.390000e-14 89.8
12 TraesCS5B01G384600 chr4B 93.023 43 3 0 2252 2294 95668608 95668650 3.260000e-06 63.9
13 TraesCS5B01G384600 chr1B 91.304 46 4 0 2252 2297 622622019 622621974 3.260000e-06 63.9
14 TraesCS5B01G384600 chr2B 92.308 39 3 0 2256 2294 364960544 364960582 5.460000e-04 56.5


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 TraesCS5B01G384600 chr5B 563331987 563335899 3912 False 3197.0 5799 100.0000 1 3913 2 chr5B.!!$F2 3912
1 TraesCS5B01G384600 chr5D 459207405 459210823 3418 False 2328.5 4368 90.2295 2 3825 2 chr5D.!!$F1 3823
2 TraesCS5B01G384600 chr5A 578446384 578449873 3489 False 2284.0 4154 90.9285 2 3901 2 chr5A.!!$F1 3899

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
963 996 0.099613 TTGTTGATTTGTGCGTGCGT 59.9 45.0 0.0 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2952 3030 0.803117 TCTAGAATCGGCGGCTATCG 59.197 55.0 7.21 0.0 42.76 2.92 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
55 56 2.280457 GATAGAGCACTGCGCCCC 60.280 66.667 4.18 0.00 44.04 5.80
130 137 2.113433 GCCTCGGACTAGCACTCGA 61.113 63.158 0.00 0.00 0.00 4.04
150 159 3.082701 GCTGCTCCTCCCTGCTCT 61.083 66.667 0.00 0.00 0.00 4.09
155 164 2.364842 TCCTCCCTGCTCTGCTCC 60.365 66.667 0.00 0.00 0.00 4.70
286 296 0.832135 TCCCTGCTTCTCCGTTCTGT 60.832 55.000 0.00 0.00 0.00 3.41
315 328 2.279517 CTGCCGGTAGGATCGTGC 60.280 66.667 12.40 0.00 41.02 5.34
370 396 3.689561 ATGGGTGGATCGACGGGGA 62.690 63.158 1.47 0.00 0.00 4.81
403 429 1.600916 GGCGGTGGTTCTTGCTTCT 60.601 57.895 0.00 0.00 0.00 2.85
451 477 2.595386 CCGGATTTTTCGAGGCTTTTG 58.405 47.619 0.00 0.00 0.00 2.44
732 763 1.098050 GGTGGCAGTGCTCTTTATGG 58.902 55.000 16.11 0.00 0.00 2.74
778 809 4.148871 CGGCATATGTATATCTACGCATGC 59.851 45.833 7.91 7.91 41.88 4.06
795 826 0.889186 TGCCTCTCCTGCGTTTTTCC 60.889 55.000 0.00 0.00 0.00 3.13
801 834 1.002468 CTCCTGCGTTTTTCCACTGTG 60.002 52.381 0.00 0.00 0.00 3.66
852 885 8.360390 GCCTGTTTTAGATATTTATTTCCCTGG 58.640 37.037 0.00 0.00 0.00 4.45
884 917 1.334869 CCCGAGTCCAATTATTGCAGC 59.665 52.381 0.00 0.00 0.00 5.25
904 937 2.545742 GCGCAGGTGTTGAATCCTTTTT 60.546 45.455 0.30 0.00 30.91 1.94
929 962 1.687494 GAGATGCGTGTGTTCGAGCC 61.687 60.000 0.00 0.00 0.00 4.70
946 979 1.856265 GCCGAGGGCTGAACAAGTTG 61.856 60.000 0.00 0.00 46.69 3.16
961 994 1.838913 AGTTGTTGATTTGTGCGTGC 58.161 45.000 0.00 0.00 0.00 5.34
962 995 0.498095 GTTGTTGATTTGTGCGTGCG 59.502 50.000 0.00 0.00 0.00 5.34
963 996 0.099613 TTGTTGATTTGTGCGTGCGT 59.900 45.000 0.00 0.00 0.00 5.24
964 997 0.590984 TGTTGATTTGTGCGTGCGTG 60.591 50.000 0.00 0.00 0.00 5.34
965 998 1.656875 TTGATTTGTGCGTGCGTGC 60.657 52.632 0.00 0.00 0.00 5.34
966 999 3.158813 GATTTGTGCGTGCGTGCG 61.159 61.111 0.00 0.00 37.81 5.34
967 1000 3.855209 GATTTGTGCGTGCGTGCGT 62.855 57.895 3.11 0.00 37.81 5.24
968 1001 4.877882 TTTGTGCGTGCGTGCGTG 62.878 61.111 3.11 0.00 37.81 5.34
1089 1122 4.864334 CCCCATGGCCAGCTCGTC 62.864 72.222 13.05 0.00 0.00 4.20
1105 1138 2.204090 TCCCCCACAAGGACCTCC 60.204 66.667 0.00 0.00 38.24 4.30
1159 1192 1.270041 GCTCCCTAGCTTCCAAGATCG 60.270 57.143 0.00 0.00 45.85 3.69
1163 1196 1.134401 CCTAGCTTCCAAGATCGGCAA 60.134 52.381 0.00 0.00 0.00 4.52
1176 1209 2.988684 GGCAACGGCAATGGTGGA 60.989 61.111 0.00 0.00 43.71 4.02
1182 1215 1.963855 CGGCAATGGTGGACGACAA 60.964 57.895 0.00 0.00 0.00 3.18
1288 1321 3.877357 CTGCCGATGCTGCTGCTG 61.877 66.667 17.00 0.77 40.48 4.41
1497 1542 2.426023 GTCCAGCCGGTGTCTGTT 59.574 61.111 1.90 0.00 0.00 3.16
1864 1909 0.972983 GCAGCAGAGGAGGAGGTGTA 60.973 60.000 0.00 0.00 33.59 2.90
1865 1910 1.786937 CAGCAGAGGAGGAGGTGTAT 58.213 55.000 0.00 0.00 0.00 2.29
1969 2015 9.948964 TGATAAATTGATATATCTGACCACTGG 57.051 33.333 13.79 0.00 31.28 4.00
1980 2026 8.917414 ATATCTGACCACTGGTATTATGGTAT 57.083 34.615 0.00 0.00 46.86 2.73
1983 2029 7.506114 TCTGACCACTGGTATTATGGTATTTC 58.494 38.462 0.00 0.00 46.86 2.17
2156 2204 2.226962 TCCCCGCATCCTAGGTATAC 57.773 55.000 9.08 0.00 0.00 1.47
2232 2284 1.822581 CATTGCACATGATGTCTGCG 58.177 50.000 0.00 0.00 0.00 5.18
2243 2295 2.002586 GATGTCTGCGCTTGCTCTTTA 58.997 47.619 9.73 0.00 40.12 1.85
2320 2375 5.527582 TGTTTTGTTCAGAGTTAGAGCTTCC 59.472 40.000 0.00 0.00 0.00 3.46
2321 2376 5.552870 TTTGTTCAGAGTTAGAGCTTCCT 57.447 39.130 0.00 0.00 0.00 3.36
2325 2380 5.760253 TGTTCAGAGTTAGAGCTTCCTTTTG 59.240 40.000 0.00 0.00 0.00 2.44
2327 2382 3.438434 CAGAGTTAGAGCTTCCTTTTGCC 59.562 47.826 0.00 0.00 0.00 4.52
2328 2383 2.750166 GAGTTAGAGCTTCCTTTTGCCC 59.250 50.000 0.00 0.00 0.00 5.36
2482 2540 8.557450 ACTTTTCTAAGGCTAGATTTTATCCCA 58.443 33.333 0.00 0.00 34.06 4.37
2485 2543 7.633018 TCTAAGGCTAGATTTTATCCCACAT 57.367 36.000 0.00 0.00 0.00 3.21
2545 2614 6.190587 AGGTTCAGATATCCTTTCCAAAAGG 58.809 40.000 11.46 11.46 38.78 3.11
2648 2717 5.925509 TGTTCTAATTCTGGTAGTATGCCC 58.074 41.667 0.00 0.00 41.90 5.36
2952 3030 2.876645 CGCAGACCGCTCTCGTTC 60.877 66.667 0.00 0.00 39.08 3.95
2954 3032 2.868196 CAGACCGCTCTCGTTCGA 59.132 61.111 0.00 0.00 32.07 3.71
2955 3033 1.429825 CAGACCGCTCTCGTTCGAT 59.570 57.895 0.00 0.00 32.07 3.59
2956 3034 0.656259 CAGACCGCTCTCGTTCGATA 59.344 55.000 0.00 0.00 32.07 2.92
2957 3035 0.938713 AGACCGCTCTCGTTCGATAG 59.061 55.000 3.79 3.79 32.07 2.08
2959 3037 1.370657 CCGCTCTCGTTCGATAGCC 60.371 63.158 20.67 8.56 32.84 3.93
2960 3038 1.722852 CGCTCTCGTTCGATAGCCG 60.723 63.158 20.67 14.34 32.84 5.52
2961 3039 2.011881 GCTCTCGTTCGATAGCCGC 61.012 63.158 17.51 4.27 38.37 6.53
2962 3040 1.370657 CTCTCGTTCGATAGCCGCC 60.371 63.158 0.00 0.00 38.37 6.13
2963 3041 2.726180 CTCGTTCGATAGCCGCCG 60.726 66.667 0.00 0.00 38.37 6.46
2964 3042 3.177272 CTCGTTCGATAGCCGCCGA 62.177 63.158 0.00 0.00 38.39 5.54
2972 3050 1.199327 CGATAGCCGCCGATTCTAGAA 59.801 52.381 7.82 7.82 0.00 2.10
2973 3051 2.729467 CGATAGCCGCCGATTCTAGAAG 60.729 54.545 11.53 0.00 0.00 2.85
2981 3059 4.261825 CCGCCGATTCTAGAAGAAGAGATT 60.262 45.833 11.53 0.00 37.69 2.40
3039 3117 9.169592 GAAGAAGAGACTAGTCTGTACATACTT 57.830 37.037 29.84 22.05 40.61 2.24
3121 3199 1.473258 TCCATGGCGAAAGGGATTTG 58.527 50.000 6.96 0.00 0.00 2.32
3123 3206 1.550072 CCATGGCGAAAGGGATTTGTT 59.450 47.619 0.00 0.00 0.00 2.83
3756 3863 3.067684 AGGAACAAAATGTACCCCTCG 57.932 47.619 0.00 0.00 0.00 4.63
3847 3954 2.670934 CCCTGGTGTCACTGCAGC 60.671 66.667 15.27 0.00 37.38 5.25
3865 3974 3.305199 GCAGCTCTTTTGTTCTCAAGCAT 60.305 43.478 0.00 0.00 34.88 3.79
3866 3975 4.795308 GCAGCTCTTTTGTTCTCAAGCATT 60.795 41.667 0.00 0.00 34.88 3.56
3867 3976 5.287226 CAGCTCTTTTGTTCTCAAGCATTT 58.713 37.500 0.00 0.00 34.88 2.32
3868 3977 5.401674 CAGCTCTTTTGTTCTCAAGCATTTC 59.598 40.000 0.00 0.00 34.88 2.17
3869 3978 5.068198 AGCTCTTTTGTTCTCAAGCATTTCA 59.932 36.000 0.00 0.00 34.88 2.69
3870 3979 5.924825 GCTCTTTTGTTCTCAAGCATTTCAT 59.075 36.000 0.00 0.00 34.88 2.57
3889 3998 5.975693 TCATTTTGATGTGTACCCCTTTC 57.024 39.130 0.00 0.00 0.00 2.62
3901 4010 3.819564 ACCCCTTTCTTGTTTTCTTGC 57.180 42.857 0.00 0.00 0.00 4.01
3902 4011 3.103742 ACCCCTTTCTTGTTTTCTTGCA 58.896 40.909 0.00 0.00 0.00 4.08
3903 4012 3.711190 ACCCCTTTCTTGTTTTCTTGCAT 59.289 39.130 0.00 0.00 0.00 3.96
3904 4013 4.060205 CCCCTTTCTTGTTTTCTTGCATG 58.940 43.478 0.00 0.00 0.00 4.06
3905 4014 3.495753 CCCTTTCTTGTTTTCTTGCATGC 59.504 43.478 11.82 11.82 0.00 4.06
3906 4015 4.121317 CCTTTCTTGTTTTCTTGCATGCA 58.879 39.130 18.46 18.46 0.00 3.96
3907 4016 4.753107 CCTTTCTTGTTTTCTTGCATGCAT 59.247 37.500 23.37 0.00 0.00 3.96
3908 4017 5.333798 CCTTTCTTGTTTTCTTGCATGCATG 60.334 40.000 23.37 23.63 0.00 4.06
3909 4018 4.587584 TCTTGTTTTCTTGCATGCATGA 57.412 36.364 30.64 27.21 0.00 3.07
3910 4019 4.946445 TCTTGTTTTCTTGCATGCATGAA 58.054 34.783 33.30 33.30 38.00 2.57
3911 4020 5.543714 TCTTGTTTTCTTGCATGCATGAAT 58.456 33.333 35.62 0.00 39.00 2.57
3912 4021 5.636121 TCTTGTTTTCTTGCATGCATGAATC 59.364 36.000 35.62 30.38 39.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.334574 TCTTTCGTTTTTCTTCTCTCGTATG 57.665 36.000 0.00 0.00 0.00 2.39
130 137 3.715097 GCAGGGAGGAGCAGCAGT 61.715 66.667 0.00 0.00 0.00 4.40
155 164 2.124487 AGAGGACGGAGAGGCGAG 60.124 66.667 0.00 0.00 0.00 5.03
191 200 3.369388 GGAGGGGAGGGGAGAGGT 61.369 72.222 0.00 0.00 0.00 3.85
192 201 4.548513 CGGAGGGGAGGGGAGAGG 62.549 77.778 0.00 0.00 0.00 3.69
266 276 0.390472 CAGAACGGAGAAGCAGGGAC 60.390 60.000 0.00 0.00 0.00 4.46
267 277 0.832135 ACAGAACGGAGAAGCAGGGA 60.832 55.000 0.00 0.00 0.00 4.20
286 296 1.600636 CCGGCAGCAAGAACAGGAA 60.601 57.895 0.00 0.00 0.00 3.36
352 378 2.965226 ATCCCCGTCGATCCACCCAT 62.965 60.000 0.00 0.00 0.00 4.00
396 422 0.821711 CCCGGGTGACAAAGAAGCAA 60.822 55.000 14.18 0.00 0.00 3.91
563 593 4.034858 GGCCTTAATCGCTACCAAAACTAC 59.965 45.833 0.00 0.00 0.00 2.73
680 710 1.377333 CCGAGGCCTGGGAAGAAAC 60.377 63.158 29.00 0.00 0.00 2.78
681 711 0.914417 ATCCGAGGCCTGGGAAGAAA 60.914 55.000 36.70 17.10 40.85 2.52
682 712 1.306997 ATCCGAGGCCTGGGAAGAA 60.307 57.895 36.70 17.49 40.85 2.52
712 743 0.729116 CATAAAGAGCACTGCCACCG 59.271 55.000 0.00 0.00 0.00 4.94
732 763 1.172812 GCTGTAATCATTCCGCCCCC 61.173 60.000 0.00 0.00 0.00 5.40
778 809 0.875059 GTGGAAAAACGCAGGAGAGG 59.125 55.000 0.00 0.00 0.00 3.69
795 826 2.031314 CGAGGATATGCTTTGCACAGTG 59.969 50.000 0.00 0.00 43.04 3.66
801 834 0.308993 GGCACGAGGATATGCTTTGC 59.691 55.000 18.13 18.13 41.74 3.68
852 885 3.288964 TGGACTCGGGTAGAAGATTCTC 58.711 50.000 0.00 0.00 38.70 2.87
884 917 3.052036 CAAAAAGGATTCAACACCTGCG 58.948 45.455 0.00 0.00 36.56 5.18
904 937 1.992667 GAACACACGCATCTCGAATCA 59.007 47.619 0.00 0.00 41.67 2.57
929 962 1.002468 CAACAACTTGTTCAGCCCTCG 60.002 52.381 4.06 0.00 38.77 4.63
940 973 2.034675 GCACGCACAAATCAACAACTTG 60.035 45.455 0.00 0.00 0.00 3.16
946 979 1.865149 GCACGCACGCACAAATCAAC 61.865 55.000 0.00 0.00 0.00 3.18
961 994 3.772000 CTGCACACACACACGCACG 62.772 63.158 0.00 0.00 0.00 5.34
962 995 2.023181 CTGCACACACACACGCAC 59.977 61.111 0.00 0.00 0.00 5.34
963 996 2.579684 TACCTGCACACACACACGCA 62.580 55.000 0.00 0.00 0.00 5.24
964 997 1.831389 CTACCTGCACACACACACGC 61.831 60.000 0.00 0.00 0.00 5.34
965 998 1.221466 CCTACCTGCACACACACACG 61.221 60.000 0.00 0.00 0.00 4.49
966 999 0.884704 CCCTACCTGCACACACACAC 60.885 60.000 0.00 0.00 0.00 3.82
967 1000 1.449782 CCCTACCTGCACACACACA 59.550 57.895 0.00 0.00 0.00 3.72
968 1001 1.302511 CCCCTACCTGCACACACAC 60.303 63.158 0.00 0.00 0.00 3.82
1089 1122 2.204151 AGGAGGTCCTTGTGGGGG 60.204 66.667 0.00 0.00 46.09 5.40
1159 1192 2.988684 TCCACCATTGCCGTTGCC 60.989 61.111 0.00 0.00 36.33 4.52
1163 1196 2.358247 GTCGTCCACCATTGCCGT 60.358 61.111 0.00 0.00 0.00 5.68
1170 1203 2.525124 ATGGCCTTGTCGTCCACCA 61.525 57.895 3.32 0.00 31.94 4.17
1171 1204 2.040544 CATGGCCTTGTCGTCCACC 61.041 63.158 10.48 0.00 31.94 4.61
1172 1205 2.690778 GCATGGCCTTGTCGTCCAC 61.691 63.158 19.05 0.00 31.94 4.02
1176 1209 1.221840 CCTAGCATGGCCTTGTCGT 59.778 57.895 19.05 7.78 0.00 4.34
1182 1215 0.543749 GTCTGAACCTAGCATGGCCT 59.456 55.000 3.32 0.00 0.00 5.19
1286 1319 2.113774 TCTTGGGTGGTGCTGCAG 59.886 61.111 10.11 10.11 0.00 4.41
1287 1320 2.203337 GTCTTGGGTGGTGCTGCA 60.203 61.111 0.00 0.00 0.00 4.41
1288 1321 1.589716 GATGTCTTGGGTGGTGCTGC 61.590 60.000 0.00 0.00 0.00 5.25
1329 1362 1.078848 CCTCGGAAACAGCTGGAGG 60.079 63.158 19.93 18.80 38.43 4.30
1476 1521 4.436998 GACACCGGCTGGACGAGG 62.437 72.222 21.41 4.50 39.21 4.63
1834 1879 2.123854 CTGCTGCATGAGGCCCAT 60.124 61.111 1.31 0.00 43.89 4.00
1864 1909 1.384502 TCCCATCCTCCTTGCCGAT 60.385 57.895 0.00 0.00 0.00 4.18
1865 1910 2.040442 TCCCATCCTCCTTGCCGA 59.960 61.111 0.00 0.00 0.00 5.54
1955 2001 8.917414 ATACCATAATACCAGTGGTCAGATAT 57.083 34.615 20.72 10.28 44.69 1.63
1956 2002 8.736097 AATACCATAATACCAGTGGTCAGATA 57.264 34.615 20.72 8.33 44.69 1.98
1983 2029 8.943909 AGGACGGTTTATTTAGAGAACATAAG 57.056 34.615 0.00 0.00 0.00 1.73
1991 2037 7.065324 TGCATACAAAGGACGGTTTATTTAGAG 59.935 37.037 0.00 0.00 0.00 2.43
1993 2039 7.079182 TGCATACAAAGGACGGTTTATTTAG 57.921 36.000 0.00 0.00 0.00 1.85
2004 2050 6.509418 TTCCTGTAATTGCATACAAAGGAC 57.491 37.500 7.58 0.00 38.31 3.85
2200 2252 7.806409 TCATGTGCAATGCAACTATATACTT 57.194 32.000 10.44 0.00 41.47 2.24
2201 2253 7.446319 ACATCATGTGCAATGCAACTATATACT 59.554 33.333 10.44 0.00 41.47 2.12
2232 2284 2.294512 ACAAAGCCAGTAAAGAGCAAGC 59.705 45.455 0.00 0.00 0.00 4.01
2243 2295 6.160576 ACATAACAAAATGACAAAGCCAGT 57.839 33.333 0.00 0.00 0.00 4.00
2280 2332 7.661847 TGAACAAAACAAAATTAAACCACCTGT 59.338 29.630 0.00 0.00 0.00 4.00
2284 2339 8.931775 ACTCTGAACAAAACAAAATTAAACCAC 58.068 29.630 0.00 0.00 0.00 4.16
2335 2390 8.782339 ATGGGTATACACTTAGTTTTACACAC 57.218 34.615 6.69 0.00 35.30 3.82
2351 2406 5.420725 TGCATCCAGTGATATGGGTATAC 57.579 43.478 0.00 0.00 41.01 1.47
2482 2540 6.223852 CGGCATCTATTACCTAAACAGATGT 58.776 40.000 10.57 0.00 39.05 3.06
2485 2543 4.344102 AGCGGCATCTATTACCTAAACAGA 59.656 41.667 1.45 0.00 0.00 3.41
2503 2572 1.599542 CCTCACTTTGCTATAAGCGGC 59.400 52.381 0.00 0.00 46.26 6.53
2545 2614 7.908230 TGACTTGATTGAAAACAAAAGCAATC 58.092 30.769 0.00 0.00 44.12 2.67
2546 2615 7.550196 ACTGACTTGATTGAAAACAAAAGCAAT 59.450 29.630 0.00 0.00 31.88 3.56
2551 2620 8.519526 ACTACACTGACTTGATTGAAAACAAAA 58.480 29.630 0.00 0.00 0.00 2.44
2648 2717 5.782047 TGTAACCTTTCTTGGATTGCAATG 58.218 37.500 18.59 1.99 0.00 2.82
2946 3024 2.459421 ATCGGCGGCTATCGAACGAG 62.459 60.000 7.21 0.00 46.52 4.18
2950 3028 1.199327 CTAGAATCGGCGGCTATCGAA 59.801 52.381 7.21 0.00 42.43 3.71
2952 3030 0.803117 TCTAGAATCGGCGGCTATCG 59.197 55.000 7.21 0.00 42.76 2.92
2954 3032 2.515854 TCTTCTAGAATCGGCGGCTAT 58.484 47.619 7.21 0.00 0.00 2.97
2955 3033 1.977056 TCTTCTAGAATCGGCGGCTA 58.023 50.000 7.21 5.99 0.00 3.93
2956 3034 1.067821 CTTCTTCTAGAATCGGCGGCT 59.932 52.381 7.21 5.01 33.13 5.52
2957 3035 1.067212 TCTTCTTCTAGAATCGGCGGC 59.933 52.381 7.21 0.00 33.13 6.53
2959 3037 3.972950 TCTCTTCTTCTAGAATCGGCG 57.027 47.619 5.44 0.00 33.13 6.46
2960 3038 8.649973 TTTTAATCTCTTCTTCTAGAATCGGC 57.350 34.615 5.44 0.00 33.13 5.54
2988 3066 8.435982 TCTTCTTCTTCTTTTCTCCAATCTTCT 58.564 33.333 0.00 0.00 0.00 2.85
2989 3067 8.614469 TCTTCTTCTTCTTTTCTCCAATCTTC 57.386 34.615 0.00 0.00 0.00 2.87
2991 3069 8.435982 TCTTCTTCTTCTTCTTTTCTCCAATCT 58.564 33.333 0.00 0.00 0.00 2.40
2992 3070 8.614469 TCTTCTTCTTCTTCTTTTCTCCAATC 57.386 34.615 0.00 0.00 0.00 2.67
2993 3071 8.986929 TTCTTCTTCTTCTTCTTTTCTCCAAT 57.013 30.769 0.00 0.00 0.00 3.16
2994 3072 8.267894 TCTTCTTCTTCTTCTTCTTTTCTCCAA 58.732 33.333 0.00 0.00 0.00 3.53
2995 3073 7.796054 TCTTCTTCTTCTTCTTCTTTTCTCCA 58.204 34.615 0.00 0.00 0.00 3.86
2996 3074 8.147704 TCTCTTCTTCTTCTTCTTCTTTTCTCC 58.852 37.037 0.00 0.00 0.00 3.71
2999 3077 8.887036 AGTCTCTTCTTCTTCTTCTTCTTTTC 57.113 34.615 0.00 0.00 0.00 2.29
3000 3078 9.981114 CTAGTCTCTTCTTCTTCTTCTTCTTTT 57.019 33.333 0.00 0.00 0.00 2.27
3001 3079 9.143155 ACTAGTCTCTTCTTCTTCTTCTTCTTT 57.857 33.333 0.00 0.00 0.00 2.52
3039 3117 3.646162 TCCTCAGCAGTTAGGAACAGAAA 59.354 43.478 0.00 0.00 38.97 2.52
3079 3157 4.199432 TCTCCTGAAAGAGCTGAATCAC 57.801 45.455 0.00 0.00 34.07 3.06
3622 3705 1.227764 ACAGCACAGCACAGGACAG 60.228 57.895 0.00 0.00 0.00 3.51
3756 3863 3.506067 ACCAATCCAATTGACCGAAAGAC 59.494 43.478 7.12 0.00 42.83 3.01
3832 3939 0.250209 AAGAGCTGCAGTGACACCAG 60.250 55.000 16.64 4.77 0.00 4.00
3847 3954 7.941795 AATGAAATGCTTGAGAACAAAAGAG 57.058 32.000 0.00 0.00 35.49 2.85
3865 3974 6.553100 AGAAAGGGGTACACATCAAAATGAAA 59.447 34.615 0.00 0.00 36.67 2.69
3866 3975 6.074648 AGAAAGGGGTACACATCAAAATGAA 58.925 36.000 0.00 0.00 36.67 2.57
3867 3976 5.640147 AGAAAGGGGTACACATCAAAATGA 58.360 37.500 0.00 0.00 36.67 2.57
3868 3977 5.982890 AGAAAGGGGTACACATCAAAATG 57.017 39.130 0.00 0.00 38.93 2.32
3869 3978 5.838521 ACAAGAAAGGGGTACACATCAAAAT 59.161 36.000 0.00 0.00 0.00 1.82
3870 3979 5.205056 ACAAGAAAGGGGTACACATCAAAA 58.795 37.500 0.00 0.00 0.00 2.44
3889 3998 5.854157 GATTCATGCATGCAAGAAAACAAG 58.146 37.500 34.08 13.20 37.23 3.16


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

AutoCloner maintained by Alex Coulton.