Multiple sequence alignment - TraesCS4A01G008400

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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 TraesCS4A01G008400 chr4A 100.000 2723 0 0 1 2723 5116264 5113542 0.000000e+00 5029.0
1 TraesCS4A01G008400 chr4B 89.349 1521 76 34 657 2131 582112441 582113921 0.000000e+00 1832.0
2 TraesCS4A01G008400 chr4B 86.012 672 72 14 1 659 582109993 582110655 0.000000e+00 701.0
3 TraesCS4A01G008400 chr4D 91.275 1020 39 18 858 1855 465357724 465358715 0.000000e+00 1345.0
4 TraesCS4A01G008400 chr4D 85.481 551 57 14 5 551 465356633 465357164 1.100000e-153 553.0
5 TraesCS4A01G008400 chr4D 90.625 320 22 4 542 860 465357374 465357686 4.190000e-113 418.0
6 TraesCS4A01G008400 chr5A 93.772 578 34 2 2148 2723 211620542 211619965 0.000000e+00 867.0
7 TraesCS4A01G008400 chr5A 93.241 577 37 2 2148 2723 616364978 616364403 0.000000e+00 848.0
8 TraesCS4A01G008400 chr5A 93.241 577 37 2 2148 2723 709217455 709218030 0.000000e+00 848.0
9 TraesCS4A01G008400 chr5A 93.217 575 38 1 2150 2723 75364404 75363830 0.000000e+00 845.0
10 TraesCS4A01G008400 chr3A 93.414 577 37 1 2148 2723 698712289 698712865 0.000000e+00 854.0
11 TraesCS4A01G008400 chr3A 100.000 28 0 0 148 175 569891243 569891216 5.000000e-03 52.8
12 TraesCS4A01G008400 chr1A 93.414 577 37 1 2148 2723 570046200 570045624 0.000000e+00 854.0
13 TraesCS4A01G008400 chr1A 77.280 669 137 14 1001 1663 337658542 337657883 1.980000e-101 379.0
14 TraesCS4A01G008400 chr1A 82.661 248 37 6 1083 1327 337629738 337629494 5.910000e-52 215.0
15 TraesCS4A01G008400 chr6A 93.554 574 34 3 2150 2723 104449703 104450273 0.000000e+00 852.0
16 TraesCS4A01G008400 chr6A 93.068 577 37 3 2148 2723 85025813 85025239 0.000000e+00 841.0
17 TraesCS4A01G008400 chr6A 82.687 335 55 1 993 1327 111449598 111449267 7.370000e-76 294.0
18 TraesCS4A01G008400 chr6A 100.000 28 0 0 148 175 166114704 166114677 5.000000e-03 52.8
19 TraesCS4A01G008400 chr2A 93.056 576 40 0 2148 2723 768968647 768969222 0.000000e+00 843.0
20 TraesCS4A01G008400 chr2A 73.763 667 138 29 1010 1657 205910923 205911571 7.590000e-56 228.0
21 TraesCS4A01G008400 chr1B 78.267 658 128 14 1012 1663 349547302 349546654 2.520000e-110 409.0
22 TraesCS4A01G008400 chr7B 74.194 651 139 21 1010 1641 27974533 27973893 7.530000e-61 244.0
23 TraesCS4A01G008400 chr2D 74.102 668 134 29 1010 1657 192186455 192185807 3.500000e-59 239.0
24 TraesCS4A01G008400 chr2B 73.913 667 137 29 1010 1657 248137080 248137728 1.630000e-57 233.0
25 TraesCS4A01G008400 chr2B 79.683 315 55 7 1019 1327 728398386 728398075 4.570000e-53 219.0
26 TraesCS4A01G008400 chr1D 84.146 246 33 6 1085 1327 262341561 262341803 1.630000e-57 233.0
27 TraesCS4A01G008400 chr6B 89.583 48 5 0 1409 1456 697438546 697438593 8.140000e-06 62.1


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 TraesCS4A01G008400 chr4A 5113542 5116264 2722 True 5029.0 5029 100.0000 1 2723 1 chr4A.!!$R1 2722
1 TraesCS4A01G008400 chr4B 582109993 582113921 3928 False 1266.5 1832 87.6805 1 2131 2 chr4B.!!$F1 2130
2 TraesCS4A01G008400 chr4D 465356633 465358715 2082 False 772.0 1345 89.1270 5 1855 3 chr4D.!!$F1 1850
3 TraesCS4A01G008400 chr5A 211619965 211620542 577 True 867.0 867 93.7720 2148 2723 1 chr5A.!!$R2 575
4 TraesCS4A01G008400 chr5A 616364403 616364978 575 True 848.0 848 93.2410 2148 2723 1 chr5A.!!$R3 575
5 TraesCS4A01G008400 chr5A 709217455 709218030 575 False 848.0 848 93.2410 2148 2723 1 chr5A.!!$F1 575
6 TraesCS4A01G008400 chr5A 75363830 75364404 574 True 845.0 845 93.2170 2150 2723 1 chr5A.!!$R1 573
7 TraesCS4A01G008400 chr3A 698712289 698712865 576 False 854.0 854 93.4140 2148 2723 1 chr3A.!!$F1 575
8 TraesCS4A01G008400 chr1A 570045624 570046200 576 True 854.0 854 93.4140 2148 2723 1 chr1A.!!$R3 575
9 TraesCS4A01G008400 chr1A 337657883 337658542 659 True 379.0 379 77.2800 1001 1663 1 chr1A.!!$R2 662
10 TraesCS4A01G008400 chr6A 104449703 104450273 570 False 852.0 852 93.5540 2150 2723 1 chr6A.!!$F1 573
11 TraesCS4A01G008400 chr6A 85025239 85025813 574 True 841.0 841 93.0680 2148 2723 1 chr6A.!!$R1 575
12 TraesCS4A01G008400 chr2A 768968647 768969222 575 False 843.0 843 93.0560 2148 2723 1 chr2A.!!$F2 575
13 TraesCS4A01G008400 chr2A 205910923 205911571 648 False 228.0 228 73.7630 1010 1657 1 chr2A.!!$F1 647
14 TraesCS4A01G008400 chr1B 349546654 349547302 648 True 409.0 409 78.2670 1012 1663 1 chr1B.!!$R1 651
15 TraesCS4A01G008400 chr7B 27973893 27974533 640 True 244.0 244 74.1940 1010 1641 1 chr7B.!!$R1 631
16 TraesCS4A01G008400 chr2D 192185807 192186455 648 True 239.0 239 74.1020 1010 1657 1 chr2D.!!$R1 647
17 TraesCS4A01G008400 chr2B 248137080 248137728 648 False 233.0 233 73.9130 1010 1657 1 chr2B.!!$F1 647

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
524 536 0.108377 GGCCCACTTTAAAATGCCCG 60.108 55.0 0.0 0.0 32.74 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 4028 0.034477 AAACCTGATAACTGGCCCGG 60.034 55.0 0.0 0.0 38.45 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
30 31 3.512033 AGTTTTGCAAAAGTTACGGCA 57.488 38.095 24.46 0.00 0.00 5.69
88 89 1.227999 CGCGGTTTTGAGAAGGAGCA 61.228 55.000 0.00 0.00 0.00 4.26
179 182 2.286772 CCTTTTCAAGCACGTACACCAC 60.287 50.000 0.00 0.00 0.00 4.16
211 215 5.671742 AAAGGTTGCGAATTTGGAAAATG 57.328 34.783 0.55 0.00 0.00 2.32
212 216 3.663025 AGGTTGCGAATTTGGAAAATGG 58.337 40.909 0.55 0.00 0.00 3.16
213 217 3.070878 AGGTTGCGAATTTGGAAAATGGT 59.929 39.130 0.55 0.00 0.00 3.55
280 284 8.679288 ATTCAATAGAAAAGTTTGCTGATTCG 57.321 30.769 6.34 0.00 37.29 3.34
291 298 6.329496 AGTTTGCTGATTCGAAAAAGTTCAA 58.671 32.000 0.00 1.22 32.89 2.69
437 449 8.492673 AAAGTGAAGAAAACCAAGAAAAATCC 57.507 30.769 0.00 0.00 0.00 3.01
441 453 5.607939 AGAAAACCAAGAAAAATCCGGTT 57.392 34.783 0.00 0.00 41.67 4.44
444 456 1.883926 ACCAAGAAAAATCCGGTTCCG 59.116 47.619 0.00 4.08 0.00 4.30
462 474 4.379339 TCCGGACAAACCAAAAGAAAAG 57.621 40.909 0.00 0.00 38.90 2.27
521 533 1.675714 GGCAGGCCCACTTTAAAATGC 60.676 52.381 0.00 0.00 0.00 3.56
523 535 1.066215 CAGGCCCACTTTAAAATGCCC 60.066 52.381 0.00 5.33 39.72 5.36
524 536 0.108377 GGCCCACTTTAAAATGCCCG 60.108 55.000 0.00 0.00 32.74 6.13
525 537 0.108377 GCCCACTTTAAAATGCCCGG 60.108 55.000 0.00 0.00 0.00 5.73
530 542 1.203075 ACTTTAAAATGCCCGGGGACA 60.203 47.619 25.28 13.68 0.00 4.02
556 786 3.506096 CTGTACGCTCCGCTCCGA 61.506 66.667 0.00 0.00 0.00 4.55
665 2683 6.370593 ACATGCGTGTGAGTTTAATAACTTG 58.629 36.000 11.65 0.00 44.51 3.16
683 2701 2.279120 CCTAGCTCGCCTTCGCTG 60.279 66.667 0.00 0.00 37.05 5.18
839 2858 7.962934 TTTGTGAAGTTTTACTGATTTGACG 57.037 32.000 0.00 0.00 0.00 4.35
897 2955 1.594564 GAGTAATTCGCGCCTCCCC 60.595 63.158 0.00 0.00 0.00 4.81
972 3058 8.528295 CAAACAAAACACAAGGTAAATCTTACG 58.472 33.333 0.00 0.00 0.00 3.18
987 3073 2.159037 TCTTACGAGCTACACAGACACG 59.841 50.000 0.00 0.00 0.00 4.49
996 3082 1.328279 ACACAGACACGATCCAGTCA 58.672 50.000 12.98 0.00 37.23 3.41
1133 3225 1.557443 GACGTCCACAACAAGAGCGG 61.557 60.000 3.51 0.00 0.00 5.52
1363 3461 2.804828 GAACTCGTCCAGGGGCAAGG 62.805 65.000 0.00 0.00 0.00 3.61
1702 3806 1.878775 GCCGCAGCTTCAACTTCAT 59.121 52.632 0.00 0.00 35.50 2.57
1703 3807 0.179179 GCCGCAGCTTCAACTTCATC 60.179 55.000 0.00 0.00 35.50 2.92
1704 3808 1.159285 CCGCAGCTTCAACTTCATCA 58.841 50.000 0.00 0.00 0.00 3.07
1709 3813 4.362279 GCAGCTTCAACTTCATCAAACAA 58.638 39.130 0.00 0.00 0.00 2.83
1710 3814 4.207841 GCAGCTTCAACTTCATCAAACAAC 59.792 41.667 0.00 0.00 0.00 3.32
1711 3815 5.342433 CAGCTTCAACTTCATCAAACAACA 58.658 37.500 0.00 0.00 0.00 3.33
1712 3816 5.806502 CAGCTTCAACTTCATCAAACAACAA 59.193 36.000 0.00 0.00 0.00 2.83
1713 3817 6.020121 CAGCTTCAACTTCATCAAACAACAAG 60.020 38.462 0.00 0.00 0.00 3.16
1714 3818 5.276536 GCTTCAACTTCATCAAACAACAAGC 60.277 40.000 0.00 0.00 0.00 4.01
1715 3819 5.321959 TCAACTTCATCAAACAACAAGCA 57.678 34.783 0.00 0.00 0.00 3.91
1716 3820 5.342433 TCAACTTCATCAAACAACAAGCAG 58.658 37.500 0.00 0.00 0.00 4.24
1717 3821 4.311816 ACTTCATCAAACAACAAGCAGG 57.688 40.909 0.00 0.00 0.00 4.85
1750 3860 1.153168 ATGGTGGCATGACCTACGC 60.153 57.895 0.00 0.00 40.22 4.42
1751 3861 2.890474 GGTGGCATGACCTACGCG 60.890 66.667 3.53 3.53 40.22 6.01
1752 3862 3.564027 GTGGCATGACCTACGCGC 61.564 66.667 5.73 0.00 40.22 6.86
1855 3965 4.745125 CAGCGGGTTGATGTAATACTACTG 59.255 45.833 0.00 0.00 0.00 2.74
1870 3980 9.843334 GTAATACTACTGCTACTGTAATGGATC 57.157 37.037 0.00 0.00 0.00 3.36
1871 3981 8.713708 AATACTACTGCTACTGTAATGGATCT 57.286 34.615 0.00 0.00 0.00 2.75
1872 3982 9.809395 AATACTACTGCTACTGTAATGGATCTA 57.191 33.333 0.00 0.00 0.00 1.98
1882 3992 7.772332 ACTGTAATGGATCTATTGACGAAAC 57.228 36.000 14.10 4.21 0.00 2.78
1907 4017 0.319986 TGCGGTTTACAGATGTGCGA 60.320 50.000 0.00 0.00 0.00 5.10
1908 4018 0.370273 GCGGTTTACAGATGTGCGAG 59.630 55.000 0.00 0.00 0.00 5.03
1916 4026 2.977914 ACAGATGTGCGAGCAGTTTAT 58.022 42.857 0.00 0.00 0.00 1.40
1917 4027 2.932614 ACAGATGTGCGAGCAGTTTATC 59.067 45.455 0.00 1.28 0.00 1.75
1918 4028 2.286294 CAGATGTGCGAGCAGTTTATCC 59.714 50.000 0.00 0.00 0.00 2.59
1919 4029 1.599542 GATGTGCGAGCAGTTTATCCC 59.400 52.381 0.00 0.00 0.00 3.85
1920 4030 0.739462 TGTGCGAGCAGTTTATCCCG 60.739 55.000 0.00 0.00 0.00 5.14
1921 4031 1.153449 TGCGAGCAGTTTATCCCGG 60.153 57.895 0.00 0.00 0.00 5.73
1950 4076 3.685139 TCAGGTTTCTCACTGGACATC 57.315 47.619 0.00 0.00 35.47 3.06
1951 4077 2.972021 TCAGGTTTCTCACTGGACATCA 59.028 45.455 0.00 0.00 35.47 3.07
1959 4085 1.002868 ACTGGACATCACCTGCTGC 60.003 57.895 0.00 0.00 33.18 5.25
1962 4088 1.748122 GGACATCACCTGCTGCTGG 60.748 63.158 22.17 22.17 0.00 4.85
1963 4089 1.297689 GACATCACCTGCTGCTGGA 59.702 57.895 29.14 10.67 0.00 3.86
1964 4090 0.107312 GACATCACCTGCTGCTGGAT 60.107 55.000 29.14 12.45 0.00 3.41
1966 4092 1.101635 CATCACCTGCTGCTGGATGG 61.102 60.000 29.14 17.97 33.47 3.51
1967 4093 1.276859 ATCACCTGCTGCTGGATGGA 61.277 55.000 29.14 21.75 0.00 3.41
1968 4094 1.226542 CACCTGCTGCTGGATGGAT 59.773 57.895 29.14 6.21 0.00 3.41
1969 4095 1.101635 CACCTGCTGCTGGATGGATG 61.102 60.000 29.14 14.26 0.00 3.51
1976 4102 0.678684 TGCTGGATGGATGCACTGTG 60.679 55.000 2.76 2.76 0.00 3.66
1998 4124 1.538876 TGGTTCAGGGTGAGGGGAG 60.539 63.158 0.00 0.00 0.00 4.30
2010 4136 3.219281 GTGAGGGGAGACTGTCTAGATC 58.781 54.545 10.86 7.45 0.00 2.75
2018 4144 4.439974 GGAGACTGTCTAGATCACTGCAAG 60.440 50.000 10.86 0.00 42.29 4.01
2022 4148 2.564504 TGTCTAGATCACTGCAAGCTGT 59.435 45.455 0.00 0.00 37.60 4.40
2023 4149 3.007290 TGTCTAGATCACTGCAAGCTGTT 59.993 43.478 0.00 0.00 37.60 3.16
2024 4150 3.370366 GTCTAGATCACTGCAAGCTGTTG 59.630 47.826 0.00 0.00 37.60 3.33
2025 4151 2.556144 AGATCACTGCAAGCTGTTGA 57.444 45.000 1.61 4.70 37.60 3.18
2026 4152 3.069079 AGATCACTGCAAGCTGTTGAT 57.931 42.857 1.61 8.68 37.60 2.57
2027 4153 4.212143 AGATCACTGCAAGCTGTTGATA 57.788 40.909 1.61 0.00 37.60 2.15
2028 4154 4.190001 AGATCACTGCAAGCTGTTGATAG 58.810 43.478 1.61 0.00 37.60 2.08
2029 4155 3.407424 TCACTGCAAGCTGTTGATAGT 57.593 42.857 1.61 0.00 37.60 2.12
2030 4156 3.069289 TCACTGCAAGCTGTTGATAGTG 58.931 45.455 13.10 13.10 44.08 2.74
2033 4159 0.097674 GCAAGCTGTTGATAGTGGCG 59.902 55.000 0.00 0.00 35.46 5.69
2034 4160 0.729116 CAAGCTGTTGATAGTGGCGG 59.271 55.000 0.00 0.00 35.46 6.13
2035 4161 1.026718 AAGCTGTTGATAGTGGCGGC 61.027 55.000 0.00 0.00 0.00 6.53
2036 4162 1.450312 GCTGTTGATAGTGGCGGCT 60.450 57.895 11.43 0.00 0.00 5.52
2037 4163 1.709147 GCTGTTGATAGTGGCGGCTG 61.709 60.000 11.43 0.00 0.00 4.85
2038 4164 1.709147 CTGTTGATAGTGGCGGCTGC 61.709 60.000 9.72 9.72 41.71 5.25
2039 4165 2.511373 TTGATAGTGGCGGCTGCG 60.511 61.111 12.29 0.00 44.10 5.18
2070 4196 0.321996 AGGGGTCAGAACGCTTTCTC 59.678 55.000 1.83 0.00 40.34 2.87
2079 4205 2.820037 CGCTTTCTCCCGGGCTTC 60.820 66.667 18.49 0.00 0.00 3.86
2118 4244 3.657350 TGGTAACTGCCCCTGCCC 61.657 66.667 0.00 0.00 36.33 5.36
2120 4246 3.339093 GTAACTGCCCCTGCCCCT 61.339 66.667 0.00 0.00 36.33 4.79
2121 4247 3.338250 TAACTGCCCCTGCCCCTG 61.338 66.667 0.00 0.00 36.33 4.45
2133 4259 3.541713 CCCCTGCCGCTAGGAGTC 61.542 72.222 9.65 0.00 40.42 3.36
2134 4260 3.905678 CCCTGCCGCTAGGAGTCG 61.906 72.222 9.65 0.00 40.42 4.18
2140 4266 3.015677 CGCTAGGAGTCGGACGAG 58.984 66.667 1.89 0.80 0.00 4.18
2141 4267 1.521010 CGCTAGGAGTCGGACGAGA 60.521 63.158 1.89 0.00 0.00 4.04
2142 4268 1.492319 CGCTAGGAGTCGGACGAGAG 61.492 65.000 1.89 0.79 0.00 3.20
2186 4312 1.118356 CCCTCAGGAAGATCTCCCCG 61.118 65.000 0.00 0.00 46.81 5.73
2189 4315 2.324541 CTCAGGAAGATCTCCCCGAAT 58.675 52.381 0.00 0.00 46.81 3.34
2214 4341 2.649843 TTTCGCGCCGGTGTCAAAAC 62.650 55.000 17.91 0.00 0.00 2.43
2240 4367 4.443266 GTCGCGCTTCCAGGAGCT 62.443 66.667 5.56 0.00 40.52 4.09
2254 4381 1.168714 GGAGCTTGATTTTCGCTGGT 58.831 50.000 0.00 0.00 33.47 4.00
2270 4397 1.228154 GGTCTGGGCCGAAAACAGT 60.228 57.895 0.00 0.00 34.02 3.55
2389 4516 2.125552 CATGGCGCCTCGTCTTCA 60.126 61.111 29.70 4.25 30.55 3.02
2390 4517 2.169789 CATGGCGCCTCGTCTTCAG 61.170 63.158 29.70 2.68 30.55 3.02
2571 4698 3.640407 ACTCGCCTGTGCCCACAT 61.640 61.111 1.04 0.00 41.01 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.624373 AGATGATTCAGTTTCTAAGCATTGTAT 57.376 29.630 0.00 0.00 32.23 2.29
88 89 2.485814 GCTTCGCCTTCAAATCAGACTT 59.514 45.455 0.00 0.00 0.00 3.01
197 201 9.149225 TCAAATTCATACCATTTTCCAAATTCG 57.851 29.630 0.00 0.00 0.00 3.34
211 215 9.696917 ATTCACAAACTTTCTCAAATTCATACC 57.303 29.630 0.00 0.00 0.00 2.73
261 265 8.188139 ACTTTTTCGAATCAGCAAACTTTTCTA 58.812 29.630 0.00 0.00 0.00 2.10
402 411 8.317891 TGGTTTTCTTCACTTTTTCCTTTTTC 57.682 30.769 0.00 0.00 0.00 2.29
441 453 4.017808 TCTTTTCTTTTGGTTTGTCCGGA 58.982 39.130 0.00 0.00 39.52 5.14
444 456 4.119862 GGCTCTTTTCTTTTGGTTTGTCC 58.880 43.478 0.00 0.00 0.00 4.02
475 487 0.035317 AGCATCTTCACCTGCAACGA 59.965 50.000 0.00 0.00 40.88 3.85
478 490 4.445453 CATACTAGCATCTTCACCTGCAA 58.555 43.478 0.00 0.00 40.88 4.08
485 497 2.369860 CCTGCCCATACTAGCATCTTCA 59.630 50.000 0.00 0.00 38.56 3.02
556 786 1.514553 GCTAACTTAGGCGACGGGT 59.485 57.895 0.00 0.00 0.00 5.28
616 846 6.657117 TGATTTTCCGTTCTTCATTATCCACA 59.343 34.615 0.00 0.00 0.00 4.17
617 847 6.967199 GTGATTTTCCGTTCTTCATTATCCAC 59.033 38.462 0.00 0.00 0.00 4.02
665 2683 4.214327 AGCGAAGGCGAGCTAGGC 62.214 66.667 12.67 12.67 46.35 3.93
750 2769 5.186021 GGAGTTGACTTGACTAATCTCCAGA 59.814 44.000 0.00 0.00 39.67 3.86
839 2858 4.740695 TGCTTTTTAAAATGTGTGCGTACC 59.259 37.500 13.53 0.00 0.00 3.34
883 2941 3.809374 GATCGGGGAGGCGCGAATT 62.809 63.158 12.10 0.00 0.00 2.17
897 2955 2.046285 GGTGCTTGGGTTGGGATCG 61.046 63.158 0.00 0.00 0.00 3.69
972 3058 1.472878 TGGATCGTGTCTGTGTAGCTC 59.527 52.381 0.00 0.00 0.00 4.09
987 3073 0.033228 CGGCCATCTCTGACTGGATC 59.967 60.000 2.24 0.00 34.24 3.36
996 3082 0.758685 CTCCTCCTTCGGCCATCTCT 60.759 60.000 2.24 0.00 0.00 3.10
1081 3167 1.153549 CGTAGCTCAGGCCCTTGAC 60.154 63.158 0.00 0.00 39.73 3.18
1394 3492 3.402681 CGGCCACCACCATCTCCT 61.403 66.667 2.24 0.00 0.00 3.69
1702 3806 2.878406 GCTACTCCTGCTTGTTGTTTGA 59.122 45.455 0.00 0.00 0.00 2.69
1703 3807 2.030805 GGCTACTCCTGCTTGTTGTTTG 60.031 50.000 0.00 0.00 0.00 2.93
1704 3808 2.230660 GGCTACTCCTGCTTGTTGTTT 58.769 47.619 0.00 0.00 0.00 2.83
1709 3813 2.982130 CCGGCTACTCCTGCTTGT 59.018 61.111 0.00 0.00 0.00 3.16
1710 3814 2.512515 GCCGGCTACTCCTGCTTG 60.513 66.667 22.15 0.00 41.31 4.01
1711 3815 2.370445 ATGCCGGCTACTCCTGCTT 61.370 57.895 29.70 0.00 44.40 3.91
1712 3816 2.765807 ATGCCGGCTACTCCTGCT 60.766 61.111 29.70 0.00 44.40 4.24
1713 3817 2.590007 CATGCCGGCTACTCCTGC 60.590 66.667 29.70 0.00 44.36 4.85
1714 3818 2.590007 GCATGCCGGCTACTCCTG 60.590 66.667 29.70 15.37 0.00 3.86
1715 3819 2.446848 ATGCATGCCGGCTACTCCT 61.447 57.895 29.70 5.00 34.04 3.69
1716 3820 2.111878 ATGCATGCCGGCTACTCC 59.888 61.111 29.70 11.81 34.04 3.85
1717 3821 2.256591 CCATGCATGCCGGCTACTC 61.257 63.158 29.70 14.33 34.04 2.59
1759 3869 4.000557 CAGTCCACACACACGCGC 62.001 66.667 5.73 0.00 0.00 6.86
1760 3870 2.584970 ACAGTCCACACACACGCG 60.585 61.111 3.53 3.53 0.00 6.01
1761 3871 1.087202 TTCACAGTCCACACACACGC 61.087 55.000 0.00 0.00 0.00 5.34
1762 3872 0.930310 CTTCACAGTCCACACACACG 59.070 55.000 0.00 0.00 0.00 4.49
1772 3882 1.021390 CATCGGCCCACTTCACAGTC 61.021 60.000 0.00 0.00 0.00 3.51
1855 3965 6.678878 TCGTCAATAGATCCATTACAGTAGC 58.321 40.000 0.00 0.00 0.00 3.58
1870 3980 2.345641 CGCAGACCAGTTTCGTCAATAG 59.654 50.000 0.00 0.00 32.41 1.73
1871 3981 2.333926 CGCAGACCAGTTTCGTCAATA 58.666 47.619 0.00 0.00 32.41 1.90
1872 3982 1.148310 CGCAGACCAGTTTCGTCAAT 58.852 50.000 0.00 0.00 32.41 2.57
1882 3992 2.002586 CATCTGTAAACCGCAGACCAG 58.997 52.381 0.00 0.00 44.52 4.00
1907 4017 2.270874 CTGGCCCGGGATAAACTGCT 62.271 60.000 29.31 0.00 0.00 4.24
1908 4018 1.823899 CTGGCCCGGGATAAACTGC 60.824 63.158 29.31 5.40 0.00 4.40
1916 4026 2.070039 CCTGATAACTGGCCCGGGA 61.070 63.158 29.31 2.11 0.00 5.14
1917 4027 1.921869 AACCTGATAACTGGCCCGGG 61.922 60.000 19.09 19.09 38.45 5.73
1918 4028 0.034477 AAACCTGATAACTGGCCCGG 60.034 55.000 0.00 0.00 38.45 5.73
1919 4029 1.065418 AGAAACCTGATAACTGGCCCG 60.065 52.381 0.00 0.00 38.45 6.13
1920 4030 2.026262 TGAGAAACCTGATAACTGGCCC 60.026 50.000 0.00 0.00 38.45 5.80
1921 4031 3.010420 GTGAGAAACCTGATAACTGGCC 58.990 50.000 0.00 0.00 38.45 5.36
1950 4076 1.101635 CATCCATCCAGCAGCAGGTG 61.102 60.000 3.35 0.64 42.78 4.00
1951 4077 1.226542 CATCCATCCAGCAGCAGGT 59.773 57.895 3.35 0.00 0.00 4.00
1959 4085 1.741706 GTTCACAGTGCATCCATCCAG 59.258 52.381 0.00 0.00 0.00 3.86
1962 4088 1.741706 CCAGTTCACAGTGCATCCATC 59.258 52.381 0.00 0.00 0.00 3.51
1963 4089 1.074405 ACCAGTTCACAGTGCATCCAT 59.926 47.619 0.00 0.00 0.00 3.41
1964 4090 0.473755 ACCAGTTCACAGTGCATCCA 59.526 50.000 0.00 0.00 0.00 3.41
1966 4092 2.221169 TGAACCAGTTCACAGTGCATC 58.779 47.619 9.12 0.00 43.90 3.91
1967 4093 2.224606 CTGAACCAGTTCACAGTGCAT 58.775 47.619 9.12 0.00 43.90 3.96
1968 4094 1.667236 CTGAACCAGTTCACAGTGCA 58.333 50.000 9.12 0.00 43.90 4.57
1969 4095 0.947244 CCTGAACCAGTTCACAGTGC 59.053 55.000 9.12 0.00 43.90 4.40
1976 4102 0.036875 CCCTCACCCTGAACCAGTTC 59.963 60.000 3.52 3.52 39.91 3.01
1998 4124 3.119173 AGCTTGCAGTGATCTAGACAGTC 60.119 47.826 0.00 0.00 0.00 3.51
2010 4136 2.161012 CCACTATCAACAGCTTGCAGTG 59.839 50.000 10.65 10.65 38.56 3.66
2018 4144 1.450312 AGCCGCCACTATCAACAGC 60.450 57.895 0.00 0.00 0.00 4.40
2022 4148 2.511373 CGCAGCCGCCACTATCAA 60.511 61.111 0.00 0.00 33.11 2.57
2023 4149 4.529219 CCGCAGCCGCCACTATCA 62.529 66.667 0.00 0.00 33.11 2.15
2035 4161 3.847602 CTCTCCCAGAGGCCGCAG 61.848 72.222 9.88 0.00 38.67 5.18
2053 4179 0.673956 GGGAGAAAGCGTTCTGACCC 60.674 60.000 19.93 19.33 44.42 4.46
2055 4181 1.014564 CCGGGAGAAAGCGTTCTGAC 61.015 60.000 19.93 11.67 44.42 3.51
2056 4182 1.292223 CCGGGAGAAAGCGTTCTGA 59.708 57.895 19.93 0.00 44.42 3.27
2094 4220 2.046604 GGCAGTTACCACGGACCC 60.047 66.667 0.00 0.00 0.00 4.46
2118 4244 3.905678 CCGACTCCTAGCGGCAGG 61.906 72.222 1.45 7.43 41.17 4.85
2120 4246 3.138798 GTCCGACTCCTAGCGGCA 61.139 66.667 1.45 0.00 46.79 5.69
2121 4247 4.253257 CGTCCGACTCCTAGCGGC 62.253 72.222 0.00 0.00 46.79 6.53
2124 4250 0.462403 ACTCTCGTCCGACTCCTAGC 60.462 60.000 0.00 0.00 0.00 3.42
2125 4251 2.886862 TACTCTCGTCCGACTCCTAG 57.113 55.000 0.00 0.00 0.00 3.02
2126 4252 2.499289 ACTTACTCTCGTCCGACTCCTA 59.501 50.000 0.00 0.00 0.00 2.94
2127 4253 1.278699 ACTTACTCTCGTCCGACTCCT 59.721 52.381 0.00 0.00 0.00 3.69
2128 4254 1.736612 ACTTACTCTCGTCCGACTCC 58.263 55.000 0.00 0.00 0.00 3.85
2129 4255 3.309410 CCTTACTTACTCTCGTCCGACTC 59.691 52.174 0.00 0.00 0.00 3.36
2130 4256 3.269178 CCTTACTTACTCTCGTCCGACT 58.731 50.000 0.00 0.00 0.00 4.18
2131 4257 2.354199 CCCTTACTTACTCTCGTCCGAC 59.646 54.545 0.00 0.00 0.00 4.79
2132 4258 2.636830 CCCTTACTTACTCTCGTCCGA 58.363 52.381 0.00 0.00 0.00 4.55
2133 4259 1.065251 GCCCTTACTTACTCTCGTCCG 59.935 57.143 0.00 0.00 0.00 4.79
2134 4260 2.097825 TGCCCTTACTTACTCTCGTCC 58.902 52.381 0.00 0.00 0.00 4.79
2135 4261 3.633065 AGATGCCCTTACTTACTCTCGTC 59.367 47.826 0.00 0.00 0.00 4.20
2136 4262 3.633065 GAGATGCCCTTACTTACTCTCGT 59.367 47.826 0.00 0.00 0.00 4.18
2137 4263 3.004944 GGAGATGCCCTTACTTACTCTCG 59.995 52.174 0.00 0.00 0.00 4.04
2138 4264 3.961408 TGGAGATGCCCTTACTTACTCTC 59.039 47.826 0.00 0.00 34.97 3.20
2139 4265 3.964031 CTGGAGATGCCCTTACTTACTCT 59.036 47.826 0.00 0.00 34.97 3.24
2140 4266 3.493524 GCTGGAGATGCCCTTACTTACTC 60.494 52.174 0.00 0.00 34.97 2.59
2141 4267 2.436173 GCTGGAGATGCCCTTACTTACT 59.564 50.000 0.00 0.00 34.97 2.24
2142 4268 2.485657 GGCTGGAGATGCCCTTACTTAC 60.486 54.545 0.00 0.00 44.32 2.34
2143 4269 1.768870 GGCTGGAGATGCCCTTACTTA 59.231 52.381 0.00 0.00 44.32 2.24
2144 4270 0.548510 GGCTGGAGATGCCCTTACTT 59.451 55.000 0.00 0.00 44.32 2.24
2145 4271 2.225792 GGCTGGAGATGCCCTTACT 58.774 57.895 0.00 0.00 44.32 2.24
2146 4272 4.887615 GGCTGGAGATGCCCTTAC 57.112 61.111 0.00 0.00 44.32 2.34
2170 4296 2.042464 CATTCGGGGAGATCTTCCTGA 58.958 52.381 25.78 25.78 45.98 3.86
2206 4332 1.398692 GACTGGGCCTTGTTTTGACA 58.601 50.000 4.53 0.00 0.00 3.58
2208 4334 1.452145 GCGACTGGGCCTTGTTTTGA 61.452 55.000 4.53 0.00 0.00 2.69
2230 4357 1.812571 GCGAAAATCAAGCTCCTGGAA 59.187 47.619 0.00 0.00 0.00 3.53
2240 4367 1.533625 CCCAGACCAGCGAAAATCAA 58.466 50.000 0.00 0.00 0.00 2.57
2254 4381 1.896660 GCACTGTTTTCGGCCCAGA 60.897 57.895 12.31 0.00 0.00 3.86
2374 4501 4.742201 GCTGAAGACGAGGCGCCA 62.742 66.667 31.54 3.45 0.00 5.69
2603 4730 1.544703 GGGAGAGGTAGGGAGAGGG 59.455 68.421 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.