Multiple sequence alignment - TraesCS5D01G433400

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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 TraesCS5D01G433400 chr5D 100.000 2819 0 0 1 2819 489187483 489190301 0.000000e+00 5206.0
1 TraesCS5D01G433400 chr5D 87.395 119 15 0 1147 1265 40023828 40023946 1.360000e-28 137.0
2 TraesCS5D01G433400 chr5A 88.529 2345 87 78 271 2497 610230305 610232585 0.000000e+00 2673.0
3 TraesCS5D01G433400 chr5A 87.888 322 17 5 2510 2819 610232796 610233107 2.670000e-95 359.0
4 TraesCS5D01G433400 chr5A 89.916 119 12 0 1147 1265 27938355 27938473 1.350000e-33 154.0
5 TraesCS5D01G433400 chr5A 95.312 64 3 0 206 269 610227408 610227471 4.970000e-18 102.0
6 TraesCS5D01G433400 chr5A 94.444 54 3 0 1 54 610227159 610227212 1.800000e-12 84.2
7 TraesCS5D01G433400 chr5B 84.063 1324 98 56 104 1372 602843084 602844349 0.000000e+00 1171.0
8 TraesCS5D01G433400 chr5B 92.331 665 18 13 2182 2817 602845343 602846003 0.000000e+00 915.0
9 TraesCS5D01G433400 chr5B 89.295 766 29 14 1354 2097 602844377 602845111 0.000000e+00 911.0
10 TraesCS5D01G433400 chr5B 87.395 119 15 0 1147 1265 33756809 33756691 1.360000e-28 137.0
11 TraesCS5D01G433400 chr4D 90.000 110 9 1 1116 1225 501675288 501675181 1.050000e-29 141.0
12 TraesCS5D01G433400 chr4D 88.288 111 13 0 1154 1264 501968480 501968590 1.760000e-27 134.0
13 TraesCS5D01G433400 chr4D 88.785 107 8 3 1120 1225 495129714 495129817 8.200000e-26 128.0
14 TraesCS5D01G433400 chr4B 90.000 110 9 1 1116 1225 645897531 645897424 1.050000e-29 141.0


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 TraesCS5D01G433400 chr5D 489187483 489190301 2818 False 5206.00 5206 100.00000 1 2819 1 chr5D.!!$F2 2818
1 TraesCS5D01G433400 chr5A 610227159 610233107 5948 False 804.55 2673 91.54325 1 2819 4 chr5A.!!$F2 2818
2 TraesCS5D01G433400 chr5B 602843084 602846003 2919 False 999.00 1171 88.56300 104 2817 3 chr5B.!!$F1 2713

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
796 3759 0.321122 AACTGCTGCTGCTACTCCAC 60.321 55.0 17.0 0.0 40.48 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2477 5713 0.319297 AGTACGTGCGTTGAGGTTCC 60.319 55.0 1.66 0.0 0.0 3.62 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
32 33 2.266554 CAGCTAGCAGAAGAAAGGTCG 58.733 52.381 18.83 0.00 0.00 4.79
38 39 1.270358 GCAGAAGAAAGGTCGGTGAGT 60.270 52.381 0.00 0.00 0.00 3.41
54 55 1.827344 TGAGTGAGCCAGATGGTAGTG 59.173 52.381 0.00 0.00 37.57 2.74
55 56 0.539051 AGTGAGCCAGATGGTAGTGC 59.461 55.000 0.00 0.00 37.57 4.40
58 59 2.034878 TGAGCCAGATGGTAGTGCTAG 58.965 52.381 0.00 0.00 37.57 3.42
59 60 2.035632 GAGCCAGATGGTAGTGCTAGT 58.964 52.381 0.00 0.00 37.57 2.57
60 61 3.223435 GAGCCAGATGGTAGTGCTAGTA 58.777 50.000 0.00 0.00 37.57 1.82
61 62 3.226777 AGCCAGATGGTAGTGCTAGTAG 58.773 50.000 0.00 0.00 37.57 2.57
62 63 2.959707 GCCAGATGGTAGTGCTAGTAGT 59.040 50.000 0.00 0.00 37.57 2.73
63 64 4.141228 AGCCAGATGGTAGTGCTAGTAGTA 60.141 45.833 0.00 0.00 37.57 1.82
64 65 4.216687 GCCAGATGGTAGTGCTAGTAGTAG 59.783 50.000 0.00 0.00 37.57 2.57
66 67 6.531923 CCAGATGGTAGTGCTAGTAGTAGTA 58.468 44.000 6.47 0.00 0.00 1.82
67 68 6.996879 CCAGATGGTAGTGCTAGTAGTAGTAA 59.003 42.308 6.47 0.00 0.00 2.24
68 69 7.501559 CCAGATGGTAGTGCTAGTAGTAGTAAA 59.498 40.741 6.47 0.00 0.00 2.01
69 70 9.069082 CAGATGGTAGTGCTAGTAGTAGTAAAT 57.931 37.037 6.47 2.80 0.00 1.40
70 71 9.287373 AGATGGTAGTGCTAGTAGTAGTAAATC 57.713 37.037 6.47 10.17 0.00 2.17
73 78 6.774656 GGTAGTGCTAGTAGTAGTAAATCCCA 59.225 42.308 6.47 0.00 0.00 4.37
89 94 8.771286 AGTAAATCCCATTTTAATTCCTGCATT 58.229 29.630 0.00 0.00 33.82 3.56
92 97 4.099266 TCCCATTTTAATTCCTGCATTCCG 59.901 41.667 0.00 0.00 0.00 4.30
101 106 1.135315 CTGCATTCCGGTTTGAGCG 59.865 57.895 0.00 0.00 39.06 5.03
103 108 0.676466 TGCATTCCGGTTTGAGCGAT 60.676 50.000 0.00 0.00 42.41 4.58
106 142 0.748005 ATTCCGGTTTGAGCGATGGG 60.748 55.000 0.00 0.00 42.41 4.00
140 176 3.362295 CAAATATGGCACGAAACGGATG 58.638 45.455 0.00 0.00 0.00 3.51
174 210 3.311110 ACGGAGAGGCGCTTTCCA 61.311 61.111 19.91 0.00 34.83 3.53
180 216 1.021390 AGAGGCGCTTTCCAATCACG 61.021 55.000 7.64 0.00 0.00 4.35
184 220 1.512734 CGCTTTCCAATCACGCAGC 60.513 57.895 0.00 0.00 0.00 5.25
189 225 0.881118 TTCCAATCACGCAGCCTTTC 59.119 50.000 0.00 0.00 0.00 2.62
194 230 2.859273 ATCACGCAGCCTTTCCTCCG 62.859 60.000 0.00 0.00 0.00 4.63
222 278 1.734748 GCTCCTGGCTACGTACTCC 59.265 63.158 0.00 0.00 38.06 3.85
535 3462 2.197577 TCGTGTGTGTGTGTGTGTATG 58.802 47.619 0.00 0.00 0.00 2.39
536 3463 1.930503 CGTGTGTGTGTGTGTGTATGT 59.069 47.619 0.00 0.00 0.00 2.29
537 3464 2.285544 CGTGTGTGTGTGTGTGTATGTG 60.286 50.000 0.00 0.00 0.00 3.21
538 3465 2.675844 GTGTGTGTGTGTGTGTATGTGT 59.324 45.455 0.00 0.00 0.00 3.72
539 3466 2.933260 TGTGTGTGTGTGTGTATGTGTC 59.067 45.455 0.00 0.00 0.00 3.67
540 3467 3.194861 GTGTGTGTGTGTGTATGTGTCT 58.805 45.455 0.00 0.00 0.00 3.41
572 3500 5.749109 CGTAAACAGAATCCCACTACATCTC 59.251 44.000 0.00 0.00 0.00 2.75
643 3587 1.755008 GTCGTAGGGCTGAGAGGCT 60.755 63.158 0.00 0.00 41.09 4.58
689 3633 2.489938 TTTATCAGCAGCGGAAAGGT 57.510 45.000 0.00 0.00 0.00 3.50
745 3697 3.390521 CCAGCCCGCCACAGTAGA 61.391 66.667 0.00 0.00 0.00 2.59
746 3698 2.185350 CAGCCCGCCACAGTAGAG 59.815 66.667 0.00 0.00 0.00 2.43
747 3699 2.283966 AGCCCGCCACAGTAGAGT 60.284 61.111 0.00 0.00 0.00 3.24
748 3700 1.000019 AGCCCGCCACAGTAGAGTA 60.000 57.895 0.00 0.00 0.00 2.59
749 3701 1.038130 AGCCCGCCACAGTAGAGTAG 61.038 60.000 0.00 0.00 0.00 2.57
750 3702 1.437986 CCCGCCACAGTAGAGTAGC 59.562 63.158 0.00 0.00 0.00 3.58
751 3703 1.437986 CCGCCACAGTAGAGTAGCC 59.562 63.158 0.00 0.00 0.00 3.93
752 3704 1.437986 CGCCACAGTAGAGTAGCCC 59.562 63.158 0.00 0.00 0.00 5.19
753 3705 1.823976 GCCACAGTAGAGTAGCCCC 59.176 63.158 0.00 0.00 0.00 5.80
754 3706 1.687297 GCCACAGTAGAGTAGCCCCC 61.687 65.000 0.00 0.00 0.00 5.40
796 3759 0.321122 AACTGCTGCTGCTACTCCAC 60.321 55.000 17.00 0.00 40.48 4.02
797 3760 1.190833 ACTGCTGCTGCTACTCCACT 61.191 55.000 17.00 0.00 40.48 4.00
838 3801 7.971168 CGTTGCCATATATAGAAAAACAAACCA 59.029 33.333 0.00 0.00 0.00 3.67
909 3880 2.285442 CTTCCCCCGACCTCCCTT 60.285 66.667 0.00 0.00 0.00 3.95
910 3881 2.285144 TTCCCCCGACCTCCCTTC 60.285 66.667 0.00 0.00 0.00 3.46
911 3882 3.937372 TTCCCCCGACCTCCCTTCC 62.937 68.421 0.00 0.00 0.00 3.46
912 3883 4.416601 CCCCCGACCTCCCTTCCT 62.417 72.222 0.00 0.00 0.00 3.36
913 3884 2.764547 CCCCGACCTCCCTTCCTC 60.765 72.222 0.00 0.00 0.00 3.71
914 3885 3.148279 CCCGACCTCCCTTCCTCG 61.148 72.222 0.00 0.00 0.00 4.63
967 3942 1.129811 CCACGACCTTGTTTAATCGCC 59.870 52.381 0.00 0.00 38.12 5.54
968 3943 1.129811 CACGACCTTGTTTAATCGCCC 59.870 52.381 0.00 0.00 38.12 6.13
969 3944 1.270947 ACGACCTTGTTTAATCGCCCA 60.271 47.619 0.00 0.00 38.12 5.36
970 3945 1.129811 CGACCTTGTTTAATCGCCCAC 59.870 52.381 0.00 0.00 0.00 4.61
971 3946 2.156098 GACCTTGTTTAATCGCCCACA 58.844 47.619 0.00 0.00 0.00 4.17
972 3947 2.554893 GACCTTGTTTAATCGCCCACAA 59.445 45.455 0.00 0.00 0.00 3.33
973 3948 2.959707 ACCTTGTTTAATCGCCCACAAA 59.040 40.909 0.00 0.00 0.00 2.83
974 3949 3.576550 ACCTTGTTTAATCGCCCACAAAT 59.423 39.130 0.00 0.00 0.00 2.32
977 3952 3.157881 TGTTTAATCGCCCACAAATCCA 58.842 40.909 0.00 0.00 0.00 3.41
1273 4258 0.597637 CTACTTCTACATGCCGCCCG 60.598 60.000 0.00 0.00 0.00 6.13
1926 4980 4.141597 ACGTAGTACCTCTACCCTTCTACC 60.142 50.000 0.00 0.00 44.30 3.18
1961 5015 2.054799 GGCTATTCATGTCCCCTACCA 58.945 52.381 0.00 0.00 0.00 3.25
1969 5023 0.546747 TGTCCCCTACCACCCTTCAG 60.547 60.000 0.00 0.00 0.00 3.02
2097 5155 2.110006 GATCGGCCCTCCTTCAGC 59.890 66.667 0.00 0.00 0.00 4.26
2104 5162 1.846712 GCCCTCCTTCAGCCAGTCTT 61.847 60.000 0.00 0.00 0.00 3.01
2105 5163 0.695347 CCCTCCTTCAGCCAGTCTTT 59.305 55.000 0.00 0.00 0.00 2.52
2110 5168 3.740115 TCCTTCAGCCAGTCTTTTGTAC 58.260 45.455 0.00 0.00 0.00 2.90
2111 5169 3.391296 TCCTTCAGCCAGTCTTTTGTACT 59.609 43.478 0.00 0.00 0.00 2.73
2112 5170 4.591498 TCCTTCAGCCAGTCTTTTGTACTA 59.409 41.667 0.00 0.00 0.00 1.82
2114 5172 5.352569 CCTTCAGCCAGTCTTTTGTACTATG 59.647 44.000 0.00 0.00 0.00 2.23
2115 5173 5.483685 TCAGCCAGTCTTTTGTACTATGT 57.516 39.130 0.00 0.00 0.00 2.29
2117 5175 6.999950 TCAGCCAGTCTTTTGTACTATGTTA 58.000 36.000 0.00 0.00 0.00 2.41
2118 5176 7.446769 TCAGCCAGTCTTTTGTACTATGTTAA 58.553 34.615 0.00 0.00 0.00 2.01
2125 5186 9.099454 AGTCTTTTGTACTATGTTAATGCTAGC 57.901 33.333 8.10 8.10 0.00 3.42
2179 5243 0.107831 TTTCACCCCCTGTTCGTCTG 59.892 55.000 0.00 0.00 0.00 3.51
2199 5404 6.367422 CGTCTGTTCATCTTTTCTTAGCTTCT 59.633 38.462 0.00 0.00 0.00 2.85
2203 5408 9.392021 CTGTTCATCTTTTCTTAGCTTCTTTTC 57.608 33.333 0.00 0.00 0.00 2.29
2214 5427 2.081462 GCTTCTTTTCCCGGATCGAAA 58.919 47.619 0.73 0.74 0.00 3.46
2215 5428 2.683362 GCTTCTTTTCCCGGATCGAAAT 59.317 45.455 0.73 0.00 0.00 2.17
2219 5432 2.791347 TTTCCCGGATCGAAATGGAA 57.209 45.000 0.73 0.00 33.44 3.53
2327 5545 4.567959 GGTTAATGAATGTTTGGCATCTGC 59.432 41.667 0.00 0.00 36.67 4.26
2436 5669 1.671901 CTCGAGTGAAGGCCCTCCTC 61.672 65.000 3.62 4.44 43.40 3.71
2437 5670 2.726351 CGAGTGAAGGCCCTCCTCC 61.726 68.421 0.00 0.00 43.40 4.30
2438 5671 1.306568 GAGTGAAGGCCCTCCTCCT 60.307 63.158 0.00 0.00 43.40 3.69
2470 5703 4.021981 TCATCACCGATCCAGCTAGTAATG 60.022 45.833 0.00 0.00 0.00 1.90
2477 5713 4.378563 CGATCCAGCTAGTAATGGTAGTCG 60.379 50.000 9.65 12.41 37.84 4.18
2508 5942 4.748892 ACGCACGTACTCTACTCTAGTAA 58.251 43.478 0.00 0.00 31.48 2.24
2513 5947 7.358270 CGCACGTACTCTACTCTAGTAATAGTG 60.358 44.444 12.04 0.00 36.16 2.74
2514 5948 7.569226 GCACGTACTCTACTCTAGTAATAGTGC 60.569 44.444 16.45 16.45 42.83 4.40
2531 5965 0.674581 TGCTACCAGTGTGATGCTGC 60.675 55.000 0.00 0.00 32.93 5.25
2536 5970 0.604511 CCAGTGTGATGCTGCAGTGA 60.605 55.000 16.64 2.45 38.05 3.41
2551 5985 0.393077 AGTGACGAACTGACCAAGGG 59.607 55.000 0.00 0.00 37.88 3.95
2597 6032 1.702299 GAACGTGTCGAATCTGGCG 59.298 57.895 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.459237 CATCTGGCTCACTCACCGAC 60.459 60.000 0.00 0.00 0.00 4.79
32 33 1.137872 CTACCATCTGGCTCACTCACC 59.862 57.143 0.00 0.00 39.32 4.02
38 39 2.034878 CTAGCACTACCATCTGGCTCA 58.965 52.381 0.00 0.00 39.32 4.26
60 61 8.914011 GCAGGAATTAAAATGGGATTTACTACT 58.086 33.333 0.00 0.00 0.00 2.57
61 62 8.691797 TGCAGGAATTAAAATGGGATTTACTAC 58.308 33.333 0.00 0.00 0.00 2.73
62 63 8.830915 TGCAGGAATTAAAATGGGATTTACTA 57.169 30.769 0.00 0.00 0.00 1.82
63 64 7.732222 TGCAGGAATTAAAATGGGATTTACT 57.268 32.000 0.00 0.00 0.00 2.24
64 65 8.962884 AATGCAGGAATTAAAATGGGATTTAC 57.037 30.769 0.00 0.00 0.00 2.01
66 67 7.056006 GGAATGCAGGAATTAAAATGGGATTT 58.944 34.615 0.00 0.00 0.00 2.17
67 68 6.594744 GGAATGCAGGAATTAAAATGGGATT 58.405 36.000 0.00 0.00 0.00 3.01
68 69 5.221501 CGGAATGCAGGAATTAAAATGGGAT 60.222 40.000 0.00 0.00 0.00 3.85
69 70 4.099266 CGGAATGCAGGAATTAAAATGGGA 59.901 41.667 0.00 0.00 0.00 4.37
70 71 4.370917 CGGAATGCAGGAATTAAAATGGG 58.629 43.478 0.00 0.00 0.00 4.00
73 78 5.675684 AACCGGAATGCAGGAATTAAAAT 57.324 34.783 9.46 0.00 33.18 1.82
78 83 2.493278 CTCAAACCGGAATGCAGGAATT 59.507 45.455 9.46 0.00 33.18 2.17
79 84 2.094675 CTCAAACCGGAATGCAGGAAT 58.905 47.619 9.46 0.00 33.18 3.01
89 94 2.267642 CCCATCGCTCAAACCGGA 59.732 61.111 9.46 0.00 0.00 5.14
92 97 2.700773 GGCACCCATCGCTCAAACC 61.701 63.158 0.00 0.00 0.00 3.27
101 106 1.153349 GGAGTTCTCGGCACCCATC 60.153 63.158 0.00 0.00 0.00 3.51
103 108 1.701031 TTTGGAGTTCTCGGCACCCA 61.701 55.000 0.00 0.00 0.00 4.51
106 142 2.614057 CCATATTTGGAGTTCTCGGCAC 59.386 50.000 0.00 0.00 46.92 5.01
174 210 0.678048 GGAGGAAAGGCTGCGTGATT 60.678 55.000 0.00 0.00 0.00 2.57
180 216 2.436824 GGACGGAGGAAAGGCTGC 60.437 66.667 0.00 0.00 0.00 5.25
182 218 2.603776 ACGGACGGAGGAAAGGCT 60.604 61.111 0.00 0.00 0.00 4.58
184 220 1.982938 AGGACGGACGGAGGAAAGG 60.983 63.158 0.00 0.00 0.00 3.11
194 230 3.775654 CCAGGAGCCAGGACGGAC 61.776 72.222 0.00 0.00 36.56 4.79
535 3462 3.054878 CTGTTTACGGTACCACAGACAC 58.945 50.000 20.35 6.62 39.25 3.67
536 3463 2.957680 TCTGTTTACGGTACCACAGACA 59.042 45.455 22.54 14.49 40.56 3.41
537 3464 3.648339 TCTGTTTACGGTACCACAGAC 57.352 47.619 22.54 11.23 40.56 3.51
538 3465 4.322198 GGATTCTGTTTACGGTACCACAGA 60.322 45.833 22.54 22.54 43.08 3.41
539 3466 3.930848 GGATTCTGTTTACGGTACCACAG 59.069 47.826 19.38 19.38 38.42 3.66
540 3467 3.306919 GGGATTCTGTTTACGGTACCACA 60.307 47.826 13.54 7.67 0.00 4.17
572 3500 4.871557 CACAAATGCCATGGTTATCAAAGG 59.128 41.667 14.67 0.00 0.00 3.11
643 3587 1.024271 GCTTGTCAAGTTGAGTGGCA 58.976 50.000 14.03 0.00 0.00 4.92
689 3633 5.485708 TCCTTTCCTTTGGTTTCTTTTTCCA 59.514 36.000 0.00 0.00 0.00 3.53
734 3686 1.437986 GGGCTACTCTACTGTGGCG 59.562 63.158 0.00 0.00 43.87 5.69
752 3704 1.005924 AGTTTGGCTAACTGATGGGGG 59.994 52.381 13.46 0.00 45.33 5.40
753 3705 2.514458 AGTTTGGCTAACTGATGGGG 57.486 50.000 13.46 0.00 45.33 4.96
776 3739 0.036952 TGGAGTAGCAGCAGCAGTTC 60.037 55.000 3.17 0.00 45.49 3.01
796 3759 0.038159 AACGGACGCAGGAGAAGAAG 60.038 55.000 0.00 0.00 0.00 2.85
797 3760 0.319555 CAACGGACGCAGGAGAAGAA 60.320 55.000 0.00 0.00 0.00 2.52
838 3801 2.592308 GCCCAGGAGAAAGGCGAT 59.408 61.111 0.00 0.00 36.84 4.58
900 3871 2.428085 GGAGCGAGGAAGGGAGGTC 61.428 68.421 0.00 0.00 0.00 3.85
901 3872 2.364448 GGAGCGAGGAAGGGAGGT 60.364 66.667 0.00 0.00 0.00 3.85
907 3878 1.078143 CAAAGGGGGAGCGAGGAAG 60.078 63.158 0.00 0.00 0.00 3.46
908 3879 1.846124 ACAAAGGGGGAGCGAGGAA 60.846 57.895 0.00 0.00 0.00 3.36
909 3880 2.203938 ACAAAGGGGGAGCGAGGA 60.204 61.111 0.00 0.00 0.00 3.71
910 3881 2.045926 CACAAAGGGGGAGCGAGG 60.046 66.667 0.00 0.00 0.00 4.63
911 3882 1.915078 ATCCACAAAGGGGGAGCGAG 61.915 60.000 0.00 0.00 36.45 5.03
912 3883 0.619255 TATCCACAAAGGGGGAGCGA 60.619 55.000 0.00 0.00 36.45 4.93
913 3884 0.474184 ATATCCACAAAGGGGGAGCG 59.526 55.000 0.00 0.00 36.45 5.03
914 3885 3.876309 TTATATCCACAAAGGGGGAGC 57.124 47.619 0.00 0.00 36.45 4.70
967 3942 2.126502 GCGGCGTTGGATTTGTGG 60.127 61.111 9.37 0.00 0.00 4.17
968 3943 2.126502 GGCGGCGTTGGATTTGTG 60.127 61.111 9.37 0.00 0.00 3.33
969 3944 3.732892 CGGCGGCGTTGGATTTGT 61.733 61.111 24.74 0.00 0.00 2.83
1273 4258 4.828925 GAGGTGCGCTGAGGAGGC 62.829 72.222 9.73 0.00 0.00 4.70
1926 4980 1.461091 TAGCCGGGCGAATAGGAGTG 61.461 60.000 14.39 0.00 0.00 3.51
1961 5015 1.288127 GTACGTCGTGCTGAAGGGT 59.712 57.895 8.47 0.00 0.00 4.34
2085 5143 1.846712 AAGACTGGCTGAAGGAGGGC 61.847 60.000 0.00 0.00 0.00 5.19
2097 5155 8.268850 AGCATTAACATAGTACAAAAGACTGG 57.731 34.615 0.00 0.00 0.00 4.00
2104 5162 6.256975 CACCGCTAGCATTAACATAGTACAAA 59.743 38.462 16.45 0.00 0.00 2.83
2105 5163 5.751509 CACCGCTAGCATTAACATAGTACAA 59.248 40.000 16.45 0.00 0.00 2.41
2110 5168 3.430218 GCTCACCGCTAGCATTAACATAG 59.570 47.826 16.45 1.91 39.83 2.23
2111 5169 3.390135 GCTCACCGCTAGCATTAACATA 58.610 45.455 16.45 0.00 39.83 2.29
2112 5170 2.213499 GCTCACCGCTAGCATTAACAT 58.787 47.619 16.45 0.00 39.83 2.71
2179 5243 7.810282 GGGAAAAGAAGCTAAGAAAAGATGAAC 59.190 37.037 0.00 0.00 0.00 3.18
2199 5404 2.791347 TCCATTTCGATCCGGGAAAA 57.209 45.000 0.00 0.00 37.00 2.29
2203 5408 2.146342 CATCTTCCATTTCGATCCGGG 58.854 52.381 0.00 0.00 0.00 5.73
2214 5427 0.886490 GCGCCGATTCCATCTTCCAT 60.886 55.000 0.00 0.00 0.00 3.41
2215 5428 1.523711 GCGCCGATTCCATCTTCCA 60.524 57.895 0.00 0.00 0.00 3.53
2219 5432 2.109799 CTGGCGCCGATTCCATCT 59.890 61.111 23.90 0.00 0.00 2.90
2436 5669 3.819564 TCGGTGATGATGAAAGGTAGG 57.180 47.619 0.00 0.00 0.00 3.18
2437 5670 4.202253 TGGATCGGTGATGATGAAAGGTAG 60.202 45.833 0.00 0.00 0.00 3.18
2438 5671 3.709141 TGGATCGGTGATGATGAAAGGTA 59.291 43.478 0.00 0.00 0.00 3.08
2470 5703 0.735287 GCGTTGAGGTTCCGACTACC 60.735 60.000 0.00 0.00 35.85 3.18
2477 5713 0.319297 AGTACGTGCGTTGAGGTTCC 60.319 55.000 1.66 0.00 0.00 3.62
2508 5942 2.768527 AGCATCACACTGGTAGCACTAT 59.231 45.455 0.00 0.00 0.00 2.12
2513 5947 0.674581 TGCAGCATCACACTGGTAGC 60.675 55.000 0.00 0.00 35.62 3.58
2514 5948 1.338484 ACTGCAGCATCACACTGGTAG 60.338 52.381 15.27 0.00 35.62 3.18
2536 5970 1.052124 TCCACCCTTGGTCAGTTCGT 61.052 55.000 0.00 0.00 44.35 3.85
2551 5985 4.084013 CGATGGACTACACAAAGTTTCCAC 60.084 45.833 0.00 0.00 41.44 4.02
2597 6032 3.799420 GTCGAAACAGCTGATATCTCCAC 59.201 47.826 23.35 0.00 0.00 4.02
2683 6118 4.477975 CGACCTGACTCCGTCGGC 62.478 72.222 6.34 0.00 46.21 5.54


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

AutoCloner maintained by Alex Coulton.