Multiple sequence alignment - TraesCS5A01G430000

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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 TraesCS5A01G430000 chr5A 100.000 4832 0 0 1 4832 613968158 613972989 0.000000e+00 8924
1 TraesCS5A01G430000 chr5B 98.980 4708 43 2 125 4832 264914596 264919298 0.000000e+00 8423
2 TraesCS5A01G430000 chr5B 97.741 4737 71 6 125 4832 371292296 371297025 0.000000e+00 8122
3 TraesCS5A01G430000 chr2A 98.367 4716 71 3 118 4832 61495399 61500109 0.000000e+00 8277
4 TraesCS5A01G430000 chr2A 93.023 129 2 2 1 122 527971244 527971372 1.070000e-41 182
5 TraesCS5A01G430000 chr2A 93.443 122 7 1 1 122 54089713 54089833 3.840000e-41 180
6 TraesCS5A01G430000 chr6B 98.322 4708 72 4 125 4832 195188168 195192868 0.000000e+00 8250
7 TraesCS5A01G430000 chr6B 98.124 4744 53 24 119 4832 56428117 56432854 0.000000e+00 8235
8 TraesCS5A01G430000 chr6B 98.079 3905 67 2 125 4026 18581659 18577760 0.000000e+00 6789
9 TraesCS5A01G430000 chr6B 96.376 3836 125 9 122 3956 645758393 645762215 0.000000e+00 6301
10 TraesCS5A01G430000 chr6B 97.412 966 21 1 3867 4832 18577863 18576902 0.000000e+00 1642
11 TraesCS5A01G430000 chr3A 97.783 4737 71 3 125 4832 684729031 684724300 0.000000e+00 8135
12 TraesCS5A01G430000 chr4A 97.563 4432 92 5 401 4832 674547767 674543352 0.000000e+00 7572
13 TraesCS5A01G430000 chr4A 96.381 967 29 3 3867 4832 731443998 731444959 0.000000e+00 1587
14 TraesCS5A01G430000 chr4A 93.023 129 2 4 1 122 607600464 607600592 1.070000e-41 182
15 TraesCS5A01G430000 chr4A 92.913 127 4 2 1 122 310328489 310328363 3.840000e-41 180
16 TraesCS5A01G430000 chr7D 93.750 128 2 2 1 122 368622743 368622870 2.300000e-43 187
17 TraesCS5A01G430000 chr4D 93.701 127 3 2 1 122 337900807 337900933 8.260000e-43 185
18 TraesCS5A01G430000 chr4D 92.913 127 4 2 1 122 388627061 388626935 3.840000e-41 180
19 TraesCS5A01G430000 chr3B 94.262 122 6 1 1 122 548781472 548781592 8.260000e-43 185
20 TraesCS5A01G430000 chr6A 92.913 127 4 2 1 122 574784636 574784510 3.840000e-41 180


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 TraesCS5A01G430000 chr5A 613968158 613972989 4831 False 8924.0 8924 100.0000 1 4832 1 chr5A.!!$F1 4831
1 TraesCS5A01G430000 chr5B 264914596 264919298 4702 False 8423.0 8423 98.9800 125 4832 1 chr5B.!!$F1 4707
2 TraesCS5A01G430000 chr5B 371292296 371297025 4729 False 8122.0 8122 97.7410 125 4832 1 chr5B.!!$F2 4707
3 TraesCS5A01G430000 chr2A 61495399 61500109 4710 False 8277.0 8277 98.3670 118 4832 1 chr2A.!!$F2 4714
4 TraesCS5A01G430000 chr6B 195188168 195192868 4700 False 8250.0 8250 98.3220 125 4832 1 chr6B.!!$F2 4707
5 TraesCS5A01G430000 chr6B 56428117 56432854 4737 False 8235.0 8235 98.1240 119 4832 1 chr6B.!!$F1 4713
6 TraesCS5A01G430000 chr6B 645758393 645762215 3822 False 6301.0 6301 96.3760 122 3956 1 chr6B.!!$F3 3834
7 TraesCS5A01G430000 chr6B 18576902 18581659 4757 True 4215.5 6789 97.7455 125 4832 2 chr6B.!!$R1 4707
8 TraesCS5A01G430000 chr3A 684724300 684729031 4731 True 8135.0 8135 97.7830 125 4832 1 chr3A.!!$R1 4707
9 TraesCS5A01G430000 chr4A 674543352 674547767 4415 True 7572.0 7572 97.5630 401 4832 1 chr4A.!!$R2 4431
10 TraesCS5A01G430000 chr4A 731443998 731444959 961 False 1587.0 1587 96.3810 3867 4832 1 chr4A.!!$F2 965

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
35 36 0.034089 ACCCTTCCACCATTGCTAGC 60.034 55.000 8.10 8.1 0.00 3.42 F
69 70 0.035247 GTGCCGGTACCATAAACCCA 60.035 55.000 12.25 0.0 33.10 4.51 F
72 73 0.619505 CCGGTACCATAAACCCACCA 59.380 55.000 13.54 0.0 33.10 4.17 F
96 97 0.961753 CCTTCCTCAAAACAGCCACC 59.038 55.000 0.00 0.0 0.00 4.61 F
727 731 1.610673 GCTGTGGAGGAGGAGGTGA 60.611 63.158 0.00 0.0 0.00 4.02 F
1284 1288 1.764134 TGGTTGTCCCTGTTAAGACGT 59.236 47.619 0.00 0.0 35.71 4.34 F
1395 1399 2.113774 CAGGGCAGTGAAGTGGCA 59.886 61.111 13.07 0.0 44.72 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1288 0.108329 GGATTCTTCGGTCTCGGCAA 60.108 55.000 0.00 0.00 36.95 4.52 R
1395 1399 3.275999 CCCGGATAAAACAATCTCGGTT 58.724 45.455 0.73 0.00 37.70 4.44 R
2636 2640 4.017130 AGAAAGAATTAGCCCCAAGATGGT 60.017 41.667 0.00 0.00 35.17 3.55 R
2654 2658 5.269313 GCTTGTTCTTGAACTGTGAGAAAG 58.731 41.667 13.65 8.45 31.79 2.62 R
3059 3063 4.040461 GGAATACAGCCTCCACAATAGCTA 59.960 45.833 0.00 0.00 33.33 3.32 R
3720 3724 0.317160 TCGATGTGGAAGCACTCGTT 59.683 50.000 0.00 0.00 32.13 3.85 R
4320 4548 2.344592 TCCAATGTACCCTCAACCAGT 58.655 47.619 0.00 0.00 0.00 4.00 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
21 22 4.323553 GATTATACGCACTCTCACCCTT 57.676 45.455 0.00 0.00 0.00 3.95
22 23 3.795623 TTATACGCACTCTCACCCTTC 57.204 47.619 0.00 0.00 0.00 3.46
23 24 0.824759 ATACGCACTCTCACCCTTCC 59.175 55.000 0.00 0.00 0.00 3.46
24 25 0.541063 TACGCACTCTCACCCTTCCA 60.541 55.000 0.00 0.00 0.00 3.53
25 26 1.374758 CGCACTCTCACCCTTCCAC 60.375 63.158 0.00 0.00 0.00 4.02
26 27 1.003233 GCACTCTCACCCTTCCACC 60.003 63.158 0.00 0.00 0.00 4.61
27 28 1.768684 GCACTCTCACCCTTCCACCA 61.769 60.000 0.00 0.00 0.00 4.17
28 29 0.987294 CACTCTCACCCTTCCACCAT 59.013 55.000 0.00 0.00 0.00 3.55
29 30 1.352352 CACTCTCACCCTTCCACCATT 59.648 52.381 0.00 0.00 0.00 3.16
30 31 1.352352 ACTCTCACCCTTCCACCATTG 59.648 52.381 0.00 0.00 0.00 2.82
31 32 0.038166 TCTCACCCTTCCACCATTGC 59.962 55.000 0.00 0.00 0.00 3.56
32 33 0.038744 CTCACCCTTCCACCATTGCT 59.961 55.000 0.00 0.00 0.00 3.91
33 34 1.281867 CTCACCCTTCCACCATTGCTA 59.718 52.381 0.00 0.00 0.00 3.49
34 35 1.281867 TCACCCTTCCACCATTGCTAG 59.718 52.381 0.00 0.00 0.00 3.42
35 36 0.034089 ACCCTTCCACCATTGCTAGC 60.034 55.000 8.10 8.10 0.00 3.42
36 37 0.753111 CCCTTCCACCATTGCTAGCC 60.753 60.000 13.29 0.00 0.00 3.93
37 38 0.257039 CCTTCCACCATTGCTAGCCT 59.743 55.000 13.29 0.00 0.00 4.58
38 39 1.490490 CCTTCCACCATTGCTAGCCTA 59.510 52.381 13.29 0.00 0.00 3.93
39 40 2.107204 CCTTCCACCATTGCTAGCCTAT 59.893 50.000 13.29 2.70 0.00 2.57
40 41 3.406764 CTTCCACCATTGCTAGCCTATC 58.593 50.000 13.29 0.00 0.00 2.08
41 42 2.694397 TCCACCATTGCTAGCCTATCT 58.306 47.619 13.29 0.00 0.00 1.98
42 43 3.856900 TCCACCATTGCTAGCCTATCTA 58.143 45.455 13.29 0.00 0.00 1.98
43 44 3.834813 TCCACCATTGCTAGCCTATCTAG 59.165 47.826 13.29 0.00 46.01 2.43
44 45 3.580458 CCACCATTGCTAGCCTATCTAGT 59.420 47.826 13.29 0.00 45.22 2.57
45 46 4.772624 CCACCATTGCTAGCCTATCTAGTA 59.227 45.833 13.29 0.00 45.22 1.82
46 47 5.336849 CCACCATTGCTAGCCTATCTAGTAC 60.337 48.000 13.29 0.00 45.22 2.73
47 48 4.773149 ACCATTGCTAGCCTATCTAGTACC 59.227 45.833 13.29 0.00 45.22 3.34
48 49 4.142359 CCATTGCTAGCCTATCTAGTACCG 60.142 50.000 13.29 0.00 45.22 4.02
49 50 2.434428 TGCTAGCCTATCTAGTACCGC 58.566 52.381 13.29 0.00 45.22 5.68
50 51 1.397692 GCTAGCCTATCTAGTACCGCG 59.602 57.143 2.29 0.00 45.22 6.46
51 52 2.697654 CTAGCCTATCTAGTACCGCGT 58.302 52.381 4.92 0.00 39.91 6.01
52 53 1.236628 AGCCTATCTAGTACCGCGTG 58.763 55.000 4.92 0.00 0.00 5.34
53 54 0.386985 GCCTATCTAGTACCGCGTGC 60.387 60.000 4.92 0.00 0.00 5.34
54 55 0.240411 CCTATCTAGTACCGCGTGCC 59.760 60.000 4.92 0.00 0.00 5.01
55 56 0.110328 CTATCTAGTACCGCGTGCCG 60.110 60.000 4.92 0.00 0.00 5.69
64 65 2.202770 CGCGTGCCGGTACCATAA 60.203 61.111 17.62 0.00 0.00 1.90
65 66 1.810441 CGCGTGCCGGTACCATAAA 60.810 57.895 17.62 0.00 0.00 1.40
66 67 1.717348 GCGTGCCGGTACCATAAAC 59.283 57.895 17.62 3.42 0.00 2.01
67 68 1.708193 GCGTGCCGGTACCATAAACC 61.708 60.000 17.62 0.00 0.00 3.27
68 69 1.091197 CGTGCCGGTACCATAAACCC 61.091 60.000 17.62 0.00 33.10 4.11
69 70 0.035247 GTGCCGGTACCATAAACCCA 60.035 55.000 12.25 0.00 33.10 4.51
70 71 0.035247 TGCCGGTACCATAAACCCAC 60.035 55.000 13.54 0.00 33.10 4.61
71 72 0.749091 GCCGGTACCATAAACCCACC 60.749 60.000 13.54 0.00 33.10 4.61
72 73 0.619505 CCGGTACCATAAACCCACCA 59.380 55.000 13.54 0.00 33.10 4.17
73 74 1.213430 CCGGTACCATAAACCCACCAT 59.787 52.381 13.54 0.00 33.10 3.55
74 75 2.357361 CCGGTACCATAAACCCACCATT 60.357 50.000 13.54 0.00 33.10 3.16
75 76 3.358118 CGGTACCATAAACCCACCATTT 58.642 45.455 13.54 0.00 33.10 2.32
76 77 4.525024 CGGTACCATAAACCCACCATTTA 58.475 43.478 13.54 0.00 33.10 1.40
77 78 4.336153 CGGTACCATAAACCCACCATTTAC 59.664 45.833 13.54 0.00 33.10 2.01
78 79 4.646040 GGTACCATAAACCCACCATTTACC 59.354 45.833 7.15 0.00 0.00 2.85
79 80 4.685513 ACCATAAACCCACCATTTACCT 57.314 40.909 0.00 0.00 0.00 3.08
80 81 5.018374 ACCATAAACCCACCATTTACCTT 57.982 39.130 0.00 0.00 0.00 3.50
81 82 5.020795 ACCATAAACCCACCATTTACCTTC 58.979 41.667 0.00 0.00 0.00 3.46
82 83 4.404394 CCATAAACCCACCATTTACCTTCC 59.596 45.833 0.00 0.00 0.00 3.46
83 84 3.915346 AAACCCACCATTTACCTTCCT 57.085 42.857 0.00 0.00 0.00 3.36
84 85 3.451402 AACCCACCATTTACCTTCCTC 57.549 47.619 0.00 0.00 0.00 3.71
85 86 2.354328 ACCCACCATTTACCTTCCTCA 58.646 47.619 0.00 0.00 0.00 3.86
86 87 2.719705 ACCCACCATTTACCTTCCTCAA 59.280 45.455 0.00 0.00 0.00 3.02
87 88 3.141272 ACCCACCATTTACCTTCCTCAAA 59.859 43.478 0.00 0.00 0.00 2.69
88 89 4.156477 CCCACCATTTACCTTCCTCAAAA 58.844 43.478 0.00 0.00 0.00 2.44
89 90 4.021456 CCCACCATTTACCTTCCTCAAAAC 60.021 45.833 0.00 0.00 0.00 2.43
90 91 4.586841 CCACCATTTACCTTCCTCAAAACA 59.413 41.667 0.00 0.00 0.00 2.83
91 92 5.278957 CCACCATTTACCTTCCTCAAAACAG 60.279 44.000 0.00 0.00 0.00 3.16
92 93 4.280929 ACCATTTACCTTCCTCAAAACAGC 59.719 41.667 0.00 0.00 0.00 4.40
93 94 4.321974 CCATTTACCTTCCTCAAAACAGCC 60.322 45.833 0.00 0.00 0.00 4.85
94 95 3.586470 TTACCTTCCTCAAAACAGCCA 57.414 42.857 0.00 0.00 0.00 4.75
95 96 1.692411 ACCTTCCTCAAAACAGCCAC 58.308 50.000 0.00 0.00 0.00 5.01
96 97 0.961753 CCTTCCTCAAAACAGCCACC 59.038 55.000 0.00 0.00 0.00 4.61
97 98 1.691196 CTTCCTCAAAACAGCCACCA 58.309 50.000 0.00 0.00 0.00 4.17
98 99 2.242043 CTTCCTCAAAACAGCCACCAT 58.758 47.619 0.00 0.00 0.00 3.55
99 100 3.420893 CTTCCTCAAAACAGCCACCATA 58.579 45.455 0.00 0.00 0.00 2.74
100 101 2.790433 TCCTCAAAACAGCCACCATAC 58.210 47.619 0.00 0.00 0.00 2.39
101 102 1.818674 CCTCAAAACAGCCACCATACC 59.181 52.381 0.00 0.00 0.00 2.73
102 103 2.555227 CCTCAAAACAGCCACCATACCT 60.555 50.000 0.00 0.00 0.00 3.08
103 104 3.308117 CCTCAAAACAGCCACCATACCTA 60.308 47.826 0.00 0.00 0.00 3.08
104 105 3.681593 TCAAAACAGCCACCATACCTAC 58.318 45.455 0.00 0.00 0.00 3.18
105 106 2.752903 CAAAACAGCCACCATACCTACC 59.247 50.000 0.00 0.00 0.00 3.18
106 107 1.966845 AACAGCCACCATACCTACCT 58.033 50.000 0.00 0.00 0.00 3.08
107 108 2.860817 ACAGCCACCATACCTACCTA 57.139 50.000 0.00 0.00 0.00 3.08
108 109 3.346146 ACAGCCACCATACCTACCTAT 57.654 47.619 0.00 0.00 0.00 2.57
109 110 3.665443 ACAGCCACCATACCTACCTATT 58.335 45.455 0.00 0.00 0.00 1.73
110 111 4.823107 ACAGCCACCATACCTACCTATTA 58.177 43.478 0.00 0.00 0.00 0.98
111 112 5.412384 ACAGCCACCATACCTACCTATTAT 58.588 41.667 0.00 0.00 0.00 1.28
112 113 5.248477 ACAGCCACCATACCTACCTATTATG 59.752 44.000 0.00 0.00 0.00 1.90
113 114 4.783227 AGCCACCATACCTACCTATTATGG 59.217 45.833 5.49 5.49 45.42 2.74
114 115 4.781087 GCCACCATACCTACCTATTATGGA 59.219 45.833 12.71 0.00 43.49 3.41
115 116 5.249852 GCCACCATACCTACCTATTATGGAA 59.750 44.000 12.71 0.00 43.49 3.53
116 117 6.069615 GCCACCATACCTACCTATTATGGAAT 60.070 42.308 12.71 0.00 43.49 3.01
117 118 7.530584 GCCACCATACCTACCTATTATGGAATT 60.531 40.741 12.71 0.00 43.49 2.17
704 708 2.294078 GGTGGTGGTGAGGAGGAGG 61.294 68.421 0.00 0.00 0.00 4.30
727 731 1.610673 GCTGTGGAGGAGGAGGTGA 60.611 63.158 0.00 0.00 0.00 4.02
881 885 7.358352 GGCGTCACAAATTTTCTCTAAATTGTG 60.358 37.037 9.51 9.51 43.84 3.33
1069 1073 6.479001 CGTTCGATATAATGAGTTGGGAGTTT 59.521 38.462 0.00 0.00 0.00 2.66
1284 1288 1.764134 TGGTTGTCCCTGTTAAGACGT 59.236 47.619 0.00 0.00 35.71 4.34
1395 1399 2.113774 CAGGGCAGTGAAGTGGCA 59.886 61.111 13.07 0.00 44.72 4.92
3059 3063 3.484407 GGAATAGAGCATTGCCACTCAT 58.516 45.455 4.70 0.00 35.28 2.90
4264 4492 6.288294 TGACATACTTTTCATAGCCGCTAAT 58.712 36.000 3.73 0.00 0.00 1.73
4265 4493 6.765989 TGACATACTTTTCATAGCCGCTAATT 59.234 34.615 3.73 0.00 0.00 1.40
4266 4494 7.929245 TGACATACTTTTCATAGCCGCTAATTA 59.071 33.333 3.73 0.00 0.00 1.40
4267 4495 8.671384 ACATACTTTTCATAGCCGCTAATTAA 57.329 30.769 3.73 0.00 0.00 1.40
4320 4548 0.606604 GACTTCTACCCTTGGCACGA 59.393 55.000 0.00 0.00 0.00 4.35
4413 4641 0.663153 ACAAGAGGCAAGTGAAACGC 59.337 50.000 0.00 0.00 45.86 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.299978 GAAGGGTGAGAGTGCGTATAATC 58.700 47.826 0.00 0.00 0.00 1.75
1 2 3.069729 GGAAGGGTGAGAGTGCGTATAAT 59.930 47.826 0.00 0.00 0.00 1.28
2 3 2.429610 GGAAGGGTGAGAGTGCGTATAA 59.570 50.000 0.00 0.00 0.00 0.98
7 8 1.374758 GTGGAAGGGTGAGAGTGCG 60.375 63.158 0.00 0.00 0.00 5.34
8 9 1.003233 GGTGGAAGGGTGAGAGTGC 60.003 63.158 0.00 0.00 0.00 4.40
9 10 0.987294 ATGGTGGAAGGGTGAGAGTG 59.013 55.000 0.00 0.00 0.00 3.51
10 11 1.352352 CAATGGTGGAAGGGTGAGAGT 59.648 52.381 0.00 0.00 0.00 3.24
11 12 1.952367 GCAATGGTGGAAGGGTGAGAG 60.952 57.143 0.00 0.00 0.00 3.20
12 13 0.038166 GCAATGGTGGAAGGGTGAGA 59.962 55.000 0.00 0.00 0.00 3.27
13 14 0.038744 AGCAATGGTGGAAGGGTGAG 59.961 55.000 0.00 0.00 0.00 3.51
14 15 1.281867 CTAGCAATGGTGGAAGGGTGA 59.718 52.381 0.00 0.00 0.00 4.02
15 16 1.755179 CTAGCAATGGTGGAAGGGTG 58.245 55.000 0.00 0.00 0.00 4.61
16 17 0.034089 GCTAGCAATGGTGGAAGGGT 60.034 55.000 10.63 0.00 0.00 4.34
17 18 0.753111 GGCTAGCAATGGTGGAAGGG 60.753 60.000 18.24 0.00 0.00 3.95
18 19 0.257039 AGGCTAGCAATGGTGGAAGG 59.743 55.000 18.24 0.00 0.00 3.46
19 20 3.072184 AGATAGGCTAGCAATGGTGGAAG 59.928 47.826 18.24 0.00 0.00 3.46
20 21 3.048600 AGATAGGCTAGCAATGGTGGAA 58.951 45.455 18.24 0.00 0.00 3.53
21 22 2.694397 AGATAGGCTAGCAATGGTGGA 58.306 47.619 18.24 0.00 0.00 4.02
22 23 4.199432 CTAGATAGGCTAGCAATGGTGG 57.801 50.000 18.24 0.00 40.15 4.61
32 33 2.420642 CACGCGGTACTAGATAGGCTA 58.579 52.381 12.47 0.00 0.00 3.93
33 34 1.236628 CACGCGGTACTAGATAGGCT 58.763 55.000 12.47 0.00 0.00 4.58
34 35 0.386985 GCACGCGGTACTAGATAGGC 60.387 60.000 12.47 0.00 0.00 3.93
35 36 0.240411 GGCACGCGGTACTAGATAGG 59.760 60.000 12.47 0.00 0.00 2.57
36 37 3.769228 GGCACGCGGTACTAGATAG 57.231 57.895 12.47 0.00 0.00 2.08
50 51 0.035247 TGGGTTTATGGTACCGGCAC 60.035 55.000 7.57 0.00 36.49 5.01
51 52 0.035247 GTGGGTTTATGGTACCGGCA 60.035 55.000 7.57 0.00 36.49 5.69
52 53 0.749091 GGTGGGTTTATGGTACCGGC 60.749 60.000 7.57 0.00 36.49 6.13
53 54 0.619505 TGGTGGGTTTATGGTACCGG 59.380 55.000 7.57 0.00 36.49 5.28
54 55 2.721425 ATGGTGGGTTTATGGTACCG 57.279 50.000 7.57 0.00 36.49 4.02
55 56 4.646040 GGTAAATGGTGGGTTTATGGTACC 59.354 45.833 4.43 4.43 34.82 3.34
56 57 5.512298 AGGTAAATGGTGGGTTTATGGTAC 58.488 41.667 0.00 0.00 0.00 3.34
57 58 5.799978 AGGTAAATGGTGGGTTTATGGTA 57.200 39.130 0.00 0.00 0.00 3.25
58 59 4.685513 AGGTAAATGGTGGGTTTATGGT 57.314 40.909 0.00 0.00 0.00 3.55
59 60 4.404394 GGAAGGTAAATGGTGGGTTTATGG 59.596 45.833 0.00 0.00 0.00 2.74
60 61 5.269189 AGGAAGGTAAATGGTGGGTTTATG 58.731 41.667 0.00 0.00 0.00 1.90
61 62 5.015817 TGAGGAAGGTAAATGGTGGGTTTAT 59.984 40.000 0.00 0.00 0.00 1.40
62 63 4.354387 TGAGGAAGGTAAATGGTGGGTTTA 59.646 41.667 0.00 0.00 0.00 2.01
63 64 3.141272 TGAGGAAGGTAAATGGTGGGTTT 59.859 43.478 0.00 0.00 0.00 3.27
64 65 2.719705 TGAGGAAGGTAAATGGTGGGTT 59.280 45.455 0.00 0.00 0.00 4.11
65 66 2.354328 TGAGGAAGGTAAATGGTGGGT 58.646 47.619 0.00 0.00 0.00 4.51
66 67 3.449746 TTGAGGAAGGTAAATGGTGGG 57.550 47.619 0.00 0.00 0.00 4.61
67 68 4.586841 TGTTTTGAGGAAGGTAAATGGTGG 59.413 41.667 0.00 0.00 0.00 4.61
68 69 5.772521 CTGTTTTGAGGAAGGTAAATGGTG 58.227 41.667 0.00 0.00 0.00 4.17
69 70 4.280929 GCTGTTTTGAGGAAGGTAAATGGT 59.719 41.667 0.00 0.00 0.00 3.55
70 71 4.321974 GGCTGTTTTGAGGAAGGTAAATGG 60.322 45.833 0.00 0.00 0.00 3.16
71 72 4.280677 TGGCTGTTTTGAGGAAGGTAAATG 59.719 41.667 0.00 0.00 0.00 2.32
72 73 4.280929 GTGGCTGTTTTGAGGAAGGTAAAT 59.719 41.667 0.00 0.00 0.00 1.40
73 74 3.634910 GTGGCTGTTTTGAGGAAGGTAAA 59.365 43.478 0.00 0.00 0.00 2.01
74 75 3.219281 GTGGCTGTTTTGAGGAAGGTAA 58.781 45.455 0.00 0.00 0.00 2.85
75 76 2.488347 GGTGGCTGTTTTGAGGAAGGTA 60.488 50.000 0.00 0.00 0.00 3.08
76 77 1.692411 GTGGCTGTTTTGAGGAAGGT 58.308 50.000 0.00 0.00 0.00 3.50
77 78 0.961753 GGTGGCTGTTTTGAGGAAGG 59.038 55.000 0.00 0.00 0.00 3.46
78 79 1.691196 TGGTGGCTGTTTTGAGGAAG 58.309 50.000 0.00 0.00 0.00 3.46
79 80 2.380064 ATGGTGGCTGTTTTGAGGAA 57.620 45.000 0.00 0.00 0.00 3.36
80 81 2.554344 GGTATGGTGGCTGTTTTGAGGA 60.554 50.000 0.00 0.00 0.00 3.71
81 82 1.818674 GGTATGGTGGCTGTTTTGAGG 59.181 52.381 0.00 0.00 0.00 3.86
82 83 2.795329 AGGTATGGTGGCTGTTTTGAG 58.205 47.619 0.00 0.00 0.00 3.02
83 84 2.969821 AGGTATGGTGGCTGTTTTGA 57.030 45.000 0.00 0.00 0.00 2.69
84 85 2.752903 GGTAGGTATGGTGGCTGTTTTG 59.247 50.000 0.00 0.00 0.00 2.44
85 86 2.647802 AGGTAGGTATGGTGGCTGTTTT 59.352 45.455 0.00 0.00 0.00 2.43
86 87 2.275466 AGGTAGGTATGGTGGCTGTTT 58.725 47.619 0.00 0.00 0.00 2.83
87 88 1.966845 AGGTAGGTATGGTGGCTGTT 58.033 50.000 0.00 0.00 0.00 3.16
88 89 2.860817 TAGGTAGGTATGGTGGCTGT 57.139 50.000 0.00 0.00 0.00 4.40
89 90 5.338381 CCATAATAGGTAGGTATGGTGGCTG 60.338 48.000 0.00 0.00 39.55 4.85
90 91 4.783227 CCATAATAGGTAGGTATGGTGGCT 59.217 45.833 0.00 0.00 39.55 4.75
91 92 4.781087 TCCATAATAGGTAGGTATGGTGGC 59.219 45.833 8.40 0.00 43.23 5.01
92 93 6.945636 TTCCATAATAGGTAGGTATGGTGG 57.054 41.667 8.40 0.00 43.23 4.61
93 94 9.449719 GAAATTCCATAATAGGTAGGTATGGTG 57.550 37.037 8.40 0.00 43.23 4.17
94 95 8.612145 GGAAATTCCATAATAGGTAGGTATGGT 58.388 37.037 7.23 0.00 43.23 3.55
95 96 8.611257 TGGAAATTCCATAATAGGTAGGTATGG 58.389 37.037 11.23 3.05 42.67 2.74
704 708 1.958902 CTCCTCCTCCACAGCTGCTC 61.959 65.000 15.27 0.00 0.00 4.26
727 731 2.909577 GCTGCTGCTCCTCCTCAT 59.090 61.111 8.53 0.00 36.03 2.90
904 908 3.462021 GCTAAAATGCCACCACAAACAA 58.538 40.909 0.00 0.00 0.00 2.83
1033 1037 3.795623 ATATCGAACGTTACCAGCACT 57.204 42.857 0.00 0.00 0.00 4.40
1035 1039 5.834169 TCATTATATCGAACGTTACCAGCA 58.166 37.500 0.00 0.00 0.00 4.41
1069 1073 6.314400 ACGCCATTTTTAAACTCGCTAAGATA 59.686 34.615 0.00 0.00 0.00 1.98
1284 1288 0.108329 GGATTCTTCGGTCTCGGCAA 60.108 55.000 0.00 0.00 36.95 4.52
1395 1399 3.275999 CCCGGATAAAACAATCTCGGTT 58.724 45.455 0.73 0.00 37.70 4.44
2636 2640 4.017130 AGAAAGAATTAGCCCCAAGATGGT 60.017 41.667 0.00 0.00 35.17 3.55
2654 2658 5.269313 GCTTGTTCTTGAACTGTGAGAAAG 58.731 41.667 13.65 8.45 31.79 2.62
3059 3063 4.040461 GGAATACAGCCTCCACAATAGCTA 59.960 45.833 0.00 0.00 33.33 3.32
3720 3724 0.317160 TCGATGTGGAAGCACTCGTT 59.683 50.000 0.00 0.00 32.13 3.85
4320 4548 2.344592 TCCAATGTACCCTCAACCAGT 58.655 47.619 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.