Multiple sequence alignment - TraesCS3A01G362400

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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 TraesCS3A01G362400 chr3A 100.000 3445 0 0 1 3445 610424498 610421054 0.000000e+00 6362
1 TraesCS3A01G362400 chr7B 99.207 3280 25 1 167 3445 204002752 204006031 0.000000e+00 5912
2 TraesCS3A01G362400 chr3B 99.207 3280 25 1 167 3445 829116457 829119736 0.000000e+00 5912
3 TraesCS3A01G362400 chr3B 99.085 3278 29 1 169 3445 813958507 813955230 0.000000e+00 5886
4 TraesCS3A01G362400 chr3B 95.783 166 7 0 1 166 622085401 622085236 5.670000e-68 268
5 TraesCS3A01G362400 chr2A 98.933 3280 34 1 167 3445 713923488 713926767 0.000000e+00 5862
6 TraesCS3A01G362400 chr2A 98.784 2631 31 1 816 3445 39363907 39361277 0.000000e+00 4680
7 TraesCS3A01G362400 chr2A 98.561 556 8 0 167 722 39364444 39363889 0.000000e+00 983
8 TraesCS3A01G362400 chr4A 98.567 3280 45 2 167 3445 586088078 586084800 0.000000e+00 5795
9 TraesCS3A01G362400 chr7D 97.312 3051 79 3 397 3445 237548459 237551508 0.000000e+00 5177
10 TraesCS3A01G362400 chr7D 96.825 189 6 0 167 355 237548280 237548468 2.000000e-82 316
11 TraesCS3A01G362400 chr5B 98.138 2524 45 2 924 3445 599616903 599614380 0.000000e+00 4399
12 TraesCS3A01G362400 chr5B 93.953 215 9 2 167 377 531864097 531864311 4.290000e-84 322
13 TraesCS3A01G362400 chr5B 91.781 73 6 0 858 930 531864453 531864525 6.080000e-18 102
14 TraesCS3A01G362400 chr3D 95.197 2519 119 2 929 3445 511280668 511278150 0.000000e+00 3980
15 TraesCS3A01G362400 chr3D 93.953 215 9 2 167 377 511281794 511281580 4.290000e-84 322
16 TraesCS3A01G362400 chr3D 95.181 166 8 0 1 166 467777579 467777414 2.640000e-66 263


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 TraesCS3A01G362400 chr3A 610421054 610424498 3444 True 6362.0 6362 100.0000 1 3445 1 chr3A.!!$R1 3444
1 TraesCS3A01G362400 chr7B 204002752 204006031 3279 False 5912.0 5912 99.2070 167 3445 1 chr7B.!!$F1 3278
2 TraesCS3A01G362400 chr3B 829116457 829119736 3279 False 5912.0 5912 99.2070 167 3445 1 chr3B.!!$F1 3278
3 TraesCS3A01G362400 chr3B 813955230 813958507 3277 True 5886.0 5886 99.0850 169 3445 1 chr3B.!!$R2 3276
4 TraesCS3A01G362400 chr2A 713923488 713926767 3279 False 5862.0 5862 98.9330 167 3445 1 chr2A.!!$F1 3278
5 TraesCS3A01G362400 chr2A 39361277 39364444 3167 True 2831.5 4680 98.6725 167 3445 2 chr2A.!!$R1 3278
6 TraesCS3A01G362400 chr4A 586084800 586088078 3278 True 5795.0 5795 98.5670 167 3445 1 chr4A.!!$R1 3278
7 TraesCS3A01G362400 chr7D 237548280 237551508 3228 False 2746.5 5177 97.0685 167 3445 2 chr7D.!!$F1 3278
8 TraesCS3A01G362400 chr5B 599614380 599616903 2523 True 4399.0 4399 98.1380 924 3445 1 chr5B.!!$R1 2521
9 TraesCS3A01G362400 chr3D 511278150 511281794 3644 True 2151.0 3980 94.5750 167 3445 2 chr3D.!!$R2 3278

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
102 103 1.197721 GGTCATTTGACAGCTCAACCG 59.802 52.381 12.43 0.0 46.47 4.44 F
111 112 1.831106 ACAGCTCAACCGATACATCCA 59.169 47.619 0.00 0.0 0.00 3.41 F
112 113 2.236146 ACAGCTCAACCGATACATCCAA 59.764 45.455 0.00 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 2322 0.035317 TCTCACCGCAGTTGAAGCAT 59.965 50.000 0.0 0.0 0.00 3.79 R
1913 2438 2.642171 TTGACCACCAGAGTATCCCT 57.358 50.000 0.0 0.0 33.66 4.20 R
2890 3415 6.438741 GTCCCATTATCTGTCCTGATCATCTA 59.561 42.308 0.0 0.0 0.00 1.98 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
24 25 5.476091 AACTCTCCTTACTTCACTCAAGG 57.524 43.478 0.00 0.00 40.23 3.61
25 26 3.259625 ACTCTCCTTACTTCACTCAAGGC 59.740 47.826 0.00 0.00 38.98 4.35
26 27 3.239449 TCTCCTTACTTCACTCAAGGCA 58.761 45.455 0.00 0.00 38.98 4.75
27 28 3.840666 TCTCCTTACTTCACTCAAGGCAT 59.159 43.478 0.00 0.00 38.98 4.40
28 29 4.287067 TCTCCTTACTTCACTCAAGGCATT 59.713 41.667 0.00 0.00 38.98 3.56
29 30 4.985538 TCCTTACTTCACTCAAGGCATTT 58.014 39.130 0.00 0.00 38.98 2.32
30 31 6.013725 TCTCCTTACTTCACTCAAGGCATTTA 60.014 38.462 0.00 0.00 38.98 1.40
31 32 6.721318 TCCTTACTTCACTCAAGGCATTTAT 58.279 36.000 0.00 0.00 38.98 1.40
32 33 7.175104 TCCTTACTTCACTCAAGGCATTTATT 58.825 34.615 0.00 0.00 38.98 1.40
33 34 7.336931 TCCTTACTTCACTCAAGGCATTTATTC 59.663 37.037 0.00 0.00 38.98 1.75
34 35 7.337942 CCTTACTTCACTCAAGGCATTTATTCT 59.662 37.037 0.00 0.00 36.26 2.40
35 36 8.635765 TTACTTCACTCAAGGCATTTATTCTT 57.364 30.769 0.00 0.00 36.26 2.52
36 37 7.530426 ACTTCACTCAAGGCATTTATTCTTT 57.470 32.000 0.00 0.00 36.26 2.52
37 38 7.955918 ACTTCACTCAAGGCATTTATTCTTTT 58.044 30.769 0.00 0.00 36.26 2.27
38 39 7.869429 ACTTCACTCAAGGCATTTATTCTTTTG 59.131 33.333 0.00 0.00 36.26 2.44
39 40 7.523293 TCACTCAAGGCATTTATTCTTTTGA 57.477 32.000 0.00 0.00 0.00 2.69
40 41 7.370383 TCACTCAAGGCATTTATTCTTTTGAC 58.630 34.615 0.00 0.00 0.00 3.18
41 42 7.231317 TCACTCAAGGCATTTATTCTTTTGACT 59.769 33.333 0.00 0.00 0.00 3.41
42 43 7.540055 CACTCAAGGCATTTATTCTTTTGACTC 59.460 37.037 0.00 0.00 0.00 3.36
43 44 7.449704 ACTCAAGGCATTTATTCTTTTGACTCT 59.550 33.333 0.00 0.00 0.00 3.24
44 45 7.820648 TCAAGGCATTTATTCTTTTGACTCTC 58.179 34.615 0.00 0.00 0.00 3.20
45 46 7.448161 TCAAGGCATTTATTCTTTTGACTCTCA 59.552 33.333 0.00 0.00 0.00 3.27
46 47 7.765695 AGGCATTTATTCTTTTGACTCTCAA 57.234 32.000 0.00 0.00 34.03 3.02
47 48 7.824672 AGGCATTTATTCTTTTGACTCTCAAG 58.175 34.615 0.00 0.00 37.70 3.02
48 49 7.031975 GGCATTTATTCTTTTGACTCTCAAGG 58.968 38.462 0.00 0.00 37.70 3.61
49 50 6.529477 GCATTTATTCTTTTGACTCTCAAGGC 59.471 38.462 0.00 0.00 37.70 4.35
50 51 7.576477 GCATTTATTCTTTTGACTCTCAAGGCT 60.576 37.037 0.00 0.00 37.70 4.58
51 52 7.823745 TTTATTCTTTTGACTCTCAAGGCTT 57.176 32.000 0.00 0.00 37.70 4.35
52 53 5.702349 ATTCTTTTGACTCTCAAGGCTTG 57.298 39.130 21.17 21.17 37.70 4.01
53 54 2.880890 TCTTTTGACTCTCAAGGCTTGC 59.119 45.455 22.31 8.51 37.70 4.01
54 55 2.645838 TTTGACTCTCAAGGCTTGCT 57.354 45.000 22.31 4.43 37.70 3.91
55 56 2.645838 TTGACTCTCAAGGCTTGCTT 57.354 45.000 22.31 5.94 31.83 3.91
56 57 2.175878 TGACTCTCAAGGCTTGCTTC 57.824 50.000 22.31 14.45 0.00 3.86
57 58 1.696336 TGACTCTCAAGGCTTGCTTCT 59.304 47.619 22.31 4.79 0.00 2.85
58 59 2.105477 TGACTCTCAAGGCTTGCTTCTT 59.895 45.455 22.31 5.22 0.00 2.52
59 60 3.145286 GACTCTCAAGGCTTGCTTCTTT 58.855 45.455 22.31 4.15 0.00 2.52
60 61 3.560105 ACTCTCAAGGCTTGCTTCTTTT 58.440 40.909 22.31 0.00 0.00 2.27
61 62 3.956848 ACTCTCAAGGCTTGCTTCTTTTT 59.043 39.130 22.31 0.00 0.00 1.94
62 63 4.037327 ACTCTCAAGGCTTGCTTCTTTTTC 59.963 41.667 22.31 0.00 0.00 2.29
63 64 4.210331 TCTCAAGGCTTGCTTCTTTTTCT 58.790 39.130 22.31 0.00 0.00 2.52
64 65 4.646492 TCTCAAGGCTTGCTTCTTTTTCTT 59.354 37.500 22.31 0.00 0.00 2.52
65 66 4.685924 TCAAGGCTTGCTTCTTTTTCTTG 58.314 39.130 22.31 0.00 33.72 3.02
66 67 3.740631 AGGCTTGCTTCTTTTTCTTGG 57.259 42.857 0.00 0.00 0.00 3.61
67 68 3.033909 AGGCTTGCTTCTTTTTCTTGGT 58.966 40.909 0.00 0.00 0.00 3.67
68 69 3.452264 AGGCTTGCTTCTTTTTCTTGGTT 59.548 39.130 0.00 0.00 0.00 3.67
69 70 3.557185 GGCTTGCTTCTTTTTCTTGGTTG 59.443 43.478 0.00 0.00 0.00 3.77
70 71 4.183865 GCTTGCTTCTTTTTCTTGGTTGT 58.816 39.130 0.00 0.00 0.00 3.32
71 72 5.348164 GCTTGCTTCTTTTTCTTGGTTGTA 58.652 37.500 0.00 0.00 0.00 2.41
72 73 5.810074 GCTTGCTTCTTTTTCTTGGTTGTAA 59.190 36.000 0.00 0.00 0.00 2.41
73 74 6.019559 GCTTGCTTCTTTTTCTTGGTTGTAAG 60.020 38.462 0.00 0.00 0.00 2.34
74 75 5.901552 TGCTTCTTTTTCTTGGTTGTAAGG 58.098 37.500 0.00 0.00 0.00 2.69
75 76 5.163457 TGCTTCTTTTTCTTGGTTGTAAGGG 60.163 40.000 0.00 0.00 0.00 3.95
76 77 5.068591 GCTTCTTTTTCTTGGTTGTAAGGGA 59.931 40.000 0.00 0.00 0.00 4.20
77 78 6.709018 TTCTTTTTCTTGGTTGTAAGGGAG 57.291 37.500 0.00 0.00 0.00 4.30
78 79 5.762279 TCTTTTTCTTGGTTGTAAGGGAGT 58.238 37.500 0.00 0.00 0.00 3.85
79 80 5.826208 TCTTTTTCTTGGTTGTAAGGGAGTC 59.174 40.000 0.00 0.00 0.00 3.36
80 81 4.781775 TTTCTTGGTTGTAAGGGAGTCA 57.218 40.909 0.00 0.00 0.00 3.41
81 82 4.351874 TTCTTGGTTGTAAGGGAGTCAG 57.648 45.455 0.00 0.00 0.00 3.51
82 83 2.637872 TCTTGGTTGTAAGGGAGTCAGG 59.362 50.000 0.00 0.00 0.00 3.86
83 84 1.358152 TGGTTGTAAGGGAGTCAGGG 58.642 55.000 0.00 0.00 0.00 4.45
84 85 1.359168 GGTTGTAAGGGAGTCAGGGT 58.641 55.000 0.00 0.00 0.00 4.34
85 86 1.278413 GGTTGTAAGGGAGTCAGGGTC 59.722 57.143 0.00 0.00 0.00 4.46
86 87 1.975680 GTTGTAAGGGAGTCAGGGTCA 59.024 52.381 0.00 0.00 0.00 4.02
87 88 2.572104 GTTGTAAGGGAGTCAGGGTCAT 59.428 50.000 0.00 0.00 0.00 3.06
88 89 2.915869 TGTAAGGGAGTCAGGGTCATT 58.084 47.619 0.00 0.00 0.00 2.57
89 90 3.256704 TGTAAGGGAGTCAGGGTCATTT 58.743 45.455 0.00 0.00 0.00 2.32
90 91 2.887151 AAGGGAGTCAGGGTCATTTG 57.113 50.000 0.00 0.00 0.00 2.32
91 92 2.044793 AGGGAGTCAGGGTCATTTGA 57.955 50.000 0.00 0.00 0.00 2.69
92 93 1.630878 AGGGAGTCAGGGTCATTTGAC 59.369 52.381 1.99 1.99 43.08 3.18
93 94 1.351017 GGGAGTCAGGGTCATTTGACA 59.649 52.381 12.43 0.00 46.47 3.58
94 95 2.616510 GGGAGTCAGGGTCATTTGACAG 60.617 54.545 12.43 2.59 46.47 3.51
95 96 2.079925 GAGTCAGGGTCATTTGACAGC 58.920 52.381 12.43 0.00 46.47 4.40
96 97 1.701847 AGTCAGGGTCATTTGACAGCT 59.298 47.619 12.43 0.00 46.47 4.24
97 98 2.079925 GTCAGGGTCATTTGACAGCTC 58.920 52.381 12.43 0.11 46.47 4.09
98 99 1.699083 TCAGGGTCATTTGACAGCTCA 59.301 47.619 12.43 0.00 46.47 4.26
99 100 2.106338 TCAGGGTCATTTGACAGCTCAA 59.894 45.455 12.43 0.00 46.47 3.02
100 101 2.227388 CAGGGTCATTTGACAGCTCAAC 59.773 50.000 12.43 0.00 46.47 3.18
101 102 1.541588 GGGTCATTTGACAGCTCAACC 59.458 52.381 12.43 0.00 46.47 3.77
102 103 1.197721 GGTCATTTGACAGCTCAACCG 59.802 52.381 12.43 0.00 46.47 4.44
103 104 2.143122 GTCATTTGACAGCTCAACCGA 58.857 47.619 5.84 0.00 44.18 4.69
104 105 2.744202 GTCATTTGACAGCTCAACCGAT 59.256 45.455 5.84 0.00 44.18 4.18
105 106 3.932710 GTCATTTGACAGCTCAACCGATA 59.067 43.478 5.84 0.00 44.18 2.92
106 107 3.932710 TCATTTGACAGCTCAACCGATAC 59.067 43.478 0.00 0.00 36.06 2.24
107 108 3.394674 TTTGACAGCTCAACCGATACA 57.605 42.857 0.00 0.00 36.06 2.29
108 109 3.610040 TTGACAGCTCAACCGATACAT 57.390 42.857 0.00 0.00 31.00 2.29
109 110 3.165058 TGACAGCTCAACCGATACATC 57.835 47.619 0.00 0.00 0.00 3.06
110 111 2.159099 TGACAGCTCAACCGATACATCC 60.159 50.000 0.00 0.00 0.00 3.51
111 112 1.831106 ACAGCTCAACCGATACATCCA 59.169 47.619 0.00 0.00 0.00 3.41
112 113 2.236146 ACAGCTCAACCGATACATCCAA 59.764 45.455 0.00 0.00 0.00 3.53
113 114 3.270027 CAGCTCAACCGATACATCCAAA 58.730 45.455 0.00 0.00 0.00 3.28
114 115 3.879295 CAGCTCAACCGATACATCCAAAT 59.121 43.478 0.00 0.00 0.00 2.32
115 116 4.024556 CAGCTCAACCGATACATCCAAATC 60.025 45.833 0.00 0.00 0.00 2.17
116 117 3.876914 GCTCAACCGATACATCCAAATCA 59.123 43.478 0.00 0.00 0.00 2.57
117 118 4.260784 GCTCAACCGATACATCCAAATCAC 60.261 45.833 0.00 0.00 0.00 3.06
118 119 4.196193 TCAACCGATACATCCAAATCACC 58.804 43.478 0.00 0.00 0.00 4.02
119 120 4.080582 TCAACCGATACATCCAAATCACCT 60.081 41.667 0.00 0.00 0.00 4.00
120 121 3.808728 ACCGATACATCCAAATCACCTG 58.191 45.455 0.00 0.00 0.00 4.00
121 122 3.454447 ACCGATACATCCAAATCACCTGA 59.546 43.478 0.00 0.00 0.00 3.86
122 123 4.103153 ACCGATACATCCAAATCACCTGAT 59.897 41.667 0.00 0.00 36.07 2.90
123 124 5.065914 CCGATACATCCAAATCACCTGATT 58.934 41.667 0.00 0.00 45.91 2.57
138 139 8.712285 ATCACCTGATTTTGCATAAAGATTTG 57.288 30.769 0.00 0.00 0.00 2.32
139 140 7.894708 TCACCTGATTTTGCATAAAGATTTGA 58.105 30.769 0.00 0.00 0.00 2.69
140 141 8.533657 TCACCTGATTTTGCATAAAGATTTGAT 58.466 29.630 0.00 0.00 0.00 2.57
141 142 8.600625 CACCTGATTTTGCATAAAGATTTGATG 58.399 33.333 0.00 0.00 0.00 3.07
142 143 7.279313 ACCTGATTTTGCATAAAGATTTGATGC 59.721 33.333 4.50 4.50 45.02 3.91
146 147 7.280730 TTTTGCATAAAGATTTGATGCGAAG 57.719 32.000 11.70 0.00 45.87 3.79
147 148 6.310956 TTTTGCATAAAGATTTGATGCGAAGG 59.689 34.615 11.70 0.00 45.87 3.46
148 149 5.173774 GCATAAAGATTTGATGCGAAGGA 57.826 39.130 0.00 0.00 36.89 3.36
149 150 5.766222 GCATAAAGATTTGATGCGAAGGAT 58.234 37.500 0.00 0.00 45.36 3.24
158 159 2.514458 ATGCGAAGGATCCAAAAGGT 57.486 45.000 15.82 0.00 25.85 3.50
159 160 2.286365 TGCGAAGGATCCAAAAGGTT 57.714 45.000 15.82 0.00 0.00 3.50
160 161 2.593026 TGCGAAGGATCCAAAAGGTTT 58.407 42.857 15.82 0.00 0.00 3.27
161 162 2.295909 TGCGAAGGATCCAAAAGGTTTG 59.704 45.455 15.82 3.28 0.00 2.93
162 163 2.556622 GCGAAGGATCCAAAAGGTTTGA 59.443 45.455 15.82 0.00 0.00 2.69
163 164 3.611766 GCGAAGGATCCAAAAGGTTTGAC 60.612 47.826 15.82 0.00 0.00 3.18
164 165 3.568007 CGAAGGATCCAAAAGGTTTGACA 59.432 43.478 15.82 0.00 0.00 3.58
165 166 4.320494 CGAAGGATCCAAAAGGTTTGACAG 60.320 45.833 15.82 0.00 0.00 3.51
536 541 4.074526 GGCGGCACTGCTCTCTCA 62.075 66.667 3.07 0.00 34.52 3.27
538 543 2.653115 CGGCACTGCTCTCTCACA 59.347 61.111 0.00 0.00 0.00 3.58
1341 1866 3.907474 TGAACTCCTTGTCTCCAACCATA 59.093 43.478 0.00 0.00 0.00 2.74
1342 1867 4.349636 TGAACTCCTTGTCTCCAACCATAA 59.650 41.667 0.00 0.00 0.00 1.90
1778 2303 3.393609 TCTCATCCAGCCTTCATAGCAAT 59.606 43.478 0.00 0.00 0.00 3.56
1797 2322 5.300539 AGCAATCGACTATAAGAGCAGAGAA 59.699 40.000 0.00 0.00 0.00 2.87
2885 3410 9.605955 TTATGTGAAAAATCAGTTCAATACACG 57.394 29.630 0.00 0.00 36.77 4.49
2890 3415 9.173021 TGAAAAATCAGTTCAATACACGGATAT 57.827 29.630 0.00 0.00 32.13 1.63
2983 3508 6.437162 AGGTATATTGCACCAAACATCTTGTT 59.563 34.615 0.00 0.00 38.62 2.83
3102 3627 4.093743 TCTTGTGGAGTGAGGCTGTAATA 58.906 43.478 0.00 0.00 0.00 0.98
3337 3862 1.837051 TGTTGGAGTCCCAGCGAGT 60.837 57.895 6.74 0.00 45.47 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.292150 CCTTGAGTGAAGTAAGGAGAGTTTT 58.708 40.000 0.00 0.00 42.82 2.43
1 2 5.743422 GCCTTGAGTGAAGTAAGGAGAGTTT 60.743 44.000 6.44 0.00 42.82 2.66
2 3 4.262678 GCCTTGAGTGAAGTAAGGAGAGTT 60.263 45.833 6.44 0.00 42.82 3.01
3 4 3.259625 GCCTTGAGTGAAGTAAGGAGAGT 59.740 47.826 6.44 0.00 42.82 3.24
4 5 3.259374 TGCCTTGAGTGAAGTAAGGAGAG 59.741 47.826 6.44 0.00 42.82 3.20
5 6 3.239449 TGCCTTGAGTGAAGTAAGGAGA 58.761 45.455 6.44 0.00 42.82 3.71
6 7 3.685139 TGCCTTGAGTGAAGTAAGGAG 57.315 47.619 6.44 0.00 42.82 3.69
7 8 4.640771 AATGCCTTGAGTGAAGTAAGGA 57.359 40.909 6.44 0.00 42.82 3.36
8 9 7.337942 AGAATAAATGCCTTGAGTGAAGTAAGG 59.662 37.037 0.00 0.00 43.00 2.69
9 10 8.273780 AGAATAAATGCCTTGAGTGAAGTAAG 57.726 34.615 0.00 0.00 0.00 2.34
10 11 8.635765 AAGAATAAATGCCTTGAGTGAAGTAA 57.364 30.769 0.00 0.00 0.00 2.24
11 12 8.635765 AAAGAATAAATGCCTTGAGTGAAGTA 57.364 30.769 0.00 0.00 0.00 2.24
12 13 7.530426 AAAGAATAAATGCCTTGAGTGAAGT 57.470 32.000 0.00 0.00 0.00 3.01
13 14 8.084073 TCAAAAGAATAAATGCCTTGAGTGAAG 58.916 33.333 0.00 0.00 0.00 3.02
14 15 7.867403 GTCAAAAGAATAAATGCCTTGAGTGAA 59.133 33.333 0.00 0.00 0.00 3.18
15 16 7.231317 AGTCAAAAGAATAAATGCCTTGAGTGA 59.769 33.333 0.00 0.00 0.00 3.41
16 17 7.373493 AGTCAAAAGAATAAATGCCTTGAGTG 58.627 34.615 0.00 0.00 0.00 3.51
17 18 7.449704 AGAGTCAAAAGAATAAATGCCTTGAGT 59.550 33.333 0.00 0.00 0.00 3.41
18 19 7.824672 AGAGTCAAAAGAATAAATGCCTTGAG 58.175 34.615 0.00 0.00 0.00 3.02
19 20 7.448161 TGAGAGTCAAAAGAATAAATGCCTTGA 59.552 33.333 0.00 0.00 0.00 3.02
20 21 7.596494 TGAGAGTCAAAAGAATAAATGCCTTG 58.404 34.615 0.00 0.00 0.00 3.61
21 22 7.765695 TGAGAGTCAAAAGAATAAATGCCTT 57.234 32.000 0.00 0.00 0.00 4.35
22 23 7.094032 CCTTGAGAGTCAAAAGAATAAATGCCT 60.094 37.037 6.44 0.00 35.73 4.75
23 24 7.031975 CCTTGAGAGTCAAAAGAATAAATGCC 58.968 38.462 6.44 0.00 35.73 4.40
24 25 6.529477 GCCTTGAGAGTCAAAAGAATAAATGC 59.471 38.462 6.44 0.00 35.73 3.56
25 26 7.824672 AGCCTTGAGAGTCAAAAGAATAAATG 58.175 34.615 6.44 0.00 35.73 2.32
26 27 8.302438 CAAGCCTTGAGAGTCAAAAGAATAAAT 58.698 33.333 0.00 0.00 35.73 1.40
27 28 7.651808 CAAGCCTTGAGAGTCAAAAGAATAAA 58.348 34.615 0.00 0.00 35.73 1.40
28 29 6.294176 GCAAGCCTTGAGAGTCAAAAGAATAA 60.294 38.462 9.04 0.00 35.73 1.40
29 30 5.182001 GCAAGCCTTGAGAGTCAAAAGAATA 59.818 40.000 9.04 0.00 35.73 1.75
30 31 4.022503 GCAAGCCTTGAGAGTCAAAAGAAT 60.023 41.667 9.04 0.00 35.73 2.40
31 32 3.316308 GCAAGCCTTGAGAGTCAAAAGAA 59.684 43.478 9.04 0.00 35.73 2.52
32 33 2.880890 GCAAGCCTTGAGAGTCAAAAGA 59.119 45.455 9.04 0.00 35.73 2.52
33 34 2.883386 AGCAAGCCTTGAGAGTCAAAAG 59.117 45.455 9.04 0.00 35.73 2.27
34 35 2.936202 AGCAAGCCTTGAGAGTCAAAA 58.064 42.857 9.04 0.00 35.73 2.44
35 36 2.645838 AGCAAGCCTTGAGAGTCAAA 57.354 45.000 9.04 0.00 35.73 2.69
36 37 2.105477 AGAAGCAAGCCTTGAGAGTCAA 59.895 45.455 9.04 0.00 34.79 3.18
37 38 1.696336 AGAAGCAAGCCTTGAGAGTCA 59.304 47.619 9.04 0.00 32.78 3.41
38 39 2.470983 AGAAGCAAGCCTTGAGAGTC 57.529 50.000 9.04 0.00 32.78 3.36
39 40 2.947127 AAGAAGCAAGCCTTGAGAGT 57.053 45.000 9.04 0.00 32.78 3.24
40 41 4.277921 AGAAAAAGAAGCAAGCCTTGAGAG 59.722 41.667 9.04 0.00 32.78 3.20
41 42 4.210331 AGAAAAAGAAGCAAGCCTTGAGA 58.790 39.130 9.04 0.00 32.78 3.27
42 43 4.581077 AGAAAAAGAAGCAAGCCTTGAG 57.419 40.909 9.04 0.00 32.78 3.02
43 44 4.441913 CCAAGAAAAAGAAGCAAGCCTTGA 60.442 41.667 9.04 0.00 33.60 3.02
44 45 3.805971 CCAAGAAAAAGAAGCAAGCCTTG 59.194 43.478 0.00 0.00 32.78 3.61
45 46 3.452264 ACCAAGAAAAAGAAGCAAGCCTT 59.548 39.130 0.00 0.00 36.19 4.35
46 47 3.033909 ACCAAGAAAAAGAAGCAAGCCT 58.966 40.909 0.00 0.00 0.00 4.58
47 48 3.459232 ACCAAGAAAAAGAAGCAAGCC 57.541 42.857 0.00 0.00 0.00 4.35
48 49 4.183865 ACAACCAAGAAAAAGAAGCAAGC 58.816 39.130 0.00 0.00 0.00 4.01
49 50 6.476706 CCTTACAACCAAGAAAAAGAAGCAAG 59.523 38.462 0.00 0.00 0.00 4.01
50 51 6.337356 CCTTACAACCAAGAAAAAGAAGCAA 58.663 36.000 0.00 0.00 0.00 3.91
51 52 5.163457 CCCTTACAACCAAGAAAAAGAAGCA 60.163 40.000 0.00 0.00 0.00 3.91
52 53 5.068591 TCCCTTACAACCAAGAAAAAGAAGC 59.931 40.000 0.00 0.00 0.00 3.86
53 54 6.321435 ACTCCCTTACAACCAAGAAAAAGAAG 59.679 38.462 0.00 0.00 0.00 2.85
54 55 6.192044 ACTCCCTTACAACCAAGAAAAAGAA 58.808 36.000 0.00 0.00 0.00 2.52
55 56 5.762279 ACTCCCTTACAACCAAGAAAAAGA 58.238 37.500 0.00 0.00 0.00 2.52
56 57 5.592688 TGACTCCCTTACAACCAAGAAAAAG 59.407 40.000 0.00 0.00 0.00 2.27
57 58 5.511363 TGACTCCCTTACAACCAAGAAAAA 58.489 37.500 0.00 0.00 0.00 1.94
58 59 5.118729 TGACTCCCTTACAACCAAGAAAA 57.881 39.130 0.00 0.00 0.00 2.29
59 60 4.445735 CCTGACTCCCTTACAACCAAGAAA 60.446 45.833 0.00 0.00 0.00 2.52
60 61 3.072476 CCTGACTCCCTTACAACCAAGAA 59.928 47.826 0.00 0.00 0.00 2.52
61 62 2.637872 CCTGACTCCCTTACAACCAAGA 59.362 50.000 0.00 0.00 0.00 3.02
62 63 2.290323 CCCTGACTCCCTTACAACCAAG 60.290 54.545 0.00 0.00 0.00 3.61
63 64 1.702957 CCCTGACTCCCTTACAACCAA 59.297 52.381 0.00 0.00 0.00 3.67
64 65 1.358152 CCCTGACTCCCTTACAACCA 58.642 55.000 0.00 0.00 0.00 3.67
65 66 1.278413 GACCCTGACTCCCTTACAACC 59.722 57.143 0.00 0.00 0.00 3.77
66 67 1.975680 TGACCCTGACTCCCTTACAAC 59.024 52.381 0.00 0.00 0.00 3.32
67 68 2.409064 TGACCCTGACTCCCTTACAA 57.591 50.000 0.00 0.00 0.00 2.41
68 69 2.642171 ATGACCCTGACTCCCTTACA 57.358 50.000 0.00 0.00 0.00 2.41
69 70 3.263425 TCAAATGACCCTGACTCCCTTAC 59.737 47.826 0.00 0.00 0.00 2.34
70 71 3.263425 GTCAAATGACCCTGACTCCCTTA 59.737 47.826 2.04 0.00 39.11 2.69
71 72 2.040412 GTCAAATGACCCTGACTCCCTT 59.960 50.000 2.04 0.00 39.11 3.95
72 73 1.630878 GTCAAATGACCCTGACTCCCT 59.369 52.381 2.04 0.00 39.11 4.20
73 74 1.351017 TGTCAAATGACCCTGACTCCC 59.649 52.381 10.83 0.00 44.15 4.30
74 75 2.704572 CTGTCAAATGACCCTGACTCC 58.295 52.381 10.83 0.00 44.15 3.85
75 76 2.079925 GCTGTCAAATGACCCTGACTC 58.920 52.381 10.83 0.00 44.15 3.36
76 77 1.701847 AGCTGTCAAATGACCCTGACT 59.298 47.619 10.83 0.00 44.15 3.41
77 78 2.079925 GAGCTGTCAAATGACCCTGAC 58.920 52.381 10.83 0.00 44.15 3.51
78 79 1.699083 TGAGCTGTCAAATGACCCTGA 59.301 47.619 10.83 0.00 44.15 3.86
79 80 2.189594 TGAGCTGTCAAATGACCCTG 57.810 50.000 10.83 3.19 44.15 4.45
80 81 2.508526 GTTGAGCTGTCAAATGACCCT 58.491 47.619 10.83 7.21 44.44 4.34
81 82 1.541588 GGTTGAGCTGTCAAATGACCC 59.458 52.381 10.83 2.71 44.44 4.46
82 83 1.197721 CGGTTGAGCTGTCAAATGACC 59.802 52.381 10.83 0.00 44.44 4.02
83 84 2.143122 TCGGTTGAGCTGTCAAATGAC 58.857 47.619 6.60 6.60 44.44 3.06
84 85 2.542020 TCGGTTGAGCTGTCAAATGA 57.458 45.000 0.00 0.00 44.44 2.57
85 86 3.684305 TGTATCGGTTGAGCTGTCAAATG 59.316 43.478 0.00 0.00 44.44 2.32
86 87 3.937814 TGTATCGGTTGAGCTGTCAAAT 58.062 40.909 0.00 0.00 44.44 2.32
87 88 3.394674 TGTATCGGTTGAGCTGTCAAA 57.605 42.857 0.00 0.00 44.44 2.69
88 89 3.521560 GATGTATCGGTTGAGCTGTCAA 58.478 45.455 0.00 0.00 40.55 3.18
89 90 2.159099 GGATGTATCGGTTGAGCTGTCA 60.159 50.000 0.00 0.00 0.00 3.58
90 91 2.159099 TGGATGTATCGGTTGAGCTGTC 60.159 50.000 0.00 0.00 0.00 3.51
91 92 1.831106 TGGATGTATCGGTTGAGCTGT 59.169 47.619 0.00 0.00 0.00 4.40
92 93 2.602257 TGGATGTATCGGTTGAGCTG 57.398 50.000 0.00 0.00 0.00 4.24
93 94 3.627395 TTTGGATGTATCGGTTGAGCT 57.373 42.857 0.00 0.00 0.00 4.09
94 95 3.876914 TGATTTGGATGTATCGGTTGAGC 59.123 43.478 0.00 0.00 0.00 4.26
95 96 4.273480 GGTGATTTGGATGTATCGGTTGAG 59.727 45.833 0.00 0.00 0.00 3.02
96 97 4.080582 AGGTGATTTGGATGTATCGGTTGA 60.081 41.667 0.00 0.00 0.00 3.18
97 98 4.035558 CAGGTGATTTGGATGTATCGGTTG 59.964 45.833 0.00 0.00 0.00 3.77
98 99 4.080582 TCAGGTGATTTGGATGTATCGGTT 60.081 41.667 0.00 0.00 0.00 4.44
99 100 3.454447 TCAGGTGATTTGGATGTATCGGT 59.546 43.478 0.00 0.00 0.00 4.69
100 101 4.071961 TCAGGTGATTTGGATGTATCGG 57.928 45.455 0.00 0.00 0.00 4.18
112 113 9.158233 CAAATCTTTATGCAAAATCAGGTGATT 57.842 29.630 0.00 0.00 45.91 2.57
113 114 8.533657 TCAAATCTTTATGCAAAATCAGGTGAT 58.466 29.630 0.00 0.00 36.07 3.06
114 115 7.894708 TCAAATCTTTATGCAAAATCAGGTGA 58.105 30.769 0.00 0.00 0.00 4.02
115 116 8.600625 CATCAAATCTTTATGCAAAATCAGGTG 58.399 33.333 0.00 0.00 0.00 4.00
116 117 7.279313 GCATCAAATCTTTATGCAAAATCAGGT 59.721 33.333 0.00 0.00 44.27 4.00
117 118 7.516155 CGCATCAAATCTTTATGCAAAATCAGG 60.516 37.037 7.24 0.00 44.95 3.86
118 119 7.221259 TCGCATCAAATCTTTATGCAAAATCAG 59.779 33.333 7.24 0.00 44.95 2.90
119 120 7.034397 TCGCATCAAATCTTTATGCAAAATCA 58.966 30.769 7.24 0.00 44.95 2.57
120 121 7.453980 TCGCATCAAATCTTTATGCAAAATC 57.546 32.000 7.24 0.00 44.95 2.17
121 122 7.010738 CCTTCGCATCAAATCTTTATGCAAAAT 59.989 33.333 7.24 0.00 44.95 1.82
122 123 6.310956 CCTTCGCATCAAATCTTTATGCAAAA 59.689 34.615 7.24 0.00 44.95 2.44
123 124 5.806502 CCTTCGCATCAAATCTTTATGCAAA 59.193 36.000 7.24 0.00 44.95 3.68
124 125 5.125257 TCCTTCGCATCAAATCTTTATGCAA 59.875 36.000 7.24 0.96 44.95 4.08
125 126 4.639755 TCCTTCGCATCAAATCTTTATGCA 59.360 37.500 7.24 0.00 44.95 3.96
126 127 5.173774 TCCTTCGCATCAAATCTTTATGC 57.826 39.130 0.00 0.00 42.02 3.14
127 128 6.016860 TGGATCCTTCGCATCAAATCTTTATG 60.017 38.462 14.23 0.00 0.00 1.90
128 129 6.064060 TGGATCCTTCGCATCAAATCTTTAT 58.936 36.000 14.23 0.00 0.00 1.40
129 130 5.436175 TGGATCCTTCGCATCAAATCTTTA 58.564 37.500 14.23 0.00 0.00 1.85
130 131 4.272489 TGGATCCTTCGCATCAAATCTTT 58.728 39.130 14.23 0.00 0.00 2.52
131 132 3.889815 TGGATCCTTCGCATCAAATCTT 58.110 40.909 14.23 0.00 0.00 2.40
132 133 3.565764 TGGATCCTTCGCATCAAATCT 57.434 42.857 14.23 0.00 0.00 2.40
133 134 4.637483 TTTGGATCCTTCGCATCAAATC 57.363 40.909 14.23 0.00 0.00 2.17
134 135 4.142093 CCTTTTGGATCCTTCGCATCAAAT 60.142 41.667 14.23 0.00 44.07 2.32
135 136 3.193267 CCTTTTGGATCCTTCGCATCAAA 59.807 43.478 14.23 0.00 44.07 2.69
136 137 2.754552 CCTTTTGGATCCTTCGCATCAA 59.245 45.455 14.23 0.00 44.07 2.57
137 138 2.290896 ACCTTTTGGATCCTTCGCATCA 60.291 45.455 14.23 0.00 44.07 3.07
138 139 2.369394 ACCTTTTGGATCCTTCGCATC 58.631 47.619 14.23 0.00 44.07 3.91
139 140 2.514458 ACCTTTTGGATCCTTCGCAT 57.486 45.000 14.23 0.00 44.07 4.73
140 141 2.286365 AACCTTTTGGATCCTTCGCA 57.714 45.000 14.23 0.00 44.07 5.10
141 142 2.556622 TCAAACCTTTTGGATCCTTCGC 59.443 45.455 14.23 0.00 44.07 4.70
142 143 3.568007 TGTCAAACCTTTTGGATCCTTCG 59.432 43.478 14.23 0.00 44.07 3.79
143 144 4.584743 ACTGTCAAACCTTTTGGATCCTTC 59.415 41.667 14.23 0.00 44.07 3.46
144 145 4.342092 CACTGTCAAACCTTTTGGATCCTT 59.658 41.667 14.23 0.00 44.07 3.36
145 146 3.891366 CACTGTCAAACCTTTTGGATCCT 59.109 43.478 14.23 0.00 44.07 3.24
146 147 3.636764 ACACTGTCAAACCTTTTGGATCC 59.363 43.478 4.20 4.20 44.07 3.36
147 148 4.918810 ACACTGTCAAACCTTTTGGATC 57.081 40.909 0.00 0.00 44.07 3.36
148 149 4.141959 CCAACACTGTCAAACCTTTTGGAT 60.142 41.667 0.00 0.00 44.07 3.41
149 150 3.194542 CCAACACTGTCAAACCTTTTGGA 59.805 43.478 0.00 0.00 44.07 3.53
151 152 3.520569 CCCAACACTGTCAAACCTTTTG 58.479 45.455 0.00 0.00 0.00 2.44
152 153 2.093711 GCCCAACACTGTCAAACCTTTT 60.094 45.455 0.00 0.00 0.00 2.27
153 154 1.480545 GCCCAACACTGTCAAACCTTT 59.519 47.619 0.00 0.00 0.00 3.11
154 155 1.111277 GCCCAACACTGTCAAACCTT 58.889 50.000 0.00 0.00 0.00 3.50
155 156 0.258774 AGCCCAACACTGTCAAACCT 59.741 50.000 0.00 0.00 0.00 3.50
156 157 0.385390 CAGCCCAACACTGTCAAACC 59.615 55.000 0.00 0.00 0.00 3.27
157 158 1.102978 ACAGCCCAACACTGTCAAAC 58.897 50.000 0.00 0.00 45.06 2.93
158 159 2.719531 TACAGCCCAACACTGTCAAA 57.280 45.000 0.00 0.00 45.06 2.69
159 160 2.949177 ATACAGCCCAACACTGTCAA 57.051 45.000 0.00 0.00 45.06 3.18
160 161 3.263170 ACATATACAGCCCAACACTGTCA 59.737 43.478 0.00 0.00 45.06 3.58
161 162 3.623060 CACATATACAGCCCAACACTGTC 59.377 47.826 0.00 0.00 45.06 3.51
163 164 3.374988 CACACATATACAGCCCAACACTG 59.625 47.826 0.00 0.00 41.08 3.66
164 165 3.263170 TCACACATATACAGCCCAACACT 59.737 43.478 0.00 0.00 0.00 3.55
165 166 3.605634 TCACACATATACAGCCCAACAC 58.394 45.455 0.00 0.00 0.00 3.32
536 541 3.121030 GCGCGCACCTCTTCATGT 61.121 61.111 29.10 0.00 0.00 3.21
1341 1866 5.220710 AGATAGTCTCAACAGTTGCAGTT 57.779 39.130 8.58 3.97 0.00 3.16
1342 1867 4.815269 GAGATAGTCTCAACAGTTGCAGT 58.185 43.478 8.58 3.39 42.90 4.40
1463 1988 5.016173 CCATCACAGAATTTTCCCCTTGTA 58.984 41.667 0.00 0.00 0.00 2.41
1797 2322 0.035317 TCTCACCGCAGTTGAAGCAT 59.965 50.000 0.00 0.00 0.00 3.79
1913 2438 2.642171 TTGACCACCAGAGTATCCCT 57.358 50.000 0.00 0.00 33.66 4.20
2890 3415 6.438741 GTCCCATTATCTGTCCTGATCATCTA 59.561 42.308 0.00 0.00 0.00 1.98
3102 3627 4.265073 GGTTGATGAGGAATGTAGCTGTT 58.735 43.478 0.00 0.00 0.00 3.16
3337 3862 2.821378 CCATGCTCACAAATGTTCTCCA 59.179 45.455 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.