Multiple sequence alignment - TraesCS5D01G313200

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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 TraesCS5D01G313200 chr5D 100.000 3602 0 0 1 3602 408547940 408551541 0.000000e+00 6652.0
1 TraesCS5D01G313200 chr5D 93.130 2722 148 6 894 3602 459919244 459921939 0.000000e+00 3954.0
2 TraesCS5D01G313200 chr5D 81.618 272 33 5 649 904 1616659 1616929 3.640000e-50 209.0
3 TraesCS5D01G313200 chr7D 97.215 3447 56 9 170 3602 631811408 631814828 0.000000e+00 5797.0
4 TraesCS5D01G313200 chr1D 95.320 3440 133 11 170 3602 335419320 335415902 0.000000e+00 5435.0
5 TraesCS5D01G313200 chr1D 97.549 3142 51 3 473 3602 414444329 414447456 0.000000e+00 5352.0
6 TraesCS5D01G313200 chr1D 96.759 2191 66 4 1413 3602 847435 845249 0.000000e+00 3648.0
7 TraesCS5D01G313200 chr4A 93.316 3456 197 16 169 3602 708328169 708331612 0.000000e+00 5072.0
8 TraesCS5D01G313200 chr4A 88.030 802 76 8 170 957 702241040 702241835 0.000000e+00 931.0
9 TraesCS5D01G313200 chr5B 93.006 3460 209 21 169 3602 708154442 708157894 0.000000e+00 5018.0
10 TraesCS5D01G313200 chr5B 93.807 2761 129 13 880 3602 498524562 498521806 0.000000e+00 4113.0
11 TraesCS5D01G313200 chr5B 92.929 99 5 2 1 97 490102929 490103027 3.750000e-30 143.0
12 TraesCS5D01G313200 chr5B 97.436 39 1 0 126 164 490103074 490103112 2.320000e-07 67.6
13 TraesCS5D01G313200 chr6D 96.306 2707 95 2 898 3601 447824505 447821801 0.000000e+00 4440.0
14 TraesCS5D01G313200 chr4D 95.665 2722 100 8 895 3602 97474833 97477550 0.000000e+00 4357.0
15 TraesCS5D01G313200 chr4D 97.403 2349 41 7 170 2505 375074949 375072608 0.000000e+00 3982.0
16 TraesCS5D01G313200 chr5A 94.265 2598 122 11 170 2746 574011486 574014077 0.000000e+00 3947.0
17 TraesCS5D01G313200 chr5A 86.667 105 6 4 1 97 514453295 514453399 3.800000e-20 110.0
18 TraesCS5D01G313200 chr7A 92.722 1113 62 9 170 1267 15541135 15542243 0.000000e+00 1589.0
19 TraesCS5D01G313200 chr3B 89.529 1232 100 12 170 1386 610168921 610167704 0.000000e+00 1533.0


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 TraesCS5D01G313200 chr5D 408547940 408551541 3601 False 6652 6652 100.000 1 3602 1 chr5D.!!$F2 3601
1 TraesCS5D01G313200 chr5D 459919244 459921939 2695 False 3954 3954 93.130 894 3602 1 chr5D.!!$F3 2708
2 TraesCS5D01G313200 chr7D 631811408 631814828 3420 False 5797 5797 97.215 170 3602 1 chr7D.!!$F1 3432
3 TraesCS5D01G313200 chr1D 335415902 335419320 3418 True 5435 5435 95.320 170 3602 1 chr1D.!!$R2 3432
4 TraesCS5D01G313200 chr1D 414444329 414447456 3127 False 5352 5352 97.549 473 3602 1 chr1D.!!$F1 3129
5 TraesCS5D01G313200 chr1D 845249 847435 2186 True 3648 3648 96.759 1413 3602 1 chr1D.!!$R1 2189
6 TraesCS5D01G313200 chr4A 708328169 708331612 3443 False 5072 5072 93.316 169 3602 1 chr4A.!!$F2 3433
7 TraesCS5D01G313200 chr4A 702241040 702241835 795 False 931 931 88.030 170 957 1 chr4A.!!$F1 787
8 TraesCS5D01G313200 chr5B 708154442 708157894 3452 False 5018 5018 93.006 169 3602 1 chr5B.!!$F1 3433
9 TraesCS5D01G313200 chr5B 498521806 498524562 2756 True 4113 4113 93.807 880 3602 1 chr5B.!!$R1 2722
10 TraesCS5D01G313200 chr6D 447821801 447824505 2704 True 4440 4440 96.306 898 3601 1 chr6D.!!$R1 2703
11 TraesCS5D01G313200 chr4D 97474833 97477550 2717 False 4357 4357 95.665 895 3602 1 chr4D.!!$F1 2707
12 TraesCS5D01G313200 chr4D 375072608 375074949 2341 True 3982 3982 97.403 170 2505 1 chr4D.!!$R1 2335
13 TraesCS5D01G313200 chr5A 574011486 574014077 2591 False 3947 3947 94.265 170 2746 1 chr5A.!!$F2 2576
14 TraesCS5D01G313200 chr7A 15541135 15542243 1108 False 1589 1589 92.722 170 1267 1 chr7A.!!$F1 1097
15 TraesCS5D01G313200 chr3B 610167704 610168921 1217 True 1533 1533 89.529 170 1386 1 chr3B.!!$R1 1216

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
152 153 0.107703 TGGAGGATGATGTGGTTCGC 60.108 55.0 0.00 0.00 0.00 4.70 F
180 181 0.529773 CGGCTGCGGAGTAAATAGCA 60.530 55.0 5.62 0.00 36.15 3.49 F
452 466 0.686112 CTCCCTCTCACCCTCACTCC 60.686 65.0 0.00 0.00 0.00 3.85 F
1773 1863 2.777832 AGAAGCTTAAGCCTGTCAGG 57.222 50.0 23.71 15.15 43.38 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1090 1147 2.244769 CCATTCCATACCCCTCCAACTT 59.755 50.000 0.00 0.0 0.00 2.66 R
1773 1863 2.492088 GTTGATAGTTGGGCCTGGTTTC 59.508 50.000 4.53 0.0 0.00 2.78 R
1883 1973 4.498177 GCAACCTTGGAACTTCTTCTTCAC 60.498 45.833 0.00 0.0 0.00 3.18 R
2783 2897 0.767375 ACCATGTCCAGCTGTCTGTT 59.233 50.000 13.81 0.0 38.66 3.16 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 9.369904 TGTTTGGTAACTTATTACTTATCGACC 57.630 33.333 0.00 0.00 40.59 4.79
31 32 9.369904 GTTTGGTAACTTATTACTTATCGACCA 57.630 33.333 0.00 0.00 40.59 4.02
32 33 9.941325 TTTGGTAACTTATTACTTATCGACCAA 57.059 29.630 0.00 0.00 40.59 3.67
33 34 9.590451 TTGGTAACTTATTACTTATCGACCAAG 57.410 33.333 6.98 6.98 40.59 3.61
34 35 8.970020 TGGTAACTTATTACTTATCGACCAAGA 58.030 33.333 13.94 0.00 40.59 3.02
35 36 9.978044 GGTAACTTATTACTTATCGACCAAGAT 57.022 33.333 13.94 2.91 40.59 2.40
38 39 9.751542 AACTTATTACTTATCGACCAAGATGAG 57.248 33.333 13.94 7.62 39.33 2.90
39 40 9.132923 ACTTATTACTTATCGACCAAGATGAGA 57.867 33.333 13.94 0.00 37.58 3.27
42 43 8.824159 ATTACTTATCGACCAAGATGAGATTG 57.176 34.615 13.94 0.00 37.58 2.67
43 44 6.471233 ACTTATCGACCAAGATGAGATTGA 57.529 37.500 13.94 0.00 37.58 2.57
44 45 7.060383 ACTTATCGACCAAGATGAGATTGAT 57.940 36.000 13.94 0.00 37.58 2.57
45 46 7.504403 ACTTATCGACCAAGATGAGATTGATT 58.496 34.615 13.94 0.00 37.58 2.57
46 47 7.440556 ACTTATCGACCAAGATGAGATTGATTG 59.559 37.037 13.94 0.00 37.58 2.67
47 48 5.089970 TCGACCAAGATGAGATTGATTGT 57.910 39.130 0.00 0.00 0.00 2.71
48 49 5.491070 TCGACCAAGATGAGATTGATTGTT 58.509 37.500 0.00 0.00 0.00 2.83
49 50 5.939883 TCGACCAAGATGAGATTGATTGTTT 59.060 36.000 0.00 0.00 0.00 2.83
50 51 7.102993 TCGACCAAGATGAGATTGATTGTTTA 58.897 34.615 0.00 0.00 0.00 2.01
51 52 7.770433 TCGACCAAGATGAGATTGATTGTTTAT 59.230 33.333 0.00 0.00 0.00 1.40
52 53 8.066595 CGACCAAGATGAGATTGATTGTTTATC 58.933 37.037 0.00 0.00 0.00 1.75
53 54 9.118300 GACCAAGATGAGATTGATTGTTTATCT 57.882 33.333 0.00 0.00 34.17 1.98
54 55 9.471702 ACCAAGATGAGATTGATTGTTTATCTT 57.528 29.630 0.00 0.00 34.87 2.40
55 56 9.947669 CCAAGATGAGATTGATTGTTTATCTTC 57.052 33.333 0.00 0.00 32.93 2.87
58 59 9.339850 AGATGAGATTGATTGTTTATCTTCTGG 57.660 33.333 0.00 0.00 34.17 3.86
59 60 9.118300 GATGAGATTGATTGTTTATCTTCTGGT 57.882 33.333 0.00 0.00 34.17 4.00
61 62 9.958180 TGAGATTGATTGTTTATCTTCTGGTAA 57.042 29.630 0.00 0.00 34.17 2.85
69 70 9.914131 ATTGTTTATCTTCTGGTAAAGAAAAGC 57.086 29.630 0.00 0.00 44.38 3.51
70 71 8.458573 TGTTTATCTTCTGGTAAAGAAAAGCA 57.541 30.769 0.00 0.00 44.38 3.91
71 72 8.567948 TGTTTATCTTCTGGTAAAGAAAAGCAG 58.432 33.333 0.00 0.00 44.38 4.24
72 73 5.635417 ATCTTCTGGTAAAGAAAAGCAGC 57.365 39.130 0.00 0.00 44.38 5.25
73 74 3.498397 TCTTCTGGTAAAGAAAAGCAGCG 59.502 43.478 0.00 0.00 44.38 5.18
74 75 2.151202 TCTGGTAAAGAAAAGCAGCGG 58.849 47.619 0.00 0.00 41.22 5.52
75 76 1.200020 CTGGTAAAGAAAAGCAGCGGG 59.800 52.381 0.00 0.00 35.86 6.13
76 77 0.526211 GGTAAAGAAAAGCAGCGGGG 59.474 55.000 0.00 0.00 0.00 5.73
77 78 1.244816 GTAAAGAAAAGCAGCGGGGT 58.755 50.000 0.00 0.00 0.00 4.95
78 79 1.611977 GTAAAGAAAAGCAGCGGGGTT 59.388 47.619 0.00 0.00 39.32 4.11
83 84 1.745890 AAAGCAGCGGGGTTTTTCC 59.254 52.632 3.26 0.00 44.39 3.13
84 85 2.082629 AAAGCAGCGGGGTTTTTCCG 62.083 55.000 3.26 0.00 44.39 4.30
85 86 4.050934 GCAGCGGGGTTTTTCCGG 62.051 66.667 0.00 0.00 46.86 5.14
88 89 3.266964 GCGGGGTTTTTCCGGTAC 58.733 61.111 0.00 0.00 46.86 3.34
104 105 2.595238 GGTACGGAGATGGTGATAGGT 58.405 52.381 0.00 0.00 0.00 3.08
105 106 2.296471 GGTACGGAGATGGTGATAGGTG 59.704 54.545 0.00 0.00 0.00 4.00
106 107 2.454336 ACGGAGATGGTGATAGGTGA 57.546 50.000 0.00 0.00 0.00 4.02
107 108 2.964209 ACGGAGATGGTGATAGGTGAT 58.036 47.619 0.00 0.00 0.00 3.06
108 109 2.630098 ACGGAGATGGTGATAGGTGATG 59.370 50.000 0.00 0.00 0.00 3.07
109 110 2.028658 CGGAGATGGTGATAGGTGATGG 60.029 54.545 0.00 0.00 0.00 3.51
110 111 3.242867 GGAGATGGTGATAGGTGATGGA 58.757 50.000 0.00 0.00 0.00 3.41
111 112 3.843027 GGAGATGGTGATAGGTGATGGAT 59.157 47.826 0.00 0.00 0.00 3.41
112 113 4.323333 GGAGATGGTGATAGGTGATGGATG 60.323 50.000 0.00 0.00 0.00 3.51
113 114 3.586174 AGATGGTGATAGGTGATGGATGG 59.414 47.826 0.00 0.00 0.00 3.51
114 115 3.059051 TGGTGATAGGTGATGGATGGA 57.941 47.619 0.00 0.00 0.00 3.41
115 116 2.705658 TGGTGATAGGTGATGGATGGAC 59.294 50.000 0.00 0.00 0.00 4.02
116 117 2.975489 GGTGATAGGTGATGGATGGACT 59.025 50.000 0.00 0.00 0.00 3.85
117 118 3.392616 GGTGATAGGTGATGGATGGACTT 59.607 47.826 0.00 0.00 0.00 3.01
118 119 4.384056 GTGATAGGTGATGGATGGACTTG 58.616 47.826 0.00 0.00 0.00 3.16
119 120 4.040047 TGATAGGTGATGGATGGACTTGT 58.960 43.478 0.00 0.00 0.00 3.16
120 121 2.795231 AGGTGATGGATGGACTTGTG 57.205 50.000 0.00 0.00 0.00 3.33
121 122 1.098050 GGTGATGGATGGACTTGTGC 58.902 55.000 0.00 0.00 0.00 4.57
122 123 1.614051 GGTGATGGATGGACTTGTGCA 60.614 52.381 0.00 0.00 0.00 4.57
123 124 1.470098 GTGATGGATGGACTTGTGCAC 59.530 52.381 10.75 10.75 0.00 4.57
124 125 1.073603 TGATGGATGGACTTGTGCACA 59.926 47.619 17.42 17.42 0.00 4.57
125 126 1.741706 GATGGATGGACTTGTGCACAG 59.258 52.381 20.59 16.04 0.00 3.66
126 127 0.473755 TGGATGGACTTGTGCACAGT 59.526 50.000 20.59 19.08 0.00 3.55
127 128 1.696884 TGGATGGACTTGTGCACAGTA 59.303 47.619 20.59 5.22 0.00 2.74
128 129 2.076863 GGATGGACTTGTGCACAGTAC 58.923 52.381 20.59 19.66 0.00 2.73
129 130 1.726791 GATGGACTTGTGCACAGTACG 59.273 52.381 20.59 12.10 0.00 3.67
130 131 0.462375 TGGACTTGTGCACAGTACGT 59.538 50.000 20.59 15.14 0.00 3.57
131 132 1.682323 TGGACTTGTGCACAGTACGTA 59.318 47.619 20.59 2.75 0.00 3.57
132 133 2.287970 TGGACTTGTGCACAGTACGTAG 60.288 50.000 20.59 15.50 0.00 3.51
134 135 2.724690 GACTTGTGCACAGTACGTAGTG 59.275 50.000 25.36 25.36 45.73 2.74
135 136 2.058798 CTTGTGCACAGTACGTAGTGG 58.941 52.381 29.05 20.06 45.73 4.00
136 137 1.320507 TGTGCACAGTACGTAGTGGA 58.679 50.000 29.05 17.81 45.73 4.02
137 138 1.268625 TGTGCACAGTACGTAGTGGAG 59.731 52.381 29.05 22.32 45.73 3.86
138 139 0.885879 TGCACAGTACGTAGTGGAGG 59.114 55.000 29.05 20.03 45.73 4.30
139 140 1.171308 GCACAGTACGTAGTGGAGGA 58.829 55.000 29.05 0.00 45.73 3.71
140 141 1.749634 GCACAGTACGTAGTGGAGGAT 59.250 52.381 29.05 9.56 45.73 3.24
141 142 2.479730 GCACAGTACGTAGTGGAGGATG 60.480 54.545 29.05 19.96 45.73 3.51
142 143 3.014623 CACAGTACGTAGTGGAGGATGA 58.985 50.000 29.05 0.00 45.73 2.92
143 144 3.632604 CACAGTACGTAGTGGAGGATGAT 59.367 47.826 29.05 7.56 45.73 2.45
144 145 3.632604 ACAGTACGTAGTGGAGGATGATG 59.367 47.826 29.05 5.60 45.73 3.07
145 146 3.632604 CAGTACGTAGTGGAGGATGATGT 59.367 47.826 20.60 0.00 45.73 3.06
146 147 3.632604 AGTACGTAGTGGAGGATGATGTG 59.367 47.826 1.10 0.00 45.73 3.21
147 148 1.757118 ACGTAGTGGAGGATGATGTGG 59.243 52.381 0.00 0.00 42.51 4.17
148 149 1.757118 CGTAGTGGAGGATGATGTGGT 59.243 52.381 0.00 0.00 0.00 4.16
149 150 2.168521 CGTAGTGGAGGATGATGTGGTT 59.831 50.000 0.00 0.00 0.00 3.67
150 151 3.738281 CGTAGTGGAGGATGATGTGGTTC 60.738 52.174 0.00 0.00 0.00 3.62
151 152 1.208052 AGTGGAGGATGATGTGGTTCG 59.792 52.381 0.00 0.00 0.00 3.95
152 153 0.107703 TGGAGGATGATGTGGTTCGC 60.108 55.000 0.00 0.00 0.00 4.70
153 154 1.154205 GGAGGATGATGTGGTTCGCG 61.154 60.000 0.00 0.00 0.00 5.87
154 155 1.766143 GAGGATGATGTGGTTCGCGC 61.766 60.000 0.00 0.00 0.00 6.86
155 156 2.106074 GGATGATGTGGTTCGCGCA 61.106 57.895 8.75 0.00 0.00 6.09
156 157 1.060937 GATGATGTGGTTCGCGCAC 59.939 57.895 8.75 0.00 0.00 5.34
157 158 2.309764 GATGATGTGGTTCGCGCACC 62.310 60.000 21.57 21.57 37.34 5.01
158 159 3.047280 GATGTGGTTCGCGCACCA 61.047 61.111 26.87 26.87 45.13 4.17
180 181 0.529773 CGGCTGCGGAGTAAATAGCA 60.530 55.000 5.62 0.00 36.15 3.49
444 446 1.379309 ACTCGCTCTCCCTCTCACC 60.379 63.158 0.00 0.00 0.00 4.02
452 466 0.686112 CTCCCTCTCACCCTCACTCC 60.686 65.000 0.00 0.00 0.00 3.85
716 732 4.996434 GCGGATCCAGATGGCGGG 62.996 72.222 13.41 0.00 34.44 6.13
1449 1506 8.356657 CAACATAGTTGTAATTTGAACAAGGGA 58.643 33.333 1.86 0.00 37.51 4.20
1773 1863 2.777832 AGAAGCTTAAGCCTGTCAGG 57.222 50.000 23.71 15.15 43.38 3.86
1883 1973 2.493278 CAGGTGATTTTGGCCTTAGTGG 59.507 50.000 3.32 0.00 39.35 4.00
2142 2232 6.715347 AGAAAGCAAGGTTGTCAGTTTTAT 57.285 33.333 0.00 0.00 0.00 1.40
2546 2640 5.238583 GTTTCACTACATGTTCTACTGCCT 58.761 41.667 2.30 0.00 0.00 4.75
2783 2897 3.691575 TGGTGTTGTTGACAAGGAAGAA 58.308 40.909 0.00 0.00 40.65 2.52
2840 2954 4.292306 AGAACTGTTATTGGGAGTGGGAAT 59.708 41.667 0.00 0.00 0.00 3.01
3310 3450 3.455910 ACAAGCCAATCAGGACTATGCTA 59.544 43.478 0.00 0.00 41.22 3.49
3554 3695 1.195115 GAGGTGGGACATGACAGCTA 58.805 55.000 16.85 0.00 44.58 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.369904 GGTCGATAAGTAATAAGTTACCAAACA 57.630 33.333 0.00 0.00 40.88 2.83
5 6 9.369904 TGGTCGATAAGTAATAAGTTACCAAAC 57.630 33.333 0.00 0.00 40.88 2.93
6 7 9.941325 TTGGTCGATAAGTAATAAGTTACCAAA 57.059 29.630 0.00 0.00 40.88 3.28
7 8 9.590451 CTTGGTCGATAAGTAATAAGTTACCAA 57.410 33.333 0.00 0.00 40.88 3.67
8 9 8.970020 TCTTGGTCGATAAGTAATAAGTTACCA 58.030 33.333 10.84 0.00 40.88 3.25
9 10 9.978044 ATCTTGGTCGATAAGTAATAAGTTACC 57.022 33.333 10.84 0.00 40.88 2.85
12 13 9.751542 CTCATCTTGGTCGATAAGTAATAAGTT 57.248 33.333 10.84 0.00 0.00 2.66
13 14 9.132923 TCTCATCTTGGTCGATAAGTAATAAGT 57.867 33.333 10.84 0.00 0.00 2.24
16 17 9.914131 CAATCTCATCTTGGTCGATAAGTAATA 57.086 33.333 10.84 0.00 0.00 0.98
17 18 8.642432 TCAATCTCATCTTGGTCGATAAGTAAT 58.358 33.333 10.84 0.00 0.00 1.89
18 19 8.007405 TCAATCTCATCTTGGTCGATAAGTAA 57.993 34.615 10.84 0.00 0.00 2.24
19 20 7.582667 TCAATCTCATCTTGGTCGATAAGTA 57.417 36.000 10.84 1.60 0.00 2.24
20 21 6.471233 TCAATCTCATCTTGGTCGATAAGT 57.529 37.500 10.84 0.00 0.00 2.24
21 22 7.440556 ACAATCAATCTCATCTTGGTCGATAAG 59.559 37.037 6.15 6.15 0.00 1.73
22 23 7.275183 ACAATCAATCTCATCTTGGTCGATAA 58.725 34.615 0.00 0.00 0.00 1.75
23 24 6.820335 ACAATCAATCTCATCTTGGTCGATA 58.180 36.000 0.00 0.00 0.00 2.92
24 25 5.678583 ACAATCAATCTCATCTTGGTCGAT 58.321 37.500 0.00 0.00 0.00 3.59
25 26 5.089970 ACAATCAATCTCATCTTGGTCGA 57.910 39.130 0.00 0.00 0.00 4.20
26 27 5.808042 AACAATCAATCTCATCTTGGTCG 57.192 39.130 0.00 0.00 0.00 4.79
27 28 9.118300 AGATAAACAATCAATCTCATCTTGGTC 57.882 33.333 0.00 0.00 37.03 4.02
28 29 9.471702 AAGATAAACAATCAATCTCATCTTGGT 57.528 29.630 0.00 0.00 37.03 3.67
29 30 9.947669 GAAGATAAACAATCAATCTCATCTTGG 57.052 33.333 0.00 0.00 37.03 3.61
32 33 9.339850 CCAGAAGATAAACAATCAATCTCATCT 57.660 33.333 0.00 0.00 37.03 2.90
33 34 9.118300 ACCAGAAGATAAACAATCAATCTCATC 57.882 33.333 0.00 0.00 37.03 2.92
35 36 9.958180 TTACCAGAAGATAAACAATCAATCTCA 57.042 29.630 0.00 0.00 37.03 3.27
43 44 9.914131 GCTTTTCTTTACCAGAAGATAAACAAT 57.086 29.630 0.00 0.00 42.76 2.71
44 45 8.908903 TGCTTTTCTTTACCAGAAGATAAACAA 58.091 29.630 0.00 0.00 42.76 2.83
45 46 8.458573 TGCTTTTCTTTACCAGAAGATAAACA 57.541 30.769 0.00 0.00 42.76 2.83
46 47 7.539022 GCTGCTTTTCTTTACCAGAAGATAAAC 59.461 37.037 0.00 0.00 42.76 2.01
47 48 7.573096 CGCTGCTTTTCTTTACCAGAAGATAAA 60.573 37.037 0.00 0.00 42.76 1.40
48 49 6.128282 CGCTGCTTTTCTTTACCAGAAGATAA 60.128 38.462 0.00 0.00 42.76 1.75
49 50 5.351465 CGCTGCTTTTCTTTACCAGAAGATA 59.649 40.000 0.00 0.00 42.76 1.98
50 51 4.154918 CGCTGCTTTTCTTTACCAGAAGAT 59.845 41.667 0.00 0.00 42.76 2.40
51 52 3.498397 CGCTGCTTTTCTTTACCAGAAGA 59.502 43.478 0.00 0.00 42.76 2.87
52 53 3.365364 CCGCTGCTTTTCTTTACCAGAAG 60.365 47.826 0.00 0.00 42.76 2.85
53 54 2.552315 CCGCTGCTTTTCTTTACCAGAA 59.448 45.455 0.00 0.00 39.99 3.02
54 55 2.151202 CCGCTGCTTTTCTTTACCAGA 58.849 47.619 0.00 0.00 0.00 3.86
55 56 1.200020 CCCGCTGCTTTTCTTTACCAG 59.800 52.381 0.00 0.00 0.00 4.00
56 57 1.243902 CCCGCTGCTTTTCTTTACCA 58.756 50.000 0.00 0.00 0.00 3.25
57 58 0.526211 CCCCGCTGCTTTTCTTTACC 59.474 55.000 0.00 0.00 0.00 2.85
58 59 1.244816 ACCCCGCTGCTTTTCTTTAC 58.755 50.000 0.00 0.00 0.00 2.01
59 60 1.989706 AACCCCGCTGCTTTTCTTTA 58.010 45.000 0.00 0.00 0.00 1.85
60 61 1.119684 AAACCCCGCTGCTTTTCTTT 58.880 45.000 0.00 0.00 0.00 2.52
61 62 1.119684 AAAACCCCGCTGCTTTTCTT 58.880 45.000 0.00 0.00 0.00 2.52
62 63 1.068588 GAAAAACCCCGCTGCTTTTCT 59.931 47.619 13.56 0.61 35.73 2.52
63 64 1.497991 GAAAAACCCCGCTGCTTTTC 58.502 50.000 7.87 7.87 32.43 2.29
64 65 0.105964 GGAAAAACCCCGCTGCTTTT 59.894 50.000 0.00 0.00 0.00 2.27
65 66 1.745890 GGAAAAACCCCGCTGCTTT 59.254 52.632 0.00 0.00 0.00 3.51
66 67 2.561037 CGGAAAAACCCCGCTGCTT 61.561 57.895 0.00 0.00 40.54 3.91
67 68 2.983592 CGGAAAAACCCCGCTGCT 60.984 61.111 0.00 0.00 40.54 4.24
68 69 4.050934 CCGGAAAAACCCCGCTGC 62.051 66.667 0.00 0.00 45.24 5.25
69 70 1.302671 TACCGGAAAAACCCCGCTG 60.303 57.895 9.46 0.00 45.24 5.18
70 71 1.302752 GTACCGGAAAAACCCCGCT 60.303 57.895 9.46 0.00 45.24 5.52
71 72 2.679934 CGTACCGGAAAAACCCCGC 61.680 63.158 9.46 0.00 45.24 6.13
72 73 3.565050 CGTACCGGAAAAACCCCG 58.435 61.111 9.46 0.00 46.10 5.73
83 84 1.540267 CCTATCACCATCTCCGTACCG 59.460 57.143 0.00 0.00 0.00 4.02
84 85 2.296471 CACCTATCACCATCTCCGTACC 59.704 54.545 0.00 0.00 0.00 3.34
85 86 3.220110 TCACCTATCACCATCTCCGTAC 58.780 50.000 0.00 0.00 0.00 3.67
86 87 3.588210 TCACCTATCACCATCTCCGTA 57.412 47.619 0.00 0.00 0.00 4.02
87 88 2.454336 TCACCTATCACCATCTCCGT 57.546 50.000 0.00 0.00 0.00 4.69
88 89 2.028658 CCATCACCTATCACCATCTCCG 60.029 54.545 0.00 0.00 0.00 4.63
89 90 3.242867 TCCATCACCTATCACCATCTCC 58.757 50.000 0.00 0.00 0.00 3.71
90 91 4.323333 CCATCCATCACCTATCACCATCTC 60.323 50.000 0.00 0.00 0.00 2.75
91 92 3.586174 CCATCCATCACCTATCACCATCT 59.414 47.826 0.00 0.00 0.00 2.90
92 93 3.584406 TCCATCCATCACCTATCACCATC 59.416 47.826 0.00 0.00 0.00 3.51
93 94 3.328931 GTCCATCCATCACCTATCACCAT 59.671 47.826 0.00 0.00 0.00 3.55
94 95 2.705658 GTCCATCCATCACCTATCACCA 59.294 50.000 0.00 0.00 0.00 4.17
95 96 2.975489 AGTCCATCCATCACCTATCACC 59.025 50.000 0.00 0.00 0.00 4.02
96 97 4.141620 ACAAGTCCATCCATCACCTATCAC 60.142 45.833 0.00 0.00 0.00 3.06
97 98 4.040047 ACAAGTCCATCCATCACCTATCA 58.960 43.478 0.00 0.00 0.00 2.15
98 99 4.384056 CACAAGTCCATCCATCACCTATC 58.616 47.826 0.00 0.00 0.00 2.08
99 100 3.434167 GCACAAGTCCATCCATCACCTAT 60.434 47.826 0.00 0.00 0.00 2.57
100 101 2.092968 GCACAAGTCCATCCATCACCTA 60.093 50.000 0.00 0.00 0.00 3.08
101 102 1.340405 GCACAAGTCCATCCATCACCT 60.340 52.381 0.00 0.00 0.00 4.00
102 103 1.098050 GCACAAGTCCATCCATCACC 58.902 55.000 0.00 0.00 0.00 4.02
103 104 1.470098 GTGCACAAGTCCATCCATCAC 59.530 52.381 13.17 0.00 0.00 3.06
104 105 1.073603 TGTGCACAAGTCCATCCATCA 59.926 47.619 19.28 0.00 0.00 3.07
105 106 1.741706 CTGTGCACAAGTCCATCCATC 59.258 52.381 21.98 0.00 0.00 3.51
106 107 1.074405 ACTGTGCACAAGTCCATCCAT 59.926 47.619 21.98 0.00 0.00 3.41
107 108 0.473755 ACTGTGCACAAGTCCATCCA 59.526 50.000 21.98 0.00 0.00 3.41
108 109 2.076863 GTACTGTGCACAAGTCCATCC 58.923 52.381 21.98 0.00 0.00 3.51
109 110 1.726791 CGTACTGTGCACAAGTCCATC 59.273 52.381 21.98 10.77 0.00 3.51
110 111 1.070134 ACGTACTGTGCACAAGTCCAT 59.930 47.619 21.98 2.10 0.00 3.41
111 112 0.462375 ACGTACTGTGCACAAGTCCA 59.538 50.000 21.98 4.61 0.00 4.02
112 113 2.288030 ACTACGTACTGTGCACAAGTCC 60.288 50.000 21.98 10.86 0.00 3.85
113 114 2.724690 CACTACGTACTGTGCACAAGTC 59.275 50.000 21.98 12.17 0.00 3.01
114 115 2.545113 CCACTACGTACTGTGCACAAGT 60.545 50.000 21.98 21.11 33.26 3.16
115 116 2.058798 CCACTACGTACTGTGCACAAG 58.941 52.381 21.98 16.12 33.26 3.16
116 117 1.682323 TCCACTACGTACTGTGCACAA 59.318 47.619 21.98 3.65 33.26 3.33
117 118 1.268625 CTCCACTACGTACTGTGCACA 59.731 52.381 20.37 20.37 33.26 4.57
118 119 1.402456 CCTCCACTACGTACTGTGCAC 60.402 57.143 10.75 10.75 33.26 4.57
119 120 0.885879 CCTCCACTACGTACTGTGCA 59.114 55.000 8.96 0.00 33.26 4.57
120 121 1.171308 TCCTCCACTACGTACTGTGC 58.829 55.000 8.96 0.00 33.26 4.57
121 122 3.014623 TCATCCTCCACTACGTACTGTG 58.985 50.000 7.75 7.75 0.00 3.66
122 123 3.361281 TCATCCTCCACTACGTACTGT 57.639 47.619 0.00 0.00 0.00 3.55
123 124 3.632604 ACATCATCCTCCACTACGTACTG 59.367 47.826 0.00 0.00 0.00 2.74
124 125 3.632604 CACATCATCCTCCACTACGTACT 59.367 47.826 0.00 0.00 0.00 2.73
125 126 3.243434 CCACATCATCCTCCACTACGTAC 60.243 52.174 0.00 0.00 0.00 3.67
126 127 2.956333 CCACATCATCCTCCACTACGTA 59.044 50.000 0.00 0.00 0.00 3.57
127 128 1.757118 CCACATCATCCTCCACTACGT 59.243 52.381 0.00 0.00 0.00 3.57
128 129 1.757118 ACCACATCATCCTCCACTACG 59.243 52.381 0.00 0.00 0.00 3.51
129 130 3.738281 CGAACCACATCATCCTCCACTAC 60.738 52.174 0.00 0.00 0.00 2.73
130 131 2.430694 CGAACCACATCATCCTCCACTA 59.569 50.000 0.00 0.00 0.00 2.74
131 132 1.208052 CGAACCACATCATCCTCCACT 59.792 52.381 0.00 0.00 0.00 4.00
132 133 1.656652 CGAACCACATCATCCTCCAC 58.343 55.000 0.00 0.00 0.00 4.02
133 134 0.107703 GCGAACCACATCATCCTCCA 60.108 55.000 0.00 0.00 0.00 3.86
134 135 1.154205 CGCGAACCACATCATCCTCC 61.154 60.000 0.00 0.00 0.00 4.30
135 136 1.766143 GCGCGAACCACATCATCCTC 61.766 60.000 12.10 0.00 0.00 3.71
136 137 1.815421 GCGCGAACCACATCATCCT 60.815 57.895 12.10 0.00 0.00 3.24
137 138 2.106074 TGCGCGAACCACATCATCC 61.106 57.895 12.10 0.00 0.00 3.51
138 139 1.060937 GTGCGCGAACCACATCATC 59.939 57.895 12.10 0.00 33.50 2.92
139 140 2.398554 GGTGCGCGAACCACATCAT 61.399 57.895 31.88 0.00 40.22 2.45
140 141 3.047280 GGTGCGCGAACCACATCA 61.047 61.111 31.88 2.54 40.22 3.07
141 142 3.027170 CTGGTGCGCGAACCACATC 62.027 63.158 35.43 11.15 45.43 3.06
142 143 3.049674 CTGGTGCGCGAACCACAT 61.050 61.111 35.43 0.00 45.43 3.21
161 162 0.529773 TGCTATTTACTCCGCAGCCG 60.530 55.000 0.00 0.00 0.00 5.52
162 163 1.663695 TTGCTATTTACTCCGCAGCC 58.336 50.000 0.00 0.00 33.48 4.85
163 164 3.757745 TTTTGCTATTTACTCCGCAGC 57.242 42.857 0.00 0.00 33.48 5.25
190 191 5.633655 TGAAACCCTAACCTGTAAACTGA 57.366 39.130 0.00 0.00 0.00 3.41
456 470 0.840722 AACCTAGGTCAGTGTGGGGG 60.841 60.000 16.64 0.00 0.00 5.40
457 471 0.324943 CAACCTAGGTCAGTGTGGGG 59.675 60.000 16.64 0.00 0.00 4.96
461 475 0.830444 TCGCCAACCTAGGTCAGTGT 60.830 55.000 16.64 0.00 0.00 3.55
626 642 1.607801 CTCGATCCACCTGAGCCACA 61.608 60.000 0.00 0.00 0.00 4.17
1090 1147 2.244769 CCATTCCATACCCCTCCAACTT 59.755 50.000 0.00 0.00 0.00 2.66
1773 1863 2.492088 GTTGATAGTTGGGCCTGGTTTC 59.508 50.000 4.53 0.00 0.00 2.78
1883 1973 4.498177 GCAACCTTGGAACTTCTTCTTCAC 60.498 45.833 0.00 0.00 0.00 3.18
2142 2232 8.336987 TCATTAGCTATTCTAGAGGCCACTATA 58.663 37.037 10.58 0.45 0.00 1.31
2546 2640 1.417145 AGCCCTCTTTGCATGCAAAAA 59.583 42.857 37.36 28.43 44.07 1.94
2783 2897 0.767375 ACCATGTCCAGCTGTCTGTT 59.233 50.000 13.81 0.00 38.66 3.16
2840 2954 8.172352 ACATAATTGTGTACTTGCCAAACTTA 57.828 30.769 5.98 0.00 33.85 2.24
3310 3450 4.985538 TCAACTTTGTTCTTATGCCCTCT 58.014 39.130 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.