Multiple sequence alignment - TraesCS3B01G491500

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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 TraesCS3B01G491500 chr3B 100.000 2322 0 0 1 2322 737836074 737833753 0.000000e+00 4289
1 TraesCS3B01G491500 chr3B 97.122 2085 60 0 238 2322 28345165 28347249 0.000000e+00 3518
2 TraesCS3B01G491500 chr3B 98.291 234 4 0 1 234 737799345 737799112 5.970000e-111 411
3 TraesCS3B01G491500 chr2B 98.274 2086 33 3 238 2322 631382327 631380244 0.000000e+00 3650
4 TraesCS3B01G491500 chr2B 98.215 2073 36 1 238 2310 90759077 90761148 0.000000e+00 3622
5 TraesCS3B01G491500 chr7B 98.167 2073 38 0 238 2310 678100957 678103029 0.000000e+00 3618
6 TraesCS3B01G491500 chr7B 97.974 2073 42 0 238 2310 134328447 134326375 0.000000e+00 3596
7 TraesCS3B01G491500 chr7B 97.554 2085 51 0 238 2322 664294831 664296915 0.000000e+00 3568
8 TraesCS3B01G491500 chr1B 98.168 2074 37 1 238 2310 615477173 615479246 0.000000e+00 3618
9 TraesCS3B01G491500 chr1B 98.167 2073 38 0 238 2310 618190790 618188718 0.000000e+00 3618
10 TraesCS3B01G491500 chr5B 97.890 2085 42 2 238 2322 415774059 415771977 0.000000e+00 3605
11 TraesCS3B01G491500 chrUn 97.436 234 6 0 1 234 249807900 249808133 1.290000e-107 399
12 TraesCS3B01G491500 chr6B 97.436 234 6 0 1 234 665596436 665596203 1.290000e-107 399
13 TraesCS3B01G491500 chr4B 97.436 234 6 0 1 234 655319417 655319184 1.290000e-107 399
14 TraesCS3B01G491500 chr7A 92.135 178 13 1 1 178 163744887 163744711 1.380000e-62 250
15 TraesCS3B01G491500 chr3A 89.600 125 13 0 54 178 684470485 684470609 2.390000e-35 159


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 TraesCS3B01G491500 chr3B 737833753 737836074 2321 True 4289 4289 100.000 1 2322 1 chr3B.!!$R2 2321
1 TraesCS3B01G491500 chr3B 28345165 28347249 2084 False 3518 3518 97.122 238 2322 1 chr3B.!!$F1 2084
2 TraesCS3B01G491500 chr2B 631380244 631382327 2083 True 3650 3650 98.274 238 2322 1 chr2B.!!$R1 2084
3 TraesCS3B01G491500 chr2B 90759077 90761148 2071 False 3622 3622 98.215 238 2310 1 chr2B.!!$F1 2072
4 TraesCS3B01G491500 chr7B 678100957 678103029 2072 False 3618 3618 98.167 238 2310 1 chr7B.!!$F2 2072
5 TraesCS3B01G491500 chr7B 134326375 134328447 2072 True 3596 3596 97.974 238 2310 1 chr7B.!!$R1 2072
6 TraesCS3B01G491500 chr7B 664294831 664296915 2084 False 3568 3568 97.554 238 2322 1 chr7B.!!$F1 2084
7 TraesCS3B01G491500 chr1B 615477173 615479246 2073 False 3618 3618 98.168 238 2310 1 chr1B.!!$F1 2072
8 TraesCS3B01G491500 chr1B 618188718 618190790 2072 True 3618 3618 98.167 238 2310 1 chr1B.!!$R1 2072
9 TraesCS3B01G491500 chr5B 415771977 415774059 2082 True 3605 3605 97.890 238 2322 1 chr5B.!!$R1 2084

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
158 159 0.463295 CGAGTGAAGCCCATGCAGAT 60.463 55.0 0.0 0.0 41.13 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1396 1397 1.06725 GGCAACGCACACACCAAAT 59.933 52.632 0.0 0.0 0.0 2.32 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
17 18 3.341043 CGAGCGAATCCCATGCGG 61.341 66.667 0.00 0.00 0.00 5.69
27 28 3.439540 CCATGCGGGTTTCCCACG 61.440 66.667 5.64 0.00 45.83 4.94
28 29 2.359354 CATGCGGGTTTCCCACGA 60.359 61.111 5.64 0.00 45.83 4.35
29 30 1.748879 CATGCGGGTTTCCCACGAT 60.749 57.895 5.64 0.00 45.83 3.73
30 31 1.748879 ATGCGGGTTTCCCACGATG 60.749 57.895 5.64 0.00 45.83 3.84
31 32 3.810896 GCGGGTTTCCCACGATGC 61.811 66.667 5.64 0.00 45.83 3.91
32 33 3.496131 CGGGTTTCCCACGATGCG 61.496 66.667 5.64 0.00 45.83 4.73
33 34 3.810896 GGGTTTCCCACGATGCGC 61.811 66.667 0.00 0.00 44.65 6.09
34 35 2.746277 GGTTTCCCACGATGCGCT 60.746 61.111 9.73 0.00 0.00 5.92
35 36 2.480555 GTTTCCCACGATGCGCTG 59.519 61.111 9.73 0.00 0.00 5.18
36 37 2.031919 TTTCCCACGATGCGCTGT 59.968 55.556 9.73 1.10 0.00 4.40
37 38 1.017177 GTTTCCCACGATGCGCTGTA 61.017 55.000 9.73 0.00 0.00 2.74
38 39 0.739462 TTTCCCACGATGCGCTGTAG 60.739 55.000 9.73 0.00 0.00 2.74
39 40 2.572095 TTCCCACGATGCGCTGTAGG 62.572 60.000 9.73 7.54 0.00 3.18
40 41 3.264897 CCACGATGCGCTGTAGGC 61.265 66.667 9.73 0.00 37.64 3.93
50 51 4.415332 CTGTAGGCGTGCGACGGT 62.415 66.667 10.02 0.00 42.82 4.83
51 52 3.909258 CTGTAGGCGTGCGACGGTT 62.909 63.158 10.02 0.00 42.82 4.44
52 53 3.177249 GTAGGCGTGCGACGGTTC 61.177 66.667 10.02 0.00 42.82 3.62
53 54 4.424566 TAGGCGTGCGACGGTTCC 62.425 66.667 10.02 4.05 42.82 3.62
58 59 4.681978 GTGCGACGGTTCCTGGCT 62.682 66.667 0.00 0.00 0.00 4.75
59 60 4.680237 TGCGACGGTTCCTGGCTG 62.680 66.667 0.00 0.00 0.00 4.85
61 62 4.003788 CGACGGTTCCTGGCTGGT 62.004 66.667 10.44 0.00 37.07 4.00
62 63 2.430367 GACGGTTCCTGGCTGGTT 59.570 61.111 10.44 0.00 37.07 3.67
63 64 1.671379 GACGGTTCCTGGCTGGTTC 60.671 63.158 10.44 4.92 37.07 3.62
64 65 2.359975 CGGTTCCTGGCTGGTTCC 60.360 66.667 10.44 12.15 37.07 3.62
65 66 2.359975 GGTTCCTGGCTGGTTCCG 60.360 66.667 10.44 0.00 37.07 4.30
66 67 3.056328 GTTCCTGGCTGGTTCCGC 61.056 66.667 10.44 0.00 37.07 5.54
67 68 4.697756 TTCCTGGCTGGTTCCGCG 62.698 66.667 10.44 0.00 37.07 6.46
90 91 4.394712 GCGGACAGGGGTGTGGAG 62.395 72.222 0.00 0.00 0.00 3.86
91 92 3.706373 CGGACAGGGGTGTGGAGG 61.706 72.222 0.00 0.00 0.00 4.30
92 93 3.330720 GGACAGGGGTGTGGAGGG 61.331 72.222 0.00 0.00 0.00 4.30
93 94 4.035102 GACAGGGGTGTGGAGGGC 62.035 72.222 0.00 0.00 0.00 5.19
94 95 4.918360 ACAGGGGTGTGGAGGGCA 62.918 66.667 0.00 0.00 0.00 5.36
95 96 4.039092 CAGGGGTGTGGAGGGCAG 62.039 72.222 0.00 0.00 0.00 4.85
96 97 4.599500 AGGGGTGTGGAGGGCAGT 62.599 66.667 0.00 0.00 0.00 4.40
97 98 4.351054 GGGGTGTGGAGGGCAGTG 62.351 72.222 0.00 0.00 0.00 3.66
110 111 3.052082 CAGTGCGGCCAGGTGAAG 61.052 66.667 2.24 0.00 0.00 3.02
111 112 3.560251 AGTGCGGCCAGGTGAAGT 61.560 61.111 2.24 0.00 0.00 3.01
112 113 3.050275 GTGCGGCCAGGTGAAGTC 61.050 66.667 2.24 0.00 0.00 3.01
113 114 4.329545 TGCGGCCAGGTGAAGTCC 62.330 66.667 2.24 0.00 0.00 3.85
115 116 4.003788 CGGCCAGGTGAAGTCCGT 62.004 66.667 2.24 0.00 35.75 4.69
116 117 2.642254 CGGCCAGGTGAAGTCCGTA 61.642 63.158 2.24 0.00 35.75 4.02
117 118 1.079336 GGCCAGGTGAAGTCCGTAC 60.079 63.158 0.00 0.00 0.00 3.67
118 119 1.445582 GCCAGGTGAAGTCCGTACG 60.446 63.158 8.69 8.69 0.00 3.67
119 120 1.214589 CCAGGTGAAGTCCGTACGG 59.785 63.158 28.66 28.66 0.00 4.02
120 121 1.246056 CCAGGTGAAGTCCGTACGGA 61.246 60.000 32.61 32.61 42.90 4.69
130 131 2.644418 CGTACGGACGGTTGGACA 59.356 61.111 13.75 0.00 45.63 4.02
131 132 1.213537 CGTACGGACGGTTGGACAT 59.786 57.895 13.75 0.00 45.63 3.06
132 133 1.074319 CGTACGGACGGTTGGACATG 61.074 60.000 13.75 0.00 45.63 3.21
133 134 1.079681 TACGGACGGTTGGACATGC 60.080 57.895 0.00 0.00 0.00 4.06
134 135 2.510064 TACGGACGGTTGGACATGCC 62.510 60.000 0.00 0.00 37.10 4.40
135 136 2.750237 GGACGGTTGGACATGCCC 60.750 66.667 0.00 0.00 34.97 5.36
136 137 3.124921 GACGGTTGGACATGCCCG 61.125 66.667 0.00 0.00 45.72 6.13
137 138 4.715523 ACGGTTGGACATGCCCGG 62.716 66.667 0.00 0.00 44.57 5.73
146 147 4.776322 CATGCCCGGCCGAGTGAA 62.776 66.667 30.73 9.92 0.00 3.18
147 148 4.473520 ATGCCCGGCCGAGTGAAG 62.474 66.667 30.73 8.54 0.00 3.02
153 154 2.825836 GGCCGAGTGAAGCCCATG 60.826 66.667 0.00 0.00 43.76 3.66
154 155 3.512516 GCCGAGTGAAGCCCATGC 61.513 66.667 0.00 0.00 37.95 4.06
155 156 2.046023 CCGAGTGAAGCCCATGCA 60.046 61.111 0.00 0.00 41.13 3.96
156 157 2.110967 CCGAGTGAAGCCCATGCAG 61.111 63.158 0.00 0.00 41.13 4.41
157 158 1.078918 CGAGTGAAGCCCATGCAGA 60.079 57.895 0.00 0.00 41.13 4.26
158 159 0.463295 CGAGTGAAGCCCATGCAGAT 60.463 55.000 0.00 0.00 41.13 2.90
159 160 1.022735 GAGTGAAGCCCATGCAGATG 58.977 55.000 0.00 0.00 41.13 2.90
160 161 1.035932 AGTGAAGCCCATGCAGATGC 61.036 55.000 0.00 0.00 41.13 3.91
161 162 2.116533 TGAAGCCCATGCAGATGCG 61.117 57.895 0.00 0.00 45.83 4.73
162 163 1.820906 GAAGCCCATGCAGATGCGA 60.821 57.895 0.00 0.00 45.83 5.10
163 164 1.378882 GAAGCCCATGCAGATGCGAA 61.379 55.000 0.00 0.00 45.83 4.70
164 165 1.660560 AAGCCCATGCAGATGCGAAC 61.661 55.000 0.00 0.00 45.83 3.95
165 166 2.117156 GCCCATGCAGATGCGAACT 61.117 57.895 0.00 0.00 45.83 3.01
166 167 0.815213 GCCCATGCAGATGCGAACTA 60.815 55.000 0.00 0.00 45.83 2.24
167 168 0.940126 CCCATGCAGATGCGAACTAC 59.060 55.000 0.00 0.00 45.83 2.73
168 169 0.578683 CCATGCAGATGCGAACTACG 59.421 55.000 0.00 0.00 45.83 3.51
196 197 4.980805 GTGCGGCGGTTCTGTCCA 62.981 66.667 9.78 0.00 0.00 4.02
197 198 4.680237 TGCGGCGGTTCTGTCCAG 62.680 66.667 9.78 0.00 0.00 3.86
199 200 4.003788 CGGCGGTTCTGTCCAGGT 62.004 66.667 0.00 0.00 0.00 4.00
200 201 2.358737 GGCGGTTCTGTCCAGGTG 60.359 66.667 0.00 0.00 0.00 4.00
201 202 3.050275 GCGGTTCTGTCCAGGTGC 61.050 66.667 0.00 0.00 0.00 5.01
202 203 2.738521 CGGTTCTGTCCAGGTGCG 60.739 66.667 0.00 0.00 0.00 5.34
203 204 2.358737 GGTTCTGTCCAGGTGCGG 60.359 66.667 0.00 0.00 0.00 5.69
204 205 3.050275 GTTCTGTCCAGGTGCGGC 61.050 66.667 0.00 0.00 0.00 6.53
205 206 3.555324 TTCTGTCCAGGTGCGGCA 61.555 61.111 0.00 0.00 0.00 5.69
206 207 3.825160 TTCTGTCCAGGTGCGGCAC 62.825 63.158 24.43 24.43 0.00 5.01
233 234 3.851955 GCATCCAGCCCCATCTTG 58.148 61.111 0.00 0.00 37.23 3.02
234 235 1.228228 GCATCCAGCCCCATCTTGA 59.772 57.895 0.00 0.00 37.23 3.02
235 236 0.822532 GCATCCAGCCCCATCTTGAG 60.823 60.000 0.00 0.00 37.23 3.02
236 237 0.549950 CATCCAGCCCCATCTTGAGT 59.450 55.000 0.00 0.00 0.00 3.41
524 525 2.288825 TGGTGAGATGACCGTCACTTTC 60.289 50.000 2.57 2.90 42.37 2.62
782 783 7.060421 CCAGGGCTTACTTATGGAATCTTTTA 58.940 38.462 0.00 0.00 32.55 1.52
1396 1397 2.839975 TGTGCTTTCGTGACCAACATA 58.160 42.857 0.00 0.00 0.00 2.29
1425 1426 0.106769 TGCGTTGCCCCATGATATGT 60.107 50.000 0.00 0.00 0.00 2.29
1494 1495 0.533308 GAGTACAACAACGCACCCCA 60.533 55.000 0.00 0.00 0.00 4.96
1495 1496 0.109723 AGTACAACAACGCACCCCAT 59.890 50.000 0.00 0.00 0.00 4.00
1614 1616 6.219473 CGATACTTCTCATGCTTTGTAGGAT 58.781 40.000 0.00 0.00 31.88 3.24
1806 1808 1.351017 CCTTAAGGGTGCTTGGACTCA 59.649 52.381 14.25 0.00 0.00 3.41
1810 1812 2.401766 GGGTGCTTGGACTCATGCG 61.402 63.158 0.00 0.00 44.16 4.73
1861 1863 2.029739 TGCTGATGGTGCATTCAACAAG 60.030 45.455 0.00 0.00 44.13 3.16
2273 2276 6.363626 CACGTGCTTAGTATAGAATGGATGTC 59.636 42.308 0.82 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.341043 CCGCATGGGATTCGCTCG 61.341 66.667 12.02 3.61 38.47 5.03
18 19 1.017177 TACAGCGCATCGTGGGAAAC 61.017 55.000 11.47 0.00 31.21 2.78
19 20 0.739462 CTACAGCGCATCGTGGGAAA 60.739 55.000 11.47 0.00 31.21 3.13
20 21 1.153647 CTACAGCGCATCGTGGGAA 60.154 57.895 11.47 0.00 31.21 3.97
21 22 2.494445 CTACAGCGCATCGTGGGA 59.506 61.111 11.47 0.00 31.21 4.37
22 23 2.586079 CCTACAGCGCATCGTGGG 60.586 66.667 11.47 11.51 0.00 4.61
23 24 3.264897 GCCTACAGCGCATCGTGG 61.265 66.667 11.47 5.54 0.00 4.94
33 34 3.909258 AACCGTCGCACGCCTACAG 62.909 63.158 3.56 0.00 40.91 2.74
34 35 3.902162 GAACCGTCGCACGCCTACA 62.902 63.158 3.56 0.00 40.91 2.74
35 36 3.177249 GAACCGTCGCACGCCTAC 61.177 66.667 3.56 0.00 40.91 3.18
36 37 4.424566 GGAACCGTCGCACGCCTA 62.425 66.667 3.56 0.00 40.91 3.93
41 42 4.681978 AGCCAGGAACCGTCGCAC 62.682 66.667 0.00 0.00 0.00 5.34
42 43 4.680237 CAGCCAGGAACCGTCGCA 62.680 66.667 0.00 0.00 0.00 5.10
44 45 3.530910 AACCAGCCAGGAACCGTCG 62.531 63.158 0.00 0.00 41.22 5.12
45 46 1.671379 GAACCAGCCAGGAACCGTC 60.671 63.158 0.00 0.00 41.22 4.79
46 47 2.430367 GAACCAGCCAGGAACCGT 59.570 61.111 0.00 0.00 41.22 4.83
47 48 2.359975 GGAACCAGCCAGGAACCG 60.360 66.667 0.00 0.00 41.22 4.44
48 49 2.359975 CGGAACCAGCCAGGAACC 60.360 66.667 0.00 2.14 41.22 3.62
49 50 3.056328 GCGGAACCAGCCAGGAAC 61.056 66.667 0.00 0.00 41.22 3.62
50 51 4.697756 CGCGGAACCAGCCAGGAA 62.698 66.667 0.00 0.00 41.22 3.36
73 74 4.394712 CTCCACACCCCTGTCCGC 62.395 72.222 0.00 0.00 0.00 5.54
74 75 3.706373 CCTCCACACCCCTGTCCG 61.706 72.222 0.00 0.00 0.00 4.79
75 76 3.330720 CCCTCCACACCCCTGTCC 61.331 72.222 0.00 0.00 0.00 4.02
76 77 4.035102 GCCCTCCACACCCCTGTC 62.035 72.222 0.00 0.00 0.00 3.51
77 78 4.918360 TGCCCTCCACACCCCTGT 62.918 66.667 0.00 0.00 0.00 4.00
78 79 4.039092 CTGCCCTCCACACCCCTG 62.039 72.222 0.00 0.00 0.00 4.45
79 80 4.599500 ACTGCCCTCCACACCCCT 62.599 66.667 0.00 0.00 0.00 4.79
80 81 4.351054 CACTGCCCTCCACACCCC 62.351 72.222 0.00 0.00 0.00 4.95
93 94 3.052082 CTTCACCTGGCCGCACTG 61.052 66.667 0.00 0.00 0.00 3.66
94 95 3.537206 GACTTCACCTGGCCGCACT 62.537 63.158 0.00 0.00 0.00 4.40
95 96 3.050275 GACTTCACCTGGCCGCAC 61.050 66.667 0.00 0.00 0.00 5.34
96 97 4.329545 GGACTTCACCTGGCCGCA 62.330 66.667 0.00 0.00 0.00 5.69
98 99 2.642254 TACGGACTTCACCTGGCCG 61.642 63.158 6.47 6.47 46.83 6.13
99 100 1.079336 GTACGGACTTCACCTGGCC 60.079 63.158 0.00 0.00 0.00 5.36
100 101 1.445582 CGTACGGACTTCACCTGGC 60.446 63.158 7.57 0.00 0.00 4.85
101 102 1.214589 CCGTACGGACTTCACCTGG 59.785 63.158 30.64 0.00 37.50 4.45
102 103 2.260247 TCCGTACGGACTTCACCTG 58.740 57.895 32.61 3.59 39.76 4.00
103 104 4.828409 TCCGTACGGACTTCACCT 57.172 55.556 32.61 0.00 39.76 4.00
114 115 1.356527 GCATGTCCAACCGTCCGTAC 61.357 60.000 0.00 0.00 0.00 3.67
115 116 1.079681 GCATGTCCAACCGTCCGTA 60.080 57.895 0.00 0.00 0.00 4.02
116 117 2.358247 GCATGTCCAACCGTCCGT 60.358 61.111 0.00 0.00 0.00 4.69
117 118 3.124921 GGCATGTCCAACCGTCCG 61.125 66.667 0.00 0.00 34.01 4.79
118 119 2.750237 GGGCATGTCCAACCGTCC 60.750 66.667 12.68 0.00 36.21 4.79
119 120 3.124921 CGGGCATGTCCAACCGTC 61.125 66.667 18.31 0.00 41.34 4.79
120 121 4.715523 CCGGGCATGTCCAACCGT 62.716 66.667 18.31 0.00 44.57 4.83
129 130 4.776322 TTCACTCGGCCGGGCATG 62.776 66.667 28.82 18.14 0.00 4.06
130 131 4.473520 CTTCACTCGGCCGGGCAT 62.474 66.667 28.82 2.55 0.00 4.40
136 137 2.825836 CATGGGCTTCACTCGGCC 60.826 66.667 0.00 0.00 46.89 6.13
137 138 3.512516 GCATGGGCTTCACTCGGC 61.513 66.667 0.00 0.00 36.96 5.54
138 139 2.046023 TGCATGGGCTTCACTCGG 60.046 61.111 0.00 0.00 41.91 4.63
139 140 0.463295 ATCTGCATGGGCTTCACTCG 60.463 55.000 0.00 0.00 41.91 4.18
140 141 1.022735 CATCTGCATGGGCTTCACTC 58.977 55.000 0.00 0.00 41.91 3.51
141 142 1.035932 GCATCTGCATGGGCTTCACT 61.036 55.000 0.00 0.00 41.91 3.41
142 143 1.436336 GCATCTGCATGGGCTTCAC 59.564 57.895 0.00 0.00 41.91 3.18
143 144 2.116533 CGCATCTGCATGGGCTTCA 61.117 57.895 2.72 0.00 42.21 3.02
144 145 1.378882 TTCGCATCTGCATGGGCTTC 61.379 55.000 2.72 0.00 41.68 3.86
145 146 1.378911 TTCGCATCTGCATGGGCTT 60.379 52.632 2.72 0.00 41.68 4.35
146 147 2.117156 GTTCGCATCTGCATGGGCT 61.117 57.895 2.72 0.00 41.68 5.19
147 148 0.815213 TAGTTCGCATCTGCATGGGC 60.815 55.000 2.72 0.00 41.68 5.36
148 149 0.940126 GTAGTTCGCATCTGCATGGG 59.060 55.000 2.72 0.00 42.98 4.00
149 150 0.578683 CGTAGTTCGCATCTGCATGG 59.421 55.000 2.72 0.00 42.21 3.66
160 161 1.726845 CGCCTACAACGCGTAGTTCG 61.727 60.000 14.46 8.51 45.40 3.95
161 162 1.986154 CGCCTACAACGCGTAGTTC 59.014 57.895 14.46 0.00 45.40 3.01
162 163 4.157817 CGCCTACAACGCGTAGTT 57.842 55.556 14.46 1.61 45.40 2.24
179 180 4.980805 TGGACAGAACCGCCGCAC 62.981 66.667 0.00 0.00 0.00 5.34
180 181 4.680237 CTGGACAGAACCGCCGCA 62.680 66.667 0.00 0.00 0.00 5.69
182 183 4.003788 ACCTGGACAGAACCGCCG 62.004 66.667 0.00 0.00 0.00 6.46
183 184 2.358737 CACCTGGACAGAACCGCC 60.359 66.667 0.00 0.00 0.00 6.13
184 185 3.050275 GCACCTGGACAGAACCGC 61.050 66.667 0.00 0.00 0.00 5.68
185 186 2.738521 CGCACCTGGACAGAACCG 60.739 66.667 0.00 0.00 0.00 4.44
186 187 2.358737 CCGCACCTGGACAGAACC 60.359 66.667 0.00 0.00 0.00 3.62
187 188 3.050275 GCCGCACCTGGACAGAAC 61.050 66.667 0.00 0.00 0.00 3.01
188 189 3.555324 TGCCGCACCTGGACAGAA 61.555 61.111 0.00 0.00 0.00 3.02
189 190 4.314440 GTGCCGCACCTGGACAGA 62.314 66.667 12.80 0.00 0.00 3.41
192 193 4.760047 ATCGTGCCGCACCTGGAC 62.760 66.667 17.81 0.00 0.00 4.02
193 194 4.758251 CATCGTGCCGCACCTGGA 62.758 66.667 17.81 9.75 0.00 3.86
206 207 2.313172 GCTGGATGCTACGCCATCG 61.313 63.158 5.56 0.00 41.95 3.84
207 208 1.963338 GGCTGGATGCTACGCCATC 60.963 63.158 7.63 3.48 42.06 3.51
208 209 2.111878 GGCTGGATGCTACGCCAT 59.888 61.111 7.63 0.00 42.06 4.40
209 210 4.175337 GGGCTGGATGCTACGCCA 62.175 66.667 12.90 0.00 44.23 5.69
210 211 4.937431 GGGGCTGGATGCTACGCC 62.937 72.222 4.63 4.63 42.39 5.68
211 212 3.482232 ATGGGGCTGGATGCTACGC 62.482 63.158 0.00 0.00 42.39 4.42
212 213 1.302033 GATGGGGCTGGATGCTACG 60.302 63.158 0.00 0.00 42.39 3.51
213 214 0.475906 AAGATGGGGCTGGATGCTAC 59.524 55.000 0.00 0.00 42.39 3.58
214 215 0.475475 CAAGATGGGGCTGGATGCTA 59.525 55.000 0.00 0.00 42.39 3.49
215 216 1.229359 CAAGATGGGGCTGGATGCT 59.771 57.895 0.00 0.00 42.39 3.79
216 217 0.822532 CTCAAGATGGGGCTGGATGC 60.823 60.000 0.00 0.00 41.94 3.91
217 218 0.549950 ACTCAAGATGGGGCTGGATG 59.450 55.000 0.00 0.00 0.00 3.51
218 219 2.196742 TACTCAAGATGGGGCTGGAT 57.803 50.000 0.00 0.00 0.00 3.41
219 220 2.196742 ATACTCAAGATGGGGCTGGA 57.803 50.000 0.00 0.00 0.00 3.86
220 221 4.202503 ACAATATACTCAAGATGGGGCTGG 60.203 45.833 0.00 0.00 0.00 4.85
221 222 4.758674 CACAATATACTCAAGATGGGGCTG 59.241 45.833 0.00 0.00 0.00 4.85
222 223 4.660303 TCACAATATACTCAAGATGGGGCT 59.340 41.667 0.00 0.00 0.00 5.19
223 224 4.973168 TCACAATATACTCAAGATGGGGC 58.027 43.478 0.00 0.00 0.00 5.80
224 225 6.179906 ACTCACAATATACTCAAGATGGGG 57.820 41.667 0.00 0.00 0.00 4.96
296 297 3.094572 CCGAAGTACTGGAGGAACCTAA 58.905 50.000 0.00 0.00 39.86 2.69
524 525 3.443037 GGAGATCATCGCAATATCCTCG 58.557 50.000 0.00 0.00 32.80 4.63
562 563 1.229400 TTCCCGGTAAGAGCCCTGT 60.229 57.895 0.00 0.00 0.00 4.00
964 965 5.801444 CCAACTGCACATTTGTATACACATG 59.199 40.000 24.07 24.07 39.30 3.21
1396 1397 1.067250 GGCAACGCACACACCAAAT 59.933 52.632 0.00 0.00 0.00 2.32
1494 1495 4.220821 ACACTTGTCTCAACATACTCCGAT 59.779 41.667 0.00 0.00 34.73 4.18
1495 1496 3.572682 ACACTTGTCTCAACATACTCCGA 59.427 43.478 0.00 0.00 34.73 4.55
1614 1616 1.723608 CTTGTTGTGTTGCCGGCTCA 61.724 55.000 29.70 22.99 0.00 4.26
1806 1808 4.624015 CATTAATTCCAAGCAATCCGCAT 58.376 39.130 0.00 0.00 46.13 4.73
1810 1812 4.405116 TGGCATTAATTCCAAGCAATCC 57.595 40.909 4.16 0.00 0.00 3.01
1861 1863 4.262678 GCTCCAATGGTCTCCCTAATAGAC 60.263 50.000 0.00 0.00 42.19 2.59
2273 2276 0.108138 ATGGACGAGCGGAAGAAAGG 60.108 55.000 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.