Multiple sequence alignment - TraesCS3B01G282100

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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 TraesCS3B01G282100 chr3B 100.000 3210 0 0 1 3210 452563308 452560099 0.000000e+00 5928
1 TraesCS3B01G282100 chr3B 98.174 3066 45 6 152 3210 73031276 73034337 0.000000e+00 5341
2 TraesCS3B01G282100 chr2B 97.876 3060 60 3 156 3210 553880196 553883255 0.000000e+00 5286
3 TraesCS3B01G282100 chr4B 97.777 3059 61 6 156 3210 629907328 629910383 0.000000e+00 5265
4 TraesCS3B01G282100 chr4B 96.709 3069 65 10 156 3210 665900182 665903228 0.000000e+00 5075
5 TraesCS3B01G282100 chr1A 97.197 3068 69 7 157 3209 444169075 444166010 0.000000e+00 5173
6 TraesCS3B01G282100 chr4A 96.905 3069 78 7 157 3210 36004230 36001164 0.000000e+00 5125
7 TraesCS3B01G282100 chr5A 96.136 1967 44 7 156 2111 705867910 705869855 0.000000e+00 3182
8 TraesCS3B01G282100 chr5A 97.826 1104 23 1 2107 3210 705883335 705884437 0.000000e+00 1905
9 TraesCS3B01G282100 chr5A 97.419 1085 28 0 1129 2213 262471612 262470528 0.000000e+00 1849
10 TraesCS3B01G282100 chr5A 91.575 724 25 4 156 843 310728836 310728113 0.000000e+00 966
11 TraesCS3B01G282100 chr2A 97.143 1085 31 0 1129 2213 694743563 694742479 0.000000e+00 1832
12 TraesCS3B01G282100 chr2A 96.113 283 8 1 852 1131 694743887 694743605 2.920000e-125 459
13 TraesCS3B01G282100 chr5D 97.972 986 19 1 2225 3210 309068222 309067238 0.000000e+00 1709
14 TraesCS3B01G282100 chr1D 97.870 986 21 0 2225 3210 97785404 97784419 0.000000e+00 1705
15 TraesCS3B01G282100 chr7A 93.705 699 31 5 157 843 699627689 699626992 0.000000e+00 1035
16 TraesCS3B01G282100 chr7A 96.140 285 8 1 850 1131 709138064 709137780 2.260000e-126 462


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 TraesCS3B01G282100 chr3B 452560099 452563308 3209 True 5928.0 5928 100.000 1 3210 1 chr3B.!!$R1 3209
1 TraesCS3B01G282100 chr3B 73031276 73034337 3061 False 5341.0 5341 98.174 152 3210 1 chr3B.!!$F1 3058
2 TraesCS3B01G282100 chr2B 553880196 553883255 3059 False 5286.0 5286 97.876 156 3210 1 chr2B.!!$F1 3054
3 TraesCS3B01G282100 chr4B 629907328 629910383 3055 False 5265.0 5265 97.777 156 3210 1 chr4B.!!$F1 3054
4 TraesCS3B01G282100 chr4B 665900182 665903228 3046 False 5075.0 5075 96.709 156 3210 1 chr4B.!!$F2 3054
5 TraesCS3B01G282100 chr1A 444166010 444169075 3065 True 5173.0 5173 97.197 157 3209 1 chr1A.!!$R1 3052
6 TraesCS3B01G282100 chr4A 36001164 36004230 3066 True 5125.0 5125 96.905 157 3210 1 chr4A.!!$R1 3053
7 TraesCS3B01G282100 chr5A 705867910 705869855 1945 False 3182.0 3182 96.136 156 2111 1 chr5A.!!$F1 1955
8 TraesCS3B01G282100 chr5A 705883335 705884437 1102 False 1905.0 1905 97.826 2107 3210 1 chr5A.!!$F2 1103
9 TraesCS3B01G282100 chr5A 262470528 262471612 1084 True 1849.0 1849 97.419 1129 2213 1 chr5A.!!$R1 1084
10 TraesCS3B01G282100 chr5A 310728113 310728836 723 True 966.0 966 91.575 156 843 1 chr5A.!!$R2 687
11 TraesCS3B01G282100 chr2A 694742479 694743887 1408 True 1145.5 1832 96.628 852 2213 2 chr2A.!!$R1 1361
12 TraesCS3B01G282100 chr5D 309067238 309068222 984 True 1709.0 1709 97.972 2225 3210 1 chr5D.!!$R1 985
13 TraesCS3B01G282100 chr1D 97784419 97785404 985 True 1705.0 1705 97.870 2225 3210 1 chr1D.!!$R1 985
14 TraesCS3B01G282100 chr7A 699626992 699627689 697 True 1035.0 1035 93.705 157 843 1 chr7A.!!$R1 686

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
122 123 0.044092 TTGGCTCCTCCCTATGGTCA 59.956 55.0 0.0 0.0 0.0 4.02 F
564 599 0.179000 GCCCTCGGTCTCACATCAAT 59.821 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1581 1.891933 TCTACCTTGCCATCCATCCA 58.108 50.0 0.00 0.00 0.0 3.41 R
2448 2542 0.112995 ATGGTGGTGGCATCAACAGT 59.887 50.0 24.44 9.57 41.9 3.55 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 2.726555 CTGCTACTGCTGCATTTACG 57.273 50.000 1.31 0.00 39.86 3.18
22 23 0.726827 TGCTACTGCTGCATTTACGC 59.273 50.000 1.31 2.82 40.48 4.42
23 24 1.009829 GCTACTGCTGCATTTACGCT 58.990 50.000 1.31 0.00 36.03 5.07
24 25 1.004504 GCTACTGCTGCATTTACGCTC 60.005 52.381 1.31 0.00 36.03 5.03
25 26 2.544685 CTACTGCTGCATTTACGCTCT 58.455 47.619 1.31 0.00 0.00 4.09
26 27 1.813513 ACTGCTGCATTTACGCTCTT 58.186 45.000 1.31 0.00 0.00 2.85
27 28 1.466167 ACTGCTGCATTTACGCTCTTG 59.534 47.619 1.31 0.00 0.00 3.02
28 29 1.733912 CTGCTGCATTTACGCTCTTGA 59.266 47.619 1.31 0.00 0.00 3.02
29 30 2.150390 TGCTGCATTTACGCTCTTGAA 58.850 42.857 0.00 0.00 0.00 2.69
30 31 2.160219 TGCTGCATTTACGCTCTTGAAG 59.840 45.455 0.00 0.00 0.00 3.02
31 32 2.476854 GCTGCATTTACGCTCTTGAAGG 60.477 50.000 0.00 0.00 0.00 3.46
32 33 1.468520 TGCATTTACGCTCTTGAAGGC 59.531 47.619 0.00 0.00 0.00 4.35
37 38 4.185413 CGCTCTTGAAGGCGCTAA 57.815 55.556 7.64 0.00 44.64 3.09
38 39 2.456000 CGCTCTTGAAGGCGCTAAA 58.544 52.632 7.64 0.00 44.64 1.85
39 40 0.371645 CGCTCTTGAAGGCGCTAAAG 59.628 55.000 7.64 6.47 44.64 1.85
40 41 1.443802 GCTCTTGAAGGCGCTAAAGT 58.556 50.000 7.64 0.00 0.00 2.66
41 42 2.618053 GCTCTTGAAGGCGCTAAAGTA 58.382 47.619 7.64 0.00 0.00 2.24
42 43 2.605366 GCTCTTGAAGGCGCTAAAGTAG 59.395 50.000 7.64 7.06 0.00 2.57
43 44 3.676324 GCTCTTGAAGGCGCTAAAGTAGA 60.676 47.826 7.64 3.02 0.00 2.59
44 45 4.109050 CTCTTGAAGGCGCTAAAGTAGAG 58.891 47.826 7.64 9.24 0.00 2.43
53 54 3.851098 CGCTAAAGTAGAGCAGAAAGGT 58.149 45.455 0.00 0.00 40.09 3.50
54 55 4.995124 CGCTAAAGTAGAGCAGAAAGGTA 58.005 43.478 0.00 0.00 40.09 3.08
55 56 5.593010 CGCTAAAGTAGAGCAGAAAGGTAT 58.407 41.667 0.00 0.00 40.09 2.73
56 57 5.460419 CGCTAAAGTAGAGCAGAAAGGTATG 59.540 44.000 0.00 0.00 40.09 2.39
57 58 5.235401 GCTAAAGTAGAGCAGAAAGGTATGC 59.765 44.000 0.00 0.00 42.52 3.14
58 59 3.828875 AGTAGAGCAGAAAGGTATGCC 57.171 47.619 0.00 0.00 43.25 4.40
59 60 3.107601 AGTAGAGCAGAAAGGTATGCCA 58.892 45.455 1.54 0.00 43.25 4.92
60 61 3.713764 AGTAGAGCAGAAAGGTATGCCAT 59.286 43.478 1.54 0.00 43.25 4.40
61 62 2.928334 AGAGCAGAAAGGTATGCCATG 58.072 47.619 1.54 0.00 43.25 3.66
62 63 2.507058 AGAGCAGAAAGGTATGCCATGA 59.493 45.455 1.54 0.00 43.25 3.07
63 64 2.877168 GAGCAGAAAGGTATGCCATGAG 59.123 50.000 1.54 0.00 43.25 2.90
64 65 2.240667 AGCAGAAAGGTATGCCATGAGT 59.759 45.455 1.54 0.00 43.25 3.41
65 66 3.019564 GCAGAAAGGTATGCCATGAGTT 58.980 45.455 1.54 0.00 35.89 3.01
66 67 3.445096 GCAGAAAGGTATGCCATGAGTTT 59.555 43.478 1.54 0.00 35.89 2.66
67 68 4.439289 GCAGAAAGGTATGCCATGAGTTTC 60.439 45.833 1.54 3.10 35.89 2.78
68 69 4.096984 CAGAAAGGTATGCCATGAGTTTCC 59.903 45.833 1.54 0.00 37.19 3.13
69 70 2.736670 AGGTATGCCATGAGTTTCCC 57.263 50.000 1.54 0.00 37.19 3.97
70 71 2.208872 AGGTATGCCATGAGTTTCCCT 58.791 47.619 1.54 0.00 37.19 4.20
71 72 2.173569 AGGTATGCCATGAGTTTCCCTC 59.826 50.000 1.54 0.00 37.74 4.30
72 73 2.173569 GGTATGCCATGAGTTTCCCTCT 59.826 50.000 0.00 0.00 36.54 3.69
73 74 3.372025 GGTATGCCATGAGTTTCCCTCTT 60.372 47.826 0.00 0.00 36.54 2.85
74 75 2.496899 TGCCATGAGTTTCCCTCTTC 57.503 50.000 0.00 0.00 41.11 2.87
75 76 1.004745 TGCCATGAGTTTCCCTCTTCC 59.995 52.381 0.00 0.00 41.11 3.46
76 77 1.004745 GCCATGAGTTTCCCTCTTCCA 59.995 52.381 0.00 0.00 41.11 3.53
77 78 2.555227 GCCATGAGTTTCCCTCTTCCAA 60.555 50.000 0.00 0.00 41.11 3.53
78 79 3.350833 CCATGAGTTTCCCTCTTCCAAG 58.649 50.000 0.00 0.00 41.11 3.61
79 80 3.245052 CCATGAGTTTCCCTCTTCCAAGT 60.245 47.826 0.00 0.00 41.11 3.16
80 81 4.401925 CATGAGTTTCCCTCTTCCAAGTT 58.598 43.478 0.00 0.00 41.11 2.66
81 82 4.519906 TGAGTTTCCCTCTTCCAAGTTT 57.480 40.909 0.00 0.00 41.11 2.66
82 83 4.867086 TGAGTTTCCCTCTTCCAAGTTTT 58.133 39.130 0.00 0.00 41.11 2.43
83 84 4.887655 TGAGTTTCCCTCTTCCAAGTTTTC 59.112 41.667 0.00 0.00 41.11 2.29
84 85 5.130705 AGTTTCCCTCTTCCAAGTTTTCT 57.869 39.130 0.00 0.00 0.00 2.52
85 86 4.889995 AGTTTCCCTCTTCCAAGTTTTCTG 59.110 41.667 0.00 0.00 0.00 3.02
86 87 4.788925 TTCCCTCTTCCAAGTTTTCTGA 57.211 40.909 0.00 0.00 0.00 3.27
87 88 4.357918 TCCCTCTTCCAAGTTTTCTGAG 57.642 45.455 0.00 0.00 0.00 3.35
88 89 2.816672 CCCTCTTCCAAGTTTTCTGAGC 59.183 50.000 0.00 0.00 0.00 4.26
89 90 3.497584 CCCTCTTCCAAGTTTTCTGAGCT 60.498 47.826 0.00 0.00 0.00 4.09
90 91 4.140536 CCTCTTCCAAGTTTTCTGAGCTT 58.859 43.478 0.00 0.00 0.00 3.74
91 92 4.215185 CCTCTTCCAAGTTTTCTGAGCTTC 59.785 45.833 0.00 0.00 0.00 3.86
92 93 5.041191 TCTTCCAAGTTTTCTGAGCTTCT 57.959 39.130 0.00 0.00 0.00 2.85
93 94 5.440610 TCTTCCAAGTTTTCTGAGCTTCTT 58.559 37.500 0.00 0.00 0.00 2.52
94 95 5.888161 TCTTCCAAGTTTTCTGAGCTTCTTT 59.112 36.000 0.00 0.00 0.00 2.52
95 96 5.505173 TCCAAGTTTTCTGAGCTTCTTTG 57.495 39.130 0.00 0.00 0.00 2.77
96 97 4.047142 CCAAGTTTTCTGAGCTTCTTTGC 58.953 43.478 0.00 0.00 0.00 3.68
97 98 3.615849 AGTTTTCTGAGCTTCTTTGCG 57.384 42.857 0.00 0.00 38.13 4.85
98 99 3.206150 AGTTTTCTGAGCTTCTTTGCGA 58.794 40.909 0.00 0.00 38.13 5.10
99 100 3.817647 AGTTTTCTGAGCTTCTTTGCGAT 59.182 39.130 0.00 0.00 38.13 4.58
100 101 4.997395 AGTTTTCTGAGCTTCTTTGCGATA 59.003 37.500 0.00 0.00 38.13 2.92
101 102 5.470098 AGTTTTCTGAGCTTCTTTGCGATAA 59.530 36.000 0.00 0.00 38.13 1.75
102 103 6.150140 AGTTTTCTGAGCTTCTTTGCGATAAT 59.850 34.615 0.00 0.00 38.13 1.28
103 104 6.500684 TTTCTGAGCTTCTTTGCGATAATT 57.499 33.333 0.00 0.00 38.13 1.40
104 105 6.500684 TTCTGAGCTTCTTTGCGATAATTT 57.499 33.333 0.00 0.00 38.13 1.82
105 106 5.872635 TCTGAGCTTCTTTGCGATAATTTG 58.127 37.500 0.00 0.00 38.13 2.32
106 107 4.985413 TGAGCTTCTTTGCGATAATTTGG 58.015 39.130 0.00 0.00 38.13 3.28
107 108 3.774066 AGCTTCTTTGCGATAATTTGGC 58.226 40.909 0.00 0.00 38.13 4.52
108 109 3.445096 AGCTTCTTTGCGATAATTTGGCT 59.555 39.130 0.00 0.00 38.13 4.75
109 110 3.793492 GCTTCTTTGCGATAATTTGGCTC 59.207 43.478 0.00 0.00 0.00 4.70
110 111 4.354587 CTTCTTTGCGATAATTTGGCTCC 58.645 43.478 0.00 0.00 0.00 4.70
111 112 3.620488 TCTTTGCGATAATTTGGCTCCT 58.380 40.909 0.00 0.00 0.00 3.69
112 113 3.627577 TCTTTGCGATAATTTGGCTCCTC 59.372 43.478 0.00 0.00 0.00 3.71
113 114 1.967319 TGCGATAATTTGGCTCCTCC 58.033 50.000 0.00 0.00 0.00 4.30
114 115 1.239347 GCGATAATTTGGCTCCTCCC 58.761 55.000 0.00 0.00 0.00 4.30
115 116 1.202818 GCGATAATTTGGCTCCTCCCT 60.203 52.381 0.00 0.00 0.00 4.20
116 117 2.038557 GCGATAATTTGGCTCCTCCCTA 59.961 50.000 0.00 0.00 0.00 3.53
117 118 3.307762 GCGATAATTTGGCTCCTCCCTAT 60.308 47.826 0.00 0.00 0.00 2.57
118 119 4.256920 CGATAATTTGGCTCCTCCCTATG 58.743 47.826 0.00 0.00 0.00 2.23
119 120 4.593956 GATAATTTGGCTCCTCCCTATGG 58.406 47.826 0.00 0.00 0.00 2.74
120 121 1.912862 ATTTGGCTCCTCCCTATGGT 58.087 50.000 0.00 0.00 0.00 3.55
121 122 1.213296 TTTGGCTCCTCCCTATGGTC 58.787 55.000 0.00 0.00 0.00 4.02
122 123 0.044092 TTGGCTCCTCCCTATGGTCA 59.956 55.000 0.00 0.00 0.00 4.02
123 124 0.268869 TGGCTCCTCCCTATGGTCAT 59.731 55.000 0.00 0.00 0.00 3.06
124 125 1.345422 TGGCTCCTCCCTATGGTCATT 60.345 52.381 0.00 0.00 0.00 2.57
125 126 1.777272 GGCTCCTCCCTATGGTCATTT 59.223 52.381 0.00 0.00 0.00 2.32
126 127 2.487986 GGCTCCTCCCTATGGTCATTTG 60.488 54.545 0.00 0.00 0.00 2.32
127 128 2.487986 GCTCCTCCCTATGGTCATTTGG 60.488 54.545 0.00 0.00 0.00 3.28
128 129 3.048600 CTCCTCCCTATGGTCATTTGGA 58.951 50.000 4.90 3.73 0.00 3.53
129 130 2.777692 TCCTCCCTATGGTCATTTGGAC 59.222 50.000 4.90 0.00 46.20 4.02
130 131 2.780010 CCTCCCTATGGTCATTTGGACT 59.220 50.000 0.00 0.00 46.16 3.85
131 132 3.181450 CCTCCCTATGGTCATTTGGACTC 60.181 52.174 0.00 0.00 46.16 3.36
132 133 3.455910 CTCCCTATGGTCATTTGGACTCA 59.544 47.826 0.00 0.00 46.16 3.41
133 134 3.199946 TCCCTATGGTCATTTGGACTCAC 59.800 47.826 0.00 0.00 46.16 3.51
134 135 3.200825 CCCTATGGTCATTTGGACTCACT 59.799 47.826 0.00 0.00 46.16 3.41
135 136 4.324563 CCCTATGGTCATTTGGACTCACTT 60.325 45.833 0.00 0.00 46.16 3.16
136 137 5.256474 CCTATGGTCATTTGGACTCACTTT 58.744 41.667 0.00 0.00 46.16 2.66
137 138 5.355350 CCTATGGTCATTTGGACTCACTTTC 59.645 44.000 0.00 0.00 46.16 2.62
138 139 3.486383 TGGTCATTTGGACTCACTTTCC 58.514 45.455 0.00 0.00 46.16 3.13
139 140 2.820197 GGTCATTTGGACTCACTTTCCC 59.180 50.000 0.00 0.00 46.16 3.97
140 141 2.484264 GTCATTTGGACTCACTTTCCCG 59.516 50.000 0.00 0.00 43.46 5.14
141 142 2.105821 TCATTTGGACTCACTTTCCCGT 59.894 45.455 0.00 0.00 31.33 5.28
142 143 1.961793 TTTGGACTCACTTTCCCGTG 58.038 50.000 0.00 0.00 36.25 4.94
143 144 0.834612 TTGGACTCACTTTCCCGTGT 59.165 50.000 0.00 0.00 36.33 4.49
144 145 0.391597 TGGACTCACTTTCCCGTGTC 59.608 55.000 0.00 0.00 36.33 3.67
145 146 0.320508 GGACTCACTTTCCCGTGTCC 60.321 60.000 0.00 0.00 38.28 4.02
146 147 0.680061 GACTCACTTTCCCGTGTCCT 59.320 55.000 0.00 0.00 36.33 3.85
147 148 1.070289 GACTCACTTTCCCGTGTCCTT 59.930 52.381 0.00 0.00 36.33 3.36
148 149 2.298163 GACTCACTTTCCCGTGTCCTTA 59.702 50.000 0.00 0.00 36.33 2.69
149 150 2.701951 ACTCACTTTCCCGTGTCCTTAA 59.298 45.455 0.00 0.00 36.33 1.85
150 151 3.244112 ACTCACTTTCCCGTGTCCTTAAG 60.244 47.826 0.00 0.00 36.33 1.85
154 155 1.053424 TTCCCGTGTCCTTAAGCAGT 58.947 50.000 0.00 0.00 0.00 4.40
251 252 3.746940 TGGTACTTCTTTGGTACTTGCC 58.253 45.455 0.00 0.00 39.36 4.52
437 445 4.883240 AAAAACCCCGCACGTACT 57.117 50.000 0.00 0.00 0.00 2.73
524 532 3.680620 CTTCATCCCTTCGCCGCCA 62.681 63.158 0.00 0.00 0.00 5.69
564 599 0.179000 GCCCTCGGTCTCACATCAAT 59.821 55.000 0.00 0.00 0.00 2.57
979 1025 3.345808 GTTTCGCGCTGCAGGTCA 61.346 61.111 17.12 0.00 0.00 4.02
1488 1581 4.080863 ACGGGAGCTCTCAATTCTGTATTT 60.081 41.667 15.40 0.00 0.00 1.40
1973 2066 5.838531 TGACGTTGTTACTTGGGAAAAAT 57.161 34.783 0.00 0.00 0.00 1.82
2448 2542 0.826715 GGCAGTAGGAGCTCATGACA 59.173 55.000 17.19 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.267732 GCGTAAATGCAGCAGTAGCAG 60.268 52.381 0.00 0.00 46.36 4.24
4 5 1.004504 GAGCGTAAATGCAGCAGTAGC 60.005 52.381 0.00 5.51 42.56 3.58
5 6 2.544685 AGAGCGTAAATGCAGCAGTAG 58.455 47.619 0.00 0.00 37.31 2.57
6 7 2.672874 CAAGAGCGTAAATGCAGCAGTA 59.327 45.455 0.00 0.00 37.31 2.74
7 8 1.466167 CAAGAGCGTAAATGCAGCAGT 59.534 47.619 0.00 0.00 37.31 4.40
8 9 1.733912 TCAAGAGCGTAAATGCAGCAG 59.266 47.619 0.00 0.00 37.31 4.24
9 10 1.807139 TCAAGAGCGTAAATGCAGCA 58.193 45.000 0.00 0.00 37.31 4.41
10 11 2.476854 CCTTCAAGAGCGTAAATGCAGC 60.477 50.000 0.00 0.00 37.31 5.25
11 12 2.476854 GCCTTCAAGAGCGTAAATGCAG 60.477 50.000 0.00 0.00 37.31 4.41
12 13 1.468520 GCCTTCAAGAGCGTAAATGCA 59.531 47.619 0.00 0.00 37.31 3.96
13 14 2.179949 GCCTTCAAGAGCGTAAATGC 57.820 50.000 0.00 0.00 0.00 3.56
21 22 1.443802 ACTTTAGCGCCTTCAAGAGC 58.556 50.000 2.29 0.00 0.00 4.09
22 23 4.109050 CTCTACTTTAGCGCCTTCAAGAG 58.891 47.826 2.29 6.33 0.00 2.85
23 24 3.676324 GCTCTACTTTAGCGCCTTCAAGA 60.676 47.826 2.29 0.00 30.57 3.02
24 25 2.605366 GCTCTACTTTAGCGCCTTCAAG 59.395 50.000 2.29 3.69 30.57 3.02
25 26 2.028476 TGCTCTACTTTAGCGCCTTCAA 60.028 45.455 2.29 0.00 43.11 2.69
26 27 1.548719 TGCTCTACTTTAGCGCCTTCA 59.451 47.619 2.29 0.00 43.11 3.02
27 28 2.159226 TCTGCTCTACTTTAGCGCCTTC 60.159 50.000 2.29 0.00 43.11 3.46
28 29 1.825474 TCTGCTCTACTTTAGCGCCTT 59.175 47.619 2.29 0.00 43.11 4.35
29 30 1.475403 TCTGCTCTACTTTAGCGCCT 58.525 50.000 2.29 0.00 43.11 5.52
30 31 2.295253 TTCTGCTCTACTTTAGCGCC 57.705 50.000 2.29 0.00 43.11 6.53
31 32 2.605366 CCTTTCTGCTCTACTTTAGCGC 59.395 50.000 0.00 0.00 43.11 5.92
32 33 3.851098 ACCTTTCTGCTCTACTTTAGCG 58.149 45.455 0.00 0.00 43.11 4.26
33 34 5.235401 GCATACCTTTCTGCTCTACTTTAGC 59.765 44.000 0.00 0.00 40.50 3.09
34 35 5.755861 GGCATACCTTTCTGCTCTACTTTAG 59.244 44.000 0.00 0.00 38.45 1.85
35 36 5.188948 TGGCATACCTTTCTGCTCTACTTTA 59.811 40.000 0.00 0.00 38.45 1.85
36 37 4.019321 TGGCATACCTTTCTGCTCTACTTT 60.019 41.667 0.00 0.00 38.45 2.66
37 38 3.519510 TGGCATACCTTTCTGCTCTACTT 59.480 43.478 0.00 0.00 38.45 2.24
38 39 3.107601 TGGCATACCTTTCTGCTCTACT 58.892 45.455 0.00 0.00 38.45 2.57
39 40 3.543680 TGGCATACCTTTCTGCTCTAC 57.456 47.619 0.00 0.00 38.45 2.59
40 41 3.711190 TCATGGCATACCTTTCTGCTCTA 59.289 43.478 0.00 0.00 38.45 2.43
41 42 2.507058 TCATGGCATACCTTTCTGCTCT 59.493 45.455 0.00 0.00 38.45 4.09
42 43 2.877168 CTCATGGCATACCTTTCTGCTC 59.123 50.000 0.00 0.00 38.45 4.26
43 44 2.240667 ACTCATGGCATACCTTTCTGCT 59.759 45.455 0.00 0.00 38.45 4.24
44 45 2.648059 ACTCATGGCATACCTTTCTGC 58.352 47.619 0.00 0.00 36.63 4.26
45 46 4.096984 GGAAACTCATGGCATACCTTTCTG 59.903 45.833 16.35 0.04 36.63 3.02
46 47 4.273318 GGAAACTCATGGCATACCTTTCT 58.727 43.478 16.35 0.00 36.63 2.52
47 48 3.381590 GGGAAACTCATGGCATACCTTTC 59.618 47.826 0.00 6.98 36.63 2.62
48 49 3.011708 AGGGAAACTCATGGCATACCTTT 59.988 43.478 0.00 0.00 36.63 3.11
49 50 2.582636 AGGGAAACTCATGGCATACCTT 59.417 45.455 0.00 0.00 36.63 3.50
50 51 2.173569 GAGGGAAACTCATGGCATACCT 59.826 50.000 0.00 0.00 45.85 3.08
51 52 2.576615 GAGGGAAACTCATGGCATACC 58.423 52.381 0.00 0.00 45.85 2.73
61 62 5.009110 CAGAAAACTTGGAAGAGGGAAACTC 59.991 44.000 0.00 0.00 46.98 3.01
62 63 4.889995 CAGAAAACTTGGAAGAGGGAAACT 59.110 41.667 0.00 0.00 0.00 2.66
63 64 4.887655 TCAGAAAACTTGGAAGAGGGAAAC 59.112 41.667 0.00 0.00 0.00 2.78
64 65 5.124036 TCAGAAAACTTGGAAGAGGGAAA 57.876 39.130 0.00 0.00 0.00 3.13
65 66 4.718961 CTCAGAAAACTTGGAAGAGGGAA 58.281 43.478 0.00 0.00 0.00 3.97
66 67 3.496870 GCTCAGAAAACTTGGAAGAGGGA 60.497 47.826 0.00 0.00 0.00 4.20
67 68 2.816672 GCTCAGAAAACTTGGAAGAGGG 59.183 50.000 0.00 0.00 0.00 4.30
68 69 3.749226 AGCTCAGAAAACTTGGAAGAGG 58.251 45.455 0.00 0.00 0.00 3.69
69 70 5.062528 AGAAGCTCAGAAAACTTGGAAGAG 58.937 41.667 0.00 0.00 0.00 2.85
70 71 5.041191 AGAAGCTCAGAAAACTTGGAAGA 57.959 39.130 0.00 0.00 0.00 2.87
71 72 5.764487 AAGAAGCTCAGAAAACTTGGAAG 57.236 39.130 0.00 0.00 0.00 3.46
72 73 5.679638 GCAAAGAAGCTCAGAAAACTTGGAA 60.680 40.000 0.00 0.00 0.00 3.53
73 74 4.202050 GCAAAGAAGCTCAGAAAACTTGGA 60.202 41.667 0.00 0.00 0.00 3.53
74 75 4.047142 GCAAAGAAGCTCAGAAAACTTGG 58.953 43.478 0.00 0.00 0.00 3.61
75 76 3.727723 CGCAAAGAAGCTCAGAAAACTTG 59.272 43.478 0.00 0.00 0.00 3.16
76 77 3.627577 TCGCAAAGAAGCTCAGAAAACTT 59.372 39.130 0.00 0.00 0.00 2.66
77 78 3.206150 TCGCAAAGAAGCTCAGAAAACT 58.794 40.909 0.00 0.00 0.00 2.66
78 79 3.609103 TCGCAAAGAAGCTCAGAAAAC 57.391 42.857 0.00 0.00 0.00 2.43
79 80 5.940192 TTATCGCAAAGAAGCTCAGAAAA 57.060 34.783 0.00 0.00 0.00 2.29
80 81 6.500684 AATTATCGCAAAGAAGCTCAGAAA 57.499 33.333 0.00 0.00 0.00 2.52
81 82 6.317088 CAAATTATCGCAAAGAAGCTCAGAA 58.683 36.000 0.00 0.00 0.00 3.02
82 83 5.163723 CCAAATTATCGCAAAGAAGCTCAGA 60.164 40.000 0.00 0.00 0.00 3.27
83 84 5.032863 CCAAATTATCGCAAAGAAGCTCAG 58.967 41.667 0.00 0.00 0.00 3.35
84 85 4.675146 GCCAAATTATCGCAAAGAAGCTCA 60.675 41.667 0.00 0.00 0.00 4.26
85 86 3.793492 GCCAAATTATCGCAAAGAAGCTC 59.207 43.478 0.00 0.00 0.00 4.09
86 87 3.445096 AGCCAAATTATCGCAAAGAAGCT 59.555 39.130 0.00 0.00 0.00 3.74
87 88 3.774066 AGCCAAATTATCGCAAAGAAGC 58.226 40.909 0.00 0.00 0.00 3.86
88 89 4.096984 AGGAGCCAAATTATCGCAAAGAAG 59.903 41.667 0.00 0.00 0.00 2.85
89 90 4.016444 AGGAGCCAAATTATCGCAAAGAA 58.984 39.130 0.00 0.00 0.00 2.52
90 91 3.620488 AGGAGCCAAATTATCGCAAAGA 58.380 40.909 0.00 0.00 0.00 2.52
91 92 3.243201 GGAGGAGCCAAATTATCGCAAAG 60.243 47.826 0.00 0.00 36.34 2.77
92 93 2.687935 GGAGGAGCCAAATTATCGCAAA 59.312 45.455 0.00 0.00 36.34 3.68
93 94 2.297701 GGAGGAGCCAAATTATCGCAA 58.702 47.619 0.00 0.00 36.34 4.85
94 95 1.476833 GGGAGGAGCCAAATTATCGCA 60.477 52.381 0.00 0.00 38.95 5.10
95 96 1.202818 AGGGAGGAGCCAAATTATCGC 60.203 52.381 0.00 0.00 38.95 4.58
96 97 2.938956 AGGGAGGAGCCAAATTATCG 57.061 50.000 0.00 0.00 38.95 2.92
97 98 4.043435 ACCATAGGGAGGAGCCAAATTATC 59.957 45.833 0.00 0.00 38.95 1.75
98 99 3.990245 ACCATAGGGAGGAGCCAAATTAT 59.010 43.478 0.00 0.00 38.95 1.28
99 100 3.394606 GACCATAGGGAGGAGCCAAATTA 59.605 47.826 0.00 0.00 38.95 1.40
100 101 2.175715 GACCATAGGGAGGAGCCAAATT 59.824 50.000 0.00 0.00 38.95 1.82
101 102 1.777272 GACCATAGGGAGGAGCCAAAT 59.223 52.381 0.00 0.00 38.95 2.32
102 103 1.213296 GACCATAGGGAGGAGCCAAA 58.787 55.000 0.00 0.00 38.95 3.28
103 104 0.044092 TGACCATAGGGAGGAGCCAA 59.956 55.000 0.00 0.00 38.95 4.52
104 105 0.268869 ATGACCATAGGGAGGAGCCA 59.731 55.000 0.00 0.00 38.95 4.75
105 106 1.439543 AATGACCATAGGGAGGAGCC 58.560 55.000 0.00 0.00 38.05 4.70
106 107 2.487986 CCAAATGACCATAGGGAGGAGC 60.488 54.545 0.00 0.00 38.05 4.70
107 108 3.048600 TCCAAATGACCATAGGGAGGAG 58.951 50.000 0.00 0.00 38.05 3.69
108 109 2.777692 GTCCAAATGACCATAGGGAGGA 59.222 50.000 0.00 0.00 38.09 3.71
109 110 2.780010 AGTCCAAATGACCATAGGGAGG 59.220 50.000 0.00 0.00 45.68 4.30
110 111 3.455910 TGAGTCCAAATGACCATAGGGAG 59.544 47.826 0.00 0.00 45.68 4.30
111 112 3.199946 GTGAGTCCAAATGACCATAGGGA 59.800 47.826 0.00 0.00 45.68 4.20
112 113 3.200825 AGTGAGTCCAAATGACCATAGGG 59.799 47.826 0.00 0.00 45.68 3.53
113 114 4.494091 AGTGAGTCCAAATGACCATAGG 57.506 45.455 0.00 0.00 45.68 2.57
114 115 5.355350 GGAAAGTGAGTCCAAATGACCATAG 59.645 44.000 0.00 0.00 45.68 2.23
115 116 5.253330 GGAAAGTGAGTCCAAATGACCATA 58.747 41.667 0.00 0.00 45.68 2.74
116 117 4.082125 GGAAAGTGAGTCCAAATGACCAT 58.918 43.478 0.00 0.00 45.68 3.55
117 118 3.486383 GGAAAGTGAGTCCAAATGACCA 58.514 45.455 0.00 0.00 45.68 4.02
118 119 2.820197 GGGAAAGTGAGTCCAAATGACC 59.180 50.000 0.00 0.00 45.68 4.02
119 120 2.484264 CGGGAAAGTGAGTCCAAATGAC 59.516 50.000 0.00 0.00 44.82 3.06
120 121 2.105821 ACGGGAAAGTGAGTCCAAATGA 59.894 45.455 0.00 0.00 36.83 2.57
121 122 2.226437 CACGGGAAAGTGAGTCCAAATG 59.774 50.000 0.00 0.00 44.43 2.32
122 123 2.158667 ACACGGGAAAGTGAGTCCAAAT 60.159 45.455 0.00 0.00 44.43 2.32
123 124 1.210967 ACACGGGAAAGTGAGTCCAAA 59.789 47.619 0.00 0.00 44.43 3.28
124 125 0.834612 ACACGGGAAAGTGAGTCCAA 59.165 50.000 0.00 0.00 44.43 3.53
125 126 0.391597 GACACGGGAAAGTGAGTCCA 59.608 55.000 0.00 0.00 44.43 4.02
126 127 0.320508 GGACACGGGAAAGTGAGTCC 60.321 60.000 0.00 0.00 44.43 3.85
127 128 0.680061 AGGACACGGGAAAGTGAGTC 59.320 55.000 0.00 0.00 44.43 3.36
128 129 1.129058 AAGGACACGGGAAAGTGAGT 58.871 50.000 0.00 0.00 44.43 3.41
129 130 3.326747 CTTAAGGACACGGGAAAGTGAG 58.673 50.000 0.00 0.00 44.43 3.51
130 131 2.549349 GCTTAAGGACACGGGAAAGTGA 60.549 50.000 4.29 0.00 44.43 3.41
131 132 1.804748 GCTTAAGGACACGGGAAAGTG 59.195 52.381 4.29 0.00 46.83 3.16
132 133 1.418637 TGCTTAAGGACACGGGAAAGT 59.581 47.619 4.29 0.00 0.00 2.66
133 134 2.076863 CTGCTTAAGGACACGGGAAAG 58.923 52.381 4.29 0.00 0.00 2.62
134 135 1.418637 ACTGCTTAAGGACACGGGAAA 59.581 47.619 4.29 0.00 0.00 3.13
135 136 1.053424 ACTGCTTAAGGACACGGGAA 58.947 50.000 4.29 0.00 0.00 3.97
136 137 1.927487 TACTGCTTAAGGACACGGGA 58.073 50.000 4.29 0.00 0.00 5.14
137 138 2.431057 AGATACTGCTTAAGGACACGGG 59.569 50.000 4.29 0.00 0.00 5.28
138 139 3.381908 AGAGATACTGCTTAAGGACACGG 59.618 47.826 4.29 0.00 0.00 4.94
139 140 4.640789 AGAGATACTGCTTAAGGACACG 57.359 45.455 4.29 0.00 0.00 4.49
140 141 6.238814 GGAGTAGAGATACTGCTTAAGGACAC 60.239 46.154 4.29 0.00 41.40 3.67
141 142 5.828859 GGAGTAGAGATACTGCTTAAGGACA 59.171 44.000 4.29 0.00 41.40 4.02
142 143 6.066032 AGGAGTAGAGATACTGCTTAAGGAC 58.934 44.000 4.29 0.00 44.64 3.85
143 144 6.268855 AGGAGTAGAGATACTGCTTAAGGA 57.731 41.667 4.29 0.00 44.64 3.36
144 145 8.519526 CATTAGGAGTAGAGATACTGCTTAAGG 58.480 40.741 13.54 5.89 44.64 2.69
145 146 9.073475 ACATTAGGAGTAGAGATACTGCTTAAG 57.927 37.037 13.54 0.00 44.64 1.85
146 147 8.998277 ACATTAGGAGTAGAGATACTGCTTAA 57.002 34.615 13.54 7.61 44.64 1.85
147 148 8.441572 AGACATTAGGAGTAGAGATACTGCTTA 58.558 37.037 13.54 6.46 44.64 3.09
148 149 7.294584 AGACATTAGGAGTAGAGATACTGCTT 58.705 38.462 13.54 0.00 44.64 3.91
150 151 6.712998 TGAGACATTAGGAGTAGAGATACTGC 59.287 42.308 0.00 0.00 38.48 4.40
154 155 7.721842 CCAACTGAGACATTAGGAGTAGAGATA 59.278 40.741 0.00 0.00 0.00 1.98
271 272 1.008329 GTGGTTTTGTCGGTTCGTGA 58.992 50.000 0.00 0.00 0.00 4.35
367 368 8.511465 TTATCGCTGGTTAATTTACGTAGATC 57.489 34.615 0.00 0.00 0.00 2.75
437 445 2.183300 GGGCATGTGACGTCGCTA 59.817 61.111 27.76 15.63 0.00 4.26
524 532 4.162690 GGCGAAGGGATGAGCGGT 62.163 66.667 0.00 0.00 0.00 5.68
979 1025 0.610174 TTGCAGAGCTCCGTGAAGAT 59.390 50.000 10.93 0.00 0.00 2.40
1488 1581 1.891933 TCTACCTTGCCATCCATCCA 58.108 50.000 0.00 0.00 0.00 3.41
1973 2066 2.655090 TTGATCTGTGGGCAGTTTCA 57.345 45.000 0.00 0.00 43.05 2.69
2448 2542 0.112995 ATGGTGGTGGCATCAACAGT 59.887 50.000 24.44 9.57 41.90 3.55


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

AutoCloner maintained by Alex Coulton.