Multiple sequence alignment - TraesCS7A01G165500

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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 TraesCS7A01G165500 chr7A 100.000 3230 0 0 1 3230 121044939 121048168 0.000000e+00 5965
1 TraesCS7A01G165500 chr2B 98.613 2956 25 2 290 3230 39425061 39428015 0.000000e+00 5217
2 TraesCS7A01G165500 chr4A 98.478 2957 30 2 289 3230 537234669 537231713 0.000000e+00 5197
3 TraesCS7A01G165500 chr4A 98.376 2955 32 3 291 3230 377591787 377594740 0.000000e+00 5177
4 TraesCS7A01G165500 chr4A 98.342 2956 34 2 290 3230 72014527 72017482 0.000000e+00 5173
5 TraesCS7A01G165500 chr4A 100.000 90 0 0 1 90 11509791 11509702 1.990000e-37 167
6 TraesCS7A01G165500 chr4A 94.059 101 5 1 1 100 151134920 151134820 5.580000e-33 152
7 TraesCS7A01G165500 chr4A 94.059 101 5 1 1 100 457515466 457515566 5.580000e-33 152
8 TraesCS7A01G165500 chr6B 98.240 2955 37 3 291 3230 660355493 660352539 0.000000e+00 5155
9 TraesCS7A01G165500 chr1B 98.240 2955 34 3 291 3230 439511016 439508065 0.000000e+00 5153
10 TraesCS7A01G165500 chr3B 98.206 2955 38 2 291 3230 149243139 149240185 0.000000e+00 5149
11 TraesCS7A01G165500 chr1A 98.173 2956 39 2 290 3230 58178563 58181518 0.000000e+00 5145
12 TraesCS7A01G165500 chr1A 97.936 2956 25 4 290 3230 449180778 449183712 0.000000e+00 5088
13 TraesCS7A01G165500 chr1A 97.287 2285 38 4 962 3230 552374795 552377071 0.000000e+00 3855
14 TraesCS7A01G165500 chr1A 98.889 90 1 0 1 90 439887334 439887245 9.270000e-36 161
15 TraesCS7A01G165500 chrUn 98.693 2296 15 2 950 3230 304158966 304156671 0.000000e+00 4060
16 TraesCS7A01G165500 chrUn 97.444 2347 36 8 899 3230 309477114 309474777 0.000000e+00 3980
17 TraesCS7A01G165500 chrUn 97.401 2347 37 8 899 3230 308090571 308092908 0.000000e+00 3975
18 TraesCS7A01G165500 chr4B 98.301 2296 24 2 950 3230 237023993 237021698 0.000000e+00 4010
19 TraesCS7A01G165500 chr3A 98.168 2238 25 3 291 2513 128148732 128146496 0.000000e+00 3892
20 TraesCS7A01G165500 chr3A 95.050 101 4 1 1 100 354380895 354380795 1.200000e-34 158
21 TraesCS7A01G165500 chr3A 94.059 101 5 1 1 100 154587366 154587266 5.580000e-33 152
22 TraesCS7A01G165500 chr5A 97.287 2285 38 4 962 3230 403293523 403295799 0.000000e+00 3855
23 TraesCS7A01G165500 chr7D 92.344 209 7 1 91 290 117132102 117132310 4.080000e-74 289
24 TraesCS7A01G165500 chr7B 91.866 209 8 2 91 290 76903271 76903479 1.900000e-72 283
25 TraesCS7A01G165500 chr6A 94.059 101 5 1 1 100 91690440 91690340 5.580000e-33 152
26 TraesCS7A01G165500 chr6A 94.059 101 5 1 1 100 390930386 390930486 5.580000e-33 152
27 TraesCS7A01G165500 chr2A 94.059 101 5 1 1 100 285700065 285699965 5.580000e-33 152


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 TraesCS7A01G165500 chr7A 121044939 121048168 3229 False 5965 5965 100.000 1 3230 1 chr7A.!!$F1 3229
1 TraesCS7A01G165500 chr2B 39425061 39428015 2954 False 5217 5217 98.613 290 3230 1 chr2B.!!$F1 2940
2 TraesCS7A01G165500 chr4A 537231713 537234669 2956 True 5197 5197 98.478 289 3230 1 chr4A.!!$R3 2941
3 TraesCS7A01G165500 chr4A 377591787 377594740 2953 False 5177 5177 98.376 291 3230 1 chr4A.!!$F2 2939
4 TraesCS7A01G165500 chr4A 72014527 72017482 2955 False 5173 5173 98.342 290 3230 1 chr4A.!!$F1 2940
5 TraesCS7A01G165500 chr6B 660352539 660355493 2954 True 5155 5155 98.240 291 3230 1 chr6B.!!$R1 2939
6 TraesCS7A01G165500 chr1B 439508065 439511016 2951 True 5153 5153 98.240 291 3230 1 chr1B.!!$R1 2939
7 TraesCS7A01G165500 chr3B 149240185 149243139 2954 True 5149 5149 98.206 291 3230 1 chr3B.!!$R1 2939
8 TraesCS7A01G165500 chr1A 58178563 58181518 2955 False 5145 5145 98.173 290 3230 1 chr1A.!!$F1 2940
9 TraesCS7A01G165500 chr1A 449180778 449183712 2934 False 5088 5088 97.936 290 3230 1 chr1A.!!$F2 2940
10 TraesCS7A01G165500 chr1A 552374795 552377071 2276 False 3855 3855 97.287 962 3230 1 chr1A.!!$F3 2268
11 TraesCS7A01G165500 chrUn 304156671 304158966 2295 True 4060 4060 98.693 950 3230 1 chrUn.!!$R1 2280
12 TraesCS7A01G165500 chrUn 309474777 309477114 2337 True 3980 3980 97.444 899 3230 1 chrUn.!!$R2 2331
13 TraesCS7A01G165500 chrUn 308090571 308092908 2337 False 3975 3975 97.401 899 3230 1 chrUn.!!$F1 2331
14 TraesCS7A01G165500 chr4B 237021698 237023993 2295 True 4010 4010 98.301 950 3230 1 chr4B.!!$R1 2280
15 TraesCS7A01G165500 chr3A 128146496 128148732 2236 True 3892 3892 98.168 291 2513 1 chr3A.!!$R1 2222
16 TraesCS7A01G165500 chr5A 403293523 403295799 2276 False 3855 3855 97.287 962 3230 1 chr5A.!!$F1 2268

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
286 287 0.110644 CTGCGCGAGTGGTTTCTTTC 60.111 55.000 12.1 0.0 0.0 2.62 F
1244 1248 1.070134 ACACACCGTACATCAAGCAGT 59.930 47.619 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1288 1.447838 GGAGCGTTCAGATTCGGCA 60.448 57.895 0.53 0.0 0.00 5.69 R
3067 3089 1.301401 GGCCTGACGCTGTAACACA 60.301 57.895 0.00 0.0 37.74 3.72 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 7.631717 GGCTCTCATTTTGATAAACTAACCT 57.368 36.000 0.00 0.00 0.00 3.50
25 26 8.056407 GGCTCTCATTTTGATAAACTAACCTT 57.944 34.615 0.00 0.00 0.00 3.50
26 27 9.174166 GGCTCTCATTTTGATAAACTAACCTTA 57.826 33.333 0.00 0.00 0.00 2.69
37 38 9.280174 TGATAAACTAACCTTAGTCAAGTTTGG 57.720 33.333 8.58 0.00 42.86 3.28
38 39 6.387041 AAACTAACCTTAGTCAAGTTTGGC 57.613 37.500 0.00 0.00 42.86 4.52
39 40 5.043737 ACTAACCTTAGTCAAGTTTGGCA 57.956 39.130 0.00 0.00 39.72 4.92
40 41 5.442391 ACTAACCTTAGTCAAGTTTGGCAA 58.558 37.500 0.00 0.00 39.72 4.52
41 42 5.889289 ACTAACCTTAGTCAAGTTTGGCAAA 59.111 36.000 8.93 8.93 39.72 3.68
42 43 5.669164 AACCTTAGTCAAGTTTGGCAAAA 57.331 34.783 15.29 0.00 34.61 2.44
43 44 5.669164 ACCTTAGTCAAGTTTGGCAAAAA 57.331 34.783 15.29 2.55 34.61 1.94
44 45 6.233905 ACCTTAGTCAAGTTTGGCAAAAAT 57.766 33.333 15.29 3.54 34.61 1.82
45 46 6.048509 ACCTTAGTCAAGTTTGGCAAAAATG 58.951 36.000 15.29 15.81 34.61 2.32
46 47 6.048509 CCTTAGTCAAGTTTGGCAAAAATGT 58.951 36.000 15.29 4.72 34.61 2.71
47 48 6.018832 CCTTAGTCAAGTTTGGCAAAAATGTG 60.019 38.462 15.29 10.16 34.61 3.21
48 49 4.831107 AGTCAAGTTTGGCAAAAATGTGT 58.169 34.783 15.29 5.91 34.61 3.72
49 50 4.630940 AGTCAAGTTTGGCAAAAATGTGTG 59.369 37.500 15.29 6.81 34.61 3.82
50 51 3.937706 TCAAGTTTGGCAAAAATGTGTGG 59.062 39.130 15.29 0.00 0.00 4.17
51 52 2.287769 AGTTTGGCAAAAATGTGTGGC 58.712 42.857 15.29 0.00 40.55 5.01
54 55 2.408271 TGGCAAAAATGTGTGGCAAA 57.592 40.000 0.00 0.00 46.13 3.68
55 56 2.286872 TGGCAAAAATGTGTGGCAAAG 58.713 42.857 0.00 0.00 46.13 2.77
56 57 2.287769 GGCAAAAATGTGTGGCAAAGT 58.712 42.857 0.00 0.00 39.93 2.66
57 58 2.031930 GGCAAAAATGTGTGGCAAAGTG 59.968 45.455 0.00 0.00 39.93 3.16
58 59 2.677337 GCAAAAATGTGTGGCAAAGTGT 59.323 40.909 0.00 0.00 0.00 3.55
59 60 3.485546 GCAAAAATGTGTGGCAAAGTGTG 60.486 43.478 0.00 0.00 0.00 3.82
60 61 2.600470 AAATGTGTGGCAAAGTGTGG 57.400 45.000 0.00 0.00 0.00 4.17
71 72 4.342352 GCAAAGTGTGGCAATACTAGTC 57.658 45.455 0.00 0.00 0.00 2.59
72 73 3.127030 GCAAAGTGTGGCAATACTAGTCC 59.873 47.826 0.00 0.00 0.00 3.85
73 74 4.579869 CAAAGTGTGGCAATACTAGTCCT 58.420 43.478 0.00 0.00 0.00 3.85
74 75 5.730550 CAAAGTGTGGCAATACTAGTCCTA 58.269 41.667 0.00 0.00 0.00 2.94
75 76 6.170506 CAAAGTGTGGCAATACTAGTCCTAA 58.829 40.000 0.00 0.00 0.00 2.69
76 77 6.368779 AAGTGTGGCAATACTAGTCCTAAA 57.631 37.500 0.00 0.00 0.00 1.85
77 78 6.368779 AGTGTGGCAATACTAGTCCTAAAA 57.631 37.500 0.00 0.00 0.00 1.52
78 79 6.171213 AGTGTGGCAATACTAGTCCTAAAAC 58.829 40.000 0.00 0.00 0.00 2.43
79 80 5.353400 GTGTGGCAATACTAGTCCTAAAACC 59.647 44.000 0.00 0.00 0.00 3.27
80 81 5.013287 TGTGGCAATACTAGTCCTAAAACCA 59.987 40.000 0.00 0.00 0.00 3.67
81 82 5.941647 GTGGCAATACTAGTCCTAAAACCAA 59.058 40.000 0.00 0.00 0.00 3.67
82 83 6.431852 GTGGCAATACTAGTCCTAAAACCAAA 59.568 38.462 0.00 0.00 0.00 3.28
83 84 6.431852 TGGCAATACTAGTCCTAAAACCAAAC 59.568 38.462 0.00 0.00 0.00 2.93
84 85 6.431852 GGCAATACTAGTCCTAAAACCAAACA 59.568 38.462 0.00 0.00 0.00 2.83
85 86 7.122204 GGCAATACTAGTCCTAAAACCAAACAT 59.878 37.037 0.00 0.00 0.00 2.71
86 87 8.182227 GCAATACTAGTCCTAAAACCAAACATC 58.818 37.037 0.00 0.00 0.00 3.06
87 88 8.674607 CAATACTAGTCCTAAAACCAAACATCC 58.325 37.037 0.00 0.00 0.00 3.51
88 89 5.567430 ACTAGTCCTAAAACCAAACATCCC 58.433 41.667 0.00 0.00 0.00 3.85
89 90 3.774734 AGTCCTAAAACCAAACATCCCC 58.225 45.455 0.00 0.00 0.00 4.81
90 91 3.141272 AGTCCTAAAACCAAACATCCCCA 59.859 43.478 0.00 0.00 0.00 4.96
91 92 3.509967 GTCCTAAAACCAAACATCCCCAG 59.490 47.826 0.00 0.00 0.00 4.45
92 93 2.233676 CCTAAAACCAAACATCCCCAGC 59.766 50.000 0.00 0.00 0.00 4.85
93 94 1.799933 AAAACCAAACATCCCCAGCA 58.200 45.000 0.00 0.00 0.00 4.41
94 95 2.028561 AAACCAAACATCCCCAGCAT 57.971 45.000 0.00 0.00 0.00 3.79
95 96 1.560505 AACCAAACATCCCCAGCATC 58.439 50.000 0.00 0.00 0.00 3.91
96 97 0.706433 ACCAAACATCCCCAGCATCT 59.294 50.000 0.00 0.00 0.00 2.90
97 98 1.108776 CCAAACATCCCCAGCATCTG 58.891 55.000 0.00 0.00 0.00 2.90
98 99 0.458669 CAAACATCCCCAGCATCTGC 59.541 55.000 0.00 0.00 42.49 4.26
99 100 0.685458 AAACATCCCCAGCATCTGCC 60.685 55.000 0.00 0.00 43.38 4.85
100 101 2.593725 CATCCCCAGCATCTGCCG 60.594 66.667 0.00 0.00 43.38 5.69
101 102 3.092511 ATCCCCAGCATCTGCCGT 61.093 61.111 0.00 0.00 43.38 5.68
102 103 3.411114 ATCCCCAGCATCTGCCGTG 62.411 63.158 0.00 0.00 43.38 4.94
106 107 3.807538 CAGCATCTGCCGTGCCAC 61.808 66.667 0.00 0.00 43.50 5.01
119 120 4.736896 GCCACCCGACTGACCGTC 62.737 72.222 0.00 0.00 39.33 4.79
120 121 4.065281 CCACCCGACTGACCGTCC 62.065 72.222 0.00 0.00 39.56 4.79
121 122 4.065281 CACCCGACTGACCGTCCC 62.065 72.222 0.00 0.00 39.56 4.46
143 144 4.457496 CGCGCTGACCAGTCCCAT 62.457 66.667 5.56 0.00 0.00 4.00
144 145 2.045926 GCGCTGACCAGTCCCATT 60.046 61.111 0.00 0.00 0.00 3.16
145 146 1.675641 GCGCTGACCAGTCCCATTT 60.676 57.895 0.00 0.00 0.00 2.32
146 147 1.648467 GCGCTGACCAGTCCCATTTC 61.648 60.000 0.00 0.00 0.00 2.17
147 148 1.026718 CGCTGACCAGTCCCATTTCC 61.027 60.000 0.00 0.00 0.00 3.13
148 149 0.329596 GCTGACCAGTCCCATTTCCT 59.670 55.000 0.00 0.00 0.00 3.36
149 150 1.559682 GCTGACCAGTCCCATTTCCTA 59.440 52.381 0.00 0.00 0.00 2.94
150 151 2.681097 GCTGACCAGTCCCATTTCCTAC 60.681 54.545 0.00 0.00 0.00 3.18
151 152 1.913419 TGACCAGTCCCATTTCCTACC 59.087 52.381 0.00 0.00 0.00 3.18
152 153 0.909623 ACCAGTCCCATTTCCTACCG 59.090 55.000 0.00 0.00 0.00 4.02
153 154 0.463833 CCAGTCCCATTTCCTACCGC 60.464 60.000 0.00 0.00 0.00 5.68
154 155 0.541863 CAGTCCCATTTCCTACCGCT 59.458 55.000 0.00 0.00 0.00 5.52
155 156 1.065418 CAGTCCCATTTCCTACCGCTT 60.065 52.381 0.00 0.00 0.00 4.68
156 157 1.633945 AGTCCCATTTCCTACCGCTTT 59.366 47.619 0.00 0.00 0.00 3.51
157 158 1.743394 GTCCCATTTCCTACCGCTTTG 59.257 52.381 0.00 0.00 0.00 2.77
158 159 0.455815 CCCATTTCCTACCGCTTTGC 59.544 55.000 0.00 0.00 0.00 3.68
159 160 0.455815 CCATTTCCTACCGCTTTGCC 59.544 55.000 0.00 0.00 0.00 4.52
160 161 1.173043 CATTTCCTACCGCTTTGCCA 58.827 50.000 0.00 0.00 0.00 4.92
161 162 1.133025 CATTTCCTACCGCTTTGCCAG 59.867 52.381 0.00 0.00 0.00 4.85
162 163 1.241315 TTTCCTACCGCTTTGCCAGC 61.241 55.000 0.00 0.00 46.31 4.85
181 182 4.115199 CCCGCCCCTCCTCCAAAG 62.115 72.222 0.00 0.00 0.00 2.77
182 183 3.330720 CCGCCCCTCCTCCAAAGT 61.331 66.667 0.00 0.00 0.00 2.66
183 184 2.757077 CGCCCCTCCTCCAAAGTT 59.243 61.111 0.00 0.00 0.00 2.66
184 185 1.675641 CGCCCCTCCTCCAAAGTTG 60.676 63.158 0.00 0.00 0.00 3.16
185 186 1.767692 GCCCCTCCTCCAAAGTTGA 59.232 57.895 0.00 0.00 0.00 3.18
186 187 0.112412 GCCCCTCCTCCAAAGTTGAA 59.888 55.000 0.00 0.00 0.00 2.69
187 188 1.480498 GCCCCTCCTCCAAAGTTGAAA 60.480 52.381 0.00 0.00 0.00 2.69
188 189 2.957474 CCCCTCCTCCAAAGTTGAAAA 58.043 47.619 0.00 0.00 0.00 2.29
199 200 2.820845 GTTGAAAACCTGCCACCCT 58.179 52.632 0.00 0.00 42.21 4.34
200 201 1.119684 GTTGAAAACCTGCCACCCTT 58.880 50.000 0.00 0.00 42.21 3.95
201 202 1.118838 TTGAAAACCTGCCACCCTTG 58.881 50.000 0.00 0.00 0.00 3.61
202 203 1.367471 GAAAACCTGCCACCCTTGC 59.633 57.895 0.00 0.00 0.00 4.01
203 204 2.420466 GAAAACCTGCCACCCTTGCG 62.420 60.000 0.00 0.00 0.00 4.85
259 260 4.405671 GCCAGCAGCAGAGCAGGA 62.406 66.667 10.63 0.00 43.20 3.86
260 261 2.125065 CCAGCAGCAGAGCAGGAG 60.125 66.667 0.00 0.00 43.20 3.69
261 262 2.820479 CAGCAGCAGAGCAGGAGC 60.820 66.667 0.00 0.00 42.56 4.70
262 263 4.098722 AGCAGCAGAGCAGGAGCC 62.099 66.667 0.00 0.00 43.56 4.70
264 265 4.486503 CAGCAGAGCAGGAGCCCC 62.487 72.222 0.00 0.00 43.56 5.80
282 283 4.090057 GCCTGCGCGAGTGGTTTC 62.090 66.667 12.10 0.00 0.00 2.78
283 284 2.357517 CCTGCGCGAGTGGTTTCT 60.358 61.111 12.10 0.00 0.00 2.52
284 285 1.961277 CCTGCGCGAGTGGTTTCTT 60.961 57.895 12.10 0.00 0.00 2.52
285 286 1.507141 CCTGCGCGAGTGGTTTCTTT 61.507 55.000 12.10 0.00 0.00 2.52
286 287 0.110644 CTGCGCGAGTGGTTTCTTTC 60.111 55.000 12.10 0.00 0.00 2.62
287 288 1.206831 GCGCGAGTGGTTTCTTTCC 59.793 57.895 12.10 0.00 0.00 3.13
310 311 4.071423 TCGGCAGAAATCACAGATTTGAA 58.929 39.130 9.49 0.00 0.00 2.69
414 415 4.373116 CGCCGCACCCTACTGTGT 62.373 66.667 0.00 0.00 38.52 3.72
472 473 1.529244 GCAGCCTTGGTCCAGTTGT 60.529 57.895 0.00 0.00 0.00 3.32
1055 1059 2.281761 CCGGGCCTACATGATGCC 60.282 66.667 0.84 13.96 44.59 4.40
1244 1248 1.070134 ACACACCGTACATCAAGCAGT 59.930 47.619 0.00 0.00 0.00 4.40
1284 1288 2.351276 GTTGGTCAGCCGGTCCAT 59.649 61.111 1.90 0.00 37.67 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.631717 AGGTTAGTTTATCAAAATGAGAGCC 57.368 36.000 0.00 0.00 0.00 4.70
11 12 9.280174 CCAAACTTGACTAAGGTTAGTTTATCA 57.720 33.333 3.93 0.00 41.80 2.15
12 13 8.235226 GCCAAACTTGACTAAGGTTAGTTTATC 58.765 37.037 3.93 0.00 41.80 1.75
13 14 7.722285 TGCCAAACTTGACTAAGGTTAGTTTAT 59.278 33.333 3.93 0.00 41.80 1.40
14 15 7.055378 TGCCAAACTTGACTAAGGTTAGTTTA 58.945 34.615 3.93 0.00 41.80 2.01
15 16 5.889289 TGCCAAACTTGACTAAGGTTAGTTT 59.111 36.000 3.93 0.00 41.80 2.66
16 17 5.442391 TGCCAAACTTGACTAAGGTTAGTT 58.558 37.500 3.93 0.00 41.80 2.24
17 18 5.043737 TGCCAAACTTGACTAAGGTTAGT 57.956 39.130 1.92 1.92 41.80 2.24
18 19 6.385649 TTTGCCAAACTTGACTAAGGTTAG 57.614 37.500 0.00 0.00 41.80 2.34
19 20 6.777213 TTTTGCCAAACTTGACTAAGGTTA 57.223 33.333 0.00 0.00 41.80 2.85
20 21 5.669164 TTTTGCCAAACTTGACTAAGGTT 57.331 34.783 0.00 0.00 44.49 3.50
21 22 5.669164 TTTTTGCCAAACTTGACTAAGGT 57.331 34.783 0.00 0.00 38.26 3.50
22 23 6.018832 CACATTTTTGCCAAACTTGACTAAGG 60.019 38.462 5.74 0.00 38.26 2.69
23 24 6.534793 ACACATTTTTGCCAAACTTGACTAAG 59.465 34.615 5.74 0.00 39.86 2.18
24 25 6.312426 CACACATTTTTGCCAAACTTGACTAA 59.688 34.615 5.74 0.00 0.00 2.24
25 26 5.809562 CACACATTTTTGCCAAACTTGACTA 59.190 36.000 5.74 0.00 0.00 2.59
26 27 4.630940 CACACATTTTTGCCAAACTTGACT 59.369 37.500 5.74 0.00 0.00 3.41
27 28 4.201802 CCACACATTTTTGCCAAACTTGAC 60.202 41.667 5.74 0.00 0.00 3.18
28 29 3.937706 CCACACATTTTTGCCAAACTTGA 59.062 39.130 5.74 0.00 0.00 3.02
29 30 3.487209 GCCACACATTTTTGCCAAACTTG 60.487 43.478 0.00 0.00 0.00 3.16
30 31 2.682352 GCCACACATTTTTGCCAAACTT 59.318 40.909 0.00 0.00 0.00 2.66
31 32 2.287769 GCCACACATTTTTGCCAAACT 58.712 42.857 0.00 0.00 0.00 2.66
32 33 2.012673 TGCCACACATTTTTGCCAAAC 58.987 42.857 0.00 0.00 0.00 2.93
33 34 2.408271 TGCCACACATTTTTGCCAAA 57.592 40.000 0.00 0.00 0.00 3.28
34 35 2.408271 TTGCCACACATTTTTGCCAA 57.592 40.000 0.00 0.00 0.00 4.52
35 36 2.286872 CTTTGCCACACATTTTTGCCA 58.713 42.857 0.00 0.00 0.00 4.92
36 37 2.031930 CACTTTGCCACACATTTTTGCC 59.968 45.455 0.00 0.00 0.00 4.52
37 38 2.677337 ACACTTTGCCACACATTTTTGC 59.323 40.909 0.00 0.00 0.00 3.68
38 39 3.063725 CCACACTTTGCCACACATTTTTG 59.936 43.478 0.00 0.00 0.00 2.44
39 40 3.269178 CCACACTTTGCCACACATTTTT 58.731 40.909 0.00 0.00 0.00 1.94
40 41 2.903798 CCACACTTTGCCACACATTTT 58.096 42.857 0.00 0.00 0.00 1.82
41 42 1.473080 GCCACACTTTGCCACACATTT 60.473 47.619 0.00 0.00 0.00 2.32
42 43 0.104671 GCCACACTTTGCCACACATT 59.895 50.000 0.00 0.00 0.00 2.71
43 44 1.042003 TGCCACACTTTGCCACACAT 61.042 50.000 0.00 0.00 0.00 3.21
44 45 1.253593 TTGCCACACTTTGCCACACA 61.254 50.000 0.00 0.00 0.00 3.72
45 46 0.104671 ATTGCCACACTTTGCCACAC 59.895 50.000 0.00 0.00 0.00 3.82
46 47 1.339610 GTATTGCCACACTTTGCCACA 59.660 47.619 0.00 0.00 0.00 4.17
47 48 1.613437 AGTATTGCCACACTTTGCCAC 59.387 47.619 0.00 0.00 0.00 5.01
48 49 1.993956 AGTATTGCCACACTTTGCCA 58.006 45.000 0.00 0.00 0.00 4.92
49 50 3.081804 ACTAGTATTGCCACACTTTGCC 58.918 45.455 0.00 0.00 0.00 4.52
50 51 3.127030 GGACTAGTATTGCCACACTTTGC 59.873 47.826 0.00 0.00 0.00 3.68
51 52 4.579869 AGGACTAGTATTGCCACACTTTG 58.420 43.478 0.00 0.00 0.00 2.77
52 53 4.910458 AGGACTAGTATTGCCACACTTT 57.090 40.909 0.00 0.00 0.00 2.66
53 54 6.368779 TTTAGGACTAGTATTGCCACACTT 57.631 37.500 0.00 0.00 0.00 3.16
54 55 6.171213 GTTTTAGGACTAGTATTGCCACACT 58.829 40.000 0.00 0.00 0.00 3.55
55 56 5.353400 GGTTTTAGGACTAGTATTGCCACAC 59.647 44.000 0.00 0.00 0.00 3.82
56 57 5.013287 TGGTTTTAGGACTAGTATTGCCACA 59.987 40.000 0.00 0.00 0.00 4.17
57 58 5.493809 TGGTTTTAGGACTAGTATTGCCAC 58.506 41.667 0.00 0.00 0.00 5.01
58 59 5.765576 TGGTTTTAGGACTAGTATTGCCA 57.234 39.130 0.00 0.00 0.00 4.92
59 60 6.431852 TGTTTGGTTTTAGGACTAGTATTGCC 59.568 38.462 0.00 0.00 0.00 4.52
60 61 7.443259 TGTTTGGTTTTAGGACTAGTATTGC 57.557 36.000 0.00 0.00 0.00 3.56
61 62 8.674607 GGATGTTTGGTTTTAGGACTAGTATTG 58.325 37.037 0.00 0.00 0.00 1.90
62 63 7.832685 GGGATGTTTGGTTTTAGGACTAGTATT 59.167 37.037 0.00 0.00 0.00 1.89
63 64 7.344134 GGGATGTTTGGTTTTAGGACTAGTAT 58.656 38.462 0.00 0.00 0.00 2.12
64 65 6.296605 GGGGATGTTTGGTTTTAGGACTAGTA 60.297 42.308 0.00 0.00 0.00 1.82
65 66 5.516062 GGGGATGTTTGGTTTTAGGACTAGT 60.516 44.000 0.00 0.00 0.00 2.57
66 67 4.948004 GGGGATGTTTGGTTTTAGGACTAG 59.052 45.833 0.00 0.00 0.00 2.57
67 68 4.354387 TGGGGATGTTTGGTTTTAGGACTA 59.646 41.667 0.00 0.00 0.00 2.59
68 69 3.141272 TGGGGATGTTTGGTTTTAGGACT 59.859 43.478 0.00 0.00 0.00 3.85
69 70 3.502356 TGGGGATGTTTGGTTTTAGGAC 58.498 45.455 0.00 0.00 0.00 3.85
70 71 3.773560 CTGGGGATGTTTGGTTTTAGGA 58.226 45.455 0.00 0.00 0.00 2.94
71 72 2.233676 GCTGGGGATGTTTGGTTTTAGG 59.766 50.000 0.00 0.00 0.00 2.69
72 73 2.896685 TGCTGGGGATGTTTGGTTTTAG 59.103 45.455 0.00 0.00 0.00 1.85
73 74 2.964209 TGCTGGGGATGTTTGGTTTTA 58.036 42.857 0.00 0.00 0.00 1.52
74 75 1.799933 TGCTGGGGATGTTTGGTTTT 58.200 45.000 0.00 0.00 0.00 2.43
75 76 1.901833 GATGCTGGGGATGTTTGGTTT 59.098 47.619 0.00 0.00 0.00 3.27
76 77 1.077663 AGATGCTGGGGATGTTTGGTT 59.922 47.619 0.00 0.00 0.00 3.67
77 78 0.706433 AGATGCTGGGGATGTTTGGT 59.294 50.000 0.00 0.00 0.00 3.67
78 79 1.108776 CAGATGCTGGGGATGTTTGG 58.891 55.000 0.00 0.00 0.00 3.28
79 80 0.458669 GCAGATGCTGGGGATGTTTG 59.541 55.000 0.00 0.00 38.21 2.93
80 81 0.685458 GGCAGATGCTGGGGATGTTT 60.685 55.000 4.59 0.00 41.70 2.83
81 82 1.076485 GGCAGATGCTGGGGATGTT 60.076 57.895 4.59 0.00 41.70 2.71
82 83 2.599597 GGCAGATGCTGGGGATGT 59.400 61.111 4.59 0.00 41.70 3.06
83 84 2.593725 CGGCAGATGCTGGGGATG 60.594 66.667 5.71 0.00 43.47 3.51
102 103 4.736896 GACGGTCAGTCGGGTGGC 62.737 72.222 2.62 0.00 40.43 5.01
126 127 3.958147 AATGGGACTGGTCAGCGCG 62.958 63.158 0.00 0.00 0.00 6.86
127 128 1.648467 GAAATGGGACTGGTCAGCGC 61.648 60.000 0.00 0.00 0.00 5.92
128 129 1.026718 GGAAATGGGACTGGTCAGCG 61.027 60.000 3.10 0.00 0.00 5.18
129 130 0.329596 AGGAAATGGGACTGGTCAGC 59.670 55.000 3.10 0.00 0.00 4.26
130 131 2.092914 GGTAGGAAATGGGACTGGTCAG 60.093 54.545 3.10 0.00 0.00 3.51
131 132 1.913419 GGTAGGAAATGGGACTGGTCA 59.087 52.381 3.10 0.00 0.00 4.02
132 133 1.134491 CGGTAGGAAATGGGACTGGTC 60.134 57.143 0.00 0.00 0.00 4.02
133 134 0.909623 CGGTAGGAAATGGGACTGGT 59.090 55.000 0.00 0.00 0.00 4.00
134 135 0.463833 GCGGTAGGAAATGGGACTGG 60.464 60.000 0.00 0.00 0.00 4.00
135 136 0.541863 AGCGGTAGGAAATGGGACTG 59.458 55.000 0.00 0.00 0.00 3.51
136 137 1.286248 AAGCGGTAGGAAATGGGACT 58.714 50.000 0.00 0.00 0.00 3.85
137 138 1.743394 CAAAGCGGTAGGAAATGGGAC 59.257 52.381 0.00 0.00 0.00 4.46
138 139 1.953311 GCAAAGCGGTAGGAAATGGGA 60.953 52.381 0.00 0.00 0.00 4.37
139 140 0.455815 GCAAAGCGGTAGGAAATGGG 59.544 55.000 0.00 0.00 0.00 4.00
140 141 0.455815 GGCAAAGCGGTAGGAAATGG 59.544 55.000 0.00 0.00 0.00 3.16
141 142 1.133025 CTGGCAAAGCGGTAGGAAATG 59.867 52.381 0.00 0.00 0.00 2.32
142 143 1.463674 CTGGCAAAGCGGTAGGAAAT 58.536 50.000 0.00 0.00 0.00 2.17
143 144 1.241315 GCTGGCAAAGCGGTAGGAAA 61.241 55.000 0.00 0.00 43.45 3.13
144 145 1.674322 GCTGGCAAAGCGGTAGGAA 60.674 57.895 0.00 0.00 43.45 3.36
145 146 2.046314 GCTGGCAAAGCGGTAGGA 60.046 61.111 0.00 0.00 43.45 2.94
164 165 4.115199 CTTTGGAGGAGGGGCGGG 62.115 72.222 0.00 0.00 0.00 6.13
165 166 2.907179 AACTTTGGAGGAGGGGCGG 61.907 63.158 0.00 0.00 0.00 6.13
166 167 1.675641 CAACTTTGGAGGAGGGGCG 60.676 63.158 0.00 0.00 0.00 6.13
167 168 0.112412 TTCAACTTTGGAGGAGGGGC 59.888 55.000 0.00 0.00 0.00 5.80
168 169 2.628178 GTTTTCAACTTTGGAGGAGGGG 59.372 50.000 0.00 0.00 0.00 4.79
169 170 2.628178 GGTTTTCAACTTTGGAGGAGGG 59.372 50.000 0.00 0.00 0.00 4.30
170 171 3.319122 CAGGTTTTCAACTTTGGAGGAGG 59.681 47.826 0.00 0.00 0.00 4.30
171 172 3.243535 GCAGGTTTTCAACTTTGGAGGAG 60.244 47.826 0.00 0.00 0.00 3.69
172 173 2.693074 GCAGGTTTTCAACTTTGGAGGA 59.307 45.455 0.00 0.00 0.00 3.71
173 174 2.224042 GGCAGGTTTTCAACTTTGGAGG 60.224 50.000 0.00 0.00 0.00 4.30
174 175 2.430332 TGGCAGGTTTTCAACTTTGGAG 59.570 45.455 0.00 0.00 0.00 3.86
175 176 2.167487 GTGGCAGGTTTTCAACTTTGGA 59.833 45.455 0.00 0.00 0.00 3.53
176 177 2.549926 GTGGCAGGTTTTCAACTTTGG 58.450 47.619 0.00 0.00 0.00 3.28
177 178 2.549926 GGTGGCAGGTTTTCAACTTTG 58.450 47.619 0.00 0.00 0.00 2.77
178 179 1.484653 GGGTGGCAGGTTTTCAACTTT 59.515 47.619 0.00 0.00 0.00 2.66
179 180 1.119684 GGGTGGCAGGTTTTCAACTT 58.880 50.000 0.00 0.00 0.00 2.66
180 181 0.261696 AGGGTGGCAGGTTTTCAACT 59.738 50.000 0.00 0.00 0.00 3.16
181 182 1.119684 AAGGGTGGCAGGTTTTCAAC 58.880 50.000 0.00 0.00 0.00 3.18
182 183 1.118838 CAAGGGTGGCAGGTTTTCAA 58.881 50.000 0.00 0.00 0.00 2.69
183 184 1.398958 GCAAGGGTGGCAGGTTTTCA 61.399 55.000 0.00 0.00 0.00 2.69
184 185 1.367471 GCAAGGGTGGCAGGTTTTC 59.633 57.895 0.00 0.00 0.00 2.29
185 186 2.498056 CGCAAGGGTGGCAGGTTTT 61.498 57.895 0.00 0.00 0.00 2.43
186 187 2.912025 CGCAAGGGTGGCAGGTTT 60.912 61.111 0.00 0.00 0.00 3.27
194 195 4.711949 AGGCTGAGCGCAAGGGTG 62.712 66.667 11.47 0.00 41.67 4.61
195 196 4.711949 CAGGCTGAGCGCAAGGGT 62.712 66.667 9.42 0.00 41.67 4.34
198 199 4.711949 ACCCAGGCTGAGCGCAAG 62.712 66.667 17.94 8.13 41.67 4.01
244 245 2.820479 GCTCCTGCTCTGCTGCTG 60.820 66.667 0.00 0.00 36.03 4.41
245 246 4.098722 GGCTCCTGCTCTGCTGCT 62.099 66.667 0.00 0.00 39.59 4.24
247 248 4.486503 GGGGCTCCTGCTCTGCTG 62.487 72.222 0.00 0.00 40.19 4.41
265 266 4.090057 GAAACCACTCGCGCAGGC 62.090 66.667 8.75 0.00 0.00 4.85
266 267 1.507141 AAAGAAACCACTCGCGCAGG 61.507 55.000 8.75 5.38 0.00 4.85
267 268 0.110644 GAAAGAAACCACTCGCGCAG 60.111 55.000 8.75 6.77 0.00 5.18
268 269 1.503818 GGAAAGAAACCACTCGCGCA 61.504 55.000 8.75 0.00 0.00 6.09
269 270 1.206831 GGAAAGAAACCACTCGCGC 59.793 57.895 0.00 0.00 0.00 6.86
270 271 0.790814 GAGGAAAGAAACCACTCGCG 59.209 55.000 0.00 0.00 0.00 5.87
271 272 0.790814 CGAGGAAAGAAACCACTCGC 59.209 55.000 0.00 0.00 43.42 5.03
273 274 1.157585 GCCGAGGAAAGAAACCACTC 58.842 55.000 0.00 0.00 0.00 3.51
274 275 0.472471 TGCCGAGGAAAGAAACCACT 59.528 50.000 0.00 0.00 0.00 4.00
275 276 0.875059 CTGCCGAGGAAAGAAACCAC 59.125 55.000 0.00 0.00 0.00 4.16
276 277 0.762418 TCTGCCGAGGAAAGAAACCA 59.238 50.000 0.00 0.00 0.00 3.67
277 278 1.892209 TTCTGCCGAGGAAAGAAACC 58.108 50.000 5.55 0.00 0.00 3.27
278 279 3.502211 TGATTTCTGCCGAGGAAAGAAAC 59.498 43.478 17.13 13.14 41.38 2.78
279 280 3.502211 GTGATTTCTGCCGAGGAAAGAAA 59.498 43.478 17.12 17.12 42.41 2.52
280 281 3.074412 GTGATTTCTGCCGAGGAAAGAA 58.926 45.455 0.00 0.00 36.35 2.52
281 282 2.038426 TGTGATTTCTGCCGAGGAAAGA 59.962 45.455 0.00 0.00 36.35 2.52
282 283 2.417933 CTGTGATTTCTGCCGAGGAAAG 59.582 50.000 0.00 0.00 36.35 2.62
283 284 2.038426 TCTGTGATTTCTGCCGAGGAAA 59.962 45.455 0.00 0.00 37.15 3.13
284 285 1.623311 TCTGTGATTTCTGCCGAGGAA 59.377 47.619 0.00 0.00 0.00 3.36
285 286 1.266178 TCTGTGATTTCTGCCGAGGA 58.734 50.000 0.00 0.00 0.00 3.71
286 287 2.322355 ATCTGTGATTTCTGCCGAGG 57.678 50.000 0.00 0.00 0.00 4.63
287 288 3.686241 TCAAATCTGTGATTTCTGCCGAG 59.314 43.478 2.92 0.00 0.00 4.63
310 311 4.401022 TGTGATTTGATTTCTGCCTCAGT 58.599 39.130 0.00 0.00 32.61 3.41
414 415 3.965660 CCTAAGGGGAAGGCGCTA 58.034 61.111 7.64 0.00 37.23 4.26
1055 1059 7.897864 ACTCATTATTACCTTATCCTTCTCGG 58.102 38.462 0.00 0.00 0.00 4.63
1284 1288 1.447838 GGAGCGTTCAGATTCGGCA 60.448 57.895 0.53 0.00 0.00 5.69
2725 2747 6.655003 CCTTTGCTAGATCCTCAAAGTTTACA 59.345 38.462 20.77 0.00 42.90 2.41
3067 3089 1.301401 GGCCTGACGCTGTAACACA 60.301 57.895 0.00 0.00 37.74 3.72


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

AutoCloner maintained by Alex Coulton.