Multiple sequence alignment - TraesCS5D01G273600

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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 TraesCS5D01G273600 chr5D 100.000 3839 0 0 1 3839 376665449 376661611 0.000000e+00 7090
1 TraesCS5D01G273600 chr5D 84.545 110 16 1 1 109 320886182 320886291 1.460000e-19 108
2 TraesCS5D01G273600 chr5B 95.468 3508 126 14 244 3734 449753333 449749842 0.000000e+00 5566
3 TraesCS5D01G273600 chr5A 96.137 3003 73 15 279 3250 477438169 477435179 0.000000e+00 4863
4 TraesCS5D01G273600 chr5A 86.189 391 29 7 3432 3816 477434481 477434110 2.150000e-107 399
5 TraesCS5D01G273600 chr5A 92.029 138 11 0 3303 3440 477434765 477434628 1.090000e-45 195
6 TraesCS5D01G273600 chr5A 86.408 103 13 1 7 108 91852701 91852803 1.130000e-20 111
7 TraesCS5D01G273600 chr7B 78.247 947 180 17 1070 2012 188604230 188603306 5.530000e-163 584
8 TraesCS5D01G273600 chr7D 79.684 822 156 6 1070 1890 213374623 213375434 1.990000e-162 582
9 TraesCS5D01G273600 chr7D 88.764 89 9 1 22 109 48534393 48534305 1.460000e-19 108
10 TraesCS5D01G273600 chr7A 78.370 920 179 12 1070 1988 224987659 224988559 2.570000e-161 579
11 TraesCS5D01G273600 chr3D 91.304 207 16 2 3635 3839 213403777 213403983 8.120000e-72 281
12 TraesCS5D01G273600 chr3D 90.291 206 18 2 3635 3839 213378572 213378776 6.320000e-68 268
13 TraesCS5D01G273600 chr2D 90.291 206 17 3 3635 3838 591992773 591992977 2.270000e-67 267
14 TraesCS5D01G273600 chr2D 88.235 102 11 1 7 107 233429666 233429767 1.870000e-23 121
15 TraesCS5D01G273600 chr2D 90.698 86 7 1 22 106 58812181 58812096 3.130000e-21 113
16 TraesCS5D01G273600 chr2D 88.542 96 8 3 22 116 393756349 393756256 3.130000e-21 113
17 TraesCS5D01G273600 chrUn 89.855 207 19 2 3635 3839 53262326 53262120 8.180000e-67 265
18 TraesCS5D01G273600 chrUn 89.855 207 19 2 3635 3839 351214890 351214684 8.180000e-67 265
19 TraesCS5D01G273600 chrUn 89.855 207 19 2 3635 3839 354743713 354743507 8.180000e-67 265
20 TraesCS5D01G273600 chr4B 89.855 207 19 2 3635 3839 151526034 151526240 8.180000e-67 265
21 TraesCS5D01G273600 chr4B 89.855 207 19 2 3635 3839 151526546 151526752 8.180000e-67 265
22 TraesCS5D01G273600 chr1D 89.855 207 19 2 3635 3839 254532696 254532902 8.180000e-67 265
23 TraesCS5D01G273600 chr1D 86.275 102 12 2 7 107 335365820 335365920 4.050000e-20 110
24 TraesCS5D01G273600 chr1A 87.619 105 11 2 6 108 21715471 21715575 1.870000e-23 121
25 TraesCS5D01G273600 chr1B 86.139 101 13 1 7 106 332136260 332136160 1.460000e-19 108


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 TraesCS5D01G273600 chr5D 376661611 376665449 3838 True 7090 7090 100.000000 1 3839 1 chr5D.!!$R1 3838
1 TraesCS5D01G273600 chr5B 449749842 449753333 3491 True 5566 5566 95.468000 244 3734 1 chr5B.!!$R1 3490
2 TraesCS5D01G273600 chr5A 477434110 477438169 4059 True 1819 4863 91.451667 279 3816 3 chr5A.!!$R1 3537
3 TraesCS5D01G273600 chr7B 188603306 188604230 924 True 584 584 78.247000 1070 2012 1 chr7B.!!$R1 942
4 TraesCS5D01G273600 chr7D 213374623 213375434 811 False 582 582 79.684000 1070 1890 1 chr7D.!!$F1 820
5 TraesCS5D01G273600 chr7A 224987659 224988559 900 False 579 579 78.370000 1070 1988 1 chr7A.!!$F1 918
6 TraesCS5D01G273600 chr4B 151526034 151526752 718 False 265 265 89.855000 3635 3839 2 chr4B.!!$F1 204

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
234 235 0.038159 GTGCCTACAAGAGAGCACGT 60.038 55.0 0.0 0.0 40.32 4.49 F
1542 1568 0.035881 CTCTGGGCTCACTGCTTTCA 59.964 55.0 0.0 0.0 42.39 2.69 F
1716 1742 0.400594 AGAAGGTTTGGAAGGTCGGG 59.599 55.0 0.0 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 2085 1.548269 CGCCCTTTCTCTGTCTCTTCT 59.452 52.381 0.00 0.0 0.0 2.85 R
2477 2503 3.010413 GCATGCAGTGGAAAGGGGC 62.010 63.158 14.21 0.0 0.0 5.80 R
3574 4135 1.972872 ACAGCAACTCAACAGGAAGG 58.027 50.000 0.00 0.0 0.0 3.46 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
26 27 9.131416 GTCCAAAATTACTTACCGTTAAAATGG 57.869 33.333 0.00 0.00 41.00 3.16
27 28 9.075678 TCCAAAATTACTTACCGTTAAAATGGA 57.924 29.630 7.96 0.00 38.48 3.41
28 29 9.863845 CCAAAATTACTTACCGTTAAAATGGAT 57.136 29.630 7.96 0.00 38.48 3.41
36 37 9.760077 ACTTACCGTTAAAATGGATGTATCTAG 57.240 33.333 7.96 0.00 38.48 2.43
37 38 9.976511 CTTACCGTTAAAATGGATGTATCTAGA 57.023 33.333 7.96 0.00 38.48 2.43
38 39 9.754382 TTACCGTTAAAATGGATGTATCTAGAC 57.246 33.333 7.96 0.00 38.48 2.59
39 40 6.921857 ACCGTTAAAATGGATGTATCTAGACG 59.078 38.462 7.96 0.00 38.48 4.18
40 41 6.921857 CCGTTAAAATGGATGTATCTAGACGT 59.078 38.462 0.00 0.00 37.24 4.34
41 42 8.077991 CCGTTAAAATGGATGTATCTAGACGTA 58.922 37.037 0.00 0.00 37.24 3.57
42 43 9.622004 CGTTAAAATGGATGTATCTAGACGTAT 57.378 33.333 0.00 0.00 0.00 3.06
78 79 9.317936 GATACATCAATTTTTCTCCATTTTCCC 57.682 33.333 0.00 0.00 0.00 3.97
79 80 6.165577 ACATCAATTTTTCTCCATTTTCCCG 58.834 36.000 0.00 0.00 0.00 5.14
80 81 6.014669 ACATCAATTTTTCTCCATTTTCCCGA 60.015 34.615 0.00 0.00 0.00 5.14
81 82 5.778862 TCAATTTTTCTCCATTTTCCCGAC 58.221 37.500 0.00 0.00 0.00 4.79
82 83 5.303078 TCAATTTTTCTCCATTTTCCCGACA 59.697 36.000 0.00 0.00 0.00 4.35
83 84 5.799827 ATTTTTCTCCATTTTCCCGACAA 57.200 34.783 0.00 0.00 0.00 3.18
84 85 4.846779 TTTTCTCCATTTTCCCGACAAG 57.153 40.909 0.00 0.00 0.00 3.16
85 86 3.502123 TTCTCCATTTTCCCGACAAGT 57.498 42.857 0.00 0.00 0.00 3.16
86 87 4.627284 TTCTCCATTTTCCCGACAAGTA 57.373 40.909 0.00 0.00 0.00 2.24
87 88 4.627284 TCTCCATTTTCCCGACAAGTAA 57.373 40.909 0.00 0.00 0.00 2.24
88 89 5.174037 TCTCCATTTTCCCGACAAGTAAT 57.826 39.130 0.00 0.00 0.00 1.89
89 90 5.566469 TCTCCATTTTCCCGACAAGTAATT 58.434 37.500 0.00 0.00 0.00 1.40
90 91 6.007703 TCTCCATTTTCCCGACAAGTAATTT 58.992 36.000 0.00 0.00 0.00 1.82
91 92 6.150474 TCTCCATTTTCCCGACAAGTAATTTC 59.850 38.462 0.00 0.00 0.00 2.17
92 93 5.092781 CCATTTTCCCGACAAGTAATTTCG 58.907 41.667 0.00 0.00 0.00 3.46
93 94 5.106475 CCATTTTCCCGACAAGTAATTTCGA 60.106 40.000 8.39 0.00 34.62 3.71
94 95 6.375377 CATTTTCCCGACAAGTAATTTCGAA 58.625 36.000 0.00 0.00 34.62 3.71
95 96 4.996062 TTCCCGACAAGTAATTTCGAAC 57.004 40.909 0.00 0.00 34.62 3.95
96 97 4.261578 TCCCGACAAGTAATTTCGAACT 57.738 40.909 0.00 0.00 34.62 3.01
97 98 3.991773 TCCCGACAAGTAATTTCGAACTG 59.008 43.478 0.00 0.00 34.62 3.16
98 99 3.991773 CCCGACAAGTAATTTCGAACTGA 59.008 43.478 0.00 0.00 34.62 3.41
99 100 4.091509 CCCGACAAGTAATTTCGAACTGAG 59.908 45.833 0.00 0.00 34.62 3.35
100 101 4.091509 CCGACAAGTAATTTCGAACTGAGG 59.908 45.833 0.00 0.00 34.62 3.86
101 102 4.091509 CGACAAGTAATTTCGAACTGAGGG 59.908 45.833 0.00 0.00 34.62 4.30
102 103 5.223449 ACAAGTAATTTCGAACTGAGGGA 57.777 39.130 0.00 0.00 0.00 4.20
103 104 5.238583 ACAAGTAATTTCGAACTGAGGGAG 58.761 41.667 0.00 0.00 0.00 4.30
104 105 5.221661 ACAAGTAATTTCGAACTGAGGGAGT 60.222 40.000 0.00 0.00 35.94 3.85
105 106 6.014840 ACAAGTAATTTCGAACTGAGGGAGTA 60.015 38.462 0.00 0.00 33.09 2.59
106 107 5.963594 AGTAATTTCGAACTGAGGGAGTAC 58.036 41.667 0.00 0.00 33.09 2.73
107 108 5.715753 AGTAATTTCGAACTGAGGGAGTACT 59.284 40.000 0.00 0.00 33.09 2.73
108 109 5.485209 AATTTCGAACTGAGGGAGTACTT 57.515 39.130 0.00 0.00 33.09 2.24
109 110 4.516365 TTTCGAACTGAGGGAGTACTTC 57.484 45.455 0.00 0.00 33.09 3.01
110 111 3.150458 TCGAACTGAGGGAGTACTTCA 57.850 47.619 2.92 0.00 33.09 3.02
111 112 3.698289 TCGAACTGAGGGAGTACTTCAT 58.302 45.455 2.92 0.00 33.09 2.57
112 113 4.851843 TCGAACTGAGGGAGTACTTCATA 58.148 43.478 2.92 0.00 33.09 2.15
113 114 5.446860 TCGAACTGAGGGAGTACTTCATAT 58.553 41.667 2.92 0.00 33.09 1.78
114 115 6.598503 TCGAACTGAGGGAGTACTTCATATA 58.401 40.000 2.92 0.00 33.09 0.86
115 116 7.058525 TCGAACTGAGGGAGTACTTCATATAA 58.941 38.462 2.92 0.00 33.09 0.98
116 117 7.724506 TCGAACTGAGGGAGTACTTCATATAAT 59.275 37.037 2.92 0.00 33.09 1.28
117 118 8.024285 CGAACTGAGGGAGTACTTCATATAATC 58.976 40.741 2.92 0.00 33.09 1.75
118 119 8.783660 AACTGAGGGAGTACTTCATATAATCA 57.216 34.615 2.92 0.00 33.09 2.57
119 120 8.783660 ACTGAGGGAGTACTTCATATAATCAA 57.216 34.615 2.92 0.00 30.86 2.57
120 121 8.865090 ACTGAGGGAGTACTTCATATAATCAAG 58.135 37.037 2.92 0.00 30.86 3.02
121 122 8.783660 TGAGGGAGTACTTCATATAATCAAGT 57.216 34.615 2.92 0.00 34.68 3.16
122 123 8.861086 TGAGGGAGTACTTCATATAATCAAGTC 58.139 37.037 2.92 0.00 32.56 3.01
123 124 9.084533 GAGGGAGTACTTCATATAATCAAGTCT 57.915 37.037 2.92 0.00 32.56 3.24
124 125 9.440761 AGGGAGTACTTCATATAATCAAGTCTT 57.559 33.333 2.92 0.00 32.56 3.01
140 141 9.778741 AATCAAGTCTTACATGTTAAGTGAAGA 57.221 29.630 2.30 2.72 0.00 2.87
141 142 9.778741 ATCAAGTCTTACATGTTAAGTGAAGAA 57.221 29.630 2.30 0.00 0.00 2.52
142 143 9.607988 TCAAGTCTTACATGTTAAGTGAAGAAA 57.392 29.630 2.30 0.00 0.00 2.52
173 174 8.418597 AGTCTAACATTTTGGTCTGTACTAGA 57.581 34.615 0.00 0.00 0.00 2.43
174 175 9.036980 AGTCTAACATTTTGGTCTGTACTAGAT 57.963 33.333 0.00 0.00 37.83 1.98
179 180 8.362464 ACATTTTGGTCTGTACTAGATACTGA 57.638 34.615 0.00 2.71 38.89 3.41
180 181 8.812972 ACATTTTGGTCTGTACTAGATACTGAA 58.187 33.333 0.00 0.00 41.74 3.02
181 182 9.653287 CATTTTGGTCTGTACTAGATACTGAAA 57.347 33.333 0.00 0.00 41.74 2.69
186 187 9.696572 TGGTCTGTACTAGATACTGAAAATAGT 57.303 33.333 0.00 0.00 41.74 2.12
215 216 6.949578 ATTGTTAAACAATGCCTTCATTCG 57.050 33.333 0.00 0.00 46.18 3.34
216 217 5.446143 TGTTAAACAATGCCTTCATTCGT 57.554 34.783 0.00 0.00 40.74 3.85
217 218 5.218885 TGTTAAACAATGCCTTCATTCGTG 58.781 37.500 0.00 0.00 40.74 4.35
218 219 2.352503 AACAATGCCTTCATTCGTGC 57.647 45.000 0.00 0.00 40.74 5.34
219 220 0.527565 ACAATGCCTTCATTCGTGCC 59.472 50.000 0.00 0.00 40.74 5.01
220 221 0.813184 CAATGCCTTCATTCGTGCCT 59.187 50.000 0.00 0.00 40.74 4.75
221 222 2.016318 CAATGCCTTCATTCGTGCCTA 58.984 47.619 0.00 0.00 40.74 3.93
222 223 1.668419 ATGCCTTCATTCGTGCCTAC 58.332 50.000 0.00 0.00 0.00 3.18
223 224 0.323302 TGCCTTCATTCGTGCCTACA 59.677 50.000 0.00 0.00 0.00 2.74
224 225 1.271108 TGCCTTCATTCGTGCCTACAA 60.271 47.619 0.00 0.00 0.00 2.41
225 226 1.398390 GCCTTCATTCGTGCCTACAAG 59.602 52.381 0.00 0.00 0.00 3.16
226 227 2.935238 GCCTTCATTCGTGCCTACAAGA 60.935 50.000 0.00 0.00 32.09 3.02
227 228 2.932614 CCTTCATTCGTGCCTACAAGAG 59.067 50.000 0.00 0.00 35.65 2.85
228 229 3.368427 CCTTCATTCGTGCCTACAAGAGA 60.368 47.826 0.00 0.00 35.65 3.10
229 230 3.510388 TCATTCGTGCCTACAAGAGAG 57.490 47.619 0.00 0.00 35.65 3.20
230 231 1.929836 CATTCGTGCCTACAAGAGAGC 59.070 52.381 0.00 0.00 35.65 4.09
231 232 0.966179 TTCGTGCCTACAAGAGAGCA 59.034 50.000 0.00 0.00 35.65 4.26
232 233 0.243907 TCGTGCCTACAAGAGAGCAC 59.756 55.000 3.96 3.96 43.44 4.40
233 234 2.743195 GTGCCTACAAGAGAGCACG 58.257 57.895 0.00 0.00 40.32 5.34
234 235 0.038159 GTGCCTACAAGAGAGCACGT 60.038 55.000 0.00 0.00 40.32 4.49
235 236 0.243907 TGCCTACAAGAGAGCACGTC 59.756 55.000 0.00 0.00 0.00 4.34
236 237 0.458716 GCCTACAAGAGAGCACGTCC 60.459 60.000 0.00 0.00 0.00 4.79
237 238 0.888619 CCTACAAGAGAGCACGTCCA 59.111 55.000 0.00 0.00 0.00 4.02
238 239 1.402984 CCTACAAGAGAGCACGTCCAC 60.403 57.143 0.00 0.00 0.00 4.02
239 240 0.601558 TACAAGAGAGCACGTCCACC 59.398 55.000 0.00 0.00 0.00 4.61
240 241 1.374758 CAAGAGAGCACGTCCACCC 60.375 63.158 0.00 0.00 0.00 4.61
241 242 2.584391 AAGAGAGCACGTCCACCCC 61.584 63.158 0.00 0.00 0.00 4.95
242 243 3.311110 GAGAGCACGTCCACCCCA 61.311 66.667 0.00 0.00 0.00 4.96
252 253 0.831711 GTCCACCCCAAACAATGCCT 60.832 55.000 0.00 0.00 0.00 4.75
369 380 0.599204 TCCGAGAAAACACACGAGCC 60.599 55.000 0.00 0.00 0.00 4.70
444 465 4.820173 TCGAGTTTCCTTCCTTTCCTTTTC 59.180 41.667 0.00 0.00 0.00 2.29
493 514 1.384525 TCCACACAAGGAAACCAACG 58.615 50.000 0.00 0.00 33.93 4.10
505 526 0.320374 AACCAACGGAATCTCGAGCA 59.680 50.000 7.81 0.00 0.00 4.26
725 747 0.171455 CCGTCTTCTTCTCTCGGGTG 59.829 60.000 0.00 0.00 37.92 4.61
829 852 2.574369 TCCATGGTCCGATTAGGTTTGT 59.426 45.455 12.58 0.00 41.99 2.83
830 853 2.943033 CCATGGTCCGATTAGGTTTGTC 59.057 50.000 2.57 0.00 41.99 3.18
831 854 3.370527 CCATGGTCCGATTAGGTTTGTCT 60.371 47.826 2.57 0.00 41.99 3.41
837 860 5.235516 GTCCGATTAGGTTTGTCTTCTTCA 58.764 41.667 0.00 0.00 41.99 3.02
925 951 1.177401 GGGAAGGCTGTTTCCATGAC 58.823 55.000 14.24 0.00 46.89 3.06
935 961 0.984230 TTTCCATGACTCCCTCGCTT 59.016 50.000 0.00 0.00 0.00 4.68
961 987 1.082206 CTAGGAGGGGTTGGGTGGA 59.918 63.158 0.00 0.00 0.00 4.02
991 1017 1.003355 CGGGATTGCGAGGCCATAT 60.003 57.895 5.01 0.00 0.00 1.78
1015 1041 3.137533 GTTCTTATGGATCAGCTGGCTC 58.862 50.000 15.13 11.06 0.00 4.70
1323 1349 1.288752 CAATGCCCGTGGGTTTGTC 59.711 57.895 6.82 0.00 37.65 3.18
1542 1568 0.035881 CTCTGGGCTCACTGCTTTCA 59.964 55.000 0.00 0.00 42.39 2.69
1716 1742 0.400594 AGAAGGTTTGGAAGGTCGGG 59.599 55.000 0.00 0.00 0.00 5.14
1857 1883 4.324719 GGAGTCCTACAGAGAGAGGAAAGA 60.325 50.000 0.41 0.00 43.52 2.52
3062 3099 4.141642 TGTTGATACCATCTGTAGCATGCT 60.142 41.667 25.99 25.99 44.72 3.79
3163 3200 6.536447 CCTACAGGGTTTAAGTTTGGAGTAA 58.464 40.000 0.00 0.00 0.00 2.24
3335 3738 9.683069 ACAATCAAGAATAAAATATTCATCGGC 57.317 29.630 11.50 0.00 0.00 5.54
3368 3771 9.445973 AATCCCTCTGTCTCTTATCTTTCTATT 57.554 33.333 0.00 0.00 0.00 1.73
3418 3822 6.816640 TCATTAGTTGATGGTAGTTACACAGC 59.183 38.462 0.00 0.00 0.00 4.40
3424 3828 3.455990 TGGTAGTTACACAGCGAAACA 57.544 42.857 0.00 0.00 0.00 2.83
3498 4059 9.167311 CTACAGTTCTGAAAATGGCTAGTATTT 57.833 33.333 6.83 0.00 34.82 1.40
3499 4060 8.409358 ACAGTTCTGAAAATGGCTAGTATTTT 57.591 30.769 15.26 15.26 39.65 1.82
3500 4061 8.860088 ACAGTTCTGAAAATGGCTAGTATTTTT 58.140 29.630 15.99 8.85 37.73 1.94
3503 4064 9.476202 GTTCTGAAAATGGCTAGTATTTTTGTT 57.524 29.630 15.99 1.08 37.73 2.83
3574 4135 3.246226 CGGTAAATGACTGCATCACTAGC 59.754 47.826 0.00 0.00 41.24 3.42
3605 4166 1.806542 AGTTGCTGTTTGGTATCTGCG 59.193 47.619 0.00 0.00 0.00 5.18
3685 4759 3.887621 TCATTGGAAAGAGGTCTACGG 57.112 47.619 0.00 0.00 0.00 4.02
3702 4776 3.007473 ACGGAGACTTTTGGGAAAACA 57.993 42.857 0.00 0.00 0.00 2.83
3704 4778 3.958147 ACGGAGACTTTTGGGAAAACATT 59.042 39.130 0.00 0.00 0.00 2.71
3734 4808 4.256110 GCTGGCTTATTTGGCAAAGAAAT 58.744 39.130 19.29 5.36 41.92 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.131416 CCATTTTAACGGTAAGTAATTTTGGAC 57.869 33.333 0.00 0.00 0.00 4.02
1 2 9.075678 TCCATTTTAACGGTAAGTAATTTTGGA 57.924 29.630 0.00 0.00 0.00 3.53
2 3 9.863845 ATCCATTTTAACGGTAAGTAATTTTGG 57.136 29.630 0.00 0.00 0.00 3.28
10 11 9.760077 CTAGATACATCCATTTTAACGGTAAGT 57.240 33.333 0.00 0.00 0.00 2.24
11 12 9.976511 TCTAGATACATCCATTTTAACGGTAAG 57.023 33.333 0.00 0.00 0.00 2.34
12 13 9.754382 GTCTAGATACATCCATTTTAACGGTAA 57.246 33.333 0.00 0.00 0.00 2.85
13 14 8.077991 CGTCTAGATACATCCATTTTAACGGTA 58.922 37.037 0.00 0.00 0.00 4.02
14 15 6.921857 CGTCTAGATACATCCATTTTAACGGT 59.078 38.462 0.00 0.00 0.00 4.83
15 16 6.921857 ACGTCTAGATACATCCATTTTAACGG 59.078 38.462 0.00 0.00 0.00 4.44
16 17 7.925703 ACGTCTAGATACATCCATTTTAACG 57.074 36.000 0.00 0.00 0.00 3.18
52 53 9.317936 GGGAAAATGGAGAAAAATTGATGTATC 57.682 33.333 0.00 0.00 0.00 2.24
53 54 7.981225 CGGGAAAATGGAGAAAAATTGATGTAT 59.019 33.333 0.00 0.00 0.00 2.29
54 55 7.177568 TCGGGAAAATGGAGAAAAATTGATGTA 59.822 33.333 0.00 0.00 0.00 2.29
55 56 6.014669 TCGGGAAAATGGAGAAAAATTGATGT 60.015 34.615 0.00 0.00 0.00 3.06
56 57 6.311200 GTCGGGAAAATGGAGAAAAATTGATG 59.689 38.462 0.00 0.00 0.00 3.07
57 58 6.014669 TGTCGGGAAAATGGAGAAAAATTGAT 60.015 34.615 0.00 0.00 0.00 2.57
58 59 5.303078 TGTCGGGAAAATGGAGAAAAATTGA 59.697 36.000 0.00 0.00 0.00 2.57
59 60 5.537188 TGTCGGGAAAATGGAGAAAAATTG 58.463 37.500 0.00 0.00 0.00 2.32
60 61 5.799827 TGTCGGGAAAATGGAGAAAAATT 57.200 34.783 0.00 0.00 0.00 1.82
61 62 5.304357 ACTTGTCGGGAAAATGGAGAAAAAT 59.696 36.000 0.00 0.00 0.00 1.82
62 63 4.647399 ACTTGTCGGGAAAATGGAGAAAAA 59.353 37.500 0.00 0.00 0.00 1.94
63 64 4.211920 ACTTGTCGGGAAAATGGAGAAAA 58.788 39.130 0.00 0.00 0.00 2.29
64 65 3.827722 ACTTGTCGGGAAAATGGAGAAA 58.172 40.909 0.00 0.00 0.00 2.52
65 66 3.502123 ACTTGTCGGGAAAATGGAGAA 57.498 42.857 0.00 0.00 0.00 2.87
66 67 4.627284 TTACTTGTCGGGAAAATGGAGA 57.373 40.909 0.00 0.00 0.00 3.71
67 68 5.897377 AATTACTTGTCGGGAAAATGGAG 57.103 39.130 0.00 0.00 0.00 3.86
68 69 5.106475 CGAAATTACTTGTCGGGAAAATGGA 60.106 40.000 0.00 0.00 0.00 3.41
69 70 5.092781 CGAAATTACTTGTCGGGAAAATGG 58.907 41.667 0.00 0.00 0.00 3.16
70 71 5.933790 TCGAAATTACTTGTCGGGAAAATG 58.066 37.500 0.00 0.00 35.51 2.32
71 72 6.206048 AGTTCGAAATTACTTGTCGGGAAAAT 59.794 34.615 0.00 0.00 35.51 1.82
72 73 5.528320 AGTTCGAAATTACTTGTCGGGAAAA 59.472 36.000 0.00 0.00 35.51 2.29
73 74 5.049954 CAGTTCGAAATTACTTGTCGGGAAA 60.050 40.000 0.00 0.00 35.51 3.13
74 75 4.449743 CAGTTCGAAATTACTTGTCGGGAA 59.550 41.667 0.00 0.00 35.51 3.97
75 76 3.991773 CAGTTCGAAATTACTTGTCGGGA 59.008 43.478 0.00 0.00 35.51 5.14
76 77 3.991773 TCAGTTCGAAATTACTTGTCGGG 59.008 43.478 0.00 0.00 35.51 5.14
77 78 4.091509 CCTCAGTTCGAAATTACTTGTCGG 59.908 45.833 0.00 0.00 35.51 4.79
78 79 4.091509 CCCTCAGTTCGAAATTACTTGTCG 59.908 45.833 0.00 0.00 36.12 4.35
79 80 5.235516 TCCCTCAGTTCGAAATTACTTGTC 58.764 41.667 0.00 0.00 0.00 3.18
80 81 5.221661 ACTCCCTCAGTTCGAAATTACTTGT 60.222 40.000 0.00 0.00 26.56 3.16
81 82 5.238583 ACTCCCTCAGTTCGAAATTACTTG 58.761 41.667 0.00 0.00 26.56 3.16
82 83 5.485209 ACTCCCTCAGTTCGAAATTACTT 57.515 39.130 0.00 0.00 26.56 2.24
83 84 5.715753 AGTACTCCCTCAGTTCGAAATTACT 59.284 40.000 0.00 0.00 36.43 2.24
84 85 5.963594 AGTACTCCCTCAGTTCGAAATTAC 58.036 41.667 0.00 0.00 36.43 1.89
85 86 6.209986 TGAAGTACTCCCTCAGTTCGAAATTA 59.790 38.462 0.00 0.00 36.43 1.40
86 87 5.011738 TGAAGTACTCCCTCAGTTCGAAATT 59.988 40.000 0.00 0.00 36.43 1.82
87 88 4.527038 TGAAGTACTCCCTCAGTTCGAAAT 59.473 41.667 0.00 0.00 36.43 2.17
88 89 3.893200 TGAAGTACTCCCTCAGTTCGAAA 59.107 43.478 0.00 0.00 36.43 3.46
89 90 3.493334 TGAAGTACTCCCTCAGTTCGAA 58.507 45.455 0.00 0.00 36.43 3.71
90 91 3.150458 TGAAGTACTCCCTCAGTTCGA 57.850 47.619 0.00 0.00 36.43 3.71
91 92 5.776173 ATATGAAGTACTCCCTCAGTTCG 57.224 43.478 0.00 0.00 36.43 3.95
92 93 8.861086 TGATTATATGAAGTACTCCCTCAGTTC 58.139 37.037 0.00 0.00 36.43 3.01
93 94 8.783660 TGATTATATGAAGTACTCCCTCAGTT 57.216 34.615 0.00 0.00 36.43 3.16
94 95 8.783660 TTGATTATATGAAGTACTCCCTCAGT 57.216 34.615 0.00 0.00 39.41 3.41
95 96 8.865090 ACTTGATTATATGAAGTACTCCCTCAG 58.135 37.037 0.00 0.00 34.92 3.35
96 97 8.783660 ACTTGATTATATGAAGTACTCCCTCA 57.216 34.615 0.00 0.00 34.92 3.86
97 98 9.084533 AGACTTGATTATATGAAGTACTCCCTC 57.915 37.037 0.00 0.00 36.84 4.30
98 99 9.440761 AAGACTTGATTATATGAAGTACTCCCT 57.559 33.333 0.00 0.00 36.84 4.20
114 115 9.778741 TCTTCACTTAACATGTAAGACTTGATT 57.221 29.630 16.84 0.00 0.00 2.57
115 116 9.778741 TTCTTCACTTAACATGTAAGACTTGAT 57.221 29.630 16.84 0.00 0.00 2.57
116 117 9.607988 TTTCTTCACTTAACATGTAAGACTTGA 57.392 29.630 16.84 10.22 0.00 3.02
147 148 8.867097 TCTAGTACAGACCAAAATGTTAGACTT 58.133 33.333 0.00 0.00 0.00 3.01
148 149 8.418597 TCTAGTACAGACCAAAATGTTAGACT 57.581 34.615 0.00 0.00 0.00 3.24
153 154 8.812972 TCAGTATCTAGTACAGACCAAAATGTT 58.187 33.333 0.00 0.00 35.62 2.71
154 155 8.362464 TCAGTATCTAGTACAGACCAAAATGT 57.638 34.615 0.00 0.00 35.62 2.71
155 156 9.653287 TTTCAGTATCTAGTACAGACCAAAATG 57.347 33.333 0.00 0.00 35.62 2.32
160 161 9.696572 ACTATTTTCAGTATCTAGTACAGACCA 57.303 33.333 0.00 0.00 35.62 4.02
181 182 8.998377 GGCATTGTTTAACAATCCAAAACTATT 58.002 29.630 19.05 0.00 44.91 1.73
182 183 8.374743 AGGCATTGTTTAACAATCCAAAACTAT 58.625 29.630 25.73 11.79 44.91 2.12
183 184 7.731054 AGGCATTGTTTAACAATCCAAAACTA 58.269 30.769 25.73 5.29 44.91 2.24
184 185 6.591001 AGGCATTGTTTAACAATCCAAAACT 58.409 32.000 25.73 14.96 44.91 2.66
185 186 6.859420 AGGCATTGTTTAACAATCCAAAAC 57.141 33.333 25.73 13.63 44.91 2.43
186 187 7.050377 TGAAGGCATTGTTTAACAATCCAAAA 58.950 30.769 25.73 15.44 44.91 2.44
187 188 6.586344 TGAAGGCATTGTTTAACAATCCAAA 58.414 32.000 25.73 15.65 44.91 3.28
188 189 6.166984 TGAAGGCATTGTTTAACAATCCAA 57.833 33.333 25.73 15.86 44.91 3.53
189 190 5.798125 TGAAGGCATTGTTTAACAATCCA 57.202 34.783 25.73 15.68 44.91 3.41
190 191 6.034898 CGAATGAAGGCATTGTTTAACAATCC 59.965 38.462 19.05 20.20 44.91 3.01
191 192 6.586082 ACGAATGAAGGCATTGTTTAACAATC 59.414 34.615 19.05 13.71 44.91 2.67
193 194 5.689514 CACGAATGAAGGCATTGTTTAACAA 59.310 36.000 13.12 13.12 44.47 2.83
194 195 5.218885 CACGAATGAAGGCATTGTTTAACA 58.781 37.500 0.00 0.00 44.47 2.41
195 196 4.089923 GCACGAATGAAGGCATTGTTTAAC 59.910 41.667 0.00 0.00 44.47 2.01
196 197 4.233789 GCACGAATGAAGGCATTGTTTAA 58.766 39.130 0.00 0.00 44.47 1.52
197 198 3.366883 GGCACGAATGAAGGCATTGTTTA 60.367 43.478 0.00 0.00 44.47 2.01
198 199 2.610232 GGCACGAATGAAGGCATTGTTT 60.610 45.455 0.00 0.00 44.47 2.83
199 200 1.067635 GGCACGAATGAAGGCATTGTT 60.068 47.619 0.00 0.00 44.47 2.83
200 201 0.527565 GGCACGAATGAAGGCATTGT 59.472 50.000 0.00 0.00 44.47 2.71
201 202 0.813184 AGGCACGAATGAAGGCATTG 59.187 50.000 0.00 0.00 44.47 2.82
202 203 2.017049 GTAGGCACGAATGAAGGCATT 58.983 47.619 0.00 0.00 47.00 3.56
203 204 1.065491 TGTAGGCACGAATGAAGGCAT 60.065 47.619 0.00 0.00 35.92 4.40
204 205 0.323302 TGTAGGCACGAATGAAGGCA 59.677 50.000 0.00 0.00 0.00 4.75
205 206 1.398390 CTTGTAGGCACGAATGAAGGC 59.602 52.381 0.00 0.00 0.00 4.35
206 207 2.932614 CTCTTGTAGGCACGAATGAAGG 59.067 50.000 0.00 0.00 0.00 3.46
207 208 3.849911 TCTCTTGTAGGCACGAATGAAG 58.150 45.455 0.00 0.00 0.00 3.02
208 209 3.849911 CTCTCTTGTAGGCACGAATGAA 58.150 45.455 0.00 0.00 0.00 2.57
209 210 2.417379 GCTCTCTTGTAGGCACGAATGA 60.417 50.000 0.00 0.00 0.00 2.57
210 211 1.929836 GCTCTCTTGTAGGCACGAATG 59.070 52.381 0.00 0.00 0.00 2.67
211 212 1.550524 TGCTCTCTTGTAGGCACGAAT 59.449 47.619 0.00 0.00 0.00 3.34
212 213 0.966179 TGCTCTCTTGTAGGCACGAA 59.034 50.000 0.00 0.00 0.00 3.85
213 214 0.243907 GTGCTCTCTTGTAGGCACGA 59.756 55.000 0.00 0.00 40.31 4.35
214 215 2.743195 GTGCTCTCTTGTAGGCACG 58.257 57.895 0.00 0.00 40.31 5.34
215 216 0.038159 ACGTGCTCTCTTGTAGGCAC 60.038 55.000 6.82 6.82 43.40 5.01
216 217 0.243907 GACGTGCTCTCTTGTAGGCA 59.756 55.000 0.00 0.00 0.00 4.75
217 218 0.458716 GGACGTGCTCTCTTGTAGGC 60.459 60.000 0.00 0.00 0.00 3.93
218 219 0.888619 TGGACGTGCTCTCTTGTAGG 59.111 55.000 8.99 0.00 0.00 3.18
219 220 1.402984 GGTGGACGTGCTCTCTTGTAG 60.403 57.143 8.99 0.00 0.00 2.74
220 221 0.601558 GGTGGACGTGCTCTCTTGTA 59.398 55.000 8.99 0.00 0.00 2.41
221 222 1.367840 GGTGGACGTGCTCTCTTGT 59.632 57.895 8.99 0.00 0.00 3.16
222 223 1.374758 GGGTGGACGTGCTCTCTTG 60.375 63.158 8.99 0.00 0.00 3.02
223 224 2.584391 GGGGTGGACGTGCTCTCTT 61.584 63.158 8.99 0.00 0.00 2.85
224 225 2.997897 GGGGTGGACGTGCTCTCT 60.998 66.667 8.99 0.00 0.00 3.10
225 226 2.391724 TTTGGGGTGGACGTGCTCTC 62.392 60.000 8.99 4.22 0.00 3.20
226 227 2.448582 TTTGGGGTGGACGTGCTCT 61.449 57.895 8.99 0.00 0.00 4.09
227 228 2.112297 TTTGGGGTGGACGTGCTC 59.888 61.111 8.99 4.31 0.00 4.26
228 229 2.203294 GTTTGGGGTGGACGTGCT 60.203 61.111 8.99 0.00 0.00 4.40
229 230 1.460273 ATTGTTTGGGGTGGACGTGC 61.460 55.000 0.00 0.00 0.00 5.34
230 231 0.313672 CATTGTTTGGGGTGGACGTG 59.686 55.000 0.00 0.00 0.00 4.49
231 232 1.460273 GCATTGTTTGGGGTGGACGT 61.460 55.000 0.00 0.00 0.00 4.34
232 233 1.288752 GCATTGTTTGGGGTGGACG 59.711 57.895 0.00 0.00 0.00 4.79
233 234 0.831711 AGGCATTGTTTGGGGTGGAC 60.832 55.000 0.00 0.00 0.00 4.02
234 235 0.105246 AAGGCATTGTTTGGGGTGGA 60.105 50.000 0.00 0.00 0.00 4.02
235 236 0.321346 GAAGGCATTGTTTGGGGTGG 59.679 55.000 0.00 0.00 0.00 4.61
236 237 1.047002 TGAAGGCATTGTTTGGGGTG 58.953 50.000 0.00 0.00 0.00 4.61
237 238 2.028561 ATGAAGGCATTGTTTGGGGT 57.971 45.000 0.00 0.00 0.00 4.95
238 239 2.302445 TGAATGAAGGCATTGTTTGGGG 59.698 45.455 0.00 0.00 44.47 4.96
239 240 3.244146 TGTGAATGAAGGCATTGTTTGGG 60.244 43.478 0.00 0.00 44.47 4.12
240 241 3.992643 TGTGAATGAAGGCATTGTTTGG 58.007 40.909 0.00 0.00 44.47 3.28
241 242 5.987777 TTTGTGAATGAAGGCATTGTTTG 57.012 34.783 0.00 0.00 44.47 2.93
242 243 6.998968 TTTTTGTGAATGAAGGCATTGTTT 57.001 29.167 0.00 0.00 44.47 2.83
369 380 1.374252 CAAACACGGGACCTCCTCG 60.374 63.158 0.00 0.00 36.31 4.63
460 481 7.846066 TCCTTGTGTGGAAATTATTTATTGGG 58.154 34.615 0.00 0.00 32.39 4.12
493 514 1.933247 CAGGTTCTGCTCGAGATTCC 58.067 55.000 18.75 10.21 0.00 3.01
505 526 0.323451 GGGGGAAATTCGCAGGTTCT 60.323 55.000 12.08 0.00 0.00 3.01
686 707 1.707200 GAGGAGGAGGGAGGAACCT 59.293 63.158 0.00 0.00 45.57 3.50
725 747 2.844348 TGGACCAATCTAGGGTTTCCTC 59.156 50.000 0.00 0.00 43.66 3.71
829 852 2.023771 CACTGCGCGCTGAAGAAGA 61.024 57.895 39.03 14.07 0.00 2.87
830 853 2.473378 CACTGCGCGCTGAAGAAG 59.527 61.111 39.03 25.89 0.00 2.85
831 854 3.716006 GCACTGCGCGCTGAAGAA 61.716 61.111 39.03 15.63 0.00 2.52
935 961 4.475444 CCCCTCCTAGTCCCGCCA 62.475 72.222 0.00 0.00 0.00 5.69
961 987 1.953559 CAATCCCGATCACGTCCAAT 58.046 50.000 0.00 0.00 37.88 3.16
991 1017 3.432749 GCCAGCTGATCCATAAGAACTGA 60.433 47.826 17.39 0.00 0.00 3.41
1015 1041 2.876645 GAACTCCGTCGCGAGCAG 60.877 66.667 10.24 8.31 32.79 4.24
1542 1568 4.277672 GGATTACAGTGCTGCATCAATGAT 59.722 41.667 23.14 8.27 35.79 2.45
1857 1883 2.248280 TGTCAATACCGTGCACAAGT 57.752 45.000 18.64 15.73 0.00 3.16
2059 2085 1.548269 CGCCCTTTCTCTGTCTCTTCT 59.452 52.381 0.00 0.00 0.00 2.85
2477 2503 3.010413 GCATGCAGTGGAAAGGGGC 62.010 63.158 14.21 0.00 0.00 5.80
3224 3266 4.079970 CAGGAGAGCATGGCATTCATATT 58.920 43.478 0.00 0.00 34.12 1.28
3342 3745 9.445973 AATAGAAAGATAAGAGACAGAGGGATT 57.554 33.333 0.00 0.00 0.00 3.01
3388 3792 8.151596 TGTAACTACCATCAACTAATGACACAA 58.848 33.333 0.00 0.00 41.93 3.33
3498 4059 9.554724 GCATATCTTCGAACTTTTATCAACAAA 57.445 29.630 0.00 0.00 0.00 2.83
3499 4060 8.726068 TGCATATCTTCGAACTTTTATCAACAA 58.274 29.630 0.00 0.00 0.00 2.83
3500 4061 8.262715 TGCATATCTTCGAACTTTTATCAACA 57.737 30.769 0.00 0.00 0.00 3.33
3503 4064 8.262715 TGTTGCATATCTTCGAACTTTTATCA 57.737 30.769 0.00 0.00 0.00 2.15
3516 4077 3.439857 ACCACCACTGTTGCATATCTT 57.560 42.857 0.00 0.00 0.00 2.40
3565 4126 3.055530 ACTCAACAGGAAGGCTAGTGATG 60.056 47.826 0.00 0.00 0.00 3.07
3574 4135 1.972872 ACAGCAACTCAACAGGAAGG 58.027 50.000 0.00 0.00 0.00 3.46
3605 4166 5.104360 AGCCATATGTCCCATATCCATGTAC 60.104 44.000 1.24 0.00 0.00 2.90
3685 4759 4.976116 CGTCAATGTTTTCCCAAAAGTCTC 59.024 41.667 0.00 0.00 0.00 3.36
3702 4776 4.236935 CAAATAAGCCAGCAAACGTCAAT 58.763 39.130 0.00 0.00 0.00 2.57
3704 4778 2.030363 CCAAATAAGCCAGCAAACGTCA 60.030 45.455 0.00 0.00 0.00 4.35
3760 4835 2.582636 ACTCCCCAATATTCAACTGGCT 59.417 45.455 0.00 0.00 0.00 4.75
3775 4850 8.672823 AATGAACGATTAAATTACTACTCCCC 57.327 34.615 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.