Multiple sequence alignment - TraesCS6A01G116300

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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 TraesCS6A01G116300 chr6A 100.000 2390 0 0 1 2390 86400502 86398113 0.000000e+00 4414.0
1 TraesCS6A01G116300 chr6D 94.654 2039 56 20 239 2247 68848899 68846884 0.000000e+00 3112.0
2 TraesCS6A01G116300 chr6D 90.351 228 15 4 1399 1623 68720519 68720296 2.320000e-75 292.0
3 TraesCS6A01G116300 chr6D 96.063 127 5 0 114 240 379557154 379557280 8.660000e-50 207.0
4 TraesCS6A01G116300 chr6D 79.344 305 30 16 1723 1994 68720133 68719829 1.460000e-42 183.0
5 TraesCS6A01G116300 chr6D 95.652 92 3 1 24 115 68848988 68848898 1.910000e-31 147.0
6 TraesCS6A01G116300 chr6D 86.458 96 13 0 429 524 68716360 68716265 3.250000e-19 106.0
7 TraesCS6A01G116300 chr6D 93.846 65 4 0 2326 2390 68689607 68689543 5.440000e-17 99.0
8 TraesCS6A01G116300 chr6D 84.375 96 14 1 429 524 68843190 68843096 2.530000e-15 93.5
9 TraesCS6A01G116300 chr6B 93.084 1605 51 26 788 2356 143751349 143749769 0.000000e+00 2294.0
10 TraesCS6A01G116300 chr6B 94.937 553 22 1 239 791 143752022 143751476 0.000000e+00 861.0
11 TraesCS6A01G116300 chr6B 95.413 109 1 2 7 115 143752125 143752021 1.140000e-38 171.0
12 TraesCS6A01G116300 chr6B 86.458 96 13 0 429 524 143667588 143667493 3.250000e-19 106.0
13 TraesCS6A01G116300 chr6B 87.179 78 9 1 447 524 143747632 143747556 1.180000e-13 87.9
14 TraesCS6A01G116300 chr5D 80.984 1199 151 35 251 1410 76003220 76004380 0.000000e+00 880.0
15 TraesCS6A01G116300 chr5D 96.094 128 5 0 114 241 460650656 460650529 2.410000e-50 209.0
16 TraesCS6A01G116300 chr5D 96.063 127 5 0 114 240 460652760 460652886 8.660000e-50 207.0
17 TraesCS6A01G116300 chr5A 80.952 1155 149 33 300 1416 71456982 71458103 0.000000e+00 848.0
18 TraesCS6A01G116300 chr5A 94.776 134 7 0 114 247 279670548 279670415 2.410000e-50 209.0
19 TraesCS6A01G116300 chr2D 78.193 1417 221 50 240 1614 21911766 21910396 0.000000e+00 824.0
20 TraesCS6A01G116300 chr2D 85.407 418 58 2 1067 1483 22107909 22107494 4.720000e-117 431.0
21 TraesCS6A01G116300 chr5B 80.017 1206 162 40 251 1416 84665019 84666185 0.000000e+00 819.0
22 TraesCS6A01G116300 chr7A 98.462 130 2 0 114 243 540886196 540886067 1.850000e-56 230.0
23 TraesCS6A01G116300 chr7A 95.455 132 5 1 109 240 222942454 222942324 2.410000e-50 209.0
24 TraesCS6A01G116300 chr7A 96.063 127 5 0 114 240 140763951 140764077 8.660000e-50 207.0
25 TraesCS6A01G116300 chr2A 96.094 128 5 0 114 241 708949045 708949172 2.410000e-50 209.0
26 TraesCS6A01G116300 chr2A 96.154 78 3 0 1112 1189 23937000 23936923 6.930000e-26 128.0
27 TraesCS6A01G116300 chr7B 95.312 128 6 0 114 241 537460871 537460998 1.120000e-48 204.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G116300 chr6A 86398113 86400502 2389 True 4414.000 4414 100.000000 1 2390 1 chr6A.!!$R1 2389
1 TraesCS6A01G116300 chr6D 68843096 68848988 5892 True 1117.500 3112 91.560333 24 2247 3 chr6D.!!$R3 2223
2 TraesCS6A01G116300 chr6B 143747556 143752125 4569 True 853.475 2294 92.653250 7 2356 4 chr6B.!!$R2 2349
3 TraesCS6A01G116300 chr5D 76003220 76004380 1160 False 880.000 880 80.984000 251 1410 1 chr5D.!!$F1 1159
4 TraesCS6A01G116300 chr5A 71456982 71458103 1121 False 848.000 848 80.952000 300 1416 1 chr5A.!!$F1 1116
5 TraesCS6A01G116300 chr2D 21910396 21911766 1370 True 824.000 824 78.193000 240 1614 1 chr2D.!!$R1 1374
6 TraesCS6A01G116300 chr5B 84665019 84666185 1166 False 819.000 819 80.017000 251 1416 1 chr5B.!!$F1 1165

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
132 133 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.0 5.23 0.00 44.66 2.17 F
133 134 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.0 5.23 0.00 44.66 1.40 F
135 136 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.00 44.66 2.12 F
236 237 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1040 1225 0.034767 TTGAGCTGCATCCCTTGGAG 60.035 55.000 1.02 0.0 45.96 3.86 R
1060 1245 1.123928 AAGCCTCTTATCCCGACCAG 58.876 55.000 0.00 0.0 0.00 4.00 R
1107 1292 4.966787 GCCGCACCACCTTTCCCA 62.967 66.667 0.00 0.0 0.00 4.37 R
1740 1972 5.013079 ACAGTCTCCTAAATCACATTCACCA 59.987 40.000 0.00 0.0 0.00 4.17 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
28 29 1.588824 CCTTCATTCGCAGCAAGGCA 61.589 55.000 0.00 0.00 0.00 4.75
63 64 7.040961 GGCGTAGATGGTCTATAGGATTAGATC 60.041 44.444 0.00 0.00 30.76 2.75
64 65 7.499563 GCGTAGATGGTCTATAGGATTAGATCA 59.500 40.741 0.00 0.00 42.09 2.92
71 72 9.607333 TGGTCTATAGGATTAGATCATGTTTCT 57.393 33.333 0.00 0.00 35.02 2.52
113 114 4.573900 CTTGATGCAGGAAGTAGTGTCTT 58.426 43.478 0.00 0.00 0.00 3.01
114 115 5.724328 CTTGATGCAGGAAGTAGTGTCTTA 58.276 41.667 0.00 0.00 0.00 2.10
115 116 5.073311 TGATGCAGGAAGTAGTGTCTTAC 57.927 43.478 0.00 0.00 0.00 2.34
116 117 4.772624 TGATGCAGGAAGTAGTGTCTTACT 59.227 41.667 0.00 0.00 38.96 2.24
117 118 4.785511 TGCAGGAAGTAGTGTCTTACTC 57.214 45.455 0.00 0.00 36.57 2.59
118 119 3.510360 TGCAGGAAGTAGTGTCTTACTCC 59.490 47.826 0.00 0.00 36.57 3.85
119 120 3.119065 GCAGGAAGTAGTGTCTTACTCCC 60.119 52.174 0.00 0.00 36.57 4.30
120 121 4.345854 CAGGAAGTAGTGTCTTACTCCCT 58.654 47.826 0.00 0.00 36.57 4.20
121 122 4.399934 CAGGAAGTAGTGTCTTACTCCCTC 59.600 50.000 0.00 0.00 36.57 4.30
122 123 3.700539 GGAAGTAGTGTCTTACTCCCTCC 59.299 52.174 0.00 0.00 40.89 4.30
123 124 3.002038 AGTAGTGTCTTACTCCCTCCG 57.998 52.381 0.00 0.00 40.89 4.63
124 125 2.308275 AGTAGTGTCTTACTCCCTCCGT 59.692 50.000 0.00 0.00 40.89 4.69
125 126 1.836802 AGTGTCTTACTCCCTCCGTC 58.163 55.000 0.00 0.00 33.17 4.79
126 127 0.816373 GTGTCTTACTCCCTCCGTCC 59.184 60.000 0.00 0.00 0.00 4.79
127 128 0.679002 TGTCTTACTCCCTCCGTCCG 60.679 60.000 0.00 0.00 0.00 4.79
128 129 1.077212 TCTTACTCCCTCCGTCCGG 60.077 63.158 0.00 0.00 0.00 5.14
129 130 1.077212 CTTACTCCCTCCGTCCGGA 60.077 63.158 0.00 0.00 42.90 5.14
130 131 0.682209 CTTACTCCCTCCGTCCGGAA 60.682 60.000 5.23 0.00 44.66 4.30
131 132 0.251742 TTACTCCCTCCGTCCGGAAA 60.252 55.000 5.23 0.00 44.66 3.13
132 133 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
133 134 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
134 135 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
135 136 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
136 137 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
137 138 2.034124 CCCTCCGTCCGGAAATACTTA 58.966 52.381 5.23 0.00 44.66 2.24
138 139 2.631545 CCCTCCGTCCGGAAATACTTAT 59.368 50.000 5.23 0.00 44.66 1.73
139 140 3.305881 CCCTCCGTCCGGAAATACTTATC 60.306 52.174 5.23 0.00 44.66 1.75
140 141 3.319972 CCTCCGTCCGGAAATACTTATCA 59.680 47.826 5.23 0.00 44.66 2.15
141 142 4.021368 CCTCCGTCCGGAAATACTTATCAT 60.021 45.833 5.23 0.00 44.66 2.45
142 143 5.130292 TCCGTCCGGAAATACTTATCATC 57.870 43.478 5.23 0.00 42.05 2.92
143 144 4.585581 TCCGTCCGGAAATACTTATCATCA 59.414 41.667 5.23 0.00 42.05 3.07
144 145 5.069383 TCCGTCCGGAAATACTTATCATCAA 59.931 40.000 5.23 0.00 42.05 2.57
145 146 5.405571 CCGTCCGGAAATACTTATCATCAAG 59.594 44.000 5.23 0.00 37.50 3.02
146 147 6.213677 CGTCCGGAAATACTTATCATCAAGA 58.786 40.000 5.23 0.00 0.00 3.02
147 148 6.868864 CGTCCGGAAATACTTATCATCAAGAT 59.131 38.462 5.23 0.00 40.86 2.40
148 149 7.148738 CGTCCGGAAATACTTATCATCAAGATG 60.149 40.741 5.23 3.67 37.57 2.90
162 163 7.828508 TCATCAAGATGAATAAAAGGGGATG 57.171 36.000 10.16 0.00 44.14 3.51
163 164 7.356680 TCATCAAGATGAATAAAAGGGGATGT 58.643 34.615 10.16 0.00 44.14 3.06
164 165 8.501904 TCATCAAGATGAATAAAAGGGGATGTA 58.498 33.333 10.16 0.00 44.14 2.29
165 166 9.305555 CATCAAGATGAATAAAAGGGGATGTAT 57.694 33.333 4.01 0.00 41.20 2.29
166 167 9.887862 ATCAAGATGAATAAAAGGGGATGTATT 57.112 29.630 0.00 0.00 0.00 1.89
167 168 9.713684 TCAAGATGAATAAAAGGGGATGTATTT 57.286 29.630 0.00 0.00 0.00 1.40
204 205 7.787028 AGTTCTAGATACACCTCTTTTCATCC 58.213 38.462 0.00 0.00 0.00 3.51
205 206 7.400339 AGTTCTAGATACACCTCTTTTCATCCA 59.600 37.037 0.00 0.00 0.00 3.41
206 207 7.921041 TCTAGATACACCTCTTTTCATCCAT 57.079 36.000 0.00 0.00 0.00 3.41
207 208 8.324191 TCTAGATACACCTCTTTTCATCCATT 57.676 34.615 0.00 0.00 0.00 3.16
208 209 8.772250 TCTAGATACACCTCTTTTCATCCATTT 58.228 33.333 0.00 0.00 0.00 2.32
209 210 9.401058 CTAGATACACCTCTTTTCATCCATTTT 57.599 33.333 0.00 0.00 0.00 1.82
210 211 8.286191 AGATACACCTCTTTTCATCCATTTTC 57.714 34.615 0.00 0.00 0.00 2.29
211 212 7.890127 AGATACACCTCTTTTCATCCATTTTCA 59.110 33.333 0.00 0.00 0.00 2.69
212 213 6.923199 ACACCTCTTTTCATCCATTTTCAT 57.077 33.333 0.00 0.00 0.00 2.57
213 214 6.694447 ACACCTCTTTTCATCCATTTTCATG 58.306 36.000 0.00 0.00 0.00 3.07
214 215 6.494491 ACACCTCTTTTCATCCATTTTCATGA 59.506 34.615 0.00 0.00 31.07 3.07
215 216 6.810182 CACCTCTTTTCATCCATTTTCATGAC 59.190 38.462 0.00 0.00 31.07 3.06
216 217 6.494491 ACCTCTTTTCATCCATTTTCATGACA 59.506 34.615 0.00 0.00 31.07 3.58
217 218 7.015487 ACCTCTTTTCATCCATTTTCATGACAA 59.985 33.333 0.00 0.00 31.07 3.18
218 219 7.544566 CCTCTTTTCATCCATTTTCATGACAAG 59.455 37.037 0.00 0.00 37.83 3.16
219 220 7.954835 TCTTTTCATCCATTTTCATGACAAGT 58.045 30.769 0.00 0.00 37.76 3.16
220 221 9.076781 TCTTTTCATCCATTTTCATGACAAGTA 57.923 29.630 0.00 0.00 37.76 2.24
221 222 9.865321 CTTTTCATCCATTTTCATGACAAGTAT 57.135 29.630 0.00 0.00 34.31 2.12
224 225 9.859427 TTCATCCATTTTCATGACAAGTATTTC 57.141 29.630 0.00 0.00 31.07 2.17
225 226 8.469200 TCATCCATTTTCATGACAAGTATTTCC 58.531 33.333 0.00 0.00 31.07 3.13
226 227 6.851609 TCCATTTTCATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 31.07 4.30
227 228 6.035843 CCATTTTCATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 31.07 5.14
228 229 6.127758 CCATTTTCATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 31.07 5.14
229 230 5.873179 TTTCATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 0.00 4.79
230 231 3.517602 TCATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
231 232 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
232 233 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
233 234 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
234 235 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
235 236 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
236 237 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
237 238 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
355 363 7.138692 ACTCAGAGACAAATTTGCTAATCAC 57.861 36.000 18.12 6.92 0.00 3.06
425 461 2.173569 GGCCTACACAGAGGGATCATTT 59.826 50.000 0.00 0.00 37.06 2.32
427 463 4.381411 GCCTACACAGAGGGATCATTTAC 58.619 47.826 0.00 0.00 37.06 2.01
487 524 5.997746 TGTTGATGTTCTTTAGGACTTCAGG 59.002 40.000 6.80 0.00 0.00 3.86
494 531 0.532573 TTAGGACTTCAGGCTGCTCG 59.467 55.000 10.34 2.76 0.00 5.03
554 591 7.839680 AGAACCTTACTTTGAATGATGGTTT 57.160 32.000 0.00 0.00 36.78 3.27
585 622 9.850198 TTACCATCATCATCTTTAATCATGTGA 57.150 29.630 0.00 0.00 0.00 3.58
686 724 8.585018 AGCCTTAAATAACACATGTAAGCTTTT 58.415 29.630 3.20 0.00 0.00 2.27
691 729 4.749245 AACACATGTAAGCTTTTCGAGG 57.251 40.909 3.20 0.00 0.00 4.63
829 1000 6.624423 GCATACTCCTTTTACACGTCTCTACA 60.624 42.308 0.00 0.00 0.00 2.74
858 1032 4.479158 ACCCTCTGTTCAAATGCCTTAAA 58.521 39.130 0.00 0.00 0.00 1.52
864 1038 7.442062 CCTCTGTTCAAATGCCTTAAATTGTTT 59.558 33.333 0.00 0.00 0.00 2.83
1040 1225 3.242543 CGAGCATTGAAGCATGGAGTTAC 60.243 47.826 0.00 0.00 36.85 2.50
1060 1245 0.322816 TCCAAGGGATGCAGCTCAAC 60.323 55.000 3.85 0.00 0.00 3.18
1107 1292 1.074296 AGGCCAAGGGAAAGAAGGGT 61.074 55.000 5.01 0.00 0.00 4.34
1764 1996 5.013079 TGGTGAATGTGATTTAGGAGACTGT 59.987 40.000 0.00 0.00 43.88 3.55
1780 2012 1.417890 ACTGTAACTTGGAGCAGCACT 59.582 47.619 0.00 0.00 32.65 4.40
1852 2088 4.445452 AAATCATGTTGTGCATCCTCAC 57.555 40.909 0.00 0.00 35.19 3.51
1860 2096 1.377594 TGCATCCTCACGCTGCATT 60.378 52.632 0.00 0.00 40.75 3.56
1861 2097 1.354506 GCATCCTCACGCTGCATTC 59.645 57.895 0.00 0.00 35.96 2.67
1913 2149 3.953612 TCCAACATTTGCTGAGAGTTTGT 59.046 39.130 0.00 0.00 0.00 2.83
1918 2154 2.849880 TTGCTGAGAGTTTGTGCAAC 57.150 45.000 0.00 0.00 38.49 4.17
2013 2249 1.852280 GCAAAAGAGAACGCCAACAAC 59.148 47.619 0.00 0.00 0.00 3.32
2024 2260 5.529800 AGAACGCCAACAACTTTACTGTAAT 59.470 36.000 0.37 0.00 0.00 1.89
2191 2427 5.368256 TTCTGAACTTCGTAGTACTGTCC 57.632 43.478 5.39 0.00 33.17 4.02
2193 2429 5.008331 TCTGAACTTCGTAGTACTGTCCAT 58.992 41.667 5.39 0.00 33.17 3.41
2197 2433 5.464030 ACTTCGTAGTACTGTCCATTGTT 57.536 39.130 5.39 0.00 31.21 2.83
2204 2440 4.389374 AGTACTGTCCATTGTTTGTGGAG 58.611 43.478 0.00 0.00 45.91 3.86
2308 2544 8.448008 AGGGAATAATAATCAGTAAGCCAATGA 58.552 33.333 0.00 0.00 0.00 2.57
2309 2545 9.247861 GGGAATAATAATCAGTAAGCCAATGAT 57.752 33.333 0.00 0.00 35.21 2.45
2313 2549 9.797642 ATAATAATCAGTAAGCCAATGATGTGA 57.202 29.630 0.21 0.00 34.02 3.58
2314 2550 5.824904 AATCAGTAAGCCAATGATGTGAC 57.175 39.130 0.21 0.00 34.02 3.67
2315 2551 4.284829 TCAGTAAGCCAATGATGTGACA 57.715 40.909 0.00 0.00 0.00 3.58
2356 2595 1.007271 CATACGGCCGGTGAGCTAG 60.007 63.158 31.76 6.14 0.00 3.42
2366 5302 3.430374 GCCGGTGAGCTAGTAAAGATTCA 60.430 47.826 1.90 0.00 0.00 2.57
2367 5303 4.755411 CCGGTGAGCTAGTAAAGATTCAA 58.245 43.478 0.00 0.00 0.00 2.69
2370 5306 5.517054 CGGTGAGCTAGTAAAGATTCAAGTC 59.483 44.000 0.00 0.00 0.00 3.01
2373 5309 7.550906 GGTGAGCTAGTAAAGATTCAAGTCAAT 59.449 37.037 0.00 0.00 0.00 2.57
2389 5325 8.642935 TCAAGTCAATATTTATTCAACCACCA 57.357 30.769 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.493350 GCTGCGAATGAAGGGATAGAAGA 60.493 47.826 0.00 0.00 0.00 2.87
1 2 2.805099 GCTGCGAATGAAGGGATAGAAG 59.195 50.000 0.00 0.00 0.00 2.85
2 3 2.170397 TGCTGCGAATGAAGGGATAGAA 59.830 45.455 0.00 0.00 0.00 2.10
3 4 1.762370 TGCTGCGAATGAAGGGATAGA 59.238 47.619 0.00 0.00 0.00 1.98
4 5 2.245159 TGCTGCGAATGAAGGGATAG 57.755 50.000 0.00 0.00 0.00 2.08
5 6 2.564771 CTTGCTGCGAATGAAGGGATA 58.435 47.619 0.00 0.00 0.00 2.59
63 64 3.300590 GCCGACGCAAAATAAGAAACATG 59.699 43.478 0.00 0.00 34.03 3.21
64 65 3.190535 AGCCGACGCAAAATAAGAAACAT 59.809 39.130 0.00 0.00 37.52 2.71
65 66 2.550606 AGCCGACGCAAAATAAGAAACA 59.449 40.909 0.00 0.00 37.52 2.83
66 67 2.908626 CAGCCGACGCAAAATAAGAAAC 59.091 45.455 0.00 0.00 37.52 2.78
69 70 2.087501 TCAGCCGACGCAAAATAAGA 57.912 45.000 0.00 0.00 37.52 2.10
70 71 2.708514 CATCAGCCGACGCAAAATAAG 58.291 47.619 0.00 0.00 37.52 1.73
71 72 1.202132 GCATCAGCCGACGCAAAATAA 60.202 47.619 0.00 0.00 37.52 1.40
72 73 0.376852 GCATCAGCCGACGCAAAATA 59.623 50.000 0.00 0.00 37.52 1.40
113 114 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
114 115 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
115 116 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
116 117 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
117 118 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
118 119 3.319972 TGATAAGTATTTCCGGACGGAGG 59.680 47.826 13.64 0.00 46.06 4.30
119 120 4.579454 TGATAAGTATTTCCGGACGGAG 57.421 45.455 13.64 0.00 46.06 4.63
120 121 4.585581 TGATGATAAGTATTTCCGGACGGA 59.414 41.667 1.83 9.76 43.52 4.69
121 122 4.878439 TGATGATAAGTATTTCCGGACGG 58.122 43.478 1.83 3.96 0.00 4.79
122 123 6.213677 TCTTGATGATAAGTATTTCCGGACG 58.786 40.000 1.83 0.00 0.00 4.79
123 124 7.872993 TCATCTTGATGATAAGTATTTCCGGAC 59.127 37.037 1.83 0.00 33.36 4.79
124 125 7.962441 TCATCTTGATGATAAGTATTTCCGGA 58.038 34.615 0.00 0.00 33.36 5.14
125 126 8.607441 TTCATCTTGATGATAAGTATTTCCGG 57.393 34.615 13.26 0.00 33.36 5.14
133 134 9.359653 CCCCTTTTATTCATCTTGATGATAAGT 57.640 33.333 13.26 4.53 33.36 2.24
134 135 9.578576 TCCCCTTTTATTCATCTTGATGATAAG 57.421 33.333 13.26 12.97 33.36 1.73
136 137 9.524496 CATCCCCTTTTATTCATCTTGATGATA 57.476 33.333 13.26 6.17 33.36 2.15
137 138 8.008922 ACATCCCCTTTTATTCATCTTGATGAT 58.991 33.333 13.26 7.25 35.40 2.45
138 139 7.356680 ACATCCCCTTTTATTCATCTTGATGA 58.643 34.615 9.02 9.02 32.39 2.92
139 140 7.592885 ACATCCCCTTTTATTCATCTTGATG 57.407 36.000 4.35 4.35 33.80 3.07
140 141 9.887862 AATACATCCCCTTTTATTCATCTTGAT 57.112 29.630 0.00 0.00 0.00 2.57
141 142 9.713684 AAATACATCCCCTTTTATTCATCTTGA 57.286 29.630 0.00 0.00 0.00 3.02
178 179 8.915036 GGATGAAAAGAGGTGTATCTAGAACTA 58.085 37.037 0.00 0.00 0.00 2.24
179 180 7.400339 TGGATGAAAAGAGGTGTATCTAGAACT 59.600 37.037 0.00 0.00 0.00 3.01
180 181 7.556844 TGGATGAAAAGAGGTGTATCTAGAAC 58.443 38.462 0.00 0.00 0.00 3.01
181 182 7.733773 TGGATGAAAAGAGGTGTATCTAGAA 57.266 36.000 0.00 0.00 0.00 2.10
182 183 7.921041 ATGGATGAAAAGAGGTGTATCTAGA 57.079 36.000 0.00 0.00 0.00 2.43
183 184 8.970859 AAATGGATGAAAAGAGGTGTATCTAG 57.029 34.615 0.00 0.00 0.00 2.43
184 185 9.396022 GAAAATGGATGAAAAGAGGTGTATCTA 57.604 33.333 0.00 0.00 0.00 1.98
185 186 7.890127 TGAAAATGGATGAAAAGAGGTGTATCT 59.110 33.333 0.00 0.00 0.00 1.98
186 187 8.055279 TGAAAATGGATGAAAAGAGGTGTATC 57.945 34.615 0.00 0.00 0.00 2.24
187 188 8.472413 CATGAAAATGGATGAAAAGAGGTGTAT 58.528 33.333 0.00 0.00 0.00 2.29
188 189 7.669304 TCATGAAAATGGATGAAAAGAGGTGTA 59.331 33.333 0.00 0.00 0.00 2.90
189 190 6.494491 TCATGAAAATGGATGAAAAGAGGTGT 59.506 34.615 0.00 0.00 0.00 4.16
190 191 6.810182 GTCATGAAAATGGATGAAAAGAGGTG 59.190 38.462 0.00 0.00 30.45 4.00
191 192 6.494491 TGTCATGAAAATGGATGAAAAGAGGT 59.506 34.615 0.00 0.00 30.45 3.85
192 193 6.927416 TGTCATGAAAATGGATGAAAAGAGG 58.073 36.000 0.00 0.00 30.45 3.69
193 194 8.086522 ACTTGTCATGAAAATGGATGAAAAGAG 58.913 33.333 15.60 0.00 42.84 2.85
194 195 7.954835 ACTTGTCATGAAAATGGATGAAAAGA 58.045 30.769 15.60 0.00 42.84 2.52
195 196 9.865321 ATACTTGTCATGAAAATGGATGAAAAG 57.135 29.630 0.00 9.42 44.54 2.27
198 199 9.859427 GAAATACTTGTCATGAAAATGGATGAA 57.141 29.630 0.00 0.00 30.45 2.57
199 200 8.469200 GGAAATACTTGTCATGAAAATGGATGA 58.531 33.333 0.00 0.00 0.00 2.92
200 201 7.433131 CGGAAATACTTGTCATGAAAATGGATG 59.567 37.037 0.00 0.00 0.00 3.51
201 202 7.416664 CCGGAAATACTTGTCATGAAAATGGAT 60.417 37.037 0.00 0.00 0.00 3.41
202 203 6.127758 CCGGAAATACTTGTCATGAAAATGGA 60.128 38.462 0.00 0.00 0.00 3.41
203 204 6.035843 CCGGAAATACTTGTCATGAAAATGG 58.964 40.000 0.00 0.00 0.00 3.16
204 205 6.747280 GTCCGGAAATACTTGTCATGAAAATG 59.253 38.462 5.23 0.00 0.00 2.32
205 206 6.403200 CGTCCGGAAATACTTGTCATGAAAAT 60.403 38.462 5.23 0.00 0.00 1.82
206 207 5.106869 CGTCCGGAAATACTTGTCATGAAAA 60.107 40.000 5.23 0.00 0.00 2.29
207 208 4.390603 CGTCCGGAAATACTTGTCATGAAA 59.609 41.667 5.23 0.00 0.00 2.69
208 209 3.930229 CGTCCGGAAATACTTGTCATGAA 59.070 43.478 5.23 0.00 0.00 2.57
209 210 3.517602 CGTCCGGAAATACTTGTCATGA 58.482 45.455 5.23 0.00 0.00 3.07
210 211 2.607635 CCGTCCGGAAATACTTGTCATG 59.392 50.000 5.23 0.00 37.50 3.07
211 212 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
212 213 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
213 214 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
214 215 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
215 216 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
216 217 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
217 218 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
218 219 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
219 220 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
220 221 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
221 222 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
222 223 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
223 224 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
224 225 1.041447 AACATACTCCCTCCGTCCGG 61.041 60.000 0.00 0.00 0.00 5.14
225 226 0.822164 AAACATACTCCCTCCGTCCG 59.178 55.000 0.00 0.00 0.00 4.79
226 227 4.186926 GTTAAAACATACTCCCTCCGTCC 58.813 47.826 0.00 0.00 0.00 4.79
227 228 4.186926 GGTTAAAACATACTCCCTCCGTC 58.813 47.826 0.00 0.00 0.00 4.79
228 229 3.368739 CGGTTAAAACATACTCCCTCCGT 60.369 47.826 0.00 0.00 0.00 4.69
229 230 3.119029 TCGGTTAAAACATACTCCCTCCG 60.119 47.826 0.00 0.00 36.30 4.63
230 231 4.476628 TCGGTTAAAACATACTCCCTCC 57.523 45.455 0.00 0.00 0.00 4.30
231 232 6.997239 AAATCGGTTAAAACATACTCCCTC 57.003 37.500 0.00 0.00 0.00 4.30
232 233 6.349860 GCAAAATCGGTTAAAACATACTCCCT 60.350 38.462 0.00 0.00 0.00 4.20
233 234 5.803461 GCAAAATCGGTTAAAACATACTCCC 59.197 40.000 0.00 0.00 0.00 4.30
234 235 6.617879 AGCAAAATCGGTTAAAACATACTCC 58.382 36.000 0.00 0.00 0.00 3.85
235 236 7.806014 TGAAGCAAAATCGGTTAAAACATACTC 59.194 33.333 0.00 0.00 0.00 2.59
236 237 7.653647 TGAAGCAAAATCGGTTAAAACATACT 58.346 30.769 0.00 0.00 0.00 2.12
237 238 7.861176 TGAAGCAAAATCGGTTAAAACATAC 57.139 32.000 0.00 0.00 0.00 2.39
355 363 5.895636 TTCAGGTAATAAGCACCACAATG 57.104 39.130 0.00 0.00 38.62 2.82
425 461 1.616725 CCCCAGCCAGAGCAAAATGTA 60.617 52.381 0.00 0.00 43.56 2.29
427 463 1.895238 CCCCAGCCAGAGCAAAATG 59.105 57.895 0.00 0.00 43.56 2.32
487 524 2.417933 ACAACATTCAGATTCGAGCAGC 59.582 45.455 0.00 0.00 0.00 5.25
494 531 7.992180 AACAGTTCAAACAACATTCAGATTC 57.008 32.000 0.00 0.00 0.00 2.52
585 622 8.771920 TGTTGATCTACAGAATACACGAATTT 57.228 30.769 5.85 0.00 0.00 1.82
627 664 4.809673 CCTCCAAGATTTTTACTGCAACC 58.190 43.478 0.00 0.00 0.00 3.77
829 1000 4.641989 GCATTTGAACAGAGGGTCATATGT 59.358 41.667 12.49 0.00 0.00 2.29
858 1032 6.165700 AGAGGTTCAAAATCTGCAAACAAT 57.834 33.333 0.00 0.00 0.00 2.71
864 1038 5.829924 AGAAGAAAGAGGTTCAAAATCTGCA 59.170 36.000 0.00 0.00 38.86 4.41
1040 1225 0.034767 TTGAGCTGCATCCCTTGGAG 60.035 55.000 1.02 0.00 45.96 3.86
1060 1245 1.123928 AAGCCTCTTATCCCGACCAG 58.876 55.000 0.00 0.00 0.00 4.00
1107 1292 4.966787 GCCGCACCACCTTTCCCA 62.967 66.667 0.00 0.00 0.00 4.37
1740 1972 5.013079 ACAGTCTCCTAAATCACATTCACCA 59.987 40.000 0.00 0.00 0.00 4.17
1860 2096 6.805713 TCTAATATGTTGAACGCATGAGAGA 58.194 36.000 2.50 0.00 0.00 3.10
1861 2097 6.699204 ACTCTAATATGTTGAACGCATGAGAG 59.301 38.462 16.16 16.16 36.36 3.20
1870 2106 6.513180 TGGATCGGACTCTAATATGTTGAAC 58.487 40.000 0.00 0.00 0.00 3.18
1913 2149 5.592282 TCTTTGACAAAATACTCTGGTTGCA 59.408 36.000 1.62 0.00 0.00 4.08
2024 2260 7.934665 TCAGTTTAAGGTTGATTGCAGTAGTTA 59.065 33.333 0.00 0.00 0.00 2.24
2180 2416 5.302360 TCCACAAACAATGGACAGTACTAC 58.698 41.667 0.00 0.00 41.47 2.73
2276 2512 9.732130 GCTTACTGATTATTATTCCCTTCTCAT 57.268 33.333 0.00 0.00 0.00 2.90
2301 2537 0.456653 GCCGTTGTCACATCATTGGC 60.457 55.000 0.00 0.00 33.33 4.52
2308 2544 0.960364 GGACATGGCCGTTGTCACAT 60.960 55.000 29.37 1.88 44.22 3.21
2309 2545 1.599518 GGACATGGCCGTTGTCACA 60.600 57.895 29.37 0.00 44.22 3.58
2310 2546 1.599518 TGGACATGGCCGTTGTCAC 60.600 57.895 29.37 21.64 44.22 3.67
2311 2547 1.599518 GTGGACATGGCCGTTGTCA 60.600 57.895 29.37 17.95 44.22 3.58
2312 2548 1.169661 TTGTGGACATGGCCGTTGTC 61.170 55.000 23.75 23.75 42.20 3.18
2313 2549 1.152860 TTGTGGACATGGCCGTTGT 60.153 52.632 14.43 10.69 0.00 3.32
2314 2550 1.285641 GTTGTGGACATGGCCGTTG 59.714 57.895 14.43 0.00 0.00 4.10
2315 2551 1.901464 GGTTGTGGACATGGCCGTT 60.901 57.895 14.43 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.