Multiple sequence alignment - TraesCS5D01G198500

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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 TraesCS5D01G198500 chr5D 100.000 3431 0 0 1 3431 301571982 301568552 0.000000e+00 6336.0
1 TraesCS5D01G198500 chr5D 100.000 30 0 0 1283 1312 301570658 301570629 4.780000e-04 56.5
2 TraesCS5D01G198500 chr5D 100.000 30 0 0 1325 1354 301570700 301570671 4.780000e-04 56.5
3 TraesCS5D01G198500 chr5A 96.499 2628 68 14 217 2832 395919780 395922395 0.000000e+00 4322.0
4 TraesCS5D01G198500 chr5A 85.915 284 23 8 3148 3431 395924435 395924701 1.560000e-73 287.0
5 TraesCS5D01G198500 chr5A 81.677 322 22 11 2820 3130 395922419 395922714 2.060000e-57 233.0
6 TraesCS5D01G198500 chr5A 90.551 127 3 5 1 127 395919646 395919763 3.540000e-35 159.0
7 TraesCS5D01G198500 chr5A 100.000 30 0 0 1325 1354 395920844 395920873 4.780000e-04 56.5
8 TraesCS5D01G198500 chr5A 100.000 30 0 0 1283 1312 395920885 395920914 4.780000e-04 56.5
9 TraesCS5D01G198500 chr5B 89.133 1822 125 35 1319 3087 344611492 344609691 0.000000e+00 2200.0
10 TraesCS5D01G198500 chr5B 89.342 1079 57 20 217 1277 344612731 344611693 0.000000e+00 1303.0
11 TraesCS5D01G198500 chr5B 88.380 284 32 1 3148 3431 344574498 344574216 1.180000e-89 340.0
12 TraesCS5D01G198500 chr5B 96.875 128 2 2 1 127 344612874 344612748 2.680000e-51 213.0
13 TraesCS5D01G198500 chrUn 100.000 422 0 0 803 1224 476732137 476731716 0.000000e+00 780.0


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 TraesCS5D01G198500 chr5D 301568552 301571982 3430 True 2149.666667 6336 100.000000 1 3431 3 chr5D.!!$R1 3430
1 TraesCS5D01G198500 chr5A 395919646 395924701 5055 False 852.333333 4322 92.440333 1 3431 6 chr5A.!!$F1 3430
2 TraesCS5D01G198500 chr5B 344609691 344612874 3183 True 1238.666667 2200 91.783333 1 3087 3 chr5B.!!$R2 3086

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
167 169 0.037419 GGGGTACGACGGCTTTGTTA 60.037 55.000 0.00 0.0 0.00 2.41 F
371 373 0.106819 CTCCTCTCCCCAATTGCCAG 60.107 60.000 0.00 0.0 0.00 4.85 F
574 594 0.453793 CGGGATAGGCTAGATCGCTG 59.546 60.000 11.22 3.5 34.87 5.18 F
801 821 3.053095 ACCTCTTGATCTCGGGGTACTTA 60.053 47.826 4.77 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 1781 1.701847 CATATGCCCAAGCTACCTCCT 59.298 52.381 0.00 0.0 40.80 3.69 R
2095 2310 7.201741 GGAATAAAGGAATTGAACACTAGAGGC 60.202 40.741 0.00 0.0 0.00 4.70 R
2393 2609 0.250209 CTTCGGATGGATGGCCTCAG 60.250 60.000 3.32 0.0 34.31 3.35 R
2583 2801 0.595053 AGCGGTGATACGATGAAGCG 60.595 55.000 0.00 0.0 35.47 4.68 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
132 134 1.228657 GCTCTTCCGACGGCTTTGTT 61.229 55.000 9.66 0.00 0.00 2.83
133 135 1.938016 GCTCTTCCGACGGCTTTGTTA 60.938 52.381 9.66 0.00 0.00 2.41
134 136 2.409975 CTCTTCCGACGGCTTTGTTAA 58.590 47.619 9.66 0.00 0.00 2.01
135 137 2.137523 TCTTCCGACGGCTTTGTTAAC 58.862 47.619 9.66 0.00 0.00 2.01
136 138 2.140717 CTTCCGACGGCTTTGTTAACT 58.859 47.619 9.66 0.00 0.00 2.24
137 139 2.243602 TCCGACGGCTTTGTTAACTT 57.756 45.000 9.66 0.00 0.00 2.66
138 140 2.563702 TCCGACGGCTTTGTTAACTTT 58.436 42.857 9.66 0.00 0.00 2.66
139 141 2.944349 TCCGACGGCTTTGTTAACTTTT 59.056 40.909 9.66 0.00 0.00 2.27
140 142 3.377798 TCCGACGGCTTTGTTAACTTTTT 59.622 39.130 9.66 0.00 0.00 1.94
160 162 3.531073 TTTTTAGGGGTACGACGGC 57.469 52.632 0.00 0.00 0.00 5.68
161 163 0.975887 TTTTTAGGGGTACGACGGCT 59.024 50.000 0.00 0.00 0.00 5.52
162 164 0.975887 TTTTAGGGGTACGACGGCTT 59.024 50.000 0.00 0.00 0.00 4.35
163 165 0.975887 TTTAGGGGTACGACGGCTTT 59.024 50.000 0.00 0.00 0.00 3.51
164 166 0.247185 TTAGGGGTACGACGGCTTTG 59.753 55.000 0.00 0.00 0.00 2.77
165 167 0.899717 TAGGGGTACGACGGCTTTGT 60.900 55.000 0.00 0.00 0.00 2.83
166 168 1.301953 GGGGTACGACGGCTTTGTT 60.302 57.895 0.00 0.00 0.00 2.83
167 169 0.037419 GGGGTACGACGGCTTTGTTA 60.037 55.000 0.00 0.00 0.00 2.41
178 180 3.003275 ACGGCTTTGTTAACTGACATGTG 59.997 43.478 1.15 0.00 0.00 3.21
179 181 3.609175 CGGCTTTGTTAACTGACATGTGG 60.609 47.826 1.15 0.00 0.00 4.17
180 182 3.305335 GGCTTTGTTAACTGACATGTGGG 60.305 47.826 1.15 0.00 0.00 4.61
181 183 3.317993 GCTTTGTTAACTGACATGTGGGT 59.682 43.478 1.15 0.00 0.00 4.51
182 184 4.556699 GCTTTGTTAACTGACATGTGGGTC 60.557 45.833 1.15 0.00 38.29 4.46
183 185 3.847671 TGTTAACTGACATGTGGGTCA 57.152 42.857 1.15 0.00 45.06 4.02
184 186 4.157849 TGTTAACTGACATGTGGGTCAA 57.842 40.909 1.15 0.00 46.36 3.18
185 187 4.527944 TGTTAACTGACATGTGGGTCAAA 58.472 39.130 1.15 0.00 46.36 2.69
186 188 4.950475 TGTTAACTGACATGTGGGTCAAAA 59.050 37.500 1.15 0.00 46.36 2.44
187 189 5.419155 TGTTAACTGACATGTGGGTCAAAAA 59.581 36.000 1.15 0.00 46.36 1.94
228 230 3.643237 TGAGAATCCGGGTCAATAGTCT 58.357 45.455 0.00 0.00 0.00 3.24
234 236 4.726035 TCCGGGTCAATAGTCTAGAGAT 57.274 45.455 0.00 0.00 0.00 2.75
242 244 6.325286 GGTCAATAGTCTAGAGATCCCTGTTT 59.675 42.308 0.00 0.00 0.00 2.83
245 247 7.228906 TCAATAGTCTAGAGATCCCTGTTTACG 59.771 40.741 0.00 0.00 0.00 3.18
263 265 0.955428 CGGACATGTGGGTCAACAGG 60.955 60.000 1.15 0.00 39.59 4.00
266 268 2.034066 ATGTGGGTCAACAGGCCG 59.966 61.111 0.00 0.00 32.52 6.13
290 292 1.623311 GTGGGCTTTACATGGGCTTTT 59.377 47.619 0.00 0.00 0.00 2.27
292 294 3.450817 GTGGGCTTTACATGGGCTTTTAT 59.549 43.478 0.00 0.00 0.00 1.40
362 364 0.772384 TCCTATCGTCTCCTCTCCCC 59.228 60.000 0.00 0.00 0.00 4.81
363 365 0.478942 CCTATCGTCTCCTCTCCCCA 59.521 60.000 0.00 0.00 0.00 4.96
364 366 1.133450 CCTATCGTCTCCTCTCCCCAA 60.133 57.143 0.00 0.00 0.00 4.12
365 367 2.491825 CCTATCGTCTCCTCTCCCCAAT 60.492 54.545 0.00 0.00 0.00 3.16
366 368 2.182516 ATCGTCTCCTCTCCCCAATT 57.817 50.000 0.00 0.00 0.00 2.32
367 369 1.195115 TCGTCTCCTCTCCCCAATTG 58.805 55.000 0.00 0.00 0.00 2.32
368 370 0.462759 CGTCTCCTCTCCCCAATTGC 60.463 60.000 0.00 0.00 0.00 3.56
369 371 0.106967 GTCTCCTCTCCCCAATTGCC 60.107 60.000 0.00 0.00 0.00 4.52
371 373 0.106819 CTCCTCTCCCCAATTGCCAG 60.107 60.000 0.00 0.00 0.00 4.85
379 381 1.373246 CCAATTGCCAGTTGCCACG 60.373 57.895 0.00 0.00 40.16 4.94
468 471 3.556306 CGACACACCCCCACAGGT 61.556 66.667 0.00 0.00 42.40 4.00
485 498 5.361427 CACAGGTACGAATCTCTCTCTCTA 58.639 45.833 0.00 0.00 0.00 2.43
492 509 4.654262 ACGAATCTCTCTCTCTACCTCTCT 59.346 45.833 0.00 0.00 0.00 3.10
497 514 2.769663 TCTCTCTCTACCTCTCTCGCTT 59.230 50.000 0.00 0.00 0.00 4.68
517 534 6.014898 CGCTTTGTTTCAAAAACTTTCTTGG 58.985 36.000 4.40 0.00 0.00 3.61
524 541 5.612725 TCAAAAACTTTCTTGGCATCCTT 57.387 34.783 0.00 0.00 0.00 3.36
529 546 4.098914 ACTTTCTTGGCATCCTTGTACA 57.901 40.909 0.00 0.00 0.00 2.90
538 558 2.489329 GCATCCTTGTACATGTGCTGTT 59.511 45.455 15.25 0.00 39.39 3.16
574 594 0.453793 CGGGATAGGCTAGATCGCTG 59.546 60.000 11.22 3.50 34.87 5.18
801 821 3.053095 ACCTCTTGATCTCGGGGTACTTA 60.053 47.826 4.77 0.00 0.00 2.24
1224 1244 9.643693 AAGTTGATGTCATTTTGCCTAATTTAG 57.356 29.630 0.00 0.00 0.00 1.85
1596 1781 4.139859 TCAGTTTTGTCCGAGGTGTTAA 57.860 40.909 0.00 0.00 0.00 2.01
2095 2310 8.904099 AATGGATAATCGTACCTCCTTTAAAG 57.096 34.615 8.32 8.32 0.00 1.85
2444 2660 1.662629 CAAGTGAAGATCGAGCGCATT 59.337 47.619 11.47 0.00 0.00 3.56
2494 2710 2.158534 TGGCTGTGAAAACTATGTGGGT 60.159 45.455 0.00 0.00 0.00 4.51
2565 2783 6.812656 TGTATTTTGCATTGCCAAACTCTATG 59.187 34.615 9.78 0.00 34.68 2.23
2583 2801 4.787999 GCTGCAAGAGCTGAATGC 57.212 55.556 0.00 0.00 45.21 3.56
2597 2815 2.796593 CTGAATGCGCTTCATCGTATCA 59.203 45.455 18.29 6.97 42.87 2.15
2602 2820 0.595053 CGCTTCATCGTATCACCGCT 60.595 55.000 0.00 0.00 0.00 5.52
2609 2827 0.248336 TCGTATCACCGCTGCTTACG 60.248 55.000 0.00 4.21 37.56 3.18
2790 3009 5.215160 GGTTGAAACACAGCTTTGATACAG 58.785 41.667 6.92 0.00 0.00 2.74
2798 3017 3.181455 ACAGCTTTGATACAGTGGTGTGA 60.181 43.478 0.00 0.00 37.52 3.58
2868 3132 4.119136 CCTTGCTTGTTTGGTCGATTTTT 58.881 39.130 0.00 0.00 0.00 1.94
2882 3146 2.350772 CGATTTTTGGAAAGAGCGCAGT 60.351 45.455 11.47 0.00 0.00 4.40
2896 3160 1.930817 GCGCAGTGACAGGGTATATCG 60.931 57.143 0.30 0.00 0.00 2.92
2964 3228 1.452108 CCTTTGGCTTAGCGGGGAG 60.452 63.158 0.00 0.00 0.00 4.30
3017 3281 5.001833 TCCCAGTGTAGGTTTAGTGTAGA 57.998 43.478 0.00 0.00 0.00 2.59
3054 3324 7.986553 AGAAGCATATATATAGCACTCCCTT 57.013 36.000 15.16 4.49 0.00 3.95
3056 3326 7.621285 AGAAGCATATATATAGCACTCCCTTCA 59.379 37.037 15.16 0.00 0.00 3.02
3143 5062 6.094048 GCAAGTTATCTATGATGGTGTTGTGT 59.906 38.462 0.00 0.00 0.00 3.72
3144 5063 7.677276 GCAAGTTATCTATGATGGTGTTGTGTC 60.677 40.741 0.00 0.00 0.00 3.67
3146 5065 3.953712 TCTATGATGGTGTTGTGTCGT 57.046 42.857 0.00 0.00 0.00 4.34
3153 5126 0.384230 GGTGTTGTGTCGTTGCATCG 60.384 55.000 10.93 10.93 0.00 3.84
3168 5141 1.126846 GCATCGACAGAACTGGAAACG 59.873 52.381 6.76 6.68 34.19 3.60
3176 5149 4.699522 ACTGGAAACGAGGCCGCC 62.700 66.667 0.00 0.00 39.95 6.13
3194 5167 2.009042 GCCAGGAAAGATGTCAGGACG 61.009 57.143 0.00 0.00 0.00 4.79
3195 5168 1.550524 CCAGGAAAGATGTCAGGACGA 59.449 52.381 0.00 0.00 0.00 4.20
3203 5176 6.015350 GGAAAGATGTCAGGACGATATTCCTA 60.015 42.308 14.41 0.00 44.90 2.94
3223 5196 1.487976 ACTGGTGATGTGGGAGCTATG 59.512 52.381 0.00 0.00 0.00 2.23
3231 5204 2.422597 TGTGGGAGCTATGAAAACACG 58.577 47.619 0.00 0.00 0.00 4.49
3238 5211 3.686016 AGCTATGAAAACACGGGAATGT 58.314 40.909 0.00 0.00 0.00 2.71
3241 5214 4.096382 GCTATGAAAACACGGGAATGTGAT 59.904 41.667 0.00 0.00 42.55 3.06
3252 5225 4.103153 ACGGGAATGTGATATGAAGGACAT 59.897 41.667 0.00 0.00 42.39 3.06
3253 5226 4.453478 CGGGAATGTGATATGAAGGACATG 59.547 45.833 0.00 0.00 39.77 3.21
3264 5237 1.667724 GAAGGACATGCGTGGAAGATG 59.332 52.381 11.36 0.00 0.00 2.90
3265 5238 0.107508 AGGACATGCGTGGAAGATGG 60.108 55.000 11.36 0.00 0.00 3.51
3266 5239 1.718757 GGACATGCGTGGAAGATGGC 61.719 60.000 11.36 0.00 0.00 4.40
3267 5240 0.745845 GACATGCGTGGAAGATGGCT 60.746 55.000 11.36 0.00 0.00 4.75
3268 5241 1.028330 ACATGCGTGGAAGATGGCTG 61.028 55.000 11.36 0.00 0.00 4.85
3269 5242 1.452651 ATGCGTGGAAGATGGCTGG 60.453 57.895 0.00 0.00 0.00 4.85
3270 5243 3.512516 GCGTGGAAGATGGCTGGC 61.513 66.667 0.00 0.00 0.00 4.85
3271 5244 2.825836 CGTGGAAGATGGCTGGCC 60.826 66.667 4.43 4.43 0.00 5.36
3272 5245 2.679716 GTGGAAGATGGCTGGCCT 59.320 61.111 13.05 0.00 36.94 5.19
3273 5246 1.915228 GTGGAAGATGGCTGGCCTA 59.085 57.895 13.05 0.04 36.94 3.93
3274 5247 0.475906 GTGGAAGATGGCTGGCCTAT 59.524 55.000 13.05 4.91 36.94 2.57
3275 5248 1.133668 GTGGAAGATGGCTGGCCTATT 60.134 52.381 13.05 4.92 36.94 1.73
3276 5249 1.143684 TGGAAGATGGCTGGCCTATTC 59.856 52.381 13.05 12.57 36.94 1.75
3277 5250 1.143684 GGAAGATGGCTGGCCTATTCA 59.856 52.381 13.05 0.00 36.94 2.57
3278 5251 2.423373 GGAAGATGGCTGGCCTATTCAA 60.423 50.000 13.05 0.00 36.94 2.69
3325 5298 1.001815 CGTTGTCAATGTGGGTGAACC 60.002 52.381 0.00 0.00 40.81 3.62
3386 5359 3.181463 GGGTGGACGTTACATAGGCATTA 60.181 47.826 0.00 0.00 0.00 1.90
3417 5390 2.119495 ACGGATACATGAGGGCTCTTT 58.881 47.619 0.00 0.00 0.00 2.52
3427 5400 3.648914 GGGCTCTTTACCCCTCCTA 57.351 57.895 0.00 0.00 42.01 2.94
3428 5401 1.129917 GGGCTCTTTACCCCTCCTAC 58.870 60.000 0.00 0.00 42.01 3.18
3429 5402 1.344189 GGGCTCTTTACCCCTCCTACT 60.344 57.143 0.00 0.00 42.01 2.57
3430 5403 2.090887 GGGCTCTTTACCCCTCCTACTA 60.091 54.545 0.00 0.00 42.01 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 144 0.975887 AGCCGTCGTACCCCTAAAAA 59.024 50.000 0.00 0.00 0.00 1.94
143 145 0.975887 AAGCCGTCGTACCCCTAAAA 59.024 50.000 0.00 0.00 0.00 1.52
144 146 0.975887 AAAGCCGTCGTACCCCTAAA 59.024 50.000 0.00 0.00 0.00 1.85
145 147 0.247185 CAAAGCCGTCGTACCCCTAA 59.753 55.000 0.00 0.00 0.00 2.69
146 148 0.899717 ACAAAGCCGTCGTACCCCTA 60.900 55.000 0.00 0.00 0.00 3.53
147 149 1.761500 AACAAAGCCGTCGTACCCCT 61.761 55.000 0.00 0.00 0.00 4.79
148 150 0.037419 TAACAAAGCCGTCGTACCCC 60.037 55.000 0.00 0.00 0.00 4.95
149 151 1.460743 GTTAACAAAGCCGTCGTACCC 59.539 52.381 0.00 0.00 0.00 3.69
150 152 2.156310 CAGTTAACAAAGCCGTCGTACC 59.844 50.000 8.61 0.00 0.00 3.34
151 153 3.052036 TCAGTTAACAAAGCCGTCGTAC 58.948 45.455 8.61 0.00 0.00 3.67
152 154 3.052036 GTCAGTTAACAAAGCCGTCGTA 58.948 45.455 8.61 0.00 0.00 3.43
153 155 1.862827 GTCAGTTAACAAAGCCGTCGT 59.137 47.619 8.61 0.00 0.00 4.34
154 156 1.862201 TGTCAGTTAACAAAGCCGTCG 59.138 47.619 8.61 0.00 0.00 5.12
155 157 3.250040 ACATGTCAGTTAACAAAGCCGTC 59.750 43.478 8.61 0.00 31.81 4.79
156 158 3.003275 CACATGTCAGTTAACAAAGCCGT 59.997 43.478 8.61 0.00 31.81 5.68
157 159 3.554524 CACATGTCAGTTAACAAAGCCG 58.445 45.455 8.61 0.00 31.81 5.52
158 160 3.305335 CCCACATGTCAGTTAACAAAGCC 60.305 47.826 8.61 0.00 31.81 4.35
159 161 3.317993 ACCCACATGTCAGTTAACAAAGC 59.682 43.478 8.61 0.00 31.81 3.51
160 162 4.578516 TGACCCACATGTCAGTTAACAAAG 59.421 41.667 8.61 0.00 40.22 2.77
161 163 4.527944 TGACCCACATGTCAGTTAACAAA 58.472 39.130 8.61 0.00 40.22 2.83
162 164 4.157849 TGACCCACATGTCAGTTAACAA 57.842 40.909 8.61 0.00 40.22 2.83
163 165 3.847671 TGACCCACATGTCAGTTAACA 57.152 42.857 8.61 0.00 40.22 2.41
164 166 5.508200 TTTTGACCCACATGTCAGTTAAC 57.492 39.130 0.00 0.00 45.37 2.01
203 205 5.566469 ACTATTGACCCGGATTCTCAAAAA 58.434 37.500 0.73 0.00 0.00 1.94
204 206 5.045869 AGACTATTGACCCGGATTCTCAAAA 60.046 40.000 0.73 0.00 0.00 2.44
205 207 4.469945 AGACTATTGACCCGGATTCTCAAA 59.530 41.667 0.73 0.00 0.00 2.69
206 208 4.030913 AGACTATTGACCCGGATTCTCAA 58.969 43.478 0.73 4.59 0.00 3.02
207 209 3.643237 AGACTATTGACCCGGATTCTCA 58.357 45.455 0.73 0.00 0.00 3.27
208 210 5.071370 TCTAGACTATTGACCCGGATTCTC 58.929 45.833 0.73 0.00 0.00 2.87
209 211 5.063017 TCTAGACTATTGACCCGGATTCT 57.937 43.478 0.73 0.00 0.00 2.40
210 212 5.071370 TCTCTAGACTATTGACCCGGATTC 58.929 45.833 0.73 0.00 0.00 2.52
211 213 5.063017 TCTCTAGACTATTGACCCGGATT 57.937 43.478 0.73 0.00 0.00 3.01
212 214 4.726035 TCTCTAGACTATTGACCCGGAT 57.274 45.455 0.73 0.00 0.00 4.18
213 215 4.506979 GGATCTCTAGACTATTGACCCGGA 60.507 50.000 0.73 0.00 0.00 5.14
214 216 3.759618 GGATCTCTAGACTATTGACCCGG 59.240 52.174 0.00 0.00 0.00 5.73
215 217 3.759618 GGGATCTCTAGACTATTGACCCG 59.240 52.174 0.00 0.00 0.00 5.28
228 230 3.972133 TGTCCGTAAACAGGGATCTCTA 58.028 45.455 0.00 0.00 34.25 2.43
234 236 1.002659 CCACATGTCCGTAAACAGGGA 59.997 52.381 0.00 0.00 35.33 4.20
242 244 1.001520 CTGTTGACCCACATGTCCGTA 59.998 52.381 0.00 0.00 34.25 4.02
245 247 1.244019 GCCTGTTGACCCACATGTCC 61.244 60.000 0.00 0.00 34.25 4.02
266 268 1.749063 GCCCATGTAAAGCCCACTTAC 59.251 52.381 0.00 0.00 34.05 2.34
290 292 2.409064 TTATTCCTCGGCCCAGGATA 57.591 50.000 20.88 11.41 42.49 2.59
292 294 1.420138 GAATTATTCCTCGGCCCAGGA 59.580 52.381 16.17 16.17 41.16 3.86
371 373 3.799755 GATGCGGACCGTGGCAAC 61.800 66.667 16.73 0.00 43.26 4.17
379 381 2.444895 AGGGGAGAGATGCGGACC 60.445 66.667 0.00 0.00 0.00 4.46
468 471 5.836898 AGAGAGGTAGAGAGAGAGATTCGTA 59.163 44.000 0.00 0.00 0.00 3.43
485 498 2.910688 TGAAACAAAGCGAGAGAGGT 57.089 45.000 0.00 0.00 0.00 3.85
492 509 6.128688 CCAAGAAAGTTTTTGAAACAAAGCGA 60.129 34.615 6.35 0.00 0.00 4.93
497 514 6.093357 GGATGCCAAGAAAGTTTTTGAAACAA 59.907 34.615 6.35 0.00 0.00 2.83
517 534 2.086869 ACAGCACATGTACAAGGATGC 58.913 47.619 0.00 7.73 41.60 3.91
524 541 4.419280 CAAACACAAACAGCACATGTACA 58.581 39.130 0.00 0.00 43.00 2.90
529 546 1.473080 GGGCAAACACAAACAGCACAT 60.473 47.619 0.00 0.00 0.00 3.21
538 558 1.969064 CGGGATCGGGCAAACACAA 60.969 57.895 0.00 0.00 0.00 3.33
574 594 0.687354 ATCGGCTGATCCCATGTACC 59.313 55.000 0.90 0.00 0.00 3.34
632 652 3.181452 ACGAACTACCCTTTAGGCAACAA 60.181 43.478 0.00 0.00 40.58 2.83
801 821 6.017687 CGTAAGGGTTAACTGTAAAAAGCACT 60.018 38.462 5.42 0.00 0.00 4.40
1224 1244 4.022849 ACAGGAAGCAATACTTGTCAAAGC 60.023 41.667 0.00 0.00 39.29 3.51
1596 1781 1.701847 CATATGCCCAAGCTACCTCCT 59.298 52.381 0.00 0.00 40.80 3.69
2095 2310 7.201741 GGAATAAAGGAATTGAACACTAGAGGC 60.202 40.741 0.00 0.00 0.00 4.70
2393 2609 0.250209 CTTCGGATGGATGGCCTCAG 60.250 60.000 3.32 0.00 34.31 3.35
2444 2660 8.445275 AAAATACTGAAGACACAATGTACACA 57.555 30.769 0.00 0.00 0.00 3.72
2536 2754 5.821995 AGTTTGGCAATGCAAAATACAAAGT 59.178 32.000 11.31 8.65 33.80 2.66
2582 2800 1.846648 CGGTGATACGATGAAGCGC 59.153 57.895 0.00 0.00 35.47 5.92
2583 2801 0.595053 AGCGGTGATACGATGAAGCG 60.595 55.000 0.00 0.00 35.47 4.68
2602 2820 1.795768 CTTCTGCTCAACCGTAAGCA 58.204 50.000 7.95 7.95 45.83 3.91
2631 2849 5.529791 AGTAGTTGTACAGTCATGTCACAC 58.470 41.667 0.00 0.00 41.01 3.82
2778 2997 3.403038 GTCACACCACTGTATCAAAGCT 58.597 45.455 0.00 0.00 0.00 3.74
2790 3009 0.597637 CTGAGACACCGTCACACCAC 60.598 60.000 0.00 0.00 34.60 4.16
2798 3017 1.269998 GCTACAGTTCTGAGACACCGT 59.730 52.381 6.83 0.00 0.00 4.83
2868 3132 0.601046 CTGTCACTGCGCTCTTTCCA 60.601 55.000 9.73 0.00 0.00 3.53
2882 3146 3.695556 TCGTTGTTCGATATACCCTGTCA 59.304 43.478 0.00 0.00 44.01 3.58
2896 3160 2.671963 GGGGTGGCCTCGTTGTTC 60.672 66.667 3.32 0.00 0.00 3.18
2958 3222 7.399245 TTTTGGTTTTAGAATTATCTCCCCG 57.601 36.000 0.00 0.00 37.10 5.73
3107 3377 9.775539 ATCATAGATAACTTGCTAATCCCTCTA 57.224 33.333 0.00 0.00 0.00 2.43
3109 3379 7.768120 CCATCATAGATAACTTGCTAATCCCTC 59.232 40.741 0.00 0.00 0.00 4.30
3113 3383 8.839310 ACACCATCATAGATAACTTGCTAATC 57.161 34.615 0.00 0.00 0.00 1.75
3115 3385 8.046708 ACAACACCATCATAGATAACTTGCTAA 58.953 33.333 0.00 0.00 0.00 3.09
3130 3400 0.660488 GCAACGACACAACACCATCA 59.340 50.000 0.00 0.00 0.00 3.07
3143 5062 1.418373 CAGTTCTGTCGATGCAACGA 58.582 50.000 15.63 15.63 40.00 3.85
3144 5063 0.439985 CCAGTTCTGTCGATGCAACG 59.560 55.000 10.48 10.48 0.00 4.10
3146 5065 2.542020 TTCCAGTTCTGTCGATGCAA 57.458 45.000 0.00 0.00 0.00 4.08
3153 5126 1.149148 GCCTCGTTTCCAGTTCTGTC 58.851 55.000 0.00 0.00 0.00 3.51
3155 5128 1.291877 CGGCCTCGTTTCCAGTTCTG 61.292 60.000 0.00 0.00 0.00 3.02
3157 5130 2.677979 GCGGCCTCGTTTCCAGTTC 61.678 63.158 0.00 0.00 38.89 3.01
3168 5141 1.821332 CATCTTTCCTGGCGGCCTC 60.821 63.158 21.46 0.00 0.00 4.70
3176 5149 3.533606 ATCGTCCTGACATCTTTCCTG 57.466 47.619 0.00 0.00 0.00 3.86
3194 5167 4.593206 TCCCACATCACCAGTAGGAATATC 59.407 45.833 0.00 0.00 38.69 1.63
3195 5168 4.566837 TCCCACATCACCAGTAGGAATAT 58.433 43.478 0.00 0.00 38.69 1.28
3203 5176 1.487976 CATAGCTCCCACATCACCAGT 59.512 52.381 0.00 0.00 0.00 4.00
3223 5196 5.811399 TCATATCACATTCCCGTGTTTTC 57.189 39.130 0.00 0.00 38.12 2.29
3231 5204 4.217118 GCATGTCCTTCATATCACATTCCC 59.783 45.833 0.00 0.00 34.67 3.97
3238 5211 2.433970 TCCACGCATGTCCTTCATATCA 59.566 45.455 0.00 0.00 34.67 2.15
3241 5214 2.499693 TCTTCCACGCATGTCCTTCATA 59.500 45.455 0.00 0.00 34.67 2.15
3252 5225 2.046023 CCAGCCATCTTCCACGCA 60.046 61.111 0.00 0.00 0.00 5.24
3253 5226 3.512516 GCCAGCCATCTTCCACGC 61.513 66.667 0.00 0.00 0.00 5.34
3264 5237 1.098050 CACACTTGAATAGGCCAGCC 58.902 55.000 5.01 0.00 0.00 4.85
3265 5238 2.113860 TCACACTTGAATAGGCCAGC 57.886 50.000 5.01 0.00 0.00 4.85
3266 5239 4.130118 GGTATCACACTTGAATAGGCCAG 58.870 47.826 5.01 0.00 34.61 4.85
3267 5240 3.521531 TGGTATCACACTTGAATAGGCCA 59.478 43.478 5.01 0.00 34.61 5.36
3268 5241 3.877508 GTGGTATCACACTTGAATAGGCC 59.122 47.826 0.00 0.00 43.13 5.19
3292 5265 1.937223 TGACAACGCGACAAAGAACAT 59.063 42.857 15.93 0.00 0.00 2.71
3293 5266 1.360820 TGACAACGCGACAAAGAACA 58.639 45.000 15.93 0.00 0.00 3.18
3303 5276 1.082169 CACCCACATTGACAACGCG 60.082 57.895 3.53 3.53 0.00 6.01
3325 5298 0.179000 AAGCATGGCTAACTCCTCCG 59.821 55.000 0.00 0.00 38.25 4.63
3386 5359 7.769044 GCCCTCATGTATCCGTTTACATATTAT 59.231 37.037 7.05 0.00 40.07 1.28
3398 5371 2.918712 AAAGAGCCCTCATGTATCCG 57.081 50.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.