Multiple sequence alignment - TraesCS3A01G228600

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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 TraesCS3A01G228600 chr3A 100.000 3715 0 0 1 3715 427335702 427331988 0.000000e+00 6861.0
1 TraesCS3A01G228600 chr3A 100.000 161 0 0 3876 4036 427331827 427331667 8.480000e-77 298.0
2 TraesCS3A01G228600 chr3A 90.625 128 12 0 2438 2565 455803790 455803663 1.930000e-38 171.0
3 TraesCS3A01G228600 chr3A 87.500 136 13 4 181 314 84037113 84036980 1.940000e-33 154.0
4 TraesCS3A01G228600 chr3D 96.119 3427 93 16 310 3713 308060004 308056595 0.000000e+00 5555.0
5 TraesCS3A01G228600 chr3D 90.055 181 13 5 2 181 308060169 308059993 3.140000e-56 230.0
6 TraesCS3A01G228600 chr3D 93.662 142 6 3 3896 4035 308056563 308056423 4.090000e-50 209.0
7 TraesCS3A01G228600 chr3D 89.844 128 13 0 2438 2565 337974607 337974480 8.970000e-37 165.0
8 TraesCS3A01G228600 chr3B 94.846 3434 98 35 310 3715 413416974 413420356 0.000000e+00 5288.0
9 TraesCS3A01G228600 chr3B 90.659 182 15 1 2 181 413416804 413416985 1.450000e-59 241.0
10 TraesCS3A01G228600 chr3B 89.922 129 11 2 2438 2565 435959560 435959433 8.970000e-37 165.0
11 TraesCS3A01G228600 chr3B 95.402 87 4 0 3896 3982 413420503 413420589 5.440000e-29 139.0
12 TraesCS3A01G228600 chr3B 100.000 59 0 0 3978 4036 413421122 413421180 4.260000e-20 110.0
13 TraesCS3A01G228600 chr1B 77.812 329 51 17 2439 2761 654716328 654716640 2.480000e-42 183.0
14 TraesCS3A01G228600 chr6D 89.844 128 9 4 181 307 121158510 121158386 1.160000e-35 161.0
15 TraesCS3A01G228600 chr6D 88.976 127 11 3 181 306 68328849 68328725 1.940000e-33 154.0
16 TraesCS3A01G228600 chr5D 88.550 131 14 1 181 311 464614673 464614802 1.500000e-34 158.0
17 TraesCS3A01G228600 chr2D 87.879 132 15 1 181 311 620552083 620552214 1.940000e-33 154.0
18 TraesCS3A01G228600 chr2D 88.372 129 13 2 181 308 641491189 641491316 1.940000e-33 154.0
19 TraesCS3A01G228600 chr2D 87.313 134 14 3 181 312 525408353 525408221 2.510000e-32 150.0
20 TraesCS3A01G228600 chr7D 87.786 131 14 2 181 310 80326560 80326431 6.990000e-33 152.0
21 TraesCS3A01G228600 chr4D 87.786 131 15 1 181 311 12696015 12695886 6.990000e-33 152.0
22 TraesCS3A01G228600 chr1A 86.667 135 14 4 2636 2768 565294204 565294336 3.250000e-31 147.0
23 TraesCS3A01G228600 chr1A 87.302 126 16 0 2439 2564 565293976 565294101 1.170000e-30 145.0
24 TraesCS3A01G228600 chr1A 100.000 29 0 0 9 37 272983285 272983257 2.000000e-03 54.7
25 TraesCS3A01G228600 chr1D 84.127 126 20 0 2439 2564 471001676 471001801 5.480000e-24 122.0
26 TraesCS3A01G228600 chr4B 86.000 100 11 2 1 99 393149902 393149999 1.980000e-18 104.0
27 TraesCS3A01G228600 chr6A 82.456 114 18 2 7 119 507658742 507658630 9.230000e-17 99.0


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 TraesCS3A01G228600 chr3A 427331667 427335702 4035 True 3579.5 6861 100.000000 1 4036 2 chr3A.!!$R3 4035
1 TraesCS3A01G228600 chr3D 308056423 308060169 3746 True 1998.0 5555 93.278667 2 4035 3 chr3D.!!$R2 4033
2 TraesCS3A01G228600 chr3B 413416804 413421180 4376 False 1444.5 5288 95.226750 2 4036 4 chr3B.!!$F1 4034

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
190 193 0.037790 GCTCCAACTCTCGCTTCAGT 60.038 55.0 0.00 0.0 0.00 3.41 F
192 195 0.319900 TCCAACTCTCGCTTCAGTGC 60.320 55.0 0.00 0.0 0.00 4.40 F
193 196 0.320247 CCAACTCTCGCTTCAGTGCT 60.320 55.0 0.00 0.0 0.00 4.40 F
1146 1160 0.322366 GCTTCTTCTTCAGCCAGCCT 60.322 55.0 0.00 0.0 0.00 4.58 F
1419 1436 1.355066 GAAAGTCTCGCCGGAGCAAG 61.355 60.0 5.05 0.0 40.26 4.01 F
2612 2661 1.416050 GAACCGGCCGTGATAACGTC 61.416 60.0 26.12 5.2 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 1776 1.472480 ACAAAAGTGTGCGTCAGCTTT 59.528 42.857 0.00 0.00 45.42 3.51 R
2190 2223 0.805322 CTGCCGAGAGTGATCAGTGC 60.805 60.000 8.05 5.71 0.00 4.40 R
2255 2288 8.343366 GCACTATATATAGCTAACTATGTCGCA 58.657 37.037 18.00 0.00 39.51 5.10 R
2631 2680 0.307146 CGGTAGTAGCTCCTGCGTAC 59.693 60.000 0.00 0.00 45.42 3.67 R
2632 2681 0.816825 CCGGTAGTAGCTCCTGCGTA 60.817 60.000 0.00 0.00 45.42 4.42 R
3446 3498 1.129998 CAAGCAGAAGTTGAGATGGCG 59.870 52.381 0.00 0.00 0.00 5.69 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
180 183 8.364142 AGATAGTACATTCATAAGCTCCAACTC 58.636 37.037 0.00 0.00 0.00 3.01
181 184 6.552445 AGTACATTCATAAGCTCCAACTCT 57.448 37.500 0.00 0.00 0.00 3.24
182 185 6.578023 AGTACATTCATAAGCTCCAACTCTC 58.422 40.000 0.00 0.00 0.00 3.20
183 186 4.437239 ACATTCATAAGCTCCAACTCTCG 58.563 43.478 0.00 0.00 0.00 4.04
184 187 2.586258 TCATAAGCTCCAACTCTCGC 57.414 50.000 0.00 0.00 0.00 5.03
185 188 2.103373 TCATAAGCTCCAACTCTCGCT 58.897 47.619 0.00 0.00 0.00 4.93
186 189 2.497675 TCATAAGCTCCAACTCTCGCTT 59.502 45.455 0.00 0.00 44.17 4.68
187 190 2.656560 TAAGCTCCAACTCTCGCTTC 57.343 50.000 0.00 0.00 41.38 3.86
188 191 0.681733 AAGCTCCAACTCTCGCTTCA 59.318 50.000 0.00 0.00 38.21 3.02
189 192 0.246086 AGCTCCAACTCTCGCTTCAG 59.754 55.000 0.00 0.00 0.00 3.02
190 193 0.037790 GCTCCAACTCTCGCTTCAGT 60.038 55.000 0.00 0.00 0.00 3.41
191 194 1.707632 CTCCAACTCTCGCTTCAGTG 58.292 55.000 0.00 0.00 0.00 3.66
192 195 0.319900 TCCAACTCTCGCTTCAGTGC 60.320 55.000 0.00 0.00 0.00 4.40
193 196 0.320247 CCAACTCTCGCTTCAGTGCT 60.320 55.000 0.00 0.00 0.00 4.40
194 197 1.506493 CAACTCTCGCTTCAGTGCTT 58.494 50.000 0.00 0.00 0.00 3.91
195 198 1.194098 CAACTCTCGCTTCAGTGCTTG 59.806 52.381 0.00 0.00 0.00 4.01
196 199 0.390860 ACTCTCGCTTCAGTGCTTGT 59.609 50.000 0.00 0.00 0.00 3.16
197 200 1.613925 ACTCTCGCTTCAGTGCTTGTA 59.386 47.619 0.00 0.00 0.00 2.41
198 201 2.257894 CTCTCGCTTCAGTGCTTGTAG 58.742 52.381 0.00 0.00 0.00 2.74
199 202 1.613925 TCTCGCTTCAGTGCTTGTAGT 59.386 47.619 0.00 0.00 0.00 2.73
200 203 1.989165 CTCGCTTCAGTGCTTGTAGTC 59.011 52.381 0.00 0.00 0.00 2.59
201 204 0.710567 CGCTTCAGTGCTTGTAGTCG 59.289 55.000 0.00 0.00 0.00 4.18
202 205 1.784525 GCTTCAGTGCTTGTAGTCGT 58.215 50.000 0.00 0.00 0.00 4.34
203 206 1.721926 GCTTCAGTGCTTGTAGTCGTC 59.278 52.381 0.00 0.00 0.00 4.20
204 207 1.979469 CTTCAGTGCTTGTAGTCGTCG 59.021 52.381 0.00 0.00 0.00 5.12
205 208 0.386858 TCAGTGCTTGTAGTCGTCGC 60.387 55.000 0.00 0.00 0.00 5.19
206 209 0.387367 CAGTGCTTGTAGTCGTCGCT 60.387 55.000 0.00 0.00 0.00 4.93
207 210 1.135774 CAGTGCTTGTAGTCGTCGCTA 60.136 52.381 0.00 0.00 0.00 4.26
208 211 1.130749 AGTGCTTGTAGTCGTCGCTAG 59.869 52.381 0.00 0.00 0.00 3.42
209 212 1.129998 GTGCTTGTAGTCGTCGCTAGA 59.870 52.381 0.00 0.00 0.00 2.43
210 213 2.014857 TGCTTGTAGTCGTCGCTAGAT 58.985 47.619 0.00 0.00 0.00 1.98
211 214 2.223272 TGCTTGTAGTCGTCGCTAGATG 60.223 50.000 0.00 0.00 34.75 2.90
212 215 2.031807 GCTTGTAGTCGTCGCTAGATGA 59.968 50.000 0.00 0.00 39.89 2.92
213 216 3.304123 GCTTGTAGTCGTCGCTAGATGAT 60.304 47.826 0.00 0.00 43.54 2.45
214 217 4.790123 GCTTGTAGTCGTCGCTAGATGATT 60.790 45.833 0.00 0.00 43.54 2.57
215 218 4.895224 TGTAGTCGTCGCTAGATGATTT 57.105 40.909 0.00 0.00 43.54 2.17
216 219 5.996669 TGTAGTCGTCGCTAGATGATTTA 57.003 39.130 0.00 0.00 43.54 1.40
217 220 5.745514 TGTAGTCGTCGCTAGATGATTTAC 58.254 41.667 0.00 2.42 43.54 2.01
218 221 4.895224 AGTCGTCGCTAGATGATTTACA 57.105 40.909 0.00 0.00 43.54 2.41
219 222 4.849883 AGTCGTCGCTAGATGATTTACAG 58.150 43.478 0.00 0.00 43.54 2.74
220 223 4.575236 AGTCGTCGCTAGATGATTTACAGA 59.425 41.667 0.00 0.00 43.54 3.41
221 224 5.066117 AGTCGTCGCTAGATGATTTACAGAA 59.934 40.000 0.00 0.00 43.54 3.02
222 225 5.171695 GTCGTCGCTAGATGATTTACAGAAC 59.828 44.000 0.00 0.00 43.54 3.01
223 226 5.066117 TCGTCGCTAGATGATTTACAGAACT 59.934 40.000 0.00 0.00 37.48 3.01
224 227 5.172232 CGTCGCTAGATGATTTACAGAACTG 59.828 44.000 0.00 0.00 35.43 3.16
225 228 5.460419 GTCGCTAGATGATTTACAGAACTGG 59.540 44.000 6.76 0.00 34.19 4.00
226 229 5.359860 TCGCTAGATGATTTACAGAACTGGA 59.640 40.000 6.76 0.00 34.19 3.86
227 230 6.040955 TCGCTAGATGATTTACAGAACTGGAT 59.959 38.462 6.76 0.00 34.19 3.41
228 231 7.230712 TCGCTAGATGATTTACAGAACTGGATA 59.769 37.037 6.76 0.00 34.19 2.59
229 232 8.031864 CGCTAGATGATTTACAGAACTGGATAT 58.968 37.037 6.76 0.00 34.19 1.63
264 267 9.562408 TTATTTCTGGTGTTTATTGTACTGTCA 57.438 29.630 0.00 0.00 0.00 3.58
265 268 8.635765 ATTTCTGGTGTTTATTGTACTGTCAT 57.364 30.769 0.00 0.00 0.00 3.06
266 269 7.433708 TTCTGGTGTTTATTGTACTGTCATG 57.566 36.000 0.00 0.00 0.00 3.07
267 270 6.764379 TCTGGTGTTTATTGTACTGTCATGA 58.236 36.000 0.00 0.00 0.00 3.07
268 271 7.394016 TCTGGTGTTTATTGTACTGTCATGAT 58.606 34.615 0.00 0.00 0.00 2.45
269 272 7.882791 TCTGGTGTTTATTGTACTGTCATGATT 59.117 33.333 0.00 0.00 0.00 2.57
270 273 7.815641 TGGTGTTTATTGTACTGTCATGATTG 58.184 34.615 0.00 0.00 0.00 2.67
271 274 7.663493 TGGTGTTTATTGTACTGTCATGATTGA 59.337 33.333 0.00 0.00 0.00 2.57
272 275 8.511321 GGTGTTTATTGTACTGTCATGATTGAA 58.489 33.333 0.00 0.00 32.48 2.69
273 276 9.546909 GTGTTTATTGTACTGTCATGATTGAAG 57.453 33.333 0.00 0.00 32.48 3.02
274 277 9.500785 TGTTTATTGTACTGTCATGATTGAAGA 57.499 29.630 0.00 0.00 32.48 2.87
288 291 9.645059 TCATGATTGAAGATAAATAGATCGACC 57.355 33.333 0.00 0.00 0.00 4.79
289 292 8.590470 CATGATTGAAGATAAATAGATCGACCG 58.410 37.037 0.00 0.00 0.00 4.79
290 293 7.658261 TGATTGAAGATAAATAGATCGACCGT 58.342 34.615 0.00 0.00 0.00 4.83
291 294 8.141909 TGATTGAAGATAAATAGATCGACCGTT 58.858 33.333 0.00 0.00 0.00 4.44
292 295 8.888579 ATTGAAGATAAATAGATCGACCGTTT 57.111 30.769 0.00 0.00 0.00 3.60
293 296 8.712285 TTGAAGATAAATAGATCGACCGTTTT 57.288 30.769 0.00 0.00 0.00 2.43
294 297 8.712285 TGAAGATAAATAGATCGACCGTTTTT 57.288 30.769 0.00 0.00 0.00 1.94
295 298 8.814235 TGAAGATAAATAGATCGACCGTTTTTC 58.186 33.333 0.00 0.00 0.00 2.29
296 299 7.390918 AGATAAATAGATCGACCGTTTTTCG 57.609 36.000 0.00 0.00 37.85 3.46
315 318 4.830826 TCGGAAAAGAAAAAGAAGCTCC 57.169 40.909 0.00 0.00 0.00 4.70
316 319 4.204012 TCGGAAAAGAAAAAGAAGCTCCA 58.796 39.130 0.00 0.00 0.00 3.86
317 320 4.642885 TCGGAAAAGAAAAAGAAGCTCCAA 59.357 37.500 0.00 0.00 0.00 3.53
318 321 4.740205 CGGAAAAGAAAAAGAAGCTCCAAC 59.260 41.667 0.00 0.00 0.00 3.77
319 322 5.450550 CGGAAAAGAAAAAGAAGCTCCAACT 60.451 40.000 0.00 0.00 0.00 3.16
404 407 3.058639 GTGGAATTATGGAATGAGAGCGC 60.059 47.826 0.00 0.00 0.00 5.92
409 412 4.607293 TTATGGAATGAGAGCGCTGTAT 57.393 40.909 18.48 1.84 0.00 2.29
413 416 3.060602 GGAATGAGAGCGCTGTATTACC 58.939 50.000 18.48 9.66 0.00 2.85
457 460 4.060205 GTCAAATTTCTTGGCTGCAACAT 58.940 39.130 0.50 0.00 0.00 2.71
478 481 3.036819 TCAGCTAGACCGTAGAGGACTA 58.963 50.000 0.00 0.00 43.07 2.59
490 493 6.485984 ACCGTAGAGGACTACAAGTATGTATG 59.514 42.308 0.00 0.00 46.47 2.39
500 503 3.214328 CAAGTATGTATGTGCCCTTCCC 58.786 50.000 0.00 0.00 0.00 3.97
501 504 2.776665 AGTATGTATGTGCCCTTCCCT 58.223 47.619 0.00 0.00 0.00 4.20
596 601 6.693113 CAGTTCGAATCAAGTATCTCGATCAA 59.307 38.462 0.00 0.00 39.80 2.57
719 724 8.947055 AATGCAAACAGAATCTTAAACAAACT 57.053 26.923 0.00 0.00 0.00 2.66
721 726 7.319646 TGCAAACAGAATCTTAAACAAACTGT 58.680 30.769 0.00 0.00 38.48 3.55
722 727 8.462811 TGCAAACAGAATCTTAAACAAACTGTA 58.537 29.630 0.00 0.00 36.36 2.74
871 884 2.622436 GTATCTTGCGCCTATCATCCC 58.378 52.381 4.18 0.00 0.00 3.85
995 1009 1.950909 CTTAGCTACCTCCCACTCTCG 59.049 57.143 0.00 0.00 0.00 4.04
1139 1153 4.183101 GACATGGAGAGCTTCTTCTTCAG 58.817 47.826 0.00 0.00 36.18 3.02
1146 1160 0.322366 GCTTCTTCTTCAGCCAGCCT 60.322 55.000 0.00 0.00 0.00 4.58
1305 1322 2.633488 GTTAGGAGCCATGACCAAGAC 58.367 52.381 0.00 0.00 0.00 3.01
1419 1436 1.355066 GAAAGTCTCGCCGGAGCAAG 61.355 60.000 5.05 0.00 40.26 4.01
1553 1570 2.503331 TCGCCTTGATTTCTTGCTTCA 58.497 42.857 0.00 0.00 0.00 3.02
1615 1632 5.772004 ACAGTGATAGATCTGGTCCTACTT 58.228 41.667 5.18 0.00 36.17 2.24
1631 1648 9.609346 TGGTCCTACTTATTGCTTAATTACTTC 57.391 33.333 0.00 0.00 0.00 3.01
1661 1678 1.885871 GTTCTGCCCCATTGTGCTC 59.114 57.895 0.00 0.00 0.00 4.26
1759 1776 2.112279 ATTAGATCCGGTTAGCCCCA 57.888 50.000 0.00 0.00 0.00 4.96
2035 2054 3.192466 CAAAAGCATCAAGGCCATTAGC 58.808 45.455 5.01 1.74 42.60 3.09
2167 2193 5.221087 GCTAGCTAACTTACTACACTCCCTG 60.221 48.000 7.70 0.00 0.00 4.45
2255 2288 9.547753 GCACCGTTCCATGAAATATATATCTAT 57.452 33.333 0.00 0.00 0.00 1.98
2320 2353 8.031864 CACGATAGATTGATTGACCTAGCTAAT 58.968 37.037 0.00 0.00 41.38 1.73
2321 2354 8.589338 ACGATAGATTGATTGACCTAGCTAATT 58.411 33.333 0.00 0.00 41.38 1.40
2364 2413 3.891366 AGTGCCTGTTCTGTGCTTATTTT 59.109 39.130 0.00 0.00 0.00 1.82
2365 2414 4.022849 AGTGCCTGTTCTGTGCTTATTTTC 60.023 41.667 0.00 0.00 0.00 2.29
2375 2424 9.689075 GTTCTGTGCTTATTTTCTTTTGTTTTC 57.311 29.630 0.00 0.00 0.00 2.29
2395 2444 4.137116 TCCGATGAACCTAACTGATTGG 57.863 45.455 0.00 0.00 0.00 3.16
2612 2661 1.416050 GAACCGGCCGTGATAACGTC 61.416 60.000 26.12 5.20 0.00 4.34
2629 2678 3.327626 ACGTCATGTAAATGGCAACGTA 58.672 40.909 8.96 0.00 39.77 3.57
2630 2679 3.936453 ACGTCATGTAAATGGCAACGTAT 59.064 39.130 8.96 0.00 39.77 3.06
2631 2680 4.201773 ACGTCATGTAAATGGCAACGTATG 60.202 41.667 8.96 2.59 39.77 2.39
2632 2681 4.201773 CGTCATGTAAATGGCAACGTATGT 60.202 41.667 0.00 0.00 42.51 2.29
2633 2682 5.005875 CGTCATGTAAATGGCAACGTATGTA 59.994 40.000 0.00 0.00 42.51 2.29
2657 2706 1.321074 GGAGCTACTACCGGTGCACT 61.321 60.000 19.93 7.28 0.00 4.40
2970 3019 3.382111 CGGGAACTCTCCAGCAGT 58.618 61.111 0.00 0.00 44.51 4.40
3009 3058 1.134699 CGCTATTGCAAGACCTCTCCA 60.135 52.381 4.94 0.00 39.64 3.86
3173 3222 1.671979 TGAGCTTGGTCTATGCATGC 58.328 50.000 11.82 11.82 32.18 4.06
3313 3365 7.321153 TGAAGCTGGTCTAATAACTAGAACAC 58.679 38.462 0.00 0.00 45.48 3.32
3383 3435 5.767816 TGTACTCGAGTGCATATGTGTAT 57.232 39.130 29.26 0.37 35.76 2.29
3421 3473 8.166422 AGGAATATTTCACTTCACTTTCGTTT 57.834 30.769 0.00 0.00 0.00 3.60
3446 3498 8.677148 TCTATGAGGAATTATTTACACAAGCC 57.323 34.615 0.00 0.00 0.00 4.35
3663 3715 1.021390 CGCCTCCTCGTGATTTGCTT 61.021 55.000 0.00 0.00 0.00 3.91
3668 3720 3.365364 CCTCCTCGTGATTTGCTTGTTTC 60.365 47.826 0.00 0.00 0.00 2.78
3941 4122 1.720301 GAGGCTGCTGCTTTGATCG 59.280 57.895 15.64 0.00 39.59 3.69
3946 4127 1.602851 GCTGCTGCTTTGATCGATGAT 59.397 47.619 0.54 0.00 36.03 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 141 6.747125 TGTACTATCTGTCCACGTTTGTTAA 58.253 36.000 0.00 0.00 0.00 2.01
143 146 5.867174 TGAATGTACTATCTGTCCACGTTTG 59.133 40.000 0.00 0.00 0.00 2.93
148 151 7.437748 AGCTTATGAATGTACTATCTGTCCAC 58.562 38.462 0.00 0.00 0.00 4.02
149 152 7.255977 GGAGCTTATGAATGTACTATCTGTCCA 60.256 40.741 0.00 0.00 0.00 4.02
156 159 8.256356 AGAGTTGGAGCTTATGAATGTACTAT 57.744 34.615 0.00 0.00 0.00 2.12
180 183 1.989165 GACTACAAGCACTGAAGCGAG 59.011 52.381 0.00 0.00 40.15 5.03
181 184 1.666023 CGACTACAAGCACTGAAGCGA 60.666 52.381 0.00 0.00 40.15 4.93
182 185 0.710567 CGACTACAAGCACTGAAGCG 59.289 55.000 0.00 0.00 40.15 4.68
183 186 1.721926 GACGACTACAAGCACTGAAGC 59.278 52.381 0.00 0.00 0.00 3.86
184 187 1.979469 CGACGACTACAAGCACTGAAG 59.021 52.381 0.00 0.00 0.00 3.02
185 188 1.929038 GCGACGACTACAAGCACTGAA 60.929 52.381 0.00 0.00 0.00 3.02
186 189 0.386858 GCGACGACTACAAGCACTGA 60.387 55.000 0.00 0.00 0.00 3.41
187 190 0.387367 AGCGACGACTACAAGCACTG 60.387 55.000 0.00 0.00 0.00 3.66
188 191 1.130749 CTAGCGACGACTACAAGCACT 59.869 52.381 0.00 0.00 0.00 4.40
189 192 1.129998 TCTAGCGACGACTACAAGCAC 59.870 52.381 0.00 0.00 0.00 4.40
190 193 1.445871 TCTAGCGACGACTACAAGCA 58.554 50.000 0.00 0.00 0.00 3.91
191 194 2.031807 TCATCTAGCGACGACTACAAGC 59.968 50.000 0.00 0.00 0.00 4.01
192 195 3.946308 TCATCTAGCGACGACTACAAG 57.054 47.619 0.00 0.00 0.00 3.16
193 196 4.895224 AATCATCTAGCGACGACTACAA 57.105 40.909 0.00 0.00 0.00 2.41
194 197 4.895224 AAATCATCTAGCGACGACTACA 57.105 40.909 0.00 0.00 0.00 2.74
195 198 5.745514 TGTAAATCATCTAGCGACGACTAC 58.254 41.667 0.00 0.00 0.00 2.73
196 199 5.756833 TCTGTAAATCATCTAGCGACGACTA 59.243 40.000 0.00 0.00 0.00 2.59
197 200 4.575236 TCTGTAAATCATCTAGCGACGACT 59.425 41.667 0.00 0.00 0.00 4.18
198 201 4.845387 TCTGTAAATCATCTAGCGACGAC 58.155 43.478 0.00 0.00 0.00 4.34
199 202 5.066117 AGTTCTGTAAATCATCTAGCGACGA 59.934 40.000 0.00 0.00 0.00 4.20
200 203 5.172232 CAGTTCTGTAAATCATCTAGCGACG 59.828 44.000 0.00 0.00 0.00 5.12
201 204 5.460419 CCAGTTCTGTAAATCATCTAGCGAC 59.540 44.000 0.00 0.00 0.00 5.19
202 205 5.359860 TCCAGTTCTGTAAATCATCTAGCGA 59.640 40.000 0.00 0.00 0.00 4.93
203 206 5.592054 TCCAGTTCTGTAAATCATCTAGCG 58.408 41.667 0.00 0.00 0.00 4.26
238 241 9.562408 TGACAGTACAATAAACACCAGAAATAA 57.438 29.630 0.00 0.00 0.00 1.40
239 242 9.733556 ATGACAGTACAATAAACACCAGAAATA 57.266 29.630 0.00 0.00 0.00 1.40
240 243 8.514594 CATGACAGTACAATAAACACCAGAAAT 58.485 33.333 0.00 0.00 0.00 2.17
241 244 7.717436 TCATGACAGTACAATAAACACCAGAAA 59.283 33.333 0.00 0.00 0.00 2.52
242 245 7.220740 TCATGACAGTACAATAAACACCAGAA 58.779 34.615 0.00 0.00 0.00 3.02
243 246 6.764379 TCATGACAGTACAATAAACACCAGA 58.236 36.000 0.00 0.00 0.00 3.86
244 247 7.615582 ATCATGACAGTACAATAAACACCAG 57.384 36.000 0.00 0.00 0.00 4.00
245 248 7.663493 TCAATCATGACAGTACAATAAACACCA 59.337 33.333 0.00 0.00 0.00 4.17
246 249 8.039603 TCAATCATGACAGTACAATAAACACC 57.960 34.615 0.00 0.00 0.00 4.16
247 250 9.546909 CTTCAATCATGACAGTACAATAAACAC 57.453 33.333 0.00 0.00 34.61 3.32
248 251 9.500785 TCTTCAATCATGACAGTACAATAAACA 57.499 29.630 0.00 0.00 34.61 2.83
262 265 9.645059 GGTCGATCTATTTATCTTCAATCATGA 57.355 33.333 0.00 0.00 0.00 3.07
263 266 8.590470 CGGTCGATCTATTTATCTTCAATCATG 58.410 37.037 0.00 0.00 0.00 3.07
264 267 8.307483 ACGGTCGATCTATTTATCTTCAATCAT 58.693 33.333 0.00 0.00 0.00 2.45
265 268 7.658261 ACGGTCGATCTATTTATCTTCAATCA 58.342 34.615 0.00 0.00 0.00 2.57
266 269 8.522178 AACGGTCGATCTATTTATCTTCAATC 57.478 34.615 0.00 0.00 0.00 2.67
267 270 8.888579 AAACGGTCGATCTATTTATCTTCAAT 57.111 30.769 0.00 0.00 0.00 2.57
268 271 8.712285 AAAACGGTCGATCTATTTATCTTCAA 57.288 30.769 0.00 0.00 0.00 2.69
269 272 8.712285 AAAAACGGTCGATCTATTTATCTTCA 57.288 30.769 0.00 0.00 0.00 3.02
270 273 7.997104 CGAAAAACGGTCGATCTATTTATCTTC 59.003 37.037 0.00 0.00 41.02 2.87
271 274 7.838498 CGAAAAACGGTCGATCTATTTATCTT 58.162 34.615 0.00 0.00 41.02 2.40
272 275 7.390918 CGAAAAACGGTCGATCTATTTATCT 57.609 36.000 0.00 0.00 41.02 1.98
288 291 6.034577 AGCTTCTTTTTCTTTTCCGAAAAACG 59.965 34.615 7.67 0.00 43.84 3.60
289 292 7.290857 AGCTTCTTTTTCTTTTCCGAAAAAC 57.709 32.000 7.67 0.31 43.84 2.43
290 293 6.533723 GGAGCTTCTTTTTCTTTTCCGAAAAA 59.466 34.615 7.67 10.04 45.46 1.94
291 294 6.040247 GGAGCTTCTTTTTCTTTTCCGAAAA 58.960 36.000 6.16 6.16 40.14 2.29
292 295 5.126384 TGGAGCTTCTTTTTCTTTTCCGAAA 59.874 36.000 0.00 0.00 0.00 3.46
293 296 4.642885 TGGAGCTTCTTTTTCTTTTCCGAA 59.357 37.500 0.00 0.00 0.00 4.30
294 297 4.204012 TGGAGCTTCTTTTTCTTTTCCGA 58.796 39.130 0.00 0.00 0.00 4.55
295 298 4.568152 TGGAGCTTCTTTTTCTTTTCCG 57.432 40.909 0.00 0.00 0.00 4.30
296 299 5.907207 AGTTGGAGCTTCTTTTTCTTTTCC 58.093 37.500 0.00 0.00 0.00 3.13
297 300 5.980116 GGAGTTGGAGCTTCTTTTTCTTTTC 59.020 40.000 0.00 0.00 0.00 2.29
298 301 5.422012 TGGAGTTGGAGCTTCTTTTTCTTTT 59.578 36.000 0.00 0.00 0.00 2.27
299 302 4.956075 TGGAGTTGGAGCTTCTTTTTCTTT 59.044 37.500 0.00 0.00 0.00 2.52
300 303 4.339530 GTGGAGTTGGAGCTTCTTTTTCTT 59.660 41.667 0.00 0.00 0.00 2.52
301 304 3.885901 GTGGAGTTGGAGCTTCTTTTTCT 59.114 43.478 0.00 0.00 0.00 2.52
302 305 3.632145 TGTGGAGTTGGAGCTTCTTTTTC 59.368 43.478 0.00 0.00 0.00 2.29
303 306 3.631250 TGTGGAGTTGGAGCTTCTTTTT 58.369 40.909 0.00 0.00 0.00 1.94
304 307 3.217626 CTGTGGAGTTGGAGCTTCTTTT 58.782 45.455 0.00 0.00 0.00 2.27
305 308 2.856222 CTGTGGAGTTGGAGCTTCTTT 58.144 47.619 0.00 0.00 0.00 2.52
306 309 1.544314 GCTGTGGAGTTGGAGCTTCTT 60.544 52.381 0.00 0.00 0.00 2.52
307 310 0.036022 GCTGTGGAGTTGGAGCTTCT 59.964 55.000 0.00 0.00 0.00 2.85
308 311 1.294659 CGCTGTGGAGTTGGAGCTTC 61.295 60.000 0.00 0.00 0.00 3.86
309 312 1.302033 CGCTGTGGAGTTGGAGCTT 60.302 57.895 0.00 0.00 0.00 3.74
310 313 2.345244 CGCTGTGGAGTTGGAGCT 59.655 61.111 0.00 0.00 0.00 4.09
311 314 2.507110 TAGCGCTGTGGAGTTGGAGC 62.507 60.000 22.90 0.00 0.00 4.70
312 315 0.176680 ATAGCGCTGTGGAGTTGGAG 59.823 55.000 22.90 0.00 0.00 3.86
313 316 1.136305 GTATAGCGCTGTGGAGTTGGA 59.864 52.381 22.90 0.00 0.00 3.53
314 317 1.134818 TGTATAGCGCTGTGGAGTTGG 60.135 52.381 22.90 0.00 0.00 3.77
315 318 1.927174 GTGTATAGCGCTGTGGAGTTG 59.073 52.381 22.90 0.00 0.00 3.16
316 319 1.469251 CGTGTATAGCGCTGTGGAGTT 60.469 52.381 22.90 0.00 0.00 3.01
317 320 0.100682 CGTGTATAGCGCTGTGGAGT 59.899 55.000 22.90 1.27 0.00 3.85
318 321 0.100682 ACGTGTATAGCGCTGTGGAG 59.899 55.000 22.90 9.56 0.00 3.86
319 322 1.381522 TACGTGTATAGCGCTGTGGA 58.618 50.000 22.90 0.00 0.00 4.02
392 395 3.060602 GGTAATACAGCGCTCTCATTCC 58.939 50.000 7.13 2.89 0.00 3.01
404 407 3.200483 GTGGCTTTACCCGGTAATACAG 58.800 50.000 10.91 6.95 37.83 2.74
409 412 0.320596 CGTGTGGCTTTACCCGGTAA 60.321 55.000 5.87 5.87 37.83 2.85
413 416 1.161563 ACAACGTGTGGCTTTACCCG 61.162 55.000 0.00 0.00 37.83 5.28
457 460 1.838715 AGTCCTCTACGGTCTAGCTGA 59.161 52.381 0.00 0.00 28.84 4.26
478 481 3.371595 GGGAAGGGCACATACATACTTGT 60.372 47.826 0.00 0.00 39.98 3.16
656 661 1.567504 CGTCAGAACAAACTGTCGGT 58.432 50.000 0.00 0.00 42.29 4.69
717 722 9.391006 TGTCAGAACAAACTAGAATTTTACAGT 57.609 29.630 0.00 0.00 30.70 3.55
718 723 9.651718 GTGTCAGAACAAACTAGAATTTTACAG 57.348 33.333 0.00 0.00 37.08 2.74
719 724 9.168451 TGTGTCAGAACAAACTAGAATTTTACA 57.832 29.630 0.00 0.00 37.08 2.41
724 729 9.003658 CCTAATGTGTCAGAACAAACTAGAATT 57.996 33.333 0.00 0.00 37.08 2.17
725 730 8.375506 TCCTAATGTGTCAGAACAAACTAGAAT 58.624 33.333 0.00 0.00 37.08 2.40
726 731 7.732025 TCCTAATGTGTCAGAACAAACTAGAA 58.268 34.615 0.00 0.00 37.08 2.10
727 732 7.297936 TCCTAATGTGTCAGAACAAACTAGA 57.702 36.000 0.00 0.00 37.08 2.43
728 733 7.962964 TTCCTAATGTGTCAGAACAAACTAG 57.037 36.000 0.00 0.00 37.08 2.57
729 734 8.783093 CAATTCCTAATGTGTCAGAACAAACTA 58.217 33.333 0.00 0.00 37.08 2.24
731 736 7.591426 GTCAATTCCTAATGTGTCAGAACAAAC 59.409 37.037 0.00 0.00 37.08 2.93
732 737 7.502226 AGTCAATTCCTAATGTGTCAGAACAAA 59.498 33.333 0.00 0.00 37.08 2.83
733 738 6.998074 AGTCAATTCCTAATGTGTCAGAACAA 59.002 34.615 0.00 0.00 37.08 2.83
734 739 6.427853 CAGTCAATTCCTAATGTGTCAGAACA 59.572 38.462 0.00 0.00 0.00 3.18
737 742 6.358974 TCAGTCAATTCCTAATGTGTCAGA 57.641 37.500 0.00 0.00 0.00 3.27
738 743 7.551974 AGAATCAGTCAATTCCTAATGTGTCAG 59.448 37.037 0.00 0.00 36.49 3.51
739 744 7.397221 AGAATCAGTCAATTCCTAATGTGTCA 58.603 34.615 0.00 0.00 36.49 3.58
907 921 1.433879 CACCTAGTCTCGCCTTCCG 59.566 63.158 0.00 0.00 38.61 4.30
995 1009 0.392998 ACCACCGGAAGACATGATGC 60.393 55.000 9.46 0.00 0.00 3.91
1438 1455 1.750930 CATCCTCCTGGTCATCCGG 59.249 63.158 0.00 0.00 39.70 5.14
1553 1570 2.413837 CTCACGACAAAAGGAATCGGT 58.586 47.619 0.00 0.00 40.16 4.69
1631 1648 2.414161 GGGGCAGAACGAAAGAAAATCG 60.414 50.000 0.00 0.00 45.47 3.34
1661 1678 2.871133 TCACGTAATAGACAAGGCACG 58.129 47.619 0.00 0.00 35.62 5.34
1737 1754 2.370849 GGGGCTAACCGGATCTAATTCA 59.629 50.000 9.46 0.00 41.60 2.57
1759 1776 1.472480 ACAAAAGTGTGCGTCAGCTTT 59.528 42.857 0.00 0.00 45.42 3.51
2147 2173 4.705991 AGACAGGGAGTGTAGTAAGTTAGC 59.294 45.833 0.00 0.00 40.56 3.09
2148 2174 5.711036 ACAGACAGGGAGTGTAGTAAGTTAG 59.289 44.000 0.00 0.00 40.56 2.34
2149 2175 5.638133 ACAGACAGGGAGTGTAGTAAGTTA 58.362 41.667 0.00 0.00 40.56 2.24
2150 2176 4.481072 ACAGACAGGGAGTGTAGTAAGTT 58.519 43.478 0.00 0.00 40.56 2.66
2190 2223 0.805322 CTGCCGAGAGTGATCAGTGC 60.805 60.000 8.05 5.71 0.00 4.40
2255 2288 8.343366 GCACTATATATAGCTAACTATGTCGCA 58.657 37.037 18.00 0.00 39.51 5.10
2320 2353 1.663911 TCCAACAGGGCCTAGCTTAA 58.336 50.000 5.28 0.00 36.21 1.85
2321 2354 1.768870 GATCCAACAGGGCCTAGCTTA 59.231 52.381 5.28 0.00 36.21 3.09
2322 2355 0.548510 GATCCAACAGGGCCTAGCTT 59.451 55.000 5.28 0.00 36.21 3.74
2323 2356 0.621571 TGATCCAACAGGGCCTAGCT 60.622 55.000 5.28 0.00 36.21 3.32
2364 2413 6.544564 AGTTAGGTTCATCGGAAAACAAAAGA 59.455 34.615 8.35 0.00 34.13 2.52
2365 2414 6.636850 CAGTTAGGTTCATCGGAAAACAAAAG 59.363 38.462 8.35 0.00 34.13 2.27
2375 2424 3.873910 ACCAATCAGTTAGGTTCATCGG 58.126 45.455 0.00 0.00 29.58 4.18
2612 2661 5.194657 CGTACATACGTTGCCATTTACATG 58.805 41.667 0.00 0.00 44.13 3.21
2629 2678 1.955080 GGTAGTAGCTCCTGCGTACAT 59.045 52.381 0.00 0.00 45.42 2.29
2630 2679 1.386533 GGTAGTAGCTCCTGCGTACA 58.613 55.000 0.00 0.00 45.42 2.90
2631 2680 0.307146 CGGTAGTAGCTCCTGCGTAC 59.693 60.000 0.00 0.00 45.42 3.67
2632 2681 0.816825 CCGGTAGTAGCTCCTGCGTA 60.817 60.000 0.00 0.00 45.42 4.42
2633 2682 2.119655 CCGGTAGTAGCTCCTGCGT 61.120 63.158 0.00 0.00 45.42 5.24
2970 3019 2.871133 CGCGTAGTCAGTGAAATGGTA 58.129 47.619 0.00 0.00 0.00 3.25
3009 3058 1.412343 GTTGTTGGGCATTGTGGAAGT 59.588 47.619 0.00 0.00 0.00 3.01
3173 3222 3.753294 ATTAGGATAACAGGACCGCAG 57.247 47.619 0.00 0.00 0.00 5.18
3421 3473 7.441157 CGGCTTGTGTAAATAATTCCTCATAGA 59.559 37.037 0.00 0.00 0.00 1.98
3424 3476 5.221048 GCGGCTTGTGTAAATAATTCCTCAT 60.221 40.000 0.00 0.00 0.00 2.90
3446 3498 1.129998 CAAGCAGAAGTTGAGATGGCG 59.870 52.381 0.00 0.00 0.00 5.69
3663 3715 9.932207 TCAGTTATAAATTCCTTCTACGAAACA 57.068 29.630 0.00 0.00 0.00 2.83
3668 3720 9.751542 ATGTCTCAGTTATAAATTCCTTCTACG 57.248 33.333 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.