Multiple sequence alignment - TraesCS2D01G093800

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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 TraesCS2D01G093800 chr2D 100.000 2751 0 0 1 2751 45540460 45537710 0.000000e+00 5081.0
1 TraesCS2D01G093800 chr2D 98.125 160 3 0 203 362 391461635 391461476 2.090000e-71 279.0
2 TraesCS2D01G093800 chr2A 91.266 2164 107 36 591 2717 48866642 48864524 0.000000e+00 2874.0
3 TraesCS2D01G093800 chr2A 97.701 87 2 0 2665 2751 48864522 48864436 1.710000e-32 150.0
4 TraesCS2D01G093800 chr2B 94.669 1782 51 20 363 2132 72581707 72579958 0.000000e+00 2724.0
5 TraesCS2D01G093800 chr2B 91.452 620 33 13 2138 2751 72579915 72579310 0.000000e+00 833.0
6 TraesCS2D01G093800 chr2B 94.203 207 7 1 1 202 72581907 72581701 7.400000e-81 311.0
7 TraesCS2D01G093800 chr2B 98.125 160 2 1 203 362 397938601 397938759 7.500000e-71 278.0
8 TraesCS2D01G093800 chr2B 97.516 161 4 0 202 362 296085573 296085733 2.700000e-70 276.0
9 TraesCS2D01G093800 chr2B 85.185 54 6 2 2398 2451 7773988 7774039 1.000000e-03 54.7
10 TraesCS2D01G093800 chr7D 99.375 160 1 0 203 362 600764281 600764440 9.640000e-75 291.0
11 TraesCS2D01G093800 chr1B 98.171 164 2 1 203 365 17384724 17384561 4.480000e-73 285.0
12 TraesCS2D01G093800 chr5B 97.561 164 4 0 199 362 655620542 655620705 5.800000e-72 281.0
13 TraesCS2D01G093800 chr1D 98.113 159 3 0 202 360 12318528 12318370 7.500000e-71 278.0
14 TraesCS2D01G093800 chr3B 94.318 176 9 1 190 365 148449881 148449707 4.520000e-68 268.0
15 TraesCS2D01G093800 chr6B 94.286 175 7 3 196 367 279332270 279332096 5.840000e-67 265.0


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 TraesCS2D01G093800 chr2D 45537710 45540460 2750 True 5081.000000 5081 100.000000 1 2751 1 chr2D.!!$R1 2750
1 TraesCS2D01G093800 chr2A 48864436 48866642 2206 True 1512.000000 2874 94.483500 591 2751 2 chr2A.!!$R1 2160
2 TraesCS2D01G093800 chr2B 72579310 72581907 2597 True 1289.333333 2724 93.441333 1 2751 3 chr2B.!!$R1 2750

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
348 354 0.035152 AACGGGATTAAACGGGACCC 60.035 55.0 0.0 0.00 37.42 4.46 F
362 368 0.106894 GGACCCGATTGACATCCCTC 59.893 60.0 0.0 0.00 0.00 4.30 F
475 481 0.108377 ATGGTGCGACGTCTTATGCA 60.108 50.0 14.7 12.75 34.44 3.96 F
1042 1070 0.320683 CCAGACGACATCAGCCACAA 60.321 55.0 0.0 0.00 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1477 1505 0.700564 TCTTCAAGCTGGGCTTCCAT 59.299 50.000 1.5 0.0 46.77 3.41 R
1565 1593 2.907910 AGATCACATTCGTTTGCAGC 57.092 45.000 0.0 0.0 0.00 5.25 R
1658 1686 3.814842 TCCGCTCTTTTGCCATGTATATG 59.185 43.478 0.0 0.0 0.00 1.78 R
2578 2652 1.530720 CATTGACACGCAAGCTACACA 59.469 47.619 0.0 0.0 40.42 3.72 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 1.286553 ACCTGTTCAAAACCCTCCACA 59.713 47.619 0.00 0.00 0.00 4.17
93 94 0.472471 TCCACAGTGAAACCCAGGAC 59.528 55.000 0.62 0.00 37.80 3.85
99 100 2.884639 CAGTGAAACCCAGGACGAAAAT 59.115 45.455 0.00 0.00 37.80 1.82
150 156 2.028748 GGGTGTCTCTGCATGCAATTTT 60.029 45.455 22.88 0.00 0.00 1.82
206 212 4.045636 GCTTAATGCACCAACATTAGGG 57.954 45.455 0.00 0.00 42.02 3.53
207 213 3.699038 GCTTAATGCACCAACATTAGGGA 59.301 43.478 0.00 0.00 42.02 4.20
208 214 4.342092 GCTTAATGCACCAACATTAGGGAT 59.658 41.667 0.00 0.00 42.02 3.85
209 215 5.737063 GCTTAATGCACCAACATTAGGGATG 60.737 44.000 0.00 0.00 42.02 3.51
210 216 8.080153 GCTTAATGCACCAACATTAGGGATGT 62.080 42.308 0.00 0.00 45.43 3.06
211 217 8.816133 GCTTAATGCACCAACATTAGGGATGTA 61.816 40.741 0.00 0.00 44.00 2.29
219 225 4.584638 ACATTAGGGATGTAAGTGGCAA 57.415 40.909 0.00 0.00 47.00 4.52
220 226 4.929479 ACATTAGGGATGTAAGTGGCAAA 58.071 39.130 0.00 0.00 47.00 3.68
221 227 5.518865 ACATTAGGGATGTAAGTGGCAAAT 58.481 37.500 0.00 0.00 47.00 2.32
222 228 6.668645 ACATTAGGGATGTAAGTGGCAAATA 58.331 36.000 0.00 0.00 47.00 1.40
223 229 7.122715 ACATTAGGGATGTAAGTGGCAAATAA 58.877 34.615 0.00 0.00 47.00 1.40
224 230 7.617723 ACATTAGGGATGTAAGTGGCAAATAAA 59.382 33.333 0.00 0.00 47.00 1.40
225 231 8.641541 CATTAGGGATGTAAGTGGCAAATAAAT 58.358 33.333 0.00 0.00 0.00 1.40
226 232 6.469782 AGGGATGTAAGTGGCAAATAAATG 57.530 37.500 0.00 0.00 0.00 2.32
227 233 5.363580 AGGGATGTAAGTGGCAAATAAATGG 59.636 40.000 0.00 0.00 0.00 3.16
228 234 5.049828 GGATGTAAGTGGCAAATAAATGGC 58.950 41.667 0.00 0.00 45.44 4.40
233 239 3.250220 GGCAAATAAATGGCGTCCG 57.750 52.632 0.00 0.00 36.07 4.79
234 240 0.869880 GGCAAATAAATGGCGTCCGC 60.870 55.000 2.45 2.45 36.07 5.54
235 241 0.179150 GCAAATAAATGGCGTCCGCA 60.179 50.000 14.19 0.24 44.11 5.69
236 242 1.734047 GCAAATAAATGGCGTCCGCAA 60.734 47.619 14.19 1.87 44.11 4.85
237 243 2.808244 CAAATAAATGGCGTCCGCAAT 58.192 42.857 14.19 4.68 44.11 3.56
238 244 2.774439 AATAAATGGCGTCCGCAATC 57.226 45.000 14.19 0.00 44.11 2.67
239 245 0.951558 ATAAATGGCGTCCGCAATCC 59.048 50.000 14.19 0.00 44.11 3.01
240 246 1.098712 TAAATGGCGTCCGCAATCCC 61.099 55.000 14.19 0.00 44.11 3.85
244 250 3.428282 GCGTCCGCAATCCCGTTT 61.428 61.111 6.82 0.00 41.49 3.60
245 251 2.101835 GCGTCCGCAATCCCGTTTA 61.102 57.895 6.82 0.00 41.49 2.01
246 252 2.003672 CGTCCGCAATCCCGTTTAG 58.996 57.895 0.00 0.00 0.00 1.85
247 253 0.738412 CGTCCGCAATCCCGTTTAGT 60.738 55.000 0.00 0.00 0.00 2.24
248 254 1.445871 GTCCGCAATCCCGTTTAGTT 58.554 50.000 0.00 0.00 0.00 2.24
249 255 2.620242 GTCCGCAATCCCGTTTAGTTA 58.380 47.619 0.00 0.00 0.00 2.24
250 256 2.606272 GTCCGCAATCCCGTTTAGTTAG 59.394 50.000 0.00 0.00 0.00 2.34
251 257 2.234414 TCCGCAATCCCGTTTAGTTAGT 59.766 45.455 0.00 0.00 0.00 2.24
252 258 3.004862 CCGCAATCCCGTTTAGTTAGTT 58.995 45.455 0.00 0.00 0.00 2.24
253 259 3.437741 CCGCAATCCCGTTTAGTTAGTTT 59.562 43.478 0.00 0.00 0.00 2.66
254 260 4.083164 CCGCAATCCCGTTTAGTTAGTTTT 60.083 41.667 0.00 0.00 0.00 2.43
255 261 5.454520 CGCAATCCCGTTTAGTTAGTTTTT 58.545 37.500 0.00 0.00 0.00 1.94
256 262 5.341196 CGCAATCCCGTTTAGTTAGTTTTTG 59.659 40.000 0.00 0.00 0.00 2.44
257 263 5.118050 GCAATCCCGTTTAGTTAGTTTTTGC 59.882 40.000 0.00 0.00 0.00 3.68
258 264 6.443792 CAATCCCGTTTAGTTAGTTTTTGCT 58.556 36.000 0.00 0.00 0.00 3.91
259 265 7.586747 CAATCCCGTTTAGTTAGTTTTTGCTA 58.413 34.615 0.00 0.00 0.00 3.49
260 266 6.790285 TCCCGTTTAGTTAGTTTTTGCTAG 57.210 37.500 0.00 0.00 0.00 3.42
261 267 5.179929 TCCCGTTTAGTTAGTTTTTGCTAGC 59.820 40.000 8.10 8.10 0.00 3.42
262 268 5.180680 CCCGTTTAGTTAGTTTTTGCTAGCT 59.819 40.000 17.23 0.00 36.65 3.32
263 269 6.293790 CCCGTTTAGTTAGTTTTTGCTAGCTT 60.294 38.462 17.23 0.00 34.92 3.74
264 270 6.577427 CCGTTTAGTTAGTTTTTGCTAGCTTG 59.423 38.462 17.23 0.00 34.92 4.01
265 271 7.349711 CGTTTAGTTAGTTTTTGCTAGCTTGA 58.650 34.615 17.23 0.00 34.92 3.02
266 272 8.015658 CGTTTAGTTAGTTTTTGCTAGCTTGAT 58.984 33.333 17.23 0.00 34.92 2.57
269 275 9.720769 TTAGTTAGTTTTTGCTAGCTTGATAGT 57.279 29.630 17.23 3.48 34.92 2.12
270 276 8.622948 AGTTAGTTTTTGCTAGCTTGATAGTT 57.377 30.769 17.23 0.00 30.04 2.24
271 277 8.722394 AGTTAGTTTTTGCTAGCTTGATAGTTC 58.278 33.333 17.23 0.95 30.04 3.01
272 278 8.504005 GTTAGTTTTTGCTAGCTTGATAGTTCA 58.496 33.333 17.23 0.00 0.00 3.18
273 279 7.693969 AGTTTTTGCTAGCTTGATAGTTCAT 57.306 32.000 17.23 0.00 0.00 2.57
274 280 8.115490 AGTTTTTGCTAGCTTGATAGTTCATT 57.885 30.769 17.23 0.00 0.00 2.57
275 281 8.579863 AGTTTTTGCTAGCTTGATAGTTCATTT 58.420 29.630 17.23 0.00 0.00 2.32
276 282 9.196552 GTTTTTGCTAGCTTGATAGTTCATTTT 57.803 29.630 17.23 0.00 0.00 1.82
277 283 9.762933 TTTTTGCTAGCTTGATAGTTCATTTTT 57.237 25.926 17.23 0.00 0.00 1.94
278 284 8.970691 TTTGCTAGCTTGATAGTTCATTTTTC 57.029 30.769 17.23 0.00 0.00 2.29
279 285 7.928307 TGCTAGCTTGATAGTTCATTTTTCT 57.072 32.000 17.23 0.00 0.00 2.52
280 286 7.978982 TGCTAGCTTGATAGTTCATTTTTCTC 58.021 34.615 17.23 0.00 0.00 2.87
281 287 7.607607 TGCTAGCTTGATAGTTCATTTTTCTCA 59.392 33.333 17.23 0.00 0.00 3.27
282 288 8.454106 GCTAGCTTGATAGTTCATTTTTCTCAA 58.546 33.333 7.70 0.00 0.00 3.02
285 291 8.632679 AGCTTGATAGTTCATTTTTCTCAAACA 58.367 29.630 0.00 0.00 0.00 2.83
286 292 9.248291 GCTTGATAGTTCATTTTTCTCAAACAA 57.752 29.630 0.00 0.00 0.00 2.83
333 339 8.657074 TCATATCATAAGTGGACTTTAAACGG 57.343 34.615 0.00 0.00 37.40 4.44
334 340 7.713507 TCATATCATAAGTGGACTTTAAACGGG 59.286 37.037 0.00 0.00 37.40 5.28
335 341 5.486735 TCATAAGTGGACTTTAAACGGGA 57.513 39.130 0.00 0.00 37.40 5.14
336 342 6.057321 TCATAAGTGGACTTTAAACGGGAT 57.943 37.500 0.00 0.00 37.40 3.85
337 343 6.478129 TCATAAGTGGACTTTAAACGGGATT 58.522 36.000 0.00 0.00 37.40 3.01
338 344 7.622713 TCATAAGTGGACTTTAAACGGGATTA 58.377 34.615 0.00 0.00 37.40 1.75
339 345 8.102047 TCATAAGTGGACTTTAAACGGGATTAA 58.898 33.333 0.00 0.00 37.40 1.40
340 346 8.732531 CATAAGTGGACTTTAAACGGGATTAAA 58.267 33.333 0.00 0.00 37.40 1.52
341 347 6.564709 AGTGGACTTTAAACGGGATTAAAC 57.435 37.500 0.00 0.00 32.77 2.01
342 348 5.179929 AGTGGACTTTAAACGGGATTAAACG 59.820 40.000 0.00 0.00 32.77 3.60
343 349 4.455190 TGGACTTTAAACGGGATTAAACGG 59.545 41.667 0.00 0.00 32.77 4.44
344 350 4.142622 GGACTTTAAACGGGATTAAACGGG 60.143 45.833 0.00 0.00 32.77 5.28
345 351 4.650734 ACTTTAAACGGGATTAAACGGGA 58.349 39.130 0.00 0.00 32.77 5.14
346 352 4.455533 ACTTTAAACGGGATTAAACGGGAC 59.544 41.667 0.00 0.00 32.77 4.46
347 353 1.825090 AAACGGGATTAAACGGGACC 58.175 50.000 0.00 0.00 0.00 4.46
348 354 0.035152 AACGGGATTAAACGGGACCC 60.035 55.000 0.00 0.00 37.42 4.46
359 365 4.878878 GGGACCCGATTGACATCC 57.121 61.111 0.00 0.00 0.00 3.51
360 366 1.148498 GGGACCCGATTGACATCCC 59.852 63.158 0.00 0.00 42.30 3.85
361 367 1.345715 GGGACCCGATTGACATCCCT 61.346 60.000 0.00 0.00 44.94 4.20
362 368 0.106894 GGACCCGATTGACATCCCTC 59.893 60.000 0.00 0.00 0.00 4.30
363 369 0.106894 GACCCGATTGACATCCCTCC 59.893 60.000 0.00 0.00 0.00 4.30
364 370 0.620410 ACCCGATTGACATCCCTCCA 60.620 55.000 0.00 0.00 0.00 3.86
365 371 0.546122 CCCGATTGACATCCCTCCAA 59.454 55.000 0.00 0.00 0.00 3.53
366 372 1.668419 CCGATTGACATCCCTCCAAC 58.332 55.000 0.00 0.00 0.00 3.77
367 373 1.065491 CCGATTGACATCCCTCCAACA 60.065 52.381 0.00 0.00 0.00 3.33
370 376 3.432749 CGATTGACATCCCTCCAACATCT 60.433 47.826 0.00 0.00 0.00 2.90
379 385 1.506493 CTCCAACATCTATCGCCAGC 58.494 55.000 0.00 0.00 0.00 4.85
396 402 2.411290 CAACCGCGGTGCTTGTTT 59.589 55.556 34.95 11.84 0.00 2.83
405 411 2.073816 CGGTGCTTGTTTCCGATAGTT 58.926 47.619 0.00 0.00 46.05 2.24
475 481 0.108377 ATGGTGCGACGTCTTATGCA 60.108 50.000 14.70 12.75 34.44 3.96
476 482 0.735978 TGGTGCGACGTCTTATGCAG 60.736 55.000 14.88 0.00 38.14 4.41
477 483 0.736325 GGTGCGACGTCTTATGCAGT 60.736 55.000 14.88 0.00 38.14 4.40
478 484 1.068474 GTGCGACGTCTTATGCAGTT 58.932 50.000 14.88 0.00 38.14 3.16
479 485 2.256174 GTGCGACGTCTTATGCAGTTA 58.744 47.619 14.88 0.00 38.14 2.24
480 486 2.858344 GTGCGACGTCTTATGCAGTTAT 59.142 45.455 14.88 0.00 38.14 1.89
481 487 2.857748 TGCGACGTCTTATGCAGTTATG 59.142 45.455 14.70 0.00 32.73 1.90
543 549 6.449635 TTGCGGCAAATAGTGATTTTATCT 57.550 33.333 13.93 0.00 32.73 1.98
588 597 8.729805 ATTTTATCTTCTGGATCTGTTCTGTC 57.270 34.615 0.00 0.00 35.98 3.51
589 598 4.751767 ATCTTCTGGATCTGTTCTGTCC 57.248 45.455 0.00 0.00 0.00 4.02
597 606 1.053835 TCTGTTCTGTCCTGTGGCCA 61.054 55.000 0.00 0.00 0.00 5.36
628 638 2.337583 CATGAACGAACACGATCCAGT 58.662 47.619 0.00 0.00 0.00 4.00
660 670 2.285026 CGTGTGGATCGTAAAGAATGCG 60.285 50.000 0.00 0.00 38.62 4.73
694 704 0.607217 TCTGTTCCTACTCCACGCGA 60.607 55.000 15.93 0.00 0.00 5.87
808 835 2.263227 CGCACGGTGTATGGGTCA 59.737 61.111 10.24 0.00 0.00 4.02
1015 1042 1.878656 CGTCGCCTTCCACTCTTCCT 61.879 60.000 0.00 0.00 0.00 3.36
1026 1054 2.364317 TCTTCCTCCCTCGGCCAG 60.364 66.667 2.24 0.00 0.00 4.85
1028 1056 2.683933 TTCCTCCCTCGGCCAGAC 60.684 66.667 2.24 0.00 0.00 3.51
1042 1070 0.320683 CCAGACGACATCAGCCACAA 60.321 55.000 0.00 0.00 0.00 3.33
1114 1142 3.512516 GGCAAGATCGTGCTGCCC 61.513 66.667 28.59 11.86 44.31 5.36
1565 1593 2.792290 CGCCAATCGACTCGTGCAG 61.792 63.158 0.00 0.00 41.67 4.41
1591 1619 6.676950 TGCAAACGAATGTGATCTTGTTTAT 58.323 32.000 0.00 0.00 0.00 1.40
1623 1651 6.690194 AAAATGGCATGTGATTAGAGACTC 57.310 37.500 0.00 0.00 0.00 3.36
1627 1655 5.423015 TGGCATGTGATTAGAGACTCTTTC 58.577 41.667 10.96 8.98 0.00 2.62
1658 1686 5.390885 CCGATTTGGTGCTGCATATATGTAC 60.391 44.000 14.14 8.33 0.00 2.90
1696 1728 4.489810 GAGCGGAGATCTTACATACATGG 58.510 47.826 0.00 0.00 41.28 3.66
1806 1838 2.926165 ACGACTGCTACGTTACAGAAC 58.074 47.619 20.49 13.54 41.18 3.01
2188 2257 5.972935 TGAATAGACGACCAAAGCATTAGA 58.027 37.500 0.00 0.00 0.00 2.10
2189 2258 6.403049 TGAATAGACGACCAAAGCATTAGAA 58.597 36.000 0.00 0.00 0.00 2.10
2190 2259 6.876789 TGAATAGACGACCAAAGCATTAGAAA 59.123 34.615 0.00 0.00 0.00 2.52
2191 2260 7.552687 TGAATAGACGACCAAAGCATTAGAAAT 59.447 33.333 0.00 0.00 0.00 2.17
2193 2262 5.245531 AGACGACCAAAGCATTAGAAATGA 58.754 37.500 3.86 0.00 0.00 2.57
2195 2264 5.883661 ACGACCAAAGCATTAGAAATGATG 58.116 37.500 3.86 0.17 0.00 3.07
2196 2265 5.163622 ACGACCAAAGCATTAGAAATGATGG 60.164 40.000 3.86 9.82 0.00 3.51
2197 2266 5.163622 CGACCAAAGCATTAGAAATGATGGT 60.164 40.000 17.58 17.58 35.67 3.55
2198 2267 6.212888 ACCAAAGCATTAGAAATGATGGTC 57.787 37.500 14.32 0.00 33.25 4.02
2199 2268 5.716228 ACCAAAGCATTAGAAATGATGGTCA 59.284 36.000 14.32 0.00 33.25 4.02
2202 2271 7.363181 CCAAAGCATTAGAAATGATGGTCAGAA 60.363 37.037 3.86 0.00 33.25 3.02
2203 2272 7.893124 AAGCATTAGAAATGATGGTCAGAAT 57.107 32.000 3.86 0.00 33.25 2.40
2204 2273 8.985315 AAGCATTAGAAATGATGGTCAGAATA 57.015 30.769 3.86 0.00 33.25 1.75
2205 2274 9.584008 AAGCATTAGAAATGATGGTCAGAATAT 57.416 29.630 3.86 0.00 33.25 1.28
2420 2491 1.932757 AGCCTCCATGGAGCCCTTT 60.933 57.895 32.97 14.48 40.69 3.11
2421 2492 1.755783 GCCTCCATGGAGCCCTTTG 60.756 63.158 32.97 20.21 40.69 2.77
2567 2641 9.474920 TGTTCACTATTTTCAAAATCACCAATC 57.525 29.630 0.00 0.00 0.00 2.67
2663 2740 7.857389 CCATATGATACTGTGGAATTTTGTTCG 59.143 37.037 3.65 0.00 33.53 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.953548 ACCCTTTTGATGATGACAATGATGA 59.046 36.000 0.00 0.00 0.00 2.92
79 80 2.721425 TTTTCGTCCTGGGTTTCACT 57.279 45.000 0.00 0.00 0.00 3.41
201 207 7.069331 CCATTTATTTGCCACTTACATCCCTAA 59.931 37.037 0.00 0.00 0.00 2.69
202 208 6.549364 CCATTTATTTGCCACTTACATCCCTA 59.451 38.462 0.00 0.00 0.00 3.53
203 209 5.363580 CCATTTATTTGCCACTTACATCCCT 59.636 40.000 0.00 0.00 0.00 4.20
204 210 5.600696 CCATTTATTTGCCACTTACATCCC 58.399 41.667 0.00 0.00 0.00 3.85
205 211 5.049828 GCCATTTATTTGCCACTTACATCC 58.950 41.667 0.00 0.00 0.00 3.51
206 212 4.739716 CGCCATTTATTTGCCACTTACATC 59.260 41.667 0.00 0.00 0.00 3.06
207 213 4.159506 ACGCCATTTATTTGCCACTTACAT 59.840 37.500 0.00 0.00 0.00 2.29
208 214 3.508012 ACGCCATTTATTTGCCACTTACA 59.492 39.130 0.00 0.00 0.00 2.41
209 215 4.102649 GACGCCATTTATTTGCCACTTAC 58.897 43.478 0.00 0.00 0.00 2.34
210 216 3.129638 GGACGCCATTTATTTGCCACTTA 59.870 43.478 0.00 0.00 0.00 2.24
211 217 2.094234 GGACGCCATTTATTTGCCACTT 60.094 45.455 0.00 0.00 0.00 3.16
212 218 1.476488 GGACGCCATTTATTTGCCACT 59.524 47.619 0.00 0.00 0.00 4.00
213 219 1.797348 CGGACGCCATTTATTTGCCAC 60.797 52.381 0.00 0.00 0.00 5.01
214 220 0.453793 CGGACGCCATTTATTTGCCA 59.546 50.000 0.00 0.00 0.00 4.92
215 221 0.869880 GCGGACGCCATTTATTTGCC 60.870 55.000 5.20 0.00 34.56 4.52
216 222 0.179150 TGCGGACGCCATTTATTTGC 60.179 50.000 14.61 0.00 41.09 3.68
217 223 2.270275 TTGCGGACGCCATTTATTTG 57.730 45.000 14.61 0.00 41.09 2.32
218 224 2.223711 GGATTGCGGACGCCATTTATTT 60.224 45.455 14.61 0.00 41.09 1.40
219 225 1.336755 GGATTGCGGACGCCATTTATT 59.663 47.619 14.61 0.00 41.09 1.40
220 226 0.951558 GGATTGCGGACGCCATTTAT 59.048 50.000 14.61 0.18 41.09 1.40
221 227 1.098712 GGGATTGCGGACGCCATTTA 61.099 55.000 14.61 0.00 41.09 1.40
222 228 2.414785 GGGATTGCGGACGCCATTT 61.415 57.895 14.61 0.00 41.09 2.32
223 229 2.828549 GGGATTGCGGACGCCATT 60.829 61.111 14.61 0.00 41.09 3.16
227 233 2.032185 CTAAACGGGATTGCGGACGC 62.032 60.000 10.13 10.13 42.35 5.19
228 234 0.738412 ACTAAACGGGATTGCGGACG 60.738 55.000 0.00 0.00 0.00 4.79
229 235 1.445871 AACTAAACGGGATTGCGGAC 58.554 50.000 0.00 0.00 0.00 4.79
230 236 2.234414 ACTAACTAAACGGGATTGCGGA 59.766 45.455 0.00 0.00 0.00 5.54
231 237 2.624636 ACTAACTAAACGGGATTGCGG 58.375 47.619 0.00 0.00 0.00 5.69
232 238 4.673534 AAACTAACTAAACGGGATTGCG 57.326 40.909 0.00 0.00 0.00 4.85
233 239 5.118050 GCAAAAACTAACTAAACGGGATTGC 59.882 40.000 0.00 0.00 0.00 3.56
234 240 6.443792 AGCAAAAACTAACTAAACGGGATTG 58.556 36.000 0.00 0.00 0.00 2.67
235 241 6.644248 AGCAAAAACTAACTAAACGGGATT 57.356 33.333 0.00 0.00 0.00 3.01
236 242 6.128090 GCTAGCAAAAACTAACTAAACGGGAT 60.128 38.462 10.63 0.00 0.00 3.85
237 243 5.179929 GCTAGCAAAAACTAACTAAACGGGA 59.820 40.000 10.63 0.00 0.00 5.14
238 244 5.180680 AGCTAGCAAAAACTAACTAAACGGG 59.819 40.000 18.83 0.00 0.00 5.28
239 245 6.237313 AGCTAGCAAAAACTAACTAAACGG 57.763 37.500 18.83 0.00 0.00 4.44
240 246 7.349711 TCAAGCTAGCAAAAACTAACTAAACG 58.650 34.615 18.83 0.00 0.00 3.60
243 249 9.720769 ACTATCAAGCTAGCAAAAACTAACTAA 57.279 29.630 18.83 0.00 0.00 2.24
244 250 9.720769 AACTATCAAGCTAGCAAAAACTAACTA 57.279 29.630 18.83 0.00 0.00 2.24
245 251 8.622948 AACTATCAAGCTAGCAAAAACTAACT 57.377 30.769 18.83 0.00 0.00 2.24
246 252 8.504005 TGAACTATCAAGCTAGCAAAAACTAAC 58.496 33.333 18.83 2.68 30.99 2.34
247 253 8.615878 TGAACTATCAAGCTAGCAAAAACTAA 57.384 30.769 18.83 0.00 30.99 2.24
248 254 8.792830 ATGAACTATCAAGCTAGCAAAAACTA 57.207 30.769 18.83 0.00 39.49 2.24
249 255 7.693969 ATGAACTATCAAGCTAGCAAAAACT 57.306 32.000 18.83 0.00 39.49 2.66
250 256 8.748380 AAATGAACTATCAAGCTAGCAAAAAC 57.252 30.769 18.83 0.00 39.49 2.43
251 257 9.762933 AAAAATGAACTATCAAGCTAGCAAAAA 57.237 25.926 18.83 0.00 39.49 1.94
252 258 9.410556 GAAAAATGAACTATCAAGCTAGCAAAA 57.589 29.630 18.83 1.00 39.49 2.44
253 259 8.796475 AGAAAAATGAACTATCAAGCTAGCAAA 58.204 29.630 18.83 1.41 39.49 3.68
254 260 8.340618 AGAAAAATGAACTATCAAGCTAGCAA 57.659 30.769 18.83 1.82 39.49 3.91
255 261 7.607607 TGAGAAAAATGAACTATCAAGCTAGCA 59.392 33.333 18.83 0.00 39.49 3.49
256 262 7.978982 TGAGAAAAATGAACTATCAAGCTAGC 58.021 34.615 6.62 6.62 39.49 3.42
259 265 8.632679 TGTTTGAGAAAAATGAACTATCAAGCT 58.367 29.630 0.00 0.00 39.49 3.74
260 266 8.801715 TGTTTGAGAAAAATGAACTATCAAGC 57.198 30.769 0.00 0.00 39.49 4.01
307 313 9.273016 CCGTTTAAAGTCCACTTATGATATGAT 57.727 33.333 0.00 0.00 34.61 2.45
308 314 7.713507 CCCGTTTAAAGTCCACTTATGATATGA 59.286 37.037 0.00 0.00 34.61 2.15
309 315 7.713507 TCCCGTTTAAAGTCCACTTATGATATG 59.286 37.037 0.00 0.00 34.61 1.78
310 316 7.798071 TCCCGTTTAAAGTCCACTTATGATAT 58.202 34.615 0.00 0.00 34.61 1.63
311 317 7.185318 TCCCGTTTAAAGTCCACTTATGATA 57.815 36.000 0.00 0.00 34.61 2.15
312 318 6.057321 TCCCGTTTAAAGTCCACTTATGAT 57.943 37.500 0.00 0.00 34.61 2.45
313 319 5.486735 TCCCGTTTAAAGTCCACTTATGA 57.513 39.130 0.00 0.00 34.61 2.15
314 320 6.753107 AATCCCGTTTAAAGTCCACTTATG 57.247 37.500 0.00 0.00 34.61 1.90
315 321 8.733458 GTTTAATCCCGTTTAAAGTCCACTTAT 58.267 33.333 0.00 0.00 34.61 1.73
316 322 7.095271 CGTTTAATCCCGTTTAAAGTCCACTTA 60.095 37.037 0.00 0.00 34.61 2.24
317 323 6.293571 CGTTTAATCCCGTTTAAAGTCCACTT 60.294 38.462 0.00 0.00 37.91 3.16
318 324 5.179929 CGTTTAATCCCGTTTAAAGTCCACT 59.820 40.000 0.00 0.00 33.07 4.00
319 325 5.384787 CGTTTAATCCCGTTTAAAGTCCAC 58.615 41.667 0.00 0.00 33.07 4.02
320 326 4.455190 CCGTTTAATCCCGTTTAAAGTCCA 59.545 41.667 0.00 0.00 33.07 4.02
321 327 4.142622 CCCGTTTAATCCCGTTTAAAGTCC 60.143 45.833 0.00 0.00 33.07 3.85
322 328 4.694982 TCCCGTTTAATCCCGTTTAAAGTC 59.305 41.667 0.00 0.00 33.07 3.01
323 329 4.455533 GTCCCGTTTAATCCCGTTTAAAGT 59.544 41.667 0.00 0.00 33.07 2.66
324 330 4.142622 GGTCCCGTTTAATCCCGTTTAAAG 60.143 45.833 0.00 0.00 33.07 1.85
325 331 3.755905 GGTCCCGTTTAATCCCGTTTAAA 59.244 43.478 0.00 0.00 0.00 1.52
326 332 3.342719 GGTCCCGTTTAATCCCGTTTAA 58.657 45.455 0.00 0.00 0.00 1.52
327 333 2.355615 GGGTCCCGTTTAATCCCGTTTA 60.356 50.000 0.00 0.00 0.00 2.01
328 334 1.614051 GGGTCCCGTTTAATCCCGTTT 60.614 52.381 0.00 0.00 0.00 3.60
329 335 0.035152 GGGTCCCGTTTAATCCCGTT 60.035 55.000 0.00 0.00 0.00 4.44
330 336 1.603842 GGGTCCCGTTTAATCCCGT 59.396 57.895 0.00 0.00 0.00 5.28
331 337 4.545929 GGGTCCCGTTTAATCCCG 57.454 61.111 0.00 0.00 0.00 5.14
332 338 4.545929 CGGGTCCCGTTTAATCCC 57.454 61.111 23.02 0.00 42.73 3.85
342 348 1.148498 GGGATGTCAATCGGGTCCC 59.852 63.158 0.00 0.00 41.55 4.46
343 349 0.106894 GAGGGATGTCAATCGGGTCC 59.893 60.000 0.00 0.00 33.18 4.46
344 350 0.106894 GGAGGGATGTCAATCGGGTC 59.893 60.000 0.00 0.00 33.18 4.46
345 351 0.620410 TGGAGGGATGTCAATCGGGT 60.620 55.000 0.00 0.00 33.18 5.28
346 352 0.546122 TTGGAGGGATGTCAATCGGG 59.454 55.000 0.00 0.00 33.18 5.14
347 353 1.065491 TGTTGGAGGGATGTCAATCGG 60.065 52.381 0.00 0.00 33.18 4.18
348 354 2.401583 TGTTGGAGGGATGTCAATCG 57.598 50.000 0.00 0.00 33.18 3.34
349 355 4.162040 AGATGTTGGAGGGATGTCAATC 57.838 45.455 0.00 0.00 0.00 2.67
350 356 5.512060 CGATAGATGTTGGAGGGATGTCAAT 60.512 44.000 0.00 0.00 39.76 2.57
351 357 4.202253 CGATAGATGTTGGAGGGATGTCAA 60.202 45.833 0.00 0.00 39.76 3.18
352 358 3.321968 CGATAGATGTTGGAGGGATGTCA 59.678 47.826 0.00 0.00 39.76 3.58
353 359 3.862642 GCGATAGATGTTGGAGGGATGTC 60.863 52.174 0.00 0.00 39.76 3.06
354 360 2.037772 GCGATAGATGTTGGAGGGATGT 59.962 50.000 0.00 0.00 39.76 3.06
355 361 2.613977 GGCGATAGATGTTGGAGGGATG 60.614 54.545 0.00 0.00 39.76 3.51
356 362 1.625818 GGCGATAGATGTTGGAGGGAT 59.374 52.381 0.00 0.00 39.76 3.85
357 363 1.048601 GGCGATAGATGTTGGAGGGA 58.951 55.000 0.00 0.00 39.76 4.20
358 364 0.758734 TGGCGATAGATGTTGGAGGG 59.241 55.000 0.00 0.00 39.76 4.30
359 365 1.875576 GCTGGCGATAGATGTTGGAGG 60.876 57.143 0.00 0.00 39.76 4.30
360 366 1.202568 TGCTGGCGATAGATGTTGGAG 60.203 52.381 0.00 0.00 39.76 3.86
361 367 0.829990 TGCTGGCGATAGATGTTGGA 59.170 50.000 0.00 0.00 39.76 3.53
362 368 1.331756 GTTGCTGGCGATAGATGTTGG 59.668 52.381 0.00 0.00 39.76 3.77
363 369 1.331756 GGTTGCTGGCGATAGATGTTG 59.668 52.381 0.00 0.00 39.76 3.33
364 370 1.668419 GGTTGCTGGCGATAGATGTT 58.332 50.000 0.00 0.00 39.76 2.71
365 371 0.530650 CGGTTGCTGGCGATAGATGT 60.531 55.000 0.00 0.00 39.76 3.06
366 372 1.835483 GCGGTTGCTGGCGATAGATG 61.835 60.000 0.00 0.00 38.39 2.90
367 373 1.595382 GCGGTTGCTGGCGATAGAT 60.595 57.895 0.00 0.00 38.39 1.98
396 402 5.140454 TCTTGATCTCATCCAACTATCGGA 58.860 41.667 0.00 0.00 36.84 4.55
405 411 4.706962 TCTTCGTCTTCTTGATCTCATCCA 59.293 41.667 0.00 0.00 0.00 3.41
585 594 1.152984 CAGTTGTGGCCACAGGACA 60.153 57.895 35.60 20.76 42.94 4.02
586 595 2.555547 GCAGTTGTGGCCACAGGAC 61.556 63.158 35.60 30.76 42.94 3.85
587 596 2.203337 GCAGTTGTGGCCACAGGA 60.203 61.111 35.60 21.92 42.94 3.86
588 597 2.079020 CTTGCAGTTGTGGCCACAGG 62.079 60.000 35.60 28.33 42.94 4.00
589 598 1.361271 CTTGCAGTTGTGGCCACAG 59.639 57.895 35.60 26.00 42.94 3.66
597 606 1.308047 TCGTTCATGCTTGCAGTTGT 58.692 45.000 0.87 0.00 0.00 3.32
628 638 2.607038 CGATCCACACGACTCACTTTCA 60.607 50.000 0.00 0.00 0.00 2.69
660 670 3.428316 GGAACAGAGATCTTCGGTCACTC 60.428 52.174 11.28 0.00 32.79 3.51
939 966 4.271816 CGTGGATCCGGCGAGAGG 62.272 72.222 19.81 0.00 0.00 3.69
1015 1042 3.957435 ATGTCGTCTGGCCGAGGGA 62.957 63.158 14.35 6.03 37.56 4.20
1026 1054 1.061131 CGAATTGTGGCTGATGTCGTC 59.939 52.381 0.00 0.00 0.00 4.20
1028 1056 0.247814 GCGAATTGTGGCTGATGTCG 60.248 55.000 0.00 0.00 0.00 4.35
1435 1463 2.125350 CTCAGGAACTCCGGCTGC 60.125 66.667 0.00 0.00 42.08 5.25
1477 1505 0.700564 TCTTCAAGCTGGGCTTCCAT 59.299 50.000 1.50 0.00 46.77 3.41
1565 1593 2.907910 AGATCACATTCGTTTGCAGC 57.092 45.000 0.00 0.00 0.00 5.25
1658 1686 3.814842 TCCGCTCTTTTGCCATGTATATG 59.185 43.478 0.00 0.00 0.00 1.78
2190 2259 8.735315 CGAGTTCTACTATATTCTGACCATCAT 58.265 37.037 0.00 0.00 0.00 2.45
2191 2260 7.937394 TCGAGTTCTACTATATTCTGACCATCA 59.063 37.037 0.00 0.00 0.00 3.07
2193 2262 8.693120 TTCGAGTTCTACTATATTCTGACCAT 57.307 34.615 0.00 0.00 0.00 3.55
2510 2581 5.277779 GCACACACTCTGCACTATAAAAACA 60.278 40.000 0.00 0.00 34.56 2.83
2578 2652 1.530720 CATTGACACGCAAGCTACACA 59.469 47.619 0.00 0.00 40.42 3.72
2587 2661 5.411053 TCATGAAGAAATACATTGACACGCA 59.589 36.000 0.00 0.00 0.00 5.24
2634 2708 9.425248 ACAAAATTCCACAGTATCATATGGATT 57.575 29.630 2.13 0.00 40.87 3.01
2639 2713 7.556275 ACCGAACAAAATTCCACAGTATCATAT 59.444 33.333 0.00 0.00 0.00 1.78
2659 2736 8.973378 TGATTCAATGTTTCAAAAATACCGAAC 58.027 29.630 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.