Multiple sequence alignment - TraesCS2B01G301900

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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 TraesCS2B01G301900 chr2B 100.000 2192 0 0 1 2192 425354423 425352232 0.000000e+00 4048.0
1 TraesCS2B01G301900 chr2B 85.691 1223 149 16 964 2177 57664587 57665792 0.000000e+00 1266.0
2 TraesCS2B01G301900 chr2B 84.272 1208 172 15 964 2166 57672640 57673834 0.000000e+00 1162.0
3 TraesCS2B01G301900 chr2D 95.727 1568 34 11 640 2192 357702136 357700587 0.000000e+00 2494.0
4 TraesCS2B01G301900 chr2D 85.364 1223 153 16 964 2177 34988082 34989287 0.000000e+00 1243.0
5 TraesCS2B01G301900 chr2D 84.578 1219 168 18 964 2177 585517380 585516177 0.000000e+00 1192.0
6 TraesCS2B01G301900 chr2D 84.483 1218 169 17 966 2177 585477114 585475911 0.000000e+00 1184.0
7 TraesCS2B01G301900 chr2D 84.507 1207 171 13 964 2166 34994837 34996031 0.000000e+00 1179.0
8 TraesCS2B01G301900 chr2D 89.870 385 11 8 2 366 357702940 357702564 9.160000e-129 470.0
9 TraesCS2B01G301900 chr2D 91.228 57 5 0 381 437 617129239 617129295 6.490000e-11 78.7
10 TraesCS2B01G301900 chr2A 95.272 1565 39 9 640 2192 478763125 478761584 0.000000e+00 2447.0
11 TraesCS2B01G301900 chr2A 85.655 1213 149 15 973 2177 38309367 38310562 0.000000e+00 1253.0
12 TraesCS2B01G301900 chr2A 91.270 378 15 9 2 366 478763742 478763370 1.170000e-137 499.0
13 TraesCS2B01G301900 chr2A 90.909 132 6 3 448 577 478763349 478763222 2.890000e-39 172.0
14 TraesCS2B01G301900 chr1B 92.857 56 3 1 381 436 8670148 8670202 1.800000e-11 80.5
15 TraesCS2B01G301900 chr1B 89.655 58 5 1 377 433 488821876 488821933 3.020000e-09 73.1
16 TraesCS2B01G301900 chr4B 95.833 48 2 0 378 425 630972735 630972782 6.490000e-11 78.7
17 TraesCS2B01G301900 chr7B 95.745 47 2 0 378 424 731191086 731191040 2.330000e-10 76.8
18 TraesCS2B01G301900 chr5B 95.652 46 2 0 381 426 657588996 657589041 8.390000e-10 75.0
19 TraesCS2B01G301900 chr4A 91.228 57 2 3 374 430 667343313 667343366 8.390000e-10 75.0
20 TraesCS2B01G301900 chr6B 93.750 48 3 0 378 425 668960268 668960221 3.020000e-09 73.1
21 TraesCS2B01G301900 chr5A 92.157 51 2 2 378 427 653056617 653056666 1.090000e-08 71.3


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 TraesCS2B01G301900 chr2B 425352232 425354423 2191 True 4048.000000 4048 100.000000 1 2192 1 chr2B.!!$R1 2191
1 TraesCS2B01G301900 chr2B 57664587 57665792 1205 False 1266.000000 1266 85.691000 964 2177 1 chr2B.!!$F1 1213
2 TraesCS2B01G301900 chr2B 57672640 57673834 1194 False 1162.000000 1162 84.272000 964 2166 1 chr2B.!!$F2 1202
3 TraesCS2B01G301900 chr2D 357700587 357702940 2353 True 1482.000000 2494 92.798500 2 2192 2 chr2D.!!$R3 2190
4 TraesCS2B01G301900 chr2D 34988082 34989287 1205 False 1243.000000 1243 85.364000 964 2177 1 chr2D.!!$F1 1213
5 TraesCS2B01G301900 chr2D 585516177 585517380 1203 True 1192.000000 1192 84.578000 964 2177 1 chr2D.!!$R2 1213
6 TraesCS2B01G301900 chr2D 585475911 585477114 1203 True 1184.000000 1184 84.483000 966 2177 1 chr2D.!!$R1 1211
7 TraesCS2B01G301900 chr2D 34994837 34996031 1194 False 1179.000000 1179 84.507000 964 2166 1 chr2D.!!$F2 1202
8 TraesCS2B01G301900 chr2A 38309367 38310562 1195 False 1253.000000 1253 85.655000 973 2177 1 chr2A.!!$F1 1204
9 TraesCS2B01G301900 chr2A 478761584 478763742 2158 True 1039.333333 2447 92.483667 2 2192 3 chr2A.!!$R1 2190

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
541 572 0.374758 CCACAATTCGAGCCATCACG 59.625 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1410 1740 1.804748 CTTTACTGGACGGCCTTTGAC 59.195 52.381 9.82 0.0 34.31 3.18 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
230 255 3.730061 GCTGTTCGCATTCTCATTTGGAG 60.730 47.826 0.00 0.00 40.98 3.86
245 270 7.013274 TCTCATTTGGAGTTTTTGGAACTACTG 59.987 37.037 3.11 0.00 44.40 2.74
246 271 6.605594 TCATTTGGAGTTTTTGGAACTACTGT 59.394 34.615 3.11 0.00 32.34 3.55
247 272 7.776030 TCATTTGGAGTTTTTGGAACTACTGTA 59.224 33.333 3.11 0.00 32.34 2.74
248 273 8.576442 CATTTGGAGTTTTTGGAACTACTGTAT 58.424 33.333 3.11 0.00 32.34 2.29
249 274 8.528044 TTTGGAGTTTTTGGAACTACTGTATT 57.472 30.769 3.11 0.00 32.34 1.89
251 276 8.161699 TGGAGTTTTTGGAACTACTGTATTTC 57.838 34.615 8.85 8.85 32.34 2.17
253 278 8.504815 GGAGTTTTTGGAACTACTGTATTTCTC 58.495 37.037 14.89 8.02 0.00 2.87
255 280 7.713942 AGTTTTTGGAACTACTGTATTTCTCGT 59.286 33.333 14.89 0.00 0.00 4.18
256 281 7.416154 TTTTGGAACTACTGTATTTCTCGTG 57.584 36.000 14.89 0.00 0.00 4.35
257 282 5.717078 TGGAACTACTGTATTTCTCGTGT 57.283 39.130 14.89 0.00 0.00 4.49
272 297 3.057734 CTCGTGTAAGTCAAAGTGGACC 58.942 50.000 0.00 0.00 38.59 4.46
285 310 2.467880 AGTGGACCCGTGATCTGTATT 58.532 47.619 0.00 0.00 0.00 1.89
366 393 5.181245 GGTTGGCATCAGCAATTACGTATAT 59.819 40.000 0.00 0.00 44.61 0.86
367 394 6.370442 GGTTGGCATCAGCAATTACGTATATA 59.630 38.462 0.00 0.00 44.61 0.86
368 395 6.961359 TGGCATCAGCAATTACGTATATAC 57.039 37.500 2.53 2.53 44.61 1.47
369 396 6.697395 TGGCATCAGCAATTACGTATATACT 58.303 36.000 11.05 1.45 44.61 2.12
370 397 6.811665 TGGCATCAGCAATTACGTATATACTC 59.188 38.462 11.05 0.00 44.61 2.59
371 398 6.255887 GGCATCAGCAATTACGTATATACTCC 59.744 42.308 11.05 0.00 44.61 3.85
372 399 6.255887 GCATCAGCAATTACGTATATACTCCC 59.744 42.308 11.05 0.00 41.58 4.30
373 400 7.548097 CATCAGCAATTACGTATATACTCCCT 58.452 38.462 11.05 0.00 0.00 4.20
374 401 7.154435 TCAGCAATTACGTATATACTCCCTC 57.846 40.000 11.05 0.00 0.00 4.30
375 402 6.152323 TCAGCAATTACGTATATACTCCCTCC 59.848 42.308 11.05 0.00 0.00 4.30
376 403 5.125097 AGCAATTACGTATATACTCCCTCCG 59.875 44.000 11.05 0.00 0.00 4.63
377 404 5.338365 CAATTACGTATATACTCCCTCCGC 58.662 45.833 11.05 0.00 0.00 5.54
378 405 1.831580 ACGTATATACTCCCTCCGCC 58.168 55.000 11.05 0.00 0.00 6.13
379 406 1.074405 ACGTATATACTCCCTCCGCCA 59.926 52.381 11.05 0.00 0.00 5.69
380 407 2.291411 ACGTATATACTCCCTCCGCCAT 60.291 50.000 11.05 0.00 0.00 4.40
381 408 2.758979 CGTATATACTCCCTCCGCCATT 59.241 50.000 11.05 0.00 0.00 3.16
382 409 3.194968 CGTATATACTCCCTCCGCCATTT 59.805 47.826 11.05 0.00 0.00 2.32
383 410 4.322499 CGTATATACTCCCTCCGCCATTTT 60.322 45.833 11.05 0.00 0.00 1.82
384 411 2.640316 ATACTCCCTCCGCCATTTTC 57.360 50.000 0.00 0.00 0.00 2.29
385 412 1.281419 TACTCCCTCCGCCATTTTCA 58.719 50.000 0.00 0.00 0.00 2.69
386 413 0.625849 ACTCCCTCCGCCATTTTCAT 59.374 50.000 0.00 0.00 0.00 2.57
387 414 1.312815 CTCCCTCCGCCATTTTCATC 58.687 55.000 0.00 0.00 0.00 2.92
388 415 0.918983 TCCCTCCGCCATTTTCATCT 59.081 50.000 0.00 0.00 0.00 2.90
389 416 2.104792 CTCCCTCCGCCATTTTCATCTA 59.895 50.000 0.00 0.00 0.00 1.98
390 417 2.711009 TCCCTCCGCCATTTTCATCTAT 59.289 45.455 0.00 0.00 0.00 1.98
391 418 3.138283 TCCCTCCGCCATTTTCATCTATT 59.862 43.478 0.00 0.00 0.00 1.73
392 419 3.891366 CCCTCCGCCATTTTCATCTATTT 59.109 43.478 0.00 0.00 0.00 1.40
393 420 4.342092 CCCTCCGCCATTTTCATCTATTTT 59.658 41.667 0.00 0.00 0.00 1.82
394 421 5.534654 CCCTCCGCCATTTTCATCTATTTTA 59.465 40.000 0.00 0.00 0.00 1.52
395 422 6.040391 CCCTCCGCCATTTTCATCTATTTTAA 59.960 38.462 0.00 0.00 0.00 1.52
396 423 7.255942 CCCTCCGCCATTTTCATCTATTTTAAT 60.256 37.037 0.00 0.00 0.00 1.40
397 424 7.596248 CCTCCGCCATTTTCATCTATTTTAATG 59.404 37.037 0.00 0.00 0.00 1.90
398 425 8.231692 TCCGCCATTTTCATCTATTTTAATGA 57.768 30.769 0.00 0.00 0.00 2.57
399 426 8.134895 TCCGCCATTTTCATCTATTTTAATGAC 58.865 33.333 0.00 0.00 31.83 3.06
400 427 7.920151 CCGCCATTTTCATCTATTTTAATGACA 59.080 33.333 0.00 0.00 31.83 3.58
401 428 9.299963 CGCCATTTTCATCTATTTTAATGACAA 57.700 29.630 0.00 0.00 31.83 3.18
415 442 8.716619 TTTTAATGACAAGTATTTTCGAACGG 57.283 30.769 0.00 0.00 0.00 4.44
416 443 7.655236 TTAATGACAAGTATTTTCGAACGGA 57.345 32.000 0.00 0.00 0.00 4.69
417 444 5.779806 ATGACAAGTATTTTCGAACGGAG 57.220 39.130 0.00 0.00 0.00 4.63
418 445 3.991773 TGACAAGTATTTTCGAACGGAGG 59.008 43.478 0.00 0.00 0.00 4.30
419 446 3.332034 ACAAGTATTTTCGAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
420 447 3.007182 ACAAGTATTTTCGAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
421 448 3.521947 AGTATTTTCGAACGGAGGGAG 57.478 47.619 0.00 0.00 0.00 4.30
422 449 2.830321 AGTATTTTCGAACGGAGGGAGT 59.170 45.455 0.00 0.00 0.00 3.85
423 450 4.019174 AGTATTTTCGAACGGAGGGAGTA 58.981 43.478 0.00 0.00 0.00 2.59
439 470 7.381678 CGGAGGGAGTACTTTATTAAGAAATCG 59.618 40.741 0.00 0.00 35.30 3.34
449 480 9.214957 ACTTTATTAAGAAATCGTCACATGTCA 57.785 29.630 0.00 0.00 35.30 3.58
450 481 9.478019 CTTTATTAAGAAATCGTCACATGTCAC 57.522 33.333 0.00 0.00 32.92 3.67
451 482 8.541133 TTATTAAGAAATCGTCACATGTCACA 57.459 30.769 0.00 0.00 0.00 3.58
468 499 4.260170 GTCACATCTCTTGGAAGATTGCT 58.740 43.478 0.00 0.00 33.68 3.91
470 501 3.015327 ACATCTCTTGGAAGATTGCTGC 58.985 45.455 0.00 0.00 33.68 5.25
471 502 2.865119 TCTCTTGGAAGATTGCTGCA 57.135 45.000 0.00 0.00 33.93 4.41
472 503 2.708051 TCTCTTGGAAGATTGCTGCAG 58.292 47.619 10.11 10.11 33.93 4.41
473 504 2.039480 TCTCTTGGAAGATTGCTGCAGT 59.961 45.455 16.64 0.00 33.93 4.40
474 505 2.419324 CTCTTGGAAGATTGCTGCAGTC 59.581 50.000 16.64 16.35 33.93 3.51
475 506 2.039480 TCTTGGAAGATTGCTGCAGTCT 59.961 45.455 20.31 20.31 31.85 3.24
485 516 4.389890 TTGCTGCAGTCTTTGTTCAAAT 57.610 36.364 16.64 0.00 0.00 2.32
511 542 7.222611 TGACGGTGTTAGTACTAAAGTTTGTTC 59.777 37.037 16.82 8.43 0.00 3.18
533 564 2.228582 TCAAATGTGCCCACAATTCGAG 59.771 45.455 5.08 0.00 45.41 4.04
541 572 0.374758 CCACAATTCGAGCCATCACG 59.625 55.000 0.00 0.00 0.00 4.35
548 581 0.952280 TCGAGCCATCACGAGATACC 59.048 55.000 0.00 0.00 34.49 2.73
593 627 6.574350 AGCTTTGATCACTATACTGTGTACC 58.426 40.000 0.00 0.00 38.90 3.34
599 633 7.544622 TGATCACTATACTGTGTACCAACTTC 58.455 38.462 0.00 0.00 38.90 3.01
600 634 5.946298 TCACTATACTGTGTACCAACTTCG 58.054 41.667 0.00 0.00 38.90 3.79
601 635 5.706833 TCACTATACTGTGTACCAACTTCGA 59.293 40.000 0.00 0.00 38.90 3.71
617 651 1.513373 CGAGATTCGTCGGCGTCAA 60.513 57.895 10.18 0.00 39.49 3.18
725 1038 1.493772 CGCCCAAGCATATGCAATTG 58.506 50.000 28.62 22.80 45.16 2.32
747 1060 4.796231 AGAGCCGTACCGCGCAAG 62.796 66.667 8.75 0.00 39.71 4.01
761 1074 1.558741 CGCAAGCAAGCAAAAAGTGA 58.441 45.000 1.32 0.00 0.00 3.41
762 1075 1.925847 CGCAAGCAAGCAAAAAGTGAA 59.074 42.857 1.32 0.00 0.00 3.18
763 1076 2.348059 CGCAAGCAAGCAAAAAGTGAAA 59.652 40.909 1.32 0.00 0.00 2.69
773 1086 5.965922 AGCAAAAAGTGAAAACACTAGCTT 58.034 33.333 0.00 0.00 34.56 3.74
860 1177 6.199908 GTCGAGATATCAACAGAATGAACAGG 59.800 42.308 5.32 0.00 39.69 4.00
875 1192 1.467920 ACAGGGCTGCTGCTATTTTC 58.532 50.000 15.64 0.00 39.59 2.29
937 1258 3.865745 CACGATGCGGTTCTCTTCTATTT 59.134 43.478 0.00 0.00 0.00 1.40
938 1259 3.865745 ACGATGCGGTTCTCTTCTATTTG 59.134 43.478 0.00 0.00 0.00 2.32
939 1260 3.865745 CGATGCGGTTCTCTTCTATTTGT 59.134 43.478 0.00 0.00 0.00 2.83
941 1262 3.334691 TGCGGTTCTCTTCTATTTGTGG 58.665 45.455 0.00 0.00 0.00 4.17
942 1263 2.096013 GCGGTTCTCTTCTATTTGTGGC 59.904 50.000 0.00 0.00 0.00 5.01
943 1264 3.334691 CGGTTCTCTTCTATTTGTGGCA 58.665 45.455 0.00 0.00 0.00 4.92
944 1265 3.941483 CGGTTCTCTTCTATTTGTGGCAT 59.059 43.478 0.00 0.00 0.00 4.40
1410 1740 1.116308 TGCCATCAGGATTGCCAATG 58.884 50.000 0.00 0.00 36.89 2.82
1434 1764 1.745489 GGCCGTCCAGTAAAGCCAG 60.745 63.158 0.00 0.00 43.32 4.85
1860 2190 7.365295 GGAGGGATACTGTCCTTTACAAATACA 60.365 40.741 0.00 0.00 46.91 2.29
1945 2275 4.202020 ACATGAACAAGATGAGATGCATGC 60.202 41.667 11.82 11.82 37.34 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 181 2.987125 GCCACCACGTCATACCCT 59.013 61.111 0.00 0.00 0.00 4.34
230 255 7.797123 CACGAGAAATACAGTAGTTCCAAAAAC 59.203 37.037 15.56 2.76 33.56 2.43
245 270 6.643770 TCCACTTTGACTTACACGAGAAATAC 59.356 38.462 0.00 0.00 0.00 1.89
246 271 6.643770 GTCCACTTTGACTTACACGAGAAATA 59.356 38.462 0.00 0.00 32.39 1.40
247 272 5.465724 GTCCACTTTGACTTACACGAGAAAT 59.534 40.000 0.00 0.00 32.39 2.17
248 273 4.807304 GTCCACTTTGACTTACACGAGAAA 59.193 41.667 0.00 0.00 32.39 2.52
249 274 4.365723 GTCCACTTTGACTTACACGAGAA 58.634 43.478 0.00 0.00 32.39 2.87
251 276 3.057734 GGTCCACTTTGACTTACACGAG 58.942 50.000 0.00 0.00 35.54 4.18
253 278 2.140717 GGGTCCACTTTGACTTACACG 58.859 52.381 0.00 0.00 35.54 4.49
255 280 1.764134 ACGGGTCCACTTTGACTTACA 59.236 47.619 0.00 0.00 35.54 2.41
256 281 2.140717 CACGGGTCCACTTTGACTTAC 58.859 52.381 0.00 0.00 35.54 2.34
257 282 2.040939 TCACGGGTCCACTTTGACTTA 58.959 47.619 0.00 0.00 35.54 2.24
272 297 3.525537 AGTTGAGCAATACAGATCACGG 58.474 45.455 0.00 0.00 33.03 4.94
285 310 2.872245 GTGCAGTTGACTTAGTTGAGCA 59.128 45.455 0.00 0.00 0.00 4.26
366 393 1.281419 TGAAAATGGCGGAGGGAGTA 58.719 50.000 0.00 0.00 0.00 2.59
367 394 0.625849 ATGAAAATGGCGGAGGGAGT 59.374 50.000 0.00 0.00 0.00 3.85
368 395 1.133976 AGATGAAAATGGCGGAGGGAG 60.134 52.381 0.00 0.00 0.00 4.30
369 396 0.918983 AGATGAAAATGGCGGAGGGA 59.081 50.000 0.00 0.00 0.00 4.20
370 397 2.638480 TAGATGAAAATGGCGGAGGG 57.362 50.000 0.00 0.00 0.00 4.30
371 398 5.520376 AAAATAGATGAAAATGGCGGAGG 57.480 39.130 0.00 0.00 0.00 4.30
372 399 8.352201 TCATTAAAATAGATGAAAATGGCGGAG 58.648 33.333 0.00 0.00 29.82 4.63
373 400 8.134895 GTCATTAAAATAGATGAAAATGGCGGA 58.865 33.333 0.00 0.00 34.34 5.54
374 401 7.920151 TGTCATTAAAATAGATGAAAATGGCGG 59.080 33.333 0.00 0.00 34.34 6.13
375 402 8.854979 TGTCATTAAAATAGATGAAAATGGCG 57.145 30.769 0.00 0.00 34.34 5.69
389 416 9.337091 CCGTTCGAAAATACTTGTCATTAAAAT 57.663 29.630 0.00 0.00 0.00 1.82
390 417 8.557864 TCCGTTCGAAAATACTTGTCATTAAAA 58.442 29.630 0.00 0.00 0.00 1.52
391 418 8.085720 TCCGTTCGAAAATACTTGTCATTAAA 57.914 30.769 0.00 0.00 0.00 1.52
392 419 7.148540 CCTCCGTTCGAAAATACTTGTCATTAA 60.149 37.037 0.00 0.00 0.00 1.40
393 420 6.311935 CCTCCGTTCGAAAATACTTGTCATTA 59.688 38.462 0.00 0.00 0.00 1.90
394 421 5.121768 CCTCCGTTCGAAAATACTTGTCATT 59.878 40.000 0.00 0.00 0.00 2.57
395 422 4.630069 CCTCCGTTCGAAAATACTTGTCAT 59.370 41.667 0.00 0.00 0.00 3.06
396 423 3.991773 CCTCCGTTCGAAAATACTTGTCA 59.008 43.478 0.00 0.00 0.00 3.58
397 424 3.370061 CCCTCCGTTCGAAAATACTTGTC 59.630 47.826 0.00 0.00 0.00 3.18
398 425 3.007182 TCCCTCCGTTCGAAAATACTTGT 59.993 43.478 0.00 0.00 0.00 3.16
399 426 3.592059 TCCCTCCGTTCGAAAATACTTG 58.408 45.455 0.00 0.00 0.00 3.16
400 427 3.260128 ACTCCCTCCGTTCGAAAATACTT 59.740 43.478 0.00 0.00 0.00 2.24
401 428 2.830321 ACTCCCTCCGTTCGAAAATACT 59.170 45.455 0.00 0.00 0.00 2.12
402 429 3.242549 ACTCCCTCCGTTCGAAAATAC 57.757 47.619 0.00 0.00 0.00 1.89
403 430 4.019174 AGTACTCCCTCCGTTCGAAAATA 58.981 43.478 0.00 0.00 0.00 1.40
404 431 2.830321 AGTACTCCCTCCGTTCGAAAAT 59.170 45.455 0.00 0.00 0.00 1.82
405 432 2.242043 AGTACTCCCTCCGTTCGAAAA 58.758 47.619 0.00 0.00 0.00 2.29
406 433 1.915141 AGTACTCCCTCCGTTCGAAA 58.085 50.000 0.00 0.00 0.00 3.46
407 434 1.915141 AAGTACTCCCTCCGTTCGAA 58.085 50.000 0.00 0.00 0.00 3.71
408 435 1.915141 AAAGTACTCCCTCCGTTCGA 58.085 50.000 0.00 0.00 0.00 3.71
409 436 4.382345 AATAAAGTACTCCCTCCGTTCG 57.618 45.455 0.00 0.00 0.00 3.95
410 437 7.105241 TCTTAATAAAGTACTCCCTCCGTTC 57.895 40.000 0.00 0.00 34.13 3.95
411 438 7.486407 TTCTTAATAAAGTACTCCCTCCGTT 57.514 36.000 0.00 0.00 34.13 4.44
412 439 7.486407 TTTCTTAATAAAGTACTCCCTCCGT 57.514 36.000 0.00 0.00 34.13 4.69
413 440 7.381678 CGATTTCTTAATAAAGTACTCCCTCCG 59.618 40.741 0.00 0.00 34.13 4.63
414 441 8.202811 ACGATTTCTTAATAAAGTACTCCCTCC 58.797 37.037 0.00 0.00 34.13 4.30
415 442 9.247126 GACGATTTCTTAATAAAGTACTCCCTC 57.753 37.037 0.00 0.00 34.13 4.30
416 443 8.755977 TGACGATTTCTTAATAAAGTACTCCCT 58.244 33.333 0.00 0.00 34.13 4.20
417 444 8.815189 GTGACGATTTCTTAATAAAGTACTCCC 58.185 37.037 0.00 0.00 34.13 4.30
418 445 9.362539 TGTGACGATTTCTTAATAAAGTACTCC 57.637 33.333 0.00 0.00 34.13 3.85
423 450 9.214957 TGACATGTGACGATTTCTTAATAAAGT 57.785 29.630 1.15 0.00 34.13 2.66
439 470 3.930336 TCCAAGAGATGTGACATGTGAC 58.070 45.455 8.67 8.67 0.00 3.67
445 476 4.005650 GCAATCTTCCAAGAGATGTGACA 58.994 43.478 0.00 0.00 38.66 3.58
447 478 4.259356 CAGCAATCTTCCAAGAGATGTGA 58.741 43.478 0.00 0.00 38.66 3.58
448 479 3.181499 GCAGCAATCTTCCAAGAGATGTG 60.181 47.826 0.00 1.23 38.66 3.21
449 480 3.015327 GCAGCAATCTTCCAAGAGATGT 58.985 45.455 0.00 0.00 38.66 3.06
450 481 3.014623 TGCAGCAATCTTCCAAGAGATG 58.985 45.455 0.00 0.00 38.66 2.90
451 482 3.280295 CTGCAGCAATCTTCCAAGAGAT 58.720 45.455 0.00 0.00 38.66 2.75
468 499 3.243035 CCGTCATTTGAACAAAGACTGCA 60.243 43.478 17.94 0.00 33.32 4.41
470 501 4.201910 ACACCGTCATTTGAACAAAGACTG 60.202 41.667 17.94 15.68 33.32 3.51
471 502 3.945285 ACACCGTCATTTGAACAAAGACT 59.055 39.130 17.94 6.86 33.32 3.24
472 503 4.287238 ACACCGTCATTTGAACAAAGAC 57.713 40.909 6.18 10.98 33.32 3.01
473 504 4.974368 AACACCGTCATTTGAACAAAGA 57.026 36.364 6.18 2.01 33.32 2.52
474 505 5.816919 ACTAACACCGTCATTTGAACAAAG 58.183 37.500 6.18 0.00 33.32 2.77
475 506 5.821516 ACTAACACCGTCATTTGAACAAA 57.178 34.783 2.48 2.48 34.46 2.83
485 516 6.572519 ACAAACTTTAGTACTAACACCGTCA 58.427 36.000 14.96 0.00 0.00 4.35
511 542 2.228582 TCGAATTGTGGGCACATTTGAG 59.771 45.455 0.00 0.00 41.52 3.02
533 564 2.906354 AGTTTGGTATCTCGTGATGGC 58.094 47.619 10.16 3.30 34.32 4.40
541 572 7.805071 CACACATTTGAAGAAGTTTGGTATCTC 59.195 37.037 0.00 0.00 0.00 2.75
548 581 4.741676 GCTCCACACATTTGAAGAAGTTTG 59.258 41.667 0.00 0.00 0.00 2.93
593 627 0.640768 GCCGACGAATCTCGAAGTTG 59.359 55.000 2.59 0.00 43.74 3.16
599 633 0.866061 ATTGACGCCGACGAATCTCG 60.866 55.000 0.00 0.00 46.93 4.04
600 634 1.278238 AATTGACGCCGACGAATCTC 58.722 50.000 0.00 0.00 43.93 2.75
601 635 1.722011 AAATTGACGCCGACGAATCT 58.278 45.000 0.00 0.00 43.93 2.40
617 651 7.361799 GGAAAACTAAATCTCACACGCCTAAAT 60.362 37.037 0.00 0.00 0.00 1.40
758 1071 4.912187 GCTTGCTTAAGCTAGTGTTTTCAC 59.088 41.667 30.58 14.18 43.92 3.18
759 1072 4.578516 TGCTTGCTTAAGCTAGTGTTTTCA 59.421 37.500 30.58 19.93 45.66 2.69
760 1073 5.108385 TGCTTGCTTAAGCTAGTGTTTTC 57.892 39.130 30.58 18.08 45.66 2.29
761 1074 5.514274 TTGCTTGCTTAAGCTAGTGTTTT 57.486 34.783 30.58 0.00 45.66 2.43
762 1075 5.514274 TTTGCTTGCTTAAGCTAGTGTTT 57.486 34.783 30.58 0.00 45.66 2.83
763 1076 5.514274 TTTTGCTTGCTTAAGCTAGTGTT 57.486 34.783 30.58 0.00 45.66 3.32
773 1086 5.006552 GCAGTTTTCACATTTTGCTTGCTTA 59.993 36.000 0.00 0.00 0.00 3.09
825 1140 3.643237 TGATATCTCGACCCCTCTGTTT 58.357 45.455 3.98 0.00 0.00 2.83
860 1177 1.064783 GGCGAAAATAGCAGCAGCC 59.935 57.895 0.00 0.00 43.56 4.85
875 1192 1.071502 CGTGTAAATCATACTGCGGCG 60.072 52.381 0.51 0.51 0.00 6.46
937 1258 2.025981 AGCTAGAATGTTGGATGCCACA 60.026 45.455 0.00 0.00 30.78 4.17
938 1259 2.648059 AGCTAGAATGTTGGATGCCAC 58.352 47.619 0.00 0.00 30.78 5.01
939 1260 3.199727 TGTAGCTAGAATGTTGGATGCCA 59.800 43.478 0.00 0.00 0.00 4.92
941 1262 4.446371 ACTGTAGCTAGAATGTTGGATGC 58.554 43.478 0.00 0.00 0.00 3.91
942 1263 5.911752 AGACTGTAGCTAGAATGTTGGATG 58.088 41.667 0.00 0.00 0.00 3.51
943 1264 7.847711 ATAGACTGTAGCTAGAATGTTGGAT 57.152 36.000 0.00 0.00 0.00 3.41
944 1265 7.661536 AATAGACTGTAGCTAGAATGTTGGA 57.338 36.000 0.00 0.00 0.00 3.53
1410 1740 1.804748 CTTTACTGGACGGCCTTTGAC 59.195 52.381 9.82 0.00 34.31 3.18
1434 1764 2.027745 TGTCATTGCTCCTCTCACCTTC 60.028 50.000 0.00 0.00 0.00 3.46
1945 2275 4.323028 CCAGGCTACCAGTATATCACATGG 60.323 50.000 0.00 0.00 38.83 3.66


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

AutoCloner maintained by Alex Coulton.