Multiple sequence alignment - TraesCS4D01G039600

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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 TraesCS4D01G039600 chr4D 100.000 2606 0 0 1 2606 16923769 16926374 0.000000e+00 4813.0
1 TraesCS4D01G039600 chr4D 94.355 124 7 0 285 408 108906370 108906247 9.520000e-45 191.0
2 TraesCS4D01G039600 chr4D 92.969 128 9 0 284 411 337136098 337135971 1.230000e-43 187.0
3 TraesCS4D01G039600 chr4D 92.366 131 9 1 285 415 120692546 120692675 4.430000e-43 185.0
4 TraesCS4D01G039600 chr4B 92.216 1336 59 23 1285 2606 28963337 28964641 0.000000e+00 1849.0
5 TraesCS4D01G039600 chr4B 85.888 659 37 14 633 1288 28961432 28962037 0.000000e+00 651.0
6 TraesCS4D01G039600 chr4B 92.126 254 12 5 1 246 28960145 28960398 4.130000e-93 351.0
7 TraesCS4D01G039600 chr4B 88.073 218 19 4 410 621 28960484 28960700 4.310000e-63 252.0
8 TraesCS4D01G039600 chr4B 78.878 303 54 9 2304 2603 387496840 387497135 2.050000e-46 196.0
9 TraesCS4D01G039600 chr4A 94.699 830 36 7 1779 2606 583524095 583523272 0.000000e+00 1282.0
10 TraesCS4D01G039600 chr4A 91.061 839 32 9 985 1792 583524938 583524112 0.000000e+00 1094.0
11 TraesCS4D01G039600 chr4A 91.860 516 37 5 415 926 583525473 583524959 0.000000e+00 715.0
12 TraesCS4D01G039600 chr4A 90.970 299 11 5 3 285 583525776 583525478 3.150000e-104 388.0
13 TraesCS4D01G039600 chr4A 97.297 37 1 0 1785 1821 583524206 583524170 2.170000e-06 63.9
14 TraesCS4D01G039600 chr3D 94.326 141 7 1 285 424 160615860 160616000 5.650000e-52 215.0
15 TraesCS4D01G039600 chr3D 95.276 127 6 0 285 411 588697587 588697461 4.400000e-48 202.0
16 TraesCS4D01G039600 chr6D 95.312 128 6 0 285 412 109243519 109243646 1.220000e-48 204.0
17 TraesCS4D01G039600 chr1D 94.531 128 7 0 285 412 465522128 465522001 5.690000e-47 198.0
18 TraesCS4D01G039600 chr1D 93.750 128 8 0 285 412 270226889 270226762 2.650000e-45 193.0
19 TraesCS4D01G039600 chr7A 89.510 143 15 0 277 419 287708635 287708777 5.730000e-42 182.0


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 TraesCS4D01G039600 chr4D 16923769 16926374 2605 False 4813.00 4813 100.00000 1 2606 1 chr4D.!!$F1 2605
1 TraesCS4D01G039600 chr4B 28960145 28964641 4496 False 775.75 1849 89.57575 1 2606 4 chr4B.!!$F2 2605
2 TraesCS4D01G039600 chr4A 583523272 583525776 2504 True 708.58 1282 93.17740 3 2606 5 chr4A.!!$R1 2603

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
936 1736 0.318441 CAGCTCCACAGTCCGAGAAA 59.682 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2432 4611 0.107643 TGTGTTCCTCGCACCATTCA 59.892 50.0 0.0 0.0 36.11 2.57 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
63 64 7.731556 AACGTACATAATAAGAGTGTCGTTC 57.268 36.000 0.00 0.00 36.18 3.95
93 95 6.566197 AAGGTCACTCTGAATCAAATGTTC 57.434 37.500 0.00 0.00 0.00 3.18
181 186 1.811965 TGTAATGTGCATTGAAGCGCT 59.188 42.857 2.64 2.64 44.96 5.92
189 194 3.545078 GTGCATTGAAGCGCTAAAGAATG 59.455 43.478 12.05 16.84 41.61 2.67
211 216 4.202040 TGTTAAAGCATGCATACTGATGGC 60.202 41.667 21.98 0.00 33.26 4.40
235 244 3.881937 CCATCTATGGCATCGAGATGA 57.118 47.619 29.30 11.69 46.31 2.92
288 341 4.810790 TCTGTCTTGCTTAGCAGTTACTC 58.189 43.478 7.08 0.00 40.61 2.59
289 342 3.926616 TGTCTTGCTTAGCAGTTACTCC 58.073 45.455 7.08 0.00 40.61 3.85
290 343 3.263261 GTCTTGCTTAGCAGTTACTCCC 58.737 50.000 7.08 0.00 40.61 4.30
291 344 3.055747 GTCTTGCTTAGCAGTTACTCCCT 60.056 47.826 7.08 0.00 40.61 4.20
292 345 3.195825 TCTTGCTTAGCAGTTACTCCCTC 59.804 47.826 7.08 0.00 40.61 4.30
293 346 2.821437 TGCTTAGCAGTTACTCCCTCT 58.179 47.619 1.39 0.00 33.32 3.69
294 347 2.497675 TGCTTAGCAGTTACTCCCTCTG 59.502 50.000 1.39 0.00 33.32 3.35
295 348 2.498078 GCTTAGCAGTTACTCCCTCTGT 59.502 50.000 0.00 0.00 0.00 3.41
296 349 3.055747 GCTTAGCAGTTACTCCCTCTGTT 60.056 47.826 0.00 0.00 0.00 3.16
297 350 4.563786 GCTTAGCAGTTACTCCCTCTGTTT 60.564 45.833 0.00 0.00 0.00 2.83
298 351 5.552178 CTTAGCAGTTACTCCCTCTGTTTT 58.448 41.667 0.00 0.00 0.00 2.43
299 352 3.744660 AGCAGTTACTCCCTCTGTTTTG 58.255 45.455 0.00 0.00 0.00 2.44
300 353 3.391296 AGCAGTTACTCCCTCTGTTTTGA 59.609 43.478 0.00 0.00 0.00 2.69
301 354 4.134563 GCAGTTACTCCCTCTGTTTTGAA 58.865 43.478 0.00 0.00 0.00 2.69
302 355 4.762251 GCAGTTACTCCCTCTGTTTTGAAT 59.238 41.667 0.00 0.00 0.00 2.57
303 356 5.241728 GCAGTTACTCCCTCTGTTTTGAATT 59.758 40.000 0.00 0.00 0.00 2.17
304 357 6.430000 GCAGTTACTCCCTCTGTTTTGAATTA 59.570 38.462 0.00 0.00 0.00 1.40
305 358 7.573283 GCAGTTACTCCCTCTGTTTTGAATTAC 60.573 40.741 0.00 0.00 0.00 1.89
306 359 7.661847 CAGTTACTCCCTCTGTTTTGAATTACT 59.338 37.037 0.00 0.00 0.00 2.24
307 360 8.218488 AGTTACTCCCTCTGTTTTGAATTACTT 58.782 33.333 0.00 0.00 0.00 2.24
308 361 6.884280 ACTCCCTCTGTTTTGAATTACTTG 57.116 37.500 0.00 0.00 0.00 3.16
309 362 6.365520 ACTCCCTCTGTTTTGAATTACTTGT 58.634 36.000 0.00 0.00 0.00 3.16
310 363 6.486993 ACTCCCTCTGTTTTGAATTACTTGTC 59.513 38.462 0.00 0.00 0.00 3.18
311 364 6.601332 TCCCTCTGTTTTGAATTACTTGTCT 58.399 36.000 0.00 0.00 0.00 3.41
312 365 7.060421 TCCCTCTGTTTTGAATTACTTGTCTT 58.940 34.615 0.00 0.00 0.00 3.01
313 366 8.215050 TCCCTCTGTTTTGAATTACTTGTCTTA 58.785 33.333 0.00 0.00 0.00 2.10
314 367 8.507249 CCCTCTGTTTTGAATTACTTGTCTTAG 58.493 37.037 0.00 0.00 0.00 2.18
315 368 9.273016 CCTCTGTTTTGAATTACTTGTCTTAGA 57.727 33.333 0.00 0.00 0.00 2.10
330 383 8.407064 ACTTGTCTTAGATTTGTCTAGATACGG 58.593 37.037 0.00 0.00 0.00 4.02
331 384 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
332 385 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
333 386 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
334 387 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
335 388 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
350 403 8.988064 ATACGGATGTATCTAGCACTAAAATG 57.012 34.615 0.00 0.00 36.56 2.32
351 404 7.050970 ACGGATGTATCTAGCACTAAAATGA 57.949 36.000 0.00 0.00 0.00 2.57
352 405 7.497595 ACGGATGTATCTAGCACTAAAATGAA 58.502 34.615 0.00 0.00 0.00 2.57
353 406 8.150945 ACGGATGTATCTAGCACTAAAATGAAT 58.849 33.333 0.00 0.00 0.00 2.57
354 407 8.651588 CGGATGTATCTAGCACTAAAATGAATC 58.348 37.037 0.00 0.00 0.00 2.52
355 408 9.717942 GGATGTATCTAGCACTAAAATGAATCT 57.282 33.333 0.00 0.00 0.00 2.40
362 415 8.350722 TCTAGCACTAAAATGAATCTAGGTACG 58.649 37.037 0.00 0.00 0.00 3.67
363 416 6.281405 AGCACTAAAATGAATCTAGGTACGG 58.719 40.000 0.00 0.00 0.00 4.02
364 417 6.097839 AGCACTAAAATGAATCTAGGTACGGA 59.902 38.462 0.00 0.00 0.00 4.69
365 418 6.929606 GCACTAAAATGAATCTAGGTACGGAT 59.070 38.462 0.00 0.00 0.00 4.18
366 419 7.095607 GCACTAAAATGAATCTAGGTACGGATG 60.096 40.741 0.00 0.00 0.00 3.51
367 420 7.926555 CACTAAAATGAATCTAGGTACGGATGT 59.073 37.037 0.00 0.00 0.00 3.06
368 421 9.139734 ACTAAAATGAATCTAGGTACGGATGTA 57.860 33.333 0.00 0.00 0.00 2.29
369 422 9.976511 CTAAAATGAATCTAGGTACGGATGTAA 57.023 33.333 0.00 0.00 30.94 2.41
370 423 8.658499 AAAATGAATCTAGGTACGGATGTAAC 57.342 34.615 0.00 0.00 38.63 2.50
372 425 8.701908 AATGAATCTAGGTACGGATGTAACTA 57.298 34.615 0.76 0.76 46.78 2.24
381 434 8.120140 AGGTACGGATGTAACTAGATAAATCC 57.880 38.462 16.09 16.09 46.78 3.01
382 435 7.727186 AGGTACGGATGTAACTAGATAAATCCA 59.273 37.037 22.61 7.36 46.78 3.41
383 436 8.362639 GGTACGGATGTAACTAGATAAATCCAA 58.637 37.037 22.61 11.55 38.95 3.53
384 437 9.408069 GTACGGATGTAACTAGATAAATCCAAG 57.592 37.037 22.61 13.26 38.95 3.61
385 438 8.246430 ACGGATGTAACTAGATAAATCCAAGA 57.754 34.615 22.61 0.00 38.95 3.02
386 439 8.142551 ACGGATGTAACTAGATAAATCCAAGAC 58.857 37.037 22.61 2.97 38.95 3.01
387 440 8.141909 CGGATGTAACTAGATAAATCCAAGACA 58.858 37.037 22.61 0.65 38.95 3.41
388 441 9.832445 GGATGTAACTAGATAAATCCAAGACAA 57.168 33.333 19.63 0.00 38.88 3.18
398 451 9.627123 AGATAAATCCAAGACAAATAATTCGGA 57.373 29.630 0.00 0.00 0.00 4.55
441 494 7.545265 TCAAGAAAACAACATTCACCTTCAAAG 59.455 33.333 0.00 0.00 0.00 2.77
448 501 6.598850 ACAACATTCACCTTCAAAGCATTTTT 59.401 30.769 0.00 0.00 35.03 1.94
508 566 2.157834 TGTGGCGTATTTCTTCACGT 57.842 45.000 0.00 0.00 40.25 4.49
529 587 0.746659 GTTTGCCAGCCAACTTCTGT 59.253 50.000 0.00 0.00 31.97 3.41
533 591 1.954528 CCAGCCAACTTCTGTGCAG 59.045 57.895 0.00 0.00 0.00 4.41
563 621 6.370453 ACTATTACAGGGTTTTGGAAGTTGT 58.630 36.000 0.00 0.00 0.00 3.32
567 625 3.447229 ACAGGGTTTTGGAAGTTGTCTTG 59.553 43.478 0.00 0.00 33.64 3.02
616 674 5.236655 GATGATTGATCGATAGCTACCGA 57.763 43.478 13.72 13.72 39.25 4.69
631 1409 1.160137 ACCGAAAAGTGAGCAGCATC 58.840 50.000 0.00 0.00 0.00 3.91
716 1497 9.651913 TTTTTGAGCTAGATCTTTTTGTTTTGT 57.348 25.926 9.79 0.00 0.00 2.83
866 1651 2.093537 GACTGCTCCATCCCCGCTAG 62.094 65.000 0.00 0.00 0.00 3.42
908 1693 1.411074 CCTCCCCGGGGAATAAAAAGG 60.411 57.143 41.16 31.66 44.66 3.11
927 1727 2.505777 CGACTCGCAGCTCCACAG 60.506 66.667 0.00 0.00 0.00 3.66
928 1728 2.653702 GACTCGCAGCTCCACAGT 59.346 61.111 0.00 0.00 0.00 3.55
929 1729 1.445238 GACTCGCAGCTCCACAGTC 60.445 63.158 0.00 0.00 0.00 3.51
930 1730 2.125753 CTCGCAGCTCCACAGTCC 60.126 66.667 0.00 0.00 0.00 3.85
931 1731 3.978723 CTCGCAGCTCCACAGTCCG 62.979 68.421 0.00 0.00 0.00 4.79
932 1732 4.056125 CGCAGCTCCACAGTCCGA 62.056 66.667 0.00 0.00 0.00 4.55
933 1733 2.125753 GCAGCTCCACAGTCCGAG 60.126 66.667 0.00 0.00 0.00 4.63
934 1734 2.640302 GCAGCTCCACAGTCCGAGA 61.640 63.158 0.00 0.00 0.00 4.04
935 1735 1.967535 CAGCTCCACAGTCCGAGAA 59.032 57.895 0.00 0.00 0.00 2.87
936 1736 0.318441 CAGCTCCACAGTCCGAGAAA 59.682 55.000 0.00 0.00 0.00 2.52
937 1737 0.318762 AGCTCCACAGTCCGAGAAAC 59.681 55.000 0.00 0.00 0.00 2.78
938 1738 0.670854 GCTCCACAGTCCGAGAAACC 60.671 60.000 0.00 0.00 0.00 3.27
939 1739 0.388649 CTCCACAGTCCGAGAAACCG 60.389 60.000 0.00 0.00 0.00 4.44
940 1740 2.027625 CCACAGTCCGAGAAACCGC 61.028 63.158 0.00 0.00 0.00 5.68
941 1741 1.300620 CACAGTCCGAGAAACCGCA 60.301 57.895 0.00 0.00 0.00 5.69
942 1742 1.300697 ACAGTCCGAGAAACCGCAC 60.301 57.895 0.00 0.00 0.00 5.34
943 1743 2.049433 AGTCCGAGAAACCGCACG 60.049 61.111 0.00 0.00 0.00 5.34
944 1744 3.774702 GTCCGAGAAACCGCACGC 61.775 66.667 0.00 0.00 0.00 5.34
948 1748 4.699522 GAGAAACCGCACGCCCCT 62.700 66.667 0.00 0.00 0.00 4.79
949 1749 4.265056 AGAAACCGCACGCCCCTT 62.265 61.111 0.00 0.00 0.00 3.95
950 1750 3.292159 GAAACCGCACGCCCCTTT 61.292 61.111 0.00 0.00 0.00 3.11
951 1751 3.263503 GAAACCGCACGCCCCTTTC 62.264 63.158 0.00 0.00 0.00 2.62
1023 1823 2.251040 CGTCCGCCGTATGATAAGATG 58.749 52.381 0.00 0.00 0.00 2.90
1100 1900 1.410882 CTTCGAGATCCTGTCTTCCCC 59.589 57.143 0.00 0.00 37.29 4.81
1201 2002 1.536766 TCTTTGAATTGACTGCCTGCG 59.463 47.619 0.00 0.00 0.00 5.18
1217 2018 0.179076 TGCGTCCTCGACCGAGTATA 60.179 55.000 16.86 1.32 40.44 1.47
1609 3750 0.393944 AGGCTCATGCATGTGACCAG 60.394 55.000 26.87 17.33 41.91 4.00
1645 3786 6.090783 TGAGTAAATTGCAGTCTGTACTACG 58.909 40.000 0.93 0.00 33.48 3.51
1671 3812 1.194547 TGAATTTGCGCGTCTTCAGAC 59.805 47.619 8.43 0.00 41.47 3.51
1672 3813 1.194547 GAATTTGCGCGTCTTCAGACA 59.805 47.619 8.43 0.00 44.99 3.41
1673 3814 0.792640 ATTTGCGCGTCTTCAGACAG 59.207 50.000 8.43 2.03 44.99 3.51
1674 3815 0.249280 TTTGCGCGTCTTCAGACAGA 60.249 50.000 8.43 0.00 44.99 3.41
1833 4006 5.724328 TGTACCACTTTTGAATTTTGCACA 58.276 33.333 0.00 0.00 0.00 4.57
1877 4050 2.991190 TCGTTCGAGTAAATTGCAGTCC 59.009 45.455 0.00 0.00 0.00 3.85
1884 4059 5.066893 TCGAGTAAATTGCAGTCCGTACTAT 59.933 40.000 0.00 0.00 33.48 2.12
1890 4065 9.037737 GTAAATTGCAGTCCGTACTATGATAAA 57.962 33.333 0.00 0.00 33.48 1.40
1902 4077 2.930230 ATGATAAATCGAGTTGCGCG 57.070 45.000 8.63 0.00 40.61 6.86
1924 4099 6.508777 GCGTCTCTTTCCTCATACTAAAGAT 58.491 40.000 0.00 0.00 38.27 2.40
1937 4112 9.138062 CTCATACTAAAGATGCACTGTCATATC 57.862 37.037 0.00 0.00 0.00 1.63
2034 4211 0.962489 CAAGACGGGATCGATAGCCT 59.038 55.000 0.00 0.00 40.11 4.58
2300 4479 7.309770 TGTAATAAAACTCCCCTGCAAAAAT 57.690 32.000 0.00 0.00 0.00 1.82
2301 4480 8.423906 TGTAATAAAACTCCCCTGCAAAAATA 57.576 30.769 0.00 0.00 0.00 1.40
2302 4481 9.041354 TGTAATAAAACTCCCCTGCAAAAATAT 57.959 29.630 0.00 0.00 0.00 1.28
2361 4540 9.754382 ACATAAAGCATGGTCATCAAATATTTC 57.246 29.630 0.00 0.00 39.13 2.17
2393 4572 3.887716 GGATGCAAAGTTCAGAGGCATAT 59.112 43.478 0.00 0.00 44.52 1.78
2484 4663 5.982516 GGCTATCGATAATATTCTGCTCTGG 59.017 44.000 6.58 0.00 0.00 3.86
2499 4678 3.006110 TGCTCTGGAAAAGGCTGAAAATG 59.994 43.478 0.00 0.00 0.00 2.32
2553 4732 6.952773 TGCAAACTGAATAAAAGTGGTACT 57.047 33.333 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 6.608610 ACGTTAAAACAATGTATCTGAAGGC 58.391 36.000 0.00 0.00 0.00 4.35
63 64 2.526304 TCAGAGTGACCTTTTGGACG 57.474 50.000 0.00 0.00 44.07 4.79
93 95 2.350522 CGAGTGAAATCCCCACAAGAG 58.649 52.381 0.00 0.00 37.01 2.85
166 171 2.150390 TCTTTAGCGCTTCAATGCACA 58.850 42.857 18.68 0.00 0.00 4.57
181 186 8.955388 TCAGTATGCATGCTTTAACATTCTTTA 58.045 29.630 20.33 0.00 34.76 1.85
189 194 4.293415 GCCATCAGTATGCATGCTTTAAC 58.707 43.478 20.33 8.73 34.76 2.01
235 244 7.821846 TCAGCAAACAAAAGGTAAATGAAACTT 59.178 29.630 0.00 0.00 0.00 2.66
246 255 5.536161 ACAGATACATCAGCAAACAAAAGGT 59.464 36.000 0.00 0.00 0.00 3.50
288 341 6.884280 AGACAAGTAATTCAAAACAGAGGG 57.116 37.500 0.00 0.00 0.00 4.30
289 342 9.273016 TCTAAGACAAGTAATTCAAAACAGAGG 57.727 33.333 0.00 0.00 0.00 3.69
304 357 8.407064 CCGTATCTAGACAAATCTAAGACAAGT 58.593 37.037 0.00 0.00 36.98 3.16
305 358 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
306 359 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
307 360 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
308 361 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
309 362 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
325 378 8.803235 TCATTTTAGTGCTAGATACATCCGTAT 58.197 33.333 0.00 0.00 41.16 3.06
326 379 8.173542 TCATTTTAGTGCTAGATACATCCGTA 57.826 34.615 0.00 0.00 0.00 4.02
327 380 7.050970 TCATTTTAGTGCTAGATACATCCGT 57.949 36.000 0.00 0.00 0.00 4.69
328 381 7.946655 TTCATTTTAGTGCTAGATACATCCG 57.053 36.000 0.00 0.00 0.00 4.18
329 382 9.717942 AGATTCATTTTAGTGCTAGATACATCC 57.282 33.333 0.00 0.00 0.00 3.51
336 389 8.350722 CGTACCTAGATTCATTTTAGTGCTAGA 58.649 37.037 0.00 0.00 0.00 2.43
337 390 7.595502 CCGTACCTAGATTCATTTTAGTGCTAG 59.404 40.741 0.00 0.00 0.00 3.42
338 391 7.286087 TCCGTACCTAGATTCATTTTAGTGCTA 59.714 37.037 0.00 0.00 0.00 3.49
339 392 6.097839 TCCGTACCTAGATTCATTTTAGTGCT 59.902 38.462 0.00 0.00 0.00 4.40
340 393 6.278363 TCCGTACCTAGATTCATTTTAGTGC 58.722 40.000 0.00 0.00 0.00 4.40
341 394 7.926555 ACATCCGTACCTAGATTCATTTTAGTG 59.073 37.037 0.00 0.00 0.00 2.74
342 395 8.019656 ACATCCGTACCTAGATTCATTTTAGT 57.980 34.615 0.00 0.00 0.00 2.24
343 396 9.976511 TTACATCCGTACCTAGATTCATTTTAG 57.023 33.333 0.00 0.00 0.00 1.85
344 397 9.754382 GTTACATCCGTACCTAGATTCATTTTA 57.246 33.333 0.00 0.00 0.00 1.52
345 398 8.483758 AGTTACATCCGTACCTAGATTCATTTT 58.516 33.333 0.00 0.00 0.00 1.82
346 399 8.019656 AGTTACATCCGTACCTAGATTCATTT 57.980 34.615 0.00 0.00 0.00 2.32
347 400 7.598759 AGTTACATCCGTACCTAGATTCATT 57.401 36.000 0.00 0.00 0.00 2.57
348 401 8.162085 TCTAGTTACATCCGTACCTAGATTCAT 58.838 37.037 3.58 0.00 41.94 2.57
349 402 7.512130 TCTAGTTACATCCGTACCTAGATTCA 58.488 38.462 3.58 0.00 41.94 2.57
350 403 7.976135 TCTAGTTACATCCGTACCTAGATTC 57.024 40.000 3.58 0.00 41.94 2.52
355 408 9.236006 GGATTTATCTAGTTACATCCGTACCTA 57.764 37.037 9.30 0.00 0.00 3.08
356 409 7.727186 TGGATTTATCTAGTTACATCCGTACCT 59.273 37.037 16.18 0.00 33.08 3.08
357 410 7.889469 TGGATTTATCTAGTTACATCCGTACC 58.111 38.462 16.18 0.00 33.08 3.34
358 411 9.408069 CTTGGATTTATCTAGTTACATCCGTAC 57.592 37.037 16.18 0.00 33.08 3.67
359 412 9.358406 TCTTGGATTTATCTAGTTACATCCGTA 57.642 33.333 16.18 9.33 33.08 4.02
360 413 8.142551 GTCTTGGATTTATCTAGTTACATCCGT 58.857 37.037 16.18 0.00 33.08 4.69
361 414 8.141909 TGTCTTGGATTTATCTAGTTACATCCG 58.858 37.037 16.18 7.54 33.08 4.18
362 415 9.832445 TTGTCTTGGATTTATCTAGTTACATCC 57.168 33.333 15.08 15.08 31.69 3.51
372 425 9.627123 TCCGAATTATTTGTCTTGGATTTATCT 57.373 29.630 0.00 0.00 0.00 1.98
375 428 8.178964 CGTTCCGAATTATTTGTCTTGGATTTA 58.821 33.333 0.00 0.00 0.00 1.40
376 429 7.027161 CGTTCCGAATTATTTGTCTTGGATTT 58.973 34.615 0.00 0.00 0.00 2.17
377 430 6.404293 CCGTTCCGAATTATTTGTCTTGGATT 60.404 38.462 0.00 0.00 0.00 3.01
378 431 5.065988 CCGTTCCGAATTATTTGTCTTGGAT 59.934 40.000 0.00 0.00 0.00 3.41
379 432 4.393680 CCGTTCCGAATTATTTGTCTTGGA 59.606 41.667 0.00 0.00 0.00 3.53
380 433 4.393680 TCCGTTCCGAATTATTTGTCTTGG 59.606 41.667 0.00 0.00 0.00 3.61
381 434 5.447279 CCTCCGTTCCGAATTATTTGTCTTG 60.447 44.000 0.00 0.00 0.00 3.02
382 435 4.634443 CCTCCGTTCCGAATTATTTGTCTT 59.366 41.667 0.00 0.00 0.00 3.01
383 436 4.189231 CCTCCGTTCCGAATTATTTGTCT 58.811 43.478 0.00 0.00 0.00 3.41
384 437 3.311596 CCCTCCGTTCCGAATTATTTGTC 59.688 47.826 0.00 0.00 0.00 3.18
385 438 3.054948 TCCCTCCGTTCCGAATTATTTGT 60.055 43.478 0.00 0.00 0.00 2.83
386 439 3.537580 TCCCTCCGTTCCGAATTATTTG 58.462 45.455 0.00 0.00 0.00 2.32
387 440 3.199289 ACTCCCTCCGTTCCGAATTATTT 59.801 43.478 0.00 0.00 0.00 1.40
388 441 2.770232 ACTCCCTCCGTTCCGAATTATT 59.230 45.455 0.00 0.00 0.00 1.40
389 442 2.395619 ACTCCCTCCGTTCCGAATTAT 58.604 47.619 0.00 0.00 0.00 1.28
390 443 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
391 444 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
392 445 1.400737 CTACTCCCTCCGTTCCGAAT 58.599 55.000 0.00 0.00 0.00 3.34
393 446 1.318158 GCTACTCCCTCCGTTCCGAA 61.318 60.000 0.00 0.00 0.00 4.30
394 447 1.751927 GCTACTCCCTCCGTTCCGA 60.752 63.158 0.00 0.00 0.00 4.55
395 448 2.050350 TGCTACTCCCTCCGTTCCG 61.050 63.158 0.00 0.00 0.00 4.30
396 449 0.971447 AGTGCTACTCCCTCCGTTCC 60.971 60.000 0.00 0.00 0.00 3.62
397 450 0.456628 GAGTGCTACTCCCTCCGTTC 59.543 60.000 5.33 0.00 39.28 3.95
398 451 0.251653 TGAGTGCTACTCCCTCCGTT 60.252 55.000 11.99 0.00 44.44 4.44
399 452 0.251653 TTGAGTGCTACTCCCTCCGT 60.252 55.000 11.99 0.00 44.44 4.69
400 453 0.457851 CTTGAGTGCTACTCCCTCCG 59.542 60.000 11.99 0.00 44.44 4.63
401 454 1.853963 TCTTGAGTGCTACTCCCTCC 58.146 55.000 11.99 0.00 44.44 4.30
402 455 3.963428 TTTCTTGAGTGCTACTCCCTC 57.037 47.619 11.99 0.00 44.44 4.30
403 456 3.391296 TGTTTTCTTGAGTGCTACTCCCT 59.609 43.478 11.99 0.00 44.44 4.20
404 457 3.740115 TGTTTTCTTGAGTGCTACTCCC 58.260 45.455 11.99 0.00 44.44 4.30
405 458 4.574828 TGTTGTTTTCTTGAGTGCTACTCC 59.425 41.667 11.99 0.00 44.44 3.85
406 459 5.734855 TGTTGTTTTCTTGAGTGCTACTC 57.265 39.130 8.75 8.75 45.26 2.59
407 460 6.318648 TGAATGTTGTTTTCTTGAGTGCTACT 59.681 34.615 0.00 0.00 0.00 2.57
408 461 6.414987 GTGAATGTTGTTTTCTTGAGTGCTAC 59.585 38.462 0.00 0.00 0.00 3.58
455 508 1.377202 CTTGTGTGATCCACCCCGG 60.377 63.158 10.60 0.00 43.85 5.73
460 513 1.000274 GGGCAAACTTGTGTGATCCAC 60.000 52.381 7.22 7.22 44.78 4.02
508 566 1.136695 CAGAAGTTGGCTGGCAAACAA 59.863 47.619 18.73 1.79 32.49 2.83
533 591 4.485163 CAAAACCCTGTAATAGTTGCAGC 58.515 43.478 0.00 0.00 41.35 5.25
582 640 1.067669 TCAATCATCGGAGAAGAGGCG 59.932 52.381 0.00 0.00 43.58 5.52
583 641 2.898729 TCAATCATCGGAGAAGAGGC 57.101 50.000 0.00 0.00 43.58 4.70
614 672 2.238245 GTGATGCTGCTCACTTTTCG 57.762 50.000 18.59 0.00 41.87 3.46
631 1409 9.612620 GAGGTAAATGTTCAAAATCTTGTAGTG 57.387 33.333 0.00 0.00 33.94 2.74
866 1651 2.125952 GCCTGCGTGATTTTGGGC 60.126 61.111 0.00 0.00 0.00 5.36
926 1726 2.049433 CGTGCGGTTTCTCGGACT 60.049 61.111 7.24 0.00 46.66 3.85
927 1727 3.774702 GCGTGCGGTTTCTCGGAC 61.775 66.667 0.00 0.00 45.67 4.79
931 1731 4.699522 AGGGGCGTGCGGTTTCTC 62.700 66.667 0.00 0.00 0.00 2.87
932 1732 3.785122 AAAGGGGCGTGCGGTTTCT 62.785 57.895 0.00 0.00 0.00 2.52
933 1733 3.263503 GAAAGGGGCGTGCGGTTTC 62.264 63.158 0.00 0.00 0.00 2.78
934 1734 3.292159 GAAAGGGGCGTGCGGTTT 61.292 61.111 0.00 0.00 0.00 3.27
979 1779 2.229792 TGTTAGAAGCTTGCCAGTTGG 58.770 47.619 2.10 0.00 38.53 3.77
980 1780 3.988379 TTGTTAGAAGCTTGCCAGTTG 57.012 42.857 2.10 0.00 0.00 3.16
981 1781 3.305608 GCATTGTTAGAAGCTTGCCAGTT 60.306 43.478 2.10 0.00 0.00 3.16
982 1782 2.229784 GCATTGTTAGAAGCTTGCCAGT 59.770 45.455 2.10 0.00 0.00 4.00
983 1783 2.730090 CGCATTGTTAGAAGCTTGCCAG 60.730 50.000 2.10 0.00 0.00 4.85
1111 1911 2.202676 CTTCGTCTCCTCCGCTGC 60.203 66.667 0.00 0.00 0.00 5.25
1112 1912 1.388065 ATCCTTCGTCTCCTCCGCTG 61.388 60.000 0.00 0.00 0.00 5.18
1113 1913 1.076632 ATCCTTCGTCTCCTCCGCT 60.077 57.895 0.00 0.00 0.00 5.52
1201 2002 4.511527 TGGATATATACTCGGTCGAGGAC 58.488 47.826 21.99 3.88 45.88 3.85
1217 2018 3.385433 TCCCGTAACACGAACATGGATAT 59.615 43.478 0.00 0.00 46.05 1.63
1244 2045 4.174009 CGTCTCATGGTGAACGTATTTCT 58.826 43.478 0.00 0.00 34.97 2.52
1259 2060 2.037772 AGCAGAACTCAAACCGTCTCAT 59.962 45.455 0.00 0.00 0.00 2.90
1444 3585 6.042777 TGATTAATGTAAGCACGGAGAAGAG 58.957 40.000 0.00 0.00 0.00 2.85
1446 3587 6.662414 TTGATTAATGTAAGCACGGAGAAG 57.338 37.500 0.00 0.00 33.28 2.85
1447 3588 7.985184 ACTATTGATTAATGTAAGCACGGAGAA 59.015 33.333 0.00 0.00 33.28 2.87
1599 3740 2.477845 TGATCACACCTGGTCACATG 57.522 50.000 0.00 0.00 32.15 3.21
1600 3741 3.726557 AATGATCACACCTGGTCACAT 57.273 42.857 0.00 0.00 40.48 3.21
1601 3742 3.148412 CAAATGATCACACCTGGTCACA 58.852 45.455 0.00 0.00 40.48 3.58
1602 3743 3.411446 TCAAATGATCACACCTGGTCAC 58.589 45.455 0.00 0.00 40.48 3.67
1609 3750 6.389091 TGCAATTTACTCAAATGATCACACC 58.611 36.000 0.00 0.00 34.53 4.16
1645 3786 0.516524 GACGCGCAAATTCAGTCGTC 60.517 55.000 5.73 0.00 39.25 4.20
1671 3812 3.599730 TGATCACACTAGTTGCCTCTG 57.400 47.619 0.00 0.00 0.00 3.35
1672 3813 4.833478 AATGATCACACTAGTTGCCTCT 57.167 40.909 0.00 0.00 0.00 3.69
1673 3814 4.937620 TCAAATGATCACACTAGTTGCCTC 59.062 41.667 0.00 0.00 0.00 4.70
1674 3815 4.910195 TCAAATGATCACACTAGTTGCCT 58.090 39.130 0.00 0.00 0.00 4.75
1731 3874 6.149308 AGTCGAAAGATTGTGCATGACATAAA 59.851 34.615 0.00 0.00 45.19 1.40
1792 3965 3.855689 ACATCCAAAAATGAGGCTTCG 57.144 42.857 0.00 0.00 0.00 3.79
1822 3995 4.171754 GCCTCTGAAGATGTGCAAAATTC 58.828 43.478 0.00 0.00 0.00 2.17
1833 4006 1.701847 ACACCAGTTGCCTCTGAAGAT 59.298 47.619 6.78 0.00 37.61 2.40
1858 4031 2.735134 ACGGACTGCAATTTACTCGAAC 59.265 45.455 0.00 0.00 0.00 3.95
1877 4050 5.441614 GCGCAACTCGATTTATCATAGTACG 60.442 44.000 0.30 10.21 41.67 3.67
1884 4059 1.586578 GACGCGCAACTCGATTTATCA 59.413 47.619 5.73 0.00 41.67 2.15
1890 4065 0.388649 AAAGAGACGCGCAACTCGAT 60.389 50.000 19.85 12.99 41.67 3.59
1902 4077 7.223777 GTGCATCTTTAGTATGAGGAAAGAGAC 59.776 40.741 0.00 0.00 41.24 3.36
1924 4099 7.568349 AGAAGATTTAAGGATATGACAGTGCA 58.432 34.615 0.00 0.00 0.00 4.57
2085 4262 3.075148 GGGACCACTACTTTTGCTTCTC 58.925 50.000 0.00 0.00 0.00 2.87
2114 4291 1.288633 TCCACCCTAAGATGTACCGGA 59.711 52.381 9.46 0.00 0.00 5.14
2269 4448 5.125417 CAGGGGAGTTTTATTACATGTGGTG 59.875 44.000 9.11 0.00 0.00 4.17
2308 4487 6.627671 GCATTCGATTTATCTGTCGGTTTTAC 59.372 38.462 0.00 0.00 38.34 2.01
2361 4540 3.904136 ACTTTGCATCCGAGTTTTCTG 57.096 42.857 0.00 0.00 0.00 3.02
2393 4572 0.825840 GGCAAGCCAACCACCTAACA 60.826 55.000 6.14 0.00 35.81 2.41
2432 4611 0.107643 TGTGTTCCTCGCACCATTCA 59.892 50.000 0.00 0.00 36.11 2.57
2484 4663 5.463392 GTCCAGTTTCATTTTCAGCCTTTTC 59.537 40.000 0.00 0.00 0.00 2.29
2499 4678 0.539438 TGGCACCCATGTCCAGTTTC 60.539 55.000 0.00 0.00 31.12 2.78
2553 4732 4.040829 TCTCTTGGAGAGCACAATCTTTCA 59.959 41.667 0.08 0.00 42.04 2.69


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

AutoCloner maintained by Alex Coulton.