Multiple sequence alignment - TraesCS5D01G420500

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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 TraesCS5D01G420500 chr5D 100.000 2372 0 0 1 2372 481156330 481158701 0.000000e+00 4381
1 TraesCS5D01G420500 chr5A 92.183 1906 100 23 483 2372 600196107 600197979 0.000000e+00 2649
2 TraesCS5D01G420500 chr5A 88.529 340 22 7 1 324 600195779 600196117 1.710000e-106 396
3 TraesCS5D01G420500 chr5A 95.266 169 8 0 319 487 644168555 644168387 3.890000e-68 268
4 TraesCS5D01G420500 chr5B 94.577 627 34 0 1746 2372 589568176 589568802 0.000000e+00 970
5 TraesCS5D01G420500 chr5B 86.762 627 41 12 829 1436 589567246 589567849 0.000000e+00 660
6 TraesCS5D01G420500 chr5B 96.933 163 5 0 325 487 318139119 318138957 8.350000e-70 274
7 TraesCS5D01G420500 chr5B 95.652 161 7 0 325 485 587459390 587459230 2.340000e-65 259
8 TraesCS5D01G420500 chr5B 88.235 187 14 4 1557 1742 589567966 589568145 1.430000e-52 217
9 TraesCS5D01G420500 chr5B 96.000 100 4 0 1475 1574 589567851 589567950 1.890000e-36 163
10 TraesCS5D01G420500 chr2B 96.341 164 6 0 324 487 8071874 8072037 1.080000e-68 270
11 TraesCS5D01G420500 chr2B 96.341 164 6 0 324 487 8227628 8227791 1.080000e-68 270
12 TraesCS5D01G420500 chr2B 96.341 164 6 0 324 487 373096899 373097062 1.080000e-68 270
13 TraesCS5D01G420500 chr6D 95.783 166 7 0 322 487 433502057 433502222 3.890000e-68 268
14 TraesCS5D01G420500 chr2A 93.220 177 6 4 317 487 50050037 50050213 3.030000e-64 255
15 TraesCS5D01G420500 chr2D 94.048 168 8 2 322 487 101335361 101335528 1.090000e-63 254


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 TraesCS5D01G420500 chr5D 481156330 481158701 2371 False 4381.0 4381 100.0000 1 2372 1 chr5D.!!$F1 2371
1 TraesCS5D01G420500 chr5A 600195779 600197979 2200 False 1522.5 2649 90.3560 1 2372 2 chr5A.!!$F1 2371
2 TraesCS5D01G420500 chr5B 589567246 589568802 1556 False 502.5 970 91.3935 829 2372 4 chr5B.!!$F1 1543

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
477 494 0.032952 TAGACAATACATCCGCCGCC 59.967 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 1657 0.823356 AGCAATGTGAGGCACGGTTT 60.823 50.0 0.0 0.0 37.14 3.27 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
58 59 1.156736 AGCTAACATCACCACAACGC 58.843 50.000 0.00 0.00 0.00 4.84
67 68 2.203139 CCACAACGCTCCCACACA 60.203 61.111 0.00 0.00 0.00 3.72
77 78 1.566211 CTCCCACACATGTCTCCTCT 58.434 55.000 0.00 0.00 0.00 3.69
79 80 0.539051 CCCACACATGTCTCCTCTCC 59.461 60.000 0.00 0.00 0.00 3.71
80 81 0.539051 CCACACATGTCTCCTCTCCC 59.461 60.000 0.00 0.00 0.00 4.30
139 146 5.907391 CGTTCGCTGAAGATTGTTAAAAACT 59.093 36.000 0.00 0.00 0.00 2.66
140 147 6.129717 CGTTCGCTGAAGATTGTTAAAAACTG 60.130 38.462 0.00 0.00 0.00 3.16
142 149 7.202016 TCGCTGAAGATTGTTAAAAACTGAT 57.798 32.000 0.00 0.00 0.00 2.90
208 215 0.719465 GTACGCCCACTGACATTTCG 59.281 55.000 0.00 0.00 0.00 3.46
216 223 3.563808 CCCACTGACATTTCGAGTGAAAA 59.436 43.478 10.93 0.00 46.53 2.29
258 275 5.494390 TTCCCCTAGAAAGTACTTTGGAC 57.506 43.478 25.17 11.11 32.11 4.02
259 276 4.495565 TCCCCTAGAAAGTACTTTGGACA 58.504 43.478 25.17 7.56 32.11 4.02
314 331 3.885901 AGAAGAAAACTGGGTGAAAGCTC 59.114 43.478 0.00 0.00 0.00 4.09
321 338 2.665603 GGTGAAAGCTCGCCCTCT 59.334 61.111 0.00 0.00 45.21 3.69
322 339 1.003233 GGTGAAAGCTCGCCCTCTT 60.003 57.895 0.00 0.00 45.21 2.85
323 340 0.606673 GGTGAAAGCTCGCCCTCTTT 60.607 55.000 0.00 0.00 45.21 2.52
324 341 1.239347 GTGAAAGCTCGCCCTCTTTT 58.761 50.000 0.00 0.00 33.14 2.27
325 342 1.609072 GTGAAAGCTCGCCCTCTTTTT 59.391 47.619 0.00 0.00 33.14 1.94
348 365 4.475051 TTTTTGAGGGAATGGCATCATG 57.525 40.909 0.00 0.00 33.18 3.07
349 366 2.076207 TTGAGGGAATGGCATCATGG 57.924 50.000 0.00 0.00 33.18 3.66
350 367 0.468585 TGAGGGAATGGCATCATGGC 60.469 55.000 3.69 3.69 44.03 4.40
361 378 4.519540 GGCATCATGGCGGTTTATATTT 57.480 40.909 0.00 0.00 31.79 1.40
362 379 4.485163 GGCATCATGGCGGTTTATATTTC 58.515 43.478 0.00 0.00 31.79 2.17
363 380 4.022416 GGCATCATGGCGGTTTATATTTCA 60.022 41.667 0.00 0.00 31.79 2.69
364 381 5.336690 GGCATCATGGCGGTTTATATTTCAT 60.337 40.000 0.00 0.00 31.79 2.57
365 382 5.574055 GCATCATGGCGGTTTATATTTCATG 59.426 40.000 0.00 0.00 33.83 3.07
366 383 6.680810 CATCATGGCGGTTTATATTTCATGT 58.319 36.000 0.00 0.00 34.11 3.21
367 384 6.707440 TCATGGCGGTTTATATTTCATGTT 57.293 33.333 0.00 0.00 34.11 2.71
368 385 7.809546 TCATGGCGGTTTATATTTCATGTTA 57.190 32.000 0.00 0.00 34.11 2.41
369 386 7.870826 TCATGGCGGTTTATATTTCATGTTAG 58.129 34.615 0.00 0.00 34.11 2.34
370 387 7.717436 TCATGGCGGTTTATATTTCATGTTAGA 59.283 33.333 0.00 0.00 34.11 2.10
371 388 7.867305 TGGCGGTTTATATTTCATGTTAGAA 57.133 32.000 0.00 0.00 0.00 2.10
372 389 8.458573 TGGCGGTTTATATTTCATGTTAGAAT 57.541 30.769 0.00 0.00 0.00 2.40
373 390 9.562408 TGGCGGTTTATATTTCATGTTAGAATA 57.438 29.630 0.00 0.00 0.00 1.75
412 429 9.603921 TTAATAAAATGTCTACTAGAAACCCCG 57.396 33.333 0.00 0.00 0.00 5.73
413 430 4.482952 AAATGTCTACTAGAAACCCCGG 57.517 45.455 0.00 0.00 0.00 5.73
414 431 2.905415 TGTCTACTAGAAACCCCGGA 57.095 50.000 0.73 0.00 0.00 5.14
415 432 2.731572 TGTCTACTAGAAACCCCGGAG 58.268 52.381 0.73 0.00 0.00 4.63
429 446 2.896443 GGAGGCTCCGACTTCCAG 59.104 66.667 19.53 0.00 35.90 3.86
430 447 1.682684 GGAGGCTCCGACTTCCAGA 60.683 63.158 19.53 0.00 35.90 3.86
431 448 1.513622 GAGGCTCCGACTTCCAGAC 59.486 63.158 2.15 0.00 0.00 3.51
432 449 1.228894 AGGCTCCGACTTCCAGACA 60.229 57.895 0.00 0.00 0.00 3.41
433 450 0.832135 AGGCTCCGACTTCCAGACAA 60.832 55.000 0.00 0.00 0.00 3.18
434 451 0.250513 GGCTCCGACTTCCAGACAAT 59.749 55.000 0.00 0.00 0.00 2.71
435 452 1.339151 GGCTCCGACTTCCAGACAATT 60.339 52.381 0.00 0.00 0.00 2.32
436 453 1.734465 GCTCCGACTTCCAGACAATTG 59.266 52.381 3.24 3.24 0.00 2.32
437 454 2.872038 GCTCCGACTTCCAGACAATTGT 60.872 50.000 11.78 11.78 0.00 2.71
438 455 3.403038 CTCCGACTTCCAGACAATTGTT 58.597 45.455 13.36 0.00 0.00 2.83
439 456 3.399330 TCCGACTTCCAGACAATTGTTC 58.601 45.455 13.36 6.25 0.00 3.18
440 457 2.157668 CCGACTTCCAGACAATTGTTCG 59.842 50.000 13.36 14.99 0.00 3.95
441 458 3.057019 CGACTTCCAGACAATTGTTCGA 58.943 45.455 17.42 9.21 0.00 3.71
442 459 3.121944 CGACTTCCAGACAATTGTTCGAG 59.878 47.826 17.42 11.72 0.00 4.04
443 460 4.307432 GACTTCCAGACAATTGTTCGAGA 58.693 43.478 13.36 5.10 0.00 4.04
444 461 4.703897 ACTTCCAGACAATTGTTCGAGAA 58.296 39.130 13.36 12.10 0.00 2.87
445 462 4.752101 ACTTCCAGACAATTGTTCGAGAAG 59.248 41.667 24.75 24.75 35.48 2.85
446 463 4.336889 TCCAGACAATTGTTCGAGAAGT 57.663 40.909 13.36 0.00 0.00 3.01
447 464 4.307432 TCCAGACAATTGTTCGAGAAGTC 58.693 43.478 13.36 0.00 0.00 3.01
448 465 4.039245 TCCAGACAATTGTTCGAGAAGTCT 59.961 41.667 13.36 0.00 35.44 3.24
449 466 4.387256 CCAGACAATTGTTCGAGAAGTCTC 59.613 45.833 13.36 0.00 39.55 3.36
450 467 4.387256 CAGACAATTGTTCGAGAAGTCTCC 59.613 45.833 13.36 0.00 39.79 3.71
451 468 3.318017 ACAATTGTTCGAGAAGTCTCCG 58.682 45.455 4.92 0.00 39.79 4.63
452 469 3.005472 ACAATTGTTCGAGAAGTCTCCGA 59.995 43.478 4.92 1.56 39.79 4.55
453 470 2.991434 TTGTTCGAGAAGTCTCCGAG 57.009 50.000 2.75 0.00 39.79 4.63
454 471 1.893544 TGTTCGAGAAGTCTCCGAGT 58.106 50.000 2.75 0.00 39.79 4.18
455 472 2.228059 TGTTCGAGAAGTCTCCGAGTT 58.772 47.619 2.75 0.00 39.79 3.01
456 473 2.225963 TGTTCGAGAAGTCTCCGAGTTC 59.774 50.000 2.75 3.78 40.97 3.01
457 474 1.451067 TCGAGAAGTCTCCGAGTTCC 58.549 55.000 7.59 0.82 41.41 3.62
458 475 1.003349 TCGAGAAGTCTCCGAGTTCCT 59.997 52.381 7.59 0.00 41.41 3.36
459 476 2.235650 TCGAGAAGTCTCCGAGTTCCTA 59.764 50.000 7.59 0.00 41.41 2.94
460 477 2.610374 CGAGAAGTCTCCGAGTTCCTAG 59.390 54.545 7.59 0.00 41.41 3.02
461 478 3.679361 CGAGAAGTCTCCGAGTTCCTAGA 60.679 52.174 7.59 0.00 41.41 2.43
462 479 3.613030 AGAAGTCTCCGAGTTCCTAGAC 58.387 50.000 7.59 0.00 41.41 2.59
463 480 3.009253 AGAAGTCTCCGAGTTCCTAGACA 59.991 47.826 7.59 0.00 41.41 3.41
464 481 3.436577 AGTCTCCGAGTTCCTAGACAA 57.563 47.619 0.00 0.00 40.65 3.18
465 482 3.970842 AGTCTCCGAGTTCCTAGACAAT 58.029 45.455 0.00 0.00 40.65 2.71
466 483 5.113446 AGTCTCCGAGTTCCTAGACAATA 57.887 43.478 0.00 0.00 40.65 1.90
467 484 4.883006 AGTCTCCGAGTTCCTAGACAATAC 59.117 45.833 0.00 0.00 40.65 1.89
468 485 4.639310 GTCTCCGAGTTCCTAGACAATACA 59.361 45.833 0.00 0.00 38.56 2.29
469 486 5.299782 GTCTCCGAGTTCCTAGACAATACAT 59.700 44.000 0.00 0.00 38.56 2.29
470 487 5.531659 TCTCCGAGTTCCTAGACAATACATC 59.468 44.000 0.00 0.00 0.00 3.06
471 488 4.583489 TCCGAGTTCCTAGACAATACATCC 59.417 45.833 0.00 0.00 0.00 3.51
472 489 4.537965 CGAGTTCCTAGACAATACATCCG 58.462 47.826 0.00 0.00 0.00 4.18
473 490 4.299978 GAGTTCCTAGACAATACATCCGC 58.700 47.826 0.00 0.00 0.00 5.54
474 491 3.069729 AGTTCCTAGACAATACATCCGCC 59.930 47.826 0.00 0.00 0.00 6.13
475 492 1.611977 TCCTAGACAATACATCCGCCG 59.388 52.381 0.00 0.00 0.00 6.46
476 493 1.419374 CTAGACAATACATCCGCCGC 58.581 55.000 0.00 0.00 0.00 6.53
477 494 0.032952 TAGACAATACATCCGCCGCC 59.967 55.000 0.00 0.00 0.00 6.13
478 495 1.522806 GACAATACATCCGCCGCCA 60.523 57.895 0.00 0.00 0.00 5.69
479 496 0.884704 GACAATACATCCGCCGCCAT 60.885 55.000 0.00 0.00 0.00 4.40
480 497 0.394938 ACAATACATCCGCCGCCATA 59.605 50.000 0.00 0.00 0.00 2.74
481 498 1.003118 ACAATACATCCGCCGCCATAT 59.997 47.619 0.00 0.00 0.00 1.78
482 499 2.083774 CAATACATCCGCCGCCATATT 58.916 47.619 0.00 0.00 0.00 1.28
483 500 1.737838 ATACATCCGCCGCCATATTG 58.262 50.000 0.00 0.00 0.00 1.90
484 501 0.321210 TACATCCGCCGCCATATTGG 60.321 55.000 0.00 0.00 41.55 3.16
503 520 5.466127 TTGGCCCCTTTATTACTCAAGAT 57.534 39.130 0.00 0.00 0.00 2.40
588 605 1.947456 CCTACTTTTAATGGGCTCGGC 59.053 52.381 0.00 0.00 0.00 5.54
595 612 2.839486 TAATGGGCTCGGCTATTCTG 57.161 50.000 5.38 0.00 0.00 3.02
601 618 1.156645 GCTCGGCTATTCTGCACAGG 61.157 60.000 0.00 0.00 34.04 4.00
603 620 2.182842 CGGCTATTCTGCACAGGCC 61.183 63.158 0.00 0.00 40.13 5.19
604 621 2.182842 GGCTATTCTGCACAGGCCG 61.183 63.158 0.00 0.00 40.13 6.13
605 622 2.182842 GCTATTCTGCACAGGCCGG 61.183 63.158 0.00 0.00 40.13 6.13
606 623 1.221840 CTATTCTGCACAGGCCGGT 59.778 57.895 1.28 1.28 40.13 5.28
652 669 1.632948 GCTTTCGTACGGGCCTTGTC 61.633 60.000 16.52 0.00 0.00 3.18
680 697 3.788766 CGCGGGCGTTCCTGAAAG 61.789 66.667 4.64 0.00 41.45 2.62
697 714 1.657804 AAGGTCTGGTGTCCCTTAGG 58.342 55.000 0.00 0.00 36.82 2.69
730 747 1.677966 TCCCCACGACGAGAAGGAG 60.678 63.158 0.00 0.00 0.00 3.69
752 769 2.550830 ATAATTCCGCCGCATCTTCT 57.449 45.000 0.00 0.00 0.00 2.85
799 816 2.676076 GCCGTTTCATTGTTGCAGAAT 58.324 42.857 0.00 0.00 0.00 2.40
802 819 3.244976 CGTTTCATTGTTGCAGAATCCC 58.755 45.455 0.00 0.00 0.00 3.85
906 923 1.880819 TTCCGCCCCTGTCGTTCTAC 61.881 60.000 0.00 0.00 0.00 2.59
1197 1214 2.044650 TACTCCACCTCCGACGGG 60.045 66.667 15.25 4.64 0.00 5.28
1341 1367 2.673893 CGTGGACAATGACGATGAGGAA 60.674 50.000 0.00 0.00 37.81 3.36
1353 1379 2.597455 GATGAGGAAGAGGAGGAGGAG 58.403 57.143 0.00 0.00 0.00 3.69
1373 1399 4.587262 GGAGGAGGAAGAGGAGAAGTAATC 59.413 50.000 0.00 0.00 0.00 1.75
1469 1505 4.442332 CGTTGCTCCAATACCCATGTACTA 60.442 45.833 0.00 0.00 0.00 1.82
1470 1506 4.682778 TGCTCCAATACCCATGTACTAC 57.317 45.455 0.00 0.00 0.00 2.73
1473 1509 5.900699 TGCTCCAATACCCATGTACTACTAA 59.099 40.000 0.00 0.00 0.00 2.24
1519 1555 5.346551 TGAACTGTCAAATAATCCGTGTACG 59.653 40.000 0.00 0.00 39.44 3.67
1588 1657 1.103803 CGGTTGTAGCAGCTCTCCTA 58.896 55.000 0.00 0.00 0.00 2.94
1600 1670 0.895530 CTCTCCTAAACCGTGCCTCA 59.104 55.000 0.00 0.00 0.00 3.86
1737 1819 3.900892 CCCGGTGGATCGAGACGG 61.901 72.222 12.15 12.15 43.89 4.79
1742 1824 1.453379 GTGGATCGAGACGGGAGGA 60.453 63.158 0.00 0.00 0.00 3.71
1743 1825 1.152943 TGGATCGAGACGGGAGGAG 60.153 63.158 0.00 0.00 0.00 3.69
1744 1826 1.148723 GGATCGAGACGGGAGGAGA 59.851 63.158 0.00 0.00 0.00 3.71
1748 1857 0.251033 TCGAGACGGGAGGAGAACAA 60.251 55.000 0.00 0.00 0.00 2.83
1752 1861 0.966920 GACGGGAGGAGAACAACTCA 59.033 55.000 0.00 0.00 46.54 3.41
1845 1954 1.662629 CTCGAAATCATTGCTCGCACT 59.337 47.619 0.00 0.00 32.66 4.40
1858 1967 0.935831 TCGCACTGACGTTACAACCG 60.936 55.000 0.00 0.00 0.00 4.44
1946 2055 4.386951 CATGGCCCACGACCACGA 62.387 66.667 0.00 0.00 40.82 4.35
2044 2153 1.531365 CCAGGGCCAACAAAGCTCA 60.531 57.895 6.18 0.00 31.12 4.26
2160 2274 2.591715 GTCAAGCTGCGGGTGTGT 60.592 61.111 0.00 0.00 0.00 3.72
2163 2277 1.968017 CAAGCTGCGGGTGTGTGAT 60.968 57.895 0.00 0.00 0.00 3.06
2181 2295 1.745087 GATGCATTCACCGGTCATGTT 59.255 47.619 19.91 11.07 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 2.110213 GTGGGAGCGTTGTGGTGA 59.890 61.111 0.00 0.00 0.00 4.02
58 59 1.480137 GAGAGGAGACATGTGTGGGAG 59.520 57.143 1.15 0.00 0.00 4.30
67 68 1.760086 CGCAGGGGAGAGGAGACAT 60.760 63.158 0.00 0.00 0.00 3.06
77 78 3.797353 GGATCTTGGCGCAGGGGA 61.797 66.667 10.83 1.45 0.00 4.81
79 80 2.191513 CATGGATCTTGGCGCAGGG 61.192 63.158 10.83 0.00 0.00 4.45
80 81 2.842256 GCATGGATCTTGGCGCAGG 61.842 63.158 10.83 0.00 0.00 4.85
124 131 7.147976 GGCTGACATCAGTTTTTAACAATCTT 58.852 34.615 10.50 0.00 45.45 2.40
139 146 4.694760 AAGTGCTATATGGCTGACATCA 57.305 40.909 12.66 0.00 41.03 3.07
140 147 5.059161 TGAAAGTGCTATATGGCTGACATC 58.941 41.667 12.66 6.53 41.03 3.06
142 149 4.486125 TGAAAGTGCTATATGGCTGACA 57.514 40.909 12.66 0.00 0.00 3.58
234 241 6.045106 TGTCCAAAGTACTTTCTAGGGGAAAT 59.955 38.462 20.21 0.00 42.25 2.17
235 242 5.370289 TGTCCAAAGTACTTTCTAGGGGAAA 59.630 40.000 20.21 14.98 41.11 3.13
238 245 4.903045 TGTCCAAAGTACTTTCTAGGGG 57.097 45.455 18.00 15.19 0.00 4.79
265 282 8.829373 ATGAAAAAGAGCAATTCCTAAGGTAT 57.171 30.769 0.00 0.00 0.00 2.73
268 285 7.121759 TCTGATGAAAAAGAGCAATTCCTAAGG 59.878 37.037 0.00 0.00 0.00 2.69
274 291 8.807667 TTTCTTCTGATGAAAAAGAGCAATTC 57.192 30.769 14.20 0.00 31.45 2.17
281 298 6.607198 ACCCAGTTTTCTTCTGATGAAAAAGA 59.393 34.615 24.31 8.30 42.59 2.52
327 344 3.198200 CCATGATGCCATTCCCTCAAAAA 59.802 43.478 0.00 0.00 0.00 1.94
328 345 2.767394 CCATGATGCCATTCCCTCAAAA 59.233 45.455 0.00 0.00 0.00 2.44
329 346 2.390696 CCATGATGCCATTCCCTCAAA 58.609 47.619 0.00 0.00 0.00 2.69
330 347 2.030571 GCCATGATGCCATTCCCTCAA 61.031 52.381 0.00 0.00 0.00 3.02
331 348 0.468585 GCCATGATGCCATTCCCTCA 60.469 55.000 0.00 0.00 0.00 3.86
332 349 1.521450 CGCCATGATGCCATTCCCTC 61.521 60.000 0.00 0.00 0.00 4.30
333 350 1.529948 CGCCATGATGCCATTCCCT 60.530 57.895 0.00 0.00 0.00 4.20
334 351 2.567497 CCGCCATGATGCCATTCCC 61.567 63.158 0.00 0.00 0.00 3.97
335 352 1.394266 AACCGCCATGATGCCATTCC 61.394 55.000 0.00 0.00 0.00 3.01
336 353 0.461135 AAACCGCCATGATGCCATTC 59.539 50.000 0.00 0.00 0.00 2.67
337 354 1.774110 TAAACCGCCATGATGCCATT 58.226 45.000 0.00 0.00 0.00 3.16
338 355 1.999648 ATAAACCGCCATGATGCCAT 58.000 45.000 0.00 0.00 0.00 4.40
339 356 2.647683 TATAAACCGCCATGATGCCA 57.352 45.000 0.00 0.00 0.00 4.92
340 357 4.022416 TGAAATATAAACCGCCATGATGCC 60.022 41.667 0.00 0.00 0.00 4.40
341 358 5.119931 TGAAATATAAACCGCCATGATGC 57.880 39.130 0.00 0.00 0.00 3.91
342 359 6.680810 ACATGAAATATAAACCGCCATGATG 58.319 36.000 0.00 0.00 35.32 3.07
343 360 6.899393 ACATGAAATATAAACCGCCATGAT 57.101 33.333 0.00 0.00 35.32 2.45
344 361 6.707440 AACATGAAATATAAACCGCCATGA 57.293 33.333 0.00 0.00 35.32 3.07
345 362 7.870826 TCTAACATGAAATATAAACCGCCATG 58.129 34.615 0.00 0.00 36.81 3.66
346 363 8.458573 TTCTAACATGAAATATAAACCGCCAT 57.541 30.769 0.00 0.00 0.00 4.40
347 364 7.867305 TTCTAACATGAAATATAAACCGCCA 57.133 32.000 0.00 0.00 0.00 5.69
386 403 9.603921 CGGGGTTTCTAGTAGACATTTTATTAA 57.396 33.333 0.00 0.00 0.00 1.40
387 404 8.206189 CCGGGGTTTCTAGTAGACATTTTATTA 58.794 37.037 0.00 0.00 0.00 0.98
388 405 7.052248 CCGGGGTTTCTAGTAGACATTTTATT 58.948 38.462 0.00 0.00 0.00 1.40
389 406 6.384886 TCCGGGGTTTCTAGTAGACATTTTAT 59.615 38.462 0.00 0.00 0.00 1.40
390 407 5.721000 TCCGGGGTTTCTAGTAGACATTTTA 59.279 40.000 0.00 0.00 0.00 1.52
391 408 4.533311 TCCGGGGTTTCTAGTAGACATTTT 59.467 41.667 0.00 0.00 0.00 1.82
392 409 4.098894 TCCGGGGTTTCTAGTAGACATTT 58.901 43.478 0.00 0.00 0.00 2.32
393 410 3.705072 CTCCGGGGTTTCTAGTAGACATT 59.295 47.826 0.00 0.00 0.00 2.71
394 411 3.297736 CTCCGGGGTTTCTAGTAGACAT 58.702 50.000 0.00 0.00 0.00 3.06
395 412 2.622452 CCTCCGGGGTTTCTAGTAGACA 60.622 54.545 0.00 0.00 0.00 3.41
396 413 2.030371 CCTCCGGGGTTTCTAGTAGAC 58.970 57.143 0.00 0.00 0.00 2.59
397 414 1.687368 GCCTCCGGGGTTTCTAGTAGA 60.687 57.143 0.00 0.00 37.43 2.59
398 415 0.751452 GCCTCCGGGGTTTCTAGTAG 59.249 60.000 0.00 0.00 37.43 2.57
399 416 0.337428 AGCCTCCGGGGTTTCTAGTA 59.663 55.000 0.00 0.00 40.98 1.82
400 417 0.976590 GAGCCTCCGGGGTTTCTAGT 60.977 60.000 0.00 0.00 44.22 2.57
401 418 1.687297 GGAGCCTCCGGGGTTTCTAG 61.687 65.000 0.00 0.00 44.22 2.43
402 419 1.688187 GGAGCCTCCGGGGTTTCTA 60.688 63.158 0.00 0.00 44.22 2.10
403 420 3.009714 GGAGCCTCCGGGGTTTCT 61.010 66.667 0.00 0.00 44.22 2.52
412 429 1.682684 TCTGGAAGTCGGAGCCTCC 60.683 63.158 0.00 0.00 33.76 4.30
413 430 1.251527 TGTCTGGAAGTCGGAGCCTC 61.252 60.000 0.00 0.00 33.76 4.70
414 431 0.832135 TTGTCTGGAAGTCGGAGCCT 60.832 55.000 0.00 0.00 33.76 4.58
415 432 0.250513 ATTGTCTGGAAGTCGGAGCC 59.749 55.000 0.00 0.00 33.76 4.70
416 433 1.734465 CAATTGTCTGGAAGTCGGAGC 59.266 52.381 0.00 0.00 33.76 4.70
417 434 3.045601 ACAATTGTCTGGAAGTCGGAG 57.954 47.619 4.92 0.00 33.76 4.63
418 435 3.399330 GAACAATTGTCTGGAAGTCGGA 58.601 45.455 12.39 0.00 33.76 4.55
419 436 2.157668 CGAACAATTGTCTGGAAGTCGG 59.842 50.000 12.39 0.00 33.76 4.79
420 437 3.057019 TCGAACAATTGTCTGGAAGTCG 58.943 45.455 12.39 14.98 33.76 4.18
421 438 4.307432 TCTCGAACAATTGTCTGGAAGTC 58.693 43.478 12.39 2.82 33.76 3.01
422 439 4.336889 TCTCGAACAATTGTCTGGAAGT 57.663 40.909 12.39 0.00 33.76 3.01
423 440 4.752101 ACTTCTCGAACAATTGTCTGGAAG 59.248 41.667 24.98 24.98 35.31 3.46
424 441 4.703897 ACTTCTCGAACAATTGTCTGGAA 58.296 39.130 12.39 12.36 0.00 3.53
425 442 4.039245 AGACTTCTCGAACAATTGTCTGGA 59.961 41.667 12.39 8.57 32.90 3.86
426 443 4.310769 AGACTTCTCGAACAATTGTCTGG 58.689 43.478 12.39 4.42 32.90 3.86
427 444 4.387256 GGAGACTTCTCGAACAATTGTCTG 59.613 45.833 12.39 7.60 43.76 3.51
428 445 4.561105 GGAGACTTCTCGAACAATTGTCT 58.439 43.478 12.39 0.67 43.76 3.41
429 446 3.365220 CGGAGACTTCTCGAACAATTGTC 59.635 47.826 12.39 4.85 43.76 3.18
430 447 3.005472 TCGGAGACTTCTCGAACAATTGT 59.995 43.478 4.92 4.92 43.76 2.71
431 448 3.575630 TCGGAGACTTCTCGAACAATTG 58.424 45.455 3.24 3.24 43.76 2.32
432 449 3.256136 ACTCGGAGACTTCTCGAACAATT 59.744 43.478 12.86 0.00 43.76 2.32
433 450 2.820787 ACTCGGAGACTTCTCGAACAAT 59.179 45.455 12.86 0.00 43.76 2.71
434 451 2.228059 ACTCGGAGACTTCTCGAACAA 58.772 47.619 12.86 0.00 43.76 2.83
435 452 1.893544 ACTCGGAGACTTCTCGAACA 58.106 50.000 12.86 0.00 43.76 3.18
436 453 2.414426 GGAACTCGGAGACTTCTCGAAC 60.414 54.545 12.86 0.00 43.76 3.95
437 454 1.811359 GGAACTCGGAGACTTCTCGAA 59.189 52.381 12.86 0.00 43.76 3.71
438 455 1.003349 AGGAACTCGGAGACTTCTCGA 59.997 52.381 12.86 1.43 43.76 4.04
439 456 1.455248 AGGAACTCGGAGACTTCTCG 58.545 55.000 12.86 0.00 43.76 4.04
440 457 3.624410 GTCTAGGAACTCGGAGACTTCTC 59.376 52.174 12.86 0.00 41.75 2.87
441 458 3.009253 TGTCTAGGAACTCGGAGACTTCT 59.991 47.826 12.86 5.06 41.75 2.85
442 459 3.345414 TGTCTAGGAACTCGGAGACTTC 58.655 50.000 12.86 5.93 41.75 3.01
443 460 3.436577 TGTCTAGGAACTCGGAGACTT 57.563 47.619 12.86 4.63 41.75 3.01
444 461 3.436577 TTGTCTAGGAACTCGGAGACT 57.563 47.619 12.86 9.12 41.75 3.24
445 462 4.639310 TGTATTGTCTAGGAACTCGGAGAC 59.361 45.833 12.86 5.30 41.75 3.36
446 463 4.851843 TGTATTGTCTAGGAACTCGGAGA 58.148 43.478 12.86 0.00 41.75 3.71
447 464 5.278561 GGATGTATTGTCTAGGAACTCGGAG 60.279 48.000 2.83 2.83 41.75 4.63
448 465 4.583489 GGATGTATTGTCTAGGAACTCGGA 59.417 45.833 0.00 0.00 41.75 4.55
449 466 4.556898 CGGATGTATTGTCTAGGAACTCGG 60.557 50.000 0.00 0.00 41.75 4.63
450 467 4.537965 CGGATGTATTGTCTAGGAACTCG 58.462 47.826 0.00 0.00 41.75 4.18
451 468 4.299978 GCGGATGTATTGTCTAGGAACTC 58.700 47.826 0.00 0.00 41.75 3.01
452 469 3.069729 GGCGGATGTATTGTCTAGGAACT 59.930 47.826 0.00 0.00 46.37 3.01
453 470 3.391049 GGCGGATGTATTGTCTAGGAAC 58.609 50.000 0.00 0.00 0.00 3.62
454 471 2.035449 CGGCGGATGTATTGTCTAGGAA 59.965 50.000 0.00 0.00 0.00 3.36
455 472 1.611977 CGGCGGATGTATTGTCTAGGA 59.388 52.381 0.00 0.00 0.00 2.94
456 473 1.935300 GCGGCGGATGTATTGTCTAGG 60.935 57.143 9.78 0.00 0.00 3.02
457 474 1.419374 GCGGCGGATGTATTGTCTAG 58.581 55.000 9.78 0.00 0.00 2.43
458 475 0.032952 GGCGGCGGATGTATTGTCTA 59.967 55.000 9.78 0.00 0.00 2.59
459 476 1.227556 GGCGGCGGATGTATTGTCT 60.228 57.895 9.78 0.00 0.00 3.41
460 477 0.884704 ATGGCGGCGGATGTATTGTC 60.885 55.000 9.78 0.00 0.00 3.18
461 478 0.394938 TATGGCGGCGGATGTATTGT 59.605 50.000 9.78 0.00 0.00 2.71
462 479 1.737838 ATATGGCGGCGGATGTATTG 58.262 50.000 9.78 0.00 0.00 1.90
463 480 2.083774 CAATATGGCGGCGGATGTATT 58.916 47.619 9.78 1.43 0.00 1.89
464 481 1.678728 CCAATATGGCGGCGGATGTAT 60.679 52.381 9.78 0.00 0.00 2.29
465 482 0.321210 CCAATATGGCGGCGGATGTA 60.321 55.000 9.78 0.00 0.00 2.29
466 483 1.600636 CCAATATGGCGGCGGATGT 60.601 57.895 9.78 0.00 0.00 3.06
467 484 3.266964 CCAATATGGCGGCGGATG 58.733 61.111 9.78 0.47 0.00 3.51
476 493 5.640147 TGAGTAATAAAGGGGCCAATATGG 58.360 41.667 4.39 0.00 41.55 2.74
477 494 7.004086 TCTTGAGTAATAAAGGGGCCAATATG 58.996 38.462 4.39 0.00 0.00 1.78
478 495 7.161715 TCTTGAGTAATAAAGGGGCCAATAT 57.838 36.000 4.39 0.00 0.00 1.28
479 496 6.584471 TCTTGAGTAATAAAGGGGCCAATA 57.416 37.500 4.39 0.00 0.00 1.90
480 497 5.466127 TCTTGAGTAATAAAGGGGCCAAT 57.534 39.130 4.39 0.00 0.00 3.16
481 498 4.938575 TCTTGAGTAATAAAGGGGCCAA 57.061 40.909 4.39 0.00 0.00 4.52
482 499 5.466127 AATCTTGAGTAATAAAGGGGCCA 57.534 39.130 4.39 0.00 0.00 5.36
483 500 6.459710 CGAAAATCTTGAGTAATAAAGGGGCC 60.460 42.308 0.00 0.00 0.00 5.80
484 501 6.095021 ACGAAAATCTTGAGTAATAAAGGGGC 59.905 38.462 0.00 0.00 0.00 5.80
561 578 5.641155 AGCCCATTAAAAGTAGGACTTGTT 58.359 37.500 0.00 0.00 38.66 2.83
588 605 0.811616 GACCGGCCTGTGCAGAATAG 60.812 60.000 3.79 0.00 40.13 1.73
595 612 2.109181 GGATAGACCGGCCTGTGC 59.891 66.667 3.79 0.00 0.00 4.57
601 618 2.171725 GCGTTGTGGATAGACCGGC 61.172 63.158 0.00 0.00 42.61 6.13
603 620 0.527817 GGAGCGTTGTGGATAGACCG 60.528 60.000 0.00 0.00 42.61 4.79
604 621 0.179081 GGGAGCGTTGTGGATAGACC 60.179 60.000 0.00 0.00 39.54 3.85
605 622 0.535335 TGGGAGCGTTGTGGATAGAC 59.465 55.000 0.00 0.00 0.00 2.59
606 623 0.535335 GTGGGAGCGTTGTGGATAGA 59.465 55.000 0.00 0.00 0.00 1.98
667 684 0.955919 CCAGACCTTTCAGGAACGCC 60.956 60.000 0.00 0.00 37.67 5.68
675 692 1.518367 AAGGGACACCAGACCTTTCA 58.482 50.000 0.00 0.00 41.65 2.69
680 697 1.652947 TTCCTAAGGGACACCAGACC 58.347 55.000 0.00 0.00 42.05 3.85
703 720 0.250166 CGTCGTGGGGACTCCTTTTT 60.250 55.000 0.00 0.00 43.79 1.94
709 726 1.507174 CTTCTCGTCGTGGGGACTC 59.493 63.158 0.00 0.00 43.79 3.36
710 727 1.977544 CCTTCTCGTCGTGGGGACT 60.978 63.158 0.00 0.00 43.79 3.85
730 747 3.251004 AGAAGATGCGGCGGAATTATTTC 59.749 43.478 4.50 5.46 0.00 2.17
752 769 1.850755 GGAGGAGGGGGTGGACAAA 60.851 63.158 0.00 0.00 0.00 2.83
799 816 4.093952 GTCGACGAACTCGCGGGA 62.094 66.667 15.95 0.92 42.62 5.14
802 819 4.434938 TCCGTCGACGAACTCGCG 62.435 66.667 37.65 19.50 42.62 5.87
883 900 4.452733 CGACAGGGGCGGAAGGAC 62.453 72.222 0.00 0.00 0.00 3.85
1341 1367 0.933700 CTTCCTCCTCCTCCTCCTCT 59.066 60.000 0.00 0.00 0.00 3.69
1353 1379 3.319689 CGGATTACTTCTCCTCTTCCTCC 59.680 52.174 0.00 0.00 0.00 4.30
1473 1509 8.784043 GTTCAACTCTTCAAATACTACCATTGT 58.216 33.333 0.00 0.00 0.00 2.71
1519 1555 3.952967 ACCAACTACTAGAATCGGGAGTC 59.047 47.826 0.00 0.00 0.00 3.36
1588 1657 0.823356 AGCAATGTGAGGCACGGTTT 60.823 50.000 0.00 0.00 37.14 3.27
1731 1813 1.202817 GAGTTGTTCTCCTCCCGTCTC 59.797 57.143 0.00 0.00 37.22 3.36
1737 1819 4.023707 CACATTGTTGAGTTGTTCTCCTCC 60.024 45.833 0.00 0.00 42.12 4.30
1742 1824 5.650543 GTTTCCACATTGTTGAGTTGTTCT 58.349 37.500 0.00 0.00 0.00 3.01
1743 1825 4.499040 CGTTTCCACATTGTTGAGTTGTTC 59.501 41.667 0.00 0.00 0.00 3.18
1744 1826 4.082463 ACGTTTCCACATTGTTGAGTTGTT 60.082 37.500 0.00 0.00 0.00 2.83
1748 1857 3.181491 CCAACGTTTCCACATTGTTGAGT 60.181 43.478 0.00 0.00 41.76 3.41
1752 1861 2.737039 GCACCAACGTTTCCACATTGTT 60.737 45.455 0.00 0.00 0.00 2.83
2160 2274 1.339920 ACATGACCGGTGAATGCATCA 60.340 47.619 14.63 0.00 35.05 3.07
2163 2277 2.080693 GTAACATGACCGGTGAATGCA 58.919 47.619 14.63 2.75 0.00 3.96
2181 2295 2.682494 GCGGGTGGGAGTGAGGTA 60.682 66.667 0.00 0.00 0.00 3.08
2199 2313 2.357760 TACACGCCGGGCAAACTC 60.358 61.111 20.71 0.00 0.00 3.01
2213 2327 1.859427 GAGCACGACGTGGAGGTACA 61.859 60.000 27.86 0.00 33.64 2.90


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

AutoCloner maintained by Alex Coulton.