Multiple sequence alignment - TraesCS6A01G353100

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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 TraesCS6A01G353100 chr6A 100.000 2812 0 0 1 2812 585055959 585058770 0.000000e+00 5193.0
1 TraesCS6A01G353100 chr6A 84.511 368 23 10 1 356 585039840 585040185 1.610000e-87 333.0
2 TraesCS6A01G353100 chr6D 91.822 1284 60 12 459 1724 436798180 436799436 0.000000e+00 1748.0
3 TraesCS6A01G353100 chr6D 90.453 1037 65 13 1784 2812 436799437 436800447 0.000000e+00 1336.0
4 TraesCS6A01G353100 chr6D 80.806 422 57 17 2327 2730 436802764 436803179 2.720000e-80 309.0
5 TraesCS6A01G353100 chr6D 88.066 243 10 7 1 236 436796583 436796813 1.280000e-68 270.0
6 TraesCS6A01G353100 chr6D 88.601 193 12 4 258 448 436796803 436796987 2.820000e-55 226.0
7 TraesCS6A01G353100 chr6D 79.091 110 9 10 118 227 436796218 436796313 2.340000e-06 63.9
8 TraesCS6A01G353100 chr6B 90.959 1283 59 14 465 1716 660455183 660456439 0.000000e+00 1674.0
9 TraesCS6A01G353100 chr6B 90.865 1040 70 9 1787 2812 660456440 660457468 0.000000e+00 1371.0
10 TraesCS6A01G353100 chr6B 90.330 455 21 11 1 445 660453504 660453945 2.430000e-160 575.0
11 TraesCS6A01G353100 chr1A 90.099 101 9 1 697 797 460970139 460970040 2.270000e-26 130.0
12 TraesCS6A01G353100 chr1D 90.625 96 7 2 689 784 361353194 361353101 2.940000e-25 126.0


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 TraesCS6A01G353100 chr6A 585055959 585058770 2811 False 5193.000000 5193 100.000000 1 2812 1 chr6A.!!$F2 2811
1 TraesCS6A01G353100 chr6D 436796218 436803179 6961 False 658.816667 1748 86.473167 1 2812 6 chr6D.!!$F1 2811
2 TraesCS6A01G353100 chr6B 660453504 660457468 3964 False 1206.666667 1674 90.718000 1 2812 3 chr6B.!!$F1 2811

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
581 2198 0.319813 CACACAGGACACAGCGATCA 60.320 55.0 0.00 0.0 0.00 2.92 F
1088 2713 0.264955 CTGCCTAGGTCCCTCCCTTA 59.735 60.0 11.31 0.0 35.97 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 3270 0.820482 TGCATGCTGTGAGTTGCTGT 60.820 50.0 20.33 0.0 36.1 4.4 R
2635 4299 2.225019 GTCAGGAGATTGGCGCATATTG 59.775 50.0 10.83 0.0 0.0 1.9 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
47 413 6.104665 CAGAGATATACTACCACATGCATGG 58.895 44.000 29.41 17.86 46.10 3.66
67 433 0.461548 TCTGCCTGTAGATTCGCCTG 59.538 55.000 0.00 0.00 0.00 4.85
70 436 2.036475 CTGCCTGTAGATTCGCCTGTAT 59.964 50.000 0.00 0.00 0.00 2.29
71 437 3.227614 TGCCTGTAGATTCGCCTGTATA 58.772 45.455 0.00 0.00 0.00 1.47
72 438 3.639561 TGCCTGTAGATTCGCCTGTATAA 59.360 43.478 0.00 0.00 0.00 0.98
74 440 4.227538 CCTGTAGATTCGCCTGTATAACG 58.772 47.826 0.00 0.00 0.00 3.18
75 441 4.227538 CTGTAGATTCGCCTGTATAACGG 58.772 47.826 0.00 0.00 0.00 4.44
81 447 3.207265 TCGCCTGTATAACGGGTAGTA 57.793 47.619 6.77 0.00 46.46 1.82
102 468 2.495409 CAAGAATTGGCGCATGCATA 57.505 45.000 19.57 0.00 43.94 3.14
104 470 2.717580 AGAATTGGCGCATGCATATG 57.282 45.000 19.57 1.75 45.35 1.78
105 471 1.271379 AGAATTGGCGCATGCATATGG 59.729 47.619 19.57 1.33 45.35 2.74
106 472 1.270274 GAATTGGCGCATGCATATGGA 59.730 47.619 19.57 1.06 45.35 3.41
108 474 0.599060 TTGGCGCATGCATATGGATG 59.401 50.000 27.58 27.58 45.18 3.51
109 475 0.537828 TGGCGCATGCATATGGATGT 60.538 50.000 30.44 1.85 44.38 3.06
110 476 1.271271 TGGCGCATGCATATGGATGTA 60.271 47.619 30.44 16.37 44.38 2.29
111 477 2.019249 GGCGCATGCATATGGATGTAT 58.981 47.619 30.44 0.76 44.38 2.29
112 478 2.032550 GGCGCATGCATATGGATGTATC 59.967 50.000 30.44 21.06 44.38 2.24
113 479 2.941064 GCGCATGCATATGGATGTATCT 59.059 45.455 30.44 0.00 44.38 1.98
114 480 4.122046 GCGCATGCATATGGATGTATCTA 58.878 43.478 30.44 0.00 44.38 1.98
115 481 4.025396 GCGCATGCATATGGATGTATCTAC 60.025 45.833 30.44 16.26 44.38 2.59
116 482 4.207841 CGCATGCATATGGATGTATCTACG 59.792 45.833 30.44 22.19 44.38 3.51
274 644 2.542597 GTTCATGGCCGTATACGAACA 58.457 47.619 26.37 22.23 43.02 3.18
277 647 1.591158 CATGGCCGTATACGAACACAC 59.409 52.381 26.37 9.72 43.02 3.82
282 652 2.701807 CCGTATACGAACACACTCTCG 58.298 52.381 26.37 1.20 43.02 4.04
289 659 1.140816 GAACACACTCTCGTCTTGCC 58.859 55.000 0.00 0.00 0.00 4.52
375 747 8.887036 TGTTCTGCAATAAATAGTCGTATCAT 57.113 30.769 0.00 0.00 0.00 2.45
390 762 8.506168 AGTCGTATCATCATTTGGTTTGTATT 57.494 30.769 0.00 0.00 0.00 1.89
391 763 8.397906 AGTCGTATCATCATTTGGTTTGTATTG 58.602 33.333 0.00 0.00 0.00 1.90
392 764 8.181573 GTCGTATCATCATTTGGTTTGTATTGT 58.818 33.333 0.00 0.00 0.00 2.71
393 765 8.735315 TCGTATCATCATTTGGTTTGTATTGTT 58.265 29.630 0.00 0.00 0.00 2.83
394 766 8.797215 CGTATCATCATTTGGTTTGTATTGTTG 58.203 33.333 0.00 0.00 0.00 3.33
395 767 9.638239 GTATCATCATTTGGTTTGTATTGTTGT 57.362 29.630 0.00 0.00 0.00 3.32
418 799 8.696410 TGTATGTATGTATTGGCGTACATATG 57.304 34.615 19.13 0.00 46.56 1.78
448 829 4.448395 GCATGTGCAAATTGAGCAAGTAAA 59.552 37.500 7.34 0.00 44.64 2.01
449 830 5.613142 GCATGTGCAAATTGAGCAAGTAAAC 60.613 40.000 7.34 0.00 44.64 2.01
450 831 4.367450 TGTGCAAATTGAGCAAGTAAACC 58.633 39.130 7.34 0.00 44.64 3.27
451 832 4.142071 TGTGCAAATTGAGCAAGTAAACCA 60.142 37.500 7.34 0.00 44.64 3.67
452 833 4.990426 GTGCAAATTGAGCAAGTAAACCAT 59.010 37.500 7.34 0.00 44.64 3.55
453 834 4.989797 TGCAAATTGAGCAAGTAAACCATG 59.010 37.500 0.00 0.00 39.39 3.66
454 835 4.990426 GCAAATTGAGCAAGTAAACCATGT 59.010 37.500 0.00 0.00 0.00 3.21
455 836 5.107375 GCAAATTGAGCAAGTAAACCATGTG 60.107 40.000 0.00 0.00 0.00 3.21
456 837 3.641437 TTGAGCAAGTAAACCATGTGC 57.359 42.857 0.00 0.00 35.41 4.57
459 840 1.613437 AGCAAGTAAACCATGTGCCAC 59.387 47.619 0.00 0.00 35.80 5.01
460 841 1.665735 GCAAGTAAACCATGTGCCACG 60.666 52.381 0.00 0.00 0.00 4.94
461 842 1.606668 CAAGTAAACCATGTGCCACGT 59.393 47.619 0.00 0.00 0.00 4.49
462 843 2.809119 CAAGTAAACCATGTGCCACGTA 59.191 45.455 0.00 0.00 0.00 3.57
463 844 3.343941 AGTAAACCATGTGCCACGTAT 57.656 42.857 0.00 0.00 0.00 3.06
492 2109 3.374402 CGAGCACCGGTCCACTCT 61.374 66.667 20.72 8.00 33.91 3.24
504 2121 2.290641 GGTCCACTCTGAGTCTCTGAGA 60.291 54.545 32.10 14.58 42.76 3.27
516 2133 2.768527 GTCTCTGAGATTCCCATGGACA 59.231 50.000 15.22 0.00 0.00 4.02
550 2167 3.769536 CATGTATCTCGCACAGTACACA 58.230 45.455 0.00 0.00 30.67 3.72
551 2168 3.487563 TGTATCTCGCACAGTACACAG 57.512 47.619 0.00 0.00 0.00 3.66
552 2169 2.817844 TGTATCTCGCACAGTACACAGT 59.182 45.455 0.00 0.00 0.00 3.55
553 2170 2.354109 ATCTCGCACAGTACACAGTG 57.646 50.000 0.00 0.00 36.58 3.66
559 2176 1.939974 CACAGTACACAGTGCACACT 58.060 50.000 21.04 10.40 43.61 3.55
560 2177 3.092334 CACAGTACACAGTGCACACTA 57.908 47.619 21.04 0.00 40.20 2.74
561 2178 3.453424 CACAGTACACAGTGCACACTAA 58.547 45.455 21.04 0.00 40.20 2.24
562 2179 3.245284 CACAGTACACAGTGCACACTAAC 59.755 47.826 21.04 10.17 40.20 2.34
563 2180 3.118920 ACAGTACACAGTGCACACTAACA 60.119 43.478 21.04 0.00 40.20 2.41
564 2181 3.245284 CAGTACACAGTGCACACTAACAC 59.755 47.826 21.04 9.30 40.20 3.32
565 2182 2.394930 ACACAGTGCACACTAACACA 57.605 45.000 21.04 0.00 40.20 3.72
566 2183 2.006888 ACACAGTGCACACTAACACAC 58.993 47.619 21.04 0.00 40.20 3.82
567 2184 2.006169 CACAGTGCACACTAACACACA 58.994 47.619 21.04 0.00 40.20 3.72
568 2185 2.030823 CACAGTGCACACTAACACACAG 59.969 50.000 21.04 0.00 40.20 3.66
569 2186 1.599071 CAGTGCACACTAACACACAGG 59.401 52.381 21.04 0.00 40.20 4.00
570 2187 1.484653 AGTGCACACTAACACACAGGA 59.515 47.619 21.04 0.00 40.43 3.86
571 2188 1.597663 GTGCACACTAACACACAGGAC 59.402 52.381 13.17 0.00 36.77 3.85
572 2189 1.208293 TGCACACTAACACACAGGACA 59.792 47.619 0.00 0.00 0.00 4.02
581 2198 0.319813 CACACAGGACACAGCGATCA 60.320 55.000 0.00 0.00 0.00 2.92
833 2450 2.721355 TGCATATCTCCTCTCCCTCTCT 59.279 50.000 0.00 0.00 0.00 3.10
1001 2618 1.082756 CAGTTCACGCCAAGTTCGC 60.083 57.895 0.00 0.00 0.00 4.70
1072 2693 1.014564 GCTACCTTGGTGTCGTCTGC 61.015 60.000 2.03 0.00 0.00 4.26
1088 2713 0.264955 CTGCCTAGGTCCCTCCCTTA 59.735 60.000 11.31 0.00 35.97 2.69
1205 2830 3.723235 GAGAGGAAGCGCGCCATCA 62.723 63.158 30.33 0.00 0.00 3.07
1307 2932 2.202492 CGTCGACGAGCAAGAGGG 60.202 66.667 33.35 0.00 43.02 4.30
1417 3042 1.251527 TGAGGAAGAGGACGCAGGTC 61.252 60.000 0.00 0.00 42.66 3.85
1442 3067 4.222847 GGATCGTCCCGGGAGTGC 62.223 72.222 27.72 14.99 0.00 4.40
1525 3150 4.081406 AGGCTCAAGTTGATGTAATGCAA 58.919 39.130 5.91 0.00 0.00 4.08
1568 3193 2.939640 GCTCCGAAACAATAGCAAGGGA 60.940 50.000 0.00 0.00 35.05 4.20
1622 3270 2.156917 TGCTTCTCTACCTTCGTTCGA 58.843 47.619 0.00 0.00 0.00 3.71
1732 3380 7.862274 TGCATATAGCTATATTATGCTCCCT 57.138 36.000 27.92 6.09 45.94 4.20
1733 3381 8.267620 TGCATATAGCTATATTATGCTCCCTT 57.732 34.615 27.92 5.67 45.94 3.95
1734 3382 8.370940 TGCATATAGCTATATTATGCTCCCTTC 58.629 37.037 27.92 9.19 45.94 3.46
1735 3383 8.592809 GCATATAGCTATATTATGCTCCCTTCT 58.407 37.037 23.76 1.56 40.04 2.85
1738 3386 6.790232 AGCTATATTATGCTCCCTTCTCTC 57.210 41.667 0.00 0.00 33.90 3.20
1739 3387 6.502138 AGCTATATTATGCTCCCTTCTCTCT 58.498 40.000 0.00 0.00 33.90 3.10
1740 3388 7.647827 AGCTATATTATGCTCCCTTCTCTCTA 58.352 38.462 0.00 0.00 33.90 2.43
1741 3389 7.779798 AGCTATATTATGCTCCCTTCTCTCTAG 59.220 40.741 0.00 0.00 33.90 2.43
1742 3390 7.777910 GCTATATTATGCTCCCTTCTCTCTAGA 59.222 40.741 0.00 0.00 0.00 2.43
1743 3391 9.342308 CTATATTATGCTCCCTTCTCTCTAGAG 57.658 40.741 13.98 13.98 43.36 2.43
1744 3392 3.971468 ATGCTCCCTTCTCTCTAGAGT 57.029 47.619 19.21 0.00 42.60 3.24
1745 3393 3.748645 TGCTCCCTTCTCTCTAGAGTT 57.251 47.619 19.21 0.00 42.60 3.01
1746 3394 4.864483 TGCTCCCTTCTCTCTAGAGTTA 57.136 45.455 19.21 6.20 42.60 2.24
1747 3395 4.528920 TGCTCCCTTCTCTCTAGAGTTAC 58.471 47.826 19.21 1.76 42.60 2.50
1748 3396 3.887110 GCTCCCTTCTCTCTAGAGTTACC 59.113 52.174 19.21 0.00 42.60 2.85
1749 3397 4.629204 GCTCCCTTCTCTCTAGAGTTACCA 60.629 50.000 19.21 0.00 42.60 3.25
1750 3398 5.701224 CTCCCTTCTCTCTAGAGTTACCAT 58.299 45.833 19.21 0.00 42.60 3.55
1751 3399 6.692008 GCTCCCTTCTCTCTAGAGTTACCATA 60.692 46.154 19.21 0.00 42.60 2.74
1752 3400 7.222180 TCCCTTCTCTCTAGAGTTACCATAA 57.778 40.000 19.21 0.00 42.60 1.90
1753 3401 7.827787 TCCCTTCTCTCTAGAGTTACCATAAT 58.172 38.462 19.21 0.00 42.60 1.28
1754 3402 7.945664 TCCCTTCTCTCTAGAGTTACCATAATC 59.054 40.741 19.21 0.00 42.60 1.75
1755 3403 7.094549 CCCTTCTCTCTAGAGTTACCATAATCG 60.095 44.444 19.21 0.00 42.60 3.34
1756 3404 7.094549 CCTTCTCTCTAGAGTTACCATAATCGG 60.095 44.444 19.21 3.24 42.60 4.18
1757 3405 6.839454 TCTCTCTAGAGTTACCATAATCGGT 58.161 40.000 19.21 0.00 42.60 4.69
1758 3406 6.935771 TCTCTCTAGAGTTACCATAATCGGTC 59.064 42.308 19.21 0.00 42.60 4.79
1759 3407 6.839454 TCTCTAGAGTTACCATAATCGGTCT 58.161 40.000 19.21 0.00 40.67 3.85
1760 3408 6.711194 TCTCTAGAGTTACCATAATCGGTCTG 59.289 42.308 19.21 0.00 40.67 3.51
1761 3409 6.363065 TCTAGAGTTACCATAATCGGTCTGT 58.637 40.000 0.00 0.00 40.67 3.41
1762 3410 5.934402 AGAGTTACCATAATCGGTCTGTT 57.066 39.130 0.00 0.00 40.67 3.16
1763 3411 5.903810 AGAGTTACCATAATCGGTCTGTTC 58.096 41.667 0.00 0.00 40.67 3.18
1764 3412 5.421056 AGAGTTACCATAATCGGTCTGTTCA 59.579 40.000 0.00 0.00 40.67 3.18
1765 3413 6.045072 AGTTACCATAATCGGTCTGTTCAA 57.955 37.500 0.00 0.00 40.67 2.69
1766 3414 5.873164 AGTTACCATAATCGGTCTGTTCAAC 59.127 40.000 0.00 0.00 40.67 3.18
1767 3415 4.280436 ACCATAATCGGTCTGTTCAACA 57.720 40.909 0.00 0.00 32.11 3.33
1768 3416 4.647611 ACCATAATCGGTCTGTTCAACAA 58.352 39.130 0.00 0.00 32.11 2.83
1769 3417 5.253330 ACCATAATCGGTCTGTTCAACAAT 58.747 37.500 0.00 0.00 32.11 2.71
1770 3418 5.123820 ACCATAATCGGTCTGTTCAACAATG 59.876 40.000 0.00 0.00 32.11 2.82
1771 3419 3.559238 AATCGGTCTGTTCAACAATGC 57.441 42.857 0.00 0.00 0.00 3.56
1772 3420 1.960417 TCGGTCTGTTCAACAATGCA 58.040 45.000 0.00 0.00 0.00 3.96
1773 3421 2.503331 TCGGTCTGTTCAACAATGCAT 58.497 42.857 0.00 0.00 0.00 3.96
1774 3422 2.226200 TCGGTCTGTTCAACAATGCATG 59.774 45.455 0.00 0.00 0.00 4.06
1775 3423 2.030893 CGGTCTGTTCAACAATGCATGT 60.031 45.455 0.00 0.00 46.82 3.21
1776 3424 3.568538 GGTCTGTTCAACAATGCATGTC 58.431 45.455 0.00 0.00 42.99 3.06
1777 3425 3.004629 GGTCTGTTCAACAATGCATGTCA 59.995 43.478 0.00 0.00 42.99 3.58
1778 3426 4.321452 GGTCTGTTCAACAATGCATGTCAT 60.321 41.667 0.00 0.00 42.99 3.06
1779 3427 5.106197 GGTCTGTTCAACAATGCATGTCATA 60.106 40.000 0.00 0.00 42.99 2.15
1780 3428 6.405065 GGTCTGTTCAACAATGCATGTCATAT 60.405 38.462 0.00 0.00 42.99 1.78
1781 3429 7.201723 GGTCTGTTCAACAATGCATGTCATATA 60.202 37.037 0.00 0.00 42.99 0.86
1782 3430 7.641411 GTCTGTTCAACAATGCATGTCATATAC 59.359 37.037 0.00 0.00 42.99 1.47
1795 3443 4.551388 TGTCATATACGCGCACATCAATA 58.449 39.130 5.73 0.00 0.00 1.90
1796 3444 4.985409 TGTCATATACGCGCACATCAATAA 59.015 37.500 5.73 0.00 0.00 1.40
1858 3506 1.636148 AAAGGACCTGTTGCATGCAT 58.364 45.000 23.37 5.68 0.00 3.96
1859 3507 0.892755 AAGGACCTGTTGCATGCATG 59.107 50.000 23.37 22.70 0.00 4.06
1920 3568 3.819564 TTGTCCAATGGATAGAGTCGG 57.180 47.619 4.81 0.00 32.73 4.79
1989 3637 9.347240 GATAATCTTGATTCTTCCCATTCTTGA 57.653 33.333 0.00 0.00 0.00 3.02
2049 3697 4.365723 GGCGTCGACTTGGATATAAGAAA 58.634 43.478 14.70 0.00 0.00 2.52
2074 3722 7.939784 AATCTTAGCCAACTTAGTTTTAGGG 57.060 36.000 0.00 0.00 0.00 3.53
2098 3746 6.372381 GGAAACCGAAAGCTATACCAAGTAAA 59.628 38.462 0.00 0.00 0.00 2.01
2099 3747 7.094677 GGAAACCGAAAGCTATACCAAGTAAAA 60.095 37.037 0.00 0.00 0.00 1.52
2100 3748 7.748691 AACCGAAAGCTATACCAAGTAAAAA 57.251 32.000 0.00 0.00 0.00 1.94
2181 3829 5.762825 ACTTCAGAACTACGTACACAAGA 57.237 39.130 0.00 0.00 0.00 3.02
2185 3833 4.521639 TCAGAACTACGTACACAAGATGGT 59.478 41.667 0.00 0.00 0.00 3.55
2271 3934 4.384846 CGGCTAACAGTAGGTAATTATGCG 59.615 45.833 0.00 0.00 0.00 4.73
2284 3947 8.232913 AGGTAATTATGCGTGGATAAAACATT 57.767 30.769 0.00 0.00 0.00 2.71
2481 4144 2.100031 CATGCGCGTAGGCTCACAA 61.100 57.895 8.43 0.00 36.59 3.33
2607 4271 1.339151 GGGGACAAAGAGCTGTCGATT 60.339 52.381 0.00 0.00 45.60 3.34
2635 4299 3.059461 CACATGGACAAAACAGCAATTGC 60.059 43.478 23.05 23.05 42.49 3.56
2768 4436 8.880991 TTTTTGCAAATGTTAGGGGTACTATA 57.119 30.769 13.65 0.00 0.00 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 413 0.461961 AGGCGAATCTACAGGCAGAC 59.538 55.000 0.00 0.00 0.00 3.51
67 433 6.703165 CCAATTCTTGGTACTACCCGTTATAC 59.297 42.308 2.59 0.00 45.93 1.47
70 436 5.088680 CCAATTCTTGGTACTACCCGTTA 57.911 43.478 2.59 0.00 45.93 3.18
71 437 3.946606 CCAATTCTTGGTACTACCCGTT 58.053 45.455 2.59 0.00 45.93 4.44
72 438 3.622166 CCAATTCTTGGTACTACCCGT 57.378 47.619 2.59 0.00 45.93 5.28
93 459 4.207841 CGTAGATACATCCATATGCATGCG 59.792 45.833 14.09 0.00 36.50 4.73
102 468 4.937201 TCACTTGCGTAGATACATCCAT 57.063 40.909 0.00 0.00 0.00 3.41
104 470 4.430007 TGTTCACTTGCGTAGATACATCC 58.570 43.478 0.00 0.00 0.00 3.51
105 471 5.577164 AGTTGTTCACTTGCGTAGATACATC 59.423 40.000 0.00 0.00 27.32 3.06
106 472 5.348724 CAGTTGTTCACTTGCGTAGATACAT 59.651 40.000 0.00 0.00 30.92 2.29
108 474 4.684703 ACAGTTGTTCACTTGCGTAGATAC 59.315 41.667 0.00 0.00 30.92 2.24
109 475 4.684242 CACAGTTGTTCACTTGCGTAGATA 59.316 41.667 0.00 0.00 30.92 1.98
110 476 3.494626 CACAGTTGTTCACTTGCGTAGAT 59.505 43.478 0.00 0.00 30.92 1.98
111 477 2.863740 CACAGTTGTTCACTTGCGTAGA 59.136 45.455 0.00 0.00 30.92 2.59
112 478 2.599848 GCACAGTTGTTCACTTGCGTAG 60.600 50.000 0.00 0.00 33.05 3.51
113 479 1.329292 GCACAGTTGTTCACTTGCGTA 59.671 47.619 0.00 0.00 33.05 4.42
114 480 0.098728 GCACAGTTGTTCACTTGCGT 59.901 50.000 0.00 0.00 33.05 5.24
115 481 0.098552 TGCACAGTTGTTCACTTGCG 59.901 50.000 0.00 0.00 40.02 4.85
116 482 1.534595 CCTGCACAGTTGTTCACTTGC 60.535 52.381 0.00 0.00 38.76 4.01
149 519 2.432628 CGGTCTCGTGGTCTTGCC 60.433 66.667 0.00 0.00 37.90 4.52
150 520 1.444553 CTCGGTCTCGTGGTCTTGC 60.445 63.158 0.00 0.00 37.69 4.01
151 521 1.444553 GCTCGGTCTCGTGGTCTTG 60.445 63.158 0.00 0.00 37.69 3.02
152 522 2.963371 GCTCGGTCTCGTGGTCTT 59.037 61.111 0.00 0.00 37.69 3.01
153 523 3.432588 CGCTCGGTCTCGTGGTCT 61.433 66.667 0.00 0.00 37.69 3.85
154 524 3.735029 ACGCTCGGTCTCGTGGTC 61.735 66.667 0.00 0.00 37.55 4.02
277 647 1.423395 GTTGAGTGGCAAGACGAGAG 58.577 55.000 0.00 0.00 37.12 3.20
342 712 7.370383 ACTATTTATTGCAGAACAACAAGTGG 58.630 34.615 0.00 0.00 42.27 4.00
390 762 6.338937 TGTACGCCAATACATACATACAACA 58.661 36.000 0.00 0.00 29.97 3.33
391 763 6.831727 TGTACGCCAATACATACATACAAC 57.168 37.500 0.00 0.00 29.97 3.32
392 764 9.145865 CATATGTACGCCAATACATACATACAA 57.854 33.333 10.67 0.00 46.00 2.41
393 765 7.762159 CCATATGTACGCCAATACATACATACA 59.238 37.037 10.67 0.00 46.00 2.29
394 766 7.223971 CCCATATGTACGCCAATACATACATAC 59.776 40.741 10.67 0.00 46.00 2.39
395 767 7.124448 TCCCATATGTACGCCAATACATACATA 59.876 37.037 10.67 5.65 46.00 2.29
396 768 6.070481 TCCCATATGTACGCCAATACATACAT 60.070 38.462 10.67 0.00 46.00 2.29
436 817 2.295909 GGCACATGGTTTACTTGCTCAA 59.704 45.455 0.00 0.00 33.55 3.02
460 841 1.299926 CTCGCTGGGCCGTACATAC 60.300 63.158 0.00 0.00 0.00 2.39
461 842 3.125607 CTCGCTGGGCCGTACATA 58.874 61.111 0.00 0.00 0.00 2.29
462 843 4.530857 GCTCGCTGGGCCGTACAT 62.531 66.667 0.00 0.00 0.00 2.29
482 2099 0.808125 CAGAGACTCAGAGTGGACCG 59.192 60.000 8.15 0.00 0.00 4.79
488 2105 3.011144 TGGGAATCTCAGAGACTCAGAGT 59.989 47.826 20.60 1.46 32.60 3.24
492 2109 3.036819 CCATGGGAATCTCAGAGACTCA 58.963 50.000 10.98 2.27 0.00 3.41
550 2167 1.484653 TCCTGTGTGTTAGTGTGCACT 59.515 47.619 19.41 9.90 45.02 4.40
551 2168 1.597663 GTCCTGTGTGTTAGTGTGCAC 59.402 52.381 10.75 10.75 36.26 4.57
552 2169 1.208293 TGTCCTGTGTGTTAGTGTGCA 59.792 47.619 0.00 0.00 0.00 4.57
553 2170 1.597663 GTGTCCTGTGTGTTAGTGTGC 59.402 52.381 0.00 0.00 0.00 4.57
554 2171 2.866156 CTGTGTCCTGTGTGTTAGTGTG 59.134 50.000 0.00 0.00 0.00 3.82
555 2172 2.741878 GCTGTGTCCTGTGTGTTAGTGT 60.742 50.000 0.00 0.00 0.00 3.55
556 2173 1.867233 GCTGTGTCCTGTGTGTTAGTG 59.133 52.381 0.00 0.00 0.00 2.74
557 2174 1.538204 CGCTGTGTCCTGTGTGTTAGT 60.538 52.381 0.00 0.00 0.00 2.24
558 2175 1.139989 CGCTGTGTCCTGTGTGTTAG 58.860 55.000 0.00 0.00 0.00 2.34
559 2176 0.747852 TCGCTGTGTCCTGTGTGTTA 59.252 50.000 0.00 0.00 0.00 2.41
560 2177 0.106708 ATCGCTGTGTCCTGTGTGTT 59.893 50.000 0.00 0.00 0.00 3.32
561 2178 0.319900 GATCGCTGTGTCCTGTGTGT 60.320 55.000 0.00 0.00 0.00 3.72
562 2179 0.319813 TGATCGCTGTGTCCTGTGTG 60.320 55.000 0.00 0.00 0.00 3.82
563 2180 0.610174 ATGATCGCTGTGTCCTGTGT 59.390 50.000 0.00 0.00 0.00 3.72
564 2181 1.004595 CATGATCGCTGTGTCCTGTG 58.995 55.000 0.00 0.00 0.00 3.66
565 2182 0.610174 ACATGATCGCTGTGTCCTGT 59.390 50.000 0.00 0.00 0.00 4.00
566 2183 1.004595 CACATGATCGCTGTGTCCTG 58.995 55.000 16.27 0.00 39.30 3.86
567 2184 3.448267 CACATGATCGCTGTGTCCT 57.552 52.632 16.27 0.00 39.30 3.85
572 2189 2.102438 CGCCACACATGATCGCTGT 61.102 57.895 0.00 0.00 0.00 4.40
581 2198 2.483876 GCTGATGTATACGCCACACAT 58.516 47.619 0.00 0.00 35.65 3.21
585 2202 0.944311 CGGGCTGATGTATACGCCAC 60.944 60.000 17.81 8.89 44.23 5.01
692 2309 2.647299 TGATAGAGGCAAAGGGTCCAAA 59.353 45.455 0.00 0.00 0.00 3.28
693 2310 2.274542 TGATAGAGGCAAAGGGTCCAA 58.725 47.619 0.00 0.00 0.00 3.53
790 2407 2.543430 TGATCGTGTGTTCATGTGTGTG 59.457 45.455 0.00 0.00 32.85 3.82
791 2408 2.832563 TGATCGTGTGTTCATGTGTGT 58.167 42.857 0.00 0.00 32.85 3.72
833 2450 2.110213 GTGCGTGTGAGTTGGGGA 59.890 61.111 0.00 0.00 0.00 4.81
977 2594 0.512952 CTTGGCGTGAACTGTAGTGC 59.487 55.000 0.00 0.00 0.00 4.40
1001 2618 3.198872 GAGGGAGCAAGAAACCTTATCG 58.801 50.000 0.00 0.00 32.42 2.92
1072 2693 3.177228 CATGATAAGGGAGGGACCTAGG 58.823 54.545 7.41 7.41 40.87 3.02
1088 2713 0.464916 TGCATCGAGCCTTGCATGAT 60.465 50.000 7.31 0.00 43.54 2.45
1121 2746 1.449956 GGAGCAGGCTCTTGAGCAG 60.450 63.158 21.97 15.12 42.38 4.24
1168 2793 0.470080 CGAGGAAGCCCATCTCCCTA 60.470 60.000 0.00 0.00 33.88 3.53
1307 2932 1.003233 GGTGGCACCTCCTCAAGAC 60.003 63.158 29.22 0.00 34.73 3.01
1397 3022 1.254284 ACCTGCGTCCTCTTCCTCAG 61.254 60.000 0.00 0.00 0.00 3.35
1442 3067 1.079819 ACTCATCGTCCACGGCTTG 60.080 57.895 0.00 0.00 40.29 4.01
1525 3150 0.980423 GAAGAGCCCTCACCAGAAGT 59.020 55.000 0.00 0.00 0.00 3.01
1568 3193 1.956170 CCGCACACGCAAAGAGACT 60.956 57.895 0.00 0.00 38.40 3.24
1622 3270 0.820482 TGCATGCTGTGAGTTGCTGT 60.820 50.000 20.33 0.00 36.10 4.40
1720 3368 7.097623 ACTCTAGAGAGAAGGGAGCATAATA 57.902 40.000 26.57 0.00 44.74 0.98
1724 3372 3.971468 ACTCTAGAGAGAAGGGAGCAT 57.029 47.619 26.57 0.00 44.74 3.79
1725 3373 3.748645 AACTCTAGAGAGAAGGGAGCA 57.251 47.619 26.57 0.00 44.74 4.26
1726 3374 3.887110 GGTAACTCTAGAGAGAAGGGAGC 59.113 52.174 26.57 8.32 44.74 4.70
1727 3375 5.118729 TGGTAACTCTAGAGAGAAGGGAG 57.881 47.826 26.57 0.00 44.74 4.30
1728 3376 5.735733 ATGGTAACTCTAGAGAGAAGGGA 57.264 43.478 26.57 4.20 44.74 4.20
1729 3377 7.094549 CGATTATGGTAACTCTAGAGAGAAGGG 60.095 44.444 26.57 0.00 44.74 3.95
1730 3378 7.094549 CCGATTATGGTAACTCTAGAGAGAAGG 60.095 44.444 26.57 9.28 44.74 3.46
1731 3379 7.446013 ACCGATTATGGTAACTCTAGAGAGAAG 59.554 40.741 26.57 0.04 41.79 2.85
1732 3380 7.288560 ACCGATTATGGTAACTCTAGAGAGAA 58.711 38.462 26.57 7.30 41.79 2.87
1733 3381 6.839454 ACCGATTATGGTAACTCTAGAGAGA 58.161 40.000 26.57 10.29 41.79 3.10
1734 3382 6.938030 AGACCGATTATGGTAACTCTAGAGAG 59.062 42.308 26.57 3.49 44.01 3.20
1735 3383 6.711194 CAGACCGATTATGGTAACTCTAGAGA 59.289 42.308 26.57 3.47 44.01 3.10
1736 3384 6.487331 ACAGACCGATTATGGTAACTCTAGAG 59.513 42.308 18.49 18.49 44.01 2.43
1737 3385 6.363065 ACAGACCGATTATGGTAACTCTAGA 58.637 40.000 0.00 0.00 44.01 2.43
1738 3386 6.636562 ACAGACCGATTATGGTAACTCTAG 57.363 41.667 0.00 0.00 44.01 2.43
1739 3387 6.604396 TGAACAGACCGATTATGGTAACTCTA 59.396 38.462 0.00 0.00 44.01 2.43
1740 3388 5.421056 TGAACAGACCGATTATGGTAACTCT 59.579 40.000 0.00 0.00 44.01 3.24
1741 3389 5.657474 TGAACAGACCGATTATGGTAACTC 58.343 41.667 0.00 0.00 44.01 3.01
1742 3390 5.670792 TGAACAGACCGATTATGGTAACT 57.329 39.130 0.00 0.00 44.01 2.24
1743 3391 5.640357 TGTTGAACAGACCGATTATGGTAAC 59.360 40.000 0.00 0.00 44.01 2.50
1744 3392 5.795972 TGTTGAACAGACCGATTATGGTAA 58.204 37.500 0.00 0.00 44.01 2.85
1745 3393 5.408880 TGTTGAACAGACCGATTATGGTA 57.591 39.130 0.00 0.00 44.01 3.25
1747 3395 5.572211 CATTGTTGAACAGACCGATTATGG 58.428 41.667 0.00 0.00 0.00 2.74
1748 3396 5.030295 GCATTGTTGAACAGACCGATTATG 58.970 41.667 0.00 0.00 0.00 1.90
1749 3397 4.699735 TGCATTGTTGAACAGACCGATTAT 59.300 37.500 0.00 0.00 0.00 1.28
1750 3398 4.068599 TGCATTGTTGAACAGACCGATTA 58.931 39.130 0.00 0.00 0.00 1.75
1751 3399 2.884012 TGCATTGTTGAACAGACCGATT 59.116 40.909 0.00 0.00 0.00 3.34
1752 3400 2.503331 TGCATTGTTGAACAGACCGAT 58.497 42.857 0.00 0.00 0.00 4.18
1753 3401 1.960417 TGCATTGTTGAACAGACCGA 58.040 45.000 0.00 0.00 0.00 4.69
1754 3402 2.030893 ACATGCATTGTTGAACAGACCG 60.031 45.455 0.00 0.00 33.74 4.79
1755 3403 3.004629 TGACATGCATTGTTGAACAGACC 59.995 43.478 0.00 0.00 39.18 3.85
1756 3404 4.227512 TGACATGCATTGTTGAACAGAC 57.772 40.909 0.00 0.00 39.18 3.51
1757 3405 6.762702 ATATGACATGCATTGTTGAACAGA 57.237 33.333 0.00 0.00 39.18 3.41
1758 3406 6.630045 CGTATATGACATGCATTGTTGAACAG 59.370 38.462 0.00 0.00 39.18 3.16
1759 3407 6.485393 CGTATATGACATGCATTGTTGAACA 58.515 36.000 0.00 0.00 39.18 3.18
1760 3408 5.396362 GCGTATATGACATGCATTGTTGAAC 59.604 40.000 0.00 0.00 39.18 3.18
1761 3409 5.509771 GCGTATATGACATGCATTGTTGAA 58.490 37.500 0.00 0.00 39.18 2.69
1762 3410 4.318689 CGCGTATATGACATGCATTGTTGA 60.319 41.667 0.00 0.00 39.18 3.18
1763 3411 3.901877 CGCGTATATGACATGCATTGTTG 59.098 43.478 0.00 0.00 39.18 3.33
1764 3412 3.606846 GCGCGTATATGACATGCATTGTT 60.607 43.478 8.43 0.00 39.18 2.83
1765 3413 2.096268 GCGCGTATATGACATGCATTGT 60.096 45.455 8.43 0.00 42.79 2.71
1766 3414 2.096318 TGCGCGTATATGACATGCATTG 60.096 45.455 8.43 0.00 38.44 2.82
1767 3415 2.096268 GTGCGCGTATATGACATGCATT 60.096 45.455 8.43 0.00 39.29 3.56
1768 3416 1.460743 GTGCGCGTATATGACATGCAT 59.539 47.619 8.43 0.00 39.29 3.96
1769 3417 0.858583 GTGCGCGTATATGACATGCA 59.141 50.000 8.43 0.00 35.95 3.96
1770 3418 0.858583 TGTGCGCGTATATGACATGC 59.141 50.000 8.43 0.00 0.00 4.06
1771 3419 2.730928 TGATGTGCGCGTATATGACATG 59.269 45.455 11.68 0.00 0.00 3.21
1772 3420 3.025287 TGATGTGCGCGTATATGACAT 57.975 42.857 11.68 4.76 0.00 3.06
1773 3421 2.500509 TGATGTGCGCGTATATGACA 57.499 45.000 11.68 1.13 0.00 3.58
1774 3422 5.509605 TTATTGATGTGCGCGTATATGAC 57.490 39.130 11.68 0.00 0.00 3.06
1775 3423 5.866633 TGATTATTGATGTGCGCGTATATGA 59.133 36.000 11.68 0.00 0.00 2.15
1776 3424 6.093532 TGATTATTGATGTGCGCGTATATG 57.906 37.500 11.68 0.00 0.00 1.78
1777 3425 6.908870 ATGATTATTGATGTGCGCGTATAT 57.091 33.333 8.43 7.17 0.00 0.86
1778 3426 6.720012 AATGATTATTGATGTGCGCGTATA 57.280 33.333 8.43 0.47 0.00 1.47
1779 3427 5.611796 AATGATTATTGATGTGCGCGTAT 57.388 34.783 8.43 0.00 0.00 3.06
1780 3428 5.416862 AAATGATTATTGATGTGCGCGTA 57.583 34.783 8.43 0.00 0.00 4.42
1781 3429 3.969117 AATGATTATTGATGTGCGCGT 57.031 38.095 8.43 0.00 0.00 6.01
1782 3430 4.734370 TGAAAATGATTATTGATGTGCGCG 59.266 37.500 0.00 0.00 0.00 6.86
1858 3506 1.974265 TTCAATTTCACCGGAGTGCA 58.026 45.000 9.46 0.00 44.16 4.57
1859 3507 3.575965 ATTTCAATTTCACCGGAGTGC 57.424 42.857 9.46 0.00 44.16 4.40
1860 3508 5.376854 AGAATTTCAATTTCACCGGAGTG 57.623 39.130 9.46 0.00 46.00 3.51
1861 3509 4.459337 GGAGAATTTCAATTTCACCGGAGT 59.541 41.667 9.46 0.00 0.00 3.85
1866 3514 5.371115 TCACGGAGAATTTCAATTTCACC 57.629 39.130 0.00 0.00 0.00 4.02
1920 3568 5.007921 ACTTGAACATTTGCAAAATCTTGGC 59.992 36.000 17.19 7.22 32.76 4.52
1989 3637 4.298103 AGTCTCCACATTGAGATTTGCT 57.702 40.909 0.00 0.00 42.97 3.91
2049 3697 8.168058 TCCCTAAAACTAAGTTGGCTAAGATTT 58.832 33.333 0.00 0.00 0.00 2.17
2067 3715 5.882000 GGTATAGCTTTCGGTTTCCCTAAAA 59.118 40.000 0.00 0.00 0.00 1.52
2074 3722 6.973229 TTACTTGGTATAGCTTTCGGTTTC 57.027 37.500 3.20 0.00 0.00 2.78
2119 3767 6.857964 CCTACAAATGAAATGATACGCAATCC 59.142 38.462 0.00 0.00 33.22 3.01
2181 3829 2.985282 CGCTGGCAACCACACCAT 60.985 61.111 0.00 0.00 34.82 3.55
2578 4242 2.505819 GCTCTTTGTCCCCTCTTGGATA 59.494 50.000 0.00 0.00 36.63 2.59
2635 4299 2.225019 GTCAGGAGATTGGCGCATATTG 59.775 50.000 10.83 0.00 0.00 1.90
2647 4311 5.538433 GGTAGCTATCTGAAAGTCAGGAGAT 59.462 44.000 0.00 5.12 44.39 2.75


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

AutoCloner maintained by Alex Coulton.