Multiple sequence alignment - TraesCS2B01G317300

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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 TraesCS2B01G317300 chr2B 100.000 4937 0 0 1 4937 453015778 453020714 0.000000e+00 9118.0
1 TraesCS2B01G317300 chr2B 94.983 598 29 1 174 770 47253633 47253036 0.000000e+00 937.0
2 TraesCS2B01G317300 chr2B 94.693 603 30 2 174 774 436266681 436266079 0.000000e+00 935.0
3 TraesCS2B01G317300 chr2B 83.824 204 25 3 4742 4937 780870045 780869842 2.350000e-43 187.0
4 TraesCS2B01G317300 chr2A 95.269 3488 115 20 768 4226 516392724 516396190 0.000000e+00 5481.0
5 TraesCS2B01G317300 chr2A 87.175 616 55 9 4236 4832 516396237 516396847 0.000000e+00 678.0
6 TraesCS2B01G317300 chr2D 95.148 3421 112 27 830 4226 382168031 382171421 0.000000e+00 5349.0
7 TraesCS2B01G317300 chr2D 87.361 720 57 14 4236 4937 382171468 382172171 0.000000e+00 795.0
8 TraesCS2B01G317300 chr2D 91.549 142 11 1 3 144 382167640 382167780 1.400000e-45 195.0
9 TraesCS2B01G317300 chr2D 95.000 40 2 0 134 173 382167966 382168005 4.130000e-06 63.9
10 TraesCS2B01G317300 chr5B 95.630 595 25 1 174 767 530709858 530709264 0.000000e+00 953.0
11 TraesCS2B01G317300 chr5B 94.702 604 29 3 174 774 677651296 677650693 0.000000e+00 935.0
12 TraesCS2B01G317300 chr3B 94.563 607 30 3 174 777 685611403 685612009 0.000000e+00 935.0
13 TraesCS2B01G317300 chr3B 81.159 207 27 7 4742 4937 105471784 105471579 6.620000e-34 156.0
14 TraesCS2B01G317300 chr3B 92.727 55 4 0 4742 4796 762587178 762587232 4.100000e-11 80.5
15 TraesCS2B01G317300 chr3B 85.526 76 6 2 4742 4817 20293043 20292973 1.910000e-09 75.0
16 TraesCS2B01G317300 chr7B 94.966 596 28 2 176 770 636462079 636461485 0.000000e+00 933.0
17 TraesCS2B01G317300 chr7B 78.947 209 30 8 4737 4932 594057562 594057769 4.010000e-26 130.0
18 TraesCS2B01G317300 chr6B 95.110 593 28 1 174 765 51383451 51384043 0.000000e+00 933.0
19 TraesCS2B01G317300 chr1B 94.781 594 30 1 174 766 499192978 499193571 0.000000e+00 924.0
20 TraesCS2B01G317300 chr4B 94.362 603 31 3 174 773 592204832 592204230 0.000000e+00 922.0
21 TraesCS2B01G317300 chr7A 83.333 204 26 3 4741 4937 205112902 205112700 1.090000e-41 182.0
22 TraesCS2B01G317300 chr3D 79.602 201 24 11 4741 4934 593120037 593119847 1.440000e-25 128.0
23 TraesCS2B01G317300 chr3A 79.798 99 17 3 4802 4897 63912082 63912180 8.870000e-08 69.4
24 TraesCS2B01G317300 chr6D 94.737 38 1 1 75 111 425996561 425996598 1.920000e-04 58.4


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 TraesCS2B01G317300 chr2B 453015778 453020714 4936 False 9118.000 9118 100.0000 1 4937 1 chr2B.!!$F1 4936
1 TraesCS2B01G317300 chr2B 47253036 47253633 597 True 937.000 937 94.9830 174 770 1 chr2B.!!$R1 596
2 TraesCS2B01G317300 chr2B 436266079 436266681 602 True 935.000 935 94.6930 174 774 1 chr2B.!!$R2 600
3 TraesCS2B01G317300 chr2A 516392724 516396847 4123 False 3079.500 5481 91.2220 768 4832 2 chr2A.!!$F1 4064
4 TraesCS2B01G317300 chr2D 382167640 382172171 4531 False 1600.725 5349 92.2645 3 4937 4 chr2D.!!$F1 4934
5 TraesCS2B01G317300 chr5B 530709264 530709858 594 True 953.000 953 95.6300 174 767 1 chr5B.!!$R1 593
6 TraesCS2B01G317300 chr5B 677650693 677651296 603 True 935.000 935 94.7020 174 774 1 chr5B.!!$R2 600
7 TraesCS2B01G317300 chr3B 685611403 685612009 606 False 935.000 935 94.5630 174 777 1 chr3B.!!$F1 603
8 TraesCS2B01G317300 chr7B 636461485 636462079 594 True 933.000 933 94.9660 176 770 1 chr7B.!!$R1 594
9 TraesCS2B01G317300 chr6B 51383451 51384043 592 False 933.000 933 95.1100 174 765 1 chr6B.!!$F1 591
10 TraesCS2B01G317300 chr1B 499192978 499193571 593 False 924.000 924 94.7810 174 766 1 chr1B.!!$F1 592
11 TraesCS2B01G317300 chr4B 592204230 592204832 602 True 922.000 922 94.3620 174 773 1 chr4B.!!$R1 599

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
410 442 0.180406 GGTGTGTGGAGGTGTGTCTT 59.820 55.000 0.00 0.00 0.00 3.01 F
411 443 1.408266 GGTGTGTGGAGGTGTGTCTTT 60.408 52.381 0.00 0.00 0.00 2.52 F
1950 1999 0.388778 TGCGTGGCAAATGCATCTTG 60.389 50.000 0.00 8.34 46.04 3.02 F
1951 2000 0.388907 GCGTGGCAAATGCATCTTGT 60.389 50.000 17.25 0.00 44.36 3.16 F
2257 2308 0.461339 CATTGCTTCATGCTTGGGCC 60.461 55.000 0.00 0.00 43.37 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2000 0.037734 TGACAGACGGAGAGGCTACA 59.962 55.0 0.00 0.0 34.57 2.74 R
1955 2004 0.318762 AACTTGACAGACGGAGAGGC 59.681 55.0 0.00 0.0 0.00 4.70 R
3405 3460 0.107654 GATTCAGTACAGCGGGCCTT 60.108 55.0 0.84 0.0 0.00 4.35 R
3407 3462 0.811616 CAGATTCAGTACAGCGGGCC 60.812 60.0 0.00 0.0 0.00 5.80 R
4111 4182 0.537143 AGCTCAAAACATGACCGGCA 60.537 50.0 0.00 0.0 33.47 5.69 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
22 23 2.941891 TGCAAAAGACGATCACGAAC 57.058 45.000 0.00 0.00 42.66 3.95
41 42 1.458064 ACCGCGACAAATTTAGTGACG 59.542 47.619 8.23 0.00 37.25 4.35
52 53 5.493133 AATTTAGTGACGTGCAAGTGAAA 57.507 34.783 10.87 5.70 0.00 2.69
169 201 3.664107 TGATGACAAAGAAACCGAGGAG 58.336 45.455 0.00 0.00 0.00 3.69
243 275 2.085042 GATCTCGGTAAGGGTCGGCC 62.085 65.000 0.00 0.00 0.00 6.13
319 351 2.559840 GAAGACGAGACGGCGACA 59.440 61.111 16.62 0.00 41.28 4.35
320 352 1.796749 GAAGACGAGACGGCGACAC 60.797 63.158 16.62 5.06 41.28 3.67
349 381 4.788075 TGAAGATGGAATAAAGGTCTCCCA 59.212 41.667 0.00 0.00 0.00 4.37
393 425 1.134401 CATCTAGCATCGTTGGTGGGT 60.134 52.381 8.40 0.00 34.79 4.51
410 442 0.180406 GGTGTGTGGAGGTGTGTCTT 59.820 55.000 0.00 0.00 0.00 3.01
411 443 1.408266 GGTGTGTGGAGGTGTGTCTTT 60.408 52.381 0.00 0.00 0.00 2.52
456 488 1.978542 CTCGGATCTCGTCGTTGTTT 58.021 50.000 0.00 0.00 40.32 2.83
457 489 2.730090 GCTCGGATCTCGTCGTTGTTTA 60.730 50.000 0.00 0.00 40.32 2.01
534 567 2.186160 CGGTTGCTGTTCTGGTGCA 61.186 57.895 0.00 0.00 34.69 4.57
731 765 4.068599 TCGTTGTACTGCCATGATTGAAA 58.931 39.130 0.00 0.00 0.00 2.69
739 773 8.747471 TGTACTGCCATGATTGAAAATGAATAA 58.253 29.630 0.00 0.00 0.00 1.40
981 1018 1.767036 CCCATGACCAGGTGACCAA 59.233 57.895 3.63 0.00 0.00 3.67
1224 1261 1.676678 GCCACTGGGATGTCGAGCTA 61.677 60.000 0.00 0.00 35.59 3.32
1354 1391 4.189231 CGGGTTAGTATCTTTGGGAACTG 58.811 47.826 0.00 0.00 0.00 3.16
1387 1424 2.025037 TCCTCCTTGGCACATGCTTTAT 60.025 45.455 3.48 0.00 39.30 1.40
1404 1442 5.301551 TGCTTTATCTTTTCAGCTGTTTGGA 59.698 36.000 14.67 8.90 33.15 3.53
1413 1451 1.463056 CAGCTGTTTGGACGCGAATTA 59.537 47.619 15.93 0.00 32.91 1.40
1515 1555 3.498397 CAGATGTTTCTAGTGTGCGGTTT 59.502 43.478 0.00 0.00 0.00 3.27
1541 1581 4.346418 GTCAGGATGGTATGATCTTGGAGT 59.654 45.833 0.00 0.00 36.16 3.85
1558 1598 7.871853 TCTTGGAGTATTACTTTTTGAACTGC 58.128 34.615 0.00 0.00 0.00 4.40
1559 1599 6.569179 TGGAGTATTACTTTTTGAACTGCC 57.431 37.500 0.00 0.00 0.00 4.85
1570 1610 4.582701 TTTGAACTGCCAAACAATCGAT 57.417 36.364 0.00 0.00 31.73 3.59
1593 1633 2.484264 AGTTTGTATCAGAAAGGCGTGC 59.516 45.455 0.00 0.00 0.00 5.34
1620 1660 3.089284 GGAGTAGGGGTTTGATTGTTGG 58.911 50.000 0.00 0.00 0.00 3.77
1630 1670 4.082245 GGTTTGATTGTTGGGTGTGGATAG 60.082 45.833 0.00 0.00 0.00 2.08
1633 1673 1.904287 TTGTTGGGTGTGGATAGTGC 58.096 50.000 0.00 0.00 0.00 4.40
1822 1863 2.993899 CTCAAAACCAGTGGCGTAGTAG 59.006 50.000 9.78 0.00 0.00 2.57
1823 1864 2.629137 TCAAAACCAGTGGCGTAGTAGA 59.371 45.455 9.78 0.00 0.00 2.59
1824 1865 2.993899 CAAAACCAGTGGCGTAGTAGAG 59.006 50.000 9.78 0.00 0.00 2.43
1825 1866 2.211250 AACCAGTGGCGTAGTAGAGA 57.789 50.000 9.78 0.00 0.00 3.10
1826 1867 2.438800 ACCAGTGGCGTAGTAGAGAT 57.561 50.000 9.78 0.00 0.00 2.75
1827 1868 2.736347 ACCAGTGGCGTAGTAGAGATT 58.264 47.619 9.78 0.00 0.00 2.40
1828 1869 2.688958 ACCAGTGGCGTAGTAGAGATTC 59.311 50.000 9.78 0.00 0.00 2.52
1829 1870 2.688446 CCAGTGGCGTAGTAGAGATTCA 59.312 50.000 0.00 0.00 0.00 2.57
1830 1871 3.319405 CCAGTGGCGTAGTAGAGATTCAT 59.681 47.826 0.00 0.00 0.00 2.57
1831 1872 4.294232 CAGTGGCGTAGTAGAGATTCATG 58.706 47.826 0.00 0.00 0.00 3.07
1879 1928 3.275999 AGTGCGTTAAGTGAACCTTGTT 58.724 40.909 0.00 0.00 34.21 2.83
1895 1944 8.584157 TGAACCTTGTTGATTAATTGTTGCTAT 58.416 29.630 0.00 0.00 0.00 2.97
1908 1957 3.221771 TGTTGCTATGGCTTCTTGTTGT 58.778 40.909 1.68 0.00 39.59 3.32
1914 1963 5.106197 TGCTATGGCTTCTTGTTGTTGTATG 60.106 40.000 1.68 0.00 39.59 2.39
1950 1999 0.388778 TGCGTGGCAAATGCATCTTG 60.389 50.000 0.00 8.34 46.04 3.02
1951 2000 0.388907 GCGTGGCAAATGCATCTTGT 60.389 50.000 17.25 0.00 44.36 3.16
1952 2001 1.342555 CGTGGCAAATGCATCTTGTG 58.657 50.000 17.25 8.58 44.36 3.33
1953 2002 1.336148 CGTGGCAAATGCATCTTGTGT 60.336 47.619 17.25 0.00 44.36 3.72
1954 2003 2.095314 CGTGGCAAATGCATCTTGTGTA 60.095 45.455 17.25 6.84 44.36 2.90
1955 2004 3.504863 GTGGCAAATGCATCTTGTGTAG 58.495 45.455 17.25 0.00 44.36 2.74
1956 2005 2.094597 TGGCAAATGCATCTTGTGTAGC 60.095 45.455 17.25 7.07 44.36 3.58
1958 2007 2.165030 GCAAATGCATCTTGTGTAGCCT 59.835 45.455 17.25 0.00 41.59 4.58
2166 2217 6.861065 TGGTGATTAGTGTTTCAAAGAGTC 57.139 37.500 0.00 0.00 0.00 3.36
2257 2308 0.461339 CATTGCTTCATGCTTGGGCC 60.461 55.000 0.00 0.00 43.37 5.80
2271 2322 0.618458 TGGGCCAGTGTATTCCTGTC 59.382 55.000 0.00 0.00 0.00 3.51
2288 2339 4.467438 TCCTGTCTGATTACTGAGCATTGA 59.533 41.667 0.00 0.00 0.00 2.57
2308 2359 5.095145 TGATGTTTCCTCTCTCAATCTGG 57.905 43.478 0.00 0.00 0.00 3.86
2315 2366 5.407407 TCCTCTCTCAATCTGGTTTACAC 57.593 43.478 0.00 0.00 0.00 2.90
2343 2394 4.986783 AGCTAACCTTCCCTAAATATGCC 58.013 43.478 0.00 0.00 0.00 4.40
2354 2405 2.179377 AAATATGCCCCCATTGTGCT 57.821 45.000 0.00 0.00 32.85 4.40
2396 2447 7.166851 AGAAGTTCATATCATGCCTCATTAGG 58.833 38.462 5.50 0.00 46.76 2.69
2439 2491 5.823861 AGGTTTATTTGGTCATGGCTTTT 57.176 34.783 0.00 0.00 0.00 2.27
2465 2517 6.030228 GCTAATTGTAACTGCCTTTGTGATC 58.970 40.000 0.00 0.00 0.00 2.92
2532 2584 4.889409 ACTTTGGCTCTCATTGTCAAGAAA 59.111 37.500 0.00 0.00 0.00 2.52
2627 2680 7.362660 CCCAGATAAATACATGCATGAATCCTG 60.363 40.741 32.75 23.64 0.00 3.86
2644 2697 7.223584 TGAATCCTGAATTCTCACACAGTTAA 58.776 34.615 7.05 0.00 43.61 2.01
2645 2698 7.173218 TGAATCCTGAATTCTCACACAGTTAAC 59.827 37.037 7.05 0.00 43.61 2.01
2646 2699 6.174720 TCCTGAATTCTCACACAGTTAACT 57.825 37.500 1.12 1.12 0.00 2.24
2647 2700 6.223852 TCCTGAATTCTCACACAGTTAACTC 58.776 40.000 4.77 0.00 0.00 3.01
2648 2701 6.042093 TCCTGAATTCTCACACAGTTAACTCT 59.958 38.462 4.77 0.00 0.00 3.24
2649 2702 6.708054 CCTGAATTCTCACACAGTTAACTCTT 59.292 38.462 4.77 0.00 0.00 2.85
2650 2703 7.872993 CCTGAATTCTCACACAGTTAACTCTTA 59.127 37.037 4.77 0.00 0.00 2.10
2651 2704 9.261180 CTGAATTCTCACACAGTTAACTCTTAA 57.739 33.333 4.77 0.00 0.00 1.85
2719 2774 1.679977 CCTGACACTGGCCAATGGG 60.680 63.158 19.99 6.35 37.18 4.00
2762 2817 1.338020 GCTTCCTGGAAGTGTTGTTGG 59.662 52.381 31.20 9.71 41.27 3.77
3018 3073 2.691011 TCCCTGGGCGCAAAAATATTAC 59.309 45.455 10.83 0.00 0.00 1.89
3065 3120 2.665649 ATTCGTGCGGTCATAGACAA 57.334 45.000 0.00 0.00 33.68 3.18
3246 3301 0.835971 ACATTTTGAGGCCAACCCCC 60.836 55.000 5.01 0.00 36.11 5.40
3383 3438 9.058424 GGTACGTAATTCATTTTACTTTTCTGC 57.942 33.333 0.00 0.00 31.28 4.26
3405 3460 4.242475 CGTTACAGCACCATAGTCTGAAA 58.758 43.478 0.00 0.00 0.00 2.69
3407 3462 5.163953 CGTTACAGCACCATAGTCTGAAAAG 60.164 44.000 0.00 0.00 0.00 2.27
3423 3479 0.328258 AAAGGCCCGCTGTACTGAAT 59.672 50.000 0.00 0.00 0.00 2.57
3612 3683 1.899814 AGTGCACAAAGGGAGATACGA 59.100 47.619 21.04 0.00 0.00 3.43
3940 4011 4.620589 TTAACCAGTGACGGGTGATTTA 57.379 40.909 8.46 0.00 39.01 1.40
3954 4025 5.817816 CGGGTGATTTAAGTTGCTAGAATCT 59.182 40.000 0.00 0.00 0.00 2.40
4004 4075 6.872020 GGTTACACTATTGTTCTCTGCAGTTA 59.128 38.462 14.67 0.00 37.15 2.24
4007 4078 6.759272 ACACTATTGTTCTCTGCAGTTAGAA 58.241 36.000 14.67 13.44 28.43 2.10
4068 4139 6.340522 AGCAAAAATGCAAGTTCAGTTTAGT 58.659 32.000 3.41 0.00 33.78 2.24
4160 4231 2.143925 GTGAACTGTAACAGTCCTGCC 58.856 52.381 0.00 0.00 44.62 4.85
4183 4255 1.118965 TTCTTCCTCTGCACCGACCA 61.119 55.000 0.00 0.00 0.00 4.02
4226 4298 5.063180 TGATGATTTGAAACATGGCAGTC 57.937 39.130 0.00 0.00 0.00 3.51
4227 4299 4.768448 TGATGATTTGAAACATGGCAGTCT 59.232 37.500 0.00 0.00 0.00 3.24
4228 4300 5.244402 TGATGATTTGAAACATGGCAGTCTT 59.756 36.000 0.00 0.00 0.00 3.01
4229 4301 5.534207 TGATTTGAAACATGGCAGTCTTT 57.466 34.783 0.00 0.00 0.00 2.52
4230 4302 6.647334 TGATTTGAAACATGGCAGTCTTTA 57.353 33.333 0.00 0.00 0.00 1.85
4231 4303 7.048629 TGATTTGAAACATGGCAGTCTTTAA 57.951 32.000 0.00 0.00 0.00 1.52
4232 4304 6.922957 TGATTTGAAACATGGCAGTCTTTAAC 59.077 34.615 0.00 0.00 0.00 2.01
4233 4305 6.463995 TTTGAAACATGGCAGTCTTTAACT 57.536 33.333 0.00 0.00 39.44 2.24
4526 4652 6.721571 AAAGTTCATGTTGGTGATACGTAG 57.278 37.500 0.08 0.00 0.00 3.51
4530 4656 6.932400 AGTTCATGTTGGTGATACGTAGAAAA 59.068 34.615 0.08 0.00 0.00 2.29
4578 4704 9.169592 GAACTAGTGAGAGAGTACAATCTAAGT 57.830 37.037 0.00 0.00 0.00 2.24
4585 4711 9.916360 TGAGAGAGTACAATCTAAGTATGGTTA 57.084 33.333 0.00 0.00 0.00 2.85
4644 4771 7.162082 TCTAGAGGGACAATTTCAAGTTCTTC 58.838 38.462 0.00 0.00 0.00 2.87
4711 4839 8.360390 ACTTTGATTTGTAGGATTCTCAAAACC 58.640 33.333 3.65 0.00 35.28 3.27
4754 4882 4.000988 CACTTGTACGAGTAGGGCATTTT 58.999 43.478 15.57 0.00 0.00 1.82
4785 4913 3.033909 GCTCCATGGAGGCCTTAATTTT 58.966 45.455 36.92 0.00 42.19 1.82
4788 4916 4.882559 TCCATGGAGGCCTTAATTTTGAT 58.117 39.130 11.44 0.00 37.29 2.57
4789 4917 5.279685 TCCATGGAGGCCTTAATTTTGATT 58.720 37.500 11.44 0.00 37.29 2.57
4790 4918 5.725822 TCCATGGAGGCCTTAATTTTGATTT 59.274 36.000 11.44 0.00 37.29 2.17
4791 4919 6.215227 TCCATGGAGGCCTTAATTTTGATTTT 59.785 34.615 11.44 0.00 37.29 1.82
4792 4920 6.885918 CCATGGAGGCCTTAATTTTGATTTTT 59.114 34.615 6.77 0.00 0.00 1.94
4837 4969 6.407475 AAAAATCTGGAAAAATACGCATGC 57.593 33.333 7.91 7.91 0.00 4.06
4863 4995 6.028146 ACAAGGATGTAATGTGTACGTGTA 57.972 37.500 0.00 0.00 38.24 2.90
4868 5000 7.948357 AGGATGTAATGTGTACGTGTACATAT 58.052 34.615 15.25 14.76 45.61 1.78
4898 5030 7.093322 AGATGAAATACCTTGAATTGTGAGC 57.907 36.000 0.00 0.00 0.00 4.26
4899 5031 5.643379 TGAAATACCTTGAATTGTGAGCC 57.357 39.130 0.00 0.00 0.00 4.70
4900 5032 5.076182 TGAAATACCTTGAATTGTGAGCCA 58.924 37.500 0.00 0.00 0.00 4.75
4901 5033 5.716228 TGAAATACCTTGAATTGTGAGCCAT 59.284 36.000 0.00 0.00 0.00 4.40
4902 5034 6.889177 TGAAATACCTTGAATTGTGAGCCATA 59.111 34.615 0.00 0.00 0.00 2.74
4903 5035 6.699575 AATACCTTGAATTGTGAGCCATAC 57.300 37.500 0.00 0.00 0.00 2.39
4904 5036 4.032960 ACCTTGAATTGTGAGCCATACA 57.967 40.909 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.798223 TCGTGATCGTCTTTTGCAAGG 59.202 47.619 0.00 0.00 38.33 3.61
1 2 3.218398 GTTCGTGATCGTCTTTTGCAAG 58.782 45.455 0.00 0.00 38.33 4.01
9 10 2.202440 CGCGGTTCGTGATCGTCT 60.202 61.111 0.00 0.00 39.94 4.18
22 23 1.458064 ACGTCACTAAATTTGTCGCGG 59.542 47.619 6.13 0.00 0.00 6.46
98 99 4.162320 TCCATGTCAACTACTCCTCCATTC 59.838 45.833 0.00 0.00 0.00 2.67
99 100 4.104086 TCCATGTCAACTACTCCTCCATT 58.896 43.478 0.00 0.00 0.00 3.16
103 104 5.361285 ACATACTCCATGTCAACTACTCCTC 59.639 44.000 0.00 0.00 44.99 3.71
140 141 8.335532 TCGGTTTCTTTGTCATCAATTATTCT 57.664 30.769 0.00 0.00 33.32 2.40
144 176 6.234920 TCCTCGGTTTCTTTGTCATCAATTA 58.765 36.000 0.00 0.00 33.32 1.40
258 290 7.746475 CCTAGCAAAACTGAAAGAAACGATTAG 59.254 37.037 0.00 0.00 37.43 1.73
319 351 4.166919 CCTTTATTCCATCTTCAGGGAGGT 59.833 45.833 0.00 0.00 34.02 3.85
320 352 4.166919 ACCTTTATTCCATCTTCAGGGAGG 59.833 45.833 0.00 0.00 34.02 4.30
374 406 1.134401 CACCCACCAACGATGCTAGAT 60.134 52.381 0.00 0.00 0.00 1.98
393 425 1.408127 CCAAAGACACACCTCCACACA 60.408 52.381 0.00 0.00 0.00 3.72
410 442 2.421388 CCACCAAAGATAGATCCGCCAA 60.421 50.000 0.00 0.00 0.00 4.52
411 443 1.140852 CCACCAAAGATAGATCCGCCA 59.859 52.381 0.00 0.00 0.00 5.69
456 488 3.181517 CCGAAGACACACGAACGTAGATA 60.182 47.826 0.00 0.00 0.00 1.98
457 489 2.413765 CCGAAGACACACGAACGTAGAT 60.414 50.000 0.00 0.00 0.00 1.98
636 669 1.536073 TACCAGCACTGAAGCGAGCT 61.536 55.000 0.00 0.00 40.15 4.09
731 765 9.352784 TGCGAGAAAATTTTCGATTTATTCATT 57.647 25.926 21.98 3.39 41.92 2.57
981 1018 1.192146 TGGCCGTGAGAGCTTAGGTT 61.192 55.000 0.00 0.00 0.00 3.50
1387 1424 1.333619 GCGTCCAAACAGCTGAAAAGA 59.666 47.619 23.35 8.92 0.00 2.52
1404 1442 2.755650 GAGATCCATGGTAATTCGCGT 58.244 47.619 12.58 0.00 0.00 6.01
1413 1451 2.692709 ATCTCTCCGAGATCCATGGT 57.307 50.000 12.58 0.00 45.03 3.55
1515 1555 4.141642 CCAAGATCATACCATCCTGACACA 60.142 45.833 0.00 0.00 0.00 3.72
1541 1581 9.255304 GATTGTTTGGCAGTTCAAAAAGTAATA 57.745 29.630 5.49 0.00 38.21 0.98
1570 1610 4.153475 GCACGCCTTTCTGATACAAACTAA 59.847 41.667 0.00 0.00 0.00 2.24
1593 1633 1.621814 TCAAACCCCTACTCCAAGACG 59.378 52.381 0.00 0.00 0.00 4.18
1620 1660 1.486726 AGCTTAGGCACTATCCACACC 59.513 52.381 0.00 0.00 42.38 4.16
1633 1673 0.460987 CTCCGCCTGTCAAGCTTAGG 60.461 60.000 9.12 9.12 34.67 2.69
1694 1734 4.512944 GCAGTCTCTGAAATGTTTCACAGA 59.487 41.667 8.71 8.71 41.88 3.41
1822 1863 9.941325 AAATATACTGTCATCTCCATGAATCTC 57.059 33.333 0.00 0.00 40.90 2.75
1825 1866 9.664332 GCTAAATATACTGTCATCTCCATGAAT 57.336 33.333 0.00 0.00 40.90 2.57
1826 1867 8.650490 TGCTAAATATACTGTCATCTCCATGAA 58.350 33.333 0.00 0.00 40.90 2.57
1827 1868 8.193953 TGCTAAATATACTGTCATCTCCATGA 57.806 34.615 0.00 0.00 36.62 3.07
1828 1869 8.880750 CATGCTAAATATACTGTCATCTCCATG 58.119 37.037 0.00 0.00 0.00 3.66
1829 1870 8.819845 TCATGCTAAATATACTGTCATCTCCAT 58.180 33.333 0.00 0.00 0.00 3.41
1830 1871 8.090831 GTCATGCTAAATATACTGTCATCTCCA 58.909 37.037 0.00 0.00 0.00 3.86
1831 1872 8.090831 TGTCATGCTAAATATACTGTCATCTCC 58.909 37.037 0.00 0.00 0.00 3.71
1850 1899 2.223144 TCACTTAACGCACTTGTCATGC 59.777 45.455 0.00 0.00 39.81 4.06
1879 1928 7.093814 ACAAGAAGCCATAGCAACAATTAATCA 60.094 33.333 0.00 0.00 43.56 2.57
1895 1944 6.892658 ATTACATACAACAACAAGAAGCCA 57.107 33.333 0.00 0.00 0.00 4.75
1908 1957 7.115520 CGCAACATTCACCAAAATTACATACAA 59.884 33.333 0.00 0.00 0.00 2.41
1914 1963 4.149747 CCACGCAACATTCACCAAAATTAC 59.850 41.667 0.00 0.00 0.00 1.89
1950 1999 0.452585 GACAGACGGAGAGGCTACAC 59.547 60.000 0.00 0.00 34.57 2.90
1951 2000 0.037734 TGACAGACGGAGAGGCTACA 59.962 55.000 0.00 0.00 34.57 2.74
1952 2001 1.133407 CTTGACAGACGGAGAGGCTAC 59.867 57.143 0.00 0.00 34.57 3.58
1953 2002 1.271982 ACTTGACAGACGGAGAGGCTA 60.272 52.381 0.00 0.00 34.57 3.93
1954 2003 0.540830 ACTTGACAGACGGAGAGGCT 60.541 55.000 0.00 0.00 40.36 4.58
1955 2004 0.318762 AACTTGACAGACGGAGAGGC 59.681 55.000 0.00 0.00 0.00 4.70
1956 2005 2.821991 AAACTTGACAGACGGAGAGG 57.178 50.000 0.00 0.00 0.00 3.69
1958 2007 6.285224 TGAAATAAAACTTGACAGACGGAGA 58.715 36.000 0.00 0.00 0.00 3.71
1998 2049 7.136822 TGTACCTCTAGCAATGACCAATAAT 57.863 36.000 0.00 0.00 0.00 1.28
2037 2088 7.156876 TCCAAAAATAGCATGGAGTAACAAG 57.843 36.000 0.00 0.00 38.30 3.16
2089 2140 9.918630 AAATAATGTGGACTTCTTTCTTCATTG 57.081 29.630 0.00 0.00 0.00 2.82
2166 2217 6.757897 TCATTGATACCTTGCTTAAACTGG 57.242 37.500 0.00 0.00 0.00 4.00
2257 2308 6.867550 TCAGTAATCAGACAGGAATACACTG 58.132 40.000 0.00 0.00 41.64 3.66
2271 2322 6.318144 AGGAAACATCAATGCTCAGTAATCAG 59.682 38.462 0.00 0.00 0.00 2.90
2288 2339 5.511386 AACCAGATTGAGAGAGGAAACAT 57.489 39.130 0.00 0.00 0.00 2.71
2308 2359 6.379386 GGAAGGTTAGCTCATTTGTGTAAAC 58.621 40.000 0.00 0.00 0.00 2.01
2315 2366 8.571336 CATATTTAGGGAAGGTTAGCTCATTTG 58.429 37.037 0.00 0.00 0.00 2.32
2343 2394 1.548081 TGTCAATGAGCACAATGGGG 58.452 50.000 0.00 0.00 0.00 4.96
2354 2405 6.259829 TGAACTTCTCGATGTTTTGTCAATGA 59.740 34.615 0.00 0.00 0.00 2.57
2396 2447 1.303561 TGCAGTCCCATCTTGCCAC 60.304 57.895 0.00 0.00 0.00 5.01
2439 2491 6.234920 TCACAAAGGCAGTTACAATTAGCTA 58.765 36.000 0.00 0.00 0.00 3.32
2532 2584 5.197682 AGTTCGTAAGTACTGCAACTCTT 57.802 39.130 0.00 0.00 46.74 2.85
2575 2628 3.504863 GAAATGAGTGCACGCAAATGAT 58.495 40.909 27.03 7.62 0.00 2.45
2576 2629 2.351641 GGAAATGAGTGCACGCAAATGA 60.352 45.455 27.03 3.47 0.00 2.57
2577 2630 1.987770 GGAAATGAGTGCACGCAAATG 59.012 47.619 27.03 0.00 0.00 2.32
2644 2697 9.690913 AAAAGGGTTTAGTTTACAGTTAAGAGT 57.309 29.630 0.00 0.00 0.00 3.24
2719 2774 5.867166 CTTCTCATTCAAAGCTAGAAGCAC 58.133 41.667 7.12 0.00 45.56 4.40
2762 2817 7.432869 AGTGATAACATGAGCTCTCAATAGAC 58.567 38.462 16.19 3.30 43.58 2.59
3018 3073 4.571984 TGTGAATCAGAAGCATATGGAACG 59.428 41.667 4.56 0.00 0.00 3.95
3246 3301 4.559063 CATGCAGGCCCCTCTCCG 62.559 72.222 0.00 0.00 0.00 4.63
3383 3438 3.503827 TCAGACTATGGTGCTGTAACG 57.496 47.619 0.00 0.00 0.00 3.18
3405 3460 0.107654 GATTCAGTACAGCGGGCCTT 60.108 55.000 0.84 0.00 0.00 4.35
3407 3462 0.811616 CAGATTCAGTACAGCGGGCC 60.812 60.000 0.00 0.00 0.00 5.80
3612 3683 1.651987 CGGTGTAATGATGCCGTTCT 58.348 50.000 0.00 0.00 39.41 3.01
3644 3715 1.129326 GATTCCGACGTAGATTGCCG 58.871 55.000 0.00 0.00 0.00 5.69
3954 4025 8.361169 CCAAGAAAATGGGGTAAAATCTAAGA 57.639 34.615 0.00 0.00 36.79 2.10
4004 4075 4.899502 AGAAATGACACTCGATGGTTTCT 58.100 39.130 13.04 13.04 35.53 2.52
4068 4139 6.993786 TCAACTTATATCAAATTGACGCCA 57.006 33.333 0.00 0.00 0.00 5.69
4111 4182 0.537143 AGCTCAAAACATGACCGGCA 60.537 50.000 0.00 0.00 33.47 5.69
4113 4184 1.608590 ACAAGCTCAAAACATGACCGG 59.391 47.619 0.00 0.00 33.47 5.28
4116 4187 3.242739 ACGACACAAGCTCAAAACATGAC 60.243 43.478 0.00 0.00 33.47 3.06
4160 4231 2.383527 GGTGCAGAGGAAGAACGCG 61.384 63.158 3.53 3.53 0.00 6.01
4214 4286 8.232913 TCTAAAAGTTAAAGACTGCCATGTTT 57.767 30.769 0.00 0.00 39.00 2.83
4400 4513 7.106439 TCTCAATGTTACTTCCTTGCAAAAA 57.894 32.000 0.00 0.00 0.00 1.94
4464 4590 7.672983 TTGAATGACTATTTCTCAGTTGACC 57.327 36.000 0.00 0.00 0.00 4.02
4517 4643 5.969423 ACCCTCGAAATTTTCTACGTATCA 58.031 37.500 7.50 0.00 0.00 2.15
4526 4652 5.276067 CGTATCGTGTACCCTCGAAATTTTC 60.276 44.000 8.47 0.00 39.69 2.29
4530 4656 2.684881 ACGTATCGTGTACCCTCGAAAT 59.315 45.455 8.47 0.00 39.18 2.17
4559 4685 8.824756 AACCATACTTAGATTGTACTCTCTCA 57.175 34.615 0.00 0.00 0.00 3.27
4602 4728 9.325248 TCCCTCTAGAAATGAAAAATGGATTTT 57.675 29.630 0.00 0.00 43.85 1.82
4616 4743 8.166726 AGAACTTGAAATTGTCCCTCTAGAAAT 58.833 33.333 0.00 0.00 0.00 2.17
4675 4803 4.112634 ACAAATCAAAGTGGCCCTAGAA 57.887 40.909 0.00 0.00 0.00 2.10
4711 4839 6.971602 AGTGGACATGACACTATATTCGTAG 58.028 40.000 20.70 0.00 46.62 3.51
4818 4949 4.924305 ATGCATGCGTATTTTTCCAGAT 57.076 36.364 11.62 0.00 0.00 2.90
4823 4954 5.577835 TCCTTGTATGCATGCGTATTTTTC 58.422 37.500 21.99 9.81 0.00 2.29
4832 4964 5.217393 CACATTACATCCTTGTATGCATGC 58.783 41.667 11.82 11.82 38.12 4.06
4837 4969 6.533723 ACACGTACACATTACATCCTTGTATG 59.466 38.462 0.00 0.00 38.12 2.39
4874 5006 6.096001 GGCTCACAATTCAAGGTATTTCATCT 59.904 38.462 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.