Multiple sequence alignment - TraesCS4A01G045100

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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 TraesCS4A01G045100 chr4A 100.000 3965 0 0 1 3965 37298925 37302889 0.000000e+00 7323.0
1 TraesCS4A01G045100 chr4A 100.000 29 0 0 3183 3211 37302047 37302075 2.000000e-03 54.7
2 TraesCS4A01G045100 chr4A 100.000 29 0 0 3123 3151 37302107 37302135 2.000000e-03 54.7
3 TraesCS4A01G045100 chr4D 92.194 3254 171 37 734 3965 428972782 428969590 0.000000e+00 4525.0
4 TraesCS4A01G045100 chr4D 96.721 61 2 0 681 741 428974250 428974190 7.010000e-18 102.0
5 TraesCS4A01G045100 chr4B 92.039 3266 167 56 735 3965 527011435 527008228 0.000000e+00 4505.0
6 TraesCS4A01G045100 chr5A 94.411 662 31 5 3 661 105460534 105461192 0.000000e+00 1013.0
7 TraesCS4A01G045100 chr5A 82.444 581 50 17 84 663 477448609 477448080 1.000000e-125 460.0
8 TraesCS4A01G045100 chr5A 76.329 414 56 18 2137 2511 523751175 523751585 2.430000e-42 183.0
9 TraesCS4A01G045100 chr5A 89.130 46 5 0 687 732 83288561 83288516 1.540000e-04 58.4
10 TraesCS4A01G045100 chr1D 92.804 667 30 5 1 663 491594430 491595082 0.000000e+00 950.0
11 TraesCS4A01G045100 chr7A 82.465 576 51 19 81 656 1980176 1980701 3.610000e-125 459.0
12 TraesCS4A01G045100 chr6B 81.095 603 87 19 81 666 705392281 705391689 1.300000e-124 457.0
13 TraesCS4A01G045100 chr3A 82.570 568 47 15 90 656 646000030 645999514 1.680000e-123 453.0
14 TraesCS4A01G045100 chr3A 81.818 165 19 6 81 235 738429784 738429947 1.160000e-25 128.0
15 TraesCS4A01G045100 chr3A 81.818 165 19 6 81 235 738519034 738519197 1.160000e-25 128.0
16 TraesCS4A01G045100 chr5D 80.196 611 78 24 81 666 458682154 458681562 6.130000e-113 418.0
17 TraesCS4A01G045100 chr5D 76.998 413 55 17 2137 2511 372296812 372297222 2.420000e-47 200.0
18 TraesCS4A01G045100 chr5D 100.000 29 0 0 694 722 539654503 539654531 2.000000e-03 54.7
19 TraesCS4A01G045100 chr6A 83.288 371 53 6 292 656 577840542 577840175 2.280000e-87 333.0
20 TraesCS4A01G045100 chr2A 80.000 370 66 5 292 656 10513366 10513000 2.350000e-67 267.0
21 TraesCS4A01G045100 chr2A 84.177 158 19 6 510 663 705552441 705552286 8.880000e-32 148.0
22 TraesCS4A01G045100 chr7D 80.989 263 37 10 403 656 561542517 561542259 3.130000e-46 196.0
23 TraesCS4A01G045100 chr7D 79.724 217 32 10 458 667 566251988 566252199 3.190000e-31 147.0
24 TraesCS4A01G045100 chr3D 76.755 413 56 17 2137 2511 275629926 275630336 1.120000e-45 195.0
25 TraesCS4A01G045100 chr2D 82.286 175 23 7 493 662 43797637 43797808 1.150000e-30 145.0
26 TraesCS4A01G045100 chr2D 81.250 176 27 5 493 664 440329179 440329006 1.920000e-28 137.0
27 TraesCS4A01G045100 chr1A 82.635 167 23 5 493 656 481676321 481676158 4.130000e-30 143.0
28 TraesCS4A01G045100 chr2B 88.158 76 8 1 1 75 733836419 733836344 5.460000e-14 89.8
29 TraesCS4A01G045100 chr7B 100.000 30 0 0 689 718 559561269 559561298 5.540000e-04 56.5


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 TraesCS4A01G045100 chr4A 37298925 37302889 3964 False 2477.466667 7323 100.0000 1 3965 3 chr4A.!!$F1 3964
1 TraesCS4A01G045100 chr4D 428969590 428974250 4660 True 2313.500000 4525 94.4575 681 3965 2 chr4D.!!$R1 3284
2 TraesCS4A01G045100 chr4B 527008228 527011435 3207 True 4505.000000 4505 92.0390 735 3965 1 chr4B.!!$R1 3230
3 TraesCS4A01G045100 chr5A 105460534 105461192 658 False 1013.000000 1013 94.4110 3 661 1 chr5A.!!$F1 658
4 TraesCS4A01G045100 chr5A 477448080 477448609 529 True 460.000000 460 82.4440 84 663 1 chr5A.!!$R2 579
5 TraesCS4A01G045100 chr1D 491594430 491595082 652 False 950.000000 950 92.8040 1 663 1 chr1D.!!$F1 662
6 TraesCS4A01G045100 chr7A 1980176 1980701 525 False 459.000000 459 82.4650 81 656 1 chr7A.!!$F1 575
7 TraesCS4A01G045100 chr6B 705391689 705392281 592 True 457.000000 457 81.0950 81 666 1 chr6B.!!$R1 585
8 TraesCS4A01G045100 chr3A 645999514 646000030 516 True 453.000000 453 82.5700 90 656 1 chr3A.!!$R1 566
9 TraesCS4A01G045100 chr5D 458681562 458682154 592 True 418.000000 418 80.1960 81 666 1 chr5D.!!$R1 585

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
179 186 0.038744 AAGATGGTGAGCAGTTGGGG 59.961 55.000 0.0 0.0 0.00 4.96 F
880 2351 1.300697 AAGGACTCAACGTGGACGC 60.301 57.895 0.0 0.0 44.43 5.19 F
1685 3169 0.388907 CCAATTGCTCGTTTGCTGGG 60.389 55.000 0.0 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1048 2520 0.102844 ATCTCTCTCAAGCTCTGCGC 59.897 55.000 0.00 0.0 39.57 6.09 R
2410 3899 1.610522 GAAGCAACAACATCCTGCAGT 59.389 47.619 13.81 0.0 38.58 4.40 R
3431 4932 0.250166 GACAGGGTACACACGCCTTT 60.250 55.000 0.00 0.0 38.34 3.11 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
27 28 5.168569 GTTGTCGATGAAATGTGTCCTAGA 58.831 41.667 0.00 0.00 0.00 2.43
66 69 2.880890 GACATATGGCATGGGTTGTCTC 59.119 50.000 10.98 0.00 32.69 3.36
67 70 2.511218 ACATATGGCATGGGTTGTCTCT 59.489 45.455 10.98 0.00 0.00 3.10
68 71 3.053395 ACATATGGCATGGGTTGTCTCTT 60.053 43.478 10.98 0.00 0.00 2.85
70 73 3.737559 ATGGCATGGGTTGTCTCTTAA 57.262 42.857 0.00 0.00 0.00 1.85
71 74 3.517296 TGGCATGGGTTGTCTCTTAAA 57.483 42.857 0.00 0.00 0.00 1.52
73 76 4.415596 TGGCATGGGTTGTCTCTTAAATT 58.584 39.130 0.00 0.00 0.00 1.82
74 77 4.837860 TGGCATGGGTTGTCTCTTAAATTT 59.162 37.500 0.00 0.00 0.00 1.82
75 78 6.013379 TGGCATGGGTTGTCTCTTAAATTTA 58.987 36.000 0.00 0.00 0.00 1.40
76 79 6.667414 TGGCATGGGTTGTCTCTTAAATTTAT 59.333 34.615 0.00 0.00 0.00 1.40
179 186 0.038744 AAGATGGTGAGCAGTTGGGG 59.961 55.000 0.00 0.00 0.00 4.96
241 275 2.341846 TTTCCTTCTTGCTCCACGTT 57.658 45.000 0.00 0.00 0.00 3.99
392 431 1.911057 AGGTGTGATCTGTCGAGTGA 58.089 50.000 0.00 0.00 0.00 3.41
410 449 1.691434 TGATTTGTGGGAAGGGTTTGC 59.309 47.619 0.00 0.00 0.00 3.68
505 557 3.042682 TCTGGAGTGGTTAGTTGTCCAA 58.957 45.455 0.00 0.00 36.86 3.53
599 654 8.882736 GTCATACATGTGTCATCTGTTCATTTA 58.117 33.333 9.11 0.00 0.00 1.40
785 2256 2.339728 TTTTGGCCTGTTTAATCGCG 57.660 45.000 3.32 0.00 0.00 5.87
815 2286 3.436001 CGTGATTCCCTACGCAACT 57.564 52.632 0.00 0.00 33.25 3.16
880 2351 1.300697 AAGGACTCAACGTGGACGC 60.301 57.895 0.00 0.00 44.43 5.19
936 2407 3.172106 TTCCAGGACCAACGGCCA 61.172 61.111 2.24 0.00 0.00 5.36
1331 2806 2.176273 GCCTTCGAGATGTGCGCAT 61.176 57.895 15.91 13.71 38.18 4.73
1341 2816 2.833794 GATGTGCGCATCCCTAAACTA 58.166 47.619 26.49 0.00 44.26 2.24
1359 2834 9.826574 CCTAAACTATACTAATTACTTGCCACA 57.173 33.333 0.00 0.00 0.00 4.17
1392 2867 7.504238 TCTTGCTTCCTTTGTTTTACCAGATTA 59.496 33.333 0.00 0.00 0.00 1.75
1485 2967 2.415168 CGATTGCACGTCTGGTTGTTAT 59.585 45.455 0.00 0.00 0.00 1.89
1495 2977 3.187227 GTCTGGTTGTTATGCAGTGACAG 59.813 47.826 0.00 0.00 0.00 3.51
1503 2985 0.539051 ATGCAGTGACAGAGCCCTAC 59.461 55.000 0.00 0.00 0.00 3.18
1516 2998 2.766828 GAGCCCTACATAGTGGTTGACT 59.233 50.000 0.00 0.00 38.88 3.41
1538 3020 7.065085 TGACTCTGTTCTGTTCTTCTTTTTCAG 59.935 37.037 0.00 0.00 0.00 3.02
1556 3038 9.766277 CTTTTTCAGTAGATTGTTCTTATCTGC 57.234 33.333 0.00 0.00 35.68 4.26
1670 3154 1.710244 TGTGATGTTCCTGTCCCCAAT 59.290 47.619 0.00 0.00 0.00 3.16
1685 3169 0.388907 CCAATTGCTCGTTTGCTGGG 60.389 55.000 0.00 0.00 0.00 4.45
1712 3196 5.472148 GTGCCATCAGAATTTTGATTCACA 58.528 37.500 22.78 14.10 37.84 3.58
1725 3209 2.159430 TGATTCACAGAAAATCACGCCG 59.841 45.455 0.00 0.00 38.02 6.46
1726 3210 0.871722 TTCACAGAAAATCACGCCGG 59.128 50.000 0.00 0.00 0.00 6.13
1759 3243 4.159135 AGGATTTCCATTGCATGTTCTGAC 59.841 41.667 0.00 0.00 38.89 3.51
1794 3278 8.519799 TGATCCAAACCCTAAAAATATCTCAC 57.480 34.615 0.00 0.00 0.00 3.51
1801 3285 5.189145 ACCCTAAAAATATCTCACCGTGTCT 59.811 40.000 0.00 0.00 0.00 3.41
1835 3319 6.248433 AGTTGTTCTTCCAACCATGTCATAT 58.752 36.000 0.00 0.00 44.60 1.78
1865 3349 9.529325 TCTGTATTCGATTAGTTTCCTTATGTG 57.471 33.333 0.00 0.00 0.00 3.21
1866 3350 8.138365 TGTATTCGATTAGTTTCCTTATGTGC 57.862 34.615 0.00 0.00 0.00 4.57
1868 3352 5.353394 TCGATTAGTTTCCTTATGTGCCT 57.647 39.130 0.00 0.00 0.00 4.75
2410 3899 4.272489 CTGAAGCATGGGTTCTATTTGGA 58.728 43.478 9.26 0.00 40.24 3.53
2473 3962 2.746362 CTGGGAAGCTGTGATGAAGAAC 59.254 50.000 0.00 0.00 0.00 3.01
2524 4013 1.656441 GCGCCCAGCCATCATTTAG 59.344 57.895 0.00 0.00 40.81 1.85
2686 4175 4.194720 GTCGTCTCGCCGGCAGAT 62.195 66.667 28.98 0.00 31.49 2.90
2779 4268 3.936203 GACCTGGTGGCCACGTCA 61.936 66.667 29.08 20.69 38.69 4.35
2825 4314 4.583871 GTTGAAGACCCTGATCATCAACT 58.416 43.478 21.93 8.06 46.43 3.16
2908 4397 1.298264 CGTTTTGCTCAAGCGTGCA 60.298 52.632 0.00 0.00 45.83 4.57
2916 4405 2.094234 TGCTCAAGCGTGCATAGTTCTA 60.094 45.455 0.00 0.00 45.83 2.10
2925 4414 7.372451 AGCGTGCATAGTTCTAAATAAAACA 57.628 32.000 0.00 0.00 0.00 2.83
2950 4439 0.536006 GCTGGCAGAGTGGTTGTTCT 60.536 55.000 20.86 0.00 0.00 3.01
2979 4468 5.560966 AGTTTCGTTTCAGCTTTTTGAGA 57.439 34.783 0.00 0.00 0.00 3.27
3102 4591 1.836391 CTGTGTGTTCACCTGGGGA 59.164 57.895 0.00 0.00 43.26 4.81
3118 4607 2.291735 TGGGGATGAACATGTTCTGCAT 60.292 45.455 32.57 21.71 40.14 3.96
3130 4619 4.690184 TGTTCTGCATGATGTTTAGCTG 57.310 40.909 0.00 0.00 0.00 4.24
3131 4620 4.074259 TGTTCTGCATGATGTTTAGCTGT 58.926 39.130 0.00 0.00 0.00 4.40
3132 4621 4.520111 TGTTCTGCATGATGTTTAGCTGTT 59.480 37.500 0.00 0.00 0.00 3.16
3134 4623 5.801350 TCTGCATGATGTTTAGCTGTTAC 57.199 39.130 0.00 0.00 0.00 2.50
3135 4624 5.491070 TCTGCATGATGTTTAGCTGTTACT 58.509 37.500 0.00 0.00 0.00 2.24
3136 4625 5.352293 TCTGCATGATGTTTAGCTGTTACTG 59.648 40.000 0.00 0.00 0.00 2.74
3137 4626 4.142622 TGCATGATGTTTAGCTGTTACTGC 60.143 41.667 6.10 6.10 0.00 4.40
3138 4627 4.142622 GCATGATGTTTAGCTGTTACTGCA 60.143 41.667 16.07 0.33 0.00 4.41
3139 4628 5.619757 GCATGATGTTTAGCTGTTACTGCAA 60.620 40.000 16.07 6.11 0.00 4.08
3140 4629 5.356882 TGATGTTTAGCTGTTACTGCAAC 57.643 39.130 16.07 12.30 37.67 4.17
3141 4630 5.063204 TGATGTTTAGCTGTTACTGCAACT 58.937 37.500 16.07 0.00 38.05 3.16
3142 4631 5.530915 TGATGTTTAGCTGTTACTGCAACTT 59.469 36.000 16.07 10.23 38.05 2.66
3151 4640 7.923888 AGCTGTTACTGCAACTTTATATGATG 58.076 34.615 16.07 0.00 38.05 3.07
3177 4666 7.363530 GGAGTTTAGTTTTCTTTTGGACTGGTT 60.364 37.037 0.00 0.00 0.00 3.67
3178 4667 7.903145 AGTTTAGTTTTCTTTTGGACTGGTTT 58.097 30.769 0.00 0.00 0.00 3.27
3188 4678 7.485810 TCTTTTGGACTGGTTTTAAGTTTAGC 58.514 34.615 0.00 0.00 0.00 3.09
3317 4807 7.290014 TCCATGCCTGAGTATCTAAATTACTCA 59.710 37.037 11.74 11.74 45.32 3.41
3331 4821 9.802039 TCTAAATTACTCAATGTGGTAAGGTTT 57.198 29.630 7.35 6.67 32.51 3.27
3348 4838 7.661027 GGTAAGGTTTGTACATAACACCTACAA 59.339 37.037 13.93 4.39 38.00 2.41
3382 4873 8.997621 TGATAGATTTTTGTAGGTACACACTC 57.002 34.615 0.00 0.00 35.64 3.51
3383 4874 8.590204 TGATAGATTTTTGTAGGTACACACTCA 58.410 33.333 0.00 0.00 35.64 3.41
3391 4892 7.718272 TTGTAGGTACACACTCATTTTACAC 57.282 36.000 0.00 0.00 35.64 2.90
3400 4901 5.740569 CACACTCATTTTACACATATGCAGC 59.259 40.000 1.58 0.00 0.00 5.25
3407 4908 9.465985 TCATTTTACACATATGCAGCAAATATG 57.534 29.630 12.64 12.64 41.69 1.78
3447 4948 1.599797 GCAAAGGCGTGTGTACCCT 60.600 57.895 0.00 0.00 0.00 4.34
3453 4954 1.070105 GCGTGTGTACCCTGTCCAA 59.930 57.895 0.00 0.00 0.00 3.53
3454 4955 0.533308 GCGTGTGTACCCTGTCCAAA 60.533 55.000 0.00 0.00 0.00 3.28
3505 5006 7.621428 ATTAACATCACTCTGAGTCATTTGG 57.379 36.000 7.49 0.00 0.00 3.28
3636 5137 4.127171 GTTGTGTCTCACTTGAGGCTTAA 58.873 43.478 11.95 4.70 46.41 1.85
3643 5144 6.377146 TGTCTCACTTGAGGCTTAAAAGTTTT 59.623 34.615 11.95 6.06 46.41 2.43
3644 5145 7.093945 TGTCTCACTTGAGGCTTAAAAGTTTTT 60.094 33.333 11.95 0.00 46.41 1.94
3645 5146 7.432545 GTCTCACTTGAGGCTTAAAAGTTTTTC 59.567 37.037 6.10 0.00 43.13 2.29
3646 5147 7.339466 TCTCACTTGAGGCTTAAAAGTTTTTCT 59.661 33.333 6.10 0.16 42.30 2.52
3686 5201 7.387643 ACATAGATACTCGAGTACTGAGCATA 58.612 38.462 26.87 12.08 36.94 3.14
3701 5216 5.932303 ACTGAGCATACGTGTTTGATTAAGT 59.068 36.000 0.00 0.00 0.00 2.24
3706 5221 6.203915 AGCATACGTGTTTGATTAAGTTGTGA 59.796 34.615 0.00 0.00 0.00 3.58
3749 5264 0.742281 CTGTGAGACCGCATTCTGGG 60.742 60.000 0.00 0.00 31.63 4.45
3764 5279 5.007724 GCATTCTGGGCAGTTAATACACTAC 59.992 44.000 0.00 0.00 0.00 2.73
3807 5322 7.319646 TGCTCAAATGTTACAAAGTTTCAACT 58.680 30.769 9.76 0.00 42.04 3.16
3810 5325 7.607250 TCAAATGTTACAAAGTTTCAACTGGT 58.393 30.769 9.76 0.00 39.66 4.00
3820 5335 6.590234 AAGTTTCAACTGGTTGTTTCTTCT 57.410 33.333 12.34 3.28 39.66 2.85
3844 5359 5.221762 TGAGAAGAAAGGGGAAATTCACGTA 60.222 40.000 0.00 0.00 0.00 3.57
3845 5360 5.816682 AGAAGAAAGGGGAAATTCACGTAT 58.183 37.500 0.00 0.00 0.00 3.06
3846 5361 6.954232 AGAAGAAAGGGGAAATTCACGTATA 58.046 36.000 0.00 0.00 0.00 1.47
3847 5362 6.822170 AGAAGAAAGGGGAAATTCACGTATAC 59.178 38.462 0.00 0.00 0.00 1.47
3848 5363 6.057321 AGAAAGGGGAAATTCACGTATACA 57.943 37.500 3.32 0.00 0.00 2.29
3849 5364 6.113411 AGAAAGGGGAAATTCACGTATACAG 58.887 40.000 3.32 0.00 0.00 2.74
3850 5365 4.417426 AGGGGAAATTCACGTATACAGG 57.583 45.455 3.32 0.00 0.00 4.00
3851 5366 3.135895 AGGGGAAATTCACGTATACAGGG 59.864 47.826 3.32 0.00 0.00 4.45
3884 5399 7.834068 TCCAGAGAAATCTTTGAATTCTACG 57.166 36.000 7.05 0.00 32.71 3.51
3928 5443 2.422479 TCTTGCTTGAATCATCTGCTGC 59.578 45.455 0.00 0.00 0.00 5.25
3929 5444 1.828979 TGCTTGAATCATCTGCTGCA 58.171 45.000 0.88 0.88 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 7.092712 CCATATGTCTGGATAACACCCTGATAT 60.093 40.741 1.24 0.00 38.69 1.63
179 186 0.607489 ATCCACAGGTCAGCAACTGC 60.607 55.000 0.00 0.00 38.25 4.40
193 200 1.106285 GGGGATTCAGCAACATCCAC 58.894 55.000 9.55 3.08 40.90 4.02
241 275 2.781757 TTCGGAGAGGAGGATGTACCTA 59.218 50.000 0.00 0.00 44.61 3.08
392 431 1.055849 GGCAAACCCTTCCCACAAAT 58.944 50.000 0.00 0.00 0.00 2.32
410 449 0.033228 TTGCAACGCATGAAAAGGGG 59.967 50.000 0.00 0.00 38.76 4.79
505 557 0.395312 AAACATCTGACCCGGTTCGT 59.605 50.000 0.00 0.00 0.00 3.85
599 654 6.573664 TCGACAACATTCAAATTTCCTGAT 57.426 33.333 0.00 0.00 0.00 2.90
741 796 1.827789 GGCCAAACTGGAGCACACA 60.828 57.895 0.00 0.00 40.96 3.72
742 797 2.564721 GGGCCAAACTGGAGCACAC 61.565 63.158 4.39 0.00 40.96 3.82
785 2256 1.140816 GAATCACGCCGCTTATCTCC 58.859 55.000 0.00 0.00 0.00 3.71
815 2286 3.374012 ATACGCGGCGGGCAGTTAA 62.374 57.895 27.37 3.15 43.84 2.01
908 2379 2.186903 CCTGGAACGGACGGATGG 59.813 66.667 0.00 0.00 36.31 3.51
927 2398 2.824041 CGGGATCTTGGCCGTTGG 60.824 66.667 0.00 0.00 0.00 3.77
961 2432 1.072505 GTTGGGGAAGGTCGCTTCA 59.927 57.895 5.35 0.00 35.19 3.02
962 2433 1.674651 GGTTGGGGAAGGTCGCTTC 60.675 63.158 0.00 0.00 0.00 3.86
1048 2520 0.102844 ATCTCTCTCAAGCTCTGCGC 59.897 55.000 0.00 0.00 39.57 6.09
1206 2681 4.954118 AGGTGGTGGCCGTGGAGA 62.954 66.667 0.00 0.00 0.00 3.71
1331 2806 9.216148 TGGCAAGTAATTAGTATAGTTTAGGGA 57.784 33.333 0.00 0.00 0.00 4.20
1333 2808 9.826574 TGTGGCAAGTAATTAGTATAGTTTAGG 57.173 33.333 0.00 0.00 0.00 2.69
1341 2816 7.380423 AGGAGATGTGGCAAGTAATTAGTAT 57.620 36.000 0.00 0.00 0.00 2.12
1355 2830 2.026449 AGGAAGCAAGAAGGAGATGTGG 60.026 50.000 0.00 0.00 0.00 4.17
1359 2834 4.379302 ACAAAGGAAGCAAGAAGGAGAT 57.621 40.909 0.00 0.00 0.00 2.75
1392 2867 6.010219 ACTATCACCAGTTTGGCAAGTAATT 58.990 36.000 0.00 0.00 42.67 1.40
1397 2872 4.853924 AAACTATCACCAGTTTGGCAAG 57.146 40.909 0.00 0.00 44.92 4.01
1485 2967 0.831711 TGTAGGGCTCTGTCACTGCA 60.832 55.000 0.00 0.00 29.58 4.41
1495 2977 2.766828 AGTCAACCACTATGTAGGGCTC 59.233 50.000 0.00 0.00 31.37 4.70
1516 2998 8.258007 TCTACTGAAAAAGAAGAACAGAACAGA 58.742 33.333 0.00 0.00 33.53 3.41
1538 3020 5.460419 CGGACAGCAGATAAGAACAATCTAC 59.540 44.000 0.00 0.00 33.77 2.59
1556 3038 4.320202 CCAATTTTGTCTTACACCGGACAG 60.320 45.833 9.46 0.00 42.31 3.51
1623 3107 6.926630 AAACATGAAGGGTGCCTAAATTAA 57.073 33.333 0.00 0.00 31.13 1.40
1624 3108 8.058847 AGATAAACATGAAGGGTGCCTAAATTA 58.941 33.333 0.00 0.00 31.13 1.40
1670 3154 1.298157 CGATCCCAGCAAACGAGCAA 61.298 55.000 0.00 0.00 36.85 3.91
1685 3169 4.621068 TCAAAATTCTGATGGCACGATC 57.379 40.909 0.00 0.00 0.00 3.69
1712 3196 3.263941 GCACCGGCGTGATTTTCT 58.736 55.556 6.01 0.00 43.14 2.52
1725 3209 5.170748 CAATGGAAATCCTAAACAAGCACC 58.829 41.667 0.44 0.00 36.82 5.01
1726 3210 4.627035 GCAATGGAAATCCTAAACAAGCAC 59.373 41.667 0.44 0.00 36.82 4.40
1794 3278 3.245797 CAACTCTACATGACAGACACGG 58.754 50.000 0.00 0.00 0.00 4.94
1801 3285 5.545063 TGGAAGAACAACTCTACATGACA 57.455 39.130 0.00 0.00 32.46 3.58
1863 3347 4.290155 CGGCATACATATGAAAAAGGCAC 58.710 43.478 10.38 0.07 35.75 5.01
1864 3348 3.243367 GCGGCATACATATGAAAAAGGCA 60.243 43.478 10.38 0.00 35.75 4.75
1865 3349 3.004734 AGCGGCATACATATGAAAAAGGC 59.995 43.478 10.38 6.11 35.75 4.35
1866 3350 4.836125 AGCGGCATACATATGAAAAAGG 57.164 40.909 10.38 0.00 35.75 3.11
1868 3352 5.347342 CCAAAGCGGCATACATATGAAAAA 58.653 37.500 10.38 0.00 35.75 1.94
2371 3860 7.341445 TGCTTCAGGTAAATAAACAACAACT 57.659 32.000 0.00 0.00 0.00 3.16
2372 3861 7.116233 CCATGCTTCAGGTAAATAAACAACAAC 59.884 37.037 0.00 0.00 0.00 3.32
2410 3899 1.610522 GAAGCAACAACATCCTGCAGT 59.389 47.619 13.81 0.00 38.58 4.40
2560 4049 9.847224 GGGAAGATAGATGAACCAAGTTATTTA 57.153 33.333 0.00 0.00 0.00 1.40
2561 4050 7.499232 CGGGAAGATAGATGAACCAAGTTATTT 59.501 37.037 0.00 0.00 0.00 1.40
2577 4066 3.292460 AGGTCTGAGAACGGGAAGATAG 58.708 50.000 0.00 0.00 0.00 2.08
2682 4171 7.012044 TCTGAATGTAATCACTGAATGCATCTG 59.988 37.037 0.00 0.70 0.00 2.90
2686 4175 6.824704 TCATCTGAATGTAATCACTGAATGCA 59.175 34.615 0.00 0.00 34.32 3.96
2779 4268 2.604686 TTGCTCTGGCCCTCGTCT 60.605 61.111 0.00 0.00 37.74 4.18
2916 4405 4.588528 TCTGCCAGCTCCTTTGTTTTATTT 59.411 37.500 0.00 0.00 0.00 1.40
2925 4414 1.377994 CCACTCTGCCAGCTCCTTT 59.622 57.895 0.00 0.00 0.00 3.11
2950 4439 6.431198 AAAGCTGAAACGAAACTAAACTCA 57.569 33.333 0.00 0.00 0.00 3.41
2979 4468 7.723172 AGAAAAAGAAGATCAAATCCTGTCTGT 59.277 33.333 0.00 0.00 0.00 3.41
3062 4551 3.576550 GCCACCAGATAAACCCTTGAAAA 59.423 43.478 0.00 0.00 0.00 2.29
3118 4607 5.063204 AGTTGCAGTAACAGCTAAACATCA 58.937 37.500 4.03 0.00 41.88 3.07
3123 4612 9.443323 TCATATAAAGTTGCAGTAACAGCTAAA 57.557 29.630 4.03 0.00 41.88 1.85
3124 4613 9.613428 ATCATATAAAGTTGCAGTAACAGCTAA 57.387 29.630 4.03 0.00 41.88 3.09
3127 4616 7.012327 TCCATCATATAAAGTTGCAGTAACAGC 59.988 37.037 4.03 0.00 41.88 4.40
3128 4617 8.437360 TCCATCATATAAAGTTGCAGTAACAG 57.563 34.615 4.03 0.00 41.88 3.16
3129 4618 8.046708 ACTCCATCATATAAAGTTGCAGTAACA 58.953 33.333 4.03 0.00 41.88 2.41
3130 4619 8.438676 ACTCCATCATATAAAGTTGCAGTAAC 57.561 34.615 0.00 0.00 39.65 2.50
3131 4620 9.461312 AAACTCCATCATATAAAGTTGCAGTAA 57.539 29.630 0.00 0.00 30.95 2.24
3134 4623 9.113838 ACTAAACTCCATCATATAAAGTTGCAG 57.886 33.333 0.00 0.00 30.95 4.41
3135 4624 9.461312 AACTAAACTCCATCATATAAAGTTGCA 57.539 29.630 0.00 0.00 30.95 4.08
3151 4640 6.096423 ACCAGTCCAAAAGAAAACTAAACTCC 59.904 38.462 0.00 0.00 0.00 3.85
3177 4666 7.562454 AGTTGCAGTAACAGCTAAACTTAAA 57.438 32.000 4.03 0.00 41.88 1.52
3178 4667 7.562454 AAGTTGCAGTAACAGCTAAACTTAA 57.438 32.000 4.03 0.00 41.88 1.85
3188 4678 8.483218 CGAGATCATATAAAGTTGCAGTAACAG 58.517 37.037 4.03 0.00 41.88 3.16
3317 4807 7.040271 GGTGTTATGTACAAACCTTACCACATT 60.040 37.037 0.00 0.00 38.80 2.71
3375 4866 6.623549 GCTGCATATGTGTAAAATGAGTGTGT 60.624 38.462 4.29 0.00 0.00 3.72
3376 4867 5.740569 GCTGCATATGTGTAAAATGAGTGTG 59.259 40.000 4.29 0.00 0.00 3.82
3382 4873 8.705134 CCATATTTGCTGCATATGTGTAAAATG 58.295 33.333 21.40 12.80 34.12 2.32
3383 4874 7.385752 GCCATATTTGCTGCATATGTGTAAAAT 59.614 33.333 21.40 10.82 34.12 1.82
3391 4892 3.985279 GTGTGCCATATTTGCTGCATATG 59.015 43.478 14.61 14.12 35.96 1.78
3400 4901 2.094390 AGCAGCTTGTGTGCCATATTTG 60.094 45.455 0.00 0.00 42.24 2.32
3407 4908 1.211190 GCTTAGCAGCTTGTGTGCC 59.789 57.895 0.00 0.00 43.51 5.01
3431 4932 0.250166 GACAGGGTACACACGCCTTT 60.250 55.000 0.00 0.00 38.34 3.11
3447 4948 3.084039 GAGTGAGGCATCAATTTGGACA 58.916 45.455 0.92 0.00 37.14 4.02
3453 4954 3.118884 GGCAAATGAGTGAGGCATCAATT 60.119 43.478 0.92 0.00 37.14 2.32
3454 4955 2.429610 GGCAAATGAGTGAGGCATCAAT 59.570 45.455 0.92 0.00 37.14 2.57
3529 5030 3.261580 CGCATACAGATCTTGTGTTCCA 58.738 45.455 0.00 0.00 41.10 3.53
3589 5090 1.312815 GGAGCAAGAGCCGCATAAAT 58.687 50.000 0.00 0.00 43.56 1.40
3655 5156 9.945904 TCAGTACTCGAGTATCTATGTATGAAT 57.054 33.333 27.02 0.00 32.54 2.57
3662 5163 6.735678 ATGCTCAGTACTCGAGTATCTATG 57.264 41.667 27.02 21.14 31.08 2.23
3686 5201 6.861065 ATCTCACAACTTAATCAAACACGT 57.139 33.333 0.00 0.00 0.00 4.49
3701 5216 7.916977 CACAACAGATTTTTCAGAATCTCACAA 59.083 33.333 0.00 0.00 42.84 3.33
3706 5221 6.489361 AGCTCACAACAGATTTTTCAGAATCT 59.511 34.615 0.00 0.00 44.94 2.40
3749 5264 7.861630 CCATGTTATGGTAGTGTATTAACTGC 58.138 38.462 0.00 0.00 45.54 4.40
3807 5322 5.590259 CCTTTCTTCTCAGAAGAAACAACCA 59.410 40.000 30.79 15.30 40.95 3.67
3810 5325 5.104109 TCCCCTTTCTTCTCAGAAGAAACAA 60.104 40.000 30.79 16.55 40.95 2.83
3820 5335 4.072131 CGTGAATTTCCCCTTTCTTCTCA 58.928 43.478 0.00 0.00 0.00 3.27
3844 5359 4.358310 TCTCTGGATGGTAGATCCCTGTAT 59.642 45.833 0.00 0.00 37.40 2.29
3845 5360 3.727391 TCTCTGGATGGTAGATCCCTGTA 59.273 47.826 0.00 0.00 37.40 2.74
3846 5361 2.520120 TCTCTGGATGGTAGATCCCTGT 59.480 50.000 0.00 0.00 37.40 4.00
3847 5362 3.251016 TCTCTGGATGGTAGATCCCTG 57.749 52.381 0.00 0.00 37.40 4.45
3848 5363 4.286813 TTTCTCTGGATGGTAGATCCCT 57.713 45.455 0.00 0.00 37.40 4.20
3849 5364 4.843516 AGATTTCTCTGGATGGTAGATCCC 59.156 45.833 0.00 0.00 37.40 3.85
3850 5365 6.432403 AAGATTTCTCTGGATGGTAGATCC 57.568 41.667 0.00 0.00 38.66 3.36
3851 5366 7.504403 TCAAAGATTTCTCTGGATGGTAGATC 58.496 38.462 0.00 0.00 0.00 2.75
3928 5443 2.879907 CCACTGGAAATGCCGCTG 59.120 61.111 0.00 0.00 40.66 5.18
3929 5444 3.064324 GCCACTGGAAATGCCGCT 61.064 61.111 0.00 0.00 40.66 5.52


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

AutoCloner maintained by Alex Coulton.