Multiple sequence alignment - TraesCS3B01G381000

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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 TraesCS3B01G381000 chr3B 100.000 2639 0 0 1 2639 598469598 598466960 0.000000e+00 4874
1 TraesCS3B01G381000 chr3A 91.955 2312 113 31 367 2639 597548359 597546082 0.000000e+00 3171
2 TraesCS3B01G381000 chr3D 90.653 1990 134 27 34 1997 455107917 455105954 0.000000e+00 2597
3 TraesCS3B01G381000 chr3D 91.969 635 17 12 2032 2639 455105823 455105196 0.000000e+00 859
4 TraesCS3B01G381000 chr1B 88.942 416 42 4 1084 1497 422563208 422562795 6.520000e-141 510
5 TraesCS3B01G381000 chr1B 87.381 420 49 4 1072 1489 529288198 529288615 1.840000e-131 479
6 TraesCS3B01G381000 chr1A 88.942 416 42 4 1084 1497 392084936 392084523 6.520000e-141 510
7 TraesCS3B01G381000 chr1A 88.067 419 46 4 1072 1488 492046051 492046467 6.560000e-136 494
8 TraesCS3B01G381000 chr1D 88.702 416 43 4 1084 1497 311988723 311988310 3.030000e-139 505
9 TraesCS3B01G381000 chr1D 88.056 427 47 4 1065 1489 393750495 393750071 1.090000e-138 503
10 TraesCS3B01G381000 chr6A 81.448 442 68 11 1043 1480 114459047 114458616 1.500000e-92 350


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 TraesCS3B01G381000 chr3B 598466960 598469598 2638 True 4874 4874 100.000 1 2639 1 chr3B.!!$R1 2638
1 TraesCS3B01G381000 chr3A 597546082 597548359 2277 True 3171 3171 91.955 367 2639 1 chr3A.!!$R1 2272
2 TraesCS3B01G381000 chr3D 455105196 455107917 2721 True 1728 2597 91.311 34 2639 2 chr3D.!!$R1 2605

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
323 347 0.040499 GTGGGGCAATGGGGTAAGAA 59.96 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1795 1869 1.740025 ACTACTACGACGCCCTGTAAC 59.26 52.381 0.0 0.0 0.0 2.5 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
19 20 0.621609 TACAAGGGGATGTTTCGGGG 59.378 55.000 0.00 0.00 34.75 5.73
20 21 1.379843 CAAGGGGATGTTTCGGGGG 60.380 63.158 0.00 0.00 0.00 5.40
21 22 3.296842 AAGGGGATGTTTCGGGGGC 62.297 63.158 0.00 0.00 0.00 5.80
22 23 4.055227 GGGGATGTTTCGGGGGCA 62.055 66.667 0.00 0.00 0.00 5.36
23 24 2.754254 GGGATGTTTCGGGGGCAC 60.754 66.667 0.00 0.00 0.00 5.01
24 25 3.131478 GGATGTTTCGGGGGCACG 61.131 66.667 0.00 0.00 0.00 5.34
25 26 2.359478 GATGTTTCGGGGGCACGT 60.359 61.111 0.91 0.00 34.94 4.49
26 27 2.671619 ATGTTTCGGGGGCACGTG 60.672 61.111 12.28 12.28 34.94 4.49
29 30 4.877619 TTTCGGGGGCACGTGCAA 62.878 61.111 38.60 22.83 44.36 4.08
30 31 4.877619 TTCGGGGGCACGTGCAAA 62.878 61.111 38.60 21.63 44.36 3.68
31 32 4.877619 TCGGGGGCACGTGCAAAA 62.878 61.111 38.60 18.01 44.36 2.44
32 33 4.639171 CGGGGGCACGTGCAAAAC 62.639 66.667 38.60 24.97 44.36 2.43
43 44 4.463209 CACGTGCAAAACATACCTACAAG 58.537 43.478 0.82 0.00 0.00 3.16
48 49 4.264172 TGCAAAACATACCTACAAGGGGAT 60.264 41.667 0.00 0.00 40.58 3.85
59 60 1.272147 ACAAGGGGATGCAACTCTTCC 60.272 52.381 4.07 0.00 38.07 3.46
67 68 2.452600 TGCAACTCTTCCCAGGTTTT 57.547 45.000 0.00 0.00 0.00 2.43
78 79 1.008995 CAGGTTTTTGTCACCGCCG 60.009 57.895 0.00 0.00 39.56 6.46
112 113 3.471306 ACACTATGGAGGAGGAAGGGATA 59.529 47.826 0.00 0.00 0.00 2.59
130 131 1.354101 TACTTGCGGGGGAAAGAAGA 58.646 50.000 0.00 0.00 0.00 2.87
143 144 3.499918 GGAAAGAAGACAGATGTGTGTGG 59.500 47.826 0.00 0.00 36.88 4.17
144 145 2.847327 AGAAGACAGATGTGTGTGGG 57.153 50.000 0.00 0.00 36.88 4.61
152 153 1.535444 ATGTGTGTGGGGGAGACGA 60.535 57.895 0.00 0.00 0.00 4.20
154 155 2.200370 TGTGTGGGGGAGACGAGT 59.800 61.111 0.00 0.00 0.00 4.18
157 158 2.214216 TGTGGGGGAGACGAGTTGG 61.214 63.158 0.00 0.00 0.00 3.77
168 169 1.673920 GACGAGTTGGGTGCTTTTTCA 59.326 47.619 0.00 0.00 0.00 2.69
183 184 2.785357 TTTCATTGGGTGAGGGGTTT 57.215 45.000 0.00 0.00 38.29 3.27
184 185 2.008242 TTCATTGGGTGAGGGGTTTG 57.992 50.000 0.00 0.00 38.29 2.93
198 199 1.371389 GTTTGAGACGCGTCGAGGT 60.371 57.895 31.56 16.11 34.09 3.85
206 207 4.059459 GCGTCGAGGTGTGCGTTG 62.059 66.667 7.01 0.00 0.00 4.10
207 208 4.059459 CGTCGAGGTGTGCGTTGC 62.059 66.667 0.00 0.00 0.00 4.17
216 217 3.116531 GTGCGTTGCGTAGGGACC 61.117 66.667 0.00 0.00 0.00 4.46
295 319 3.833732 GGGACCAGAAGTTTCCTTTTCT 58.166 45.455 0.00 0.00 34.09 2.52
301 325 4.152580 CCAGAAGTTTCCTTTTCTAGCGTC 59.847 45.833 0.00 0.00 32.62 5.19
311 335 3.390521 CTAGCGTCAGGTGGGGCA 61.391 66.667 0.00 0.00 0.00 5.36
319 343 2.204385 AGGTGGGGCAATGGGGTA 60.204 61.111 0.00 0.00 0.00 3.69
323 347 0.040499 GTGGGGCAATGGGGTAAGAA 59.960 55.000 0.00 0.00 0.00 2.52
328 352 2.959030 GGGCAATGGGGTAAGAATCTTC 59.041 50.000 0.00 0.00 0.00 2.87
330 354 3.885901 GGCAATGGGGTAAGAATCTTCTC 59.114 47.826 0.00 0.00 36.28 2.87
333 357 5.994668 GCAATGGGGTAAGAATCTTCTCTAG 59.005 44.000 0.00 0.00 36.28 2.43
335 359 6.739331 ATGGGGTAAGAATCTTCTCTAGTG 57.261 41.667 0.00 0.00 36.28 2.74
345 369 4.244425 TCTTCTCTAGTGAAGTGTGTGC 57.756 45.455 25.95 0.00 42.76 4.57
346 370 3.891977 TCTTCTCTAGTGAAGTGTGTGCT 59.108 43.478 25.95 0.00 42.76 4.40
403 427 1.563924 ACACACTTACCGGATAGGCA 58.436 50.000 9.46 0.00 46.52 4.75
408 432 1.551883 ACTTACCGGATAGGCACGTTT 59.448 47.619 9.46 0.00 46.52 3.60
444 468 6.952773 AAATACAAACTTACTGGCAAGACA 57.047 33.333 0.00 0.00 0.00 3.41
449 473 2.480845 ACTTACTGGCAAGACACGTTC 58.519 47.619 0.00 0.00 0.00 3.95
483 549 9.681062 ACTATAAATACACACATACCAGCTTTT 57.319 29.630 0.00 0.00 0.00 2.27
531 597 2.510768 ATTTCCTGGATAGACGCGTC 57.489 50.000 31.30 31.30 0.00 5.19
552 618 9.451853 CGCGTCCGTATAAAATTATAAATACAC 57.548 33.333 0.00 0.00 0.00 2.90
569 635 1.135746 ACACGCTTACTGACTAGACGC 60.136 52.381 0.00 0.00 0.00 5.19
580 646 6.315091 ACTGACTAGACGCGTTCATATAAT 57.685 37.500 15.53 0.00 0.00 1.28
581 647 6.736123 ACTGACTAGACGCGTTCATATAATT 58.264 36.000 15.53 0.00 0.00 1.40
582 648 7.868775 ACTGACTAGACGCGTTCATATAATTA 58.131 34.615 15.53 0.00 0.00 1.40
586 655 9.775060 GACTAGACGCGTTCATATAATTAAAAC 57.225 33.333 15.53 0.00 0.00 2.43
620 689 6.459670 TGTTGGATATACGCGTCCATATAT 57.540 37.500 18.63 13.89 43.61 0.86
661 730 1.080025 GACCTACACGGAGCCACAC 60.080 63.158 0.00 0.00 36.31 3.82
711 784 1.128200 ATGCACTTCTATACGCCCCA 58.872 50.000 0.00 0.00 0.00 4.96
944 1018 0.669077 ACTGGTCACTCACTCGTCAC 59.331 55.000 0.00 0.00 0.00 3.67
1558 1632 2.439883 GGGACGTCGAGGGTAGCT 60.440 66.667 9.92 0.00 0.00 3.32
1559 1633 2.050934 GGGACGTCGAGGGTAGCTT 61.051 63.158 9.92 0.00 0.00 3.74
1725 1799 6.731467 AGATTTGAGCTTTCCCTTTGGTATA 58.269 36.000 0.00 0.00 0.00 1.47
1733 1807 6.208797 AGCTTTCCCTTTGGTATACTTTGTTC 59.791 38.462 2.25 0.00 0.00 3.18
1883 1957 8.768397 TCATTATCCCATACATATCCTGGTAAC 58.232 37.037 0.00 0.00 0.00 2.50
1913 1987 9.911788 AGAAATTGAGATTTGTGGTCATATACT 57.088 29.630 0.00 0.00 35.65 2.12
1915 1989 9.685276 AAATTGAGATTTGTGGTCATATACTCA 57.315 29.630 0.00 0.00 34.26 3.41
1916 1990 9.857656 AATTGAGATTTGTGGTCATATACTCAT 57.142 29.630 0.00 0.00 33.12 2.90
1951 2025 3.386078 TCTTATGCTACCTCTCAGCTTGG 59.614 47.826 0.00 0.00 39.83 3.61
1954 2028 0.898320 GCTACCTCTCAGCTTGGTCA 59.102 55.000 1.34 0.00 36.07 4.02
1955 2029 1.484240 GCTACCTCTCAGCTTGGTCAT 59.516 52.381 1.34 0.00 36.07 3.06
1963 2038 2.499289 CTCAGCTTGGTCATGTACTCCT 59.501 50.000 0.00 0.00 0.00 3.69
1997 2074 9.774742 CTTATTAGAGGTGTTTAATTTGTGCTC 57.225 33.333 0.00 0.00 0.00 4.26
1999 2076 7.759489 TTAGAGGTGTTTAATTTGTGCTCAT 57.241 32.000 0.00 0.00 0.00 2.90
2000 2077 6.655078 AGAGGTGTTTAATTTGTGCTCATT 57.345 33.333 0.00 0.00 0.00 2.57
2001 2078 7.759489 AGAGGTGTTTAATTTGTGCTCATTA 57.241 32.000 0.00 0.00 0.00 1.90
2002 2079 7.820648 AGAGGTGTTTAATTTGTGCTCATTAG 58.179 34.615 0.00 0.00 0.00 1.73
2029 2134 6.206048 TCATTAGCTCATACATCCATTGCAAG 59.794 38.462 4.94 0.00 0.00 4.01
2052 2225 7.024340 AGCTAGTAATCAATTCTTGCACATG 57.976 36.000 0.00 0.00 33.79 3.21
2117 2293 3.087031 CAGAAGCACTGGATGAATGGTT 58.913 45.455 3.48 0.00 42.39 3.67
2118 2294 3.508793 CAGAAGCACTGGATGAATGGTTT 59.491 43.478 3.48 0.00 42.39 3.27
2119 2295 3.760684 AGAAGCACTGGATGAATGGTTTC 59.239 43.478 0.00 0.00 34.37 2.78
2120 2296 3.446442 AGCACTGGATGAATGGTTTCT 57.554 42.857 0.00 0.00 32.78 2.52
2121 2297 3.771216 AGCACTGGATGAATGGTTTCTT 58.229 40.909 0.00 0.00 32.78 2.52
2122 2298 3.508793 AGCACTGGATGAATGGTTTCTTG 59.491 43.478 0.00 0.00 32.78 3.02
2123 2299 3.841643 CACTGGATGAATGGTTTCTTGC 58.158 45.455 0.00 0.00 32.78 4.01
2174 2352 5.141182 AGTAGATCGCTAGGAAGAATGGAA 58.859 41.667 0.00 0.00 0.00 3.53
2176 2354 4.954875 AGATCGCTAGGAAGAATGGAAAG 58.045 43.478 0.00 0.00 0.00 2.62
2177 2355 4.651503 AGATCGCTAGGAAGAATGGAAAGA 59.348 41.667 0.00 0.00 0.00 2.52
2424 2612 0.595588 AGAGCGTGTGTGTGAGAGAG 59.404 55.000 0.00 0.00 0.00 3.20
2437 2625 5.069648 TGTGTGAGAGAGAGATGAACAGTTT 59.930 40.000 0.00 0.00 0.00 2.66
2494 2698 2.872245 CAGTTCTTGCGGTTTGAGAGAA 59.128 45.455 0.00 0.00 0.00 2.87
2499 2703 2.169832 TGCGGTTTGAGAGAAAGAGG 57.830 50.000 0.00 0.00 0.00 3.69
2503 2707 2.354203 CGGTTTGAGAGAAAGAGGGAGG 60.354 54.545 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.621609 CCCCGAAACATCCCCTTGTA 59.378 55.000 0.00 0.00 0.00 2.41
2 3 1.379843 CCCCCGAAACATCCCCTTG 60.380 63.158 0.00 0.00 0.00 3.61
4 5 3.739613 GCCCCCGAAACATCCCCT 61.740 66.667 0.00 0.00 0.00 4.79
5 6 4.055227 TGCCCCCGAAACATCCCC 62.055 66.667 0.00 0.00 0.00 4.81
6 7 2.754254 GTGCCCCCGAAACATCCC 60.754 66.667 0.00 0.00 0.00 3.85
7 8 3.131478 CGTGCCCCCGAAACATCC 61.131 66.667 0.00 0.00 0.00 3.51
8 9 2.359478 ACGTGCCCCCGAAACATC 60.359 61.111 0.00 0.00 0.00 3.06
9 10 2.671619 CACGTGCCCCCGAAACAT 60.672 61.111 0.82 0.00 0.00 2.71
12 13 4.877619 TTGCACGTGCCCCCGAAA 62.878 61.111 35.72 20.26 41.18 3.46
13 14 4.877619 TTTGCACGTGCCCCCGAA 62.878 61.111 35.72 21.00 41.18 4.30
14 15 4.877619 TTTTGCACGTGCCCCCGA 62.878 61.111 35.72 15.93 41.18 5.14
15 16 4.639171 GTTTTGCACGTGCCCCCG 62.639 66.667 35.72 0.15 41.18 5.73
16 17 1.528292 TATGTTTTGCACGTGCCCCC 61.528 55.000 35.72 21.15 41.18 5.40
17 18 0.388006 GTATGTTTTGCACGTGCCCC 60.388 55.000 35.72 20.82 41.18 5.80
18 19 0.388006 GGTATGTTTTGCACGTGCCC 60.388 55.000 35.72 23.05 40.49 5.36
19 20 0.596082 AGGTATGTTTTGCACGTGCC 59.404 50.000 35.72 21.40 45.41 5.01
20 21 2.224549 TGTAGGTATGTTTTGCACGTGC 59.775 45.455 33.11 33.11 42.50 5.34
21 22 4.463209 CTTGTAGGTATGTTTTGCACGTG 58.537 43.478 12.28 12.28 0.00 4.49
22 23 3.500680 CCTTGTAGGTATGTTTTGCACGT 59.499 43.478 0.00 0.00 0.00 4.49
23 24 3.119990 CCCTTGTAGGTATGTTTTGCACG 60.120 47.826 0.00 0.00 31.93 5.34
24 25 3.192633 CCCCTTGTAGGTATGTTTTGCAC 59.807 47.826 0.00 0.00 31.93 4.57
25 26 3.074687 TCCCCTTGTAGGTATGTTTTGCA 59.925 43.478 0.00 0.00 31.93 4.08
26 27 3.692690 TCCCCTTGTAGGTATGTTTTGC 58.307 45.455 0.00 0.00 31.93 3.68
27 28 4.097892 GCATCCCCTTGTAGGTATGTTTTG 59.902 45.833 0.00 0.00 32.44 2.44
28 29 4.264172 TGCATCCCCTTGTAGGTATGTTTT 60.264 41.667 0.00 0.00 32.44 2.43
29 30 3.268334 TGCATCCCCTTGTAGGTATGTTT 59.732 43.478 0.00 0.00 32.44 2.83
30 31 2.849943 TGCATCCCCTTGTAGGTATGTT 59.150 45.455 0.00 0.00 32.44 2.71
31 32 2.487775 TGCATCCCCTTGTAGGTATGT 58.512 47.619 0.00 0.00 32.44 2.29
32 33 3.117888 AGTTGCATCCCCTTGTAGGTATG 60.118 47.826 0.00 0.00 31.93 2.39
43 44 4.666105 GGGAAGAGTTGCATCCCC 57.334 61.111 10.79 1.47 45.96 4.81
48 49 2.430332 CAAAAACCTGGGAAGAGTTGCA 59.570 45.455 0.00 0.00 0.00 4.08
59 60 1.362355 GGCGGTGACAAAAACCTGG 59.638 57.895 0.00 0.00 35.39 4.45
61 62 0.536460 ATCGGCGGTGACAAAAACCT 60.536 50.000 7.21 0.00 35.39 3.50
67 68 0.537653 TGGATTATCGGCGGTGACAA 59.462 50.000 7.21 0.00 0.00 3.18
112 113 0.250770 GTCTTCTTTCCCCCGCAAGT 60.251 55.000 0.00 0.00 0.00 3.16
130 131 0.473694 TCTCCCCCACACACATCTGT 60.474 55.000 0.00 0.00 0.00 3.41
143 144 2.663196 CACCCAACTCGTCTCCCC 59.337 66.667 0.00 0.00 0.00 4.81
144 145 2.047179 GCACCCAACTCGTCTCCC 60.047 66.667 0.00 0.00 0.00 4.30
152 153 2.104622 CCCAATGAAAAAGCACCCAACT 59.895 45.455 0.00 0.00 0.00 3.16
154 155 2.122768 ACCCAATGAAAAAGCACCCAA 58.877 42.857 0.00 0.00 0.00 4.12
157 158 2.289010 CCTCACCCAATGAAAAAGCACC 60.289 50.000 0.00 0.00 36.69 5.01
168 169 1.075536 GTCTCAAACCCCTCACCCAAT 59.924 52.381 0.00 0.00 0.00 3.16
183 184 2.976350 ACACCTCGACGCGTCTCA 60.976 61.111 33.94 20.55 0.00 3.27
184 185 2.502080 CACACCTCGACGCGTCTC 60.502 66.667 33.94 12.84 0.00 3.36
198 199 2.356553 GTCCCTACGCAACGCACA 60.357 61.111 0.00 0.00 0.00 4.57
216 217 1.672030 TGCACGCCAATGGACTCTG 60.672 57.895 2.05 0.00 0.00 3.35
265 289 3.883822 TTCTGGTCCCCCTCCACCC 62.884 68.421 0.00 0.00 0.00 4.61
268 292 0.402861 AAACTTCTGGTCCCCCTCCA 60.403 55.000 0.00 0.00 0.00 3.86
269 293 0.328592 GAAACTTCTGGTCCCCCTCC 59.671 60.000 0.00 0.00 0.00 4.30
270 294 0.328592 GGAAACTTCTGGTCCCCCTC 59.671 60.000 0.00 0.00 0.00 4.30
287 311 1.275291 CCACCTGACGCTAGAAAAGGA 59.725 52.381 0.00 0.00 0.00 3.36
295 319 2.297895 ATTGCCCCACCTGACGCTA 61.298 57.895 0.00 0.00 0.00 4.26
301 325 2.161713 TTACCCCATTGCCCCACCTG 62.162 60.000 0.00 0.00 0.00 4.00
311 335 6.903534 TCACTAGAGAAGATTCTTACCCCATT 59.096 38.462 0.00 0.00 37.73 3.16
319 343 7.151308 CACACACTTCACTAGAGAAGATTCTT 58.849 38.462 29.45 9.81 46.18 2.52
323 347 4.526262 AGCACACACTTCACTAGAGAAGAT 59.474 41.667 29.45 17.31 46.18 2.40
328 352 3.055591 CACAGCACACACTTCACTAGAG 58.944 50.000 0.00 0.00 0.00 2.43
330 354 2.138320 CCACAGCACACACTTCACTAG 58.862 52.381 0.00 0.00 0.00 2.57
333 357 0.940126 CTCCACAGCACACACTTCAC 59.060 55.000 0.00 0.00 0.00 3.18
335 359 1.944778 GCTCCACAGCACACACTTC 59.055 57.895 0.00 0.00 46.06 3.01
376 400 8.255905 GCCTATCCGGTAAGTGTGTATTAATAT 58.744 37.037 0.00 0.00 34.25 1.28
385 409 1.801395 CGTGCCTATCCGGTAAGTGTG 60.801 57.143 0.00 0.00 34.25 3.82
387 411 0.458669 ACGTGCCTATCCGGTAAGTG 59.541 55.000 0.00 0.00 38.53 3.16
394 418 7.647907 AGTTTTATATAAACGTGCCTATCCG 57.352 36.000 7.43 0.00 35.42 4.18
468 492 1.730064 CGCGTAAAAGCTGGTATGTGT 59.270 47.619 0.00 0.00 34.40 3.72
516 582 1.162181 TACGGACGCGTCTATCCAGG 61.162 60.000 35.50 18.73 34.35 4.45
517 583 0.873054 ATACGGACGCGTCTATCCAG 59.127 55.000 35.50 21.67 34.35 3.86
524 590 9.662157 GTATTTATAATTTTATACGGACGCGTC 57.338 33.333 30.67 30.67 0.00 5.19
525 591 9.190858 TGTATTTATAATTTTATACGGACGCGT 57.809 29.630 13.85 13.85 0.00 6.01
527 593 9.451853 CGTGTATTTATAATTTTATACGGACGC 57.548 33.333 9.81 0.00 0.00 5.19
541 607 9.941664 GTCTAGTCAGTAAGCGTGTATTTATAA 57.058 33.333 0.00 0.00 0.00 0.98
549 615 1.135746 GCGTCTAGTCAGTAAGCGTGT 60.136 52.381 0.00 0.00 0.00 4.49
552 618 2.842995 CGCGTCTAGTCAGTAAGCG 58.157 57.895 0.00 0.00 40.14 4.68
560 626 9.775060 GTTTTAATTATATGAACGCGTCTAGTC 57.225 33.333 14.44 7.02 0.00 2.59
561 627 9.525409 AGTTTTAATTATATGAACGCGTCTAGT 57.475 29.630 14.44 0.00 0.00 2.57
591 660 5.992829 TGGACGCGTATATCCAACAAATATT 59.007 36.000 13.97 0.00 42.14 1.28
592 661 5.543714 TGGACGCGTATATCCAACAAATAT 58.456 37.500 13.97 0.00 42.14 1.28
593 662 4.946445 TGGACGCGTATATCCAACAAATA 58.054 39.130 13.97 0.00 42.14 1.40
620 689 9.850628 GGTCGTATGAGCATGTATTTATAGTTA 57.149 33.333 9.27 0.00 42.23 2.24
991 1065 2.549754 CGGAGGAATCCATATGCAACAC 59.450 50.000 0.61 0.00 0.00 3.32
1374 1448 2.434359 GCGAAGGGGTTGGACTCG 60.434 66.667 0.00 0.00 0.00 4.18
1558 1632 1.741401 CAAGAGCACCATCGCCGAA 60.741 57.895 0.00 0.00 0.00 4.30
1559 1633 2.125552 CAAGAGCACCATCGCCGA 60.126 61.111 0.00 0.00 0.00 5.54
1633 1707 7.178628 AGGTTTGCAAGTCTACTATACTCAAGA 59.821 37.037 0.00 0.00 0.00 3.02
1695 1769 4.268359 AGGGAAAGCTCAAATCTTGCTAG 58.732 43.478 0.00 0.00 35.85 3.42
1795 1869 1.740025 ACTACTACGACGCCCTGTAAC 59.260 52.381 0.00 0.00 0.00 2.50
1917 1991 9.762381 AGAGGTAGCATAAGAAGTAGCTATAAT 57.238 33.333 0.00 0.00 41.14 1.28
1918 1992 9.233649 GAGAGGTAGCATAAGAAGTAGCTATAA 57.766 37.037 0.00 0.00 41.14 0.98
1919 1993 8.383947 TGAGAGGTAGCATAAGAAGTAGCTATA 58.616 37.037 0.00 0.00 41.14 1.31
1920 1994 7.235079 TGAGAGGTAGCATAAGAAGTAGCTAT 58.765 38.462 0.00 0.00 41.14 2.97
1924 1998 5.534654 AGCTGAGAGGTAGCATAAGAAGTAG 59.465 44.000 0.00 0.00 43.53 2.57
2003 2080 5.704053 TGCAATGGATGTATGAGCTAATGAG 59.296 40.000 0.00 0.00 0.00 2.90
2004 2081 5.623169 TGCAATGGATGTATGAGCTAATGA 58.377 37.500 0.00 0.00 0.00 2.57
2008 2085 3.817084 GCTTGCAATGGATGTATGAGCTA 59.183 43.478 0.00 0.00 0.00 3.32
2009 2086 2.621998 GCTTGCAATGGATGTATGAGCT 59.378 45.455 0.00 0.00 0.00 4.09
2052 2225 8.848528 GCTTCGAACGGTACTAGAAATATTATC 58.151 37.037 0.00 0.00 0.00 1.75
2118 2294 9.331282 GCTAGGAGAAAATAGAAATAAGCAAGA 57.669 33.333 0.00 0.00 0.00 3.02
2119 2295 9.336171 AGCTAGGAGAAAATAGAAATAAGCAAG 57.664 33.333 0.00 0.00 0.00 4.01
2121 2297 9.765795 GTAGCTAGGAGAAAATAGAAATAAGCA 57.234 33.333 0.00 0.00 0.00 3.91
2122 2298 9.990360 AGTAGCTAGGAGAAAATAGAAATAAGC 57.010 33.333 0.00 0.00 0.00 3.09
2174 2352 4.140536 CCTCTCTTTTCCTTTGCACTCTT 58.859 43.478 0.00 0.00 0.00 2.85
2176 2354 2.816672 CCCTCTCTTTTCCTTTGCACTC 59.183 50.000 0.00 0.00 0.00 3.51
2177 2355 2.489802 CCCCTCTCTTTTCCTTTGCACT 60.490 50.000 0.00 0.00 0.00 4.40
2424 2612 3.626028 ACCGCAAAAACTGTTCATCTC 57.374 42.857 0.00 0.00 0.00 2.75
2437 2625 1.466950 CTCGCCATTAGAAACCGCAAA 59.533 47.619 0.00 0.00 0.00 3.68
2494 2698 2.629909 CCTAGCCCTAAACCTCCCTCTT 60.630 54.545 0.00 0.00 0.00 2.85
2499 2703 1.141185 ATGCCTAGCCCTAAACCTCC 58.859 55.000 0.00 0.00 0.00 4.30
2503 2707 1.025041 GTGCATGCCTAGCCCTAAAC 58.975 55.000 16.68 0.00 0.00 2.01
2526 2730 1.900545 CTCTCCGGACAAACCCCTCC 61.901 65.000 0.00 0.00 34.64 4.30


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

AutoCloner maintained by Alex Coulton.