Multiple sequence alignment - TraesCS6D01G308200

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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 TraesCS6D01G308200 chr6D 100.000 2918 0 0 1 2918 419262237 419265154 0.000000e+00 5389.0
1 TraesCS6D01G308200 chr6B 92.964 2274 94 22 644 2872 632176430 632178682 0.000000e+00 3253.0
2 TraesCS6D01G308200 chr6B 85.833 480 52 10 155 628 632175861 632176330 2.020000e-136 496.0
3 TraesCS6D01G308200 chr6A 95.096 1509 47 11 644 2136 562682805 562684302 0.000000e+00 2351.0
4 TraesCS6D01G308200 chr6A 92.005 763 47 7 2164 2918 562684285 562685041 0.000000e+00 1059.0
5 TraesCS6D01G308200 chr7A 80.777 489 73 18 150 625 526618898 526618418 2.140000e-96 363.0
6 TraesCS6D01G308200 chr3A 79.266 545 67 21 115 629 446319301 446319829 3.600000e-89 339.0
7 TraesCS6D01G308200 chr3A 72.131 427 88 16 196 612 477146167 477146572 1.850000e-17 100.0
8 TraesCS6D01G308200 chr7D 86.992 246 31 1 2233 2478 223980351 223980107 2.860000e-70 276.0
9 TraesCS6D01G308200 chr7D 74.603 504 81 26 118 609 607029799 607030267 8.310000e-41 178.0
10 TraesCS6D01G308200 chr7D 76.689 296 53 10 339 623 101784533 101784243 1.810000e-32 150.0
11 TraesCS6D01G308200 chr1D 76.301 519 68 27 115 623 475813650 475814123 2.930000e-55 226.0
12 TraesCS6D01G308200 chr4B 75.915 519 80 26 115 611 527012572 527012077 1.050000e-54 224.0
13 TraesCS6D01G308200 chr2D 83.254 209 33 2 115 323 83097392 83097186 1.070000e-44 191.0
14 TraesCS6D01G308200 chr2D 74.168 511 98 18 118 612 135280925 135281417 6.420000e-42 182.0
15 TraesCS6D01G308200 chr2B 75.050 505 70 27 115 582 153707821 153707336 1.790000e-42 183.0
16 TraesCS6D01G308200 chr2A 83.425 181 30 0 120 300 483626262 483626082 5.000000e-38 169.0
17 TraesCS6D01G308200 chr5B 85.333 150 22 0 115 264 440202542 440202691 3.890000e-34 156.0
18 TraesCS6D01G308200 chr5B 76.680 253 46 12 185 433 355894690 355894933 8.490000e-26 128.0
19 TraesCS6D01G308200 chr5B 82.243 107 17 2 507 612 620297200 620297305 1.110000e-14 91.6
20 TraesCS6D01G308200 chr5D 73.715 506 71 33 118 612 502653685 502654139 1.090000e-29 141.0
21 TraesCS6D01G308200 chr5D 76.207 290 42 11 318 597 449684963 449684691 8.490000e-26 128.0
22 TraesCS6D01G308200 chr5D 75.410 305 51 12 315 610 231410345 231410634 3.050000e-25 126.0
23 TraesCS6D01G308200 chr5A 79.612 206 32 7 116 316 513250695 513250495 3.920000e-29 139.0
24 TraesCS6D01G308200 chr5A 74.185 399 70 21 210 596 553167985 553167608 5.070000e-28 135.0
25 TraesCS6D01G308200 chr4A 75.000 320 53 14 314 623 119065481 119065783 3.950000e-24 122.0
26 TraesCS6D01G308200 chr3B 74.706 340 49 15 279 603 706913179 706912862 1.840000e-22 117.0


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 TraesCS6D01G308200 chr6D 419262237 419265154 2917 False 5389.0 5389 100.0000 1 2918 1 chr6D.!!$F1 2917
1 TraesCS6D01G308200 chr6B 632175861 632178682 2821 False 1874.5 3253 89.3985 155 2872 2 chr6B.!!$F1 2717
2 TraesCS6D01G308200 chr6A 562682805 562685041 2236 False 1705.0 2351 93.5505 644 2918 2 chr6A.!!$F1 2274
3 TraesCS6D01G308200 chr3A 446319301 446319829 528 False 339.0 339 79.2660 115 629 1 chr3A.!!$F1 514

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
110 111 0.039074 CACTCTTGTTCGAGACCGCT 60.039 55.0 0.0 0.0 35.06 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 2097 1.131883 GCAGACCAGATGCAACATGAC 59.868 52.381 0.0 0.0 43.31 3.06 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
25 26 3.762407 AACCCCAAAATACCTTGTTGC 57.238 42.857 0.00 0.00 0.00 4.17
26 27 2.683768 ACCCCAAAATACCTTGTTGCA 58.316 42.857 0.00 0.00 0.00 4.08
27 28 2.367241 ACCCCAAAATACCTTGTTGCAC 59.633 45.455 0.00 0.00 0.00 4.57
28 29 2.632512 CCCCAAAATACCTTGTTGCACT 59.367 45.455 0.00 0.00 0.00 4.40
29 30 3.070878 CCCCAAAATACCTTGTTGCACTT 59.929 43.478 0.00 0.00 0.00 3.16
30 31 4.444164 CCCCAAAATACCTTGTTGCACTTT 60.444 41.667 0.00 0.00 0.00 2.66
31 32 5.221541 CCCCAAAATACCTTGTTGCACTTTA 60.222 40.000 0.00 0.00 0.00 1.85
32 33 6.463360 CCCAAAATACCTTGTTGCACTTTAT 58.537 36.000 0.00 0.00 0.00 1.40
33 34 6.934083 CCCAAAATACCTTGTTGCACTTTATT 59.066 34.615 0.00 0.00 0.00 1.40
34 35 7.443879 CCCAAAATACCTTGTTGCACTTTATTT 59.556 33.333 0.00 0.00 0.00 1.40
35 36 9.482627 CCAAAATACCTTGTTGCACTTTATTTA 57.517 29.630 0.00 0.00 0.00 1.40
67 68 9.845740 ACTTTGGTTTGCCTTTTTATTTATCTT 57.154 25.926 0.00 0.00 35.27 2.40
98 99 9.739276 ACCTATCTCTATTAGATCTCACTCTTG 57.261 37.037 0.00 0.00 44.17 3.02
99 100 9.739276 CCTATCTCTATTAGATCTCACTCTTGT 57.261 37.037 0.00 0.00 44.17 3.16
102 103 8.148807 TCTCTATTAGATCTCACTCTTGTTCG 57.851 38.462 0.00 0.00 0.00 3.95
103 104 7.988028 TCTCTATTAGATCTCACTCTTGTTCGA 59.012 37.037 0.00 0.00 0.00 3.71
104 105 8.148807 TCTATTAGATCTCACTCTTGTTCGAG 57.851 38.462 0.00 0.00 37.07 4.04
105 106 7.988028 TCTATTAGATCTCACTCTTGTTCGAGA 59.012 37.037 0.00 0.00 38.78 4.04
106 107 4.695217 AGATCTCACTCTTGTTCGAGAC 57.305 45.455 0.00 0.00 37.34 3.36
107 108 3.442273 AGATCTCACTCTTGTTCGAGACC 59.558 47.826 0.00 0.00 37.34 3.85
108 109 1.535896 TCTCACTCTTGTTCGAGACCG 59.464 52.381 0.00 0.00 35.06 4.79
109 110 0.039437 TCACTCTTGTTCGAGACCGC 60.039 55.000 0.00 0.00 35.06 5.68
110 111 0.039074 CACTCTTGTTCGAGACCGCT 60.039 55.000 0.00 0.00 35.06 5.52
111 112 0.674534 ACTCTTGTTCGAGACCGCTT 59.325 50.000 0.00 0.00 35.06 4.68
112 113 1.063806 CTCTTGTTCGAGACCGCTTG 58.936 55.000 0.00 0.00 32.74 4.01
113 114 0.319555 TCTTGTTCGAGACCGCTTGG 60.320 55.000 0.00 0.00 39.35 3.61
134 135 2.047844 CCTCATCCATAGCCGCGG 60.048 66.667 24.05 24.05 0.00 6.46
246 247 4.521062 GATCGCCTGCTGCTCCGT 62.521 66.667 0.00 0.00 38.05 4.69
260 261 4.193334 CCGTCTGCAGATCCGCGA 62.193 66.667 21.47 0.00 33.35 5.87
273 274 2.264480 CGCGACCCCAATGTCTCA 59.736 61.111 0.00 0.00 32.97 3.27
292 299 3.273654 ACGTCCTCCTCCTCCCCA 61.274 66.667 0.00 0.00 0.00 4.96
309 316 2.363147 ACCCTCGTGCTCCTCCTC 60.363 66.667 0.00 0.00 0.00 3.71
310 317 2.043450 CCCTCGTGCTCCTCCTCT 60.043 66.667 0.00 0.00 0.00 3.69
324 354 1.000496 TCCTCTTCCTCTTCCTCCGA 59.000 55.000 0.00 0.00 0.00 4.55
331 361 5.459505 TCTTCCTCTTCCTCCGAATCTAAT 58.540 41.667 0.00 0.00 0.00 1.73
504 534 3.866582 GGCGGTGGAGGATGGGAG 61.867 72.222 0.00 0.00 0.00 4.30
505 535 3.866582 GCGGTGGAGGATGGGAGG 61.867 72.222 0.00 0.00 0.00 4.30
506 536 3.164269 CGGTGGAGGATGGGAGGG 61.164 72.222 0.00 0.00 0.00 4.30
507 537 2.774351 GGTGGAGGATGGGAGGGG 60.774 72.222 0.00 0.00 0.00 4.79
508 538 2.372688 GTGGAGGATGGGAGGGGA 59.627 66.667 0.00 0.00 0.00 4.81
509 539 1.768077 GTGGAGGATGGGAGGGGAG 60.768 68.421 0.00 0.00 0.00 4.30
564 594 2.222592 CGGCGGTCGGCTTAAATAG 58.777 57.895 14.55 0.00 42.94 1.73
636 666 2.647297 GACGTCCGTCGGGTTTCT 59.353 61.111 12.29 0.00 44.69 2.52
637 667 1.731969 GACGTCCGTCGGGTTTCTG 60.732 63.158 12.29 0.00 44.69 3.02
638 668 3.110178 CGTCCGTCGGGTTTCTGC 61.110 66.667 12.29 0.00 35.71 4.26
639 669 2.741211 GTCCGTCGGGTTTCTGCC 60.741 66.667 12.29 0.00 33.83 4.85
640 670 4.367023 TCCGTCGGGTTTCTGCCG 62.367 66.667 12.29 0.00 33.83 5.69
657 771 4.307908 GCGCGCCAAACGTTGACT 62.308 61.111 23.24 0.00 46.11 3.41
661 775 1.602191 GCGCCAAACGTTGACTATTG 58.398 50.000 0.00 0.00 46.11 1.90
713 827 9.660180 GTCATAAGTCAAATCTAGAAAGGTCTT 57.340 33.333 0.00 2.67 35.12 3.01
730 844 7.399245 AAGGTCTTAGCAAGTTTACACAAAA 57.601 32.000 0.00 0.00 0.00 2.44
738 852 5.463061 AGCAAGTTTACACAAAATGCATCAC 59.537 36.000 0.00 0.00 39.47 3.06
767 881 4.872691 GCGGCATATATGAGAGCAAATACT 59.127 41.667 17.10 0.00 0.00 2.12
779 893 4.392138 AGAGCAAATACTAACGTTTCTGCC 59.608 41.667 5.91 2.20 0.00 4.85
801 915 3.383761 GTGTGTCAGGCAGGAAATTTTG 58.616 45.455 0.00 0.00 0.00 2.44
1432 1591 2.202610 CGCTCTTCGACGCCATCA 60.203 61.111 0.00 0.00 41.67 3.07
1444 1603 2.429058 CCATCAGGGGCTCCATCG 59.571 66.667 4.79 0.00 34.83 3.84
1937 2096 3.169099 AGCTCTGGTATGACTGTCAACT 58.831 45.455 15.31 1.60 0.00 3.16
1938 2097 3.056250 AGCTCTGGTATGACTGTCAACTG 60.056 47.826 15.31 11.64 0.00 3.16
1939 2098 3.306364 GCTCTGGTATGACTGTCAACTGT 60.306 47.826 15.31 0.43 0.00 3.55
1957 2119 2.418976 CTGTCATGTTGCATCTGGTCTG 59.581 50.000 0.00 0.00 0.00 3.51
1966 2128 1.612726 GCATCTGGTCTGCAGGAAACT 60.613 52.381 15.13 0.00 46.44 2.66
1969 2131 1.623811 TCTGGTCTGCAGGAAACTACC 59.376 52.381 15.13 13.31 40.21 3.18
2049 2212 4.985413 TGCTGTGCATTCTGTTATTTAGC 58.015 39.130 0.00 0.00 31.71 3.09
2052 2215 5.216566 TGTGCATTCTGTTATTTAGCGTC 57.783 39.130 0.00 0.00 0.00 5.19
2162 2325 6.391227 AGCACATTAACTTTACAGTTGCTT 57.609 33.333 4.49 0.00 43.54 3.91
2257 2424 9.268268 AGTATGACTTCGTTTCACAAAATTAGA 57.732 29.630 0.00 0.00 0.00 2.10
2348 2516 3.667261 CGAACGAAGTAACATCTTGTCGT 59.333 43.478 0.00 0.00 45.00 4.34
2349 2517 4.147653 CGAACGAAGTAACATCTTGTCGTT 59.852 41.667 8.79 8.79 45.00 3.85
2358 2526 5.493133 AACATCTTGTCGTTAAAACTGCA 57.507 34.783 0.00 0.00 0.00 4.41
2365 2533 7.254852 TCTTGTCGTTAAAACTGCAAAAGATT 58.745 30.769 0.00 0.00 0.00 2.40
2373 2541 9.087424 GTTAAAACTGCAAAAGATTTGAACTCT 57.913 29.630 6.99 0.00 33.37 3.24
2411 2579 4.675933 GCTTGGTTTCCGTTTGTTTACACT 60.676 41.667 0.00 0.00 0.00 3.55
2424 2592 5.811796 TGTTTACACTACTAAGCCCAGAA 57.188 39.130 0.00 0.00 0.00 3.02
2532 2700 4.812626 TCGGTTCTTTGTTTTCCTGTACTC 59.187 41.667 0.00 0.00 0.00 2.59
2565 2733 4.406648 TCGATATATCCATGCACATCCC 57.593 45.455 7.15 0.00 0.00 3.85
2579 2747 4.641541 TGCACATCCCATTCTCAAATACAG 59.358 41.667 0.00 0.00 0.00 2.74
2617 2785 6.040247 CAGCCATCTATTCAACACGTTACTA 58.960 40.000 0.00 0.00 0.00 1.82
2618 2786 6.019801 CAGCCATCTATTCAACACGTTACTAC 60.020 42.308 0.00 0.00 0.00 2.73
2619 2787 6.040878 GCCATCTATTCAACACGTTACTACT 58.959 40.000 0.00 0.00 0.00 2.57
2620 2788 7.067859 AGCCATCTATTCAACACGTTACTACTA 59.932 37.037 0.00 0.00 0.00 1.82
2646 2814 3.519510 ACTGAGAAGCCAGGCATAGTTAA 59.480 43.478 15.80 0.00 38.44 2.01
2656 2824 5.308014 CCAGGCATAGTTAATGATACAGCA 58.692 41.667 0.00 0.00 37.86 4.41
2671 2839 1.406539 ACAGCAAAGGCAGAAACAGTG 59.593 47.619 0.00 0.00 44.61 3.66
2749 2925 2.844348 TCCCTACCCCACTTGAAATCTC 59.156 50.000 0.00 0.00 0.00 2.75
2751 2927 3.267031 CCCTACCCCACTTGAAATCTCTT 59.733 47.826 0.00 0.00 0.00 2.85
2752 2928 4.265073 CCTACCCCACTTGAAATCTCTTG 58.735 47.826 0.00 0.00 0.00 3.02
2753 2929 3.884037 ACCCCACTTGAAATCTCTTGT 57.116 42.857 0.00 0.00 0.00 3.16
2766 2942 5.686159 AATCTCTTGTTGTGCTTCTTCTG 57.314 39.130 0.00 0.00 0.00 3.02
2775 2951 2.950975 TGTGCTTCTTCTGTGCAATGAA 59.049 40.909 0.00 0.00 38.50 2.57
2873 3049 4.511826 GGTTTCATATTCCTTAGAGCACCG 59.488 45.833 0.00 0.00 0.00 4.94
2875 3051 3.572642 TCATATTCCTTAGAGCACCGGA 58.427 45.455 9.46 0.00 0.00 5.14
2883 3059 4.654262 TCCTTAGAGCACCGGAATTATCTT 59.346 41.667 9.46 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.884744 GCAACAAGGTATTTTGGGGTTTTT 59.115 37.500 0.00 0.00 32.32 1.94
3 4 4.080299 TGCAACAAGGTATTTTGGGGTTTT 60.080 37.500 0.00 0.00 32.32 2.43
4 5 3.456277 TGCAACAAGGTATTTTGGGGTTT 59.544 39.130 0.00 0.00 32.32 3.27
5 6 3.041946 TGCAACAAGGTATTTTGGGGTT 58.958 40.909 0.00 0.00 32.32 4.11
6 7 2.367241 GTGCAACAAGGTATTTTGGGGT 59.633 45.455 0.00 0.00 36.32 4.95
7 8 2.632512 AGTGCAACAAGGTATTTTGGGG 59.367 45.455 0.00 0.00 41.43 4.96
8 9 4.335400 AAGTGCAACAAGGTATTTTGGG 57.665 40.909 0.00 0.00 41.43 4.12
9 10 7.961325 AATAAAGTGCAACAAGGTATTTTGG 57.039 32.000 0.00 0.00 41.43 3.28
41 42 9.845740 AAGATAAATAAAAAGGCAAACCAAAGT 57.154 25.926 0.00 0.00 39.06 2.66
72 73 9.739276 CAAGAGTGAGATCTAATAGAGATAGGT 57.261 37.037 0.00 0.00 45.48 3.08
73 74 9.739276 ACAAGAGTGAGATCTAATAGAGATAGG 57.261 37.037 0.00 0.00 45.48 2.57
77 78 7.988028 TCGAACAAGAGTGAGATCTAATAGAGA 59.012 37.037 0.00 0.00 39.01 3.10
78 79 8.148807 TCGAACAAGAGTGAGATCTAATAGAG 57.851 38.462 0.00 0.00 0.00 2.43
79 80 7.988028 TCTCGAACAAGAGTGAGATCTAATAGA 59.012 37.037 0.00 0.00 39.21 1.98
80 81 8.067784 GTCTCGAACAAGAGTGAGATCTAATAG 58.932 40.741 0.00 0.00 39.46 1.73
81 82 7.012515 GGTCTCGAACAAGAGTGAGATCTAATA 59.987 40.741 0.00 0.00 39.46 0.98
82 83 6.183360 GGTCTCGAACAAGAGTGAGATCTAAT 60.183 42.308 0.00 0.00 39.46 1.73
83 84 5.124138 GGTCTCGAACAAGAGTGAGATCTAA 59.876 44.000 0.00 0.00 39.46 2.10
84 85 4.636648 GGTCTCGAACAAGAGTGAGATCTA 59.363 45.833 0.00 0.00 39.46 1.98
85 86 3.442273 GGTCTCGAACAAGAGTGAGATCT 59.558 47.826 0.00 0.00 39.46 2.75
86 87 3.729462 CGGTCTCGAACAAGAGTGAGATC 60.729 52.174 0.00 0.00 39.46 2.75
87 88 2.162608 CGGTCTCGAACAAGAGTGAGAT 59.837 50.000 0.00 0.00 39.46 2.75
88 89 1.535896 CGGTCTCGAACAAGAGTGAGA 59.464 52.381 0.00 0.00 39.21 3.27
89 90 1.970447 CGGTCTCGAACAAGAGTGAG 58.030 55.000 0.00 0.00 39.21 3.51
90 91 0.039437 GCGGTCTCGAACAAGAGTGA 60.039 55.000 0.00 0.00 39.21 3.41
91 92 0.039074 AGCGGTCTCGAACAAGAGTG 60.039 55.000 0.00 0.00 39.21 3.51
92 93 0.674534 AAGCGGTCTCGAACAAGAGT 59.325 50.000 0.00 0.00 39.21 3.24
93 94 1.063806 CAAGCGGTCTCGAACAAGAG 58.936 55.000 0.00 0.00 39.00 2.85
94 95 0.319555 CCAAGCGGTCTCGAACAAGA 60.320 55.000 0.00 0.00 39.00 3.02
95 96 1.901650 GCCAAGCGGTCTCGAACAAG 61.902 60.000 0.00 0.00 39.00 3.16
96 97 1.959226 GCCAAGCGGTCTCGAACAA 60.959 57.895 0.00 0.00 39.00 2.83
97 98 2.357034 GCCAAGCGGTCTCGAACA 60.357 61.111 0.00 0.00 39.00 3.18
98 99 3.119096 GGCCAAGCGGTCTCGAAC 61.119 66.667 0.00 0.00 39.00 3.95
104 105 2.932130 GATGAGGAGGCCAAGCGGTC 62.932 65.000 5.01 0.00 37.05 4.79
105 106 3.011517 ATGAGGAGGCCAAGCGGT 61.012 61.111 5.01 0.00 33.28 5.68
106 107 2.203126 GATGAGGAGGCCAAGCGG 60.203 66.667 5.01 0.00 0.00 5.52
107 108 2.203126 GGATGAGGAGGCCAAGCG 60.203 66.667 5.01 0.00 0.00 4.68
108 109 0.767375 TATGGATGAGGAGGCCAAGC 59.233 55.000 5.01 0.00 34.95 4.01
109 110 1.271271 GCTATGGATGAGGAGGCCAAG 60.271 57.143 5.01 0.00 34.95 3.61
110 111 0.767375 GCTATGGATGAGGAGGCCAA 59.233 55.000 5.01 0.00 34.95 4.52
111 112 1.130054 GGCTATGGATGAGGAGGCCA 61.130 60.000 5.01 0.00 38.16 5.36
112 113 1.682257 GGCTATGGATGAGGAGGCC 59.318 63.158 0.00 0.00 0.00 5.19
113 114 1.294780 CGGCTATGGATGAGGAGGC 59.705 63.158 0.00 0.00 0.00 4.70
134 135 2.278013 GGACGTCGACGAGATGCC 60.278 66.667 41.52 27.30 43.02 4.40
246 247 3.838271 GGGTCGCGGATCTGCAGA 61.838 66.667 25.69 20.79 34.15 4.26
260 261 0.034896 GACGTGTGAGACATTGGGGT 59.965 55.000 0.00 0.00 0.00 4.95
273 274 2.037527 GGGAGGAGGAGGACGTGT 59.962 66.667 0.00 0.00 0.00 4.49
292 299 2.363147 GAGGAGGAGCACGAGGGT 60.363 66.667 0.00 0.00 0.00 4.34
309 316 5.537188 CATTAGATTCGGAGGAAGAGGAAG 58.463 45.833 0.00 0.00 35.19 3.46
310 317 4.202264 GCATTAGATTCGGAGGAAGAGGAA 60.202 45.833 0.00 0.00 35.19 3.36
324 354 3.307059 GCTACCTCCGGATGCATTAGATT 60.307 47.826 3.57 0.00 0.00 2.40
331 361 3.161450 GGGCTACCTCCGGATGCA 61.161 66.667 3.57 0.00 0.00 3.96
376 406 1.439543 ACTCCTTGAGCAGGTCCTTT 58.560 50.000 0.00 0.00 44.37 3.11
377 407 1.072965 CAACTCCTTGAGCAGGTCCTT 59.927 52.381 0.00 0.00 44.37 3.36
429 459 3.071837 TATGCTCCCACGCCGTCA 61.072 61.111 0.00 0.00 0.00 4.35
436 466 1.068194 CGCTAGTAGCTATGCTCCCAC 60.068 57.143 19.66 0.00 39.60 4.61
441 471 4.363999 CACTTTTCGCTAGTAGCTATGCT 58.636 43.478 19.66 0.00 39.60 3.79
466 496 1.373497 CACTTTCTGCTCGCCGTCT 60.373 57.895 0.00 0.00 0.00 4.18
492 522 2.705410 CTCCCCTCCCATCCTCCA 59.295 66.667 0.00 0.00 0.00 3.86
496 526 4.928520 CCCCCTCCCCTCCCATCC 62.929 77.778 0.00 0.00 0.00 3.51
514 544 0.401395 TACCCATCCACATCCCCCTC 60.401 60.000 0.00 0.00 0.00 4.30
515 545 0.401979 CTACCCATCCACATCCCCCT 60.402 60.000 0.00 0.00 0.00 4.79
569 599 2.042230 ACCCCGTAGTGCCCTAGG 60.042 66.667 0.06 0.06 0.00 3.02
640 670 2.235536 ATAGTCAACGTTTGGCGCGC 62.236 55.000 25.94 25.94 46.11 6.86
641 671 0.165079 AATAGTCAACGTTTGGCGCG 59.835 50.000 0.00 0.00 46.11 6.86
713 827 6.640499 GTGATGCATTTTGTGTAAACTTGCTA 59.360 34.615 0.00 0.00 36.68 3.49
730 844 2.592574 CCGCGGATGGTGATGCAT 60.593 61.111 24.07 0.00 0.00 3.96
738 852 1.136891 TCTCATATATGCCGCGGATGG 59.863 52.381 33.48 16.06 0.00 3.51
767 881 1.210870 GACACACGGCAGAAACGTTA 58.789 50.000 0.00 0.00 43.58 3.18
779 893 1.238439 AATTTCCTGCCTGACACACG 58.762 50.000 0.00 0.00 0.00 4.49
801 915 0.593008 GCGTCGGTTTGGTTTTGGAC 60.593 55.000 0.00 0.00 0.00 4.02
1632 1791 2.124487 CGCTCCTCCTCCTCGTCT 60.124 66.667 0.00 0.00 0.00 4.18
1937 2096 2.429478 CAGACCAGATGCAACATGACA 58.571 47.619 0.00 0.00 0.00 3.58
1938 2097 1.131883 GCAGACCAGATGCAACATGAC 59.868 52.381 0.00 0.00 43.31 3.06
1939 2098 1.456296 GCAGACCAGATGCAACATGA 58.544 50.000 0.00 0.00 43.31 3.07
1957 2119 3.268023 AGCATACTGGTAGTTTCCTGC 57.732 47.619 0.00 0.00 0.00 4.85
2049 2212 4.817517 ACTGTAATTGACCCTAACAGACG 58.182 43.478 8.82 0.00 39.93 4.18
2052 2215 8.883731 CAAATCTACTGTAATTGACCCTAACAG 58.116 37.037 0.00 0.00 42.53 3.16
2162 2325 6.149308 CCAGACACTACATAACAAGAATGCAA 59.851 38.462 0.00 0.00 0.00 4.08
2274 2441 3.887352 ACAGTATCTTCTAGCTGACGGA 58.113 45.455 0.00 0.00 33.57 4.69
2349 2517 9.950680 CTAGAGTTCAAATCTTTTGCAGTTTTA 57.049 29.630 0.00 0.00 0.00 1.52
2358 2526 4.757149 AGCACGCTAGAGTTCAAATCTTTT 59.243 37.500 0.00 0.00 0.00 2.27
2365 2533 6.887376 CTATTTTAGCACGCTAGAGTTCAA 57.113 37.500 0.00 0.00 0.00 2.69
2398 2566 4.751098 TGGGCTTAGTAGTGTAAACAAACG 59.249 41.667 0.00 0.00 0.00 3.60
2411 2579 6.889722 AGTTATGCAATTTTCTGGGCTTAGTA 59.110 34.615 0.00 0.00 0.00 1.82
2424 2592 7.893124 ATCTGAGATCCAAGTTATGCAATTT 57.107 32.000 0.00 0.00 0.00 1.82
2505 2673 3.630312 CAGGAAAACAAAGAACCGAGGAA 59.370 43.478 0.00 0.00 0.00 3.36
2511 2679 7.255035 GGTTAGAGTACAGGAAAACAAAGAACC 60.255 40.741 0.00 0.00 0.00 3.62
2532 2700 9.046296 GCATGGATATATCGAATTAAGGGTTAG 57.954 37.037 6.64 0.00 0.00 2.34
2579 2747 9.796120 GAATAGATGGCTGAAGTAGTATGTATC 57.204 37.037 0.00 0.00 0.00 2.24
2617 2785 2.498078 GCCTGGCTTCTCAGTTACTAGT 59.502 50.000 12.43 0.00 33.14 2.57
2618 2786 2.497675 TGCCTGGCTTCTCAGTTACTAG 59.502 50.000 21.03 0.00 33.14 2.57
2619 2787 2.536066 TGCCTGGCTTCTCAGTTACTA 58.464 47.619 21.03 0.00 33.14 1.82
2620 2788 1.352083 TGCCTGGCTTCTCAGTTACT 58.648 50.000 21.03 0.00 33.14 2.24
2646 2814 4.081406 TGTTTCTGCCTTTGCTGTATCAT 58.919 39.130 0.00 0.00 38.71 2.45
2656 2824 5.852282 ATAACAACACTGTTTCTGCCTTT 57.148 34.783 0.00 0.00 43.45 3.11
2671 2839 7.905493 GCATAGAAGAAGCACAGTTATAACAAC 59.095 37.037 17.65 4.09 0.00 3.32
2749 2925 2.097954 TGCACAGAAGAAGCACAACAAG 59.902 45.455 0.00 0.00 32.55 3.16
2751 2927 1.748950 TGCACAGAAGAAGCACAACA 58.251 45.000 0.00 0.00 32.55 3.33
2752 2928 2.849880 TTGCACAGAAGAAGCACAAC 57.150 45.000 0.00 0.00 38.11 3.32
2753 2929 2.950975 TCATTGCACAGAAGAAGCACAA 59.049 40.909 0.00 0.00 38.11 3.33
2766 2942 3.057736 ACAGCATCTCAGTTTCATTGCAC 60.058 43.478 0.00 0.00 32.66 4.57
2775 2951 2.255406 AGTCCAGACAGCATCTCAGTT 58.745 47.619 0.00 0.00 34.41 3.16
2873 3049 6.586844 GTCTACTATGGCGTCAAGATAATTCC 59.413 42.308 0.00 0.00 0.00 3.01
2875 3051 7.050970 TGTCTACTATGGCGTCAAGATAATT 57.949 36.000 0.00 0.00 0.00 1.40
2883 3059 4.207955 AGAAGATGTCTACTATGGCGTCA 58.792 43.478 0.00 0.00 33.56 4.35


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

AutoCloner maintained by Alex Coulton.