Multiple sequence alignment - TraesCS2D01G024800

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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 TraesCS2D01G024800 chr2D 100.000 2983 0 0 1 2983 10907702 10904720 0.000000e+00 5509.0
1 TraesCS2D01G024800 chr2D 84.722 72 8 3 2 70 641227719 641227648 5.340000e-08 69.4
2 TraesCS2D01G024800 chr2A 91.099 2101 100 27 570 2642 11614319 11612278 0.000000e+00 2763.0
3 TraesCS2D01G024800 chr2A 83.203 512 65 11 77 569 451012584 451012075 1.630000e-122 449.0
4 TraesCS2D01G024800 chr2A 96.581 117 3 1 2868 2983 11611971 11611855 3.030000e-45 193.0
5 TraesCS2D01G024800 chr2B 94.292 1717 87 7 564 2278 16335664 16333957 0.000000e+00 2617.0
6 TraesCS2D01G024800 chr2B 84.071 226 16 1 2424 2629 16331918 16331693 1.810000e-47 200.0
7 TraesCS2D01G024800 chr2B 93.846 65 4 0 2311 2375 16333957 16333893 6.800000e-17 99.0
8 TraesCS2D01G024800 chr5D 83.597 506 70 11 74 570 484702066 484701565 2.090000e-126 462.0
9 TraesCS2D01G024800 chr7B 80.952 525 73 13 70 570 22536878 22536357 1.000000e-104 390.0
10 TraesCS2D01G024800 chr7B 87.500 72 7 2 2 71 162931958 162931887 6.850000e-12 82.4
11 TraesCS2D01G024800 chr7A 81.081 518 73 12 70 570 80323909 80323400 1.000000e-104 390.0
12 TraesCS2D01G024800 chr7A 81.141 403 43 14 181 569 254431463 254431846 2.910000e-75 292.0
13 TraesCS2D01G024800 chr7A 81.424 323 57 3 250 571 8544444 8544124 8.200000e-66 261.0
14 TraesCS2D01G024800 chr3A 83.129 326 51 4 250 574 165095946 165095624 8.090000e-76 294.0
15 TraesCS2D01G024800 chr3A 96.970 33 1 0 40 72 185814 185782 4.150000e-04 56.5
16 TraesCS2D01G024800 chr5A 83.178 321 51 3 250 569 682896815 682897133 1.050000e-74 291.0
17 TraesCS2D01G024800 chr5A 87.611 113 11 2 244 356 607947458 607947567 8.680000e-26 128.0
18 TraesCS2D01G024800 chr5A 87.234 94 11 1 207 300 671555844 671555752 4.070000e-19 106.0
19 TraesCS2D01G024800 chr6B 87.383 214 23 4 367 578 22560033 22559822 2.970000e-60 243.0
20 TraesCS2D01G024800 chr6B 95.122 41 2 0 28 68 47426116 47426156 6.900000e-07 65.8
21 TraesCS2D01G024800 chr3D 87.368 95 8 3 272 365 540883524 540883433 4.070000e-19 106.0
22 TraesCS2D01G024800 chr3D 84.000 75 9 3 2 73 3191546 3191472 5.340000e-08 69.4
23 TraesCS2D01G024800 chr6A 86.567 67 7 2 4 68 455943092 455943026 4.120000e-09 73.1
24 TraesCS2D01G024800 chr3B 85.507 69 8 2 7 73 59707475 59707407 1.480000e-08 71.3
25 TraesCS2D01G024800 chr3B 89.583 48 3 2 22 68 790391950 790391904 3.210000e-05 60.2
26 TraesCS2D01G024800 chr1D 83.562 73 9 3 2 71 364514263 364514191 6.900000e-07 65.8


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 TraesCS2D01G024800 chr2D 10904720 10907702 2982 True 5509 5509 100.000000 1 2983 1 chr2D.!!$R1 2982
1 TraesCS2D01G024800 chr2A 11611855 11614319 2464 True 1478 2763 93.840000 570 2983 2 chr2A.!!$R2 2413
2 TraesCS2D01G024800 chr2A 451012075 451012584 509 True 449 449 83.203000 77 569 1 chr2A.!!$R1 492
3 TraesCS2D01G024800 chr2B 16331693 16335664 3971 True 972 2617 90.736333 564 2629 3 chr2B.!!$R1 2065
4 TraesCS2D01G024800 chr5D 484701565 484702066 501 True 462 462 83.597000 74 570 1 chr5D.!!$R1 496
5 TraesCS2D01G024800 chr7B 22536357 22536878 521 True 390 390 80.952000 70 570 1 chr7B.!!$R1 500
6 TraesCS2D01G024800 chr7A 80323400 80323909 509 True 390 390 81.081000 70 570 1 chr7A.!!$R2 500

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
30 31 0.105039 GCTCGTCCCAGGATCGATTT 59.895 55.0 0.0 0.0 33.26 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2061 1.069204 TCGAAGTGCCATCCATAGAGC 59.931 52.381 0.0 0.0 0.0 4.09 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 3.917760 CCGGCTCGTCCCAGGATC 61.918 72.222 0.00 0.00 0.00 3.36
26 27 4.271816 CGGCTCGTCCCAGGATCG 62.272 72.222 0.00 0.00 0.00 3.69
27 28 2.833582 GGCTCGTCCCAGGATCGA 60.834 66.667 9.81 9.81 0.00 3.59
28 29 2.203771 GGCTCGTCCCAGGATCGAT 61.204 63.158 0.00 0.00 33.26 3.59
29 30 1.742768 GCTCGTCCCAGGATCGATT 59.257 57.895 0.00 0.00 33.26 3.34
30 31 0.105039 GCTCGTCCCAGGATCGATTT 59.895 55.000 0.00 0.00 33.26 2.17
31 32 1.473434 GCTCGTCCCAGGATCGATTTT 60.473 52.381 0.00 0.00 33.26 1.82
32 33 2.906354 CTCGTCCCAGGATCGATTTTT 58.094 47.619 0.00 0.00 33.26 1.94
33 34 3.740141 GCTCGTCCCAGGATCGATTTTTA 60.740 47.826 0.00 0.00 33.26 1.52
34 35 4.632153 CTCGTCCCAGGATCGATTTTTAT 58.368 43.478 0.00 0.00 33.26 1.40
35 36 4.377021 TCGTCCCAGGATCGATTTTTATG 58.623 43.478 0.00 0.00 0.00 1.90
36 37 3.058914 CGTCCCAGGATCGATTTTTATGC 60.059 47.826 0.00 0.00 0.00 3.14
37 38 3.882888 GTCCCAGGATCGATTTTTATGCA 59.117 43.478 0.00 0.00 0.00 3.96
38 39 4.520492 GTCCCAGGATCGATTTTTATGCAT 59.480 41.667 3.79 3.79 0.00 3.96
39 40 4.761739 TCCCAGGATCGATTTTTATGCATC 59.238 41.667 0.19 0.00 0.00 3.91
40 41 4.082571 CCCAGGATCGATTTTTATGCATCC 60.083 45.833 0.19 0.00 0.00 3.51
41 42 4.763793 CCAGGATCGATTTTTATGCATCCT 59.236 41.667 0.19 0.00 40.71 3.24
42 43 5.696822 CAGGATCGATTTTTATGCATCCTG 58.303 41.667 0.19 6.89 46.77 3.86
43 44 5.624159 AGGATCGATTTTTATGCATCCTGA 58.376 37.500 0.19 0.00 38.97 3.86
44 45 6.064060 AGGATCGATTTTTATGCATCCTGAA 58.936 36.000 0.19 0.00 38.97 3.02
45 46 6.206243 AGGATCGATTTTTATGCATCCTGAAG 59.794 38.462 0.19 0.00 38.97 3.02
46 47 5.756195 TCGATTTTTATGCATCCTGAAGG 57.244 39.130 0.19 0.00 0.00 3.46
47 48 4.580167 TCGATTTTTATGCATCCTGAAGGG 59.420 41.667 0.19 0.00 35.41 3.95
48 49 4.625028 GATTTTTATGCATCCTGAAGGGC 58.375 43.478 0.19 0.00 35.41 5.19
49 50 2.071778 TTTATGCATCCTGAAGGGCC 57.928 50.000 0.19 0.00 35.41 5.80
50 51 0.925558 TTATGCATCCTGAAGGGCCA 59.074 50.000 6.18 0.00 35.41 5.36
51 52 0.925558 TATGCATCCTGAAGGGCCAA 59.074 50.000 6.18 0.00 35.41 4.52
52 53 0.685458 ATGCATCCTGAAGGGCCAAC 60.685 55.000 6.18 0.00 35.41 3.77
53 54 2.409870 GCATCCTGAAGGGCCAACG 61.410 63.158 6.18 0.00 35.41 4.10
54 55 1.750399 CATCCTGAAGGGCCAACGG 60.750 63.158 6.18 3.88 35.41 4.44
66 67 3.805267 CAACGGCTGGAGATGCTC 58.195 61.111 0.00 0.00 0.00 4.26
67 68 1.220206 CAACGGCTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
68 69 0.461548 CAACGGCTGGAGATGCTCTA 59.538 55.000 0.00 0.00 0.00 2.43
72 73 1.134699 CGGCTGGAGATGCTCTAAACA 60.135 52.381 0.00 0.00 0.00 2.83
84 85 2.866460 GCTCTAAACAAGCAGGACACGA 60.866 50.000 0.00 0.00 39.61 4.35
112 113 1.457303 GCTATTGCGTCCTAATCAGCG 59.543 52.381 0.00 0.00 0.00 5.18
118 119 3.466314 TCCTAATCAGCGGCGCCA 61.466 61.111 30.40 16.73 0.00 5.69
132 133 3.558411 GCCATCGTCGCTGCAGTC 61.558 66.667 16.64 6.83 0.00 3.51
135 136 3.071206 ATCGTCGCTGCAGTCCCT 61.071 61.111 16.64 0.00 0.00 4.20
138 139 2.343758 GTCGCTGCAGTCCCTTCA 59.656 61.111 16.64 0.00 0.00 3.02
139 140 1.739562 GTCGCTGCAGTCCCTTCAG 60.740 63.158 16.64 0.00 0.00 3.02
152 156 2.284331 TTCAGGGTGCCCTCGCTA 60.284 61.111 6.84 0.00 46.28 4.26
166 170 2.863153 GCTACTTGTGCCTGCGTG 59.137 61.111 0.00 0.00 0.00 5.34
179 183 3.279116 GCGTGGCTTGTGTGCAGA 61.279 61.111 0.00 0.00 34.04 4.26
186 190 4.560743 TTGTGTGCAGAGGCCGCA 62.561 61.111 9.88 4.12 40.13 5.69
211 215 0.370273 CGACTTGATCGCCGGAAAAG 59.630 55.000 5.05 2.89 45.52 2.27
219 223 0.742990 TCGCCGGAAAAGCAATCGAT 60.743 50.000 5.05 0.00 0.00 3.59
224 228 3.003275 GCCGGAAAAGCAATCGATTGATA 59.997 43.478 36.10 0.00 40.14 2.15
244 251 9.658799 ATTGATAACATATGTACTAGTGCATCC 57.341 33.333 26.98 11.01 37.16 3.51
245 252 7.312899 TGATAACATATGTACTAGTGCATCCG 58.687 38.462 26.98 20.83 37.16 4.18
259 266 1.462283 GCATCCGGACATGATCAATCG 59.538 52.381 6.12 1.48 0.00 3.34
294 313 2.233676 GGTGATTTCCTCGGCCAAAAAT 59.766 45.455 2.24 2.29 0.00 1.82
316 335 4.064973 TCCGGCAAGGATCCATGA 57.935 55.556 21.00 0.00 45.98 3.07
318 337 0.846015 TCCGGCAAGGATCCATGAAT 59.154 50.000 21.00 0.00 45.98 2.57
335 356 6.929049 TCCATGAATTATGTACAATCGTCTCC 59.071 38.462 0.00 0.00 34.87 3.71
336 357 6.705825 CCATGAATTATGTACAATCGTCTCCA 59.294 38.462 0.00 0.00 34.87 3.86
356 377 2.106938 GCATCTCATGTCCGCCGA 59.893 61.111 0.00 0.00 0.00 5.54
362 383 1.156736 CTCATGTCCGCCGAAAAGTT 58.843 50.000 0.00 0.00 0.00 2.66
365 400 1.535462 CATGTCCGCCGAAAAGTTTCT 59.465 47.619 2.53 0.00 35.07 2.52
374 409 2.224314 CCGAAAAGTTTCTCTGCAGTCC 59.776 50.000 14.67 0.00 35.07 3.85
391 426 0.324738 TCCCGTCAGAGCAGGAGAAT 60.325 55.000 0.00 0.00 0.00 2.40
396 431 3.868077 CCGTCAGAGCAGGAGAATAAAAG 59.132 47.826 0.00 0.00 0.00 2.27
413 448 8.454106 AGAATAAAAGACACGGATTTCTCAATG 58.546 33.333 0.00 0.00 0.00 2.82
427 462 6.371809 TTTCTCAATGCGTGTAGAGTTTTT 57.628 33.333 0.00 0.00 0.00 1.94
609 646 2.030274 AGGCCAAACAAGTTATGAACGC 60.030 45.455 5.01 0.00 36.23 4.84
630 667 3.554934 CATTGCTTACTATCAAGGGCCA 58.445 45.455 6.18 0.00 0.00 5.36
633 670 2.777114 TGCTTACTATCAAGGGCCATCA 59.223 45.455 6.18 0.00 0.00 3.07
637 674 5.440610 CTTACTATCAAGGGCCATCAGTTT 58.559 41.667 6.18 0.00 0.00 2.66
638 675 4.322057 ACTATCAAGGGCCATCAGTTTT 57.678 40.909 6.18 0.00 0.00 2.43
639 676 4.019174 ACTATCAAGGGCCATCAGTTTTG 58.981 43.478 6.18 0.00 0.00 2.44
640 677 2.673775 TCAAGGGCCATCAGTTTTGA 57.326 45.000 6.18 1.60 37.81 2.69
641 678 2.956132 TCAAGGGCCATCAGTTTTGAA 58.044 42.857 6.18 0.00 36.78 2.69
642 679 2.627699 TCAAGGGCCATCAGTTTTGAAC 59.372 45.455 6.18 0.00 36.78 3.18
651 688 6.147656 GGCCATCAGTTTTGAACTTTTTATGG 59.852 38.462 0.00 12.42 40.46 2.74
687 724 4.751098 TGGTTATTGTGGTAGTCGTCAAAC 59.249 41.667 0.00 0.00 0.00 2.93
703 740 8.126700 AGTCGTCAAACCTACAAATAAGTTTTG 58.873 33.333 0.00 0.00 30.27 2.44
759 796 1.378531 TCACAAAGTCAGCACACACC 58.621 50.000 0.00 0.00 0.00 4.16
765 802 0.390860 AGTCAGCACACACCAGAGAC 59.609 55.000 0.00 0.00 0.00 3.36
823 866 3.694566 AGTTGACCTGTGGAAGTTTTGTC 59.305 43.478 0.00 0.00 0.00 3.18
859 902 7.176075 CGTGTGTAGCTATCAAAGAAATGAAG 58.824 38.462 0.00 0.00 32.06 3.02
860 903 7.467623 GTGTGTAGCTATCAAAGAAATGAAGG 58.532 38.462 0.00 0.00 32.06 3.46
894 937 4.260620 CCTTGAACAAGTCGTACCAACAAG 60.261 45.833 12.54 0.00 36.72 3.16
928 971 3.814842 TCATATAAGTGCCTCCAAATGCG 59.185 43.478 0.00 0.00 0.00 4.73
972 1015 8.952278 ACTCACATAGTAACAGAAGTAGAAGAG 58.048 37.037 0.00 0.00 36.36 2.85
975 1018 7.700234 CACATAGTAACAGAAGTAGAAGAGCAG 59.300 40.741 0.00 0.00 0.00 4.24
1494 1537 9.675464 AATCATTCCAACTTAATTACTCCGTTA 57.325 29.630 0.00 0.00 0.00 3.18
1740 1784 8.507524 AAAGGGAGTCATATTAAGCTAACAAC 57.492 34.615 0.00 0.00 0.00 3.32
1781 1825 7.503566 ACTTCAATGGTTACTCATGGGATAATG 59.496 37.037 0.00 0.00 0.00 1.90
1983 2027 0.872388 AAAAATCACCGTCCGCTGAC 59.128 50.000 0.00 0.00 38.18 3.51
1993 2037 1.607148 CGTCCGCTGACCAGTCATATA 59.393 52.381 0.04 0.00 39.13 0.86
2189 2233 4.554960 TTGTCCGTATGTTGTAATGGGA 57.445 40.909 0.00 0.00 0.00 4.37
2280 2327 3.403038 ACTTCAACTCCCAACTGAATCG 58.597 45.455 0.00 0.00 0.00 3.34
2343 2395 3.551496 CTTGGGGCTGTTGAGGCGA 62.551 63.158 0.00 0.00 45.92 5.54
2381 2433 5.593010 CAGTGGAACGGGTTATTTGAAAAA 58.407 37.500 0.00 0.00 45.86 1.94
2412 2496 0.250989 AGGGCGAAATCAAAACGGGA 60.251 50.000 0.00 0.00 0.00 5.14
2449 4427 0.325860 TGTAAGTACAGGGGGCGGAT 60.326 55.000 0.00 0.00 0.00 4.18
2457 4435 0.537371 CAGGGGGCGGATCAATAACC 60.537 60.000 0.00 0.00 0.00 2.85
2538 4536 0.737715 CGGCTGCAGTCCACTTCTAC 60.738 60.000 21.86 0.86 0.00 2.59
2545 4543 0.537188 AGTCCACTTCTACGCATGGG 59.463 55.000 8.44 8.44 32.73 4.00
2719 4717 5.502079 TCTCTCTCTACCTCGAATTCAACT 58.498 41.667 6.22 0.00 0.00 3.16
2729 4727 1.327303 GAATTCAACTGGTGTGGCCA 58.673 50.000 0.00 0.00 46.95 5.36
2760 4758 7.689299 TCCACCTATTACCAATCATAATCCTG 58.311 38.462 0.00 0.00 0.00 3.86
2778 4776 3.943381 TCCTGCACATCAGCTTATTTCTG 59.057 43.478 0.00 0.00 41.50 3.02
2779 4777 3.066342 CCTGCACATCAGCTTATTTCTGG 59.934 47.826 0.00 0.00 41.50 3.86
2783 4781 5.243507 TGCACATCAGCTTATTTCTGGAAAA 59.756 36.000 0.00 0.00 32.77 2.29
2784 4782 6.158598 GCACATCAGCTTATTTCTGGAAAAA 58.841 36.000 0.00 0.00 33.56 1.94
2815 4820 0.179121 CGTAGCATTACTCGGTGGCA 60.179 55.000 0.00 0.00 0.00 4.92
2839 4844 1.115326 AAGGAGCAAAACACCCCAGC 61.115 55.000 0.00 0.00 0.00 4.85
2841 4846 2.123897 AGCAAAACACCCCAGCGT 60.124 55.556 0.00 0.00 0.00 5.07
2843 4848 2.727544 CAAAACACCCCAGCGTGG 59.272 61.111 0.00 0.00 38.11 4.94
2863 4868 3.244112 TGGAAGAGGGAACGTTCTTTCTC 60.244 47.826 26.32 25.47 34.04 2.87
2889 4998 0.533085 TTGGGATGACACGCGAACAA 60.533 50.000 15.93 2.83 0.00 2.83
2894 5003 3.485216 GGGATGACACGCGAACAAATAAG 60.485 47.826 15.93 0.00 0.00 1.73
2967 5077 2.037641 TCAACCTGTGACTGTGAGGATG 59.962 50.000 0.00 0.00 32.36 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.917760 GATCCTGGGACGAGCCGG 61.918 72.222 0.00 0.00 37.63 6.13
9 10 4.271816 CGATCCTGGGACGAGCCG 62.272 72.222 7.44 0.00 37.63 5.52
10 11 1.749334 AATCGATCCTGGGACGAGCC 61.749 60.000 17.31 0.00 39.31 4.70
11 12 0.105039 AAATCGATCCTGGGACGAGC 59.895 55.000 17.31 0.00 39.31 5.03
12 13 2.604046 AAAATCGATCCTGGGACGAG 57.396 50.000 17.31 2.50 39.31 4.18
13 14 4.377021 CATAAAAATCGATCCTGGGACGA 58.623 43.478 15.47 15.47 40.18 4.20
14 15 3.058914 GCATAAAAATCGATCCTGGGACG 60.059 47.826 0.00 0.23 0.00 4.79
15 16 3.882888 TGCATAAAAATCGATCCTGGGAC 59.117 43.478 0.00 0.00 0.00 4.46
16 17 4.163441 TGCATAAAAATCGATCCTGGGA 57.837 40.909 0.00 0.00 0.00 4.37
17 18 4.082571 GGATGCATAAAAATCGATCCTGGG 60.083 45.833 0.00 0.00 0.00 4.45
18 19 4.763793 AGGATGCATAAAAATCGATCCTGG 59.236 41.667 0.00 0.00 38.60 4.45
19 20 5.696822 CAGGATGCATAAAAATCGATCCTG 58.303 41.667 10.38 10.38 46.39 3.86
20 21 5.624159 TCAGGATGCATAAAAATCGATCCT 58.376 37.500 0.00 0.00 40.29 3.24
21 22 5.947228 TCAGGATGCATAAAAATCGATCC 57.053 39.130 0.00 0.00 34.76 3.36
22 23 6.376978 CCTTCAGGATGCATAAAAATCGATC 58.623 40.000 0.00 0.00 37.39 3.69
23 24 5.242393 CCCTTCAGGATGCATAAAAATCGAT 59.758 40.000 0.00 0.00 38.24 3.59
24 25 4.580167 CCCTTCAGGATGCATAAAAATCGA 59.420 41.667 0.00 0.00 38.24 3.59
25 26 4.794003 GCCCTTCAGGATGCATAAAAATCG 60.794 45.833 0.00 0.00 38.24 3.34
26 27 4.502087 GGCCCTTCAGGATGCATAAAAATC 60.502 45.833 0.00 0.00 38.24 2.17
27 28 3.389002 GGCCCTTCAGGATGCATAAAAAT 59.611 43.478 0.00 0.00 38.24 1.82
28 29 2.765699 GGCCCTTCAGGATGCATAAAAA 59.234 45.455 0.00 0.00 38.24 1.94
29 30 2.292126 TGGCCCTTCAGGATGCATAAAA 60.292 45.455 0.00 0.00 38.24 1.52
30 31 1.287442 TGGCCCTTCAGGATGCATAAA 59.713 47.619 0.00 0.00 38.24 1.40
31 32 0.925558 TGGCCCTTCAGGATGCATAA 59.074 50.000 0.00 0.00 38.24 1.90
32 33 0.925558 TTGGCCCTTCAGGATGCATA 59.074 50.000 0.00 0.00 38.24 3.14
33 34 0.685458 GTTGGCCCTTCAGGATGCAT 60.685 55.000 0.00 0.00 38.24 3.96
34 35 1.304381 GTTGGCCCTTCAGGATGCA 60.304 57.895 0.00 0.00 38.24 3.96
35 36 2.409870 CGTTGGCCCTTCAGGATGC 61.410 63.158 0.00 0.00 38.24 3.91
36 37 1.750399 CCGTTGGCCCTTCAGGATG 60.750 63.158 0.00 0.00 38.24 3.51
37 38 2.677228 CCGTTGGCCCTTCAGGAT 59.323 61.111 0.00 0.00 38.24 3.24
38 39 4.344865 GCCGTTGGCCCTTCAGGA 62.345 66.667 0.00 0.00 44.06 3.86
49 50 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
63 64 1.461127 CGTGTCCTGCTTGTTTAGAGC 59.539 52.381 0.00 0.00 40.53 4.09
64 65 3.026630 TCGTGTCCTGCTTGTTTAGAG 57.973 47.619 0.00 0.00 0.00 2.43
65 66 3.390135 CTTCGTGTCCTGCTTGTTTAGA 58.610 45.455 0.00 0.00 0.00 2.10
66 67 2.096218 GCTTCGTGTCCTGCTTGTTTAG 60.096 50.000 0.00 0.00 0.00 1.85
67 68 1.871039 GCTTCGTGTCCTGCTTGTTTA 59.129 47.619 0.00 0.00 0.00 2.01
68 69 0.663153 GCTTCGTGTCCTGCTTGTTT 59.337 50.000 0.00 0.00 0.00 2.83
72 73 2.357517 CGGCTTCGTGTCCTGCTT 60.358 61.111 0.00 0.00 0.00 3.91
91 92 2.483876 GCTGATTAGGACGCAATAGCA 58.516 47.619 0.00 0.00 42.27 3.49
96 97 1.813753 GCCGCTGATTAGGACGCAA 60.814 57.895 0.00 0.00 0.00 4.85
97 98 2.202878 GCCGCTGATTAGGACGCA 60.203 61.111 0.00 0.00 0.00 5.24
105 106 4.838152 ACGATGGCGCCGCTGATT 62.838 61.111 23.90 1.28 42.48 2.57
118 119 2.564553 GAAGGGACTGCAGCGACGAT 62.565 60.000 15.27 0.00 40.86 3.73
146 150 3.479370 GCAGGCACAAGTAGCGAG 58.521 61.111 0.00 0.00 0.00 5.03
166 170 3.368571 GGCCTCTGCACACAAGCC 61.369 66.667 0.00 0.00 40.13 4.35
194 198 0.605319 TGCTTTTCCGGCGATCAAGT 60.605 50.000 9.30 0.00 0.00 3.16
219 223 7.812669 CGGATGCACTAGTACATATGTTATCAA 59.187 37.037 14.77 0.00 0.00 2.57
224 228 4.587262 TCCGGATGCACTAGTACATATGTT 59.413 41.667 14.77 0.00 0.00 2.71
259 266 8.125448 CGAGGAAATCACCATTTAGAAAAGATC 58.875 37.037 0.00 0.00 31.94 2.75
262 269 6.555315 CCGAGGAAATCACCATTTAGAAAAG 58.445 40.000 0.00 0.00 31.94 2.27
263 270 5.105917 GCCGAGGAAATCACCATTTAGAAAA 60.106 40.000 0.00 0.00 31.94 2.29
264 271 4.398044 GCCGAGGAAATCACCATTTAGAAA 59.602 41.667 0.00 0.00 31.94 2.52
265 272 3.945285 GCCGAGGAAATCACCATTTAGAA 59.055 43.478 0.00 0.00 31.94 2.10
266 273 3.541632 GCCGAGGAAATCACCATTTAGA 58.458 45.455 0.00 0.00 31.94 2.10
267 274 2.618709 GGCCGAGGAAATCACCATTTAG 59.381 50.000 0.00 0.00 31.94 1.85
294 313 2.428925 GGATCCTTGCCGGACGGTA 61.429 63.158 5.05 4.82 46.80 4.02
315 334 7.072030 GCAATGGAGACGATTGTACATAATTC 58.928 38.462 0.00 0.00 33.88 2.17
316 335 6.542005 TGCAATGGAGACGATTGTACATAATT 59.458 34.615 0.00 0.00 33.88 1.40
318 337 5.423886 TGCAATGGAGACGATTGTACATAA 58.576 37.500 0.00 0.00 33.88 1.90
335 356 0.309922 GGCGGACATGAGATGCAATG 59.690 55.000 0.00 0.00 0.00 2.82
336 357 1.162181 CGGCGGACATGAGATGCAAT 61.162 55.000 0.00 0.00 0.00 3.56
356 377 2.222027 CGGGACTGCAGAGAAACTTTT 58.778 47.619 23.35 0.00 0.00 2.27
362 383 0.539669 TCTGACGGGACTGCAGAGAA 60.540 55.000 23.35 0.00 34.02 2.87
365 400 2.640302 GCTCTGACGGGACTGCAGA 61.640 63.158 23.35 0.00 37.17 4.26
374 409 3.526931 TTTATTCTCCTGCTCTGACGG 57.473 47.619 0.00 0.00 0.00 4.79
391 426 5.390461 CGCATTGAGAAATCCGTGTCTTTTA 60.390 40.000 0.00 0.00 0.00 1.52
396 431 1.732259 ACGCATTGAGAAATCCGTGTC 59.268 47.619 0.00 0.00 0.00 3.67
442 477 5.068215 TCAAGGGGTAAAATTGGAAGACA 57.932 39.130 0.00 0.00 0.00 3.41
508 545 4.142093 CCATTTCCAGTCATTCAATGGACC 60.142 45.833 0.00 0.00 44.63 4.46
520 557 2.479566 TGAGCTGTCCATTTCCAGTC 57.520 50.000 0.00 0.00 0.00 3.51
609 646 3.554934 TGGCCCTTGATAGTAAGCAATG 58.445 45.455 0.00 0.00 29.04 2.82
630 667 8.149647 TGCATCCATAAAAAGTTCAAAACTGAT 58.850 29.630 0.00 0.00 41.91 2.90
633 670 8.907222 ATTGCATCCATAAAAAGTTCAAAACT 57.093 26.923 0.00 0.00 45.46 2.66
660 697 7.585579 TGACGACTACCACAATAACCATATA 57.414 36.000 0.00 0.00 0.00 0.86
759 796 0.469144 GCTCCCCCTCTAGGTCTCTG 60.469 65.000 0.00 0.00 0.00 3.35
765 802 1.739750 AATCATGCTCCCCCTCTAGG 58.260 55.000 0.00 0.00 0.00 3.02
800 843 4.086457 ACAAAACTTCCACAGGTCAACTT 58.914 39.130 0.00 0.00 0.00 2.66
823 866 0.732880 CTACACACGGCTCGGTCAAG 60.733 60.000 0.00 0.00 0.00 3.02
859 902 5.783111 ACTTGTTCAAGGTGATTAATTGCC 58.217 37.500 15.51 0.00 0.00 4.52
860 903 5.569059 CGACTTGTTCAAGGTGATTAATTGC 59.431 40.000 15.51 0.00 0.00 3.56
894 937 4.212214 GCACTTATATGACAGCCAACTAGC 59.788 45.833 0.00 0.00 0.00 3.42
932 975 0.598419 GTGAGTTTGCCAGCTTTGCC 60.598 55.000 2.68 0.00 0.00 4.52
940 983 5.222079 TCTGTTACTATGTGAGTTTGCCA 57.778 39.130 0.00 0.00 39.81 4.92
941 984 5.701290 ACTTCTGTTACTATGTGAGTTTGCC 59.299 40.000 0.00 0.00 39.81 4.52
942 985 6.787085 ACTTCTGTTACTATGTGAGTTTGC 57.213 37.500 0.00 0.00 39.81 3.68
972 1015 4.115516 TCGATTCTTCACTCTATTGCTGC 58.884 43.478 0.00 0.00 0.00 5.25
975 1018 3.181377 CGCTCGATTCTTCACTCTATTGC 59.819 47.826 0.00 0.00 0.00 3.56
1192 1235 2.935849 TCGCATTATACACAAGGCACAG 59.064 45.455 0.00 0.00 34.99 3.66
1697 1741 3.982891 TGGTCCGGGTTGTACCAA 58.017 55.556 9.42 0.00 41.02 3.67
1952 1996 6.128929 GGACGGTGATTTTTGCAGTAAATTTC 60.129 38.462 9.42 6.70 0.00 2.17
1983 2027 5.731406 GCACACAATTGCTGTATATGACTGG 60.731 44.000 5.05 0.00 39.59 4.00
2017 2061 1.069204 TCGAAGTGCCATCCATAGAGC 59.931 52.381 0.00 0.00 0.00 4.09
2343 2395 5.221048 CGTTCCACTGGTCTTTCTTGAAATT 60.221 40.000 0.00 0.00 0.00 1.82
2381 2433 5.192927 TGATTTCGCCCTATCAAATCTGTT 58.807 37.500 0.00 0.00 37.40 3.16
2382 2434 4.780815 TGATTTCGCCCTATCAAATCTGT 58.219 39.130 0.00 0.00 37.40 3.41
2383 2435 5.756195 TTGATTTCGCCCTATCAAATCTG 57.244 39.130 0.00 0.00 37.71 2.90
2392 2476 1.003349 TCCCGTTTTGATTTCGCCCTA 59.997 47.619 0.00 0.00 0.00 3.53
2397 2481 2.550606 TCCACTTCCCGTTTTGATTTCG 59.449 45.455 0.00 0.00 0.00 3.46
2412 2496 1.274650 ACATCATCCCCTCCTCCACTT 60.275 52.381 0.00 0.00 0.00 3.16
2449 4427 4.827692 ACGCACAGTAGATTGGTTATTGA 58.172 39.130 0.00 0.00 0.00 2.57
2457 4435 4.352039 AGAATCGTACGCACAGTAGATTG 58.648 43.478 11.24 0.00 35.42 2.67
2504 4502 1.134521 CAGCCGGCCACTTGATTAGTA 60.135 52.381 26.15 0.00 34.56 1.82
2529 4527 3.813596 GCCCATGCGTAGAAGTGG 58.186 61.111 0.00 0.00 0.00 4.00
2545 4543 6.539649 TTTTTGTATGACATATCTAGCCGC 57.460 37.500 0.00 0.00 0.00 6.53
2551 4549 7.445096 TGCATCCGATTTTTGTATGACATATCT 59.555 33.333 0.00 0.00 0.00 1.98
2589 4587 0.608130 TTGGTCGAGTGCTGCTATGT 59.392 50.000 0.00 0.00 0.00 2.29
2659 4657 8.724229 GGAAAGTTAGGTATAAACATTGTCGTT 58.276 33.333 0.00 0.00 0.00 3.85
2660 4658 7.879160 TGGAAAGTTAGGTATAAACATTGTCGT 59.121 33.333 0.00 0.00 0.00 4.34
2661 4659 8.173130 GTGGAAAGTTAGGTATAAACATTGTCG 58.827 37.037 0.00 0.00 0.00 4.35
2662 4660 9.005777 TGTGGAAAGTTAGGTATAAACATTGTC 57.994 33.333 0.00 0.00 0.00 3.18
2684 4682 7.094975 CGAGGTAGAGAGAGAGTTATAATGTGG 60.095 44.444 0.00 0.00 0.00 4.17
2692 4690 6.651086 TGAATTCGAGGTAGAGAGAGAGTTA 58.349 40.000 0.04 0.00 0.00 2.24
2695 4693 5.588648 AGTTGAATTCGAGGTAGAGAGAGAG 59.411 44.000 0.04 0.00 0.00 3.20
2729 4727 6.575244 TGATTGGTAATAGGTGGATGAAGT 57.425 37.500 0.00 0.00 0.00 3.01
2739 4737 6.942005 TGTGCAGGATTATGATTGGTAATAGG 59.058 38.462 0.00 0.00 0.00 2.57
2760 4758 4.970662 TTCCAGAAATAAGCTGATGTGC 57.029 40.909 0.00 0.00 35.39 4.57
2787 4785 5.870978 ACCGAGTAATGCTACGTTTACATTT 59.129 36.000 13.38 0.52 35.68 2.32
2788 4786 5.290158 CACCGAGTAATGCTACGTTTACATT 59.710 40.000 9.79 11.44 37.71 2.71
2809 4814 0.322816 TTGCTCCTTCATCTGCCACC 60.323 55.000 0.00 0.00 0.00 4.61
2815 4820 2.519013 GGGTGTTTTGCTCCTTCATCT 58.481 47.619 0.00 0.00 0.00 2.90
2839 4844 0.317479 AGAACGTTCCCTCTTCCACG 59.683 55.000 24.22 0.00 38.62 4.94
2841 4846 2.704065 AGAAAGAACGTTCCCTCTTCCA 59.296 45.455 24.22 0.00 30.57 3.53
2843 4848 4.260139 AGAGAAAGAACGTTCCCTCTTC 57.740 45.455 26.41 21.51 30.57 2.87
2863 4868 2.159707 CGCGTGTCATCCCAAGTAAAAG 60.160 50.000 0.00 0.00 0.00 2.27
2889 4998 2.868253 GGCAGGTTGGCGTCTTATT 58.132 52.632 0.00 0.00 31.79 1.40


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

AutoCloner maintained by Alex Coulton.