Multiple sequence alignment - TraesCS6A01G358800

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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 TraesCS6A01G358800 chr6A 100.000 3992 0 0 936 4927 588755704 588759695 0.000000e+00 7372.0
1 TraesCS6A01G358800 chr6A 96.077 2549 85 6 936 3470 32534262 32531715 0.000000e+00 4139.0
2 TraesCS6A01G358800 chr6A 95.998 2549 87 6 936 3470 32560455 32557908 0.000000e+00 4128.0
3 TraesCS6A01G358800 chr6A 95.842 2549 88 7 936 3470 32426664 32424120 0.000000e+00 4104.0
4 TraesCS6A01G358800 chr6A 96.788 1183 26 3 3462 4636 32530831 32529653 0.000000e+00 1964.0
5 TraesCS6A01G358800 chr6A 96.453 1184 29 3 3462 4636 32423217 32422038 0.000000e+00 1941.0
6 TraesCS6A01G358800 chr6A 96.447 1182 29 3 3462 4634 32557017 32555840 0.000000e+00 1938.0
7 TraesCS6A01G358800 chr6A 100.000 558 0 0 1 558 588754769 588755326 0.000000e+00 1031.0
8 TraesCS6A01G358800 chr6A 96.085 562 16 5 1 558 32427409 32426850 0.000000e+00 911.0
9 TraesCS6A01G358800 chr6A 95.907 562 18 4 1 558 32561201 32560641 0.000000e+00 905.0
10 TraesCS6A01G358800 chr6A 95.536 560 21 4 1 558 32535004 32534447 0.000000e+00 893.0
11 TraesCS6A01G358800 chr6A 97.447 235 6 0 4639 4873 32555315 32555081 7.680000e-108 401.0
12 TraesCS6A01G358800 chr6A 97.021 235 7 0 4639 4873 32421514 32421280 3.570000e-106 396.0
13 TraesCS6A01G358800 chr6A 94.898 196 8 1 2343 2538 514350960 514350767 6.200000e-79 305.0
14 TraesCS6A01G358800 chr4A 95.507 3494 126 13 1161 4636 592048856 592045376 0.000000e+00 5553.0
15 TraesCS6A01G358800 chr4A 90.664 557 50 2 4 558 592073922 592073366 0.000000e+00 739.0
16 TraesCS6A01G358800 chr4A 100.000 55 0 0 4873 4927 141472340 141472286 8.730000e-18 102.0
17 TraesCS6A01G358800 chr2B 94.887 1897 68 6 2753 4636 691133793 691135673 0.000000e+00 2939.0
18 TraesCS6A01G358800 chr2B 83.308 671 49 27 1530 2184 653016749 653017372 1.200000e-155 560.0
19 TraesCS6A01G358800 chr2B 84.890 364 26 16 1121 1456 490617656 490617294 1.700000e-89 340.0
20 TraesCS6A01G358800 chr7B 96.222 1350 37 4 3297 4636 707972806 707974151 0.000000e+00 2198.0
21 TraesCS6A01G358800 chr7B 95.361 1121 38 6 2756 3864 27766400 27765282 0.000000e+00 1770.0
22 TraesCS6A01G358800 chr7B 96.178 968 29 4 3672 4636 605712178 605711216 0.000000e+00 1576.0
23 TraesCS6A01G358800 chr7B 92.092 822 59 4 1519 2337 306216483 306215665 0.000000e+00 1153.0
24 TraesCS6A01G358800 chr7B 92.628 529 37 2 4 530 559714278 559713750 0.000000e+00 760.0
25 TraesCS6A01G358800 chr7B 89.242 567 52 5 960 1519 559713275 559712711 0.000000e+00 701.0
26 TraesCS6A01G358800 chr7B 93.642 173 5 1 2551 2723 559712704 559712538 2.280000e-63 254.0
27 TraesCS6A01G358800 chr7B 95.312 64 2 1 2756 2818 697784506 697784443 3.140000e-17 100.0
28 TraesCS6A01G358800 chr7B 97.778 45 1 0 1476 1520 493131944 493131900 1.470000e-10 78.7
29 TraesCS6A01G358800 chr7B 96.875 32 1 0 936 967 559713311 559713280 2.000000e-03 54.7
30 TraesCS6A01G358800 chr2A 96.894 966 25 2 3672 4636 481859456 481858495 0.000000e+00 1613.0
31 TraesCS6A01G358800 chr2A 82.678 687 62 33 1530 2184 687049186 687049847 1.550000e-154 556.0
32 TraesCS6A01G358800 chr2A 97.458 236 6 0 4639 4874 66626287 66626522 2.140000e-108 403.0
33 TraesCS6A01G358800 chr2A 82.051 117 9 5 936 1040 655840291 655840175 6.790000e-14 89.8
34 TraesCS6A01G358800 chr5A 96.498 971 29 2 3672 4642 6906408 6905443 0.000000e+00 1600.0
35 TraesCS6A01G358800 chr5A 95.708 932 27 4 2753 3672 41526594 41527524 0.000000e+00 1487.0
36 TraesCS6A01G358800 chr5A 89.297 327 22 5 1183 1496 345324263 345323937 9.940000e-107 398.0
37 TraesCS6A01G358800 chr5A 94.444 36 2 0 2796 2831 41526574 41526539 6.890000e-04 56.5
38 TraesCS6A01G358800 chr1D 95.289 934 26 4 2862 3781 463400809 463401738 0.000000e+00 1465.0
39 TraesCS6A01G358800 chr1D 94.450 937 34 4 2862 3784 26249386 26248454 0.000000e+00 1426.0
40 TraesCS6A01G358800 chr1D 89.502 562 55 4 1 558 41780599 41781160 0.000000e+00 708.0
41 TraesCS6A01G358800 chr1D 89.247 558 57 3 4 558 79843159 79842602 0.000000e+00 695.0
42 TraesCS6A01G358800 chr1D 80.342 117 11 5 936 1040 412908087 412907971 1.470000e-10 78.7
43 TraesCS6A01G358800 chr1D 97.778 45 0 1 2827 2870 26249383 26249427 5.290000e-10 76.8
44 TraesCS6A01G358800 chr1D 97.778 45 0 1 2827 2870 463400812 463400768 5.290000e-10 76.8
45 TraesCS6A01G358800 chr1D 100.000 31 0 0 936 966 412824530 412824500 1.920000e-04 58.4
46 TraesCS6A01G358800 chr4D 95.192 936 27 6 2862 3785 275234587 275235516 0.000000e+00 1463.0
47 TraesCS6A01G358800 chr4D 94.855 933 30 9 2862 3781 143276401 143277328 0.000000e+00 1441.0
48 TraesCS6A01G358800 chr4D 97.778 45 0 1 2827 2870 143276404 143276360 5.290000e-10 76.8
49 TraesCS6A01G358800 chr4D 97.778 45 0 1 2827 2870 275234590 275234546 5.290000e-10 76.8
50 TraesCS6A01G358800 chr1A 95.070 933 29 4 2862 3781 30575706 30576634 0.000000e+00 1452.0
51 TraesCS6A01G358800 chr1A 97.458 236 6 0 4639 4874 412535585 412535820 2.140000e-108 403.0
52 TraesCS6A01G358800 chr1A 97.021 235 7 0 4639 4873 531836843 531836609 3.570000e-106 396.0
53 TraesCS6A01G358800 chr1A 97.021 235 7 0 4639 4873 560100601 560100367 3.570000e-106 396.0
54 TraesCS6A01G358800 chr1A 85.375 253 27 6 1197 1439 7151462 7151714 2.280000e-63 254.0
55 TraesCS6A01G358800 chr1B 89.157 747 68 6 1591 2337 146428112 146427379 0.000000e+00 918.0
56 TraesCS6A01G358800 chr7D 89.661 561 55 3 1 558 76198756 76199316 0.000000e+00 712.0
57 TraesCS6A01G358800 chr7A 89.464 560 56 3 1 558 57476163 57476721 0.000000e+00 704.0
58 TraesCS6A01G358800 chr7A 97.034 236 7 0 4639 4874 10812783 10813018 9.940000e-107 398.0
59 TraesCS6A01G358800 chr7A 95.408 196 5 2 2343 2538 172071443 172071634 4.790000e-80 309.0
60 TraesCS6A01G358800 chr7A 93.367 196 11 1 2343 2538 675743374 675743181 6.240000e-74 289.0
61 TraesCS6A01G358800 chr7A 85.455 275 38 2 1185 1457 498452311 498452037 8.070000e-73 285.0
62 TraesCS6A01G358800 chr7A 83.871 279 35 8 1178 1447 480452641 480452364 1.760000e-64 257.0
63 TraesCS6A01G358800 chr7A 95.349 43 2 0 2681 2723 700209522 700209480 8.850000e-08 69.4
64 TraesCS6A01G358800 chr6B 87.852 568 58 6 960 1520 693622084 693622647 0.000000e+00 656.0
65 TraesCS6A01G358800 chr6B 91.620 179 9 3 2545 2723 693622647 693622819 4.930000e-60 243.0
66 TraesCS6A01G358800 chr2D 88.309 556 48 11 1530 2075 546208747 546209295 0.000000e+00 651.0
67 TraesCS6A01G358800 chr2D 88.889 63 3 2 2125 2184 546209340 546209401 1.900000e-09 75.0
68 TraesCS6A01G358800 chr6D 96.354 384 12 1 2337 2720 223690392 223690773 9.000000e-177 630.0
69 TraesCS6A01G358800 chr5D 97.872 235 5 0 4639 4873 107305041 107304807 1.650000e-109 407.0
70 TraesCS6A01G358800 chr5D 97.778 45 0 1 2827 2870 403969356 403969312 5.290000e-10 76.8
71 TraesCS6A01G358800 chr3A 97.458 236 6 0 4639 4874 42398278 42398043 2.140000e-108 403.0
72 TraesCS6A01G358800 chr4B 84.478 393 30 17 1519 1907 267356342 267355977 4.690000e-95 359.0
73 TraesCS6A01G358800 chr4B 93.220 177 6 1 2545 2721 603004487 603004657 6.330000e-64 255.0
74 TraesCS6A01G358800 chr4B 93.333 90 6 0 2145 2234 632835110 632835021 3.090000e-27 134.0
75 TraesCS6A01G358800 chrUn 94.898 196 8 1 2343 2538 329059237 329059044 6.200000e-79 305.0
76 TraesCS6A01G358800 chrUn 100.000 54 0 0 4874 4927 74575070 74575123 3.140000e-17 100.0
77 TraesCS6A01G358800 chrUn 100.000 54 0 0 4874 4927 111864369 111864316 3.140000e-17 100.0
78 TraesCS6A01G358800 chrUn 100.000 54 0 0 4874 4927 111883595 111883542 3.140000e-17 100.0
79 TraesCS6A01G358800 chrUn 100.000 54 0 0 4874 4927 209641098 209641045 3.140000e-17 100.0
80 TraesCS6A01G358800 chrUn 100.000 54 0 0 4874 4927 337975715 337975662 3.140000e-17 100.0
81 TraesCS6A01G358800 chrUn 100.000 54 0 0 4874 4927 337978329 337978276 3.140000e-17 100.0
82 TraesCS6A01G358800 chrUn 100.000 54 0 0 4874 4927 359224682 359224735 3.140000e-17 100.0
83 TraesCS6A01G358800 chrUn 100.000 54 0 0 4874 4927 371087507 371087454 3.140000e-17 100.0


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 TraesCS6A01G358800 chr6A 588754769 588759695 4926 False 4201.500 7372 100.000000 1 4927 2 chr6A.!!$F1 4926
1 TraesCS6A01G358800 chr6A 32529653 32535004 5351 True 2332.000 4139 96.133667 1 4636 3 chr6A.!!$R3 4635
2 TraesCS6A01G358800 chr6A 32555081 32561201 6120 True 1843.000 4128 96.449750 1 4873 4 chr6A.!!$R4 4872
3 TraesCS6A01G358800 chr6A 32421280 32427409 6129 True 1838.000 4104 96.350250 1 4873 4 chr6A.!!$R2 4872
4 TraesCS6A01G358800 chr4A 592045376 592048856 3480 True 5553.000 5553 95.507000 1161 4636 1 chr4A.!!$R2 3475
5 TraesCS6A01G358800 chr4A 592073366 592073922 556 True 739.000 739 90.664000 4 558 1 chr4A.!!$R3 554
6 TraesCS6A01G358800 chr2B 691133793 691135673 1880 False 2939.000 2939 94.887000 2753 4636 1 chr2B.!!$F2 1883
7 TraesCS6A01G358800 chr2B 653016749 653017372 623 False 560.000 560 83.308000 1530 2184 1 chr2B.!!$F1 654
8 TraesCS6A01G358800 chr7B 707972806 707974151 1345 False 2198.000 2198 96.222000 3297 4636 1 chr7B.!!$F1 1339
9 TraesCS6A01G358800 chr7B 27765282 27766400 1118 True 1770.000 1770 95.361000 2756 3864 1 chr7B.!!$R1 1108
10 TraesCS6A01G358800 chr7B 605711216 605712178 962 True 1576.000 1576 96.178000 3672 4636 1 chr7B.!!$R4 964
11 TraesCS6A01G358800 chr7B 306215665 306216483 818 True 1153.000 1153 92.092000 1519 2337 1 chr7B.!!$R2 818
12 TraesCS6A01G358800 chr7B 559712538 559714278 1740 True 442.425 760 93.096750 4 2723 4 chr7B.!!$R6 2719
13 TraesCS6A01G358800 chr2A 481858495 481859456 961 True 1613.000 1613 96.894000 3672 4636 1 chr2A.!!$R1 964
14 TraesCS6A01G358800 chr2A 687049186 687049847 661 False 556.000 556 82.678000 1530 2184 1 chr2A.!!$F2 654
15 TraesCS6A01G358800 chr5A 6905443 6906408 965 True 1600.000 1600 96.498000 3672 4642 1 chr5A.!!$R1 970
16 TraesCS6A01G358800 chr5A 41526594 41527524 930 False 1487.000 1487 95.708000 2753 3672 1 chr5A.!!$F1 919
17 TraesCS6A01G358800 chr1D 463400809 463401738 929 False 1465.000 1465 95.289000 2862 3781 1 chr1D.!!$F3 919
18 TraesCS6A01G358800 chr1D 26248454 26249386 932 True 1426.000 1426 94.450000 2862 3784 1 chr1D.!!$R1 922
19 TraesCS6A01G358800 chr1D 41780599 41781160 561 False 708.000 708 89.502000 1 558 1 chr1D.!!$F2 557
20 TraesCS6A01G358800 chr1D 79842602 79843159 557 True 695.000 695 89.247000 4 558 1 chr1D.!!$R2 554
21 TraesCS6A01G358800 chr4D 275234587 275235516 929 False 1463.000 1463 95.192000 2862 3785 1 chr4D.!!$F2 923
22 TraesCS6A01G358800 chr4D 143276401 143277328 927 False 1441.000 1441 94.855000 2862 3781 1 chr4D.!!$F1 919
23 TraesCS6A01G358800 chr1A 30575706 30576634 928 False 1452.000 1452 95.070000 2862 3781 1 chr1A.!!$F2 919
24 TraesCS6A01G358800 chr1B 146427379 146428112 733 True 918.000 918 89.157000 1591 2337 1 chr1B.!!$R1 746
25 TraesCS6A01G358800 chr7D 76198756 76199316 560 False 712.000 712 89.661000 1 558 1 chr7D.!!$F1 557
26 TraesCS6A01G358800 chr7A 57476163 57476721 558 False 704.000 704 89.464000 1 558 1 chr7A.!!$F2 557
27 TraesCS6A01G358800 chr6B 693622084 693622819 735 False 449.500 656 89.736000 960 2723 2 chr6B.!!$F1 1763
28 TraesCS6A01G358800 chr2D 546208747 546209401 654 False 363.000 651 88.599000 1530 2184 2 chr2D.!!$F1 654

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
329 339 0.755698 AGACCGTCGGATACTGCCAT 60.756 55.000 20.51 0.00 0.00 4.40 F
1604 1900 0.033504 CTTCACGGTGGCACAGTACT 59.966 55.000 22.59 0.00 41.80 2.73 F
2117 2450 1.228552 GTCTTTGCTTGGGCCAGGA 60.229 57.895 21.24 6.46 37.74 3.86 F
2586 2945 0.621082 AGGGCTTAGGCAGGAACTTC 59.379 55.000 8.32 0.00 40.87 3.01 F
3379 3748 2.134789 AAGGCCCTGTTCATGTGATC 57.865 50.000 0.00 0.00 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 2003 0.911769 TGGTGGTAGAAGCATGAGGG 59.088 55.000 0.00 0.00 0.00 4.30 R
2409 2761 0.752658 CATACCAGAGATGGCCGTCA 59.247 55.000 26.70 5.25 0.00 4.35 R
3716 5014 1.008194 CTGCATGCCACACACACAC 60.008 57.895 16.68 0.00 0.00 3.82 R
3758 5058 3.242867 CCAGAGGTCTTCCAGGCATATA 58.757 50.000 0.00 0.00 35.89 0.86 R
4765 6592 2.736670 ACAGAAGGTCAAAAGCTGGT 57.263 45.000 0.00 0.00 32.35 4.00 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
294 304 1.188871 TGGTCTACGGGCATGTCACA 61.189 55.000 0.00 0.00 0.00 3.58
329 339 0.755698 AGACCGTCGGATACTGCCAT 60.756 55.000 20.51 0.00 0.00 4.40
364 374 3.077556 CCTCACCCTCTCCCCACG 61.078 72.222 0.00 0.00 0.00 4.94
530 545 4.704833 CCCCGCACACCACTCCTG 62.705 72.222 0.00 0.00 0.00 3.86
1032 1305 1.767088 CTCTCCATCTCTTCCATGGCA 59.233 52.381 6.96 0.00 40.77 4.92
1040 1313 1.211212 CTCTTCCATGGCACCAGATCA 59.789 52.381 6.96 0.00 0.00 2.92
1113 1386 4.508128 ATCCGCGCCGTTGTCGAT 62.508 61.111 0.00 0.00 39.71 3.59
1323 1610 4.856801 GGACATGCGCGACCCCAT 62.857 66.667 12.10 0.00 0.00 4.00
1362 1649 1.134189 TGAAGAGGAGATCGCCGAGTA 60.134 52.381 10.07 0.00 0.00 2.59
1555 1845 2.747822 GCAGCAGCACACGATGAGG 61.748 63.158 0.00 0.00 41.58 3.86
1604 1900 0.033504 CTTCACGGTGGCACAGTACT 59.966 55.000 22.59 0.00 41.80 2.73
1706 2003 2.436824 GCGGCTTTGACTCCCTCC 60.437 66.667 0.00 0.00 0.00 4.30
1826 2144 3.439825 TGCGATTTGCTCAGCTTGATTAA 59.560 39.130 0.00 0.00 46.63 1.40
2055 2381 4.488126 TGTTTTGATTCAAGAAGCCTCG 57.512 40.909 0.00 0.00 0.00 4.63
2111 2444 2.951642 TGAGTTTGAGTCTTTGCTTGGG 59.048 45.455 0.00 0.00 0.00 4.12
2117 2450 1.228552 GTCTTTGCTTGGGCCAGGA 60.229 57.895 21.24 6.46 37.74 3.86
2238 2590 8.963725 TGCATCTCATTCAGATTAGATTGTTTT 58.036 29.630 0.00 0.00 40.20 2.43
2409 2761 2.034879 CGCTGACCCAGTCGCAAAT 61.035 57.895 10.51 0.00 34.95 2.32
2586 2945 0.621082 AGGGCTTAGGCAGGAACTTC 59.379 55.000 8.32 0.00 40.87 3.01
2919 3278 6.607198 CAGAGTTTCAAACCATATAACCCCAT 59.393 38.462 0.00 0.00 0.00 4.00
3337 3706 6.037786 TGTCTTTCTAATGGTACTGGACTG 57.962 41.667 0.00 0.00 0.00 3.51
3379 3748 2.134789 AAGGCCCTGTTCATGTGATC 57.865 50.000 0.00 0.00 0.00 2.92
3715 5013 7.545965 GTCTGTATGTAATCTAACTTGCAGTGT 59.454 37.037 7.48 0.00 37.98 3.55
3716 5014 7.545615 TCTGTATGTAATCTAACTTGCAGTGTG 59.454 37.037 7.48 0.00 37.98 3.82
3757 5057 1.988107 AGGTGGTGATCAGGTGAACAT 59.012 47.619 0.00 0.00 0.00 2.71
3758 5058 2.376518 AGGTGGTGATCAGGTGAACATT 59.623 45.455 0.00 0.00 0.00 2.71
3818 5118 0.745486 CATGCACCTTGGCGAGATCA 60.745 55.000 2.43 0.00 36.28 2.92
3852 5152 0.946221 CGCCTGCCTCGTATCATTCC 60.946 60.000 0.00 0.00 0.00 3.01
3955 5255 5.827797 TGGTACTTCAGTCAAATCTGCTTTT 59.172 36.000 0.00 0.00 35.63 2.27
4287 5588 9.672673 ATTCTACTGCACACTATTCAGTTATTT 57.327 29.630 0.00 0.00 40.96 1.40
4405 5711 7.997107 AAGTAAAATGCAATGCACATAGATG 57.003 32.000 11.23 0.00 43.04 2.90
4429 5735 5.939883 GGACATGCATCATAGGCAATACTTA 59.060 40.000 0.00 0.00 45.60 2.24
4516 5822 3.141398 TGTGTTCTGGTCTTGCTTCATC 58.859 45.455 0.00 0.00 0.00 2.92
4672 6499 1.305046 CTACGTGGTCTGGGGAGGT 60.305 63.158 0.00 0.00 0.00 3.85
4683 6510 0.178903 TGGGGAGGTTGCTAGTGACT 60.179 55.000 0.00 0.00 0.00 3.41
4699 6526 8.564574 TGCTAGTGACTAAAACAAAACAATAGG 58.435 33.333 0.00 0.00 0.00 2.57
4724 6551 4.891277 ATTTTGGTCGTAAACGTCTACG 57.109 40.909 15.13 15.13 44.78 3.51
4873 6700 8.773645 CACAAGTTGACATATTTCTTGTAGTGA 58.226 33.333 10.54 0.00 44.11 3.41
4874 6701 8.993121 ACAAGTTGACATATTTCTTGTAGTGAG 58.007 33.333 10.54 0.00 44.11 3.51
4875 6702 8.446273 CAAGTTGACATATTTCTTGTAGTGAGG 58.554 37.037 0.00 0.00 33.27 3.86
4876 6703 7.907389 AGTTGACATATTTCTTGTAGTGAGGA 58.093 34.615 0.00 0.00 0.00 3.71
4877 6704 8.375506 AGTTGACATATTTCTTGTAGTGAGGAA 58.624 33.333 0.00 0.00 0.00 3.36
4878 6705 9.167311 GTTGACATATTTCTTGTAGTGAGGAAT 57.833 33.333 0.00 0.00 0.00 3.01
4881 6708 9.482627 GACATATTTCTTGTAGTGAGGAATAGG 57.517 37.037 0.00 0.00 34.26 2.57
4882 6709 8.993424 ACATATTTCTTGTAGTGAGGAATAGGT 58.007 33.333 0.00 0.00 35.73 3.08
4886 6713 7.973048 TTCTTGTAGTGAGGAATAGGTATGT 57.027 36.000 0.00 0.00 0.00 2.29
4887 6714 7.348080 TCTTGTAGTGAGGAATAGGTATGTG 57.652 40.000 0.00 0.00 0.00 3.21
4888 6715 6.323996 TCTTGTAGTGAGGAATAGGTATGTGG 59.676 42.308 0.00 0.00 0.00 4.17
4889 6716 5.525484 TGTAGTGAGGAATAGGTATGTGGT 58.475 41.667 0.00 0.00 0.00 4.16
4890 6717 6.675565 TGTAGTGAGGAATAGGTATGTGGTA 58.324 40.000 0.00 0.00 0.00 3.25
4891 6718 6.548622 TGTAGTGAGGAATAGGTATGTGGTAC 59.451 42.308 0.00 0.00 0.00 3.34
4892 6719 4.583489 AGTGAGGAATAGGTATGTGGTACG 59.417 45.833 0.00 0.00 33.94 3.67
4893 6720 3.893200 TGAGGAATAGGTATGTGGTACGG 59.107 47.826 0.00 0.00 33.94 4.02
4894 6721 3.893813 GAGGAATAGGTATGTGGTACGGT 59.106 47.826 0.00 0.00 33.94 4.83
4895 6722 5.065613 AGGAATAGGTATGTGGTACGGTA 57.934 43.478 0.00 0.00 33.94 4.02
4896 6723 5.457686 AGGAATAGGTATGTGGTACGGTAA 58.542 41.667 0.00 0.00 33.94 2.85
4897 6724 5.537674 AGGAATAGGTATGTGGTACGGTAAG 59.462 44.000 0.00 0.00 33.94 2.34
4898 6725 5.302823 GGAATAGGTATGTGGTACGGTAAGT 59.697 44.000 0.00 0.00 33.94 2.24
4899 6726 6.490040 GGAATAGGTATGTGGTACGGTAAGTA 59.510 42.308 0.00 0.00 33.94 2.24
4900 6727 7.014230 GGAATAGGTATGTGGTACGGTAAGTAA 59.986 40.741 0.00 0.00 37.02 2.24
4901 6728 7.896383 ATAGGTATGTGGTACGGTAAGTAAA 57.104 36.000 0.00 0.00 37.02 2.01
4902 6729 5.965922 AGGTATGTGGTACGGTAAGTAAAC 58.034 41.667 0.00 0.00 37.02 2.01
4903 6730 5.105351 AGGTATGTGGTACGGTAAGTAAACC 60.105 44.000 0.00 0.00 37.02 3.27
4914 6741 5.348418 GGTAAGTAAACCGACTCCAAAAC 57.652 43.478 0.00 0.00 0.00 2.43
4915 6742 4.815846 GGTAAGTAAACCGACTCCAAAACA 59.184 41.667 0.00 0.00 0.00 2.83
4916 6743 5.049886 GGTAAGTAAACCGACTCCAAAACAG 60.050 44.000 0.00 0.00 0.00 3.16
4917 6744 4.146745 AGTAAACCGACTCCAAAACAGT 57.853 40.909 0.00 0.00 0.00 3.55
4918 6745 4.520179 AGTAAACCGACTCCAAAACAGTT 58.480 39.130 0.00 0.00 0.00 3.16
4919 6746 4.945543 AGTAAACCGACTCCAAAACAGTTT 59.054 37.500 0.00 0.00 0.00 2.66
4920 6747 4.794278 AAACCGACTCCAAAACAGTTTT 57.206 36.364 5.37 5.37 0.00 2.43
4921 6748 4.794278 AACCGACTCCAAAACAGTTTTT 57.206 36.364 8.65 0.00 35.15 1.94
4922 6749 5.900865 AACCGACTCCAAAACAGTTTTTA 57.099 34.783 8.65 0.00 32.90 1.52
4923 6750 5.900865 ACCGACTCCAAAACAGTTTTTAA 57.099 34.783 8.65 0.00 32.90 1.52
4924 6751 5.886992 ACCGACTCCAAAACAGTTTTTAAG 58.113 37.500 8.65 11.09 32.90 1.85
4925 6752 5.163591 ACCGACTCCAAAACAGTTTTTAAGG 60.164 40.000 8.65 7.77 32.90 2.69
4926 6753 4.738252 CGACTCCAAAACAGTTTTTAAGGC 59.262 41.667 8.65 10.07 32.90 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
294 304 2.223829 CGGTCTCTAATGCTTGATCCGT 60.224 50.000 0.00 0.00 0.00 4.69
329 339 2.672295 GGTGTGGGCCGTTGGATA 59.328 61.111 0.00 0.00 0.00 2.59
391 401 5.185442 TCATTAACGACATGTGGTGTAGGTA 59.815 40.000 14.66 0.00 42.36 3.08
530 545 2.203351 GGATTCGGGTCATGGGCC 60.203 66.667 0.00 0.00 0.00 5.80
1032 1305 0.036010 CCTCGTTGGCTTGATCTGGT 60.036 55.000 0.00 0.00 0.00 4.00
1040 1313 1.371558 GGACTGACCTCGTTGGCTT 59.628 57.895 0.00 0.00 40.22 4.35
1066 1339 2.360350 CTGTGGCCGTGGCAGATT 60.360 61.111 13.76 0.00 44.11 2.40
1113 1386 3.849951 GGAGGGCGCGGATCAAGA 61.850 66.667 8.83 0.00 0.00 3.02
1535 1825 1.296755 CTCATCGTGTGCTGCTGCTT 61.297 55.000 17.00 0.00 40.48 3.91
1706 2003 0.911769 TGGTGGTAGAAGCATGAGGG 59.088 55.000 0.00 0.00 0.00 4.30
1826 2144 1.343478 ACCTGAATCTCTCGACCCCAT 60.343 52.381 0.00 0.00 0.00 4.00
1871 2190 6.418057 AATGACTGGGAGCAATTAACAAAA 57.582 33.333 0.00 0.00 0.00 2.44
2055 2381 5.730568 GCCATCTAATCAAATCGAACCACAC 60.731 44.000 0.00 0.00 0.00 3.82
2238 2590 9.823647 TTGCACAGAACATTTAATAAAGGAAAA 57.176 25.926 4.32 0.00 0.00 2.29
2281 2633 4.846779 TGCGATAGATGTATGTACAGCA 57.153 40.909 10.61 3.44 44.49 4.41
2394 2746 0.948623 CGTCATTTGCGACTGGGTCA 60.949 55.000 0.00 0.00 33.54 4.02
2409 2761 0.752658 CATACCAGAGATGGCCGTCA 59.247 55.000 26.70 5.25 0.00 4.35
2782 3141 0.790207 CAGCATTCACACTACGCGTT 59.210 50.000 20.78 0.00 0.00 4.84
3189 3556 2.171659 TGTGGCTTCACACTAACTTGGA 59.828 45.455 0.00 0.00 45.47 3.53
3337 3706 4.708726 ATGCACATTTTTCTCTACCAGC 57.291 40.909 0.00 0.00 0.00 4.85
3379 3748 3.726291 AACTTGTGGGAAATTTGGTCG 57.274 42.857 0.00 0.00 0.00 4.79
3715 5013 1.726533 CTGCATGCCACACACACACA 61.727 55.000 16.68 0.00 0.00 3.72
3716 5014 1.008194 CTGCATGCCACACACACAC 60.008 57.895 16.68 0.00 0.00 3.82
3757 5057 3.648067 CCAGAGGTCTTCCAGGCATATAA 59.352 47.826 0.00 0.00 35.89 0.98
3758 5058 3.242867 CCAGAGGTCTTCCAGGCATATA 58.757 50.000 0.00 0.00 35.89 0.86
3852 5152 5.525378 GCCACACTAGAATGTTATCCAGAAG 59.475 44.000 0.00 0.00 0.00 2.85
3955 5255 4.523083 AGGTGCACAGTTGTTTAGAAAGA 58.477 39.130 20.43 0.00 0.00 2.52
4069 5369 6.660521 TGCCTGAATATTCATCAACTCTTGTT 59.339 34.615 18.26 0.00 36.46 2.83
4111 5411 6.479884 ACTTCTGCAGTTCTAGAATTTCCAT 58.520 36.000 14.67 0.00 32.92 3.41
4405 5711 4.330250 AGTATTGCCTATGATGCATGTCC 58.670 43.478 2.46 0.00 38.76 4.02
4672 6499 9.944663 CTATTGTTTTGTTTTAGTCACTAGCAA 57.055 29.630 0.00 0.00 0.00 3.91
4699 6526 5.212589 AGACGTTTACGACCAAAATATGC 57.787 39.130 9.53 0.00 43.02 3.14
4765 6592 2.736670 ACAGAAGGTCAAAAGCTGGT 57.263 45.000 0.00 0.00 32.35 4.00
4800 6627 6.285790 GGTCATTGTTTTTCATTTGTGACC 57.714 37.500 5.57 5.57 45.01 4.02
4873 6700 3.919834 ACCGTACCACATACCTATTCCT 58.080 45.455 0.00 0.00 0.00 3.36
4874 6701 5.302823 ACTTACCGTACCACATACCTATTCC 59.697 44.000 0.00 0.00 0.00 3.01
4875 6702 6.396829 ACTTACCGTACCACATACCTATTC 57.603 41.667 0.00 0.00 0.00 1.75
4876 6703 7.896383 TTACTTACCGTACCACATACCTATT 57.104 36.000 0.00 0.00 0.00 1.73
4877 6704 7.201911 GGTTTACTTACCGTACCACATACCTAT 60.202 40.741 0.00 0.00 0.00 2.57
4878 6705 6.096282 GGTTTACTTACCGTACCACATACCTA 59.904 42.308 0.00 0.00 0.00 3.08
4879 6706 5.105351 GGTTTACTTACCGTACCACATACCT 60.105 44.000 0.00 0.00 0.00 3.08
4880 6707 5.109210 GGTTTACTTACCGTACCACATACC 58.891 45.833 0.00 0.00 0.00 2.73
4892 6719 4.815846 TGTTTTGGAGTCGGTTTACTTACC 59.184 41.667 0.00 0.00 34.72 2.85
4893 6720 5.525012 ACTGTTTTGGAGTCGGTTTACTTAC 59.475 40.000 0.00 0.00 0.00 2.34
4894 6721 5.673514 ACTGTTTTGGAGTCGGTTTACTTA 58.326 37.500 0.00 0.00 0.00 2.24
4895 6722 4.520179 ACTGTTTTGGAGTCGGTTTACTT 58.480 39.130 0.00 0.00 0.00 2.24
4896 6723 4.146745 ACTGTTTTGGAGTCGGTTTACT 57.853 40.909 0.00 0.00 0.00 2.24
4897 6724 4.888038 AACTGTTTTGGAGTCGGTTTAC 57.112 40.909 0.00 0.00 0.00 2.01
4898 6725 5.900865 AAAACTGTTTTGGAGTCGGTTTA 57.099 34.783 17.06 0.00 38.96 2.01
4899 6726 4.794278 AAAACTGTTTTGGAGTCGGTTT 57.206 36.364 17.06 0.00 40.77 3.27
4900 6727 4.794278 AAAAACTGTTTTGGAGTCGGTT 57.206 36.364 18.33 0.00 35.58 4.44
4901 6728 5.163591 CCTTAAAAACTGTTTTGGAGTCGGT 60.164 40.000 18.33 3.92 37.51 4.69
4902 6729 5.278604 CCTTAAAAACTGTTTTGGAGTCGG 58.721 41.667 18.33 9.89 37.51 4.79
4903 6730 4.738252 GCCTTAAAAACTGTTTTGGAGTCG 59.262 41.667 18.33 9.06 37.51 4.18


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

AutoCloner maintained by Alex Coulton.