Multiple sequence alignment - TraesCS6D01G106900

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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 TraesCS6D01G106900 chr6D 100.000 3119 0 0 1 3119 69942297 69945415 0.000000e+00 5760.0
1 TraesCS6D01G106900 chr6D 100.000 2911 0 0 3419 6329 69945715 69948625 0.000000e+00 5376.0
2 TraesCS6D01G106900 chr6D 82.819 1880 219 46 3512 5329 48856869 48858706 0.000000e+00 1587.0
3 TraesCS6D01G106900 chr6D 82.727 1291 135 45 1864 3119 48855573 48856810 0.000000e+00 1068.0
4 TraesCS6D01G106900 chr6D 87.500 880 100 8 996 1866 48854435 48855313 0.000000e+00 1007.0
5 TraesCS6D01G106900 chr6D 83.649 740 91 22 4624 5345 63730172 63730899 0.000000e+00 669.0
6 TraesCS6D01G106900 chr6D 88.070 570 46 8 3715 4279 63729178 63729730 0.000000e+00 656.0
7 TraesCS6D01G106900 chr6D 88.252 349 24 9 4278 4625 63729794 63730126 9.880000e-108 401.0
8 TraesCS6D01G106900 chr6D 82.243 321 40 14 5649 5953 63730983 63731302 1.750000e-65 261.0
9 TraesCS6D01G106900 chr6D 89.610 77 8 0 3038 3114 48856639 48856715 1.450000e-16 99.0
10 TraesCS6D01G106900 chr6D 87.013 77 10 0 3038 3114 69945250 69945326 3.140000e-13 87.9
11 TraesCS6D01G106900 chr6D 87.013 77 10 0 2954 3030 69945334 69945410 3.140000e-13 87.9
12 TraesCS6D01G106900 chr6D 87.013 77 8 2 6254 6329 91038404 91038479 1.130000e-12 86.1
13 TraesCS6D01G106900 chr6D 80.000 120 18 5 6213 6328 80797544 80797427 4.070000e-12 84.2
14 TraesCS6D01G106900 chr6D 85.366 82 6 1 2954 3029 48856723 48856804 5.260000e-11 80.5
15 TraesCS6D01G106900 chr6A 96.126 3123 65 14 1 3110 87755705 87758784 0.000000e+00 5046.0
16 TraesCS6D01G106900 chr6A 96.019 2361 68 11 3451 5794 87759203 87761554 0.000000e+00 3816.0
17 TraesCS6D01G106900 chr6A 82.941 1870 219 49 3512 5329 65803828 65802007 0.000000e+00 1594.0
18 TraesCS6D01G106900 chr6A 82.676 1293 131 46 1864 3119 65805122 65803886 0.000000e+00 1061.0
19 TraesCS6D01G106900 chr6A 89.392 641 65 3 1228 1866 65806022 65805383 0.000000e+00 804.0
20 TraesCS6D01G106900 chr6A 89.431 492 36 14 5848 6329 87761546 87762031 1.950000e-169 606.0
21 TraesCS6D01G106900 chr6A 87.441 422 46 6 4473 4891 80879309 80879726 4.440000e-131 479.0
22 TraesCS6D01G106900 chr6A 84.416 385 48 10 4970 5345 80879761 80880142 1.000000e-97 368.0
23 TraesCS6D01G106900 chr6A 83.799 358 40 10 2478 2824 22034991 22034641 2.200000e-84 324.0
24 TraesCS6D01G106900 chr6A 83.799 358 40 11 2478 2824 77508399 77508749 2.200000e-84 324.0
25 TraesCS6D01G106900 chr6A 84.252 254 27 7 3733 3979 80879067 80879314 1.060000e-57 235.0
26 TraesCS6D01G106900 chr6A 84.167 240 22 6 1638 1876 22035787 22035563 1.070000e-52 219.0
27 TraesCS6D01G106900 chr6A 83.983 231 21 2 1638 1867 77507344 77507559 2.310000e-49 207.0
28 TraesCS6D01G106900 chr6A 78.378 222 43 3 5351 5568 16232636 16232416 8.560000e-29 139.0
29 TraesCS6D01G106900 chr6A 88.750 80 9 0 3038 3117 65804058 65803979 1.450000e-16 99.0
30 TraesCS6D01G106900 chr6A 87.013 77 10 0 3038 3114 87758628 87758704 3.140000e-13 87.9
31 TraesCS6D01G106900 chr6B 97.444 2700 56 4 421 3116 144960936 144963626 0.000000e+00 4591.0
32 TraesCS6D01G106900 chr6B 95.775 2296 62 11 3425 5718 144963910 144966172 0.000000e+00 3670.0
33 TraesCS6D01G106900 chr6B 88.056 1348 105 30 3715 5044 137383681 137384990 0.000000e+00 1546.0
34 TraesCS6D01G106900 chr6B 82.149 1871 223 52 3512 5329 122296460 122294648 0.000000e+00 1502.0
35 TraesCS6D01G106900 chr6B 82.123 1281 146 58 1864 3119 122297741 122296519 0.000000e+00 1020.0
36 TraesCS6D01G106900 chr6B 89.168 637 69 0 1231 1867 122298655 122298019 0.000000e+00 795.0
37 TraesCS6D01G106900 chr6B 92.562 484 31 3 5716 6196 144966302 144966783 0.000000e+00 689.0
38 TraesCS6D01G106900 chr6B 86.093 151 18 2 5564 5713 137385066 137385214 6.570000e-35 159.0
39 TraesCS6D01G106900 chr6B 96.296 81 1 1 1 81 144960863 144960941 1.430000e-26 132.0
40 TraesCS6D01G106900 chr6B 86.585 82 5 1 2954 3029 122296606 122296525 1.130000e-12 86.1
41 TraesCS6D01G106900 chr6B 85.714 77 11 0 3038 3114 144963472 144963548 1.460000e-11 82.4
42 TraesCS6D01G106900 chr2D 88.631 431 31 12 3419 3836 543110061 543110486 5.660000e-140 508.0
43 TraesCS6D01G106900 chr2D 80.000 395 46 17 1477 1867 543109380 543109745 1.750000e-65 261.0
44 TraesCS6D01G106900 chr2D 83.929 168 22 1 309 471 645528839 645529006 8.500000e-34 156.0
45 TraesCS6D01G106900 chr2D 80.319 188 31 4 5352 5534 200366954 200366768 3.080000e-28 137.0
46 TraesCS6D01G106900 chr2D 94.444 36 2 0 6293 6328 492718534 492718569 8.860000e-04 56.5
47 TraesCS6D01G106900 chr5D 88.859 377 35 4 3420 3795 23824563 23824933 2.080000e-124 457.0
48 TraesCS6D01G106900 chr5D 84.507 213 21 8 5358 5566 232411949 232411745 3.870000e-47 200.0
49 TraesCS6D01G106900 chr5D 78.125 224 41 6 5350 5567 451133147 451132926 1.110000e-27 135.0
50 TraesCS6D01G106900 chr5D 87.069 116 12 3 6213 6326 117765369 117765255 1.850000e-25 128.0
51 TraesCS6D01G106900 chr5D 90.000 60 6 0 4 63 437354701 437354642 1.890000e-10 78.7
52 TraesCS6D01G106900 chr3A 88.095 378 38 4 3419 3795 723439594 723439223 5.820000e-120 442.0
53 TraesCS6D01G106900 chr3A 83.898 354 40 10 2481 2824 20205112 20205458 7.920000e-84 322.0
54 TraesCS6D01G106900 chr3A 84.848 231 19 6 1638 1867 20204312 20204527 1.070000e-52 219.0
55 TraesCS6D01G106900 chr3A 77.578 223 44 4 5352 5569 51968801 51968580 5.150000e-26 130.0
56 TraesCS6D01G106900 chr1A 87.812 361 32 7 3577 3926 513428541 513428182 4.570000e-111 412.0
57 TraesCS6D01G106900 chr1A 81.560 423 43 22 1449 1867 513429364 513428973 3.680000e-82 316.0
58 TraesCS6D01G106900 chr1A 90.511 137 11 2 3419 3555 513428668 513428534 5.040000e-41 180.0
59 TraesCS6D01G106900 chr5A 83.402 241 22 4 1638 1876 456472692 456472468 2.310000e-49 207.0
60 TraesCS6D01G106900 chr5A 89.062 64 7 0 5 68 552549513 552549450 5.260000e-11 80.5
61 TraesCS6D01G106900 chr5A 83.333 78 7 5 6255 6328 216973230 216973305 4.090000e-07 67.6
62 TraesCS6D01G106900 chr1D 79.452 219 40 3 5352 5566 182614472 182614689 3.950000e-32 150.0
63 TraesCS6D01G106900 chr4B 78.222 225 44 3 5350 5570 634730535 634730312 8.560000e-29 139.0
64 TraesCS6D01G106900 chr7A 82.759 116 18 2 6213 6326 582383381 582383496 1.120000e-17 102.0
65 TraesCS6D01G106900 chr7A 88.889 72 7 1 5476 5546 546431669 546431598 3.140000e-13 87.9
66 TraesCS6D01G106900 chr7A 76.866 134 29 2 6197 6328 197975492 197975625 2.450000e-09 75.0
67 TraesCS6D01G106900 chr3D 83.036 112 17 2 6217 6326 108206763 108206652 4.040000e-17 100.0
68 TraesCS6D01G106900 chr5B 91.525 59 5 0 908 966 655298049 655298107 1.460000e-11 82.4
69 TraesCS6D01G106900 chr5B 79.167 120 21 4 6213 6329 503281797 503281679 5.260000e-11 80.5


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 TraesCS6D01G106900 chr6D 69942297 69948625 6328 False 2827.950000 5760 93.506500 1 6329 4 chr6D.!!$F4 6328
1 TraesCS6D01G106900 chr6D 48854435 48858706 4271 False 768.300000 1587 85.604400 996 5329 5 chr6D.!!$F2 4333
2 TraesCS6D01G106900 chr6D 63729178 63731302 2124 False 496.750000 669 85.553500 3715 5953 4 chr6D.!!$F3 2238
3 TraesCS6D01G106900 chr6A 87755705 87762031 6326 False 2388.975000 5046 92.147250 1 6329 4 chr6A.!!$F3 6328
4 TraesCS6D01G106900 chr6A 65802007 65806022 4015 True 889.500000 1594 85.939750 1228 5329 4 chr6A.!!$R3 4101
5 TraesCS6D01G106900 chr6A 80879067 80880142 1075 False 360.666667 479 85.369667 3733 5345 3 chr6A.!!$F2 1612
6 TraesCS6D01G106900 chr6A 22034641 22035787 1146 True 271.500000 324 83.983000 1638 2824 2 chr6A.!!$R2 1186
7 TraesCS6D01G106900 chr6A 77507344 77508749 1405 False 265.500000 324 83.891000 1638 2824 2 chr6A.!!$F1 1186
8 TraesCS6D01G106900 chr6B 144960863 144966783 5920 False 1832.880000 4591 93.558200 1 6196 5 chr6B.!!$F2 6195
9 TraesCS6D01G106900 chr6B 137383681 137385214 1533 False 852.500000 1546 87.074500 3715 5713 2 chr6B.!!$F1 1998
10 TraesCS6D01G106900 chr6B 122294648 122298655 4007 True 850.775000 1502 85.006250 1231 5329 4 chr6B.!!$R1 4098
11 TraesCS6D01G106900 chr2D 543109380 543110486 1106 False 384.500000 508 84.315500 1477 3836 2 chr2D.!!$F3 2359
12 TraesCS6D01G106900 chr3A 20204312 20205458 1146 False 270.500000 322 84.373000 1638 2824 2 chr3A.!!$F1 1186
13 TraesCS6D01G106900 chr1A 513428182 513429364 1182 True 302.666667 412 86.627667 1449 3926 3 chr1A.!!$R1 2477

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
175 176 0.313672 TCACCGTTGCTGCCAATTTC 59.686 50.000 0.00 0.0 32.75 2.17 F
687 689 0.686769 GCCGGTTAAGGAGAGGGAGA 60.687 60.000 1.90 0.0 0.00 3.71 F
2198 2771 1.133915 TGCCAATAAACCCGGATCTCC 60.134 52.381 0.73 0.0 0.00 3.71 F
2707 3308 6.183359 GCTCGCTGCATAATGTTATAATTTGC 60.183 38.462 0.00 0.0 42.31 3.68 F
4403 5187 0.321996 AGCGTCTCAAGGGGAAAGTC 59.678 55.000 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1153 1158 0.322546 GGGGCATCAACGAAGGAGTT 60.323 55.000 0.00 0.00 34.15 3.01 R
2389 2970 1.112113 GAGCGGGAGATGTGTTAGGA 58.888 55.000 0.00 0.00 0.00 2.94 R
3073 3678 1.822990 AGCAAGTCAATCAGGCCATTG 59.177 47.619 5.01 7.57 35.39 2.82 R
4635 5510 1.090728 TGTTTCTGCACAAACAGCGA 58.909 45.000 15.25 0.00 40.57 4.93 R
5749 6808 0.232303 GACAAGTCACAACCGAAGCG 59.768 55.000 0.00 0.00 0.00 4.68 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
150 151 1.149782 AGACAGGAGGGACCAGAGGA 61.150 60.000 0.00 0.00 42.04 3.71
151 152 0.686112 GACAGGAGGGACCAGAGGAG 60.686 65.000 0.00 0.00 42.04 3.69
167 168 2.943345 GAGTGCGTCACCGTTGCTG 61.943 63.158 6.39 0.00 34.49 4.41
175 176 0.313672 TCACCGTTGCTGCCAATTTC 59.686 50.000 0.00 0.00 32.75 2.17
414 415 4.762289 ACTGAGTTCCTCTGACTTTTGT 57.238 40.909 5.31 0.00 34.33 2.83
587 588 2.957680 TCAAACTTTGGCATTCTCAGCA 59.042 40.909 1.62 0.00 0.00 4.41
619 620 1.774254 TGATCTTCACCACCCAACTGT 59.226 47.619 0.00 0.00 0.00 3.55
687 689 0.686769 GCCGGTTAAGGAGAGGGAGA 60.687 60.000 1.90 0.00 0.00 3.71
779 784 1.267261 CTTCGACTCCGGCATAGGTAG 59.733 57.143 0.00 0.00 36.24 3.18
806 811 1.461127 CGGTTTCTCTCCTTTGCTTCG 59.539 52.381 0.00 0.00 0.00 3.79
882 887 2.127271 TGGGTTGTGCTGATGGTATG 57.873 50.000 0.00 0.00 0.00 2.39
936 941 7.771826 CCGTTTTAGTGGATTTATCCCTTAAGA 59.228 37.037 3.36 0.00 46.59 2.10
1153 1158 2.994995 TCCTCGCCCGCTTCTTCA 60.995 61.111 0.00 0.00 0.00 3.02
1164 1169 2.135933 CGCTTCTTCAACTCCTTCGTT 58.864 47.619 0.00 0.00 0.00 3.85
1287 1308 1.144936 GCTGCTAGGGTTCAGCGAT 59.855 57.895 4.60 0.00 44.94 4.58
1318 1339 3.469863 GACAACCCGGAGCACCACA 62.470 63.158 0.73 0.00 35.59 4.17
1319 1340 2.034066 CAACCCGGAGCACCACAT 59.966 61.111 0.73 0.00 35.59 3.21
1972 2543 1.489649 ACTGAGAGCCAAGCATGCTAT 59.510 47.619 23.00 8.64 39.69 2.97
2198 2771 1.133915 TGCCAATAAACCCGGATCTCC 60.134 52.381 0.73 0.00 0.00 3.71
2707 3308 6.183359 GCTCGCTGCATAATGTTATAATTTGC 60.183 38.462 0.00 0.00 42.31 3.68
3083 3688 3.418047 CATATCTGCATCAATGGCCTGA 58.582 45.455 3.32 0.00 0.00 3.86
3099 3710 4.082081 TGGCCTGATTGACTTGCTAAATTG 60.082 41.667 3.32 0.00 0.00 2.32
4062 4778 6.476378 ACATGAACAGGTAAGAACAGCTAAT 58.524 36.000 0.00 0.00 0.00 1.73
4254 4970 3.037549 TGTTGATTGGCAAGGAAAAGGT 58.962 40.909 5.96 0.00 37.12 3.50
4403 5187 0.321996 AGCGTCTCAAGGGGAAAGTC 59.678 55.000 0.00 0.00 0.00 3.01
4577 5377 8.280909 TGCTTGTTCGAACTTAAAATCATTTC 57.719 30.769 27.32 0.00 0.00 2.17
4635 5510 6.833416 TGTGAGGCCTTATTAGCATTTATTGT 59.167 34.615 6.77 0.00 0.00 2.71
4655 5531 1.470494 TCGCTGTTTGTGCAGAAACAA 59.530 42.857 33.44 21.40 43.48 2.83
4758 5642 9.241317 CCTGAAAATAACTGACATATTGCATTC 57.759 33.333 0.00 0.00 0.00 2.67
4933 5828 8.604640 TCAATAAAGCATGCATCTTTTCAAAA 57.395 26.923 21.98 9.77 35.58 2.44
5053 5952 2.678336 GGTTAGATCACCGAGCTTTTGG 59.322 50.000 0.00 0.00 28.73 3.28
5134 6042 7.081349 CAGACTGAATATAGTCCAAGTCGATC 58.919 42.308 12.36 0.00 46.48 3.69
5152 6061 4.401202 TCGATCTGTACCTGCTTCACAATA 59.599 41.667 0.00 0.00 0.00 1.90
5249 6158 3.473647 CGCCTCTGCCCCTGATCA 61.474 66.667 0.00 0.00 0.00 2.92
5360 6285 0.035343 GCCAACCCAGTACTCCCTTC 60.035 60.000 0.00 0.00 0.00 3.46
5408 6333 6.973474 CGTAGTTCTAGGGTGAATTTGACTAG 59.027 42.308 0.00 0.00 34.03 2.57
5585 6510 8.612619 GGGAGTACATATCTTTGTTTATGTGTG 58.387 37.037 0.00 0.00 38.96 3.82
5586 6511 9.162764 GGAGTACATATCTTTGTTTATGTGTGT 57.837 33.333 0.00 0.00 38.96 3.72
5610 6535 1.757118 TGATGCTGTAGTAGTGCCTCC 59.243 52.381 0.00 0.00 0.00 4.30
5749 6808 5.277925 CCACATTTTTGGCACTTCCATTTTC 60.278 40.000 0.00 0.00 46.04 2.29
5784 6843 6.418226 GTGACTTGTCATCAGATACGATTACC 59.582 42.308 6.74 0.00 0.00 2.85
5789 6848 6.873997 TGTCATCAGATACGATTACCTTGTT 58.126 36.000 0.00 0.00 0.00 2.83
5795 6854 7.383687 TCAGATACGATTACCTTGTTGTCTTT 58.616 34.615 0.00 0.00 0.00 2.52
5796 6855 8.525316 TCAGATACGATTACCTTGTTGTCTTTA 58.475 33.333 0.00 0.00 0.00 1.85
5798 6857 8.529476 AGATACGATTACCTTGTTGTCTTTACT 58.471 33.333 0.00 0.00 0.00 2.24
5799 6858 6.780706 ACGATTACCTTGTTGTCTTTACTG 57.219 37.500 0.00 0.00 0.00 2.74
5800 6859 6.518493 ACGATTACCTTGTTGTCTTTACTGA 58.482 36.000 0.00 0.00 0.00 3.41
5801 6860 7.159372 ACGATTACCTTGTTGTCTTTACTGAT 58.841 34.615 0.00 0.00 0.00 2.90
5802 6861 7.117812 ACGATTACCTTGTTGTCTTTACTGATG 59.882 37.037 0.00 0.00 0.00 3.07
5803 6862 6.554334 TTACCTTGTTGTCTTTACTGATGC 57.446 37.500 0.00 0.00 0.00 3.91
5804 6863 4.460263 ACCTTGTTGTCTTTACTGATGCA 58.540 39.130 0.00 0.00 0.00 3.96
5805 6864 4.887071 ACCTTGTTGTCTTTACTGATGCAA 59.113 37.500 0.00 0.00 0.00 4.08
5806 6865 5.536161 ACCTTGTTGTCTTTACTGATGCAAT 59.464 36.000 0.00 0.00 0.00 3.56
5807 6866 5.860182 CCTTGTTGTCTTTACTGATGCAATG 59.140 40.000 0.00 0.00 0.00 2.82
5808 6867 5.375417 TGTTGTCTTTACTGATGCAATGG 57.625 39.130 0.00 0.00 0.00 3.16
5809 6868 4.218200 TGTTGTCTTTACTGATGCAATGGG 59.782 41.667 0.00 0.00 0.00 4.00
5810 6869 4.299586 TGTCTTTACTGATGCAATGGGA 57.700 40.909 0.00 0.00 0.00 4.37
5811 6870 4.661222 TGTCTTTACTGATGCAATGGGAA 58.339 39.130 0.00 0.00 0.00 3.97
5812 6871 4.458989 TGTCTTTACTGATGCAATGGGAAC 59.541 41.667 0.00 0.00 0.00 3.62
5825 6884 2.363297 GGGAACCGGACACTCTTCT 58.637 57.895 9.46 0.00 40.86 2.85
5826 6885 0.685660 GGGAACCGGACACTCTTCTT 59.314 55.000 9.46 0.00 40.86 2.52
5827 6886 1.071857 GGGAACCGGACACTCTTCTTT 59.928 52.381 9.46 0.00 40.86 2.52
5828 6887 2.414806 GGAACCGGACACTCTTCTTTC 58.585 52.381 9.46 0.00 0.00 2.62
5829 6888 2.059541 GAACCGGACACTCTTCTTTCG 58.940 52.381 9.46 0.00 0.00 3.46
5830 6889 1.038280 ACCGGACACTCTTCTTTCGT 58.962 50.000 9.46 0.00 0.00 3.85
5831 6890 1.411612 ACCGGACACTCTTCTTTCGTT 59.588 47.619 9.46 0.00 0.00 3.85
5832 6891 1.792949 CCGGACACTCTTCTTTCGTTG 59.207 52.381 0.00 0.00 0.00 4.10
5833 6892 2.545113 CCGGACACTCTTCTTTCGTTGA 60.545 50.000 0.00 0.00 0.00 3.18
5834 6893 2.726760 CGGACACTCTTCTTTCGTTGAG 59.273 50.000 0.00 0.00 0.00 3.02
5835 6894 2.476997 GGACACTCTTCTTTCGTTGAGC 59.523 50.000 0.00 0.00 0.00 4.26
5836 6895 3.123804 GACACTCTTCTTTCGTTGAGCA 58.876 45.455 0.00 0.00 0.00 4.26
5837 6896 3.531538 ACACTCTTCTTTCGTTGAGCAA 58.468 40.909 0.00 0.00 0.00 3.91
5838 6897 3.938963 ACACTCTTCTTTCGTTGAGCAAA 59.061 39.130 0.00 0.00 0.00 3.68
5839 6898 4.034510 ACACTCTTCTTTCGTTGAGCAAAG 59.965 41.667 0.00 0.00 0.00 2.77
5840 6899 4.034510 CACTCTTCTTTCGTTGAGCAAAGT 59.965 41.667 0.00 0.00 32.37 2.66
5841 6900 4.034510 ACTCTTCTTTCGTTGAGCAAAGTG 59.965 41.667 0.00 0.00 32.37 3.16
5842 6901 4.188462 TCTTCTTTCGTTGAGCAAAGTGA 58.812 39.130 0.00 0.00 32.37 3.41
5843 6902 4.634004 TCTTCTTTCGTTGAGCAAAGTGAA 59.366 37.500 0.00 0.00 32.37 3.18
5844 6903 4.536364 TCTTTCGTTGAGCAAAGTGAAG 57.464 40.909 0.00 0.00 32.37 3.02
5845 6904 3.312421 TCTTTCGTTGAGCAAAGTGAAGG 59.688 43.478 0.00 0.00 32.37 3.46
5846 6905 2.613026 TCGTTGAGCAAAGTGAAGGA 57.387 45.000 0.00 0.00 0.00 3.36
5970 7091 2.755103 CAGATAGGTTGGGCCTCAAAAC 59.245 50.000 4.53 0.00 46.96 2.43
6008 7129 6.728200 TGAAACAAACATCATCTGACACTTC 58.272 36.000 0.00 0.00 0.00 3.01
6135 7261 4.026744 TCCCAAACCAGTTTCAAACATCA 58.973 39.130 2.41 0.00 0.00 3.07
6147 7273 1.608590 CAAACATCAGGGCGAACAACT 59.391 47.619 0.00 0.00 0.00 3.16
6171 7297 5.068460 TCGGTCACATTGGTCAGAAAAATTT 59.932 36.000 0.00 0.00 0.00 1.82
6211 7343 3.948719 GGACGTCCAGGTTGGCCA 61.949 66.667 29.75 0.00 37.47 5.36
6215 7347 2.985847 GTCCAGGTTGGCCAGCAC 60.986 66.667 22.07 10.67 37.47 4.40
6248 7381 2.378038 CCCAAATGTAGGGTGGACATG 58.622 52.381 0.00 0.00 41.61 3.21
6258 7391 2.124612 TGGACATGCTGATGCCCG 60.125 61.111 0.00 0.00 34.87 6.13
6281 7414 2.181021 GTCCGCCACGTCGAATCT 59.819 61.111 0.00 0.00 0.00 2.40
6315 7448 2.425539 CCCACAAATTGCACCAAATCC 58.574 47.619 0.00 0.00 0.00 3.01
6321 7454 3.853355 AATTGCACCAAATCCACCAAA 57.147 38.095 0.00 0.00 0.00 3.28
6325 7458 1.715785 CACCAAATCCACCAAACCCT 58.284 50.000 0.00 0.00 0.00 4.34
6327 7460 1.266178 CCAAATCCACCAAACCCTCC 58.734 55.000 0.00 0.00 0.00 4.30
6328 7461 1.266178 CAAATCCACCAAACCCTCCC 58.734 55.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 5.697473 TGTTGTTTGAAGTGTCAACAAGA 57.303 34.783 7.04 0.00 43.52 3.02
167 168 0.317020 GCTACGGATGCGAAATTGGC 60.317 55.000 15.49 0.00 0.00 4.52
175 176 1.065701 ACTGAAGTAGCTACGGATGCG 59.934 52.381 17.99 4.58 35.28 4.73
315 316 5.468409 TCGCTGTTTTGATGTGAGATTTACA 59.532 36.000 0.00 0.00 0.00 2.41
424 425 5.991933 AGAGAGAGAAGACATGCAACTTA 57.008 39.130 0.00 0.00 0.00 2.24
587 588 3.007398 GGTGAAGATCAAGGTGTGAGTCT 59.993 47.826 0.00 0.00 40.43 3.24
619 620 1.005037 CACGCTTGTGCAGGACCTA 60.005 57.895 0.00 0.00 39.64 3.08
687 689 2.332654 GCCGAGCCACAAAACGGAT 61.333 57.895 0.00 0.00 46.94 4.18
779 784 1.079057 GGAGAGAAACCGAGTGGCC 60.079 63.158 0.00 0.00 39.70 5.36
806 811 0.953727 TGGCACACAAAGCATGAGAC 59.046 50.000 0.00 0.00 0.00 3.36
882 887 5.376854 AGAAGTACAAATGTTGGCATCAC 57.623 39.130 0.00 0.00 33.50 3.06
1153 1158 0.322546 GGGGCATCAACGAAGGAGTT 60.323 55.000 0.00 0.00 34.15 3.01
1164 1169 1.790635 TTTGTTACCCGGGGGCATCA 61.791 55.000 27.92 13.40 39.32 3.07
1287 1308 1.754745 GTTGTCCAGCACCTCCAGA 59.245 57.895 0.00 0.00 0.00 3.86
1972 2543 7.733773 TTTGATCAGAAACTCCTAGACCATA 57.266 36.000 0.00 0.00 0.00 2.74
2198 2771 5.951747 TCAGGTTTCAAAAAGGATCCTATGG 59.048 40.000 16.55 5.03 0.00 2.74
2389 2970 1.112113 GAGCGGGAGATGTGTTAGGA 58.888 55.000 0.00 0.00 0.00 2.94
2707 3308 3.184541 GCAGCAGGAAACATAAATGCAG 58.815 45.455 0.00 0.00 39.34 4.41
3073 3678 1.822990 AGCAAGTCAATCAGGCCATTG 59.177 47.619 5.01 7.57 35.39 2.82
3083 3688 9.729281 ATGGAAAAATCAATTTAGCAAGTCAAT 57.271 25.926 0.00 0.00 0.00 2.57
4062 4778 5.447624 CAGCTATGGAATTCAATCATGCA 57.552 39.130 7.93 0.00 0.00 3.96
4635 5510 1.090728 TGTTTCTGCACAAACAGCGA 58.909 45.000 15.25 0.00 40.57 4.93
4655 5531 6.382570 AGTCAAAGAGATGGACAGCTAGTATT 59.617 38.462 0.00 0.00 34.04 1.89
4729 5613 7.147863 TGCAATATGTCAGTTATTTTCAGGCAT 60.148 33.333 0.00 0.00 0.00 4.40
4758 5642 4.156455 AGCCTATGTGGTGACATAAAGG 57.844 45.455 0.00 0.00 43.13 3.11
5053 5952 2.688446 GCACAAGGTATTTAGAAGGCCC 59.312 50.000 0.00 0.00 0.00 5.80
5134 6042 6.810911 AGTCTATATTGTGAAGCAGGTACAG 58.189 40.000 0.00 0.00 0.00 2.74
5152 6061 4.500499 AATTCTCTGGCTGCAAGTCTAT 57.500 40.909 3.55 0.00 41.06 1.98
5249 6158 2.031919 TTGTGACGGCGGCAGATT 59.968 55.556 19.67 0.00 0.00 2.40
5360 6285 2.279517 GCCCTATGCACCGAGACG 60.280 66.667 0.00 0.00 40.77 4.18
5382 6307 5.245526 AGTCAAATTCACCCTAGAACTACGT 59.754 40.000 0.00 0.00 0.00 3.57
5508 6433 7.254353 GCGTAGTTCTAGGTCATCAATTTAACC 60.254 40.741 0.00 0.00 0.00 2.85
5551 6476 3.702792 AGATATGTACTCCCTCCATCCG 58.297 50.000 0.00 0.00 0.00 4.18
5555 6480 6.636454 AAACAAAGATATGTACTCCCTCCA 57.364 37.500 0.00 0.00 32.02 3.86
5586 6511 5.009829 AGGCACTACTACAGCATCATGCA 62.010 47.826 13.38 0.00 42.16 3.96
5610 6535 2.757686 CAGCACATGAATAGCAGCTG 57.242 50.000 10.11 10.11 42.69 4.24
5736 6794 1.606606 CGAAGCGAAAATGGAAGTGC 58.393 50.000 0.00 0.00 0.00 4.40
5749 6808 0.232303 GACAAGTCACAACCGAAGCG 59.768 55.000 0.00 0.00 0.00 4.68
5784 6843 5.860182 CCATTGCATCAGTAAAGACAACAAG 59.140 40.000 0.00 0.00 0.00 3.16
5789 6848 4.299586 TCCCATTGCATCAGTAAAGACA 57.700 40.909 0.00 0.00 0.00 3.41
5795 6854 1.408127 CCGGTTCCCATTGCATCAGTA 60.408 52.381 0.00 0.00 0.00 2.74
5796 6855 0.680921 CCGGTTCCCATTGCATCAGT 60.681 55.000 0.00 0.00 0.00 3.41
5798 6857 0.679640 GTCCGGTTCCCATTGCATCA 60.680 55.000 0.00 0.00 0.00 3.07
5799 6858 0.679640 TGTCCGGTTCCCATTGCATC 60.680 55.000 0.00 0.00 0.00 3.91
5800 6859 0.965363 GTGTCCGGTTCCCATTGCAT 60.965 55.000 0.00 0.00 0.00 3.96
5801 6860 1.602323 GTGTCCGGTTCCCATTGCA 60.602 57.895 0.00 0.00 0.00 4.08
5802 6861 1.303317 AGTGTCCGGTTCCCATTGC 60.303 57.895 0.00 0.00 0.00 3.56
5803 6862 0.324943 AGAGTGTCCGGTTCCCATTG 59.675 55.000 0.00 0.00 0.00 2.82
5804 6863 1.003233 GAAGAGTGTCCGGTTCCCATT 59.997 52.381 0.00 0.00 0.00 3.16
5805 6864 0.613777 GAAGAGTGTCCGGTTCCCAT 59.386 55.000 0.00 0.00 0.00 4.00
5806 6865 0.471211 AGAAGAGTGTCCGGTTCCCA 60.471 55.000 0.00 0.00 0.00 4.37
5807 6866 0.685660 AAGAAGAGTGTCCGGTTCCC 59.314 55.000 0.00 0.00 0.00 3.97
5808 6867 2.414806 GAAAGAAGAGTGTCCGGTTCC 58.585 52.381 0.00 0.00 0.00 3.62
5809 6868 2.059541 CGAAAGAAGAGTGTCCGGTTC 58.940 52.381 0.00 0.00 0.00 3.62
5810 6869 1.411612 ACGAAAGAAGAGTGTCCGGTT 59.588 47.619 0.00 0.00 0.00 4.44
5811 6870 1.038280 ACGAAAGAAGAGTGTCCGGT 58.962 50.000 0.00 0.00 0.00 5.28
5812 6871 1.792949 CAACGAAAGAAGAGTGTCCGG 59.207 52.381 0.00 0.00 0.00 5.14
5813 6872 2.726760 CTCAACGAAAGAAGAGTGTCCG 59.273 50.000 0.00 0.00 33.29 4.79
5814 6873 2.476997 GCTCAACGAAAGAAGAGTGTCC 59.523 50.000 0.00 0.00 37.66 4.02
5815 6874 3.123804 TGCTCAACGAAAGAAGAGTGTC 58.876 45.455 0.00 0.00 37.66 3.67
5816 6875 3.179443 TGCTCAACGAAAGAAGAGTGT 57.821 42.857 0.00 0.00 37.66 3.55
5817 6876 4.034510 ACTTTGCTCAACGAAAGAAGAGTG 59.965 41.667 0.00 0.00 37.66 3.51
5818 6877 4.034510 CACTTTGCTCAACGAAAGAAGAGT 59.965 41.667 0.00 0.00 37.66 3.24
5819 6878 4.271049 TCACTTTGCTCAACGAAAGAAGAG 59.729 41.667 0.00 0.00 38.12 2.85
5820 6879 4.188462 TCACTTTGCTCAACGAAAGAAGA 58.812 39.130 0.00 0.00 34.02 2.87
5821 6880 4.536364 TCACTTTGCTCAACGAAAGAAG 57.464 40.909 0.00 0.00 34.02 2.85
5822 6881 4.201910 CCTTCACTTTGCTCAACGAAAGAA 60.202 41.667 0.00 0.00 34.02 2.52
5823 6882 3.312421 CCTTCACTTTGCTCAACGAAAGA 59.688 43.478 0.00 0.00 34.02 2.52
5824 6883 3.312421 TCCTTCACTTTGCTCAACGAAAG 59.688 43.478 0.00 0.00 35.64 2.62
5825 6884 3.275143 TCCTTCACTTTGCTCAACGAAA 58.725 40.909 0.00 0.00 0.00 3.46
5826 6885 2.912771 TCCTTCACTTTGCTCAACGAA 58.087 42.857 0.00 0.00 0.00 3.85
5827 6886 2.613026 TCCTTCACTTTGCTCAACGA 57.387 45.000 0.00 0.00 0.00 3.85
5828 6887 2.549754 ACATCCTTCACTTTGCTCAACG 59.450 45.455 0.00 0.00 0.00 4.10
5829 6888 5.182001 ACATACATCCTTCACTTTGCTCAAC 59.818 40.000 0.00 0.00 0.00 3.18
5830 6889 5.316167 ACATACATCCTTCACTTTGCTCAA 58.684 37.500 0.00 0.00 0.00 3.02
5831 6890 4.910195 ACATACATCCTTCACTTTGCTCA 58.090 39.130 0.00 0.00 0.00 4.26
5832 6891 5.181748 AGACATACATCCTTCACTTTGCTC 58.818 41.667 0.00 0.00 0.00 4.26
5833 6892 5.171339 AGACATACATCCTTCACTTTGCT 57.829 39.130 0.00 0.00 0.00 3.91
5834 6893 6.985188 TTAGACATACATCCTTCACTTTGC 57.015 37.500 0.00 0.00 0.00 3.68
5835 6894 8.553459 AGTTTAGACATACATCCTTCACTTTG 57.447 34.615 0.00 0.00 0.00 2.77
5836 6895 9.220767 GAAGTTTAGACATACATCCTTCACTTT 57.779 33.333 0.00 0.00 0.00 2.66
5837 6896 8.375506 TGAAGTTTAGACATACATCCTTCACTT 58.624 33.333 0.00 0.00 33.97 3.16
5838 6897 7.907389 TGAAGTTTAGACATACATCCTTCACT 58.093 34.615 0.00 0.00 33.97 3.41
5839 6898 8.547967 TTGAAGTTTAGACATACATCCTTCAC 57.452 34.615 0.00 0.00 37.41 3.18
5840 6899 8.999431 GTTTGAAGTTTAGACATACATCCTTCA 58.001 33.333 0.00 0.00 36.29 3.02
5841 6900 8.999431 TGTTTGAAGTTTAGACATACATCCTTC 58.001 33.333 0.00 0.00 0.00 3.46
5842 6901 8.918202 TGTTTGAAGTTTAGACATACATCCTT 57.082 30.769 0.00 0.00 0.00 3.36
5843 6902 9.167311 GATGTTTGAAGTTTAGACATACATCCT 57.833 33.333 1.53 0.00 41.88 3.24
5844 6903 8.946085 TGATGTTTGAAGTTTAGACATACATCC 58.054 33.333 18.88 3.37 44.28 3.51
5886 7006 7.229506 CAGTTTCAGGAATTCAGAGGTTAGTTT 59.770 37.037 7.93 0.00 0.00 2.66
5970 7091 6.279882 TGTTTGTTTCAGGAATTAGCCTTTG 58.720 36.000 0.00 0.00 35.66 2.77
6105 7231 0.610232 ACTGGTTTGGGATGCTGAGC 60.610 55.000 0.00 0.00 0.00 4.26
6108 7234 1.962807 TGAAACTGGTTTGGGATGCTG 59.037 47.619 3.30 0.00 32.11 4.41
6109 7235 2.380064 TGAAACTGGTTTGGGATGCT 57.620 45.000 3.30 0.00 32.11 3.79
6113 7239 4.026744 TGATGTTTGAAACTGGTTTGGGA 58.973 39.130 9.69 0.00 32.11 4.37
6147 7273 2.920724 TTTCTGACCAATGTGACCGA 57.079 45.000 0.00 0.00 0.00 4.69
6199 7331 4.284550 GGTGCTGGCCAACCTGGA 62.285 66.667 17.98 0.00 40.96 3.86
6211 7343 2.064581 GGTGGATACGAGGGGTGCT 61.065 63.158 0.00 0.00 42.51 4.40
6215 7347 0.843984 ATTTGGGTGGATACGAGGGG 59.156 55.000 0.00 0.00 42.51 4.79
6269 7402 1.603172 GGCCTATCAGATTCGACGTGG 60.603 57.143 0.00 0.00 0.00 4.94
6297 7430 2.807392 GGTGGATTTGGTGCAATTTGTG 59.193 45.455 0.00 0.00 0.00 3.33
6303 7436 1.139853 GGTTTGGTGGATTTGGTGCAA 59.860 47.619 0.00 0.00 0.00 4.08
6304 7437 0.755686 GGTTTGGTGGATTTGGTGCA 59.244 50.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.