Multiple sequence alignment - TraesCS7B01G466200

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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 TraesCS7B01G466200 chr7B 100.000 2515 0 0 1 2515 723752301 723754815 0.000000e+00 4645.0
1 TraesCS7B01G466200 chr7B 84.000 600 61 20 1935 2515 714066010 714066593 6.120000e-151 544.0
2 TraesCS7B01G466200 chr7B 96.970 99 2 1 3 101 552932054 552932151 5.570000e-37 165.0
3 TraesCS7B01G466200 chr7B 78.788 264 39 13 1748 2000 665211160 665211417 7.200000e-36 161.0
4 TraesCS7B01G466200 chr7D 88.727 1029 88 13 93 1111 625298112 625297102 0.000000e+00 1232.0
5 TraesCS7B01G466200 chr7D 93.322 614 36 4 1128 1739 625296623 625296013 0.000000e+00 902.0
6 TraesCS7B01G466200 chr7D 84.615 481 60 4 1125 1603 629236792 629237260 1.360000e-127 466.0
7 TraesCS7B01G466200 chr7D 81.607 473 56 13 1131 1599 625283634 625283189 1.840000e-96 363.0
8 TraesCS7B01G466200 chr7D 94.444 108 5 1 3 109 439634649 439634542 5.570000e-37 165.0
9 TraesCS7B01G466200 chr7A 85.005 987 117 16 170 1129 720844998 720845980 0.000000e+00 974.0
10 TraesCS7B01G466200 chr7A 83.446 592 64 19 1935 2507 165902444 165901868 1.030000e-143 520.0
11 TraesCS7B01G466200 chr7A 86.013 479 54 4 1125 1603 720846062 720846527 3.730000e-138 501.0
12 TraesCS7B01G466200 chr6D 85.069 797 78 19 1753 2514 4057982 4057192 0.000000e+00 774.0
13 TraesCS7B01G466200 chr4D 87.661 543 53 5 1980 2512 398287362 398286824 9.880000e-174 619.0
14 TraesCS7B01G466200 chr5A 84.433 591 59 19 1935 2507 698459700 698460275 3.660000e-153 551.0
15 TraesCS7B01G466200 chr5A 84.775 289 22 10 2237 2511 455273442 455273162 1.150000e-68 270.0
16 TraesCS7B01G466200 chr5A 93.478 46 3 0 1903 1948 338283289 338283244 4.490000e-08 69.4
17 TraesCS7B01G466200 chr3A 84.087 597 63 21 1935 2515 646470775 646471355 4.730000e-152 547.0
18 TraesCS7B01G466200 chr3B 86.373 499 48 10 2030 2515 752208788 752208297 6.160000e-146 527.0
19 TraesCS7B01G466200 chr4A 85.743 498 48 13 2033 2515 27192569 27192080 2.890000e-139 505.0
20 TraesCS7B01G466200 chr4A 86.851 289 17 10 2237 2511 75921863 75922144 1.130000e-78 303.0
21 TraesCS7B01G466200 chr4A 88.646 229 25 1 1748 1975 716959578 716959806 6.850000e-71 278.0
22 TraesCS7B01G466200 chr2A 82.792 523 58 16 1935 2440 758406512 758406005 2.970000e-119 438.0
23 TraesCS7B01G466200 chr2A 94.828 58 2 1 2459 2515 758406009 758405952 3.450000e-14 89.8
24 TraesCS7B01G466200 chr6B 79.606 559 73 19 1886 2412 244585284 244584735 1.840000e-96 363.0
25 TraesCS7B01G466200 chr3D 97.980 99 1 1 3 101 475116306 475116403 1.200000e-38 171.0
26 TraesCS7B01G466200 chr3D 96.000 100 4 0 6 105 527509763 527509664 2.000000e-36 163.0
27 TraesCS7B01G466200 chr2D 97.030 101 2 1 3 102 238966731 238966831 4.300000e-38 169.0
28 TraesCS7B01G466200 chr2D 92.437 119 7 2 3 119 645066685 645066567 4.300000e-38 169.0
29 TraesCS7B01G466200 chr2D 93.458 107 7 0 3 109 604128840 604128946 2.590000e-35 159.0
30 TraesCS7B01G466200 chr5D 96.970 99 3 0 3 101 84221066 84221164 1.550000e-37 167.0
31 TraesCS7B01G466200 chr5D 90.566 53 5 0 1896 1948 255071955 255071903 1.250000e-08 71.3
32 TraesCS7B01G466200 chr2B 96.117 103 2 2 3 104 173488967 173488866 1.550000e-37 167.0
33 TraesCS7B01G466200 chr5B 92.683 41 3 0 1893 1933 287440972 287441012 2.700000e-05 60.2


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 TraesCS7B01G466200 chr7B 723752301 723754815 2514 False 4645.0 4645 100.0000 1 2515 1 chr7B.!!$F4 2514
1 TraesCS7B01G466200 chr7B 714066010 714066593 583 False 544.0 544 84.0000 1935 2515 1 chr7B.!!$F3 580
2 TraesCS7B01G466200 chr7D 625296013 625298112 2099 True 1067.0 1232 91.0245 93 1739 2 chr7D.!!$R3 1646
3 TraesCS7B01G466200 chr7A 720844998 720846527 1529 False 737.5 974 85.5090 170 1603 2 chr7A.!!$F1 1433
4 TraesCS7B01G466200 chr7A 165901868 165902444 576 True 520.0 520 83.4460 1935 2507 1 chr7A.!!$R1 572
5 TraesCS7B01G466200 chr6D 4057192 4057982 790 True 774.0 774 85.0690 1753 2514 1 chr6D.!!$R1 761
6 TraesCS7B01G466200 chr4D 398286824 398287362 538 True 619.0 619 87.6610 1980 2512 1 chr4D.!!$R1 532
7 TraesCS7B01G466200 chr5A 698459700 698460275 575 False 551.0 551 84.4330 1935 2507 1 chr5A.!!$F1 572
8 TraesCS7B01G466200 chr3A 646470775 646471355 580 False 547.0 547 84.0870 1935 2515 1 chr3A.!!$F1 580
9 TraesCS7B01G466200 chr2A 758405952 758406512 560 True 263.9 438 88.8100 1935 2515 2 chr2A.!!$R1 580
10 TraesCS7B01G466200 chr6B 244584735 244585284 549 True 363.0 363 79.6060 1886 2412 1 chr6B.!!$R1 526

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
45 46 0.035152 ACAATTCGCATCTGAGGGCA 60.035 50.0 5.18 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 2394 0.171455 GTCTGAGAAGGATCACGCGT 59.829 55.0 5.58 5.58 0.0 6.01 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
17 18 4.931292 TCCATGGACTAGGGGCAA 57.069 55.556 11.44 0.00 0.00 4.52
18 19 3.112878 TCCATGGACTAGGGGCAAA 57.887 52.632 11.44 0.00 0.00 3.68
19 20 1.377690 TCCATGGACTAGGGGCAAAA 58.622 50.000 11.44 0.00 0.00 2.44
20 21 1.005450 TCCATGGACTAGGGGCAAAAC 59.995 52.381 11.44 0.00 0.00 2.43
21 22 1.005924 CCATGGACTAGGGGCAAAACT 59.994 52.381 5.56 0.00 0.00 2.66
22 23 2.094675 CATGGACTAGGGGCAAAACTG 58.905 52.381 0.00 0.00 0.00 3.16
23 24 1.440618 TGGACTAGGGGCAAAACTGA 58.559 50.000 0.00 0.00 0.00 3.41
24 25 1.351017 TGGACTAGGGGCAAAACTGAG 59.649 52.381 0.00 0.00 0.00 3.35
25 26 1.454201 GACTAGGGGCAAAACTGAGC 58.546 55.000 0.00 0.00 0.00 4.26
26 27 0.771127 ACTAGGGGCAAAACTGAGCA 59.229 50.000 0.00 0.00 0.00 4.26
27 28 1.168714 CTAGGGGCAAAACTGAGCAC 58.831 55.000 0.00 0.00 0.00 4.40
28 29 0.476338 TAGGGGCAAAACTGAGCACA 59.524 50.000 0.00 0.00 35.37 4.57
29 30 0.396974 AGGGGCAAAACTGAGCACAA 60.397 50.000 0.00 0.00 35.37 3.33
30 31 0.681175 GGGGCAAAACTGAGCACAAT 59.319 50.000 0.00 0.00 35.37 2.71
31 32 1.070601 GGGGCAAAACTGAGCACAATT 59.929 47.619 0.00 0.00 35.37 2.32
32 33 2.407090 GGGCAAAACTGAGCACAATTC 58.593 47.619 0.00 0.00 33.42 2.17
33 34 2.053627 GGCAAAACTGAGCACAATTCG 58.946 47.619 0.00 0.00 0.00 3.34
34 35 1.453148 GCAAAACTGAGCACAATTCGC 59.547 47.619 0.00 0.00 0.00 4.70
35 36 2.730069 CAAAACTGAGCACAATTCGCA 58.270 42.857 0.00 0.00 0.00 5.10
36 37 3.311106 CAAAACTGAGCACAATTCGCAT 58.689 40.909 0.00 0.00 0.00 4.73
37 38 2.907910 AACTGAGCACAATTCGCATC 57.092 45.000 0.00 0.00 0.00 3.91
38 39 2.105006 ACTGAGCACAATTCGCATCT 57.895 45.000 0.00 0.00 0.00 2.90
39 40 1.736126 ACTGAGCACAATTCGCATCTG 59.264 47.619 0.00 2.00 0.00 2.90
40 41 2.004733 CTGAGCACAATTCGCATCTGA 58.995 47.619 0.00 0.00 0.00 3.27
41 42 2.004733 TGAGCACAATTCGCATCTGAG 58.995 47.619 0.00 0.00 0.00 3.35
42 43 1.329906 GAGCACAATTCGCATCTGAGG 59.670 52.381 0.00 0.00 0.00 3.86
43 44 0.379669 GCACAATTCGCATCTGAGGG 59.620 55.000 0.00 0.00 0.00 4.30
44 45 0.379669 CACAATTCGCATCTGAGGGC 59.620 55.000 0.00 0.00 0.00 5.19
45 46 0.035152 ACAATTCGCATCTGAGGGCA 60.035 50.000 5.18 0.00 0.00 5.36
46 47 1.097232 CAATTCGCATCTGAGGGCAA 58.903 50.000 5.18 0.25 0.00 4.52
47 48 1.473677 CAATTCGCATCTGAGGGCAAA 59.526 47.619 5.18 0.00 0.00 3.68
48 49 1.838112 ATTCGCATCTGAGGGCAAAA 58.162 45.000 5.18 0.00 0.00 2.44
49 50 0.881118 TTCGCATCTGAGGGCAAAAC 59.119 50.000 5.18 0.00 0.00 2.43
50 51 0.036732 TCGCATCTGAGGGCAAAACT 59.963 50.000 5.18 0.00 0.00 2.66
51 52 0.169672 CGCATCTGAGGGCAAAACTG 59.830 55.000 5.18 0.00 0.00 3.16
52 53 1.538047 GCATCTGAGGGCAAAACTGA 58.462 50.000 0.00 0.00 0.00 3.41
53 54 1.471684 GCATCTGAGGGCAAAACTGAG 59.528 52.381 0.00 0.00 0.00 3.35
54 55 1.471684 CATCTGAGGGCAAAACTGAGC 59.528 52.381 0.00 0.00 0.00 4.26
55 56 0.473755 TCTGAGGGCAAAACTGAGCA 59.526 50.000 0.00 0.00 0.00 4.26
56 57 0.595095 CTGAGGGCAAAACTGAGCAC 59.405 55.000 0.00 0.00 0.00 4.40
57 58 0.106769 TGAGGGCAAAACTGAGCACA 60.107 50.000 0.00 0.00 36.38 4.57
58 59 0.312102 GAGGGCAAAACTGAGCACAC 59.688 55.000 0.00 0.00 36.38 3.82
59 60 1.008538 GGGCAAAACTGAGCACACG 60.009 57.895 0.00 0.00 33.42 4.49
60 61 1.008538 GGCAAAACTGAGCACACGG 60.009 57.895 0.00 0.00 0.00 4.94
61 62 1.444119 GGCAAAACTGAGCACACGGA 61.444 55.000 0.00 0.00 0.00 4.69
62 63 0.317020 GCAAAACTGAGCACACGGAC 60.317 55.000 0.00 0.00 0.00 4.79
63 64 1.013596 CAAAACTGAGCACACGGACA 58.986 50.000 0.00 0.00 0.00 4.02
64 65 1.014352 AAAACTGAGCACACGGACAC 58.986 50.000 0.00 0.00 0.00 3.67
65 66 0.814010 AAACTGAGCACACGGACACC 60.814 55.000 0.00 0.00 0.00 4.16
66 67 1.966901 AACTGAGCACACGGACACCA 61.967 55.000 0.00 0.00 0.00 4.17
67 68 1.956170 CTGAGCACACGGACACCAC 60.956 63.158 0.00 0.00 0.00 4.16
68 69 2.369257 CTGAGCACACGGACACCACT 62.369 60.000 0.00 0.00 0.00 4.00
69 70 1.956170 GAGCACACGGACACCACTG 60.956 63.158 0.00 0.00 0.00 3.66
70 71 2.108157 GCACACGGACACCACTGA 59.892 61.111 0.00 0.00 0.00 3.41
71 72 1.956170 GCACACGGACACCACTGAG 60.956 63.158 0.00 0.00 0.00 3.35
72 73 1.300931 CACACGGACACCACTGAGG 60.301 63.158 0.00 0.00 45.67 3.86
73 74 2.343758 CACGGACACCACTGAGGG 59.656 66.667 0.00 0.00 43.89 4.30
74 75 3.626924 ACGGACACCACTGAGGGC 61.627 66.667 0.00 0.00 43.89 5.19
75 76 3.625897 CGGACACCACTGAGGGCA 61.626 66.667 0.00 0.00 43.89 5.36
76 77 2.836154 GGACACCACTGAGGGCAA 59.164 61.111 0.00 0.00 43.89 4.52
77 78 1.150536 GGACACCACTGAGGGCAAA 59.849 57.895 0.00 0.00 43.89 3.68
78 79 0.467290 GGACACCACTGAGGGCAAAA 60.467 55.000 0.00 0.00 43.89 2.44
79 80 0.954452 GACACCACTGAGGGCAAAAG 59.046 55.000 0.00 0.00 43.89 2.27
80 81 0.468029 ACACCACTGAGGGCAAAAGG 60.468 55.000 0.00 0.00 43.89 3.11
81 82 0.178992 CACCACTGAGGGCAAAAGGA 60.179 55.000 0.00 0.00 43.89 3.36
82 83 0.779997 ACCACTGAGGGCAAAAGGAT 59.220 50.000 0.00 0.00 43.89 3.24
83 84 1.992557 ACCACTGAGGGCAAAAGGATA 59.007 47.619 0.00 0.00 43.89 2.59
84 85 2.378547 ACCACTGAGGGCAAAAGGATAA 59.621 45.455 0.00 0.00 43.89 1.75
85 86 3.011708 ACCACTGAGGGCAAAAGGATAAT 59.988 43.478 0.00 0.00 43.89 1.28
86 87 4.026052 CCACTGAGGGCAAAAGGATAATT 58.974 43.478 0.00 0.00 0.00 1.40
87 88 5.200483 CCACTGAGGGCAAAAGGATAATTA 58.800 41.667 0.00 0.00 0.00 1.40
88 89 5.656416 CCACTGAGGGCAAAAGGATAATTAA 59.344 40.000 0.00 0.00 0.00 1.40
89 90 6.405842 CCACTGAGGGCAAAAGGATAATTAAC 60.406 42.308 0.00 0.00 0.00 2.01
90 91 5.656859 ACTGAGGGCAAAAGGATAATTAACC 59.343 40.000 3.60 3.60 0.00 2.85
91 92 4.959839 TGAGGGCAAAAGGATAATTAACCC 59.040 41.667 8.09 3.96 34.91 4.11
113 114 7.981142 ACCCTTTAGTTTTCTATGGAACTACA 58.019 34.615 0.00 0.00 37.90 2.74
139 142 8.862325 TTTTATCTTGTTGGTAGATGACATGT 57.138 30.769 0.00 0.00 34.35 3.21
140 143 9.952030 TTTTATCTTGTTGGTAGATGACATGTA 57.048 29.630 0.00 0.00 34.35 2.29
143 146 8.668510 ATCTTGTTGGTAGATGACATGTATTC 57.331 34.615 0.00 0.00 31.32 1.75
144 147 6.756542 TCTTGTTGGTAGATGACATGTATTCG 59.243 38.462 0.00 0.00 0.00 3.34
152 156 9.077674 GGTAGATGACATGTATTCGCTTTATAG 57.922 37.037 0.00 0.00 0.00 1.31
160 164 8.873830 ACATGTATTCGCTTTATAGACATATGC 58.126 33.333 1.58 0.00 0.00 3.14
161 165 9.091784 CATGTATTCGCTTTATAGACATATGCT 57.908 33.333 1.58 3.84 0.00 3.79
321 326 2.814336 GGTTGACCTCCATGTTGAGTTC 59.186 50.000 0.00 0.00 0.00 3.01
378 383 4.835615 TGATAGGTAGGCTCCTGAATCTTC 59.164 45.833 13.65 4.50 38.41 2.87
542 550 8.046107 CCCTAAAGAAATAAATTTTGCCCATCA 58.954 33.333 0.00 0.00 0.00 3.07
548 556 7.706179 AGAAATAAATTTTGCCCATCATGTACG 59.294 33.333 0.00 0.00 0.00 3.67
551 559 4.572985 ATTTTGCCCATCATGTACGATG 57.427 40.909 4.30 4.30 42.09 3.84
579 591 4.504826 GCTTCGAGGACTCTTATGCTTTAC 59.495 45.833 0.00 0.00 0.00 2.01
616 628 6.004408 TGAATAAATGCATGATGTCCATCG 57.996 37.500 0.00 0.00 40.63 3.84
768 791 5.531287 ACCAAACCAAGACAAGACATACTTC 59.469 40.000 0.00 0.00 36.61 3.01
786 815 8.296713 ACATACTTCCAACACACATTAAATGAC 58.703 33.333 0.00 0.00 0.00 3.06
795 824 9.467258 CAACACACATTAAATGACAGATCTTTT 57.533 29.630 0.00 0.00 36.47 2.27
896 948 5.825679 TGTATAATACATTGAGGGTGTTGCC 59.174 40.000 0.00 0.00 32.89 4.52
904 956 2.265367 TGAGGGTGTTGCCAAGATCTA 58.735 47.619 0.00 0.00 39.65 1.98
985 1037 2.086869 CCTTCGGTCTGCACATCATTT 58.913 47.619 0.00 0.00 0.00 2.32
1036 1088 1.729484 GCGGTTTTGCTCGCCTTTC 60.729 57.895 0.00 0.00 45.42 2.62
1063 1115 5.236478 GGTATGTGAAATCGAATCATCCGTT 59.764 40.000 7.44 0.00 0.00 4.44
1064 1116 4.857871 TGTGAAATCGAATCATCCGTTC 57.142 40.909 7.44 0.00 0.00 3.95
1075 1127 5.536554 AATCATCCGTTCATCGCATATTC 57.463 39.130 0.00 0.00 38.35 1.75
1099 1151 7.478322 TCTGTACTTCATCTTGATACGGTTAC 58.522 38.462 0.00 0.00 0.00 2.50
1151 1665 6.153067 TGCCTTGTTAATTTCGTATTTGGTG 58.847 36.000 0.00 0.00 0.00 4.17
1182 1696 2.167075 GGCCCAATCAAAGGAGAACATG 59.833 50.000 0.00 0.00 0.00 3.21
1206 1720 1.973281 GATGCAGGTGGTGGTGGTG 60.973 63.158 0.00 0.00 0.00 4.17
1209 1723 2.280797 CAGGTGGTGGTGGTGTCG 60.281 66.667 0.00 0.00 0.00 4.35
1228 1742 4.554036 GGCGCCTCCACCTGATCC 62.554 72.222 22.15 0.00 34.01 3.36
1247 1761 1.227205 CGAGAGCAGTCATCTGGCC 60.227 63.158 0.00 0.00 41.57 5.36
1518 2032 6.273825 ACTAGTCCGTCATTACATTGATGTC 58.726 40.000 0.00 0.00 41.97 3.06
1569 2083 9.184523 TGGTCAATAAAATAGTAAAGGATGTGG 57.815 33.333 0.00 0.00 0.00 4.17
1641 2155 5.596836 TTTTTGAAAGATCCAGCAACTGT 57.403 34.783 0.00 0.00 0.00 3.55
1642 2156 4.572985 TTTGAAAGATCCAGCAACTGTG 57.427 40.909 0.00 0.00 0.00 3.66
1660 2174 6.515272 ACTGTGGGCTTTTGTATTATCAAG 57.485 37.500 0.00 0.00 0.00 3.02
1678 2192 5.609533 TCAAGGTAGGGAGCAGTATTTAC 57.390 43.478 0.00 0.00 0.00 2.01
1683 2197 5.246429 AGGTAGGGAGCAGTATTTACATAGC 59.754 44.000 0.00 0.00 0.00 2.97
1685 2199 5.630415 AGGGAGCAGTATTTACATAGCAA 57.370 39.130 0.00 0.00 0.00 3.91
1688 2202 4.211374 GGAGCAGTATTTACATAGCAACCG 59.789 45.833 0.00 0.00 0.00 4.44
1689 2203 3.560068 AGCAGTATTTACATAGCAACCGC 59.440 43.478 0.00 0.00 38.99 5.68
1722 2236 8.194769 GTCTTAAGGAGAGAAGTTAGAGGAATG 58.805 40.741 1.85 0.00 34.31 2.67
1783 2297 3.800685 TTCGGCTGGTCACACCACG 62.801 63.158 0.00 0.00 44.79 4.94
1800 2314 3.053291 GCCCGCACGATTTGGACA 61.053 61.111 0.00 0.00 0.00 4.02
1805 2319 1.393539 CCGCACGATTTGGACAGTTAG 59.606 52.381 0.00 0.00 0.00 2.34
1810 2324 1.927174 CGATTTGGACAGTTAGAGCCG 59.073 52.381 0.00 0.00 0.00 5.52
1818 2332 1.141881 AGTTAGAGCCGTGCGATGG 59.858 57.895 0.00 0.00 0.00 3.51
1827 2341 0.673644 CCGTGCGATGGTCTTCCTTT 60.674 55.000 0.00 0.00 34.23 3.11
1841 2355 6.012508 TGGTCTTCCTTTCCATAACTGATTCT 60.013 38.462 0.00 0.00 34.23 2.40
1868 2382 4.834496 AGAACATGAAGGAAAAAGGCATGA 59.166 37.500 0.00 0.00 38.82 3.07
1882 2396 0.725784 GCATGACGCCAAGTTCAACG 60.726 55.000 0.00 0.00 32.94 4.10
1894 2408 1.000955 AGTTCAACGCGTGATCCTTCT 59.999 47.619 14.98 2.49 35.70 2.85
1970 2507 2.580815 CCTCATCGCCAGTGCTCA 59.419 61.111 0.00 0.00 34.43 4.26
2056 2595 0.107703 CGTCCCTATCCTTGCAGCAA 60.108 55.000 7.81 7.81 0.00 3.91
2096 2635 3.490759 GTCCATCGCAGCACCACG 61.491 66.667 0.00 0.00 0.00 4.94
2120 2659 1.005630 GCAGACCGCAACTCTCACT 60.006 57.895 0.00 0.00 41.79 3.41
2127 2666 0.317854 CGCAACTCTCACTGTCGTCA 60.318 55.000 0.00 0.00 0.00 4.35
2176 2718 1.002624 GAAGGCCACCCAATCGACA 60.003 57.895 5.01 0.00 0.00 4.35
2217 2760 0.465287 AAAACGTCACCGGTGGTAGT 59.535 50.000 33.40 25.55 38.78 2.73
2269 2820 4.492160 GCCGTCGTCCATCTGCGA 62.492 66.667 0.00 0.00 34.54 5.10
2283 2834 4.996758 CCATCTGCGACATTAATGGATGTA 59.003 41.667 19.37 7.29 40.21 2.29
2301 2852 3.655486 TGTAAGCAAATTTCCTCGTCGA 58.345 40.909 0.00 0.00 0.00 4.20
2337 2892 1.270412 ACGACCGTCAGCAAATAACCA 60.270 47.619 0.00 0.00 0.00 3.67
2385 2942 2.811431 CGTCAAGGAAAACATACAGCCA 59.189 45.455 0.00 0.00 0.00 4.75
2390 2947 4.574674 AGGAAAACATACAGCCAGATGA 57.425 40.909 0.00 0.00 0.00 2.92
2416 2974 3.772387 TCCCATGGTAGCAAAAATGTGA 58.228 40.909 11.73 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.005924 AGTTTTGCCCCTAGTCCATGG 59.994 52.381 4.97 4.97 0.00 3.66
2 3 2.094675 CAGTTTTGCCCCTAGTCCATG 58.905 52.381 0.00 0.00 0.00 3.66
3 4 1.992557 TCAGTTTTGCCCCTAGTCCAT 59.007 47.619 0.00 0.00 0.00 3.41
4 5 1.351017 CTCAGTTTTGCCCCTAGTCCA 59.649 52.381 0.00 0.00 0.00 4.02
6 7 1.271379 TGCTCAGTTTTGCCCCTAGTC 60.271 52.381 0.00 0.00 0.00 2.59
7 8 0.771127 TGCTCAGTTTTGCCCCTAGT 59.229 50.000 0.00 0.00 0.00 2.57
8 9 1.168714 GTGCTCAGTTTTGCCCCTAG 58.831 55.000 0.00 0.00 0.00 3.02
9 10 0.476338 TGTGCTCAGTTTTGCCCCTA 59.524 50.000 0.00 0.00 0.00 3.53
10 11 0.396974 TTGTGCTCAGTTTTGCCCCT 60.397 50.000 0.00 0.00 0.00 4.79
11 12 0.681175 ATTGTGCTCAGTTTTGCCCC 59.319 50.000 0.00 0.00 0.00 5.80
12 13 2.407090 GAATTGTGCTCAGTTTTGCCC 58.593 47.619 0.00 0.00 0.00 5.36
13 14 2.053627 CGAATTGTGCTCAGTTTTGCC 58.946 47.619 0.00 0.00 0.00 4.52
14 15 1.453148 GCGAATTGTGCTCAGTTTTGC 59.547 47.619 8.90 8.90 0.00 3.68
15 16 2.730069 TGCGAATTGTGCTCAGTTTTG 58.270 42.857 0.00 0.00 0.00 2.44
16 17 3.254166 AGATGCGAATTGTGCTCAGTTTT 59.746 39.130 0.00 0.00 0.00 2.43
17 18 2.816087 AGATGCGAATTGTGCTCAGTTT 59.184 40.909 0.00 0.00 0.00 2.66
18 19 2.161012 CAGATGCGAATTGTGCTCAGTT 59.839 45.455 0.00 0.00 0.00 3.16
19 20 1.736126 CAGATGCGAATTGTGCTCAGT 59.264 47.619 0.00 0.00 0.00 3.41
20 21 2.004733 TCAGATGCGAATTGTGCTCAG 58.995 47.619 0.00 0.00 0.00 3.35
21 22 2.004733 CTCAGATGCGAATTGTGCTCA 58.995 47.619 0.00 0.00 0.00 4.26
22 23 1.329906 CCTCAGATGCGAATTGTGCTC 59.670 52.381 0.00 0.00 0.00 4.26
23 24 1.376543 CCTCAGATGCGAATTGTGCT 58.623 50.000 0.00 0.00 0.00 4.40
24 25 0.379669 CCCTCAGATGCGAATTGTGC 59.620 55.000 0.00 0.00 0.00 4.57
25 26 0.379669 GCCCTCAGATGCGAATTGTG 59.620 55.000 0.00 0.00 0.00 3.33
26 27 0.035152 TGCCCTCAGATGCGAATTGT 60.035 50.000 0.00 0.00 0.00 2.71
27 28 1.097232 TTGCCCTCAGATGCGAATTG 58.903 50.000 0.00 0.00 0.00 2.32
28 29 1.838112 TTTGCCCTCAGATGCGAATT 58.162 45.000 0.00 0.00 0.00 2.17
29 30 1.474077 GTTTTGCCCTCAGATGCGAAT 59.526 47.619 0.00 0.00 31.25 3.34
30 31 0.881118 GTTTTGCCCTCAGATGCGAA 59.119 50.000 0.00 0.00 0.00 4.70
31 32 0.036732 AGTTTTGCCCTCAGATGCGA 59.963 50.000 0.00 0.00 0.00 5.10
32 33 0.169672 CAGTTTTGCCCTCAGATGCG 59.830 55.000 0.00 0.00 0.00 4.73
33 34 1.471684 CTCAGTTTTGCCCTCAGATGC 59.528 52.381 0.00 0.00 0.00 3.91
34 35 1.471684 GCTCAGTTTTGCCCTCAGATG 59.528 52.381 0.00 0.00 0.00 2.90
35 36 1.074405 TGCTCAGTTTTGCCCTCAGAT 59.926 47.619 0.00 0.00 0.00 2.90
36 37 0.473755 TGCTCAGTTTTGCCCTCAGA 59.526 50.000 0.00 0.00 0.00 3.27
37 38 0.595095 GTGCTCAGTTTTGCCCTCAG 59.405 55.000 0.00 0.00 0.00 3.35
38 39 0.106769 TGTGCTCAGTTTTGCCCTCA 60.107 50.000 0.00 0.00 0.00 3.86
39 40 0.312102 GTGTGCTCAGTTTTGCCCTC 59.688 55.000 0.00 0.00 0.00 4.30
40 41 1.447317 CGTGTGCTCAGTTTTGCCCT 61.447 55.000 0.00 0.00 0.00 5.19
41 42 1.008538 CGTGTGCTCAGTTTTGCCC 60.009 57.895 0.00 0.00 0.00 5.36
42 43 1.008538 CCGTGTGCTCAGTTTTGCC 60.009 57.895 0.00 0.00 0.00 4.52
43 44 0.317020 GTCCGTGTGCTCAGTTTTGC 60.317 55.000 0.00 0.00 0.00 3.68
44 45 1.013596 TGTCCGTGTGCTCAGTTTTG 58.986 50.000 0.00 0.00 0.00 2.44
45 46 1.014352 GTGTCCGTGTGCTCAGTTTT 58.986 50.000 0.00 0.00 0.00 2.43
46 47 0.814010 GGTGTCCGTGTGCTCAGTTT 60.814 55.000 0.00 0.00 0.00 2.66
47 48 1.227556 GGTGTCCGTGTGCTCAGTT 60.228 57.895 0.00 0.00 0.00 3.16
48 49 2.421739 GGTGTCCGTGTGCTCAGT 59.578 61.111 0.00 0.00 0.00 3.41
49 50 1.956170 GTGGTGTCCGTGTGCTCAG 60.956 63.158 0.00 0.00 0.00 3.35
50 51 2.108157 GTGGTGTCCGTGTGCTCA 59.892 61.111 0.00 0.00 0.00 4.26
51 52 1.956170 CAGTGGTGTCCGTGTGCTC 60.956 63.158 0.00 0.00 0.00 4.26
52 53 2.108976 CAGTGGTGTCCGTGTGCT 59.891 61.111 0.00 0.00 0.00 4.40
53 54 1.956170 CTCAGTGGTGTCCGTGTGC 60.956 63.158 0.00 0.00 0.00 4.57
54 55 1.300931 CCTCAGTGGTGTCCGTGTG 60.301 63.158 0.00 0.00 0.00 3.82
55 56 2.507854 CCCTCAGTGGTGTCCGTGT 61.508 63.158 0.00 0.00 0.00 4.49
56 57 2.343758 CCCTCAGTGGTGTCCGTG 59.656 66.667 0.00 0.00 0.00 4.94
57 58 3.626924 GCCCTCAGTGGTGTCCGT 61.627 66.667 0.00 0.00 0.00 4.69
58 59 2.674563 TTTGCCCTCAGTGGTGTCCG 62.675 60.000 0.00 0.00 0.00 4.79
59 60 0.467290 TTTTGCCCTCAGTGGTGTCC 60.467 55.000 0.00 0.00 0.00 4.02
60 61 0.954452 CTTTTGCCCTCAGTGGTGTC 59.046 55.000 0.00 0.00 0.00 3.67
61 62 0.468029 CCTTTTGCCCTCAGTGGTGT 60.468 55.000 0.00 0.00 0.00 4.16
62 63 0.178992 TCCTTTTGCCCTCAGTGGTG 60.179 55.000 0.00 0.00 0.00 4.17
63 64 0.779997 ATCCTTTTGCCCTCAGTGGT 59.220 50.000 0.00 0.00 0.00 4.16
64 65 2.806945 TATCCTTTTGCCCTCAGTGG 57.193 50.000 0.00 0.00 0.00 4.00
65 66 6.405842 GGTTAATTATCCTTTTGCCCTCAGTG 60.406 42.308 5.46 0.00 0.00 3.66
66 67 5.656859 GGTTAATTATCCTTTTGCCCTCAGT 59.343 40.000 5.46 0.00 0.00 3.41
67 68 5.069119 GGGTTAATTATCCTTTTGCCCTCAG 59.931 44.000 11.51 0.00 0.00 3.35
68 69 4.959839 GGGTTAATTATCCTTTTGCCCTCA 59.040 41.667 11.51 0.00 0.00 3.86
69 70 5.208890 AGGGTTAATTATCCTTTTGCCCTC 58.791 41.667 11.51 0.00 39.57 4.30
70 71 5.220872 AGGGTTAATTATCCTTTTGCCCT 57.779 39.130 11.51 0.00 38.99 5.19
71 72 5.950544 AAGGGTTAATTATCCTTTTGCCC 57.049 39.130 11.51 0.00 37.60 5.36
72 73 8.074613 ACTAAAGGGTTAATTATCCTTTTGCC 57.925 34.615 25.41 7.17 45.46 4.52
73 74 9.938280 AAACTAAAGGGTTAATTATCCTTTTGC 57.062 29.630 25.41 7.70 45.46 3.68
86 87 9.948964 GTAGTTCCATAGAAAACTAAAGGGTTA 57.051 33.333 0.00 0.00 39.11 2.85
87 88 8.442374 TGTAGTTCCATAGAAAACTAAAGGGTT 58.558 33.333 0.00 0.00 39.11 4.11
88 89 7.981142 TGTAGTTCCATAGAAAACTAAAGGGT 58.019 34.615 0.00 0.00 39.11 4.34
89 90 9.462606 AATGTAGTTCCATAGAAAACTAAAGGG 57.537 33.333 0.00 0.00 39.11 3.95
113 114 9.466497 ACATGTCATCTACCAACAAGATAAAAT 57.534 29.630 0.00 0.00 32.40 1.82
117 118 9.764363 GAATACATGTCATCTACCAACAAGATA 57.236 33.333 0.00 0.00 32.40 1.98
277 282 8.465273 ACCTTGATTTAACTAGCAAAGTTCTT 57.535 30.769 7.65 0.00 45.64 2.52
279 284 8.349983 TCAACCTTGATTTAACTAGCAAAGTTC 58.650 33.333 7.65 0.00 39.63 3.01
283 288 6.775629 AGGTCAACCTTGATTTAACTAGCAAA 59.224 34.615 0.00 0.00 46.09 3.68
321 326 1.135972 CGCATTCAAACCCGTTCTGAG 60.136 52.381 0.00 0.00 0.00 3.35
444 450 7.461182 TGAACCCATTCGACAATCTAAAAAT 57.539 32.000 0.00 0.00 37.69 1.82
525 533 7.106439 TCGTACATGATGGGCAAAATTTATT 57.894 32.000 0.00 0.00 0.00 1.40
560 568 4.288670 TCGTAAAGCATAAGAGTCCTCG 57.711 45.455 0.00 0.00 34.09 4.63
579 591 6.252441 TGCATTTATTCAACGGCTTTATTTCG 59.748 34.615 0.00 0.00 0.00 3.46
591 603 6.361481 CGATGGACATCATGCATTTATTCAAC 59.639 38.462 12.33 0.00 39.93 3.18
719 733 9.677567 GTGCTCATAAAGTTTGAATTTAGTCAA 57.322 29.630 0.00 0.00 35.72 3.18
734 748 4.278170 TGTCTTGGTTTGGTGCTCATAAAG 59.722 41.667 0.00 0.00 0.00 1.85
768 791 7.149569 AGATCTGTCATTTAATGTGTGTTGG 57.850 36.000 4.77 0.00 0.00 3.77
872 920 5.825679 GGCAACACCCTCAATGTATTATACA 59.174 40.000 7.56 7.56 43.80 2.29
915 967 8.331931 ACCTACATTTATAGATTCTTGGACCA 57.668 34.615 0.00 0.00 0.00 4.02
985 1037 2.441375 TCAACATGGTGGTCCTTCTCAA 59.559 45.455 11.68 0.00 34.23 3.02
1036 1088 5.180117 GGATGATTCGATTTCACATACCTGG 59.820 44.000 1.09 0.00 0.00 4.45
1063 1115 6.986250 AGATGAAGTACAGAATATGCGATGA 58.014 36.000 0.00 0.00 0.00 2.92
1064 1116 7.383300 TCAAGATGAAGTACAGAATATGCGATG 59.617 37.037 0.00 0.00 0.00 3.84
1075 1127 7.481642 AGTAACCGTATCAAGATGAAGTACAG 58.518 38.462 0.00 0.00 0.00 2.74
1099 1151 8.178313 TGGTGTTGACTGTATAGTGGATATAG 57.822 38.462 0.00 0.00 37.25 1.31
1151 1665 1.327303 TGATTGGGCCTGTTGTTCAC 58.673 50.000 4.53 0.00 0.00 3.18
1182 1696 0.819582 CCACCACCTGCATCCAAATC 59.180 55.000 0.00 0.00 0.00 2.17
1228 1742 1.227205 GCCAGATGACTGCTCTCGG 60.227 63.158 0.00 0.00 42.25 4.63
1247 1761 2.639839 TGGAGAAGTTTGAGGAGAAGGG 59.360 50.000 0.00 0.00 0.00 3.95
1413 1927 2.357154 GGCCGCCCTTATATGATTCCAT 60.357 50.000 0.00 0.00 36.81 3.41
1454 1968 3.007506 TGAGACAATAGCAAGGACCGAAA 59.992 43.478 0.00 0.00 0.00 3.46
1518 2032 5.375417 TGAAAACTCAAGCCACATGTATG 57.625 39.130 0.00 0.00 0.00 2.39
1557 2071 8.904099 AATACTATAAGCACCACATCCTTTAC 57.096 34.615 0.00 0.00 0.00 2.01
1558 2072 8.154856 GGAATACTATAAGCACCACATCCTTTA 58.845 37.037 0.00 0.00 0.00 1.85
1562 2076 6.115448 AGGAATACTATAAGCACCACATCC 57.885 41.667 0.00 0.00 0.00 3.51
1563 2077 5.864474 CGAGGAATACTATAAGCACCACATC 59.136 44.000 0.00 0.00 0.00 3.06
1622 2136 2.886523 CCACAGTTGCTGGATCTTTCAA 59.113 45.455 1.08 0.00 35.51 2.69
1624 2138 1.815003 CCCACAGTTGCTGGATCTTTC 59.185 52.381 1.08 0.00 35.51 2.62
1625 2139 1.915141 CCCACAGTTGCTGGATCTTT 58.085 50.000 1.08 0.00 35.51 2.52
1641 2155 6.126409 CCTACCTTGATAATACAAAAGCCCA 58.874 40.000 0.00 0.00 0.00 5.36
1642 2156 5.535030 CCCTACCTTGATAATACAAAAGCCC 59.465 44.000 0.00 0.00 0.00 5.19
1660 2174 5.011738 TGCTATGTAAATACTGCTCCCTACC 59.988 44.000 0.00 0.00 0.00 3.18
1683 2197 2.864343 CCTTAAGACGGATAAGCGGTTG 59.136 50.000 10.73 0.00 0.00 3.77
1685 2199 2.361438 CTCCTTAAGACGGATAAGCGGT 59.639 50.000 3.36 0.00 0.00 5.68
1688 2202 5.068067 ACTTCTCTCCTTAAGACGGATAAGC 59.932 44.000 3.36 0.00 0.00 3.09
1689 2203 6.702716 ACTTCTCTCCTTAAGACGGATAAG 57.297 41.667 3.36 9.19 0.00 1.73
1691 2205 7.571919 TCTAACTTCTCTCCTTAAGACGGATA 58.428 38.462 3.36 0.00 0.00 2.59
1694 2208 5.066764 CCTCTAACTTCTCTCCTTAAGACGG 59.933 48.000 3.36 0.00 0.00 4.79
1697 2211 7.343316 CCATTCCTCTAACTTCTCTCCTTAAGA 59.657 40.741 3.36 0.00 0.00 2.10
1734 2248 1.134226 CGTGCCGTACTCGTCTTTTT 58.866 50.000 0.00 0.00 35.01 1.94
1749 2263 4.413800 AAATTTCGGCCGGCGTGC 62.414 61.111 27.83 5.60 0.00 5.34
1750 2264 2.202427 GAAATTTCGGCCGGCGTG 60.202 61.111 27.83 16.16 0.00 5.34
1751 2265 3.795342 CGAAATTTCGGCCGGCGT 61.795 61.111 28.73 8.41 46.30 5.68
1781 2295 4.690719 TCCAAATCGTGCGGGCGT 62.691 61.111 0.00 0.00 0.00 5.68
1783 2297 3.039202 CTGTCCAAATCGTGCGGGC 62.039 63.158 0.00 0.00 0.00 6.13
1800 2314 1.141881 CCATCGCACGGCTCTAACT 59.858 57.895 0.00 0.00 0.00 2.24
1805 2319 2.125512 AAGACCATCGCACGGCTC 60.126 61.111 0.00 0.00 0.00 4.70
1810 2324 1.087501 GGAAAGGAAGACCATCGCAC 58.912 55.000 0.00 0.00 38.94 5.34
1818 2332 7.929941 AAGAATCAGTTATGGAAAGGAAGAC 57.070 36.000 0.00 0.00 0.00 3.01
1827 2341 9.958180 TCATGTTCTTAAAGAATCAGTTATGGA 57.042 29.630 0.00 0.00 36.50 3.41
1841 2355 7.118496 TGCCTTTTTCCTTCATGTTCTTAAA 57.882 32.000 0.00 0.00 0.00 1.52
1849 2363 3.504863 CGTCATGCCTTTTTCCTTCATG 58.495 45.455 0.00 0.00 36.71 3.07
1851 2365 1.269448 GCGTCATGCCTTTTTCCTTCA 59.731 47.619 0.00 0.00 37.76 3.02
1877 2391 0.601057 TGAGAAGGATCACGCGTTGA 59.399 50.000 10.22 11.72 39.11 3.18
1880 2394 0.171455 GTCTGAGAAGGATCACGCGT 59.829 55.000 5.58 5.58 0.00 6.01
1882 2396 0.171455 ACGTCTGAGAAGGATCACGC 59.829 55.000 0.00 0.00 0.00 5.34
1894 2408 2.965783 GAGCTGGCTGACGTCTGA 59.034 61.111 24.65 5.24 0.00 3.27
1942 2479 4.530857 GATGAGGGTGGCGACCGG 62.531 72.222 12.15 0.00 44.23 5.28
1943 2480 4.873129 CGATGAGGGTGGCGACCG 62.873 72.222 12.15 0.00 44.23 4.79
1963 2500 2.029666 GCTGTGACGGTGAGCACT 59.970 61.111 0.16 0.00 36.05 4.40
1970 2507 3.785189 GACGGTGTGCTGTGACGGT 62.785 63.158 0.00 0.00 33.67 4.83
2012 2550 1.195900 GTGTTTTGCTACGATGGCGAA 59.804 47.619 0.00 0.00 41.64 4.70
2056 2595 1.099879 ATACGAAGGCGACGGCTAGT 61.100 55.000 25.26 26.14 37.50 2.57
2069 2608 0.452585 TGCGATGGACGTGATACGAA 59.547 50.000 8.48 0.00 46.05 3.85
2104 2643 0.315568 GACAGTGAGAGTTGCGGTCT 59.684 55.000 0.00 0.00 0.00 3.85
2106 2645 1.007271 CGACAGTGAGAGTTGCGGT 60.007 57.895 0.00 0.00 0.00 5.68
2146 2686 2.251642 GGCCTTCGTTCGTGCAACT 61.252 57.895 0.00 0.00 32.09 3.16
2227 2770 4.099266 ACAGTGATTTTGCTGCAACCTTAA 59.901 37.500 15.72 7.14 36.26 1.85
2228 2771 3.636300 ACAGTGATTTTGCTGCAACCTTA 59.364 39.130 15.72 0.00 36.26 2.69
2230 2773 2.034124 ACAGTGATTTTGCTGCAACCT 58.966 42.857 15.72 5.01 36.26 3.50
2269 2820 8.761689 AGGAAATTTGCTTACATCCATTAATGT 58.238 29.630 14.25 0.00 42.41 2.71
2283 2834 2.348666 CGATCGACGAGGAAATTTGCTT 59.651 45.455 13.87 0.00 45.77 3.91
2375 2932 3.539604 GAAGCTTCATCTGGCTGTATGT 58.460 45.455 21.67 0.00 38.91 2.29
2385 2942 2.158696 GCTACCATGGGAAGCTTCATCT 60.159 50.000 27.02 8.31 33.40 2.90
2390 2947 2.603075 TTTGCTACCATGGGAAGCTT 57.397 45.000 30.33 0.00 37.16 3.74
2416 2974 5.446143 TTTTTGCTACATCCATTCAACGT 57.554 34.783 0.00 0.00 0.00 3.99
2442 3001 5.634859 GTCATTTTTGCTTTGACCGATGATT 59.365 36.000 0.00 0.00 34.95 2.57
2443 3002 5.163513 GTCATTTTTGCTTTGACCGATGAT 58.836 37.500 0.00 0.00 34.95 2.45
2454 3013 2.607180 GCAACCGTTGTCATTTTTGCTT 59.393 40.909 12.77 0.00 37.08 3.91


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

AutoCloner maintained by Alex Coulton.