Multiple sequence alignment - TraesCS3B01G015200

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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 TraesCS3B01G015200 chr3B 100.000 2938 0 0 1 2938 6335915 6338852 0.000000e+00 5426.0
1 TraesCS3B01G015200 chr3B 94.939 1956 60 12 361 2285 6405371 6407318 0.000000e+00 3027.0
2 TraesCS3B01G015200 chr3B 84.149 776 84 25 1686 2433 6533859 6534623 0.000000e+00 715.0
3 TraesCS3B01G015200 chr3B 96.639 357 12 0 2582 2938 6415421 6415777 7.010000e-166 593.0
4 TraesCS3B01G015200 chr3B 84.797 592 65 14 1519 2101 6469700 6470275 3.280000e-159 571.0
5 TraesCS3B01G015200 chr3B 83.657 618 51 24 366 960 6467876 6468466 1.200000e-148 536.0
6 TraesCS3B01G015200 chr3B 79.697 660 66 38 364 972 6532307 6532949 5.860000e-112 414.0
7 TraesCS3B01G015200 chr3B 90.288 278 18 3 2670 2938 6536444 6536721 3.600000e-94 355.0
8 TraesCS3B01G015200 chr3B 90.476 231 22 0 973 1203 6532983 6533213 3.680000e-79 305.0
9 TraesCS3B01G015200 chr3B 90.667 225 17 2 2431 2654 6534653 6534874 2.210000e-76 296.0
10 TraesCS3B01G015200 chr3B 98.710 155 2 0 2431 2585 6413212 6413366 2.880000e-70 276.0
11 TraesCS3B01G015200 chr3B 96.129 155 5 1 2280 2433 6413028 6413182 4.860000e-63 252.0
12 TraesCS3B01G015200 chr3B 91.463 164 8 4 1242 1404 6468972 6469130 1.370000e-53 220.0
13 TraesCS3B01G015200 chr3B 87.363 182 19 4 1440 1619 6533668 6533847 3.840000e-49 206.0
14 TraesCS3B01G015200 chr3B 93.814 97 6 0 1270 1366 6533298 6533394 2.360000e-31 147.0
15 TraesCS3B01G015200 chr3B 88.525 61 5 2 2092 2150 6470333 6470393 4.060000e-09 73.1
16 TraesCS3B01G015200 chr3D 89.688 1765 103 24 361 2064 4111217 4112963 0.000000e+00 2178.0
17 TraesCS3B01G015200 chr3D 88.554 498 50 4 1607 2098 4134996 4135492 5.420000e-167 597.0
18 TraesCS3B01G015200 chr3D 87.955 357 33 8 1606 1955 4139545 4139898 2.110000e-111 412.0
19 TraesCS3B01G015200 chr3D 92.857 224 13 1 2431 2654 4136595 4136815 3.650000e-84 322.0
20 TraesCS3B01G015200 chr3D 90.909 231 21 0 973 1203 4138737 4138967 7.910000e-81 311.0
21 TraesCS3B01G015200 chr3D 92.202 218 17 0 986 1203 4134328 4134545 2.840000e-80 309.0
22 TraesCS3B01G015200 chr3D 85.621 306 27 6 2431 2722 4157114 4157416 3.680000e-79 305.0
23 TraesCS3B01G015200 chr3D 80.441 363 47 11 624 972 4133932 4134284 3.760000e-64 255.0
24 TraesCS3B01G015200 chr3D 94.309 123 7 0 1242 1364 4139172 4139294 3.870000e-44 189.0
25 TraesCS3B01G015200 chr3D 84.000 200 18 10 1423 1617 4134851 4135041 2.330000e-41 180.0
26 TraesCS3B01G015200 chr3D 85.811 148 9 6 1270 1407 4134647 4134792 2.360000e-31 147.0
27 TraesCS3B01G015200 chr3D 87.879 99 7 3 2091 2189 4153366 4153459 8.610000e-21 111.0
28 TraesCS3B01G015200 chr3D 78.142 183 25 7 1439 1619 4139423 4139592 5.180000e-18 102.0
29 TraesCS3B01G015200 chr3A 89.522 1088 72 13 361 1408 9627284 9628369 0.000000e+00 1339.0
30 TraesCS3B01G015200 chr3A 88.073 1048 81 16 1421 2433 9630889 9631927 0.000000e+00 1203.0
31 TraesCS3B01G015200 chr3A 92.141 509 28 6 2433 2938 9631959 9632458 0.000000e+00 708.0
32 TraesCS3B01G015200 chr3A 88.430 121 13 1 2748 2868 644498182 644498063 8.490000e-31 145.0
33 TraesCS3B01G015200 chrUn 84.797 592 65 14 1519 2101 35828911 35829486 3.280000e-159 571.0
34 TraesCS3B01G015200 chrUn 83.657 618 51 24 366 960 35827087 35827677 1.200000e-148 536.0
35 TraesCS3B01G015200 chrUn 91.463 164 8 4 1242 1404 35828183 35828341 1.370000e-53 220.0
36 TraesCS3B01G015200 chrUn 88.525 61 5 2 2092 2150 35829544 35829604 4.060000e-09 73.1
37 TraesCS3B01G015200 chr2B 95.798 357 9 4 1 351 211868779 211869135 3.280000e-159 571.0
38 TraesCS3B01G015200 chr2B 88.533 375 17 14 3 351 106165803 106166177 5.820000e-117 431.0
39 TraesCS3B01G015200 chr2B 83.727 381 23 16 3 351 664369853 664370226 1.020000e-84 324.0
40 TraesCS3B01G015200 chr2B 82.162 370 41 16 1009 1354 707377353 707377721 7.960000e-76 294.0
41 TraesCS3B01G015200 chr2B 73.961 361 62 23 12 350 731035353 731035703 1.850000e-22 117.0
42 TraesCS3B01G015200 chr2B 88.298 94 8 1 3 96 526382529 526382619 3.100000e-20 110.0
43 TraesCS3B01G015200 chr2B 90.361 83 5 1 12 94 602096166 602096087 4.000000e-19 106.0
44 TraesCS3B01G015200 chr1B 89.488 371 17 14 3 351 623676318 623676688 1.610000e-122 449.0
45 TraesCS3B01G015200 chr6B 88.736 364 16 14 3 351 217153908 217154261 3.500000e-114 422.0
46 TraesCS3B01G015200 chr6B 87.297 370 25 14 4 351 148479986 148479617 1.270000e-108 403.0
47 TraesCS3B01G015200 chr5B 86.849 365 25 13 3 351 569767966 569768323 1.280000e-103 387.0
48 TraesCS3B01G015200 chr5B 85.549 346 25 12 3 339 661909767 661909438 3.630000e-89 339.0
49 TraesCS3B01G015200 chr2A 89.157 249 21 3 1700 1948 719994275 719994517 3.680000e-79 305.0
50 TraesCS3B01G015200 chr2A 82.474 388 26 21 3 351 240480756 240480372 4.760000e-78 302.0
51 TraesCS3B01G015200 chr2A 89.231 195 21 0 1009 1203 719993378 719993572 8.130000e-61 244.0
52 TraesCS3B01G015200 chr7B 91.892 222 11 4 137 351 26646603 26646382 1.320000e-78 303.0
53 TraesCS3B01G015200 chr7B 81.694 366 22 20 3 351 169267216 169266879 2.250000e-66 263.0
54 TraesCS3B01G015200 chr2D 81.967 366 43 12 1010 1354 585860394 585860757 3.700000e-74 289.0
55 TraesCS3B01G015200 chr5A 87.500 112 14 0 1415 1526 699318673 699318784 2.380000e-26 130.0
56 TraesCS3B01G015200 chr5A 85.455 110 2 3 557 666 699313887 699313982 5.180000e-18 102.0


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 TraesCS3B01G015200 chr3B 6335915 6338852 2937 False 5426.000000 5426 100.000000 1 2938 1 chr3B.!!$F1 2937
1 TraesCS3B01G015200 chr3B 6405371 6407318 1947 False 3027.000000 3027 94.939000 361 2285 1 chr3B.!!$F2 1924
2 TraesCS3B01G015200 chr3B 6413028 6415777 2749 False 373.666667 593 97.159333 2280 2938 3 chr3B.!!$F3 658
3 TraesCS3B01G015200 chr3B 6467876 6470393 2517 False 350.025000 571 87.110500 366 2150 4 chr3B.!!$F4 1784
4 TraesCS3B01G015200 chr3B 6532307 6536721 4414 False 348.285714 715 88.064857 364 2938 7 chr3B.!!$F5 2574
5 TraesCS3B01G015200 chr3D 4111217 4112963 1746 False 2178.000000 2178 89.688000 361 2064 1 chr3D.!!$F1 1703
6 TraesCS3B01G015200 chr3D 4133932 4139898 5966 False 282.400000 597 87.518000 624 2654 10 chr3D.!!$F2 2030
7 TraesCS3B01G015200 chr3D 4153366 4157416 4050 False 208.000000 305 86.750000 2091 2722 2 chr3D.!!$F3 631
8 TraesCS3B01G015200 chr3A 9627284 9632458 5174 False 1083.333333 1339 89.912000 361 2938 3 chr3A.!!$F1 2577
9 TraesCS3B01G015200 chrUn 35827087 35829604 2517 False 350.025000 571 87.110500 366 2150 4 chrUn.!!$F1 1784
10 TraesCS3B01G015200 chr2A 719993378 719994517 1139 False 274.500000 305 89.194000 1009 1948 2 chr2A.!!$F1 939

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
75 76 0.104855 GGTGATGATGCTGGTAGCGA 59.895 55.0 0.0 0.0 46.26 4.93 F
80 81 0.108186 TGATGCTGGTAGCGACTTGG 60.108 55.0 0.0 0.0 46.26 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1498 4457 1.283613 TGATTTCTTACCACGGCCCAT 59.716 47.619 0.0 0.0 0.0 4.00 R
2297 9633 0.121197 TCCCAACCCTCCATCCTCTT 59.879 55.000 0.0 0.0 0.0 2.85 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
23 24 3.802948 GTTGGGACGACATATGACTCT 57.197 47.619 10.38 0.00 0.00 3.24
24 25 3.707793 GTTGGGACGACATATGACTCTC 58.292 50.000 10.38 3.95 0.00 3.20
25 26 3.012934 TGGGACGACATATGACTCTCA 57.987 47.619 10.38 6.43 0.00 3.27
26 27 3.361786 TGGGACGACATATGACTCTCAA 58.638 45.455 10.38 0.00 0.00 3.02
27 28 3.130516 TGGGACGACATATGACTCTCAAC 59.869 47.826 10.38 0.00 0.00 3.18
28 29 3.491104 GGGACGACATATGACTCTCAACC 60.491 52.174 10.38 2.91 0.00 3.77
29 30 3.381908 GGACGACATATGACTCTCAACCT 59.618 47.826 10.38 0.00 0.00 3.50
30 31 4.498345 GGACGACATATGACTCTCAACCTC 60.498 50.000 10.38 0.00 0.00 3.85
31 32 3.065510 ACGACATATGACTCTCAACCTCG 59.934 47.826 10.38 6.60 0.00 4.63
32 33 3.549019 CGACATATGACTCTCAACCTCGG 60.549 52.174 10.38 0.00 0.00 4.63
33 34 3.632333 ACATATGACTCTCAACCTCGGA 58.368 45.455 10.38 0.00 0.00 4.55
34 35 4.023980 ACATATGACTCTCAACCTCGGAA 58.976 43.478 10.38 0.00 0.00 4.30
35 36 4.098654 ACATATGACTCTCAACCTCGGAAG 59.901 45.833 10.38 0.00 0.00 3.46
36 37 2.287977 TGACTCTCAACCTCGGAAGA 57.712 50.000 0.00 0.00 39.12 2.87
37 38 1.887198 TGACTCTCAACCTCGGAAGAC 59.113 52.381 0.00 0.00 35.39 3.01
38 39 1.887198 GACTCTCAACCTCGGAAGACA 59.113 52.381 0.00 0.00 35.39 3.41
39 40 1.614413 ACTCTCAACCTCGGAAGACAC 59.386 52.381 0.00 0.00 35.39 3.67
40 41 0.966920 TCTCAACCTCGGAAGACACC 59.033 55.000 0.00 0.00 35.39 4.16
48 49 3.677527 GGAAGACACCGACGAGGA 58.322 61.111 8.56 0.00 45.00 3.71
49 50 2.190756 GGAAGACACCGACGAGGAT 58.809 57.895 8.56 0.00 45.00 3.24
50 51 0.179134 GGAAGACACCGACGAGGATG 60.179 60.000 8.56 5.92 45.00 3.51
51 52 0.809385 GAAGACACCGACGAGGATGA 59.191 55.000 8.56 0.00 45.00 2.92
52 53 1.405821 GAAGACACCGACGAGGATGAT 59.594 52.381 8.56 0.00 45.00 2.45
53 54 0.741326 AGACACCGACGAGGATGATG 59.259 55.000 8.56 0.00 45.00 3.07
54 55 0.738975 GACACCGACGAGGATGATGA 59.261 55.000 8.56 0.00 45.00 2.92
55 56 1.338337 GACACCGACGAGGATGATGAT 59.662 52.381 8.56 0.00 45.00 2.45
56 57 1.067669 ACACCGACGAGGATGATGATG 59.932 52.381 8.56 0.00 45.00 3.07
57 58 0.676184 ACCGACGAGGATGATGATGG 59.324 55.000 8.56 0.00 45.00 3.51
58 59 0.676184 CCGACGAGGATGATGATGGT 59.324 55.000 0.00 0.00 45.00 3.55
59 60 1.603931 CCGACGAGGATGATGATGGTG 60.604 57.143 0.00 0.00 45.00 4.17
60 61 1.338020 CGACGAGGATGATGATGGTGA 59.662 52.381 0.00 0.00 0.00 4.02
61 62 2.029560 CGACGAGGATGATGATGGTGAT 60.030 50.000 0.00 0.00 0.00 3.06
62 63 3.324117 GACGAGGATGATGATGGTGATG 58.676 50.000 0.00 0.00 0.00 3.07
63 64 2.967887 ACGAGGATGATGATGGTGATGA 59.032 45.455 0.00 0.00 0.00 2.92
64 65 3.581770 ACGAGGATGATGATGGTGATGAT 59.418 43.478 0.00 0.00 0.00 2.45
65 66 3.933332 CGAGGATGATGATGGTGATGATG 59.067 47.826 0.00 0.00 0.00 3.07
66 67 3.687125 AGGATGATGATGGTGATGATGC 58.313 45.455 0.00 0.00 0.00 3.91
67 68 3.330998 AGGATGATGATGGTGATGATGCT 59.669 43.478 0.00 0.00 0.00 3.79
68 69 3.440522 GGATGATGATGGTGATGATGCTG 59.559 47.826 0.00 0.00 0.00 4.41
69 70 2.858745 TGATGATGGTGATGATGCTGG 58.141 47.619 0.00 0.00 0.00 4.85
70 71 2.173996 TGATGATGGTGATGATGCTGGT 59.826 45.455 0.00 0.00 0.00 4.00
71 72 3.391955 TGATGATGGTGATGATGCTGGTA 59.608 43.478 0.00 0.00 0.00 3.25
72 73 3.480505 TGATGGTGATGATGCTGGTAG 57.519 47.619 0.00 0.00 0.00 3.18
73 74 2.149578 GATGGTGATGATGCTGGTAGC 58.850 52.381 0.00 0.00 42.82 3.58
74 75 0.179076 TGGTGATGATGCTGGTAGCG 60.179 55.000 0.00 0.00 46.26 4.26
75 76 0.104855 GGTGATGATGCTGGTAGCGA 59.895 55.000 0.00 0.00 46.26 4.93
76 77 1.212616 GTGATGATGCTGGTAGCGAC 58.787 55.000 0.00 0.00 46.26 5.19
77 78 1.114627 TGATGATGCTGGTAGCGACT 58.885 50.000 0.00 0.00 46.26 4.18
78 79 1.482182 TGATGATGCTGGTAGCGACTT 59.518 47.619 0.00 0.00 46.26 3.01
79 80 1.863454 GATGATGCTGGTAGCGACTTG 59.137 52.381 0.00 0.00 46.26 3.16
80 81 0.108186 TGATGCTGGTAGCGACTTGG 60.108 55.000 0.00 0.00 46.26 3.61
81 82 0.175760 GATGCTGGTAGCGACTTGGA 59.824 55.000 0.00 0.00 46.26 3.53
82 83 0.176680 ATGCTGGTAGCGACTTGGAG 59.823 55.000 0.00 0.00 46.26 3.86
83 84 1.185618 TGCTGGTAGCGACTTGGAGT 61.186 55.000 0.00 0.00 46.26 3.85
84 85 0.815734 GCTGGTAGCGACTTGGAGTA 59.184 55.000 0.00 0.00 0.00 2.59
85 86 1.202313 GCTGGTAGCGACTTGGAGTAG 60.202 57.143 0.00 0.00 0.00 2.57
86 87 2.093106 CTGGTAGCGACTTGGAGTAGT 58.907 52.381 0.00 0.00 0.00 2.73
87 88 2.492484 CTGGTAGCGACTTGGAGTAGTT 59.508 50.000 0.00 0.00 0.00 2.24
88 89 2.895404 TGGTAGCGACTTGGAGTAGTTT 59.105 45.455 0.00 0.00 0.00 2.66
89 90 3.057033 TGGTAGCGACTTGGAGTAGTTTC 60.057 47.826 0.00 0.00 0.00 2.78
90 91 3.193056 GGTAGCGACTTGGAGTAGTTTCT 59.807 47.826 0.00 0.00 0.00 2.52
91 92 4.397417 GGTAGCGACTTGGAGTAGTTTCTA 59.603 45.833 0.00 0.00 0.00 2.10
92 93 5.067544 GGTAGCGACTTGGAGTAGTTTCTAT 59.932 44.000 0.00 0.00 0.00 1.98
93 94 5.251601 AGCGACTTGGAGTAGTTTCTATC 57.748 43.478 0.00 0.00 0.00 2.08
94 95 4.951094 AGCGACTTGGAGTAGTTTCTATCT 59.049 41.667 0.00 0.00 0.00 1.98
95 96 6.120905 AGCGACTTGGAGTAGTTTCTATCTA 58.879 40.000 0.00 0.00 0.00 1.98
96 97 6.773685 AGCGACTTGGAGTAGTTTCTATCTAT 59.226 38.462 0.00 0.00 0.00 1.98
97 98 7.040961 AGCGACTTGGAGTAGTTTCTATCTATC 60.041 40.741 0.00 0.00 0.00 2.08
98 99 7.040961 GCGACTTGGAGTAGTTTCTATCTATCT 60.041 40.741 0.00 0.00 0.00 1.98
99 100 9.491675 CGACTTGGAGTAGTTTCTATCTATCTA 57.508 37.037 0.00 0.00 0.00 1.98
159 160 8.870879 TGTCGAACTATCTATCTATGTATGTCG 58.129 37.037 0.00 0.00 0.00 4.35
160 161 9.085250 GTCGAACTATCTATCTATGTATGTCGA 57.915 37.037 0.00 0.00 0.00 4.20
161 162 9.649167 TCGAACTATCTATCTATGTATGTCGAA 57.351 33.333 0.00 0.00 0.00 3.71
162 163 9.691795 CGAACTATCTATCTATGTATGTCGAAC 57.308 37.037 0.00 0.00 0.00 3.95
234 235 2.546821 AATGTTTTAAAAACGCGCGC 57.453 40.000 32.58 23.91 0.00 6.86
235 236 1.761206 ATGTTTTAAAAACGCGCGCT 58.239 40.000 32.58 17.02 0.00 5.92
236 237 0.840729 TGTTTTAAAAACGCGCGCTG 59.159 45.000 32.58 23.88 0.00 5.18
237 238 0.446625 GTTTTAAAAACGCGCGCTGC 60.447 50.000 32.58 10.17 41.47 5.25
238 239 0.866061 TTTTAAAAACGCGCGCTGCA 60.866 45.000 32.58 8.85 46.97 4.41
239 240 0.661780 TTTAAAAACGCGCGCTGCAT 60.662 45.000 32.58 15.25 46.97 3.96
240 241 0.661780 TTAAAAACGCGCGCTGCATT 60.662 45.000 32.58 19.52 46.97 3.56
241 242 0.661780 TAAAAACGCGCGCTGCATTT 60.662 45.000 32.58 23.43 41.45 2.32
242 243 1.948635 AAAACGCGCGCTGCATTTT 60.949 47.368 32.58 24.27 43.53 1.82
243 244 1.486644 AAAACGCGCGCTGCATTTTT 61.487 45.000 32.58 23.54 45.86 1.94
244 245 0.661780 AAACGCGCGCTGCATTTTTA 60.662 45.000 32.58 0.00 46.97 1.52
245 246 1.334288 AACGCGCGCTGCATTTTTAC 61.334 50.000 32.58 0.00 46.97 2.01
246 247 2.496257 CGCGCGCTGCATTTTTACC 61.496 57.895 30.48 0.00 46.97 2.85
247 248 2.496257 GCGCGCTGCATTTTTACCG 61.496 57.895 26.67 0.00 45.45 4.02
248 249 2.496257 CGCGCTGCATTTTTACCGC 61.496 57.895 5.56 0.00 38.23 5.68
249 250 2.496257 GCGCTGCATTTTTACCGCG 61.496 57.895 0.00 0.00 43.03 6.46
250 251 2.496257 CGCTGCATTTTTACCGCGC 61.496 57.895 0.00 0.00 34.05 6.86
251 252 2.158330 GCTGCATTTTTACCGCGCC 61.158 57.895 0.00 0.00 0.00 6.53
252 253 1.506262 CTGCATTTTTACCGCGCCT 59.494 52.632 0.00 0.00 0.00 5.52
253 254 0.798009 CTGCATTTTTACCGCGCCTG 60.798 55.000 0.00 0.00 0.00 4.85
254 255 2.158330 GCATTTTTACCGCGCCTGC 61.158 57.895 0.00 0.00 37.91 4.85
255 256 1.506262 CATTTTTACCGCGCCTGCT 59.494 52.632 0.00 0.00 39.65 4.24
256 257 0.798009 CATTTTTACCGCGCCTGCTG 60.798 55.000 0.00 0.00 39.65 4.41
257 258 1.933115 ATTTTTACCGCGCCTGCTGG 61.933 55.000 0.00 5.03 39.65 4.85
258 259 3.538785 TTTTACCGCGCCTGCTGGA 62.539 57.895 14.77 0.00 39.65 3.86
259 260 3.950794 TTTACCGCGCCTGCTGGAG 62.951 63.158 14.77 11.77 39.65 3.86
347 348 4.759096 GCGCGCGCCAAATCAGTT 62.759 61.111 42.83 0.00 34.56 3.16
348 349 2.126888 CGCGCGCCAAATCAGTTT 60.127 55.556 27.72 0.00 0.00 2.66
349 350 1.729131 CGCGCGCCAAATCAGTTTT 60.729 52.632 27.72 0.00 0.00 2.43
350 351 1.274798 CGCGCGCCAAATCAGTTTTT 61.275 50.000 27.72 0.00 0.00 1.94
351 352 0.161446 GCGCGCCAAATCAGTTTTTG 59.839 50.000 23.24 0.00 36.55 2.44
362 363 6.453092 CAAATCAGTTTTTGGAGATGCTCTT 58.547 36.000 0.00 0.00 33.81 2.85
463 469 6.102663 AGACCAGACAACTGATCGAATAAAG 58.897 40.000 0.00 0.00 46.03 1.85
550 561 3.129638 CACGTGGGGGTATACATTTTTGG 59.870 47.826 7.95 0.00 0.00 3.28
649 670 6.423182 TGAACTTATTGGGATGGACCTTTAG 58.577 40.000 0.00 0.00 38.98 1.85
669 690 8.579863 CCTTTAGAGAAAGTTTGATTCCACAAT 58.420 33.333 0.00 0.00 40.53 2.71
684 705 0.546122 ACAATAGGGGCGATGAAGCA 59.454 50.000 0.00 0.00 39.27 3.91
764 810 4.191544 CAGCCGATCAGAAATCAGGTAAA 58.808 43.478 0.00 0.00 0.00 2.01
768 814 5.992217 GCCGATCAGAAATCAGGTAAACTAT 59.008 40.000 0.00 0.00 0.00 2.12
770 816 7.210174 CCGATCAGAAATCAGGTAAACTATGA 58.790 38.462 0.00 0.00 0.00 2.15
788 834 6.344500 ACTATGACAACAGATTCCATGAGAC 58.656 40.000 0.00 0.00 0.00 3.36
820 875 3.021269 TCACATGTTAGTGTCGTCCAC 57.979 47.619 0.00 0.60 44.89 4.02
835 890 4.809426 GTCGTCCACTGGGTCTTATAATTG 59.191 45.833 0.00 0.00 34.93 2.32
837 892 4.570772 CGTCCACTGGGTCTTATAATTGTG 59.429 45.833 0.00 0.00 34.93 3.33
887 950 3.243301 TGAACCGTAGTCACACTCAAGAC 60.243 47.826 0.00 0.00 35.02 3.01
1044 1185 0.686441 TCATCGGGAGGATCGTTGGT 60.686 55.000 0.00 0.00 34.37 3.67
1215 1356 2.512745 AGTGCAAACGCGTCCACA 60.513 55.556 27.71 18.13 0.00 4.17
1227 1372 1.326548 GCGTCCACATTTCGGTCATAC 59.673 52.381 0.00 0.00 0.00 2.39
1366 1798 7.041372 CCATTGGTACGTGCTAAATTAAGCTAT 60.041 37.037 6.52 0.00 43.19 2.97
1367 1799 8.984764 CATTGGTACGTGCTAAATTAAGCTATA 58.015 33.333 6.52 0.00 43.19 1.31
1498 4457 2.832129 GACATACCAGAAGGAGGTGACA 59.168 50.000 0.00 0.00 40.26 3.58
1727 4988 1.596934 CACTGAGGTGGTGGCGTAT 59.403 57.895 0.00 0.00 39.59 3.06
2098 5365 3.323979 CCCTACTTGTGGCCGAATATACT 59.676 47.826 0.00 0.00 0.00 2.12
2099 5366 4.307432 CCTACTTGTGGCCGAATATACTG 58.693 47.826 0.00 0.00 0.00 2.74
2390 9752 3.379372 CGAATCATTCAGTTGGCATCCTT 59.621 43.478 0.00 0.00 0.00 3.36
2427 9789 6.038825 TGGTTCTGAAAGCTCGTTATTTCAAA 59.961 34.615 10.99 7.33 42.96 2.69
2534 9932 3.119637 ACCTTAATTAATGTGCACCACGC 60.120 43.478 15.69 0.00 37.14 5.34
2656 12112 8.323140 CAGAAACTTGAAACAATGTTCACAATC 58.677 33.333 15.02 11.52 37.24 2.67
2668 14172 2.093306 TCACAATCACACCGGATGAC 57.907 50.000 9.46 0.00 0.00 3.06
2743 14265 5.957842 TCGCATGGAACTTTACAAAGAAT 57.042 34.783 8.65 0.00 39.31 2.40
2745 14267 4.858692 CGCATGGAACTTTACAAAGAATGG 59.141 41.667 8.65 0.00 39.31 3.16
2914 14445 3.006940 CACCTGCTGGCGACTTATTAAA 58.993 45.455 9.95 0.00 36.63 1.52
2920 14451 5.398169 TGCTGGCGACTTATTAAAAATGTG 58.602 37.500 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.130516 TGAGAGTCATATGTCGTCCCAAC 59.869 47.826 1.90 0.00 0.00 3.77
4 5 3.361786 TGAGAGTCATATGTCGTCCCAA 58.638 45.455 1.90 0.00 0.00 4.12
5 6 3.012934 TGAGAGTCATATGTCGTCCCA 57.987 47.619 1.90 0.00 0.00 4.37
6 7 3.491104 GGTTGAGAGTCATATGTCGTCCC 60.491 52.174 1.90 0.00 0.00 4.46
7 8 3.381908 AGGTTGAGAGTCATATGTCGTCC 59.618 47.826 1.90 0.47 0.00 4.79
8 9 4.602995 GAGGTTGAGAGTCATATGTCGTC 58.397 47.826 1.90 1.08 0.00 4.20
9 10 3.065510 CGAGGTTGAGAGTCATATGTCGT 59.934 47.826 1.90 0.00 0.00 4.34
10 11 3.549019 CCGAGGTTGAGAGTCATATGTCG 60.549 52.174 1.90 0.63 0.00 4.35
11 12 3.632604 TCCGAGGTTGAGAGTCATATGTC 59.367 47.826 1.90 0.00 0.00 3.06
12 13 3.632333 TCCGAGGTTGAGAGTCATATGT 58.368 45.455 1.90 0.00 0.00 2.29
13 14 4.339530 TCTTCCGAGGTTGAGAGTCATATG 59.660 45.833 0.00 0.00 0.00 1.78
14 15 4.339814 GTCTTCCGAGGTTGAGAGTCATAT 59.660 45.833 0.00 0.00 0.00 1.78
15 16 3.695060 GTCTTCCGAGGTTGAGAGTCATA 59.305 47.826 0.00 0.00 0.00 2.15
16 17 2.494073 GTCTTCCGAGGTTGAGAGTCAT 59.506 50.000 0.00 0.00 0.00 3.06
17 18 1.887198 GTCTTCCGAGGTTGAGAGTCA 59.113 52.381 0.00 0.00 0.00 3.41
18 19 1.887198 TGTCTTCCGAGGTTGAGAGTC 59.113 52.381 0.00 0.00 0.00 3.36
19 20 1.614413 GTGTCTTCCGAGGTTGAGAGT 59.386 52.381 0.00 0.00 0.00 3.24
20 21 1.067495 GGTGTCTTCCGAGGTTGAGAG 60.067 57.143 0.00 0.00 0.00 3.20
21 22 0.966920 GGTGTCTTCCGAGGTTGAGA 59.033 55.000 0.00 0.00 0.00 3.27
22 23 3.516578 GGTGTCTTCCGAGGTTGAG 57.483 57.895 0.00 0.00 0.00 3.02
31 32 0.179134 CATCCTCGTCGGTGTCTTCC 60.179 60.000 0.00 0.00 0.00 3.46
32 33 0.809385 TCATCCTCGTCGGTGTCTTC 59.191 55.000 0.00 0.00 0.00 2.87
33 34 1.135139 CATCATCCTCGTCGGTGTCTT 59.865 52.381 0.00 0.00 0.00 3.01
34 35 0.741326 CATCATCCTCGTCGGTGTCT 59.259 55.000 0.00 0.00 0.00 3.41
35 36 0.738975 TCATCATCCTCGTCGGTGTC 59.261 55.000 0.00 0.00 0.00 3.67
36 37 1.067669 CATCATCATCCTCGTCGGTGT 59.932 52.381 0.00 0.00 0.00 4.16
37 38 1.603931 CCATCATCATCCTCGTCGGTG 60.604 57.143 0.00 0.00 0.00 4.94
38 39 0.676184 CCATCATCATCCTCGTCGGT 59.324 55.000 0.00 0.00 0.00 4.69
39 40 0.676184 ACCATCATCATCCTCGTCGG 59.324 55.000 0.00 0.00 0.00 4.79
40 41 1.338020 TCACCATCATCATCCTCGTCG 59.662 52.381 0.00 0.00 0.00 5.12
41 42 3.006217 TCATCACCATCATCATCCTCGTC 59.994 47.826 0.00 0.00 0.00 4.20
42 43 2.967887 TCATCACCATCATCATCCTCGT 59.032 45.455 0.00 0.00 0.00 4.18
43 44 3.672767 TCATCACCATCATCATCCTCG 57.327 47.619 0.00 0.00 0.00 4.63
44 45 3.690139 GCATCATCACCATCATCATCCTC 59.310 47.826 0.00 0.00 0.00 3.71
45 46 3.330998 AGCATCATCACCATCATCATCCT 59.669 43.478 0.00 0.00 0.00 3.24
46 47 3.440522 CAGCATCATCACCATCATCATCC 59.559 47.826 0.00 0.00 0.00 3.51
47 48 3.440522 CCAGCATCATCACCATCATCATC 59.559 47.826 0.00 0.00 0.00 2.92
48 49 3.181433 ACCAGCATCATCACCATCATCAT 60.181 43.478 0.00 0.00 0.00 2.45
49 50 2.173996 ACCAGCATCATCACCATCATCA 59.826 45.455 0.00 0.00 0.00 3.07
50 51 2.860009 ACCAGCATCATCACCATCATC 58.140 47.619 0.00 0.00 0.00 2.92
51 52 3.809678 GCTACCAGCATCATCACCATCAT 60.810 47.826 0.00 0.00 41.89 2.45
52 53 2.486013 GCTACCAGCATCATCACCATCA 60.486 50.000 0.00 0.00 41.89 3.07
53 54 2.149578 GCTACCAGCATCATCACCATC 58.850 52.381 0.00 0.00 41.89 3.51
54 55 1.541889 CGCTACCAGCATCATCACCAT 60.542 52.381 0.00 0.00 42.58 3.55
55 56 0.179076 CGCTACCAGCATCATCACCA 60.179 55.000 0.00 0.00 42.58 4.17
56 57 0.104855 TCGCTACCAGCATCATCACC 59.895 55.000 0.00 0.00 42.58 4.02
57 58 1.202463 AGTCGCTACCAGCATCATCAC 60.202 52.381 0.00 0.00 42.58 3.06
58 59 1.114627 AGTCGCTACCAGCATCATCA 58.885 50.000 0.00 0.00 42.58 3.07
59 60 1.863454 CAAGTCGCTACCAGCATCATC 59.137 52.381 0.00 0.00 42.58 2.92
60 61 1.473965 CCAAGTCGCTACCAGCATCAT 60.474 52.381 0.00 0.00 42.58 2.45
61 62 0.108186 CCAAGTCGCTACCAGCATCA 60.108 55.000 0.00 0.00 42.58 3.07
62 63 0.175760 TCCAAGTCGCTACCAGCATC 59.824 55.000 0.00 0.00 42.58 3.91
63 64 0.176680 CTCCAAGTCGCTACCAGCAT 59.823 55.000 0.00 0.00 42.58 3.79
64 65 1.185618 ACTCCAAGTCGCTACCAGCA 61.186 55.000 0.00 0.00 42.58 4.41
65 66 0.815734 TACTCCAAGTCGCTACCAGC 59.184 55.000 0.00 0.00 38.02 4.85
66 67 2.093106 ACTACTCCAAGTCGCTACCAG 58.907 52.381 0.00 0.00 0.00 4.00
67 68 2.211250 ACTACTCCAAGTCGCTACCA 57.789 50.000 0.00 0.00 0.00 3.25
68 69 3.193056 AGAAACTACTCCAAGTCGCTACC 59.807 47.826 0.00 0.00 0.00 3.18
69 70 4.437772 AGAAACTACTCCAAGTCGCTAC 57.562 45.455 0.00 0.00 0.00 3.58
70 71 6.120905 AGATAGAAACTACTCCAAGTCGCTA 58.879 40.000 0.00 0.00 0.00 4.26
71 72 4.951094 AGATAGAAACTACTCCAAGTCGCT 59.049 41.667 0.00 0.00 0.00 4.93
72 73 5.251601 AGATAGAAACTACTCCAAGTCGC 57.748 43.478 0.00 0.00 0.00 5.19
73 74 8.385898 AGATAGATAGAAACTACTCCAAGTCG 57.614 38.462 0.00 0.00 0.00 4.18
133 134 8.870879 CGACATACATAGATAGATAGTTCGACA 58.129 37.037 0.00 0.00 0.00 4.35
134 135 9.085250 TCGACATACATAGATAGATAGTTCGAC 57.915 37.037 0.00 0.00 0.00 4.20
135 136 9.649167 TTCGACATACATAGATAGATAGTTCGA 57.351 33.333 0.00 0.00 0.00 3.71
136 137 9.691795 GTTCGACATACATAGATAGATAGTTCG 57.308 37.037 0.00 0.00 0.00 3.95
212 213 3.714981 GCGCGCGTTTTTAAAACATTTTT 59.285 34.783 32.35 0.00 0.00 1.94
213 214 3.000423 AGCGCGCGTTTTTAAAACATTTT 60.000 34.783 32.35 0.00 0.00 1.82
214 215 2.536393 AGCGCGCGTTTTTAAAACATTT 59.464 36.364 32.35 0.00 0.00 2.32
215 216 2.097637 CAGCGCGCGTTTTTAAAACATT 60.098 40.909 32.35 0.00 0.00 2.71
216 217 1.450161 CAGCGCGCGTTTTTAAAACAT 59.550 42.857 32.35 0.00 0.00 2.71
217 218 0.840729 CAGCGCGCGTTTTTAAAACA 59.159 45.000 32.35 0.00 0.00 2.83
218 219 0.446625 GCAGCGCGCGTTTTTAAAAC 60.447 50.000 32.35 11.09 0.00 2.43
219 220 0.866061 TGCAGCGCGCGTTTTTAAAA 60.866 45.000 32.35 6.37 46.97 1.52
220 221 0.661780 ATGCAGCGCGCGTTTTTAAA 60.662 45.000 32.35 11.20 46.97 1.52
221 222 1.081774 ATGCAGCGCGCGTTTTTAA 60.082 47.368 32.35 12.88 46.97 1.52
222 223 2.558821 ATGCAGCGCGCGTTTTTA 59.441 50.000 32.35 14.01 46.97 1.52
227 228 1.795962 GTAAAAATGCAGCGCGCGT 60.796 52.632 32.35 15.53 46.97 6.01
228 229 2.496257 GGTAAAAATGCAGCGCGCG 61.496 57.895 28.44 28.44 46.97 6.86
229 230 2.496257 CGGTAAAAATGCAGCGCGC 61.496 57.895 26.66 26.66 42.89 6.86
230 231 3.661764 CGGTAAAAATGCAGCGCG 58.338 55.556 0.00 0.00 0.00 6.86
232 233 3.661764 CGCGGTAAAAATGCAGCG 58.338 55.556 0.00 0.00 41.92 5.18
233 234 2.158330 GGCGCGGTAAAAATGCAGC 61.158 57.895 8.83 0.00 0.00 5.25
234 235 0.798009 CAGGCGCGGTAAAAATGCAG 60.798 55.000 8.83 0.00 0.00 4.41
235 236 1.211449 CAGGCGCGGTAAAAATGCA 59.789 52.632 8.83 0.00 0.00 3.96
236 237 2.158330 GCAGGCGCGGTAAAAATGC 61.158 57.895 8.83 0.00 0.00 3.56
237 238 0.798009 CAGCAGGCGCGGTAAAAATG 60.798 55.000 8.83 0.00 45.49 2.32
238 239 1.506262 CAGCAGGCGCGGTAAAAAT 59.494 52.632 8.83 0.00 45.49 1.82
239 240 2.622011 CCAGCAGGCGCGGTAAAAA 61.622 57.895 8.83 0.00 45.49 1.94
240 241 3.053291 CCAGCAGGCGCGGTAAAA 61.053 61.111 8.83 0.00 45.49 1.52
241 242 3.950794 CTCCAGCAGGCGCGGTAAA 62.951 63.158 8.83 0.00 45.49 2.01
242 243 4.451150 CTCCAGCAGGCGCGGTAA 62.451 66.667 8.83 0.00 45.49 2.85
314 315 3.451894 GCCCATCGCCTGGTTTGG 61.452 66.667 0.00 0.14 44.30 3.28
315 316 3.814268 CGCCCATCGCCTGGTTTG 61.814 66.667 0.00 0.00 44.30 2.93
330 331 4.759096 AACTGATTTGGCGCGCGC 62.759 61.111 44.40 44.40 41.06 6.86
331 332 1.274798 AAAAACTGATTTGGCGCGCG 61.275 50.000 28.44 28.44 0.00 6.86
332 333 0.161446 CAAAAACTGATTTGGCGCGC 59.839 50.000 25.94 25.94 36.79 6.86
351 352 9.583756 CAACTGTTTGGTTGTAAGAGCATCTCC 62.584 44.444 0.00 0.00 42.34 3.71
352 353 6.785341 CAACTGTTTGGTTGTAAGAGCATCTC 60.785 42.308 0.00 0.00 42.34 2.75
353 354 5.009010 CAACTGTTTGGTTGTAAGAGCATCT 59.991 40.000 0.00 0.00 43.70 2.90
354 355 5.215160 CAACTGTTTGGTTGTAAGAGCATC 58.785 41.667 0.00 0.00 40.92 3.91
355 356 5.186996 CAACTGTTTGGTTGTAAGAGCAT 57.813 39.130 0.00 0.00 40.92 3.79
356 357 4.630894 CAACTGTTTGGTTGTAAGAGCA 57.369 40.909 0.00 0.00 40.92 4.26
381 382 5.513267 GGAAAGGGCAAAGAAGAAGAGAGTA 60.513 44.000 0.00 0.00 0.00 2.59
382 383 4.393834 GAAAGGGCAAAGAAGAAGAGAGT 58.606 43.478 0.00 0.00 0.00 3.24
383 384 3.755905 GGAAAGGGCAAAGAAGAAGAGAG 59.244 47.826 0.00 0.00 0.00 3.20
415 421 3.209410 AGACTTCCACAAGAGCAAACTG 58.791 45.455 0.00 0.00 33.34 3.16
490 500 3.603532 CTTGACAGCACATATGTGGACT 58.396 45.455 31.63 20.56 45.72 3.85
550 561 1.237285 ACGTGCTGGAGATTGCAACC 61.237 55.000 0.00 0.00 41.10 3.77
649 670 6.127619 CCCCTATTGTGGAATCAAACTTTCTC 60.128 42.308 0.00 0.00 0.00 2.87
669 690 1.070134 GTGTATGCTTCATCGCCCCTA 59.930 52.381 0.00 0.00 0.00 3.53
720 766 4.947147 ATGTGTTGCCGCCGGTGT 62.947 61.111 15.14 0.00 0.00 4.16
722 768 3.669344 CAATGTGTTGCCGCCGGT 61.669 61.111 4.45 0.00 0.00 5.28
744 790 4.192317 AGTTTACCTGATTTCTGATCGGC 58.808 43.478 0.00 0.00 0.00 5.54
764 810 6.344500 GTCTCATGGAATCTGTTGTCATAGT 58.656 40.000 0.00 0.00 0.00 2.12
768 814 3.006859 ACGTCTCATGGAATCTGTTGTCA 59.993 43.478 0.00 0.00 0.00 3.58
770 816 3.006859 TGACGTCTCATGGAATCTGTTGT 59.993 43.478 17.92 0.00 0.00 3.32
788 834 3.909957 CATGTGATGGCATGTGACG 57.090 52.632 3.81 0.00 40.81 4.35
820 875 7.777910 TCCCAATAACACAATTATAAGACCCAG 59.222 37.037 0.00 0.00 0.00 4.45
835 890 4.284485 GTGTGACGTTTTCCCAATAACAC 58.716 43.478 0.00 0.00 0.00 3.32
837 892 3.315749 TGGTGTGACGTTTTCCCAATAAC 59.684 43.478 0.00 0.00 0.00 1.89
972 1048 7.959175 TCCCACTACGTATGCTTATTAGATTT 58.041 34.615 0.00 0.00 0.00 2.17
1044 1185 1.866601 TCGAAGTAGTCAACGACGTCA 59.133 47.619 17.16 0.00 37.67 4.35
1105 1246 2.048503 CTCCGACCCAACCGTGAC 60.049 66.667 0.00 0.00 0.00 3.67
1204 1345 1.562575 GACCGAAATGTGGACGCGTT 61.563 55.000 15.53 0.00 0.00 4.84
1227 1372 4.155099 TGGACAAATAACTATGTGCAACGG 59.845 41.667 0.00 0.00 43.53 4.44
1366 1798 6.816640 AGTGCACGAATAATTGAAAGTAGCTA 59.183 34.615 12.01 0.00 0.00 3.32
1367 1799 5.643777 AGTGCACGAATAATTGAAAGTAGCT 59.356 36.000 12.01 0.00 0.00 3.32
1377 1820 3.613910 GCCCACAAAGTGCACGAATAATT 60.614 43.478 12.01 0.00 31.34 1.40
1498 4457 1.283613 TGATTTCTTACCACGGCCCAT 59.716 47.619 0.00 0.00 0.00 4.00
2296 9632 1.002857 CCCAACCCTCCATCCTCTTT 58.997 55.000 0.00 0.00 0.00 2.52
2297 9633 0.121197 TCCCAACCCTCCATCCTCTT 59.879 55.000 0.00 0.00 0.00 2.85
2298 9634 0.348370 ATCCCAACCCTCCATCCTCT 59.652 55.000 0.00 0.00 0.00 3.69
2299 9635 1.143889 GAATCCCAACCCTCCATCCTC 59.856 57.143 0.00 0.00 0.00 3.71
2301 9637 0.186143 GGAATCCCAACCCTCCATCC 59.814 60.000 0.00 0.00 0.00 3.51
2390 9752 6.042143 GCTTTCAGAACCATTTCACAAAGAA 58.958 36.000 10.19 0.00 36.04 2.52
2427 9789 5.661759 ACTACGGAAAGTAAAGGATCCATCT 59.338 40.000 15.82 3.40 34.45 2.90
2656 12112 0.522705 CGAGTACGTCATCCGGTGTG 60.523 60.000 0.00 1.81 42.24 3.82
2668 14172 4.144051 GCAATTTGTTTTGTGTCGAGTACG 59.856 41.667 0.00 0.00 41.26 3.67
2914 14445 3.192001 CAGCACCAATCACTAGCACATTT 59.808 43.478 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.