Multiple sequence alignment - TraesCS4A01G162400

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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 TraesCS4A01G162400 chr4A 100.000 4365 0 0 1 4365 357263996 357259632 0.000000e+00 8061.0
1 TraesCS4A01G162400 chr4A 83.065 868 89 25 3504 4336 141113091 141113935 0.000000e+00 736.0
2 TraesCS4A01G162400 chr4A 91.089 404 25 2 3860 4252 713135622 713135219 1.790000e-148 536.0
3 TraesCS4A01G162400 chr2A 96.979 3012 79 9 1223 4227 64383451 64386457 0.000000e+00 5048.0
4 TraesCS4A01G162400 chr2A 93.981 1030 61 1 200 1228 64377104 64378133 0.000000e+00 1557.0
5 TraesCS4A01G162400 chr2A 88.581 578 57 6 3505 4080 744538280 744538850 0.000000e+00 693.0
6 TraesCS4A01G162400 chr2A 89.141 396 35 8 3011 3405 522504529 522504141 1.820000e-133 486.0
7 TraesCS4A01G162400 chr2A 84.858 317 32 5 4031 4332 744538841 744539156 5.480000e-79 305.0
8 TraesCS4A01G162400 chr2A 98.333 60 1 0 1 60 548445168 548445227 5.970000e-19 106.0
9 TraesCS4A01G162400 chr6B 94.900 3216 145 11 202 3405 91029637 91026429 0.000000e+00 5012.0
10 TraesCS4A01G162400 chr6B 94.602 2816 111 10 599 3405 91035213 91032430 0.000000e+00 4320.0
11 TraesCS4A01G162400 chr6B 96.058 964 32 4 3405 4364 91031740 91030779 0.000000e+00 1565.0
12 TraesCS4A01G162400 chr6B 95.426 962 42 2 3405 4365 91025739 91024779 0.000000e+00 1531.0
13 TraesCS4A01G162400 chr6B 98.113 53 1 0 3 55 605824101 605824049 4.650000e-15 93.5
14 TraesCS4A01G162400 chr5B 94.918 2263 96 8 387 2645 35424190 35426437 0.000000e+00 3524.0
15 TraesCS4A01G162400 chr5B 88.689 2166 167 26 801 2906 362138101 362140248 0.000000e+00 2571.0
16 TraesCS4A01G162400 chr5B 96.237 744 20 2 2669 3405 35426433 35427175 0.000000e+00 1212.0
17 TraesCS4A01G162400 chr5B 92.623 488 31 4 2922 3405 362141385 362141871 0.000000e+00 697.0
18 TraesCS4A01G162400 chr5B 79.076 779 104 37 1842 2570 335413803 335414572 8.490000e-132 481.0
19 TraesCS4A01G162400 chr5B 98.930 187 0 2 3405 3591 35427865 35428049 2.520000e-87 333.0
20 TraesCS4A01G162400 chr5B 87.329 292 32 3 844 1135 455275779 455276065 3.250000e-86 329.0
21 TraesCS4A01G162400 chr2D 92.759 2182 101 16 1041 3169 70020277 70022454 0.000000e+00 3101.0
22 TraesCS4A01G162400 chr2D 91.142 508 29 4 3751 4242 70022450 70022957 0.000000e+00 675.0
23 TraesCS4A01G162400 chr2D 89.121 239 21 5 202 437 7049873 7050109 4.270000e-75 292.0
24 TraesCS4A01G162400 chr2B 90.918 1960 134 17 477 2409 773901561 773903503 0.000000e+00 2593.0
25 TraesCS4A01G162400 chr2B 95.670 970 36 5 2440 3405 773907649 773908616 0.000000e+00 1554.0
26 TraesCS4A01G162400 chr2B 93.233 931 51 7 3407 4327 773909153 773910081 0.000000e+00 1360.0
27 TraesCS4A01G162400 chr2B 94.545 55 3 0 1 55 285449575 285449629 7.780000e-13 86.1
28 TraesCS4A01G162400 chr3B 89.025 1221 91 19 2226 3405 270856199 270857417 0.000000e+00 1472.0
29 TraesCS4A01G162400 chr3B 95.804 143 6 0 61 203 194618692 194618550 9.440000e-57 231.0
30 TraesCS4A01G162400 chr3B 92.929 99 7 0 3405 3503 270858104 270858202 1.270000e-30 145.0
31 TraesCS4A01G162400 chr3B 96.364 55 1 1 1 55 502392468 502392415 6.010000e-14 89.8
32 TraesCS4A01G162400 chr7D 93.814 970 51 8 2443 3405 277554492 277555459 0.000000e+00 1450.0
33 TraesCS4A01G162400 chr7D 92.627 651 47 1 848 1498 277545538 277546187 0.000000e+00 935.0
34 TraesCS4A01G162400 chr7D 89.608 510 27 3 1920 2414 277549200 277549698 3.710000e-175 625.0
35 TraesCS4A01G162400 chr7D 86.768 461 32 2 1490 1921 277548616 277549076 1.820000e-133 486.0
36 TraesCS4A01G162400 chr7D 86.981 361 40 4 477 836 277523486 277523840 2.450000e-107 399.0
37 TraesCS4A01G162400 chr7D 95.804 143 6 0 61 203 163713602 163713460 9.440000e-57 231.0
38 TraesCS4A01G162400 chr7D 95.172 145 7 0 59 203 169065820 169065964 3.400000e-56 230.0
39 TraesCS4A01G162400 chr7D 87.879 99 0 3 3405 3503 277556149 277556235 5.970000e-19 106.0
40 TraesCS4A01G162400 chr3A 88.471 850 71 19 3503 4332 718383678 718382836 0.000000e+00 1002.0
41 TraesCS4A01G162400 chr5A 80.830 892 106 35 3496 4350 11251668 11250805 1.320000e-179 640.0
42 TraesCS4A01G162400 chr6A 81.780 719 87 23 3504 4204 428722612 428723304 2.950000e-156 562.0
43 TraesCS4A01G162400 chr1A 81.085 719 95 23 3508 4204 52537672 52536973 1.790000e-148 536.0
44 TraesCS4A01G162400 chr1A 90.714 280 24 2 202 480 412040468 412040190 5.330000e-99 372.0
45 TraesCS4A01G162400 chr1A 88.070 285 29 5 201 483 45650648 45650367 2.520000e-87 333.0
46 TraesCS4A01G162400 chr1A 95.804 143 6 0 61 203 482404480 482404622 9.440000e-57 231.0
47 TraesCS4A01G162400 chr4B 89.448 417 42 2 719 1135 165816122 165816536 3.870000e-145 525.0
48 TraesCS4A01G162400 chr4B 96.226 53 2 0 3 55 503937298 503937350 2.160000e-13 87.9
49 TraesCS4A01G162400 chr4B 96.226 53 2 0 3 55 503997388 503997440 2.160000e-13 87.9
50 TraesCS4A01G162400 chr4B 94.545 55 3 0 1 55 17180621 17180675 7.780000e-13 86.1
51 TraesCS4A01G162400 chr3D 87.167 413 46 5 724 1135 308779597 308779191 3.080000e-126 462.0
52 TraesCS4A01G162400 chr6D 92.199 282 19 2 202 480 413771160 413771441 3.160000e-106 396.0
53 TraesCS4A01G162400 chrUn 88.070 285 29 5 201 483 324407747 324408028 2.520000e-87 333.0
54 TraesCS4A01G162400 chrUn 84.892 278 36 6 202 474 297297529 297297805 4.300000e-70 276.0
55 TraesCS4A01G162400 chr7B 84.892 278 36 6 202 474 206268842 206269118 4.300000e-70 276.0
56 TraesCS4A01G162400 chr7B 94.643 56 3 0 1 56 35626267 35626322 2.160000e-13 87.9
57 TraesCS4A01G162400 chr5D 95.862 145 6 0 59 203 393742911 393743055 7.300000e-58 235.0
58 TraesCS4A01G162400 chr5D 95.172 145 7 0 59 203 116901975 116901831 3.400000e-56 230.0
59 TraesCS4A01G162400 chr5D 94.558 147 8 0 57 203 232129784 232129638 1.220000e-55 228.0
60 TraesCS4A01G162400 chr5D 92.810 153 11 0 51 203 337502634 337502482 5.680000e-54 222.0
61 TraesCS4A01G162400 chr1D 95.139 144 7 0 60 203 349846362 349846219 1.220000e-55 228.0
62 TraesCS4A01G162400 chr1B 94.915 59 3 0 2 60 45352719 45352661 4.650000e-15 93.5


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 TraesCS4A01G162400 chr4A 357259632 357263996 4364 True 8061.000000 8061 100.000000 1 4365 1 chr4A.!!$R1 4364
1 TraesCS4A01G162400 chr4A 141113091 141113935 844 False 736.000000 736 83.065000 3504 4336 1 chr4A.!!$F1 832
2 TraesCS4A01G162400 chr2A 64383451 64386457 3006 False 5048.000000 5048 96.979000 1223 4227 1 chr2A.!!$F2 3004
3 TraesCS4A01G162400 chr2A 64377104 64378133 1029 False 1557.000000 1557 93.981000 200 1228 1 chr2A.!!$F1 1028
4 TraesCS4A01G162400 chr2A 744538280 744539156 876 False 499.000000 693 86.719500 3505 4332 2 chr2A.!!$F4 827
5 TraesCS4A01G162400 chr6B 91024779 91035213 10434 True 3107.000000 5012 95.246500 202 4365 4 chr6B.!!$R2 4163
6 TraesCS4A01G162400 chr5B 35424190 35428049 3859 False 1689.666667 3524 96.695000 387 3591 3 chr5B.!!$F3 3204
7 TraesCS4A01G162400 chr5B 362138101 362141871 3770 False 1634.000000 2571 90.656000 801 3405 2 chr5B.!!$F4 2604
8 TraesCS4A01G162400 chr5B 335413803 335414572 769 False 481.000000 481 79.076000 1842 2570 1 chr5B.!!$F1 728
9 TraesCS4A01G162400 chr2D 70020277 70022957 2680 False 1888.000000 3101 91.950500 1041 4242 2 chr2D.!!$F2 3201
10 TraesCS4A01G162400 chr2B 773901561 773903503 1942 False 2593.000000 2593 90.918000 477 2409 1 chr2B.!!$F2 1932
11 TraesCS4A01G162400 chr2B 773907649 773910081 2432 False 1457.000000 1554 94.451500 2440 4327 2 chr2B.!!$F3 1887
12 TraesCS4A01G162400 chr3B 270856199 270858202 2003 False 808.500000 1472 90.977000 2226 3503 2 chr3B.!!$F1 1277
13 TraesCS4A01G162400 chr7D 277554492 277556235 1743 False 778.000000 1450 90.846500 2443 3503 2 chr7D.!!$F4 1060
14 TraesCS4A01G162400 chr7D 277545538 277549698 4160 False 682.000000 935 89.667667 848 2414 3 chr7D.!!$F3 1566
15 TraesCS4A01G162400 chr3A 718382836 718383678 842 True 1002.000000 1002 88.471000 3503 4332 1 chr3A.!!$R1 829
16 TraesCS4A01G162400 chr5A 11250805 11251668 863 True 640.000000 640 80.830000 3496 4350 1 chr5A.!!$R1 854
17 TraesCS4A01G162400 chr6A 428722612 428723304 692 False 562.000000 562 81.780000 3504 4204 1 chr6A.!!$F1 700
18 TraesCS4A01G162400 chr1A 52536973 52537672 699 True 536.000000 536 81.085000 3508 4204 1 chr1A.!!$R2 696

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
192 193 0.029834 GTGTCAAGTGCCAGTTGCTG 59.970 55.000 7.41 0.0 42.0 4.41 F
716 6109 0.107897 AACATACAATCTCGCCGCCA 60.108 50.000 0.00 0.0 0.0 5.69 F
1082 6475 0.035739 TTTCCCTACTCCCGTGCAAC 59.964 55.000 0.00 0.0 0.0 4.17 F
2220 10239 2.047274 CATCCAACCGACGTGCCT 60.047 61.111 0.00 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1063 6456 0.035739 GTTGCACGGGAGTAGGGAAA 59.964 55.000 0.00 0.00 44.67 3.13 R
2142 10142 1.608336 CCACCCGTGTACTCCTCCA 60.608 63.158 0.00 0.00 0.00 3.86 R
2863 10935 2.828549 CACGGTTAGGCATGCCCC 60.829 66.667 33.14 24.81 36.58 5.80 R
4058 14005 0.685458 GCAGAATCCAATGCCCAGGT 60.685 55.000 0.00 0.00 36.41 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
31 32 9.504708 AATTGAGAATTATTTTTGAACATGGCA 57.495 25.926 0.00 0.00 0.00 4.92
32 33 8.899427 TTGAGAATTATTTTTGAACATGGCAA 57.101 26.923 0.00 0.00 0.00 4.52
33 34 8.537049 TGAGAATTATTTTTGAACATGGCAAG 57.463 30.769 0.00 0.00 0.00 4.01
35 36 7.678837 AGAATTATTTTTGAACATGGCAAGGA 58.321 30.769 0.00 0.00 0.00 3.36
36 37 8.156165 AGAATTATTTTTGAACATGGCAAGGAA 58.844 29.630 0.00 1.57 0.00 3.36
37 38 8.688747 AATTATTTTTGAACATGGCAAGGAAA 57.311 26.923 0.00 0.89 0.00 3.13
38 39 8.688747 ATTATTTTTGAACATGGCAAGGAAAA 57.311 26.923 0.00 0.22 0.00 2.29
40 41 4.751767 TTTGAACATGGCAAGGAAAAGT 57.248 36.364 0.00 0.00 0.00 2.66
41 42 4.751767 TTGAACATGGCAAGGAAAAGTT 57.248 36.364 0.00 0.00 0.00 2.66
42 43 4.751767 TGAACATGGCAAGGAAAAGTTT 57.248 36.364 0.00 0.00 0.00 2.66
43 44 5.096443 TGAACATGGCAAGGAAAAGTTTT 57.904 34.783 0.00 0.00 0.00 2.43
52 53 6.558771 GCAAGGAAAAGTTTTGCCATATTT 57.441 33.333 15.37 1.42 40.89 1.40
53 54 6.372981 GCAAGGAAAAGTTTTGCCATATTTG 58.627 36.000 15.37 13.32 40.89 2.32
54 55 6.204495 GCAAGGAAAAGTTTTGCCATATTTGA 59.796 34.615 15.37 0.00 40.89 2.69
55 56 7.571798 GCAAGGAAAAGTTTTGCCATATTTGAG 60.572 37.037 15.37 0.00 40.89 3.02
56 57 7.066307 AGGAAAAGTTTTGCCATATTTGAGT 57.934 32.000 15.37 0.00 38.42 3.41
57 58 8.189119 AGGAAAAGTTTTGCCATATTTGAGTA 57.811 30.769 15.37 0.00 38.42 2.59
58 59 8.646900 AGGAAAAGTTTTGCCATATTTGAGTAA 58.353 29.630 15.37 0.00 38.42 2.24
59 60 8.925700 GGAAAAGTTTTGCCATATTTGAGTAAG 58.074 33.333 5.36 0.00 35.80 2.34
60 61 9.476202 GAAAAGTTTTGCCATATTTGAGTAAGT 57.524 29.630 5.36 0.00 0.00 2.24
62 63 7.759489 AGTTTTGCCATATTTGAGTAAGTGA 57.241 32.000 0.00 0.00 0.00 3.41
64 65 9.461312 AGTTTTGCCATATTTGAGTAAGTGATA 57.539 29.630 0.00 0.00 0.00 2.15
66 67 7.477144 TTGCCATATTTGAGTAAGTGATACG 57.523 36.000 0.00 0.00 39.62 3.06
68 69 5.107065 GCCATATTTGAGTAAGTGATACGCC 60.107 44.000 0.00 0.00 39.62 5.68
69 70 6.223852 CCATATTTGAGTAAGTGATACGCCT 58.776 40.000 0.00 0.00 39.62 5.52
70 71 6.706270 CCATATTTGAGTAAGTGATACGCCTT 59.294 38.462 0.00 0.00 39.62 4.35
71 72 7.095607 CCATATTTGAGTAAGTGATACGCCTTC 60.096 40.741 0.00 0.00 39.62 3.46
72 73 4.794278 TTGAGTAAGTGATACGCCTTCA 57.206 40.909 0.00 0.00 39.62 3.02
73 74 4.794278 TGAGTAAGTGATACGCCTTCAA 57.206 40.909 0.00 0.00 39.62 2.69
75 76 4.021807 TGAGTAAGTGATACGCCTTCAACA 60.022 41.667 0.00 0.00 39.62 3.33
76 77 5.086104 AGTAAGTGATACGCCTTCAACAT 57.914 39.130 0.00 0.00 39.62 2.71
77 78 6.127563 TGAGTAAGTGATACGCCTTCAACATA 60.128 38.462 0.00 0.00 39.62 2.29
80 81 5.537300 AGTGATACGCCTTCAACATATCT 57.463 39.130 0.00 0.00 0.00 1.98
83 84 8.349568 AGTGATACGCCTTCAACATATCTATA 57.650 34.615 0.00 0.00 0.00 1.31
84 85 8.803235 AGTGATACGCCTTCAACATATCTATAA 58.197 33.333 0.00 0.00 0.00 0.98
85 86 9.419297 GTGATACGCCTTCAACATATCTATAAA 57.581 33.333 0.00 0.00 0.00 1.40
175 176 9.661563 TTTTGGTACTAACCTATTGACATAGTG 57.338 33.333 0.00 0.00 46.91 2.74
176 177 7.966339 TGGTACTAACCTATTGACATAGTGT 57.034 36.000 0.00 0.00 46.91 3.55
187 188 3.045601 GACATAGTGTCAAGTGCCAGT 57.954 47.619 5.28 0.00 46.22 4.00
188 189 3.403038 GACATAGTGTCAAGTGCCAGTT 58.597 45.455 5.28 0.00 46.22 3.16
189 190 3.141398 ACATAGTGTCAAGTGCCAGTTG 58.859 45.455 5.90 5.90 0.00 3.16
190 191 1.593196 TAGTGTCAAGTGCCAGTTGC 58.407 50.000 7.41 3.94 41.77 4.17
192 193 0.029834 GTGTCAAGTGCCAGTTGCTG 59.970 55.000 7.41 0.00 42.00 4.41
195 196 1.134946 GTCAAGTGCCAGTTGCTGTTT 59.865 47.619 7.41 0.00 42.00 2.83
196 197 1.824230 TCAAGTGCCAGTTGCTGTTTT 59.176 42.857 7.41 0.00 42.00 2.43
197 198 2.233431 TCAAGTGCCAGTTGCTGTTTTT 59.767 40.909 7.41 0.00 42.00 1.94
252 5628 2.147958 AGTCTGCGCGGTTTATTTTCA 58.852 42.857 17.37 0.00 0.00 2.69
281 5657 2.575921 TTCATCATCCTCCCACCTCT 57.424 50.000 0.00 0.00 0.00 3.69
329 5705 2.292267 CGTTAACTCGCTACCCTCCTA 58.708 52.381 3.71 0.00 0.00 2.94
407 5785 4.335647 CTCCACCGCCAACCAGCT 62.336 66.667 0.00 0.00 0.00 4.24
411 5789 1.221840 CACCGCCAACCAGCTCTAT 59.778 57.895 0.00 0.00 0.00 1.98
462 5840 1.391933 CGACCGATCCATCCCTGTGA 61.392 60.000 0.00 0.00 0.00 3.58
465 5843 1.676678 CCGATCCATCCCTGTGACGT 61.677 60.000 0.00 0.00 0.00 4.34
506 5884 3.866582 CCTCCTCCGCCACCATCC 61.867 72.222 0.00 0.00 0.00 3.51
507 5885 2.765807 CTCCTCCGCCACCATCCT 60.766 66.667 0.00 0.00 0.00 3.24
508 5886 1.457643 CTCCTCCGCCACCATCCTA 60.458 63.158 0.00 0.00 0.00 2.94
515 5894 0.474184 CGCCACCATCCTATTCCCTT 59.526 55.000 0.00 0.00 0.00 3.95
528 5907 0.909610 TTCCCTTCGCTCCCATCTGT 60.910 55.000 0.00 0.00 0.00 3.41
536 5915 1.109920 GCTCCCATCTGTCGCCTCTA 61.110 60.000 0.00 0.00 0.00 2.43
664 6043 2.233566 TGCCCTGCATCTGGTTCCT 61.234 57.895 0.00 0.00 31.71 3.36
667 6046 1.500474 CCCTGCATCTGGTTCCTCTA 58.500 55.000 0.00 0.00 0.00 2.43
678 6057 0.683504 GTTCCTCTACGCTCCCCTCA 60.684 60.000 0.00 0.00 0.00 3.86
700 6079 1.299648 CCCTTCATCGCCTCCAACA 59.700 57.895 0.00 0.00 0.00 3.33
716 6109 0.107897 AACATACAATCTCGCCGCCA 60.108 50.000 0.00 0.00 0.00 5.69
766 6159 2.464459 GCCTCCATCGCGTTCCTTG 61.464 63.158 5.77 0.00 0.00 3.61
822 6215 0.978146 AGCTATGGTTCTCACCCGCT 60.978 55.000 0.00 0.00 43.49 5.52
838 6231 4.711949 CTGCCGCTTCCCTGCTGT 62.712 66.667 0.00 0.00 0.00 4.40
842 6235 1.003839 CCGCTTCCCTGCTGTTACA 60.004 57.895 0.00 0.00 0.00 2.41
869 6262 1.811266 CGATGCCCTCCACGAACAG 60.811 63.158 0.00 0.00 0.00 3.16
908 6301 1.201429 GGAAGAGCAAGAGGGGGTCA 61.201 60.000 0.00 0.00 35.30 4.02
969 6362 0.461163 CGGTGATGGTATTGTGGCGA 60.461 55.000 0.00 0.00 0.00 5.54
1044 6437 1.808512 CGTGCCAACAAGACAGGTACA 60.809 52.381 0.00 0.00 37.82 2.90
1081 6474 0.988832 ATTTCCCTACTCCCGTGCAA 59.011 50.000 0.00 0.00 0.00 4.08
1082 6475 0.035739 TTTCCCTACTCCCGTGCAAC 59.964 55.000 0.00 0.00 0.00 4.17
1235 6629 3.446516 TGTTGTGCTATTATGCATTGCCA 59.553 39.130 3.54 3.20 45.23 4.92
1269 6663 6.961131 TCCGGGTGAAGTAATATATTGGGATA 59.039 38.462 8.28 0.00 0.00 2.59
1426 6828 2.261671 CTAGCCACGTTCTGCCGT 59.738 61.111 0.00 0.00 42.87 5.68
1503 9342 6.480763 TCTGGTGATAAAAATGCTGAAGGTA 58.519 36.000 0.00 0.00 0.00 3.08
1543 9382 3.679824 ATATGCGGTTCTTACCTAGCC 57.320 47.619 0.00 0.00 42.66 3.93
1877 9746 2.887152 AGGTTTCACAGACCATTTCAGC 59.113 45.455 0.00 0.00 39.71 4.26
1888 9757 8.045507 CACAGACCATTTCAGCCATAGATATAT 58.954 37.037 0.00 0.00 0.00 0.86
2108 10108 6.579666 AGTGTTCTATTTGTGCATTGTGAT 57.420 33.333 0.00 0.00 0.00 3.06
2139 10139 3.130516 TCTTGGATAACAGACGAAGCGAT 59.869 43.478 0.00 0.00 0.00 4.58
2142 10142 5.196341 TGGATAACAGACGAAGCGATATT 57.804 39.130 0.00 0.00 0.00 1.28
2220 10239 2.047274 CATCCAACCGACGTGCCT 60.047 61.111 0.00 0.00 0.00 4.75
2387 10434 2.228822 CTCGCTTGTATTGCAGGGTTTT 59.771 45.455 0.00 0.00 0.00 2.43
2389 10436 2.595386 GCTTGTATTGCAGGGTTTTCG 58.405 47.619 0.00 0.00 0.00 3.46
2391 10438 3.189702 GCTTGTATTGCAGGGTTTTCGTA 59.810 43.478 0.00 0.00 0.00 3.43
2414 10461 4.161565 AGGAACATAATTCAGTGTCCGCTA 59.838 41.667 0.00 0.00 0.00 4.26
2906 10978 7.654116 GCCTAGGACAATATCTGAAACTTACTC 59.346 40.741 14.75 0.00 0.00 2.59
2907 10979 8.696374 CCTAGGACAATATCTGAAACTTACTCA 58.304 37.037 1.05 0.00 0.00 3.41
2936 12129 5.505780 TGCCTAACTATGTGCCAAACTAAT 58.494 37.500 0.00 0.00 0.00 1.73
3023 12218 4.928020 AGGCTTTAAGTTTCAGCTACGTAC 59.072 41.667 0.00 0.00 33.76 3.67
3027 12222 7.127686 GCTTTAAGTTTCAGCTACGTACAAAA 58.872 34.615 0.00 0.00 0.00 2.44
3036 12234 8.815141 TTCAGCTACGTACAAAATAACACTAA 57.185 30.769 0.00 0.00 0.00 2.24
3667 13570 1.614241 CCCAGCTAGCCCGTTACTGT 61.614 60.000 12.13 0.00 0.00 3.55
3733 13656 3.915437 TTCTTGTCCTTTCGCATTTCC 57.085 42.857 0.00 0.00 0.00 3.13
3845 13779 1.076332 GATTTCCGTTCCAGTGTCGG 58.924 55.000 10.90 10.90 44.76 4.79
3901 13835 3.692690 TCCCCCTTGAATTTCGTTTAGG 58.307 45.455 0.00 0.00 0.00 2.69
3917 13851 7.102847 TCGTTTAGGTCTTTTGGTTTGATTT 57.897 32.000 0.00 0.00 0.00 2.17
4022 13969 2.557056 GGTAGTAGCATGGATGTAGCGA 59.443 50.000 0.00 0.00 0.00 4.93
4058 14005 4.340950 CCCTGTTGGTTTTCTTTCTGCTAA 59.659 41.667 0.00 0.00 0.00 3.09
4173 14177 6.098124 ACTGTTCAATTTCAGTGGAATTTCCA 59.902 34.615 14.24 14.24 42.30 3.53
4220 14235 4.646945 TGCAATTTCCAGAGTTAACCACAA 59.353 37.500 0.88 0.00 0.00 3.33
4265 14280 6.016610 TCTGTGATTTTTAGTTTACAGCCACC 60.017 38.462 0.00 0.00 36.41 4.61
4285 14300 6.020201 GCCACCGCAATTACAATGTAATTTAC 60.020 38.462 24.05 18.55 30.81 2.01
4287 14302 6.962116 CACCGCAATTACAATGTAATTTACGA 59.038 34.615 31.36 6.83 31.22 3.43
4288 14303 7.163520 CACCGCAATTACAATGTAATTTACGAG 59.836 37.037 31.36 25.93 31.22 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.504708 TGCCATGTTCAAAAATAATTCTCAATT 57.495 25.926 0.00 0.00 34.90 2.32
6 7 9.504708 TTGCCATGTTCAAAAATAATTCTCAAT 57.495 25.926 0.00 0.00 0.00 2.57
7 8 8.899427 TTGCCATGTTCAAAAATAATTCTCAA 57.101 26.923 0.00 0.00 0.00 3.02
10 11 7.678837 TCCTTGCCATGTTCAAAAATAATTCT 58.321 30.769 0.00 0.00 0.00 2.40
12 13 8.688747 TTTCCTTGCCATGTTCAAAAATAATT 57.311 26.923 0.00 0.00 0.00 1.40
13 14 8.688747 TTTTCCTTGCCATGTTCAAAAATAAT 57.311 26.923 0.00 0.00 0.00 1.28
14 15 7.772757 ACTTTTCCTTGCCATGTTCAAAAATAA 59.227 29.630 0.00 0.00 0.00 1.40
15 16 7.278875 ACTTTTCCTTGCCATGTTCAAAAATA 58.721 30.769 0.00 0.00 0.00 1.40
16 17 6.121590 ACTTTTCCTTGCCATGTTCAAAAAT 58.878 32.000 0.00 0.00 0.00 1.82
17 18 5.495640 ACTTTTCCTTGCCATGTTCAAAAA 58.504 33.333 0.00 0.00 0.00 1.94
20 21 4.751767 AACTTTTCCTTGCCATGTTCAA 57.248 36.364 0.00 0.00 0.00 2.69
21 22 4.751767 AAACTTTTCCTTGCCATGTTCA 57.248 36.364 0.00 0.00 0.00 3.18
22 23 4.260743 GCAAAACTTTTCCTTGCCATGTTC 60.261 41.667 0.00 0.00 39.62 3.18
23 24 3.627123 GCAAAACTTTTCCTTGCCATGTT 59.373 39.130 0.00 0.00 39.62 2.71
24 25 3.205338 GCAAAACTTTTCCTTGCCATGT 58.795 40.909 0.00 0.00 39.62 3.21
30 31 7.442062 ACTCAAATATGGCAAAACTTTTCCTTG 59.558 33.333 0.00 0.00 0.00 3.61
31 32 7.508687 ACTCAAATATGGCAAAACTTTTCCTT 58.491 30.769 0.00 0.00 0.00 3.36
32 33 7.066307 ACTCAAATATGGCAAAACTTTTCCT 57.934 32.000 0.00 0.00 0.00 3.36
33 34 8.825667 TTACTCAAATATGGCAAAACTTTTCC 57.174 30.769 0.00 0.00 0.00 3.13
35 36 9.260002 CACTTACTCAAATATGGCAAAACTTTT 57.740 29.630 0.00 0.00 0.00 2.27
36 37 8.637986 TCACTTACTCAAATATGGCAAAACTTT 58.362 29.630 0.00 0.00 0.00 2.66
37 38 8.177119 TCACTTACTCAAATATGGCAAAACTT 57.823 30.769 0.00 0.00 0.00 2.66
38 39 7.759489 TCACTTACTCAAATATGGCAAAACT 57.241 32.000 0.00 0.00 0.00 2.66
40 41 8.394877 CGTATCACTTACTCAAATATGGCAAAA 58.605 33.333 0.00 0.00 0.00 2.44
41 42 7.466725 GCGTATCACTTACTCAAATATGGCAAA 60.467 37.037 0.00 0.00 0.00 3.68
42 43 6.018262 GCGTATCACTTACTCAAATATGGCAA 60.018 38.462 0.00 0.00 0.00 4.52
43 44 5.465390 GCGTATCACTTACTCAAATATGGCA 59.535 40.000 0.00 0.00 0.00 4.92
47 48 7.497595 TGAAGGCGTATCACTTACTCAAATAT 58.502 34.615 0.00 0.00 0.00 1.28
49 50 5.730550 TGAAGGCGTATCACTTACTCAAAT 58.269 37.500 0.00 0.00 0.00 2.32
50 51 5.142061 TGAAGGCGTATCACTTACTCAAA 57.858 39.130 0.00 0.00 0.00 2.69
51 52 4.794278 TGAAGGCGTATCACTTACTCAA 57.206 40.909 0.00 0.00 0.00 3.02
52 53 4.021807 TGTTGAAGGCGTATCACTTACTCA 60.022 41.667 0.00 0.00 0.00 3.41
53 54 4.491676 TGTTGAAGGCGTATCACTTACTC 58.508 43.478 0.00 0.00 0.00 2.59
54 55 4.530710 TGTTGAAGGCGTATCACTTACT 57.469 40.909 0.00 0.00 0.00 2.24
55 56 6.924060 AGATATGTTGAAGGCGTATCACTTAC 59.076 38.462 0.00 0.00 37.32 2.34
56 57 7.050970 AGATATGTTGAAGGCGTATCACTTA 57.949 36.000 0.00 0.00 37.32 2.24
57 58 5.918608 AGATATGTTGAAGGCGTATCACTT 58.081 37.500 0.00 0.00 37.32 3.16
58 59 5.537300 AGATATGTTGAAGGCGTATCACT 57.463 39.130 0.00 0.00 37.32 3.41
59 60 8.981724 TTATAGATATGTTGAAGGCGTATCAC 57.018 34.615 0.00 0.00 37.32 3.06
151 152 8.472413 GACACTATGTCAATAGGTTAGTACCAA 58.528 37.037 4.08 0.00 46.22 3.67
152 153 8.004087 GACACTATGTCAATAGGTTAGTACCA 57.996 38.462 4.08 0.00 46.22 3.25
167 168 6.375151 GCAACTGGCACTTGACACTATGTC 62.375 50.000 10.53 1.90 44.37 3.06
168 169 3.141398 CAACTGGCACTTGACACTATGT 58.859 45.455 1.12 0.00 0.00 2.29
170 171 2.154462 GCAACTGGCACTTGACACTAT 58.846 47.619 10.53 0.00 43.97 2.12
172 173 2.408333 GCAACTGGCACTTGACACT 58.592 52.632 10.53 0.00 43.97 3.55
195 196 6.560003 TCCATTAGGAGTAGAGATGCAAAA 57.440 37.500 0.00 0.00 39.61 2.44
265 5641 2.277008 AACAGAGGTGGGAGGATGAT 57.723 50.000 0.00 0.00 0.00 2.45
281 5657 5.182380 GTGGGAGGATGACGAAAATAAAACA 59.818 40.000 0.00 0.00 0.00 2.83
407 5785 0.030773 GTGGATCGCGAGTGCATAGA 59.969 55.000 16.66 0.00 42.97 1.98
411 5789 4.451150 GGGTGGATCGCGAGTGCA 62.451 66.667 16.66 11.60 42.97 4.57
462 5840 1.623542 GGGGTTAGGATCTGCCACGT 61.624 60.000 0.00 0.00 40.02 4.49
465 5843 2.070039 CCGGGGTTAGGATCTGCCA 61.070 63.158 0.00 0.00 40.02 4.92
506 5884 1.974236 AGATGGGAGCGAAGGGAATAG 59.026 52.381 0.00 0.00 0.00 1.73
507 5885 1.694150 CAGATGGGAGCGAAGGGAATA 59.306 52.381 0.00 0.00 0.00 1.75
508 5886 0.471617 CAGATGGGAGCGAAGGGAAT 59.528 55.000 0.00 0.00 0.00 3.01
515 5894 3.838271 GGCGACAGATGGGAGCGA 61.838 66.667 0.00 0.00 0.00 4.93
528 5907 2.155279 CTCCGATCTTGATAGAGGCGA 58.845 52.381 0.00 0.00 35.41 5.54
584 5963 1.774217 TGCCTTGTCCTGGGGTTCT 60.774 57.895 0.00 0.00 0.00 3.01
592 5971 2.833913 CCACACCCTGCCTTGTCCT 61.834 63.158 0.00 0.00 0.00 3.85
664 6043 0.759436 GGGATTGAGGGGAGCGTAGA 60.759 60.000 0.00 0.00 0.00 2.59
667 6046 3.090532 GGGGATTGAGGGGAGCGT 61.091 66.667 0.00 0.00 0.00 5.07
678 6057 0.988145 TGGAGGCGATGAAGGGGATT 60.988 55.000 0.00 0.00 0.00 3.01
700 6079 0.603707 CCATGGCGGCGAGATTGTAT 60.604 55.000 12.98 0.00 0.00 2.29
735 6128 1.568504 TGGAGGCAATCTCGTACCTT 58.431 50.000 0.00 0.00 43.34 3.50
822 6215 2.889606 TAACAGCAGGGAAGCGGCA 61.890 57.895 1.45 0.00 40.15 5.69
838 6231 2.266372 CATCGGGTGGCGGTGTAA 59.734 61.111 0.00 0.00 0.00 2.41
942 6335 0.836606 ATACCATCACCGTGCATGGA 59.163 50.000 31.74 10.64 42.11 3.41
1062 6455 0.988832 TTGCACGGGAGTAGGGAAAT 59.011 50.000 0.00 0.00 44.67 2.17
1063 6456 0.035739 GTTGCACGGGAGTAGGGAAA 59.964 55.000 0.00 0.00 44.67 3.13
1081 6474 3.845781 CCATACAGGCTTGACCATAGT 57.154 47.619 1.40 0.00 43.14 2.12
1185 6579 9.975218 TCTATGCTTCTTAAAAGTTAAATCCCT 57.025 29.630 0.00 0.00 0.00 4.20
1235 6629 1.354368 ACTTCACCCGGACCAAATCAT 59.646 47.619 0.73 0.00 0.00 2.45
1246 6640 9.681062 AAATATCCCAATATATTACTTCACCCG 57.319 33.333 0.00 0.00 32.86 5.28
1269 6663 8.223330 AGAAGCAATATAATCTCCTCCACAAAT 58.777 33.333 0.00 0.00 0.00 2.32
1426 6828 2.347322 GCAAATAGGGTGCCCGCAA 61.347 57.895 0.98 0.00 41.95 4.85
1503 9342 7.226720 CGCATATAACCTGGTAAGAAATCAAGT 59.773 37.037 0.00 0.00 0.00 3.16
1505 9344 6.485313 CCGCATATAACCTGGTAAGAAATCAA 59.515 38.462 0.00 0.00 0.00 2.57
1543 9382 2.947652 AGAAGAAATCATCACCATGCCG 59.052 45.455 0.00 0.00 0.00 5.69
1858 9727 2.622942 TGGCTGAAATGGTCTGTGAAAC 59.377 45.455 0.00 0.00 37.35 2.78
1888 9757 8.768397 ACTAGGATACCAATTCAACATAGTTGA 58.232 33.333 8.39 8.39 37.17 3.18
2027 10027 6.368779 AAGTATGTTACACACAGGTATGGT 57.631 37.500 0.00 0.00 39.40 3.55
2108 10108 5.335583 CGTCTGTTATCCAAGAAAATTGCCA 60.336 40.000 0.00 0.00 0.00 4.92
2139 10139 2.104967 CACCCGTGTACTCCTCCAATA 58.895 52.381 0.00 0.00 0.00 1.90
2142 10142 1.608336 CCACCCGTGTACTCCTCCA 60.608 63.158 0.00 0.00 0.00 3.86
2220 10239 4.592778 TCATGCCAATATGTAGCCTGTCTA 59.407 41.667 0.00 0.00 0.00 2.59
2387 10434 5.657474 GGACACTGAATTATGTTCCTACGA 58.343 41.667 0.00 0.00 0.00 3.43
2389 10436 4.270325 GCGGACACTGAATTATGTTCCTAC 59.730 45.833 0.00 0.00 0.00 3.18
2391 10438 3.055094 AGCGGACACTGAATTATGTTCCT 60.055 43.478 0.00 0.00 0.00 3.36
2430 10479 7.141363 GTGACAAGCAAGAAGAACAAATATGT 58.859 34.615 0.00 0.00 43.14 2.29
2842 10914 5.104527 CCCCTGAAATGGTTATCTGTACTCA 60.105 44.000 0.00 0.00 0.00 3.41
2862 10934 3.015145 ACGGTTAGGCATGCCCCT 61.015 61.111 33.14 18.49 39.05 4.79
2863 10935 2.828549 CACGGTTAGGCATGCCCC 60.829 66.667 33.14 24.81 36.58 5.80
2906 10978 7.686438 TTGGCACATAGTTAGGCATATTATG 57.314 36.000 0.00 0.00 39.30 1.90
2907 10979 7.944554 AGTTTGGCACATAGTTAGGCATATTAT 59.055 33.333 0.00 0.00 39.30 1.28
2955 12148 9.218440 AGCCCAAATGAAAAACAAAACTATATG 57.782 29.630 0.00 0.00 0.00 1.78
3733 13656 1.067985 TCTCAGCTTCAACTCTCGCAG 60.068 52.381 0.00 0.00 0.00 5.18
3845 13779 4.399303 CCAGGATAACCAACTGAAATCACC 59.601 45.833 0.00 0.00 38.94 4.02
3901 13835 5.700832 GGGGAATCAAATCAAACCAAAAGAC 59.299 40.000 0.00 0.00 0.00 3.01
3917 13851 9.135189 CATCTAAATCAAATACAAGGGGAATCA 57.865 33.333 0.00 0.00 0.00 2.57
4022 13969 1.143684 CAACAGGGGAATCGGATCCAT 59.856 52.381 13.41 1.55 41.55 3.41
4058 14005 0.685458 GCAGAATCCAATGCCCAGGT 60.685 55.000 0.00 0.00 36.41 4.00
4173 14177 5.303078 AGTGTCACTACTCTGTGATTTGAGT 59.697 40.000 2.87 0.00 46.77 3.41
4261 14276 6.195613 CGTAAATTACATTGTAATTGCGGTGG 59.804 38.462 28.72 17.29 0.00 4.61
4265 14280 9.858247 ATACTCGTAAATTACATTGTAATTGCG 57.142 29.630 29.52 29.52 32.59 4.85


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

AutoCloner maintained by Alex Coulton.