Multiple sequence alignment - TraesCS4B01G246400

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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 TraesCS4B01G246400 chr4B 100.000 2961 0 0 1 2961 510436029 510433069 0.000000e+00 5469.0
1 TraesCS4B01G246400 chr4B 84.989 1399 147 29 871 2233 510482342 510480971 0.000000e+00 1362.0
2 TraesCS4B01G246400 chr4B 88.080 1099 108 9 871 1960 510562810 510561726 0.000000e+00 1282.0
3 TraesCS4B01G246400 chr4B 81.746 378 39 7 370 734 510482823 510482463 3.730000e-74 289.0
4 TraesCS4B01G246400 chr4B 80.679 383 40 12 370 734 510563288 510562922 1.750000e-67 267.0
5 TraesCS4B01G246400 chr4B 79.012 162 12 10 2013 2172 510529818 510529677 1.130000e-14 91.6
6 TraesCS4B01G246400 chr4A 91.659 2086 128 25 318 2376 49199101 49201167 0.000000e+00 2846.0
7 TraesCS4B01G246400 chr4A 84.302 981 106 30 1293 2244 49040330 49041291 0.000000e+00 915.0
8 TraesCS4B01G246400 chr4A 92.720 522 36 2 2385 2906 49202267 49202786 0.000000e+00 752.0
9 TraesCS4B01G246400 chr4A 82.114 369 44 10 370 734 49039430 49039780 2.230000e-76 296.0
10 TraesCS4B01G246400 chr4A 84.175 297 27 7 871 1152 49039892 49040183 1.350000e-68 270.0
11 TraesCS4B01G246400 chr4D 95.609 1708 73 2 670 2376 414329016 414327310 0.000000e+00 2737.0
12 TraesCS4B01G246400 chr4D 88.128 1095 109 11 871 1960 414337361 414336283 0.000000e+00 1282.0
13 TraesCS4B01G246400 chr4D 88.026 1094 112 9 871 1960 414365736 414364658 0.000000e+00 1277.0
14 TraesCS4B01G246400 chr4D 84.628 1249 139 27 1021 2240 414359382 414358158 0.000000e+00 1194.0
15 TraesCS4B01G246400 chr4D 94.628 484 21 3 211 689 414329507 414329024 0.000000e+00 745.0
16 TraesCS4B01G246400 chr4D 83.119 622 91 9 1330 1949 414349710 414349101 3.330000e-154 555.0
17 TraesCS4B01G246400 chr4D 81.963 377 39 11 370 734 414366211 414365852 2.890000e-75 292.0
18 TraesCS4B01G246400 chr4D 76.367 512 65 28 1768 2245 414369786 414369297 1.070000e-54 224.0
19 TraesCS4B01G246400 chr4D 82.723 191 17 10 555 734 414337658 414337473 3.950000e-34 156.0
20 TraesCS4B01G246400 chr4D 76.271 236 29 14 2013 2245 414349019 414348808 1.880000e-17 100.0
21 TraesCS4B01G246400 chr4D 95.161 62 3 0 2383 2444 414327079 414327018 6.750000e-17 99.0
22 TraesCS4B01G246400 chr4D 94.444 54 3 0 1 54 414330746 414330693 1.890000e-12 84.2
23 TraesCS4B01G246400 chr4D 100.000 34 0 0 232 265 414367156 414367123 2.460000e-06 63.9
24 TraesCS4B01G246400 chr6D 78.378 481 90 9 2485 2961 255013574 255013104 1.730000e-77 300.0
25 TraesCS4B01G246400 chr6A 78.170 481 91 9 2485 2961 330053635 330054105 8.030000e-76 294.0
26 TraesCS4B01G246400 chr6B 78.947 418 78 8 2485 2898 352091089 352091500 2.910000e-70 276.0
27 TraesCS4B01G246400 chr5D 77.316 313 56 12 2627 2933 214367168 214366865 1.410000e-38 171.0
28 TraesCS4B01G246400 chr1D 74.888 223 33 17 1 218 465549854 465550058 2.450000e-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 TraesCS4B01G246400 chr4B 510433069 510436029 2960 True 5469.000000 5469 100.000000 1 2961 1 chr4B.!!$R1 2960
1 TraesCS4B01G246400 chr4B 510480971 510482823 1852 True 825.500000 1362 83.367500 370 2233 2 chr4B.!!$R3 1863
2 TraesCS4B01G246400 chr4B 510561726 510563288 1562 True 774.500000 1282 84.379500 370 1960 2 chr4B.!!$R4 1590
3 TraesCS4B01G246400 chr4A 49199101 49202786 3685 False 1799.000000 2846 92.189500 318 2906 2 chr4A.!!$F2 2588
4 TraesCS4B01G246400 chr4A 49039430 49041291 1861 False 493.666667 915 83.530333 370 2244 3 chr4A.!!$F1 1874
5 TraesCS4B01G246400 chr4D 414358158 414359382 1224 True 1194.000000 1194 84.628000 1021 2240 1 chr4D.!!$R1 1219
6 TraesCS4B01G246400 chr4D 414327018 414330746 3728 True 916.300000 2737 94.960500 1 2444 4 chr4D.!!$R2 2443
7 TraesCS4B01G246400 chr4D 414336283 414337658 1375 True 719.000000 1282 85.425500 555 1960 2 chr4D.!!$R3 1405
8 TraesCS4B01G246400 chr4D 414364658 414369786 5128 True 464.225000 1277 86.589000 232 2245 4 chr4D.!!$R5 2013
9 TraesCS4B01G246400 chr4D 414348808 414349710 902 True 327.500000 555 79.695000 1330 2245 2 chr4D.!!$R4 915

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
63 64 0.040781 GTGCTATCTCGACGAGGCTC 60.041 60.0 23.92 15.86 0.00 4.70 F
64 65 0.179043 TGCTATCTCGACGAGGCTCT 60.179 55.0 23.92 9.63 0.00 4.09 F
72 73 0.179150 CGACGAGGCTCTCTTTGAGG 60.179 60.0 13.50 0.00 42.87 3.86 F
75 76 0.459489 CGAGGCTCTCTTTGAGGAGG 59.541 60.0 13.50 0.00 42.87 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1391 4809 0.314935 CGCCAGGTTTGCAGAACATT 59.685 50.000 11.93 0.51 0.00 2.71 R
1520 4938 0.329261 CACCAATCTTCTCCCAGGCA 59.671 55.000 0.00 0.00 0.00 4.75 R
1877 5296 0.823356 AACACAAGCGTCTGCCCATT 60.823 50.000 0.00 0.00 44.31 3.16 R
2109 5563 6.603201 ACACATACATAAAAGGATGTTGGAGG 59.397 38.462 0.00 0.00 40.54 4.30 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 0.554305 ATGATGCATGCTTGGGGAGA 59.446 50.000 20.33 0.00 0.00 3.71
41 42 1.065199 GCTTGGGGAGATGATGACACA 60.065 52.381 0.00 0.00 0.00 3.72
43 44 1.956869 TGGGGAGATGATGACACAGT 58.043 50.000 0.00 0.00 0.00 3.55
45 46 1.556911 GGGGAGATGATGACACAGTGT 59.443 52.381 5.68 5.68 0.00 3.55
46 47 2.625737 GGGAGATGATGACACAGTGTG 58.374 52.381 21.77 21.77 39.75 3.82
47 48 2.005451 GGAGATGATGACACAGTGTGC 58.995 52.381 23.21 15.66 36.98 4.57
48 49 2.354503 GGAGATGATGACACAGTGTGCT 60.355 50.000 23.21 9.94 36.98 4.40
49 50 3.118992 GGAGATGATGACACAGTGTGCTA 60.119 47.826 23.21 12.52 36.98 3.49
50 51 4.442612 GGAGATGATGACACAGTGTGCTAT 60.443 45.833 23.21 16.67 36.98 2.97
51 52 4.691175 AGATGATGACACAGTGTGCTATC 58.309 43.478 23.21 23.33 36.98 2.08
53 54 4.115401 TGATGACACAGTGTGCTATCTC 57.885 45.455 27.11 17.75 36.98 2.75
55 56 2.159382 TGACACAGTGTGCTATCTCGA 58.841 47.619 23.21 1.81 36.98 4.04
57 58 1.135660 ACACAGTGTGCTATCTCGACG 60.136 52.381 23.21 0.00 36.98 5.12
58 59 1.130561 CACAGTGTGCTATCTCGACGA 59.869 52.381 10.97 0.00 0.00 4.20
59 60 1.398739 ACAGTGTGCTATCTCGACGAG 59.601 52.381 18.91 18.91 0.00 4.18
60 61 1.018148 AGTGTGCTATCTCGACGAGG 58.982 55.000 23.92 9.89 0.00 4.63
62 63 0.748367 TGTGCTATCTCGACGAGGCT 60.748 55.000 23.92 14.26 0.00 4.58
63 64 0.040781 GTGCTATCTCGACGAGGCTC 60.041 60.000 23.92 15.86 0.00 4.70
64 65 0.179043 TGCTATCTCGACGAGGCTCT 60.179 55.000 23.92 9.63 0.00 4.09
65 66 0.515564 GCTATCTCGACGAGGCTCTC 59.484 60.000 23.92 8.26 0.00 3.20
66 67 1.876416 GCTATCTCGACGAGGCTCTCT 60.876 57.143 23.92 5.79 0.00 3.10
67 68 2.489971 CTATCTCGACGAGGCTCTCTT 58.510 52.381 23.92 0.00 0.00 2.85
68 69 1.757682 ATCTCGACGAGGCTCTCTTT 58.242 50.000 23.92 0.00 0.00 2.52
69 70 0.805614 TCTCGACGAGGCTCTCTTTG 59.194 55.000 23.92 0.00 0.00 2.77
70 71 0.805614 CTCGACGAGGCTCTCTTTGA 59.194 55.000 17.27 5.32 0.00 2.69
71 72 0.805614 TCGACGAGGCTCTCTTTGAG 59.194 55.000 13.50 0.00 45.33 3.02
72 73 0.179150 CGACGAGGCTCTCTTTGAGG 60.179 60.000 13.50 0.00 42.87 3.86
73 74 1.178276 GACGAGGCTCTCTTTGAGGA 58.822 55.000 13.50 0.00 42.87 3.71
74 75 1.134175 GACGAGGCTCTCTTTGAGGAG 59.866 57.143 13.50 0.00 42.87 3.69
75 76 0.459489 CGAGGCTCTCTTTGAGGAGG 59.541 60.000 13.50 0.00 42.87 4.30
76 77 1.567357 GAGGCTCTCTTTGAGGAGGT 58.433 55.000 7.40 0.00 42.87 3.85
77 78 1.206849 GAGGCTCTCTTTGAGGAGGTG 59.793 57.143 7.40 0.00 42.87 4.00
78 79 0.980423 GGCTCTCTTTGAGGAGGTGT 59.020 55.000 0.00 0.00 42.87 4.16
84 85 1.140852 TCTTTGAGGAGGTGTGTGTGG 59.859 52.381 0.00 0.00 0.00 4.17
88 89 1.203250 TGAGGAGGTGTGTGTGGGATA 60.203 52.381 0.00 0.00 0.00 2.59
89 90 1.482593 GAGGAGGTGTGTGTGGGATAG 59.517 57.143 0.00 0.00 0.00 2.08
101 102 0.764890 TGGGATAGCCTATGTGTGCC 59.235 55.000 0.00 0.00 0.00 5.01
150 151 9.457436 TTTTCTGGTTTCTCTTTAGTTAACTGT 57.543 29.630 18.56 0.00 0.00 3.55
194 195 7.548780 TGCTTAATTTTAATGGATGAGGCAAAC 59.451 33.333 0.00 0.00 0.00 2.93
209 210 2.220824 GGCAAACCTTTTGCATTCGTTC 59.779 45.455 21.67 2.84 46.58 3.95
213 214 5.405269 GCAAACCTTTTGCATTCGTTCTAAT 59.595 36.000 16.79 0.00 44.34 1.73
216 217 8.973378 CAAACCTTTTGCATTCGTTCTAATAAA 58.027 29.630 0.00 0.00 0.00 1.40
217 218 9.535878 AAACCTTTTGCATTCGTTCTAATAAAA 57.464 25.926 0.00 0.00 0.00 1.52
218 219 8.742554 ACCTTTTGCATTCGTTCTAATAAAAG 57.257 30.769 0.00 0.00 35.05 2.27
219 220 8.573035 ACCTTTTGCATTCGTTCTAATAAAAGA 58.427 29.630 0.00 0.00 36.50 2.52
220 221 8.850452 CCTTTTGCATTCGTTCTAATAAAAGAC 58.150 33.333 0.00 0.00 36.50 3.01
270 2679 9.851686 AATCATGCTTATTCCATTCTACTAACA 57.148 29.630 0.00 0.00 0.00 2.41
307 2727 1.871676 CCGTGCAATCTCTGATGATGG 59.128 52.381 0.00 0.00 0.00 3.51
340 3520 7.045126 ACTTAGCAGACGATAAATCTAGCTT 57.955 36.000 0.00 0.00 34.53 3.74
355 3535 2.740714 GCTTGATCACGCACCCGTC 61.741 63.158 18.52 0.00 46.39 4.79
418 3625 3.961838 TACGTTCCGGCATGCCCAC 62.962 63.158 30.79 22.11 0.00 4.61
447 3654 1.278127 CCGATGTTTAGGACCAGGTGT 59.722 52.381 0.00 0.00 0.00 4.16
668 3906 8.594550 ACCGATAAATAGCTGATGTTATAAGGT 58.405 33.333 0.00 5.64 0.00 3.50
695 3966 1.445410 GACCATACGTGTCTGCGCA 60.445 57.895 10.98 10.98 34.88 6.09
748 4027 2.202932 ATGGTGCGGCTCGACATC 60.203 61.111 0.00 0.00 0.00 3.06
760 4059 2.954868 GACATCCGCACGCTACCG 60.955 66.667 0.00 0.00 41.14 4.02
855 4161 2.100584 GCACACACACCTTCATCCAAAA 59.899 45.455 0.00 0.00 0.00 2.44
1159 4482 3.633525 CACCATGGGTACGTAACTAGCTA 59.366 47.826 18.09 0.00 32.11 3.32
1166 4492 5.530171 TGGGTACGTAACTAGCTAATCTCAG 59.470 44.000 11.05 0.00 0.00 3.35
1192 4610 5.162637 TCCCTGTATAGGCCAATAGAACAT 58.837 41.667 5.01 0.00 43.16 2.71
1207 4625 9.559732 CCAATAGAACATTGAATACCACATCTA 57.440 33.333 0.00 0.00 0.00 1.98
1406 4824 2.827921 GGATCCAATGTTCTGCAAACCT 59.172 45.455 6.95 0.00 0.00 3.50
1487 4905 2.594592 AACGGAGGCTGGTGCAAC 60.595 61.111 0.00 0.00 41.91 4.17
1488 4906 4.988598 ACGGAGGCTGGTGCAACG 62.989 66.667 0.00 0.00 41.91 4.10
1627 5045 3.009026 TGTTATATGTGCCTGTGTGCAG 58.991 45.455 0.00 0.00 43.02 4.41
1675 5094 0.606401 CATGCGTGAAGAAGGGTGGT 60.606 55.000 0.00 0.00 0.00 4.16
1790 5209 2.836372 AGCTCTGATTCAGACACATGGA 59.164 45.455 12.38 0.00 35.39 3.41
1877 5296 3.753815 TCATTCAGATTGACCAGCACAA 58.246 40.909 0.00 0.00 0.00 3.33
1960 5380 6.984740 TTTGCGAGCAAATTACAGTTTTAG 57.015 33.333 18.01 0.00 40.51 1.85
1989 5409 6.219473 ACACTCTCAACAGAACAATCTAGTG 58.781 40.000 0.00 0.00 39.25 2.74
2109 5563 4.757657 TGGTCACCACATGTAACATTGTAC 59.242 41.667 0.00 0.00 0.00 2.90
2123 5577 4.998051 ACATTGTACCTCCAACATCCTTT 58.002 39.130 0.00 0.00 0.00 3.11
2268 5728 5.329399 TGCCTTGGGTGACTAACAAATAAT 58.671 37.500 0.00 0.00 0.00 1.28
2362 5822 9.453572 AAAAGCATGAGAATTCTACATCTAACA 57.546 29.630 8.25 0.00 0.00 2.41
2363 5823 9.624373 AAAGCATGAGAATTCTACATCTAACAT 57.376 29.630 8.25 2.13 0.00 2.71
2381 5841 9.743057 ATCTAACATCTCAACTAAGAATTCTCG 57.257 33.333 8.78 5.83 0.00 4.04
2461 7012 3.021177 AGACCTAGCTTCCCACTCTAC 57.979 52.381 0.00 0.00 0.00 2.59
2468 7019 0.173708 CTTCCCACTCTACTGTCGGC 59.826 60.000 0.00 0.00 0.00 5.54
2473 7024 3.528370 CTCTACTGTCGGCGGGGG 61.528 72.222 7.21 0.00 0.00 5.40
2514 7065 7.064134 GTGGTGTGTCGATGATAAGTTAAATCA 59.936 37.037 0.00 1.47 37.73 2.57
2521 7072 8.356526 GTCGATGATAAGTTAAATCACGTATCG 58.643 37.037 0.00 0.00 39.60 2.92
2522 7073 7.536281 TCGATGATAAGTTAAATCACGTATCGG 59.464 37.037 0.00 0.00 39.60 4.18
2526 7077 3.454375 AGTTAAATCACGTATCGGCCTG 58.546 45.455 0.00 0.00 0.00 4.85
2549 7100 1.871772 CCTTTGCTGCCAAGACGAG 59.128 57.895 14.41 0.00 31.52 4.18
2556 7107 4.388499 GCCAAGACGAGCCCCGAA 62.388 66.667 2.99 0.00 41.76 4.30
2577 7128 1.954362 GCTCGAGACAGCCCAGTGAT 61.954 60.000 18.75 0.00 32.76 3.06
2580 7131 1.107114 CGAGACAGCCCAGTGATACT 58.893 55.000 0.00 0.00 0.00 2.12
2581 7132 1.202348 CGAGACAGCCCAGTGATACTG 60.202 57.143 2.05 2.05 45.53 2.74
2603 7154 1.530655 GGTTCACCACCACCTTGGG 60.531 63.158 0.00 0.00 46.42 4.12
2638 7189 6.267471 ACCACCATACAACACATCAGAAAAAT 59.733 34.615 0.00 0.00 0.00 1.82
2660 7211 4.205587 TGGAGGAGTCTACGAATAAGGAC 58.794 47.826 0.00 0.00 0.00 3.85
2685 7236 1.678101 GACCCTGCATGCATCCTAAAC 59.322 52.381 22.97 5.77 0.00 2.01
2690 7241 3.276857 CTGCATGCATCCTAAACAGACT 58.723 45.455 22.97 0.00 0.00 3.24
2742 7293 1.675641 GCACCGACATGGAAGCCTT 60.676 57.895 0.00 0.00 42.00 4.35
2758 7309 4.538746 AGCCTTCCACAAGTAGTTCTAC 57.461 45.455 2.14 2.14 0.00 2.59
2812 7363 0.535335 TCTCCCGCACCATTGTAGTC 59.465 55.000 0.00 0.00 0.00 2.59
2848 7399 0.507358 GATTTCGACGCTTATCGCCC 59.493 55.000 0.00 0.00 41.97 6.13
2873 7424 2.024868 CCGCCGTGTCATTTCGTCA 61.025 57.895 0.00 0.00 0.00 4.35
2890 7441 5.743026 TCGTCAAGATACTCTGTCTCATC 57.257 43.478 0.00 0.00 0.00 2.92
2914 7465 4.499116 CCCCCTCCCCTCGACCAT 62.499 72.222 0.00 0.00 0.00 3.55
2915 7466 3.164269 CCCCTCCCCTCGACCATG 61.164 72.222 0.00 0.00 0.00 3.66
2916 7467 2.365635 CCCTCCCCTCGACCATGT 60.366 66.667 0.00 0.00 0.00 3.21
2917 7468 1.075525 CCCTCCCCTCGACCATGTA 60.076 63.158 0.00 0.00 0.00 2.29
2918 7469 0.689745 CCCTCCCCTCGACCATGTAA 60.690 60.000 0.00 0.00 0.00 2.41
2919 7470 1.424638 CCTCCCCTCGACCATGTAAT 58.575 55.000 0.00 0.00 0.00 1.89
2920 7471 1.344763 CCTCCCCTCGACCATGTAATC 59.655 57.143 0.00 0.00 0.00 1.75
2921 7472 2.320781 CTCCCCTCGACCATGTAATCT 58.679 52.381 0.00 0.00 0.00 2.40
2922 7473 2.700897 CTCCCCTCGACCATGTAATCTT 59.299 50.000 0.00 0.00 0.00 2.40
2923 7474 2.698797 TCCCCTCGACCATGTAATCTTC 59.301 50.000 0.00 0.00 0.00 2.87
2924 7475 2.700897 CCCCTCGACCATGTAATCTTCT 59.299 50.000 0.00 0.00 0.00 2.85
2925 7476 3.493350 CCCCTCGACCATGTAATCTTCTG 60.493 52.174 0.00 0.00 0.00 3.02
2926 7477 3.126831 CCTCGACCATGTAATCTTCTGC 58.873 50.000 0.00 0.00 0.00 4.26
2927 7478 2.791560 CTCGACCATGTAATCTTCTGCG 59.208 50.000 0.00 0.00 0.00 5.18
2928 7479 2.165641 TCGACCATGTAATCTTCTGCGT 59.834 45.455 0.00 0.00 0.00 5.24
2929 7480 2.930040 CGACCATGTAATCTTCTGCGTT 59.070 45.455 0.00 0.00 0.00 4.84
2930 7481 3.000322 CGACCATGTAATCTTCTGCGTTC 60.000 47.826 0.00 0.00 0.00 3.95
2931 7482 4.184629 GACCATGTAATCTTCTGCGTTCT 58.815 43.478 0.00 0.00 0.00 3.01
2932 7483 4.184629 ACCATGTAATCTTCTGCGTTCTC 58.815 43.478 0.00 0.00 0.00 2.87
2933 7484 3.557595 CCATGTAATCTTCTGCGTTCTCC 59.442 47.826 0.00 0.00 0.00 3.71
2934 7485 3.953712 TGTAATCTTCTGCGTTCTCCA 57.046 42.857 0.00 0.00 0.00 3.86
2935 7486 3.585862 TGTAATCTTCTGCGTTCTCCAC 58.414 45.455 0.00 0.00 0.00 4.02
2936 7487 2.839486 AATCTTCTGCGTTCTCCACA 57.161 45.000 0.00 0.00 0.00 4.17
2937 7488 3.340814 AATCTTCTGCGTTCTCCACAT 57.659 42.857 0.00 0.00 0.00 3.21
2938 7489 4.471904 AATCTTCTGCGTTCTCCACATA 57.528 40.909 0.00 0.00 0.00 2.29
2939 7490 4.679373 ATCTTCTGCGTTCTCCACATAT 57.321 40.909 0.00 0.00 0.00 1.78
2940 7491 5.791336 ATCTTCTGCGTTCTCCACATATA 57.209 39.130 0.00 0.00 0.00 0.86
2941 7492 5.791336 TCTTCTGCGTTCTCCACATATAT 57.209 39.130 0.00 0.00 0.00 0.86
2942 7493 6.894339 TCTTCTGCGTTCTCCACATATATA 57.106 37.500 0.00 0.00 0.00 0.86
2943 7494 7.284919 TCTTCTGCGTTCTCCACATATATAA 57.715 36.000 0.00 0.00 0.00 0.98
2944 7495 7.371159 TCTTCTGCGTTCTCCACATATATAAG 58.629 38.462 0.00 0.00 0.00 1.73
2945 7496 6.894339 TCTGCGTTCTCCACATATATAAGA 57.106 37.500 0.00 0.00 0.00 2.10
2946 7497 7.284919 TCTGCGTTCTCCACATATATAAGAA 57.715 36.000 0.00 0.00 0.00 2.52
2947 7498 7.896811 TCTGCGTTCTCCACATATATAAGAAT 58.103 34.615 0.00 0.00 0.00 2.40
2948 7499 7.814587 TCTGCGTTCTCCACATATATAAGAATG 59.185 37.037 8.20 8.20 36.50 2.67
2949 7500 6.873605 TGCGTTCTCCACATATATAAGAATGG 59.126 38.462 12.24 6.90 34.85 3.16
2950 7501 7.097192 GCGTTCTCCACATATATAAGAATGGA 58.903 38.462 12.24 9.77 34.85 3.41
2955 7506 8.489990 CTCCACATATATAAGAATGGAGCAAG 57.510 38.462 16.08 2.20 44.87 4.01
2956 7507 7.397221 TCCACATATATAAGAATGGAGCAAGG 58.603 38.462 4.39 0.00 32.50 3.61
2957 7508 6.094603 CCACATATATAAGAATGGAGCAAGGC 59.905 42.308 0.00 0.00 0.00 4.35
2958 7509 6.656270 CACATATATAAGAATGGAGCAAGGCA 59.344 38.462 0.00 0.00 0.00 4.75
2959 7510 6.883217 ACATATATAAGAATGGAGCAAGGCAG 59.117 38.462 0.00 0.00 0.00 4.85
2960 7511 2.425143 TAAGAATGGAGCAAGGCAGG 57.575 50.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.691175 GAGATAGCACACTGTGTCATCAT 58.309 43.478 11.12 2.21 35.75 2.45
41 42 1.018148 CCTCGTCGAGATAGCACACT 58.982 55.000 23.74 0.00 0.00 3.55
43 44 0.748367 AGCCTCGTCGAGATAGCACA 60.748 55.000 23.74 0.00 32.31 4.57
45 46 0.179043 AGAGCCTCGTCGAGATAGCA 60.179 55.000 23.74 0.00 32.31 3.49
46 47 0.515564 GAGAGCCTCGTCGAGATAGC 59.484 60.000 23.74 17.45 0.00 2.97
47 48 2.163818 AGAGAGCCTCGTCGAGATAG 57.836 55.000 23.74 8.16 35.36 2.08
48 49 2.614520 CAAAGAGAGCCTCGTCGAGATA 59.385 50.000 23.74 0.00 35.36 1.98
49 50 1.403679 CAAAGAGAGCCTCGTCGAGAT 59.596 52.381 23.74 11.51 35.36 2.75
50 51 0.805614 CAAAGAGAGCCTCGTCGAGA 59.194 55.000 23.74 0.00 35.36 4.04
51 52 0.805614 TCAAAGAGAGCCTCGTCGAG 59.194 55.000 15.53 15.53 35.36 4.04
53 54 0.179150 CCTCAAAGAGAGCCTCGTCG 60.179 60.000 0.00 0.00 43.31 5.12
55 56 1.181786 CTCCTCAAAGAGAGCCTCGT 58.818 55.000 0.00 0.00 43.31 4.18
57 58 1.206849 CACCTCCTCAAAGAGAGCCTC 59.793 57.143 0.00 0.00 43.31 4.70
58 59 1.274712 CACCTCCTCAAAGAGAGCCT 58.725 55.000 0.00 0.00 43.31 4.58
59 60 0.980423 ACACCTCCTCAAAGAGAGCC 59.020 55.000 0.00 0.00 43.31 4.70
60 61 1.346068 ACACACCTCCTCAAAGAGAGC 59.654 52.381 0.00 0.00 43.31 4.09
62 63 2.103094 CACACACACCTCCTCAAAGAGA 59.897 50.000 0.00 0.00 35.82 3.10
63 64 2.487934 CACACACACCTCCTCAAAGAG 58.512 52.381 0.00 0.00 0.00 2.85
64 65 1.140852 CCACACACACCTCCTCAAAGA 59.859 52.381 0.00 0.00 0.00 2.52
65 66 1.597742 CCACACACACCTCCTCAAAG 58.402 55.000 0.00 0.00 0.00 2.77
66 67 0.182537 CCCACACACACCTCCTCAAA 59.817 55.000 0.00 0.00 0.00 2.69
67 68 0.692756 TCCCACACACACCTCCTCAA 60.693 55.000 0.00 0.00 0.00 3.02
68 69 0.473694 ATCCCACACACACCTCCTCA 60.474 55.000 0.00 0.00 0.00 3.86
69 70 1.482593 CTATCCCACACACACCTCCTC 59.517 57.143 0.00 0.00 0.00 3.71
70 71 1.573108 CTATCCCACACACACCTCCT 58.427 55.000 0.00 0.00 0.00 3.69
71 72 0.107654 GCTATCCCACACACACCTCC 60.108 60.000 0.00 0.00 0.00 4.30
72 73 0.107654 GGCTATCCCACACACACCTC 60.108 60.000 0.00 0.00 0.00 3.85
73 74 0.547712 AGGCTATCCCACACACACCT 60.548 55.000 0.00 0.00 35.39 4.00
74 75 1.200519 TAGGCTATCCCACACACACC 58.799 55.000 0.00 0.00 35.39 4.16
75 76 2.170607 ACATAGGCTATCCCACACACAC 59.829 50.000 3.47 0.00 35.39 3.82
76 77 2.170397 CACATAGGCTATCCCACACACA 59.830 50.000 3.47 0.00 35.39 3.72
77 78 2.170607 ACACATAGGCTATCCCACACAC 59.829 50.000 3.47 0.00 35.39 3.82
78 79 2.170397 CACACATAGGCTATCCCACACA 59.830 50.000 3.47 0.00 35.39 3.72
84 85 0.951040 GCGGCACACATAGGCTATCC 60.951 60.000 3.47 1.56 0.00 2.59
88 89 0.179073 CTTAGCGGCACACATAGGCT 60.179 55.000 1.45 0.00 37.73 4.58
89 90 1.776034 GCTTAGCGGCACACATAGGC 61.776 60.000 1.45 0.00 0.00 3.93
164 165 9.762933 GCCTCATCCATTAAAATTAAGCAATTA 57.237 29.630 0.00 0.00 33.09 1.40
167 168 7.180322 TGCCTCATCCATTAAAATTAAGCAA 57.820 32.000 0.00 0.00 0.00 3.91
168 169 6.788598 TGCCTCATCCATTAAAATTAAGCA 57.211 33.333 0.00 0.00 0.00 3.91
169 170 7.011389 GGTTTGCCTCATCCATTAAAATTAAGC 59.989 37.037 0.00 0.00 0.00 3.09
170 171 8.260114 AGGTTTGCCTCATCCATTAAAATTAAG 58.740 33.333 0.00 0.00 42.67 1.85
174 175 6.625532 AAGGTTTGCCTCATCCATTAAAAT 57.374 33.333 0.00 0.00 46.33 1.82
175 176 6.432403 AAAGGTTTGCCTCATCCATTAAAA 57.568 33.333 0.00 0.00 46.33 1.52
176 177 6.229733 CAAAAGGTTTGCCTCATCCATTAAA 58.770 36.000 0.00 0.00 46.33 1.52
182 183 1.344114 TGCAAAAGGTTTGCCTCATCC 59.656 47.619 19.86 0.00 46.33 3.51
194 195 8.850452 GTCTTTTATTAGAACGAATGCAAAAGG 58.150 33.333 0.00 0.00 31.30 3.11
202 203 7.601508 AGTTCGTGGTCTTTTATTAGAACGAAT 59.398 33.333 13.20 4.47 43.49 3.34
204 205 6.364165 CAGTTCGTGGTCTTTTATTAGAACGA 59.636 38.462 0.00 0.00 40.86 3.85
206 207 6.147328 AGCAGTTCGTGGTCTTTTATTAGAAC 59.853 38.462 0.00 0.00 37.56 3.01
209 210 6.147164 TCAAGCAGTTCGTGGTCTTTTATTAG 59.853 38.462 0.00 0.00 35.15 1.73
213 214 3.799366 TCAAGCAGTTCGTGGTCTTTTA 58.201 40.909 0.00 0.00 35.15 1.52
216 217 2.550830 ATCAAGCAGTTCGTGGTCTT 57.449 45.000 0.00 0.00 35.15 3.01
217 218 2.671351 CGTATCAAGCAGTTCGTGGTCT 60.671 50.000 0.00 0.00 35.15 3.85
218 219 1.654105 CGTATCAAGCAGTTCGTGGTC 59.346 52.381 0.00 0.00 35.15 4.02
219 220 1.671850 CCGTATCAAGCAGTTCGTGGT 60.672 52.381 0.00 0.00 39.08 4.16
220 221 0.999406 CCGTATCAAGCAGTTCGTGG 59.001 55.000 0.00 0.00 0.00 4.94
270 2679 4.100344 TGCACGGTATGGTAGTAACATGAT 59.900 41.667 11.11 0.00 0.00 2.45
307 2727 0.714439 GTCTGCTAAGTTTCGTCGGC 59.286 55.000 0.00 0.00 0.00 5.54
340 3520 3.307108 TGGACGGGTGCGTGATCA 61.307 61.111 0.00 0.00 0.00 2.92
355 3535 0.532862 AGTTGTCGTTGAGGCAGTGG 60.533 55.000 0.00 0.00 34.99 4.00
447 3654 2.616960 CTTGAATCGAACGGATCACCA 58.383 47.619 0.00 0.00 33.02 4.17
748 4027 4.849329 GGAGACGGTAGCGTGCGG 62.849 72.222 26.54 0.00 0.00 5.69
760 4059 2.996621 CAAGGTCATCACGAAAGGAGAC 59.003 50.000 0.00 0.00 0.00 3.36
855 4161 4.847198 TGATGGTTAGCTGTGTGATGATT 58.153 39.130 0.00 0.00 0.00 2.57
942 4253 6.508246 CGCGGACTAATCTATACGTAGATGAG 60.508 46.154 10.16 10.16 44.89 2.90
1110 4433 3.365291 ATCAGCGCCGCCGTAGAAA 62.365 57.895 4.98 0.00 36.67 2.52
1159 4482 4.534103 GGCCTATACAGGGATTCTGAGATT 59.466 45.833 0.00 0.00 46.18 2.40
1166 4492 6.174049 GTTCTATTGGCCTATACAGGGATTC 58.826 44.000 3.32 0.00 42.88 2.52
1192 4610 4.191544 GCAGCAGTAGATGTGGTATTCAA 58.808 43.478 0.00 0.00 32.61 2.69
1207 4625 1.882623 GCTTTTAGAACAGGCAGCAGT 59.117 47.619 0.00 0.00 0.00 4.40
1208 4626 1.881973 TGCTTTTAGAACAGGCAGCAG 59.118 47.619 0.00 0.00 32.38 4.24
1379 4797 2.086869 CAGAACATTGGATCCGCAAGT 58.913 47.619 7.39 0.00 0.00 3.16
1391 4809 0.314935 CGCCAGGTTTGCAGAACATT 59.685 50.000 11.93 0.51 0.00 2.71
1520 4938 0.329261 CACCAATCTTCTCCCAGGCA 59.671 55.000 0.00 0.00 0.00 4.75
1627 5045 7.659799 ACCCTGCAAAAATCAATTTTAGTAACC 59.340 33.333 1.36 0.00 39.20 2.85
1638 5057 3.806507 GCATGGAACCCTGCAAAAATCAA 60.807 43.478 14.37 0.00 38.28 2.57
1639 5058 2.289569 GCATGGAACCCTGCAAAAATCA 60.290 45.455 14.37 0.00 38.28 2.57
1726 5145 2.202690 CCATCCGCTGCGACGTTA 60.203 61.111 25.45 3.54 0.00 3.18
1877 5296 0.823356 AACACAAGCGTCTGCCCATT 60.823 50.000 0.00 0.00 44.31 3.16
2109 5563 6.603201 ACACATACATAAAAGGATGTTGGAGG 59.397 38.462 0.00 0.00 40.54 4.30
2173 5632 4.155099 CCAGACGTGTTTTATATGCACCAA 59.845 41.667 0.00 0.00 0.00 3.67
2362 5822 4.098044 TCGGCGAGAATTCTTAGTTGAGAT 59.902 41.667 9.87 0.00 0.00 2.75
2363 5823 3.442625 TCGGCGAGAATTCTTAGTTGAGA 59.557 43.478 9.87 1.19 0.00 3.27
2376 5836 0.237235 GCACAAATGTTCGGCGAGAA 59.763 50.000 10.46 2.41 36.31 2.87
2378 5838 0.238289 AAGCACAAATGTTCGGCGAG 59.762 50.000 10.46 0.00 0.00 5.03
2379 5839 1.514003 TAAGCACAAATGTTCGGCGA 58.486 45.000 4.99 4.99 0.00 5.54
2381 5841 2.159572 ACGATAAGCACAAATGTTCGGC 60.160 45.455 8.80 0.00 0.00 5.54
2468 7019 1.257055 AATTGTGATTGCCACCCCCG 61.257 55.000 0.00 0.00 45.09 5.73
2514 7065 2.494918 GCAGACAGGCCGATACGT 59.505 61.111 0.00 0.00 0.00 3.57
2522 7073 2.960170 CAGCAAAGGCAGACAGGC 59.040 61.111 0.00 0.00 44.61 4.85
2526 7077 1.174712 TCTTGGCAGCAAAGGCAGAC 61.175 55.000 9.84 0.00 45.28 3.51
2532 7083 1.208614 GCTCGTCTTGGCAGCAAAG 59.791 57.895 2.64 2.64 33.06 2.77
2549 7100 2.509561 GTCTCGAGCTTTCGGGGC 60.510 66.667 7.81 0.00 33.80 5.80
2556 7107 1.910772 ACTGGGCTGTCTCGAGCTT 60.911 57.895 7.81 0.00 39.11 3.74
2590 7141 1.847968 CTCCTCCCAAGGTGGTGGT 60.848 63.158 1.88 0.00 43.82 4.16
2603 7154 2.972348 TGTATGGTGGTATCCCTCCTC 58.028 52.381 0.00 0.00 43.59 3.71
2627 7178 5.521735 CGTAGACTCCTCCATTTTTCTGATG 59.478 44.000 0.00 0.00 0.00 3.07
2638 7189 4.205587 GTCCTTATTCGTAGACTCCTCCA 58.794 47.826 0.00 0.00 34.32 3.86
2660 7211 0.379669 GATGCATGCAGGGTCTTTCG 59.620 55.000 26.69 0.00 0.00 3.46
2671 7222 5.220931 CCTTAAGTCTGTTTAGGATGCATGC 60.221 44.000 11.82 11.82 0.00 4.06
2685 7236 2.303022 TGGAGTCTTGCCCTTAAGTCTG 59.697 50.000 0.97 0.00 0.00 3.51
2690 7241 1.271926 GGCTTGGAGTCTTGCCCTTAA 60.272 52.381 9.40 0.00 39.49 1.85
2742 7293 5.105064 GCCCTTATGTAGAACTACTTGTGGA 60.105 44.000 12.25 0.00 37.00 4.02
2758 7309 0.552848 ATGGTCCTGGTGCCCTTATG 59.447 55.000 7.40 0.00 0.00 1.90
2798 7349 2.165641 TGGTCTAGACTACAATGGTGCG 59.834 50.000 21.88 0.00 0.00 5.34
2812 7363 5.360144 TCGAAATCCTTTCTAGGTGGTCTAG 59.640 44.000 0.00 0.00 45.25 2.43
2848 7399 0.806102 AATGACACGGCGGAGATTCG 60.806 55.000 13.24 0.00 0.00 3.34
2901 7452 2.320781 AGATTACATGGTCGAGGGGAG 58.679 52.381 0.00 0.00 0.00 4.30
2902 7453 2.471815 AGATTACATGGTCGAGGGGA 57.528 50.000 0.00 0.00 0.00 4.81
2905 7456 3.126831 GCAGAAGATTACATGGTCGAGG 58.873 50.000 0.00 0.00 0.00 4.63
2906 7457 2.791560 CGCAGAAGATTACATGGTCGAG 59.208 50.000 0.00 0.00 0.00 4.04
2907 7458 2.165641 ACGCAGAAGATTACATGGTCGA 59.834 45.455 0.00 0.00 0.00 4.20
2908 7459 2.540515 ACGCAGAAGATTACATGGTCG 58.459 47.619 0.00 0.00 0.00 4.79
2909 7460 4.184629 AGAACGCAGAAGATTACATGGTC 58.815 43.478 0.00 0.00 0.00 4.02
2910 7461 4.184629 GAGAACGCAGAAGATTACATGGT 58.815 43.478 0.00 0.00 0.00 3.55
2911 7462 3.557595 GGAGAACGCAGAAGATTACATGG 59.442 47.826 0.00 0.00 0.00 3.66
2912 7463 4.033358 GTGGAGAACGCAGAAGATTACATG 59.967 45.833 0.00 0.00 0.00 3.21
2913 7464 4.184629 GTGGAGAACGCAGAAGATTACAT 58.815 43.478 0.00 0.00 0.00 2.29
2914 7465 3.006430 TGTGGAGAACGCAGAAGATTACA 59.994 43.478 0.00 0.00 33.95 2.41
2915 7466 3.585862 TGTGGAGAACGCAGAAGATTAC 58.414 45.455 0.00 0.00 33.95 1.89
2916 7467 3.953712 TGTGGAGAACGCAGAAGATTA 57.046 42.857 0.00 0.00 33.95 1.75
2917 7468 2.839486 TGTGGAGAACGCAGAAGATT 57.161 45.000 0.00 0.00 33.95 2.40
2918 7469 4.679373 ATATGTGGAGAACGCAGAAGAT 57.321 40.909 0.00 0.00 43.91 2.40
2919 7470 5.791336 ATATATGTGGAGAACGCAGAAGA 57.209 39.130 0.00 0.00 43.91 2.87
2920 7471 7.371159 TCTTATATATGTGGAGAACGCAGAAG 58.629 38.462 0.00 0.00 43.91 2.85
2921 7472 7.284919 TCTTATATATGTGGAGAACGCAGAA 57.715 36.000 0.00 0.00 43.91 3.02
2922 7473 6.894339 TCTTATATATGTGGAGAACGCAGA 57.106 37.500 0.00 0.00 43.91 4.26
2923 7474 7.063898 CCATTCTTATATATGTGGAGAACGCAG 59.936 40.741 0.00 0.00 43.91 5.18
2924 7475 6.873605 CCATTCTTATATATGTGGAGAACGCA 59.126 38.462 0.00 0.00 44.94 5.24
2925 7476 7.097192 TCCATTCTTATATATGTGGAGAACGC 58.903 38.462 0.00 0.00 32.38 4.84
2931 7482 7.397221 CCTTGCTCCATTCTTATATATGTGGA 58.603 38.462 0.00 7.40 34.77 4.02
2932 7483 6.094603 GCCTTGCTCCATTCTTATATATGTGG 59.905 42.308 0.00 0.00 0.00 4.17
2933 7484 6.656270 TGCCTTGCTCCATTCTTATATATGTG 59.344 38.462 0.00 0.00 0.00 3.21
2934 7485 6.782986 TGCCTTGCTCCATTCTTATATATGT 58.217 36.000 0.00 0.00 0.00 2.29
2935 7486 6.318144 CCTGCCTTGCTCCATTCTTATATATG 59.682 42.308 0.00 0.00 0.00 1.78
2936 7487 6.421485 CCTGCCTTGCTCCATTCTTATATAT 58.579 40.000 0.00 0.00 0.00 0.86
2937 7488 5.809001 CCTGCCTTGCTCCATTCTTATATA 58.191 41.667 0.00 0.00 0.00 0.86
2938 7489 4.660168 CCTGCCTTGCTCCATTCTTATAT 58.340 43.478 0.00 0.00 0.00 0.86
2939 7490 4.090761 CCTGCCTTGCTCCATTCTTATA 57.909 45.455 0.00 0.00 0.00 0.98
2940 7491 2.941480 CCTGCCTTGCTCCATTCTTAT 58.059 47.619 0.00 0.00 0.00 1.73
2941 7492 2.425143 CCTGCCTTGCTCCATTCTTA 57.575 50.000 0.00 0.00 0.00 2.10
2942 7493 3.277962 CCTGCCTTGCTCCATTCTT 57.722 52.632 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.