Multiple sequence alignment - TraesCS5A01G282100

Loading Multiple Alignment...

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 TraesCS5A01G282100 chr5A 100.000 5800 0 0 1 5800 491250030 491255829 0.000000e+00 10711.0
1 TraesCS5A01G282100 chr5A 91.877 751 33 6 2416 3150 60747374 60748112 0.000000e+00 1024.0
2 TraesCS5A01G282100 chr5A 90.153 721 55 9 1700 2416 493376390 493377098 0.000000e+00 924.0
3 TraesCS5A01G282100 chr5A 89.744 702 50 9 993 1676 493375312 493376009 0.000000e+00 878.0
4 TraesCS5A01G282100 chr5A 87.863 758 50 16 2417 3148 452427615 452426874 0.000000e+00 852.0
5 TraesCS5A01G282100 chr5A 89.877 405 36 4 566 967 493374912 493375314 3.100000e-142 516.0
6 TraesCS5A01G282100 chr5A 82.558 258 41 3 1868 2123 491239333 491239588 2.100000e-54 224.0
7 TraesCS5A01G282100 chr5B 90.200 1898 139 22 10 1868 466756178 466758067 0.000000e+00 2431.0
8 TraesCS5A01G282100 chr5B 92.274 1618 92 12 3149 4756 466769869 466771463 0.000000e+00 2265.0
9 TraesCS5A01G282100 chr5B 91.956 721 49 5 1700 2416 470115394 470116109 0.000000e+00 1002.0
10 TraesCS5A01G282100 chr5B 91.137 677 54 6 5127 5800 550554136 550553463 0.000000e+00 913.0
11 TraesCS5A01G282100 chr5B 91.962 423 25 3 993 1410 470112815 470113233 8.370000e-163 584.0
12 TraesCS5A01G282100 chr5B 91.534 378 26 5 4753 5129 466771529 466771901 3.100000e-142 516.0
13 TraesCS5A01G282100 chr5B 97.260 292 8 0 1861 2152 466769368 466769659 4.040000e-136 496.0
14 TraesCS5A01G282100 chr5B 93.636 220 10 2 2197 2416 466769662 466769877 5.600000e-85 326.0
15 TraesCS5A01G282100 chr5B 82.403 233 38 2 1867 2099 265431592 265431821 3.540000e-47 200.0
16 TraesCS5A01G282100 chr5B 87.425 167 18 3 574 740 470091264 470091427 7.670000e-44 189.0
17 TraesCS5A01G282100 chr5B 85.027 187 23 3 1882 2067 466654659 466654841 9.920000e-43 185.0
18 TraesCS5A01G282100 chr5B 92.373 118 5 3 736 851 470093209 470093324 1.290000e-36 165.0
19 TraesCS5A01G282100 chr5B 94.444 54 3 0 4934 4987 466638193 466638246 3.720000e-12 84.2
20 TraesCS5A01G282100 chr5D 90.296 1556 105 23 3442 4994 388093064 388094576 0.000000e+00 1995.0
21 TraesCS5A01G282100 chr5D 85.724 1492 151 21 2 1479 388089566 388091009 0.000000e+00 1519.0
22 TraesCS5A01G282100 chr5D 90.385 676 58 7 5127 5800 560487098 560486428 0.000000e+00 881.0
23 TraesCS5A01G282100 chr5D 87.892 702 52 16 1724 2412 388092038 388092719 0.000000e+00 795.0
24 TraesCS5A01G282100 chr5D 81.884 276 43 5 1850 2123 388051533 388051803 5.850000e-55 226.0
25 TraesCS5A01G282100 chr5D 92.708 96 7 0 5034 5129 388094981 388095076 7.840000e-29 139.0
26 TraesCS5A01G282100 chr5D 80.172 116 18 4 3158 3271 388052766 388052878 1.340000e-11 82.4
27 TraesCS5A01G282100 chr3A 91.478 751 40 11 2416 3151 126127823 126128564 0.000000e+00 1011.0
28 TraesCS5A01G282100 chr3A 88.801 759 38 12 2417 3148 125831053 125831791 0.000000e+00 887.0
29 TraesCS5A01G282100 chr2A 90.775 748 46 16 2417 3151 316792980 316793717 0.000000e+00 977.0
30 TraesCS5A01G282100 chr3D 90.283 741 44 16 2417 3148 576277815 576278536 0.000000e+00 944.0
31 TraesCS5A01G282100 chr3D 90.133 750 38 20 2417 3150 189080693 189081422 0.000000e+00 942.0
32 TraesCS5A01G282100 chr7B 91.876 677 51 4 5127 5800 65665521 65666196 0.000000e+00 942.0
33 TraesCS5A01G282100 chr7B 77.818 275 46 12 295 563 595295932 595295667 7.780000e-34 156.0
34 TraesCS5A01G282100 chr4D 89.382 744 58 16 2417 3148 304573693 304574427 0.000000e+00 917.0
35 TraesCS5A01G282100 chr4D 90.680 676 58 5 5127 5800 97440273 97440945 0.000000e+00 894.0
36 TraesCS5A01G282100 chr2B 91.285 677 52 7 5127 5800 63843336 63842664 0.000000e+00 917.0
37 TraesCS5A01G282100 chr2B 90.519 675 61 2 5127 5800 776235654 776236326 0.000000e+00 889.0
38 TraesCS5A01G282100 chr4B 91.246 674 52 6 5127 5799 42941721 42941054 0.000000e+00 911.0
39 TraesCS5A01G282100 chr4B 77.778 225 40 9 297 516 427362694 427362475 4.720000e-26 130.0
40 TraesCS5A01G282100 chr6D 90.976 676 54 6 5127 5800 81778178 81778848 0.000000e+00 904.0
41 TraesCS5A01G282100 chrUn 90.251 677 60 6 5127 5800 50893870 50893197 0.000000e+00 880.0
42 TraesCS5A01G282100 chr1A 87.467 750 65 16 2417 3152 434582381 434581647 0.000000e+00 837.0
43 TraesCS5A01G282100 chr7D 81.159 207 34 5 1881 2086 548132393 548132191 1.670000e-35 161.0


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 TraesCS5A01G282100 chr5A 491250030 491255829 5799 False 10711.000000 10711 100.000000 1 5800 1 chr5A.!!$F3 5799
1 TraesCS5A01G282100 chr5A 60747374 60748112 738 False 1024.000000 1024 91.877000 2416 3150 1 chr5A.!!$F1 734
2 TraesCS5A01G282100 chr5A 452426874 452427615 741 True 852.000000 852 87.863000 2417 3148 1 chr5A.!!$R1 731
3 TraesCS5A01G282100 chr5A 493374912 493377098 2186 False 772.666667 924 89.924667 566 2416 3 chr5A.!!$F4 1850
4 TraesCS5A01G282100 chr5B 466756178 466758067 1889 False 2431.000000 2431 90.200000 10 1868 1 chr5B.!!$F4 1858
5 TraesCS5A01G282100 chr5B 550553463 550554136 673 True 913.000000 913 91.137000 5127 5800 1 chr5B.!!$R1 673
6 TraesCS5A01G282100 chr5B 466769368 466771901 2533 False 900.750000 2265 93.676000 1861 5129 4 chr5B.!!$F5 3268
7 TraesCS5A01G282100 chr5B 470112815 470116109 3294 False 793.000000 1002 91.959000 993 2416 2 chr5B.!!$F7 1423
8 TraesCS5A01G282100 chr5D 388089566 388095076 5510 False 1112.000000 1995 89.155000 2 5129 4 chr5D.!!$F2 5127
9 TraesCS5A01G282100 chr5D 560486428 560487098 670 True 881.000000 881 90.385000 5127 5800 1 chr5D.!!$R1 673
10 TraesCS5A01G282100 chr3A 126127823 126128564 741 False 1011.000000 1011 91.478000 2416 3151 1 chr3A.!!$F2 735
11 TraesCS5A01G282100 chr3A 125831053 125831791 738 False 887.000000 887 88.801000 2417 3148 1 chr3A.!!$F1 731
12 TraesCS5A01G282100 chr2A 316792980 316793717 737 False 977.000000 977 90.775000 2417 3151 1 chr2A.!!$F1 734
13 TraesCS5A01G282100 chr3D 576277815 576278536 721 False 944.000000 944 90.283000 2417 3148 1 chr3D.!!$F2 731
14 TraesCS5A01G282100 chr3D 189080693 189081422 729 False 942.000000 942 90.133000 2417 3150 1 chr3D.!!$F1 733
15 TraesCS5A01G282100 chr7B 65665521 65666196 675 False 942.000000 942 91.876000 5127 5800 1 chr7B.!!$F1 673
16 TraesCS5A01G282100 chr4D 304573693 304574427 734 False 917.000000 917 89.382000 2417 3148 1 chr4D.!!$F2 731
17 TraesCS5A01G282100 chr4D 97440273 97440945 672 False 894.000000 894 90.680000 5127 5800 1 chr4D.!!$F1 673
18 TraesCS5A01G282100 chr2B 63842664 63843336 672 True 917.000000 917 91.285000 5127 5800 1 chr2B.!!$R1 673
19 TraesCS5A01G282100 chr2B 776235654 776236326 672 False 889.000000 889 90.519000 5127 5800 1 chr2B.!!$F1 673
20 TraesCS5A01G282100 chr4B 42941054 42941721 667 True 911.000000 911 91.246000 5127 5799 1 chr4B.!!$R1 672
21 TraesCS5A01G282100 chr6D 81778178 81778848 670 False 904.000000 904 90.976000 5127 5800 1 chr6D.!!$F1 673
22 TraesCS5A01G282100 chrUn 50893197 50893870 673 True 880.000000 880 90.251000 5127 5800 1 chrUn.!!$R1 673
23 TraesCS5A01G282100 chr1A 434581647 434582381 734 True 837.000000 837 87.467000 2417 3152 1 chr1A.!!$R1 735

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
685 695 0.248289 CCCAACTATCCGAACCACGT 59.752 55.000 0.00 0.0 40.78 4.49 F
928 941 0.548682 ATTCACAGCCCCCACTCTCT 60.549 55.000 0.00 0.0 0.00 3.10 F
932 945 1.920325 CAGCCCCCACTCTCTGGAA 60.920 63.158 0.00 0.0 43.95 3.53 F
2847 5329 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.0 0.00 4.57 F
4201 6806 0.537653 GAGGCCACAGTAGAGGTTCC 59.462 60.000 5.01 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2328 4702 0.824109 GCCCCTTTGAATACCAAGGC 59.176 55.000 0.00 0.00 36.75 4.35 R
2700 5112 2.098298 GCACATAGGCACGCAACG 59.902 61.111 0.00 0.00 0.00 4.10 R
3010 5508 8.070034 TCATTCATTTTGAGCCTAAATGACAT 57.930 30.769 17.44 13.31 46.19 3.06 R
4594 7201 0.529773 GTCACAAGCACACGACTCCA 60.530 55.000 0.00 0.00 0.00 3.86 R
5142 8193 0.326264 AAGCCGGATTCTGCTTGAGT 59.674 50.000 5.05 0.00 45.60 3.41 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
52 53 1.456165 GACCAAAGTTCGACGAAGAGC 59.544 52.381 11.25 0.00 0.00 4.09
78 79 2.420687 CCTCTGTGAGGGGCAATTACTC 60.421 54.545 5.75 0.00 45.43 2.59
85 86 0.455815 GGGGCAATTACTCGCTTTGG 59.544 55.000 0.00 0.00 0.00 3.28
101 102 1.622607 TTGGCCTAGGGACACGATGG 61.623 60.000 11.72 0.00 42.46 3.51
122 123 5.387788 TGGGATCGGATGAATGAATCAATT 58.612 37.500 0.00 0.00 42.54 2.32
123 124 5.242171 TGGGATCGGATGAATGAATCAATTG 59.758 40.000 0.00 0.00 42.54 2.32
179 180 2.308570 TGTCCAACTATCTGGGCATGTT 59.691 45.455 0.00 0.00 46.19 2.71
211 212 9.321562 GTCTTTAATCCAATGGTCGATTACTTA 57.678 33.333 0.00 0.00 32.15 2.24
219 220 6.857964 CCAATGGTCGATTACTTATTGCAATC 59.142 38.462 16.86 0.00 34.31 2.67
222 223 4.510340 GGTCGATTACTTATTGCAATCGGT 59.490 41.667 16.86 17.16 46.39 4.69
252 257 3.634397 CCTCTTGGGCTTGATCTTACA 57.366 47.619 0.00 0.00 0.00 2.41
254 259 3.539604 CTCTTGGGCTTGATCTTACAGG 58.460 50.000 0.00 0.00 0.00 4.00
258 263 1.340991 GGGCTTGATCTTACAGGGCAA 60.341 52.381 0.00 0.00 42.39 4.52
266 271 2.871453 TCTTACAGGGCAAAGGGTTTC 58.129 47.619 0.00 0.00 0.00 2.78
273 278 2.242452 AGGGCAAAGGGTTTCCTCTATC 59.758 50.000 0.00 0.00 44.07 2.08
289 294 1.200716 CTATCGGCCGGCGACTAATTA 59.799 52.381 27.83 6.81 0.00 1.40
331 336 8.976986 AGATGAAATTATCTTTTGAAGCACAC 57.023 30.769 0.00 0.00 33.74 3.82
387 392 4.774660 TGTTAGTTTTGGAGTGGGTACA 57.225 40.909 0.00 0.00 0.00 2.90
434 439 2.487265 GGAAGCCTTTCAGGTGTGAAGA 60.487 50.000 0.00 0.00 43.66 2.87
438 443 2.034685 GCCTTTCAGGTGTGAAGAAACC 59.965 50.000 0.00 0.00 43.66 3.27
452 457 8.617809 GTGTGAAGAAACCAAGAAGTTTGTATA 58.382 33.333 0.00 0.00 40.01 1.47
463 468 7.492994 CCAAGAAGTTTGTATAGGCTTAGAGAC 59.507 40.741 0.00 0.00 0.00 3.36
465 470 8.368962 AGAAGTTTGTATAGGCTTAGAGACTT 57.631 34.615 0.00 1.26 33.88 3.01
486 491 7.177041 AGACTTCCTACTTCGTGAAAATCTACT 59.823 37.037 0.00 0.00 0.00 2.57
523 528 3.627577 ACCTTCGTGATTGTATTCCATGC 59.372 43.478 0.00 0.00 0.00 4.06
579 586 1.066430 GGGTTAGTCCTTCATGCGTCA 60.066 52.381 0.00 0.00 36.25 4.35
611 619 3.500680 GGAACTTGTAGCCGTGATTTTCA 59.499 43.478 0.00 0.00 0.00 2.69
632 642 4.840680 TCATGATCCTAGAACCATAGTGGG 59.159 45.833 0.00 0.00 43.37 4.61
685 695 0.248289 CCCAACTATCCGAACCACGT 59.752 55.000 0.00 0.00 40.78 4.49
728 738 4.724399 TCCTGTGTTTGCATTCCTCTAAA 58.276 39.130 0.00 0.00 0.00 1.85
808 818 2.292569 CCGCGCCTGTACTCTATTAGAA 59.707 50.000 0.00 0.00 0.00 2.10
915 928 7.397892 TTGGTTTTCTTGTAGTCAATTCACA 57.602 32.000 0.00 0.00 32.82 3.58
928 941 0.548682 ATTCACAGCCCCCACTCTCT 60.549 55.000 0.00 0.00 0.00 3.10
932 945 1.920325 CAGCCCCCACTCTCTGGAA 60.920 63.158 0.00 0.00 43.95 3.53
1019 1032 3.219176 CACTCCCATGTGGCTCATTAT 57.781 47.619 0.00 0.00 34.09 1.28
1262 1282 3.483421 CACTACATCATGTCCATGGCAT 58.517 45.455 6.96 11.28 39.24 4.40
1263 1283 4.505390 CCACTACATCATGTCCATGGCATA 60.505 45.833 17.70 9.61 39.24 3.14
1264 1284 4.453478 CACTACATCATGTCCATGGCATAC 59.547 45.833 17.70 8.01 39.24 2.39
1530 1726 6.780031 TTCTTATAAGATCTCAGCTAGTGGCT 59.220 38.462 15.82 0.00 42.91 4.75
1585 1786 9.930158 AATTACCTATTACTAGGAAATTGCCAA 57.070 29.630 12.85 0.00 46.66 4.52
1610 1813 7.055667 AGTTGTCGTCAATACTATGGATGAT 57.944 36.000 0.00 0.00 35.92 2.45
1676 1879 4.298332 CCACACAAAGTTAAGGACAATGC 58.702 43.478 0.00 0.00 0.00 3.56
1689 3799 5.733620 AGGACAATGCTTTTGACAATGAT 57.266 34.783 6.92 0.00 0.00 2.45
1699 3809 8.801715 TGCTTTTGACAATGATACTCTTTTTC 57.198 30.769 0.00 0.00 0.00 2.29
1701 3811 7.867403 GCTTTTGACAATGATACTCTTTTTCCA 59.133 33.333 0.00 0.00 0.00 3.53
1702 3812 9.918630 CTTTTGACAATGATACTCTTTTTCCAT 57.081 29.630 0.00 0.00 0.00 3.41
1703 3813 9.695526 TTTTGACAATGATACTCTTTTTCCATG 57.304 29.630 0.00 0.00 0.00 3.66
1704 3814 8.634335 TTGACAATGATACTCTTTTTCCATGA 57.366 30.769 0.00 0.00 0.00 3.07
1705 3815 8.634335 TGACAATGATACTCTTTTTCCATGAA 57.366 30.769 0.00 0.00 0.00 2.57
1706 3816 9.246670 TGACAATGATACTCTTTTTCCATGAAT 57.753 29.630 0.00 0.00 0.00 2.57
1748 4108 7.678947 CTCTAAGTGAGGTGTTCAAATGATT 57.321 36.000 0.00 0.00 37.61 2.57
1787 4153 4.451096 ACATTTCGAACAGCGTGTATTCTT 59.549 37.500 0.00 0.00 41.80 2.52
1795 4161 6.299966 CGAACAGCGTGTATTCTTTTACTTTG 59.700 38.462 0.00 0.00 34.64 2.77
1917 4283 3.823304 GCTATGGCTAAAATTCCTCAGGG 59.177 47.826 0.00 0.00 35.22 4.45
1925 4291 3.372440 AAATTCCTCAGGGTGATGACC 57.628 47.619 0.00 0.00 42.27 4.02
1970 4336 2.809665 GCAGTGTGGGATGATCTGGATC 60.810 54.545 3.83 3.83 38.29 3.36
2041 4407 2.633488 GAGAAGGTGCACATCCTTACC 58.367 52.381 20.43 4.77 44.19 2.85
2168 4542 3.304057 GCCCATTAAAAGCATCGACTAGC 60.304 47.826 0.00 0.00 0.00 3.42
2205 4579 6.316390 ACATTTGGATAGTTTCGGAGAATGTC 59.684 38.462 0.00 0.00 45.90 3.06
2274 4648 6.477033 CCACTCCAAAGTCTATGATTTAGACG 59.523 42.308 7.03 0.00 46.24 4.18
2303 4677 8.044060 TGGAATTCACAAGTCAAATATCAGAC 57.956 34.615 7.93 0.47 35.02 3.51
2328 4702 7.660208 ACTTGTGTGTTAATTAAGTAGACCAGG 59.340 37.037 0.00 0.00 30.45 4.45
2456 4834 4.762251 GGCACTGTCTTAAAATCTGGTTCT 59.238 41.667 0.00 0.00 0.00 3.01
2700 5112 4.589700 CGTGCGTGTGTGTGTGCC 62.590 66.667 0.00 0.00 0.00 5.01
2839 5321 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2840 5322 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2841 5323 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2842 5324 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2843 5325 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2844 5326 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2845 5327 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2846 5328 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2847 5329 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
2848 5330 1.225991 GTGTGTGTGTGTGTGTGCG 60.226 57.895 0.00 0.00 0.00 5.34
2849 5331 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
2850 5332 3.858989 TGTGTGTGTGTGTGCGCG 61.859 61.111 0.00 0.00 0.00 6.86
3010 5508 3.117512 AGGGGCAAAAGAGTCTTTTCAGA 60.118 43.478 24.77 0.00 0.00 3.27
3177 5677 7.508687 ACATCCATGCATAGAACACTACATTA 58.491 34.615 0.00 0.00 0.00 1.90
3198 5698 3.683365 TCTCTAGACATGCTGCAACAA 57.317 42.857 6.36 0.00 0.00 2.83
3358 5868 9.585099 TCATTGTTCCATGAGTATTTATTTTGC 57.415 29.630 0.00 0.00 0.00 3.68
3418 5928 1.271856 TGCTTCCCCGTGTCATTAGA 58.728 50.000 0.00 0.00 0.00 2.10
3421 5931 2.429610 GCTTCCCCGTGTCATTAGACTA 59.570 50.000 0.00 0.00 45.20 2.59
3435 5945 9.967346 TGTCATTAGACTATTCATAAGTAGCAC 57.033 33.333 0.00 0.00 45.20 4.40
3550 6155 9.784531 ACTAATGGAGTATGATGTATTCCAAAG 57.215 33.333 3.84 6.95 40.96 2.77
3680 6285 4.261801 CCCCATCACTAGAACATTCGTTT 58.738 43.478 0.00 0.00 34.75 3.60
3683 6288 5.088739 CCATCACTAGAACATTCGTTTTGC 58.911 41.667 0.00 0.00 34.75 3.68
3768 6373 0.676736 GCCAATTTTCCCGGTCACAA 59.323 50.000 0.00 0.00 0.00 3.33
3804 6409 7.613585 TCTGTATCCATTTTGTTGAATGCATT 58.386 30.769 12.83 12.83 36.04 3.56
3813 6418 9.536558 CATTTTGTTGAATGCATTACAAAGATG 57.463 29.630 27.10 25.88 40.38 2.90
3819 6424 6.389091 TGAATGCATTACAAAGATGTTGGTC 58.611 36.000 12.97 0.00 41.05 4.02
3834 6439 6.992063 ATGTTGGTCATCAGTTGTAAGATC 57.008 37.500 0.00 0.00 29.76 2.75
3868 6473 6.893759 TGTTTTTACACGTGAACCATCATAG 58.106 36.000 25.01 0.00 38.01 2.23
3870 6475 2.760634 ACACGTGAACCATCATAGCA 57.239 45.000 25.01 0.00 38.01 3.49
3990 6595 5.457778 GGTCCTAGGCGAGGGATATATATGA 60.458 48.000 14.03 0.00 46.70 2.15
3995 6600 6.412362 AGGCGAGGGATATATATGAATGAC 57.588 41.667 0.00 0.00 0.00 3.06
4039 6644 1.068434 GAGGATCAAGAGAGGAAGGCG 59.932 57.143 0.00 0.00 33.17 5.52
4140 6745 2.285773 ATCTCTGGCGACTGTGGCA 61.286 57.895 16.54 10.87 42.76 4.92
4172 6777 7.171678 GTCGCCATAACTTTAGCATATCTTTCT 59.828 37.037 0.00 0.00 0.00 2.52
4201 6806 0.537653 GAGGCCACAGTAGAGGTTCC 59.462 60.000 5.01 0.00 0.00 3.62
4203 6808 1.218316 GCCACAGTAGAGGTTCCCG 59.782 63.158 0.00 0.00 0.00 5.14
4248 6853 8.394121 GTTTCCATATGTCTCTCAGATGTTTTC 58.606 37.037 1.24 0.00 42.25 2.29
4252 6857 4.916041 TGTCTCTCAGATGTTTTCCCAT 57.084 40.909 0.00 0.00 0.00 4.00
4258 6863 4.290985 TCTCAGATGTTTTCCCATTGGGTA 59.709 41.667 21.31 9.47 44.74 3.69
4290 6895 4.838152 GGCTCTTCGATGGCGCCA 62.838 66.667 34.80 34.80 40.41 5.69
4310 6915 1.967319 TTGTCAAGTCTTGTGCCCTC 58.033 50.000 12.30 0.00 0.00 4.30
4365 6970 7.360361 GTCTTCCATACGTTTGAAATTCAAGT 58.640 34.615 8.51 7.11 37.70 3.16
4374 6979 5.060816 CGTTTGAAATTCAAGTTATGCGCAT 59.939 36.000 28.23 28.23 37.70 4.73
4376 6981 4.341935 TGAAATTCAAGTTATGCGCATCG 58.658 39.130 29.11 11.49 0.00 3.84
4397 7002 1.156330 ATCCGGATCCGAGTCCCAT 59.844 57.895 35.42 13.28 42.83 4.00
4427 7032 4.792087 TTCAAGGCGAAGACCCAC 57.208 55.556 0.00 0.00 31.70 4.61
4496 7103 1.300697 GGTCACTTGGTCGACGCTT 60.301 57.895 9.92 0.00 32.74 4.68
4498 7105 1.300620 TCACTTGGTCGACGCTTGG 60.301 57.895 9.92 0.00 0.00 3.61
4543 7150 2.845363 AGGTTTGTCCGACCGTAAAT 57.155 45.000 0.00 0.00 42.11 1.40
4554 7161 2.668001 CGACCGTAAATGTGTGTCCGTA 60.668 50.000 0.00 0.00 0.00 4.02
4594 7201 1.818642 ACGACGTACTTAGGCAGACT 58.181 50.000 0.00 0.00 0.00 3.24
4756 7371 3.561503 GCAACACGGATTAGGTCAAAAC 58.438 45.455 0.00 0.00 0.00 2.43
4775 7460 3.473093 ACGAGAGTGAACGATGTACAG 57.527 47.619 0.33 0.00 46.97 2.74
4805 7491 7.174946 TCCTGTTTCTGACTGATTAAATGTTCC 59.825 37.037 0.00 0.00 0.00 3.62
4853 7539 9.712305 ATTATGTATGCTGTACATCTAAACTCC 57.288 33.333 15.49 0.00 40.38 3.85
4873 7559 2.810274 CCGTATGGAAGCCATTCATGAG 59.190 50.000 4.03 0.00 42.23 2.90
4970 7656 2.339712 GCATGTGGTGGTTGCACC 59.660 61.111 0.00 0.00 45.20 5.01
4974 7660 0.106268 ATGTGGTGGTTGCACCTTGA 60.106 50.000 0.00 0.00 45.21 3.02
5091 8142 1.843376 CACTCAGGACTGGGGTGGT 60.843 63.158 3.97 0.00 34.74 4.16
5153 8205 3.735237 AGAACGAAGACTCAAGCAGAA 57.265 42.857 0.00 0.00 0.00 3.02
5154 8206 4.264460 AGAACGAAGACTCAAGCAGAAT 57.736 40.909 0.00 0.00 0.00 2.40
5170 8222 4.646492 AGCAGAATCCGGCTTTGAATTAAT 59.354 37.500 0.00 0.00 40.96 1.40
5186 8238 5.654650 TGAATTAATAAAGCCATCAACCGGT 59.345 36.000 0.00 0.00 0.00 5.28
5190 8242 0.400213 AAAGCCATCAACCGGTCAGA 59.600 50.000 8.04 10.26 0.00 3.27
5195 8247 3.117888 AGCCATCAACCGGTCAGAATTAT 60.118 43.478 8.04 0.00 0.00 1.28
5201 8253 7.067008 CCATCAACCGGTCAGAATTATAACTTT 59.933 37.037 8.04 0.00 0.00 2.66
5261 8314 1.024579 ACAAAGATACAAGGGCGCCG 61.025 55.000 22.54 9.65 0.00 6.46
5354 8411 0.739813 ATAACCTCTTGCACGCCGAC 60.740 55.000 0.00 0.00 0.00 4.79
5414 8471 3.112075 CGACGATGCAAGGCACGT 61.112 61.111 14.99 14.99 43.04 4.49
5449 8508 1.876156 CTGGGCTTGAAGAAGACACAC 59.124 52.381 0.00 0.00 39.27 3.82
5470 8529 2.039480 CCCATCCAGATCCATCGTCAAT 59.961 50.000 0.00 0.00 0.00 2.57
5479 8538 0.107017 CCATCGTCAATGAAGGCCCT 60.107 55.000 0.00 0.00 37.59 5.19
5553 8612 2.263545 CCCTAGAGCATGGATGGATGA 58.736 52.381 0.00 0.00 0.00 2.92
5569 8628 3.244387 TGGATGACATCGAAGAAACCACA 60.244 43.478 9.31 0.00 43.58 4.17
5582 8642 2.282816 CCACATGGGCGGAACCAA 60.283 61.111 0.00 0.00 45.13 3.67
5669 8729 0.107945 GAAAGAGGGCGAGCAGTCAT 60.108 55.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.530720 TGATGTTGTTGCTGCTACACG 59.469 47.619 16.15 0.00 0.00 4.49
6 7 3.189080 GTGATGATGTTGTTGCTGCTACA 59.811 43.478 12.74 12.74 0.00 2.74
7 8 3.725895 CGTGATGATGTTGTTGCTGCTAC 60.726 47.826 7.29 7.29 0.00 3.58
8 9 2.416202 CGTGATGATGTTGTTGCTGCTA 59.584 45.455 0.00 0.00 0.00 3.49
71 72 2.421529 CCCTAGGCCAAAGCGAGTAATT 60.422 50.000 5.01 0.00 41.24 1.40
72 73 1.141053 CCCTAGGCCAAAGCGAGTAAT 59.859 52.381 5.01 0.00 41.24 1.89
73 74 0.539986 CCCTAGGCCAAAGCGAGTAA 59.460 55.000 5.01 0.00 41.24 2.24
78 79 1.745489 GTGTCCCTAGGCCAAAGCG 60.745 63.158 5.01 0.00 41.24 4.68
85 86 1.122019 ATCCCATCGTGTCCCTAGGC 61.122 60.000 2.05 0.00 0.00 3.93
101 102 6.206243 AGACAATTGATTCATTCATCCGATCC 59.794 38.462 13.59 0.00 33.34 3.36
108 109 5.008415 GCGAGGAGACAATTGATTCATTCAT 59.992 40.000 13.59 0.00 33.34 2.57
179 180 3.010808 ACCATTGGATTAAAGACCCGGAA 59.989 43.478 10.37 0.00 0.00 4.30
211 212 0.602562 CACCACCAACCGATTGCAAT 59.397 50.000 12.83 12.83 34.17 3.56
219 220 3.491598 AAGAGGCCACCACCAACCG 62.492 63.158 5.01 0.00 0.00 4.44
222 223 2.520458 CCAAGAGGCCACCACCAA 59.480 61.111 5.01 0.00 0.00 3.67
252 257 1.755200 TAGAGGAAACCCTTTGCCCT 58.245 50.000 0.00 0.00 33.25 5.19
254 259 2.289565 CGATAGAGGAAACCCTTTGCC 58.710 52.381 0.00 0.00 33.25 4.52
258 263 0.837940 GGCCGATAGAGGAAACCCTT 59.162 55.000 0.00 0.00 33.25 3.95
273 278 2.297912 CGTAATTAGTCGCCGGCCG 61.298 63.158 23.46 21.04 38.61 6.13
289 294 9.436957 AATTTCATCTACACTCAAAACTATCGT 57.563 29.630 0.00 0.00 0.00 3.73
331 336 5.869344 TGTTTGGTGATGAATCTCTTACTCG 59.131 40.000 0.00 0.00 0.00 4.18
434 439 8.161425 TCTAAGCCTATACAAACTTCTTGGTTT 58.839 33.333 0.00 0.00 39.62 3.27
438 443 8.254508 AGTCTCTAAGCCTATACAAACTTCTTG 58.745 37.037 0.00 0.00 0.00 3.02
452 457 3.949113 CGAAGTAGGAAGTCTCTAAGCCT 59.051 47.826 0.00 0.00 0.00 4.58
463 468 6.752815 GGAGTAGATTTTCACGAAGTAGGAAG 59.247 42.308 0.00 0.00 41.61 3.46
465 470 5.163683 CGGAGTAGATTTTCACGAAGTAGGA 60.164 44.000 0.00 0.00 41.61 2.94
486 491 2.516460 GGTCTAGCCTCGCTCGGA 60.516 66.667 0.00 0.00 40.44 4.55
507 512 2.613595 TGCGAGCATGGAATACAATCAC 59.386 45.455 0.00 0.00 0.00 3.06
523 528 1.009829 GGAGCAAACACCTATGCGAG 58.990 55.000 0.00 0.00 46.98 5.03
597 604 4.422073 AGGATCATGAAAATCACGGCTA 57.578 40.909 0.00 0.00 0.00 3.93
611 619 4.832492 ACCCACTATGGTTCTAGGATCAT 58.168 43.478 1.45 1.45 33.91 2.45
632 642 2.821969 ACACATTGATGGAGGCTTCAAC 59.178 45.455 0.00 0.00 34.87 3.18
685 695 5.718130 AGGATGGCTTGATGAAGATTTTTCA 59.282 36.000 0.00 0.00 0.00 2.69
728 738 6.567602 ATCATCTCCTTGCTTAGGTAAAGT 57.432 37.500 5.52 0.00 45.03 2.66
808 818 6.012858 TCCTAGAAACACCCTACACATGAAAT 60.013 38.462 0.00 0.00 0.00 2.17
928 941 8.375493 AGTGTAGGATTGTTTAGTCTATTCCA 57.625 34.615 0.00 0.00 0.00 3.53
1019 1032 1.615651 GCCCATGTACCAATGTCCACA 60.616 52.381 0.00 0.00 0.00 4.17
1096 1109 6.420913 AACACACTTCTGTACAAGGTATCT 57.579 37.500 0.00 0.00 0.00 1.98
1290 1310 9.913310 TCACAAAGTATCCCACATTGAATAATA 57.087 29.630 0.00 0.00 37.93 0.98
1297 1317 6.513806 TCATTCACAAAGTATCCCACATTG 57.486 37.500 0.00 0.00 40.78 2.82
1530 1726 5.657745 TGACGACTGGTAGGGTAAATGAATA 59.342 40.000 0.00 0.00 0.00 1.75
1538 1734 2.812836 TGATGACGACTGGTAGGGTA 57.187 50.000 0.00 0.00 0.00 3.69
1585 1786 6.873997 TCATCCATAGTATTGACGACAACTT 58.126 36.000 1.63 0.00 38.90 2.66
1656 1859 5.852282 AAGCATTGTCCTTAACTTTGTGT 57.148 34.783 0.00 0.00 0.00 3.72
1676 1879 9.918630 ATGGAAAAAGAGTATCATTGTCAAAAG 57.081 29.630 0.00 0.00 31.86 2.27
1699 3809 6.600822 GGGTCAGAATGGACATATATTCATGG 59.399 42.308 0.00 0.00 39.59 3.66
1701 3811 7.460402 AGAGGGTCAGAATGGACATATATTCAT 59.540 37.037 0.00 0.00 39.59 2.57
1702 3812 6.789457 AGAGGGTCAGAATGGACATATATTCA 59.211 38.462 0.00 0.00 39.59 2.57
1703 3813 7.251321 AGAGGGTCAGAATGGACATATATTC 57.749 40.000 0.00 0.00 39.59 1.75
1704 3814 8.742125 TTAGAGGGTCAGAATGGACATATATT 57.258 34.615 0.00 0.00 39.59 1.28
1705 3815 7.958583 ACTTAGAGGGTCAGAATGGACATATAT 59.041 37.037 0.00 0.00 39.59 0.86
1706 3816 7.233553 CACTTAGAGGGTCAGAATGGACATATA 59.766 40.741 0.00 0.00 39.59 0.86
1707 3817 6.042552 CACTTAGAGGGTCAGAATGGACATAT 59.957 42.308 0.00 0.00 39.59 1.78
1708 3818 5.363868 CACTTAGAGGGTCAGAATGGACATA 59.636 44.000 0.00 0.00 39.59 2.29
1917 4283 6.546403 TCCATACAACTCTACTAGGTCATCAC 59.454 42.308 0.00 0.00 0.00 3.06
1925 4291 9.232473 TGCTATGTATCCATACAACTCTACTAG 57.768 37.037 3.54 1.46 45.40 2.57
1970 4336 9.935682 AATATTGACGACATAATTAAGCAACAG 57.064 29.630 0.00 0.00 0.00 3.16
2041 4407 9.865321 CTTATTCCTCCAAATAATTGCATATGG 57.135 33.333 4.56 0.00 35.10 2.74
2168 4542 6.049149 ACTATCCAAATGTGTGATTAGGACG 58.951 40.000 0.00 0.00 0.00 4.79
2251 4625 6.574350 CCGTCTAAATCATAGACTTTGGAGT 58.426 40.000 12.34 0.00 41.19 3.85
2274 4648 3.940209 TTGACTTGTGAATTCCATGCC 57.060 42.857 2.27 0.00 0.00 4.40
2303 4677 7.360946 GCCTGGTCTACTTAATTAACACACAAG 60.361 40.741 0.00 0.00 0.00 3.16
2328 4702 0.824109 GCCCCTTTGAATACCAAGGC 59.176 55.000 0.00 0.00 36.75 4.35
2334 4708 4.230745 TCTACTTGGCCCCTTTGAATAC 57.769 45.455 0.00 0.00 0.00 1.89
2376 4750 9.088512 CAGCCCTATATTACGAAGTGAATAATC 57.911 37.037 0.00 0.00 45.73 1.75
2434 4812 5.948992 AGAACCAGATTTTAAGACAGTGC 57.051 39.130 0.00 0.00 0.00 4.40
2529 4907 4.394920 GTCATTTAGGCTCAAAATGGACGA 59.605 41.667 18.10 1.82 42.17 4.20
2700 5112 2.098298 GCACATAGGCACGCAACG 59.902 61.111 0.00 0.00 0.00 4.10
3010 5508 8.070034 TCATTCATTTTGAGCCTAAATGACAT 57.930 30.769 17.44 13.31 46.19 3.06
3062 5560 7.839680 ATTCTTCCCTATTTGACACAAGTTT 57.160 32.000 0.00 0.00 0.00 2.66
3177 5677 3.900966 TGTTGCAGCATGTCTAGAGAT 57.099 42.857 0.00 0.00 39.31 2.75
3234 5734 8.986477 AGAGCACAAATAATACAAAATTCACC 57.014 30.769 0.00 0.00 0.00 4.02
3267 5774 9.332502 TGAAAACTGAGCTTTATGTTTACTACA 57.667 29.630 0.00 0.00 41.97 2.74
3268 5775 9.595357 GTGAAAACTGAGCTTTATGTTTACTAC 57.405 33.333 0.00 0.00 33.07 2.73
3373 5883 3.352648 TCCTGCAGGTAAGGCAAAATAC 58.647 45.455 31.58 0.00 41.39 1.89
3381 5891 2.827921 AGCATTTTTCCTGCAGGTAAGG 59.172 45.455 31.58 23.72 42.15 2.69
3443 5953 9.903682 TCGCTTATACAATCCAAAGTACTATAC 57.096 33.333 0.00 0.00 0.00 1.47
3445 5955 8.639761 ACTCGCTTATACAATCCAAAGTACTAT 58.360 33.333 0.00 0.00 0.00 2.12
3446 5956 8.004087 ACTCGCTTATACAATCCAAAGTACTA 57.996 34.615 0.00 0.00 0.00 1.82
3447 5957 6.875076 ACTCGCTTATACAATCCAAAGTACT 58.125 36.000 0.00 0.00 0.00 2.73
3448 5958 7.919621 AGTACTCGCTTATACAATCCAAAGTAC 59.080 37.037 0.00 0.00 36.97 2.73
3454 6059 8.859236 AGTATAGTACTCGCTTATACAATCCA 57.141 34.615 12.91 0.00 32.47 3.41
3533 6138 9.651718 GTTCGATTTCTTTGGAATACATCATAC 57.348 33.333 0.00 0.00 0.00 2.39
3534 6139 9.389755 TGTTCGATTTCTTTGGAATACATCATA 57.610 29.630 0.00 0.00 0.00 2.15
3535 6140 8.279970 TGTTCGATTTCTTTGGAATACATCAT 57.720 30.769 0.00 0.00 0.00 2.45
3550 6155 4.083271 CCCAAAGGAACTCTGTTCGATTTC 60.083 45.833 4.65 0.00 38.49 2.17
3813 6418 8.547967 TTAAGATCTTACAACTGATGACCAAC 57.452 34.615 14.85 0.00 0.00 3.77
3854 6459 3.525537 ACTTCTGCTATGATGGTTCACG 58.474 45.455 0.00 0.00 33.85 4.35
3990 6595 7.653713 GTCATACTCAATTAGACCATCGTCATT 59.346 37.037 0.00 0.00 41.87 2.57
3995 6600 7.147976 TCATGTCATACTCAATTAGACCATCG 58.852 38.462 0.00 0.00 0.00 3.84
4034 6639 0.827368 GGTCATCTCCTTCTCGCCTT 59.173 55.000 0.00 0.00 0.00 4.35
4101 6706 1.068816 GTTAAATGTGAACGGCCGCTT 60.069 47.619 28.58 18.95 0.00 4.68
4140 6745 2.185004 AAAGTTATGGCGACTGCACT 57.815 45.000 0.00 0.00 45.35 4.40
4172 6777 4.752879 GTGGCCTCAACCGCGCTA 62.753 66.667 5.56 0.00 0.00 4.26
4203 6808 1.204941 ACCACTCTGCACTTCCGATAC 59.795 52.381 0.00 0.00 0.00 2.24
4220 6825 5.426509 ACATCTGAGAGACATATGGAAACCA 59.573 40.000 7.80 0.00 37.39 3.67
4252 6857 3.257375 CCGGATCTCGTCATAATACCCAA 59.743 47.826 0.00 0.00 37.11 4.12
4258 6863 2.520069 AGAGCCGGATCTCGTCATAAT 58.480 47.619 18.52 0.00 38.12 1.28
4289 6894 2.227388 GAGGGCACAAGACTTGACAATG 59.773 50.000 21.95 10.30 0.00 2.82
4290 6895 2.158623 TGAGGGCACAAGACTTGACAAT 60.159 45.455 21.95 5.72 0.00 2.71
4310 6915 1.230635 CGGCAACCACAGACCTCTTG 61.231 60.000 0.00 0.00 0.00 3.02
4376 6981 1.660917 GGACTCGGATCCGGATGAC 59.339 63.158 32.79 21.17 40.25 3.06
4397 7002 1.603678 GCCTTGAAGGTACAACGACGA 60.604 52.381 13.58 0.00 37.80 4.20
4427 7032 0.738975 TCTCTCGAGTGTTATGCCCG 59.261 55.000 13.13 0.00 0.00 6.13
4498 7105 1.065126 AGGAAAGCTACCTGGCATCAC 60.065 52.381 10.97 0.00 36.30 3.06
4521 7128 3.959535 TTACGGTCGGACAAACCTTAT 57.040 42.857 10.76 0.00 34.45 1.73
4543 7150 3.116073 CGCTCATTACGGACACACA 57.884 52.632 0.00 0.00 0.00 3.72
4554 7161 0.625849 AATCCCTTGGTCCGCTCATT 59.374 50.000 0.00 0.00 0.00 2.57
4594 7201 0.529773 GTCACAAGCACACGACTCCA 60.530 55.000 0.00 0.00 0.00 3.86
4604 7211 1.311859 CTCCAAGCTTGTCACAAGCA 58.688 50.000 37.59 20.25 45.30 3.91
4756 7371 2.418976 TCCTGTACATCGTTCACTCTCG 59.581 50.000 0.00 0.00 0.00 4.04
4775 7460 3.971245 ATCAGTCAGAAACAGGAGTCC 57.029 47.619 0.00 0.00 0.00 3.85
4853 7539 2.810274 CCTCATGAATGGCTTCCATACG 59.190 50.000 0.00 0.00 44.40 3.06
4873 7559 9.087424 GAGTCCAATTTTAACAGCATAATTTCC 57.913 33.333 0.00 0.00 0.00 3.13
5142 8193 0.326264 AAGCCGGATTCTGCTTGAGT 59.674 50.000 5.05 0.00 45.60 3.41
5170 8222 1.626321 TCTGACCGGTTGATGGCTTTA 59.374 47.619 9.42 0.00 0.00 1.85
5195 8247 8.623030 GTTGGTGAGTGGTGTAATTTAAAGTTA 58.377 33.333 0.00 0.00 0.00 2.24
5201 8253 8.212312 TCTTTAGTTGGTGAGTGGTGTAATTTA 58.788 33.333 0.00 0.00 0.00 1.40
5261 8314 1.682005 TGCATTGTAAGCTGCCCCC 60.682 57.895 0.00 0.00 37.59 5.40
5271 8325 5.937540 ACTAGCTTGTTGTATGTGCATTGTA 59.062 36.000 0.00 0.00 0.00 2.41
5335 8391 0.739813 GTCGGCGTGCAAGAGGTTAT 60.740 55.000 6.85 0.00 0.00 1.89
5354 8411 1.083489 TATCGCTTTCGCCTTGGTTG 58.917 50.000 0.00 0.00 35.26 3.77
5422 8479 1.981256 TCTTCAAGCCCAGGTGTTTC 58.019 50.000 0.00 0.00 0.00 2.78
5449 8508 1.051008 TGACGATGGATCTGGATGGG 58.949 55.000 0.00 0.00 0.00 4.00
5470 8529 0.976073 CGAGGAGGTAAGGGCCTTCA 60.976 60.000 24.77 6.70 39.34 3.02
5479 8538 2.038975 AGCCAGGCGAGGAGGTAA 59.961 61.111 5.55 0.00 0.00 2.85
5542 8601 4.694760 TTCTTCGATGTCATCCATCCAT 57.305 40.909 7.25 0.00 46.10 3.41
5553 8612 2.436417 CCCATGTGGTTTCTTCGATGT 58.564 47.619 0.00 0.00 0.00 3.06
5569 8628 1.305213 AATGCTTGGTTCCGCCCAT 60.305 52.632 0.00 0.00 33.60 4.00
5669 8729 3.181462 TGTTGTTGCCCAATTGTGCATTA 60.181 39.130 16.48 6.02 37.33 1.90


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

AutoCloner maintained by Alex Coulton.