Multiple sequence alignment - TraesCS3B01G086300

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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 TraesCS3B01G086300 chr3B 100.000 3958 0 0 1 3958 54737377 54741334 0.000000e+00 7310.0
1 TraesCS3B01G086300 chr3B 86.900 229 20 7 469 694 658933647 658933426 8.490000e-62 248.0
2 TraesCS3B01G086300 chr3B 80.000 230 36 10 1103 1325 744340634 744340408 1.140000e-35 161.0
3 TraesCS3B01G086300 chr3D 97.976 1729 9 9 2135 3863 32147874 32149576 0.000000e+00 2976.0
4 TraesCS3B01G086300 chr3D 95.806 1383 16 10 722 2075 32146486 32147855 0.000000e+00 2194.0
5 TraesCS3B01G086300 chr3D 95.923 417 15 1 42 458 32145576 32145990 0.000000e+00 675.0
6 TraesCS3B01G086300 chr3D 96.581 234 4 1 466 699 32146184 32146413 6.200000e-103 385.0
7 TraesCS3B01G086300 chr3D 84.483 174 23 4 1154 1325 560827070 560827241 6.800000e-38 169.0
8 TraesCS3B01G086300 chr3D 80.349 229 36 9 1103 1325 560198818 560198593 8.800000e-37 165.0
9 TraesCS3B01G086300 chr3D 94.845 97 2 1 3859 3955 32149938 32150031 8.860000e-32 148.0
10 TraesCS3B01G086300 chr3D 96.721 61 2 0 2081 2141 84562665 84562605 7.000000e-18 102.0
11 TraesCS3B01G086300 chr3D 95.238 63 2 1 2081 2143 606484157 606484218 9.050000e-17 99.0
12 TraesCS3B01G086300 chr3D 87.500 56 7 0 1420 1475 134963996 134963941 9.180000e-07 65.8
13 TraesCS3B01G086300 chr4D 97.860 1729 11 9 2135 3863 35654668 35652966 0.000000e+00 2964.0
14 TraesCS3B01G086300 chr4D 95.540 1390 18 12 722 2082 35656056 35654682 0.000000e+00 2183.0
15 TraesCS3B01G086300 chr4D 96.135 414 14 1 45 458 35656847 35656436 0.000000e+00 675.0
16 TraesCS3B01G086300 chr4D 95.299 234 7 1 466 699 35656359 35656130 6.250000e-98 368.0
17 TraesCS3B01G086300 chr4D 86.061 165 22 1 1156 1320 93761213 93761050 4.060000e-40 176.0
18 TraesCS3B01G086300 chr4D 96.875 64 1 1 2079 2141 505937254 505937191 5.410000e-19 106.0
19 TraesCS3B01G086300 chr4D 95.161 62 2 1 2079 2140 114549435 114549495 3.260000e-16 97.1
20 TraesCS3B01G086300 chr4D 96.552 58 2 0 2081 2138 298539115 298539058 3.260000e-16 97.1
21 TraesCS3B01G086300 chr4D 93.750 64 4 0 2084 2147 418725522 418725585 3.260000e-16 97.1
22 TraesCS3B01G086300 chr4D 96.552 58 2 0 2079 2136 478510056 478509999 3.260000e-16 97.1
23 TraesCS3B01G086300 chr4D 95.000 60 3 0 2081 2140 417670815 417670874 1.170000e-15 95.3
24 TraesCS3B01G086300 chr4D 94.915 59 3 0 2079 2137 441684631 441684689 4.210000e-15 93.5
25 TraesCS3B01G086300 chr4D 88.889 72 6 2 2081 2150 144894863 144894792 1.960000e-13 87.9
26 TraesCS3B01G086300 chr4D 86.538 52 7 0 1420 1471 98015409 98015358 1.540000e-04 58.4
27 TraesCS3B01G086300 chr3A 96.542 1735 17 15 2135 3863 44551169 44552866 0.000000e+00 2832.0
28 TraesCS3B01G086300 chr3A 93.946 1404 29 17 722 2087 44549765 44551150 0.000000e+00 2071.0
29 TraesCS3B01G086300 chr3A 81.140 228 35 8 1103 1325 696290076 696289852 4.060000e-40 176.0
30 TraesCS3B01G086300 chr3A 93.939 66 3 1 2079 2144 679179473 679179409 9.050000e-17 99.0
31 TraesCS3B01G086300 chr3A 90.385 52 4 1 1420 1471 149716650 149716600 2.550000e-07 67.6
32 TraesCS3B01G086300 chr6D 96.535 202 7 0 1 202 462884282 462884081 6.340000e-88 335.0
33 TraesCS3B01G086300 chr6D 86.842 228 20 7 466 690 337807535 337807755 3.050000e-61 246.0
34 TraesCS3B01G086300 chr6D 98.214 56 1 0 2081 2136 332501456 332501511 9.050000e-17 99.0
35 TraesCS3B01G086300 chr6D 94.915 59 3 0 2079 2137 468308125 468308067 4.210000e-15 93.5
36 TraesCS3B01G086300 chr6D 93.548 62 3 1 2079 2140 53035659 53035719 1.510000e-14 91.6
37 TraesCS3B01G086300 chr6D 93.548 62 3 1 2079 2140 103327071 103327131 1.510000e-14 91.6
38 TraesCS3B01G086300 chr6D 93.548 62 3 1 2079 2140 109470322 109470382 1.510000e-14 91.6
39 TraesCS3B01G086300 chr6D 93.548 62 3 1 2079 2140 127951578 127951638 1.510000e-14 91.6
40 TraesCS3B01G086300 chr6D 87.500 56 7 0 1420 1475 61003321 61003376 9.180000e-07 65.8
41 TraesCS3B01G086300 chr1D 96.985 199 6 0 1 199 352400425 352400227 6.340000e-88 335.0
42 TraesCS3B01G086300 chr1D 96.610 59 2 0 2081 2139 7179617 7179559 9.050000e-17 99.0
43 TraesCS3B01G086300 chr1D 98.214 56 1 0 2081 2136 491052590 491052535 9.050000e-17 99.0
44 TraesCS3B01G086300 chr1D 95.161 62 2 1 2079 2140 336626927 336626987 3.260000e-16 97.1
45 TraesCS3B01G086300 chr1D 95.161 62 2 1 2079 2140 449997713 449997653 3.260000e-16 97.1
46 TraesCS3B01G086300 chr1D 91.176 68 5 1 2081 2148 247418639 247418573 1.510000e-14 91.6
47 TraesCS3B01G086300 chr2D 96.970 198 6 0 1 198 119766596 119766793 2.280000e-87 333.0
48 TraesCS3B01G086300 chr2D 96.020 201 8 0 1 201 137569691 137569891 1.060000e-85 327.0
49 TraesCS3B01G086300 chr2D 95.169 207 8 2 1 205 133054877 133054671 3.810000e-85 326.0
50 TraesCS3B01G086300 chr2D 86.842 228 19 8 466 690 33261597 33261816 1.100000e-60 244.0
51 TraesCS3B01G086300 chr2D 100.000 28 0 0 3833 3860 558797762 558797789 7.000000e-03 52.8
52 TraesCS3B01G086300 chr5D 96.020 201 8 0 1 201 452571653 452571853 1.060000e-85 327.0
53 TraesCS3B01G086300 chr5D 86.842 228 20 8 466 690 204082002 204082222 3.050000e-61 246.0
54 TraesCS3B01G086300 chr5D 96.610 59 2 0 2081 2139 455608000 455608058 9.050000e-17 99.0
55 TraesCS3B01G086300 chr5D 95.082 61 2 1 2081 2141 256849799 256849740 1.170000e-15 95.3
56 TraesCS3B01G086300 chr7D 94.712 208 11 0 1 208 65656644 65656437 1.370000e-84 324.0
57 TraesCS3B01G086300 chr7D 87.558 217 21 4 475 690 72118361 72118150 3.050000e-61 246.0
58 TraesCS3B01G086300 chr7D 87.111 225 19 7 469 690 489035544 489035327 3.050000e-61 246.0
59 TraesCS3B01G086300 chr6B 86.207 232 22 7 466 694 138885148 138885372 3.950000e-60 243.0
60 TraesCS3B01G086300 chr6B 100.000 57 0 0 2081 2137 714074607 714074551 5.410000e-19 106.0
61 TraesCS3B01G086300 chr6B 94.030 67 2 2 2081 2146 625918239 625918304 2.520000e-17 100.0
62 TraesCS3B01G086300 chr6B 87.500 56 7 0 1420 1475 134838679 134838734 9.180000e-07 65.8
63 TraesCS3B01G086300 chr4B 86.061 165 22 1 1156 1320 132294956 132294793 4.060000e-40 176.0
64 TraesCS3B01G086300 chr4B 98.305 59 1 0 2081 2139 89386016 89385958 1.950000e-18 104.0
65 TraesCS3B01G086300 chr4B 96.721 61 2 0 2079 2139 518087660 518087720 7.000000e-18 102.0
66 TraesCS3B01G086300 chr4B 98.276 58 1 0 2081 2138 653214347 653214290 7.000000e-18 102.0
67 TraesCS3B01G086300 chr4B 93.750 64 4 0 2081 2144 329074133 329074196 3.260000e-16 97.1
68 TraesCS3B01G086300 chr4B 86.275 51 5 2 1423 1471 139593650 139593600 2.000000e-03 54.7
69 TraesCS3B01G086300 chr7A 100.000 58 0 0 2081 2138 675331767 675331824 1.500000e-19 108.0
70 TraesCS3B01G086300 chr7A 95.238 63 2 1 2079 2141 247275330 247275391 9.050000e-17 99.0
71 TraesCS3B01G086300 chr7A 100.000 28 0 0 3833 3860 700786189 700786162 7.000000e-03 52.8
72 TraesCS3B01G086300 chr1B 100.000 58 0 0 2079 2136 175682539 175682596 1.500000e-19 108.0
73 TraesCS3B01G086300 chr1B 100.000 56 0 0 2081 2136 563743774 563743719 1.950000e-18 104.0
74 TraesCS3B01G086300 chr1B 91.429 70 4 2 2081 2148 28065505 28065436 1.170000e-15 95.3
75 TraesCS3B01G086300 chr5A 95.238 63 3 0 2079 2141 652657783 652657845 2.520000e-17 100.0
76 TraesCS3B01G086300 chr5A 95.238 63 2 1 2079 2141 343241940 343242001 9.050000e-17 99.0
77 TraesCS3B01G086300 chr1A 98.246 57 1 0 2081 2137 456318121 456318065 2.520000e-17 100.0
78 TraesCS3B01G086300 chr1A 95.238 63 2 1 2079 2141 286659476 286659537 9.050000e-17 99.0
79 TraesCS3B01G086300 chr1A 95.161 62 2 1 2079 2140 538050362 538050302 3.260000e-16 97.1
80 TraesCS3B01G086300 chr1A 94.286 35 1 1 3827 3860 107481943 107481977 7.000000e-03 52.8
81 TraesCS3B01G086300 chr6A 95.161 62 2 1 2079 2140 595114703 595114643 3.260000e-16 97.1
82 TraesCS3B01G086300 chr6A 100.000 30 0 0 3831 3860 129336922 129336893 5.530000e-04 56.5
83 TraesCS3B01G086300 chr2B 89.744 78 4 4 2081 2158 146921814 146921741 3.260000e-16 97.1
84 TraesCS3B01G086300 chr2B 92.308 39 1 1 3824 3860 182707636 182707674 2.000000e-03 54.7
85 TraesCS3B01G086300 chrUn 96.429 56 2 0 2081 2136 10314533 10314478 4.210000e-15 93.5
86 TraesCS3B01G086300 chrUn 96.429 56 2 0 2081 2136 16475891 16475836 4.210000e-15 93.5
87 TraesCS3B01G086300 chrUn 96.429 56 2 0 2081 2136 23715068 23715013 4.210000e-15 93.5
88 TraesCS3B01G086300 chrUn 94.915 59 3 0 2079 2137 34537886 34537828 4.210000e-15 93.5
89 TraesCS3B01G086300 chrUn 94.915 59 3 0 2079 2137 58368641 58368699 4.210000e-15 93.5
90 TraesCS3B01G086300 chrUn 96.429 56 2 0 2081 2136 299762065 299762010 4.210000e-15 93.5
91 TraesCS3B01G086300 chrUn 94.915 59 3 0 2079 2137 303488279 303488221 4.210000e-15 93.5
92 TraesCS3B01G086300 chrUn 96.429 56 2 0 2081 2136 319723550 319723605 4.210000e-15 93.5
93 TraesCS3B01G086300 chrUn 96.429 56 2 0 2081 2136 319750691 319750746 4.210000e-15 93.5
94 TraesCS3B01G086300 chrUn 93.548 62 3 1 2079 2140 1522175 1522115 1.510000e-14 91.6
95 TraesCS3B01G086300 chrUn 93.548 62 3 1 2079 2140 97886580 97886520 1.510000e-14 91.6
96 TraesCS3B01G086300 chrUn 93.548 62 3 1 2079 2140 101532548 101532608 1.510000e-14 91.6
97 TraesCS3B01G086300 chrUn 92.188 64 3 2 2081 2143 191163379 191163441 5.450000e-14 89.8
98 TraesCS3B01G086300 chrUn 88.732 71 6 2 2081 2151 38147148 38147080 7.050000e-13 86.1
99 TraesCS3B01G086300 chr5B 87.500 80 8 2 2081 2158 480764979 480765058 1.510000e-14 91.6
100 TraesCS3B01G086300 chr5B 100.000 29 0 0 3832 3860 426991482 426991510 2.000000e-03 54.7
101 TraesCS3B01G086300 chr4A 96.970 33 1 0 3828 3860 649897871 649897903 5.530000e-04 56.5


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 TraesCS3B01G086300 chr3B 54737377 54741334 3957 False 7310.0 7310 100.0000 1 3958 1 chr3B.!!$F1 3957
1 TraesCS3B01G086300 chr3D 32145576 32150031 4455 False 1275.6 2976 96.2262 42 3955 5 chr3D.!!$F3 3913
2 TraesCS3B01G086300 chr4D 35652966 35656847 3881 True 1547.5 2964 96.2085 45 3863 4 chr4D.!!$R7 3818
3 TraesCS3B01G086300 chr3A 44549765 44552866 3101 False 2451.5 2832 95.2440 722 3863 2 chr3A.!!$F1 3141

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
409 410 0.110486 GGCAACTCTCCCAGGAACAA 59.890 55.0 0.00 0.0 0.00 2.83 F
2079 2377 0.677731 CCATCATGGTCCGTGTGCTT 60.678 55.0 10.97 0.0 31.35 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 2417 0.256752 TCATACTCCCTCCGTCCGAA 59.743 55.000 0.0 0.0 0.00 4.30 R
3529 3833 1.065926 TGCCAGAGCACATGGTAGAAG 60.066 52.381 0.0 0.0 46.52 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
20 21 4.882396 GCGCGAGGGCCTCTTCTC 62.882 72.222 29.81 13.49 35.02 2.87
21 22 3.144193 CGCGAGGGCCTCTTCTCT 61.144 66.667 29.81 0.00 35.02 3.10
22 23 2.716017 CGCGAGGGCCTCTTCTCTT 61.716 63.158 29.81 0.00 35.02 2.85
23 24 1.142965 GCGAGGGCCTCTTCTCTTC 59.857 63.158 29.81 3.42 0.00 2.87
24 25 1.326951 GCGAGGGCCTCTTCTCTTCT 61.327 60.000 29.81 0.00 0.00 2.85
25 26 0.744281 CGAGGGCCTCTTCTCTTCTC 59.256 60.000 29.81 1.86 0.00 2.87
26 27 1.859302 GAGGGCCTCTTCTCTTCTCA 58.141 55.000 26.44 0.00 0.00 3.27
27 28 2.183679 GAGGGCCTCTTCTCTTCTCAA 58.816 52.381 26.44 0.00 0.00 3.02
28 29 1.905894 AGGGCCTCTTCTCTTCTCAAC 59.094 52.381 0.00 0.00 0.00 3.18
29 30 1.065782 GGGCCTCTTCTCTTCTCAACC 60.066 57.143 0.84 0.00 0.00 3.77
30 31 1.905894 GGCCTCTTCTCTTCTCAACCT 59.094 52.381 0.00 0.00 0.00 3.50
31 32 2.093711 GGCCTCTTCTCTTCTCAACCTC 60.094 54.545 0.00 0.00 0.00 3.85
32 33 2.093711 GCCTCTTCTCTTCTCAACCTCC 60.094 54.545 0.00 0.00 0.00 4.30
33 34 3.169099 CCTCTTCTCTTCTCAACCTCCA 58.831 50.000 0.00 0.00 0.00 3.86
34 35 3.580458 CCTCTTCTCTTCTCAACCTCCAA 59.420 47.826 0.00 0.00 0.00 3.53
35 36 4.224818 CCTCTTCTCTTCTCAACCTCCAAT 59.775 45.833 0.00 0.00 0.00 3.16
36 37 5.423610 CCTCTTCTCTTCTCAACCTCCAATA 59.576 44.000 0.00 0.00 0.00 1.90
37 38 6.406849 CCTCTTCTCTTCTCAACCTCCAATAG 60.407 46.154 0.00 0.00 0.00 1.73
38 39 4.744795 TCTCTTCTCAACCTCCAATAGC 57.255 45.455 0.00 0.00 0.00 2.97
39 40 4.096681 TCTCTTCTCAACCTCCAATAGCA 58.903 43.478 0.00 0.00 0.00 3.49
40 41 4.718774 TCTCTTCTCAACCTCCAATAGCAT 59.281 41.667 0.00 0.00 0.00 3.79
41 42 4.774124 TCTTCTCAACCTCCAATAGCATG 58.226 43.478 0.00 0.00 0.00 4.06
42 43 4.225942 TCTTCTCAACCTCCAATAGCATGT 59.774 41.667 0.00 0.00 0.00 3.21
43 44 3.877559 TCTCAACCTCCAATAGCATGTG 58.122 45.455 0.00 0.00 0.00 3.21
88 89 3.045634 TCCAACTCCTCTTCCACTTTCA 58.954 45.455 0.00 0.00 0.00 2.69
138 139 2.782925 AGTGCCATATAACCCACATGGA 59.217 45.455 0.00 0.00 41.53 3.41
278 279 5.290386 CCCTCATCTGGAAATAACGAGTAC 58.710 45.833 0.00 0.00 0.00 2.73
307 308 2.190578 GCCCGCAGCCATTCTACT 59.809 61.111 0.00 0.00 34.35 2.57
409 410 0.110486 GGCAACTCTCCCAGGAACAA 59.890 55.000 0.00 0.00 0.00 2.83
543 730 3.255642 CCCTTTGACCGTTTGATTGTCAT 59.744 43.478 0.00 0.00 38.68 3.06
647 834 3.446310 TGCATGTCATTTGCATCCATC 57.554 42.857 0.00 0.00 44.73 3.51
648 835 2.101750 TGCATGTCATTTGCATCCATCC 59.898 45.455 0.00 0.00 44.73 3.51
649 836 2.101750 GCATGTCATTTGCATCCATCCA 59.898 45.455 0.00 0.00 39.90 3.41
650 837 3.244078 GCATGTCATTTGCATCCATCCAT 60.244 43.478 0.00 0.00 39.90 3.41
716 930 4.159135 ACATCCCACAGCTTCATTTTCATC 59.841 41.667 0.00 0.00 0.00 2.92
789 1036 9.777297 ATTTCAAATTAAATGCACCAAGTAAGT 57.223 25.926 0.00 0.00 0.00 2.24
864 1124 1.607148 CCGACAAGGAAGGAACCAAAC 59.393 52.381 0.00 0.00 45.00 2.93
865 1125 1.607148 CGACAAGGAAGGAACCAAACC 59.393 52.381 0.00 0.00 0.00 3.27
866 1126 2.661718 GACAAGGAAGGAACCAAACCA 58.338 47.619 0.00 0.00 0.00 3.67
867 1127 3.028130 GACAAGGAAGGAACCAAACCAA 58.972 45.455 0.00 0.00 0.00 3.67
868 1128 3.445987 ACAAGGAAGGAACCAAACCAAA 58.554 40.909 0.00 0.00 0.00 3.28
909 1169 3.435186 GACCAAAGCAGCCGCCTC 61.435 66.667 0.00 0.00 39.83 4.70
1698 1996 4.537433 CTCCCGCCTACTGCTGCC 62.537 72.222 0.00 0.00 38.05 4.85
1807 2105 1.483827 AGAAGCTCATGATCGCCAGAA 59.516 47.619 0.00 0.00 0.00 3.02
2050 2348 3.507233 TGGAATGCACCAACTTGAGATTC 59.493 43.478 0.00 0.00 36.96 2.52
2075 2373 1.078214 CAGCCATCATGGTCCGTGT 60.078 57.895 5.31 0.00 40.46 4.49
2076 2374 1.078214 AGCCATCATGGTCCGTGTG 60.078 57.895 5.31 8.45 40.46 3.82
2077 2375 2.764314 GCCATCATGGTCCGTGTGC 61.764 63.158 5.31 8.71 40.46 4.57
2079 2377 0.677731 CCATCATGGTCCGTGTGCTT 60.678 55.000 10.97 0.00 31.35 3.91
2080 2378 1.167851 CATCATGGTCCGTGTGCTTT 58.832 50.000 10.97 0.00 0.00 3.51
2081 2379 2.355197 CATCATGGTCCGTGTGCTTTA 58.645 47.619 10.97 0.00 0.00 1.85
2082 2380 2.093306 TCATGGTCCGTGTGCTTTAG 57.907 50.000 10.97 0.00 0.00 1.85
2083 2381 1.621317 TCATGGTCCGTGTGCTTTAGA 59.379 47.619 10.97 0.00 0.00 2.10
2085 2383 3.449377 TCATGGTCCGTGTGCTTTAGATA 59.551 43.478 10.97 0.00 0.00 1.98
2086 2384 3.241067 TGGTCCGTGTGCTTTAGATAC 57.759 47.619 0.00 0.00 0.00 2.24
2088 2386 3.196901 TGGTCCGTGTGCTTTAGATACAT 59.803 43.478 0.00 0.00 0.00 2.29
2089 2387 3.802685 GGTCCGTGTGCTTTAGATACATC 59.197 47.826 0.00 0.00 0.00 3.06
2090 2388 3.802685 GTCCGTGTGCTTTAGATACATCC 59.197 47.826 0.00 0.00 0.00 3.51
2091 2389 3.131396 CCGTGTGCTTTAGATACATCCC 58.869 50.000 0.00 0.00 0.00 3.85
2092 2390 3.131396 CGTGTGCTTTAGATACATCCCC 58.869 50.000 0.00 0.00 0.00 4.81
2094 2392 4.683400 CGTGTGCTTTAGATACATCCCCTT 60.683 45.833 0.00 0.00 0.00 3.95
2095 2393 5.193679 GTGTGCTTTAGATACATCCCCTTT 58.806 41.667 0.00 0.00 0.00 3.11
2096 2394 5.652452 GTGTGCTTTAGATACATCCCCTTTT 59.348 40.000 0.00 0.00 0.00 2.27
2097 2395 6.826741 GTGTGCTTTAGATACATCCCCTTTTA 59.173 38.462 0.00 0.00 0.00 1.52
2098 2396 7.502561 GTGTGCTTTAGATACATCCCCTTTTAT 59.497 37.037 0.00 0.00 0.00 1.40
2099 2397 7.719633 TGTGCTTTAGATACATCCCCTTTTATC 59.280 37.037 0.00 0.00 0.00 1.75
2100 2398 7.939588 GTGCTTTAGATACATCCCCTTTTATCT 59.060 37.037 0.00 0.00 35.79 1.98
2101 2399 9.166222 TGCTTTAGATACATCCCCTTTTATCTA 57.834 33.333 0.00 0.00 34.04 1.98
2111 2409 9.136323 ACATCCCCTTTTATCTATTTTGATGAC 57.864 33.333 0.00 0.00 32.39 3.06
2112 2410 9.135189 CATCCCCTTTTATCTATTTTGATGACA 57.865 33.333 0.00 0.00 0.00 3.58
2113 2411 9.713684 ATCCCCTTTTATCTATTTTGATGACAA 57.286 29.630 0.00 0.00 0.00 3.18
2114 2412 9.189156 TCCCCTTTTATCTATTTTGATGACAAG 57.811 33.333 0.00 0.00 37.32 3.16
2115 2413 8.971073 CCCCTTTTATCTATTTTGATGACAAGT 58.029 33.333 0.00 0.00 37.32 3.16
2124 2422 9.443323 TCTATTTTGATGACAAGTATTTTCGGA 57.557 29.630 0.00 0.00 37.32 4.55
2125 2423 9.490663 CTATTTTGATGACAAGTATTTTCGGAC 57.509 33.333 0.00 0.00 37.32 4.79
2126 2424 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2127 2425 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2128 2426 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2129 2427 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2130 2428 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2131 2429 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2132 2430 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2133 2431 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2173 2471 8.402472 TCATTCCGAATCACCATGTTTTAATAC 58.598 33.333 0.00 0.00 0.00 1.89
2461 2761 0.961019 GTCTGCCTGCACCAAATGAA 59.039 50.000 0.00 0.00 0.00 2.57
2462 2762 1.547372 GTCTGCCTGCACCAAATGAAT 59.453 47.619 0.00 0.00 0.00 2.57
2463 2763 2.028748 GTCTGCCTGCACCAAATGAATT 60.029 45.455 0.00 0.00 0.00 2.17
2464 2764 2.028839 TCTGCCTGCACCAAATGAATTG 60.029 45.455 0.00 0.00 38.84 2.32
2465 2765 1.969208 TGCCTGCACCAAATGAATTGA 59.031 42.857 0.00 0.00 41.85 2.57
2493 2793 4.082733 GCTACTCATGACGTGCCATCTATA 60.083 45.833 0.00 0.00 0.00 1.31
2494 2794 5.393569 GCTACTCATGACGTGCCATCTATAT 60.394 44.000 0.00 0.00 0.00 0.86
2502 2802 3.256879 ACGTGCCATCTATATGTCCTCTG 59.743 47.826 0.00 0.00 0.00 3.35
2966 3266 2.557924 TGCTGCCCATTAGTTTTCTGTG 59.442 45.455 0.00 0.00 0.00 3.66
2967 3267 2.558359 GCTGCCCATTAGTTTTCTGTGT 59.442 45.455 0.00 0.00 0.00 3.72
2968 3268 3.005791 GCTGCCCATTAGTTTTCTGTGTT 59.994 43.478 0.00 0.00 0.00 3.32
2969 3269 4.549458 CTGCCCATTAGTTTTCTGTGTTG 58.451 43.478 0.00 0.00 0.00 3.33
3433 3737 3.030291 TGATTGTTGCTTCAACTGGGTT 58.970 40.909 10.52 0.00 43.85 4.11
3529 3833 8.839310 ACAAATATATATCTTGGTCAGTCTGC 57.161 34.615 15.75 0.00 0.00 4.26
3575 3879 9.962809 ATTTTGTTTTGAAATGATGGACCATAT 57.037 25.926 7.05 0.00 0.00 1.78
3618 3922 4.816385 AGTCCAATTTATCACTATGCCACG 59.184 41.667 0.00 0.00 0.00 4.94
3707 4011 7.669722 ACTCAGAGGGAAACAAATGCTAAAATA 59.330 33.333 1.53 0.00 0.00 1.40
3863 4167 4.154195 CCTCCGTTTGGAATTACTTGACTG 59.846 45.833 0.00 0.00 45.87 3.51
3864 4168 4.710324 TCCGTTTGGAATTACTTGACTGT 58.290 39.130 0.00 0.00 42.85 3.55
3865 4169 4.513692 TCCGTTTGGAATTACTTGACTGTG 59.486 41.667 0.00 0.00 42.85 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.882396 GAGAAGAGGCCCTCGCGC 62.882 72.222 4.80 0.00 35.36 6.86
4 5 2.621371 GAAGAGAAGAGGCCCTCGCG 62.621 65.000 4.80 0.00 35.36 5.87
5 6 1.142965 GAAGAGAAGAGGCCCTCGC 59.857 63.158 4.80 1.57 35.36 5.03
6 7 0.744281 GAGAAGAGAAGAGGCCCTCG 59.256 60.000 4.80 0.00 35.36 4.63
7 8 1.859302 TGAGAAGAGAAGAGGCCCTC 58.141 55.000 1.26 1.26 0.00 4.30
8 9 1.905894 GTTGAGAAGAGAAGAGGCCCT 59.094 52.381 0.00 0.00 0.00 5.19
9 10 1.065782 GGTTGAGAAGAGAAGAGGCCC 60.066 57.143 0.00 0.00 0.00 5.80
10 11 1.905894 AGGTTGAGAAGAGAAGAGGCC 59.094 52.381 0.00 0.00 0.00 5.19
11 12 2.093711 GGAGGTTGAGAAGAGAAGAGGC 60.094 54.545 0.00 0.00 0.00 4.70
12 13 3.169099 TGGAGGTTGAGAAGAGAAGAGG 58.831 50.000 0.00 0.00 0.00 3.69
13 14 4.881019 TTGGAGGTTGAGAAGAGAAGAG 57.119 45.455 0.00 0.00 0.00 2.85
14 15 5.105146 GCTATTGGAGGTTGAGAAGAGAAGA 60.105 44.000 0.00 0.00 0.00 2.87
15 16 5.115480 GCTATTGGAGGTTGAGAAGAGAAG 58.885 45.833 0.00 0.00 0.00 2.85
16 17 4.532126 TGCTATTGGAGGTTGAGAAGAGAA 59.468 41.667 0.00 0.00 0.00 2.87
17 18 4.096681 TGCTATTGGAGGTTGAGAAGAGA 58.903 43.478 0.00 0.00 0.00 3.10
18 19 4.478206 TGCTATTGGAGGTTGAGAAGAG 57.522 45.455 0.00 0.00 0.00 2.85
19 20 4.225942 ACATGCTATTGGAGGTTGAGAAGA 59.774 41.667 0.00 0.00 0.00 2.87
20 21 4.334759 CACATGCTATTGGAGGTTGAGAAG 59.665 45.833 0.00 0.00 0.00 2.85
21 22 4.264253 CACATGCTATTGGAGGTTGAGAA 58.736 43.478 0.00 0.00 0.00 2.87
22 23 3.370846 CCACATGCTATTGGAGGTTGAGA 60.371 47.826 0.00 0.00 34.46 3.27
23 24 2.947652 CCACATGCTATTGGAGGTTGAG 59.052 50.000 0.00 0.00 34.46 3.02
24 25 2.575735 TCCACATGCTATTGGAGGTTGA 59.424 45.455 0.00 0.00 36.96 3.18
25 26 3.003394 TCCACATGCTATTGGAGGTTG 57.997 47.619 0.00 0.00 36.96 3.77
26 27 3.266772 TCTTCCACATGCTATTGGAGGTT 59.733 43.478 10.72 0.00 42.93 3.50
27 28 2.846206 TCTTCCACATGCTATTGGAGGT 59.154 45.455 10.72 0.00 42.93 3.85
28 29 3.135348 TCTCTTCCACATGCTATTGGAGG 59.865 47.826 6.00 6.00 42.93 4.30
29 30 4.412796 TCTCTTCCACATGCTATTGGAG 57.587 45.455 3.28 0.64 42.93 3.86
30 31 4.842531 TTCTCTTCCACATGCTATTGGA 57.157 40.909 0.00 0.00 40.30 3.53
31 32 4.096984 GGTTTCTCTTCCACATGCTATTGG 59.903 45.833 0.00 0.00 0.00 3.16
32 33 4.096984 GGGTTTCTCTTCCACATGCTATTG 59.903 45.833 0.00 0.00 0.00 1.90
33 34 4.018050 AGGGTTTCTCTTCCACATGCTATT 60.018 41.667 0.00 0.00 0.00 1.73
34 35 3.525199 AGGGTTTCTCTTCCACATGCTAT 59.475 43.478 0.00 0.00 0.00 2.97
35 36 2.912956 AGGGTTTCTCTTCCACATGCTA 59.087 45.455 0.00 0.00 0.00 3.49
36 37 1.707427 AGGGTTTCTCTTCCACATGCT 59.293 47.619 0.00 0.00 0.00 3.79
37 38 2.206576 AGGGTTTCTCTTCCACATGC 57.793 50.000 0.00 0.00 0.00 4.06
38 39 6.543831 CCTTATAAGGGTTTCTCTTCCACATG 59.456 42.308 22.09 0.00 42.66 3.21
39 40 6.447084 TCCTTATAAGGGTTTCTCTTCCACAT 59.553 38.462 27.65 0.00 46.47 3.21
40 41 5.788533 TCCTTATAAGGGTTTCTCTTCCACA 59.211 40.000 27.65 3.96 46.47 4.17
41 42 6.309389 TCCTTATAAGGGTTTCTCTTCCAC 57.691 41.667 27.65 0.00 46.47 4.02
42 43 5.428783 CCTCCTTATAAGGGTTTCTCTTCCA 59.571 44.000 27.65 6.36 46.47 3.53
43 44 5.429109 ACCTCCTTATAAGGGTTTCTCTTCC 59.571 44.000 27.65 0.00 46.47 3.46
138 139 8.864087 AGCAATTTCTGAAAAATCTCTAAAGGT 58.136 29.630 6.95 0.00 0.00 3.50
186 187 5.634896 CAGATGGTGTACTGCTGAAATTTC 58.365 41.667 11.41 11.41 0.00 2.17
200 201 1.072266 TTACTTGGGGCAGATGGTGT 58.928 50.000 0.00 0.00 0.00 4.16
201 202 1.271871 TGTTACTTGGGGCAGATGGTG 60.272 52.381 0.00 0.00 0.00 4.17
278 279 2.133742 CTGCGGGCTGGTGACAAAAG 62.134 60.000 0.00 0.00 42.06 2.27
409 410 7.329588 AGAAAGAGTTGGAAATTTTACGTGT 57.670 32.000 0.00 0.00 0.00 4.49
458 459 8.601476 ACGCGTGTTTTTGGAAATTAATAAAAA 58.399 25.926 12.93 3.53 31.72 1.94
459 460 8.128016 ACGCGTGTTTTTGGAAATTAATAAAA 57.872 26.923 12.93 0.00 0.00 1.52
460 461 7.695869 ACGCGTGTTTTTGGAAATTAATAAA 57.304 28.000 12.93 0.00 0.00 1.40
461 462 7.434307 TGAACGCGTGTTTTTGGAAATTAATAA 59.566 29.630 14.98 0.00 38.78 1.40
462 463 6.916387 TGAACGCGTGTTTTTGGAAATTAATA 59.084 30.769 14.98 0.00 38.78 0.98
463 464 5.749109 TGAACGCGTGTTTTTGGAAATTAAT 59.251 32.000 14.98 0.00 38.78 1.40
464 465 5.100259 TGAACGCGTGTTTTTGGAAATTAA 58.900 33.333 14.98 0.00 38.78 1.40
606 793 3.062639 CACATGTAGGTGATGTTTCTCGC 59.937 47.826 0.00 0.00 41.32 5.03
647 834 7.341769 TGGGACTTTCCAATACTTTTATCATGG 59.658 37.037 0.00 0.00 38.64 3.66
648 835 8.292444 TGGGACTTTCCAATACTTTTATCATG 57.708 34.615 0.00 0.00 38.64 3.07
649 836 8.893563 TTGGGACTTTCCAATACTTTTATCAT 57.106 30.769 0.00 0.00 41.44 2.45
679 866 4.216687 TGTGGGATGTTTTAGCTTAAACCG 59.783 41.667 21.89 0.00 37.24 4.44
716 930 5.520376 AGTTTGTCAAATGAGGGAGTTTG 57.480 39.130 0.40 0.00 36.82 2.93
787 1034 1.961180 GCCCATCACACGCTCCTACT 61.961 60.000 0.00 0.00 0.00 2.57
788 1035 1.521681 GCCCATCACACGCTCCTAC 60.522 63.158 0.00 0.00 0.00 3.18
789 1036 2.731571 GGCCCATCACACGCTCCTA 61.732 63.158 0.00 0.00 0.00 2.94
790 1037 4.101448 GGCCCATCACACGCTCCT 62.101 66.667 0.00 0.00 0.00 3.69
864 1124 4.706476 TGAATGATTGAGCTAGGGTTTTGG 59.294 41.667 0.00 0.00 0.00 3.28
865 1125 5.183713 TGTGAATGATTGAGCTAGGGTTTTG 59.816 40.000 0.00 0.00 0.00 2.44
866 1126 5.324409 TGTGAATGATTGAGCTAGGGTTTT 58.676 37.500 0.00 0.00 0.00 2.43
867 1127 4.922206 TGTGAATGATTGAGCTAGGGTTT 58.078 39.130 0.00 0.00 0.00 3.27
868 1128 4.574674 TGTGAATGATTGAGCTAGGGTT 57.425 40.909 0.00 0.00 0.00 4.11
910 1170 4.459089 GTGGAGTGGAGGCGAGGC 62.459 72.222 0.00 0.00 0.00 4.70
911 1171 1.831652 AAAGTGGAGTGGAGGCGAGG 61.832 60.000 0.00 0.00 0.00 4.63
912 1172 0.390472 GAAAGTGGAGTGGAGGCGAG 60.390 60.000 0.00 0.00 0.00 5.03
913 1173 1.671742 GAAAGTGGAGTGGAGGCGA 59.328 57.895 0.00 0.00 0.00 5.54
1496 1794 0.397941 CCAGAGCTCCAACTTGTCCA 59.602 55.000 10.93 0.00 0.00 4.02
1604 1902 1.294659 GGTGCAGTTGAAGAGCTCGG 61.295 60.000 8.37 0.00 0.00 4.63
1605 1903 1.621301 CGGTGCAGTTGAAGAGCTCG 61.621 60.000 8.37 0.00 0.00 5.03
1606 1904 1.905922 GCGGTGCAGTTGAAGAGCTC 61.906 60.000 5.27 5.27 0.00 4.09
2050 2348 1.138036 CCATGATGGCTGTGTTGCG 59.862 57.895 0.00 0.00 0.00 4.85
2075 2373 8.045720 AGATAAAAGGGGATGTATCTAAAGCA 57.954 34.615 0.00 0.00 32.73 3.91
2085 2383 9.136323 GTCATCAAAATAGATAAAAGGGGATGT 57.864 33.333 0.00 0.00 32.47 3.06
2086 2384 9.135189 TGTCATCAAAATAGATAAAAGGGGATG 57.865 33.333 0.00 0.00 0.00 3.51
2088 2386 9.189156 CTTGTCATCAAAATAGATAAAAGGGGA 57.811 33.333 0.00 0.00 32.87 4.81
2089 2387 8.971073 ACTTGTCATCAAAATAGATAAAAGGGG 58.029 33.333 0.00 0.00 32.87 4.79
2098 2396 9.443323 TCCGAAAATACTTGTCATCAAAATAGA 57.557 29.630 0.00 0.00 32.87 1.98
2099 2397 9.490663 GTCCGAAAATACTTGTCATCAAAATAG 57.509 33.333 0.00 0.00 32.87 1.73
2100 2398 8.172484 CGTCCGAAAATACTTGTCATCAAAATA 58.828 33.333 0.00 0.00 32.87 1.40
2101 2399 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2102 2400 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2103 2401 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2104 2402 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2105 2403 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2106 2404 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2107 2405 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2108 2406 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2109 2407 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2110 2408 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2111 2409 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2112 2410 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2113 2411 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2114 2412 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2115 2413 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2116 2414 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2117 2415 1.479323 CATACTCCCTCCGTCCGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
2118 2416 1.108776 CATACTCCCTCCGTCCGAAA 58.891 55.000 0.00 0.00 0.00 3.46
2119 2417 0.256752 TCATACTCCCTCCGTCCGAA 59.743 55.000 0.00 0.00 0.00 4.30
2120 2418 0.256752 TTCATACTCCCTCCGTCCGA 59.743 55.000 0.00 0.00 0.00 4.55
2121 2419 1.269998 GATTCATACTCCCTCCGTCCG 59.730 57.143 0.00 0.00 0.00 4.79
2122 2420 2.599677 AGATTCATACTCCCTCCGTCC 58.400 52.381 0.00 0.00 0.00 4.79
2123 2421 3.892588 AGAAGATTCATACTCCCTCCGTC 59.107 47.826 0.00 0.00 0.00 4.79
2124 2422 3.917300 AGAAGATTCATACTCCCTCCGT 58.083 45.455 0.00 0.00 0.00 4.69
2125 2423 4.946478 AAGAAGATTCATACTCCCTCCG 57.054 45.455 0.00 0.00 0.00 4.63
2126 2424 6.240549 TGAAAGAAGATTCATACTCCCTCC 57.759 41.667 0.00 0.00 34.50 4.30
2127 2425 7.443879 GGAATGAAAGAAGATTCATACTCCCTC 59.556 40.741 3.21 0.00 46.57 4.30
2128 2426 7.286313 GGAATGAAAGAAGATTCATACTCCCT 58.714 38.462 3.21 0.00 46.57 4.20
2129 2427 6.203723 CGGAATGAAAGAAGATTCATACTCCC 59.796 42.308 12.02 7.39 46.57 4.30
2130 2428 6.986817 TCGGAATGAAAGAAGATTCATACTCC 59.013 38.462 3.21 6.77 46.57 3.85
2131 2429 8.425577 TTCGGAATGAAAGAAGATTCATACTC 57.574 34.615 3.21 0.00 46.57 2.59
2132 2430 8.970859 ATTCGGAATGAAAGAAGATTCATACT 57.029 30.769 1.68 0.00 46.57 2.12
2133 2431 8.830580 TGATTCGGAATGAAAGAAGATTCATAC 58.169 33.333 8.18 0.35 46.57 2.39
2250 2550 9.770926 CTTGCCTTGGTGTTAACCTGCAAATTA 62.771 40.741 15.59 0.00 46.10 1.40
2252 2552 7.701328 CTTGCCTTGGTGTTAACCTGCAAAT 62.701 44.000 15.59 0.00 46.10 2.32
2422 2722 5.347093 CAGACACAAACATGAGTAGCTAGTG 59.653 44.000 5.62 4.19 0.00 2.74
2424 2724 4.328440 GCAGACACAAACATGAGTAGCTAG 59.672 45.833 0.00 0.00 0.00 3.42
2425 2725 4.245660 GCAGACACAAACATGAGTAGCTA 58.754 43.478 0.00 0.00 0.00 3.32
2426 2726 3.070018 GCAGACACAAACATGAGTAGCT 58.930 45.455 0.00 0.00 0.00 3.32
2427 2727 2.160417 GGCAGACACAAACATGAGTAGC 59.840 50.000 0.00 0.00 0.00 3.58
2461 2761 3.445450 ACGTCATGAGTAGCAGTCTCAAT 59.555 43.478 0.00 0.00 43.65 2.57
2462 2762 2.820197 ACGTCATGAGTAGCAGTCTCAA 59.180 45.455 0.00 0.00 43.65 3.02
2463 2763 2.162408 CACGTCATGAGTAGCAGTCTCA 59.838 50.000 0.00 7.69 44.37 3.27
2464 2764 2.791567 CACGTCATGAGTAGCAGTCTC 58.208 52.381 0.00 0.00 0.00 3.36
2465 2765 1.135257 GCACGTCATGAGTAGCAGTCT 60.135 52.381 0.00 0.00 0.00 3.24
2494 2794 9.638239 GCAAATTAATAAATCAAACAGAGGACA 57.362 29.630 0.00 0.00 0.00 4.02
2502 2802 8.682128 TCGGACTGCAAATTAATAAATCAAAC 57.318 30.769 0.00 0.00 0.00 2.93
2966 3266 7.335491 GCAGTACGTTATAGATGCTTAACAAC 58.665 38.462 0.00 0.00 0.00 3.32
2967 3267 6.477688 GGCAGTACGTTATAGATGCTTAACAA 59.522 38.462 0.00 0.00 34.19 2.83
2968 3268 5.981315 GGCAGTACGTTATAGATGCTTAACA 59.019 40.000 0.00 0.00 34.19 2.41
2969 3269 6.214399 AGGCAGTACGTTATAGATGCTTAAC 58.786 40.000 0.00 0.00 34.19 2.01
3529 3833 1.065926 TGCCAGAGCACATGGTAGAAG 60.066 52.381 0.00 0.00 46.52 2.85
3863 4167 7.803189 CACCATAAATCAACAGTGAAGTTACAC 59.197 37.037 0.00 0.00 37.30 2.90
3864 4168 7.521423 GCACCATAAATCAACAGTGAAGTTACA 60.521 37.037 0.00 0.00 37.30 2.41
3865 4169 6.801862 GCACCATAAATCAACAGTGAAGTTAC 59.198 38.462 0.00 0.00 37.30 2.50


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

AutoCloner maintained by Alex Coulton.