Multiple sequence alignment - TraesCS5A01G200800

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 TraesCS5A01G200800 chr5A 100.000 6094 0 0 990 7083 406672895 406666802 0.000000e+00 11254.0
1 TraesCS5A01G200800 chr5A 100.000 532 0 0 1 532 406673884 406673353 0.000000e+00 983.0
2 TraesCS5A01G200800 chr5A 94.215 121 7 0 1 121 406678945 406678825 1.210000e-42 185.0
3 TraesCS5A01G200800 chr5A 86.585 82 9 2 6708 6789 6479770 6479849 9.790000e-14 89.8
4 TraesCS5A01G200800 chr5B 94.274 6078 211 46 990 6992 359314471 359308456 0.000000e+00 9169.0
5 TraesCS5A01G200800 chr5B 95.316 918 30 6 1606 2521 648736964 648737870 0.000000e+00 1445.0
6 TraesCS5A01G200800 chr5B 92.925 424 17 3 122 532 359314940 359314517 7.860000e-169 604.0
7 TraesCS5A01G200800 chr5B 93.443 122 8 0 1 122 214942257 214942136 1.570000e-41 182.0
8 TraesCS5A01G200800 chr5D 97.843 3014 48 11 990 3999 312609182 312606182 0.000000e+00 5190.0
9 TraesCS5A01G200800 chr5D 95.910 3154 68 19 3958 7083 312606190 312603070 0.000000e+00 5053.0
10 TraesCS5A01G200800 chr5D 88.652 423 32 8 122 532 312609657 312609239 1.060000e-137 501.0
11 TraesCS5A01G200800 chr7B 94.798 1288 54 6 1236 2521 263150378 263151654 0.000000e+00 1995.0
12 TraesCS5A01G200800 chr7B 84.177 158 21 3 142 295 150838700 150838857 4.430000e-32 150.0
13 TraesCS5A01G200800 chr1B 92.062 1285 60 21 1239 2521 372098872 372097628 0.000000e+00 1770.0
14 TraesCS5A01G200800 chr1B 82.653 98 16 1 6894 6991 502386100 502386196 1.270000e-12 86.1
15 TraesCS5A01G200800 chr7D 95.628 915 27 6 1609 2521 513996142 513995239 0.000000e+00 1456.0
16 TraesCS5A01G200800 chr7D 85.065 154 19 3 145 294 4181370 4181523 3.420000e-33 154.0
17 TraesCS5A01G200800 chr7A 95.207 918 31 6 1606 2521 673066056 673066962 0.000000e+00 1439.0
18 TraesCS5A01G200800 chr3D 95.098 918 32 6 1606 2521 208830981 208831887 0.000000e+00 1434.0
19 TraesCS5A01G200800 chr6B 94.754 915 35 6 1609 2521 388076505 388075602 0.000000e+00 1411.0
20 TraesCS5A01G200800 chr6B 86.275 153 18 3 145 294 683376234 683376082 5.690000e-36 163.0
21 TraesCS5A01G200800 chr6B 85.714 154 16 5 145 292 6004336 6004489 2.650000e-34 158.0
22 TraesCS5A01G200800 chr4A 82.375 817 103 24 1116 1927 654360456 654361236 0.000000e+00 673.0
23 TraesCS5A01G200800 chr4A 80.128 312 37 11 1116 1426 654249407 654249694 7.200000e-50 209.0
24 TraesCS5A01G200800 chr2D 93.333 120 8 0 1 120 331307593 331307474 2.030000e-40 178.0
25 TraesCS5A01G200800 chr2D 84.277 159 20 5 140 294 7402785 7402628 4.430000e-32 150.0
26 TraesCS5A01G200800 chr2D 91.860 86 6 1 6704 6789 14027793 14027877 1.250000e-22 119.0
27 TraesCS5A01G200800 chr2D 95.455 44 1 1 79 121 331181720 331181677 1.270000e-07 69.4
28 TraesCS5A01G200800 chr6D 85.714 154 17 5 145 294 431160668 431160820 2.650000e-34 158.0
29 TraesCS5A01G200800 chr6D 92.208 77 5 1 1 76 454003512 454003436 2.700000e-19 108.0
30 TraesCS5A01G200800 chr6D 82.540 126 13 8 1 121 454008465 454008344 1.260000e-17 102.0
31 TraesCS5A01G200800 chr2A 85.256 156 16 7 144 294 367649322 367649169 3.420000e-33 154.0
32 TraesCS5A01G200800 chr2A 88.372 86 7 3 6708 6792 187205961 187205878 4.520000e-17 100.0
33 TraesCS5A01G200800 chr2A 97.778 45 1 0 1239 1283 37030425 37030381 2.120000e-10 78.7
34 TraesCS5A01G200800 chrUn 84.868 152 21 2 145 294 96478384 96478233 1.230000e-32 152.0
35 TraesCS5A01G200800 chr4D 84.277 159 19 5 144 298 42146452 42146296 4.430000e-32 150.0
36 TraesCS5A01G200800 chr1A 92.593 81 6 0 6708 6788 584582645 584582725 4.490000e-22 117.0
37 TraesCS5A01G200800 chr1A 95.833 48 2 0 1236 1283 561614310 561614357 2.120000e-10 78.7
38 TraesCS5A01G200800 chr3A 91.358 81 7 0 6708 6788 67901736 67901816 2.090000e-20 111.0
39 TraesCS5A01G200800 chr3A 95.833 48 2 0 1236 1283 10617878 10617925 2.120000e-10 78.7
40 TraesCS5A01G200800 chr2B 90.123 81 7 1 6708 6788 534924157 534924078 3.490000e-18 104.0
41 TraesCS5A01G200800 chr1D 85.366 82 11 1 6708 6789 22162903 22162823 4.550000e-12 84.2
42 TraesCS5A01G200800 chr3B 84.211 76 11 1 6908 6983 271929188 271929114 9.860000e-09 73.1


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 TraesCS5A01G200800 chr5A 406666802 406673884 7082 True 6118.500000 11254 100.0000 1 7083 2 chr5A.!!$R2 7082
1 TraesCS5A01G200800 chr5B 359308456 359314940 6484 True 4886.500000 9169 93.5995 122 6992 2 chr5B.!!$R2 6870
2 TraesCS5A01G200800 chr5B 648736964 648737870 906 False 1445.000000 1445 95.3160 1606 2521 1 chr5B.!!$F1 915
3 TraesCS5A01G200800 chr5D 312603070 312609657 6587 True 3581.333333 5190 94.1350 122 7083 3 chr5D.!!$R1 6961
4 TraesCS5A01G200800 chr7B 263150378 263151654 1276 False 1995.000000 1995 94.7980 1236 2521 1 chr7B.!!$F2 1285
5 TraesCS5A01G200800 chr1B 372097628 372098872 1244 True 1770.000000 1770 92.0620 1239 2521 1 chr1B.!!$R1 1282
6 TraesCS5A01G200800 chr7D 513995239 513996142 903 True 1456.000000 1456 95.6280 1609 2521 1 chr7D.!!$R1 912
7 TraesCS5A01G200800 chr7A 673066056 673066962 906 False 1439.000000 1439 95.2070 1606 2521 1 chr7A.!!$F1 915
8 TraesCS5A01G200800 chr3D 208830981 208831887 906 False 1434.000000 1434 95.0980 1606 2521 1 chr3D.!!$F1 915
9 TraesCS5A01G200800 chr6B 388075602 388076505 903 True 1411.000000 1411 94.7540 1609 2521 1 chr6B.!!$R1 912
10 TraesCS5A01G200800 chr4A 654360456 654361236 780 False 673.000000 673 82.3750 1116 1927 1 chr4A.!!$F2 811

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
93 94 0.037232 CCGGGTCTCTGTCCTTTGTC 60.037 60.000 0.00 0.00 0.00 3.18 F
100 101 0.318441 TCTGTCCTTTGTCGAGCCTG 59.682 55.000 0.00 0.00 0.00 4.85 F
119 120 0.952984 GAGCTGTCTGTGGCCTTGAC 60.953 60.000 3.32 10.22 0.00 3.18 F
120 121 1.227943 GCTGTCTGTGGCCTTGACA 60.228 57.895 19.40 19.40 38.24 3.58 F
1008 1029 2.699938 ATCCCCACCCCACCATCC 60.700 66.667 0.00 0.00 0.00 3.51 F
1011 1032 4.109675 CCCACCCCACCATCCGAC 62.110 72.222 0.00 0.00 0.00 4.79 F
2737 2799 1.977594 GACCCTTGCGCACCGTATTG 61.978 60.000 11.12 0.00 0.00 1.90 F
3297 3367 5.839063 TGTCTACCTCCTGAATTACCCATAG 59.161 44.000 0.00 0.00 0.00 2.23 F
4149 4266 7.654116 TGTAAATGTGACATCTCAAACGACTTA 59.346 33.333 0.00 0.00 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 1591 0.802494 CCGATCAAAACCTGGAACCG 59.198 55.000 0.00 0.00 0.00 4.44 R
1845 1875 3.011566 TCTCAAACCAAAGGAAGCACA 57.988 42.857 0.00 0.00 0.00 4.57 R
1848 1878 3.254411 CCTCTTCTCAAACCAAAGGAAGC 59.746 47.826 0.00 0.00 34.98 3.86 R
1855 1885 4.445735 CCAAGGTACCTCTTCTCAAACCAA 60.446 45.833 16.64 0.00 0.00 3.67 R
2737 2799 2.222445 ACAAACGTGCGGAGTTATCAAC 59.778 45.455 0.00 0.00 0.00 3.18 R
3287 3357 3.676750 ACTGTAAGGCCCTATGGGTAAT 58.323 45.455 0.00 0.00 41.12 1.89 R
4149 4266 1.068333 GTCACAAACGGATGCTGCAAT 60.068 47.619 6.36 0.00 0.00 3.56 R
4524 4642 2.028203 ACACATGTCATCGTCATCACCA 60.028 45.455 0.00 0.00 0.00 4.17 R
6236 6363 0.037882 TGCAGCTGCTCAGAGTGTAC 60.038 55.000 36.61 6.43 42.66 2.90 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
17 18 2.032071 GGTTCACACCCACTCCGG 59.968 66.667 0.00 0.00 37.03 5.14
18 19 2.668550 GTTCACACCCACTCCGGC 60.669 66.667 0.00 0.00 0.00 6.13
19 20 3.948719 TTCACACCCACTCCGGCC 61.949 66.667 0.00 0.00 0.00 6.13
20 21 4.954118 TCACACCCACTCCGGCCT 62.954 66.667 0.00 0.00 0.00 5.19
21 22 4.704833 CACACCCACTCCGGCCTG 62.705 72.222 0.00 0.00 0.00 4.85
26 27 4.767255 CCACTCCGGCCTGCTGAC 62.767 72.222 0.00 0.00 0.00 3.51
27 28 4.767255 CACTCCGGCCTGCTGACC 62.767 72.222 0.00 0.00 0.00 4.02
34 35 4.341783 GCCTGCTGACCCTGCTGT 62.342 66.667 0.00 0.00 0.00 4.40
35 36 2.433446 CCTGCTGACCCTGCTGTT 59.567 61.111 0.00 0.00 0.00 3.16
36 37 1.970114 CCTGCTGACCCTGCTGTTG 60.970 63.158 0.00 0.00 0.00 3.33
37 38 1.970114 CTGCTGACCCTGCTGTTGG 60.970 63.158 0.00 0.00 0.00 3.77
45 46 3.741476 CTGCTGTTGGGCCGCTTC 61.741 66.667 0.00 0.00 0.00 3.86
46 47 4.269523 TGCTGTTGGGCCGCTTCT 62.270 61.111 0.00 0.00 0.00 2.85
47 48 3.741476 GCTGTTGGGCCGCTTCTG 61.741 66.667 0.00 0.00 0.00 3.02
48 49 3.741476 CTGTTGGGCCGCTTCTGC 61.741 66.667 0.00 0.00 0.00 4.26
54 55 3.207669 GGCCGCTTCTGCCTGATG 61.208 66.667 0.00 0.00 45.70 3.07
55 56 3.207669 GCCGCTTCTGCCTGATGG 61.208 66.667 0.00 0.00 35.36 3.51
56 57 2.515523 CCGCTTCTGCCTGATGGG 60.516 66.667 0.00 0.00 35.36 4.00
82 83 4.083862 GTGGTGAGGCCGGGTCTC 62.084 72.222 21.70 21.70 41.21 3.36
83 84 4.316823 TGGTGAGGCCGGGTCTCT 62.317 66.667 27.54 8.19 41.21 3.10
84 85 3.775654 GGTGAGGCCGGGTCTCTG 61.776 72.222 27.54 0.00 35.05 3.35
85 86 2.997897 GTGAGGCCGGGTCTCTGT 60.998 66.667 27.54 0.00 35.05 3.41
86 87 2.680352 TGAGGCCGGGTCTCTGTC 60.680 66.667 27.54 4.41 35.05 3.51
87 88 3.462678 GAGGCCGGGTCTCTGTCC 61.463 72.222 21.25 0.00 30.76 4.02
88 89 3.966930 GAGGCCGGGTCTCTGTCCT 62.967 68.421 21.25 4.00 30.76 3.85
89 90 3.003763 GGCCGGGTCTCTGTCCTT 61.004 66.667 2.18 0.00 0.00 3.36
90 91 2.593956 GGCCGGGTCTCTGTCCTTT 61.594 63.158 2.18 0.00 0.00 3.11
91 92 1.376037 GCCGGGTCTCTGTCCTTTG 60.376 63.158 2.18 0.00 0.00 2.77
92 93 2.058675 CCGGGTCTCTGTCCTTTGT 58.941 57.895 0.00 0.00 0.00 2.83
93 94 0.037232 CCGGGTCTCTGTCCTTTGTC 60.037 60.000 0.00 0.00 0.00 3.18
94 95 0.388649 CGGGTCTCTGTCCTTTGTCG 60.389 60.000 0.00 0.00 0.00 4.35
95 96 0.966920 GGGTCTCTGTCCTTTGTCGA 59.033 55.000 0.00 0.00 0.00 4.20
96 97 1.067495 GGGTCTCTGTCCTTTGTCGAG 60.067 57.143 0.00 0.00 0.00 4.04
97 98 1.670380 GGTCTCTGTCCTTTGTCGAGC 60.670 57.143 0.00 0.00 0.00 5.03
98 99 0.603569 TCTCTGTCCTTTGTCGAGCC 59.396 55.000 0.00 0.00 0.00 4.70
99 100 0.605589 CTCTGTCCTTTGTCGAGCCT 59.394 55.000 0.00 0.00 0.00 4.58
100 101 0.318441 TCTGTCCTTTGTCGAGCCTG 59.682 55.000 0.00 0.00 0.00 4.85
101 102 0.318441 CTGTCCTTTGTCGAGCCTGA 59.682 55.000 0.00 0.00 0.00 3.86
102 103 0.318441 TGTCCTTTGTCGAGCCTGAG 59.682 55.000 0.00 0.00 0.00 3.35
103 104 1.016653 GTCCTTTGTCGAGCCTGAGC 61.017 60.000 0.00 0.00 40.32 4.26
113 114 2.745492 GCCTGAGCTGTCTGTGGC 60.745 66.667 0.00 0.00 35.50 5.01
114 115 2.046507 CCTGAGCTGTCTGTGGCC 60.047 66.667 0.00 0.00 0.00 5.36
115 116 2.591072 CCTGAGCTGTCTGTGGCCT 61.591 63.158 3.32 0.00 0.00 5.19
116 117 1.374190 CTGAGCTGTCTGTGGCCTT 59.626 57.895 3.32 0.00 0.00 4.35
117 118 0.954449 CTGAGCTGTCTGTGGCCTTG 60.954 60.000 3.32 0.00 0.00 3.61
118 119 1.372683 GAGCTGTCTGTGGCCTTGA 59.627 57.895 3.32 0.00 0.00 3.02
119 120 0.952984 GAGCTGTCTGTGGCCTTGAC 60.953 60.000 3.32 10.22 0.00 3.18
120 121 1.227943 GCTGTCTGTGGCCTTGACA 60.228 57.895 19.40 19.40 38.24 3.58
134 135 4.246458 GCCTTGACATTCGTACTCTCTTT 58.754 43.478 0.00 0.00 0.00 2.52
170 171 7.199078 ACTCCGTCCGTTCTTAAATATAAGTC 58.801 38.462 0.00 0.00 39.65 3.01
215 218 6.408858 ACTACATACGAAGCAAAATGAGTG 57.591 37.500 0.00 0.00 0.00 3.51
227 230 6.906659 AGCAAAATGAGTGAATGTACTCTTG 58.093 36.000 10.05 7.85 45.70 3.02
322 336 7.283127 GGCTGATTTAGTATGGATTTGAACTGA 59.717 37.037 0.00 0.00 0.00 3.41
345 359 3.436924 CTTCATGGCAGCAGCGCA 61.437 61.111 11.47 0.00 43.41 6.09
1008 1029 2.699938 ATCCCCACCCCACCATCC 60.700 66.667 0.00 0.00 0.00 3.51
1011 1032 4.109675 CCCACCCCACCATCCGAC 62.110 72.222 0.00 0.00 0.00 4.79
1012 1033 4.467084 CCACCCCACCATCCGACG 62.467 72.222 0.00 0.00 0.00 5.12
1544 1572 5.125097 TGGAGTCATTCGTTAGACTAACTCC 59.875 44.000 20.36 17.90 44.61 3.85
1555 1583 4.949966 AGACTAACTCCTCTCCCTTGTA 57.050 45.455 0.00 0.00 0.00 2.41
1563 1591 5.995446 ACTCCTCTCCCTTGTATGATTTTC 58.005 41.667 0.00 0.00 0.00 2.29
1845 1875 8.299990 ACTGCTAGACTAGTTGTTTGATCTAT 57.700 34.615 11.15 0.00 0.00 1.98
1846 1876 8.194104 ACTGCTAGACTAGTTGTTTGATCTATG 58.806 37.037 11.15 0.00 0.00 2.23
1847 1877 8.067751 TGCTAGACTAGTTGTTTGATCTATGT 57.932 34.615 11.15 0.00 0.00 2.29
1848 1878 7.976175 TGCTAGACTAGTTGTTTGATCTATGTG 59.024 37.037 11.15 0.00 0.00 3.21
1855 1885 6.006449 AGTTGTTTGATCTATGTGCTTCCTT 58.994 36.000 0.00 0.00 0.00 3.36
1999 2031 5.590259 GGCAGTAAGTAACCATCAATCATGT 59.410 40.000 0.00 0.00 0.00 3.21
2737 2799 1.977594 GACCCTTGCGCACCGTATTG 61.978 60.000 11.12 0.00 0.00 1.90
3094 3163 7.743116 TCCCAGAGTACCATATTTTAGTTCA 57.257 36.000 0.00 0.00 0.00 3.18
3287 3357 6.667848 TCAGAACAATATGTCTACCTCCTGAA 59.332 38.462 0.00 0.00 0.00 3.02
3297 3367 5.839063 TGTCTACCTCCTGAATTACCCATAG 59.161 44.000 0.00 0.00 0.00 2.23
4149 4266 7.654116 TGTAAATGTGACATCTCAAACGACTTA 59.346 33.333 0.00 0.00 0.00 2.24
4659 4777 7.615582 TCTACTCTGCATTTCAAAATTCGAT 57.384 32.000 0.00 0.00 0.00 3.59
4685 4803 6.727824 ATGAAAGAAGTTGTTATGTCCTCG 57.272 37.500 0.00 0.00 0.00 4.63
5235 5353 1.276421 AGCAGTACGATGGCTGAAAGT 59.724 47.619 0.00 0.00 36.34 2.66
5461 5580 6.019748 CTGGTACATGATCTAATAGGGGACT 58.980 44.000 0.00 0.00 41.63 3.85
5470 5589 9.621239 ATGATCTAATAGGGGACTTATTTCTGA 57.379 33.333 0.00 0.00 43.67 3.27
5562 5681 5.810080 AAGAGGTAAGTGTAGCTTCTGTT 57.190 39.130 0.00 0.00 38.19 3.16
5830 5951 0.675837 CATATCCAGATGGCTGCCCG 60.676 60.000 17.53 1.74 40.91 6.13
5837 5958 1.895707 GATGGCTGCCCGAATCAGG 60.896 63.158 17.53 0.00 32.41 3.86
5987 6114 0.758685 TTTCCTGCCAAGGGTTGTGG 60.759 55.000 0.00 0.00 44.62 4.17
6021 6148 3.264897 CGGTGCTATGCGTGCTCC 61.265 66.667 9.87 9.87 39.76 4.70
6142 6269 6.099341 GGTTTTGTATGGAGCTTGTTTATGG 58.901 40.000 0.00 0.00 0.00 2.74
6174 6301 7.645340 GTGTAATAAGCCAAGTAATGCAGATTG 59.355 37.037 0.00 0.00 0.00 2.67
6219 6346 1.909700 AATTTCCTTCAGGCGCTTCA 58.090 45.000 7.64 0.00 34.44 3.02
6220 6347 1.457346 ATTTCCTTCAGGCGCTTCAG 58.543 50.000 7.64 0.00 34.44 3.02
6221 6348 0.108585 TTTCCTTCAGGCGCTTCAGT 59.891 50.000 7.64 0.00 34.44 3.41
6237 6364 5.059404 CTTCAGTTTGGTGAAGTTGTTGT 57.941 39.130 5.60 0.00 45.73 3.32
6246 6373 4.081365 TGGTGAAGTTGTTGTACACTCTGA 60.081 41.667 0.00 0.00 0.00 3.27
6254 6381 0.037882 TGTACACTCTGAGCAGCTGC 60.038 55.000 31.53 31.53 42.49 5.25
6264 6391 2.079158 TGAGCAGCTGCAATACTGAAC 58.921 47.619 38.24 17.52 45.16 3.18
6298 6435 8.402472 ACTATGTAAGTTTGATTCTCTCTCTCG 58.598 37.037 0.00 0.00 33.35 4.04
6344 6488 7.172875 CGAGGATATGATTTGCTTCTTTCTCAT 59.827 37.037 0.00 0.00 0.00 2.90
6379 6523 1.027357 CAACATCAGGGCCTGCATAC 58.973 55.000 29.02 0.00 0.00 2.39
6380 6524 0.921896 AACATCAGGGCCTGCATACT 59.078 50.000 29.02 8.81 0.00 2.12
6383 6527 0.763652 ATCAGGGCCTGCATACTCTG 59.236 55.000 29.02 9.24 0.00 3.35
6480 6636 4.462834 TGTGTTCATCGAGTAGACAGGATT 59.537 41.667 0.00 0.00 0.00 3.01
6484 6640 6.321435 TGTTCATCGAGTAGACAGGATTACAT 59.679 38.462 0.00 0.00 0.00 2.29
6531 6687 1.235281 GGGAGGGCGACAGTTTCAAC 61.235 60.000 0.00 0.00 0.00 3.18
6534 6690 0.818040 AGGGCGACAGTTTCAACACC 60.818 55.000 0.00 0.00 0.00 4.16
6562 6718 3.178865 CTGTTTAGGGGAGGGAGTACAA 58.821 50.000 0.00 0.00 0.00 2.41
6602 6759 3.260205 TGAGATCCTCCAAGTCCCTTTT 58.740 45.455 0.00 0.00 0.00 2.27
6677 6835 3.691118 TCATGTGAGCATTTACAAGAGGC 59.309 43.478 0.00 0.00 31.99 4.70
6750 6908 5.880887 TGCTTAGTCTCTTCTAACAGATCGA 59.119 40.000 0.00 0.00 0.00 3.59
6758 6916 7.971168 GTCTCTTCTAACAGATCGATCTTTTGA 59.029 37.037 28.71 23.52 34.22 2.69
6771 6929 5.125257 TCGATCTTTTGATTGCATTGGCTAA 59.875 36.000 0.00 0.00 39.67 3.09
6781 6939 1.930567 CATTGGCTAAAGCATGCACC 58.069 50.000 21.98 13.04 44.36 5.01
6998 7176 3.899052 TTACCCAAAGTACGATCCCAG 57.101 47.619 0.00 0.00 0.00 4.45
7057 7236 2.785713 AACACAAAACCACCGTATGC 57.214 45.000 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.032071 CCGGAGTGGGTGTGAACC 59.968 66.667 0.00 0.00 0.00 3.62
1 2 2.668550 GCCGGAGTGGGTGTGAAC 60.669 66.667 5.05 0.00 38.63 3.18
3 4 4.954118 AGGCCGGAGTGGGTGTGA 62.954 66.667 5.05 0.00 38.63 3.58
9 10 4.767255 GTCAGCAGGCCGGAGTGG 62.767 72.222 5.05 0.00 42.50 4.00
10 11 4.767255 GGTCAGCAGGCCGGAGTG 62.767 72.222 5.05 1.39 0.00 3.51
17 18 3.857309 AACAGCAGGGTCAGCAGGC 62.857 63.158 0.00 0.00 0.00 4.85
18 19 1.970114 CAACAGCAGGGTCAGCAGG 60.970 63.158 0.00 0.00 0.00 4.85
19 20 1.970114 CCAACAGCAGGGTCAGCAG 60.970 63.158 0.00 0.00 0.00 4.24
20 21 2.113774 CCAACAGCAGGGTCAGCA 59.886 61.111 0.00 0.00 0.00 4.41
21 22 2.674380 CCCAACAGCAGGGTCAGC 60.674 66.667 0.00 0.00 41.61 4.26
28 29 3.741476 GAAGCGGCCCAACAGCAG 61.741 66.667 0.00 0.00 42.62 4.24
29 30 4.269523 AGAAGCGGCCCAACAGCA 62.270 61.111 0.00 0.00 42.62 4.41
30 31 3.741476 CAGAAGCGGCCCAACAGC 61.741 66.667 0.00 0.00 40.15 4.40
31 32 3.741476 GCAGAAGCGGCCCAACAG 61.741 66.667 0.00 0.00 0.00 3.16
38 39 3.207669 CCATCAGGCAGAAGCGGC 61.208 66.667 0.00 0.00 43.41 6.53
39 40 2.515523 CCCATCAGGCAGAAGCGG 60.516 66.667 0.00 0.00 43.41 5.52
65 66 4.083862 GAGACCCGGCCTCACCAC 62.084 72.222 14.80 0.00 39.03 4.16
66 67 4.316823 AGAGACCCGGCCTCACCA 62.317 66.667 19.84 0.00 39.03 4.17
67 68 3.775654 CAGAGACCCGGCCTCACC 61.776 72.222 19.84 4.07 33.25 4.02
68 69 2.997897 ACAGAGACCCGGCCTCAC 60.998 66.667 19.84 5.93 33.25 3.51
69 70 2.680352 GACAGAGACCCGGCCTCA 60.680 66.667 19.84 0.00 33.25 3.86
70 71 3.462678 GGACAGAGACCCGGCCTC 61.463 72.222 12.56 12.56 0.00 4.70
71 72 3.547787 AAGGACAGAGACCCGGCCT 62.548 63.158 0.00 0.00 0.00 5.19
72 73 2.593956 AAAGGACAGAGACCCGGCC 61.594 63.158 0.00 0.00 0.00 6.13
73 74 1.376037 CAAAGGACAGAGACCCGGC 60.376 63.158 0.00 0.00 0.00 6.13
74 75 0.037232 GACAAAGGACAGAGACCCGG 60.037 60.000 0.00 0.00 0.00 5.73
75 76 0.388649 CGACAAAGGACAGAGACCCG 60.389 60.000 0.00 0.00 0.00 5.28
76 77 0.966920 TCGACAAAGGACAGAGACCC 59.033 55.000 0.00 0.00 0.00 4.46
77 78 1.670380 GCTCGACAAAGGACAGAGACC 60.670 57.143 0.00 0.00 0.00 3.85
78 79 1.670380 GGCTCGACAAAGGACAGAGAC 60.670 57.143 0.00 0.00 0.00 3.36
79 80 0.603569 GGCTCGACAAAGGACAGAGA 59.396 55.000 0.00 0.00 0.00 3.10
80 81 0.605589 AGGCTCGACAAAGGACAGAG 59.394 55.000 0.00 0.00 0.00 3.35
81 82 0.318441 CAGGCTCGACAAAGGACAGA 59.682 55.000 0.00 0.00 0.00 3.41
82 83 0.318441 TCAGGCTCGACAAAGGACAG 59.682 55.000 0.00 0.00 0.00 3.51
83 84 0.318441 CTCAGGCTCGACAAAGGACA 59.682 55.000 0.00 0.00 0.00 4.02
84 85 1.016653 GCTCAGGCTCGACAAAGGAC 61.017 60.000 0.00 0.00 35.22 3.85
85 86 1.293498 GCTCAGGCTCGACAAAGGA 59.707 57.895 0.00 0.00 35.22 3.36
86 87 3.882025 GCTCAGGCTCGACAAAGG 58.118 61.111 0.00 0.00 35.22 3.11
96 97 2.745492 GCCACAGACAGCTCAGGC 60.745 66.667 0.00 0.00 34.94 4.85
97 98 2.046507 GGCCACAGACAGCTCAGG 60.047 66.667 0.00 0.00 0.00 3.86
98 99 0.954449 CAAGGCCACAGACAGCTCAG 60.954 60.000 5.01 0.00 0.00 3.35
99 100 1.071987 CAAGGCCACAGACAGCTCA 59.928 57.895 5.01 0.00 0.00 4.26
100 101 0.952984 GTCAAGGCCACAGACAGCTC 60.953 60.000 5.01 0.00 32.68 4.09
101 102 1.072159 GTCAAGGCCACAGACAGCT 59.928 57.895 5.01 0.00 32.68 4.24
102 103 0.607489 ATGTCAAGGCCACAGACAGC 60.607 55.000 23.30 2.37 44.51 4.40
103 104 1.808945 GAATGTCAAGGCCACAGACAG 59.191 52.381 23.30 0.12 44.51 3.51
104 105 1.877680 CGAATGTCAAGGCCACAGACA 60.878 52.381 21.94 21.94 45.26 3.41
105 106 0.798776 CGAATGTCAAGGCCACAGAC 59.201 55.000 5.01 10.50 0.00 3.51
106 107 0.396435 ACGAATGTCAAGGCCACAGA 59.604 50.000 5.01 0.00 0.00 3.41
107 108 1.732259 GTACGAATGTCAAGGCCACAG 59.268 52.381 5.01 0.00 0.00 3.66
108 109 1.346395 AGTACGAATGTCAAGGCCACA 59.654 47.619 5.01 0.00 0.00 4.17
109 110 2.000447 GAGTACGAATGTCAAGGCCAC 59.000 52.381 5.01 0.00 0.00 5.01
110 111 1.899814 AGAGTACGAATGTCAAGGCCA 59.100 47.619 5.01 0.00 0.00 5.36
111 112 2.166664 AGAGAGTACGAATGTCAAGGCC 59.833 50.000 0.00 0.00 0.00 5.19
112 113 3.512033 AGAGAGTACGAATGTCAAGGC 57.488 47.619 0.00 0.00 0.00 4.35
113 114 6.697892 GGATAAAGAGAGTACGAATGTCAAGG 59.302 42.308 0.00 0.00 0.00 3.61
114 115 6.697892 GGGATAAAGAGAGTACGAATGTCAAG 59.302 42.308 0.00 0.00 0.00 3.02
115 116 6.153851 TGGGATAAAGAGAGTACGAATGTCAA 59.846 38.462 0.00 0.00 0.00 3.18
116 117 5.655090 TGGGATAAAGAGAGTACGAATGTCA 59.345 40.000 0.00 0.00 0.00 3.58
117 118 6.145338 TGGGATAAAGAGAGTACGAATGTC 57.855 41.667 0.00 0.00 0.00 3.06
118 119 6.540438 TTGGGATAAAGAGAGTACGAATGT 57.460 37.500 0.00 0.00 0.00 2.71
119 120 7.843490 TTTTGGGATAAAGAGAGTACGAATG 57.157 36.000 0.00 0.00 0.00 2.67
120 121 9.543783 GTATTTTGGGATAAAGAGAGTACGAAT 57.456 33.333 0.00 0.00 0.00 3.34
170 171 7.873739 AGTCCGCATTGAAATCTTTAAAAAG 57.126 32.000 0.00 0.00 37.36 2.27
187 190 0.812549 TGCTTCGTATGTAGTCCGCA 59.187 50.000 0.00 0.00 0.00 5.69
189 192 4.565166 TCATTTTGCTTCGTATGTAGTCCG 59.435 41.667 0.00 0.00 0.00 4.79
322 336 0.677098 CTGCTGCCATGAAGCTCAGT 60.677 55.000 17.76 0.00 41.42 3.41
345 359 4.145052 GTCAAGTGGACAGGGAAAAGAAT 58.855 43.478 0.00 0.00 46.19 2.40
1544 1572 4.770795 ACCGAAAATCATACAAGGGAGAG 58.229 43.478 0.00 0.00 0.00 3.20
1555 1583 4.586841 TCAAAACCTGGAACCGAAAATCAT 59.413 37.500 0.00 0.00 0.00 2.45
1563 1591 0.802494 CCGATCAAAACCTGGAACCG 59.198 55.000 0.00 0.00 0.00 4.44
1845 1875 3.011566 TCTCAAACCAAAGGAAGCACA 57.988 42.857 0.00 0.00 0.00 4.57
1846 1876 3.632145 TCTTCTCAAACCAAAGGAAGCAC 59.368 43.478 0.00 0.00 34.98 4.40
1847 1877 3.885297 CTCTTCTCAAACCAAAGGAAGCA 59.115 43.478 0.00 0.00 34.98 3.91
1848 1878 3.254411 CCTCTTCTCAAACCAAAGGAAGC 59.746 47.826 0.00 0.00 34.98 3.86
1855 1885 4.445735 CCAAGGTACCTCTTCTCAAACCAA 60.446 45.833 16.64 0.00 0.00 3.67
2180 2212 4.662468 TTAGCACAGCCAAACAATCAAA 57.338 36.364 0.00 0.00 0.00 2.69
2737 2799 2.222445 ACAAACGTGCGGAGTTATCAAC 59.778 45.455 0.00 0.00 0.00 3.18
3287 3357 3.676750 ACTGTAAGGCCCTATGGGTAAT 58.323 45.455 0.00 0.00 41.12 1.89
3297 3367 3.161866 TCAAAATGGAACTGTAAGGCCC 58.838 45.455 0.00 0.00 39.30 5.80
4149 4266 1.068333 GTCACAAACGGATGCTGCAAT 60.068 47.619 6.36 0.00 0.00 3.56
4336 4453 4.021368 AGTTACTTACATCTCTGTTGGCGT 60.021 41.667 0.00 0.00 36.79 5.68
4524 4642 2.028203 ACACATGTCATCGTCATCACCA 60.028 45.455 0.00 0.00 0.00 4.17
4659 4777 9.529325 CGAGGACATAACAACTTCTTTCATATA 57.471 33.333 0.00 0.00 0.00 0.86
4685 4803 4.394729 TGACAGACCCCAGAATTAAACAC 58.605 43.478 0.00 0.00 0.00 3.32
5562 5681 6.155221 TGAGTCGACTTACTTAGGAGTAGGTA 59.845 42.308 21.08 0.00 45.45 3.08
5788 5909 0.310543 TGTGTGGCGAACAATGAAGC 59.689 50.000 0.00 0.00 41.57 3.86
5792 5913 0.661187 GCACTGTGTGGCGAACAATG 60.661 55.000 9.86 0.00 41.57 2.82
5830 5951 2.012673 CTACTTGCACCAGCCTGATTC 58.987 52.381 0.00 0.00 41.13 2.52
5837 5958 3.258971 AGAAGATCTACTTGCACCAGC 57.741 47.619 0.00 0.00 39.13 4.85
5987 6114 3.665060 GCACCGCAAAGAATGAAAAATGC 60.665 43.478 0.00 0.00 0.00 3.56
6021 6148 1.075542 TAAGCCATGCGACTGAAACG 58.924 50.000 0.00 0.00 0.00 3.60
6142 6269 4.680171 ACTTGGCTTATTACACGCTTTC 57.320 40.909 0.00 0.00 0.00 2.62
6174 6301 5.977129 ACAATCAACAAACGAAATCTTCCAC 59.023 36.000 0.00 0.00 0.00 4.02
6219 6346 5.007682 AGTGTACAACAACTTCACCAAACT 58.992 37.500 0.00 0.00 0.00 2.66
6220 6347 5.123344 AGAGTGTACAACAACTTCACCAAAC 59.877 40.000 0.00 0.00 0.00 2.93
6221 6348 5.123186 CAGAGTGTACAACAACTTCACCAAA 59.877 40.000 0.00 0.00 0.00 3.28
6236 6363 0.037882 TGCAGCTGCTCAGAGTGTAC 60.038 55.000 36.61 6.43 42.66 2.90
6237 6364 0.681175 TTGCAGCTGCTCAGAGTGTA 59.319 50.000 36.61 12.87 42.66 2.90
6246 6373 1.808945 GTGTTCAGTATTGCAGCTGCT 59.191 47.619 36.61 21.93 42.66 4.24
6254 6381 5.355071 ACATAGTGGCATGTGTTCAGTATTG 59.645 40.000 0.00 1.00 37.74 1.90
6264 6391 5.878332 TCAAACTTACATAGTGGCATGTG 57.122 39.130 2.56 0.00 39.46 3.21
6298 6435 8.589335 TCCTCGTATCATTTTATACTTTCAGC 57.411 34.615 0.00 0.00 31.38 4.26
6331 6475 2.998670 CAGCTCGAATGAGAAAGAAGCA 59.001 45.455 0.00 0.00 45.57 3.91
6344 6488 2.013400 TGTTGCTTTGTTCAGCTCGAA 58.987 42.857 0.00 0.00 40.79 3.71
6379 6523 4.692625 AGCAATGTTAAGTGTGTAGCAGAG 59.307 41.667 0.00 0.00 0.00 3.35
6380 6524 4.452114 CAGCAATGTTAAGTGTGTAGCAGA 59.548 41.667 0.00 0.00 0.00 4.26
6383 6527 5.179368 TCTTCAGCAATGTTAAGTGTGTAGC 59.821 40.000 0.00 0.00 0.00 3.58
6430 6586 5.549742 AGAGCAATTTCACCAATTTCCAA 57.450 34.783 0.00 0.00 32.24 3.53
6445 6601 4.275689 TCGATGAACACAACAAAGAGCAAT 59.724 37.500 0.00 0.00 0.00 3.56
6449 6605 5.920840 TCTACTCGATGAACACAACAAAGAG 59.079 40.000 0.00 0.00 34.03 2.85
6480 6636 7.719193 TGTTTTCTCATTGTCCTCTTTCATGTA 59.281 33.333 0.00 0.00 0.00 2.29
6484 6640 6.356556 TCTGTTTTCTCATTGTCCTCTTTCA 58.643 36.000 0.00 0.00 0.00 2.69
6531 6687 2.107552 TCCCCTAAACAGGACTTTGGTG 59.892 50.000 0.00 0.00 0.00 4.17
6534 6690 2.290960 CCCTCCCCTAAACAGGACTTTG 60.291 54.545 0.00 0.00 0.00 2.77
6742 6900 6.263344 CAATGCAATCAAAAGATCGATCTGT 58.737 36.000 27.93 20.59 37.19 3.41
6750 6908 5.583457 GCTTTAGCCAATGCAATCAAAAGAT 59.417 36.000 11.47 0.00 41.13 2.40
6758 6916 2.557317 GCATGCTTTAGCCAATGCAAT 58.443 42.857 11.37 0.00 44.74 3.56
6771 6929 5.760253 GTGTTATATGTAGAGGTGCATGCTT 59.240 40.000 20.33 4.32 30.67 3.91
7018 7196 6.071334 TGTGTTTTTGTTTAGTGTGGGATTCA 60.071 34.615 0.00 0.00 0.00 2.57
7019 7197 6.334202 TGTGTTTTTGTTTAGTGTGGGATTC 58.666 36.000 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.