Multiple sequence alignment - TraesCS6A01G084800

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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 TraesCS6A01G084800 chr6A 100.000 4829 0 0 1 4829 53131930 53127102 0.000000e+00 8918
1 TraesCS6A01G084800 chr6B 98.709 3254 35 2 721 3967 56428715 56431968 0.000000e+00 5770
2 TraesCS6A01G084800 chr6B 98.463 3254 41 4 721 3967 195188760 195192011 0.000000e+00 5723
3 TraesCS6A01G084800 chr6B 98.463 3254 38 3 721 3967 18581064 18577816 0.000000e+00 5722
4 TraesCS6A01G084800 chr6B 98.758 966 12 0 3864 4829 18577807 18576842 0.000000e+00 1718
5 TraesCS6A01G084800 chr6B 98.447 966 14 1 3864 4829 195191964 195192928 0.000000e+00 1700
6 TraesCS6A01G084800 chr6B 98.240 966 17 0 3864 4829 57427341 57426376 0.000000e+00 1690
7 TraesCS6A01G084800 chr6B 97.930 966 20 0 3864 4829 56431949 56432914 0.000000e+00 1674
8 TraesCS6A01G084800 chr6B 97.671 601 10 2 160 756 18581662 18581062 0.000000e+00 1029
9 TraesCS6A01G084800 chr6B 97.492 598 14 1 160 756 52028758 52028161 0.000000e+00 1020
10 TraesCS6A01G084800 chr6B 97.804 592 12 1 163 753 56428123 56428714 0.000000e+00 1020
11 TraesCS6A01G084800 chr6B 97.315 596 15 1 159 753 195188164 195188759 0.000000e+00 1011
12 TraesCS6A01G084800 chr6B 99.379 161 1 0 1 161 17946320 17946480 4.730000e-75 292
13 TraesCS6A01G084800 chr3A 98.586 3254 39 2 721 3967 684728439 684725186 0.000000e+00 5747
14 TraesCS6A01G084800 chr3A 98.447 966 15 0 3864 4829 684725205 684724240 0.000000e+00 1701
15 TraesCS6A01G084800 chr3A 96.833 600 18 1 158 756 684729036 684728437 0.000000e+00 1002
16 TraesCS6A01G084800 chr3A 100.000 161 0 0 1 161 729865048 729865208 1.020000e-76 298
17 TraesCS6A01G084800 chr3A 88.043 92 7 3 721 808 16062912 16063003 6.610000e-19 106
18 TraesCS6A01G084800 chr2A 98.556 3254 39 3 721 3967 61495999 61499251 0.000000e+00 5742
19 TraesCS6A01G084800 chr2A 98.344 966 16 0 3864 4829 61499204 61500169 0.000000e+00 1696
20 TraesCS6A01G084800 chr2A 97.647 595 13 1 160 753 61495404 61495998 0.000000e+00 1020
21 TraesCS6A01G084800 chr2A 100.000 161 0 0 1 161 83922267 83922427 1.020000e-76 298
22 TraesCS6A01G084800 chr5B 98.496 3259 42 2 716 3967 264915182 264918440 0.000000e+00 5740
23 TraesCS6A01G084800 chr5B 98.525 3254 40 3 721 3967 371292888 371296140 0.000000e+00 5736
24 TraesCS6A01G084800 chr5B 98.447 966 14 1 3864 4829 371296121 371297085 0.000000e+00 1700
25 TraesCS6A01G084800 chr5B 98.758 161 2 0 1 161 669972537 669972697 2.200000e-73 287
26 TraesCS6A01G084800 chr5A 98.172 3282 53 2 693 3967 613968846 613972127 0.000000e+00 5722
27 TraesCS6A01G084800 chr5A 97.635 592 13 1 163 753 613968282 613968873 0.000000e+00 1014
28 TraesCS6A01G084800 chr4A 97.935 3245 58 4 723 3960 674547459 674544217 0.000000e+00 5613
29 TraesCS6A01G084800 chr4A 97.930 966 20 0 3864 4829 674544257 674543292 0.000000e+00 1674
30 TraesCS6A01G084800 chr3B 99.069 967 8 1 3864 4829 2425780 2426746 0.000000e+00 1735
31 TraesCS6A01G084800 chr7A 97.171 601 16 1 154 753 356409148 356409748 0.000000e+00 1014
32 TraesCS6A01G084800 chr4B 97.162 599 15 2 157 753 644578720 644579318 0.000000e+00 1011
33 TraesCS6A01G084800 chr4B 100.000 161 0 0 1 161 16697845 16698005 1.020000e-76 298
34 TraesCS6A01G084800 chr4D 98.758 161 2 0 1 161 504097685 504097525 2.200000e-73 287
35 TraesCS6A01G084800 chr1D 98.758 161 2 0 1 161 28582515 28582675 2.200000e-73 287
36 TraesCS6A01G084800 chr5D 97.516 161 4 0 1 161 525580720 525580560 4.760000e-70 276
37 TraesCS6A01G084800 chr5D 96.894 161 5 0 1 161 485761179 485761019 2.220000e-68 270


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 TraesCS6A01G084800 chr6A 53127102 53131930 4828 True 8918.000000 8918 100.000000 1 4829 1 chr6A.!!$R1 4828
1 TraesCS6A01G084800 chr6B 18576842 18581662 4820 True 2823.000000 5722 98.297333 160 4829 3 chr6B.!!$R3 4669
2 TraesCS6A01G084800 chr6B 56428123 56432914 4791 False 2821.333333 5770 98.147667 163 4829 3 chr6B.!!$F2 4666
3 TraesCS6A01G084800 chr6B 195188164 195192928 4764 False 2811.333333 5723 98.075000 159 4829 3 chr6B.!!$F3 4670
4 TraesCS6A01G084800 chr6B 57426376 57427341 965 True 1690.000000 1690 98.240000 3864 4829 1 chr6B.!!$R2 965
5 TraesCS6A01G084800 chr6B 52028161 52028758 597 True 1020.000000 1020 97.492000 160 756 1 chr6B.!!$R1 596
6 TraesCS6A01G084800 chr3A 684724240 684729036 4796 True 2816.666667 5747 97.955333 158 4829 3 chr3A.!!$R1 4671
7 TraesCS6A01G084800 chr2A 61495404 61500169 4765 False 2819.333333 5742 98.182333 160 4829 3 chr2A.!!$F2 4669
8 TraesCS6A01G084800 chr5B 264915182 264918440 3258 False 5740.000000 5740 98.496000 716 3967 1 chr5B.!!$F1 3251
9 TraesCS6A01G084800 chr5B 371292888 371297085 4197 False 3718.000000 5736 98.486000 721 4829 2 chr5B.!!$F3 4108
10 TraesCS6A01G084800 chr5A 613968282 613972127 3845 False 3368.000000 5722 97.903500 163 3967 2 chr5A.!!$F1 3804
11 TraesCS6A01G084800 chr4A 674543292 674547459 4167 True 3643.500000 5613 97.932500 723 4829 2 chr4A.!!$R1 4106
12 TraesCS6A01G084800 chr3B 2425780 2426746 966 False 1735.000000 1735 99.069000 3864 4829 1 chr3B.!!$F1 965
13 TraesCS6A01G084800 chr7A 356409148 356409748 600 False 1014.000000 1014 97.171000 154 753 1 chr7A.!!$F1 599
14 TraesCS6A01G084800 chr4B 644578720 644579318 598 False 1011.000000 1011 97.162000 157 753 1 chr4B.!!$F2 596

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
408 409 0.032017 AGGCCTAGACCGAAGTGGAT 60.032 55.000 1.29 0.0 42.00 3.41 F
1092 1135 7.681939 TGATCTTAGCGAGTTTAAAAATGGT 57.318 32.000 0.00 0.0 0.00 3.55 F
1452 1495 1.128200 TGTATGCTAGCCAACCCGAT 58.872 50.000 13.29 0.0 0.00 4.18 F
1945 1988 1.542547 GGGTTGTCACCATTGTCGTCT 60.543 52.381 0.00 0.0 46.43 4.18 F
2163 2206 2.691526 GGAAAGGTTTGGGACGTTCTTT 59.308 45.455 0.00 0.0 35.43 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1452 1495 1.470098 GGCACGTACTCCGACTCTTTA 59.530 52.381 0.00 0.00 40.70 1.85 R
2655 2701 2.354510 CCGCTTGTTCTTGAACTGTGAA 59.645 45.455 13.65 0.72 0.00 3.18 R
3328 3374 2.131972 GCATGTACACTCACACGTTGA 58.868 47.619 0.00 0.00 0.00 3.18 R
3740 3786 0.937304 TCTTGCTCTTGTTGTCGCAC 59.063 50.000 0.00 0.00 31.24 5.34 R
4091 4305 3.054361 CAGCCAGTTAGTCTTTGGGGTAT 60.054 47.826 0.00 0.00 32.53 2.73 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
23 24 6.308371 CAATGAACAACCTAACCGTAAACT 57.692 37.500 0.00 0.00 0.00 2.66
24 25 6.731164 CAATGAACAACCTAACCGTAAACTT 58.269 36.000 0.00 0.00 0.00 2.66
25 26 5.989551 TGAACAACCTAACCGTAAACTTC 57.010 39.130 0.00 0.00 0.00 3.01
26 27 4.507388 TGAACAACCTAACCGTAAACTTCG 59.493 41.667 0.00 0.00 0.00 3.79
27 28 4.320608 ACAACCTAACCGTAAACTTCGA 57.679 40.909 0.00 0.00 0.00 3.71
28 29 4.692228 ACAACCTAACCGTAAACTTCGAA 58.308 39.130 0.00 0.00 0.00 3.71
29 30 5.299949 ACAACCTAACCGTAAACTTCGAAT 58.700 37.500 0.00 0.00 0.00 3.34
30 31 6.454795 ACAACCTAACCGTAAACTTCGAATA 58.545 36.000 0.00 0.00 0.00 1.75
31 32 7.099120 ACAACCTAACCGTAAACTTCGAATAT 58.901 34.615 0.00 0.00 0.00 1.28
32 33 7.603784 ACAACCTAACCGTAAACTTCGAATATT 59.396 33.333 0.00 0.00 0.00 1.28
33 34 8.445493 CAACCTAACCGTAAACTTCGAATATTT 58.555 33.333 0.00 5.57 0.00 1.40
34 35 8.189709 ACCTAACCGTAAACTTCGAATATTTC 57.810 34.615 9.99 1.56 0.00 2.17
35 36 7.818930 ACCTAACCGTAAACTTCGAATATTTCA 59.181 33.333 9.99 0.00 0.00 2.69
36 37 8.112449 CCTAACCGTAAACTTCGAATATTTCAC 58.888 37.037 9.99 7.31 0.00 3.18
37 38 7.662604 AACCGTAAACTTCGAATATTTCACT 57.337 32.000 9.99 0.00 0.00 3.41
38 39 7.057149 ACCGTAAACTTCGAATATTTCACTG 57.943 36.000 9.99 7.26 0.00 3.66
39 40 6.647895 ACCGTAAACTTCGAATATTTCACTGT 59.352 34.615 9.99 7.69 0.00 3.55
40 41 7.814107 ACCGTAAACTTCGAATATTTCACTGTA 59.186 33.333 9.99 0.00 0.00 2.74
41 42 8.318876 CCGTAAACTTCGAATATTTCACTGTAG 58.681 37.037 9.99 0.00 0.00 2.74
42 43 8.318876 CGTAAACTTCGAATATTTCACTGTAGG 58.681 37.037 9.99 0.00 0.00 3.18
43 44 7.611213 AAACTTCGAATATTTCACTGTAGGG 57.389 36.000 0.00 0.00 0.00 3.53
44 45 6.295719 ACTTCGAATATTTCACTGTAGGGT 57.704 37.500 0.00 0.00 0.00 4.34
45 46 6.106673 ACTTCGAATATTTCACTGTAGGGTG 58.893 40.000 0.00 0.00 38.44 4.61
46 47 5.925506 TCGAATATTTCACTGTAGGGTGA 57.074 39.130 0.00 0.00 43.41 4.02
51 52 2.839486 TTCACTGTAGGGTGAAGCAG 57.161 50.000 6.03 0.00 46.91 4.24
52 53 0.321671 TCACTGTAGGGTGAAGCAGC 59.678 55.000 0.00 0.00 42.35 5.25
59 60 4.481195 GGTGAAGCAGCCTGTTCA 57.519 55.556 5.86 5.86 0.00 3.18
60 61 2.952714 GGTGAAGCAGCCTGTTCAT 58.047 52.632 11.18 0.00 35.22 2.57
61 62 0.524862 GGTGAAGCAGCCTGTTCATG 59.475 55.000 11.18 0.00 35.22 3.07
62 63 1.242076 GTGAAGCAGCCTGTTCATGT 58.758 50.000 11.18 0.00 35.22 3.21
63 64 1.610522 GTGAAGCAGCCTGTTCATGTT 59.389 47.619 11.18 0.00 35.22 2.71
64 65 2.813754 GTGAAGCAGCCTGTTCATGTTA 59.186 45.455 11.18 0.00 35.22 2.41
65 66 3.253188 GTGAAGCAGCCTGTTCATGTTAA 59.747 43.478 11.18 0.00 35.22 2.01
66 67 3.253188 TGAAGCAGCCTGTTCATGTTAAC 59.747 43.478 0.00 0.00 0.00 2.01
67 68 2.862541 AGCAGCCTGTTCATGTTAACA 58.137 42.857 11.41 11.41 37.75 2.41
68 69 3.424703 AGCAGCCTGTTCATGTTAACAT 58.575 40.909 15.47 15.47 38.61 2.71
69 70 3.828451 AGCAGCCTGTTCATGTTAACATT 59.172 39.130 18.50 1.72 38.61 2.71
70 71 5.009631 AGCAGCCTGTTCATGTTAACATTA 58.990 37.500 18.50 8.40 38.61 1.90
71 72 5.476599 AGCAGCCTGTTCATGTTAACATTAA 59.523 36.000 18.50 14.16 38.61 1.40
72 73 6.015519 AGCAGCCTGTTCATGTTAACATTAAA 60.016 34.615 18.50 12.71 38.61 1.52
73 74 6.308766 GCAGCCTGTTCATGTTAACATTAAAG 59.691 38.462 18.50 13.03 38.61 1.85
74 75 7.370383 CAGCCTGTTCATGTTAACATTAAAGT 58.630 34.615 18.50 0.00 38.61 2.66
75 76 7.867403 CAGCCTGTTCATGTTAACATTAAAGTT 59.133 33.333 18.50 5.44 38.61 2.66
76 77 9.073475 AGCCTGTTCATGTTAACATTAAAGTTA 57.927 29.630 18.50 0.00 38.61 2.24
77 78 9.341899 GCCTGTTCATGTTAACATTAAAGTTAG 57.658 33.333 18.50 12.21 38.61 2.34
93 94 9.765795 ATTAAAGTTAGAGTTCTTCCATATCGG 57.234 33.333 0.00 0.00 0.00 4.18
94 95 5.793030 AGTTAGAGTTCTTCCATATCGGG 57.207 43.478 0.00 0.00 34.36 5.14
95 96 4.039366 AGTTAGAGTTCTTCCATATCGGGC 59.961 45.833 0.00 0.00 34.36 6.13
96 97 1.694696 AGAGTTCTTCCATATCGGGCC 59.305 52.381 0.00 0.00 34.36 5.80
97 98 1.416401 GAGTTCTTCCATATCGGGCCA 59.584 52.381 4.39 0.00 34.36 5.36
98 99 2.039084 GAGTTCTTCCATATCGGGCCAT 59.961 50.000 4.39 0.00 34.36 4.40
99 100 2.154462 GTTCTTCCATATCGGGCCATG 58.846 52.381 4.39 0.00 34.36 3.66
100 101 0.036732 TCTTCCATATCGGGCCATGC 59.963 55.000 4.39 0.00 34.36 4.06
101 102 0.037303 CTTCCATATCGGGCCATGCT 59.963 55.000 4.39 0.00 34.36 3.79
102 103 0.478072 TTCCATATCGGGCCATGCTT 59.522 50.000 4.39 0.00 34.36 3.91
103 104 0.250858 TCCATATCGGGCCATGCTTG 60.251 55.000 4.39 0.00 34.36 4.01
104 105 1.582968 CATATCGGGCCATGCTTGC 59.417 57.895 4.39 0.00 0.00 4.01
105 106 0.892358 CATATCGGGCCATGCTTGCT 60.892 55.000 4.39 0.00 0.00 3.91
106 107 0.892358 ATATCGGGCCATGCTTGCTG 60.892 55.000 4.39 0.00 0.00 4.41
107 108 1.981951 TATCGGGCCATGCTTGCTGA 61.982 55.000 4.39 0.00 0.00 4.26
108 109 2.635787 ATCGGGCCATGCTTGCTGAT 62.636 55.000 4.39 0.00 0.00 2.90
109 110 2.812499 GGGCCATGCTTGCTGATG 59.188 61.111 4.39 0.00 0.00 3.07
110 111 2.792947 GGGCCATGCTTGCTGATGG 61.793 63.158 4.39 7.38 41.95 3.51
112 113 2.411701 CCATGCTTGCTGATGGCG 59.588 61.111 0.00 0.00 45.43 5.69
113 114 2.278596 CATGCTTGCTGATGGCGC 60.279 61.111 0.00 0.00 45.43 6.53
114 115 3.524606 ATGCTTGCTGATGGCGCC 61.525 61.111 22.73 22.73 45.43 6.53
117 118 3.570638 CTTGCTGATGGCGCCGAG 61.571 66.667 23.90 18.23 45.43 4.63
120 121 4.838152 GCTGATGGCGCCGAGGAA 62.838 66.667 23.90 3.26 0.00 3.36
121 122 2.892425 CTGATGGCGCCGAGGAAC 60.892 66.667 23.90 9.49 0.00 3.62
122 123 3.664025 CTGATGGCGCCGAGGAACA 62.664 63.158 23.90 13.52 0.00 3.18
123 124 2.435938 GATGGCGCCGAGGAACAA 60.436 61.111 23.90 0.49 0.00 2.83
124 125 2.033448 ATGGCGCCGAGGAACAAA 59.967 55.556 23.90 0.00 0.00 2.83
125 126 1.376609 GATGGCGCCGAGGAACAAAT 61.377 55.000 23.90 5.79 0.00 2.32
126 127 1.656818 ATGGCGCCGAGGAACAAATG 61.657 55.000 23.90 0.00 0.00 2.32
127 128 2.485122 GCGCCGAGGAACAAATGG 59.515 61.111 0.00 0.00 0.00 3.16
128 129 2.038269 GCGCCGAGGAACAAATGGA 61.038 57.895 0.00 0.00 0.00 3.41
129 130 1.982073 GCGCCGAGGAACAAATGGAG 61.982 60.000 0.00 0.00 0.00 3.86
130 131 1.803289 GCCGAGGAACAAATGGAGC 59.197 57.895 0.00 0.00 0.00 4.70
131 132 1.982073 GCCGAGGAACAAATGGAGCG 61.982 60.000 0.00 0.00 0.00 5.03
132 133 1.369091 CCGAGGAACAAATGGAGCGG 61.369 60.000 0.00 0.00 0.00 5.52
133 134 1.803289 GAGGAACAAATGGAGCGGC 59.197 57.895 0.00 0.00 0.00 6.53
134 135 0.960364 GAGGAACAAATGGAGCGGCA 60.960 55.000 1.45 0.00 0.00 5.69
135 136 0.962356 AGGAACAAATGGAGCGGCAG 60.962 55.000 1.45 0.00 0.00 4.85
136 137 1.508088 GAACAAATGGAGCGGCAGG 59.492 57.895 1.45 0.00 0.00 4.85
137 138 0.960364 GAACAAATGGAGCGGCAGGA 60.960 55.000 1.45 0.00 0.00 3.86
138 139 0.323725 AACAAATGGAGCGGCAGGAT 60.324 50.000 1.45 0.00 0.00 3.24
139 140 0.546122 ACAAATGGAGCGGCAGGATA 59.454 50.000 1.45 0.00 0.00 2.59
140 141 1.143684 ACAAATGGAGCGGCAGGATAT 59.856 47.619 1.45 0.00 0.00 1.63
141 142 2.233271 CAAATGGAGCGGCAGGATATT 58.767 47.619 1.45 0.00 0.00 1.28
142 143 1.901591 AATGGAGCGGCAGGATATTG 58.098 50.000 1.45 0.00 0.00 1.90
143 144 1.059098 ATGGAGCGGCAGGATATTGA 58.941 50.000 1.45 0.00 0.00 2.57
144 145 0.836606 TGGAGCGGCAGGATATTGAA 59.163 50.000 1.45 0.00 0.00 2.69
145 146 1.211703 TGGAGCGGCAGGATATTGAAA 59.788 47.619 1.45 0.00 0.00 2.69
146 147 2.158623 TGGAGCGGCAGGATATTGAAAT 60.159 45.455 1.45 0.00 0.00 2.17
147 148 2.227388 GGAGCGGCAGGATATTGAAATG 59.773 50.000 1.45 0.00 0.00 2.32
148 149 1.610522 AGCGGCAGGATATTGAAATGC 59.389 47.619 1.45 0.00 36.16 3.56
149 150 1.337703 GCGGCAGGATATTGAAATGCA 59.662 47.619 0.00 0.00 38.63 3.96
150 151 2.606308 GCGGCAGGATATTGAAATGCAG 60.606 50.000 0.00 0.00 38.63 4.41
151 152 2.880268 CGGCAGGATATTGAAATGCAGA 59.120 45.455 0.00 0.00 38.63 4.26
152 153 3.504906 CGGCAGGATATTGAAATGCAGAT 59.495 43.478 0.00 0.00 38.63 2.90
153 154 4.022589 CGGCAGGATATTGAAATGCAGATT 60.023 41.667 0.00 0.00 38.63 2.40
154 155 5.181811 CGGCAGGATATTGAAATGCAGATTA 59.818 40.000 0.00 0.00 38.63 1.75
155 156 6.618811 GGCAGGATATTGAAATGCAGATTAG 58.381 40.000 0.00 0.00 38.63 1.73
156 157 6.432162 GGCAGGATATTGAAATGCAGATTAGA 59.568 38.462 0.00 0.00 38.63 2.10
407 408 0.970937 CAGGCCTAGACCGAAGTGGA 60.971 60.000 3.98 0.00 42.00 4.02
408 409 0.032017 AGGCCTAGACCGAAGTGGAT 60.032 55.000 1.29 0.00 42.00 3.41
924 967 8.652463 GTTAATATGTTTGTGGTGGCATTTTAC 58.348 33.333 0.00 0.00 0.00 2.01
1092 1135 7.681939 TGATCTTAGCGAGTTTAAAAATGGT 57.318 32.000 0.00 0.00 0.00 3.55
1151 1194 8.950210 CATTAGACAATTGAAGTACTGGTTGAT 58.050 33.333 13.59 6.94 0.00 2.57
1452 1495 1.128200 TGTATGCTAGCCAACCCGAT 58.872 50.000 13.29 0.00 0.00 4.18
1945 1988 1.542547 GGGTTGTCACCATTGTCGTCT 60.543 52.381 0.00 0.00 46.43 4.18
2163 2206 2.691526 GGAAAGGTTTGGGACGTTCTTT 59.308 45.455 0.00 0.00 35.43 2.52
2915 2961 5.658634 AGAAGGGAAGGGCAATAAAGAATTC 59.341 40.000 0.00 0.00 0.00 2.17
3101 3147 4.336433 CCACGGCACTTTGAGATATTTCAT 59.664 41.667 0.00 0.00 0.00 2.57
3740 3786 2.100631 GTGCTTCCACATCGACGGG 61.101 63.158 0.00 0.00 41.67 5.28
4091 4305 2.691526 ACTTAGACGTGTTGGTCACTCA 59.308 45.455 0.00 0.00 44.16 3.41
4154 4368 9.884636 GGTTGATAGGTATGTGTGCATATAATA 57.115 33.333 0.00 0.00 39.49 0.98
4536 4751 1.702401 TCTGGGTGGCAAACAGTGATA 59.298 47.619 16.33 0.00 34.02 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.308371 AGTTTACGGTTAGGTTGTTCATTG 57.692 37.500 0.00 0.00 0.00 2.82
3 4 4.507388 CGAAGTTTACGGTTAGGTTGTTCA 59.493 41.667 0.00 0.00 0.00 3.18
4 5 4.744631 TCGAAGTTTACGGTTAGGTTGTTC 59.255 41.667 0.00 0.00 0.00 3.18
6 7 4.320608 TCGAAGTTTACGGTTAGGTTGT 57.679 40.909 0.00 0.00 0.00 3.32
7 8 5.851047 ATTCGAAGTTTACGGTTAGGTTG 57.149 39.130 3.35 0.00 0.00 3.77
8 9 8.552083 AAATATTCGAAGTTTACGGTTAGGTT 57.448 30.769 3.35 0.00 0.00 3.50
9 10 7.818930 TGAAATATTCGAAGTTTACGGTTAGGT 59.181 33.333 3.35 0.00 0.00 3.08
10 11 8.112449 GTGAAATATTCGAAGTTTACGGTTAGG 58.888 37.037 3.35 0.00 0.00 2.69
11 12 8.866956 AGTGAAATATTCGAAGTTTACGGTTAG 58.133 33.333 3.35 0.00 0.00 2.34
12 13 8.649841 CAGTGAAATATTCGAAGTTTACGGTTA 58.350 33.333 3.35 0.00 0.00 2.85
13 14 7.172019 ACAGTGAAATATTCGAAGTTTACGGTT 59.828 33.333 3.35 0.00 0.00 4.44
14 15 6.647895 ACAGTGAAATATTCGAAGTTTACGGT 59.352 34.615 3.35 8.54 0.00 4.83
15 16 7.057149 ACAGTGAAATATTCGAAGTTTACGG 57.943 36.000 3.35 7.97 0.00 4.02
16 17 8.318876 CCTACAGTGAAATATTCGAAGTTTACG 58.681 37.037 3.35 4.71 0.00 3.18
17 18 8.601476 CCCTACAGTGAAATATTCGAAGTTTAC 58.399 37.037 3.35 5.08 0.00 2.01
18 19 8.316214 ACCCTACAGTGAAATATTCGAAGTTTA 58.684 33.333 3.35 0.00 0.00 2.01
19 20 7.119262 CACCCTACAGTGAAATATTCGAAGTTT 59.881 37.037 3.35 7.48 40.34 2.66
20 21 6.594159 CACCCTACAGTGAAATATTCGAAGTT 59.406 38.462 3.35 0.00 40.34 2.66
21 22 6.070995 TCACCCTACAGTGAAATATTCGAAGT 60.071 38.462 3.35 0.00 43.65 3.01
22 23 6.338146 TCACCCTACAGTGAAATATTCGAAG 58.662 40.000 3.35 0.00 43.65 3.79
23 24 6.288941 TCACCCTACAGTGAAATATTCGAA 57.711 37.500 0.00 0.00 43.65 3.71
24 25 5.925506 TCACCCTACAGTGAAATATTCGA 57.074 39.130 0.00 0.00 43.65 3.71
33 34 0.321671 GCTGCTTCACCCTACAGTGA 59.678 55.000 0.00 0.00 44.89 3.41
34 35 0.674895 GGCTGCTTCACCCTACAGTG 60.675 60.000 0.00 0.00 39.20 3.66
35 36 0.838122 AGGCTGCTTCACCCTACAGT 60.838 55.000 0.00 0.00 32.65 3.55
36 37 0.392193 CAGGCTGCTTCACCCTACAG 60.392 60.000 0.00 0.00 0.00 2.74
37 38 1.127567 ACAGGCTGCTTCACCCTACA 61.128 55.000 15.89 0.00 0.00 2.74
38 39 0.036875 AACAGGCTGCTTCACCCTAC 59.963 55.000 15.89 0.00 0.00 3.18
39 40 0.324943 GAACAGGCTGCTTCACCCTA 59.675 55.000 15.89 0.00 0.00 3.53
40 41 1.073897 GAACAGGCTGCTTCACCCT 59.926 57.895 15.89 0.00 0.00 4.34
41 42 0.610232 ATGAACAGGCTGCTTCACCC 60.610 55.000 24.60 6.55 0.00 4.61
42 43 0.524862 CATGAACAGGCTGCTTCACC 59.475 55.000 24.60 7.67 0.00 4.02
43 44 1.242076 ACATGAACAGGCTGCTTCAC 58.758 50.000 24.60 10.74 0.00 3.18
44 45 1.985473 AACATGAACAGGCTGCTTCA 58.015 45.000 24.43 24.43 0.00 3.02
45 46 3.253188 TGTTAACATGAACAGGCTGCTTC 59.747 43.478 15.89 16.87 34.40 3.86
46 47 3.221771 TGTTAACATGAACAGGCTGCTT 58.778 40.909 15.89 8.23 34.40 3.91
47 48 2.862541 TGTTAACATGAACAGGCTGCT 58.137 42.857 15.89 0.78 34.40 4.24
48 49 3.855689 ATGTTAACATGAACAGGCTGC 57.144 42.857 20.19 0.00 42.38 5.25
49 50 7.370383 ACTTTAATGTTAACATGAACAGGCTG 58.630 34.615 21.46 14.16 42.38 4.85
50 51 7.524717 ACTTTAATGTTAACATGAACAGGCT 57.475 32.000 21.46 6.16 42.38 4.58
51 52 9.341899 CTAACTTTAATGTTAACATGAACAGGC 57.658 33.333 21.46 0.00 42.38 4.85
67 68 9.765795 CCGATATGGAAGAACTCTAACTTTAAT 57.234 33.333 0.00 0.00 42.00 1.40
68 69 8.202137 CCCGATATGGAAGAACTCTAACTTTAA 58.798 37.037 0.00 0.00 42.00 1.52
69 70 7.686127 GCCCGATATGGAAGAACTCTAACTTTA 60.686 40.741 0.00 0.00 42.00 1.85
70 71 6.583562 CCCGATATGGAAGAACTCTAACTTT 58.416 40.000 0.00 0.00 42.00 2.66
71 72 5.453480 GCCCGATATGGAAGAACTCTAACTT 60.453 44.000 0.00 0.00 42.00 2.66
72 73 4.039366 GCCCGATATGGAAGAACTCTAACT 59.961 45.833 0.00 0.00 42.00 2.24
73 74 4.308265 GCCCGATATGGAAGAACTCTAAC 58.692 47.826 0.00 0.00 42.00 2.34
74 75 3.323979 GGCCCGATATGGAAGAACTCTAA 59.676 47.826 0.00 0.00 42.00 2.10
75 76 2.897969 GGCCCGATATGGAAGAACTCTA 59.102 50.000 0.00 0.00 42.00 2.43
76 77 1.694696 GGCCCGATATGGAAGAACTCT 59.305 52.381 0.00 0.00 42.00 3.24
77 78 1.416401 TGGCCCGATATGGAAGAACTC 59.584 52.381 0.00 0.00 42.00 3.01
78 79 1.507140 TGGCCCGATATGGAAGAACT 58.493 50.000 0.00 0.00 42.00 3.01
79 80 2.154462 CATGGCCCGATATGGAAGAAC 58.846 52.381 0.00 0.00 42.00 3.01
80 81 1.545428 GCATGGCCCGATATGGAAGAA 60.545 52.381 0.00 0.00 42.00 2.52
81 82 0.036732 GCATGGCCCGATATGGAAGA 59.963 55.000 0.00 0.00 42.00 2.87
82 83 0.037303 AGCATGGCCCGATATGGAAG 59.963 55.000 0.00 0.00 42.00 3.46
83 84 0.478072 AAGCATGGCCCGATATGGAA 59.522 50.000 0.00 0.00 42.00 3.53
84 85 0.250858 CAAGCATGGCCCGATATGGA 60.251 55.000 0.00 0.00 42.00 3.41
85 86 1.870055 GCAAGCATGGCCCGATATGG 61.870 60.000 0.00 0.00 37.55 2.74
86 87 0.892358 AGCAAGCATGGCCCGATATG 60.892 55.000 0.00 0.00 33.19 1.78
87 88 0.892358 CAGCAAGCATGGCCCGATAT 60.892 55.000 0.00 0.00 33.19 1.63
88 89 1.526686 CAGCAAGCATGGCCCGATA 60.527 57.895 0.00 0.00 33.19 2.92
89 90 2.635787 ATCAGCAAGCATGGCCCGAT 62.636 55.000 0.00 0.00 33.19 4.18
90 91 3.348554 ATCAGCAAGCATGGCCCGA 62.349 57.895 0.00 0.00 33.19 5.14
91 92 2.831742 ATCAGCAAGCATGGCCCG 60.832 61.111 0.00 0.00 33.19 6.13
92 93 2.792947 CCATCAGCAAGCATGGCCC 61.793 63.158 0.00 0.00 33.19 5.80
93 94 2.812499 CCATCAGCAAGCATGGCC 59.188 61.111 0.00 0.00 33.19 5.36
95 96 2.411701 CGCCATCAGCAAGCATGG 59.588 61.111 6.96 6.96 44.04 3.66
96 97 2.278596 GCGCCATCAGCAAGCATG 60.279 61.111 0.00 0.00 44.04 4.06
97 98 3.524606 GGCGCCATCAGCAAGCAT 61.525 61.111 24.80 0.00 44.04 3.79
100 101 3.570638 CTCGGCGCCATCAGCAAG 61.571 66.667 28.98 7.38 44.04 4.01
103 104 4.838152 TTCCTCGGCGCCATCAGC 62.838 66.667 28.98 0.00 38.52 4.26
104 105 2.892425 GTTCCTCGGCGCCATCAG 60.892 66.667 28.98 18.21 0.00 2.90
105 106 2.739849 TTTGTTCCTCGGCGCCATCA 62.740 55.000 28.98 9.27 0.00 3.07
106 107 1.376609 ATTTGTTCCTCGGCGCCATC 61.377 55.000 28.98 6.42 0.00 3.51
107 108 1.378514 ATTTGTTCCTCGGCGCCAT 60.379 52.632 28.98 5.67 0.00 4.40
108 109 2.033448 ATTTGTTCCTCGGCGCCA 59.967 55.556 28.98 12.94 0.00 5.69
109 110 2.485122 CATTTGTTCCTCGGCGCC 59.515 61.111 19.07 19.07 0.00 6.53
110 111 1.982073 CTCCATTTGTTCCTCGGCGC 61.982 60.000 0.00 0.00 0.00 6.53
111 112 1.982073 GCTCCATTTGTTCCTCGGCG 61.982 60.000 0.00 0.00 0.00 6.46
112 113 1.803289 GCTCCATTTGTTCCTCGGC 59.197 57.895 0.00 0.00 0.00 5.54
113 114 1.369091 CCGCTCCATTTGTTCCTCGG 61.369 60.000 0.00 0.00 0.00 4.63
114 115 1.982073 GCCGCTCCATTTGTTCCTCG 61.982 60.000 0.00 0.00 0.00 4.63
115 116 0.960364 TGCCGCTCCATTTGTTCCTC 60.960 55.000 0.00 0.00 0.00 3.71
116 117 0.962356 CTGCCGCTCCATTTGTTCCT 60.962 55.000 0.00 0.00 0.00 3.36
117 118 1.508088 CTGCCGCTCCATTTGTTCC 59.492 57.895 0.00 0.00 0.00 3.62
118 119 0.960364 TCCTGCCGCTCCATTTGTTC 60.960 55.000 0.00 0.00 0.00 3.18
119 120 0.323725 ATCCTGCCGCTCCATTTGTT 60.324 50.000 0.00 0.00 0.00 2.83
120 121 0.546122 TATCCTGCCGCTCCATTTGT 59.454 50.000 0.00 0.00 0.00 2.83
121 122 1.901591 ATATCCTGCCGCTCCATTTG 58.098 50.000 0.00 0.00 0.00 2.32
122 123 2.158623 TCAATATCCTGCCGCTCCATTT 60.159 45.455 0.00 0.00 0.00 2.32
123 124 1.421268 TCAATATCCTGCCGCTCCATT 59.579 47.619 0.00 0.00 0.00 3.16
124 125 1.059098 TCAATATCCTGCCGCTCCAT 58.941 50.000 0.00 0.00 0.00 3.41
125 126 0.836606 TTCAATATCCTGCCGCTCCA 59.163 50.000 0.00 0.00 0.00 3.86
126 127 1.967319 TTTCAATATCCTGCCGCTCC 58.033 50.000 0.00 0.00 0.00 4.70
127 128 2.351157 GCATTTCAATATCCTGCCGCTC 60.351 50.000 0.00 0.00 0.00 5.03
128 129 1.610522 GCATTTCAATATCCTGCCGCT 59.389 47.619 0.00 0.00 0.00 5.52
129 130 1.337703 TGCATTTCAATATCCTGCCGC 59.662 47.619 0.00 0.00 31.89 6.53
130 131 2.880268 TCTGCATTTCAATATCCTGCCG 59.120 45.455 0.00 0.00 31.89 5.69
131 132 5.464030 AATCTGCATTTCAATATCCTGCC 57.536 39.130 0.00 0.00 31.89 4.85
132 133 7.444629 TCTAATCTGCATTTCAATATCCTGC 57.555 36.000 0.00 0.00 0.00 4.85
133 134 8.459635 CCATCTAATCTGCATTTCAATATCCTG 58.540 37.037 0.00 0.00 0.00 3.86
134 135 8.388589 TCCATCTAATCTGCATTTCAATATCCT 58.611 33.333 0.00 0.00 0.00 3.24
135 136 8.571461 TCCATCTAATCTGCATTTCAATATCC 57.429 34.615 0.00 0.00 0.00 2.59
407 408 2.750237 GGGCTGGCCGAAAACGAT 60.750 61.111 3.84 0.00 36.85 3.73
924 967 1.582937 CGCTACACTGACTACGCGG 60.583 63.158 12.47 0.00 37.25 6.46
1092 1135 1.550524 GGGTCTGCTAGTGTCATGACA 59.449 52.381 24.56 24.56 39.32 3.58
1151 1194 3.773119 AGGATCAAGCCCGAAACTAGTTA 59.227 43.478 8.92 0.00 0.00 2.24
1452 1495 1.470098 GGCACGTACTCCGACTCTTTA 59.530 52.381 0.00 0.00 40.70 1.85
1826 1869 4.967036 TGTTGGACTTGATATGTGTGTCA 58.033 39.130 0.00 0.00 0.00 3.58
2053 2096 2.880268 CTGCTGTCTGGATGTGTTTTGA 59.120 45.455 0.00 0.00 0.00 2.69
2163 2206 6.816136 ACGGACAACATTATCATATGAGTCA 58.184 36.000 11.78 0.00 36.62 3.41
2655 2701 2.354510 CCGCTTGTTCTTGAACTGTGAA 59.645 45.455 13.65 0.72 0.00 3.18
2915 2961 5.451798 GGCTCTTTCTCTATCCACTCAGAAG 60.452 48.000 0.00 0.00 0.00 2.85
3101 3147 3.671008 TTGCTAACTCGTGCCTTTCTA 57.329 42.857 0.00 0.00 0.00 2.10
3328 3374 2.131972 GCATGTACACTCACACGTTGA 58.868 47.619 0.00 0.00 0.00 3.18
3740 3786 0.937304 TCTTGCTCTTGTTGTCGCAC 59.063 50.000 0.00 0.00 31.24 5.34
4091 4305 3.054361 CAGCCAGTTAGTCTTTGGGGTAT 60.054 47.826 0.00 0.00 32.53 2.73


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

AutoCloner maintained by Alex Coulton.