Multiple sequence alignment - TraesCS2B01G390100

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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 TraesCS2B01G390100 chr2B 100.000 3210 0 0 1 3210 553880046 553883255 0.000000e+00 5928
1 TraesCS2B01G390100 chr2B 98.684 152 2 0 1 152 456048205 456048356 1.470000e-68 270
2 TraesCS2B01G390100 chr3B 97.876 3060 60 3 151 3210 452563153 452560099 0.000000e+00 5286
3 TraesCS2B01G390100 chr3B 97.683 3064 63 4 150 3210 73031279 73034337 0.000000e+00 5258
4 TraesCS2B01G390100 chr3B 100.000 152 0 0 1 152 562708487 562708638 6.780000e-72 281
5 TraesCS2B01G390100 chr3B 98.684 152 2 0 1 152 24400116 24399965 1.470000e-68 270
6 TraesCS2B01G390100 chr4B 97.128 3064 84 4 147 3210 629907324 629910383 0.000000e+00 5168
7 TraesCS2B01G390100 chr4B 95.930 3071 92 16 150 3210 665900181 665903228 0.000000e+00 4948
8 TraesCS2B01G390100 chr1A 96.742 3069 86 6 152 3209 444169075 444166010 0.000000e+00 5101
9 TraesCS2B01G390100 chr4A 96.156 3070 104 6 152 3210 36004230 36001164 0.000000e+00 5003
10 TraesCS2B01G390100 chr5A 95.582 1969 58 13 150 2111 705867909 705869855 0.000000e+00 3127
11 TraesCS2B01G390100 chr5A 96.649 1104 36 1 2107 3210 705883335 705884437 0.000000e+00 1832
12 TraesCS2B01G390100 chr5A 96.959 1085 33 0 1129 2213 262471612 262470528 0.000000e+00 1821
13 TraesCS2B01G390100 chr5A 90.922 727 30 4 149 840 310728838 310728113 0.000000e+00 944
14 TraesCS2B01G390100 chr2A 96.682 1085 36 0 1129 2213 694743563 694742479 0.000000e+00 1805
15 TraesCS2B01G390100 chr2A 96.466 283 10 0 849 1131 694743887 694743605 4.850000e-128 468
16 TraesCS2B01G390100 chr5D 96.957 986 29 1 2225 3210 309068222 309067238 0.000000e+00 1653
17 TraesCS2B01G390100 chr1D 96.856 986 31 0 2225 3210 97785404 97784419 0.000000e+00 1650
18 TraesCS2B01G390100 chr7A 93.295 701 32 7 152 840 699627689 699626992 0.000000e+00 1020
19 TraesCS2B01G390100 chr7A 96.491 285 10 0 847 1131 709138064 709137780 3.750000e-129 472
20 TraesCS2B01G390100 chr7B 99.342 152 1 0 1 152 730414500 730414349 3.150000e-70 276
21 TraesCS2B01G390100 chr5B 99.342 152 1 0 1 152 314355431 314355582 3.150000e-70 276
22 TraesCS2B01G390100 chr5B 99.342 152 1 0 1 152 458028693 458028542 3.150000e-70 276
23 TraesCS2B01G390100 chr5B 99.342 152 1 0 1 152 572382538 572382689 3.150000e-70 276
24 TraesCS2B01G390100 chr6B 98.684 152 2 0 1 152 79048486 79048637 1.470000e-68 270
25 TraesCS2B01G390100 chr1B 98.684 152 2 0 1 152 602886557 602886406 1.470000e-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 TraesCS2B01G390100 chr2B 553880046 553883255 3209 False 5928.0 5928 100.000 1 3210 1 chr2B.!!$F2 3209
1 TraesCS2B01G390100 chr3B 452560099 452563153 3054 True 5286.0 5286 97.876 151 3210 1 chr3B.!!$R2 3059
2 TraesCS2B01G390100 chr3B 73031279 73034337 3058 False 5258.0 5258 97.683 150 3210 1 chr3B.!!$F1 3060
3 TraesCS2B01G390100 chr4B 629907324 629910383 3059 False 5168.0 5168 97.128 147 3210 1 chr4B.!!$F1 3063
4 TraesCS2B01G390100 chr4B 665900181 665903228 3047 False 4948.0 4948 95.930 150 3210 1 chr4B.!!$F2 3060
5 TraesCS2B01G390100 chr1A 444166010 444169075 3065 True 5101.0 5101 96.742 152 3209 1 chr1A.!!$R1 3057
6 TraesCS2B01G390100 chr4A 36001164 36004230 3066 True 5003.0 5003 96.156 152 3210 1 chr4A.!!$R1 3058
7 TraesCS2B01G390100 chr5A 705867909 705869855 1946 False 3127.0 3127 95.582 150 2111 1 chr5A.!!$F1 1961
8 TraesCS2B01G390100 chr5A 705883335 705884437 1102 False 1832.0 1832 96.649 2107 3210 1 chr5A.!!$F2 1103
9 TraesCS2B01G390100 chr5A 262470528 262471612 1084 True 1821.0 1821 96.959 1129 2213 1 chr5A.!!$R1 1084
10 TraesCS2B01G390100 chr5A 310728113 310728838 725 True 944.0 944 90.922 149 840 1 chr5A.!!$R2 691
11 TraesCS2B01G390100 chr2A 694742479 694743887 1408 True 1136.5 1805 96.574 849 2213 2 chr2A.!!$R1 1364
12 TraesCS2B01G390100 chr5D 309067238 309068222 984 True 1653.0 1653 96.957 2225 3210 1 chr5D.!!$R1 985
13 TraesCS2B01G390100 chr1D 97784419 97785404 985 True 1650.0 1650 96.856 2225 3210 1 chr1D.!!$R1 985
14 TraesCS2B01G390100 chr7A 699626992 699627689 697 True 1020.0 1020 93.295 152 840 1 chr7A.!!$R1 688

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
116 117 0.038892 TACCAACACGAACCTCGAGC 60.039 55.000 6.99 0.0 43.74 5.03 F
126 127 0.614979 AACCTCGAGCCAGAGCCTAA 60.615 55.000 6.99 0.0 41.25 2.69 F
618 673 0.687354 AGCCGAAAGCCGATCCATAT 59.313 50.000 0.00 0.0 45.47 1.78 F
1086 1148 1.211457 GGATTGCAGGGTGAGTCTCAT 59.789 52.381 5.68 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2075 2.695147 CTGTGGGCAGTTTCCTTTTTCT 59.305 45.455 0.00 0.00 37.92 2.52 R
2058 2168 8.973182 GTTGGTAGATATTTATTGGGGAAAACA 58.027 33.333 0.00 0.00 0.00 2.83 R
2178 2288 0.457851 CTCTTCGTTCCCAGCGAGAT 59.542 55.000 0.00 0.00 39.61 2.75 R
2831 2941 1.460504 CAAGTGATGCTGCAGGTCAT 58.539 50.000 17.12 11.28 0.00 3.06 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
24 25 7.889589 AAAGCACAAAATCAGTAAATAAGCC 57.110 32.000 0.00 0.00 0.00 4.35
25 26 6.588719 AGCACAAAATCAGTAAATAAGCCA 57.411 33.333 0.00 0.00 0.00 4.75
26 27 7.174107 AGCACAAAATCAGTAAATAAGCCAT 57.826 32.000 0.00 0.00 0.00 4.40
27 28 7.260603 AGCACAAAATCAGTAAATAAGCCATC 58.739 34.615 0.00 0.00 0.00 3.51
28 29 6.476706 GCACAAAATCAGTAAATAAGCCATCC 59.523 38.462 0.00 0.00 0.00 3.51
29 30 7.546358 CACAAAATCAGTAAATAAGCCATCCA 58.454 34.615 0.00 0.00 0.00 3.41
30 31 8.199449 CACAAAATCAGTAAATAAGCCATCCAT 58.801 33.333 0.00 0.00 0.00 3.41
31 32 8.416329 ACAAAATCAGTAAATAAGCCATCCATC 58.584 33.333 0.00 0.00 0.00 3.51
32 33 8.636213 CAAAATCAGTAAATAAGCCATCCATCT 58.364 33.333 0.00 0.00 0.00 2.90
33 34 7.992754 AATCAGTAAATAAGCCATCCATCTC 57.007 36.000 0.00 0.00 0.00 2.75
34 35 6.499106 TCAGTAAATAAGCCATCCATCTCA 57.501 37.500 0.00 0.00 0.00 3.27
35 36 6.291377 TCAGTAAATAAGCCATCCATCTCAC 58.709 40.000 0.00 0.00 0.00 3.51
36 37 6.100279 TCAGTAAATAAGCCATCCATCTCACT 59.900 38.462 0.00 0.00 0.00 3.41
37 38 6.204301 CAGTAAATAAGCCATCCATCTCACTG 59.796 42.308 0.00 0.00 0.00 3.66
38 39 3.784511 ATAAGCCATCCATCTCACTGG 57.215 47.619 0.00 0.00 37.66 4.00
39 40 1.293062 AAGCCATCCATCTCACTGGT 58.707 50.000 0.00 0.00 37.57 4.00
40 41 0.835941 AGCCATCCATCTCACTGGTC 59.164 55.000 0.00 0.00 37.57 4.02
41 42 0.179034 GCCATCCATCTCACTGGTCC 60.179 60.000 0.00 0.00 37.57 4.46
42 43 1.504912 CCATCCATCTCACTGGTCCT 58.495 55.000 0.00 0.00 37.57 3.85
43 44 1.140452 CCATCCATCTCACTGGTCCTG 59.860 57.143 0.00 0.00 37.57 3.86
44 45 1.836166 CATCCATCTCACTGGTCCTGT 59.164 52.381 0.00 0.00 37.57 4.00
45 46 1.561643 TCCATCTCACTGGTCCTGTC 58.438 55.000 0.00 0.00 37.57 3.51
46 47 1.077828 TCCATCTCACTGGTCCTGTCT 59.922 52.381 0.00 0.00 37.57 3.41
47 48 2.311841 TCCATCTCACTGGTCCTGTCTA 59.688 50.000 0.00 0.00 37.57 2.59
48 49 2.428890 CCATCTCACTGGTCCTGTCTAC 59.571 54.545 0.00 0.00 0.00 2.59
49 50 2.971901 TCTCACTGGTCCTGTCTACA 57.028 50.000 0.00 0.00 0.00 2.74
50 51 3.238788 TCTCACTGGTCCTGTCTACAA 57.761 47.619 0.00 0.00 0.00 2.41
51 52 3.572642 TCTCACTGGTCCTGTCTACAAA 58.427 45.455 0.00 0.00 0.00 2.83
52 53 3.964688 TCTCACTGGTCCTGTCTACAAAA 59.035 43.478 0.00 0.00 0.00 2.44
53 54 4.039245 TCTCACTGGTCCTGTCTACAAAAG 59.961 45.833 0.00 0.00 0.00 2.27
54 55 2.808543 CACTGGTCCTGTCTACAAAAGC 59.191 50.000 0.00 0.00 0.00 3.51
55 56 2.438021 ACTGGTCCTGTCTACAAAAGCA 59.562 45.455 0.00 0.00 0.00 3.91
56 57 3.118038 ACTGGTCCTGTCTACAAAAGCAA 60.118 43.478 0.00 0.00 0.00 3.91
57 58 4.074970 CTGGTCCTGTCTACAAAAGCAAT 58.925 43.478 0.00 0.00 0.00 3.56
58 59 4.469657 TGGTCCTGTCTACAAAAGCAATT 58.530 39.130 0.00 0.00 0.00 2.32
59 60 4.892934 TGGTCCTGTCTACAAAAGCAATTT 59.107 37.500 0.00 0.00 0.00 1.82
60 61 5.362430 TGGTCCTGTCTACAAAAGCAATTTT 59.638 36.000 0.00 0.00 0.00 1.82
61 62 5.920840 GGTCCTGTCTACAAAAGCAATTTTC 59.079 40.000 0.00 0.00 0.00 2.29
62 63 5.920840 GTCCTGTCTACAAAAGCAATTTTCC 59.079 40.000 0.00 0.00 0.00 3.13
63 64 5.833131 TCCTGTCTACAAAAGCAATTTTCCT 59.167 36.000 0.00 0.00 0.00 3.36
64 65 6.016276 TCCTGTCTACAAAAGCAATTTTCCTC 60.016 38.462 0.00 0.00 0.00 3.71
65 66 6.239008 CCTGTCTACAAAAGCAATTTTCCTCA 60.239 38.462 0.00 0.00 0.00 3.86
66 67 7.288810 TGTCTACAAAAGCAATTTTCCTCAT 57.711 32.000 0.00 0.00 0.00 2.90
67 68 8.402798 TGTCTACAAAAGCAATTTTCCTCATA 57.597 30.769 0.00 0.00 0.00 2.15
68 69 9.023962 TGTCTACAAAAGCAATTTTCCTCATAT 57.976 29.630 0.00 0.00 0.00 1.78
69 70 9.508567 GTCTACAAAAGCAATTTTCCTCATATC 57.491 33.333 0.00 0.00 0.00 1.63
70 71 8.686334 TCTACAAAAGCAATTTTCCTCATATCC 58.314 33.333 0.00 0.00 0.00 2.59
71 72 6.643388 ACAAAAGCAATTTTCCTCATATCCC 58.357 36.000 0.00 0.00 0.00 3.85
72 73 6.213195 ACAAAAGCAATTTTCCTCATATCCCA 59.787 34.615 0.00 0.00 0.00 4.37
73 74 6.475596 AAAGCAATTTTCCTCATATCCCAG 57.524 37.500 0.00 0.00 0.00 4.45
74 75 4.477249 AGCAATTTTCCTCATATCCCAGG 58.523 43.478 0.00 0.00 0.00 4.45
75 76 4.078980 AGCAATTTTCCTCATATCCCAGGT 60.079 41.667 0.00 0.00 0.00 4.00
76 77 4.651045 GCAATTTTCCTCATATCCCAGGTT 59.349 41.667 0.00 0.00 0.00 3.50
77 78 5.452356 GCAATTTTCCTCATATCCCAGGTTG 60.452 44.000 0.00 0.00 0.00 3.77
78 79 3.951563 TTTCCTCATATCCCAGGTTGG 57.048 47.619 0.00 0.00 37.25 3.77
79 80 1.140312 TCCTCATATCCCAGGTTGGC 58.860 55.000 0.00 0.00 35.79 4.52
80 81 0.846015 CCTCATATCCCAGGTTGGCA 59.154 55.000 0.00 0.00 35.79 4.92
81 82 1.215173 CCTCATATCCCAGGTTGGCAA 59.785 52.381 0.00 0.00 35.79 4.52
82 83 2.301346 CTCATATCCCAGGTTGGCAAC 58.699 52.381 21.92 21.92 35.79 4.17
94 95 2.911484 GTTGGCAACCAATTTGTTCCA 58.089 42.857 19.57 8.52 45.80 3.53
95 96 2.611225 TGGCAACCAATTTGTTCCAC 57.389 45.000 8.52 0.00 37.54 4.02
96 97 1.833630 TGGCAACCAATTTGTTCCACA 59.166 42.857 8.52 0.22 37.54 4.17
97 98 2.437281 TGGCAACCAATTTGTTCCACAT 59.563 40.909 8.52 0.00 37.54 3.21
98 99 3.643320 TGGCAACCAATTTGTTCCACATA 59.357 39.130 8.52 0.00 37.54 2.29
99 100 3.993736 GGCAACCAATTTGTTCCACATAC 59.006 43.478 0.00 0.00 37.54 2.39
100 101 3.993736 GCAACCAATTTGTTCCACATACC 59.006 43.478 0.00 0.00 37.54 2.73
101 102 4.502259 GCAACCAATTTGTTCCACATACCA 60.502 41.667 0.00 0.00 37.54 3.25
102 103 5.605534 CAACCAATTTGTTCCACATACCAA 58.394 37.500 0.00 0.00 0.00 3.67
103 104 5.208463 ACCAATTTGTTCCACATACCAAC 57.792 39.130 0.00 0.00 0.00 3.77
104 105 4.651503 ACCAATTTGTTCCACATACCAACA 59.348 37.500 0.00 0.00 0.00 3.33
105 106 4.987912 CCAATTTGTTCCACATACCAACAC 59.012 41.667 0.00 0.00 29.74 3.32
106 107 3.972950 TTTGTTCCACATACCAACACG 57.027 42.857 0.00 0.00 29.74 4.49
107 108 2.912690 TGTTCCACATACCAACACGA 57.087 45.000 0.00 0.00 0.00 4.35
108 109 3.195471 TGTTCCACATACCAACACGAA 57.805 42.857 0.00 0.00 0.00 3.85
109 110 2.873472 TGTTCCACATACCAACACGAAC 59.127 45.455 0.00 0.00 0.00 3.95
110 111 2.172851 TCCACATACCAACACGAACC 57.827 50.000 0.00 0.00 0.00 3.62
111 112 1.695242 TCCACATACCAACACGAACCT 59.305 47.619 0.00 0.00 0.00 3.50
112 113 2.073816 CCACATACCAACACGAACCTC 58.926 52.381 0.00 0.00 0.00 3.85
113 114 1.724623 CACATACCAACACGAACCTCG 59.275 52.381 0.00 0.00 46.93 4.63
114 115 1.614903 ACATACCAACACGAACCTCGA 59.385 47.619 2.59 0.00 43.74 4.04
115 116 2.259618 CATACCAACACGAACCTCGAG 58.740 52.381 5.13 5.13 43.74 4.04
116 117 0.038892 TACCAACACGAACCTCGAGC 60.039 55.000 6.99 0.00 43.74 5.03
117 118 2.027625 CCAACACGAACCTCGAGCC 61.028 63.158 6.99 0.00 43.74 4.70
118 119 1.300620 CAACACGAACCTCGAGCCA 60.301 57.895 6.99 0.00 43.74 4.75
119 120 1.006102 AACACGAACCTCGAGCCAG 60.006 57.895 6.99 0.26 43.74 4.85
120 121 1.461091 AACACGAACCTCGAGCCAGA 61.461 55.000 6.99 0.00 43.74 3.86
121 122 1.153939 CACGAACCTCGAGCCAGAG 60.154 63.158 6.99 0.00 43.74 3.35
122 123 2.202676 CGAACCTCGAGCCAGAGC 60.203 66.667 6.99 0.00 43.74 4.09
123 124 2.185608 GAACCTCGAGCCAGAGCC 59.814 66.667 6.99 0.00 41.25 4.70
124 125 2.284258 AACCTCGAGCCAGAGCCT 60.284 61.111 6.99 0.00 41.25 4.58
125 126 1.000486 AACCTCGAGCCAGAGCCTA 60.000 57.895 6.99 0.00 41.25 3.93
126 127 0.614979 AACCTCGAGCCAGAGCCTAA 60.615 55.000 6.99 0.00 41.25 2.69
127 128 1.040339 ACCTCGAGCCAGAGCCTAAG 61.040 60.000 6.99 0.00 41.25 2.18
128 129 0.753479 CCTCGAGCCAGAGCCTAAGA 60.753 60.000 6.99 0.00 41.25 2.10
129 130 1.327303 CTCGAGCCAGAGCCTAAGAT 58.673 55.000 0.00 0.00 41.25 2.40
130 131 2.509569 CTCGAGCCAGAGCCTAAGATA 58.490 52.381 0.00 0.00 41.25 1.98
131 132 2.227865 CTCGAGCCAGAGCCTAAGATAC 59.772 54.545 0.00 0.00 41.25 2.24
132 133 2.158593 TCGAGCCAGAGCCTAAGATACT 60.159 50.000 0.00 0.00 41.25 2.12
133 134 3.072622 TCGAGCCAGAGCCTAAGATACTA 59.927 47.826 0.00 0.00 41.25 1.82
134 135 3.821600 CGAGCCAGAGCCTAAGATACTAA 59.178 47.826 0.00 0.00 41.25 2.24
135 136 4.320641 CGAGCCAGAGCCTAAGATACTAAC 60.321 50.000 0.00 0.00 41.25 2.34
136 137 3.570550 AGCCAGAGCCTAAGATACTAACG 59.429 47.826 0.00 0.00 41.25 3.18
137 138 3.318557 GCCAGAGCCTAAGATACTAACGT 59.681 47.826 0.00 0.00 0.00 3.99
138 139 4.518211 GCCAGAGCCTAAGATACTAACGTA 59.482 45.833 0.00 0.00 0.00 3.57
139 140 5.009410 GCCAGAGCCTAAGATACTAACGTAA 59.991 44.000 0.00 0.00 0.00 3.18
140 141 8.864515 AGCCAGAGCCTAAGATACTAACGTAAG 61.865 44.444 0.00 0.00 41.25 2.34
141 142 6.485984 CCAGAGCCTAAGATACTAACGTAAGA 59.514 42.308 0.00 0.00 43.62 2.10
142 143 7.175293 CCAGAGCCTAAGATACTAACGTAAGAT 59.825 40.741 0.00 0.00 43.62 2.40
143 144 8.231837 CAGAGCCTAAGATACTAACGTAAGATC 58.768 40.741 0.00 0.00 43.62 2.75
144 145 8.158789 AGAGCCTAAGATACTAACGTAAGATCT 58.841 37.037 0.00 0.00 43.62 2.75
145 146 8.101654 AGCCTAAGATACTAACGTAAGATCTG 57.898 38.462 0.00 0.00 43.62 2.90
182 183 4.466370 CCTAATGTCTCAGTTGGTAGGTCA 59.534 45.833 0.00 0.00 0.00 4.02
498 505 4.052229 CCTGCCCTCGTTCGTCGT 62.052 66.667 0.00 0.00 40.80 4.34
618 673 0.687354 AGCCGAAAGCCGATCCATAT 59.313 50.000 0.00 0.00 45.47 1.78
707 769 4.414956 ACCCCTCGGATGCCTCCA 62.415 66.667 8.86 0.00 42.19 3.86
754 816 1.886422 GGATCCACCTCTTCCTCCTT 58.114 55.000 6.95 0.00 35.41 3.36
798 860 2.502492 CCGGCATCGACCTCATCCT 61.502 63.158 0.00 0.00 39.00 3.24
852 914 4.602259 CGCCACCTGGTCGTGTGT 62.602 66.667 0.00 0.00 37.57 3.72
964 1026 3.319122 AGGTTGATGCCTTTGTTTCTGTC 59.681 43.478 0.00 0.00 34.71 3.51
1086 1148 1.211457 GGATTGCAGGGTGAGTCTCAT 59.789 52.381 5.68 0.00 0.00 2.90
1222 1331 2.224378 CGCTCATAGGTGTCATGGGAAT 60.224 50.000 0.00 0.00 0.00 3.01
1277 1386 4.089408 AGCCAAGCAAAATTGAATGGTT 57.911 36.364 14.91 9.17 37.59 3.67
1376 1485 6.530120 TCACCAATAGAAGCTGAACTTGTTA 58.470 36.000 0.00 0.00 39.29 2.41
1755 1864 5.428131 AGAAATGCTAACAGAGGAGGAGAAT 59.572 40.000 0.00 0.00 0.00 2.40
1768 1877 4.910304 AGGAGGAGAATACCATGCAAGTAT 59.090 41.667 6.88 6.88 31.71 2.12
1871 1980 5.598830 TGTAGGAGATAGCAAAAGGACTAGG 59.401 44.000 0.00 0.00 0.00 3.02
1966 2075 6.900189 TGAAAAGTTTGACGTTGTTACTTGA 58.100 32.000 0.00 0.00 0.00 3.02
2058 2168 6.655078 AACTTCAGTCATGCTTTATTGGTT 57.345 33.333 0.00 0.00 0.00 3.67
2178 2288 2.584064 CGGCACCTGCATAGACCA 59.416 61.111 0.00 0.00 44.36 4.02
2824 2934 7.105588 TGTTGATTCTTATAGAGCTTCTGCAA 58.894 34.615 0.00 0.00 42.74 4.08
2962 3072 2.959421 AGTTCCCTTCCTCTCTCCAT 57.041 50.000 0.00 0.00 0.00 3.41
2971 3081 2.176045 TCCTCTCTCCATGCAACGTTA 58.824 47.619 0.00 0.00 0.00 3.18
3015 3125 1.142667 TCATCAGGCCCATTATTGCGA 59.857 47.619 0.00 0.00 0.00 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.441017 TGGCTTATTTACTGATTTTGTGCTTT 58.559 30.769 0.00 0.00 0.00 3.51
1 2 6.991938 TGGCTTATTTACTGATTTTGTGCTT 58.008 32.000 0.00 0.00 0.00 3.91
2 3 6.588719 TGGCTTATTTACTGATTTTGTGCT 57.411 33.333 0.00 0.00 0.00 4.40
3 4 6.476706 GGATGGCTTATTTACTGATTTTGTGC 59.523 38.462 0.00 0.00 0.00 4.57
4 5 7.546358 TGGATGGCTTATTTACTGATTTTGTG 58.454 34.615 0.00 0.00 0.00 3.33
5 6 7.716799 TGGATGGCTTATTTACTGATTTTGT 57.283 32.000 0.00 0.00 0.00 2.83
6 7 8.636213 AGATGGATGGCTTATTTACTGATTTTG 58.364 33.333 0.00 0.00 0.00 2.44
7 8 8.773033 AGATGGATGGCTTATTTACTGATTTT 57.227 30.769 0.00 0.00 0.00 1.82
8 9 8.000709 TGAGATGGATGGCTTATTTACTGATTT 58.999 33.333 0.00 0.00 0.00 2.17
9 10 7.446625 GTGAGATGGATGGCTTATTTACTGATT 59.553 37.037 0.00 0.00 0.00 2.57
10 11 6.939163 GTGAGATGGATGGCTTATTTACTGAT 59.061 38.462 0.00 0.00 0.00 2.90
11 12 6.100279 AGTGAGATGGATGGCTTATTTACTGA 59.900 38.462 0.00 0.00 0.00 3.41
12 13 6.204301 CAGTGAGATGGATGGCTTATTTACTG 59.796 42.308 0.00 0.00 0.00 2.74
13 14 6.294473 CAGTGAGATGGATGGCTTATTTACT 58.706 40.000 0.00 0.00 0.00 2.24
14 15 5.471456 CCAGTGAGATGGATGGCTTATTTAC 59.529 44.000 0.00 0.00 43.57 2.01
15 16 5.132648 ACCAGTGAGATGGATGGCTTATTTA 59.867 40.000 0.00 0.00 43.57 1.40
16 17 4.079558 ACCAGTGAGATGGATGGCTTATTT 60.080 41.667 0.00 0.00 43.57 1.40
17 18 3.461085 ACCAGTGAGATGGATGGCTTATT 59.539 43.478 0.00 0.00 43.57 1.40
18 19 3.051581 ACCAGTGAGATGGATGGCTTAT 58.948 45.455 0.00 0.00 43.57 1.73
19 20 2.435805 GACCAGTGAGATGGATGGCTTA 59.564 50.000 0.00 0.00 43.57 3.09
20 21 1.211457 GACCAGTGAGATGGATGGCTT 59.789 52.381 0.00 0.00 43.57 4.35
21 22 0.835941 GACCAGTGAGATGGATGGCT 59.164 55.000 0.00 0.00 43.57 4.75
22 23 0.179034 GGACCAGTGAGATGGATGGC 60.179 60.000 0.00 0.00 43.57 4.40
23 24 1.140452 CAGGACCAGTGAGATGGATGG 59.860 57.143 0.00 0.00 43.57 3.51
24 25 1.836166 ACAGGACCAGTGAGATGGATG 59.164 52.381 0.00 0.00 43.57 3.51
25 26 2.114616 GACAGGACCAGTGAGATGGAT 58.885 52.381 0.00 0.00 43.57 3.41
26 27 1.077828 AGACAGGACCAGTGAGATGGA 59.922 52.381 0.00 0.00 43.57 3.41
27 28 1.566211 AGACAGGACCAGTGAGATGG 58.434 55.000 0.00 0.00 46.47 3.51
28 29 3.092301 TGTAGACAGGACCAGTGAGATG 58.908 50.000 0.00 0.00 0.00 2.90
29 30 3.458044 TGTAGACAGGACCAGTGAGAT 57.542 47.619 0.00 0.00 0.00 2.75
30 31 2.971901 TGTAGACAGGACCAGTGAGA 57.028 50.000 0.00 0.00 0.00 3.27
31 32 4.310769 CTTTTGTAGACAGGACCAGTGAG 58.689 47.826 0.00 0.00 0.00 3.51
32 33 3.494398 GCTTTTGTAGACAGGACCAGTGA 60.494 47.826 0.00 0.00 0.00 3.41
33 34 2.808543 GCTTTTGTAGACAGGACCAGTG 59.191 50.000 0.00 0.00 0.00 3.66
34 35 2.438021 TGCTTTTGTAGACAGGACCAGT 59.562 45.455 0.00 0.00 0.00 4.00
35 36 3.126001 TGCTTTTGTAGACAGGACCAG 57.874 47.619 0.00 0.00 0.00 4.00
36 37 3.569194 TTGCTTTTGTAGACAGGACCA 57.431 42.857 0.00 0.00 0.00 4.02
37 38 5.453567 AAATTGCTTTTGTAGACAGGACC 57.546 39.130 0.00 0.00 0.00 4.46
38 39 5.920840 GGAAAATTGCTTTTGTAGACAGGAC 59.079 40.000 0.00 0.00 34.73 3.85
39 40 5.833131 AGGAAAATTGCTTTTGTAGACAGGA 59.167 36.000 0.00 0.00 34.73 3.86
40 41 6.089249 AGGAAAATTGCTTTTGTAGACAGG 57.911 37.500 0.00 0.00 34.73 4.00
41 42 6.738114 TGAGGAAAATTGCTTTTGTAGACAG 58.262 36.000 0.00 0.00 34.73 3.51
42 43 6.707440 TGAGGAAAATTGCTTTTGTAGACA 57.293 33.333 0.00 0.00 34.73 3.41
43 44 9.508567 GATATGAGGAAAATTGCTTTTGTAGAC 57.491 33.333 0.00 0.00 34.73 2.59
44 45 8.686334 GGATATGAGGAAAATTGCTTTTGTAGA 58.314 33.333 0.00 0.00 34.73 2.59
45 46 7.922811 GGGATATGAGGAAAATTGCTTTTGTAG 59.077 37.037 0.00 0.00 34.73 2.74
46 47 7.398618 TGGGATATGAGGAAAATTGCTTTTGTA 59.601 33.333 0.00 0.00 34.73 2.41
47 48 6.213195 TGGGATATGAGGAAAATTGCTTTTGT 59.787 34.615 0.00 0.00 34.73 2.83
48 49 6.642430 TGGGATATGAGGAAAATTGCTTTTG 58.358 36.000 0.00 0.00 34.73 2.44
49 50 6.126968 CCTGGGATATGAGGAAAATTGCTTTT 60.127 38.462 0.00 0.00 37.28 2.27
50 51 5.364735 CCTGGGATATGAGGAAAATTGCTTT 59.635 40.000 0.00 0.00 0.00 3.51
51 52 4.897670 CCTGGGATATGAGGAAAATTGCTT 59.102 41.667 0.00 0.00 0.00 3.91
52 53 4.078980 ACCTGGGATATGAGGAAAATTGCT 60.079 41.667 0.00 0.00 33.16 3.91
53 54 4.218312 ACCTGGGATATGAGGAAAATTGC 58.782 43.478 0.00 0.00 33.16 3.56
54 55 5.069516 CCAACCTGGGATATGAGGAAAATTG 59.930 44.000 0.00 0.00 32.67 2.32
55 56 5.211201 CCAACCTGGGATATGAGGAAAATT 58.789 41.667 0.00 0.00 32.67 1.82
56 57 4.808042 CCAACCTGGGATATGAGGAAAAT 58.192 43.478 0.00 0.00 32.67 1.82
57 58 3.627237 GCCAACCTGGGATATGAGGAAAA 60.627 47.826 0.00 0.00 38.19 2.29
58 59 2.091885 GCCAACCTGGGATATGAGGAAA 60.092 50.000 0.00 0.00 38.19 3.13
59 60 1.494721 GCCAACCTGGGATATGAGGAA 59.505 52.381 0.00 0.00 38.19 3.36
60 61 1.140312 GCCAACCTGGGATATGAGGA 58.860 55.000 0.00 0.00 38.19 3.71
61 62 0.846015 TGCCAACCTGGGATATGAGG 59.154 55.000 0.00 0.00 38.19 3.86
62 63 2.301346 GTTGCCAACCTGGGATATGAG 58.699 52.381 0.00 0.00 37.82 2.90
63 64 2.435372 GTTGCCAACCTGGGATATGA 57.565 50.000 0.00 0.00 37.82 2.15
71 72 6.727587 TGGAACAAATTGGTTGCCAACCTG 62.728 45.833 26.03 18.07 44.76 4.00
72 73 4.707857 TGGAACAAATTGGTTGCCAACCT 61.708 43.478 26.03 5.32 44.76 3.50
73 74 2.217750 GGAACAAATTGGTTGCCAACC 58.782 47.619 19.89 19.89 46.95 3.77
74 75 2.611751 GTGGAACAAATTGGTTGCCAAC 59.388 45.455 14.01 0.00 44.14 3.77
75 76 2.911484 GTGGAACAAATTGGTTGCCAA 58.089 42.857 14.01 2.86 45.09 4.52
76 77 2.611225 GTGGAACAAATTGGTTGCCA 57.389 45.000 14.01 12.27 44.16 4.92
89 90 2.224784 GGTTCGTGTTGGTATGTGGAAC 59.775 50.000 0.00 0.00 33.43 3.62
90 91 2.105134 AGGTTCGTGTTGGTATGTGGAA 59.895 45.455 0.00 0.00 0.00 3.53
91 92 1.695242 AGGTTCGTGTTGGTATGTGGA 59.305 47.619 0.00 0.00 0.00 4.02
92 93 2.073816 GAGGTTCGTGTTGGTATGTGG 58.926 52.381 0.00 0.00 0.00 4.17
93 94 1.724623 CGAGGTTCGTGTTGGTATGTG 59.275 52.381 0.00 0.00 34.72 3.21
94 95 1.614903 TCGAGGTTCGTGTTGGTATGT 59.385 47.619 0.00 0.00 41.35 2.29
95 96 2.259618 CTCGAGGTTCGTGTTGGTATG 58.740 52.381 3.91 0.00 41.35 2.39
96 97 1.403780 GCTCGAGGTTCGTGTTGGTAT 60.404 52.381 15.58 0.00 41.35 2.73
97 98 0.038892 GCTCGAGGTTCGTGTTGGTA 60.039 55.000 15.58 0.00 41.35 3.25
98 99 1.300697 GCTCGAGGTTCGTGTTGGT 60.301 57.895 15.58 0.00 41.35 3.67
99 100 2.027625 GGCTCGAGGTTCGTGTTGG 61.028 63.158 15.58 0.00 41.35 3.77
100 101 1.284982 CTGGCTCGAGGTTCGTGTTG 61.285 60.000 15.58 0.00 41.35 3.33
101 102 1.006102 CTGGCTCGAGGTTCGTGTT 60.006 57.895 15.58 0.00 41.35 3.32
102 103 1.867919 CTCTGGCTCGAGGTTCGTGT 61.868 60.000 15.58 0.00 41.35 4.49
103 104 1.153939 CTCTGGCTCGAGGTTCGTG 60.154 63.158 15.58 0.00 41.35 4.35
104 105 2.995872 GCTCTGGCTCGAGGTTCGT 61.996 63.158 15.58 0.00 41.35 3.85
105 106 2.202676 GCTCTGGCTCGAGGTTCG 60.203 66.667 15.58 0.00 42.10 3.95
106 107 1.038130 TAGGCTCTGGCTCGAGGTTC 61.038 60.000 15.58 0.00 39.70 3.62
107 108 0.614979 TTAGGCTCTGGCTCGAGGTT 60.615 55.000 15.58 0.00 39.70 3.50
108 109 1.000486 TTAGGCTCTGGCTCGAGGT 60.000 57.895 15.58 0.00 39.70 3.85
109 110 0.753479 TCTTAGGCTCTGGCTCGAGG 60.753 60.000 15.58 0.00 39.70 4.63
110 111 1.327303 ATCTTAGGCTCTGGCTCGAG 58.673 55.000 8.45 8.45 39.70 4.04
111 112 2.158593 AGTATCTTAGGCTCTGGCTCGA 60.159 50.000 0.00 0.00 39.70 4.04
112 113 2.235016 AGTATCTTAGGCTCTGGCTCG 58.765 52.381 0.00 0.00 39.70 5.03
113 114 4.320641 CGTTAGTATCTTAGGCTCTGGCTC 60.321 50.000 0.00 0.00 39.70 4.70
114 115 3.570550 CGTTAGTATCTTAGGCTCTGGCT 59.429 47.826 0.00 0.00 42.39 4.75
115 116 3.318557 ACGTTAGTATCTTAGGCTCTGGC 59.681 47.826 0.00 0.00 37.82 4.85
116 117 6.485984 TCTTACGTTAGTATCTTAGGCTCTGG 59.514 42.308 0.00 0.00 32.12 3.86
117 118 7.493743 TCTTACGTTAGTATCTTAGGCTCTG 57.506 40.000 0.00 0.00 32.12 3.35
118 119 8.158789 AGATCTTACGTTAGTATCTTAGGCTCT 58.841 37.037 0.00 0.00 32.12 4.09
119 120 8.231837 CAGATCTTACGTTAGTATCTTAGGCTC 58.768 40.741 11.35 0.00 32.12 4.70
120 121 7.720515 ACAGATCTTACGTTAGTATCTTAGGCT 59.279 37.037 11.35 0.00 32.12 4.58
121 122 7.804129 CACAGATCTTACGTTAGTATCTTAGGC 59.196 40.741 11.35 0.00 32.12 3.93
122 123 9.053840 TCACAGATCTTACGTTAGTATCTTAGG 57.946 37.037 11.35 6.26 32.12 2.69
126 127 9.953697 GATTTCACAGATCTTACGTTAGTATCT 57.046 33.333 0.00 2.08 32.12 1.98
127 128 9.953697 AGATTTCACAGATCTTACGTTAGTATC 57.046 33.333 0.00 0.00 29.77 2.24
128 129 9.953697 GAGATTTCACAGATCTTACGTTAGTAT 57.046 33.333 0.00 0.00 34.13 2.12
129 130 9.175312 AGAGATTTCACAGATCTTACGTTAGTA 57.825 33.333 0.00 0.00 34.13 1.82
130 131 8.057536 AGAGATTTCACAGATCTTACGTTAGT 57.942 34.615 0.00 0.00 34.13 2.24
131 132 9.440784 GTAGAGATTTCACAGATCTTACGTTAG 57.559 37.037 0.00 0.00 34.13 2.34
132 133 9.175312 AGTAGAGATTTCACAGATCTTACGTTA 57.825 33.333 0.00 0.00 34.13 3.18
133 134 8.057536 AGTAGAGATTTCACAGATCTTACGTT 57.942 34.615 0.00 0.00 34.13 3.99
134 135 7.201750 GGAGTAGAGATTTCACAGATCTTACGT 60.202 40.741 0.00 0.00 34.13 3.57
135 136 7.012894 AGGAGTAGAGATTTCACAGATCTTACG 59.987 40.741 0.00 0.00 34.13 3.18
136 137 8.232913 AGGAGTAGAGATTTCACAGATCTTAC 57.767 38.462 0.00 0.00 34.13 2.34
137 138 9.922477 TTAGGAGTAGAGATTTCACAGATCTTA 57.078 33.333 0.00 0.00 34.13 2.10
138 139 8.830915 TTAGGAGTAGAGATTTCACAGATCTT 57.169 34.615 0.00 0.00 34.13 2.40
139 140 8.859090 CATTAGGAGTAGAGATTTCACAGATCT 58.141 37.037 0.00 0.00 36.60 2.75
140 141 8.637986 ACATTAGGAGTAGAGATTTCACAGATC 58.362 37.037 0.00 0.00 0.00 2.75
141 142 8.546083 ACATTAGGAGTAGAGATTTCACAGAT 57.454 34.615 0.00 0.00 0.00 2.90
142 143 7.836685 AGACATTAGGAGTAGAGATTTCACAGA 59.163 37.037 0.00 0.00 0.00 3.41
143 144 8.006298 AGACATTAGGAGTAGAGATTTCACAG 57.994 38.462 0.00 0.00 0.00 3.66
144 145 7.615757 TGAGACATTAGGAGTAGAGATTTCACA 59.384 37.037 0.00 0.00 0.00 3.58
145 146 8.001881 TGAGACATTAGGAGTAGAGATTTCAC 57.998 38.462 0.00 0.00 0.00 3.18
182 183 4.526625 GACGAAAATAAAACCCGAAACGT 58.473 39.130 0.00 0.00 0.00 3.99
240 241 4.785453 CGGGAGGTGGGAGCAAGC 62.785 72.222 0.00 0.00 0.00 4.01
318 319 1.660560 CGATCGGTGGTTACGACCCT 61.661 60.000 10.85 0.00 45.92 4.34
498 505 2.186903 GCGAAGGGATGAAGGCGA 59.813 61.111 0.00 0.00 0.00 5.54
618 673 2.867855 GCGCGTCCAGATGGGGATA 61.868 63.158 8.43 0.00 39.62 2.59
689 751 3.551407 GGAGGCATCCGAGGGGTC 61.551 72.222 0.00 0.00 35.37 4.46
707 769 0.620556 AGCAATGGATCCACGAAGGT 59.379 50.000 18.99 9.91 39.02 3.50
798 860 4.063967 CGACCAGGTAGGCGTGCA 62.064 66.667 0.00 0.00 43.14 4.57
852 914 0.033504 GCGTCCCAAGAGACAAGACA 59.966 55.000 0.00 0.00 36.52 3.41
1086 1148 5.304614 AGAGCAAGTAACTGAGGTTAGTCAA 59.695 40.000 0.00 0.00 39.75 3.18
1277 1386 9.829507 AATTTACATCAATTCAACAAGGTTTGA 57.170 25.926 0.00 0.00 33.55 2.69
1755 1864 4.133820 GGCACATACATACTTGCATGGTA 58.866 43.478 4.44 3.73 36.66 3.25
1871 1980 8.925700 GTGTTTTTAAATCAATGGATCCTTCAC 58.074 33.333 14.23 2.99 31.88 3.18
1966 2075 2.695147 CTGTGGGCAGTTTCCTTTTTCT 59.305 45.455 0.00 0.00 37.92 2.52
2058 2168 8.973182 GTTGGTAGATATTTATTGGGGAAAACA 58.027 33.333 0.00 0.00 0.00 2.83
2178 2288 0.457851 CTCTTCGTTCCCAGCGAGAT 59.542 55.000 0.00 0.00 39.61 2.75
2588 2698 5.757320 CAGATTACCTAGAGTGAAGGCATTG 59.243 44.000 0.00 0.00 37.67 2.82
2589 2699 5.426833 ACAGATTACCTAGAGTGAAGGCATT 59.573 40.000 0.00 0.00 37.67 3.56
2831 2941 1.460504 CAAGTGATGCTGCAGGTCAT 58.539 50.000 17.12 11.28 0.00 3.06
2971 3081 6.664428 ATTAACAACTTAGCAACAATGGGT 57.336 33.333 0.00 0.00 0.00 4.51
3015 3125 5.423610 AGGCAAGATGAACAGACTATGTAGT 59.576 40.000 0.00 0.00 43.00 2.73


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

AutoCloner maintained by Alex Coulton.