Multiple sequence alignment - TraesCS3A01G482700

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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 TraesCS3A01G482700 chr3A 100.000 2447 0 0 1 2447 713309210 713306764 0.000000e+00 4519.0
1 TraesCS3A01G482700 chr3A 87.444 1561 161 25 906 2447 713342779 713341235 0.000000e+00 1764.0
2 TraesCS3A01G482700 chr3A 89.677 620 54 5 697 1311 713418385 713417771 0.000000e+00 782.0
3 TraesCS3A01G482700 chr3A 83.824 816 107 17 1341 2147 713417774 713416975 0.000000e+00 752.0
4 TraesCS3A01G482700 chr3A 84.911 676 61 23 165 807 713344043 713343376 0.000000e+00 645.0
5 TraesCS3A01G482700 chr3A 90.984 122 11 0 581 702 713419079 713418958 5.410000e-37 165.0
6 TraesCS3A01G482700 chr3A 90.000 50 4 1 119 168 746406548 746406596 2.030000e-06 63.9
7 TraesCS3A01G482700 chr3A 85.484 62 6 3 118 179 424730570 424730628 7.310000e-06 62.1
8 TraesCS3A01G482700 chr3D 88.821 1798 148 30 670 2447 577669002 577667238 0.000000e+00 2158.0
9 TraesCS3A01G482700 chr3D 88.387 1240 95 13 580 1814 577753120 577751925 0.000000e+00 1447.0
10 TraesCS3A01G482700 chr3D 89.019 1111 87 14 701 1806 578040810 578041890 0.000000e+00 1343.0
11 TraesCS3A01G482700 chr3D 87.733 1125 92 15 698 1814 577779883 577778797 0.000000e+00 1271.0
12 TraesCS3A01G482700 chr3D 85.041 615 69 16 1840 2447 578041894 578042492 2.690000e-169 604.0
13 TraesCS3A01G482700 chr3D 79.865 591 96 18 1872 2447 577778787 577778205 6.300000e-111 411.0
14 TraesCS3A01G482700 chr3D 93.780 209 12 1 165 373 577760929 577760722 1.830000e-81 313.0
15 TraesCS3A01G482700 chr3D 92.823 209 14 1 165 373 577741106 577740899 3.950000e-78 302.0
16 TraesCS3A01G482700 chr3D 88.800 125 14 0 579 703 577780160 577780036 1.170000e-33 154.0
17 TraesCS3A01G482700 chr3D 92.135 89 7 0 373 461 577740456 577740368 2.550000e-25 126.0
18 TraesCS3A01G482700 chr3D 84.946 93 13 1 1898 1989 558739588 558739680 2.590000e-15 93.5
19 TraesCS3A01G482700 chr3B 87.556 1776 158 28 698 2447 771241738 771243476 0.000000e+00 1997.0
20 TraesCS3A01G482700 chr3B 90.812 1121 77 17 698 1806 770964980 770963874 0.000000e+00 1476.0
21 TraesCS3A01G482700 chr3B 87.182 944 62 24 698 1630 771178204 771179099 0.000000e+00 1018.0
22 TraesCS3A01G482700 chr3B 85.222 812 97 17 1628 2426 771179185 771179986 0.000000e+00 813.0
23 TraesCS3A01G482700 chr3B 84.098 610 72 19 1846 2447 770963865 770963273 1.270000e-157 566.0
24 TraesCS3A01G482700 chr1B 88.304 171 18 2 1 170 525804316 525804485 1.150000e-48 204.0
25 TraesCS3A01G482700 chr5D 75.989 354 66 15 1949 2292 46308271 46308615 5.410000e-37 165.0
26 TraesCS3A01G482700 chr2D 72.979 470 93 24 1888 2349 118561299 118560856 1.530000e-27 134.0
27 TraesCS3A01G482700 chr7D 72.857 420 101 11 1887 2297 136705297 136704882 5.490000e-27 132.0
28 TraesCS3A01G482700 chr1A 76.000 250 54 5 1888 2133 345061935 345062182 9.190000e-25 124.0
29 TraesCS3A01G482700 chr1A 95.349 43 2 0 129 171 110060351 110060309 4.370000e-08 69.4
30 TraesCS3A01G482700 chr1A 85.075 67 7 3 102 168 504268039 504268102 5.650000e-07 65.8
31 TraesCS3A01G482700 chr5A 95.455 44 2 0 130 173 769560 769517 1.210000e-08 71.3
32 TraesCS3A01G482700 chr5A 89.091 55 4 2 118 171 549322181 549322128 1.570000e-07 67.6
33 TraesCS3A01G482700 chr6D 89.091 55 4 2 120 174 468565055 468565107 1.570000e-07 67.6
34 TraesCS3A01G482700 chr2B 90.385 52 4 1 118 168 99958542 99958593 1.570000e-07 67.6


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 TraesCS3A01G482700 chr3A 713306764 713309210 2446 True 4519.000000 4519 100.000000 1 2447 1 chr3A.!!$R1 2446
1 TraesCS3A01G482700 chr3A 713341235 713344043 2808 True 1204.500000 1764 86.177500 165 2447 2 chr3A.!!$R2 2282
2 TraesCS3A01G482700 chr3A 713416975 713419079 2104 True 566.333333 782 88.161667 581 2147 3 chr3A.!!$R3 1566
3 TraesCS3A01G482700 chr3D 577667238 577669002 1764 True 2158.000000 2158 88.821000 670 2447 1 chr3D.!!$R1 1777
4 TraesCS3A01G482700 chr3D 577751925 577753120 1195 True 1447.000000 1447 88.387000 580 1814 1 chr3D.!!$R2 1234
5 TraesCS3A01G482700 chr3D 578040810 578042492 1682 False 973.500000 1343 87.030000 701 2447 2 chr3D.!!$F2 1746
6 TraesCS3A01G482700 chr3D 577778205 577780160 1955 True 612.000000 1271 85.466000 579 2447 3 chr3D.!!$R5 1868
7 TraesCS3A01G482700 chr3D 577740368 577741106 738 True 214.000000 302 92.479000 165 461 2 chr3D.!!$R4 296
8 TraesCS3A01G482700 chr3B 771241738 771243476 1738 False 1997.000000 1997 87.556000 698 2447 1 chr3B.!!$F1 1749
9 TraesCS3A01G482700 chr3B 770963273 770964980 1707 True 1021.000000 1476 87.455000 698 2447 2 chr3B.!!$R1 1749
10 TraesCS3A01G482700 chr3B 771178204 771179986 1782 False 915.500000 1018 86.202000 698 2426 2 chr3B.!!$F2 1728

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
26 27 0.102481 CCGTCTCCGTGAATAGGTGG 59.898 60.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 3098 0.526524 GTGATCGAAGAGGCGGACTG 60.527 60.0 0.0 0.0 43.63 3.51 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
18 19 2.957060 ATGTTCTCCGTCTCCGTGA 58.043 52.632 0.00 0.00 0.00 4.35
19 20 1.254026 ATGTTCTCCGTCTCCGTGAA 58.746 50.000 0.00 0.00 0.00 3.18
20 21 1.254026 TGTTCTCCGTCTCCGTGAAT 58.746 50.000 0.00 0.00 31.05 2.57
21 22 2.439409 TGTTCTCCGTCTCCGTGAATA 58.561 47.619 0.00 0.00 31.05 1.75
22 23 2.422479 TGTTCTCCGTCTCCGTGAATAG 59.578 50.000 0.00 0.00 31.05 1.73
23 24 1.676746 TCTCCGTCTCCGTGAATAGG 58.323 55.000 0.00 0.00 0.00 2.57
24 25 1.064906 TCTCCGTCTCCGTGAATAGGT 60.065 52.381 0.00 0.00 0.00 3.08
25 26 1.065701 CTCCGTCTCCGTGAATAGGTG 59.934 57.143 0.00 0.00 0.00 4.00
26 27 0.102481 CCGTCTCCGTGAATAGGTGG 59.898 60.000 0.00 0.00 0.00 4.61
27 28 0.527817 CGTCTCCGTGAATAGGTGGC 60.528 60.000 0.00 0.00 0.00 5.01
28 29 0.179081 GTCTCCGTGAATAGGTGGCC 60.179 60.000 0.00 0.00 0.00 5.36
29 30 1.146263 CTCCGTGAATAGGTGGCCC 59.854 63.158 0.00 0.00 0.00 5.80
30 31 1.306654 TCCGTGAATAGGTGGCCCT 60.307 57.895 0.00 0.00 45.51 5.19
32 33 0.106149 CCGTGAATAGGTGGCCCTAC 59.894 60.000 0.00 0.00 46.14 3.18
33 34 1.120530 CGTGAATAGGTGGCCCTACT 58.879 55.000 0.00 0.00 46.14 2.57
34 35 1.202533 CGTGAATAGGTGGCCCTACTG 60.203 57.143 0.00 0.00 46.14 2.74
35 36 2.116238 GTGAATAGGTGGCCCTACTGA 58.884 52.381 0.00 0.00 46.14 3.41
36 37 2.706190 GTGAATAGGTGGCCCTACTGAT 59.294 50.000 0.00 0.00 46.14 2.90
37 38 2.972713 TGAATAGGTGGCCCTACTGATC 59.027 50.000 0.00 0.00 46.14 2.92
38 39 2.795291 ATAGGTGGCCCTACTGATCA 57.205 50.000 0.00 0.00 46.14 2.92
39 40 2.561209 TAGGTGGCCCTACTGATCAA 57.439 50.000 0.00 0.00 42.66 2.57
40 41 0.912486 AGGTGGCCCTACTGATCAAC 59.088 55.000 0.00 0.00 40.19 3.18
41 42 0.618458 GGTGGCCCTACTGATCAACA 59.382 55.000 0.00 0.00 0.00 3.33
42 43 3.748631 AGGTGGCCCTACTGATCAACAG 61.749 54.545 0.00 0.00 40.19 3.16
52 53 3.719083 CTGATCAACAGCAACGAAGAG 57.281 47.619 0.00 0.00 39.86 2.85
53 54 2.414481 CTGATCAACAGCAACGAAGAGG 59.586 50.000 0.00 0.00 39.86 3.69
54 55 1.734465 GATCAACAGCAACGAAGAGGG 59.266 52.381 0.00 0.00 0.00 4.30
55 56 0.884704 TCAACAGCAACGAAGAGGGC 60.885 55.000 0.00 0.00 0.00 5.19
56 57 1.148273 AACAGCAACGAAGAGGGCA 59.852 52.632 0.00 0.00 0.00 5.36
57 58 1.166531 AACAGCAACGAAGAGGGCAC 61.167 55.000 0.00 0.00 0.00 5.01
58 59 2.357517 AGCAACGAAGAGGGCACG 60.358 61.111 0.00 0.00 0.00 5.34
59 60 2.665185 GCAACGAAGAGGGCACGT 60.665 61.111 0.00 0.00 41.97 4.49
60 61 2.954753 GCAACGAAGAGGGCACGTG 61.955 63.158 12.28 12.28 40.10 4.49
61 62 2.030562 AACGAAGAGGGCACGTGG 59.969 61.111 18.88 0.00 40.10 4.94
62 63 4.681978 ACGAAGAGGGCACGTGGC 62.682 66.667 32.17 32.17 38.79 5.01
76 77 4.342427 TGGCAACATGGATGGCTC 57.658 55.556 22.03 5.68 46.17 4.70
77 78 1.383409 TGGCAACATGGATGGCTCA 59.617 52.632 22.03 6.19 46.17 4.26
78 79 0.966875 TGGCAACATGGATGGCTCAC 60.967 55.000 22.03 0.00 46.17 3.51
79 80 0.682209 GGCAACATGGATGGCTCACT 60.682 55.000 16.75 0.00 39.99 3.41
80 81 1.408683 GGCAACATGGATGGCTCACTA 60.409 52.381 16.75 0.00 39.99 2.74
81 82 1.945394 GCAACATGGATGGCTCACTAG 59.055 52.381 0.00 0.00 0.00 2.57
96 97 5.679734 CTCACTAGCAGTGTGAATTTGTT 57.320 39.130 13.59 0.00 46.03 2.83
97 98 6.064846 CTCACTAGCAGTGTGAATTTGTTT 57.935 37.500 13.59 0.00 46.03 2.83
98 99 6.060028 TCACTAGCAGTGTGAATTTGTTTC 57.940 37.500 13.59 0.00 46.03 2.78
99 100 5.822519 TCACTAGCAGTGTGAATTTGTTTCT 59.177 36.000 13.59 0.00 46.03 2.52
100 101 6.318648 TCACTAGCAGTGTGAATTTGTTTCTT 59.681 34.615 13.59 0.00 46.03 2.52
101 102 6.634436 CACTAGCAGTGTGAATTTGTTTCTTC 59.366 38.462 7.80 0.00 41.19 2.87
102 103 4.936891 AGCAGTGTGAATTTGTTTCTTCC 58.063 39.130 0.00 0.00 35.23 3.46
103 104 4.402155 AGCAGTGTGAATTTGTTTCTTCCA 59.598 37.500 0.00 0.00 35.23 3.53
104 105 5.069516 AGCAGTGTGAATTTGTTTCTTCCAT 59.930 36.000 0.00 0.00 35.23 3.41
105 106 5.754890 GCAGTGTGAATTTGTTTCTTCCATT 59.245 36.000 0.00 0.00 35.23 3.16
106 107 6.292488 GCAGTGTGAATTTGTTTCTTCCATTG 60.292 38.462 0.00 0.00 35.23 2.82
107 108 5.754890 AGTGTGAATTTGTTTCTTCCATTGC 59.245 36.000 0.00 0.00 35.23 3.56
108 109 5.754890 GTGTGAATTTGTTTCTTCCATTGCT 59.245 36.000 0.00 0.00 35.23 3.91
109 110 5.984926 TGTGAATTTGTTTCTTCCATTGCTC 59.015 36.000 0.00 0.00 35.23 4.26
110 111 5.984926 GTGAATTTGTTTCTTCCATTGCTCA 59.015 36.000 0.00 0.00 35.23 4.26
111 112 5.984926 TGAATTTGTTTCTTCCATTGCTCAC 59.015 36.000 0.00 0.00 35.23 3.51
112 113 5.796424 ATTTGTTTCTTCCATTGCTCACT 57.204 34.783 0.00 0.00 0.00 3.41
113 114 5.596836 TTTGTTTCTTCCATTGCTCACTT 57.403 34.783 0.00 0.00 0.00 3.16
114 115 4.572985 TGTTTCTTCCATTGCTCACTTG 57.427 40.909 0.00 0.00 0.00 3.16
115 116 3.243501 TGTTTCTTCCATTGCTCACTTGC 60.244 43.478 0.00 0.00 0.00 4.01
116 117 2.275134 TCTTCCATTGCTCACTTGCA 57.725 45.000 0.00 0.00 41.65 4.08
117 118 2.156917 TCTTCCATTGCTCACTTGCAG 58.843 47.619 0.00 0.00 44.27 4.41
118 119 1.884579 CTTCCATTGCTCACTTGCAGT 59.115 47.619 0.00 0.00 44.27 4.40
120 121 0.956633 CCATTGCTCACTTGCAGTGT 59.043 50.000 13.59 2.96 46.03 3.55
121 122 1.335597 CCATTGCTCACTTGCAGTGTG 60.336 52.381 13.59 13.59 46.03 3.82
122 123 0.956633 ATTGCTCACTTGCAGTGTGG 59.043 50.000 17.82 11.62 46.03 4.17
123 124 0.107263 TTGCTCACTTGCAGTGTGGA 60.107 50.000 17.82 12.78 46.03 4.02
124 125 0.109153 TGCTCACTTGCAGTGTGGAT 59.891 50.000 17.82 0.00 46.03 3.41
125 126 1.242076 GCTCACTTGCAGTGTGGATT 58.758 50.000 17.82 0.00 46.03 3.01
126 127 1.610522 GCTCACTTGCAGTGTGGATTT 59.389 47.619 17.82 0.00 46.03 2.17
127 128 2.606308 GCTCACTTGCAGTGTGGATTTG 60.606 50.000 17.82 7.98 46.03 2.32
128 129 2.620115 CTCACTTGCAGTGTGGATTTGT 59.380 45.455 17.82 0.00 46.03 2.83
129 130 3.023119 TCACTTGCAGTGTGGATTTGTT 58.977 40.909 17.82 0.00 46.03 2.83
130 131 3.446873 TCACTTGCAGTGTGGATTTGTTT 59.553 39.130 17.82 0.00 46.03 2.83
131 132 4.081752 TCACTTGCAGTGTGGATTTGTTTT 60.082 37.500 17.82 0.00 46.03 2.43
132 133 4.630940 CACTTGCAGTGTGGATTTGTTTTT 59.369 37.500 12.37 0.00 41.19 1.94
146 147 2.328639 TTTTTCCGGTCGCAACGC 59.671 55.556 0.00 0.00 0.00 4.84
147 148 2.470362 TTTTTCCGGTCGCAACGCA 61.470 52.632 0.00 0.00 0.00 5.24
148 149 2.649843 TTTTTCCGGTCGCAACGCAC 62.650 55.000 0.00 0.00 0.00 5.34
156 157 4.698651 CGCAACGCACGGGCATTT 62.699 61.111 11.77 0.00 41.24 2.32
157 158 2.355718 GCAACGCACGGGCATTTT 60.356 55.556 11.77 0.00 41.24 1.82
158 159 1.953642 GCAACGCACGGGCATTTTT 60.954 52.632 11.77 0.00 41.24 1.94
159 160 1.851978 CAACGCACGGGCATTTTTG 59.148 52.632 11.77 2.90 41.24 2.44
160 161 1.953642 AACGCACGGGCATTTTTGC 60.954 52.632 11.77 0.00 41.24 3.68
161 162 2.049248 CGCACGGGCATTTTTGCT 60.049 55.556 11.77 0.00 41.24 3.91
162 163 1.211449 CGCACGGGCATTTTTGCTA 59.789 52.632 11.77 0.00 41.24 3.49
163 164 0.798009 CGCACGGGCATTTTTGCTAG 60.798 55.000 11.77 0.00 41.24 3.42
201 202 0.315568 GATTCTCCATCCCTCGACGG 59.684 60.000 0.00 0.00 0.00 4.79
240 241 2.557869 TGGCCTACCTACAGAATGGTT 58.442 47.619 3.32 0.00 37.33 3.67
352 355 6.561945 TTTGTAGTTGAAAATCGTTTGTGC 57.438 33.333 0.00 0.00 0.00 4.57
353 356 5.236655 TGTAGTTGAAAATCGTTTGTGCA 57.763 34.783 0.00 0.00 0.00 4.57
519 966 9.974750 GTGTTGATCTATCTGTTAAAAAGTAGC 57.025 33.333 0.00 0.00 0.00 3.58
549 996 2.953821 CACGTTGGGTGTCATGGC 59.046 61.111 0.00 0.00 41.89 4.40
567 1014 1.621814 GGCCTATACATTGCCGGTAGA 59.378 52.381 1.90 0.00 35.08 2.59
568 1015 2.353803 GGCCTATACATTGCCGGTAGAG 60.354 54.545 1.90 0.00 35.08 2.43
570 1017 2.897969 CCTATACATTGCCGGTAGAGGT 59.102 50.000 1.90 0.30 42.51 3.85
571 1018 2.910688 ATACATTGCCGGTAGAGGTG 57.089 50.000 1.90 0.00 0.00 4.00
572 1019 1.563924 TACATTGCCGGTAGAGGTGT 58.436 50.000 1.90 5.31 0.00 4.16
573 1020 0.690762 ACATTGCCGGTAGAGGTGTT 59.309 50.000 1.90 0.00 0.00 3.32
574 1021 1.086696 CATTGCCGGTAGAGGTGTTG 58.913 55.000 1.90 0.00 0.00 3.33
575 1022 0.981183 ATTGCCGGTAGAGGTGTTGA 59.019 50.000 1.90 0.00 0.00 3.18
577 1024 0.830444 TGCCGGTAGAGGTGTTGAGT 60.830 55.000 1.90 0.00 0.00 3.41
587 1061 0.531974 GGTGTTGAGTGTCGCCTTGA 60.532 55.000 0.00 0.00 0.00 3.02
591 1065 1.197721 GTTGAGTGTCGCCTTGAATGG 59.802 52.381 0.00 0.00 0.00 3.16
594 1068 1.880027 GAGTGTCGCCTTGAATGGTTT 59.120 47.619 0.00 0.00 0.00 3.27
612 1087 1.096416 TTAAAAGGTATTGCGGGCCG 58.904 50.000 24.35 24.35 0.00 6.13
629 1104 5.424757 CGGGCCGAGATAAATAATAATGGA 58.575 41.667 24.41 0.00 0.00 3.41
651 1126 0.991920 TCGGGGCCTTTGAGAAGAAT 59.008 50.000 0.84 0.00 34.71 2.40
732 1794 4.908601 TCCACCTCAATGAATGTACAGT 57.091 40.909 0.33 0.00 0.00 3.55
733 1795 6.367374 TTCCACCTCAATGAATGTACAGTA 57.633 37.500 0.33 0.00 0.00 2.74
734 1796 6.367374 TCCACCTCAATGAATGTACAGTAA 57.633 37.500 0.33 0.00 0.00 2.24
735 1797 6.774673 TCCACCTCAATGAATGTACAGTAAA 58.225 36.000 0.33 0.00 0.00 2.01
736 1798 6.878923 TCCACCTCAATGAATGTACAGTAAAG 59.121 38.462 0.33 0.00 0.00 1.85
737 1799 6.878923 CCACCTCAATGAATGTACAGTAAAGA 59.121 38.462 0.33 0.00 0.00 2.52
738 1800 7.554118 CCACCTCAATGAATGTACAGTAAAGAT 59.446 37.037 0.33 0.00 0.00 2.40
739 1801 8.950210 CACCTCAATGAATGTACAGTAAAGATT 58.050 33.333 0.33 0.00 0.00 2.40
937 2546 6.684897 ATCTCTCTATAGCCTGCATCTTTT 57.315 37.500 0.00 0.00 0.00 2.27
944 2553 1.000506 AGCCTGCATCTTTTTGTGCTG 59.999 47.619 0.00 0.00 41.78 4.41
1224 2839 4.796830 CACTTCTCCGATGAATGCAAATTG 59.203 41.667 0.00 0.00 0.00 2.32
1265 2880 1.330655 ATCCACTACAGCACTCGGGG 61.331 60.000 0.00 0.00 0.00 5.73
1327 2942 4.082125 AGGCATTAAGGTGAAGGTCTTTG 58.918 43.478 0.00 0.00 0.00 2.77
1359 2974 0.679960 GCATAAAGGAGGTTGGCCGT 60.680 55.000 0.00 0.00 40.50 5.68
1413 3028 4.228010 TGATATCCAAGTCATTCCCGGTA 58.772 43.478 0.00 0.00 0.00 4.02
1416 3031 2.759355 TCCAAGTCATTCCCGGTAGAT 58.241 47.619 0.00 0.00 0.00 1.98
1483 3098 1.767692 ACACAAGTGTCCCCATCCC 59.232 57.895 0.00 0.00 40.24 3.85
1540 3155 6.947464 TCCTTCTTTCTTCGTAGGATTGATT 58.053 36.000 0.00 0.00 30.30 2.57
1551 3172 4.318760 CGTAGGATTGATTATGCACGTTGG 60.319 45.833 0.00 0.00 30.57 3.77
1570 3191 0.177836 GTGCTTGTTTTGCAACCCCT 59.822 50.000 0.00 0.00 42.41 4.79
1572 3193 2.111384 TGCTTGTTTTGCAACCCCTTA 58.889 42.857 0.00 0.00 37.51 2.69
1601 3222 7.410174 TCTTACCAATTCATGTACTCCCATTT 58.590 34.615 0.00 0.00 0.00 2.32
1602 3223 7.893302 TCTTACCAATTCATGTACTCCCATTTT 59.107 33.333 0.00 0.00 0.00 1.82
1603 3224 9.184523 CTTACCAATTCATGTACTCCCATTTTA 57.815 33.333 0.00 0.00 0.00 1.52
1714 3425 2.427812 TGGACGGTGAATGCGTTATCTA 59.572 45.455 0.00 0.00 0.00 1.98
1780 3491 5.093457 TCACTTAATTAGCTCTCAACGTCG 58.907 41.667 0.00 0.00 0.00 5.12
1836 3551 5.625150 AGATAGCTTACCACATTTCCCATC 58.375 41.667 0.00 0.00 0.00 3.51
1869 3586 4.909696 TTTGCGAGGAAACTTTTGATCA 57.090 36.364 0.00 0.00 44.43 2.92
1870 3587 5.452078 TTTGCGAGGAAACTTTTGATCAT 57.548 34.783 0.00 0.00 44.43 2.45
1878 3595 9.624697 CGAGGAAACTTTTGATCATTTAATCAA 57.375 29.630 0.00 0.00 44.43 2.57
1883 3600 8.538409 AACTTTTGATCATTTAATCAAGCCAC 57.462 30.769 0.00 0.00 44.23 5.01
1992 3712 1.227674 CTCATCGTGCTAAGGCCCC 60.228 63.158 0.00 0.00 37.74 5.80
2004 3724 3.017581 GGCCCCCACAGGATCAGT 61.018 66.667 0.00 0.00 38.24 3.41
2012 3732 0.675837 CACAGGATCAGTGCACCAGG 60.676 60.000 14.63 3.59 0.00 4.45
2022 3742 1.202770 AGTGCACCAGGACAGTAAACC 60.203 52.381 14.63 0.00 38.75 3.27
2039 3759 7.286775 ACAGTAAACCTTGCCTATGAAGAAAAA 59.713 33.333 0.00 0.00 0.00 1.94
2076 3797 1.501169 CAGCATGAAGACACACGACA 58.499 50.000 0.00 0.00 39.69 4.35
2126 3847 1.234615 CCACCAAACACTAGCACCGG 61.235 60.000 0.00 0.00 0.00 5.28
2141 3862 1.134580 CACCGGCTGAATCTCATGAGT 60.135 52.381 21.92 3.90 0.00 3.41
2142 3863 1.137872 ACCGGCTGAATCTCATGAGTC 59.862 52.381 21.92 13.70 37.75 3.36
2144 3865 2.471818 CGGCTGAATCTCATGAGTCTG 58.528 52.381 21.92 16.71 38.06 3.51
2191 3918 1.863454 GACGCTAGATGCATCACCAAG 59.137 52.381 27.81 18.63 43.06 3.61
2239 3966 8.651389 CCTTATTCCATCTTTAGAGTGATACCA 58.349 37.037 0.00 0.00 0.00 3.25
2274 4001 2.808543 CTGAGCAAGACACAAACCCTAC 59.191 50.000 0.00 0.00 0.00 3.18
2292 4019 5.244178 ACCCTACACAAACTCACAAAAACAA 59.756 36.000 0.00 0.00 0.00 2.83
2300 4030 5.913137 AACTCACAAAAACAACTGATGGA 57.087 34.783 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.179081 GGCCACCTATTCACGGAGAC 60.179 60.000 0.00 0.00 0.00 3.36
10 11 1.335132 GGGCCACCTATTCACGGAGA 61.335 60.000 4.39 0.00 0.00 3.71
11 12 1.146263 GGGCCACCTATTCACGGAG 59.854 63.158 4.39 0.00 0.00 4.63
12 13 3.316029 GGGCCACCTATTCACGGA 58.684 61.111 4.39 0.00 0.00 4.69
20 21 4.451035 CTGTTGATCAGTAGGGCCACCTA 61.451 52.174 6.18 0.00 41.34 3.08
21 22 3.748631 CTGTTGATCAGTAGGGCCACCT 61.749 54.545 6.18 0.00 41.93 4.00
22 23 0.618458 TGTTGATCAGTAGGGCCACC 59.382 55.000 6.18 0.00 0.00 4.61
23 24 2.014068 GCTGTTGATCAGTAGGGCCAC 61.014 57.143 6.18 1.63 45.23 5.01
24 25 0.253044 GCTGTTGATCAGTAGGGCCA 59.747 55.000 6.18 0.00 45.23 5.36
25 26 0.253044 TGCTGTTGATCAGTAGGGCC 59.747 55.000 0.00 0.00 45.23 5.80
26 27 1.740025 GTTGCTGTTGATCAGTAGGGC 59.260 52.381 0.00 0.00 45.23 5.19
27 28 2.002586 CGTTGCTGTTGATCAGTAGGG 58.997 52.381 0.00 0.00 45.23 3.53
28 29 2.959516 TCGTTGCTGTTGATCAGTAGG 58.040 47.619 0.00 0.00 45.23 3.18
29 30 4.237724 TCTTCGTTGCTGTTGATCAGTAG 58.762 43.478 0.00 0.00 45.23 2.57
30 31 4.237724 CTCTTCGTTGCTGTTGATCAGTA 58.762 43.478 0.00 0.00 45.23 2.74
31 32 3.062763 CTCTTCGTTGCTGTTGATCAGT 58.937 45.455 0.00 0.00 45.23 3.41
32 33 2.414481 CCTCTTCGTTGCTGTTGATCAG 59.586 50.000 0.00 0.00 46.12 2.90
33 34 2.416747 CCTCTTCGTTGCTGTTGATCA 58.583 47.619 0.00 0.00 0.00 2.92
34 35 1.734465 CCCTCTTCGTTGCTGTTGATC 59.266 52.381 0.00 0.00 0.00 2.92
35 36 1.813513 CCCTCTTCGTTGCTGTTGAT 58.186 50.000 0.00 0.00 0.00 2.57
36 37 0.884704 GCCCTCTTCGTTGCTGTTGA 60.885 55.000 0.00 0.00 0.00 3.18
37 38 1.165907 TGCCCTCTTCGTTGCTGTTG 61.166 55.000 0.00 0.00 0.00 3.33
38 39 1.148273 TGCCCTCTTCGTTGCTGTT 59.852 52.632 0.00 0.00 0.00 3.16
39 40 1.598130 GTGCCCTCTTCGTTGCTGT 60.598 57.895 0.00 0.00 0.00 4.40
40 41 2.671177 CGTGCCCTCTTCGTTGCTG 61.671 63.158 0.00 0.00 0.00 4.41
41 42 2.357517 CGTGCCCTCTTCGTTGCT 60.358 61.111 0.00 0.00 0.00 3.91
42 43 2.665185 ACGTGCCCTCTTCGTTGC 60.665 61.111 0.00 0.00 34.07 4.17
43 44 2.317609 CCACGTGCCCTCTTCGTTG 61.318 63.158 10.91 0.00 35.62 4.10
44 45 2.030562 CCACGTGCCCTCTTCGTT 59.969 61.111 10.91 0.00 35.62 3.85
45 46 4.681978 GCCACGTGCCCTCTTCGT 62.682 66.667 10.91 0.00 38.34 3.85
46 47 4.680237 TGCCACGTGCCCTCTTCG 62.680 66.667 10.91 0.00 40.16 3.79
47 48 2.281484 TTGCCACGTGCCCTCTTC 60.281 61.111 10.91 0.00 40.16 2.87
48 49 2.594592 GTTGCCACGTGCCCTCTT 60.595 61.111 10.91 0.00 40.16 2.85
49 50 3.196207 ATGTTGCCACGTGCCCTCT 62.196 57.895 10.91 0.00 40.16 3.69
50 51 2.672996 ATGTTGCCACGTGCCCTC 60.673 61.111 10.91 1.08 40.16 4.30
51 52 2.985282 CATGTTGCCACGTGCCCT 60.985 61.111 10.91 0.00 40.16 5.19
52 53 4.054825 CCATGTTGCCACGTGCCC 62.055 66.667 10.91 3.59 38.46 5.36
53 54 2.342650 ATCCATGTTGCCACGTGCC 61.343 57.895 10.91 0.00 38.46 5.01
54 55 1.153978 CATCCATGTTGCCACGTGC 60.154 57.895 10.91 6.53 38.46 5.34
55 56 1.507630 CCATCCATGTTGCCACGTG 59.492 57.895 9.08 9.08 39.38 4.49
56 57 2.342650 GCCATCCATGTTGCCACGT 61.343 57.895 0.00 0.00 0.00 4.49
57 58 1.996786 GAGCCATCCATGTTGCCACG 61.997 60.000 0.00 0.00 0.00 4.94
58 59 0.966875 TGAGCCATCCATGTTGCCAC 60.967 55.000 0.00 0.00 0.00 5.01
59 60 0.966875 GTGAGCCATCCATGTTGCCA 60.967 55.000 0.00 0.00 0.00 4.92
60 61 0.682209 AGTGAGCCATCCATGTTGCC 60.682 55.000 0.00 0.00 0.00 4.52
61 62 1.945394 CTAGTGAGCCATCCATGTTGC 59.055 52.381 0.00 0.00 0.00 4.17
62 63 1.945394 GCTAGTGAGCCATCCATGTTG 59.055 52.381 0.00 0.00 43.49 3.33
63 64 2.338577 GCTAGTGAGCCATCCATGTT 57.661 50.000 0.00 0.00 43.49 2.71
73 74 9.323484 AGAAACAAATTCACACTGCTAGTGAGC 62.323 40.741 19.01 0.00 45.72 4.26
74 75 6.017605 AGAAACAAATTCACACTGCTAGTGAG 60.018 38.462 19.01 13.01 45.72 3.51
75 76 5.822519 AGAAACAAATTCACACTGCTAGTGA 59.177 36.000 19.01 11.55 43.48 3.41
76 77 6.064846 AGAAACAAATTCACACTGCTAGTG 57.935 37.500 12.81 12.81 42.58 2.74
77 78 6.238759 GGAAGAAACAAATTCACACTGCTAGT 60.239 38.462 0.00 0.00 40.72 2.57
78 79 6.145535 GGAAGAAACAAATTCACACTGCTAG 58.854 40.000 0.00 0.00 40.72 3.42
79 80 5.592282 TGGAAGAAACAAATTCACACTGCTA 59.408 36.000 0.00 0.00 40.72 3.49
80 81 4.402155 TGGAAGAAACAAATTCACACTGCT 59.598 37.500 0.00 0.00 40.72 4.24
81 82 4.681744 TGGAAGAAACAAATTCACACTGC 58.318 39.130 0.00 0.00 40.72 4.40
82 83 6.292488 GCAATGGAAGAAACAAATTCACACTG 60.292 38.462 0.00 0.00 40.72 3.66
83 84 5.754890 GCAATGGAAGAAACAAATTCACACT 59.245 36.000 0.00 0.00 40.72 3.55
84 85 5.754890 AGCAATGGAAGAAACAAATTCACAC 59.245 36.000 0.00 0.00 40.72 3.82
85 86 5.916318 AGCAATGGAAGAAACAAATTCACA 58.084 33.333 0.00 0.00 40.72 3.58
86 87 5.984926 TGAGCAATGGAAGAAACAAATTCAC 59.015 36.000 0.00 0.00 40.72 3.18
87 88 5.984926 GTGAGCAATGGAAGAAACAAATTCA 59.015 36.000 0.00 0.00 40.72 2.57
88 89 6.218746 AGTGAGCAATGGAAGAAACAAATTC 58.781 36.000 0.00 0.00 38.39 2.17
89 90 6.165700 AGTGAGCAATGGAAGAAACAAATT 57.834 33.333 0.00 0.00 0.00 1.82
90 91 5.796424 AGTGAGCAATGGAAGAAACAAAT 57.204 34.783 0.00 0.00 0.00 2.32
91 92 5.350633 CAAGTGAGCAATGGAAGAAACAAA 58.649 37.500 0.00 0.00 0.00 2.83
92 93 4.737352 GCAAGTGAGCAATGGAAGAAACAA 60.737 41.667 0.00 0.00 0.00 2.83
93 94 3.243501 GCAAGTGAGCAATGGAAGAAACA 60.244 43.478 0.00 0.00 0.00 2.83
94 95 3.243501 TGCAAGTGAGCAATGGAAGAAAC 60.244 43.478 0.00 0.00 42.46 2.78
95 96 2.957680 TGCAAGTGAGCAATGGAAGAAA 59.042 40.909 0.00 0.00 42.46 2.52
96 97 2.555325 CTGCAAGTGAGCAATGGAAGAA 59.445 45.455 0.00 0.00 45.13 2.52
97 98 2.156917 CTGCAAGTGAGCAATGGAAGA 58.843 47.619 0.00 0.00 45.13 2.87
98 99 2.631418 CTGCAAGTGAGCAATGGAAG 57.369 50.000 0.00 0.00 45.13 3.46
129 130 2.328639 GCGTTGCGACCGGAAAAA 59.671 55.556 9.46 0.00 0.00 1.94
130 131 2.895865 TGCGTTGCGACCGGAAAA 60.896 55.556 9.46 0.00 0.00 2.29
131 132 3.641986 GTGCGTTGCGACCGGAAA 61.642 61.111 9.46 0.00 0.00 3.13
139 140 4.698651 AAATGCCCGTGCGTTGCG 62.699 61.111 0.00 0.00 45.88 4.85
140 141 1.953642 AAAAATGCCCGTGCGTTGC 60.954 52.632 0.00 0.00 45.88 4.17
141 142 1.851978 CAAAAATGCCCGTGCGTTG 59.148 52.632 0.00 0.00 45.88 4.10
143 144 1.519751 TAGCAAAAATGCCCGTGCGT 61.520 50.000 0.00 0.00 41.90 5.24
144 145 0.798009 CTAGCAAAAATGCCCGTGCG 60.798 55.000 0.00 0.00 41.90 5.34
145 146 0.243636 ACTAGCAAAAATGCCCGTGC 59.756 50.000 0.00 0.00 37.26 5.34
146 147 3.840890 TTACTAGCAAAAATGCCCGTG 57.159 42.857 0.00 0.00 34.90 4.94
147 148 6.709018 ATAATTACTAGCAAAAATGCCCGT 57.291 33.333 0.00 0.00 34.90 5.28
148 149 9.128107 CATAATAATTACTAGCAAAAATGCCCG 57.872 33.333 0.00 0.00 34.90 6.13
201 202 0.107848 AAATCGGACGACCACCCATC 60.108 55.000 4.48 0.00 35.59 3.51
407 853 6.705381 CCCAAATTGCTTTGAATAGAACACAA 59.295 34.615 0.22 0.00 43.71 3.33
416 862 4.961438 ACTCACCCAAATTGCTTTGAAT 57.039 36.364 0.22 0.00 43.71 2.57
508 955 7.011669 GTGTACACTGGTCAAGCTACTTTTTAA 59.988 37.037 18.92 0.00 0.00 1.52
515 962 2.288030 ACGTGTACACTGGTCAAGCTAC 60.288 50.000 23.01 0.00 0.00 3.58
519 966 1.864711 CCAACGTGTACACTGGTCAAG 59.135 52.381 23.01 8.65 0.00 3.02
522 969 0.105408 ACCCAACGTGTACACTGGTC 59.895 55.000 24.86 2.51 0.00 4.02
548 995 2.353803 CCTCTACCGGCAATGTATAGGC 60.354 54.545 0.00 0.00 29.28 3.93
549 996 2.897969 ACCTCTACCGGCAATGTATAGG 59.102 50.000 0.00 0.00 38.11 2.57
567 1014 0.532862 CAAGGCGACACTCAACACCT 60.533 55.000 0.00 0.00 0.00 4.00
568 1015 0.531974 TCAAGGCGACACTCAACACC 60.532 55.000 0.00 0.00 0.00 4.16
570 1017 1.872952 CATTCAAGGCGACACTCAACA 59.127 47.619 0.00 0.00 0.00 3.33
571 1018 1.197721 CCATTCAAGGCGACACTCAAC 59.802 52.381 0.00 0.00 0.00 3.18
572 1019 1.202758 ACCATTCAAGGCGACACTCAA 60.203 47.619 0.00 0.00 0.00 3.02
573 1020 0.396435 ACCATTCAAGGCGACACTCA 59.604 50.000 0.00 0.00 0.00 3.41
574 1021 1.523758 AACCATTCAAGGCGACACTC 58.476 50.000 0.00 0.00 0.00 3.51
575 1022 1.981256 AAACCATTCAAGGCGACACT 58.019 45.000 0.00 0.00 0.00 3.55
577 1024 4.261825 CCTTTTAAACCATTCAAGGCGACA 60.262 41.667 0.00 0.00 0.00 4.35
587 1061 4.621983 GCCCGCAATACCTTTTAAACCATT 60.622 41.667 0.00 0.00 0.00 3.16
591 1065 2.732912 CGGCCCGCAATACCTTTTAAAC 60.733 50.000 0.00 0.00 0.00 2.01
594 1068 0.252479 TCGGCCCGCAATACCTTTTA 59.748 50.000 0.00 0.00 0.00 1.52
612 1087 7.048512 CCCCGAGGTCCATTATTATTTATCTC 58.951 42.308 0.00 0.00 0.00 2.75
629 1104 1.842381 CTTCTCAAAGGCCCCGAGGT 61.842 60.000 12.40 0.00 34.57 3.85
856 2452 9.787435 TGTATTCAGTACTCACCAAAGTTAATT 57.213 29.630 0.00 0.00 34.27 1.40
909 2516 8.378115 AGATGCAGGCTATAGAGAGATAAATT 57.622 34.615 3.21 0.00 0.00 1.82
920 2527 4.337555 AGCACAAAAAGATGCAGGCTATAG 59.662 41.667 0.00 0.00 44.59 1.31
944 2553 7.816945 AGCTTTGCAAATATATTTGTGTGTC 57.183 32.000 29.73 19.55 46.63 3.67
959 2570 3.490761 GGCTGACAACTAAAGCTTTGCAA 60.491 43.478 22.02 0.00 37.12 4.08
1193 2808 3.017442 TCATCGGAGAAGTGTACCTCAG 58.983 50.000 0.00 0.00 43.58 3.35
1224 2839 1.731969 GTACTGGCCGTCGACACAC 60.732 63.158 17.16 4.89 0.00 3.82
1298 2913 4.397417 CCTTCACCTTAATGCCTTCAAGAG 59.603 45.833 0.00 0.00 0.00 2.85
1299 2914 4.202567 ACCTTCACCTTAATGCCTTCAAGA 60.203 41.667 0.00 0.00 0.00 3.02
1327 2942 0.878416 TTTATGCTGACCCACGCAAC 59.122 50.000 0.00 0.00 39.89 4.17
1359 2974 0.767375 GCCTAAGCTCATCCCCATCA 59.233 55.000 0.00 0.00 35.50 3.07
1413 3028 3.730269 AGGGCTAGAGGAGAAAACATCT 58.270 45.455 0.00 0.00 42.61 2.90
1416 3031 4.223032 CACTTAGGGCTAGAGGAGAAAACA 59.777 45.833 0.00 0.00 0.00 2.83
1476 3091 3.866582 GAGGCGGACTGGGATGGG 61.867 72.222 0.00 0.00 0.00 4.00
1483 3098 0.526524 GTGATCGAAGAGGCGGACTG 60.527 60.000 0.00 0.00 43.63 3.51
1570 3191 7.990886 GGAGTACATGAATTGGTAAGATGGTAA 59.009 37.037 0.00 0.00 0.00 2.85
1572 3193 6.357367 GGAGTACATGAATTGGTAAGATGGT 58.643 40.000 0.00 0.00 0.00 3.55
1601 3222 7.290014 TCATTCAATCTCAGCCCATACTACTAA 59.710 37.037 0.00 0.00 0.00 2.24
1602 3223 6.782494 TCATTCAATCTCAGCCCATACTACTA 59.218 38.462 0.00 0.00 0.00 1.82
1603 3224 5.604231 TCATTCAATCTCAGCCCATACTACT 59.396 40.000 0.00 0.00 0.00 2.57
1714 3425 7.230108 CACAATACCATTATGCCTTCTCTGATT 59.770 37.037 0.00 0.00 0.00 2.57
1811 3525 5.826643 TGGGAAATGTGGTAAGCTATCTTT 58.173 37.500 0.00 0.00 33.85 2.52
1869 3586 3.081061 TGCTGACGTGGCTTGATTAAAT 58.919 40.909 0.00 0.00 0.00 1.40
1870 3587 2.499197 TGCTGACGTGGCTTGATTAAA 58.501 42.857 0.00 0.00 0.00 1.52
1878 3595 1.376424 CTCCAATGCTGACGTGGCT 60.376 57.895 0.00 0.00 32.10 4.75
1883 3600 2.806856 GCTCGCTCCAATGCTGACG 61.807 63.158 0.00 0.00 0.00 4.35
1974 3694 1.227674 GGGGCCTTAGCACGATGAG 60.228 63.158 0.84 0.00 46.55 2.90
1992 3712 0.675837 CTGGTGCACTGATCCTGTGG 60.676 60.000 17.98 0.00 34.61 4.17
2004 3724 1.136828 AGGTTTACTGTCCTGGTGCA 58.863 50.000 0.00 0.00 32.29 4.57
2012 3732 5.488341 TCTTCATAGGCAAGGTTTACTGTC 58.512 41.667 0.00 0.00 0.00 3.51
2039 3759 6.382282 TCATGCTGGATCCTTTCGATCTATAT 59.618 38.462 14.23 0.00 45.90 0.86
2059 3779 2.543848 TCTTTGTCGTGTGTCTTCATGC 59.456 45.455 0.00 0.00 0.00 4.06
2076 3797 4.042062 TGGATCCAGTCTGTGTTCATCTTT 59.958 41.667 11.44 0.00 0.00 2.52
2126 3847 2.211806 GGCAGACTCATGAGATTCAGC 58.788 52.381 29.27 22.31 35.92 4.26
2141 3862 1.993701 ATGTGGTGGTGTGTGGCAGA 61.994 55.000 0.00 0.00 0.00 4.26
2142 3863 1.529010 ATGTGGTGGTGTGTGGCAG 60.529 57.895 0.00 0.00 0.00 4.85
2144 3865 2.563798 CCATGTGGTGGTGTGTGGC 61.564 63.158 0.00 0.00 43.44 5.01
2145 3866 3.762293 CCATGTGGTGGTGTGTGG 58.238 61.111 0.00 0.00 43.44 4.17
2162 3888 1.413382 CATCTAGCGTCATCGAAGGC 58.587 55.000 0.00 0.00 39.71 4.35
2209 3936 8.146053 TCACTCTAAAGATGGAATAAGGTTCA 57.854 34.615 0.00 0.00 0.00 3.18
2239 3966 0.179062 GCTCAGGAAGACCATGCGAT 60.179 55.000 0.00 0.00 38.94 4.58
2274 4001 6.183360 CCATCAGTTGTTTTTGTGAGTTTGTG 60.183 38.462 0.00 0.00 0.00 3.33
2292 4019 0.842635 GGGATCTTGCCTCCATCAGT 59.157 55.000 0.00 0.00 34.24 3.41
2300 4030 3.483869 GCGGGAGGGATCTTGCCT 61.484 66.667 6.71 0.00 42.67 4.75
2327 4057 0.836400 GAAGGAGTGGTGGACCCTGA 60.836 60.000 0.00 0.00 34.29 3.86
2420 4150 9.529325 GAGTGTGTAGAATATTACATTGCTACA 57.471 33.333 7.86 7.86 36.08 2.74


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

AutoCloner maintained by Alex Coulton.