Multiple sequence alignment - TraesCS7B01G293900

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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 TraesCS7B01G293900 chr7B 100.000 2504 0 0 1 2504 530591829 530589326 0.000000e+00 4625
1 TraesCS7B01G293900 chr7B 90.123 1620 89 34 134 1715 530435783 530434197 0.000000e+00 2039
2 TraesCS7B01G293900 chr7B 95.489 133 6 0 1 133 589922924 589922792 1.950000e-51 213
3 TraesCS7B01G293900 chr7B 95.489 133 6 0 1 133 589923249 589923117 1.950000e-51 213
4 TraesCS7B01G293900 chr7A 85.579 1692 115 63 134 1751 567592336 567590700 0.000000e+00 1653
5 TraesCS7B01G293900 chr7D 85.172 1659 71 70 134 1710 501109332 501107767 0.000000e+00 1539
6 TraesCS7B01G293900 chr5B 95.883 753 29 2 1752 2503 692928802 692929553 0.000000e+00 1218
7 TraesCS7B01G293900 chr5B 93.103 754 47 4 1751 2503 46718065 46717316 0.000000e+00 1099
8 TraesCS7B01G293900 chr5B 94.737 133 7 0 1 133 77707838 77707706 9.080000e-50 207
9 TraesCS7B01G293900 chr5B 94.737 133 7 0 1 133 441669954 441670086 9.080000e-50 207
10 TraesCS7B01G293900 chr5B 94.737 133 7 0 1 133 534218159 534218027 9.080000e-50 207
11 TraesCS7B01G293900 chr2B 95.219 753 33 3 1752 2503 526525141 526525891 0.000000e+00 1188
12 TraesCS7B01G293900 chr2B 93.227 753 37 8 1752 2503 731271888 731272627 0.000000e+00 1096
13 TraesCS7B01G293900 chr2B 93.094 753 36 8 1752 2503 40895727 40896464 0.000000e+00 1088
14 TraesCS7B01G293900 chr2B 92.563 753 42 4 1752 2503 105895370 105894631 0.000000e+00 1068
15 TraesCS7B01G293900 chr2B 95.489 133 5 1 1 133 800511388 800511519 7.020000e-51 211
16 TraesCS7B01G293900 chr2B 94.815 135 6 1 1 135 800511712 800511845 2.520000e-50 209
17 TraesCS7B01G293900 chrUn 94.555 753 39 2 1752 2503 212364751 212364000 0.000000e+00 1162
18 TraesCS7B01G293900 chrUn 93.985 133 8 0 1 133 313027407 313027539 4.220000e-48 202
19 TraesCS7B01G293900 chrUn 93.233 133 9 0 1 133 67918192 67918324 1.960000e-46 196
20 TraesCS7B01G293900 chrUn 93.233 133 9 0 1 133 67918517 67918649 1.960000e-46 196
21 TraesCS7B01G293900 chrUn 92.481 133 10 0 1 133 65794742 65794874 9.140000e-45 191
22 TraesCS7B01G293900 chrUn 94.118 85 4 1 1 85 137769654 137769737 7.270000e-26 128
23 TraesCS7B01G293900 chr4A 94.157 753 42 2 1752 2503 620071252 620072003 0.000000e+00 1146
24 TraesCS7B01G293900 chr4A 92.563 753 33 9 1752 2503 620133953 620134683 0.000000e+00 1059
25 TraesCS7B01G293900 chr4A 94.776 134 7 0 1 134 727713830 727713963 2.520000e-50 209
26 TraesCS7B01G293900 chr4A 91.724 145 10 2 1 144 737296964 737296821 1.520000e-47 200
27 TraesCS7B01G293900 chr6B 93.923 757 42 4 1749 2503 679124956 679124202 0.000000e+00 1140
28 TraesCS7B01G293900 chr6B 96.241 133 5 0 1 133 140674470 140674338 4.190000e-53 219
29 TraesCS7B01G293900 chr6B 94.737 133 7 0 1 133 213154059 213153927 9.080000e-50 207
30 TraesCS7B01G293900 chr6B 94.737 133 7 0 1 133 688775823 688775691 9.080000e-50 207
31 TraesCS7B01G293900 chr3B 92.021 752 55 4 1754 2503 64620164 64620912 0.000000e+00 1051
32 TraesCS7B01G293900 chr3B 96.324 136 5 0 1 136 800853573 800853708 9.010000e-55 224
33 TraesCS7B01G293900 chr4B 91.633 753 49 4 1752 2503 188514756 188514017 0.000000e+00 1029
34 TraesCS7B01G293900 chr4B 95.489 133 6 0 1 133 562876902 562876770 1.950000e-51 213
35 TraesCS7B01G293900 chr4B 93.284 134 8 1 1 133 562877228 562877095 1.960000e-46 196
36 TraesCS7B01G293900 chr4B 92.481 133 10 0 1 133 417210036 417209904 9.140000e-45 191
37 TraesCS7B01G293900 chr1B 94.737 133 7 0 1 133 14550552 14550420 9.080000e-50 207
38 TraesCS7B01G293900 chr1B 93.985 133 8 0 1 133 550695836 550695968 4.220000e-48 202
39 TraesCS7B01G293900 chr1B 93.985 133 8 0 1 133 593206988 593206856 4.220000e-48 202
40 TraesCS7B01G293900 chr1B 93.985 133 8 0 1 133 636803022 636802890 4.220000e-48 202
41 TraesCS7B01G293900 chr1B 93.333 135 9 0 1 135 6570622 6570488 1.520000e-47 200
42 TraesCS7B01G293900 chr3D 94.030 134 8 0 1 134 18795270 18795403 1.170000e-48 204
43 TraesCS7B01G293900 chr4D 93.233 133 8 1 1 133 387445620 387445751 7.070000e-46 195
44 TraesCS7B01G293900 chr4D 92.481 133 9 1 1 133 387445298 387445429 3.290000e-44 189
45 TraesCS7B01G293900 chr4D 89.474 133 13 1 1 133 71013128 71013259 1.540000e-37 167
46 TraesCS7B01G293900 chr5D 91.729 133 11 0 1 133 204525998 204525866 4.250000e-43 185
47 TraesCS7B01G293900 chr1D 91.667 132 11 0 1 132 3339725 3339594 1.530000e-42 183
48 TraesCS7B01G293900 chr1D 90.000 140 14 0 1 140 3339400 3339261 5.500000e-42 182
49 TraesCS7B01G293900 chr6D 92.126 127 10 0 1 127 126441760 126441886 1.980000e-41 180
50 TraesCS7B01G293900 chr6D 89.313 131 12 2 3 133 64928770 64928642 1.990000e-36 163
51 TraesCS7B01G293900 chr6D 89.764 127 10 2 1 124 2789058 2789184 2.580000e-35 159
52 TraesCS7B01G293900 chr6D 87.121 132 15 2 2 133 34091778 34091649 5.580000e-32 148


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 TraesCS7B01G293900 chr7B 530589326 530591829 2503 True 4625 4625 100.000 1 2504 1 chr7B.!!$R2 2503
1 TraesCS7B01G293900 chr7B 530434197 530435783 1586 True 2039 2039 90.123 134 1715 1 chr7B.!!$R1 1581
2 TraesCS7B01G293900 chr7A 567590700 567592336 1636 True 1653 1653 85.579 134 1751 1 chr7A.!!$R1 1617
3 TraesCS7B01G293900 chr7D 501107767 501109332 1565 True 1539 1539 85.172 134 1710 1 chr7D.!!$R1 1576
4 TraesCS7B01G293900 chr5B 692928802 692929553 751 False 1218 1218 95.883 1752 2503 1 chr5B.!!$F2 751
5 TraesCS7B01G293900 chr5B 46717316 46718065 749 True 1099 1099 93.103 1751 2503 1 chr5B.!!$R1 752
6 TraesCS7B01G293900 chr2B 526525141 526525891 750 False 1188 1188 95.219 1752 2503 1 chr2B.!!$F2 751
7 TraesCS7B01G293900 chr2B 731271888 731272627 739 False 1096 1096 93.227 1752 2503 1 chr2B.!!$F3 751
8 TraesCS7B01G293900 chr2B 40895727 40896464 737 False 1088 1088 93.094 1752 2503 1 chr2B.!!$F1 751
9 TraesCS7B01G293900 chr2B 105894631 105895370 739 True 1068 1068 92.563 1752 2503 1 chr2B.!!$R1 751
10 TraesCS7B01G293900 chrUn 212364000 212364751 751 True 1162 1162 94.555 1752 2503 1 chrUn.!!$R1 751
11 TraesCS7B01G293900 chr4A 620071252 620072003 751 False 1146 1146 94.157 1752 2503 1 chr4A.!!$F1 751
12 TraesCS7B01G293900 chr4A 620133953 620134683 730 False 1059 1059 92.563 1752 2503 1 chr4A.!!$F2 751
13 TraesCS7B01G293900 chr6B 679124202 679124956 754 True 1140 1140 93.923 1749 2503 1 chr6B.!!$R3 754
14 TraesCS7B01G293900 chr3B 64620164 64620912 748 False 1051 1051 92.021 1754 2503 1 chr3B.!!$F1 749
15 TraesCS7B01G293900 chr4B 188514017 188514756 739 True 1029 1029 91.633 1752 2503 1 chr4B.!!$R1 751

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
52 53 0.034089 GCCCAAGGCCTGTCATAAGT 60.034 55.0 5.69 0.0 44.06 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 1744 0.677731 CGAGCAATTCCAAGAGCCCA 60.678 55.0 0.0 0.0 0.0 5.36 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 5.859495 CCTCCTAATAGGCTAGTCTTTTGG 58.141 45.833 0.11 2.74 34.61 3.28
24 25 5.221742 CCTCCTAATAGGCTAGTCTTTTGGG 60.222 48.000 19.50 19.50 34.61 4.12
25 26 4.658901 TCCTAATAGGCTAGTCTTTTGGGG 59.341 45.833 23.24 17.28 34.61 4.96
26 27 3.953542 AATAGGCTAGTCTTTTGGGGG 57.046 47.619 0.11 0.00 0.00 5.40
51 52 2.799176 GCCCAAGGCCTGTCATAAG 58.201 57.895 5.69 0.00 44.06 1.73
52 53 0.034089 GCCCAAGGCCTGTCATAAGT 60.034 55.000 5.69 0.00 44.06 2.24
53 54 2.019156 GCCCAAGGCCTGTCATAAGTC 61.019 57.143 5.69 0.00 44.06 3.01
54 55 1.656652 CCAAGGCCTGTCATAAGTCG 58.343 55.000 5.69 0.00 0.00 4.18
55 56 1.656652 CAAGGCCTGTCATAAGTCGG 58.343 55.000 5.69 0.00 0.00 4.79
56 57 1.066143 CAAGGCCTGTCATAAGTCGGT 60.066 52.381 5.69 0.00 0.00 4.69
57 58 0.537188 AGGCCTGTCATAAGTCGGTG 59.463 55.000 3.11 0.00 0.00 4.94
58 59 0.249398 GGCCTGTCATAAGTCGGTGT 59.751 55.000 0.00 0.00 0.00 4.16
59 60 1.338769 GGCCTGTCATAAGTCGGTGTT 60.339 52.381 0.00 0.00 0.00 3.32
60 61 1.732259 GCCTGTCATAAGTCGGTGTTG 59.268 52.381 0.00 0.00 0.00 3.33
61 62 1.732259 CCTGTCATAAGTCGGTGTTGC 59.268 52.381 0.00 0.00 0.00 4.17
62 63 2.612972 CCTGTCATAAGTCGGTGTTGCT 60.613 50.000 0.00 0.00 0.00 3.91
63 64 2.668457 CTGTCATAAGTCGGTGTTGCTC 59.332 50.000 0.00 0.00 0.00 4.26
64 65 2.299013 TGTCATAAGTCGGTGTTGCTCT 59.701 45.455 0.00 0.00 0.00 4.09
65 66 3.244078 TGTCATAAGTCGGTGTTGCTCTT 60.244 43.478 0.00 0.00 0.00 2.85
66 67 3.368236 GTCATAAGTCGGTGTTGCTCTTC 59.632 47.826 0.00 0.00 0.00 2.87
67 68 2.060326 TAAGTCGGTGTTGCTCTTCG 57.940 50.000 0.00 0.00 0.00 3.79
68 69 0.600255 AAGTCGGTGTTGCTCTTCGG 60.600 55.000 0.00 0.00 0.00 4.30
69 70 1.300697 GTCGGTGTTGCTCTTCGGT 60.301 57.895 0.00 0.00 0.00 4.69
70 71 0.878961 GTCGGTGTTGCTCTTCGGTT 60.879 55.000 0.00 0.00 0.00 4.44
71 72 0.878523 TCGGTGTTGCTCTTCGGTTG 60.879 55.000 0.00 0.00 0.00 3.77
72 73 1.841663 CGGTGTTGCTCTTCGGTTGG 61.842 60.000 0.00 0.00 0.00 3.77
73 74 1.515521 GGTGTTGCTCTTCGGTTGGG 61.516 60.000 0.00 0.00 0.00 4.12
74 75 1.896660 TGTTGCTCTTCGGTTGGGC 60.897 57.895 0.00 0.00 0.00 5.36
75 76 2.282180 TTGCTCTTCGGTTGGGCC 60.282 61.111 0.00 0.00 0.00 5.80
76 77 2.829384 TTGCTCTTCGGTTGGGCCT 61.829 57.895 4.53 0.00 34.25 5.19
77 78 2.747855 GCTCTTCGGTTGGGCCTG 60.748 66.667 4.53 0.00 34.25 4.85
78 79 2.045926 CTCTTCGGTTGGGCCTGG 60.046 66.667 4.53 0.00 34.25 4.45
79 80 2.852075 TCTTCGGTTGGGCCTGGT 60.852 61.111 4.53 0.00 34.25 4.00
80 81 2.115266 CTTCGGTTGGGCCTGGTT 59.885 61.111 4.53 0.00 34.25 3.67
81 82 2.203422 TTCGGTTGGGCCTGGTTG 60.203 61.111 4.53 0.00 34.25 3.77
82 83 2.690653 CTTCGGTTGGGCCTGGTTGA 62.691 60.000 4.53 0.00 34.25 3.18
83 84 2.969300 TTCGGTTGGGCCTGGTTGAC 62.969 60.000 4.53 0.00 34.25 3.18
84 85 2.983592 GGTTGGGCCTGGTTGACG 60.984 66.667 4.53 0.00 0.00 4.35
85 86 2.203294 GTTGGGCCTGGTTGACGT 60.203 61.111 4.53 0.00 0.00 4.34
86 87 1.071814 GTTGGGCCTGGTTGACGTA 59.928 57.895 4.53 0.00 0.00 3.57
87 88 0.322187 GTTGGGCCTGGTTGACGTAT 60.322 55.000 4.53 0.00 0.00 3.06
88 89 1.065998 GTTGGGCCTGGTTGACGTATA 60.066 52.381 4.53 0.00 0.00 1.47
89 90 1.502690 TGGGCCTGGTTGACGTATAT 58.497 50.000 4.53 0.00 0.00 0.86
90 91 1.140052 TGGGCCTGGTTGACGTATATG 59.860 52.381 4.53 0.00 0.00 1.78
91 92 1.542547 GGGCCTGGTTGACGTATATGG 60.543 57.143 0.84 0.00 0.00 2.74
92 93 1.542547 GGCCTGGTTGACGTATATGGG 60.543 57.143 0.00 0.00 0.00 4.00
93 94 1.140252 GCCTGGTTGACGTATATGGGT 59.860 52.381 0.00 0.00 0.00 4.51
94 95 2.805657 GCCTGGTTGACGTATATGGGTC 60.806 54.545 0.00 2.07 0.00 4.46
95 96 2.545113 CCTGGTTGACGTATATGGGTCG 60.545 54.545 0.00 0.00 35.95 4.79
96 97 1.409790 TGGTTGACGTATATGGGTCGG 59.590 52.381 0.00 0.00 35.95 4.79
97 98 1.682854 GGTTGACGTATATGGGTCGGA 59.317 52.381 0.00 0.00 35.95 4.55
98 99 2.101249 GGTTGACGTATATGGGTCGGAA 59.899 50.000 0.00 0.00 35.95 4.30
99 100 3.430651 GGTTGACGTATATGGGTCGGAAA 60.431 47.826 0.00 0.00 35.95 3.13
100 101 3.441496 TGACGTATATGGGTCGGAAAC 57.559 47.619 0.00 0.00 35.95 2.78
118 119 4.683432 GCTGATGATAGCGGACCC 57.317 61.111 0.00 0.00 33.46 4.46
119 120 1.373497 GCTGATGATAGCGGACCCG 60.373 63.158 3.73 3.73 43.09 5.28
120 121 1.290324 CTGATGATAGCGGACCCGG 59.710 63.158 10.70 0.00 40.19 5.73
121 122 1.152631 TGATGATAGCGGACCCGGA 60.153 57.895 0.73 0.00 40.19 5.14
122 123 0.757561 TGATGATAGCGGACCCGGAA 60.758 55.000 0.73 0.00 40.19 4.30
123 124 0.608640 GATGATAGCGGACCCGGAAT 59.391 55.000 0.73 0.00 40.19 3.01
124 125 1.002087 GATGATAGCGGACCCGGAATT 59.998 52.381 0.73 0.00 40.19 2.17
125 126 0.105964 TGATAGCGGACCCGGAATTG 59.894 55.000 0.73 0.00 40.19 2.32
126 127 1.227853 ATAGCGGACCCGGAATTGC 60.228 57.895 0.73 0.99 40.19 3.56
127 128 2.989055 ATAGCGGACCCGGAATTGCG 62.989 60.000 12.93 12.93 40.19 4.85
129 130 2.184836 CGGACCCGGAATTGCGTA 59.815 61.111 18.34 0.00 35.56 4.42
130 131 1.448189 CGGACCCGGAATTGCGTAA 60.448 57.895 18.34 0.00 35.56 3.18
131 132 1.698714 CGGACCCGGAATTGCGTAAC 61.699 60.000 18.34 8.24 35.56 2.50
132 133 0.674269 GGACCCGGAATTGCGTAACA 60.674 55.000 18.34 0.00 0.00 2.41
197 198 2.103538 CGCATCATGCACCCAAGC 59.896 61.111 11.00 0.00 45.36 4.01
209 216 2.028925 CCAAGCGGTGGCCAAAAC 59.971 61.111 7.24 0.00 41.72 2.43
210 217 2.790791 CCAAGCGGTGGCCAAAACA 61.791 57.895 7.24 0.00 41.72 2.83
211 218 1.300080 CAAGCGGTGGCCAAAACAG 60.300 57.895 7.24 0.00 41.24 3.16
212 219 3.150647 AAGCGGTGGCCAAAACAGC 62.151 57.895 7.24 8.12 41.24 4.40
213 220 3.605664 GCGGTGGCCAAAACAGCT 61.606 61.111 7.24 0.00 36.06 4.24
214 221 2.265182 GCGGTGGCCAAAACAGCTA 61.265 57.895 7.24 0.00 36.06 3.32
216 223 1.745232 CGGTGGCCAAAACAGCTATA 58.255 50.000 7.24 0.00 34.37 1.31
380 394 3.923017 AAAAGTTTGGCTGAAGATCGG 57.077 42.857 0.00 0.00 0.00 4.18
439 483 5.411669 AGCCAAGTCACTAACGGAAATTAAG 59.588 40.000 0.00 0.00 0.00 1.85
470 514 6.644347 AGATGTTCAGACTCCACGATTTAAT 58.356 36.000 0.00 0.00 0.00 1.40
520 564 3.452264 TCTCGATGGTGAATTGGTGATCT 59.548 43.478 0.00 0.00 0.00 2.75
521 565 4.649218 TCTCGATGGTGAATTGGTGATCTA 59.351 41.667 0.00 0.00 0.00 1.98
522 566 4.948847 TCGATGGTGAATTGGTGATCTAG 58.051 43.478 0.00 0.00 0.00 2.43
659 719 3.424861 ACGACGACGACGATCTATTCTAG 59.575 47.826 25.15 0.00 42.66 2.43
660 720 3.424861 CGACGACGACGATCTATTCTAGT 59.575 47.826 15.32 0.00 42.66 2.57
661 721 4.614702 CGACGACGACGATCTATTCTAGTA 59.385 45.833 15.32 0.00 42.66 1.82
690 750 1.335496 GCAAAGAGTTTACCGCAACCA 59.665 47.619 0.00 0.00 0.00 3.67
746 814 6.471146 CAGCAGGATAGGTAATATCAAAGCT 58.529 40.000 0.00 0.00 41.94 3.74
860 940 1.087771 CGGTTTAAAGCGGCGGAGAT 61.088 55.000 27.53 0.00 45.30 2.75
866 954 1.608717 AAAGCGGCGGAGATCAGTCT 61.609 55.000 9.78 0.00 37.42 3.24
869 957 0.741221 GCGGCGGAGATCAGTCTTTT 60.741 55.000 9.78 0.00 33.97 2.27
875 963 3.172229 GGAGATCAGTCTTTTCCTCCG 57.828 52.381 0.00 0.00 33.97 4.63
1600 1710 2.922740 ATTACGGGGCGTGTGAATAT 57.077 45.000 0.00 0.00 41.39 1.28
1630 1744 6.949352 AGCTGGATTATGTTTTCATCGATT 57.051 33.333 0.00 0.00 41.25 3.34
1649 1763 0.677731 TGGGCTCTTGGAATTGCTCG 60.678 55.000 0.00 0.00 0.00 5.03
1650 1764 0.392998 GGGCTCTTGGAATTGCTCGA 60.393 55.000 0.00 0.00 0.00 4.04
1655 1769 3.493350 GCTCTTGGAATTGCTCGATCCTA 60.493 47.826 3.79 0.00 34.24 2.94
1656 1770 4.802248 GCTCTTGGAATTGCTCGATCCTAT 60.802 45.833 3.79 0.00 34.24 2.57
1657 1771 4.635223 TCTTGGAATTGCTCGATCCTATG 58.365 43.478 3.79 0.00 34.24 2.23
1658 1772 3.407424 TGGAATTGCTCGATCCTATGG 57.593 47.619 3.79 0.00 34.24 2.74
1660 1774 1.728971 GAATTGCTCGATCCTATGGCG 59.271 52.381 0.00 0.00 0.00 5.69
1661 1775 0.681733 ATTGCTCGATCCTATGGCGT 59.318 50.000 0.00 0.00 0.00 5.68
1663 1777 0.032130 TGCTCGATCCTATGGCGTTC 59.968 55.000 0.00 0.00 0.00 3.95
1664 1778 0.315568 GCTCGATCCTATGGCGTTCT 59.684 55.000 0.00 0.00 0.00 3.01
1665 1779 1.269831 GCTCGATCCTATGGCGTTCTT 60.270 52.381 0.00 0.00 0.00 2.52
1666 1780 2.398498 CTCGATCCTATGGCGTTCTTG 58.602 52.381 0.00 0.00 0.00 3.02
1671 1785 0.729116 CCTATGGCGTTCTTGCACTG 59.271 55.000 0.00 0.00 36.28 3.66
1715 1833 1.800586 GCTGCAACATCGTTCTTGAGA 59.199 47.619 0.00 0.00 0.00 3.27
1725 1843 4.584327 TCGTTCTTGAGATTGAGTGACA 57.416 40.909 0.00 0.00 0.00 3.58
1744 1862 4.402474 TGACACTCATATAGTCCCACTGTG 59.598 45.833 0.00 0.00 35.76 3.66
1855 1975 1.604378 CCGAGATCCAAGCCCTGTT 59.396 57.895 0.00 0.00 0.00 3.16
1892 2022 1.203262 TGTCTAGCCCTGTACAACCCT 60.203 52.381 0.00 0.00 0.00 4.34
1920 2050 3.659183 ATACGTACAGTACCCTGGTCT 57.341 47.619 5.07 0.00 43.36 3.85
1921 2051 4.778213 ATACGTACAGTACCCTGGTCTA 57.222 45.455 5.07 0.00 43.36 2.59
2025 2155 2.988010 TCACGCAGCTCCATAATTCT 57.012 45.000 0.00 0.00 0.00 2.40
2084 2214 2.791927 CGATCTCGTCGGACAGCA 59.208 61.111 9.10 0.00 46.47 4.41
2125 2255 2.656646 CAGCGCTCACAGGTACCA 59.343 61.111 15.94 0.00 0.00 3.25
2272 2402 1.653151 GATCTTGTTCCGGTAGTGCC 58.347 55.000 0.00 0.00 0.00 5.01
2480 2610 1.207089 CGTGGCCATCTTCCTGACTTA 59.793 52.381 9.72 0.00 0.00 2.24
2503 2633 1.078143 GGCAGATCTGAACGGCCTT 60.078 57.895 27.04 0.00 43.24 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.221742 CCCAAAAGACTAGCCTATTAGGAGG 60.222 48.000 14.16 4.95 37.67 4.30
1 2 5.221742 CCCCAAAAGACTAGCCTATTAGGAG 60.222 48.000 14.16 5.48 37.67 3.69
2 3 4.658901 CCCCAAAAGACTAGCCTATTAGGA 59.341 45.833 14.16 0.00 37.67 2.94
3 4 4.202472 CCCCCAAAAGACTAGCCTATTAGG 60.202 50.000 5.28 5.28 38.80 2.69
4 5 4.974399 CCCCCAAAAGACTAGCCTATTAG 58.026 47.826 0.00 0.00 0.00 1.73
6 7 3.953542 CCCCCAAAAGACTAGCCTATT 57.046 47.619 0.00 0.00 0.00 1.73
34 35 1.743772 CGACTTATGACAGGCCTTGGG 60.744 57.143 0.00 0.00 0.00 4.12
35 36 1.656652 CGACTTATGACAGGCCTTGG 58.343 55.000 0.00 0.00 0.00 3.61
36 37 1.066143 ACCGACTTATGACAGGCCTTG 60.066 52.381 0.00 0.66 0.00 3.61
37 38 1.066143 CACCGACTTATGACAGGCCTT 60.066 52.381 0.00 0.00 0.00 4.35
38 39 0.537188 CACCGACTTATGACAGGCCT 59.463 55.000 0.00 0.00 0.00 5.19
39 40 0.249398 ACACCGACTTATGACAGGCC 59.751 55.000 0.00 0.00 0.00 5.19
40 41 1.732259 CAACACCGACTTATGACAGGC 59.268 52.381 0.00 0.00 0.00 4.85
41 42 1.732259 GCAACACCGACTTATGACAGG 59.268 52.381 0.00 0.00 0.00 4.00
42 43 2.668457 GAGCAACACCGACTTATGACAG 59.332 50.000 0.00 0.00 0.00 3.51
43 44 2.299013 AGAGCAACACCGACTTATGACA 59.701 45.455 0.00 0.00 0.00 3.58
44 45 2.960819 AGAGCAACACCGACTTATGAC 58.039 47.619 0.00 0.00 0.00 3.06
45 46 3.585862 GAAGAGCAACACCGACTTATGA 58.414 45.455 0.00 0.00 0.00 2.15
46 47 2.345641 CGAAGAGCAACACCGACTTATG 59.654 50.000 0.00 0.00 0.00 1.90
47 48 2.607187 CGAAGAGCAACACCGACTTAT 58.393 47.619 0.00 0.00 0.00 1.73
48 49 1.336517 CCGAAGAGCAACACCGACTTA 60.337 52.381 0.00 0.00 0.00 2.24
49 50 0.600255 CCGAAGAGCAACACCGACTT 60.600 55.000 0.00 0.00 0.00 3.01
50 51 1.006102 CCGAAGAGCAACACCGACT 60.006 57.895 0.00 0.00 0.00 4.18
51 52 0.878961 AACCGAAGAGCAACACCGAC 60.879 55.000 0.00 0.00 0.00 4.79
52 53 0.878523 CAACCGAAGAGCAACACCGA 60.879 55.000 0.00 0.00 0.00 4.69
53 54 1.569493 CAACCGAAGAGCAACACCG 59.431 57.895 0.00 0.00 0.00 4.94
54 55 1.515521 CCCAACCGAAGAGCAACACC 61.516 60.000 0.00 0.00 0.00 4.16
55 56 1.949257 CCCAACCGAAGAGCAACAC 59.051 57.895 0.00 0.00 0.00 3.32
56 57 1.896660 GCCCAACCGAAGAGCAACA 60.897 57.895 0.00 0.00 0.00 3.33
57 58 2.626780 GGCCCAACCGAAGAGCAAC 61.627 63.158 0.00 0.00 0.00 4.17
58 59 2.282180 GGCCCAACCGAAGAGCAA 60.282 61.111 0.00 0.00 0.00 3.91
59 60 3.249189 AGGCCCAACCGAAGAGCA 61.249 61.111 0.00 0.00 46.52 4.26
60 61 2.747855 CAGGCCCAACCGAAGAGC 60.748 66.667 0.00 0.00 46.52 4.09
61 62 2.045926 CCAGGCCCAACCGAAGAG 60.046 66.667 0.00 0.00 46.52 2.85
62 63 2.457323 AACCAGGCCCAACCGAAGA 61.457 57.895 0.00 0.00 46.52 2.87
63 64 2.115266 AACCAGGCCCAACCGAAG 59.885 61.111 0.00 0.00 46.52 3.79
64 65 2.203422 CAACCAGGCCCAACCGAA 60.203 61.111 0.00 0.00 46.52 4.30
65 66 3.172106 TCAACCAGGCCCAACCGA 61.172 61.111 0.00 0.00 46.52 4.69
66 67 2.983592 GTCAACCAGGCCCAACCG 60.984 66.667 0.00 0.00 46.52 4.44
67 68 2.400269 TACGTCAACCAGGCCCAACC 62.400 60.000 0.00 0.00 39.61 3.77
68 69 0.322187 ATACGTCAACCAGGCCCAAC 60.322 55.000 0.00 0.00 0.00 3.77
69 70 1.277579 TATACGTCAACCAGGCCCAA 58.722 50.000 0.00 0.00 0.00 4.12
70 71 1.140052 CATATACGTCAACCAGGCCCA 59.860 52.381 0.00 0.00 0.00 5.36
71 72 1.542547 CCATATACGTCAACCAGGCCC 60.543 57.143 0.00 0.00 0.00 5.80
72 73 1.542547 CCCATATACGTCAACCAGGCC 60.543 57.143 0.00 0.00 0.00 5.19
73 74 1.140252 ACCCATATACGTCAACCAGGC 59.860 52.381 0.00 0.00 0.00 4.85
74 75 2.545113 CGACCCATATACGTCAACCAGG 60.545 54.545 0.00 0.00 0.00 4.45
75 76 2.545113 CCGACCCATATACGTCAACCAG 60.545 54.545 0.00 0.00 0.00 4.00
76 77 1.409790 CCGACCCATATACGTCAACCA 59.590 52.381 0.00 0.00 0.00 3.67
77 78 1.682854 TCCGACCCATATACGTCAACC 59.317 52.381 0.00 0.00 0.00 3.77
78 79 3.441496 TTCCGACCCATATACGTCAAC 57.559 47.619 0.00 0.00 0.00 3.18
79 80 3.734597 CGTTTCCGACCCATATACGTCAA 60.735 47.826 0.00 0.00 35.63 3.18
80 81 2.223548 CGTTTCCGACCCATATACGTCA 60.224 50.000 0.00 0.00 35.63 4.35
81 82 2.388121 CGTTTCCGACCCATATACGTC 58.612 52.381 0.00 0.00 35.63 4.34
82 83 1.536709 GCGTTTCCGACCCATATACGT 60.537 52.381 0.00 0.00 35.63 3.57
83 84 1.134226 GCGTTTCCGACCCATATACG 58.866 55.000 0.00 0.00 35.63 3.06
84 85 2.132762 CAGCGTTTCCGACCCATATAC 58.867 52.381 0.00 0.00 35.63 1.47
85 86 2.033372 TCAGCGTTTCCGACCCATATA 58.967 47.619 0.00 0.00 35.63 0.86
86 87 0.828022 TCAGCGTTTCCGACCCATAT 59.172 50.000 0.00 0.00 35.63 1.78
87 88 0.828022 ATCAGCGTTTCCGACCCATA 59.172 50.000 0.00 0.00 35.63 2.74
88 89 0.744414 CATCAGCGTTTCCGACCCAT 60.744 55.000 0.00 0.00 35.63 4.00
89 90 1.375396 CATCAGCGTTTCCGACCCA 60.375 57.895 0.00 0.00 35.63 4.51
90 91 0.462047 ATCATCAGCGTTTCCGACCC 60.462 55.000 0.00 0.00 35.63 4.46
91 92 2.128035 CTATCATCAGCGTTTCCGACC 58.872 52.381 0.00 0.00 35.63 4.79
92 93 1.523095 GCTATCATCAGCGTTTCCGAC 59.477 52.381 0.00 0.00 35.63 4.79
93 94 1.852942 GCTATCATCAGCGTTTCCGA 58.147 50.000 0.00 0.00 35.63 4.55
101 102 1.373497 CGGGTCCGCTATCATCAGC 60.373 63.158 0.00 0.00 38.23 4.26
102 103 1.179174 TCCGGGTCCGCTATCATCAG 61.179 60.000 0.00 0.00 38.24 2.90
103 104 0.757561 TTCCGGGTCCGCTATCATCA 60.758 55.000 0.00 0.00 38.24 3.07
104 105 0.608640 ATTCCGGGTCCGCTATCATC 59.391 55.000 0.00 0.00 38.24 2.92
105 106 1.056660 AATTCCGGGTCCGCTATCAT 58.943 50.000 0.00 0.00 38.24 2.45
106 107 0.105964 CAATTCCGGGTCCGCTATCA 59.894 55.000 0.00 0.00 38.24 2.15
107 108 1.228657 GCAATTCCGGGTCCGCTATC 61.229 60.000 0.00 0.00 38.24 2.08
108 109 1.227853 GCAATTCCGGGTCCGCTAT 60.228 57.895 0.00 0.00 38.24 2.97
109 110 2.188469 GCAATTCCGGGTCCGCTA 59.812 61.111 0.00 0.00 38.24 4.26
112 113 1.448189 TTACGCAATTCCGGGTCCG 60.448 57.895 0.00 1.86 39.44 4.79
113 114 0.674269 TGTTACGCAATTCCGGGTCC 60.674 55.000 0.00 0.00 33.58 4.46
114 115 1.329599 GATGTTACGCAATTCCGGGTC 59.670 52.381 0.00 0.00 33.58 4.46
115 116 1.065709 AGATGTTACGCAATTCCGGGT 60.066 47.619 0.00 0.00 35.95 5.28
116 117 1.663695 AGATGTTACGCAATTCCGGG 58.336 50.000 0.00 0.00 0.00 5.73
117 118 3.000925 GTGTAGATGTTACGCAATTCCGG 59.999 47.826 0.00 0.00 0.00 5.14
118 119 3.301579 CGTGTAGATGTTACGCAATTCCG 60.302 47.826 0.00 0.00 0.00 4.30
119 120 3.861113 TCGTGTAGATGTTACGCAATTCC 59.139 43.478 0.00 0.00 37.70 3.01
120 121 4.026804 CCTCGTGTAGATGTTACGCAATTC 60.027 45.833 0.00 0.00 37.70 2.17
121 122 3.863424 CCTCGTGTAGATGTTACGCAATT 59.137 43.478 0.00 0.00 37.70 2.32
122 123 3.129813 TCCTCGTGTAGATGTTACGCAAT 59.870 43.478 0.00 0.00 37.70 3.56
123 124 2.488937 TCCTCGTGTAGATGTTACGCAA 59.511 45.455 0.00 0.00 37.70 4.85
124 125 2.086094 TCCTCGTGTAGATGTTACGCA 58.914 47.619 0.00 0.00 37.70 5.24
125 126 2.541178 CCTCCTCGTGTAGATGTTACGC 60.541 54.545 0.00 0.00 37.70 4.42
126 127 2.033049 CCCTCCTCGTGTAGATGTTACG 59.967 54.545 0.00 0.00 39.04 3.18
127 128 3.066481 GTCCCTCCTCGTGTAGATGTTAC 59.934 52.174 0.00 0.00 0.00 2.50
128 129 3.053842 AGTCCCTCCTCGTGTAGATGTTA 60.054 47.826 0.00 0.00 0.00 2.41
129 130 2.100989 GTCCCTCCTCGTGTAGATGTT 58.899 52.381 0.00 0.00 0.00 2.71
130 131 1.285373 AGTCCCTCCTCGTGTAGATGT 59.715 52.381 0.00 0.00 0.00 3.06
131 132 1.678627 CAGTCCCTCCTCGTGTAGATG 59.321 57.143 0.00 0.00 0.00 2.90
132 133 1.564818 TCAGTCCCTCCTCGTGTAGAT 59.435 52.381 0.00 0.00 0.00 1.98
197 198 1.670811 CTATAGCTGTTTTGGCCACCG 59.329 52.381 3.88 0.00 0.00 4.94
208 215 0.031111 TGCCAGGACCCTATAGCTGT 60.031 55.000 0.00 0.00 0.00 4.40
209 216 1.277557 GATGCCAGGACCCTATAGCTG 59.722 57.143 0.00 0.00 0.00 4.24
210 217 1.150986 AGATGCCAGGACCCTATAGCT 59.849 52.381 0.00 0.00 0.00 3.32
211 218 1.277557 CAGATGCCAGGACCCTATAGC 59.722 57.143 0.00 0.00 0.00 2.97
212 219 1.905215 CCAGATGCCAGGACCCTATAG 59.095 57.143 0.00 0.00 0.00 1.31
213 220 2.030027 CCAGATGCCAGGACCCTATA 57.970 55.000 0.00 0.00 0.00 1.31
214 221 1.422161 GCCAGATGCCAGGACCCTAT 61.422 60.000 0.00 0.00 0.00 2.57
216 223 3.415087 GCCAGATGCCAGGACCCT 61.415 66.667 0.00 0.00 0.00 4.34
237 244 6.599244 ACGCCACACAGTACTAGTAGTATAAA 59.401 38.462 13.09 0.00 32.65 1.40
240 247 4.521146 ACGCCACACAGTACTAGTAGTAT 58.479 43.478 13.09 0.00 32.65 2.12
241 248 3.935203 GACGCCACACAGTACTAGTAGTA 59.065 47.826 9.94 5.90 0.00 1.82
242 249 2.746362 GACGCCACACAGTACTAGTAGT 59.254 50.000 8.14 8.14 0.00 2.73
243 250 2.745821 TGACGCCACACAGTACTAGTAG 59.254 50.000 1.87 0.00 0.00 2.57
358 372 3.983344 CCGATCTTCAGCCAAACTTTTTG 59.017 43.478 0.00 0.00 0.00 2.44
359 373 3.552890 GCCGATCTTCAGCCAAACTTTTT 60.553 43.478 0.00 0.00 0.00 1.94
380 394 6.194285 AGGAAATTTTCTCCTATAGAGGGC 57.806 41.667 2.96 0.00 41.73 5.19
439 483 2.626840 GAGTCTGAACATCTTGCCCTC 58.373 52.381 0.00 0.00 0.00 4.30
470 514 0.179032 TTTCTTGGCGGTTGCAGAGA 60.179 50.000 0.00 0.00 45.35 3.10
520 564 3.786516 TGGTCGCATTGAATCGTACTA 57.213 42.857 0.00 0.00 0.00 1.82
521 565 2.665649 TGGTCGCATTGAATCGTACT 57.334 45.000 0.00 0.00 0.00 2.73
522 566 2.222953 GGTTGGTCGCATTGAATCGTAC 60.223 50.000 0.00 0.00 0.00 3.67
706 766 3.094572 CTGCTGGTTTTTCTGGGATCAT 58.905 45.455 0.00 0.00 0.00 2.45
746 814 1.314534 CCCATTGCCATTGCGTCTGA 61.315 55.000 0.00 0.00 41.78 3.27
857 937 2.498078 GGACGGAGGAAAAGACTGATCT 59.502 50.000 0.00 0.00 36.42 2.75
860 940 1.712056 TGGACGGAGGAAAAGACTGA 58.288 50.000 0.00 0.00 0.00 3.41
866 954 2.088950 GTCGAATGGACGGAGGAAAA 57.911 50.000 0.00 0.00 35.61 2.29
915 1005 4.649088 TGCTATGTCAAGTAGCGTATGT 57.351 40.909 1.93 0.00 45.82 2.29
963 1053 2.326897 CCGCAGATCGCAATGCTG 59.673 61.111 2.94 0.00 42.60 4.41
1102 1192 2.660802 GACCAACCACCCGTCGAT 59.339 61.111 0.00 0.00 0.00 3.59
1131 1221 4.738998 CCATTGTCGCCAGCCCCA 62.739 66.667 0.00 0.00 0.00 4.96
1200 1290 4.724602 GTCTCGCTCACTGCCGCA 62.725 66.667 0.00 0.00 38.78 5.69
1439 1529 4.361971 TGGCCTCCTCCTCGACGT 62.362 66.667 3.32 0.00 0.00 4.34
1630 1744 0.677731 CGAGCAATTCCAAGAGCCCA 60.678 55.000 0.00 0.00 0.00 5.36
1649 1763 1.599542 GTGCAAGAACGCCATAGGATC 59.400 52.381 0.00 0.00 0.00 3.36
1650 1764 1.210478 AGTGCAAGAACGCCATAGGAT 59.790 47.619 0.00 0.00 0.00 3.24
1655 1769 1.580845 GAGCAGTGCAAGAACGCCAT 61.581 55.000 19.20 0.00 0.00 4.40
1656 1770 2.203195 AGCAGTGCAAGAACGCCA 60.203 55.556 19.20 0.00 0.00 5.69
1657 1771 2.558313 GAGCAGTGCAAGAACGCC 59.442 61.111 19.20 0.00 0.00 5.68
1658 1772 2.558313 GGAGCAGTGCAAGAACGC 59.442 61.111 19.20 0.00 0.00 4.84
1660 1774 1.661112 GATACGGAGCAGTGCAAGAAC 59.339 52.381 19.20 2.98 0.00 3.01
1661 1775 1.275010 TGATACGGAGCAGTGCAAGAA 59.725 47.619 19.20 0.00 0.00 2.52
1663 1777 1.284657 CTGATACGGAGCAGTGCAAG 58.715 55.000 19.20 10.31 34.24 4.01
1664 1778 3.441244 CTGATACGGAGCAGTGCAA 57.559 52.632 19.20 0.00 34.24 4.08
1671 1785 3.767278 ACGAAGTTAACTGATACGGAGC 58.233 45.455 9.34 0.00 37.78 4.70
1725 1843 4.265856 TCCACAGTGGGACTATATGAGT 57.734 45.455 20.14 0.00 38.32 3.41
1729 1847 5.467738 TCTCATTCCACAGTGGGACTATAT 58.532 41.667 20.14 0.00 38.32 0.86
1732 1850 3.099905 CTCTCATTCCACAGTGGGACTA 58.900 50.000 20.14 1.68 38.32 2.59
1839 1959 2.293170 GCTAAACAGGGCTTGGATCTC 58.707 52.381 0.44 0.00 0.00 2.75
1855 1975 2.941025 AGGGCTTGGCAGGGCTAA 60.941 61.111 22.04 0.00 0.00 3.09
1892 2022 5.295787 CAGGGTACTGTACGTATACGGTTTA 59.704 44.000 27.62 9.84 46.88 2.01
2480 2610 1.813513 CCGTTCAGATCTGCCAAACT 58.186 50.000 18.36 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.