Multiple sequence alignment - TraesCS7A01G456400

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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 TraesCS7A01G456400 chr7A 100.000 2741 0 0 1 2741 652483081 652485821 0.000000e+00 5062.0
1 TraesCS7A01G456400 chr7A 91.228 1026 73 10 945 1955 652490515 652491538 0.000000e+00 1380.0
2 TraesCS7A01G456400 chr7A 79.851 134 19 7 262 391 491222773 491222902 1.050000e-14 91.6
3 TraesCS7A01G456400 chr7D 94.669 1163 51 8 945 2101 566133114 566134271 0.000000e+00 1794.0
4 TraesCS7A01G456400 chr7D 91.933 1190 75 11 920 2089 566123586 566124774 0.000000e+00 1646.0
5 TraesCS7A01G456400 chr7D 86.759 793 43 21 146 913 566122782 566123537 0.000000e+00 826.0
6 TraesCS7A01G456400 chr7D 80.843 522 36 25 146 637 112008885 112008398 4.340000e-93 351.0
7 TraesCS7A01G456400 chr7D 83.601 311 18 23 632 917 111801530 111801228 7.530000e-66 261.0
8 TraesCS7A01G456400 chr7D 86.869 99 8 4 222 318 529587454 529587549 3.730000e-19 106.0
9 TraesCS7A01G456400 chr7D 94.286 70 3 1 2117 2185 566134255 566134324 3.730000e-19 106.0
10 TraesCS7A01G456400 chr7B 89.691 1164 94 11 945 2089 617782894 617784050 0.000000e+00 1461.0
11 TraesCS7A01G456400 chr7B 96.892 547 12 4 2197 2741 669216203 669216746 0.000000e+00 911.0
12 TraesCS7A01G456400 chr7B 96.527 547 13 5 2197 2741 669283255 669283797 0.000000e+00 900.0
13 TraesCS7A01G456400 chr7B 94.836 213 9 2 1866 2077 617787713 617787924 5.660000e-87 331.0
14 TraesCS7A01G456400 chr7B 92.891 211 11 3 949 1156 617787467 617787676 1.230000e-78 303.0
15 TraesCS7A01G456400 chr5B 95.985 548 20 2 2196 2741 489308054 489308601 0.000000e+00 889.0
16 TraesCS7A01G456400 chr5B 88.000 200 22 2 2201 2399 685309738 685309936 4.560000e-58 235.0
17 TraesCS7A01G456400 chr2B 83.395 813 78 31 146 925 25077819 25077031 0.000000e+00 701.0
18 TraesCS7A01G456400 chr2B 89.005 191 21 0 2200 2390 663917249 663917059 1.270000e-58 237.0
19 TraesCS7A01G456400 chr5D 84.462 502 60 13 2201 2690 390129390 390128895 1.910000e-131 479.0
20 TraesCS7A01G456400 chr1B 81.409 511 58 21 2192 2687 581105502 581105990 1.540000e-102 383.0
21 TraesCS7A01G456400 chr3B 81.139 509 63 19 2200 2690 15048293 15047800 7.160000e-101 377.0
22 TraesCS7A01G456400 chr3B 80.658 517 59 24 2192 2687 733252967 733253463 2.010000e-96 363.0
23 TraesCS7A01G456400 chr2A 83.959 293 29 9 632 911 261666723 261666436 5.820000e-67 265.0
24 TraesCS7A01G456400 chr2A 73.740 377 52 34 262 616 734500813 734501164 1.340000e-18 104.0
25 TraesCS7A01G456400 chr5A 83.612 299 29 12 632 911 31131430 31131133 2.090000e-66 263.0
26 TraesCS7A01G456400 chr6D 83.444 302 28 12 632 915 379977108 379976811 7.530000e-66 261.0
27 TraesCS7A01G456400 chr3A 82.724 301 31 13 632 915 733189444 733189148 5.860000e-62 248.0
28 TraesCS7A01G456400 chr3A 87.778 90 7 3 226 313 680762871 680762784 4.830000e-18 102.0
29 TraesCS7A01G456400 chr6A 89.157 83 5 4 1 83 456982687 456982765 1.740000e-17 100.0
30 TraesCS7A01G456400 chr1D 82.500 120 14 6 238 350 236630927 236631046 6.250000e-17 99.0


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 TraesCS7A01G456400 chr7A 652483081 652485821 2740 False 5062.000000 5062 100.000000 1 2741 1 chr7A.!!$F2 2740
1 TraesCS7A01G456400 chr7A 652490515 652491538 1023 False 1380.000000 1380 91.228000 945 1955 1 chr7A.!!$F3 1010
2 TraesCS7A01G456400 chr7D 566122782 566124774 1992 False 1236.000000 1646 89.346000 146 2089 2 chr7D.!!$F2 1943
3 TraesCS7A01G456400 chr7D 566133114 566134324 1210 False 950.000000 1794 94.477500 945 2185 2 chr7D.!!$F3 1240
4 TraesCS7A01G456400 chr7B 669216203 669216746 543 False 911.000000 911 96.892000 2197 2741 1 chr7B.!!$F1 544
5 TraesCS7A01G456400 chr7B 669283255 669283797 542 False 900.000000 900 96.527000 2197 2741 1 chr7B.!!$F2 544
6 TraesCS7A01G456400 chr7B 617782894 617787924 5030 False 698.333333 1461 92.472667 945 2089 3 chr7B.!!$F3 1144
7 TraesCS7A01G456400 chr5B 489308054 489308601 547 False 889.000000 889 95.985000 2196 2741 1 chr5B.!!$F1 545
8 TraesCS7A01G456400 chr2B 25077031 25077819 788 True 701.000000 701 83.395000 146 925 1 chr2B.!!$R1 779

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
947 1028 0.03213 TCTGGATTCGCCGCTGATAC 59.968 55.0 0.0 0.0 40.66 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2077 2186 2.163815 CCCGTTATTCGAGATCGGCTAT 59.836 50.0 11.49 0.0 42.86 2.97 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
20 21 2.143925 AGGAAAGAACGAAAAGCGAGG 58.856 47.619 0.00 0.00 44.57 4.63
21 22 1.197036 GGAAAGAACGAAAAGCGAGGG 59.803 52.381 0.00 0.00 44.57 4.30
22 23 2.140717 GAAAGAACGAAAAGCGAGGGA 58.859 47.619 0.00 0.00 44.57 4.20
23 24 1.797025 AAGAACGAAAAGCGAGGGAG 58.203 50.000 0.00 0.00 44.57 4.30
24 25 0.037232 AGAACGAAAAGCGAGGGAGG 60.037 55.000 0.00 0.00 44.57 4.30
25 26 1.636570 GAACGAAAAGCGAGGGAGGC 61.637 60.000 0.00 0.00 44.57 4.70
26 27 3.188786 CGAAAAGCGAGGGAGGCG 61.189 66.667 0.00 0.00 44.57 5.52
27 28 2.264794 GAAAAGCGAGGGAGGCGA 59.735 61.111 0.00 0.00 35.00 5.54
28 29 1.375523 GAAAAGCGAGGGAGGCGAA 60.376 57.895 0.00 0.00 35.00 4.70
29 30 1.362406 GAAAAGCGAGGGAGGCGAAG 61.362 60.000 0.00 0.00 35.00 3.79
30 31 2.804828 AAAAGCGAGGGAGGCGAAGG 62.805 60.000 0.00 0.00 35.00 3.46
32 33 4.516195 GCGAGGGAGGCGAAGGTC 62.516 72.222 0.00 0.00 0.00 3.85
33 34 4.194720 CGAGGGAGGCGAAGGTCG 62.195 72.222 0.00 0.00 43.89 4.79
42 43 4.680237 CGAAGGTCGCAGCACCCA 62.680 66.667 9.63 0.00 37.09 4.51
43 44 3.050275 GAAGGTCGCAGCACCCAC 61.050 66.667 9.63 2.71 37.09 4.61
44 45 3.825160 GAAGGTCGCAGCACCCACA 62.825 63.158 9.63 0.00 37.09 4.17
45 46 3.196207 AAGGTCGCAGCACCCACAT 62.196 57.895 9.63 0.00 37.09 3.21
46 47 3.434319 GGTCGCAGCACCCACATG 61.434 66.667 0.00 0.00 0.00 3.21
47 48 3.434319 GTCGCAGCACCCACATGG 61.434 66.667 0.00 0.00 41.37 3.66
51 52 4.682334 CAGCACCCACATGGCCCA 62.682 66.667 0.00 0.00 37.83 5.36
52 53 3.913445 AGCACCCACATGGCCCAA 61.913 61.111 0.00 0.00 37.83 4.12
53 54 3.694538 GCACCCACATGGCCCAAC 61.695 66.667 0.00 0.00 37.83 3.77
54 55 2.118076 CACCCACATGGCCCAACT 59.882 61.111 0.00 0.00 37.83 3.16
55 56 1.978617 CACCCACATGGCCCAACTC 60.979 63.158 0.00 0.00 37.83 3.01
56 57 2.362889 CCCACATGGCCCAACTCC 60.363 66.667 0.00 0.00 0.00 3.85
57 58 2.362889 CCACATGGCCCAACTCCC 60.363 66.667 0.00 0.00 0.00 4.30
58 59 2.765969 CACATGGCCCAACTCCCT 59.234 61.111 0.00 0.00 0.00 4.20
59 60 1.077265 CACATGGCCCAACTCCCTT 59.923 57.895 0.00 0.00 0.00 3.95
60 61 1.077265 ACATGGCCCAACTCCCTTG 59.923 57.895 0.00 0.00 33.74 3.61
61 62 2.037847 ATGGCCCAACTCCCTTGC 59.962 61.111 0.00 0.00 0.00 4.01
62 63 2.855770 ATGGCCCAACTCCCTTGCA 61.856 57.895 0.00 0.00 0.00 4.08
63 64 2.203625 GGCCCAACTCCCTTGCAA 60.204 61.111 0.00 0.00 0.00 4.08
64 65 2.574018 GGCCCAACTCCCTTGCAAC 61.574 63.158 0.00 0.00 0.00 4.17
65 66 2.919494 GCCCAACTCCCTTGCAACG 61.919 63.158 0.00 0.00 0.00 4.10
66 67 2.644992 CCAACTCCCTTGCAACGC 59.355 61.111 0.00 0.00 0.00 4.84
67 68 2.192861 CCAACTCCCTTGCAACGCA 61.193 57.895 0.00 0.00 36.47 5.24
68 69 1.526575 CCAACTCCCTTGCAACGCAT 61.527 55.000 0.00 0.00 38.76 4.73
69 70 0.387622 CAACTCCCTTGCAACGCATG 60.388 55.000 0.00 0.00 38.76 4.06
78 79 4.853507 CAACGCATGCTCCACTTG 57.146 55.556 17.13 5.46 0.00 3.16
79 80 1.443194 CAACGCATGCTCCACTTGC 60.443 57.895 17.13 0.00 44.03 4.01
80 81 1.898094 AACGCATGCTCCACTTGCA 60.898 52.632 17.13 0.00 46.97 4.08
81 82 1.859427 AACGCATGCTCCACTTGCAG 61.859 55.000 17.13 0.00 46.97 4.41
82 83 2.181021 GCATGCTCCACTTGCAGC 59.819 61.111 11.37 0.00 46.12 5.25
83 84 2.882876 CATGCTCCACTTGCAGCC 59.117 61.111 0.00 0.00 44.04 4.85
84 85 2.362120 ATGCTCCACTTGCAGCCC 60.362 61.111 0.00 0.00 44.04 5.19
85 86 3.214190 ATGCTCCACTTGCAGCCCA 62.214 57.895 0.00 0.00 44.04 5.36
86 87 3.060615 GCTCCACTTGCAGCCCAG 61.061 66.667 0.00 0.00 0.00 4.45
87 88 3.060615 CTCCACTTGCAGCCCAGC 61.061 66.667 0.00 0.00 0.00 4.85
88 89 4.666253 TCCACTTGCAGCCCAGCC 62.666 66.667 0.00 0.00 0.00 4.85
90 91 4.980702 CACTTGCAGCCCAGCCCA 62.981 66.667 0.00 0.00 0.00 5.36
91 92 4.673375 ACTTGCAGCCCAGCCCAG 62.673 66.667 0.00 0.00 0.00 4.45
92 93 4.355720 CTTGCAGCCCAGCCCAGA 62.356 66.667 0.00 0.00 0.00 3.86
93 94 3.873679 CTTGCAGCCCAGCCCAGAA 62.874 63.158 0.00 0.00 0.00 3.02
94 95 3.873679 TTGCAGCCCAGCCCAGAAG 62.874 63.158 0.00 0.00 0.00 2.85
95 96 4.039092 GCAGCCCAGCCCAGAAGA 62.039 66.667 0.00 0.00 0.00 2.87
96 97 3.004951 CAGCCCAGCCCAGAAGAT 58.995 61.111 0.00 0.00 0.00 2.40
97 98 1.987807 GCAGCCCAGCCCAGAAGATA 61.988 60.000 0.00 0.00 0.00 1.98
98 99 0.179034 CAGCCCAGCCCAGAAGATAC 60.179 60.000 0.00 0.00 0.00 2.24
99 100 0.327000 AGCCCAGCCCAGAAGATACT 60.327 55.000 0.00 0.00 0.00 2.12
100 101 0.179034 GCCCAGCCCAGAAGATACTG 60.179 60.000 0.00 0.00 37.61 2.74
101 102 1.500474 CCCAGCCCAGAAGATACTGA 58.500 55.000 0.00 0.00 39.94 3.41
102 103 1.415659 CCCAGCCCAGAAGATACTGAG 59.584 57.143 0.00 0.00 39.94 3.35
103 104 2.392662 CCAGCCCAGAAGATACTGAGA 58.607 52.381 0.00 0.00 39.94 3.27
104 105 2.102252 CCAGCCCAGAAGATACTGAGAC 59.898 54.545 0.00 0.00 39.94 3.36
105 106 2.762887 CAGCCCAGAAGATACTGAGACA 59.237 50.000 0.00 0.00 39.94 3.41
106 107 3.030291 AGCCCAGAAGATACTGAGACAG 58.970 50.000 0.00 0.00 39.94 3.51
107 108 2.102252 GCCCAGAAGATACTGAGACAGG 59.898 54.545 0.00 0.00 39.94 4.00
108 109 3.636679 CCCAGAAGATACTGAGACAGGA 58.363 50.000 0.00 0.00 39.94 3.86
109 110 3.383185 CCCAGAAGATACTGAGACAGGAC 59.617 52.174 0.00 0.00 39.94 3.85
110 111 4.019858 CCAGAAGATACTGAGACAGGACA 58.980 47.826 0.00 0.00 39.94 4.02
111 112 4.097741 CCAGAAGATACTGAGACAGGACAG 59.902 50.000 0.00 0.00 39.94 3.51
112 113 4.097741 CAGAAGATACTGAGACAGGACAGG 59.902 50.000 0.00 0.00 39.94 4.00
113 114 2.383855 AGATACTGAGACAGGACAGGC 58.616 52.381 0.00 0.00 38.30 4.85
114 115 2.024464 AGATACTGAGACAGGACAGGCT 60.024 50.000 0.00 0.00 38.30 4.58
115 116 2.310779 TACTGAGACAGGACAGGCTT 57.689 50.000 0.00 0.00 38.30 4.35
116 117 0.683973 ACTGAGACAGGACAGGCTTG 59.316 55.000 0.00 0.00 38.30 4.01
117 118 0.036577 CTGAGACAGGACAGGCTTGG 60.037 60.000 0.00 0.00 0.00 3.61
118 119 0.471780 TGAGACAGGACAGGCTTGGA 60.472 55.000 0.00 0.00 0.00 3.53
119 120 0.908198 GAGACAGGACAGGCTTGGAT 59.092 55.000 0.00 0.00 0.00 3.41
120 121 0.617413 AGACAGGACAGGCTTGGATG 59.383 55.000 0.00 0.00 0.00 3.51
121 122 0.393537 GACAGGACAGGCTTGGATGG 60.394 60.000 0.00 0.00 0.00 3.51
122 123 1.077212 CAGGACAGGCTTGGATGGG 60.077 63.158 0.00 0.00 0.00 4.00
123 124 2.440980 GGACAGGCTTGGATGGGC 60.441 66.667 0.00 0.00 0.00 5.36
124 125 2.679716 GACAGGCTTGGATGGGCT 59.320 61.111 0.00 0.00 40.24 5.19
125 126 1.452833 GACAGGCTTGGATGGGCTC 60.453 63.158 0.00 0.00 37.49 4.70
126 127 2.202236 GACAGGCTTGGATGGGCTCA 62.202 60.000 0.00 0.00 37.49 4.26
127 128 1.453379 CAGGCTTGGATGGGCTCAG 60.453 63.158 0.00 0.00 37.49 3.35
128 129 2.123982 GGCTTGGATGGGCTCAGG 60.124 66.667 0.00 0.00 0.00 3.86
129 130 2.832201 GCTTGGATGGGCTCAGGC 60.832 66.667 0.00 0.00 37.82 4.85
140 141 4.020617 CTCAGGCCTGCCGTCCAA 62.021 66.667 28.91 7.95 41.95 3.53
141 142 3.551496 CTCAGGCCTGCCGTCCAAA 62.551 63.158 28.91 7.14 41.95 3.28
142 143 2.597217 CAGGCCTGCCGTCCAAAA 60.597 61.111 22.33 0.00 41.95 2.44
143 144 1.978617 CAGGCCTGCCGTCCAAAAT 60.979 57.895 22.33 0.00 41.95 1.82
144 145 1.678970 AGGCCTGCCGTCCAAAATC 60.679 57.895 3.11 0.00 41.95 2.17
172 173 0.332632 TGCAGCCTAGCCCAGAAAAT 59.667 50.000 0.00 0.00 0.00 1.82
202 204 0.036732 CTGCTCAGCCCCTGTAAACA 59.963 55.000 0.00 0.00 32.61 2.83
203 205 0.476338 TGCTCAGCCCCTGTAAACAA 59.524 50.000 0.00 0.00 32.61 2.83
204 206 1.133637 TGCTCAGCCCCTGTAAACAAA 60.134 47.619 0.00 0.00 32.61 2.83
205 207 1.269723 GCTCAGCCCCTGTAAACAAAC 59.730 52.381 0.00 0.00 32.61 2.93
208 210 1.176619 AGCCCCTGTAAACAAACGCC 61.177 55.000 0.00 0.00 0.00 5.68
527 560 4.899239 GCCGGCTCATCAGGTCCG 62.899 72.222 22.15 0.00 41.41 4.79
528 561 3.147595 CCGGCTCATCAGGTCCGA 61.148 66.667 0.65 0.00 44.23 4.55
536 569 1.410517 TCATCAGGTCCGATTCAGAGC 59.589 52.381 0.00 0.00 0.00 4.09
537 570 0.755686 ATCAGGTCCGATTCAGAGCC 59.244 55.000 0.00 0.00 32.08 4.70
578 612 1.486726 GCTGCTCCTACCTACCATTGT 59.513 52.381 0.00 0.00 0.00 2.71
579 613 2.092914 GCTGCTCCTACCTACCATTGTT 60.093 50.000 0.00 0.00 0.00 2.83
580 614 3.622455 GCTGCTCCTACCTACCATTGTTT 60.622 47.826 0.00 0.00 0.00 2.83
581 615 4.589908 CTGCTCCTACCTACCATTGTTTT 58.410 43.478 0.00 0.00 0.00 2.43
582 616 4.993028 TGCTCCTACCTACCATTGTTTTT 58.007 39.130 0.00 0.00 0.00 1.94
608 642 5.818136 TTTGCAGAATTCCAGTAGCATAC 57.182 39.130 0.65 0.00 43.47 2.39
637 671 5.642491 CCTTGCCCAGTTTAGTTCTAGTTAC 59.358 44.000 0.00 0.00 0.00 2.50
654 688 8.378172 TCTAGTTACTTTGACAAAATGTCCAG 57.622 34.615 7.94 6.63 46.40 3.86
692 726 8.961294 AGATTGTCATTCAAAACAAAATCCAA 57.039 26.923 0.00 0.00 38.74 3.53
769 805 6.818644 CGACAATATGATTAGGGGATAACAGG 59.181 42.308 0.00 0.00 0.00 4.00
885 923 6.588348 AAAGTTTGAGCTTATTTGCACAAC 57.412 33.333 0.00 0.00 41.63 3.32
889 927 2.557924 TGAGCTTATTTGCACAACAGGG 59.442 45.455 0.00 0.00 31.14 4.45
939 1020 2.785679 CATTTTCGTTCTGGATTCGCC 58.214 47.619 0.00 0.00 37.10 5.54
947 1028 0.032130 TCTGGATTCGCCGCTGATAC 59.968 55.000 0.00 0.00 40.66 2.24
1028 1112 1.153369 ATGCTTCATCCACGACGGG 60.153 57.895 0.00 0.00 34.36 5.28
1086 1173 2.822707 TCTACCTCCTCGGCTACTTT 57.177 50.000 0.00 0.00 35.61 2.66
1278 1365 1.185618 TCAGCACGGCCTACTTCACT 61.186 55.000 0.00 0.00 0.00 3.41
1408 1495 3.771160 CCTACGGGTTGCTCGCCT 61.771 66.667 0.00 0.00 0.00 5.52
1528 1615 0.735287 GTTGTCGCTCCCGTTCTACC 60.735 60.000 0.00 0.00 35.54 3.18
1593 1680 5.614324 TCGTGAGGATGGTGAAATTCTAT 57.386 39.130 0.00 0.00 0.00 1.98
1721 1817 2.716424 ACTTCAGACAAAGGATGGGGAA 59.284 45.455 0.00 0.00 0.00 3.97
1754 1850 4.279420 GGAACAATGATGGGCTCCTTAATC 59.721 45.833 0.00 0.00 0.00 1.75
1760 1856 7.786464 ACAATGATGGGCTCCTTAATCTTAATT 59.214 33.333 0.00 0.00 0.00 1.40
1787 1883 2.890311 CTCATAGGGTGTTTGGTTTGCA 59.110 45.455 0.00 0.00 0.00 4.08
1788 1884 3.300388 TCATAGGGTGTTTGGTTTGCAA 58.700 40.909 0.00 0.00 0.00 4.08
2068 2177 9.690913 GGGGATTTGTAACCTTAGTTTTAGTAT 57.309 33.333 0.00 0.00 37.42 2.12
2089 2198 4.174411 TGGTTTGATATAGCCGATCTCG 57.826 45.455 0.00 0.00 39.44 4.04
2090 2199 3.824443 TGGTTTGATATAGCCGATCTCGA 59.176 43.478 0.22 0.00 43.02 4.04
2091 2200 4.279922 TGGTTTGATATAGCCGATCTCGAA 59.720 41.667 0.22 0.00 43.02 3.71
2092 2201 5.047306 TGGTTTGATATAGCCGATCTCGAAT 60.047 40.000 0.22 0.00 43.02 3.34
2093 2202 6.152154 TGGTTTGATATAGCCGATCTCGAATA 59.848 38.462 0.22 0.00 43.02 1.75
2094 2203 7.033791 GGTTTGATATAGCCGATCTCGAATAA 58.966 38.462 0.22 0.00 43.02 1.40
2095 2204 7.009357 GGTTTGATATAGCCGATCTCGAATAAC 59.991 40.741 0.22 0.00 43.02 1.89
2096 2205 5.807344 TGATATAGCCGATCTCGAATAACG 58.193 41.667 0.22 0.00 43.02 3.18
2097 2206 2.983402 TAGCCGATCTCGAATAACGG 57.017 50.000 10.64 10.64 45.26 4.44
2098 2207 0.314302 AGCCGATCTCGAATAACGGG 59.686 55.000 15.08 0.00 44.81 5.28
2145 2296 8.141909 TCGGATAACAGGAGTTAGATTTACATG 58.858 37.037 0.00 0.00 43.02 3.21
2166 2317 2.625737 CACTTGAGATGAGTGCCGATT 58.374 47.619 0.00 0.00 38.20 3.34
2185 2337 4.681978 GGCGCGAGTGGGAGTGTT 62.682 66.667 12.10 0.00 0.00 3.32
2188 2340 2.426023 GCGAGTGGGAGTGTTGGT 59.574 61.111 0.00 0.00 0.00 3.67
2189 2341 1.668151 GCGAGTGGGAGTGTTGGTC 60.668 63.158 0.00 0.00 0.00 4.02
2190 2342 1.004918 CGAGTGGGAGTGTTGGTCC 60.005 63.158 0.00 0.00 0.00 4.46
2191 2343 1.472662 CGAGTGGGAGTGTTGGTCCT 61.473 60.000 0.00 0.00 34.16 3.85
2192 2344 0.765510 GAGTGGGAGTGTTGGTCCTT 59.234 55.000 0.00 0.00 34.16 3.36
2193 2345 0.474184 AGTGGGAGTGTTGGTCCTTG 59.526 55.000 0.00 0.00 34.16 3.61
2194 2346 0.472471 GTGGGAGTGTTGGTCCTTGA 59.528 55.000 0.00 0.00 34.16 3.02
2195 2347 0.764890 TGGGAGTGTTGGTCCTTGAG 59.235 55.000 0.00 0.00 34.16 3.02
2247 2399 0.541863 AGAGGTTCGGCGAAATGGAT 59.458 50.000 25.48 8.41 0.00 3.41
2571 4280 3.320129 ACAACTAACCACCAGGGACTAA 58.680 45.455 0.00 0.00 41.15 2.24
2573 4282 4.166531 ACAACTAACCACCAGGGACTAAAA 59.833 41.667 0.00 0.00 41.15 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.143925 CCTCGCTTTTCGTTCTTTCCT 58.856 47.619 0.00 0.00 39.67 3.36
3 4 2.143925 CTCCCTCGCTTTTCGTTCTTT 58.856 47.619 0.00 0.00 39.67 2.52
4 5 1.608283 CCTCCCTCGCTTTTCGTTCTT 60.608 52.381 0.00 0.00 39.67 2.52
5 6 0.037232 CCTCCCTCGCTTTTCGTTCT 60.037 55.000 0.00 0.00 39.67 3.01
6 7 1.636570 GCCTCCCTCGCTTTTCGTTC 61.637 60.000 0.00 0.00 39.67 3.95
7 8 1.671379 GCCTCCCTCGCTTTTCGTT 60.671 57.895 0.00 0.00 39.67 3.85
8 9 2.047179 GCCTCCCTCGCTTTTCGT 60.047 61.111 0.00 0.00 39.67 3.85
9 10 3.188786 CGCCTCCCTCGCTTTTCG 61.189 66.667 0.00 0.00 40.15 3.46
10 11 1.362406 CTTCGCCTCCCTCGCTTTTC 61.362 60.000 0.00 0.00 0.00 2.29
11 12 1.376037 CTTCGCCTCCCTCGCTTTT 60.376 57.895 0.00 0.00 0.00 2.27
12 13 2.266055 CTTCGCCTCCCTCGCTTT 59.734 61.111 0.00 0.00 0.00 3.51
13 14 3.775654 CCTTCGCCTCCCTCGCTT 61.776 66.667 0.00 0.00 0.00 4.68
15 16 4.516195 GACCTTCGCCTCCCTCGC 62.516 72.222 0.00 0.00 0.00 5.03
16 17 4.194720 CGACCTTCGCCTCCCTCG 62.195 72.222 0.00 0.00 31.14 4.63
25 26 4.680237 TGGGTGCTGCGACCTTCG 62.680 66.667 16.88 0.00 43.89 3.79
26 27 3.050275 GTGGGTGCTGCGACCTTC 61.050 66.667 16.88 9.37 36.14 3.46
27 28 3.196207 ATGTGGGTGCTGCGACCTT 62.196 57.895 16.88 1.07 36.14 3.50
28 29 3.640407 ATGTGGGTGCTGCGACCT 61.640 61.111 16.88 0.04 36.14 3.85
29 30 3.434319 CATGTGGGTGCTGCGACC 61.434 66.667 11.32 11.32 34.96 4.79
30 31 3.434319 CCATGTGGGTGCTGCGAC 61.434 66.667 0.00 0.00 0.00 5.19
34 35 4.682334 TGGGCCATGTGGGTGCTG 62.682 66.667 0.00 0.00 39.65 4.41
35 36 3.913445 TTGGGCCATGTGGGTGCT 61.913 61.111 7.26 0.00 39.65 4.40
36 37 3.694538 GTTGGGCCATGTGGGTGC 61.695 66.667 7.26 0.00 39.65 5.01
37 38 1.978617 GAGTTGGGCCATGTGGGTG 60.979 63.158 7.26 0.00 39.65 4.61
38 39 2.440599 GAGTTGGGCCATGTGGGT 59.559 61.111 7.26 0.00 39.65 4.51
39 40 2.362889 GGAGTTGGGCCATGTGGG 60.363 66.667 7.26 0.00 40.85 4.61
40 41 2.362889 GGGAGTTGGGCCATGTGG 60.363 66.667 7.26 0.00 38.53 4.17
41 42 1.077265 AAGGGAGTTGGGCCATGTG 59.923 57.895 7.26 0.00 0.00 3.21
42 43 1.077265 CAAGGGAGTTGGGCCATGT 59.923 57.895 7.26 0.00 31.82 3.21
43 44 2.353610 GCAAGGGAGTTGGGCCATG 61.354 63.158 7.26 0.94 36.56 3.66
44 45 2.037847 GCAAGGGAGTTGGGCCAT 59.962 61.111 7.26 0.00 36.56 4.40
45 46 3.080158 TTGCAAGGGAGTTGGGCCA 62.080 57.895 0.00 0.00 36.56 5.36
46 47 2.203625 TTGCAAGGGAGTTGGGCC 60.204 61.111 0.00 0.00 36.56 5.80
47 48 2.919494 CGTTGCAAGGGAGTTGGGC 61.919 63.158 11.31 0.00 36.56 5.36
48 49 2.919494 GCGTTGCAAGGGAGTTGGG 61.919 63.158 19.88 0.00 36.56 4.12
49 50 1.526575 ATGCGTTGCAAGGGAGTTGG 61.527 55.000 19.88 0.00 43.62 3.77
50 51 0.387622 CATGCGTTGCAAGGGAGTTG 60.388 55.000 19.88 10.09 43.62 3.16
51 52 1.959085 CATGCGTTGCAAGGGAGTT 59.041 52.632 19.88 1.14 43.62 3.01
52 53 3.672293 CATGCGTTGCAAGGGAGT 58.328 55.556 19.88 5.67 43.62 3.85
61 62 1.443194 GCAAGTGGAGCATGCGTTG 60.443 57.895 13.01 12.68 31.94 4.10
62 63 1.859427 CTGCAAGTGGAGCATGCGTT 61.859 55.000 13.01 0.00 44.01 4.84
63 64 2.281692 TGCAAGTGGAGCATGCGT 60.282 55.556 13.01 0.00 44.01 5.24
64 65 2.483745 CTGCAAGTGGAGCATGCG 59.516 61.111 13.01 0.00 44.01 4.73
70 71 3.060615 GCTGGGCTGCAAGTGGAG 61.061 66.667 0.50 0.00 35.30 3.86
71 72 4.666253 GGCTGGGCTGCAAGTGGA 62.666 66.667 0.50 0.00 35.30 4.02
73 74 4.980702 TGGGCTGGGCTGCAAGTG 62.981 66.667 0.50 0.00 35.30 3.16
74 75 4.673375 CTGGGCTGGGCTGCAAGT 62.673 66.667 0.50 0.00 35.30 3.16
75 76 3.873679 TTCTGGGCTGGGCTGCAAG 62.874 63.158 0.50 0.00 34.04 4.01
76 77 3.873679 CTTCTGGGCTGGGCTGCAA 62.874 63.158 0.50 0.00 34.04 4.08
77 78 4.355720 CTTCTGGGCTGGGCTGCA 62.356 66.667 0.50 0.00 34.04 4.41
78 79 1.987807 TATCTTCTGGGCTGGGCTGC 61.988 60.000 0.00 0.00 0.00 5.25
79 80 0.179034 GTATCTTCTGGGCTGGGCTG 60.179 60.000 0.00 0.00 0.00 4.85
80 81 0.327000 AGTATCTTCTGGGCTGGGCT 60.327 55.000 0.00 0.00 0.00 5.19
81 82 0.179034 CAGTATCTTCTGGGCTGGGC 60.179 60.000 0.00 0.00 0.00 5.36
82 83 1.415659 CTCAGTATCTTCTGGGCTGGG 59.584 57.143 0.00 0.00 36.25 4.45
83 84 2.102252 GTCTCAGTATCTTCTGGGCTGG 59.898 54.545 0.00 0.00 36.03 4.85
84 85 2.762887 TGTCTCAGTATCTTCTGGGCTG 59.237 50.000 0.00 0.00 36.03 4.85
85 86 3.030291 CTGTCTCAGTATCTTCTGGGCT 58.970 50.000 0.00 0.00 36.03 5.19
86 87 2.102252 CCTGTCTCAGTATCTTCTGGGC 59.898 54.545 0.00 0.00 36.03 5.36
87 88 3.383185 GTCCTGTCTCAGTATCTTCTGGG 59.617 52.174 0.00 0.00 37.28 4.45
88 89 4.019858 TGTCCTGTCTCAGTATCTTCTGG 58.980 47.826 0.00 0.00 36.25 3.86
89 90 4.097741 CCTGTCCTGTCTCAGTATCTTCTG 59.902 50.000 0.00 0.00 36.85 3.02
90 91 4.277476 CCTGTCCTGTCTCAGTATCTTCT 58.723 47.826 0.00 0.00 0.00 2.85
91 92 3.181480 GCCTGTCCTGTCTCAGTATCTTC 60.181 52.174 0.00 0.00 0.00 2.87
92 93 2.763448 GCCTGTCCTGTCTCAGTATCTT 59.237 50.000 0.00 0.00 0.00 2.40
93 94 2.024464 AGCCTGTCCTGTCTCAGTATCT 60.024 50.000 0.00 0.00 0.00 1.98
94 95 2.383855 AGCCTGTCCTGTCTCAGTATC 58.616 52.381 0.00 0.00 0.00 2.24
95 96 2.499289 CAAGCCTGTCCTGTCTCAGTAT 59.501 50.000 0.00 0.00 0.00 2.12
96 97 1.895798 CAAGCCTGTCCTGTCTCAGTA 59.104 52.381 0.00 0.00 0.00 2.74
97 98 0.683973 CAAGCCTGTCCTGTCTCAGT 59.316 55.000 0.00 0.00 0.00 3.41
98 99 0.036577 CCAAGCCTGTCCTGTCTCAG 60.037 60.000 0.00 0.00 0.00 3.35
99 100 0.471780 TCCAAGCCTGTCCTGTCTCA 60.472 55.000 0.00 0.00 0.00 3.27
100 101 0.908198 ATCCAAGCCTGTCCTGTCTC 59.092 55.000 0.00 0.00 0.00 3.36
101 102 0.617413 CATCCAAGCCTGTCCTGTCT 59.383 55.000 0.00 0.00 0.00 3.41
102 103 0.393537 CCATCCAAGCCTGTCCTGTC 60.394 60.000 0.00 0.00 0.00 3.51
103 104 1.687612 CCATCCAAGCCTGTCCTGT 59.312 57.895 0.00 0.00 0.00 4.00
104 105 1.077212 CCCATCCAAGCCTGTCCTG 60.077 63.158 0.00 0.00 0.00 3.86
105 106 2.988839 GCCCATCCAAGCCTGTCCT 61.989 63.158 0.00 0.00 0.00 3.85
106 107 2.440980 GCCCATCCAAGCCTGTCC 60.441 66.667 0.00 0.00 0.00 4.02
107 108 1.452833 GAGCCCATCCAAGCCTGTC 60.453 63.158 0.00 0.00 0.00 3.51
108 109 2.207501 CTGAGCCCATCCAAGCCTGT 62.208 60.000 0.00 0.00 0.00 4.00
109 110 1.453379 CTGAGCCCATCCAAGCCTG 60.453 63.158 0.00 0.00 0.00 4.85
110 111 2.687610 CCTGAGCCCATCCAAGCCT 61.688 63.158 0.00 0.00 0.00 4.58
111 112 2.123982 CCTGAGCCCATCCAAGCC 60.124 66.667 0.00 0.00 0.00 4.35
112 113 2.832201 GCCTGAGCCCATCCAAGC 60.832 66.667 0.00 0.00 0.00 4.01
128 129 1.657751 GAGGATTTTGGACGGCAGGC 61.658 60.000 0.00 0.00 0.00 4.85
129 130 0.322456 TGAGGATTTTGGACGGCAGG 60.322 55.000 0.00 0.00 0.00 4.85
130 131 1.672881 GATGAGGATTTTGGACGGCAG 59.327 52.381 0.00 0.00 0.00 4.85
131 132 1.004161 TGATGAGGATTTTGGACGGCA 59.996 47.619 0.00 0.00 0.00 5.69
132 133 1.672881 CTGATGAGGATTTTGGACGGC 59.327 52.381 0.00 0.00 0.00 5.68
133 134 2.679837 CACTGATGAGGATTTTGGACGG 59.320 50.000 0.00 0.00 0.00 4.79
134 135 2.096496 GCACTGATGAGGATTTTGGACG 59.904 50.000 0.00 0.00 0.00 4.79
135 136 3.084039 TGCACTGATGAGGATTTTGGAC 58.916 45.455 0.00 0.00 0.00 4.02
136 137 3.349927 CTGCACTGATGAGGATTTTGGA 58.650 45.455 0.00 0.00 0.00 3.53
137 138 2.159282 GCTGCACTGATGAGGATTTTGG 60.159 50.000 0.00 0.00 0.00 3.28
138 139 2.159282 GGCTGCACTGATGAGGATTTTG 60.159 50.000 0.50 0.00 0.00 2.44
139 140 2.097825 GGCTGCACTGATGAGGATTTT 58.902 47.619 0.50 0.00 0.00 1.82
140 141 1.284198 AGGCTGCACTGATGAGGATTT 59.716 47.619 0.50 0.00 0.00 2.17
141 142 0.917533 AGGCTGCACTGATGAGGATT 59.082 50.000 0.50 0.00 0.00 3.01
142 143 1.693062 CTAGGCTGCACTGATGAGGAT 59.307 52.381 0.50 0.00 0.00 3.24
143 144 1.117994 CTAGGCTGCACTGATGAGGA 58.882 55.000 0.50 0.00 0.00 3.71
144 145 0.532417 GCTAGGCTGCACTGATGAGG 60.532 60.000 0.50 0.00 0.00 3.86
172 173 1.976132 GCTGAGCAGATGGGCCTGTA 61.976 60.000 4.53 0.00 36.57 2.74
654 688 9.859427 TTGAATGACAATCTATGAACCAAAATC 57.141 29.630 0.00 0.00 33.18 2.17
703 737 9.596308 TTCCCAGATTACTACTATAAGCATGTA 57.404 33.333 0.00 0.00 0.00 2.29
704 738 8.492415 TTCCCAGATTACTACTATAAGCATGT 57.508 34.615 0.00 0.00 0.00 3.21
705 739 9.950496 AATTCCCAGATTACTACTATAAGCATG 57.050 33.333 0.00 0.00 0.00 4.06
760 796 6.374333 TCAGTTGAGCAAAATACCTGTTATCC 59.626 38.462 0.00 0.00 0.00 2.59
769 805 9.860898 AAAATTAGGATCAGTTGAGCAAAATAC 57.139 29.630 0.00 0.00 30.87 1.89
885 923 5.728637 AAAGCAATTTTCTCCTAACCCTG 57.271 39.130 0.00 0.00 0.00 4.45
913 952 5.391523 CGAATCCAGAACGAAAATGCCTTAA 60.392 40.000 0.00 0.00 0.00 1.85
915 954 3.119849 CGAATCCAGAACGAAAATGCCTT 60.120 43.478 0.00 0.00 0.00 4.35
916 955 2.420022 CGAATCCAGAACGAAAATGCCT 59.580 45.455 0.00 0.00 0.00 4.75
917 956 2.785679 CGAATCCAGAACGAAAATGCC 58.214 47.619 0.00 0.00 0.00 4.40
918 957 2.177173 GCGAATCCAGAACGAAAATGC 58.823 47.619 0.00 0.00 0.00 3.56
926 1007 0.811616 ATCAGCGGCGAATCCAGAAC 60.812 55.000 12.98 0.00 34.01 3.01
939 1020 6.634805 AGACCAAGATATAATGGTATCAGCG 58.365 40.000 10.98 0.00 34.27 5.18
947 1028 4.021104 TCGCTGGAGACCAAGATATAATGG 60.021 45.833 5.00 5.00 30.80 3.16
1028 1112 1.177401 GAAAGGCAGGAACATGGACC 58.823 55.000 0.00 0.00 0.00 4.46
1086 1173 4.680237 CAGCGCCGGAAGACCACA 62.680 66.667 5.05 0.00 35.59 4.17
1278 1365 1.005569 AGGTAGTGGATGAGGTCGACA 59.994 52.381 18.91 0.00 37.96 4.35
1408 1495 4.069232 CTCGGCGAGCACCTCCAA 62.069 66.667 25.31 0.00 0.00 3.53
1508 1595 0.038892 GTAGAACGGGAGCGACAACA 60.039 55.000 0.00 0.00 0.00 3.33
1510 1597 1.588082 GGTAGAACGGGAGCGACAA 59.412 57.895 0.00 0.00 0.00 3.18
1721 1817 4.281688 CCCATCATTGTTCCTTCTTGTTGT 59.718 41.667 0.00 0.00 0.00 3.32
1760 1856 7.524698 GCAAACCAAACACCCTATGAGAAAATA 60.525 37.037 0.00 0.00 0.00 1.40
2008 2115 7.732222 ACACCAATAACCATAAACATCCATT 57.268 32.000 0.00 0.00 0.00 3.16
2009 2116 8.058847 AGTACACCAATAACCATAAACATCCAT 58.941 33.333 0.00 0.00 0.00 3.41
2010 2117 7.406916 AGTACACCAATAACCATAAACATCCA 58.593 34.615 0.00 0.00 0.00 3.41
2011 2118 7.875327 AGTACACCAATAACCATAAACATCC 57.125 36.000 0.00 0.00 0.00 3.51
2018 2125 7.340743 CCCAAATCAAGTACACCAATAACCATA 59.659 37.037 0.00 0.00 0.00 2.74
2068 2177 3.824443 TCGAGATCGGCTATATCAAACCA 59.176 43.478 1.91 0.00 40.29 3.67
2077 2186 2.163815 CCCGTTATTCGAGATCGGCTAT 59.836 50.000 11.49 0.00 42.86 2.97
2108 2217 6.940298 ACTCCTGTTATCCGAGATTTCAAAAA 59.060 34.615 0.00 0.00 0.00 1.94
2109 2218 6.472887 ACTCCTGTTATCCGAGATTTCAAAA 58.527 36.000 0.00 0.00 0.00 2.44
2110 2219 6.049955 ACTCCTGTTATCCGAGATTTCAAA 57.950 37.500 0.00 0.00 0.00 2.69
2111 2220 5.677319 ACTCCTGTTATCCGAGATTTCAA 57.323 39.130 0.00 0.00 0.00 2.69
2112 2221 5.677319 AACTCCTGTTATCCGAGATTTCA 57.323 39.130 0.00 0.00 34.15 2.69
2113 2222 7.040473 TCTAACTCCTGTTATCCGAGATTTC 57.960 40.000 0.00 0.00 37.92 2.17
2115 2224 7.604657 AATCTAACTCCTGTTATCCGAGATT 57.395 36.000 0.00 0.00 37.92 2.40
2247 2399 3.557054 CGACTGGGATTTTGACTTGAGGA 60.557 47.826 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.