Multiple sequence alignment - TraesCS7B01G011100

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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 TraesCS7B01G011100 chr7B 100.000 2897 0 0 1 2897 7029959 7032855 0.000000e+00 5350
1 TraesCS7B01G011100 chr7B 88.277 1544 114 16 710 2230 7349859 7351358 0.000000e+00 1786
2 TraesCS7B01G011100 chr7B 94.313 844 48 0 1232 2075 6864556 6863713 0.000000e+00 1293
3 TraesCS7B01G011100 chr7B 90.977 532 40 4 741 1271 7311802 7311278 0.000000e+00 710
4 TraesCS7B01G011100 chr7B 88.010 392 17 6 1705 2066 7054044 7054435 1.230000e-118 436
5 TraesCS7B01G011100 chr7B 84.673 398 33 15 316 695 7312185 7311798 3.530000e-99 372
6 TraesCS7B01G011100 chr7B 82.072 251 24 13 450 696 7349643 7349876 8.190000e-46 195
7 TraesCS7B01G011100 chr7D 94.689 2071 87 9 828 2896 65442180 65440131 0.000000e+00 3193
8 TraesCS7B01G011100 chr7D 88.154 1815 149 29 524 2303 65449255 65447472 0.000000e+00 2100
9 TraesCS7B01G011100 chr7D 87.326 1436 146 14 746 2154 65621801 65623227 0.000000e+00 1611
10 TraesCS7B01G011100 chr7D 78.788 660 99 28 2246 2893 65623974 65624604 3.480000e-109 405
11 TraesCS7B01G011100 chr7A 89.010 1556 121 17 709 2227 69956667 69958209 0.000000e+00 1881
12 TraesCS7B01G011100 chr7A 85.024 1489 163 30 739 2195 69557362 69555902 0.000000e+00 1459
13 TraesCS7B01G011100 chr7A 95.229 545 23 2 2356 2897 69629273 69628729 0.000000e+00 859
14 TraesCS7B01G011100 chr7A 81.841 391 41 12 310 696 69956321 69956685 4.690000e-78 302
15 TraesCS7B01G011100 chr2D 83.759 1213 161 23 712 1904 574448333 574447137 0.000000e+00 1116
16 TraesCS7B01G011100 chr2B 88.526 889 102 0 1016 1904 690683072 690682184 0.000000e+00 1077


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 TraesCS7B01G011100 chr7B 7029959 7032855 2896 False 5350.0 5350 100.0000 1 2897 1 chr7B.!!$F1 2896
1 TraesCS7B01G011100 chr7B 6863713 6864556 843 True 1293.0 1293 94.3130 1232 2075 1 chr7B.!!$R1 843
2 TraesCS7B01G011100 chr7B 7349643 7351358 1715 False 990.5 1786 85.1745 450 2230 2 chr7B.!!$F3 1780
3 TraesCS7B01G011100 chr7B 7311278 7312185 907 True 541.0 710 87.8250 316 1271 2 chr7B.!!$R2 955
4 TraesCS7B01G011100 chr7D 65440131 65442180 2049 True 3193.0 3193 94.6890 828 2896 1 chr7D.!!$R1 2068
5 TraesCS7B01G011100 chr7D 65447472 65449255 1783 True 2100.0 2100 88.1540 524 2303 1 chr7D.!!$R2 1779
6 TraesCS7B01G011100 chr7D 65621801 65624604 2803 False 1008.0 1611 83.0570 746 2893 2 chr7D.!!$F1 2147
7 TraesCS7B01G011100 chr7A 69555902 69557362 1460 True 1459.0 1459 85.0240 739 2195 1 chr7A.!!$R1 1456
8 TraesCS7B01G011100 chr7A 69956321 69958209 1888 False 1091.5 1881 85.4255 310 2227 2 chr7A.!!$F1 1917
9 TraesCS7B01G011100 chr7A 69628729 69629273 544 True 859.0 859 95.2290 2356 2897 1 chr7A.!!$R2 541
10 TraesCS7B01G011100 chr2D 574447137 574448333 1196 True 1116.0 1116 83.7590 712 1904 1 chr2D.!!$R1 1192
11 TraesCS7B01G011100 chr2B 690682184 690683072 888 True 1077.0 1077 88.5260 1016 1904 1 chr2B.!!$R1 888

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
92 93 0.030638 GTGTGGGTTGTGTGACATGC 59.969 55.0 0.00 0.00 0.00 4.06 F
96 97 0.031994 GGGTTGTGTGACATGCCAAC 59.968 55.0 8.52 8.52 37.14 3.77 F
468 479 0.385751 TCGCTGAGCCATAGCAGTAC 59.614 55.0 0.00 0.00 43.56 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1245 1361 0.108329 CGGAGGTTAGGTTCGTGCAT 60.108 55.0 0.0 0.00 0.00 3.96 R
1667 1783 1.565305 CTTCCATGCGTCAGCTAGAC 58.435 55.0 0.0 6.31 45.42 2.59 R
2396 3204 2.159627 GCAGTATGTTCCACAAAGTCCG 59.840 50.0 0.0 0.00 39.31 4.79 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
26 27 9.638176 AAATATGAAAACTGCTAGAAGATGGAT 57.362 29.630 4.16 0.00 0.00 3.41
27 28 6.939132 ATGAAAACTGCTAGAAGATGGATG 57.061 37.500 4.16 0.00 0.00 3.51
28 29 6.053632 TGAAAACTGCTAGAAGATGGATGA 57.946 37.500 4.16 0.00 0.00 2.92
29 30 6.475504 TGAAAACTGCTAGAAGATGGATGAA 58.524 36.000 4.16 0.00 0.00 2.57
30 31 6.942005 TGAAAACTGCTAGAAGATGGATGAAA 59.058 34.615 4.16 0.00 0.00 2.69
31 32 7.613022 TGAAAACTGCTAGAAGATGGATGAAAT 59.387 33.333 4.16 0.00 0.00 2.17
32 33 6.939132 AACTGCTAGAAGATGGATGAAATG 57.061 37.500 4.16 0.00 0.00 2.32
33 34 5.374921 ACTGCTAGAAGATGGATGAAATGG 58.625 41.667 4.16 0.00 0.00 3.16
34 35 5.131642 ACTGCTAGAAGATGGATGAAATGGA 59.868 40.000 4.16 0.00 0.00 3.41
35 36 6.183361 ACTGCTAGAAGATGGATGAAATGGAT 60.183 38.462 4.16 0.00 0.00 3.41
36 37 6.607970 TGCTAGAAGATGGATGAAATGGATT 58.392 36.000 0.00 0.00 0.00 3.01
37 38 7.748677 TGCTAGAAGATGGATGAAATGGATTA 58.251 34.615 0.00 0.00 0.00 1.75
38 39 8.219868 TGCTAGAAGATGGATGAAATGGATTAA 58.780 33.333 0.00 0.00 0.00 1.40
39 40 9.071276 GCTAGAAGATGGATGAAATGGATTAAA 57.929 33.333 0.00 0.00 0.00 1.52
42 43 9.705103 AGAAGATGGATGAAATGGATTAAAAGA 57.295 29.630 0.00 0.00 0.00 2.52
45 46 8.699130 AGATGGATGAAATGGATTAAAAGAACC 58.301 33.333 0.00 0.00 0.00 3.62
46 47 8.613922 ATGGATGAAATGGATTAAAAGAACCT 57.386 30.769 0.00 0.00 0.00 3.50
47 48 7.839907 TGGATGAAATGGATTAAAAGAACCTG 58.160 34.615 0.00 0.00 0.00 4.00
48 49 7.093377 TGGATGAAATGGATTAAAAGAACCTGG 60.093 37.037 0.00 0.00 0.00 4.45
49 50 6.036577 TGAAATGGATTAAAAGAACCTGGC 57.963 37.500 0.00 0.00 0.00 4.85
50 51 5.779771 TGAAATGGATTAAAAGAACCTGGCT 59.220 36.000 0.00 0.00 0.00 4.75
51 52 5.921962 AATGGATTAAAAGAACCTGGCTC 57.078 39.130 0.00 0.00 0.00 4.70
52 53 3.697166 TGGATTAAAAGAACCTGGCTCC 58.303 45.455 0.00 0.00 0.00 4.70
53 54 3.075283 TGGATTAAAAGAACCTGGCTCCA 59.925 43.478 0.00 0.00 0.00 3.86
54 55 4.264352 TGGATTAAAAGAACCTGGCTCCAT 60.264 41.667 0.00 0.00 0.00 3.41
55 56 4.098501 GGATTAAAAGAACCTGGCTCCATG 59.901 45.833 0.00 0.00 0.00 3.66
56 57 1.928868 AAAAGAACCTGGCTCCATGG 58.071 50.000 4.97 4.97 0.00 3.66
57 58 0.040204 AAAGAACCTGGCTCCATGGG 59.960 55.000 13.02 3.69 0.00 4.00
58 59 2.440980 GAACCTGGCTCCATGGGC 60.441 66.667 13.02 14.08 0.00 5.36
73 74 4.681978 GGCCGGCCCATAGTAGCG 62.682 72.222 36.64 0.00 0.00 4.26
74 75 3.925090 GCCGGCCCATAGTAGCGT 61.925 66.667 18.11 0.00 0.00 5.07
75 76 2.029073 CCGGCCCATAGTAGCGTG 59.971 66.667 0.00 0.00 0.00 5.34
76 77 2.792947 CCGGCCCATAGTAGCGTGT 61.793 63.158 0.00 0.00 0.00 4.49
77 78 1.591594 CGGCCCATAGTAGCGTGTG 60.592 63.158 0.00 0.00 0.00 3.82
78 79 1.227556 GGCCCATAGTAGCGTGTGG 60.228 63.158 0.00 0.00 0.00 4.17
80 81 2.208527 CCCATAGTAGCGTGTGGGT 58.791 57.895 9.54 0.00 45.04 4.51
81 82 0.539986 CCCATAGTAGCGTGTGGGTT 59.460 55.000 9.54 0.00 45.04 4.11
82 83 1.651987 CCATAGTAGCGTGTGGGTTG 58.348 55.000 0.00 0.00 0.00 3.77
83 84 1.066430 CCATAGTAGCGTGTGGGTTGT 60.066 52.381 0.00 0.00 0.00 3.32
84 85 1.999735 CATAGTAGCGTGTGGGTTGTG 59.000 52.381 0.00 0.00 0.00 3.33
85 86 1.042229 TAGTAGCGTGTGGGTTGTGT 58.958 50.000 0.00 0.00 0.00 3.72
86 87 0.531974 AGTAGCGTGTGGGTTGTGTG 60.532 55.000 0.00 0.00 0.00 3.82
87 88 0.531090 GTAGCGTGTGGGTTGTGTGA 60.531 55.000 0.00 0.00 0.00 3.58
88 89 0.531090 TAGCGTGTGGGTTGTGTGAC 60.531 55.000 0.00 0.00 0.00 3.67
89 90 2.109739 GCGTGTGGGTTGTGTGACA 61.110 57.895 0.00 0.00 0.00 3.58
90 91 1.444119 GCGTGTGGGTTGTGTGACAT 61.444 55.000 0.00 0.00 0.00 3.06
91 92 0.307453 CGTGTGGGTTGTGTGACATG 59.693 55.000 0.00 0.00 0.00 3.21
92 93 0.030638 GTGTGGGTTGTGTGACATGC 59.969 55.000 0.00 0.00 0.00 4.06
93 94 1.106351 TGTGGGTTGTGTGACATGCC 61.106 55.000 0.00 0.00 0.00 4.40
94 95 1.106351 GTGGGTTGTGTGACATGCCA 61.106 55.000 0.00 0.00 0.00 4.92
95 96 0.396278 TGGGTTGTGTGACATGCCAA 60.396 50.000 0.00 0.00 0.00 4.52
96 97 0.031994 GGGTTGTGTGACATGCCAAC 59.968 55.000 8.52 8.52 37.14 3.77
97 98 0.743688 GGTTGTGTGACATGCCAACA 59.256 50.000 16.13 4.12 39.08 3.33
98 99 1.340889 GGTTGTGTGACATGCCAACAT 59.659 47.619 16.13 0.00 39.08 2.71
99 100 2.607771 GGTTGTGTGACATGCCAACATC 60.608 50.000 16.13 0.82 39.08 3.06
100 101 2.275134 TGTGTGACATGCCAACATCT 57.725 45.000 0.00 0.00 32.87 2.90
101 102 2.585330 TGTGTGACATGCCAACATCTT 58.415 42.857 0.00 0.00 32.87 2.40
102 103 2.293955 TGTGTGACATGCCAACATCTTG 59.706 45.455 0.00 0.00 32.87 3.02
103 104 2.294233 GTGTGACATGCCAACATCTTGT 59.706 45.455 0.00 0.00 32.87 3.16
104 105 2.553602 TGTGACATGCCAACATCTTGTC 59.446 45.455 0.00 0.00 38.40 3.18
105 106 1.805943 TGACATGCCAACATCTTGTCG 59.194 47.619 0.00 0.00 39.82 4.35
106 107 0.523072 ACATGCCAACATCTTGTCGC 59.477 50.000 0.00 0.00 32.87 5.19
107 108 0.522626 CATGCCAACATCTTGTCGCA 59.477 50.000 5.24 5.24 39.05 5.10
108 109 1.133598 CATGCCAACATCTTGTCGCAT 59.866 47.619 8.52 8.52 42.99 4.73
109 110 2.106477 TGCCAACATCTTGTCGCATA 57.894 45.000 0.00 0.00 32.73 3.14
110 111 2.431454 TGCCAACATCTTGTCGCATAA 58.569 42.857 0.00 0.00 32.73 1.90
111 112 2.419673 TGCCAACATCTTGTCGCATAAG 59.580 45.455 0.00 0.00 32.73 1.73
112 113 2.792542 GCCAACATCTTGTCGCATAAGC 60.793 50.000 0.00 0.00 37.42 3.09
113 114 2.419673 CCAACATCTTGTCGCATAAGCA 59.580 45.455 0.00 0.00 42.27 3.91
114 115 3.119884 CCAACATCTTGTCGCATAAGCAA 60.120 43.478 0.00 0.00 42.27 3.91
115 116 3.747099 ACATCTTGTCGCATAAGCAAC 57.253 42.857 0.00 0.00 42.27 4.17
116 117 3.073678 ACATCTTGTCGCATAAGCAACA 58.926 40.909 0.00 0.00 42.27 3.33
117 118 3.501828 ACATCTTGTCGCATAAGCAACAA 59.498 39.130 0.00 0.00 44.82 2.83
118 119 4.023279 ACATCTTGTCGCATAAGCAACAAA 60.023 37.500 0.00 0.00 46.11 2.83
119 120 4.145876 TCTTGTCGCATAAGCAACAAAG 57.854 40.909 0.00 0.00 46.11 2.77
120 121 2.330231 TGTCGCATAAGCAACAAAGC 57.670 45.000 0.00 0.00 34.10 3.51
121 122 1.250476 GTCGCATAAGCAACAAAGCG 58.750 50.000 0.00 0.00 45.79 4.68
122 123 5.139046 TTGTCGCATAAGCAACAAAGCGA 62.139 43.478 3.00 3.00 44.12 4.93
126 127 4.908966 GCATAAGCAACAAAGCGAAATT 57.091 36.364 0.00 0.00 41.58 1.82
127 128 5.268107 GCATAAGCAACAAAGCGAAATTT 57.732 34.783 0.00 0.00 41.58 1.82
128 129 6.388259 GCATAAGCAACAAAGCGAAATTTA 57.612 33.333 0.00 0.00 41.58 1.40
129 130 6.233500 GCATAAGCAACAAAGCGAAATTTAC 58.766 36.000 0.00 0.00 41.58 2.01
130 131 6.669741 GCATAAGCAACAAAGCGAAATTTACC 60.670 38.462 0.00 0.00 41.58 2.85
131 132 4.584327 AGCAACAAAGCGAAATTTACCT 57.416 36.364 0.00 0.00 40.15 3.08
132 133 4.944048 AGCAACAAAGCGAAATTTACCTT 58.056 34.783 0.00 0.00 40.15 3.50
133 134 5.356426 AGCAACAAAGCGAAATTTACCTTT 58.644 33.333 8.83 8.83 40.15 3.11
134 135 6.508777 AGCAACAAAGCGAAATTTACCTTTA 58.491 32.000 12.55 0.00 40.15 1.85
135 136 6.640907 AGCAACAAAGCGAAATTTACCTTTAG 59.359 34.615 12.55 10.46 40.15 1.85
136 137 6.419710 GCAACAAAGCGAAATTTACCTTTAGT 59.580 34.615 12.55 10.88 0.00 2.24
137 138 7.042992 GCAACAAAGCGAAATTTACCTTTAGTT 60.043 33.333 12.55 14.23 0.00 2.24
138 139 8.813282 CAACAAAGCGAAATTTACCTTTAGTTT 58.187 29.630 12.55 6.58 0.00 2.66
139 140 8.570096 ACAAAGCGAAATTTACCTTTAGTTTC 57.430 30.769 12.55 0.00 0.00 2.78
140 141 8.410912 ACAAAGCGAAATTTACCTTTAGTTTCT 58.589 29.630 12.55 0.00 0.00 2.52
141 142 9.887406 CAAAGCGAAATTTACCTTTAGTTTCTA 57.113 29.630 12.55 0.00 0.00 2.10
297 298 9.859427 TGATGATTTTTGATGTGGTAAGAAATC 57.141 29.630 0.00 0.00 34.37 2.17
298 299 9.305925 GATGATTTTTGATGTGGTAAGAAATCC 57.694 33.333 0.00 0.00 33.39 3.01
299 300 8.187913 TGATTTTTGATGTGGTAAGAAATCCA 57.812 30.769 0.00 0.00 33.39 3.41
300 301 8.646004 TGATTTTTGATGTGGTAAGAAATCCAA 58.354 29.630 0.00 0.00 35.38 3.53
301 302 9.487790 GATTTTTGATGTGGTAAGAAATCCAAA 57.512 29.630 0.00 0.00 35.38 3.28
302 303 8.655651 TTTTTGATGTGGTAAGAAATCCAAAC 57.344 30.769 0.00 0.00 35.38 2.93
303 304 6.968263 TTGATGTGGTAAGAAATCCAAACA 57.032 33.333 0.00 0.00 35.38 2.83
304 305 6.968263 TGATGTGGTAAGAAATCCAAACAA 57.032 33.333 0.00 0.00 35.38 2.83
305 306 6.744112 TGATGTGGTAAGAAATCCAAACAAC 58.256 36.000 0.00 0.00 35.38 3.32
306 307 6.549364 TGATGTGGTAAGAAATCCAAACAACT 59.451 34.615 0.00 0.00 35.38 3.16
307 308 7.721842 TGATGTGGTAAGAAATCCAAACAACTA 59.278 33.333 0.00 0.00 35.38 2.24
308 309 7.883391 TGTGGTAAGAAATCCAAACAACTAA 57.117 32.000 0.00 0.00 35.38 2.24
309 310 8.294954 TGTGGTAAGAAATCCAAACAACTAAA 57.705 30.769 0.00 0.00 35.38 1.85
310 311 8.750298 TGTGGTAAGAAATCCAAACAACTAAAA 58.250 29.630 0.00 0.00 35.38 1.52
311 312 9.589111 GTGGTAAGAAATCCAAACAACTAAAAA 57.411 29.630 0.00 0.00 35.38 1.94
375 379 7.125113 ACGCACAAATTTTAAAAATCTTGCTG 58.875 30.769 18.20 15.16 0.00 4.41
440 451 1.589414 CCTTCTTCCCCCTGTCTCAT 58.411 55.000 0.00 0.00 0.00 2.90
468 479 0.385751 TCGCTGAGCCATAGCAGTAC 59.614 55.000 0.00 0.00 43.56 2.73
485 499 1.134560 GTACAGCACCTACGCTAGCTT 59.865 52.381 13.93 5.97 41.38 3.74
695 728 5.677178 CGTTCAAGCAGTACAAAGAAAACTC 59.323 40.000 0.00 0.00 0.00 3.01
696 729 6.551736 GTTCAAGCAGTACAAAGAAAACTCA 58.448 36.000 0.00 0.00 0.00 3.41
701 734 7.801716 AGCAGTACAAAGAAAACTCATGTTA 57.198 32.000 0.00 0.00 34.96 2.41
794 828 2.001812 TGATTCGAAGCTGAGAGCAC 57.998 50.000 15.31 0.00 45.56 4.40
818 862 2.032550 GGCATTCTCATGTGTTCATCCG 59.967 50.000 0.00 0.00 32.28 4.18
822 866 1.899142 TCTCATGTGTTCATCCGTCCA 59.101 47.619 0.00 0.00 31.15 4.02
823 867 2.501316 TCTCATGTGTTCATCCGTCCAT 59.499 45.455 0.00 0.00 31.15 3.41
824 868 2.610833 CTCATGTGTTCATCCGTCCATG 59.389 50.000 0.00 0.00 31.15 3.66
825 869 2.027285 TCATGTGTTCATCCGTCCATGT 60.027 45.455 0.00 0.00 33.27 3.21
826 870 1.807139 TGTGTTCATCCGTCCATGTG 58.193 50.000 0.00 0.00 0.00 3.21
900 958 2.773993 TTTCACATTACGAGTCCCCC 57.226 50.000 0.00 0.00 0.00 5.40
949 1007 5.678583 CCCAAACTCAGATCATCATACACT 58.321 41.667 0.00 0.00 0.00 3.55
988 1092 3.685550 GCATACACAGAAGCAATAGGGGT 60.686 47.826 0.00 0.00 0.00 4.95
1005 1121 1.202746 GGGTTTGCTCCAAAAATGGCA 60.203 47.619 0.00 0.00 35.03 4.92
1023 1139 1.627329 GCAGGCAGATCATCATCCCTA 59.373 52.381 0.00 0.00 0.00 3.53
1159 1275 3.371591 CGCTACCGGCAACTACAAATTTA 59.628 43.478 0.00 0.00 41.91 1.40
1215 1331 2.750350 CCGCCAGTCCTCAACCTT 59.250 61.111 0.00 0.00 0.00 3.50
1259 1375 1.084289 GGTGGATGCACGAACCTAAC 58.916 55.000 11.52 0.00 0.00 2.34
1667 1783 6.651643 CAGTATACCTCAGGTAGCACTACTAG 59.348 46.154 16.95 8.22 41.83 2.57
1878 1994 2.911484 CAGGATGGCTACAGTTCTTCC 58.089 52.381 0.00 0.00 0.00 3.46
1923 2039 5.537295 GGGTTACCTTACCTTTGATTTGTGT 59.463 40.000 0.00 0.00 38.30 3.72
2061 2209 3.762407 TCATTCAGAACGAGGAAACCA 57.238 42.857 0.00 0.00 0.00 3.67
2396 3204 6.945938 TCTTCTGCTCTACTCCTAACATAC 57.054 41.667 0.00 0.00 0.00 2.39
2574 3382 1.134098 CCTAAGCACCCATTGGTCGAT 60.134 52.381 1.20 0.00 45.57 3.59
2601 3409 4.391830 GTGTGTCCATGTAGGTATTGTGTG 59.608 45.833 0.00 0.00 39.02 3.82
2678 3486 8.087750 TGTGGCAAAATGGAAAATAGTTTCTAG 58.912 33.333 14.68 0.00 42.45 2.43
2721 3529 6.983474 AATAATTATGGCAGGTTGTTTTGC 57.017 33.333 0.00 0.00 39.56 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.795047 TCATCCATCTTCTAGCAGTTTTCATA 58.205 34.615 0.00 0.00 0.00 2.15
4 5 6.656902 TCATCCATCTTCTAGCAGTTTTCAT 58.343 36.000 0.00 0.00 0.00 2.57
6 7 6.992063 TTCATCCATCTTCTAGCAGTTTTC 57.008 37.500 0.00 0.00 0.00 2.29
7 8 7.147949 CCATTTCATCCATCTTCTAGCAGTTTT 60.148 37.037 0.00 0.00 0.00 2.43
8 9 6.320672 CCATTTCATCCATCTTCTAGCAGTTT 59.679 38.462 0.00 0.00 0.00 2.66
9 10 5.826737 CCATTTCATCCATCTTCTAGCAGTT 59.173 40.000 0.00 0.00 0.00 3.16
10 11 5.131642 TCCATTTCATCCATCTTCTAGCAGT 59.868 40.000 0.00 0.00 0.00 4.40
11 12 5.618236 TCCATTTCATCCATCTTCTAGCAG 58.382 41.667 0.00 0.00 0.00 4.24
12 13 5.635278 TCCATTTCATCCATCTTCTAGCA 57.365 39.130 0.00 0.00 0.00 3.49
13 14 8.627208 TTAATCCATTTCATCCATCTTCTAGC 57.373 34.615 0.00 0.00 0.00 3.42
16 17 9.705103 TCTTTTAATCCATTTCATCCATCTTCT 57.295 29.630 0.00 0.00 0.00 2.85
19 20 8.699130 GGTTCTTTTAATCCATTTCATCCATCT 58.301 33.333 0.00 0.00 0.00 2.90
20 21 8.699130 AGGTTCTTTTAATCCATTTCATCCATC 58.301 33.333 0.00 0.00 0.00 3.51
21 22 8.480501 CAGGTTCTTTTAATCCATTTCATCCAT 58.519 33.333 0.00 0.00 0.00 3.41
22 23 7.093377 CCAGGTTCTTTTAATCCATTTCATCCA 60.093 37.037 0.00 0.00 0.00 3.41
23 24 7.267857 CCAGGTTCTTTTAATCCATTTCATCC 58.732 38.462 0.00 0.00 0.00 3.51
24 25 6.758416 GCCAGGTTCTTTTAATCCATTTCATC 59.242 38.462 0.00 0.00 0.00 2.92
25 26 6.441604 AGCCAGGTTCTTTTAATCCATTTCAT 59.558 34.615 0.00 0.00 0.00 2.57
26 27 5.779771 AGCCAGGTTCTTTTAATCCATTTCA 59.220 36.000 0.00 0.00 0.00 2.69
27 28 6.286240 AGCCAGGTTCTTTTAATCCATTTC 57.714 37.500 0.00 0.00 0.00 2.17
28 29 5.187772 GGAGCCAGGTTCTTTTAATCCATTT 59.812 40.000 2.91 0.00 0.00 2.32
29 30 4.711846 GGAGCCAGGTTCTTTTAATCCATT 59.288 41.667 2.91 0.00 0.00 3.16
30 31 4.264352 TGGAGCCAGGTTCTTTTAATCCAT 60.264 41.667 2.91 0.00 29.63 3.41
31 32 3.075283 TGGAGCCAGGTTCTTTTAATCCA 59.925 43.478 2.91 0.00 32.10 3.41
32 33 3.697166 TGGAGCCAGGTTCTTTTAATCC 58.303 45.455 2.91 0.00 0.00 3.01
33 34 4.098501 CCATGGAGCCAGGTTCTTTTAATC 59.901 45.833 5.56 0.00 0.00 1.75
34 35 4.026052 CCATGGAGCCAGGTTCTTTTAAT 58.974 43.478 5.56 0.00 0.00 1.40
35 36 3.430453 CCATGGAGCCAGGTTCTTTTAA 58.570 45.455 5.56 0.00 0.00 1.52
36 37 2.291540 CCCATGGAGCCAGGTTCTTTTA 60.292 50.000 15.22 0.00 0.00 1.52
37 38 1.550869 CCCATGGAGCCAGGTTCTTTT 60.551 52.381 15.22 0.00 0.00 2.27
38 39 0.040204 CCCATGGAGCCAGGTTCTTT 59.960 55.000 15.22 0.00 0.00 2.52
39 40 1.693640 CCCATGGAGCCAGGTTCTT 59.306 57.895 15.22 0.00 0.00 2.52
40 41 2.988839 GCCCATGGAGCCAGGTTCT 61.989 63.158 15.22 0.00 0.00 3.01
41 42 2.440980 GCCCATGGAGCCAGGTTC 60.441 66.667 15.22 0.00 0.00 3.62
56 57 4.681978 CGCTACTATGGGCCGGCC 62.682 72.222 38.57 38.57 0.00 6.13
57 58 3.925090 ACGCTACTATGGGCCGGC 61.925 66.667 21.18 21.18 0.00 6.13
58 59 2.029073 CACGCTACTATGGGCCGG 59.971 66.667 0.00 0.00 0.00 6.13
59 60 1.591594 CACACGCTACTATGGGCCG 60.592 63.158 0.00 0.00 0.00 6.13
60 61 1.227556 CCACACGCTACTATGGGCC 60.228 63.158 0.00 0.00 0.00 5.80
61 62 1.227556 CCCACACGCTACTATGGGC 60.228 63.158 0.00 0.00 45.26 5.36
63 64 1.066430 ACAACCCACACGCTACTATGG 60.066 52.381 0.00 0.00 0.00 2.74
64 65 1.999735 CACAACCCACACGCTACTATG 59.000 52.381 0.00 0.00 0.00 2.23
65 66 1.621814 ACACAACCCACACGCTACTAT 59.378 47.619 0.00 0.00 0.00 2.12
66 67 1.042229 ACACAACCCACACGCTACTA 58.958 50.000 0.00 0.00 0.00 1.82
67 68 0.531974 CACACAACCCACACGCTACT 60.532 55.000 0.00 0.00 0.00 2.57
68 69 0.531090 TCACACAACCCACACGCTAC 60.531 55.000 0.00 0.00 0.00 3.58
69 70 0.531090 GTCACACAACCCACACGCTA 60.531 55.000 0.00 0.00 0.00 4.26
70 71 1.817941 GTCACACAACCCACACGCT 60.818 57.895 0.00 0.00 0.00 5.07
71 72 1.444119 ATGTCACACAACCCACACGC 61.444 55.000 0.00 0.00 0.00 5.34
72 73 0.307453 CATGTCACACAACCCACACG 59.693 55.000 0.00 0.00 0.00 4.49
73 74 0.030638 GCATGTCACACAACCCACAC 59.969 55.000 0.00 0.00 0.00 3.82
74 75 1.106351 GGCATGTCACACAACCCACA 61.106 55.000 0.00 0.00 0.00 4.17
75 76 1.106351 TGGCATGTCACACAACCCAC 61.106 55.000 0.00 0.00 30.63 4.61
76 77 0.396278 TTGGCATGTCACACAACCCA 60.396 50.000 0.00 0.00 32.74 4.51
77 78 0.031994 GTTGGCATGTCACACAACCC 59.968 55.000 0.00 0.00 37.75 4.11
78 79 0.743688 TGTTGGCATGTCACACAACC 59.256 50.000 0.00 0.00 41.74 3.77
79 80 2.294233 AGATGTTGGCATGTCACACAAC 59.706 45.455 15.78 13.75 42.51 3.32
80 81 2.585330 AGATGTTGGCATGTCACACAA 58.415 42.857 15.78 3.13 35.07 3.33
81 82 2.275134 AGATGTTGGCATGTCACACA 57.725 45.000 14.66 14.66 35.07 3.72
82 83 2.294233 ACAAGATGTTGGCATGTCACAC 59.706 45.455 0.00 2.46 38.07 3.82
83 84 2.553602 GACAAGATGTTGGCATGTCACA 59.446 45.455 0.00 1.88 41.96 3.58
84 85 2.413239 CGACAAGATGTTGGCATGTCAC 60.413 50.000 9.41 0.00 42.59 3.67
85 86 1.805943 CGACAAGATGTTGGCATGTCA 59.194 47.619 9.41 0.00 42.59 3.58
86 87 1.466360 GCGACAAGATGTTGGCATGTC 60.466 52.381 9.41 6.59 42.59 3.06
87 88 0.523072 GCGACAAGATGTTGGCATGT 59.477 50.000 9.41 0.00 42.59 3.21
88 89 0.522626 TGCGACAAGATGTTGGCATG 59.477 50.000 9.41 0.00 42.59 4.06
89 90 1.466856 ATGCGACAAGATGTTGGCAT 58.533 45.000 9.41 10.81 42.59 4.40
90 91 2.106477 TATGCGACAAGATGTTGGCA 57.894 45.000 9.41 8.93 42.59 4.92
91 92 2.792542 GCTTATGCGACAAGATGTTGGC 60.793 50.000 7.59 2.45 38.49 4.52
92 93 2.419673 TGCTTATGCGACAAGATGTTGG 59.580 45.455 7.59 0.00 43.34 3.77
93 94 3.745332 TGCTTATGCGACAAGATGTTG 57.255 42.857 0.13 0.13 43.34 3.33
103 104 3.674225 CGCTTTGTTGCTTATGCGA 57.326 47.368 0.00 0.00 45.15 5.10
104 105 1.962412 TTCGCTTTGTTGCTTATGCG 58.038 45.000 0.00 0.00 43.34 4.73
105 106 4.908966 AATTTCGCTTTGTTGCTTATGC 57.091 36.364 0.00 0.00 40.20 3.14
106 107 6.586082 AGGTAAATTTCGCTTTGTTGCTTATG 59.414 34.615 0.00 0.00 0.00 1.90
107 108 6.687604 AGGTAAATTTCGCTTTGTTGCTTAT 58.312 32.000 0.00 0.00 0.00 1.73
108 109 6.079424 AGGTAAATTTCGCTTTGTTGCTTA 57.921 33.333 0.00 0.00 0.00 3.09
109 110 4.944048 AGGTAAATTTCGCTTTGTTGCTT 58.056 34.783 0.00 0.00 0.00 3.91
110 111 4.584327 AGGTAAATTTCGCTTTGTTGCT 57.416 36.364 0.00 0.00 0.00 3.91
111 112 5.651172 AAAGGTAAATTTCGCTTTGTTGC 57.349 34.783 0.00 0.00 0.00 4.17
112 113 7.924103 ACTAAAGGTAAATTTCGCTTTGTTG 57.076 32.000 0.00 0.00 0.00 3.33
113 114 8.936070 AAACTAAAGGTAAATTTCGCTTTGTT 57.064 26.923 0.00 0.00 0.00 2.83
114 115 8.410912 AGAAACTAAAGGTAAATTTCGCTTTGT 58.589 29.630 0.00 0.00 35.03 2.83
115 116 8.797266 AGAAACTAAAGGTAAATTTCGCTTTG 57.203 30.769 0.00 0.00 35.03 2.77
271 272 9.859427 GATTTCTTACCACATCAAAAATCATCA 57.141 29.630 0.00 0.00 33.80 3.07
272 273 9.305925 GGATTTCTTACCACATCAAAAATCATC 57.694 33.333 0.00 0.00 34.76 2.92
273 274 8.814931 TGGATTTCTTACCACATCAAAAATCAT 58.185 29.630 0.00 0.00 34.76 2.45
274 275 8.187913 TGGATTTCTTACCACATCAAAAATCA 57.812 30.769 0.00 0.00 34.76 2.57
275 276 9.487790 TTTGGATTTCTTACCACATCAAAAATC 57.512 29.630 0.00 0.00 35.81 2.17
276 277 9.271828 GTTTGGATTTCTTACCACATCAAAAAT 57.728 29.630 0.00 0.00 35.81 1.82
277 278 8.260818 TGTTTGGATTTCTTACCACATCAAAAA 58.739 29.630 0.00 0.00 35.81 1.94
278 279 7.786030 TGTTTGGATTTCTTACCACATCAAAA 58.214 30.769 0.00 0.00 35.81 2.44
279 280 7.353414 TGTTTGGATTTCTTACCACATCAAA 57.647 32.000 0.00 0.00 35.81 2.69
280 281 6.968263 TGTTTGGATTTCTTACCACATCAA 57.032 33.333 0.00 0.00 35.81 2.57
281 282 6.549364 AGTTGTTTGGATTTCTTACCACATCA 59.451 34.615 0.00 0.00 35.81 3.07
282 283 6.981722 AGTTGTTTGGATTTCTTACCACATC 58.018 36.000 0.00 0.00 35.81 3.06
283 284 6.976934 AGTTGTTTGGATTTCTTACCACAT 57.023 33.333 0.00 0.00 35.81 3.21
284 285 7.883391 TTAGTTGTTTGGATTTCTTACCACA 57.117 32.000 0.00 0.00 35.81 4.17
285 286 9.589111 TTTTTAGTTGTTTGGATTTCTTACCAC 57.411 29.630 0.00 0.00 35.81 4.16
348 352 8.987890 AGCAAGATTTTTAAAATTTGTGCGTAT 58.012 25.926 18.78 7.61 0.00 3.06
349 353 8.272176 CAGCAAGATTTTTAAAATTTGTGCGTA 58.728 29.630 18.78 0.00 0.00 4.42
350 354 7.010923 TCAGCAAGATTTTTAAAATTTGTGCGT 59.989 29.630 18.78 10.78 0.00 5.24
351 355 7.343691 TCAGCAAGATTTTTAAAATTTGTGCG 58.656 30.769 18.78 15.62 0.00 5.34
352 356 9.500864 TTTCAGCAAGATTTTTAAAATTTGTGC 57.499 25.926 17.96 17.96 0.00 4.57
395 399 6.782298 TGACACCACGATATTTTAAAACGA 57.218 33.333 14.18 2.34 0.00 3.85
396 400 6.303733 GGTTGACACCACGATATTTTAAAACG 59.696 38.462 1.97 5.39 43.61 3.60
402 406 4.028993 AGGGTTGACACCACGATATTTT 57.971 40.909 0.00 0.00 46.43 1.82
404 408 3.263425 AGAAGGGTTGACACCACGATATT 59.737 43.478 0.00 0.00 46.43 1.28
406 410 2.253610 AGAAGGGTTGACACCACGATA 58.746 47.619 0.00 0.00 46.43 2.92
407 411 1.056660 AGAAGGGTTGACACCACGAT 58.943 50.000 0.00 0.00 46.43 3.73
408 412 0.834612 AAGAAGGGTTGACACCACGA 59.165 50.000 0.00 0.00 46.43 4.35
409 413 1.226746 GAAGAAGGGTTGACACCACG 58.773 55.000 0.00 0.00 46.43 4.94
410 414 1.605753 GGAAGAAGGGTTGACACCAC 58.394 55.000 0.00 0.00 46.43 4.16
440 451 4.074526 GCTCAGCGACCTCTGGCA 62.075 66.667 0.00 0.00 34.91 4.92
468 479 0.457851 AGAAGCTAGCGTAGGTGCTG 59.542 55.000 9.55 0.00 46.70 4.41
485 499 1.387539 CGGAGCAGATCAGACTCAGA 58.612 55.000 10.61 0.00 31.88 3.27
563 591 0.178906 TGGAGAGGTGATGGTGACCA 60.179 55.000 6.84 6.84 38.19 4.02
794 828 4.439700 GGATGAACACATGAGAATGCCTTG 60.440 45.833 0.00 0.00 0.00 3.61
818 862 1.660560 GCTGGGCACATCACATGGAC 61.661 60.000 0.00 0.00 33.60 4.02
822 866 1.601419 GCTTGCTGGGCACATCACAT 61.601 55.000 0.00 0.00 38.71 3.21
823 867 2.270257 GCTTGCTGGGCACATCACA 61.270 57.895 0.00 0.00 38.71 3.58
824 868 2.570181 GCTTGCTGGGCACATCAC 59.430 61.111 0.00 0.00 38.71 3.06
825 869 2.677524 GGCTTGCTGGGCACATCA 60.678 61.111 0.00 0.00 38.71 3.07
826 870 2.677524 TGGCTTGCTGGGCACATC 60.678 61.111 0.00 0.00 38.71 3.06
988 1092 1.542987 GCCTGCCATTTTTGGAGCAAA 60.543 47.619 0.00 0.00 34.26 3.68
1005 1121 2.905085 CAGTAGGGATGATGATCTGCCT 59.095 50.000 9.18 9.18 0.00 4.75
1023 1139 0.250467 CCAGTACCAGCAGTTGCAGT 60.250 55.000 6.90 6.02 45.16 4.40
1126 1242 3.450115 GGTAGCGCAGGTCTCCGT 61.450 66.667 11.47 0.00 40.68 4.69
1159 1275 1.517832 CGAGGAAGGCGAGGTTGAT 59.482 57.895 0.00 0.00 0.00 2.57
1215 1331 4.269523 GGGTCACAGTGGCCTGCA 62.270 66.667 23.72 0.00 43.05 4.41
1245 1361 0.108329 CGGAGGTTAGGTTCGTGCAT 60.108 55.000 0.00 0.00 0.00 3.96
1667 1783 1.565305 CTTCCATGCGTCAGCTAGAC 58.435 55.000 0.00 6.31 45.42 2.59
1878 1994 3.677121 CCTCTCAAACATCACTCTTCACG 59.323 47.826 0.00 0.00 0.00 4.35
2396 3204 2.159627 GCAGTATGTTCCACAAAGTCCG 59.840 50.000 0.00 0.00 39.31 4.79
2505 3313 4.589908 AGGGTGGATGTGTTAACTTCATC 58.410 43.478 23.33 23.33 37.72 2.92
2574 3382 5.486063 ACAATACCTACATGGACACACCTTA 59.514 40.000 0.00 0.00 39.71 2.69
2601 3409 3.181511 TGTTGAATCATCATCGAAACGGC 60.182 43.478 0.00 0.00 34.96 5.68
2721 3529 6.405842 GGAAGTGACTTGGCAATTATAAAGGG 60.406 42.308 0.90 0.00 0.00 3.95
2723 3531 7.396540 AGGAAGTGACTTGGCAATTATAAAG 57.603 36.000 0.90 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.