Multiple sequence alignment - TraesCS2D01G258600

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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 TraesCS2D01G258600 chr2D 100.000 2266 0 0 1 2266 314480425 314478160 0.000000e+00 4185.0
1 TraesCS2D01G258600 chr2D 89.416 2173 159 39 127 2266 50978653 50976519 0.000000e+00 2673.0
2 TraesCS2D01G258600 chr2D 88.377 2039 157 48 127 2138 519139898 519141883 0.000000e+00 2379.0
3 TraesCS2D01G258600 chr2D 98.507 134 2 0 1 134 314488006 314487873 1.050000e-58 237.0
4 TraesCS2D01G258600 chr7D 90.689 2148 167 15 127 2258 29611335 29613465 0.000000e+00 2828.0
5 TraesCS2D01G258600 chr7D 92.266 1836 107 12 127 1932 411315675 411313845 0.000000e+00 2571.0
6 TraesCS2D01G258600 chr7D 89.297 327 35 0 1940 2266 411313873 411313547 5.830000e-111 411.0
7 TraesCS2D01G258600 chr7D 93.182 176 12 0 2086 2261 411313408 411313233 2.230000e-65 259.0
8 TraesCS2D01G258600 chr5D 90.367 2180 163 24 127 2266 522787270 522789442 0.000000e+00 2819.0
9 TraesCS2D01G258600 chr5D 89.925 2144 158 16 127 2240 517099106 517101221 0.000000e+00 2710.0
10 TraesCS2D01G258600 chr5D 89.447 2170 172 22 127 2266 452401397 452399255 0.000000e+00 2686.0
11 TraesCS2D01G258600 chr5D 91.899 1222 85 10 452 1660 46684446 46683226 0.000000e+00 1696.0
12 TraesCS2D01G258600 chr5D 97.761 134 3 0 1 134 268761472 268761339 4.870000e-57 231.0
13 TraesCS2D01G258600 chr5D 85.106 141 18 3 1 139 276992929 276993068 8.440000e-30 141.0
14 TraesCS2D01G258600 chr3B 90.035 2027 158 22 128 2137 738417953 738419952 0.000000e+00 2584.0
15 TraesCS2D01G258600 chr3B 86.933 2181 223 31 127 2264 213720010 213717849 0.000000e+00 2392.0
16 TraesCS2D01G258600 chr3B 86.500 200 23 4 1777 1973 715193966 715193768 1.360000e-52 217.0
17 TraesCS2D01G258600 chr6B 89.315 2059 165 29 127 2154 472600132 472602166 0.000000e+00 2532.0
18 TraesCS2D01G258600 chr6B 84.524 84 3 1 127 200 288473735 288473818 8.680000e-10 75.0
19 TraesCS2D01G258600 chr3D 88.110 2153 172 43 127 2238 16222245 16220136 0.000000e+00 2481.0
20 TraesCS2D01G258600 chr3D 84.340 447 56 10 1733 2170 416000234 416000675 2.080000e-115 425.0
21 TraesCS2D01G258600 chr3D 97.778 135 3 0 1 135 314181301 314181167 1.350000e-57 233.0
22 TraesCS2D01G258600 chr4D 88.042 2074 159 51 127 2156 422950169 422948141 0.000000e+00 2374.0
23 TraesCS2D01G258600 chr4D 86.123 1643 182 26 165 1794 343945794 343947403 0.000000e+00 1729.0
24 TraesCS2D01G258600 chr4D 98.507 134 2 0 1 134 333711301 333711434 1.050000e-58 237.0
25 TraesCS2D01G258600 chr1D 88.958 1929 148 35 127 2034 392033514 392035398 0.000000e+00 2322.0
26 TraesCS2D01G258600 chr1D 84.668 587 63 16 1688 2266 20009332 20008765 5.470000e-156 560.0
27 TraesCS2D01G258600 chr1D 97.015 134 4 0 1 134 64848897 64849030 2.260000e-55 226.0
28 TraesCS2D01G258600 chr6D 88.364 1925 153 38 127 2034 327605268 327603398 0.000000e+00 2248.0
29 TraesCS2D01G258600 chr6D 90.244 328 22 5 127 444 471473696 471473369 9.680000e-114 420.0
30 TraesCS2D01G258600 chr7B 88.033 1713 157 22 127 1818 122757001 122758686 0.000000e+00 1984.0
31 TraesCS2D01G258600 chr7B 97.744 133 3 0 1 133 214625 214493 1.750000e-56 230.0
32 TraesCS2D01G258600 chr2B 88.086 982 88 19 1177 2138 82426784 82425812 0.000000e+00 1138.0
33 TraesCS2D01G258600 chr5A 87.215 219 26 2 2048 2266 353253385 353253601 4.830000e-62 248.0
34 TraesCS2D01G258600 chr1A 88.742 151 17 0 2111 2261 215652546 215652396 3.840000e-43 185.0
35 TraesCS2D01G258600 chr2A 84.615 143 18 4 1 142 453986817 453986956 3.030000e-29 139.0
36 TraesCS2D01G258600 chr3A 83.688 141 20 3 1 139 384253394 384253533 1.830000e-26 130.0
37 TraesCS2D01G258600 chrUn 97.500 40 1 0 127 166 12507765 12507804 4.040000e-08 69.4


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 TraesCS2D01G258600 chr2D 314478160 314480425 2265 True 4185.000000 4185 100.000000 1 2266 1 chr2D.!!$R2 2265
1 TraesCS2D01G258600 chr2D 50976519 50978653 2134 True 2673.000000 2673 89.416000 127 2266 1 chr2D.!!$R1 2139
2 TraesCS2D01G258600 chr2D 519139898 519141883 1985 False 2379.000000 2379 88.377000 127 2138 1 chr2D.!!$F1 2011
3 TraesCS2D01G258600 chr7D 29611335 29613465 2130 False 2828.000000 2828 90.689000 127 2258 1 chr7D.!!$F1 2131
4 TraesCS2D01G258600 chr7D 411313233 411315675 2442 True 1080.333333 2571 91.581667 127 2266 3 chr7D.!!$R1 2139
5 TraesCS2D01G258600 chr5D 522787270 522789442 2172 False 2819.000000 2819 90.367000 127 2266 1 chr5D.!!$F3 2139
6 TraesCS2D01G258600 chr5D 517099106 517101221 2115 False 2710.000000 2710 89.925000 127 2240 1 chr5D.!!$F2 2113
7 TraesCS2D01G258600 chr5D 452399255 452401397 2142 True 2686.000000 2686 89.447000 127 2266 1 chr5D.!!$R3 2139
8 TraesCS2D01G258600 chr5D 46683226 46684446 1220 True 1696.000000 1696 91.899000 452 1660 1 chr5D.!!$R1 1208
9 TraesCS2D01G258600 chr3B 738417953 738419952 1999 False 2584.000000 2584 90.035000 128 2137 1 chr3B.!!$F1 2009
10 TraesCS2D01G258600 chr3B 213717849 213720010 2161 True 2392.000000 2392 86.933000 127 2264 1 chr3B.!!$R1 2137
11 TraesCS2D01G258600 chr6B 472600132 472602166 2034 False 2532.000000 2532 89.315000 127 2154 1 chr6B.!!$F2 2027
12 TraesCS2D01G258600 chr3D 16220136 16222245 2109 True 2481.000000 2481 88.110000 127 2238 1 chr3D.!!$R1 2111
13 TraesCS2D01G258600 chr4D 422948141 422950169 2028 True 2374.000000 2374 88.042000 127 2156 1 chr4D.!!$R1 2029
14 TraesCS2D01G258600 chr4D 343945794 343947403 1609 False 1729.000000 1729 86.123000 165 1794 1 chr4D.!!$F2 1629
15 TraesCS2D01G258600 chr1D 392033514 392035398 1884 False 2322.000000 2322 88.958000 127 2034 1 chr1D.!!$F2 1907
16 TraesCS2D01G258600 chr1D 20008765 20009332 567 True 560.000000 560 84.668000 1688 2266 1 chr1D.!!$R1 578
17 TraesCS2D01G258600 chr6D 327603398 327605268 1870 True 2248.000000 2248 88.364000 127 2034 1 chr6D.!!$R1 1907
18 TraesCS2D01G258600 chr7B 122757001 122758686 1685 False 1984.000000 1984 88.033000 127 1818 1 chr7B.!!$F1 1691
19 TraesCS2D01G258600 chr2B 82425812 82426784 972 True 1138.000000 1138 88.086000 1177 2138 1 chr2B.!!$R1 961

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
634 648 0.172578 CGGACCGATGCTAACACTCA 59.827 55.0 8.64 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 2183 0.035458 CAGGGGAGCGTTTCTGTTCT 59.965 55.0 0.0 0.0 0.0 3.01 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 5.886960 ACAACAGCAAGAAATCCTCATAC 57.113 39.130 0.00 0.00 0.00 2.39
24 25 5.316167 ACAACAGCAAGAAATCCTCATACA 58.684 37.500 0.00 0.00 0.00 2.29
25 26 5.769662 ACAACAGCAAGAAATCCTCATACAA 59.230 36.000 0.00 0.00 0.00 2.41
26 27 6.265196 ACAACAGCAAGAAATCCTCATACAAA 59.735 34.615 0.00 0.00 0.00 2.83
27 28 7.039504 ACAACAGCAAGAAATCCTCATACAAAT 60.040 33.333 0.00 0.00 0.00 2.32
28 29 6.860080 ACAGCAAGAAATCCTCATACAAATG 58.140 36.000 0.00 0.00 0.00 2.32
29 30 6.660521 ACAGCAAGAAATCCTCATACAAATGA 59.339 34.615 0.00 0.00 39.87 2.57
30 31 6.971184 CAGCAAGAAATCCTCATACAAATGAC 59.029 38.462 0.00 0.00 37.20 3.06
31 32 6.888632 AGCAAGAAATCCTCATACAAATGACT 59.111 34.615 0.00 0.00 37.20 3.41
32 33 6.971184 GCAAGAAATCCTCATACAAATGACTG 59.029 38.462 0.00 0.00 37.20 3.51
33 34 7.362401 GCAAGAAATCCTCATACAAATGACTGT 60.362 37.037 0.00 0.00 37.20 3.55
34 35 7.621428 AGAAATCCTCATACAAATGACTGTG 57.379 36.000 0.00 0.00 37.20 3.66
35 36 7.397221 AGAAATCCTCATACAAATGACTGTGA 58.603 34.615 0.00 0.00 37.20 3.58
36 37 8.051535 AGAAATCCTCATACAAATGACTGTGAT 58.948 33.333 0.00 0.00 37.20 3.06
37 38 7.563888 AATCCTCATACAAATGACTGTGATG 57.436 36.000 0.00 0.00 37.20 3.07
38 39 4.877823 TCCTCATACAAATGACTGTGATGC 59.122 41.667 0.00 0.00 37.20 3.91
39 40 4.637091 CCTCATACAAATGACTGTGATGCA 59.363 41.667 0.00 0.00 37.20 3.96
40 41 5.298527 CCTCATACAAATGACTGTGATGCAT 59.701 40.000 0.00 0.00 37.20 3.96
41 42 6.484308 CCTCATACAAATGACTGTGATGCATA 59.516 38.462 0.00 0.00 37.20 3.14
42 43 7.174426 CCTCATACAAATGACTGTGATGCATAT 59.826 37.037 0.00 0.00 37.20 1.78
43 44 9.211485 CTCATACAAATGACTGTGATGCATATA 57.789 33.333 0.00 0.00 37.20 0.86
44 45 8.992073 TCATACAAATGACTGTGATGCATATAC 58.008 33.333 0.00 2.59 37.20 1.47
45 46 8.996271 CATACAAATGACTGTGATGCATATACT 58.004 33.333 0.00 0.00 34.84 2.12
46 47 7.870509 ACAAATGACTGTGATGCATATACTT 57.129 32.000 0.00 0.00 0.00 2.24
47 48 8.962884 ACAAATGACTGTGATGCATATACTTA 57.037 30.769 0.00 0.00 0.00 2.24
48 49 8.830580 ACAAATGACTGTGATGCATATACTTAC 58.169 33.333 0.00 0.00 0.00 2.34
49 50 7.969536 AATGACTGTGATGCATATACTTACC 57.030 36.000 0.00 0.00 0.00 2.85
50 51 6.731292 TGACTGTGATGCATATACTTACCT 57.269 37.500 0.00 0.00 0.00 3.08
51 52 7.124573 TGACTGTGATGCATATACTTACCTT 57.875 36.000 0.00 0.00 0.00 3.50
52 53 6.986231 TGACTGTGATGCATATACTTACCTTG 59.014 38.462 0.00 0.00 0.00 3.61
53 54 6.889198 ACTGTGATGCATATACTTACCTTGT 58.111 36.000 0.00 0.00 0.00 3.16
54 55 6.763135 ACTGTGATGCATATACTTACCTTGTG 59.237 38.462 0.00 0.00 0.00 3.33
55 56 6.054941 TGTGATGCATATACTTACCTTGTGG 58.945 40.000 0.00 0.00 39.83 4.17
57 58 6.202954 GTGATGCATATACTTACCTTGTGGTC 59.797 42.308 0.00 0.00 44.78 4.02
58 59 5.950544 TGCATATACTTACCTTGTGGTCT 57.049 39.130 0.00 0.00 44.78 3.85
59 60 6.308015 TGCATATACTTACCTTGTGGTCTT 57.692 37.500 0.00 0.00 44.78 3.01
60 61 6.112734 TGCATATACTTACCTTGTGGTCTTG 58.887 40.000 0.00 0.00 44.78 3.02
61 62 6.070481 TGCATATACTTACCTTGTGGTCTTGA 60.070 38.462 0.00 0.00 44.78 3.02
62 63 6.480320 GCATATACTTACCTTGTGGTCTTGAG 59.520 42.308 0.00 0.00 44.78 3.02
63 64 7.556844 CATATACTTACCTTGTGGTCTTGAGT 58.443 38.462 0.00 0.00 44.78 3.41
64 65 4.772886 ACTTACCTTGTGGTCTTGAGTT 57.227 40.909 0.00 0.00 44.78 3.01
65 66 4.451900 ACTTACCTTGTGGTCTTGAGTTG 58.548 43.478 0.00 0.00 44.78 3.16
66 67 2.348411 ACCTTGTGGTCTTGAGTTGG 57.652 50.000 0.00 0.00 44.78 3.77
67 68 0.954452 CCTTGTGGTCTTGAGTTGGC 59.046 55.000 0.00 0.00 0.00 4.52
68 69 1.477558 CCTTGTGGTCTTGAGTTGGCT 60.478 52.381 0.00 0.00 0.00 4.75
69 70 2.301346 CTTGTGGTCTTGAGTTGGCTT 58.699 47.619 0.00 0.00 0.00 4.35
70 71 3.476552 CTTGTGGTCTTGAGTTGGCTTA 58.523 45.455 0.00 0.00 0.00 3.09
71 72 3.126001 TGTGGTCTTGAGTTGGCTTAG 57.874 47.619 0.00 0.00 0.00 2.18
72 73 2.224523 TGTGGTCTTGAGTTGGCTTAGG 60.225 50.000 0.00 0.00 0.00 2.69
73 74 2.038557 GTGGTCTTGAGTTGGCTTAGGA 59.961 50.000 0.00 0.00 0.00 2.94
74 75 2.708861 TGGTCTTGAGTTGGCTTAGGAA 59.291 45.455 0.00 0.00 0.00 3.36
75 76 3.244561 TGGTCTTGAGTTGGCTTAGGAAG 60.245 47.826 0.00 0.00 0.00 3.46
76 77 3.339141 GTCTTGAGTTGGCTTAGGAAGG 58.661 50.000 0.00 0.00 0.00 3.46
77 78 3.008049 GTCTTGAGTTGGCTTAGGAAGGA 59.992 47.826 0.00 0.00 0.00 3.36
78 79 3.261897 TCTTGAGTTGGCTTAGGAAGGAG 59.738 47.826 0.00 0.00 0.00 3.69
79 80 2.621070 TGAGTTGGCTTAGGAAGGAGT 58.379 47.619 0.00 0.00 0.00 3.85
80 81 2.303022 TGAGTTGGCTTAGGAAGGAGTG 59.697 50.000 0.00 0.00 0.00 3.51
81 82 2.567615 GAGTTGGCTTAGGAAGGAGTGA 59.432 50.000 0.00 0.00 0.00 3.41
82 83 2.979678 AGTTGGCTTAGGAAGGAGTGAA 59.020 45.455 0.00 0.00 0.00 3.18
83 84 3.075148 GTTGGCTTAGGAAGGAGTGAAC 58.925 50.000 0.00 0.00 0.00 3.18
84 85 1.628846 TGGCTTAGGAAGGAGTGAACC 59.371 52.381 0.00 0.00 0.00 3.62
85 86 1.909986 GGCTTAGGAAGGAGTGAACCT 59.090 52.381 0.00 0.00 42.69 3.50
86 87 2.355209 GGCTTAGGAAGGAGTGAACCTG 60.355 54.545 0.00 0.00 40.49 4.00
87 88 2.567615 GCTTAGGAAGGAGTGAACCTGA 59.432 50.000 0.00 0.00 40.49 3.86
88 89 3.368948 GCTTAGGAAGGAGTGAACCTGAG 60.369 52.174 0.00 0.00 40.49 3.35
89 90 2.407340 AGGAAGGAGTGAACCTGAGT 57.593 50.000 0.00 0.00 40.49 3.41
90 91 3.544698 AGGAAGGAGTGAACCTGAGTA 57.455 47.619 0.00 0.00 40.49 2.59
91 92 3.858135 AGGAAGGAGTGAACCTGAGTAA 58.142 45.455 0.00 0.00 40.49 2.24
92 93 4.232091 AGGAAGGAGTGAACCTGAGTAAA 58.768 43.478 0.00 0.00 40.49 2.01
93 94 4.040584 AGGAAGGAGTGAACCTGAGTAAAC 59.959 45.833 0.00 0.00 40.49 2.01
94 95 4.202326 GGAAGGAGTGAACCTGAGTAAACA 60.202 45.833 0.00 0.00 40.49 2.83
95 96 5.365619 GAAGGAGTGAACCTGAGTAAACAA 58.634 41.667 0.00 0.00 40.49 2.83
96 97 4.962155 AGGAGTGAACCTGAGTAAACAAG 58.038 43.478 0.00 0.00 39.01 3.16
97 98 4.065789 GGAGTGAACCTGAGTAAACAAGG 58.934 47.826 1.46 1.46 0.00 3.61
98 99 4.444449 GGAGTGAACCTGAGTAAACAAGGT 60.444 45.833 2.55 2.55 0.00 3.50
99 100 5.112129 AGTGAACCTGAGTAAACAAGGTT 57.888 39.130 16.00 16.00 44.51 3.50
100 101 6.243216 AGTGAACCTGAGTAAACAAGGTTA 57.757 37.500 16.02 6.55 42.23 2.85
101 102 6.289064 AGTGAACCTGAGTAAACAAGGTTAG 58.711 40.000 16.02 0.00 42.23 2.34
102 103 6.099269 AGTGAACCTGAGTAAACAAGGTTAGA 59.901 38.462 16.02 7.22 42.23 2.10
103 104 6.935208 GTGAACCTGAGTAAACAAGGTTAGAT 59.065 38.462 16.02 0.44 42.23 1.98
104 105 8.092687 GTGAACCTGAGTAAACAAGGTTAGATA 58.907 37.037 16.02 5.45 42.23 1.98
105 106 8.653191 TGAACCTGAGTAAACAAGGTTAGATAA 58.347 33.333 16.02 3.21 42.23 1.75
106 107 8.843885 AACCTGAGTAAACAAGGTTAGATAAC 57.156 34.615 14.99 0.00 40.62 1.89
107 108 7.970102 ACCTGAGTAAACAAGGTTAGATAACA 58.030 34.615 5.19 0.00 37.92 2.41
108 109 7.876582 ACCTGAGTAAACAAGGTTAGATAACAC 59.123 37.037 5.19 0.00 37.92 3.32
109 110 7.876068 CCTGAGTAAACAAGGTTAGATAACACA 59.124 37.037 5.19 0.00 37.92 3.72
110 111 8.827177 TGAGTAAACAAGGTTAGATAACACAG 57.173 34.615 5.19 0.00 37.92 3.66
111 112 8.644216 TGAGTAAACAAGGTTAGATAACACAGA 58.356 33.333 5.19 0.00 37.92 3.41
112 113 9.654663 GAGTAAACAAGGTTAGATAACACAGAT 57.345 33.333 5.19 0.00 37.92 2.90
116 117 8.773404 AACAAGGTTAGATAACACAGATACAC 57.227 34.615 5.19 0.00 37.92 2.90
117 118 7.328737 ACAAGGTTAGATAACACAGATACACC 58.671 38.462 5.19 0.00 37.92 4.16
118 119 7.180408 ACAAGGTTAGATAACACAGATACACCT 59.820 37.037 5.19 0.00 37.92 4.00
119 120 8.692710 CAAGGTTAGATAACACAGATACACCTA 58.307 37.037 5.19 0.00 37.92 3.08
120 121 8.235359 AGGTTAGATAACACAGATACACCTAC 57.765 38.462 5.19 0.00 37.92 3.18
121 122 8.060075 AGGTTAGATAACACAGATACACCTACT 58.940 37.037 5.19 0.00 37.92 2.57
122 123 9.347240 GGTTAGATAACACAGATACACCTACTA 57.653 37.037 5.19 0.00 37.92 1.82
124 125 7.513371 AGATAACACAGATACACCTACTAGC 57.487 40.000 0.00 0.00 0.00 3.42
125 126 6.490721 AGATAACACAGATACACCTACTAGCC 59.509 42.308 0.00 0.00 0.00 3.93
226 237 1.345741 CCAGTGGTGTCAGTGTGAGAT 59.654 52.381 0.00 0.00 41.52 2.75
255 266 1.210478 AGTATCATTGGCCTTGCTCGT 59.790 47.619 3.32 0.00 0.00 4.18
272 283 2.108157 TATGTGATGACCGCCGCC 59.892 61.111 0.00 0.00 0.00 6.13
382 393 2.436173 GGTTTCATCCCTTCCTCGATCT 59.564 50.000 0.00 0.00 0.00 2.75
383 394 3.641906 GGTTTCATCCCTTCCTCGATCTA 59.358 47.826 0.00 0.00 0.00 1.98
404 415 2.256306 TCACAGTGGCCTGAGTATGAA 58.744 47.619 3.32 0.00 41.50 2.57
626 640 2.748058 AAAAGCCACGGACCGATGCT 62.748 55.000 23.38 23.13 38.36 3.79
634 648 0.172578 CGGACCGATGCTAACACTCA 59.827 55.000 8.64 0.00 0.00 3.41
646 663 3.643792 GCTAACACTCAGGATCCCACTAT 59.356 47.826 8.55 0.00 0.00 2.12
694 711 4.453454 TGGCACACGAGGAGGTAT 57.547 55.556 0.00 0.00 0.00 2.73
718 747 1.567649 TGGTAGTGGACGAGGAGGTAT 59.432 52.381 0.00 0.00 0.00 2.73
754 783 0.462047 GGACGGATGAATCTTGGCGT 60.462 55.000 0.00 0.00 0.00 5.68
1155 1205 5.594725 TGTTTGCAAAGTTAAGGTATCCACA 59.405 36.000 13.26 0.00 0.00 4.17
1173 1223 1.470098 ACAGACCGCAAGAAATCATGC 59.530 47.619 0.72 0.72 43.02 4.06
1262 1313 2.277084 GATGTACCGCTGGTAAGTTGG 58.723 52.381 8.68 0.00 40.12 3.77
1273 1324 4.278419 GCTGGTAAGTTGGTGAAGTTCAAT 59.722 41.667 7.25 0.00 0.00 2.57
1374 1429 4.995487 CCTCCACTTTGTAAGTACTTCACC 59.005 45.833 12.39 2.21 40.46 4.02
1457 1512 1.065551 GCAGCGGTTGTTTGAAGAAGT 59.934 47.619 0.00 0.00 0.00 3.01
1473 1528 7.482169 TGAAGAAGTATTTCAGAGAGGCTTA 57.518 36.000 0.44 0.00 35.70 3.09
1594 1656 1.302033 CTGCAAGGGCTCGTGAAGT 60.302 57.895 2.76 0.00 41.91 3.01
1714 1839 5.289434 TCGATTCGAGAAACATGTGATGAAG 59.711 40.000 4.29 0.00 0.00 3.02
1983 2183 0.040058 TAGGTGGCCGAACTGTCCTA 59.960 55.000 0.00 0.00 0.00 2.94
2005 2205 1.053424 ACAGAAACGCTCCCCTGTTA 58.947 50.000 0.00 0.00 36.57 2.41
2112 2632 3.493002 CCAAATCAGCCACTTTTTCTGCA 60.493 43.478 0.00 0.00 0.00 4.41
2121 2734 4.394729 CCACTTTTTCTGCAGTAGGGTTA 58.605 43.478 14.67 0.00 0.00 2.85
2188 2801 2.663796 CTGCTCTGCTGCCTGTCT 59.336 61.111 0.00 0.00 0.00 3.41
2203 2816 2.549992 CCTGTCTTGTGACCAAATCGGA 60.550 50.000 0.00 0.00 42.28 4.55
2217 2831 2.163818 ATCGGACACTTTTTCTGCGA 57.836 45.000 0.00 0.00 0.00 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.472016 TGTATGAGGATTTCTTGCTGTTGTA 58.528 36.000 0.00 0.00 0.00 2.41
1 2 5.316167 TGTATGAGGATTTCTTGCTGTTGT 58.684 37.500 0.00 0.00 0.00 3.32
2 3 5.885230 TGTATGAGGATTTCTTGCTGTTG 57.115 39.130 0.00 0.00 0.00 3.33
3 4 6.899393 TTTGTATGAGGATTTCTTGCTGTT 57.101 33.333 0.00 0.00 0.00 3.16
4 5 6.660521 TCATTTGTATGAGGATTTCTTGCTGT 59.339 34.615 0.00 0.00 35.87 4.40
5 6 6.971184 GTCATTTGTATGAGGATTTCTTGCTG 59.029 38.462 0.00 0.00 41.33 4.41
6 7 6.888632 AGTCATTTGTATGAGGATTTCTTGCT 59.111 34.615 0.00 0.00 41.33 3.91
7 8 6.971184 CAGTCATTTGTATGAGGATTTCTTGC 59.029 38.462 0.00 0.00 41.33 4.01
8 9 7.966753 CACAGTCATTTGTATGAGGATTTCTTG 59.033 37.037 0.00 0.00 41.33 3.02
9 10 7.884877 TCACAGTCATTTGTATGAGGATTTCTT 59.115 33.333 0.00 0.00 41.33 2.52
10 11 7.397221 TCACAGTCATTTGTATGAGGATTTCT 58.603 34.615 0.00 0.00 41.33 2.52
11 12 7.615582 TCACAGTCATTTGTATGAGGATTTC 57.384 36.000 0.00 0.00 41.33 2.17
12 13 7.415989 GCATCACAGTCATTTGTATGAGGATTT 60.416 37.037 0.00 0.00 41.33 2.17
13 14 6.039047 GCATCACAGTCATTTGTATGAGGATT 59.961 38.462 0.00 0.00 41.33 3.01
14 15 5.530171 GCATCACAGTCATTTGTATGAGGAT 59.470 40.000 0.00 0.00 41.33 3.24
15 16 4.877823 GCATCACAGTCATTTGTATGAGGA 59.122 41.667 0.00 0.00 41.33 3.71
16 17 4.637091 TGCATCACAGTCATTTGTATGAGG 59.363 41.667 0.00 0.00 41.33 3.86
17 18 5.806366 TGCATCACAGTCATTTGTATGAG 57.194 39.130 0.00 0.00 41.33 2.90
18 19 8.992073 GTATATGCATCACAGTCATTTGTATGA 58.008 33.333 0.19 0.00 38.45 2.15
19 20 8.996271 AGTATATGCATCACAGTCATTTGTATG 58.004 33.333 0.19 0.00 0.00 2.39
20 21 9.565090 AAGTATATGCATCACAGTCATTTGTAT 57.435 29.630 0.19 0.00 0.00 2.29
21 22 8.962884 AAGTATATGCATCACAGTCATTTGTA 57.037 30.769 0.19 0.00 0.00 2.41
22 23 7.870509 AAGTATATGCATCACAGTCATTTGT 57.129 32.000 0.19 0.00 0.00 2.83
23 24 8.285394 GGTAAGTATATGCATCACAGTCATTTG 58.715 37.037 0.19 0.00 0.00 2.32
24 25 8.213679 AGGTAAGTATATGCATCACAGTCATTT 58.786 33.333 0.19 0.00 0.00 2.32
25 26 7.739825 AGGTAAGTATATGCATCACAGTCATT 58.260 34.615 0.19 0.00 0.00 2.57
26 27 7.308450 AGGTAAGTATATGCATCACAGTCAT 57.692 36.000 0.19 0.00 0.00 3.06
27 28 6.731292 AGGTAAGTATATGCATCACAGTCA 57.269 37.500 0.19 0.00 0.00 3.41
28 29 6.986817 ACAAGGTAAGTATATGCATCACAGTC 59.013 38.462 0.19 0.00 0.00 3.51
29 30 6.763135 CACAAGGTAAGTATATGCATCACAGT 59.237 38.462 0.19 0.00 0.00 3.55
30 31 6.203530 CCACAAGGTAAGTATATGCATCACAG 59.796 42.308 0.19 0.00 0.00 3.66
31 32 6.054941 CCACAAGGTAAGTATATGCATCACA 58.945 40.000 0.19 0.00 0.00 3.58
32 33 6.545504 CCACAAGGTAAGTATATGCATCAC 57.454 41.667 0.19 2.42 0.00 3.06
48 49 0.954452 GCCAACTCAAGACCACAAGG 59.046 55.000 0.00 0.00 42.21 3.61
49 50 1.972872 AGCCAACTCAAGACCACAAG 58.027 50.000 0.00 0.00 0.00 3.16
50 51 2.435372 AAGCCAACTCAAGACCACAA 57.565 45.000 0.00 0.00 0.00 3.33
51 52 2.224523 CCTAAGCCAACTCAAGACCACA 60.225 50.000 0.00 0.00 0.00 4.17
52 53 2.038557 TCCTAAGCCAACTCAAGACCAC 59.961 50.000 0.00 0.00 0.00 4.16
53 54 2.334977 TCCTAAGCCAACTCAAGACCA 58.665 47.619 0.00 0.00 0.00 4.02
54 55 3.339141 CTTCCTAAGCCAACTCAAGACC 58.661 50.000 0.00 0.00 0.00 3.85
55 56 3.008049 TCCTTCCTAAGCCAACTCAAGAC 59.992 47.826 0.00 0.00 0.00 3.01
56 57 3.248024 TCCTTCCTAAGCCAACTCAAGA 58.752 45.455 0.00 0.00 0.00 3.02
57 58 3.008485 ACTCCTTCCTAAGCCAACTCAAG 59.992 47.826 0.00 0.00 0.00 3.02
58 59 2.979678 ACTCCTTCCTAAGCCAACTCAA 59.020 45.455 0.00 0.00 0.00 3.02
59 60 2.303022 CACTCCTTCCTAAGCCAACTCA 59.697 50.000 0.00 0.00 0.00 3.41
60 61 2.567615 TCACTCCTTCCTAAGCCAACTC 59.432 50.000 0.00 0.00 0.00 3.01
61 62 2.621070 TCACTCCTTCCTAAGCCAACT 58.379 47.619 0.00 0.00 0.00 3.16
62 63 3.075148 GTTCACTCCTTCCTAAGCCAAC 58.925 50.000 0.00 0.00 0.00 3.77
63 64 2.039879 GGTTCACTCCTTCCTAAGCCAA 59.960 50.000 0.00 0.00 0.00 4.52
64 65 1.628846 GGTTCACTCCTTCCTAAGCCA 59.371 52.381 0.00 0.00 0.00 4.75
65 66 1.909986 AGGTTCACTCCTTCCTAAGCC 59.090 52.381 0.00 0.00 33.52 4.35
66 67 2.567615 TCAGGTTCACTCCTTCCTAAGC 59.432 50.000 0.00 0.00 35.37 3.09
67 68 3.835395 ACTCAGGTTCACTCCTTCCTAAG 59.165 47.826 0.00 0.00 35.37 2.18
68 69 3.858135 ACTCAGGTTCACTCCTTCCTAA 58.142 45.455 0.00 0.00 35.37 2.69
69 70 3.544698 ACTCAGGTTCACTCCTTCCTA 57.455 47.619 0.00 0.00 35.37 2.94
70 71 2.407340 ACTCAGGTTCACTCCTTCCT 57.593 50.000 0.00 0.00 35.37 3.36
71 72 4.202326 TGTTTACTCAGGTTCACTCCTTCC 60.202 45.833 0.00 0.00 35.37 3.46
72 73 4.957296 TGTTTACTCAGGTTCACTCCTTC 58.043 43.478 0.00 0.00 35.37 3.46
73 74 5.367945 TTGTTTACTCAGGTTCACTCCTT 57.632 39.130 0.00 0.00 35.37 3.36
74 75 4.202367 CCTTGTTTACTCAGGTTCACTCCT 60.202 45.833 0.00 0.00 38.51 3.69
75 76 4.065789 CCTTGTTTACTCAGGTTCACTCC 58.934 47.826 0.00 0.00 0.00 3.85
76 77 4.704965 ACCTTGTTTACTCAGGTTCACTC 58.295 43.478 0.00 0.00 0.00 3.51
77 78 4.772886 ACCTTGTTTACTCAGGTTCACT 57.227 40.909 0.00 0.00 0.00 3.41
78 79 6.285990 TCTAACCTTGTTTACTCAGGTTCAC 58.714 40.000 15.85 0.00 42.20 3.18
79 80 6.488769 TCTAACCTTGTTTACTCAGGTTCA 57.511 37.500 15.85 6.34 42.20 3.18
80 81 8.933807 GTTATCTAACCTTGTTTACTCAGGTTC 58.066 37.037 15.85 3.33 42.20 3.62
81 82 8.434392 TGTTATCTAACCTTGTTTACTCAGGTT 58.566 33.333 16.34 16.34 44.11 3.50
82 83 7.876582 GTGTTATCTAACCTTGTTTACTCAGGT 59.123 37.037 0.00 0.00 35.37 4.00
83 84 7.876068 TGTGTTATCTAACCTTGTTTACTCAGG 59.124 37.037 0.00 0.00 35.37 3.86
84 85 8.827177 TGTGTTATCTAACCTTGTTTACTCAG 57.173 34.615 0.00 0.00 35.37 3.35
85 86 8.644216 TCTGTGTTATCTAACCTTGTTTACTCA 58.356 33.333 0.00 0.00 35.37 3.41
86 87 9.654663 ATCTGTGTTATCTAACCTTGTTTACTC 57.345 33.333 0.00 0.00 35.37 2.59
90 91 9.216117 GTGTATCTGTGTTATCTAACCTTGTTT 57.784 33.333 0.00 0.00 35.37 2.83
91 92 7.822822 GGTGTATCTGTGTTATCTAACCTTGTT 59.177 37.037 0.00 0.00 35.37 2.83
92 93 7.180408 AGGTGTATCTGTGTTATCTAACCTTGT 59.820 37.037 0.00 0.00 35.37 3.16
93 94 7.556844 AGGTGTATCTGTGTTATCTAACCTTG 58.443 38.462 0.00 0.00 35.37 3.61
94 95 7.735326 AGGTGTATCTGTGTTATCTAACCTT 57.265 36.000 0.00 0.00 35.37 3.50
95 96 8.060075 AGTAGGTGTATCTGTGTTATCTAACCT 58.940 37.037 0.00 0.00 37.95 3.50
96 97 8.235359 AGTAGGTGTATCTGTGTTATCTAACC 57.765 38.462 0.00 0.00 35.37 2.85
98 99 9.064706 GCTAGTAGGTGTATCTGTGTTATCTAA 57.935 37.037 0.00 0.00 0.00 2.10
99 100 7.664731 GGCTAGTAGGTGTATCTGTGTTATCTA 59.335 40.741 0.00 0.00 0.00 1.98
100 101 6.490721 GGCTAGTAGGTGTATCTGTGTTATCT 59.509 42.308 0.00 0.00 0.00 1.98
101 102 6.264744 TGGCTAGTAGGTGTATCTGTGTTATC 59.735 42.308 0.00 0.00 0.00 1.75
102 103 6.134055 TGGCTAGTAGGTGTATCTGTGTTAT 58.866 40.000 0.00 0.00 0.00 1.89
103 104 5.512298 TGGCTAGTAGGTGTATCTGTGTTA 58.488 41.667 0.00 0.00 0.00 2.41
104 105 4.350245 TGGCTAGTAGGTGTATCTGTGTT 58.650 43.478 0.00 0.00 0.00 3.32
105 106 3.954904 CTGGCTAGTAGGTGTATCTGTGT 59.045 47.826 0.00 0.00 0.00 3.72
106 107 4.207955 TCTGGCTAGTAGGTGTATCTGTG 58.792 47.826 0.00 0.00 0.00 3.66
107 108 4.521536 TCTGGCTAGTAGGTGTATCTGT 57.478 45.455 0.00 0.00 0.00 3.41
108 109 4.645136 TGTTCTGGCTAGTAGGTGTATCTG 59.355 45.833 0.00 0.00 0.00 2.90
109 110 4.868268 TGTTCTGGCTAGTAGGTGTATCT 58.132 43.478 0.00 0.00 0.00 1.98
110 111 5.593679 TTGTTCTGGCTAGTAGGTGTATC 57.406 43.478 0.00 0.00 0.00 2.24
111 112 6.384305 AGATTTGTTCTGGCTAGTAGGTGTAT 59.616 38.462 0.00 0.00 31.79 2.29
112 113 5.720041 AGATTTGTTCTGGCTAGTAGGTGTA 59.280 40.000 0.00 0.00 31.79 2.90
113 114 4.532521 AGATTTGTTCTGGCTAGTAGGTGT 59.467 41.667 0.00 0.00 31.79 4.16
114 115 5.091261 AGATTTGTTCTGGCTAGTAGGTG 57.909 43.478 0.00 0.00 31.79 4.00
115 116 5.128991 GGTAGATTTGTTCTGGCTAGTAGGT 59.871 44.000 0.00 0.00 35.79 3.08
116 117 5.128827 TGGTAGATTTGTTCTGGCTAGTAGG 59.871 44.000 0.00 0.00 35.79 3.18
117 118 6.222038 TGGTAGATTTGTTCTGGCTAGTAG 57.778 41.667 0.00 0.00 35.79 2.57
118 119 6.212791 ACTTGGTAGATTTGTTCTGGCTAGTA 59.787 38.462 0.00 0.00 35.79 1.82
119 120 5.013183 ACTTGGTAGATTTGTTCTGGCTAGT 59.987 40.000 0.00 0.00 35.79 2.57
120 121 5.491982 ACTTGGTAGATTTGTTCTGGCTAG 58.508 41.667 0.00 0.00 35.79 3.42
121 122 5.488341 GACTTGGTAGATTTGTTCTGGCTA 58.512 41.667 0.00 0.00 35.79 3.93
122 123 4.327680 GACTTGGTAGATTTGTTCTGGCT 58.672 43.478 0.00 0.00 35.79 4.75
123 124 3.125316 CGACTTGGTAGATTTGTTCTGGC 59.875 47.826 0.00 0.00 35.79 4.85
124 125 4.566004 TCGACTTGGTAGATTTGTTCTGG 58.434 43.478 0.00 0.00 35.79 3.86
125 126 5.869344 TCATCGACTTGGTAGATTTGTTCTG 59.131 40.000 0.00 0.00 35.79 3.02
162 163 2.846039 ACTCCATCGTACGTCATGTC 57.154 50.000 16.05 0.00 0.00 3.06
226 237 3.780294 AGGCCAATGATACTTGTGAGGTA 59.220 43.478 5.01 0.00 0.00 3.08
255 266 2.108157 GGCGGCGGTCATCACATA 59.892 61.111 9.78 0.00 0.00 2.29
341 352 1.561542 CTAGGAGCCCATGTCAACCTT 59.438 52.381 0.00 0.00 0.00 3.50
382 393 3.642141 TCATACTCAGGCCACTGTGATA 58.358 45.455 9.86 0.00 45.14 2.15
383 394 2.470990 TCATACTCAGGCCACTGTGAT 58.529 47.619 9.86 0.00 45.14 3.06
404 415 3.717294 GGGACGATGTGTGGCCCT 61.717 66.667 0.00 0.00 35.86 5.19
548 562 6.149973 CACATTGACCACAACTATTGATGTCT 59.850 38.462 12.74 0.00 38.90 3.41
626 640 5.277250 TGAATAGTGGGATCCTGAGTGTTA 58.723 41.667 12.58 0.00 0.00 2.41
634 648 2.172717 CCCGTTTGAATAGTGGGATCCT 59.827 50.000 12.58 0.00 42.77 3.24
694 711 0.402887 TCCTCGTCCACTACCACTCA 59.597 55.000 0.00 0.00 0.00 3.41
718 747 2.421314 CTCCACGTGCACCACTCA 59.579 61.111 10.91 0.00 31.34 3.41
754 783 2.581216 AGTGTCTCCTCGTCCACTAA 57.419 50.000 0.00 0.00 36.44 2.24
816 845 3.437795 CGTCCTACGACCACGGCT 61.438 66.667 0.00 0.00 46.05 5.52
837 866 0.474614 GGCCTTCCTCTATCAACCCC 59.525 60.000 0.00 0.00 0.00 4.95
1155 1205 1.470098 GTGCATGATTTCTTGCGGTCT 59.530 47.619 12.15 0.00 46.27 3.85
1262 1313 7.865707 ACAGTTGAATACTCATTGAACTTCAC 58.134 34.615 0.34 3.08 43.42 3.18
1273 1324 6.288294 AGTTGTAGCAACAGTTGAATACTCA 58.712 36.000 17.99 7.27 36.83 3.41
1374 1429 4.040095 TCTGGCACATCTTGATCTATCCAG 59.960 45.833 0.00 0.00 38.20 3.86
1457 1512 7.471260 GCTCTTCATCTAAGCCTCTCTGAAATA 60.471 40.741 0.00 0.00 34.97 1.40
1594 1656 0.043183 TGCCTCATCCTCCTCTTGGA 59.957 55.000 0.00 0.00 40.69 3.53
1714 1839 5.650543 AGGTTTCACAAATCAAAGACACAC 58.349 37.500 0.00 0.00 0.00 3.82
1788 1938 7.760131 AGTTTCATCACAAGTTTCACAAATG 57.240 32.000 0.00 0.00 0.00 2.32
1850 2009 4.690748 TCCTCGTGTTCATCATTTCAAGTC 59.309 41.667 0.00 0.00 0.00 3.01
1969 2148 0.606604 TGTTCTAGGACAGTTCGGCC 59.393 55.000 0.00 0.00 0.00 6.13
1983 2183 0.035458 CAGGGGAGCGTTTCTGTTCT 59.965 55.000 0.00 0.00 0.00 3.01
2005 2205 2.624674 GATGGCCAACCCTACCGCAT 62.625 60.000 10.96 0.00 33.59 4.73
2203 2816 3.418684 ACCCTATCGCAGAAAAAGTGT 57.581 42.857 0.00 0.00 43.58 3.55
2217 2831 1.353394 GGTAGGCTGGCCAACCCTAT 61.353 60.000 26.32 11.80 38.92 2.57


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

AutoCloner maintained by Alex Coulton.