Multiple sequence alignment - TraesCS1B01G104200

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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 TraesCS1B01G104200 chr1B 100.000 2873 0 0 1 2873 114685573 114688445 0.000000e+00 5306.0
1 TraesCS1B01G104200 chr1B 83.301 509 56 22 2378 2873 143837991 143837499 2.630000e-120 442.0
2 TraesCS1B01G104200 chr6A 92.783 1441 76 15 1442 2873 206039510 206040931 0.000000e+00 2060.0
3 TraesCS1B01G104200 chr6A 85.200 1223 107 37 239 1423 390133350 390132164 0.000000e+00 1188.0
4 TraesCS1B01G104200 chr6A 89.138 847 69 9 1431 2269 149925646 149924815 0.000000e+00 1033.0
5 TraesCS1B01G104200 chr6A 79.200 125 13 13 223 342 167867782 167867898 1.100000e-09 75.0
6 TraesCS1B01G104200 chr6A 85.714 56 8 0 233 288 513610185 513610240 3.090000e-05 60.2
7 TraesCS1B01G104200 chr5A 92.249 1445 78 23 1442 2873 150629234 150630657 0.000000e+00 2017.0
8 TraesCS1B01G104200 chr5A 82.995 394 46 19 2312 2692 323082693 323082308 1.280000e-88 337.0
9 TraesCS1B01G104200 chr5A 81.633 98 17 1 515 611 628572865 628572962 2.370000e-11 80.5
10 TraesCS1B01G104200 chr3A 86.953 1211 88 35 247 1423 411058045 411059219 0.000000e+00 1297.0
11 TraesCS1B01G104200 chr3A 84.241 514 63 15 2371 2873 218070010 218069504 4.300000e-133 484.0
12 TraesCS1B01G104200 chr4A 89.268 1025 84 19 422 1423 389304291 389305312 0.000000e+00 1260.0
13 TraesCS1B01G104200 chr4A 84.971 346 43 7 2312 2653 732337415 732337075 2.740000e-90 342.0
14 TraesCS1B01G104200 chr4A 81.726 394 52 18 2312 2691 113484699 113484312 7.730000e-81 311.0
15 TraesCS1B01G104200 chr7A 86.885 1037 82 26 401 1423 431484690 431483694 0.000000e+00 1112.0
16 TraesCS1B01G104200 chr7A 89.831 59 3 3 233 289 236640292 236640235 3.970000e-09 73.1
17 TraesCS1B01G104200 chr6D 90.577 849 56 9 1432 2269 122256107 122256942 0.000000e+00 1103.0
18 TraesCS1B01G104200 chr6D 83.548 620 75 13 418 1026 238477679 238478282 3.230000e-154 555.0
19 TraesCS1B01G104200 chr6B 86.330 1068 73 42 327 1351 154908478 154907441 0.000000e+00 1096.0
20 TraesCS1B01G104200 chr6B 89.965 847 64 7 1432 2269 214028154 214028988 0.000000e+00 1074.0
21 TraesCS1B01G104200 chr1A 93.224 487 29 3 937 1423 380358384 380358866 0.000000e+00 713.0
22 TraesCS1B01G104200 chr1A 82.808 698 77 31 239 899 380357688 380358379 4.130000e-163 584.0
23 TraesCS1B01G104200 chr1A 90.950 221 19 1 1 220 72753390 72753610 2.160000e-76 296.0
24 TraesCS1B01G104200 chr4D 84.402 577 62 19 2312 2873 131715251 131714688 2.520000e-150 542.0
25 TraesCS1B01G104200 chr3B 83.566 572 65 25 2312 2869 370538118 370537562 2.550000e-140 508.0
26 TraesCS1B01G104200 chr3B 82.353 510 69 17 2378 2873 334650709 334650207 9.520000e-115 424.0
27 TraesCS1B01G104200 chr3B 91.935 62 5 0 233 294 523589802 523589741 1.420000e-13 87.9
28 TraesCS1B01G104200 chr2A 82.664 473 54 18 2378 2835 202764942 202765401 7.460000e-106 394.0
29 TraesCS1B01G104200 chr1D 93.182 220 14 1 1 219 72882330 72882549 3.570000e-84 322.0
30 TraesCS1B01G104200 chr5B 85.172 290 30 9 2594 2873 240822919 240823205 4.690000e-73 285.0


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 TraesCS1B01G104200 chr1B 114685573 114688445 2872 False 5306.0 5306 100.000 1 2873 1 chr1B.!!$F1 2872
1 TraesCS1B01G104200 chr6A 206039510 206040931 1421 False 2060.0 2060 92.783 1442 2873 1 chr6A.!!$F2 1431
2 TraesCS1B01G104200 chr6A 390132164 390133350 1186 True 1188.0 1188 85.200 239 1423 1 chr6A.!!$R2 1184
3 TraesCS1B01G104200 chr6A 149924815 149925646 831 True 1033.0 1033 89.138 1431 2269 1 chr6A.!!$R1 838
4 TraesCS1B01G104200 chr5A 150629234 150630657 1423 False 2017.0 2017 92.249 1442 2873 1 chr5A.!!$F1 1431
5 TraesCS1B01G104200 chr3A 411058045 411059219 1174 False 1297.0 1297 86.953 247 1423 1 chr3A.!!$F1 1176
6 TraesCS1B01G104200 chr3A 218069504 218070010 506 True 484.0 484 84.241 2371 2873 1 chr3A.!!$R1 502
7 TraesCS1B01G104200 chr4A 389304291 389305312 1021 False 1260.0 1260 89.268 422 1423 1 chr4A.!!$F1 1001
8 TraesCS1B01G104200 chr7A 431483694 431484690 996 True 1112.0 1112 86.885 401 1423 1 chr7A.!!$R2 1022
9 TraesCS1B01G104200 chr6D 122256107 122256942 835 False 1103.0 1103 90.577 1432 2269 1 chr6D.!!$F1 837
10 TraesCS1B01G104200 chr6D 238477679 238478282 603 False 555.0 555 83.548 418 1026 1 chr6D.!!$F2 608
11 TraesCS1B01G104200 chr6B 154907441 154908478 1037 True 1096.0 1096 86.330 327 1351 1 chr6B.!!$R1 1024
12 TraesCS1B01G104200 chr6B 214028154 214028988 834 False 1074.0 1074 89.965 1432 2269 1 chr6B.!!$F1 837
13 TraesCS1B01G104200 chr1A 380357688 380358866 1178 False 648.5 713 88.016 239 1423 2 chr1A.!!$F2 1184
14 TraesCS1B01G104200 chr4D 131714688 131715251 563 True 542.0 542 84.402 2312 2873 1 chr4D.!!$R1 561
15 TraesCS1B01G104200 chr3B 370537562 370538118 556 True 508.0 508 83.566 2312 2869 1 chr3B.!!$R2 557
16 TraesCS1B01G104200 chr3B 334650207 334650709 502 True 424.0 424 82.353 2378 2873 1 chr3B.!!$R1 495

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
350 351 0.108615 ACTTCCCGAACTCGCAGATG 60.109 55.0 0.00 0.00 38.18 2.90 F
1429 1568 0.107066 TGCTCTGTACATGGGCCATG 60.107 55.0 38.37 38.37 46.18 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 1794 0.108186 CTAACATCAGTGCCTGCGGA 60.108 55.000 0.0 0.0 0.0 5.54 R
2610 2787 8.926710 CCTTGTACTTCTCTGTTATTGTAGTTG 58.073 37.037 0.0 0.0 0.0 3.16 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
27 28 9.836864 ATTCTTTTTATTTCCTTTGAGCTGTTT 57.163 25.926 0.00 0.00 0.00 2.83
31 32 8.964420 TTTTATTTCCTTTGAGCTGTTTATCG 57.036 30.769 0.00 0.00 0.00 2.92
32 33 4.419522 TTTCCTTTGAGCTGTTTATCGC 57.580 40.909 0.00 0.00 0.00 4.58
33 34 3.334583 TCCTTTGAGCTGTTTATCGCT 57.665 42.857 0.00 0.00 39.61 4.93
34 35 3.002791 TCCTTTGAGCTGTTTATCGCTG 58.997 45.455 0.00 0.00 36.45 5.18
35 36 2.096496 CCTTTGAGCTGTTTATCGCTGG 59.904 50.000 0.00 0.00 36.45 4.85
36 37 2.760634 TTGAGCTGTTTATCGCTGGA 57.239 45.000 0.00 0.00 36.45 3.86
37 38 2.760634 TGAGCTGTTTATCGCTGGAA 57.239 45.000 0.00 0.00 36.45 3.53
38 39 3.266510 TGAGCTGTTTATCGCTGGAAT 57.733 42.857 0.00 0.00 36.45 3.01
39 40 3.198068 TGAGCTGTTTATCGCTGGAATC 58.802 45.455 0.00 0.00 36.45 2.52
40 41 3.198068 GAGCTGTTTATCGCTGGAATCA 58.802 45.455 0.00 0.00 36.45 2.57
41 42 3.609853 AGCTGTTTATCGCTGGAATCAA 58.390 40.909 0.00 0.00 34.69 2.57
42 43 3.624861 AGCTGTTTATCGCTGGAATCAAG 59.375 43.478 0.00 0.00 34.69 3.02
43 44 3.623060 GCTGTTTATCGCTGGAATCAAGA 59.377 43.478 0.00 0.00 0.00 3.02
44 45 4.094887 GCTGTTTATCGCTGGAATCAAGAA 59.905 41.667 0.00 0.00 0.00 2.52
45 46 5.391950 GCTGTTTATCGCTGGAATCAAGAAA 60.392 40.000 0.00 0.00 0.00 2.52
46 47 6.678900 GCTGTTTATCGCTGGAATCAAGAAAT 60.679 38.462 0.00 0.00 0.00 2.17
47 48 6.785191 TGTTTATCGCTGGAATCAAGAAATC 58.215 36.000 0.00 0.00 0.00 2.17
48 49 6.374053 TGTTTATCGCTGGAATCAAGAAATCA 59.626 34.615 0.00 0.00 0.00 2.57
49 50 7.067372 TGTTTATCGCTGGAATCAAGAAATCAT 59.933 33.333 0.00 0.00 0.00 2.45
50 51 5.686159 ATCGCTGGAATCAAGAAATCATC 57.314 39.130 0.00 0.00 0.00 2.92
51 52 3.879295 TCGCTGGAATCAAGAAATCATCC 59.121 43.478 0.00 0.00 0.00 3.51
52 53 3.303593 CGCTGGAATCAAGAAATCATCCG 60.304 47.826 0.00 0.00 0.00 4.18
53 54 3.629398 GCTGGAATCAAGAAATCATCCGT 59.371 43.478 0.00 0.00 0.00 4.69
54 55 4.816385 GCTGGAATCAAGAAATCATCCGTA 59.184 41.667 0.00 0.00 0.00 4.02
55 56 5.296780 GCTGGAATCAAGAAATCATCCGTAA 59.703 40.000 0.00 0.00 0.00 3.18
56 57 6.512415 GCTGGAATCAAGAAATCATCCGTAAG 60.512 42.308 0.00 0.00 0.00 2.34
57 58 6.414732 TGGAATCAAGAAATCATCCGTAAGT 58.585 36.000 0.00 0.00 0.00 2.24
58 59 7.561251 TGGAATCAAGAAATCATCCGTAAGTA 58.439 34.615 0.00 0.00 0.00 2.24
59 60 8.044309 TGGAATCAAGAAATCATCCGTAAGTAA 58.956 33.333 0.00 0.00 0.00 2.24
60 61 8.889717 GGAATCAAGAAATCATCCGTAAGTAAA 58.110 33.333 0.00 0.00 0.00 2.01
63 64 9.613428 ATCAAGAAATCATCCGTAAGTAAATGA 57.387 29.630 0.00 0.00 34.70 2.57
64 65 9.443323 TCAAGAAATCATCCGTAAGTAAATGAA 57.557 29.630 0.00 0.00 34.16 2.57
68 69 9.503427 GAAATCATCCGTAAGTAAATGAAAAGG 57.497 33.333 0.00 0.00 34.16 3.11
69 70 8.575649 AATCATCCGTAAGTAAATGAAAAGGT 57.424 30.769 0.00 0.00 34.16 3.50
70 71 7.372451 TCATCCGTAAGTAAATGAAAAGGTG 57.628 36.000 0.00 0.00 0.00 4.00
71 72 7.162761 TCATCCGTAAGTAAATGAAAAGGTGA 58.837 34.615 0.00 0.00 0.00 4.02
72 73 7.827236 TCATCCGTAAGTAAATGAAAAGGTGAT 59.173 33.333 0.00 0.00 0.00 3.06
73 74 7.605410 TCCGTAAGTAAATGAAAAGGTGATC 57.395 36.000 0.00 0.00 0.00 2.92
74 75 7.391620 TCCGTAAGTAAATGAAAAGGTGATCT 58.608 34.615 0.00 0.00 0.00 2.75
75 76 7.548075 TCCGTAAGTAAATGAAAAGGTGATCTC 59.452 37.037 0.00 0.00 0.00 2.75
76 77 7.201617 CCGTAAGTAAATGAAAAGGTGATCTCC 60.202 40.741 5.64 5.64 0.00 3.71
77 78 7.333423 CGTAAGTAAATGAAAAGGTGATCTCCA 59.667 37.037 15.93 0.00 0.00 3.86
78 79 7.454260 AAGTAAATGAAAAGGTGATCTCCAC 57.546 36.000 15.93 2.35 44.95 4.02
79 80 6.784031 AGTAAATGAAAAGGTGATCTCCACT 58.216 36.000 15.93 4.52 45.03 4.00
80 81 7.918076 AGTAAATGAAAAGGTGATCTCCACTA 58.082 34.615 15.93 0.00 45.03 2.74
81 82 8.383175 AGTAAATGAAAAGGTGATCTCCACTAA 58.617 33.333 15.93 0.00 45.03 2.24
82 83 7.693969 AAATGAAAAGGTGATCTCCACTAAG 57.306 36.000 15.93 0.00 45.03 2.18
83 84 4.579869 TGAAAAGGTGATCTCCACTAAGC 58.420 43.478 15.93 1.48 45.03 3.09
84 85 4.287067 TGAAAAGGTGATCTCCACTAAGCT 59.713 41.667 15.93 0.00 45.03 3.74
85 86 5.483937 TGAAAAGGTGATCTCCACTAAGCTA 59.516 40.000 15.93 0.00 45.03 3.32
86 87 6.013725 TGAAAAGGTGATCTCCACTAAGCTAA 60.014 38.462 15.93 0.00 45.03 3.09
87 88 6.374417 AAAGGTGATCTCCACTAAGCTAAA 57.626 37.500 15.93 0.00 45.03 1.85
88 89 6.374417 AAGGTGATCTCCACTAAGCTAAAA 57.626 37.500 15.93 0.00 45.03 1.52
89 90 6.567602 AGGTGATCTCCACTAAGCTAAAAT 57.432 37.500 15.93 0.00 45.03 1.82
90 91 6.352516 AGGTGATCTCCACTAAGCTAAAATG 58.647 40.000 15.93 0.00 45.03 2.32
91 92 6.069963 AGGTGATCTCCACTAAGCTAAAATGT 60.070 38.462 15.93 0.00 45.03 2.71
92 93 6.258947 GGTGATCTCCACTAAGCTAAAATGTC 59.741 42.308 8.97 0.00 45.03 3.06
93 94 6.818644 GTGATCTCCACTAAGCTAAAATGTCA 59.181 38.462 0.00 0.00 42.44 3.58
94 95 6.818644 TGATCTCCACTAAGCTAAAATGTCAC 59.181 38.462 0.00 0.00 0.00 3.67
95 96 6.109156 TCTCCACTAAGCTAAAATGTCACA 57.891 37.500 0.00 0.00 0.00 3.58
96 97 6.711277 TCTCCACTAAGCTAAAATGTCACAT 58.289 36.000 0.00 0.00 0.00 3.21
97 98 6.818644 TCTCCACTAAGCTAAAATGTCACATC 59.181 38.462 0.00 0.00 0.00 3.06
98 99 6.472016 TCCACTAAGCTAAAATGTCACATCA 58.528 36.000 0.00 0.00 0.00 3.07
99 100 6.939730 TCCACTAAGCTAAAATGTCACATCAA 59.060 34.615 0.00 0.00 0.00 2.57
100 101 7.023575 CCACTAAGCTAAAATGTCACATCAAC 58.976 38.462 0.00 0.00 0.00 3.18
101 102 7.308529 CCACTAAGCTAAAATGTCACATCAACA 60.309 37.037 0.00 0.00 0.00 3.33
102 103 7.535258 CACTAAGCTAAAATGTCACATCAACAC 59.465 37.037 0.00 0.00 0.00 3.32
103 104 6.389830 AAGCTAAAATGTCACATCAACACA 57.610 33.333 0.00 0.00 0.00 3.72
104 105 6.005583 AGCTAAAATGTCACATCAACACAG 57.994 37.500 0.00 0.00 0.00 3.66
105 106 5.764686 AGCTAAAATGTCACATCAACACAGA 59.235 36.000 0.00 0.00 0.00 3.41
106 107 6.262944 AGCTAAAATGTCACATCAACACAGAA 59.737 34.615 0.00 0.00 0.00 3.02
107 108 7.040201 AGCTAAAATGTCACATCAACACAGAAT 60.040 33.333 0.00 0.00 0.00 2.40
108 109 7.272084 GCTAAAATGTCACATCAACACAGAATC 59.728 37.037 0.00 0.00 0.00 2.52
109 110 6.638096 AAATGTCACATCAACACAGAATCA 57.362 33.333 0.00 0.00 0.00 2.57
110 111 6.829229 AATGTCACATCAACACAGAATCAT 57.171 33.333 0.00 0.00 0.00 2.45
111 112 5.616488 TGTCACATCAACACAGAATCATG 57.384 39.130 0.00 0.00 0.00 3.07
112 113 4.083164 TGTCACATCAACACAGAATCATGC 60.083 41.667 0.00 0.00 0.00 4.06
113 114 4.073549 TCACATCAACACAGAATCATGCA 58.926 39.130 0.00 0.00 0.00 3.96
114 115 4.703093 TCACATCAACACAGAATCATGCAT 59.297 37.500 0.00 0.00 0.00 3.96
115 116 5.881443 TCACATCAACACAGAATCATGCATA 59.119 36.000 0.00 0.00 0.00 3.14
116 117 6.374894 TCACATCAACACAGAATCATGCATAA 59.625 34.615 0.00 0.00 0.00 1.90
117 118 7.030768 CACATCAACACAGAATCATGCATAAA 58.969 34.615 0.00 0.00 0.00 1.40
118 119 7.542824 CACATCAACACAGAATCATGCATAAAA 59.457 33.333 0.00 0.00 0.00 1.52
119 120 8.089597 ACATCAACACAGAATCATGCATAAAAA 58.910 29.630 0.00 0.00 0.00 1.94
120 121 8.592155 CATCAACACAGAATCATGCATAAAAAG 58.408 33.333 0.00 0.00 0.00 2.27
121 122 7.092079 TCAACACAGAATCATGCATAAAAAGG 58.908 34.615 0.00 0.00 0.00 3.11
122 123 6.839124 ACACAGAATCATGCATAAAAAGGA 57.161 33.333 0.00 0.00 0.00 3.36
123 124 6.624423 ACACAGAATCATGCATAAAAAGGAC 58.376 36.000 0.00 0.00 0.00 3.85
124 125 6.038356 CACAGAATCATGCATAAAAAGGACC 58.962 40.000 0.00 0.00 0.00 4.46
125 126 5.127682 ACAGAATCATGCATAAAAAGGACCC 59.872 40.000 0.00 0.00 0.00 4.46
126 127 5.127519 CAGAATCATGCATAAAAAGGACCCA 59.872 40.000 0.00 0.00 0.00 4.51
127 128 5.901276 AGAATCATGCATAAAAAGGACCCAT 59.099 36.000 0.00 0.00 0.00 4.00
128 129 5.540400 ATCATGCATAAAAAGGACCCATG 57.460 39.130 0.00 0.00 0.00 3.66
129 130 3.132646 TCATGCATAAAAAGGACCCATGC 59.867 43.478 0.00 0.00 41.81 4.06
131 132 2.902486 TGCATAAAAAGGACCCATGCAA 59.098 40.909 5.15 0.00 46.47 4.08
132 133 3.518705 TGCATAAAAAGGACCCATGCAAT 59.481 39.130 5.15 0.00 46.47 3.56
133 134 4.122046 GCATAAAAAGGACCCATGCAATC 58.878 43.478 0.00 0.00 41.25 2.67
134 135 4.382901 GCATAAAAAGGACCCATGCAATCA 60.383 41.667 0.00 0.00 41.25 2.57
135 136 5.685599 GCATAAAAAGGACCCATGCAATCAT 60.686 40.000 0.00 0.00 41.25 2.45
136 137 9.938135 TGCATAAAAAGGACCCATGCAATCATG 62.938 40.741 5.15 0.00 46.47 3.07
231 232 9.515020 ACAACAAAATAAATCTTACACACACAG 57.485 29.630 0.00 0.00 0.00 3.66
232 233 9.729023 CAACAAAATAAATCTTACACACACAGA 57.271 29.630 0.00 0.00 0.00 3.41
302 303 2.664402 ATTTGAACCACAGTCAGCCT 57.336 45.000 0.00 0.00 0.00 4.58
317 318 1.301479 GCCTTATAAGGGCCCGACG 60.301 63.158 28.81 2.71 46.56 5.12
346 347 0.942410 CGAAACTTCCCGAACTCGCA 60.942 55.000 0.00 0.00 38.18 5.10
350 351 0.108615 ACTTCCCGAACTCGCAGATG 60.109 55.000 0.00 0.00 38.18 2.90
351 352 0.173481 CTTCCCGAACTCGCAGATGA 59.827 55.000 0.00 0.00 38.18 2.92
388 390 4.410400 CGCCCACCACTTCCCCTC 62.410 72.222 0.00 0.00 0.00 4.30
394 396 3.400054 CCACTTCCCCTCCCCGAC 61.400 72.222 0.00 0.00 0.00 4.79
615 729 2.273179 CCCTGGAGACGAACACGGA 61.273 63.158 0.00 0.00 0.00 4.69
681 802 2.629656 CCTGCCCACTGCCTTTTCG 61.630 63.158 0.00 0.00 40.16 3.46
698 819 2.276409 GTCCATGCATGCCCTCCA 59.724 61.111 21.69 0.00 0.00 3.86
755 877 4.402528 CGCCCGGGATCCACACAA 62.403 66.667 29.31 0.00 0.00 3.33
814 937 0.685097 CAACCTTGACCTTCCCGAGA 59.315 55.000 0.00 0.00 0.00 4.04
815 938 1.279271 CAACCTTGACCTTCCCGAGAT 59.721 52.381 0.00 0.00 0.00 2.75
908 1040 2.258591 CGTCACCAGTACGCTGCT 59.741 61.111 0.00 0.00 41.26 4.24
1078 1216 4.362677 TCCCCTTCTTCTACTACAGCAAT 58.637 43.478 0.00 0.00 0.00 3.56
1085 1223 3.060978 TCTACTACAGCAATACGCACG 57.939 47.619 0.00 0.00 46.13 5.34
1108 1246 3.411351 GCGTTGCACATCCGTCGT 61.411 61.111 0.00 0.00 0.00 4.34
1112 1250 3.816367 TTGCACATCCGTCGTGGCA 62.816 57.895 0.00 0.00 37.80 4.92
1155 1293 1.732941 CCAAGGTGTGTATTGCGCTA 58.267 50.000 9.73 0.00 0.00 4.26
1171 1309 5.673337 TGCGCTACTCATTCAATAAATCC 57.327 39.130 9.73 0.00 0.00 3.01
1208 1346 0.824759 GGGTACGTCATGCCTCTTCT 59.175 55.000 0.00 0.00 32.53 2.85
1223 1361 0.240411 CTTCTTTGCCTGCTCACTGC 59.760 55.000 0.00 0.00 43.25 4.40
1315 1453 7.226441 TCCTGAATCATATAGTGGTTGATTGG 58.774 38.462 3.76 1.39 39.52 3.16
1322 1460 8.642935 TCATATAGTGGTTGATTGGTTTTTCA 57.357 30.769 0.00 0.00 0.00 2.69
1423 1562 4.696877 TCTGATTTGTTGCTCTGTACATGG 59.303 41.667 0.00 0.00 0.00 3.66
1424 1563 3.758023 TGATTTGTTGCTCTGTACATGGG 59.242 43.478 0.00 0.00 0.00 4.00
1425 1564 1.533625 TTGTTGCTCTGTACATGGGC 58.466 50.000 9.46 9.46 0.00 5.36
1426 1565 0.322456 TGTTGCTCTGTACATGGGCC 60.322 55.000 12.69 0.00 0.00 5.80
1427 1566 0.322456 GTTGCTCTGTACATGGGCCA 60.322 55.000 9.61 9.61 0.00 5.36
1428 1567 0.625316 TTGCTCTGTACATGGGCCAT 59.375 50.000 14.78 14.78 0.00 4.40
1429 1568 0.107066 TGCTCTGTACATGGGCCATG 60.107 55.000 38.37 38.37 46.18 3.66
1440 1579 4.049546 CATGGGCCATGTTGTAATTCAG 57.950 45.455 33.65 7.94 37.12 3.02
1601 1740 2.742372 CCGAAGCCTTGGACACCG 60.742 66.667 0.00 0.00 0.00 4.94
1655 1794 5.524281 GGAGTCTTCGAGTTTGAGAAGTTTT 59.476 40.000 5.30 0.00 43.07 2.43
1871 2014 3.563808 GCCGACAATATGAGCCACATTTA 59.436 43.478 0.00 0.00 40.07 1.40
2046 2197 8.483758 ACGTTATATGGAAACTTTGAGATAGGT 58.516 33.333 0.00 0.00 0.00 3.08
2047 2198 9.326413 CGTTATATGGAAACTTTGAGATAGGTT 57.674 33.333 0.00 0.00 0.00 3.50
2050 2201 6.840780 ATGGAAACTTTGAGATAGGTTTGG 57.159 37.500 0.00 0.00 32.95 3.28
2051 2202 5.076873 TGGAAACTTTGAGATAGGTTTGGG 58.923 41.667 0.00 0.00 32.95 4.12
2079 2230 4.335315 TCGCCAATTTTTGCTAGTAGATGG 59.665 41.667 0.00 0.00 0.00 3.51
2133 2284 4.321718 AGTGAAGTGATGTGACTGGAATG 58.678 43.478 0.00 0.00 0.00 2.67
2138 2289 5.227569 AGTGATGTGACTGGAATGTAACA 57.772 39.130 0.00 0.00 35.93 2.41
2178 2331 5.948992 ATGGTTTTAAGCTCTGTGTCTTC 57.051 39.130 0.00 0.00 0.00 2.87
2216 2369 5.636837 TCTGTGTTGTTTGCTCTGTTTTAC 58.363 37.500 0.00 0.00 0.00 2.01
2441 2609 7.334171 ACTGAAAAACCAAGAAAGTCCAAATTG 59.666 33.333 0.00 0.00 0.00 2.32
2848 3045 7.745620 ACCAAGAAGTTCAGTTCGAAATAAT 57.254 32.000 0.00 0.00 34.69 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.405587 CGATAAACAGCTCAAAGGAAATAAAAA 57.594 29.630 0.00 0.00 0.00 1.94
6 7 7.540745 GCGATAAACAGCTCAAAGGAAATAAAA 59.459 33.333 0.00 0.00 0.00 1.52
7 8 7.027161 GCGATAAACAGCTCAAAGGAAATAAA 58.973 34.615 0.00 0.00 0.00 1.40
8 9 6.374333 AGCGATAAACAGCTCAAAGGAAATAA 59.626 34.615 0.00 0.00 39.98 1.40
9 10 5.880332 AGCGATAAACAGCTCAAAGGAAATA 59.120 36.000 0.00 0.00 39.98 1.40
10 11 4.702131 AGCGATAAACAGCTCAAAGGAAAT 59.298 37.500 0.00 0.00 39.98 2.17
11 12 4.072131 AGCGATAAACAGCTCAAAGGAAA 58.928 39.130 0.00 0.00 39.98 3.13
12 13 3.436704 CAGCGATAAACAGCTCAAAGGAA 59.563 43.478 0.00 0.00 42.52 3.36
13 14 3.002791 CAGCGATAAACAGCTCAAAGGA 58.997 45.455 0.00 0.00 42.52 3.36
14 15 2.096496 CCAGCGATAAACAGCTCAAAGG 59.904 50.000 0.00 0.00 42.52 3.11
15 16 3.002791 TCCAGCGATAAACAGCTCAAAG 58.997 45.455 0.00 0.00 42.52 2.77
16 17 3.052455 TCCAGCGATAAACAGCTCAAA 57.948 42.857 0.00 0.00 42.52 2.69
17 18 2.760634 TCCAGCGATAAACAGCTCAA 57.239 45.000 0.00 0.00 42.52 3.02
18 19 2.760634 TTCCAGCGATAAACAGCTCA 57.239 45.000 0.00 0.00 42.52 4.26
19 20 3.198068 TGATTCCAGCGATAAACAGCTC 58.802 45.455 0.00 0.00 42.52 4.09
20 21 3.266510 TGATTCCAGCGATAAACAGCT 57.733 42.857 0.00 0.00 45.74 4.24
21 22 3.623060 TCTTGATTCCAGCGATAAACAGC 59.377 43.478 0.00 0.00 0.00 4.40
22 23 5.801350 TTCTTGATTCCAGCGATAAACAG 57.199 39.130 0.00 0.00 0.00 3.16
23 24 6.374053 TGATTTCTTGATTCCAGCGATAAACA 59.626 34.615 0.00 0.00 0.00 2.83
24 25 6.785191 TGATTTCTTGATTCCAGCGATAAAC 58.215 36.000 0.00 0.00 0.00 2.01
25 26 7.255242 GGATGATTTCTTGATTCCAGCGATAAA 60.255 37.037 0.00 0.00 0.00 1.40
26 27 6.205464 GGATGATTTCTTGATTCCAGCGATAA 59.795 38.462 0.00 0.00 0.00 1.75
27 28 5.702670 GGATGATTTCTTGATTCCAGCGATA 59.297 40.000 0.00 0.00 0.00 2.92
28 29 4.518211 GGATGATTTCTTGATTCCAGCGAT 59.482 41.667 0.00 0.00 0.00 4.58
29 30 3.879295 GGATGATTTCTTGATTCCAGCGA 59.121 43.478 0.00 0.00 0.00 4.93
30 31 3.303593 CGGATGATTTCTTGATTCCAGCG 60.304 47.826 0.00 0.00 0.00 5.18
31 32 3.629398 ACGGATGATTTCTTGATTCCAGC 59.371 43.478 0.00 0.00 0.00 4.85
32 33 6.540189 ACTTACGGATGATTTCTTGATTCCAG 59.460 38.462 0.00 0.00 0.00 3.86
33 34 6.414732 ACTTACGGATGATTTCTTGATTCCA 58.585 36.000 0.00 0.00 0.00 3.53
34 35 6.927294 ACTTACGGATGATTTCTTGATTCC 57.073 37.500 0.00 0.00 0.00 3.01
37 38 9.613428 TCATTTACTTACGGATGATTTCTTGAT 57.387 29.630 0.00 0.00 0.00 2.57
38 39 9.443323 TTCATTTACTTACGGATGATTTCTTGA 57.557 29.630 0.00 0.00 0.00 3.02
42 43 9.503427 CCTTTTCATTTACTTACGGATGATTTC 57.497 33.333 0.00 0.00 0.00 2.17
43 44 9.020731 ACCTTTTCATTTACTTACGGATGATTT 57.979 29.630 0.00 0.00 0.00 2.17
44 45 8.458843 CACCTTTTCATTTACTTACGGATGATT 58.541 33.333 0.00 0.00 0.00 2.57
45 46 7.827236 TCACCTTTTCATTTACTTACGGATGAT 59.173 33.333 0.00 0.00 0.00 2.45
46 47 7.162761 TCACCTTTTCATTTACTTACGGATGA 58.837 34.615 0.00 0.00 0.00 2.92
47 48 7.372451 TCACCTTTTCATTTACTTACGGATG 57.628 36.000 0.00 0.00 0.00 3.51
48 49 8.047310 AGATCACCTTTTCATTTACTTACGGAT 58.953 33.333 0.00 0.00 0.00 4.18
49 50 7.391620 AGATCACCTTTTCATTTACTTACGGA 58.608 34.615 0.00 0.00 0.00 4.69
50 51 7.201617 GGAGATCACCTTTTCATTTACTTACGG 60.202 40.741 1.33 0.00 0.00 4.02
51 52 7.333423 TGGAGATCACCTTTTCATTTACTTACG 59.667 37.037 10.73 0.00 0.00 3.18
52 53 8.451748 GTGGAGATCACCTTTTCATTTACTTAC 58.548 37.037 10.73 0.00 40.39 2.34
53 54 8.561738 GTGGAGATCACCTTTTCATTTACTTA 57.438 34.615 10.73 0.00 40.39 2.24
54 55 7.454260 GTGGAGATCACCTTTTCATTTACTT 57.546 36.000 10.73 0.00 40.39 2.24
68 69 6.818644 TGACATTTTAGCTTAGTGGAGATCAC 59.181 38.462 0.00 0.00 46.39 3.06
69 70 6.818644 GTGACATTTTAGCTTAGTGGAGATCA 59.181 38.462 0.00 0.00 0.00 2.92
70 71 6.818644 TGTGACATTTTAGCTTAGTGGAGATC 59.181 38.462 0.00 0.00 0.00 2.75
71 72 6.711277 TGTGACATTTTAGCTTAGTGGAGAT 58.289 36.000 0.00 0.00 0.00 2.75
72 73 6.109156 TGTGACATTTTAGCTTAGTGGAGA 57.891 37.500 0.00 0.00 0.00 3.71
73 74 6.595326 TGATGTGACATTTTAGCTTAGTGGAG 59.405 38.462 0.00 0.00 0.00 3.86
74 75 6.472016 TGATGTGACATTTTAGCTTAGTGGA 58.528 36.000 0.00 0.00 0.00 4.02
75 76 6.741992 TGATGTGACATTTTAGCTTAGTGG 57.258 37.500 0.00 0.00 0.00 4.00
76 77 7.535258 GTGTTGATGTGACATTTTAGCTTAGTG 59.465 37.037 0.00 0.00 0.00 2.74
77 78 7.228507 TGTGTTGATGTGACATTTTAGCTTAGT 59.771 33.333 0.00 0.00 0.00 2.24
78 79 7.584108 TGTGTTGATGTGACATTTTAGCTTAG 58.416 34.615 0.00 0.00 0.00 2.18
79 80 7.443879 TCTGTGTTGATGTGACATTTTAGCTTA 59.556 33.333 0.00 0.00 0.00 3.09
80 81 6.262944 TCTGTGTTGATGTGACATTTTAGCTT 59.737 34.615 0.00 0.00 0.00 3.74
81 82 5.764686 TCTGTGTTGATGTGACATTTTAGCT 59.235 36.000 0.00 0.00 0.00 3.32
82 83 6.000891 TCTGTGTTGATGTGACATTTTAGC 57.999 37.500 0.00 0.00 0.00 3.09
83 84 8.291740 TGATTCTGTGTTGATGTGACATTTTAG 58.708 33.333 0.00 0.00 0.00 1.85
84 85 8.164058 TGATTCTGTGTTGATGTGACATTTTA 57.836 30.769 0.00 0.00 0.00 1.52
85 86 7.041635 TGATTCTGTGTTGATGTGACATTTT 57.958 32.000 0.00 0.00 0.00 1.82
86 87 6.638096 TGATTCTGTGTTGATGTGACATTT 57.362 33.333 0.00 0.00 0.00 2.32
87 88 6.617879 CATGATTCTGTGTTGATGTGACATT 58.382 36.000 0.00 0.00 0.00 2.71
88 89 5.392703 GCATGATTCTGTGTTGATGTGACAT 60.393 40.000 0.00 0.00 0.00 3.06
89 90 4.083164 GCATGATTCTGTGTTGATGTGACA 60.083 41.667 0.00 0.00 0.00 3.58
90 91 4.083164 TGCATGATTCTGTGTTGATGTGAC 60.083 41.667 0.00 0.00 0.00 3.67
91 92 4.073549 TGCATGATTCTGTGTTGATGTGA 58.926 39.130 0.00 0.00 0.00 3.58
92 93 4.428615 TGCATGATTCTGTGTTGATGTG 57.571 40.909 0.00 0.00 0.00 3.21
93 94 6.762702 TTATGCATGATTCTGTGTTGATGT 57.237 33.333 10.16 0.00 0.00 3.06
94 95 8.468720 TTTTTATGCATGATTCTGTGTTGATG 57.531 30.769 10.16 0.00 0.00 3.07
95 96 7.762615 CCTTTTTATGCATGATTCTGTGTTGAT 59.237 33.333 10.16 0.00 0.00 2.57
96 97 7.039853 TCCTTTTTATGCATGATTCTGTGTTGA 60.040 33.333 10.16 0.00 0.00 3.18
97 98 7.062605 GTCCTTTTTATGCATGATTCTGTGTTG 59.937 37.037 10.16 0.00 0.00 3.33
98 99 7.092716 GTCCTTTTTATGCATGATTCTGTGTT 58.907 34.615 10.16 0.00 0.00 3.32
99 100 6.350445 GGTCCTTTTTATGCATGATTCTGTGT 60.350 38.462 10.16 0.00 0.00 3.72
100 101 6.038356 GGTCCTTTTTATGCATGATTCTGTG 58.962 40.000 10.16 0.00 0.00 3.66
101 102 5.127682 GGGTCCTTTTTATGCATGATTCTGT 59.872 40.000 10.16 0.00 0.00 3.41
102 103 5.127519 TGGGTCCTTTTTATGCATGATTCTG 59.872 40.000 10.16 0.00 0.00 3.02
103 104 5.271598 TGGGTCCTTTTTATGCATGATTCT 58.728 37.500 10.16 0.00 0.00 2.40
104 105 5.596836 TGGGTCCTTTTTATGCATGATTC 57.403 39.130 10.16 0.00 0.00 2.52
105 106 5.685599 GCATGGGTCCTTTTTATGCATGATT 60.686 40.000 10.16 0.00 42.63 2.57
106 107 4.202284 GCATGGGTCCTTTTTATGCATGAT 60.202 41.667 10.16 0.00 42.63 2.45
107 108 3.132646 GCATGGGTCCTTTTTATGCATGA 59.867 43.478 10.16 0.00 42.63 3.07
108 109 3.118702 TGCATGGGTCCTTTTTATGCATG 60.119 43.478 10.16 0.00 46.31 4.06
109 110 3.106054 TGCATGGGTCCTTTTTATGCAT 58.894 40.909 3.79 3.79 46.31 3.96
111 112 3.608316 TTGCATGGGTCCTTTTTATGC 57.392 42.857 0.00 0.00 43.21 3.14
112 113 5.341872 TGATTGCATGGGTCCTTTTTATG 57.658 39.130 0.00 0.00 0.00 1.90
113 114 5.920903 CATGATTGCATGGGTCCTTTTTAT 58.079 37.500 0.00 0.00 46.45 1.40
114 115 5.341872 CATGATTGCATGGGTCCTTTTTA 57.658 39.130 0.00 0.00 46.45 1.52
115 116 4.210724 CATGATTGCATGGGTCCTTTTT 57.789 40.909 0.00 0.00 46.45 1.94
116 117 3.899052 CATGATTGCATGGGTCCTTTT 57.101 42.857 0.00 0.00 46.45 2.27
127 128 7.012515 GAAATAATTTTCCCATGCATGATTGCA 59.987 33.333 28.31 9.12 46.86 4.08
128 129 7.357303 GAAATAATTTTCCCATGCATGATTGC 58.643 34.615 28.31 11.42 41.03 3.56
205 206 9.515020 CTGTGTGTGTAAGATTTATTTTGTTGT 57.485 29.630 0.00 0.00 0.00 3.32
206 207 9.729023 TCTGTGTGTGTAAGATTTATTTTGTTG 57.271 29.630 0.00 0.00 0.00 3.33
280 281 3.821033 AGGCTGACTGTGGTTCAAATAAC 59.179 43.478 0.00 0.00 0.00 1.89
281 282 4.098914 AGGCTGACTGTGGTTCAAATAA 57.901 40.909 0.00 0.00 0.00 1.40
288 289 3.054361 CCCTTATAAGGCTGACTGTGGTT 60.054 47.826 24.05 0.00 45.10 3.67
290 291 3.199880 CCCTTATAAGGCTGACTGTGG 57.800 52.381 24.05 5.27 45.10 4.17
317 318 1.166129 GGAAGTTTCGGAAGGAAGCC 58.834 55.000 0.00 0.00 36.61 4.35
321 322 1.050204 TTCGGGAAGTTTCGGAAGGA 58.950 50.000 0.13 0.00 0.00 3.36
322 323 1.154197 GTTCGGGAAGTTTCGGAAGG 58.846 55.000 4.46 0.00 0.00 3.46
324 325 1.603678 CGAGTTCGGGAAGTTTCGGAA 60.604 52.381 0.13 0.13 35.37 4.30
328 329 0.790814 CTGCGAGTTCGGGAAGTTTC 59.209 55.000 3.50 0.00 40.23 2.78
478 566 4.410400 GGGGTTGCTCGGTGGAGG 62.410 72.222 0.00 0.00 40.80 4.30
479 567 4.760047 CGGGGTTGCTCGGTGGAG 62.760 72.222 0.00 0.00 43.46 3.86
681 802 1.152610 ATGGAGGGCATGCATGGAC 60.153 57.895 27.34 12.00 38.74 4.02
908 1040 4.155733 CCCGTCAGCCATGCGGTA 62.156 66.667 7.74 0.00 41.55 4.02
935 1067 4.082523 CCAGCCCGGACGTGATGT 62.083 66.667 0.73 0.00 36.56 3.06
1108 1246 1.227943 GCTGGACAGTGAGTTGCCA 60.228 57.895 0.00 0.00 0.00 4.92
1155 1293 6.604396 TGCACATCAGGATTTATTGAATGAGT 59.396 34.615 0.00 0.00 0.00 3.41
1239 1377 2.623889 GAGATAGAACAAGGAGCCGCTA 59.376 50.000 0.00 0.00 0.00 4.26
1315 1453 1.857837 CACCAACACGCCATGAAAAAC 59.142 47.619 0.00 0.00 0.00 2.43
1322 1460 0.881118 GAACATCACCAACACGCCAT 59.119 50.000 0.00 0.00 0.00 4.40
1371 1510 7.795047 AGTGAAAAACAGAAAAATTGGAGGAT 58.205 30.769 0.00 0.00 0.00 3.24
1423 1562 2.754552 TCAGCTGAATTACAACATGGCC 59.245 45.455 15.67 0.00 0.00 5.36
1424 1563 3.191162 TGTCAGCTGAATTACAACATGGC 59.809 43.478 20.19 1.27 0.00 4.40
1425 1564 5.571784 ATGTCAGCTGAATTACAACATGG 57.428 39.130 20.19 0.00 28.86 3.66
1426 1565 7.620600 GCAAAATGTCAGCTGAATTACAACATG 60.621 37.037 20.19 12.98 29.99 3.21
1427 1566 6.366877 GCAAAATGTCAGCTGAATTACAACAT 59.633 34.615 20.19 13.34 30.50 2.71
1428 1567 5.691305 GCAAAATGTCAGCTGAATTACAACA 59.309 36.000 20.19 11.42 0.00 3.33
1429 1568 5.691305 TGCAAAATGTCAGCTGAATTACAAC 59.309 36.000 20.19 5.15 0.00 3.32
1440 1579 2.223782 TGTTCTGGTGCAAAATGTCAGC 60.224 45.455 0.00 0.00 0.00 4.26
1601 1740 2.673368 CGTTCCAGATAACAGTCTTGGC 59.327 50.000 0.00 0.00 0.00 4.52
1655 1794 0.108186 CTAACATCAGTGCCTGCGGA 60.108 55.000 0.00 0.00 0.00 5.54
1857 2000 2.769663 ACCGGTCTAAATGTGGCTCATA 59.230 45.455 0.00 0.00 35.48 2.15
1898 2041 3.984732 GGGGCTTGCCTTCCACCT 61.985 66.667 11.71 0.00 0.00 4.00
2079 2230 7.711339 AGAGGAAGTTGATAATTATTCACGACC 59.289 37.037 0.00 8.27 0.00 4.79
2133 2284 3.054655 ACACATCCACAGGGGTATGTTAC 60.055 47.826 4.50 0.00 36.13 2.50
2138 2289 2.711009 CCATACACATCCACAGGGGTAT 59.289 50.000 0.00 0.00 38.11 2.73
2178 2331 0.249741 ACAGAAGGAAACCGGACACG 60.250 55.000 9.46 0.00 40.55 4.49
2216 2369 7.323656 GGTACGTGACAAGATTTCATTTCAAAG 59.676 37.037 0.00 0.00 0.00 2.77
2610 2787 8.926710 CCTTGTACTTCTCTGTTATTGTAGTTG 58.073 37.037 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.