Multiple sequence alignment - TraesCS7D01G412300

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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 TraesCS7D01G412300 chr7D 100.000 3187 0 0 708 3894 530741569 530738383 0.000000e+00 5886.0
1 TraesCS7D01G412300 chr7D 97.352 2417 53 5 708 3122 340173012 340175419 0.000000e+00 4098.0
2 TraesCS7D01G412300 chr7D 100.000 431 0 0 1 431 530742276 530741846 0.000000e+00 797.0
3 TraesCS7D01G412300 chr7D 93.860 228 13 1 3121 3347 621806259 621806486 3.730000e-90 342.0
4 TraesCS7D01G412300 chr5D 97.435 2417 54 4 708 3122 127940625 127938215 0.000000e+00 4113.0
5 TraesCS7D01G412300 chr5D 92.949 1092 71 5 1981 3068 27284055 27285144 0.000000e+00 1585.0
6 TraesCS7D01G412300 chr1D 97.447 2076 50 3 1049 3122 415596273 415598347 0.000000e+00 3537.0
7 TraesCS7D01G412300 chr1D 97.037 270 8 0 708 977 415595646 415595915 4.590000e-124 455.0
8 TraesCS7D01G412300 chr1D 94.152 171 6 1 205 371 415595241 415595411 1.390000e-64 257.0
9 TraesCS7D01G412300 chr1D 90.230 174 13 1 203 372 62893009 62893182 1.410000e-54 224.0
10 TraesCS7D01G412300 chr1D 94.565 92 2 1 708 799 62893369 62893457 5.250000e-29 139.0
11 TraesCS7D01G412300 chr6D 97.515 2052 48 3 1073 3122 450189601 450187551 0.000000e+00 3504.0
12 TraesCS7D01G412300 chr6D 96.486 313 11 0 708 1020 450189914 450189602 5.770000e-143 518.0
13 TraesCS7D01G412300 chr6D 88.265 196 13 5 185 372 13475040 13475233 3.910000e-55 226.0
14 TraesCS7D01G412300 chr6D 94.565 92 2 1 708 799 13475420 13475508 5.250000e-29 139.0
15 TraesCS7D01G412300 chr7B 96.397 1943 62 5 854 2796 593350733 593348799 0.000000e+00 3193.0
16 TraesCS7D01G412300 chr7B 92.495 493 34 1 1326 1818 228801503 228801992 0.000000e+00 702.0
17 TraesCS7D01G412300 chr7B 93.567 171 7 3 205 371 593351224 593351054 6.460000e-63 252.0
18 TraesCS7D01G412300 chr7B 86.603 209 19 7 1 205 570103429 570103226 5.060000e-54 222.0
19 TraesCS7D01G412300 chr7B 98.901 91 1 0 708 798 593350823 593350733 3.110000e-36 163.0
20 TraesCS7D01G412300 chr7B 97.826 46 0 1 373 417 593351034 593350989 1.160000e-10 78.7
21 TraesCS7D01G412300 chr4D 92.514 1750 109 9 1326 3068 85851885 85850151 0.000000e+00 2486.0
22 TraesCS7D01G412300 chr2D 93.484 1642 104 3 1430 3068 29096340 29094699 0.000000e+00 2436.0
23 TraesCS7D01G412300 chr2D 89.210 519 42 7 3385 3894 364922418 364922931 1.530000e-178 636.0
24 TraesCS7D01G412300 chr3B 91.504 1742 111 19 800 2529 775660020 775658304 0.000000e+00 2362.0
25 TraesCS7D01G412300 chr3B 90.811 555 43 2 3346 3892 507488772 507488218 0.000000e+00 736.0
26 TraesCS7D01G412300 chr3B 93.133 233 15 1 3119 3350 507489281 507489049 1.340000e-89 340.0
27 TraesCS7D01G412300 chr2B 92.933 1500 93 10 1326 2818 134342241 134343734 0.000000e+00 2170.0
28 TraesCS7D01G412300 chr2B 89.231 520 44 6 3385 3894 432974201 432974718 1.180000e-179 640.0
29 TraesCS7D01G412300 chr7A 92.542 1475 100 8 1601 3068 658272015 658273486 0.000000e+00 2106.0
30 TraesCS7D01G412300 chr7A 93.860 228 13 1 3119 3345 28817440 28817213 3.730000e-90 342.0
31 TraesCS7D01G412300 chr7A 92.754 207 11 2 2 205 611010097 611009892 2.940000e-76 296.0
32 TraesCS7D01G412300 chr7A 88.827 179 15 2 198 372 41466135 41465958 8.470000e-52 215.0
33 TraesCS7D01G412300 chr7A 84.762 210 24 5 1 205 610960943 610960737 1.830000e-48 204.0
34 TraesCS7D01G412300 chr5A 98.335 781 11 2 3116 3894 470948297 470949077 0.000000e+00 1369.0
35 TraesCS7D01G412300 chr5A 97.222 144 4 0 854 997 470928156 470928299 1.080000e-60 244.0
36 TraesCS7D01G412300 chr5A 90.751 173 12 1 204 372 707254302 707254474 1.090000e-55 228.0
37 TraesCS7D01G412300 chr5A 89.865 148 4 2 224 371 470927699 470927835 3.090000e-41 180.0
38 TraesCS7D01G412300 chr5A 100.000 91 0 0 708 798 470928066 470928156 6.690000e-38 169.0
39 TraesCS7D01G412300 chr5A 100.000 30 0 0 1049 1078 470928787 470928816 5.440000e-04 56.5
40 TraesCS7D01G412300 chr3A 97.943 778 14 2 3119 3894 662566953 662566176 0.000000e+00 1347.0
41 TraesCS7D01G412300 chr3A 97.439 781 18 2 3116 3894 703821471 703822251 0.000000e+00 1330.0
42 TraesCS7D01G412300 chr3A 93.506 231 14 1 3116 3345 574292221 574292451 3.730000e-90 342.0
43 TraesCS7D01G412300 chr3A 88.953 172 5 3 204 371 662600847 662600686 2.370000e-47 200.0
44 TraesCS7D01G412300 chr3A 78.453 181 27 4 1068 1239 632623091 632622914 1.480000e-19 108.0
45 TraesCS7D01G412300 chr3A 100.000 40 0 0 1039 1078 662600066 662600027 1.500000e-09 75.0
46 TraesCS7D01G412300 chr1B 87.856 667 55 16 800 1461 289692783 289693428 0.000000e+00 760.0
47 TraesCS7D01G412300 chr2A 92.085 518 32 3 3385 3894 491478640 491479156 0.000000e+00 721.0
48 TraesCS7D01G412300 chr3D 94.017 234 12 2 3119 3350 577278485 577278252 1.720000e-93 353.0
49 TraesCS7D01G412300 chr3D 93.860 228 13 1 3121 3347 583603712 583603939 3.730000e-90 342.0
50 TraesCS7D01G412300 chr3D 78.756 193 30 3 1055 1239 489552459 489552270 6.830000e-23 119.0
51 TraesCS7D01G412300 chr4A 95.556 180 6 2 854 1032 742010839 742010661 1.770000e-73 287.0
52 TraesCS7D01G412300 chr4A 94.798 173 5 2 203 371 742011296 742011124 2.310000e-67 267.0
53 TraesCS7D01G412300 chr4A 96.703 91 3 0 708 798 742010929 742010839 6.740000e-33 152.0
54 TraesCS7D01G412300 chrUn 89.560 182 14 2 196 372 344421167 344421348 3.910000e-55 226.0
55 TraesCS7D01G412300 chrUn 89.560 182 14 2 196 372 408147030 408147211 3.910000e-55 226.0


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 TraesCS7D01G412300 chr7D 530738383 530742276 3893 True 3341.500000 5886 100.000000 1 3894 2 chr7D.!!$R1 3893
1 TraesCS7D01G412300 chr7D 340173012 340175419 2407 False 4098.000000 4098 97.352000 708 3122 1 chr7D.!!$F1 2414
2 TraesCS7D01G412300 chr5D 127938215 127940625 2410 True 4113.000000 4113 97.435000 708 3122 1 chr5D.!!$R1 2414
3 TraesCS7D01G412300 chr5D 27284055 27285144 1089 False 1585.000000 1585 92.949000 1981 3068 1 chr5D.!!$F1 1087
4 TraesCS7D01G412300 chr1D 415595241 415598347 3106 False 1416.333333 3537 96.212000 205 3122 3 chr1D.!!$F2 2917
5 TraesCS7D01G412300 chr6D 450187551 450189914 2363 True 2011.000000 3504 97.000500 708 3122 2 chr6D.!!$R1 2414
6 TraesCS7D01G412300 chr7B 593348799 593351224 2425 True 921.675000 3193 96.672750 205 2796 4 chr7B.!!$R2 2591
7 TraesCS7D01G412300 chr4D 85850151 85851885 1734 True 2486.000000 2486 92.514000 1326 3068 1 chr4D.!!$R1 1742
8 TraesCS7D01G412300 chr2D 29094699 29096340 1641 True 2436.000000 2436 93.484000 1430 3068 1 chr2D.!!$R1 1638
9 TraesCS7D01G412300 chr2D 364922418 364922931 513 False 636.000000 636 89.210000 3385 3894 1 chr2D.!!$F1 509
10 TraesCS7D01G412300 chr3B 775658304 775660020 1716 True 2362.000000 2362 91.504000 800 2529 1 chr3B.!!$R1 1729
11 TraesCS7D01G412300 chr3B 507488218 507489281 1063 True 538.000000 736 91.972000 3119 3892 2 chr3B.!!$R2 773
12 TraesCS7D01G412300 chr2B 134342241 134343734 1493 False 2170.000000 2170 92.933000 1326 2818 1 chr2B.!!$F1 1492
13 TraesCS7D01G412300 chr2B 432974201 432974718 517 False 640.000000 640 89.231000 3385 3894 1 chr2B.!!$F2 509
14 TraesCS7D01G412300 chr7A 658272015 658273486 1471 False 2106.000000 2106 92.542000 1601 3068 1 chr7A.!!$F1 1467
15 TraesCS7D01G412300 chr5A 470948297 470949077 780 False 1369.000000 1369 98.335000 3116 3894 1 chr5A.!!$F1 778
16 TraesCS7D01G412300 chr3A 662566176 662566953 777 True 1347.000000 1347 97.943000 3119 3894 1 chr3A.!!$R2 775
17 TraesCS7D01G412300 chr3A 703821471 703822251 780 False 1330.000000 1330 97.439000 3116 3894 1 chr3A.!!$F2 778
18 TraesCS7D01G412300 chr1B 289692783 289693428 645 False 760.000000 760 87.856000 800 1461 1 chr1B.!!$F1 661
19 TraesCS7D01G412300 chr2A 491478640 491479156 516 False 721.000000 721 92.085000 3385 3894 1 chr2A.!!$F1 509
20 TraesCS7D01G412300 chr4A 742010661 742011296 635 True 235.333333 287 95.685667 203 1032 3 chr4A.!!$R1 829

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
965 1003 0.036388 GAGATCGCCCAGGTTGACAA 60.036 55.0 0.00 0.0 0.00 3.18 F
2071 2405 0.469705 ACATTGTGGAGCAAGGCCAA 60.470 50.0 5.01 0.0 42.07 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2258 2594 0.03779 GTTCTCTGCCGAGTGCTTCT 60.038 55.0 4.97 0.00 42.0 2.85 R
3234 3593 6.05236 GCCAAGTTCAAATTTGTTTCCCTAA 58.948 36.0 17.47 0.38 0.0 2.69 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
30 31 9.435688 AGTTGGGAAATTTGATTAAAAGCATAC 57.564 29.630 0.00 0.00 0.00 2.39
31 32 9.213799 GTTGGGAAATTTGATTAAAAGCATACA 57.786 29.630 0.00 0.00 0.00 2.29
32 33 9.784531 TTGGGAAATTTGATTAAAAGCATACAA 57.215 25.926 0.00 0.00 0.00 2.41
33 34 9.784531 TGGGAAATTTGATTAAAAGCATACAAA 57.215 25.926 0.00 0.00 0.00 2.83
62 63 6.668541 AATCAATGTAGTGAATTCAGTCGG 57.331 37.500 19.01 6.22 0.00 4.79
63 64 3.932710 TCAATGTAGTGAATTCAGTCGGC 59.067 43.478 19.01 11.23 0.00 5.54
64 65 3.610040 ATGTAGTGAATTCAGTCGGCA 57.390 42.857 19.01 15.84 0.00 5.69
65 66 3.394674 TGTAGTGAATTCAGTCGGCAA 57.605 42.857 19.01 0.00 0.00 4.52
66 67 3.734463 TGTAGTGAATTCAGTCGGCAAA 58.266 40.909 19.01 0.00 0.00 3.68
67 68 4.130857 TGTAGTGAATTCAGTCGGCAAAA 58.869 39.130 19.01 0.00 0.00 2.44
68 69 4.576873 TGTAGTGAATTCAGTCGGCAAAAA 59.423 37.500 19.01 0.00 0.00 1.94
91 92 9.905713 AAAAATTCTGGTATTGTAGCATCTAGA 57.094 29.630 0.00 0.00 35.39 2.43
94 95 9.499479 AATTCTGGTATTGTAGCATCTAGATTG 57.501 33.333 1.33 0.25 35.39 2.67
95 96 7.839680 TCTGGTATTGTAGCATCTAGATTGA 57.160 36.000 1.33 0.00 35.39 2.57
96 97 8.250143 TCTGGTATTGTAGCATCTAGATTGAA 57.750 34.615 1.33 0.00 35.39 2.69
97 98 8.704668 TCTGGTATTGTAGCATCTAGATTGAAA 58.295 33.333 1.33 0.00 35.39 2.69
98 99 9.499479 CTGGTATTGTAGCATCTAGATTGAAAT 57.501 33.333 1.33 2.43 35.39 2.17
108 109 9.678260 AGCATCTAGATTGAAATAAAGAGTGTT 57.322 29.630 1.33 0.00 0.00 3.32
121 122 8.443953 AATAAAGAGTGTTATCATCTCAAGGC 57.556 34.615 0.00 0.00 0.00 4.35
122 123 4.414337 AGAGTGTTATCATCTCAAGGCC 57.586 45.455 0.00 0.00 0.00 5.19
123 124 3.126831 GAGTGTTATCATCTCAAGGCCG 58.873 50.000 0.00 0.00 0.00 6.13
124 125 2.501723 AGTGTTATCATCTCAAGGCCGT 59.498 45.455 0.00 0.00 0.00 5.68
125 126 2.866762 GTGTTATCATCTCAAGGCCGTC 59.133 50.000 0.00 0.00 0.00 4.79
126 127 2.158957 TGTTATCATCTCAAGGCCGTCC 60.159 50.000 0.00 0.00 0.00 4.79
128 129 0.755686 ATCATCTCAAGGCCGTCCTC 59.244 55.000 0.00 0.00 43.40 3.71
129 130 0.614697 TCATCTCAAGGCCGTCCTCA 60.615 55.000 0.00 0.00 43.40 3.86
130 131 0.467384 CATCTCAAGGCCGTCCTCAT 59.533 55.000 0.00 0.00 43.40 2.90
131 132 0.755686 ATCTCAAGGCCGTCCTCATC 59.244 55.000 0.00 0.00 43.40 2.92
132 133 1.144936 CTCAAGGCCGTCCTCATCC 59.855 63.158 0.00 0.00 43.40 3.51
133 134 1.306141 TCAAGGCCGTCCTCATCCT 60.306 57.895 0.00 0.00 43.40 3.24
134 135 1.153289 CAAGGCCGTCCTCATCCTG 60.153 63.158 0.00 0.00 43.40 3.86
135 136 2.370445 AAGGCCGTCCTCATCCTGG 61.370 63.158 0.00 0.00 43.40 4.45
136 137 3.866582 GGCCGTCCTCATCCTGGG 61.867 72.222 0.00 0.00 0.00 4.45
137 138 4.554036 GCCGTCCTCATCCTGGGC 62.554 72.222 0.00 0.00 0.00 5.36
138 139 2.765807 CCGTCCTCATCCTGGGCT 60.766 66.667 0.00 0.00 0.00 5.19
139 140 2.370445 CCGTCCTCATCCTGGGCTT 61.370 63.158 0.00 0.00 0.00 4.35
140 141 1.153289 CGTCCTCATCCTGGGCTTG 60.153 63.158 0.00 0.00 0.00 4.01
141 142 1.452833 GTCCTCATCCTGGGCTTGC 60.453 63.158 0.00 0.00 0.00 4.01
142 143 1.924939 TCCTCATCCTGGGCTTGCA 60.925 57.895 0.00 0.00 0.00 4.08
143 144 1.453379 CCTCATCCTGGGCTTGCAG 60.453 63.158 0.00 0.00 0.00 4.41
144 145 1.302285 CTCATCCTGGGCTTGCAGT 59.698 57.895 0.00 0.00 0.00 4.40
145 146 0.323178 CTCATCCTGGGCTTGCAGTT 60.323 55.000 0.00 0.00 0.00 3.16
146 147 0.322816 TCATCCTGGGCTTGCAGTTC 60.323 55.000 0.00 0.00 0.00 3.01
147 148 1.000396 ATCCTGGGCTTGCAGTTCC 60.000 57.895 0.00 0.00 0.00 3.62
148 149 1.792757 ATCCTGGGCTTGCAGTTCCA 61.793 55.000 0.00 4.35 0.00 3.53
149 150 2.270986 CCTGGGCTTGCAGTTCCAC 61.271 63.158 0.66 0.00 0.00 4.02
150 151 1.529010 CTGGGCTTGCAGTTCCACA 60.529 57.895 0.66 0.00 0.00 4.17
151 152 1.799258 CTGGGCTTGCAGTTCCACAC 61.799 60.000 0.66 0.00 0.00 3.82
152 153 2.564721 GGGCTTGCAGTTCCACACC 61.565 63.158 3.85 0.00 0.00 4.16
153 154 1.827789 GGCTTGCAGTTCCACACCA 60.828 57.895 0.00 0.00 0.00 4.17
154 155 1.181098 GGCTTGCAGTTCCACACCAT 61.181 55.000 0.00 0.00 0.00 3.55
155 156 0.675633 GCTTGCAGTTCCACACCATT 59.324 50.000 0.00 0.00 0.00 3.16
156 157 1.885887 GCTTGCAGTTCCACACCATTA 59.114 47.619 0.00 0.00 0.00 1.90
157 158 2.351738 GCTTGCAGTTCCACACCATTAC 60.352 50.000 0.00 0.00 0.00 1.89
158 159 1.904287 TGCAGTTCCACACCATTACC 58.096 50.000 0.00 0.00 0.00 2.85
159 160 1.143889 TGCAGTTCCACACCATTACCA 59.856 47.619 0.00 0.00 0.00 3.25
160 161 1.812571 GCAGTTCCACACCATTACCAG 59.187 52.381 0.00 0.00 0.00 4.00
161 162 2.552155 GCAGTTCCACACCATTACCAGA 60.552 50.000 0.00 0.00 0.00 3.86
162 163 3.873801 GCAGTTCCACACCATTACCAGAT 60.874 47.826 0.00 0.00 0.00 2.90
163 164 4.335416 CAGTTCCACACCATTACCAGATT 58.665 43.478 0.00 0.00 0.00 2.40
164 165 4.766891 CAGTTCCACACCATTACCAGATTT 59.233 41.667 0.00 0.00 0.00 2.17
165 166 5.010282 AGTTCCACACCATTACCAGATTTC 58.990 41.667 0.00 0.00 0.00 2.17
166 167 4.927267 TCCACACCATTACCAGATTTCT 57.073 40.909 0.00 0.00 0.00 2.52
167 168 5.255397 TCCACACCATTACCAGATTTCTT 57.745 39.130 0.00 0.00 0.00 2.52
168 169 5.640147 TCCACACCATTACCAGATTTCTTT 58.360 37.500 0.00 0.00 0.00 2.52
169 170 6.074648 TCCACACCATTACCAGATTTCTTTT 58.925 36.000 0.00 0.00 0.00 2.27
170 171 6.208599 TCCACACCATTACCAGATTTCTTTTC 59.791 38.462 0.00 0.00 0.00 2.29
171 172 6.015519 CCACACCATTACCAGATTTCTTTTCA 60.016 38.462 0.00 0.00 0.00 2.69
172 173 7.309990 CCACACCATTACCAGATTTCTTTTCAT 60.310 37.037 0.00 0.00 0.00 2.57
173 174 7.756722 CACACCATTACCAGATTTCTTTTCATC 59.243 37.037 0.00 0.00 0.00 2.92
174 175 7.451255 ACACCATTACCAGATTTCTTTTCATCA 59.549 33.333 0.00 0.00 0.00 3.07
175 176 7.756722 CACCATTACCAGATTTCTTTTCATCAC 59.243 37.037 0.00 0.00 0.00 3.06
176 177 7.671398 ACCATTACCAGATTTCTTTTCATCACT 59.329 33.333 0.00 0.00 0.00 3.41
177 178 8.186821 CCATTACCAGATTTCTTTTCATCACTC 58.813 37.037 0.00 0.00 0.00 3.51
178 179 8.733458 CATTACCAGATTTCTTTTCATCACTCA 58.267 33.333 0.00 0.00 0.00 3.41
179 180 8.868522 TTACCAGATTTCTTTTCATCACTCAT 57.131 30.769 0.00 0.00 0.00 2.90
180 181 7.388460 ACCAGATTTCTTTTCATCACTCATC 57.612 36.000 0.00 0.00 0.00 2.92
181 182 6.376581 ACCAGATTTCTTTTCATCACTCATCC 59.623 38.462 0.00 0.00 0.00 3.51
182 183 6.376299 CCAGATTTCTTTTCATCACTCATCCA 59.624 38.462 0.00 0.00 0.00 3.41
183 184 7.249147 CAGATTTCTTTTCATCACTCATCCAC 58.751 38.462 0.00 0.00 0.00 4.02
184 185 7.120873 CAGATTTCTTTTCATCACTCATCCACT 59.879 37.037 0.00 0.00 0.00 4.00
185 186 6.564709 TTTCTTTTCATCACTCATCCACTG 57.435 37.500 0.00 0.00 0.00 3.66
186 187 5.488262 TCTTTTCATCACTCATCCACTGA 57.512 39.130 0.00 0.00 0.00 3.41
187 188 6.058553 TCTTTTCATCACTCATCCACTGAT 57.941 37.500 0.00 0.00 32.10 2.90
188 189 6.479006 TCTTTTCATCACTCATCCACTGATT 58.521 36.000 0.00 0.00 32.10 2.57
189 190 7.623630 TCTTTTCATCACTCATCCACTGATTA 58.376 34.615 0.00 0.00 32.10 1.75
190 191 7.767659 TCTTTTCATCACTCATCCACTGATTAG 59.232 37.037 0.00 0.00 32.10 1.73
191 192 6.550938 TTCATCACTCATCCACTGATTAGT 57.449 37.500 0.00 0.00 36.16 2.24
326 331 6.317642 TGAAATCACAAATAACTATGGGACCG 59.682 38.462 0.00 0.00 30.46 4.79
371 376 8.138074 GCTAATCATTTTCCAAAAGGGTAGATC 58.862 37.037 10.01 0.00 38.11 2.75
965 1003 0.036388 GAGATCGCCCAGGTTGACAA 60.036 55.000 0.00 0.00 0.00 3.18
1213 1538 2.101582 CAGTTACCCTGGAGAGGAATCG 59.898 54.545 0.00 0.00 42.93 3.34
1420 1750 5.130350 CCTTCTGGTTTAGGAAAGTGACAA 58.870 41.667 0.00 0.00 33.13 3.18
1433 1763 7.725251 AGGAAAGTGACAATTTTCAGCAATTA 58.275 30.769 9.22 0.00 34.56 1.40
1478 1810 6.018433 ACAACATATCCCTTTATTCTGCCT 57.982 37.500 0.00 0.00 0.00 4.75
1767 2100 4.567959 GCGCATTTAAAATGCCAGAGAAAT 59.432 37.500 0.30 0.00 41.71 2.17
2071 2405 0.469705 ACATTGTGGAGCAAGGCCAA 60.470 50.000 5.01 0.00 42.07 4.52
2258 2594 2.424601 GCATTGACATAGCCAAGCTGAA 59.575 45.455 0.00 0.00 40.10 3.02
2609 2952 1.764854 ACCCAACAGACACCGAGGT 60.765 57.895 0.00 0.00 0.00 3.85
2611 2954 1.372997 CCAACAGACACCGAGGTCG 60.373 63.158 0.00 0.00 42.62 4.79
2636 2980 4.441792 GAGGCAAGAACACCAACATTTTT 58.558 39.130 0.00 0.00 0.00 1.94
2719 3064 3.056179 TCATGTTCGTGGTGCAGATTCTA 60.056 43.478 0.00 0.00 0.00 2.10
3234 3593 1.202891 GGCCCAACACAGAAGTAGGTT 60.203 52.381 0.00 0.00 0.00 3.50
3855 4504 5.654603 TGTATCAGAACATAAGGACGTGT 57.345 39.130 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.435688 GTATGCTTTTAATCAAATTTCCCAACT 57.564 29.630 0.00 0.00 0.00 3.16
5 6 9.213799 TGTATGCTTTTAATCAAATTTCCCAAC 57.786 29.630 0.00 0.00 0.00 3.77
6 7 9.784531 TTGTATGCTTTTAATCAAATTTCCCAA 57.215 25.926 0.00 0.00 0.00 4.12
7 8 9.784531 TTTGTATGCTTTTAATCAAATTTCCCA 57.215 25.926 0.00 0.00 0.00 4.37
36 37 8.664798 CCGACTGAATTCACTACATTGATTTTA 58.335 33.333 3.38 0.00 0.00 1.52
37 38 7.530010 CCGACTGAATTCACTACATTGATTTT 58.470 34.615 3.38 0.00 0.00 1.82
38 39 6.403636 GCCGACTGAATTCACTACATTGATTT 60.404 38.462 3.38 0.00 0.00 2.17
39 40 5.065218 GCCGACTGAATTCACTACATTGATT 59.935 40.000 3.38 0.00 0.00 2.57
40 41 4.572389 GCCGACTGAATTCACTACATTGAT 59.428 41.667 3.38 0.00 0.00 2.57
41 42 3.932710 GCCGACTGAATTCACTACATTGA 59.067 43.478 3.38 0.00 0.00 2.57
42 43 3.684305 TGCCGACTGAATTCACTACATTG 59.316 43.478 3.38 0.00 0.00 2.82
43 44 3.937814 TGCCGACTGAATTCACTACATT 58.062 40.909 3.38 0.00 0.00 2.71
44 45 3.610040 TGCCGACTGAATTCACTACAT 57.390 42.857 3.38 0.00 0.00 2.29
45 46 3.394674 TTGCCGACTGAATTCACTACA 57.605 42.857 3.38 0.00 0.00 2.74
46 47 4.742438 TTTTGCCGACTGAATTCACTAC 57.258 40.909 3.38 0.00 0.00 2.73
65 66 9.905713 TCTAGATGCTACAATACCAGAATTTTT 57.094 29.630 0.00 0.00 0.00 1.94
68 69 9.499479 CAATCTAGATGCTACAATACCAGAATT 57.501 33.333 5.86 0.00 0.00 2.17
69 70 8.874156 TCAATCTAGATGCTACAATACCAGAAT 58.126 33.333 5.86 0.00 0.00 2.40
70 71 8.250143 TCAATCTAGATGCTACAATACCAGAA 57.750 34.615 5.86 0.00 0.00 3.02
71 72 7.839680 TCAATCTAGATGCTACAATACCAGA 57.160 36.000 5.86 0.00 0.00 3.86
72 73 8.893219 TTTCAATCTAGATGCTACAATACCAG 57.107 34.615 5.86 0.00 0.00 4.00
82 83 9.678260 AACACTCTTTATTTCAATCTAGATGCT 57.322 29.630 5.86 0.00 0.00 3.79
95 96 8.897752 GCCTTGAGATGATAACACTCTTTATTT 58.102 33.333 0.00 0.00 0.00 1.40
96 97 7.500559 GGCCTTGAGATGATAACACTCTTTATT 59.499 37.037 0.00 0.00 0.00 1.40
97 98 6.995091 GGCCTTGAGATGATAACACTCTTTAT 59.005 38.462 0.00 0.00 0.00 1.40
98 99 6.349300 GGCCTTGAGATGATAACACTCTTTA 58.651 40.000 0.00 0.00 0.00 1.85
99 100 5.189180 GGCCTTGAGATGATAACACTCTTT 58.811 41.667 0.00 0.00 0.00 2.52
100 101 4.681781 CGGCCTTGAGATGATAACACTCTT 60.682 45.833 0.00 0.00 0.00 2.85
101 102 3.181471 CGGCCTTGAGATGATAACACTCT 60.181 47.826 0.00 0.00 0.00 3.24
102 103 3.126831 CGGCCTTGAGATGATAACACTC 58.873 50.000 0.00 0.00 0.00 3.51
103 104 2.501723 ACGGCCTTGAGATGATAACACT 59.498 45.455 0.00 0.00 0.00 3.55
104 105 2.866762 GACGGCCTTGAGATGATAACAC 59.133 50.000 0.00 0.00 0.00 3.32
105 106 2.158957 GGACGGCCTTGAGATGATAACA 60.159 50.000 0.00 0.00 0.00 2.41
106 107 2.103263 AGGACGGCCTTGAGATGATAAC 59.897 50.000 2.12 0.00 43.90 1.89
107 108 2.398588 AGGACGGCCTTGAGATGATAA 58.601 47.619 2.12 0.00 43.90 1.75
108 109 2.088104 AGGACGGCCTTGAGATGATA 57.912 50.000 2.12 0.00 43.90 2.15
109 110 2.922162 AGGACGGCCTTGAGATGAT 58.078 52.632 2.12 0.00 43.90 2.45
110 111 4.461119 AGGACGGCCTTGAGATGA 57.539 55.556 2.12 0.00 43.90 2.92
119 120 3.866582 CCCAGGATGAGGACGGCC 61.867 72.222 0.00 0.00 39.69 6.13
120 121 4.554036 GCCCAGGATGAGGACGGC 62.554 72.222 0.00 0.00 39.69 5.68
121 122 2.370445 AAGCCCAGGATGAGGACGG 61.370 63.158 0.00 0.00 39.69 4.79
122 123 1.153289 CAAGCCCAGGATGAGGACG 60.153 63.158 0.00 0.00 39.69 4.79
123 124 1.452833 GCAAGCCCAGGATGAGGAC 60.453 63.158 0.00 0.00 39.69 3.85
124 125 1.918467 CTGCAAGCCCAGGATGAGGA 61.918 60.000 0.00 0.00 39.69 3.71
125 126 1.453379 CTGCAAGCCCAGGATGAGG 60.453 63.158 0.00 0.00 39.69 3.86
126 127 0.323178 AACTGCAAGCCCAGGATGAG 60.323 55.000 0.00 0.00 35.45 2.90
127 128 0.322816 GAACTGCAAGCCCAGGATGA 60.323 55.000 0.00 0.00 35.45 2.92
128 129 1.318158 GGAACTGCAAGCCCAGGATG 61.318 60.000 0.00 0.00 37.60 3.51
129 130 1.000396 GGAACTGCAAGCCCAGGAT 60.000 57.895 0.00 0.00 37.60 3.24
130 131 2.436109 GGAACTGCAAGCCCAGGA 59.564 61.111 0.00 0.00 37.60 3.86
131 132 2.115910 TGGAACTGCAAGCCCAGG 59.884 61.111 0.00 0.00 35.44 4.45
132 133 1.529010 TGTGGAACTGCAAGCCCAG 60.529 57.895 1.33 0.00 40.05 4.45
133 134 1.827789 GTGTGGAACTGCAAGCCCA 60.828 57.895 0.00 0.00 37.60 5.36
134 135 2.564721 GGTGTGGAACTGCAAGCCC 61.565 63.158 0.00 0.00 37.60 5.19
135 136 1.181098 ATGGTGTGGAACTGCAAGCC 61.181 55.000 0.00 0.00 37.60 4.35
136 137 0.675633 AATGGTGTGGAACTGCAAGC 59.324 50.000 0.00 0.00 37.60 4.01
137 138 2.228822 GGTAATGGTGTGGAACTGCAAG 59.771 50.000 0.00 0.00 38.04 4.01
138 139 2.235016 GGTAATGGTGTGGAACTGCAA 58.765 47.619 0.00 0.00 38.04 4.08
139 140 1.143889 TGGTAATGGTGTGGAACTGCA 59.856 47.619 0.00 0.00 38.04 4.41
140 141 1.812571 CTGGTAATGGTGTGGAACTGC 59.187 52.381 0.00 0.00 38.04 4.40
141 142 3.417069 TCTGGTAATGGTGTGGAACTG 57.583 47.619 0.00 0.00 38.04 3.16
142 143 4.657814 AATCTGGTAATGGTGTGGAACT 57.342 40.909 0.00 0.00 38.04 3.01
143 144 5.010282 AGAAATCTGGTAATGGTGTGGAAC 58.990 41.667 0.00 0.00 37.35 3.62
144 145 5.255397 AGAAATCTGGTAATGGTGTGGAA 57.745 39.130 0.00 0.00 0.00 3.53
145 146 4.927267 AGAAATCTGGTAATGGTGTGGA 57.073 40.909 0.00 0.00 0.00 4.02
146 147 5.982890 AAAGAAATCTGGTAATGGTGTGG 57.017 39.130 0.00 0.00 0.00 4.17
147 148 6.980593 TGAAAAGAAATCTGGTAATGGTGTG 58.019 36.000 0.00 0.00 0.00 3.82
148 149 7.451255 TGATGAAAAGAAATCTGGTAATGGTGT 59.549 33.333 0.00 0.00 0.00 4.16
149 150 7.756722 GTGATGAAAAGAAATCTGGTAATGGTG 59.243 37.037 0.00 0.00 0.00 4.17
150 151 7.671398 AGTGATGAAAAGAAATCTGGTAATGGT 59.329 33.333 0.00 0.00 0.00 3.55
151 152 8.059798 AGTGATGAAAAGAAATCTGGTAATGG 57.940 34.615 0.00 0.00 0.00 3.16
152 153 8.733458 TGAGTGATGAAAAGAAATCTGGTAATG 58.267 33.333 0.00 0.00 0.00 1.90
153 154 8.868522 TGAGTGATGAAAAGAAATCTGGTAAT 57.131 30.769 0.00 0.00 0.00 1.89
154 155 8.868522 ATGAGTGATGAAAAGAAATCTGGTAA 57.131 30.769 0.00 0.00 0.00 2.85
155 156 7.554118 GGATGAGTGATGAAAAGAAATCTGGTA 59.446 37.037 0.00 0.00 0.00 3.25
156 157 6.376581 GGATGAGTGATGAAAAGAAATCTGGT 59.623 38.462 0.00 0.00 0.00 4.00
157 158 6.376299 TGGATGAGTGATGAAAAGAAATCTGG 59.624 38.462 0.00 0.00 0.00 3.86
158 159 7.120873 AGTGGATGAGTGATGAAAAGAAATCTG 59.879 37.037 0.00 0.00 0.00 2.90
159 160 7.120873 CAGTGGATGAGTGATGAAAAGAAATCT 59.879 37.037 0.00 0.00 0.00 2.40
160 161 7.120285 TCAGTGGATGAGTGATGAAAAGAAATC 59.880 37.037 0.00 0.00 32.77 2.17
161 162 6.944290 TCAGTGGATGAGTGATGAAAAGAAAT 59.056 34.615 0.00 0.00 32.77 2.17
162 163 6.298361 TCAGTGGATGAGTGATGAAAAGAAA 58.702 36.000 0.00 0.00 32.77 2.52
163 164 5.868454 TCAGTGGATGAGTGATGAAAAGAA 58.132 37.500 0.00 0.00 32.77 2.52
164 165 5.488262 TCAGTGGATGAGTGATGAAAAGA 57.512 39.130 0.00 0.00 32.77 2.52
165 166 6.754702 AATCAGTGGATGAGTGATGAAAAG 57.245 37.500 0.00 0.00 42.98 2.27
166 167 7.397221 ACTAATCAGTGGATGAGTGATGAAAA 58.603 34.615 0.00 0.00 42.61 2.29
167 168 6.950842 ACTAATCAGTGGATGAGTGATGAAA 58.049 36.000 0.00 0.00 42.61 2.69
168 169 6.550938 ACTAATCAGTGGATGAGTGATGAA 57.449 37.500 0.00 0.00 42.61 2.57
196 197 9.251792 CGCCACTGTAACAGTTGTATTTATATA 57.748 33.333 0.00 0.00 42.59 0.86
197 198 7.982919 TCGCCACTGTAACAGTTGTATTTATAT 59.017 33.333 0.00 0.00 42.59 0.86
198 199 7.321908 TCGCCACTGTAACAGTTGTATTTATA 58.678 34.615 0.00 0.00 42.59 0.98
199 200 6.167685 TCGCCACTGTAACAGTTGTATTTAT 58.832 36.000 0.00 0.00 42.59 1.40
200 201 5.539979 TCGCCACTGTAACAGTTGTATTTA 58.460 37.500 0.00 0.00 42.59 1.40
201 202 4.382291 TCGCCACTGTAACAGTTGTATTT 58.618 39.130 0.00 0.00 42.59 1.40
307 312 5.875910 TGTAACGGTCCCATAGTTATTTGTG 59.124 40.000 0.00 0.00 33.63 3.33
318 323 4.165372 ACCATAATCTTGTAACGGTCCCAT 59.835 41.667 0.00 0.00 0.00 4.00
326 331 3.898482 AGCCCCACCATAATCTTGTAAC 58.102 45.455 0.00 0.00 0.00 2.50
371 376 1.234615 TTTCCTTTTCTCCCAGCGCG 61.235 55.000 0.00 0.00 0.00 6.86
949 987 1.671054 CGTTGTCAACCTGGGCGAT 60.671 57.895 10.12 0.00 0.00 4.58
1032 1074 1.068352 ACATAGGGGATGAAGGGGGC 61.068 60.000 0.00 0.00 39.06 5.80
1420 1750 7.425606 CCTACGGCTAAATAATTGCTGAAAAT 58.574 34.615 0.00 0.00 36.92 1.82
1433 1763 4.772886 ATGTTCTTCCCTACGGCTAAAT 57.227 40.909 0.00 0.00 0.00 1.40
1478 1810 2.760650 ACTGCTCCATCAGACACGAATA 59.239 45.455 0.00 0.00 37.51 1.75
1606 1938 3.062763 CAGTCTAGTGGCAGAACAACAG 58.937 50.000 0.00 0.00 0.00 3.16
1660 1993 5.896922 AGAAGAGTTCAATTGCGATATCG 57.103 39.130 20.79 20.79 43.27 2.92
1666 1999 5.613358 ACCTTAAGAAGAGTTCAATTGCG 57.387 39.130 3.36 0.00 0.00 4.85
1767 2100 8.547069 CGTGAAAATTAAAGAGATTGGCAAAAA 58.453 29.630 3.01 0.00 0.00 1.94
2071 2405 9.846248 GCAAATGTAGATGAAGAAACATAGTTT 57.154 29.630 0.00 0.00 32.44 2.66
2258 2594 0.037790 GTTCTCTGCCGAGTGCTTCT 60.038 55.000 4.97 0.00 42.00 2.85
2521 2864 7.792364 TGTCCCTAGTAGAAGAAGAAAATCA 57.208 36.000 0.00 0.00 0.00 2.57
2609 2952 1.006571 GGTGTTCTTGCCTCGTCGA 60.007 57.895 0.00 0.00 0.00 4.20
2611 2954 0.586802 GTTGGTGTTCTTGCCTCGTC 59.413 55.000 0.00 0.00 0.00 4.20
2636 2980 4.099266 ACAAATGCAGCTTAGTTTTGTGGA 59.901 37.500 10.63 0.00 38.64 4.02
2719 3064 2.113986 AGCACGCCCTTCTTTGCT 59.886 55.556 0.00 0.00 40.53 3.91
3234 3593 6.052360 GCCAAGTTCAAATTTGTTTCCCTAA 58.948 36.000 17.47 0.38 0.00 2.69
3370 4010 8.466617 AATTCGAGATACACAACTCCTAGTAT 57.533 34.615 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.