Multiple sequence alignment - TraesCS2D01G386600

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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 TraesCS2D01G386600 chr2D 100.000 7526 0 0 806 8331 491802220 491809745 0.000000e+00 13899.0
1 TraesCS2D01G386600 chr2D 100.000 394 0 0 1 394 491801415 491801808 0.000000e+00 728.0
2 TraesCS2D01G386600 chr2D 92.857 70 3 1 1456 1523 79056232 79056163 5.320000e-17 100.0
3 TraesCS2D01G386600 chr2D 89.231 65 7 0 8244 8308 506172025 506172089 1.930000e-11 82.4
4 TraesCS2D01G386600 chr2A 97.712 7344 115 27 806 8128 636904038 636911349 0.000000e+00 12582.0
5 TraesCS2D01G386600 chr2A 96.606 383 7 2 1 380 636903117 636903496 1.530000e-176 630.0
6 TraesCS2D01G386600 chr2A 96.139 259 10 0 1198 1456 232387130 232387388 2.780000e-114 424.0
7 TraesCS2D01G386600 chr2A 79.008 262 43 8 2613 2870 726594395 726594648 1.440000e-37 169.0
8 TraesCS2D01G386600 chr2A 91.892 74 4 1 1450 1521 141506399 141506472 1.480000e-17 102.0
9 TraesCS2D01G386600 chr2B 97.963 4565 76 7 806 5365 576084772 576089324 0.000000e+00 7899.0
10 TraesCS2D01G386600 chr2B 96.461 2713 70 8 5503 8191 576089730 576092440 0.000000e+00 4455.0
11 TraesCS2D01G386600 chr2B 95.965 347 5 1 1 338 576083807 576084153 9.450000e-154 555.0
12 TraesCS2D01G386600 chr2B 98.611 144 2 0 5364 5507 576089486 576089629 1.070000e-63 255.0
13 TraesCS2D01G386600 chr2B 95.652 69 2 1 1456 1523 122742494 122742426 8.840000e-20 110.0
14 TraesCS2D01G386600 chr2B 91.935 62 4 1 8250 8311 662900006 662899946 1.490000e-12 86.1
15 TraesCS2D01G386600 chr7B 87.685 609 53 11 3622 4216 584316865 584317465 0.000000e+00 689.0
16 TraesCS2D01G386600 chr7A 95.785 261 11 0 1195 1455 595822975 595822715 1.000000e-113 422.0
17 TraesCS2D01G386600 chr7A 80.159 126 17 4 2621 2744 55130127 55130246 4.140000e-13 87.9
18 TraesCS2D01G386600 chr7A 93.333 60 3 1 8252 8311 128829523 128829465 4.140000e-13 87.9
19 TraesCS2D01G386600 chr6A 95.131 267 13 0 1189 1455 599623039 599623305 1.000000e-113 422.0
20 TraesCS2D01G386600 chr6A 77.305 282 50 9 2615 2892 186238648 186238919 4.030000e-33 154.0
21 TraesCS2D01G386600 chr1A 95.076 264 12 1 1193 1455 533465019 533464756 1.670000e-111 414.0
22 TraesCS2D01G386600 chr1A 92.063 126 10 0 5463 5588 218526967 218526842 2.390000e-40 178.0
23 TraesCS2D01G386600 chr1A 89.744 78 7 1 1450 1526 116698461 116698538 1.910000e-16 99.0
24 TraesCS2D01G386600 chr4D 96.047 253 10 0 1203 1455 252186814 252187066 6.020000e-111 412.0
25 TraesCS2D01G386600 chr4D 90.226 133 11 2 5463 5594 29833611 29833480 1.110000e-38 172.0
26 TraesCS2D01G386600 chr3B 94.118 272 13 2 1185 1456 144814327 144814595 2.160000e-110 411.0
27 TraesCS2D01G386600 chr3B 92.063 126 10 0 5463 5588 42630944 42630819 2.390000e-40 178.0
28 TraesCS2D01G386600 chr3B 76.953 256 51 6 2620 2874 664910910 664911158 1.130000e-28 139.0
29 TraesCS2D01G386600 chr5A 95.312 256 11 1 1200 1455 477975540 477975286 1.010000e-108 405.0
30 TraesCS2D01G386600 chr5A 76.800 125 20 6 2623 2743 248527483 248527602 2.510000e-05 62.1
31 TraesCS2D01G386600 chr7D 91.065 291 22 3 4053 4342 540858154 540858441 2.820000e-104 390.0
32 TraesCS2D01G386600 chr7D 92.969 256 18 0 3622 3877 540857895 540858150 2.840000e-99 374.0
33 TraesCS2D01G386600 chr7D 92.188 64 4 1 8249 8312 610805274 610805336 1.150000e-13 89.8
34 TraesCS2D01G386600 chr3D 92.857 126 9 0 5463 5588 426451985 426451860 5.140000e-42 183.0
35 TraesCS2D01G386600 chr3D 92.063 126 10 0 5463 5588 25133061 25132936 2.390000e-40 178.0
36 TraesCS2D01G386600 chr3D 92.063 126 10 0 5463 5588 71517804 71517679 2.390000e-40 178.0
37 TraesCS2D01G386600 chr3D 89.706 68 6 1 8244 8311 210615441 210615375 1.490000e-12 86.1
38 TraesCS2D01G386600 chr3A 92.857 126 9 0 5463 5588 34532575 34532450 5.140000e-42 183.0
39 TraesCS2D01G386600 chr3A 91.026 78 4 2 1450 1524 509865334 509865411 1.480000e-17 102.0
40 TraesCS2D01G386600 chr6B 91.781 73 4 1 1449 1519 537553913 537553841 5.320000e-17 100.0
41 TraesCS2D01G386600 chr6B 92.063 63 4 1 8249 8311 288654618 288654679 4.140000e-13 87.9
42 TraesCS2D01G386600 chr6B 91.667 60 4 1 8252 8311 459599615 459599673 1.930000e-11 82.4
43 TraesCS2D01G386600 chr6B 94.737 38 2 0 2620 2657 615551908 615551871 9.030000e-05 60.2
44 TraesCS2D01G386600 chr4B 90.000 80 5 3 1456 1534 189421865 189421788 5.320000e-17 100.0
45 TraesCS2D01G386600 chr4A 88.750 80 4 3 8229 8308 12207275 12207349 8.900000e-15 93.5
46 TraesCS2D01G386600 chr5B 92.982 57 4 0 8252 8308 588539080 588539136 5.360000e-12 84.2


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 TraesCS2D01G386600 chr2D 491801415 491809745 8330 False 7313.5 13899 100.000 1 8331 2 chr2D.!!$F2 8330
1 TraesCS2D01G386600 chr2A 636903117 636911349 8232 False 6606.0 12582 97.159 1 8128 2 chr2A.!!$F4 8127
2 TraesCS2D01G386600 chr2B 576083807 576092440 8633 False 3291.0 7899 97.250 1 8191 4 chr2B.!!$F1 8190
3 TraesCS2D01G386600 chr7B 584316865 584317465 600 False 689.0 689 87.685 3622 4216 1 chr7B.!!$F1 594
4 TraesCS2D01G386600 chr7D 540857895 540858441 546 False 382.0 390 92.017 3622 4342 2 chr7D.!!$F2 720


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
84 85 1.974236 CCTCCTCCACATGGTAGATCC 59.026 57.143 0.00 0.00 36.34 3.36 F
1005 1568 3.058983 TGAAAGTTACACGAGCAATGCAG 60.059 43.478 8.35 3.33 0.00 4.41 F
1554 2117 4.788100 CAGTCGCGAAAACAATCCAAATAG 59.212 41.667 12.06 0.00 0.00 1.73 F
1809 2372 3.062042 CCAATGCAAGTGAAAAAGGAGC 58.938 45.455 0.00 0.00 30.28 4.70 F
1868 2431 4.141287 TGTTCACCTGGTATGGAAACTTG 58.859 43.478 0.00 0.00 32.09 3.16 F
3697 4268 2.145536 GGCAACAAAGAAATGCTTGGG 58.854 47.619 0.00 0.00 39.94 4.12 F
4429 5014 0.744414 CTTCACCACTGGCCATACCG 60.744 60.000 5.51 0.00 43.94 4.02 F
5588 6443 1.205893 CTAGCACTGGGTCTGTCCTTC 59.794 57.143 0.00 0.00 36.25 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1005 1568 2.066999 ATCCGCCCAGAGACTTCCC 61.067 63.158 0.00 0.0 0.00 3.97 R
1809 2372 2.856032 CTGAGCCACGCTTCGTTG 59.144 61.111 0.00 0.0 39.88 4.10 R
3005 3576 7.654568 ACAAGTTTACACTTAAGCAAATACCC 58.345 34.615 1.29 0.0 41.69 3.69 R
3697 4268 9.705290 AATATTAAACCAACCTGTTCACATTTC 57.295 29.630 0.00 0.0 0.00 2.17 R
3877 4449 8.877864 AATCCAAGTAAATTAACTGATGGACA 57.122 30.769 0.00 0.0 38.56 4.02 R
5609 6464 5.181748 AGAAAGATAAGGTAAGCTGCACAG 58.818 41.667 1.02 0.0 0.00 3.66 R
6426 7281 1.616865 CGAAGGTCACAACTCCTACCA 59.383 52.381 0.00 0.0 34.29 3.25 R
7437 8296 1.995484 CTGACATTACACCTCTGCGTG 59.005 52.381 0.00 0.0 39.75 5.34 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
84 85 1.974236 CCTCCTCCACATGGTAGATCC 59.026 57.143 0.00 0.00 36.34 3.36
1005 1568 3.058983 TGAAAGTTACACGAGCAATGCAG 60.059 43.478 8.35 3.33 0.00 4.41
1465 2028 8.124823 GCACACATTTACTAGTACGTGTCTATA 58.875 37.037 20.92 0.00 35.52 1.31
1554 2117 4.788100 CAGTCGCGAAAACAATCCAAATAG 59.212 41.667 12.06 0.00 0.00 1.73
1809 2372 3.062042 CCAATGCAAGTGAAAAAGGAGC 58.938 45.455 0.00 0.00 30.28 4.70
1868 2431 4.141287 TGTTCACCTGGTATGGAAACTTG 58.859 43.478 0.00 0.00 32.09 3.16
2090 2654 9.151471 GTGGTAATACGATATGCATGATTACTT 57.849 33.333 10.16 0.00 32.73 2.24
2263 2828 8.221251 AGGGACTTTTGAATAGTTTTCTCTCTT 58.779 33.333 0.00 0.00 27.25 2.85
3188 3759 6.837048 TCATACAGTGGTCTAACATTAGGCTA 59.163 38.462 3.42 0.00 35.74 3.93
3697 4268 2.145536 GGCAACAAAGAAATGCTTGGG 58.854 47.619 0.00 0.00 39.94 4.12
3877 4449 2.014128 CAACACAGGTCCGTTGTCTTT 58.986 47.619 0.00 0.00 38.14 2.52
4016 4588 3.976169 TGCAACAAAAGAGGTACAATGC 58.024 40.909 0.00 0.00 0.00 3.56
4034 4606 7.934855 ACAATGCTGTATCATCTCTTTCTTT 57.065 32.000 0.00 0.00 32.54 2.52
4429 5014 0.744414 CTTCACCACTGGCCATACCG 60.744 60.000 5.51 0.00 43.94 4.02
4602 5187 4.091549 AGTTGGGAATCATGCATCTTGTT 58.908 39.130 0.00 0.00 0.00 2.83
4706 5291 6.102006 TCTAAAACCGTTTGAATATCAGCG 57.898 37.500 0.00 0.00 0.00 5.18
4844 5429 9.105844 AGCTCTGGGTGTATCAATTACTAATAT 57.894 33.333 0.00 0.00 0.00 1.28
4938 5523 1.629861 TGATGGCTGGATTCAGTGTCA 59.370 47.619 2.16 2.22 42.78 3.58
5071 5656 3.439476 GTCTGAGCGTAGAACTGGAACTA 59.561 47.826 0.00 0.00 0.00 2.24
5250 5835 2.460669 TCTGCCAGTTCTCTGCATAGA 58.539 47.619 0.00 0.00 40.09 1.98
5588 6443 1.205893 CTAGCACTGGGTCTGTCCTTC 59.794 57.143 0.00 0.00 36.25 3.46
5835 6690 3.005050 TCCAATTGAAGTTGCTTGCTGAG 59.995 43.478 7.12 0.00 0.00 3.35
7011 7868 2.937469 TTGTTGTCCAAACAGTGCAG 57.063 45.000 0.00 0.00 36.57 4.41
7037 7894 4.326413 TCGAATCGAATTGCTGTTTCTG 57.674 40.909 1.57 0.00 31.06 3.02
7110 7967 4.818534 TGAGTCAACATGCTTCTGTTTC 57.181 40.909 0.00 0.00 37.25 2.78
7367 8224 4.338879 CAATCTTCCATCTTTGTGACCCT 58.661 43.478 0.00 0.00 0.00 4.34
7437 8296 6.611381 TGCTTTTTGATGCTCAATGTAGTAC 58.389 36.000 0.00 0.00 36.11 2.73
7822 8684 1.255667 TTCTCACTAGCGGGTGGGTC 61.256 60.000 10.78 0.00 38.69 4.46
7823 8685 1.682684 CTCACTAGCGGGTGGGTCT 60.683 63.158 11.10 0.00 37.75 3.85
7863 8725 1.619827 CAAAATGCAGGGAGGCTTCAA 59.380 47.619 0.00 0.00 34.04 2.69
8120 9000 1.065854 AGGATGTGTCTGGTGCTAAGC 60.066 52.381 0.00 0.00 0.00 3.09
8137 9018 3.386932 AAGCAGGGCCTAATTCATGAA 57.613 42.857 11.26 11.26 0.00 2.57
8193 9074 6.893958 CAGACGTATTCTGTTTCATAGCTT 57.106 37.500 0.00 0.00 46.12 3.74
8194 9075 6.927746 CAGACGTATTCTGTTTCATAGCTTC 58.072 40.000 0.00 0.00 46.12 3.86
8195 9076 6.531594 CAGACGTATTCTGTTTCATAGCTTCA 59.468 38.462 0.00 0.00 46.12 3.02
8196 9077 7.063426 CAGACGTATTCTGTTTCATAGCTTCAA 59.937 37.037 0.00 0.00 46.12 2.69
8197 9078 7.602644 AGACGTATTCTGTTTCATAGCTTCAAA 59.397 33.333 0.00 0.00 31.12 2.69
8198 9079 7.743104 ACGTATTCTGTTTCATAGCTTCAAAG 58.257 34.615 0.00 0.00 0.00 2.77
8212 9093 3.636381 CTTCAAAGCTGAACCAGAAAGC 58.364 45.455 0.00 0.00 36.62 3.51
8213 9094 2.653726 TCAAAGCTGAACCAGAAAGCA 58.346 42.857 0.00 0.00 39.47 3.91
8214 9095 3.023119 TCAAAGCTGAACCAGAAAGCAA 58.977 40.909 0.00 0.00 39.47 3.91
8215 9096 3.067180 TCAAAGCTGAACCAGAAAGCAAG 59.933 43.478 0.00 0.00 39.47 4.01
8216 9097 2.645838 AGCTGAACCAGAAAGCAAGA 57.354 45.000 0.00 0.00 39.47 3.02
8217 9098 2.936202 AGCTGAACCAGAAAGCAAGAA 58.064 42.857 0.00 0.00 39.47 2.52
8218 9099 2.883386 AGCTGAACCAGAAAGCAAGAAG 59.117 45.455 0.00 0.00 39.47 2.85
8219 9100 2.620585 GCTGAACCAGAAAGCAAGAAGT 59.379 45.455 0.00 0.00 36.91 3.01
8220 9101 3.815401 GCTGAACCAGAAAGCAAGAAGTA 59.185 43.478 0.00 0.00 36.91 2.24
8221 9102 4.457257 GCTGAACCAGAAAGCAAGAAGTAT 59.543 41.667 0.00 0.00 36.91 2.12
8222 9103 5.643777 GCTGAACCAGAAAGCAAGAAGTATA 59.356 40.000 0.00 0.00 36.91 1.47
8223 9104 6.317391 GCTGAACCAGAAAGCAAGAAGTATAT 59.683 38.462 0.00 0.00 36.91 0.86
8224 9105 7.615582 TGAACCAGAAAGCAAGAAGTATATG 57.384 36.000 0.00 0.00 0.00 1.78
8225 9106 7.168219 TGAACCAGAAAGCAAGAAGTATATGT 58.832 34.615 0.00 0.00 0.00 2.29
8226 9107 7.665559 TGAACCAGAAAGCAAGAAGTATATGTT 59.334 33.333 0.00 0.00 0.00 2.71
8227 9108 8.409358 AACCAGAAAGCAAGAAGTATATGTTT 57.591 30.769 0.00 0.00 0.00 2.83
8228 9109 9.515226 AACCAGAAAGCAAGAAGTATATGTTTA 57.485 29.630 0.00 0.00 0.00 2.01
8229 9110 9.515226 ACCAGAAAGCAAGAAGTATATGTTTAA 57.485 29.630 0.00 0.00 0.00 1.52
8230 9111 9.774742 CCAGAAAGCAAGAAGTATATGTTTAAC 57.225 33.333 0.00 0.00 0.00 2.01
8258 9139 9.596308 AAATTTTGTGTTTAGGTAATACTCCCT 57.404 29.630 0.00 0.00 34.74 4.20
8259 9140 8.803397 ATTTTGTGTTTAGGTAATACTCCCTC 57.197 34.615 0.00 0.00 32.08 4.30
8260 9141 5.945144 TGTGTTTAGGTAATACTCCCTCC 57.055 43.478 0.00 0.00 32.08 4.30
8261 9142 5.596763 TGTGTTTAGGTAATACTCCCTCCT 58.403 41.667 0.00 0.00 32.08 3.69
8262 9143 6.027482 TGTGTTTAGGTAATACTCCCTCCTT 58.973 40.000 0.00 0.00 32.08 3.36
8263 9144 6.155737 TGTGTTTAGGTAATACTCCCTCCTTC 59.844 42.308 0.00 0.00 32.08 3.46
8264 9145 5.664457 TGTTTAGGTAATACTCCCTCCTTCC 59.336 44.000 0.00 0.00 32.08 3.46
8265 9146 3.347759 AGGTAATACTCCCTCCTTCCC 57.652 52.381 0.00 0.00 0.00 3.97
8266 9147 2.595380 AGGTAATACTCCCTCCTTCCCA 59.405 50.000 0.00 0.00 0.00 4.37
8267 9148 3.014807 AGGTAATACTCCCTCCTTCCCAA 59.985 47.826 0.00 0.00 0.00 4.12
8268 9149 3.784202 GGTAATACTCCCTCCTTCCCAAA 59.216 47.826 0.00 0.00 0.00 3.28
8269 9150 4.228895 GGTAATACTCCCTCCTTCCCAAAA 59.771 45.833 0.00 0.00 0.00 2.44
8270 9151 5.103643 GGTAATACTCCCTCCTTCCCAAAAT 60.104 44.000 0.00 0.00 0.00 1.82
8271 9152 6.102174 GGTAATACTCCCTCCTTCCCAAAATA 59.898 42.308 0.00 0.00 0.00 1.40
8272 9153 6.865651 AATACTCCCTCCTTCCCAAAATAT 57.134 37.500 0.00 0.00 0.00 1.28
8273 9154 7.964730 AATACTCCCTCCTTCCCAAAATATA 57.035 36.000 0.00 0.00 0.00 0.86
8274 9155 7.964730 ATACTCCCTCCTTCCCAAAATATAA 57.035 36.000 0.00 0.00 0.00 0.98
8275 9156 6.267492 ACTCCCTCCTTCCCAAAATATAAG 57.733 41.667 0.00 0.00 0.00 1.73
8276 9157 5.134509 ACTCCCTCCTTCCCAAAATATAAGG 59.865 44.000 0.00 0.00 39.93 2.69
8277 9158 4.141018 TCCCTCCTTCCCAAAATATAAGGC 60.141 45.833 0.00 0.00 38.70 4.35
8278 9159 3.821033 CCTCCTTCCCAAAATATAAGGCG 59.179 47.826 0.00 0.00 38.70 5.52
8279 9160 4.461198 CTCCTTCCCAAAATATAAGGCGT 58.539 43.478 0.00 0.00 38.70 5.68
8280 9161 4.204012 TCCTTCCCAAAATATAAGGCGTG 58.796 43.478 0.00 0.00 38.70 5.34
8281 9162 4.080243 TCCTTCCCAAAATATAAGGCGTGA 60.080 41.667 0.00 0.00 38.70 4.35
8282 9163 4.827284 CCTTCCCAAAATATAAGGCGTGAT 59.173 41.667 0.00 0.00 32.66 3.06
8283 9164 5.301805 CCTTCCCAAAATATAAGGCGTGATT 59.698 40.000 0.00 0.00 32.66 2.57
8284 9165 5.766150 TCCCAAAATATAAGGCGTGATTG 57.234 39.130 0.00 0.00 0.00 2.67
8285 9166 5.441500 TCCCAAAATATAAGGCGTGATTGA 58.558 37.500 0.00 0.00 0.00 2.57
8286 9167 5.298276 TCCCAAAATATAAGGCGTGATTGAC 59.702 40.000 0.00 0.00 0.00 3.18
8287 9168 5.299279 CCCAAAATATAAGGCGTGATTGACT 59.701 40.000 0.00 0.00 0.00 3.41
8288 9169 6.201517 CCAAAATATAAGGCGTGATTGACTG 58.798 40.000 0.00 0.00 0.00 3.51
8289 9170 6.183360 CCAAAATATAAGGCGTGATTGACTGT 60.183 38.462 0.00 0.00 0.00 3.55
8290 9171 5.991328 AATATAAGGCGTGATTGACTGTG 57.009 39.130 0.00 0.00 0.00 3.66
8291 9172 1.438651 TAAGGCGTGATTGACTGTGC 58.561 50.000 0.00 0.00 0.00 4.57
8292 9173 0.534877 AAGGCGTGATTGACTGTGCA 60.535 50.000 0.00 0.00 0.00 4.57
8293 9174 1.207593 GGCGTGATTGACTGTGCAC 59.792 57.895 10.75 10.75 0.00 4.57
8294 9175 1.506309 GGCGTGATTGACTGTGCACA 61.506 55.000 20.37 20.37 0.00 4.57
8308 9189 5.213913 CTGTGCACAGTCTTTGATACATC 57.786 43.478 34.04 0.00 39.09 3.06
8309 9190 3.679502 TGTGCACAGTCTTTGATACATCG 59.320 43.478 17.42 0.00 0.00 3.84
8310 9191 3.926527 GTGCACAGTCTTTGATACATCGA 59.073 43.478 13.17 0.00 0.00 3.59
8311 9192 4.388773 GTGCACAGTCTTTGATACATCGAA 59.611 41.667 13.17 0.00 0.00 3.71
8312 9193 4.627035 TGCACAGTCTTTGATACATCGAAG 59.373 41.667 11.53 11.53 45.55 3.79
8313 9194 4.627467 GCACAGTCTTTGATACATCGAAGT 59.373 41.667 15.64 0.00 44.82 3.01
8314 9195 5.805486 GCACAGTCTTTGATACATCGAAGTA 59.195 40.000 15.64 2.58 44.82 2.24
8315 9196 6.237595 GCACAGTCTTTGATACATCGAAGTAC 60.238 42.308 15.64 12.83 44.82 2.73
8316 9197 6.806739 CACAGTCTTTGATACATCGAAGTACA 59.193 38.462 15.64 1.38 44.82 2.90
8317 9198 7.489435 CACAGTCTTTGATACATCGAAGTACAT 59.511 37.037 15.64 0.00 44.82 2.29
8318 9199 7.489435 ACAGTCTTTGATACATCGAAGTACATG 59.511 37.037 15.64 12.73 44.82 3.21
8319 9200 6.980978 AGTCTTTGATACATCGAAGTACATGG 59.019 38.462 15.64 1.47 44.82 3.66
8320 9201 6.978659 GTCTTTGATACATCGAAGTACATGGA 59.021 38.462 15.64 0.00 44.82 3.41
8321 9202 7.653713 GTCTTTGATACATCGAAGTACATGGAT 59.346 37.037 15.64 0.00 44.82 3.41
8322 9203 8.204160 TCTTTGATACATCGAAGTACATGGATT 58.796 33.333 15.64 0.00 44.82 3.01
8323 9204 9.476202 CTTTGATACATCGAAGTACATGGATTA 57.524 33.333 2.07 0.00 41.38 1.75
8324 9205 9.825109 TTTGATACATCGAAGTACATGGATTAA 57.175 29.630 2.07 0.00 0.00 1.40
8325 9206 9.825109 TTGATACATCGAAGTACATGGATTAAA 57.175 29.630 2.07 0.00 0.00 1.52
8326 9207 9.256477 TGATACATCGAAGTACATGGATTAAAC 57.744 33.333 2.07 0.00 0.00 2.01
8327 9208 9.256477 GATACATCGAAGTACATGGATTAAACA 57.744 33.333 2.07 0.00 0.00 2.83
8328 9209 9.778741 ATACATCGAAGTACATGGATTAAACAT 57.221 29.630 2.07 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 2.023673 TGTTCAGTTGAAAGGCCACAG 58.976 47.619 5.01 0.00 35.58 3.66
1005 1568 2.066999 ATCCGCCCAGAGACTTCCC 61.067 63.158 0.00 0.00 0.00 3.97
1309 1872 8.273557 GGTATGATATTAACTGCACACTAAACG 58.726 37.037 0.00 0.00 0.00 3.60
1508 2071 6.136857 TGTAGCATGATATATACTCCCTCCC 58.863 44.000 0.00 0.00 0.00 4.30
1809 2372 2.856032 CTGAGCCACGCTTCGTTG 59.144 61.111 0.00 0.00 39.88 4.10
1868 2431 8.748380 AAAGAAAATAAGTGCATTAAGAGTGC 57.252 30.769 0.00 0.00 42.81 4.40
1919 2482 5.163713 GCTTAAGGTAGAAGCACAAGAATGG 60.164 44.000 4.29 0.00 46.97 3.16
3005 3576 7.654568 ACAAGTTTACACTTAAGCAAATACCC 58.345 34.615 1.29 0.00 41.69 3.69
3697 4268 9.705290 AATATTAAACCAACCTGTTCACATTTC 57.295 29.630 0.00 0.00 0.00 2.17
3877 4449 8.877864 AATCCAAGTAAATTAACTGATGGACA 57.122 30.769 0.00 0.00 38.56 4.02
4429 5014 6.208644 CCTAACCAGCATTGTATTATTGTGC 58.791 40.000 0.00 0.00 36.11 4.57
4844 5429 8.682710 GCACCCTATTATTGTTTGTTTGATCTA 58.317 33.333 0.00 0.00 0.00 1.98
4938 5523 9.498176 AACTTACAATCGACCAGTAAATTTACT 57.502 29.630 22.49 22.49 44.42 2.24
5609 6464 5.181748 AGAAAGATAAGGTAAGCTGCACAG 58.818 41.667 1.02 0.00 0.00 3.66
5835 6690 5.469760 ACCTTTGTTTATTGCTTGCATTTCC 59.530 36.000 0.00 0.00 0.00 3.13
6426 7281 1.616865 CGAAGGTCACAACTCCTACCA 59.383 52.381 0.00 0.00 34.29 3.25
6939 7796 4.899898 AGGGATTAGGGGCAATACTTTT 57.100 40.909 0.00 0.00 0.00 2.27
7037 7894 2.749800 GCCACTTGATAGACCATTCCCC 60.750 54.545 0.00 0.00 0.00 4.81
7437 8296 1.995484 CTGACATTACACCTCTGCGTG 59.005 52.381 0.00 0.00 39.75 5.34
7633 8495 6.158598 ACAAACAGTAAATAAGCCTGCAATG 58.841 36.000 0.00 0.00 0.00 2.82
7822 8684 3.181477 TGTTTCAGGAATGTTTGCCACAG 60.181 43.478 0.00 0.00 39.40 3.66
7823 8685 2.762887 TGTTTCAGGAATGTTTGCCACA 59.237 40.909 0.00 0.00 40.71 4.17
7863 8725 0.677288 TGTACAACACTACAGCGGCT 59.323 50.000 0.00 0.00 0.00 5.52
8074 8954 1.061857 CGCGCACTGCATATAACAACA 59.938 47.619 8.75 0.00 46.97 3.33
8120 9000 6.051074 GGAATTTTTCATGAATTAGGCCCTG 58.949 40.000 9.40 0.00 0.00 4.45
8171 9052 6.631016 TGAAGCTATGAAACAGAATACGTCT 58.369 36.000 0.00 0.00 36.88 4.18
8191 9072 3.067180 TGCTTTCTGGTTCAGCTTTGAAG 59.933 43.478 0.00 0.00 34.42 3.02
8192 9073 3.023119 TGCTTTCTGGTTCAGCTTTGAA 58.977 40.909 0.00 0.00 34.42 2.69
8193 9074 2.653726 TGCTTTCTGGTTCAGCTTTGA 58.346 42.857 0.00 0.00 34.42 2.69
8194 9075 3.067180 TCTTGCTTTCTGGTTCAGCTTTG 59.933 43.478 0.00 0.00 34.42 2.77
8195 9076 3.290710 TCTTGCTTTCTGGTTCAGCTTT 58.709 40.909 0.00 0.00 34.42 3.51
8196 9077 2.936202 TCTTGCTTTCTGGTTCAGCTT 58.064 42.857 0.00 0.00 34.42 3.74
8197 9078 2.645838 TCTTGCTTTCTGGTTCAGCT 57.354 45.000 0.00 0.00 34.42 4.24
8198 9079 2.620585 ACTTCTTGCTTTCTGGTTCAGC 59.379 45.455 0.00 0.00 0.00 4.26
8199 9080 7.335422 ACATATACTTCTTGCTTTCTGGTTCAG 59.665 37.037 0.00 0.00 0.00 3.02
8200 9081 7.168219 ACATATACTTCTTGCTTTCTGGTTCA 58.832 34.615 0.00 0.00 0.00 3.18
8201 9082 7.617041 ACATATACTTCTTGCTTTCTGGTTC 57.383 36.000 0.00 0.00 0.00 3.62
8202 9083 8.409358 AAACATATACTTCTTGCTTTCTGGTT 57.591 30.769 0.00 0.00 0.00 3.67
8203 9084 9.515226 TTAAACATATACTTCTTGCTTTCTGGT 57.485 29.630 0.00 0.00 0.00 4.00
8204 9085 9.774742 GTTAAACATATACTTCTTGCTTTCTGG 57.225 33.333 0.00 0.00 0.00 3.86
8232 9113 9.596308 AGGGAGTATTACCTAAACACAAAATTT 57.404 29.630 0.00 0.00 34.71 1.82
8233 9114 9.239551 GAGGGAGTATTACCTAAACACAAAATT 57.760 33.333 0.00 0.00 37.18 1.82
8234 9115 7.832685 GGAGGGAGTATTACCTAAACACAAAAT 59.167 37.037 0.00 0.00 37.18 1.82
8235 9116 7.017850 AGGAGGGAGTATTACCTAAACACAAAA 59.982 37.037 0.00 0.00 37.18 2.44
8236 9117 6.502863 AGGAGGGAGTATTACCTAAACACAAA 59.497 38.462 0.00 0.00 37.18 2.83
8237 9118 6.027482 AGGAGGGAGTATTACCTAAACACAA 58.973 40.000 0.00 0.00 37.18 3.33
8238 9119 5.596763 AGGAGGGAGTATTACCTAAACACA 58.403 41.667 0.00 0.00 37.18 3.72
8239 9120 6.407865 GGAAGGAGGGAGTATTACCTAAACAC 60.408 46.154 0.00 0.00 37.18 3.32
8240 9121 5.664457 GGAAGGAGGGAGTATTACCTAAACA 59.336 44.000 0.00 0.00 37.18 2.83
8241 9122 5.071519 GGGAAGGAGGGAGTATTACCTAAAC 59.928 48.000 0.00 0.00 37.18 2.01
8242 9123 5.222086 GGGAAGGAGGGAGTATTACCTAAA 58.778 45.833 0.00 0.00 37.18 1.85
8243 9124 4.235873 TGGGAAGGAGGGAGTATTACCTAA 59.764 45.833 0.00 0.00 37.18 2.69
8244 9125 3.801317 TGGGAAGGAGGGAGTATTACCTA 59.199 47.826 0.00 0.00 37.18 3.08
8245 9126 2.595380 TGGGAAGGAGGGAGTATTACCT 59.405 50.000 0.00 0.00 40.54 3.08
8246 9127 3.056201 TGGGAAGGAGGGAGTATTACC 57.944 52.381 0.00 0.00 0.00 2.85
8247 9128 5.446260 TTTTGGGAAGGAGGGAGTATTAC 57.554 43.478 0.00 0.00 0.00 1.89
8248 9129 7.964730 ATATTTTGGGAAGGAGGGAGTATTA 57.035 36.000 0.00 0.00 0.00 0.98
8249 9130 6.865651 ATATTTTGGGAAGGAGGGAGTATT 57.134 37.500 0.00 0.00 0.00 1.89
8250 9131 7.018650 CCTTATATTTTGGGAAGGAGGGAGTAT 59.981 40.741 0.00 0.00 40.88 2.12
8251 9132 6.331837 CCTTATATTTTGGGAAGGAGGGAGTA 59.668 42.308 0.00 0.00 40.88 2.59
8252 9133 5.134509 CCTTATATTTTGGGAAGGAGGGAGT 59.865 44.000 0.00 0.00 40.88 3.85
8253 9134 5.635120 CCTTATATTTTGGGAAGGAGGGAG 58.365 45.833 0.00 0.00 40.88 4.30
8254 9135 4.141018 GCCTTATATTTTGGGAAGGAGGGA 60.141 45.833 3.71 0.00 40.88 4.20
8255 9136 4.152647 GCCTTATATTTTGGGAAGGAGGG 58.847 47.826 3.71 0.00 40.88 4.30
8256 9137 3.821033 CGCCTTATATTTTGGGAAGGAGG 59.179 47.826 3.71 0.00 40.88 4.30
8257 9138 4.275936 CACGCCTTATATTTTGGGAAGGAG 59.724 45.833 3.71 2.94 40.88 3.69
8258 9139 4.080243 TCACGCCTTATATTTTGGGAAGGA 60.080 41.667 3.71 0.00 40.88 3.36
8259 9140 4.204012 TCACGCCTTATATTTTGGGAAGG 58.796 43.478 0.00 0.00 41.26 3.46
8260 9141 6.039270 TCAATCACGCCTTATATTTTGGGAAG 59.961 38.462 0.00 0.00 0.00 3.46
8261 9142 5.888724 TCAATCACGCCTTATATTTTGGGAA 59.111 36.000 0.00 0.00 0.00 3.97
8262 9143 5.298276 GTCAATCACGCCTTATATTTTGGGA 59.702 40.000 0.00 0.00 0.00 4.37
8263 9144 5.299279 AGTCAATCACGCCTTATATTTTGGG 59.701 40.000 0.00 0.00 0.00 4.12
8264 9145 6.183360 ACAGTCAATCACGCCTTATATTTTGG 60.183 38.462 0.00 0.00 0.00 3.28
8265 9146 6.688385 CACAGTCAATCACGCCTTATATTTTG 59.312 38.462 0.00 0.00 0.00 2.44
8266 9147 6.677920 GCACAGTCAATCACGCCTTATATTTT 60.678 38.462 0.00 0.00 0.00 1.82
8267 9148 5.220854 GCACAGTCAATCACGCCTTATATTT 60.221 40.000 0.00 0.00 0.00 1.40
8268 9149 4.273480 GCACAGTCAATCACGCCTTATATT 59.727 41.667 0.00 0.00 0.00 1.28
8269 9150 3.809832 GCACAGTCAATCACGCCTTATAT 59.190 43.478 0.00 0.00 0.00 0.86
8270 9151 3.194861 GCACAGTCAATCACGCCTTATA 58.805 45.455 0.00 0.00 0.00 0.98
8271 9152 2.009774 GCACAGTCAATCACGCCTTAT 58.990 47.619 0.00 0.00 0.00 1.73
8272 9153 1.270571 TGCACAGTCAATCACGCCTTA 60.271 47.619 0.00 0.00 0.00 2.69
8273 9154 0.534877 TGCACAGTCAATCACGCCTT 60.535 50.000 0.00 0.00 0.00 4.35
8274 9155 1.071299 TGCACAGTCAATCACGCCT 59.929 52.632 0.00 0.00 0.00 5.52
8275 9156 1.207593 GTGCACAGTCAATCACGCC 59.792 57.895 13.17 0.00 0.00 5.68
8276 9157 0.110509 CTGTGCACAGTCAATCACGC 60.111 55.000 34.04 0.00 39.09 5.34
8287 9168 3.679502 CGATGTATCAAAGACTGTGCACA 59.320 43.478 20.37 20.37 0.00 4.57
8288 9169 3.926527 TCGATGTATCAAAGACTGTGCAC 59.073 43.478 10.75 10.75 0.00 4.57
8289 9170 4.186856 TCGATGTATCAAAGACTGTGCA 57.813 40.909 0.00 0.00 0.00 4.57
8290 9171 4.627467 ACTTCGATGTATCAAAGACTGTGC 59.373 41.667 1.47 0.00 0.00 4.57
8291 9172 6.806739 TGTACTTCGATGTATCAAAGACTGTG 59.193 38.462 13.59 0.00 0.00 3.66
8292 9173 6.920817 TGTACTTCGATGTATCAAAGACTGT 58.079 36.000 13.59 0.00 0.00 3.55
8293 9174 7.043125 CCATGTACTTCGATGTATCAAAGACTG 60.043 40.741 13.59 8.55 0.00 3.51
8294 9175 6.980978 CCATGTACTTCGATGTATCAAAGACT 59.019 38.462 13.59 0.00 0.00 3.24
8295 9176 6.978659 TCCATGTACTTCGATGTATCAAAGAC 59.021 38.462 13.59 3.42 0.00 3.01
8296 9177 7.107639 TCCATGTACTTCGATGTATCAAAGA 57.892 36.000 13.59 10.99 0.00 2.52
8297 9178 7.953158 ATCCATGTACTTCGATGTATCAAAG 57.047 36.000 13.59 10.20 0.00 2.77
8298 9179 9.825109 TTAATCCATGTACTTCGATGTATCAAA 57.175 29.630 13.59 2.53 0.00 2.69
8299 9180 9.825109 TTTAATCCATGTACTTCGATGTATCAA 57.175 29.630 13.59 4.65 0.00 2.57
8300 9181 9.256477 GTTTAATCCATGTACTTCGATGTATCA 57.744 33.333 13.59 12.99 0.00 2.15
8301 9182 9.256477 TGTTTAATCCATGTACTTCGATGTATC 57.744 33.333 13.59 8.62 0.00 2.24
8302 9183 9.778741 ATGTTTAATCCATGTACTTCGATGTAT 57.221 29.630 13.59 0.00 0.00 2.29
8303 9184 9.040939 CATGTTTAATCCATGTACTTCGATGTA 57.959 33.333 7.05 7.05 35.94 2.29
8304 9185 7.919690 CATGTTTAATCCATGTACTTCGATGT 58.080 34.615 9.12 9.12 35.94 3.06



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

AutoCloner maintained by Alex Coulton.