Multiple sequence alignment - TraesCS3B01G268100

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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 TraesCS3B01G268100 chr3B 100.000 2594 0 0 1 2594 431518263 431515670 0.000000e+00 4791
1 TraesCS3B01G268100 chr3B 89.425 435 34 2 1709 2132 431259893 431259460 2.940000e-149 538
2 TraesCS3B01G268100 chr3B 88.800 250 23 5 2335 2582 431259307 431259061 4.200000e-78 302
3 TraesCS3B01G268100 chr3B 88.321 137 16 0 2204 2340 798537470 798537334 5.740000e-37 165
4 TraesCS3B01G268100 chr3B 94.286 70 3 1 2120 2189 431259442 431259374 3.530000e-19 106
5 TraesCS3B01G268100 chr3D 95.014 1745 45 18 478 2202 332327529 332325807 0.000000e+00 2702
6 TraesCS3B01G268100 chr3D 95.366 410 18 1 2186 2594 332325772 332325363 0.000000e+00 651
7 TraesCS3B01G268100 chr3D 89.152 507 40 4 1709 2202 332169727 332169223 3.670000e-173 617
8 TraesCS3B01G268100 chr3D 88.046 435 36 3 1709 2132 332237370 332236941 3.850000e-138 501
9 TraesCS3B01G268100 chr3D 91.228 342 30 0 1 342 332328748 332328407 1.410000e-127 466
10 TraesCS3B01G268100 chr3D 89.200 250 23 4 2335 2582 332236789 332236542 2.510000e-80 309
11 TraesCS3B01G268100 chr3D 95.312 128 5 1 334 460 332327643 332327516 4.380000e-48 202
12 TraesCS3B01G268100 chr3D 82.329 249 19 14 2335 2582 332169170 332168946 2.630000e-45 193
13 TraesCS3B01G268100 chr3D 93.333 75 5 0 2115 2189 332236930 332236856 7.590000e-21 111
14 TraesCS3B01G268100 chr3A 94.938 1284 38 8 940 2202 449656996 449655719 0.000000e+00 1986
15 TraesCS3B01G268100 chr3A 88.046 435 40 2 1709 2132 449514077 449513644 2.980000e-139 505
16 TraesCS3B01G268100 chr3A 94.231 260 15 0 2335 2594 449655666 449655407 5.200000e-107 398
17 TraesCS3B01G268100 chr3A 95.279 233 9 2 478 708 449658733 449658501 4.080000e-98 368
18 TraesCS3B01G268100 chr3A 93.625 251 7 4 699 949 449658478 449658237 1.470000e-97 366
19 TraesCS3B01G268100 chr3A 95.455 198 9 0 1 198 449659458 449659261 1.500000e-82 316
20 TraesCS3B01G268100 chr3A 89.600 250 22 4 2335 2582 449513490 449513243 5.390000e-82 315
21 TraesCS3B01G268100 chr3A 77.265 563 108 12 1010 1556 449514952 449514394 1.940000e-81 313
22 TraesCS3B01G268100 chr3A 89.641 251 16 3 213 460 449658963 449658720 6.970000e-81 311
23 TraesCS3B01G268100 chr3A 94.286 70 4 0 2120 2189 449513626 449513557 9.820000e-20 108
24 TraesCS3B01G268100 chr7A 80.833 600 103 6 1001 1588 424534696 424535295 6.540000e-126 460
25 TraesCS3B01G268100 chr5A 80.288 624 101 16 996 1601 4080757 4081376 3.940000e-123 451
26 TraesCS3B01G268100 chr5A 89.344 122 13 0 2220 2341 54638371 54638250 1.240000e-33 154
27 TraesCS3B01G268100 chr4A 80.421 618 100 15 1001 1601 17887880 17888493 3.940000e-123 451
28 TraesCS3B01G268100 chr7D 80.500 600 104 7 1001 1588 376941126 376941724 5.090000e-122 448
29 TraesCS3B01G268100 chr2A 80.328 610 103 14 994 1588 764913447 764914054 1.830000e-121 446
30 TraesCS3B01G268100 chr7B 80.000 600 108 6 1001 1588 372008150 372008749 1.430000e-117 433
31 TraesCS3B01G268100 chr6A 92.537 134 10 0 2204 2337 149859972 149859839 2.630000e-45 193
32 TraesCS3B01G268100 chr6B 90.299 134 13 0 2204 2337 214085918 214086051 2.650000e-40 176
33 TraesCS3B01G268100 chr6B 89.899 99 10 0 2206 2304 687365217 687365315 7.530000e-26 128
34 TraesCS3B01G268100 chr5B 90.667 75 7 0 2230 2304 636344682 636344756 1.640000e-17 100


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 TraesCS3B01G268100 chr3B 431515670 431518263 2593 True 4791.000000 4791 100.00000 1 2594 1 chr3B.!!$R1 2593
1 TraesCS3B01G268100 chr3B 431259061 431259893 832 True 315.333333 538 90.83700 1709 2582 3 chr3B.!!$R3 873
2 TraesCS3B01G268100 chr3D 332325363 332328748 3385 True 1005.250000 2702 94.23000 1 2594 4 chr3D.!!$R3 2593
3 TraesCS3B01G268100 chr3D 332168946 332169727 781 True 405.000000 617 85.74050 1709 2582 2 chr3D.!!$R1 873
4 TraesCS3B01G268100 chr3D 332236542 332237370 828 True 307.000000 501 90.19300 1709 2582 3 chr3D.!!$R2 873
5 TraesCS3B01G268100 chr3A 449655407 449659458 4051 True 624.166667 1986 93.86150 1 2594 6 chr3A.!!$R2 2593
6 TraesCS3B01G268100 chr3A 449513243 449514952 1709 True 310.250000 505 87.29925 1010 2582 4 chr3A.!!$R1 1572
7 TraesCS3B01G268100 chr7A 424534696 424535295 599 False 460.000000 460 80.83300 1001 1588 1 chr7A.!!$F1 587
8 TraesCS3B01G268100 chr5A 4080757 4081376 619 False 451.000000 451 80.28800 996 1601 1 chr5A.!!$F1 605
9 TraesCS3B01G268100 chr4A 17887880 17888493 613 False 451.000000 451 80.42100 1001 1601 1 chr4A.!!$F1 600
10 TraesCS3B01G268100 chr7D 376941126 376941724 598 False 448.000000 448 80.50000 1001 1588 1 chr7D.!!$F1 587
11 TraesCS3B01G268100 chr2A 764913447 764914054 607 False 446.000000 446 80.32800 994 1588 1 chr2A.!!$F1 594
12 TraesCS3B01G268100 chr7B 372008150 372008749 599 False 433.000000 433 80.00000 1001 1588 1 chr7B.!!$F1 587

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
443 1502 0.527565 GCCATGGCAACCTGTACAAG 59.472 55.0 32.08 0.0 41.49 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2248 4917 0.03601 TCTAGGAGCCAGCAAACAGC 60.036 55.0 0.0 0.0 46.19 4.4 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
53 54 6.994421 ATTACAAACCTTTGGTGATCCTTT 57.006 33.333 2.94 0.00 42.34 3.11
75 76 7.331687 CCTTTGTAAACAAATTTGATAGCAGGG 59.668 37.037 24.64 16.19 43.92 4.45
92 93 1.134401 AGGGCATGTGAACATACGGAG 60.134 52.381 0.00 0.00 34.26 4.63
153 154 0.694444 AGCCCCCGAGTCCATTGTAT 60.694 55.000 0.00 0.00 0.00 2.29
183 184 6.198591 GGAAATCTACATAGAAGTACACACGC 59.801 42.308 0.00 0.00 35.69 5.34
201 202 3.994392 CACGCCATAGGAACATATACCAC 59.006 47.826 0.00 0.00 0.00 4.16
235 519 6.704493 CCAATAGCATGATGAAATTGAAAGGG 59.296 38.462 16.78 2.26 30.77 3.95
256 540 4.626172 GGGAAAGCTAACGAAACTGTAGAG 59.374 45.833 0.00 0.00 0.00 2.43
261 545 3.368236 GCTAACGAAACTGTAGAGGCAAG 59.632 47.826 0.00 0.00 0.00 4.01
286 572 4.323336 CACAAAATAATTGTAGTGGCGTGC 59.677 41.667 0.00 0.00 0.00 5.34
312 599 0.927029 GGTAGGGAAAGGGAGCCAAT 59.073 55.000 0.00 0.00 0.00 3.16
319 606 4.089361 GGGAAAGGGAGCCAATAATATGG 58.911 47.826 0.00 0.00 43.70 2.74
378 1437 8.224025 TCTTATCAGGATCATCAGACTACTCTT 58.776 37.037 0.00 0.00 0.00 2.85
443 1502 0.527565 GCCATGGCAACCTGTACAAG 59.472 55.000 32.08 0.00 41.49 3.16
444 1503 1.886222 GCCATGGCAACCTGTACAAGA 60.886 52.381 32.08 0.00 41.49 3.02
445 1504 2.726821 CCATGGCAACCTGTACAAGAT 58.273 47.619 0.00 0.00 0.00 2.40
446 1505 2.424601 CCATGGCAACCTGTACAAGATG 59.575 50.000 0.00 0.00 0.00 2.90
447 1506 2.198827 TGGCAACCTGTACAAGATGG 57.801 50.000 0.00 0.00 0.00 3.51
448 1507 1.702401 TGGCAACCTGTACAAGATGGA 59.298 47.619 5.91 0.00 0.00 3.41
449 1508 2.290260 TGGCAACCTGTACAAGATGGAG 60.290 50.000 5.91 0.17 0.00 3.86
450 1509 1.740025 GCAACCTGTACAAGATGGAGC 59.260 52.381 5.91 5.80 0.00 4.70
451 1510 2.616510 GCAACCTGTACAAGATGGAGCT 60.617 50.000 5.91 0.00 0.00 4.09
452 1511 3.679389 CAACCTGTACAAGATGGAGCTT 58.321 45.455 5.91 0.00 0.00 3.74
453 1512 4.832248 CAACCTGTACAAGATGGAGCTTA 58.168 43.478 5.91 0.00 0.00 3.09
454 1513 5.245531 CAACCTGTACAAGATGGAGCTTAA 58.754 41.667 5.91 0.00 0.00 1.85
455 1514 4.833390 ACCTGTACAAGATGGAGCTTAAC 58.167 43.478 5.91 0.00 0.00 2.01
456 1515 3.865745 CCTGTACAAGATGGAGCTTAACG 59.134 47.826 0.00 0.00 0.00 3.18
457 1516 3.259064 TGTACAAGATGGAGCTTAACGC 58.741 45.455 0.00 0.00 39.57 4.84
458 1517 1.739067 ACAAGATGGAGCTTAACGCC 58.261 50.000 0.00 0.00 40.39 5.68
459 1518 1.279271 ACAAGATGGAGCTTAACGCCT 59.721 47.619 0.00 0.00 39.39 5.52
460 1519 2.290323 ACAAGATGGAGCTTAACGCCTT 60.290 45.455 0.00 0.00 39.39 4.35
461 1520 2.749621 CAAGATGGAGCTTAACGCCTTT 59.250 45.455 0.00 0.00 39.39 3.11
462 1521 3.073274 AGATGGAGCTTAACGCCTTTT 57.927 42.857 0.00 0.00 39.39 2.27
463 1522 3.421844 AGATGGAGCTTAACGCCTTTTT 58.578 40.909 0.00 0.00 39.39 1.94
534 1594 5.821470 CAGAAGCAGATGGTCAAACATATCT 59.179 40.000 0.00 0.00 0.00 1.98
615 1675 2.632987 AGTAACCCAAAAGCACGAGT 57.367 45.000 0.00 0.00 0.00 4.18
655 1715 5.712446 GCTATTCTTCAGAAAACCCCTCTTT 59.288 40.000 0.00 0.00 37.61 2.52
657 1717 6.656632 ATTCTTCAGAAAACCCCTCTTTTC 57.343 37.500 0.00 0.00 39.50 2.29
777 1878 5.300792 TCGAATAGTTGCCCTTTTCTTTTGT 59.699 36.000 0.00 0.00 31.23 2.83
778 1879 6.487331 TCGAATAGTTGCCCTTTTCTTTTGTA 59.513 34.615 0.00 0.00 31.23 2.41
779 1880 7.013464 TCGAATAGTTGCCCTTTTCTTTTGTAA 59.987 33.333 0.00 0.00 31.23 2.41
780 1881 7.812669 CGAATAGTTGCCCTTTTCTTTTGTAAT 59.187 33.333 3.46 0.00 31.23 1.89
787 1888 9.838339 TTGCCCTTTTCTTTTGTAATAATTTCA 57.162 25.926 0.00 0.00 0.00 2.69
811 1912 8.877195 TCAAACTAGTAAGAGGGTTTATTCTGT 58.123 33.333 0.00 0.00 31.80 3.41
984 3347 3.072468 TAGCCCAGAACCGACGGG 61.072 66.667 20.00 0.00 43.42 5.28
1173 3548 1.609239 CAGCTACAGCCCATCCCAA 59.391 57.895 0.00 0.00 43.38 4.12
1296 3671 1.530655 CCCCAACCTCCGCTTTGTT 60.531 57.895 0.00 0.00 0.00 2.83
1350 3725 2.885861 GACGACCACAGCCTCGAT 59.114 61.111 0.00 0.00 33.96 3.59
1653 4035 6.852345 GCATTCTTAAGTCTAGCTCGTACTAC 59.148 42.308 1.63 0.00 0.00 2.73
1655 4037 9.258826 CATTCTTAAGTCTAGCTCGTACTACTA 57.741 37.037 1.63 0.00 0.00 1.82
1657 4039 9.829507 TTCTTAAGTCTAGCTCGTACTACTATT 57.170 33.333 1.63 0.00 0.00 1.73
1661 4043 7.945033 AGTCTAGCTCGTACTACTATTGTAC 57.055 40.000 0.00 0.00 37.50 2.90
1788 4328 2.472695 AAGATTGCGCCTACAACTGA 57.527 45.000 4.18 0.00 31.03 3.41
1971 4519 6.084326 TCCTTTGTTCTAAAGTTGCCATTC 57.916 37.500 0.00 0.00 0.00 2.67
2058 4606 3.976793 AATTGACGGCATGAGCATTAG 57.023 42.857 0.00 0.00 44.61 1.73
2190 4807 5.130311 TGGGATGTTTCAGATTTCCGATAGA 59.870 40.000 0.00 0.00 39.76 1.98
2191 4808 5.698545 GGGATGTTTCAGATTTCCGATAGAG 59.301 44.000 0.00 0.00 39.76 2.43
2203 4872 4.884668 TCCGATAGAGTTTTGGTCTGTT 57.115 40.909 0.00 0.00 39.76 3.16
2204 4873 5.223449 TCCGATAGAGTTTTGGTCTGTTT 57.777 39.130 0.00 0.00 39.76 2.83
2205 4874 6.349243 TCCGATAGAGTTTTGGTCTGTTTA 57.651 37.500 0.00 0.00 39.76 2.01
2206 4875 6.395629 TCCGATAGAGTTTTGGTCTGTTTAG 58.604 40.000 0.00 0.00 39.76 1.85
2207 4876 5.581085 CCGATAGAGTTTTGGTCTGTTTAGG 59.419 44.000 0.00 0.00 39.76 2.69
2208 4877 5.063564 CGATAGAGTTTTGGTCTGTTTAGGC 59.936 44.000 0.00 0.00 39.76 3.93
2209 4878 7.831078 CGATAGAGTTTTGGTCTGTTTAGGCC 61.831 46.154 0.00 0.00 44.70 5.19
2215 4884 1.822506 GGTCTGTTTAGGCCCTGTTC 58.177 55.000 0.00 0.00 43.16 3.18
2216 4885 1.439679 GTCTGTTTAGGCCCTGTTCG 58.560 55.000 0.00 0.00 0.00 3.95
2217 4886 1.053424 TCTGTTTAGGCCCTGTTCGT 58.947 50.000 0.00 0.00 0.00 3.85
2218 4887 1.156736 CTGTTTAGGCCCTGTTCGTG 58.843 55.000 0.00 0.00 0.00 4.35
2219 4888 0.759959 TGTTTAGGCCCTGTTCGTGA 59.240 50.000 0.00 0.00 0.00 4.35
2220 4889 1.141254 TGTTTAGGCCCTGTTCGTGAA 59.859 47.619 0.00 0.00 0.00 3.18
2221 4890 2.224670 TGTTTAGGCCCTGTTCGTGAAT 60.225 45.455 0.00 0.00 0.00 2.57
2222 4891 2.396590 TTAGGCCCTGTTCGTGAATC 57.603 50.000 0.00 0.00 0.00 2.52
2223 4892 0.539986 TAGGCCCTGTTCGTGAATCC 59.460 55.000 0.00 0.00 0.00 3.01
2224 4893 1.002624 GGCCCTGTTCGTGAATCCA 60.003 57.895 0.00 0.00 0.00 3.41
2225 4894 1.305930 GGCCCTGTTCGTGAATCCAC 61.306 60.000 0.00 0.00 39.86 4.02
2226 4895 1.305930 GCCCTGTTCGTGAATCCACC 61.306 60.000 0.00 0.00 40.12 4.61
2227 4896 1.019278 CCCTGTTCGTGAATCCACCG 61.019 60.000 0.00 0.00 40.12 4.94
2228 4897 1.635663 CCTGTTCGTGAATCCACCGC 61.636 60.000 0.00 0.00 40.12 5.68
2229 4898 0.670546 CTGTTCGTGAATCCACCGCT 60.671 55.000 0.00 0.00 40.12 5.52
2230 4899 0.669318 TGTTCGTGAATCCACCGCTC 60.669 55.000 0.00 0.00 40.12 5.03
2231 4900 1.079405 TTCGTGAATCCACCGCTCC 60.079 57.895 0.00 0.00 40.12 4.70
2232 4901 1.541310 TTCGTGAATCCACCGCTCCT 61.541 55.000 0.00 0.00 40.12 3.69
2233 4902 0.681887 TCGTGAATCCACCGCTCCTA 60.682 55.000 0.00 0.00 40.12 2.94
2234 4903 0.174845 CGTGAATCCACCGCTCCTAA 59.825 55.000 0.00 0.00 40.12 2.69
2235 4904 1.802880 CGTGAATCCACCGCTCCTAAG 60.803 57.143 0.00 0.00 40.12 2.18
2236 4905 1.480954 GTGAATCCACCGCTCCTAAGA 59.519 52.381 0.00 0.00 37.33 2.10
2237 4906 2.103263 GTGAATCCACCGCTCCTAAGAT 59.897 50.000 0.00 0.00 37.33 2.40
2238 4907 2.365617 TGAATCCACCGCTCCTAAGATC 59.634 50.000 0.00 0.00 0.00 2.75
2239 4908 2.390225 ATCCACCGCTCCTAAGATCT 57.610 50.000 0.00 0.00 0.00 2.75
2240 4909 1.403814 TCCACCGCTCCTAAGATCTG 58.596 55.000 0.00 0.00 0.00 2.90
2241 4910 1.063942 TCCACCGCTCCTAAGATCTGA 60.064 52.381 0.00 0.00 0.00 3.27
2242 4911 1.339610 CCACCGCTCCTAAGATCTGAG 59.660 57.143 0.00 0.00 0.00 3.35
2243 4912 1.339610 CACCGCTCCTAAGATCTGAGG 59.660 57.143 19.39 19.39 0.00 3.86
2244 4913 1.215673 ACCGCTCCTAAGATCTGAGGA 59.784 52.381 25.22 25.22 39.63 3.71
2248 4917 1.988293 TCCTAAGATCTGAGGAGCGG 58.012 55.000 23.48 0.22 36.92 5.52
2249 4918 0.316841 CCTAAGATCTGAGGAGCGGC 59.683 60.000 20.68 0.00 34.46 6.53
2250 4919 1.327303 CTAAGATCTGAGGAGCGGCT 58.673 55.000 0.00 0.00 32.47 5.52
2251 4920 1.000385 CTAAGATCTGAGGAGCGGCTG 60.000 57.143 7.50 0.00 32.47 4.85
2252 4921 0.975040 AAGATCTGAGGAGCGGCTGT 60.975 55.000 7.50 0.00 32.47 4.40
2253 4922 0.975040 AGATCTGAGGAGCGGCTGTT 60.975 55.000 7.50 0.00 32.47 3.16
2254 4923 0.107945 GATCTGAGGAGCGGCTGTTT 60.108 55.000 7.50 0.00 0.00 2.83
2255 4924 0.392193 ATCTGAGGAGCGGCTGTTTG 60.392 55.000 7.50 0.00 0.00 2.93
2256 4925 2.669569 TGAGGAGCGGCTGTTTGC 60.670 61.111 7.50 0.00 41.94 3.68
2257 4926 2.359230 GAGGAGCGGCTGTTTGCT 60.359 61.111 7.50 0.00 45.90 3.91
2263 4932 3.741476 CGGCTGTTTGCTGGCTCC 61.741 66.667 0.00 0.00 44.06 4.70
2264 4933 2.282745 GGCTGTTTGCTGGCTCCT 60.283 61.111 0.00 0.00 42.39 3.69
2265 4934 1.002134 GGCTGTTTGCTGGCTCCTA 60.002 57.895 0.00 0.00 42.39 2.94
2266 4935 1.028868 GGCTGTTTGCTGGCTCCTAG 61.029 60.000 0.00 0.00 42.39 3.02
2267 4936 0.036010 GCTGTTTGCTGGCTCCTAGA 60.036 55.000 0.00 0.00 38.95 2.43
2268 4937 1.407989 GCTGTTTGCTGGCTCCTAGAT 60.408 52.381 0.00 0.00 38.95 1.98
2269 4938 2.943199 GCTGTTTGCTGGCTCCTAGATT 60.943 50.000 0.00 0.00 38.95 2.40
2270 4939 3.350833 CTGTTTGCTGGCTCCTAGATTT 58.649 45.455 0.00 0.00 0.00 2.17
2271 4940 3.760684 CTGTTTGCTGGCTCCTAGATTTT 59.239 43.478 0.00 0.00 0.00 1.82
2272 4941 3.507233 TGTTTGCTGGCTCCTAGATTTTG 59.493 43.478 0.00 0.00 0.00 2.44
2273 4942 1.755179 TGCTGGCTCCTAGATTTTGC 58.245 50.000 0.00 0.00 0.00 3.68
2274 4943 1.004628 TGCTGGCTCCTAGATTTTGCA 59.995 47.619 0.00 0.00 0.00 4.08
2275 4944 2.305009 GCTGGCTCCTAGATTTTGCAT 58.695 47.619 0.00 0.00 0.00 3.96
2276 4945 2.692041 GCTGGCTCCTAGATTTTGCATT 59.308 45.455 0.00 0.00 0.00 3.56
2277 4946 3.885297 GCTGGCTCCTAGATTTTGCATTA 59.115 43.478 0.00 0.00 0.00 1.90
2278 4947 4.261363 GCTGGCTCCTAGATTTTGCATTAC 60.261 45.833 0.00 0.00 0.00 1.89
2279 4948 4.854173 TGGCTCCTAGATTTTGCATTACA 58.146 39.130 0.00 0.00 0.00 2.41
2280 4949 4.883585 TGGCTCCTAGATTTTGCATTACAG 59.116 41.667 0.00 0.00 0.00 2.74
2281 4950 4.261363 GGCTCCTAGATTTTGCATTACAGC 60.261 45.833 0.00 0.00 0.00 4.40
2282 4951 4.578105 GCTCCTAGATTTTGCATTACAGCT 59.422 41.667 0.00 0.00 34.99 4.24
2283 4952 5.277731 GCTCCTAGATTTTGCATTACAGCTC 60.278 44.000 0.00 0.00 34.99 4.09
2284 4953 5.126067 TCCTAGATTTTGCATTACAGCTCC 58.874 41.667 0.00 0.00 34.99 4.70
2285 4954 4.024556 CCTAGATTTTGCATTACAGCTCCG 60.025 45.833 0.00 0.00 34.99 4.63
2286 4955 3.347216 AGATTTTGCATTACAGCTCCGT 58.653 40.909 0.00 0.00 34.99 4.69
2287 4956 3.375299 AGATTTTGCATTACAGCTCCGTC 59.625 43.478 0.00 0.00 34.99 4.79
2288 4957 1.448985 TTTGCATTACAGCTCCGTCC 58.551 50.000 0.00 0.00 34.99 4.79
2289 4958 0.739462 TTGCATTACAGCTCCGTCCG 60.739 55.000 0.00 0.00 34.99 4.79
2290 4959 2.526120 GCATTACAGCTCCGTCCGC 61.526 63.158 0.00 0.00 0.00 5.54
2291 4960 1.141881 CATTACAGCTCCGTCCGCT 59.858 57.895 0.00 0.00 38.49 5.52
2292 4961 0.872021 CATTACAGCTCCGTCCGCTC 60.872 60.000 0.00 0.00 35.07 5.03
2293 4962 1.038130 ATTACAGCTCCGTCCGCTCT 61.038 55.000 0.00 0.00 35.07 4.09
2294 4963 1.248785 TTACAGCTCCGTCCGCTCTT 61.249 55.000 0.00 0.00 35.07 2.85
2295 4964 1.934220 TACAGCTCCGTCCGCTCTTG 61.934 60.000 0.00 0.00 35.07 3.02
2296 4965 3.764466 AGCTCCGTCCGCTCTTGG 61.764 66.667 0.00 0.00 30.49 3.61
2297 4966 3.760035 GCTCCGTCCGCTCTTGGA 61.760 66.667 0.00 0.00 35.04 3.53
2298 4967 2.492090 CTCCGTCCGCTCTTGGAG 59.508 66.667 0.00 0.00 41.82 3.86
2316 4985 3.933722 CGGAGCCATGGAGCGGAT 61.934 66.667 18.40 0.00 38.01 4.18
2317 4986 2.512896 GGAGCCATGGAGCGGATT 59.487 61.111 18.40 0.00 38.01 3.01
2318 4987 1.895707 GGAGCCATGGAGCGGATTG 60.896 63.158 18.40 0.00 38.01 2.67
2319 4988 1.146930 GAGCCATGGAGCGGATTGA 59.853 57.895 18.40 0.00 38.01 2.57
2320 4989 1.153086 AGCCATGGAGCGGATTGAC 60.153 57.895 18.40 0.00 38.01 3.18
2321 4990 2.537560 GCCATGGAGCGGATTGACG 61.538 63.158 18.40 0.00 0.00 4.35
2322 4991 1.143838 CCATGGAGCGGATTGACGA 59.856 57.895 5.56 0.00 35.47 4.20
2323 4992 1.154205 CCATGGAGCGGATTGACGAC 61.154 60.000 5.56 0.00 35.47 4.34
2324 4993 1.226974 ATGGAGCGGATTGACGACG 60.227 57.895 0.00 0.00 35.47 5.12
2325 4994 1.663379 ATGGAGCGGATTGACGACGA 61.663 55.000 0.00 0.00 35.47 4.20
2326 4995 1.153901 GGAGCGGATTGACGACGAA 60.154 57.895 0.00 0.00 35.47 3.85
2327 4996 1.411493 GGAGCGGATTGACGACGAAC 61.411 60.000 0.00 0.00 35.47 3.95
2474 5275 9.295214 CTTCAGTATACATGTCAGAAGTTACTG 57.705 37.037 0.00 9.56 37.63 2.74
2576 5378 5.615925 AGTCAACTCCTCACTGTTTAGTT 57.384 39.130 0.00 0.00 34.07 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 5.244851 TGCCCTGCTATCAAATTTGTTTACA 59.755 36.000 17.47 11.11 0.00 2.41
75 76 4.332543 TGATTTCTCCGTATGTTCACATGC 59.667 41.667 2.50 0.29 37.15 4.06
153 154 9.871238 GTGTACTTCTATGTAGATTTCCTTTCA 57.129 33.333 0.00 0.00 31.40 2.69
183 184 9.793259 AAGTAAATGTGGTATATGTTCCTATGG 57.207 33.333 0.00 0.00 0.00 2.74
201 202 9.976511 ATTTCATCATGCTATTGGAAGTAAATG 57.023 29.630 0.00 0.00 0.00 2.32
210 211 6.704493 CCCTTTCAATTTCATCATGCTATTGG 59.296 38.462 10.08 0.00 0.00 3.16
211 212 7.494211 TCCCTTTCAATTTCATCATGCTATTG 58.506 34.615 5.59 5.59 0.00 1.90
235 519 4.091655 GCCTCTACAGTTTCGTTAGCTTTC 59.908 45.833 0.00 0.00 0.00 2.62
256 540 5.348451 CACTACAATTATTTTGTGGCTTGCC 59.652 40.000 4.43 4.43 34.76 4.52
286 572 2.766828 CTCCCTTTCCCTACCACACTAG 59.233 54.545 0.00 0.00 0.00 2.57
312 599 4.502604 GCTACTTTGCCTCGGTCCATATTA 60.503 45.833 0.00 0.00 0.00 0.98
319 606 1.362406 GCTGCTACTTTGCCTCGGTC 61.362 60.000 0.00 0.00 0.00 4.79
378 1437 8.725405 TGATATGCCAAGTTAATTACGAAGAA 57.275 30.769 0.00 0.00 0.00 2.52
464 1523 0.188342 AAGCTCCTGCCCCTCAAAAA 59.812 50.000 0.00 0.00 40.80 1.94
465 1524 1.072266 TAAGCTCCTGCCCCTCAAAA 58.928 50.000 0.00 0.00 40.80 2.44
466 1525 1.072266 TTAAGCTCCTGCCCCTCAAA 58.928 50.000 0.00 0.00 40.80 2.69
467 1526 0.328258 GTTAAGCTCCTGCCCCTCAA 59.672 55.000 0.00 0.00 40.80 3.02
468 1527 1.899437 CGTTAAGCTCCTGCCCCTCA 61.899 60.000 0.00 0.00 40.80 3.86
469 1528 1.153349 CGTTAAGCTCCTGCCCCTC 60.153 63.158 0.00 0.00 40.80 4.30
470 1529 2.990479 CGTTAAGCTCCTGCCCCT 59.010 61.111 0.00 0.00 40.80 4.79
471 1530 2.824489 GCGTTAAGCTCCTGCCCC 60.824 66.667 0.00 0.00 44.04 5.80
472 1531 3.330992 AGGCGTTAAGCTCCTGCCC 62.331 63.158 13.66 0.91 46.92 5.36
473 1532 2.109126 CAGGCGTTAAGCTCCTGCC 61.109 63.158 5.53 8.09 42.41 4.85
474 1533 2.109126 CCAGGCGTTAAGCTCCTGC 61.109 63.158 11.98 2.68 46.11 4.85
475 1534 0.535335 TACCAGGCGTTAAGCTCCTG 59.465 55.000 10.73 10.73 46.81 3.86
534 1594 3.849911 CGTAGGAATCAAGCTGTCAGAA 58.150 45.455 3.32 0.00 0.00 3.02
825 1926 4.489810 GACCAGCCTGACATTATATCTCG 58.510 47.826 0.00 0.00 0.00 4.04
963 3326 1.381928 CGTCGGTTCTGGGCTAGCTA 61.382 60.000 15.72 3.29 0.00 3.32
984 3347 2.759783 CATCGGATGATGGATCGCC 58.240 57.895 12.67 0.00 46.76 5.54
1167 3542 2.360726 GCGACGGGGTTTTGGGAT 60.361 61.111 0.00 0.00 0.00 3.85
1209 3584 1.519246 CTGGAAGATGAGGCAGCGA 59.481 57.895 0.00 0.00 34.07 4.93
1657 4039 9.907229 TGAGATGAAGAACTAGATCTAAGTACA 57.093 33.333 2.55 1.04 0.00 2.90
1971 4519 5.991328 TGCTAGGCAGATCGAAAAATTAG 57.009 39.130 0.00 0.00 33.32 1.73
2058 4606 3.715628 ACACAATCAGCACAAAAGGAC 57.284 42.857 0.00 0.00 0.00 3.85
2190 4807 2.177016 AGGGCCTAAACAGACCAAAACT 59.823 45.455 2.82 0.00 0.00 2.66
2191 4808 2.296190 CAGGGCCTAAACAGACCAAAAC 59.704 50.000 5.28 0.00 0.00 2.43
2203 4872 1.065709 GGATTCACGAACAGGGCCTAA 60.066 52.381 5.28 0.00 0.00 2.69
2204 4873 0.539986 GGATTCACGAACAGGGCCTA 59.460 55.000 5.28 0.00 0.00 3.93
2205 4874 1.299976 GGATTCACGAACAGGGCCT 59.700 57.895 0.00 0.00 0.00 5.19
2206 4875 1.002624 TGGATTCACGAACAGGGCC 60.003 57.895 0.00 0.00 0.00 5.80
2207 4876 1.305930 GGTGGATTCACGAACAGGGC 61.306 60.000 0.00 0.00 44.50 5.19
2208 4877 1.019278 CGGTGGATTCACGAACAGGG 61.019 60.000 0.00 0.00 44.50 4.45
2209 4878 1.635663 GCGGTGGATTCACGAACAGG 61.636 60.000 0.00 0.00 44.50 4.00
2210 4879 0.670546 AGCGGTGGATTCACGAACAG 60.671 55.000 0.00 0.00 44.50 3.16
2211 4880 0.669318 GAGCGGTGGATTCACGAACA 60.669 55.000 0.00 0.00 44.50 3.18
2212 4881 1.359459 GGAGCGGTGGATTCACGAAC 61.359 60.000 0.00 0.00 44.50 3.95
2213 4882 1.079405 GGAGCGGTGGATTCACGAA 60.079 57.895 0.00 0.00 44.50 3.85
2214 4883 0.681887 TAGGAGCGGTGGATTCACGA 60.682 55.000 0.00 0.00 44.50 4.35
2215 4884 0.174845 TTAGGAGCGGTGGATTCACG 59.825 55.000 0.00 0.00 44.50 4.35
2216 4885 1.480954 TCTTAGGAGCGGTGGATTCAC 59.519 52.381 0.00 0.00 42.91 3.18
2217 4886 1.860641 TCTTAGGAGCGGTGGATTCA 58.139 50.000 0.00 0.00 0.00 2.57
2218 4887 2.630580 AGATCTTAGGAGCGGTGGATTC 59.369 50.000 0.00 0.00 32.47 2.52
2219 4888 2.366916 CAGATCTTAGGAGCGGTGGATT 59.633 50.000 0.00 0.00 32.47 3.01
2220 4889 1.967066 CAGATCTTAGGAGCGGTGGAT 59.033 52.381 0.00 0.00 32.47 3.41
2221 4890 1.063942 TCAGATCTTAGGAGCGGTGGA 60.064 52.381 0.00 0.00 32.47 4.02
2222 4891 1.339610 CTCAGATCTTAGGAGCGGTGG 59.660 57.143 0.00 0.00 32.47 4.61
2223 4892 1.339610 CCTCAGATCTTAGGAGCGGTG 59.660 57.143 16.82 0.00 34.58 4.94
2224 4893 1.215673 TCCTCAGATCTTAGGAGCGGT 59.784 52.381 19.83 0.00 36.97 5.68
2225 4894 1.988293 TCCTCAGATCTTAGGAGCGG 58.012 55.000 19.83 0.88 36.97 5.52
2229 4898 1.988293 CCGCTCCTCAGATCTTAGGA 58.012 55.000 21.82 21.82 39.63 2.94
2230 4899 0.316841 GCCGCTCCTCAGATCTTAGG 59.683 60.000 15.81 15.81 0.00 2.69
2231 4900 1.000385 CAGCCGCTCCTCAGATCTTAG 60.000 57.143 0.00 0.00 0.00 2.18
2232 4901 1.035923 CAGCCGCTCCTCAGATCTTA 58.964 55.000 0.00 0.00 0.00 2.10
2233 4902 0.975040 ACAGCCGCTCCTCAGATCTT 60.975 55.000 0.00 0.00 0.00 2.40
2234 4903 0.975040 AACAGCCGCTCCTCAGATCT 60.975 55.000 0.00 0.00 0.00 2.75
2235 4904 0.107945 AAACAGCCGCTCCTCAGATC 60.108 55.000 0.00 0.00 0.00 2.75
2236 4905 0.392193 CAAACAGCCGCTCCTCAGAT 60.392 55.000 0.00 0.00 0.00 2.90
2237 4906 1.004560 CAAACAGCCGCTCCTCAGA 60.005 57.895 0.00 0.00 0.00 3.27
2238 4907 2.684843 GCAAACAGCCGCTCCTCAG 61.685 63.158 0.00 0.00 37.23 3.35
2239 4908 2.669569 GCAAACAGCCGCTCCTCA 60.670 61.111 0.00 0.00 37.23 3.86
2248 4917 0.036010 TCTAGGAGCCAGCAAACAGC 60.036 55.000 0.00 0.00 46.19 4.40
2249 4918 2.706339 ATCTAGGAGCCAGCAAACAG 57.294 50.000 0.00 0.00 0.00 3.16
2250 4919 3.439857 AAATCTAGGAGCCAGCAAACA 57.560 42.857 0.00 0.00 0.00 2.83
2251 4920 3.674410 GCAAAATCTAGGAGCCAGCAAAC 60.674 47.826 0.00 0.00 0.00 2.93
2252 4921 2.493278 GCAAAATCTAGGAGCCAGCAAA 59.507 45.455 0.00 0.00 0.00 3.68
2253 4922 2.094675 GCAAAATCTAGGAGCCAGCAA 58.905 47.619 0.00 0.00 0.00 3.91
2254 4923 1.004628 TGCAAAATCTAGGAGCCAGCA 59.995 47.619 0.00 0.00 0.00 4.41
2255 4924 1.755179 TGCAAAATCTAGGAGCCAGC 58.245 50.000 0.00 0.00 0.00 4.85
2256 4925 4.883585 TGTAATGCAAAATCTAGGAGCCAG 59.116 41.667 0.00 0.00 0.00 4.85
2257 4926 4.854173 TGTAATGCAAAATCTAGGAGCCA 58.146 39.130 0.00 0.00 0.00 4.75
2258 4927 4.261363 GCTGTAATGCAAAATCTAGGAGCC 60.261 45.833 0.00 0.00 0.00 4.70
2259 4928 4.578105 AGCTGTAATGCAAAATCTAGGAGC 59.422 41.667 0.00 0.00 34.99 4.70
2260 4929 5.238214 GGAGCTGTAATGCAAAATCTAGGAG 59.762 44.000 0.00 0.00 34.99 3.69
2261 4930 5.126067 GGAGCTGTAATGCAAAATCTAGGA 58.874 41.667 0.00 0.00 34.99 2.94
2262 4931 4.024556 CGGAGCTGTAATGCAAAATCTAGG 60.025 45.833 0.00 0.00 34.99 3.02
2263 4932 4.572389 ACGGAGCTGTAATGCAAAATCTAG 59.428 41.667 0.00 0.00 34.99 2.43
2264 4933 4.513442 ACGGAGCTGTAATGCAAAATCTA 58.487 39.130 0.00 0.00 34.99 1.98
2265 4934 3.347216 ACGGAGCTGTAATGCAAAATCT 58.653 40.909 0.00 0.00 34.99 2.40
2266 4935 3.487544 GGACGGAGCTGTAATGCAAAATC 60.488 47.826 0.00 0.00 34.99 2.17
2267 4936 2.423538 GGACGGAGCTGTAATGCAAAAT 59.576 45.455 0.00 0.00 34.99 1.82
2268 4937 1.810151 GGACGGAGCTGTAATGCAAAA 59.190 47.619 0.00 0.00 34.99 2.44
2269 4938 1.448985 GGACGGAGCTGTAATGCAAA 58.551 50.000 0.00 0.00 34.99 3.68
2270 4939 0.739462 CGGACGGAGCTGTAATGCAA 60.739 55.000 0.00 0.00 34.99 4.08
2271 4940 1.153647 CGGACGGAGCTGTAATGCA 60.154 57.895 0.00 0.00 34.99 3.96
2272 4941 2.526120 GCGGACGGAGCTGTAATGC 61.526 63.158 0.00 0.00 0.00 3.56
2273 4942 0.872021 GAGCGGACGGAGCTGTAATG 60.872 60.000 6.28 0.00 46.13 1.90
2274 4943 1.038130 AGAGCGGACGGAGCTGTAAT 61.038 55.000 6.28 0.00 46.13 1.89
2275 4944 1.248785 AAGAGCGGACGGAGCTGTAA 61.249 55.000 6.28 0.00 46.13 2.41
2276 4945 1.677966 AAGAGCGGACGGAGCTGTA 60.678 57.895 6.28 0.00 46.13 2.74
2277 4946 2.992114 AAGAGCGGACGGAGCTGT 60.992 61.111 6.28 0.00 46.13 4.40
2278 4947 2.507992 CAAGAGCGGACGGAGCTG 60.508 66.667 6.28 0.00 46.13 4.24
2280 4949 3.708220 CTCCAAGAGCGGACGGAGC 62.708 68.421 2.92 0.00 38.74 4.70
2281 4950 2.492090 CTCCAAGAGCGGACGGAG 59.508 66.667 0.00 0.00 39.20 4.63
2282 4951 3.760035 GCTCCAAGAGCGGACGGA 61.760 66.667 0.06 0.00 45.85 4.69
2290 4959 1.523258 CATGGCTCCGCTCCAAGAG 60.523 63.158 0.00 0.00 37.13 2.85
2291 4960 2.586245 CATGGCTCCGCTCCAAGA 59.414 61.111 0.00 0.00 37.13 3.02
2292 4961 2.515523 CCATGGCTCCGCTCCAAG 60.516 66.667 0.00 0.00 37.13 3.61
2293 4962 3.008517 TCCATGGCTCCGCTCCAA 61.009 61.111 6.96 0.00 37.13 3.53
2294 4963 3.473647 CTCCATGGCTCCGCTCCA 61.474 66.667 6.96 0.00 38.09 3.86
2295 4964 4.925861 GCTCCATGGCTCCGCTCC 62.926 72.222 6.96 0.00 0.00 4.70
2299 4968 3.466791 AATCCGCTCCATGGCTCCG 62.467 63.158 6.96 9.13 0.00 4.63
2300 4969 1.895707 CAATCCGCTCCATGGCTCC 60.896 63.158 6.96 0.00 0.00 4.70
2301 4970 1.146930 TCAATCCGCTCCATGGCTC 59.853 57.895 6.96 0.00 0.00 4.70
2302 4971 1.153086 GTCAATCCGCTCCATGGCT 60.153 57.895 6.96 0.00 0.00 4.75
2303 4972 2.537560 CGTCAATCCGCTCCATGGC 61.538 63.158 6.96 0.00 0.00 4.40
2304 4973 1.143838 TCGTCAATCCGCTCCATGG 59.856 57.895 4.97 4.97 0.00 3.66
2305 4974 1.482621 CGTCGTCAATCCGCTCCATG 61.483 60.000 0.00 0.00 0.00 3.66
2306 4975 1.226974 CGTCGTCAATCCGCTCCAT 60.227 57.895 0.00 0.00 0.00 3.41
2307 4976 1.868987 TTCGTCGTCAATCCGCTCCA 61.869 55.000 0.00 0.00 0.00 3.86
2308 4977 1.153901 TTCGTCGTCAATCCGCTCC 60.154 57.895 0.00 0.00 0.00 4.70
2309 4978 1.730593 CGTTCGTCGTCAATCCGCTC 61.731 60.000 0.00 0.00 34.52 5.03
2310 4979 1.800315 CGTTCGTCGTCAATCCGCT 60.800 57.895 0.00 0.00 34.52 5.52
2311 4980 2.687436 CGTTCGTCGTCAATCCGC 59.313 61.111 0.00 0.00 34.52 5.54
2312 4981 2.156446 CCCGTTCGTCGTCAATCCG 61.156 63.158 0.00 0.00 37.94 4.18
2313 4982 1.808390 CCCCGTTCGTCGTCAATCC 60.808 63.158 0.00 0.00 37.94 3.01
2314 4983 2.450345 GCCCCGTTCGTCGTCAATC 61.450 63.158 0.00 0.00 37.94 2.67
2315 4984 2.433664 GCCCCGTTCGTCGTCAAT 60.434 61.111 0.00 0.00 37.94 2.57
2316 4985 4.668118 GGCCCCGTTCGTCGTCAA 62.668 66.667 0.00 0.00 37.94 3.18
2318 4987 2.879039 CTAAGGCCCCGTTCGTCGTC 62.879 65.000 0.00 0.00 37.94 4.20
2319 4988 2.990967 TAAGGCCCCGTTCGTCGT 60.991 61.111 0.00 0.00 37.94 4.34
2320 4989 1.656818 TACTAAGGCCCCGTTCGTCG 61.657 60.000 0.00 0.00 39.52 5.12
2321 4990 0.749049 ATACTAAGGCCCCGTTCGTC 59.251 55.000 0.00 0.00 0.00 4.20
2322 4991 1.197812 AATACTAAGGCCCCGTTCGT 58.802 50.000 0.00 0.00 0.00 3.85
2323 4992 1.937899 CAAATACTAAGGCCCCGTTCG 59.062 52.381 0.00 0.00 0.00 3.95
2324 4993 2.294979 CCAAATACTAAGGCCCCGTTC 58.705 52.381 0.00 0.00 0.00 3.95
2325 4994 1.683938 GCCAAATACTAAGGCCCCGTT 60.684 52.381 0.00 0.00 42.58 4.44
2326 4995 0.106868 GCCAAATACTAAGGCCCCGT 60.107 55.000 0.00 0.00 42.58 5.28
2327 4996 2.715536 GCCAAATACTAAGGCCCCG 58.284 57.895 0.00 0.00 42.58 5.73
2331 5000 8.359642 TCAAATTATGATGCCAAATACTAAGGC 58.640 33.333 0.00 0.00 40.05 4.35
2447 5248 9.244292 AGTAACTTCTGACATGTATACTGAAGA 57.756 33.333 25.89 11.70 39.88 2.87
2474 5275 6.278363 TCTTCTGGCCGTAGTAATTGATAAC 58.722 40.000 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.