Multiple sequence alignment - TraesCS5D01G016800

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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 TraesCS5D01G016800 chr5D 100.000 2483 0 0 1 2483 9527780 9525298 0.000000e+00 4586.0
1 TraesCS5D01G016800 chr5D 81.081 444 76 6 1 440 477991572 477992011 5.080000e-92 348.0
2 TraesCS5D01G016800 chr5D 94.231 208 8 2 1318 1524 9329832 9329628 5.150000e-82 315.0
3 TraesCS5D01G016800 chr5D 83.529 85 11 3 434 518 518924381 518924300 2.650000e-10 76.8
4 TraesCS5D01G016800 chr5D 86.207 58 4 4 2367 2424 520290587 520290534 2.670000e-05 60.2
5 TraesCS5D01G016800 chr5A 88.440 1635 99 35 434 2002 7656240 7654630 0.000000e+00 1890.0
6 TraesCS5D01G016800 chr5A 88.312 385 19 12 2030 2399 7654631 7654258 2.930000e-119 438.0
7 TraesCS5D01G016800 chr5B 92.030 803 45 9 735 1521 9524485 9523686 0.000000e+00 1110.0
8 TraesCS5D01G016800 chr5B 81.867 739 82 22 7 697 9525229 9524495 2.140000e-160 575.0
9 TraesCS5D01G016800 chr5B 91.317 334 15 6 2077 2397 9522811 9522479 6.300000e-121 444.0
10 TraesCS5D01G016800 chr5B 84.483 406 36 15 1674 2065 9523449 9523057 2.330000e-100 375.0
11 TraesCS5D01G016800 chr5B 90.110 273 15 4 1730 1995 327937117 327937384 6.570000e-91 344.0
12 TraesCS5D01G016800 chr5B 96.721 61 2 0 2423 2483 164677645 164677705 4.370000e-18 102.0
13 TraesCS5D01G016800 chr5B 96.721 61 2 0 2333 2393 327937394 327937454 4.370000e-18 102.0
14 TraesCS5D01G016800 chr5B 96.721 61 2 0 2423 2483 435663387 435663327 4.370000e-18 102.0
15 TraesCS5D01G016800 chr5B 97.674 43 1 0 2389 2431 40069390 40069348 9.520000e-10 75.0
16 TraesCS5D01G016800 chr5B 97.674 43 1 0 2389 2431 426874444 426874402 9.520000e-10 75.0
17 TraesCS5D01G016800 chr2A 83.144 439 66 7 7 440 459549189 459548754 6.440000e-106 394.0
18 TraesCS5D01G016800 chr4A 82.093 430 66 10 7 430 599611319 599610895 8.440000e-95 357.0
19 TraesCS5D01G016800 chr2B 90.476 273 14 4 1730 1995 70465427 70465694 1.410000e-92 350.0
20 TraesCS5D01G016800 chr2B 90.110 273 15 4 1730 1995 64571992 64571725 6.570000e-91 344.0
21 TraesCS5D01G016800 chr2B 90.110 273 15 4 1730 1995 71092139 71091872 6.570000e-91 344.0
22 TraesCS5D01G016800 chr2B 89.744 273 16 4 1730 1995 734423296 734423563 3.060000e-89 339.0
23 TraesCS5D01G016800 chr2B 96.721 61 2 0 2333 2393 64571715 64571655 4.370000e-18 102.0
24 TraesCS5D01G016800 chr2B 96.721 61 2 0 2333 2393 70465704 70465764 4.370000e-18 102.0
25 TraesCS5D01G016800 chr2B 96.721 61 2 0 2333 2393 71091862 71091802 4.370000e-18 102.0
26 TraesCS5D01G016800 chr2B 92.754 69 3 2 2417 2483 778983872 778983804 5.650000e-17 99.0
27 TraesCS5D01G016800 chr7B 90.110 273 15 4 1730 1995 66910672 66910939 6.570000e-91 344.0
28 TraesCS5D01G016800 chr7B 95.385 65 3 0 2419 2483 634520721 634520657 1.210000e-18 104.0
29 TraesCS5D01G016800 chr7B 96.721 61 2 0 2333 2393 66910949 66911009 4.370000e-18 102.0
30 TraesCS5D01G016800 chr4B 81.236 437 73 7 7 440 100844204 100843774 6.570000e-91 344.0
31 TraesCS5D01G016800 chr4B 96.721 61 2 0 2423 2483 650936390 650936450 4.370000e-18 102.0
32 TraesCS5D01G016800 chr6B 90.074 272 15 4 1730 1994 95105084 95105350 2.360000e-90 342.0
33 TraesCS5D01G016800 chr6B 80.804 448 71 12 1 440 695926181 695926621 1.100000e-88 337.0
34 TraesCS5D01G016800 chr6B 89.011 273 18 8 1730 1995 191056260 191055993 6.620000e-86 327.0
35 TraesCS5D01G016800 chr6B 96.721 61 2 0 2333 2393 95105361 95105421 4.370000e-18 102.0
36 TraesCS5D01G016800 chr6B 96.721 61 2 0 2333 2393 191055983 191055923 4.370000e-18 102.0
37 TraesCS5D01G016800 chr6B 96.721 61 2 0 2423 2483 419780853 419780913 4.370000e-18 102.0
38 TraesCS5D01G016800 chr6B 96.721 61 2 0 2423 2483 678117868 678117928 4.370000e-18 102.0
39 TraesCS5D01G016800 chr3D 81.412 425 71 6 7 429 84576704 84577122 8.500000e-90 340.0
40 TraesCS5D01G016800 chr3D 100.000 31 0 0 799 829 446113916 446113886 9.590000e-05 58.4
41 TraesCS5D01G016800 chr6A 80.866 439 77 7 7 440 610855751 610855315 3.060000e-89 339.0
42 TraesCS5D01G016800 chr3B 80.493 446 76 7 1 440 615729024 615729464 5.120000e-87 331.0
43 TraesCS5D01G016800 chr6D 96.721 61 2 0 2423 2483 431112962 431112902 4.370000e-18 102.0
44 TraesCS5D01G016800 chr1D 96.721 61 2 0 2423 2483 464800330 464800270 4.370000e-18 102.0
45 TraesCS5D01G016800 chr2D 95.556 45 2 0 2387 2431 455269006 455269050 3.430000e-09 73.1
46 TraesCS5D01G016800 chrUn 95.349 43 2 0 2389 2431 119229296 119229254 4.430000e-08 69.4
47 TraesCS5D01G016800 chr4D 95.349 43 2 0 2389 2431 22433566 22433608 4.430000e-08 69.4
48 TraesCS5D01G016800 chr4D 95.349 43 2 0 2389 2431 291023735 291023777 4.430000e-08 69.4
49 TraesCS5D01G016800 chr1B 95.349 43 2 0 2389 2431 426604206 426604248 4.430000e-08 69.4
50 TraesCS5D01G016800 chr1B 95.349 43 2 0 2389 2431 446767184 446767142 4.430000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G016800 chr5D 9525298 9527780 2482 True 4586 4586 100.00000 1 2483 1 chr5D.!!$R2 2482
1 TraesCS5D01G016800 chr5A 7654258 7656240 1982 True 1164 1890 88.37600 434 2399 2 chr5A.!!$R1 1965
2 TraesCS5D01G016800 chr5B 9522479 9525229 2750 True 626 1110 87.42425 7 2397 4 chr5B.!!$R4 2390

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
730 782 0.033601 AAAGCATAACCGCCCATGGA 60.034 50.0 15.22 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2173 0.824109 ATAGACCGCAGCAGCAGTTA 59.176 50.0 0.82 0.0 42.27 2.24 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
45 52 2.481449 GCACCCCTACATGACTAAGACG 60.481 54.545 0.00 0.00 0.00 4.18
54 61 5.821516 ACATGACTAAGACGTTAGAGGAG 57.178 43.478 0.00 0.00 38.39 3.69
79 86 2.669781 CCATACCTGGCATCCACAAAT 58.330 47.619 0.00 0.00 35.23 2.32
82 89 1.549203 ACCTGGCATCCACAAATCAC 58.451 50.000 0.00 0.00 0.00 3.06
89 96 2.158559 CATCCACAAATCACGAACCCA 58.841 47.619 0.00 0.00 0.00 4.51
90 97 2.350057 TCCACAAATCACGAACCCAA 57.650 45.000 0.00 0.00 0.00 4.12
95 102 2.357637 ACAAATCACGAACCCAACACAG 59.642 45.455 0.00 0.00 0.00 3.66
109 116 3.012518 CAACACAGGATCCACCATCTTC 58.987 50.000 15.82 0.00 42.04 2.87
125 132 0.463295 CTTCCAGATGCCGCTGATGT 60.463 55.000 4.63 0.00 38.14 3.06
127 134 0.390492 TCCAGATGCCGCTGATGTAG 59.610 55.000 4.63 0.00 38.14 2.74
131 138 0.104855 GATGCCGCTGATGTAGACCA 59.895 55.000 0.00 0.00 0.00 4.02
137 144 2.159043 CCGCTGATGTAGACCACAATCT 60.159 50.000 0.00 0.00 41.55 2.40
139 146 2.611292 GCTGATGTAGACCACAATCTGC 59.389 50.000 0.00 0.00 41.55 4.26
143 150 4.767578 ATGTAGACCACAATCTGCATCT 57.232 40.909 1.10 0.00 45.57 2.90
144 151 3.865446 TGTAGACCACAATCTGCATCTG 58.135 45.455 0.00 0.00 36.53 2.90
146 153 0.376152 GACCACAATCTGCATCTGCG 59.624 55.000 0.00 0.00 45.83 5.18
159 166 0.461961 ATCTGCGCTTGGACTACCTC 59.538 55.000 9.73 0.00 37.04 3.85
161 168 2.187163 GCGCTTGGACTACCTCCC 59.813 66.667 0.00 0.00 38.49 4.30
169 176 0.617820 GGACTACCTCCCAAGCTCCA 60.618 60.000 0.00 0.00 31.83 3.86
170 177 0.537653 GACTACCTCCCAAGCTCCAC 59.462 60.000 0.00 0.00 0.00 4.02
180 187 3.612247 AAGCTCCACGCCGATGCTT 62.612 57.895 0.00 0.00 40.39 3.91
210 217 1.444250 GTCACAACGACAGACCCCA 59.556 57.895 0.00 0.00 44.69 4.96
257 264 1.977594 GCCGCCACACAATCCTTACG 61.978 60.000 0.00 0.00 0.00 3.18
260 267 1.519408 GCCACACAATCCTTACGTGT 58.481 50.000 0.00 0.00 44.45 4.49
263 270 3.655486 CCACACAATCCTTACGTGTACA 58.345 45.455 0.00 0.00 41.79 2.90
264 271 4.059511 CCACACAATCCTTACGTGTACAA 58.940 43.478 0.00 0.00 41.79 2.41
269 276 5.063438 CACAATCCTTACGTGTACAATCTGG 59.937 44.000 0.00 0.00 0.00 3.86
272 279 5.981088 TCCTTACGTGTACAATCTGGTTA 57.019 39.130 0.00 0.00 0.00 2.85
286 293 3.940335 TCTGGTTATCAGATCCATCCCA 58.060 45.455 0.00 0.00 46.71 4.37
288 295 4.103153 TCTGGTTATCAGATCCATCCCAAC 59.897 45.833 0.00 0.00 46.71 3.77
290 297 3.138283 GGTTATCAGATCCATCCCAACCA 59.862 47.826 4.67 0.00 35.38 3.67
291 298 4.202609 GGTTATCAGATCCATCCCAACCAT 60.203 45.833 4.67 0.00 35.38 3.55
292 299 5.014123 GGTTATCAGATCCATCCCAACCATA 59.986 44.000 4.67 0.00 35.38 2.74
293 300 4.923516 ATCAGATCCATCCCAACCATAG 57.076 45.455 0.00 0.00 0.00 2.23
294 301 2.981784 TCAGATCCATCCCAACCATAGG 59.018 50.000 0.00 0.00 0.00 2.57
296 303 2.982488 AGATCCATCCCAACCATAGGAC 59.018 50.000 0.00 0.00 34.20 3.85
297 304 2.587060 TCCATCCCAACCATAGGACT 57.413 50.000 0.00 0.00 34.20 3.85
299 306 1.477558 CCATCCCAACCATAGGACTGC 60.478 57.143 0.00 0.00 34.20 4.40
302 309 0.744414 CCCAACCATAGGACTGCACG 60.744 60.000 0.00 0.00 0.00 5.34
303 310 1.369091 CCAACCATAGGACTGCACGC 61.369 60.000 0.00 0.00 0.00 5.34
320 332 1.817209 GCCTCGTCGGAGAAGGATT 59.183 57.895 9.27 0.00 43.27 3.01
341 353 9.745018 AGGATTTGAAGAATCTTTATTCAGTGA 57.255 29.630 0.00 0.00 43.44 3.41
349 361 4.471904 TCTTTATTCAGTGACGCCATCT 57.528 40.909 0.00 0.00 0.00 2.90
351 363 2.492019 TATTCAGTGACGCCATCTCG 57.508 50.000 0.00 0.00 0.00 4.04
352 364 0.817654 ATTCAGTGACGCCATCTCGA 59.182 50.000 0.00 0.00 0.00 4.04
354 366 1.869574 CAGTGACGCCATCTCGACG 60.870 63.158 0.00 0.00 0.00 5.12
377 389 1.391485 CGAAGCCAAGACGATGAACAG 59.609 52.381 0.00 0.00 0.00 3.16
378 390 1.129437 GAAGCCAAGACGATGAACAGC 59.871 52.381 0.00 0.00 0.00 4.40
379 391 0.035317 AGCCAAGACGATGAACAGCA 59.965 50.000 0.00 0.00 0.00 4.41
387 399 5.296813 AGACGATGAACAGCATAAAAACC 57.703 39.130 0.00 0.00 37.34 3.27
416 428 1.223487 GGGCCTAAAGCGATCCACA 59.777 57.895 0.84 0.00 45.17 4.17
424 436 2.505337 GCGATCCACACGCGTGTA 60.505 61.111 41.12 28.91 46.05 2.90
425 437 1.876714 GCGATCCACACGCGTGTAT 60.877 57.895 41.12 32.02 46.05 2.29
426 438 1.808234 GCGATCCACACGCGTGTATC 61.808 60.000 41.12 35.45 46.05 2.24
428 440 1.206745 GATCCACACGCGTGTATCCG 61.207 60.000 41.12 28.66 42.83 4.18
429 441 2.622903 ATCCACACGCGTGTATCCGG 62.623 60.000 41.12 35.09 42.83 5.14
430 442 2.126228 CACACGCGTGTATCCGGT 60.126 61.111 41.12 17.49 42.83 5.28
431 443 2.126228 ACACGCGTGTATCCGGTG 60.126 61.111 41.14 14.65 42.90 4.94
432 444 2.179767 CACGCGTGTATCCGGTGA 59.820 61.111 30.50 0.00 33.63 4.02
499 536 3.077359 CTGGCGAGATCACCTTTCTTTT 58.923 45.455 0.00 0.00 0.00 2.27
590 630 1.416373 TCATTAACACGCGCGTACAA 58.584 45.000 37.24 27.28 0.00 2.41
591 631 1.387420 TCATTAACACGCGCGTACAAG 59.613 47.619 37.24 25.32 0.00 3.16
592 632 0.094046 ATTAACACGCGCGTACAAGC 59.906 50.000 37.24 0.00 0.00 4.01
593 633 0.940519 TTAACACGCGCGTACAAGCT 60.941 50.000 37.24 17.05 34.40 3.74
619 659 5.806366 ATACAATACGGTTGCAAAGTACC 57.194 39.130 15.51 6.69 0.00 3.34
699 751 0.333993 TTAGCCGTCCCTCCACTACT 59.666 55.000 0.00 0.00 0.00 2.57
701 753 0.333993 AGCCGTCCCTCCACTACTAA 59.666 55.000 0.00 0.00 0.00 2.24
704 756 2.295629 GCCGTCCCTCCACTACTAATAC 59.704 54.545 0.00 0.00 0.00 1.89
705 757 3.830121 CCGTCCCTCCACTACTAATACT 58.170 50.000 0.00 0.00 0.00 2.12
706 758 3.568853 CCGTCCCTCCACTACTAATACTG 59.431 52.174 0.00 0.00 0.00 2.74
730 782 0.033601 AAAGCATAACCGCCCATGGA 60.034 50.000 15.22 0.00 0.00 3.41
824 886 0.415429 TTGCCCTCTCCTCTCCTCTT 59.585 55.000 0.00 0.00 0.00 2.85
859 925 1.394618 TCCTCAAAAACCAACCACCG 58.605 50.000 0.00 0.00 0.00 4.94
872 938 0.826672 ACCACCGTCGTCCTCTTTCT 60.827 55.000 0.00 0.00 0.00 2.52
1008 1078 0.685660 TGTGTACGTACATGGGGCAA 59.314 50.000 29.58 8.57 38.63 4.52
1103 1173 3.311110 GGTCCTGTCGTGGGAGCA 61.311 66.667 14.55 0.00 46.82 4.26
1105 1175 2.523168 TCCTGTCGTGGGAGCACA 60.523 61.111 0.00 0.00 0.00 4.57
1173 1249 3.009115 CGGGAGGGCCAGAGGAAA 61.009 66.667 6.18 0.00 35.15 3.13
1287 1363 3.305177 TTTCCTGGCGGCGTACCTC 62.305 63.158 9.37 0.00 0.00 3.85
1303 1379 3.889134 CTCGCCTGCACCAAGAGCA 62.889 63.158 0.00 0.00 40.19 4.26
1412 1494 3.730761 GCTGTCCTGCAAGCGGTG 61.731 66.667 0.00 0.00 0.00 4.94
1581 1700 7.898014 AGTTTCTTCCTGATAAACTTTGGTT 57.102 32.000 0.00 0.00 39.74 3.67
1582 1701 8.990163 AGTTTCTTCCTGATAAACTTTGGTTA 57.010 30.769 0.00 0.00 39.74 2.85
1620 1758 8.911247 AAGTTTGAGAACACACTAAATTTGTC 57.089 30.769 0.00 0.00 36.23 3.18
1666 1840 6.044046 GCATCATCTCATCTTCCTATAGCTG 58.956 44.000 0.00 0.00 0.00 4.24
1668 1842 5.022122 TCATCTCATCTTCCTATAGCTGGG 58.978 45.833 0.00 0.00 0.00 4.45
1670 1844 4.820775 TCTCATCTTCCTATAGCTGGGTT 58.179 43.478 0.00 0.00 0.00 4.11
1672 1846 5.667626 TCTCATCTTCCTATAGCTGGGTTTT 59.332 40.000 0.00 0.00 0.00 2.43
1673 1847 6.158695 TCTCATCTTCCTATAGCTGGGTTTTT 59.841 38.462 0.00 0.00 0.00 1.94
1674 1848 6.357367 TCATCTTCCTATAGCTGGGTTTTTC 58.643 40.000 0.00 0.00 0.00 2.29
1675 1849 5.772393 TCTTCCTATAGCTGGGTTTTTCA 57.228 39.130 0.00 0.00 0.00 2.69
1676 1850 5.745227 TCTTCCTATAGCTGGGTTTTTCAG 58.255 41.667 0.00 0.00 35.49 3.02
1677 1851 5.487488 TCTTCCTATAGCTGGGTTTTTCAGA 59.513 40.000 0.00 0.00 34.36 3.27
1678 1852 5.975988 TCCTATAGCTGGGTTTTTCAGAT 57.024 39.130 0.00 0.00 34.36 2.90
1679 1853 6.327386 TCCTATAGCTGGGTTTTTCAGATT 57.673 37.500 0.00 0.00 34.36 2.40
1686 1880 5.539955 AGCTGGGTTTTTCAGATTATTGTGT 59.460 36.000 0.00 0.00 34.36 3.72
1712 1906 5.063944 TCGCATAAGCATCTTGTTTCTTCTC 59.936 40.000 0.00 0.00 42.27 2.87
1713 1907 5.064452 CGCATAAGCATCTTGTTTCTTCTCT 59.936 40.000 0.00 0.00 42.27 3.10
1714 1908 6.256686 GCATAAGCATCTTGTTTCTTCTCTG 58.743 40.000 0.00 0.00 41.58 3.35
1717 1911 4.965814 AGCATCTTGTTTCTTCTCTGTGA 58.034 39.130 0.00 0.00 0.00 3.58
1719 1913 5.411977 AGCATCTTGTTTCTTCTCTGTGATG 59.588 40.000 0.00 0.00 33.93 3.07
1720 1914 5.629097 CATCTTGTTTCTTCTCTGTGATGC 58.371 41.667 0.00 0.00 0.00 3.91
1758 1973 1.188219 TGACACTGACTCTCTGCCCC 61.188 60.000 0.00 0.00 0.00 5.80
1766 1981 3.965539 CTCTCTGCCCCGCACTTGG 62.966 68.421 0.00 0.00 33.79 3.61
1769 1984 3.365265 CTGCCCCGCACTTGGAAC 61.365 66.667 0.00 0.00 33.79 3.62
1775 1990 1.318576 CCCGCACTTGGAACTTTCTT 58.681 50.000 0.00 0.00 0.00 2.52
1808 2023 4.153117 GTCAATCAACCAGACAGTGACATC 59.847 45.833 0.00 0.00 36.56 3.06
1809 2024 4.040829 TCAATCAACCAGACAGTGACATCT 59.959 41.667 0.00 0.00 0.00 2.90
1823 2038 3.017442 TGACATCTAGAGGTTGACCGAG 58.983 50.000 11.96 0.00 42.08 4.63
1824 2039 3.280295 GACATCTAGAGGTTGACCGAGA 58.720 50.000 11.96 5.38 42.08 4.04
1825 2040 3.018149 ACATCTAGAGGTTGACCGAGAC 58.982 50.000 3.73 0.00 42.08 3.36
1865 2080 3.631686 TGCTAATTGCTTGTGTCTGTGTT 59.368 39.130 0.00 0.00 43.37 3.32
1874 2089 1.330213 TGTGTCTGTGTTCATTGTGCG 59.670 47.619 0.00 0.00 0.00 5.34
1903 2121 5.455326 GGAATATGGATCACTGCTTGGTAGT 60.455 44.000 0.00 0.00 0.00 2.73
1945 2163 4.153411 CAGATTAGGTAGGGGGTCTAGTG 58.847 52.174 0.00 0.00 0.00 2.74
1946 2164 3.798422 AGATTAGGTAGGGGGTCTAGTGT 59.202 47.826 0.00 0.00 0.00 3.55
1955 2173 1.279271 GGGGTCTAGTGTCACAAGCAT 59.721 52.381 5.62 0.00 0.00 3.79
2005 2223 5.675684 TGCACATAGTACCTGAATCTCAA 57.324 39.130 0.34 0.00 0.00 3.02
2020 2238 1.063912 TCTCAAAAGTGCAGTGCAACG 59.936 47.619 21.67 6.76 45.86 4.10
2039 2257 1.971357 CGGAGGCTGGTCCATAGTAAT 59.029 52.381 0.00 0.00 36.23 1.89
2057 2275 6.793505 AGTAATTTAGTACTAGCTGCTGGT 57.206 37.500 22.26 22.26 32.42 4.00
2060 2278 8.414778 AGTAATTTAGTACTAGCTGCTGGTAAG 58.585 37.037 24.60 11.14 32.42 2.34
2070 2288 4.835927 CTGGTAAGCTACAGCCCG 57.164 61.111 0.00 0.00 43.38 6.13
2123 2581 4.590222 ACTGCCATTTTCTCTGACCATTTT 59.410 37.500 0.00 0.00 0.00 1.82
2139 2597 4.336433 ACCATTTTCATGCCGTGAGATAAG 59.664 41.667 0.00 0.00 38.29 1.73
2383 2849 4.453478 TGACTTTGTGATCATTCTGTGAGC 59.547 41.667 0.00 0.00 43.51 4.26
2399 2865 3.898123 TGTGAGCAGGAATATACTCCCTC 59.102 47.826 0.00 0.00 35.95 4.30
2400 2866 3.259625 GTGAGCAGGAATATACTCCCTCC 59.740 52.174 0.00 0.00 35.95 4.30
2401 2867 3.116746 TGAGCAGGAATATACTCCCTCCA 60.117 47.826 0.00 0.00 35.95 3.86
2402 2868 4.100373 GAGCAGGAATATACTCCCTCCAT 58.900 47.826 0.00 0.00 35.95 3.41
2403 2869 4.507342 AGCAGGAATATACTCCCTCCATT 58.493 43.478 0.00 0.00 35.95 3.16
2404 2870 4.534103 AGCAGGAATATACTCCCTCCATTC 59.466 45.833 0.00 0.00 35.95 2.67
2405 2871 4.323868 GCAGGAATATACTCCCTCCATTCC 60.324 50.000 0.00 3.91 43.25 3.01
2406 2872 5.376653 AGGAATATACTCCCTCCATTCCT 57.623 43.478 8.08 8.08 46.45 3.36
2409 2875 7.569599 GGAATATACTCCCTCCATTCCTAAA 57.430 40.000 4.73 0.00 40.89 1.85
2410 2876 8.164057 GGAATATACTCCCTCCATTCCTAAAT 57.836 38.462 4.73 0.00 40.89 1.40
2411 2877 9.280456 GGAATATACTCCCTCCATTCCTAAATA 57.720 37.037 4.73 0.00 40.89 1.40
2418 2884 9.411848 ACTCCCTCCATTCCTAAATATTTATCT 57.588 33.333 8.34 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.071385 CATGTAGGGGTGCCAGATCTC 59.929 57.143 0.00 0.00 0.00 2.75
18 19 1.131638 TCATGTAGGGGTGCCAGATC 58.868 55.000 0.00 0.00 0.00 2.75
45 52 4.141688 CCAGGTATGGTTTCCTCCTCTAAC 60.142 50.000 0.00 0.00 42.17 2.34
68 75 1.135402 GGGTTCGTGATTTGTGGATGC 60.135 52.381 0.00 0.00 0.00 3.91
69 76 2.158559 TGGGTTCGTGATTTGTGGATG 58.841 47.619 0.00 0.00 0.00 3.51
79 86 0.762418 ATCCTGTGTTGGGTTCGTGA 59.238 50.000 0.00 0.00 0.00 4.35
82 89 0.036164 TGGATCCTGTGTTGGGTTCG 59.964 55.000 14.23 0.00 0.00 3.95
89 96 2.025887 GGAAGATGGTGGATCCTGTGTT 60.026 50.000 14.23 1.05 37.07 3.32
90 97 1.561542 GGAAGATGGTGGATCCTGTGT 59.438 52.381 14.23 0.00 37.07 3.72
109 116 0.390492 TCTACATCAGCGGCATCTGG 59.610 55.000 1.45 0.00 34.91 3.86
118 125 2.611292 GCAGATTGTGGTCTACATCAGC 59.389 50.000 0.00 0.00 39.48 4.26
119 126 3.865446 TGCAGATTGTGGTCTACATCAG 58.135 45.455 0.00 0.00 39.48 2.90
125 132 2.739609 CGCAGATGCAGATTGTGGTCTA 60.740 50.000 5.55 0.00 42.21 2.59
127 134 0.376152 CGCAGATGCAGATTGTGGTC 59.624 55.000 5.55 0.00 42.21 4.02
131 138 0.450583 CAAGCGCAGATGCAGATTGT 59.549 50.000 11.47 0.00 42.21 2.71
137 144 0.740868 GTAGTCCAAGCGCAGATGCA 60.741 55.000 11.47 0.00 42.21 3.96
139 146 0.176680 AGGTAGTCCAAGCGCAGATG 59.823 55.000 11.47 5.42 35.89 2.90
143 150 2.978824 GGAGGTAGTCCAAGCGCA 59.021 61.111 11.47 0.00 46.10 6.09
201 208 0.474184 CTTGTGTCCTTGGGGTCTGT 59.526 55.000 0.00 0.00 0.00 3.41
240 247 0.442310 CACGTAAGGATTGTGTGGCG 59.558 55.000 0.00 0.00 46.39 5.69
247 254 5.175859 ACCAGATTGTACACGTAAGGATTG 58.824 41.667 0.00 0.00 46.39 2.67
248 255 5.416271 ACCAGATTGTACACGTAAGGATT 57.584 39.130 0.00 0.00 46.39 3.01
269 276 4.437682 TGGTTGGGATGGATCTGATAAC 57.562 45.455 0.00 0.00 0.00 1.89
272 279 3.590630 CCTATGGTTGGGATGGATCTGAT 59.409 47.826 0.00 0.00 0.00 2.90
278 285 2.126882 CAGTCCTATGGTTGGGATGGA 58.873 52.381 0.00 0.00 34.64 3.41
282 289 0.618458 GTGCAGTCCTATGGTTGGGA 59.382 55.000 0.00 0.00 0.00 4.37
286 293 1.078426 GGCGTGCAGTCCTATGGTT 60.078 57.895 0.00 0.00 0.00 3.67
288 295 1.227380 GAGGCGTGCAGTCCTATGG 60.227 63.158 6.66 0.00 31.71 2.74
290 297 2.005960 GACGAGGCGTGCAGTCCTAT 62.006 60.000 6.66 0.00 41.37 2.57
291 298 2.675423 ACGAGGCGTGCAGTCCTA 60.675 61.111 6.66 0.00 39.18 2.94
292 299 4.057428 GACGAGGCGTGCAGTCCT 62.057 66.667 6.39 6.39 41.37 3.85
299 306 2.202492 CTTCTCCGACGAGGCGTG 60.202 66.667 0.00 0.00 41.37 5.34
302 309 0.175989 AAATCCTTCTCCGACGAGGC 59.824 55.000 0.00 0.00 40.77 4.70
303 310 1.476891 TCAAATCCTTCTCCGACGAGG 59.523 52.381 0.00 0.00 42.97 4.63
320 332 6.128282 GGCGTCACTGAATAAAGATTCTTCAA 60.128 38.462 0.00 0.00 41.87 2.69
338 350 2.579787 CCGTCGAGATGGCGTCAC 60.580 66.667 9.78 1.29 0.00 3.67
357 369 1.391485 CTGTTCATCGTCTTGGCTTCG 59.609 52.381 0.00 0.00 0.00 3.79
369 381 7.713764 AGTTTTGGTTTTTATGCTGTTCATC 57.286 32.000 0.00 0.00 36.63 2.92
377 389 6.097356 GCCCTAGTAGTTTTGGTTTTTATGC 58.903 40.000 0.00 0.00 0.00 3.14
378 390 6.436218 AGGCCCTAGTAGTTTTGGTTTTTATG 59.564 38.462 0.00 0.00 0.00 1.90
379 391 6.558498 AGGCCCTAGTAGTTTTGGTTTTTAT 58.442 36.000 0.00 0.00 0.00 1.40
387 399 3.621715 CGCTTTAGGCCCTAGTAGTTTTG 59.378 47.826 0.00 0.00 37.74 2.44
416 428 1.153901 CTTCACCGGATACACGCGT 60.154 57.895 9.46 5.58 0.00 6.01
422 434 2.509422 GGGGGCTTCACCGGATAC 59.491 66.667 9.46 0.00 40.62 2.24
423 435 3.158648 CGGGGGCTTCACCGGATA 61.159 66.667 9.46 0.00 46.08 2.59
429 441 4.097361 GTCCTCCGGGGGCTTCAC 62.097 72.222 18.55 4.39 36.61 3.18
499 536 3.572642 GTTTTCTTTCTCCCCCTCCAAA 58.427 45.455 0.00 0.00 0.00 3.28
568 608 0.299300 TACGCGCGTGTTAATGATGC 59.701 50.000 42.78 0.00 0.00 3.91
590 630 5.018539 TGCAACCGTATTGTATTCTAGCT 57.981 39.130 0.00 0.00 0.00 3.32
591 631 5.728351 TTGCAACCGTATTGTATTCTAGC 57.272 39.130 0.00 0.00 0.00 3.42
592 632 7.303634 ACTTTGCAACCGTATTGTATTCTAG 57.696 36.000 0.00 0.00 0.00 2.43
593 633 7.278424 GGTACTTTGCAACCGTATTGTATTCTA 59.722 37.037 0.00 0.00 0.00 2.10
619 659 6.708285 AGACCAAGGGTTATTTGTACTACTG 58.292 40.000 0.00 0.00 35.25 2.74
699 751 6.017440 GGCGGTTATGCTTTTGATCAGTATTA 60.017 38.462 0.00 0.00 34.52 0.98
701 753 4.275936 GGCGGTTATGCTTTTGATCAGTAT 59.724 41.667 0.00 0.00 34.52 2.12
704 756 2.223572 GGGCGGTTATGCTTTTGATCAG 60.224 50.000 0.00 0.00 34.52 2.90
705 757 1.748493 GGGCGGTTATGCTTTTGATCA 59.252 47.619 0.00 0.00 34.52 2.92
706 758 1.748493 TGGGCGGTTATGCTTTTGATC 59.252 47.619 0.00 0.00 34.52 2.92
730 782 5.716703 GGCCCAACTAAATGGATATTATGCT 59.283 40.000 0.00 0.00 43.54 3.79
784 836 4.761235 AATGGATCATGAATGCATCGTC 57.239 40.909 0.00 0.00 44.81 4.20
785 837 4.794981 GCAAATGGATCATGAATGCATCGT 60.795 41.667 0.00 0.00 44.81 3.73
786 838 3.673338 GCAAATGGATCATGAATGCATCG 59.327 43.478 0.00 2.88 44.81 3.84
824 886 3.319198 GAAGTGGTGGGGCGAGGA 61.319 66.667 0.00 0.00 0.00 3.71
859 925 3.058085 ACGAAGAAGAGAAAGAGGACGAC 60.058 47.826 0.00 0.00 0.00 4.34
872 938 2.051879 CGTGAGCAAGACGAAGAAGA 57.948 50.000 0.00 0.00 39.21 2.87
1008 1078 1.985116 GGTCAGGGCGTCCTCTTCT 60.985 63.158 5.00 0.00 42.67 2.85
1035 1105 2.680352 TCCTCCTGCTCCCACGAC 60.680 66.667 0.00 0.00 0.00 4.34
1103 1173 3.469863 TTCTTCACGGCCGGCTTGT 62.470 57.895 31.76 22.28 0.00 3.16
1105 1175 2.358737 CTTCTTCACGGCCGGCTT 60.359 61.111 31.76 11.31 0.00 4.35
1269 1345 3.305177 GAGGTACGCCGCCAGGAAA 62.305 63.158 0.00 0.00 41.02 3.13
1357 1439 4.803426 CACGCTCCACCGCCTCTC 62.803 72.222 0.00 0.00 0.00 3.20
1412 1494 4.166011 GCTCCATGACGCCGTTGC 62.166 66.667 0.00 0.00 0.00 4.17
1422 1504 0.107361 TCACCATGCTCTGCTCCATG 60.107 55.000 0.00 0.00 38.78 3.66
1515 1599 5.182001 CCAAACAAAAAGAGGAGATGACGAT 59.818 40.000 0.00 0.00 0.00 3.73
1551 1642 8.754230 AAGTTTATCAGGAAGAAACTACGTAC 57.246 34.615 11.03 0.00 41.39 3.67
1552 1643 9.199982 CAAAGTTTATCAGGAAGAAACTACGTA 57.800 33.333 11.03 0.00 41.39 3.57
1553 1644 7.172703 CCAAAGTTTATCAGGAAGAAACTACGT 59.827 37.037 11.03 0.00 41.39 3.57
1554 1645 7.172703 ACCAAAGTTTATCAGGAAGAAACTACG 59.827 37.037 11.03 7.12 41.39 3.51
1620 1758 1.155042 GCTTCCTCTTCAGCACACAG 58.845 55.000 0.00 0.00 35.95 3.66
1666 1840 5.856455 CGACACACAATAATCTGAAAAACCC 59.144 40.000 0.00 0.00 0.00 4.11
1668 1842 5.912396 TGCGACACACAATAATCTGAAAAAC 59.088 36.000 0.00 0.00 0.00 2.43
1670 1844 5.681337 TGCGACACACAATAATCTGAAAA 57.319 34.783 0.00 0.00 0.00 2.29
1672 1846 6.456853 GCTTATGCGACACACAATAATCTGAA 60.457 38.462 0.00 0.00 0.00 3.02
1673 1847 5.006649 GCTTATGCGACACACAATAATCTGA 59.993 40.000 0.00 0.00 0.00 3.27
1674 1848 5.200454 GCTTATGCGACACACAATAATCTG 58.800 41.667 0.00 0.00 0.00 2.90
1675 1849 4.875536 TGCTTATGCGACACACAATAATCT 59.124 37.500 0.00 0.00 43.34 2.40
1676 1850 5.155509 TGCTTATGCGACACACAATAATC 57.844 39.130 0.00 0.00 43.34 1.75
1677 1851 5.528690 AGATGCTTATGCGACACACAATAAT 59.471 36.000 0.00 0.00 43.34 1.28
1678 1852 4.875536 AGATGCTTATGCGACACACAATAA 59.124 37.500 0.00 0.00 43.34 1.40
1679 1853 4.441792 AGATGCTTATGCGACACACAATA 58.558 39.130 0.00 0.00 43.34 1.90
1686 1880 4.002982 AGAAACAAGATGCTTATGCGACA 58.997 39.130 0.00 0.00 43.34 4.35
1712 1906 2.927028 TCAATCCATCCAGCATCACAG 58.073 47.619 0.00 0.00 0.00 3.66
1713 1907 3.588210 ATCAATCCATCCAGCATCACA 57.412 42.857 0.00 0.00 0.00 3.58
1714 1908 4.261909 GGAAATCAATCCATCCAGCATCAC 60.262 45.833 0.00 0.00 39.42 3.06
1717 1911 3.918566 TGGAAATCAATCCATCCAGCAT 58.081 40.909 0.00 0.00 44.52 3.79
1758 1973 2.031682 CAGGAAGAAAGTTCCAAGTGCG 60.032 50.000 6.56 0.00 41.00 5.34
1766 1981 4.442706 TGACACTGACAGGAAGAAAGTTC 58.557 43.478 7.51 0.00 0.00 3.01
1769 1984 5.059161 TGATTGACACTGACAGGAAGAAAG 58.941 41.667 7.51 0.00 0.00 2.62
1775 1990 2.437651 TGGTTGATTGACACTGACAGGA 59.562 45.455 7.51 0.00 0.00 3.86
1808 2023 1.397692 GTCGTCTCGGTCAACCTCTAG 59.602 57.143 0.00 0.00 0.00 2.43
1809 2024 1.002888 AGTCGTCTCGGTCAACCTCTA 59.997 52.381 0.00 0.00 0.00 2.43
1851 2066 3.365832 CACAATGAACACAGACACAAGC 58.634 45.455 0.00 0.00 0.00 4.01
1865 2080 4.285775 TCCATATTCCTATCCGCACAATGA 59.714 41.667 0.00 0.00 0.00 2.57
1874 2089 5.690464 AGCAGTGATCCATATTCCTATCC 57.310 43.478 0.00 0.00 0.00 2.59
1955 2173 0.824109 ATAGACCGCAGCAGCAGTTA 59.176 50.000 0.82 0.00 42.27 2.24
1987 2205 6.595326 TGCACTTTTGAGATTCAGGTACTATG 59.405 38.462 0.00 0.00 36.02 2.23
2005 2223 1.447317 CCTCCGTTGCACTGCACTTT 61.447 55.000 2.26 0.00 38.71 2.66
2020 2238 4.439253 AAATTACTATGGACCAGCCTCC 57.561 45.455 0.00 0.00 37.63 4.30
2039 2257 5.007385 GCTTACCAGCAGCTAGTACTAAA 57.993 43.478 3.76 0.00 46.49 1.85
2057 2275 3.476419 GGGCCGGGCTGTAGCTTA 61.476 66.667 28.80 0.00 41.70 3.09
2123 2581 2.034878 AGCTCTTATCTCACGGCATGA 58.965 47.619 0.00 0.00 35.45 3.07
2139 2597 1.540267 TGACGTGTCCTGTCTTAGCTC 59.460 52.381 0.00 0.00 37.26 4.09
2260 2725 3.889196 TTTTTCCATTGACCGTTCGAG 57.111 42.857 0.00 0.00 0.00 4.04
2284 2750 5.680619 TGTTTCAGAGTGTGTAATGTTCCT 58.319 37.500 0.00 0.00 0.00 3.36
2376 2842 3.900601 AGGGAGTATATTCCTGCTCACAG 59.099 47.826 13.49 0.00 44.05 3.66
2383 2849 5.428184 GGAATGGAGGGAGTATATTCCTG 57.572 47.826 13.49 0.00 42.10 3.86


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

AutoCloner maintained by Alex Coulton.