Multiple sequence alignment - TraesCS1A01G214100

Loading Multiple Alignment...

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 TraesCS1A01G214100 chr1A 100.000 4187 0 0 1 4187 377217267 377213081 0.000000e+00 7733.0
1 TraesCS1A01G214100 chr1A 98.571 140 2 0 1 140 520505788 520505649 8.990000e-62 248.0
2 TraesCS1A01G214100 chr1A 98.571 140 2 0 1 140 537737948 537737809 8.990000e-62 248.0
3 TraesCS1A01G214100 chr1B 94.926 3725 132 23 487 4187 409608171 409604480 0.000000e+00 5779.0
4 TraesCS1A01G214100 chr1B 91.234 308 12 5 141 433 409608477 409608170 5.040000e-109 405.0
5 TraesCS1A01G214100 chr1B 84.848 99 8 5 3743 3841 539869619 539869528 4.460000e-15 93.5
6 TraesCS1A01G214100 chr1D 96.847 3394 74 6 807 4187 302699452 302696079 0.000000e+00 5644.0
7 TraesCS1A01G214100 chr1D 88.312 77 7 1 3756 3830 493932391 493932315 1.600000e-14 91.6
8 TraesCS1A01G214100 chr1D 83.516 91 11 4 3753 3841 468830222 468830134 9.650000e-12 82.4
9 TraesCS1A01G214100 chr5A 98.582 141 2 0 1 141 632926379 632926239 2.500000e-62 250.0
10 TraesCS1A01G214100 chr3A 97.917 144 3 0 1 144 467768697 467768554 2.500000e-62 250.0
11 TraesCS1A01G214100 chr3A 97.241 145 3 1 1 145 660229846 660229989 1.160000e-60 244.0
12 TraesCS1A01G214100 chr3A 82.418 91 13 3 3753 3841 491189515 491189426 4.490000e-10 76.8
13 TraesCS1A01G214100 chr2A 98.582 141 2 0 1 141 101617571 101617431 2.500000e-62 250.0
14 TraesCS1A01G214100 chr2A 98.582 141 2 0 1 141 180047506 180047366 2.500000e-62 250.0
15 TraesCS1A01G214100 chr2A 97.260 146 3 1 1 145 244289690 244289545 3.230000e-61 246.0
16 TraesCS1A01G214100 chr6B 96.026 151 4 2 1 151 186424072 186423924 1.160000e-60 244.0
17 TraesCS1A01G214100 chr6B 83.133 83 12 2 3754 3835 707294021 707294102 1.610000e-09 75.0
18 TraesCS1A01G214100 chr4A 89.773 88 7 2 3755 3841 75437851 75437765 1.230000e-20 111.0
19 TraesCS1A01G214100 chr2D 84.091 88 10 4 3755 3841 29167764 29167680 9.650000e-12 82.4


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 TraesCS1A01G214100 chr1A 377213081 377217267 4186 True 7733 7733 100.000 1 4187 1 chr1A.!!$R1 4186
1 TraesCS1A01G214100 chr1B 409604480 409608477 3997 True 3092 5779 93.080 141 4187 2 chr1B.!!$R2 4046
2 TraesCS1A01G214100 chr1D 302696079 302699452 3373 True 5644 5644 96.847 807 4187 1 chr1D.!!$R1 3380

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
202 205 0.105401 CCTCTAACCCTCTCCCCTCC 60.105 65.0 0.00 0.0 0.0 4.30 F
790 810 0.320421 TGCGCTTACACTCAGGTTCC 60.320 55.0 9.73 0.0 0.0 3.62 F
2049 2072 0.035317 TGCTCGCCAATGTCTGTCTT 59.965 50.0 0.00 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 1829 0.594284 CCGAGCGGACTAAATCGACC 60.594 60.000 2.00 0.00 37.35 4.79 R
2259 2282 0.519999 GCTTTCGAATCACTGCAGCG 60.520 55.000 15.27 9.11 0.00 5.18 R
3876 3925 1.681264 CAGGGGTTTCCGCATTTATCC 59.319 52.381 5.70 0.00 41.52 2.59 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
28 29 6.638021 AGGTGAGCCTAGTTATTTTAGGTT 57.362 37.500 0.77 0.00 44.90 3.50
29 30 7.029053 AGGTGAGCCTAGTTATTTTAGGTTT 57.971 36.000 0.77 0.00 44.90 3.27
30 31 7.467650 AGGTGAGCCTAGTTATTTTAGGTTTT 58.532 34.615 0.77 0.00 44.90 2.43
31 32 7.393515 AGGTGAGCCTAGTTATTTTAGGTTTTG 59.606 37.037 0.77 0.00 44.90 2.44
32 33 7.176165 GGTGAGCCTAGTTATTTTAGGTTTTGT 59.824 37.037 0.77 0.00 39.91 2.83
33 34 8.021396 GTGAGCCTAGTTATTTTAGGTTTTGTG 58.979 37.037 0.77 0.00 39.91 3.33
34 35 6.920817 AGCCTAGTTATTTTAGGTTTTGTGC 58.079 36.000 0.77 0.00 39.91 4.57
35 36 6.719829 AGCCTAGTTATTTTAGGTTTTGTGCT 59.280 34.615 0.77 0.00 39.91 4.40
36 37 7.232737 AGCCTAGTTATTTTAGGTTTTGTGCTT 59.767 33.333 0.77 0.00 39.91 3.91
37 38 7.328493 GCCTAGTTATTTTAGGTTTTGTGCTTG 59.672 37.037 0.77 0.00 39.91 4.01
38 39 8.573035 CCTAGTTATTTTAGGTTTTGTGCTTGA 58.427 33.333 0.00 0.00 34.27 3.02
39 40 9.394477 CTAGTTATTTTAGGTTTTGTGCTTGAC 57.606 33.333 0.00 0.00 0.00 3.18
40 41 7.777095 AGTTATTTTAGGTTTTGTGCTTGACA 58.223 30.769 0.00 0.00 0.00 3.58
41 42 8.254508 AGTTATTTTAGGTTTTGTGCTTGACAA 58.745 29.630 0.00 0.00 43.11 3.18
51 52 4.764679 TGTGCTTGACAAATTAATCGCT 57.235 36.364 0.00 0.00 0.00 4.93
52 53 5.871465 TGTGCTTGACAAATTAATCGCTA 57.129 34.783 0.00 0.00 0.00 4.26
53 54 5.868257 TGTGCTTGACAAATTAATCGCTAG 58.132 37.500 0.00 0.00 0.00 3.42
54 55 5.163764 TGTGCTTGACAAATTAATCGCTAGG 60.164 40.000 0.00 0.00 0.00 3.02
55 56 4.941263 TGCTTGACAAATTAATCGCTAGGT 59.059 37.500 0.00 0.00 0.00 3.08
56 57 5.414454 TGCTTGACAAATTAATCGCTAGGTT 59.586 36.000 0.00 0.00 0.00 3.50
57 58 6.072175 TGCTTGACAAATTAATCGCTAGGTTT 60.072 34.615 0.00 0.00 0.00 3.27
58 59 7.119992 TGCTTGACAAATTAATCGCTAGGTTTA 59.880 33.333 0.00 0.00 0.00 2.01
59 60 8.129211 GCTTGACAAATTAATCGCTAGGTTTAT 58.871 33.333 0.00 0.00 0.00 1.40
61 62 9.997482 TTGACAAATTAATCGCTAGGTTTATTC 57.003 29.630 0.00 0.00 0.00 1.75
62 63 8.617809 TGACAAATTAATCGCTAGGTTTATTCC 58.382 33.333 0.00 0.00 0.00 3.01
63 64 7.636326 ACAAATTAATCGCTAGGTTTATTCCG 58.364 34.615 0.00 0.00 0.00 4.30
64 65 5.857822 ATTAATCGCTAGGTTTATTCCGC 57.142 39.130 0.00 0.00 0.00 5.54
65 66 2.902705 ATCGCTAGGTTTATTCCGCA 57.097 45.000 0.00 0.00 0.00 5.69
66 67 2.902705 TCGCTAGGTTTATTCCGCAT 57.097 45.000 0.00 0.00 0.00 4.73
67 68 3.188159 TCGCTAGGTTTATTCCGCATT 57.812 42.857 0.00 0.00 0.00 3.56
68 69 3.537580 TCGCTAGGTTTATTCCGCATTT 58.462 40.909 0.00 0.00 0.00 2.32
69 70 3.311322 TCGCTAGGTTTATTCCGCATTTG 59.689 43.478 0.00 0.00 0.00 2.32
70 71 3.064820 CGCTAGGTTTATTCCGCATTTGT 59.935 43.478 0.00 0.00 0.00 2.83
71 72 4.438200 CGCTAGGTTTATTCCGCATTTGTT 60.438 41.667 0.00 0.00 0.00 2.83
72 73 5.034797 GCTAGGTTTATTCCGCATTTGTTC 58.965 41.667 0.00 0.00 0.00 3.18
73 74 5.392595 GCTAGGTTTATTCCGCATTTGTTCA 60.393 40.000 0.00 0.00 0.00 3.18
74 75 5.461032 AGGTTTATTCCGCATTTGTTCAA 57.539 34.783 0.00 0.00 0.00 2.69
75 76 5.469479 AGGTTTATTCCGCATTTGTTCAAG 58.531 37.500 0.00 0.00 0.00 3.02
76 77 4.091365 GGTTTATTCCGCATTTGTTCAAGC 59.909 41.667 0.00 0.00 0.00 4.01
77 78 2.368655 ATTCCGCATTTGTTCAAGCC 57.631 45.000 0.00 0.00 0.00 4.35
78 79 1.327303 TTCCGCATTTGTTCAAGCCT 58.673 45.000 0.00 0.00 0.00 4.58
79 80 2.192664 TCCGCATTTGTTCAAGCCTA 57.807 45.000 0.00 0.00 0.00 3.93
80 81 2.509569 TCCGCATTTGTTCAAGCCTAA 58.490 42.857 0.00 0.00 0.00 2.69
81 82 2.887783 TCCGCATTTGTTCAAGCCTAAA 59.112 40.909 0.00 0.00 0.00 1.85
82 83 3.509575 TCCGCATTTGTTCAAGCCTAAAT 59.490 39.130 0.00 0.00 0.00 1.40
83 84 3.859386 CCGCATTTGTTCAAGCCTAAATC 59.141 43.478 0.00 0.00 0.00 2.17
84 85 3.543494 CGCATTTGTTCAAGCCTAAATCG 59.457 43.478 0.00 0.00 0.00 3.34
85 86 4.485163 GCATTTGTTCAAGCCTAAATCGT 58.515 39.130 0.00 0.00 0.00 3.73
86 87 5.636837 GCATTTGTTCAAGCCTAAATCGTA 58.363 37.500 0.00 0.00 0.00 3.43
87 88 6.090129 GCATTTGTTCAAGCCTAAATCGTAA 58.910 36.000 0.00 0.00 0.00 3.18
88 89 6.751888 GCATTTGTTCAAGCCTAAATCGTAAT 59.248 34.615 0.00 0.00 0.00 1.89
89 90 7.275560 GCATTTGTTCAAGCCTAAATCGTAATT 59.724 33.333 0.00 0.00 0.00 1.40
90 91 9.781834 CATTTGTTCAAGCCTAAATCGTAATTA 57.218 29.630 0.00 0.00 0.00 1.40
111 112 8.936070 AATTATTTTAAAACGCCTATTCACCC 57.064 30.769 1.97 0.00 0.00 4.61
112 113 4.787260 TTTTAAAACGCCTATTCACCCC 57.213 40.909 0.00 0.00 0.00 4.95
113 114 2.423446 TAAAACGCCTATTCACCCCC 57.577 50.000 0.00 0.00 0.00 5.40
127 128 3.460995 CCCCCTCTAGGCGACATC 58.539 66.667 0.00 0.00 0.00 3.06
128 129 2.210711 CCCCCTCTAGGCGACATCC 61.211 68.421 0.00 0.00 0.00 3.51
129 130 1.457643 CCCCTCTAGGCGACATCCA 60.458 63.158 0.00 0.00 0.00 3.41
130 131 1.742768 CCCTCTAGGCGACATCCAC 59.257 63.158 0.00 0.00 0.00 4.02
131 132 1.360551 CCTCTAGGCGACATCCACG 59.639 63.158 0.00 0.00 0.00 4.94
132 133 1.101635 CCTCTAGGCGACATCCACGA 61.102 60.000 0.00 0.00 0.00 4.35
133 134 0.955178 CTCTAGGCGACATCCACGAT 59.045 55.000 0.00 0.00 0.00 3.73
134 135 0.952280 TCTAGGCGACATCCACGATC 59.048 55.000 0.00 0.00 0.00 3.69
135 136 0.955178 CTAGGCGACATCCACGATCT 59.045 55.000 0.00 0.00 0.00 2.75
136 137 1.338337 CTAGGCGACATCCACGATCTT 59.662 52.381 0.00 0.00 0.00 2.40
137 138 0.537188 AGGCGACATCCACGATCTTT 59.463 50.000 0.00 0.00 0.00 2.52
138 139 0.931005 GGCGACATCCACGATCTTTC 59.069 55.000 0.00 0.00 0.00 2.62
139 140 1.640428 GCGACATCCACGATCTTTCA 58.360 50.000 0.00 0.00 0.00 2.69
156 157 3.872511 TTCACCTTTCGTATCGCCTTA 57.127 42.857 0.00 0.00 0.00 2.69
173 174 0.399949 TTATCGAGCCATCACCCCCT 60.400 55.000 0.00 0.00 0.00 4.79
174 175 0.399949 TATCGAGCCATCACCCCCTT 60.400 55.000 0.00 0.00 0.00 3.95
177 180 2.285368 AGCCATCACCCCCTTCGA 60.285 61.111 0.00 0.00 0.00 3.71
202 205 0.105401 CCTCTAACCCTCTCCCCTCC 60.105 65.000 0.00 0.00 0.00 4.30
208 211 2.037367 CCTCTCCCCTCCGACACA 59.963 66.667 0.00 0.00 0.00 3.72
271 277 4.406173 CAGTGCCTCGCTCGACGT 62.406 66.667 0.00 0.00 44.19 4.34
272 278 3.671411 AGTGCCTCGCTCGACGTT 61.671 61.111 0.00 0.00 44.19 3.99
287 293 1.443702 CGTTGTCTCGCCATCGTCA 60.444 57.895 0.00 0.00 36.96 4.35
323 329 1.875576 GCCGCTAGGTCCATGAAGATG 60.876 57.143 0.00 0.00 40.50 2.90
365 381 2.808958 CGCTGTTCCGCCCATAACG 61.809 63.158 0.00 0.00 0.00 3.18
383 399 6.238103 CCATAACGTGTAGAATTTGCCTACTG 60.238 42.308 0.00 0.00 37.84 2.74
425 441 6.576662 TTATTTGCCGAAAATACACCTTGA 57.423 33.333 3.57 0.00 39.84 3.02
431 447 4.437390 GCCGAAAATACACCTTGAGACATG 60.437 45.833 0.00 0.00 0.00 3.21
432 448 4.094887 CCGAAAATACACCTTGAGACATGG 59.905 45.833 0.00 0.00 35.21 3.66
433 449 4.935205 CGAAAATACACCTTGAGACATGGA 59.065 41.667 9.97 0.00 33.58 3.41
434 450 5.586243 CGAAAATACACCTTGAGACATGGAT 59.414 40.000 9.97 0.00 33.58 3.41
435 451 6.457392 CGAAAATACACCTTGAGACATGGATG 60.457 42.308 9.97 7.36 33.58 3.51
436 452 2.119801 ACACCTTGAGACATGGATGC 57.880 50.000 9.97 0.00 33.58 3.91
437 453 1.340405 ACACCTTGAGACATGGATGCC 60.340 52.381 9.97 0.00 33.58 4.40
438 454 1.064906 CACCTTGAGACATGGATGCCT 60.065 52.381 9.97 0.00 33.58 4.75
439 455 2.171237 CACCTTGAGACATGGATGCCTA 59.829 50.000 9.97 0.00 33.58 3.93
440 456 3.051581 ACCTTGAGACATGGATGCCTAT 58.948 45.455 9.97 0.00 33.58 2.57
441 457 3.181447 ACCTTGAGACATGGATGCCTATG 60.181 47.826 9.97 0.00 33.58 2.23
442 458 3.181447 CCTTGAGACATGGATGCCTATGT 60.181 47.826 0.00 0.00 40.04 2.29
443 459 4.040829 CCTTGAGACATGGATGCCTATGTA 59.959 45.833 0.00 0.00 37.63 2.29
444 460 4.607293 TGAGACATGGATGCCTATGTAC 57.393 45.455 0.00 0.00 37.63 2.90
445 461 3.324846 TGAGACATGGATGCCTATGTACC 59.675 47.826 0.00 0.00 37.63 3.34
446 462 2.639839 AGACATGGATGCCTATGTACCC 59.360 50.000 0.00 0.00 37.63 3.69
447 463 1.347707 ACATGGATGCCTATGTACCCG 59.652 52.381 0.00 0.00 35.86 5.28
448 464 1.623311 CATGGATGCCTATGTACCCGA 59.377 52.381 0.00 0.00 0.00 5.14
449 465 1.796017 TGGATGCCTATGTACCCGAA 58.204 50.000 0.00 0.00 0.00 4.30
450 466 2.334977 TGGATGCCTATGTACCCGAAT 58.665 47.619 0.00 0.00 0.00 3.34
451 467 2.708861 TGGATGCCTATGTACCCGAATT 59.291 45.455 0.00 0.00 0.00 2.17
452 468 3.074412 GGATGCCTATGTACCCGAATTG 58.926 50.000 0.00 0.00 0.00 2.32
453 469 1.961793 TGCCTATGTACCCGAATTGC 58.038 50.000 0.00 0.00 0.00 3.56
454 470 1.210722 TGCCTATGTACCCGAATTGCA 59.789 47.619 0.00 0.00 0.00 4.08
455 471 2.294074 GCCTATGTACCCGAATTGCAA 58.706 47.619 0.00 0.00 0.00 4.08
456 472 2.685897 GCCTATGTACCCGAATTGCAAA 59.314 45.455 1.71 0.00 0.00 3.68
457 473 3.129638 GCCTATGTACCCGAATTGCAAAA 59.870 43.478 1.71 0.00 0.00 2.44
458 474 4.381079 GCCTATGTACCCGAATTGCAAAAA 60.381 41.667 1.71 0.00 0.00 1.94
459 475 5.681179 GCCTATGTACCCGAATTGCAAAAAT 60.681 40.000 1.71 0.00 0.00 1.82
460 476 6.460399 GCCTATGTACCCGAATTGCAAAAATA 60.460 38.462 1.71 0.00 0.00 1.40
461 477 7.484975 CCTATGTACCCGAATTGCAAAAATAA 58.515 34.615 1.71 0.00 0.00 1.40
462 478 7.976734 CCTATGTACCCGAATTGCAAAAATAAA 59.023 33.333 1.71 0.00 0.00 1.40
463 479 9.528018 CTATGTACCCGAATTGCAAAAATAAAT 57.472 29.630 1.71 0.00 0.00 1.40
465 481 9.877178 ATGTACCCGAATTGCAAAAATAAATAA 57.123 25.926 1.71 0.00 0.00 1.40
466 482 9.706691 TGTACCCGAATTGCAAAAATAAATAAA 57.293 25.926 1.71 0.00 0.00 1.40
523 540 5.000591 TGATCTTTGTCGGAACAAGCATAA 58.999 37.500 0.00 0.00 45.72 1.90
584 602 4.188462 TGACTTGCGTGGTATTCTAATGG 58.812 43.478 0.00 0.00 0.00 3.16
641 661 9.626045 AGCTTAAAATTCATAGTTTGTAGTTGC 57.374 29.630 0.00 0.00 0.00 4.17
656 676 6.324522 TGTAGTTGCAATTTTGTCGTTTTG 57.675 33.333 0.59 0.00 0.00 2.44
660 680 3.002791 TGCAATTTTGTCGTTTTGCCAA 58.997 36.364 4.26 0.00 42.87 4.52
670 690 7.436430 TTGTCGTTTTGCCAATAATACTACA 57.564 32.000 0.00 0.00 0.00 2.74
790 810 0.320421 TGCGCTTACACTCAGGTTCC 60.320 55.000 9.73 0.00 0.00 3.62
798 818 5.564848 GCTTACACTCAGGTTCCAAAAATCC 60.565 44.000 0.00 0.00 0.00 3.01
809 829 1.533756 CCAAAAATCCGCACCGCTATG 60.534 52.381 0.00 0.00 0.00 2.23
812 832 0.392461 AAATCCGCACCGCTATGTGT 60.392 50.000 0.00 0.00 38.52 3.72
1072 1095 3.260100 CCTCCCTTGCCCACCACT 61.260 66.667 0.00 0.00 0.00 4.00
1182 1205 3.576259 AACCCCTTGGACCCCACG 61.576 66.667 0.00 0.00 30.78 4.94
1605 1628 2.263852 CTCCTGCTGCTGCTCGAA 59.736 61.111 17.00 0.00 40.48 3.71
1611 1634 1.963338 GCTGCTGCTCGAACCAGTT 60.963 57.895 8.53 0.00 36.03 3.16
1752 1775 2.273449 CCGCTGCTTGATTCCCCT 59.727 61.111 0.00 0.00 0.00 4.79
1806 1829 2.287644 TGATGTGCGTGACAAGAAAGTG 59.712 45.455 0.00 0.00 38.36 3.16
1827 1850 1.226859 CGATTTAGTCCGCTCGGCA 60.227 57.895 2.96 0.00 34.68 5.69
1851 1874 1.823169 TTACTCCAGTGGTGACCGCC 61.823 60.000 17.99 0.00 33.99 6.13
2049 2072 0.035317 TGCTCGCCAATGTCTGTCTT 59.965 50.000 0.00 0.00 0.00 3.01
2058 2081 4.142730 GCCAATGTCTGTCTTGATGAGTTC 60.143 45.833 0.00 0.00 0.00 3.01
2238 2261 0.817013 GCGGGCATTTCTTGATTGGA 59.183 50.000 0.00 0.00 0.00 3.53
2241 2264 3.278574 CGGGCATTTCTTGATTGGAGTA 58.721 45.455 0.00 0.00 0.00 2.59
2247 2270 3.366052 TTCTTGATTGGAGTAAGGGGC 57.634 47.619 0.00 0.00 0.00 5.80
2271 2294 3.121030 GCCGACGCTGCAGTGATT 61.121 61.111 32.90 12.45 0.00 2.57
2385 2408 4.609947 TGTTTCTTGATCATGTGTTGTGC 58.390 39.130 8.33 0.00 0.00 4.57
2469 2492 1.267121 GGGTTGGTACTCTGCTCTCA 58.733 55.000 0.00 0.00 0.00 3.27
2640 2663 3.677148 CGATGGCAGAATGGTATCGCTAT 60.677 47.826 0.00 0.00 34.98 2.97
2902 2925 4.215908 TCCTGATCCTGACTATACACCAC 58.784 47.826 0.00 0.00 0.00 4.16
3184 3207 0.712380 AGGCCATCAGGGTTTTCCAT 59.288 50.000 5.01 0.00 42.91 3.41
3186 3209 2.091665 AGGCCATCAGGGTTTTCCATAG 60.092 50.000 5.01 0.00 42.91 2.23
3188 3211 2.949963 GCCATCAGGGTTTTCCATAGCA 60.950 50.000 0.00 0.00 42.91 3.49
3298 3321 0.391263 GACCAACTCACCGATGGACC 60.391 60.000 0.00 0.00 37.76 4.46
3409 3432 4.443881 CCTGCTCAAGGTCATGACATATCA 60.444 45.833 26.47 13.96 41.74 2.15
3515 3562 3.929002 GCATCTGCATCAAGGCCA 58.071 55.556 5.01 0.00 41.59 5.36
3516 3563 1.734137 GCATCTGCATCAAGGCCAG 59.266 57.895 5.01 0.00 41.59 4.85
3569 3616 8.888579 TTAGTAAGACTTTATCAAGCCTATGC 57.111 34.615 0.00 0.00 32.57 3.14
3573 3620 9.273016 GTAAGACTTTATCAAGCCTATGCATTA 57.727 33.333 3.54 0.00 41.13 1.90
3577 3624 9.971922 GACTTTATCAAGCCTATGCATTAAAAT 57.028 29.630 3.54 0.00 41.13 1.82
3876 3925 1.812235 TTGCAGTGTGTGAGCCATAG 58.188 50.000 0.00 0.00 0.00 2.23
4078 4128 4.548451 TGGCATTCAACCATATTTTGCA 57.452 36.364 0.00 0.00 30.29 4.08
4145 4196 6.140377 TCCTTTTCTATTTGTTTTCCCCTGT 58.860 36.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.176165 ACAAAACCTAAAATAACTAGGCTCACC 59.824 37.037 0.00 0.00 39.78 4.02
7 8 8.021396 CACAAAACCTAAAATAACTAGGCTCAC 58.979 37.037 0.00 0.00 39.78 3.51
8 9 7.308951 GCACAAAACCTAAAATAACTAGGCTCA 60.309 37.037 0.00 0.00 39.78 4.26
9 10 7.027760 GCACAAAACCTAAAATAACTAGGCTC 58.972 38.462 0.00 0.00 39.78 4.70
10 11 6.719829 AGCACAAAACCTAAAATAACTAGGCT 59.280 34.615 0.00 0.00 39.78 4.58
11 12 6.920817 AGCACAAAACCTAAAATAACTAGGC 58.079 36.000 0.00 0.00 39.78 3.93
12 13 8.573035 TCAAGCACAAAACCTAAAATAACTAGG 58.427 33.333 0.00 0.00 41.61 3.02
13 14 9.394477 GTCAAGCACAAAACCTAAAATAACTAG 57.606 33.333 0.00 0.00 0.00 2.57
14 15 8.904834 TGTCAAGCACAAAACCTAAAATAACTA 58.095 29.630 0.00 0.00 29.30 2.24
15 16 7.777095 TGTCAAGCACAAAACCTAAAATAACT 58.223 30.769 0.00 0.00 29.30 2.24
16 17 7.995463 TGTCAAGCACAAAACCTAAAATAAC 57.005 32.000 0.00 0.00 29.30 1.89
29 30 5.119931 AGCGATTAATTTGTCAAGCACAA 57.880 34.783 0.00 0.00 43.68 3.33
30 31 4.764679 AGCGATTAATTTGTCAAGCACA 57.235 36.364 0.00 0.00 0.00 4.57
31 32 5.163754 ACCTAGCGATTAATTTGTCAAGCAC 60.164 40.000 0.00 0.00 0.00 4.40
32 33 4.941263 ACCTAGCGATTAATTTGTCAAGCA 59.059 37.500 0.00 0.00 0.00 3.91
33 34 5.485662 ACCTAGCGATTAATTTGTCAAGC 57.514 39.130 0.00 0.00 0.00 4.01
35 36 9.997482 GAATAAACCTAGCGATTAATTTGTCAA 57.003 29.630 0.00 0.00 0.00 3.18
36 37 8.617809 GGAATAAACCTAGCGATTAATTTGTCA 58.382 33.333 0.00 0.00 0.00 3.58
37 38 7.797123 CGGAATAAACCTAGCGATTAATTTGTC 59.203 37.037 0.00 0.00 0.00 3.18
38 39 7.636326 CGGAATAAACCTAGCGATTAATTTGT 58.364 34.615 0.00 0.00 0.00 2.83
39 40 6.577427 GCGGAATAAACCTAGCGATTAATTTG 59.423 38.462 0.00 0.00 0.00 2.32
40 41 6.261381 TGCGGAATAAACCTAGCGATTAATTT 59.739 34.615 0.00 0.00 0.00 1.82
41 42 5.761234 TGCGGAATAAACCTAGCGATTAATT 59.239 36.000 0.00 0.00 0.00 1.40
42 43 5.302360 TGCGGAATAAACCTAGCGATTAAT 58.698 37.500 0.00 0.00 0.00 1.40
43 44 4.695396 TGCGGAATAAACCTAGCGATTAA 58.305 39.130 0.00 0.00 0.00 1.40
44 45 4.325028 TGCGGAATAAACCTAGCGATTA 57.675 40.909 0.00 0.00 0.00 1.75
45 46 3.188159 TGCGGAATAAACCTAGCGATT 57.812 42.857 0.00 0.00 0.00 3.34
46 47 2.902705 TGCGGAATAAACCTAGCGAT 57.097 45.000 0.00 0.00 0.00 4.58
47 48 2.902705 ATGCGGAATAAACCTAGCGA 57.097 45.000 0.00 0.00 0.00 4.93
48 49 3.064820 ACAAATGCGGAATAAACCTAGCG 59.935 43.478 0.00 0.00 0.00 4.26
49 50 4.632538 ACAAATGCGGAATAAACCTAGC 57.367 40.909 0.00 0.00 0.00 3.42
50 51 6.189677 TGAACAAATGCGGAATAAACCTAG 57.810 37.500 0.00 0.00 0.00 3.02
51 52 6.576662 TTGAACAAATGCGGAATAAACCTA 57.423 33.333 0.00 0.00 0.00 3.08
52 53 5.461032 TTGAACAAATGCGGAATAAACCT 57.539 34.783 0.00 0.00 0.00 3.50
53 54 4.091365 GCTTGAACAAATGCGGAATAAACC 59.909 41.667 0.00 0.00 0.00 3.27
54 55 4.091365 GGCTTGAACAAATGCGGAATAAAC 59.909 41.667 0.00 0.00 0.00 2.01
55 56 4.021544 AGGCTTGAACAAATGCGGAATAAA 60.022 37.500 0.00 0.00 0.00 1.40
56 57 3.509575 AGGCTTGAACAAATGCGGAATAA 59.490 39.130 0.00 0.00 0.00 1.40
57 58 3.088532 AGGCTTGAACAAATGCGGAATA 58.911 40.909 0.00 0.00 0.00 1.75
58 59 1.895131 AGGCTTGAACAAATGCGGAAT 59.105 42.857 0.00 0.00 0.00 3.01
59 60 1.327303 AGGCTTGAACAAATGCGGAA 58.673 45.000 0.00 0.00 0.00 4.30
60 61 2.192664 TAGGCTTGAACAAATGCGGA 57.807 45.000 0.00 0.00 0.00 5.54
61 62 3.296322 TTTAGGCTTGAACAAATGCGG 57.704 42.857 0.00 0.00 0.00 5.69
62 63 3.543494 CGATTTAGGCTTGAACAAATGCG 59.457 43.478 0.00 0.00 0.00 4.73
63 64 4.485163 ACGATTTAGGCTTGAACAAATGC 58.515 39.130 0.00 0.00 0.00 3.56
64 65 8.687824 AATTACGATTTAGGCTTGAACAAATG 57.312 30.769 0.00 0.00 0.00 2.32
86 87 7.982919 GGGGTGAATAGGCGTTTTAAAATAATT 59.017 33.333 3.52 0.88 0.00 1.40
87 88 7.418139 GGGGGTGAATAGGCGTTTTAAAATAAT 60.418 37.037 3.52 0.00 0.00 1.28
88 89 6.127394 GGGGGTGAATAGGCGTTTTAAAATAA 60.127 38.462 3.52 0.00 0.00 1.40
89 90 5.360429 GGGGGTGAATAGGCGTTTTAAAATA 59.640 40.000 3.52 0.00 0.00 1.40
90 91 4.160814 GGGGGTGAATAGGCGTTTTAAAAT 59.839 41.667 3.52 0.00 0.00 1.82
91 92 3.510753 GGGGGTGAATAGGCGTTTTAAAA 59.489 43.478 0.00 0.00 0.00 1.52
92 93 3.090790 GGGGGTGAATAGGCGTTTTAAA 58.909 45.455 0.00 0.00 0.00 1.52
93 94 2.725637 GGGGGTGAATAGGCGTTTTAA 58.274 47.619 0.00 0.00 0.00 1.52
94 95 2.423446 GGGGGTGAATAGGCGTTTTA 57.577 50.000 0.00 0.00 0.00 1.52
95 96 3.276281 GGGGGTGAATAGGCGTTTT 57.724 52.632 0.00 0.00 0.00 2.43
110 111 2.210711 GGATGTCGCCTAGAGGGGG 61.211 68.421 12.32 0.23 46.90 5.40
112 113 1.742768 GTGGATGTCGCCTAGAGGG 59.257 63.158 0.00 0.00 35.18 4.30
113 114 1.101635 TCGTGGATGTCGCCTAGAGG 61.102 60.000 0.00 0.00 38.53 3.69
114 115 0.955178 ATCGTGGATGTCGCCTAGAG 59.045 55.000 0.00 0.00 0.00 2.43
115 116 0.952280 GATCGTGGATGTCGCCTAGA 59.048 55.000 0.00 0.00 0.00 2.43
116 117 0.955178 AGATCGTGGATGTCGCCTAG 59.045 55.000 0.00 0.00 0.00 3.02
117 118 1.399714 AAGATCGTGGATGTCGCCTA 58.600 50.000 0.00 0.00 0.00 3.93
118 119 0.537188 AAAGATCGTGGATGTCGCCT 59.463 50.000 0.00 0.00 0.00 5.52
119 120 0.931005 GAAAGATCGTGGATGTCGCC 59.069 55.000 0.00 0.00 0.00 5.54
120 121 1.324736 GTGAAAGATCGTGGATGTCGC 59.675 52.381 0.00 0.00 0.00 5.19
121 122 1.927174 GGTGAAAGATCGTGGATGTCG 59.073 52.381 0.00 0.00 0.00 4.35
122 123 3.252974 AGGTGAAAGATCGTGGATGTC 57.747 47.619 0.00 0.00 0.00 3.06
123 124 3.703001 AAGGTGAAAGATCGTGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
124 125 3.062639 CGAAAGGTGAAAGATCGTGGATG 59.937 47.826 0.00 0.00 0.00 3.51
125 126 3.262420 CGAAAGGTGAAAGATCGTGGAT 58.738 45.455 0.00 0.00 0.00 3.41
126 127 2.036733 ACGAAAGGTGAAAGATCGTGGA 59.963 45.455 0.00 0.00 44.20 4.02
127 128 2.413837 ACGAAAGGTGAAAGATCGTGG 58.586 47.619 0.00 0.00 44.20 4.94
128 129 4.027621 CGATACGAAAGGTGAAAGATCGTG 60.028 45.833 9.14 0.00 45.30 4.35
130 131 3.061139 GCGATACGAAAGGTGAAAGATCG 60.061 47.826 0.00 0.00 38.32 3.69
131 132 3.245519 GGCGATACGAAAGGTGAAAGATC 59.754 47.826 0.00 0.00 0.00 2.75
132 133 3.118738 AGGCGATACGAAAGGTGAAAGAT 60.119 43.478 0.00 0.00 0.00 2.40
133 134 2.232941 AGGCGATACGAAAGGTGAAAGA 59.767 45.455 0.00 0.00 0.00 2.52
134 135 2.618053 AGGCGATACGAAAGGTGAAAG 58.382 47.619 0.00 0.00 0.00 2.62
135 136 2.754946 AGGCGATACGAAAGGTGAAA 57.245 45.000 0.00 0.00 0.00 2.69
136 137 2.754946 AAGGCGATACGAAAGGTGAA 57.245 45.000 0.00 0.00 0.00 3.18
137 138 3.549423 CGATAAGGCGATACGAAAGGTGA 60.549 47.826 0.00 0.00 0.00 4.02
138 139 2.724690 CGATAAGGCGATACGAAAGGTG 59.275 50.000 0.00 0.00 0.00 4.00
139 140 2.620115 TCGATAAGGCGATACGAAAGGT 59.380 45.455 0.00 0.00 35.01 3.50
156 157 1.694169 AAGGGGGTGATGGCTCGAT 60.694 57.895 0.00 0.00 0.00 3.59
173 174 1.078324 AGGGTTAGAGGGAAGGTCGAA 59.922 52.381 0.00 0.00 0.00 3.71
174 175 0.708802 AGGGTTAGAGGGAAGGTCGA 59.291 55.000 0.00 0.00 0.00 4.20
177 180 1.008571 GGAGAGGGTTAGAGGGAAGGT 59.991 57.143 0.00 0.00 0.00 3.50
208 211 1.837051 TGAGCGGTTCAGGTCACCT 60.837 57.895 0.00 0.00 42.80 4.00
271 277 0.109272 GAGTGACGATGGCGAGACAA 60.109 55.000 0.00 0.00 41.64 3.18
272 278 1.506718 GAGTGACGATGGCGAGACA 59.493 57.895 0.00 0.00 41.64 3.41
336 342 1.276844 GAACAGCGAGCACACACAC 59.723 57.895 0.00 0.00 0.00 3.82
337 343 1.887242 GGAACAGCGAGCACACACA 60.887 57.895 0.00 0.00 0.00 3.72
365 381 6.313744 ACAAACAGTAGGCAAATTCTACAC 57.686 37.500 5.80 0.00 39.48 2.90
425 441 2.639839 GGGTACATAGGCATCCATGTCT 59.360 50.000 0.00 0.00 46.01 3.41
431 447 3.074412 CAATTCGGGTACATAGGCATCC 58.926 50.000 0.00 0.00 0.00 3.51
432 448 2.484264 GCAATTCGGGTACATAGGCATC 59.516 50.000 0.00 0.00 0.00 3.91
433 449 2.158682 TGCAATTCGGGTACATAGGCAT 60.159 45.455 0.00 0.00 0.00 4.40
434 450 1.210722 TGCAATTCGGGTACATAGGCA 59.789 47.619 0.00 0.00 0.00 4.75
435 451 1.961793 TGCAATTCGGGTACATAGGC 58.038 50.000 0.00 0.00 0.00 3.93
436 452 4.974368 TTTTGCAATTCGGGTACATAGG 57.026 40.909 0.00 0.00 0.00 2.57
437 453 8.918961 TTTATTTTTGCAATTCGGGTACATAG 57.081 30.769 0.00 0.00 0.00 2.23
439 455 9.877178 TTATTTATTTTTGCAATTCGGGTACAT 57.123 25.926 0.00 0.00 0.00 2.29
440 456 9.706691 TTTATTTATTTTTGCAATTCGGGTACA 57.293 25.926 0.00 0.00 0.00 2.90
485 501 9.855021 CGACAAAGATCAAAAATATTTTACCCT 57.145 29.630 13.68 6.55 0.00 4.34
503 519 5.245531 AGATTATGCTTGTTCCGACAAAGA 58.754 37.500 0.00 0.00 44.65 2.52
594 612 6.940739 AGCTCCGCTTGATATATTATCAGTT 58.059 36.000 0.00 0.00 33.89 3.16
612 630 8.665685 ACTACAAACTATGAATTTTAAGCTCCG 58.334 33.333 0.00 0.00 0.00 4.63
628 646 6.787225 ACGACAAAATTGCAACTACAAACTA 58.213 32.000 0.00 0.00 32.27 2.24
686 706 8.301720 ACTATATCACTCACGTGTAAAGTTTCA 58.698 33.333 16.51 0.00 41.89 2.69
752 772 6.639563 AGCGCACCCAATTATTAAGAAAATT 58.360 32.000 11.47 0.00 0.00 1.82
753 773 6.220726 AGCGCACCCAATTATTAAGAAAAT 57.779 33.333 11.47 0.00 0.00 1.82
755 775 5.652994 AAGCGCACCCAATTATTAAGAAA 57.347 34.783 11.47 0.00 0.00 2.52
756 776 5.648526 TGTAAGCGCACCCAATTATTAAGAA 59.351 36.000 11.47 0.00 0.00 2.52
757 777 5.065474 GTGTAAGCGCACCCAATTATTAAGA 59.935 40.000 11.47 0.00 33.53 2.10
758 778 5.065988 AGTGTAAGCGCACCCAATTATTAAG 59.934 40.000 11.47 0.00 40.04 1.85
759 779 4.944930 AGTGTAAGCGCACCCAATTATTAA 59.055 37.500 11.47 0.00 40.04 1.40
760 780 4.519213 AGTGTAAGCGCACCCAATTATTA 58.481 39.130 11.47 0.00 40.04 0.98
761 781 3.352648 AGTGTAAGCGCACCCAATTATT 58.647 40.909 11.47 0.00 40.04 1.40
762 782 2.943033 GAGTGTAAGCGCACCCAATTAT 59.057 45.455 11.47 0.00 40.04 1.28
763 783 2.289756 TGAGTGTAAGCGCACCCAATTA 60.290 45.455 11.47 0.00 40.04 1.40
764 784 1.165270 GAGTGTAAGCGCACCCAATT 58.835 50.000 11.47 0.00 40.04 2.32
765 785 0.036164 TGAGTGTAAGCGCACCCAAT 59.964 50.000 11.47 0.69 40.04 3.16
766 786 0.602638 CTGAGTGTAAGCGCACCCAA 60.603 55.000 11.47 0.00 40.04 4.12
767 787 1.005037 CTGAGTGTAAGCGCACCCA 60.005 57.895 11.47 0.00 40.04 4.51
790 810 1.132262 ACATAGCGGTGCGGATTTTTG 59.868 47.619 0.00 0.00 0.00 2.44
812 832 2.215625 CCCATTGGGCTTTGTGGCA 61.216 57.895 9.28 0.00 43.83 4.92
836 856 2.591715 GCCACCACGCTCACAGTT 60.592 61.111 0.00 0.00 0.00 3.16
944 967 2.048312 GATGGCTAAAACCCTCGCGC 62.048 60.000 0.00 0.00 0.00 6.86
1024 1047 2.200092 GCGGAGGAGGGAGGAGAT 59.800 66.667 0.00 0.00 0.00 2.75
1461 1484 2.768769 GGGGAGTGGAGGTAGGGC 60.769 72.222 0.00 0.00 0.00 5.19
1560 1583 4.353437 ACGACGCGGTCCTGGAAC 62.353 66.667 12.47 0.28 0.00 3.62
1605 1628 1.449601 CCGCGCCTCATAAACTGGT 60.450 57.895 0.00 0.00 0.00 4.00
1611 1634 1.226859 CGAGAACCGCGCCTCATAA 60.227 57.895 17.26 0.00 0.00 1.90
1806 1829 0.594284 CCGAGCGGACTAAATCGACC 60.594 60.000 2.00 0.00 37.35 4.79
1827 1850 1.344763 GTCACCACTGGAGTAAGCAGT 59.655 52.381 0.71 0.00 0.00 4.40
1851 1874 1.605753 CATCATCATCACCAGGCCTG 58.394 55.000 26.87 26.87 0.00 4.85
2028 2051 1.089920 GACAGACATTGGCGAGCAAT 58.910 50.000 0.00 0.00 0.00 3.56
2049 2072 5.991606 GTCCATCCATTTATCGAACTCATCA 59.008 40.000 0.00 0.00 0.00 3.07
2058 2081 4.871513 TCTTCTCGTCCATCCATTTATCG 58.128 43.478 0.00 0.00 0.00 2.92
2256 2279 1.344226 TTCGAATCACTGCAGCGTCG 61.344 55.000 15.27 16.89 0.00 5.12
2259 2282 0.519999 GCTTTCGAATCACTGCAGCG 60.520 55.000 15.27 9.11 0.00 5.18
2271 2294 4.771590 AAATTCAATGAGCTGCTTTCGA 57.228 36.364 2.53 0.00 0.00 3.71
2385 2408 2.126734 GGGTACACGACACGACGG 60.127 66.667 0.00 0.00 37.61 4.79
2469 2492 2.880890 CTGCTTCAAACTGGCTGTAACT 59.119 45.455 0.00 0.00 0.00 2.24
2640 2663 2.235016 ACCTTTTTGCGGTTATCAGCA 58.765 42.857 0.00 0.00 42.37 4.41
3184 3207 6.701340 ACACTCAAGACATTTCAGTATGCTA 58.299 36.000 0.00 0.00 34.76 3.49
3186 3209 5.409520 TGACACTCAAGACATTTCAGTATGC 59.590 40.000 0.00 0.00 34.76 3.14
3188 3211 9.725019 TTATTGACACTCAAGACATTTCAGTAT 57.275 29.630 0.00 0.00 40.05 2.12
3409 3432 2.042464 TCTTGAAGGATAGAGCCGCAT 58.958 47.619 0.00 0.00 0.00 4.73
3516 3563 2.876550 TGAATGATGTATGAGCAGCTGC 59.123 45.455 31.53 31.53 42.49 5.25
3791 3839 9.533831 AGATGTTTTTGATACTCCCTTTGTATT 57.466 29.630 0.00 0.00 31.55 1.89
3876 3925 1.681264 CAGGGGTTTCCGCATTTATCC 59.319 52.381 5.70 0.00 41.52 2.59
4076 4126 3.827008 TCTAGGACATGGATCAGTTGC 57.173 47.619 0.00 0.00 0.00 4.17
4077 4127 5.990386 CAGATTCTAGGACATGGATCAGTTG 59.010 44.000 0.00 0.00 0.00 3.16
4078 4128 5.664908 ACAGATTCTAGGACATGGATCAGTT 59.335 40.000 0.00 0.00 0.00 3.16
4123 4174 7.865889 GTGTACAGGGGAAAACAAATAGAAAAG 59.134 37.037 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.