Multiple sequence alignment - TraesCS7D01G049200

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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 TraesCS7D01G049200 chr7D 100.000 1900 0 0 386 2285 25285202 25287101 0.000000e+00 3509.0
1 TraesCS7D01G049200 chr7D 84.273 763 86 15 804 1548 25276692 25277438 0.000000e+00 713.0
2 TraesCS7D01G049200 chr7D 100.000 128 0 0 1 128 25284817 25284944 1.060000e-58 237.0
3 TraesCS7D01G049200 chr7D 89.362 94 10 0 5 98 513204888 513204981 3.990000e-23 119.0
4 TraesCS7D01G049200 chr4A 90.848 1344 100 16 952 2285 709264430 709265760 0.000000e+00 1779.0
5 TraesCS7D01G049200 chr4A 90.583 1338 102 15 952 2279 709262869 709264192 0.000000e+00 1751.0
6 TraesCS7D01G049200 chr4A 86.573 499 42 6 804 1285 709203314 709203804 5.590000e-146 527.0
7 TraesCS7D01G049200 chr4A 87.213 305 33 3 386 690 709242463 709242761 2.170000e-90 342.0
8 TraesCS7D01G049200 chr4A 90.625 160 12 3 2059 2218 709265690 709265846 2.300000e-50 209.0
9 TraesCS7D01G049200 chr4A 91.304 92 7 1 2059 2150 709264128 709264218 8.570000e-25 124.0
10 TraesCS7D01G049200 chr4A 92.308 65 5 0 2215 2279 709263973 709264037 2.420000e-15 93.5
11 TraesCS7D01G049200 chr7A 82.105 1235 126 47 1021 2215 26099657 26100836 0.000000e+00 968.0
12 TraesCS7D01G049200 chr7A 84.483 754 72 15 804 1535 26049398 26050128 0.000000e+00 702.0
13 TraesCS7D01G049200 chr7A 85.252 556 40 20 414 936 26099108 26099654 3.340000e-148 534.0
14 TraesCS7D01G049200 chr7A 89.362 94 10 0 5 98 705473967 705474060 3.990000e-23 119.0
15 TraesCS7D01G049200 chr2B 93.103 87 6 0 12 98 10604035 10603949 6.630000e-26 128.0
16 TraesCS7D01G049200 chr2B 89.247 93 10 0 5 97 17089572 17089664 1.430000e-22 117.0
17 TraesCS7D01G049200 chr1D 91.398 93 8 0 5 97 437274208 437274300 6.630000e-26 128.0
18 TraesCS7D01G049200 chr1D 89.362 94 10 0 5 98 228825170 228825263 3.990000e-23 119.0
19 TraesCS7D01G049200 chr1A 91.398 93 8 0 5 97 380270972 380271064 6.630000e-26 128.0
20 TraesCS7D01G049200 chr1B 91.954 87 7 0 12 98 592854655 592854741 3.080000e-24 122.0
21 TraesCS7D01G049200 chr5B 89.247 93 10 0 5 97 678295449 678295357 1.430000e-22 117.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G049200 chr7D 25284817 25287101 2284 False 1873.0 3509 100.0000 1 2285 2 chr7D.!!$F3 2284
1 TraesCS7D01G049200 chr7D 25276692 25277438 746 False 713.0 713 84.2730 804 1548 1 chr7D.!!$F1 744
2 TraesCS7D01G049200 chr4A 709262869 709265846 2977 False 791.3 1779 91.1336 952 2285 5 chr4A.!!$F3 1333
3 TraesCS7D01G049200 chr7A 26099108 26100836 1728 False 751.0 968 83.6785 414 2215 2 chr7A.!!$F3 1801
4 TraesCS7D01G049200 chr7A 26049398 26050128 730 False 702.0 702 84.4830 804 1535 1 chr7A.!!$F1 731

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
80 81 0.110238 TCGCGCTCTCAAAACAATGC 60.11 50.0 5.56 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 2425 0.321671 CTTCGACACTGACCCACCAT 59.678 55.0 0.0 0.0 0.0 3.55 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
22 23 4.463597 GCACATGCACCGTCATTG 57.536 55.556 0.00 0.00 41.59 2.82
23 24 1.580942 GCACATGCACCGTCATTGT 59.419 52.632 0.00 0.00 41.59 2.71
25 26 1.159285 CACATGCACCGTCATTGTCT 58.841 50.000 0.00 0.00 0.00 3.41
28 29 3.374988 CACATGCACCGTCATTGTCTAAT 59.625 43.478 0.00 0.00 0.00 1.73
31 32 2.236146 TGCACCGTCATTGTCTAATCCT 59.764 45.455 0.00 0.00 0.00 3.24
32 33 3.449377 TGCACCGTCATTGTCTAATCCTA 59.551 43.478 0.00 0.00 0.00 2.94
33 34 4.051922 GCACCGTCATTGTCTAATCCTAG 58.948 47.826 0.00 0.00 0.00 3.02
34 35 4.202121 GCACCGTCATTGTCTAATCCTAGA 60.202 45.833 0.00 0.00 0.00 2.43
35 36 5.509840 GCACCGTCATTGTCTAATCCTAGAT 60.510 44.000 0.00 0.00 36.54 1.98
36 37 6.153067 CACCGTCATTGTCTAATCCTAGATC 58.847 44.000 0.00 0.00 36.54 2.75
37 38 6.015856 CACCGTCATTGTCTAATCCTAGATCT 60.016 42.308 0.00 0.00 36.54 2.75
39 40 7.724506 ACCGTCATTGTCTAATCCTAGATCTTA 59.275 37.037 0.00 0.00 36.54 2.10
40 41 8.240682 CCGTCATTGTCTAATCCTAGATCTTAG 58.759 40.741 0.00 0.00 36.54 2.18
42 43 9.084533 GTCATTGTCTAATCCTAGATCTTAGGT 57.915 37.037 0.00 0.00 36.54 3.08
43 44 9.661954 TCATTGTCTAATCCTAGATCTTAGGTT 57.338 33.333 0.00 0.00 36.54 3.50
48 49 9.752961 GTCTAATCCTAGATCTTAGGTTTTCAC 57.247 37.037 0.00 4.63 36.54 3.18
49 50 8.925338 TCTAATCCTAGATCTTAGGTTTTCACC 58.075 37.037 0.00 0.00 44.67 4.02
50 51 5.952347 TCCTAGATCTTAGGTTTTCACCC 57.048 43.478 0.00 0.00 45.63 4.61
51 52 5.600749 TCCTAGATCTTAGGTTTTCACCCT 58.399 41.667 0.00 0.00 45.63 4.34
52 53 5.425539 TCCTAGATCTTAGGTTTTCACCCTG 59.574 44.000 0.00 0.00 45.63 4.45
53 54 5.189934 CCTAGATCTTAGGTTTTCACCCTGT 59.810 44.000 0.00 0.00 45.63 4.00
54 55 6.383147 CCTAGATCTTAGGTTTTCACCCTGTA 59.617 42.308 0.00 0.00 45.63 2.74
55 56 6.697641 AGATCTTAGGTTTTCACCCTGTAA 57.302 37.500 0.00 0.00 45.63 2.41
59 60 6.902408 TCTTAGGTTTTCACCCTGTAAAAGA 58.098 36.000 0.00 0.00 45.63 2.52
60 61 7.523415 TCTTAGGTTTTCACCCTGTAAAAGAT 58.477 34.615 0.00 0.00 45.63 2.40
61 62 8.002459 TCTTAGGTTTTCACCCTGTAAAAGATT 58.998 33.333 0.00 0.00 45.63 2.40
62 63 6.650427 AGGTTTTCACCCTGTAAAAGATTC 57.350 37.500 0.00 0.00 45.63 2.52
64 65 4.759516 TTTCACCCTGTAAAAGATTCGC 57.240 40.909 0.00 0.00 0.00 4.70
65 66 2.343101 TCACCCTGTAAAAGATTCGCG 58.657 47.619 0.00 0.00 0.00 5.87
66 67 1.084289 ACCCTGTAAAAGATTCGCGC 58.916 50.000 0.00 0.00 0.00 6.86
67 68 1.338769 ACCCTGTAAAAGATTCGCGCT 60.339 47.619 5.56 0.00 0.00 5.92
68 69 1.327764 CCCTGTAAAAGATTCGCGCTC 59.672 52.381 5.56 0.00 0.00 5.03
69 70 2.271800 CCTGTAAAAGATTCGCGCTCT 58.728 47.619 5.56 2.72 0.00 4.09
70 71 2.282820 CCTGTAAAAGATTCGCGCTCTC 59.717 50.000 5.56 0.00 0.00 3.20
71 72 2.923655 CTGTAAAAGATTCGCGCTCTCA 59.076 45.455 5.56 0.00 0.00 3.27
72 73 3.322369 TGTAAAAGATTCGCGCTCTCAA 58.678 40.909 5.56 0.00 0.00 3.02
75 76 2.882742 AAGATTCGCGCTCTCAAAAC 57.117 45.000 5.56 0.00 0.00 2.43
76 77 1.795768 AGATTCGCGCTCTCAAAACA 58.204 45.000 5.56 0.00 0.00 2.83
78 79 2.744202 AGATTCGCGCTCTCAAAACAAT 59.256 40.909 5.56 0.00 0.00 2.71
79 80 2.314561 TTCGCGCTCTCAAAACAATG 57.685 45.000 5.56 0.00 0.00 2.82
80 81 0.110238 TCGCGCTCTCAAAACAATGC 60.110 50.000 5.56 0.00 0.00 3.56
82 83 0.242017 GCGCTCTCAAAACAATGCCT 59.758 50.000 0.00 0.00 0.00 4.75
83 84 1.336240 GCGCTCTCAAAACAATGCCTT 60.336 47.619 0.00 0.00 0.00 4.35
84 85 2.589014 CGCTCTCAAAACAATGCCTTC 58.411 47.619 0.00 0.00 0.00 3.46
86 87 3.550639 CGCTCTCAAAACAATGCCTTCAA 60.551 43.478 0.00 0.00 0.00 2.69
88 89 4.737352 GCTCTCAAAACAATGCCTTCAACA 60.737 41.667 0.00 0.00 0.00 3.33
89 90 5.336150 TCTCAAAACAATGCCTTCAACAA 57.664 34.783 0.00 0.00 0.00 2.83
100 101 2.643551 CCTTCAACAAGGTCACTGTGT 58.356 47.619 7.79 0.00 44.11 3.72
101 102 3.016736 CCTTCAACAAGGTCACTGTGTT 58.983 45.455 7.79 0.00 44.11 3.32
104 105 3.135414 CAACAAGGTCACTGTGTTGTG 57.865 47.619 13.76 8.37 44.51 3.33
106 107 0.381801 CAAGGTCACTGTGTTGTGGC 59.618 55.000 7.79 0.00 41.38 5.01
107 108 0.255890 AAGGTCACTGTGTTGTGGCT 59.744 50.000 7.79 0.00 41.76 4.75
108 109 0.255890 AGGTCACTGTGTTGTGGCTT 59.744 50.000 7.79 0.00 41.76 4.35
109 110 1.102978 GGTCACTGTGTTGTGGCTTT 58.897 50.000 7.79 0.00 41.76 3.51
110 111 1.065551 GGTCACTGTGTTGTGGCTTTC 59.934 52.381 7.79 0.00 41.76 2.62
111 112 1.742831 GTCACTGTGTTGTGGCTTTCA 59.257 47.619 7.79 0.00 39.26 2.69
112 113 2.358898 GTCACTGTGTTGTGGCTTTCAT 59.641 45.455 7.79 0.00 39.26 2.57
113 114 2.618241 TCACTGTGTTGTGGCTTTCATC 59.382 45.455 7.79 0.00 38.40 2.92
114 115 1.956477 ACTGTGTTGTGGCTTTCATCC 59.044 47.619 0.00 0.00 0.00 3.51
115 116 1.955778 CTGTGTTGTGGCTTTCATCCA 59.044 47.619 0.00 0.00 0.00 3.41
117 118 2.229792 GTGTTGTGGCTTTCATCCAGA 58.770 47.619 0.00 0.00 33.63 3.86
118 119 2.030805 GTGTTGTGGCTTTCATCCAGAC 60.031 50.000 0.00 0.00 33.63 3.51
119 120 2.158623 TGTTGTGGCTTTCATCCAGACT 60.159 45.455 0.00 0.00 33.63 3.24
120 121 2.887152 GTTGTGGCTTTCATCCAGACTT 59.113 45.455 0.00 0.00 33.63 3.01
121 122 3.228188 TGTGGCTTTCATCCAGACTTT 57.772 42.857 0.00 0.00 33.63 2.66
122 123 3.565307 TGTGGCTTTCATCCAGACTTTT 58.435 40.909 0.00 0.00 33.63 2.27
123 124 3.569701 TGTGGCTTTCATCCAGACTTTTC 59.430 43.478 0.00 0.00 33.63 2.29
124 125 3.823304 GTGGCTTTCATCCAGACTTTTCT 59.177 43.478 0.00 0.00 33.63 2.52
126 127 4.895297 TGGCTTTCATCCAGACTTTTCTTT 59.105 37.500 0.00 0.00 0.00 2.52
127 128 5.010012 TGGCTTTCATCCAGACTTTTCTTTC 59.990 40.000 0.00 0.00 0.00 2.62
408 409 4.351111 TCTCTGTTTCTAGGGGCTTTTCTT 59.649 41.667 0.00 0.00 0.00 2.52
409 410 5.061721 TCTGTTTCTAGGGGCTTTTCTTT 57.938 39.130 0.00 0.00 0.00 2.52
410 411 5.070685 TCTGTTTCTAGGGGCTTTTCTTTC 58.929 41.667 0.00 0.00 0.00 2.62
411 412 4.149598 TGTTTCTAGGGGCTTTTCTTTCC 58.850 43.478 0.00 0.00 0.00 3.13
412 413 4.141018 TGTTTCTAGGGGCTTTTCTTTCCT 60.141 41.667 0.00 0.00 0.00 3.36
424 425 7.316640 GGCTTTTCTTTCCTCTCTTTATTTCC 58.683 38.462 0.00 0.00 0.00 3.13
428 429 7.668525 TTCTTTCCTCTCTTTATTTCCGTTC 57.331 36.000 0.00 0.00 0.00 3.95
435 436 6.210287 TCTCTTTATTTCCGTTCTCTCCTC 57.790 41.667 0.00 0.00 0.00 3.71
469 470 5.957842 AGCATTTCGTCACCATCTTTTAA 57.042 34.783 0.00 0.00 0.00 1.52
470 471 6.515272 AGCATTTCGTCACCATCTTTTAAT 57.485 33.333 0.00 0.00 0.00 1.40
486 487 9.421806 CATCTTTTAATTGCCATTGTTCAACTA 57.578 29.630 0.00 0.00 0.00 2.24
487 488 8.810652 TCTTTTAATTGCCATTGTTCAACTAC 57.189 30.769 0.00 0.00 0.00 2.73
494 495 9.777297 AATTGCCATTGTTCAACTACTAATTTT 57.223 25.926 0.00 0.00 0.00 1.82
547 548 5.818136 TTCTTTCTATGCTCCATTTTCGG 57.182 39.130 0.00 0.00 0.00 4.30
549 550 5.984725 TCTTTCTATGCTCCATTTTCGGTA 58.015 37.500 0.00 0.00 0.00 4.02
550 551 6.049149 TCTTTCTATGCTCCATTTTCGGTAG 58.951 40.000 0.00 0.00 0.00 3.18
552 553 5.607939 TCTATGCTCCATTTTCGGTAGAA 57.392 39.130 0.00 0.00 33.98 2.10
553 554 5.357257 TCTATGCTCCATTTTCGGTAGAAC 58.643 41.667 0.00 0.00 35.86 3.01
556 557 3.260884 TGCTCCATTTTCGGTAGAACTCT 59.739 43.478 0.00 0.00 35.86 3.24
605 610 3.470709 CATTTCGTGGGCATGTCTAGAT 58.529 45.455 0.00 0.00 0.00 1.98
664 669 6.324770 GTCCCAATCCAATCCAAGTATCAATT 59.675 38.462 0.00 0.00 0.00 2.32
712 746 0.687354 AGCTTTCCACGTGACCATCT 59.313 50.000 19.30 5.46 0.00 2.90
739 773 3.620427 TTTGCAGGTATCCACGTGTAT 57.380 42.857 15.65 6.86 41.56 2.29
755 789 2.480419 GTGTATGCACGCATCTATTCCC 59.520 50.000 7.99 0.00 37.82 3.97
788 822 3.751479 TTCCTCCATCCATATCGTGTG 57.249 47.619 0.00 0.00 0.00 3.82
894 928 0.757935 GGACCACCACTCCGCCTATA 60.758 60.000 0.00 0.00 35.97 1.31
895 929 1.339097 GACCACCACTCCGCCTATAT 58.661 55.000 0.00 0.00 0.00 0.86
897 931 2.492484 GACCACCACTCCGCCTATATAG 59.508 54.545 2.46 2.46 0.00 1.31
922 956 2.737252 GTTGAAACTCACCCTGATCGAC 59.263 50.000 0.00 0.00 0.00 4.20
991 1606 2.228822 CCCAAGAAAACCACAAGGATCG 59.771 50.000 0.00 0.00 38.69 3.69
1029 1644 1.339151 GCGAAGGTGAAGGTGAAGGAT 60.339 52.381 0.00 0.00 0.00 3.24
1266 1881 2.118404 CCACAACCACAAGCACGGT 61.118 57.895 0.00 0.00 36.98 4.83
1288 1903 1.089481 CGGTGGCGTGCACTGATATT 61.089 55.000 16.19 0.00 0.00 1.28
1361 1990 6.986817 TCTATTCTTTTAGCTGATGTACTGCC 59.013 38.462 0.00 0.00 43.01 4.85
1434 2063 4.512198 TGTGATTTTGTTGACGTTATCGGT 59.488 37.500 0.00 0.00 41.85 4.69
1536 2185 3.499338 TCATGTCCATGTTTTTGCTCCT 58.501 40.909 7.13 0.00 39.72 3.69
1543 2192 6.491745 TGTCCATGTTTTTGCTCCTATACAAA 59.508 34.615 0.00 0.00 34.11 2.83
1544 2193 7.014711 TGTCCATGTTTTTGCTCCTATACAAAA 59.985 33.333 0.00 0.00 42.37 2.44
1586 2235 1.359475 GAAGCTACGGACCTAGGCG 59.641 63.158 9.30 8.07 0.00 5.52
1587 2236 2.680693 GAAGCTACGGACCTAGGCGC 62.681 65.000 9.30 0.00 0.00 6.53
1588 2237 3.524606 GCTACGGACCTAGGCGCA 61.525 66.667 10.83 0.00 0.00 6.09
1589 2238 2.412112 CTACGGACCTAGGCGCAC 59.588 66.667 10.83 0.00 0.00 5.34
1606 2258 3.671971 GCGCACCAAGCAAACAACATATA 60.672 43.478 0.30 0.00 46.13 0.86
1616 2268 9.416794 CAAGCAAACAACATATACCATGTAAAA 57.583 29.630 0.00 0.00 0.00 1.52
1643 2295 8.877779 CAAAATTATAATTCCGCAATGAAACCA 58.122 29.630 11.08 0.00 0.00 3.67
1686 2338 5.763876 ACCCTAGAATCTAATATGGTGGC 57.236 43.478 0.00 0.00 0.00 5.01
1689 2341 5.411781 CCTAGAATCTAATATGGTGGCGTC 58.588 45.833 0.00 0.00 0.00 5.19
1783 2436 7.324178 GCTACTATTATCTTATGGTGGGTCAG 58.676 42.308 0.00 0.00 0.00 3.51
1794 2447 0.608640 GTGGGTCAGTGTCGAAGGAT 59.391 55.000 0.00 0.00 0.00 3.24
1856 2515 1.477014 GCCAAAGCCCCTACTATGTCC 60.477 57.143 0.00 0.00 0.00 4.02
1857 2516 1.143073 CCAAAGCCCCTACTATGTCCC 59.857 57.143 0.00 0.00 0.00 4.46
1870 2529 2.795231 ATGTCCCATGACTCCTGTTG 57.205 50.000 0.00 0.00 42.28 3.33
1885 2544 0.034337 TGTTGGTACTCCTCAACCGC 59.966 55.000 9.36 0.00 41.64 5.68
1886 2545 0.034337 GTTGGTACTCCTCAACCGCA 59.966 55.000 0.00 0.00 38.70 5.69
1887 2546 0.981183 TTGGTACTCCTCAACCGCAT 59.019 50.000 0.00 0.00 38.70 4.73
1888 2547 0.981183 TGGTACTCCTCAACCGCATT 59.019 50.000 0.00 0.00 38.70 3.56
1889 2548 1.066430 TGGTACTCCTCAACCGCATTC 60.066 52.381 0.00 0.00 38.70 2.67
1890 2549 1.278238 GTACTCCTCAACCGCATTCG 58.722 55.000 0.00 0.00 0.00 3.34
1891 2550 0.459585 TACTCCTCAACCGCATTCGC 60.460 55.000 0.00 0.00 0.00 4.70
1902 2561 3.909137 GCATTCGCGCTTACTATCG 57.091 52.632 5.56 0.00 0.00 2.92
1903 2562 0.435008 GCATTCGCGCTTACTATCGG 59.565 55.000 5.56 0.00 0.00 4.18
1904 2563 1.929038 GCATTCGCGCTTACTATCGGA 60.929 52.381 5.56 0.00 0.00 4.55
1905 2564 2.596452 CATTCGCGCTTACTATCGGAT 58.404 47.619 5.56 0.00 0.00 4.18
1906 2565 2.327081 TTCGCGCTTACTATCGGATC 57.673 50.000 5.56 0.00 0.00 3.36
1907 2566 0.520404 TCGCGCTTACTATCGGATCC 59.480 55.000 5.56 0.00 0.00 3.36
1908 2567 0.522180 CGCGCTTACTATCGGATCCT 59.478 55.000 10.75 0.00 0.00 3.24
1909 2568 1.466024 CGCGCTTACTATCGGATCCTC 60.466 57.143 10.75 0.00 0.00 3.71
1910 2569 1.135344 GCGCTTACTATCGGATCCTCC 60.135 57.143 10.75 0.00 0.00 4.30
1911 2570 1.473278 CGCTTACTATCGGATCCTCCC 59.527 57.143 10.75 0.00 31.13 4.30
1936 2622 1.070914 GAGGGATCCGATTGTTCCTCC 59.929 57.143 5.45 0.00 35.89 4.30
1995 2681 7.808218 TCTTAAGAAGAAGTAACCAAGGGAAA 58.192 34.615 1.68 0.00 33.83 3.13
2015 2707 5.747197 GGAAAGACGATATGCTAGACGAAAA 59.253 40.000 0.00 0.00 0.00 2.29
2023 2717 4.521130 ATGCTAGACGAAAACACTGAGA 57.479 40.909 0.00 0.00 0.00 3.27
2090 2784 4.545610 GATTCTCTCTCGCTGATAAGTGG 58.454 47.826 0.00 0.00 0.00 4.00
2123 2817 3.424703 CAAGGGAAGCATGAGAAAGGAA 58.575 45.455 0.00 0.00 0.00 3.36
2125 2819 3.425659 AGGGAAGCATGAGAAAGGAAAC 58.574 45.455 0.00 0.00 0.00 2.78
2203 2897 2.124278 GGGGAGGCCGAAACATCC 60.124 66.667 0.00 0.00 0.00 3.51
2204 2898 2.513897 GGGAGGCCGAAACATCCG 60.514 66.667 0.00 0.00 32.30 4.18
2227 2921 4.451096 GCTTTGTTTGGAGAACTCACGATA 59.549 41.667 4.23 0.00 0.00 2.92
2246 2940 4.449405 CGATACTCTCTCGCTGATAAGTGA 59.551 45.833 0.00 0.00 0.00 3.41
2272 2966 1.271597 ACTAGGCAAGGGAAGCACAAG 60.272 52.381 0.00 0.00 0.00 3.16
2279 2973 2.278332 AGGGAAGCACAAGAAAGGAC 57.722 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.454957 GACAATGACGGTGCATGTGC 60.455 55.000 0.00 0.00 42.50 4.57
6 7 1.159285 AGACAATGACGGTGCATGTG 58.841 50.000 0.00 0.00 0.00 3.21
9 10 3.118261 AGGATTAGACAATGACGGTGCAT 60.118 43.478 0.00 0.00 0.00 3.96
10 11 2.236146 AGGATTAGACAATGACGGTGCA 59.764 45.455 0.00 0.00 0.00 4.57
12 13 5.515797 TCTAGGATTAGACAATGACGGTG 57.484 43.478 0.00 0.00 30.96 4.94
14 15 6.582677 AGATCTAGGATTAGACAATGACGG 57.417 41.667 0.00 0.00 38.69 4.79
15 16 8.240682 CCTAAGATCTAGGATTAGACAATGACG 58.759 40.741 10.96 0.00 38.69 4.35
21 22 9.488762 TGAAAACCTAAGATCTAGGATTAGACA 57.511 33.333 19.24 13.27 38.69 3.41
22 23 9.752961 GTGAAAACCTAAGATCTAGGATTAGAC 57.247 37.037 19.24 12.12 38.69 2.59
23 24 8.925338 GGTGAAAACCTAAGATCTAGGATTAGA 58.075 37.037 19.24 6.62 40.10 2.10
25 26 7.849904 AGGGTGAAAACCTAAGATCTAGGATTA 59.150 37.037 19.24 0.00 36.32 1.75
28 29 5.425539 CAGGGTGAAAACCTAAGATCTAGGA 59.574 44.000 19.24 0.00 36.32 2.94
31 32 7.801893 TTACAGGGTGAAAACCTAAGATCTA 57.198 36.000 0.00 0.00 36.32 1.98
32 33 6.697641 TTACAGGGTGAAAACCTAAGATCT 57.302 37.500 0.00 0.00 36.32 2.75
33 34 7.664318 TCTTTTACAGGGTGAAAACCTAAGATC 59.336 37.037 0.00 0.00 36.32 2.75
34 35 7.523415 TCTTTTACAGGGTGAAAACCTAAGAT 58.477 34.615 0.00 0.00 36.32 2.40
35 36 6.902408 TCTTTTACAGGGTGAAAACCTAAGA 58.098 36.000 0.00 0.00 36.32 2.10
36 37 7.761038 ATCTTTTACAGGGTGAAAACCTAAG 57.239 36.000 0.00 0.00 36.32 2.18
37 38 7.040961 CGAATCTTTTACAGGGTGAAAACCTAA 60.041 37.037 0.00 0.00 36.32 2.69
39 40 5.240844 CGAATCTTTTACAGGGTGAAAACCT 59.759 40.000 0.00 0.00 39.43 3.50
40 41 5.458015 CGAATCTTTTACAGGGTGAAAACC 58.542 41.667 0.00 0.00 0.00 3.27
42 43 4.319911 CGCGAATCTTTTACAGGGTGAAAA 60.320 41.667 0.00 0.00 0.00 2.29
43 44 3.187637 CGCGAATCTTTTACAGGGTGAAA 59.812 43.478 0.00 0.00 0.00 2.69
44 45 2.739913 CGCGAATCTTTTACAGGGTGAA 59.260 45.455 0.00 0.00 0.00 3.18
45 46 2.343101 CGCGAATCTTTTACAGGGTGA 58.657 47.619 0.00 0.00 0.00 4.02
46 47 1.202031 GCGCGAATCTTTTACAGGGTG 60.202 52.381 12.10 0.00 0.00 4.61
48 49 1.327764 GAGCGCGAATCTTTTACAGGG 59.672 52.381 12.10 0.00 0.00 4.45
49 50 2.271800 AGAGCGCGAATCTTTTACAGG 58.728 47.619 12.10 0.00 0.00 4.00
50 51 2.923655 TGAGAGCGCGAATCTTTTACAG 59.076 45.455 12.10 0.00 0.00 2.74
51 52 2.954316 TGAGAGCGCGAATCTTTTACA 58.046 42.857 12.10 3.52 0.00 2.41
52 53 3.991605 TTGAGAGCGCGAATCTTTTAC 57.008 42.857 12.10 0.66 0.00 2.01
53 54 4.212425 TGTTTTGAGAGCGCGAATCTTTTA 59.788 37.500 12.10 0.40 0.00 1.52
54 55 3.003275 TGTTTTGAGAGCGCGAATCTTTT 59.997 39.130 12.10 0.00 0.00 2.27
55 56 2.548057 TGTTTTGAGAGCGCGAATCTTT 59.452 40.909 12.10 0.00 0.00 2.52
59 60 2.855180 CATTGTTTTGAGAGCGCGAAT 58.145 42.857 12.10 0.00 0.00 3.34
60 61 1.662876 GCATTGTTTTGAGAGCGCGAA 60.663 47.619 12.10 0.00 0.00 4.70
61 62 0.110238 GCATTGTTTTGAGAGCGCGA 60.110 50.000 12.10 0.00 0.00 5.87
62 63 1.067199 GGCATTGTTTTGAGAGCGCG 61.067 55.000 0.00 0.00 0.00 6.86
64 65 2.030893 TGAAGGCATTGTTTTGAGAGCG 60.031 45.455 0.00 0.00 0.00 5.03
65 66 3.648339 TGAAGGCATTGTTTTGAGAGC 57.352 42.857 0.00 0.00 0.00 4.09
66 67 4.935702 TGTTGAAGGCATTGTTTTGAGAG 58.064 39.130 0.00 0.00 0.00 3.20
67 68 4.998671 TGTTGAAGGCATTGTTTTGAGA 57.001 36.364 0.00 0.00 0.00 3.27
68 69 4.508861 CCTTGTTGAAGGCATTGTTTTGAG 59.491 41.667 0.00 0.00 42.60 3.02
69 70 4.440880 CCTTGTTGAAGGCATTGTTTTGA 58.559 39.130 0.00 0.00 42.60 2.69
70 71 4.799419 CCTTGTTGAAGGCATTGTTTTG 57.201 40.909 0.00 0.00 42.60 2.44
86 87 1.750193 CCACAACACAGTGACCTTGT 58.250 50.000 7.81 4.84 42.05 3.16
88 89 0.255890 AGCCACAACACAGTGACCTT 59.744 50.000 7.81 0.00 42.05 3.50
89 90 0.255890 AAGCCACAACACAGTGACCT 59.744 50.000 7.81 0.00 42.05 3.85
91 92 1.742831 TGAAAGCCACAACACAGTGAC 59.257 47.619 7.81 0.00 42.05 3.67
93 94 2.287788 GGATGAAAGCCACAACACAGTG 60.288 50.000 0.00 0.00 46.15 3.66
95 96 2.712057 GGATGAAAGCCACAACACAG 57.288 50.000 0.00 0.00 46.15 3.66
385 386 3.910627 AGAAAAGCCCCTAGAAACAGAGA 59.089 43.478 0.00 0.00 0.00 3.10
386 387 4.293662 AGAAAAGCCCCTAGAAACAGAG 57.706 45.455 0.00 0.00 0.00 3.35
390 391 4.408276 AGGAAAGAAAAGCCCCTAGAAAC 58.592 43.478 0.00 0.00 0.00 2.78
393 394 3.519913 GAGAGGAAAGAAAAGCCCCTAGA 59.480 47.826 0.00 0.00 0.00 2.43
394 395 3.521531 AGAGAGGAAAGAAAAGCCCCTAG 59.478 47.826 0.00 0.00 0.00 3.02
395 396 3.532102 AGAGAGGAAAGAAAAGCCCCTA 58.468 45.455 0.00 0.00 0.00 3.53
396 397 2.353349 AGAGAGGAAAGAAAAGCCCCT 58.647 47.619 0.00 0.00 0.00 4.79
398 399 6.842437 AATAAAGAGAGGAAAGAAAAGCCC 57.158 37.500 0.00 0.00 0.00 5.19
401 402 8.100508 ACGGAAATAAAGAGAGGAAAGAAAAG 57.899 34.615 0.00 0.00 0.00 2.27
402 403 8.459911 AACGGAAATAAAGAGAGGAAAGAAAA 57.540 30.769 0.00 0.00 0.00 2.29
403 404 7.937394 AGAACGGAAATAAAGAGAGGAAAGAAA 59.063 33.333 0.00 0.00 0.00 2.52
405 406 7.005709 AGAACGGAAATAAAGAGAGGAAAGA 57.994 36.000 0.00 0.00 0.00 2.52
408 409 6.351117 GGAGAGAACGGAAATAAAGAGAGGAA 60.351 42.308 0.00 0.00 0.00 3.36
409 410 5.127356 GGAGAGAACGGAAATAAAGAGAGGA 59.873 44.000 0.00 0.00 0.00 3.71
410 411 5.128008 AGGAGAGAACGGAAATAAAGAGAGG 59.872 44.000 0.00 0.00 0.00 3.69
411 412 6.096282 AGAGGAGAGAACGGAAATAAAGAGAG 59.904 42.308 0.00 0.00 0.00 3.20
412 413 5.952947 AGAGGAGAGAACGGAAATAAAGAGA 59.047 40.000 0.00 0.00 0.00 3.10
424 425 1.099689 GGTGGAGAGAGGAGAGAACG 58.900 60.000 0.00 0.00 0.00 3.95
428 429 2.627699 GCTATTGGTGGAGAGAGGAGAG 59.372 54.545 0.00 0.00 0.00 3.20
435 436 3.535561 ACGAAATGCTATTGGTGGAGAG 58.464 45.455 0.00 0.00 0.00 3.20
469 470 9.206870 CAAAATTAGTAGTTGAACAATGGCAAT 57.793 29.630 0.00 0.00 0.00 3.56
470 471 8.417106 TCAAAATTAGTAGTTGAACAATGGCAA 58.583 29.630 0.00 0.00 0.00 4.52
486 487 7.708752 TCAAGCGGAACAAATTTCAAAATTAGT 59.291 29.630 1.36 0.00 37.62 2.24
487 488 8.071122 TCAAGCGGAACAAATTTCAAAATTAG 57.929 30.769 1.36 0.00 37.62 1.73
494 495 8.519526 ACTAAATATCAAGCGGAACAAATTTCA 58.480 29.630 0.00 0.00 0.00 2.69
527 528 6.049149 TCTACCGAAAATGGAGCATAGAAAG 58.951 40.000 0.00 0.00 0.00 2.62
545 546 6.586844 CCAACTAGAAGAAAAGAGTTCTACCG 59.413 42.308 0.00 0.00 34.76 4.02
546 547 7.668492 TCCAACTAGAAGAAAAGAGTTCTACC 58.332 38.462 0.00 0.00 34.76 3.18
549 550 9.713713 GTTATCCAACTAGAAGAAAAGAGTTCT 57.286 33.333 0.00 0.00 36.90 3.01
550 551 9.713713 AGTTATCCAACTAGAAGAAAAGAGTTC 57.286 33.333 0.00 0.00 43.33 3.01
552 553 9.713713 GAAGTTATCCAACTAGAAGAAAAGAGT 57.286 33.333 0.00 0.00 44.41 3.24
553 554 9.712305 TGAAGTTATCCAACTAGAAGAAAAGAG 57.288 33.333 0.00 0.00 44.41 2.85
556 557 9.621629 TTGTGAAGTTATCCAACTAGAAGAAAA 57.378 29.630 0.00 0.00 44.41 2.29
631 636 3.638627 GGATTGGATTGGGACAGGAAATC 59.361 47.826 0.00 0.00 42.39 2.17
664 669 3.433306 AAGTGGATTTGGTCGGAATGA 57.567 42.857 0.00 0.00 0.00 2.57
724 758 2.596904 GTGCATACACGTGGATACCT 57.403 50.000 21.57 0.00 36.98 3.08
739 773 1.209261 TGAAGGGAATAGATGCGTGCA 59.791 47.619 0.00 0.00 0.00 4.57
755 789 5.945784 TGGATGGAGGAAATACAAAGTGAAG 59.054 40.000 0.00 0.00 0.00 3.02
788 822 1.299976 CCTGGCCTGGTAACTGTCC 59.700 63.158 20.28 0.00 37.61 4.02
894 928 6.187727 TCAGGGTGAGTTTCAACTTTCTAT 57.812 37.500 0.00 0.00 39.88 1.98
895 929 5.623956 TCAGGGTGAGTTTCAACTTTCTA 57.376 39.130 0.00 0.00 39.88 2.10
897 931 4.083802 CGATCAGGGTGAGTTTCAACTTTC 60.084 45.833 0.00 0.00 39.88 2.62
922 956 6.020041 GCTTGAGCTTCTTCTTTGTTTTCTTG 60.020 38.462 0.00 0.00 38.21 3.02
991 1606 1.136147 CTTGCTGCATCTCGTTGGC 59.864 57.895 1.84 0.00 0.00 4.52
1047 1662 1.448540 CACGATCTTCGCCTTGGCT 60.449 57.895 10.12 0.00 45.12 4.75
1586 2235 4.173256 GGTATATGTTGTTTGCTTGGTGC 58.827 43.478 0.00 0.00 43.25 5.01
1587 2236 5.384063 TGGTATATGTTGTTTGCTTGGTG 57.616 39.130 0.00 0.00 0.00 4.17
1588 2237 5.480073 ACATGGTATATGTTGTTTGCTTGGT 59.520 36.000 0.00 0.00 0.00 3.67
1589 2238 5.964758 ACATGGTATATGTTGTTTGCTTGG 58.035 37.500 0.00 0.00 0.00 3.61
1616 2268 8.878769 GGTTTCATTGCGGAATTATAATTTTGT 58.121 29.630 11.92 0.00 0.00 2.83
1631 2283 4.398044 ACCTTATTACCTGGTTTCATTGCG 59.602 41.667 3.84 0.00 0.00 4.85
1638 2290 7.466804 TCAAGATGAACCTTATTACCTGGTTT 58.533 34.615 3.84 0.00 43.28 3.27
1686 2338 2.561733 ATAGTGTCATCACCACGACG 57.438 50.000 0.00 0.00 44.83 5.12
1689 2341 3.245518 TCCAATAGTGTCATCACCACG 57.754 47.619 0.00 0.00 44.83 4.94
1762 2415 7.067496 ACACTGACCCACCATAAGATAATAG 57.933 40.000 0.00 0.00 0.00 1.73
1765 2418 4.142026 CGACACTGACCCACCATAAGATAA 60.142 45.833 0.00 0.00 0.00 1.75
1772 2425 0.321671 CTTCGACACTGACCCACCAT 59.678 55.000 0.00 0.00 0.00 3.55
1778 2431 0.741221 GGCATCCTTCGACACTGACC 60.741 60.000 0.00 0.00 0.00 4.02
1783 2436 1.718757 GGCATGGCATCCTTCGACAC 61.719 60.000 15.47 0.00 0.00 3.67
1856 2515 2.093447 GGAGTACCAACAGGAGTCATGG 60.093 54.545 9.95 5.92 38.91 3.66
1857 2516 2.834549 AGGAGTACCAACAGGAGTCATG 59.165 50.000 2.61 2.61 38.94 3.07
1870 2529 1.653151 GAATGCGGTTGAGGAGTACC 58.347 55.000 0.00 0.00 0.00 3.34
1885 2544 2.046283 TCCGATAGTAAGCGCGAATG 57.954 50.000 12.10 0.00 31.79 2.67
1886 2545 2.415625 GGATCCGATAGTAAGCGCGAAT 60.416 50.000 12.10 0.00 31.79 3.34
1887 2546 1.068748 GGATCCGATAGTAAGCGCGAA 60.069 52.381 12.10 0.00 31.79 4.70
1888 2547 0.520404 GGATCCGATAGTAAGCGCGA 59.480 55.000 12.10 0.00 31.79 5.87
1889 2548 0.522180 AGGATCCGATAGTAAGCGCG 59.478 55.000 5.98 0.00 31.79 6.86
1890 2549 2.265647 GAGGATCCGATAGTAAGCGC 57.734 55.000 5.98 0.00 31.79 5.92
1911 2570 0.767375 ACAATCGGATCCCTCCATGG 59.233 55.000 4.97 4.97 42.19 3.66
1936 2622 4.986587 TCGACACCGTTCGCACCG 62.987 66.667 0.00 0.00 38.95 4.94
1995 2681 5.035443 GTGTTTTCGTCTAGCATATCGTCT 58.965 41.667 0.00 0.00 0.00 4.18
2023 2717 3.285484 CCTGCATCCAAGATTTACTGCT 58.715 45.455 0.00 0.00 0.00 4.24
2090 2784 2.044946 CCCTTGCCTAGTGGTGCC 60.045 66.667 0.00 0.00 35.27 5.01
2123 2817 3.704381 GACTCATGTCGCTCTCGTT 57.296 52.632 0.00 0.00 36.96 3.85
2203 2897 2.599848 CGTGAGTTCTCCAAACAAAGCG 60.600 50.000 0.00 0.00 0.00 4.68
2204 2898 2.612212 TCGTGAGTTCTCCAAACAAAGC 59.388 45.455 0.00 0.00 0.00 3.51
2227 2921 2.357637 GCTCACTTATCAGCGAGAGAGT 59.642 50.000 0.00 0.00 31.62 3.24
2246 2940 1.133809 TTCCCTTGCCTAGTGGTGCT 61.134 55.000 0.00 0.00 35.27 4.40


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

AutoCloner maintained by Alex Coulton.