Multiple sequence alignment - TraesCS7D01G135800

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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 TraesCS7D01G135800 chr7D 100.000 3210 0 0 1 3210 87219529 87222738 0.000000e+00 5928.0
1 TraesCS7D01G135800 chr7D 95.328 899 36 5 947 1842 87206445 87207340 0.000000e+00 1423.0
2 TraesCS7D01G135800 chr7D 100.000 457 0 0 3645 4101 87223173 87223629 0.000000e+00 845.0
3 TraesCS7D01G135800 chr7D 92.056 428 32 2 1416 1842 86919030 86919456 5.870000e-168 601.0
4 TraesCS7D01G135800 chr7D 91.355 428 34 3 1416 1842 86755540 86755965 2.120000e-162 582.0
5 TraesCS7D01G135800 chr7D 88.981 481 33 9 1371 1842 86292328 86292797 9.880000e-161 577.0
6 TraesCS7D01G135800 chr7D 90.789 380 21 8 789 1162 86754993 86755364 2.850000e-136 496.0
7 TraesCS7D01G135800 chr7D 90.000 380 25 7 789 1162 86918482 86918854 2.870000e-131 479.0
8 TraesCS7D01G135800 chr7D 85.613 424 44 6 1 409 91778983 91779404 2.930000e-116 429.0
9 TraesCS7D01G135800 chr7D 85.142 424 44 6 1 409 91748651 91749070 2.280000e-112 416.0
10 TraesCS7D01G135800 chr7D 96.316 190 7 0 1203 1392 86918849 86919038 3.080000e-81 313.0
11 TraesCS7D01G135800 chr7D 86.809 235 28 3 2091 2325 86292911 86293142 4.070000e-65 259.0
12 TraesCS7D01G135800 chr7D 91.803 183 14 1 2091 2272 87207453 87207635 1.890000e-63 254.0
13 TraesCS7D01G135800 chr7D 84.082 245 33 5 485 727 86753556 86753796 8.870000e-57 231.0
14 TraesCS7D01G135800 chr7D 100.000 28 0 0 924 951 87206170 87206197 7.000000e-03 52.8
15 TraesCS7D01G135800 chr7A 96.007 1177 36 7 762 1931 88500082 88501254 0.000000e+00 1903.0
16 TraesCS7D01G135800 chr7A 95.688 1090 33 11 762 1842 88435713 88436797 0.000000e+00 1740.0
17 TraesCS7D01G135800 chr7A 96.169 1018 30 5 2200 3209 88501276 88502292 0.000000e+00 1655.0
18 TraesCS7D01G135800 chr7A 92.779 914 58 7 933 1842 88315480 88316389 0.000000e+00 1315.0
19 TraesCS7D01G135800 chr7A 88.622 791 69 6 1 778 88188139 88188921 0.000000e+00 942.0
20 TraesCS7D01G135800 chr7A 82.677 1143 99 50 731 1842 87451043 87452117 0.000000e+00 922.0
21 TraesCS7D01G135800 chr7A 87.990 791 73 6 1 778 88144209 88144990 0.000000e+00 915.0
22 TraesCS7D01G135800 chr7A 93.729 606 31 3 189 790 88435110 88435712 0.000000e+00 902.0
23 TraesCS7D01G135800 chr7A 93.698 603 34 2 189 790 88499482 88500081 0.000000e+00 900.0
24 TraesCS7D01G135800 chr7A 89.327 609 34 14 789 1392 88008334 88008916 0.000000e+00 736.0
25 TraesCS7D01G135800 chr7A 94.588 425 22 1 3663 4086 88502294 88502718 0.000000e+00 656.0
26 TraesCS7D01G135800 chr7A 88.462 520 29 11 878 1392 88172469 88172962 2.110000e-167 599.0
27 TraesCS7D01G135800 chr7A 89.027 401 32 3 1 389 88035307 88035707 1.710000e-133 486.0
28 TraesCS7D01G135800 chr7A 88.342 386 37 4 393 778 88047215 88047592 1.340000e-124 457.0
29 TraesCS7D01G135800 chr7A 85.804 317 40 3 412 727 88119764 88120076 8.500000e-87 331.0
30 TraesCS7D01G135800 chr7A 89.524 210 10 1 1 198 88429757 88429966 5.260000e-64 255.0
31 TraesCS7D01G135800 chr7A 89.048 210 11 1 1 198 88494102 88494311 2.450000e-62 250.0
32 TraesCS7D01G135800 chr7A 90.164 183 17 1 2091 2272 88316502 88316684 1.910000e-58 237.0
33 TraesCS7D01G135800 chr7A 90.164 183 15 3 2091 2272 88436910 88437090 6.850000e-58 235.0
34 TraesCS7D01G135800 chr7A 84.375 160 19 5 789 947 88121353 88121507 7.100000e-33 152.0
35 TraesCS7D01G135800 chr7B 96.338 1147 38 4 2065 3209 35638327 35639471 0.000000e+00 1882.0
36 TraesCS7D01G135800 chr7B 92.736 1239 56 10 721 1931 35637095 35638327 0.000000e+00 1759.0
37 TraesCS7D01G135800 chr7B 85.730 904 61 22 947 1842 35307638 35308481 0.000000e+00 893.0
38 TraesCS7D01G135800 chr7B 90.539 687 43 11 721 1395 35507037 35507713 0.000000e+00 889.0
39 TraesCS7D01G135800 chr7B 88.529 741 63 6 1 727 35636338 35637070 0.000000e+00 878.0
40 TraesCS7D01G135800 chr7B 96.073 331 13 0 3663 3993 35639473 35639803 1.300000e-149 540.0
41 TraesCS7D01G135800 chr7B 89.019 428 43 4 1416 1842 35507702 35508126 1.010000e-145 527.0
42 TraesCS7D01G135800 chr7B 88.050 318 34 3 412 728 35506699 35507013 1.390000e-99 374.0
43 TraesCS7D01G135800 chr7B 95.556 225 9 1 3862 4086 35639802 35640025 3.900000e-95 359.0
44 TraesCS7D01G135800 chr7B 89.677 155 12 2 809 963 35301965 35302115 1.160000e-45 195.0
45 TraesCS7D01G135800 chr1D 86.588 425 45 3 1 413 439108547 439108971 3.740000e-125 459.0
46 TraesCS7D01G135800 chr1D 86.260 393 41 2 2 381 293617395 293617003 8.200000e-112 414.0
47 TraesCS7D01G135800 chr3D 86.667 420 43 4 1 408 123618627 123619045 1.740000e-123 453.0
48 TraesCS7D01G135800 chr2B 84.186 430 39 9 1 410 741122198 741121778 1.380000e-104 390.0
49 TraesCS7D01G135800 chr1B 84.635 384 57 2 11 393 532405962 532406344 8.320000e-102 381.0
50 TraesCS7D01G135800 chr2D 83.092 414 57 10 1 408 645994568 645994974 8.380000e-97 364.0
51 TraesCS7D01G135800 chr2D 98.519 135 2 0 1931 2065 33935356 33935490 5.300000e-59 239.0
52 TraesCS7D01G135800 chr2D 98.519 135 2 0 1931 2065 630271832 630271966 5.300000e-59 239.0
53 TraesCS7D01G135800 chr4A 99.259 135 1 0 1931 2065 310763952 310764086 1.140000e-60 244.0
54 TraesCS7D01G135800 chrUn 98.519 135 2 0 1931 2065 371049993 371050127 5.300000e-59 239.0
55 TraesCS7D01G135800 chr5B 98.519 135 2 0 1931 2065 429038227 429038361 5.300000e-59 239.0
56 TraesCS7D01G135800 chr5B 98.519 135 2 0 1931 2065 432878267 432878401 5.300000e-59 239.0
57 TraesCS7D01G135800 chr5B 86.765 136 6 4 1 124 387146022 387145887 1.540000e-29 141.0
58 TraesCS7D01G135800 chr3B 97.183 142 2 1 1931 2072 201559228 201559089 5.300000e-59 239.0
59 TraesCS7D01G135800 chr1A 98.519 135 2 0 1931 2065 371922680 371922814 5.300000e-59 239.0
60 TraesCS7D01G135800 chr3A 97.183 142 1 2 1931 2072 672876888 672876750 1.910000e-58 237.0


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 TraesCS7D01G135800 chr7D 87219529 87223629 4100 False 3386.500000 5928 100.000000 1 4101 2 chr7D.!!$F7 4100
1 TraesCS7D01G135800 chr7D 87206170 87207635 1465 False 576.600000 1423 95.710333 924 2272 3 chr7D.!!$F6 1348
2 TraesCS7D01G135800 chr7D 86918482 86919456 974 False 464.333333 601 92.790667 789 1842 3 chr7D.!!$F5 1053
3 TraesCS7D01G135800 chr7D 86753556 86755965 2409 False 436.333333 582 88.742000 485 1842 3 chr7D.!!$F4 1357
4 TraesCS7D01G135800 chr7D 86292328 86293142 814 False 418.000000 577 87.895000 1371 2325 2 chr7D.!!$F3 954
5 TraesCS7D01G135800 chr7A 88499482 88502718 3236 False 1278.500000 1903 95.115500 189 4086 4 chr7A.!!$F13 3897
6 TraesCS7D01G135800 chr7A 88435110 88437090 1980 False 959.000000 1740 93.193667 189 2272 3 chr7A.!!$F12 2083
7 TraesCS7D01G135800 chr7A 88188139 88188921 782 False 942.000000 942 88.622000 1 778 1 chr7A.!!$F7 777
8 TraesCS7D01G135800 chr7A 87451043 87452117 1074 False 922.000000 922 82.677000 731 1842 1 chr7A.!!$F1 1111
9 TraesCS7D01G135800 chr7A 88144209 88144990 781 False 915.000000 915 87.990000 1 778 1 chr7A.!!$F5 777
10 TraesCS7D01G135800 chr7A 88315480 88316684 1204 False 776.000000 1315 91.471500 933 2272 2 chr7A.!!$F11 1339
11 TraesCS7D01G135800 chr7A 88008334 88008916 582 False 736.000000 736 89.327000 789 1392 1 chr7A.!!$F2 603
12 TraesCS7D01G135800 chr7A 88119764 88121507 1743 False 241.500000 331 85.089500 412 947 2 chr7A.!!$F10 535
13 TraesCS7D01G135800 chr7B 35636338 35640025 3687 False 1083.600000 1882 93.846400 1 4086 5 chr7B.!!$F4 4085
14 TraesCS7D01G135800 chr7B 35307638 35308481 843 False 893.000000 893 85.730000 947 1842 1 chr7B.!!$F2 895
15 TraesCS7D01G135800 chr7B 35506699 35508126 1427 False 596.666667 889 89.202667 412 1842 3 chr7B.!!$F3 1430

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
88 101 0.180406 ACGGCTTGCACTTATAGGGG 59.820 55.000 0.0 0.0 0.00 4.79 F
191 204 1.071542 TCATGCGGGTGAAAGAGTGAA 59.928 47.619 0.0 0.0 0.00 3.18 F
1772 3384 1.737793 GTACCTGTGGGCATCTTTTCG 59.262 52.381 0.0 0.0 35.63 3.46 F
2212 3885 0.684535 TTGTCCACGAGATCTGGCAA 59.315 50.000 0.0 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 3226 1.000955 GCCTTTCTTCTCCGAGTCACA 59.999 52.381 0.00 0.0 0.00 3.58 R
2073 3746 1.619827 ACCAACGTCCTACCATTCGAA 59.380 47.619 0.00 0.0 0.00 3.71 R
2926 4609 1.070445 GCGCTGGTGAGCCTCATAT 59.930 57.895 0.00 0.0 42.91 1.78 R
3809 5493 0.252148 TCAGGGGGCAATGCATTTCA 60.252 50.000 9.83 0.0 0.00 2.69 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
88 101 0.180406 ACGGCTTGCACTTATAGGGG 59.820 55.000 0.00 0.00 0.00 4.79
126 139 3.077484 TCAAGGCTTCCCATCTTTCTG 57.923 47.619 0.00 0.00 0.00 3.02
129 142 1.283321 AGGCTTCCCATCTTTCTGGAC 59.717 52.381 0.00 0.00 38.69 4.02
155 168 4.060205 CCACTCAAGGCATTTTGAAAAGG 58.940 43.478 0.00 0.00 36.69 3.11
191 204 1.071542 TCATGCGGGTGAAAGAGTGAA 59.928 47.619 0.00 0.00 0.00 3.18
368 382 6.801862 GTCAAAATCACTGTACCTGTAATTGC 59.198 38.462 0.00 0.00 0.00 3.56
516 531 5.408356 TCATACTCGAAGAACAAACCTAGC 58.592 41.667 0.00 0.00 34.09 3.42
528 543 4.523083 ACAAACCTAGCTTGAACAGTTCA 58.477 39.130 12.24 12.24 38.04 3.18
529 544 5.133221 ACAAACCTAGCTTGAACAGTTCAT 58.867 37.500 16.89 5.03 39.84 2.57
559 579 3.518634 TTTTTGTTCTGGGTCAACTGC 57.481 42.857 0.00 0.00 0.00 4.40
1387 2998 5.573337 AGCTGGCAAAATTAGAGATCAAC 57.427 39.130 0.00 0.00 0.00 3.18
1406 3018 2.051804 CTTGGACGGGAATCGCATGC 62.052 60.000 7.91 7.91 43.89 4.06
1527 3139 3.961480 TGGGTGTCTAGTTCTGATGTG 57.039 47.619 0.00 0.00 0.00 3.21
1614 3226 2.270205 CTGGGCTCTCCGCATTGT 59.730 61.111 0.00 0.00 41.67 2.71
1772 3384 1.737793 GTACCTGTGGGCATCTTTTCG 59.262 52.381 0.00 0.00 35.63 3.46
1850 3523 4.396166 CAGAACTAGAATTTTGTGGCCGAT 59.604 41.667 0.00 0.00 0.00 4.18
1865 3538 2.035961 GGCCGATCACTGCTACTGAATA 59.964 50.000 0.00 0.00 0.00 1.75
1894 3567 7.768120 GTGATCTCCAAACAGTTATCTGAGAAT 59.232 37.037 7.81 0.00 43.76 2.40
1920 3593 9.208022 TGTTTGTGTTATTGTTCATTGTTTTCA 57.792 25.926 0.00 0.00 0.00 2.69
1930 3603 7.509141 TGTTCATTGTTTTCAAGATAGCTGA 57.491 32.000 0.00 0.00 43.41 4.26
1931 3604 7.587629 TGTTCATTGTTTTCAAGATAGCTGAG 58.412 34.615 0.00 0.00 43.41 3.35
1932 3605 7.229306 TGTTCATTGTTTTCAAGATAGCTGAGT 59.771 33.333 0.00 0.00 43.41 3.41
1933 3606 8.721478 GTTCATTGTTTTCAAGATAGCTGAGTA 58.279 33.333 0.00 0.00 43.41 2.59
1934 3607 8.256611 TCATTGTTTTCAAGATAGCTGAGTAC 57.743 34.615 0.00 0.00 43.41 2.73
1935 3608 7.877612 TCATTGTTTTCAAGATAGCTGAGTACA 59.122 33.333 0.00 0.00 43.41 2.90
1936 3609 8.506437 CATTGTTTTCAAGATAGCTGAGTACAA 58.494 33.333 0.00 0.90 43.41 2.41
1937 3610 8.445275 TTGTTTTCAAGATAGCTGAGTACAAA 57.555 30.769 0.00 0.00 34.60 2.83
1938 3611 8.621532 TGTTTTCAAGATAGCTGAGTACAAAT 57.378 30.769 0.00 0.00 0.00 2.32
1939 3612 9.066892 TGTTTTCAAGATAGCTGAGTACAAATT 57.933 29.630 0.00 0.00 0.00 1.82
1951 3624 9.177608 AGCTGAGTACAAATTATAAGAATTGCA 57.822 29.630 0.00 0.00 0.00 4.08
1952 3625 9.787532 GCTGAGTACAAATTATAAGAATTGCAA 57.212 29.630 0.00 0.00 0.00 4.08
2011 3684 8.677148 GATTTAGTAAAATCCATCTACTGCCA 57.323 34.615 0.00 0.00 43.49 4.92
2012 3685 9.120538 GATTTAGTAAAATCCATCTACTGCCAA 57.879 33.333 0.00 0.00 43.49 4.52
2013 3686 7.859325 TTAGTAAAATCCATCTACTGCCAAC 57.141 36.000 0.00 0.00 0.00 3.77
2014 3687 5.815581 AGTAAAATCCATCTACTGCCAACA 58.184 37.500 0.00 0.00 0.00 3.33
2015 3688 6.245408 AGTAAAATCCATCTACTGCCAACAA 58.755 36.000 0.00 0.00 0.00 2.83
2016 3689 6.719370 AGTAAAATCCATCTACTGCCAACAAA 59.281 34.615 0.00 0.00 0.00 2.83
2017 3690 6.610075 AAAATCCATCTACTGCCAACAAAT 57.390 33.333 0.00 0.00 0.00 2.32
2018 3691 7.716799 AAAATCCATCTACTGCCAACAAATA 57.283 32.000 0.00 0.00 0.00 1.40
2019 3692 6.699575 AATCCATCTACTGCCAACAAATAC 57.300 37.500 0.00 0.00 0.00 1.89
2020 3693 4.523083 TCCATCTACTGCCAACAAATACC 58.477 43.478 0.00 0.00 0.00 2.73
2021 3694 4.227300 TCCATCTACTGCCAACAAATACCT 59.773 41.667 0.00 0.00 0.00 3.08
2022 3695 4.576463 CCATCTACTGCCAACAAATACCTC 59.424 45.833 0.00 0.00 0.00 3.85
2023 3696 4.216411 TCTACTGCCAACAAATACCTCC 57.784 45.455 0.00 0.00 0.00 4.30
2024 3697 3.844211 TCTACTGCCAACAAATACCTCCT 59.156 43.478 0.00 0.00 0.00 3.69
2025 3698 3.525800 ACTGCCAACAAATACCTCCTT 57.474 42.857 0.00 0.00 0.00 3.36
2026 3699 3.844640 ACTGCCAACAAATACCTCCTTT 58.155 40.909 0.00 0.00 0.00 3.11
2027 3700 4.993028 ACTGCCAACAAATACCTCCTTTA 58.007 39.130 0.00 0.00 0.00 1.85
2028 3701 5.580022 ACTGCCAACAAATACCTCCTTTAT 58.420 37.500 0.00 0.00 0.00 1.40
2029 3702 6.016555 ACTGCCAACAAATACCTCCTTTATT 58.983 36.000 0.00 0.00 0.00 1.40
2030 3703 6.496911 ACTGCCAACAAATACCTCCTTTATTT 59.503 34.615 0.00 0.00 30.70 1.40
2031 3704 7.016170 ACTGCCAACAAATACCTCCTTTATTTT 59.984 33.333 0.00 0.00 28.55 1.82
2032 3705 8.423906 TGCCAACAAATACCTCCTTTATTTTA 57.576 30.769 0.00 0.00 28.55 1.52
2033 3706 9.041354 TGCCAACAAATACCTCCTTTATTTTAT 57.959 29.630 0.00 0.00 28.55 1.40
2034 3707 9.529325 GCCAACAAATACCTCCTTTATTTTATC 57.471 33.333 0.00 0.00 28.55 1.75
2044 3717 9.981114 ACCTCCTTTATTTTATCTTTTGTTGTG 57.019 29.630 0.00 0.00 0.00 3.33
2045 3718 9.981114 CCTCCTTTATTTTATCTTTTGTTGTGT 57.019 29.630 0.00 0.00 0.00 3.72
2212 3885 0.684535 TTGTCCACGAGATCTGGCAA 59.315 50.000 0.00 0.00 0.00 4.52
2259 3934 3.844577 AGCTCATTTGACATGTGAAGC 57.155 42.857 1.15 0.00 0.00 3.86
2330 4012 5.247110 TGCTCCTCTGAATCAGTCTTAGTTT 59.753 40.000 10.36 0.00 32.61 2.66
2331 4013 5.580297 GCTCCTCTGAATCAGTCTTAGTTTG 59.420 44.000 10.36 0.00 32.61 2.93
2430 4112 7.686438 TTGATCAATGTGCAGTTTAGTGTAT 57.314 32.000 3.38 0.00 0.00 2.29
2431 4113 7.686438 TGATCAATGTGCAGTTTAGTGTATT 57.314 32.000 0.00 0.00 0.00 1.89
2535 4217 7.066284 AGAGCTTACCTTTATGTGCATTTAGTG 59.934 37.037 0.00 0.00 0.00 2.74
2585 4267 7.227512 ACTTCCTTTTCAATCCGAGCAATATAG 59.772 37.037 0.00 0.00 0.00 1.31
2827 4509 6.450545 GGAGTCTACTACGGTAGTTTTGTTT 58.549 40.000 24.46 7.58 44.13 2.83
2828 4510 6.364435 GGAGTCTACTACGGTAGTTTTGTTTG 59.636 42.308 24.46 8.07 44.13 2.93
2829 4511 6.218746 AGTCTACTACGGTAGTTTTGTTTGG 58.781 40.000 24.46 1.89 44.13 3.28
2926 4609 1.345741 GGATTCTCTGGATGCCATCGA 59.654 52.381 0.00 0.00 30.82 3.59
2929 4612 4.141756 GGATTCTCTGGATGCCATCGATAT 60.142 45.833 0.00 0.00 30.82 1.63
2974 4657 0.387622 CAACCATCCGCTGCAAAGTG 60.388 55.000 0.00 0.00 0.00 3.16
3114 4797 1.934589 CGATGAATCGGTGGTTAGCA 58.065 50.000 4.77 0.00 45.93 3.49
3203 4887 7.511959 AAAAACTTTCTCCTCCTGTAATCAC 57.488 36.000 0.00 0.00 0.00 3.06
3209 4893 9.386122 ACTTTCTCCTCCTGTAATCACATATAT 57.614 33.333 0.00 0.00 33.14 0.86
3670 5354 4.216472 TGTGTGTGTGTGTGTGTGTAAATT 59.784 37.500 0.00 0.00 0.00 1.82
3717 5401 2.504461 CTTGTTCAGCTGGCGCTTCG 62.504 60.000 15.13 0.00 46.47 3.79
3736 5420 1.136147 GCTCCTTCTGTTGCATGCG 59.864 57.895 14.09 0.00 0.00 4.73
3767 5451 2.427095 ACAACTCTGTTTGGGCAAGAAC 59.573 45.455 0.00 0.00 28.57 3.01
3802 5486 0.983378 GGGTGGAGTGCAGGGTCTAT 60.983 60.000 0.00 0.00 0.00 1.98
3809 5493 3.435890 GGAGTGCAGGGTCTATACTCTCT 60.436 52.174 0.00 0.00 32.55 3.10
3863 5547 1.488705 TTCAGGGCCATTCGGAGTGT 61.489 55.000 6.18 0.00 0.00 3.55
3964 5649 3.556004 CCTCAGAAAACAGTGGAGTCTCC 60.556 52.174 12.40 12.40 36.96 3.71
3978 5792 4.479056 TGGAGTCTCCCTACTCACTAGATT 59.521 45.833 16.60 0.00 46.40 2.40
4029 5843 6.540551 GGTCCAATGAAGGAAGAAGTTCTATC 59.459 42.308 5.65 6.22 39.92 2.08
4086 5900 2.033194 GCTACACCCCGTGTTCAGC 61.033 63.158 2.29 3.54 45.08 4.26
4087 5901 1.375523 CTACACCCCGTGTTCAGCC 60.376 63.158 2.29 0.00 45.08 4.85
4088 5902 2.798148 CTACACCCCGTGTTCAGCCC 62.798 65.000 2.29 0.00 45.08 5.19
4091 5905 4.096003 CCCCGTGTTCAGCCCGAT 62.096 66.667 0.00 0.00 0.00 4.18
4092 5906 2.511600 CCCGTGTTCAGCCCGATC 60.512 66.667 0.00 0.00 0.00 3.69
4093 5907 2.579201 CCGTGTTCAGCCCGATCT 59.421 61.111 0.00 0.00 0.00 2.75
4094 5908 1.672854 CCCGTGTTCAGCCCGATCTA 61.673 60.000 0.00 0.00 0.00 1.98
4095 5909 0.527817 CCGTGTTCAGCCCGATCTAC 60.528 60.000 0.00 0.00 0.00 2.59
4096 5910 0.527817 CGTGTTCAGCCCGATCTACC 60.528 60.000 0.00 0.00 0.00 3.18
4097 5911 0.179081 GTGTTCAGCCCGATCTACCC 60.179 60.000 0.00 0.00 0.00 3.69
4098 5912 1.335132 TGTTCAGCCCGATCTACCCC 61.335 60.000 0.00 0.00 0.00 4.95
4099 5913 1.002403 TTCAGCCCGATCTACCCCA 59.998 57.895 0.00 0.00 0.00 4.96
4100 5914 1.335132 TTCAGCCCGATCTACCCCAC 61.335 60.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 5.349817 CGAATCACTATATCTTCACCATGGC 59.650 44.000 13.04 0.00 0.00 4.40
88 101 2.536365 TGATCGATGAACGTACTTGGC 58.464 47.619 0.54 0.00 43.13 4.52
191 204 3.678056 TGGACTAGAGCAACGATGTTT 57.322 42.857 0.00 0.00 0.00 2.83
404 418 7.015584 ACTCATACAAAGGAATGGCTTCTTTTT 59.984 33.333 4.78 0.00 38.27 1.94
405 419 6.494835 ACTCATACAAAGGAATGGCTTCTTTT 59.505 34.615 0.00 2.55 40.23 2.27
409 424 5.904362 AACTCATACAAAGGAATGGCTTC 57.096 39.130 0.00 0.00 0.00 3.86
540 558 1.403679 CGCAGTTGACCCAGAACAAAA 59.596 47.619 0.00 0.00 0.00 2.44
541 559 1.021202 CGCAGTTGACCCAGAACAAA 58.979 50.000 0.00 0.00 0.00 2.83
559 579 4.621034 GGTATGTTTCAAAGTGAAATGGCG 59.379 41.667 6.69 0.00 46.55 5.69
1387 2998 2.016961 CATGCGATTCCCGTCCAAG 58.983 57.895 0.00 0.00 41.15 3.61
1406 3018 1.672441 CGCCCAATTGGACACCATTTG 60.672 52.381 26.60 14.54 41.65 2.32
1527 3139 5.127693 TCAAGAGCAGAGACTGAACTTAC 57.872 43.478 2.81 0.00 32.44 2.34
1614 3226 1.000955 GCCTTTCTTCTCCGAGTCACA 59.999 52.381 0.00 0.00 0.00 3.58
1865 3538 6.014242 TCAGATAACTGTTTGGAGATCACTGT 60.014 38.462 0.00 0.00 43.81 3.55
1894 3567 9.208022 TGAAAACAATGAACAATAACACAAACA 57.792 25.926 0.00 0.00 0.00 2.83
1986 3659 8.677148 TGGCAGTAGATGGATTTTACTAAATC 57.323 34.615 0.00 0.00 45.81 2.17
1987 3660 8.903820 GTTGGCAGTAGATGGATTTTACTAAAT 58.096 33.333 0.00 0.00 36.68 1.40
1988 3661 7.885922 TGTTGGCAGTAGATGGATTTTACTAAA 59.114 33.333 0.00 0.00 0.00 1.85
1989 3662 7.398829 TGTTGGCAGTAGATGGATTTTACTAA 58.601 34.615 0.00 0.00 0.00 2.24
1990 3663 6.953101 TGTTGGCAGTAGATGGATTTTACTA 58.047 36.000 0.00 0.00 0.00 1.82
1991 3664 5.815581 TGTTGGCAGTAGATGGATTTTACT 58.184 37.500 0.00 0.00 0.00 2.24
1992 3665 6.509418 TTGTTGGCAGTAGATGGATTTTAC 57.491 37.500 0.00 0.00 0.00 2.01
1993 3666 7.716799 ATTTGTTGGCAGTAGATGGATTTTA 57.283 32.000 0.00 0.00 0.00 1.52
1994 3667 6.610075 ATTTGTTGGCAGTAGATGGATTTT 57.390 33.333 0.00 0.00 0.00 1.82
1995 3668 6.096846 GGTATTTGTTGGCAGTAGATGGATTT 59.903 38.462 0.00 0.00 0.00 2.17
1996 3669 5.594317 GGTATTTGTTGGCAGTAGATGGATT 59.406 40.000 0.00 0.00 0.00 3.01
1997 3670 5.103940 AGGTATTTGTTGGCAGTAGATGGAT 60.104 40.000 0.00 0.00 0.00 3.41
1998 3671 4.227300 AGGTATTTGTTGGCAGTAGATGGA 59.773 41.667 0.00 0.00 0.00 3.41
1999 3672 4.526970 AGGTATTTGTTGGCAGTAGATGG 58.473 43.478 0.00 0.00 0.00 3.51
2000 3673 4.576463 GGAGGTATTTGTTGGCAGTAGATG 59.424 45.833 0.00 0.00 0.00 2.90
2001 3674 4.475016 AGGAGGTATTTGTTGGCAGTAGAT 59.525 41.667 0.00 0.00 0.00 1.98
2002 3675 3.844211 AGGAGGTATTTGTTGGCAGTAGA 59.156 43.478 0.00 0.00 0.00 2.59
2003 3676 4.222124 AGGAGGTATTTGTTGGCAGTAG 57.778 45.455 0.00 0.00 0.00 2.57
2004 3677 4.650972 AAGGAGGTATTTGTTGGCAGTA 57.349 40.909 0.00 0.00 0.00 2.74
2005 3678 3.525800 AAGGAGGTATTTGTTGGCAGT 57.474 42.857 0.00 0.00 0.00 4.40
2006 3679 6.530019 AATAAAGGAGGTATTTGTTGGCAG 57.470 37.500 0.00 0.00 0.00 4.85
2007 3680 6.926630 AAATAAAGGAGGTATTTGTTGGCA 57.073 33.333 0.00 0.00 31.48 4.92
2008 3681 9.529325 GATAAAATAAAGGAGGTATTTGTTGGC 57.471 33.333 0.00 0.00 32.71 4.52
2018 3691 9.981114 CACAACAAAAGATAAAATAAAGGAGGT 57.019 29.630 0.00 0.00 0.00 3.85
2019 3692 9.981114 ACACAACAAAAGATAAAATAAAGGAGG 57.019 29.630 0.00 0.00 0.00 4.30
2055 3728 9.748708 CCATTCGAAATCAATGGTAATTACAAT 57.251 29.630 17.16 8.81 43.77 2.71
2073 3746 1.619827 ACCAACGTCCTACCATTCGAA 59.380 47.619 0.00 0.00 0.00 3.71
2259 3934 0.035317 TACTGCTGCAGGTGAACAGG 59.965 55.000 31.00 6.41 35.51 4.00
2430 4112 2.749076 AGCATCTTATTCAACAGCGCAA 59.251 40.909 11.47 0.00 0.00 4.85
2431 4113 2.358957 AGCATCTTATTCAACAGCGCA 58.641 42.857 11.47 0.00 0.00 6.09
2535 4217 6.753897 GCTAAATGCACATAAAATGGCTAC 57.246 37.500 0.00 0.00 42.31 3.58
2585 4267 7.064371 TCACATGTTAAATGCACATAAAATGGC 59.936 33.333 19.90 0.00 32.88 4.40
2827 4509 3.373001 GGGGAATGACCAATTGAGATCCA 60.373 47.826 7.12 0.00 41.20 3.41
2828 4510 3.225940 GGGGAATGACCAATTGAGATCC 58.774 50.000 7.12 7.04 41.20 3.36
2829 4511 3.633986 GTGGGGAATGACCAATTGAGATC 59.366 47.826 7.12 2.27 40.24 2.75
2926 4609 1.070445 GCGCTGGTGAGCCTCATAT 59.930 57.895 0.00 0.00 42.91 1.78
2929 4612 2.230994 CTAAGCGCTGGTGAGCCTCA 62.231 60.000 12.58 0.00 42.91 3.86
2945 4628 1.200519 CGGATGGTTGGGAGTCCTAA 58.799 55.000 9.58 6.48 0.00 2.69
2974 4657 1.512156 TTTCTTTTGTCCCTCGGCGC 61.512 55.000 0.00 0.00 0.00 6.53
3134 4817 2.157421 CTTCGTGGCTGAAGCAGTC 58.843 57.895 4.43 0.00 44.36 3.51
3644 5328 3.339141 ACACACACACACACACACATTA 58.661 40.909 0.00 0.00 0.00 1.90
3645 5329 2.158559 ACACACACACACACACACATT 58.841 42.857 0.00 0.00 0.00 2.71
3646 5330 1.819928 ACACACACACACACACACAT 58.180 45.000 0.00 0.00 0.00 3.21
3647 5331 2.457366 TACACACACACACACACACA 57.543 45.000 0.00 0.00 0.00 3.72
3648 5332 3.815337 TTTACACACACACACACACAC 57.185 42.857 0.00 0.00 0.00 3.82
3649 5333 5.378292 AAATTTACACACACACACACACA 57.622 34.783 0.00 0.00 0.00 3.72
3650 5334 6.251801 GGTAAAATTTACACACACACACACAC 59.748 38.462 16.55 0.00 0.00 3.82
3651 5335 6.323266 GGTAAAATTTACACACACACACACA 58.677 36.000 16.55 0.00 0.00 3.72
3652 5336 5.744819 GGGTAAAATTTACACACACACACAC 59.255 40.000 16.55 0.00 0.00 3.82
3653 5337 5.417894 TGGGTAAAATTTACACACACACACA 59.582 36.000 16.05 0.00 0.00 3.72
3654 5338 5.892568 TGGGTAAAATTTACACACACACAC 58.107 37.500 16.05 0.00 0.00 3.82
3655 5339 6.525578 TTGGGTAAAATTTACACACACACA 57.474 33.333 19.23 3.09 29.45 3.72
3656 5340 6.643360 GGATTGGGTAAAATTTACACACACAC 59.357 38.462 19.23 10.97 29.45 3.82
3657 5341 6.323996 TGGATTGGGTAAAATTTACACACACA 59.676 34.615 19.23 14.94 29.45 3.72
3658 5342 6.750148 TGGATTGGGTAAAATTTACACACAC 58.250 36.000 19.23 15.12 29.45 3.82
3659 5343 6.978674 TGGATTGGGTAAAATTTACACACA 57.021 33.333 19.23 12.02 29.45 3.72
3660 5344 7.875554 ACATTGGATTGGGTAAAATTTACACAC 59.124 33.333 19.23 9.73 29.45 3.82
3661 5345 7.875041 CACATTGGATTGGGTAAAATTTACACA 59.125 33.333 16.05 16.05 0.00 3.72
3717 5401 1.509923 GCATGCAACAGAAGGAGCC 59.490 57.895 14.21 0.00 0.00 4.70
3736 5420 5.875359 CCCAAACAGAGTTGTAGAGATTACC 59.125 44.000 0.00 0.00 36.23 2.85
3802 5486 3.282021 GGGCAATGCATTTCAGAGAGTA 58.718 45.455 9.83 0.00 0.00 2.59
3809 5493 0.252148 TCAGGGGGCAATGCATTTCA 60.252 50.000 9.83 0.00 0.00 2.69
3841 5525 1.312815 CTCCGAATGGCCCTGAATTC 58.687 55.000 0.00 1.34 34.14 2.17
3978 5792 9.224267 CTCTTCTGGAAACATTTTATCTTCAGA 57.776 33.333 0.00 0.00 41.51 3.27
4029 5843 2.354805 GCACCCTACCACTACCAAGAAG 60.355 54.545 0.00 0.00 0.00 2.85
4070 5884 2.745037 GGCTGAACACGGGGTGTA 59.255 61.111 1.32 0.00 46.79 2.90


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

AutoCloner maintained by Alex Coulton.