Multiple sequence alignment - TraesCS6A01G167400

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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 TraesCS6A01G167400 chr6A 100.000 6435 0 0 1 6435 171461672 171455238 0.000000e+00 11884.0
1 TraesCS6A01G167400 chr6A 100.000 71 0 0 5806 5876 171455795 171455725 1.460000e-26 132.0
2 TraesCS6A01G167400 chr6A 100.000 71 0 0 5878 5948 171455867 171455797 1.460000e-26 132.0
3 TraesCS6A01G167400 chr6A 88.000 50 6 0 6366 6415 127090627 127090578 6.970000e-05 60.2
4 TraesCS6A01G167400 chr6A 100.000 29 0 0 6366 6394 531375939 531375967 3.000000e-03 54.7
5 TraesCS6A01G167400 chr6D 97.465 5286 97 12 1 5274 132314545 132309285 0.000000e+00 8985.0
6 TraesCS6A01G167400 chr6D 97.579 3552 67 8 2335 5876 132413291 132409749 0.000000e+00 6065.0
7 TraesCS6A01G167400 chr6D 96.913 2041 42 12 1 2036 132415319 132413295 0.000000e+00 3400.0
8 TraesCS6A01G167400 chr6D 95.059 506 15 7 5878 6379 132409819 132409320 0.000000e+00 787.0
9 TraesCS6A01G167400 chr6D 95.436 482 17 4 5878 6357 132302642 132302164 0.000000e+00 763.0
10 TraesCS6A01G167400 chr6D 95.711 443 10 3 5435 5876 132303006 132302572 0.000000e+00 704.0
11 TraesCS6A01G167400 chr6B 94.418 3637 144 25 1 3602 229730414 229726802 0.000000e+00 5537.0
12 TraesCS6A01G167400 chr6B 88.960 2192 142 48 3692 5833 229726803 229724662 0.000000e+00 2615.0
13 TraesCS6A01G167400 chr6B 100.000 30 0 0 6318 6347 229724559 229724530 1.000000e-03 56.5
14 TraesCS6A01G167400 chr6B 100.000 28 0 0 5878 5905 229724689 229724662 1.200000e-02 52.8
15 TraesCS6A01G167400 chr4A 89.488 371 36 3 5924 6293 626320216 626319848 3.510000e-127 466.0
16 TraesCS6A01G167400 chr4A 78.276 290 52 11 199 485 516487631 516487912 6.630000e-40 176.0
17 TraesCS6A01G167400 chr4A 96.875 32 0 1 5846 5876 596787377 596787346 1.200000e-02 52.8
18 TraesCS6A01G167400 chr5D 88.889 378 33 8 5921 6293 370117039 370117412 2.110000e-124 457.0
19 TraesCS6A01G167400 chr5D 78.058 515 93 16 1136 1635 74090878 74090369 2.250000e-79 307.0
20 TraesCS6A01G167400 chr5D 80.385 260 44 7 2144 2397 315936231 315935973 2.370000e-44 191.0
21 TraesCS6A01G167400 chr5D 92.308 39 2 1 6357 6394 453423193 453423155 3.000000e-03 54.7
22 TraesCS6A01G167400 chr3D 88.859 377 35 6 5921 6293 94246284 94245911 2.110000e-124 457.0
23 TraesCS6A01G167400 chr3D 84.286 140 20 2 2261 2399 159794640 159794502 1.130000e-27 135.0
24 TraesCS6A01G167400 chr3D 100.000 29 0 0 6366 6394 294343242 294343214 3.000000e-03 54.7
25 TraesCS6A01G167400 chr5A 88.503 374 41 2 5921 6293 1951099 1950727 9.840000e-123 451.0
26 TraesCS6A01G167400 chr5A 76.494 502 102 12 1134 1625 69103998 69103503 6.400000e-65 259.0
27 TraesCS6A01G167400 chr5A 94.286 35 1 1 5843 5876 9464614 9464648 1.200000e-02 52.8
28 TraesCS6A01G167400 chr1D 88.235 374 40 3 5921 6293 143544923 143545293 1.650000e-120 444.0
29 TraesCS6A01G167400 chr1D 80.645 155 25 4 2235 2385 404253054 404253207 1.470000e-21 115.0
30 TraesCS6A01G167400 chr1D 76.437 174 33 7 2232 2399 478140149 478140320 3.200000e-13 87.9
31 TraesCS6A01G167400 chr1D 100.000 28 0 0 5849 5876 18816365 18816392 1.200000e-02 52.8
32 TraesCS6A01G167400 chr1D 100.000 28 0 0 5849 5876 455089311 455089338 1.200000e-02 52.8
33 TraesCS6A01G167400 chr3B 88.032 376 40 4 5921 6293 13423064 13422691 2.130000e-119 440.0
34 TraesCS6A01G167400 chr2D 87.664 381 42 3 5918 6293 618123866 618123486 7.660000e-119 438.0
35 TraesCS6A01G167400 chr2D 85.000 120 11 4 4869 4987 166197115 166197228 1.470000e-21 115.0
36 TraesCS6A01G167400 chr2D 100.000 29 0 0 6366 6394 131774885 131774857 3.000000e-03 54.7
37 TraesCS6A01G167400 chr2D 96.875 32 0 1 5846 5876 618123866 618123835 1.200000e-02 52.8
38 TraesCS6A01G167400 chr5B 78.622 421 77 9 1134 1548 78420696 78421109 3.820000e-67 267.0
39 TraesCS6A01G167400 chr5B 100.000 29 0 0 6366 6394 440209526 440209498 3.000000e-03 54.7
40 TraesCS6A01G167400 chr5B 94.286 35 1 1 5843 5876 12660479 12660445 1.200000e-02 52.8
41 TraesCS6A01G167400 chr4D 84.351 262 35 4 2144 2399 301756303 301756564 1.070000e-62 252.0
42 TraesCS6A01G167400 chr4D 76.299 308 56 16 193 492 67358128 67357830 1.450000e-31 148.0
43 TraesCS6A01G167400 chr4B 82.061 262 41 4 2144 2399 376157709 376157970 1.090000e-52 219.0
44 TraesCS6A01G167400 chr4B 77.320 291 51 14 199 481 99430388 99430671 2.400000e-34 158.0
45 TraesCS6A01G167400 chr4B 84.892 139 13 6 2145 2278 93286449 93286314 4.050000e-27 134.0
46 TraesCS6A01G167400 chr2A 81.273 267 30 14 2144 2400 386294347 386294603 1.420000e-46 198.0
47 TraesCS6A01G167400 chr1B 80.303 264 43 7 2146 2403 104349882 104349622 2.370000e-44 191.0
48 TraesCS6A01G167400 chr1B 100.000 30 0 0 6365 6394 169001864 169001893 1.000000e-03 56.5
49 TraesCS6A01G167400 chr7A 84.112 107 15 2 2144 2248 700824169 700824063 1.140000e-17 102.0
50 TraesCS6A01G167400 chr2B 93.182 44 3 0 6366 6409 19446375 19446332 1.500000e-06 65.8


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 TraesCS6A01G167400 chr6A 171455238 171461672 6434 True 11884.000000 11884 100.0000 1 6435 1 chr6A.!!$R2 6434
1 TraesCS6A01G167400 chr6D 132309285 132314545 5260 True 8985.000000 8985 97.4650 1 5274 1 chr6D.!!$R1 5273
2 TraesCS6A01G167400 chr6D 132409320 132415319 5999 True 3417.333333 6065 96.5170 1 6379 3 chr6D.!!$R3 6378
3 TraesCS6A01G167400 chr6D 132302164 132303006 842 True 733.500000 763 95.5735 5435 6357 2 chr6D.!!$R2 922
4 TraesCS6A01G167400 chr6B 229724530 229730414 5884 True 2065.325000 5537 95.8445 1 6347 4 chr6B.!!$R1 6346
5 TraesCS6A01G167400 chr5D 74090369 74090878 509 True 307.000000 307 78.0580 1136 1635 1 chr5D.!!$R1 499

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
384 386 4.070716 GTGGGAGGCATAGATGAATCAAG 58.929 47.826 0.00 0.00 0.00 3.02 F
1737 1777 1.372087 CGCAATCTGGGGCTCAAGTC 61.372 60.000 0.00 0.00 0.00 3.01 F
1968 2008 1.204941 ACGTATCCAGTGAGTTCCTGC 59.795 52.381 0.00 0.00 0.00 4.85 F
2772 2817 2.490903 TCGTCCTAGACCTGCTGTAAAC 59.509 50.000 0.00 0.00 0.00 2.01 F
3595 3642 0.040157 TTTTCATGTCAGTGCGCTGC 60.040 50.000 22.58 17.01 42.29 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 1990 1.204941 ACGCAGGAACTCACTGGATAC 59.795 52.381 0.0 0.0 34.6 2.24 R
2630 2675 0.383949 TTTTTGCCCGCTTCTGTGTC 59.616 50.000 0.0 0.0 0.0 3.67 R
3058 3103 1.352622 TGCAGACCCCCTTGTGAAGT 61.353 55.000 0.0 0.0 0.0 3.01 R
4606 4656 0.893447 AGCCAGCTCCTTCATTTTGC 59.107 50.000 0.0 0.0 0.0 3.68 R
5536 5631 4.917906 AATCAAACTTAGGGTCTCAGCT 57.082 40.909 0.0 0.0 0.0 4.24 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
189 190 5.300034 ACTGAACTCAAGTTGATGCATTTCA 59.700 36.000 5.91 9.21 38.56 2.69
197 198 9.361315 CTCAAGTTGATGCATTTCATTTTATCA 57.639 29.630 5.91 0.00 35.05 2.15
384 386 4.070716 GTGGGAGGCATAGATGAATCAAG 58.929 47.826 0.00 0.00 0.00 3.02
573 576 4.365514 TCAGTGCTTAGATTTTGGTCCA 57.634 40.909 0.00 0.00 0.00 4.02
1058 1088 6.146021 CCCTTCACTGCAAATTCAATAAACAC 59.854 38.462 0.00 0.00 0.00 3.32
1172 1202 8.690840 CATTCATTTTTAACTCCGTTTCTTGTC 58.309 33.333 0.00 0.00 0.00 3.18
1253 1287 2.344592 TGGAAGTAGTGGACATTGGGT 58.655 47.619 0.00 0.00 0.00 4.51
1730 1770 1.377202 TCAACTCGCAATCTGGGGC 60.377 57.895 0.00 0.00 0.00 5.80
1737 1777 1.372087 CGCAATCTGGGGCTCAAGTC 61.372 60.000 0.00 0.00 0.00 3.01
1752 1792 6.116126 GGCTCAAGTCACCATAGTATTTCTT 58.884 40.000 0.00 0.00 0.00 2.52
1784 1824 2.223735 CCTTGTCCATCATTGAGCATGC 60.224 50.000 10.51 10.51 32.13 4.06
1949 1989 7.278646 TCTGACATGATTTTATGCAGTAGTGAC 59.721 37.037 0.00 0.00 35.56 3.67
1950 1990 6.035975 TGACATGATTTTATGCAGTAGTGACG 59.964 38.462 0.00 0.00 0.00 4.35
1968 2008 1.204941 ACGTATCCAGTGAGTTCCTGC 59.795 52.381 0.00 0.00 0.00 4.85
2036 2078 5.698089 CCATAGGCTACATGACAATACACAG 59.302 44.000 0.00 0.00 0.00 3.66
2630 2675 6.140110 CCCAAAAAGTGATACAACAACTACG 58.860 40.000 0.00 0.00 0.00 3.51
2772 2817 2.490903 TCGTCCTAGACCTGCTGTAAAC 59.509 50.000 0.00 0.00 0.00 2.01
3058 3103 0.178301 TCGTTGTGCTGTAACCCACA 59.822 50.000 0.00 0.00 39.95 4.17
3131 3176 8.028938 CACATAAATATATTGCAACTAAGGGGC 58.971 37.037 0.00 0.00 0.00 5.80
3132 3177 7.728083 ACATAAATATATTGCAACTAAGGGGCA 59.272 33.333 0.00 0.00 35.41 5.36
3323 3370 3.608316 GGCATAAACTTGGCAATGGAA 57.392 42.857 0.00 0.00 41.53 3.53
3411 3458 3.242867 TGGATCGATAAAGGGAGAGCAT 58.757 45.455 0.00 0.00 0.00 3.79
3578 3625 3.854994 AGGAAGGATTCTCCATGACCTTT 59.145 43.478 0.00 0.00 46.56 3.11
3595 3642 0.040157 TTTTCATGTCAGTGCGCTGC 60.040 50.000 22.58 17.01 42.29 5.25
3618 3665 3.747099 CGATAGCCAACAAACCTTCAG 57.253 47.619 0.00 0.00 0.00 3.02
3636 3683 2.571528 GAGCTGTGCTCGTATGACG 58.428 57.895 3.73 0.00 45.85 4.35
3670 3717 1.412343 CTGAGGCCTCCTAGCTTCTTC 59.588 57.143 29.95 1.40 39.46 2.87
3907 3955 2.224744 TGTGACTTTCATAGCCAAGCCA 60.225 45.455 0.00 0.00 0.00 4.75
4062 4110 4.990257 ACATGAAGTGAAACATATGCTGC 58.010 39.130 1.58 0.00 41.43 5.25
4680 4730 3.079478 AGCAGGGAGCATCTCGCA 61.079 61.111 12.37 0.00 43.84 5.10
5134 5211 1.205417 GCCACCCTTTTGATGATGTGG 59.795 52.381 0.00 0.00 44.70 4.17
5173 5262 8.023706 GGATAGAAATGTTGAAAAGGAAGTGTC 58.976 37.037 0.00 0.00 0.00 3.67
5349 5444 4.201628 GCAGGATATTATGAACGATCGCAC 60.202 45.833 16.60 10.09 0.00 5.34
5536 5631 2.090760 TGCAAATGAGCGCCTCAAATA 58.909 42.857 2.29 0.00 44.04 1.40
5569 5664 3.004024 AGTTTGATTTTGTGCGAGCTG 57.996 42.857 0.00 0.00 0.00 4.24
5689 5792 8.408043 TTGTCAGGTAAAGATGTGAATGAAAT 57.592 30.769 0.00 0.00 0.00 2.17
5795 5898 4.322080 TCCATCGTATGATCACTCAACC 57.678 45.455 0.00 0.00 34.37 3.77
5860 6045 8.679288 AAGATGCTATTTCGAAATTCACTTTG 57.321 30.769 27.10 6.38 0.00 2.77
5861 6046 7.253422 AGATGCTATTTCGAAATTCACTTTGG 58.747 34.615 27.10 6.56 0.00 3.28
5862 6047 5.160641 TGCTATTTCGAAATTCACTTTGGC 58.839 37.500 27.10 16.05 0.00 4.52
5863 6048 5.160641 GCTATTTCGAAATTCACTTTGGCA 58.839 37.500 27.10 5.68 0.00 4.92
5864 6049 5.060940 GCTATTTCGAAATTCACTTTGGCAC 59.939 40.000 27.10 2.10 0.00 5.01
5865 6050 4.377839 TTTCGAAATTCACTTTGGCACA 57.622 36.364 6.47 0.00 0.00 4.57
5866 6051 4.582701 TTCGAAATTCACTTTGGCACAT 57.417 36.364 0.00 0.00 39.30 3.21
5867 6052 3.899734 TCGAAATTCACTTTGGCACATG 58.100 40.909 0.00 0.00 39.30 3.21
5868 6053 2.988493 CGAAATTCACTTTGGCACATGG 59.012 45.455 0.00 0.00 39.30 3.66
5869 6054 3.328505 GAAATTCACTTTGGCACATGGG 58.671 45.455 0.00 0.00 39.30 4.00
5870 6055 2.307496 ATTCACTTTGGCACATGGGA 57.693 45.000 0.00 0.00 39.30 4.37
5871 6056 1.619654 TTCACTTTGGCACATGGGAG 58.380 50.000 0.00 0.00 39.30 4.30
5872 6057 0.895100 TCACTTTGGCACATGGGAGC 60.895 55.000 0.00 0.00 39.30 4.70
5873 6058 1.153524 ACTTTGGCACATGGGAGCA 59.846 52.632 0.00 0.00 39.30 4.26
5874 6059 0.251922 ACTTTGGCACATGGGAGCAT 60.252 50.000 0.00 0.00 39.30 3.79
5875 6060 1.005805 ACTTTGGCACATGGGAGCATA 59.994 47.619 0.00 0.00 39.30 3.14
5876 6061 2.101783 CTTTGGCACATGGGAGCATAA 58.898 47.619 0.00 0.00 39.30 1.90
5877 6062 2.457813 TTGGCACATGGGAGCATAAT 57.542 45.000 0.00 0.00 39.30 1.28
5878 6063 3.591695 TTGGCACATGGGAGCATAATA 57.408 42.857 0.00 0.00 39.30 0.98
5879 6064 3.812611 TGGCACATGGGAGCATAATAT 57.187 42.857 0.00 0.00 31.64 1.28
5880 6065 3.423749 TGGCACATGGGAGCATAATATG 58.576 45.455 0.00 0.00 31.64 1.78
5881 6066 3.074242 TGGCACATGGGAGCATAATATGA 59.926 43.478 0.00 0.00 31.64 2.15
5882 6067 4.264038 TGGCACATGGGAGCATAATATGAT 60.264 41.667 0.00 0.00 31.64 2.45
5883 6068 4.708421 GGCACATGGGAGCATAATATGATT 59.292 41.667 0.00 0.00 31.64 2.57
5884 6069 5.186409 GGCACATGGGAGCATAATATGATTT 59.814 40.000 0.00 0.00 31.64 2.17
5885 6070 6.327934 GCACATGGGAGCATAATATGATTTC 58.672 40.000 0.00 0.00 0.00 2.17
5886 6071 6.626623 GCACATGGGAGCATAATATGATTTCC 60.627 42.308 0.00 7.27 0.00 3.13
5887 6072 6.434965 CACATGGGAGCATAATATGATTTCCA 59.565 38.462 13.72 13.72 36.96 3.53
5888 6073 7.123697 CACATGGGAGCATAATATGATTTCCAT 59.876 37.037 16.08 16.08 40.78 3.41
5889 6074 7.676893 ACATGGGAGCATAATATGATTTCCATT 59.323 33.333 17.97 10.96 39.33 3.16
5890 6075 8.537016 CATGGGAGCATAATATGATTTCCATTT 58.463 33.333 17.97 4.40 39.33 2.32
5891 6076 9.772605 ATGGGAGCATAATATGATTTCCATTTA 57.227 29.630 16.08 5.12 38.73 1.40
5892 6077 9.246670 TGGGAGCATAATATGATTTCCATTTAG 57.753 33.333 4.14 0.00 36.71 1.85
5893 6078 9.247861 GGGAGCATAATATGATTTCCATTTAGT 57.752 33.333 4.14 0.00 36.71 2.24
5895 6080 9.979270 GAGCATAATATGATTTCCATTTAGTCG 57.021 33.333 4.14 0.00 36.71 4.18
5896 6081 9.507329 AGCATAATATGATTTCCATTTAGTCGT 57.493 29.630 4.14 0.00 36.71 4.34
5897 6082 9.546909 GCATAATATGATTTCCATTTAGTCGTG 57.453 33.333 4.14 0.00 36.71 4.35
5900 6085 8.731275 AATATGATTTCCATTTAGTCGTGTCA 57.269 30.769 0.00 0.00 36.71 3.58
5901 6086 8.731275 ATATGATTTCCATTTAGTCGTGTCAA 57.269 30.769 0.00 0.00 36.71 3.18
5902 6087 6.236017 TGATTTCCATTTAGTCGTGTCAAC 57.764 37.500 0.00 0.00 0.00 3.18
5903 6088 5.995282 TGATTTCCATTTAGTCGTGTCAACT 59.005 36.000 0.00 0.00 0.00 3.16
5904 6089 7.156000 TGATTTCCATTTAGTCGTGTCAACTA 58.844 34.615 0.00 0.00 0.00 2.24
5905 6090 7.822334 TGATTTCCATTTAGTCGTGTCAACTAT 59.178 33.333 0.00 0.00 0.00 2.12
5906 6091 9.309516 GATTTCCATTTAGTCGTGTCAACTATA 57.690 33.333 0.00 0.00 0.00 1.31
5907 6092 9.661563 ATTTCCATTTAGTCGTGTCAACTATAA 57.338 29.630 0.00 0.00 0.00 0.98
5908 6093 9.491675 TTTCCATTTAGTCGTGTCAACTATAAA 57.508 29.630 0.00 0.00 0.00 1.40
5909 6094 8.697846 TCCATTTAGTCGTGTCAACTATAAAG 57.302 34.615 0.00 0.00 0.00 1.85
5910 6095 8.525316 TCCATTTAGTCGTGTCAACTATAAAGA 58.475 33.333 0.00 0.00 0.00 2.52
5911 6096 9.314321 CCATTTAGTCGTGTCAACTATAAAGAT 57.686 33.333 0.00 0.00 0.00 2.40
5913 6098 7.751047 TTAGTCGTGTCAACTATAAAGATGC 57.249 36.000 0.00 0.00 0.00 3.91
5914 6099 5.967088 AGTCGTGTCAACTATAAAGATGCT 58.033 37.500 0.00 0.00 0.00 3.79
5915 6100 7.096884 AGTCGTGTCAACTATAAAGATGCTA 57.903 36.000 0.00 0.00 0.00 3.49
5916 6101 7.717568 AGTCGTGTCAACTATAAAGATGCTAT 58.282 34.615 0.00 0.00 0.00 2.97
5917 6102 8.198109 AGTCGTGTCAACTATAAAGATGCTATT 58.802 33.333 0.00 0.00 0.00 1.73
5918 6103 8.818057 GTCGTGTCAACTATAAAGATGCTATTT 58.182 33.333 0.00 0.00 0.00 1.40
5919 6104 9.031360 TCGTGTCAACTATAAAGATGCTATTTC 57.969 33.333 0.00 0.00 0.00 2.17
5920 6105 7.998767 CGTGTCAACTATAAAGATGCTATTTCG 59.001 37.037 0.00 0.00 0.00 3.46
5921 6106 9.031360 GTGTCAACTATAAAGATGCTATTTCGA 57.969 33.333 0.00 0.00 0.00 3.71
6042 6227 2.098298 GTATGTGCGCACGCCAAG 59.902 61.111 33.22 0.00 41.09 3.61
6168 6355 6.094325 TGACATAAAAGTTGTCGGTTTTCTGT 59.906 34.615 0.00 0.00 45.14 3.41
6188 6375 3.312828 GTGAAACAAGTTTGTGTGCACA 58.687 40.909 17.42 17.42 41.31 4.57
6225 6412 6.778834 TGTATGCAGGAATCATTTTGTCAT 57.221 33.333 0.00 0.00 0.00 3.06
6315 6503 2.223433 GCATATGCTCTGCCACTGAAAC 60.223 50.000 20.64 0.00 38.21 2.78
6364 6552 9.606631 TCTTTGCAGTTTTTACCATTTAACAAT 57.393 25.926 0.00 0.00 0.00 2.71
6383 6571 7.701539 AACAATCTAAATGATAAGTGCCACA 57.298 32.000 0.00 0.00 34.45 4.17
6384 6572 7.088589 ACAATCTAAATGATAAGTGCCACAC 57.911 36.000 0.00 0.00 34.45 3.82
6385 6573 5.991328 ATCTAAATGATAAGTGCCACACG 57.009 39.130 0.00 0.00 34.93 4.49
6386 6574 4.827692 TCTAAATGATAAGTGCCACACGT 58.172 39.130 0.00 0.00 39.64 4.49
6387 6575 3.829886 AAATGATAAGTGCCACACGTG 57.170 42.857 15.48 15.48 39.64 4.49
6388 6576 2.472695 ATGATAAGTGCCACACGTGT 57.527 45.000 17.22 17.22 39.64 4.49
6389 6577 1.507562 TGATAAGTGCCACACGTGTG 58.492 50.000 36.13 36.13 45.23 3.82
6398 6586 3.817960 CACACGTGTGGCACTTAAC 57.182 52.632 35.65 7.86 42.10 2.01
6399 6587 1.010580 CACACGTGTGGCACTTAACA 58.989 50.000 35.65 0.00 42.10 2.41
6400 6588 1.398739 CACACGTGTGGCACTTAACAA 59.601 47.619 35.65 0.00 42.10 2.83
6401 6589 1.399089 ACACGTGTGGCACTTAACAAC 59.601 47.619 22.71 6.32 34.19 3.32
6402 6590 1.668751 CACGTGTGGCACTTAACAACT 59.331 47.619 19.83 0.00 31.34 3.16
6403 6591 2.096819 CACGTGTGGCACTTAACAACTT 59.903 45.455 19.83 0.00 31.34 2.66
6404 6592 2.096819 ACGTGTGGCACTTAACAACTTG 59.903 45.455 19.83 0.00 31.34 3.16
6405 6593 2.540769 CGTGTGGCACTTAACAACTTGG 60.541 50.000 19.83 0.00 31.34 3.61
6406 6594 2.028130 TGTGGCACTTAACAACTTGGG 58.972 47.619 19.83 0.00 0.00 4.12
6407 6595 1.036707 TGGCACTTAACAACTTGGGC 58.963 50.000 0.00 0.00 0.00 5.36
6408 6596 0.317160 GGCACTTAACAACTTGGGCC 59.683 55.000 0.00 0.00 0.00 5.80
6409 6597 0.039527 GCACTTAACAACTTGGGCCG 60.040 55.000 0.00 0.00 0.00 6.13
6410 6598 1.600023 CACTTAACAACTTGGGCCGA 58.400 50.000 0.00 0.00 0.00 5.54
6411 6599 1.950909 CACTTAACAACTTGGGCCGAA 59.049 47.619 0.00 0.00 0.00 4.30
6412 6600 1.951602 ACTTAACAACTTGGGCCGAAC 59.048 47.619 0.00 0.00 0.00 3.95
6413 6601 0.945813 TTAACAACTTGGGCCGAACG 59.054 50.000 0.00 0.00 0.00 3.95
6414 6602 1.508808 TAACAACTTGGGCCGAACGC 61.509 55.000 0.00 0.00 0.00 4.84
6415 6603 3.283684 CAACTTGGGCCGAACGCA 61.284 61.111 0.00 0.00 40.31 5.24
6416 6604 2.978010 AACTTGGGCCGAACGCAG 60.978 61.111 0.00 0.00 42.90 5.18
6418 6606 3.726517 CTTGGGCCGAACGCAGTG 61.727 66.667 0.00 0.00 45.00 3.66
6419 6607 4.243008 TTGGGCCGAACGCAGTGA 62.243 61.111 0.00 0.00 45.00 3.41
6420 6608 3.545124 TTGGGCCGAACGCAGTGAT 62.545 57.895 0.00 0.00 45.00 3.06
6421 6609 3.195698 GGGCCGAACGCAGTGATC 61.196 66.667 0.00 0.00 45.00 2.92
6422 6610 2.125512 GGCCGAACGCAGTGATCT 60.126 61.111 0.00 0.00 45.00 2.75
6423 6611 2.167861 GGCCGAACGCAGTGATCTC 61.168 63.158 0.00 0.00 45.00 2.75
6424 6612 2.167861 GCCGAACGCAGTGATCTCC 61.168 63.158 0.00 0.00 45.00 3.71
6425 6613 1.215382 CCGAACGCAGTGATCTCCA 59.785 57.895 0.00 0.00 45.00 3.86
6426 6614 0.179100 CCGAACGCAGTGATCTCCAT 60.179 55.000 0.00 0.00 45.00 3.41
6427 6615 1.645034 CGAACGCAGTGATCTCCATT 58.355 50.000 0.00 0.00 45.00 3.16
6428 6616 1.590238 CGAACGCAGTGATCTCCATTC 59.410 52.381 0.00 0.00 45.00 2.67
6429 6617 2.621338 GAACGCAGTGATCTCCATTCA 58.379 47.619 0.00 0.00 45.00 2.57
6430 6618 2.996249 ACGCAGTGATCTCCATTCAT 57.004 45.000 0.00 0.00 42.51 2.57
6431 6619 3.272574 ACGCAGTGATCTCCATTCATT 57.727 42.857 0.00 0.00 42.51 2.57
6432 6620 3.614092 ACGCAGTGATCTCCATTCATTT 58.386 40.909 0.00 0.00 42.51 2.32
6433 6621 4.012374 ACGCAGTGATCTCCATTCATTTT 58.988 39.130 0.00 0.00 42.51 1.82
6434 6622 4.095483 ACGCAGTGATCTCCATTCATTTTC 59.905 41.667 0.00 0.00 42.51 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 198 6.814954 TTGAGAGACCTATAGGCTTGAAAT 57.185 37.500 19.25 0.00 39.32 2.17
384 386 3.125316 CGAAAGAGTACCAAATCAGTGGC 59.875 47.826 0.00 0.00 43.00 5.01
536 539 3.378427 GCACTGATAGCTACCCCAAAAAG 59.622 47.826 0.00 0.00 0.00 2.27
573 576 4.465886 ACTATTATCGGTGAGCAGACTCT 58.534 43.478 0.00 0.00 43.85 3.24
812 839 5.071250 TCTCTGGTACAAACTAAAGGCTCAA 59.929 40.000 0.00 0.00 38.70 3.02
1253 1287 5.984926 GCAGAATTTGGTCTGAAATTTGTGA 59.015 36.000 6.39 0.00 46.76 3.58
1415 1449 2.817901 AGGCGTCGATATAAACACCAC 58.182 47.619 0.00 0.00 0.00 4.16
1730 1770 7.106239 ACCAAGAAATACTATGGTGACTTGAG 58.894 38.462 15.19 10.51 44.25 3.02
1752 1792 5.512942 TGATGGACAAGGAATTTAGACCA 57.487 39.130 0.00 0.00 0.00 4.02
1784 1824 5.971763 ACTTTACTCAGTCTGCATCCTAAG 58.028 41.667 0.00 0.00 0.00 2.18
1949 1989 1.799181 CGCAGGAACTCACTGGATACG 60.799 57.143 0.00 0.00 34.60 3.06
1950 1990 1.204941 ACGCAGGAACTCACTGGATAC 59.795 52.381 0.00 0.00 34.60 2.24
1968 2008 7.850982 GTGTGCAAACCTTCATAAATAGATACG 59.149 37.037 0.00 0.00 0.00 3.06
2036 2078 6.651975 AAGGACACATATACTACAGCTACC 57.348 41.667 0.00 0.00 0.00 3.18
2630 2675 0.383949 TTTTTGCCCGCTTCTGTGTC 59.616 50.000 0.00 0.00 0.00 3.67
2772 2817 3.444034 TCTTCGAACAGGAGTATCACAGG 59.556 47.826 0.00 0.00 36.25 4.00
3058 3103 1.352622 TGCAGACCCCCTTGTGAAGT 61.353 55.000 0.00 0.00 0.00 3.01
3131 3176 1.750399 CATCCGGAAAGCCTGGGTG 60.750 63.158 9.01 0.00 34.34 4.61
3132 3177 1.923395 TCATCCGGAAAGCCTGGGT 60.923 57.895 9.01 0.00 0.00 4.51
3323 3370 5.304686 TCAACGATATCAAGGCCCTAATT 57.695 39.130 0.00 0.00 0.00 1.40
3411 3458 5.760131 TGAGATCACATCAGACCTTCTCTA 58.240 41.667 0.00 0.00 31.61 2.43
3595 3642 1.453155 AGGTTTGTTGGCTATCGCTG 58.547 50.000 0.00 0.00 36.09 5.18
3636 3683 5.360649 AGGCCTCAGGATTCTTAACTTAC 57.639 43.478 0.00 0.00 0.00 2.34
3866 3914 5.298276 TCACATTGTTTGTCTGGTCCTAAAC 59.702 40.000 0.00 0.00 36.00 2.01
4062 4110 2.053627 GAAAACAGGAATGCTTGTGCG 58.946 47.619 0.00 0.00 43.34 5.34
4606 4656 0.893447 AGCCAGCTCCTTCATTTTGC 59.107 50.000 0.00 0.00 0.00 3.68
4680 4730 9.136323 GGAAAGGAAATATGGACTGACAATAAT 57.864 33.333 0.00 0.00 0.00 1.28
4747 4799 9.177608 CATTTTAGAACTATCCATCCAGACAAA 57.822 33.333 0.00 0.00 0.00 2.83
4748 4800 8.328758 ACATTTTAGAACTATCCATCCAGACAA 58.671 33.333 0.00 0.00 0.00 3.18
4749 4801 7.861629 ACATTTTAGAACTATCCATCCAGACA 58.138 34.615 0.00 0.00 0.00 3.41
5091 5166 7.448777 TGGCTGTTCCTGTAGATCTACTTATAG 59.551 40.741 28.53 18.90 37.00 1.31
5173 5262 7.576923 CGTTAATACGTAGCAAACAAAATTCG 58.423 34.615 0.08 0.00 42.72 3.34
5322 5417 6.565811 GCGATCGTTCATAATATCCTGCAAAA 60.566 38.462 17.81 0.00 0.00 2.44
5422 5517 7.889873 TTGTCTTTCCCATCAAGAGTAAAAA 57.110 32.000 0.00 0.00 30.72 1.94
5536 5631 4.917906 AATCAAACTTAGGGTCTCAGCT 57.082 40.909 0.00 0.00 0.00 4.24
5627 5723 7.021196 CCATATCTACAAACTGAACAAAACCG 58.979 38.462 0.00 0.00 0.00 4.44
5689 5792 7.395772 TGCCCTTCACATTGATTAAATTGAGTA 59.604 33.333 0.00 0.00 0.00 2.59
5705 5808 1.913951 ATCTCCGCATGCCCTTCACA 61.914 55.000 13.15 0.00 0.00 3.58
5795 5898 1.308998 GGAAATCATACCACAGCGGG 58.691 55.000 0.00 0.00 40.22 6.13
5851 6036 2.173519 CTCCCATGTGCCAAAGTGAAT 58.826 47.619 0.00 0.00 0.00 2.57
5853 6038 0.895100 GCTCCCATGTGCCAAAGTGA 60.895 55.000 0.00 0.00 0.00 3.41
5854 6039 1.180456 TGCTCCCATGTGCCAAAGTG 61.180 55.000 0.00 0.00 0.00 3.16
5855 6040 0.251922 ATGCTCCCATGTGCCAAAGT 60.252 50.000 0.00 0.00 0.00 2.66
5856 6041 1.766494 TATGCTCCCATGTGCCAAAG 58.234 50.000 0.00 0.00 32.85 2.77
5857 6042 2.228545 TTATGCTCCCATGTGCCAAA 57.771 45.000 0.00 0.00 32.85 3.28
5858 6043 2.457813 ATTATGCTCCCATGTGCCAA 57.542 45.000 0.00 0.00 32.85 4.52
5859 6044 3.074242 TCATATTATGCTCCCATGTGCCA 59.926 43.478 0.00 0.00 32.85 4.92
5860 6045 3.689347 TCATATTATGCTCCCATGTGCC 58.311 45.455 0.00 0.00 32.85 5.01
5861 6046 5.909621 AATCATATTATGCTCCCATGTGC 57.090 39.130 0.00 0.00 32.85 4.57
5862 6047 6.434965 TGGAAATCATATTATGCTCCCATGTG 59.565 38.462 12.80 0.00 32.85 3.21
5863 6048 6.554784 TGGAAATCATATTATGCTCCCATGT 58.445 36.000 12.80 0.00 32.85 3.21
5864 6049 7.655521 ATGGAAATCATATTATGCTCCCATG 57.344 36.000 13.73 0.00 33.61 3.66
5865 6050 8.674925 AAATGGAAATCATATTATGCTCCCAT 57.325 30.769 12.80 11.83 34.44 4.00
5866 6051 9.246670 CTAAATGGAAATCATATTATGCTCCCA 57.753 33.333 12.80 10.62 34.44 4.37
5867 6052 9.247861 ACTAAATGGAAATCATATTATGCTCCC 57.752 33.333 12.80 6.89 34.44 4.30
5869 6054 9.979270 CGACTAAATGGAAATCATATTATGCTC 57.021 33.333 0.00 0.00 34.44 4.26
5870 6055 9.507329 ACGACTAAATGGAAATCATATTATGCT 57.493 29.630 0.00 0.00 34.44 3.79
5871 6056 9.546909 CACGACTAAATGGAAATCATATTATGC 57.453 33.333 0.00 0.00 34.44 3.14
5874 6059 9.825109 TGACACGACTAAATGGAAATCATATTA 57.175 29.630 0.00 0.00 34.44 0.98
5875 6060 8.731275 TGACACGACTAAATGGAAATCATATT 57.269 30.769 0.00 0.00 34.44 1.28
5876 6061 8.612619 GTTGACACGACTAAATGGAAATCATAT 58.387 33.333 0.00 0.00 34.44 1.78
5877 6062 7.822334 AGTTGACACGACTAAATGGAAATCATA 59.178 33.333 0.00 0.00 34.44 2.15
5878 6063 6.655003 AGTTGACACGACTAAATGGAAATCAT 59.345 34.615 0.00 0.00 37.79 2.45
5879 6064 5.995282 AGTTGACACGACTAAATGGAAATCA 59.005 36.000 0.00 0.00 0.00 2.57
5880 6065 6.481954 AGTTGACACGACTAAATGGAAATC 57.518 37.500 0.00 0.00 0.00 2.17
5881 6066 9.661563 TTATAGTTGACACGACTAAATGGAAAT 57.338 29.630 0.00 0.00 33.66 2.17
5882 6067 9.491675 TTTATAGTTGACACGACTAAATGGAAA 57.508 29.630 0.00 0.00 33.66 3.13
5883 6068 9.146984 CTTTATAGTTGACACGACTAAATGGAA 57.853 33.333 0.00 0.00 33.66 3.53
5884 6069 8.525316 TCTTTATAGTTGACACGACTAAATGGA 58.475 33.333 0.00 0.00 33.66 3.41
5885 6070 8.697846 TCTTTATAGTTGACACGACTAAATGG 57.302 34.615 0.00 0.00 33.66 3.16
5887 6072 8.818057 GCATCTTTATAGTTGACACGACTAAAT 58.182 33.333 0.00 0.00 33.66 1.40
5888 6073 8.033038 AGCATCTTTATAGTTGACACGACTAAA 58.967 33.333 0.00 0.00 33.66 1.85
5889 6074 7.544622 AGCATCTTTATAGTTGACACGACTAA 58.455 34.615 0.00 0.00 33.66 2.24
5890 6075 7.096884 AGCATCTTTATAGTTGACACGACTA 57.903 36.000 0.00 0.00 34.38 2.59
5891 6076 5.967088 AGCATCTTTATAGTTGACACGACT 58.033 37.500 0.00 0.00 0.00 4.18
5892 6077 7.932120 ATAGCATCTTTATAGTTGACACGAC 57.068 36.000 0.00 0.00 0.00 4.34
5893 6078 8.942338 AAATAGCATCTTTATAGTTGACACGA 57.058 30.769 0.00 0.00 0.00 4.35
5894 6079 7.998767 CGAAATAGCATCTTTATAGTTGACACG 59.001 37.037 0.00 0.00 0.00 4.49
5895 6080 9.031360 TCGAAATAGCATCTTTATAGTTGACAC 57.969 33.333 0.00 0.00 0.00 3.67
5896 6081 9.594478 TTCGAAATAGCATCTTTATAGTTGACA 57.406 29.630 0.00 0.00 0.00 3.58
5906 6091 9.132521 CAAAGTGAATTTCGAAATAGCATCTTT 57.867 29.630 22.99 24.12 0.00 2.52
5907 6092 7.756722 CCAAAGTGAATTTCGAAATAGCATCTT 59.243 33.333 22.99 21.18 0.00 2.40
5908 6093 7.253422 CCAAAGTGAATTTCGAAATAGCATCT 58.747 34.615 22.99 17.86 0.00 2.90
5909 6094 6.020360 GCCAAAGTGAATTTCGAAATAGCATC 60.020 38.462 22.99 16.62 0.00 3.91
5910 6095 5.807011 GCCAAAGTGAATTTCGAAATAGCAT 59.193 36.000 22.99 8.13 0.00 3.79
5911 6096 5.160641 GCCAAAGTGAATTTCGAAATAGCA 58.839 37.500 22.99 19.79 0.00 3.49
5912 6097 5.060940 GTGCCAAAGTGAATTTCGAAATAGC 59.939 40.000 22.99 17.66 0.00 2.97
5913 6098 6.148948 TGTGCCAAAGTGAATTTCGAAATAG 58.851 36.000 22.99 7.86 0.00 1.73
5914 6099 6.078202 TGTGCCAAAGTGAATTTCGAAATA 57.922 33.333 22.99 6.53 0.00 1.40
5915 6100 4.942852 TGTGCCAAAGTGAATTTCGAAAT 58.057 34.783 17.60 17.60 0.00 2.17
5916 6101 4.377839 TGTGCCAAAGTGAATTTCGAAA 57.622 36.364 13.91 13.91 0.00 3.46
5917 6102 4.297510 CATGTGCCAAAGTGAATTTCGAA 58.702 39.130 0.00 0.00 0.00 3.71
5918 6103 3.305267 CCATGTGCCAAAGTGAATTTCGA 60.305 43.478 0.00 0.00 0.00 3.71
5919 6104 2.988493 CCATGTGCCAAAGTGAATTTCG 59.012 45.455 0.00 0.00 0.00 3.46
5920 6105 3.006752 TCCCATGTGCCAAAGTGAATTTC 59.993 43.478 0.00 0.00 0.00 2.17
5921 6106 2.971330 TCCCATGTGCCAAAGTGAATTT 59.029 40.909 0.00 0.00 0.00 1.82
6149 6336 5.379732 TTCACAGAAAACCGACAACTTTT 57.620 34.783 0.00 0.00 0.00 2.27
6150 6337 5.158494 GTTTCACAGAAAACCGACAACTTT 58.842 37.500 0.00 0.00 33.86 2.66
6168 6355 3.650070 TGTGCACACAAACTTGTTTCA 57.350 38.095 17.42 0.00 39.91 2.69
6188 6375 5.478332 TCCTGCATACATCTCGACATTCTAT 59.522 40.000 0.00 0.00 0.00 1.98
6253 6440 5.006649 GCTCCTGGTTTTCAAAATGTGTTTC 59.993 40.000 0.00 0.00 0.00 2.78
6364 6552 4.629634 CACGTGTGGCACTTATCATTTAGA 59.370 41.667 19.83 0.00 31.34 2.10
6380 6568 1.010580 TGTTAAGTGCCACACGTGTG 58.989 50.000 36.13 36.13 45.23 3.82
6381 6569 1.399089 GTTGTTAAGTGCCACACGTGT 59.601 47.619 17.22 17.22 39.64 4.49
6382 6570 1.668751 AGTTGTTAAGTGCCACACGTG 59.331 47.619 15.48 15.48 39.64 4.49
6383 6571 2.032680 AGTTGTTAAGTGCCACACGT 57.967 45.000 0.00 0.00 39.64 4.49
6384 6572 2.540769 CCAAGTTGTTAAGTGCCACACG 60.541 50.000 1.45 0.00 39.64 4.49
6385 6573 2.223711 CCCAAGTTGTTAAGTGCCACAC 60.224 50.000 1.45 0.00 34.10 3.82
6386 6574 2.028130 CCCAAGTTGTTAAGTGCCACA 58.972 47.619 1.45 0.00 0.00 4.17
6387 6575 1.269569 GCCCAAGTTGTTAAGTGCCAC 60.270 52.381 1.45 0.00 0.00 5.01
6388 6576 1.036707 GCCCAAGTTGTTAAGTGCCA 58.963 50.000 1.45 0.00 0.00 4.92
6389 6577 0.317160 GGCCCAAGTTGTTAAGTGCC 59.683 55.000 1.45 0.70 0.00 5.01
6390 6578 0.039527 CGGCCCAAGTTGTTAAGTGC 60.040 55.000 0.00 0.00 0.00 4.40
6391 6579 1.600023 TCGGCCCAAGTTGTTAAGTG 58.400 50.000 0.00 0.00 0.00 3.16
6392 6580 1.951602 GTTCGGCCCAAGTTGTTAAGT 59.048 47.619 0.00 0.00 0.00 2.24
6393 6581 1.069500 CGTTCGGCCCAAGTTGTTAAG 60.069 52.381 0.00 0.00 0.00 1.85
6394 6582 0.945813 CGTTCGGCCCAAGTTGTTAA 59.054 50.000 0.00 0.00 0.00 2.01
6395 6583 1.508808 GCGTTCGGCCCAAGTTGTTA 61.509 55.000 0.00 0.00 34.80 2.41
6396 6584 2.841160 GCGTTCGGCCCAAGTTGTT 61.841 57.895 0.00 0.00 34.80 2.83
6397 6585 3.284449 GCGTTCGGCCCAAGTTGT 61.284 61.111 0.00 0.00 34.80 3.32
6398 6586 3.254014 CTGCGTTCGGCCCAAGTTG 62.254 63.158 0.00 0.00 42.61 3.16
6399 6587 2.978010 CTGCGTTCGGCCCAAGTT 60.978 61.111 0.00 0.00 42.61 2.66
6400 6588 4.250305 ACTGCGTTCGGCCCAAGT 62.250 61.111 0.00 0.00 42.61 3.16
6401 6589 3.726517 CACTGCGTTCGGCCCAAG 61.727 66.667 0.00 0.00 42.61 3.61
6402 6590 3.545124 ATCACTGCGTTCGGCCCAA 62.545 57.895 0.00 0.00 42.61 4.12
6403 6591 3.950794 GATCACTGCGTTCGGCCCA 62.951 63.158 0.00 0.00 42.61 5.36
6404 6592 3.195698 GATCACTGCGTTCGGCCC 61.196 66.667 0.00 0.00 42.61 5.80
6405 6593 2.125512 AGATCACTGCGTTCGGCC 60.126 61.111 0.00 0.00 42.61 6.13
6406 6594 2.167861 GGAGATCACTGCGTTCGGC 61.168 63.158 0.00 0.00 43.96 5.54
6407 6595 0.179100 ATGGAGATCACTGCGTTCGG 60.179 55.000 0.00 0.00 37.28 4.30
6408 6596 1.590238 GAATGGAGATCACTGCGTTCG 59.410 52.381 0.00 0.00 45.32 3.95
6410 6598 2.768253 TGAATGGAGATCACTGCGTT 57.232 45.000 0.00 0.00 44.20 4.84
6411 6599 2.996249 ATGAATGGAGATCACTGCGT 57.004 45.000 0.00 0.00 37.28 5.24
6412 6600 4.595116 GAAAATGAATGGAGATCACTGCG 58.405 43.478 0.00 0.00 37.28 5.18


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

AutoCloner maintained by Alex Coulton.