Multiple sequence alignment - TraesCS7D01G504900

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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 TraesCS7D01G504900 chr7D 100.000 7199 0 0 1 7199 610773631 610780829 0.000000e+00 13295.0
1 TraesCS7D01G504900 chr7D 96.980 298 9 0 2528 2825 610775863 610776160 1.080000e-137 501.0
2 TraesCS7D01G504900 chr7D 96.980 298 9 0 2233 2530 610776158 610776455 1.080000e-137 501.0
3 TraesCS7D01G504900 chr7A 94.889 5439 135 40 1686 7065 700672819 700678173 0.000000e+00 8371.0
4 TraesCS7D01G504900 chr7A 97.471 1107 28 0 589 1695 700671674 700672780 0.000000e+00 1890.0
5 TraesCS7D01G504900 chr7A 92.500 440 26 5 1 439 700671176 700671609 2.210000e-174 623.0
6 TraesCS7D01G504900 chr7A 95.427 328 13 2 3835 4162 631667067 631666742 8.280000e-144 521.0
7 TraesCS7D01G504900 chr7A 94.753 324 17 0 3835 4158 683559840 683560163 8.330000e-139 505.0
8 TraesCS7D01G504900 chr7A 94.136 324 19 0 3835 4158 721272993 721273316 1.800000e-135 494.0
9 TraesCS7D01G504900 chr7A 95.973 298 12 0 2528 2825 700673366 700673663 1.090000e-132 484.0
10 TraesCS7D01G504900 chr7A 94.737 304 9 2 2233 2530 700673661 700673963 3.930000e-127 466.0
11 TraesCS7D01G504900 chr7A 93.407 273 17 1 3466 3738 683559572 683559843 3.130000e-108 403.0
12 TraesCS7D01G504900 chr7A 92.963 270 18 1 3469 3738 631667332 631667064 6.770000e-105 392.0
13 TraesCS7D01G504900 chr7B 93.807 3601 135 36 3553 7099 699377315 699373749 0.000000e+00 5334.0
14 TraesCS7D01G504900 chr7B 96.078 2983 100 11 589 3561 699381297 699378322 0.000000e+00 4844.0
15 TraesCS7D01G504900 chr7B 92.624 583 38 4 2912 3490 703575925 703576506 0.000000e+00 833.0
16 TraesCS7D01G504900 chr7B 92.167 600 30 9 1 591 699382019 699381428 0.000000e+00 832.0
17 TraesCS7D01G504900 chr7B 92.740 551 26 6 2952 3490 619069303 619068755 0.000000e+00 784.0
18 TraesCS7D01G504900 chr7B 96.309 298 11 0 2528 2825 699379644 699379347 2.330000e-134 490.0
19 TraesCS7D01G504900 chr7B 96.309 298 8 1 2233 2530 699379349 699379055 3.020000e-133 486.0
20 TraesCS7D01G504900 chr7B 100.000 64 0 0 2848 2911 54052624 54052687 1.270000e-22 119.0
21 TraesCS7D01G504900 chr6B 93.664 584 31 5 2912 3490 72321506 72320924 0.000000e+00 869.0
22 TraesCS7D01G504900 chr6B 93.482 583 33 4 2912 3490 72318712 72318131 0.000000e+00 861.0
23 TraesCS7D01G504900 chr6B 93.322 584 33 5 2912 3490 72315919 72315337 0.000000e+00 857.0
24 TraesCS7D01G504900 chr6B 93.322 584 33 5 2912 3490 72327102 72326520 0.000000e+00 857.0
25 TraesCS7D01G504900 chr6B 93.151 584 34 5 2912 3490 72324306 72323724 0.000000e+00 852.0
26 TraesCS7D01G504900 chr6B 95.217 230 11 0 3929 4158 687274859 687274630 1.480000e-96 364.0
27 TraesCS7D01G504900 chr6B 94.608 204 11 0 3469 3672 687275070 687274867 4.190000e-82 316.0
28 TraesCS7D01G504900 chr3A 95.988 324 13 0 3835 4158 497908878 497909201 1.780000e-145 527.0
29 TraesCS7D01G504900 chr3A 93.040 273 18 1 3466 3738 497908610 497908881 1.460000e-106 398.0
30 TraesCS7D01G504900 chr5A 94.444 324 18 0 3835 4158 195559037 195559360 3.880000e-137 499.0
31 TraesCS7D01G504900 chr5A 93.407 273 17 1 3466 3738 195558769 195559040 3.130000e-108 403.0
32 TraesCS7D01G504900 chr5A 96.429 56 2 0 7143 7198 386163004 386163059 7.690000e-15 93.5
33 TraesCS7D01G504900 chr5A 92.063 63 5 0 7137 7199 495395608 495395546 9.950000e-14 89.8
34 TraesCS7D01G504900 chr1A 94.207 328 18 1 3835 4162 174399850 174399524 3.880000e-137 499.0
35 TraesCS7D01G504900 chr1A 92.963 270 18 1 3469 3738 174400115 174399847 6.770000e-105 392.0
36 TraesCS7D01G504900 chr1A 100.000 64 0 0 2848 2911 94578141 94578078 1.270000e-22 119.0
37 TraesCS7D01G504900 chr1A 100.000 64 0 0 2848 2911 94666691 94666754 1.270000e-22 119.0
38 TraesCS7D01G504900 chr1A 93.548 62 2 2 7139 7199 133163551 133163611 2.770000e-14 91.6
39 TraesCS7D01G504900 chr1A 91.045 67 4 2 7133 7199 337152800 337152864 9.950000e-14 89.8
40 TraesCS7D01G504900 chrUn 93.009 329 17 5 2912 3236 69801110 69800784 6.530000e-130 475.0
41 TraesCS7D01G504900 chrUn 100.000 64 0 0 2848 2911 171005526 171005463 1.270000e-22 119.0
42 TraesCS7D01G504900 chr3B 93.301 209 14 0 3464 3672 752874051 752874259 7.010000e-80 309.0
43 TraesCS7D01G504900 chr3B 96.491 57 1 1 7144 7199 586527278 586527334 7.690000e-15 93.5
44 TraesCS7D01G504900 chr4D 100.000 64 0 0 2848 2911 123398764 123398701 1.270000e-22 119.0
45 TraesCS7D01G504900 chr4B 100.000 64 0 0 2848 2911 623344603 623344540 1.270000e-22 119.0
46 TraesCS7D01G504900 chr1D 100.000 64 0 0 2848 2911 212448328 212448391 1.270000e-22 119.0
47 TraesCS7D01G504900 chr5D 96.552 58 2 0 7142 7199 406201093 406201150 5.940000e-16 97.1
48 TraesCS7D01G504900 chr5D 94.915 59 1 2 7142 7199 502656319 502656262 2.770000e-14 91.6
49 TraesCS7D01G504900 chr6D 95.082 61 1 2 7141 7199 75402904 75402964 2.140000e-15 95.3
50 TraesCS7D01G504900 chr6A 92.063 63 4 1 7138 7199 63210492 63210430 3.580000e-13 87.9


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 TraesCS7D01G504900 chr7D 610773631 610780829 7198 False 13295.0 13295 100.000000 1 7199 1 chr7D.!!$F1 7198
1 TraesCS7D01G504900 chr7D 610775863 610776455 592 False 501.0 501 96.980000 2233 2825 2 chr7D.!!$F2 592
2 TraesCS7D01G504900 chr7A 700671176 700678173 6997 False 3628.0 8371 94.953333 1 7065 3 chr7A.!!$F3 7064
3 TraesCS7D01G504900 chr7A 700673366 700673963 597 False 475.0 484 95.355000 2233 2825 2 chr7A.!!$F4 592
4 TraesCS7D01G504900 chr7A 631666742 631667332 590 True 456.5 521 94.195000 3469 4162 2 chr7A.!!$R1 693
5 TraesCS7D01G504900 chr7A 683559572 683560163 591 False 454.0 505 94.080000 3466 4158 2 chr7A.!!$F2 692
6 TraesCS7D01G504900 chr7B 699373749 699382019 8270 True 2397.2 5334 94.934000 1 7099 5 chr7B.!!$R2 7098
7 TraesCS7D01G504900 chr7B 703575925 703576506 581 False 833.0 833 92.624000 2912 3490 1 chr7B.!!$F2 578
8 TraesCS7D01G504900 chr7B 619068755 619069303 548 True 784.0 784 92.740000 2952 3490 1 chr7B.!!$R1 538
9 TraesCS7D01G504900 chr6B 72315337 72327102 11765 True 859.2 869 93.388200 2912 3490 5 chr6B.!!$R1 578
10 TraesCS7D01G504900 chr3A 497908610 497909201 591 False 462.5 527 94.514000 3466 4158 2 chr3A.!!$F1 692
11 TraesCS7D01G504900 chr5A 195558769 195559360 591 False 451.0 499 93.925500 3466 4158 2 chr5A.!!$F2 692
12 TraesCS7D01G504900 chr1A 174399524 174400115 591 True 445.5 499 93.585000 3469 4162 2 chr1A.!!$R2 693

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
529 539 0.250901 AAGGCCACGTGCAGATTCTT 60.251 50.000 10.91 4.00 43.89 2.52 F
1269 1412 1.408702 ACCGTGGATTGCAATAATGGC 59.591 47.619 23.60 9.01 0.00 4.40 F
1585 1728 2.239907 GCTATGGATACCCCCAAGGATC 59.760 54.545 0.00 0.00 40.04 3.36 F
3494 9310 0.681175 AGCTTGCATGTTTGTTCCCC 59.319 50.000 1.14 0.00 0.00 4.81 F
3844 11043 2.937149 GCGAAACTTTAGGAGATGGGTC 59.063 50.000 0.00 0.00 0.00 4.46 F
5484 17134 0.835971 TCACTAAGCACTCCCAGCCA 60.836 55.000 0.00 0.00 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2289 1.747355 CATGACTGGTTCATCCTTGCC 59.253 52.381 0.00 0.00 43.68 4.52 R
2841 3047 5.541484 AGGTCTTTCTCCTTACCGTTCTTTA 59.459 40.000 0.00 0.00 37.09 1.85 R
3535 9353 5.570205 TGGTTCAAGGAATGGTAACTACA 57.430 39.130 0.00 0.00 37.61 2.74 R
4514 16158 0.258774 AGGCTTTACCGGATTGGCAT 59.741 50.000 9.46 1.51 46.52 4.40 R
5607 17257 0.326264 AACCCTGGATCAGCTGTGAC 59.674 55.000 14.67 5.50 34.75 3.67 R
6761 18435 0.109342 CCCCACACAGGCATCTATCC 59.891 60.000 0.00 0.00 35.39 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
89 90 0.611714 GTGGTGACCGTTGGGACTAT 59.388 55.000 0.00 0.00 36.97 2.12
91 92 1.826720 TGGTGACCGTTGGGACTATAC 59.173 52.381 0.00 0.00 36.97 1.47
107 108 6.462067 GGGACTATACAGGTTGCGTTATTACT 60.462 42.308 0.00 0.00 0.00 2.24
188 193 1.203287 GGGTTTCTCGGTTACGTAGCT 59.797 52.381 9.39 0.00 41.85 3.32
290 299 5.817296 TGAAGATGATTTTATCGTGGAGGTG 59.183 40.000 0.00 0.00 32.33 4.00
291 300 4.130118 AGATGATTTTATCGTGGAGGTGC 58.870 43.478 0.00 0.00 32.33 5.01
292 301 3.342377 TGATTTTATCGTGGAGGTGCA 57.658 42.857 0.00 0.00 0.00 4.57
293 302 3.884895 TGATTTTATCGTGGAGGTGCAT 58.115 40.909 0.00 0.00 0.00 3.96
319 328 4.706035 AGGTGTCGATCGTAGATAGAAGT 58.294 43.478 15.94 0.00 45.12 3.01
403 412 3.832276 CGATTTTCGCCCTTCAAATGAA 58.168 40.909 0.00 0.00 31.14 2.57
415 424 6.369890 GCCCTTCAAATGAATTTCCTTTTCTC 59.630 38.462 0.00 0.00 33.01 2.87
433 443 9.821662 CCTTTTCTCTTAAAGTTTTATGTACCG 57.178 33.333 0.00 0.00 34.11 4.02
439 449 8.789825 TCTTAAAGTTTTATGTACCGCCAATA 57.210 30.769 0.00 0.00 0.00 1.90
466 476 9.944376 GGAAGGTATAAATATCAGCATTAGTCA 57.056 33.333 0.00 0.00 0.00 3.41
529 539 0.250901 AAGGCCACGTGCAGATTCTT 60.251 50.000 10.91 4.00 43.89 2.52
534 544 3.234386 GCCACGTGCAGATTCTTTTTAC 58.766 45.455 10.91 0.00 40.77 2.01
545 555 8.941977 TGCAGATTCTTTTTACGTACATAATGT 58.058 29.630 0.00 0.00 0.00 2.71
563 573 8.157476 ACATAATGTATTGGTGGGAGTAGATTC 58.843 37.037 0.00 0.00 0.00 2.52
670 813 6.199557 TGCCCTAAGCCTATTTTGATGATA 57.800 37.500 0.00 0.00 42.71 2.15
689 832 1.645710 ATCGACAGGACTTCCCTTGT 58.354 50.000 0.00 0.00 44.85 3.16
1269 1412 1.408702 ACCGTGGATTGCAATAATGGC 59.591 47.619 23.60 9.01 0.00 4.40
1288 1431 2.608268 GCCCTTCTTCTAGAACACGAC 58.392 52.381 0.00 0.00 29.89 4.34
1585 1728 2.239907 GCTATGGATACCCCCAAGGATC 59.760 54.545 0.00 0.00 40.04 3.36
1637 1783 3.081409 ACGCCCCGCTGATAAGGT 61.081 61.111 0.00 0.00 0.00 3.50
1685 1831 2.839486 TGTTTGTTTTGGGTGCAACA 57.161 40.000 3.06 0.00 39.98 3.33
2089 2289 6.127054 TGACTCATTCCATTACTAGGTTCAGG 60.127 42.308 0.00 0.00 0.00 3.86
2841 3047 6.588719 TGTGGCTGTGCTTTATTTTAATCT 57.411 33.333 0.00 0.00 0.00 2.40
3091 8894 5.471456 TCATTCTCAAGGACTTTCAAGAAGC 59.529 40.000 0.00 0.00 0.00 3.86
3248 9064 9.612066 AATTTTCCTTGACATTGTTTTGTGTAT 57.388 25.926 0.00 0.00 0.00 2.29
3493 9309 2.295909 TGTAGCTTGCATGTTTGTTCCC 59.704 45.455 0.00 0.00 0.00 3.97
3494 9310 0.681175 AGCTTGCATGTTTGTTCCCC 59.319 50.000 1.14 0.00 0.00 4.81
3513 9329 5.930135 TCCCCTAGAACATAGAAAGAATGC 58.070 41.667 0.00 0.00 0.00 3.56
3535 9353 6.826668 TGCAAGTGCTATGTATGTAGGTATT 58.173 36.000 4.69 0.00 42.66 1.89
3844 11043 2.937149 GCGAAACTTTAGGAGATGGGTC 59.063 50.000 0.00 0.00 0.00 4.46
4056 15694 9.342308 TCTCTTATATATGTGGCTTCCTTTTTG 57.658 33.333 0.00 0.00 0.00 2.44
4514 16158 3.342377 TGAGCCGACCATTGTAAATCA 57.658 42.857 0.00 0.00 0.00 2.57
4523 16167 5.280654 ACCATTGTAAATCATGCCAATCC 57.719 39.130 0.00 0.00 0.00 3.01
5317 16967 1.582968 GCTGTGAACCACATGCAGG 59.417 57.895 0.00 0.00 43.71 4.85
5365 17015 1.722011 ACAATTAGGTCAAGCCGACG 58.278 50.000 0.00 0.00 46.42 5.12
5388 17038 2.359214 TGTGAAGCAAATGCAAACCGTA 59.641 40.909 8.28 0.00 45.16 4.02
5478 17128 5.105310 TCAGGAATACTTCACTAAGCACTCC 60.105 44.000 0.00 0.00 36.05 3.85
5484 17134 0.835971 TCACTAAGCACTCCCAGCCA 60.836 55.000 0.00 0.00 0.00 4.75
5547 17197 1.296056 ACACCGCCAATCAACTACGC 61.296 55.000 0.00 0.00 0.00 4.42
5570 17220 4.511617 TCAGTCAAGCTAACTCTGTCAG 57.488 45.455 0.00 0.00 0.00 3.51
5571 17221 2.992543 CAGTCAAGCTAACTCTGTCAGC 59.007 50.000 0.00 0.00 35.49 4.26
5607 17257 2.356135 CAGGAAAATACCACCAGTCGG 58.644 52.381 0.00 0.00 38.77 4.79
5646 17296 6.608002 AGGGTTTAACTGTCAACCAAATACAA 59.392 34.615 18.52 0.00 43.89 2.41
5689 17339 4.368315 CAGATACTTGCAGCCACGTTATA 58.632 43.478 0.00 0.00 0.00 0.98
5839 17489 1.002134 CCCATTGCAACCTCCTCGT 60.002 57.895 0.00 0.00 0.00 4.18
5850 17500 3.045601 ACCTCCTCGTCAAATGTTGAG 57.954 47.619 0.00 0.00 41.01 3.02
5898 17548 1.135141 GTTTTGCCAACACAGACTGCA 60.135 47.619 1.25 0.00 0.00 4.41
5900 17550 0.107263 TTGCCAACACAGACTGCAGA 60.107 50.000 23.35 0.00 32.88 4.26
5946 17596 2.788640 CGCCCTGCCATCATTTGGG 61.789 63.158 0.00 0.00 46.55 4.12
5967 17617 0.257039 ATTCCTGGTCAGACCCATGC 59.743 55.000 17.59 0.00 37.50 4.06
6233 17883 1.001068 TGAATGGACGAACCGCTTGTA 59.999 47.619 0.00 0.00 42.61 2.41
6243 17893 2.774439 ACCGCTTGTACTTGCAAAAG 57.226 45.000 0.00 2.16 0.00 2.27
6245 17895 1.408422 CGCTTGTACTTGCAAAAGGC 58.592 50.000 9.93 3.69 45.13 4.35
6254 17906 2.961062 ACTTGCAAAAGGCTGATGTTCT 59.039 40.909 0.00 0.00 45.15 3.01
6261 17913 2.283145 AGGCTGATGTTCTGCTTGTT 57.717 45.000 6.38 0.00 40.57 2.83
6326 17978 1.131504 CGAGCTCGAAGCAGTAGTCTT 59.868 52.381 32.06 0.00 45.56 3.01
6327 17979 2.525055 GAGCTCGAAGCAGTAGTCTTG 58.475 52.381 0.00 0.00 45.56 3.02
6328 17980 0.995728 GCTCGAAGCAGTAGTCTTGC 59.004 55.000 2.53 0.00 41.89 4.01
6329 17981 1.403514 GCTCGAAGCAGTAGTCTTGCT 60.404 52.381 0.00 0.00 41.89 3.91
6330 17982 2.159366 GCTCGAAGCAGTAGTCTTGCTA 60.159 50.000 0.00 0.00 41.89 3.49
6331 17983 3.690422 CTCGAAGCAGTAGTCTTGCTAG 58.310 50.000 0.00 0.00 38.01 3.42
6332 17984 2.159366 TCGAAGCAGTAGTCTTGCTAGC 60.159 50.000 8.10 8.10 38.01 3.42
6333 17985 2.189342 GAAGCAGTAGTCTTGCTAGCG 58.811 52.381 10.77 0.00 38.01 4.26
6334 17986 0.179124 AGCAGTAGTCTTGCTAGCGC 60.179 55.000 10.77 0.00 37.11 5.92
6335 17987 0.179124 GCAGTAGTCTTGCTAGCGCT 60.179 55.000 17.26 17.26 36.97 5.92
6336 17988 1.833860 CAGTAGTCTTGCTAGCGCTC 58.166 55.000 16.34 0.00 36.97 5.03
6337 17989 1.403679 CAGTAGTCTTGCTAGCGCTCT 59.596 52.381 16.34 5.29 36.97 4.09
6338 17990 2.096248 AGTAGTCTTGCTAGCGCTCTT 58.904 47.619 16.34 0.00 36.97 2.85
6339 17991 2.159310 AGTAGTCTTGCTAGCGCTCTTG 60.159 50.000 16.34 6.94 36.97 3.02
6340 17992 0.739112 AGTCTTGCTAGCGCTCTTGC 60.739 55.000 16.34 18.03 40.66 4.01
6359 18011 2.287547 TGCGTTTTTGTGATCCTTCTGC 60.288 45.455 0.00 0.00 0.00 4.26
6513 18170 8.917415 TTTGTTTTCTGTTTTGTTTTGCTTTT 57.083 23.077 0.00 0.00 0.00 2.27
6566 18223 3.202818 TGATGTATCATCAGGGCCAACTT 59.797 43.478 6.18 0.00 0.00 2.66
6579 18236 0.040425 CCAACTTGCTAACACACCGC 60.040 55.000 0.00 0.00 0.00 5.68
6721 18395 4.392940 AGCAATACCATTGCCAGTATCTC 58.607 43.478 17.79 0.00 45.98 2.75
6722 18396 4.103785 AGCAATACCATTGCCAGTATCTCT 59.896 41.667 17.79 0.00 45.98 3.10
6723 18397 5.307976 AGCAATACCATTGCCAGTATCTCTA 59.692 40.000 17.79 0.00 45.98 2.43
6724 18398 5.641209 GCAATACCATTGCCAGTATCTCTAG 59.359 44.000 11.89 0.00 39.38 2.43
6761 18435 8.547894 CAAAAGTGCATTTTCATATGATGGATG 58.452 33.333 7.72 11.59 39.11 3.51
6762 18436 6.340962 AGTGCATTTTCATATGATGGATGG 57.659 37.500 6.17 0.00 0.00 3.51
6763 18437 6.072649 AGTGCATTTTCATATGATGGATGGA 58.927 36.000 6.17 9.40 0.00 3.41
6764 18438 6.724441 AGTGCATTTTCATATGATGGATGGAT 59.276 34.615 6.17 1.76 0.00 3.41
6774 18448 3.254089 TGATGGATGGATAGATGCCTGT 58.746 45.455 0.00 0.00 0.00 4.00
6775 18449 3.008704 TGATGGATGGATAGATGCCTGTG 59.991 47.826 0.00 0.00 0.00 3.66
6787 18461 3.297620 CCTGTGTGGGGCAGTTGC 61.298 66.667 0.00 0.00 41.14 4.17
6897 18573 4.900635 AGTTTTGCTTCGTGTTCTTCAT 57.099 36.364 0.00 0.00 0.00 2.57
6898 18574 4.601019 AGTTTTGCTTCGTGTTCTTCATG 58.399 39.130 0.00 0.00 34.61 3.07
6900 18576 5.009010 AGTTTTGCTTCGTGTTCTTCATGAT 59.991 36.000 0.00 0.00 41.08 2.45
6901 18577 4.408993 TTGCTTCGTGTTCTTCATGATG 57.591 40.909 0.00 0.00 41.08 3.07
6971 18676 5.708948 TCTCAGCAAAAATAACCGAAATGG 58.291 37.500 0.00 0.00 46.41 3.16
7019 18724 4.820897 TCAGTGGCAGTCATACAAACTAG 58.179 43.478 0.00 0.00 0.00 2.57
7025 18730 5.932303 TGGCAGTCATACAAACTAGAGAAAC 59.068 40.000 0.00 0.00 0.00 2.78
7027 18732 6.128526 GGCAGTCATACAAACTAGAGAAACAC 60.129 42.308 0.00 0.00 0.00 3.32
7053 18759 6.150140 AGCACCATCAGTCAGTTAAAATCTTC 59.850 38.462 0.00 0.00 0.00 2.87
7078 18784 1.485838 GATGACGCACGGCTCATCTG 61.486 60.000 18.99 0.00 38.67 2.90
7099 18805 1.066358 TGCCTCAGAGATTCTGCAGTG 60.066 52.381 14.67 3.29 43.95 3.66
7100 18806 1.206610 GCCTCAGAGATTCTGCAGTGA 59.793 52.381 14.67 7.93 43.95 3.41
7101 18807 2.739287 GCCTCAGAGATTCTGCAGTGAG 60.739 54.545 18.25 18.25 43.95 3.51
7102 18808 2.496871 CCTCAGAGATTCTGCAGTGAGT 59.503 50.000 21.54 5.35 43.95 3.41
7103 18809 3.513662 CTCAGAGATTCTGCAGTGAGTG 58.486 50.000 14.67 5.51 43.95 3.51
7119 18825 3.865446 TGAGTGCAGTCCTCACATATTG 58.135 45.455 18.82 0.00 36.93 1.90
7120 18826 2.611292 GAGTGCAGTCCTCACATATTGC 59.389 50.000 10.66 0.00 36.93 3.56
7121 18827 1.328680 GTGCAGTCCTCACATATTGCG 59.671 52.381 0.00 0.00 34.44 4.85
7122 18828 1.066215 TGCAGTCCTCACATATTGCGT 60.066 47.619 0.00 0.00 34.44 5.24
7123 18829 1.594862 GCAGTCCTCACATATTGCGTC 59.405 52.381 0.00 0.00 0.00 5.19
7124 18830 2.892374 CAGTCCTCACATATTGCGTCA 58.108 47.619 0.00 0.00 0.00 4.35
7125 18831 2.604914 CAGTCCTCACATATTGCGTCAC 59.395 50.000 0.00 0.00 0.00 3.67
7126 18832 2.233676 AGTCCTCACATATTGCGTCACA 59.766 45.455 0.00 0.00 0.00 3.58
7127 18833 3.118629 AGTCCTCACATATTGCGTCACAT 60.119 43.478 0.00 0.00 0.00 3.21
7128 18834 3.246226 GTCCTCACATATTGCGTCACATC 59.754 47.826 0.00 0.00 0.00 3.06
7129 18835 3.118811 TCCTCACATATTGCGTCACATCA 60.119 43.478 0.00 0.00 0.00 3.07
7130 18836 3.001634 CCTCACATATTGCGTCACATCAC 59.998 47.826 0.00 0.00 0.00 3.06
7131 18837 3.594134 TCACATATTGCGTCACATCACA 58.406 40.909 0.00 0.00 0.00 3.58
7132 18838 3.370672 TCACATATTGCGTCACATCACAC 59.629 43.478 0.00 0.00 0.00 3.82
7133 18839 3.124976 CACATATTGCGTCACATCACACA 59.875 43.478 0.00 0.00 0.00 3.72
7134 18840 3.940852 ACATATTGCGTCACATCACACAT 59.059 39.130 0.00 0.00 0.00 3.21
7135 18841 5.006552 CACATATTGCGTCACATCACACATA 59.993 40.000 0.00 0.00 0.00 2.29
7136 18842 5.584251 ACATATTGCGTCACATCACACATAA 59.416 36.000 0.00 0.00 0.00 1.90
7137 18843 3.804518 TTGCGTCACATCACACATAAC 57.195 42.857 0.00 0.00 0.00 1.89
7138 18844 2.760374 TGCGTCACATCACACATAACA 58.240 42.857 0.00 0.00 0.00 2.41
7139 18845 3.333804 TGCGTCACATCACACATAACAT 58.666 40.909 0.00 0.00 0.00 2.71
7140 18846 3.124976 TGCGTCACATCACACATAACATG 59.875 43.478 0.00 0.00 0.00 3.21
7141 18847 3.125146 GCGTCACATCACACATAACATGT 59.875 43.478 0.00 0.00 46.22 3.21
7142 18848 4.328712 GCGTCACATCACACATAACATGTA 59.671 41.667 0.00 0.00 42.70 2.29
7143 18849 5.006649 GCGTCACATCACACATAACATGTAT 59.993 40.000 0.00 0.00 42.70 2.29
7144 18850 6.200097 GCGTCACATCACACATAACATGTATA 59.800 38.462 0.00 0.00 42.70 1.47
7145 18851 7.254286 GCGTCACATCACACATAACATGTATAA 60.254 37.037 0.00 0.00 42.70 0.98
7146 18852 8.764287 CGTCACATCACACATAACATGTATAAT 58.236 33.333 0.00 0.00 42.70 1.28
7168 18874 9.845214 ATAATAATGGGAGTACCTAGAACTCAT 57.155 33.333 20.28 9.26 44.25 2.90
7169 18875 7.784470 ATAATGGGAGTACCTAGAACTCATC 57.216 40.000 20.28 14.32 44.25 2.92
7170 18876 4.883021 TGGGAGTACCTAGAACTCATCT 57.117 45.455 20.28 0.00 44.25 2.90
7171 18877 5.988865 TGGGAGTACCTAGAACTCATCTA 57.011 43.478 20.28 5.84 44.25 1.98
7189 18895 7.348080 TCATCTAGATGAGACGTAATTTGGT 57.652 36.000 27.93 0.00 42.42 3.67
7190 18896 7.426410 TCATCTAGATGAGACGTAATTTGGTC 58.574 38.462 27.93 1.46 42.42 4.02
7191 18897 6.145338 TCTAGATGAGACGTAATTTGGTCC 57.855 41.667 0.00 0.00 33.66 4.46
7192 18898 4.138487 AGATGAGACGTAATTTGGTCCC 57.862 45.455 0.00 0.00 33.66 4.46
7193 18899 3.517901 AGATGAGACGTAATTTGGTCCCA 59.482 43.478 0.00 1.31 33.66 4.37
7194 18900 3.992943 TGAGACGTAATTTGGTCCCAT 57.007 42.857 0.00 0.00 33.66 4.00
7195 18901 4.295141 TGAGACGTAATTTGGTCCCATT 57.705 40.909 0.00 0.00 33.66 3.16
7196 18902 4.258543 TGAGACGTAATTTGGTCCCATTC 58.741 43.478 0.00 0.00 33.66 2.67
7197 18903 4.258543 GAGACGTAATTTGGTCCCATTCA 58.741 43.478 0.00 0.00 33.66 2.57
7198 18904 4.007659 AGACGTAATTTGGTCCCATTCAC 58.992 43.478 0.00 0.00 33.66 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 6.019640 GCGAATAAGTAATAACGCAACCTGTA 60.020 38.462 0.00 0.00 40.50 2.74
91 92 5.195379 GCGAATAAGTAATAACGCAACCTG 58.805 41.667 0.00 0.00 40.50 4.00
107 108 3.302434 CGTCTGTCTTTTAGCGCGAATAA 59.698 43.478 12.10 5.01 0.00 1.40
243 248 4.574828 ACGCATCCATCAATACACTAAACC 59.425 41.667 0.00 0.00 0.00 3.27
290 299 1.922570 ACGATCGACACCTTACATGC 58.077 50.000 24.34 0.00 0.00 4.06
291 300 4.547406 TCTACGATCGACACCTTACATG 57.453 45.455 24.34 0.00 0.00 3.21
292 301 6.228995 TCTATCTACGATCGACACCTTACAT 58.771 40.000 24.34 0.00 0.00 2.29
293 302 5.604565 TCTATCTACGATCGACACCTTACA 58.395 41.667 24.34 0.00 0.00 2.41
319 328 2.107343 CACACGACAACACGGGGA 59.893 61.111 0.00 0.00 41.28 4.81
415 424 8.126700 CCTATTGGCGGTACATAAAACTTTAAG 58.873 37.037 0.00 0.00 0.00 1.85
433 443 7.829211 TGCTGATATTTATACCTTCCTATTGGC 59.171 37.037 0.00 0.00 0.00 4.52
514 524 3.059188 ACGTAAAAAGAATCTGCACGTGG 60.059 43.478 18.88 0.92 39.43 4.94
529 539 8.045507 TCCCACCAATACATTATGTACGTAAAA 58.954 33.333 11.45 1.73 35.42 1.52
534 544 5.607477 ACTCCCACCAATACATTATGTACG 58.393 41.667 7.26 2.28 35.42 3.67
545 555 6.143915 AGCTAAGAATCTACTCCCACCAATA 58.856 40.000 0.00 0.00 0.00 1.90
689 832 1.704628 TCCATTCAGCCCTTTCTGTGA 59.295 47.619 0.00 0.00 35.63 3.58
1269 1412 2.228343 ACGTCGTGTTCTAGAAGAAGGG 59.772 50.000 14.07 9.73 34.42 3.95
1288 1431 1.175983 TTTGCCCTAACAAGCCCACG 61.176 55.000 0.00 0.00 0.00 4.94
1549 1692 5.860941 TCCATAGCAGAGTTTCCTCTAAG 57.139 43.478 0.00 0.00 46.52 2.18
1637 1783 8.593945 AAGGGAACAATTTAGAGATTTGCATA 57.406 30.769 0.00 0.00 0.00 3.14
1704 1898 7.654923 GCAAGGAAAAGAGAAGTGATGATTTTT 59.345 33.333 0.00 0.00 0.00 1.94
1745 1944 3.591527 ACCCCTTAATGACTGGTTCATCA 59.408 43.478 0.00 0.00 44.86 3.07
2089 2289 1.747355 CATGACTGGTTCATCCTTGCC 59.253 52.381 0.00 0.00 43.68 4.52
2841 3047 5.541484 AGGTCTTTCTCCTTACCGTTCTTTA 59.459 40.000 0.00 0.00 37.09 1.85
3118 8921 6.114221 GCTAATTGCTATCAACACGGTTAA 57.886 37.500 0.00 0.00 38.95 2.01
3255 9071 7.939784 ATTAGAGGTAAAACAAGGGATTCAC 57.060 36.000 0.00 0.00 0.00 3.18
3260 9076 8.856103 CAAAAGAATTAGAGGTAAAACAAGGGA 58.144 33.333 0.00 0.00 0.00 4.20
3493 9309 7.678218 GCACTTGCATTCTTTCTATGTTCTAGG 60.678 40.741 0.00 0.00 41.59 3.02
3494 9310 7.065563 AGCACTTGCATTCTTTCTATGTTCTAG 59.934 37.037 3.62 0.00 45.16 2.43
3513 9329 9.411801 CTACAATACCTACATACATAGCACTTG 57.588 37.037 0.00 0.00 0.00 3.16
3535 9353 5.570205 TGGTTCAAGGAATGGTAACTACA 57.430 39.130 0.00 0.00 37.61 2.74
3603 10802 3.552875 AGAATTGCCACATGATGAGGAG 58.447 45.455 13.24 0.00 28.90 3.69
3823 11022 2.937149 GACCCATCTCCTAAAGTTTCGC 59.063 50.000 0.00 0.00 0.00 4.70
4514 16158 0.258774 AGGCTTTACCGGATTGGCAT 59.741 50.000 9.46 1.51 46.52 4.40
4550 16194 6.703319 TCAGGATTAACTTTTCGTACATCCA 58.297 36.000 6.02 0.00 37.04 3.41
4652 16296 2.513204 CTGCCTGGCTCACATCCG 60.513 66.667 21.03 0.00 0.00 4.18
5317 16967 0.672711 GCGGTGTTCTCCTGGTTACC 60.673 60.000 0.00 0.00 0.00 2.85
5388 17038 2.158900 CCGATCAGTGCTATTTCCCTGT 60.159 50.000 0.00 0.00 0.00 4.00
5444 17094 8.779354 AGTGAAGTATTCCTGAATAGTTTGTC 57.221 34.615 16.94 8.71 46.93 3.18
5478 17128 2.024414 GTATTTACTGGGCTTGGCTGG 58.976 52.381 0.00 0.00 0.00 4.85
5547 17197 4.876125 TGACAGAGTTAGCTTGACTGAAG 58.124 43.478 7.12 0.89 33.53 3.02
5570 17220 1.403249 CCTGCATAGTTTGTGCCTTGC 60.403 52.381 0.00 0.00 41.83 4.01
5571 17221 2.161855 TCCTGCATAGTTTGTGCCTTG 58.838 47.619 0.00 0.00 41.83 3.61
5607 17257 0.326264 AACCCTGGATCAGCTGTGAC 59.674 55.000 14.67 5.50 34.75 3.67
5646 17296 4.850680 TGGTATTGTTTTCCCGAATAGCT 58.149 39.130 0.00 0.00 33.29 3.32
5689 17339 6.176183 CAGACTGTTGGATAGGATTTTCAGT 58.824 40.000 0.00 0.00 37.56 3.41
5839 17489 2.177394 TACTGCGGCTCAACATTTGA 57.823 45.000 0.00 0.00 38.17 2.69
5866 17516 0.759060 GGCAAAACAGGTTCTGGGGT 60.759 55.000 0.00 0.00 35.51 4.95
5898 17548 2.121385 TCAGCACCTCCAGGCTCT 59.879 61.111 0.00 0.00 38.56 4.09
5900 17550 3.325753 GGTCAGCACCTCCAGGCT 61.326 66.667 0.00 0.00 40.00 4.58
5946 17596 2.648059 CATGGGTCTGACCAGGAATTC 58.352 52.381 26.94 9.33 44.73 2.17
5967 17617 1.057847 GTCTTGAACGCGAACTCGATG 59.942 52.381 15.93 1.07 43.02 3.84
6233 17883 2.961062 AGAACATCAGCCTTTTGCAAGT 59.039 40.909 0.00 0.00 44.83 3.16
6243 17893 2.157738 AGAACAAGCAGAACATCAGCC 58.842 47.619 0.00 0.00 28.14 4.85
6245 17895 3.004002 TGCAAGAACAAGCAGAACATCAG 59.996 43.478 0.00 0.00 35.51 2.90
6254 17906 2.093553 AGCCTTTTTGCAAGAACAAGCA 60.094 40.909 13.69 0.00 39.32 3.91
6261 17913 2.694628 ACATCACAGCCTTTTTGCAAGA 59.305 40.909 0.00 0.00 0.00 3.02
6333 17985 2.030805 AGGATCACAAAAACGCAAGAGC 60.031 45.455 0.00 0.00 43.62 4.09
6334 17986 3.904136 AGGATCACAAAAACGCAAGAG 57.096 42.857 0.00 0.00 43.62 2.85
6335 17987 3.882888 AGAAGGATCACAAAAACGCAAGA 59.117 39.130 0.00 0.00 43.62 3.02
6337 17989 3.795150 GCAGAAGGATCACAAAAACGCAA 60.795 43.478 0.00 0.00 0.00 4.85
6338 17990 2.287547 GCAGAAGGATCACAAAAACGCA 60.288 45.455 0.00 0.00 0.00 5.24
6339 17991 2.319472 GCAGAAGGATCACAAAAACGC 58.681 47.619 0.00 0.00 0.00 4.84
6340 17992 2.223144 TCGCAGAAGGATCACAAAAACG 59.777 45.455 0.00 0.00 0.00 3.60
6341 17993 3.896648 TCGCAGAAGGATCACAAAAAC 57.103 42.857 0.00 0.00 0.00 2.43
6342 17994 8.450578 AATATATCGCAGAAGGATCACAAAAA 57.549 30.769 0.00 0.00 43.58 1.94
6343 17995 8.450578 AAATATATCGCAGAAGGATCACAAAA 57.549 30.769 0.00 0.00 43.58 2.44
6344 17996 8.344831 CAAAATATATCGCAGAAGGATCACAAA 58.655 33.333 0.00 0.00 43.58 2.83
6359 18011 6.377327 ACAGCCCTTTCACAAAATATATCG 57.623 37.500 0.00 0.00 0.00 2.92
6513 18170 1.134037 ACCGGGCAACTACACAGAAAA 60.134 47.619 6.32 0.00 0.00 2.29
6566 18223 1.506309 CTTGCAGCGGTGTGTTAGCA 61.506 55.000 17.07 3.48 0.00 3.49
6579 18236 2.816087 AGTCAAACTATGGTGCTTGCAG 59.184 45.455 0.00 0.00 0.00 4.41
6761 18435 0.109342 CCCCACACAGGCATCTATCC 59.891 60.000 0.00 0.00 35.39 2.59
6762 18436 3.713902 CCCCACACAGGCATCTATC 57.286 57.895 0.00 0.00 35.39 2.08
6787 18461 1.688197 ACACAAACAATGAGCAAGGGG 59.312 47.619 0.00 0.00 0.00 4.79
6817 18493 7.919690 TGTGTGAACTTTAGAACTGAAATGAG 58.080 34.615 0.00 0.00 0.00 2.90
6894 18570 3.200483 CTGTGAATCGGAAGCATCATGA 58.800 45.455 0.00 0.00 0.00 3.07
6895 18571 2.286831 GCTGTGAATCGGAAGCATCATG 60.287 50.000 0.00 0.00 35.69 3.07
6897 18573 1.338960 TGCTGTGAATCGGAAGCATCA 60.339 47.619 0.00 0.00 40.59 3.07
6898 18574 1.063174 GTGCTGTGAATCGGAAGCATC 59.937 52.381 4.77 0.00 46.50 3.91
6900 18576 0.250252 TGTGCTGTGAATCGGAAGCA 60.250 50.000 0.00 0.00 43.10 3.91
6901 18577 0.166814 GTGTGCTGTGAATCGGAAGC 59.833 55.000 0.00 0.00 36.18 3.86
6902 18578 0.798776 GGTGTGCTGTGAATCGGAAG 59.201 55.000 0.00 0.00 0.00 3.46
6971 18676 0.384309 TCGTGGTCCATAGCATCGAC 59.616 55.000 0.00 0.00 34.28 4.20
7019 18724 2.481952 GACTGATGGTGCTGTGTTTCTC 59.518 50.000 0.00 0.00 0.00 2.87
7025 18730 1.888215 AACTGACTGATGGTGCTGTG 58.112 50.000 0.00 0.00 0.00 3.66
7027 18732 5.413833 AGATTTTAACTGACTGATGGTGCTG 59.586 40.000 0.00 0.00 0.00 4.41
7099 18805 2.611292 GCAATATGTGAGGACTGCACTC 59.389 50.000 0.00 0.00 37.18 3.51
7100 18806 2.636830 GCAATATGTGAGGACTGCACT 58.363 47.619 0.00 0.00 37.18 4.40
7101 18807 1.328680 CGCAATATGTGAGGACTGCAC 59.671 52.381 0.00 0.00 36.81 4.57
7102 18808 1.066215 ACGCAATATGTGAGGACTGCA 60.066 47.619 0.00 0.00 0.00 4.41
7103 18809 1.594862 GACGCAATATGTGAGGACTGC 59.405 52.381 0.00 0.00 0.00 4.40
7104 18810 2.604914 GTGACGCAATATGTGAGGACTG 59.395 50.000 0.00 0.00 0.00 3.51
7105 18811 2.233676 TGTGACGCAATATGTGAGGACT 59.766 45.455 0.00 0.00 0.00 3.85
7106 18812 2.616960 TGTGACGCAATATGTGAGGAC 58.383 47.619 0.00 0.00 0.00 3.85
7107 18813 3.118811 TGATGTGACGCAATATGTGAGGA 60.119 43.478 0.00 0.00 0.00 3.71
7108 18814 3.001634 GTGATGTGACGCAATATGTGAGG 59.998 47.826 0.00 0.00 0.00 3.86
7109 18815 3.618150 TGTGATGTGACGCAATATGTGAG 59.382 43.478 0.00 0.00 0.00 3.51
7110 18816 3.370672 GTGTGATGTGACGCAATATGTGA 59.629 43.478 0.00 0.00 32.08 3.58
7111 18817 3.124976 TGTGTGATGTGACGCAATATGTG 59.875 43.478 0.00 0.00 33.45 3.21
7112 18818 3.333804 TGTGTGATGTGACGCAATATGT 58.666 40.909 0.00 0.00 33.45 2.29
7113 18819 4.541085 ATGTGTGATGTGACGCAATATG 57.459 40.909 0.00 0.00 39.68 1.78
7114 18820 5.584251 TGTTATGTGTGATGTGACGCAATAT 59.416 36.000 0.00 0.00 39.68 1.28
7115 18821 4.932200 TGTTATGTGTGATGTGACGCAATA 59.068 37.500 0.00 0.00 39.68 1.90
7116 18822 3.750652 TGTTATGTGTGATGTGACGCAAT 59.249 39.130 0.00 0.00 39.68 3.56
7117 18823 3.134458 TGTTATGTGTGATGTGACGCAA 58.866 40.909 0.00 0.00 39.68 4.85
7118 18824 2.760374 TGTTATGTGTGATGTGACGCA 58.240 42.857 0.00 0.00 40.50 5.24
7119 18825 3.125146 ACATGTTATGTGTGATGTGACGC 59.875 43.478 0.00 0.00 43.01 5.19
7120 18826 4.926860 ACATGTTATGTGTGATGTGACG 57.073 40.909 0.00 0.00 43.01 4.35
7142 18848 9.845214 ATGAGTTCTAGGTACTCCCATTATTAT 57.155 33.333 17.72 5.14 41.02 1.28
7143 18849 9.310449 GATGAGTTCTAGGTACTCCCATTATTA 57.690 37.037 17.72 3.53 41.02 0.98
7144 18850 8.013667 AGATGAGTTCTAGGTACTCCCATTATT 58.986 37.037 17.72 1.66 41.02 1.40
7145 18851 7.540183 AGATGAGTTCTAGGTACTCCCATTAT 58.460 38.462 17.72 8.48 41.02 1.28
7146 18852 6.923670 AGATGAGTTCTAGGTACTCCCATTA 58.076 40.000 17.72 5.09 41.02 1.90
7147 18853 5.782925 AGATGAGTTCTAGGTACTCCCATT 58.217 41.667 17.72 5.87 41.02 3.16
7148 18854 5.411103 AGATGAGTTCTAGGTACTCCCAT 57.589 43.478 17.72 9.94 41.02 4.00
7149 18855 4.883021 AGATGAGTTCTAGGTACTCCCA 57.117 45.455 17.72 6.62 41.02 4.37
7150 18856 6.657541 CATCTAGATGAGTTCTAGGTACTCCC 59.342 46.154 25.78 12.05 44.99 4.30
7151 18857 7.455058 TCATCTAGATGAGTTCTAGGTACTCC 58.545 42.308 27.93 8.04 44.99 3.85
7165 18871 7.348080 ACCAAATTACGTCTCATCTAGATGA 57.652 36.000 29.17 29.17 42.99 2.92
7166 18872 6.642950 GGACCAAATTACGTCTCATCTAGATG 59.357 42.308 24.32 24.32 45.40 2.90
7167 18873 6.239345 GGGACCAAATTACGTCTCATCTAGAT 60.239 42.308 0.00 0.00 36.36 1.98
7168 18874 5.068723 GGGACCAAATTACGTCTCATCTAGA 59.931 44.000 0.00 0.00 29.40 2.43
7169 18875 5.163447 TGGGACCAAATTACGTCTCATCTAG 60.163 44.000 0.00 0.00 34.55 2.43
7170 18876 4.712829 TGGGACCAAATTACGTCTCATCTA 59.287 41.667 0.00 0.00 34.55 1.98
7171 18877 3.517901 TGGGACCAAATTACGTCTCATCT 59.482 43.478 0.00 0.00 34.55 2.90
7172 18878 3.869065 TGGGACCAAATTACGTCTCATC 58.131 45.455 0.00 0.00 34.55 2.92
7173 18879 3.992943 TGGGACCAAATTACGTCTCAT 57.007 42.857 0.00 0.00 34.55 2.90
7174 18880 3.992943 ATGGGACCAAATTACGTCTCA 57.007 42.857 9.23 9.23 43.40 3.27
7175 18881 4.094442 GTGAATGGGACCAAATTACGTCTC 59.906 45.833 0.00 2.20 0.00 3.36
7176 18882 4.007659 GTGAATGGGACCAAATTACGTCT 58.992 43.478 0.00 0.00 0.00 4.18
7177 18883 4.351131 GTGAATGGGACCAAATTACGTC 57.649 45.455 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.