Multiple sequence alignment - TraesCS5A01G074400

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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 TraesCS5A01G074400 chr5A 100.000 5757 0 0 1 5757 87431376 87425620 0.000000e+00 10632
1 TraesCS5A01G074400 chr5A 82.191 2291 281 65 447 2669 87896698 87894467 0.000000e+00 1853
2 TraesCS5A01G074400 chr5A 87.041 926 97 12 2863 3767 87894239 87893316 0.000000e+00 1024
3 TraesCS5A01G074400 chr5A 87.424 493 51 9 4304 4792 87891650 87891165 1.810000e-154 556
4 TraesCS5A01G074400 chr5A 87.500 400 37 9 3852 4249 87893271 87892883 3.160000e-122 449
5 TraesCS5A01G074400 chr5A 84.966 439 55 6 1 434 87897185 87896753 8.860000e-118 435
6 TraesCS5A01G074400 chr5A 85.714 189 23 4 4891 5076 631470342 631470529 4.550000e-46 196
7 TraesCS5A01G074400 chr5D 94.082 3430 161 15 1 3393 93991159 93987735 0.000000e+00 5171
8 TraesCS5A01G074400 chr5D 93.498 323 20 1 5436 5757 204403847 204403525 4.040000e-131 479
9 TraesCS5A01G074400 chr5D 92.945 326 21 2 5433 5757 342648125 342647801 1.880000e-129 473
10 TraesCS5A01G074400 chr5B 92.705 2769 169 15 1081 3824 101155135 101152375 0.000000e+00 3964
11 TraesCS5A01G074400 chr5B 94.314 897 50 1 1 897 101230209 101229314 0.000000e+00 1373
12 TraesCS5A01G074400 chr5B 93.464 918 56 4 3928 4843 101152137 101151222 0.000000e+00 1360
13 TraesCS5A01G074400 chr5B 92.593 837 54 5 4835 5670 101151190 101150361 0.000000e+00 1195
14 TraesCS5A01G074400 chr5B 80.380 1473 221 38 905 2359 364799056 364797634 0.000000e+00 1057
15 TraesCS5A01G074400 chr5B 81.947 986 135 29 2803 3756 364797333 364796359 0.000000e+00 795
16 TraesCS5A01G074400 chr5B 85.150 532 70 6 4304 4832 364795701 364795176 2.360000e-148 536
17 TraesCS5A01G074400 chr5B 92.879 323 21 2 5436 5757 208591601 208591280 8.730000e-128 468
18 TraesCS5A01G074400 chr5B 83.854 384 53 6 3871 4252 364796304 364795928 1.970000e-94 357
19 TraesCS5A01G074400 chr5B 95.495 222 9 1 864 1085 101229304 101229084 2.550000e-93 353
20 TraesCS5A01G074400 chr5B 85.028 354 41 5 442 792 364799435 364799091 3.300000e-92 350
21 TraesCS5A01G074400 chr2D 81.931 2983 384 79 871 3767 81659229 81656316 0.000000e+00 2379
22 TraesCS5A01G074400 chr2D 89.958 478 46 2 4304 4780 81655540 81655064 2.950000e-172 616
23 TraesCS5A01G074400 chr2D 93.189 323 19 3 5436 5757 154117172 154116852 6.750000e-129 472
24 TraesCS5A01G074400 chr2D 89.918 367 32 4 442 806 81659560 81659197 8.730000e-128 468
25 TraesCS5A01G074400 chr2D 92.879 323 21 2 5436 5757 410618240 410618561 8.730000e-128 468
26 TraesCS5A01G074400 chr2D 85.749 407 50 3 3848 4252 81656277 81655877 1.920000e-114 424
27 TraesCS5A01G074400 chr2D 83.632 446 59 11 1 441 81660038 81659602 1.930000e-109 407
28 TraesCS5A01G074400 chr2B 81.650 2981 395 83 874 3765 155176905 155173988 0.000000e+00 2335
29 TraesCS5A01G074400 chr2B 89.036 529 56 2 4304 4831 155159174 155158647 0.000000e+00 654
30 TraesCS5A01G074400 chr2B 86.243 189 22 4 4891 5076 534924145 534924332 9.780000e-48 202
31 TraesCS5A01G074400 chr2B 84.925 199 24 6 4885 5079 383640052 383640248 4.550000e-46 196
32 TraesCS5A01G074400 chr2A 81.433 3000 380 89 871 3767 139518533 139521458 0.000000e+00 2290
33 TraesCS5A01G074400 chr2A 89.414 529 54 2 4304 4831 139522221 139522748 0.000000e+00 665
34 TraesCS5A01G074400 chr2A 89.751 361 33 3 442 800 139518201 139518559 5.260000e-125 459
35 TraesCS5A01G074400 chr2A 84.451 328 34 9 3848 4174 139521497 139521808 2.010000e-79 307
36 TraesCS5A01G074400 chr1D 93.519 324 20 1 5435 5757 278293019 278292696 1.120000e-131 481
37 TraesCS5A01G074400 chr4B 92.593 324 23 1 5435 5757 128570384 128570707 1.130000e-126 464
38 TraesCS5A01G074400 chr7D 91.867 332 23 4 5429 5757 351417923 351418253 1.460000e-125 460
39 TraesCS5A01G074400 chr3B 89.759 166 17 0 4847 5012 392762571 392762406 4.520000e-51 213
40 TraesCS5A01G074400 chr3B 85.204 196 23 6 4888 5079 335842811 335843004 4.550000e-46 196
41 TraesCS5A01G074400 chr1B 82.833 233 35 5 4835 5064 510786089 510785859 2.720000e-48 204
42 TraesCS5A01G074400 chr1B 93.056 72 4 1 4835 4906 510785900 510785830 2.840000e-18 104
43 TraesCS5A01G074400 chr1A 86.813 182 20 4 4898 5076 91042782 91042962 3.520000e-47 200
44 TraesCS5A01G074400 chr4A 85.417 192 22 6 4891 5078 618189370 618189559 1.640000e-45 195
45 TraesCS5A01G074400 chr3D 84.694 196 24 6 4888 5079 111983635 111983442 2.120000e-44 191


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 TraesCS5A01G074400 chr5A 87425620 87431376 5756 True 10632.00 10632 100.000000 1 5757 1 chr5A.!!$R1 5756
1 TraesCS5A01G074400 chr5A 87891165 87897185 6020 True 863.40 1853 85.824400 1 4792 5 chr5A.!!$R2 4791
2 TraesCS5A01G074400 chr5D 93987735 93991159 3424 True 5171.00 5171 94.082000 1 3393 1 chr5D.!!$R1 3392
3 TraesCS5A01G074400 chr5B 101150361 101155135 4774 True 2173.00 3964 92.920667 1081 5670 3 chr5B.!!$R2 4589
4 TraesCS5A01G074400 chr5B 101229084 101230209 1125 True 863.00 1373 94.904500 1 1085 2 chr5B.!!$R3 1084
5 TraesCS5A01G074400 chr5B 364795176 364799435 4259 True 619.00 1057 83.271800 442 4832 5 chr5B.!!$R4 4390
6 TraesCS5A01G074400 chr2D 81655064 81660038 4974 True 858.80 2379 86.237600 1 4780 5 chr2D.!!$R2 4779
7 TraesCS5A01G074400 chr2B 155173988 155176905 2917 True 2335.00 2335 81.650000 874 3765 1 chr2B.!!$R2 2891
8 TraesCS5A01G074400 chr2B 155158647 155159174 527 True 654.00 654 89.036000 4304 4831 1 chr2B.!!$R1 527
9 TraesCS5A01G074400 chr2A 139518201 139522748 4547 False 930.25 2290 86.262250 442 4831 4 chr2A.!!$F1 4389

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
349 357 0.609406 AGCGTGTCAGCTCACTAGGA 60.609 55.000 4.26 0.0 45.67 2.94 F
2191 2408 0.485099 AGCCCCATTTGTGTTACCCA 59.515 50.000 0.00 0.0 0.00 4.51 F
2585 2835 3.395639 TGCTACTACCACCACTTTTTCG 58.604 45.455 0.00 0.0 0.00 3.46 F
3204 3552 0.031716 ACTGGATAGCTGGCTGGAGA 60.032 55.000 5.25 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2316 2534 0.178873 AGGCTAAGGTTGACCCCTCA 60.179 55.0 0.00 0.00 36.42 3.86 R
3204 3552 0.033504 CGTGGCTACTCAGTGTGGTT 59.966 55.0 0.00 0.00 0.00 3.67 R
3791 4345 0.386478 GCAGTAGCAGCAGCAACAAC 60.386 55.0 3.17 0.00 45.49 3.32 R
4909 6809 0.107800 CTGAGGGAGCCACATGTGAG 60.108 60.0 27.46 17.31 0.00 3.51 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
216 224 9.211485 CACTGAAATTGGCAAGAAAATAAATCT 57.789 29.630 5.96 0.00 0.00 2.40
326 334 2.136026 AGGGGAAAGAGTGGTGAGTTT 58.864 47.619 0.00 0.00 0.00 2.66
349 357 0.609406 AGCGTGTCAGCTCACTAGGA 60.609 55.000 4.26 0.00 45.67 2.94
357 365 1.134848 CAGCTCACTAGGAGTGGCTTC 60.135 57.143 15.51 1.95 44.51 3.86
494 544 3.276857 CATCTCCACATTCCCTTGTCAG 58.723 50.000 0.00 0.00 0.00 3.51
607 657 2.167662 CACCCCTATCAAACCAACACC 58.832 52.381 0.00 0.00 0.00 4.16
785 840 5.962031 TGGGAAGACTACTACCAATGTATGT 59.038 40.000 0.00 0.00 32.81 2.29
800 855 8.934697 ACCAATGTATGTATACTTCCACACTAT 58.065 33.333 4.17 0.00 34.41 2.12
827 882 8.803397 ACCACCATACCTTATTAACTCTTTTC 57.197 34.615 0.00 0.00 0.00 2.29
835 890 7.582352 ACCTTATTAACTCTTTTCGCACTTTC 58.418 34.615 0.00 0.00 0.00 2.62
856 911 9.791801 ACTTTCCAACATACATATATGCATACA 57.208 29.630 8.99 0.00 41.83 2.29
894 1034 9.979897 ATAACCAATATATGCATACTTCCACAT 57.020 29.630 8.99 0.00 0.00 3.21
930 1089 8.689251 ATATACAATCGAAATAGTCCGATGTG 57.311 34.615 0.00 0.00 43.72 3.21
935 1094 3.446161 TCGAAATAGTCCGATGTGTTCCT 59.554 43.478 0.00 0.00 0.00 3.36
1060 1225 2.495669 TGTGCATCCAACGATCTCAGTA 59.504 45.455 0.00 0.00 0.00 2.74
1198 1380 9.837681 TCAGTAAGGTTTAGGATATGGATCATA 57.162 33.333 0.00 0.00 33.27 2.15
1246 1428 8.463930 AAGTCTCCATGTATTTTTCACAAAGA 57.536 30.769 0.00 0.00 0.00 2.52
1629 1835 9.136323 ACTTCAACCTCTGATGTTTCTAAAAAT 57.864 29.630 0.00 0.00 38.88 1.82
1636 1842 7.201565 CCTCTGATGTTTCTAAAAATCGACTCC 60.202 40.741 0.00 0.00 35.77 3.85
1652 1858 3.427233 CGACTCCCTTCACCTAAACTACG 60.427 52.174 0.00 0.00 0.00 3.51
1971 2186 7.324856 GTCTCTAGCTATTGTGATTGATACACG 59.675 40.741 0.00 0.00 40.61 4.49
2091 2308 6.774673 TGTCCCTATGATTTACTTCACACAA 58.225 36.000 0.00 0.00 0.00 3.33
2130 2347 6.015519 TCCCATTTGTTGAAAAGTAGGTGATG 60.016 38.462 0.00 0.00 0.00 3.07
2191 2408 0.485099 AGCCCCATTTGTGTTACCCA 59.515 50.000 0.00 0.00 0.00 4.51
2311 2529 8.144478 ACTAATGACGACATGCTACATTTATCT 58.856 33.333 0.05 0.00 36.79 1.98
2316 2534 7.495606 TGACGACATGCTACATTTATCTGAAAT 59.504 33.333 0.00 0.00 0.00 2.17
2317 2535 7.633621 ACGACATGCTACATTTATCTGAAATG 58.366 34.615 8.17 8.17 41.91 2.32
2585 2835 3.395639 TGCTACTACCACCACTTTTTCG 58.604 45.455 0.00 0.00 0.00 3.46
2615 2865 9.706691 TCCTATAAGTTGAAAGACTACAAGTTG 57.293 33.333 17.90 0.00 39.15 3.16
2619 2869 6.364945 AGTTGAAAGACTACAAGTTGCTTC 57.635 37.500 1.81 0.00 0.00 3.86
2743 3045 9.658799 CCTCCGATCTATATTAATTGACATTGT 57.341 33.333 0.00 0.00 0.00 2.71
2763 3065 8.545420 ACATTGTTTCAGTACAAAGTTAGTACG 58.455 33.333 0.00 0.00 44.92 3.67
3171 3515 9.929180 TGTATATGAGCTAACAAGCCTATTTAG 57.071 33.333 0.00 0.00 34.90 1.85
3204 3552 0.031716 ACTGGATAGCTGGCTGGAGA 60.032 55.000 5.25 0.00 0.00 3.71
3220 3568 1.066787 GGAGAACCACACTGAGTAGCC 60.067 57.143 0.00 0.00 35.97 3.93
3265 3613 2.999185 ATGGGGTTCACAAGGACAAT 57.001 45.000 0.00 0.00 0.00 2.71
3270 3618 2.554032 GGGTTCACAAGGACAATGTCAG 59.446 50.000 15.86 6.92 33.68 3.51
3499 3850 8.156820 TGATGTCCATTTCTTTATACGATGGAT 58.843 33.333 6.65 0.00 45.60 3.41
3553 3904 7.230108 TGGGGTAAATGTAAATGTTGTCGTTTA 59.770 33.333 0.00 0.00 34.95 2.01
3743 4095 5.062683 CGCTACATAACTATTAGCCTGCATG 59.937 44.000 0.00 0.00 35.75 4.06
3798 4376 8.038492 ACTACTACTACTACTACTGTTGTTGC 57.962 38.462 0.00 0.00 34.32 4.17
3815 4393 0.108472 TGCTGCTGCTACTGCTACTG 60.108 55.000 17.00 0.00 40.48 2.74
3817 4395 0.809241 CTGCTGCTACTGCTACTGCC 60.809 60.000 0.00 0.00 40.48 4.85
3821 4399 0.247460 TGCTACTGCTACTGCCACTG 59.753 55.000 0.00 0.00 40.48 3.66
3840 4418 5.879223 CCACTGCTCTCATAATCTCAGTTTT 59.121 40.000 0.00 0.00 33.08 2.43
3845 4423 8.939201 TGCTCTCATAATCTCAGTTTTTAGAG 57.061 34.615 0.00 0.00 0.00 2.43
3846 4424 7.984050 TGCTCTCATAATCTCAGTTTTTAGAGG 59.016 37.037 0.00 0.00 32.76 3.69
3895 4491 6.805016 TGTGTATGCAAATATTTTCCCCAT 57.195 33.333 0.00 2.52 0.00 4.00
4029 4626 9.734620 TTCTTGCATATTGTAAATGTATGAAGC 57.265 29.630 0.00 0.00 32.30 3.86
4041 4638 5.746307 ATGTATGAAGCATGTGTGTGATC 57.254 39.130 0.00 0.00 0.00 2.92
4147 4744 9.247861 GGGCATATTAATCTTGAATTGGTCTAT 57.752 33.333 0.00 0.00 0.00 1.98
4507 6366 3.307059 CCGGAGTAGGATGGATTGGATTC 60.307 52.174 0.00 0.00 0.00 2.52
4510 6369 4.527038 GGAGTAGGATGGATTGGATTCGTA 59.473 45.833 0.00 0.00 0.00 3.43
4519 6378 7.827236 GGATGGATTGGATTCGTATATTACCAA 59.173 37.037 0.00 0.00 40.74 3.67
4663 6522 1.002544 GCCTTGGCTAGACTTGTCAGT 59.997 52.381 4.11 0.00 35.17 3.41
4726 6585 7.603024 GCTAGAAAGGACGGCTATATGTTTTAT 59.397 37.037 0.00 0.00 0.00 1.40
4764 6623 5.416271 AGTTGTATGGGTTGACGAGTATT 57.584 39.130 0.00 0.00 0.00 1.89
4820 6680 7.128234 TCATTGACCATACATCTCTCATGAA 57.872 36.000 0.00 0.00 0.00 2.57
4845 6745 5.626142 TGAGTAATTTAGGCACAAGTCCAA 58.374 37.500 0.00 0.00 0.00 3.53
4857 6757 4.370917 CACAAGTCCAATTCACCCAAAAG 58.629 43.478 0.00 0.00 0.00 2.27
4895 6795 7.390718 GGGGAAAGGTGTACTATGCATTTATAG 59.609 40.741 3.54 0.00 36.83 1.31
4909 6809 4.338400 GCATTTATAGGTCAACACTTCCCC 59.662 45.833 0.00 0.00 0.00 4.81
4913 6813 0.765510 AGGTCAACACTTCCCCTCAC 59.234 55.000 0.00 0.00 0.00 3.51
4914 6814 0.472471 GGTCAACACTTCCCCTCACA 59.528 55.000 0.00 0.00 0.00 3.58
4936 6836 1.224870 GGCTCCCTCAGGCCTAAAC 59.775 63.158 3.98 0.00 44.48 2.01
4937 6837 1.562672 GGCTCCCTCAGGCCTAAACA 61.563 60.000 3.98 0.00 44.48 2.83
4944 6844 0.251916 TCAGGCCTAAACATGGACCG 59.748 55.000 3.98 0.00 31.51 4.79
4952 6852 0.251165 AAACATGGACCGGAAGTGGG 60.251 55.000 9.46 0.00 0.00 4.61
4960 6860 0.039618 ACCGGAAGTGGGATGCAATT 59.960 50.000 9.46 0.00 0.00 2.32
4976 6876 1.928503 CAATTTAATTGCGCCAGCCAG 59.071 47.619 4.18 0.00 44.33 4.85
5048 6948 2.154462 AGCCAACTCATCCAAAAGTCG 58.846 47.619 0.00 0.00 0.00 4.18
5050 6950 2.095718 GCCAACTCATCCAAAAGTCGAC 60.096 50.000 7.70 7.70 0.00 4.20
5069 6969 1.028905 CCTGATGGAGAGAGTCGGAC 58.971 60.000 0.00 0.00 34.57 4.79
5082 6982 8.091449 GGAGAGAGTCGGACAATATATTTCAAT 58.909 37.037 11.27 0.00 0.00 2.57
5170 7070 7.616150 AGAGTTTCCATGACTTAGTAGCTAAGA 59.384 37.037 19.14 2.32 44.24 2.10
5241 7141 0.106519 AAAAGGAGCAGCACACCACT 60.107 50.000 0.00 0.00 0.00 4.00
5242 7142 0.820891 AAAGGAGCAGCACACCACTG 60.821 55.000 0.00 0.00 38.22 3.66
5304 7204 7.013823 AGTAGTACTAGTACAAGTCCTCACA 57.986 40.000 29.87 4.06 38.48 3.58
5321 7221 2.987413 ACAAACTGTGTGTGTGTGTG 57.013 45.000 2.08 0.00 44.87 3.82
5322 7222 2.226330 ACAAACTGTGTGTGTGTGTGT 58.774 42.857 2.08 0.00 44.87 3.72
5323 7223 2.031245 ACAAACTGTGTGTGTGTGTGTG 60.031 45.455 2.08 0.00 44.87 3.82
5324 7224 0.521291 AACTGTGTGTGTGTGTGTGC 59.479 50.000 0.00 0.00 0.00 4.57
5337 7237 1.800586 GTGTGTGCATGTGTAGACTGG 59.199 52.381 0.00 0.00 0.00 4.00
5354 7254 5.994250 AGACTGGACTACATGTTTATGCAT 58.006 37.500 2.30 3.79 37.85 3.96
5367 7267 4.635765 TGTTTATGCATCTGCTACACTTCC 59.364 41.667 0.19 0.00 42.66 3.46
5383 7283 5.515106 ACACTTCCTCATCTAGCTACTCTT 58.485 41.667 0.00 0.00 0.00 2.85
5394 7294 2.107366 AGCTACTCTTTGCTCCTCCTC 58.893 52.381 0.00 0.00 33.90 3.71
5395 7295 1.827969 GCTACTCTTTGCTCCTCCTCA 59.172 52.381 0.00 0.00 0.00 3.86
5420 7320 7.667043 TCTTATACTGGCAACACTACAAAAG 57.333 36.000 0.00 0.00 46.17 2.27
5427 7327 4.095782 TGGCAACACTACAAAAGACACTTC 59.904 41.667 0.00 0.00 46.17 3.01
5428 7328 4.497507 GGCAACACTACAAAAGACACTTCC 60.498 45.833 0.00 0.00 0.00 3.46
5454 7354 2.672874 TGTGCTACTTATTGAGCTTGCG 59.327 45.455 0.00 0.00 39.54 4.85
5467 7367 0.179097 GCTTGCGTTGGTTTTTCCCA 60.179 50.000 0.00 0.00 34.77 4.37
5555 7455 4.346709 TCAATCCAGTAAGAGGAACACACA 59.653 41.667 0.00 0.00 38.93 3.72
5561 7461 4.508124 CAGTAAGAGGAACACACAAGTCAC 59.492 45.833 0.00 0.00 0.00 3.67
5571 7471 2.426738 CACACAAGTCACCAATGGTTGT 59.573 45.455 0.16 1.19 35.16 3.32
5615 7515 1.303091 GCACCCAACGCGATAAAGGT 61.303 55.000 15.93 9.28 0.00 3.50
5616 7516 2.008045 GCACCCAACGCGATAAAGGTA 61.008 52.381 15.93 0.00 0.00 3.08
5625 7525 6.255215 CAACGCGATAAAGGTATTGTCAATT 58.745 36.000 15.93 0.00 0.00 2.32
5655 7556 4.038042 CGGTACTTGCAAGGATGAGATCTA 59.962 45.833 29.18 7.41 0.00 1.98
5657 7558 5.755861 GGTACTTGCAAGGATGAGATCTAAC 59.244 44.000 29.18 9.07 0.00 2.34
5661 7562 5.426689 TGCAAGGATGAGATCTAACAGTT 57.573 39.130 0.00 0.00 0.00 3.16
5665 7566 8.363390 TGCAAGGATGAGATCTAACAGTTATAG 58.637 37.037 0.00 0.00 0.00 1.31
5721 7622 9.807649 AGATAAAGGTAAATAAATTGCAGCAAG 57.192 29.630 14.47 0.00 0.00 4.01
5722 7623 8.947055 ATAAAGGTAAATAAATTGCAGCAAGG 57.053 30.769 14.47 0.00 0.00 3.61
5723 7624 6.358974 AAGGTAAATAAATTGCAGCAAGGT 57.641 33.333 14.47 6.29 0.00 3.50
5724 7625 7.475137 AAGGTAAATAAATTGCAGCAAGGTA 57.525 32.000 14.47 8.37 0.00 3.08
5725 7626 7.660030 AGGTAAATAAATTGCAGCAAGGTAT 57.340 32.000 14.47 10.29 0.00 2.73
5726 7627 8.078060 AGGTAAATAAATTGCAGCAAGGTATT 57.922 30.769 14.47 15.20 0.00 1.89
5727 7628 8.539544 AGGTAAATAAATTGCAGCAAGGTATTT 58.460 29.630 26.59 26.59 34.12 1.40
5728 7629 9.161629 GGTAAATAAATTGCAGCAAGGTATTTT 57.838 29.630 27.62 19.52 33.00 1.82
5731 7632 5.945466 AAATTGCAGCAAGGTATTTTTGG 57.055 34.783 14.47 0.00 0.00 3.28
5732 7633 3.399440 TTGCAGCAAGGTATTTTTGGG 57.601 42.857 2.83 0.00 0.00 4.12
5733 7634 2.324541 TGCAGCAAGGTATTTTTGGGT 58.675 42.857 0.00 0.00 0.00 4.51
5734 7635 2.703007 TGCAGCAAGGTATTTTTGGGTT 59.297 40.909 0.00 0.00 0.00 4.11
5735 7636 3.135530 TGCAGCAAGGTATTTTTGGGTTT 59.864 39.130 0.00 0.00 0.00 3.27
5736 7637 4.133820 GCAGCAAGGTATTTTTGGGTTTT 58.866 39.130 0.00 0.00 0.00 2.43
5737 7638 4.578516 GCAGCAAGGTATTTTTGGGTTTTT 59.421 37.500 0.00 0.00 0.00 1.94
5738 7639 5.505489 GCAGCAAGGTATTTTTGGGTTTTTG 60.505 40.000 0.00 0.00 0.00 2.44
5739 7640 5.819901 CAGCAAGGTATTTTTGGGTTTTTGA 59.180 36.000 0.00 0.00 0.00 2.69
5740 7641 6.486320 CAGCAAGGTATTTTTGGGTTTTTGAT 59.514 34.615 0.00 0.00 0.00 2.57
5741 7642 7.013178 CAGCAAGGTATTTTTGGGTTTTTGATT 59.987 33.333 0.00 0.00 0.00 2.57
5742 7643 7.559533 AGCAAGGTATTTTTGGGTTTTTGATTT 59.440 29.630 0.00 0.00 0.00 2.17
5743 7644 8.194104 GCAAGGTATTTTTGGGTTTTTGATTTT 58.806 29.630 0.00 0.00 0.00 1.82
5744 7645 9.513727 CAAGGTATTTTTGGGTTTTTGATTTTG 57.486 29.630 0.00 0.00 0.00 2.44
5745 7646 8.815565 AGGTATTTTTGGGTTTTTGATTTTGT 57.184 26.923 0.00 0.00 0.00 2.83
5746 7647 9.907229 AGGTATTTTTGGGTTTTTGATTTTGTA 57.093 25.926 0.00 0.00 0.00 2.41
5751 7652 9.898152 TTTTTGGGTTTTTGATTTTGTAGATCT 57.102 25.926 0.00 0.00 0.00 2.75
5752 7653 8.885494 TTTGGGTTTTTGATTTTGTAGATCTG 57.115 30.769 5.18 0.00 0.00 2.90
5753 7654 7.831691 TGGGTTTTTGATTTTGTAGATCTGA 57.168 32.000 5.18 0.00 0.00 3.27
5754 7655 8.243961 TGGGTTTTTGATTTTGTAGATCTGAA 57.756 30.769 5.18 0.00 0.00 3.02
5755 7656 8.700051 TGGGTTTTTGATTTTGTAGATCTGAAA 58.300 29.630 5.18 4.47 0.00 2.69
5756 7657 9.541143 GGGTTTTTGATTTTGTAGATCTGAAAA 57.459 29.630 5.18 10.74 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
223 231 9.232473 GGAAGAACTTTTGGTAAGATTGATAGT 57.768 33.333 0.00 0.00 0.00 2.12
286 294 7.475299 TCCCCTTACTAAATTCAGGTCAAAAT 58.525 34.615 0.00 0.00 0.00 1.82
297 305 6.045106 TCACCACTCTTTCCCCTTACTAAATT 59.955 38.462 0.00 0.00 0.00 1.82
303 311 2.638363 ACTCACCACTCTTTCCCCTTAC 59.362 50.000 0.00 0.00 0.00 2.34
326 334 1.177401 AGTGAGCTGACACGCTATCA 58.823 50.000 5.98 0.00 44.35 2.15
349 357 2.417243 GCAAAACACTTGTGAAGCCACT 60.417 45.455 7.83 0.00 43.55 4.00
357 365 3.713858 TGGAGATGCAAAACACTTGTG 57.286 42.857 0.00 0.00 0.00 3.33
409 417 9.774742 CAAAACATTTATTACTCTAGCCAAGTC 57.225 33.333 0.00 0.00 0.00 3.01
607 657 4.499183 GAAAGTGTCATGAGGTAGACTGG 58.501 47.826 0.00 0.00 35.81 4.00
785 840 5.274015 TGGTGGTCATAGTGTGGAAGTATA 58.726 41.667 0.00 0.00 0.00 1.47
800 855 7.504926 AAGAGTTAATAAGGTATGGTGGTCA 57.495 36.000 0.00 0.00 0.00 4.02
827 882 6.079763 GCATATATGTATGTTGGAAAGTGCG 58.920 40.000 14.14 0.00 39.90 5.34
835 890 8.615211 GTGGATGTATGCATATATGTATGTTGG 58.385 37.037 22.27 0.00 39.90 3.77
856 911 9.618890 GCATATATTGGTTATCATAGTGTGGAT 57.381 33.333 0.00 0.00 0.00 3.41
993 1158 3.129287 CCACCTTGTAATCCATTGCTGTC 59.871 47.826 0.00 0.00 0.00 3.51
1060 1225 1.382522 CGCCCAAATGCATCTACTGT 58.617 50.000 0.00 0.00 0.00 3.55
1198 1380 3.444029 ACATAAAGGGAAAATGGCAGCT 58.556 40.909 0.00 0.00 0.00 4.24
1246 1428 7.054751 AGTTCACTTTTAGAAAGTAGCAACCT 58.945 34.615 5.81 0.00 0.00 3.50
1629 1835 2.885616 AGTTTAGGTGAAGGGAGTCGA 58.114 47.619 0.00 0.00 0.00 4.20
1652 1858 8.695456 ACATGGATTAAATGAAGTTCCCATAAC 58.305 33.333 0.00 0.00 32.46 1.89
1971 2186 6.985059 GGGACAGACCTACACATATAAGTTTC 59.015 42.308 0.00 0.00 38.98 2.78
2091 2308 6.484364 ACAAATGGGAGAAACAACAGAAAT 57.516 33.333 0.00 0.00 0.00 2.17
2191 2408 8.523658 GCTTTTGTATTGACTTTTATTCCTCCT 58.476 33.333 0.00 0.00 0.00 3.69
2311 2529 3.561313 GCTAAGGTTGACCCCTCATTTCA 60.561 47.826 0.00 0.00 36.42 2.69
2316 2534 0.178873 AGGCTAAGGTTGACCCCTCA 60.179 55.000 0.00 0.00 36.42 3.86
2317 2535 1.875488 TAGGCTAAGGTTGACCCCTC 58.125 55.000 0.00 0.00 36.42 4.30
2454 2674 4.044426 GCGAATTAATTGATGCAACCTCC 58.956 43.478 5.17 0.00 0.00 4.30
2585 2835 8.718102 TGTAGTCTTTCAACTTATAGGATTGC 57.282 34.615 0.00 0.00 0.00 3.56
2743 3045 8.931385 AAAGTCGTACTAACTTTGTACTGAAA 57.069 30.769 17.50 0.00 43.46 2.69
2801 3110 5.841957 TTGGTCCTCGTAGAAATACTACC 57.158 43.478 0.00 0.00 46.09 3.18
2876 3195 5.936372 TCATGATATTTAGCACTCAGGATGC 59.064 40.000 0.00 0.00 43.74 3.91
3045 3383 6.055588 TCCTTCACTGTCACCTAAGAAAAAG 58.944 40.000 0.00 0.00 0.00 2.27
3171 3515 9.736023 CCAGCTATCCAGTAATGAAAAATAAAC 57.264 33.333 0.00 0.00 0.00 2.01
3182 3530 2.636893 CTCCAGCCAGCTATCCAGTAAT 59.363 50.000 0.00 0.00 0.00 1.89
3188 3536 0.107643 GGTTCTCCAGCCAGCTATCC 59.892 60.000 0.00 0.00 0.00 2.59
3204 3552 0.033504 CGTGGCTACTCAGTGTGGTT 59.966 55.000 0.00 0.00 0.00 3.67
3220 3568 0.165079 ATTTTAACTCGTGCGCCGTG 59.835 50.000 16.00 15.70 37.94 4.94
3321 3669 5.443283 TCTTGGATCAAATTGATGGAGGAG 58.557 41.667 13.82 4.54 37.20 3.69
3441 3792 6.890979 ATATAAGTCGGGAAGTACCTACAC 57.109 41.667 0.00 0.00 38.98 2.90
3528 3879 5.632244 ACGACAACATTTACATTTACCCC 57.368 39.130 0.00 0.00 0.00 4.95
3743 4095 4.828387 AGTAGTAGTAGAAGGGCATACTGC 59.172 45.833 0.00 0.00 44.08 4.40
3791 4345 0.386478 GCAGTAGCAGCAGCAACAAC 60.386 55.000 3.17 0.00 45.49 3.32
3792 4346 0.535780 AGCAGTAGCAGCAGCAACAA 60.536 50.000 3.17 0.00 45.49 2.83
3795 4373 0.610174 AGTAGCAGTAGCAGCAGCAA 59.390 50.000 3.17 0.00 45.49 3.91
3798 4376 0.809241 GGCAGTAGCAGTAGCAGCAG 60.809 60.000 0.00 0.00 45.49 4.24
3815 4393 3.181467 ACTGAGATTATGAGAGCAGTGGC 60.181 47.826 0.00 0.00 35.49 5.01
3817 4395 6.981762 AAAACTGAGATTATGAGAGCAGTG 57.018 37.500 0.00 0.00 36.77 3.66
3821 4399 7.440856 CCCTCTAAAAACTGAGATTATGAGAGC 59.559 40.741 0.00 0.00 32.44 4.09
3878 4473 9.917887 ATTTTTATGATGGGGAAAATATTTGCA 57.082 25.926 8.47 0.00 31.86 4.08
3895 4491 5.649557 CAACAGGCGATGGAATTTTTATGA 58.350 37.500 0.00 0.00 0.00 2.15
4008 4605 8.908678 CACATGCTTCATACATTTACAATATGC 58.091 33.333 0.00 0.00 0.00 3.14
4021 4618 5.114780 AGAGATCACACACATGCTTCATAC 58.885 41.667 0.00 0.00 0.00 2.39
4029 4626 9.971922 TGACTATATTTAGAGATCACACACATG 57.028 33.333 0.00 0.00 0.00 3.21
4103 4700 6.622427 ATGCCCTAATACACCCTAAGATAC 57.378 41.667 0.00 0.00 0.00 2.24
4507 6366 8.198109 CCTTGATCCCTATCTTGGTAATATACG 58.802 40.741 0.00 0.00 32.93 3.06
4510 6369 7.037297 CCACCTTGATCCCTATCTTGGTAATAT 60.037 40.741 0.00 0.00 36.76 1.28
4519 6378 2.695585 GGACCACCTTGATCCCTATCT 58.304 52.381 0.00 0.00 32.93 1.98
4663 6522 2.225491 GACTTTGTAACATCTTGGCGCA 59.775 45.455 10.83 0.00 0.00 6.09
4726 6585 3.450904 ACAACTAGCTGGACCTCCATAA 58.549 45.455 3.17 0.00 46.46 1.90
4742 6601 5.416271 AATACTCGTCAACCCATACAACT 57.584 39.130 0.00 0.00 0.00 3.16
4820 6680 6.245408 TGGACTTGTGCCTAAATTACTCATT 58.755 36.000 0.00 0.00 0.00 2.57
4845 6745 3.960102 TCAACTTGAGCTTTTGGGTGAAT 59.040 39.130 0.00 0.00 0.00 2.57
4857 6757 1.821136 CCTTTCCCCATCAACTTGAGC 59.179 52.381 0.00 0.00 0.00 4.26
4895 6795 0.472471 TGTGAGGGGAAGTGTTGACC 59.528 55.000 0.00 0.00 0.00 4.02
4909 6809 0.107800 CTGAGGGAGCCACATGTGAG 60.108 60.000 27.46 17.31 0.00 3.51
4913 6813 2.124403 GCCTGAGGGAGCCACATG 60.124 66.667 0.00 0.00 33.58 3.21
4936 6836 0.464373 CATCCCACTTCCGGTCCATG 60.464 60.000 0.00 0.00 0.00 3.66
4937 6837 1.915228 CATCCCACTTCCGGTCCAT 59.085 57.895 0.00 0.00 0.00 3.41
4960 6860 1.024271 GATCTGGCTGGCGCAATTAA 58.976 50.000 10.83 0.00 38.10 1.40
5027 6927 2.554032 CGACTTTTGGATGAGTTGGCTT 59.446 45.455 0.00 0.00 0.00 4.35
5048 6948 1.028905 CCGACTCTCTCCATCAGGTC 58.971 60.000 0.00 0.00 35.89 3.85
5050 6950 1.028905 GTCCGACTCTCTCCATCAGG 58.971 60.000 0.00 0.00 0.00 3.86
5203 7103 8.353423 TCCTTTTATACGAGTACTTACCAACT 57.647 34.615 0.00 0.00 0.00 3.16
5204 7104 7.221645 GCTCCTTTTATACGAGTACTTACCAAC 59.778 40.741 0.00 0.00 0.00 3.77
5205 7105 7.093814 TGCTCCTTTTATACGAGTACTTACCAA 60.094 37.037 0.00 0.00 0.00 3.67
5206 7106 6.377996 TGCTCCTTTTATACGAGTACTTACCA 59.622 38.462 0.00 0.00 0.00 3.25
5215 7115 3.307242 GTGTGCTGCTCCTTTTATACGAG 59.693 47.826 0.00 0.00 0.00 4.18
5216 7116 3.259064 GTGTGCTGCTCCTTTTATACGA 58.741 45.455 0.00 0.00 0.00 3.43
5241 7141 4.321899 GCTGGATGGCTTGATTTACAAACA 60.322 41.667 0.00 0.00 38.08 2.83
5242 7142 4.176271 GCTGGATGGCTTGATTTACAAAC 58.824 43.478 0.00 0.00 38.08 2.93
5304 7204 1.068610 GCACACACACACACACAGTTT 60.069 47.619 0.00 0.00 0.00 2.66
5320 7220 1.970640 AGTCCAGTCTACACATGCACA 59.029 47.619 0.00 0.00 0.00 4.57
5321 7221 2.751166 AGTCCAGTCTACACATGCAC 57.249 50.000 0.00 0.00 0.00 4.57
5322 7222 3.161866 TGTAGTCCAGTCTACACATGCA 58.838 45.455 0.00 0.00 43.26 3.96
5323 7223 3.868757 TGTAGTCCAGTCTACACATGC 57.131 47.619 0.00 0.00 43.26 4.06
5337 7237 5.998454 AGCAGATGCATAAACATGTAGTC 57.002 39.130 7.68 0.00 45.16 2.59
5354 7254 3.634448 GCTAGATGAGGAAGTGTAGCAGA 59.366 47.826 0.00 0.00 37.22 4.26
5367 7267 4.584325 AGGAGCAAAGAGTAGCTAGATGAG 59.416 45.833 0.00 0.00 42.04 2.90
5383 7283 4.590647 CCAGTATAAGATGAGGAGGAGCAA 59.409 45.833 0.00 0.00 0.00 3.91
5394 7294 7.609760 TTTGTAGTGTTGCCAGTATAAGATG 57.390 36.000 0.00 0.00 31.69 2.90
5395 7295 8.100791 TCTTTTGTAGTGTTGCCAGTATAAGAT 58.899 33.333 0.00 0.00 31.69 2.40
5427 7327 3.246226 GCTCAATAAGTAGCACATCACGG 59.754 47.826 0.00 0.00 38.63 4.94
5428 7328 4.115516 AGCTCAATAAGTAGCACATCACG 58.884 43.478 0.00 0.00 41.32 4.35
5454 7354 3.895041 TCCTCTTCATGGGAAAAACCAAC 59.105 43.478 0.00 0.00 45.13 3.77
5467 7367 2.309755 TGCATCACCCTTTCCTCTTCAT 59.690 45.455 0.00 0.00 0.00 2.57
5524 7424 6.202331 TCCTCTTACTGGATTGATACCTTGA 58.798 40.000 0.00 0.00 0.00 3.02
5543 7443 1.837439 TGGTGACTTGTGTGTTCCTCT 59.163 47.619 0.00 0.00 0.00 3.69
5555 7455 3.876309 AGGTACAACCATTGGTGACTT 57.124 42.857 9.62 2.03 41.95 3.01
5561 7461 4.580995 TGTTTGTGTAGGTACAACCATTGG 59.419 41.667 0.00 0.00 41.95 3.16
5571 7471 7.916450 GCAAGTATTTGTTTGTTTGTGTAGGTA 59.084 33.333 0.00 0.00 36.65 3.08
5615 7515 6.045072 AGTACCGTGAAGGAATTGACAATA 57.955 37.500 0.00 0.00 45.00 1.90
5616 7516 4.906618 AGTACCGTGAAGGAATTGACAAT 58.093 39.130 0.00 0.00 45.00 2.71
5625 7525 1.270625 CCTTGCAAGTACCGTGAAGGA 60.271 52.381 24.35 0.00 45.00 3.36
5695 7596 9.807649 CTTGCTGCAATTTATTTACCTTTATCT 57.192 29.630 16.38 0.00 0.00 1.98
5696 7597 9.034544 CCTTGCTGCAATTTATTTACCTTTATC 57.965 33.333 16.38 0.00 0.00 1.75
5697 7598 8.539544 ACCTTGCTGCAATTTATTTACCTTTAT 58.460 29.630 16.38 0.00 0.00 1.40
5698 7599 7.902087 ACCTTGCTGCAATTTATTTACCTTTA 58.098 30.769 16.38 0.00 0.00 1.85
5699 7600 6.768483 ACCTTGCTGCAATTTATTTACCTTT 58.232 32.000 16.38 0.00 0.00 3.11
5700 7601 6.358974 ACCTTGCTGCAATTTATTTACCTT 57.641 33.333 16.38 0.00 0.00 3.50
5701 7602 7.660030 ATACCTTGCTGCAATTTATTTACCT 57.340 32.000 16.38 0.00 0.00 3.08
5702 7603 8.716646 AAATACCTTGCTGCAATTTATTTACC 57.283 30.769 25.02 0.00 0.00 2.85
5705 7606 8.513774 CCAAAAATACCTTGCTGCAATTTATTT 58.486 29.630 22.83 22.83 29.39 1.40
5706 7607 7.121020 CCCAAAAATACCTTGCTGCAATTTATT 59.879 33.333 16.38 16.64 0.00 1.40
5707 7608 6.598850 CCCAAAAATACCTTGCTGCAATTTAT 59.401 34.615 16.38 11.97 0.00 1.40
5708 7609 5.936956 CCCAAAAATACCTTGCTGCAATTTA 59.063 36.000 16.38 10.19 0.00 1.40
5709 7610 4.761227 CCCAAAAATACCTTGCTGCAATTT 59.239 37.500 16.38 10.44 0.00 1.82
5710 7611 4.202451 ACCCAAAAATACCTTGCTGCAATT 60.202 37.500 16.38 8.59 0.00 2.32
5711 7612 3.327464 ACCCAAAAATACCTTGCTGCAAT 59.673 39.130 16.38 4.53 0.00 3.56
5712 7613 2.703007 ACCCAAAAATACCTTGCTGCAA 59.297 40.909 15.16 15.16 0.00 4.08
5713 7614 2.324541 ACCCAAAAATACCTTGCTGCA 58.675 42.857 0.00 0.00 0.00 4.41
5714 7615 3.401033 AACCCAAAAATACCTTGCTGC 57.599 42.857 0.00 0.00 0.00 5.25
5715 7616 5.819901 TCAAAAACCCAAAAATACCTTGCTG 59.180 36.000 0.00 0.00 0.00 4.41
5716 7617 5.995446 TCAAAAACCCAAAAATACCTTGCT 58.005 33.333 0.00 0.00 0.00 3.91
5717 7618 6.875948 ATCAAAAACCCAAAAATACCTTGC 57.124 33.333 0.00 0.00 0.00 4.01
5718 7619 9.513727 CAAAATCAAAAACCCAAAAATACCTTG 57.486 29.630 0.00 0.00 0.00 3.61
5719 7620 9.249053 ACAAAATCAAAAACCCAAAAATACCTT 57.751 25.926 0.00 0.00 0.00 3.50
5720 7621 8.815565 ACAAAATCAAAAACCCAAAAATACCT 57.184 26.923 0.00 0.00 0.00 3.08
5725 7626 9.898152 AGATCTACAAAATCAAAAACCCAAAAA 57.102 25.926 0.00 0.00 0.00 1.94
5726 7627 9.323985 CAGATCTACAAAATCAAAAACCCAAAA 57.676 29.630 0.00 0.00 0.00 2.44
5727 7628 8.700051 TCAGATCTACAAAATCAAAAACCCAAA 58.300 29.630 0.00 0.00 0.00 3.28
5728 7629 8.243961 TCAGATCTACAAAATCAAAAACCCAA 57.756 30.769 0.00 0.00 0.00 4.12
5729 7630 7.831691 TCAGATCTACAAAATCAAAAACCCA 57.168 32.000 0.00 0.00 0.00 4.51
5730 7631 9.541143 TTTTCAGATCTACAAAATCAAAAACCC 57.459 29.630 0.00 0.00 0.00 4.11


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

AutoCloner maintained by Alex Coulton.