Multiple sequence alignment - TraesCS6D01G201700

Loading Multiple Alignment...

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 TraesCS6D01G201700 chr6D 100.000 5404 0 0 1 5404 283818195 283812792 0.000000e+00 9980.0
1 TraesCS6D01G201700 chr6D 86.842 76 6 2 4992 5066 128896655 128896727 1.250000e-11 82.4
2 TraesCS6D01G201700 chr6D 86.842 76 6 2 4992 5066 429499684 429499756 1.250000e-11 82.4
3 TraesCS6D01G201700 chr6A 96.451 2705 85 5 2180 4876 404455082 404457783 0.000000e+00 4453.0
4 TraesCS6D01G201700 chr6A 93.224 1343 58 13 772 2097 404453760 404455086 0.000000e+00 1945.0
5 TraesCS6D01G201700 chr6A 87.667 300 30 5 5061 5357 404458175 404458470 5.180000e-90 342.0
6 TraesCS6D01G201700 chr6A 87.912 91 5 2 4935 5025 404458086 404458170 9.580000e-18 102.0
7 TraesCS6D01G201700 chr6A 86.842 76 6 2 4992 5066 163137573 163137645 1.250000e-11 82.4
8 TraesCS6D01G201700 chr6B 94.664 2680 87 17 2501 5176 444748348 444745721 0.000000e+00 4106.0
9 TraesCS6D01G201700 chr6B 95.514 1672 35 7 867 2516 444750019 444748366 0.000000e+00 2636.0
10 TraesCS6D01G201700 chr6B 88.428 1158 86 15 6 1133 444752317 444751178 0.000000e+00 1352.0
11 TraesCS6D01G201700 chr6B 87.030 825 79 13 31 833 444751200 444750382 0.000000e+00 905.0
12 TraesCS6D01G201700 chr6B 74.449 544 120 14 127 659 622727953 622727418 3.280000e-52 217.0
13 TraesCS6D01G201700 chr6B 95.000 40 2 0 608 647 605558185 605558146 4.520000e-06 63.9
14 TraesCS6D01G201700 chr2A 76.491 570 96 17 129 664 552499500 552498935 5.330000e-70 276.0
15 TraesCS6D01G201700 chr2A 87.671 73 7 1 5085 5157 611316592 611316662 3.470000e-12 84.2
16 TraesCS6D01G201700 chr7B 83.270 263 41 3 326 587 733716073 733715813 7.000000e-59 239.0
17 TraesCS6D01G201700 chr1B 79.128 321 55 9 350 664 161987301 161986987 1.520000e-50 211.0
18 TraesCS6D01G201700 chr1B 93.333 45 3 0 167 211 344352706 344352662 3.490000e-07 67.6
19 TraesCS6D01G201700 chr5D 83.333 216 35 1 372 586 224866143 224865928 1.190000e-46 198.0
20 TraesCS6D01G201700 chr2B 82.474 194 33 1 333 525 732073 731880 9.310000e-38 169.0
21 TraesCS6D01G201700 chr2D 77.821 257 48 9 445 698 375581706 375581956 3.370000e-32 150.0
22 TraesCS6D01G201700 chr2D 77.626 219 46 3 354 570 166603366 166603583 4.390000e-26 130.0
23 TraesCS6D01G201700 chr2D 85.526 76 9 1 5082 5157 470043819 470043892 1.610000e-10 78.7
24 TraesCS6D01G201700 chr3A 80.488 123 22 2 4766 4887 699855915 699855794 5.760000e-15 93.5
25 TraesCS6D01G201700 chr3A 77.686 121 23 4 4766 4884 9341890 9342008 2.700000e-08 71.3
26 TraesCS6D01G201700 chr5A 85.556 90 8 4 5069 5156 46961268 46961182 7.460000e-14 89.8
27 TraesCS6D01G201700 chr5A 88.158 76 5 2 4992 5066 143581201 143581129 2.680000e-13 87.9
28 TraesCS6D01G201700 chr1D 88.158 76 5 2 4992 5066 308177442 308177514 2.680000e-13 87.9
29 TraesCS6D01G201700 chr7D 88.000 75 6 1 4992 5066 184267116 184267045 9.640000e-13 86.1
30 TraesCS6D01G201700 chr4D 73.684 247 52 11 422 659 507879425 507879667 3.470000e-12 84.2
31 TraesCS6D01G201700 chr4D 86.842 76 6 2 4992 5066 108856484 108856412 1.250000e-11 82.4
32 TraesCS6D01G201700 chr3D 79.661 118 22 2 4766 4882 565636169 565636053 3.470000e-12 84.2
33 TraesCS6D01G201700 chr4A 87.013 77 4 4 4992 5066 214094459 214094531 1.250000e-11 82.4
34 TraesCS6D01G201700 chrUn 91.228 57 4 1 608 664 28639926 28639871 5.800000e-10 76.8
35 TraesCS6D01G201700 chr3B 77.982 109 22 2 4775 4882 753745310 753745203 3.490000e-07 67.6
36 TraesCS6D01G201700 chr3B 87.719 57 6 1 608 664 390894164 390894109 1.260000e-06 65.8
37 TraesCS6D01G201700 chr7A 95.122 41 2 0 607 647 21351084 21351124 1.260000e-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 TraesCS6D01G201700 chr6D 283812792 283818195 5403 True 9980.00 9980 100.0000 1 5404 1 chr6D.!!$R1 5403
1 TraesCS6D01G201700 chr6A 404453760 404458470 4710 False 1710.50 4453 91.3135 772 5357 4 chr6A.!!$F2 4585
2 TraesCS6D01G201700 chr6B 444745721 444752317 6596 True 2249.75 4106 91.4090 6 5176 4 chr6B.!!$R3 5170
3 TraesCS6D01G201700 chr6B 622727418 622727953 535 True 217.00 217 74.4490 127 659 1 chr6B.!!$R2 532
4 TraesCS6D01G201700 chr2A 552498935 552499500 565 True 276.00 276 76.4910 129 664 1 chr2A.!!$R1 535

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
42 43 0.105778 GAGATGGCCCTCTGCACTAC 59.894 60.000 16.06 0.00 43.89 2.73 F
43 44 0.618680 AGATGGCCCTCTGCACTACA 60.619 55.000 10.08 0.00 43.89 2.74 F
104 110 0.764271 TCATGCGGGAATCCATAGCA 59.236 50.000 16.10 16.10 42.28 3.49 F
109 115 1.002430 GCGGGAATCCATAGCATCAGA 59.998 52.381 0.09 0.00 0.00 3.27 F
1587 3064 1.087202 TGGTGTCTGTGTGTGCGTTC 61.087 55.000 0.00 0.00 0.00 3.95 F
2246 3760 2.125685 CAGTAGAGCGTGCATGATCTG 58.874 52.381 31.70 15.75 35.01 2.90 F
3197 4749 4.045636 ACATGTTCTGTGTGCCTTTTTC 57.954 40.909 0.00 0.00 36.48 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 3253 0.036671 CGGGTCACCCAACCTAGTTC 60.037 60.000 15.17 0.0 45.83 3.01 R
1964 3474 3.510459 TCTGAGGAATGAAGGAGTGACA 58.490 45.455 0.00 0.0 0.00 3.58 R
2077 3590 4.142966 GGCGTACTAAACAACATGGACTTC 60.143 45.833 0.00 0.0 0.00 3.01 R
2158 3671 6.637657 ACTACCTCCGTTTCTAAATGTAAGG 58.362 40.000 9.90 9.9 34.55 2.69 R
3197 4749 0.249657 GCCTTCACTGCTCTATCCCG 60.250 60.000 0.00 0.0 0.00 5.14 R
3305 4860 2.304761 AGGAAATAGACCAACCGAAGCA 59.695 45.455 0.00 0.0 0.00 3.91 R
4883 6439 0.037232 AGCAGTCCGTAACAAGAGGC 60.037 55.000 0.00 0.0 0.00 4.70 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
39 40 2.191641 GGAGATGGCCCTCTGCAC 59.808 66.667 21.91 5.77 43.89 4.57
41 42 1.050988 GGAGATGGCCCTCTGCACTA 61.051 60.000 21.91 0.00 43.89 2.74
42 43 0.105778 GAGATGGCCCTCTGCACTAC 59.894 60.000 16.06 0.00 43.89 2.73
43 44 0.618680 AGATGGCCCTCTGCACTACA 60.619 55.000 10.08 0.00 43.89 2.74
45 46 1.915078 ATGGCCCTCTGCACTACACC 61.915 60.000 0.00 0.00 43.89 4.16
46 47 2.125512 GCCCTCTGCACTACACCG 60.126 66.667 0.00 0.00 40.77 4.94
71 77 2.153913 CGAGAAGAACGCCCAACAG 58.846 57.895 0.00 0.00 0.00 3.16
90 96 1.202394 AGCAGTCTGACTCGATCATGC 60.202 52.381 7.49 7.55 39.97 4.06
104 110 0.764271 TCATGCGGGAATCCATAGCA 59.236 50.000 16.10 16.10 42.28 3.49
107 113 0.764271 TGCGGGAATCCATAGCATCA 59.236 50.000 11.22 0.00 32.43 3.07
108 114 1.271001 TGCGGGAATCCATAGCATCAG 60.271 52.381 11.22 0.00 32.43 2.90
109 115 1.002430 GCGGGAATCCATAGCATCAGA 59.998 52.381 0.09 0.00 0.00 3.27
169 191 3.770040 CGGTCCGTCTGGCATCCA 61.770 66.667 2.08 0.00 34.14 3.41
232 261 1.376609 CGGAGCTAAACCATGTGGCC 61.377 60.000 0.00 0.00 39.32 5.36
249 286 1.530013 GCCCGTCCGCTAAGGCTATA 61.530 60.000 0.00 0.00 42.34 1.31
305 1435 2.110213 GGCCGTGACAGACCACAA 59.890 61.111 0.00 0.00 36.89 3.33
550 1686 3.118454 CGGCGACCGCAACTTCAT 61.118 61.111 16.47 0.00 41.17 2.57
575 1711 4.109675 GGCTTAGCCGGCCTCCAA 62.110 66.667 26.15 11.52 45.57 3.53
727 1875 8.586273 CAATTGTGCAATAGGAAATTTAAGACG 58.414 33.333 0.00 0.00 0.00 4.18
768 1916 8.846943 CCAGATTTGGTATATTGTGCTGTATA 57.153 34.615 0.00 0.00 39.79 1.47
769 1917 9.453572 CCAGATTTGGTATATTGTGCTGTATAT 57.546 33.333 0.00 0.00 39.79 0.86
794 1942 6.611381 ACTGTTATGTACACACATTGCAATC 58.389 36.000 9.53 0.00 42.98 2.67
796 1944 7.040478 ACTGTTATGTACACACATTGCAATCTT 60.040 33.333 9.53 0.00 42.98 2.40
835 1983 7.833682 TGAGGAAGCATATTTGTTCCAGAATAA 59.166 33.333 14.82 0.00 42.03 1.40
937 2414 2.558359 GACCCCACAAGATTTCCACTTG 59.442 50.000 0.00 0.00 46.69 3.16
1546 3023 6.420588 TCCATTTCAACGTTGTTTAGTTACG 58.579 36.000 26.47 7.84 40.85 3.18
1558 3035 5.908106 TGTTTAGTTACGCAATTCTCGTTC 58.092 37.500 7.47 3.24 40.89 3.95
1587 3064 1.087202 TGGTGTCTGTGTGTGCGTTC 61.087 55.000 0.00 0.00 0.00 3.95
1749 3253 5.994668 AGCAAGAAGGAGAAGTTTCAGTAAG 59.005 40.000 0.00 0.00 0.00 2.34
2077 3590 3.244033 TGTTTGCAAAAGTTGGTCTGG 57.756 42.857 14.67 0.00 0.00 3.86
2104 3617 3.596214 CATGTTGTTTAGTACGCCCTCT 58.404 45.455 0.00 0.00 0.00 3.69
2179 3692 4.259356 GCCTTACATTTAGAAACGGAGGT 58.741 43.478 0.00 0.00 0.00 3.85
2222 3736 8.383619 CAACTGTACTCTATTGTTTACTCATGC 58.616 37.037 0.00 0.00 0.00 4.06
2246 3760 2.125685 CAGTAGAGCGTGCATGATCTG 58.874 52.381 31.70 15.75 35.01 2.90
2340 3854 7.915293 TTGAAAACATTGAGTGGTCGTATAT 57.085 32.000 0.00 0.00 0.00 0.86
2779 4331 6.771076 TGTTTTATCTGATTCGATTTGTCCG 58.229 36.000 0.00 0.00 0.00 4.79
3080 4632 5.263599 ACACCCATCAAGATTCTGCAATTA 58.736 37.500 0.00 0.00 0.00 1.40
3083 4635 4.646040 CCCATCAAGATTCTGCAATTACCA 59.354 41.667 0.00 0.00 0.00 3.25
3197 4749 4.045636 ACATGTTCTGTGTGCCTTTTTC 57.954 40.909 0.00 0.00 36.48 2.29
3403 4958 8.504815 GTTGCCAAACTAAAACTTTAACCAAAA 58.495 29.630 0.00 0.00 33.22 2.44
3405 4960 8.669243 TGCCAAACTAAAACTTTAACCAAAATG 58.331 29.630 0.00 0.00 0.00 2.32
3487 5042 7.329471 CCTTTTGAAGTTAGCTTATTTTCCAGC 59.671 37.037 0.00 0.00 34.61 4.85
3526 5081 6.402222 TGATTTCTCTCTTCCTTTCAGCTAC 58.598 40.000 0.00 0.00 0.00 3.58
3687 5242 4.094590 CAGTTTTGCTCATCATCCTGTCTC 59.905 45.833 0.00 0.00 0.00 3.36
3703 5258 5.419155 TCCTGTCTCACTTACTATTGGAGTG 59.581 44.000 6.61 6.61 39.39 3.51
3737 5292 6.541641 AGAAATAGGCAGAATTAGCAACTCAG 59.458 38.462 4.92 0.00 0.00 3.35
3772 5327 6.658816 TCTCTTAATGGTTGCATGCTAAAAGA 59.341 34.615 20.33 15.12 0.00 2.52
4319 5874 5.426689 AGACTGCACCTATGAAGATGAAA 57.573 39.130 0.00 0.00 34.64 2.69
4326 5881 5.645497 GCACCTATGAAGATGAAAGTTCAGT 59.355 40.000 0.00 0.00 41.08 3.41
4718 6273 1.221840 CGAGGCTAAGGGTGCATGT 59.778 57.895 0.00 0.00 0.00 3.21
4740 6295 2.355716 CCATGGTACCGTGAACTGGAAT 60.356 50.000 31.83 1.90 35.09 3.01
4765 6320 2.558359 ACCTTTGGCTTAGTGCAATGTC 59.442 45.455 0.00 0.00 45.15 3.06
4837 6392 4.624015 TGAAACCCATACGATATCGGAAC 58.376 43.478 27.58 8.23 44.95 3.62
4841 6396 6.600882 AACCCATACGATATCGGAACTTAT 57.399 37.500 27.58 13.54 44.95 1.73
4848 6403 5.479306 ACGATATCGGAACTTATTCATGGG 58.521 41.667 27.58 0.00 44.95 4.00
4859 6415 0.609662 ATTCATGGGTTGGCACTTGC 59.390 50.000 0.00 0.00 41.14 4.01
4863 6419 1.135527 CATGGGTTGGCACTTGCATAG 59.864 52.381 3.15 0.00 44.36 2.23
4864 6420 0.611618 TGGGTTGGCACTTGCATAGG 60.612 55.000 3.15 0.00 44.36 2.57
4883 6439 1.737793 GGTAACTTTCACGCATCCCTG 59.262 52.381 0.00 0.00 0.00 4.45
4884 6440 1.130561 GTAACTTTCACGCATCCCTGC 59.869 52.381 0.00 0.00 45.31 4.85
4901 6457 0.320421 TGCCTCTTGTTACGGACTGC 60.320 55.000 0.00 0.00 0.00 4.40
4903 6459 1.608283 GCCTCTTGTTACGGACTGCTT 60.608 52.381 0.00 0.00 0.00 3.91
4911 6467 2.605837 TACGGACTGCTTGTGTCAAA 57.394 45.000 0.00 0.00 36.26 2.69
5077 6897 9.253832 TCATGTATATCATCAGGGTTTTGTTTT 57.746 29.630 0.00 0.00 34.09 2.43
5098 6918 7.398332 TGTTTTGGTACACCCCTTAAAAGTTTA 59.602 33.333 0.00 0.00 39.29 2.01
5105 6925 7.849322 ACACCCCTTAAAAGTTTACATGAAT 57.151 32.000 0.00 0.00 0.00 2.57
5207 7027 7.996098 TTTTGATTGAAGGGGTACTTTCTAG 57.004 36.000 0.00 0.00 40.21 2.43
5213 7036 6.973460 TGAAGGGGTACTTTCTAGCTATAC 57.027 41.667 0.00 0.00 40.21 1.47
5227 7050 7.841282 TCTAGCTATACCTTTAATCTGCACT 57.159 36.000 0.00 0.00 0.00 4.40
5236 7059 4.346129 CTTTAATCTGCACTGAAATCCGC 58.654 43.478 0.00 0.00 0.00 5.54
5242 7065 1.680735 TGCACTGAAATCCGCAAACTT 59.319 42.857 0.00 0.00 0.00 2.66
5259 7082 5.382616 CAAACTTTTCTAGGGGGTGTAACT 58.617 41.667 0.00 0.00 36.74 2.24
5273 7096 4.278419 GGGTGTAACTGAAGCAAAGTTCAT 59.722 41.667 2.40 0.00 38.73 2.57
5281 7104 7.317842 ACTGAAGCAAAGTTCATATCATCAG 57.682 36.000 0.00 0.00 35.88 2.90
5285 7108 5.748402 AGCAAAGTTCATATCATCAGTCCA 58.252 37.500 0.00 0.00 0.00 4.02
5286 7109 5.821470 AGCAAAGTTCATATCATCAGTCCAG 59.179 40.000 0.00 0.00 0.00 3.86
5291 7114 7.370905 AGTTCATATCATCAGTCCAGATCAA 57.629 36.000 0.00 0.00 0.00 2.57
5292 7115 7.799081 AGTTCATATCATCAGTCCAGATCAAA 58.201 34.615 0.00 0.00 0.00 2.69
5332 7155 5.321516 CACATATCAACATGCGCATATCTG 58.678 41.667 24.84 19.26 0.00 2.90
5339 7162 2.224137 ACATGCGCATATCTGCTACACT 60.224 45.455 24.84 0.00 46.65 3.55
5344 7167 4.270084 TGCGCATATCTGCTACACTTTAAC 59.730 41.667 5.66 0.00 46.65 2.01
5346 7169 5.557136 GCGCATATCTGCTACACTTTAACTG 60.557 44.000 0.30 0.00 46.65 3.16
5357 7180 7.663905 TGCTACACTTTAACTGTTGGACATATT 59.336 33.333 2.69 0.00 0.00 1.28
5358 7181 7.962918 GCTACACTTTAACTGTTGGACATATTG 59.037 37.037 2.69 0.00 0.00 1.90
5359 7182 6.677913 ACACTTTAACTGTTGGACATATTGC 58.322 36.000 2.69 0.00 0.00 3.56
5360 7183 6.490040 ACACTTTAACTGTTGGACATATTGCT 59.510 34.615 2.69 0.00 0.00 3.91
5361 7184 7.014230 ACACTTTAACTGTTGGACATATTGCTT 59.986 33.333 2.69 0.00 0.00 3.91
5362 7185 7.867403 CACTTTAACTGTTGGACATATTGCTTT 59.133 33.333 2.69 0.00 0.00 3.51
5363 7186 8.421002 ACTTTAACTGTTGGACATATTGCTTTT 58.579 29.630 2.69 0.00 0.00 2.27
5364 7187 9.260002 CTTTAACTGTTGGACATATTGCTTTTT 57.740 29.630 2.69 0.00 0.00 1.94
5366 7189 9.906660 TTAACTGTTGGACATATTGCTTTTTAG 57.093 29.630 2.69 0.00 0.00 1.85
5367 7190 7.524717 ACTGTTGGACATATTGCTTTTTAGT 57.475 32.000 0.00 0.00 0.00 2.24
5368 7191 7.951591 ACTGTTGGACATATTGCTTTTTAGTT 58.048 30.769 0.00 0.00 0.00 2.24
5369 7192 8.421002 ACTGTTGGACATATTGCTTTTTAGTTT 58.579 29.630 0.00 0.00 0.00 2.66
5370 7193 8.586570 TGTTGGACATATTGCTTTTTAGTTTG 57.413 30.769 0.00 0.00 0.00 2.93
5371 7194 7.170658 TGTTGGACATATTGCTTTTTAGTTTGC 59.829 33.333 0.00 0.00 0.00 3.68
5372 7195 6.162777 TGGACATATTGCTTTTTAGTTTGCC 58.837 36.000 0.00 0.00 0.00 4.52
5373 7196 6.162777 GGACATATTGCTTTTTAGTTTGCCA 58.837 36.000 0.00 0.00 0.00 4.92
5374 7197 6.648725 GGACATATTGCTTTTTAGTTTGCCAA 59.351 34.615 0.00 0.00 0.00 4.52
5375 7198 7.360017 GGACATATTGCTTTTTAGTTTGCCAAC 60.360 37.037 0.00 0.00 0.00 3.77
5376 7199 6.989169 ACATATTGCTTTTTAGTTTGCCAACA 59.011 30.769 3.22 0.00 35.05 3.33
5377 7200 7.661027 ACATATTGCTTTTTAGTTTGCCAACAT 59.339 29.630 3.22 0.00 35.05 2.71
5378 7201 6.940831 ATTGCTTTTTAGTTTGCCAACATT 57.059 29.167 3.22 0.00 35.05 2.71
5379 7202 6.749923 TTGCTTTTTAGTTTGCCAACATTT 57.250 29.167 3.22 0.00 35.05 2.32
5380 7203 6.116680 TGCTTTTTAGTTTGCCAACATTTG 57.883 33.333 3.22 0.00 35.05 2.32
5381 7204 4.969395 GCTTTTTAGTTTGCCAACATTTGC 59.031 37.500 3.22 0.00 35.05 3.68
5382 7205 4.785669 TTTTAGTTTGCCAACATTTGCG 57.214 36.364 3.22 0.00 35.05 4.85
5383 7206 1.777101 TAGTTTGCCAACATTTGCGC 58.223 45.000 0.00 0.00 35.05 6.09
5384 7207 0.879839 AGTTTGCCAACATTTGCGCC 60.880 50.000 4.18 0.00 35.05 6.53
5385 7208 1.144716 TTTGCCAACATTTGCGCCA 59.855 47.368 4.18 0.00 0.00 5.69
5386 7209 0.250209 TTTGCCAACATTTGCGCCAT 60.250 45.000 4.18 0.00 0.00 4.40
5387 7210 0.605083 TTGCCAACATTTGCGCCATA 59.395 45.000 4.18 0.00 0.00 2.74
5388 7211 0.108898 TGCCAACATTTGCGCCATAC 60.109 50.000 4.18 0.00 0.00 2.39
5389 7212 0.108898 GCCAACATTTGCGCCATACA 60.109 50.000 4.18 0.00 0.00 2.29
5390 7213 1.671261 GCCAACATTTGCGCCATACAA 60.671 47.619 4.18 0.00 0.00 2.41
5391 7214 1.991965 CCAACATTTGCGCCATACAAC 59.008 47.619 4.18 0.00 0.00 3.32
5392 7215 1.648191 CAACATTTGCGCCATACAACG 59.352 47.619 4.18 0.00 0.00 4.10
5393 7216 0.878416 ACATTTGCGCCATACAACGT 59.122 45.000 4.18 0.00 0.00 3.99
5394 7217 1.135803 ACATTTGCGCCATACAACGTC 60.136 47.619 4.18 0.00 0.00 4.34
5395 7218 0.096281 ATTTGCGCCATACAACGTCG 59.904 50.000 4.18 0.00 0.00 5.12
5396 7219 2.501607 TTTGCGCCATACAACGTCGC 62.502 55.000 4.18 8.41 45.23 5.19
5397 7220 3.483665 GCGCCATACAACGTCGCA 61.484 61.111 10.21 0.00 44.50 5.10
5398 7221 3.017656 GCGCCATACAACGTCGCAA 62.018 57.895 10.21 0.00 44.50 4.85
5399 7222 1.713246 CGCCATACAACGTCGCAAT 59.287 52.632 0.00 0.00 0.00 3.56
5400 7223 0.096281 CGCCATACAACGTCGCAATT 59.904 50.000 0.00 0.00 0.00 2.32
5401 7224 1.325037 CGCCATACAACGTCGCAATTA 59.675 47.619 0.00 0.00 0.00 1.40
5402 7225 2.222841 CGCCATACAACGTCGCAATTAA 60.223 45.455 0.00 0.00 0.00 1.40
5403 7226 3.725305 CGCCATACAACGTCGCAATTAAA 60.725 43.478 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.016393 CTCAAGCCCGCGTAGGATGA 62.016 60.000 4.92 7.64 45.00 2.92
1 2 1.592669 CTCAAGCCCGCGTAGGATG 60.593 63.158 4.92 3.43 45.00 3.51
2 3 2.797278 CCTCAAGCCCGCGTAGGAT 61.797 63.158 4.92 0.00 45.00 3.24
3 4 3.458163 CCTCAAGCCCGCGTAGGA 61.458 66.667 4.92 0.00 45.00 2.94
4 5 3.432051 CTCCTCAAGCCCGCGTAGG 62.432 68.421 4.92 0.00 40.63 3.18
11 12 1.835693 CCATCTCCTCCTCAAGCCC 59.164 63.158 0.00 0.00 0.00 5.19
12 13 1.148048 GCCATCTCCTCCTCAAGCC 59.852 63.158 0.00 0.00 0.00 4.35
63 69 0.952984 GAGTCAGACTGCTGTTGGGC 60.953 60.000 8.15 0.00 42.84 5.36
67 73 1.889170 TGATCGAGTCAGACTGCTGTT 59.111 47.619 8.15 0.00 42.84 3.16
71 77 1.207390 GCATGATCGAGTCAGACTGC 58.793 55.000 8.15 0.00 40.92 4.40
90 96 2.613977 GGTCTGATGCTATGGATTCCCG 60.614 54.545 0.00 0.00 34.29 5.14
104 110 2.086869 CCAAGCGTCATTTGGTCTGAT 58.913 47.619 0.00 0.00 40.15 2.90
107 113 2.359900 GATCCAAGCGTCATTTGGTCT 58.640 47.619 4.14 0.00 44.35 3.85
108 114 1.062587 CGATCCAAGCGTCATTTGGTC 59.937 52.381 4.14 1.67 44.35 4.02
109 115 1.086696 CGATCCAAGCGTCATTTGGT 58.913 50.000 4.14 0.00 44.35 3.67
169 191 3.284449 GCCTCCGCCACAACGTTT 61.284 61.111 0.00 0.00 0.00 3.60
208 230 1.899814 ACATGGTTTAGCTCCGAGTCA 59.100 47.619 0.00 0.00 0.00 3.41
218 240 1.029947 GGACGGGCCACATGGTTTAG 61.030 60.000 4.39 0.00 37.57 1.85
232 261 0.109226 GCTATAGCCTTAGCGGACGG 60.109 60.000 14.13 0.00 46.67 4.79
285 1412 3.311110 TGGTCTGTCACGGCCTCC 61.311 66.667 0.00 0.00 0.00 4.30
386 1520 0.683179 TGGATCTGTCGTGGTCGGAT 60.683 55.000 0.00 0.00 37.69 4.18
443 1577 4.377760 TCTTCCTCGTCGGGGCCT 62.378 66.667 6.17 0.00 0.00 5.19
544 1680 1.486726 CTAAGCCCCTCGGAATGAAGT 59.513 52.381 0.00 0.00 0.00 3.01
575 1711 2.668212 CACGCCCGTGTCCATGTT 60.668 61.111 12.31 0.00 40.91 2.71
700 1848 8.872845 GTCTTAAATTTCCTATTGCACAATTGG 58.127 33.333 15.14 15.14 42.48 3.16
701 1849 8.586273 CGTCTTAAATTTCCTATTGCACAATTG 58.414 33.333 3.24 3.24 32.50 2.32
702 1850 8.303876 ACGTCTTAAATTTCCTATTGCACAATT 58.696 29.630 0.47 0.00 32.50 2.32
709 1857 6.185399 CGCTCACGTCTTAAATTTCCTATTG 58.815 40.000 0.00 0.00 33.53 1.90
768 1916 7.680442 TTGCAATGTGTGTACATAACAGTAT 57.320 32.000 16.50 6.20 46.54 2.12
769 1917 7.606073 AGATTGCAATGTGTGTACATAACAGTA 59.394 33.333 18.59 4.76 46.54 2.74
770 1918 6.430925 AGATTGCAATGTGTGTACATAACAGT 59.569 34.615 18.59 12.61 46.54 3.55
794 1942 1.613925 TCCTCACTTCCTCACGACAAG 59.386 52.381 0.00 0.00 0.00 3.16
796 1944 1.613925 CTTCCTCACTTCCTCACGACA 59.386 52.381 0.00 0.00 0.00 4.35
835 1983 3.623453 GCCTTATTCTTCTGGTTCTGGCT 60.623 47.826 0.00 0.00 34.42 4.75
917 2394 2.597455 CAAGTGGAAATCTTGTGGGGT 58.403 47.619 0.00 0.00 37.90 4.95
937 2414 2.103941 AGAATCGAATGGAGGAAGAGGC 59.896 50.000 0.00 0.00 0.00 4.70
1187 2664 4.840005 GCCTCCTGTACCGCTGCC 62.840 72.222 0.00 0.00 0.00 4.85
1515 2992 1.135315 CGTTGAAATGGAGGCGCAG 59.865 57.895 10.83 0.00 0.00 5.18
1546 3023 2.427506 AGGTCCTTGAACGAGAATTGC 58.572 47.619 0.00 0.00 0.00 3.56
1558 3035 2.303022 ACACAGACACCATAGGTCCTTG 59.697 50.000 0.00 0.00 35.89 3.61
1587 3064 6.632834 CACTTTCCATCGTCAAAAGTAACAAG 59.367 38.462 0.00 0.00 40.32 3.16
1749 3253 0.036671 CGGGTCACCCAACCTAGTTC 60.037 60.000 15.17 0.00 45.83 3.01
1944 3454 9.231297 AGTGACAACTATAATACATTTTGTGCT 57.769 29.630 0.00 0.00 33.79 4.40
1964 3474 3.510459 TCTGAGGAATGAAGGAGTGACA 58.490 45.455 0.00 0.00 0.00 3.58
1965 3475 4.543590 TTCTGAGGAATGAAGGAGTGAC 57.456 45.455 0.00 0.00 0.00 3.67
1966 3476 5.768980 ATTTCTGAGGAATGAAGGAGTGA 57.231 39.130 0.00 0.00 0.00 3.41
1975 3488 9.458727 AGTGGCATATATAATTTCTGAGGAATG 57.541 33.333 0.00 0.00 0.00 2.67
2050 3563 6.315144 AGACCAACTTTTGCAAACATTTTACC 59.685 34.615 12.39 0.00 0.00 2.85
2077 3590 4.142966 GGCGTACTAAACAACATGGACTTC 60.143 45.833 0.00 0.00 0.00 3.01
2158 3671 6.637657 ACTACCTCCGTTTCTAAATGTAAGG 58.362 40.000 9.90 9.90 34.55 2.69
2179 3692 9.071276 AGTACAGTTGTAAGCTGTAAGTTACTA 57.929 33.333 14.00 0.62 46.81 1.82
2222 3736 4.190350 TGCACGCTCTACTGCATG 57.810 55.556 0.00 0.00 38.49 4.06
2246 3760 2.609747 TCTGGATATAGGTGGCCTCAC 58.390 52.381 3.32 0.00 42.91 3.51
2779 4331 4.142609 TCATTGTCCTGCCATAGAGAAC 57.857 45.455 0.00 0.00 0.00 3.01
2935 4487 5.644188 AGATTTTGGGAGAAGAAATGGTCA 58.356 37.500 0.00 0.00 0.00 4.02
3080 4632 5.103940 AGGTAGGATTATGAACATGCTTGGT 60.104 40.000 4.44 0.00 0.00 3.67
3083 4635 6.662755 TGAAGGTAGGATTATGAACATGCTT 58.337 36.000 0.00 0.00 0.00 3.91
3197 4749 0.249657 GCCTTCACTGCTCTATCCCG 60.250 60.000 0.00 0.00 0.00 5.14
3305 4860 2.304761 AGGAAATAGACCAACCGAAGCA 59.695 45.455 0.00 0.00 0.00 3.91
3403 4958 6.708054 GCCTACTTGCAGACTATATTTCACAT 59.292 38.462 0.00 0.00 0.00 3.21
3405 4960 6.049149 TGCCTACTTGCAGACTATATTTCAC 58.951 40.000 0.00 0.00 36.04 3.18
3462 5017 7.061094 CGCTGGAAAATAAGCTAACTTCAAAAG 59.939 37.037 0.00 0.00 37.33 2.27
3467 5022 5.796350 TCGCTGGAAAATAAGCTAACTTC 57.204 39.130 0.00 0.00 37.33 3.01
3487 5042 5.350914 AGAGAAATCAGCACAGAAAGATTCG 59.649 40.000 0.00 0.00 30.87 3.34
3526 5081 6.480524 TCATCAGTGTCGAAGTTAAAATGG 57.519 37.500 0.00 0.00 0.00 3.16
3687 5242 7.672983 AATTCACACACTCCAATAGTAAGTG 57.327 36.000 3.99 3.99 44.68 3.16
3737 5292 7.826690 TGCAACCATTAAGAGATAGGAAAAAC 58.173 34.615 0.00 0.00 0.00 2.43
3772 5327 5.018539 TGAAATATTCAGACGAATCGGGT 57.981 39.130 7.80 0.00 41.09 5.28
3825 5380 7.619965 AGAAAAGAAGTATTAGAGCTCTGCTT 58.380 34.615 26.78 21.51 39.88 3.91
4098 5653 7.755822 AGCTCTGTTACAGTCTTAAAATACTCG 59.244 37.037 12.41 0.00 32.61 4.18
4231 5786 4.747108 GTGTTCAGGTTCATGGATAGATCG 59.253 45.833 0.00 0.00 0.00 3.69
4319 5874 3.503748 GCACCTGAAGCATAAACTGAACT 59.496 43.478 0.00 0.00 0.00 3.01
4502 6057 7.647715 ACCAAAATACATGATAAAATAGCACGC 59.352 33.333 0.00 0.00 0.00 5.34
4718 6273 0.611200 CCAGTTCACGGTACCATGGA 59.389 55.000 21.47 0.00 0.00 3.41
4740 6295 2.660572 TGCACTAAGCCAAAGGTCAAA 58.339 42.857 0.00 0.00 44.83 2.69
4765 6320 3.143807 TGAAAGGCTTTGTTGTCGTTG 57.856 42.857 18.79 0.00 0.00 4.10
4837 6392 3.676873 GCAAGTGCCAACCCATGAATAAG 60.677 47.826 0.00 0.00 34.31 1.73
4841 6396 0.758310 TGCAAGTGCCAACCCATGAA 60.758 50.000 0.00 0.00 41.18 2.57
4848 6403 3.081804 AGTTACCTATGCAAGTGCCAAC 58.918 45.455 0.00 0.00 41.18 3.77
4859 6415 3.560068 GGGATGCGTGAAAGTTACCTATG 59.440 47.826 0.00 0.00 0.00 2.23
4863 6419 1.737793 CAGGGATGCGTGAAAGTTACC 59.262 52.381 0.00 0.00 0.00 2.85
4864 6420 1.130561 GCAGGGATGCGTGAAAGTTAC 59.869 52.381 11.38 0.00 0.00 2.50
4883 6439 0.037232 AGCAGTCCGTAACAAGAGGC 60.037 55.000 0.00 0.00 0.00 4.70
4884 6440 2.069273 CAAGCAGTCCGTAACAAGAGG 58.931 52.381 0.00 0.00 0.00 3.69
4901 6457 6.483307 TCAGAGTAGACCAAATTTGACACAAG 59.517 38.462 19.86 4.15 0.00 3.16
4903 6459 5.758296 GTCAGAGTAGACCAAATTTGACACA 59.242 40.000 19.86 0.00 35.13 3.72
4954 6774 3.197766 TGTAGAACTCCTGAAATGCCGAT 59.802 43.478 0.00 0.00 0.00 4.18
4955 6775 2.565391 TGTAGAACTCCTGAAATGCCGA 59.435 45.455 0.00 0.00 0.00 5.54
4956 6776 2.972625 TGTAGAACTCCTGAAATGCCG 58.027 47.619 0.00 0.00 0.00 5.69
4957 6777 4.702131 ACAATGTAGAACTCCTGAAATGCC 59.298 41.667 0.00 0.00 0.00 4.40
4958 6778 5.886960 ACAATGTAGAACTCCTGAAATGC 57.113 39.130 0.00 0.00 0.00 3.56
4999 6819 5.316167 AGCTTGTCCAACATTATTGTCTGA 58.684 37.500 0.00 0.00 34.06 3.27
5048 6868 9.507329 ACAAAACCCTGATGATATACATGATAC 57.493 33.333 0.00 0.00 39.56 2.24
5077 6897 6.011122 TGTAAACTTTTAAGGGGTGTACCA 57.989 37.500 3.11 0.00 42.91 3.25
5122 6942 6.744537 GCAAGCTAATATGGCGATAATCTTTG 59.255 38.462 0.00 0.00 34.52 2.77
5127 6947 5.491070 TCTGCAAGCTAATATGGCGATAAT 58.509 37.500 0.00 0.00 34.52 1.28
5182 7002 7.039993 GCTAGAAAGTACCCCTTCAATCAAAAA 60.040 37.037 0.00 0.00 31.27 1.94
5192 7012 6.040662 AGGTATAGCTAGAAAGTACCCCTT 57.959 41.667 14.29 0.00 36.34 3.95
5201 7021 8.705594 AGTGCAGATTAAAGGTATAGCTAGAAA 58.294 33.333 4.57 0.83 0.00 2.52
5207 7027 7.553881 TTTCAGTGCAGATTAAAGGTATAGC 57.446 36.000 0.00 0.00 0.00 2.97
5213 7036 4.731773 GCGGATTTCAGTGCAGATTAAAGG 60.732 45.833 0.00 0.00 0.00 3.11
5227 7050 4.217550 CCCTAGAAAAGTTTGCGGATTTCA 59.782 41.667 3.99 0.00 34.91 2.69
5236 7059 5.240844 CAGTTACACCCCCTAGAAAAGTTTG 59.759 44.000 0.00 0.00 0.00 2.93
5242 7065 3.008704 GCTTCAGTTACACCCCCTAGAAA 59.991 47.826 0.00 0.00 0.00 2.52
5259 7082 6.317140 GGACTGATGATATGAACTTTGCTTCA 59.683 38.462 0.00 0.00 34.65 3.02
5273 7096 7.384524 AAGGATTTGATCTGGACTGATGATA 57.615 36.000 0.00 0.00 0.00 2.15
5281 7104 7.201767 CCACATAAGAAAGGATTTGATCTGGAC 60.202 40.741 0.00 0.00 39.27 4.02
5285 7108 5.595952 GGCCACATAAGAAAGGATTTGATCT 59.404 40.000 0.00 0.00 39.27 2.75
5286 7109 5.360714 TGGCCACATAAGAAAGGATTTGATC 59.639 40.000 0.00 0.00 39.27 2.92
5291 7114 4.046286 TGTGGCCACATAAGAAAGGATT 57.954 40.909 34.74 0.00 36.21 3.01
5292 7115 3.737559 TGTGGCCACATAAGAAAGGAT 57.262 42.857 34.74 0.00 36.21 3.24
5314 7137 2.501261 AGCAGATATGCGCATGTTGAT 58.499 42.857 32.48 21.58 40.27 2.57
5320 7143 2.827800 AGTGTAGCAGATATGCGCAT 57.172 45.000 28.23 28.23 40.27 4.73
5332 7155 5.941948 ATGTCCAACAGTTAAAGTGTAGC 57.058 39.130 0.00 0.00 30.24 3.58
5344 7167 8.702438 CAAACTAAAAAGCAATATGTCCAACAG 58.298 33.333 0.00 0.00 0.00 3.16
5346 7169 7.360017 GGCAAACTAAAAAGCAATATGTCCAAC 60.360 37.037 0.00 0.00 0.00 3.77
5357 7180 5.448360 GCAAATGTTGGCAAACTAAAAAGCA 60.448 36.000 0.00 0.00 37.19 3.91
5358 7181 4.969395 GCAAATGTTGGCAAACTAAAAAGC 59.031 37.500 0.00 0.00 37.19 3.51
5359 7182 5.196825 CGCAAATGTTGGCAAACTAAAAAG 58.803 37.500 0.00 0.00 37.19 2.27
5360 7183 4.494855 GCGCAAATGTTGGCAAACTAAAAA 60.495 37.500 0.30 0.00 37.19 1.94
5361 7184 3.001736 GCGCAAATGTTGGCAAACTAAAA 59.998 39.130 0.30 0.00 37.19 1.52
5362 7185 2.541762 GCGCAAATGTTGGCAAACTAAA 59.458 40.909 0.30 0.00 37.19 1.85
5363 7186 2.131183 GCGCAAATGTTGGCAAACTAA 58.869 42.857 0.30 0.00 37.19 2.24
5364 7187 1.604185 GGCGCAAATGTTGGCAAACTA 60.604 47.619 10.83 0.00 37.19 2.24
5365 7188 0.879839 GGCGCAAATGTTGGCAAACT 60.880 50.000 10.83 0.00 37.19 2.66
5366 7189 1.156645 TGGCGCAAATGTTGGCAAAC 61.157 50.000 10.83 0.00 35.04 2.93
5367 7190 0.250209 ATGGCGCAAATGTTGGCAAA 60.250 45.000 10.83 0.00 41.73 3.68
5368 7191 0.605083 TATGGCGCAAATGTTGGCAA 59.395 45.000 10.83 0.00 41.73 4.52
5369 7192 0.108898 GTATGGCGCAAATGTTGGCA 60.109 50.000 10.83 6.53 42.64 4.92
5370 7193 0.108898 TGTATGGCGCAAATGTTGGC 60.109 50.000 10.83 0.00 0.00 4.52
5371 7194 1.991965 GTTGTATGGCGCAAATGTTGG 59.008 47.619 10.83 0.00 0.00 3.77
5372 7195 1.648191 CGTTGTATGGCGCAAATGTTG 59.352 47.619 10.83 0.00 0.00 3.33
5373 7196 1.268352 ACGTTGTATGGCGCAAATGTT 59.732 42.857 10.83 0.00 0.00 2.71
5374 7197 0.878416 ACGTTGTATGGCGCAAATGT 59.122 45.000 10.83 3.95 0.00 2.71
5375 7198 1.534028 GACGTTGTATGGCGCAAATG 58.466 50.000 10.83 3.29 0.00 2.32
5376 7199 0.096281 CGACGTTGTATGGCGCAAAT 59.904 50.000 10.83 4.67 0.00 2.32
5377 7200 1.493750 CGACGTTGTATGGCGCAAA 59.506 52.632 10.83 0.00 0.00 3.68
5378 7201 3.017656 GCGACGTTGTATGGCGCAA 62.018 57.895 10.83 0.00 46.19 4.85
5379 7202 3.483665 GCGACGTTGTATGGCGCA 61.484 61.111 10.83 0.00 46.19 6.09
5381 7204 0.096281 AATTGCGACGTTGTATGGCG 59.904 50.000 4.37 0.00 0.00 5.69
5382 7205 3.392769 TTAATTGCGACGTTGTATGGC 57.607 42.857 4.37 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.