Multiple sequence alignment - TraesCS2A01G129900

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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 TraesCS2A01G129900 chr2A 100.000 8255 0 0 1 8255 77749895 77758149 0.000000e+00 15245.0
1 TraesCS2A01G129900 chr2A 88.421 285 19 11 7890 8172 77767626 77767898 1.720000e-86 331.0
2 TraesCS2A01G129900 chr2B 97.640 5043 95 12 1 5035 118686725 118691751 0.000000e+00 8632.0
3 TraesCS2A01G129900 chr2B 93.306 2181 101 32 5101 7261 118691756 118693911 0.000000e+00 3177.0
4 TraesCS2A01G129900 chr2B 83.626 684 38 34 7618 8246 118694389 118695053 7.190000e-160 575.0
5 TraesCS2A01G129900 chr2B 88.356 292 18 12 7898 8186 118825849 118826127 3.690000e-88 337.0
6 TraesCS2A01G129900 chr2B 97.143 35 0 1 256 290 118687105 118687072 3.220000e-04 58.4
7 TraesCS2A01G129900 chr2D 98.220 2303 31 6 605 2905 76893039 76895333 0.000000e+00 4017.0
8 TraesCS2A01G129900 chr2D 97.546 2078 28 4 2959 5035 76895329 76897384 0.000000e+00 3533.0
9 TraesCS2A01G129900 chr2D 91.033 1907 109 32 6364 8243 76898752 76900623 0.000000e+00 2518.0
10 TraesCS2A01G129900 chr2D 97.008 1270 33 5 5101 6366 76897389 76898657 0.000000e+00 2130.0
11 TraesCS2A01G129900 chr2D 96.607 560 17 2 6 564 76892480 76893038 0.000000e+00 928.0
12 TraesCS2A01G129900 chr2D 82.295 305 50 2 6517 6818 76898845 76899148 2.290000e-65 261.0
13 TraesCS2A01G129900 chr2D 89.888 178 10 7 7997 8171 76988226 76988398 1.080000e-53 222.0
14 TraesCS2A01G129900 chr2D 97.143 35 0 1 256 290 76892853 76892820 3.220000e-04 58.4
15 TraesCS2A01G129900 chr5B 86.165 824 83 16 4253 5067 586786954 586787755 0.000000e+00 861.0
16 TraesCS2A01G129900 chr5B 88.509 644 70 3 5119 5758 586787738 586788381 0.000000e+00 776.0
17 TraesCS2A01G129900 chr5B 95.906 342 12 2 5767 6107 586788467 586788807 3.370000e-153 553.0
18 TraesCS2A01G129900 chr1D 88.131 674 64 10 3972 4637 66752910 66752245 0.000000e+00 787.0
19 TraesCS2A01G129900 chr3B 87.143 210 15 5 1610 1816 823953934 823953734 2.320000e-55 228.0
20 TraesCS2A01G129900 chr5A 88.050 159 16 2 4480 4637 426302507 426302351 1.410000e-42 185.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G129900 chr2A 77749895 77758149 8254 False 15245.000000 15245 100.000000 1 8255 1 chr2A.!!$F1 8254
1 TraesCS2A01G129900 chr2B 118686725 118695053 8328 False 4128.000000 8632 91.524000 1 8246 3 chr2B.!!$F2 8245
2 TraesCS2A01G129900 chr2D 76892480 76900623 8143 False 2231.166667 4017 93.784833 6 8243 6 chr2D.!!$F2 8237
3 TraesCS2A01G129900 chr5B 586786954 586788807 1853 False 730.000000 861 90.193333 4253 6107 3 chr5B.!!$F1 1854
4 TraesCS2A01G129900 chr1D 66752245 66752910 665 True 787.000000 787 88.131000 3972 4637 1 chr1D.!!$R1 665

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
213 215 1.518325 TGTCATACAAGTGGTTGCCG 58.482 50.000 0.00 0.00 37.14 5.69 F
1304 1309 1.517242 GGATCATGAATCTGGTCGCC 58.483 55.000 0.00 0.00 34.56 5.54 F
1722 1727 1.711206 GCACTGACCCGAAAGACTAC 58.289 55.000 0.00 0.00 0.00 2.73 F
3223 3229 5.227908 AGGTGTACTTTGACAACTGTATCG 58.772 41.667 0.00 0.00 45.77 2.92 F
3670 3676 4.015872 TCCGGAGAAAATATGGTATGGC 57.984 45.455 0.00 0.00 0.00 4.40 F
3775 3781 4.569943 TCAGTTCTGTATTCAGTGCCTTC 58.430 43.478 0.00 0.00 41.91 3.46 F
4792 4805 3.703556 TGACATGATGAAGGTCTCTCTCC 59.296 47.826 0.00 0.00 32.84 3.71 F
6282 6394 1.346068 GAAACTCTGCTGAGGGTGAGT 59.654 52.381 22.75 0.64 44.29 3.41 F
6502 6715 1.355381 TCCTTCAGTGGATGGCAATGT 59.645 47.619 0.00 0.00 38.05 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 1727 0.738762 CACCAGCACCATCTCTCACG 60.739 60.000 0.00 0.0 0.00 4.35 R
3223 3229 1.204704 GGCCTAGGAAAACATTGGTGC 59.795 52.381 14.75 0.0 0.00 5.01 R
3670 3676 5.435557 GCACTTATAGCTTTATCTGTTGCG 58.564 41.667 0.00 0.0 0.00 4.85 R
4328 4334 0.036732 ACCGCAGAGAGCAATGGAAA 59.963 50.000 0.00 0.0 46.13 3.13 R
4792 4805 0.627986 AAAGAGAGATTGGCAGGGGG 59.372 55.000 0.00 0.0 0.00 5.40 R
5051 5079 1.064758 ACTGACACAGTTGCCAAAGGA 60.065 47.619 0.00 0.0 42.59 3.36 R
6476 6689 2.300152 GCCATCCACTGAAGGATCGATA 59.700 50.000 0.00 0.0 45.16 2.92 R
7127 7344 0.034380 TAGTGAGCAGGACGGCTAGT 60.034 55.000 0.00 0.0 45.99 2.57 R
7829 8210 0.185901 TCCTCCTGCATTATTGGGGC 59.814 55.000 0.00 0.0 0.00 5.80 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
87 88 3.141398 TGGACTCAATCTTTGCTCACAC 58.859 45.455 0.00 0.00 0.00 3.82
168 170 6.463995 AGTCACTTATCTTTCCAGAGCTAG 57.536 41.667 0.00 0.00 30.36 3.42
213 215 1.518325 TGTCATACAAGTGGTTGCCG 58.482 50.000 0.00 0.00 37.14 5.69
231 233 2.742053 GCCGACTTTCATGTGCTCTAAA 59.258 45.455 0.00 0.00 0.00 1.85
232 234 3.424962 GCCGACTTTCATGTGCTCTAAAC 60.425 47.826 0.00 0.00 0.00 2.01
233 235 3.997021 CCGACTTTCATGTGCTCTAAACT 59.003 43.478 0.00 0.00 0.00 2.66
234 236 4.143030 CCGACTTTCATGTGCTCTAAACTG 60.143 45.833 0.00 0.00 0.00 3.16
236 238 5.050091 CGACTTTCATGTGCTCTAAACTGTT 60.050 40.000 0.00 0.00 0.00 3.16
237 239 6.305693 ACTTTCATGTGCTCTAAACTGTTC 57.694 37.500 0.00 0.00 0.00 3.18
238 240 5.822519 ACTTTCATGTGCTCTAAACTGTTCA 59.177 36.000 0.00 0.00 0.00 3.18
336 339 5.595257 AACTACTCCCTCGGTAAAGAATC 57.405 43.478 0.00 0.00 0.00 2.52
380 383 3.072211 GGTTACCTTGTGTAGTGGAAGC 58.928 50.000 0.00 0.00 0.00 3.86
420 423 7.831691 TGAAGGAAACATAATGGAAAAGACA 57.168 32.000 0.00 0.00 0.00 3.41
432 435 7.654022 AATGGAAAAGACAGTACTGGAAAAA 57.346 32.000 26.12 5.19 34.19 1.94
558 561 8.443937 CCTAATGTTGAACTAAAGTTGCTCTAC 58.556 37.037 0.00 0.00 38.56 2.59
593 596 4.319177 CAGTACAGCCAGTTAGCTTTCTT 58.681 43.478 0.00 0.00 42.61 2.52
603 606 5.073428 CAGTTAGCTTTCTTTTCCTCCCTT 58.927 41.667 0.00 0.00 0.00 3.95
629 632 8.525316 TGATGTTTTCAGATTTGATGCATTACT 58.475 29.630 0.00 0.00 32.27 2.24
630 633 9.362539 GATGTTTTCAGATTTGATGCATTACTT 57.637 29.630 0.00 0.00 32.27 2.24
632 635 9.624697 TGTTTTCAGATTTGATGCATTACTTAC 57.375 29.630 0.00 0.00 32.27 2.34
689 692 7.330262 AGGAAACATTTGCACCAATATTTAGG 58.670 34.615 0.00 0.00 0.00 2.69
697 700 5.858381 TGCACCAATATTTAGGCTCTCTAG 58.142 41.667 0.00 0.00 0.00 2.43
715 718 8.384365 GCTCTCTAGACTATTTTAGTTTGTTGC 58.616 37.037 0.00 0.00 39.59 4.17
852 855 4.070716 CTGACAAGGAACTCTTCTGCATT 58.929 43.478 0.00 0.00 38.49 3.56
1170 1173 5.591472 TGTCCAAAGCATATGATTCTTCAGG 59.409 40.000 6.68 6.66 34.73 3.86
1175 1178 8.469200 CCAAAGCATATGATTCTTCAGGTTTTA 58.531 33.333 6.68 0.00 34.73 1.52
1304 1309 1.517242 GGATCATGAATCTGGTCGCC 58.483 55.000 0.00 0.00 34.56 5.54
1450 1455 8.559536 TGTTCTTATAGTGACTTTGCTTTCTTG 58.440 33.333 0.00 0.00 0.00 3.02
1722 1727 1.711206 GCACTGACCCGAAAGACTAC 58.289 55.000 0.00 0.00 0.00 2.73
2253 2258 8.482852 AGAAATTGGAAGAAAAGGAATCTCAA 57.517 30.769 0.00 0.00 0.00 3.02
2941 2946 7.625817 GCAATGCTATGCACTCTTTCATATAGG 60.626 40.741 0.00 0.00 45.70 2.57
2947 2952 9.716531 CTATGCACTCTTTCATATAGGATTCAA 57.283 33.333 0.00 0.00 0.00 2.69
3052 3057 8.058847 TCCAAGATAGGGTTATTAACTTGCATT 58.941 33.333 6.52 0.00 34.09 3.56
3223 3229 5.227908 AGGTGTACTTTGACAACTGTATCG 58.772 41.667 0.00 0.00 45.77 2.92
3670 3676 4.015872 TCCGGAGAAAATATGGTATGGC 57.984 45.455 0.00 0.00 0.00 4.40
3775 3781 4.569943 TCAGTTCTGTATTCAGTGCCTTC 58.430 43.478 0.00 0.00 41.91 3.46
3788 3794 4.984194 CCTTCGGAATGGATGGCA 57.016 55.556 0.00 0.00 0.00 4.92
4328 4334 6.627395 TCGTACATCTTTGAAATGTTTGGT 57.373 33.333 0.00 0.00 38.31 3.67
4792 4805 3.703556 TGACATGATGAAGGTCTCTCTCC 59.296 47.826 0.00 0.00 32.84 3.71
4839 4866 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4840 4867 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4841 4868 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4842 4869 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5038 5066 9.686683 AATTTAATACTGCAGTTAGACTTCCAT 57.313 29.630 27.06 5.86 0.00 3.41
5043 5071 9.686683 AATACTGCAGTTAGACTTCCATTAATT 57.313 29.630 27.06 10.16 0.00 1.40
5045 5073 8.045176 ACTGCAGTTAGACTTCCATTAATTTC 57.955 34.615 15.25 0.00 0.00 2.17
5046 5074 7.885399 ACTGCAGTTAGACTTCCATTAATTTCT 59.115 33.333 15.25 0.00 0.00 2.52
5047 5075 8.635765 TGCAGTTAGACTTCCATTAATTTCTT 57.364 30.769 0.00 0.00 0.00 2.52
5049 5077 9.914131 GCAGTTAGACTTCCATTAATTTCTTTT 57.086 29.630 0.00 0.00 0.00 2.27
5067 5095 3.971245 TTTTTCCTTTGGCAACTGTGT 57.029 38.095 0.00 0.00 37.61 3.72
5068 5096 3.518634 TTTTCCTTTGGCAACTGTGTC 57.481 42.857 0.00 0.00 37.61 3.67
5069 5097 2.136298 TTCCTTTGGCAACTGTGTCA 57.864 45.000 0.00 0.00 37.67 3.58
5070 5098 1.679139 TCCTTTGGCAACTGTGTCAG 58.321 50.000 0.00 0.00 41.33 3.51
5072 5100 2.171659 TCCTTTGGCAACTGTGTCAGTA 59.828 45.455 0.00 0.00 44.62 2.74
5073 5101 2.290641 CCTTTGGCAACTGTGTCAGTAC 59.709 50.000 0.00 0.00 44.62 2.73
5074 5102 2.700722 TTGGCAACTGTGTCAGTACA 57.299 45.000 0.00 1.34 44.62 2.90
5075 5103 2.928801 TGGCAACTGTGTCAGTACAT 57.071 45.000 2.80 0.00 44.62 2.29
5076 5104 2.493035 TGGCAACTGTGTCAGTACATG 58.507 47.619 2.80 0.00 44.62 3.21
5077 5105 2.158827 TGGCAACTGTGTCAGTACATGT 60.159 45.455 2.69 2.69 44.62 3.21
5078 5106 3.070302 TGGCAACTGTGTCAGTACATGTA 59.930 43.478 0.08 0.08 44.62 2.29
5079 5107 4.253685 GGCAACTGTGTCAGTACATGTAT 58.746 43.478 9.18 0.00 44.62 2.29
5080 5108 5.046950 TGGCAACTGTGTCAGTACATGTATA 60.047 40.000 9.18 0.00 44.62 1.47
5081 5109 5.872617 GGCAACTGTGTCAGTACATGTATAA 59.127 40.000 9.18 0.00 44.62 0.98
5082 5110 6.370442 GGCAACTGTGTCAGTACATGTATAAA 59.630 38.462 9.18 0.00 44.62 1.40
5083 5111 7.094975 GGCAACTGTGTCAGTACATGTATAAAA 60.095 37.037 9.18 0.00 44.62 1.52
5084 5112 8.450964 GCAACTGTGTCAGTACATGTATAAAAT 58.549 33.333 9.18 0.00 44.62 1.82
5085 5113 9.759259 CAACTGTGTCAGTACATGTATAAAATG 57.241 33.333 9.18 0.00 44.62 2.32
5086 5114 9.502091 AACTGTGTCAGTACATGTATAAAATGT 57.498 29.630 9.18 7.31 44.62 2.71
5087 5115 8.935844 ACTGTGTCAGTACATGTATAAAATGTG 58.064 33.333 9.18 0.74 43.46 3.21
5088 5116 8.840833 TGTGTCAGTACATGTATAAAATGTGT 57.159 30.769 9.18 0.00 38.67 3.72
5089 5117 8.931775 TGTGTCAGTACATGTATAAAATGTGTC 58.068 33.333 9.18 0.00 38.67 3.67
5090 5118 8.931775 GTGTCAGTACATGTATAAAATGTGTCA 58.068 33.333 9.18 0.95 38.67 3.58
5091 5119 9.150348 TGTCAGTACATGTATAAAATGTGTCAG 57.850 33.333 9.18 0.00 38.67 3.51
5092 5120 9.151471 GTCAGTACATGTATAAAATGTGTCAGT 57.849 33.333 9.18 0.00 38.67 3.41
5275 5304 2.488153 GGTCTAACATGCCGCTTCTTTT 59.512 45.455 0.00 0.00 0.00 2.27
5284 5313 1.733718 GCCGCTTCTTTTTCTGCCATC 60.734 52.381 0.00 0.00 0.00 3.51
5406 5435 6.152154 AGGTTTGCTGGTGTAAATGGTATTAC 59.848 38.462 0.00 0.00 36.52 1.89
5459 5488 8.089115 TGAATATTTATGTTGTTCGTGTGTGA 57.911 30.769 0.00 0.00 0.00 3.58
5496 5528 1.478916 TCAACTGTTGACCACTCGACA 59.521 47.619 18.69 0.00 38.33 4.35
5513 5545 6.147821 CACTCGACATCTGTTTAAGAAACCAT 59.852 38.462 0.00 0.00 40.67 3.55
5520 5552 9.167311 ACATCTGTTTAAGAAACCATGAGATAC 57.833 33.333 13.81 0.00 40.67 2.24
6282 6394 1.346068 GAAACTCTGCTGAGGGTGAGT 59.654 52.381 22.75 0.64 44.29 3.41
6361 6475 3.185188 CCATGCGAGTACTTCATGTATGC 59.815 47.826 24.83 10.66 36.70 3.14
6382 6593 6.325919 TGCTTACTTCATTACAACCCAAAG 57.674 37.500 0.00 0.00 0.00 2.77
6402 6613 5.484173 AAGTGGTGTTTATGATGTATGCG 57.516 39.130 0.00 0.00 0.00 4.73
6413 6626 7.631717 TTATGATGTATGCGCTAGAGTAGAT 57.368 36.000 9.73 0.00 0.00 1.98
6454 6667 4.092237 TCACTTATTTATGCGTGTTCCGTG 59.908 41.667 0.00 0.00 39.32 4.94
6502 6715 1.355381 TCCTTCAGTGGATGGCAATGT 59.645 47.619 0.00 0.00 38.05 2.71
6562 6775 1.831106 TCCGTCAGTGGATAGCAATGT 59.169 47.619 0.00 0.00 31.53 2.71
6669 6882 5.069781 GCTACTGAGGTTACTGATCCTTCAT 59.930 44.000 0.00 0.00 33.83 2.57
6674 6887 4.111577 AGGTTACTGATCCTTCATTGGGA 58.888 43.478 0.00 0.00 37.26 4.37
6704 6920 3.679389 TGAAAATGAGACAGAGGAAGGC 58.321 45.455 0.00 0.00 0.00 4.35
6707 6923 8.916973 CTGAAAATGAGACAGAGGAAGGCACT 62.917 46.154 0.00 0.00 35.03 4.40
6794 7010 3.692257 ATTGATCCTTCAGCGGATAGG 57.308 47.619 8.17 8.17 43.71 2.57
6869 7085 5.006386 GGAAAAAGTCAGACATCATCCACT 58.994 41.667 2.66 0.00 0.00 4.00
6878 7094 3.131223 AGACATCATCCACTGTTACGGAG 59.869 47.826 0.00 0.00 33.97 4.63
6952 7168 2.851195 AGGTAAGCCATAATTCCAGCG 58.149 47.619 0.00 0.00 37.19 5.18
6958 7174 1.610522 GCCATAATTCCAGCGCAGATT 59.389 47.619 11.47 6.49 0.00 2.40
6969 7185 2.028523 CAGCGCAGATTACTGAAGAACG 59.971 50.000 11.47 0.00 46.03 3.95
7126 7343 1.996191 CTCAAGTAGAAGGTGCGCTTC 59.004 52.381 9.73 4.06 0.00 3.86
7127 7344 1.343142 TCAAGTAGAAGGTGCGCTTCA 59.657 47.619 9.73 0.00 33.57 3.02
7128 7345 1.461127 CAAGTAGAAGGTGCGCTTCAC 59.539 52.381 9.73 0.00 44.90 3.18
7129 7346 0.969894 AGTAGAAGGTGCGCTTCACT 59.030 50.000 9.73 7.86 44.98 3.41
7131 7348 2.164624 AGTAGAAGGTGCGCTTCACTAG 59.835 50.000 9.73 0.00 44.98 2.57
7144 7363 1.153745 CACTAGCCGTCCTGCTCAC 60.154 63.158 0.00 0.00 41.68 3.51
7145 7364 1.304547 ACTAGCCGTCCTGCTCACT 60.305 57.895 0.00 0.00 41.68 3.41
7147 7366 1.103803 CTAGCCGTCCTGCTCACTAA 58.896 55.000 0.00 0.00 41.68 2.24
7183 7402 3.347443 CGTCACACACCGTGTTTAAAAG 58.653 45.455 0.00 0.00 45.08 2.27
7185 7404 3.011119 TCACACACCGTGTTTAAAAGCT 58.989 40.909 0.00 0.00 45.08 3.74
7188 7407 4.271533 CACACACCGTGTTTAAAAGCTCTA 59.728 41.667 0.00 0.00 45.08 2.43
7189 7408 4.877251 ACACACCGTGTTTAAAAGCTCTAA 59.123 37.500 0.00 0.00 45.08 2.10
7216 7435 7.502120 GCTCTTGCTTATCCATGATTTTCTA 57.498 36.000 0.00 0.00 36.03 2.10
7222 7441 9.820725 TTGCTTATCCATGATTTTCTAATTTGG 57.179 29.630 0.00 0.00 32.61 3.28
7262 7537 2.156917 TGGCAGACAATGAAGCTGAAG 58.843 47.619 0.00 0.00 0.00 3.02
7484 7807 8.135382 ACCATTTGTATCTCTGTAGTAACACT 57.865 34.615 0.00 0.00 0.00 3.55
7498 7858 4.884247 AGTAACACTTTGGCTCTAGTCAC 58.116 43.478 0.00 0.00 0.00 3.67
7573 7933 7.861372 ACAATTCTATACTCTACACACGCATAC 59.139 37.037 0.00 0.00 0.00 2.39
7575 7935 5.370679 TCTATACTCTACACACGCATACCA 58.629 41.667 0.00 0.00 0.00 3.25
7589 7949 4.154195 ACGCATACCATTTCTGTGTTTCTC 59.846 41.667 0.00 0.00 29.81 2.87
7609 7969 2.079158 CTATGCACACAGGTTCACCAG 58.921 52.381 0.00 0.00 38.89 4.00
7612 7972 0.463654 GCACACAGGTTCACCAGTCA 60.464 55.000 0.00 0.00 38.89 3.41
7653 8013 0.951558 AGAAAATGACCGCGCAACTT 59.048 45.000 8.75 0.00 0.00 2.66
7729 8093 3.010138 TGGACCAGGAACTATTTTCCCTG 59.990 47.826 0.00 0.00 44.29 4.45
7734 8098 4.263506 CCAGGAACTATTTTCCCTGACAGT 60.264 45.833 8.68 0.00 46.84 3.55
7735 8099 4.938226 CAGGAACTATTTTCCCTGACAGTC 59.062 45.833 0.93 0.00 46.84 3.51
7736 8100 4.597507 AGGAACTATTTTCCCTGACAGTCA 59.402 41.667 2.48 2.48 39.39 3.41
7737 8101 4.695928 GGAACTATTTTCCCTGACAGTCAC 59.304 45.833 0.00 0.00 32.48 3.67
7738 8102 5.513267 GGAACTATTTTCCCTGACAGTCACT 60.513 44.000 0.00 0.00 32.48 3.41
7790 8164 2.521958 TAGAGGGGCGAGCAAGCAAC 62.522 60.000 5.80 0.00 39.27 4.17
7829 8210 1.069823 CAGCCACTGGTGCTAGATAGG 59.930 57.143 0.00 0.00 36.81 2.57
7856 8237 0.251474 AATGCAGGAGGAAAGCAGCA 60.251 50.000 0.00 0.00 42.14 4.41
7857 8238 0.680280 ATGCAGGAGGAAAGCAGCAG 60.680 55.000 0.00 0.00 42.14 4.24
7858 8239 2.698763 GCAGGAGGAAAGCAGCAGC 61.699 63.158 0.00 0.00 42.56 5.25
7889 8293 3.450115 GACCCTCGTCCCCGTGAG 61.450 72.222 0.00 0.00 32.40 3.51
7980 8387 2.755542 ATCTCGCTTATCCGCTGCCG 62.756 60.000 0.00 0.00 0.00 5.69
8027 8434 1.291877 CCAGCCACGTTTTCTCCTCG 61.292 60.000 0.00 0.00 0.00 4.63
8061 8471 3.245518 TCGCGAGATGGAGATGAAAAA 57.754 42.857 3.71 0.00 33.31 1.94
8221 8642 1.446272 GACGGCTCTAGTGGTGTGC 60.446 63.158 0.00 0.00 0.00 4.57
8224 8645 0.391661 CGGCTCTAGTGGTGTGCAAT 60.392 55.000 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.886247 TTAAGGAACACCAGAAACAACG 57.114 40.909 0.00 0.00 0.00 4.10
87 88 1.272490 TGCAGACTAGGTTTCTGTCCG 59.728 52.381 9.78 0.00 42.26 4.79
205 207 0.950836 CACATGAAAGTCGGCAACCA 59.049 50.000 0.00 0.00 0.00 3.67
213 215 5.931441 ACAGTTTAGAGCACATGAAAGTC 57.069 39.130 0.00 0.00 0.00 3.01
311 314 5.813513 TCTTTACCGAGGGAGTAGTTTTT 57.186 39.130 0.00 0.00 0.00 1.94
336 339 8.238481 ACCAATATTTTGCAAAACGTCTTATG 57.762 30.769 26.05 16.42 0.00 1.90
357 360 4.710324 CTTCCACTACACAAGGTAACCAA 58.290 43.478 0.00 0.00 37.17 3.67
593 596 5.060427 TCTGAAAACATCAAGGGAGGAAA 57.940 39.130 0.00 0.00 37.67 3.13
603 606 8.525316 AGTAATGCATCAAATCTGAAAACATCA 58.475 29.630 0.00 0.00 34.49 3.07
629 632 9.571810 GACATGCTCATTTGATTGTTAATGTAA 57.428 29.630 0.00 0.00 34.25 2.41
630 633 8.738106 TGACATGCTCATTTGATTGTTAATGTA 58.262 29.630 0.00 0.00 34.25 2.29
631 634 7.604549 TGACATGCTCATTTGATTGTTAATGT 58.395 30.769 0.00 0.00 34.25 2.71
632 635 8.377681 GTTGACATGCTCATTTGATTGTTAATG 58.622 33.333 0.00 0.00 33.96 1.90
689 692 8.384365 GCAACAAACTAAAATAGTCTAGAGAGC 58.616 37.037 0.00 0.00 38.26 4.09
852 855 5.880332 GCTATTAAACACATCCTGTTCCTCA 59.120 40.000 0.00 0.00 42.70 3.86
877 880 5.048294 TGAAGTCACGCACAAGAGAGTATAA 60.048 40.000 0.00 0.00 0.00 0.98
1203 1208 4.016444 GTCACCTAAATCCAAATGGCAGA 58.984 43.478 0.00 0.00 34.44 4.26
1304 1309 7.227512 AGTGTAAGGTCAACTTCAAGAGAATTG 59.772 37.037 0.00 0.00 40.64 2.32
1450 1455 6.574350 AGAGAACATAAGTACACCTATGCAC 58.426 40.000 0.00 0.00 0.00 4.57
1647 1652 5.451798 GCTTCCATCACCAAACTTTTTCTCA 60.452 40.000 0.00 0.00 0.00 3.27
1722 1727 0.738762 CACCAGCACCATCTCTCACG 60.739 60.000 0.00 0.00 0.00 4.35
2671 2676 7.074653 ACTTGTCCTGAGAAAATACCTACAA 57.925 36.000 0.00 0.00 0.00 2.41
2672 2677 6.269077 TGACTTGTCCTGAGAAAATACCTACA 59.731 38.462 0.00 0.00 0.00 2.74
2941 2946 7.715265 ATCAGTATTCGGTACACATTGAATC 57.285 36.000 0.00 0.00 35.67 2.52
2947 2952 7.867909 CACATCTAATCAGTATTCGGTACACAT 59.132 37.037 0.00 0.00 35.67 3.21
3052 3057 8.812972 TGTTCTAAAATTAGCTCTCTCACCTAA 58.187 33.333 0.00 0.00 0.00 2.69
3188 3193 7.172532 TGTCAAAGTACACCTTAATAGCACAAG 59.827 37.037 0.00 0.00 31.48 3.16
3200 3206 5.227908 CGATACAGTTGTCAAAGTACACCT 58.772 41.667 0.00 0.00 0.00 4.00
3223 3229 1.204704 GGCCTAGGAAAACATTGGTGC 59.795 52.381 14.75 0.00 0.00 5.01
3670 3676 5.435557 GCACTTATAGCTTTATCTGTTGCG 58.564 41.667 0.00 0.00 0.00 4.85
3775 3781 2.549064 TAGACATGCCATCCATTCCG 57.451 50.000 0.00 0.00 29.71 4.30
3788 3794 5.762179 TCAAGTTCCACTCCATTAGACAT 57.238 39.130 0.00 0.00 0.00 3.06
4328 4334 0.036732 ACCGCAGAGAGCAATGGAAA 59.963 50.000 0.00 0.00 46.13 3.13
4522 4535 7.358765 GCATATAATGAGATTCAGTGTCGTCAC 60.359 40.741 4.52 4.52 44.15 3.67
4792 4805 0.627986 AAAGAGAGATTGGCAGGGGG 59.372 55.000 0.00 0.00 0.00 5.40
4839 4866 2.223971 ACGTGTTTCAGTGGTGGTAGAG 60.224 50.000 0.00 0.00 0.00 2.43
4840 4867 1.758280 ACGTGTTTCAGTGGTGGTAGA 59.242 47.619 0.00 0.00 0.00 2.59
4841 4868 2.234300 ACGTGTTTCAGTGGTGGTAG 57.766 50.000 0.00 0.00 0.00 3.18
4842 4869 2.553086 GAACGTGTTTCAGTGGTGGTA 58.447 47.619 0.00 0.00 33.94 3.25
5047 5075 3.259374 TGACACAGTTGCCAAAGGAAAAA 59.741 39.130 0.00 0.00 0.00 1.94
5049 5077 2.426738 CTGACACAGTTGCCAAAGGAAA 59.573 45.455 0.00 0.00 0.00 3.13
5050 5078 2.023673 CTGACACAGTTGCCAAAGGAA 58.976 47.619 0.00 0.00 0.00 3.36
5051 5079 1.064758 ACTGACACAGTTGCCAAAGGA 60.065 47.619 0.00 0.00 42.59 3.36
5052 5080 1.392589 ACTGACACAGTTGCCAAAGG 58.607 50.000 0.00 0.00 42.59 3.11
5053 5081 2.942376 TGTACTGACACAGTTGCCAAAG 59.058 45.455 9.63 0.00 42.59 2.77
5054 5082 2.992593 TGTACTGACACAGTTGCCAAA 58.007 42.857 9.63 0.00 42.59 3.28
5055 5083 2.700722 TGTACTGACACAGTTGCCAA 57.299 45.000 9.63 0.00 42.59 4.52
5056 5084 2.158827 ACATGTACTGACACAGTTGCCA 60.159 45.455 9.63 5.64 42.59 4.92
5057 5085 2.494059 ACATGTACTGACACAGTTGCC 58.506 47.619 9.63 0.60 42.59 4.52
5058 5086 6.961359 TTATACATGTACTGACACAGTTGC 57.039 37.500 7.96 4.87 42.59 4.17
5059 5087 9.759259 CATTTTATACATGTACTGACACAGTTG 57.241 33.333 7.96 5.34 42.59 3.16
5060 5088 9.502091 ACATTTTATACATGTACTGACACAGTT 57.498 29.630 7.96 0.00 42.59 3.16
5062 5090 8.935844 ACACATTTTATACATGTACTGACACAG 58.064 33.333 7.96 0.00 38.76 3.66
5063 5091 8.840833 ACACATTTTATACATGTACTGACACA 57.159 30.769 7.96 0.00 38.76 3.72
5064 5092 8.931775 TGACACATTTTATACATGTACTGACAC 58.068 33.333 7.96 0.00 38.76 3.67
5065 5093 9.150348 CTGACACATTTTATACATGTACTGACA 57.850 33.333 7.96 1.89 40.72 3.58
5066 5094 9.151471 ACTGACACATTTTATACATGTACTGAC 57.849 33.333 7.96 0.00 32.88 3.51
5088 5116 9.826574 GGAGGTAACATTTTATACATGTACTGA 57.173 33.333 7.96 0.00 33.54 3.41
5089 5117 9.832445 AGGAGGTAACATTTTATACATGTACTG 57.168 33.333 7.96 4.02 33.54 2.74
5275 5304 1.610038 CAAAGTGCACTGATGGCAGAA 59.390 47.619 22.49 0.00 45.17 3.02
5284 5313 7.277539 TCAAGAAATAAAAACCAAAGTGCACTG 59.722 33.333 22.49 10.86 0.00 3.66
5332 5361 7.603784 GCTTCCATTTGTTTGTCCTGAAATAAT 59.396 33.333 0.00 0.00 0.00 1.28
5459 5488 9.590451 CAACAGTTGATTAGCAATTAATGGAAT 57.410 29.630 7.61 0.00 39.03 3.01
5496 5528 9.911788 ATGTATCTCATGGTTTCTTAAACAGAT 57.088 29.630 5.03 6.60 43.15 2.90
5513 5545 9.904198 TCCATTCATCAAAGTTTATGTATCTCA 57.096 29.630 0.00 0.00 0.00 3.27
5910 6021 6.270156 TCTTCACATAATGCATGCTCAAAA 57.730 33.333 20.33 0.00 38.29 2.44
6337 6451 3.827008 ACATGAAGTACTCGCATGGAT 57.173 42.857 28.15 14.95 42.70 3.41
6361 6475 6.264518 ACCACTTTGGGTTGTAATGAAGTAAG 59.735 38.462 0.00 0.00 43.37 2.34
6382 6593 3.312421 AGCGCATACATCATAAACACCAC 59.688 43.478 11.47 0.00 0.00 4.16
6454 6667 2.772287 CCTCACTGGTTTCCTCTGTTC 58.228 52.381 0.00 0.00 0.00 3.18
6476 6689 2.300152 GCCATCCACTGAAGGATCGATA 59.700 50.000 0.00 0.00 45.16 2.92
6502 6715 3.576861 TCCTCTGTCTCCTTGTCTTCAA 58.423 45.455 0.00 0.00 0.00 2.69
6562 6775 2.652348 TCCTCTGCCCCCTTATTTTCAA 59.348 45.455 0.00 0.00 0.00 2.69
6669 6882 3.324268 TCATTTTCAGCATTGCTTCCCAA 59.676 39.130 8.83 0.24 36.40 4.12
6674 6887 4.521639 TCTGTCTCATTTTCAGCATTGCTT 59.478 37.500 8.83 0.00 36.40 3.91
6704 6920 2.632996 TGAAGGACCAGTAACCTCAGTG 59.367 50.000 0.00 0.00 35.25 3.66
6707 6923 2.632996 CACTGAAGGACCAGTAACCTCA 59.367 50.000 0.00 0.00 44.87 3.86
6794 7010 3.758554 TGTTCTCCTTATTTTCAGCAGCC 59.241 43.478 0.00 0.00 0.00 4.85
6869 7085 5.221067 GCTATCATCTTCTGACTCCGTAACA 60.221 44.000 0.00 0.00 36.48 2.41
6878 7094 4.099266 ACCTCTGTGCTATCATCTTCTGAC 59.901 45.833 0.00 0.00 36.48 3.51
6952 7168 1.993370 ACGCGTTCTTCAGTAATCTGC 59.007 47.619 5.58 0.00 41.10 4.26
6958 7174 4.261072 GGATCTATGACGCGTTCTTCAGTA 60.261 45.833 15.53 1.02 0.00 2.74
6969 7185 2.131183 GAGCAACTGGATCTATGACGC 58.869 52.381 0.00 0.00 0.00 5.19
7010 7227 0.179171 ATCGCGTCGAACCTGTACAG 60.179 55.000 16.34 16.34 39.99 2.74
7126 7343 1.153745 GTGAGCAGGACGGCTAGTG 60.154 63.158 0.00 0.00 45.99 2.74
7127 7344 0.034380 TAGTGAGCAGGACGGCTAGT 60.034 55.000 0.00 0.00 45.99 2.57
7128 7345 1.103803 TTAGTGAGCAGGACGGCTAG 58.896 55.000 0.00 0.00 45.99 3.42
7129 7346 1.681793 GATTAGTGAGCAGGACGGCTA 59.318 52.381 0.00 0.00 45.99 3.93
7131 7348 0.461961 AGATTAGTGAGCAGGACGGC 59.538 55.000 0.00 0.00 0.00 5.68
7157 7376 3.892122 ACGGTGTGTGACGCAAAA 58.108 50.000 0.00 0.00 0.00 2.44
7202 7421 9.093458 GGTATCCCAAATTAGAAAATCATGGAT 57.907 33.333 0.00 0.00 35.48 3.41
7204 7423 7.670364 GGGTATCCCAAATTAGAAAATCATGG 58.330 38.462 0.00 0.00 44.65 3.66
7222 7441 2.614057 CAATTTGTCAGCGAGGGTATCC 59.386 50.000 0.00 0.00 0.00 2.59
7262 7537 0.947244 CGCCACTTGCTCCATATTCC 59.053 55.000 0.00 0.00 38.05 3.01
7281 7556 1.103803 TCATACAGCGACAGGGAGTC 58.896 55.000 0.00 0.00 44.02 3.36
7297 7572 1.393603 TCTCAAGCCGAGATCGTCAT 58.606 50.000 1.09 0.00 46.18 3.06
7484 7807 3.007614 GGTTACAGGTGACTAGAGCCAAA 59.992 47.826 0.00 0.00 40.21 3.28
7498 7858 9.862149 ATAAATATCAACTTAAGGGGTTACAGG 57.138 33.333 7.53 0.00 0.00 4.00
7567 7927 4.393062 AGAGAAACACAGAAATGGTATGCG 59.607 41.667 0.00 0.00 0.00 4.73
7573 7933 5.181811 TGTGCATAGAGAAACACAGAAATGG 59.818 40.000 0.00 0.00 38.07 3.16
7575 7935 5.764686 TGTGTGCATAGAGAAACACAGAAAT 59.235 36.000 3.50 0.00 45.82 2.17
7589 7949 2.079158 CTGGTGAACCTGTGTGCATAG 58.921 52.381 0.37 0.00 30.96 2.23
7653 8013 1.503818 GCTTGCTCGTCGGTTGGAAA 61.504 55.000 0.00 0.00 0.00 3.13
7704 8064 4.262617 GGAAAATAGTTCCTGGTCCAGAC 58.737 47.826 21.23 11.39 35.73 3.51
7705 8065 3.265995 GGGAAAATAGTTCCTGGTCCAGA 59.734 47.826 21.23 3.69 38.61 3.86
7707 8067 3.010138 CAGGGAAAATAGTTCCTGGTCCA 59.990 47.826 5.17 0.00 42.12 4.02
7720 8080 4.642429 GTGTAGTGACTGTCAGGGAAAAT 58.358 43.478 11.41 0.00 0.00 1.82
7754 8118 4.171234 CCTCTATCCTGTTGGTCCCATAT 58.829 47.826 0.00 0.00 34.23 1.78
7756 8120 2.412591 CCTCTATCCTGTTGGTCCCAT 58.587 52.381 0.00 0.00 34.23 4.00
7757 8121 1.625228 CCCTCTATCCTGTTGGTCCCA 60.625 57.143 0.00 0.00 34.23 4.37
7758 8122 1.132500 CCCTCTATCCTGTTGGTCCC 58.868 60.000 0.00 0.00 34.23 4.46
7761 8125 1.338136 CGCCCCTCTATCCTGTTGGT 61.338 60.000 0.00 0.00 34.23 3.67
7790 8164 6.035758 GTGGCTGTTACTATTAACTTTCTCCG 59.964 42.308 4.80 0.00 38.78 4.63
7829 8210 0.185901 TCCTCCTGCATTATTGGGGC 59.814 55.000 0.00 0.00 0.00 5.80
7889 8293 4.074526 TGCTGCTGCTCGTCCTCC 62.075 66.667 17.00 0.00 40.48 4.30
7890 8294 2.508887 CTGCTGCTGCTCGTCCTC 60.509 66.667 17.00 0.00 40.48 3.71
7891 8295 4.756458 GCTGCTGCTGCTCGTCCT 62.756 66.667 22.10 0.00 40.48 3.85


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

AutoCloner maintained by Alex Coulton.