Multiple sequence alignment - TraesCS5D01G065500

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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 TraesCS5D01G065500 chr5D 100.000 4051 0 0 931 4981 60896685 60900735 0.000000e+00 7481.0
1 TraesCS5D01G065500 chr5D 100.000 603 0 0 1 603 60895755 60896357 0.000000e+00 1114.0
2 TraesCS5D01G065500 chr5A 91.571 2266 112 35 931 3169 50743506 50745719 0.000000e+00 3053.0
3 TraesCS5D01G065500 chr5A 91.382 1288 54 28 3163 4419 50745757 50747018 0.000000e+00 1711.0
4 TraesCS5D01G065500 chr5A 91.190 420 12 11 4447 4849 50747018 50747429 9.430000e-152 547.0
5 TraesCS5D01G065500 chr5A 85.400 500 47 17 52 541 50742733 50743216 3.460000e-136 496.0
6 TraesCS5D01G065500 chr5A 92.188 64 2 2 4851 4913 547220797 547220736 2.470000e-13 87.9
7 TraesCS5D01G065500 chr5B 95.451 1275 25 12 3163 4418 69856987 69855727 0.000000e+00 2002.0
8 TraesCS5D01G065500 chr5B 96.000 1175 27 7 1873 3027 69858467 69857293 0.000000e+00 1892.0
9 TraesCS5D01G065500 chr5B 93.426 867 54 3 957 1823 69859506 69858643 0.000000e+00 1282.0
10 TraesCS5D01G065500 chr5B 86.268 619 50 22 1 603 69860393 69859794 1.510000e-179 640.0
11 TraesCS5D01G065500 chr5B 92.000 400 12 7 4456 4835 69855717 69855318 1.220000e-150 544.0
12 TraesCS5D01G065500 chr5B 96.528 144 2 2 3026 3166 69857169 69857026 8.340000e-58 235.0
13 TraesCS5D01G065500 chr3D 91.716 169 11 1 121 289 526050624 526050789 1.080000e-56 231.0
14 TraesCS5D01G065500 chr3D 91.176 170 12 1 121 290 409892009 409891843 1.390000e-55 228.0
15 TraesCS5D01G065500 chr3D 89.655 58 5 1 4850 4906 608681625 608681568 6.920000e-09 73.1
16 TraesCS5D01G065500 chr7A 90.173 173 14 1 121 293 5678230 5678399 6.490000e-54 222.0
17 TraesCS5D01G065500 chr7A 92.958 71 3 2 4849 4918 156131026 156131095 8.820000e-18 102.0
18 TraesCS5D01G065500 chr6A 90.173 173 14 1 121 293 420829338 420829507 6.490000e-54 222.0
19 TraesCS5D01G065500 chr4A 89.444 180 13 4 118 295 665604119 665604294 6.490000e-54 222.0
20 TraesCS5D01G065500 chr4B 88.950 181 16 2 122 302 9545124 9545300 2.330000e-53 220.0
21 TraesCS5D01G065500 chr1D 88.398 181 18 1 115 295 362598063 362597886 1.090000e-51 215.0
22 TraesCS5D01G065500 chr1D 92.188 64 5 0 4851 4914 323866230 323866293 1.910000e-14 91.6
23 TraesCS5D01G065500 chr1D 88.889 72 5 3 4846 4914 485482394 485482465 8.880000e-13 86.1
24 TraesCS5D01G065500 chr2D 91.603 131 11 0 4850 4980 284804512 284804642 1.100000e-41 182.0
25 TraesCS5D01G065500 chr7D 92.537 67 5 0 4850 4916 227569951 227570017 4.100000e-16 97.1
26 TraesCS5D01G065500 chr1A 91.935 62 5 0 4850 4911 508629049 508628988 2.470000e-13 87.9
27 TraesCS5D01G065500 chr1B 90.000 60 3 3 4849 4906 675770064 675770122 1.920000e-09 75.0


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 TraesCS5D01G065500 chr5D 60895755 60900735 4980 False 4297.500000 7481 100.000000 1 4981 2 chr5D.!!$F1 4980
1 TraesCS5D01G065500 chr5A 50742733 50747429 4696 False 1451.750000 3053 89.885750 52 4849 4 chr5A.!!$F1 4797
2 TraesCS5D01G065500 chr5B 69855318 69860393 5075 True 1099.166667 2002 93.278833 1 4835 6 chr5B.!!$R1 4834

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
457 468 0.249911 CCCGAATCCTAAAGCCCTCG 60.250 60.000 0.0 0.0 0.00 4.63 F
1171 1407 0.248458 CTTTTGGTTCGTTGCGTGCT 60.248 50.000 0.0 0.0 0.00 4.40 F
1340 1576 0.608130 ACTGTCTCGCCAGTAATGCA 59.392 50.000 0.0 0.0 43.71 3.96 F
1388 1624 1.065418 CGCCAGAATTTAGTGAGGGGT 60.065 52.381 0.0 0.0 0.00 4.95 F
1865 2102 1.068943 TTTCAGGCAGGGGGTGGTTA 61.069 55.000 0.0 0.0 0.00 2.85 F
1867 2104 1.304134 CAGGCAGGGGGTGGTTAAC 60.304 63.158 0.0 0.0 0.00 2.01 F
2590 2968 2.755650 CAACTCTTGGAACTAGTGCGT 58.244 47.619 0.0 0.0 0.00 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1518 1755 0.036388 TCTGAAATGCTCGACCACCC 60.036 55.000 0.00 0.00 0.00 4.61 R
2051 2427 0.738389 ACCCAGAAGCAAAACACACG 59.262 50.000 0.00 0.00 0.00 4.49 R
3068 3583 4.650588 ACCGTAACACCATATAGCCAGTTA 59.349 41.667 0.00 0.00 0.00 2.24 R
3179 3742 4.667948 CGCAATAGAATTCATCAAGCGAAC 59.332 41.667 20.17 0.00 44.76 3.95 R
3566 4136 0.999406 CAGTATGGACTTCAACGCCG 59.001 55.000 0.00 0.00 31.73 6.46 R
3578 4148 1.064463 AGGTGCCCATTCACAGTATGG 60.064 52.381 0.00 0.00 43.62 2.74 R
4151 4725 0.107017 CAGGCTGGGTCCCAATACAG 60.107 60.000 12.96 0.31 30.80 2.74 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
42 43 3.243068 GCGGGCTGTTCGATCAAATTTAT 60.243 43.478 0.00 0.00 0.00 1.40
43 44 4.527564 CGGGCTGTTCGATCAAATTTATC 58.472 43.478 0.00 0.00 0.00 1.75
45 46 5.514279 GGGCTGTTCGATCAAATTTATCTG 58.486 41.667 0.00 0.00 0.00 2.90
46 47 5.296780 GGGCTGTTCGATCAAATTTATCTGA 59.703 40.000 0.00 0.00 0.00 3.27
47 48 6.195165 GGCTGTTCGATCAAATTTATCTGAC 58.805 40.000 0.00 0.00 0.00 3.51
48 49 5.898606 GCTGTTCGATCAAATTTATCTGACG 59.101 40.000 0.00 0.00 0.00 4.35
49 50 6.344572 TGTTCGATCAAATTTATCTGACGG 57.655 37.500 0.00 0.00 0.00 4.79
50 51 5.198274 GTTCGATCAAATTTATCTGACGGC 58.802 41.667 0.00 0.00 0.00 5.68
71 72 2.535984 CCAACGCGCTAAGAGTTATCAG 59.464 50.000 5.73 0.00 40.91 2.90
82 83 6.183360 GCTAAGAGTTATCAGCTGACTGTTTG 60.183 42.308 20.97 17.46 44.77 2.93
90 91 2.286294 CAGCTGACTGTTTGTGAGTGTC 59.714 50.000 8.42 0.00 39.22 3.67
98 99 4.636206 ACTGTTTGTGAGTGTCTTCCTTTC 59.364 41.667 0.00 0.00 0.00 2.62
99 100 4.843728 TGTTTGTGAGTGTCTTCCTTTCT 58.156 39.130 0.00 0.00 0.00 2.52
102 103 4.753516 TGTGAGTGTCTTCCTTTCTGAA 57.246 40.909 0.00 0.00 0.00 3.02
138 143 3.675348 TGATACTCCCTCCGTTCCTAA 57.325 47.619 0.00 0.00 0.00 2.69
139 144 3.985127 TGATACTCCCTCCGTTCCTAAA 58.015 45.455 0.00 0.00 0.00 1.85
140 145 4.553678 TGATACTCCCTCCGTTCCTAAAT 58.446 43.478 0.00 0.00 0.00 1.40
147 152 8.731591 ACTCCCTCCGTTCCTAAATAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
150 155 9.162733 TCCCTCCGTTCCTAAATAATATAAGTT 57.837 33.333 0.00 0.00 0.00 2.66
177 182 8.754991 TTTTAGAGGTTTCAAATGGACTACAA 57.245 30.769 0.00 0.00 0.00 2.41
190 197 7.969536 AATGGACTACAATATACAGATGCAC 57.030 36.000 0.00 0.00 0.00 4.57
212 219 9.750125 TGCACATAGACATATTTTAGAGTGTAG 57.250 33.333 0.00 0.00 0.00 2.74
243 250 8.529476 ACTCATTTTACTCCGTATGTAGTCTTT 58.471 33.333 0.00 0.00 0.00 2.52
244 251 9.367444 CTCATTTTACTCCGTATGTAGTCTTTT 57.633 33.333 0.00 0.00 0.00 2.27
245 252 9.146984 TCATTTTACTCCGTATGTAGTCTTTTG 57.853 33.333 0.00 0.00 0.00 2.44
253 260 9.146984 CTCCGTATGTAGTCTTTTGTTGAAATA 57.853 33.333 0.00 0.00 0.00 1.40
255 262 9.916397 CCGTATGTAGTCTTTTGTTGAAATATC 57.084 33.333 0.00 0.00 0.00 1.63
304 312 9.635520 CGGATGGAGTAAATAATTTAGTACGAT 57.364 33.333 0.00 0.00 32.99 3.73
329 337 2.572173 GTGTACTACACTTTGTGCGC 57.428 50.000 11.50 0.00 45.27 6.09
333 341 3.562141 TGTACTACACTTTGTGCGCAATT 59.438 39.130 14.00 0.81 36.98 2.32
334 342 4.750598 TGTACTACACTTTGTGCGCAATTA 59.249 37.500 14.00 0.00 36.98 1.40
335 343 4.822036 ACTACACTTTGTGCGCAATTAA 57.178 36.364 14.00 5.11 36.98 1.40
457 468 0.249911 CCCGAATCCTAAAGCCCTCG 60.250 60.000 0.00 0.00 0.00 4.63
1101 1337 0.673956 GGAAGAAGAAGTCGGTGCCC 60.674 60.000 0.00 0.00 0.00 5.36
1171 1407 0.248458 CTTTTGGTTCGTTGCGTGCT 60.248 50.000 0.00 0.00 0.00 4.40
1244 1480 5.007682 GTGTTTGGTTATAGGAGGAAAGCA 58.992 41.667 0.00 0.00 0.00 3.91
1331 1567 1.128692 CGAATTTTCCACTGTCTCGCC 59.871 52.381 0.00 0.00 0.00 5.54
1340 1576 0.608130 ACTGTCTCGCCAGTAATGCA 59.392 50.000 0.00 0.00 43.71 3.96
1362 1598 4.794278 AAATGCTGCAAATGTCTCATCA 57.206 36.364 6.36 0.00 0.00 3.07
1388 1624 1.065418 CGCCAGAATTTAGTGAGGGGT 60.065 52.381 0.00 0.00 0.00 4.95
1389 1625 2.618045 CGCCAGAATTTAGTGAGGGGTT 60.618 50.000 0.00 0.00 0.00 4.11
1398 1634 9.398921 AGAATTTAGTGAGGGGTTGAGATATAT 57.601 33.333 0.00 0.00 0.00 0.86
1399 1635 9.442047 GAATTTAGTGAGGGGTTGAGATATATG 57.558 37.037 0.00 0.00 0.00 1.78
1406 1642 4.042187 AGGGGTTGAGATATATGGTGCTTC 59.958 45.833 0.00 0.00 0.00 3.86
1474 1710 2.169832 TCCAGCACTAGTTCAGTTGC 57.830 50.000 0.00 0.00 34.26 4.17
1539 1776 2.158957 GGGTGGTCGAGCATTTCAGATA 60.159 50.000 21.66 0.00 0.00 1.98
1552 1789 9.837525 GAGCATTTCAGATATTTGATGGATAAC 57.162 33.333 0.00 0.00 0.00 1.89
1587 1824 5.087323 AGCCAATCGAGATCCCTAAAGATA 58.913 41.667 0.00 0.00 0.00 1.98
1676 1913 8.891720 ACAACTTTATGCAAACATGTTGATTTT 58.108 25.926 12.82 0.00 38.80 1.82
1717 1954 7.311408 GTTCACCTGTACTTACTAGTTACTGG 58.689 42.308 19.74 19.74 35.78 4.00
1756 1993 7.063544 CACTTGAAGCACACCTAAGATTAGTAC 59.936 40.741 0.00 0.00 0.00 2.73
1762 1999 6.070194 AGCACACCTAAGATTAGTACATTGGT 60.070 38.462 0.00 0.00 0.00 3.67
1785 2022 3.301274 GGGATTCTGGTCTAGCTGTACT 58.699 50.000 0.00 0.00 0.00 2.73
1816 2053 4.662145 GTGTTAGTGCCATGTATTGCTTC 58.338 43.478 0.00 0.00 0.00 3.86
1850 2087 3.754965 CAATGGAGGGAACTGAGTTTCA 58.245 45.455 5.89 0.00 44.43 2.69
1860 2097 1.774217 TGAGTTTCAGGCAGGGGGT 60.774 57.895 0.00 0.00 0.00 4.95
1861 2098 1.303643 GAGTTTCAGGCAGGGGGTG 60.304 63.158 0.00 0.00 0.00 4.61
1862 2099 2.283173 GTTTCAGGCAGGGGGTGG 60.283 66.667 0.00 0.00 0.00 4.61
1863 2100 2.780924 TTTCAGGCAGGGGGTGGT 60.781 61.111 0.00 0.00 0.00 4.16
1864 2101 2.399607 TTTCAGGCAGGGGGTGGTT 61.400 57.895 0.00 0.00 0.00 3.67
1865 2102 1.068943 TTTCAGGCAGGGGGTGGTTA 61.069 55.000 0.00 0.00 0.00 2.85
1866 2103 1.068943 TTCAGGCAGGGGGTGGTTAA 61.069 55.000 0.00 0.00 0.00 2.01
1867 2104 1.304134 CAGGCAGGGGGTGGTTAAC 60.304 63.158 0.00 0.00 0.00 2.01
1887 2250 2.821969 ACTGGTGATGCATGGAAAAGAC 59.178 45.455 2.46 0.00 0.00 3.01
1950 2326 8.506196 AACATACACCATACCTATCTAACCAT 57.494 34.615 0.00 0.00 0.00 3.55
2210 2586 7.644157 GGTCAAAATTCAGCGGTATAAATCTTC 59.356 37.037 0.00 0.00 0.00 2.87
2590 2968 2.755650 CAACTCTTGGAACTAGTGCGT 58.244 47.619 0.00 0.00 0.00 5.24
2591 2969 3.909430 CAACTCTTGGAACTAGTGCGTA 58.091 45.455 0.00 0.00 0.00 4.42
2592 2970 3.572604 ACTCTTGGAACTAGTGCGTAC 57.427 47.619 0.00 0.00 0.00 3.67
2719 3102 8.219868 TCATGAATGGGTAGTCACAATATGAAT 58.780 33.333 0.00 0.00 39.72 2.57
2986 3374 9.747293 AAGATAAGCTAACTCGGTACTTAAATC 57.253 33.333 0.00 0.00 0.00 2.17
3022 3411 8.910351 AGATGGTTTAGTTTATAGGAGAATGC 57.090 34.615 0.00 0.00 0.00 3.56
3068 3583 6.528537 TGCTTAATCATTGGCAGTGTTTAT 57.471 33.333 9.95 0.00 0.00 1.40
3159 3677 6.099701 ACCACATACTAACTCTGGAATGCATA 59.900 38.462 0.00 0.00 0.00 3.14
3179 3742 5.934625 GCATACTGGTTAGGATATGTTGGAG 59.065 44.000 0.00 0.00 0.00 3.86
3566 4136 4.707448 TCATTCCAACAGGAGACTCTAGTC 59.293 45.833 1.74 1.72 45.08 2.59
3578 4148 1.199558 ACTCTAGTCGGCGTTGAAGTC 59.800 52.381 6.85 0.00 0.00 3.01
3740 4310 0.530650 ATGCTATGGAAGGACACGCG 60.531 55.000 3.53 3.53 0.00 6.01
3848 4421 2.045708 GGTGATGAACGGCATGGCA 61.046 57.895 20.37 0.00 37.34 4.92
3984 4557 2.451490 TGAGGAGCCTTGTGTAGAGAG 58.549 52.381 0.00 0.00 0.00 3.20
3985 4558 2.041755 TGAGGAGCCTTGTGTAGAGAGA 59.958 50.000 0.00 0.00 0.00 3.10
3986 4559 2.687935 GAGGAGCCTTGTGTAGAGAGAG 59.312 54.545 0.00 0.00 0.00 3.20
4262 4855 5.880332 GGTCTGCTTTCAAGGTTCATGTATA 59.120 40.000 0.00 0.00 0.00 1.47
4306 4903 0.252881 AAGGGGCATCTGTCTCTGGA 60.253 55.000 0.00 0.00 26.17 3.86
4337 4934 6.154534 AGAGCCACTGATTGTACATACAGTTA 59.845 38.462 23.54 0.00 40.84 2.24
4338 4935 6.341316 AGCCACTGATTGTACATACAGTTAG 58.659 40.000 23.54 19.76 40.84 2.34
4340 4937 6.594159 GCCACTGATTGTACATACAGTTAGTT 59.406 38.462 23.54 7.83 39.52 2.24
4341 4938 7.413000 GCCACTGATTGTACATACAGTTAGTTG 60.413 40.741 23.54 15.72 39.52 3.16
4342 4939 7.064609 CCACTGATTGTACATACAGTTAGTTGG 59.935 40.741 23.54 19.01 39.52 3.77
4419 5021 4.352298 AGGTTGACAGGAAGGAAAAGAGAT 59.648 41.667 0.00 0.00 0.00 2.75
4420 5022 4.457257 GGTTGACAGGAAGGAAAAGAGATG 59.543 45.833 0.00 0.00 0.00 2.90
4421 5023 4.292186 TGACAGGAAGGAAAAGAGATGG 57.708 45.455 0.00 0.00 0.00 3.51
4422 5024 3.652869 TGACAGGAAGGAAAAGAGATGGT 59.347 43.478 0.00 0.00 0.00 3.55
4423 5025 4.006319 GACAGGAAGGAAAAGAGATGGTG 58.994 47.826 0.00 0.00 0.00 4.17
4424 5026 3.395941 ACAGGAAGGAAAAGAGATGGTGT 59.604 43.478 0.00 0.00 0.00 4.16
4425 5027 3.755378 CAGGAAGGAAAAGAGATGGTGTG 59.245 47.826 0.00 0.00 0.00 3.82
4426 5028 3.395941 AGGAAGGAAAAGAGATGGTGTGT 59.604 43.478 0.00 0.00 0.00 3.72
4427 5029 3.503748 GGAAGGAAAAGAGATGGTGTGTG 59.496 47.826 0.00 0.00 0.00 3.82
4428 5030 2.508526 AGGAAAAGAGATGGTGTGTGC 58.491 47.619 0.00 0.00 0.00 4.57
4429 5031 1.541588 GGAAAAGAGATGGTGTGTGCC 59.458 52.381 0.00 0.00 0.00 5.01
4430 5032 1.541588 GAAAAGAGATGGTGTGTGCCC 59.458 52.381 0.00 0.00 0.00 5.36
4431 5033 0.773644 AAAGAGATGGTGTGTGCCCT 59.226 50.000 0.00 0.00 0.00 5.19
4432 5034 0.037303 AAGAGATGGTGTGTGCCCTG 59.963 55.000 0.00 0.00 0.00 4.45
4433 5035 1.377725 GAGATGGTGTGTGCCCTGG 60.378 63.158 0.00 0.00 0.00 4.45
4434 5036 1.841302 GAGATGGTGTGTGCCCTGGA 61.841 60.000 0.00 0.00 0.00 3.86
4435 5037 1.074775 GATGGTGTGTGCCCTGGAA 59.925 57.895 0.00 0.00 0.00 3.53
4436 5038 0.539438 GATGGTGTGTGCCCTGGAAA 60.539 55.000 0.00 0.00 0.00 3.13
4437 5039 0.114954 ATGGTGTGTGCCCTGGAAAT 59.885 50.000 0.00 0.00 0.00 2.17
4438 5040 0.827089 TGGTGTGTGCCCTGGAAATG 60.827 55.000 0.00 0.00 0.00 2.32
4439 5041 1.290009 GTGTGTGCCCTGGAAATGC 59.710 57.895 0.00 0.00 0.00 3.56
4440 5042 1.152589 TGTGTGCCCTGGAAATGCA 60.153 52.632 0.00 0.00 0.00 3.96
4443 5045 2.853316 TGCCCTGGAAATGCACCT 59.147 55.556 0.00 0.00 0.00 4.00
4444 5046 2.082834 TGCCCTGGAAATGCACCTA 58.917 52.632 0.00 0.00 0.00 3.08
4445 5047 0.323360 TGCCCTGGAAATGCACCTAC 60.323 55.000 0.00 0.00 0.00 3.18
4446 5048 0.323360 GCCCTGGAAATGCACCTACA 60.323 55.000 0.00 0.00 0.00 2.74
4568 5180 0.835276 CATGTGAGCCATGGAGGAGA 59.165 55.000 18.40 0.00 46.03 3.71
4669 5281 6.682861 GCTCTTTTTCTTCCTTGGCTTAACAA 60.683 38.462 0.00 0.00 0.00 2.83
4681 5300 1.060698 GCTTAACAAGGATGTCGACGC 59.939 52.381 11.62 5.34 39.40 5.19
4760 5383 2.670414 CTGTCCGTGCTCATCTTTTCTC 59.330 50.000 0.00 0.00 0.00 2.87
4870 5493 2.969821 TTTTTAGGGAAGCAGCAGGA 57.030 45.000 0.00 0.00 0.00 3.86
4871 5494 2.200373 TTTTAGGGAAGCAGCAGGAC 57.800 50.000 0.00 0.00 0.00 3.85
4872 5495 1.362224 TTTAGGGAAGCAGCAGGACT 58.638 50.000 0.00 0.00 0.00 3.85
4873 5496 0.905357 TTAGGGAAGCAGCAGGACTC 59.095 55.000 0.00 0.00 0.00 3.36
4874 5497 0.041833 TAGGGAAGCAGCAGGACTCT 59.958 55.000 0.00 0.00 0.00 3.24
4875 5498 1.078567 GGGAAGCAGCAGGACTCTG 60.079 63.158 0.00 0.00 43.64 3.35
4889 5512 6.992063 CAGGACTCTGCTGTGTATTTTTAT 57.008 37.500 0.00 0.00 33.86 1.40
4890 5513 7.383102 CAGGACTCTGCTGTGTATTTTTATT 57.617 36.000 0.00 0.00 33.86 1.40
4891 5514 7.246311 CAGGACTCTGCTGTGTATTTTTATTG 58.754 38.462 0.00 0.00 33.86 1.90
4892 5515 7.119699 CAGGACTCTGCTGTGTATTTTTATTGA 59.880 37.037 0.00 0.00 33.86 2.57
4893 5516 7.831193 AGGACTCTGCTGTGTATTTTTATTGAT 59.169 33.333 0.00 0.00 0.00 2.57
4894 5517 8.462016 GGACTCTGCTGTGTATTTTTATTGATT 58.538 33.333 0.00 0.00 0.00 2.57
4895 5518 9.846248 GACTCTGCTGTGTATTTTTATTGATTT 57.154 29.630 0.00 0.00 0.00 2.17
4924 5547 2.738587 TGGTACAAAAGGTCCTTGCA 57.261 45.000 4.45 0.00 31.92 4.08
4925 5548 3.019799 TGGTACAAAAGGTCCTTGCAA 57.980 42.857 4.45 0.00 31.92 4.08
4926 5549 3.366396 TGGTACAAAAGGTCCTTGCAAA 58.634 40.909 4.45 0.00 31.92 3.68
4927 5550 3.769844 TGGTACAAAAGGTCCTTGCAAAA 59.230 39.130 4.45 0.00 31.92 2.44
4928 5551 4.142049 TGGTACAAAAGGTCCTTGCAAAAG 60.142 41.667 4.45 0.00 31.92 2.27
4929 5552 4.098807 GGTACAAAAGGTCCTTGCAAAAGA 59.901 41.667 4.45 0.00 0.00 2.52
4930 5553 4.817318 ACAAAAGGTCCTTGCAAAAGAA 57.183 36.364 4.45 0.00 0.00 2.52
4931 5554 5.159273 ACAAAAGGTCCTTGCAAAAGAAA 57.841 34.783 4.45 0.00 0.00 2.52
4932 5555 5.555966 ACAAAAGGTCCTTGCAAAAGAAAA 58.444 33.333 4.45 0.00 0.00 2.29
4933 5556 5.643348 ACAAAAGGTCCTTGCAAAAGAAAAG 59.357 36.000 4.45 0.00 0.00 2.27
4934 5557 5.675684 AAAGGTCCTTGCAAAAGAAAAGA 57.324 34.783 4.45 0.00 0.00 2.52
4935 5558 5.675684 AAGGTCCTTGCAAAAGAAAAGAA 57.324 34.783 2.38 0.00 0.00 2.52
4936 5559 5.268118 AGGTCCTTGCAAAAGAAAAGAAG 57.732 39.130 0.00 0.00 0.00 2.85
4937 5560 3.804325 GGTCCTTGCAAAAGAAAAGAAGC 59.196 43.478 0.00 0.00 0.00 3.86
4938 5561 4.442052 GGTCCTTGCAAAAGAAAAGAAGCT 60.442 41.667 0.00 0.00 0.00 3.74
4939 5562 5.221244 GGTCCTTGCAAAAGAAAAGAAGCTA 60.221 40.000 0.00 0.00 0.00 3.32
4940 5563 6.450545 GTCCTTGCAAAAGAAAAGAAGCTAT 58.549 36.000 0.00 0.00 0.00 2.97
4941 5564 7.309194 GGTCCTTGCAAAAGAAAAGAAGCTATA 60.309 37.037 0.00 0.00 0.00 1.31
4942 5565 7.539022 GTCCTTGCAAAAGAAAAGAAGCTATAC 59.461 37.037 0.00 0.00 0.00 1.47
4943 5566 7.230510 TCCTTGCAAAAGAAAAGAAGCTATACA 59.769 33.333 0.00 0.00 0.00 2.29
4944 5567 7.540055 CCTTGCAAAAGAAAAGAAGCTATACAG 59.460 37.037 0.00 0.00 0.00 2.74
4945 5568 7.744087 TGCAAAAGAAAAGAAGCTATACAGA 57.256 32.000 0.00 0.00 0.00 3.41
4946 5569 8.165239 TGCAAAAGAAAAGAAGCTATACAGAA 57.835 30.769 0.00 0.00 0.00 3.02
4947 5570 8.629158 TGCAAAAGAAAAGAAGCTATACAGAAA 58.371 29.630 0.00 0.00 0.00 2.52
4948 5571 9.463443 GCAAAAGAAAAGAAGCTATACAGAAAA 57.537 29.630 0.00 0.00 0.00 2.29
4980 5603 6.502136 CTAGGAAAACTAGGAAAGCAAAGG 57.498 41.667 0.00 0.00 44.50 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.298157 TTTGATCGAACAGCCCGCAG 61.298 55.000 0.00 0.00 0.00 5.18
26 27 5.220586 GCCGTCAGATAAATTTGATCGAACA 60.221 40.000 0.00 0.00 0.00 3.18
45 46 3.849953 CTTAGCGCGTTGGCCGTC 61.850 66.667 8.43 0.00 39.32 4.79
46 47 4.367023 TCTTAGCGCGTTGGCCGT 62.367 61.111 8.43 0.00 39.32 5.68
47 48 3.554692 CTCTTAGCGCGTTGGCCG 61.555 66.667 8.43 0.00 40.40 6.13
48 49 0.738412 TAACTCTTAGCGCGTTGGCC 60.738 55.000 8.43 0.00 35.02 5.36
49 50 1.258197 GATAACTCTTAGCGCGTTGGC 59.742 52.381 8.43 0.00 0.00 4.52
50 51 2.535984 CTGATAACTCTTAGCGCGTTGG 59.464 50.000 8.43 0.00 0.00 3.77
59 60 6.646653 CACAAACAGTCAGCTGATAACTCTTA 59.353 38.462 21.47 0.00 45.28 2.10
71 72 2.555199 AGACACTCACAAACAGTCAGC 58.445 47.619 0.00 0.00 0.00 4.26
82 83 6.625873 AATTTCAGAAAGGAAGACACTCAC 57.374 37.500 1.28 0.00 0.00 3.51
125 130 9.788889 AAACTTATATTATTTAGGAACGGAGGG 57.211 33.333 0.00 0.00 0.00 4.30
164 169 8.285394 GTGCATCTGTATATTGTAGTCCATTTG 58.715 37.037 0.00 0.00 0.00 2.32
166 171 7.508687 TGTGCATCTGTATATTGTAGTCCATT 58.491 34.615 0.00 0.00 0.00 3.16
169 174 8.523658 TCTATGTGCATCTGTATATTGTAGTCC 58.476 37.037 0.00 0.00 0.00 3.85
170 175 9.347934 GTCTATGTGCATCTGTATATTGTAGTC 57.652 37.037 0.00 0.00 0.00 2.59
171 176 8.860088 TGTCTATGTGCATCTGTATATTGTAGT 58.140 33.333 0.00 0.00 0.00 2.73
172 177 9.866798 ATGTCTATGTGCATCTGTATATTGTAG 57.133 33.333 0.00 0.00 0.00 2.74
317 325 6.007936 TCTTATTAATTGCGCACAAAGTGT 57.992 33.333 11.12 0.00 39.77 3.55
333 341 9.998106 GTAAGAAGGCCATTAGTGATCTTATTA 57.002 33.333 5.01 0.00 0.00 0.98
334 342 8.494433 TGTAAGAAGGCCATTAGTGATCTTATT 58.506 33.333 5.01 0.00 0.00 1.40
335 343 8.034313 TGTAAGAAGGCCATTAGTGATCTTAT 57.966 34.615 5.01 0.00 0.00 1.73
1101 1337 2.297880 CCGAAAAGGGTAAAAAGTGGGG 59.702 50.000 0.00 0.00 35.97 4.96
1171 1407 5.373812 GGGAATCCCAGAGAAAATACTCA 57.626 43.478 14.67 0.00 44.65 3.41
1244 1480 3.382832 CACCCTTCGCCGTCCTCT 61.383 66.667 0.00 0.00 0.00 3.69
1340 1576 5.142061 TGATGAGACATTTGCAGCATTTT 57.858 34.783 0.00 0.00 0.00 1.82
1362 1598 5.360591 CCTCACTAAATTCTGGCGTTCTAT 58.639 41.667 0.00 0.00 0.00 1.98
1388 1624 6.997655 AGAATCGAAGCACCATATATCTCAA 58.002 36.000 0.00 0.00 0.00 3.02
1389 1625 6.209391 TGAGAATCGAAGCACCATATATCTCA 59.791 38.462 0.00 0.00 38.61 3.27
1398 1634 2.560981 TGTACTGAGAATCGAAGCACCA 59.439 45.455 0.00 0.00 38.61 4.17
1399 1635 3.232213 TGTACTGAGAATCGAAGCACC 57.768 47.619 0.00 0.00 38.61 5.01
1406 1642 8.864069 ACAATTAGAAGATGTACTGAGAATCG 57.136 34.615 0.00 0.00 38.61 3.34
1458 1694 2.620251 TGTGCAACTGAACTAGTGCT 57.380 45.000 1.64 0.00 40.26 4.40
1474 1710 2.418976 CACCAGACTCATTGCAGATGTG 59.581 50.000 8.19 8.32 0.00 3.21
1511 1748 1.496060 TGCTCGACCACCCAATCTAT 58.504 50.000 0.00 0.00 0.00 1.98
1518 1755 0.036388 TCTGAAATGCTCGACCACCC 60.036 55.000 0.00 0.00 0.00 4.61
1539 1776 3.011566 TGGGTGCGTTATCCATCAAAT 57.988 42.857 0.00 0.00 33.53 2.32
1552 1789 0.381801 GATTGGCTACATTGGGTGCG 59.618 55.000 0.00 0.00 0.00 5.34
1587 1824 7.458409 AAACATGCTCAAATAGAGTCACAAT 57.542 32.000 0.00 0.00 46.47 2.71
1676 1913 7.091443 ACAGGTGAACGTAAAATTGAAACAAA 58.909 30.769 0.00 0.00 0.00 2.83
1717 1954 3.365832 CTTCAAGTGTGTGACATTGCAC 58.634 45.455 0.00 0.00 39.22 4.57
1756 1993 3.091633 AGACCAGAATCCCAACCAATG 57.908 47.619 0.00 0.00 0.00 2.82
1762 1999 2.551270 ACAGCTAGACCAGAATCCCAA 58.449 47.619 0.00 0.00 0.00 4.12
1785 2022 1.667830 GCACTAACACGCAGGCTGA 60.668 57.895 20.86 0.00 0.00 4.26
1850 2087 1.465387 AGTTAACCACCCCCTGCCT 60.465 57.895 0.88 0.00 0.00 4.75
1860 2097 2.040947 TCCATGCATCACCAGTTAACCA 59.959 45.455 0.00 0.00 0.00 3.67
1861 2098 2.722094 TCCATGCATCACCAGTTAACC 58.278 47.619 0.00 0.00 0.00 2.85
1862 2099 4.782019 TTTCCATGCATCACCAGTTAAC 57.218 40.909 0.00 0.00 0.00 2.01
1863 2100 5.048083 GTCTTTTCCATGCATCACCAGTTAA 60.048 40.000 0.00 0.00 0.00 2.01
1864 2101 4.458989 GTCTTTTCCATGCATCACCAGTTA 59.541 41.667 0.00 0.00 0.00 2.24
1865 2102 3.256631 GTCTTTTCCATGCATCACCAGTT 59.743 43.478 0.00 0.00 0.00 3.16
1866 2103 2.821969 GTCTTTTCCATGCATCACCAGT 59.178 45.455 0.00 0.00 0.00 4.00
1867 2104 2.159476 CGTCTTTTCCATGCATCACCAG 60.159 50.000 0.00 0.00 0.00 4.00
1887 2250 1.403679 TGCGAAAATTAGCATTCCCCG 59.596 47.619 0.00 0.00 38.59 5.73
2051 2427 0.738389 ACCCAGAAGCAAAACACACG 59.262 50.000 0.00 0.00 0.00 4.49
2210 2586 7.801547 GACATTTACCATGTCATGTTTGAAG 57.198 36.000 11.84 0.00 45.61 3.02
2588 2966 8.851960 TTAACATCTTGCAATCTAGTAGTACG 57.148 34.615 0.00 0.00 0.00 3.67
2591 2969 9.372369 GACTTTAACATCTTGCAATCTAGTAGT 57.628 33.333 0.00 0.00 0.00 2.73
2592 2970 9.371136 TGACTTTAACATCTTGCAATCTAGTAG 57.629 33.333 0.00 0.00 0.00 2.57
2996 3385 8.994170 GCATTCTCCTATAAACTAAACCATCTC 58.006 37.037 0.00 0.00 0.00 2.75
3068 3583 4.650588 ACCGTAACACCATATAGCCAGTTA 59.349 41.667 0.00 0.00 0.00 2.24
3159 3677 5.395324 CGAACTCCAACATATCCTAACCAGT 60.395 44.000 0.00 0.00 0.00 4.00
3179 3742 4.667948 CGCAATAGAATTCATCAAGCGAAC 59.332 41.667 20.17 0.00 44.76 3.95
3566 4136 0.999406 CAGTATGGACTTCAACGCCG 59.001 55.000 0.00 0.00 31.73 6.46
3578 4148 1.064463 AGGTGCCCATTCACAGTATGG 60.064 52.381 0.00 0.00 43.62 2.74
3740 4310 3.019564 CTGATGATGAAACTTGGGGTCC 58.980 50.000 0.00 0.00 0.00 4.46
3848 4421 4.361971 TCCACCGGCGAGAGGTCT 62.362 66.667 9.30 0.00 40.59 3.85
3984 4557 1.371881 GCGGCGGTGCTACTATCTC 60.372 63.158 9.78 0.00 0.00 2.75
3985 4558 2.728817 GCGGCGGTGCTACTATCT 59.271 61.111 9.78 0.00 0.00 1.98
3986 4559 2.729862 CGCGGCGGTGCTACTATC 60.730 66.667 15.84 0.00 0.00 2.08
4146 4720 3.117663 GGCTGGGTCCCAATACAGATTTA 60.118 47.826 12.96 0.00 30.80 1.40
4147 4721 2.358195 GGCTGGGTCCCAATACAGATTT 60.358 50.000 12.96 0.00 30.80 2.17
4148 4722 1.215423 GGCTGGGTCCCAATACAGATT 59.785 52.381 12.96 0.00 30.80 2.40
4149 4723 0.846693 GGCTGGGTCCCAATACAGAT 59.153 55.000 12.96 0.00 30.80 2.90
4150 4724 0.253160 AGGCTGGGTCCCAATACAGA 60.253 55.000 12.96 0.00 30.80 3.41
4151 4725 0.107017 CAGGCTGGGTCCCAATACAG 60.107 60.000 12.96 0.31 30.80 2.74
4152 4726 0.844661 ACAGGCTGGGTCCCAATACA 60.845 55.000 20.34 0.00 30.80 2.29
4153 4727 0.331616 AACAGGCTGGGTCCCAATAC 59.668 55.000 20.34 5.05 30.80 1.89
4262 4855 3.582208 AGAAGAAGGCAGACAGACAGATT 59.418 43.478 0.00 0.00 0.00 2.40
4306 4903 2.522185 ACAATCAGTGGCTCTTGCATT 58.478 42.857 0.00 0.00 41.91 3.56
4419 5021 0.827089 CATTTCCAGGGCACACACCA 60.827 55.000 0.00 0.00 0.00 4.17
4420 5022 1.966762 CATTTCCAGGGCACACACC 59.033 57.895 0.00 0.00 0.00 4.16
4421 5023 1.290009 GCATTTCCAGGGCACACAC 59.710 57.895 0.00 0.00 0.00 3.82
4422 5024 1.152589 TGCATTTCCAGGGCACACA 60.153 52.632 0.00 0.00 31.58 3.72
4423 5025 3.776158 TGCATTTCCAGGGCACAC 58.224 55.556 0.00 0.00 31.58 3.82
4426 5028 0.323360 GTAGGTGCATTTCCAGGGCA 60.323 55.000 0.00 0.00 34.70 5.36
4427 5029 0.323360 TGTAGGTGCATTTCCAGGGC 60.323 55.000 0.00 0.00 0.00 5.19
4428 5030 1.755179 CTGTAGGTGCATTTCCAGGG 58.245 55.000 0.00 0.00 0.00 4.45
4429 5031 1.098050 GCTGTAGGTGCATTTCCAGG 58.902 55.000 0.00 0.00 0.00 4.45
4430 5032 0.729116 CGCTGTAGGTGCATTTCCAG 59.271 55.000 0.00 0.00 0.00 3.86
4431 5033 2.853159 CGCTGTAGGTGCATTTCCA 58.147 52.632 0.00 0.00 0.00 3.53
4439 5041 2.014857 TCACTAGTAGCGCTGTAGGTG 58.985 52.381 22.90 21.66 0.00 4.00
4440 5042 2.290464 CTCACTAGTAGCGCTGTAGGT 58.710 52.381 22.90 11.04 0.00 3.08
4441 5043 1.604755 CCTCACTAGTAGCGCTGTAGG 59.395 57.143 22.90 13.77 0.00 3.18
4442 5044 1.604755 CCCTCACTAGTAGCGCTGTAG 59.395 57.143 22.90 21.76 0.00 2.74
4443 5045 1.064906 ACCCTCACTAGTAGCGCTGTA 60.065 52.381 22.90 10.72 0.00 2.74
4444 5046 0.323542 ACCCTCACTAGTAGCGCTGT 60.324 55.000 22.90 10.02 0.00 4.40
4445 5047 0.818296 AACCCTCACTAGTAGCGCTG 59.182 55.000 22.90 5.37 0.00 5.18
4446 5048 0.818296 CAACCCTCACTAGTAGCGCT 59.182 55.000 17.26 17.26 0.00 5.92
4521 5124 2.488153 GGTTTGTCTCATTGGGCTACAC 59.512 50.000 0.00 0.00 0.00 2.90
4669 5281 1.132643 GTTACTGAGCGTCGACATCCT 59.867 52.381 17.16 8.22 0.00 3.24
4681 5300 4.728882 GCTCATGCCGAAAATGTTACTGAG 60.729 45.833 0.00 0.00 0.00 3.35
4760 5383 5.221303 TGCACAAATCTCAGAAGGAAAAAGG 60.221 40.000 0.00 0.00 0.00 3.11
4851 5474 2.108250 AGTCCTGCTGCTTCCCTAAAAA 59.892 45.455 0.00 0.00 0.00 1.94
4852 5475 1.705186 AGTCCTGCTGCTTCCCTAAAA 59.295 47.619 0.00 0.00 0.00 1.52
4853 5476 1.279271 GAGTCCTGCTGCTTCCCTAAA 59.721 52.381 0.00 0.00 0.00 1.85
4854 5477 0.905357 GAGTCCTGCTGCTTCCCTAA 59.095 55.000 0.00 0.00 0.00 2.69
4855 5478 0.041833 AGAGTCCTGCTGCTTCCCTA 59.958 55.000 0.00 0.00 0.00 3.53
4856 5479 1.229464 AGAGTCCTGCTGCTTCCCT 60.229 57.895 0.00 0.00 0.00 4.20
4857 5480 1.078567 CAGAGTCCTGCTGCTTCCC 60.079 63.158 0.00 0.00 33.07 3.97
4858 5481 4.613929 CAGAGTCCTGCTGCTTCC 57.386 61.111 0.00 0.00 33.07 3.46
4866 5489 6.992063 ATAAAAATACACAGCAGAGTCCTG 57.008 37.500 0.00 0.00 43.22 3.86
4867 5490 7.168219 TCAATAAAAATACACAGCAGAGTCCT 58.832 34.615 0.00 0.00 0.00 3.85
4868 5491 7.377766 TCAATAAAAATACACAGCAGAGTCC 57.622 36.000 0.00 0.00 0.00 3.85
4869 5492 9.846248 AAATCAATAAAAATACACAGCAGAGTC 57.154 29.630 0.00 0.00 0.00 3.36
4893 5516 9.549078 GGACCTTTTGTACCATTTATTTGAAAA 57.451 29.630 0.00 0.00 0.00 2.29
4894 5517 8.929487 AGGACCTTTTGTACCATTTATTTGAAA 58.071 29.630 0.00 0.00 0.00 2.69
4895 5518 8.485578 AGGACCTTTTGTACCATTTATTTGAA 57.514 30.769 0.00 0.00 0.00 2.69
4896 5519 8.364142 CAAGGACCTTTTGTACCATTTATTTGA 58.636 33.333 3.21 0.00 0.00 2.69
4897 5520 7.117667 GCAAGGACCTTTTGTACCATTTATTTG 59.882 37.037 3.21 0.00 0.00 2.32
4898 5521 7.158697 GCAAGGACCTTTTGTACCATTTATTT 58.841 34.615 3.21 0.00 0.00 1.40
4899 5522 6.268847 TGCAAGGACCTTTTGTACCATTTATT 59.731 34.615 3.21 0.00 0.00 1.40
4900 5523 5.777732 TGCAAGGACCTTTTGTACCATTTAT 59.222 36.000 3.21 0.00 0.00 1.40
4901 5524 5.141182 TGCAAGGACCTTTTGTACCATTTA 58.859 37.500 3.21 0.00 0.00 1.40
4902 5525 3.964031 TGCAAGGACCTTTTGTACCATTT 59.036 39.130 3.21 0.00 0.00 2.32
4903 5526 3.571590 TGCAAGGACCTTTTGTACCATT 58.428 40.909 3.21 0.00 0.00 3.16
4904 5527 3.237268 TGCAAGGACCTTTTGTACCAT 57.763 42.857 3.21 0.00 0.00 3.55
4905 5528 2.738587 TGCAAGGACCTTTTGTACCA 57.261 45.000 3.21 0.00 0.00 3.25
4906 5529 4.098807 TCTTTTGCAAGGACCTTTTGTACC 59.901 41.667 3.21 0.00 0.00 3.34
4907 5530 5.257082 TCTTTTGCAAGGACCTTTTGTAC 57.743 39.130 3.21 0.00 0.00 2.90
4908 5531 5.923733 TTCTTTTGCAAGGACCTTTTGTA 57.076 34.783 3.21 0.00 0.00 2.41
4909 5532 4.817318 TTCTTTTGCAAGGACCTTTTGT 57.183 36.364 3.21 0.00 0.00 2.83
4910 5533 5.874261 TCTTTTCTTTTGCAAGGACCTTTTG 59.126 36.000 3.21 0.00 0.00 2.44
4911 5534 6.048732 TCTTTTCTTTTGCAAGGACCTTTT 57.951 33.333 3.21 0.00 0.00 2.27
4912 5535 5.675684 TCTTTTCTTTTGCAAGGACCTTT 57.324 34.783 3.21 0.00 0.00 3.11
4913 5536 5.664457 CTTCTTTTCTTTTGCAAGGACCTT 58.336 37.500 0.00 0.00 0.00 3.50
4914 5537 4.442052 GCTTCTTTTCTTTTGCAAGGACCT 60.442 41.667 0.00 0.00 0.00 3.85
4915 5538 3.804325 GCTTCTTTTCTTTTGCAAGGACC 59.196 43.478 0.00 0.00 0.00 4.46
4916 5539 4.686972 AGCTTCTTTTCTTTTGCAAGGAC 58.313 39.130 0.00 0.00 0.00 3.85
4917 5540 6.655078 ATAGCTTCTTTTCTTTTGCAAGGA 57.345 33.333 0.00 0.00 0.00 3.36
4918 5541 7.370383 TGTATAGCTTCTTTTCTTTTGCAAGG 58.630 34.615 0.00 0.00 0.00 3.61
4919 5542 8.292448 TCTGTATAGCTTCTTTTCTTTTGCAAG 58.708 33.333 0.00 0.00 0.00 4.01
4920 5543 8.165239 TCTGTATAGCTTCTTTTCTTTTGCAA 57.835 30.769 0.00 0.00 0.00 4.08
4921 5544 7.744087 TCTGTATAGCTTCTTTTCTTTTGCA 57.256 32.000 0.00 0.00 0.00 4.08
4922 5545 9.463443 TTTTCTGTATAGCTTCTTTTCTTTTGC 57.537 29.630 0.00 0.00 0.00 3.68
4957 5580 6.502136 CCTTTGCTTTCCTAGTTTTCCTAG 57.498 41.667 0.00 0.00 42.51 3.02


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

AutoCloner maintained by Alex Coulton.