Multiple sequence alignment - TraesCS2D01G352300

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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 TraesCS2D01G352300 chr2D 100.000 2285 0 0 1 2285 450398083 450400367 0.000000e+00 4220.0
1 TraesCS2D01G352300 chr2D 88.752 809 66 3 1479 2285 498867944 498867159 0.000000e+00 966.0
2 TraesCS2D01G352300 chr2D 86.862 647 62 9 549 1184 498869713 498869079 0.000000e+00 702.0
3 TraesCS2D01G352300 chr2D 92.511 227 17 0 1235 1461 498869078 498868852 2.190000e-85 326.0
4 TraesCS2D01G352300 chr5A 94.066 2039 75 13 251 2285 220900304 220898308 0.000000e+00 3053.0
5 TraesCS2D01G352300 chr5A 84.244 622 81 14 1476 2089 626270471 626269859 7.030000e-165 590.0
6 TraesCS2D01G352300 chr5A 85.185 135 11 2 1109 1243 567297228 567297103 1.840000e-26 130.0
7 TraesCS2D01G352300 chr2B 94.240 816 22 6 1457 2266 17860922 17861718 0.000000e+00 1223.0
8 TraesCS2D01G352300 chr2B 95.338 622 27 2 607 1227 17859516 17860136 0.000000e+00 987.0
9 TraesCS2D01G352300 chr2B 91.093 247 11 6 1 243 530730048 530730287 7.870000e-85 324.0
10 TraesCS2D01G352300 chr2B 88.293 205 16 3 250 449 17859315 17859516 2.930000e-59 239.0
11 TraesCS2D01G352300 chr2B 86.047 86 11 1 240 325 747676944 747676860 8.690000e-15 91.6
12 TraesCS2D01G352300 chr3B 90.199 806 76 2 543 1345 279694684 279693879 0.000000e+00 1048.0
13 TraesCS2D01G352300 chr3B 94.306 562 20 3 900 1461 27506515 27505966 0.000000e+00 850.0
14 TraesCS2D01G352300 chr3B 85.366 697 35 25 254 913 27508098 27507432 0.000000e+00 660.0
15 TraesCS2D01G352300 chr6A 89.104 569 41 15 907 1461 206346444 206347005 0.000000e+00 688.0
16 TraesCS2D01G352300 chr6D 88.401 569 45 15 907 1461 153857267 153857828 0.000000e+00 665.0
17 TraesCS2D01G352300 chr6D 82.308 130 20 3 243 370 300217860 300217988 2.400000e-20 110.0
18 TraesCS2D01G352300 chr1D 85.569 589 53 14 891 1461 10548962 10548388 2.530000e-164 588.0
19 TraesCS2D01G352300 chr1D 82.927 246 28 7 1 243 202276835 202277069 2.300000e-50 209.0
20 TraesCS2D01G352300 chr1D 91.176 136 12 0 907 1042 10457142 10457007 3.880000e-43 185.0
21 TraesCS2D01G352300 chr5D 82.476 622 93 12 1477 2089 501038034 501038648 4.320000e-147 531.0
22 TraesCS2D01G352300 chr5D 84.653 202 25 3 1453 1649 50013418 50013618 1.790000e-46 196.0
23 TraesCS2D01G352300 chr5D 84.653 202 25 3 1453 1649 50179353 50179553 1.790000e-46 196.0
24 TraesCS2D01G352300 chr4A 81.695 590 74 20 713 1282 353083901 353083326 5.750000e-126 460.0
25 TraesCS2D01G352300 chr5B 87.073 410 48 4 543 949 248673943 248673536 2.070000e-125 459.0
26 TraesCS2D01G352300 chr5B 85.024 207 24 4 1449 1649 52555029 52555234 1.070000e-48 204.0
27 TraesCS2D01G352300 chr3A 79.332 629 106 17 1470 2086 712339339 712338723 9.760000e-114 420.0
28 TraesCS2D01G352300 chr2A 85.425 247 22 7 1 243 598970280 598970044 6.310000e-61 244.0
29 TraesCS2D01G352300 chr7D 83.240 179 25 4 1913 2086 469084405 469084583 2.350000e-35 159.0
30 TraesCS2D01G352300 chr7B 84.328 134 18 3 240 370 367827763 367827630 6.630000e-26 128.0
31 TraesCS2D01G352300 chr4B 86.486 111 13 2 241 350 207101496 207101387 1.110000e-23 121.0
32 TraesCS2D01G352300 chr6B 86.538 104 9 4 2170 2271 547649203 547649303 2.400000e-20 110.0
33 TraesCS2D01G352300 chr6B 81.513 119 17 3 239 356 564369871 564369757 2.420000e-15 93.5
34 TraesCS2D01G352300 chr6B 80.000 115 21 2 244 356 267030643 267030757 1.450000e-12 84.2
35 TraesCS2D01G352300 chr3D 83.158 95 15 1 253 346 325517883 325517789 4.040000e-13 86.1


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 TraesCS2D01G352300 chr2D 450398083 450400367 2284 False 4220.000000 4220 100.000000 1 2285 1 chr2D.!!$F1 2284
1 TraesCS2D01G352300 chr2D 498867159 498869713 2554 True 664.666667 966 89.375000 549 2285 3 chr2D.!!$R1 1736
2 TraesCS2D01G352300 chr5A 220898308 220900304 1996 True 3053.000000 3053 94.066000 251 2285 1 chr5A.!!$R1 2034
3 TraesCS2D01G352300 chr5A 626269859 626270471 612 True 590.000000 590 84.244000 1476 2089 1 chr5A.!!$R3 613
4 TraesCS2D01G352300 chr2B 17859315 17861718 2403 False 816.333333 1223 92.623667 250 2266 3 chr2B.!!$F2 2016
5 TraesCS2D01G352300 chr3B 279693879 279694684 805 True 1048.000000 1048 90.199000 543 1345 1 chr3B.!!$R1 802
6 TraesCS2D01G352300 chr3B 27505966 27508098 2132 True 755.000000 850 89.836000 254 1461 2 chr3B.!!$R2 1207
7 TraesCS2D01G352300 chr6A 206346444 206347005 561 False 688.000000 688 89.104000 907 1461 1 chr6A.!!$F1 554
8 TraesCS2D01G352300 chr6D 153857267 153857828 561 False 665.000000 665 88.401000 907 1461 1 chr6D.!!$F1 554
9 TraesCS2D01G352300 chr1D 10548388 10548962 574 True 588.000000 588 85.569000 891 1461 1 chr1D.!!$R2 570
10 TraesCS2D01G352300 chr5D 501038034 501038648 614 False 531.000000 531 82.476000 1477 2089 1 chr5D.!!$F3 612
11 TraesCS2D01G352300 chr4A 353083326 353083901 575 True 460.000000 460 81.695000 713 1282 1 chr4A.!!$R1 569
12 TraesCS2D01G352300 chr3A 712338723 712339339 616 True 420.000000 420 79.332000 1470 2086 1 chr3A.!!$R1 616

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
181 182 0.038526 GCAGTCTGCAAATTGCTGCT 60.039 50.0 20.16 15.5 46.2 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 4424 0.46546 GGGGAACACACTGCACTGAA 60.465 55.0 0.0 0.0 0.0 3.02 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
20 21 1.303309 ATACAAGGCTTCTGATGCGC 58.697 50.000 0.00 0.00 0.00 6.09
21 22 0.744414 TACAAGGCTTCTGATGCGCC 60.744 55.000 4.18 7.14 44.09 6.53
22 23 2.439156 AAGGCTTCTGATGCGCCC 60.439 61.111 4.18 0.00 44.84 6.13
23 24 2.976490 AAGGCTTCTGATGCGCCCT 61.976 57.895 4.18 0.00 44.84 5.19
24 25 2.439156 GGCTTCTGATGCGCCCTT 60.439 61.111 4.18 0.00 37.86 3.95
25 26 2.048603 GGCTTCTGATGCGCCCTTT 61.049 57.895 4.18 0.00 37.86 3.11
26 27 1.138247 GCTTCTGATGCGCCCTTTG 59.862 57.895 4.18 0.00 0.00 2.77
27 28 1.589716 GCTTCTGATGCGCCCTTTGT 61.590 55.000 4.18 0.00 0.00 2.83
28 29 1.737838 CTTCTGATGCGCCCTTTGTA 58.262 50.000 4.18 0.00 0.00 2.41
29 30 2.292267 CTTCTGATGCGCCCTTTGTAT 58.708 47.619 4.18 0.00 0.00 2.29
30 31 2.418368 TCTGATGCGCCCTTTGTATT 57.582 45.000 4.18 0.00 0.00 1.89
31 32 2.722094 TCTGATGCGCCCTTTGTATTT 58.278 42.857 4.18 0.00 0.00 1.40
32 33 2.682856 TCTGATGCGCCCTTTGTATTTC 59.317 45.455 4.18 0.00 0.00 2.17
33 34 2.423185 CTGATGCGCCCTTTGTATTTCA 59.577 45.455 4.18 0.00 0.00 2.69
34 35 3.023119 TGATGCGCCCTTTGTATTTCAT 58.977 40.909 4.18 0.00 0.00 2.57
35 36 3.446873 TGATGCGCCCTTTGTATTTCATT 59.553 39.130 4.18 0.00 0.00 2.57
36 37 3.951775 TGCGCCCTTTGTATTTCATTT 57.048 38.095 4.18 0.00 0.00 2.32
37 38 4.264460 TGCGCCCTTTGTATTTCATTTT 57.736 36.364 4.18 0.00 0.00 1.82
38 39 4.241681 TGCGCCCTTTGTATTTCATTTTC 58.758 39.130 4.18 0.00 0.00 2.29
39 40 3.616821 GCGCCCTTTGTATTTCATTTTCC 59.383 43.478 0.00 0.00 0.00 3.13
40 41 4.815269 CGCCCTTTGTATTTCATTTTCCA 58.185 39.130 0.00 0.00 0.00 3.53
41 42 4.864247 CGCCCTTTGTATTTCATTTTCCAG 59.136 41.667 0.00 0.00 0.00 3.86
42 43 5.336372 CGCCCTTTGTATTTCATTTTCCAGA 60.336 40.000 0.00 0.00 0.00 3.86
43 44 6.627953 CGCCCTTTGTATTTCATTTTCCAGAT 60.628 38.462 0.00 0.00 0.00 2.90
44 45 7.105588 GCCCTTTGTATTTCATTTTCCAGATT 58.894 34.615 0.00 0.00 0.00 2.40
45 46 7.278646 GCCCTTTGTATTTCATTTTCCAGATTC 59.721 37.037 0.00 0.00 0.00 2.52
46 47 8.313292 CCCTTTGTATTTCATTTTCCAGATTCA 58.687 33.333 0.00 0.00 0.00 2.57
47 48 9.143631 CCTTTGTATTTCATTTTCCAGATTCAC 57.856 33.333 0.00 0.00 0.00 3.18
48 49 9.695526 CTTTGTATTTCATTTTCCAGATTCACA 57.304 29.630 0.00 0.00 0.00 3.58
63 64 9.904198 TCCAGATTCACAAATATACTCATTTCA 57.096 29.630 0.00 0.00 0.00 2.69
69 70 9.685276 TTCACAAATATACTCATTTCATCAGGT 57.315 29.630 0.00 0.00 0.00 4.00
70 71 9.330063 TCACAAATATACTCATTTCATCAGGTC 57.670 33.333 0.00 0.00 0.00 3.85
71 72 9.112725 CACAAATATACTCATTTCATCAGGTCA 57.887 33.333 0.00 0.00 0.00 4.02
72 73 9.685276 ACAAATATACTCATTTCATCAGGTCAA 57.315 29.630 0.00 0.00 0.00 3.18
77 78 6.506500 ACTCATTTCATCAGGTCAATTCAC 57.493 37.500 0.00 0.00 0.00 3.18
78 79 6.243900 ACTCATTTCATCAGGTCAATTCACT 58.756 36.000 0.00 0.00 0.00 3.41
79 80 6.718454 ACTCATTTCATCAGGTCAATTCACTT 59.282 34.615 0.00 0.00 0.00 3.16
80 81 6.916440 TCATTTCATCAGGTCAATTCACTTG 58.084 36.000 0.00 0.00 36.09 3.16
81 82 4.771590 TTCATCAGGTCAATTCACTTGC 57.228 40.909 0.00 0.00 34.66 4.01
82 83 3.753815 TCATCAGGTCAATTCACTTGCA 58.246 40.909 0.00 0.00 34.66 4.08
83 84 4.143543 TCATCAGGTCAATTCACTTGCAA 58.856 39.130 0.00 0.00 34.66 4.08
84 85 4.216902 TCATCAGGTCAATTCACTTGCAAG 59.783 41.667 24.84 24.84 34.66 4.01
85 86 3.819368 TCAGGTCAATTCACTTGCAAGA 58.181 40.909 32.50 11.28 34.66 3.02
86 87 3.817084 TCAGGTCAATTCACTTGCAAGAG 59.183 43.478 32.50 24.50 34.66 2.85
87 88 3.817084 CAGGTCAATTCACTTGCAAGAGA 59.183 43.478 32.50 26.43 34.66 3.10
88 89 4.276678 CAGGTCAATTCACTTGCAAGAGAA 59.723 41.667 32.16 32.16 39.36 2.87
89 90 4.518211 AGGTCAATTCACTTGCAAGAGAAG 59.482 41.667 32.73 24.01 38.63 2.85
90 91 4.276926 GGTCAATTCACTTGCAAGAGAAGT 59.723 41.667 32.73 29.82 38.63 3.01
91 92 5.470098 GGTCAATTCACTTGCAAGAGAAGTA 59.530 40.000 32.73 21.97 38.63 2.24
92 93 6.017109 GGTCAATTCACTTGCAAGAGAAGTAA 60.017 38.462 32.73 21.19 38.63 2.24
93 94 6.853362 GTCAATTCACTTGCAAGAGAAGTAAC 59.147 38.462 32.73 26.45 38.63 2.50
94 95 6.542005 TCAATTCACTTGCAAGAGAAGTAACA 59.458 34.615 32.73 20.06 38.63 2.41
95 96 5.991328 TTCACTTGCAAGAGAAGTAACAG 57.009 39.130 32.50 2.47 32.03 3.16
96 97 4.380531 TCACTTGCAAGAGAAGTAACAGG 58.619 43.478 32.50 2.55 32.27 4.00
97 98 4.130118 CACTTGCAAGAGAAGTAACAGGT 58.870 43.478 32.50 3.25 32.27 4.00
98 99 4.576463 CACTTGCAAGAGAAGTAACAGGTT 59.424 41.667 32.50 1.82 32.27 3.50
99 100 5.066505 CACTTGCAAGAGAAGTAACAGGTTT 59.933 40.000 32.50 1.12 32.27 3.27
100 101 6.260050 CACTTGCAAGAGAAGTAACAGGTTTA 59.740 38.462 32.50 0.00 32.27 2.01
101 102 6.483640 ACTTGCAAGAGAAGTAACAGGTTTAG 59.516 38.462 32.50 0.00 31.72 1.85
102 103 5.305585 TGCAAGAGAAGTAACAGGTTTAGG 58.694 41.667 0.00 0.00 0.00 2.69
103 104 4.154375 GCAAGAGAAGTAACAGGTTTAGGC 59.846 45.833 0.00 0.00 0.00 3.93
104 105 5.552178 CAAGAGAAGTAACAGGTTTAGGCT 58.448 41.667 0.00 0.00 0.00 4.58
105 106 5.827326 AGAGAAGTAACAGGTTTAGGCTT 57.173 39.130 0.00 0.00 0.00 4.35
106 107 5.552178 AGAGAAGTAACAGGTTTAGGCTTG 58.448 41.667 0.00 0.00 0.00 4.01
107 108 5.071923 AGAGAAGTAACAGGTTTAGGCTTGT 59.928 40.000 0.00 0.00 0.00 3.16
108 109 5.306394 AGAAGTAACAGGTTTAGGCTTGTC 58.694 41.667 0.00 0.00 0.00 3.18
109 110 3.660865 AGTAACAGGTTTAGGCTTGTCG 58.339 45.455 0.00 0.00 0.00 4.35
110 111 2.922740 AACAGGTTTAGGCTTGTCGA 57.077 45.000 0.00 0.00 0.00 4.20
111 112 2.922740 ACAGGTTTAGGCTTGTCGAA 57.077 45.000 0.00 0.00 0.00 3.71
112 113 3.418684 ACAGGTTTAGGCTTGTCGAAT 57.581 42.857 0.00 0.00 0.00 3.34
113 114 3.335579 ACAGGTTTAGGCTTGTCGAATC 58.664 45.455 0.00 0.00 0.00 2.52
114 115 2.678336 CAGGTTTAGGCTTGTCGAATCC 59.322 50.000 0.00 0.00 0.00 3.01
115 116 2.572104 AGGTTTAGGCTTGTCGAATCCT 59.428 45.455 0.00 0.00 32.30 3.24
116 117 3.773119 AGGTTTAGGCTTGTCGAATCCTA 59.227 43.478 0.00 0.00 30.13 2.94
117 118 4.224370 AGGTTTAGGCTTGTCGAATCCTAA 59.776 41.667 0.00 10.21 37.90 2.69
118 119 5.104485 AGGTTTAGGCTTGTCGAATCCTAAT 60.104 40.000 13.33 1.74 38.92 1.73
119 120 5.589050 GGTTTAGGCTTGTCGAATCCTAATT 59.411 40.000 13.33 0.00 38.92 1.40
120 121 6.764560 GGTTTAGGCTTGTCGAATCCTAATTA 59.235 38.462 13.33 0.00 38.92 1.40
121 122 7.444487 GGTTTAGGCTTGTCGAATCCTAATTAT 59.556 37.037 13.33 0.00 38.92 1.28
122 123 8.837389 GTTTAGGCTTGTCGAATCCTAATTATT 58.163 33.333 13.33 0.00 38.92 1.40
123 124 8.603242 TTAGGCTTGTCGAATCCTAATTATTC 57.397 34.615 0.00 0.00 35.78 1.75
124 125 6.831976 AGGCTTGTCGAATCCTAATTATTCT 58.168 36.000 0.00 0.00 32.29 2.40
125 126 7.963532 AGGCTTGTCGAATCCTAATTATTCTA 58.036 34.615 0.00 0.00 32.29 2.10
126 127 7.873505 AGGCTTGTCGAATCCTAATTATTCTAC 59.126 37.037 0.00 0.00 32.51 2.59
127 128 7.656137 GGCTTGTCGAATCCTAATTATTCTACA 59.344 37.037 3.78 3.78 37.30 2.74
128 129 9.209175 GCTTGTCGAATCCTAATTATTCTACAT 57.791 33.333 7.31 0.00 38.24 2.29
138 139 9.998106 TCCTAATTATTCTACATTAGCAGTTCC 57.002 33.333 0.00 0.00 33.33 3.62
144 145 9.515226 TTATTCTACATTAGCAGTTCCTTTTGT 57.485 29.630 0.00 0.00 0.00 2.83
145 146 7.817418 TTCTACATTAGCAGTTCCTTTTGTT 57.183 32.000 0.00 0.00 0.00 2.83
146 147 7.435068 TCTACATTAGCAGTTCCTTTTGTTC 57.565 36.000 0.00 0.00 0.00 3.18
147 148 6.995686 TCTACATTAGCAGTTCCTTTTGTTCA 59.004 34.615 0.00 0.00 0.00 3.18
148 149 5.831997 ACATTAGCAGTTCCTTTTGTTCAC 58.168 37.500 0.00 0.00 0.00 3.18
149 150 5.594317 ACATTAGCAGTTCCTTTTGTTCACT 59.406 36.000 0.00 0.00 0.00 3.41
150 151 5.499139 TTAGCAGTTCCTTTTGTTCACTG 57.501 39.130 0.00 0.00 38.32 3.66
151 152 3.356290 AGCAGTTCCTTTTGTTCACTGT 58.644 40.909 0.00 0.00 37.71 3.55
152 153 3.129287 AGCAGTTCCTTTTGTTCACTGTG 59.871 43.478 0.17 0.17 37.71 3.66
153 154 3.128589 GCAGTTCCTTTTGTTCACTGTGA 59.871 43.478 6.36 6.36 37.71 3.58
154 155 4.662145 CAGTTCCTTTTGTTCACTGTGAC 58.338 43.478 10.56 6.70 31.91 3.67
155 156 3.694566 AGTTCCTTTTGTTCACTGTGACC 59.305 43.478 10.56 3.87 0.00 4.02
156 157 2.285083 TCCTTTTGTTCACTGTGACCG 58.715 47.619 10.56 0.00 0.00 4.79
157 158 1.268539 CCTTTTGTTCACTGTGACCGC 60.269 52.381 10.56 4.76 0.00 5.68
158 159 1.400142 CTTTTGTTCACTGTGACCGCA 59.600 47.619 10.56 7.33 0.00 5.69
159 160 1.013596 TTTGTTCACTGTGACCGCAG 58.986 50.000 10.56 8.85 41.92 5.18
160 161 0.176910 TTGTTCACTGTGACCGCAGA 59.823 50.000 10.56 0.00 39.62 4.26
161 162 0.392706 TGTTCACTGTGACCGCAGAT 59.607 50.000 10.56 0.00 39.62 2.90
162 163 0.792640 GTTCACTGTGACCGCAGATG 59.207 55.000 10.56 10.83 39.62 2.90
163 164 0.950555 TTCACTGTGACCGCAGATGC 60.951 55.000 10.56 0.00 39.62 3.91
164 165 1.668793 CACTGTGACCGCAGATGCA 60.669 57.895 16.45 0.00 42.21 3.96
165 166 1.375140 ACTGTGACCGCAGATGCAG 60.375 57.895 16.45 0.00 42.21 4.41
166 167 1.375140 CTGTGACCGCAGATGCAGT 60.375 57.895 5.55 0.00 42.21 4.40
167 168 1.357258 CTGTGACCGCAGATGCAGTC 61.357 60.000 13.10 13.10 42.21 3.51
168 169 1.079543 GTGACCGCAGATGCAGTCT 60.080 57.895 18.99 0.00 42.21 3.24
180 181 2.442084 GCAGTCTGCAAATTGCTGC 58.558 52.632 20.16 15.79 45.31 5.25
181 182 0.038526 GCAGTCTGCAAATTGCTGCT 60.039 50.000 20.16 15.50 46.20 4.24
182 183 1.200716 GCAGTCTGCAAATTGCTGCTA 59.799 47.619 20.16 0.91 46.20 3.49
183 184 2.159282 GCAGTCTGCAAATTGCTGCTAT 60.159 45.455 20.16 5.19 46.20 2.97
184 185 3.065786 GCAGTCTGCAAATTGCTGCTATA 59.934 43.478 20.16 0.00 46.20 1.31
185 186 4.788840 GCAGTCTGCAAATTGCTGCTATAG 60.789 45.833 20.16 6.94 46.20 1.31
186 187 4.573607 CAGTCTGCAAATTGCTGCTATAGA 59.426 41.667 19.34 9.24 45.31 1.98
187 188 5.238868 CAGTCTGCAAATTGCTGCTATAGAT 59.761 40.000 19.34 0.92 45.31 1.98
188 189 6.426025 CAGTCTGCAAATTGCTGCTATAGATA 59.574 38.462 19.34 0.00 45.31 1.98
189 190 7.119407 CAGTCTGCAAATTGCTGCTATAGATAT 59.881 37.037 19.34 3.20 45.31 1.63
190 191 7.664731 AGTCTGCAAATTGCTGCTATAGATATT 59.335 33.333 19.34 0.76 45.31 1.28
191 192 8.939929 GTCTGCAAATTGCTGCTATAGATATTA 58.060 33.333 19.34 0.00 45.31 0.98
192 193 9.676861 TCTGCAAATTGCTGCTATAGATATTAT 57.323 29.630 19.34 0.00 45.31 1.28
280 281 0.180406 AAGCACGGGTTGAGTCTGTT 59.820 50.000 0.00 0.00 0.00 3.16
417 438 0.613292 CCTCCCGATCCCATCTCGAT 60.613 60.000 0.00 0.00 38.38 3.59
418 439 0.529833 CTCCCGATCCCATCTCGATG 59.470 60.000 0.00 0.00 38.38 3.84
419 440 0.112412 TCCCGATCCCATCTCGATGA 59.888 55.000 8.42 0.00 41.20 2.92
989 1989 8.316946 TCAGAGATTAGGCCATGTATATCTTTG 58.683 37.037 5.01 8.84 0.00 2.77
1010 2020 0.244721 CACGCTCTCATGTCCACAGA 59.755 55.000 0.00 0.00 0.00 3.41
1163 2186 3.056179 GTGGAGTCTAAGCAGAAGAAGCT 60.056 47.826 0.00 0.00 45.97 3.74
1167 2190 4.565022 AGTCTAAGCAGAAGAAGCTGAAC 58.435 43.478 0.00 0.00 42.53 3.18
1233 2307 4.275936 GCTGTTGTATTTGTGAGTTCCAGT 59.724 41.667 0.00 0.00 0.00 4.00
1299 2377 5.269554 TGGAGTAATTTCCATTCAGGGTT 57.730 39.130 0.00 0.00 42.24 4.11
1652 4255 3.181461 CCTCAGCTAATTCAGTAGGGGTG 60.181 52.174 0.00 0.00 0.00 4.61
1882 4496 1.002251 GTCTCTCGCCTATTGGACTCG 60.002 57.143 0.00 0.00 34.57 4.18
2099 4720 6.667370 ACATAACATAATGTGTGTGTGTGTG 58.333 36.000 1.80 0.00 41.14 3.82
2100 4721 6.262049 ACATAACATAATGTGTGTGTGTGTGT 59.738 34.615 1.80 0.00 41.14 3.72
2101 4722 4.550577 ACATAATGTGTGTGTGTGTGTG 57.449 40.909 0.00 0.00 40.28 3.82
2102 4723 3.944650 ACATAATGTGTGTGTGTGTGTGT 59.055 39.130 0.00 0.00 40.28 3.72
2103 4724 2.917701 AATGTGTGTGTGTGTGTGTG 57.082 45.000 0.00 0.00 0.00 3.82
2104 4725 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
2105 4726 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2106 4727 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2107 4728 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2108 4729 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2109 4730 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2110 4731 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2111 4732 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2112 4733 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2113 4734 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2114 4735 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2115 4736 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2141 4762 9.415544 GTTACTAATCTGAAAGTCGAACCTAAA 57.584 33.333 0.00 0.00 33.76 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.672881 GCGCATCAGAAGCCTTGTATT 59.327 47.619 0.30 0.00 0.00 1.89
2 3 0.744414 GGCGCATCAGAAGCCTTGTA 60.744 55.000 10.83 0.00 46.83 2.41
3 4 2.042831 GGCGCATCAGAAGCCTTGT 61.043 57.895 10.83 0.00 46.83 3.16
4 5 2.796651 GGCGCATCAGAAGCCTTG 59.203 61.111 10.83 0.00 46.83 3.61
8 9 1.138247 CAAAGGGCGCATCAGAAGC 59.862 57.895 10.83 0.00 0.00 3.86
9 10 1.737838 TACAAAGGGCGCATCAGAAG 58.262 50.000 10.83 0.00 0.00 2.85
10 11 2.418368 ATACAAAGGGCGCATCAGAA 57.582 45.000 10.83 0.00 0.00 3.02
11 12 2.418368 AATACAAAGGGCGCATCAGA 57.582 45.000 10.83 0.00 0.00 3.27
12 13 2.423185 TGAAATACAAAGGGCGCATCAG 59.577 45.455 10.83 0.00 0.00 2.90
13 14 2.441410 TGAAATACAAAGGGCGCATCA 58.559 42.857 10.83 0.00 0.00 3.07
14 15 3.715628 ATGAAATACAAAGGGCGCATC 57.284 42.857 10.83 0.00 0.00 3.91
15 16 4.470334 AAATGAAATACAAAGGGCGCAT 57.530 36.364 10.83 0.00 0.00 4.73
16 17 3.951775 AAATGAAATACAAAGGGCGCA 57.048 38.095 10.83 0.00 0.00 6.09
17 18 3.616821 GGAAAATGAAATACAAAGGGCGC 59.383 43.478 0.00 0.00 0.00 6.53
18 19 4.815269 TGGAAAATGAAATACAAAGGGCG 58.185 39.130 0.00 0.00 0.00 6.13
19 20 6.036577 TCTGGAAAATGAAATACAAAGGGC 57.963 37.500 0.00 0.00 0.00 5.19
20 21 8.313292 TGAATCTGGAAAATGAAATACAAAGGG 58.687 33.333 0.00 0.00 0.00 3.95
21 22 9.143631 GTGAATCTGGAAAATGAAATACAAAGG 57.856 33.333 0.00 0.00 0.00 3.11
22 23 9.695526 TGTGAATCTGGAAAATGAAATACAAAG 57.304 29.630 0.00 0.00 0.00 2.77
37 38 9.904198 TGAAATGAGTATATTTGTGAATCTGGA 57.096 29.630 0.00 0.00 30.78 3.86
43 44 9.685276 ACCTGATGAAATGAGTATATTTGTGAA 57.315 29.630 0.00 0.00 30.78 3.18
44 45 9.330063 GACCTGATGAAATGAGTATATTTGTGA 57.670 33.333 0.00 0.00 30.78 3.58
45 46 9.112725 TGACCTGATGAAATGAGTATATTTGTG 57.887 33.333 0.00 0.00 30.78 3.33
46 47 9.685276 TTGACCTGATGAAATGAGTATATTTGT 57.315 29.630 0.00 0.00 30.78 2.83
51 52 9.330063 GTGAATTGACCTGATGAAATGAGTATA 57.670 33.333 0.00 0.00 0.00 1.47
52 53 8.051535 AGTGAATTGACCTGATGAAATGAGTAT 58.948 33.333 0.00 0.00 0.00 2.12
53 54 7.397221 AGTGAATTGACCTGATGAAATGAGTA 58.603 34.615 0.00 0.00 0.00 2.59
54 55 6.243900 AGTGAATTGACCTGATGAAATGAGT 58.756 36.000 0.00 0.00 0.00 3.41
55 56 6.754702 AGTGAATTGACCTGATGAAATGAG 57.245 37.500 0.00 0.00 0.00 2.90
56 57 6.570957 GCAAGTGAATTGACCTGATGAAATGA 60.571 38.462 0.00 0.00 41.83 2.57
57 58 5.575606 GCAAGTGAATTGACCTGATGAAATG 59.424 40.000 0.00 0.00 41.83 2.32
58 59 5.244402 TGCAAGTGAATTGACCTGATGAAAT 59.756 36.000 0.00 0.00 41.83 2.17
59 60 4.583907 TGCAAGTGAATTGACCTGATGAAA 59.416 37.500 0.00 0.00 41.83 2.69
60 61 4.143543 TGCAAGTGAATTGACCTGATGAA 58.856 39.130 0.00 0.00 41.83 2.57
61 62 3.753815 TGCAAGTGAATTGACCTGATGA 58.246 40.909 0.00 0.00 41.83 2.92
62 63 4.216902 TCTTGCAAGTGAATTGACCTGATG 59.783 41.667 25.19 0.00 41.83 3.07
63 64 4.401022 TCTTGCAAGTGAATTGACCTGAT 58.599 39.130 25.19 0.00 41.83 2.90
64 65 3.817084 CTCTTGCAAGTGAATTGACCTGA 59.183 43.478 25.19 1.32 41.83 3.86
65 66 3.817084 TCTCTTGCAAGTGAATTGACCTG 59.183 43.478 24.84 0.00 41.83 4.00
66 67 4.090761 TCTCTTGCAAGTGAATTGACCT 57.909 40.909 24.84 0.00 41.83 3.85
67 68 4.276926 ACTTCTCTTGCAAGTGAATTGACC 59.723 41.667 32.64 0.00 41.83 4.02
68 69 5.429957 ACTTCTCTTGCAAGTGAATTGAC 57.570 39.130 32.64 0.00 41.83 3.18
69 70 6.542005 TGTTACTTCTCTTGCAAGTGAATTGA 59.458 34.615 32.64 24.50 41.83 2.57
70 71 6.728200 TGTTACTTCTCTTGCAAGTGAATTG 58.272 36.000 32.64 26.14 37.73 2.32
71 72 6.016777 CCTGTTACTTCTCTTGCAAGTGAATT 60.017 38.462 32.64 29.54 37.73 2.17
72 73 5.471456 CCTGTTACTTCTCTTGCAAGTGAAT 59.529 40.000 32.64 25.54 37.73 2.57
73 74 4.816385 CCTGTTACTTCTCTTGCAAGTGAA 59.184 41.667 31.25 31.25 36.50 3.18
74 75 4.141711 ACCTGTTACTTCTCTTGCAAGTGA 60.142 41.667 25.19 24.36 35.63 3.41
75 76 4.130118 ACCTGTTACTTCTCTTGCAAGTG 58.870 43.478 25.19 22.48 35.63 3.16
76 77 4.423625 ACCTGTTACTTCTCTTGCAAGT 57.576 40.909 25.19 9.76 37.80 3.16
77 78 5.757850 AAACCTGTTACTTCTCTTGCAAG 57.242 39.130 20.81 20.81 0.00 4.01
78 79 5.763204 CCTAAACCTGTTACTTCTCTTGCAA 59.237 40.000 0.00 0.00 0.00 4.08
79 80 5.305585 CCTAAACCTGTTACTTCTCTTGCA 58.694 41.667 0.00 0.00 0.00 4.08
80 81 4.154375 GCCTAAACCTGTTACTTCTCTTGC 59.846 45.833 0.00 0.00 0.00 4.01
81 82 5.552178 AGCCTAAACCTGTTACTTCTCTTG 58.448 41.667 0.00 0.00 0.00 3.02
82 83 5.827326 AGCCTAAACCTGTTACTTCTCTT 57.173 39.130 0.00 0.00 0.00 2.85
83 84 5.071923 ACAAGCCTAAACCTGTTACTTCTCT 59.928 40.000 0.00 0.00 0.00 3.10
84 85 5.306394 ACAAGCCTAAACCTGTTACTTCTC 58.694 41.667 0.00 0.00 0.00 2.87
85 86 5.306114 ACAAGCCTAAACCTGTTACTTCT 57.694 39.130 0.00 0.00 0.00 2.85
86 87 4.151867 CGACAAGCCTAAACCTGTTACTTC 59.848 45.833 0.00 0.00 0.00 3.01
87 88 4.062991 CGACAAGCCTAAACCTGTTACTT 58.937 43.478 0.00 0.00 0.00 2.24
88 89 3.322828 TCGACAAGCCTAAACCTGTTACT 59.677 43.478 0.00 0.00 0.00 2.24
89 90 3.656559 TCGACAAGCCTAAACCTGTTAC 58.343 45.455 0.00 0.00 0.00 2.50
90 91 4.339872 TTCGACAAGCCTAAACCTGTTA 57.660 40.909 0.00 0.00 0.00 2.41
91 92 2.922740 TCGACAAGCCTAAACCTGTT 57.077 45.000 0.00 0.00 0.00 3.16
92 93 2.922740 TTCGACAAGCCTAAACCTGT 57.077 45.000 0.00 0.00 0.00 4.00
93 94 2.678336 GGATTCGACAAGCCTAAACCTG 59.322 50.000 0.00 0.00 34.94 4.00
94 95 2.987232 GGATTCGACAAGCCTAAACCT 58.013 47.619 0.00 0.00 34.94 3.50
101 102 7.656137 TGTAGAATAATTAGGATTCGACAAGCC 59.344 37.037 10.94 0.00 42.33 4.35
102 103 8.589335 TGTAGAATAATTAGGATTCGACAAGC 57.411 34.615 10.94 0.00 42.33 4.01
112 113 9.998106 GGAACTGCTAATGTAGAATAATTAGGA 57.002 33.333 4.98 1.67 37.02 2.94
118 119 9.515226 ACAAAAGGAACTGCTAATGTAGAATAA 57.485 29.630 0.00 0.00 40.86 1.40
119 120 9.515226 AACAAAAGGAACTGCTAATGTAGAATA 57.485 29.630 0.00 0.00 40.86 1.75
120 121 8.409358 AACAAAAGGAACTGCTAATGTAGAAT 57.591 30.769 0.00 0.00 40.86 2.40
121 122 7.500892 TGAACAAAAGGAACTGCTAATGTAGAA 59.499 33.333 0.00 0.00 40.86 2.10
122 123 6.995686 TGAACAAAAGGAACTGCTAATGTAGA 59.004 34.615 0.00 0.00 40.86 2.59
123 124 7.041098 AGTGAACAAAAGGAACTGCTAATGTAG 60.041 37.037 0.00 0.00 40.86 2.74
124 125 6.770785 AGTGAACAAAAGGAACTGCTAATGTA 59.229 34.615 0.00 0.00 40.86 2.29
125 126 5.594317 AGTGAACAAAAGGAACTGCTAATGT 59.406 36.000 0.00 0.00 40.86 2.71
126 127 5.916883 CAGTGAACAAAAGGAACTGCTAATG 59.083 40.000 0.00 0.00 40.86 1.90
127 128 5.594317 ACAGTGAACAAAAGGAACTGCTAAT 59.406 36.000 0.00 0.00 41.53 1.73
128 129 4.947388 ACAGTGAACAAAAGGAACTGCTAA 59.053 37.500 0.00 0.00 41.53 3.09
129 130 4.335315 CACAGTGAACAAAAGGAACTGCTA 59.665 41.667 0.00 0.00 41.53 3.49
130 131 3.129287 CACAGTGAACAAAAGGAACTGCT 59.871 43.478 0.00 0.00 41.53 4.24
131 132 3.128589 TCACAGTGAACAAAAGGAACTGC 59.871 43.478 0.00 0.00 41.53 4.40
132 133 4.438744 GGTCACAGTGAACAAAAGGAACTG 60.439 45.833 14.17 0.00 43.07 3.16
133 134 3.694566 GGTCACAGTGAACAAAAGGAACT 59.305 43.478 14.17 0.00 34.72 3.01
134 135 3.486875 CGGTCACAGTGAACAAAAGGAAC 60.487 47.826 18.89 0.00 32.48 3.62
135 136 2.680841 CGGTCACAGTGAACAAAAGGAA 59.319 45.455 18.89 0.00 32.48 3.36
136 137 2.285083 CGGTCACAGTGAACAAAAGGA 58.715 47.619 18.89 0.00 32.48 3.36
137 138 1.268539 GCGGTCACAGTGAACAAAAGG 60.269 52.381 18.89 2.84 32.48 3.11
138 139 1.400142 TGCGGTCACAGTGAACAAAAG 59.600 47.619 18.89 3.22 32.48 2.27
139 140 1.400142 CTGCGGTCACAGTGAACAAAA 59.600 47.619 18.89 2.30 32.48 2.44
140 141 1.013596 CTGCGGTCACAGTGAACAAA 58.986 50.000 18.89 4.81 32.48 2.83
141 142 0.176910 TCTGCGGTCACAGTGAACAA 59.823 50.000 18.89 5.17 38.84 2.83
142 143 0.392706 ATCTGCGGTCACAGTGAACA 59.607 50.000 18.89 10.15 38.84 3.18
143 144 0.792640 CATCTGCGGTCACAGTGAAC 59.207 55.000 8.73 8.73 38.84 3.18
144 145 0.950555 GCATCTGCGGTCACAGTGAA 60.951 55.000 4.32 0.00 38.84 3.18
145 146 1.374631 GCATCTGCGGTCACAGTGA 60.375 57.895 0.00 0.00 38.84 3.41
146 147 1.632948 CTGCATCTGCGGTCACAGTG 61.633 60.000 2.75 0.00 45.83 3.66
147 148 1.375140 CTGCATCTGCGGTCACAGT 60.375 57.895 2.75 0.00 45.83 3.55
148 149 3.482809 CTGCATCTGCGGTCACAG 58.517 61.111 2.75 0.00 45.83 3.66
242 243 9.280174 CCGTGCTTTATTATTATTAGGGAAAGA 57.720 33.333 0.00 0.00 0.00 2.52
243 244 8.512138 CCCGTGCTTTATTATTATTAGGGAAAG 58.488 37.037 0.00 0.00 36.18 2.62
244 245 8.000127 ACCCGTGCTTTATTATTATTAGGGAAA 59.000 33.333 0.00 0.00 37.46 3.13
245 246 7.519927 ACCCGTGCTTTATTATTATTAGGGAA 58.480 34.615 0.00 0.00 37.46 3.97
246 247 7.081857 ACCCGTGCTTTATTATTATTAGGGA 57.918 36.000 0.00 0.00 37.46 4.20
247 248 7.446013 TCAACCCGTGCTTTATTATTATTAGGG 59.554 37.037 0.00 0.00 39.75 3.53
248 249 8.385898 TCAACCCGTGCTTTATTATTATTAGG 57.614 34.615 0.00 0.00 0.00 2.69
252 253 7.226720 CAGACTCAACCCGTGCTTTATTATTAT 59.773 37.037 0.00 0.00 0.00 1.28
388 409 1.258676 GATCGGGAGGTAGGGTGATC 58.741 60.000 0.00 0.00 0.00 2.92
417 438 3.005539 GCTGGAGGCTGGAGGTCA 61.006 66.667 0.00 0.00 38.06 4.02
418 439 3.005539 TGCTGGAGGCTGGAGGTC 61.006 66.667 0.00 0.00 42.39 3.85
419 440 3.325753 GTGCTGGAGGCTGGAGGT 61.326 66.667 0.00 0.00 42.39 3.85
989 1989 2.103042 GTGGACATGAGAGCGTGCC 61.103 63.158 0.00 0.00 34.29 5.01
1010 2020 5.717078 ACTGTTGCTGAAAACATCATGAT 57.283 34.783 1.18 1.18 39.25 2.45
1081 2101 4.018688 ACCTAGGTTCCCACAAGAAATACC 60.019 45.833 9.21 0.00 0.00 2.73
1233 2307 4.635223 CTTCAGACAAGAGATCACCAACA 58.365 43.478 0.00 0.00 0.00 3.33
1447 2865 6.542005 TGAATGTGTCGCTGGTGAATATATTT 59.458 34.615 0.00 0.00 0.00 1.40
1652 4255 2.162681 CACTTGGACAGGGAATGAACC 58.837 52.381 0.00 0.00 0.00 3.62
1690 4293 9.491675 CTAGATGAGAATAAACAGATGAAGCAT 57.508 33.333 0.00 0.00 0.00 3.79
1770 4377 2.908073 CGCCTTCACCGCAAAGCTT 61.908 57.895 0.00 0.00 0.00 3.74
1817 4424 0.465460 GGGGAACACACTGCACTGAA 60.465 55.000 0.00 0.00 0.00 3.02
2099 4720 2.739913 AGTAACACACACACACACACAC 59.260 45.455 0.00 0.00 0.00 3.82
2100 4721 3.046968 AGTAACACACACACACACACA 57.953 42.857 0.00 0.00 0.00 3.72
2101 4722 5.522460 AGATTAGTAACACACACACACACAC 59.478 40.000 0.00 0.00 0.00 3.82
2102 4723 5.522097 CAGATTAGTAACACACACACACACA 59.478 40.000 0.00 0.00 0.00 3.72
2103 4724 5.751509 TCAGATTAGTAACACACACACACAC 59.248 40.000 0.00 0.00 0.00 3.82
2104 4725 5.908341 TCAGATTAGTAACACACACACACA 58.092 37.500 0.00 0.00 0.00 3.72
2105 4726 6.838198 TTCAGATTAGTAACACACACACAC 57.162 37.500 0.00 0.00 0.00 3.82
2106 4727 7.045416 ACTTTCAGATTAGTAACACACACACA 58.955 34.615 0.00 0.00 0.00 3.72
2107 4728 7.478520 ACTTTCAGATTAGTAACACACACAC 57.521 36.000 0.00 0.00 0.00 3.82
2108 4729 6.419710 CGACTTTCAGATTAGTAACACACACA 59.580 38.462 0.00 0.00 0.00 3.72
2109 4730 6.639686 TCGACTTTCAGATTAGTAACACACAC 59.360 38.462 0.00 0.00 0.00 3.82
2110 4731 6.741109 TCGACTTTCAGATTAGTAACACACA 58.259 36.000 0.00 0.00 0.00 3.72
2111 4732 7.359014 GGTTCGACTTTCAGATTAGTAACACAC 60.359 40.741 0.00 0.00 0.00 3.82
2112 4733 6.643770 GGTTCGACTTTCAGATTAGTAACACA 59.356 38.462 0.00 0.00 0.00 3.72
2113 4734 6.867293 AGGTTCGACTTTCAGATTAGTAACAC 59.133 38.462 0.00 0.00 0.00 3.32
2114 4735 6.989659 AGGTTCGACTTTCAGATTAGTAACA 58.010 36.000 0.00 0.00 0.00 2.41
2115 4736 8.976986 TTAGGTTCGACTTTCAGATTAGTAAC 57.023 34.615 0.00 0.00 0.00 2.50
2226 4847 4.391830 GCTGAACAGTCATTCCGTGATAAA 59.608 41.667 3.77 0.00 39.48 1.40
2234 4855 1.808945 CAGTGGCTGAACAGTCATTCC 59.191 52.381 12.15 0.45 45.65 3.01


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

AutoCloner maintained by Alex Coulton.