Multiple sequence alignment - TraesCS1A01G312400

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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 TraesCS1A01G312400 chr1A 100.000 4537 0 0 1 4537 504312343 504316879 0.000000e+00 8379.0
1 TraesCS1A01G312400 chr1A 80.847 945 111 38 2987 3896 504406379 504407288 0.000000e+00 678.0
2 TraesCS1A01G312400 chr1A 85.380 684 64 16 3096 3773 504418844 504419497 0.000000e+00 676.0
3 TraesCS1A01G312400 chr1A 80.469 384 46 23 3450 3833 504519545 504519899 2.690000e-67 267.0
4 TraesCS1A01G312400 chr1A 80.786 229 27 15 4014 4231 569488650 569488428 3.630000e-36 163.0
5 TraesCS1A01G312400 chr1A 84.932 146 20 2 57 200 328258711 328258856 3.660000e-31 147.0
6 TraesCS1A01G312400 chr1A 83.007 153 21 5 52 200 397108097 397108248 2.850000e-27 134.0
7 TraesCS1A01G312400 chr1A 93.548 62 4 0 3830 3891 504521214 504521275 4.830000e-15 93.5
8 TraesCS1A01G312400 chr1A 91.667 60 5 0 3832 3891 504440775 504440834 2.910000e-12 84.2
9 TraesCS1A01G312400 chr1D 91.341 2506 115 35 1 2464 408431307 408433752 0.000000e+00 3332.0
10 TraesCS1A01G312400 chr1D 88.112 1430 93 33 2470 3876 408433828 408435203 0.000000e+00 1628.0
11 TraesCS1A01G312400 chr1D 85.119 672 53 24 3197 3852 408454078 408454718 1.060000e-180 643.0
12 TraesCS1A01G312400 chr1D 98.361 61 1 0 3908 3968 408435203 408435263 1.730000e-19 108.0
13 TraesCS1A01G312400 chr1B 90.385 1768 126 18 2211 3969 549610737 549612469 0.000000e+00 2283.0
14 TraesCS1A01G312400 chr1B 89.418 1134 53 27 1004 2103 549518332 549519432 0.000000e+00 1367.0
15 TraesCS1A01G312400 chr1B 89.057 923 64 12 3053 3966 549520553 549521447 0.000000e+00 1110.0
16 TraesCS1A01G312400 chr1B 82.867 893 94 36 3102 3969 549733439 549734297 0.000000e+00 747.0
17 TraesCS1A01G312400 chr1B 86.379 602 51 16 3124 3720 549635476 549636051 2.980000e-176 628.0
18 TraesCS1A01G312400 chr1B 87.500 576 15 16 345 899 549517409 549517948 3.000000e-171 612.0
19 TraesCS1A01G312400 chr1B 97.248 327 9 0 2729 3055 549520145 549520471 5.130000e-154 555.0
20 TraesCS1A01G312400 chr1B 94.429 359 14 3 2134 2490 549519431 549519785 8.580000e-152 547.0
21 TraesCS1A01G312400 chr1B 91.393 244 18 2 2485 2728 549519820 549520060 9.410000e-87 331.0
22 TraesCS1A01G312400 chr1B 89.105 257 24 2 3327 3579 549703947 549704203 2.630000e-82 316.0
23 TraesCS1A01G312400 chr1B 87.500 224 26 2 2486 2707 549719202 549719425 1.620000e-64 257.0
24 TraesCS1A01G312400 chr1B 89.634 164 12 4 2676 2838 549722102 549722261 2.140000e-48 204.0
25 TraesCS1A01G312400 chr1B 83.425 181 17 9 3681 3852 549705837 549706013 6.080000e-34 156.0
26 TraesCS1A01G312400 chr1B 92.045 88 7 0 3804 3891 549636052 549636139 1.710000e-24 124.0
27 TraesCS1A01G312400 chr7A 93.299 582 28 3 3967 4537 539997988 539997407 0.000000e+00 848.0
28 TraesCS1A01G312400 chr7A 93.431 137 7 2 3966 4100 539992638 539992502 7.700000e-48 202.0
29 TraesCS1A01G312400 chr7A 82.386 176 17 10 3966 4133 40852662 40852831 1.700000e-29 141.0
30 TraesCS1A01G312400 chr7A 84.106 151 18 6 56 203 40986858 40986711 1.700000e-29 141.0
31 TraesCS1A01G312400 chr3D 86.644 599 75 3 1060 1657 437218219 437217625 0.000000e+00 658.0
32 TraesCS1A01G312400 chr3D 77.448 572 124 3 1069 1639 575129812 575129245 2.020000e-88 337.0
33 TraesCS1A01G312400 chr3D 81.860 215 23 14 4014 4217 441198638 441198847 2.810000e-37 167.0
34 TraesCS1A01G312400 chr3B 86.455 598 76 3 1060 1656 572488198 572487605 0.000000e+00 651.0
35 TraesCS1A01G312400 chr3B 78.284 571 121 1 1069 1639 764693729 764694296 9.280000e-97 364.0
36 TraesCS1A01G312400 chr3B 80.198 202 23 15 3966 4158 113922443 113922636 7.920000e-28 135.0
37 TraesCS1A01G312400 chr3A 86.455 598 76 3 1060 1656 575314269 575313676 0.000000e+00 651.0
38 TraesCS1A01G312400 chr3A 77.622 572 123 3 1069 1639 710274395 710274962 4.350000e-90 342.0
39 TraesCS1A01G312400 chr7B 76.817 578 78 34 3967 4519 715711202 715710656 1.610000e-69 274.0
40 TraesCS1A01G312400 chrUn 83.721 215 19 14 3965 4173 328744683 328744887 5.990000e-44 189.0
41 TraesCS1A01G312400 chrUn 85.616 146 19 2 57 200 379959502 379959357 7.860000e-33 152.0
42 TraesCS1A01G312400 chr5D 81.778 225 26 13 3997 4212 483615065 483615283 1.680000e-39 174.0
43 TraesCS1A01G312400 chr5A 83.756 197 18 11 3967 4158 554072957 554073144 1.680000e-39 174.0
44 TraesCS1A01G312400 chr5A 85.632 174 13 10 3966 4133 326959217 326959050 6.030000e-39 172.0
45 TraesCS1A01G312400 chr4D 82.524 206 26 9 4014 4212 389498014 389498216 6.030000e-39 172.0
46 TraesCS1A01G312400 chr6D 82.212 208 24 12 4014 4212 465775639 465775436 2.810000e-37 167.0
47 TraesCS1A01G312400 chr2A 86.301 146 18 2 57 200 539305007 539305152 1.690000e-34 158.0
48 TraesCS1A01G312400 chr2A 84.932 146 19 3 57 200 188909276 188909420 1.320000e-30 145.0
49 TraesCS1A01G312400 chr2B 85.161 155 20 2 57 208 76026646 76026492 6.080000e-34 156.0
50 TraesCS1A01G312400 chr7D 83.019 159 21 5 54 208 614392834 614392990 6.120000e-29 139.0
51 TraesCS1A01G312400 chr5B 83.117 154 22 4 49 200 445493384 445493535 2.200000e-28 137.0


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 TraesCS1A01G312400 chr1A 504312343 504316879 4536 False 8379.000000 8379 100.000000 1 4537 1 chr1A.!!$F3 4536
1 TraesCS1A01G312400 chr1A 504406379 504407288 909 False 678.000000 678 80.847000 2987 3896 1 chr1A.!!$F4 909
2 TraesCS1A01G312400 chr1A 504418844 504419497 653 False 676.000000 676 85.380000 3096 3773 1 chr1A.!!$F5 677
3 TraesCS1A01G312400 chr1D 408431307 408435263 3956 False 1689.333333 3332 92.604667 1 3968 3 chr1D.!!$F2 3967
4 TraesCS1A01G312400 chr1D 408454078 408454718 640 False 643.000000 643 85.119000 3197 3852 1 chr1D.!!$F1 655
5 TraesCS1A01G312400 chr1B 549610737 549612469 1732 False 2283.000000 2283 90.385000 2211 3969 1 chr1B.!!$F1 1758
6 TraesCS1A01G312400 chr1B 549517409 549521447 4038 False 753.666667 1367 91.507500 345 3966 6 chr1B.!!$F3 3621
7 TraesCS1A01G312400 chr1B 549733439 549734297 858 False 747.000000 747 82.867000 3102 3969 1 chr1B.!!$F2 867
8 TraesCS1A01G312400 chr1B 549635476 549636139 663 False 376.000000 628 89.212000 3124 3891 2 chr1B.!!$F4 767
9 TraesCS1A01G312400 chr1B 549703947 549706013 2066 False 236.000000 316 86.265000 3327 3852 2 chr1B.!!$F5 525
10 TraesCS1A01G312400 chr1B 549719202 549722261 3059 False 230.500000 257 88.567000 2486 2838 2 chr1B.!!$F6 352
11 TraesCS1A01G312400 chr7A 539997407 539997988 581 True 848.000000 848 93.299000 3967 4537 1 chr7A.!!$R3 570
12 TraesCS1A01G312400 chr3D 437217625 437218219 594 True 658.000000 658 86.644000 1060 1657 1 chr3D.!!$R1 597
13 TraesCS1A01G312400 chr3D 575129245 575129812 567 True 337.000000 337 77.448000 1069 1639 1 chr3D.!!$R2 570
14 TraesCS1A01G312400 chr3B 572487605 572488198 593 True 651.000000 651 86.455000 1060 1656 1 chr3B.!!$R1 596
15 TraesCS1A01G312400 chr3B 764693729 764694296 567 False 364.000000 364 78.284000 1069 1639 1 chr3B.!!$F2 570
16 TraesCS1A01G312400 chr3A 575313676 575314269 593 True 651.000000 651 86.455000 1060 1656 1 chr3A.!!$R1 596
17 TraesCS1A01G312400 chr3A 710274395 710274962 567 False 342.000000 342 77.622000 1069 1639 1 chr3A.!!$F1 570
18 TraesCS1A01G312400 chr7B 715710656 715711202 546 True 274.000000 274 76.817000 3967 4519 1 chr7B.!!$R1 552

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
279 286 0.388907 TAGGCGTCTGCGTTTGTACC 60.389 55.000 0.00 0.00 44.10 3.34 F
650 677 0.818296 GCTCTCCTGTAGAAGCGGAA 59.182 55.000 0.00 0.00 32.46 4.30 F
652 679 1.202200 CTCTCCTGTAGAAGCGGAACG 60.202 57.143 0.00 0.00 45.51 3.95 F
2276 2624 1.005037 AAACGCTCGCATCTGTGGA 60.005 52.632 0.00 0.00 0.00 4.02 F
3045 6265 0.949105 ACAGGTTTGTGTCGCGATCC 60.949 55.000 14.06 6.55 35.83 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2276 2624 0.036022 GCTTCCTCCACTTGTCAGCT 59.964 55.0 0.00 0.0 0.00 4.24 R
2277 2625 0.957888 GGCTTCCTCCACTTGTCAGC 60.958 60.0 0.00 0.0 0.00 4.26 R
2594 3018 2.155924 GCAAGTAGCGTGTGAAAGAGAC 59.844 50.0 0.00 0.0 0.00 3.36 R
3388 6712 0.034089 GGTACCAAGCTCCCTGCAAT 60.034 55.0 7.15 0.0 45.94 3.56 R
3858 8783 0.458716 GAACTACAGGCGTCCTCTGC 60.459 60.0 0.00 0.0 35.78 4.26 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
38 39 5.471257 GTTGAAGACGAATAGGAAGTCTGT 58.529 41.667 0.00 0.00 43.60 3.41
56 57 4.629200 GTCTGTAAGTTGAAGATGAGCAGG 59.371 45.833 0.00 0.00 33.76 4.85
61 62 1.129437 GTTGAAGATGAGCAGGCGAAC 59.871 52.381 0.00 0.00 0.00 3.95
66 67 0.955428 GATGAGCAGGCGAACCAACA 60.955 55.000 0.00 0.00 39.06 3.33
70 71 1.081242 GCAGGCGAACCAACATGTG 60.081 57.895 0.00 0.00 39.06 3.21
86 87 4.934356 ACATGTGGTTGGATTGTTAGGAT 58.066 39.130 0.00 0.00 0.00 3.24
87 88 6.073447 ACATGTGGTTGGATTGTTAGGATA 57.927 37.500 0.00 0.00 0.00 2.59
90 91 5.882040 TGTGGTTGGATTGTTAGGATAACA 58.118 37.500 0.00 0.00 0.00 2.41
93 94 5.943416 TGGTTGGATTGTTAGGATAACAGTG 59.057 40.000 2.85 0.00 0.00 3.66
94 95 5.357032 GGTTGGATTGTTAGGATAACAGTGG 59.643 44.000 2.85 0.00 0.00 4.00
95 96 5.772393 TGGATTGTTAGGATAACAGTGGT 57.228 39.130 2.85 0.00 0.00 4.16
96 97 6.877668 TGGATTGTTAGGATAACAGTGGTA 57.122 37.500 2.85 0.00 0.00 3.25
97 98 7.446106 TGGATTGTTAGGATAACAGTGGTAT 57.554 36.000 0.00 0.00 0.00 2.73
103 104 3.318313 AGGATAACAGTGGTATCCCCAG 58.682 50.000 34.28 0.00 46.45 4.45
106 107 1.571773 AACAGTGGTATCCCCAGCCC 61.572 60.000 0.00 0.00 46.45 5.19
108 109 2.001269 AGTGGTATCCCCAGCCCAC 61.001 63.158 0.00 0.00 46.45 4.61
113 114 3.281975 TATCCCCAGCCCACCAGGT 62.282 63.158 0.00 0.00 38.26 4.00
118 119 1.604593 CCAGCCCACCAGGTTTCAG 60.605 63.158 0.00 0.00 38.26 3.02
119 120 1.604593 CAGCCCACCAGGTTTCAGG 60.605 63.158 0.00 0.00 38.26 3.86
123 124 1.074951 CCACCAGGTTTCAGGTCCC 59.925 63.158 0.00 0.00 35.52 4.46
139 140 2.561373 CCGGTGCTCGCCTTTTTC 59.439 61.111 0.00 0.00 37.59 2.29
140 141 1.966451 CCGGTGCTCGCCTTTTTCT 60.966 57.895 0.00 0.00 37.59 2.52
141 142 1.207593 CGGTGCTCGCCTTTTTCTG 59.792 57.895 0.00 0.00 0.00 3.02
142 143 1.581447 GGTGCTCGCCTTTTTCTGG 59.419 57.895 0.00 0.00 0.00 3.86
143 144 0.889186 GGTGCTCGCCTTTTTCTGGA 60.889 55.000 0.00 0.00 0.00 3.86
151 154 5.516696 GCTCGCCTTTTTCTGGATTTATTTC 59.483 40.000 0.00 0.00 0.00 2.17
158 161 9.948964 CCTTTTTCTGGATTTATTTCAGGATTT 57.051 29.630 0.00 0.00 0.00 2.17
162 165 9.723601 TTTCTGGATTTATTTCAGGATTTTTGG 57.276 29.630 0.00 0.00 0.00 3.28
168 171 8.871686 ATTTATTTCAGGATTTTTGGCGATAC 57.128 30.769 0.00 0.00 0.00 2.24
169 172 5.913137 ATTTCAGGATTTTTGGCGATACA 57.087 34.783 0.00 0.00 0.00 2.29
170 173 5.913137 TTTCAGGATTTTTGGCGATACAT 57.087 34.783 0.00 0.00 0.00 2.29
179 182 2.022764 TGGCGATACATGTTCAGTGG 57.977 50.000 2.30 0.00 0.00 4.00
180 183 1.299541 GGCGATACATGTTCAGTGGG 58.700 55.000 2.30 0.00 0.00 4.61
184 187 3.678806 GCGATACATGTTCAGTGGGAGAA 60.679 47.826 2.30 0.00 0.00 2.87
192 195 2.801111 GTTCAGTGGGAGAAGACGTTTC 59.199 50.000 0.00 0.00 0.00 2.78
210 213 2.626780 CCGTCGACTGAGGTGCTCA 61.627 63.158 14.70 0.00 38.25 4.26
220 223 1.291033 TGAGGTGCTCATAGGGGTAGT 59.709 52.381 0.00 0.00 35.39 2.73
223 226 1.413077 GGTGCTCATAGGGGTAGTGTC 59.587 57.143 0.00 0.00 0.00 3.67
226 229 4.153411 GTGCTCATAGGGGTAGTGTCTAT 58.847 47.826 0.00 0.00 0.00 1.98
238 245 7.070821 AGGGGTAGTGTCTATGTGTTTATAAGG 59.929 40.741 0.00 0.00 0.00 2.69
239 246 7.070322 GGGGTAGTGTCTATGTGTTTATAAGGA 59.930 40.741 0.00 0.00 0.00 3.36
240 247 8.648693 GGGTAGTGTCTATGTGTTTATAAGGAT 58.351 37.037 0.00 0.00 0.00 3.24
273 280 3.438087 ACGTATATATAGGCGTCTGCGTT 59.562 43.478 0.00 0.00 44.10 4.84
275 282 4.262277 CGTATATATAGGCGTCTGCGTTTG 59.738 45.833 0.00 0.00 44.10 2.93
278 285 1.636988 ATAGGCGTCTGCGTTTGTAC 58.363 50.000 0.00 0.00 44.10 2.90
279 286 0.388907 TAGGCGTCTGCGTTTGTACC 60.389 55.000 0.00 0.00 44.10 3.34
282 289 1.485514 CGTCTGCGTTTGTACCGTG 59.514 57.895 0.00 0.00 0.00 4.94
283 290 1.203313 GTCTGCGTTTGTACCGTGC 59.797 57.895 0.00 0.00 0.00 5.34
290 297 2.159881 GCGTTTGTACCGTGCTCTAAAG 60.160 50.000 0.00 0.00 0.00 1.85
292 299 3.737266 CGTTTGTACCGTGCTCTAAAGAA 59.263 43.478 0.00 0.00 0.00 2.52
306 313 8.345565 GTGCTCTAAAGAAAAGTTGAAGATGAA 58.654 33.333 0.00 0.00 0.00 2.57
317 324 9.594478 AAAAGTTGAAGATGAACCGTTAAATTT 57.406 25.926 0.00 0.00 0.00 1.82
322 329 8.964420 TGAAGATGAACCGTTAAATTTCAATC 57.036 30.769 0.00 0.00 33.13 2.67
324 331 7.141100 AGATGAACCGTTAAATTTCAATCGT 57.859 32.000 0.00 0.00 33.13 3.73
373 380 7.350110 ACAAAATTATTTTCATGCAACCGAG 57.650 32.000 0.00 0.00 0.00 4.63
376 383 8.494347 CAAAATTATTTTCATGCAACCGAGAAA 58.506 29.630 0.00 0.00 0.00 2.52
378 385 9.868277 AAATTATTTTCATGCAACCGAGAAATA 57.132 25.926 0.00 0.24 30.92 1.40
390 403 3.199071 ACCGAGAAATAATGTGGCCAGTA 59.801 43.478 5.11 0.00 0.00 2.74
395 408 6.347969 CGAGAAATAATGTGGCCAGTATGATG 60.348 42.308 5.11 0.00 39.69 3.07
406 428 1.004610 CAGTATGATGTTTGCGAGCGG 60.005 52.381 0.00 0.00 39.69 5.52
499 521 4.570663 CCCGTCCGTCGCCATCTC 62.571 72.222 0.00 0.00 38.35 2.75
650 677 0.818296 GCTCTCCTGTAGAAGCGGAA 59.182 55.000 0.00 0.00 32.46 4.30
651 678 1.470112 GCTCTCCTGTAGAAGCGGAAC 60.470 57.143 0.00 0.00 32.46 3.62
652 679 1.202200 CTCTCCTGTAGAAGCGGAACG 60.202 57.143 0.00 0.00 45.51 3.95
653 680 4.397731 CTCTCCTGTAGAAGCGGAACGG 62.398 59.091 0.00 0.00 43.62 4.44
698 725 1.923227 GCTCGCCAACTTTACTGCCC 61.923 60.000 0.00 0.00 0.00 5.36
805 832 2.503809 CAATTCAAACGGGCGGCG 60.504 61.111 0.51 0.51 0.00 6.46
1044 1352 3.160748 GGAGCAGGAGGAGGAGGC 61.161 72.222 0.00 0.00 0.00 4.70
1531 1839 3.467226 TGTTCGGGGAGATCGGGC 61.467 66.667 0.00 0.00 0.00 6.13
1713 2029 8.472007 TGGTTGATACTTTCTTTTGGTTACAT 57.528 30.769 0.00 0.00 0.00 2.29
1732 2048 4.780815 ACATCAAATCCGGAGCTGAATAA 58.219 39.130 19.12 0.76 0.00 1.40
1896 2244 6.072452 TGTCTACAGCACATTCTCTATATCCG 60.072 42.308 0.00 0.00 0.00 4.18
1901 2249 7.093354 ACAGCACATTCTCTATATCCGTTATG 58.907 38.462 0.00 0.00 0.00 1.90
1932 2280 5.918608 TGAAGAGCTAGTTAATGCCCTTAG 58.081 41.667 0.00 0.00 27.62 2.18
1977 2325 2.884012 CCAAGTGTTATGTCCTGCAACA 59.116 45.455 0.00 0.00 0.00 3.33
2069 2417 9.471084 GAATAATAAGCAGTCTAGTTTCCTCTC 57.529 37.037 0.00 0.00 0.00 3.20
2147 2495 2.716217 ACTGCAATTTAGGCTCTGACC 58.284 47.619 0.00 0.00 0.00 4.02
2174 2522 8.567285 TGTTTTGTTTGTCATGGGTTTTATTT 57.433 26.923 0.00 0.00 0.00 1.40
2175 2523 9.667107 TGTTTTGTTTGTCATGGGTTTTATTTA 57.333 25.926 0.00 0.00 0.00 1.40
2213 2561 8.997323 GTTCCATTGGAGAATATTCTGTATCTG 58.003 37.037 22.61 12.15 37.73 2.90
2240 2588 4.500375 GGCCCTAACATTGCATCTGAAATC 60.500 45.833 0.00 0.00 0.00 2.17
2276 2624 1.005037 AAACGCTCGCATCTGTGGA 60.005 52.632 0.00 0.00 0.00 4.02
2277 2625 1.016130 AAACGCTCGCATCTGTGGAG 61.016 55.000 0.00 0.00 0.00 3.86
2339 2687 4.037208 CAGCCTCATTTCATTGTATGGGAC 59.963 45.833 3.87 0.00 0.00 4.46
2475 2857 7.881751 TGCCTCATATTATCTTGATCAGGAAAG 59.118 37.037 11.98 0.00 0.00 2.62
2594 3018 6.671190 TCTACTGTTTCTTGCATTGATGTTG 58.329 36.000 0.00 0.00 0.00 3.33
2695 5832 7.816640 TGAATTCAGTATTAAACTTGGCAGAC 58.183 34.615 3.38 0.00 35.76 3.51
2700 5837 7.390823 TCAGTATTAAACTTGGCAGACATGTA 58.609 34.615 0.00 0.00 35.76 2.29
2757 5977 3.504520 TGGCCTAATCTTTCAACGGTTTC 59.495 43.478 3.32 0.00 0.00 2.78
2846 6066 4.351192 CAGTGTACTTTTCACTTTGCACC 58.649 43.478 0.00 0.00 43.14 5.01
2873 6093 6.298361 TGAAATGATATACATCACCCACCTG 58.702 40.000 0.00 0.00 43.89 4.00
3045 6265 0.949105 ACAGGTTTGTGTCGCGATCC 60.949 55.000 14.06 6.55 35.83 3.36
3128 6441 6.038271 TGCTAAGTTCTCTGTGTTCTTTTTCC 59.962 38.462 0.00 0.00 0.00 3.13
3131 6444 4.640647 AGTTCTCTGTGTTCTTTTTCCACC 59.359 41.667 0.00 0.00 0.00 4.61
3256 6569 4.055360 TGTGTCCGATACTCAAAACACTG 58.945 43.478 0.00 0.00 38.22 3.66
3309 6622 5.178096 TCTTGCTTCTTGGATCACCATTA 57.822 39.130 0.00 0.00 46.34 1.90
3378 6702 4.449068 ACAGCTGTCTGAATTTTCTGTACG 59.551 41.667 15.25 0.00 42.95 3.67
3388 6712 7.386573 TCTGAATTTTCTGTACGACTTATGCAA 59.613 33.333 0.00 0.00 0.00 4.08
3425 6749 1.425066 ACCAGTTCCATTCTTGAGGCA 59.575 47.619 0.00 0.00 0.00 4.75
3556 6881 7.605410 TGTAGTAGTTGCAGCCTTTATTTAC 57.395 36.000 0.00 0.00 0.00 2.01
3617 8203 2.428622 GGTGTACCCCGCAAGTGT 59.571 61.111 0.00 0.00 0.00 3.55
3622 8208 3.321682 GGTGTACCCCGCAAGTGTATATA 59.678 47.826 0.00 0.00 0.00 0.86
3624 8210 5.185635 GGTGTACCCCGCAAGTGTATATATA 59.814 44.000 0.00 0.00 0.00 0.86
3627 8213 8.636213 GTGTACCCCGCAAGTGTATATATATAT 58.364 37.037 10.10 10.10 0.00 0.86
3628 8214 9.865152 TGTACCCCGCAAGTGTATATATATATA 57.135 33.333 8.16 8.16 0.00 0.86
3799 8698 2.418334 GGGAAACGAGGTACCTGTGATC 60.418 54.545 22.10 17.20 0.00 2.92
3800 8699 2.496470 GGAAACGAGGTACCTGTGATCT 59.504 50.000 22.10 0.00 0.00 2.75
3808 8707 5.643777 CGAGGTACCTGTGATCTTTTTGAAT 59.356 40.000 22.10 0.00 0.00 2.57
3849 8774 4.681483 GCTTTAGTTGATTGGCAGTGTTTC 59.319 41.667 0.00 0.00 0.00 2.78
3858 8783 2.575532 TGGCAGTGTTTCCTTCAGAAG 58.424 47.619 2.78 2.78 35.40 2.85
3891 8816 7.013942 ACGCCTGTAGTTCTGTATATGTAATGA 59.986 37.037 0.00 0.00 0.00 2.57
3990 8932 8.428063 AGTGTTAGACTGTATATACGTACCTCT 58.572 37.037 8.33 5.84 31.75 3.69
4011 8953 7.057894 CCTCTGTACCTCTCTGTATATATCCC 58.942 46.154 0.00 0.00 0.00 3.85
4027 8969 9.765795 GTATATATCCCATATTGTACCTCTTGC 57.234 37.037 0.00 0.00 0.00 4.01
4033 8975 6.157994 TCCCATATTGTACCTCTTGCTACTTT 59.842 38.462 0.00 0.00 0.00 2.66
4079 9037 0.468226 TCAGGGTGTCGAGCAGTTTT 59.532 50.000 0.00 0.00 0.00 2.43
4093 9052 5.296813 AGCAGTTTTCCAAACATATCGTC 57.703 39.130 2.38 0.00 0.00 4.20
4195 9163 4.400961 GGCGCCAGCTCCTGTCTT 62.401 66.667 24.80 0.00 44.37 3.01
4212 9180 4.722535 TGCCCTTCCTCGCCTCCT 62.723 66.667 0.00 0.00 0.00 3.69
4334 9308 1.352156 GCTCGACCAACCACATCGTC 61.352 60.000 0.00 0.00 37.16 4.20
4523 9515 2.490217 CCGCTCCAGGACGTACTG 59.510 66.667 21.53 21.53 38.21 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.178912 TTCGTCTTCAACCATGACCC 57.821 50.000 0.00 0.00 34.61 4.46
9 10 4.755411 TCCTATTCGTCTTCAACCATGAC 58.245 43.478 0.00 0.00 34.61 3.06
12 13 5.187967 AGACTTCCTATTCGTCTTCAACCAT 59.812 40.000 0.00 0.00 34.55 3.55
13 14 4.527038 AGACTTCCTATTCGTCTTCAACCA 59.473 41.667 0.00 0.00 34.55 3.67
38 39 2.233676 TCGCCTGCTCATCTTCAACTTA 59.766 45.455 0.00 0.00 0.00 2.24
66 67 6.489603 TGTTATCCTAACAATCCAACCACAT 58.510 36.000 0.00 0.00 0.00 3.21
70 71 5.357032 CCACTGTTATCCTAACAATCCAACC 59.643 44.000 1.80 0.00 0.00 3.77
94 95 2.757124 CCTGGTGGGCTGGGGATAC 61.757 68.421 0.00 0.00 0.00 2.24
95 96 2.368192 CCTGGTGGGCTGGGGATA 60.368 66.667 0.00 0.00 0.00 2.59
96 97 4.701437 ACCTGGTGGGCTGGGGAT 62.701 66.667 0.00 0.00 39.10 3.85
97 98 4.938756 AACCTGGTGGGCTGGGGA 62.939 66.667 0.00 0.00 39.10 4.81
103 104 1.603739 GACCTGAAACCTGGTGGGC 60.604 63.158 0.00 0.00 36.22 5.36
106 107 1.302511 CGGGACCTGAAACCTGGTG 60.303 63.158 0.00 0.00 36.22 4.17
108 109 2.351276 CCGGGACCTGAAACCTGG 59.649 66.667 0.31 0.00 44.78 4.45
113 114 2.747686 GAGCACCGGGACCTGAAA 59.252 61.111 6.32 0.00 0.00 2.69
119 120 4.699522 AAAGGCGAGCACCGGGAC 62.700 66.667 6.32 0.00 39.04 4.46
123 124 1.207593 CAGAAAAAGGCGAGCACCG 59.792 57.895 0.00 0.00 42.21 4.94
132 133 9.948964 AAATCCTGAAATAAATCCAGAAAAAGG 57.051 29.630 0.00 0.00 0.00 3.11
139 140 6.256321 CGCCAAAAATCCTGAAATAAATCCAG 59.744 38.462 0.00 0.00 0.00 3.86
140 141 6.071108 TCGCCAAAAATCCTGAAATAAATCCA 60.071 34.615 0.00 0.00 0.00 3.41
141 142 6.337356 TCGCCAAAAATCCTGAAATAAATCC 58.663 36.000 0.00 0.00 0.00 3.01
142 143 8.968242 GTATCGCCAAAAATCCTGAAATAAATC 58.032 33.333 0.00 0.00 0.00 2.17
143 144 8.474025 TGTATCGCCAAAAATCCTGAAATAAAT 58.526 29.630 0.00 0.00 0.00 1.40
151 154 4.637483 ACATGTATCGCCAAAAATCCTG 57.363 40.909 0.00 0.00 0.00 3.86
158 161 2.746904 CCACTGAACATGTATCGCCAAA 59.253 45.455 0.00 0.00 0.00 3.28
160 163 1.406751 CCCACTGAACATGTATCGCCA 60.407 52.381 0.00 0.00 0.00 5.69
162 165 2.159099 TCTCCCACTGAACATGTATCGC 60.159 50.000 0.00 0.00 0.00 4.58
168 171 2.289072 ACGTCTTCTCCCACTGAACATG 60.289 50.000 0.00 0.00 0.00 3.21
169 172 1.971357 ACGTCTTCTCCCACTGAACAT 59.029 47.619 0.00 0.00 0.00 2.71
170 173 1.410004 ACGTCTTCTCCCACTGAACA 58.590 50.000 0.00 0.00 0.00 3.18
192 195 1.938657 ATGAGCACCTCAGTCGACGG 61.939 60.000 10.46 10.03 44.08 4.79
210 213 9.664777 TTATAAACACATAGACACTACCCCTAT 57.335 33.333 0.00 0.00 0.00 2.57
244 251 8.929746 GCAGACGCCTATATATACGTATATACA 58.070 37.037 28.95 20.80 39.16 2.29
245 252 8.106956 CGCAGACGCCTATATATACGTATATAC 58.893 40.741 28.95 18.62 39.16 1.47
246 253 7.814587 ACGCAGACGCCTATATATACGTATATA 59.185 37.037 28.67 28.67 45.53 0.86
247 254 6.648310 ACGCAGACGCCTATATATACGTATAT 59.352 38.462 26.67 26.67 45.53 0.86
248 255 5.985530 ACGCAGACGCCTATATATACGTATA 59.014 40.000 17.24 17.24 45.53 1.47
249 256 4.813161 ACGCAGACGCCTATATATACGTAT 59.187 41.667 13.54 13.54 45.53 3.06
250 257 4.183865 ACGCAGACGCCTATATATACGTA 58.816 43.478 8.02 0.00 45.53 3.57
251 258 3.005554 ACGCAGACGCCTATATATACGT 58.994 45.455 7.83 7.83 45.53 3.57
252 259 3.670311 ACGCAGACGCCTATATATACG 57.330 47.619 2.20 2.20 45.53 3.06
253 260 5.159209 ACAAACGCAGACGCCTATATATAC 58.841 41.667 0.00 0.00 45.53 1.47
254 261 5.381174 ACAAACGCAGACGCCTATATATA 57.619 39.130 0.00 0.00 45.53 0.86
255 262 4.252971 ACAAACGCAGACGCCTATATAT 57.747 40.909 0.00 0.00 45.53 0.86
256 263 3.720949 ACAAACGCAGACGCCTATATA 57.279 42.857 0.00 0.00 45.53 0.86
257 264 2.596904 ACAAACGCAGACGCCTATAT 57.403 45.000 0.00 0.00 45.53 0.86
258 265 2.480073 GGTACAAACGCAGACGCCTATA 60.480 50.000 0.00 0.00 45.53 1.31
259 266 1.636988 GTACAAACGCAGACGCCTAT 58.363 50.000 0.00 0.00 45.53 2.57
260 267 0.388907 GGTACAAACGCAGACGCCTA 60.389 55.000 0.00 0.00 45.53 3.93
261 268 1.666872 GGTACAAACGCAGACGCCT 60.667 57.895 0.00 0.00 45.53 5.52
262 269 2.858158 GGTACAAACGCAGACGCC 59.142 61.111 0.00 0.00 45.53 5.68
265 272 1.203313 GCACGGTACAAACGCAGAC 59.797 57.895 0.00 0.00 34.00 3.51
267 274 0.944311 AGAGCACGGTACAAACGCAG 60.944 55.000 0.00 0.00 34.00 5.18
268 275 0.314618 TAGAGCACGGTACAAACGCA 59.685 50.000 0.00 0.00 34.00 5.24
273 280 5.362263 ACTTTTCTTTAGAGCACGGTACAA 58.638 37.500 0.00 0.00 0.00 2.41
275 282 5.464389 TCAACTTTTCTTTAGAGCACGGTAC 59.536 40.000 0.00 0.00 0.00 3.34
278 285 5.236478 TCTTCAACTTTTCTTTAGAGCACGG 59.764 40.000 0.00 0.00 0.00 4.94
279 286 6.287107 TCTTCAACTTTTCTTTAGAGCACG 57.713 37.500 0.00 0.00 0.00 5.34
282 289 7.805542 GGTTCATCTTCAACTTTTCTTTAGAGC 59.194 37.037 0.00 0.00 0.00 4.09
283 290 8.012241 CGGTTCATCTTCAACTTTTCTTTAGAG 58.988 37.037 0.00 0.00 0.00 2.43
290 297 8.797266 ATTTAACGGTTCATCTTCAACTTTTC 57.203 30.769 0.00 0.00 0.00 2.29
292 299 9.244799 GAAATTTAACGGTTCATCTTCAACTTT 57.755 29.630 0.00 0.00 0.00 2.66
306 313 4.789784 CCACACGATTGAAATTTAACGGT 58.210 39.130 0.00 0.00 0.00 4.83
317 324 1.403814 TTTTTGGGCCACACGATTGA 58.596 45.000 5.23 0.00 0.00 2.57
355 362 9.299963 CATTATTTCTCGGTTGCATGAAAATAA 57.700 29.630 0.00 15.81 33.09 1.40
370 377 5.056480 TCATACTGGCCACATTATTTCTCG 58.944 41.667 0.00 0.00 0.00 4.04
373 380 6.639632 ACATCATACTGGCCACATTATTTC 57.360 37.500 0.00 0.00 0.00 2.17
376 383 5.221303 GCAAACATCATACTGGCCACATTAT 60.221 40.000 0.00 0.00 0.00 1.28
378 385 3.119029 GCAAACATCATACTGGCCACATT 60.119 43.478 0.00 0.00 0.00 2.71
390 403 1.078497 TCCCGCTCGCAAACATCAT 60.078 52.632 0.00 0.00 0.00 2.45
395 408 3.479269 CTCGTCCCGCTCGCAAAC 61.479 66.667 0.00 0.00 0.00 2.93
546 572 1.149627 CCGGGTCAAAACAGGTGGA 59.850 57.895 0.00 0.00 0.00 4.02
650 677 1.816572 GCTTTGTACTGGGGTTTCCGT 60.817 52.381 0.00 0.00 38.76 4.69
651 678 0.879090 GCTTTGTACTGGGGTTTCCG 59.121 55.000 0.00 0.00 38.76 4.30
652 679 1.203013 AGGCTTTGTACTGGGGTTTCC 60.203 52.381 0.00 0.00 0.00 3.13
653 680 2.160205 GAGGCTTTGTACTGGGGTTTC 58.840 52.381 0.00 0.00 0.00 2.78
654 681 1.203013 GGAGGCTTTGTACTGGGGTTT 60.203 52.381 0.00 0.00 0.00 3.27
968 1003 2.760385 ACTAGCTCAGTCCGCCCC 60.760 66.667 0.00 0.00 28.33 5.80
1026 1334 2.445654 CCTCCTCCTCCTGCTCCC 60.446 72.222 0.00 0.00 0.00 4.30
1291 1599 4.803426 GAGCCTGCGGAGGACGTG 62.803 72.222 29.09 0.00 42.93 4.49
1531 1839 1.957877 GATCCTCTCCTTCCAGTACCG 59.042 57.143 0.00 0.00 0.00 4.02
1713 2029 6.773976 AAAATTATTCAGCTCCGGATTTGA 57.226 33.333 3.57 9.44 0.00 2.69
1901 2249 9.670719 GGCATTAACTAGCTCTTCAATTATTTC 57.329 33.333 0.00 0.00 0.00 2.17
1977 2325 0.687354 CCACTACACCAGCTCAAGGT 59.313 55.000 0.00 0.00 40.85 3.50
2054 2402 8.816894 TGAATTAACATGAGAGGAAACTAGACT 58.183 33.333 0.00 0.00 44.43 3.24
2147 2495 6.434018 AAAACCCATGACAAACAAAACATG 57.566 33.333 0.00 0.00 39.51 3.21
2213 2561 0.106015 ATGCAATGTTAGGGCCTCCC 60.106 55.000 10.74 1.53 45.90 4.30
2240 2588 5.245850 GCGTTTGCGTACTCTTTATTGTAG 58.754 41.667 0.00 0.00 40.81 2.74
2276 2624 0.036022 GCTTCCTCCACTTGTCAGCT 59.964 55.000 0.00 0.00 0.00 4.24
2277 2625 0.957888 GGCTTCCTCCACTTGTCAGC 60.958 60.000 0.00 0.00 0.00 4.26
2339 2687 9.761504 ACTTCATGAGTAATGAGATCACTATTG 57.238 33.333 0.00 0.00 46.01 1.90
2475 2857 5.004726 GCAGAAATGGCAATAACGATTTCAC 59.995 40.000 12.44 3.37 37.30 3.18
2569 2993 6.882610 ACATCAATGCAAGAAACAGTAGAA 57.117 33.333 0.00 0.00 0.00 2.10
2594 3018 2.155924 GCAAGTAGCGTGTGAAAGAGAC 59.844 50.000 0.00 0.00 0.00 3.36
2725 5862 8.854117 GTTGAAAGATTAGGCCATGAATAGAAT 58.146 33.333 5.01 0.00 0.00 2.40
2757 5977 4.957971 ACAAGAAAATACGATGTTCAGCG 58.042 39.130 8.87 8.87 0.00 5.18
2846 6066 6.652481 GGTGGGTGATGTATATCATTTCAGAG 59.348 42.308 5.38 0.00 44.62 3.35
3114 6427 4.275936 CCTACAGGTGGAAAAAGAACACAG 59.724 45.833 0.00 0.00 36.87 3.66
3131 6444 1.203523 GACTGCAGAGACACCCTACAG 59.796 57.143 23.35 0.00 0.00 2.74
3256 6569 9.974980 TCCAACCTCTTGATTAAAATTTTGTAC 57.025 29.630 13.76 5.16 0.00 2.90
3309 6622 4.097892 AGAAAAACTGCGACAACAAGGAAT 59.902 37.500 0.00 0.00 0.00 3.01
3388 6712 0.034089 GGTACCAAGCTCCCTGCAAT 60.034 55.000 7.15 0.00 45.94 3.56
3425 6749 3.184379 CGGACATTGATTCATCGCGTATT 59.816 43.478 5.77 0.00 0.00 1.89
3689 8582 3.526534 AGAAGTTTATCTCGCCTTGCTC 58.473 45.455 0.00 0.00 0.00 4.26
3799 8698 7.010091 AGTGGCAACGAGTTTAAATTCAAAAAG 59.990 33.333 10.84 0.00 42.51 2.27
3800 8699 6.814146 AGTGGCAACGAGTTTAAATTCAAAAA 59.186 30.769 10.84 0.00 42.51 1.94
3808 8707 2.294074 AGCAGTGGCAACGAGTTTAAA 58.706 42.857 0.00 0.00 44.61 1.52
3849 8774 0.739112 GCGTCCTCTGCTTCTGAAGG 60.739 60.000 18.38 2.84 0.00 3.46
3858 8783 0.458716 GAACTACAGGCGTCCTCTGC 60.459 60.000 0.00 0.00 35.78 4.26
3916 8857 5.480422 TGGATCTCAAACTAGCACACTCTTA 59.520 40.000 0.00 0.00 0.00 2.10
4033 8975 9.715119 ACAGGTGTGGCTATCTCATATATATAA 57.285 33.333 0.00 0.00 0.00 0.98
4079 9037 5.984725 ACCATGTAAGACGATATGTTTGGA 58.015 37.500 0.00 0.00 0.00 3.53
4093 9052 8.192774 TCGTAACCTAAACTGATACCATGTAAG 58.807 37.037 0.00 0.00 0.00 2.34
4195 9163 4.722535 AGGAGGCGAGGAAGGGCA 62.723 66.667 0.00 0.00 0.00 5.36
4227 9195 4.052518 GGACTGGGCCTGCCACAT 62.053 66.667 10.71 0.00 37.98 3.21
4362 9354 4.109675 GTACATGGGCGGGGCAGT 62.110 66.667 0.00 0.00 0.00 4.40
4397 9389 1.338200 GCATACCCAGACGGATGGATC 60.338 57.143 9.56 0.00 43.57 3.36
4471 9463 1.072806 TCATCACAGGAGCAGCTTGTT 59.927 47.619 0.00 0.00 34.14 2.83


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

AutoCloner maintained by Alex Coulton.