Multiple sequence alignment - TraesCS1B01G109900

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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 TraesCS1B01G109900 chr1B 100.000 3191 0 0 1 3191 121792256 121789066 0.000000e+00 5893.0
1 TraesCS1B01G109900 chr1B 91.606 2049 135 17 344 2368 122978320 122976285 0.000000e+00 2796.0
2 TraesCS1B01G109900 chr1B 91.150 2034 140 29 344 2360 122359646 122357636 0.000000e+00 2723.0
3 TraesCS1B01G109900 chr1B 90.565 2035 131 25 316 2325 121850652 121848654 0.000000e+00 2638.0
4 TraesCS1B01G109900 chr1B 88.866 1967 166 30 422 2360 123352973 123351032 0.000000e+00 2370.0
5 TraesCS1B01G109900 chr1B 92.437 833 45 6 2363 3191 662561168 662561986 0.000000e+00 1173.0
6 TraesCS1B01G109900 chr1B 86.406 743 74 18 2365 3084 392754449 392753711 0.000000e+00 787.0
7 TraesCS1B01G109900 chr1B 83.652 838 79 37 2366 3191 646866229 646865438 0.000000e+00 736.0
8 TraesCS1B01G109900 chr1B 92.523 321 16 4 1 318 41823582 41823267 1.350000e-123 453.0
9 TraesCS1B01G109900 chr1B 100.000 31 0 0 316 346 122978370 122978340 1.240000e-04 58.4
10 TraesCS1B01G109900 chr1D 88.693 2043 165 25 344 2368 78131434 78129440 0.000000e+00 2433.0
11 TraesCS1B01G109900 chr1D 100.000 30 0 0 316 345 78131484 78131455 4.450000e-04 56.5
12 TraesCS1B01G109900 chr2B 86.993 715 69 15 2363 3067 147497762 147498462 0.000000e+00 784.0
13 TraesCS1B01G109900 chr2B 82.088 843 104 32 2365 3191 4888042 4888853 0.000000e+00 676.0
14 TraesCS1B01G109900 chr2B 90.329 486 34 10 2366 2844 47691780 47691301 2.700000e-175 625.0
15 TraesCS1B01G109900 chr2B 90.020 491 32 14 2364 2844 787521450 787520967 1.260000e-173 619.0
16 TraesCS1B01G109900 chr2B 89.918 486 36 10 2366 2844 47718166 47717687 5.850000e-172 614.0
17 TraesCS1B01G109900 chr2B 92.097 329 19 5 1 324 138529621 138529295 1.040000e-124 457.0
18 TraesCS1B01G109900 chr2B 76.415 636 98 40 2365 2987 733241341 733240745 2.410000e-76 296.0
19 TraesCS1B01G109900 chr4A 91.529 484 29 11 2366 2842 650608111 650608589 0.000000e+00 656.0
20 TraesCS1B01G109900 chr4A 94.688 320 15 1 1 318 697736043 697735724 2.210000e-136 496.0
21 TraesCS1B01G109900 chr4A 93.750 320 18 2 1 318 697751123 697750804 2.230000e-131 479.0
22 TraesCS1B01G109900 chr4A 92.879 323 17 3 1 318 660466580 660466901 6.230000e-127 464.0
23 TraesCS1B01G109900 chr5B 81.785 818 95 33 2392 3191 640142985 640142204 1.250000e-178 636.0
24 TraesCS1B01G109900 chr3B 89.759 498 38 10 2366 2855 800119521 800120013 2.700000e-175 625.0
25 TraesCS1B01G109900 chrUn 89.733 487 39 8 2365 2844 38374348 38374830 2.100000e-171 612.0
26 TraesCS1B01G109900 chrUn 72.656 384 88 11 1671 2043 155963890 155964267 9.360000e-21 111.0
27 TraesCS1B01G109900 chr4B 93.168 322 15 4 1 320 28495872 28495556 1.730000e-127 466.0
28 TraesCS1B01G109900 chr6B 92.879 323 16 4 1 321 657251511 657251194 2.240000e-126 462.0
29 TraesCS1B01G109900 chr7B 92.308 325 17 4 1 322 84208498 84208817 3.750000e-124 455.0
30 TraesCS1B01G109900 chr7B 92.523 321 16 4 1 318 693861383 693861698 1.350000e-123 453.0
31 TraesCS1B01G109900 chr7D 79.050 716 107 35 2366 3068 53322931 53322246 4.850000e-123 451.0
32 TraesCS1B01G109900 chr3D 92.908 282 19 1 2911 3191 604597377 604597096 2.960000e-110 409.0
33 TraesCS1B01G109900 chr7A 81.481 432 74 5 1000 1428 79335023 79334595 1.820000e-92 350.0
34 TraesCS1B01G109900 chr5A 73.641 368 88 8 1025 1389 18680397 18680758 2.000000e-27 134.0
35 TraesCS1B01G109900 chr5D 73.370 368 89 8 1025 1389 27054593 27054954 9.290000e-26 128.0
36 TraesCS1B01G109900 chr5D 73.025 367 92 6 1025 1389 22796748 22797109 4.320000e-24 122.0
37 TraesCS1B01G109900 chr5D 77.000 200 46 0 1211 1410 27260325 27260126 7.230000e-22 115.0


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 TraesCS1B01G109900 chr1B 121789066 121792256 3190 True 5893.00 5893 100.0000 1 3191 1 chr1B.!!$R2 3190
1 TraesCS1B01G109900 chr1B 122357636 122359646 2010 True 2723.00 2723 91.1500 344 2360 1 chr1B.!!$R4 2016
2 TraesCS1B01G109900 chr1B 121848654 121850652 1998 True 2638.00 2638 90.5650 316 2325 1 chr1B.!!$R3 2009
3 TraesCS1B01G109900 chr1B 123351032 123352973 1941 True 2370.00 2370 88.8660 422 2360 1 chr1B.!!$R5 1938
4 TraesCS1B01G109900 chr1B 122976285 122978370 2085 True 1427.20 2796 95.8030 316 2368 2 chr1B.!!$R8 2052
5 TraesCS1B01G109900 chr1B 662561168 662561986 818 False 1173.00 1173 92.4370 2363 3191 1 chr1B.!!$F1 828
6 TraesCS1B01G109900 chr1B 392753711 392754449 738 True 787.00 787 86.4060 2365 3084 1 chr1B.!!$R6 719
7 TraesCS1B01G109900 chr1B 646865438 646866229 791 True 736.00 736 83.6520 2366 3191 1 chr1B.!!$R7 825
8 TraesCS1B01G109900 chr1D 78129440 78131484 2044 True 1244.75 2433 94.3465 316 2368 2 chr1D.!!$R1 2052
9 TraesCS1B01G109900 chr2B 147497762 147498462 700 False 784.00 784 86.9930 2363 3067 1 chr2B.!!$F2 704
10 TraesCS1B01G109900 chr2B 4888042 4888853 811 False 676.00 676 82.0880 2365 3191 1 chr2B.!!$F1 826
11 TraesCS1B01G109900 chr2B 733240745 733241341 596 True 296.00 296 76.4150 2365 2987 1 chr2B.!!$R4 622
12 TraesCS1B01G109900 chr5B 640142204 640142985 781 True 636.00 636 81.7850 2392 3191 1 chr5B.!!$R1 799
13 TraesCS1B01G109900 chr7D 53322246 53322931 685 True 451.00 451 79.0500 2366 3068 1 chr7D.!!$R1 702

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
556 585 0.033503 GTGGGAACGGGATTGGGATT 60.034 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2466 2536 0.301687 CTTTATGTAGCGCTGCGTGG 59.698 55.0 27.69 14.65 0.0 4.94 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
18 19 4.711949 CCCAGCACCGAAGCAGCT 62.712 66.667 0.00 0.00 36.60 4.24
19 20 3.123620 CCAGCACCGAAGCAGCTC 61.124 66.667 0.00 0.00 34.06 4.09
20 21 3.123620 CAGCACCGAAGCAGCTCC 61.124 66.667 0.00 0.00 34.06 4.70
21 22 4.749310 AGCACCGAAGCAGCTCCG 62.749 66.667 0.00 0.00 36.85 4.63
22 23 4.742201 GCACCGAAGCAGCTCCGA 62.742 66.667 0.92 0.00 0.00 4.55
23 24 2.811317 CACCGAAGCAGCTCCGAC 60.811 66.667 0.92 0.00 0.00 4.79
24 25 3.303135 ACCGAAGCAGCTCCGACA 61.303 61.111 0.92 0.00 0.00 4.35
25 26 2.811317 CCGAAGCAGCTCCGACAC 60.811 66.667 0.92 0.00 0.00 3.67
26 27 2.811317 CGAAGCAGCTCCGACACC 60.811 66.667 0.00 0.00 0.00 4.16
27 28 2.811317 GAAGCAGCTCCGACACCG 60.811 66.667 0.00 0.00 0.00 4.94
31 32 4.680237 CAGCTCCGACACCGCCAA 62.680 66.667 0.00 0.00 0.00 4.52
32 33 4.379243 AGCTCCGACACCGCCAAG 62.379 66.667 0.00 0.00 0.00 3.61
34 35 4.379243 CTCCGACACCGCCAAGCT 62.379 66.667 0.00 0.00 0.00 3.74
35 36 4.373116 TCCGACACCGCCAAGCTC 62.373 66.667 0.00 0.00 0.00 4.09
83 84 4.367023 CGACCCCGCCGAGTGAAA 62.367 66.667 0.00 0.00 0.00 2.69
84 85 2.741211 GACCCCGCCGAGTGAAAC 60.741 66.667 0.00 0.00 0.00 2.78
85 86 4.675029 ACCCCGCCGAGTGAAACG 62.675 66.667 0.00 0.00 45.86 3.60
94 95 3.058457 GAGTGAAACGCGAACTTGC 57.942 52.632 15.93 0.00 45.86 4.01
114 115 4.025401 CGGCGGCGCTCTGTTTTT 62.025 61.111 32.30 0.00 0.00 1.94
132 133 2.798976 TTTGTAACGCCAGACTACGT 57.201 45.000 0.00 0.00 46.07 3.57
133 134 2.336554 TTGTAACGCCAGACTACGTC 57.663 50.000 0.00 0.00 42.68 4.34
134 135 0.523072 TGTAACGCCAGACTACGTCC 59.477 55.000 0.00 0.00 42.68 4.79
135 136 0.522076 GTAACGCCAGACTACGTCCG 60.522 60.000 0.00 0.00 42.68 4.79
136 137 0.673333 TAACGCCAGACTACGTCCGA 60.673 55.000 0.00 0.00 42.68 4.55
137 138 1.310933 AACGCCAGACTACGTCCGAT 61.311 55.000 0.00 0.00 42.68 4.18
138 139 1.009900 CGCCAGACTACGTCCGATC 60.010 63.158 0.00 0.00 32.18 3.69
139 140 1.009900 GCCAGACTACGTCCGATCG 60.010 63.158 8.51 8.51 32.18 3.69
140 141 1.009900 CCAGACTACGTCCGATCGC 60.010 63.158 10.32 0.00 32.18 4.58
141 142 1.009900 CAGACTACGTCCGATCGCC 60.010 63.158 10.32 0.86 32.18 5.54
142 143 2.052414 GACTACGTCCGATCGCCG 60.052 66.667 19.54 19.54 38.18 6.46
156 157 4.413800 GCCGGATTTGCGGCGTTT 62.414 61.111 19.53 0.00 41.61 3.60
157 158 2.257067 CCGGATTTGCGGCGTTTT 59.743 55.556 9.37 0.00 0.00 2.43
158 159 1.372375 CCGGATTTGCGGCGTTTTT 60.372 52.632 9.37 0.00 0.00 1.94
187 188 4.316205 GGGAACGACCAAGTTTGAATTT 57.684 40.909 0.00 0.00 41.20 1.82
188 189 4.295870 GGGAACGACCAAGTTTGAATTTC 58.704 43.478 0.00 0.00 41.20 2.17
189 190 4.295870 GGAACGACCAAGTTTGAATTTCC 58.704 43.478 0.00 0.00 38.79 3.13
190 191 4.295870 GAACGACCAAGTTTGAATTTCCC 58.704 43.478 0.00 0.00 34.00 3.97
191 192 2.292292 ACGACCAAGTTTGAATTTCCCG 59.708 45.455 0.00 0.00 0.00 5.14
192 193 2.672714 GACCAAGTTTGAATTTCCCGC 58.327 47.619 0.00 0.00 0.00 6.13
193 194 2.035321 GACCAAGTTTGAATTTCCCGCA 59.965 45.455 0.00 0.00 0.00 5.69
194 195 2.632512 ACCAAGTTTGAATTTCCCGCAT 59.367 40.909 0.00 0.00 0.00 4.73
195 196 3.253230 CCAAGTTTGAATTTCCCGCATC 58.747 45.455 0.00 0.00 0.00 3.91
196 197 3.253230 CAAGTTTGAATTTCCCGCATCC 58.747 45.455 0.00 0.00 0.00 3.51
197 198 2.807676 AGTTTGAATTTCCCGCATCCT 58.192 42.857 0.00 0.00 0.00 3.24
198 199 2.493278 AGTTTGAATTTCCCGCATCCTG 59.507 45.455 0.00 0.00 0.00 3.86
199 200 1.473258 TTGAATTTCCCGCATCCTGG 58.527 50.000 0.00 0.00 0.00 4.45
230 231 3.075005 GGGCGTGACTGGGAGCTA 61.075 66.667 0.00 0.00 0.00 3.32
231 232 2.496817 GGCGTGACTGGGAGCTAG 59.503 66.667 0.00 0.00 0.00 3.42
232 233 2.496817 GCGTGACTGGGAGCTAGG 59.503 66.667 0.00 0.00 0.00 3.02
233 234 2.352032 GCGTGACTGGGAGCTAGGT 61.352 63.158 0.00 0.00 0.00 3.08
234 235 1.810532 CGTGACTGGGAGCTAGGTC 59.189 63.158 13.67 13.67 0.00 3.85
235 236 1.810532 GTGACTGGGAGCTAGGTCG 59.189 63.158 15.43 4.94 0.00 4.79
236 237 2.052690 TGACTGGGAGCTAGGTCGC 61.053 63.158 26.90 26.90 0.00 5.19
237 238 2.760385 ACTGGGAGCTAGGTCGCC 60.760 66.667 29.34 23.22 0.00 5.54
238 239 3.541713 CTGGGAGCTAGGTCGCCC 61.542 72.222 29.34 20.74 45.10 6.13
242 243 3.541713 GAGCTAGGTCGCCCCCAG 61.542 72.222 6.12 0.00 0.00 4.45
254 255 2.683475 CCCCAGGGGCCAAACTAG 59.317 66.667 13.35 0.00 35.35 2.57
255 256 2.043953 CCCAGGGGCCAAACTAGC 60.044 66.667 4.39 0.00 0.00 3.42
256 257 2.438434 CCAGGGGCCAAACTAGCG 60.438 66.667 4.39 0.00 0.00 4.26
257 258 3.134127 CAGGGGCCAAACTAGCGC 61.134 66.667 4.39 0.00 42.07 5.92
263 264 3.799755 CCAAACTAGCGCCGGCAC 61.800 66.667 28.98 18.62 43.41 5.01
282 283 3.171388 CCCCCAGGCCGCTCTATT 61.171 66.667 0.00 0.00 0.00 1.73
283 284 2.757124 CCCCCAGGCCGCTCTATTT 61.757 63.158 0.00 0.00 0.00 1.40
284 285 1.415672 CCCCCAGGCCGCTCTATTTA 61.416 60.000 0.00 0.00 0.00 1.40
285 286 0.035458 CCCCAGGCCGCTCTATTTAG 59.965 60.000 0.00 0.00 0.00 1.85
286 287 0.035458 CCCAGGCCGCTCTATTTAGG 59.965 60.000 0.00 0.00 0.00 2.69
289 290 3.245084 GCCGCTCTATTTAGGCGC 58.755 61.111 0.00 0.00 46.29 6.53
290 291 2.318352 GCCGCTCTATTTAGGCGCC 61.318 63.158 21.89 21.89 46.29 6.53
291 292 1.668151 CCGCTCTATTTAGGCGCCC 60.668 63.158 26.15 5.07 46.29 6.13
292 293 1.367840 CGCTCTATTTAGGCGCCCT 59.632 57.895 26.15 13.52 42.28 5.19
293 294 0.946221 CGCTCTATTTAGGCGCCCTG 60.946 60.000 26.15 7.22 42.28 4.45
294 295 0.603975 GCTCTATTTAGGCGCCCTGG 60.604 60.000 26.15 7.92 34.61 4.45
295 296 0.035458 CTCTATTTAGGCGCCCTGGG 59.965 60.000 26.15 8.86 34.61 4.45
296 297 1.073199 CTATTTAGGCGCCCTGGGG 59.927 63.158 26.15 5.60 34.61 4.96
538 567 1.893544 TCTCTCTTTCCTGTCGTCGT 58.106 50.000 0.00 0.00 0.00 4.34
556 585 0.033503 GTGGGAACGGGATTGGGATT 60.034 55.000 0.00 0.00 0.00 3.01
629 662 1.702957 TCTCCAGTCCAAATTTCCCGT 59.297 47.619 0.00 0.00 0.00 5.28
630 663 2.907696 TCTCCAGTCCAAATTTCCCGTA 59.092 45.455 0.00 0.00 0.00 4.02
687 727 3.082701 AGCTGAGCTCAGGCCTCC 61.083 66.667 37.86 23.88 43.94 4.30
1354 1395 3.389329 TGAGAAGTCTGAGCTTCACCTTT 59.611 43.478 15.43 0.00 45.28 3.11
1434 1475 3.761897 AGAGCCGATCTTAGATAGTGCT 58.238 45.455 14.24 14.24 32.99 4.40
1551 1592 0.694444 ATCCACCCACGGGAAGCTAT 60.694 55.000 9.72 0.00 38.09 2.97
1579 1620 4.721274 TGGTTATCATCCACAATCCAGAGA 59.279 41.667 0.00 0.00 0.00 3.10
1681 1722 4.996758 TGGATGGTCTATTGTATGCATTCG 59.003 41.667 3.54 0.00 0.00 3.34
1702 1743 3.736433 CGCAGAAACTGGAGGAGTCTATG 60.736 52.174 0.00 0.00 31.73 2.23
1713 1754 5.163364 TGGAGGAGTCTATGCTTTTGATCTC 60.163 44.000 0.00 0.00 0.00 2.75
1730 1771 1.063190 TCTCACCGGTCCTACCATCAT 60.063 52.381 2.59 0.00 38.47 2.45
1731 1772 1.069204 CTCACCGGTCCTACCATCATG 59.931 57.143 2.59 0.00 38.47 3.07
1734 1775 1.343075 ACCGGTCCTACCATCATGAGT 60.343 52.381 0.00 0.00 38.47 3.41
1735 1776 1.762957 CCGGTCCTACCATCATGAGTT 59.237 52.381 0.09 0.00 38.47 3.01
1772 1813 8.373981 AGATGAGATGGAGAATTACATTAGTGG 58.626 37.037 0.00 0.00 0.00 4.00
1779 1820 5.019785 AGAATTACATTAGTGGGACGGAC 57.980 43.478 0.00 0.00 0.00 4.79
1783 1824 2.062177 ATTAGTGGGACGGACGGGG 61.062 63.158 0.00 0.00 0.00 5.73
1870 1914 0.808125 AGAGCTGCTCGTACAGACTG 59.192 55.000 22.77 0.00 40.25 3.51
1879 1923 4.700692 TGCTCGTACAGACTGAGAAAGTAT 59.299 41.667 10.08 0.00 40.07 2.12
1986 2030 2.179764 GCAATGCCTTAGTGCGGAA 58.820 52.632 0.00 0.00 40.87 4.30
2006 2050 5.123820 CGGAAGCTTATCCACAATTGAAGAA 59.876 40.000 13.59 0.20 39.61 2.52
2010 2054 8.593492 AAGCTTATCCACAATTGAAGAAAAAC 57.407 30.769 13.59 1.17 0.00 2.43
2036 2080 6.873605 TGTGTTTATTTCACAGATGACGAGAT 59.126 34.615 0.00 0.00 40.26 2.75
2047 2091 5.859114 ACAGATGACGAGATATATGTTTCGC 59.141 40.000 11.54 6.22 36.58 4.70
2049 2093 5.859114 AGATGACGAGATATATGTTTCGCAC 59.141 40.000 11.54 7.49 36.58 5.34
2090 2134 6.574465 CGGGATATAGGTATTCTCAACTTGGG 60.574 46.154 0.00 0.00 0.00 4.12
2102 2146 5.305585 TCTCAACTTGGGAAATGACAGTAC 58.694 41.667 0.00 0.00 0.00 2.73
2172 2216 3.309954 GGATAACACCAAATCTCACGAGC 59.690 47.826 0.00 0.00 0.00 5.03
2179 2223 3.376234 ACCAAATCTCACGAGCATGAATG 59.624 43.478 0.00 0.00 0.00 2.67
2199 2253 9.687210 ATGAATGCAAATAGCTAACATATTGTG 57.313 29.630 0.00 0.00 45.94 3.33
2224 2278 3.251479 TGTACGTAGGTAGCTTCTCGA 57.749 47.619 16.35 0.00 0.00 4.04
2248 2310 7.441157 CGAATGCTATTAGAAACTGTCCCATAA 59.559 37.037 0.00 0.00 0.00 1.90
2252 2314 2.808906 AGAAACTGTCCCATAAGGCC 57.191 50.000 0.00 0.00 34.51 5.19
2256 2318 1.819632 CTGTCCCATAAGGCCGTGC 60.820 63.158 0.00 0.00 34.51 5.34
2260 2322 1.136828 TCCCATAAGGCCGTGCTAAT 58.863 50.000 0.00 0.00 34.51 1.73
2270 2332 2.481276 GGCCGTGCTAATCAAAATTCCC 60.481 50.000 0.00 0.00 0.00 3.97
2273 2335 4.815269 CCGTGCTAATCAAAATTCCCAAA 58.185 39.130 0.00 0.00 0.00 3.28
2295 2357 4.822685 TTTGTGGGCAAATGCTATGAAT 57.177 36.364 5.25 0.00 39.43 2.57
2317 2383 1.871080 GGAGGCATGTTCCGTATCTG 58.129 55.000 0.00 0.00 0.00 2.90
2321 2387 2.501723 AGGCATGTTCCGTATCTGTTCT 59.498 45.455 0.00 0.00 0.00 3.01
2322 2388 3.055094 AGGCATGTTCCGTATCTGTTCTT 60.055 43.478 0.00 0.00 0.00 2.52
2323 2389 3.309954 GGCATGTTCCGTATCTGTTCTTC 59.690 47.826 0.00 0.00 0.00 2.87
2328 2394 4.039973 TGTTCCGTATCTGTTCTTCACCTT 59.960 41.667 0.00 0.00 0.00 3.50
2383 2449 5.087323 TGAACTGTTAGGTTGATCTCTCCT 58.913 41.667 0.00 1.90 35.60 3.69
2728 2803 3.074675 TGATCTAGCCTACTCCGATCC 57.925 52.381 0.00 0.00 34.47 3.36
2729 2804 2.011222 GATCTAGCCTACTCCGATCCG 58.989 57.143 0.00 0.00 31.56 4.18
2758 2835 3.959495 AACAATGGTATCAGGCCATCT 57.041 42.857 5.01 0.00 45.21 2.90
2815 2897 0.683179 GGAAAAGGATCCCCAACCCG 60.683 60.000 8.55 0.00 33.05 5.28
2841 2937 4.040645 CCTAGCAGGGCACAGAGA 57.959 61.111 0.00 0.00 0.00 3.10
2842 2938 2.290847 CCTAGCAGGGCACAGAGAA 58.709 57.895 0.00 0.00 0.00 2.87
2843 2939 0.615331 CCTAGCAGGGCACAGAGAAA 59.385 55.000 0.00 0.00 0.00 2.52
2844 2940 1.003580 CCTAGCAGGGCACAGAGAAAA 59.996 52.381 0.00 0.00 0.00 2.29
2845 2941 2.354259 CTAGCAGGGCACAGAGAAAAG 58.646 52.381 0.00 0.00 0.00 2.27
2846 2942 0.892814 AGCAGGGCACAGAGAAAAGC 60.893 55.000 0.00 0.00 0.00 3.51
2847 2943 1.174712 GCAGGGCACAGAGAAAAGCA 61.175 55.000 0.00 0.00 0.00 3.91
2848 2944 1.321474 CAGGGCACAGAGAAAAGCAA 58.679 50.000 0.00 0.00 0.00 3.91
2849 2945 1.682854 CAGGGCACAGAGAAAAGCAAA 59.317 47.619 0.00 0.00 0.00 3.68
2850 2946 1.683385 AGGGCACAGAGAAAAGCAAAC 59.317 47.619 0.00 0.00 0.00 2.93
3088 3214 3.902162 GACCACGACGCCGCAGTAA 62.902 63.158 0.00 0.00 39.95 2.24
3134 3261 2.440599 GGGCAGAAGGGGCAAAGA 59.559 61.111 0.00 0.00 34.52 2.52
3155 3282 1.797441 CCTCGTCCTCTCTGTCACG 59.203 63.158 0.00 0.00 0.00 4.35
3161 3288 0.989602 TCCTCTCTGTCACGGTAGGA 59.010 55.000 6.43 6.43 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.711949 AGCTGCTTCGGTGCTGGG 62.712 66.667 0.00 0.00 35.54 4.45
3 4 3.123620 GGAGCTGCTTCGGTGCTG 61.124 66.667 2.53 3.29 37.16 4.41
4 5 4.749310 CGGAGCTGCTTCGGTGCT 62.749 66.667 22.39 0.00 40.02 4.40
6 7 2.811317 GTCGGAGCTGCTTCGGTG 60.811 66.667 28.41 2.65 32.62 4.94
7 8 3.303135 TGTCGGAGCTGCTTCGGT 61.303 61.111 28.41 0.00 32.62 4.69
8 9 2.811317 GTGTCGGAGCTGCTTCGG 60.811 66.667 28.41 11.47 32.62 4.30
9 10 2.811317 GGTGTCGGAGCTGCTTCG 60.811 66.667 23.99 23.99 33.10 3.79
10 11 2.811317 CGGTGTCGGAGCTGCTTC 60.811 66.667 2.53 0.00 0.00 3.86
14 15 4.680237 TTGGCGGTGTCGGAGCTG 62.680 66.667 0.00 0.00 36.79 4.24
15 16 4.379243 CTTGGCGGTGTCGGAGCT 62.379 66.667 0.00 0.00 36.79 4.09
17 18 4.379243 AGCTTGGCGGTGTCGGAG 62.379 66.667 0.00 0.00 36.79 4.63
18 19 4.373116 GAGCTTGGCGGTGTCGGA 62.373 66.667 0.00 0.00 36.79 4.55
66 67 4.367023 TTTCACTCGGCGGGGTCG 62.367 66.667 13.20 0.00 39.81 4.79
67 68 2.741211 GTTTCACTCGGCGGGGTC 60.741 66.667 13.20 0.00 0.00 4.46
68 69 4.675029 CGTTTCACTCGGCGGGGT 62.675 66.667 13.20 6.13 0.00 4.95
72 73 3.399770 TTCGCGTTTCACTCGGCG 61.400 61.111 5.77 0.00 0.00 6.46
73 74 1.828331 AAGTTCGCGTTTCACTCGGC 61.828 55.000 5.77 0.00 0.00 5.54
74 75 0.111266 CAAGTTCGCGTTTCACTCGG 60.111 55.000 5.77 0.00 0.00 4.63
75 76 0.718220 GCAAGTTCGCGTTTCACTCG 60.718 55.000 5.77 0.00 0.00 4.18
76 77 3.058457 GCAAGTTCGCGTTTCACTC 57.942 52.632 5.77 0.00 0.00 3.51
97 98 4.025401 AAAAACAGAGCGCCGCCG 62.025 61.111 4.98 0.00 37.57 6.46
111 112 3.456280 ACGTAGTCTGGCGTTACAAAAA 58.544 40.909 0.00 0.00 29.74 1.94
112 113 3.096489 ACGTAGTCTGGCGTTACAAAA 57.904 42.857 0.00 0.00 29.74 2.44
113 114 2.798976 ACGTAGTCTGGCGTTACAAA 57.201 45.000 0.00 0.00 29.74 2.83
141 142 4.236724 AAAAACGCCGCAAATCCG 57.763 50.000 0.00 0.00 0.00 4.18
155 156 3.539604 TGGTCGTTCCCGTTCTTAAAAA 58.460 40.909 0.00 0.00 34.77 1.94
156 157 3.191078 TGGTCGTTCCCGTTCTTAAAA 57.809 42.857 0.00 0.00 34.77 1.52
157 158 2.906691 TGGTCGTTCCCGTTCTTAAA 57.093 45.000 0.00 0.00 34.77 1.52
158 159 2.102925 ACTTGGTCGTTCCCGTTCTTAA 59.897 45.455 0.00 0.00 34.77 1.85
159 160 1.688197 ACTTGGTCGTTCCCGTTCTTA 59.312 47.619 0.00 0.00 34.77 2.10
160 161 0.466963 ACTTGGTCGTTCCCGTTCTT 59.533 50.000 0.00 0.00 34.77 2.52
161 162 0.466963 AACTTGGTCGTTCCCGTTCT 59.533 50.000 0.00 0.00 34.77 3.01
162 163 1.003223 CAAACTTGGTCGTTCCCGTTC 60.003 52.381 0.00 0.00 34.77 3.95
163 164 1.018910 CAAACTTGGTCGTTCCCGTT 58.981 50.000 0.00 0.00 34.77 4.44
164 165 0.178533 TCAAACTTGGTCGTTCCCGT 59.821 50.000 0.00 0.00 34.77 5.28
165 166 1.301423 TTCAAACTTGGTCGTTCCCG 58.699 50.000 0.00 0.00 34.77 5.14
166 167 4.295870 GAAATTCAAACTTGGTCGTTCCC 58.704 43.478 0.00 0.00 34.77 3.97
167 168 4.295870 GGAAATTCAAACTTGGTCGTTCC 58.704 43.478 0.00 0.00 0.00 3.62
168 169 4.295870 GGGAAATTCAAACTTGGTCGTTC 58.704 43.478 0.00 0.00 0.00 3.95
169 170 3.243267 CGGGAAATTCAAACTTGGTCGTT 60.243 43.478 0.00 0.00 0.00 3.85
170 171 2.292292 CGGGAAATTCAAACTTGGTCGT 59.708 45.455 0.00 0.00 0.00 4.34
171 172 2.920647 GCGGGAAATTCAAACTTGGTCG 60.921 50.000 0.00 0.00 0.00 4.79
172 173 2.035321 TGCGGGAAATTCAAACTTGGTC 59.965 45.455 0.00 0.00 0.00 4.02
173 174 2.035632 TGCGGGAAATTCAAACTTGGT 58.964 42.857 0.00 0.00 0.00 3.67
174 175 2.810439 TGCGGGAAATTCAAACTTGG 57.190 45.000 0.00 0.00 0.00 3.61
175 176 3.056607 AGGATGCGGGAAATTCAAACTTG 60.057 43.478 0.00 0.00 0.00 3.16
176 177 3.056607 CAGGATGCGGGAAATTCAAACTT 60.057 43.478 0.00 0.00 0.00 2.66
177 178 2.493278 CAGGATGCGGGAAATTCAAACT 59.507 45.455 0.00 0.00 0.00 2.66
178 179 2.417243 CCAGGATGCGGGAAATTCAAAC 60.417 50.000 0.00 0.00 31.97 2.93
179 180 1.824230 CCAGGATGCGGGAAATTCAAA 59.176 47.619 0.00 0.00 31.97 2.69
180 181 1.473258 CCAGGATGCGGGAAATTCAA 58.527 50.000 0.00 0.00 31.97 2.69
181 182 3.189568 CCAGGATGCGGGAAATTCA 57.810 52.632 0.00 0.00 31.97 2.57
213 214 3.075005 TAGCTCCCAGTCACGCCC 61.075 66.667 0.00 0.00 0.00 6.13
214 215 2.496817 CTAGCTCCCAGTCACGCC 59.503 66.667 0.00 0.00 0.00 5.68
215 216 2.286127 GACCTAGCTCCCAGTCACGC 62.286 65.000 0.00 0.00 0.00 5.34
216 217 1.810532 GACCTAGCTCCCAGTCACG 59.189 63.158 0.00 0.00 0.00 4.35
217 218 1.810532 CGACCTAGCTCCCAGTCAC 59.189 63.158 0.00 0.00 0.00 3.67
218 219 2.052690 GCGACCTAGCTCCCAGTCA 61.053 63.158 0.00 0.00 0.00 3.41
219 220 2.787567 GGCGACCTAGCTCCCAGTC 61.788 68.421 0.00 0.00 37.29 3.51
220 221 2.760385 GGCGACCTAGCTCCCAGT 60.760 66.667 0.00 0.00 37.29 4.00
238 239 2.043953 GCTAGTTTGGCCCCTGGG 60.044 66.667 5.50 5.50 38.57 4.45
239 240 2.438434 CGCTAGTTTGGCCCCTGG 60.438 66.667 0.00 0.00 0.00 4.45
240 241 3.134127 GCGCTAGTTTGGCCCCTG 61.134 66.667 0.00 0.00 0.00 4.45
241 242 4.426313 GGCGCTAGTTTGGCCCCT 62.426 66.667 7.64 0.00 41.01 4.79
246 247 3.799755 GTGCCGGCGCTAGTTTGG 61.800 66.667 32.27 0.98 35.36 3.28
247 248 4.147322 CGTGCCGGCGCTAGTTTG 62.147 66.667 35.04 16.62 35.36 2.93
265 266 1.415672 TAAATAGAGCGGCCTGGGGG 61.416 60.000 0.00 0.00 0.00 5.40
266 267 0.035458 CTAAATAGAGCGGCCTGGGG 59.965 60.000 0.00 0.00 0.00 4.96
267 268 0.035458 CCTAAATAGAGCGGCCTGGG 59.965 60.000 0.00 0.00 0.00 4.45
268 269 0.603975 GCCTAAATAGAGCGGCCTGG 60.604 60.000 0.00 0.00 36.56 4.45
269 270 0.946221 CGCCTAAATAGAGCGGCCTG 60.946 60.000 0.00 0.00 45.88 4.85
270 271 1.367840 CGCCTAAATAGAGCGGCCT 59.632 57.895 0.00 0.00 45.88 5.19
271 272 3.952811 CGCCTAAATAGAGCGGCC 58.047 61.111 12.51 0.00 45.88 6.13
275 276 0.603975 CCAGGGCGCCTAAATAGAGC 60.604 60.000 28.56 5.83 29.64 4.09
276 277 0.035458 CCCAGGGCGCCTAAATAGAG 59.965 60.000 28.56 6.58 29.64 2.43
277 278 1.415672 CCCCAGGGCGCCTAAATAGA 61.416 60.000 28.56 0.00 29.64 1.98
278 279 1.073199 CCCCAGGGCGCCTAAATAG 59.927 63.158 28.56 10.47 29.64 1.73
279 280 3.246687 CCCCAGGGCGCCTAAATA 58.753 61.111 28.56 0.00 29.64 1.40
304 305 2.124529 GGTAAGGGCAGCTCCAGC 60.125 66.667 0.00 0.00 42.49 4.85
305 306 2.187946 CGGTAAGGGCAGCTCCAG 59.812 66.667 0.00 0.00 36.21 3.86
306 307 4.096003 GCGGTAAGGGCAGCTCCA 62.096 66.667 0.00 0.00 36.21 3.86
538 567 0.257616 GAATCCCAATCCCGTTCCCA 59.742 55.000 0.00 0.00 0.00 4.37
556 585 2.745100 ACTACGCGGCTCAGACGA 60.745 61.111 2.43 0.00 35.20 4.20
629 662 3.087031 AGTCCGAATCCAAGAACGACTA 58.913 45.455 0.00 0.00 0.00 2.59
630 663 1.893801 AGTCCGAATCCAAGAACGACT 59.106 47.619 0.00 0.00 0.00 4.18
687 727 0.391263 GGAAGCTCAACCCACCTACG 60.391 60.000 0.00 0.00 0.00 3.51
1354 1395 3.244387 TGTTGACCAGTGATCGGATTGAA 60.244 43.478 0.00 0.00 0.00 2.69
1434 1475 8.892723 CACATCTTAATCTTATTAACTGCACCA 58.107 33.333 0.00 0.00 0.00 4.17
1579 1620 7.340999 ACCTACCCTTGCAAACGAAATATATTT 59.659 33.333 10.51 10.51 0.00 1.40
1585 1626 2.556622 CACCTACCCTTGCAAACGAAAT 59.443 45.455 0.00 0.00 0.00 2.17
1633 1674 7.701539 TGTGGATGCATTGTTTATAGTTCTT 57.298 32.000 0.00 0.00 0.00 2.52
1681 1722 3.791245 CATAGACTCCTCCAGTTTCTGC 58.209 50.000 0.00 0.00 34.41 4.26
1702 1743 1.087501 GGACCGGTGAGATCAAAAGC 58.912 55.000 14.63 0.00 0.00 3.51
1713 1754 1.069204 CTCATGATGGTAGGACCGGTG 59.931 57.143 14.63 0.00 42.58 4.94
1730 1771 9.662947 CCATCTCATCTGCAATAATATAACTCA 57.337 33.333 0.00 0.00 0.00 3.41
1731 1772 9.881649 TCCATCTCATCTGCAATAATATAACTC 57.118 33.333 0.00 0.00 0.00 3.01
1772 1813 2.053865 TACATGTCCCCGTCCGTCC 61.054 63.158 0.00 0.00 0.00 4.79
1779 1820 1.073177 GAACAACGTACATGTCCCCG 58.927 55.000 0.00 6.27 0.00 5.73
1783 1824 2.412089 GAGCCTGAACAACGTACATGTC 59.588 50.000 0.00 0.00 0.00 3.06
1833 1874 5.063691 CAGCTCTTCTGTGACATCAGATTTC 59.936 44.000 8.07 0.00 42.84 2.17
1853 1897 0.808125 CTCAGTCTGTACGAGCAGCT 59.192 55.000 0.00 0.00 36.49 4.24
1854 1898 0.805614 TCTCAGTCTGTACGAGCAGC 59.194 55.000 0.00 0.00 36.49 5.25
1855 1899 3.057876 ACTTTCTCAGTCTGTACGAGCAG 60.058 47.826 0.00 0.00 37.81 4.24
1856 1900 2.885266 ACTTTCTCAGTCTGTACGAGCA 59.115 45.455 0.00 0.00 0.00 4.26
1858 1902 6.613233 ACAATACTTTCTCAGTCTGTACGAG 58.387 40.000 0.00 0.00 36.88 4.18
1909 1953 5.600696 CAAGCCATTTACTTCCACAAGTTT 58.399 37.500 0.00 0.00 40.16 2.66
1921 1965 4.743151 CACATGATCATGCAAGCCATTTAC 59.257 41.667 31.17 0.00 42.39 2.01
1923 1967 3.196901 ACACATGATCATGCAAGCCATTT 59.803 39.130 31.17 9.42 42.39 2.32
1983 2027 6.515272 TTCTTCAATTGTGGATAAGCTTCC 57.485 37.500 0.00 0.00 36.24 3.46
1986 2030 7.869429 CAGTTTTTCTTCAATTGTGGATAAGCT 59.131 33.333 5.13 10.06 0.00 3.74
1988 2032 8.971321 CACAGTTTTTCTTCAATTGTGGATAAG 58.029 33.333 5.13 1.48 37.90 1.73
1989 2033 8.474025 ACACAGTTTTTCTTCAATTGTGGATAA 58.526 29.630 5.13 4.24 42.93 1.75
1999 2043 9.698309 TGTGAAATAAACACAGTTTTTCTTCAA 57.302 25.926 9.57 2.36 42.20 2.69
2028 2072 5.183014 AGTGCGAAACATATATCTCGTCA 57.817 39.130 9.11 6.11 33.87 4.35
2041 2085 6.297353 GGCGATTATTCTTATAGTGCGAAAC 58.703 40.000 0.00 0.00 0.00 2.78
2047 2091 5.068234 TCCCGGCGATTATTCTTATAGTG 57.932 43.478 9.30 0.00 0.00 2.74
2049 2093 8.244802 CCTATATCCCGGCGATTATTCTTATAG 58.755 40.741 9.30 7.37 31.92 1.31
2062 2106 3.021695 TGAGAATACCTATATCCCGGCG 58.978 50.000 0.00 0.00 0.00 6.46
2063 2107 4.466726 AGTTGAGAATACCTATATCCCGGC 59.533 45.833 0.00 0.00 0.00 6.13
2090 2134 6.899114 ACAATTTCTTCCGTACTGTCATTTC 58.101 36.000 0.00 0.00 0.00 2.17
2102 2146 6.253746 CAAAGCTGAGATACAATTTCTTCCG 58.746 40.000 0.00 0.00 0.00 4.30
2172 2216 9.687210 ACAATATGTTAGCTATTTGCATTCATG 57.313 29.630 0.00 0.00 45.94 3.07
2192 2246 9.458727 AGCTACCTACGTACATATACACAATAT 57.541 33.333 0.00 0.00 0.00 1.28
2197 2251 7.432350 AGAAGCTACCTACGTACATATACAC 57.568 40.000 0.00 0.00 0.00 2.90
2199 2253 6.587990 TCGAGAAGCTACCTACGTACATATAC 59.412 42.308 0.00 0.00 0.00 1.47
2201 2255 5.545588 TCGAGAAGCTACCTACGTACATAT 58.454 41.667 0.00 0.00 0.00 1.78
2205 2259 4.525686 CATTCGAGAAGCTACCTACGTAC 58.474 47.826 0.00 0.00 0.00 3.67
2206 2260 3.003068 GCATTCGAGAAGCTACCTACGTA 59.997 47.826 0.00 0.00 0.00 3.57
2207 2261 2.223525 GCATTCGAGAAGCTACCTACGT 60.224 50.000 0.00 0.00 0.00 3.57
2208 2262 2.033550 AGCATTCGAGAAGCTACCTACG 59.966 50.000 6.55 0.00 36.73 3.51
2248 2310 2.427095 GGAATTTTGATTAGCACGGCCT 59.573 45.455 0.00 0.00 0.00 5.19
2252 2314 6.966435 AATTTGGGAATTTTGATTAGCACG 57.034 33.333 0.00 0.00 31.48 5.34
2356 2422 7.251321 AGAGATCAACCTAACAGTTCAGAAT 57.749 36.000 0.00 0.00 0.00 2.40
2443 2513 1.733526 GGCCCGTCAACCATATTGC 59.266 57.895 0.00 0.00 0.00 3.56
2466 2536 0.301687 CTTTATGTAGCGCTGCGTGG 59.698 55.000 27.69 14.65 0.00 4.94
2728 2803 5.928839 CCTGATACCATTGTTAGATCCTTCG 59.071 44.000 0.00 0.00 0.00 3.79
2729 2804 5.703130 GCCTGATACCATTGTTAGATCCTTC 59.297 44.000 0.00 0.00 0.00 3.46
2973 3085 0.682852 CCGTGTGGGGTAGTTCTTCA 59.317 55.000 0.00 0.00 0.00 3.02
3059 3185 3.075005 CGTGGTCATCCCCCTCGT 61.075 66.667 0.00 0.00 35.01 4.18
3088 3214 2.049063 GACGACGGCAGAGCACTT 60.049 61.111 0.00 0.00 0.00 3.16
3134 3261 0.251386 TGACAGAGAGGACGAGGCTT 60.251 55.000 0.00 0.00 0.00 4.35
3155 3282 1.041437 CCGTTCCATCTCCTCCTACC 58.959 60.000 0.00 0.00 0.00 3.18
3161 3288 0.912486 CTTTCCCCGTTCCATCTCCT 59.088 55.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.