Multiple sequence alignment - TraesCS6D01G206800

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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 TraesCS6D01G206800 chr6D 100.000 4610 0 0 1 4610 292373591 292378200 0.000000e+00 8514.0
1 TraesCS6D01G206800 chr6D 84.979 233 20 7 1006 1237 292305178 292305396 6.000000e-54 222.0
2 TraesCS6D01G206800 chr6D 81.181 271 31 13 254 515 6861617 6861876 2.810000e-47 200.0
3 TraesCS6D01G206800 chr6D 79.927 274 47 7 253 523 471334061 471333793 1.310000e-45 195.0
4 TraesCS6D01G206800 chr6D 78.947 190 38 2 3023 3211 457346056 457345868 1.350000e-25 128.0
5 TraesCS6D01G206800 chr6D 78.392 199 41 2 3018 3215 457472166 457471969 1.350000e-25 128.0
6 TraesCS6D01G206800 chr6D 77.647 170 26 8 364 529 393581078 393580917 4.910000e-15 93.5
7 TraesCS6D01G206800 chr6D 85.227 88 13 0 1754 1841 457472614 457472527 1.770000e-14 91.6
8 TraesCS6D01G206800 chr6B 90.434 1798 97 39 633 2383 455413290 455415059 0.000000e+00 2298.0
9 TraesCS6D01G206800 chr6B 92.489 892 35 13 2396 3277 455415106 455415975 0.000000e+00 1247.0
10 TraesCS6D01G206800 chr6B 88.855 978 86 13 3649 4610 9309391 9310361 0.000000e+00 1181.0
11 TraesCS6D01G206800 chr6B 88.208 653 48 14 1 639 455412625 455413262 0.000000e+00 752.0
12 TraesCS6D01G206800 chr6B 85.131 612 74 9 33 639 455402206 455402805 1.100000e-170 610.0
13 TraesCS6D01G206800 chr6B 89.112 349 31 4 1 347 455402898 455403241 1.190000e-115 427.0
14 TraesCS6D01G206800 chr6B 86.093 302 34 5 343 639 455412234 455412532 7.440000e-83 318.0
15 TraesCS6D01G206800 chr6B 90.698 215 19 1 3427 3640 455417056 455417270 7.550000e-73 285.0
16 TraesCS6D01G206800 chr6B 84.810 158 21 2 1157 1314 695937064 695937218 6.180000e-34 156.0
17 TraesCS6D01G206800 chr6B 84.375 64 8 2 3321 3383 656566703 656566641 1.380000e-05 62.1
18 TraesCS6D01G206800 chr6A 92.900 1507 73 16 2154 3644 430342442 430340954 0.000000e+00 2159.0
19 TraesCS6D01G206800 chr6A 91.557 1066 46 17 1040 2074 430343528 430342476 0.000000e+00 1430.0
20 TraesCS6D01G206800 chr6A 87.741 726 44 24 286 982 430344249 430343540 0.000000e+00 806.0
21 TraesCS6D01G206800 chr6A 77.835 194 41 2 3023 3215 604295939 604296131 8.100000e-23 119.0
22 TraesCS6D01G206800 chr6A 85.106 94 14 0 1748 1841 604295480 604295573 3.800000e-16 97.1
23 TraesCS6D01G206800 chr6A 85.106 94 14 0 1748 1841 604385293 604385386 3.800000e-16 97.1
24 TraesCS6D01G206800 chr6A 83.696 92 10 3 428 515 286424020 286423930 1.060000e-11 82.4
25 TraesCS6D01G206800 chr1A 94.840 969 43 4 3649 4610 396446955 396445987 0.000000e+00 1506.0
26 TraesCS6D01G206800 chr1A 83.582 268 32 8 254 516 4700257 4700517 1.660000e-59 241.0
27 TraesCS6D01G206800 chr1A 76.371 474 95 15 1459 1922 251376676 251377142 5.960000e-59 239.0
28 TraesCS6D01G206800 chr1A 82.353 272 32 12 254 518 19518001 19518263 6.000000e-54 222.0
29 TraesCS6D01G206800 chr1A 78.058 278 54 7 248 522 53445282 53445009 7.930000e-38 169.0
30 TraesCS6D01G206800 chr1D 94.547 972 42 7 3649 4610 236267292 236268262 0.000000e+00 1491.0
31 TraesCS6D01G206800 chr1D 77.407 270 47 11 254 517 57931291 57931552 1.030000e-31 148.0
32 TraesCS6D01G206800 chr1D 77.200 250 55 2 1667 1915 199624486 199624734 1.340000e-30 145.0
33 TraesCS6D01G206800 chr1D 79.024 205 32 6 314 514 401024952 401025149 3.740000e-26 130.0
34 TraesCS6D01G206800 chr1D 83.168 101 9 4 420 515 229408615 229408712 8.220000e-13 86.1
35 TraesCS6D01G206800 chr1D 89.831 59 5 1 458 515 42143026 42143084 1.780000e-09 75.0
36 TraesCS6D01G206800 chr1D 88.710 62 6 1 458 518 269856728 269856667 1.780000e-09 75.0
37 TraesCS6D01G206800 chr2A 94.473 977 36 8 3649 4610 179281763 179282736 0.000000e+00 1489.0
38 TraesCS6D01G206800 chr2A 88.496 226 24 2 3000 3224 607479988 607480212 5.880000e-69 272.0
39 TraesCS6D01G206800 chr2A 76.190 483 86 25 1466 1923 607476472 607476950 1.290000e-55 228.0
40 TraesCS6D01G206800 chr2A 88.830 188 16 3 1154 1340 607476176 607476359 4.640000e-55 226.0
41 TraesCS6D01G206800 chr2A 82.463 268 35 8 253 515 711885512 711885252 1.670000e-54 224.0
42 TraesCS6D01G206800 chr2A 86.432 199 25 2 2999 3196 610066609 610066806 2.790000e-52 217.0
43 TraesCS6D01G206800 chr2A 87.766 188 18 4 1154 1340 610058585 610058768 1.000000e-51 215.0
44 TraesCS6D01G206800 chr5B 94.342 972 45 6 3649 4610 48315003 48315974 0.000000e+00 1482.0
45 TraesCS6D01G206800 chr5B 82.582 976 131 23 3647 4610 248401390 248402338 0.000000e+00 824.0
46 TraesCS6D01G206800 chr7B 93.168 966 60 4 3649 4610 200481372 200482335 0.000000e+00 1413.0
47 TraesCS6D01G206800 chr7B 87.848 971 100 12 3647 4610 490603434 490602475 0.000000e+00 1123.0
48 TraesCS6D01G206800 chr5A 88.454 970 94 12 3649 4606 341135983 341136946 0.000000e+00 1155.0
49 TraesCS6D01G206800 chr5A 83.146 267 33 8 254 515 529182579 529182838 2.770000e-57 233.0
50 TraesCS6D01G206800 chr7D 88.235 969 98 10 3647 4610 466054272 466053315 0.000000e+00 1144.0
51 TraesCS6D01G206800 chr7D 81.550 271 38 7 250 515 364683079 364682816 3.610000e-51 213.0
52 TraesCS6D01G206800 chr7D 74.845 485 90 24 1466 1923 525350368 525350847 1.690000e-44 191.0
53 TraesCS6D01G206800 chr2D 88.261 230 25 2 2996 3224 462200391 462200619 1.630000e-69 274.0
54 TraesCS6D01G206800 chr2D 76.939 477 85 20 1466 1923 462197730 462198200 9.900000e-62 248.0
55 TraesCS6D01G206800 chr2D 89.894 188 14 4 1154 1340 462197431 462197614 2.140000e-58 237.0
56 TraesCS6D01G206800 chr2B 88.053 226 25 2 3000 3224 544984246 544984470 2.730000e-67 267.0
57 TraesCS6D01G206800 chr2B 83.088 272 30 12 254 518 57025349 57025087 2.770000e-57 233.0
58 TraesCS6D01G206800 chr2B 88.298 188 17 4 1154 1340 544981722 544981905 2.160000e-53 220.0
59 TraesCS6D01G206800 chr2B 75.884 481 87 20 1466 1923 544982009 544982483 7.770000e-53 219.0
60 TraesCS6D01G206800 chr3D 82.593 270 35 6 251 515 67721034 67721296 1.290000e-55 228.0
61 TraesCS6D01G206800 chr3D 81.227 277 40 8 244 515 297466842 297466573 3.610000e-51 213.0
62 TraesCS6D01G206800 chr3D 75.258 485 88 24 1466 1923 459311355 459311834 7.820000e-48 202.0
63 TraesCS6D01G206800 chr3D 80.071 281 41 10 249 523 487225907 487226178 1.310000e-45 195.0
64 TraesCS6D01G206800 chr4A 82.397 267 35 8 254 515 395037306 395037565 6.000000e-54 222.0
65 TraesCS6D01G206800 chr4A 82.759 261 33 8 260 515 454119751 454120004 6.000000e-54 222.0
66 TraesCS6D01G206800 chr4A 82.117 274 33 9 254 520 438615260 438615524 2.160000e-53 220.0
67 TraesCS6D01G206800 chr7A 81.139 281 39 7 249 523 418669676 418669404 3.610000e-51 213.0
68 TraesCS6D01G206800 chr4D 75.258 485 88 24 1466 1923 475139971 475140450 7.820000e-48 202.0
69 TraesCS6D01G206800 chr4D 74.845 485 90 24 1466 1923 462625928 462626407 1.690000e-44 191.0
70 TraesCS6D01G206800 chr4D 79.134 254 47 6 1673 1923 461226270 461226520 2.210000e-38 171.0
71 TraesCS6D01G206800 chr1B 87.943 141 17 0 1462 1602 280182258 280182398 2.850000e-37 167.0
72 TraesCS6D01G206800 chr4B 77.985 268 42 12 255 515 168181398 168181655 7.990000e-33 152.0
73 TraesCS6D01G206800 chr4B 82.143 140 25 0 1784 1923 652369503 652369364 2.250000e-23 121.0
74 TraesCS6D01G206800 chr5D 76.707 249 46 8 1673 1915 353763229 353763471 1.350000e-25 128.0
75 TraesCS6D01G206800 chrUn 89.655 58 5 1 460 516 287443516 287443573 6.400000e-09 73.1


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 TraesCS6D01G206800 chr6D 292373591 292378200 4609 False 8514.000000 8514 100.000000 1 4610 1 chr6D.!!$F3 4609
1 TraesCS6D01G206800 chr6B 9309391 9310361 970 False 1181.000000 1181 88.855000 3649 4610 1 chr6B.!!$F1 961
2 TraesCS6D01G206800 chr6B 455412234 455417270 5036 False 980.000000 2298 89.584400 1 3640 5 chr6B.!!$F4 3639
3 TraesCS6D01G206800 chr6B 455402206 455403241 1035 False 518.500000 610 87.121500 1 639 2 chr6B.!!$F3 638
4 TraesCS6D01G206800 chr6A 430340954 430344249 3295 True 1465.000000 2159 90.732667 286 3644 3 chr6A.!!$R2 3358
5 TraesCS6D01G206800 chr1A 396445987 396446955 968 True 1506.000000 1506 94.840000 3649 4610 1 chr1A.!!$R2 961
6 TraesCS6D01G206800 chr1D 236267292 236268262 970 False 1491.000000 1491 94.547000 3649 4610 1 chr1D.!!$F5 961
7 TraesCS6D01G206800 chr2A 179281763 179282736 973 False 1489.000000 1489 94.473000 3649 4610 1 chr2A.!!$F1 961
8 TraesCS6D01G206800 chr2A 607476176 607480212 4036 False 242.000000 272 84.505333 1154 3224 3 chr2A.!!$F4 2070
9 TraesCS6D01G206800 chr5B 48315003 48315974 971 False 1482.000000 1482 94.342000 3649 4610 1 chr5B.!!$F1 961
10 TraesCS6D01G206800 chr5B 248401390 248402338 948 False 824.000000 824 82.582000 3647 4610 1 chr5B.!!$F2 963
11 TraesCS6D01G206800 chr7B 200481372 200482335 963 False 1413.000000 1413 93.168000 3649 4610 1 chr7B.!!$F1 961
12 TraesCS6D01G206800 chr7B 490602475 490603434 959 True 1123.000000 1123 87.848000 3647 4610 1 chr7B.!!$R1 963
13 TraesCS6D01G206800 chr5A 341135983 341136946 963 False 1155.000000 1155 88.454000 3649 4606 1 chr5A.!!$F1 957
14 TraesCS6D01G206800 chr7D 466053315 466054272 957 True 1144.000000 1144 88.235000 3647 4610 1 chr7D.!!$R2 963
15 TraesCS6D01G206800 chr2D 462197431 462200619 3188 False 253.000000 274 85.031333 1154 3224 3 chr2D.!!$F1 2070
16 TraesCS6D01G206800 chr2B 544981722 544984470 2748 False 235.333333 267 84.078333 1154 3224 3 chr2B.!!$F1 2070

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
298 1038 0.379669 CGCCCATGACTTTGCAGATC 59.620 55.0 0.0 0.0 0.00 2.75 F
1323 2134 0.400213 TCTCCAACGGCCTCAACATT 59.600 50.0 0.0 0.0 0.00 2.71 F
2451 5054 0.901580 AATGGAGCCAGCAAAGGGTG 60.902 55.0 0.0 0.0 40.02 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 2179 0.101759 ATGCATGCATGGCGAAAGAC 59.898 50.0 31.74 9.08 42.12 3.01 R
2631 5242 0.522180 CTCGTACAGCCTCTGAACGT 59.478 55.0 0.29 0.00 35.18 3.99 R
3967 8382 0.398318 ACTCAAAGCTGACCCCTGAC 59.602 55.0 0.00 0.00 0.00 3.51 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
64 65 9.243637 TGAAAATTATAGTCAAAGTTGTGCAAC 57.756 29.630 6.94 6.94 41.45 4.17
104 105 7.215085 TCGAAAGAAAATATTAGCCTAGACCC 58.785 38.462 0.00 0.00 37.03 4.46
112 113 9.487442 AAAATATTAGCCTAGACCCAATGAAAA 57.513 29.630 0.00 0.00 0.00 2.29
113 114 9.487442 AAATATTAGCCTAGACCCAATGAAAAA 57.513 29.630 0.00 0.00 0.00 1.94
149 150 8.934825 GTCCTATGAATCAAATGATAGCTCTTC 58.065 37.037 0.00 0.00 33.73 2.87
155 156 8.878211 TGAATCAAATGATAGCTCTTCCTCTAT 58.122 33.333 0.00 0.00 33.73 1.98
187 188 7.712264 GAGATACATTTCATCTCACTTCCTG 57.288 40.000 7.33 0.00 45.17 3.86
188 189 6.054295 AGATACATTTCATCTCACTTCCTGC 58.946 40.000 0.00 0.00 0.00 4.85
190 191 1.442769 TTTCATCTCACTTCCTGCGC 58.557 50.000 0.00 0.00 0.00 6.09
192 193 0.610174 TCATCTCACTTCCTGCGCTT 59.390 50.000 9.73 0.00 0.00 4.68
204 205 2.415168 TCCTGCGCTTTTTCTATTCACG 59.585 45.455 9.73 0.00 0.00 4.35
210 211 5.005394 TGCGCTTTTTCTATTCACGAGATAC 59.995 40.000 9.73 0.00 0.00 2.24
258 259 6.017830 GCCTAGGGGTCATTTATACTACTCT 58.982 44.000 11.72 0.00 34.45 3.24
260 261 7.471890 CCTAGGGGTCATTTATACTACTCTCT 58.528 42.308 0.00 0.00 0.00 3.10
266 267 7.039574 GGGTCATTTATACTACTCTCTCCTTCC 60.040 44.444 0.00 0.00 0.00 3.46
273 274 5.428184 ACTACTCTCTCCTTCCCAAAATG 57.572 43.478 0.00 0.00 0.00 2.32
277 278 5.810095 ACTCTCTCCTTCCCAAAATGTAAG 58.190 41.667 0.00 0.00 0.00 2.34
278 279 5.548056 ACTCTCTCCTTCCCAAAATGTAAGA 59.452 40.000 0.00 0.00 0.00 2.10
279 280 5.805728 TCTCTCCTTCCCAAAATGTAAGAC 58.194 41.667 0.00 0.00 0.00 3.01
282 283 2.163613 CCTTCCCAAAATGTAAGACGCC 59.836 50.000 0.00 0.00 0.00 5.68
284 285 1.074084 TCCCAAAATGTAAGACGCCCA 59.926 47.619 0.00 0.00 0.00 5.36
298 1038 0.379669 CGCCCATGACTTTGCAGATC 59.620 55.000 0.00 0.00 0.00 2.75
307 1047 4.064388 TGACTTTGCAGATCGTTGATGAA 58.936 39.130 0.00 0.00 0.00 2.57
385 1127 8.549548 TGACATCGTCGTATTTTTCTTACAAAA 58.450 29.630 0.00 0.00 34.95 2.44
462 1207 5.725110 AGTGAAAATCATAGTCATCGTGC 57.275 39.130 0.00 0.00 0.00 5.34
505 1251 2.031157 CCGCGCCTTATATTTTGGGAAG 60.031 50.000 0.00 0.00 0.00 3.46
506 1252 2.031157 CGCGCCTTATATTTTGGGAAGG 60.031 50.000 0.00 0.00 41.26 3.46
507 1253 3.219281 GCGCCTTATATTTTGGGAAGGA 58.781 45.455 0.00 0.00 40.88 3.36
508 1254 3.253432 GCGCCTTATATTTTGGGAAGGAG 59.747 47.826 0.00 1.55 40.88 3.69
509 1255 3.821033 CGCCTTATATTTTGGGAAGGAGG 59.179 47.826 3.71 0.00 40.88 4.30
510 1256 4.152647 GCCTTATATTTTGGGAAGGAGGG 58.847 47.826 3.71 0.00 40.88 4.30
511 1257 4.141018 GCCTTATATTTTGGGAAGGAGGGA 60.141 45.833 3.71 0.00 40.88 4.20
512 1258 5.635120 CCTTATATTTTGGGAAGGAGGGAG 58.365 45.833 0.00 0.00 40.88 4.30
527 1273 4.079096 AGGAGGGAGTAGTACTGTAGCAAT 60.079 45.833 7.76 0.00 0.00 3.56
601 1356 4.915085 ACGGCAATTTCAACTGAATTAACG 59.085 37.500 0.00 0.00 33.54 3.18
681 1470 7.493971 ACTCATCATAACTGAAATTCTCTTCCG 59.506 37.037 0.00 0.00 34.37 4.30
682 1471 6.258727 TCATCATAACTGAAATTCTCTTCCGC 59.741 38.462 0.00 0.00 34.37 5.54
683 1472 5.734720 TCATAACTGAAATTCTCTTCCGCT 58.265 37.500 0.00 0.00 0.00 5.52
684 1473 6.873997 TCATAACTGAAATTCTCTTCCGCTA 58.126 36.000 0.00 0.00 0.00 4.26
722 1511 1.200020 AGCCGTGAAGCAAAGCATTAC 59.800 47.619 0.00 0.00 34.23 1.89
723 1512 1.200020 GCCGTGAAGCAAAGCATTACT 59.800 47.619 0.00 0.00 0.00 2.24
724 1513 2.418628 GCCGTGAAGCAAAGCATTACTA 59.581 45.455 0.00 0.00 0.00 1.82
877 1675 2.330745 GATCGAGCGTACGTCCCC 59.669 66.667 17.90 0.00 34.70 4.81
878 1676 2.124403 ATCGAGCGTACGTCCCCT 60.124 61.111 17.90 4.87 34.70 4.79
879 1677 2.115533 GATCGAGCGTACGTCCCCTC 62.116 65.000 17.90 13.17 34.70 4.30
880 1678 3.885521 CGAGCGTACGTCCCCTCC 61.886 72.222 17.90 0.00 0.00 4.30
881 1679 3.525545 GAGCGTACGTCCCCTCCC 61.526 72.222 17.90 0.00 0.00 4.30
905 1707 2.768344 CGCCACCTACCCATCCCT 60.768 66.667 0.00 0.00 0.00 4.20
917 1719 1.221840 CATCCCTCAACCACCTCGG 59.778 63.158 0.00 0.00 42.50 4.63
978 1789 1.701545 GCCTGTATAAAGCGCACGCA 61.702 55.000 18.24 0.00 44.88 5.24
996 1807 0.457166 CACGTTCGATCGCCACCTTA 60.457 55.000 15.45 0.00 0.00 2.69
1072 1883 1.153667 CTCTCCAGGTCTCAAGCGC 60.154 63.158 0.00 0.00 0.00 5.92
1132 1943 1.025113 CCTCGTCTCCGTAGTGCTCA 61.025 60.000 0.00 0.00 35.01 4.26
1191 2002 3.864686 CCGCGGGCATTCTTCGTG 61.865 66.667 20.10 0.00 0.00 4.35
1284 2095 2.202892 GGCATCGACTTCCCGTCC 60.203 66.667 0.00 0.00 39.56 4.79
1323 2134 0.400213 TCTCCAACGGCCTCAACATT 59.600 50.000 0.00 0.00 0.00 2.71
1347 2158 6.304624 TCCCGACATCATCAGTAATACTACT 58.695 40.000 0.00 0.00 39.04 2.57
1348 2159 6.430308 TCCCGACATCATCAGTAATACTACTC 59.570 42.308 0.00 0.00 36.14 2.59
1368 2179 1.599071 CCTACAATACACTGCATGCCG 59.401 52.381 16.68 12.01 0.00 5.69
1369 2180 2.279741 CTACAATACACTGCATGCCGT 58.720 47.619 16.68 12.81 0.00 5.68
1620 2439 1.457346 GTGCTCCATTTCCCTGACAG 58.543 55.000 0.00 0.00 0.00 3.51
1648 2478 4.023792 ACATGCATTGACGGCTTATGTATG 60.024 41.667 23.15 23.15 43.53 2.39
1659 2495 4.632688 CGGCTTATGTATGATGATGCATGA 59.367 41.667 2.46 0.00 35.82 3.07
1970 2824 2.548875 TGCTTCCAAATTTGTGCACAC 58.451 42.857 21.56 4.29 0.00 3.82
1993 2899 6.366332 CACTGCGCTAGGTAATTAGGAATTAG 59.634 42.308 9.73 0.00 34.23 1.73
1996 2925 7.954835 TGCGCTAGGTAATTAGGAATTAGTAA 58.045 34.615 9.73 0.00 34.23 2.24
2063 3325 4.536765 ACATGGCCATAAGAAGTAAAGGG 58.463 43.478 20.30 3.41 0.00 3.95
2064 3326 3.012934 TGGCCATAAGAAGTAAAGGGC 57.987 47.619 0.00 0.00 37.16 5.19
2065 3327 2.310349 TGGCCATAAGAAGTAAAGGGCA 59.690 45.455 0.00 0.00 41.37 5.36
2080 3343 2.751436 GCATGTGGCACCCGTCAT 60.751 61.111 16.26 0.00 43.97 3.06
2109 3372 6.164876 CACATGAAGAAGAGAGTGACAGATT 58.835 40.000 0.00 0.00 0.00 2.40
2130 3393 8.533965 CAGATTTGGTATTTTGATTTATGCACG 58.466 33.333 0.00 0.00 0.00 5.34
2232 4302 7.584123 CACGCTGCAATAGAATTATAACAGAAC 59.416 37.037 10.57 0.00 29.88 3.01
2308 4761 2.177977 CAACGATCGAGTACTGCTCAC 58.822 52.381 24.34 0.00 44.33 3.51
2451 5054 0.901580 AATGGAGCCAGCAAAGGGTG 60.902 55.000 0.00 0.00 40.02 4.61
2524 5135 2.747460 GCATTCACTCCTGGCGCA 60.747 61.111 10.83 0.00 0.00 6.09
2538 5149 3.035503 CGCACTGCAGCACGTACA 61.036 61.111 15.27 0.00 0.00 2.90
2559 5170 3.035727 CATGTGCTGTGCAGTGCA 58.964 55.556 15.37 15.37 40.08 4.57
2560 5171 1.081442 CATGTGCTGTGCAGTGCAG 60.081 57.895 20.42 9.23 40.08 4.41
2561 5172 1.228033 ATGTGCTGTGCAGTGCAGA 60.228 52.632 20.42 17.48 40.08 4.26
2587 5198 1.396301 CAGCAGCTTCTCGAATTCACC 59.604 52.381 6.22 0.00 0.00 4.02
2598 5209 1.025041 GAATTCACCCGCCTTCCATC 58.975 55.000 0.00 0.00 0.00 3.51
2896 6311 4.396854 CCGCAGAGCTACGGTAAC 57.603 61.111 12.84 0.00 44.46 2.50
2908 6323 0.032403 ACGGTAACTACGTGCTTGCA 59.968 50.000 0.00 0.00 43.78 4.08
2909 6324 0.713883 CGGTAACTACGTGCTTGCAG 59.286 55.000 0.00 0.00 0.00 4.41
2946 6361 3.691744 GACGGTCGAGCCTGCAGAG 62.692 68.421 17.39 6.56 34.25 3.35
2971 6386 2.598589 GCCGTGTGATCGTTGTTACTA 58.401 47.619 0.00 0.00 0.00 1.82
3251 6675 2.962421 CAGGAGGGTCCTCTTTAGCTAG 59.038 54.545 15.74 0.00 45.66 3.42
3333 6890 2.266279 AGTAGTTTGCTCCTAGGGCAA 58.734 47.619 25.11 25.11 46.12 4.52
3361 6918 2.935849 TGCATGTGCGTTTATAGGAGTG 59.064 45.455 0.01 0.00 45.83 3.51
3380 6937 5.932303 GGAGTGAGTGTATTTGTGTATGTGT 59.068 40.000 0.00 0.00 0.00 3.72
3516 7899 1.662517 TTTCTGTTCTGCGTGCAAGA 58.337 45.000 2.99 0.00 0.00 3.02
3570 7954 4.386867 TTCTATCTCGATGGTCACAACC 57.613 45.455 0.00 0.00 46.66 3.77
3689 8073 5.163814 GCTTAAGAAGAATGACAAGCGTGAT 60.164 40.000 6.65 0.00 30.29 3.06
3730 8114 1.685765 CCTGGGAGGTCGACCATGA 60.686 63.158 35.00 15.33 38.89 3.07
3733 8117 1.003118 CTGGGAGGTCGACCATGAAAA 59.997 52.381 35.00 14.77 38.89 2.29
3800 8187 3.878778 AGAAGGACTTGCATATGGTGTC 58.121 45.455 4.56 0.00 0.00 3.67
3967 8382 2.557056 TCCCGATTAAGATAGGACTGCG 59.443 50.000 0.00 0.00 30.20 5.18
3986 8401 0.398318 GTCAGGGGTCAGCTTTGAGT 59.602 55.000 0.00 0.00 0.00 3.41
4059 8476 3.449018 AGATATCCGATGGTGTATGCTCC 59.551 47.826 0.00 0.00 0.00 4.70
4147 8568 7.133346 TGGAGACAAACCTTGAAATCGAAAGA 61.133 38.462 0.00 0.00 41.45 2.52
4221 8655 1.827969 CTAGGTGTGAGGAGGAGGTTG 59.172 57.143 0.00 0.00 0.00 3.77
4244 8678 1.858739 TTGATGGCCAGGTGGTACCC 61.859 60.000 13.05 0.11 39.75 3.69
4256 8690 0.104882 TGGTACCCCAGAAGGACACA 60.105 55.000 10.07 0.00 38.24 3.72
4269 8703 5.411361 CAGAAGGACACATTTCGGTATTTGA 59.589 40.000 0.00 0.00 0.00 2.69
4328 8763 4.075682 TGTAAACCATCGAATCAAAGCCA 58.924 39.130 0.00 0.00 0.00 4.75
4348 8783 1.442526 GATGGATGAAGTGGCGCCAG 61.443 60.000 33.73 0.00 31.23 4.85
4367 8802 1.630369 AGGCTTCTGGCATTCTGTGTA 59.370 47.619 0.00 0.00 44.01 2.90
4490 8926 2.685897 GTTCAACAGTTAGGTGTGGCAA 59.314 45.455 0.00 0.00 35.97 4.52
4594 9033 3.766545 AGCACCAATTGAAGGAAGCTTA 58.233 40.909 7.12 0.00 37.62 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 9.979578 TGCACAACTTTGACTATAATTTTCAAT 57.020 25.926 0.00 0.00 0.00 2.57
45 46 7.561021 TCTTTGTTGCACAACTTTGACTATA 57.439 32.000 14.16 0.00 37.90 1.31
51 52 7.754069 TTCTAATCTTTGTTGCACAACTTTG 57.246 32.000 14.16 4.90 37.90 2.77
60 61 9.180678 TCTTTCGATTTTTCTAATCTTTGTTGC 57.819 29.630 0.00 0.00 0.00 4.17
80 81 6.990349 TGGGTCTAGGCTAATATTTTCTTTCG 59.010 38.462 0.00 0.00 0.00 3.46
81 82 8.747538 TTGGGTCTAGGCTAATATTTTCTTTC 57.252 34.615 0.00 0.00 0.00 2.62
123 124 8.845413 AAGAGCTATCATTTGATTCATAGGAC 57.155 34.615 0.00 0.00 36.05 3.85
125 126 8.102047 AGGAAGAGCTATCATTTGATTCATAGG 58.898 37.037 0.00 0.00 36.05 2.57
163 164 6.202570 GCAGGAAGTGAGATGAAATGTATCTC 59.797 42.308 7.80 7.80 46.82 2.75
172 173 0.610174 AGCGCAGGAAGTGAGATGAA 59.390 50.000 11.47 0.00 0.00 2.57
187 188 3.991605 TCTCGTGAATAGAAAAAGCGC 57.008 42.857 0.00 0.00 0.00 5.92
188 189 6.074782 GGAGTATCTCGTGAATAGAAAAAGCG 60.075 42.308 0.00 0.00 33.73 4.68
210 211 8.261522 GGCCTCCTTTAGTTCATATAATAGGAG 58.738 40.741 0.00 0.00 44.50 3.69
217 218 6.023603 CCCTAGGCCTCCTTTAGTTCATATA 58.976 44.000 9.68 0.00 34.61 0.86
218 219 4.846940 CCCTAGGCCTCCTTTAGTTCATAT 59.153 45.833 9.68 0.00 34.61 1.78
258 259 4.575885 CGTCTTACATTTTGGGAAGGAGA 58.424 43.478 0.00 0.00 0.00 3.71
260 261 3.078837 GCGTCTTACATTTTGGGAAGGA 58.921 45.455 0.00 0.00 0.00 3.36
266 267 2.752354 TCATGGGCGTCTTACATTTTGG 59.248 45.455 0.00 0.00 0.00 3.28
273 274 1.130561 GCAAAGTCATGGGCGTCTTAC 59.869 52.381 0.00 0.00 0.00 2.34
277 278 0.955428 TCTGCAAAGTCATGGGCGTC 60.955 55.000 0.00 0.00 0.00 5.19
278 279 0.322816 ATCTGCAAAGTCATGGGCGT 60.323 50.000 0.00 0.00 0.00 5.68
279 280 0.379669 GATCTGCAAAGTCATGGGCG 59.620 55.000 0.00 0.00 0.00 6.13
282 283 2.743664 TCAACGATCTGCAAAGTCATGG 59.256 45.455 0.00 0.00 0.00 3.66
284 285 4.256110 TCATCAACGATCTGCAAAGTCAT 58.744 39.130 0.00 0.00 0.00 3.06
329 1069 9.812347 ATACATATTCAATCCATGTAATGTGGT 57.188 29.630 0.00 0.00 44.81 4.16
437 1179 7.119997 GCACGATGACTATGATTTTCACTTAC 58.880 38.462 0.00 0.00 0.00 2.34
455 1197 1.872952 TCTGGTCTTTGTTGCACGATG 59.127 47.619 0.00 0.00 0.00 3.84
457 1199 2.031258 TTCTGGTCTTTGTTGCACGA 57.969 45.000 0.00 0.00 0.00 4.35
458 1200 2.842208 TTTCTGGTCTTTGTTGCACG 57.158 45.000 0.00 0.00 0.00 5.34
462 1207 5.102313 GGTTCACTTTTCTGGTCTTTGTTG 58.898 41.667 0.00 0.00 0.00 3.33
505 1251 3.294038 TGCTACAGTACTACTCCCTCC 57.706 52.381 0.00 0.00 0.00 4.30
506 1252 7.884354 AGTATATTGCTACAGTACTACTCCCTC 59.116 40.741 0.00 0.00 0.00 4.30
507 1253 7.666388 CAGTATATTGCTACAGTACTACTCCCT 59.334 40.741 0.00 0.00 0.00 4.20
508 1254 7.664731 TCAGTATATTGCTACAGTACTACTCCC 59.335 40.741 0.00 0.00 0.00 4.30
509 1255 8.618702 TCAGTATATTGCTACAGTACTACTCC 57.381 38.462 0.00 0.00 0.00 3.85
601 1356 1.873591 AGTTTGGCATCACGACAGTTC 59.126 47.619 0.00 0.00 30.55 3.01
681 1470 2.289547 TGTCTCGTTTGCTGGTTTTAGC 59.710 45.455 0.00 0.00 43.95 3.09
682 1471 3.607078 GCTGTCTCGTTTGCTGGTTTTAG 60.607 47.826 0.00 0.00 0.00 1.85
683 1472 2.289547 GCTGTCTCGTTTGCTGGTTTTA 59.710 45.455 0.00 0.00 0.00 1.52
684 1473 1.065551 GCTGTCTCGTTTGCTGGTTTT 59.934 47.619 0.00 0.00 0.00 2.43
722 1511 3.131755 AGGGTTCGTACGGAAGGAAATAG 59.868 47.826 16.52 0.00 34.69 1.73
723 1512 3.099141 AGGGTTCGTACGGAAGGAAATA 58.901 45.455 16.52 0.00 34.69 1.40
724 1513 1.904537 AGGGTTCGTACGGAAGGAAAT 59.095 47.619 16.52 0.00 34.69 2.17
889 1687 1.279025 TTGAGGGATGGGTAGGTGGC 61.279 60.000 0.00 0.00 0.00 5.01
905 1707 1.100510 CGTAGATCCGAGGTGGTTGA 58.899 55.000 0.00 0.00 39.52 3.18
937 1748 2.125552 CGGGCAGCTTGATCGACA 60.126 61.111 0.00 0.00 0.00 4.35
978 1789 0.458669 ATAAGGTGGCGATCGAACGT 59.541 50.000 21.57 14.47 35.59 3.99
996 1807 1.084370 GCGCGCACTAGGAAACTGAT 61.084 55.000 29.10 0.00 43.88 2.90
1323 2134 6.304624 AGTAGTATTACTGATGATGTCGGGA 58.695 40.000 6.60 0.00 38.69 5.14
1347 2158 2.741553 CGGCATGCAGTGTATTGTAGGA 60.742 50.000 21.36 0.00 0.00 2.94
1348 2159 1.599071 CGGCATGCAGTGTATTGTAGG 59.401 52.381 21.36 0.00 0.00 3.18
1368 2179 0.101759 ATGCATGCATGGCGAAAGAC 59.898 50.000 31.74 9.08 42.12 3.01
1369 2180 0.382873 GATGCATGCATGGCGAAAGA 59.617 50.000 36.73 3.35 36.70 2.52
1430 2241 3.490759 GTGACATGCCGTGCTCCG 61.491 66.667 0.00 0.00 0.00 4.63
1620 2439 3.698029 AGCCGTCAATGCATGTTAATC 57.302 42.857 0.00 0.00 0.00 1.75
1648 2478 4.214758 TCGACCAATCATTCATGCATCATC 59.785 41.667 0.00 0.00 0.00 2.92
1659 2495 1.278985 TCACCTGCTCGACCAATCATT 59.721 47.619 0.00 0.00 0.00 2.57
1793 2647 3.050275 GTTGCCTCCCAGCGTGAC 61.050 66.667 0.00 0.00 34.65 3.67
1931 2785 7.092716 GGAAGCAACATCAACTGTAAATTCAT 58.907 34.615 0.00 0.00 36.98 2.57
1970 2824 6.456501 ACTAATTCCTAATTACCTAGCGCAG 58.543 40.000 11.47 4.88 32.38 5.18
2063 3325 2.751436 ATGACGGGTGCCACATGC 60.751 61.111 0.00 0.00 41.77 4.06
2064 3326 1.377072 TCATGACGGGTGCCACATG 60.377 57.895 0.00 0.00 38.39 3.21
2065 3327 1.377202 GTCATGACGGGTGCCACAT 60.377 57.895 10.69 0.00 0.00 3.21
2080 3343 4.342092 TCACTCTCTTCTTCATGTGTGTCA 59.658 41.667 0.00 0.00 0.00 3.58
2109 3372 6.096036 CACCGTGCATAAATCAAAATACCAA 58.904 36.000 0.00 0.00 0.00 3.67
2143 3406 9.605955 CAACAACTCGAATATACATTCACAAAA 57.394 29.630 0.00 0.00 40.61 2.44
2144 3407 7.748683 GCAACAACTCGAATATACATTCACAAA 59.251 33.333 0.00 0.00 40.61 2.83
2232 4302 3.451902 AGAGATCTTCCTTCTGGCTTCAG 59.548 47.826 0.00 0.00 39.78 3.02
2239 4309 8.646004 TCCATTTATGTAGAGATCTTCCTTCTG 58.354 37.037 0.00 0.00 0.00 3.02
2308 4761 7.621832 TTTTCATGTGCTCAAACTTAATTCG 57.378 32.000 0.00 0.00 0.00 3.34
2345 4798 0.959372 AGGTCATCAAGTGCTGCTGC 60.959 55.000 8.89 8.89 40.20 5.25
2383 4840 1.464219 TGTGTGTGTATTCATGCTGCG 59.536 47.619 0.00 0.00 0.00 5.18
2451 5054 3.119029 TGTCTTTACCCTGTACGTATGGC 60.119 47.826 0.00 0.00 0.00 4.40
2454 5057 3.131755 GGCTGTCTTTACCCTGTACGTAT 59.868 47.826 0.00 0.00 0.00 3.06
2460 5063 1.636148 TACGGCTGTCTTTACCCTGT 58.364 50.000 0.00 0.00 0.00 4.00
2524 5135 0.884259 TGCATTGTACGTGCTGCAGT 60.884 50.000 16.64 6.28 42.92 4.40
2564 5175 0.801251 AATTCGAGAAGCTGCTGCAC 59.199 50.000 18.42 11.01 42.74 4.57
2565 5176 1.081892 GAATTCGAGAAGCTGCTGCA 58.918 50.000 18.42 0.88 42.74 4.41
2587 5198 1.893808 CATTCGGGATGGAAGGCGG 60.894 63.158 0.00 0.00 31.83 6.13
2598 5209 0.801067 GTTCGTCGGTCTCATTCGGG 60.801 60.000 0.00 0.00 0.00 5.14
2631 5242 0.522180 CTCGTACAGCCTCTGAACGT 59.478 55.000 0.29 0.00 35.18 3.99
2783 6195 3.737172 GCGCACCATGTCCACCAC 61.737 66.667 0.30 0.00 0.00 4.16
2971 6386 4.038642 ACGAACCACAAGCACCAATTAATT 59.961 37.500 0.00 0.00 0.00 1.40
3157 6581 1.003839 GGACCCGTGCATGAACTGA 60.004 57.895 7.72 0.00 0.00 3.41
3333 6890 1.383456 AAACGCACATGCACACACCT 61.383 50.000 4.49 0.00 42.21 4.00
3361 6918 6.954944 ACACAACACATACACAAATACACTC 58.045 36.000 0.00 0.00 0.00 3.51
3399 6956 5.736951 ACATTATGCTTTTACTTGGCCAA 57.263 34.783 19.25 19.25 0.00 4.52
3411 6968 8.421002 ACAAAAAGGTACTGAAACATTATGCTT 58.579 29.630 0.00 0.00 40.86 3.91
3516 7899 6.550854 TCATGACCTTTTCTTTTGGACAGAAT 59.449 34.615 0.00 0.00 30.26 2.40
3640 8024 2.038659 CTCAATGACTCTCCCTCCTCC 58.961 57.143 0.00 0.00 0.00 4.30
3641 8025 1.412343 GCTCAATGACTCTCCCTCCTC 59.588 57.143 0.00 0.00 0.00 3.71
3642 8026 1.273495 TGCTCAATGACTCTCCCTCCT 60.273 52.381 0.00 0.00 0.00 3.69
3643 8027 1.134551 GTGCTCAATGACTCTCCCTCC 60.135 57.143 0.00 0.00 0.00 4.30
3644 8028 1.134551 GGTGCTCAATGACTCTCCCTC 60.135 57.143 0.00 0.00 0.00 4.30
3645 8029 0.908198 GGTGCTCAATGACTCTCCCT 59.092 55.000 0.00 0.00 0.00 4.20
3696 8080 1.688197 CCAGGCATGAAACCAAACTGT 59.312 47.619 0.00 0.00 0.00 3.55
3800 8187 1.005215 AGGCCTTCTCCAAGTCAATGG 59.995 52.381 0.00 0.00 42.12 3.16
3967 8382 0.398318 ACTCAAAGCTGACCCCTGAC 59.602 55.000 0.00 0.00 0.00 3.51
3986 8401 6.351202 CCATCACCAATGCAAAAAGATAAGGA 60.351 38.462 0.00 0.00 33.71 3.36
4045 8462 0.940126 CGCAAGGAGCATACACCATC 59.060 55.000 0.00 0.00 46.13 3.51
4059 8476 1.028330 AGCACCACATCATCCGCAAG 61.028 55.000 0.00 0.00 0.00 4.01
4147 8568 9.905171 CGGTTTTAGTTCTACTAAGACTAAACT 57.095 33.333 15.49 0.00 42.25 2.66
4244 8678 2.185004 ACCGAAATGTGTCCTTCTGG 57.815 50.000 0.00 0.00 0.00 3.86
4256 8690 4.949856 AGCATTGACCTCAAATACCGAAAT 59.050 37.500 0.00 0.00 39.55 2.17
4269 8703 1.203441 TCCTCCTGCAGCATTGACCT 61.203 55.000 8.66 0.00 0.00 3.85
4328 8763 1.153086 GGCGCCACTTCATCCATCT 60.153 57.895 24.80 0.00 0.00 2.90
4348 8783 2.113860 TACACAGAATGCCAGAAGCC 57.886 50.000 0.00 0.00 42.53 4.35
4363 8798 2.833794 TGTGGCACTCTCTTGTTACAC 58.166 47.619 19.83 0.00 0.00 2.90
4367 8802 2.099756 GCTTTTGTGGCACTCTCTTGTT 59.900 45.455 19.83 0.00 0.00 2.83
4490 8926 6.206829 CACATCCATCTCAACATATGCATCTT 59.793 38.462 0.19 0.00 0.00 2.40
4497 8933 4.139786 GCCACACATCCATCTCAACATAT 58.860 43.478 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.