Multiple sequence alignment - TraesCS1D01G225700

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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 TraesCS1D01G225700 chr1D 100.000 2594 0 0 1 2594 314195164 314197757 0.000000e+00 4791.0
1 TraesCS1D01G225700 chr1D 88.795 589 60 2 190 777 487944256 487944839 0.000000e+00 717.0
2 TraesCS1D01G225700 chr1D 88.776 588 60 3 192 778 18666886 18666304 0.000000e+00 715.0
3 TraesCS1D01G225700 chr1D 86.446 332 23 9 1941 2263 202558837 202559155 6.870000e-91 344.0
4 TraesCS1D01G225700 chr1D 95.480 177 8 0 1315 1491 314419163 314419339 1.520000e-72 283.0
5 TraesCS1D01G225700 chr1D 93.820 178 11 0 1321 1498 314426554 314426731 4.250000e-68 268.0
6 TraesCS1D01G225700 chr1D 82.836 134 19 3 1096 1229 314418939 314419068 1.630000e-22 117.0
7 TraesCS1D01G225700 chr1D 82.927 123 18 1 1100 1222 314426343 314426462 9.820000e-20 108.0
8 TraesCS1D01G225700 chr1B 89.511 696 39 16 1256 1928 424414437 424415121 0.000000e+00 850.0
9 TraesCS1D01G225700 chr1B 92.825 446 18 7 795 1230 424414004 424414445 3.640000e-178 634.0
10 TraesCS1D01G225700 chr1B 94.565 184 10 0 1315 1498 424531661 424531844 4.220000e-73 285.0
11 TraesCS1D01G225700 chr1B 83.077 130 16 4 1100 1228 424535365 424535489 2.110000e-21 113.0
12 TraesCS1D01G225700 chr1B 82.222 135 20 2 1939 2072 566709302 566709433 2.110000e-21 113.0
13 TraesCS1D01G225700 chr1A 87.959 681 50 20 1270 1929 394444640 394445309 0.000000e+00 774.0
14 TraesCS1D01G225700 chr1A 87.959 681 50 20 1270 1929 394533034 394533703 0.000000e+00 774.0
15 TraesCS1D01G225700 chr1A 92.699 452 22 5 780 1230 394444187 394444628 2.180000e-180 641.0
16 TraesCS1D01G225700 chr1A 92.699 452 22 5 780 1230 394532581 394533022 2.180000e-180 641.0
17 TraesCS1D01G225700 chr1A 94.872 195 6 3 1 191 394443842 394444036 4.200000e-78 302.0
18 TraesCS1D01G225700 chr1A 94.872 195 6 3 1 191 394532236 394532430 4.200000e-78 302.0
19 TraesCS1D01G225700 chr1A 93.564 202 9 3 1315 1516 394482337 394482534 5.430000e-77 298.0
20 TraesCS1D01G225700 chr1A 93.564 202 9 3 1315 1516 394567010 394567207 5.430000e-77 298.0
21 TraesCS1D01G225700 chr1A 92.857 196 10 3 1321 1516 394588117 394588308 5.470000e-72 281.0
22 TraesCS1D01G225700 chr1A 83.333 132 18 3 1096 1227 394482135 394482262 4.530000e-23 119.0
23 TraesCS1D01G225700 chr1A 89.474 95 8 1 1585 1679 394534779 394534871 4.530000e-23 119.0
24 TraesCS1D01G225700 chr1A 83.333 132 18 3 1096 1227 394566808 394566935 4.530000e-23 119.0
25 TraesCS1D01G225700 chr4D 89.897 584 53 2 199 781 459073048 459072470 0.000000e+00 747.0
26 TraesCS1D01G225700 chr4D 89.116 588 58 2 191 777 368465220 368464638 0.000000e+00 726.0
27 TraesCS1D01G225700 chr4D 85.303 347 22 16 1941 2263 69134969 69134628 5.350000e-87 331.0
28 TraesCS1D01G225700 chr4D 84.900 351 23 16 1937 2263 507897431 507897775 6.920000e-86 327.0
29 TraesCS1D01G225700 chr7D 89.134 589 56 4 192 778 242767723 242768305 0.000000e+00 726.0
30 TraesCS1D01G225700 chr7D 88.481 599 60 5 184 778 120524538 120525131 0.000000e+00 715.0
31 TraesCS1D01G225700 chr7D 88.851 583 54 7 192 773 449156746 449157318 0.000000e+00 706.0
32 TraesCS1D01G225700 chr7D 92.420 343 14 2 2264 2594 349949721 349949379 1.810000e-131 479.0
33 TraesCS1D01G225700 chr7D 90.671 343 20 2 2264 2594 254900253 254900595 1.830000e-121 446.0
34 TraesCS1D01G225700 chr7D 87.988 333 25 9 1941 2263 426556021 426556348 1.880000e-101 379.0
35 TraesCS1D01G225700 chr7D 88.591 298 20 8 1939 2226 45200097 45200390 1.480000e-92 350.0
36 TraesCS1D01G225700 chr7D 84.874 357 25 15 1932 2263 172258702 172259054 1.490000e-87 333.0
37 TraesCS1D01G225700 chr3A 89.116 588 56 4 192 778 316573959 316574539 0.000000e+00 725.0
38 TraesCS1D01G225700 chr3A 88.795 589 59 3 192 779 87441666 87441084 0.000000e+00 715.0
39 TraesCS1D01G225700 chr3A 81.618 136 19 4 1939 2072 669179828 669179697 9.820000e-20 108.0
40 TraesCS1D01G225700 chr5D 90.962 343 19 2 2264 2594 381787956 381788298 3.940000e-123 451.0
41 TraesCS1D01G225700 chr5D 85.044 341 31 10 1939 2263 293511602 293511938 1.920000e-86 329.0
42 TraesCS1D01G225700 chr2D 90.379 343 21 2 2264 2594 74972721 74973063 8.520000e-120 440.0
43 TraesCS1D01G225700 chr2D 88.498 313 22 8 1939 2244 74972464 74972769 1.470000e-97 366.0
44 TraesCS1D01G225700 chr6D 90.087 343 22 5 2264 2594 428424901 428424559 3.960000e-118 435.0
45 TraesCS1D01G225700 chr6D 86.646 322 29 10 1936 2250 428425161 428424847 6.870000e-91 344.0
46 TraesCS1D01G225700 chr3D 90.087 343 22 5 2264 2594 556937033 556937375 3.960000e-118 435.0
47 TraesCS1D01G225700 chr3D 90.087 343 22 3 2264 2594 580086146 580086488 3.960000e-118 435.0
48 TraesCS1D01G225700 chr2A 90.179 336 26 5 2264 2594 5702018 5701685 5.130000e-117 431.0
49 TraesCS1D01G225700 chr7A 89.213 343 25 6 2264 2594 571362561 571362219 3.990000e-113 418.0
50 TraesCS1D01G225700 chr5A 100.000 30 0 0 2234 2263 407782755 407782784 3.610000e-04 56.5


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 TraesCS1D01G225700 chr1D 314195164 314197757 2593 False 4791.000000 4791 100.000000 1 2594 1 chr1D.!!$F2 2593
1 TraesCS1D01G225700 chr1D 487944256 487944839 583 False 717.000000 717 88.795000 190 777 1 chr1D.!!$F3 587
2 TraesCS1D01G225700 chr1D 18666304 18666886 582 True 715.000000 715 88.776000 192 778 1 chr1D.!!$R1 586
3 TraesCS1D01G225700 chr1B 424414004 424415121 1117 False 742.000000 850 91.168000 795 1928 2 chr1B.!!$F2 1133
4 TraesCS1D01G225700 chr1A 394443842 394445309 1467 False 572.333333 774 91.843333 1 1929 3 chr1A.!!$F2 1928
5 TraesCS1D01G225700 chr1A 394532236 394534871 2635 False 459.000000 774 91.251000 1 1929 4 chr1A.!!$F4 1928
6 TraesCS1D01G225700 chr4D 459072470 459073048 578 True 747.000000 747 89.897000 199 781 1 chr4D.!!$R3 582
7 TraesCS1D01G225700 chr4D 368464638 368465220 582 True 726.000000 726 89.116000 191 777 1 chr4D.!!$R2 586
8 TraesCS1D01G225700 chr7D 242767723 242768305 582 False 726.000000 726 89.134000 192 778 1 chr7D.!!$F4 586
9 TraesCS1D01G225700 chr7D 120524538 120525131 593 False 715.000000 715 88.481000 184 778 1 chr7D.!!$F2 594
10 TraesCS1D01G225700 chr7D 449156746 449157318 572 False 706.000000 706 88.851000 192 773 1 chr7D.!!$F7 581
11 TraesCS1D01G225700 chr3A 316573959 316574539 580 False 725.000000 725 89.116000 192 778 1 chr3A.!!$F1 586
12 TraesCS1D01G225700 chr3A 87441084 87441666 582 True 715.000000 715 88.795000 192 779 1 chr3A.!!$R1 587
13 TraesCS1D01G225700 chr2D 74972464 74973063 599 False 403.000000 440 89.438500 1939 2594 2 chr2D.!!$F1 655
14 TraesCS1D01G225700 chr6D 428424559 428425161 602 True 389.500000 435 88.366500 1936 2594 2 chr6D.!!$R1 658

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
521 537 0.515564 ACGAACAAGTATGCGTTGCC 59.484 50.0 0.0 0.0 32.42 4.52 F
1043 1071 0.110295 AGCAGTTGCATACACCACCA 59.890 50.0 6.9 0.0 45.16 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1581 1617 0.037303 TCCGAGTACCTGACGACCTT 59.963 55.0 0.0 0.0 0.00 3.50 R
2226 3005 0.668706 GATGACGATGGCGAGGATGG 60.669 60.0 0.0 0.0 41.64 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
79 82 2.566913 ACGTTGTGAGCAAACCATACA 58.433 42.857 0.00 0.00 36.22 2.29
82 85 3.974401 CGTTGTGAGCAAACCATACAAAG 59.026 43.478 0.00 0.00 36.22 2.77
100 103 0.744414 AGAAATGGCATGACGGTCGG 60.744 55.000 0.00 0.00 0.00 4.79
113 116 2.737376 GTCGGTTCACGGCCAGTC 60.737 66.667 2.24 0.00 42.53 3.51
195 200 2.451490 CCAGCAGAGTCTTGAGTAGGA 58.549 52.381 0.00 0.00 0.00 2.94
223 228 1.522130 GGTACCCATTACCCGCGTG 60.522 63.158 4.92 0.00 44.41 5.34
260 265 2.972348 CCTAGTAGGGCAAGGGTATGA 58.028 52.381 8.50 0.00 0.00 2.15
508 524 1.742411 GCAATAGCTAGCCCACGAACA 60.742 52.381 12.13 0.00 37.91 3.18
521 537 0.515564 ACGAACAAGTATGCGTTGCC 59.484 50.000 0.00 0.00 32.42 4.52
611 627 9.345517 CAAATTGATGTGTTGTAAATCTAGGTG 57.654 33.333 0.00 0.00 0.00 4.00
728 744 4.310022 AAGATTTGGGATGACGGGTAAA 57.690 40.909 0.00 0.00 0.00 2.01
818 835 1.574339 TCCCCTTCCTCGGATAACTCT 59.426 52.381 0.00 0.00 0.00 3.24
857 875 1.730064 CCCATTACGTGTTGTCTTCCG 59.270 52.381 0.00 0.00 0.00 4.30
1042 1070 0.523072 CAGCAGTTGCATACACCACC 59.477 55.000 6.90 0.00 45.16 4.61
1043 1071 0.110295 AGCAGTTGCATACACCACCA 59.890 50.000 6.90 0.00 45.16 4.17
1044 1072 0.240945 GCAGTTGCATACACCACCAC 59.759 55.000 0.00 0.00 41.59 4.16
1053 1081 0.680061 TACACCACCACACACGCATA 59.320 50.000 0.00 0.00 0.00 3.14
1056 1084 0.602638 ACCACCACACACGCATACAG 60.603 55.000 0.00 0.00 0.00 2.74
1097 1125 1.153823 CGGTCGAGCACCTGTTAGG 60.154 63.158 15.89 0.00 44.21 2.69
1140 1168 1.979693 GAGGTCGGAGCTGGACAGT 60.980 63.158 15.38 3.40 36.12 3.55
1234 1262 2.840296 CGAAGGTAACGTACTCCCTC 57.160 55.000 0.00 0.00 46.39 4.30
1235 1263 1.403323 CGAAGGTAACGTACTCCCTCC 59.597 57.143 0.00 0.00 46.39 4.30
1236 1264 1.403323 GAAGGTAACGTACTCCCTCCG 59.597 57.143 0.00 0.00 46.39 4.63
1237 1265 0.329596 AGGTAACGTACTCCCTCCGT 59.670 55.000 0.00 0.00 46.39 4.69
1238 1266 1.177401 GGTAACGTACTCCCTCCGTT 58.823 55.000 0.00 0.00 45.65 4.44
1239 1267 1.133216 GGTAACGTACTCCCTCCGTTC 59.867 57.143 0.00 0.00 43.09 3.95
1240 1268 1.133216 GTAACGTACTCCCTCCGTTCC 59.867 57.143 0.00 0.00 43.09 3.62
1241 1269 0.251519 AACGTACTCCCTCCGTTCCT 60.252 55.000 0.00 0.00 40.46 3.36
1242 1270 0.620556 ACGTACTCCCTCCGTTCCTA 59.379 55.000 0.00 0.00 0.00 2.94
1243 1271 1.213926 ACGTACTCCCTCCGTTCCTAT 59.786 52.381 0.00 0.00 0.00 2.57
1244 1272 2.439507 ACGTACTCCCTCCGTTCCTATA 59.560 50.000 0.00 0.00 0.00 1.31
1245 1273 3.117888 ACGTACTCCCTCCGTTCCTATAA 60.118 47.826 0.00 0.00 0.00 0.98
1246 1274 3.501445 CGTACTCCCTCCGTTCCTATAAG 59.499 52.174 0.00 0.00 0.00 1.73
1247 1275 3.684408 ACTCCCTCCGTTCCTATAAGT 57.316 47.619 0.00 0.00 0.00 2.24
1248 1276 3.564264 ACTCCCTCCGTTCCTATAAGTC 58.436 50.000 0.00 0.00 0.00 3.01
1249 1277 3.204831 ACTCCCTCCGTTCCTATAAGTCT 59.795 47.826 0.00 0.00 0.00 3.24
1250 1278 4.414846 ACTCCCTCCGTTCCTATAAGTCTA 59.585 45.833 0.00 0.00 0.00 2.59
1251 1279 4.983053 TCCCTCCGTTCCTATAAGTCTAG 58.017 47.826 0.00 0.00 0.00 2.43
1252 1280 4.080687 CCCTCCGTTCCTATAAGTCTAGG 58.919 52.174 0.00 0.00 39.81 3.02
1253 1281 4.080687 CCTCCGTTCCTATAAGTCTAGGG 58.919 52.174 0.00 0.00 39.08 3.53
1254 1282 4.202545 CCTCCGTTCCTATAAGTCTAGGGA 60.203 50.000 0.00 0.00 39.08 4.20
1255 1283 4.983053 TCCGTTCCTATAAGTCTAGGGAG 58.017 47.826 0.00 0.00 39.08 4.30
1256 1284 4.414846 TCCGTTCCTATAAGTCTAGGGAGT 59.585 45.833 0.00 0.00 39.08 3.85
1257 1285 5.608437 TCCGTTCCTATAAGTCTAGGGAGTA 59.392 44.000 0.00 0.00 39.08 2.59
1313 1346 0.111045 CATTGTTGTAACACGCGCGA 60.111 50.000 39.36 11.73 38.92 5.87
1316 1349 0.111045 TGTTGTAACACGCGCGAATG 60.111 50.000 39.36 27.47 33.17 2.67
1415 1448 2.045926 GGGCTGAGCACCAACGAT 60.046 61.111 6.82 0.00 0.00 3.73
1510 1546 2.289072 TGTTCAGTTCAGTGCCTAGCTC 60.289 50.000 0.00 0.00 0.00 4.09
1520 1556 0.675837 TGCCTAGCTCAGCAAAGCAG 60.676 55.000 8.06 7.62 45.00 4.24
1543 1579 1.956170 CTGCTCGCTCGTGTTTGGT 60.956 57.895 0.00 0.00 0.00 3.67
1558 1594 4.571984 GTGTTTGGTTGTAGTCCGTTTAGT 59.428 41.667 0.00 0.00 0.00 2.24
1732 1781 6.106673 GTGACCAAGCTATGTAATGTAGTGT 58.893 40.000 0.00 0.00 0.00 3.55
1741 1790 7.545965 AGCTATGTAATGTAGTGTGTCTGTTTC 59.454 37.037 0.00 0.00 0.00 2.78
1777 1830 1.202639 TCCGTCTGTGTGCAATGTTCT 60.203 47.619 0.00 0.00 0.00 3.01
1778 1831 1.603802 CCGTCTGTGTGCAATGTTCTT 59.396 47.619 0.00 0.00 0.00 2.52
1779 1832 2.805671 CCGTCTGTGTGCAATGTTCTTA 59.194 45.455 0.00 0.00 0.00 2.10
1780 1833 3.363970 CCGTCTGTGTGCAATGTTCTTAC 60.364 47.826 0.00 0.00 0.00 2.34
1781 1834 3.494626 CGTCTGTGTGCAATGTTCTTACT 59.505 43.478 0.00 0.00 0.00 2.24
1782 1835 4.376413 CGTCTGTGTGCAATGTTCTTACTC 60.376 45.833 0.00 0.00 0.00 2.59
1783 1836 4.065088 TCTGTGTGCAATGTTCTTACTCC 58.935 43.478 0.00 0.00 0.00 3.85
1784 1837 3.814625 TGTGTGCAATGTTCTTACTCCA 58.185 40.909 0.00 0.00 0.00 3.86
1785 1838 3.814842 TGTGTGCAATGTTCTTACTCCAG 59.185 43.478 0.00 0.00 0.00 3.86
1786 1839 2.813754 TGTGCAATGTTCTTACTCCAGC 59.186 45.455 0.00 0.00 0.00 4.85
1787 1840 3.077359 GTGCAATGTTCTTACTCCAGCT 58.923 45.455 0.00 0.00 0.00 4.24
1788 1841 3.503748 GTGCAATGTTCTTACTCCAGCTT 59.496 43.478 0.00 0.00 0.00 3.74
1789 1842 4.022849 GTGCAATGTTCTTACTCCAGCTTT 60.023 41.667 0.00 0.00 0.00 3.51
1790 1843 5.181245 GTGCAATGTTCTTACTCCAGCTTTA 59.819 40.000 0.00 0.00 0.00 1.85
1791 1844 5.181245 TGCAATGTTCTTACTCCAGCTTTAC 59.819 40.000 0.00 0.00 0.00 2.01
1792 1845 5.412904 GCAATGTTCTTACTCCAGCTTTACT 59.587 40.000 0.00 0.00 0.00 2.24
1807 1860 3.484229 GCTTTACTGCTCAGCAATGTACG 60.484 47.826 0.00 0.00 38.41 3.67
1808 1861 2.293677 TACTGCTCAGCAATGTACGG 57.706 50.000 0.00 0.00 38.41 4.02
1810 1863 1.709147 CTGCTCAGCAATGTACGGGC 61.709 60.000 0.00 0.00 38.41 6.13
1811 1864 1.745115 GCTCAGCAATGTACGGGCA 60.745 57.895 0.00 0.00 0.00 5.36
1812 1865 1.097547 GCTCAGCAATGTACGGGCAT 61.098 55.000 0.00 0.00 0.00 4.40
1813 1866 1.810031 GCTCAGCAATGTACGGGCATA 60.810 52.381 0.00 0.00 0.00 3.14
1814 1867 2.771089 CTCAGCAATGTACGGGCATAT 58.229 47.619 6.08 0.00 0.00 1.78
1815 1868 3.864540 GCTCAGCAATGTACGGGCATATA 60.865 47.826 0.00 0.00 0.00 0.86
1817 1870 3.576550 TCAGCAATGTACGGGCATATAGA 59.423 43.478 6.08 0.00 0.00 1.98
1925 1993 2.963432 ACCGGTGGTACTACAATTTCG 58.037 47.619 6.12 4.98 32.11 3.46
1926 1994 2.562298 ACCGGTGGTACTACAATTTCGA 59.438 45.455 6.12 0.00 32.11 3.71
1927 1995 2.925563 CCGGTGGTACTACAATTTCGAC 59.074 50.000 11.80 0.00 0.00 4.20
1928 1996 2.595536 CGGTGGTACTACAATTTCGACG 59.404 50.000 11.80 0.00 0.00 5.12
1930 1998 3.578688 GTGGTACTACAATTTCGACGGT 58.421 45.455 4.23 0.00 0.00 4.83
1931 1999 4.380444 GGTGGTACTACAATTTCGACGGTA 60.380 45.833 11.80 0.00 0.00 4.02
1933 2001 5.230726 GTGGTACTACAATTTCGACGGTATG 59.769 44.000 4.23 0.00 0.00 2.39
1934 2002 4.741676 GGTACTACAATTTCGACGGTATGG 59.258 45.833 0.00 0.00 0.00 2.74
1994 2062 0.107214 CTAAAATCGCAGCCTGGGGA 60.107 55.000 9.07 0.00 0.00 4.81
2005 2073 3.083349 CTGGGGATGAGCCGGTGA 61.083 66.667 1.90 0.00 37.63 4.02
2130 2500 2.867456 AACACGACTAAATTTCGGCG 57.133 45.000 15.74 15.74 40.92 6.46
2177 2956 5.238432 TCGCGGATTTTCATTACATAGCAAT 59.762 36.000 6.13 0.00 0.00 3.56
2221 3000 4.074454 GCTGAACGCCGAGTAGTC 57.926 61.111 0.00 0.00 0.00 2.59
2222 3001 1.868251 GCTGAACGCCGAGTAGTCG 60.868 63.158 13.16 13.16 46.39 4.18
2223 3002 1.868251 CTGAACGCCGAGTAGTCGC 60.868 63.158 14.65 9.06 45.41 5.19
2224 3003 2.578981 GAACGCCGAGTAGTCGCC 60.579 66.667 14.65 2.21 45.41 5.54
2229 3008 3.900892 CCGAGTAGTCGCCGCCAT 61.901 66.667 14.65 0.00 45.41 4.40
2230 3009 2.353607 CGAGTAGTCGCCGCCATC 60.354 66.667 7.09 0.00 39.88 3.51
2231 3010 2.027751 GAGTAGTCGCCGCCATCC 59.972 66.667 0.00 0.00 0.00 3.51
2232 3011 2.442272 AGTAGTCGCCGCCATCCT 60.442 61.111 0.00 0.00 0.00 3.24
2233 3012 2.027751 GTAGTCGCCGCCATCCTC 59.972 66.667 0.00 0.00 0.00 3.71
2234 3013 3.592814 TAGTCGCCGCCATCCTCG 61.593 66.667 0.00 0.00 0.00 4.63
2241 3020 4.592192 CGCCATCCTCGCCATCGT 62.592 66.667 0.00 0.00 36.96 3.73
2242 3021 2.663188 GCCATCCTCGCCATCGTC 60.663 66.667 0.00 0.00 36.96 4.20
2246 3025 1.005804 CATCCTCGCCATCGTCATCG 61.006 60.000 0.00 0.00 36.96 3.84
2248 3027 1.658717 CCTCGCCATCGTCATCGTC 60.659 63.158 0.00 0.00 38.33 4.20
2249 3028 2.006062 CTCGCCATCGTCATCGTCG 61.006 63.158 0.00 0.00 38.33 5.12
2250 3029 3.024609 CGCCATCGTCATCGTCGG 61.025 66.667 0.00 0.00 38.33 4.79
2251 3030 3.330853 GCCATCGTCATCGTCGGC 61.331 66.667 0.00 7.11 43.42 5.54
2252 3031 2.658593 CCATCGTCATCGTCGGCC 60.659 66.667 0.00 0.00 38.33 6.13
2254 3033 1.226974 CATCGTCATCGTCGGCCTT 60.227 57.895 0.00 0.00 38.33 4.35
2257 3036 1.586564 CGTCATCGTCGGCCTTCTC 60.587 63.158 0.00 0.00 0.00 2.87
2258 3037 1.227002 GTCATCGTCGGCCTTCTCC 60.227 63.158 0.00 0.00 0.00 3.71
2259 3038 1.379977 TCATCGTCGGCCTTCTCCT 60.380 57.895 0.00 0.00 0.00 3.69
2260 3039 1.066587 CATCGTCGGCCTTCTCCTC 59.933 63.158 0.00 0.00 0.00 3.71
2261 3040 2.128507 ATCGTCGGCCTTCTCCTCC 61.129 63.158 0.00 0.00 0.00 4.30
2262 3041 2.575455 ATCGTCGGCCTTCTCCTCCT 62.575 60.000 0.00 0.00 0.00 3.69
2263 3042 1.453379 CGTCGGCCTTCTCCTCCTA 60.453 63.158 0.00 0.00 0.00 2.94
2265 3044 0.747852 GTCGGCCTTCTCCTCCTAAG 59.252 60.000 0.00 0.00 0.00 2.18
2266 3045 0.629596 TCGGCCTTCTCCTCCTAAGA 59.370 55.000 0.00 0.00 0.00 2.10
2269 3048 2.436173 CGGCCTTCTCCTCCTAAGAAAT 59.564 50.000 0.00 0.00 32.60 2.17
2425 3216 1.134901 GTCGCTGTCGTCGATGACT 59.865 57.895 31.83 0.00 39.64 3.41
2426 3217 0.858135 GTCGCTGTCGTCGATGACTC 60.858 60.000 31.83 23.21 39.64 3.36
2428 3219 1.803943 GCTGTCGTCGATGACTCCT 59.196 57.895 31.83 0.00 39.64 3.69
2429 3220 0.248296 GCTGTCGTCGATGACTCCTC 60.248 60.000 31.83 17.33 39.64 3.71
2442 3233 0.410270 ACTCCTCCTCCTCCTTCGTT 59.590 55.000 0.00 0.00 0.00 3.85
2508 3299 0.740868 CGCTTCCTCGCCATCTTCAA 60.741 55.000 0.00 0.00 0.00 2.69
2557 3348 3.429141 TCGTCGTCGAGCTCCACC 61.429 66.667 8.47 0.00 41.35 4.61
2560 3351 2.033602 TCGTCGAGCTCCACCTCA 59.966 61.111 8.47 0.00 0.00 3.86
2589 3380 3.382832 CTTCACGGCGGGGAGACT 61.383 66.667 13.47 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 82 1.468520 CGACCGTCATGCCATTTCTTT 59.531 47.619 0.00 0.00 0.00 2.52
82 85 1.024579 ACCGACCGTCATGCCATTTC 61.025 55.000 0.00 0.00 0.00 2.17
100 103 2.432628 CGGAGACTGGCCGTGAAC 60.433 66.667 4.94 0.00 43.66 3.18
244 249 2.116238 TGACTCATACCCTTGCCCTAC 58.884 52.381 0.00 0.00 0.00 3.18
285 290 8.082242 CCGATGGGTATGAAATTTTCCTATTTC 58.918 37.037 6.68 0.00 42.29 2.17
445 460 6.885918 TGAATGCATGATGAGGTCTTTTTAGA 59.114 34.615 0.00 0.00 0.00 2.10
488 504 0.938008 GTTCGTGGGCTAGCTATTGC 59.062 55.000 15.72 0.00 40.05 3.56
607 623 4.019141 TGGTACCCACGAATAAAATCACCT 60.019 41.667 10.07 0.00 0.00 4.00
611 627 7.916977 GGTAAATTGGTACCCACGAATAAAATC 59.083 37.037 10.07 0.00 38.08 2.17
642 658 1.798283 TTTTCCATACACGTCACCCG 58.202 50.000 0.00 0.00 44.03 5.28
669 685 4.021192 CCCATACCATATTTGTTGATGGGC 60.021 45.833 11.64 0.00 45.94 5.36
680 696 5.104527 CCATCATCCGTACCCATACCATATT 60.105 44.000 0.00 0.00 0.00 1.28
681 697 4.408921 CCATCATCCGTACCCATACCATAT 59.591 45.833 0.00 0.00 0.00 1.78
682 698 3.772572 CCATCATCCGTACCCATACCATA 59.227 47.826 0.00 0.00 0.00 2.74
683 699 2.571653 CCATCATCCGTACCCATACCAT 59.428 50.000 0.00 0.00 0.00 3.55
684 700 1.974957 CCATCATCCGTACCCATACCA 59.025 52.381 0.00 0.00 0.00 3.25
728 744 2.544768 GTGGAGCCACCCCATATCT 58.455 57.895 8.48 0.00 40.79 1.98
968 986 1.638133 TACGCCGCGTTTTTATAGCA 58.362 45.000 25.47 0.00 41.54 3.49
1042 1070 0.708370 GACGTCTGTATGCGTGTGTG 59.292 55.000 8.70 0.00 41.70 3.82
1043 1071 0.388134 GGACGTCTGTATGCGTGTGT 60.388 55.000 16.46 0.00 41.70 3.72
1044 1072 1.403225 CGGACGTCTGTATGCGTGTG 61.403 60.000 16.54 0.00 41.70 3.82
1053 1081 0.748450 TTCCTGAAACGGACGTCTGT 59.252 50.000 24.31 24.31 36.96 3.41
1056 1084 0.033090 AGGTTCCTGAAACGGACGTC 59.967 55.000 7.13 7.13 38.87 4.34
1097 1125 2.511600 CCTGACCGGACGCCATTC 60.512 66.667 9.46 0.00 33.16 2.67
1223 1251 0.620556 TAGGAACGGAGGGAGTACGT 59.379 55.000 0.00 0.00 43.43 3.57
1224 1252 1.978454 ATAGGAACGGAGGGAGTACG 58.022 55.000 0.00 0.00 0.00 3.67
1225 1253 4.468713 ACTTATAGGAACGGAGGGAGTAC 58.531 47.826 0.00 0.00 0.00 2.73
1226 1254 4.414846 AGACTTATAGGAACGGAGGGAGTA 59.585 45.833 0.00 0.00 0.00 2.59
1227 1255 3.204831 AGACTTATAGGAACGGAGGGAGT 59.795 47.826 0.00 0.00 0.00 3.85
1228 1256 3.834938 AGACTTATAGGAACGGAGGGAG 58.165 50.000 0.00 0.00 0.00 4.30
1229 1257 3.967467 AGACTTATAGGAACGGAGGGA 57.033 47.619 0.00 0.00 0.00 4.20
1230 1258 4.080687 CCTAGACTTATAGGAACGGAGGG 58.919 52.174 0.00 0.00 44.50 4.30
1231 1259 4.080687 CCCTAGACTTATAGGAACGGAGG 58.919 52.174 0.00 0.00 44.50 4.30
1232 1260 4.983053 TCCCTAGACTTATAGGAACGGAG 58.017 47.826 0.00 0.00 44.50 4.63
1233 1261 4.414846 ACTCCCTAGACTTATAGGAACGGA 59.585 45.833 0.00 0.00 44.50 4.69
1234 1262 4.727677 ACTCCCTAGACTTATAGGAACGG 58.272 47.826 0.00 0.00 44.50 4.44
1235 1263 6.532826 ACTACTCCCTAGACTTATAGGAACG 58.467 44.000 0.00 0.00 44.50 3.95
1236 1264 8.659527 AGTACTACTCCCTAGACTTATAGGAAC 58.340 40.741 0.00 0.00 44.50 3.62
1237 1265 8.811341 AGTACTACTCCCTAGACTTATAGGAA 57.189 38.462 0.00 0.00 44.50 3.36
1238 1266 8.811341 AAGTACTACTCCCTAGACTTATAGGA 57.189 38.462 0.00 0.00 44.50 2.94
1247 1275 9.956640 GCATTATACTAAGTACTACTCCCTAGA 57.043 37.037 0.00 0.00 0.00 2.43
1248 1276 9.736414 TGCATTATACTAAGTACTACTCCCTAG 57.264 37.037 0.00 0.00 0.00 3.02
1250 1278 9.603189 ATTGCATTATACTAAGTACTACTCCCT 57.397 33.333 0.00 0.00 0.00 4.20
1281 1314 3.153919 ACAACAATGCCGGTTCAGTATT 58.846 40.909 1.90 0.00 0.00 1.89
1337 1370 3.068691 TCCTTCCGAGTCTGCCCG 61.069 66.667 0.00 0.00 0.00 6.13
1520 1556 3.177920 CACGAGCGAGCAGTCAGC 61.178 66.667 0.00 0.00 46.19 4.26
1543 1579 3.243839 GGGACACACTAAACGGACTACAA 60.244 47.826 0.00 0.00 0.00 2.41
1558 1594 6.877668 TTATTATTCAGTACCTGGGACACA 57.122 37.500 12.53 0.00 31.51 3.72
1580 1616 0.886563 CCGAGTACCTGACGACCTTT 59.113 55.000 0.00 0.00 0.00 3.11
1581 1617 0.037303 TCCGAGTACCTGACGACCTT 59.963 55.000 0.00 0.00 0.00 3.50
1623 1659 3.958147 TCACGGTACACATGATCACCTAT 59.042 43.478 0.00 0.00 0.00 2.57
1732 1781 9.376075 GAGATTCAGATTCATAAGAAACAGACA 57.624 33.333 0.00 0.00 37.29 3.41
1741 1790 6.420306 CACAGACGGAGATTCAGATTCATAAG 59.580 42.308 0.00 0.00 0.00 1.73
1777 1830 3.617531 GCTGAGCAGTAAAGCTGGAGTAA 60.618 47.826 0.00 0.00 46.75 2.24
1778 1831 2.093973 GCTGAGCAGTAAAGCTGGAGTA 60.094 50.000 0.00 0.00 46.75 2.59
1779 1832 1.338579 GCTGAGCAGTAAAGCTGGAGT 60.339 52.381 0.00 0.00 46.75 3.85
1780 1833 1.338484 TGCTGAGCAGTAAAGCTGGAG 60.338 52.381 1.40 0.00 46.75 3.86
1781 1834 0.686789 TGCTGAGCAGTAAAGCTGGA 59.313 50.000 1.40 0.00 46.75 3.86
1782 1835 1.527034 TTGCTGAGCAGTAAAGCTGG 58.473 50.000 7.39 0.00 46.75 4.85
1783 1836 2.486982 ACATTGCTGAGCAGTAAAGCTG 59.513 45.455 7.39 2.71 46.75 4.24
1785 1838 3.484229 CGTACATTGCTGAGCAGTAAAGC 60.484 47.826 7.39 0.00 40.61 3.51
1786 1839 3.062639 CCGTACATTGCTGAGCAGTAAAG 59.937 47.826 7.39 5.59 40.61 1.85
1787 1840 3.000041 CCGTACATTGCTGAGCAGTAAA 59.000 45.455 7.39 0.00 40.61 2.01
1788 1841 2.616960 CCGTACATTGCTGAGCAGTAA 58.383 47.619 7.39 3.56 40.61 2.24
1789 1842 1.134818 CCCGTACATTGCTGAGCAGTA 60.135 52.381 7.39 4.74 40.61 2.74
1790 1843 0.391661 CCCGTACATTGCTGAGCAGT 60.392 55.000 7.39 0.59 40.61 4.40
1791 1844 1.709147 GCCCGTACATTGCTGAGCAG 61.709 60.000 7.39 0.00 40.61 4.24
1792 1845 1.745115 GCCCGTACATTGCTGAGCA 60.745 57.895 1.40 1.40 36.47 4.26
1925 1993 3.241067 TGCTCTAACAACCATACCGTC 57.759 47.619 0.00 0.00 0.00 4.79
1926 1994 3.451178 AGATGCTCTAACAACCATACCGT 59.549 43.478 0.00 0.00 0.00 4.83
1927 1995 4.060038 AGATGCTCTAACAACCATACCG 57.940 45.455 0.00 0.00 0.00 4.02
1928 1996 5.428253 TGAAGATGCTCTAACAACCATACC 58.572 41.667 0.00 0.00 0.00 2.73
1930 1998 5.118990 GCTGAAGATGCTCTAACAACCATA 58.881 41.667 0.00 0.00 0.00 2.74
1931 1999 3.944015 GCTGAAGATGCTCTAACAACCAT 59.056 43.478 0.00 0.00 0.00 3.55
1933 2001 2.680339 GGCTGAAGATGCTCTAACAACC 59.320 50.000 0.00 0.00 0.00 3.77
1934 2002 2.349886 CGGCTGAAGATGCTCTAACAAC 59.650 50.000 0.00 0.00 0.00 3.32
2012 2080 2.185310 AACTCGCTCCAGGCCGATTT 62.185 55.000 0.00 1.85 37.74 2.17
2013 2081 2.660064 AACTCGCTCCAGGCCGATT 61.660 57.895 0.00 0.00 37.74 3.34
2014 2082 3.077556 AACTCGCTCCAGGCCGAT 61.078 61.111 0.00 0.00 37.74 4.18
2083 2189 6.073440 GCCGAACTTCCGAAATTTGCTATATA 60.073 38.462 0.00 0.00 0.00 0.86
2130 2500 6.511767 CGAACATGTCTAATATGCCCAAGTTC 60.512 42.308 0.00 0.00 33.05 3.01
2206 2985 2.177531 GCGACTACTCGGCGTTCA 59.822 61.111 6.85 0.00 40.53 3.18
2212 2991 3.825833 GATGGCGGCGACTACTCGG 62.826 68.421 16.45 0.00 40.53 4.63
2213 2992 2.353607 GATGGCGGCGACTACTCG 60.354 66.667 16.45 0.00 43.28 4.18
2214 2993 2.027751 GGATGGCGGCGACTACTC 59.972 66.667 16.45 8.21 0.00 2.59
2216 2995 2.027751 GAGGATGGCGGCGACTAC 59.972 66.667 16.45 7.84 0.00 2.73
2224 3003 4.592192 ACGATGGCGAGGATGGCG 62.592 66.667 0.00 0.00 42.57 5.69
2225 3004 2.663188 GACGATGGCGAGGATGGC 60.663 66.667 0.00 0.00 41.64 4.40
2226 3005 0.668706 GATGACGATGGCGAGGATGG 60.669 60.000 0.00 0.00 41.64 3.51
2229 3008 2.060004 GACGATGACGATGGCGAGGA 62.060 60.000 0.00 0.00 42.66 3.71
2230 3009 1.658717 GACGATGACGATGGCGAGG 60.659 63.158 0.00 0.00 42.66 4.63
2231 3010 2.006062 CGACGATGACGATGGCGAG 61.006 63.158 0.00 0.00 42.66 5.03
2232 3011 2.024163 CGACGATGACGATGGCGA 59.976 61.111 0.00 0.00 42.66 5.54
2233 3012 3.024609 CCGACGATGACGATGGCG 61.025 66.667 0.00 0.00 42.66 5.69
2235 3014 2.629050 AAGGCCGACGATGACGATGG 62.629 60.000 0.00 0.00 42.66 3.51
2236 3015 1.209275 GAAGGCCGACGATGACGATG 61.209 60.000 0.00 0.00 42.66 3.84
2238 3017 1.989966 GAGAAGGCCGACGATGACGA 61.990 60.000 0.00 0.00 42.66 4.20
2239 3018 1.586564 GAGAAGGCCGACGATGACG 60.587 63.158 0.00 0.00 45.75 4.35
2240 3019 1.227002 GGAGAAGGCCGACGATGAC 60.227 63.158 0.00 0.00 0.00 3.06
2241 3020 1.379977 AGGAGAAGGCCGACGATGA 60.380 57.895 0.00 0.00 0.00 2.92
2242 3021 1.066587 GAGGAGAAGGCCGACGATG 59.933 63.158 0.00 0.00 0.00 3.84
2246 3025 0.747852 CTTAGGAGGAGAAGGCCGAC 59.252 60.000 0.00 0.00 0.00 4.79
2248 3027 1.486211 TTCTTAGGAGGAGAAGGCCG 58.514 55.000 0.00 0.00 0.00 6.13
2249 3028 4.203226 CAATTTCTTAGGAGGAGAAGGCC 58.797 47.826 0.00 0.00 34.84 5.19
2250 3029 4.203226 CCAATTTCTTAGGAGGAGAAGGC 58.797 47.826 0.00 0.00 34.84 4.35
2251 3030 4.080072 AGCCAATTTCTTAGGAGGAGAAGG 60.080 45.833 0.00 0.00 34.84 3.46
2252 3031 4.880696 CAGCCAATTTCTTAGGAGGAGAAG 59.119 45.833 0.00 0.00 34.84 2.85
2254 3033 4.104086 TCAGCCAATTTCTTAGGAGGAGA 58.896 43.478 0.00 0.00 0.00 3.71
2257 3036 3.375299 CGTTCAGCCAATTTCTTAGGAGG 59.625 47.826 0.00 0.00 0.00 4.30
2258 3037 3.181506 GCGTTCAGCCAATTTCTTAGGAG 60.182 47.826 0.00 0.00 40.81 3.69
2259 3038 2.747446 GCGTTCAGCCAATTTCTTAGGA 59.253 45.455 0.00 0.00 40.81 2.94
2260 3039 3.136808 GCGTTCAGCCAATTTCTTAGG 57.863 47.619 0.00 0.00 40.81 2.69
2314 3096 1.065928 GAAGGCCGACGATGACGAT 59.934 57.895 0.00 0.00 42.66 3.73
2425 3216 1.258445 GCAACGAAGGAGGAGGAGGA 61.258 60.000 0.00 0.00 0.00 3.71
2426 3217 1.219393 GCAACGAAGGAGGAGGAGG 59.781 63.158 0.00 0.00 0.00 4.30
2428 3219 2.646175 CCGCAACGAAGGAGGAGGA 61.646 63.158 0.00 0.00 0.00 3.71
2429 3220 2.125512 CCGCAACGAAGGAGGAGG 60.126 66.667 0.00 0.00 0.00 4.30
2493 3284 0.826715 CTCCTTGAAGATGGCGAGGA 59.173 55.000 0.00 0.00 42.36 3.71


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

AutoCloner maintained by Alex Coulton.