Multiple sequence alignment - TraesCS5A01G207600

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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 TraesCS5A01G207600 chr5A 100.000 2468 0 0 1 2468 419694059 419691592 0.000000e+00 4558.0
1 TraesCS5A01G207600 chr5A 86.818 220 26 3 1807 2026 549204577 549204361 2.450000e-60 243.0
2 TraesCS5A01G207600 chr5A 86.547 223 25 5 1807 2027 429122769 429122550 8.820000e-60 241.0
3 TraesCS5A01G207600 chr5A 90.909 44 2 2 2082 2125 338924047 338924006 9.530000e-05 58.4
4 TraesCS5A01G207600 chr5D 87.481 2013 160 43 482 2421 322975566 322973573 0.000000e+00 2237.0
5 TraesCS5A01G207600 chr5D 87.363 364 39 6 4 363 107774732 107774372 6.350000e-111 411.0
6 TraesCS5A01G207600 chr5D 86.721 369 43 5 1 363 315917782 315917414 2.960000e-109 405.0
7 TraesCS5A01G207600 chr5D 81.230 309 30 11 1751 2048 315823696 315823987 8.880000e-55 224.0
8 TraesCS5A01G207600 chr5D 92.500 40 2 1 2079 2118 564987927 564987965 3.430000e-04 56.5
9 TraesCS5A01G207600 chr5B 87.048 1328 71 43 508 1746 375179578 375178263 0.000000e+00 1406.0
10 TraesCS5A01G207600 chr5B 86.948 521 54 9 1 512 375191746 375191231 7.660000e-160 573.0
11 TraesCS5A01G207600 chr5B 86.933 375 40 6 1 368 7033342 7032970 1.770000e-111 412.0
12 TraesCS5A01G207600 chr5B 81.494 308 28 15 1753 2049 90506588 90506877 2.470000e-55 226.0
13 TraesCS5A01G207600 chr5B 94.737 38 2 0 2078 2115 95757517 95757554 2.650000e-05 60.2
14 TraesCS5A01G207600 chr1D 88.108 370 36 4 1 363 28554901 28555269 1.360000e-117 433.0
15 TraesCS5A01G207600 chr1D 87.027 370 39 7 2 363 431510634 431511002 2.280000e-110 409.0
16 TraesCS5A01G207600 chr1D 84.937 239 28 4 1803 2040 374241603 374241834 4.100000e-58 235.0
17 TraesCS5A01G207600 chr1D 89.256 121 12 1 363 482 301924802 301924922 1.530000e-32 150.0
18 TraesCS5A01G207600 chr7D 87.805 369 35 7 4 363 91554230 91553863 8.160000e-115 424.0
19 TraesCS5A01G207600 chr7D 87.805 369 36 6 4 363 565217783 565217415 8.160000e-115 424.0
20 TraesCS5A01G207600 chr7D 87.466 367 40 5 2 363 469521106 469521471 3.800000e-113 418.0
21 TraesCS5A01G207600 chr7D 82.428 313 51 4 2157 2468 251378111 251378420 1.120000e-68 270.0
22 TraesCS5A01G207600 chr7D 81.879 298 34 8 2171 2468 101791224 101791501 1.480000e-57 233.0
23 TraesCS5A01G207600 chr7D 94.262 122 7 0 363 484 156900162 156900041 1.170000e-43 187.0
24 TraesCS5A01G207600 chr7D 88.525 122 14 0 363 484 254430078 254430199 5.500000e-32 148.0
25 TraesCS5A01G207600 chr6D 86.863 373 40 6 1 364 464851910 464852282 2.280000e-110 409.0
26 TraesCS5A01G207600 chr6D 83.871 310 50 0 2159 2468 285795980 285795671 1.860000e-76 296.0
27 TraesCS5A01G207600 chr6D 82.828 297 30 7 1751 2042 21075877 21075597 1.900000e-61 246.0
28 TraesCS5A01G207600 chr6D 88.525 122 14 0 363 484 108213294 108213173 5.500000e-32 148.0
29 TraesCS5A01G207600 chr6D 82.065 184 20 7 1874 2045 407203016 407203198 7.110000e-31 145.0
30 TraesCS5A01G207600 chr6A 85.256 312 43 3 2157 2467 560708565 560708256 3.960000e-83 318.0
31 TraesCS5A01G207600 chr6A 84.026 313 47 2 2157 2468 208785735 208786045 5.160000e-77 298.0
32 TraesCS5A01G207600 chr6A 88.525 122 14 0 363 484 229981276 229981397 5.500000e-32 148.0
33 TraesCS5A01G207600 chr6A 94.872 39 2 0 2077 2115 143970905 143970943 7.370000e-06 62.1
34 TraesCS5A01G207600 chr4D 86.777 242 30 1 2225 2466 351373230 351373469 4.050000e-68 268.0
35 TraesCS5A01G207600 chr4D 86.818 220 26 3 1807 2026 50326253 50326037 2.450000e-60 243.0
36 TraesCS5A01G207600 chr4D 88.525 122 14 0 363 484 259454738 259454859 5.500000e-32 148.0
37 TraesCS5A01G207600 chr4D 81.319 182 15 7 2114 2283 487071756 487071582 1.990000e-26 130.0
38 TraesCS5A01G207600 chr6B 82.848 309 29 10 2157 2465 408698321 408698605 3.150000e-64 255.0
39 TraesCS5A01G207600 chr6B 91.111 45 3 1 2072 2115 598007690 598007646 2.650000e-05 60.2
40 TraesCS5A01G207600 chr1A 87.273 220 26 2 1807 2026 518802362 518802579 1.470000e-62 250.0
41 TraesCS5A01G207600 chr1A 83.696 276 30 9 1751 2026 536896516 536896256 1.900000e-61 246.0
42 TraesCS5A01G207600 chr1A 82.645 242 27 3 2225 2466 580149796 580150022 1.500000e-47 200.0
43 TraesCS5A01G207600 chr1A 85.556 180 24 2 2289 2468 63732565 63732742 1.170000e-43 187.0
44 TraesCS5A01G207600 chr1A 86.441 59 4 4 2074 2131 572390174 572390119 7.370000e-06 62.1
45 TraesCS5A01G207600 chr4B 86.425 221 28 2 1807 2027 461583183 461583401 8.820000e-60 241.0
46 TraesCS5A01G207600 chr4B 88.525 122 14 0 363 484 542157628 542157749 5.500000e-32 148.0
47 TraesCS5A01G207600 chr4A 81.613 310 27 16 1755 2052 590230249 590230540 1.910000e-56 230.0
48 TraesCS5A01G207600 chr3B 80.368 326 35 16 1755 2068 11552100 11551792 1.150000e-53 220.0
49 TraesCS5A01G207600 chr2A 87.500 168 19 2 2302 2468 416914848 416914682 2.500000e-45 193.0
50 TraesCS5A01G207600 chr3D 90.351 114 11 0 371 484 2487572 2487459 1.530000e-32 150.0
51 TraesCS5A01G207600 chr3A 92.857 42 3 0 2074 2115 149713942 149713983 7.370000e-06 62.1
52 TraesCS5A01G207600 chr7B 92.500 40 2 1 2079 2118 492490500 492490538 3.430000e-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 TraesCS5A01G207600 chr5A 419691592 419694059 2467 True 4558 4558 100.000 1 2468 1 chr5A.!!$R2 2467
1 TraesCS5A01G207600 chr5D 322973573 322975566 1993 True 2237 2237 87.481 482 2421 1 chr5D.!!$R3 1939
2 TraesCS5A01G207600 chr5B 375178263 375179578 1315 True 1406 1406 87.048 508 1746 1 chr5B.!!$R2 1238
3 TraesCS5A01G207600 chr5B 375191231 375191746 515 True 573 573 86.948 1 512 1 chr5B.!!$R3 511

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
870 930 0.768622 AAATCACCCACCGAGGACAA 59.231 50.0 0.0 0.0 41.22 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2423 2570 0.030908 CCGACGATGAAGAGTAGGGC 59.969 60.0 0.0 0.0 30.89 5.19 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
73 79 5.627499 TTGTGAGGTAGACAATTTGATGC 57.373 39.130 2.79 0.00 0.00 3.91
78 84 3.935203 AGGTAGACAATTTGATGCGTGAG 59.065 43.478 2.79 0.00 0.00 3.51
105 111 7.678454 GCCCGCTCCAATTTTTAAATTATTTGG 60.678 37.037 0.00 10.45 36.52 3.28
145 152 5.365314 TCAGCAAAAAGACAAATTAGGGGTT 59.635 36.000 0.00 0.00 0.00 4.11
162 169 5.912892 AGGGGTTTGTAAAAATGTTCACTG 58.087 37.500 0.00 0.00 0.00 3.66
163 170 5.423931 AGGGGTTTGTAAAAATGTTCACTGT 59.576 36.000 0.00 0.00 0.00 3.55
165 172 6.036626 GGGGTTTGTAAAAATGTTCACTGTTG 59.963 38.462 0.00 0.00 0.00 3.33
179 186 6.150307 TGTTCACTGTTGATGTACTGTTTTGT 59.850 34.615 0.00 0.00 0.00 2.83
182 189 5.971202 CACTGTTGATGTACTGTTTTGTTCC 59.029 40.000 0.00 0.00 0.00 3.62
217 224 2.290514 TGCTGAGACCTGCTAAAATGCT 60.291 45.455 0.00 0.00 37.99 3.79
228 235 5.575606 CCTGCTAAAATGCTCAAATGACTTG 59.424 40.000 0.00 0.00 36.25 3.16
243 250 1.886542 GACTTGAAATTTGGAGCGGGT 59.113 47.619 0.00 0.00 0.00 5.28
244 251 1.886542 ACTTGAAATTTGGAGCGGGTC 59.113 47.619 0.00 0.00 0.00 4.46
245 252 2.162681 CTTGAAATTTGGAGCGGGTCT 58.837 47.619 7.19 0.00 0.00 3.85
246 253 1.821216 TGAAATTTGGAGCGGGTCTC 58.179 50.000 7.19 0.00 41.15 3.36
248 255 1.468914 GAAATTTGGAGCGGGTCTCAC 59.531 52.381 7.19 0.00 43.70 3.51
263 270 3.932710 GGTCTCACGCATCAAATTGTCTA 59.067 43.478 0.00 0.00 0.00 2.59
265 272 3.932710 TCTCACGCATCAAATTGTCTACC 59.067 43.478 0.00 0.00 0.00 3.18
269 276 2.785679 GCATCAAATTGTCTACCGCAC 58.214 47.619 0.00 0.00 0.00 5.34
272 279 4.675146 GCATCAAATTGTCTACCGCACAAT 60.675 41.667 0.00 0.00 44.67 2.71
367 375 2.306512 ACCAAAACGCCCTACTCCATAA 59.693 45.455 0.00 0.00 0.00 1.90
567 575 6.403615 CAGAGCTCGTTAAATTAAACTAGCG 58.596 40.000 8.37 0.03 46.90 4.26
630 638 2.505819 ACTTCTGACTGGAACAACACCT 59.494 45.455 0.00 0.00 38.70 4.00
636 644 1.343465 ACTGGAACAACACCTACTCCG 59.657 52.381 0.00 0.00 38.70 4.63
706 739 4.124851 AGTGGATCGTATCAAACACTCC 57.875 45.455 0.00 0.00 34.37 3.85
709 742 3.195661 GGATCGTATCAAACACTCCCAC 58.804 50.000 0.00 0.00 0.00 4.61
710 743 3.118738 GGATCGTATCAAACACTCCCACT 60.119 47.826 0.00 0.00 0.00 4.00
711 744 3.587797 TCGTATCAAACACTCCCACTC 57.412 47.619 0.00 0.00 0.00 3.51
712 745 3.162666 TCGTATCAAACACTCCCACTCT 58.837 45.455 0.00 0.00 0.00 3.24
713 746 3.192844 TCGTATCAAACACTCCCACTCTC 59.807 47.826 0.00 0.00 0.00 3.20
714 747 2.751166 ATCAAACACTCCCACTCTCG 57.249 50.000 0.00 0.00 0.00 4.04
854 914 4.353777 TCCTCCGGCTATATAGAGCAAAT 58.646 43.478 20.32 0.00 44.76 2.32
864 924 1.271856 TAGAGCAAATCACCCACCGA 58.728 50.000 0.00 0.00 0.00 4.69
870 930 0.768622 AAATCACCCACCGAGGACAA 59.231 50.000 0.00 0.00 41.22 3.18
872 932 0.991920 ATCACCCACCGAGGACAAAT 59.008 50.000 0.00 0.00 41.22 2.32
990 1078 2.433145 AGCACATCACAGTCCGCG 60.433 61.111 0.00 0.00 0.00 6.46
991 1079 2.738521 GCACATCACAGTCCGCGT 60.739 61.111 4.92 0.00 0.00 6.01
992 1080 3.015293 GCACATCACAGTCCGCGTG 62.015 63.158 4.92 0.00 35.63 5.34
993 1081 2.738521 ACATCACAGTCCGCGTGC 60.739 61.111 4.92 0.00 34.27 5.34
1311 1399 2.359975 GTGTCCGGCAAGAAGGGG 60.360 66.667 0.00 0.00 0.00 4.79
1335 1423 3.971702 GGCAGGGGCAACAGGTCT 61.972 66.667 0.00 0.00 43.71 3.85
1470 1558 3.452627 ACACCATCTTCGAGGCTTAGATT 59.547 43.478 5.35 0.00 0.00 2.40
1488 1583 1.983119 TTGATCATGGCCCCCGTCTC 61.983 60.000 0.00 0.00 0.00 3.36
1493 1588 3.023045 ATGGCCCCCGTCTCTAGGT 62.023 63.158 0.00 0.00 0.00 3.08
1572 1675 4.437682 TTTTCAAGCAAGGAGAGAAGGA 57.562 40.909 0.00 0.00 0.00 3.36
1579 1682 3.008485 AGCAAGGAGAGAAGGAATTCGTT 59.992 43.478 12.98 12.98 0.00 3.85
1606 1712 5.114081 ACGTGTACTGTCTTGTAAAGCTTT 58.886 37.500 17.30 17.30 45.70 3.51
1672 1781 7.759489 AATTGTCAAACCTAAATGCTACTCA 57.241 32.000 0.00 0.00 0.00 3.41
1673 1782 7.944729 ATTGTCAAACCTAAATGCTACTCAT 57.055 32.000 0.00 0.00 36.87 2.90
1676 1785 7.168219 TGTCAAACCTAAATGCTACTCATTCT 58.832 34.615 0.00 0.00 44.23 2.40
1679 1788 6.992063 AACCTAAATGCTACTCATTCTGTG 57.008 37.500 0.00 0.00 44.23 3.66
1749 1871 9.269453 AGTGTATAGAGAAAAATATTTACGCCC 57.731 33.333 0.01 0.00 0.00 6.13
1764 1902 6.613755 TTTACGCCCTAGAAAAATCATAGC 57.386 37.500 0.00 0.00 0.00 2.97
1767 1905 5.133221 ACGCCCTAGAAAAATCATAGCAAT 58.867 37.500 0.00 0.00 0.00 3.56
1769 1907 6.428159 ACGCCCTAGAAAAATCATAGCAATAG 59.572 38.462 0.00 0.00 0.00 1.73
1770 1908 6.650807 CGCCCTAGAAAAATCATAGCAATAGA 59.349 38.462 0.00 0.00 0.00 1.98
1772 1910 8.850156 GCCCTAGAAAAATCATAGCAATAGAAA 58.150 33.333 0.00 0.00 0.00 2.52
1860 1998 7.785033 AGAAAAGAAGATGTTGTTTGGTTCAT 58.215 30.769 0.00 0.00 29.91 2.57
1867 2005 9.941664 GAAGATGTTGTTTGGTTCATATCATAG 57.058 33.333 0.00 0.00 0.00 2.23
1870 2008 9.071276 GATGTTGTTTGGTTCATATCATAGGAT 57.929 33.333 0.00 0.00 37.55 3.24
1871 2009 8.821686 TGTTGTTTGGTTCATATCATAGGATT 57.178 30.769 0.00 0.00 34.89 3.01
1872 2010 9.253832 TGTTGTTTGGTTCATATCATAGGATTT 57.746 29.630 0.00 0.00 34.89 2.17
1929 2067 7.690454 TTCCTATGAAATGTGGAGGATAGAA 57.310 36.000 0.00 0.00 36.22 2.10
1931 2069 8.101309 TCCTATGAAATGTGGAGGATAGAAAA 57.899 34.615 0.00 0.00 31.25 2.29
1975 2113 9.280456 AGGATTCTATTCCTACAAACTAAAGGA 57.720 33.333 0.00 0.00 44.50 3.36
1984 2122 7.904205 TCCTACAAACTAAAGGACTCTAAAGG 58.096 38.462 0.00 0.00 34.46 3.11
1987 2125 9.945904 CTACAAACTAAAGGACTCTAAAGGAAT 57.054 33.333 0.00 0.00 0.00 3.01
2042 2181 2.178106 TCCAAACCAAAGGAGGCCTTAA 59.822 45.455 6.77 0.00 43.92 1.85
2043 2182 2.299013 CCAAACCAAAGGAGGCCTTAAC 59.701 50.000 6.77 0.00 43.92 2.01
2044 2183 2.962421 CAAACCAAAGGAGGCCTTAACA 59.038 45.455 6.77 0.00 43.92 2.41
2046 2185 3.087370 ACCAAAGGAGGCCTTAACATC 57.913 47.619 6.77 0.00 43.92 3.06
2050 2189 4.080299 CCAAAGGAGGCCTTAACATCTAGT 60.080 45.833 6.77 0.00 43.92 2.57
2053 2192 7.016268 CCAAAGGAGGCCTTAACATCTAGTATA 59.984 40.741 6.77 0.00 43.92 1.47
2133 2272 3.585862 GAGCATCTACAACCGAACTTGA 58.414 45.455 0.00 0.00 0.00 3.02
2134 2273 3.589988 AGCATCTACAACCGAACTTGAG 58.410 45.455 0.00 0.00 0.00 3.02
2144 2283 2.000447 CCGAACTTGAGAAATCCGACC 59.000 52.381 0.00 0.00 0.00 4.79
2145 2284 2.000447 CGAACTTGAGAAATCCGACCC 59.000 52.381 0.00 0.00 0.00 4.46
2162 2309 3.118454 CCTCAAACACGCGCGGAT 61.118 61.111 35.22 19.11 0.00 4.18
2170 2317 3.445687 ACGCGCGGATAGTGACCA 61.446 61.111 35.22 0.00 0.00 4.02
2216 2363 8.972458 TTTCACATCCGGATATCTCAAATTAA 57.028 30.769 18.63 0.00 0.00 1.40
2220 2367 9.450807 CACATCCGGATATCTCAAATTAAAAAC 57.549 33.333 18.63 0.00 0.00 2.43
2221 2368 9.184523 ACATCCGGATATCTCAAATTAAAAACA 57.815 29.630 18.63 0.00 0.00 2.83
2248 2395 9.964303 TGAAATCCATATTATTACATGCAACAC 57.036 29.630 0.00 0.00 0.00 3.32
2249 2396 9.117145 GAAATCCATATTATTACATGCAACACG 57.883 33.333 0.00 0.00 0.00 4.49
2281 2428 4.493747 GAGCTTCGTCCGGGTCCG 62.494 72.222 0.00 1.86 39.44 4.79
2346 2493 3.691342 CGCCCCTCGGAGTGTTGA 61.691 66.667 4.02 0.00 33.78 3.18
2350 2497 1.264749 CCCCTCGGAGTGTTGATCCA 61.265 60.000 4.02 0.00 36.57 3.41
2356 2503 0.741221 GGAGTGTTGATCCAGTCGCC 60.741 60.000 0.00 0.00 35.94 5.54
2358 2505 2.100631 GTGTTGATCCAGTCGCCGG 61.101 63.158 0.00 0.00 0.00 6.13
2371 2518 0.966875 TCGCCGGCAAGGTAGAGTAA 60.967 55.000 28.98 0.00 43.70 2.24
2376 2523 1.139058 CGGCAAGGTAGAGTAAGGCAT 59.861 52.381 0.00 0.00 0.00 4.40
2422 2569 2.264794 GGCGTTGTCGTCTCCCAT 59.735 61.111 0.00 0.00 38.74 4.00
2423 2570 2.100631 GGCGTTGTCGTCTCCCATG 61.101 63.158 0.00 0.00 38.74 3.66
2424 2571 2.740714 GCGTTGTCGTCTCCCATGC 61.741 63.158 0.00 0.00 39.49 4.06
2425 2572 2.100631 CGTTGTCGTCTCCCATGCC 61.101 63.158 0.00 0.00 0.00 4.40
2426 2573 1.745489 GTTGTCGTCTCCCATGCCC 60.745 63.158 0.00 0.00 0.00 5.36
2427 2574 1.918293 TTGTCGTCTCCCATGCCCT 60.918 57.895 0.00 0.00 0.00 5.19
2428 2575 0.616395 TTGTCGTCTCCCATGCCCTA 60.616 55.000 0.00 0.00 0.00 3.53
2429 2576 1.327690 TGTCGTCTCCCATGCCCTAC 61.328 60.000 0.00 0.00 0.00 3.18
2430 2577 1.043673 GTCGTCTCCCATGCCCTACT 61.044 60.000 0.00 0.00 0.00 2.57
2431 2578 0.755698 TCGTCTCCCATGCCCTACTC 60.756 60.000 0.00 0.00 0.00 2.59
2432 2579 0.757188 CGTCTCCCATGCCCTACTCT 60.757 60.000 0.00 0.00 0.00 3.24
2433 2580 1.501582 GTCTCCCATGCCCTACTCTT 58.498 55.000 0.00 0.00 0.00 2.85
2434 2581 1.414550 GTCTCCCATGCCCTACTCTTC 59.585 57.143 0.00 0.00 0.00 2.87
2435 2582 1.008327 TCTCCCATGCCCTACTCTTCA 59.992 52.381 0.00 0.00 0.00 3.02
2436 2583 2.053244 CTCCCATGCCCTACTCTTCAT 58.947 52.381 0.00 0.00 0.00 2.57
2437 2584 2.038295 CTCCCATGCCCTACTCTTCATC 59.962 54.545 0.00 0.00 0.00 2.92
2438 2585 1.270518 CCCATGCCCTACTCTTCATCG 60.271 57.143 0.00 0.00 0.00 3.84
2439 2586 1.414181 CCATGCCCTACTCTTCATCGT 59.586 52.381 0.00 0.00 0.00 3.73
2440 2587 2.546795 CCATGCCCTACTCTTCATCGTC 60.547 54.545 0.00 0.00 0.00 4.20
2441 2588 0.738975 TGCCCTACTCTTCATCGTCG 59.261 55.000 0.00 0.00 0.00 5.12
2442 2589 0.030908 GCCCTACTCTTCATCGTCGG 59.969 60.000 0.00 0.00 0.00 4.79
2443 2590 1.676746 CCCTACTCTTCATCGTCGGA 58.323 55.000 0.00 0.00 0.00 4.55
2444 2591 1.604755 CCCTACTCTTCATCGTCGGAG 59.395 57.143 0.00 0.00 0.00 4.63
2445 2592 1.002251 CCTACTCTTCATCGTCGGAGC 60.002 57.143 0.00 0.00 0.00 4.70
2446 2593 1.002251 CTACTCTTCATCGTCGGAGCC 60.002 57.143 0.00 0.00 0.00 4.70
2447 2594 1.066587 CTCTTCATCGTCGGAGCCC 59.933 63.158 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 42 9.665719 ATTGTCTACCTCACAAAAATTGTTTTT 57.334 25.926 0.00 0.00 43.23 1.94
42 44 9.665719 AAATTGTCTACCTCACAAAAATTGTTT 57.334 25.926 0.00 0.00 43.23 2.83
44 46 8.474025 TCAAATTGTCTACCTCACAAAAATTGT 58.526 29.630 0.00 0.00 46.75 2.71
45 47 8.870160 TCAAATTGTCTACCTCACAAAAATTG 57.130 30.769 0.00 0.00 37.30 2.32
46 48 9.480053 CATCAAATTGTCTACCTCACAAAAATT 57.520 29.630 0.00 0.00 37.30 1.82
47 49 7.599998 GCATCAAATTGTCTACCTCACAAAAAT 59.400 33.333 0.00 0.00 37.30 1.82
73 79 3.976701 AATTGGAGCGGGCCTCACG 62.977 63.158 0.84 0.00 42.62 4.35
78 84 2.753055 TTTAAAAATTGGAGCGGGCC 57.247 45.000 0.00 0.00 0.00 5.80
117 123 6.015940 CCCTAATTTGTCTTTTTGCTGAGAGT 60.016 38.462 0.00 0.00 0.00 3.24
124 130 5.820423 ACAAACCCCTAATTTGTCTTTTTGC 59.180 36.000 0.00 0.00 44.97 3.68
145 152 9.509855 GTACATCAACAGTGAACATTTTTACAA 57.490 29.630 0.00 0.00 37.30 2.41
162 169 5.412526 TCGGAACAAAACAGTACATCAAC 57.587 39.130 0.00 0.00 0.00 3.18
163 170 6.627395 AATCGGAACAAAACAGTACATCAA 57.373 33.333 0.00 0.00 0.00 2.57
165 172 6.435428 ACAAATCGGAACAAAACAGTACATC 58.565 36.000 0.00 0.00 0.00 3.06
204 211 5.320549 AGTCATTTGAGCATTTTAGCAGG 57.679 39.130 0.00 0.00 36.85 4.85
210 217 8.347035 CCAAATTTCAAGTCATTTGAGCATTTT 58.653 29.630 6.25 0.00 46.01 1.82
217 224 5.221880 CGCTCCAAATTTCAAGTCATTTGA 58.778 37.500 6.25 0.00 43.92 2.69
228 235 1.468914 GTGAGACCCGCTCCAAATTTC 59.531 52.381 0.00 0.00 43.26 2.17
243 250 3.932710 GGTAGACAATTTGATGCGTGAGA 59.067 43.478 2.79 0.00 0.00 3.27
244 251 3.242091 CGGTAGACAATTTGATGCGTGAG 60.242 47.826 2.79 0.00 0.00 3.51
245 252 2.670905 CGGTAGACAATTTGATGCGTGA 59.329 45.455 2.79 0.00 0.00 4.35
246 253 2.787723 GCGGTAGACAATTTGATGCGTG 60.788 50.000 2.79 0.00 0.00 5.34
248 255 1.396648 TGCGGTAGACAATTTGATGCG 59.603 47.619 2.79 0.00 0.00 4.73
315 323 6.240894 ACTCATCTGCATCTGGTTAGAAAAA 58.759 36.000 0.00 0.00 36.32 1.94
316 324 5.809001 ACTCATCTGCATCTGGTTAGAAAA 58.191 37.500 0.00 0.00 36.32 2.29
317 325 5.188555 AGACTCATCTGCATCTGGTTAGAAA 59.811 40.000 0.00 0.00 32.84 2.52
318 326 4.713814 AGACTCATCTGCATCTGGTTAGAA 59.286 41.667 0.00 0.00 32.84 2.10
320 328 4.370049 CAGACTCATCTGCATCTGGTTAG 58.630 47.826 5.06 0.00 45.83 2.34
321 329 4.397481 CAGACTCATCTGCATCTGGTTA 57.603 45.455 5.06 0.00 45.83 2.85
322 330 3.263489 CAGACTCATCTGCATCTGGTT 57.737 47.619 5.06 0.00 45.83 3.67
323 331 2.983907 CAGACTCATCTGCATCTGGT 57.016 50.000 5.06 0.00 45.83 4.00
344 352 0.250597 GGAGTAGGGCGTTTTGGTGT 60.251 55.000 0.00 0.00 0.00 4.16
393 401 6.114767 GGTTGAATTCATAACAATGGCCAAT 58.885 36.000 10.96 0.00 0.00 3.16
426 434 7.514721 TGTCCCTTTGGTATTATGGAGATTAC 58.485 38.462 0.00 0.00 0.00 1.89
442 450 7.099266 TGTTGATATTAGCATTGTCCCTTTG 57.901 36.000 0.00 0.00 0.00 2.77
444 452 7.902920 AATGTTGATATTAGCATTGTCCCTT 57.097 32.000 8.47 0.00 31.52 3.95
477 485 4.513442 TGATGCCGAGTGCTTAATTTACT 58.487 39.130 0.00 0.00 42.00 2.24
480 488 3.505680 TGTTGATGCCGAGTGCTTAATTT 59.494 39.130 0.00 0.00 42.00 1.82
512 520 2.618053 GACGATCGGGTCAGTTTGATT 58.382 47.619 20.98 0.00 36.91 2.57
630 638 1.605058 GGTGCAGAGCCTTCGGAGTA 61.605 60.000 0.00 0.00 0.00 2.59
714 747 2.511600 ATTGGACGTAGCGGCAGC 60.512 61.111 0.00 0.00 45.58 5.25
802 862 2.203788 AGGCAGGACGAAGGTGGA 60.204 61.111 0.00 0.00 0.00 4.02
854 914 0.323629 GATTTGTCCTCGGTGGGTGA 59.676 55.000 0.00 0.00 36.20 4.02
864 924 4.725810 AGGAATCTGGAGATGATTTGTCCT 59.274 41.667 1.07 1.07 34.67 3.85
870 930 6.324601 AGTGAAAGGAATCTGGAGATGATT 57.675 37.500 0.00 0.00 36.91 2.57
872 932 5.494724 CAAGTGAAAGGAATCTGGAGATGA 58.505 41.667 0.00 0.00 34.49 2.92
955 1043 3.241059 CGTGCTGCGACGTAGAGC 61.241 66.667 17.59 12.22 44.77 4.09
958 1046 3.241059 GCTCGTGCTGCGACGTAG 61.241 66.667 18.80 8.74 45.68 3.51
979 1067 1.646624 TATACGCACGCGGACTGTGA 61.647 55.000 16.70 0.00 44.69 3.58
990 1078 3.558418 CCAAGTTACCCATGTATACGCAC 59.442 47.826 0.00 0.00 0.00 5.34
991 1079 3.198200 ACCAAGTTACCCATGTATACGCA 59.802 43.478 0.00 0.00 0.00 5.24
992 1080 3.800531 ACCAAGTTACCCATGTATACGC 58.199 45.455 0.00 0.00 0.00 4.42
993 1081 5.272283 AGACCAAGTTACCCATGTATACG 57.728 43.478 0.00 0.00 0.00 3.06
1048 1136 3.374402 CAGGACGACCAGCGGACT 61.374 66.667 6.71 0.00 46.49 3.85
1328 1416 2.350863 AATCCTTCTCCCAGACCTGT 57.649 50.000 0.00 0.00 0.00 4.00
1470 1558 2.366837 AGACGGGGGCCATGATCA 60.367 61.111 4.39 0.00 0.00 2.92
1488 1583 9.197694 CGAATGAATGTTCCTATTCTAACCTAG 57.802 37.037 0.00 0.00 37.81 3.02
1579 1682 5.005971 GCTTTACAAGACAGTACACGTCAAA 59.994 40.000 15.40 7.82 35.77 2.69
1606 1712 8.983702 ACAACCTTGTACTCCAAAATAAGTTA 57.016 30.769 0.00 0.00 40.16 2.24
1623 1729 6.402222 ACTATTTCTAGCTCTGACAACCTTG 58.598 40.000 0.00 0.00 0.00 3.61
1676 1785 5.764686 ACTTCTCAACAAATCTGTATGCACA 59.235 36.000 0.00 0.00 33.45 4.57
1679 1788 6.486253 TGACTTCTCAACAAATCTGTATGC 57.514 37.500 0.00 0.00 33.45 3.14
1739 1861 7.934665 TGCTATGATTTTTCTAGGGCGTAAATA 59.065 33.333 0.00 0.00 0.00 1.40
1841 1979 9.941664 CTATGATATGAACCAAACAACATCTTC 57.058 33.333 0.00 0.00 0.00 2.87
1842 1980 8.906867 CCTATGATATGAACCAAACAACATCTT 58.093 33.333 0.00 0.00 0.00 2.40
2003 2141 7.898636 TGGTTTGGAGGAATTTTGTAGGATAAT 59.101 33.333 0.00 0.00 0.00 1.28
2004 2142 7.242359 TGGTTTGGAGGAATTTTGTAGGATAA 58.758 34.615 0.00 0.00 0.00 1.75
2021 2159 0.560688 AAGGCCTCCTTTGGTTTGGA 59.439 50.000 5.23 0.00 41.69 3.53
2022 2160 2.299013 GTTAAGGCCTCCTTTGGTTTGG 59.701 50.000 5.23 0.00 41.69 3.28
2071 2210 8.950007 TTAGAAACAAAGGGAGGACATTTTAT 57.050 30.769 0.00 0.00 0.00 1.40
2110 2249 3.963428 AGTTCGGTTGTAGATGCTCTT 57.037 42.857 0.00 0.00 0.00 2.85
2122 2261 3.064931 GTCGGATTTCTCAAGTTCGGTT 58.935 45.455 0.00 0.00 0.00 4.44
2123 2262 2.612221 GGTCGGATTTCTCAAGTTCGGT 60.612 50.000 0.00 0.00 0.00 4.69
2124 2263 2.000447 GGTCGGATTTCTCAAGTTCGG 59.000 52.381 0.00 0.00 0.00 4.30
2127 2266 1.985895 AGGGGTCGGATTTCTCAAGTT 59.014 47.619 0.00 0.00 0.00 2.66
2133 2272 1.702957 TGTTTGAGGGGTCGGATTTCT 59.297 47.619 0.00 0.00 0.00 2.52
2134 2273 1.810755 GTGTTTGAGGGGTCGGATTTC 59.189 52.381 0.00 0.00 0.00 2.17
2145 2284 1.752501 CTATCCGCGCGTGTTTGAGG 61.753 60.000 29.95 10.76 0.00 3.86
2189 2336 7.678947 ATTTGAGATATCCGGATGTGAAATC 57.321 36.000 27.55 19.89 0.00 2.17
2223 2370 9.117145 CGTGTTGCATGTAATAATATGGATTTC 57.883 33.333 0.00 0.00 0.00 2.17
2247 2394 2.509336 CCGCTCAAAGATCGCCGT 60.509 61.111 0.00 0.00 0.00 5.68
2248 2395 2.202743 TCCGCTCAAAGATCGCCG 60.203 61.111 0.00 0.00 0.00 6.46
2249 2396 2.529619 GCTCCGCTCAAAGATCGCC 61.530 63.158 0.00 0.00 0.00 5.54
2281 2428 4.273257 GCTAGACGAGCGGGGAGC 62.273 72.222 0.00 0.00 42.62 4.70
2346 2493 4.473520 CCTTGCCGGCGACTGGAT 62.474 66.667 23.90 0.00 0.00 3.41
2350 2497 2.678934 TCTACCTTGCCGGCGACT 60.679 61.111 23.90 8.20 35.61 4.18
2356 2503 0.535335 TGCCTTACTCTACCTTGCCG 59.465 55.000 0.00 0.00 0.00 5.69
2358 2505 2.565841 CCATGCCTTACTCTACCTTGC 58.434 52.381 0.00 0.00 0.00 4.01
2371 2518 1.524002 CGACTCATGTCCCATGCCT 59.476 57.895 0.00 0.00 39.94 4.75
2376 2523 3.298958 GAGCCGACTCATGTCCCA 58.701 61.111 0.00 0.00 42.93 4.37
2396 2543 2.853914 GACAACGCCTTGAGTCGC 59.146 61.111 2.26 0.00 0.00 5.19
2397 2544 3.147294 CGACAACGCCTTGAGTCG 58.853 61.111 2.26 0.00 46.12 4.18
2409 2556 0.616395 TAGGGCATGGGAGACGACAA 60.616 55.000 0.00 0.00 0.00 3.18
2410 2557 1.001120 TAGGGCATGGGAGACGACA 59.999 57.895 0.00 0.00 0.00 4.35
2418 2565 1.270518 CGATGAAGAGTAGGGCATGGG 60.271 57.143 0.00 0.00 0.00 4.00
2421 2568 1.338337 CGACGATGAAGAGTAGGGCAT 59.662 52.381 0.00 0.00 0.00 4.40
2422 2569 0.738975 CGACGATGAAGAGTAGGGCA 59.261 55.000 0.00 0.00 0.00 5.36
2423 2570 0.030908 CCGACGATGAAGAGTAGGGC 59.969 60.000 0.00 0.00 30.89 5.19
2424 2571 1.604755 CTCCGACGATGAAGAGTAGGG 59.395 57.143 0.00 0.00 34.52 3.53
2425 2572 1.002251 GCTCCGACGATGAAGAGTAGG 60.002 57.143 0.00 0.00 34.97 3.18
2426 2573 1.002251 GGCTCCGACGATGAAGAGTAG 60.002 57.143 0.00 0.00 0.00 2.57
2427 2574 1.022735 GGCTCCGACGATGAAGAGTA 58.977 55.000 0.00 0.00 0.00 2.59
2428 2575 1.668101 GGGCTCCGACGATGAAGAGT 61.668 60.000 0.00 0.00 0.00 3.24
2429 2576 1.066587 GGGCTCCGACGATGAAGAG 59.933 63.158 0.00 0.00 0.00 2.85
2430 2577 3.207354 GGGCTCCGACGATGAAGA 58.793 61.111 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.