Multiple sequence alignment - TraesCS5B01G347400

Loading Multiple Alignment...

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 TraesCS5B01G347400 chr5B 100.000 2435 0 0 1 2435 528587389 528584955 0.000000e+00 4497
1 TraesCS5B01G347400 chr5B 88.331 1594 103 27 391 1912 528580167 528578585 0.000000e+00 1836
2 TraesCS5B01G347400 chr5B 88.867 503 44 6 1939 2435 528578588 528578092 2.070000e-170 608
3 TraesCS5B01G347400 chr5B 83.623 403 43 10 1 393 528580584 528580195 8.280000e-95 357
4 TraesCS5B01G347400 chr5B 75.069 361 82 5 1000 1353 528539299 528539658 6.970000e-36 161
5 TraesCS5B01G347400 chr5D 95.521 2456 85 7 1 2435 435275076 435272625 0.000000e+00 3903
6 TraesCS5B01G347400 chr5D 86.627 2550 196 61 1 2435 435269128 435266609 0.000000e+00 2686
7 TraesCS5B01G347400 chr5A 94.465 2475 81 15 4 2435 549216083 549213622 0.000000e+00 3760
8 TraesCS5B01G347400 chr5A 88.562 2072 137 48 443 2435 549211302 549209252 0.000000e+00 2422
9 TraesCS5B01G347400 chr5A 88.851 1480 100 22 391 1813 549206116 549204645 0.000000e+00 1759
10 TraesCS5B01G347400 chr5A 82.669 652 68 20 1815 2435 549204327 549203690 9.910000e-149 536
11 TraesCS5B01G347400 chr5A 85.149 404 45 8 1 393 549206543 549206144 1.360000e-107 399


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 TraesCS5B01G347400 chr5B 528584955 528587389 2434 True 4497.000000 4497 100.000000 1 2435 1 chr5B.!!$R1 2434
1 TraesCS5B01G347400 chr5B 528578092 528580584 2492 True 933.666667 1836 86.940333 1 2435 3 chr5B.!!$R2 2434
2 TraesCS5B01G347400 chr5D 435266609 435275076 8467 True 3294.500000 3903 91.074000 1 2435 2 chr5D.!!$R1 2434
3 TraesCS5B01G347400 chr5A 549203690 549216083 12393 True 1775.200000 3760 87.939200 1 2435 5 chr5A.!!$R1 2434

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
380 9948 0.037232 AGAACTGCTTACCGCTCACC 60.037 55.0 0.0 0.0 40.11 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 11924 1.748493 TCAGTGGTCCAAACAACTTGC 59.252 47.619 0.0 0.0 37.59 4.01 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
35 36 7.977853 GCAGACCAAATGATAATTTCACTGAAT 59.022 33.333 13.19 0.00 37.11 2.57
36 37 9.865321 CAGACCAAATGATAATTTCACTGAATT 57.135 29.630 7.06 0.00 37.11 2.17
112 9671 7.255312 CGCTAAATGTTCTAGATAGGACTCAGT 60.255 40.741 0.00 0.00 32.86 3.41
117 9676 5.130350 GTTCTAGATAGGACTCAGTCAGCT 58.870 45.833 7.24 0.00 33.68 4.24
164 9723 6.563381 GCTGAACTTTGAAAGATGTTTGCATG 60.563 38.462 12.53 0.00 35.07 4.06
169 9728 6.477688 ACTTTGAAAGATGTTTGCATGAGTTG 59.522 34.615 12.53 0.00 35.07 3.16
181 9740 7.599621 TGTTTGCATGAGTTGAAAATTAGATGG 59.400 33.333 0.00 0.00 35.27 3.51
186 9745 8.677300 GCATGAGTTGAAAATTAGATGGTTAGA 58.323 33.333 0.00 0.00 0.00 2.10
201 9760 7.168219 AGATGGTTAGACATTGTTAAGCAAGA 58.832 34.615 18.46 5.55 39.71 3.02
202 9761 6.801539 TGGTTAGACATTGTTAAGCAAGAG 57.198 37.500 15.08 0.00 40.86 2.85
203 9762 6.296026 TGGTTAGACATTGTTAAGCAAGAGT 58.704 36.000 15.08 0.00 40.86 3.24
207 9766 6.699575 AGACATTGTTAAGCAAGAGTTGTT 57.300 33.333 0.00 0.00 40.86 2.83
217 9776 6.515272 AAGCAAGAGTTGTTCAGAAAGAAA 57.485 33.333 0.00 0.00 38.13 2.52
220 9779 8.401490 AGCAAGAGTTGTTCAGAAAGAAATAT 57.599 30.769 0.00 0.00 38.13 1.28
231 9790 5.812642 TCAGAAAGAAATATGAACCTCTCGC 59.187 40.000 0.00 0.00 0.00 5.03
232 9791 4.806247 AGAAAGAAATATGAACCTCTCGCG 59.194 41.667 0.00 0.00 0.00 5.87
235 9794 4.504858 AGAAATATGAACCTCTCGCGTTT 58.495 39.130 5.77 0.00 0.00 3.60
241 9800 2.223157 TGAACCTCTCGCGTTTTGTTTG 60.223 45.455 5.77 0.00 0.00 2.93
242 9801 1.375551 ACCTCTCGCGTTTTGTTTGT 58.624 45.000 5.77 0.00 0.00 2.83
245 9804 3.374678 ACCTCTCGCGTTTTGTTTGTTTA 59.625 39.130 5.77 0.00 0.00 2.01
246 9805 4.035909 ACCTCTCGCGTTTTGTTTGTTTAT 59.964 37.500 5.77 0.00 0.00 1.40
247 9806 5.236911 ACCTCTCGCGTTTTGTTTGTTTATA 59.763 36.000 5.77 0.00 0.00 0.98
251 9810 8.206516 TCTCGCGTTTTGTTTGTTTATATTTC 57.793 30.769 5.77 0.00 0.00 2.17
253 9812 8.563289 TCGCGTTTTGTTTGTTTATATTTCTT 57.437 26.923 5.77 0.00 0.00 2.52
272 9840 6.827586 TTCTTTTGTTGTGTAAGTTCCTGT 57.172 33.333 0.00 0.00 0.00 4.00
312 9880 4.996788 CAGCTTTCCTGCTATTTTCCAT 57.003 40.909 0.00 0.00 41.98 3.41
313 9881 4.929781 CAGCTTTCCTGCTATTTTCCATC 58.070 43.478 0.00 0.00 41.98 3.51
323 9891 8.443176 TCCTGCTATTTTCCATCAAAGAGATAT 58.557 33.333 0.00 0.00 34.43 1.63
326 9894 9.803507 TGCTATTTTCCATCAAAGAGATATGAT 57.196 29.630 0.00 0.00 36.74 2.45
334 9902 7.444487 TCCATCAAAGAGATATGATTGCTTCAG 59.556 37.037 0.00 0.00 34.20 3.02
339 9907 6.497624 AGAGATATGATTGCTTCAGGTCTT 57.502 37.500 7.85 0.00 37.89 3.01
348 9916 5.489792 TTGCTTCAGGTCTTAACTGAGAT 57.510 39.130 0.00 0.00 44.91 2.75
353 9921 8.363390 TGCTTCAGGTCTTAACTGAGATATATG 58.637 37.037 0.00 0.00 44.91 1.78
374 9942 2.416972 GGTCCAGTAGAACTGCTTACCG 60.417 54.545 1.43 0.00 44.63 4.02
379 9947 2.094649 AGTAGAACTGCTTACCGCTCAC 60.095 50.000 0.00 0.00 40.11 3.51
380 9948 0.037232 AGAACTGCTTACCGCTCACC 60.037 55.000 0.00 0.00 40.11 4.02
386 9954 1.065491 TGCTTACCGCTCACCAATGAT 60.065 47.619 0.00 0.00 40.11 2.45
393 9961 3.815401 ACCGCTCACCAATGATAATAAGC 59.185 43.478 0.00 0.00 33.22 3.09
406 10004 9.988815 CAATGATAATAAGCTAGTTGTAGTCCT 57.011 33.333 0.00 0.00 0.00 3.85
412 10010 4.587976 AGCTAGTTGTAGTCCTGTAGGA 57.412 45.455 0.00 0.00 43.08 2.94
451 10049 1.639298 AAGCAGCGACGAAATGGAGC 61.639 55.000 0.00 0.00 0.00 4.70
492 10090 4.734398 TCAAACAGACAACCAGCAAAAT 57.266 36.364 0.00 0.00 0.00 1.82
509 10107 7.851963 CCAGCAAAATATTTTATGAAATTGCCG 59.148 33.333 19.53 9.07 37.57 5.69
526 10124 0.605319 CCGGGCAAGCTGTTCACTTA 60.605 55.000 0.00 0.00 0.00 2.24
531 10129 3.255642 GGGCAAGCTGTTCACTTATTTGA 59.744 43.478 0.00 0.00 0.00 2.69
554 10159 8.057536 TGAACCACTAAACACATTAAAACTGT 57.942 30.769 0.00 0.00 0.00 3.55
555 10160 8.185505 TGAACCACTAAACACATTAAAACTGTC 58.814 33.333 0.00 0.00 0.00 3.51
574 10179 2.622942 GTCTGTTCAGAAACAATGGGCA 59.377 45.455 3.99 0.00 44.53 5.36
575 10180 3.068024 GTCTGTTCAGAAACAATGGGCAA 59.932 43.478 3.99 0.00 44.53 4.52
597 10202 5.326200 AGGAAAACCGTCAGACTATGTAG 57.674 43.478 0.00 0.00 0.00 2.74
598 10203 4.771054 AGGAAAACCGTCAGACTATGTAGT 59.229 41.667 0.00 0.00 39.71 2.73
601 10227 7.776969 AGGAAAACCGTCAGACTATGTAGTATA 59.223 37.037 0.00 0.00 36.50 1.47
638 10264 0.976641 TCATCTCCCGCAGAACTGTT 59.023 50.000 0.00 0.00 33.62 3.16
639 10265 1.066858 TCATCTCCCGCAGAACTGTTC 60.067 52.381 12.54 12.54 33.62 3.18
676 10302 3.343941 TGGACCCAACTTACATGTAGC 57.656 47.619 5.56 0.00 0.00 3.58
678 10304 2.238898 GGACCCAACTTACATGTAGCCT 59.761 50.000 5.56 0.00 0.00 4.58
683 10309 4.336433 CCCAACTTACATGTAGCCTTCATG 59.664 45.833 9.49 9.49 45.41 3.07
684 10310 5.185454 CCAACTTACATGTAGCCTTCATGA 58.815 41.667 16.97 0.00 43.47 3.07
685 10311 5.065218 CCAACTTACATGTAGCCTTCATGAC 59.935 44.000 16.97 0.00 43.47 3.06
686 10312 5.683876 ACTTACATGTAGCCTTCATGACT 57.316 39.130 16.97 0.00 43.47 3.41
687 10313 5.665459 ACTTACATGTAGCCTTCATGACTC 58.335 41.667 16.97 0.00 43.47 3.36
688 10314 5.187772 ACTTACATGTAGCCTTCATGACTCA 59.812 40.000 16.97 0.00 43.47 3.41
710 10336 1.151760 AGCATGCCCCTGATCCATTA 58.848 50.000 15.66 0.00 0.00 1.90
717 10343 1.496429 CCCCTGATCCATTAAGCAGGT 59.504 52.381 7.35 0.00 0.00 4.00
747 10373 3.243501 GCGGCACATTGTGATATCCAATT 60.244 43.478 20.77 6.38 35.23 2.32
748 10374 4.292599 CGGCACATTGTGATATCCAATTG 58.707 43.478 20.77 14.52 35.23 2.32
765 10391 1.686355 TTGCCCAAACACTACCACTG 58.314 50.000 0.00 0.00 0.00 3.66
769 10395 1.476833 CCCAAACACTACCACTGCTGT 60.477 52.381 0.00 0.00 0.00 4.40
772 10398 2.533266 AACACTACCACTGCTGTCTG 57.467 50.000 0.00 0.00 0.00 3.51
773 10399 1.414158 ACACTACCACTGCTGTCTGT 58.586 50.000 0.00 0.00 0.00 3.41
778 10404 3.386726 ACTACCACTGCTGTCTGTAACAA 59.613 43.478 0.00 0.00 37.45 2.83
840 10476 1.228675 CCTTGTCCCTTGCCAGCTT 60.229 57.895 0.00 0.00 0.00 3.74
909 10545 7.071196 ACCTATAAATACATCAGCTCTGAACCA 59.929 37.037 3.47 0.00 43.58 3.67
954 10590 3.444034 CACTACCACTAGCTTAGCACTCA 59.556 47.826 7.07 0.00 0.00 3.41
993 10629 3.576078 TCTGCCAAGAAAGAAGGTGAA 57.424 42.857 0.00 0.00 0.00 3.18
1033 10669 7.066766 GTGCCAAGAGACTTTCTCAAATGATAT 59.933 37.037 5.99 0.00 45.73 1.63
1155 10791 1.003464 TGCACCATGTACACTGCTGAT 59.997 47.619 18.10 0.00 0.00 2.90
1294 10930 3.642848 TGATGCAGCTGTGATGGACTATA 59.357 43.478 16.64 0.00 0.00 1.31
1564 11201 5.359194 TTTGACTCTTGTCTTGACTCCTT 57.641 39.130 2.35 0.00 43.29 3.36
1568 11205 6.304624 TGACTCTTGTCTTGACTCCTTACTA 58.695 40.000 2.35 0.00 43.29 1.82
1569 11206 6.776116 TGACTCTTGTCTTGACTCCTTACTAA 59.224 38.462 2.35 0.00 43.29 2.24
1578 11215 8.751242 GTCTTGACTCCTTACTAATTAGTTCCT 58.249 37.037 22.66 1.07 37.73 3.36
1579 11216 8.968969 TCTTGACTCCTTACTAATTAGTTCCTC 58.031 37.037 22.66 9.91 37.73 3.71
1587 11224 9.945904 CCTTACTAATTAGTTCCTCAACTCTTT 57.054 33.333 22.66 0.00 42.27 2.52
1593 11230 8.753497 AATTAGTTCCTCAACTCTTTTTGTCT 57.247 30.769 0.00 0.00 42.27 3.41
1594 11231 7.553881 TTAGTTCCTCAACTCTTTTTGTCTG 57.446 36.000 0.00 0.00 42.27 3.51
1595 11232 5.745227 AGTTCCTCAACTCTTTTTGTCTGA 58.255 37.500 0.00 0.00 38.62 3.27
1596 11233 5.819901 AGTTCCTCAACTCTTTTTGTCTGAG 59.180 40.000 0.00 0.00 38.62 3.35
1597 11234 5.359194 TCCTCAACTCTTTTTGTCTGAGT 57.641 39.130 0.00 0.00 42.12 3.41
1600 11237 7.509546 TCCTCAACTCTTTTTGTCTGAGTAAT 58.490 34.615 0.00 0.00 39.78 1.89
1605 11243 8.830580 CAACTCTTTTTGTCTGAGTAATCAAGA 58.169 33.333 0.00 0.00 39.78 3.02
1619 11258 7.875041 TGAGTAATCAAGATAAGGCTCTATTGC 59.125 37.037 0.00 0.00 0.00 3.56
1625 11264 5.140747 AGATAAGGCTCTATTGCGTAAGG 57.859 43.478 0.00 0.00 38.28 2.69
1661 11322 2.514205 AAAGTTGATGCAAGCACACC 57.486 45.000 0.00 0.00 0.00 4.16
1667 11328 3.472283 TGATGCAAGCACACCAAAATT 57.528 38.095 0.00 0.00 0.00 1.82
1705 11366 7.066525 TGGTACTAGTTTAGCAAAATGGTATGC 59.933 37.037 0.00 0.00 42.87 3.14
1728 11389 7.482474 TGCAATCATGGTCATGTAAAGTTATG 58.518 34.615 10.32 0.00 39.72 1.90
1893 11875 8.463930 AATCAAACAGACCATCAACTAAAGAA 57.536 30.769 0.00 0.00 0.00 2.52
1913 11925 7.551035 AAGAAGTGATGTGAGATTATTGAGC 57.449 36.000 0.00 0.00 0.00 4.26
1914 11926 6.647229 AGAAGTGATGTGAGATTATTGAGCA 58.353 36.000 0.00 0.00 0.00 4.26
1915 11927 7.108194 AGAAGTGATGTGAGATTATTGAGCAA 58.892 34.615 0.00 0.00 0.00 3.91
1916 11928 6.922247 AGTGATGTGAGATTATTGAGCAAG 57.078 37.500 0.00 0.00 0.00 4.01
1917 11929 6.413052 AGTGATGTGAGATTATTGAGCAAGT 58.587 36.000 0.00 0.00 0.00 3.16
1918 11930 6.883217 AGTGATGTGAGATTATTGAGCAAGTT 59.117 34.615 0.00 0.00 0.00 2.66
1919 11931 6.965500 GTGATGTGAGATTATTGAGCAAGTTG 59.035 38.462 0.00 0.00 0.00 3.16
1920 11932 6.656270 TGATGTGAGATTATTGAGCAAGTTGT 59.344 34.615 4.48 0.00 0.00 3.32
1921 11933 6.882610 TGTGAGATTATTGAGCAAGTTGTT 57.117 33.333 4.48 0.00 0.00 2.83
1922 11934 7.275888 TGTGAGATTATTGAGCAAGTTGTTT 57.724 32.000 4.48 0.00 0.00 2.83
1923 11935 7.140705 TGTGAGATTATTGAGCAAGTTGTTTG 58.859 34.615 4.48 0.00 39.88 2.93
1924 11936 6.583806 GTGAGATTATTGAGCAAGTTGTTTGG 59.416 38.462 4.48 0.00 37.26 3.28
1925 11937 6.489700 TGAGATTATTGAGCAAGTTGTTTGGA 59.510 34.615 4.48 0.00 37.26 3.53
1926 11938 6.681777 AGATTATTGAGCAAGTTGTTTGGAC 58.318 36.000 4.48 0.00 37.26 4.02
1927 11939 3.733443 ATTGAGCAAGTTGTTTGGACC 57.267 42.857 4.48 0.00 37.26 4.46
1928 11940 2.136298 TGAGCAAGTTGTTTGGACCA 57.864 45.000 4.48 0.00 37.26 4.02
1929 11941 1.748493 TGAGCAAGTTGTTTGGACCAC 59.252 47.619 4.48 0.00 37.26 4.16
1930 11942 2.024414 GAGCAAGTTGTTTGGACCACT 58.976 47.619 4.48 0.00 37.26 4.00
1931 11943 1.750778 AGCAAGTTGTTTGGACCACTG 59.249 47.619 4.48 0.00 37.26 3.66
1932 11944 1.748493 GCAAGTTGTTTGGACCACTGA 59.252 47.619 4.48 0.00 37.26 3.41
1933 11945 2.165437 GCAAGTTGTTTGGACCACTGAA 59.835 45.455 4.48 0.00 37.26 3.02
1934 11946 3.734902 GCAAGTTGTTTGGACCACTGAAG 60.735 47.826 4.48 0.00 37.26 3.02
1935 11947 3.644966 AGTTGTTTGGACCACTGAAGA 57.355 42.857 0.00 0.00 31.15 2.87
1936 11948 3.279434 AGTTGTTTGGACCACTGAAGAC 58.721 45.455 0.00 0.00 31.15 3.01
1937 11949 2.341846 TGTTTGGACCACTGAAGACC 57.658 50.000 0.00 0.00 0.00 3.85
1938 11950 1.843851 TGTTTGGACCACTGAAGACCT 59.156 47.619 0.00 0.00 0.00 3.85
1939 11951 2.241176 TGTTTGGACCACTGAAGACCTT 59.759 45.455 0.00 0.00 0.00 3.50
1940 11952 2.618709 GTTTGGACCACTGAAGACCTTG 59.381 50.000 0.00 0.00 0.00 3.61
1941 11953 1.801242 TGGACCACTGAAGACCTTGA 58.199 50.000 0.00 0.00 0.00 3.02
1972 11984 3.120321 TCAGCAACAACTCGTTATGGT 57.880 42.857 0.00 0.00 35.52 3.55
1977 11989 4.870426 AGCAACAACTCGTTATGGTCATAG 59.130 41.667 0.00 0.00 35.52 2.23
1986 11998 4.634004 TCGTTATGGTCATAGCCAACTTTG 59.366 41.667 0.00 0.00 42.48 2.77
1996 12008 7.600752 GGTCATAGCCAACTTTGAGACTATATC 59.399 40.741 0.00 0.00 34.97 1.63
2011 12023 2.711895 ATATCTCTCCACCTCAGGGG 57.288 55.000 0.00 0.00 41.89 4.79
2036 12048 7.128263 GGCCACCCTATATATTTAACCAGGATA 59.872 40.741 0.00 0.00 0.00 2.59
2047 12059 6.942532 TTTAACCAGGATATAAGCAAGCAG 57.057 37.500 0.00 0.00 0.00 4.24
2209 12241 3.030291 GGTTATTTGACATGGGGATGCA 58.970 45.455 0.00 0.00 0.00 3.96
2226 12258 1.339920 TGCAGCATTTCCAAGATCCGA 60.340 47.619 0.00 0.00 0.00 4.55
2228 12260 2.358957 CAGCATTTCCAAGATCCGACA 58.641 47.619 0.00 0.00 0.00 4.35
2245 12277 2.550208 CGACAAGGGCCAGAAGTTACTT 60.550 50.000 6.18 0.00 0.00 2.24
2281 12313 2.240667 AGCTGCCATTACCTCTGAATGT 59.759 45.455 0.00 0.00 33.27 2.71
2292 12324 7.562454 TTACCTCTGAATGTTTTCGTCTTTT 57.438 32.000 0.00 0.00 34.39 2.27
2298 12330 7.132213 TCTGAATGTTTTCGTCTTTTCACATC 58.868 34.615 0.00 0.00 34.39 3.06
2299 12331 6.205784 TGAATGTTTTCGTCTTTTCACATCC 58.794 36.000 0.00 0.00 34.39 3.51
2330 12362 7.426929 TGATTTCAGACTCTGCTTTTTCTAC 57.573 36.000 0.62 0.00 0.00 2.59
2333 12365 5.791336 TCAGACTCTGCTTTTTCTACAGA 57.209 39.130 0.62 0.00 38.09 3.41
2369 12402 7.482169 ACAATGTCTCAAAGTAGGATGTAGA 57.518 36.000 0.00 0.00 0.00 2.59
2371 12404 8.543774 ACAATGTCTCAAAGTAGGATGTAGATT 58.456 33.333 0.00 0.00 0.00 2.40
2372 12405 8.824781 CAATGTCTCAAAGTAGGATGTAGATTG 58.175 37.037 0.00 0.00 0.00 2.67
2373 12406 6.341316 TGTCTCAAAGTAGGATGTAGATTGC 58.659 40.000 0.00 0.00 0.00 3.56
2374 12407 5.460419 GTCTCAAAGTAGGATGTAGATTGCG 59.540 44.000 0.00 0.00 0.00 4.85
2393 12432 3.627123 TGCGTTTGATATGGATTGTCCTG 59.373 43.478 0.00 0.00 37.46 3.86
2418 12459 3.901222 TGTGTACTGTTTCAGAGGATCCA 59.099 43.478 15.82 0.00 35.18 3.41
2423 12464 3.054065 ACTGTTTCAGAGGATCCAATCCC 60.054 47.826 15.82 0.00 41.57 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 9671 2.236644 AGTCGGTCAGTCTACTAGCTGA 59.763 50.000 0.00 6.26 39.17 4.26
117 9676 4.142447 GCAATGAAGTCGGTCAGTCTACTA 60.142 45.833 0.00 0.00 0.00 1.82
181 9740 7.639945 ACAACTCTTGCTTAACAATGTCTAAC 58.360 34.615 0.00 0.00 37.72 2.34
186 9745 6.318648 TCTGAACAACTCTTGCTTAACAATGT 59.681 34.615 0.00 0.00 37.72 2.71
201 9760 8.697507 AGGTTCATATTTCTTTCTGAACAACT 57.302 30.769 14.14 3.04 45.83 3.16
202 9761 8.787852 AGAGGTTCATATTTCTTTCTGAACAAC 58.212 33.333 14.14 8.42 45.83 3.32
203 9762 8.924511 AGAGGTTCATATTTCTTTCTGAACAA 57.075 30.769 14.14 0.00 45.83 2.83
207 9766 5.812642 GCGAGAGGTTCATATTTCTTTCTGA 59.187 40.000 0.00 0.00 0.00 3.27
217 9776 3.596214 ACAAAACGCGAGAGGTTCATAT 58.404 40.909 15.93 0.00 0.00 1.78
220 9779 1.658994 AACAAAACGCGAGAGGTTCA 58.341 45.000 15.93 0.00 0.00 3.18
245 9804 9.965824 CAGGAACTTACACAACAAAAGAAATAT 57.034 29.630 0.00 0.00 34.60 1.28
246 9805 8.962679 ACAGGAACTTACACAACAAAAGAAATA 58.037 29.630 0.00 0.00 34.60 1.40
247 9806 7.836842 ACAGGAACTTACACAACAAAAGAAAT 58.163 30.769 0.00 0.00 34.60 2.17
251 9810 7.596995 TCAAAACAGGAACTTACACAACAAAAG 59.403 33.333 0.00 0.00 34.60 2.27
253 9812 6.982852 TCAAAACAGGAACTTACACAACAAA 58.017 32.000 0.00 0.00 34.60 2.83
268 9836 7.201496 GCTGCTAAATTCATTGATCAAAACAGG 60.201 37.037 13.09 0.52 0.00 4.00
272 9840 8.836268 AAAGCTGCTAAATTCATTGATCAAAA 57.164 26.923 13.09 3.45 0.00 2.44
312 9880 6.656902 ACCTGAAGCAATCATATCTCTTTGA 58.343 36.000 0.00 0.00 37.44 2.69
313 9881 6.766944 AGACCTGAAGCAATCATATCTCTTTG 59.233 38.462 0.00 0.00 37.44 2.77
323 9891 5.012046 TCTCAGTTAAGACCTGAAGCAATCA 59.988 40.000 0.00 0.00 36.38 2.57
326 9894 4.955811 TCTCAGTTAAGACCTGAAGCAA 57.044 40.909 0.00 0.00 0.00 3.91
334 9902 7.233757 ACTGGACCATATATCTCAGTTAAGACC 59.766 40.741 0.00 0.00 32.34 3.85
339 9907 9.298250 GTTCTACTGGACCATATATCTCAGTTA 57.702 37.037 0.00 1.52 36.87 2.24
348 9916 6.267014 GGTAAGCAGTTCTACTGGACCATATA 59.733 42.308 8.73 0.00 46.01 0.86
353 9921 2.416972 CGGTAAGCAGTTCTACTGGACC 60.417 54.545 8.73 0.00 46.01 4.46
374 9942 7.227512 ACAACTAGCTTATTATCATTGGTGAGC 59.772 37.037 0.00 0.00 37.87 4.26
379 9947 9.209175 GGACTACAACTAGCTTATTATCATTGG 57.791 37.037 0.00 0.00 0.00 3.16
380 9948 9.988815 AGGACTACAACTAGCTTATTATCATTG 57.011 33.333 0.00 0.00 0.00 2.82
386 9954 8.277197 TCCTACAGGACTACAACTAGCTTATTA 58.723 37.037 0.00 0.00 39.78 0.98
406 10004 5.664815 ACACTCTCCTATATGGTCCTACA 57.335 43.478 0.00 0.00 37.07 2.74
412 10010 6.136857 TGCTTCTTACACTCTCCTATATGGT 58.863 40.000 0.00 0.00 37.07 3.55
414 10012 6.155827 GCTGCTTCTTACACTCTCCTATATG 58.844 44.000 0.00 0.00 0.00 1.78
419 10017 1.203523 CGCTGCTTCTTACACTCTCCT 59.796 52.381 0.00 0.00 0.00 3.69
422 10020 1.401670 CGTCGCTGCTTCTTACACTCT 60.402 52.381 0.00 0.00 0.00 3.24
451 10049 7.493645 TGTTTGATTAGTAGCATCTCATGTGAG 59.506 37.037 3.61 3.61 43.36 3.51
492 10090 5.344743 TTGCCCGGCAATTTCATAAAATA 57.655 34.783 21.31 0.00 43.99 1.40
509 10107 3.255642 TCAAATAAGTGAACAGCTTGCCC 59.744 43.478 0.00 0.00 0.00 5.36
531 10129 8.188139 CAGACAGTTTTAATGTGTTTAGTGGTT 58.812 33.333 0.00 0.00 0.00 3.67
554 10159 2.942804 TGCCCATTGTTTCTGAACAGA 58.057 42.857 0.00 0.00 45.80 3.41
555 10160 3.553508 CCTTGCCCATTGTTTCTGAACAG 60.554 47.826 0.00 0.00 45.80 3.16
574 10179 4.618920 ACATAGTCTGACGGTTTTCCTT 57.381 40.909 1.52 0.00 37.95 3.36
575 10180 4.771054 ACTACATAGTCTGACGGTTTTCCT 59.229 41.667 1.52 0.00 37.95 3.36
613 10239 4.460731 CAGTTCTGCGGGAGATGAGATATA 59.539 45.833 0.00 0.00 0.00 0.86
623 10249 0.390472 GAGGAACAGTTCTGCGGGAG 60.390 60.000 13.13 0.00 0.00 4.30
628 10254 2.246719 ACAGTGAGGAACAGTTCTGC 57.753 50.000 13.13 6.18 0.00 4.26
638 10264 2.437651 TCCAACATGTGAACAGTGAGGA 59.562 45.455 0.00 0.00 0.00 3.71
639 10265 2.549754 GTCCAACATGTGAACAGTGAGG 59.450 50.000 0.00 0.00 0.00 3.86
676 10302 2.355132 GCATGCTTCTGAGTCATGAAGG 59.645 50.000 22.71 13.54 38.53 3.46
678 10304 2.362736 GGCATGCTTCTGAGTCATGAA 58.637 47.619 18.92 0.00 38.53 2.57
683 10309 0.747283 CAGGGGCATGCTTCTGAGTC 60.747 60.000 25.67 6.41 0.00 3.36
684 10310 1.203441 TCAGGGGCATGCTTCTGAGT 61.203 55.000 27.24 4.11 33.07 3.41
685 10311 0.183014 ATCAGGGGCATGCTTCTGAG 59.817 55.000 30.99 15.61 39.26 3.35
686 10312 0.182061 GATCAGGGGCATGCTTCTGA 59.818 55.000 30.40 30.40 40.04 3.27
687 10313 0.822532 GGATCAGGGGCATGCTTCTG 60.823 60.000 24.62 24.62 0.00 3.02
688 10314 1.284111 TGGATCAGGGGCATGCTTCT 61.284 55.000 18.92 12.31 0.00 2.85
710 10336 1.221840 CCGCCATACTGACCTGCTT 59.778 57.895 0.00 0.00 0.00 3.91
717 10343 0.035534 ACAATGTGCCGCCATACTGA 60.036 50.000 0.00 0.00 0.00 3.41
747 10373 0.821711 GCAGTGGTAGTGTTTGGGCA 60.822 55.000 0.00 0.00 0.00 5.36
748 10374 0.537371 AGCAGTGGTAGTGTTTGGGC 60.537 55.000 0.00 0.00 0.00 5.36
765 10391 1.593196 TGGCACTTGTTACAGACAGC 58.407 50.000 0.00 0.00 39.94 4.40
769 10395 2.582052 CCCTTTGGCACTTGTTACAGA 58.418 47.619 0.00 0.00 0.00 3.41
810 10446 0.322816 GGACAAGGCCATGAGCTTCA 60.323 55.000 16.33 0.00 43.05 3.02
853 10489 2.042686 TAGGCATGCAGCTTAAGTGG 57.957 50.000 21.36 0.00 44.79 4.00
909 10545 0.478072 TGCTTGTGGATGGAACTGGT 59.522 50.000 0.00 0.00 0.00 4.00
954 10590 4.439289 GCAGAAAGCTCAGAGTTTTGTGTT 60.439 41.667 27.14 3.84 40.23 3.32
993 10629 0.106268 TGGCACTGACCATGGTTGTT 60.106 50.000 20.85 2.77 33.75 2.83
1033 10669 0.823356 GCCACTCTTTGCCACTTCCA 60.823 55.000 0.00 0.00 0.00 3.53
1138 10774 1.065199 CCCATCAGCAGTGTACATGGT 60.065 52.381 0.00 1.49 33.38 3.55
1155 10791 2.852075 ACCTCAAACCGCCTCCCA 60.852 61.111 0.00 0.00 0.00 4.37
1294 10930 2.026542 TCCTTCTGAGCAAGCACATGAT 60.027 45.455 0.00 0.00 0.00 2.45
1357 10993 2.481441 TCCATAGTGGCAAGGTCTCAT 58.519 47.619 0.00 0.00 37.47 2.90
1568 11205 8.624776 CAGACAAAAAGAGTTGAGGAACTAATT 58.375 33.333 0.00 0.00 42.80 1.40
1569 11206 7.993183 TCAGACAAAAAGAGTTGAGGAACTAAT 59.007 33.333 0.00 0.00 42.80 1.73
1578 11215 8.731275 TTGATTACTCAGACAAAAAGAGTTGA 57.269 30.769 0.00 0.00 42.25 3.18
1579 11216 8.830580 TCTTGATTACTCAGACAAAAAGAGTTG 58.169 33.333 0.00 0.00 42.25 3.16
1587 11224 7.624549 AGCCTTATCTTGATTACTCAGACAAA 58.375 34.615 0.00 0.00 31.68 2.83
1590 11227 7.049799 AGAGCCTTATCTTGATTACTCAGAC 57.950 40.000 0.00 0.00 31.68 3.51
1592 11229 9.421806 CAATAGAGCCTTATCTTGATTACTCAG 57.578 37.037 0.00 0.00 31.68 3.35
1593 11230 7.875041 GCAATAGAGCCTTATCTTGATTACTCA 59.125 37.037 0.00 0.00 0.00 3.41
1594 11231 7.062839 CGCAATAGAGCCTTATCTTGATTACTC 59.937 40.741 0.00 0.00 0.00 2.59
1595 11232 6.870965 CGCAATAGAGCCTTATCTTGATTACT 59.129 38.462 0.00 0.00 0.00 2.24
1596 11233 6.647067 ACGCAATAGAGCCTTATCTTGATTAC 59.353 38.462 0.00 0.00 0.00 1.89
1597 11234 6.759272 ACGCAATAGAGCCTTATCTTGATTA 58.241 36.000 0.00 0.00 0.00 1.75
1600 11237 4.672587 ACGCAATAGAGCCTTATCTTGA 57.327 40.909 0.00 0.00 0.00 3.02
1605 11243 3.665190 GCCTTACGCAATAGAGCCTTAT 58.335 45.455 0.00 0.00 37.47 1.73
1619 11258 3.560068 AGTCTGAACTTTGTTGCCTTACG 59.440 43.478 0.00 0.00 28.74 3.18
1625 11264 6.551736 TCAACTTTAGTCTGAACTTTGTTGC 58.448 36.000 0.00 0.00 37.92 4.17
1629 11268 6.728200 TGCATCAACTTTAGTCTGAACTTTG 58.272 36.000 0.00 0.00 36.92 2.77
1630 11269 6.942532 TGCATCAACTTTAGTCTGAACTTT 57.057 33.333 0.00 0.00 36.92 2.66
1661 11322 9.450807 CTAGTACCAAGTTCTGTTCAAATTTTG 57.549 33.333 2.59 2.59 0.00 2.44
1667 11328 7.440255 GCTAAACTAGTACCAAGTTCTGTTCAA 59.560 37.037 10.68 0.00 36.17 2.69
1705 11366 9.859427 AAACATAACTTTACATGACCATGATTG 57.141 29.630 16.07 6.34 41.20 2.67
1728 11389 7.200455 AGAGGTTGTAACAGTTATTGCAAAAC 58.800 34.615 1.71 9.60 36.18 2.43
1746 11407 7.555554 AGAATAAGATTGGTGATCAAGAGGTTG 59.444 37.037 0.00 0.00 38.95 3.77
1813 11479 9.398170 CACATTTTGTTCTTACAGTTTCCTATG 57.602 33.333 0.00 0.00 35.28 2.23
1893 11875 6.413052 ACTTGCTCAATAATCTCACATCACT 58.587 36.000 0.00 0.00 0.00 3.41
1912 11924 1.748493 TCAGTGGTCCAAACAACTTGC 59.252 47.619 0.00 0.00 37.59 4.01
1913 11925 3.694072 TCTTCAGTGGTCCAAACAACTTG 59.306 43.478 0.00 0.00 37.59 3.16
1914 11926 3.694566 GTCTTCAGTGGTCCAAACAACTT 59.305 43.478 0.00 0.00 37.59 2.66
1915 11927 3.279434 GTCTTCAGTGGTCCAAACAACT 58.721 45.455 0.00 0.00 40.51 3.16
1916 11928 2.357952 GGTCTTCAGTGGTCCAAACAAC 59.642 50.000 0.00 0.00 0.00 3.32
1917 11929 2.241176 AGGTCTTCAGTGGTCCAAACAA 59.759 45.455 0.00 0.00 0.00 2.83
1918 11930 1.843851 AGGTCTTCAGTGGTCCAAACA 59.156 47.619 0.00 0.00 0.00 2.83
1919 11931 2.618709 CAAGGTCTTCAGTGGTCCAAAC 59.381 50.000 0.00 0.00 0.00 2.93
1920 11932 2.507886 TCAAGGTCTTCAGTGGTCCAAA 59.492 45.455 0.00 0.00 0.00 3.28
1921 11933 2.123589 TCAAGGTCTTCAGTGGTCCAA 58.876 47.619 0.00 0.00 0.00 3.53
1922 11934 1.801242 TCAAGGTCTTCAGTGGTCCA 58.199 50.000 0.00 0.00 0.00 4.02
1923 11935 2.930826 TTCAAGGTCTTCAGTGGTCC 57.069 50.000 0.00 0.00 0.00 4.46
1924 11936 3.999663 CAGATTCAAGGTCTTCAGTGGTC 59.000 47.826 0.00 0.00 0.00 4.02
1925 11937 3.244700 CCAGATTCAAGGTCTTCAGTGGT 60.245 47.826 0.00 0.00 0.00 4.16
1926 11938 3.244700 ACCAGATTCAAGGTCTTCAGTGG 60.245 47.826 0.00 0.00 30.79 4.00
1927 11939 3.750130 CACCAGATTCAAGGTCTTCAGTG 59.250 47.826 0.00 0.00 35.52 3.66
1928 11940 3.244700 CCACCAGATTCAAGGTCTTCAGT 60.245 47.826 0.00 0.00 35.52 3.41
1929 11941 3.244700 ACCACCAGATTCAAGGTCTTCAG 60.245 47.826 0.00 0.00 35.52 3.02
1930 11942 2.711009 ACCACCAGATTCAAGGTCTTCA 59.289 45.455 0.00 0.00 35.52 3.02
1931 11943 3.425162 ACCACCAGATTCAAGGTCTTC 57.575 47.619 0.00 0.00 35.52 2.87
1932 11944 3.138283 TGAACCACCAGATTCAAGGTCTT 59.862 43.478 0.00 0.00 35.52 3.01
1933 11945 2.711009 TGAACCACCAGATTCAAGGTCT 59.289 45.455 0.00 0.00 35.52 3.85
1934 11946 3.077359 CTGAACCACCAGATTCAAGGTC 58.923 50.000 0.00 0.00 35.52 3.85
1935 11947 2.815589 GCTGAACCACCAGATTCAAGGT 60.816 50.000 0.00 0.00 39.10 3.50
1936 11948 1.815003 GCTGAACCACCAGATTCAAGG 59.185 52.381 0.00 0.00 34.52 3.61
1937 11949 2.507484 TGCTGAACCACCAGATTCAAG 58.493 47.619 0.00 0.00 34.52 3.02
1938 11950 2.622942 GTTGCTGAACCACCAGATTCAA 59.377 45.455 0.00 0.00 34.52 2.69
1939 11951 2.229792 GTTGCTGAACCACCAGATTCA 58.770 47.619 0.00 0.00 36.29 2.57
1940 11952 2.229792 TGTTGCTGAACCACCAGATTC 58.770 47.619 0.00 0.00 36.29 2.52
1941 11953 2.362077 GTTGTTGCTGAACCACCAGATT 59.638 45.455 0.00 0.00 36.29 2.40
1972 11984 8.484214 AGATATAGTCTCAAAGTTGGCTATGA 57.516 34.615 0.00 0.00 28.45 2.15
1996 12008 3.086600 GGCCCCTGAGGTGGAGAG 61.087 72.222 9.82 0.00 38.26 3.20
2011 12023 6.382919 TCCTGGTTAAATATATAGGGTGGC 57.617 41.667 0.00 0.00 0.00 5.01
2040 12052 8.537223 CATGATACAAATTATTTGACTGCTTGC 58.463 33.333 22.53 5.32 43.26 4.01
2047 12059 9.518906 TGTGCATCATGATACAAATTATTTGAC 57.481 29.630 22.53 13.54 43.26 3.18
2076 12088 8.575649 TCACTGACAATGTATACTCTCTTGTA 57.424 34.615 4.17 0.00 30.63 2.41
2209 12241 2.787473 TGTCGGATCTTGGAAATGCT 57.213 45.000 0.00 0.00 0.00 3.79
2226 12258 3.487372 GAAAGTAACTTCTGGCCCTTGT 58.513 45.455 0.00 0.00 0.00 3.16
2228 12260 2.779506 CGAAAGTAACTTCTGGCCCTT 58.220 47.619 0.00 0.00 0.00 3.95
2281 12313 7.504924 ACTTATGGATGTGAAAAGACGAAAA 57.495 32.000 0.00 0.00 0.00 2.29
2292 12324 7.397221 AGTCTGAAATCAACTTATGGATGTGA 58.603 34.615 0.00 0.00 0.00 3.58
2298 12330 5.879223 AGCAGAGTCTGAAATCAACTTATGG 59.121 40.000 24.55 0.00 32.44 2.74
2299 12331 6.981762 AGCAGAGTCTGAAATCAACTTATG 57.018 37.500 24.55 0.00 32.44 1.90
2333 12365 9.125026 ACTTTGAGACATTGTTTTCAGAATAGT 57.875 29.630 0.00 0.15 0.00 2.12
2369 12402 4.889409 AGGACAATCCATATCAAACGCAAT 59.111 37.500 0.00 0.00 39.61 3.56
2371 12404 3.627123 CAGGACAATCCATATCAAACGCA 59.373 43.478 0.00 0.00 39.61 5.24
2372 12405 3.548818 GCAGGACAATCCATATCAAACGC 60.549 47.826 0.00 0.00 39.61 4.84
2373 12406 3.879295 AGCAGGACAATCCATATCAAACG 59.121 43.478 0.00 0.00 39.61 3.60
2374 12407 5.126061 ACAAGCAGGACAATCCATATCAAAC 59.874 40.000 0.00 0.00 39.61 2.93
2393 12432 3.728845 TCCTCTGAAACAGTACACAAGC 58.271 45.455 0.00 0.00 32.61 4.01


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

AutoCloner maintained by Alex Coulton.