Multiple sequence alignment - TraesCS7D01G149500

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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 TraesCS7D01G149500 chr7D 100.000 5165 0 0 1 5165 98412417 98407253 0.000000e+00 9539.0
1 TraesCS7D01G149500 chr7D 100.000 59 0 0 4698 4756 98407661 98407603 5.470000e-20 110.0
2 TraesCS7D01G149500 chr7D 100.000 59 0 0 4757 4815 98407720 98407662 5.470000e-20 110.0
3 TraesCS7D01G149500 chr7D 84.034 119 12 5 594 709 66838232 66838346 1.970000e-19 108.0
4 TraesCS7D01G149500 chr7D 80.303 132 17 8 593 720 295044839 295044713 1.980000e-14 91.6
5 TraesCS7D01G149500 chr7A 93.195 1587 67 18 2327 3884 100714648 100713074 0.000000e+00 2294.0
6 TraesCS7D01G149500 chr7A 90.670 1447 73 16 918 2337 100716110 100714699 0.000000e+00 1868.0
7 TraesCS7D01G149500 chr7A 90.922 694 41 8 3935 4619 100712862 100712182 0.000000e+00 913.0
8 TraesCS7D01G149500 chr7A 92.476 412 28 2 4756 5165 100711852 100711442 2.070000e-163 586.0
9 TraesCS7D01G149500 chr7A 83.453 556 59 16 39 576 100718229 100717689 2.160000e-133 486.0
10 TraesCS7D01G149500 chr7A 83.333 162 9 8 765 926 100717682 100717539 3.240000e-27 134.0
11 TraesCS7D01G149500 chr7A 81.679 131 17 5 593 720 73771432 73771306 9.150000e-18 102.0
12 TraesCS7D01G149500 chr7A 97.727 44 1 0 3889 3932 100712932 100712889 5.550000e-10 76.8
13 TraesCS7D01G149500 chr7B 91.480 1608 78 23 748 2338 53256463 53254898 0.000000e+00 2156.0
14 TraesCS7D01G149500 chr7B 95.274 804 23 6 3091 3888 53254063 53253269 0.000000e+00 1260.0
15 TraesCS7D01G149500 chr7B 92.725 701 39 8 3935 4625 53253119 53252421 0.000000e+00 1002.0
16 TraesCS7D01G149500 chr7B 92.994 471 17 5 2332 2788 53254842 53254374 0.000000e+00 673.0
17 TraesCS7D01G149500 chr7B 89.258 391 30 3 4787 5165 53252126 53251736 3.620000e-131 479.0
18 TraesCS7D01G149500 chr7B 89.308 318 20 5 2787 3092 53254061 53254376 2.260000e-103 387.0
19 TraesCS7D01G149500 chr7B 90.000 280 27 1 441 720 53257181 53256903 1.370000e-95 361.0
20 TraesCS7D01G149500 chr7B 90.299 268 23 3 33 298 53258314 53258048 1.060000e-91 348.0
21 TraesCS7D01G149500 chr7B 97.917 48 1 0 3885 3932 53253193 53253146 3.310000e-12 84.2
22 TraesCS7D01G149500 chr5D 83.848 712 79 17 2981 3672 501033290 501032595 0.000000e+00 645.0
23 TraesCS7D01G149500 chr5D 77.447 235 40 6 3728 3955 501032578 501032350 1.510000e-25 128.0
24 TraesCS7D01G149500 chr2A 92.126 127 9 1 594 720 145379360 145379235 1.480000e-40 178.0
25 TraesCS7D01G149500 chr6D 82.203 118 13 5 4356 4468 159234475 159234589 1.530000e-15 95.3
26 TraesCS7D01G149500 chr5A 77.632 152 28 6 4380 4526 325199376 325199526 2.560000e-13 87.9
27 TraesCS7D01G149500 chr4A 86.207 58 3 4 4357 4411 739069153 739069098 2.010000e-04 58.4
28 TraesCS7D01G149500 chr3D 100.000 31 0 0 4380 4410 7237951 7237981 2.010000e-04 58.4
29 TraesCS7D01G149500 chr1B 97.059 34 0 1 1 34 473562951 473562919 7.220000e-04 56.5
30 TraesCS7D01G149500 chr3B 96.875 32 0 1 4380 4410 654437469 654437438 9.000000e-03 52.8


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 TraesCS7D01G149500 chr7D 98407253 98412417 5164 True 9539.000000 9539 100.000000 1 5165 1 chr7D.!!$R1 5164
1 TraesCS7D01G149500 chr7A 100711442 100718229 6787 True 908.257143 2294 90.253714 39 5165 7 chr7A.!!$R2 5126
2 TraesCS7D01G149500 chr7B 53251736 53258314 6578 True 795.400000 2156 92.493375 33 5165 8 chr7B.!!$R1 5132
3 TraesCS7D01G149500 chr5D 501032350 501033290 940 True 386.500000 645 80.647500 2981 3955 2 chr5D.!!$R1 974

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
347 773 1.202533 AGACTCAACCAACGTGACCAG 60.203 52.381 0.00 0.0 0.00 4.00 F
1119 3695 0.094730 CTAAACGGAAAGCGGCGAAG 59.905 55.000 12.98 0.0 0.00 3.79 F
1207 3784 0.250553 AAATGAAACGTCTCGCCCCA 60.251 50.000 0.00 0.0 0.00 4.96 F
1300 3885 0.464916 GTCTCGTCCTCCTCCTCCTC 60.465 65.000 0.00 0.0 0.00 3.71 F
1934 4537 0.661483 GAACTTGTTTGCTGCGGCTC 60.661 55.000 20.27 9.8 39.59 4.70 F
2009 4613 0.661483 GTGCTTCTGCTTCGGTTTGC 60.661 55.000 0.00 0.0 40.48 3.68 F
2179 4783 0.823356 TGCTGCTGGTGGTCCTTTTC 60.823 55.000 0.00 0.0 34.23 2.29 F
2213 4825 1.293924 GCAGTCGTTATGCTCATGCT 58.706 50.000 0.00 0.0 40.59 3.79 F
3932 6878 2.095567 GTCATCAACGCATCTGCAGTTT 60.096 45.455 14.67 0.0 42.21 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 3938 0.533032 CGTGGGAGAAGGAAGAGGAC 59.467 60.000 0.00 0.0 0.00 3.85 R
2288 4900 0.687354 CAAGAGCACCACTACAGGGT 59.313 55.000 0.00 0.0 39.88 4.34 R
2376 5050 0.915872 AGTCCTGGTGATGGATGCCA 60.916 55.000 0.00 0.0 38.19 4.92 R
2628 5317 1.691434 GCACAAGGGGGAAAATGTGAA 59.309 47.619 8.78 0.0 44.52 3.18 R
3782 6585 3.857093 ACATTGTTTGCTTTTGTCACGAC 59.143 39.130 0.00 0.0 0.00 4.34 R
3960 6930 2.671351 CGACGTGCAACTACCTTCAGAT 60.671 50.000 0.00 0.0 31.75 2.90 R
3980 6950 6.544038 TCATGGCATACTATTTTGATCACG 57.456 37.500 0.00 0.0 0.00 4.35 R
4016 6989 7.807907 ACTAAATAAATGGAGAACGCAAACTTG 59.192 33.333 0.00 0.0 0.00 3.16 R
4979 8162 0.257039 GTTGGCCTCCCATCACTGAT 59.743 55.000 3.32 0.0 41.78 2.90 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
17 18 3.376078 TAGACGCACCACCGGGAC 61.376 66.667 6.32 0.00 38.05 4.46
30 31 4.828296 GGGACGGGGACTAGGCGA 62.828 72.222 0.00 0.00 0.00 5.54
31 32 3.217743 GGACGGGGACTAGGCGAG 61.218 72.222 0.00 0.00 0.00 5.03
117 120 8.969260 TTCATGCAACATAGAGAACATTAGAT 57.031 30.769 0.00 0.00 0.00 1.98
202 205 6.947733 ACAGATAAATGAATGTCCAAACCTCA 59.052 34.615 0.00 0.00 0.00 3.86
259 262 9.224267 CCAAACTTAGTGGATTATCATATCCTG 57.776 37.037 0.00 0.00 43.75 3.86
266 269 7.780064 AGTGGATTATCATATCCTGAAGATCG 58.220 38.462 0.00 0.00 43.75 3.69
281 284 3.045601 AGATCGCCCCTTCATTTATCG 57.954 47.619 0.00 0.00 0.00 2.92
284 287 1.208535 TCGCCCCTTCATTTATCGTGT 59.791 47.619 0.00 0.00 0.00 4.49
338 764 8.977412 TCACATGTATATAAGAGACTCAACCAA 58.023 33.333 5.02 0.00 0.00 3.67
339 765 9.035607 CACATGTATATAAGAGACTCAACCAAC 57.964 37.037 5.02 0.00 0.00 3.77
341 767 7.400599 TGTATATAAGAGACTCAACCAACGT 57.599 36.000 5.02 0.00 0.00 3.99
347 773 1.202533 AGACTCAACCAACGTGACCAG 60.203 52.381 0.00 0.00 0.00 4.00
376 802 5.186198 ACCCAGTAACTTCTGTTATGATGC 58.814 41.667 0.00 0.00 40.31 3.91
377 803 5.185454 CCCAGTAACTTCTGTTATGATGCA 58.815 41.667 0.00 0.00 40.31 3.96
379 805 6.992123 CCCAGTAACTTCTGTTATGATGCATA 59.008 38.462 0.00 0.00 40.31 3.14
380 806 7.498900 CCCAGTAACTTCTGTTATGATGCATAA 59.501 37.037 0.00 0.00 40.31 1.90
381 807 9.060347 CCAGTAACTTCTGTTATGATGCATAAT 57.940 33.333 0.00 0.00 40.31 1.28
431 857 1.909700 TGGCCGCATTTTCTTCTTCT 58.090 45.000 0.00 0.00 0.00 2.85
438 1165 5.280945 CCGCATTTTCTTCTTCTTTCACAA 58.719 37.500 0.00 0.00 0.00 3.33
439 1166 5.748152 CCGCATTTTCTTCTTCTTTCACAAA 59.252 36.000 0.00 0.00 0.00 2.83
466 1193 6.627395 TGTTGATCTTATTGGTGTCGTTTT 57.373 33.333 0.00 0.00 0.00 2.43
468 1195 7.802738 TGTTGATCTTATTGGTGTCGTTTTAG 58.197 34.615 0.00 0.00 0.00 1.85
475 1202 7.496591 TCTTATTGGTGTCGTTTTAGTTCACTT 59.503 33.333 0.00 0.00 0.00 3.16
485 1212 8.008279 GTCGTTTTAGTTCACTTAGATGTTTCC 58.992 37.037 0.00 0.00 0.00 3.13
516 1243 4.276678 CCATATGACCGCATTTCTGTGAAT 59.723 41.667 3.65 0.00 35.94 2.57
535 1262 5.047092 GTGAATTGAGGACCACATTTTCCAT 60.047 40.000 10.54 0.00 33.92 3.41
539 1266 4.335416 TGAGGACCACATTTTCCATCTTC 58.665 43.478 0.00 0.00 33.92 2.87
541 1268 4.338879 AGGACCACATTTTCCATCTTCAG 58.661 43.478 0.00 0.00 33.92 3.02
585 1312 6.160576 AGAGAGCAATTCACTCTATCCTTC 57.839 41.667 7.37 0.00 44.50 3.46
590 1317 7.289782 AGAGCAATTCACTCTATCCTTCACTAT 59.710 37.037 5.84 0.00 42.69 2.12
591 1318 8.484214 AGCAATTCACTCTATCCTTCACTATA 57.516 34.615 0.00 0.00 0.00 1.31
621 1348 4.592485 ACGATAAGGCCTTCATGTCTAG 57.408 45.455 24.49 8.51 0.00 2.43
629 1356 5.128919 AGGCCTTCATGTCTAGCTTTATTG 58.871 41.667 0.00 0.00 0.00 1.90
639 1366 8.886719 CATGTCTAGCTTTATTGACTCAAATCA 58.113 33.333 0.00 0.00 0.00 2.57
690 1417 9.998106 GAATAATAAAGCTAAGAGGTGTATCCA 57.002 33.333 0.00 0.00 39.02 3.41
705 1432 1.604604 ATCCAACCACAAAGTCGGTG 58.395 50.000 0.00 0.00 35.08 4.94
737 1475 1.741706 CCACTCATGAGCAACCATGTC 59.258 52.381 22.83 0.00 43.22 3.06
748 1486 2.357154 GCAACCATGTCCAACTCCCTAT 60.357 50.000 0.00 0.00 0.00 2.57
868 2007 4.066646 TGCGCCATAATAGCTTTCACTA 57.933 40.909 4.18 0.00 0.00 2.74
928 3504 9.111519 TGATACTGGGCCAGATATTTTCTATTA 57.888 33.333 38.99 16.95 35.18 0.98
958 3534 1.473258 TTCCTTCGGCCCATTCAATG 58.527 50.000 0.00 0.00 0.00 2.82
966 3542 1.450531 GCCCATTCAATGCCTCTCCG 61.451 60.000 0.00 0.00 0.00 4.63
1024 3600 2.622436 GTTCTCCCTCAAACAGATCCG 58.378 52.381 0.00 0.00 0.00 4.18
1104 3680 3.792736 ATCCAGGCGGCGGCTAAA 61.793 61.111 35.69 25.42 36.44 1.85
1119 3695 0.094730 CTAAACGGAAAGCGGCGAAG 59.905 55.000 12.98 0.00 0.00 3.79
1128 3704 0.828677 AAGCGGCGAAGGTAGGTAAT 59.171 50.000 12.98 0.00 0.00 1.89
1207 3784 0.250553 AAATGAAACGTCTCGCCCCA 60.251 50.000 0.00 0.00 0.00 4.96
1300 3885 0.464916 GTCTCGTCCTCCTCCTCCTC 60.465 65.000 0.00 0.00 0.00 3.71
1301 3886 0.914902 TCTCGTCCTCCTCCTCCTCA 60.915 60.000 0.00 0.00 0.00 3.86
1302 3887 0.750182 CTCGTCCTCCTCCTCCTCAC 60.750 65.000 0.00 0.00 0.00 3.51
1303 3888 2.115911 CGTCCTCCTCCTCCTCACG 61.116 68.421 0.00 0.00 0.00 4.35
1304 3889 1.303615 GTCCTCCTCCTCCTCACGA 59.696 63.158 0.00 0.00 0.00 4.35
1463 4049 1.000359 TCCGCCTCATCCAGAGTCA 60.000 57.895 0.00 0.00 43.12 3.41
1482 4068 4.457257 AGTCAATTTAGCAGAGAACAAGGC 59.543 41.667 0.00 0.00 0.00 4.35
1612 4207 7.556275 TGAGAAAATGTTTGTTAGTTGGAGACT 59.444 33.333 0.00 0.00 42.55 3.24
1624 4219 3.119459 AGTTGGAGACTAGTGCGTGTATG 60.119 47.826 0.00 0.00 36.65 2.39
1652 4255 1.502690 TGTATATGGCCCCGTGTTCT 58.497 50.000 0.00 0.00 0.00 3.01
1851 4454 5.106515 GCACTTTGTATCTTCTTGGTTCCTC 60.107 44.000 0.00 0.00 0.00 3.71
1893 4496 1.918957 AGCAGGGGAGCTTTGTAATCT 59.081 47.619 0.00 0.00 43.70 2.40
1933 4536 1.360192 GAACTTGTTTGCTGCGGCT 59.640 52.632 20.27 0.00 39.59 5.52
1934 4537 0.661483 GAACTTGTTTGCTGCGGCTC 60.661 55.000 20.27 9.80 39.59 4.70
1935 4538 1.383456 AACTTGTTTGCTGCGGCTCA 61.383 50.000 20.27 12.33 39.59 4.26
1936 4539 1.370900 CTTGTTTGCTGCGGCTCAC 60.371 57.895 20.27 15.24 39.59 3.51
1937 4540 2.737932 CTTGTTTGCTGCGGCTCACC 62.738 60.000 20.27 4.64 39.59 4.02
1938 4541 3.286751 GTTTGCTGCGGCTCACCA 61.287 61.111 20.27 0.00 39.59 4.17
1939 4542 2.518112 TTTGCTGCGGCTCACCAA 60.518 55.556 20.27 0.33 39.59 3.67
1940 4543 2.844451 TTTGCTGCGGCTCACCAAC 61.844 57.895 20.27 0.00 39.59 3.77
1943 4546 2.743928 CTGCGGCTCACCAACCTC 60.744 66.667 0.00 0.00 34.57 3.85
1944 4547 4.329545 TGCGGCTCACCAACCTCC 62.330 66.667 0.00 0.00 34.57 4.30
2009 4613 0.661483 GTGCTTCTGCTTCGGTTTGC 60.661 55.000 0.00 0.00 40.48 3.68
2019 4623 4.749976 TGCTTCGGTTTGCTTTAGTTTTT 58.250 34.783 0.00 0.00 0.00 1.94
2058 4662 9.847706 CCTATGCTATGTAGTCACTAACATTAG 57.152 37.037 5.55 0.00 36.82 1.73
2059 4663 9.847706 CTATGCTATGTAGTCACTAACATTAGG 57.152 37.037 3.79 0.00 35.08 2.69
2060 4664 7.050970 TGCTATGTAGTCACTAACATTAGGG 57.949 40.000 3.79 0.00 35.48 3.53
2102 4706 5.047092 ACCCATCATTGTTTTCTGGATCAAC 60.047 40.000 0.00 0.00 0.00 3.18
2179 4783 0.823356 TGCTGCTGGTGGTCCTTTTC 60.823 55.000 0.00 0.00 34.23 2.29
2184 4788 2.306847 GCTGGTGGTCCTTTTCTTGAA 58.693 47.619 0.00 0.00 34.23 2.69
2185 4789 2.693074 GCTGGTGGTCCTTTTCTTGAAA 59.307 45.455 0.00 0.00 34.23 2.69
2213 4825 1.293924 GCAGTCGTTATGCTCATGCT 58.706 50.000 0.00 0.00 40.59 3.79
2314 4926 5.482908 CTGTAGTGGTGCTCTTGTATTTCT 58.517 41.667 0.00 0.00 0.00 2.52
2330 4942 6.908825 TGTATTTCTATTTTCACCTGTGCAC 58.091 36.000 10.75 10.75 0.00 4.57
2480 5167 5.772672 TGTGACCACAGGCTTAAAATAATGT 59.227 36.000 0.00 0.00 36.21 2.71
2482 5169 7.448777 TGTGACCACAGGCTTAAAATAATGTAA 59.551 33.333 0.00 0.00 36.21 2.41
2559 5246 5.282055 TGACTCTTGATACTTGCCCTATG 57.718 43.478 0.00 0.00 0.00 2.23
2576 5263 8.404107 TGCCCTATGTTTTATCTTATTAAGGC 57.596 34.615 3.66 0.00 0.00 4.35
2628 5317 3.553828 TTTGGAAGGACGAGAACTTGT 57.446 42.857 0.00 0.00 0.00 3.16
2674 5363 3.814005 ATTTGATTGGAATGCAGCTCC 57.186 42.857 10.14 10.14 0.00 4.70
2863 5552 7.280205 TCGTTGGATTTCCTAAAGATCTAAAGC 59.720 37.037 0.00 0.00 36.82 3.51
2874 5563 9.383519 CCTAAAGATCTAAAGCATGTGTCTTAA 57.616 33.333 0.00 0.00 0.00 1.85
2938 5700 6.854892 CCGCAGATCATAAGAATTCACAATTC 59.145 38.462 8.44 1.37 45.98 2.17
3722 6521 2.772287 GGATACCCACTCTTATGCTGC 58.228 52.381 0.00 0.00 0.00 5.25
3724 6523 3.181450 GGATACCCACTCTTATGCTGCTT 60.181 47.826 0.00 0.00 0.00 3.91
3725 6524 4.040461 GGATACCCACTCTTATGCTGCTTA 59.960 45.833 0.00 0.00 0.00 3.09
3726 6525 5.454755 GGATACCCACTCTTATGCTGCTTAA 60.455 44.000 0.00 4.46 0.00 1.85
3782 6585 5.462068 TGTTGTTTCAGACTATCTGTTGACG 59.538 40.000 5.77 0.00 44.58 4.35
3784 6587 5.220381 TGTTTCAGACTATCTGTTGACGTC 58.780 41.667 9.11 9.11 44.58 4.34
3826 6633 5.416013 TGTTTTCCAGTGTATTGTCACAACA 59.584 36.000 0.00 0.00 40.37 3.33
3932 6878 2.095567 GTCATCAACGCATCTGCAGTTT 60.096 45.455 14.67 0.00 42.21 2.66
3960 6930 9.280174 CACTGGTAAGAATAACCTGAAACTTTA 57.720 33.333 6.20 0.00 38.80 1.85
3980 6950 2.433868 TCTGAAGGTAGTTGCACGTC 57.566 50.000 0.00 0.00 0.00 4.34
4021 6994 7.520798 TGCCATGATTAATCTATCTCCAAGTT 58.479 34.615 16.24 0.00 0.00 2.66
4218 7193 6.877855 AGACATATGATAGAAATTCGCATGCT 59.122 34.615 17.13 0.00 0.00 3.79
4263 7238 3.213206 TGCGGATTCAATTATGAGCCT 57.787 42.857 0.00 0.00 36.78 4.58
4349 7326 1.955778 TGCAACATGCTTAAGTGTGCT 59.044 42.857 4.02 0.00 45.31 4.40
4367 7344 5.063312 GTGTGCTAGTTGTGTGCAAAATTTT 59.937 36.000 0.00 0.00 38.50 1.82
4426 7406 3.501445 AGAAAATGAGCTCTGAACAGTGC 59.499 43.478 16.19 17.41 45.38 4.40
4470 7453 2.223144 GCCCGAAATTTGTCTTTTTGCC 59.777 45.455 0.00 0.00 0.00 4.52
4488 7471 7.859325 TTTTGCCGAGAGCTACTAAAATATT 57.141 32.000 0.00 0.00 44.23 1.28
4527 7511 1.667236 CACGGGCATCACACACATAT 58.333 50.000 0.00 0.00 0.00 1.78
4597 7582 1.279496 TTACTGGGAGCATCTGCACT 58.721 50.000 4.79 0.00 45.16 4.40
4598 7583 0.826715 TACTGGGAGCATCTGCACTC 59.173 55.000 4.79 0.00 45.16 3.51
4671 7714 0.322456 CATCCTTGTTCCGCTTGGGA 60.322 55.000 0.00 0.00 45.40 4.37
4691 7734 1.421268 AGATGAGTGTGTTGGCTTGGA 59.579 47.619 0.00 0.00 0.00 3.53
4692 7735 1.808945 GATGAGTGTGTTGGCTTGGAG 59.191 52.381 0.00 0.00 0.00 3.86
4693 7736 0.819259 TGAGTGTGTTGGCTTGGAGC 60.819 55.000 0.00 0.00 41.46 4.70
4695 7738 0.820891 AGTGTGTTGGCTTGGAGCAG 60.821 55.000 2.04 0.00 44.75 4.24
4696 7739 0.819259 GTGTGTTGGCTTGGAGCAGA 60.819 55.000 2.04 0.00 44.75 4.26
4698 7741 0.524862 GTGTTGGCTTGGAGCAGATG 59.475 55.000 2.04 0.00 44.75 2.90
4704 7747 0.106819 GCTTGGAGCAGATGGACCAT 60.107 55.000 6.71 6.71 41.89 3.55
4706 7749 0.994247 TTGGAGCAGATGGACCATGT 59.006 50.000 12.99 4.62 32.31 3.21
4707 7750 0.543277 TGGAGCAGATGGACCATGTC 59.457 55.000 12.99 0.00 0.00 3.06
4708 7751 0.531532 GGAGCAGATGGACCATGTCG 60.532 60.000 12.99 4.31 32.65 4.35
4711 7754 1.524621 CAGATGGACCATGTCGGGC 60.525 63.158 12.99 0.00 45.59 6.13
4735 7785 1.690219 GAGCAGATGGATGTCGGGGT 61.690 60.000 0.00 0.00 0.00 4.95
4736 7786 1.524621 GCAGATGGATGTCGGGGTG 60.525 63.158 0.00 0.00 0.00 4.61
4762 7812 2.874664 CGAGGGTTTCGGTGGACCA 61.875 63.158 0.00 0.00 45.54 4.02
4763 7813 1.683441 GAGGGTTTCGGTGGACCAT 59.317 57.895 0.00 0.00 37.68 3.55
4764 7814 0.676782 GAGGGTTTCGGTGGACCATG 60.677 60.000 0.00 0.00 37.68 3.66
4765 7815 1.074248 GGGTTTCGGTGGACCATGT 59.926 57.895 0.00 0.00 37.68 3.21
4766 7816 0.958876 GGGTTTCGGTGGACCATGTC 60.959 60.000 0.00 0.00 37.68 3.06
4767 7817 1.296056 GGTTTCGGTGGACCATGTCG 61.296 60.000 0.00 2.90 35.95 4.35
4794 7952 1.690219 GAGCAGATGGATGTCGGGGT 61.690 60.000 0.00 0.00 0.00 4.95
4842 8024 6.017357 GCATTGAGAGCATTGATCTTGTATCA 60.017 38.462 5.81 0.00 0.00 2.15
4927 8110 5.221925 TGGAGTGCCTACTTCTTGATCTTTT 60.222 40.000 0.00 0.00 37.25 2.27
4933 8116 6.169800 GCCTACTTCTTGATCTTTTCAGTCT 58.830 40.000 0.00 0.00 35.27 3.24
4979 8162 3.389329 GCAGATATGACTTCTTCTCCCCA 59.611 47.826 0.00 0.00 0.00 4.96
5067 8261 3.694734 CGCTTCTTGTTGTGTTGTCATT 58.305 40.909 0.00 0.00 0.00 2.57
5155 8349 6.239772 GGGTTTTGCCTAGTTTTCCCTAATTT 60.240 38.462 0.00 0.00 37.43 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.376078 GTCCCGGTGGTGCGTCTA 61.376 66.667 0.00 0.00 0.00 2.59
8 9 4.764771 TAGTCCCCGTCCCGGTGG 62.765 72.222 0.00 0.00 46.80 4.61
9 10 3.145551 CTAGTCCCCGTCCCGGTG 61.146 72.222 0.00 0.00 46.80 4.94
10 11 4.453892 CCTAGTCCCCGTCCCGGT 62.454 72.222 0.00 0.00 46.80 5.28
13 14 4.828296 TCGCCTAGTCCCCGTCCC 62.828 72.222 0.00 0.00 0.00 4.46
14 15 3.217743 CTCGCCTAGTCCCCGTCC 61.218 72.222 0.00 0.00 0.00 4.79
15 16 3.217743 CCTCGCCTAGTCCCCGTC 61.218 72.222 0.00 0.00 0.00 4.79
16 17 3.717924 CTCCTCGCCTAGTCCCCGT 62.718 68.421 0.00 0.00 0.00 5.28
17 18 2.907917 CTCCTCGCCTAGTCCCCG 60.908 72.222 0.00 0.00 0.00 5.73
18 19 1.529713 CTCTCCTCGCCTAGTCCCC 60.530 68.421 0.00 0.00 0.00 4.81
19 20 1.529713 CCTCTCCTCGCCTAGTCCC 60.530 68.421 0.00 0.00 0.00 4.46
20 21 2.197605 GCCTCTCCTCGCCTAGTCC 61.198 68.421 0.00 0.00 0.00 3.85
21 22 0.108963 TAGCCTCTCCTCGCCTAGTC 59.891 60.000 0.00 0.00 0.00 2.59
22 23 0.109723 CTAGCCTCTCCTCGCCTAGT 59.890 60.000 0.00 0.00 0.00 2.57
23 24 1.241315 GCTAGCCTCTCCTCGCCTAG 61.241 65.000 2.29 0.00 0.00 3.02
24 25 1.228306 GCTAGCCTCTCCTCGCCTA 60.228 63.158 2.29 0.00 0.00 3.93
25 26 2.520741 GCTAGCCTCTCCTCGCCT 60.521 66.667 2.29 0.00 0.00 5.52
26 27 2.520741 AGCTAGCCTCTCCTCGCC 60.521 66.667 12.13 0.00 0.00 5.54
27 28 1.388065 TTGAGCTAGCCTCTCCTCGC 61.388 60.000 12.13 0.00 41.35 5.03
28 29 1.000385 CATTGAGCTAGCCTCTCCTCG 60.000 57.143 12.13 0.00 41.35 4.63
29 30 1.344114 CCATTGAGCTAGCCTCTCCTC 59.656 57.143 12.13 1.34 41.35 3.71
30 31 1.422531 CCATTGAGCTAGCCTCTCCT 58.577 55.000 12.13 0.00 41.35 3.69
31 32 0.250252 GCCATTGAGCTAGCCTCTCC 60.250 60.000 12.13 0.00 41.35 3.71
61 62 2.215196 TCATGTCCATGCATGTCATCG 58.785 47.619 24.58 19.02 44.68 3.84
101 102 9.513727 CGGTCATCATATCTAATGTTCTCTATG 57.486 37.037 0.00 0.00 0.00 2.23
117 120 1.244816 CGGCTACCTCGGTCATCATA 58.755 55.000 0.00 0.00 0.00 2.15
259 262 3.433615 CGATAAATGAAGGGGCGATCTTC 59.566 47.826 6.84 6.84 40.57 2.87
266 269 2.097466 CACACACGATAAATGAAGGGGC 59.903 50.000 0.00 0.00 0.00 5.80
315 318 7.921214 ACGTTGGTTGAGTCTCTTATATACATG 59.079 37.037 0.65 0.00 0.00 3.21
317 320 7.121611 TCACGTTGGTTGAGTCTCTTATATACA 59.878 37.037 0.65 0.00 0.00 2.29
318 321 7.431668 GTCACGTTGGTTGAGTCTCTTATATAC 59.568 40.741 0.65 0.00 0.00 1.47
431 857 9.258826 CCAATAAGATCAACATTGTTTGTGAAA 57.741 29.630 0.00 0.00 38.99 2.69
438 1165 6.206634 ACGACACCAATAAGATCAACATTGTT 59.793 34.615 0.00 0.00 0.00 2.83
439 1166 5.705441 ACGACACCAATAAGATCAACATTGT 59.295 36.000 0.00 0.00 0.00 2.71
466 1193 8.145767 TCTTTTCGGAAACATCTAAGTGAACTA 58.854 33.333 1.96 0.00 0.00 2.24
468 1195 7.070183 GTCTTTTCGGAAACATCTAAGTGAAC 58.930 38.462 1.96 0.00 0.00 3.18
475 1202 7.494625 GTCATATGGTCTTTTCGGAAACATCTA 59.505 37.037 1.96 0.00 0.00 1.98
485 1212 2.276201 TGCGGTCATATGGTCTTTTCG 58.724 47.619 2.13 0.00 0.00 3.46
516 1243 4.387026 AGATGGAAAATGTGGTCCTCAA 57.613 40.909 0.00 0.00 34.77 3.02
535 1262 6.736110 TCATACCATCATGATCACTGAAGA 57.264 37.500 4.86 0.00 29.93 2.87
539 1266 7.664758 TCTACTTCATACCATCATGATCACTG 58.335 38.462 4.86 1.77 34.95 3.66
541 1268 7.890515 TCTCTACTTCATACCATCATGATCAC 58.109 38.462 4.86 0.00 34.95 3.06
598 1325 5.509163 GCTAGACATGAAGGCCTTATCGTAA 60.509 44.000 20.54 6.51 0.00 3.18
599 1326 4.022242 GCTAGACATGAAGGCCTTATCGTA 60.022 45.833 20.54 4.88 0.00 3.43
600 1327 3.243907 GCTAGACATGAAGGCCTTATCGT 60.244 47.826 20.54 15.34 0.00 3.73
601 1328 3.006323 AGCTAGACATGAAGGCCTTATCG 59.994 47.826 20.54 11.94 0.00 2.92
603 1330 5.379706 AAAGCTAGACATGAAGGCCTTAT 57.620 39.130 20.54 9.70 0.00 1.73
604 1331 4.844349 AAAGCTAGACATGAAGGCCTTA 57.156 40.909 20.54 7.57 0.00 2.69
617 1344 9.507329 AGTTTGATTTGAGTCAATAAAGCTAGA 57.493 29.630 6.36 0.00 37.88 2.43
621 1348 9.677567 TGTAAGTTTGATTTGAGTCAATAAAGC 57.322 29.630 6.36 4.26 37.88 3.51
639 1366 6.915843 CCTTTGTTAGCAAACGATGTAAGTTT 59.084 34.615 0.00 0.00 41.90 2.66
649 1376 8.583765 GCTTTATTATTCCTTTGTTAGCAAACG 58.416 33.333 0.00 0.00 39.43 3.60
705 1432 1.415659 CATGAGTGGGAGGAGTGATCC 59.584 57.143 0.00 0.00 35.99 3.36
709 1436 0.177604 GCTCATGAGTGGGAGGAGTG 59.822 60.000 23.38 0.00 0.00 3.51
737 1475 6.180472 ACAGAACATTGTAATAGGGAGTTGG 58.820 40.000 0.00 0.00 0.00 3.77
748 1486 9.841295 AAGTTAGTTAAGGACAGAACATTGTAA 57.159 29.630 0.00 0.00 32.00 2.41
831 1970 4.732784 TGGCGCATTTTATTGAGTTCTTC 58.267 39.130 10.83 0.00 0.00 2.87
834 1973 7.061094 GCTATTATGGCGCATTTTATTGAGTTC 59.939 37.037 10.83 0.00 0.00 3.01
958 3534 1.458588 AGGGGAGAATCGGAGAGGC 60.459 63.158 0.00 0.00 43.63 4.70
966 3542 0.182299 CTGGGCTTGAGGGGAGAATC 59.818 60.000 0.00 0.00 0.00 2.52
1024 3600 0.319900 TGCGAGGTGAGAACAGAAGC 60.320 55.000 0.00 0.00 0.00 3.86
1104 3680 2.830704 CTACCTTCGCCGCTTTCCGT 62.831 60.000 0.00 0.00 34.38 4.69
1108 3684 0.609662 TTACCTACCTTCGCCGCTTT 59.390 50.000 0.00 0.00 0.00 3.51
1119 3695 3.241156 GAGGGGAAGGAGATTACCTACC 58.759 54.545 0.00 0.00 42.35 3.18
1128 3704 1.305887 GGAACGGAGGGGAAGGAGA 60.306 63.158 0.00 0.00 0.00 3.71
1189 3766 0.953960 GTGGGGCGAGACGTTTCATT 60.954 55.000 6.91 0.00 0.00 2.57
1190 3767 1.375523 GTGGGGCGAGACGTTTCAT 60.376 57.895 6.91 0.00 0.00 2.57
1303 3888 1.154338 CGGGTACGACGACACACTC 60.154 63.158 0.00 0.00 44.60 3.51
1304 3889 2.620112 CCGGGTACGACGACACACT 61.620 63.158 0.00 0.00 44.60 3.55
1353 3938 0.533032 CGTGGGAGAAGGAAGAGGAC 59.467 60.000 0.00 0.00 0.00 3.85
1389 3974 5.404946 GCGAAATCCCCTAAACCTAAAAAC 58.595 41.667 0.00 0.00 0.00 2.43
1463 4049 2.749621 CGGCCTTGTTCTCTGCTAAATT 59.250 45.455 0.00 0.00 0.00 1.82
1482 4068 2.476185 GCACGAGGAACAAATTGATCGG 60.476 50.000 0.00 0.00 34.63 4.18
1612 4207 4.177783 CAACATACACCATACACGCACTA 58.822 43.478 0.00 0.00 0.00 2.74
1624 4219 3.418047 GGGGCCATATACAACATACACC 58.582 50.000 4.39 0.00 0.00 4.16
1652 4255 4.521075 GCCAGCAGCAGTCGAATA 57.479 55.556 0.00 0.00 42.97 1.75
1710 4313 3.943671 TCTCCTTGAGTTTCCCAAACA 57.056 42.857 2.16 0.00 43.79 2.83
1976 4580 7.452880 AGCAGAAGCACAAAATGAATAACTA 57.547 32.000 0.00 0.00 45.49 2.24
2019 4623 7.661536 ACATAGCATAGGACTTCTAAAGACA 57.338 36.000 0.00 0.00 0.00 3.41
2059 4663 3.769300 GGGTATGCATGATAATTTCCCCC 59.231 47.826 10.16 0.00 0.00 5.40
2060 4664 4.415596 TGGGTATGCATGATAATTTCCCC 58.584 43.478 10.16 5.09 0.00 4.81
2073 4677 4.160065 CCAGAAAACAATGATGGGTATGCA 59.840 41.667 0.00 0.00 0.00 3.96
2102 4706 4.934001 GTGGTGATGTAGCTGATGATATGG 59.066 45.833 0.00 0.00 0.00 2.74
2276 4888 3.055094 CACTACAGGGTTGCTATTCTGGT 60.055 47.826 0.00 0.00 0.00 4.00
2278 4890 3.055094 ACCACTACAGGGTTGCTATTCTG 60.055 47.826 0.00 0.00 34.10 3.02
2284 4896 1.073199 GCACCACTACAGGGTTGCT 59.927 57.895 0.00 0.00 36.19 3.91
2288 4900 0.687354 CAAGAGCACCACTACAGGGT 59.313 55.000 0.00 0.00 39.88 4.34
2314 4926 7.701539 ATTAATCTGTGCACAGGTGAAAATA 57.298 32.000 39.04 22.52 43.91 1.40
2358 5032 9.836864 TGGATGCCATCAAACATATAGATATAC 57.163 33.333 7.06 0.00 0.00 1.47
2376 5050 0.915872 AGTCCTGGTGATGGATGCCA 60.916 55.000 0.00 0.00 38.19 4.92
2389 5063 5.879223 AGCAAGATTTCATCAACTAGTCCTG 59.121 40.000 0.00 0.00 0.00 3.86
2480 5167 7.118496 ACCAACAAACAAGAATTCCATGTTA 57.882 32.000 21.08 0.00 36.33 2.41
2482 5169 5.612725 ACCAACAAACAAGAATTCCATGT 57.387 34.783 0.65 5.26 0.00 3.21
2628 5317 1.691434 GCACAAGGGGGAAAATGTGAA 59.309 47.619 8.78 0.00 44.52 3.18
2674 5363 8.877808 TCCTGAATATATGCTATAAAGATGCG 57.122 34.615 0.00 0.00 0.00 4.73
2719 5408 5.361857 CCAAGGATTAATGAACCATTCTGCT 59.638 40.000 0.00 0.00 35.54 4.24
2828 5517 8.446599 TTTAGGAAATCCAACGATTATCCTTC 57.553 34.615 15.43 0.16 41.36 3.46
2839 5528 8.281212 TGCTTTAGATCTTTAGGAAATCCAAC 57.719 34.615 0.00 0.00 38.89 3.77
2863 5552 8.085296 AGAACTACAAGACTCTTAAGACACATG 58.915 37.037 0.00 4.73 0.00 3.21
2874 5563 4.896482 AGGTGACAAGAACTACAAGACTCT 59.104 41.667 0.00 0.00 0.00 3.24
2875 5564 4.985409 CAGGTGACAAGAACTACAAGACTC 59.015 45.833 0.00 0.00 0.00 3.36
2876 5565 4.740934 GCAGGTGACAAGAACTACAAGACT 60.741 45.833 0.00 0.00 0.00 3.24
3129 5908 8.509690 CGAAGACAATCAAATCATAGCCATTAT 58.490 33.333 0.00 0.00 0.00 1.28
3130 5909 7.714813 TCGAAGACAATCAAATCATAGCCATTA 59.285 33.333 0.00 0.00 0.00 1.90
3147 5926 5.301805 TCTCCATACAGCATATCGAAGACAA 59.698 40.000 0.00 0.00 42.51 3.18
3218 5997 5.697473 TCAGCATATCTTTAGACTCCTCG 57.303 43.478 0.00 0.00 0.00 4.63
3224 6003 6.347240 CCGCATTCTTCAGCATATCTTTAGAC 60.347 42.308 0.00 0.00 0.00 2.59
3724 6523 8.932791 GCTTATTTCTGCGGTATAGCTTAATTA 58.067 33.333 0.00 0.00 38.13 1.40
3725 6524 7.807680 GCTTATTTCTGCGGTATAGCTTAATT 58.192 34.615 0.00 0.00 38.13 1.40
3726 6525 7.365840 GCTTATTTCTGCGGTATAGCTTAAT 57.634 36.000 0.00 0.00 38.13 1.40
3782 6585 3.857093 ACATTGTTTGCTTTTGTCACGAC 59.143 39.130 0.00 0.00 0.00 4.34
3784 6587 4.838665 AACATTGTTTGCTTTTGTCACG 57.161 36.364 0.00 0.00 0.00 4.35
3826 6633 3.864789 AGTCAGAAACACAGGGACAAT 57.135 42.857 0.00 0.00 0.00 2.71
3932 6878 7.514721 AGTTTCAGGTTATTCTTACCAGTGAA 58.485 34.615 0.00 0.00 38.16 3.18
3960 6930 2.671351 CGACGTGCAACTACCTTCAGAT 60.671 50.000 0.00 0.00 31.75 2.90
3980 6950 6.544038 TCATGGCATACTATTTTGATCACG 57.456 37.500 0.00 0.00 0.00 4.35
4016 6989 7.807907 ACTAAATAAATGGAGAACGCAAACTTG 59.192 33.333 0.00 0.00 0.00 3.16
4218 7193 7.750229 AATGAGTAAGCATCTGTCTTTTTGA 57.250 32.000 0.00 0.00 0.00 2.69
4263 7238 1.276859 ATCAGGTGCAGATGAGCCCA 61.277 55.000 6.88 0.00 0.00 5.36
4349 7326 4.032217 CGCACAAAATTTTGCACACAACTA 59.968 37.500 26.94 0.00 41.79 2.24
4367 7344 4.496360 TCCTCGAATGTTATTTACGCACA 58.504 39.130 0.00 0.00 0.00 4.57
4426 7406 7.127686 GGCATGTGAGAAAATTTTGAAAACAG 58.872 34.615 8.47 3.88 0.00 3.16
4470 7453 8.756864 GGAGTTTGAATATTTTAGTAGCTCTCG 58.243 37.037 0.00 0.00 0.00 4.04
4488 7471 2.690497 TGCCAAATTTCGTGGAGTTTGA 59.310 40.909 0.00 0.00 38.54 2.69
4597 7582 0.937699 CGTGTCGTTTTGGCTCTCGA 60.938 55.000 0.00 0.00 0.00 4.04
4598 7583 1.213094 ACGTGTCGTTTTGGCTCTCG 61.213 55.000 0.00 0.00 36.35 4.04
4671 7714 1.421268 TCCAAGCCAACACACTCATCT 59.579 47.619 0.00 0.00 0.00 2.90
4673 7716 1.901591 CTCCAAGCCAACACACTCAT 58.098 50.000 0.00 0.00 0.00 2.90
4691 7734 1.524002 CCGACATGGTCCATCTGCT 59.476 57.895 0.00 0.00 0.00 4.24
4692 7735 1.524621 CCCGACATGGTCCATCTGC 60.525 63.158 0.00 0.00 35.15 4.26
4693 7736 1.524621 GCCCGACATGGTCCATCTG 60.525 63.158 0.00 0.00 35.15 2.90
4695 7738 2.203209 GGCCCGACATGGTCCATC 60.203 66.667 0.00 0.00 35.15 3.51
4696 7739 4.175337 CGGCCCGACATGGTCCAT 62.175 66.667 0.00 0.00 35.15 3.41
4711 7754 2.664185 CATCCATCTGCTCCGCGG 60.664 66.667 22.12 22.12 36.06 6.46
4712 7755 1.953138 GACATCCATCTGCTCCGCG 60.953 63.158 0.00 0.00 0.00 6.46
4714 7757 1.300465 CCGACATCCATCTGCTCCG 60.300 63.158 0.00 0.00 0.00 4.63
4717 7760 1.690633 ACCCCGACATCCATCTGCT 60.691 57.895 0.00 0.00 0.00 4.24
4719 7762 1.146930 CCACCCCGACATCCATCTG 59.853 63.158 0.00 0.00 0.00 2.90
4720 7763 2.746375 GCCACCCCGACATCCATCT 61.746 63.158 0.00 0.00 0.00 2.90
4722 7765 4.175337 CGCCACCCCGACATCCAT 62.175 66.667 0.00 0.00 0.00 3.41
4747 7797 0.958876 GACATGGTCCACCGAAACCC 60.959 60.000 0.00 0.00 39.43 4.11
4748 7798 1.296056 CGACATGGTCCACCGAAACC 61.296 60.000 0.00 0.00 39.43 3.27
4749 7799 1.296056 CCGACATGGTCCACCGAAAC 61.296 60.000 10.64 0.00 39.43 2.78
4751 7801 2.660206 CCGACATGGTCCACCGAA 59.340 61.111 10.64 0.00 39.43 4.30
4770 7820 2.664185 CATCCATCTGCTCCGCGG 60.664 66.667 22.12 22.12 36.06 6.46
4773 7823 1.300465 CCGACATCCATCTGCTCCG 60.300 63.158 0.00 0.00 0.00 4.63
4774 7824 1.070445 CCCGACATCCATCTGCTCC 59.930 63.158 0.00 0.00 0.00 4.70
4775 7825 1.070445 CCCCGACATCCATCTGCTC 59.930 63.158 0.00 0.00 0.00 4.26
4777 7827 1.524621 CACCCCGACATCCATCTGC 60.525 63.158 0.00 0.00 0.00 4.26
4778 7828 1.146930 CCACCCCGACATCCATCTG 59.853 63.158 0.00 0.00 0.00 2.90
4779 7829 2.746375 GCCACCCCGACATCCATCT 61.746 63.158 0.00 0.00 0.00 2.90
4781 7831 4.175337 CGCCACCCCGACATCCAT 62.175 66.667 0.00 0.00 0.00 3.41
4817 7999 4.634184 ACAAGATCAATGCTCTCAATGC 57.366 40.909 0.00 0.00 0.00 3.56
4897 8080 3.034635 AGAAGTAGGCACTCCACATAGG 58.965 50.000 0.00 0.00 41.75 2.57
4927 8110 3.085533 GAGCAGACCTAGAACAGACTGA 58.914 50.000 10.08 0.00 33.39 3.41
4933 8116 1.619977 GGGAGGAGCAGACCTAGAACA 60.620 57.143 0.00 0.00 40.73 3.18
4979 8162 0.257039 GTTGGCCTCCCATCACTGAT 59.743 55.000 3.32 0.00 41.78 2.90


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

AutoCloner maintained by Alex Coulton.