Multiple sequence alignment - TraesCS1B01G085300

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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 TraesCS1B01G085300 chr1B 100.000 4379 0 0 1 4379 70168866 70173244 0.000000e+00 8087.0
1 TraesCS1B01G085300 chr1B 86.308 3177 351 41 1253 4366 70185802 70188957 0.000000e+00 3380.0
2 TraesCS1B01G085300 chr1A 91.231 3581 218 35 851 4348 49245090 49248657 0.000000e+00 4785.0
3 TraesCS1B01G085300 chr1A 83.030 2640 405 30 812 3436 49354700 49357311 0.000000e+00 2353.0
4 TraesCS1B01G085300 chr1A 81.748 2586 426 34 851 3423 49293340 49295892 0.000000e+00 2119.0
5 TraesCS1B01G085300 chr1D 86.540 3670 388 50 767 4366 49616882 49620515 0.000000e+00 3943.0
6 TraesCS1B01G085300 chr1D 83.977 2565 376 29 899 3456 49973228 49975764 0.000000e+00 2427.0
7 TraesCS1B01G085300 chr1D 83.989 2467 359 24 917 3372 50022600 50025041 0.000000e+00 2335.0
8 TraesCS1B01G085300 chr1D 82.330 2592 416 34 843 3425 49956215 49958773 0.000000e+00 2211.0
9 TraesCS1B01G085300 chr1D 81.753 2658 428 41 908 3552 49426338 49423725 0.000000e+00 2169.0
10 TraesCS1B01G085300 chr1D 89.916 595 41 10 90 679 49609193 49609773 0.000000e+00 749.0
11 TraesCS1B01G085300 chr1D 91.991 462 30 5 73 533 49614381 49614836 3.690000e-180 641.0
12 TraesCS1B01G085300 chr1D 89.401 217 14 7 764 979 49611044 49611252 9.340000e-67 265.0
13 TraesCS1B01G085300 chr1D 93.333 90 6 0 679 768 49610930 49611019 2.750000e-27 134.0
14 TraesCS1B01G085300 chr2B 87.755 49 5 1 445 492 458621026 458621074 6.120000e-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 TraesCS1B01G085300 chr1B 70168866 70173244 4378 False 8087.0 8087 100.0000 1 4379 1 chr1B.!!$F1 4378
1 TraesCS1B01G085300 chr1B 70185802 70188957 3155 False 3380.0 3380 86.3080 1253 4366 1 chr1B.!!$F2 3113
2 TraesCS1B01G085300 chr1A 49245090 49248657 3567 False 4785.0 4785 91.2310 851 4348 1 chr1A.!!$F1 3497
3 TraesCS1B01G085300 chr1A 49354700 49357311 2611 False 2353.0 2353 83.0300 812 3436 1 chr1A.!!$F3 2624
4 TraesCS1B01G085300 chr1A 49293340 49295892 2552 False 2119.0 2119 81.7480 851 3423 1 chr1A.!!$F2 2572
5 TraesCS1B01G085300 chr1D 49973228 49975764 2536 False 2427.0 2427 83.9770 899 3456 1 chr1D.!!$F2 2557
6 TraesCS1B01G085300 chr1D 50022600 50025041 2441 False 2335.0 2335 83.9890 917 3372 1 chr1D.!!$F3 2455
7 TraesCS1B01G085300 chr1D 49956215 49958773 2558 False 2211.0 2211 82.3300 843 3425 1 chr1D.!!$F1 2582
8 TraesCS1B01G085300 chr1D 49423725 49426338 2613 True 2169.0 2169 81.7530 908 3552 1 chr1D.!!$R1 2644
9 TraesCS1B01G085300 chr1D 49609193 49620515 11322 False 1146.4 3943 90.2362 73 4366 5 chr1D.!!$F4 4293

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
835 2027 0.031111 CCTCCAGATCCACCTACCCA 60.031 60.0 0.0 0.0 0.0 4.51 F
842 2034 0.118346 ATCCACCTACCCAGTGTCCA 59.882 55.0 0.0 0.0 33.2 4.02 F
1110 8164 0.250124 TTGCTACAACAGACCACCCG 60.250 55.0 0.0 0.0 0.0 5.28 F
1565 8637 0.322456 CGGGTGATGGCAAAAGGAGA 60.322 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 8759 2.224281 ACGTCACCACATCAGACACAAT 60.224 45.455 0.00 0.0 32.68 2.71 R
2827 9910 4.024809 GCTCACTACTGTTCCACTTTCAAC 60.025 45.833 0.00 0.0 0.00 3.18 R
3106 10189 1.593196 TTGTCAGCTTCTTCCAACGG 58.407 50.000 0.00 0.0 0.00 4.44 R
3492 10575 1.301244 AGAGCAGAACACTGTGGCG 60.301 57.895 13.09 0.0 34.51 5.69 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
22 23 3.093278 GGCAAATCTGACGGCTCG 58.907 61.111 0.00 0.00 0.00 5.03
23 24 1.741770 GGCAAATCTGACGGCTCGT 60.742 57.895 0.00 0.00 45.10 4.18
24 25 1.421485 GCAAATCTGACGGCTCGTG 59.579 57.895 4.94 0.00 41.37 4.35
25 26 1.014044 GCAAATCTGACGGCTCGTGA 61.014 55.000 4.94 0.00 41.37 4.35
26 27 1.645034 CAAATCTGACGGCTCGTGAT 58.355 50.000 4.94 0.79 41.37 3.06
27 28 1.590238 CAAATCTGACGGCTCGTGATC 59.410 52.381 4.94 0.00 41.37 2.92
28 29 1.107114 AATCTGACGGCTCGTGATCT 58.893 50.000 4.94 0.00 41.37 2.75
29 30 0.383590 ATCTGACGGCTCGTGATCTG 59.616 55.000 4.94 0.00 41.37 2.90
30 31 1.226802 CTGACGGCTCGTGATCTGG 60.227 63.158 4.94 0.00 41.37 3.86
31 32 2.583593 GACGGCTCGTGATCTGGC 60.584 66.667 4.94 0.00 41.37 4.85
32 33 3.069980 GACGGCTCGTGATCTGGCT 62.070 63.158 4.94 0.00 41.37 4.75
33 34 2.185350 CGGCTCGTGATCTGGCTT 59.815 61.111 0.00 0.00 0.00 4.35
34 35 1.320344 ACGGCTCGTGATCTGGCTTA 61.320 55.000 0.00 0.00 39.18 3.09
35 36 0.032678 CGGCTCGTGATCTGGCTTAT 59.967 55.000 0.00 0.00 0.00 1.73
36 37 1.506493 GGCTCGTGATCTGGCTTATG 58.494 55.000 0.00 0.00 0.00 1.90
37 38 1.069204 GGCTCGTGATCTGGCTTATGA 59.931 52.381 0.00 0.00 0.00 2.15
38 39 2.289320 GGCTCGTGATCTGGCTTATGAT 60.289 50.000 0.00 0.00 0.00 2.45
39 40 3.397482 GCTCGTGATCTGGCTTATGATT 58.603 45.455 0.00 0.00 0.00 2.57
40 41 4.560128 GCTCGTGATCTGGCTTATGATTA 58.440 43.478 0.00 0.00 0.00 1.75
41 42 4.991056 GCTCGTGATCTGGCTTATGATTAA 59.009 41.667 0.00 0.00 0.00 1.40
42 43 5.107298 GCTCGTGATCTGGCTTATGATTAAC 60.107 44.000 0.00 0.00 0.00 2.01
43 44 5.912892 TCGTGATCTGGCTTATGATTAACA 58.087 37.500 0.00 0.00 0.00 2.41
44 45 6.524734 TCGTGATCTGGCTTATGATTAACAT 58.475 36.000 0.00 0.00 42.39 2.71
45 46 6.992123 TCGTGATCTGGCTTATGATTAACATT 59.008 34.615 0.00 0.00 40.07 2.71
46 47 7.041848 TCGTGATCTGGCTTATGATTAACATTG 60.042 37.037 0.00 0.00 40.07 2.82
47 48 7.254898 CGTGATCTGGCTTATGATTAACATTGT 60.255 37.037 0.00 0.00 40.07 2.71
48 49 8.408601 GTGATCTGGCTTATGATTAACATTGTT 58.591 33.333 7.30 7.30 40.07 2.83
49 50 8.407832 TGATCTGGCTTATGATTAACATTGTTG 58.592 33.333 12.30 0.00 40.07 3.33
50 51 7.099266 TCTGGCTTATGATTAACATTGTTGG 57.901 36.000 12.30 0.00 40.07 3.77
51 52 6.889177 TCTGGCTTATGATTAACATTGTTGGA 59.111 34.615 12.30 1.45 40.07 3.53
52 53 7.395772 TCTGGCTTATGATTAACATTGTTGGAA 59.604 33.333 12.30 0.00 40.07 3.53
53 54 7.319646 TGGCTTATGATTAACATTGTTGGAAC 58.680 34.615 12.30 1.07 40.07 3.62
54 55 7.039434 TGGCTTATGATTAACATTGTTGGAACA 60.039 33.333 12.30 6.29 40.07 3.18
55 56 7.981225 GGCTTATGATTAACATTGTTGGAACAT 59.019 33.333 12.30 12.10 38.20 2.71
66 67 8.593945 ACATTGTTGGAACATATATTGGAACT 57.406 30.769 0.00 0.00 39.30 3.01
67 68 9.034800 ACATTGTTGGAACATATATTGGAACTT 57.965 29.630 0.00 0.00 39.30 2.66
241 242 7.294473 TCACACACACATTAATACATTTGTCG 58.706 34.615 0.00 0.00 0.00 4.35
248 249 9.720667 ACACATTAATACATTTGTCGAATGATG 57.279 29.630 18.09 12.75 46.59 3.07
249 250 9.934190 CACATTAATACATTTGTCGAATGATGA 57.066 29.630 18.09 4.94 46.59 2.92
391 393 6.910536 TTTTAATGGCACGAACATTGTTTT 57.089 29.167 3.08 0.00 38.84 2.43
392 394 6.910536 TTTAATGGCACGAACATTGTTTTT 57.089 29.167 3.08 0.00 38.84 1.94
393 395 8.420374 TTTTAATGGCACGAACATTGTTTTTA 57.580 26.923 3.08 0.00 38.84 1.52
520 525 6.757947 ACATTATACACCTTTTCAATGCATGC 59.242 34.615 11.82 11.82 0.00 4.06
525 530 4.273969 ACACCTTTTCAATGCATGCTTTTG 59.726 37.500 20.33 20.73 0.00 2.44
629 635 4.842531 TGAGGAAGCTACATCCAATGAA 57.157 40.909 5.73 0.00 39.55 2.57
688 1851 2.618053 ACGAAAAGGAATACTGAGCCG 58.382 47.619 0.00 0.00 0.00 5.52
698 1861 4.537433 CTGAGCCGGCCCAGTAGC 62.537 72.222 28.38 7.90 0.00 3.58
807 1999 2.824041 CACCATTCCCCTTCGCCG 60.824 66.667 0.00 0.00 0.00 6.46
822 2014 4.521062 CCGCCGCTCTTCCTCCAG 62.521 72.222 0.00 0.00 0.00 3.86
835 2027 0.031111 CCTCCAGATCCACCTACCCA 60.031 60.000 0.00 0.00 0.00 4.51
836 2028 1.418334 CTCCAGATCCACCTACCCAG 58.582 60.000 0.00 0.00 0.00 4.45
842 2034 0.118346 ATCCACCTACCCAGTGTCCA 59.882 55.000 0.00 0.00 33.20 4.02
847 2039 1.203262 ACCTACCCAGTGTCCAGCTTA 60.203 52.381 0.00 0.00 0.00 3.09
858 2050 2.202932 CAGCTTACGCCTCCGCAT 60.203 61.111 0.00 0.00 38.22 4.73
1007 8061 1.482593 GATCCTCACGGTCATGGTCTT 59.517 52.381 0.00 0.00 0.00 3.01
1099 8153 2.811431 CCTGTTCGACCAATTGCTACAA 59.189 45.455 0.00 0.00 0.00 2.41
1103 8157 3.394674 TCGACCAATTGCTACAACAGA 57.605 42.857 0.00 0.00 0.00 3.41
1110 8164 0.250124 TTGCTACAACAGACCACCCG 60.250 55.000 0.00 0.00 0.00 5.28
1135 8189 4.166888 GAGCGCTCCCTGCATGGA 62.167 66.667 27.22 10.56 43.06 3.41
1136 8190 3.472943 GAGCGCTCCCTGCATGGAT 62.473 63.158 27.22 0.00 43.06 3.41
1269 8329 2.986290 CCGCCCACAGTCCATACA 59.014 61.111 0.00 0.00 0.00 2.29
1298 8358 0.677098 CTGATGAACTGCTGCTGCCT 60.677 55.000 13.47 0.00 38.71 4.75
1353 8413 2.435693 CCGCCTCCTAAGGACAGGG 61.436 68.421 0.00 0.00 46.67 4.45
1384 8444 3.356639 GAGATCGTCGCCAGCACCA 62.357 63.158 0.00 0.00 0.00 4.17
1435 8496 3.728845 ACAGATGAAGCAGTAAACGTGT 58.271 40.909 0.00 0.00 0.00 4.49
1490 8556 5.643348 TGCCTAATGTGTTCTCATACAACAG 59.357 40.000 0.00 0.00 34.40 3.16
1561 8633 1.937546 GCTCCGGGTGATGGCAAAAG 61.938 60.000 0.00 0.00 0.00 2.27
1562 8634 1.304052 TCCGGGTGATGGCAAAAGG 60.304 57.895 0.00 0.00 0.00 3.11
1563 8635 1.304052 CCGGGTGATGGCAAAAGGA 60.304 57.895 0.00 0.00 0.00 3.36
1564 8636 1.315257 CCGGGTGATGGCAAAAGGAG 61.315 60.000 0.00 0.00 0.00 3.69
1565 8637 0.322456 CGGGTGATGGCAAAAGGAGA 60.322 55.000 0.00 0.00 0.00 3.71
1566 8638 1.683011 CGGGTGATGGCAAAAGGAGAT 60.683 52.381 0.00 0.00 0.00 2.75
1681 8759 1.171549 TGAAATGACGCAGCAAGGCA 61.172 50.000 0.00 0.00 0.00 4.75
1818 8898 6.203530 CGAATGGAGTGACATATACTGCAATT 59.796 38.462 2.87 0.00 46.96 2.32
1961 9041 3.494332 AGCATGGAAGAAGCAAAGAAGT 58.506 40.909 0.00 0.00 0.00 3.01
1988 9068 5.416952 CAGAACTTCTTTATTCCATGGCTGT 59.583 40.000 6.96 0.00 0.00 4.40
2827 9910 5.632347 GCAAAGAAGTTGTTCAATGAGATGG 59.368 40.000 0.00 0.00 39.63 3.51
3158 10241 3.136443 TCAATGGAGAAGAGTGGTTGTGT 59.864 43.478 0.00 0.00 0.00 3.72
3213 10296 3.529216 ACGTTATTGGAAAAGGGGGAA 57.471 42.857 0.00 0.00 0.00 3.97
3244 10327 8.965819 TCAAGGCAGCAAATTATATGTCTAAAA 58.034 29.630 0.00 0.00 0.00 1.52
3391 10474 4.147321 AGTCATTTGATGCACTGGACTTT 58.853 39.130 0.00 0.00 30.53 2.66
3431 10514 2.290134 GGTTCGGAGCTCCCTTTTAACT 60.290 50.000 27.20 0.00 0.00 2.24
3461 10544 4.202503 ACATGTGTTCTCTTCCATCCACTT 60.203 41.667 0.00 0.00 0.00 3.16
3476 10559 2.159043 TCCACTTGCCAAGATCGATCTC 60.159 50.000 27.43 15.91 35.76 2.75
3497 10580 2.327940 GATAATGCCGTGCGCCAC 59.672 61.111 4.18 1.96 36.24 5.01
3498 10581 2.437537 ATAATGCCGTGCGCCACA 60.438 55.556 4.18 0.00 36.24 4.17
3545 10630 1.217882 GGCGTGTATGCTATGGTCAC 58.782 55.000 0.00 0.00 34.52 3.67
3561 10648 1.202582 GTCACTGCTCCGTCTACATGT 59.797 52.381 2.69 2.69 0.00 3.21
3593 10686 3.497884 AAGGGCTGTCTGGTGTGGC 62.498 63.158 0.00 0.00 0.00 5.01
3607 10700 1.231296 TGTGGCGCGTTTGCTAATGA 61.231 50.000 8.43 0.00 39.65 2.57
3611 10704 1.467374 GGCGCGTTTGCTAATGACAAT 60.467 47.619 8.43 0.00 39.65 2.71
3612 10705 1.840141 GCGCGTTTGCTAATGACAATC 59.160 47.619 8.43 0.00 39.65 2.67
3616 10709 4.666176 CGCGTTTGCTAATGACAATCATAC 59.334 41.667 0.00 0.00 35.86 2.39
3621 10735 7.409697 GTTTGCTAATGACAATCATACGATGT 58.590 34.615 0.00 0.00 35.76 3.06
3632 10746 6.599244 ACAATCATACGATGTTGGATCTTGTT 59.401 34.615 0.00 0.00 30.13 2.83
3644 10758 4.582869 TGGATCTTGTTCCAGAGTTCATG 58.417 43.478 0.00 0.00 40.90 3.07
3653 10767 2.909006 TCCAGAGTTCATGGAGCTCTTT 59.091 45.455 14.64 0.00 45.43 2.52
3657 10771 4.081531 CAGAGTTCATGGAGCTCTTTCTCT 60.082 45.833 14.64 14.09 45.43 3.10
3665 10779 1.134175 GAGCTCTTTCTCTCGGTGGAG 59.866 57.143 6.43 0.00 41.89 3.86
3668 10782 1.131504 CTCTTTCTCTCGGTGGAGTCG 59.868 57.143 0.00 0.00 41.26 4.18
3670 10784 0.538977 TTTCTCTCGGTGGAGTCGGT 60.539 55.000 0.00 0.00 41.26 4.69
3671 10785 0.959372 TTCTCTCGGTGGAGTCGGTC 60.959 60.000 0.00 0.00 41.26 4.79
3672 10786 1.377463 CTCTCGGTGGAGTCGGTCT 60.377 63.158 0.00 0.00 41.26 3.85
3673 10787 1.370587 CTCTCGGTGGAGTCGGTCTC 61.371 65.000 0.00 0.00 41.26 3.36
3674 10788 2.745100 TCGGTGGAGTCGGTCTCG 60.745 66.667 0.00 0.00 43.60 4.04
3681 10797 4.406173 AGTCGGTCTCGCTGCACG 62.406 66.667 0.00 2.79 45.62 5.34
3700 10816 2.009051 CGCTGATGTGCTTGATGGTAA 58.991 47.619 0.00 0.00 0.00 2.85
3719 10835 0.178953 ATGTTTGGAACCCAGCTGCT 60.179 50.000 8.66 0.00 33.81 4.24
3745 10868 3.430790 GGTCTCCATTTGGCTAAATTGGC 60.431 47.826 5.14 1.23 34.34 4.52
3759 10882 1.311859 ATTGGCGTATGATGTGCAGG 58.688 50.000 0.00 0.00 0.00 4.85
3792 10915 2.766313 TGCCATCGCATAATGTACCTC 58.234 47.619 0.00 0.00 41.12 3.85
3793 10916 2.368548 TGCCATCGCATAATGTACCTCT 59.631 45.455 0.00 0.00 41.12 3.69
3794 10917 3.576550 TGCCATCGCATAATGTACCTCTA 59.423 43.478 0.00 0.00 41.12 2.43
3808 10931 8.738645 AATGTACCTCTATTGTTTCTCAATCC 57.261 34.615 0.00 0.00 44.50 3.01
3811 10934 8.041323 TGTACCTCTATTGTTTCTCAATCCTTC 58.959 37.037 0.00 0.00 44.50 3.46
3813 10936 5.007136 CCTCTATTGTTTCTCAATCCTTCGC 59.993 44.000 0.00 0.00 44.50 4.70
3815 10938 1.821216 TGTTTCTCAATCCTTCGCCC 58.179 50.000 0.00 0.00 0.00 6.13
3816 10939 1.095600 GTTTCTCAATCCTTCGCCCC 58.904 55.000 0.00 0.00 0.00 5.80
3840 10967 4.567747 GGGGAATGTGACTATGTCAGGTTT 60.568 45.833 0.20 0.00 43.57 3.27
3855 10982 1.154197 GGTTTGTGACCCGTTAGAGC 58.846 55.000 0.00 0.00 43.06 4.09
3862 10989 2.479275 GTGACCCGTTAGAGCAAAGAAC 59.521 50.000 0.00 0.00 0.00 3.01
3864 10991 2.994578 GACCCGTTAGAGCAAAGAACTC 59.005 50.000 0.00 0.00 0.00 3.01
3865 10992 2.367567 ACCCGTTAGAGCAAAGAACTCA 59.632 45.455 0.00 0.00 36.58 3.41
3869 10996 2.370281 TAGAGCAAAGAACTCAGGCG 57.630 50.000 0.00 0.00 36.58 5.52
3870 10997 0.321122 AGAGCAAAGAACTCAGGCGG 60.321 55.000 0.00 0.00 36.58 6.13
3891 11018 1.070445 CTCGCAGGAGCATAAGGGG 59.930 63.158 0.00 0.00 42.27 4.79
3899 11026 0.107643 GAGCATAAGGGGAGGTCTGC 59.892 60.000 0.00 0.00 0.00 4.26
3908 11036 1.133136 GGGGAGGTCTGCACTATCCTA 60.133 57.143 0.00 0.00 32.09 2.94
3927 11055 4.225942 TCCTAAAATGCTGTGAGATCTGGT 59.774 41.667 0.00 0.00 0.00 4.00
3947 11075 4.184629 GGTGTGAGTGTAACATGAGGATC 58.815 47.826 0.00 0.00 41.43 3.36
3956 11084 7.177878 AGTGTAACATGAGGATCTTGGAATTT 58.822 34.615 0.00 0.00 43.84 1.82
3972 11100 5.579047 TGGAATTTAAAAGCCTCCTGATCA 58.421 37.500 10.08 0.00 0.00 2.92
3987 11115 2.617308 CTGATCAACAGGTGGATGATGC 59.383 50.000 0.00 0.00 42.39 3.91
3994 11122 5.357878 TCAACAGGTGGATGATGCTAATTTC 59.642 40.000 0.00 0.00 0.00 2.17
3995 11123 4.858850 ACAGGTGGATGATGCTAATTTCA 58.141 39.130 0.00 0.00 0.00 2.69
4006 11140 4.032960 TGCTAATTTCAGAGGAGGCAAA 57.967 40.909 0.00 0.00 0.00 3.68
4008 11142 5.018809 TGCTAATTTCAGAGGAGGCAAATT 58.981 37.500 0.00 0.00 33.89 1.82
4039 11173 5.962031 TCCTAGCTGGAGTAAAATTCTACCA 59.038 40.000 0.00 0.00 40.56 3.25
4041 11175 7.127339 TCCTAGCTGGAGTAAAATTCTACCAAT 59.873 37.037 0.00 0.00 40.56 3.16
4045 11180 8.107095 AGCTGGAGTAAAATTCTACCAATGTAA 58.893 33.333 0.00 0.00 0.00 2.41
4053 11188 4.853468 TTCTACCAATGTAATCAGGGCA 57.147 40.909 0.00 0.00 0.00 5.36
4069 11204 1.172812 GGCACCAACACCACCTCTTC 61.173 60.000 0.00 0.00 0.00 2.87
4074 11209 1.140852 CCAACACCACCTCTTCTGACA 59.859 52.381 0.00 0.00 0.00 3.58
4124 11259 6.530019 TGTAGAGAACTTGCAGATGATACA 57.470 37.500 0.00 0.00 0.00 2.29
4126 11261 6.982724 TGTAGAGAACTTGCAGATGATACATG 59.017 38.462 0.00 0.00 0.00 3.21
4149 11284 5.652014 TGCTGGTTTATATGGAACTTCTTGG 59.348 40.000 4.46 0.00 0.00 3.61
4154 11289 6.262496 GGTTTATATGGAACTTCTTGGCCTAC 59.738 42.308 3.32 0.00 0.00 3.18
4162 11306 4.143986 ACTTCTTGGCCTACAGATTAGC 57.856 45.455 3.32 0.00 0.00 3.09
4186 11330 5.471116 CAGGCAATATAAGCTCTGCAATGTA 59.529 40.000 0.00 0.00 36.50 2.29
4196 11340 7.693969 AAGCTCTGCAATGTAGAAAGTAAAT 57.306 32.000 2.17 0.00 0.00 1.40
4226 11378 0.248843 GAGAGAAGTGGAGGCAGGTG 59.751 60.000 0.00 0.00 0.00 4.00
4228 11380 0.321122 GAGAAGTGGAGGCAGGTGTG 60.321 60.000 0.00 0.00 0.00 3.82
4269 11424 0.179043 TTTGTCTGGCGCTTGTACCA 60.179 50.000 7.64 0.00 0.00 3.25
4282 11437 5.460748 GCGCTTGTACCACTTTTAAAATGTT 59.539 36.000 0.00 0.00 0.00 2.71
4323 11478 5.820423 TGACGATATTTTGGGGTGTTGATAG 59.180 40.000 0.00 0.00 0.00 2.08
4326 11481 7.060421 ACGATATTTTGGGGTGTTGATAGATT 58.940 34.615 0.00 0.00 0.00 2.40
4329 11484 6.715347 ATTTTGGGGTGTTGATAGATTAGC 57.285 37.500 0.00 0.00 0.00 3.09
4333 11488 3.322828 GGGGTGTTGATAGATTAGCGGTA 59.677 47.826 0.00 0.00 0.00 4.02
4366 11527 1.522668 TTGACCAAGCAGGATGAACG 58.477 50.000 1.83 0.00 39.69 3.95
4367 11528 0.396435 TGACCAAGCAGGATGAACGT 59.604 50.000 1.83 0.00 39.69 3.99
4368 11529 1.202758 TGACCAAGCAGGATGAACGTT 60.203 47.619 0.00 0.00 39.69 3.99
4369 11530 2.037902 TGACCAAGCAGGATGAACGTTA 59.962 45.455 0.00 0.00 39.69 3.18
4370 11531 3.071479 GACCAAGCAGGATGAACGTTAA 58.929 45.455 0.00 0.00 39.69 2.01
4371 11532 2.812011 ACCAAGCAGGATGAACGTTAAC 59.188 45.455 0.00 0.00 39.69 2.01
4372 11533 3.074412 CCAAGCAGGATGAACGTTAACT 58.926 45.455 0.00 0.00 39.69 2.24
4373 11534 4.250464 CCAAGCAGGATGAACGTTAACTA 58.750 43.478 0.00 0.00 39.69 2.24
4374 11535 4.693566 CCAAGCAGGATGAACGTTAACTAA 59.306 41.667 0.00 0.00 39.69 2.24
4375 11536 5.163854 CCAAGCAGGATGAACGTTAACTAAG 60.164 44.000 0.00 0.00 39.69 2.18
4376 11537 4.504858 AGCAGGATGAACGTTAACTAAGG 58.495 43.478 0.00 0.00 39.69 2.69
4377 11538 3.063588 GCAGGATGAACGTTAACTAAGGC 59.936 47.826 0.00 0.00 39.69 4.35
4378 11539 4.250464 CAGGATGAACGTTAACTAAGGCA 58.750 43.478 0.00 0.00 39.69 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.582005 GCCGTCAGATTTGCCGTATC 59.418 55.000 0.00 0.00 0.00 2.24
1 2 0.178068 AGCCGTCAGATTTGCCGTAT 59.822 50.000 0.00 0.00 0.00 3.06
3 4 1.741770 GAGCCGTCAGATTTGCCGT 60.742 57.895 0.00 0.00 0.00 5.68
4 5 2.802667 CGAGCCGTCAGATTTGCCG 61.803 63.158 0.00 0.00 0.00 5.69
5 6 1.741770 ACGAGCCGTCAGATTTGCC 60.742 57.895 0.00 0.00 33.69 4.52
6 7 1.014044 TCACGAGCCGTCAGATTTGC 61.014 55.000 0.00 0.00 38.32 3.68
7 8 1.590238 GATCACGAGCCGTCAGATTTG 59.410 52.381 0.00 0.00 38.32 2.32
8 9 1.478510 AGATCACGAGCCGTCAGATTT 59.521 47.619 0.00 0.00 38.32 2.17
9 10 1.107114 AGATCACGAGCCGTCAGATT 58.893 50.000 0.00 0.00 38.32 2.40
10 11 0.383590 CAGATCACGAGCCGTCAGAT 59.616 55.000 0.00 0.00 38.32 2.90
11 12 1.657751 CCAGATCACGAGCCGTCAGA 61.658 60.000 0.00 0.00 38.32 3.27
12 13 1.226802 CCAGATCACGAGCCGTCAG 60.227 63.158 0.00 0.00 38.32 3.51
13 14 2.885113 CCAGATCACGAGCCGTCA 59.115 61.111 0.00 0.00 38.32 4.35
14 15 2.564553 AAGCCAGATCACGAGCCGTC 62.565 60.000 0.00 0.00 38.32 4.79
15 16 1.320344 TAAGCCAGATCACGAGCCGT 61.320 55.000 0.00 0.00 42.36 5.68
16 17 0.032678 ATAAGCCAGATCACGAGCCG 59.967 55.000 0.00 0.00 0.00 5.52
17 18 1.069204 TCATAAGCCAGATCACGAGCC 59.931 52.381 0.00 0.00 0.00 4.70
18 19 2.515926 TCATAAGCCAGATCACGAGC 57.484 50.000 0.00 0.00 0.00 5.03
19 20 5.985530 TGTTAATCATAAGCCAGATCACGAG 59.014 40.000 0.00 0.00 0.00 4.18
20 21 5.912892 TGTTAATCATAAGCCAGATCACGA 58.087 37.500 0.00 0.00 0.00 4.35
21 22 6.791887 ATGTTAATCATAAGCCAGATCACG 57.208 37.500 0.00 0.00 34.67 4.35
22 23 7.934457 ACAATGTTAATCATAAGCCAGATCAC 58.066 34.615 0.00 0.00 35.48 3.06
23 24 8.407832 CAACAATGTTAATCATAAGCCAGATCA 58.592 33.333 0.00 0.00 35.48 2.92
24 25 7.864379 CCAACAATGTTAATCATAAGCCAGATC 59.136 37.037 0.00 0.00 35.48 2.75
25 26 7.560991 TCCAACAATGTTAATCATAAGCCAGAT 59.439 33.333 0.00 0.00 35.48 2.90
26 27 6.889177 TCCAACAATGTTAATCATAAGCCAGA 59.111 34.615 0.00 0.00 35.48 3.86
27 28 7.099266 TCCAACAATGTTAATCATAAGCCAG 57.901 36.000 0.00 0.00 35.48 4.85
28 29 7.039434 TGTTCCAACAATGTTAATCATAAGCCA 60.039 33.333 0.00 0.00 35.67 4.75
29 30 7.319646 TGTTCCAACAATGTTAATCATAAGCC 58.680 34.615 0.00 0.00 35.67 4.35
30 31 8.931385 ATGTTCCAACAATGTTAATCATAAGC 57.069 30.769 0.00 0.00 43.03 3.09
40 41 9.034800 AGTTCCAATATATGTTCCAACAATGTT 57.965 29.630 0.00 0.00 43.03 2.71
41 42 8.593945 AGTTCCAATATATGTTCCAACAATGT 57.406 30.769 0.00 0.00 43.03 2.71
293 294 8.819015 TCATCACATTTTGAAACAATCTTTGTG 58.181 29.630 0.00 0.00 39.23 3.33
356 358 8.682128 TCGTGCCATTAAAAAGAAATTCATAC 57.318 30.769 0.00 0.00 0.00 2.39
358 360 7.655328 TGTTCGTGCCATTAAAAAGAAATTCAT 59.345 29.630 0.00 0.00 0.00 2.57
363 365 6.758886 ACAATGTTCGTGCCATTAAAAAGAAA 59.241 30.769 0.00 0.00 31.52 2.52
498 503 6.528537 AGCATGCATTGAAAAGGTGTATAA 57.471 33.333 21.98 0.00 0.00 0.98
500 505 5.410355 AAGCATGCATTGAAAAGGTGTAT 57.590 34.783 21.98 0.00 0.00 2.29
641 647 4.855340 TCCTCCAGTTGTTTCTTCACTTT 58.145 39.130 0.00 0.00 0.00 2.66
643 649 4.503714 TTCCTCCAGTTGTTTCTTCACT 57.496 40.909 0.00 0.00 0.00 3.41
688 1851 3.851128 GGGAGACGCTACTGGGCC 61.851 72.222 0.00 0.00 0.00 5.80
698 1861 2.046892 CCAAGCCACAGGGAGACG 60.047 66.667 0.00 0.00 35.59 4.18
725 1888 2.005960 GACCGTCAGTATCAGCGCCT 62.006 60.000 2.29 0.00 0.00 5.52
786 1978 2.440247 GAAGGGGAATGGTGGCCG 60.440 66.667 0.00 0.00 0.00 6.13
787 1979 2.440247 CGAAGGGGAATGGTGGCC 60.440 66.667 0.00 0.00 0.00 5.36
789 1981 2.440247 GGCGAAGGGGAATGGTGG 60.440 66.667 0.00 0.00 0.00 4.61
790 1982 2.824041 CGGCGAAGGGGAATGGTG 60.824 66.667 0.00 0.00 0.00 4.17
791 1983 4.796495 GCGGCGAAGGGGAATGGT 62.796 66.667 12.98 0.00 0.00 3.55
807 1999 1.068921 GATCTGGAGGAAGAGCGGC 59.931 63.158 0.00 0.00 0.00 6.53
822 2014 0.831307 GGACACTGGGTAGGTGGATC 59.169 60.000 0.00 0.00 38.83 3.36
847 2039 3.077556 AAGGAGATGCGGAGGCGT 61.078 61.111 0.00 0.00 44.10 5.68
858 2050 1.257743 CGTGGTGGAAGAGAAGGAGA 58.742 55.000 0.00 0.00 0.00 3.71
890 2090 3.119096 GGAGTTGCGGAGGCGAAC 61.119 66.667 0.00 0.00 44.10 3.95
1130 8184 1.021390 GGCGGCGAGGAATATCCATG 61.021 60.000 12.98 0.00 39.61 3.66
1135 8189 1.071471 CAAGGGCGGCGAGGAATAT 59.929 57.895 12.98 0.00 0.00 1.28
1136 8190 2.504032 CAAGGGCGGCGAGGAATA 59.496 61.111 12.98 0.00 0.00 1.75
1266 8326 3.641436 AGTTCATCAGGATGCCGTATGTA 59.359 43.478 4.39 0.00 38.65 2.29
1269 8329 2.808202 GCAGTTCATCAGGATGCCGTAT 60.808 50.000 4.39 0.00 38.65 3.06
1298 8358 1.174078 TAGGTCTGGACGACGCACAA 61.174 55.000 0.00 0.00 43.79 3.33
1353 8413 4.084507 CGACGATCTCATTTGTTTTGAGC 58.915 43.478 0.00 0.00 40.35 4.26
1384 8444 0.252479 CAGCAGAGGCACTTGAGGAT 59.748 55.000 0.00 0.00 41.55 3.24
1435 8496 2.158957 GGTCGGACATCCTATGAAGCAA 60.159 50.000 10.76 0.00 0.00 3.91
1475 8541 8.638873 TCTTTAGAACTCTGTTGTATGAGAACA 58.361 33.333 0.00 0.00 34.65 3.18
1490 8556 5.986135 TCTTCACACAAGCTCTTTAGAACTC 59.014 40.000 0.00 0.00 0.00 3.01
1561 8633 0.035176 GAGCAGCCATCTCCATCTCC 59.965 60.000 0.00 0.00 0.00 3.71
1562 8634 3.610637 GAGCAGCCATCTCCATCTC 57.389 57.895 0.00 0.00 0.00 2.75
1681 8759 2.224281 ACGTCACCACATCAGACACAAT 60.224 45.455 0.00 0.00 32.68 2.71
1961 9041 5.336690 GCCATGGAATAAAGAAGTTCTGCAA 60.337 40.000 18.40 0.00 0.00 4.08
2827 9910 4.024809 GCTCACTACTGTTCCACTTTCAAC 60.025 45.833 0.00 0.00 0.00 3.18
3106 10189 1.593196 TTGTCAGCTTCTTCCAACGG 58.407 50.000 0.00 0.00 0.00 4.44
3158 10241 5.362717 TCATTTATAAGACGAGAGCTGGGAA 59.637 40.000 0.00 0.00 0.00 3.97
3213 10296 8.469309 ACATATAATTTGCTGCCTTGACTATT 57.531 30.769 0.00 0.00 0.00 1.73
3391 10474 4.235079 ACCATGCCAAAGCTTATCTACA 57.765 40.909 0.00 0.00 40.80 2.74
3431 10514 5.863965 TGGAAGAGAACACATGTTGACATA 58.136 37.500 1.07 0.00 38.56 2.29
3492 10575 1.301244 AGAGCAGAACACTGTGGCG 60.301 57.895 13.09 0.00 34.51 5.69
3497 10580 2.479275 CACACATCAGAGCAGAACACTG 59.521 50.000 0.00 0.00 38.24 3.66
3498 10581 2.549563 CCACACATCAGAGCAGAACACT 60.550 50.000 0.00 0.00 0.00 3.55
3545 10630 2.094494 AGACAACATGTAGACGGAGCAG 60.094 50.000 0.00 0.00 0.00 4.24
3583 10670 3.276091 CAAACGCGCCACACCAGA 61.276 61.111 5.73 0.00 0.00 3.86
3593 10686 3.116063 TGATTGTCATTAGCAAACGCG 57.884 42.857 3.53 3.53 0.00 6.01
3596 10689 7.409697 ACATCGTATGATTGTCATTAGCAAAC 58.590 34.615 0.00 0.00 38.26 2.93
3607 10700 6.115446 ACAAGATCCAACATCGTATGATTGT 58.885 36.000 0.00 0.00 30.49 2.71
3611 10704 5.116180 GGAACAAGATCCAACATCGTATGA 58.884 41.667 0.00 0.00 39.42 2.15
3612 10705 4.875536 TGGAACAAGATCCAACATCGTATG 59.124 41.667 0.00 0.00 46.36 2.39
3632 10746 2.244486 AGAGCTCCATGAACTCTGGA 57.756 50.000 10.93 0.00 39.29 3.86
3644 10758 0.174617 CCACCGAGAGAAAGAGCTCC 59.825 60.000 10.93 0.00 35.49 4.70
3653 10767 1.376942 GACCGACTCCACCGAGAGA 60.377 63.158 4.39 0.00 38.52 3.10
3657 10771 2.745100 CGAGACCGACTCCACCGA 60.745 66.667 0.00 0.00 42.18 4.69
3681 10797 3.379372 ACATTACCATCAAGCACATCAGC 59.621 43.478 0.00 0.00 0.00 4.26
3700 10816 0.178953 AGCAGCTGGGTTCCAAACAT 60.179 50.000 17.12 0.00 30.80 2.71
3719 10835 4.314522 TTTAGCCAAATGGAGACCATCA 57.685 40.909 2.98 0.00 44.40 3.07
3726 10849 2.166254 ACGCCAATTTAGCCAAATGGAG 59.834 45.455 2.98 4.03 34.53 3.86
3745 10868 1.935873 CTTGGACCTGCACATCATACG 59.064 52.381 0.00 0.00 0.00 3.06
3759 10882 4.251246 TGGCACAACACCTTGGAC 57.749 55.556 0.00 0.00 31.92 4.02
3808 10931 4.109675 ACATTCCCCGGGGCGAAG 62.110 66.667 36.68 24.90 34.68 3.79
3813 10936 0.108585 CATAGTCACATTCCCCGGGG 59.891 60.000 35.80 35.80 0.00 5.73
3815 10938 1.484653 TGACATAGTCACATTCCCCGG 59.515 52.381 0.00 0.00 37.67 5.73
3816 10939 2.483714 CCTGACATAGTCACATTCCCCG 60.484 54.545 0.00 0.00 37.67 5.73
3840 10967 1.689813 TCTTTGCTCTAACGGGTCACA 59.310 47.619 0.00 0.00 0.00 3.58
3847 10974 2.413453 GCCTGAGTTCTTTGCTCTAACG 59.587 50.000 0.00 0.00 34.30 3.18
3855 10982 0.321122 AGCTCCGCCTGAGTTCTTTG 60.321 55.000 0.41 0.00 43.48 2.77
3876 11003 1.348775 ACCTCCCCTTATGCTCCTGC 61.349 60.000 0.00 0.00 40.20 4.85
3886 11013 1.501582 GATAGTGCAGACCTCCCCTT 58.498 55.000 0.00 0.00 0.00 3.95
3887 11014 0.399233 GGATAGTGCAGACCTCCCCT 60.399 60.000 0.00 0.00 0.00 4.79
3891 11018 4.513318 GCATTTTAGGATAGTGCAGACCTC 59.487 45.833 4.55 0.00 35.93 3.85
3899 11026 7.171167 CAGATCTCACAGCATTTTAGGATAGTG 59.829 40.741 0.00 0.00 0.00 2.74
3908 11036 3.504906 CACACCAGATCTCACAGCATTTT 59.495 43.478 0.00 0.00 0.00 1.82
3927 11055 5.482006 CAAGATCCTCATGTTACACTCACA 58.518 41.667 0.00 0.00 0.00 3.58
3947 11075 5.982890 TCAGGAGGCTTTTAAATTCCAAG 57.017 39.130 8.42 0.00 0.00 3.61
3972 11100 5.263599 TGAAATTAGCATCATCCACCTGTT 58.736 37.500 0.00 0.00 0.00 3.16
3979 11107 5.002516 CCTCCTCTGAAATTAGCATCATCC 58.997 45.833 0.00 0.00 0.00 3.51
3987 11115 7.332678 CCAAAAATTTGCCTCCTCTGAAATTAG 59.667 37.037 0.29 0.00 36.86 1.73
3994 11122 2.301009 AGCCAAAAATTTGCCTCCTCTG 59.699 45.455 0.29 0.00 36.86 3.35
3995 11123 2.564504 GAGCCAAAAATTTGCCTCCTCT 59.435 45.455 5.75 0.00 36.84 3.69
4015 11149 5.962031 TGGTAGAATTTTACTCCAGCTAGGA 59.038 40.000 6.15 5.03 46.75 2.94
4027 11161 7.836685 TGCCCTGATTACATTGGTAGAATTTTA 59.163 33.333 0.00 0.00 0.00 1.52
4028 11162 6.667414 TGCCCTGATTACATTGGTAGAATTTT 59.333 34.615 0.00 0.00 0.00 1.82
4031 11165 5.133221 GTGCCCTGATTACATTGGTAGAAT 58.867 41.667 0.00 0.00 0.00 2.40
4039 11173 2.825532 GTGTTGGTGCCCTGATTACATT 59.174 45.455 0.00 0.00 0.00 2.71
4041 11175 1.546773 GGTGTTGGTGCCCTGATTACA 60.547 52.381 0.00 0.00 0.00 2.41
4045 11180 1.228552 GTGGTGTTGGTGCCCTGAT 60.229 57.895 0.00 0.00 0.00 2.90
4053 11188 1.141053 GTCAGAAGAGGTGGTGTTGGT 59.859 52.381 0.00 0.00 0.00 3.67
4069 11204 6.016024 TGGTTTGATTCATTTTCCTCTGTCAG 60.016 38.462 0.00 0.00 0.00 3.51
4074 11209 7.236225 AGGAAATGGTTTGATTCATTTTCCTCT 59.764 33.333 15.25 0.23 41.80 3.69
4082 11217 7.890127 TCTCTACAAGGAAATGGTTTGATTCAT 59.110 33.333 0.00 0.00 0.00 2.57
4124 11259 6.322201 CCAAGAAGTTCCATATAAACCAGCAT 59.678 38.462 0.00 0.00 0.00 3.79
4126 11261 5.450550 GCCAAGAAGTTCCATATAAACCAGC 60.451 44.000 0.00 0.00 0.00 4.85
4154 11289 6.092396 CAGAGCTTATATTGCCTGCTAATCTG 59.908 42.308 0.00 0.00 33.83 2.90
4162 11306 4.277672 ACATTGCAGAGCTTATATTGCCTG 59.722 41.667 0.00 11.09 35.75 4.85
4186 11330 7.069578 TCTCTCCCTACGCATTATTTACTTTCT 59.930 37.037 0.00 0.00 0.00 2.52
4196 11340 2.693591 CCACTTCTCTCCCTACGCATTA 59.306 50.000 0.00 0.00 0.00 1.90
4226 11378 2.643551 ACCTGGTTGCATATACAGCAC 58.356 47.619 0.00 0.00 42.54 4.40
4228 11380 6.391227 AATTTACCTGGTTGCATATACAGC 57.609 37.500 3.84 0.00 0.00 4.40
4229 11381 7.771183 ACAAATTTACCTGGTTGCATATACAG 58.229 34.615 3.84 0.00 0.00 2.74
4235 11387 4.021192 CCAGACAAATTTACCTGGTTGCAT 60.021 41.667 21.22 0.00 40.84 3.96
4295 11450 2.752354 CACCCCAAAATATCGTCAAGCA 59.248 45.455 0.00 0.00 0.00 3.91
4299 11454 4.022413 TCAACACCCCAAAATATCGTCA 57.978 40.909 0.00 0.00 0.00 4.35
4351 11507 3.074412 AGTTAACGTTCATCCTGCTTGG 58.926 45.455 2.82 0.00 37.10 3.61


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

AutoCloner maintained by Alex Coulton.