Multiple sequence alignment - TraesCS4B01G122000

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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 TraesCS4B01G122000 chr4B 100.000 4057 0 0 3736 7792 144753056 144757112 0.000000e+00 7492.0
1 TraesCS4B01G122000 chr4B 100.000 3571 0 0 1 3571 144749321 144752891 0.000000e+00 6595.0
2 TraesCS4B01G122000 chr4B 99.362 784 4 1 7010 7792 181527595 181526812 0.000000e+00 1419.0
3 TraesCS4B01G122000 chr4D 94.537 3240 121 15 3787 7010 101029628 101032827 0.000000e+00 4951.0
4 TraesCS4B01G122000 chr4D 94.299 3175 102 23 441 3569 101025933 101029074 0.000000e+00 4787.0
5 TraesCS4B01G122000 chr4D 98.633 439 6 0 1 439 101025462 101025900 0.000000e+00 778.0
6 TraesCS4B01G122000 chr4D 88.024 334 33 5 1440 1768 231979239 231978908 9.480000e-104 388.0
7 TraesCS4B01G122000 chr4A 94.531 2706 99 21 441 3115 474739591 474736904 0.000000e+00 4132.0
8 TraesCS4B01G122000 chr4A 93.455 1375 58 13 3787 5158 474735349 474734004 0.000000e+00 2012.0
9 TraesCS4B01G122000 chr4A 94.957 1170 42 10 5143 6298 474728537 474727371 0.000000e+00 1818.0
10 TraesCS4B01G122000 chr4A 95.257 759 21 7 6254 7010 474727372 474726627 0.000000e+00 1188.0
11 TraesCS4B01G122000 chr4A 94.080 473 17 5 3107 3571 474736052 474735583 0.000000e+00 708.0
12 TraesCS4B01G122000 chr4A 98.447 322 4 1 1 322 474740479 474740159 4.080000e-157 566.0
13 TraesCS4B01G122000 chr4A 96.774 93 0 1 347 439 474739713 474739624 1.350000e-32 152.0
14 TraesCS4B01G122000 chr4A 96.226 53 2 0 3736 3788 474735559 474735507 3.870000e-13 87.9
15 TraesCS4B01G122000 chr2A 99.365 787 4 1 7007 7792 78216874 78217660 0.000000e+00 1424.0
16 TraesCS4B01G122000 chr2A 99.238 787 5 1 7007 7792 194167765 194166979 0.000000e+00 1419.0
17 TraesCS4B01G122000 chr2A 93.289 149 9 1 1 148 13020640 13020788 1.320000e-52 219.0
18 TraesCS4B01G122000 chr7B 99.364 786 4 1 7008 7792 603980686 603979901 0.000000e+00 1423.0
19 TraesCS4B01G122000 chr7B 99.364 786 4 1 7008 7792 603983035 603982250 0.000000e+00 1423.0
20 TraesCS4B01G122000 chr7B 92.568 148 11 0 1 148 446166357 446166504 6.120000e-51 213.0
21 TraesCS4B01G122000 chr5A 99.363 785 4 1 7009 7792 219313276 219314060 0.000000e+00 1421.0
22 TraesCS4B01G122000 chr5A 88.427 337 31 6 1440 1770 74706589 74706923 4.380000e-107 399.0
23 TraesCS4B01G122000 chr5A 94.483 145 8 0 4 148 141878702 141878846 2.830000e-54 224.0
24 TraesCS4B01G122000 chr5A 93.243 148 10 0 1 148 438144783 438144636 1.320000e-52 219.0
25 TraesCS4B01G122000 chr7A 99.237 786 6 0 7007 7792 287520457 287519672 0.000000e+00 1419.0
26 TraesCS4B01G122000 chr2B 98.742 795 9 1 6999 7792 642462158 642462952 0.000000e+00 1411.0
27 TraesCS4B01G122000 chr2B 98.742 795 8 2 6999 7792 767326153 767326946 0.000000e+00 1411.0
28 TraesCS4B01G122000 chrUn 90.390 333 25 5 1440 1767 108422805 108422475 1.550000e-116 431.0
29 TraesCS4B01G122000 chr3D 90.390 333 25 5 1440 1767 251689732 251690062 1.550000e-116 431.0
30 TraesCS4B01G122000 chr5D 88.955 335 29 6 1440 1768 156586163 156586495 2.620000e-109 407.0
31 TraesCS4B01G122000 chr5D 94.483 145 8 0 4 148 126570096 126570240 2.830000e-54 224.0
32 TraesCS4B01G122000 chr3A 88.462 338 33 4 1434 1766 691062142 691062478 3.390000e-108 403.0
33 TraesCS4B01G122000 chr3A 88.889 333 30 5 1440 1767 737582350 737582680 3.390000e-108 403.0
34 TraesCS4B01G122000 chr1D 93.919 148 9 0 1 148 148657602 148657455 2.830000e-54 224.0
35 TraesCS4B01G122000 chr6B 93.151 146 10 0 3 148 432489748 432489603 1.700000e-51 215.0


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 TraesCS4B01G122000 chr4B 144749321 144757112 7791 False 7043.500000 7492 100.0000 1 7792 2 chr4B.!!$F1 7791
1 TraesCS4B01G122000 chr4B 181526812 181527595 783 True 1419.000000 1419 99.3620 7010 7792 1 chr4B.!!$R1 782
2 TraesCS4B01G122000 chr4D 101025462 101032827 7365 False 3505.333333 4951 95.8230 1 7010 3 chr4D.!!$F1 7009
3 TraesCS4B01G122000 chr4A 474726627 474728537 1910 True 1503.000000 1818 95.1070 5143 7010 2 chr4A.!!$R1 1867
4 TraesCS4B01G122000 chr4A 474734004 474740479 6475 True 1276.316667 4132 95.5855 1 5158 6 chr4A.!!$R2 5157
5 TraesCS4B01G122000 chr2A 78216874 78217660 786 False 1424.000000 1424 99.3650 7007 7792 1 chr2A.!!$F2 785
6 TraesCS4B01G122000 chr2A 194166979 194167765 786 True 1419.000000 1419 99.2380 7007 7792 1 chr2A.!!$R1 785
7 TraesCS4B01G122000 chr7B 603979901 603983035 3134 True 1423.000000 1423 99.3640 7008 7792 2 chr7B.!!$R1 784
8 TraesCS4B01G122000 chr5A 219313276 219314060 784 False 1421.000000 1421 99.3630 7009 7792 1 chr5A.!!$F3 783
9 TraesCS4B01G122000 chr7A 287519672 287520457 785 True 1419.000000 1419 99.2370 7007 7792 1 chr7A.!!$R1 785
10 TraesCS4B01G122000 chr2B 642462158 642462952 794 False 1411.000000 1411 98.7420 6999 7792 1 chr2B.!!$F1 793
11 TraesCS4B01G122000 chr2B 767326153 767326946 793 False 1411.000000 1411 98.7420 6999 7792 1 chr2B.!!$F2 793

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
773 1237 0.966920 ATTGTCGAACGTGGAGGTCT 59.033 50.000 0.00 0.0 33.40 3.85 F
1561 2052 0.035056 GGTGGCAGCATAACCTCTGT 60.035 55.000 12.58 0.0 33.09 3.41 F
2482 2987 0.620556 CAGAACACCCCCTACAGCAT 59.379 55.000 0.00 0.0 0.00 3.79 F
2483 2988 1.837439 CAGAACACCCCCTACAGCATA 59.163 52.381 0.00 0.0 0.00 3.14 F
3522 4902 2.052468 ACGTCCTGGGTAAGAAGGTTT 58.948 47.619 0.00 0.0 34.94 3.27 F
3904 5622 2.224475 TGGCAAATGTTCAATGGTTGGG 60.224 45.455 0.00 0.0 0.00 4.12 F
4865 6587 0.960364 TGTCATTTGCTTCCCCTCGC 60.960 55.000 0.00 0.0 0.00 5.03 F
5958 7697 1.113517 TCCCTATGTAGCGCCTCACC 61.114 60.000 2.29 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 2392 1.285078 GTTCTGGAGGGCCCTACAAAT 59.715 52.381 36.74 8.76 36.31 2.32 R
2697 3203 3.441572 ACAAAACTAGCAGCCTAGCAATG 59.558 43.478 0.00 0.00 44.00 2.82 R
4316 6034 2.041620 AGGGAACATTGCTTCTGCCTTA 59.958 45.455 0.00 0.00 38.71 2.69 R
4342 6060 8.931568 GGACCTAACTAACTAATTTATCCTCCA 58.068 37.037 0.00 0.00 0.00 3.86 R
4856 6578 0.764890 CCAGGATTATGCGAGGGGAA 59.235 55.000 0.00 0.00 0.00 3.97 R
5098 6823 1.081092 TCAGCTAGAAGGCCCCACT 59.919 57.895 0.00 0.00 0.00 4.00 R
5973 7712 1.279271 CGACCCCAACTCTTTCTGGAT 59.721 52.381 0.00 0.00 34.35 3.41 R
6929 8714 0.459237 CCAGAGCGCAAGAGTACTGG 60.459 60.000 11.47 12.14 43.02 4.00 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
322 323 2.674380 CCTTGCCCCAGCTCACAC 60.674 66.667 0.00 0.00 40.80 3.82
439 861 4.440663 CGAGATGACAAACTCAGCTATCCA 60.441 45.833 11.63 0.00 46.02 3.41
690 1151 1.762460 CCACGGACAGCCCCTATCT 60.762 63.158 0.00 0.00 0.00 1.98
773 1237 0.966920 ATTGTCGAACGTGGAGGTCT 59.033 50.000 0.00 0.00 33.40 3.85
817 1291 2.126618 CGTCGACGGCAGCAGTTA 60.127 61.111 29.70 0.00 35.37 2.24
916 1395 2.032030 CCTGACCGCTTAAACACACTTG 60.032 50.000 0.00 0.00 0.00 3.16
1048 1533 0.616679 CCGGTACTTCCCCTCTTCCA 60.617 60.000 0.00 0.00 0.00 3.53
1107 1592 1.948104 CTGTGGTCACGTTTTCTCCA 58.052 50.000 0.00 0.00 0.00 3.86
1209 1694 0.105039 GCGTAGACTTCCCCATCCTG 59.895 60.000 0.00 0.00 0.00 3.86
1330 1820 5.064707 ACAGTCGCGCATCTAATTATGTTTT 59.935 36.000 8.75 0.00 0.00 2.43
1375 1865 2.278596 GATTGCGGCGCGTCTAGA 60.279 61.111 28.09 5.10 0.00 2.43
1423 1913 2.048503 GCTTTTGCTGCTGCCTGG 60.049 61.111 13.47 2.28 43.35 4.45
1481 1971 0.316204 CCGTACGGAGTTCCAACTGT 59.684 55.000 30.64 0.00 37.78 3.55
1492 1983 2.136298 TCCAACTGTTGTTCAAGGCA 57.864 45.000 18.38 0.00 33.52 4.75
1530 2021 1.632018 CGAGGGGCCATGGAGGTTTA 61.632 60.000 18.40 0.00 40.61 2.01
1559 2050 1.207488 TGGGTGGCAGCATAACCTCT 61.207 55.000 19.48 0.00 34.24 3.69
1560 2051 0.749454 GGGTGGCAGCATAACCTCTG 60.749 60.000 19.48 0.00 34.24 3.35
1561 2052 0.035056 GGTGGCAGCATAACCTCTGT 60.035 55.000 12.58 0.00 33.09 3.41
1562 2053 1.209504 GGTGGCAGCATAACCTCTGTA 59.790 52.381 12.58 0.00 33.09 2.74
1563 2054 2.158755 GGTGGCAGCATAACCTCTGTAT 60.159 50.000 12.58 0.00 33.09 2.29
1573 2069 1.290324 CCTCTGTATCGGCCCATCG 59.710 63.158 0.00 0.00 0.00 3.84
1589 2085 1.609072 CATCGCCTCCTTCGACATAGA 59.391 52.381 0.00 0.00 38.88 1.98
1634 2130 2.779755 ACTGGTGCCGATATGTCAAA 57.220 45.000 0.00 0.00 0.00 2.69
1694 2190 1.901159 CATCCTAGCTATGCAGAGGCT 59.099 52.381 10.92 12.62 41.91 4.58
1730 2230 5.993055 TCATGATTTCCTCTTGATGCTACA 58.007 37.500 0.00 0.00 34.17 2.74
1804 2307 3.660970 TGGGCTTTTAGCATATCACCA 57.339 42.857 0.67 0.00 44.75 4.17
1871 2374 4.580580 ACTCAGCTTTCTTTTGATTCGGTT 59.419 37.500 0.00 0.00 0.00 4.44
1884 2387 4.960329 TGATTCGGTTATGCGTGTAAAAC 58.040 39.130 0.00 0.00 0.00 2.43
1889 2392 3.125487 CGGTTATGCGTGTAAAACATCCA 59.875 43.478 0.00 0.00 0.00 3.41
1965 2470 7.579726 TGCAAAATTATTGTTGGTTTACATGC 58.420 30.769 0.00 0.00 0.00 4.06
2009 2514 6.569179 ATGTCGCAAACTTTAACCTTACAT 57.431 33.333 0.00 0.00 0.00 2.29
2037 2542 8.341892 TGTTATGTATACACTTTTGGCATTCA 57.658 30.769 7.96 0.00 0.00 2.57
2121 2626 8.626526 ACAAATTAGTTTACTTCGACAATGGTT 58.373 29.630 0.00 0.00 0.00 3.67
2257 2762 6.071616 TCCTTTATGTCTTAATTGGGTGTTGC 60.072 38.462 0.00 0.00 0.00 4.17
2330 2835 5.304614 TCTCTAAGTGTGAGTAAAGCAAGGT 59.695 40.000 0.00 0.00 33.59 3.50
2482 2987 0.620556 CAGAACACCCCCTACAGCAT 59.379 55.000 0.00 0.00 0.00 3.79
2483 2988 1.837439 CAGAACACCCCCTACAGCATA 59.163 52.381 0.00 0.00 0.00 3.14
2551 3057 5.310409 TCTTCTGTGATTTCCCCCATATC 57.690 43.478 0.00 0.00 0.00 1.63
2596 3102 8.491134 AGGTATGGTAGTGCTCACATAATTTTA 58.509 33.333 2.63 0.00 0.00 1.52
2627 3133 4.501571 GGACAATGATGCTATAGGTGTCGT 60.502 45.833 1.04 0.00 35.79 4.34
2634 3140 4.260139 TGCTATAGGTGTCGTGTTTTGA 57.740 40.909 1.04 0.00 0.00 2.69
2697 3203 6.909357 GCAGTTGATTTGCTTCATAGTATGTC 59.091 38.462 9.94 0.00 38.51 3.06
2784 3290 5.004821 GCGAGCTATGTGCATATGTATACAC 59.995 44.000 7.96 4.54 45.94 2.90
3040 3547 3.041211 TGCTCTACCTGCCAGTCATAAT 58.959 45.455 0.00 0.00 0.00 1.28
3095 3602 9.850628 ATCATGAATATTGTTCTTCAAACACTG 57.149 29.630 0.00 0.00 39.62 3.66
3096 3603 8.849168 TCATGAATATTGTTCTTCAAACACTGT 58.151 29.630 0.00 0.00 39.62 3.55
3097 3604 9.467258 CATGAATATTGTTCTTCAAACACTGTT 57.533 29.630 0.00 0.00 39.62 3.16
3104 3611 4.963276 TCTTCAAACACTGTTTGACCTG 57.037 40.909 29.07 22.31 38.05 4.00
3155 4529 9.777297 ATTATTTTCCTCATCTCTTTCTAGCTC 57.223 33.333 0.00 0.00 0.00 4.09
3161 4535 7.721402 TCCTCATCTCTTTCTAGCTCATTAAC 58.279 38.462 0.00 0.00 0.00 2.01
3260 4634 8.586570 TGTCACCAAACATTGATTTTTATCAC 57.413 30.769 0.00 0.00 0.00 3.06
3522 4902 2.052468 ACGTCCTGGGTAAGAAGGTTT 58.948 47.619 0.00 0.00 34.94 3.27
3523 4903 2.440627 ACGTCCTGGGTAAGAAGGTTTT 59.559 45.455 0.00 0.00 34.94 2.43
3524 4904 3.117776 ACGTCCTGGGTAAGAAGGTTTTT 60.118 43.478 0.00 0.00 34.94 1.94
3864 5582 5.679792 CACGATGACGAGTTACGAATTATGA 59.320 40.000 0.00 0.00 45.77 2.15
3865 5583 5.680229 ACGATGACGAGTTACGAATTATGAC 59.320 40.000 0.00 0.00 45.77 3.06
3866 5584 5.679792 CGATGACGAGTTACGAATTATGACA 59.320 40.000 0.00 0.00 45.77 3.58
3904 5622 2.224475 TGGCAAATGTTCAATGGTTGGG 60.224 45.455 0.00 0.00 0.00 4.12
3925 5643 6.650120 TGGGTCCTGTCATTCTAACTTTATC 58.350 40.000 0.00 0.00 0.00 1.75
4089 5807 4.263462 TGTCAAAGTGTTCCTCATATGCCT 60.263 41.667 0.00 0.00 0.00 4.75
4157 5875 7.598278 TCGCATAAGGTTTGTGTTATCAATTT 58.402 30.769 0.00 0.00 0.00 1.82
4182 5900 6.409704 TCTGCTAGCAACAAATTCATAGTCT 58.590 36.000 19.86 0.00 0.00 3.24
4184 5902 7.391554 TCTGCTAGCAACAAATTCATAGTCTTT 59.608 33.333 19.86 0.00 0.00 2.52
4285 6003 5.514204 GCATGGAAAATTTGAGATCTTGTCG 59.486 40.000 0.00 0.00 0.00 4.35
4316 6034 6.098552 GGAGCCTTTCTTAGGTAAGATACTGT 59.901 42.308 0.29 0.00 46.61 3.55
4335 6053 2.819608 TGTAAGGCAGAAGCAATGTTCC 59.180 45.455 0.00 0.00 44.61 3.62
4342 6060 3.507622 GCAGAAGCAATGTTCCCTACTTT 59.492 43.478 0.00 0.00 41.58 2.66
4343 6061 4.616835 GCAGAAGCAATGTTCCCTACTTTG 60.617 45.833 0.00 0.00 42.06 2.77
4404 6122 7.334858 ACAGAGCCTTCCTATTTAAGAGAAAG 58.665 38.462 0.00 0.00 0.00 2.62
4527 6245 4.673968 TCTAGGTGAGGAAGCAAGTTCTA 58.326 43.478 0.00 0.00 35.25 2.10
4542 6260 9.822185 AAGCAAGTTCTATTTGTTTTGATCTTT 57.178 25.926 0.00 0.00 0.00 2.52
4579 6297 8.302438 TCATATCTGTCACTGTATGCTATCAAG 58.698 37.037 0.00 0.00 0.00 3.02
4595 6313 7.195646 TGCTATCAAGTTTTGTGAACAAAGAG 58.804 34.615 8.49 2.00 45.34 2.85
4712 6434 6.555812 TCGCAGGTTAGATATGTAGTGTAG 57.444 41.667 0.00 0.00 0.00 2.74
4717 6439 7.364200 CAGGTTAGATATGTAGTGTAGCTGTC 58.636 42.308 0.00 0.00 0.00 3.51
4749 6471 3.576078 AAAGAACACCTCCACATGTGA 57.424 42.857 27.46 12.04 36.35 3.58
4815 6537 4.406003 TCCTAACAAGGTATCAGAAGAGGC 59.594 45.833 0.00 0.00 0.00 4.70
4829 6551 6.653020 TCAGAAGAGGCATACACATGTTATT 58.347 36.000 0.00 0.00 34.40 1.40
4834 6556 4.718961 AGGCATACACATGTTATTCCTCC 58.281 43.478 0.00 0.00 34.40 4.30
4844 6566 5.994054 ACATGTTATTCCTCCTGATTGATCG 59.006 40.000 0.00 0.00 0.00 3.69
4856 6578 4.275196 CCTGATTGATCGATGTCATTTGCT 59.725 41.667 0.54 0.00 0.00 3.91
4865 6587 0.960364 TGTCATTTGCTTCCCCTCGC 60.960 55.000 0.00 0.00 0.00 5.03
4868 6590 1.211703 TCATTTGCTTCCCCTCGCATA 59.788 47.619 0.00 0.00 35.85 3.14
4884 6606 2.744202 CGCATAATCCTGGCAACTATCC 59.256 50.000 0.00 0.00 37.61 2.59
4938 6660 2.621338 CGCTGCCTTACTCTTTCATGA 58.379 47.619 0.00 0.00 0.00 3.07
4957 6679 2.280052 GCCGCCTCTGCTCTCATC 60.280 66.667 0.00 0.00 34.43 2.92
5098 6823 3.706373 GGGTCCTCTTCGCTGCCA 61.706 66.667 0.00 0.00 0.00 4.92
5101 6826 1.739562 GTCCTCTTCGCTGCCAGTG 60.740 63.158 0.00 0.00 0.00 3.66
5205 6930 6.587608 GGAACTGATCAATTGCCAACTAAAAG 59.412 38.462 0.00 0.00 0.00 2.27
5352 7078 4.812626 CGGGCGTGTTTATAGGACTAATTT 59.187 41.667 0.00 0.00 0.00 1.82
5462 7188 6.433766 GTTAGCAATGCCATCTCAATCTTAC 58.566 40.000 0.00 0.00 0.00 2.34
5464 7190 3.633525 GCAATGCCATCTCAATCTTACCA 59.366 43.478 0.00 0.00 0.00 3.25
5591 7319 9.750882 GTTTCTACAGTTCCATTATACGTTTTC 57.249 33.333 0.00 0.00 0.00 2.29
5627 7355 7.038659 TCCCTTGACAGTTGTTAAAATTTGTG 58.961 34.615 0.00 0.00 0.00 3.33
5774 7511 2.454772 TGGAGAGGCTATAGGATTGGGA 59.545 50.000 1.04 0.00 0.00 4.37
5958 7697 1.113517 TCCCTATGTAGCGCCTCACC 61.114 60.000 2.29 0.00 0.00 4.02
5973 7712 3.808728 CCTCACCTGTCTTTTTCTGTCA 58.191 45.455 0.00 0.00 0.00 3.58
6041 7780 5.295787 TGTTCCAAATGTTCGTATCTATGGC 59.704 40.000 0.00 0.00 0.00 4.40
6160 7899 4.941263 GGTATGCTGATGTTTCAACCACTA 59.059 41.667 0.00 0.00 31.83 2.74
6189 7929 6.643770 CAGATGCAAATGCTAGTTCTGTTTTT 59.356 34.615 6.97 0.00 42.66 1.94
6302 8087 6.491394 GCATATGCGTTTTTGGTATTACTCA 58.509 36.000 12.82 0.00 0.00 3.41
6440 8225 4.278170 TGTAGATTTTTGGTGAGGCAAGTG 59.722 41.667 0.00 0.00 0.00 3.16
6477 8262 5.104024 AGAGATCTCATTTTCCAGAGGCATT 60.104 40.000 24.39 0.00 32.76 3.56
6544 8329 5.843673 TGTTTGGTCAAATTGCTGTCTTA 57.156 34.783 0.00 0.00 32.36 2.10
6627 8412 3.836949 ACTATTTTGTTTCAGCATGGCG 58.163 40.909 0.00 0.00 36.16 5.69
6713 8498 0.951040 CCCGTGCCAGTCTTCACTTC 60.951 60.000 0.00 0.00 0.00 3.01
6879 8664 2.613977 CCTACCTGCTCAAACTGTCTGG 60.614 54.545 0.00 0.00 0.00 3.86
6928 8713 2.629051 GCACGGGCAAGTTTATCTACT 58.371 47.619 3.77 0.00 40.72 2.57
6929 8714 2.608090 GCACGGGCAAGTTTATCTACTC 59.392 50.000 3.77 0.00 40.72 2.59
6930 8715 3.195661 CACGGGCAAGTTTATCTACTCC 58.804 50.000 0.00 0.00 0.00 3.85
6931 8716 2.835764 ACGGGCAAGTTTATCTACTCCA 59.164 45.455 0.00 0.00 0.00 3.86
6932 8717 3.118738 ACGGGCAAGTTTATCTACTCCAG 60.119 47.826 0.00 0.00 0.00 3.86
6962 8755 3.109619 CGCTCTGGAAGTTTCGAGATAC 58.890 50.000 6.98 3.15 40.48 2.24
7113 11256 2.525629 TCCTTCCGTCTGCCACCA 60.526 61.111 0.00 0.00 0.00 4.17
7152 11295 6.154445 ACTTTGTGCTGCTCTTATTGATTTG 58.846 36.000 0.00 0.00 0.00 2.32
7287 11430 2.686816 GCCCAACGAACATGGACGG 61.687 63.158 15.73 0.08 40.56 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
322 323 0.607489 CAAAGGGAGGAGGCACTGTG 60.607 60.000 2.76 2.76 41.55 3.66
439 861 7.624360 TTATATGAAGCAAATTCTCCGTGTT 57.376 32.000 0.00 0.00 38.83 3.32
1048 1533 0.394565 GGATAGCTGCGGTTCCTGAT 59.605 55.000 0.00 0.00 0.00 2.90
1227 1712 2.180862 CGAGACGAGCCGGAGATGA 61.181 63.158 5.05 0.00 0.00 2.92
1336 1826 9.746711 CAATCAAGAACGATCCGATAATTTATC 57.253 33.333 6.37 6.37 0.00 1.75
1442 1932 4.096682 ACGGTGAAGCATAGACTCTCTTAC 59.903 45.833 0.00 0.00 0.00 2.34
1449 1939 1.404391 CCGTACGGTGAAGCATAGACT 59.596 52.381 26.39 0.00 0.00 3.24
1481 1971 1.937223 CGTACACACTGCCTTGAACAA 59.063 47.619 0.00 0.00 0.00 2.83
1492 1983 1.156736 GCTCCAATTGCGTACACACT 58.843 50.000 0.00 0.00 0.00 3.55
1515 2006 1.704641 GGAATAAACCTCCATGGCCC 58.295 55.000 6.96 0.00 40.22 5.80
1573 2069 3.570550 ACTATGTCTATGTCGAAGGAGGC 59.429 47.826 0.00 0.00 0.00 4.70
1589 2085 4.710375 AGTCAAATAGGACCGTCACTATGT 59.290 41.667 0.00 0.00 38.59 2.29
1694 2190 2.812836 ATCATGATGAGCAACACCCA 57.187 45.000 7.59 0.00 0.00 4.51
1871 2374 6.260870 ACAAATGGATGTTTTACACGCATA 57.739 33.333 0.00 0.00 0.00 3.14
1884 2387 1.479389 GGAGGGCCCTACAAATGGATG 60.479 57.143 30.89 0.00 0.00 3.51
1889 2392 1.285078 GTTCTGGAGGGCCCTACAAAT 59.715 52.381 36.74 8.76 36.31 2.32
1965 2470 8.691727 CGACATAGTAATAACGAAAGAATCCAG 58.308 37.037 0.00 0.00 0.00 3.86
2009 2514 9.988815 AATGCCAAAAGTGTATACATAACAAAA 57.011 25.926 9.18 0.00 0.00 2.44
2121 2626 3.390967 TGAGAGGGTTTCTGTGATGTTGA 59.609 43.478 0.00 0.00 35.87 3.18
2257 2762 7.388437 TGGTACTAGTGGGTATTTTACACTTG 58.612 38.462 5.39 3.22 42.38 3.16
2330 2835 4.446167 CCAGATATTACATCAGGGCCACAA 60.446 45.833 6.18 0.00 0.00 3.33
2404 2909 9.063615 GTAAAAGGGTAATCTTCTGTTTCTCAA 57.936 33.333 0.00 0.00 0.00 3.02
2405 2910 8.437575 AGTAAAAGGGTAATCTTCTGTTTCTCA 58.562 33.333 0.00 0.00 0.00 3.27
2551 3057 3.941483 ACCTCACAAAACAGACAAGTCAG 59.059 43.478 2.72 0.00 0.00 3.51
2608 3114 4.672587 ACACGACACCTATAGCATCATT 57.327 40.909 0.00 0.00 0.00 2.57
2634 3140 7.447594 TGCACACAGTTGATCATCATATATCT 58.552 34.615 6.55 0.00 0.00 1.98
2654 3160 7.500141 TCAACTGCTATATCTTTCTATGCACA 58.500 34.615 0.00 0.00 0.00 4.57
2655 3161 7.953158 TCAACTGCTATATCTTTCTATGCAC 57.047 36.000 0.00 0.00 0.00 4.57
2697 3203 3.441572 ACAAAACTAGCAGCCTAGCAATG 59.558 43.478 0.00 0.00 44.00 2.82
2784 3290 4.456911 ACATGTCAGTAGGAGCAAAACATG 59.543 41.667 10.17 10.17 44.90 3.21
2952 3459 5.503002 TGTTTTAAGTTAGATAGGCCCCAC 58.497 41.667 0.00 0.00 0.00 4.61
3040 3547 9.410556 GCATCAAAGTAGAAGCATAAAAAGAAA 57.589 29.630 0.00 0.00 32.81 2.52
3094 3601 7.812191 GCATAAATACATGAAACAGGTCAAACA 59.188 33.333 0.00 0.00 29.18 2.83
3095 3602 7.812191 TGCATAAATACATGAAACAGGTCAAAC 59.188 33.333 0.00 0.00 29.18 2.93
3096 3603 7.890515 TGCATAAATACATGAAACAGGTCAAA 58.109 30.769 0.00 0.00 29.18 2.69
3097 3604 7.459795 TGCATAAATACATGAAACAGGTCAA 57.540 32.000 0.00 0.00 29.18 3.18
3104 3611 6.403866 TGGGGATGCATAAATACATGAAAC 57.596 37.500 0.00 0.00 0.00 2.78
3161 4535 9.926158 ATGAATCACTATATGAAGAGTTAGCAG 57.074 33.333 0.00 0.00 41.93 4.24
3236 4610 7.593273 TCGTGATAAAAATCAATGTTTGGTGAC 59.407 33.333 0.00 0.00 31.60 3.67
3842 5560 5.679792 TGTCATAATTCGTAACTCGTCATCG 59.320 40.000 0.00 0.00 40.80 3.84
3864 5582 4.896482 TGCCATAAAACTACCCTTTGTTGT 59.104 37.500 0.00 0.00 34.24 3.32
3865 5583 5.461032 TGCCATAAAACTACCCTTTGTTG 57.539 39.130 0.00 0.00 0.00 3.33
3866 5584 6.487299 TTTGCCATAAAACTACCCTTTGTT 57.513 33.333 0.00 0.00 0.00 2.83
3904 5622 7.770897 ACATGGATAAAGTTAGAATGACAGGAC 59.229 37.037 0.00 0.00 0.00 3.85
3925 5643 9.829507 ATTCTCTCTAAGACAGAAATAACATGG 57.170 33.333 0.00 0.00 32.27 3.66
3983 5701 4.032960 AGCATTGAACCTGGTAATGACA 57.967 40.909 21.10 6.53 34.55 3.58
3984 5702 4.142381 GGAAGCATTGAACCTGGTAATGAC 60.142 45.833 21.10 13.92 34.55 3.06
3990 5708 4.019174 CAATAGGAAGCATTGAACCTGGT 58.981 43.478 0.00 0.00 35.77 4.00
4089 5807 3.316029 CACCAAGCTTCTGAACATCAACA 59.684 43.478 0.00 0.00 0.00 3.33
4157 5875 6.881065 AGACTATGAATTTGTTGCTAGCAGAA 59.119 34.615 18.45 14.13 0.00 3.02
4182 5900 3.960102 AGGTCATTTTGCTGTTCTGGAAA 59.040 39.130 0.00 0.00 0.00 3.13
4184 5902 3.228188 AGGTCATTTTGCTGTTCTGGA 57.772 42.857 0.00 0.00 0.00 3.86
4316 6034 2.041620 AGGGAACATTGCTTCTGCCTTA 59.958 45.455 0.00 0.00 38.71 2.69
4342 6060 8.931568 GGACCTAACTAACTAATTTATCCTCCA 58.068 37.037 0.00 0.00 0.00 3.86
4343 6061 9.156940 AGGACCTAACTAACTAATTTATCCTCC 57.843 37.037 0.00 0.00 0.00 4.30
4542 6260 9.634021 ACAGTGACAGATATGAATTAGTCTAGA 57.366 33.333 0.00 0.00 0.00 2.43
4579 6297 8.736751 TTTTGTACTCTCTTTGTTCACAAAAC 57.263 30.769 6.57 2.05 44.24 2.43
4650 6368 9.803315 GACTGTGATTCTAGATACATGTAACAA 57.197 33.333 10.14 0.00 0.00 2.83
4683 6401 7.224753 CACTACATATCTAACCTGCGAAACATT 59.775 37.037 0.00 0.00 0.00 2.71
4712 6434 6.757478 GTGTTCTTTAAGGATACCTAGACAGC 59.243 42.308 0.00 0.00 31.13 4.40
4717 6439 6.383147 TGGAGGTGTTCTTTAAGGATACCTAG 59.617 42.308 19.63 0.00 35.09 3.02
4815 6537 7.716560 TCAATCAGGAGGAATAACATGTGTATG 59.283 37.037 0.00 0.00 40.24 2.39
4829 6551 3.299503 TGACATCGATCAATCAGGAGGA 58.700 45.455 0.00 0.00 0.00 3.71
4834 6556 5.419760 AGCAAATGACATCGATCAATCAG 57.580 39.130 0.00 0.00 30.82 2.90
4844 6566 1.672881 CGAGGGGAAGCAAATGACATC 59.327 52.381 0.00 0.00 0.00 3.06
4856 6578 0.764890 CCAGGATTATGCGAGGGGAA 59.235 55.000 0.00 0.00 0.00 3.97
4865 6587 4.647564 AGGGATAGTTGCCAGGATTATG 57.352 45.455 0.00 0.00 35.36 1.90
4868 6590 2.175715 GGAAGGGATAGTTGCCAGGATT 59.824 50.000 0.00 0.00 35.36 3.01
4884 6606 1.679898 GAGGTGGTGGTCTGGAAGG 59.320 63.158 0.00 0.00 0.00 3.46
4957 6679 1.670406 GTGGTGACAGCAGCTCAGG 60.670 63.158 7.77 0.00 44.46 3.86
5075 6800 2.948720 GCGAAGAGGACCCTGCAGT 61.949 63.158 13.81 0.00 0.00 4.40
5098 6823 1.081092 TCAGCTAGAAGGCCCCACT 59.919 57.895 0.00 0.00 0.00 4.00
5101 6826 1.524482 CAGTCAGCTAGAAGGCCCC 59.476 63.158 0.00 0.00 0.00 5.80
5205 6930 9.167311 AGTTATCTTGTGATATTCTTGTTCCAC 57.833 33.333 0.00 0.00 35.36 4.02
5334 7060 9.341899 CAGCAAACAAATTAGTCCTATAAACAC 57.658 33.333 0.00 0.00 0.00 3.32
5352 7078 1.371512 CGCCGCAATTCAGCAAACA 60.372 52.632 0.00 0.00 0.00 2.83
5462 7188 6.143758 CGAACTGTTCAATTTGTTACCAATGG 59.856 38.462 19.56 0.00 0.00 3.16
5464 7190 6.695278 CACGAACTGTTCAATTTGTTACCAAT 59.305 34.615 19.56 0.00 0.00 3.16
5482 7209 1.961394 TGCTCTAAGGTCACACGAACT 59.039 47.619 0.00 0.00 42.67 3.01
5627 7355 3.360249 AGCAAACAATGTGAAGCAGAC 57.640 42.857 7.50 0.00 0.00 3.51
5701 7429 9.575783 TTTTCAGAACACATTACAGTTAAAACC 57.424 29.630 0.00 0.00 0.00 3.27
5714 7451 5.537674 AGCCTCAAATCTTTTCAGAACACAT 59.462 36.000 0.00 0.00 30.76 3.21
5759 7496 2.784347 GCAACTCCCAATCCTATAGCC 58.216 52.381 0.00 0.00 0.00 3.93
5774 7511 5.980116 GTGTGACAGATAATCTATCGCAACT 59.020 40.000 0.00 0.00 41.40 3.16
5874 7611 7.027760 TCGTAACAATAGCACAGAGACTAAAG 58.972 38.462 0.00 0.00 0.00 1.85
5884 7621 4.503910 AGCAGAATCGTAACAATAGCACA 58.496 39.130 0.00 0.00 0.00 4.57
5973 7712 1.279271 CGACCCCAACTCTTTCTGGAT 59.721 52.381 0.00 0.00 34.35 3.41
6017 7756 5.295787 GCCATAGATACGAACATTTGGAACA 59.704 40.000 0.00 0.00 0.00 3.18
6119 7858 5.824624 GCATACCTGGAGATCAAGAATTTCA 59.175 40.000 0.00 0.00 0.00 2.69
6160 7899 6.152323 ACAGAACTAGCATTTGCATCTGATTT 59.848 34.615 22.70 8.10 45.16 2.17
6189 7929 3.264706 TGGGGCAGTACAACTATTGCTAA 59.735 43.478 0.00 0.00 36.19 3.09
6190 7930 2.841266 TGGGGCAGTACAACTATTGCTA 59.159 45.455 0.00 0.00 36.19 3.49
6208 7948 2.401967 GCACAGAGCTAGCATTGGG 58.598 57.895 18.83 16.25 41.15 4.12
6266 8006 5.574891 AACGCATATGCTGGAAAATACAA 57.425 34.783 24.56 0.00 39.32 2.41
6291 8076 9.521841 CAGTTCCTAGATAGATGAGTAATACCA 57.478 37.037 0.00 0.00 0.00 3.25
6302 8087 8.948401 TGATTAAGAGCAGTTCCTAGATAGAT 57.052 34.615 0.00 0.00 0.00 1.98
6314 8099 4.574013 GCAACATAGCTGATTAAGAGCAGT 59.426 41.667 10.92 4.79 41.32 4.40
6440 8225 1.969923 AGATCTCTCACTATGCCTGGC 59.030 52.381 12.87 12.87 0.00 4.85
6477 8262 2.897271 ATGTCAACATGGGGCAACTA 57.103 45.000 0.00 0.00 34.83 2.24
6487 8272 7.229306 TCAGCAGTTCTTTTTCTATGTCAACAT 59.771 33.333 0.70 0.70 40.22 2.71
6544 8329 9.590451 GACATATTTCACAAAATCCATCACAAT 57.410 29.630 0.00 0.00 36.49 2.71
6627 8412 1.591863 GCCCTGACCGAATCGCTAC 60.592 63.158 0.00 0.00 0.00 3.58
6701 8486 6.662414 TTTGTGTTGTAGAAGTGAAGACTG 57.338 37.500 0.00 0.00 30.61 3.51
6713 8498 3.815401 CCACCTCCTCTTTTGTGTTGTAG 59.185 47.826 0.00 0.00 0.00 2.74
6879 8664 4.016113 ACACGAAAAAGCTGAAAGACAC 57.984 40.909 0.00 0.00 34.07 3.67
6925 8710 1.743958 GAGCGCAAGAGTACTGGAGTA 59.256 52.381 11.47 0.00 43.02 2.59
6926 8711 0.528470 GAGCGCAAGAGTACTGGAGT 59.472 55.000 11.47 0.00 43.02 3.85
6927 8712 0.814457 AGAGCGCAAGAGTACTGGAG 59.186 55.000 11.47 0.00 43.02 3.86
6928 8713 0.528017 CAGAGCGCAAGAGTACTGGA 59.472 55.000 11.47 0.00 43.02 3.86
6929 8714 0.459237 CCAGAGCGCAAGAGTACTGG 60.459 60.000 11.47 12.14 43.02 4.00
6930 8715 0.528017 TCCAGAGCGCAAGAGTACTG 59.472 55.000 11.47 7.02 43.02 2.74
6931 8716 1.203523 CTTCCAGAGCGCAAGAGTACT 59.796 52.381 11.47 0.00 43.02 2.73
6932 8717 1.067495 ACTTCCAGAGCGCAAGAGTAC 60.067 52.381 11.47 0.00 43.02 2.73
7113 11256 3.325135 CACAAAGTCTAGGTCCCTGTCTT 59.675 47.826 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.