Multiple sequence alignment - TraesCS2B01G287400

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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 TraesCS2B01G287400 chr2B 100.000 7408 0 0 1 7408 396572421 396565014 0.000000e+00 13681
1 TraesCS2B01G287400 chr2D 96.754 5514 127 16 759 6260 327073326 327067853 0.000000e+00 9143
2 TraesCS2B01G287400 chr2D 89.278 485 27 14 6274 6739 327067706 327067228 1.070000e-162 584
3 TraesCS2B01G287400 chr2A 95.954 5512 128 26 759 6260 431658920 431653494 0.000000e+00 8855
4 TraesCS2B01G287400 chr2A 87.058 1159 101 18 6274 7408 431581247 431580114 0.000000e+00 1264
5 TraesCS2B01G287400 chrUn 97.233 759 21 0 1 759 221514893 221515651 0.000000e+00 1286
6 TraesCS2B01G287400 chrUn 95.268 317 15 0 443 759 392292814 392292498 3.090000e-138 503
7 TraesCS2B01G287400 chr4B 97.233 759 21 0 1 759 630128308 630129066 0.000000e+00 1286
8 TraesCS2B01G287400 chr6B 95.675 763 22 4 1 763 708116135 708115384 0.000000e+00 1216
9 TraesCS2B01G287400 chr3D 86.810 743 90 4 6672 7408 379766753 379766013 0.000000e+00 822
10 TraesCS2B01G287400 chr3B 84.853 746 105 7 6669 7408 495499627 495500370 0.000000e+00 745
11 TraesCS2B01G287400 chr7A 82.672 756 129 2 1 755 679792251 679793005 0.000000e+00 669
12 TraesCS2B01G287400 chr7A 81.686 759 133 6 1 756 23818535 23819290 1.750000e-175 627
13 TraesCS2B01G287400 chr5A 81.987 755 132 4 1 753 330878148 330877396 8.110000e-179 638
14 TraesCS2B01G287400 chr5D 80.784 510 95 3 58 565 449507086 449506578 5.390000e-106 396


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 TraesCS2B01G287400 chr2B 396565014 396572421 7407 True 13681.0 13681 100.000 1 7408 1 chr2B.!!$R1 7407
1 TraesCS2B01G287400 chr2D 327067228 327073326 6098 True 4863.5 9143 93.016 759 6739 2 chr2D.!!$R1 5980
2 TraesCS2B01G287400 chr2A 431653494 431658920 5426 True 8855.0 8855 95.954 759 6260 1 chr2A.!!$R2 5501
3 TraesCS2B01G287400 chr2A 431580114 431581247 1133 True 1264.0 1264 87.058 6274 7408 1 chr2A.!!$R1 1134
4 TraesCS2B01G287400 chrUn 221514893 221515651 758 False 1286.0 1286 97.233 1 759 1 chrUn.!!$F1 758
5 TraesCS2B01G287400 chr4B 630128308 630129066 758 False 1286.0 1286 97.233 1 759 1 chr4B.!!$F1 758
6 TraesCS2B01G287400 chr6B 708115384 708116135 751 True 1216.0 1216 95.675 1 763 1 chr6B.!!$R1 762
7 TraesCS2B01G287400 chr3D 379766013 379766753 740 True 822.0 822 86.810 6672 7408 1 chr3D.!!$R1 736
8 TraesCS2B01G287400 chr3B 495499627 495500370 743 False 745.0 745 84.853 6669 7408 1 chr3B.!!$F1 739
9 TraesCS2B01G287400 chr7A 679792251 679793005 754 False 669.0 669 82.672 1 755 1 chr7A.!!$F2 754
10 TraesCS2B01G287400 chr7A 23818535 23819290 755 False 627.0 627 81.686 1 756 1 chr7A.!!$F1 755
11 TraesCS2B01G287400 chr5A 330877396 330878148 752 True 638.0 638 81.987 1 753 1 chr5A.!!$R1 752
12 TraesCS2B01G287400 chr5D 449506578 449507086 508 True 396.0 396 80.784 58 565 1 chr5D.!!$R1 507

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
355 358 0.618458 AGCCGGAGCAGGTAATTTGA 59.382 50.000 5.05 0.00 43.56 2.69 F
1684 1689 0.471191 CATGGAGGCAGCCAGATACA 59.529 55.000 15.80 0.00 42.15 2.29 F
2967 2974 2.383683 TCTATCCCCTCTCTACCCATGG 59.616 54.545 4.14 4.14 0.00 3.66 F
3581 3589 1.402325 GGAAACCTAATTGCGCGCTTT 60.402 47.619 33.29 25.86 0.00 3.51 F
4777 4790 2.167281 CAGTGAGGTGTGTGATAGGGAG 59.833 54.545 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 1936 1.564348 ACCAACATAGTGCTAAGGGGG 59.436 52.381 0.00 0.00 0.00 5.40 R
3570 3578 0.310543 TTGAGACAAAAGCGCGCAAT 59.689 45.000 35.10 19.45 0.00 3.56 R
3815 3828 8.469200 AGATCTCTGACTTTCTATTCTGAACAG 58.531 37.037 0.00 0.00 0.00 3.16 R
5524 5540 1.701847 ACTGCAGGGAGAATGTTGACT 59.298 47.619 19.93 0.00 0.00 3.41 R
6453 6606 0.239082 CCGCCAAAGGGTTTTACGAC 59.761 55.000 0.00 0.00 36.17 4.34 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
123 124 3.609853 TGTTGGTGATGCTATGAGAACC 58.390 45.455 0.00 0.00 0.00 3.62
355 358 0.618458 AGCCGGAGCAGGTAATTTGA 59.382 50.000 5.05 0.00 43.56 2.69
471 474 1.159285 CTGATTCGCTGGTGCTGAAA 58.841 50.000 0.00 0.00 36.17 2.69
507 510 6.975196 TCTGAAGCTTATAATCTCTCTGCT 57.025 37.500 0.00 0.00 0.00 4.24
520 523 1.066573 TCTCTGCTTTAGGTGCTCTGC 60.067 52.381 0.00 0.00 0.00 4.26
522 525 1.085091 CTGCTTTAGGTGCTCTGCTG 58.915 55.000 0.00 0.00 0.00 4.41
551 554 7.552687 AGAGATTAAATTTCAGTTACGCATGGA 59.447 33.333 0.00 0.00 0.00 3.41
745 748 9.237187 TGTAATGGAATGCATAAGTGTTTCTTA 57.763 29.630 0.00 0.00 41.98 2.10
798 801 2.261671 CAGTTGGACGGACGAGGG 59.738 66.667 0.00 0.00 0.00 4.30
926 929 2.284847 GGTCCCGTGGTTCCCCTA 60.285 66.667 0.00 0.00 0.00 3.53
1092 1095 2.438795 GACGAGCCGGAGACCTCT 60.439 66.667 5.05 0.00 0.00 3.69
1245 1248 2.100631 CGCCGAGAACCGCTTCATT 61.101 57.895 0.00 0.00 36.84 2.57
1314 1318 2.753296 CCATCGATTGCCTCTCTTCTC 58.247 52.381 0.00 0.00 0.00 2.87
1684 1689 0.471191 CATGGAGGCAGCCAGATACA 59.529 55.000 15.80 0.00 42.15 2.29
1749 1754 2.550208 CCTCAGCCGGACACTAAACTTT 60.550 50.000 5.05 0.00 0.00 2.66
1756 1761 3.502211 CCGGACACTAAACTTTTGCTGAT 59.498 43.478 0.00 0.00 0.00 2.90
1757 1762 4.466828 CGGACACTAAACTTTTGCTGATG 58.533 43.478 0.00 0.00 0.00 3.07
1783 1788 8.947055 AACTTTTTGTTCTGAATTAAGTGCAT 57.053 26.923 0.00 0.00 32.63 3.96
1818 1823 6.313744 ACAAGACAGAACGGAAAATTTAGG 57.686 37.500 0.00 0.00 0.00 2.69
1860 1865 3.886505 AGTTGTACTGGCGATTTTGGAAA 59.113 39.130 0.00 0.00 0.00 3.13
1861 1866 4.339814 AGTTGTACTGGCGATTTTGGAAAA 59.660 37.500 0.00 0.00 0.00 2.29
1863 1868 5.461032 TGTACTGGCGATTTTGGAAAATT 57.539 34.783 0.00 0.00 38.64 1.82
1864 1869 6.576662 TGTACTGGCGATTTTGGAAAATTA 57.423 33.333 0.00 0.00 38.64 1.40
1866 1871 4.481463 ACTGGCGATTTTGGAAAATTACG 58.519 39.130 0.00 1.32 38.64 3.18
1867 1872 4.022676 ACTGGCGATTTTGGAAAATTACGT 60.023 37.500 0.00 0.00 38.64 3.57
1868 1873 4.230657 TGGCGATTTTGGAAAATTACGTG 58.769 39.130 0.00 0.00 38.64 4.49
1869 1874 4.231439 GGCGATTTTGGAAAATTACGTGT 58.769 39.130 0.00 0.00 38.64 4.49
1870 1875 4.682401 GGCGATTTTGGAAAATTACGTGTT 59.318 37.500 0.00 0.00 38.64 3.32
1871 1876 5.857517 GGCGATTTTGGAAAATTACGTGTTA 59.142 36.000 0.00 0.00 38.64 2.41
1872 1877 6.183359 GGCGATTTTGGAAAATTACGTGTTAC 60.183 38.462 0.00 0.00 38.64 2.50
1873 1878 6.579666 GCGATTTTGGAAAATTACGTGTTACT 59.420 34.615 0.00 0.00 38.64 2.24
1874 1879 7.408921 GCGATTTTGGAAAATTACGTGTTACTG 60.409 37.037 0.00 0.00 38.64 2.74
1875 1880 7.588488 CGATTTTGGAAAATTACGTGTTACTGT 59.412 33.333 0.00 0.00 38.64 3.55
1876 1881 9.881529 GATTTTGGAAAATTACGTGTTACTGTA 57.118 29.630 0.00 0.00 38.64 2.74
1878 1883 9.881529 TTTTGGAAAATTACGTGTTACTGTATC 57.118 29.630 0.00 0.00 0.00 2.24
1879 1884 7.599630 TGGAAAATTACGTGTTACTGTATCC 57.400 36.000 0.00 0.00 0.00 2.59
1902 1907 5.228579 TGTGATGTGGTAAATATTGTGCG 57.771 39.130 0.00 0.00 0.00 5.34
1913 1918 7.860373 TGGTAAATATTGTGCGCATTCTAAATC 59.140 33.333 15.91 0.00 0.00 2.17
1951 1957 2.775384 CCCCCTTAGCACTATGTTGGTA 59.225 50.000 0.00 0.00 0.00 3.25
2003 2009 5.416013 TCATGTTACTCGAGTCTTGTCAGAT 59.584 40.000 23.89 1.80 0.00 2.90
2006 2012 6.171213 TGTTACTCGAGTCTTGTCAGATAGA 58.829 40.000 23.89 0.00 0.00 1.98
2045 2051 4.207891 TGAACCTCCTCTTAGTTGCATC 57.792 45.455 0.00 0.00 0.00 3.91
2046 2052 3.840666 TGAACCTCCTCTTAGTTGCATCT 59.159 43.478 2.28 2.28 0.00 2.90
2047 2053 4.287067 TGAACCTCCTCTTAGTTGCATCTT 59.713 41.667 1.93 0.00 0.00 2.40
2048 2054 4.213564 ACCTCCTCTTAGTTGCATCTTG 57.786 45.455 1.93 0.00 0.00 3.02
2049 2055 2.941720 CCTCCTCTTAGTTGCATCTTGC 59.058 50.000 1.93 0.00 45.29 4.01
2099 2105 9.334693 GTGTCATGATTCAGTAAATTTCTCAAC 57.665 33.333 0.00 0.00 0.00 3.18
2413 2419 7.710676 AGAAGGACGTATCATATGCTAGATT 57.289 36.000 0.00 0.00 0.00 2.40
2414 2420 7.542890 AGAAGGACGTATCATATGCTAGATTG 58.457 38.462 0.00 0.00 0.00 2.67
2415 2421 6.842437 AGGACGTATCATATGCTAGATTGT 57.158 37.500 0.00 0.00 0.00 2.71
2416 2422 7.233389 AGGACGTATCATATGCTAGATTGTT 57.767 36.000 0.00 0.00 0.00 2.83
2417 2423 7.093354 AGGACGTATCATATGCTAGATTGTTG 58.907 38.462 0.00 0.00 0.00 3.33
2418 2424 7.039714 AGGACGTATCATATGCTAGATTGTTGA 60.040 37.037 0.00 0.00 0.00 3.18
2419 2425 7.761704 GGACGTATCATATGCTAGATTGTTGAT 59.238 37.037 0.00 0.00 0.00 2.57
2420 2426 9.144747 GACGTATCATATGCTAGATTGTTGATT 57.855 33.333 0.00 0.00 0.00 2.57
2421 2427 9.144747 ACGTATCATATGCTAGATTGTTGATTC 57.855 33.333 0.00 0.00 0.00 2.52
2645 2651 7.287512 TCAGTCTTAGATGAGATTGGATCTG 57.712 40.000 0.00 0.00 40.38 2.90
2674 2680 7.768120 GGATTCTGGACTATATGATGCTTTAGG 59.232 40.741 0.00 0.00 0.00 2.69
2733 2739 7.935338 ATCTCATTTGTTGATGTTTTCACAC 57.065 32.000 0.00 0.00 35.03 3.82
2967 2974 2.383683 TCTATCCCCTCTCTACCCATGG 59.616 54.545 4.14 4.14 0.00 3.66
3016 3023 4.933400 TCTTTGTTACATACGCCTTCCTTC 59.067 41.667 0.00 0.00 0.00 3.46
3031 3039 4.098960 CCTTCCTTCAATTCACCATGGATG 59.901 45.833 21.47 13.20 0.00 3.51
3034 3042 5.085920 TCCTTCAATTCACCATGGATGTTT 58.914 37.500 21.47 8.66 0.00 2.83
3128 3136 7.928706 CCTTAAAATGGAGGTCACTGACTATAG 59.071 40.741 9.08 0.00 32.47 1.31
3158 3166 4.839121 TGGATGGTTCGTATTACTTTGCT 58.161 39.130 0.00 0.00 0.00 3.91
3234 3242 5.527951 TCATGTGCAACTAAAATCACAACC 58.472 37.500 0.00 0.00 41.92 3.77
3235 3243 5.301551 TCATGTGCAACTAAAATCACAACCT 59.698 36.000 0.00 0.00 41.92 3.50
3284 3292 9.454859 ACTTGTCTAAGGAGATTTAATTCTTGG 57.545 33.333 1.60 0.00 38.26 3.61
3293 3301 9.981460 AGGAGATTTAATTCTTGGTTTATCACT 57.019 29.630 1.60 0.00 0.00 3.41
3570 3578 3.071023 CAGTGTCTCTGGTGGAAACCTAA 59.929 47.826 0.00 0.00 40.23 2.69
3581 3589 1.402325 GGAAACCTAATTGCGCGCTTT 60.402 47.619 33.29 25.86 0.00 3.51
3582 3590 2.324860 GAAACCTAATTGCGCGCTTTT 58.675 42.857 33.29 25.51 0.00 2.27
3598 3606 4.437930 GCGCTTTTGTCTCAATGCTCTATT 60.438 41.667 0.00 0.00 0.00 1.73
3599 3607 5.220662 GCGCTTTTGTCTCAATGCTCTATTA 60.221 40.000 0.00 0.00 0.00 0.98
3600 3608 6.188175 CGCTTTTGTCTCAATGCTCTATTAC 58.812 40.000 0.00 0.00 0.00 1.89
3601 3609 6.036517 CGCTTTTGTCTCAATGCTCTATTACT 59.963 38.462 0.00 0.00 0.00 2.24
3602 3610 7.413438 CGCTTTTGTCTCAATGCTCTATTACTT 60.413 37.037 0.00 0.00 0.00 2.24
3603 3611 7.907563 GCTTTTGTCTCAATGCTCTATTACTTC 59.092 37.037 0.00 0.00 0.00 3.01
3604 3612 9.160496 CTTTTGTCTCAATGCTCTATTACTTCT 57.840 33.333 0.00 0.00 0.00 2.85
3607 3615 7.487484 TGTCTCAATGCTCTATTACTTCTCAG 58.513 38.462 0.00 0.00 0.00 3.35
3624 3632 7.488322 ACTTCTCAGTTCTCACTTATCTATGC 58.512 38.462 0.00 0.00 0.00 3.14
3642 3650 2.184579 GCTCTGTCCCACGGCTAC 59.815 66.667 0.00 0.00 0.00 3.58
3709 3719 5.932619 TTGAAGTTCCTCTGATCCGATTA 57.067 39.130 0.00 0.00 0.00 1.75
3722 3732 8.593492 TCTGATCCGATTACATTTAGTTGATG 57.407 34.615 0.00 0.00 0.00 3.07
3987 4000 3.189495 GGCCTAGAAGTTTCAGAAGTTGC 59.811 47.826 0.00 0.00 0.00 4.17
4301 4314 6.466812 CATGTACCATGGTATGCTGATTCTA 58.533 40.000 27.03 0.00 32.82 2.10
4777 4790 2.167281 CAGTGAGGTGTGTGATAGGGAG 59.833 54.545 0.00 0.00 0.00 4.30
4997 5013 2.283173 CCCAGTCACCTTTGGGCC 60.283 66.667 0.00 0.00 46.96 5.80
5524 5540 0.034186 CATCAAGCAACCCCCAGCTA 60.034 55.000 0.00 0.00 40.90 3.32
5652 5668 5.441718 TTTCATGTGGCTTATCTCTCCTT 57.558 39.130 0.00 0.00 0.00 3.36
5653 5669 5.441718 TTCATGTGGCTTATCTCTCCTTT 57.558 39.130 0.00 0.00 0.00 3.11
5837 5853 7.803189 GCGTTTACGGAATTTGATGATATCAAT 59.197 33.333 9.99 0.00 43.10 2.57
5962 5978 9.548631 ACTTGTATCTACATGGTAATAGGCTAT 57.451 33.333 0.00 0.00 36.14 2.97
6025 6042 0.396278 GCTTCCCTGCCCAGCTAAAT 60.396 55.000 0.00 0.00 0.00 1.40
6118 6135 1.594518 CGTGTGCAACTCCTCGTTTTG 60.595 52.381 0.00 0.00 38.04 2.44
6154 6171 1.548582 CCCAAGGGAGCTTGTGTTGAT 60.549 52.381 0.00 0.00 37.50 2.57
6165 6182 4.083855 AGCTTGTGTTGATATGTTGTGTCG 60.084 41.667 0.00 0.00 0.00 4.35
6207 6224 0.824109 ATGGTTTGGCGAGAGATCGA 59.176 50.000 1.17 0.00 34.64 3.59
6213 6230 4.511826 GGTTTGGCGAGAGATCGAAAATAT 59.488 41.667 1.17 0.00 34.64 1.28
6260 6278 9.982651 TTTTTGGAATGGAATATTCGTAAAACA 57.017 25.926 9.32 1.25 31.23 2.83
6262 6280 9.579768 TTTGGAATGGAATATTCGTAAAACATG 57.420 29.630 9.32 0.00 0.00 3.21
6264 6282 7.340743 TGGAATGGAATATTCGTAAAACATGGT 59.659 33.333 9.32 0.00 0.00 3.55
6265 6283 8.194769 GGAATGGAATATTCGTAAAACATGGTT 58.805 33.333 9.32 0.00 0.00 3.67
6266 6284 9.233232 GAATGGAATATTCGTAAAACATGGTTC 57.767 33.333 9.32 0.00 0.00 3.62
6267 6285 7.090953 TGGAATATTCGTAAAACATGGTTCC 57.909 36.000 9.32 0.00 33.71 3.62
6268 6286 6.183360 TGGAATATTCGTAAAACATGGTTCCG 60.183 38.462 9.32 2.55 35.37 4.30
6269 6287 2.973419 TTCGTAAAACATGGTTCCGC 57.027 45.000 9.88 0.00 0.00 5.54
6270 6288 0.791422 TCGTAAAACATGGTTCCGCG 59.209 50.000 9.88 0.00 0.00 6.46
6272 6290 1.723384 CGTAAAACATGGTTCCGCGTG 60.723 52.381 4.92 0.00 0.00 5.34
6343 6495 0.947244 GCGAATGCCAGGGAATACAG 59.053 55.000 0.00 0.00 33.98 2.74
6453 6606 4.821260 CCATTGAAAAGTTTTCCCCCAAAG 59.179 41.667 22.47 9.83 0.00 2.77
6454 6607 5.436175 CATTGAAAAGTTTTCCCCCAAAGT 58.564 37.500 22.47 0.52 0.00 2.66
6470 6623 3.377439 CAAAGTCGTAAAACCCTTTGGC 58.623 45.455 0.00 0.00 39.87 4.52
6507 6660 0.949397 GGGTTTTGACCGTGGAACTC 59.051 55.000 0.00 0.00 31.75 3.01
6508 6661 0.584876 GGTTTTGACCGTGGAACTCG 59.415 55.000 0.00 0.00 45.50 4.18
6509 6662 0.041576 GTTTTGACCGTGGAACTCGC 60.042 55.000 0.00 0.00 44.50 5.03
6510 6663 0.179067 TTTTGACCGTGGAACTCGCT 60.179 50.000 0.00 0.00 44.50 4.93
6511 6664 0.878523 TTTGACCGTGGAACTCGCTG 60.879 55.000 0.00 0.00 44.50 5.18
6551 6704 2.362369 GGGGCTGAGAGCTAGTGCA 61.362 63.158 0.00 0.00 41.99 4.57
6636 6806 0.988063 GGAAGAAGTTGGAGGAGGCT 59.012 55.000 0.00 0.00 0.00 4.58
6641 6811 1.073923 GAAGTTGGAGGAGGCTTTGGA 59.926 52.381 0.00 0.00 0.00 3.53
6736 6906 3.088532 TGGCTACTGGCTGGTAAAATTG 58.911 45.455 0.00 0.00 41.46 2.32
6748 6918 6.589907 GGCTGGTAAAATTGTTCATCGAAATT 59.410 34.615 0.00 0.00 0.00 1.82
6767 6937 9.706691 TCGAAATTAATTCCATATCCAGACTAC 57.293 33.333 0.10 0.00 34.34 2.73
6783 6953 2.257409 CTACAGCCAATGCCCTCCGT 62.257 60.000 0.00 0.00 38.69 4.69
6784 6954 1.847798 TACAGCCAATGCCCTCCGTT 61.848 55.000 0.00 0.00 38.69 4.44
6885 7055 4.331443 CGAGACATAGATCGAGTATGGGAG 59.669 50.000 17.50 6.45 41.40 4.30
6891 7061 1.746220 GATCGAGTATGGGAGGGATCG 59.254 57.143 0.00 0.00 0.00 3.69
6895 7065 1.122019 AGTATGGGAGGGATCGCCAC 61.122 60.000 6.09 0.00 34.28 5.01
6908 7083 0.602638 TCGCCACGTCAGCAAGAATT 60.603 50.000 7.78 0.00 0.00 2.17
7031 7206 2.922283 AGGGATGACTCTTGGTGGATTT 59.078 45.455 0.00 0.00 0.00 2.17
7101 7276 0.110486 AATGGTGGGTTCTTGCGAGT 59.890 50.000 0.00 0.00 0.00 4.18
7119 7294 0.931005 GTTCGGATCACCATCGAAGC 59.069 55.000 4.31 0.00 42.38 3.86
7225 7400 5.659440 TCCCATATTTTTGTTTCTCCTGC 57.341 39.130 0.00 0.00 0.00 4.85
7385 7560 4.215109 ACAAAACTCAAGTGCCAATACCT 58.785 39.130 0.00 0.00 0.00 3.08
7391 7566 0.251916 AAGTGCCAATACCTAGCGCA 59.748 50.000 11.47 0.00 39.46 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
355 358 2.351738 GCAATGGCTCAGCTACGTTTTT 60.352 45.455 0.00 0.00 36.96 1.94
471 474 4.484537 AGCTTCAGAAGTGATAGCATGT 57.515 40.909 11.94 0.00 38.37 3.21
507 510 3.324846 TCTCTTTCAGCAGAGCACCTAAA 59.675 43.478 0.00 0.00 40.33 1.85
522 525 9.774742 ATGCGTAACTGAAATTTAATCTCTTTC 57.225 29.630 0.00 0.00 0.00 2.62
562 565 8.407832 TGATCTTTGGCAATGTTTGATACATAG 58.592 33.333 12.22 0.00 46.75 2.23
759 762 2.520458 CCCTGCAGTTTGGTCCCA 59.480 61.111 13.81 0.00 0.00 4.37
762 765 2.594592 ACGCCCTGCAGTTTGGTC 60.595 61.111 13.81 2.85 0.00 4.02
763 766 2.906897 CACGCCCTGCAGTTTGGT 60.907 61.111 13.81 1.98 0.00 3.67
798 801 1.540435 GCCCCGATCCATCCTCTCTC 61.540 65.000 0.00 0.00 0.00 3.20
926 929 1.821753 CAAGATGAGACAGGAGACGGT 59.178 52.381 0.00 0.00 43.23 4.83
1092 1095 2.771639 CGCTCCTCGTTCCGATCCA 61.772 63.158 0.00 0.00 34.61 3.41
1343 1347 2.037367 CCCACCTCCGAGACCTCA 59.963 66.667 0.00 0.00 0.00 3.86
1684 1689 7.667219 CACAATATCCTCTGGCAGGTATAAAAT 59.333 37.037 15.73 2.18 43.95 1.82
1775 1780 9.243637 GTCTTGTTTTGTTATTTGATGCACTTA 57.756 29.630 0.00 0.00 0.00 2.24
1783 1788 6.970043 CCGTTCTGTCTTGTTTTGTTATTTGA 59.030 34.615 0.00 0.00 0.00 2.69
1797 1802 5.705905 CCTCCTAAATTTTCCGTTCTGTCTT 59.294 40.000 0.00 0.00 0.00 3.01
1818 1823 8.668510 ACAACTACATGATGATACATTTCCTC 57.331 34.615 0.00 0.00 0.00 3.71
1860 1865 6.927416 TCACAGGATACAGTAACACGTAATT 58.073 36.000 0.00 0.00 41.41 1.40
1861 1866 6.519679 TCACAGGATACAGTAACACGTAAT 57.480 37.500 0.00 0.00 41.41 1.89
1863 1868 5.416639 ACATCACAGGATACAGTAACACGTA 59.583 40.000 0.00 0.00 41.41 3.57
1864 1869 4.219944 ACATCACAGGATACAGTAACACGT 59.780 41.667 0.00 0.00 41.41 4.49
1866 1871 4.870426 CCACATCACAGGATACAGTAACAC 59.130 45.833 0.00 0.00 41.41 3.32
1867 1872 4.530553 ACCACATCACAGGATACAGTAACA 59.469 41.667 0.00 0.00 41.41 2.41
1868 1873 5.086104 ACCACATCACAGGATACAGTAAC 57.914 43.478 0.00 0.00 41.41 2.50
1869 1874 6.860790 TTACCACATCACAGGATACAGTAA 57.139 37.500 0.00 0.00 41.41 2.24
1870 1875 6.860790 TTTACCACATCACAGGATACAGTA 57.139 37.500 0.00 0.00 41.41 2.74
1871 1876 5.755409 TTTACCACATCACAGGATACAGT 57.245 39.130 0.00 0.00 41.41 3.55
1872 1877 8.777413 CAATATTTACCACATCACAGGATACAG 58.223 37.037 0.00 0.00 41.41 2.74
1873 1878 8.271458 ACAATATTTACCACATCACAGGATACA 58.729 33.333 0.00 0.00 41.41 2.29
1874 1879 8.559536 CACAATATTTACCACATCACAGGATAC 58.440 37.037 0.00 0.00 30.87 2.24
1875 1880 7.228507 GCACAATATTTACCACATCACAGGATA 59.771 37.037 0.00 0.00 30.87 2.59
1876 1881 6.039717 GCACAATATTTACCACATCACAGGAT 59.960 38.462 0.00 0.00 0.00 3.24
1877 1882 5.356751 GCACAATATTTACCACATCACAGGA 59.643 40.000 0.00 0.00 0.00 3.86
1878 1883 5.581605 GCACAATATTTACCACATCACAGG 58.418 41.667 0.00 0.00 0.00 4.00
1879 1884 5.265477 CGCACAATATTTACCACATCACAG 58.735 41.667 0.00 0.00 0.00 3.66
1902 1907 2.291465 TGCTGCGATGGATTTAGAATGC 59.709 45.455 0.00 0.00 0.00 3.56
1930 1936 1.564348 ACCAACATAGTGCTAAGGGGG 59.436 52.381 0.00 0.00 0.00 5.40
1951 1957 5.685511 GCAACAATTTGACGACTTATGTTGT 59.314 36.000 14.76 1.33 44.75 3.32
2003 2009 7.363880 GGTTCATCACTTAACCAGACTGATCTA 60.364 40.741 3.32 0.00 43.84 1.98
2006 2012 5.249393 AGGTTCATCACTTAACCAGACTGAT 59.751 40.000 3.32 0.00 46.29 2.90
2045 2051 6.889301 ATGACATACTAATTCCCATGCAAG 57.111 37.500 0.00 0.00 0.00 4.01
2046 2052 6.832900 TGAATGACATACTAATTCCCATGCAA 59.167 34.615 0.00 0.00 30.75 4.08
2047 2053 6.363882 TGAATGACATACTAATTCCCATGCA 58.636 36.000 0.00 0.00 30.75 3.96
2048 2054 6.882610 TGAATGACATACTAATTCCCATGC 57.117 37.500 0.00 0.00 30.75 4.06
2049 2055 8.347771 CACTTGAATGACATACTAATTCCCATG 58.652 37.037 0.00 0.00 30.75 3.66
2050 2056 8.055181 ACACTTGAATGACATACTAATTCCCAT 58.945 33.333 0.00 0.00 30.75 4.00
2051 2057 7.402054 ACACTTGAATGACATACTAATTCCCA 58.598 34.615 0.00 0.00 30.75 4.37
2110 2116 5.975693 ATGTTCGGTTTGTTATGGATTGT 57.024 34.783 0.00 0.00 0.00 2.71
2126 2132 7.201530 GGTGACTACAGAAAATAGGAATGTTCG 60.202 40.741 0.00 0.00 34.89 3.95
2621 2627 6.838090 ACAGATCCAATCTCATCTAAGACTGA 59.162 38.462 0.00 0.00 37.58 3.41
2645 2651 7.416964 AGCATCATATAGTCCAGAATCCTAC 57.583 40.000 0.00 0.00 0.00 3.18
3016 3023 8.658609 GTTGATAAAAACATCCATGGTGAATTG 58.341 33.333 12.58 5.83 0.00 2.32
3031 3039 7.220108 GCCGATGGTAGAAATGTTGATAAAAAC 59.780 37.037 0.00 0.00 0.00 2.43
3034 3042 5.883115 TGCCGATGGTAGAAATGTTGATAAA 59.117 36.000 0.00 0.00 0.00 1.40
3128 3136 7.208080 AGTAATACGAACCATCCATAGTCAAC 58.792 38.462 0.00 0.00 0.00 3.18
3195 3203 4.618489 GCACATGAGCAAATCTACAACAAC 59.382 41.667 10.48 0.00 0.00 3.32
3234 3242 1.101635 CCAGATCATGGCACTGGCAG 61.102 60.000 14.16 14.16 43.83 4.85
3235 3243 1.077285 CCAGATCATGGCACTGGCA 60.077 57.895 7.88 7.88 43.83 4.92
3284 3292 8.364129 TGATTTTTCCTTTGCAAGTGATAAAC 57.636 30.769 13.83 10.39 0.00 2.01
3462 3470 4.443394 CACCAACGTACAGTACTTGAAGAC 59.557 45.833 17.66 0.00 0.00 3.01
3478 3486 7.537306 CAGACTTTCATAAAATAACCACCAACG 59.463 37.037 0.00 0.00 0.00 4.10
3570 3578 0.310543 TTGAGACAAAAGCGCGCAAT 59.689 45.000 35.10 19.45 0.00 3.56
3581 3589 7.840931 TGAGAAGTAATAGAGCATTGAGACAA 58.159 34.615 0.00 0.00 0.00 3.18
3582 3590 7.123397 ACTGAGAAGTAATAGAGCATTGAGACA 59.877 37.037 0.00 0.00 0.00 3.41
3598 3606 8.625651 GCATAGATAAGTGAGAACTGAGAAGTA 58.374 37.037 0.00 0.00 0.00 2.24
3599 3607 7.488322 GCATAGATAAGTGAGAACTGAGAAGT 58.512 38.462 0.00 0.00 0.00 3.01
3600 3608 6.636447 CGCATAGATAAGTGAGAACTGAGAAG 59.364 42.308 0.00 0.00 0.00 2.85
3601 3609 6.499172 CGCATAGATAAGTGAGAACTGAGAA 58.501 40.000 0.00 0.00 0.00 2.87
3602 3610 5.506483 GCGCATAGATAAGTGAGAACTGAGA 60.506 44.000 0.30 0.00 0.00 3.27
3603 3611 4.679197 GCGCATAGATAAGTGAGAACTGAG 59.321 45.833 0.30 0.00 0.00 3.35
3604 3612 4.339530 AGCGCATAGATAAGTGAGAACTGA 59.660 41.667 11.47 0.00 0.00 3.41
3607 3615 4.679197 CAGAGCGCATAGATAAGTGAGAAC 59.321 45.833 11.47 0.00 0.00 3.01
3618 3626 1.816537 GTGGGACAGAGCGCATAGA 59.183 57.895 11.47 0.00 41.80 1.98
3624 3632 3.449227 TAGCCGTGGGACAGAGCG 61.449 66.667 0.00 0.00 41.80 5.03
3815 3828 8.469200 AGATCTCTGACTTTCTATTCTGAACAG 58.531 37.037 0.00 0.00 0.00 3.16
4997 5013 5.056480 TGATACTTCATTTGATACCAGCGG 58.944 41.667 0.00 0.00 0.00 5.52
5524 5540 1.701847 ACTGCAGGGAGAATGTTGACT 59.298 47.619 19.93 0.00 0.00 3.41
5652 5668 7.394016 TGCATGTTCACCTATTAAAGAGAGAA 58.606 34.615 0.00 0.00 0.00 2.87
5653 5669 6.946340 TGCATGTTCACCTATTAAAGAGAGA 58.054 36.000 0.00 0.00 0.00 3.10
5804 5820 4.454847 TCAAATTCCGTAAACGCAACCATA 59.545 37.500 0.00 0.00 38.18 2.74
5837 5853 2.359169 GGGCTGATCACGGTCTCCA 61.359 63.158 0.00 0.00 0.00 3.86
5962 5978 3.680490 TCATCGTATTGCCAAAACCAGA 58.320 40.909 0.00 0.00 0.00 3.86
5963 5979 4.637483 ATCATCGTATTGCCAAAACCAG 57.363 40.909 0.00 0.00 0.00 4.00
6025 6042 3.894427 ACATTTAACAACCACATCAGCCA 59.106 39.130 0.00 0.00 0.00 4.75
6118 6135 3.274288 CTTGGGCACTAAATGGAGAGAC 58.726 50.000 0.00 0.00 0.00 3.36
6154 6171 1.336056 TGTAGCGCACGACACAACATA 60.336 47.619 11.47 0.00 0.00 2.29
6165 6182 1.933181 TGTCTGCATAATGTAGCGCAC 59.067 47.619 11.47 6.60 29.77 5.34
6207 6224 7.610580 TTTTCAGAACTGGTGGGAATATTTT 57.389 32.000 1.93 0.00 0.00 1.82
6213 6230 7.610580 AAAATATTTTCAGAACTGGTGGGAA 57.389 32.000 7.64 0.00 0.00 3.97
6260 6278 1.452145 AAAAGCACACGCGGAACCAT 61.452 50.000 12.47 0.00 45.49 3.55
6262 6280 0.933047 GAAAAAGCACACGCGGAACC 60.933 55.000 12.47 0.00 45.49 3.62
6264 6282 0.665835 ATGAAAAAGCACACGCGGAA 59.334 45.000 12.47 0.00 45.49 4.30
6265 6283 1.463056 CTATGAAAAAGCACACGCGGA 59.537 47.619 12.47 0.00 45.49 5.54
6266 6284 1.465689 CCTATGAAAAAGCACACGCGG 60.466 52.381 12.47 1.27 45.49 6.46
6267 6285 1.463056 TCCTATGAAAAAGCACACGCG 59.537 47.619 3.53 3.53 45.49 6.01
6268 6286 3.375299 AGATCCTATGAAAAAGCACACGC 59.625 43.478 0.00 0.00 38.99 5.34
6269 6287 4.393062 ACAGATCCTATGAAAAAGCACACG 59.607 41.667 0.00 0.00 0.00 4.49
6270 6288 5.634896 CACAGATCCTATGAAAAAGCACAC 58.365 41.667 0.00 0.00 0.00 3.82
6272 6290 4.156556 TGCACAGATCCTATGAAAAAGCAC 59.843 41.667 0.00 0.00 0.00 4.40
6343 6495 0.447801 CAAAGCATGTACGCTCACCC 59.552 55.000 0.00 0.00 42.89 4.61
6364 6516 2.158667 AGCCTGGATTTATTACGTGGGG 60.159 50.000 0.00 0.00 0.00 4.96
6453 6606 0.239082 CCGCCAAAGGGTTTTACGAC 59.761 55.000 0.00 0.00 36.17 4.34
6454 6607 1.517210 GCCGCCAAAGGGTTTTACGA 61.517 55.000 0.00 0.00 36.17 3.43
6470 6623 2.047655 TAAACACCAGAGGCGCCG 60.048 61.111 23.20 9.47 0.00 6.46
6484 6637 2.950975 GTTCCACGGTCAAAACCCTAAA 59.049 45.455 0.00 0.00 43.21 1.85
6509 6662 2.452813 CGAATCCCCGTGCGAACAG 61.453 63.158 0.00 0.00 0.00 3.16
6510 6663 2.433491 CGAATCCCCGTGCGAACA 60.433 61.111 0.00 0.00 0.00 3.18
6511 6664 2.030958 AACGAATCCCCGTGCGAAC 61.031 57.895 0.00 0.00 42.54 3.95
6551 6704 3.254024 ATCCGTTTCCGCCTGCAGT 62.254 57.895 13.81 0.00 0.00 4.40
6736 6906 9.831737 CTGGATATGGAATTAATTTCGATGAAC 57.168 33.333 1.43 0.00 34.89 3.18
6748 6918 5.843969 TGGCTGTAGTCTGGATATGGAATTA 59.156 40.000 0.00 0.00 0.00 1.40
6767 6937 2.361610 AACGGAGGGCATTGGCTG 60.362 61.111 10.31 1.09 40.87 4.85
6769 6939 3.508840 CGAACGGAGGGCATTGGC 61.509 66.667 0.70 0.70 40.13 4.52
6812 6982 0.807496 GCTGCCAACTGGTCTGAATC 59.193 55.000 0.00 0.00 37.57 2.52
6885 7055 3.950794 TTGCTGACGTGGCGATCCC 62.951 63.158 0.00 0.00 0.00 3.85
6891 7061 0.169009 GGAATTCTTGCTGACGTGGC 59.831 55.000 5.23 0.00 0.00 5.01
6895 7065 2.086869 ACCATGGAATTCTTGCTGACG 58.913 47.619 21.47 0.00 0.00 4.35
6908 7083 4.100084 CTCCGCTGCCACCATGGA 62.100 66.667 21.47 0.00 40.96 3.41
7018 7193 7.121168 TGTTTAGCTATTGAAATCCACCAAGAG 59.879 37.037 0.00 0.00 35.42 2.85
7031 7206 6.946340 TCTTGTCCATCTGTTTAGCTATTGA 58.054 36.000 0.00 0.00 0.00 2.57
7101 7276 0.824109 AGCTTCGATGGTGATCCGAA 59.176 50.000 1.79 4.15 39.58 4.30
7119 7294 3.539604 CACCTCCTTAATGGCTTCTCAG 58.460 50.000 0.00 0.00 35.26 3.35
7201 7376 6.101997 GCAGGAGAAACAAAAATATGGGAAG 58.898 40.000 0.00 0.00 0.00 3.46
7202 7377 5.336372 CGCAGGAGAAACAAAAATATGGGAA 60.336 40.000 0.00 0.00 0.00 3.97
7204 7379 4.423732 CGCAGGAGAAACAAAAATATGGG 58.576 43.478 0.00 0.00 0.00 4.00
7225 7400 1.019673 CAGAATGTCCCAATCTGCCG 58.980 55.000 0.00 0.00 35.13 5.69
7294 7469 0.093026 CGCGCAGTTTAGGTCGAAAG 59.907 55.000 8.75 0.00 0.00 2.62
7298 7473 4.191485 CGCGCGCAGTTTAGGTCG 62.191 66.667 32.61 6.38 0.00 4.79
7326 7501 1.741770 GATGACGCCGCCTTTCTGT 60.742 57.895 0.00 0.00 0.00 3.41
7385 7560 1.938577 CGAGTTCCTAGTAGTGCGCTA 59.061 52.381 9.73 1.99 0.00 4.26


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

AutoCloner maintained by Alex Coulton.