Multiple sequence alignment - TraesCS3B01G133800

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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 TraesCS3B01G133800 chr3B 100.000 5111 0 0 1 5111 116107176 116112286 0.000000e+00 9439.0
1 TraesCS3B01G133800 chr3D 90.950 4232 230 58 907 5101 70242168 70246283 0.000000e+00 5552.0
2 TraesCS3B01G133800 chr3D 93.766 385 15 2 1 376 70239985 70239601 2.060000e-158 569.0
3 TraesCS3B01G133800 chr3D 89.305 374 29 6 379 748 70240287 70240653 4.660000e-125 459.0
4 TraesCS3B01G133800 chr3D 95.865 266 10 1 1 266 70238249 70238513 3.660000e-116 429.0
5 TraesCS3B01G133800 chr3D 90.385 156 13 1 377 530 70237947 70237792 2.410000e-48 204.0
6 TraesCS3B01G133800 chr3D 96.226 53 1 1 709 761 70237790 70237739 9.120000e-13 86.1
7 TraesCS3B01G133800 chr3A 93.716 1273 65 8 2582 3846 81693975 81695240 0.000000e+00 1893.0
8 TraesCS3B01G133800 chr3A 93.750 1056 41 15 4062 5103 81695239 81696283 0.000000e+00 1561.0
9 TraesCS3B01G133800 chr3A 88.677 892 61 23 796 1661 81691944 81692821 0.000000e+00 1051.0
10 TraesCS3B01G133800 chr3A 91.092 348 29 2 2211 2556 81693309 81693656 2.150000e-128 470.0
11 TraesCS3B01G133800 chr3A 87.032 401 39 8 1795 2194 81692865 81693253 1.690000e-119 440.0
12 TraesCS3B01G133800 chr3A 95.489 266 12 0 1 266 81685155 81684890 4.730000e-115 425.0
13 TraesCS3B01G133800 chr3A 85.333 375 38 10 395 764 81675795 81675433 6.250000e-99 372.0
14 TraesCS3B01G133800 chr3A 89.831 236 18 6 379 610 81691372 81691605 1.080000e-76 298.0
15 TraesCS3B01G133800 chr1B 77.318 701 133 24 4352 5041 677913912 677914597 1.730000e-104 390.0
16 TraesCS3B01G133800 chr6A 86.136 339 35 8 1274 1608 73678826 73679156 6.290000e-94 355.0
17 TraesCS3B01G133800 chr6A 87.121 264 33 1 3 266 563488212 563488474 1.080000e-76 298.0
18 TraesCS3B01G133800 chr6A 93.750 112 4 3 264 373 591518340 591518230 1.140000e-36 165.0
19 TraesCS3B01G133800 chr5D 90.234 256 21 3 1 254 356096211 356096464 1.060000e-86 331.0
20 TraesCS3B01G133800 chr1A 83.573 347 54 3 4697 5041 584374170 584374515 6.380000e-84 322.0
21 TraesCS3B01G133800 chr1A 91.892 111 8 1 264 373 8360618 8360728 2.460000e-33 154.0
22 TraesCS3B01G133800 chr5B 87.925 265 30 2 3 266 487444083 487443820 1.380000e-80 311.0
23 TraesCS3B01G133800 chr5B 86.700 203 27 0 64 266 551737868 551737666 5.150000e-55 226.0
24 TraesCS3B01G133800 chr4B 87.259 259 33 0 8 266 168271298 168271040 3.870000e-76 296.0
25 TraesCS3B01G133800 chr4B 89.655 116 9 3 264 376 168269786 168269901 1.480000e-30 145.0
26 TraesCS3B01G133800 chr2A 87.259 259 32 1 8 266 21993567 21993310 1.390000e-75 294.0
27 TraesCS3B01G133800 chr7A 88.793 116 10 3 264 376 106409162 106409277 6.900000e-29 139.0
28 TraesCS3B01G133800 chr6B 83.750 80 12 1 679 757 701612010 701612089 1.970000e-09 75.0


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 TraesCS3B01G133800 chr3B 116107176 116112286 5110 False 9439.000000 9439 100.000 1 5111 1 chr3B.!!$F1 5110
1 TraesCS3B01G133800 chr3D 70238249 70246283 8034 False 2146.666667 5552 92.040 1 5101 3 chr3D.!!$F1 5100
2 TraesCS3B01G133800 chr3D 70237739 70239985 2246 True 286.366667 569 93.459 1 761 3 chr3D.!!$R1 760
3 TraesCS3B01G133800 chr3A 81691372 81696283 4911 False 952.166667 1893 90.683 379 5103 6 chr3A.!!$F1 4724
4 TraesCS3B01G133800 chr1B 677913912 677914597 685 False 390.000000 390 77.318 4352 5041 1 chr1B.!!$F1 689

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
681 3409 0.032952 TGCTGTTAGTCCACCACGTC 59.967 55.000 0.00 0.0 0.00 4.34 F
782 3771 3.209410 TGGCCATTTTCGCATTGTTTTT 58.791 36.364 0.00 0.0 0.00 1.94 F
1737 6109 1.201965 GCTTCAATTTCGGCTCTGTCG 60.202 52.381 0.00 0.0 0.00 4.35 F
3035 7751 0.255890 GGAATGCTAACAGGGAGGCA 59.744 55.000 0.00 0.0 39.06 4.75 F
3693 8412 1.153289 CAGCCCTGGGATCGTGAAG 60.153 63.158 19.27 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 6077 0.178924 ATTGAAGCAAACCCCAGGCT 60.179 50.0 0.00 0.0 40.14 4.58 R
1860 6235 0.391661 ATTGAGCGACCGAAGCACAT 60.392 50.0 0.00 0.0 35.34 3.21 R
3693 8412 0.321122 CTGTGAGGCTGACAAGGGAC 60.321 60.0 8.44 0.0 0.00 4.46 R
3846 8566 0.240945 GTTGCTCAACCCACCGAATG 59.759 55.0 1.45 0.0 35.36 2.67 R
4646 9393 0.464036 TCTTTCAGACCGTGCTGTGT 59.536 50.0 0.00 0.0 37.20 3.72 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
383 3108 6.318648 GTGAGCAAAATACAATACTGGGATGA 59.681 38.462 0.00 0.00 0.00 2.92
384 3109 7.013655 GTGAGCAAAATACAATACTGGGATGAT 59.986 37.037 0.00 0.00 0.00 2.45
432 3157 2.662596 GTCGTGAGGATGTGGGCA 59.337 61.111 0.00 0.00 0.00 5.36
517 3244 2.808206 GCGTGGTAGGGGGAGATGG 61.808 68.421 0.00 0.00 0.00 3.51
547 3274 3.515286 GGGACGAGACGGATGCGA 61.515 66.667 15.49 0.00 0.00 5.10
597 3325 1.343431 GGGGCTAGACCTAACCACCC 61.343 65.000 16.16 0.71 39.10 4.61
615 3343 1.543802 CCCGGTTGATGCTAGCAAAAA 59.456 47.619 23.54 15.96 0.00 1.94
662 3390 0.548031 ATCAGCGTCCATGTTGGGAT 59.452 50.000 0.00 0.00 39.62 3.85
669 3397 2.722094 GTCCATGTTGGGATGCTGTTA 58.278 47.619 0.00 0.00 39.62 2.41
681 3409 0.032952 TGCTGTTAGTCCACCACGTC 59.967 55.000 0.00 0.00 0.00 4.34
694 3422 3.744426 CCACCACGTCCTTACTAGTTTTG 59.256 47.826 0.00 0.00 0.00 2.44
703 3431 8.347771 ACGTCCTTACTAGTTTTGAAATTTTCC 58.652 33.333 0.00 0.00 0.00 3.13
777 3766 3.264104 AGAATTGGCCATTTTCGCATTG 58.736 40.909 6.09 0.00 0.00 2.82
782 3771 3.209410 TGGCCATTTTCGCATTGTTTTT 58.791 36.364 0.00 0.00 0.00 1.94
813 4035 6.876804 AGAAACTTTCGCATTTAACATTTGC 58.123 32.000 0.00 0.00 34.02 3.68
910 5271 4.990426 GGATGTGGAATGTTTTTCCTTGTG 59.010 41.667 6.00 0.00 39.31 3.33
1024 5385 3.576004 CAGGCTTGCAGCAGTCTC 58.424 61.111 9.78 0.00 44.75 3.36
1332 5693 9.169468 GTATGATTAAATATGTGGAAAACTGCG 57.831 33.333 0.00 0.00 0.00 5.18
1426 5795 8.744652 TGAGTTGAAATTAAAACTGAAGGTGAA 58.255 29.630 9.71 0.00 36.77 3.18
1469 5838 4.359434 TGTGTAGTTATGGGAAGCACAA 57.641 40.909 0.00 0.00 33.28 3.33
1528 5897 9.017669 GTCTCCACGTACTATTATTTGTACTTG 57.982 37.037 0.00 8.07 38.10 3.16
1678 6050 6.542370 TCTTGGATAGTTATAAGTGCCAAAGC 59.458 38.462 20.71 0.71 33.96 3.51
1708 6080 7.391148 TCATGTTACTGAGGAAAAATTAGCC 57.609 36.000 0.00 0.00 0.00 3.93
1709 6081 7.175104 TCATGTTACTGAGGAAAAATTAGCCT 58.825 34.615 0.00 0.00 33.97 4.58
1711 6083 5.710099 TGTTACTGAGGAAAAATTAGCCTGG 59.290 40.000 0.00 0.00 30.70 4.45
1727 6099 2.871637 GCCTGGGGTTTGCTTCAATTTC 60.872 50.000 0.00 0.00 0.00 2.17
1735 6107 1.896220 TGCTTCAATTTCGGCTCTGT 58.104 45.000 0.00 0.00 0.00 3.41
1737 6109 1.201965 GCTTCAATTTCGGCTCTGTCG 60.202 52.381 0.00 0.00 0.00 4.35
1738 6110 2.337583 CTTCAATTTCGGCTCTGTCGA 58.662 47.619 0.00 0.00 38.09 4.20
1756 6128 2.890847 GATGCACAGTAGCGCGGACT 62.891 60.000 8.83 11.68 37.31 3.85
1764 6136 1.756950 TAGCGCGGACTCTTCCCAT 60.757 57.895 8.83 0.00 38.99 4.00
1774 6146 3.309121 GGACTCTTCCCATTTTCCATCCA 60.309 47.826 0.00 0.00 35.57 3.41
1778 6150 5.433051 ACTCTTCCCATTTTCCATCCAGATA 59.567 40.000 0.00 0.00 0.00 1.98
1779 6151 6.103797 ACTCTTCCCATTTTCCATCCAGATAT 59.896 38.462 0.00 0.00 0.00 1.63
1780 6152 6.546484 TCTTCCCATTTTCCATCCAGATATC 58.454 40.000 0.00 0.00 0.00 1.63
1787 6162 3.458044 TCCATCCAGATATCGCTAGGT 57.542 47.619 0.00 0.00 0.00 3.08
1791 6166 4.262635 CCATCCAGATATCGCTAGGTTTGT 60.263 45.833 0.00 0.00 0.00 2.83
1793 6168 3.321111 TCCAGATATCGCTAGGTTTGTCC 59.679 47.826 0.00 0.00 0.00 4.02
1819 6194 7.006509 TCCTGATTTTTCTCTGAAACCTGAAT 58.993 34.615 0.00 0.00 0.00 2.57
1860 6235 7.878127 CAGTTACTAATTTCTTTCCAGGACTGA 59.122 37.037 0.00 0.00 31.59 3.41
1870 6245 0.742281 CCAGGACTGATGTGCTTCGG 60.742 60.000 0.00 0.00 42.28 4.30
1874 6249 1.687494 GACTGATGTGCTTCGGTCGC 61.687 60.000 10.07 0.00 40.98 5.19
1887 6264 1.754803 TCGGTCGCTCAATAGGTTGAT 59.245 47.619 0.00 0.00 43.08 2.57
1924 6301 1.791785 GACTATGAAGCTGCGATCTGC 59.208 52.381 9.33 3.07 46.70 4.26
1938 6315 5.175127 TGCGATCTGCTAACTGAAAATACA 58.825 37.500 10.16 0.00 46.63 2.29
1942 6319 7.777816 GCGATCTGCTAACTGAAAATACATCAG 60.778 40.741 2.17 2.17 44.24 2.90
1943 6320 6.668541 TCTGCTAACTGAAAATACATCAGC 57.331 37.500 3.57 0.00 46.56 4.26
1944 6321 6.409704 TCTGCTAACTGAAAATACATCAGCT 58.590 36.000 3.57 0.00 46.56 4.24
1956 6333 8.538409 AAAATACATCAGCTGGTTGAAAATTC 57.462 30.769 15.13 0.00 0.00 2.17
1996 6373 6.999272 GGATCTTCAGTAGAGGACATAGTGTA 59.001 42.308 0.00 0.00 36.02 2.90
2000 6377 6.392625 TCAGTAGAGGACATAGTGTAATGC 57.607 41.667 0.00 0.00 0.00 3.56
2001 6378 6.129874 TCAGTAGAGGACATAGTGTAATGCT 58.870 40.000 0.00 0.00 0.00 3.79
2002 6379 6.607600 TCAGTAGAGGACATAGTGTAATGCTT 59.392 38.462 0.00 0.00 0.00 3.91
2003 6380 7.124298 TCAGTAGAGGACATAGTGTAATGCTTT 59.876 37.037 0.00 0.00 0.00 3.51
2004 6381 8.414003 CAGTAGAGGACATAGTGTAATGCTTTA 58.586 37.037 0.00 0.00 0.00 1.85
2005 6382 9.148879 AGTAGAGGACATAGTGTAATGCTTTAT 57.851 33.333 0.00 0.00 0.00 1.40
2006 6383 9.765795 GTAGAGGACATAGTGTAATGCTTTATT 57.234 33.333 0.00 0.00 0.00 1.40
2007 6384 8.668510 AGAGGACATAGTGTAATGCTTTATTG 57.331 34.615 0.00 0.00 0.00 1.90
2008 6385 7.227512 AGAGGACATAGTGTAATGCTTTATTGC 59.772 37.037 0.00 0.00 32.65 3.56
2033 6410 8.846211 GCTTTTGCATTATAAGGGTATCAGTTA 58.154 33.333 0.00 0.00 46.58 2.24
2109 6486 9.678260 AGAGAAGTAGCAAGAAAATGTATTCAT 57.322 29.630 0.00 0.00 35.59 2.57
2126 6503 3.998099 TCATTAGACCTGAGATGCTCG 57.002 47.619 0.00 0.00 32.35 5.03
2147 6524 2.310577 GCTAGTTTGCTTGCTGAAACG 58.689 47.619 0.00 0.00 39.71 3.60
2158 6535 3.673746 TGCTGAAACGTTGACTCTTTG 57.326 42.857 0.00 0.00 0.00 2.77
2179 6556 3.444742 TGAATAAGATTTGCTGGTGCCTG 59.555 43.478 0.00 0.00 38.71 4.85
2180 6557 1.176527 TAAGATTTGCTGGTGCCTGC 58.823 50.000 12.33 12.33 40.57 4.85
2183 6560 1.228644 ATTTGCTGGTGCCTGCTGA 60.229 52.632 18.45 9.22 40.75 4.26
2184 6561 1.248785 ATTTGCTGGTGCCTGCTGAG 61.249 55.000 18.45 0.00 40.75 3.35
2209 6594 2.941720 CTGATGCCTTAGTTGCCTCTTC 59.058 50.000 0.00 0.00 0.00 2.87
2259 6675 4.161333 GCTTGCAGCAGTACTTTGTTATG 58.839 43.478 0.00 0.00 41.89 1.90
2263 6679 5.518812 TGCAGCAGTACTTTGTTATGTTTG 58.481 37.500 0.00 0.00 0.00 2.93
2270 6686 7.484959 GCAGTACTTTGTTATGTTTGCCTAATC 59.515 37.037 0.00 0.00 0.00 1.75
2283 6699 6.040278 TGTTTGCCTAATCACACAATTTCAGA 59.960 34.615 0.00 0.00 0.00 3.27
2312 6728 7.479980 TGCCATTGCAATAGTATTTTGTAGAC 58.520 34.615 12.53 0.00 46.66 2.59
2329 6745 2.657143 AGACGCAAAAGGGTTTTACCA 58.343 42.857 0.00 0.00 41.02 3.25
2491 6908 9.212641 CTTATCGATCTATTCCATTGTGATTGT 57.787 33.333 0.00 0.00 0.00 2.71
2772 7488 7.940688 TGGTATGCAGATGATTGTATTCTGAAT 59.059 33.333 8.14 8.14 39.36 2.57
2987 7703 6.371809 TCTTATGGTTTGTTCTTGTGTGAC 57.628 37.500 0.00 0.00 0.00 3.67
3035 7751 0.255890 GGAATGCTAACAGGGAGGCA 59.744 55.000 0.00 0.00 39.06 4.75
3215 7931 7.237471 TGGCTAATGTTTCCAGGATCAGATATA 59.763 37.037 0.00 0.00 0.00 0.86
3305 8022 1.336440 TGAAGTTGGTGCATTTCGGTG 59.664 47.619 0.00 0.00 0.00 4.94
3372 8089 9.025041 AGGAGGGTTTATTTCAAGTTTATTCAG 57.975 33.333 0.00 0.00 0.00 3.02
3390 8107 6.645790 ATTCAGAAGTCTGTTGAATTGCTT 57.354 33.333 8.14 0.00 44.12 3.91
3391 8108 5.428496 TCAGAAGTCTGTTGAATTGCTTG 57.572 39.130 8.14 0.00 44.12 4.01
3393 8110 5.357878 TCAGAAGTCTGTTGAATTGCTTGTT 59.642 36.000 8.14 0.00 44.12 2.83
3406 8123 1.612950 TGCTTGTTTTCACCGCATGAT 59.387 42.857 0.00 0.00 37.11 2.45
3434 8153 4.287766 ACCTGGTGAAAAGTAGTGATCC 57.712 45.455 0.00 0.00 0.00 3.36
3444 8163 4.564940 AAGTAGTGATCCGATTCCGTAC 57.435 45.455 0.00 0.00 0.00 3.67
3454 8173 2.603110 CCGATTCCGTACTTGTGTCATG 59.397 50.000 0.00 0.00 0.00 3.07
3525 8244 2.027100 GGTCAGGGTTAGCAAGCTTAGT 60.027 50.000 0.00 0.00 0.00 2.24
3636 8355 2.734079 GAGCTTTGTGAAGGAGAAGTCG 59.266 50.000 0.00 0.00 33.34 4.18
3648 8367 4.340617 AGGAGAAGTCGTTTCTGATCTCT 58.659 43.478 9.15 0.00 46.12 3.10
3669 8388 2.036256 AAAGGCGCCCTTGCTGAT 59.964 55.556 26.15 0.00 43.92 2.90
3693 8412 1.153289 CAGCCCTGGGATCGTGAAG 60.153 63.158 19.27 0.00 0.00 3.02
3747 8466 1.486310 CTAGGCACATTACAGGAGGCA 59.514 52.381 0.00 0.00 0.00 4.75
3787 8507 2.037902 TGCCGAGTAGTCCACATGAAAA 59.962 45.455 0.00 0.00 0.00 2.29
3797 8517 5.630121 AGTCCACATGAAAATTCACACCTA 58.370 37.500 0.00 0.00 40.49 3.08
3852 8572 4.764679 TTTCTGGAAACATGTCATTCGG 57.235 40.909 0.00 0.00 41.51 4.30
3853 8573 3.417069 TCTGGAAACATGTCATTCGGT 57.583 42.857 0.00 0.00 41.51 4.69
3878 8598 4.869861 GGTTGAGCAACTGAAATGTTGTTT 59.130 37.500 12.54 0.00 46.33 2.83
3881 8601 6.691754 TGAGCAACTGAAATGTTGTTTCTA 57.308 33.333 8.78 0.00 46.33 2.10
3885 8605 7.771183 AGCAACTGAAATGTTGTTTCTAGAAA 58.229 30.769 13.99 13.99 46.33 2.52
3901 8621 6.618287 TCTAGAAACATGTGGTTCAGTTTG 57.382 37.500 12.83 0.00 43.92 2.93
3903 8623 4.277476 AGAAACATGTGGTTCAGTTTGGA 58.723 39.130 12.83 0.00 43.92 3.53
3904 8624 4.097892 AGAAACATGTGGTTCAGTTTGGAC 59.902 41.667 12.83 0.00 43.92 4.02
3905 8625 3.297134 ACATGTGGTTCAGTTTGGACT 57.703 42.857 0.00 0.00 36.25 3.85
3906 8626 3.631250 ACATGTGGTTCAGTTTGGACTT 58.369 40.909 0.00 0.00 32.54 3.01
3907 8627 4.787551 ACATGTGGTTCAGTTTGGACTTA 58.212 39.130 0.00 0.00 32.54 2.24
3908 8628 5.197451 ACATGTGGTTCAGTTTGGACTTAA 58.803 37.500 0.00 0.00 32.54 1.85
3911 8631 6.783708 TGTGGTTCAGTTTGGACTTAAAAT 57.216 33.333 0.00 0.00 32.54 1.82
3914 8634 7.762159 TGTGGTTCAGTTTGGACTTAAAATTTC 59.238 33.333 0.00 0.00 32.54 2.17
3935 8655 8.786937 ATTTCGATCATGATTTTAAATCGTGG 57.213 30.769 28.71 18.24 39.98 4.94
3937 8657 4.911610 CGATCATGATTTTAAATCGTGGGC 59.088 41.667 28.71 21.79 36.12 5.36
3956 8676 1.709182 GATTTTGCCGCAATTGCCG 59.291 52.632 24.24 18.71 37.91 5.69
3961 8681 4.418401 GCCGCAATTGCCGCTGAA 62.418 61.111 28.95 0.00 41.04 3.02
3962 8682 2.491152 CCGCAATTGCCGCTGAAT 59.509 55.556 24.24 0.00 37.91 2.57
3963 8683 1.587088 CCGCAATTGCCGCTGAATC 60.587 57.895 24.24 0.00 37.91 2.52
3964 8684 1.935917 CGCAATTGCCGCTGAATCG 60.936 57.895 24.24 3.35 37.91 3.34
3965 8685 2.226225 GCAATTGCCGCTGAATCGC 61.226 57.895 20.06 0.00 34.31 4.58
3966 8686 1.137194 CAATTGCCGCTGAATCGCA 59.863 52.632 0.00 0.00 0.00 5.10
3967 8687 1.135699 CAATTGCCGCTGAATCGCAC 61.136 55.000 0.00 0.00 0.00 5.34
3968 8688 2.270297 AATTGCCGCTGAATCGCACC 62.270 55.000 0.00 0.00 0.00 5.01
3969 8689 4.695993 TGCCGCTGAATCGCACCA 62.696 61.111 0.00 0.00 0.00 4.17
3970 8690 3.204827 GCCGCTGAATCGCACCAT 61.205 61.111 0.00 0.00 0.00 3.55
3979 8699 2.427812 TGAATCGCACCATGATTTGCAT 59.572 40.909 12.54 4.74 38.76 3.96
3995 8715 0.171903 GCATGCAGGTGAAAATCGCT 59.828 50.000 14.21 0.00 0.00 4.93
4003 8723 2.237143 AGGTGAAAATCGCTGGAGATCA 59.763 45.455 0.00 0.00 0.00 2.92
4004 8724 2.611292 GGTGAAAATCGCTGGAGATCAG 59.389 50.000 0.00 0.00 46.03 2.90
4005 8725 2.611292 GTGAAAATCGCTGGAGATCAGG 59.389 50.000 0.00 0.00 43.54 3.86
4006 8726 1.601430 GAAAATCGCTGGAGATCAGGC 59.399 52.381 0.00 0.00 43.54 4.85
4007 8727 0.179034 AAATCGCTGGAGATCAGGCC 60.179 55.000 0.00 0.00 43.54 5.19
4008 8728 2.374830 AATCGCTGGAGATCAGGCCG 62.375 60.000 0.00 0.00 43.54 6.13
4009 8729 4.598894 CGCTGGAGATCAGGCCGG 62.599 72.222 0.00 0.00 43.54 6.13
4016 8746 1.120530 GAGATCAGGCCGGTTTAGGA 58.879 55.000 1.90 0.00 0.00 2.94
4028 8758 4.276460 CCGGTTTAGGATAAAATTTCGCG 58.724 43.478 0.00 0.00 0.00 5.87
4140 8870 1.162181 GCTCACAAGTGCAGTGCAGA 61.162 55.000 20.42 10.98 40.08 4.26
4148 8883 1.227943 TGCAGTGCAGAACAGGACC 60.228 57.895 15.37 0.00 33.32 4.46
4169 8907 2.492881 CACAGCATCATTGGTAAGGCAA 59.507 45.455 0.00 0.00 30.88 4.52
4170 8908 3.056678 CACAGCATCATTGGTAAGGCAAA 60.057 43.478 0.00 0.00 30.88 3.68
4171 8909 3.056607 ACAGCATCATTGGTAAGGCAAAC 60.057 43.478 0.00 0.00 30.88 2.93
4172 8910 2.164219 AGCATCATTGGTAAGGCAAACG 59.836 45.455 0.00 0.00 0.00 3.60
4194 8932 3.270877 AGCCAATTACATGACTCGGAAC 58.729 45.455 0.00 0.00 0.00 3.62
4448 9187 4.758251 CTGTCCGTCATGGCGCCA 62.758 66.667 34.80 34.80 37.80 5.69
4629 9376 3.242518 CAGCAAAGATTCACTCGTCGTA 58.757 45.455 0.00 0.00 0.00 3.43
4865 9613 4.335647 AAGTCCAGCGGGCACAGG 62.336 66.667 0.00 0.00 0.00 4.00
5061 9809 0.095245 AAGCACAAACGCATCGATCG 59.905 50.000 9.36 9.36 0.00 3.69
5090 9838 6.221659 TCAGATGATGATGAGATACACTTGC 58.778 40.000 0.00 0.00 31.12 4.01
5091 9839 6.041751 TCAGATGATGATGAGATACACTTGCT 59.958 38.462 0.00 0.00 31.12 3.91
5103 9851 2.681706 ACACTTGCTCACTTCTCGATG 58.318 47.619 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
227 237 7.606456 CCTAGGCAGTTAGTGAAATCAGTAAAA 59.394 37.037 11.28 0.00 41.73 1.52
337 1399 7.062605 GCTCACCAAATTGTTACTCATCATTTG 59.937 37.037 0.00 0.00 35.61 2.32
409 3134 3.461773 CATCCTCACGACCGCCCT 61.462 66.667 0.00 0.00 0.00 5.19
547 3274 2.187946 GATAGTGCTGGCGGCTGT 59.812 61.111 20.66 9.02 42.39 4.40
597 3325 4.037690 GCTATTTTTGCTAGCATCAACCG 58.962 43.478 20.13 7.64 41.03 4.44
601 3329 3.312421 GGACGCTATTTTTGCTAGCATCA 59.688 43.478 20.13 5.55 41.35 3.07
615 3343 2.041922 TCCCAGCCTGGACGCTAT 60.042 61.111 13.74 0.00 40.96 2.97
622 3350 1.094785 CAAATAACGTCCCAGCCTGG 58.905 55.000 2.91 2.91 37.25 4.45
662 3390 0.032952 GACGTGGTGGACTAACAGCA 59.967 55.000 0.00 0.00 45.57 4.41
664 3392 0.966920 AGGACGTGGTGGACTAACAG 59.033 55.000 0.00 0.00 0.00 3.16
669 3397 2.224967 ACTAGTAAGGACGTGGTGGACT 60.225 50.000 0.00 0.00 0.00 3.85
694 3422 8.534954 AGTAATAAAGGGCTAGGGAAAATTTC 57.465 34.615 0.00 0.00 0.00 2.17
757 3746 3.002102 ACAATGCGAAAATGGCCAATTC 58.998 40.909 10.96 16.80 0.00 2.17
783 3772 8.467402 TGTTAAATGCGAAAGTTTCTCAAAAA 57.533 26.923 12.01 4.88 0.00 1.94
784 3773 8.641499 ATGTTAAATGCGAAAGTTTCTCAAAA 57.359 26.923 12.01 5.18 0.00 2.44
785 3774 8.641499 AATGTTAAATGCGAAAGTTTCTCAAA 57.359 26.923 12.01 0.44 0.00 2.69
786 3775 8.538856 CAAATGTTAAATGCGAAAGTTTCTCAA 58.461 29.630 12.01 0.00 0.00 3.02
788 3777 7.003648 GCAAATGTTAAATGCGAAAGTTTCTC 58.996 34.615 13.56 6.35 0.00 2.87
832 4054 9.979578 AGCTCAATCTGTCTGTATATTCTAAAG 57.020 33.333 0.00 0.00 0.00 1.85
841 4063 4.100189 GGGTACAGCTCAATCTGTCTGTAT 59.900 45.833 0.00 0.00 45.32 2.29
842 4064 3.447586 GGGTACAGCTCAATCTGTCTGTA 59.552 47.826 0.00 0.00 45.32 2.74
843 4065 2.234908 GGGTACAGCTCAATCTGTCTGT 59.765 50.000 0.00 0.00 45.32 3.41
844 4066 2.419297 GGGGTACAGCTCAATCTGTCTG 60.419 54.545 0.00 0.00 45.32 3.51
845 4067 1.834263 GGGGTACAGCTCAATCTGTCT 59.166 52.381 0.00 0.00 45.32 3.41
846 4068 1.555075 TGGGGTACAGCTCAATCTGTC 59.445 52.381 0.00 0.00 45.32 3.51
887 5230 4.990426 CACAAGGAAAAACATTCCACATCC 59.010 41.667 9.69 0.00 41.00 3.51
889 5232 4.101430 AGCACAAGGAAAAACATTCCACAT 59.899 37.500 9.69 0.00 41.00 3.21
905 5248 4.431131 ATCCGGGCCCAGCACAAG 62.431 66.667 24.92 2.52 0.00 3.16
1437 5806 2.713863 AACTACACAAAACCGGTGGA 57.286 45.000 8.52 0.00 40.54 4.02
1438 5807 3.189702 CCATAACTACACAAAACCGGTGG 59.810 47.826 8.52 3.27 40.54 4.61
1469 5838 9.777297 AGTACCAAATCAATTGTTTGCTTTATT 57.223 25.926 19.51 4.25 37.32 1.40
1501 5870 8.284945 AGTACAAATAATAGTACGTGGAGACA 57.715 34.615 0.00 0.00 43.98 3.41
1502 5871 9.017669 CAAGTACAAATAATAGTACGTGGAGAC 57.982 37.037 0.00 0.00 42.78 3.36
1507 5876 8.692110 TGTCCAAGTACAAATAATAGTACGTG 57.308 34.615 0.00 10.32 44.63 4.49
1603 5972 3.700038 ACCCCATACGAAAACACACAAAA 59.300 39.130 0.00 0.00 0.00 2.44
1684 6056 7.121168 CAGGCTAATTTTTCCTCAGTAACATGA 59.879 37.037 0.00 0.00 0.00 3.07
1685 6057 7.253422 CAGGCTAATTTTTCCTCAGTAACATG 58.747 38.462 0.00 0.00 0.00 3.21
1691 6063 3.564352 CCCCAGGCTAATTTTTCCTCAGT 60.564 47.826 0.00 0.00 0.00 3.41
1697 6069 3.007940 AGCAAACCCCAGGCTAATTTTTC 59.992 43.478 0.00 0.00 35.82 2.29
1705 6077 0.178924 ATTGAAGCAAACCCCAGGCT 60.179 50.000 0.00 0.00 40.14 4.58
1708 6080 2.610232 CCGAAATTGAAGCAAACCCCAG 60.610 50.000 0.00 0.00 0.00 4.45
1709 6081 1.342819 CCGAAATTGAAGCAAACCCCA 59.657 47.619 0.00 0.00 0.00 4.96
1711 6083 1.000843 AGCCGAAATTGAAGCAAACCC 59.999 47.619 0.00 0.00 0.00 4.11
1727 6099 2.125952 TGTGCATCGACAGAGCCG 60.126 61.111 0.00 0.00 0.00 5.52
1756 6128 4.886755 ATCTGGATGGAAAATGGGAAGA 57.113 40.909 0.00 0.00 0.00 2.87
1764 6136 4.593206 ACCTAGCGATATCTGGATGGAAAA 59.407 41.667 0.34 0.00 0.00 2.29
1787 6162 5.940617 TCAGAGAAAAATCAGGAGGACAAA 58.059 37.500 0.00 0.00 0.00 2.83
1791 6166 5.073691 AGGTTTCAGAGAAAAATCAGGAGGA 59.926 40.000 0.00 0.00 0.00 3.71
1793 6168 6.000219 TCAGGTTTCAGAGAAAAATCAGGAG 59.000 40.000 0.00 0.00 0.00 3.69
1819 6194 1.186200 AACTGCTATGACCTCTCGCA 58.814 50.000 0.00 0.00 0.00 5.10
1860 6235 0.391661 ATTGAGCGACCGAAGCACAT 60.392 50.000 0.00 0.00 35.34 3.21
1924 6301 6.992063 ACCAGCTGATGTATTTTCAGTTAG 57.008 37.500 17.39 0.00 42.12 2.34
1956 6333 4.573607 TGAAGATCCAGATCGAAGCAATTG 59.426 41.667 0.00 0.00 42.48 2.32
2000 6377 8.947055 ACCCTTATAATGCAAAAGCAATAAAG 57.053 30.769 0.00 0.00 0.00 1.85
2003 6380 9.360901 TGATACCCTTATAATGCAAAAGCAATA 57.639 29.630 0.00 0.00 0.00 1.90
2004 6381 8.248904 TGATACCCTTATAATGCAAAAGCAAT 57.751 30.769 0.00 0.00 0.00 3.56
2005 6382 7.341769 ACTGATACCCTTATAATGCAAAAGCAA 59.658 33.333 0.00 0.00 0.00 3.91
2006 6383 6.833416 ACTGATACCCTTATAATGCAAAAGCA 59.167 34.615 0.00 0.00 0.00 3.91
2007 6384 7.277174 ACTGATACCCTTATAATGCAAAAGC 57.723 36.000 0.00 0.00 0.00 3.51
2033 6410 8.635765 TCAATCATTTAGCTAGAAAACACCTT 57.364 30.769 0.00 0.00 0.00 3.50
2109 6486 0.747255 GCCGAGCATCTCAGGTCTAA 59.253 55.000 0.00 0.00 34.00 2.10
2126 6503 2.666026 GTTTCAGCAAGCAAACTAGCC 58.334 47.619 0.00 0.00 34.23 3.93
2147 6524 7.540055 CCAGCAAATCTTATTCAAAGAGTCAAC 59.460 37.037 0.00 0.00 0.00 3.18
2158 6535 3.736126 GCAGGCACCAGCAAATCTTATTC 60.736 47.826 0.00 0.00 44.61 1.75
2209 6594 8.004344 TGACATACAAAACAAAACACGTTTTTG 58.996 29.630 22.78 22.78 42.41 2.44
2254 6670 8.532977 AAATTGTGTGATTAGGCAAACATAAC 57.467 30.769 0.00 0.00 36.00 1.89
2259 6675 6.446318 TCTGAAATTGTGTGATTAGGCAAAC 58.554 36.000 0.00 0.00 0.00 2.93
2263 6679 6.441093 TGATCTGAAATTGTGTGATTAGGC 57.559 37.500 0.00 0.00 0.00 3.93
2270 6686 4.443913 TGGCATGATCTGAAATTGTGTG 57.556 40.909 0.00 0.00 0.00 3.82
2297 6713 6.882678 ACCCTTTTGCGTCTACAAAATACTAT 59.117 34.615 3.18 0.00 45.66 2.12
2312 6728 1.334243 TCGTGGTAAAACCCTTTTGCG 59.666 47.619 0.00 0.00 37.50 4.85
2446 6862 7.611855 TCGATAAGCATTAGGATATGAGAGACA 59.388 37.037 0.00 0.00 31.76 3.41
2630 7341 5.826601 TGTGTTGTGCAAAAGTATGAGAA 57.173 34.783 0.00 0.00 0.00 2.87
2987 7703 2.991190 GTCATTTTGCACAAGCTGATGG 59.009 45.455 0.00 0.00 42.74 3.51
3289 8006 4.243383 GCACCGAAATGCACCAAC 57.757 55.556 0.00 0.00 45.39 3.77
3305 8022 2.094417 GCATCAAACCTACTTCGACAGC 59.906 50.000 0.00 0.00 0.00 4.40
3372 8089 6.531240 TGAAAACAAGCAATTCAACAGACTTC 59.469 34.615 0.00 0.00 30.60 3.01
3390 8107 2.890311 AGGAAATCATGCGGTGAAAACA 59.110 40.909 0.00 0.00 40.97 2.83
3391 8108 3.575965 AGGAAATCATGCGGTGAAAAC 57.424 42.857 0.00 0.00 40.97 2.43
3393 8110 3.442273 GGTAAGGAAATCATGCGGTGAAA 59.558 43.478 0.00 0.00 40.97 2.69
3406 8123 6.059484 CACTACTTTTCACCAGGTAAGGAAA 58.941 40.000 5.70 3.07 0.00 3.13
3434 8153 2.603110 CCATGACACAAGTACGGAATCG 59.397 50.000 0.00 0.00 43.02 3.34
3444 8163 1.081242 GCCGCAACCATGACACAAG 60.081 57.895 0.00 0.00 0.00 3.16
3454 8173 0.512518 GCAAAGAAAATGCCGCAACC 59.487 50.000 0.00 0.00 37.85 3.77
3525 8244 7.936847 AGGAATTGCATAATCATTAGTAACGGA 59.063 33.333 0.00 0.00 0.00 4.69
3555 8274 4.052608 CTGCAACATTGTGAAGAAATGCA 58.947 39.130 9.11 9.11 38.36 3.96
3636 8355 3.616379 CGCCTTTCTCAGAGATCAGAAAC 59.384 47.826 0.00 0.00 34.39 2.78
3648 8367 2.672996 GCAAGGGCGCCTTTCTCA 60.673 61.111 28.56 0.00 41.69 3.27
3669 8388 1.342074 CGATCCCAGGGCTGATCTTA 58.658 55.000 0.00 0.00 36.15 2.10
3693 8412 0.321122 CTGTGAGGCTGACAAGGGAC 60.321 60.000 8.44 0.00 0.00 4.46
3787 8507 4.154195 GCATCGAACAGTTTAGGTGTGAAT 59.846 41.667 0.00 0.00 0.00 2.57
3797 8517 1.069906 GCTGAACGCATCGAACAGTTT 60.070 47.619 0.00 0.00 38.92 2.66
3846 8566 0.240945 GTTGCTCAACCCACCGAATG 59.759 55.000 1.45 0.00 35.36 2.67
3852 8572 2.362077 ACATTTCAGTTGCTCAACCCAC 59.638 45.455 8.95 0.00 42.06 4.61
3853 8573 2.665165 ACATTTCAGTTGCTCAACCCA 58.335 42.857 8.95 0.00 42.06 4.51
3878 8598 5.530915 CCAAACTGAACCACATGTTTCTAGA 59.469 40.000 10.75 0.00 37.29 2.43
3881 8601 4.097892 GTCCAAACTGAACCACATGTTTCT 59.902 41.667 10.75 0.00 37.29 2.52
3885 8605 3.297134 AGTCCAAACTGAACCACATGT 57.703 42.857 0.00 0.00 33.32 3.21
3889 8609 7.043656 CGAAATTTTAAGTCCAAACTGAACCAC 60.044 37.037 0.00 0.00 35.36 4.16
3895 8615 8.853345 CATGATCGAAATTTTAAGTCCAAACTG 58.147 33.333 0.00 0.00 35.36 3.16
3896 8616 8.792633 TCATGATCGAAATTTTAAGTCCAAACT 58.207 29.630 0.00 0.00 37.32 2.66
3911 8631 7.192913 CCCACGATTTAAAATCATGATCGAAA 58.807 34.615 16.97 13.43 41.37 3.46
3914 8634 4.911610 GCCCACGATTTAAAATCATGATCG 59.088 41.667 9.06 9.78 43.65 3.69
3937 8657 1.709182 GGCAATTGCGGCAAAATCG 59.291 52.632 23.48 9.29 43.26 3.34
3939 8659 3.873449 CGGCAATTGCGGCAAAAT 58.127 50.000 23.48 9.01 43.26 1.82
3947 8667 2.226225 GCGATTCAGCGGCAATTGC 61.226 57.895 22.47 22.47 41.14 3.56
3948 8668 1.135699 GTGCGATTCAGCGGCAATTG 61.136 55.000 1.45 0.00 38.58 2.32
3949 8669 1.137404 GTGCGATTCAGCGGCAATT 59.863 52.632 1.45 0.00 38.58 2.32
3950 8670 2.764314 GGTGCGATTCAGCGGCAAT 61.764 57.895 1.45 0.00 38.58 3.56
3953 8673 3.204827 ATGGTGCGATTCAGCGGC 61.205 61.111 0.00 0.00 45.75 6.53
3954 8674 1.162181 ATCATGGTGCGATTCAGCGG 61.162 55.000 0.00 0.00 45.75 5.52
3956 8676 2.456989 CAAATCATGGTGCGATTCAGC 58.543 47.619 0.00 0.00 43.23 4.26
3960 8680 2.816689 CATGCAAATCATGGTGCGATT 58.183 42.857 10.87 0.00 46.81 3.34
3961 8681 2.502213 CATGCAAATCATGGTGCGAT 57.498 45.000 10.87 5.02 46.81 4.58
3969 8689 3.965379 TTTCACCTGCATGCAAATCAT 57.035 38.095 22.88 2.36 35.31 2.45
3970 8690 3.747854 TTTTCACCTGCATGCAAATCA 57.252 38.095 22.88 3.29 0.00 2.57
3979 8699 0.250684 TCCAGCGATTTTCACCTGCA 60.251 50.000 0.00 0.00 0.00 4.41
3982 8702 2.237143 TGATCTCCAGCGATTTTCACCT 59.763 45.455 0.00 0.00 0.00 4.00
3995 8715 0.830648 CTAAACCGGCCTGATCTCCA 59.169 55.000 0.00 0.00 0.00 3.86
4003 8723 4.337274 CGAAATTTTATCCTAAACCGGCCT 59.663 41.667 0.00 0.00 0.00 5.19
4004 8724 4.603985 CGAAATTTTATCCTAAACCGGCC 58.396 43.478 0.00 0.00 0.00 6.13
4005 8725 4.039703 GCGAAATTTTATCCTAAACCGGC 58.960 43.478 0.00 0.00 0.00 6.13
4006 8726 4.276460 CGCGAAATTTTATCCTAAACCGG 58.724 43.478 0.00 0.00 0.00 5.28
4007 8727 4.276460 CCGCGAAATTTTATCCTAAACCG 58.724 43.478 8.23 0.00 0.00 4.44
4008 8728 4.039703 GCCGCGAAATTTTATCCTAAACC 58.960 43.478 8.23 0.00 0.00 3.27
4009 8729 4.664188 TGCCGCGAAATTTTATCCTAAAC 58.336 39.130 8.23 0.00 0.00 2.01
4046 8776 7.533289 TTAAAATCACGGGAGAAAGGAAATT 57.467 32.000 0.00 0.00 0.00 1.82
4051 8781 5.648092 ACTGATTAAAATCACGGGAGAAAGG 59.352 40.000 0.00 0.00 40.32 3.11
4052 8782 6.371548 TCACTGATTAAAATCACGGGAGAAAG 59.628 38.462 0.00 0.00 40.32 2.62
4140 8870 2.165167 CAATGATGCTGTGGTCCTGTT 58.835 47.619 0.00 0.00 0.00 3.16
4148 8883 2.093890 TGCCTTACCAATGATGCTGTG 58.906 47.619 0.00 0.00 0.00 3.66
4172 8910 3.179443 TCCGAGTCATGTAATTGGCTC 57.821 47.619 0.00 0.00 43.41 4.70
4176 8914 5.163854 GGAGTTGTTCCGAGTCATGTAATTG 60.164 44.000 0.00 0.00 35.91 2.32
4207 8945 3.669536 CCCTTTCTCCTGTGACTTCTTC 58.330 50.000 0.00 0.00 0.00 2.87
4208 8946 2.224646 GCCCTTTCTCCTGTGACTTCTT 60.225 50.000 0.00 0.00 0.00 2.52
4209 8947 1.349357 GCCCTTTCTCCTGTGACTTCT 59.651 52.381 0.00 0.00 0.00 2.85
4210 8948 1.349357 AGCCCTTTCTCCTGTGACTTC 59.651 52.381 0.00 0.00 0.00 3.01
4253 8992 2.668120 GCCCCAGCTCTGCTCTTCT 61.668 63.158 0.00 0.00 36.40 2.85
4448 9187 1.617322 TCTCCGATACCGCTGCTATT 58.383 50.000 0.00 0.00 0.00 1.73
4629 9376 5.174395 GCTGTGTGTGATCTACTGATCTTT 58.826 41.667 7.42 0.00 46.84 2.52
4646 9393 0.464036 TCTTTCAGACCGTGCTGTGT 59.536 50.000 0.00 0.00 37.20 3.72
4865 9613 2.125793 GACGGGTACAACGAGGCC 60.126 66.667 14.89 0.00 34.93 5.19
5052 9800 3.826466 TCATCTGATGTACGATCGATGC 58.174 45.455 24.34 11.42 33.45 3.91
5075 9823 5.659463 AGAAGTGAGCAAGTGTATCTCATC 58.341 41.667 0.00 0.00 38.85 2.92
5077 9825 4.379918 CGAGAAGTGAGCAAGTGTATCTCA 60.380 45.833 0.00 0.00 33.40 3.27
5078 9826 4.101942 CGAGAAGTGAGCAAGTGTATCTC 58.898 47.826 0.00 0.00 0.00 2.75
5079 9827 3.759086 TCGAGAAGTGAGCAAGTGTATCT 59.241 43.478 0.00 0.00 0.00 1.98
5080 9828 4.098055 TCGAGAAGTGAGCAAGTGTATC 57.902 45.455 0.00 0.00 0.00 2.24
5081 9829 4.428209 CATCGAGAAGTGAGCAAGTGTAT 58.572 43.478 0.00 0.00 0.00 2.29
5082 9830 3.367395 CCATCGAGAAGTGAGCAAGTGTA 60.367 47.826 0.00 0.00 0.00 2.90
5083 9831 2.611473 CCATCGAGAAGTGAGCAAGTGT 60.611 50.000 0.00 0.00 0.00 3.55
5084 9832 1.998315 CCATCGAGAAGTGAGCAAGTG 59.002 52.381 0.00 0.00 0.00 3.16
5085 9833 1.674221 GCCATCGAGAAGTGAGCAAGT 60.674 52.381 0.00 0.00 0.00 3.16
5086 9834 1.005340 GCCATCGAGAAGTGAGCAAG 58.995 55.000 0.00 0.00 0.00 4.01
5087 9835 0.610174 AGCCATCGAGAAGTGAGCAA 59.390 50.000 0.00 0.00 0.00 3.91
5088 9836 0.610174 AAGCCATCGAGAAGTGAGCA 59.390 50.000 0.00 0.00 0.00 4.26
5089 9837 1.134848 AGAAGCCATCGAGAAGTGAGC 60.135 52.381 0.00 0.00 0.00 4.26
5090 9838 2.808244 GAGAAGCCATCGAGAAGTGAG 58.192 52.381 0.00 0.00 0.00 3.51
5091 9839 2.949451 GAGAAGCCATCGAGAAGTGA 57.051 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.