Multiple sequence alignment - TraesCS7A01G245900

Loading Multiple Alignment...

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 TraesCS7A01G245900 chr7A 100.000 4832 0 0 1 4832 224092877 224088046 0.000000e+00 8924
1 TraesCS7A01G245900 chr7D 92.428 3962 156 48 213 4106 212812255 212808370 0.000000e+00 5522
2 TraesCS7A01G245900 chr7D 91.156 735 57 6 4100 4832 212632046 212631318 0.000000e+00 990
3 TraesCS7A01G245900 chr7B 93.500 2154 95 12 1959 4106 188974418 188976532 0.000000e+00 3160
4 TraesCS7A01G245900 chr7B 92.829 753 35 6 855 1590 188973232 188973982 0.000000e+00 1074
5 TraesCS7A01G245900 chr7B 83.705 896 45 27 12 850 188972269 188973120 0.000000e+00 752
6 TraesCS7A01G245900 chr7B 85.857 700 60 20 4136 4832 189202197 189202860 0.000000e+00 708
7 TraesCS7A01G245900 chr7B 93.030 330 20 2 1637 1963 188973978 188974307 3.380000e-131 479


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 TraesCS7A01G245900 chr7A 224088046 224092877 4831 True 8924.00 8924 100.000 1 4832 1 chr7A.!!$R1 4831
1 TraesCS7A01G245900 chr7D 212808370 212812255 3885 True 5522.00 5522 92.428 213 4106 1 chr7D.!!$R2 3893
2 TraesCS7A01G245900 chr7D 212631318 212632046 728 True 990.00 990 91.156 4100 4832 1 chr7D.!!$R1 732
3 TraesCS7A01G245900 chr7B 188972269 188976532 4263 False 1366.25 3160 90.766 12 4106 4 chr7B.!!$F2 4094
4 TraesCS7A01G245900 chr7B 189202197 189202860 663 False 708.00 708 85.857 4136 4832 1 chr7B.!!$F1 696

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
398 430 0.026156 GCCAAAAACGCAACTGCAAC 59.974 50.0 2.12 0.0 42.21 4.17 F
1644 1850 0.836606 TGTCAGTCAGGGTTTGCTCA 59.163 50.0 0.00 0.0 0.00 4.26 F
2666 2996 0.749454 CCTGCCACAATCAGTAGGGC 60.749 60.0 0.00 0.0 44.82 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 1985 0.961019 TGGCTGTTCTGGAATGTTGC 59.039 50.0 0.0 0.0 0.0 4.17 R
2713 3043 0.034896 GGGTGGTGATTCGACTGTGT 59.965 55.0 0.0 0.0 0.0 3.72 R
3852 4182 0.250640 GGCATGATACCAGCTCAGGG 60.251 60.0 0.0 0.0 0.0 4.45 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
21 22 1.845809 CGTGTCCCTGTGCTTTGCTC 61.846 60.000 0.00 0.00 0.00 4.26
67 68 2.176055 GCGACGTCTCTGAAGCGA 59.824 61.111 14.70 0.00 0.00 4.93
81 82 2.501128 GCGACCTGCCTGCTATGA 59.499 61.111 0.00 0.00 37.76 2.15
82 83 1.593750 GCGACCTGCCTGCTATGAG 60.594 63.158 0.00 0.00 37.76 2.90
83 84 1.593750 CGACCTGCCTGCTATGAGC 60.594 63.158 0.00 0.00 42.82 4.26
84 85 1.227793 GACCTGCCTGCTATGAGCC 60.228 63.158 0.00 0.00 41.51 4.70
85 86 2.112718 CCTGCCTGCTATGAGCCC 59.887 66.667 0.00 0.00 41.51 5.19
86 87 2.112718 CTGCCTGCTATGAGCCCC 59.887 66.667 0.00 0.00 41.51 5.80
127 138 2.766828 ACCTTAAAGAGACCCGGATCTG 59.233 50.000 0.64 0.00 0.00 2.90
168 179 1.865865 TCGCTCACCTTTTCTGTGAC 58.134 50.000 0.00 0.00 37.80 3.67
174 185 3.194861 TCACCTTTTCTGTGACGACTTG 58.805 45.455 0.00 0.00 37.80 3.16
191 202 3.486383 ACTTGGCTCGAATTTTTCTCCA 58.514 40.909 0.00 0.00 0.00 3.86
196 207 3.005367 GGCTCGAATTTTTCTCCAAACCA 59.995 43.478 0.00 0.00 0.00 3.67
204 215 8.647226 CGAATTTTTCTCCAAACCATTTCATAC 58.353 33.333 0.00 0.00 0.00 2.39
210 221 3.085533 CCAAACCATTTCATACACCGGA 58.914 45.455 9.46 0.00 0.00 5.14
211 222 3.128589 CCAAACCATTTCATACACCGGAG 59.871 47.826 9.46 1.26 0.00 4.63
361 393 4.704103 TGCTCCTCGGCCCTCTGT 62.704 66.667 0.00 0.00 0.00 3.41
383 415 1.741401 CTCGCCGATCAACAGCCAA 60.741 57.895 0.00 0.00 0.00 4.52
386 418 0.039617 CGCCGATCAACAGCCAAAAA 60.040 50.000 0.00 0.00 0.00 1.94
398 430 0.026156 GCCAAAAACGCAACTGCAAC 59.974 50.000 2.12 0.00 42.21 4.17
419 451 6.400568 CAACTAGTCCGTATAAAAACCTCCA 58.599 40.000 0.00 0.00 0.00 3.86
420 452 6.803366 ACTAGTCCGTATAAAAACCTCCAT 57.197 37.500 0.00 0.00 0.00 3.41
422 454 5.687166 AGTCCGTATAAAAACCTCCATCA 57.313 39.130 0.00 0.00 0.00 3.07
424 456 5.878669 AGTCCGTATAAAAACCTCCATCAAC 59.121 40.000 0.00 0.00 0.00 3.18
426 458 5.045432 TCCGTATAAAAACCTCCATCAACCT 60.045 40.000 0.00 0.00 0.00 3.50
434 469 2.582636 ACCTCCATCAACCTTAGCCATT 59.417 45.455 0.00 0.00 0.00 3.16
452 487 1.024271 TTCCAGCAACAACAGACAGC 58.976 50.000 0.00 0.00 0.00 4.40
456 494 1.655350 GCAACAACAGACAGCGCAC 60.655 57.895 11.47 0.00 0.00 5.34
484 522 3.058293 GCACAGCACAGTATACAGCAAAA 60.058 43.478 5.50 0.00 0.00 2.44
664 729 3.041946 CCCTCCCATCTGTAAAGCTACT 58.958 50.000 0.00 0.00 0.00 2.57
677 751 5.878116 TGTAAAGCTACTCTCTCTCTCTCAC 59.122 44.000 0.00 0.00 0.00 3.51
678 752 4.568072 AAGCTACTCTCTCTCTCTCACA 57.432 45.455 0.00 0.00 0.00 3.58
679 753 3.873910 AGCTACTCTCTCTCTCTCACAC 58.126 50.000 0.00 0.00 0.00 3.82
680 754 3.263170 AGCTACTCTCTCTCTCTCACACA 59.737 47.826 0.00 0.00 0.00 3.72
681 755 3.374058 GCTACTCTCTCTCTCTCACACAC 59.626 52.174 0.00 0.00 0.00 3.82
682 756 3.500448 ACTCTCTCTCTCTCACACACA 57.500 47.619 0.00 0.00 0.00 3.72
683 757 3.146066 ACTCTCTCTCTCTCACACACAC 58.854 50.000 0.00 0.00 0.00 3.82
684 758 3.145286 CTCTCTCTCTCTCACACACACA 58.855 50.000 0.00 0.00 0.00 3.72
685 759 2.881513 TCTCTCTCTCTCACACACACAC 59.118 50.000 0.00 0.00 0.00 3.82
686 760 2.620585 CTCTCTCTCTCACACACACACA 59.379 50.000 0.00 0.00 0.00 3.72
730 804 2.125673 CTACGTTGGTCCAGCCCG 60.126 66.667 0.00 3.38 36.04 6.13
741 820 1.078497 CCAGCCCGCACTATCAACA 60.078 57.895 0.00 0.00 0.00 3.33
755 834 6.459298 GCACTATCAACATCTCAAAATCCAGG 60.459 42.308 0.00 0.00 0.00 4.45
760 839 1.753073 CATCTCAAAATCCAGGGCCAC 59.247 52.381 6.18 0.00 0.00 5.01
794 873 2.540228 GCGCCGGTACCCATTTAGC 61.540 63.158 6.25 0.00 0.00 3.09
800 879 1.810412 CGGTACCCATTTAGCAGGAGC 60.810 57.143 6.25 0.00 42.56 4.70
834 916 2.113860 AGCATGATTACCGCACAGTT 57.886 45.000 0.00 0.00 0.00 3.16
835 917 1.739466 AGCATGATTACCGCACAGTTG 59.261 47.619 0.00 0.00 0.00 3.16
836 918 1.737236 GCATGATTACCGCACAGTTGA 59.263 47.619 0.00 0.00 0.00 3.18
850 932 6.533723 CCGCACAGTTGAGATACAAAATACTA 59.466 38.462 0.00 0.00 40.36 1.82
852 934 7.275779 CGCACAGTTGAGATACAAAATACTACT 59.724 37.037 0.00 0.00 40.36 2.57
853 935 8.383619 GCACAGTTGAGATACAAAATACTACTG 58.616 37.037 0.00 0.00 40.36 2.74
899 1088 5.594317 ACATACAACAAGCCATTATTCCCTC 59.406 40.000 0.00 0.00 0.00 4.30
910 1099 2.032356 TATTCCCTCCCTCCCTCCGG 62.032 65.000 0.00 0.00 0.00 5.14
1334 1532 2.231478 TGTTTCTCGGTCTAAGGAGCAG 59.769 50.000 0.00 0.00 39.68 4.24
1336 1534 1.064946 CTCGGTCTAAGGAGCAGCG 59.935 63.158 0.00 0.00 39.68 5.18
1395 1593 1.131126 CACTGTCCGCCATGCTAAAAG 59.869 52.381 0.00 0.00 0.00 2.27
1430 1628 3.695606 ATCTGGCTGTCGTGGCGT 61.696 61.111 0.00 0.00 35.06 5.68
1468 1666 4.630894 TTGCTTATTCTTATTGTGGGCG 57.369 40.909 0.00 0.00 0.00 6.13
1480 1678 1.299089 GTGGGCGTGTTCTTTGTGC 60.299 57.895 0.00 0.00 0.00 4.57
1534 1740 5.247792 ACTTTCTTTACCGATAGTCCTTGGT 59.752 40.000 0.00 0.00 38.51 3.67
1541 1747 5.687166 ACCGATAGTCCTTGGTTGAAATA 57.313 39.130 0.00 0.00 0.00 1.40
1542 1748 6.057321 ACCGATAGTCCTTGGTTGAAATAA 57.943 37.500 0.00 0.00 0.00 1.40
1576 1782 5.188434 ACAGTGTGCTCAAATATGCTATGT 58.812 37.500 0.00 0.00 0.00 2.29
1590 1796 4.439305 TGCTATGTTGATTGGAGTTTGC 57.561 40.909 0.00 0.00 0.00 3.68
1591 1797 3.193267 TGCTATGTTGATTGGAGTTTGCC 59.807 43.478 0.00 0.00 0.00 4.52
1596 1802 3.153919 GTTGATTGGAGTTTGCCAGGTA 58.846 45.455 0.00 0.00 39.52 3.08
1597 1803 3.517296 TGATTGGAGTTTGCCAGGTAA 57.483 42.857 0.00 0.00 39.52 2.85
1606 1812 3.897505 AGTTTGCCAGGTAAAAGCTCAAT 59.102 39.130 3.97 0.00 0.00 2.57
1612 1818 4.400567 GCCAGGTAAAAGCTCAATCTTGAT 59.599 41.667 0.00 0.00 36.46 2.57
1614 1820 6.095440 GCCAGGTAAAAGCTCAATCTTGATTA 59.905 38.462 0.00 0.00 36.46 1.75
1631 1837 5.241403 TGATTAACAAGGTGGATGTCAGT 57.759 39.130 0.00 0.00 0.00 3.41
1644 1850 0.836606 TGTCAGTCAGGGTTTGCTCA 59.163 50.000 0.00 0.00 0.00 4.26
1704 1910 7.938140 ACAAGCAAGGCTATTTTCTTGTATA 57.062 32.000 14.00 0.00 41.31 1.47
1755 1961 3.689872 AATAGGTGTCTAGAGCCCTGA 57.310 47.619 16.93 5.34 0.00 3.86
1779 1985 4.326826 TGTCTTCTGCCTGGTCTAATTTG 58.673 43.478 0.00 0.00 0.00 2.32
1798 2004 0.961019 GCAACATTCCAGAACAGCCA 59.039 50.000 0.00 0.00 0.00 4.75
1799 2005 1.547372 GCAACATTCCAGAACAGCCAT 59.453 47.619 0.00 0.00 0.00 4.40
1819 2028 5.009010 GCCATCTTATACAGGTTGGTGAATG 59.991 44.000 0.00 0.00 31.82 2.67
1870 2079 1.859080 CTAAATCGTACCGCCAAGCTC 59.141 52.381 0.00 0.00 0.00 4.09
1895 2104 7.875554 TCTTTGGTTGGCTATAAATGTTTTTCC 59.124 33.333 0.00 0.00 0.00 3.13
1937 2146 7.331791 AGGAACCACTAGTAATCTGAACAATC 58.668 38.462 0.00 0.00 0.00 2.67
1968 2292 6.267496 ACCATTTTAGCATGTACTTGGTTC 57.733 37.500 17.30 0.00 32.48 3.62
1969 2293 6.010219 ACCATTTTAGCATGTACTTGGTTCT 58.990 36.000 17.30 5.85 32.48 3.01
2027 2351 6.709018 ATGTTGCCCTTTGTTGGTATATAC 57.291 37.500 4.14 4.14 0.00 1.47
2173 2498 6.818142 ACTGCAAAAGAAAGCAAAACAGTAAT 59.182 30.769 0.00 0.00 40.73 1.89
2174 2499 7.978975 ACTGCAAAAGAAAGCAAAACAGTAATA 59.021 29.630 0.00 0.00 40.73 0.98
2175 2500 8.709386 TGCAAAAGAAAGCAAAACAGTAATAA 57.291 26.923 0.00 0.00 37.90 1.40
2237 2562 4.574013 TGAACCACATTCATTTTGTTTGCC 59.426 37.500 0.00 0.00 42.62 4.52
2248 2573 6.222389 TCATTTTGTTTGCCGAATCATCTTT 58.778 32.000 0.00 0.00 0.00 2.52
2439 2769 1.556911 GAAGATGAGGTGGCCTTCTCA 59.443 52.381 23.82 23.82 43.15 3.27
2443 2773 0.907486 TGAGGTGGCCTTCTCAGATG 59.093 55.000 19.81 0.00 35.37 2.90
2631 2961 0.892755 AATCGAAGGCTACGACCACA 59.107 50.000 0.00 0.00 42.37 4.17
2661 2991 1.530013 GCAAGCCTGCCACAATCAGT 61.530 55.000 0.00 0.00 43.26 3.41
2666 2996 0.749454 CCTGCCACAATCAGTAGGGC 60.749 60.000 0.00 0.00 44.82 5.19
2713 3043 1.486310 AGAACCTCAGCAGTGTTGTGA 59.514 47.619 10.22 1.88 0.00 3.58
2943 3273 0.749649 ATAGGGACGCTGCTCTTCAG 59.250 55.000 1.57 0.00 45.62 3.02
3006 3336 2.350134 CTGCTGAGCCTGGAAGCA 59.650 61.111 15.46 15.46 44.36 3.91
3060 3390 2.200899 GCAACGAGCACCAAAAACAAT 58.799 42.857 0.00 0.00 44.79 2.71
3135 3465 0.742281 CATTGCCCGTCAGTCAGGAG 60.742 60.000 0.00 0.00 0.00 3.69
3168 3498 5.163301 GGAAGGGTTCTTGCAGATAGTATCA 60.163 44.000 12.66 0.00 40.47 2.15
3177 3507 2.928731 GCAGATAGTATCAGAAGCCCGC 60.929 54.545 12.66 0.00 0.00 6.13
3202 3532 3.817084 CTCCATCAAACAGTTCTGCAAGA 59.183 43.478 0.00 0.00 44.68 3.02
3246 3576 2.401766 CGACAATGGGCTGGCAGAC 61.402 63.158 20.86 17.26 0.00 3.51
3288 3618 1.126890 CATATCAGCTGACACTCGCG 58.873 55.000 20.97 0.00 0.00 5.87
3339 3669 2.235650 TCTGGAAGCTCTGATGAACCAG 59.764 50.000 0.00 0.00 42.97 4.00
3342 3672 0.034670 AAGCTCTGATGAACCAGGCC 60.035 55.000 0.00 0.00 33.66 5.19
3351 3681 0.327924 TGAACCAGGCCATGTACCAG 59.672 55.000 5.01 0.00 0.00 4.00
3390 3720 2.809601 CAGAAGAACGGGTCGCCG 60.810 66.667 0.00 0.00 39.31 6.46
3438 3768 0.031721 AGGAGAACTTCGCGTCGTTT 59.968 50.000 5.77 2.39 0.00 3.60
3441 3771 0.575390 AGAACTTCGCGTCGTTTGTG 59.425 50.000 5.77 0.00 0.00 3.33
3519 3849 1.122019 AGGACTTCAGCCGGTTCTGT 61.122 55.000 1.90 0.00 35.63 3.41
3630 3960 1.451567 CATCTGGCTGCTCCACCTG 60.452 63.158 0.00 0.00 40.72 4.00
3636 3966 4.340246 CTGCTCCACCTGCTGGCA 62.340 66.667 9.95 0.40 40.39 4.92
3642 3972 1.751927 CCACCTGCTGGCATTCTCC 60.752 63.158 9.95 0.00 36.63 3.71
3750 4080 4.373116 TCGCAGCAGAACCCGTCC 62.373 66.667 0.00 0.00 0.00 4.79
3768 4098 1.526917 CCGGGTGAAGATCATGGCC 60.527 63.158 0.00 0.00 0.00 5.36
3789 4119 2.890371 CCCGGGTTCTACGTCCAG 59.110 66.667 14.18 0.00 0.00 3.86
3836 4166 4.666412 TCTGCAGATATAGCTAGACCCT 57.334 45.455 13.74 0.00 0.00 4.34
3837 4167 4.339748 TCTGCAGATATAGCTAGACCCTG 58.660 47.826 13.74 12.67 0.00 4.45
3838 4168 4.085733 CTGCAGATATAGCTAGACCCTGT 58.914 47.826 8.42 0.00 0.00 4.00
3839 4169 3.829026 TGCAGATATAGCTAGACCCTGTG 59.171 47.826 16.30 2.10 0.00 3.66
3840 4170 3.367910 GCAGATATAGCTAGACCCTGTGC 60.368 52.174 16.30 7.40 0.00 4.57
3841 4171 3.194542 CAGATATAGCTAGACCCTGTGCC 59.805 52.174 0.00 0.00 0.00 5.01
3852 4182 2.036089 GACCCTGTGCCTGTAGTATAGC 59.964 54.545 0.00 0.00 0.00 2.97
3874 4204 0.390492 TGAGCTGGTATCATGCCTCG 59.610 55.000 0.00 0.00 0.00 4.63
3894 4224 5.008217 CCTCGTGGTTTTGTTTTGACTGATA 59.992 40.000 0.00 0.00 0.00 2.15
3938 4268 2.800096 GCATTTGCGTGTTGAGTGG 58.200 52.632 0.00 0.00 0.00 4.00
3939 4269 0.310543 GCATTTGCGTGTTGAGTGGA 59.689 50.000 0.00 0.00 0.00 4.02
3940 4270 1.068333 GCATTTGCGTGTTGAGTGGAT 60.068 47.619 0.00 0.00 0.00 3.41
3941 4271 2.587956 CATTTGCGTGTTGAGTGGATG 58.412 47.619 0.00 0.00 0.00 3.51
3942 4272 1.674359 TTTGCGTGTTGAGTGGATGT 58.326 45.000 0.00 0.00 0.00 3.06
3943 4273 1.674359 TTGCGTGTTGAGTGGATGTT 58.326 45.000 0.00 0.00 0.00 2.71
3944 4274 0.943673 TGCGTGTTGAGTGGATGTTG 59.056 50.000 0.00 0.00 0.00 3.33
3945 4275 0.238289 GCGTGTTGAGTGGATGTTGG 59.762 55.000 0.00 0.00 0.00 3.77
3946 4276 1.593196 CGTGTTGAGTGGATGTTGGT 58.407 50.000 0.00 0.00 0.00 3.67
3947 4277 1.946768 CGTGTTGAGTGGATGTTGGTT 59.053 47.619 0.00 0.00 0.00 3.67
3948 4278 2.032030 CGTGTTGAGTGGATGTTGGTTC 60.032 50.000 0.00 0.00 0.00 3.62
3949 4279 2.948979 GTGTTGAGTGGATGTTGGTTCA 59.051 45.455 0.00 0.00 0.00 3.18
4013 4343 6.590677 GCTAATCCTTAACGGGTAGATTGATC 59.409 42.308 0.00 0.00 0.00 2.92
4014 4344 4.579454 TCCTTAACGGGTAGATTGATCG 57.421 45.455 0.00 0.00 0.00 3.69
4015 4345 4.209538 TCCTTAACGGGTAGATTGATCGA 58.790 43.478 0.00 0.00 0.00 3.59
4016 4346 4.831155 TCCTTAACGGGTAGATTGATCGAT 59.169 41.667 0.00 0.00 0.00 3.59
4024 4354 6.479001 ACGGGTAGATTGATCGATAGTTTTTG 59.521 38.462 0.00 0.00 37.40 2.44
4027 4357 9.057089 GGGTAGATTGATCGATAGTTTTTGATT 57.943 33.333 0.00 0.00 37.40 2.57
4033 4363 6.649155 TGATCGATAGTTTTTGATTCCTCCA 58.351 36.000 0.00 0.00 37.40 3.86
4044 4374 3.544684 TGATTCCTCCATGGTTTGATCG 58.455 45.455 12.58 0.00 37.07 3.69
4088 4418 4.242475 CATGCATTTGAACTGCTGATGTT 58.758 39.130 8.94 0.00 40.34 2.71
4127 4457 9.550811 GTTTTAGGAGTTTGTATATTTTGACGG 57.449 33.333 0.00 0.00 0.00 4.79
4204 4536 2.292292 GAGACTGAGGTATCTTCGGCTC 59.708 54.545 0.00 0.00 31.65 4.70
4278 4610 2.798148 AAACCGACTGCCGATCCACC 62.798 60.000 0.00 0.00 41.76 4.61
4284 4616 1.144936 CTGCCGATCCACCTTCTCC 59.855 63.158 0.00 0.00 0.00 3.71
4289 4621 1.264749 CGATCCACCTTCTCCCACCA 61.265 60.000 0.00 0.00 0.00 4.17
4367 4699 3.936203 AAGGACTCAACGGCGGCA 61.936 61.111 13.24 0.00 0.00 5.69
4368 4700 3.469863 AAGGACTCAACGGCGGCAA 62.470 57.895 13.24 0.00 0.00 4.52
4421 4753 1.173043 CAGCAGCCGAATGGGTTTTA 58.827 50.000 0.00 0.00 45.97 1.52
4424 4756 1.268539 GCAGCCGAATGGGTTTTATCG 60.269 52.381 0.00 0.00 45.97 2.92
4432 4764 2.051334 TGGGTTTTATCGGCATCTGG 57.949 50.000 0.00 0.00 0.00 3.86
4450 4782 3.186047 CGCGACTTTAGTGGGCCG 61.186 66.667 0.00 0.00 0.00 6.13
4453 4785 1.590147 CGACTTTAGTGGGCCGACT 59.410 57.895 24.69 24.69 0.00 4.18
4537 4869 9.687210 GAAAATACTTTTAGAAACGGGTTGAAT 57.313 29.630 0.00 0.00 31.94 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.972505 AAAGCACAGGGACACGCG 60.973 61.111 3.53 3.53 0.00 6.01
1 2 2.639286 CAAAGCACAGGGACACGC 59.361 61.111 0.00 0.00 0.00 5.34
2 3 1.845809 GAGCAAAGCACAGGGACACG 61.846 60.000 0.00 0.00 0.00 4.49
3 4 0.536006 AGAGCAAAGCACAGGGACAC 60.536 55.000 0.00 0.00 0.00 3.67
4 5 0.250467 GAGAGCAAAGCACAGGGACA 60.250 55.000 0.00 0.00 0.00 4.02
5 6 1.294659 CGAGAGCAAAGCACAGGGAC 61.295 60.000 0.00 0.00 0.00 4.46
6 7 1.004560 CGAGAGCAAAGCACAGGGA 60.005 57.895 0.00 0.00 0.00 4.20
7 8 3.571119 CGAGAGCAAAGCACAGGG 58.429 61.111 0.00 0.00 0.00 4.45
21 22 4.923893 TGGAAAATAATTGATGCTGCGAG 58.076 39.130 0.00 0.00 0.00 5.03
27 28 4.768583 TGGGCTTGGAAAATAATTGATGC 58.231 39.130 0.00 0.00 0.00 3.91
40 41 4.373116 GACGTCGCTGGGCTTGGA 62.373 66.667 0.00 0.00 0.00 3.53
41 42 4.379243 AGACGTCGCTGGGCTTGG 62.379 66.667 10.46 0.00 0.00 3.61
67 68 2.750657 GGGCTCATAGCAGGCAGGT 61.751 63.158 0.78 0.00 44.75 4.00
74 75 3.865383 CTGCGGGGGCTCATAGCA 61.865 66.667 0.78 1.70 44.75 3.49
75 76 4.632974 CCTGCGGGGGCTCATAGC 62.633 72.222 2.57 0.00 41.46 2.97
95 106 0.676782 CTTTAAGGTGGCGGTCCCTG 60.677 60.000 0.00 0.00 0.00 4.45
102 113 0.739813 CGGGTCTCTTTAAGGTGGCG 60.740 60.000 0.00 0.00 0.00 5.69
103 114 0.392595 CCGGGTCTCTTTAAGGTGGC 60.393 60.000 0.00 0.00 0.00 5.01
107 118 3.031736 TCAGATCCGGGTCTCTTTAAGG 58.968 50.000 16.33 1.32 0.00 2.69
127 138 0.625849 TCCCTCCCTGCTGGAAATTC 59.374 55.000 11.88 0.00 44.57 2.17
157 168 2.213499 AGCCAAGTCGTCACAGAAAAG 58.787 47.619 0.00 0.00 0.00 2.27
168 179 3.424962 GGAGAAAAATTCGAGCCAAGTCG 60.425 47.826 0.00 0.00 41.51 4.18
174 185 3.005367 TGGTTTGGAGAAAAATTCGAGCC 59.995 43.478 0.00 0.00 34.02 4.70
191 202 3.352648 CCTCCGGTGTATGAAATGGTTT 58.647 45.455 0.00 0.00 0.00 3.27
196 207 0.916086 TGGCCTCCGGTGTATGAAAT 59.084 50.000 3.32 0.00 0.00 2.17
204 215 1.526917 GGAATCATGGCCTCCGGTG 60.527 63.158 3.32 0.00 0.00 4.94
210 221 1.152881 GCTTCCGGAATCATGGCCT 60.153 57.895 19.21 0.00 0.00 5.19
211 222 2.196245 GGCTTCCGGAATCATGGCC 61.196 63.158 23.81 23.81 0.00 5.36
355 387 0.528684 GATCGGCGAGGAAACAGAGG 60.529 60.000 17.22 0.00 0.00 3.69
361 393 1.019278 GCTGTTGATCGGCGAGGAAA 61.019 55.000 17.22 6.67 38.74 3.13
383 415 2.032924 GGACTAGTTGCAGTTGCGTTTT 59.967 45.455 0.00 0.00 45.83 2.43
386 418 0.944311 CGGACTAGTTGCAGTTGCGT 60.944 55.000 0.00 0.00 45.83 5.24
398 430 6.812998 TGATGGAGGTTTTTATACGGACTAG 58.187 40.000 0.00 0.00 0.00 2.57
419 451 2.025037 TGCTGGAATGGCTAAGGTTGAT 60.025 45.455 0.00 0.00 0.00 2.57
420 452 1.354031 TGCTGGAATGGCTAAGGTTGA 59.646 47.619 0.00 0.00 0.00 3.18
422 454 2.171003 GTTGCTGGAATGGCTAAGGTT 58.829 47.619 0.00 0.00 0.00 3.50
424 456 1.838112 TGTTGCTGGAATGGCTAAGG 58.162 50.000 0.00 0.00 0.00 2.69
426 458 2.557924 CTGTTGTTGCTGGAATGGCTAA 59.442 45.455 0.00 0.00 0.00 3.09
434 469 1.159713 CGCTGTCTGTTGTTGCTGGA 61.160 55.000 0.00 0.00 0.00 3.86
475 513 4.083217 ACGTTTGACAGTGTTTTTGCTGTA 60.083 37.500 0.00 0.00 44.89 2.74
484 522 1.741145 GTTGGGACGTTTGACAGTGTT 59.259 47.619 0.00 0.00 0.00 3.32
602 663 5.570320 CCATCTACTGAAAGGAAAGGGAAA 58.430 41.667 0.00 0.00 39.30 3.13
605 666 3.282885 GCCATCTACTGAAAGGAAAGGG 58.717 50.000 0.00 0.00 39.30 3.95
606 667 3.691609 GTGCCATCTACTGAAAGGAAAGG 59.308 47.826 0.00 0.00 39.30 3.11
607 668 3.372206 CGTGCCATCTACTGAAAGGAAAG 59.628 47.826 0.00 0.00 39.30 2.62
664 729 2.881513 GTGTGTGTGTGAGAGAGAGAGA 59.118 50.000 0.00 0.00 0.00 3.10
680 754 5.474532 ACAGAATGATAAAGCACATGTGTGT 59.525 36.000 26.01 14.69 43.49 3.72
681 755 5.946298 ACAGAATGATAAAGCACATGTGTG 58.054 37.500 26.01 14.08 44.12 3.82
682 756 6.207221 TCAACAGAATGATAAAGCACATGTGT 59.793 34.615 26.01 10.04 39.69 3.72
683 757 6.525628 GTCAACAGAATGATAAAGCACATGTG 59.474 38.462 21.83 21.83 39.69 3.21
684 758 6.207221 TGTCAACAGAATGATAAAGCACATGT 59.793 34.615 0.00 0.00 39.69 3.21
685 759 6.525628 GTGTCAACAGAATGATAAAGCACATG 59.474 38.462 0.00 0.00 39.69 3.21
686 760 6.432162 AGTGTCAACAGAATGATAAAGCACAT 59.568 34.615 0.00 0.00 39.69 3.21
730 804 6.441093 TGGATTTTGAGATGTTGATAGTGC 57.559 37.500 0.00 0.00 0.00 4.40
741 820 1.683011 CGTGGCCCTGGATTTTGAGAT 60.683 52.381 0.00 0.00 0.00 2.75
760 839 3.818787 GCCAATGCAGGACCAGCG 61.819 66.667 4.22 0.00 37.47 5.18
794 873 0.179134 GGTGCTACGTAGTGCTCCTG 60.179 60.000 22.98 0.00 45.73 3.86
800 879 1.660607 CATGCTTGGTGCTACGTAGTG 59.339 52.381 22.98 7.01 41.03 2.74
850 932 3.508402 TGTCCGTGTATGTCATGTACAGT 59.492 43.478 0.33 0.00 42.70 3.55
852 934 4.522722 TTGTCCGTGTATGTCATGTACA 57.477 40.909 0.00 0.00 43.86 2.90
853 935 5.177881 TGTTTTGTCCGTGTATGTCATGTAC 59.822 40.000 0.00 0.00 0.00 2.90
1286 1484 1.727022 CGCAAAACAGGCAAGAGCG 60.727 57.895 0.00 0.00 43.41 5.03
1348 1546 3.818787 GCACCAATGGAGCTGCCG 61.819 66.667 14.43 0.00 40.66 5.69
1468 1666 1.278637 CGACCCGCACAAAGAACAC 59.721 57.895 0.00 0.00 0.00 3.32
1576 1782 2.380064 ACCTGGCAAACTCCAATCAA 57.620 45.000 0.00 0.00 35.36 2.57
1590 1796 6.521151 AATCAAGATTGAGCTTTTACCTGG 57.479 37.500 1.32 0.00 41.08 4.45
1591 1797 8.514594 TGTTAATCAAGATTGAGCTTTTACCTG 58.485 33.333 5.59 0.00 41.08 4.00
1612 1818 4.504864 CCTGACTGACATCCACCTTGTTAA 60.505 45.833 0.00 0.00 0.00 2.01
1614 1820 2.224621 CCTGACTGACATCCACCTTGTT 60.225 50.000 0.00 0.00 0.00 2.83
1627 1833 1.131638 AGTGAGCAAACCCTGACTGA 58.868 50.000 0.00 0.00 27.90 3.41
1628 1834 2.839486 TAGTGAGCAAACCCTGACTG 57.161 50.000 0.00 0.00 31.66 3.51
1629 1835 3.409026 CTTAGTGAGCAAACCCTGACT 57.591 47.619 0.00 0.00 33.78 3.41
1704 1910 6.515272 AAAAGATCATTGCCTTTCGTATGT 57.485 33.333 0.00 0.00 32.01 2.29
1755 1961 2.310779 TAGACCAGGCAGAAGACAGT 57.689 50.000 0.00 0.00 0.00 3.55
1779 1985 0.961019 TGGCTGTTCTGGAATGTTGC 59.039 50.000 0.00 0.00 0.00 4.17
1798 2004 6.058183 GCTCATTCACCAACCTGTATAAGAT 58.942 40.000 0.00 0.00 0.00 2.40
1799 2005 5.189736 AGCTCATTCACCAACCTGTATAAGA 59.810 40.000 0.00 0.00 0.00 2.10
1819 2028 1.634702 CACTGCGGAGAAGTTAGCTC 58.365 55.000 12.26 0.00 0.00 4.09
1870 2079 7.148656 CGGAAAAACATTTATAGCCAACCAAAG 60.149 37.037 0.00 0.00 0.00 2.77
1912 2121 6.681729 TTGTTCAGATTACTAGTGGTTCCT 57.318 37.500 5.39 0.00 0.00 3.36
1937 2146 9.638239 AAGTACATGCTAAAATGGTTTGTTATG 57.362 29.630 0.00 0.00 31.46 1.90
1947 2156 8.268850 ACTAGAACCAAGTACATGCTAAAATG 57.731 34.615 0.00 0.00 0.00 2.32
1968 2292 7.656412 AGAATGCAGACATAGTGACATACTAG 58.344 38.462 0.00 0.00 44.69 2.57
1969 2293 7.588497 AGAATGCAGACATAGTGACATACTA 57.412 36.000 0.00 0.00 45.50 1.82
2173 2498 9.349145 GTGACTTTTGCTTCTTTGTTTTAGTTA 57.651 29.630 0.00 0.00 0.00 2.24
2174 2499 7.330946 GGTGACTTTTGCTTCTTTGTTTTAGTT 59.669 33.333 0.00 0.00 0.00 2.24
2175 2500 6.811665 GGTGACTTTTGCTTCTTTGTTTTAGT 59.188 34.615 0.00 0.00 0.00 2.24
2197 2522 0.970937 TCAGCTCTAACCCCTCGGTG 60.971 60.000 0.00 0.00 43.71 4.94
2272 2602 7.986085 AGCAACAAGTGTCAATATTAGAAGT 57.014 32.000 0.00 0.00 0.00 3.01
2439 2769 3.727726 TGTGTTGTGATTGTCGACATCT 58.272 40.909 20.80 10.10 32.76 2.90
2443 2773 4.449068 AGAGAATGTGTTGTGATTGTCGAC 59.551 41.667 9.11 9.11 29.44 4.20
2652 2982 0.107017 CAGGGGCCCTACTGATTGTG 60.107 60.000 28.28 6.51 36.86 3.33
2661 2991 1.004758 ATCAGCTTCAGGGGCCCTA 59.995 57.895 28.28 10.38 29.64 3.53
2666 2996 0.396695 ATTGGCATCAGCTTCAGGGG 60.397 55.000 0.00 0.00 41.70 4.79
2713 3043 0.034896 GGGTGGTGATTCGACTGTGT 59.965 55.000 0.00 0.00 0.00 3.72
2748 3078 2.935849 GTTTGTCCCTTTTTGCCTTGTG 59.064 45.455 0.00 0.00 0.00 3.33
2889 3219 2.028203 AGCAAGCTCCTTCTTCAGAGAC 60.028 50.000 0.00 0.00 31.43 3.36
2943 3273 5.540911 GATGATCTCATCTCTCCAACTTCC 58.459 45.833 11.99 0.00 46.88 3.46
2968 3298 3.196685 AGCTTGCTAGTTAGTTCTCCCAG 59.803 47.826 0.00 0.00 0.00 4.45
2998 3328 4.815308 CAGTTCTGAGGAATATGCTTCCAG 59.185 45.833 6.05 0.00 41.00 3.86
3006 3336 5.428131 AGCCTTCTTCAGTTCTGAGGAATAT 59.572 40.000 21.42 11.62 34.24 1.28
3060 3390 2.558359 TCTCTTCGAGTGAGATTGCACA 59.442 45.455 13.81 0.00 41.19 4.57
3084 3414 1.153549 GACACCCACTGATCTCGCC 60.154 63.158 0.00 0.00 0.00 5.54
3135 3465 3.089284 CAAGAACCCTTCCACCATTACC 58.911 50.000 0.00 0.00 0.00 2.85
3168 3498 2.366167 ATGGAGAGGCGGGCTTCT 60.366 61.111 5.24 4.87 35.00 2.85
3177 3507 2.746362 GCAGAACTGTTTGATGGAGAGG 59.254 50.000 0.00 0.00 0.00 3.69
3246 3576 1.584380 GCAGGAGCAGGTTCAGCTTG 61.584 60.000 0.00 0.00 43.58 4.01
3288 3618 1.865865 TCACTTTCGAGTGCTTGTCC 58.134 50.000 1.78 0.00 39.49 4.02
3339 3669 0.462047 CGAAGTCCTGGTACATGGCC 60.462 60.000 0.00 0.00 38.20 5.36
3342 3672 3.193691 AGTTCTCGAAGTCCTGGTACATG 59.806 47.826 0.00 0.00 38.20 3.21
3351 3681 0.318784 ACGTGCAGTTCTCGAAGTCC 60.319 55.000 0.24 0.00 35.79 3.85
3390 3720 3.316573 CTTGGGGTCGAGGCACCTC 62.317 68.421 6.62 6.62 37.45 3.85
3519 3849 0.978907 TGCAGCTCATCTTCTGGTCA 59.021 50.000 0.00 0.00 0.00 4.02
3630 3960 1.382692 GGCTGAAGGAGAATGCCAGC 61.383 60.000 0.00 0.00 46.71 4.85
3636 3966 2.592308 GGCGGGCTGAAGGAGAAT 59.408 61.111 0.00 0.00 0.00 2.40
3720 4050 3.071206 TGCGACCTCTGCCTCTCC 61.071 66.667 0.00 0.00 0.00 3.71
3729 4059 2.435059 GGGTTCTGCTGCGACCTC 60.435 66.667 15.93 6.18 33.90 3.85
3750 4080 1.526917 GGCCATGATCTTCACCCGG 60.527 63.158 0.00 0.00 0.00 5.73
3768 4098 1.520787 GACGTAGAACCCGGGCATG 60.521 63.158 24.08 11.52 0.00 4.06
3789 4119 2.700773 GCATTTCAGCACCCGGTCC 61.701 63.158 0.00 0.00 0.00 4.46
3810 4140 5.652014 GGTCTAGCTATATCTGCAGATCACT 59.348 44.000 31.92 23.93 36.05 3.41
3836 4166 2.039418 CAGGGCTATACTACAGGCACA 58.961 52.381 0.00 0.00 40.21 4.57
3837 4167 2.297597 CTCAGGGCTATACTACAGGCAC 59.702 54.545 0.00 0.00 40.21 5.01
3838 4168 2.598565 CTCAGGGCTATACTACAGGCA 58.401 52.381 0.00 0.00 40.21 4.75
3839 4169 1.273886 GCTCAGGGCTATACTACAGGC 59.726 57.143 0.00 0.00 38.06 4.85
3852 4182 0.250640 GGCATGATACCAGCTCAGGG 60.251 60.000 0.00 0.00 0.00 4.45
3915 4245 2.813754 ACTCAACACGCAAATGCTACAT 59.186 40.909 3.63 0.00 39.32 2.29
3916 4246 2.032117 CACTCAACACGCAAATGCTACA 60.032 45.455 3.63 0.00 39.32 2.74
3928 4258 2.948979 TGAACCAACATCCACTCAACAC 59.051 45.455 0.00 0.00 0.00 3.32
3930 4260 3.214328 AGTGAACCAACATCCACTCAAC 58.786 45.455 0.00 0.00 35.15 3.18
3931 4261 3.576078 AGTGAACCAACATCCACTCAA 57.424 42.857 0.00 0.00 35.15 3.02
3934 4264 1.878102 GCGAGTGAACCAACATCCACT 60.878 52.381 0.00 0.00 41.96 4.00
3935 4265 0.517316 GCGAGTGAACCAACATCCAC 59.483 55.000 0.00 0.00 0.00 4.02
3936 4266 0.948623 CGCGAGTGAACCAACATCCA 60.949 55.000 0.00 0.00 0.00 3.41
3937 4267 0.949105 ACGCGAGTGAACCAACATCC 60.949 55.000 15.93 0.00 46.97 3.51
3938 4268 2.528797 ACGCGAGTGAACCAACATC 58.471 52.632 15.93 0.00 46.97 3.06
3939 4269 4.771127 ACGCGAGTGAACCAACAT 57.229 50.000 15.93 0.00 46.97 2.71
4013 4343 5.590259 ACCATGGAGGAATCAAAAACTATCG 59.410 40.000 21.47 0.00 41.22 2.92
4014 4344 7.410120 AACCATGGAGGAATCAAAAACTATC 57.590 36.000 21.47 0.00 41.22 2.08
4015 4345 7.454380 TCAAACCATGGAGGAATCAAAAACTAT 59.546 33.333 21.47 0.00 41.22 2.12
4016 4346 6.780031 TCAAACCATGGAGGAATCAAAAACTA 59.220 34.615 21.47 0.00 41.22 2.24
4024 4354 3.808728 TCGATCAAACCATGGAGGAATC 58.191 45.455 21.47 14.12 41.22 2.52
4027 4357 2.187958 ACTCGATCAAACCATGGAGGA 58.812 47.619 21.47 12.83 41.22 3.71
4033 4363 5.476599 TCCATCAAAAACTCGATCAAACCAT 59.523 36.000 0.00 0.00 0.00 3.55
4044 4374 5.531634 TGCATTTCTGTCCATCAAAAACTC 58.468 37.500 0.00 0.00 0.00 3.01
4122 4452 5.184287 TCATGTGTTCTATACTCAACCGTCA 59.816 40.000 0.00 0.00 34.25 4.35
4124 4454 5.185249 ACTCATGTGTTCTATACTCAACCGT 59.815 40.000 0.00 0.00 34.25 4.83
4127 4457 6.183360 GCCAACTCATGTGTTCTATACTCAAC 60.183 42.308 10.12 0.00 34.25 3.18
4158 4488 1.037030 AGGCTCTCTCGAGAAGGCAG 61.037 60.000 32.19 21.19 39.74 4.85
4204 4536 3.127030 GCCTGACCCAATTTCGACTTTAG 59.873 47.826 0.00 0.00 0.00 1.85
4278 4610 2.742372 CGCCGTTGGTGGGAGAAG 60.742 66.667 0.00 0.00 0.00 2.85
4336 4668 1.009335 TCCTTGTCACACGACGACG 60.009 57.895 5.58 5.58 45.80 5.12
4413 4745 2.021723 GCCAGATGCCGATAAAACCCA 61.022 52.381 0.00 0.00 0.00 4.51
4415 4747 0.307760 CGCCAGATGCCGATAAAACC 59.692 55.000 0.00 0.00 36.24 3.27
4424 4756 1.766143 CTAAAGTCGCGCCAGATGCC 61.766 60.000 0.00 0.00 36.24 4.40
4432 4764 3.497031 GGCCCACTAAAGTCGCGC 61.497 66.667 0.00 0.00 0.00 6.86
4702 5035 6.523840 ACAATGTGAAAAGTGTTGGCATAAT 58.476 32.000 0.00 0.00 0.00 1.28
4704 5037 5.528043 ACAATGTGAAAAGTGTTGGCATA 57.472 34.783 0.00 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.