Multiple sequence alignment - TraesCS5D01G149700

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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 TraesCS5D01G149700 chr5D 100.000 4624 0 0 1 4624 238588004 238583381 0.000000e+00 8540
1 TraesCS5D01G149700 chr5A 96.424 3691 107 11 895 4574 315982138 315985814 0.000000e+00 6061
2 TraesCS5D01G149700 chrUn 96.188 3594 109 14 987 4574 284251002 284254573 0.000000e+00 5853
3 TraesCS5D01G149700 chrUn 89.438 729 67 6 1 726 430916080 430915359 0.000000e+00 911
4 TraesCS5D01G149700 chr5B 96.188 3594 109 14 987 4574 266348666 266352237 0.000000e+00 5853
5 TraesCS5D01G149700 chr5B 87.132 1018 109 12 1 1006 266347063 266348070 0.000000e+00 1134
6 TraesCS5D01G149700 chr5B 79.394 495 94 7 15 505 441572880 441572390 4.430000e-90 342
7 TraesCS5D01G149700 chr4D 83.536 577 76 12 20 585 79709830 79709262 5.300000e-144 521
8 TraesCS5D01G149700 chr4B 81.773 598 94 12 1 591 111046584 111045995 1.930000e-133 486
9 TraesCS5D01G149700 chr2B 80.030 671 113 19 8 668 468438241 468437582 1.160000e-130 477
10 TraesCS5D01G149700 chr3A 79.793 579 107 7 35 608 579119795 579120368 3.330000e-111 412
11 TraesCS5D01G149700 chr1D 80.943 509 83 13 161 662 22849645 22850146 1.560000e-104 390
12 TraesCS5D01G149700 chr2D 79.359 499 84 17 177 664 413943852 413944342 2.670000e-87 333


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 TraesCS5D01G149700 chr5D 238583381 238588004 4623 True 8540.0 8540 100.000 1 4624 1 chr5D.!!$R1 4623
1 TraesCS5D01G149700 chr5A 315982138 315985814 3676 False 6061.0 6061 96.424 895 4574 1 chr5A.!!$F1 3679
2 TraesCS5D01G149700 chrUn 284251002 284254573 3571 False 5853.0 5853 96.188 987 4574 1 chrUn.!!$F1 3587
3 TraesCS5D01G149700 chrUn 430915359 430916080 721 True 911.0 911 89.438 1 726 1 chrUn.!!$R1 725
4 TraesCS5D01G149700 chr5B 266347063 266352237 5174 False 3493.5 5853 91.660 1 4574 2 chr5B.!!$F1 4573
5 TraesCS5D01G149700 chr4D 79709262 79709830 568 True 521.0 521 83.536 20 585 1 chr4D.!!$R1 565
6 TraesCS5D01G149700 chr4B 111045995 111046584 589 True 486.0 486 81.773 1 591 1 chr4B.!!$R1 590
7 TraesCS5D01G149700 chr2B 468437582 468438241 659 True 477.0 477 80.030 8 668 1 chr2B.!!$R1 660
8 TraesCS5D01G149700 chr3A 579119795 579120368 573 False 412.0 412 79.793 35 608 1 chr3A.!!$F1 573
9 TraesCS5D01G149700 chr1D 22849645 22850146 501 False 390.0 390 80.943 161 662 1 chr1D.!!$F1 501

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
681 696 0.243365 TGATGGCAAACAACGATGGC 59.757 50.0 0.00 0.0 42.03 4.40 F
774 795 0.446616 GGGCGTCTCCAAACGAATTC 59.553 55.0 0.00 0.0 45.37 2.17 F
1197 1834 0.544357 TCCTCTCATCGGTGGTTGGT 60.544 55.0 0.00 0.0 0.00 3.67 F
2202 2839 0.106318 ATCTGCAGGAAGGAATGCCC 60.106 55.0 15.13 0.0 41.85 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 2306 1.194772 CAAAGAGAACCCGAGCGAAAC 59.805 52.381 0.0 0.0 0.00 2.78 R
1880 2517 1.884926 GCGGTACATCTGCTCTGCC 60.885 63.158 0.0 0.0 44.39 4.85 R
3004 3645 0.170561 CTGCTGCCTTGCTGAATCAC 59.829 55.000 0.0 0.0 34.47 3.06 R
3666 4307 1.808945 GAATGACAAGGTGCAGGACAG 59.191 52.381 0.0 0.0 0.00 3.51 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
80 81 2.076863 CAACCCTGCTTTTCCGTAGAG 58.923 52.381 0.00 0.00 0.00 2.43
106 107 2.814336 GGAGAGAAAGTTGTCCGCAATT 59.186 45.455 0.00 0.00 36.92 2.32
107 108 3.253432 GGAGAGAAAGTTGTCCGCAATTT 59.747 43.478 0.00 0.00 36.32 1.82
109 110 5.262588 AGAGAAAGTTGTCCGCAATTTTT 57.737 34.783 3.15 0.00 42.14 1.94
164 166 2.130395 CGATAGTCATGATGCGCAAGT 58.870 47.619 17.11 2.19 41.68 3.16
272 276 1.948104 CGCCAACGATCCTATTCCAA 58.052 50.000 0.00 0.00 43.93 3.53
316 320 4.993705 TGGAACCCTTGAAGTTCAGTAT 57.006 40.909 5.56 0.00 44.40 2.12
325 329 4.623932 TGAAGTTCAGTATGTGCTCCTT 57.376 40.909 0.08 0.00 37.40 3.36
357 367 4.444449 CCATCTTCTCTTGGATGCTCATCA 60.444 45.833 11.49 0.00 39.54 3.07
358 368 5.309638 CATCTTCTCTTGGATGCTCATCAT 58.690 41.667 11.49 0.00 39.54 2.45
373 383 6.062095 TGCTCATCATCATCATCATTTCAGT 58.938 36.000 0.00 0.00 0.00 3.41
433 443 8.554835 TCGTTGAATATGAATTTGTCAAGGTA 57.445 30.769 0.00 0.00 40.50 3.08
446 456 4.979335 TGTCAAGGTATGTGTTTCCATGA 58.021 39.130 0.00 0.00 0.00 3.07
598 613 0.465460 GTTGGCAGTGACCTTGTCCA 60.465 55.000 0.00 0.00 0.00 4.02
610 625 1.078497 TTGTCCAGTGGCGGCATAG 60.078 57.895 17.19 10.93 0.00 2.23
611 626 1.836999 TTGTCCAGTGGCGGCATAGT 61.837 55.000 17.19 0.00 0.00 2.12
612 627 1.815421 GTCCAGTGGCGGCATAGTG 60.815 63.158 17.19 13.20 0.00 2.74
662 677 1.384191 GAAGCTGTGGGTTGGGGAT 59.616 57.895 0.00 0.00 32.93 3.85
663 678 0.967380 GAAGCTGTGGGTTGGGGATG 60.967 60.000 0.00 0.00 32.93 3.51
665 680 1.217057 AGCTGTGGGTTGGGGATGAT 61.217 55.000 0.00 0.00 0.00 2.45
680 695 2.480073 GGATGATGGCAAACAACGATGG 60.480 50.000 0.00 0.00 0.00 3.51
681 696 0.243365 TGATGGCAAACAACGATGGC 59.757 50.000 0.00 0.00 42.03 4.40
701 716 2.829914 TGGAGCAATGATGGCGGC 60.830 61.111 0.00 0.00 36.08 6.53
727 742 4.040461 TGTGGACGAGGAAGAAAAGAGAAT 59.960 41.667 0.00 0.00 0.00 2.40
728 743 5.245301 TGTGGACGAGGAAGAAAAGAGAATA 59.755 40.000 0.00 0.00 0.00 1.75
743 758 8.773033 AAAAGAGAATAGGAACATGGCATATT 57.227 30.769 0.00 0.00 0.00 1.28
763 784 4.475135 GCAAGGAGGGGGCGTCTC 62.475 72.222 0.00 0.00 0.00 3.36
774 795 0.446616 GGGCGTCTCCAAACGAATTC 59.553 55.000 0.00 0.00 45.37 2.17
775 796 1.153353 GGCGTCTCCAAACGAATTCA 58.847 50.000 6.22 0.00 45.37 2.57
780 801 1.004277 TCTCCAAACGAATTCAGGGGG 59.996 52.381 6.22 0.95 0.00 5.40
786 807 1.250840 ACGAATTCAGGGGGCTTTGC 61.251 55.000 6.22 0.00 0.00 3.68
788 809 1.948721 GAATTCAGGGGGCTTTGCGG 61.949 60.000 0.00 0.00 0.00 5.69
792 813 4.351054 AGGGGGCTTTGCGGTCAG 62.351 66.667 0.00 0.00 0.00 3.51
799 820 1.291132 GCTTTGCGGTCAGTCCTATC 58.709 55.000 0.00 0.00 0.00 2.08
802 823 1.847328 TTGCGGTCAGTCCTATCTGA 58.153 50.000 0.00 0.00 41.40 3.27
840 861 1.372997 CCCGGCGTCTTCATATCCG 60.373 63.158 6.01 0.00 39.79 4.18
845 867 1.745890 CGTCTTCATATCCGCCCCA 59.254 57.895 0.00 0.00 0.00 4.96
846 868 0.600255 CGTCTTCATATCCGCCCCAC 60.600 60.000 0.00 0.00 0.00 4.61
847 869 0.600255 GTCTTCATATCCGCCCCACG 60.600 60.000 0.00 0.00 43.15 4.94
861 883 2.189521 CACGTGGGTAGGGGATGC 59.810 66.667 7.95 0.00 0.00 3.91
867 889 1.767268 GGGTAGGGGATGCGGGTTA 60.767 63.158 0.00 0.00 0.00 2.85
868 890 1.131928 GGGTAGGGGATGCGGGTTAT 61.132 60.000 0.00 0.00 0.00 1.89
870 892 1.053424 GTAGGGGATGCGGGTTATCA 58.947 55.000 0.00 0.00 0.00 2.15
871 893 1.002087 GTAGGGGATGCGGGTTATCAG 59.998 57.143 0.00 0.00 0.00 2.90
876 898 1.202486 GGATGCGGGTTATCAGTTCGA 60.202 52.381 0.00 0.00 0.00 3.71
877 899 1.859080 GATGCGGGTTATCAGTTCGAC 59.141 52.381 0.00 0.00 0.00 4.20
879 901 1.278238 GCGGGTTATCAGTTCGACAG 58.722 55.000 0.00 0.00 0.00 3.51
882 904 2.100916 CGGGTTATCAGTTCGACAGGAT 59.899 50.000 0.00 0.00 0.00 3.24
883 905 3.458189 GGGTTATCAGTTCGACAGGATG 58.542 50.000 0.00 0.00 46.00 3.51
921 943 7.328277 GTAGATGCTCTACAGAAGAAGAGAA 57.672 40.000 14.65 0.00 46.47 2.87
922 944 6.849085 AGATGCTCTACAGAAGAAGAGAAA 57.151 37.500 3.60 0.00 41.51 2.52
923 945 7.238486 AGATGCTCTACAGAAGAAGAGAAAA 57.762 36.000 3.60 0.00 41.51 2.29
965 987 0.819259 GTGCAACCAAGGCTGACAGA 60.819 55.000 6.65 0.00 0.00 3.41
990 1627 6.015688 ACGGGCCATATAATATATACGACAGG 60.016 42.308 4.39 2.12 0.00 4.00
991 1628 6.015688 CGGGCCATATAATATATACGACAGGT 60.016 42.308 4.39 0.00 0.00 4.00
992 1629 7.152645 GGGCCATATAATATATACGACAGGTG 58.847 42.308 4.39 0.00 0.00 4.00
1128 1765 2.515991 AATACACCCATGGCCGCG 60.516 61.111 6.09 0.00 0.00 6.46
1197 1834 0.544357 TCCTCTCATCGGTGGTTGGT 60.544 55.000 0.00 0.00 0.00 3.67
1203 1840 1.903183 TCATCGGTGGTTGGTGACATA 59.097 47.619 0.00 0.00 42.32 2.29
1262 1899 4.162690 GTACGGCCCTGCTCCCAG 62.163 72.222 0.00 0.00 38.85 4.45
1506 2143 3.476552 TGCTGCTATACCAAACCATAGC 58.523 45.455 0.00 6.63 46.44 2.97
1535 2172 2.740447 GACTACGCGAGGGTTTCATTTT 59.260 45.455 15.93 0.00 0.00 1.82
1539 2176 2.050691 CGCGAGGGTTTCATTTTGTTG 58.949 47.619 0.00 0.00 0.00 3.33
1575 2212 7.044181 TGAGAGATGTTGAGATTGATTGGTAC 58.956 38.462 0.00 0.00 0.00 3.34
1577 2214 6.820656 AGAGATGTTGAGATTGATTGGTACAC 59.179 38.462 0.00 0.00 39.29 2.90
1669 2306 2.002586 CACCACAGTTATTGAGCTCCG 58.997 52.381 12.15 0.00 0.00 4.63
1844 2481 5.308825 AGAGCTGCGTTTTATATGGCTTAT 58.691 37.500 0.00 0.00 0.00 1.73
1880 2517 1.187087 AGCGTAGGAGGTTTCAGGAG 58.813 55.000 0.00 0.00 0.00 3.69
1919 2556 3.681594 GCGTGGGAATCCAGAAGTAATCA 60.682 47.826 0.09 0.00 45.05 2.57
1927 2564 6.126739 GGAATCCAGAAGTAATCACTTACCCT 60.127 42.308 0.00 0.00 45.18 4.34
1963 2600 5.109903 GGATACTGTCGTTTGCTTCTACAT 58.890 41.667 0.00 0.00 0.00 2.29
2015 2652 7.512746 TCTGATTATGTAAGCCTGGGTACTTAT 59.487 37.037 0.00 0.00 31.44 1.73
2074 2711 6.942005 AGGAGTTACACAAATCACATGATCAA 59.058 34.615 0.00 0.00 32.75 2.57
2100 2737 4.696899 TCTATCGCATGGAGTTATACCG 57.303 45.455 0.00 0.00 0.00 4.02
2132 2769 8.204836 GGAAAGATAAAGTATGGCTCTCACTTA 58.795 37.037 0.00 0.00 32.35 2.24
2151 2788 5.348451 CACTTAACCTTGGCAAATATTGTGC 59.652 40.000 0.00 11.76 41.45 4.57
2152 2789 5.011533 ACTTAACCTTGGCAAATATTGTGCA 59.988 36.000 18.16 0.00 44.07 4.57
2154 2791 4.556592 ACCTTGGCAAATATTGTGCATT 57.443 36.364 18.16 0.00 44.07 3.56
2202 2839 0.106318 ATCTGCAGGAAGGAATGCCC 60.106 55.000 15.13 0.00 41.85 5.36
2576 3214 2.154567 ATGCTTGTCATCATGGCCTT 57.845 45.000 3.32 0.00 0.00 4.35
2672 3310 2.221169 ACAATGCTCAAGAAACGCTCA 58.779 42.857 0.00 0.00 0.00 4.26
2706 3344 3.256631 ACCAAAGTTTAATCAGCAGGCAG 59.743 43.478 0.00 0.00 0.00 4.85
2851 3492 7.395190 TTGTTGATGAAGATTGTCCTAATGG 57.605 36.000 0.00 0.00 0.00 3.16
2899 3540 6.863275 ACAGGAAAAGTAACAAGGAAAACAG 58.137 36.000 0.00 0.00 0.00 3.16
2986 3627 5.423886 TGTCATGTGTCACAAGAACACTAA 58.576 37.500 12.23 0.00 35.59 2.24
2997 3638 4.230657 CAAGAACACTAAGTGTCCTCGAG 58.769 47.826 5.13 5.13 46.79 4.04
3004 3645 2.279582 AAGTGTCCTCGAGCATTACG 57.720 50.000 6.99 0.00 0.00 3.18
3250 3891 5.541845 ACTTCGAGAAGACACAATCATTCA 58.458 37.500 18.54 0.00 40.79 2.57
3460 4101 2.551459 CAGCTCCTGTTTCTGGTTTCTG 59.449 50.000 0.00 0.00 0.00 3.02
3651 4292 7.915923 GCACTTGCTTAGAGGGAATTTAATTAC 59.084 37.037 0.00 0.00 38.21 1.89
3684 4325 1.059098 TCTGTCCTGCACCTTGTCAT 58.941 50.000 0.00 0.00 0.00 3.06
3698 4339 6.460123 GCACCTTGTCATTCTTTTCTTGAGAA 60.460 38.462 0.00 0.00 37.52 2.87
3786 4427 9.533253 TGCAATCGATATGGAATATATGTACTG 57.467 33.333 0.00 0.00 40.26 2.74
3858 4499 4.839121 AGTTGGCGACTGGTGAATATTTA 58.161 39.130 6.59 0.00 37.17 1.40
3884 4525 5.794687 AACTGATCATTCGCGTTTATCAA 57.205 34.783 5.77 0.00 0.00 2.57
3937 4578 6.658188 TTTTCCTTGATAAAATTGGGACGT 57.342 33.333 0.00 0.00 0.00 4.34
3997 4638 7.011389 CCTTGATATCGTGATGTTTTTGCTCTA 59.989 37.037 0.00 0.00 0.00 2.43
4111 4752 2.423373 GGGAATGATACCATGCCTGTGT 60.423 50.000 0.00 0.00 46.14 3.72
4164 4805 6.127366 GGATATTTTCCACAAAATGAGCTCCA 60.127 38.462 12.15 0.00 44.74 3.86
4187 4829 1.144913 TCTTTGTTTAGCACCAGGCCT 59.855 47.619 0.00 0.00 46.50 5.19
4292 4934 7.557719 CCCCACTGTATTTTGTTCATTAGATCT 59.442 37.037 0.00 0.00 0.00 2.75
4324 4966 1.027357 GGTGATGCTGCCCATTACAG 58.973 55.000 10.22 0.00 40.99 2.74
4325 4967 1.408683 GGTGATGCTGCCCATTACAGA 60.409 52.381 10.22 0.00 40.99 3.41
4574 5223 2.550208 GGGGAGACTGACGTGAAACAAT 60.550 50.000 0.00 0.00 35.74 2.71
4575 5224 3.139077 GGGAGACTGACGTGAAACAATT 58.861 45.455 0.00 0.00 35.74 2.32
4576 5225 3.058914 GGGAGACTGACGTGAAACAATTG 60.059 47.826 3.24 3.24 35.74 2.32
4577 5226 3.807622 GGAGACTGACGTGAAACAATTGA 59.192 43.478 13.59 0.00 35.74 2.57
4578 5227 4.452455 GGAGACTGACGTGAAACAATTGAT 59.548 41.667 13.59 0.00 35.74 2.57
4579 5228 5.389935 GGAGACTGACGTGAAACAATTGATC 60.390 44.000 13.59 10.44 35.74 2.92
4580 5229 4.150627 AGACTGACGTGAAACAATTGATCG 59.849 41.667 13.59 10.85 35.74 3.69
4581 5230 3.155998 CTGACGTGAAACAATTGATCGC 58.844 45.455 13.59 14.55 35.74 4.58
4582 5231 2.545946 TGACGTGAAACAATTGATCGCA 59.454 40.909 13.59 0.00 35.74 5.10
4583 5232 3.155998 GACGTGAAACAATTGATCGCAG 58.844 45.455 13.59 13.56 35.74 5.18
4584 5233 1.906966 CGTGAAACAATTGATCGCAGC 59.093 47.619 13.59 2.14 35.74 5.25
4585 5234 2.665245 CGTGAAACAATTGATCGCAGCA 60.665 45.455 13.59 0.00 35.74 4.41
4586 5235 2.912967 GTGAAACAATTGATCGCAGCAG 59.087 45.455 13.59 0.00 36.32 4.24
4587 5236 1.916000 GAAACAATTGATCGCAGCAGC 59.084 47.619 13.59 0.00 37.42 5.25
4588 5237 1.171308 AACAATTGATCGCAGCAGCT 58.829 45.000 13.59 0.00 39.10 4.24
4589 5238 2.028420 ACAATTGATCGCAGCAGCTA 57.972 45.000 13.59 0.00 39.10 3.32
4590 5239 2.569059 ACAATTGATCGCAGCAGCTAT 58.431 42.857 13.59 0.00 39.10 2.97
4591 5240 2.947652 ACAATTGATCGCAGCAGCTATT 59.052 40.909 13.59 0.00 39.10 1.73
4592 5241 3.242969 ACAATTGATCGCAGCAGCTATTG 60.243 43.478 13.59 9.39 39.10 1.90
4593 5242 2.028420 TTGATCGCAGCAGCTATTGT 57.972 45.000 0.00 0.00 39.10 2.71
4594 5243 2.028420 TGATCGCAGCAGCTATTGTT 57.972 45.000 0.00 0.00 39.10 2.83
4595 5244 1.667212 TGATCGCAGCAGCTATTGTTG 59.333 47.619 0.00 0.00 40.61 3.33
4596 5245 1.935873 GATCGCAGCAGCTATTGTTGA 59.064 47.619 0.00 0.00 40.12 3.18
4597 5246 2.028420 TCGCAGCAGCTATTGTTGAT 57.972 45.000 0.00 0.00 40.12 2.57
4598 5247 2.358957 TCGCAGCAGCTATTGTTGATT 58.641 42.857 0.00 0.00 40.12 2.57
4599 5248 2.749076 TCGCAGCAGCTATTGTTGATTT 59.251 40.909 0.00 0.00 40.12 2.17
4600 5249 3.103738 CGCAGCAGCTATTGTTGATTTC 58.896 45.455 0.00 0.00 40.12 2.17
4601 5250 3.426560 CGCAGCAGCTATTGTTGATTTCA 60.427 43.478 0.00 0.00 40.12 2.69
4602 5251 4.679662 GCAGCAGCTATTGTTGATTTCAT 58.320 39.130 0.00 0.00 40.12 2.57
4603 5252 4.738740 GCAGCAGCTATTGTTGATTTCATC 59.261 41.667 0.00 0.00 40.12 2.92
4604 5253 5.677852 GCAGCAGCTATTGTTGATTTCATCA 60.678 40.000 0.00 0.00 40.12 3.07
4605 5254 6.327154 CAGCAGCTATTGTTGATTTCATCAA 58.673 36.000 0.00 6.54 46.30 2.57
4606 5255 8.828772 GCAGCAGCTATTGTTGATTTCATCAAG 61.829 40.741 0.00 0.21 42.89 3.02
4616 5265 5.587388 TGATTTCATCAAGGATCAAAGCC 57.413 39.130 0.00 0.00 36.11 4.35
4617 5266 5.266788 TGATTTCATCAAGGATCAAAGCCT 58.733 37.500 0.00 0.00 36.11 4.58
4618 5267 6.425735 TGATTTCATCAAGGATCAAAGCCTA 58.574 36.000 0.00 0.00 36.11 3.93
4619 5268 6.319658 TGATTTCATCAAGGATCAAAGCCTAC 59.680 38.462 0.00 0.00 36.11 3.18
4620 5269 4.842531 TCATCAAGGATCAAAGCCTACA 57.157 40.909 0.00 0.00 33.76 2.74
4621 5270 4.774124 TCATCAAGGATCAAAGCCTACAG 58.226 43.478 0.00 0.00 33.76 2.74
4622 5271 4.225942 TCATCAAGGATCAAAGCCTACAGT 59.774 41.667 0.00 0.00 33.76 3.55
4623 5272 5.425217 TCATCAAGGATCAAAGCCTACAGTA 59.575 40.000 0.00 0.00 33.76 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 4.785453 CAGGGTTGCTCTCGGGGC 62.785 72.222 0.00 0.00 0.00 5.80
62 63 0.613777 CCTCTACGGAAAAGCAGGGT 59.386 55.000 0.00 0.00 33.16 4.34
65 66 0.107654 CCCCCTCTACGGAAAAGCAG 60.108 60.000 0.00 0.00 33.16 4.24
107 108 7.340743 TGATGACAACTTCAACCTAAGGAAAAA 59.659 33.333 0.00 0.00 37.92 1.94
109 110 6.361433 TGATGACAACTTCAACCTAAGGAAA 58.639 36.000 0.00 0.00 37.92 3.13
141 143 0.162507 GCGCATCATGACTATCGTGC 59.837 55.000 0.30 1.56 33.54 5.34
164 166 3.284617 TCCGGATGAGTCGAGATTTGTA 58.715 45.455 0.00 0.00 0.00 2.41
272 276 7.236847 TCCATAAAGGGTCGGATAGTTATTCAT 59.763 37.037 0.00 0.00 38.24 2.57
316 320 0.250901 GGAGAAGGCAAAGGAGCACA 60.251 55.000 0.00 0.00 35.83 4.57
325 329 3.307975 CCAAGAGAAGATGGAGAAGGCAA 60.308 47.826 0.00 0.00 39.12 4.52
357 367 7.328005 CGACGAAGATACTGAAATGATGATGAT 59.672 37.037 0.00 0.00 0.00 2.45
358 368 6.638468 CGACGAAGATACTGAAATGATGATGA 59.362 38.462 0.00 0.00 0.00 2.92
359 369 6.615208 GCGACGAAGATACTGAAATGATGATG 60.615 42.308 0.00 0.00 0.00 3.07
446 456 0.842635 GCTCCTCCTGGAATGATGGT 59.157 55.000 0.00 0.00 42.66 3.55
509 524 5.276395 GGTCTATGTGTTCGATGAAATGTCG 60.276 44.000 0.00 0.00 40.30 4.35
548 563 1.825474 CCAGTACGTCCAACTCCTCAT 59.175 52.381 0.00 0.00 0.00 2.90
549 564 1.254026 CCAGTACGTCCAACTCCTCA 58.746 55.000 0.00 0.00 0.00 3.86
598 613 2.187946 GCTCACTATGCCGCCACT 59.812 61.111 0.00 0.00 0.00 4.00
611 626 4.555709 AACCCACAACGCCGCTCA 62.556 61.111 0.00 0.00 0.00 4.26
612 627 3.723348 GAACCCACAACGCCGCTC 61.723 66.667 0.00 0.00 0.00 5.03
619 634 3.723348 GAGGCGCGAACCCACAAC 61.723 66.667 12.10 0.00 0.00 3.32
638 653 1.675641 AACCCACAGCTTCGCCATC 60.676 57.895 0.00 0.00 0.00 3.51
641 656 3.365265 CCAACCCACAGCTTCGCC 61.365 66.667 0.00 0.00 0.00 5.54
648 663 0.396139 CCATCATCCCCAACCCACAG 60.396 60.000 0.00 0.00 0.00 3.66
662 677 0.243365 GCCATCGTTGTTTGCCATCA 59.757 50.000 0.00 0.00 0.00 3.07
663 678 0.798009 CGCCATCGTTGTTTGCCATC 60.798 55.000 0.00 0.00 0.00 3.51
665 680 2.642129 CGCCATCGTTGTTTGCCA 59.358 55.556 0.00 0.00 0.00 4.92
680 695 3.113745 CCATCATTGCTCCACCGC 58.886 61.111 0.00 0.00 0.00 5.68
681 696 2.827051 CGCCATCATTGCTCCACCG 61.827 63.158 0.00 0.00 0.00 4.94
689 704 1.138036 CACACAGCCGCCATCATTG 59.862 57.895 0.00 0.00 0.00 2.82
701 716 2.526304 TTTCTTCCTCGTCCACACAG 57.474 50.000 0.00 0.00 0.00 3.66
711 726 7.281999 CCATGTTCCTATTCTCTTTTCTTCCTC 59.718 40.741 0.00 0.00 0.00 3.71
727 742 2.176581 TGCCCAATATGCCATGTTCCTA 59.823 45.455 0.00 0.00 0.00 2.94
728 743 1.063038 TGCCCAATATGCCATGTTCCT 60.063 47.619 0.00 0.00 0.00 3.36
763 784 0.611896 AGCCCCCTGAATTCGTTTGG 60.612 55.000 0.04 0.51 0.00 3.28
774 795 4.659172 TGACCGCAAAGCCCCCTG 62.659 66.667 0.00 0.00 0.00 4.45
775 796 4.351054 CTGACCGCAAAGCCCCCT 62.351 66.667 0.00 0.00 0.00 4.79
780 801 1.134670 AGATAGGACTGACCGCAAAGC 60.135 52.381 0.00 0.00 44.74 3.51
792 813 3.728268 CGAACACGAGTGTCAGATAGGAC 60.728 52.174 9.48 0.00 44.13 3.85
799 820 2.022129 GCCCGAACACGAGTGTCAG 61.022 63.158 9.48 6.69 44.13 3.51
824 845 3.538841 GCGGATATGAAGACGCCG 58.461 61.111 0.00 0.00 45.70 6.46
832 853 2.802724 CCACGTGGGGCGGATATGA 61.803 63.158 27.57 0.00 46.52 2.15
845 867 3.467226 CGCATCCCCTACCCACGT 61.467 66.667 0.00 0.00 0.00 4.49
846 868 4.235762 CCGCATCCCCTACCCACG 62.236 72.222 0.00 0.00 0.00 4.94
847 869 3.873812 CCCGCATCCCCTACCCAC 61.874 72.222 0.00 0.00 0.00 4.61
851 873 1.002087 CTGATAACCCGCATCCCCTAC 59.998 57.143 0.00 0.00 0.00 3.18
852 874 1.348064 CTGATAACCCGCATCCCCTA 58.652 55.000 0.00 0.00 0.00 3.53
853 875 0.694444 ACTGATAACCCGCATCCCCT 60.694 55.000 0.00 0.00 0.00 4.79
857 879 1.859080 GTCGAACTGATAACCCGCATC 59.141 52.381 0.00 0.00 0.00 3.91
861 883 1.475280 TCCTGTCGAACTGATAACCCG 59.525 52.381 0.00 0.00 0.00 5.28
867 889 3.244561 ACCAAACATCCTGTCGAACTGAT 60.245 43.478 0.00 0.00 0.00 2.90
868 890 2.104111 ACCAAACATCCTGTCGAACTGA 59.896 45.455 0.00 0.00 0.00 3.41
870 892 2.878406 CAACCAAACATCCTGTCGAACT 59.122 45.455 0.00 0.00 0.00 3.01
871 893 2.031157 CCAACCAAACATCCTGTCGAAC 60.031 50.000 0.00 0.00 0.00 3.95
876 898 3.966665 ACAAATCCAACCAAACATCCTGT 59.033 39.130 0.00 0.00 0.00 4.00
877 899 4.605640 ACAAATCCAACCAAACATCCTG 57.394 40.909 0.00 0.00 0.00 3.86
879 901 5.975693 TCTACAAATCCAACCAAACATCC 57.024 39.130 0.00 0.00 0.00 3.51
882 904 4.832266 AGCATCTACAAATCCAACCAAACA 59.168 37.500 0.00 0.00 0.00 2.83
883 905 5.391312 AGCATCTACAAATCCAACCAAAC 57.609 39.130 0.00 0.00 0.00 2.93
922 944 3.336138 GGTCTGGTCCGAGATCTTTTT 57.664 47.619 0.00 0.00 0.00 1.94
947 969 0.819259 GTCTGTCAGCCTTGGTTGCA 60.819 55.000 0.00 0.00 0.00 4.08
965 987 6.015688 CCTGTCGTATATATTATATGGCCCGT 60.016 42.308 0.00 0.00 0.00 5.28
990 1627 4.380531 CATATACTGACATGTGGGTCCAC 58.619 47.826 1.15 12.89 46.33 4.02
991 1628 3.181455 GCATATACTGACATGTGGGTCCA 60.181 47.826 1.15 0.00 36.97 4.02
992 1629 3.403038 GCATATACTGACATGTGGGTCC 58.597 50.000 1.15 0.00 36.97 4.46
1197 1834 1.133598 CCGGAGTAACAGCGTATGTCA 59.866 52.381 0.00 0.00 43.00 3.58
1203 1840 1.291272 GGAACCGGAGTAACAGCGT 59.709 57.895 9.46 0.00 0.00 5.07
1282 1919 4.840005 GAGGAAAGGAGGGGCGCG 62.840 72.222 0.00 0.00 0.00 6.86
1293 1930 2.761208 GGTTCGATCAGAGAGGAGGAAA 59.239 50.000 0.00 0.00 0.00 3.13
1450 2087 1.179814 GGATCCAGACGCGGAGGTAT 61.180 60.000 12.47 4.90 38.83 2.73
1506 2143 4.111016 TCGCGTAGTCAGCCGGTG 62.111 66.667 5.77 0.00 0.00 4.94
1535 2172 3.526899 TCTCTCAGTAAATCCCCCAACA 58.473 45.455 0.00 0.00 0.00 3.33
1539 2176 4.164221 TCAACATCTCTCAGTAAATCCCCC 59.836 45.833 0.00 0.00 0.00 5.40
1669 2306 1.194772 CAAAGAGAACCCGAGCGAAAC 59.805 52.381 0.00 0.00 0.00 2.78
1844 2481 6.317893 TCCTACGCTTCTCATAATATATCGCA 59.682 38.462 0.00 0.00 0.00 5.10
1880 2517 1.884926 GCGGTACATCTGCTCTGCC 60.885 63.158 0.00 0.00 44.39 4.85
1919 2556 2.824341 CTCTACAACGTGGAGGGTAAGT 59.176 50.000 0.00 0.00 37.48 2.24
1927 2564 3.693085 GACAGTATCCTCTACAACGTGGA 59.307 47.826 0.00 0.00 0.00 4.02
2002 2639 7.277396 TGAACACTTATAATAAGTACCCAGGC 58.723 38.462 0.00 0.00 0.00 4.85
2015 2652 7.109501 TCTGCAAGGCTATTGAACACTTATAA 58.890 34.615 6.41 0.00 0.00 0.98
2074 2711 7.921214 CGGTATAACTCCATGCGATAGATAAAT 59.079 37.037 0.00 0.00 39.76 1.40
2100 2737 6.596621 AGCCATACTTTATCTTTCCTCTTCC 58.403 40.000 0.00 0.00 0.00 3.46
2132 2769 4.556592 ATGCACAATATTTGCCAAGGTT 57.443 36.364 15.43 0.00 39.39 3.50
2202 2839 3.744660 AGGAAGTGGTTTAACTCTGCTG 58.255 45.455 0.00 0.00 0.00 4.41
2276 2914 7.344612 TCCACTAGAAACTGATTTAGATAGCCA 59.655 37.037 0.00 0.00 0.00 4.75
2369 3007 5.127845 TGAACTACTTCCCAATTTTTGCACA 59.872 36.000 0.00 0.00 0.00 4.57
2576 3214 7.776030 TCCTTCAAGTTTATAGTTGGTTCAACA 59.224 33.333 12.46 0.81 45.66 3.33
2672 3310 4.385358 AAACTTTGGTTGATCACGCTTT 57.615 36.364 0.00 0.00 35.63 3.51
2706 3344 5.627499 TCAACAAAGATATGAAGTGCACC 57.373 39.130 14.63 0.00 0.00 5.01
2851 3492 1.001520 GGCCCACATTTTGGTTGGTAC 59.998 52.381 0.00 0.00 45.25 3.34
2899 3540 2.539476 CAAACCCACTTGTTTGCTGAC 58.461 47.619 3.97 0.00 45.89 3.51
2986 3627 1.135373 CACGTAATGCTCGAGGACACT 60.135 52.381 15.58 2.33 0.00 3.55
2997 3638 2.792542 GCCTTGCTGAATCACGTAATGC 60.793 50.000 0.00 0.00 0.00 3.56
3004 3645 0.170561 CTGCTGCCTTGCTGAATCAC 59.829 55.000 0.00 0.00 34.47 3.06
3250 3891 2.578021 ACAGCAGATCCCACAAACCTAT 59.422 45.455 0.00 0.00 0.00 2.57
3404 4045 3.626028 ACTGCATTCGTTTTCCTGTTC 57.374 42.857 0.00 0.00 0.00 3.18
3460 4101 7.065443 TGCTAATGTCATCATCAGCTAATATGC 59.935 37.037 5.20 0.00 43.64 3.14
3651 4292 2.894126 AGGACAGACAGTACCTGTTGAG 59.106 50.000 4.97 0.00 45.44 3.02
3666 4307 1.808945 GAATGACAAGGTGCAGGACAG 59.191 52.381 0.00 0.00 0.00 3.51
3698 4339 8.188799 CACATCTTGAATGCAGAATACAAAGAT 58.811 33.333 0.00 0.00 0.00 2.40
3786 4427 6.327934 CCAAGCTATTATATCAGCAAATGGC 58.672 40.000 8.36 2.10 40.36 4.40
3912 4553 7.602265 CACGTCCCAATTTTATCAAGGAAAATT 59.398 33.333 0.00 1.27 43.77 1.82
3937 4578 2.076100 CAAGCTAGTCACCATTTCGCA 58.924 47.619 0.00 0.00 0.00 5.10
3997 4638 7.573843 CGTCAAGAGAAGCATTTTTCAGGTAAT 60.574 37.037 0.00 0.00 0.00 1.89
4111 4752 8.559536 GGAAAATTATGATATCAGCGAGAACAA 58.440 33.333 11.78 0.00 0.00 2.83
4162 4803 3.441572 CCTGGTGCTAAACAAAGATCTGG 59.558 47.826 0.00 0.00 0.00 3.86
4164 4805 3.084786 GCCTGGTGCTAAACAAAGATCT 58.915 45.455 0.00 0.00 36.87 2.75
4324 4966 5.817816 TGACTTCCAACAAAGAGAAAGTCTC 59.182 40.000 12.61 0.00 43.70 3.36
4325 4967 5.586643 GTGACTTCCAACAAAGAGAAAGTCT 59.413 40.000 12.61 0.00 36.94 3.24
4517 5166 5.107760 GCAATATGTTGTCAACAAACAGCAG 60.108 40.000 21.71 9.67 45.86 4.24
4574 5223 2.028420 ACAATAGCTGCTGCGATCAA 57.972 45.000 13.43 0.00 45.42 2.57
4575 5224 1.667212 CAACAATAGCTGCTGCGATCA 59.333 47.619 13.43 0.00 45.42 2.92
4576 5225 1.935873 TCAACAATAGCTGCTGCGATC 59.064 47.619 13.43 0.00 45.42 3.69
4577 5226 2.028420 TCAACAATAGCTGCTGCGAT 57.972 45.000 13.43 7.68 45.42 4.58
4578 5227 2.028420 ATCAACAATAGCTGCTGCGA 57.972 45.000 13.43 5.28 45.42 5.10
4579 5228 2.838386 AATCAACAATAGCTGCTGCG 57.162 45.000 13.43 2.77 45.42 5.18
4580 5229 4.100707 TGAAATCAACAATAGCTGCTGC 57.899 40.909 13.43 7.62 40.05 5.25
4595 5244 5.848833 AGGCTTTGATCCTTGATGAAATC 57.151 39.130 0.00 0.00 45.83 2.17
4596 5245 6.189859 TGTAGGCTTTGATCCTTGATGAAAT 58.810 36.000 0.00 0.00 35.21 2.17
4597 5246 5.569355 TGTAGGCTTTGATCCTTGATGAAA 58.431 37.500 0.00 0.00 35.21 2.69
4598 5247 5.178096 TGTAGGCTTTGATCCTTGATGAA 57.822 39.130 0.00 0.00 35.21 2.57
4599 5248 4.225942 ACTGTAGGCTTTGATCCTTGATGA 59.774 41.667 0.00 0.00 35.21 2.92
4600 5249 4.521146 ACTGTAGGCTTTGATCCTTGATG 58.479 43.478 0.00 0.00 35.21 3.07
4601 5250 4.851639 ACTGTAGGCTTTGATCCTTGAT 57.148 40.909 0.00 0.00 35.21 2.57


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

AutoCloner maintained by Alex Coulton.