Multiple sequence alignment - TraesCS3A01G256600

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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 TraesCS3A01G256600 chr3A 100.000 3190 0 0 1 3190 478664579 478667768 0.000000e+00 5891.0
1 TraesCS3A01G256600 chr3B 90.305 2589 116 41 1 2513 465067602 465070131 0.000000e+00 3265.0
2 TraesCS3A01G256600 chr3B 84.672 685 65 17 2511 3177 465092943 465093605 0.000000e+00 647.0
3 TraesCS3A01G256600 chr3D 91.464 2308 93 24 4 2255 359091223 359093482 0.000000e+00 3075.0
4 TraesCS3A01G256600 chr3D 86.172 687 64 16 2511 3177 359105845 359106520 0.000000e+00 713.0
5 TraesCS3A01G256600 chr3D 84.155 284 22 4 2252 2513 359093766 359094048 1.470000e-63 254.0
6 TraesCS3A01G256600 chr5B 84.312 1447 161 39 933 2339 561693675 561692255 0.000000e+00 1354.0
7 TraesCS3A01G256600 chr5B 84.925 1340 144 33 882 2201 561713770 561712469 0.000000e+00 1303.0
8 TraesCS3A01G256600 chr5B 76.327 245 50 8 1727 1967 353015784 353016024 1.200000e-24 124.0
9 TraesCS3A01G256600 chr5B 88.679 53 6 0 3018 3070 674335799 674335747 7.390000e-07 65.8
10 TraesCS3A01G256600 chr5D 85.281 1352 154 25 933 2253 458459681 458458344 0.000000e+00 1352.0
11 TraesCS3A01G256600 chr5D 83.708 178 20 6 2081 2253 458457463 458457290 3.290000e-35 159.0
12 TraesCS3A01G256600 chr5D 75.918 245 51 8 1727 1967 308220215 308220455 5.590000e-23 119.0
13 TraesCS3A01G256600 chr5A 85.165 364 47 4 926 1282 576340536 576340173 1.810000e-97 366.0
14 TraesCS3A01G256600 chr5A 76.016 246 49 10 1727 1967 389724965 389724725 5.590000e-23 119.0
15 TraesCS3A01G256600 chr7A 91.071 56 5 0 3015 3070 642378769 642378824 3.410000e-10 76.8
16 TraesCS3A01G256600 chr6B 93.617 47 3 0 3016 3062 416732885 416732839 1.590000e-08 71.3
17 TraesCS3A01G256600 chr6B 87.719 57 6 1 3014 3070 26089257 26089312 7.390000e-07 65.8
18 TraesCS3A01G256600 chr7D 86.667 60 7 1 3007 3065 47118249 47118308 7.390000e-07 65.8
19 TraesCS3A01G256600 chr7D 87.500 56 7 0 3015 3070 556776446 556776501 7.390000e-07 65.8
20 TraesCS3A01G256600 chr7B 85.714 56 8 0 3015 3070 84384231 84384286 3.440000e-05 60.2


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 TraesCS3A01G256600 chr3A 478664579 478667768 3189 False 5891.0 5891 100.0000 1 3190 1 chr3A.!!$F1 3189
1 TraesCS3A01G256600 chr3B 465067602 465070131 2529 False 3265.0 3265 90.3050 1 2513 1 chr3B.!!$F1 2512
2 TraesCS3A01G256600 chr3B 465092943 465093605 662 False 647.0 647 84.6720 2511 3177 1 chr3B.!!$F2 666
3 TraesCS3A01G256600 chr3D 359091223 359094048 2825 False 1664.5 3075 87.8095 4 2513 2 chr3D.!!$F2 2509
4 TraesCS3A01G256600 chr3D 359105845 359106520 675 False 713.0 713 86.1720 2511 3177 1 chr3D.!!$F1 666
5 TraesCS3A01G256600 chr5B 561692255 561693675 1420 True 1354.0 1354 84.3120 933 2339 1 chr5B.!!$R1 1406
6 TraesCS3A01G256600 chr5B 561712469 561713770 1301 True 1303.0 1303 84.9250 882 2201 1 chr5B.!!$R2 1319
7 TraesCS3A01G256600 chr5D 458457290 458459681 2391 True 755.5 1352 84.4945 933 2253 2 chr5D.!!$R1 1320

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
209 234 0.239879 CAATCCCCAAAACCACGACG 59.760 55.0 0.00 0.0 0.00 5.12 F
264 289 0.249489 CAGGGACTAATCGAAGCCCG 60.249 60.0 9.55 0.0 43.64 6.13 F
824 862 0.458197 TCACGTCACGTCACGGTTTT 60.458 50.0 18.20 0.0 44.41 2.43 F
1689 1786 0.178068 CCCGGAGATGACGAACCAAT 59.822 55.0 0.73 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1574 1653 0.454600 TGAAGTAGACATCGCCGGTC 59.545 55.000 1.9 0.0 35.5 4.79 R
1655 1752 0.808755 CCGGGGTTCATGCTACAAAC 59.191 55.000 0.0 0.0 0.0 2.93 R
1693 1790 0.871722 GTTGAACCTGCACGCACATA 59.128 50.000 0.0 0.0 0.0 2.29 R
2745 3779 1.008538 CTTCCGCATTTATGGCCGC 60.009 57.895 0.0 0.0 0.0 6.53 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
74 75 3.126858 TCCAACTTAACGATTGCTCATGC 59.873 43.478 0.00 0.00 40.20 4.06
144 169 2.280628 GAAAGCTACCATGGACCGAAG 58.719 52.381 21.47 8.45 0.00 3.79
209 234 0.239879 CAATCCCCAAAACCACGACG 59.760 55.000 0.00 0.00 0.00 5.12
219 244 3.853330 CCACGACGCAATCAGCCG 61.853 66.667 0.00 0.00 41.38 5.52
242 267 1.153549 AAGCAAGCGATCTCGGGAC 60.154 57.895 1.34 0.00 40.23 4.46
264 289 0.249489 CAGGGACTAATCGAAGCCCG 60.249 60.000 9.55 0.00 43.64 6.13
307 332 2.108566 CCCATGCTCGAGCTCCAG 59.891 66.667 35.27 21.72 42.66 3.86
380 418 2.905935 TAAGACGGAGGAGGCGGAGG 62.906 65.000 0.00 0.00 0.00 4.30
388 426 1.076923 GGAGGCGGAGGTGTAGAGA 60.077 63.158 0.00 0.00 0.00 3.10
734 772 0.725117 GCGAACAATACCTGAACCGG 59.275 55.000 0.00 0.00 0.00 5.28
735 773 1.942586 GCGAACAATACCTGAACCGGT 60.943 52.381 0.00 0.00 41.10 5.28
821 859 2.025156 GTCACGTCACGTCACGGT 59.975 61.111 18.20 0.00 44.41 4.83
822 860 1.587088 GTCACGTCACGTCACGGTT 60.587 57.895 18.20 0.00 44.41 4.44
823 861 1.139308 TCACGTCACGTCACGGTTT 59.861 52.632 18.20 0.00 44.41 3.27
824 862 0.458197 TCACGTCACGTCACGGTTTT 60.458 50.000 18.20 0.00 44.41 2.43
825 863 1.198767 CACGTCACGTCACGGTTTTA 58.801 50.000 18.20 0.00 44.41 1.52
826 864 1.071959 CACGTCACGTCACGGTTTTAC 60.072 52.381 18.20 0.00 44.41 2.01
827 865 1.202290 ACGTCACGTCACGGTTTTACT 60.202 47.619 18.20 0.00 44.41 2.24
828 866 1.854126 CGTCACGTCACGGTTTTACTT 59.146 47.619 3.22 0.00 36.07 2.24
829 867 3.042189 CGTCACGTCACGGTTTTACTTA 58.958 45.455 3.22 0.00 36.07 2.24
830 868 3.121696 CGTCACGTCACGGTTTTACTTAC 60.122 47.826 3.22 0.00 36.07 2.34
831 869 3.796178 GTCACGTCACGGTTTTACTTACA 59.204 43.478 0.35 0.00 0.00 2.41
832 870 4.043750 TCACGTCACGGTTTTACTTACAG 58.956 43.478 0.35 0.00 0.00 2.74
833 871 3.798337 CACGTCACGGTTTTACTTACAGT 59.202 43.478 0.35 0.00 0.00 3.55
834 872 4.268405 CACGTCACGGTTTTACTTACAGTT 59.732 41.667 0.35 0.00 0.00 3.16
835 873 4.504097 ACGTCACGGTTTTACTTACAGTTC 59.496 41.667 0.35 0.00 0.00 3.01
836 874 4.374309 CGTCACGGTTTTACTTACAGTTCG 60.374 45.833 0.00 0.00 0.00 3.95
837 875 4.504097 GTCACGGTTTTACTTACAGTTCGT 59.496 41.667 0.00 0.00 0.00 3.85
838 876 4.739716 TCACGGTTTTACTTACAGTTCGTC 59.260 41.667 0.00 0.00 0.00 4.20
839 877 4.503734 CACGGTTTTACTTACAGTTCGTCA 59.496 41.667 0.00 0.00 0.00 4.35
840 878 4.504097 ACGGTTTTACTTACAGTTCGTCAC 59.496 41.667 0.00 0.00 0.00 3.67
841 879 4.374309 CGGTTTTACTTACAGTTCGTCACG 60.374 45.833 0.00 0.00 0.00 4.35
842 880 4.084900 GGTTTTACTTACAGTTCGTCACGG 60.085 45.833 0.00 0.00 0.00 4.94
874 912 2.803956 AGTTCGTGTGGGATTTTACGTG 59.196 45.455 0.00 0.00 37.74 4.49
905 943 5.421212 GTAGGATTACTACCGTGTCTCTG 57.579 47.826 0.00 0.00 45.15 3.35
906 944 3.288964 AGGATTACTACCGTGTCTCTGG 58.711 50.000 0.00 0.00 0.00 3.86
907 945 3.022406 GGATTACTACCGTGTCTCTGGT 58.978 50.000 0.00 0.00 42.34 4.00
908 946 3.066481 GGATTACTACCGTGTCTCTGGTC 59.934 52.174 0.00 0.00 39.70 4.02
909 947 3.430042 TTACTACCGTGTCTCTGGTCT 57.570 47.619 0.00 0.00 39.70 3.85
955 1000 2.358090 CCCATAAAAGGCATGGAGGTGA 60.358 50.000 3.28 0.00 44.95 4.02
985 1030 5.221864 ACGACTTCCCATAGAGGAAAACTTT 60.222 40.000 0.00 0.00 45.25 2.66
993 1038 5.337652 CCATAGAGGAAAACTTTCGAGGACT 60.338 44.000 0.00 0.00 41.22 3.85
1056 1119 4.735132 TGCCTCGTTTCCCTCGCG 62.735 66.667 0.00 0.00 0.00 5.87
1233 1296 2.045926 GGCTGGACCACATTCGCT 60.046 61.111 0.00 0.00 38.86 4.93
1254 1317 2.949177 ACAATGCCAACTACAGGTCA 57.051 45.000 0.00 0.00 0.00 4.02
1282 1350 9.522804 TGTAATTAAAAGCTCAAAATCGTGTTT 57.477 25.926 0.00 0.00 0.00 2.83
1317 1396 4.046462 TCGACCGCGATCTAAAATTTAGG 58.954 43.478 8.23 0.00 42.51 2.69
1327 1406 7.396419 CGATCTAAAATTTAGGTTACGTGTGG 58.604 38.462 12.29 0.00 0.00 4.17
1574 1653 1.874019 CCTCGACGTTGATCAGGCG 60.874 63.158 16.68 16.68 0.00 5.52
1636 1727 4.367023 GAGGTACCGCACACGCCA 62.367 66.667 11.20 0.00 38.22 5.69
1655 1752 3.788797 GCCAGATCACGCCTTAAAAATCG 60.789 47.826 0.00 0.00 0.00 3.34
1688 1785 1.594833 CCCGGAGATGACGAACCAA 59.405 57.895 0.73 0.00 0.00 3.67
1689 1786 0.178068 CCCGGAGATGACGAACCAAT 59.822 55.000 0.73 0.00 0.00 3.16
1690 1787 1.290203 CCGGAGATGACGAACCAATG 58.710 55.000 0.00 0.00 0.00 2.82
1691 1788 1.405526 CCGGAGATGACGAACCAATGT 60.406 52.381 0.00 0.00 0.00 2.71
1692 1789 2.346803 CGGAGATGACGAACCAATGTT 58.653 47.619 0.00 0.00 37.42 2.71
1693 1790 2.742053 CGGAGATGACGAACCAATGTTT 59.258 45.455 0.00 0.00 33.97 2.83
1709 1806 1.265635 TGTTTATGTGCGTGCAGGTTC 59.734 47.619 8.40 2.48 0.00 3.62
1769 1866 3.887327 CTCAAGTACGACGCGCGC 61.887 66.667 32.58 23.91 46.04 6.86
2183 2283 6.039616 CGAGCTTGATTATATAGGCCTCTTC 58.960 44.000 9.68 0.00 0.00 2.87
2201 2301 5.389642 TCTTCGTTTGATCGATTATGTGC 57.610 39.130 0.00 0.00 39.57 4.57
2210 2311 1.439353 CGATTATGTGCCAGCGCCTT 61.439 55.000 2.29 0.00 0.00 4.35
2211 2312 0.740737 GATTATGTGCCAGCGCCTTT 59.259 50.000 2.29 0.00 0.00 3.11
2212 2313 1.946768 GATTATGTGCCAGCGCCTTTA 59.053 47.619 2.29 0.00 0.00 1.85
2259 2676 6.586844 GTGGTTGTCTCATTGAGTTAGTAGAC 59.413 42.308 13.23 3.68 35.13 2.59
2284 2701 4.251268 AGTTAAAGGTCATGGCTTCGTAC 58.749 43.478 0.00 0.00 0.00 3.67
2400 3426 9.884465 ATTTTTCTTTCTGAACTTCGACTATTG 57.116 29.630 0.00 0.00 33.88 1.90
2408 3434 7.017645 TCTGAACTTCGACTATTGTTACGTAC 58.982 38.462 0.00 0.00 0.00 3.67
2412 3438 9.329913 GAACTTCGACTATTGTTACGTACTTAA 57.670 33.333 0.00 0.00 0.00 1.85
2413 3439 9.846248 AACTTCGACTATTGTTACGTACTTAAT 57.154 29.630 0.00 0.00 0.00 1.40
2445 3475 9.320295 ACCATTAATTAGGAAAACATGAAAGGA 57.680 29.630 0.00 0.00 0.00 3.36
2481 3511 6.538742 AGTCATCCATAATTCTTTGTACACGG 59.461 38.462 0.00 0.00 0.00 4.94
2497 3527 4.104696 ACACGGAAAAGGACAACAAAAG 57.895 40.909 0.00 0.00 0.00 2.27
2499 3529 4.401202 ACACGGAAAAGGACAACAAAAGAT 59.599 37.500 0.00 0.00 0.00 2.40
2537 3567 1.270907 GCCAGTTCTCTCTTCTCCCA 58.729 55.000 0.00 0.00 0.00 4.37
2556 3586 3.193479 CCCATCCAGAAAAGTTGGCTTAC 59.807 47.826 0.00 0.00 35.62 2.34
2612 3643 4.693283 TGGACTGACAACTACAGTTTCTG 58.307 43.478 0.00 0.00 46.57 3.02
2624 3655 8.495949 CAACTACAGTTTCTGTATGGTTTAGTG 58.504 37.037 9.55 0.00 44.49 2.74
2654 3685 1.878953 TCAACCGTGAAAAGGCTCTC 58.121 50.000 0.00 0.00 40.05 3.20
2659 3690 5.105106 TCAACCGTGAAAAGGCTCTCATATA 60.105 40.000 2.92 0.00 40.05 0.86
2667 3698 7.798982 GTGAAAAGGCTCTCATATATAAAACGC 59.201 37.037 2.92 0.00 0.00 4.84
2683 3714 3.478857 AACGCGGGGATATGATGTAAA 57.521 42.857 12.47 0.00 0.00 2.01
2687 3718 2.290323 GCGGGGATATGATGTAAAGGCT 60.290 50.000 0.00 0.00 0.00 4.58
2688 3719 3.338249 CGGGGATATGATGTAAAGGCTG 58.662 50.000 0.00 0.00 0.00 4.85
2690 3721 3.498481 GGGGATATGATGTAAAGGCTGCA 60.498 47.826 0.50 0.00 0.00 4.41
2691 3722 4.144297 GGGATATGATGTAAAGGCTGCAA 58.856 43.478 0.50 0.00 0.00 4.08
2692 3723 4.768968 GGGATATGATGTAAAGGCTGCAAT 59.231 41.667 0.50 0.00 0.00 3.56
2693 3724 5.336213 GGGATATGATGTAAAGGCTGCAATG 60.336 44.000 0.50 0.00 0.00 2.82
2702 3736 3.058160 GCTGCAATGCTGACCCGT 61.058 61.111 16.29 0.00 0.00 5.28
2706 3740 1.745087 CTGCAATGCTGACCCGTAAAT 59.255 47.619 6.82 0.00 0.00 1.40
2735 3769 0.461870 CATCCATCCGCGGACAGAAA 60.462 55.000 33.75 17.12 38.07 2.52
2736 3770 0.179073 ATCCATCCGCGGACAGAAAG 60.179 55.000 33.75 15.37 38.07 2.62
2737 3771 1.218047 CCATCCGCGGACAGAAAGA 59.782 57.895 33.75 5.46 0.00 2.52
2738 3772 1.084370 CCATCCGCGGACAGAAAGAC 61.084 60.000 33.75 0.00 0.00 3.01
2739 3773 0.108615 CATCCGCGGACAGAAAGACT 60.109 55.000 33.75 8.42 0.00 3.24
2740 3774 1.134367 CATCCGCGGACAGAAAGACTA 59.866 52.381 33.75 2.92 0.00 2.59
2741 3775 0.809385 TCCGCGGACAGAAAGACTAG 59.191 55.000 27.28 0.00 0.00 2.57
2742 3776 0.526662 CCGCGGACAGAAAGACTAGT 59.473 55.000 24.07 0.00 0.00 2.57
2743 3777 1.467713 CCGCGGACAGAAAGACTAGTC 60.468 57.143 24.07 15.41 0.00 2.59
2744 3778 1.469308 CGCGGACAGAAAGACTAGTCT 59.531 52.381 20.00 20.00 42.75 3.24
2745 3779 2.729467 CGCGGACAGAAAGACTAGTCTG 60.729 54.545 25.83 16.10 45.59 3.51
2746 3780 2.869897 CGGACAGAAAGACTAGTCTGC 58.130 52.381 25.83 19.61 44.25 4.26
2747 3781 2.729467 CGGACAGAAAGACTAGTCTGCG 60.729 54.545 25.83 15.51 44.25 5.18
2748 3782 2.416162 GGACAGAAAGACTAGTCTGCGG 60.416 54.545 25.83 21.22 44.25 5.69
2753 3787 1.776662 AAGACTAGTCTGCGGCCATA 58.223 50.000 25.83 0.00 40.36 2.74
2761 3795 2.124529 TGCGGCCATAAATGCGGA 60.125 55.556 2.24 0.00 0.00 5.54
2780 3814 3.744660 GGAAGGCGGACATCTTCAATAT 58.255 45.455 0.00 0.00 40.65 1.28
2818 3856 3.470709 ACCGAGTATGCCATCTTCAATG 58.529 45.455 0.00 0.00 0.00 2.82
2822 3860 4.751600 CGAGTATGCCATCTTCAATGCTAA 59.248 41.667 0.00 0.00 0.00 3.09
2823 3861 5.107182 CGAGTATGCCATCTTCAATGCTAAG 60.107 44.000 0.00 0.00 0.00 2.18
2851 3889 4.701171 TGCATGTATGTTTGATTGAGCTCA 59.299 37.500 13.74 13.74 0.00 4.26
2852 3890 5.163693 TGCATGTATGTTTGATTGAGCTCAG 60.164 40.000 17.43 0.90 0.00 3.35
2898 3936 7.874528 ACAAGATTGGAGTGGATGAAAATTTTC 59.125 33.333 21.60 21.60 37.69 2.29
2900 3938 8.198807 AGATTGGAGTGGATGAAAATTTTCTT 57.801 30.769 26.73 21.84 38.02 2.52
2902 3940 9.358872 GATTGGAGTGGATGAAAATTTTCTTAC 57.641 33.333 26.73 22.22 38.02 2.34
2925 3963 5.357032 ACGAAATCCAGTACAAATGAATCCC 59.643 40.000 0.00 0.00 0.00 3.85
3000 4039 4.799564 ATTCTTTTAATCAAAGCGGCCA 57.200 36.364 2.24 0.00 41.72 5.36
3004 4043 6.463995 TCTTTTAATCAAAGCGGCCATATT 57.536 33.333 2.24 0.00 41.72 1.28
3027 4066 6.683974 TTCTTTAAGCAACTAGATGATGCC 57.316 37.500 3.85 0.00 44.25 4.40
3030 4069 0.107456 AGCAACTAGATGATGCCCCG 59.893 55.000 3.85 0.00 44.25 5.73
3033 4072 1.399744 AACTAGATGATGCCCCGCGA 61.400 55.000 8.23 0.00 0.00 5.87
3050 4089 1.298157 CGAGTTGCTGCGGGAATCAA 61.298 55.000 1.67 0.00 0.00 2.57
3172 4220 4.640771 AATTGTATGTGGTGGTGAGTCT 57.359 40.909 0.00 0.00 0.00 3.24
3177 4225 5.931294 TGTATGTGGTGGTGAGTCTTTTTA 58.069 37.500 0.00 0.00 0.00 1.52
3178 4226 5.761234 TGTATGTGGTGGTGAGTCTTTTTAC 59.239 40.000 0.00 0.00 0.00 2.01
3179 4227 4.223556 TGTGGTGGTGAGTCTTTTTACA 57.776 40.909 0.00 0.00 0.00 2.41
3180 4228 4.787551 TGTGGTGGTGAGTCTTTTTACAT 58.212 39.130 0.00 0.00 0.00 2.29
3181 4229 5.931294 TGTGGTGGTGAGTCTTTTTACATA 58.069 37.500 0.00 0.00 0.00 2.29
3182 4230 5.761234 TGTGGTGGTGAGTCTTTTTACATAC 59.239 40.000 0.00 0.00 0.00 2.39
3183 4231 5.761234 GTGGTGGTGAGTCTTTTTACATACA 59.239 40.000 0.00 0.00 0.00 2.29
3184 4232 6.430000 GTGGTGGTGAGTCTTTTTACATACAT 59.570 38.462 0.00 0.00 0.00 2.29
3185 4233 6.429692 TGGTGGTGAGTCTTTTTACATACATG 59.570 38.462 0.00 0.00 0.00 3.21
3186 4234 6.128007 GGTGGTGAGTCTTTTTACATACATGG 60.128 42.308 0.00 0.00 0.00 3.66
3187 4235 6.430000 GTGGTGAGTCTTTTTACATACATGGT 59.570 38.462 0.00 0.00 0.00 3.55
3188 4236 7.001674 TGGTGAGTCTTTTTACATACATGGTT 58.998 34.615 0.00 0.00 0.00 3.67
3189 4237 7.040755 TGGTGAGTCTTTTTACATACATGGTTG 60.041 37.037 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 1.734885 GCTTAACGCATGAGCAATCG 58.265 50.000 0.00 0.00 42.27 3.34
144 169 3.371702 GGGGATTTAGTGAAAGGAGGTCC 60.372 52.174 0.00 0.00 0.00 4.46
209 234 2.180017 CTTGCCACGGCTGATTGC 59.820 61.111 9.92 0.00 42.51 3.56
219 244 1.427020 GAGATCGCTTGCTTGCCAC 59.573 57.895 0.00 0.00 0.00 5.01
242 267 1.069358 GGCTTCGATTAGTCCCTGGAG 59.931 57.143 0.00 0.00 0.00 3.86
264 289 2.443577 GTAGGACCCGACCCCTCC 60.444 72.222 0.00 0.00 34.11 4.30
307 332 3.274288 CTGTAGCTGAGAACCCATTTCC 58.726 50.000 0.00 0.00 34.32 3.13
380 418 1.355916 CGCCCTACGCTCTCTACAC 59.644 63.158 0.00 0.00 34.21 2.90
381 419 1.822613 CCGCCCTACGCTCTCTACA 60.823 63.158 0.00 0.00 41.76 2.74
388 426 4.444081 AGTCTCCCGCCCTACGCT 62.444 66.667 0.00 0.00 41.76 5.07
687 725 2.460853 CCCACACCCACTCCAACCT 61.461 63.158 0.00 0.00 0.00 3.50
746 784 0.598562 GTGGTCTCTGCTGAGTTCGA 59.401 55.000 18.82 9.11 40.98 3.71
801 839 2.728383 GTGACGTGACGTGACGGG 60.728 66.667 30.00 5.49 43.84 5.28
826 864 4.741676 AGTAAAACCGTGACGAACTGTAAG 59.258 41.667 6.54 0.00 42.29 2.34
827 865 4.681744 AGTAAAACCGTGACGAACTGTAA 58.318 39.130 6.54 0.00 0.00 2.41
828 866 4.305989 AGTAAAACCGTGACGAACTGTA 57.694 40.909 6.54 0.00 0.00 2.74
829 867 3.169355 AGTAAAACCGTGACGAACTGT 57.831 42.857 6.54 0.00 0.00 3.55
830 868 4.503734 TGTAAGTAAAACCGTGACGAACTG 59.496 41.667 6.54 0.00 0.00 3.16
831 869 4.681744 TGTAAGTAAAACCGTGACGAACT 58.318 39.130 6.54 0.00 0.00 3.01
832 870 4.998295 CTGTAAGTAAAACCGTGACGAAC 58.002 43.478 6.54 0.00 0.00 3.95
874 912 4.202090 CGGTAGTAATCCTACACCAACTCC 60.202 50.000 2.31 0.00 46.68 3.85
903 941 2.038689 CCCATGGATCAGATCAGACCAG 59.961 54.545 15.22 7.08 34.08 4.00
904 942 2.052468 CCCATGGATCAGATCAGACCA 58.948 52.381 15.22 10.34 35.09 4.02
905 943 2.038295 GACCCATGGATCAGATCAGACC 59.962 54.545 15.22 0.00 0.00 3.85
906 944 2.288702 CGACCCATGGATCAGATCAGAC 60.289 54.545 15.22 0.00 0.00 3.51
907 945 1.966354 CGACCCATGGATCAGATCAGA 59.034 52.381 15.22 0.00 0.00 3.27
908 946 1.690893 ACGACCCATGGATCAGATCAG 59.309 52.381 15.22 0.00 0.00 2.90
909 947 1.413812 CACGACCCATGGATCAGATCA 59.586 52.381 15.22 0.00 0.00 2.92
955 1000 0.669077 CTATGGGAAGTCGTAGCGCT 59.331 55.000 17.26 17.26 0.00 5.92
985 1030 1.605753 CCCATCGTCATAGTCCTCGA 58.394 55.000 0.00 0.00 36.77 4.04
993 1038 1.522806 GTTGCGCCCCATCGTCATA 60.523 57.895 4.18 0.00 0.00 2.15
1023 1086 3.782244 CAGGCAAGCACGACGAGC 61.782 66.667 9.38 9.38 0.00 5.03
1062 1125 2.375766 CGTCGTCTTGACCTGCTGC 61.376 63.158 0.00 0.00 45.23 5.25
1223 1286 1.472082 TGGCATTGTAAGCGAATGTGG 59.528 47.619 0.00 0.00 33.96 4.17
1227 1290 4.006989 TGTAGTTGGCATTGTAAGCGAAT 58.993 39.130 0.00 0.00 32.47 3.34
1233 1296 4.202419 ACTGACCTGTAGTTGGCATTGTAA 60.202 41.667 0.00 0.00 0.00 2.41
1254 1317 8.349983 ACACGATTTTGAGCTTTTAATTACACT 58.650 29.630 0.00 0.00 0.00 3.55
1285 1353 1.097232 TCGCGGTCGATCCTAAGAAA 58.903 50.000 6.13 0.00 40.21 2.52
1287 1355 4.545929 TCGCGGTCGATCCTAAGA 57.454 55.556 6.13 0.00 40.21 2.10
1299 1378 5.232838 ACGTAACCTAAATTTTAGATCGCGG 59.767 40.000 16.13 3.60 0.00 6.46
1306 1385 6.243811 TGCCACACGTAACCTAAATTTTAG 57.756 37.500 8.88 8.88 0.00 1.85
1317 1396 0.604243 TCCCACATGCCACACGTAAC 60.604 55.000 0.00 0.00 0.00 2.50
1327 1406 1.019278 CCTACACACGTCCCACATGC 61.019 60.000 0.00 0.00 0.00 4.06
1527 1606 1.789576 AAGTGGAAGGGGATGCCGTT 61.790 55.000 11.30 11.30 0.00 4.44
1533 1612 1.636003 GTTGAGGAAGTGGAAGGGGAT 59.364 52.381 0.00 0.00 0.00 3.85
1574 1653 0.454600 TGAAGTAGACATCGCCGGTC 59.545 55.000 1.90 0.00 35.50 4.79
1629 1720 1.884075 TAAGGCGTGATCTGGCGTGT 61.884 55.000 9.74 2.58 36.92 4.49
1636 1727 5.048991 ACAAACGATTTTTAAGGCGTGATCT 60.049 36.000 0.00 0.00 37.03 2.75
1655 1752 0.808755 CCGGGGTTCATGCTACAAAC 59.191 55.000 0.00 0.00 0.00 2.93
1688 1785 1.533625 ACCTGCACGCACATAAACAT 58.466 45.000 0.00 0.00 0.00 2.71
1689 1786 1.265635 GAACCTGCACGCACATAAACA 59.734 47.619 0.00 0.00 0.00 2.83
1690 1787 1.265635 TGAACCTGCACGCACATAAAC 59.734 47.619 0.00 0.00 0.00 2.01
1691 1788 1.598882 TGAACCTGCACGCACATAAA 58.401 45.000 0.00 0.00 0.00 1.40
1692 1789 1.265635 GTTGAACCTGCACGCACATAA 59.734 47.619 0.00 0.00 0.00 1.90
1693 1790 0.871722 GTTGAACCTGCACGCACATA 59.128 50.000 0.00 0.00 0.00 2.29
1709 1806 3.000623 CGTTCATGATGATCTCCGTGTTG 59.999 47.826 0.00 0.00 0.00 3.33
1773 1870 2.505118 GAGCACCGTGACGAGCTC 60.505 66.667 26.90 26.90 43.07 4.09
2183 2283 3.846023 GCTGGCACATAATCGATCAAACG 60.846 47.826 0.00 0.00 38.20 3.60
2201 2301 1.750778 ACAAATCCATAAAGGCGCTGG 59.249 47.619 7.64 6.86 37.29 4.85
2259 2676 3.372206 CGAAGCCATGACCTTTAACTCTG 59.628 47.826 0.00 0.00 0.00 3.35
2284 2701 2.093306 TGCATGTAGTCCTGAAACCG 57.907 50.000 0.00 0.00 0.00 4.44
2497 3527 3.458189 CCCTCCAGTATCGAACAACATC 58.542 50.000 0.00 0.00 0.00 3.06
2499 3529 1.066430 GCCCTCCAGTATCGAACAACA 60.066 52.381 0.00 0.00 0.00 3.33
2537 3567 3.081804 CGGTAAGCCAACTTTTCTGGAT 58.918 45.455 0.00 0.00 37.33 3.41
2556 3586 1.318576 AAACAAGAGGCTGTTTCCGG 58.681 50.000 0.00 0.00 44.32 5.14
2612 3643 6.707608 TGATGCATCATCTCACTAAACCATAC 59.292 38.462 25.42 0.00 41.06 2.39
2624 3655 2.554142 TCACGGTTGATGCATCATCTC 58.446 47.619 29.13 20.54 41.06 2.75
2654 3685 7.441157 ACATCATATCCCCGCGTTTTATATATG 59.559 37.037 4.92 9.53 0.00 1.78
2659 3690 4.015872 ACATCATATCCCCGCGTTTTAT 57.984 40.909 4.92 0.00 0.00 1.40
2667 3698 3.338249 CAGCCTTTACATCATATCCCCG 58.662 50.000 0.00 0.00 0.00 5.73
2683 3714 2.362120 GGGTCAGCATTGCAGCCT 60.362 61.111 11.91 0.00 34.23 4.58
2687 3718 1.742831 GATTTACGGGTCAGCATTGCA 59.257 47.619 11.91 0.00 0.00 4.08
2688 3719 1.268032 CGATTTACGGGTCAGCATTGC 60.268 52.381 0.00 0.00 38.46 3.56
2702 3736 4.196193 GGATGGATGTTGTGTCCGATTTA 58.804 43.478 0.00 0.00 38.64 1.40
2706 3740 3.853104 GGATGGATGTTGTGTCCGA 57.147 52.632 0.00 0.00 38.64 4.55
2714 3748 1.153369 CTGTCCGCGGATGGATGTT 60.153 57.895 33.58 0.00 40.91 2.71
2715 3749 1.613317 TTCTGTCCGCGGATGGATGT 61.613 55.000 33.58 0.00 40.91 3.06
2719 3753 1.084370 GTCTTTCTGTCCGCGGATGG 61.084 60.000 33.58 25.38 0.00 3.51
2735 3769 1.776662 TTATGGCCGCAGACTAGTCT 58.223 50.000 20.00 20.00 41.37 3.24
2736 3770 2.596904 TTTATGGCCGCAGACTAGTC 57.403 50.000 15.41 15.41 0.00 2.59
2737 3771 2.838736 CATTTATGGCCGCAGACTAGT 58.161 47.619 0.00 0.00 0.00 2.57
2738 3772 1.532868 GCATTTATGGCCGCAGACTAG 59.467 52.381 0.00 0.00 0.00 2.57
2739 3773 1.593196 GCATTTATGGCCGCAGACTA 58.407 50.000 0.00 0.00 0.00 2.59
2740 3774 1.439353 CGCATTTATGGCCGCAGACT 61.439 55.000 0.00 0.00 0.00 3.24
2741 3775 1.009675 CGCATTTATGGCCGCAGAC 60.010 57.895 0.00 0.00 0.00 3.51
2742 3776 2.186160 CCGCATTTATGGCCGCAGA 61.186 57.895 0.00 0.00 0.00 4.26
2743 3777 1.723608 TTCCGCATTTATGGCCGCAG 61.724 55.000 0.00 0.00 0.00 5.18
2744 3778 1.723608 CTTCCGCATTTATGGCCGCA 61.724 55.000 0.00 0.00 0.00 5.69
2745 3779 1.008538 CTTCCGCATTTATGGCCGC 60.009 57.895 0.00 0.00 0.00 6.53
2746 3780 1.654220 CCTTCCGCATTTATGGCCG 59.346 57.895 0.00 0.00 0.00 6.13
2747 3781 1.363807 GCCTTCCGCATTTATGGCC 59.636 57.895 0.00 0.00 37.47 5.36
2748 3782 1.008538 CGCCTTCCGCATTTATGGC 60.009 57.895 0.00 0.00 37.30 4.40
2753 3787 1.376609 GATGTCCGCCTTCCGCATTT 61.377 55.000 0.00 0.00 37.30 2.32
2761 3795 6.530019 AAAAATATTGAAGATGTCCGCCTT 57.470 33.333 0.00 0.00 0.00 4.35
2818 3856 5.067674 TCAAACATACATGCAATCCCTTAGC 59.932 40.000 0.00 0.00 0.00 3.09
2822 3860 5.657745 TCAATCAAACATACATGCAATCCCT 59.342 36.000 0.00 0.00 0.00 4.20
2823 3861 5.904941 TCAATCAAACATACATGCAATCCC 58.095 37.500 0.00 0.00 0.00 3.85
2851 3889 9.739276 TCTTGTGTGAATATTCCTATGTTTTCT 57.261 29.630 12.90 0.00 0.00 2.52
2898 3936 8.122952 GGATTCATTTGTACTGGATTTCGTAAG 58.877 37.037 0.00 0.00 0.00 2.34
2900 3938 6.540914 GGGATTCATTTGTACTGGATTTCGTA 59.459 38.462 0.00 0.00 0.00 3.43
2902 3940 5.356751 TGGGATTCATTTGTACTGGATTTCG 59.643 40.000 0.00 0.00 0.00 3.46
2986 4025 6.463995 AAAGAAATATGGCCGCTTTGATTA 57.536 33.333 0.00 0.00 0.00 1.75
3004 4043 5.590259 GGGCATCATCTAGTTGCTTAAAGAA 59.410 40.000 0.00 0.00 41.61 2.52
3030 4069 3.100862 GATTCCCGCAGCAACTCGC 62.101 63.158 0.00 0.00 42.91 5.03
3033 4072 1.203052 CAATTGATTCCCGCAGCAACT 59.797 47.619 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.