Multiple sequence alignment - TraesCS3B01G150000

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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 TraesCS3B01G150000 chr3B 100.000 2996 0 0 1 2996 141136108 141133113 0.000000e+00 5533
1 TraesCS3B01G150000 chr3B 82.100 1000 132 25 993 1964 141285605 141286585 0.000000e+00 811
2 TraesCS3B01G150000 chr3B 82.091 966 143 16 1022 1963 141735411 141736370 0.000000e+00 798
3 TraesCS3B01G150000 chr3B 81.474 1004 147 20 987 1963 141288915 141289906 0.000000e+00 787
4 TraesCS3B01G150000 chr3D 93.050 1367 64 6 909 2251 91683105 91681746 0.000000e+00 1969
5 TraesCS3B01G150000 chr3D 89.886 702 69 1 1 700 596069593 596070294 0.000000e+00 902
6 TraesCS3B01G150000 chr3D 81.747 767 117 9 1219 1963 91797729 91798494 1.180000e-173 619
7 TraesCS3B01G150000 chr3D 86.334 461 44 10 2549 2996 91679666 91679212 4.490000e-133 484
8 TraesCS3B01G150000 chr3D 84.759 374 43 9 989 1361 91690874 91691234 2.200000e-96 363
9 TraesCS3B01G150000 chr3A 91.005 1423 76 20 841 2236 107757245 107755848 0.000000e+00 1871
10 TraesCS3B01G150000 chr3A 82.435 1002 142 14 987 1963 545281334 545282326 0.000000e+00 845
11 TraesCS3B01G150000 chr3A 82.010 995 143 18 993 1964 545257489 545258470 0.000000e+00 813
12 TraesCS3B01G150000 chr3A 81.056 966 150 16 1022 1963 545331387 545332343 0.000000e+00 739
13 TraesCS3B01G150000 chr3A 87.188 601 47 12 2419 2996 107755571 107754978 0.000000e+00 656
14 TraesCS3B01G150000 chrUn 92.170 728 51 5 1 724 90094658 90093933 0.000000e+00 1024
15 TraesCS3B01G150000 chr2D 92.181 729 49 7 1 724 59840953 59840228 0.000000e+00 1024
16 TraesCS3B01G150000 chr2D 87.010 816 86 14 1 800 43734451 43735262 0.000000e+00 902
17 TraesCS3B01G150000 chr7B 91.322 726 59 3 1 724 229198322 229199045 0.000000e+00 989
18 TraesCS3B01G150000 chr4D 90.883 702 62 1 1 700 72576484 72575783 0.000000e+00 941
19 TraesCS3B01G150000 chr6B 87.623 816 85 11 1 803 84669584 84670396 0.000000e+00 933
20 TraesCS3B01G150000 chr4B 90.741 702 62 2 1 700 628584429 628583729 0.000000e+00 933
21 TraesCS3B01G150000 chr2B 89.889 722 64 7 2 716 107037350 107038069 0.000000e+00 920
22 TraesCS3B01G150000 chr6A 88.372 731 75 9 1 724 162548325 162549052 0.000000e+00 870


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 TraesCS3B01G150000 chr3B 141133113 141136108 2995 True 5533.0 5533 100.0000 1 2996 1 chr3B.!!$R1 2995
1 TraesCS3B01G150000 chr3B 141285605 141289906 4301 False 799.0 811 81.7870 987 1964 2 chr3B.!!$F2 977
2 TraesCS3B01G150000 chr3B 141735411 141736370 959 False 798.0 798 82.0910 1022 1963 1 chr3B.!!$F1 941
3 TraesCS3B01G150000 chr3D 91679212 91683105 3893 True 1226.5 1969 89.6920 909 2996 2 chr3D.!!$R1 2087
4 TraesCS3B01G150000 chr3D 596069593 596070294 701 False 902.0 902 89.8860 1 700 1 chr3D.!!$F3 699
5 TraesCS3B01G150000 chr3D 91797729 91798494 765 False 619.0 619 81.7470 1219 1963 1 chr3D.!!$F2 744
6 TraesCS3B01G150000 chr3A 107754978 107757245 2267 True 1263.5 1871 89.0965 841 2996 2 chr3A.!!$R1 2155
7 TraesCS3B01G150000 chr3A 545281334 545282326 992 False 845.0 845 82.4350 987 1963 1 chr3A.!!$F2 976
8 TraesCS3B01G150000 chr3A 545257489 545258470 981 False 813.0 813 82.0100 993 1964 1 chr3A.!!$F1 971
9 TraesCS3B01G150000 chr3A 545331387 545332343 956 False 739.0 739 81.0560 1022 1963 1 chr3A.!!$F3 941
10 TraesCS3B01G150000 chrUn 90093933 90094658 725 True 1024.0 1024 92.1700 1 724 1 chrUn.!!$R1 723
11 TraesCS3B01G150000 chr2D 59840228 59840953 725 True 1024.0 1024 92.1810 1 724 1 chr2D.!!$R1 723
12 TraesCS3B01G150000 chr2D 43734451 43735262 811 False 902.0 902 87.0100 1 800 1 chr2D.!!$F1 799
13 TraesCS3B01G150000 chr7B 229198322 229199045 723 False 989.0 989 91.3220 1 724 1 chr7B.!!$F1 723
14 TraesCS3B01G150000 chr4D 72575783 72576484 701 True 941.0 941 90.8830 1 700 1 chr4D.!!$R1 699
15 TraesCS3B01G150000 chr6B 84669584 84670396 812 False 933.0 933 87.6230 1 803 1 chr6B.!!$F1 802
16 TraesCS3B01G150000 chr4B 628583729 628584429 700 True 933.0 933 90.7410 1 700 1 chr4B.!!$R1 699
17 TraesCS3B01G150000 chr2B 107037350 107038069 719 False 920.0 920 89.8890 2 716 1 chr2B.!!$F1 714
18 TraesCS3B01G150000 chr6A 162548325 162549052 727 False 870.0 870 88.3720 1 724 1 chr6A.!!$F1 723

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
829 856 0.106335 ATCCTCTCATGCGCTTCCAG 59.894 55.0 9.73 0.35 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2342 7559 0.251787 TGGTGACAGCAGCTAGAGGA 60.252 55.0 2.5 0.0 42.84 3.71 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
53 54 8.793592 ACTTTAACCAGACCAGATATTTGTTTC 58.206 33.333 0.00 0.00 0.00 2.78
75 76 5.487433 TCTCAGTCAACAAAGTTTGTCAGA 58.513 37.500 21.10 18.04 44.59 3.27
93 94 1.069823 AGATCCTTCATGCGCCTACTG 59.930 52.381 4.18 0.00 0.00 2.74
94 95 1.069204 GATCCTTCATGCGCCTACTGA 59.931 52.381 4.18 0.00 0.00 3.41
324 330 6.542735 AGCTATTGTGTCTAGATCGAGTACAA 59.457 38.462 20.73 20.73 32.97 2.41
423 429 2.341257 GTCACTCATCTGCAACGTCAT 58.659 47.619 0.00 0.00 0.00 3.06
493 499 4.988065 TGCTAGGACGAAGCACAC 57.012 55.556 0.00 0.00 44.78 3.82
498 504 0.888619 TAGGACGAAGCACACTGAGG 59.111 55.000 0.00 0.00 0.00 3.86
550 556 7.315890 GTGGCTAACAAGCTTTTGAATATTCT 58.684 34.615 16.24 0.00 34.73 2.40
559 565 9.252962 CAAGCTTTTGAATATTCTGTTTGTTCT 57.747 29.630 16.24 1.75 0.00 3.01
599 605 3.621715 CGGATGGCTTTACTAAACCACTC 59.378 47.826 5.49 5.41 34.36 3.51
618 624 2.031012 CACTGCGGCAACTGGAGA 59.969 61.111 3.44 0.00 33.99 3.71
629 635 3.368531 GGCAACTGGAGATCTTTAGACGT 60.369 47.826 12.51 0.00 0.00 4.34
676 687 4.400120 TGAGGGGGTGTTAAACATTGTAC 58.600 43.478 0.00 0.00 0.00 2.90
689 706 4.260139 ACATTGTACATCACGGTGTGTA 57.740 40.909 8.17 12.47 34.79 2.90
707 724 6.536224 GGTGTGTATATAAACCGTGCTAGTTT 59.464 38.462 0.43 5.02 40.43 2.66
708 725 7.706179 GGTGTGTATATAAACCGTGCTAGTTTA 59.294 37.037 0.43 8.34 42.25 2.01
724 742 1.463444 GTTTAGGATGTGGCGTGTGTC 59.537 52.381 0.00 0.00 0.00 3.67
725 743 0.973632 TTAGGATGTGGCGTGTGTCT 59.026 50.000 0.00 0.00 0.00 3.41
726 744 0.530744 TAGGATGTGGCGTGTGTCTC 59.469 55.000 0.00 0.00 0.00 3.36
727 745 1.741770 GGATGTGGCGTGTGTCTCC 60.742 63.158 0.00 0.00 0.00 3.71
730 757 0.108585 ATGTGGCGTGTGTCTCCTTT 59.891 50.000 0.00 0.00 0.00 3.11
731 758 0.531974 TGTGGCGTGTGTCTCCTTTC 60.532 55.000 0.00 0.00 0.00 2.62
735 762 1.000506 GGCGTGTGTCTCCTTTCTGTA 59.999 52.381 0.00 0.00 0.00 2.74
738 765 3.368236 GCGTGTGTCTCCTTTCTGTAATC 59.632 47.826 0.00 0.00 0.00 1.75
746 773 8.470805 GTGTCTCCTTTCTGTAATCTGATCTTA 58.529 37.037 0.00 0.00 0.00 2.10
747 774 8.470805 TGTCTCCTTTCTGTAATCTGATCTTAC 58.529 37.037 0.00 0.00 0.00 2.34
791 818 1.904537 CACCTAACCGAACCCTAACCT 59.095 52.381 0.00 0.00 0.00 3.50
792 819 2.303890 CACCTAACCGAACCCTAACCTT 59.696 50.000 0.00 0.00 0.00 3.50
793 820 2.981784 ACCTAACCGAACCCTAACCTTT 59.018 45.455 0.00 0.00 0.00 3.11
803 830 6.171213 CGAACCCTAACCTTTCTGTAATCTT 58.829 40.000 0.00 0.00 0.00 2.40
804 831 6.313164 CGAACCCTAACCTTTCTGTAATCTTC 59.687 42.308 0.00 0.00 0.00 2.87
805 832 5.731591 ACCCTAACCTTTCTGTAATCTTCG 58.268 41.667 0.00 0.00 0.00 3.79
806 833 4.571176 CCCTAACCTTTCTGTAATCTTCGC 59.429 45.833 0.00 0.00 0.00 4.70
807 834 4.571176 CCTAACCTTTCTGTAATCTTCGCC 59.429 45.833 0.00 0.00 0.00 5.54
808 835 3.695830 ACCTTTCTGTAATCTTCGCCA 57.304 42.857 0.00 0.00 0.00 5.69
809 836 3.335579 ACCTTTCTGTAATCTTCGCCAC 58.664 45.455 0.00 0.00 0.00 5.01
810 837 3.244422 ACCTTTCTGTAATCTTCGCCACA 60.244 43.478 0.00 0.00 0.00 4.17
811 838 3.941483 CCTTTCTGTAATCTTCGCCACAT 59.059 43.478 0.00 0.00 0.00 3.21
812 839 4.034510 CCTTTCTGTAATCTTCGCCACATC 59.965 45.833 0.00 0.00 0.00 3.06
813 840 3.179443 TCTGTAATCTTCGCCACATCC 57.821 47.619 0.00 0.00 0.00 3.51
814 841 2.766263 TCTGTAATCTTCGCCACATCCT 59.234 45.455 0.00 0.00 0.00 3.24
815 842 3.126831 CTGTAATCTTCGCCACATCCTC 58.873 50.000 0.00 0.00 0.00 3.71
816 843 2.766263 TGTAATCTTCGCCACATCCTCT 59.234 45.455 0.00 0.00 0.00 3.69
817 844 2.611225 AATCTTCGCCACATCCTCTC 57.389 50.000 0.00 0.00 0.00 3.20
818 845 1.489481 ATCTTCGCCACATCCTCTCA 58.511 50.000 0.00 0.00 0.00 3.27
819 846 1.489481 TCTTCGCCACATCCTCTCAT 58.511 50.000 0.00 0.00 0.00 2.90
820 847 1.137675 TCTTCGCCACATCCTCTCATG 59.862 52.381 0.00 0.00 0.00 3.07
821 848 0.462581 TTCGCCACATCCTCTCATGC 60.463 55.000 0.00 0.00 0.00 4.06
822 849 2.242572 CGCCACATCCTCTCATGCG 61.243 63.158 0.00 0.00 0.00 4.73
823 850 2.541120 GCCACATCCTCTCATGCGC 61.541 63.158 0.00 0.00 0.00 6.09
824 851 1.145598 CCACATCCTCTCATGCGCT 59.854 57.895 9.73 0.00 0.00 5.92
825 852 0.463295 CCACATCCTCTCATGCGCTT 60.463 55.000 9.73 0.00 0.00 4.68
826 853 0.935898 CACATCCTCTCATGCGCTTC 59.064 55.000 9.73 0.00 0.00 3.86
827 854 0.179062 ACATCCTCTCATGCGCTTCC 60.179 55.000 9.73 0.00 0.00 3.46
828 855 0.179065 CATCCTCTCATGCGCTTCCA 60.179 55.000 9.73 0.00 0.00 3.53
829 856 0.106335 ATCCTCTCATGCGCTTCCAG 59.894 55.000 9.73 0.35 0.00 3.86
830 857 2.178890 CCTCTCATGCGCTTCCAGC 61.179 63.158 9.73 0.00 38.02 4.85
831 858 2.124983 TCTCATGCGCTTCCAGCC 60.125 61.111 9.73 0.00 38.18 4.85
832 859 2.124819 CTCATGCGCTTCCAGCCT 60.125 61.111 9.73 0.00 38.18 4.58
833 860 2.124983 TCATGCGCTTCCAGCCTC 60.125 61.111 9.73 0.00 38.18 4.70
834 861 2.124819 CATGCGCTTCCAGCCTCT 60.125 61.111 9.73 0.00 38.18 3.69
835 862 1.748122 CATGCGCTTCCAGCCTCTT 60.748 57.895 9.73 0.00 38.18 2.85
836 863 1.001641 ATGCGCTTCCAGCCTCTTT 60.002 52.632 9.73 0.00 38.18 2.52
837 864 1.028868 ATGCGCTTCCAGCCTCTTTC 61.029 55.000 9.73 0.00 38.18 2.62
838 865 1.672356 GCGCTTCCAGCCTCTTTCA 60.672 57.895 0.00 0.00 38.18 2.69
839 866 1.916697 GCGCTTCCAGCCTCTTTCAC 61.917 60.000 0.00 0.00 38.18 3.18
844 871 0.687354 TCCAGCCTCTTTCACACCTC 59.313 55.000 0.00 0.00 0.00 3.85
867 894 2.046507 GACCAGAGCTGCCACCAG 60.047 66.667 0.00 0.00 42.13 4.00
892 919 1.869574 CGTGCCGTCTGATCGACAG 60.870 63.158 14.90 8.24 46.97 3.51
906 933 1.009389 CGACAGGAACCTTCGTGAGC 61.009 60.000 13.31 5.44 43.66 4.26
918 945 8.086522 GGAACCTTCGTGAGCACTAATAATATA 58.913 37.037 0.00 0.00 0.00 0.86
940 967 3.524095 ATAAATCCGATGCCCCATTGA 57.476 42.857 0.00 0.00 0.00 2.57
1048 1075 2.038813 TCATGGAGGACCTGCCGA 59.961 61.111 10.94 4.33 43.43 5.54
1156 1183 3.555324 TGCAGTGGAAGGACGCCA 61.555 61.111 0.00 0.00 0.00 5.69
1263 1305 2.341176 GTGTACTTCCACGGCGGT 59.659 61.111 13.24 0.64 35.57 5.68
1426 1468 1.682257 GCTTTCCTCTCCTGGCTGT 59.318 57.895 0.00 0.00 0.00 4.40
1584 1628 4.388499 GACGTCCACCCGGTGCAT 62.388 66.667 12.54 0.00 31.34 3.96
1620 1664 0.888619 TCATCTCTGCGTTCTTCGGT 59.111 50.000 0.00 0.00 40.26 4.69
1623 1667 1.006102 CTCTGCGTTCTTCGGTGGT 60.006 57.895 0.00 0.00 40.26 4.16
1627 1671 2.280524 CGTTCTTCGGTGGTGCCA 60.281 61.111 0.00 0.00 36.97 4.92
1695 5061 1.191535 TCGAGGGATCCGACATGTTT 58.808 50.000 5.45 0.00 0.00 2.83
1967 5396 0.386476 AAGCGGTTCGTGTACACAGA 59.614 50.000 24.98 18.92 0.00 3.41
1997 5426 3.624861 CGTAATAGTACGTCCCACTGAGT 59.375 47.826 14.24 0.00 46.49 3.41
2028 5457 4.043310 TGTTTGGTGATCTCCTGATCCTTT 59.957 41.667 14.65 0.00 46.34 3.11
2036 5466 3.415212 TCTCCTGATCCTTTTGTGCAAG 58.585 45.455 0.00 0.00 0.00 4.01
2042 5473 3.380004 TGATCCTTTTGTGCAAGTCGTTT 59.620 39.130 0.00 0.00 0.00 3.60
2074 5508 4.566545 TGCAATAATGTAAATCCAGCCG 57.433 40.909 0.00 0.00 0.00 5.52
2085 5519 0.676782 ATCCAGCCGCACAACCTAAC 60.677 55.000 0.00 0.00 0.00 2.34
2158 5592 2.604914 CCGTATGTGAGATGTTCTGTGC 59.395 50.000 0.00 0.00 0.00 4.57
2181 5615 5.482006 CTGTCTCATTAGTGATGTTGTGGA 58.518 41.667 0.00 0.00 37.06 4.02
2196 5630 5.132502 TGTTGTGGATGTGTTGAGATCTTT 58.867 37.500 0.00 0.00 0.00 2.52
2197 5631 5.239306 TGTTGTGGATGTGTTGAGATCTTTC 59.761 40.000 0.00 0.00 0.00 2.62
2198 5632 3.996363 TGTGGATGTGTTGAGATCTTTCG 59.004 43.478 0.00 0.00 0.00 3.46
2215 5649 5.853936 TCTTTCGACTTTCTCCAGATTTCA 58.146 37.500 0.00 0.00 0.00 2.69
2258 5753 5.816919 ACTATTTCAACACAAAAGGACACG 58.183 37.500 0.00 0.00 0.00 4.49
2267 5762 6.445357 ACACAAAAGGACACGAAAACTAAT 57.555 33.333 0.00 0.00 0.00 1.73
2275 5770 8.732746 AAGGACACGAAAACTAATATAAGCAT 57.267 30.769 0.00 0.00 0.00 3.79
2323 5820 9.736023 AAATAATTTATGAGCAATTCGACTTCC 57.264 29.630 0.00 0.00 0.00 3.46
2330 7547 3.600388 AGCAATTCGACTTCCCTAACAG 58.400 45.455 0.00 0.00 0.00 3.16
2331 7548 2.096013 GCAATTCGACTTCCCTAACAGC 59.904 50.000 0.00 0.00 0.00 4.40
2333 7550 0.245539 TTCGACTTCCCTAACAGCCG 59.754 55.000 0.00 0.00 0.00 5.52
2334 7551 1.810030 CGACTTCCCTAACAGCCGC 60.810 63.158 0.00 0.00 0.00 6.53
2336 7553 2.511600 CTTCCCTAACAGCCGCCG 60.512 66.667 0.00 0.00 0.00 6.46
2337 7554 3.310860 CTTCCCTAACAGCCGCCGT 62.311 63.158 0.00 0.00 0.00 5.68
2338 7555 3.305177 TTCCCTAACAGCCGCCGTC 62.305 63.158 0.00 0.00 0.00 4.79
2341 7558 4.796231 CTAACAGCCGCCGTCGCT 62.796 66.667 0.00 0.00 0.00 4.93
2342 7559 4.367023 TAACAGCCGCCGTCGCTT 62.367 61.111 0.00 0.00 0.00 4.68
2362 7579 0.829333 CCTCTAGCTGCTGTCACCAT 59.171 55.000 13.43 0.00 0.00 3.55
2366 7583 1.607801 TAGCTGCTGTCACCATCGCT 61.608 55.000 13.43 0.00 0.00 4.93
2387 7604 4.196971 CTGGTTTAAAATCCCTACCTCGG 58.803 47.826 0.00 0.00 0.00 4.63
2392 7619 1.109609 AAATCCCTACCTCGGTCGAC 58.890 55.000 7.13 7.13 0.00 4.20
2443 7705 2.642129 CCGGACGCATTTTGCACA 59.358 55.556 0.00 0.00 45.36 4.57
2445 7707 0.388391 CCGGACGCATTTTGCACAAT 60.388 50.000 0.00 0.00 45.36 2.71
2450 7712 2.663119 GACGCATTTTGCACAATTCCTC 59.337 45.455 0.00 0.00 45.36 3.71
2451 7713 2.297033 ACGCATTTTGCACAATTCCTCT 59.703 40.909 0.00 0.00 45.36 3.69
2485 7747 4.769488 GGGCTGACTCATCTATCTATGTCA 59.231 45.833 0.00 0.00 34.04 3.58
2502 7764 7.410174 TCTATGTCAAATTAACAATGGACCCT 58.590 34.615 0.00 0.00 0.00 4.34
2504 7766 7.645058 ATGTCAAATTAACAATGGACCCTAG 57.355 36.000 0.00 0.00 0.00 3.02
2508 7770 6.435904 TCAAATTAACAATGGACCCTAGTTGG 59.564 38.462 0.00 0.00 0.00 3.77
2514 7776 0.690762 TGGACCCTAGTTGGCAGAAC 59.309 55.000 0.00 0.00 0.00 3.01
2565 7827 5.242795 AGACCAACTTGCTTAACTATGGT 57.757 39.130 0.00 0.00 42.09 3.55
2567 7829 6.958767 AGACCAACTTGCTTAACTATGGTAT 58.041 36.000 0.00 0.00 39.65 2.73
2628 7890 9.793252 CAAGAAATATCCCAAATTGACACTTAG 57.207 33.333 0.00 0.00 0.00 2.18
2653 7915 8.971073 AGGGAGTAAAATTTGGAATTCACTATG 58.029 33.333 7.93 0.00 0.00 2.23
2654 7916 8.966868 GGGAGTAAAATTTGGAATTCACTATGA 58.033 33.333 7.93 0.00 0.00 2.15
2666 7938 9.066892 TGGAATTCACTATGAATAACTTATGGC 57.933 33.333 7.93 0.00 45.57 4.40
2674 7946 9.547753 ACTATGAATAACTTATGGCAGTAAGTG 57.452 33.333 17.26 8.99 42.48 3.16
2678 7950 8.946085 TGAATAACTTATGGCAGTAAGTGAAAG 58.054 33.333 17.26 4.52 42.48 2.62
2683 7955 7.450903 ACTTATGGCAGTAAGTGAAAGTAGTT 58.549 34.615 16.36 0.00 41.90 2.24
2696 7968 5.234543 GTGAAAGTAGTTCCAAGTCACTCAC 59.765 44.000 5.25 0.00 35.12 3.51
2700 7972 6.859112 AGTAGTTCCAAGTCACTCACATAT 57.141 37.500 0.00 0.00 0.00 1.78
2701 7973 6.634805 AGTAGTTCCAAGTCACTCACATATG 58.365 40.000 0.00 0.00 0.00 1.78
2702 7974 5.745312 AGTTCCAAGTCACTCACATATGA 57.255 39.130 10.38 0.00 0.00 2.15
2767 8039 5.044476 TGGAATTCTAAAATAGGGAGCACCA 60.044 40.000 5.23 0.00 43.89 4.17
2775 8047 5.653255 AAATAGGGAGCACCAAGTCATAT 57.347 39.130 1.58 0.00 43.89 1.78
2776 8048 4.630644 ATAGGGAGCACCAAGTCATATG 57.369 45.455 1.58 0.00 43.89 1.78
2791 8063 4.590850 TCATATGTGAATGACTCCCTCG 57.409 45.455 1.90 0.00 30.92 4.63
2827 8099 0.741221 GGCGAGCATTCTTCTTCGGT 60.741 55.000 0.00 0.00 0.00 4.69
2923 8196 7.611467 AGAATCCATACATACACAAACACACAT 59.389 33.333 0.00 0.00 0.00 3.21
2928 8201 9.684448 CCATACATACACAAACACACATAAAAA 57.316 29.630 0.00 0.00 0.00 1.94
2961 8245 2.143876 ACTTGAGCAAAACCACCACT 57.856 45.000 0.00 0.00 0.00 4.00
2979 8263 6.318900 CCACCACTTAAAAGTTCAAAGACTCT 59.681 38.462 4.62 0.00 37.08 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 5.801350 TCTGACAAACTTTGTTGACTGAG 57.199 39.130 8.56 0.32 45.52 3.35
75 76 1.123077 TCAGTAGGCGCATGAAGGAT 58.877 50.000 10.83 0.00 0.00 3.24
93 94 8.999431 TCTTTTTACTGTTGTCCAATGAGTATC 58.001 33.333 0.00 0.00 0.00 2.24
94 95 8.918202 TCTTTTTACTGTTGTCCAATGAGTAT 57.082 30.769 0.00 0.00 0.00 2.12
304 306 5.862323 GCTTTTGTACTCGATCTAGACACAA 59.138 40.000 0.47 7.89 0.00 3.33
324 330 2.959465 AAGGCCTTGTACTCAGCTTT 57.041 45.000 19.73 0.00 0.00 3.51
423 429 3.430098 GCACCAAGATTGTCACACCAAAA 60.430 43.478 0.00 0.00 0.00 2.44
493 499 7.482743 CACGAACAAAATGATAATCAACCTCAG 59.517 37.037 0.00 0.00 0.00 3.35
498 504 7.693951 CCTCTCACGAACAAAATGATAATCAAC 59.306 37.037 0.00 0.00 0.00 3.18
550 556 6.038161 CACTTGATCACCAGTAAGAACAAACA 59.962 38.462 0.00 0.00 0.00 2.83
559 565 2.894765 TCCGTCACTTGATCACCAGTAA 59.105 45.455 0.00 0.00 0.00 2.24
599 605 2.031012 TCCAGTTGCCGCAGTGAG 59.969 61.111 0.00 0.00 0.00 3.51
676 687 5.570262 CGGTTTATATACACACCGTGATG 57.430 43.478 5.28 2.73 45.85 3.07
689 706 7.656137 CACATCCTAAACTAGCACGGTTTATAT 59.344 37.037 8.56 4.89 38.12 0.86
707 724 0.530744 GAGACACACGCCACATCCTA 59.469 55.000 0.00 0.00 0.00 2.94
708 725 1.293498 GAGACACACGCCACATCCT 59.707 57.895 0.00 0.00 0.00 3.24
725 743 9.702253 ACTAGTAAGATCAGATTACAGAAAGGA 57.298 33.333 0.00 0.00 35.92 3.36
730 757 9.854668 AGCTAACTAGTAAGATCAGATTACAGA 57.145 33.333 0.00 0.00 35.92 3.41
746 773 7.665559 TGTGGATTGATTTTCAAGCTAACTAGT 59.334 33.333 5.59 0.00 42.01 2.57
747 774 7.965107 GTGTGGATTGATTTTCAAGCTAACTAG 59.035 37.037 5.59 0.00 42.01 2.57
759 786 4.658063 TCGGTTAGGTGTGGATTGATTTT 58.342 39.130 0.00 0.00 0.00 1.82
761 788 3.992943 TCGGTTAGGTGTGGATTGATT 57.007 42.857 0.00 0.00 0.00 2.57
791 818 3.938963 GGATGTGGCGAAGATTACAGAAA 59.061 43.478 0.00 0.00 0.00 2.52
792 819 3.197766 AGGATGTGGCGAAGATTACAGAA 59.802 43.478 0.00 0.00 0.00 3.02
793 820 2.766263 AGGATGTGGCGAAGATTACAGA 59.234 45.455 0.00 0.00 0.00 3.41
803 830 1.144716 GCATGAGAGGATGTGGCGA 59.855 57.895 0.00 0.00 0.00 5.54
804 831 2.242572 CGCATGAGAGGATGTGGCG 61.243 63.158 0.00 0.00 36.93 5.69
805 832 2.541120 GCGCATGAGAGGATGTGGC 61.541 63.158 0.30 0.00 34.89 5.01
806 833 0.463295 AAGCGCATGAGAGGATGTGG 60.463 55.000 11.47 0.00 34.89 4.17
807 834 0.935898 GAAGCGCATGAGAGGATGTG 59.064 55.000 11.47 0.00 36.99 3.21
808 835 0.179062 GGAAGCGCATGAGAGGATGT 60.179 55.000 11.47 0.00 0.00 3.06
809 836 0.179065 TGGAAGCGCATGAGAGGATG 60.179 55.000 11.47 0.00 0.00 3.51
810 837 0.106335 CTGGAAGCGCATGAGAGGAT 59.894 55.000 11.47 0.00 0.00 3.24
811 838 1.519246 CTGGAAGCGCATGAGAGGA 59.481 57.895 11.47 0.00 0.00 3.71
812 839 4.121691 CTGGAAGCGCATGAGAGG 57.878 61.111 11.47 0.00 0.00 3.69
823 850 1.072965 AGGTGTGAAAGAGGCTGGAAG 59.927 52.381 0.00 0.00 0.00 3.46
824 851 1.072331 GAGGTGTGAAAGAGGCTGGAA 59.928 52.381 0.00 0.00 0.00 3.53
825 852 0.687354 GAGGTGTGAAAGAGGCTGGA 59.313 55.000 0.00 0.00 0.00 3.86
826 853 0.671781 CGAGGTGTGAAAGAGGCTGG 60.672 60.000 0.00 0.00 0.00 4.85
827 854 0.318441 TCGAGGTGTGAAAGAGGCTG 59.682 55.000 0.00 0.00 0.00 4.85
828 855 0.605589 CTCGAGGTGTGAAAGAGGCT 59.394 55.000 3.91 0.00 0.00 4.58
829 856 0.603569 TCTCGAGGTGTGAAAGAGGC 59.396 55.000 13.56 0.00 0.00 4.70
830 857 2.558795 TCTTCTCGAGGTGTGAAAGAGG 59.441 50.000 13.56 0.00 30.27 3.69
831 858 3.570559 GTCTTCTCGAGGTGTGAAAGAG 58.429 50.000 13.56 0.00 30.27 2.85
832 859 2.296471 GGTCTTCTCGAGGTGTGAAAGA 59.704 50.000 13.56 10.09 30.27 2.52
833 860 2.035961 TGGTCTTCTCGAGGTGTGAAAG 59.964 50.000 13.56 7.75 30.27 2.62
834 861 2.035961 CTGGTCTTCTCGAGGTGTGAAA 59.964 50.000 13.56 0.00 30.27 2.69
835 862 1.613925 CTGGTCTTCTCGAGGTGTGAA 59.386 52.381 13.56 0.00 0.00 3.18
836 863 1.202891 TCTGGTCTTCTCGAGGTGTGA 60.203 52.381 13.56 3.19 0.00 3.58
837 864 1.201181 CTCTGGTCTTCTCGAGGTGTG 59.799 57.143 13.56 0.70 0.00 3.82
838 865 1.540267 CTCTGGTCTTCTCGAGGTGT 58.460 55.000 13.56 0.00 0.00 4.16
839 866 0.172352 GCTCTGGTCTTCTCGAGGTG 59.828 60.000 13.56 5.92 0.00 4.00
844 871 1.153667 GGCAGCTCTGGTCTTCTCG 60.154 63.158 0.00 0.00 0.00 4.04
892 919 2.450609 TTAGTGCTCACGAAGGTTCC 57.549 50.000 0.00 0.00 36.20 3.62
918 945 5.191727 TCAATGGGGCATCGGATTTATAT 57.808 39.130 0.00 0.00 0.00 0.86
940 967 1.066143 AGGTTGTCGCGATTCCTGAAT 60.066 47.619 22.24 5.31 0.00 2.57
1048 1075 1.603236 CTGAGGAGCTTGAGGACGCT 61.603 60.000 0.00 0.00 39.61 5.07
1263 1305 2.501128 GAGCCGATGCAGTAGCCA 59.499 61.111 0.00 0.00 41.13 4.75
1446 1488 4.988598 CACGGGTCAGCGCCAACT 62.989 66.667 2.29 0.00 0.00 3.16
1583 1627 1.228367 AGGACGTACCCGGCGATAT 60.228 57.895 9.30 0.00 45.55 1.63
1584 1628 1.893808 GAGGACGTACCCGGCGATA 60.894 63.158 9.30 0.00 45.55 2.92
1836 5265 0.327000 CCTTCCCCATCTCCCTCAGT 60.327 60.000 0.00 0.00 0.00 3.41
1923 5352 2.816958 CGCATCAGCTCGTTGGCT 60.817 61.111 0.00 0.00 44.10 4.75
1997 5426 3.882888 GGAGATCACCAAACACTTCAACA 59.117 43.478 4.05 0.00 0.00 3.33
2028 5457 6.326375 AGTAAAAATCAAACGACTTGCACAA 58.674 32.000 0.00 0.00 34.76 3.33
2036 5466 9.726034 CATTATTGCAAGTAAAAATCAAACGAC 57.274 29.630 4.94 0.00 0.00 4.34
2074 5508 3.003897 TCAAATGGTTCGTTAGGTTGTGC 59.996 43.478 0.00 0.00 0.00 4.57
2119 5553 3.349022 ACGGTTTTCACTTTTCAGACCA 58.651 40.909 0.00 0.00 0.00 4.02
2158 5592 5.482006 TCCACAACATCACTAATGAGACAG 58.518 41.667 0.00 0.00 38.57 3.51
2181 5615 6.226787 AGAAAGTCGAAAGATCTCAACACAT 58.773 36.000 0.00 0.00 45.19 3.21
2196 5630 5.793817 TCAATGAAATCTGGAGAAAGTCGA 58.206 37.500 0.00 0.00 0.00 4.20
2197 5631 6.486253 TTCAATGAAATCTGGAGAAAGTCG 57.514 37.500 0.00 0.00 0.00 4.18
2198 5632 7.880105 AGTTTCAATGAAATCTGGAGAAAGTC 58.120 34.615 11.87 0.00 33.97 3.01
2236 5670 6.055231 TCGTGTCCTTTTGTGTTGAAATAG 57.945 37.500 0.00 0.00 0.00 1.73
2238 5672 4.974368 TCGTGTCCTTTTGTGTTGAAAT 57.026 36.364 0.00 0.00 0.00 2.17
2239 5673 4.768130 TTCGTGTCCTTTTGTGTTGAAA 57.232 36.364 0.00 0.00 0.00 2.69
2240 5674 4.768130 TTTCGTGTCCTTTTGTGTTGAA 57.232 36.364 0.00 0.00 0.00 2.69
2242 5676 4.481463 AGTTTTCGTGTCCTTTTGTGTTG 58.519 39.130 0.00 0.00 0.00 3.33
2243 5677 4.776795 AGTTTTCGTGTCCTTTTGTGTT 57.223 36.364 0.00 0.00 0.00 3.32
2247 5681 9.274065 GCTTATATTAGTTTTCGTGTCCTTTTG 57.726 33.333 0.00 0.00 0.00 2.44
2248 5682 9.005777 TGCTTATATTAGTTTTCGTGTCCTTTT 57.994 29.630 0.00 0.00 0.00 2.27
2312 5809 2.677037 CGGCTGTTAGGGAAGTCGAATT 60.677 50.000 0.00 0.00 44.07 2.17
2317 5814 1.449778 GGCGGCTGTTAGGGAAGTC 60.450 63.158 0.00 0.00 0.00 3.01
2331 7548 3.471244 CTAGAGGAAGCGACGGCGG 62.471 68.421 15.06 0.00 46.35 6.13
2333 7550 2.278923 GCTAGAGGAAGCGACGGC 60.279 66.667 0.00 0.00 40.37 5.68
2339 7556 0.534412 TGACAGCAGCTAGAGGAAGC 59.466 55.000 0.00 0.00 43.11 3.86
2340 7557 1.134848 GGTGACAGCAGCTAGAGGAAG 60.135 57.143 0.00 0.00 39.38 3.46
2341 7558 0.898320 GGTGACAGCAGCTAGAGGAA 59.102 55.000 0.00 0.00 39.38 3.36
2342 7559 0.251787 TGGTGACAGCAGCTAGAGGA 60.252 55.000 2.50 0.00 42.84 3.71
2343 7560 2.280835 TGGTGACAGCAGCTAGAGG 58.719 57.895 2.50 0.00 42.84 3.69
2362 7579 3.264964 AGGTAGGGATTTTAAACCAGCGA 59.735 43.478 0.00 0.00 32.43 4.93
2366 7583 3.588396 ACCGAGGTAGGGATTTTAAACCA 59.412 43.478 0.00 0.00 35.02 3.67
2368 7585 3.867493 CGACCGAGGTAGGGATTTTAAAC 59.133 47.826 0.00 0.00 35.02 2.01
2371 7588 2.689983 GTCGACCGAGGTAGGGATTTTA 59.310 50.000 3.51 0.00 35.02 1.52
2372 7589 1.479730 GTCGACCGAGGTAGGGATTTT 59.520 52.381 3.51 0.00 35.02 1.82
2387 7604 2.045143 AGTCCCCTCTCCGTCGAC 60.045 66.667 5.18 5.18 0.00 4.20
2392 7619 3.151022 GAGCCAGTCCCCTCTCCG 61.151 72.222 0.00 0.00 0.00 4.63
2443 7705 2.322355 CTCACATCGGCAGAGGAATT 57.678 50.000 5.30 0.00 31.71 2.17
2485 7747 5.186992 GCCAACTAGGGTCCATTGTTAATTT 59.813 40.000 3.05 0.00 38.09 1.82
2498 7760 1.066143 CATCGTTCTGCCAACTAGGGT 60.066 52.381 0.00 0.00 38.09 4.34
2502 7764 2.177394 TTGCATCGTTCTGCCAACTA 57.823 45.000 0.00 0.00 41.58 2.24
2504 7766 1.786579 GTTTTGCATCGTTCTGCCAAC 59.213 47.619 0.00 5.03 41.58 3.77
2508 7770 5.820926 TTTAATGTTTTGCATCGTTCTGC 57.179 34.783 0.00 1.35 42.62 4.26
2541 7803 6.407202 ACCATAGTTAAGCAAGTTGGTCTAG 58.593 40.000 8.24 0.00 29.70 2.43
2600 7862 5.812127 GTGTCAATTTGGGATATTTCTTGCC 59.188 40.000 0.00 0.00 0.00 4.52
2628 7890 8.966868 TCATAGTGAATTCCAAATTTTACTCCC 58.033 33.333 2.27 0.00 0.00 4.30
2653 7915 8.947115 ACTTTCACTTACTGCCATAAGTTATTC 58.053 33.333 6.92 0.00 41.62 1.75
2654 7916 8.863872 ACTTTCACTTACTGCCATAAGTTATT 57.136 30.769 6.92 0.00 41.62 1.40
2666 7938 6.984474 TGACTTGGAACTACTTTCACTTACTG 59.016 38.462 0.00 0.00 35.70 2.74
2674 7946 5.357257 TGTGAGTGACTTGGAACTACTTTC 58.643 41.667 0.00 0.00 0.00 2.62
2678 7950 6.531948 GTCATATGTGAGTGACTTGGAACTAC 59.468 42.308 1.90 0.00 41.10 2.73
2701 7973 9.743057 CGATATCATATTTATGAGGAAGGAGTC 57.257 37.037 3.12 0.00 45.01 3.36
2702 7974 9.480861 TCGATATCATATTTATGAGGAAGGAGT 57.519 33.333 3.12 0.00 45.01 3.85
2744 8016 5.445964 TGGTGCTCCCTATTTTAGAATTCC 58.554 41.667 0.65 0.00 0.00 3.01
2759 8031 3.266510 TCACATATGACTTGGTGCTCC 57.733 47.619 10.38 0.00 0.00 4.70
2760 8032 4.877823 TCATTCACATATGACTTGGTGCTC 59.122 41.667 10.38 0.00 33.38 4.26
2775 8047 0.252057 TCCCGAGGGAGTCATTCACA 60.252 55.000 6.80 0.00 39.76 3.58
2776 8048 2.591915 TCCCGAGGGAGTCATTCAC 58.408 57.895 6.80 0.00 39.76 3.18
2791 8063 1.472376 CGCCTCAAGAGAGAACATCCC 60.472 57.143 0.00 0.00 44.98 3.85
2827 8099 2.422479 CGTCCTGTCGGATGTCTTTCTA 59.578 50.000 0.00 0.00 42.43 2.10
2898 8170 7.139896 TGTGTGTTTGTGTATGTATGGATTC 57.860 36.000 0.00 0.00 0.00 2.52
2928 8201 6.463995 TTGCTCAAGTTGGTGATTTACTTT 57.536 33.333 2.34 0.00 30.08 2.66


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

AutoCloner maintained by Alex Coulton.