Multiple sequence alignment - TraesCS1D01G270700

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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 TraesCS1D01G270700 chr1D 100.000 3516 0 0 1 3516 365539279 365542794 0.000000e+00 6493.0
1 TraesCS1D01G270700 chr1D 88.904 712 63 6 57 753 198903118 198902408 0.000000e+00 863.0
2 TraesCS1D01G270700 chr1A 90.524 1889 102 34 958 2780 464794657 464796534 0.000000e+00 2425.0
3 TraesCS1D01G270700 chr1A 92.962 611 25 3 2910 3516 464797003 464797599 0.000000e+00 874.0
4 TraesCS1D01G270700 chr1A 87.500 96 3 3 830 925 464794566 464794652 6.210000e-18 102.0
5 TraesCS1D01G270700 chr1B 90.397 1083 68 18 958 2018 489198659 489199727 0.000000e+00 1391.0
6 TraesCS1D01G270700 chr1B 89.974 768 60 8 1 753 350634985 350635750 0.000000e+00 976.0
7 TraesCS1D01G270700 chr1B 97.282 515 14 0 3002 3516 489201289 489201803 0.000000e+00 874.0
8 TraesCS1D01G270700 chr1B 96.060 533 14 2 2002 2533 489199889 489200415 0.000000e+00 861.0
9 TraesCS1D01G270700 chr1B 93.725 255 9 2 2558 2812 489200410 489200657 3.310000e-100 375.0
10 TraesCS1D01G270700 chr1B 87.288 118 4 4 822 939 489198560 489198666 1.330000e-24 124.0
11 TraesCS1D01G270700 chr1B 100.000 28 0 0 3017 3044 32430032 32430059 6.000000e-03 52.8
12 TraesCS1D01G270700 chr4D 90.352 767 59 1 1 752 425281799 425281033 0.000000e+00 992.0
13 TraesCS1D01G270700 chr5D 89.700 767 63 2 1 752 389442679 389441914 0.000000e+00 965.0
14 TraesCS1D01G270700 chr5D 88.287 572 52 1 1 557 463266349 463265778 0.000000e+00 671.0
15 TraesCS1D01G270700 chr3D 87.898 785 69 9 1 767 587508916 587508140 0.000000e+00 900.0
16 TraesCS1D01G270700 chr6D 88.828 734 66 4 1 719 35026362 35025630 0.000000e+00 887.0
17 TraesCS1D01G270700 chr6D 92.608 487 35 1 267 753 288592328 288592813 0.000000e+00 699.0
18 TraesCS1D01G270700 chr7D 88.599 728 77 3 1 727 400446299 400447021 0.000000e+00 880.0
19 TraesCS1D01G270700 chr7D 86.606 769 83 4 1 752 554470629 554471394 0.000000e+00 832.0
20 TraesCS1D01G270700 chr7D 90.984 488 42 1 267 752 503939633 503939146 0.000000e+00 656.0
21 TraesCS1D01G270700 chrUn 87.646 769 78 2 1 752 31727050 31727818 0.000000e+00 878.0
22 TraesCS1D01G270700 chr3B 86.381 771 86 4 1 753 50156199 50156968 0.000000e+00 824.0
23 TraesCS1D01G270700 chr4A 86.140 772 83 7 1 752 618129962 618130729 0.000000e+00 811.0
24 TraesCS1D01G270700 chr2B 86.963 652 68 2 1 635 799275062 799274411 0.000000e+00 717.0
25 TraesCS1D01G270700 chr2A 89.837 551 52 4 208 756 673129817 673129269 0.000000e+00 704.0
26 TraesCS1D01G270700 chr7B 87.867 511 47 1 1 496 69543378 69543888 1.410000e-163 586.0
27 TraesCS1D01G270700 chr4B 88.462 52 6 0 3001 3052 596373410 596373461 2.930000e-06 63.9
28 TraesCS1D01G270700 chr3A 94.444 36 2 0 3009 3044 71221349 71221314 4.900000e-04 56.5


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 TraesCS1D01G270700 chr1D 365539279 365542794 3515 False 6493.000000 6493 100.000000 1 3516 1 chr1D.!!$F1 3515
1 TraesCS1D01G270700 chr1D 198902408 198903118 710 True 863.000000 863 88.904000 57 753 1 chr1D.!!$R1 696
2 TraesCS1D01G270700 chr1A 464794566 464797599 3033 False 1133.666667 2425 90.328667 830 3516 3 chr1A.!!$F1 2686
3 TraesCS1D01G270700 chr1B 350634985 350635750 765 False 976.000000 976 89.974000 1 753 1 chr1B.!!$F2 752
4 TraesCS1D01G270700 chr1B 489198560 489201803 3243 False 725.000000 1391 92.950400 822 3516 5 chr1B.!!$F3 2694
5 TraesCS1D01G270700 chr4D 425281033 425281799 766 True 992.000000 992 90.352000 1 752 1 chr4D.!!$R1 751
6 TraesCS1D01G270700 chr5D 389441914 389442679 765 True 965.000000 965 89.700000 1 752 1 chr5D.!!$R1 751
7 TraesCS1D01G270700 chr5D 463265778 463266349 571 True 671.000000 671 88.287000 1 557 1 chr5D.!!$R2 556
8 TraesCS1D01G270700 chr3D 587508140 587508916 776 True 900.000000 900 87.898000 1 767 1 chr3D.!!$R1 766
9 TraesCS1D01G270700 chr6D 35025630 35026362 732 True 887.000000 887 88.828000 1 719 1 chr6D.!!$R1 718
10 TraesCS1D01G270700 chr7D 400446299 400447021 722 False 880.000000 880 88.599000 1 727 1 chr7D.!!$F1 726
11 TraesCS1D01G270700 chr7D 554470629 554471394 765 False 832.000000 832 86.606000 1 752 1 chr7D.!!$F2 751
12 TraesCS1D01G270700 chrUn 31727050 31727818 768 False 878.000000 878 87.646000 1 752 1 chrUn.!!$F1 751
13 TraesCS1D01G270700 chr3B 50156199 50156968 769 False 824.000000 824 86.381000 1 753 1 chr3B.!!$F1 752
14 TraesCS1D01G270700 chr4A 618129962 618130729 767 False 811.000000 811 86.140000 1 752 1 chr4A.!!$F1 751
15 TraesCS1D01G270700 chr2B 799274411 799275062 651 True 717.000000 717 86.963000 1 635 1 chr2B.!!$R1 634
16 TraesCS1D01G270700 chr2A 673129269 673129817 548 True 704.000000 704 89.837000 208 756 1 chr2A.!!$R1 548
17 TraesCS1D01G270700 chr7B 69543378 69543888 510 False 586.000000 586 87.867000 1 496 1 chr7B.!!$F1 495


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
936 959 0.03582 AACGCGACCTCTCTCTCTCT 60.036 55.0 15.93 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2691 2971 0.323725 CCCAAGTTGATGACCCCAGG 60.324 60.0 3.87 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
25 26 2.696989 TGAAGGCATCGTCATGTGAT 57.303 45.000 0.00 0.00 31.86 3.06
92 93 1.676529 GTCTTCCAGATCGGACGATGA 59.323 52.381 12.40 0.60 46.36 2.92
135 136 5.423290 TCTCTCTTAGGAGCATCATTTGTGA 59.577 40.000 0.00 0.00 39.31 3.58
181 182 0.670854 GGTGGAGTGGCTTCGTCTTC 60.671 60.000 0.00 0.00 0.00 2.87
424 441 0.313672 GGGCAAAGTTGATGCGTCAA 59.686 50.000 17.41 17.41 44.75 3.18
446 463 2.533916 ACAGCTCTGAAGATGGAGTGA 58.466 47.619 3.60 0.00 43.33 3.41
524 542 2.736531 CAAGTGGCTTGGTTGGGC 59.263 61.111 1.23 0.00 37.77 5.36
545 563 3.493524 GCCCTCAGGTCTTAGATGTTAGC 60.494 52.174 0.00 0.00 34.57 3.09
558 576 1.055849 TGTTAGCCTTGGCTGTGAGA 58.944 50.000 23.03 5.94 0.00 3.27
583 605 3.181419 TGTGGTATTAGGCCCGGACTATA 60.181 47.826 0.73 0.00 0.00 1.31
612 634 4.164988 CCCTTCATCAACTGGATAGGAGTT 59.835 45.833 0.00 0.00 34.78 3.01
637 660 1.066858 CAGATGTTGCCTAGACGGTGT 60.067 52.381 0.00 0.00 34.25 4.16
715 738 0.604511 CTGCATGCATCGCCCAGATA 60.605 55.000 22.97 0.00 37.52 1.98
723 746 0.760567 ATCGCCCAGATACAGAGGCA 60.761 55.000 0.30 0.00 46.08 4.75
748 771 5.477291 GGGGGTCTTCCTTCTTTTCTAAAAG 59.523 44.000 8.58 8.58 40.09 2.27
776 799 8.567285 ACTAATGAAATAGGTTTGTCTTGAGG 57.433 34.615 0.00 0.00 0.00 3.86
777 800 8.164070 ACTAATGAAATAGGTTTGTCTTGAGGT 58.836 33.333 0.00 0.00 0.00 3.85
778 801 7.454260 AATGAAATAGGTTTGTCTTGAGGTC 57.546 36.000 0.00 0.00 0.00 3.85
779 802 5.935945 TGAAATAGGTTTGTCTTGAGGTCA 58.064 37.500 0.00 0.00 0.00 4.02
780 803 6.361433 TGAAATAGGTTTGTCTTGAGGTCAA 58.639 36.000 0.00 0.00 0.00 3.18
781 804 6.831353 TGAAATAGGTTTGTCTTGAGGTCAAA 59.169 34.615 0.00 0.00 35.15 2.69
782 805 7.505585 TGAAATAGGTTTGTCTTGAGGTCAAAT 59.494 33.333 0.00 0.00 35.15 2.32
783 806 7.839680 AATAGGTTTGTCTTGAGGTCAAATT 57.160 32.000 0.00 0.00 35.15 1.82
784 807 7.839680 ATAGGTTTGTCTTGAGGTCAAATTT 57.160 32.000 0.00 0.00 35.15 1.82
785 808 8.934023 ATAGGTTTGTCTTGAGGTCAAATTTA 57.066 30.769 0.00 0.00 35.15 1.40
786 809 7.839680 AGGTTTGTCTTGAGGTCAAATTTAT 57.160 32.000 0.00 0.00 35.15 1.40
787 810 7.661040 AGGTTTGTCTTGAGGTCAAATTTATG 58.339 34.615 0.00 0.00 35.15 1.90
788 811 6.366061 GGTTTGTCTTGAGGTCAAATTTATGC 59.634 38.462 0.00 0.00 35.15 3.14
789 812 5.643379 TGTCTTGAGGTCAAATTTATGCC 57.357 39.130 0.00 0.00 35.15 4.40
790 813 5.324409 TGTCTTGAGGTCAAATTTATGCCT 58.676 37.500 6.97 6.97 35.15 4.75
791 814 5.774690 TGTCTTGAGGTCAAATTTATGCCTT 59.225 36.000 8.25 0.00 35.15 4.35
792 815 6.267471 TGTCTTGAGGTCAAATTTATGCCTTT 59.733 34.615 8.25 0.00 35.15 3.11
793 816 7.154656 GTCTTGAGGTCAAATTTATGCCTTTT 58.845 34.615 8.25 0.00 35.15 2.27
794 817 7.116805 GTCTTGAGGTCAAATTTATGCCTTTTG 59.883 37.037 8.25 0.00 35.15 2.44
795 818 5.237048 TGAGGTCAAATTTATGCCTTTTGC 58.763 37.500 8.25 0.00 41.77 3.68
796 819 4.578871 AGGTCAAATTTATGCCTTTTGCC 58.421 39.130 0.00 0.00 40.16 4.52
797 820 4.286808 AGGTCAAATTTATGCCTTTTGCCT 59.713 37.500 0.00 0.00 40.16 4.75
798 821 5.003160 GGTCAAATTTATGCCTTTTGCCTT 58.997 37.500 0.00 0.00 40.16 4.35
799 822 5.473162 GGTCAAATTTATGCCTTTTGCCTTT 59.527 36.000 0.00 0.00 40.16 3.11
800 823 6.016360 GGTCAAATTTATGCCTTTTGCCTTTT 60.016 34.615 0.00 0.00 40.16 2.27
801 824 7.424803 GTCAAATTTATGCCTTTTGCCTTTTT 58.575 30.769 0.00 0.00 40.16 1.94
854 877 3.761218 CAGTAGATCTGACGAGGGCATAT 59.239 47.826 5.18 0.00 46.27 1.78
855 878 4.944317 CAGTAGATCTGACGAGGGCATATA 59.056 45.833 5.18 0.00 46.27 0.86
856 879 4.944930 AGTAGATCTGACGAGGGCATATAC 59.055 45.833 5.18 0.00 0.00 1.47
857 880 4.040936 AGATCTGACGAGGGCATATACT 57.959 45.455 0.00 0.00 0.00 2.12
858 881 4.411927 AGATCTGACGAGGGCATATACTT 58.588 43.478 0.00 0.00 0.00 2.24
859 882 4.219507 AGATCTGACGAGGGCATATACTTG 59.780 45.833 0.00 0.00 0.00 3.16
860 883 2.628178 TCTGACGAGGGCATATACTTGG 59.372 50.000 0.00 0.00 0.00 3.61
861 884 2.365617 CTGACGAGGGCATATACTTGGT 59.634 50.000 0.00 0.00 0.00 3.67
862 885 3.568443 TGACGAGGGCATATACTTGGTA 58.432 45.455 0.00 0.00 0.00 3.25
925 948 1.206831 GCAGAAGGAAAACGCGACC 59.793 57.895 15.93 10.71 0.00 4.79
926 949 1.228657 GCAGAAGGAAAACGCGACCT 61.229 55.000 15.93 12.98 35.36 3.85
927 950 0.790814 CAGAAGGAAAACGCGACCTC 59.209 55.000 15.93 5.22 33.16 3.85
928 951 0.680061 AGAAGGAAAACGCGACCTCT 59.320 50.000 15.93 11.54 33.16 3.69
929 952 1.069255 GAAGGAAAACGCGACCTCTC 58.931 55.000 15.93 11.52 33.16 3.20
930 953 0.680061 AAGGAAAACGCGACCTCTCT 59.320 50.000 15.93 0.00 33.16 3.10
931 954 0.244178 AGGAAAACGCGACCTCTCTC 59.756 55.000 15.93 0.00 0.00 3.20
932 955 0.244178 GGAAAACGCGACCTCTCTCT 59.756 55.000 15.93 0.00 0.00 3.10
933 956 1.619983 GAAAACGCGACCTCTCTCTC 58.380 55.000 15.93 0.00 0.00 3.20
934 957 1.200484 GAAAACGCGACCTCTCTCTCT 59.800 52.381 15.93 0.00 0.00 3.10
935 958 0.806241 AAACGCGACCTCTCTCTCTC 59.194 55.000 15.93 0.00 0.00 3.20
936 959 0.035820 AACGCGACCTCTCTCTCTCT 60.036 55.000 15.93 0.00 0.00 3.10
937 960 0.461339 ACGCGACCTCTCTCTCTCTC 60.461 60.000 15.93 0.00 0.00 3.20
938 961 0.179084 CGCGACCTCTCTCTCTCTCT 60.179 60.000 0.00 0.00 0.00 3.10
939 962 1.583054 GCGACCTCTCTCTCTCTCTC 58.417 60.000 0.00 0.00 0.00 3.20
940 963 1.139058 GCGACCTCTCTCTCTCTCTCT 59.861 57.143 0.00 0.00 0.00 3.10
941 964 2.803492 GCGACCTCTCTCTCTCTCTCTC 60.803 59.091 0.00 0.00 0.00 3.20
942 965 2.695666 CGACCTCTCTCTCTCTCTCTCT 59.304 54.545 0.00 0.00 0.00 3.10
943 966 3.243569 CGACCTCTCTCTCTCTCTCTCTC 60.244 56.522 0.00 0.00 0.00 3.20
944 967 3.964031 GACCTCTCTCTCTCTCTCTCTCT 59.036 52.174 0.00 0.00 0.00 3.10
945 968 3.964031 ACCTCTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 0.00 3.20
946 969 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
947 970 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
948 971 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
949 972 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
950 973 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
951 974 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
952 975 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
953 976 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
954 977 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
955 978 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
956 979 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
960 983 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
971 994 0.322906 TCTCTCTCTCTCTGCGGCAA 60.323 55.000 3.44 0.00 0.00 4.52
1056 1079 2.047844 CAGGTGTCAGGCCTCGTG 60.048 66.667 0.00 0.00 33.31 4.35
1163 1191 1.095807 CCCCGCGAAAAATCTCCCTC 61.096 60.000 8.23 0.00 0.00 4.30
1185 1221 4.161754 TCTCTCCCCGTCTATTTTTCCTTC 59.838 45.833 0.00 0.00 0.00 3.46
1201 1237 3.285484 TCCTTCGGAGCTAACTAACGAT 58.715 45.455 0.00 0.00 35.92 3.73
1248 1285 2.270257 GCTGGTGTGCTTGATGGCA 61.270 57.895 0.00 0.00 40.15 4.92
1349 1386 2.828520 GTGAGTTCTCATCTCTGGGACA 59.171 50.000 5.80 0.00 29.26 4.02
1362 1399 0.105709 TGGGACAGGACAGACACAGA 60.106 55.000 0.00 0.00 0.00 3.41
1363 1400 0.318762 GGGACAGGACAGACACAGAC 59.681 60.000 0.00 0.00 0.00 3.51
1365 1402 1.689273 GGACAGGACAGACACAGACTT 59.311 52.381 0.00 0.00 0.00 3.01
1375 1412 7.990886 AGGACAGACACAGACTTGTAAATTTTA 59.009 33.333 0.00 0.00 35.25 1.52
1386 1423 5.239963 ACTTGTAAATTTTACCGGGAGTGTG 59.760 40.000 14.99 0.79 0.00 3.82
1418 1468 9.444600 GATTTATGAGTTCCAACTACTAACCAA 57.555 33.333 0.00 0.00 39.88 3.67
1439 1489 3.469739 AGGCAGCTTTTGTCCAATTTTG 58.530 40.909 0.00 0.00 29.16 2.44
1463 1513 9.461312 TTGGCTTTACTAATGTTTCATATCACT 57.539 29.630 0.00 0.00 0.00 3.41
1495 1545 7.045126 AGAGCAGTATGTAGTCCAGTTATTC 57.955 40.000 0.00 0.00 39.31 1.75
1501 1551 3.845178 TGTAGTCCAGTTATTCGTGCAG 58.155 45.455 0.00 0.00 0.00 4.41
1600 1651 2.555757 GGCATGATCCACTAATTGGCTC 59.444 50.000 0.00 0.00 46.47 4.70
1701 1779 5.062183 CCATAGATGTCGTATTGTATTGCCG 59.938 44.000 0.00 0.00 0.00 5.69
1702 1780 2.800544 AGATGTCGTATTGTATTGCCGC 59.199 45.455 0.00 0.00 0.00 6.53
1717 1795 1.362406 GCCGCTCTAGTTCTTGCCAC 61.362 60.000 0.00 0.00 0.00 5.01
1742 1820 8.311109 ACAAGAGTTAAGGTTTGACAAAATTGT 58.689 29.630 1.27 0.00 45.65 2.71
1844 1923 5.123820 TGAATGGGAACGATGTGAGAAATTC 59.876 40.000 0.00 0.00 0.00 2.17
1868 1966 5.237344 CAGCTTGTTACAGTAGAAAAGTGCT 59.763 40.000 0.00 0.00 31.00 4.40
1915 2013 4.034510 ACGCAGAGAAAGCATGCTATAAAC 59.965 41.667 23.00 11.69 37.81 2.01
1916 2014 4.272018 CGCAGAGAAAGCATGCTATAAACT 59.728 41.667 23.00 15.10 37.81 2.66
1917 2015 5.463392 CGCAGAGAAAGCATGCTATAAACTA 59.537 40.000 23.00 0.00 37.81 2.24
1969 2067 3.386486 CGTGGAACTGTAGTTGTTAGCA 58.614 45.455 1.35 0.00 38.56 3.49
1998 2096 8.200792 TGCTCCTCAACTTTGCTTTAATTTTTA 58.799 29.630 0.00 0.00 0.00 1.52
1999 2097 8.703336 GCTCCTCAACTTTGCTTTAATTTTTAG 58.297 33.333 0.00 0.00 0.00 1.85
2000 2098 8.587952 TCCTCAACTTTGCTTTAATTTTTAGC 57.412 30.769 0.00 0.00 35.50 3.09
2366 2646 4.735822 CCTTTTCGTCTATTAGAGTCTGCG 59.264 45.833 1.86 0.00 0.00 5.18
2434 2714 4.698575 GGTTCCAGGTTAGCTCTCTTATG 58.301 47.826 0.00 0.00 0.00 1.90
2487 2767 0.815615 GCAGAACTAAGGCATCGGGG 60.816 60.000 0.00 0.00 0.00 5.73
2545 2825 5.860648 TCCTATTTTGGAAGAAGGGAAGT 57.139 39.130 0.00 0.00 32.39 3.01
2708 2988 0.698238 TCCCTGGGGTCATCAACTTG 59.302 55.000 14.00 0.00 36.47 3.16
2725 3005 7.752518 TCAACTTGGGTAATGGTTAGGTATA 57.247 36.000 0.00 0.00 0.00 1.47
2727 3007 6.165700 ACTTGGGTAATGGTTAGGTATACG 57.834 41.667 0.00 0.00 0.00 3.06
2782 3062 7.416326 CCATCCTGTTTTATTTGTAGCTAACCC 60.416 40.741 0.00 0.00 0.00 4.11
2800 3080 3.469739 ACCCGACGATGTAAGTTTGTTT 58.530 40.909 0.00 0.00 0.00 2.83
2806 3086 7.117454 CCGACGATGTAAGTTTGTTTGATATC 58.883 38.462 0.00 0.00 0.00 1.63
2823 3228 8.877779 GTTTGATATCTGGTATGATACATCTGC 58.122 37.037 4.83 0.00 32.51 4.26
2846 3251 5.633182 GCAAAACCACACATCGATACATTTT 59.367 36.000 0.00 0.00 0.00 1.82
2847 3252 6.145371 GCAAAACCACACATCGATACATTTTT 59.855 34.615 0.00 0.00 0.00 1.94
2883 3586 5.239744 TGCAAAGGTTATTTTCTGTAGCGAA 59.760 36.000 0.00 0.00 0.00 4.70
2891 3594 4.404507 TTTTCTGTAGCGAAATGAGTGC 57.595 40.909 0.00 0.00 33.33 4.40
2900 3616 6.983890 TGTAGCGAAATGAGTGCTAAATATCA 59.016 34.615 0.00 0.00 42.36 2.15
2904 3620 8.663025 AGCGAAATGAGTGCTAAATATCATATG 58.337 33.333 0.00 0.00 37.15 1.78
3015 4115 7.232534 TGTTCCTAAATGTTTAAACTGCCAGAT 59.767 33.333 18.72 0.67 0.00 2.90
3035 4135 7.656137 GCCAGATCGTCTTATATTTAGGAACAA 59.344 37.037 0.00 0.00 0.00 2.83
3056 4156 7.849322 ACAAAGGGTGTAATTCCTAAAACAT 57.151 32.000 0.00 0.00 39.29 2.71
3077 4177 2.409948 AACTTGGAGGAGTAGCATGC 57.590 50.000 10.51 10.51 0.00 4.06
3506 4606 2.930023 GCACTGTGACTCTCATCCTGTG 60.930 54.545 12.86 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 6.822676 ACAAATGATGCTCCTAAGAGAGAAAG 59.177 38.462 0.00 0.00 43.39 2.62
135 136 1.670406 CTGACTTCCAGCGCTGCTT 60.670 57.895 31.96 14.59 36.40 3.91
231 232 1.236616 CGACCAGGCATGACAAAGCA 61.237 55.000 0.00 0.00 0.00 3.91
392 409 1.192146 TTTGCCCGGTCTAGCTGTCT 61.192 55.000 0.00 0.00 0.00 3.41
424 441 4.285020 TCACTCCATCTTCAGAGCTGTAT 58.715 43.478 0.00 0.00 33.18 2.29
524 542 3.070302 GGCTAACATCTAAGACCTGAGGG 59.930 52.174 2.38 0.00 38.88 4.30
545 563 1.542915 CCACAAATCTCACAGCCAAGG 59.457 52.381 0.00 0.00 0.00 3.61
558 576 1.847737 TCCGGGCCTAATACCACAAAT 59.152 47.619 0.84 0.00 0.00 2.32
583 605 2.309755 TCCAGTTGATGAAGGGATGCTT 59.690 45.455 0.00 0.00 0.00 3.91
612 634 0.894835 TCTAGGCAACATCTGTCGCA 59.105 50.000 0.00 0.00 41.41 5.10
637 660 9.832445 AAAGAAATACAACAGTAAGTCTGAAGA 57.168 29.630 1.79 0.00 46.27 2.87
715 738 1.920835 GAAGACCCCCTGCCTCTGT 60.921 63.158 0.00 0.00 0.00 3.41
723 746 2.719676 AGAAAAGAAGGAAGACCCCCT 58.280 47.619 0.00 0.00 36.73 4.79
753 776 8.160765 TGACCTCAAGACAAACCTATTTCATTA 58.839 33.333 0.00 0.00 0.00 1.90
754 777 7.004086 TGACCTCAAGACAAACCTATTTCATT 58.996 34.615 0.00 0.00 0.00 2.57
756 779 5.935945 TGACCTCAAGACAAACCTATTTCA 58.064 37.500 0.00 0.00 0.00 2.69
757 780 6.877611 TTGACCTCAAGACAAACCTATTTC 57.122 37.500 0.00 0.00 0.00 2.17
758 781 7.839680 ATTTGACCTCAAGACAAACCTATTT 57.160 32.000 0.00 0.00 37.15 1.40
759 782 7.839680 AATTTGACCTCAAGACAAACCTATT 57.160 32.000 0.00 0.00 37.15 1.73
761 784 8.792633 CATAAATTTGACCTCAAGACAAACCTA 58.207 33.333 0.00 0.00 37.15 3.08
762 785 7.661040 CATAAATTTGACCTCAAGACAAACCT 58.339 34.615 0.00 0.00 37.15 3.50
763 786 6.366061 GCATAAATTTGACCTCAAGACAAACC 59.634 38.462 0.00 0.00 37.15 3.27
764 787 6.366061 GGCATAAATTTGACCTCAAGACAAAC 59.634 38.462 0.00 0.00 37.15 2.93
765 788 6.267471 AGGCATAAATTTGACCTCAAGACAAA 59.733 34.615 0.00 0.00 37.15 2.83
766 789 5.774690 AGGCATAAATTTGACCTCAAGACAA 59.225 36.000 0.00 0.00 37.15 3.18
767 790 5.324409 AGGCATAAATTTGACCTCAAGACA 58.676 37.500 0.00 0.00 37.15 3.41
768 791 5.904362 AGGCATAAATTTGACCTCAAGAC 57.096 39.130 0.00 0.00 37.15 3.01
770 793 6.128472 GCAAAAGGCATAAATTTGACCTCAAG 60.128 38.462 0.00 0.49 43.97 3.02
771 794 5.700373 GCAAAAGGCATAAATTTGACCTCAA 59.300 36.000 0.00 0.00 43.97 3.02
772 795 5.237048 GCAAAAGGCATAAATTTGACCTCA 58.763 37.500 0.00 0.00 43.97 3.86
773 796 5.784750 GCAAAAGGCATAAATTTGACCTC 57.215 39.130 0.00 0.00 43.97 3.85
809 832 4.916358 GGAAGAGCATCCCCATGG 57.084 61.111 4.14 4.14 33.66 3.66
815 838 1.834263 ACTGTACTGGGAAGAGCATCC 59.166 52.381 4.66 0.00 38.86 3.51
816 839 3.954904 TCTACTGTACTGGGAAGAGCATC 59.045 47.826 4.66 0.00 0.00 3.91
817 840 3.982516 TCTACTGTACTGGGAAGAGCAT 58.017 45.455 4.66 0.00 0.00 3.79
818 841 3.451402 TCTACTGTACTGGGAAGAGCA 57.549 47.619 4.66 0.00 0.00 4.26
819 842 4.037446 CAGATCTACTGTACTGGGAAGAGC 59.963 50.000 0.00 6.88 41.30 4.09
820 843 5.298276 GTCAGATCTACTGTACTGGGAAGAG 59.702 48.000 0.00 0.00 45.86 2.85
825 848 3.542648 TCGTCAGATCTACTGTACTGGG 58.457 50.000 0.00 0.00 45.86 4.45
854 877 4.042311 TGATGCTTTCCCAAGTACCAAGTA 59.958 41.667 0.00 0.00 31.86 2.24
855 878 3.181434 TGATGCTTTCCCAAGTACCAAGT 60.181 43.478 0.00 0.00 31.86 3.16
856 879 3.420893 TGATGCTTTCCCAAGTACCAAG 58.579 45.455 0.00 0.00 31.86 3.61
857 880 3.517296 TGATGCTTTCCCAAGTACCAA 57.483 42.857 0.00 0.00 31.86 3.67
858 881 3.517296 TTGATGCTTTCCCAAGTACCA 57.483 42.857 0.00 0.00 31.86 3.25
859 882 3.367395 GCTTTGATGCTTTCCCAAGTACC 60.367 47.826 0.00 0.00 31.86 3.34
860 883 3.507622 AGCTTTGATGCTTTCCCAAGTAC 59.492 43.478 0.00 0.00 40.93 2.73
861 884 3.507233 CAGCTTTGATGCTTTCCCAAGTA 59.493 43.478 0.00 0.00 41.98 2.24
862 885 2.298163 CAGCTTTGATGCTTTCCCAAGT 59.702 45.455 0.00 0.00 41.98 3.16
925 948 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
926 949 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
927 950 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
928 951 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
929 952 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
930 953 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
931 954 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
932 955 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
933 956 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
934 957 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
935 958 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
936 959 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
937 960 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
938 961 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
939 962 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
940 963 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
941 964 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
942 965 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
943 966 4.501229 GCAGAGAGAGAGAGAGAGAGAGAG 60.501 54.167 0.00 0.00 0.00 3.20
944 967 3.386078 GCAGAGAGAGAGAGAGAGAGAGA 59.614 52.174 0.00 0.00 0.00 3.10
945 968 3.726607 GCAGAGAGAGAGAGAGAGAGAG 58.273 54.545 0.00 0.00 0.00 3.20
946 969 2.101415 CGCAGAGAGAGAGAGAGAGAGA 59.899 54.545 0.00 0.00 0.00 3.10
947 970 2.477825 CGCAGAGAGAGAGAGAGAGAG 58.522 57.143 0.00 0.00 0.00 3.20
948 971 1.138859 CCGCAGAGAGAGAGAGAGAGA 59.861 57.143 0.00 0.00 0.00 3.10
949 972 1.586422 CCGCAGAGAGAGAGAGAGAG 58.414 60.000 0.00 0.00 0.00 3.20
950 973 0.463654 GCCGCAGAGAGAGAGAGAGA 60.464 60.000 0.00 0.00 0.00 3.10
951 974 0.747644 TGCCGCAGAGAGAGAGAGAG 60.748 60.000 0.00 0.00 0.00 3.20
952 975 0.322906 TTGCCGCAGAGAGAGAGAGA 60.323 55.000 0.00 0.00 0.00 3.10
953 976 0.179140 GTTGCCGCAGAGAGAGAGAG 60.179 60.000 0.00 0.00 0.00 3.20
954 977 1.599606 GGTTGCCGCAGAGAGAGAGA 61.600 60.000 0.00 0.00 0.00 3.10
955 978 1.153667 GGTTGCCGCAGAGAGAGAG 60.154 63.158 0.00 0.00 0.00 3.20
956 979 2.650116 GGGTTGCCGCAGAGAGAGA 61.650 63.158 0.00 0.00 0.00 3.10
1163 1191 4.443621 GAAGGAAAAATAGACGGGGAGAG 58.556 47.826 0.00 0.00 0.00 3.20
1185 1221 1.779724 GCGAATCGTTAGTTAGCTCCG 59.220 52.381 4.07 0.00 0.00 4.63
1349 1386 5.552870 ATTTACAAGTCTGTGTCTGTCCT 57.447 39.130 0.00 0.00 36.96 3.85
1362 1399 5.239963 CACACTCCCGGTAAAATTTACAAGT 59.760 40.000 16.55 10.91 0.00 3.16
1363 1400 5.335348 CCACACTCCCGGTAAAATTTACAAG 60.335 44.000 16.55 10.02 0.00 3.16
1365 1402 4.073549 CCACACTCCCGGTAAAATTTACA 58.926 43.478 16.55 0.00 0.00 2.41
1375 1412 0.691078 ATCATAGCCACACTCCCGGT 60.691 55.000 0.00 0.00 0.00 5.28
1386 1423 7.934120 AGTAGTTGGAACTCATAAATCATAGCC 59.066 37.037 0.00 0.00 40.37 3.93
1418 1468 3.469739 CAAAATTGGACAAAAGCTGCCT 58.530 40.909 0.00 0.00 0.00 4.75
1459 1509 8.827758 ACTACATACTGCTCTCCTATATAGTGA 58.172 37.037 8.92 5.91 0.00 3.41
1460 1510 9.104965 GACTACATACTGCTCTCCTATATAGTG 57.895 40.741 8.92 1.93 0.00 2.74
1461 1511 8.269317 GGACTACATACTGCTCTCCTATATAGT 58.731 40.741 8.92 0.00 0.00 2.12
1463 1513 8.159229 TGGACTACATACTGCTCTCCTATATA 57.841 38.462 0.00 0.00 0.00 0.86
1465 1515 6.044520 ACTGGACTACATACTGCTCTCCTATA 59.955 42.308 0.00 0.00 0.00 1.31
1466 1516 5.163034 ACTGGACTACATACTGCTCTCCTAT 60.163 44.000 0.00 0.00 0.00 2.57
1475 1525 5.459107 GCACGAATAACTGGACTACATACTG 59.541 44.000 0.00 0.00 0.00 2.74
1477 1527 5.345702 TGCACGAATAACTGGACTACATAC 58.654 41.667 0.00 0.00 0.00 2.39
1495 1545 3.430895 AGTTATACAAAACGGACTGCACG 59.569 43.478 0.00 0.00 34.46 5.34
1501 1551 9.968743 CTAAGAATTGAGTTATACAAAACGGAC 57.031 33.333 0.00 0.00 34.46 4.79
1619 1670 1.001158 GCGAGATACACCTAGACCAGC 60.001 57.143 0.00 0.00 0.00 4.85
1701 1779 2.999355 CTCTTGTGGCAAGAACTAGAGC 59.001 50.000 11.93 0.00 39.48 4.09
1702 1780 4.264460 ACTCTTGTGGCAAGAACTAGAG 57.736 45.455 11.93 11.68 46.42 2.43
1717 1795 8.594687 CACAATTTTGTCAAACCTTAACTCTTG 58.405 33.333 0.00 0.00 39.91 3.02
1742 1820 6.816136 TCGAATCTTAGATAAGGCAATGTCA 58.184 36.000 0.00 0.00 34.14 3.58
1844 1923 5.237344 AGCACTTTTCTACTGTAACAAGCTG 59.763 40.000 0.00 0.00 0.00 4.24
1969 2067 2.283145 AGCAAAGTTGAGGAGCACAT 57.717 45.000 0.00 0.00 0.00 3.21
1982 2080 7.437124 GCTGTACGCTAAAAATTAAAGCAAAG 58.563 34.615 7.21 1.42 35.98 2.77
1999 2097 4.813296 ATTATGGCTTAAAGCTGTACGC 57.187 40.909 3.78 3.78 41.99 4.42
2000 2098 5.455525 GCAAATTATGGCTTAAAGCTGTACG 59.544 40.000 0.00 0.00 41.99 3.67
2366 2646 4.860907 ACAAAGCTGAATCGCAAATTGATC 59.139 37.500 0.00 0.00 0.00 2.92
2487 2767 1.190323 CTTTGTCACGAGCAAGACGAC 59.810 52.381 0.00 0.00 37.58 4.34
2544 2824 9.209175 ACTAAGATCAACAATTCAACACTCTAC 57.791 33.333 0.00 0.00 0.00 2.59
2545 2825 9.424319 GACTAAGATCAACAATTCAACACTCTA 57.576 33.333 0.00 0.00 0.00 2.43
2646 2926 2.695127 AAGAGCAGCTGAAGATGGAG 57.305 50.000 20.43 0.00 31.02 3.86
2647 2927 2.570752 AGAAAGAGCAGCTGAAGATGGA 59.429 45.455 20.43 0.00 31.02 3.41
2648 2928 2.988570 AGAAAGAGCAGCTGAAGATGG 58.011 47.619 20.43 0.00 31.02 3.51
2649 2929 5.177326 ACTAAGAAAGAGCAGCTGAAGATG 58.823 41.667 20.43 0.00 34.00 2.90
2691 2971 0.323725 CCCAAGTTGATGACCCCAGG 60.324 60.000 3.87 0.00 0.00 4.45
2708 2988 5.806654 TTCCGTATACCTAACCATTACCC 57.193 43.478 0.00 0.00 0.00 3.69
2725 3005 8.915036 AGATACAACATCTATCTAGTTTTCCGT 58.085 33.333 0.00 0.00 30.51 4.69
2727 3007 9.482627 CCAGATACAACATCTATCTAGTTTTCC 57.517 37.037 0.00 0.00 31.02 3.13
2782 3062 7.841277 CAGATATCAAACAAACTTACATCGTCG 59.159 37.037 5.32 0.00 0.00 5.12
2800 3080 7.722949 TGCAGATGTATCATACCAGATATCA 57.277 36.000 5.32 0.00 33.42 2.15
2806 3086 5.589855 TGGTTTTGCAGATGTATCATACCAG 59.410 40.000 0.00 0.00 0.00 4.00
2823 3228 7.636259 AAAAATGTATCGATGTGTGGTTTTG 57.364 32.000 8.54 0.00 0.00 2.44
2858 3561 5.414454 TCGCTACAGAAAATAACCTTTGCAT 59.586 36.000 0.00 0.00 0.00 3.96
2943 3736 4.142071 TGCATTTTGCTTGTTCTGGTGTTA 60.142 37.500 0.75 0.00 45.31 2.41
3015 4115 7.767198 CACCCTTTGTTCCTAAATATAAGACGA 59.233 37.037 0.00 0.00 0.00 4.20
3035 4135 9.596308 AGTTTATGTTTTAGGAATTACACCCTT 57.404 29.630 0.00 0.00 34.11 3.95
3056 4156 3.370527 GGCATGCTACTCCTCCAAGTTTA 60.371 47.826 18.92 0.00 0.00 2.01
3067 4167 1.740025 GGTCAAGTTGGCATGCTACTC 59.260 52.381 18.92 7.47 0.00 2.59
3077 4177 9.996554 AAAGGAAATAATAAAAGGTCAAGTTGG 57.003 29.630 2.34 0.00 0.00 3.77
3273 4373 1.271840 ATCTTGGCCCTTGCTCGGTA 61.272 55.000 0.00 0.00 37.74 4.02
3452 4552 1.123077 AGCGGCACAGAGGATAATGA 58.877 50.000 1.45 0.00 0.00 2.57



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

AutoCloner maintained by Alex Coulton.