Multiple sequence alignment - TraesCS6D01G022700

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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 TraesCS6D01G022700 chr6D 100.000 2543 0 0 1 2543 8788629 8786087 0.000000e+00 4697.0
1 TraesCS6D01G022700 chr6D 91.429 945 70 6 964 1905 8743569 8742633 0.000000e+00 1286.0
2 TraesCS6D01G022700 chr6D 91.703 928 69 3 980 1905 8732868 8731947 0.000000e+00 1280.0
3 TraesCS6D01G022700 chr6D 87.363 641 71 8 1908 2543 8725263 8724628 0.000000e+00 726.0
4 TraesCS6D01G022700 chrUn 92.241 928 64 3 980 1905 357590835 357589914 0.000000e+00 1308.0
5 TraesCS6D01G022700 chrUn 91.487 928 71 3 980 1905 355457517 355456596 0.000000e+00 1269.0
6 TraesCS6D01G022700 chrUn 91.574 902 68 3 980 1879 461056163 461057058 0.000000e+00 1238.0
7 TraesCS6D01G022700 chrUn 87.676 641 68 9 1908 2543 80050940 80051574 0.000000e+00 736.0
8 TraesCS6D01G022700 chrUn 87.676 641 68 9 1908 2543 230374518 230375152 0.000000e+00 736.0
9 TraesCS6D01G022700 chrUn 87.676 641 68 9 1908 2543 364470942 364470308 0.000000e+00 736.0
10 TraesCS6D01G022700 chrUn 87.363 641 71 8 1908 2543 351902535 351901900 0.000000e+00 726.0
11 TraesCS6D01G022700 chrUn 87.363 641 71 8 1908 2543 357589627 357588992 0.000000e+00 726.0
12 TraesCS6D01G022700 chrUn 87.051 641 73 8 1908 2543 393621037 393620402 0.000000e+00 715.0
13 TraesCS6D01G022700 chrUn 86.089 381 49 2 2166 2543 80053126 80053505 8.470000e-110 407.0
14 TraesCS6D01G022700 chr6A 94.649 841 44 1 980 1819 9054312 9055152 0.000000e+00 1303.0
15 TraesCS6D01G022700 chr6A 91.703 928 68 5 980 1905 9134508 9135428 0.000000e+00 1279.0
16 TraesCS6D01G022700 chr6A 88.263 639 70 4 1908 2543 9135712 9136348 0.000000e+00 760.0
17 TraesCS6D01G022700 chr6A 94.276 297 17 0 1806 2102 9055185 9055481 2.980000e-124 455.0
18 TraesCS6D01G022700 chr6A 87.143 350 16 11 222 543 9053269 9053617 1.110000e-98 370.0
19 TraesCS6D01G022700 chr6A 94.118 221 8 2 1 221 9053026 9053241 5.240000e-87 331.0
20 TraesCS6D01G022700 chr6A 83.383 337 47 4 538 871 9053685 9054015 1.140000e-78 303.0
21 TraesCS6D01G022700 chr6B 91.909 927 58 5 980 1905 15890522 15889612 0.000000e+00 1280.0
22 TraesCS6D01G022700 chr6B 90.530 792 69 5 980 1766 15899547 15898757 0.000000e+00 1042.0
23 TraesCS6D01G022700 chr6B 86.150 917 69 26 1 873 15929698 15928796 0.000000e+00 937.0
24 TraesCS6D01G022700 chr6B 86.111 144 15 2 842 980 15928795 15928652 1.580000e-32 150.0
25 TraesCS6D01G022700 chr4A 92.683 41 2 1 888 928 624289893 624289932 9.830000e-05 58.4
26 TraesCS6D01G022700 chr4A 100.000 28 0 0 888 915 448524910 448524883 5.000000e-03 52.8
27 TraesCS6D01G022700 chr5A 100.000 28 0 0 888 915 59700886 59700859 5.000000e-03 52.8
28 TraesCS6D01G022700 chr4D 100.000 28 0 0 888 915 122192896 122192923 5.000000e-03 52.8


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 TraesCS6D01G022700 chr6D 8786087 8788629 2542 True 4697.0 4697 100.0000 1 2543 1 chr6D.!!$R4 2542
1 TraesCS6D01G022700 chr6D 8742633 8743569 936 True 1286.0 1286 91.4290 964 1905 1 chr6D.!!$R3 941
2 TraesCS6D01G022700 chr6D 8731947 8732868 921 True 1280.0 1280 91.7030 980 1905 1 chr6D.!!$R2 925
3 TraesCS6D01G022700 chr6D 8724628 8725263 635 True 726.0 726 87.3630 1908 2543 1 chr6D.!!$R1 635
4 TraesCS6D01G022700 chrUn 355456596 355457517 921 True 1269.0 1269 91.4870 980 1905 1 chrUn.!!$R2 925
5 TraesCS6D01G022700 chrUn 461056163 461057058 895 False 1238.0 1238 91.5740 980 1879 1 chrUn.!!$F2 899
6 TraesCS6D01G022700 chrUn 357588992 357590835 1843 True 1017.0 1308 89.8020 980 2543 2 chrUn.!!$R5 1563
7 TraesCS6D01G022700 chrUn 230374518 230375152 634 False 736.0 736 87.6760 1908 2543 1 chrUn.!!$F1 635
8 TraesCS6D01G022700 chrUn 364470308 364470942 634 True 736.0 736 87.6760 1908 2543 1 chrUn.!!$R3 635
9 TraesCS6D01G022700 chrUn 351901900 351902535 635 True 726.0 726 87.3630 1908 2543 1 chrUn.!!$R1 635
10 TraesCS6D01G022700 chrUn 393620402 393621037 635 True 715.0 715 87.0510 1908 2543 1 chrUn.!!$R4 635
11 TraesCS6D01G022700 chrUn 80050940 80053505 2565 False 571.5 736 86.8825 1908 2543 2 chrUn.!!$F3 635
12 TraesCS6D01G022700 chr6A 9134508 9136348 1840 False 1019.5 1279 89.9830 980 2543 2 chr6A.!!$F2 1563
13 TraesCS6D01G022700 chr6A 9053026 9055481 2455 False 552.4 1303 90.7138 1 2102 5 chr6A.!!$F1 2101
14 TraesCS6D01G022700 chr6B 15889612 15890522 910 True 1280.0 1280 91.9090 980 1905 1 chr6B.!!$R1 925
15 TraesCS6D01G022700 chr6B 15898757 15899547 790 True 1042.0 1042 90.5300 980 1766 1 chr6B.!!$R2 786
16 TraesCS6D01G022700 chr6B 15928652 15929698 1046 True 543.5 937 86.1305 1 980 2 chr6B.!!$R3 979

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
443 505 0.325933 TGGTGGTCTGCAGGATTCTG 59.674 55.0 15.13 0.0 43.64 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 2638 0.321671 CTGTCCAGAACCATGTCCGT 59.678 55.0 0.0 0.0 0.0 4.69 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
79 82 7.840342 ACTGTCATGCTAGAGAAATAAGTTG 57.160 36.000 0.00 0.00 0.00 3.16
80 83 7.390027 ACTGTCATGCTAGAGAAATAAGTTGT 58.610 34.615 0.00 0.00 0.00 3.32
81 84 8.531982 ACTGTCATGCTAGAGAAATAAGTTGTA 58.468 33.333 0.00 0.00 0.00 2.41
82 85 8.703604 TGTCATGCTAGAGAAATAAGTTGTAC 57.296 34.615 0.00 0.00 0.00 2.90
83 86 8.531982 TGTCATGCTAGAGAAATAAGTTGTACT 58.468 33.333 0.00 0.00 0.00 2.73
84 87 8.812329 GTCATGCTAGAGAAATAAGTTGTACTG 58.188 37.037 0.00 0.00 0.00 2.74
169 172 4.327627 GCAGAGACGTCCTGACTTATTTTC 59.672 45.833 27.67 10.53 33.65 2.29
195 199 9.140286 CGCGAGATTATCCTATTTTTGATTCTA 57.860 33.333 0.00 0.00 0.00 2.10
232 263 0.447801 CGCCAGTGTAACAAGATGCC 59.552 55.000 0.00 0.00 41.43 4.40
333 368 2.093973 AGCTCGGTTTGTGATACTGAGG 60.094 50.000 12.32 0.00 45.17 3.86
343 378 5.159273 TGTGATACTGAGGTGTATGCAAA 57.841 39.130 0.00 0.00 33.74 3.68
443 505 0.325933 TGGTGGTCTGCAGGATTCTG 59.674 55.000 15.13 0.00 43.64 3.02
446 508 2.079925 GTGGTCTGCAGGATTCTGAAC 58.920 52.381 15.13 1.25 43.49 3.18
460 522 8.260818 CAGGATTCTGAACTTCCAAGTAAGATA 58.739 37.037 11.52 0.73 43.49 1.98
469 531 8.868635 AACTTCCAAGTAAGATATTACTACGC 57.131 34.615 12.93 0.00 38.57 4.42
493 555 6.679884 GCCAATGAAATCTGAGGATGAAACTC 60.680 42.308 0.00 0.00 35.55 3.01
534 598 4.500477 GCTCAAATGGCGAAAATATGTGTC 59.500 41.667 0.00 0.00 0.00 3.67
578 718 8.130671 TCTGGTGGTAAGGTAGCATTATATAC 57.869 38.462 0.00 0.00 38.57 1.47
584 724 8.863086 TGGTAAGGTAGCATTATATACGTTCTT 58.137 33.333 0.00 0.00 33.45 2.52
599 739 3.813166 ACGTTCTTCCCAAGTTGTACATG 59.187 43.478 0.00 0.00 0.00 3.21
601 741 4.084013 CGTTCTTCCCAAGTTGTACATGTC 60.084 45.833 0.00 0.00 0.00 3.06
602 742 3.659786 TCTTCCCAAGTTGTACATGTCG 58.340 45.455 0.00 0.00 0.00 4.35
609 749 4.992319 CCAAGTTGTACATGTCGTTTCCTA 59.008 41.667 0.00 0.00 0.00 2.94
610 750 5.467399 CCAAGTTGTACATGTCGTTTCCTAA 59.533 40.000 0.00 0.00 0.00 2.69
611 751 6.017770 CCAAGTTGTACATGTCGTTTCCTAAA 60.018 38.462 0.00 0.00 0.00 1.85
626 766 8.410141 TCGTTTCCTAAAGTGTGAAATTGAATT 58.590 29.630 0.00 0.00 31.35 2.17
667 807 7.487189 CCTAACATTTTGAAGAGCACATGAATC 59.513 37.037 0.00 0.00 0.00 2.52
670 810 5.381174 TTTTGAAGAGCACATGAATCAGG 57.619 39.130 0.00 0.00 0.00 3.86
722 862 2.223782 GGAAGCTTTGCATGAACACACA 60.224 45.455 0.00 0.00 0.00 3.72
725 865 4.062677 AGCTTTGCATGAACACACAAAT 57.937 36.364 0.00 0.00 32.07 2.32
736 876 2.867624 ACACACAAATGAGACCTGCAT 58.132 42.857 0.00 0.00 0.00 3.96
744 884 5.181009 CAAATGAGACCTGCATGAACTAGA 58.819 41.667 0.00 0.00 0.00 2.43
745 885 3.876274 TGAGACCTGCATGAACTAGAC 57.124 47.619 0.00 0.00 0.00 2.59
748 888 4.040339 TGAGACCTGCATGAACTAGACAAA 59.960 41.667 0.00 0.00 0.00 2.83
749 889 4.319177 AGACCTGCATGAACTAGACAAAC 58.681 43.478 0.00 0.00 0.00 2.93
752 892 4.516698 ACCTGCATGAACTAGACAAACTTG 59.483 41.667 0.00 0.00 0.00 3.16
753 893 4.470462 CTGCATGAACTAGACAAACTTGC 58.530 43.478 0.00 4.22 34.07 4.01
754 894 3.882288 TGCATGAACTAGACAAACTTGCA 59.118 39.130 0.00 6.66 38.56 4.08
755 895 4.337836 TGCATGAACTAGACAAACTTGCAA 59.662 37.500 0.00 0.00 38.18 4.08
756 896 4.913924 GCATGAACTAGACAAACTTGCAAG 59.086 41.667 24.84 24.84 33.80 4.01
757 897 5.277974 GCATGAACTAGACAAACTTGCAAGA 60.278 40.000 32.50 7.52 33.80 3.02
758 898 6.728200 CATGAACTAGACAAACTTGCAAGAA 58.272 36.000 32.50 7.72 0.00 2.52
759 899 6.751514 TGAACTAGACAAACTTGCAAGAAA 57.248 33.333 32.50 8.37 0.00 2.52
762 902 7.754924 TGAACTAGACAAACTTGCAAGAAAAAG 59.245 33.333 32.50 19.35 0.00 2.27
763 903 6.564328 ACTAGACAAACTTGCAAGAAAAAGG 58.436 36.000 32.50 16.30 0.00 3.11
764 904 4.758688 AGACAAACTTGCAAGAAAAAGGG 58.241 39.130 32.50 15.34 0.00 3.95
808 951 5.048083 TGTTGCTACCAATTCATTCAGTTCC 60.048 40.000 0.00 0.00 32.75 3.62
809 952 4.922206 TGCTACCAATTCATTCAGTTCCT 58.078 39.130 0.00 0.00 0.00 3.36
812 955 5.393461 GCTACCAATTCATTCAGTTCCTTGG 60.393 44.000 0.00 0.00 38.08 3.61
815 958 4.523943 CCAATTCATTCAGTTCCTTGGACA 59.476 41.667 0.00 0.00 34.88 4.02
820 963 4.520111 TCATTCAGTTCCTTGGACATGTTG 59.480 41.667 0.00 0.00 0.00 3.33
822 965 4.698201 TCAGTTCCTTGGACATGTTGTA 57.302 40.909 0.00 0.00 0.00 2.41
878 1030 4.694037 TCATTGTCTGTCTTTCATGCTCAG 59.306 41.667 0.00 0.00 0.00 3.35
884 1036 3.657634 TGTCTTTCATGCTCAGTGAGAC 58.342 45.455 24.55 14.89 0.00 3.36
890 1042 1.925185 CATGCTCAGTGAGACACGATG 59.075 52.381 24.55 11.92 39.64 3.84
892 1044 2.159382 TGCTCAGTGAGACACGATGTA 58.841 47.619 24.55 0.00 39.64 2.29
893 1045 2.095212 TGCTCAGTGAGACACGATGTAC 60.095 50.000 24.55 2.36 39.64 2.90
894 1046 2.162608 GCTCAGTGAGACACGATGTACT 59.837 50.000 24.55 0.00 39.64 2.73
896 1048 4.407818 CTCAGTGAGACACGATGTACTTC 58.592 47.826 15.46 0.00 39.64 3.01
898 1050 3.191581 CAGTGAGACACGATGTACTTCCT 59.808 47.826 3.35 0.00 39.64 3.36
899 1051 3.440872 AGTGAGACACGATGTACTTCCTC 59.559 47.826 3.35 4.94 39.64 3.71
901 1053 1.743958 AGACACGATGTACTTCCTCCG 59.256 52.381 3.35 0.00 0.00 4.63
902 1054 1.471684 GACACGATGTACTTCCTCCGT 59.528 52.381 3.35 0.00 0.00 4.69
903 1055 1.471684 ACACGATGTACTTCCTCCGTC 59.528 52.381 3.35 0.00 0.00 4.79
904 1056 1.743958 CACGATGTACTTCCTCCGTCT 59.256 52.381 3.35 0.00 0.00 4.18
906 1058 2.014857 CGATGTACTTCCTCCGTCTCA 58.985 52.381 3.35 0.00 0.00 3.27
909 1063 4.275196 CGATGTACTTCCTCCGTCTCATAA 59.725 45.833 3.35 0.00 0.00 1.90
918 1072 8.142551 ACTTCCTCCGTCTCATAATATAACAAC 58.857 37.037 0.00 0.00 0.00 3.32
919 1073 7.591421 TCCTCCGTCTCATAATATAACAACA 57.409 36.000 0.00 0.00 0.00 3.33
920 1074 8.190326 TCCTCCGTCTCATAATATAACAACAT 57.810 34.615 0.00 0.00 0.00 2.71
921 1075 8.647796 TCCTCCGTCTCATAATATAACAACATT 58.352 33.333 0.00 0.00 0.00 2.71
956 1110 9.421806 TGTTTTAGCTTGAAAATGTTATCATGG 57.578 29.630 0.00 0.00 34.19 3.66
957 1111 8.872845 GTTTTAGCTTGAAAATGTTATCATGGG 58.127 33.333 0.00 0.00 34.19 4.00
960 1114 6.812998 AGCTTGAAAATGTTATCATGGGATG 58.187 36.000 0.00 0.00 34.89 3.51
961 1115 5.987347 GCTTGAAAATGTTATCATGGGATGG 59.013 40.000 0.00 0.00 34.89 3.51
962 1116 6.482898 TTGAAAATGTTATCATGGGATGGG 57.517 37.500 0.00 0.00 34.89 4.00
963 1117 4.900652 TGAAAATGTTATCATGGGATGGGG 59.099 41.667 0.00 0.00 34.89 4.96
964 1118 4.557899 AAATGTTATCATGGGATGGGGT 57.442 40.909 0.00 0.00 34.89 4.95
966 1120 4.934797 ATGTTATCATGGGATGGGGTAG 57.065 45.455 0.00 0.00 34.89 3.18
968 1122 4.833672 TGTTATCATGGGATGGGGTAGTA 58.166 43.478 0.00 0.00 34.89 1.82
969 1123 5.420455 TGTTATCATGGGATGGGGTAGTAT 58.580 41.667 0.00 0.00 34.89 2.12
970 1124 6.576360 TGTTATCATGGGATGGGGTAGTATA 58.424 40.000 0.00 0.00 34.89 1.47
972 1126 4.495459 TCATGGGATGGGGTAGTATACA 57.505 45.455 5.50 0.00 45.43 2.29
973 1127 4.164981 TCATGGGATGGGGTAGTATACAC 58.835 47.826 5.50 1.57 46.65 2.90
975 1129 9.618612 TATCATGGGATGGGGTAGTATACACGT 62.619 44.444 5.50 0.00 39.41 4.49
1017 1348 2.173356 CACCATGGCAATCTTCCTCCTA 59.827 50.000 13.04 0.00 0.00 2.94
1093 1424 1.374252 CGTGCGAGTGGCTACCTTT 60.374 57.895 0.00 0.00 44.05 3.11
1103 1434 3.138468 AGTGGCTACCTTTCAGGAAAGTT 59.862 43.478 17.76 8.66 44.66 2.66
1106 1437 2.229062 GCTACCTTTCAGGAAAGTTGGC 59.771 50.000 17.76 14.31 44.66 4.52
1180 1511 2.989824 AGTACCACTGCTCGCCGT 60.990 61.111 0.00 0.00 0.00 5.68
1215 1546 3.373226 AAGGCCGTCTTGACGCTA 58.627 55.556 16.59 0.00 33.76 4.26
1223 1554 1.387084 CGTCTTGACGCTAAACAGCTC 59.613 52.381 10.23 0.00 0.00 4.09
1331 1662 0.187117 TGGTTCAAGAACATGGCCCA 59.813 50.000 14.25 0.00 42.85 5.36
1358 1689 0.740868 CACCGCATCAAGATCACCGT 60.741 55.000 0.00 0.00 0.00 4.83
1403 1734 2.338984 GGTGGACGAGTGCGACTT 59.661 61.111 0.00 0.00 41.64 3.01
1464 1795 0.796312 GTGCCAACAACATCGTCGAT 59.204 50.000 0.75 0.75 0.00 3.59
1519 1850 1.215382 CAGAACGTCGGCATGGAGA 59.785 57.895 0.00 0.00 0.00 3.71
1669 2004 4.408182 ACTCGGGAGGTTTATCAGATTG 57.592 45.455 0.00 0.00 0.00 2.67
1814 2153 3.584406 ATGAAACACACGAGAGAGAGG 57.416 47.619 0.00 0.00 0.00 3.69
1830 2215 3.103742 GAGAGGGAGACACCTGAGAAAT 58.896 50.000 0.00 0.00 42.10 2.17
1851 2236 4.265904 TCTACACGCTCATTTTCAAGGA 57.734 40.909 0.00 0.00 0.00 3.36
1854 2239 6.403049 TCTACACGCTCATTTTCAAGGATAA 58.597 36.000 0.00 0.00 0.00 1.75
1969 2638 5.820423 AGTAATGTGTTACAAGCACTCAACA 59.180 36.000 0.00 0.00 42.13 3.33
1973 2642 2.206750 GTTACAAGCACTCAACACGGA 58.793 47.619 0.00 0.00 0.00 4.69
1995 2664 5.431765 GACATGGTTCTGGACAGATGTAAT 58.568 41.667 2.42 0.00 37.29 1.89
1996 2665 5.188434 ACATGGTTCTGGACAGATGTAATG 58.812 41.667 2.42 7.73 37.29 1.90
2073 2744 3.803778 CCAGCCATTTTTCTTCACACAAC 59.196 43.478 0.00 0.00 0.00 3.32
2075 2746 2.218530 GCCATTTTTCTTCACACAACGC 59.781 45.455 0.00 0.00 0.00 4.84
2122 2793 7.189693 TGTTGCTAACTGTTTGAAGAGTATG 57.810 36.000 6.17 0.00 31.58 2.39
2144 2815 2.159254 GCTGCCCGAGATAATTTTTGCA 60.159 45.455 0.00 0.00 0.00 4.08
2193 2864 6.978080 GGTGCATGGTTACGAATAATGATTTT 59.022 34.615 0.00 0.00 0.00 1.82
2206 2877 6.942532 ATAATGATTTTGTGGCATACGAGT 57.057 33.333 0.00 0.00 0.00 4.18
2251 2922 7.123383 AGAAAAGGAAAGGAAGGTTTTGTCTA 58.877 34.615 0.00 0.00 0.00 2.59
2253 2924 6.901081 AAGGAAAGGAAGGTTTTGTCTATG 57.099 37.500 0.00 0.00 0.00 2.23
2275 2946 4.334481 TGTGATGTCAAGCTTGATATGCAG 59.666 41.667 34.78 6.62 38.83 4.41
2281 2952 5.203370 GTCAAGCTTGATATGCAGAATTCG 58.797 41.667 30.65 0.00 39.73 3.34
2310 2981 4.338879 CAGGTGGAGTGGAATTTCTTGAT 58.661 43.478 0.00 0.00 0.00 2.57
2331 3002 9.113838 CTTGATAAGTATTATGTTGAAGCTGGT 57.886 33.333 0.00 0.00 42.35 4.00
2351 3022 2.758423 GTTTTTGACTCCAAGTGGGTGT 59.242 45.455 0.00 0.00 45.80 4.16
2353 3024 4.447138 TTTTGACTCCAAGTGGGTGTAT 57.553 40.909 0.00 0.00 43.26 2.29
2360 3031 5.030147 ACTCCAAGTGGGTGTATCTCATTA 58.970 41.667 0.00 0.00 41.48 1.90
2373 3044 6.363626 GTGTATCTCATTATCGAATGCGTCTT 59.636 38.462 0.00 0.00 42.01 3.01
2374 3045 5.835911 ATCTCATTATCGAATGCGTCTTG 57.164 39.130 0.00 0.00 42.01 3.02
2379 3050 0.676466 ATCGAATGCGTCTTGCCCAA 60.676 50.000 0.00 0.00 45.60 4.12
2398 3069 6.126332 TGCCCAATAAATATCAGGTCCAGTTA 60.126 38.462 0.00 0.00 0.00 2.24
2410 3081 6.785076 TCAGGTCCAGTTAAATTAATGGTCA 58.215 36.000 11.28 0.00 34.32 4.02
2487 3159 5.192722 TCACCATAAGTATTCCCATTCCACA 59.807 40.000 0.00 0.00 0.00 4.17
2492 3164 7.445402 CCATAAGTATTCCCATTCCACAGTAAG 59.555 40.741 0.00 0.00 0.00 2.34
2496 3168 0.999712 CCCATTCCACAGTAAGGGGT 59.000 55.000 0.00 0.00 41.91 4.95
2514 3186 7.849322 AAGGGGTTTTTGAGCTTATTTAAGA 57.151 32.000 1.52 0.00 35.33 2.10
2526 3201 9.823647 TGAGCTTATTTAAGAATGAGGAGTTAG 57.176 33.333 1.52 0.00 35.33 2.34
2528 3203 7.717436 AGCTTATTTAAGAATGAGGAGTTAGGC 59.283 37.037 1.52 0.00 35.33 3.93
2532 3207 8.829373 ATTTAAGAATGAGGAGTTAGGCAATT 57.171 30.769 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 82 5.407691 GCAACAGGTTTACTTCCTACAGTAC 59.592 44.000 0.00 0.00 33.54 2.73
80 83 5.544650 GCAACAGGTTTACTTCCTACAGTA 58.455 41.667 0.00 0.00 33.54 2.74
81 84 4.386711 GCAACAGGTTTACTTCCTACAGT 58.613 43.478 0.00 0.00 33.54 3.55
82 85 3.432252 CGCAACAGGTTTACTTCCTACAG 59.568 47.826 0.00 0.00 33.54 2.74
83 86 3.395639 CGCAACAGGTTTACTTCCTACA 58.604 45.455 0.00 0.00 33.54 2.74
84 87 2.740447 CCGCAACAGGTTTACTTCCTAC 59.260 50.000 0.00 0.00 33.54 3.18
169 172 8.023050 AGAATCAAAAATAGGATAATCTCGCG 57.977 34.615 0.00 0.00 0.00 5.87
195 199 1.556564 CGTTACATCCGAATGCGACT 58.443 50.000 0.00 0.00 40.82 4.18
199 203 0.304705 CTGGCGTTACATCCGAATGC 59.695 55.000 0.00 0.00 37.96 3.56
232 263 1.699343 GTCGAGTTTGAAGTCCTCCG 58.301 55.000 0.00 0.00 0.00 4.63
333 368 5.176223 GGCATGCTTGATTATTTGCATACAC 59.824 40.000 18.92 0.00 43.24 2.90
343 378 3.907221 AGAACAGGGCATGCTTGATTAT 58.093 40.909 23.30 11.82 0.00 1.28
387 422 6.923508 TGAATGTACTACTGCACTGCATATAC 59.076 38.462 3.64 5.82 38.13 1.47
388 423 7.049799 TGAATGTACTACTGCACTGCATATA 57.950 36.000 3.64 0.00 38.13 0.86
443 505 8.966194 GCGTAGTAATATCTTACTTGGAAGTTC 58.034 37.037 8.62 0.00 44.07 3.01
446 508 7.431249 TGGCGTAGTAATATCTTACTTGGAAG 58.569 38.462 8.62 0.00 44.07 3.46
460 522 5.760253 CCTCAGATTTCATTGGCGTAGTAAT 59.240 40.000 0.00 0.00 0.00 1.89
469 531 6.602406 AGAGTTTCATCCTCAGATTTCATTGG 59.398 38.462 0.00 0.00 0.00 3.16
493 555 4.326826 TGAGCAATTTACCTTGAGACCAG 58.673 43.478 0.00 0.00 0.00 4.00
534 598 2.639286 GTGTTCCTTGCTGGTGCG 59.361 61.111 0.00 0.00 43.34 5.34
559 699 9.351570 GAAGAACGTATATAATGCTACCTTACC 57.648 37.037 0.00 0.00 0.00 2.85
560 700 9.351570 GGAAGAACGTATATAATGCTACCTTAC 57.648 37.037 0.00 0.00 0.00 2.34
561 701 8.526147 GGGAAGAACGTATATAATGCTACCTTA 58.474 37.037 0.00 0.00 0.00 2.69
562 702 7.015877 TGGGAAGAACGTATATAATGCTACCTT 59.984 37.037 0.00 0.00 0.00 3.50
563 703 6.495872 TGGGAAGAACGTATATAATGCTACCT 59.504 38.462 0.00 0.00 0.00 3.08
578 718 3.813166 ACATGTACAACTTGGGAAGAACG 59.187 43.478 0.00 0.00 0.00 3.95
584 724 3.478857 AACGACATGTACAACTTGGGA 57.521 42.857 0.00 0.00 0.00 4.37
599 739 6.721321 TCAATTTCACACTTTAGGAAACGAC 58.279 36.000 0.00 0.00 33.78 4.34
601 741 8.574196 AATTCAATTTCACACTTTAGGAAACG 57.426 30.769 0.00 0.00 33.78 3.60
642 782 8.024865 TGATTCATGTGCTCTTCAAAATGTTAG 58.975 33.333 0.00 0.00 0.00 2.34
655 795 1.404391 CCAAGCCTGATTCATGTGCTC 59.596 52.381 6.10 0.00 0.00 4.26
657 797 1.133790 GTCCAAGCCTGATTCATGTGC 59.866 52.381 0.00 0.00 0.00 4.57
707 847 5.042593 GTCTCATTTGTGTGTTCATGCAAA 58.957 37.500 0.00 0.00 35.66 3.68
722 862 5.181748 GTCTAGTTCATGCAGGTCTCATTT 58.818 41.667 0.00 0.00 0.00 2.32
725 865 3.165071 TGTCTAGTTCATGCAGGTCTCA 58.835 45.455 0.00 0.00 0.00 3.27
736 876 6.751514 TTTCTTGCAAGTTTGTCTAGTTCA 57.248 33.333 25.19 0.00 0.00 3.18
744 884 4.252878 CACCCTTTTTCTTGCAAGTTTGT 58.747 39.130 25.19 11.38 0.00 2.83
745 885 3.622612 CCACCCTTTTTCTTGCAAGTTTG 59.377 43.478 25.19 12.14 0.00 2.93
748 888 2.466846 ACCACCCTTTTTCTTGCAAGT 58.533 42.857 25.19 1.95 0.00 3.16
749 889 3.888930 TCTACCACCCTTTTTCTTGCAAG 59.111 43.478 20.81 20.81 0.00 4.01
752 892 4.929819 TTTCTACCACCCTTTTTCTTGC 57.070 40.909 0.00 0.00 0.00 4.01
753 893 7.996098 TCTATTTCTACCACCCTTTTTCTTG 57.004 36.000 0.00 0.00 0.00 3.02
755 895 9.907229 CTATTCTATTTCTACCACCCTTTTTCT 57.093 33.333 0.00 0.00 0.00 2.52
756 896 9.901172 TCTATTCTATTTCTACCACCCTTTTTC 57.099 33.333 0.00 0.00 0.00 2.29
759 899 9.853177 CATTCTATTCTATTTCTACCACCCTTT 57.147 33.333 0.00 0.00 0.00 3.11
762 902 9.057089 CAACATTCTATTCTATTTCTACCACCC 57.943 37.037 0.00 0.00 0.00 4.61
763 903 8.560374 GCAACATTCTATTCTATTTCTACCACC 58.440 37.037 0.00 0.00 0.00 4.61
764 904 9.331282 AGCAACATTCTATTCTATTTCTACCAC 57.669 33.333 0.00 0.00 0.00 4.16
792 935 4.523943 TGTCCAAGGAACTGAATGAATTGG 59.476 41.667 0.00 0.00 40.86 3.16
822 965 8.626526 GGGTTACACCGATGATAAAAATATTGT 58.373 33.333 0.00 0.00 39.83 2.71
828 971 5.648960 GGAAGGGTTACACCGATGATAAAAA 59.351 40.000 0.00 0.00 39.83 1.94
839 982 3.081804 CAATGACAGGAAGGGTTACACC 58.918 50.000 0.00 0.00 37.60 4.16
846 989 2.304180 AGACAGACAATGACAGGAAGGG 59.696 50.000 0.00 0.00 0.00 3.95
847 990 3.692257 AGACAGACAATGACAGGAAGG 57.308 47.619 0.00 0.00 0.00 3.46
848 991 5.059161 TGAAAGACAGACAATGACAGGAAG 58.941 41.667 0.00 0.00 0.00 3.46
849 992 5.034852 TGAAAGACAGACAATGACAGGAA 57.965 39.130 0.00 0.00 0.00 3.36
857 1000 4.454847 CACTGAGCATGAAAGACAGACAAT 59.545 41.667 0.00 0.00 33.53 2.71
858 1001 3.811497 CACTGAGCATGAAAGACAGACAA 59.189 43.478 0.00 0.00 33.53 3.18
878 1030 3.427773 GGAGGAAGTACATCGTGTCTCAC 60.428 52.174 0.00 0.00 0.00 3.51
884 1036 1.743958 AGACGGAGGAAGTACATCGTG 59.256 52.381 0.00 0.00 0.00 4.35
890 1042 8.790718 TGTTATATTATGAGACGGAGGAAGTAC 58.209 37.037 0.00 0.00 0.00 2.73
892 1044 7.834881 TGTTATATTATGAGACGGAGGAAGT 57.165 36.000 0.00 0.00 0.00 3.01
893 1045 8.141909 TGTTGTTATATTATGAGACGGAGGAAG 58.858 37.037 0.00 0.00 0.00 3.46
894 1046 8.014070 TGTTGTTATATTATGAGACGGAGGAA 57.986 34.615 0.00 0.00 0.00 3.36
896 1048 8.833231 AATGTTGTTATATTATGAGACGGAGG 57.167 34.615 0.00 0.00 0.00 4.30
928 1082 9.143631 ATGATAACATTTTCAAGCTAAAACAGC 57.856 29.630 0.00 0.00 41.35 4.40
930 1084 9.421806 CCATGATAACATTTTCAAGCTAAAACA 57.578 29.630 0.00 0.00 34.15 2.83
931 1085 8.872845 CCCATGATAACATTTTCAAGCTAAAAC 58.127 33.333 0.00 0.00 34.15 2.43
933 1087 8.359875 TCCCATGATAACATTTTCAAGCTAAA 57.640 30.769 0.00 0.00 34.15 1.85
934 1088 7.953005 TCCCATGATAACATTTTCAAGCTAA 57.047 32.000 0.00 0.00 34.15 3.09
935 1089 7.014518 CCATCCCATGATAACATTTTCAAGCTA 59.985 37.037 0.00 0.00 34.15 3.32
936 1090 6.183360 CCATCCCATGATAACATTTTCAAGCT 60.183 38.462 0.00 0.00 34.15 3.74
937 1091 5.987347 CCATCCCATGATAACATTTTCAAGC 59.013 40.000 0.00 0.00 34.15 4.01
938 1092 6.463331 CCCCATCCCATGATAACATTTTCAAG 60.463 42.308 0.00 0.00 34.15 3.02
939 1093 5.366186 CCCCATCCCATGATAACATTTTCAA 59.634 40.000 0.00 0.00 34.15 2.69
940 1094 4.900652 CCCCATCCCATGATAACATTTTCA 59.099 41.667 0.00 0.00 34.15 2.69
942 1096 4.894622 ACCCCATCCCATGATAACATTTT 58.105 39.130 0.00 0.00 34.15 1.82
943 1097 4.557899 ACCCCATCCCATGATAACATTT 57.442 40.909 0.00 0.00 34.15 2.32
944 1098 4.669768 ACTACCCCATCCCATGATAACATT 59.330 41.667 0.00 0.00 34.15 2.71
945 1099 4.251169 ACTACCCCATCCCATGATAACAT 58.749 43.478 0.00 0.00 37.19 2.71
946 1100 3.675613 ACTACCCCATCCCATGATAACA 58.324 45.455 0.00 0.00 0.00 2.41
947 1101 6.442564 TGTATACTACCCCATCCCATGATAAC 59.557 42.308 4.17 0.00 0.00 1.89
948 1102 6.442564 GTGTATACTACCCCATCCCATGATAA 59.557 42.308 4.17 0.00 0.00 1.75
950 1104 4.783227 GTGTATACTACCCCATCCCATGAT 59.217 45.833 4.17 0.00 0.00 2.45
952 1106 3.056107 CGTGTATACTACCCCATCCCATG 60.056 52.174 4.17 0.00 0.00 3.66
954 1108 2.091166 ACGTGTATACTACCCCATCCCA 60.091 50.000 4.17 0.00 0.00 4.37
955 1109 2.560105 GACGTGTATACTACCCCATCCC 59.440 54.545 4.17 0.00 0.00 3.85
956 1110 2.560105 GGACGTGTATACTACCCCATCC 59.440 54.545 4.17 0.00 0.00 3.51
957 1111 2.227388 CGGACGTGTATACTACCCCATC 59.773 54.545 4.17 0.00 0.00 3.51
960 1114 1.604278 GTCGGACGTGTATACTACCCC 59.396 57.143 4.17 0.32 0.00 4.95
961 1115 2.289002 CAGTCGGACGTGTATACTACCC 59.711 54.545 4.17 0.00 0.00 3.69
962 1116 2.286654 GCAGTCGGACGTGTATACTACC 60.287 54.545 4.17 1.96 0.00 3.18
963 1117 2.352651 TGCAGTCGGACGTGTATACTAC 59.647 50.000 4.17 0.36 0.00 2.73
964 1118 2.631267 TGCAGTCGGACGTGTATACTA 58.369 47.619 4.17 0.00 0.00 1.82
966 1120 2.159476 TCTTGCAGTCGGACGTGTATAC 60.159 50.000 0.00 0.00 0.00 1.47
968 1122 0.885879 TCTTGCAGTCGGACGTGTAT 59.114 50.000 0.00 0.00 0.00 2.29
969 1123 0.240145 CTCTTGCAGTCGGACGTGTA 59.760 55.000 0.00 0.00 0.00 2.90
970 1124 1.007271 CTCTTGCAGTCGGACGTGT 60.007 57.895 0.00 0.00 0.00 4.49
972 1126 2.049063 GCTCTTGCAGTCGGACGT 60.049 61.111 1.89 0.00 39.41 4.34
973 1127 1.803519 GAGCTCTTGCAGTCGGACG 60.804 63.158 6.43 0.00 42.74 4.79
975 1129 1.098869 CTAGAGCTCTTGCAGTCGGA 58.901 55.000 23.84 0.00 42.74 4.55
976 1130 0.527385 GCTAGAGCTCTTGCAGTCGG 60.527 60.000 35.28 12.94 42.75 4.79
977 1131 0.527385 GGCTAGAGCTCTTGCAGTCG 60.527 60.000 38.45 15.29 44.52 4.18
978 1132 0.534412 TGGCTAGAGCTCTTGCAGTC 59.466 55.000 38.45 25.56 44.52 3.51
1065 1396 4.700365 CTCGCACGGCAGACACGA 62.700 66.667 0.00 0.00 34.93 4.35
1103 1434 0.250467 GCTCTTCTCACAGTTGGCCA 60.250 55.000 0.00 0.00 0.00 5.36
1106 1437 1.528586 CGTTGCTCTTCTCACAGTTGG 59.471 52.381 0.00 0.00 0.00 3.77
1215 1546 1.003233 GCCCTTCTCGGAGCTGTTT 60.003 57.895 0.00 0.00 33.16 2.83
1223 1554 2.125512 CGTCCTTGCCCTTCTCGG 60.126 66.667 0.00 0.00 0.00 4.63
1331 1662 1.597797 CTTGATGCGGTGCCCACAAT 61.598 55.000 0.40 0.00 0.00 2.71
1358 1689 2.749076 GCATACACAGACTTGCCATTGA 59.251 45.455 0.00 0.00 0.00 2.57
1814 2153 4.675671 CGTGTAGATTTCTCAGGTGTCTCC 60.676 50.000 0.00 0.00 0.00 3.71
1830 2215 4.265904 TCCTTGAAAATGAGCGTGTAGA 57.734 40.909 0.00 0.00 0.00 2.59
1851 2236 9.059260 ACCGTTTTGTTATACTTGTTCAGTTAT 57.941 29.630 0.00 0.00 36.88 1.89
1854 2239 6.930667 ACCGTTTTGTTATACTTGTTCAGT 57.069 33.333 0.00 0.00 39.87 3.41
1969 2638 0.321671 CTGTCCAGAACCATGTCCGT 59.678 55.000 0.00 0.00 0.00 4.69
1973 2642 4.908601 TTACATCTGTCCAGAACCATGT 57.091 40.909 0.37 4.09 41.36 3.21
1995 2664 7.841282 TTGGAATAGAAACCAACATTTACCA 57.159 32.000 0.00 0.00 40.59 3.25
1996 2665 8.364894 ACTTTGGAATAGAAACCAACATTTACC 58.635 33.333 0.00 0.00 44.34 2.85
2122 2793 2.799562 GCAAAAATTATCTCGGGCAGCC 60.800 50.000 1.26 1.26 0.00 4.85
2144 2815 5.726980 TGGAATGAAAGTGCTTGCTTATT 57.273 34.783 0.00 0.00 0.00 1.40
2176 2847 7.985634 ATGCCACAAAATCATTATTCGTAAC 57.014 32.000 0.00 0.00 0.00 2.50
2193 2864 3.878160 TGATAACACTCGTATGCCACA 57.122 42.857 0.00 0.00 0.00 4.17
2251 2922 4.885325 TGCATATCAAGCTTGACATCACAT 59.115 37.500 30.66 15.69 40.49 3.21
2253 2924 4.573607 TCTGCATATCAAGCTTGACATCAC 59.426 41.667 30.66 18.64 40.49 3.06
2275 2946 3.118738 ACTCCACCTGGTCATACGAATTC 60.119 47.826 0.00 0.00 36.34 2.17
2281 2952 1.568504 TCCACTCCACCTGGTCATAC 58.431 55.000 0.00 0.00 36.34 2.39
2310 2981 9.906660 CAAAAACCAGCTTCAACATAATACTTA 57.093 29.630 0.00 0.00 0.00 2.24
2323 2994 3.381590 ACTTGGAGTCAAAAACCAGCTTC 59.618 43.478 0.00 0.00 35.08 3.86
2331 3002 3.094484 ACACCCACTTGGAGTCAAAAA 57.906 42.857 0.00 0.00 31.55 1.94
2351 3022 5.346011 GCAAGACGCATTCGATAATGAGATA 59.654 40.000 7.69 0.00 44.50 1.98
2353 3024 3.490896 GCAAGACGCATTCGATAATGAGA 59.509 43.478 7.69 0.00 44.50 3.27
2360 3031 0.676466 TTGGGCAAGACGCATTCGAT 60.676 50.000 0.00 0.00 45.17 3.59
2373 3044 4.167892 ACTGGACCTGATATTTATTGGGCA 59.832 41.667 5.22 0.00 0.00 5.36
2374 3045 4.729868 ACTGGACCTGATATTTATTGGGC 58.270 43.478 5.22 0.00 0.00 5.36
2410 3081 4.219919 GGGAGAGAATAGAGCAGGTACTT 58.780 47.826 0.00 0.00 34.60 2.24
2462 3134 5.531287 GTGGAATGGGAATACTTATGGTGAC 59.469 44.000 0.00 0.00 0.00 3.67
2487 3159 8.715190 TTAAATAAGCTCAAAAACCCCTTACT 57.285 30.769 0.00 0.00 0.00 2.24
2492 3164 8.311109 TCATTCTTAAATAAGCTCAAAAACCCC 58.689 33.333 0.00 0.00 33.40 4.95
2514 3186 7.514127 TCCTAGATAATTGCCTAACTCCTCATT 59.486 37.037 0.00 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.