Multiple sequence alignment - TraesCS7B01G078800

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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 TraesCS7B01G078800 chr7B 100.000 2591 0 0 1 2591 88881488 88878898 0.000000e+00 4785.0
1 TraesCS7B01G078800 chr7B 93.656 867 47 5 992 1851 89208694 89209559 0.000000e+00 1290.0
2 TraesCS7B01G078800 chr7B 95.652 138 2 1 1 138 498177477 498177610 4.340000e-53 219.0
3 TraesCS7B01G078800 chr7B 80.383 209 37 3 2353 2561 45268520 45268316 3.450000e-34 156.0
4 TraesCS7B01G078800 chr7B 85.714 105 12 3 2473 2576 16521270 16521372 9.800000e-20 108.0
5 TraesCS7B01G078800 chr7A 89.714 1400 97 25 991 2354 127907374 127905986 0.000000e+00 1744.0
6 TraesCS7B01G078800 chr7A 92.060 806 44 9 991 1786 128153959 128154754 0.000000e+00 1116.0
7 TraesCS7B01G078800 chr7A 86.713 715 79 11 141 845 679051209 679050501 0.000000e+00 780.0
8 TraesCS7B01G078800 chr7A 80.899 534 73 13 1033 1565 24928081 24928586 6.720000e-106 394.0
9 TraesCS7B01G078800 chr7A 94.821 251 13 0 2341 2591 127905968 127905718 2.420000e-105 392.0
10 TraesCS7B01G078800 chr7D 92.904 916 49 8 951 1851 127420930 127421844 0.000000e+00 1317.0
11 TraesCS7B01G078800 chr7D 87.952 747 53 18 139 852 568652887 568652145 0.000000e+00 846.0
12 TraesCS7B01G078800 chr7D 87.256 769 39 15 1875 2591 127280666 127279905 0.000000e+00 822.0
13 TraesCS7B01G078800 chr7D 80.284 563 81 11 1033 1592 24427822 24428357 5.200000e-107 398.0
14 TraesCS7B01G078800 chr7D 94.595 74 4 0 1875 1948 127280778 127280705 5.860000e-22 115.0
15 TraesCS7B01G078800 chr2D 87.390 912 48 21 1 851 590328782 590329687 0.000000e+00 985.0
16 TraesCS7B01G078800 chr6B 85.699 944 77 32 2 890 644389334 644388394 0.000000e+00 942.0
17 TraesCS7B01G078800 chr6B 89.048 557 35 18 1 532 142208243 142207688 0.000000e+00 667.0
18 TraesCS7B01G078800 chr6B 88.112 572 50 14 294 852 130969954 130969388 0.000000e+00 664.0
19 TraesCS7B01G078800 chr6B 95.652 138 2 1 1 138 68248934 68248801 4.340000e-53 219.0
20 TraesCS7B01G078800 chr6B 95.652 138 1 2 1 138 431709566 431709434 1.560000e-52 217.0
21 TraesCS7B01G078800 chr6B 83.333 114 16 3 2475 2587 205338818 205338929 4.560000e-18 102.0
22 TraesCS7B01G078800 chr6B 82.906 117 16 3 2475 2591 539188346 539188234 4.560000e-18 102.0
23 TraesCS7B01G078800 chr4B 86.924 803 70 17 139 908 534981947 534981147 0.000000e+00 869.0
24 TraesCS7B01G078800 chr4B 84.232 964 74 39 1 890 193541654 193542613 0.000000e+00 867.0
25 TraesCS7B01G078800 chr4B 85.047 107 8 8 2463 2563 552583990 552584094 4.560000e-18 102.0
26 TraesCS7B01G078800 chr4B 82.906 117 16 4 2473 2587 608387037 608387151 4.560000e-18 102.0
27 TraesCS7B01G078800 chr4B 82.051 117 19 2 2472 2587 2339395 2339510 5.900000e-17 99.0
28 TraesCS7B01G078800 chr4B 86.170 94 8 5 2472 2562 668096163 668096254 2.120000e-16 97.1
29 TraesCS7B01G078800 chr4B 83.810 105 12 4 2475 2577 644396907 644396806 7.630000e-16 95.3
30 TraesCS7B01G078800 chr2B 85.006 907 65 19 1 852 430218019 430217129 0.000000e+00 856.0
31 TraesCS7B01G078800 chr2B 95.000 140 3 1 1 140 273060066 273059931 1.560000e-52 217.0
32 TraesCS7B01G078800 chr2B 85.965 114 13 3 2475 2587 65025186 65025075 4.530000e-23 119.0
33 TraesCS7B01G078800 chr2B 85.345 116 13 4 2473 2587 58872456 58872344 1.630000e-22 117.0
34 TraesCS7B01G078800 chr2B 83.621 116 16 3 2473 2587 49409089 49408976 3.530000e-19 106.0
35 TraesCS7B01G078800 chr1B 87.929 729 67 12 139 858 26588734 26588018 0.000000e+00 839.0
36 TraesCS7B01G078800 chr1B 86.667 480 46 15 426 890 669910158 669910634 1.370000e-142 516.0
37 TraesCS7B01G078800 chr1B 88.043 92 8 3 2473 2563 539877633 539877722 3.530000e-19 106.0
38 TraesCS7B01G078800 chr1B 82.203 118 17 4 2472 2587 549718231 549718116 5.900000e-17 99.0
39 TraesCS7B01G078800 chr1B 81.897 116 18 3 2473 2587 630514468 630514581 7.630000e-16 95.3
40 TraesCS7B01G078800 chrUn 85.901 766 77 21 139 890 264052465 264053213 0.000000e+00 787.0
41 TraesCS7B01G078800 chrUn 85.901 766 77 21 139 890 308780908 308780160 0.000000e+00 787.0
42 TraesCS7B01G078800 chrUn 85.901 766 77 21 139 890 362458981 362458233 0.000000e+00 787.0
43 TraesCS7B01G078800 chrUn 88.764 89 7 3 2475 2563 329542846 329542931 3.530000e-19 106.0
44 TraesCS7B01G078800 chrUn 83.051 118 14 4 2475 2591 262550235 262550123 4.560000e-18 102.0
45 TraesCS7B01G078800 chrUn 87.640 89 7 3 2475 2563 369547317 369547401 1.640000e-17 100.0
46 TraesCS7B01G078800 chrUn 87.640 89 7 3 2475 2563 376542547 376542631 1.640000e-17 100.0
47 TraesCS7B01G078800 chrUn 87.640 89 7 3 2475 2563 376688401 376688485 1.640000e-17 100.0
48 TraesCS7B01G078800 chrUn 86.517 89 8 3 2475 2563 60716422 60716338 7.630000e-16 95.3
49 TraesCS7B01G078800 chrUn 85.714 91 10 2 2475 2563 60658936 60658847 2.750000e-15 93.5
50 TraesCS7B01G078800 chrUn 85.714 91 10 2 2475 2563 256881375 256881286 2.750000e-15 93.5
51 TraesCS7B01G078800 chrUn 86.420 81 10 1 2475 2555 231863032 231863111 1.280000e-13 87.9
52 TraesCS7B01G078800 chrUn 80.870 115 14 7 2475 2587 15380442 15380334 1.650000e-12 84.2
53 TraesCS7B01G078800 chr4D 82.474 970 80 39 1 905 421043388 421044332 0.000000e+00 767.0
54 TraesCS7B01G078800 chr4D 80.870 115 15 7 2477 2587 283073624 283073513 1.650000e-12 84.2
55 TraesCS7B01G078800 chr6D 84.774 775 84 24 141 890 36566082 36565317 0.000000e+00 747.0
56 TraesCS7B01G078800 chr6D 96.429 140 1 1 1 140 36566245 36566110 7.210000e-56 228.0
57 TraesCS7B01G078800 chr6D 82.500 200 26 5 711 901 143084268 143084069 1.590000e-37 167.0
58 TraesCS7B01G078800 chr2A 85.736 659 64 19 1 633 713349489 713348835 0.000000e+00 669.0
59 TraesCS7B01G078800 chr2A 84.211 114 15 3 2475 2587 524141371 524141260 9.800000e-20 108.0
60 TraesCS7B01G078800 chr4A 78.906 512 81 11 1081 1592 707248446 707247962 3.220000e-84 322.0
61 TraesCS7B01G078800 chr4A 95.714 140 2 1 1 140 464761356 464761491 3.360000e-54 222.0
62 TraesCS7B01G078800 chr5D 95.000 140 3 1 1 140 242920776 242920641 1.560000e-52 217.0
63 TraesCS7B01G078800 chr3D 95.000 140 3 1 1 140 446356344 446356209 1.560000e-52 217.0
64 TraesCS7B01G078800 chr3D 80.870 230 37 6 2354 2582 547459089 547459312 9.530000e-40 174.0
65 TraesCS7B01G078800 chr1D 95.000 140 3 1 1 140 453550974 453550839 1.560000e-52 217.0
66 TraesCS7B01G078800 chr1D 77.824 239 45 7 2354 2590 250957081 250956849 9.670000e-30 141.0
67 TraesCS7B01G078800 chr1D 81.651 109 15 5 2475 2582 444920867 444920763 4.590000e-13 86.1
68 TraesCS7B01G078800 chr1D 80.165 121 16 6 2472 2587 35576456 35576573 1.650000e-12 84.2
69 TraesCS7B01G078800 chr3B 83.740 123 13 7 2473 2591 29349408 29349289 2.730000e-20 110.0
70 TraesCS7B01G078800 chr5B 83.621 116 16 3 2473 2587 118428606 118428719 3.530000e-19 106.0
71 TraesCS7B01G078800 chr5B 84.404 109 14 3 2475 2582 466988407 466988301 1.270000e-18 104.0
72 TraesCS7B01G078800 chr5B 82.906 117 16 3 2475 2591 711555647 711555535 4.560000e-18 102.0


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 TraesCS7B01G078800 chr7B 88878898 88881488 2590 True 4785.0 4785 100.0000 1 2591 1 chr7B.!!$R2 2590
1 TraesCS7B01G078800 chr7B 89208694 89209559 865 False 1290.0 1290 93.6560 992 1851 1 chr7B.!!$F2 859
2 TraesCS7B01G078800 chr7A 128153959 128154754 795 False 1116.0 1116 92.0600 991 1786 1 chr7A.!!$F2 795
3 TraesCS7B01G078800 chr7A 127905718 127907374 1656 True 1068.0 1744 92.2675 991 2591 2 chr7A.!!$R2 1600
4 TraesCS7B01G078800 chr7A 679050501 679051209 708 True 780.0 780 86.7130 141 845 1 chr7A.!!$R1 704
5 TraesCS7B01G078800 chr7A 24928081 24928586 505 False 394.0 394 80.8990 1033 1565 1 chr7A.!!$F1 532
6 TraesCS7B01G078800 chr7D 127420930 127421844 914 False 1317.0 1317 92.9040 951 1851 1 chr7D.!!$F2 900
7 TraesCS7B01G078800 chr7D 568652145 568652887 742 True 846.0 846 87.9520 139 852 1 chr7D.!!$R1 713
8 TraesCS7B01G078800 chr7D 127279905 127280778 873 True 468.5 822 90.9255 1875 2591 2 chr7D.!!$R2 716
9 TraesCS7B01G078800 chr7D 24427822 24428357 535 False 398.0 398 80.2840 1033 1592 1 chr7D.!!$F1 559
10 TraesCS7B01G078800 chr2D 590328782 590329687 905 False 985.0 985 87.3900 1 851 1 chr2D.!!$F1 850
11 TraesCS7B01G078800 chr6B 644388394 644389334 940 True 942.0 942 85.6990 2 890 1 chr6B.!!$R6 888
12 TraesCS7B01G078800 chr6B 142207688 142208243 555 True 667.0 667 89.0480 1 532 1 chr6B.!!$R3 531
13 TraesCS7B01G078800 chr6B 130969388 130969954 566 True 664.0 664 88.1120 294 852 1 chr6B.!!$R2 558
14 TraesCS7B01G078800 chr4B 534981147 534981947 800 True 869.0 869 86.9240 139 908 1 chr4B.!!$R1 769
15 TraesCS7B01G078800 chr4B 193541654 193542613 959 False 867.0 867 84.2320 1 890 1 chr4B.!!$F2 889
16 TraesCS7B01G078800 chr2B 430217129 430218019 890 True 856.0 856 85.0060 1 852 1 chr2B.!!$R5 851
17 TraesCS7B01G078800 chr1B 26588018 26588734 716 True 839.0 839 87.9290 139 858 1 chr1B.!!$R1 719
18 TraesCS7B01G078800 chrUn 264052465 264053213 748 False 787.0 787 85.9010 139 890 1 chrUn.!!$F2 751
19 TraesCS7B01G078800 chrUn 308780160 308780908 748 True 787.0 787 85.9010 139 890 1 chrUn.!!$R6 751
20 TraesCS7B01G078800 chrUn 362458233 362458981 748 True 787.0 787 85.9010 139 890 1 chrUn.!!$R7 751
21 TraesCS7B01G078800 chr4D 421043388 421044332 944 False 767.0 767 82.4740 1 905 1 chr4D.!!$F1 904
22 TraesCS7B01G078800 chr6D 36565317 36566245 928 True 487.5 747 90.6015 1 890 2 chr6D.!!$R2 889
23 TraesCS7B01G078800 chr2A 713348835 713349489 654 True 669.0 669 85.7360 1 633 1 chr2A.!!$R2 632

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
941 1042 0.037975 GTTACTCTTTGGCGGACGGA 60.038 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 2043 1.081892 CAGGAAGACCAGTTGATGCG 58.918 55.0 0.0 0.0 38.94 4.73 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
83 84 3.646946 TGATCATCAACTAGATCAGCGC 58.353 45.455 0.00 0.00 44.04 5.92
200 229 0.602638 AATGCGCCTGAACAACTCGA 60.603 50.000 4.18 0.00 0.00 4.04
288 323 2.756207 TCATCAATCTGTTGTGGGCATG 59.244 45.455 0.00 0.00 36.69 4.06
302 337 3.055328 TGGGCATGAATTCTATCCCTCA 58.945 45.455 21.59 7.69 34.89 3.86
395 433 1.686052 CAAGATCCTCCTCCTCTTCCG 59.314 57.143 0.00 0.00 0.00 4.30
410 448 6.574350 TCCTCTTCCGTATCAAATTCTTCTC 58.426 40.000 0.00 0.00 0.00 2.87
639 727 3.456317 GGTGACGCGGGGATAGAT 58.544 61.111 12.47 0.00 0.00 1.98
640 728 2.649831 GGTGACGCGGGGATAGATA 58.350 57.895 12.47 0.00 0.00 1.98
674 763 1.017177 CGGTCGGCGAAAGAAATGGA 61.017 55.000 12.92 0.00 0.00 3.41
675 764 1.161843 GGTCGGCGAAAGAAATGGAA 58.838 50.000 12.92 0.00 0.00 3.53
725 817 3.450904 TGGATAGGTAGGTGAAGTTGCT 58.549 45.455 0.00 0.00 0.00 3.91
806 899 2.554636 TTTTGGCCAGCGTGCTGAG 61.555 57.895 22.79 13.52 46.30 3.35
825 918 4.337060 TAGATATGCCGCGCGCGT 62.337 61.111 45.51 32.67 42.08 6.01
842 935 1.065109 GTGGTTTTTGCGCCTTCGT 59.935 52.632 4.18 0.00 38.14 3.85
853 947 1.896660 GCCTTCGTTGAGTGCCCAA 60.897 57.895 0.00 0.00 0.00 4.12
858 952 0.181587 TCGTTGAGTGCCCAAAAGGA 59.818 50.000 0.00 0.00 38.24 3.36
859 953 0.310854 CGTTGAGTGCCCAAAAGGAC 59.689 55.000 0.00 0.00 38.24 3.85
901 1002 2.434884 CGCGGCTGTTGGAGATGT 60.435 61.111 0.00 0.00 0.00 3.06
908 1009 3.125316 CGGCTGTTGGAGATGTTCTAAAC 59.875 47.826 0.00 0.00 0.00 2.01
909 1010 4.072131 GGCTGTTGGAGATGTTCTAAACA 58.928 43.478 0.00 0.00 46.94 2.83
910 1011 4.518970 GGCTGTTGGAGATGTTCTAAACAA 59.481 41.667 0.00 0.00 45.86 2.83
911 1012 5.009610 GGCTGTTGGAGATGTTCTAAACAAA 59.990 40.000 0.00 0.00 45.86 2.83
912 1013 5.915196 GCTGTTGGAGATGTTCTAAACAAAC 59.085 40.000 0.00 0.00 45.86 2.93
913 1014 6.459573 GCTGTTGGAGATGTTCTAAACAAACA 60.460 38.462 0.00 2.55 45.86 2.83
914 1015 6.791303 TGTTGGAGATGTTCTAAACAAACAC 58.209 36.000 0.00 0.00 45.86 3.32
915 1016 5.666969 TGGAGATGTTCTAAACAAACACG 57.333 39.130 0.00 0.00 45.86 4.49
916 1017 4.024387 TGGAGATGTTCTAAACAAACACGC 60.024 41.667 0.00 0.00 45.86 5.34
917 1018 4.464112 GAGATGTTCTAAACAAACACGCC 58.536 43.478 0.00 0.00 45.86 5.68
918 1019 3.880490 AGATGTTCTAAACAAACACGCCA 59.120 39.130 0.00 0.00 45.86 5.69
919 1020 3.684103 TGTTCTAAACAAACACGCCAG 57.316 42.857 0.00 0.00 38.72 4.85
920 1021 3.271729 TGTTCTAAACAAACACGCCAGA 58.728 40.909 0.00 0.00 38.72 3.86
921 1022 3.064271 TGTTCTAAACAAACACGCCAGAC 59.936 43.478 0.00 0.00 38.72 3.51
922 1023 6.247124 TGTTCTAAACAAACACGCCAGACG 62.247 45.833 0.00 0.00 42.99 4.18
933 1034 1.068474 CGCCAGACGTTACTCTTTGG 58.932 55.000 0.00 0.00 36.87 3.28
934 1035 0.796927 GCCAGACGTTACTCTTTGGC 59.203 55.000 0.00 0.00 43.54 4.52
935 1036 1.068474 CCAGACGTTACTCTTTGGCG 58.932 55.000 0.00 0.00 0.00 5.69
936 1037 1.068474 CAGACGTTACTCTTTGGCGG 58.932 55.000 0.00 0.00 0.00 6.13
937 1038 0.963962 AGACGTTACTCTTTGGCGGA 59.036 50.000 0.00 0.00 0.00 5.54
938 1039 1.066136 GACGTTACTCTTTGGCGGAC 58.934 55.000 0.00 0.00 0.00 4.79
939 1040 0.665369 ACGTTACTCTTTGGCGGACG 60.665 55.000 0.00 0.00 35.39 4.79
940 1041 1.349259 CGTTACTCTTTGGCGGACGG 61.349 60.000 0.00 0.00 0.00 4.79
941 1042 0.037975 GTTACTCTTTGGCGGACGGA 60.038 55.000 0.00 0.00 0.00 4.69
942 1043 0.245539 TTACTCTTTGGCGGACGGAG 59.754 55.000 0.00 0.00 0.00 4.63
943 1044 1.601419 TACTCTTTGGCGGACGGAGG 61.601 60.000 0.00 0.00 0.00 4.30
944 1045 3.665675 CTCTTTGGCGGACGGAGGG 62.666 68.421 0.00 0.00 0.00 4.30
945 1046 3.702048 CTTTGGCGGACGGAGGGA 61.702 66.667 0.00 0.00 0.00 4.20
946 1047 3.665675 CTTTGGCGGACGGAGGGAG 62.666 68.421 0.00 0.00 0.00 4.30
948 1049 3.588817 TTGGCGGACGGAGGGAGTA 62.589 63.158 0.00 0.00 0.00 2.59
949 1050 3.525545 GGCGGACGGAGGGAGTAC 61.526 72.222 0.00 0.00 0.00 2.73
964 1065 7.008941 GGAGGGAGTACTACAAAGTCCATATA 58.991 42.308 7.57 0.00 38.08 0.86
968 1069 8.088981 GGGAGTACTACAAAGTCCATATACATG 58.911 40.741 7.57 0.00 38.08 3.21
981 1082 4.683320 CCATATACATGTCGACAGCTTCTG 59.317 45.833 24.41 18.28 37.52 3.02
1281 1392 4.742201 CTGCGGGTGTACAGCGCT 62.742 66.667 28.46 2.64 32.58 5.92
1393 1511 2.095252 GCCTTCTTCGACCTGCGTC 61.095 63.158 0.00 0.00 41.80 5.19
1479 1597 3.319198 GTGAGGGCCCAAGTCCGA 61.319 66.667 27.56 0.00 45.21 4.55
1552 1671 1.080025 CCCGTCGACTTCTTCACCC 60.080 63.158 14.70 0.00 0.00 4.61
1770 1892 6.987404 GGTTTCCTTCCATCTACAGAATAGAC 59.013 42.308 0.00 0.00 0.00 2.59
1796 1918 8.537049 TGCATTAAAGAAAATTGTTGATGGAG 57.463 30.769 0.00 0.00 0.00 3.86
1802 1924 4.907269 AGAAAATTGTTGATGGAGGGGTTT 59.093 37.500 0.00 0.00 0.00 3.27
1803 1925 4.622260 AAATTGTTGATGGAGGGGTTTG 57.378 40.909 0.00 0.00 0.00 2.93
1805 1927 2.765689 TGTTGATGGAGGGGTTTGTT 57.234 45.000 0.00 0.00 0.00 2.83
1806 1928 2.315176 TGTTGATGGAGGGGTTTGTTG 58.685 47.619 0.00 0.00 0.00 3.33
1807 1929 1.000843 GTTGATGGAGGGGTTTGTTGC 59.999 52.381 0.00 0.00 0.00 4.17
1809 1931 1.707989 TGATGGAGGGGTTTGTTGCTA 59.292 47.619 0.00 0.00 0.00 3.49
1810 1932 2.290896 TGATGGAGGGGTTTGTTGCTAG 60.291 50.000 0.00 0.00 0.00 3.42
1846 1974 3.181440 ACTCCACCAAGAAATGCAGAGAA 60.181 43.478 0.00 0.00 0.00 2.87
1981 2110 5.007332 ACAGAGTTGTTCCGATAAAACACAC 59.993 40.000 0.00 0.00 36.41 3.82
1999 2128 2.512476 ACACTACAGGAAACAAACCCCT 59.488 45.455 0.00 0.00 0.00 4.79
2003 2132 1.203013 ACAGGAAACAAACCCCTAGCC 60.203 52.381 0.00 0.00 0.00 3.93
2200 2357 9.674068 GATAAATGAGAAGGGAGAAAAGTAGTT 57.326 33.333 0.00 0.00 0.00 2.24
2202 2359 5.228945 TGAGAAGGGAGAAAAGTAGTTGG 57.771 43.478 0.00 0.00 0.00 3.77
2204 2361 2.881111 AGGGAGAAAAGTAGTTGGCC 57.119 50.000 0.00 0.00 0.00 5.36
2205 2362 2.349445 AGGGAGAAAAGTAGTTGGCCT 58.651 47.619 3.32 0.00 0.00 5.19
2283 2440 0.548682 AAGCCCATCCACCTGACTCT 60.549 55.000 0.00 0.00 0.00 3.24
2284 2441 0.339859 AGCCCATCCACCTGACTCTA 59.660 55.000 0.00 0.00 0.00 2.43
2285 2442 0.466124 GCCCATCCACCTGACTCTAC 59.534 60.000 0.00 0.00 0.00 2.59
2286 2443 1.123928 CCCATCCACCTGACTCTACC 58.876 60.000 0.00 0.00 0.00 3.18
2287 2444 1.622449 CCCATCCACCTGACTCTACCA 60.622 57.143 0.00 0.00 0.00 3.25
2405 2593 3.976911 TCGTCGTCGATTCGCATG 58.023 55.556 0.00 0.00 41.35 4.06
2412 2600 2.025156 CGATTCGCATGGGCAAGC 59.975 61.111 4.59 2.91 41.24 4.01
2435 2623 0.976641 CCTATCGAGCAATAGGGCCA 59.023 55.000 6.18 0.00 43.13 5.36
2450 2638 1.318576 GGCCAACCCATGTATAGCAC 58.681 55.000 0.00 0.00 0.00 4.40
2479 2667 5.458015 GCAGCATTCTAGTAAACCGTTTTT 58.542 37.500 0.96 0.00 0.00 1.94
2570 2758 6.056236 CCGGGTTTTCCTTTTTCCAATTTAA 58.944 36.000 0.00 0.00 40.46 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 5.597806 ATGTTGGCATATATACGGTATCCG 58.402 41.667 3.47 6.64 42.59 4.18
95 96 3.354089 GCTTTGCGTATGTTGGCATAT 57.646 42.857 0.00 0.00 39.49 1.78
200 229 0.532862 CGCCGGTTTAGGATGAGCAT 60.533 55.000 1.90 0.00 0.00 3.79
288 323 7.708322 GGCAGAAAATTTTGAGGGATAGAATTC 59.292 37.037 8.47 0.00 0.00 2.17
302 337 4.322424 GGTTATGGGTCGGCAGAAAATTTT 60.322 41.667 2.28 2.28 0.00 1.82
410 448 2.768833 TCGTCGTATGATTCTTCCGG 57.231 50.000 0.00 0.00 0.00 5.14
465 522 4.991153 TTTGGTGCATGTTGTTTGTAGA 57.009 36.364 0.00 0.00 0.00 2.59
624 712 0.611062 CCCTATCTATCCCCGCGTCA 60.611 60.000 4.92 0.00 0.00 4.35
626 714 0.113776 TTCCCTATCTATCCCCGCGT 59.886 55.000 4.92 0.00 0.00 6.01
639 727 4.137872 CGTTCCGGCGCTTCCCTA 62.138 66.667 7.64 0.00 0.00 3.53
661 750 1.548986 CGCCATTCCATTTCTTTCGC 58.451 50.000 0.00 0.00 0.00 4.70
709 800 1.204941 CGCTAGCAACTTCACCTACCT 59.795 52.381 16.45 0.00 0.00 3.08
796 889 1.336702 GCATATCTAGCTCAGCACGCT 60.337 52.381 0.00 0.24 41.35 5.07
806 899 3.843240 GCGCGCGGCATATCTAGC 61.843 66.667 33.06 6.36 42.87 3.42
825 918 0.526524 CAACGAAGGCGCAAAAACCA 60.527 50.000 10.83 0.00 42.48 3.67
853 947 6.628919 ATTAGTGCTTTTAACGTGTCCTTT 57.371 33.333 0.00 0.00 0.00 3.11
858 952 7.043656 GCTGAAAAATTAGTGCTTTTAACGTGT 60.044 33.333 0.00 0.00 0.00 4.49
859 953 7.273659 GCTGAAAAATTAGTGCTTTTAACGTG 58.726 34.615 0.00 0.00 0.00 4.49
901 1002 2.285756 CGTCTGGCGTGTTTGTTTAGAA 59.714 45.455 0.00 0.00 35.54 2.10
915 1016 0.796927 GCCAAAGAGTAACGTCTGGC 59.203 55.000 0.00 0.00 30.75 4.85
916 1017 1.068474 CGCCAAAGAGTAACGTCTGG 58.932 55.000 0.00 0.00 0.00 3.86
917 1018 1.068474 CCGCCAAAGAGTAACGTCTG 58.932 55.000 0.00 0.00 0.00 3.51
918 1019 0.963962 TCCGCCAAAGAGTAACGTCT 59.036 50.000 0.00 0.00 0.00 4.18
919 1020 1.066136 GTCCGCCAAAGAGTAACGTC 58.934 55.000 0.00 0.00 0.00 4.34
920 1021 0.665369 CGTCCGCCAAAGAGTAACGT 60.665 55.000 0.00 0.00 0.00 3.99
921 1022 1.349259 CCGTCCGCCAAAGAGTAACG 61.349 60.000 0.00 0.00 0.00 3.18
922 1023 0.037975 TCCGTCCGCCAAAGAGTAAC 60.038 55.000 0.00 0.00 0.00 2.50
923 1024 0.245539 CTCCGTCCGCCAAAGAGTAA 59.754 55.000 0.00 0.00 0.00 2.24
924 1025 1.601419 CCTCCGTCCGCCAAAGAGTA 61.601 60.000 0.00 0.00 0.00 2.59
925 1026 2.657237 CTCCGTCCGCCAAAGAGT 59.343 61.111 0.00 0.00 0.00 3.24
926 1027 2.125512 CCTCCGTCCGCCAAAGAG 60.126 66.667 0.00 0.00 0.00 2.85
927 1028 3.702048 CCCTCCGTCCGCCAAAGA 61.702 66.667 0.00 0.00 0.00 2.52
928 1029 3.665675 CTCCCTCCGTCCGCCAAAG 62.666 68.421 0.00 0.00 0.00 2.77
929 1030 3.702048 CTCCCTCCGTCCGCCAAA 61.702 66.667 0.00 0.00 0.00 3.28
930 1031 3.588817 TACTCCCTCCGTCCGCCAA 62.589 63.158 0.00 0.00 0.00 4.52
931 1032 4.051167 TACTCCCTCCGTCCGCCA 62.051 66.667 0.00 0.00 0.00 5.69
932 1033 2.615227 TAGTACTCCCTCCGTCCGCC 62.615 65.000 0.00 0.00 0.00 6.13
933 1034 1.153086 TAGTACTCCCTCCGTCCGC 60.153 63.158 0.00 0.00 0.00 5.54
934 1035 0.107508 TGTAGTACTCCCTCCGTCCG 60.108 60.000 0.00 0.00 0.00 4.79
935 1036 2.134789 TTGTAGTACTCCCTCCGTCC 57.865 55.000 0.00 0.00 0.00 4.79
936 1037 3.087781 ACTTTGTAGTACTCCCTCCGTC 58.912 50.000 0.00 0.00 31.21 4.79
937 1038 3.087781 GACTTTGTAGTACTCCCTCCGT 58.912 50.000 0.00 0.00 33.84 4.69
938 1039 2.426381 GGACTTTGTAGTACTCCCTCCG 59.574 54.545 0.00 0.00 33.84 4.63
939 1040 3.438183 TGGACTTTGTAGTACTCCCTCC 58.562 50.000 0.00 0.00 36.10 4.30
940 1041 6.980416 ATATGGACTTTGTAGTACTCCCTC 57.020 41.667 0.00 0.00 36.10 4.30
941 1042 7.359849 TGTATATGGACTTTGTAGTACTCCCT 58.640 38.462 0.00 0.00 36.10 4.20
942 1043 7.592885 TGTATATGGACTTTGTAGTACTCCC 57.407 40.000 0.00 0.00 36.10 4.30
943 1044 8.639761 ACATGTATATGGACTTTGTAGTACTCC 58.360 37.037 0.00 0.75 36.10 3.85
944 1045 9.680315 GACATGTATATGGACTTTGTAGTACTC 57.320 37.037 0.00 0.00 36.10 2.59
945 1046 8.350722 CGACATGTATATGGACTTTGTAGTACT 58.649 37.037 0.00 0.00 36.10 2.73
946 1047 8.347771 TCGACATGTATATGGACTTTGTAGTAC 58.652 37.037 0.00 0.00 38.66 2.73
947 1048 8.347771 GTCGACATGTATATGGACTTTGTAGTA 58.652 37.037 11.55 0.00 38.66 1.82
948 1049 7.147966 TGTCGACATGTATATGGACTTTGTAGT 60.148 37.037 15.76 0.00 38.66 2.73
949 1050 7.200455 TGTCGACATGTATATGGACTTTGTAG 58.800 38.462 15.76 0.00 38.66 2.74
964 1065 0.671781 GCCAGAAGCTGTCGACATGT 60.672 55.000 20.40 6.32 38.99 3.21
981 1082 4.137543 CCATGGACAATAAACTCCTAGCC 58.862 47.826 5.56 0.00 0.00 3.93
1015 1116 1.220206 CGCCATCAGTGAGCTTCCT 59.780 57.895 0.00 0.00 0.00 3.36
1042 1143 0.108138 GCCAGGATGTAGTGCTTCGT 60.108 55.000 0.00 0.00 0.00 3.85
1296 1407 4.539083 ACCGTCTGCACCAACGCA 62.539 61.111 6.11 0.00 40.32 5.24
1301 1412 3.936203 GGACCACCGTCTGCACCA 61.936 66.667 0.00 0.00 39.15 4.17
1393 1511 2.734492 CGCCGGAGTTACTAACCAAGAG 60.734 54.545 5.05 0.00 0.00 2.85
1479 1597 2.044946 GCCAGCCCGACCTTGAAT 60.045 61.111 0.00 0.00 0.00 2.57
1584 1703 0.239613 ATCGATCGATCTGTCAGGCG 59.760 55.000 24.60 8.09 0.00 5.52
1733 1855 3.214328 GAAGGAAACCAGAAGAGCACAA 58.786 45.455 0.00 0.00 0.00 3.33
1738 1860 4.566426 AGATGGAAGGAAACCAGAAGAG 57.434 45.455 0.00 0.00 40.89 2.85
1770 1892 8.537049 TCCATCAACAATTTTCTTTAATGCAG 57.463 30.769 0.00 0.00 0.00 4.41
1790 1912 2.369394 CTAGCAACAAACCCCTCCATC 58.631 52.381 0.00 0.00 0.00 3.51
1796 1918 2.024414 CCATAGCTAGCAACAAACCCC 58.976 52.381 18.83 0.00 0.00 4.95
1802 1924 7.039923 GGAGTAAGTATACCATAGCTAGCAACA 60.040 40.741 18.83 1.36 32.08 3.33
1803 1925 7.039923 TGGAGTAAGTATACCATAGCTAGCAAC 60.040 40.741 18.83 1.86 32.08 4.17
1805 1927 6.433404 GTGGAGTAAGTATACCATAGCTAGCA 59.567 42.308 18.83 3.19 34.87 3.49
1806 1928 6.127675 GGTGGAGTAAGTATACCATAGCTAGC 60.128 46.154 6.62 6.62 34.87 3.42
1807 1929 6.946583 TGGTGGAGTAAGTATACCATAGCTAG 59.053 42.308 0.00 0.00 36.56 3.42
1809 1931 5.712752 TGGTGGAGTAAGTATACCATAGCT 58.287 41.667 0.00 0.00 36.56 3.32
1810 1932 6.267014 TCTTGGTGGAGTAAGTATACCATAGC 59.733 42.308 0.00 0.00 40.75 2.97
1846 1974 6.653320 TGCGTAAGTTCAGGTAATCAAGAAAT 59.347 34.615 0.00 0.00 41.68 2.17
1868 1996 5.900339 ATGGTATTGTACGTCTAAATGCG 57.100 39.130 0.00 0.00 0.00 4.73
1915 2043 1.081892 CAGGAAGACCAGTTGATGCG 58.918 55.000 0.00 0.00 38.94 4.73
1981 2110 3.344515 GCTAGGGGTTTGTTTCCTGTAG 58.655 50.000 0.00 0.00 32.46 2.74
2051 2180 5.532406 CCTTGATCTTCTGAAGTGTTTTCCA 59.468 40.000 16.43 3.94 0.00 3.53
2052 2181 5.765182 TCCTTGATCTTCTGAAGTGTTTTCC 59.235 40.000 16.43 1.75 0.00 3.13
2165 2294 7.826252 TCTCCCTTCTCATTTATCTCAAAACAG 59.174 37.037 0.00 0.00 0.00 3.16
2286 2443 4.806640 AAATGTAGAAGGGCCAACAATG 57.193 40.909 6.18 0.00 0.00 2.82
2287 2444 6.098266 GGAATAAATGTAGAAGGGCCAACAAT 59.902 38.462 6.18 0.00 0.00 2.71
2328 2485 5.931724 TCCGGTATGTCATATATGCAAACAG 59.068 40.000 7.92 4.67 0.00 3.16
2357 2545 3.757493 CGTAGAGAGCGGTAAATAGGGAT 59.243 47.826 0.00 0.00 0.00 3.85
2404 2592 2.908015 GATAGGTCGGCTTGCCCA 59.092 61.111 6.02 0.00 0.00 5.36
2405 2593 2.280186 CGATAGGTCGGCTTGCCC 60.280 66.667 6.02 0.00 44.00 5.36
2435 2623 2.545113 CGCGTAGTGCTATACATGGGTT 60.545 50.000 0.00 0.00 43.27 4.11
2450 2638 2.401017 TACTAGAATGCTGCGCGTAG 57.599 50.000 20.60 20.60 0.00 3.51
2479 2667 2.758979 GGTGACGATCTAGAAGGTTCCA 59.241 50.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.