Multiple sequence alignment - TraesCS5D01G356400

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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 TraesCS5D01G356400 chr5D 100.000 3794 0 0 1 3794 437531653 437527860 0.000000e+00 7007.0
1 TraesCS5D01G356400 chr5D 86.582 708 85 5 3087 3789 421110041 421110743 0.000000e+00 773.0
2 TraesCS5D01G356400 chr5D 86.383 705 88 3 3092 3792 245182513 245181813 0.000000e+00 763.0
3 TraesCS5D01G356400 chr5D 76.552 290 52 9 2336 2616 24575473 24575191 1.100000e-30 145.0
4 TraesCS5D01G356400 chr5B 95.825 1892 64 8 1203 3084 531613603 531611717 0.000000e+00 3042.0
5 TraesCS5D01G356400 chr5B 91.205 2058 138 17 960 3004 100039504 100037477 0.000000e+00 2758.0
6 TraesCS5D01G356400 chr5B 92.275 712 47 3 3087 3794 339553033 339553740 0.000000e+00 1003.0
7 TraesCS5D01G356400 chr5B 81.739 920 126 28 1 896 528269891 528270792 0.000000e+00 730.0
8 TraesCS5D01G356400 chr5B 91.787 207 14 3 972 1178 531613798 531613595 6.200000e-73 285.0
9 TraesCS5D01G356400 chr5A 90.609 2119 138 20 965 3082 396225637 396223579 0.000000e+00 2754.0
10 TraesCS5D01G356400 chr6B 95.679 1134 44 3 1203 2333 607125013 607123882 0.000000e+00 1818.0
11 TraesCS5D01G356400 chr6B 97.460 748 19 0 2328 3075 607123718 607122971 0.000000e+00 1277.0
12 TraesCS5D01G356400 chr6B 92.135 712 43 6 3087 3794 708109562 708108860 0.000000e+00 992.0
13 TraesCS5D01G356400 chr6B 79.315 730 135 12 1242 1963 711333433 711332712 7.320000e-137 497.0
14 TraesCS5D01G356400 chr6B 76.344 744 149 20 1225 1957 711360212 711360939 1.290000e-99 374.0
15 TraesCS5D01G356400 chr6B 93.750 208 10 3 971 1178 607125209 607125005 3.680000e-80 309.0
16 TraesCS5D01G356400 chr6B 76.054 664 106 30 2000 2620 711332709 711332056 2.870000e-76 296.0
17 TraesCS5D01G356400 chr6B 75.285 615 111 27 2000 2598 711757184 711757773 4.860000e-64 255.0
18 TraesCS5D01G356400 chr6B 75.000 624 101 31 2000 2577 710682857 710682243 1.760000e-58 237.0
19 TraesCS5D01G356400 chr6B 76.149 457 95 10 965 1414 705520816 705520367 1.060000e-55 228.0
20 TraesCS5D01G356400 chr7B 92.342 679 44 3 3087 3761 517319898 517319224 0.000000e+00 959.0
21 TraesCS5D01G356400 chr3B 84.228 894 113 20 1 886 351998774 351997901 0.000000e+00 845.0
22 TraesCS5D01G356400 chr2B 83.849 873 123 11 1 859 793993646 793992778 0.000000e+00 815.0
23 TraesCS5D01G356400 chr2B 85.915 710 91 4 3087 3792 402621282 402620578 0.000000e+00 749.0
24 TraesCS5D01G356400 chr2B 82.105 285 43 4 315 593 793992787 793992505 1.760000e-58 237.0
25 TraesCS5D01G356400 chr2B 84.722 72 11 0 191 262 742092420 742092349 5.260000e-09 73.1
26 TraesCS5D01G356400 chr3D 86.396 713 84 9 3087 3793 7522491 7523196 0.000000e+00 767.0
27 TraesCS5D01G356400 chr3D 84.603 617 70 13 7 613 567230078 567229477 1.170000e-164 590.0
28 TraesCS5D01G356400 chr7D 86.552 699 86 3 3092 3786 395184714 395185408 0.000000e+00 763.0
29 TraesCS5D01G356400 chr7D 86.479 355 36 2 4 352 26502550 26502202 2.770000e-101 379.0
30 TraesCS5D01G356400 chr2A 86.319 709 87 5 3089 3792 417096446 417097149 0.000000e+00 763.0
31 TraesCS5D01G356400 chr2A 80.286 350 38 15 460 781 722732743 722733089 6.340000e-58 235.0
32 TraesCS5D01G356400 chr6D 77.224 1023 186 35 968 1962 465966587 465965584 4.280000e-154 555.0
33 TraesCS5D01G356400 chr6D 75.507 739 169 9 1227 1956 466818831 466818096 6.030000e-93 351.0
34 TraesCS5D01G356400 chr6D 75.791 632 100 33 2000 2615 465965579 465964985 1.740000e-68 270.0
35 TraesCS5D01G356400 chr6D 74.363 628 135 20 965 1579 466130902 466130288 1.050000e-60 244.0
36 TraesCS5D01G356400 chr6D 77.670 412 71 12 965 1366 462839821 462840221 8.200000e-57 231.0
37 TraesCS5D01G356400 chr1B 85.236 508 68 4 1 502 8553048 8553554 2.020000e-142 516.0
38 TraesCS5D01G356400 chr1B 84.259 108 10 4 138 238 134427277 134427384 8.670000e-17 99.0
39 TraesCS5D01G356400 chr6A 75.906 635 99 34 2000 2611 612301254 612301857 3.730000e-70 276.0
40 TraesCS5D01G356400 chr6A 72.467 977 216 40 965 1915 612125485 612124536 8.080000e-67 265.0
41 TraesCS5D01G356400 chr6A 78.450 413 77 9 968 1374 612109048 612108642 3.760000e-65 259.0
42 TraesCS5D01G356400 chr6A 78.114 297 50 9 2324 2612 125261612 125261901 1.400000e-39 174.0
43 TraesCS5D01G356400 chr6A 83.060 183 29 2 2002 2183 611903106 611903287 8.430000e-37 165.0
44 TraesCS5D01G356400 chr6A 77.895 285 49 7 2336 2612 611903393 611903671 8.430000e-37 165.0
45 TraesCS5D01G356400 chr6A 79.091 220 44 2 1738 1956 612676241 612676459 2.360000e-32 150.0
46 TraesCS5D01G356400 chr4B 74.817 409 58 32 56 457 255385473 255385103 3.950000e-30 143.0


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 TraesCS5D01G356400 chr5D 437527860 437531653 3793 True 7007.000000 7007 100.000000 1 3794 1 chr5D.!!$R3 3793
1 TraesCS5D01G356400 chr5D 421110041 421110743 702 False 773.000000 773 86.582000 3087 3789 1 chr5D.!!$F1 702
2 TraesCS5D01G356400 chr5D 245181813 245182513 700 True 763.000000 763 86.383000 3092 3792 1 chr5D.!!$R2 700
3 TraesCS5D01G356400 chr5B 100037477 100039504 2027 True 2758.000000 2758 91.205000 960 3004 1 chr5B.!!$R1 2044
4 TraesCS5D01G356400 chr5B 531611717 531613798 2081 True 1663.500000 3042 93.806000 972 3084 2 chr5B.!!$R2 2112
5 TraesCS5D01G356400 chr5B 339553033 339553740 707 False 1003.000000 1003 92.275000 3087 3794 1 chr5B.!!$F1 707
6 TraesCS5D01G356400 chr5B 528269891 528270792 901 False 730.000000 730 81.739000 1 896 1 chr5B.!!$F2 895
7 TraesCS5D01G356400 chr5A 396223579 396225637 2058 True 2754.000000 2754 90.609000 965 3082 1 chr5A.!!$R1 2117
8 TraesCS5D01G356400 chr6B 607122971 607125209 2238 True 1134.666667 1818 95.629667 971 3075 3 chr6B.!!$R4 2104
9 TraesCS5D01G356400 chr6B 708108860 708109562 702 True 992.000000 992 92.135000 3087 3794 1 chr6B.!!$R2 707
10 TraesCS5D01G356400 chr6B 711332056 711333433 1377 True 396.500000 497 77.684500 1242 2620 2 chr6B.!!$R5 1378
11 TraesCS5D01G356400 chr6B 711360212 711360939 727 False 374.000000 374 76.344000 1225 1957 1 chr6B.!!$F1 732
12 TraesCS5D01G356400 chr6B 711757184 711757773 589 False 255.000000 255 75.285000 2000 2598 1 chr6B.!!$F2 598
13 TraesCS5D01G356400 chr6B 710682243 710682857 614 True 237.000000 237 75.000000 2000 2577 1 chr6B.!!$R3 577
14 TraesCS5D01G356400 chr7B 517319224 517319898 674 True 959.000000 959 92.342000 3087 3761 1 chr7B.!!$R1 674
15 TraesCS5D01G356400 chr3B 351997901 351998774 873 True 845.000000 845 84.228000 1 886 1 chr3B.!!$R1 885
16 TraesCS5D01G356400 chr2B 402620578 402621282 704 True 749.000000 749 85.915000 3087 3792 1 chr2B.!!$R1 705
17 TraesCS5D01G356400 chr2B 793992505 793993646 1141 True 526.000000 815 82.977000 1 859 2 chr2B.!!$R3 858
18 TraesCS5D01G356400 chr3D 7522491 7523196 705 False 767.000000 767 86.396000 3087 3793 1 chr3D.!!$F1 706
19 TraesCS5D01G356400 chr3D 567229477 567230078 601 True 590.000000 590 84.603000 7 613 1 chr3D.!!$R1 606
20 TraesCS5D01G356400 chr7D 395184714 395185408 694 False 763.000000 763 86.552000 3092 3786 1 chr7D.!!$F1 694
21 TraesCS5D01G356400 chr2A 417096446 417097149 703 False 763.000000 763 86.319000 3089 3792 1 chr2A.!!$F1 703
22 TraesCS5D01G356400 chr6D 465964985 465966587 1602 True 412.500000 555 76.507500 968 2615 2 chr6D.!!$R3 1647
23 TraesCS5D01G356400 chr6D 466818096 466818831 735 True 351.000000 351 75.507000 1227 1956 1 chr6D.!!$R2 729
24 TraesCS5D01G356400 chr6D 466130288 466130902 614 True 244.000000 244 74.363000 965 1579 1 chr6D.!!$R1 614
25 TraesCS5D01G356400 chr1B 8553048 8553554 506 False 516.000000 516 85.236000 1 502 1 chr1B.!!$F1 501
26 TraesCS5D01G356400 chr6A 612301254 612301857 603 False 276.000000 276 75.906000 2000 2611 1 chr6A.!!$F2 611
27 TraesCS5D01G356400 chr6A 612124536 612125485 949 True 265.000000 265 72.467000 965 1915 1 chr6A.!!$R2 950

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
576 610 0.252742 GGGGAAGAGAAGGACTCCCA 60.253 60.0 8.21 0.0 45.96 4.37 F
899 951 0.594110 CGAGAGCGGGAGGATAAGAC 59.406 60.0 0.00 0.0 0.00 3.01 F
902 954 0.594110 GAGCGGGAGGATAAGACTCG 59.406 60.0 0.00 0.0 35.82 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2309 2456 2.169144 TGCCACTCATAGGACATCTGTG 59.831 50.000 0.00 0.0 36.14 3.66 R
2583 3070 4.556898 GCCAGTCTATCATACAGGTACACG 60.557 50.000 0.00 0.0 0.00 4.49 R
3288 3781 1.612442 GCCTCCTCAGGTGGGTACA 60.612 63.158 13.96 0.0 42.74 2.90 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
37 38 2.730550 ACGAAAGTAACGACCGGATT 57.269 45.000 9.46 1.42 46.88 3.01
58 62 1.212441 ACGAGGAGTAGGATCGAAGGT 59.788 52.381 0.30 0.00 39.66 3.50
60 64 2.232399 GAGGAGTAGGATCGAAGGTCC 58.768 57.143 0.00 0.00 35.94 4.46
99 103 3.660111 GCCAACGCCGAACAAGCT 61.660 61.111 0.00 0.00 0.00 3.74
152 157 3.392595 CTACTCACCGACGGCCGAC 62.393 68.421 35.90 26.45 41.76 4.79
166 171 3.744719 CGACGCCGGAGAAGACCA 61.745 66.667 13.83 0.00 0.00 4.02
173 178 3.706373 GGAGAAGACCAGCCGCCA 61.706 66.667 0.00 0.00 0.00 5.69
189 211 3.367743 CACCGAGGAACGACCCGA 61.368 66.667 0.00 0.00 45.77 5.14
209 237 2.032528 CATGAGCCACCACCACGT 59.967 61.111 0.00 0.00 0.00 4.49
210 238 1.600636 CATGAGCCACCACCACGTT 60.601 57.895 0.00 0.00 0.00 3.99
239 267 3.009115 CATCCACACCGGGACCCT 61.009 66.667 9.41 0.00 40.44 4.34
240 268 1.687840 CATCCACACCGGGACCCTA 60.688 63.158 9.41 0.00 40.44 3.53
304 332 2.045926 GTTGATCTGGCCGGCACT 60.046 61.111 30.85 9.09 0.00 4.40
368 396 1.227943 CATAGCCATGACCCCACCG 60.228 63.158 0.00 0.00 33.67 4.94
369 397 1.383943 ATAGCCATGACCCCACCGA 60.384 57.895 0.00 0.00 0.00 4.69
382 410 3.231736 ACCGAGTCACAACCCGCT 61.232 61.111 0.00 0.00 0.00 5.52
431 460 0.600255 CATAACGGATCTGGACGGGC 60.600 60.000 6.47 0.00 0.00 6.13
464 493 2.521708 GCACACCCCCAGCACTTT 60.522 61.111 0.00 0.00 0.00 2.66
576 610 0.252742 GGGGAAGAGAAGGACTCCCA 60.253 60.000 8.21 0.00 45.96 4.37
579 613 1.645710 GAAGAGAAGGACTCCCACCA 58.354 55.000 0.00 0.00 45.96 4.17
655 706 3.593794 GACGGCCGGAGCTATCGT 61.594 66.667 31.76 3.99 37.16 3.73
662 713 1.519234 CGGAGCTATCGTTGCAGCA 60.519 57.895 0.24 0.00 40.36 4.41
667 718 2.047750 TATCGTTGCAGCACCGCA 60.048 55.556 7.60 0.00 41.03 5.69
766 818 3.390521 CCGCTAGCCACCACCAGA 61.391 66.667 9.66 0.00 0.00 3.86
817 869 4.862823 GGGGAGACGGGAGAGGGG 62.863 77.778 0.00 0.00 0.00 4.79
818 870 4.862823 GGGAGACGGGAGAGGGGG 62.863 77.778 0.00 0.00 0.00 5.40
835 887 4.394712 GGGTGCTGGGGACGTGAG 62.395 72.222 0.00 0.00 0.00 3.51
836 888 4.394712 GGTGCTGGGGACGTGAGG 62.395 72.222 0.00 0.00 0.00 3.86
837 889 3.626924 GTGCTGGGGACGTGAGGT 61.627 66.667 0.00 0.00 0.00 3.85
838 890 3.625897 TGCTGGGGACGTGAGGTG 61.626 66.667 0.00 0.00 0.00 4.00
839 891 4.394712 GCTGGGGACGTGAGGTGG 62.395 72.222 0.00 0.00 0.00 4.61
840 892 4.394712 CTGGGGACGTGAGGTGGC 62.395 72.222 0.00 0.00 0.00 5.01
898 950 3.022940 CGAGAGCGGGAGGATAAGA 57.977 57.895 0.00 0.00 0.00 2.10
899 951 0.594110 CGAGAGCGGGAGGATAAGAC 59.406 60.000 0.00 0.00 0.00 3.01
900 952 1.816183 CGAGAGCGGGAGGATAAGACT 60.816 57.143 0.00 0.00 0.00 3.24
901 953 1.883926 GAGAGCGGGAGGATAAGACTC 59.116 57.143 0.00 0.00 0.00 3.36
902 954 0.594110 GAGCGGGAGGATAAGACTCG 59.406 60.000 0.00 0.00 35.82 4.18
903 955 0.824182 AGCGGGAGGATAAGACTCGG 60.824 60.000 0.00 0.00 35.82 4.63
904 956 1.108132 GCGGGAGGATAAGACTCGGT 61.108 60.000 0.00 0.00 35.82 4.69
905 957 1.816961 GCGGGAGGATAAGACTCGGTA 60.817 57.143 0.00 0.00 35.82 4.02
906 958 2.579873 CGGGAGGATAAGACTCGGTAA 58.420 52.381 0.00 0.00 35.82 2.85
907 959 2.292845 CGGGAGGATAAGACTCGGTAAC 59.707 54.545 0.00 0.00 35.82 2.50
908 960 3.294214 GGGAGGATAAGACTCGGTAACA 58.706 50.000 0.00 0.00 35.82 2.41
909 961 3.318557 GGGAGGATAAGACTCGGTAACAG 59.681 52.174 0.00 0.00 35.82 3.16
910 962 3.318557 GGAGGATAAGACTCGGTAACAGG 59.681 52.174 0.00 0.00 35.82 4.00
911 963 4.205587 GAGGATAAGACTCGGTAACAGGA 58.794 47.826 0.00 0.00 0.00 3.86
912 964 3.952967 AGGATAAGACTCGGTAACAGGAC 59.047 47.826 0.00 0.00 0.00 3.85
913 965 3.952967 GGATAAGACTCGGTAACAGGACT 59.047 47.826 0.00 0.00 0.00 3.85
914 966 4.036616 GGATAAGACTCGGTAACAGGACTC 59.963 50.000 0.00 0.00 0.00 3.36
915 967 1.836802 AGACTCGGTAACAGGACTCC 58.163 55.000 0.00 0.00 0.00 3.85
916 968 1.355043 AGACTCGGTAACAGGACTCCT 59.645 52.381 0.00 0.00 0.00 3.69
917 969 1.744522 GACTCGGTAACAGGACTCCTC 59.255 57.143 0.00 0.00 0.00 3.71
918 970 1.355043 ACTCGGTAACAGGACTCCTCT 59.645 52.381 0.00 0.00 0.00 3.69
919 971 2.225066 ACTCGGTAACAGGACTCCTCTT 60.225 50.000 0.00 0.00 0.00 2.85
920 972 2.826725 CTCGGTAACAGGACTCCTCTTT 59.173 50.000 0.00 0.00 0.00 2.52
921 973 3.236896 TCGGTAACAGGACTCCTCTTTT 58.763 45.455 0.00 0.00 0.00 2.27
922 974 3.006537 TCGGTAACAGGACTCCTCTTTTG 59.993 47.826 0.00 0.00 0.00 2.44
923 975 3.244112 CGGTAACAGGACTCCTCTTTTGT 60.244 47.826 0.00 0.00 0.00 2.83
924 976 4.065789 GGTAACAGGACTCCTCTTTTGTG 58.934 47.826 0.00 0.00 0.00 3.33
925 977 3.933861 AACAGGACTCCTCTTTTGTGT 57.066 42.857 0.00 0.00 0.00 3.72
926 978 5.221581 GGTAACAGGACTCCTCTTTTGTGTA 60.222 44.000 0.00 0.00 0.00 2.90
927 979 5.568620 AACAGGACTCCTCTTTTGTGTAT 57.431 39.130 0.00 0.00 0.00 2.29
928 980 5.568620 ACAGGACTCCTCTTTTGTGTATT 57.431 39.130 0.00 0.00 0.00 1.89
929 981 6.681729 ACAGGACTCCTCTTTTGTGTATTA 57.318 37.500 0.00 0.00 0.00 0.98
930 982 6.465084 ACAGGACTCCTCTTTTGTGTATTAC 58.535 40.000 0.00 0.00 0.00 1.89
931 983 5.875359 CAGGACTCCTCTTTTGTGTATTACC 59.125 44.000 0.00 0.00 0.00 2.85
932 984 4.868734 GGACTCCTCTTTTGTGTATTACCG 59.131 45.833 0.00 0.00 0.00 4.02
933 985 5.337009 GGACTCCTCTTTTGTGTATTACCGA 60.337 44.000 0.00 0.00 0.00 4.69
934 986 6.105397 ACTCCTCTTTTGTGTATTACCGAA 57.895 37.500 0.00 0.00 0.00 4.30
935 987 6.708285 ACTCCTCTTTTGTGTATTACCGAAT 58.292 36.000 0.00 0.00 0.00 3.34
936 988 6.817140 ACTCCTCTTTTGTGTATTACCGAATC 59.183 38.462 0.00 0.00 0.00 2.52
937 989 6.703319 TCCTCTTTTGTGTATTACCGAATCA 58.297 36.000 0.00 0.00 0.00 2.57
938 990 7.162761 TCCTCTTTTGTGTATTACCGAATCAA 58.837 34.615 0.00 0.00 0.00 2.57
939 991 7.662258 TCCTCTTTTGTGTATTACCGAATCAAA 59.338 33.333 0.00 0.00 0.00 2.69
940 992 8.458843 CCTCTTTTGTGTATTACCGAATCAAAT 58.541 33.333 0.00 0.00 0.00 2.32
941 993 9.840427 CTCTTTTGTGTATTACCGAATCAAATT 57.160 29.630 0.00 0.00 0.00 1.82
944 996 7.804614 TTGTGTATTACCGAATCAAATTTGC 57.195 32.000 13.54 0.00 0.00 3.68
945 997 7.151999 TGTGTATTACCGAATCAAATTTGCT 57.848 32.000 13.54 0.29 0.00 3.91
946 998 7.598278 TGTGTATTACCGAATCAAATTTGCTT 58.402 30.769 13.54 10.18 0.00 3.91
947 999 7.753132 TGTGTATTACCGAATCAAATTTGCTTC 59.247 33.333 19.98 19.98 31.79 3.86
948 1000 7.968405 GTGTATTACCGAATCAAATTTGCTTCT 59.032 33.333 24.57 14.18 32.68 2.85
949 1001 8.519526 TGTATTACCGAATCAAATTTGCTTCTT 58.480 29.630 24.57 16.77 32.68 2.52
950 1002 9.010366 GTATTACCGAATCAAATTTGCTTCTTC 57.990 33.333 24.57 17.01 32.68 2.87
951 1003 4.809673 ACCGAATCAAATTTGCTTCTTCC 58.190 39.130 24.57 7.02 32.68 3.46
952 1004 4.280677 ACCGAATCAAATTTGCTTCTTCCA 59.719 37.500 24.57 4.26 32.68 3.53
953 1005 4.860907 CCGAATCAAATTTGCTTCTTCCAG 59.139 41.667 24.57 13.29 32.68 3.86
954 1006 4.325472 CGAATCAAATTTGCTTCTTCCAGC 59.675 41.667 24.57 5.60 40.55 4.85
963 1015 1.749634 GCTTCTTCCAGCATGCTTGAT 59.250 47.619 19.98 0.00 39.83 2.57
1016 1070 2.923020 GCCAAATGCAGAAATACAACGG 59.077 45.455 0.00 0.00 40.77 4.44
1017 1071 3.366883 GCCAAATGCAGAAATACAACGGA 60.367 43.478 0.00 0.00 40.77 4.69
1020 1074 5.163622 CCAAATGCAGAAATACAACGGAGAT 60.164 40.000 0.00 0.00 0.00 2.75
1189 1252 1.184970 TGATGGTGTGTCTCGCTCCA 61.185 55.000 6.57 6.57 40.85 3.86
1215 1278 3.937706 CCAACATCTCTGATGGTGACTTC 59.062 47.826 22.55 0.00 39.75 3.01
1330 1414 4.709397 CCTTCTACTTGAGAGGTGATGTCT 59.291 45.833 0.00 0.00 34.93 3.41
1374 1458 2.433145 AGCGCCATGACGACACAG 60.433 61.111 5.30 0.00 34.06 3.66
1393 1477 3.999663 ACAGAAGATTGAGAAAGCCGAAG 59.000 43.478 0.00 0.00 0.00 3.79
1425 1509 1.300697 AGTGAAGGAACGCCGACAC 60.301 57.895 0.00 0.00 41.66 3.67
1533 1620 4.133078 GCCTCTACATGGAGAATTTGAGG 58.867 47.826 9.45 6.69 41.78 3.86
2102 2205 1.546029 GTTTGCATTCCTGAAGGGTCC 59.454 52.381 0.00 0.00 36.25 4.46
2214 2332 7.741785 TGTTCTTTTTCTATGGGTTACTCTGA 58.258 34.615 0.00 0.00 0.00 3.27
2333 2673 3.624861 CAGATGTCCTATGAGTGGCAAAC 59.375 47.826 0.00 0.00 0.00 2.93
2583 3070 1.363744 CAGCGGTGAATCTGAAGGAC 58.636 55.000 9.50 0.00 32.26 3.85
3084 3574 4.122776 GAGGCTGAACTATACATGTGGTG 58.877 47.826 9.11 0.32 0.00 4.17
3085 3575 3.519510 AGGCTGAACTATACATGTGGTGT 59.480 43.478 9.11 0.99 44.95 4.16
3154 3644 4.840545 GGGTCTCCCTCCTCCAAT 57.159 61.111 0.00 0.00 41.34 3.16
3155 3645 3.970426 GGGTCTCCCTCCTCCAATA 57.030 57.895 0.00 0.00 41.34 1.90
3156 3646 2.424684 GGGTCTCCCTCCTCCAATAT 57.575 55.000 0.00 0.00 41.34 1.28
3166 3656 5.901853 TCCCTCCTCCAATATATATGCTGAG 59.098 44.000 0.00 3.29 0.00 3.35
3288 3781 2.499289 AGAGCGAAGTGATGATCCTTGT 59.501 45.455 1.72 0.00 0.00 3.16
3391 3886 0.384309 CCATTAGTGACTCGCGGCTA 59.616 55.000 6.13 0.00 0.00 3.93
3432 3927 1.058748 CAGTAACGCGGATGCAACG 59.941 57.895 12.47 9.51 42.97 4.10
3504 4000 2.497675 TCTCATTAACTCCTCGCTTGCT 59.502 45.455 0.00 0.00 0.00 3.91
3597 4094 1.763770 CAGGTTCTTCTGGGCAGGT 59.236 57.895 0.00 0.00 0.00 4.00
3646 4143 2.180017 GCTGGCCTGACATTTGCG 59.820 61.111 14.77 0.00 0.00 4.85
3683 4180 2.838202 GTGGTCTTGGGATCTTGTCCTA 59.162 50.000 0.00 0.00 46.91 2.94
3730 4227 0.179048 CCATTGGCTCTGGCGTATCA 60.179 55.000 0.00 0.00 39.81 2.15
3781 4278 5.592688 ACCATTGTCCGGAATAAATACCTTG 59.407 40.000 5.23 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.882761 ACTTTCGTTAAAGGGCTGGTTC 59.117 45.455 3.19 0.00 45.39 3.62
17 18 2.730550 ATCCGGTCGTTACTTTCGTT 57.269 45.000 0.00 0.00 0.00 3.85
30 31 1.492176 TCCTACTCCTCGTAATCCGGT 59.508 52.381 0.00 0.00 37.11 5.28
36 37 3.118112 ACCTTCGATCCTACTCCTCGTAA 60.118 47.826 0.00 0.00 34.19 3.18
37 38 2.437281 ACCTTCGATCCTACTCCTCGTA 59.563 50.000 0.00 0.00 34.19 3.43
58 62 1.174078 TCGTAAGCGGTCTGTGTGGA 61.174 55.000 0.00 0.00 38.89 4.02
60 64 1.344942 GCTCGTAAGCGGTCTGTGTG 61.345 60.000 0.00 0.00 39.10 3.82
135 140 3.434319 GTCGGCCGTCGGTGAGTA 61.434 66.667 27.15 0.00 39.77 2.59
173 178 2.598394 TTCGGGTCGTTCCTCGGT 60.598 61.111 0.00 0.00 40.32 4.69
189 211 1.228552 GTGGTGGTGGCTCATGGTT 60.229 57.895 0.00 0.00 0.00 3.67
368 396 2.047179 GGGAGCGGGTTGTGACTC 60.047 66.667 0.00 0.00 0.00 3.36
369 397 4.003788 CGGGAGCGGGTTGTGACT 62.004 66.667 0.00 0.00 0.00 3.41
414 443 2.428925 GGCCCGTCCAGATCCGTTA 61.429 63.158 0.00 0.00 34.01 3.18
454 483 2.281761 AGCGGTGAAAGTGCTGGG 60.282 61.111 0.00 0.00 37.62 4.45
457 486 2.980233 GGCAGCGGTGAAAGTGCT 60.980 61.111 20.69 0.00 40.16 4.40
458 487 4.389576 CGGCAGCGGTGAAAGTGC 62.390 66.667 20.69 0.47 35.07 4.40
549 578 1.151987 TTCTCTTCCCCGTTCCCCA 60.152 57.895 0.00 0.00 0.00 4.96
550 579 1.602771 CTTCTCTTCCCCGTTCCCC 59.397 63.158 0.00 0.00 0.00 4.81
557 586 0.252742 TGGGAGTCCTTCTCTTCCCC 60.253 60.000 9.58 0.00 42.40 4.81
639 673 3.145551 AACGATAGCTCCGGCCGT 61.146 61.111 26.12 7.98 39.73 5.68
800 852 4.862823 CCCCTCTCCCGTCTCCCC 62.863 77.778 0.00 0.00 0.00 4.81
801 853 4.862823 CCCCCTCTCCCGTCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
818 870 4.394712 CTCACGTCCCCAGCACCC 62.395 72.222 0.00 0.00 0.00 4.61
819 871 4.394712 CCTCACGTCCCCAGCACC 62.395 72.222 0.00 0.00 0.00 5.01
820 872 3.626924 ACCTCACGTCCCCAGCAC 61.627 66.667 0.00 0.00 0.00 4.40
821 873 3.625897 CACCTCACGTCCCCAGCA 61.626 66.667 0.00 0.00 0.00 4.41
822 874 4.394712 CCACCTCACGTCCCCAGC 62.395 72.222 0.00 0.00 0.00 4.85
823 875 4.394712 GCCACCTCACGTCCCCAG 62.395 72.222 0.00 0.00 0.00 4.45
878 930 2.148558 CTTATCCTCCCGCTCTCGCC 62.149 65.000 0.00 0.00 0.00 5.54
879 931 1.173444 TCTTATCCTCCCGCTCTCGC 61.173 60.000 0.00 0.00 0.00 5.03
880 932 0.594110 GTCTTATCCTCCCGCTCTCG 59.406 60.000 0.00 0.00 0.00 4.04
881 933 1.883926 GAGTCTTATCCTCCCGCTCTC 59.116 57.143 0.00 0.00 0.00 3.20
882 934 1.816183 CGAGTCTTATCCTCCCGCTCT 60.816 57.143 0.00 0.00 0.00 4.09
883 935 0.594110 CGAGTCTTATCCTCCCGCTC 59.406 60.000 0.00 0.00 0.00 5.03
884 936 0.824182 CCGAGTCTTATCCTCCCGCT 60.824 60.000 0.00 0.00 0.00 5.52
885 937 1.108132 ACCGAGTCTTATCCTCCCGC 61.108 60.000 0.00 0.00 0.00 6.13
886 938 2.267174 TACCGAGTCTTATCCTCCCG 57.733 55.000 0.00 0.00 0.00 5.14
887 939 3.294214 TGTTACCGAGTCTTATCCTCCC 58.706 50.000 0.00 0.00 0.00 4.30
888 940 3.318557 CCTGTTACCGAGTCTTATCCTCC 59.681 52.174 0.00 0.00 0.00 4.30
889 941 4.036616 GTCCTGTTACCGAGTCTTATCCTC 59.963 50.000 0.00 0.00 0.00 3.71
890 942 3.952967 GTCCTGTTACCGAGTCTTATCCT 59.047 47.826 0.00 0.00 0.00 3.24
891 943 3.952967 AGTCCTGTTACCGAGTCTTATCC 59.047 47.826 0.00 0.00 0.00 2.59
892 944 4.036616 GGAGTCCTGTTACCGAGTCTTATC 59.963 50.000 0.41 0.00 0.00 1.75
893 945 3.952967 GGAGTCCTGTTACCGAGTCTTAT 59.047 47.826 0.41 0.00 0.00 1.73
894 946 3.009916 AGGAGTCCTGTTACCGAGTCTTA 59.990 47.826 12.07 0.00 29.57 2.10
895 947 2.169330 GGAGTCCTGTTACCGAGTCTT 58.831 52.381 0.41 0.00 0.00 3.01
896 948 1.355043 AGGAGTCCTGTTACCGAGTCT 59.645 52.381 12.07 0.00 29.57 3.24
897 949 1.744522 GAGGAGTCCTGTTACCGAGTC 59.255 57.143 18.90 0.00 31.76 3.36
898 950 1.355043 AGAGGAGTCCTGTTACCGAGT 59.645 52.381 18.90 0.00 31.76 4.18
899 951 2.131776 AGAGGAGTCCTGTTACCGAG 57.868 55.000 18.90 0.00 31.76 4.63
900 952 2.599408 AAGAGGAGTCCTGTTACCGA 57.401 50.000 19.65 0.00 35.27 4.69
901 953 3.244112 ACAAAAGAGGAGTCCTGTTACCG 60.244 47.826 21.17 14.45 36.03 4.02
902 954 4.065789 CACAAAAGAGGAGTCCTGTTACC 58.934 47.826 21.17 4.35 36.03 2.85
903 955 4.704965 ACACAAAAGAGGAGTCCTGTTAC 58.295 43.478 21.17 4.74 36.03 2.50
904 956 6.681729 ATACACAAAAGAGGAGTCCTGTTA 57.318 37.500 21.17 5.76 36.03 2.41
905 957 3.933861 ACACAAAAGAGGAGTCCTGTT 57.066 42.857 18.90 17.13 38.85 3.16
906 958 5.568620 AATACACAAAAGAGGAGTCCTGT 57.431 39.130 18.90 10.47 31.76 4.00
907 959 5.875359 GGTAATACACAAAAGAGGAGTCCTG 59.125 44.000 18.90 4.96 31.76 3.86
908 960 5.337330 CGGTAATACACAAAAGAGGAGTCCT 60.337 44.000 12.85 12.85 36.03 3.85
909 961 4.868734 CGGTAATACACAAAAGAGGAGTCC 59.131 45.833 0.00 0.00 0.00 3.85
910 962 5.717119 TCGGTAATACACAAAAGAGGAGTC 58.283 41.667 0.00 0.00 0.00 3.36
911 963 5.733620 TCGGTAATACACAAAAGAGGAGT 57.266 39.130 0.00 0.00 0.00 3.85
912 964 6.816640 TGATTCGGTAATACACAAAAGAGGAG 59.183 38.462 0.00 0.00 0.00 3.69
913 965 6.703319 TGATTCGGTAATACACAAAAGAGGA 58.297 36.000 0.00 0.00 0.00 3.71
914 966 6.978343 TGATTCGGTAATACACAAAAGAGG 57.022 37.500 0.00 0.00 0.00 3.69
915 967 9.840427 AATTTGATTCGGTAATACACAAAAGAG 57.160 29.630 0.00 0.00 31.45 2.85
918 970 8.704234 GCAAATTTGATTCGGTAATACACAAAA 58.296 29.630 22.31 0.00 31.45 2.44
919 971 8.085296 AGCAAATTTGATTCGGTAATACACAAA 58.915 29.630 22.31 0.00 0.00 2.83
920 972 7.598278 AGCAAATTTGATTCGGTAATACACAA 58.402 30.769 22.31 0.00 0.00 3.33
921 973 7.151999 AGCAAATTTGATTCGGTAATACACA 57.848 32.000 22.31 0.00 0.00 3.72
922 974 8.104222 GAAGCAAATTTGATTCGGTAATACAC 57.896 34.615 27.67 7.28 42.66 2.90
943 995 1.171308 TCAAGCATGCTGGAAGAAGC 58.829 50.000 22.84 0.00 43.82 3.86
944 996 4.639310 ACTAATCAAGCATGCTGGAAGAAG 59.361 41.667 28.18 24.09 34.07 2.85
945 997 4.397103 CACTAATCAAGCATGCTGGAAGAA 59.603 41.667 28.18 15.09 34.07 2.52
946 998 3.943381 CACTAATCAAGCATGCTGGAAGA 59.057 43.478 28.18 19.48 34.07 2.87
947 999 3.693085 ACACTAATCAAGCATGCTGGAAG 59.307 43.478 28.18 22.77 28.62 3.46
948 1000 3.441222 CACACTAATCAAGCATGCTGGAA 59.559 43.478 28.18 12.39 28.62 3.53
949 1001 3.011818 CACACTAATCAAGCATGCTGGA 58.988 45.455 26.79 26.79 0.00 3.86
950 1002 3.011818 TCACACTAATCAAGCATGCTGG 58.988 45.455 23.48 19.91 0.00 4.85
951 1003 4.690184 TTCACACTAATCAAGCATGCTG 57.310 40.909 23.48 15.40 0.00 4.41
952 1004 5.416639 TGATTTCACACTAATCAAGCATGCT 59.583 36.000 16.30 16.30 38.64 3.79
953 1005 5.643664 TGATTTCACACTAATCAAGCATGC 58.356 37.500 10.51 10.51 38.64 4.06
954 1006 7.310664 AGTTGATTTCACACTAATCAAGCATG 58.689 34.615 10.34 0.00 46.74 4.06
955 1007 7.392673 AGAGTTGATTTCACACTAATCAAGCAT 59.607 33.333 10.34 2.26 46.74 3.79
956 1008 6.712095 AGAGTTGATTTCACACTAATCAAGCA 59.288 34.615 10.34 0.00 46.74 3.91
957 1009 7.020010 CAGAGTTGATTTCACACTAATCAAGC 58.980 38.462 10.34 6.97 46.74 4.01
958 1010 8.315391 TCAGAGTTGATTTCACACTAATCAAG 57.685 34.615 10.34 1.72 46.74 3.02
1009 1063 7.524717 TGATTCTATCATCATCTCCGTTGTA 57.475 36.000 0.00 0.00 33.59 2.41
1015 1069 5.046448 AGGTGCTGATTCTATCATCATCTCC 60.046 44.000 1.53 0.00 41.57 3.71
1016 1070 6.040209 AGGTGCTGATTCTATCATCATCTC 57.960 41.667 1.53 0.00 41.57 2.75
1017 1071 6.231951 CAAGGTGCTGATTCTATCATCATCT 58.768 40.000 1.53 1.53 45.77 2.90
1020 1074 4.132336 GCAAGGTGCTGATTCTATCATCA 58.868 43.478 0.00 0.00 40.96 3.07
1189 1252 3.584406 TCACCATCAGAGATGTTGGAGTT 59.416 43.478 11.34 0.00 33.91 3.01
1215 1278 0.027194 CAGCTGCATTGATCCGAACG 59.973 55.000 0.00 0.00 0.00 3.95
1330 1414 3.758425 CAGCATGTCCAATGGATATGGA 58.242 45.455 31.07 7.93 46.70 3.41
1374 1458 3.997021 TGACTTCGGCTTTCTCAATCTTC 59.003 43.478 0.00 0.00 0.00 2.87
1425 1509 3.749609 TCAACACATCATCAAGAGTGCAG 59.250 43.478 0.00 0.00 35.47 4.41
1797 1892 7.095397 CGACTAAGACCAACATTTGTGATGTTA 60.095 37.037 4.28 0.00 39.94 2.41
1801 1896 4.695455 CCGACTAAGACCAACATTTGTGAT 59.305 41.667 0.00 0.00 0.00 3.06
2102 2205 3.431912 TGAAAATTGTCCACGTGAGATCG 59.568 43.478 19.30 0.00 0.00 3.69
2214 2332 4.101645 AGCTCTAGGTACCGTCATGTAT 57.898 45.455 6.18 0.00 0.00 2.29
2309 2456 2.169144 TGCCACTCATAGGACATCTGTG 59.831 50.000 0.00 0.00 36.14 3.66
2333 2673 7.336176 GGACATAGGTAAAAGAAACAGGTTAGG 59.664 40.741 0.00 0.00 0.00 2.69
2583 3070 4.556898 GCCAGTCTATCATACAGGTACACG 60.557 50.000 0.00 0.00 0.00 4.49
3288 3781 1.612442 GCCTCCTCAGGTGGGTACA 60.612 63.158 13.96 0.00 42.74 2.90
3391 3886 2.251642 GCGAAGGTCAGCAACGGTT 61.252 57.895 0.00 0.00 0.00 4.44
3460 3956 1.301401 CCCGAGTTGCCTTCGACAA 60.301 57.895 3.54 0.00 40.36 3.18
3504 4000 4.935578 TCATGAGAAACCAGAGGAGACTA 58.064 43.478 0.00 0.00 44.43 2.59
3597 4094 4.962362 TGATACTTCTGCTTATCACCCTCA 59.038 41.667 0.00 0.00 31.17 3.86
3683 4180 2.876955 CAATGTTCATGCGCCGGT 59.123 55.556 4.18 0.00 0.00 5.28
3730 4227 3.023735 GCCTCCCTCCCCATTGGT 61.024 66.667 1.20 0.00 34.77 3.67


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

AutoCloner maintained by Alex Coulton.