Multiple sequence alignment - TraesCS6D01G347700

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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 TraesCS6D01G347700 chr6D 100.000 3248 0 0 1 3248 446150924 446147677 0.000000e+00 5999.0
1 TraesCS6D01G347700 chr6D 84.777 1524 167 41 384 1874 446097891 446099382 0.000000e+00 1469.0
2 TraesCS6D01G347700 chr6D 91.755 473 36 2 1836 2308 446099383 446099852 0.000000e+00 654.0
3 TraesCS6D01G347700 chr6B 96.078 1326 49 2 986 2308 674378327 674377002 0.000000e+00 2158.0
4 TraesCS6D01G347700 chr6B 88.855 1310 136 6 1000 2308 674196097 674197397 0.000000e+00 1602.0
5 TraesCS6D01G347700 chr6B 93.691 951 45 10 2306 3248 674375938 674374995 0.000000e+00 1410.0
6 TraesCS6D01G347700 chr6B 75.168 149 31 5 633 778 143454478 143454333 7.520000e-07 65.8
7 TraesCS6D01G347700 chr6A 90.377 956 49 18 2306 3248 592823286 592822361 0.000000e+00 1216.0
8 TraesCS6D01G347700 chr6A 89.545 660 67 2 1216 1874 592716408 592717066 0.000000e+00 835.0
9 TraesCS6D01G347700 chr6A 91.489 564 45 3 1744 2307 592856755 592856195 0.000000e+00 773.0
10 TraesCS6D01G347700 chr6A 90.182 275 27 0 1836 2110 592717067 592717341 3.080000e-95 359.0
11 TraesCS6D01G347700 chr6A 93.722 223 14 0 962 1184 592866652 592866430 5.190000e-88 335.0
12 TraesCS6D01G347700 chr6A 88.506 261 28 2 963 1221 592710692 592710952 6.760000e-82 315.0
13 TraesCS6D01G347700 chr6A 78.385 421 51 13 401 811 592867090 592866700 1.510000e-58 237.0
14 TraesCS6D01G347700 chr7B 82.215 298 44 5 1067 1361 749460016 749459725 6.960000e-62 248.0
15 TraesCS6D01G347700 chr7D 75.000 600 111 23 1048 1629 33089070 33088492 1.160000e-59 241.0
16 TraesCS6D01G347700 chr7D 81.210 314 44 9 1067 1374 633394498 633394194 4.190000e-59 239.0
17 TraesCS6D01G347700 chr7D 79.268 328 55 8 1039 1361 633399849 633399530 1.960000e-52 217.0
18 TraesCS6D01G347700 chr2D 71.872 903 175 48 1058 1910 73865197 73864324 1.540000e-43 187.0
19 TraesCS6D01G347700 chr2D 94.231 52 3 0 1 52 308770708 308770759 2.690000e-11 80.5
20 TraesCS6D01G347700 chr2B 71.736 605 124 28 1058 1633 112204529 112203943 3.400000e-25 126.0
21 TraesCS6D01G347700 chr3A 98.077 52 1 0 1 52 548261865 548261814 1.240000e-14 91.6
22 TraesCS6D01G347700 chr3A 97.872 47 1 0 1 47 548121226 548121180 7.470000e-12 82.4
23 TraesCS6D01G347700 chr5B 96.970 33 1 0 666 698 665687077 665687109 4.530000e-04 56.5
24 TraesCS6D01G347700 chr1B 82.090 67 8 3 630 694 503595057 503595121 2.000000e-03 54.7


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 TraesCS6D01G347700 chr6D 446147677 446150924 3247 True 5999.0 5999 100.0000 1 3248 1 chr6D.!!$R1 3247
1 TraesCS6D01G347700 chr6D 446097891 446099852 1961 False 1061.5 1469 88.2660 384 2308 2 chr6D.!!$F1 1924
2 TraesCS6D01G347700 chr6B 674374995 674378327 3332 True 1784.0 2158 94.8845 986 3248 2 chr6B.!!$R2 2262
3 TraesCS6D01G347700 chr6B 674196097 674197397 1300 False 1602.0 1602 88.8550 1000 2308 1 chr6B.!!$F1 1308
4 TraesCS6D01G347700 chr6A 592822361 592823286 925 True 1216.0 1216 90.3770 2306 3248 1 chr6A.!!$R1 942
5 TraesCS6D01G347700 chr6A 592856195 592856755 560 True 773.0 773 91.4890 1744 2307 1 chr6A.!!$R2 563
6 TraesCS6D01G347700 chr6A 592716408 592717341 933 False 597.0 835 89.8635 1216 2110 2 chr6A.!!$F2 894
7 TraesCS6D01G347700 chr6A 592866430 592867090 660 True 286.0 335 86.0535 401 1184 2 chr6A.!!$R3 783
8 TraesCS6D01G347700 chr7D 33088492 33089070 578 True 241.0 241 75.0000 1048 1629 1 chr7D.!!$R1 581

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
978 1022 0.377203 GAACCCTAAATCCGCTTGCG 59.623 55.0 8.14 8.14 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2967 4186 1.173043 TGCATTAGAAACAAGCCCCG 58.827 50.0 0.0 0.0 0.0 5.73 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
24 25 4.181010 CCCTCCTGGCGGGTCATG 62.181 72.222 13.89 1.58 36.91 3.07
25 26 3.402681 CCTCCTGGCGGGTCATGT 61.403 66.667 13.14 0.00 36.25 3.21
26 27 2.187946 CTCCTGGCGGGTCATGTC 59.812 66.667 13.14 0.00 36.25 3.06
27 28 2.284625 TCCTGGCGGGTCATGTCT 60.285 61.111 13.14 0.00 36.25 3.41
28 29 2.124983 CCTGGCGGGTCATGTCTG 60.125 66.667 3.48 0.00 0.00 3.51
29 30 2.659063 CCTGGCGGGTCATGTCTGA 61.659 63.158 3.48 0.00 0.00 3.27
30 31 1.524002 CTGGCGGGTCATGTCTGAT 59.476 57.895 0.00 0.00 32.98 2.90
31 32 0.752658 CTGGCGGGTCATGTCTGATA 59.247 55.000 0.00 0.00 32.98 2.15
32 33 0.752658 TGGCGGGTCATGTCTGATAG 59.247 55.000 0.00 0.00 32.98 2.08
33 34 0.753262 GGCGGGTCATGTCTGATAGT 59.247 55.000 0.00 0.00 32.98 2.12
34 35 1.269831 GGCGGGTCATGTCTGATAGTC 60.270 57.143 0.00 0.00 32.98 2.59
35 36 1.409064 GCGGGTCATGTCTGATAGTCA 59.591 52.381 0.00 0.00 32.98 3.41
36 37 2.036475 GCGGGTCATGTCTGATAGTCAT 59.964 50.000 0.00 0.00 32.98 3.06
37 38 3.255888 GCGGGTCATGTCTGATAGTCATA 59.744 47.826 0.00 0.00 32.98 2.15
38 39 4.081972 GCGGGTCATGTCTGATAGTCATAT 60.082 45.833 0.00 0.00 32.98 1.78
39 40 5.645624 CGGGTCATGTCTGATAGTCATATC 58.354 45.833 0.00 0.00 38.66 1.63
40 41 5.393569 CGGGTCATGTCTGATAGTCATATCC 60.394 48.000 0.00 0.00 37.58 2.59
41 42 5.105146 GGGTCATGTCTGATAGTCATATCCC 60.105 48.000 0.00 0.00 37.58 3.85
42 43 5.105146 GGTCATGTCTGATAGTCATATCCCC 60.105 48.000 0.00 0.00 37.58 4.81
43 44 5.481824 GTCATGTCTGATAGTCATATCCCCA 59.518 44.000 0.00 0.00 37.58 4.96
44 45 6.014242 GTCATGTCTGATAGTCATATCCCCAA 60.014 42.308 0.00 0.00 37.58 4.12
45 46 5.808366 TGTCTGATAGTCATATCCCCAAC 57.192 43.478 0.00 0.00 37.58 3.77
46 47 5.215845 TGTCTGATAGTCATATCCCCAACA 58.784 41.667 0.00 0.00 37.58 3.33
47 48 5.665360 TGTCTGATAGTCATATCCCCAACAA 59.335 40.000 0.00 0.00 37.58 2.83
48 49 6.329986 TGTCTGATAGTCATATCCCCAACAAT 59.670 38.462 0.00 0.00 37.58 2.71
49 50 7.512402 TGTCTGATAGTCATATCCCCAACAATA 59.488 37.037 0.00 0.00 37.58 1.90
50 51 8.037758 GTCTGATAGTCATATCCCCAACAATAG 58.962 40.741 0.00 0.00 37.58 1.73
51 52 7.180946 TCTGATAGTCATATCCCCAACAATAGG 59.819 40.741 0.00 0.00 37.58 2.57
52 53 6.215431 TGATAGTCATATCCCCAACAATAGGG 59.785 42.308 0.00 0.00 46.36 3.53
63 64 5.482163 CCAACAATAGGGGAACACATTTT 57.518 39.130 0.00 0.00 0.00 1.82
64 65 6.597832 CCAACAATAGGGGAACACATTTTA 57.402 37.500 0.00 0.00 0.00 1.52
65 66 6.630071 CCAACAATAGGGGAACACATTTTAG 58.370 40.000 0.00 0.00 0.00 1.85
66 67 6.435904 CCAACAATAGGGGAACACATTTTAGA 59.564 38.462 0.00 0.00 0.00 2.10
67 68 7.039363 CCAACAATAGGGGAACACATTTTAGAA 60.039 37.037 0.00 0.00 0.00 2.10
68 69 8.364142 CAACAATAGGGGAACACATTTTAGAAA 58.636 33.333 0.00 0.00 0.00 2.52
69 70 7.892609 ACAATAGGGGAACACATTTTAGAAAC 58.107 34.615 0.00 0.00 0.00 2.78
70 71 7.507616 ACAATAGGGGAACACATTTTAGAAACA 59.492 33.333 0.00 0.00 0.00 2.83
71 72 5.784578 AGGGGAACACATTTTAGAAACAC 57.215 39.130 0.00 0.00 0.00 3.32
72 73 5.205056 AGGGGAACACATTTTAGAAACACA 58.795 37.500 0.00 0.00 0.00 3.72
73 74 5.068591 AGGGGAACACATTTTAGAAACACAC 59.931 40.000 0.00 0.00 0.00 3.82
74 75 5.163499 GGGGAACACATTTTAGAAACACACA 60.163 40.000 0.00 0.00 0.00 3.72
75 76 6.334202 GGGAACACATTTTAGAAACACACAA 58.666 36.000 0.00 0.00 0.00 3.33
76 77 6.814146 GGGAACACATTTTAGAAACACACAAA 59.186 34.615 0.00 0.00 0.00 2.83
77 78 7.494298 GGGAACACATTTTAGAAACACACAAAT 59.506 33.333 0.00 0.00 0.00 2.32
78 79 9.522804 GGAACACATTTTAGAAACACACAAATA 57.477 29.630 0.00 0.00 0.00 1.40
132 133 4.899516 GTGTGAACACGTTTTGTATGACA 58.100 39.130 0.00 0.00 37.51 3.58
133 134 5.507077 GTGTGAACACGTTTTGTATGACAT 58.493 37.500 0.00 0.00 37.51 3.06
134 135 5.968848 GTGTGAACACGTTTTGTATGACATT 59.031 36.000 0.00 0.00 37.51 2.71
135 136 7.127042 GTGTGAACACGTTTTGTATGACATTA 58.873 34.615 0.00 0.00 37.51 1.90
136 137 7.640630 GTGTGAACACGTTTTGTATGACATTAA 59.359 33.333 0.00 0.00 37.51 1.40
137 138 8.346300 TGTGAACACGTTTTGTATGACATTAAT 58.654 29.630 0.00 0.00 37.51 1.40
138 139 9.814507 GTGAACACGTTTTGTATGACATTAATA 57.185 29.630 0.00 0.00 37.51 0.98
234 235 8.941977 ACAGTATCAATACTTTTTAATGCGTGA 58.058 29.630 0.00 0.00 41.44 4.35
235 236 9.935682 CAGTATCAATACTTTTTAATGCGTGAT 57.064 29.630 0.00 0.00 41.44 3.06
254 255 9.541143 TGCGTGATAGATATTTCTTGAAATACA 57.459 29.630 15.39 8.04 33.17 2.29
255 256 9.798885 GCGTGATAGATATTTCTTGAAATACAC 57.201 33.333 15.39 15.67 33.17 2.90
256 257 9.995379 CGTGATAGATATTTCTTGAAATACACG 57.005 33.333 24.34 24.34 35.67 4.49
367 368 9.383519 TGATCTAAATGAACATTCTTCCTGTAC 57.616 33.333 0.45 0.00 0.00 2.90
368 369 9.606631 GATCTAAATGAACATTCTTCCTGTACT 57.393 33.333 0.45 0.00 0.00 2.73
369 370 9.965902 ATCTAAATGAACATTCTTCCTGTACTT 57.034 29.630 0.45 0.00 0.00 2.24
370 371 9.793259 TCTAAATGAACATTCTTCCTGTACTTT 57.207 29.630 0.45 0.00 0.00 2.66
371 372 9.831737 CTAAATGAACATTCTTCCTGTACTTTG 57.168 33.333 0.45 0.00 0.00 2.77
372 373 7.823745 AATGAACATTCTTCCTGTACTTTGT 57.176 32.000 0.00 0.00 0.00 2.83
373 374 8.918202 AATGAACATTCTTCCTGTACTTTGTA 57.082 30.769 0.00 0.00 0.00 2.41
374 375 8.918202 ATGAACATTCTTCCTGTACTTTGTAA 57.082 30.769 0.00 0.00 0.00 2.41
375 376 8.378172 TGAACATTCTTCCTGTACTTTGTAAG 57.622 34.615 0.00 0.00 0.00 2.34
376 377 7.990886 TGAACATTCTTCCTGTACTTTGTAAGT 59.009 33.333 0.00 0.00 45.40 2.24
377 378 7.964604 ACATTCTTCCTGTACTTTGTAAGTC 57.035 36.000 0.00 0.00 41.77 3.01
378 379 7.506114 ACATTCTTCCTGTACTTTGTAAGTCA 58.494 34.615 0.00 0.00 41.77 3.41
379 380 7.657761 ACATTCTTCCTGTACTTTGTAAGTCAG 59.342 37.037 0.00 4.32 41.77 3.51
380 381 6.726490 TCTTCCTGTACTTTGTAAGTCAGT 57.274 37.500 0.00 0.00 41.77 3.41
381 382 7.120923 TCTTCCTGTACTTTGTAAGTCAGTT 57.879 36.000 0.00 0.00 41.77 3.16
382 383 7.562135 TCTTCCTGTACTTTGTAAGTCAGTTT 58.438 34.615 0.00 0.00 41.77 2.66
383 384 8.044908 TCTTCCTGTACTTTGTAAGTCAGTTTT 58.955 33.333 0.00 0.00 41.77 2.43
384 385 8.570068 TTCCTGTACTTTGTAAGTCAGTTTTT 57.430 30.769 0.00 0.00 41.77 1.94
428 429 5.767816 TTTGCCCAAAAGAGTAGAGAAAC 57.232 39.130 0.00 0.00 0.00 2.78
437 440 4.993029 AGAGTAGAGAAACCCGAAGATG 57.007 45.455 0.00 0.00 0.00 2.90
441 444 5.866207 AGTAGAGAAACCCGAAGATGTTTT 58.134 37.500 0.00 0.00 33.71 2.43
442 445 6.296803 AGTAGAGAAACCCGAAGATGTTTTT 58.703 36.000 0.00 0.00 33.71 1.94
447 450 8.638873 AGAGAAACCCGAAGATGTTTTTAAAAT 58.361 29.630 0.55 0.00 33.71 1.82
520 523 4.725556 TTTTAGTGAAGTGCGTTGCTAG 57.274 40.909 0.00 0.00 0.00 3.42
553 560 3.115554 GGCAGTGTGTTGCTAGTTTTTG 58.884 45.455 0.00 0.00 43.57 2.44
555 562 4.173256 GCAGTGTGTTGCTAGTTTTTGTT 58.827 39.130 0.00 0.00 40.89 2.83
562 569 5.983118 GTGTTGCTAGTTTTTGTTAAGGCAT 59.017 36.000 0.00 0.00 0.00 4.40
566 573 7.141100 TGCTAGTTTTTGTTAAGGCATACTC 57.859 36.000 0.00 0.00 0.00 2.59
571 578 6.433093 AGTTTTTGTTAAGGCATACTCGGAAT 59.567 34.615 0.00 0.00 0.00 3.01
572 579 5.811399 TTTGTTAAGGCATACTCGGAATG 57.189 39.130 0.00 0.00 0.00 2.67
593 600 9.651913 GGAATGCTTTATTCAACCAGAAAATAA 57.348 29.630 0.00 0.00 45.70 1.40
631 642 5.483685 TTGGATCGTATAGCTGGCTAAAT 57.516 39.130 6.39 0.00 31.73 1.40
633 644 4.526650 TGGATCGTATAGCTGGCTAAATCA 59.473 41.667 6.39 0.00 31.73 2.57
634 645 5.105752 GGATCGTATAGCTGGCTAAATCAG 58.894 45.833 6.39 0.00 35.49 2.90
635 646 5.105716 GGATCGTATAGCTGGCTAAATCAGA 60.106 44.000 6.39 3.52 34.36 3.27
636 647 5.122512 TCGTATAGCTGGCTAAATCAGAC 57.877 43.478 6.39 0.00 34.36 3.51
637 648 4.583073 TCGTATAGCTGGCTAAATCAGACA 59.417 41.667 6.39 0.00 41.31 3.41
638 649 5.243954 TCGTATAGCTGGCTAAATCAGACAT 59.756 40.000 6.39 0.00 43.15 3.06
639 650 5.347093 CGTATAGCTGGCTAAATCAGACATG 59.653 44.000 6.39 0.00 43.15 3.21
640 651 2.928334 AGCTGGCTAAATCAGACATGG 58.072 47.619 0.00 0.00 43.15 3.66
641 652 1.336125 GCTGGCTAAATCAGACATGGC 59.664 52.381 0.00 0.00 43.15 4.40
645 656 1.667236 CTAAATCAGACATGGCGGCA 58.333 50.000 16.34 16.34 0.00 5.69
695 711 5.403466 GCAAGGTTGTGAGCTTCAAAATTAG 59.597 40.000 6.81 0.43 41.44 1.73
701 717 8.349983 GGTTGTGAGCTTCAAAATTAGAGTTTA 58.650 33.333 6.81 0.00 0.00 2.01
764 780 7.068593 GGGAATGTTCCTTGATTTCATGTATGA 59.931 37.037 11.32 0.00 46.72 2.15
767 783 9.811995 AATGTTCCTTGATTTCATGTATGATTG 57.188 29.630 0.00 0.00 36.56 2.67
768 784 7.259882 TGTTCCTTGATTTCATGTATGATTGC 58.740 34.615 0.00 0.00 36.56 3.56
769 785 7.093858 TGTTCCTTGATTTCATGTATGATTGCA 60.094 33.333 0.00 0.00 36.56 4.08
770 786 7.591421 TCCTTGATTTCATGTATGATTGCAT 57.409 32.000 0.00 0.00 36.56 3.96
771 787 7.654568 TCCTTGATTTCATGTATGATTGCATC 58.345 34.615 0.00 0.00 36.56 3.91
772 788 7.285858 TCCTTGATTTCATGTATGATTGCATCA 59.714 33.333 0.00 0.00 44.55 3.07
793 811 2.990479 CTAGCTGCCGACCCCTTT 59.010 61.111 0.00 0.00 0.00 3.11
811 829 5.470098 CCCCTTTTCAATATCGTCGATCATT 59.530 40.000 11.82 7.43 0.00 2.57
812 830 6.017109 CCCCTTTTCAATATCGTCGATCATTT 60.017 38.462 11.82 1.75 0.00 2.32
813 831 7.417612 CCCTTTTCAATATCGTCGATCATTTT 58.582 34.615 11.82 0.00 0.00 1.82
814 832 7.915397 CCCTTTTCAATATCGTCGATCATTTTT 59.085 33.333 11.82 0.00 0.00 1.94
850 868 4.271049 AGAAACATCGATCATTACCTTGCG 59.729 41.667 0.00 0.00 0.00 4.85
858 876 5.242171 TCGATCATTACCTTGCGGACTAATA 59.758 40.000 0.00 0.00 0.00 0.98
864 900 2.829720 ACCTTGCGGACTAATACAGTGA 59.170 45.455 0.00 0.00 37.72 3.41
870 906 3.001330 GCGGACTAATACAGTGATGTTGC 59.999 47.826 0.00 0.00 37.72 4.17
900 936 4.747529 GGTACCCACGTCCGGCAC 62.748 72.222 0.00 0.00 0.00 5.01
902 938 2.035469 TACCCACGTCCGGCACTA 59.965 61.111 0.00 0.00 0.00 2.74
903 939 2.342650 TACCCACGTCCGGCACTAC 61.343 63.158 0.00 0.00 0.00 2.73
904 940 4.789075 CCCACGTCCGGCACTACG 62.789 72.222 11.47 11.47 44.47 3.51
905 941 3.740397 CCACGTCCGGCACTACGA 61.740 66.667 19.01 0.00 41.55 3.43
906 942 2.202440 CACGTCCGGCACTACGAG 60.202 66.667 19.01 8.29 41.55 4.18
907 943 4.112341 ACGTCCGGCACTACGAGC 62.112 66.667 19.01 0.00 41.55 5.03
908 944 3.812019 CGTCCGGCACTACGAGCT 61.812 66.667 7.60 0.00 41.55 4.09
911 947 0.669625 GTCCGGCACTACGAGCTTTT 60.670 55.000 0.00 0.00 35.47 2.27
937 973 2.044946 GGCCCATTTGTCGGAGCT 60.045 61.111 0.00 0.00 0.00 4.09
942 978 1.339055 CCCATTTGTCGGAGCTCTGAA 60.339 52.381 26.70 12.31 32.23 3.02
944 980 2.813754 CCATTTGTCGGAGCTCTGAAAA 59.186 45.455 26.70 24.28 32.23 2.29
945 981 3.253188 CCATTTGTCGGAGCTCTGAAAAA 59.747 43.478 33.18 33.18 41.30 1.94
978 1022 0.377203 GAACCCTAAATCCGCTTGCG 59.623 55.000 8.14 8.14 0.00 4.85
1137 1182 3.391382 GCCTGTCCTACCCTGCGT 61.391 66.667 0.00 0.00 0.00 5.24
1214 1259 1.760613 TCTCCTCGGCATAATTTCCGT 59.239 47.619 11.50 0.00 45.44 4.69
1626 1683 1.131504 CTGGTCCTCTTCGTCTTCTCG 59.868 57.143 0.00 0.00 0.00 4.04
1776 1833 1.301401 TTGGGCTGTTTCTCCGTCG 60.301 57.895 0.00 0.00 0.00 5.12
1848 1905 1.674322 CCCACGTCAACATGTCCCC 60.674 63.158 0.00 0.00 0.00 4.81
1998 2133 1.202510 GGTGCAAACAAGTGGCAATCA 60.203 47.619 0.00 0.00 39.57 2.57
2003 2138 2.071778 AACAAGTGGCAATCAGTGGT 57.928 45.000 0.00 0.00 34.50 4.16
2103 2238 4.759205 AACCTGCATTCGGCCCCC 62.759 66.667 0.00 0.00 43.89 5.40
2254 2393 2.159254 CCACCAACTGTTTGAAGTGGTG 60.159 50.000 16.48 16.48 42.62 4.17
2270 2412 1.270625 TGGTGAGTAAGCTTGTTCCCG 60.271 52.381 9.86 0.00 0.00 5.14
2356 3564 6.716628 CCATGTTATGCCTAAATAGATGGTGT 59.283 38.462 0.00 0.00 0.00 4.16
2571 3781 8.408043 AATTACCTGATCTATGAGACTGAGAG 57.592 38.462 0.00 0.00 0.00 3.20
2604 3814 6.659242 CCACTTAAACCAGTTGGATTATGACT 59.341 38.462 16.01 0.00 38.94 3.41
2691 3901 2.016318 CCATGCAAACTGATAGGCGAA 58.984 47.619 0.00 0.00 0.00 4.70
2849 4068 4.099881 ACTGACATTTGAACCAAACTGCAT 59.900 37.500 0.00 0.00 36.13 3.96
2929 4148 0.963225 TACGTCTAACAGCAGTGGCA 59.037 50.000 0.00 0.00 44.61 4.92
2933 4152 2.704572 GTCTAACAGCAGTGGCATCTT 58.295 47.619 0.00 0.00 44.61 2.40
2938 4157 1.241165 CAGCAGTGGCATCTTGTTGA 58.759 50.000 7.37 0.00 44.61 3.18
2975 4194 1.392589 AATCTGCATAACGGGGCTTG 58.607 50.000 0.00 0.00 0.00 4.01
2979 4199 0.885196 TGCATAACGGGGCTTGTTTC 59.115 50.000 0.60 0.00 0.00 2.78
3130 4351 3.518590 AGCCGTGCGTTATATATAAGCC 58.481 45.455 17.14 8.78 0.00 4.35
3131 4352 3.194968 AGCCGTGCGTTATATATAAGCCT 59.805 43.478 17.14 9.19 0.00 4.58
3141 4362 7.653713 GCGTTATATATAAGCCTCTGCATGTAT 59.346 37.037 5.39 0.00 41.13 2.29
3154 4375 3.148412 TGCATGTATGGATGTGTATGCC 58.852 45.455 0.00 0.00 39.96 4.40
3176 4397 7.676947 TGCCAATACCTTCTGTTAGATATACC 58.323 38.462 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.391665 GACATGACCCGCCAGGAGG 62.392 68.421 1.14 1.14 41.02 4.30
9 10 2.187946 GACATGACCCGCCAGGAG 59.812 66.667 0.00 0.00 41.02 3.69
10 11 2.284625 AGACATGACCCGCCAGGA 60.285 61.111 0.00 0.00 41.02 3.86
11 12 1.976132 ATCAGACATGACCCGCCAGG 61.976 60.000 0.00 0.00 38.57 4.45
12 13 0.752658 TATCAGACATGACCCGCCAG 59.247 55.000 0.00 0.00 38.57 4.85
13 14 0.752658 CTATCAGACATGACCCGCCA 59.247 55.000 0.00 0.00 38.57 5.69
14 15 0.753262 ACTATCAGACATGACCCGCC 59.247 55.000 0.00 0.00 38.57 6.13
15 16 1.409064 TGACTATCAGACATGACCCGC 59.591 52.381 0.00 0.00 38.57 6.13
16 17 5.393569 GGATATGACTATCAGACATGACCCG 60.394 48.000 0.00 0.00 38.57 5.28
17 18 5.105146 GGGATATGACTATCAGACATGACCC 60.105 48.000 0.00 13.79 38.51 4.46
18 19 5.105146 GGGGATATGACTATCAGACATGACC 60.105 48.000 0.00 5.04 38.57 4.02
19 20 5.481824 TGGGGATATGACTATCAGACATGAC 59.518 44.000 0.00 0.00 38.57 3.06
20 21 5.654370 TGGGGATATGACTATCAGACATGA 58.346 41.667 0.00 0.00 40.50 3.07
21 22 6.169094 GTTGGGGATATGACTATCAGACATG 58.831 44.000 0.00 0.00 36.27 3.21
22 23 5.846164 TGTTGGGGATATGACTATCAGACAT 59.154 40.000 0.00 0.00 36.27 3.06
23 24 5.215845 TGTTGGGGATATGACTATCAGACA 58.784 41.667 0.00 0.00 36.27 3.41
24 25 5.808366 TGTTGGGGATATGACTATCAGAC 57.192 43.478 0.00 0.00 36.27 3.51
25 26 7.180946 CCTATTGTTGGGGATATGACTATCAGA 59.819 40.741 0.00 0.00 36.27 3.27
26 27 7.334090 CCTATTGTTGGGGATATGACTATCAG 58.666 42.308 0.00 0.00 36.27 2.90
27 28 6.215431 CCCTATTGTTGGGGATATGACTATCA 59.785 42.308 0.00 0.00 46.62 2.15
28 29 6.653989 CCCTATTGTTGGGGATATGACTATC 58.346 44.000 0.00 0.00 46.62 2.08
29 30 6.642733 CCCTATTGTTGGGGATATGACTAT 57.357 41.667 0.00 0.00 46.62 2.12
40 41 2.595750 TGTGTTCCCCTATTGTTGGG 57.404 50.000 0.00 0.00 44.19 4.12
41 42 5.482163 AAAATGTGTTCCCCTATTGTTGG 57.518 39.130 0.00 0.00 0.00 3.77
42 43 7.461182 TCTAAAATGTGTTCCCCTATTGTTG 57.539 36.000 0.00 0.00 0.00 3.33
43 44 8.364894 GTTTCTAAAATGTGTTCCCCTATTGTT 58.635 33.333 0.00 0.00 0.00 2.83
44 45 7.507616 TGTTTCTAAAATGTGTTCCCCTATTGT 59.492 33.333 0.00 0.00 0.00 2.71
45 46 7.812669 GTGTTTCTAAAATGTGTTCCCCTATTG 59.187 37.037 0.00 0.00 0.00 1.90
46 47 7.507616 TGTGTTTCTAAAATGTGTTCCCCTATT 59.492 33.333 0.00 0.00 0.00 1.73
47 48 7.007723 TGTGTTTCTAAAATGTGTTCCCCTAT 58.992 34.615 0.00 0.00 0.00 2.57
48 49 6.263617 GTGTGTTTCTAAAATGTGTTCCCCTA 59.736 38.462 0.00 0.00 0.00 3.53
49 50 5.068591 GTGTGTTTCTAAAATGTGTTCCCCT 59.931 40.000 0.00 0.00 0.00 4.79
50 51 5.163499 TGTGTGTTTCTAAAATGTGTTCCCC 60.163 40.000 0.00 0.00 0.00 4.81
51 52 5.897050 TGTGTGTTTCTAAAATGTGTTCCC 58.103 37.500 0.00 0.00 0.00 3.97
52 53 7.820044 TTTGTGTGTTTCTAAAATGTGTTCC 57.180 32.000 0.00 0.00 0.00 3.62
104 105 7.542477 TCATACAAAACGTGTTCACACATTTTT 59.458 29.630 12.82 11.92 46.00 1.94
106 107 6.470877 GTCATACAAAACGTGTTCACACATTT 59.529 34.615 10.61 4.67 43.01 2.32
107 108 5.968848 GTCATACAAAACGTGTTCACACATT 59.031 36.000 10.61 0.00 46.75 2.71
108 109 5.065346 TGTCATACAAAACGTGTTCACACAT 59.935 36.000 10.61 0.00 46.75 3.21
109 110 4.392138 TGTCATACAAAACGTGTTCACACA 59.608 37.500 10.61 0.00 46.75 3.72
110 111 4.899516 TGTCATACAAAACGTGTTCACAC 58.100 39.130 0.00 0.00 41.98 3.82
111 112 5.743026 ATGTCATACAAAACGTGTTCACA 57.257 34.783 0.00 0.00 41.98 3.58
112 113 8.722342 ATTAATGTCATACAAAACGTGTTCAC 57.278 30.769 0.00 0.00 41.98 3.18
208 209 8.941977 TCACGCATTAAAAAGTATTGATACTGT 58.058 29.630 4.52 0.00 42.47 3.55
209 210 9.935682 ATCACGCATTAAAAAGTATTGATACTG 57.064 29.630 4.52 0.00 42.47 2.74
228 229 9.541143 TGTATTTCAAGAAATATCTATCACGCA 57.459 29.630 15.87 5.85 42.93 5.24
229 230 9.798885 GTGTATTTCAAGAAATATCTATCACGC 57.201 33.333 15.87 8.59 42.93 5.34
230 231 9.995379 CGTGTATTTCAAGAAATATCTATCACG 57.005 33.333 24.53 24.53 43.57 4.35
341 342 9.383519 GTACAGGAAGAATGTTCATTTAGATCA 57.616 33.333 0.00 0.00 32.02 2.92
342 343 9.606631 AGTACAGGAAGAATGTTCATTTAGATC 57.393 33.333 0.00 0.00 32.02 2.75
343 344 9.965902 AAGTACAGGAAGAATGTTCATTTAGAT 57.034 29.630 0.00 0.00 32.02 1.98
344 345 9.793259 AAAGTACAGGAAGAATGTTCATTTAGA 57.207 29.630 0.00 0.00 32.02 2.10
345 346 9.831737 CAAAGTACAGGAAGAATGTTCATTTAG 57.168 33.333 0.00 0.00 32.02 1.85
346 347 9.349713 ACAAAGTACAGGAAGAATGTTCATTTA 57.650 29.630 0.00 0.00 32.02 1.40
347 348 8.237811 ACAAAGTACAGGAAGAATGTTCATTT 57.762 30.769 0.00 0.00 32.02 2.32
348 349 7.823745 ACAAAGTACAGGAAGAATGTTCATT 57.176 32.000 0.00 0.00 32.02 2.57
349 350 8.918202 TTACAAAGTACAGGAAGAATGTTCAT 57.082 30.769 0.00 0.00 32.02 2.57
350 351 7.990886 ACTTACAAAGTACAGGAAGAATGTTCA 59.009 33.333 10.74 0.00 40.69 3.18
351 352 8.379457 ACTTACAAAGTACAGGAAGAATGTTC 57.621 34.615 10.74 0.00 40.69 3.18
352 353 7.990886 TGACTTACAAAGTACAGGAAGAATGTT 59.009 33.333 10.74 0.00 43.03 2.71
353 354 7.506114 TGACTTACAAAGTACAGGAAGAATGT 58.494 34.615 10.74 0.00 43.03 2.71
354 355 7.657761 ACTGACTTACAAAGTACAGGAAGAATG 59.342 37.037 10.74 4.30 43.03 2.67
355 356 7.736893 ACTGACTTACAAAGTACAGGAAGAAT 58.263 34.615 10.74 0.00 43.03 2.40
356 357 7.120923 ACTGACTTACAAAGTACAGGAAGAA 57.879 36.000 10.74 0.79 43.03 2.52
357 358 6.726490 ACTGACTTACAAAGTACAGGAAGA 57.274 37.500 10.74 0.00 43.03 2.87
358 359 7.787725 AAACTGACTTACAAAGTACAGGAAG 57.212 36.000 16.43 0.00 43.03 3.46
359 360 8.570068 AAAAACTGACTTACAAAGTACAGGAA 57.430 30.769 16.43 0.00 43.03 3.36
409 410 3.082548 GGGTTTCTCTACTCTTTTGGGC 58.917 50.000 0.00 0.00 0.00 5.36
413 414 5.803237 TCTTCGGGTTTCTCTACTCTTTT 57.197 39.130 0.00 0.00 0.00 2.27
428 429 8.682710 TCCAGATATTTTAAAAACATCTTCGGG 58.317 33.333 18.71 17.15 0.00 5.14
534 541 6.472163 CCTTAACAAAAACTAGCAACACACTG 59.528 38.462 0.00 0.00 0.00 3.66
539 546 5.584253 TGCCTTAACAAAAACTAGCAACA 57.416 34.783 0.00 0.00 0.00 3.33
540 547 7.368059 AGTATGCCTTAACAAAAACTAGCAAC 58.632 34.615 0.00 0.00 31.99 4.17
553 560 3.879932 GCATTCCGAGTATGCCTTAAC 57.120 47.619 0.00 0.00 41.94 2.01
562 569 5.492895 TGGTTGAATAAAGCATTCCGAGTA 58.507 37.500 0.00 0.00 42.17 2.59
566 573 4.963276 TCTGGTTGAATAAAGCATTCCG 57.037 40.909 0.00 0.00 44.90 4.30
571 578 9.995003 AACATTATTTTCTGGTTGAATAAAGCA 57.005 25.926 0.00 0.00 43.85 3.91
598 605 8.297426 CAGCTATACGATCCAATTCTAGTTGTA 58.703 37.037 0.00 0.00 0.00 2.41
599 606 7.148641 CAGCTATACGATCCAATTCTAGTTGT 58.851 38.462 0.00 0.00 0.00 3.32
600 607 6.587990 CCAGCTATACGATCCAATTCTAGTTG 59.412 42.308 0.00 0.00 0.00 3.16
603 614 5.105554 AGCCAGCTATACGATCCAATTCTAG 60.106 44.000 0.00 0.00 0.00 2.43
604 615 4.772624 AGCCAGCTATACGATCCAATTCTA 59.227 41.667 0.00 0.00 0.00 2.10
610 621 4.526650 TGATTTAGCCAGCTATACGATCCA 59.473 41.667 0.00 0.00 0.00 3.41
616 627 5.641209 CCATGTCTGATTTAGCCAGCTATAC 59.359 44.000 0.00 0.00 0.00 1.47
620 631 2.928334 CCATGTCTGATTTAGCCAGCT 58.072 47.619 0.00 0.00 0.00 4.24
631 642 2.334946 GCTTTGCCGCCATGTCTGA 61.335 57.895 0.00 0.00 0.00 3.27
673 684 6.547510 ACTCTAATTTTGAAGCTCACAACCTT 59.452 34.615 5.91 5.78 0.00 3.50
695 711 5.007528 GCTTCATCCATGAGCTTCTAAACTC 59.992 44.000 0.00 0.00 38.19 3.01
701 717 3.453717 TGTAGCTTCATCCATGAGCTTCT 59.546 43.478 10.74 4.17 39.84 2.85
767 783 0.037882 TCGGCAGCTAGCTATGATGC 60.038 55.000 18.86 16.89 44.89 3.91
768 784 1.671261 GGTCGGCAGCTAGCTATGATG 60.671 57.143 18.86 6.74 44.79 3.07
769 785 0.605589 GGTCGGCAGCTAGCTATGAT 59.394 55.000 18.86 0.00 44.79 2.45
770 786 1.464376 GGGTCGGCAGCTAGCTATGA 61.464 60.000 18.86 12.55 44.79 2.15
771 787 1.005630 GGGTCGGCAGCTAGCTATG 60.006 63.158 18.86 8.40 44.79 2.23
772 788 2.210711 GGGGTCGGCAGCTAGCTAT 61.211 63.158 18.86 0.00 44.79 2.97
821 839 8.335532 AGGTAATGATCGATGTTTCTCAAAAA 57.664 30.769 0.54 0.00 0.00 1.94
822 840 7.921786 AGGTAATGATCGATGTTTCTCAAAA 57.078 32.000 0.54 0.00 0.00 2.44
823 841 7.626240 GCAAGGTAATGATCGATGTTTCTCAAA 60.626 37.037 0.54 0.00 0.00 2.69
824 842 6.183360 GCAAGGTAATGATCGATGTTTCTCAA 60.183 38.462 0.54 0.00 0.00 3.02
825 843 5.294306 GCAAGGTAATGATCGATGTTTCTCA 59.706 40.000 0.54 0.00 0.00 3.27
826 844 5.557136 CGCAAGGTAATGATCGATGTTTCTC 60.557 44.000 0.54 0.00 0.00 2.87
827 845 4.271049 CGCAAGGTAATGATCGATGTTTCT 59.729 41.667 0.54 0.00 0.00 2.52
828 846 4.518217 CGCAAGGTAATGATCGATGTTTC 58.482 43.478 0.54 0.00 0.00 2.78
829 847 4.536364 CGCAAGGTAATGATCGATGTTT 57.464 40.909 0.54 0.00 0.00 2.83
845 863 4.433615 ACATCACTGTATTAGTCCGCAAG 58.566 43.478 0.00 0.00 37.60 4.01
850 868 4.572389 CCAGCAACATCACTGTATTAGTCC 59.428 45.833 0.00 0.00 37.60 3.85
858 876 1.604593 GGCCCAGCAACATCACTGT 60.605 57.895 0.00 0.00 37.12 3.55
885 921 2.035469 TAGTGCCGGACGTGGGTA 59.965 61.111 5.05 0.00 0.00 3.69
887 923 4.789075 CGTAGTGCCGGACGTGGG 62.789 72.222 5.05 0.00 34.39 4.61
888 924 3.678717 CTCGTAGTGCCGGACGTGG 62.679 68.421 5.05 0.18 40.00 4.94
889 925 2.202440 CTCGTAGTGCCGGACGTG 60.202 66.667 5.05 2.93 40.00 4.49
890 926 4.112341 GCTCGTAGTGCCGGACGT 62.112 66.667 5.05 0.00 41.67 4.34
900 936 2.159170 CCAGAGAGGGAAAAGCTCGTAG 60.159 54.545 0.00 0.00 33.98 3.51
902 938 0.610687 CCAGAGAGGGAAAAGCTCGT 59.389 55.000 0.00 0.00 33.98 4.18
903 939 0.742635 GCCAGAGAGGGAAAAGCTCG 60.743 60.000 0.00 0.00 38.09 5.03
904 940 0.393673 GGCCAGAGAGGGAAAAGCTC 60.394 60.000 0.00 0.00 38.09 4.09
905 941 1.688211 GGCCAGAGAGGGAAAAGCT 59.312 57.895 0.00 0.00 38.09 3.74
906 942 1.379176 GGGCCAGAGAGGGAAAAGC 60.379 63.158 4.39 0.00 38.09 3.51
907 943 0.627986 ATGGGCCAGAGAGGGAAAAG 59.372 55.000 13.78 0.00 38.09 2.27
908 944 1.084018 AATGGGCCAGAGAGGGAAAA 58.916 50.000 13.78 0.00 38.09 2.29
911 947 0.846427 ACAAATGGGCCAGAGAGGGA 60.846 55.000 13.78 0.00 38.09 4.20
946 982 5.975693 TTTAGGGTTCTCGATGCATTTTT 57.024 34.783 0.00 0.00 0.00 1.94
947 983 5.067805 GGATTTAGGGTTCTCGATGCATTTT 59.932 40.000 0.00 0.00 0.00 1.82
948 984 4.580580 GGATTTAGGGTTCTCGATGCATTT 59.419 41.667 0.00 0.00 0.00 2.32
949 985 4.137543 GGATTTAGGGTTCTCGATGCATT 58.862 43.478 0.00 0.00 0.00 3.56
950 986 3.744660 GGATTTAGGGTTCTCGATGCAT 58.255 45.455 0.00 0.00 0.00 3.96
951 987 2.483013 CGGATTTAGGGTTCTCGATGCA 60.483 50.000 0.00 0.00 0.00 3.96
952 988 2.135933 CGGATTTAGGGTTCTCGATGC 58.864 52.381 0.00 0.00 0.00 3.91
953 989 2.135933 GCGGATTTAGGGTTCTCGATG 58.864 52.381 0.00 0.00 0.00 3.84
954 990 2.040178 AGCGGATTTAGGGTTCTCGAT 58.960 47.619 0.00 0.00 0.00 3.59
978 1022 1.682344 GGTGGAGGGTGGAAATGCC 60.682 63.158 0.00 0.00 37.10 4.40
1137 1182 3.366915 TGGTCGGTGATGACGCGA 61.367 61.111 15.93 0.00 39.83 5.87
1455 1506 0.682209 TGGGAGGTAGCAGACGGTAC 60.682 60.000 0.00 0.00 43.89 3.34
1776 1833 3.243168 TGTCAAGCATGAGCAACTTGTTC 60.243 43.478 0.00 0.00 45.49 3.18
1848 1905 1.401761 TCATTGGGATCATTTGGCCG 58.598 50.000 0.00 0.00 0.00 6.13
1998 2133 3.118531 AGGCAAGGAGATTATCACCACT 58.881 45.455 11.06 1.46 28.86 4.00
2003 2138 3.269381 ACCCAAAGGCAAGGAGATTATCA 59.731 43.478 0.00 0.00 36.11 2.15
2254 2393 1.275573 AGACCGGGAACAAGCTTACTC 59.724 52.381 6.32 0.00 0.00 2.59
2270 2412 6.237915 GCATATGCAAAATACAAGCAAAGACC 60.238 38.462 22.84 0.00 42.15 3.85
2356 3564 4.441356 CCTTTTAGCAAAACTGGCACTTCA 60.441 41.667 0.00 0.00 0.00 3.02
2423 3632 6.476706 TGCATCTACGTTACAATCATGAGAAG 59.523 38.462 0.09 0.00 0.00 2.85
2503 3713 5.163703 CCACGGCAGCAATATGTTTAGTTTA 60.164 40.000 0.00 0.00 0.00 2.01
2571 3781 5.449999 CCAACTGGTTTAAGTGGTGTCTTTC 60.450 44.000 0.00 0.00 0.00 2.62
2849 4068 1.339055 ACTATGCTGAAAAGGCGAGCA 60.339 47.619 0.00 0.00 46.32 4.26
2929 4148 5.484715 CCCTGCAATTCAATTCAACAAGAT 58.515 37.500 0.00 0.00 0.00 2.40
2933 4152 2.367894 TGCCCTGCAATTCAATTCAACA 59.632 40.909 0.00 0.00 34.76 3.33
2938 4157 5.607477 CAGATTATGCCCTGCAATTCAATT 58.393 37.500 0.00 0.00 43.62 2.32
2966 4185 1.173913 GCATTAGAAACAAGCCCCGT 58.826 50.000 0.00 0.00 0.00 5.28
2967 4186 1.173043 TGCATTAGAAACAAGCCCCG 58.827 50.000 0.00 0.00 0.00 5.73
2975 4194 3.382546 ACAGCCATCCATGCATTAGAAAC 59.617 43.478 0.00 0.00 0.00 2.78
2979 4199 2.545113 GCAACAGCCATCCATGCATTAG 60.545 50.000 0.00 0.00 37.00 1.73
3110 4331 3.518590 AGGCTTATATATAACGCACGGC 58.481 45.455 19.56 13.95 0.00 5.68
3130 4351 4.153655 GCATACACATCCATACATGCAGAG 59.846 45.833 0.00 0.00 38.84 3.35
3131 4352 4.067192 GCATACACATCCATACATGCAGA 58.933 43.478 0.00 0.00 38.84 4.26
3141 4362 4.165950 AGAAGGTATTGGCATACACATCCA 59.834 41.667 0.00 0.00 37.59 3.41
3181 4406 3.359033 CTTGGCCCATGATTCTCAGAAA 58.641 45.455 0.00 0.00 0.00 2.52
3196 4421 0.678048 ATGTCGGAAGAAGCTTGGCC 60.678 55.000 2.10 0.00 45.01 5.36


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

AutoCloner maintained by Alex Coulton.