Multiple sequence alignment - TraesCS5D01G380800

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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 TraesCS5D01G380800 chr5D 100.000 3231 0 0 1 3231 451039545 451042775 0.000000e+00 5967.0
1 TraesCS5D01G380800 chr5D 93.443 122 8 0 2425 2546 451066634 451066755 7.120000e-42 182.0
2 TraesCS5D01G380800 chr5D 83.851 161 22 3 252 411 393737081 393737238 2.010000e-32 150.0
3 TraesCS5D01G380800 chr5B 93.193 1660 80 16 785 2425 551297642 551299287 0.000000e+00 2409.0
4 TraesCS5D01G380800 chr5B 91.572 439 25 4 117 553 551294878 551295306 2.150000e-166 595.0
5 TraesCS5D01G380800 chr5B 95.378 238 8 1 543 780 551297367 551297601 3.040000e-100 375.0
6 TraesCS5D01G380800 chr5B 85.965 57 8 0 350 406 475474657 475474601 9.680000e-06 62.1
7 TraesCS5D01G380800 chr5A 91.095 1662 78 20 772 2430 570249744 570251338 0.000000e+00 2185.0
8 TraesCS5D01G380800 chr5A 88.474 321 30 7 1 319 570237787 570238102 6.540000e-102 381.0
9 TraesCS5D01G380800 chr5A 88.294 299 34 1 483 780 570249425 570249723 1.100000e-94 357.0
10 TraesCS5D01G380800 chr5A 79.767 257 35 14 116 365 573618417 573618171 1.540000e-38 171.0
11 TraesCS5D01G380800 chr6B 87.931 812 83 7 2427 3231 357129026 357129829 0.000000e+00 942.0
12 TraesCS5D01G380800 chr7D 89.482 656 65 3 2576 3229 8559058 8558405 0.000000e+00 826.0
13 TraesCS5D01G380800 chr7D 79.646 113 18 3 80 188 46827725 46827836 3.460000e-10 76.8
14 TraesCS5D01G380800 chr6A 83.128 812 127 6 2425 3229 218134561 218135369 0.000000e+00 732.0
15 TraesCS5D01G380800 chr6A 97.222 36 1 0 347 382 67840138 67840173 9.680000e-06 62.1
16 TraesCS5D01G380800 chr2A 83.251 812 114 14 2425 3229 644450435 644449639 0.000000e+00 726.0
17 TraesCS5D01G380800 chr2A 80.800 125 20 4 2425 2547 116077305 116077183 9.540000e-16 95.3
18 TraesCS5D01G380800 chr2A 86.792 53 3 1 127 175 655739202 655739150 4.500000e-04 56.5
19 TraesCS5D01G380800 chr1D 82.924 814 112 15 2431 3229 359496089 359495288 0.000000e+00 708.0
20 TraesCS5D01G380800 chr1D 81.898 801 133 11 2425 3219 15057302 15056508 0.000000e+00 665.0
21 TraesCS5D01G380800 chr1D 77.859 822 153 16 2425 3229 200224659 200225468 1.740000e-132 483.0
22 TraesCS5D01G380800 chr6D 85.802 648 92 0 2582 3229 67406472 67407119 0.000000e+00 688.0
23 TraesCS5D01G380800 chr6D 87.379 206 18 3 2427 2626 234428560 234428763 2.510000e-56 230.0
24 TraesCS5D01G380800 chr3A 85.263 665 93 3 2569 3229 682338701 682339364 0.000000e+00 680.0
25 TraesCS5D01G380800 chr3A 80.952 147 23 5 216 359 7200388 7200244 9.480000e-21 111.0
26 TraesCS5D01G380800 chr4A 81.852 799 139 6 2431 3227 413512796 413512002 0.000000e+00 667.0
27 TraesCS5D01G380800 chr1A 76.903 381 60 23 40 408 300932921 300932557 1.180000e-44 191.0
28 TraesCS5D01G380800 chr2B 88.333 120 12 1 2431 2550 198762643 198762526 3.360000e-30 143.0
29 TraesCS5D01G380800 chr4D 79.213 178 31 6 235 411 51607957 51608129 5.660000e-23 119.0
30 TraesCS5D01G380800 chr4D 77.027 148 30 3 216 362 394360252 394360108 7.430000e-12 82.4
31 TraesCS5D01G380800 chr7B 89.655 87 9 0 292 378 531815213 531815127 9.480000e-21 111.0
32 TraesCS5D01G380800 chr1B 83.186 113 19 0 2425 2537 600525958 600526070 1.590000e-18 104.0
33 TraesCS5D01G380800 chr4B 80.198 101 20 0 432 532 621096018 621095918 3.460000e-10 76.8


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 TraesCS5D01G380800 chr5D 451039545 451042775 3230 False 5967.000000 5967 100.0000 1 3231 1 chr5D.!!$F2 3230
1 TraesCS5D01G380800 chr5B 551294878 551299287 4409 False 1126.333333 2409 93.3810 117 2425 3 chr5B.!!$F1 2308
2 TraesCS5D01G380800 chr5A 570249425 570251338 1913 False 1271.000000 2185 89.6945 483 2430 2 chr5A.!!$F2 1947
3 TraesCS5D01G380800 chr6B 357129026 357129829 803 False 942.000000 942 87.9310 2427 3231 1 chr6B.!!$F1 804
4 TraesCS5D01G380800 chr7D 8558405 8559058 653 True 826.000000 826 89.4820 2576 3229 1 chr7D.!!$R1 653
5 TraesCS5D01G380800 chr6A 218134561 218135369 808 False 732.000000 732 83.1280 2425 3229 1 chr6A.!!$F2 804
6 TraesCS5D01G380800 chr2A 644449639 644450435 796 True 726.000000 726 83.2510 2425 3229 1 chr2A.!!$R2 804
7 TraesCS5D01G380800 chr1D 359495288 359496089 801 True 708.000000 708 82.9240 2431 3229 1 chr1D.!!$R2 798
8 TraesCS5D01G380800 chr1D 15056508 15057302 794 True 665.000000 665 81.8980 2425 3219 1 chr1D.!!$R1 794
9 TraesCS5D01G380800 chr1D 200224659 200225468 809 False 483.000000 483 77.8590 2425 3229 1 chr1D.!!$F1 804
10 TraesCS5D01G380800 chr6D 67406472 67407119 647 False 688.000000 688 85.8020 2582 3229 1 chr6D.!!$F1 647
11 TraesCS5D01G380800 chr3A 682338701 682339364 663 False 680.000000 680 85.2630 2569 3229 1 chr3A.!!$F1 660
12 TraesCS5D01G380800 chr4A 413512002 413512796 794 True 667.000000 667 81.8520 2431 3227 1 chr4A.!!$R1 796

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
276 279 0.105246 CTAGAGAGATGGCTGGGGGT 60.105 60.0 0.0 0.0 0.0 4.95 F
720 2795 0.316841 TGCAACCGAAAGATTTGGCC 59.683 50.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 3774 0.252974 TCCTTCTCCATTTCCCCCGA 60.253 55.0 0.00 0.0 0.00 5.14 R
2592 4755 1.067295 ACTGCATTCCAGGAGTTCCA 58.933 50.0 0.28 0.0 46.14 3.53 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
20 21 3.535280 TGCCCAAAGAAACCAGTTTTC 57.465 42.857 0.00 0.00 43.67 2.29
21 22 2.834549 TGCCCAAAGAAACCAGTTTTCA 59.165 40.909 0.00 0.00 45.50 2.69
22 23 3.454082 TGCCCAAAGAAACCAGTTTTCAT 59.546 39.130 0.00 0.00 45.50 2.57
23 24 3.809279 GCCCAAAGAAACCAGTTTTCATG 59.191 43.478 0.00 0.00 45.50 3.07
24 25 3.809279 CCCAAAGAAACCAGTTTTCATGC 59.191 43.478 0.00 0.00 45.50 4.06
25 26 3.809279 CCAAAGAAACCAGTTTTCATGCC 59.191 43.478 0.00 0.00 45.50 4.40
26 27 4.443315 CCAAAGAAACCAGTTTTCATGCCT 60.443 41.667 0.00 0.00 45.50 4.75
27 28 5.221422 CCAAAGAAACCAGTTTTCATGCCTA 60.221 40.000 0.00 0.00 45.50 3.93
28 29 6.458210 CAAAGAAACCAGTTTTCATGCCTAT 58.542 36.000 0.00 0.00 45.50 2.57
29 30 6.670695 AAGAAACCAGTTTTCATGCCTATT 57.329 33.333 0.00 0.00 45.50 1.73
30 31 6.670695 AGAAACCAGTTTTCATGCCTATTT 57.329 33.333 0.00 0.00 45.50 1.40
31 32 7.066307 AGAAACCAGTTTTCATGCCTATTTT 57.934 32.000 0.00 0.00 45.50 1.82
32 33 7.508687 AGAAACCAGTTTTCATGCCTATTTTT 58.491 30.769 0.00 0.00 45.50 1.94
62 63 9.502091 ACAATAGCTAAATGTAAGTCACTTGAA 57.498 29.630 12.43 0.00 0.00 2.69
75 76 9.482627 GTAAGTCACTTGAATATAGAATCTGGG 57.517 37.037 0.00 0.00 0.00 4.45
76 77 6.529220 AGTCACTTGAATATAGAATCTGGGC 58.471 40.000 0.00 0.00 0.00 5.36
77 78 5.703130 GTCACTTGAATATAGAATCTGGGCC 59.297 44.000 0.00 0.00 0.00 5.80
78 79 5.369404 TCACTTGAATATAGAATCTGGGCCA 59.631 40.000 5.85 5.85 0.00 5.36
79 80 5.704515 CACTTGAATATAGAATCTGGGCCAG 59.295 44.000 28.01 28.01 0.00 4.85
80 81 5.370880 ACTTGAATATAGAATCTGGGCCAGT 59.629 40.000 31.60 15.22 32.61 4.00
81 82 5.489792 TGAATATAGAATCTGGGCCAGTC 57.510 43.478 31.60 22.74 32.61 3.51
82 83 4.907269 TGAATATAGAATCTGGGCCAGTCA 59.093 41.667 31.60 21.09 32.61 3.41
83 84 5.369404 TGAATATAGAATCTGGGCCAGTCAA 59.631 40.000 31.60 14.73 32.61 3.18
84 85 6.044754 TGAATATAGAATCTGGGCCAGTCAAT 59.955 38.462 31.60 16.44 32.61 2.57
85 86 4.803329 ATAGAATCTGGGCCAGTCAATT 57.197 40.909 31.60 23.49 32.61 2.32
86 87 3.463048 AGAATCTGGGCCAGTCAATTT 57.537 42.857 31.60 18.02 32.61 1.82
87 88 3.782992 AGAATCTGGGCCAGTCAATTTT 58.217 40.909 31.60 16.85 32.61 1.82
88 89 3.766051 AGAATCTGGGCCAGTCAATTTTC 59.234 43.478 31.60 22.27 32.61 2.29
89 90 2.673775 TCTGGGCCAGTCAATTTTCA 57.326 45.000 31.60 7.59 32.61 2.69
90 91 2.238521 TCTGGGCCAGTCAATTTTCAC 58.761 47.619 31.60 0.00 32.61 3.18
91 92 0.958091 TGGGCCAGTCAATTTTCACG 59.042 50.000 0.00 0.00 0.00 4.35
92 93 0.958822 GGGCCAGTCAATTTTCACGT 59.041 50.000 4.39 0.00 0.00 4.49
93 94 1.335872 GGGCCAGTCAATTTTCACGTG 60.336 52.381 9.94 9.94 0.00 4.49
94 95 1.606668 GGCCAGTCAATTTTCACGTGA 59.393 47.619 15.76 15.76 0.00 4.35
95 96 2.034053 GGCCAGTCAATTTTCACGTGAA 59.966 45.455 26.53 26.53 0.00 3.18
96 97 3.300009 GCCAGTCAATTTTCACGTGAAG 58.700 45.455 28.21 18.08 35.21 3.02
97 98 3.853307 GCCAGTCAATTTTCACGTGAAGG 60.853 47.826 28.21 23.22 35.21 3.46
98 99 3.563808 CCAGTCAATTTTCACGTGAAGGA 59.436 43.478 28.21 21.48 35.21 3.36
99 100 4.036262 CCAGTCAATTTTCACGTGAAGGAA 59.964 41.667 28.21 21.64 35.21 3.36
100 101 5.207768 CAGTCAATTTTCACGTGAAGGAAG 58.792 41.667 28.21 19.83 35.21 3.46
101 102 4.275936 AGTCAATTTTCACGTGAAGGAAGG 59.724 41.667 28.21 18.35 35.21 3.46
102 103 4.274950 GTCAATTTTCACGTGAAGGAAGGA 59.725 41.667 28.21 20.02 35.21 3.36
103 104 5.048713 GTCAATTTTCACGTGAAGGAAGGAT 60.049 40.000 28.21 14.66 35.21 3.24
104 105 5.534654 TCAATTTTCACGTGAAGGAAGGATT 59.465 36.000 28.21 18.58 35.21 3.01
105 106 6.712998 TCAATTTTCACGTGAAGGAAGGATTA 59.287 34.615 28.21 10.00 35.21 1.75
106 107 6.743575 ATTTTCACGTGAAGGAAGGATTAG 57.256 37.500 28.21 0.00 35.21 1.73
107 108 3.247006 TCACGTGAAGGAAGGATTAGC 57.753 47.619 17.62 0.00 0.00 3.09
108 109 2.093658 TCACGTGAAGGAAGGATTAGCC 60.094 50.000 17.62 0.00 0.00 3.93
109 110 1.134788 ACGTGAAGGAAGGATTAGCCG 60.135 52.381 0.00 0.00 43.43 5.52
110 111 1.806623 CGTGAAGGAAGGATTAGCCGG 60.807 57.143 0.00 0.00 43.43 6.13
111 112 1.485066 GTGAAGGAAGGATTAGCCGGA 59.515 52.381 5.05 0.00 43.43 5.14
112 113 1.762957 TGAAGGAAGGATTAGCCGGAG 59.237 52.381 5.05 0.00 43.43 4.63
113 114 1.763545 GAAGGAAGGATTAGCCGGAGT 59.236 52.381 5.05 0.00 43.43 3.85
114 115 1.123928 AGGAAGGATTAGCCGGAGTG 58.876 55.000 5.05 0.00 43.43 3.51
115 116 1.120530 GGAAGGATTAGCCGGAGTGA 58.879 55.000 5.05 0.00 43.43 3.41
125 126 1.021920 GCCGGAGTGAAGGAAGAAGC 61.022 60.000 5.05 0.00 0.00 3.86
150 151 1.681486 GGAGGGAAGGAAGGAGCTCG 61.681 65.000 7.83 0.00 0.00 5.03
151 152 2.188207 GGGAAGGAAGGAGCTCGC 59.812 66.667 7.83 0.47 0.00 5.03
178 179 5.071370 CGACCCCACTATCTATCTTACTGT 58.929 45.833 0.00 0.00 0.00 3.55
179 180 5.048643 CGACCCCACTATCTATCTTACTGTG 60.049 48.000 0.00 0.00 0.00 3.66
180 181 5.148502 ACCCCACTATCTATCTTACTGTGG 58.851 45.833 0.00 0.00 41.99 4.17
181 182 4.021016 CCCCACTATCTATCTTACTGTGGC 60.021 50.000 0.00 0.00 41.27 5.01
182 183 4.588951 CCCACTATCTATCTTACTGTGGCA 59.411 45.833 0.00 0.00 41.27 4.92
183 184 5.279206 CCCACTATCTATCTTACTGTGGCAG 60.279 48.000 0.00 0.00 41.27 4.85
184 185 5.279206 CCACTATCTATCTTACTGTGGCAGG 60.279 48.000 0.00 0.00 37.31 4.85
185 186 4.835615 ACTATCTATCTTACTGTGGCAGGG 59.164 45.833 0.00 0.00 35.51 4.45
186 187 2.398588 TCTATCTTACTGTGGCAGGGG 58.601 52.381 0.00 0.00 35.51 4.79
190 191 2.521958 CTTACTGTGGCAGGGGGACG 62.522 65.000 0.00 0.00 35.51 4.79
210 211 4.426704 ACGCCCATTATCTATCTTAGGGT 58.573 43.478 0.00 0.00 37.16 4.34
211 212 4.759782 CGCCCATTATCTATCTTAGGGTG 58.240 47.826 0.00 0.00 38.77 4.61
212 213 4.223032 CGCCCATTATCTATCTTAGGGTGT 59.777 45.833 0.00 0.00 39.77 4.16
232 235 2.890474 GGTGGTGCAGTATCGCCG 60.890 66.667 0.00 0.00 39.42 6.46
263 266 2.912542 CATCGCCGGGGCTAGAGA 60.913 66.667 14.85 0.00 39.32 3.10
275 278 1.479368 GCTAGAGAGATGGCTGGGGG 61.479 65.000 0.00 0.00 0.00 5.40
276 279 0.105246 CTAGAGAGATGGCTGGGGGT 60.105 60.000 0.00 0.00 0.00 4.95
278 281 2.693864 AGAGATGGCTGGGGGTGG 60.694 66.667 0.00 0.00 0.00 4.61
279 282 4.512914 GAGATGGCTGGGGGTGGC 62.513 72.222 0.00 0.00 0.00 5.01
316 319 3.787001 GAGGTTGAGGGGAGGGCG 61.787 72.222 0.00 0.00 0.00 6.13
453 456 6.258230 TGAAGAAGCAATCTAAACCACATG 57.742 37.500 0.00 0.00 37.42 3.21
487 490 2.066262 GGCTGAAACGAAATCGACTGA 58.934 47.619 10.16 0.00 43.02 3.41
569 2644 6.723977 TCAACTTTTGATGCCCTAAAATAGGT 59.276 34.615 2.93 0.00 38.34 3.08
613 2688 1.214367 CGGTCCCGGAAAATACATCG 58.786 55.000 0.73 0.00 35.56 3.84
624 2699 5.329493 GGAAAATACATCGAAGGGAAAACG 58.671 41.667 0.00 0.00 0.00 3.60
676 2751 3.126225 GCGAGACGAGACGACCCT 61.126 66.667 0.00 0.00 0.00 4.34
718 2793 1.265635 TCGTGCAACCGAAAGATTTGG 59.734 47.619 0.00 0.00 33.15 3.28
719 2794 1.418373 GTGCAACCGAAAGATTTGGC 58.582 50.000 0.00 0.00 0.00 4.52
720 2795 0.316841 TGCAACCGAAAGATTTGGCC 59.683 50.000 0.00 0.00 0.00 5.36
751 2829 1.026182 TCGTGGTAGTACCGACGCAT 61.026 55.000 26.27 0.00 42.58 4.73
824 2938 3.737172 CGAAGTTTGGCTGGCCGG 61.737 66.667 7.41 7.41 39.42 6.13
825 2939 4.056125 GAAGTTTGGCTGGCCGGC 62.056 66.667 29.49 29.49 39.42 6.13
888 3002 1.090625 CATGTCTGCTGCTCTGCTCC 61.091 60.000 0.00 0.00 0.00 4.70
948 3062 2.917227 CCCCGCCCCAATAATGGC 60.917 66.667 0.00 0.00 46.09 4.40
1018 3144 2.414785 CCATTTAAGCGCGGCCCTT 61.415 57.895 8.83 5.37 0.00 3.95
1045 3171 0.400594 ACCCACGCTTTAAGCTTCCT 59.599 50.000 15.29 0.00 39.60 3.36
1047 3173 1.087501 CCACGCTTTAAGCTTCCTCC 58.912 55.000 15.29 0.00 39.60 4.30
1049 3175 0.984995 ACGCTTTAAGCTTCCTCCCT 59.015 50.000 15.29 0.00 39.60 4.20
1051 3177 1.744114 CGCTTTAAGCTTCCTCCCTCC 60.744 57.143 15.29 0.00 39.60 4.30
1347 3473 2.967076 CACCAACGCTGCGACAGT 60.967 61.111 30.47 18.21 33.43 3.55
1437 3563 3.969802 GCCGTGTGCTGCTGCTTT 61.970 61.111 17.00 0.00 40.48 3.51
1680 3806 0.178958 AGAAGGAGGTGTGGTCGAGT 60.179 55.000 0.00 0.00 0.00 4.18
1815 3941 3.247006 TCTTGATTCTTGCTCGGGTAC 57.753 47.619 0.00 0.00 0.00 3.34
1816 3942 1.927174 CTTGATTCTTGCTCGGGTACG 59.073 52.381 0.00 0.00 42.74 3.67
1817 3943 0.892755 TGATTCTTGCTCGGGTACGT 59.107 50.000 0.00 0.00 41.85 3.57
1818 3944 2.093890 TGATTCTTGCTCGGGTACGTA 58.906 47.619 0.00 0.00 41.85 3.57
1965 4092 3.504906 TCTTGTTGGTGTACGTCCTCTAG 59.495 47.826 0.00 7.59 0.00 2.43
1980 4107 5.423886 GTCCTCTAGAAGGGAAATGAACAG 58.576 45.833 2.39 0.00 46.23 3.16
1995 4122 7.201875 GGAAATGAACAGTTCCCTTCTTTGTTA 60.202 37.037 19.16 0.00 46.57 2.41
2106 4235 1.781555 GACGGACACAAGCACATCG 59.218 57.895 0.00 0.00 0.00 3.84
2172 4301 2.483106 GACCTTAACAACTTCTTCGCCC 59.517 50.000 0.00 0.00 0.00 6.13
2191 4320 4.440525 CGCCCATAAAGCATTTGATGAGTT 60.441 41.667 0.00 0.00 39.63 3.01
2210 4339 9.224058 GATGAGTTTTCGTGAGACTAGTATTAC 57.776 37.037 2.47 2.47 41.84 1.89
2212 4341 8.449397 TGAGTTTTCGTGAGACTAGTATTACTC 58.551 37.037 10.28 6.61 41.84 2.59
2219 4348 8.923683 TCGTGAGACTAGTATTACTCATATTCG 58.076 37.037 13.38 12.04 40.61 3.34
2220 4349 7.688989 CGTGAGACTAGTATTACTCATATTCGC 59.311 40.741 13.38 1.89 40.61 4.70
2224 4353 6.622549 ACTAGTATTACTCATATTCGCAGGC 58.377 40.000 0.00 0.00 0.00 4.85
2226 4355 3.769739 ATTACTCATATTCGCAGGCCA 57.230 42.857 5.01 0.00 0.00 5.36
2263 4393 4.632688 GCAATTGTTTGGCTATCTTTGCAT 59.367 37.500 7.40 0.00 38.40 3.96
2279 4409 3.517296 TGCATGGGTGAAAGGTAGAAA 57.483 42.857 0.00 0.00 0.00 2.52
2282 4412 5.192927 TGCATGGGTGAAAGGTAGAAATAG 58.807 41.667 0.00 0.00 0.00 1.73
2300 4431 7.466804 AGAAATAGGACATGGTTAGGTTTTGA 58.533 34.615 0.00 0.00 0.00 2.69
2312 4443 6.045106 TGGTTAGGTTTTGATCCTCCTAAAGT 59.955 38.462 12.99 0.00 41.96 2.66
2322 4453 2.303022 TCCTCCTAAAGTTGTGGAGCTG 59.697 50.000 15.33 6.62 44.32 4.24
2348 4479 6.649973 GCTAGCTCTGATTGTAATCATGATGT 59.350 38.462 9.46 2.46 43.87 3.06
2366 4497 8.729756 TCATGATGTGGTTTGAGTAATACAAAG 58.270 33.333 0.00 0.00 37.80 2.77
2454 4585 1.726865 TTGCGTGACAAGCCAACTG 59.273 52.632 10.95 0.00 33.24 3.16
2491 4622 9.875708 ATCTCTAAGAGTCAATCTATACAAGGT 57.124 33.333 0.00 0.00 37.23 3.50
2551 4695 1.065410 TGTCATGGTCAACACCCCCT 61.065 55.000 0.00 0.00 42.99 4.79
2592 4755 1.098050 GGCGATGCAAAGACTGGAAT 58.902 50.000 0.00 0.00 0.00 3.01
2650 4814 4.518970 AGTCATAATGTCGGCAAACTGTTT 59.481 37.500 0.00 0.00 0.00 2.83
2655 4819 2.366533 TGTCGGCAAACTGTTTGGTAA 58.633 42.857 28.61 8.42 40.94 2.85
2667 4831 9.804324 CAAACTGTTTGGTAATCGGTACGTGAC 62.804 44.444 22.38 0.00 44.56 3.67
2710 4874 0.106149 ACCTTCTCGCGGACAAAGTT 59.894 50.000 6.13 0.00 0.00 2.66
2752 4919 1.669437 TGCGCTTATGTTGCACCGA 60.669 52.632 9.73 0.00 32.86 4.69
2771 4938 0.180406 AATTGGCCGCGAGATAGGTT 59.820 50.000 8.23 0.00 0.00 3.50
2889 5056 2.559840 CGACAGTGCGGTACTCGT 59.440 61.111 0.00 0.00 37.60 4.18
2965 5133 0.733223 GAGTCGCCGAAGAAGACACC 60.733 60.000 0.00 0.00 36.50 4.16
2997 5165 0.749649 GGATCAGCGAGTGTCAGGAT 59.250 55.000 0.00 0.00 0.00 3.24
3025 5193 1.134401 CCAATCTGCATCCGTGTAGGT 60.134 52.381 0.00 0.00 41.99 3.08
3034 5202 1.629043 TCCGTGTAGGTGAGAAGCTT 58.371 50.000 0.00 0.00 41.99 3.74
3068 5236 0.955178 CGCAGAGACGGAGACCATAT 59.045 55.000 0.00 0.00 0.00 1.78
3171 5339 0.040157 TTGCTGCATCGCAAACTGAC 60.040 50.000 10.65 0.00 46.00 3.51
3184 5352 1.051812 AACTGACTGTCTGGTCTGGG 58.948 55.000 17.32 0.00 38.76 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.834549 TGAAAACTGGTTTCTTTGGGCA 59.165 40.909 18.15 0.00 45.14 5.36
1 2 3.535280 TGAAAACTGGTTTCTTTGGGC 57.465 42.857 18.15 0.00 45.14 5.36
2 3 3.809279 GCATGAAAACTGGTTTCTTTGGG 59.191 43.478 18.15 3.31 45.14 4.12
3 4 3.809279 GGCATGAAAACTGGTTTCTTTGG 59.191 43.478 18.15 7.05 45.14 3.28
4 5 4.696455 AGGCATGAAAACTGGTTTCTTTG 58.304 39.130 18.15 15.62 45.14 2.77
5 6 6.670695 ATAGGCATGAAAACTGGTTTCTTT 57.329 33.333 18.15 4.36 45.14 2.52
6 7 6.670695 AATAGGCATGAAAACTGGTTTCTT 57.329 33.333 18.15 9.91 45.14 2.52
7 8 6.670695 AAATAGGCATGAAAACTGGTTTCT 57.329 33.333 18.15 1.39 45.14 2.52
8 9 7.728847 AAAAATAGGCATGAAAACTGGTTTC 57.271 32.000 11.18 11.18 45.13 2.78
36 37 9.502091 TTCAAGTGACTTACATTTAGCTATTGT 57.498 29.630 12.80 12.80 0.00 2.71
49 50 9.482627 CCCAGATTCTATATTCAAGTGACTTAC 57.517 37.037 0.00 0.00 0.00 2.34
50 51 8.150945 GCCCAGATTCTATATTCAAGTGACTTA 58.849 37.037 0.00 0.00 0.00 2.24
51 52 6.995091 GCCCAGATTCTATATTCAAGTGACTT 59.005 38.462 0.00 0.00 0.00 3.01
52 53 6.465035 GGCCCAGATTCTATATTCAAGTGACT 60.465 42.308 0.00 0.00 0.00 3.41
53 54 5.703130 GGCCCAGATTCTATATTCAAGTGAC 59.297 44.000 0.00 0.00 0.00 3.67
54 55 5.369404 TGGCCCAGATTCTATATTCAAGTGA 59.631 40.000 0.00 0.00 0.00 3.41
55 56 5.624159 TGGCCCAGATTCTATATTCAAGTG 58.376 41.667 0.00 0.00 0.00 3.16
56 57 5.370880 ACTGGCCCAGATTCTATATTCAAGT 59.629 40.000 19.90 0.00 35.18 3.16
57 58 5.874093 ACTGGCCCAGATTCTATATTCAAG 58.126 41.667 19.90 0.00 35.18 3.02
58 59 5.369404 TGACTGGCCCAGATTCTATATTCAA 59.631 40.000 19.90 0.00 35.18 2.69
59 60 4.907269 TGACTGGCCCAGATTCTATATTCA 59.093 41.667 19.90 4.14 35.18 2.57
60 61 5.489792 TGACTGGCCCAGATTCTATATTC 57.510 43.478 19.90 1.15 35.18 1.75
61 62 5.912149 TTGACTGGCCCAGATTCTATATT 57.088 39.130 19.90 0.00 35.18 1.28
62 63 6.460103 AATTGACTGGCCCAGATTCTATAT 57.540 37.500 19.90 0.00 35.18 0.86
63 64 5.912149 AATTGACTGGCCCAGATTCTATA 57.088 39.130 19.90 0.00 35.18 1.31
64 65 4.803329 AATTGACTGGCCCAGATTCTAT 57.197 40.909 19.90 5.11 35.18 1.98
65 66 4.591321 AAATTGACTGGCCCAGATTCTA 57.409 40.909 19.90 2.61 35.18 2.10
66 67 3.463048 AAATTGACTGGCCCAGATTCT 57.537 42.857 19.90 0.00 35.18 2.40
67 68 3.511146 TGAAAATTGACTGGCCCAGATTC 59.489 43.478 19.90 6.03 35.18 2.52
68 69 3.259123 GTGAAAATTGACTGGCCCAGATT 59.741 43.478 19.90 3.83 35.18 2.40
69 70 2.827921 GTGAAAATTGACTGGCCCAGAT 59.172 45.455 19.90 0.96 35.18 2.90
70 71 2.238521 GTGAAAATTGACTGGCCCAGA 58.761 47.619 19.90 0.00 35.18 3.86
71 72 1.068333 CGTGAAAATTGACTGGCCCAG 60.068 52.381 9.83 9.83 37.52 4.45
72 73 0.958091 CGTGAAAATTGACTGGCCCA 59.042 50.000 0.00 0.00 0.00 5.36
73 74 0.958822 ACGTGAAAATTGACTGGCCC 59.041 50.000 0.00 0.00 0.00 5.80
74 75 1.606668 TCACGTGAAAATTGACTGGCC 59.393 47.619 17.62 0.00 0.00 5.36
75 76 3.300009 CTTCACGTGAAAATTGACTGGC 58.700 45.455 29.32 0.00 33.07 4.85
76 77 3.563808 TCCTTCACGTGAAAATTGACTGG 59.436 43.478 29.32 23.12 33.07 4.00
77 78 4.811555 TCCTTCACGTGAAAATTGACTG 57.188 40.909 29.32 15.94 33.07 3.51
78 79 4.275936 CCTTCCTTCACGTGAAAATTGACT 59.724 41.667 29.32 0.00 33.07 3.41
79 80 4.274950 TCCTTCCTTCACGTGAAAATTGAC 59.725 41.667 29.32 0.00 33.07 3.18
80 81 4.456535 TCCTTCCTTCACGTGAAAATTGA 58.543 39.130 29.32 19.97 33.07 2.57
81 82 4.829064 TCCTTCCTTCACGTGAAAATTG 57.171 40.909 29.32 18.29 33.07 2.32
82 83 6.349363 GCTAATCCTTCCTTCACGTGAAAATT 60.349 38.462 29.32 21.17 33.07 1.82
83 84 5.123979 GCTAATCCTTCCTTCACGTGAAAAT 59.876 40.000 29.32 11.17 33.07 1.82
84 85 4.454504 GCTAATCCTTCCTTCACGTGAAAA 59.545 41.667 29.32 20.81 33.07 2.29
85 86 4.000988 GCTAATCCTTCCTTCACGTGAAA 58.999 43.478 29.32 14.99 33.07 2.69
86 87 3.596214 GCTAATCCTTCCTTCACGTGAA 58.404 45.455 28.07 28.07 0.00 3.18
87 88 2.093658 GGCTAATCCTTCCTTCACGTGA 60.094 50.000 15.76 15.76 0.00 4.35
88 89 2.280628 GGCTAATCCTTCCTTCACGTG 58.719 52.381 9.94 9.94 0.00 4.49
89 90 1.134788 CGGCTAATCCTTCCTTCACGT 60.135 52.381 0.00 0.00 0.00 4.49
90 91 1.571919 CGGCTAATCCTTCCTTCACG 58.428 55.000 0.00 0.00 0.00 4.35
91 92 1.485066 TCCGGCTAATCCTTCCTTCAC 59.515 52.381 0.00 0.00 0.00 3.18
92 93 1.762957 CTCCGGCTAATCCTTCCTTCA 59.237 52.381 0.00 0.00 0.00 3.02
93 94 1.763545 ACTCCGGCTAATCCTTCCTTC 59.236 52.381 0.00 0.00 0.00 3.46
94 95 1.486726 CACTCCGGCTAATCCTTCCTT 59.513 52.381 0.00 0.00 0.00 3.36
95 96 1.123928 CACTCCGGCTAATCCTTCCT 58.876 55.000 0.00 0.00 0.00 3.36
96 97 1.120530 TCACTCCGGCTAATCCTTCC 58.879 55.000 0.00 0.00 0.00 3.46
97 98 2.483889 CCTTCACTCCGGCTAATCCTTC 60.484 54.545 0.00 0.00 0.00 3.46
98 99 1.486726 CCTTCACTCCGGCTAATCCTT 59.513 52.381 0.00 0.00 0.00 3.36
99 100 1.123928 CCTTCACTCCGGCTAATCCT 58.876 55.000 0.00 0.00 0.00 3.24
100 101 1.120530 TCCTTCACTCCGGCTAATCC 58.879 55.000 0.00 0.00 0.00 3.01
101 102 2.431057 TCTTCCTTCACTCCGGCTAATC 59.569 50.000 0.00 0.00 0.00 1.75
102 103 2.467880 TCTTCCTTCACTCCGGCTAAT 58.532 47.619 0.00 0.00 0.00 1.73
103 104 1.933021 TCTTCCTTCACTCCGGCTAA 58.067 50.000 0.00 0.00 0.00 3.09
104 105 1.825474 CTTCTTCCTTCACTCCGGCTA 59.175 52.381 0.00 0.00 0.00 3.93
105 106 0.610687 CTTCTTCCTTCACTCCGGCT 59.389 55.000 0.00 0.00 0.00 5.52
106 107 1.021920 GCTTCTTCCTTCACTCCGGC 61.022 60.000 0.00 0.00 0.00 6.13
107 108 0.610687 AGCTTCTTCCTTCACTCCGG 59.389 55.000 0.00 0.00 0.00 5.14
108 109 1.734047 CGAGCTTCTTCCTTCACTCCG 60.734 57.143 0.00 0.00 0.00 4.63
109 110 2.003196 CGAGCTTCTTCCTTCACTCC 57.997 55.000 0.00 0.00 0.00 3.85
110 111 1.355005 GCGAGCTTCTTCCTTCACTC 58.645 55.000 0.00 0.00 0.00 3.51
111 112 0.036858 GGCGAGCTTCTTCCTTCACT 60.037 55.000 0.00 0.00 0.00 3.41
112 113 1.355066 CGGCGAGCTTCTTCCTTCAC 61.355 60.000 0.00 0.00 0.00 3.18
113 114 1.079819 CGGCGAGCTTCTTCCTTCA 60.080 57.895 0.00 0.00 0.00 3.02
114 115 1.811679 CCGGCGAGCTTCTTCCTTC 60.812 63.158 9.30 0.00 0.00 3.46
115 116 2.232298 CTCCGGCGAGCTTCTTCCTT 62.232 60.000 9.30 0.00 0.00 3.36
125 126 3.075005 TTCCTTCCCTCCGGCGAG 61.075 66.667 9.30 3.68 35.72 5.03
150 151 4.603946 GATAGTGGGGTCGCCGGC 62.604 72.222 19.07 19.07 0.00 6.13
151 152 0.898789 ATAGATAGTGGGGTCGCCGG 60.899 60.000 0.00 0.00 0.00 6.13
185 186 3.983044 AAGATAGATAATGGGCGTCCC 57.017 47.619 2.12 5.67 45.71 4.46
186 187 4.141914 CCCTAAGATAGATAATGGGCGTCC 60.142 50.000 0.00 0.00 0.00 4.79
190 191 5.491982 CACACCCTAAGATAGATAATGGGC 58.508 45.833 0.00 0.00 36.78 5.36
210 211 1.682849 GATACTGCACCACCCCACA 59.317 57.895 0.00 0.00 0.00 4.17
211 212 1.449601 CGATACTGCACCACCCCAC 60.450 63.158 0.00 0.00 0.00 4.61
212 213 2.986290 CGATACTGCACCACCCCA 59.014 61.111 0.00 0.00 0.00 4.96
251 254 2.578714 GCCATCTCTCTAGCCCCGG 61.579 68.421 0.00 0.00 0.00 5.73
252 255 1.532794 AGCCATCTCTCTAGCCCCG 60.533 63.158 0.00 0.00 0.00 5.73
275 278 2.260869 ACCATTGTGCTGTCGCCAC 61.261 57.895 0.00 0.00 34.43 5.01
276 279 2.112928 ACCATTGTGCTGTCGCCA 59.887 55.556 0.00 0.00 34.43 5.69
278 281 2.562912 CCACCATTGTGCTGTCGC 59.437 61.111 0.00 0.00 41.35 5.19
279 282 1.300971 CTCCCACCATTGTGCTGTCG 61.301 60.000 0.00 0.00 41.35 4.35
281 284 1.075482 CCTCCCACCATTGTGCTGT 59.925 57.895 0.00 0.00 41.35 4.40
282 285 0.679002 CTCCTCCCACCATTGTGCTG 60.679 60.000 0.00 0.00 41.35 4.41
284 287 1.379044 CCTCCTCCCACCATTGTGC 60.379 63.158 0.00 0.00 41.35 4.57
285 288 0.405585 AACCTCCTCCCACCATTGTG 59.594 55.000 0.00 0.00 42.39 3.33
286 289 0.405585 CAACCTCCTCCCACCATTGT 59.594 55.000 0.00 0.00 0.00 2.71
287 290 0.698238 TCAACCTCCTCCCACCATTG 59.302 55.000 0.00 0.00 0.00 2.82
288 291 0.995024 CTCAACCTCCTCCCACCATT 59.005 55.000 0.00 0.00 0.00 3.16
289 292 0.916358 CCTCAACCTCCTCCCACCAT 60.916 60.000 0.00 0.00 0.00 3.55
382 385 1.897615 CCCCAACCGCCAAACGTAA 60.898 57.895 0.00 0.00 41.42 3.18
453 456 1.243902 TCAGCCGTTGGATGGAAAAC 58.756 50.000 0.72 0.00 39.86 2.43
502 506 2.289444 TGGCTAGTGGTAAGTTGACTGC 60.289 50.000 0.00 0.00 0.00 4.40
569 2644 0.689055 AGAGCATGTCCAACAGCTGA 59.311 50.000 23.35 0.00 34.43 4.26
613 2688 2.144482 TCTCGTGTCGTTTTCCCTTC 57.856 50.000 0.00 0.00 0.00 3.46
624 2699 0.731514 TTGCGTCCGATTCTCGTGTC 60.732 55.000 0.00 0.00 38.40 3.67
674 2749 3.190849 CTCCGTGTCGCATGCAGG 61.191 66.667 19.57 12.10 0.00 4.85
676 2751 3.529341 AACCTCCGTGTCGCATGCA 62.529 57.895 19.57 1.73 0.00 3.96
751 2829 3.411446 ACACTGTTTGCTTGCTATGCTA 58.589 40.909 0.00 0.00 0.00 3.49
825 2939 3.702048 TTTCGTGGGAGGAGCCGG 61.702 66.667 0.00 0.00 37.63 6.13
826 2940 2.434359 GTTTCGTGGGAGGAGCCG 60.434 66.667 0.00 0.00 37.63 5.52
827 2941 2.434359 CGTTTCGTGGGAGGAGCC 60.434 66.667 0.00 0.00 0.00 4.70
1018 3144 0.687920 TAAAGCGTGGGTGGATGACA 59.312 50.000 0.00 0.00 0.00 3.58
1047 3173 3.536917 TATGTGCGCTCGGGGAGG 61.537 66.667 9.73 0.00 0.00 4.30
1049 3175 1.454295 TAGTATGTGCGCTCGGGGA 60.454 57.895 9.73 0.00 0.00 4.81
1051 3177 0.102481 AAGTAGTATGTGCGCTCGGG 59.898 55.000 9.73 0.00 0.00 5.14
1062 3188 1.202498 GCCCGCCGAAGAAAGTAGTAT 60.202 52.381 0.00 0.00 0.00 2.12
1437 3563 2.606213 TCCACCATGACGCAGGGA 60.606 61.111 15.63 3.75 37.52 4.20
1549 3675 1.214589 GCTCGTACATGTCCACGGT 59.785 57.895 18.40 0.00 38.66 4.83
1551 3677 1.413767 GCAGCTCGTACATGTCCACG 61.414 60.000 13.74 13.74 39.48 4.94
1645 3771 0.905809 TTCTCCATTTCCCCCGACGA 60.906 55.000 0.00 0.00 0.00 4.20
1646 3772 0.462047 CTTCTCCATTTCCCCCGACG 60.462 60.000 0.00 0.00 0.00 5.12
1648 3774 0.252974 TCCTTCTCCATTTCCCCCGA 60.253 55.000 0.00 0.00 0.00 5.14
1680 3806 4.382320 AAGCCGGCGCCGTAGAAA 62.382 61.111 43.12 0.00 37.81 2.52
1815 3941 1.730612 GGAAAACGAAGGAAGCCTACG 59.269 52.381 0.00 0.00 31.13 3.51
1816 3942 3.001414 GAGGAAAACGAAGGAAGCCTAC 58.999 50.000 0.00 0.00 31.13 3.18
1817 3943 2.353406 CGAGGAAAACGAAGGAAGCCTA 60.353 50.000 0.00 0.00 31.13 3.93
1818 3944 1.608283 CGAGGAAAACGAAGGAAGCCT 60.608 52.381 0.00 0.00 33.87 4.58
2106 4235 4.439057 TCCCAACGTAAATCTCTGTATGC 58.561 43.478 0.00 0.00 0.00 3.14
2172 4301 7.538334 TCACGAAAACTCATCAAATGCTTTATG 59.462 33.333 0.00 0.00 0.00 1.90
2210 4339 5.633830 ATTTTATGGCCTGCGAATATGAG 57.366 39.130 3.32 0.00 0.00 2.90
2212 4341 7.370383 ACTTTATTTTATGGCCTGCGAATATG 58.630 34.615 3.32 3.66 0.00 1.78
2219 4348 5.901552 TGCTAACTTTATTTTATGGCCTGC 58.098 37.500 3.32 0.00 0.00 4.85
2220 4349 8.819974 CAATTGCTAACTTTATTTTATGGCCTG 58.180 33.333 3.32 0.00 0.00 4.85
2263 4393 4.847512 TGTCCTATTTCTACCTTTCACCCA 59.152 41.667 0.00 0.00 0.00 4.51
2279 4409 6.160459 AGGATCAAAACCTAACCATGTCCTAT 59.840 38.462 0.00 0.00 35.84 2.57
2282 4412 4.600062 AGGATCAAAACCTAACCATGTCC 58.400 43.478 0.00 0.00 35.84 4.02
2454 4585 6.544650 TGACTCTTAGAGATATGGTAGGGTC 58.455 44.000 16.95 0.00 34.49 4.46
2516 4660 9.539194 TGACCATGACATATCTGTATCTATCTT 57.461 33.333 0.00 0.00 35.14 2.40
2558 4711 3.512516 GCCGATGCTTGGACTGCC 61.513 66.667 0.00 0.00 33.53 4.85
2592 4755 1.067295 ACTGCATTCCAGGAGTTCCA 58.933 50.000 0.28 0.00 46.14 3.53
2650 4814 1.447945 TCGTCACGTACCGATTACCA 58.552 50.000 0.00 0.00 0.00 3.25
2655 4819 3.389741 GTGTTCGTCACGTACCGAT 57.610 52.632 4.36 0.00 37.31 4.18
2667 4831 1.284982 CTGGGTCAGCTTCGTGTTCG 61.285 60.000 0.00 0.00 38.55 3.95
2710 4874 7.625395 GCACCAAACATATTGAACTCGATGTTA 60.625 37.037 0.00 0.00 40.68 2.41
2752 4919 0.180406 AACCTATCTCGCGGCCAATT 59.820 50.000 6.13 0.00 0.00 2.32
2771 4938 5.457140 GTTTTCTGTGATAATGTTTCGGCA 58.543 37.500 0.00 0.00 0.00 5.69
2841 5008 1.078567 CTGAGACCTCTTGGCTGCC 60.079 63.158 12.87 12.87 36.63 4.85
2870 5037 2.567049 GAGTACCGCACTGTCGCT 59.433 61.111 0.00 0.00 37.72 4.93
2878 5045 2.697761 GCTGAGGACGAGTACCGCA 61.698 63.158 0.00 0.00 43.32 5.69
2889 5056 3.443925 CCGCTCGAGTGCTGAGGA 61.444 66.667 20.61 0.00 33.99 3.71
2965 5133 0.319040 CTGATCCACATCGGGCTACG 60.319 60.000 0.00 0.00 46.11 3.51
2997 5165 1.349026 GGATGCAGATTGGGCTAGCTA 59.651 52.381 15.72 0.96 0.00 3.32
3025 5193 1.376466 GCCTCCACCAAGCTTCTCA 59.624 57.895 0.00 0.00 0.00 3.27
3052 5220 2.222886 CGACATATGGTCTCCGTCTCT 58.777 52.381 7.80 0.00 44.68 3.10
3171 5339 2.985456 GCTCCCCAGACCAGACAG 59.015 66.667 0.00 0.00 0.00 3.51
3184 5352 1.798079 CGCTTCAGTACCTTACGCTCC 60.798 57.143 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.