Multiple sequence alignment - TraesCS5B01G083000

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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 TraesCS5B01G083000 chr5B 100.000 5311 0 0 1 5311 103568714 103574024 0.000000e+00 9808
1 TraesCS5B01G083000 chr5B 94.074 2548 98 25 787 3318 105767788 105770298 0.000000e+00 3819
2 TraesCS5B01G083000 chr5B 97.149 947 23 4 4364 5309 105771341 105772284 0.000000e+00 1596
3 TraesCS5B01G083000 chr5B 98.354 790 11 2 1 788 52919368 52920157 0.000000e+00 1386
4 TraesCS5B01G083000 chr5B 80.710 902 127 37 3457 4335 105712739 105713616 0.000000e+00 658
5 TraesCS5B01G083000 chr5B 95.990 399 13 2 3425 3823 105770328 105770723 0.000000e+00 645
6 TraesCS5B01G083000 chr5B 97.721 351 7 1 3954 4304 105770731 105771080 2.120000e-168 603
7 TraesCS5B01G083000 chr5B 83.759 431 63 5 2883 3307 105712250 105712679 8.280000e-108 401
8 TraesCS5B01G083000 chr5B 86.141 368 46 5 3457 3822 103473460 103473824 4.990000e-105 392
9 TraesCS5B01G083000 chr5B 82.022 356 53 10 2483 2834 105711816 105712164 5.200000e-75 292
10 TraesCS5B01G083000 chr5B 76.234 547 103 22 1507 2043 103471579 103472108 1.130000e-66 265
11 TraesCS5B01G083000 chr5B 75.956 549 100 27 1507 2043 105710864 105711392 2.450000e-63 254
12 TraesCS5B01G083000 chr5B 85.629 167 21 3 2193 2357 103472239 103472404 7.070000e-39 172
13 TraesCS5B01G083000 chr5B 97.753 89 2 0 3341 3429 559465933 559465845 2.560000e-33 154
14 TraesCS5B01G083000 chr5D 93.586 2588 91 33 787 3343 97323073 97325616 0.000000e+00 3790
15 TraesCS5B01G083000 chr5D 96.041 884 34 1 3424 4307 97325614 97326496 0.000000e+00 1437
16 TraesCS5B01G083000 chr5D 96.526 806 25 3 4506 5311 97327471 97328273 0.000000e+00 1330
17 TraesCS5B01G083000 chr5D 86.059 373 47 5 3457 3827 97277714 97278083 3.850000e-106 396
18 TraesCS5B01G083000 chr5D 83.372 433 61 9 2883 3307 97277225 97277654 1.790000e-104 390
19 TraesCS5B01G083000 chr5D 96.835 158 5 0 4353 4510 97326945 97327102 1.130000e-66 265
20 TraesCS5B01G083000 chr5D 81.121 339 52 9 2483 2813 97276790 97277124 1.470000e-65 261
21 TraesCS5B01G083000 chr5D 75.681 551 98 29 1507 2043 97275834 97276362 5.310000e-60 243
22 TraesCS5B01G083000 chr5D 85.629 167 21 3 2193 2357 97276492 97276657 7.070000e-39 172
23 TraesCS5B01G083000 chr5D 96.667 90 3 0 3341 3430 34074200 34074111 3.310000e-32 150
24 TraesCS5B01G083000 chr5D 94.737 95 4 1 3333 3426 57225953 57226047 4.290000e-31 147
25 TraesCS5B01G083000 chr5D 89.908 109 10 1 3327 3434 120889981 120889873 7.170000e-29 139
26 TraesCS5B01G083000 chr5A 93.541 2570 92 26 787 3340 106751207 106748696 0.000000e+00 3759
27 TraesCS5B01G083000 chr5A 94.979 1892 83 7 3426 5309 106748693 106746806 0.000000e+00 2957
28 TraesCS5B01G083000 chr5A 86.413 368 45 5 3457 3822 92445769 92446133 1.070000e-106 398
29 TraesCS5B01G083000 chr5A 83.102 432 65 5 2883 3307 92445279 92445709 2.320000e-103 387
30 TraesCS5B01G083000 chr5A 82.789 337 48 9 2483 2813 92444846 92445178 5.200000e-75 292
31 TraesCS5B01G083000 chr5A 75.671 559 105 27 1507 2049 92443877 92444420 3.180000e-62 250
32 TraesCS5B01G083000 chr5A 85.629 167 21 3 2193 2357 92444548 92444713 7.070000e-39 172
33 TraesCS5B01G083000 chr2B 98.858 788 9 0 1 788 491546896 491546109 0.000000e+00 1406
34 TraesCS5B01G083000 chr2B 97.753 89 2 0 3339 3427 49649221 49649133 2.560000e-33 154
35 TraesCS5B01G083000 chr6B 98.608 790 9 2 1 788 717603272 717604061 0.000000e+00 1397
36 TraesCS5B01G083000 chr6B 98.479 789 12 0 1 789 191972770 191971982 0.000000e+00 1391
37 TraesCS5B01G083000 chr2A 98.606 789 11 0 1 789 36006926 36007714 0.000000e+00 1397
38 TraesCS5B01G083000 chr2A 98.479 789 12 0 1 789 753423661 753424449 0.000000e+00 1391
39 TraesCS5B01G083000 chr2A 98.354 790 11 2 1 788 401104270 401105059 0.000000e+00 1386
40 TraesCS5B01G083000 chr6A 98.354 790 11 2 1 788 362710530 362711319 0.000000e+00 1386
41 TraesCS5B01G083000 chr6A 95.556 90 3 1 3337 3426 73454840 73454928 5.540000e-30 143
42 TraesCS5B01G083000 chr6A 93.684 95 6 0 3337 3431 542602877 542602783 5.540000e-30 143
43 TraesCS5B01G083000 chr4A 98.354 790 11 2 1 788 115902053 115901264 0.000000e+00 1386
44 TraesCS5B01G083000 chr4A 77.966 295 57 6 3478 3767 48302060 48302351 1.520000e-40 178
45 TraesCS5B01G083000 chr4A 96.629 89 3 0 3338 3426 650839237 650839325 1.190000e-31 148
46 TraesCS5B01G083000 chr4B 78.305 295 54 7 3479 3767 512162873 512162583 1.170000e-41 182
47 TraesCS5B01G083000 chr4B 97.802 91 2 0 3339 3429 2431982 2431892 1.980000e-34 158
48 TraesCS5B01G083000 chr4B 96.667 90 3 0 3337 3426 136939786 136939875 3.310000e-32 150
49 TraesCS5B01G083000 chr4D 80.263 228 39 5 3543 3767 415290805 415290581 3.290000e-37 167
50 TraesCS5B01G083000 chr4D 96.774 93 3 0 3334 3426 498898054 498897962 7.120000e-34 156
51 TraesCS5B01G083000 chr4D 95.506 89 4 0 3341 3429 26481779 26481867 5.540000e-30 143
52 TraesCS5B01G083000 chr4D 96.512 86 3 0 3341 3426 270678548 270678633 5.540000e-30 143
53 TraesCS5B01G083000 chr4D 93.617 94 6 0 3333 3426 99160559 99160652 1.990000e-29 141
54 TraesCS5B01G083000 chr3B 96.739 92 3 0 3339 3430 54592547 54592456 2.560000e-33 154
55 TraesCS5B01G083000 chr2D 96.629 89 3 0 3338 3426 82187152 82187240 1.190000e-31 148
56 TraesCS5B01G083000 chr1D 96.629 89 3 0 3341 3429 447863805 447863717 1.190000e-31 148
57 TraesCS5B01G083000 chr1D 96.512 86 3 0 3342 3427 463576612 463576527 5.540000e-30 143
58 TraesCS5B01G083000 chr3A 90.909 110 8 2 3322 3431 427713546 427713653 4.290000e-31 147
59 TraesCS5B01G083000 chr1A 97.647 85 2 0 3342 3426 133417547 133417463 4.290000e-31 147
60 TraesCS5B01G083000 chr1A 93.069 101 6 1 3328 3428 498400833 498400932 4.290000e-31 147
61 TraesCS5B01G083000 chr1A 94.565 92 4 1 3336 3427 90167760 90167850 1.990000e-29 141
62 TraesCS5B01G083000 chr1A 89.474 114 9 3 3341 3451 286008393 286008280 1.990000e-29 141
63 TraesCS5B01G083000 chr1A 90.654 107 8 2 3341 3447 550138441 550138337 1.990000e-29 141
64 TraesCS5B01G083000 chr1A 92.784 97 6 1 3330 3426 542440302 542440397 7.170000e-29 139
65 TraesCS5B01G083000 chrUn 96.512 86 3 0 3342 3427 16901625 16901710 5.540000e-30 143
66 TraesCS5B01G083000 chrUn 95.506 89 4 0 3341 3429 316200624 316200536 5.540000e-30 143
67 TraesCS5B01G083000 chrUn 96.471 85 3 0 3342 3426 8111450 8111534 1.990000e-29 141
68 TraesCS5B01G083000 chrUn 93.617 94 5 1 3337 3429 60935156 60935249 7.170000e-29 139
69 TraesCS5B01G083000 chrUn 94.382 89 5 0 3339 3427 180382666 180382754 2.580000e-28 137
70 TraesCS5B01G083000 chrUn 94.318 88 5 0 3340 3427 244923898 244923811 9.280000e-28 135
71 TraesCS5B01G083000 chrUn 94.318 88 5 0 3340 3427 287095786 287095699 9.280000e-28 135
72 TraesCS5B01G083000 chrUn 93.333 90 6 0 3342 3431 230602168 230602079 3.340000e-27 134
73 TraesCS5B01G083000 chrUn 93.333 90 5 1 3341 3429 15908528 15908439 1.200000e-26 132
74 TraesCS5B01G083000 chrUn 94.186 86 5 0 3342 3427 47471788 47471703 1.200000e-26 132
75 TraesCS5B01G083000 chrUn 89.899 99 10 0 3328 3426 371558035 371558133 1.550000e-25 128
76 TraesCS5B01G083000 chrUn 89.899 99 10 0 3328 3426 371616842 371616940 1.550000e-25 128
77 TraesCS5B01G083000 chr6D 96.512 86 3 0 3341 3426 27308698 27308613 5.540000e-30 143
78 TraesCS5B01G083000 chr6D 96.512 86 3 0 3341 3426 460470431 460470346 5.540000e-30 143
79 TraesCS5B01G083000 chr6D 96.471 85 3 0 3342 3426 11067939 11067855 1.990000e-29 141
80 TraesCS5B01G083000 chr6D 95.455 88 4 0 3342 3429 99730289 99730202 1.990000e-29 141
81 TraesCS5B01G083000 chr6D 95.402 87 4 0 3342 3428 170947554 170947640 7.170000e-29 139
82 TraesCS5B01G083000 chr6D 91.837 98 6 2 3333 3429 231497261 231497357 9.280000e-28 135
83 TraesCS5B01G083000 chr3D 90.000 110 8 3 3319 3426 560920326 560920434 7.170000e-29 139


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 TraesCS5B01G083000 chr5B 103568714 103574024 5310 False 9808.000000 9808 100.00000 1 5311 1 chr5B.!!$F2 5310
1 TraesCS5B01G083000 chr5B 105767788 105772284 4496 False 1665.750000 3819 96.23350 787 5309 4 chr5B.!!$F5 4522
2 TraesCS5B01G083000 chr5B 52919368 52920157 789 False 1386.000000 1386 98.35400 1 788 1 chr5B.!!$F1 787
3 TraesCS5B01G083000 chr5B 105710864 105713616 2752 False 401.250000 658 80.61175 1507 4335 4 chr5B.!!$F4 2828
4 TraesCS5B01G083000 chr5B 103471579 103473824 2245 False 276.333333 392 82.66800 1507 3822 3 chr5B.!!$F3 2315
5 TraesCS5B01G083000 chr5D 97323073 97328273 5200 False 1705.500000 3790 95.74700 787 5311 4 chr5D.!!$F3 4524
6 TraesCS5B01G083000 chr5D 97275834 97278083 2249 False 292.400000 396 82.37240 1507 3827 5 chr5D.!!$F2 2320
7 TraesCS5B01G083000 chr5A 106746806 106751207 4401 True 3358.000000 3759 94.26000 787 5309 2 chr5A.!!$R1 4522
8 TraesCS5B01G083000 chr5A 92443877 92446133 2256 False 299.800000 398 82.72080 1507 3822 5 chr5A.!!$F1 2315
9 TraesCS5B01G083000 chr2B 491546109 491546896 787 True 1406.000000 1406 98.85800 1 788 1 chr2B.!!$R2 787
10 TraesCS5B01G083000 chr6B 717603272 717604061 789 False 1397.000000 1397 98.60800 1 788 1 chr6B.!!$F1 787
11 TraesCS5B01G083000 chr6B 191971982 191972770 788 True 1391.000000 1391 98.47900 1 789 1 chr6B.!!$R1 788
12 TraesCS5B01G083000 chr2A 36006926 36007714 788 False 1397.000000 1397 98.60600 1 789 1 chr2A.!!$F1 788
13 TraesCS5B01G083000 chr2A 753423661 753424449 788 False 1391.000000 1391 98.47900 1 789 1 chr2A.!!$F3 788
14 TraesCS5B01G083000 chr2A 401104270 401105059 789 False 1386.000000 1386 98.35400 1 788 1 chr2A.!!$F2 787
15 TraesCS5B01G083000 chr6A 362710530 362711319 789 False 1386.000000 1386 98.35400 1 788 1 chr6A.!!$F2 787
16 TraesCS5B01G083000 chr4A 115901264 115902053 789 True 1386.000000 1386 98.35400 1 788 1 chr4A.!!$R1 787

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
892 901 0.032815 TTGGTTCACTCGATCGCACA 59.967 50.000 11.09 0.0 0.00 4.57 F
1822 1866 1.435563 TCTGGGGGTCTCTTGAAGGTA 59.564 52.381 0.00 0.0 0.00 3.08 F
1995 2045 1.045911 TTGTGAACCCAAAGGCACCC 61.046 55.000 0.00 0.0 36.11 4.61 F
3803 3945 1.140252 GTCCAGTGTACCAGGTGTGTT 59.860 52.381 0.76 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2045 2.377310 CGCCAAACGTGGGTAGACG 61.377 63.158 8.18 0.00 46.09 4.18 R
3228 3355 0.534412 CGCATTCTCCACCAGAGTCT 59.466 55.000 0.00 0.00 43.71 3.24 R
3935 4077 0.807496 GTAAGCCTGAGCCTGCAAAG 59.193 55.000 0.00 0.00 41.25 2.77 R
4697 5629 1.335810 ACTGTTTGCATCACACAGCTG 59.664 47.619 13.48 13.48 43.43 4.24 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
405 408 8.122952 GTCTATTATTTGTTTCCTTCACATCCG 58.877 37.037 0.00 0.00 0.00 4.18
690 693 1.364269 AATGAAACGGGTGGGAGGTA 58.636 50.000 0.00 0.00 0.00 3.08
742 747 1.797025 GAGTGAGGTGGGACGAAAAG 58.203 55.000 0.00 0.00 0.00 2.27
762 768 3.100671 AGAAACCTGGAAGCGAGACTAT 58.899 45.455 0.00 0.00 0.00 2.12
773 779 1.862008 GCGAGACTATCAACTGCTCCG 60.862 57.143 0.00 0.00 0.00 4.63
791 797 5.066634 TGCTCCGTTAAGAGTAGAGATTCTG 59.933 44.000 0.00 0.00 36.20 3.02
880 889 3.211045 CGTCCCTTTCTTTCTTGGTTCA 58.789 45.455 0.00 0.00 0.00 3.18
881 890 3.003378 CGTCCCTTTCTTTCTTGGTTCAC 59.997 47.826 0.00 0.00 0.00 3.18
882 891 4.207955 GTCCCTTTCTTTCTTGGTTCACT 58.792 43.478 0.00 0.00 0.00 3.41
883 892 4.276183 GTCCCTTTCTTTCTTGGTTCACTC 59.724 45.833 0.00 0.00 0.00 3.51
884 893 3.251004 CCCTTTCTTTCTTGGTTCACTCG 59.749 47.826 0.00 0.00 0.00 4.18
885 894 4.127171 CCTTTCTTTCTTGGTTCACTCGA 58.873 43.478 0.00 0.00 0.00 4.04
886 895 4.757149 CCTTTCTTTCTTGGTTCACTCGAT 59.243 41.667 0.00 0.00 0.00 3.59
887 896 5.106908 CCTTTCTTTCTTGGTTCACTCGATC 60.107 44.000 0.00 0.00 0.00 3.69
888 897 3.575630 TCTTTCTTGGTTCACTCGATCG 58.424 45.455 9.36 9.36 0.00 3.69
889 898 1.710013 TTCTTGGTTCACTCGATCGC 58.290 50.000 11.09 0.00 0.00 4.58
890 899 0.601057 TCTTGGTTCACTCGATCGCA 59.399 50.000 11.09 0.00 0.00 5.10
891 900 0.716108 CTTGGTTCACTCGATCGCAC 59.284 55.000 11.09 1.65 0.00 5.34
892 901 0.032815 TTGGTTCACTCGATCGCACA 59.967 50.000 11.09 0.00 0.00 4.57
925 934 4.460873 GAAGCCGCCGCCTTTTCG 62.461 66.667 0.00 0.00 34.57 3.46
937 946 1.533965 GCCTTTTCGCGGAATCATTCC 60.534 52.381 6.32 6.32 46.62 3.01
1147 1156 3.692406 ACGTCAAGGCGTCCCCTC 61.692 66.667 0.00 0.00 45.62 4.30
1438 1470 8.230472 AGTTCAGAAAAATTCAGTTCAGATGT 57.770 30.769 0.00 0.00 0.00 3.06
1440 1472 9.387123 GTTCAGAAAAATTCAGTTCAGATGTAC 57.613 33.333 0.00 0.00 0.00 2.90
1487 1519 6.054295 GGATTTGATGCTGTTCTATGTCTCT 58.946 40.000 0.00 0.00 0.00 3.10
1488 1520 6.541641 GGATTTGATGCTGTTCTATGTCTCTT 59.458 38.462 0.00 0.00 0.00 2.85
1489 1521 7.712639 GGATTTGATGCTGTTCTATGTCTCTTA 59.287 37.037 0.00 0.00 0.00 2.10
1822 1866 1.435563 TCTGGGGGTCTCTTGAAGGTA 59.564 52.381 0.00 0.00 0.00 3.08
1995 2045 1.045911 TTGTGAACCCAAAGGCACCC 61.046 55.000 0.00 0.00 36.11 4.61
2397 2457 8.909671 GTTTTTCTTTGAGATGAACATAAGCTG 58.090 33.333 0.00 0.00 0.00 4.24
2399 2459 4.637534 TCTTTGAGATGAACATAAGCTGGC 59.362 41.667 0.00 0.00 0.00 4.85
2610 2693 5.321927 TCCTGTTTAACCCCTTCTGAAATC 58.678 41.667 0.00 0.00 0.00 2.17
2632 2715 2.324541 GGATCCATCCAGCTACTCAGT 58.675 52.381 6.95 0.00 46.38 3.41
3228 3355 7.510675 AACTGGTTCCTTCTATGGAAATCTA 57.489 36.000 0.00 0.00 46.34 1.98
3321 3454 6.451292 TTTTGGTAATAGTGGTAGTTGGGA 57.549 37.500 0.00 0.00 0.00 4.37
3347 3480 9.574516 AATACAAATTCCTTCATATGTACTCCC 57.425 33.333 1.90 0.00 0.00 4.30
3349 3482 7.283329 ACAAATTCCTTCATATGTACTCCCTC 58.717 38.462 1.90 0.00 0.00 4.30
3350 3483 7.127955 ACAAATTCCTTCATATGTACTCCCTCT 59.872 37.037 1.90 0.00 0.00 3.69
3351 3484 6.678568 ATTCCTTCATATGTACTCCCTCTG 57.321 41.667 1.90 0.00 0.00 3.35
3352 3485 5.144159 TCCTTCATATGTACTCCCTCTGT 57.856 43.478 1.90 0.00 0.00 3.41
3354 3487 6.679542 TCCTTCATATGTACTCCCTCTGTTA 58.320 40.000 1.90 0.00 0.00 2.41
3355 3488 7.130099 TCCTTCATATGTACTCCCTCTGTTAA 58.870 38.462 1.90 0.00 0.00 2.01
3356 3489 7.069578 TCCTTCATATGTACTCCCTCTGTTAAC 59.930 40.741 1.90 0.00 0.00 2.01
3358 3491 9.132923 CTTCATATGTACTCCCTCTGTTAACTA 57.867 37.037 7.22 0.00 0.00 2.24
3360 3493 9.656323 TCATATGTACTCCCTCTGTTAACTAAT 57.344 33.333 7.22 0.00 0.00 1.73
3368 3501 8.862085 ACTCCCTCTGTTAACTAATATAAGAGC 58.138 37.037 7.22 0.00 0.00 4.09
3369 3502 7.883217 TCCCTCTGTTAACTAATATAAGAGCG 58.117 38.462 7.22 1.79 0.00 5.03
3370 3503 7.504911 TCCCTCTGTTAACTAATATAAGAGCGT 59.495 37.037 7.22 0.00 0.00 5.07
3371 3504 8.142551 CCCTCTGTTAACTAATATAAGAGCGTT 58.857 37.037 7.22 0.00 0.00 4.84
3372 3505 9.530633 CCTCTGTTAACTAATATAAGAGCGTTT 57.469 33.333 7.22 0.00 0.00 3.60
3387 3520 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
3388 3521 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
3402 3535 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
3403 3536 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
3404 3537 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
3405 3538 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
3420 3553 9.490379 AAACGCTCTTATATTAGTTTATGGAGG 57.510 33.333 0.00 0.00 31.14 4.30
3421 3554 7.612677 ACGCTCTTATATTAGTTTATGGAGGG 58.387 38.462 0.00 0.00 35.06 4.30
3422 3555 7.453752 ACGCTCTTATATTAGTTTATGGAGGGA 59.546 37.037 0.00 0.00 34.22 4.20
3467 3609 8.188139 TGTCTTAGGAAAAACAATTTCTGACAC 58.812 33.333 0.00 0.00 0.00 3.67
3468 3610 8.188139 GTCTTAGGAAAAACAATTTCTGACACA 58.812 33.333 1.47 0.00 0.00 3.72
3493 3635 6.008331 ACATATATCCTTCTGTAGGTACGCA 58.992 40.000 0.00 0.00 45.03 5.24
3514 3656 1.831106 ACCGACTATGGCATGTTCAGA 59.169 47.619 10.98 0.00 0.00 3.27
3667 3809 5.221009 CGGGTACTCATCCAACTCTTACTAC 60.221 48.000 0.00 0.00 0.00 2.73
3803 3945 1.140252 GTCCAGTGTACCAGGTGTGTT 59.860 52.381 0.76 0.00 0.00 3.32
3846 3988 9.993881 CATGAGATCAAAACGTTTAATTTTGTC 57.006 29.630 15.03 8.55 44.08 3.18
3896 4038 6.617782 ACTACTATGGCAGCATCTGATAAT 57.382 37.500 0.00 0.00 32.44 1.28
3933 4075 7.087639 GGTAATGCTACAGTACAAAATTTGCA 58.912 34.615 5.52 0.00 36.76 4.08
3935 4077 4.545610 TGCTACAGTACAAAATTTGCAGC 58.454 39.130 5.52 5.99 0.00 5.25
4331 4487 2.279173 AGGCCCAATACTTTCAGAGGT 58.721 47.619 0.00 0.00 0.00 3.85
4335 4491 2.357154 CCCAATACTTTCAGAGGTGGGG 60.357 54.545 0.00 0.00 40.11 4.96
4338 4494 4.265073 CAATACTTTCAGAGGTGGGGAAG 58.735 47.826 0.00 0.00 0.00 3.46
4340 4496 0.674895 CTTTCAGAGGTGGGGAAGCG 60.675 60.000 0.00 0.00 0.00 4.68
4343 4500 1.144936 CAGAGGTGGGGAAGCGATC 59.855 63.158 0.00 0.00 0.00 3.69
4357 4916 1.364171 CGATCGATGGGTGGAGACC 59.636 63.158 10.26 0.00 42.27 3.85
4748 5680 1.273381 TGGACCGGAGAGAACCCAATA 60.273 52.381 9.46 0.00 0.00 1.90
4784 5716 3.513515 ACAAGGAGAAGTCCAGCTAGAAG 59.486 47.826 0.00 0.00 46.80 2.85
4793 5725 3.149981 GTCCAGCTAGAAGCAAAAAGGT 58.850 45.455 1.22 0.00 45.56 3.50
4798 5730 3.823304 AGCTAGAAGCAAAAAGGTCCAAG 59.177 43.478 1.22 0.00 45.56 3.61
4801 5733 5.221244 GCTAGAAGCAAAAAGGTCCAAGAAA 60.221 40.000 0.00 0.00 41.89 2.52
4983 5915 5.860611 TCTGGGTTATCTTCTTCGTTTTCA 58.139 37.500 0.00 0.00 0.00 2.69
5252 6184 7.883559 TCCATGCCATGATATAGGATCATAT 57.116 36.000 6.18 5.09 36.69 1.78
5292 6224 1.818959 GCAGGTGCAGATGCCCAAAA 61.819 55.000 11.22 0.00 41.18 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
405 408 9.364989 TGCAATTTGCTTTAGGAAACATATAAC 57.635 29.630 21.19 0.00 45.31 1.89
690 693 4.531339 GGTACTTCTTTGGTACTTCCTCCT 59.469 45.833 0.00 0.00 39.36 3.69
724 729 1.420430 TCTTTTCGTCCCACCTCACT 58.580 50.000 0.00 0.00 0.00 3.41
742 747 3.119101 TGATAGTCTCGCTTCCAGGTTTC 60.119 47.826 0.00 0.00 0.00 2.78
762 768 4.077108 TCTACTCTTAACGGAGCAGTTGA 58.923 43.478 3.05 0.00 36.87 3.18
773 779 5.251601 ACGGCAGAATCTCTACTCTTAAC 57.748 43.478 0.00 0.00 0.00 2.01
791 797 1.007618 GACTGCGGGTAGATACGGC 60.008 63.158 0.00 0.00 0.00 5.68
858 867 3.211865 GAACCAAGAAAGAAAGGGACGT 58.788 45.455 0.00 0.00 0.00 4.34
880 889 1.983196 CTCGGAGTGTGCGATCGAGT 61.983 60.000 21.57 0.00 40.01 4.18
881 890 1.297967 CTCGGAGTGTGCGATCGAG 60.298 63.158 21.57 0.00 40.01 4.04
882 891 1.303091 TTCTCGGAGTGTGCGATCGA 61.303 55.000 21.57 0.59 40.01 3.59
883 892 0.863538 CTTCTCGGAGTGTGCGATCG 60.864 60.000 11.69 11.69 40.01 3.69
884 893 0.452184 TCTTCTCGGAGTGTGCGATC 59.548 55.000 4.69 0.00 40.01 3.69
885 894 0.171455 GTCTTCTCGGAGTGTGCGAT 59.829 55.000 4.69 0.00 40.01 4.58
886 895 1.579932 GTCTTCTCGGAGTGTGCGA 59.420 57.895 4.69 0.00 38.05 5.10
887 896 1.444553 GGTCTTCTCGGAGTGTGCG 60.445 63.158 4.69 0.00 0.00 5.34
888 897 1.079750 GGGTCTTCTCGGAGTGTGC 60.080 63.158 4.69 0.00 0.00 4.57
889 898 0.244994 CAGGGTCTTCTCGGAGTGTG 59.755 60.000 4.69 0.00 0.00 3.82
890 899 0.112606 TCAGGGTCTTCTCGGAGTGT 59.887 55.000 4.69 0.00 0.00 3.55
891 900 1.203523 CTTCAGGGTCTTCTCGGAGTG 59.796 57.143 4.69 0.00 0.00 3.51
892 901 1.551452 CTTCAGGGTCTTCTCGGAGT 58.449 55.000 4.69 0.00 0.00 3.85
937 946 4.811557 AGGAAACAGAAACAAGAACTCGAG 59.188 41.667 11.84 11.84 0.00 4.04
1147 1156 1.296715 CCTCCAGTCCAAGAACCGG 59.703 63.158 0.00 0.00 0.00 5.28
1438 1470 3.815962 TGCTTTGCCATTTCAAGTACGTA 59.184 39.130 0.00 0.00 0.00 3.57
1440 1472 3.281341 TGCTTTGCCATTTCAAGTACG 57.719 42.857 0.00 0.00 0.00 3.67
1487 1519 5.238214 GGCACTGGAAATTTGCAAACAATAA 59.762 36.000 15.41 0.00 38.04 1.40
1488 1520 4.754114 GGCACTGGAAATTTGCAAACAATA 59.246 37.500 15.41 0.00 38.04 1.90
1489 1521 3.565063 GGCACTGGAAATTTGCAAACAAT 59.435 39.130 15.41 3.28 38.04 2.71
1995 2045 2.377310 CGCCAAACGTGGGTAGACG 61.377 63.158 8.18 0.00 46.09 4.18
2190 2249 8.033038 TCTACAATGGTACTAATTCAGTCACAC 58.967 37.037 0.00 0.00 38.80 3.82
2632 2715 4.056740 CAATGTTGCAGCAACCATGTTTA 58.943 39.130 31.05 14.23 42.96 2.01
3028 3149 0.904649 TGAACTGATCCCACTGCGAT 59.095 50.000 0.00 0.00 0.00 4.58
3129 3250 3.874543 CATTAAGCAATGCATGGCAACAT 59.125 39.130 27.59 12.71 45.12 2.71
3171 3298 2.549563 CCTCTCATGATTACCGCTGCAT 60.550 50.000 0.00 0.00 0.00 3.96
3228 3355 0.534412 CGCATTCTCCACCAGAGTCT 59.466 55.000 0.00 0.00 43.71 3.24
3282 3409 2.470999 CCAAAATTTTGCACGGTTCTCG 59.529 45.455 22.90 4.14 39.68 4.04
3321 3454 9.574516 GGGAGTACATATGAAGGAATTTGTATT 57.425 33.333 10.38 0.00 30.20 1.89
3343 3476 8.024285 CGCTCTTATATTAGTTAACAGAGGGAG 58.976 40.741 20.28 12.42 36.40 4.30
3344 3477 7.504911 ACGCTCTTATATTAGTTAACAGAGGGA 59.495 37.037 26.61 9.25 37.30 4.20
3346 3479 9.530633 AAACGCTCTTATATTAGTTAACAGAGG 57.469 33.333 8.61 6.21 0.00 3.69
3363 3496 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
3364 3497 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
3378 3511 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
3379 3512 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
3394 3527 9.490379 CCTCCATAAACTAATATAAGAGCGTTT 57.510 33.333 0.00 0.00 0.00 3.60
3395 3528 8.095169 CCCTCCATAAACTAATATAAGAGCGTT 58.905 37.037 0.00 0.00 0.00 4.84
3396 3529 7.453752 TCCCTCCATAAACTAATATAAGAGCGT 59.546 37.037 0.00 0.00 0.00 5.07
3397 3530 7.837863 TCCCTCCATAAACTAATATAAGAGCG 58.162 38.462 0.00 0.00 0.00 5.03
3398 3531 8.817876 ACTCCCTCCATAAACTAATATAAGAGC 58.182 37.037 0.00 0.00 0.00 4.09
3404 3537 9.900112 AGAACTACTCCCTCCATAAACTAATAT 57.100 33.333 0.00 0.00 0.00 1.28
3405 3538 9.144298 CAGAACTACTCCCTCCATAAACTAATA 57.856 37.037 0.00 0.00 0.00 0.98
3406 3539 7.844779 TCAGAACTACTCCCTCCATAAACTAAT 59.155 37.037 0.00 0.00 0.00 1.73
3407 3540 7.186972 TCAGAACTACTCCCTCCATAAACTAA 58.813 38.462 0.00 0.00 0.00 2.24
3408 3541 6.738635 TCAGAACTACTCCCTCCATAAACTA 58.261 40.000 0.00 0.00 0.00 2.24
3409 3542 5.590818 TCAGAACTACTCCCTCCATAAACT 58.409 41.667 0.00 0.00 0.00 2.66
3410 3543 5.934402 TCAGAACTACTCCCTCCATAAAC 57.066 43.478 0.00 0.00 0.00 2.01
3411 3544 6.023603 ACTTCAGAACTACTCCCTCCATAAA 58.976 40.000 0.00 0.00 0.00 1.40
3412 3545 5.590818 ACTTCAGAACTACTCCCTCCATAA 58.409 41.667 0.00 0.00 0.00 1.90
3413 3546 5.208294 ACTTCAGAACTACTCCCTCCATA 57.792 43.478 0.00 0.00 0.00 2.74
3414 3547 4.067944 ACTTCAGAACTACTCCCTCCAT 57.932 45.455 0.00 0.00 0.00 3.41
3415 3548 3.544698 ACTTCAGAACTACTCCCTCCA 57.455 47.619 0.00 0.00 0.00 3.86
3416 3549 4.893829 AAACTTCAGAACTACTCCCTCC 57.106 45.455 0.00 0.00 0.00 4.30
3417 3550 6.593268 AGTAAACTTCAGAACTACTCCCTC 57.407 41.667 0.00 0.00 0.00 4.30
3418 3551 6.326843 ACAAGTAAACTTCAGAACTACTCCCT 59.673 38.462 0.00 0.00 33.11 4.20
3419 3552 6.522946 ACAAGTAAACTTCAGAACTACTCCC 58.477 40.000 0.00 0.00 33.11 4.30
3420 3553 7.435305 AGACAAGTAAACTTCAGAACTACTCC 58.565 38.462 0.00 0.00 33.11 3.85
3421 3554 8.874744 AAGACAAGTAAACTTCAGAACTACTC 57.125 34.615 0.00 0.00 33.11 2.59
3422 3555 9.968870 CTAAGACAAGTAAACTTCAGAACTACT 57.031 33.333 0.00 0.00 33.11 2.57
3493 3635 2.236146 TCTGAACATGCCATAGTCGGTT 59.764 45.455 0.00 0.00 0.00 4.44
3514 3656 6.882610 TCTTCTGTGTGAGCAATACAAAAT 57.117 33.333 0.00 0.00 0.00 1.82
3667 3809 1.265635 TCAAACGTGCCTTCAAATCCG 59.734 47.619 0.00 0.00 0.00 4.18
3803 3945 6.225981 TCTCATGCAAATGCTAGTTAGAGA 57.774 37.500 6.97 7.25 42.66 3.10
3896 4038 2.717390 AGCATTACCGGCAATTGTACA 58.283 42.857 0.00 0.00 0.00 2.90
3933 4075 2.675772 GCCTGAGCCTGCAAAGCT 60.676 61.111 10.53 10.53 45.23 3.74
3935 4077 0.807496 GTAAGCCTGAGCCTGCAAAG 59.193 55.000 0.00 0.00 41.25 2.77
4217 4373 4.163552 TCGTGAAGTGATCGTACACATTC 58.836 43.478 14.46 13.86 42.45 2.67
4331 4487 2.807107 CCCATCGATCGCTTCCCCA 61.807 63.158 11.09 0.00 0.00 4.96
4335 4491 0.598680 CTCCACCCATCGATCGCTTC 60.599 60.000 11.09 0.00 0.00 3.86
4338 4494 1.300233 GTCTCCACCCATCGATCGC 60.300 63.158 11.09 0.00 0.00 4.58
4340 4496 0.830648 TTGGTCTCCACCCATCGATC 59.169 55.000 0.00 0.00 42.99 3.69
4343 4500 0.176680 CTCTTGGTCTCCACCCATCG 59.823 60.000 0.00 0.00 42.99 3.84
4357 4916 5.542779 ACAGTAACTAGCTTGTTCCTCTTG 58.457 41.667 16.89 11.26 0.00 3.02
4428 4987 7.552687 TCAGAATTTAGTATAACCCTTGTGCTG 59.447 37.037 0.00 0.00 0.00 4.41
4695 5627 2.549329 CTGTTTGCATCACACAGCTGTA 59.451 45.455 21.20 4.30 35.79 2.74
4697 5629 1.335810 ACTGTTTGCATCACACAGCTG 59.664 47.619 13.48 13.48 43.43 4.24
4734 5666 5.010282 ACACAACAATATTGGGTTCTCTCC 58.990 41.667 19.37 0.00 30.76 3.71
4748 5680 3.136443 TCTCCTTGTCCTCACACAACAAT 59.864 43.478 0.00 0.00 32.85 2.71
4784 5716 2.158971 TGGCTTTCTTGGACCTTTTTGC 60.159 45.455 0.00 0.00 0.00 3.68
4793 5725 2.890945 GCTAGGTTTTGGCTTTCTTGGA 59.109 45.455 0.00 0.00 0.00 3.53
4798 5730 4.584327 TTTCTGCTAGGTTTTGGCTTTC 57.416 40.909 0.00 0.00 0.00 2.62
4801 5733 3.321968 CCTTTTTCTGCTAGGTTTTGGCT 59.678 43.478 0.00 0.00 0.00 4.75
4983 5915 7.033185 AGAAGAATTTTGTAAACTGCGTTTGT 58.967 30.769 14.23 0.00 36.37 2.83
5252 6184 6.265196 CCTGCACCTTGATGGCTATTAATAAA 59.735 38.462 0.00 0.00 40.22 1.40


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

AutoCloner maintained by Alex Coulton.