Multiple sequence alignment - TraesCS3D01G457500

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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 TraesCS3D01G457500 chr3D 100.000 4693 0 0 1 4693 562705593 562710285 0.000000e+00 8667
1 TraesCS3D01G457500 chr3A 90.680 2060 112 30 873 2895 697782644 697784660 0.000000e+00 2667
2 TraesCS3D01G457500 chr3A 92.373 826 43 7 1 813 697781408 697782226 0.000000e+00 1158
3 TraesCS3D01G457500 chr3A 87.935 978 62 24 3047 4015 697784664 697785594 0.000000e+00 1101
4 TraesCS3D01G457500 chr3A 89.516 248 16 5 4446 4693 697786519 697786756 5.900000e-79 305
5 TraesCS3D01G457500 chr3B 92.188 1472 66 16 1939 3378 750355724 750357178 0.000000e+00 2036
6 TraesCS3D01G457500 chr3B 86.522 1521 123 32 1 1471 750353682 750355170 0.000000e+00 1598
7 TraesCS3D01G457500 chr3B 91.015 601 27 7 3377 3974 750357530 750358106 0.000000e+00 785
8 TraesCS3D01G457500 chr3B 93.793 435 24 1 1502 1933 750355166 750355600 0.000000e+00 651
9 TraesCS3D01G457500 chr3B 87.742 155 9 6 4545 4693 750361188 750361338 6.240000e-39 172
10 TraesCS3D01G457500 chr7B 77.778 1008 144 51 854 1818 622670119 622671089 8.880000e-152 547
11 TraesCS3D01G457500 chr7B 77.778 1008 144 51 854 1818 622682879 622683849 8.880000e-152 547
12 TraesCS3D01G457500 chr7B 84.437 302 38 7 2009 2307 622671296 622671591 5.940000e-74 289
13 TraesCS3D01G457500 chr7B 84.437 302 38 7 2009 2307 622684056 622684351 5.940000e-74 289
14 TraesCS3D01G457500 chr5B 76.868 696 135 16 30 707 698020713 698020026 2.060000e-98 370
15 TraesCS3D01G457500 chr5B 80.000 435 70 11 27 456 709120980 709121402 5.900000e-79 305
16 TraesCS3D01G457500 chr5B 79.770 435 71 11 27 456 709015687 709016109 2.740000e-77 300
17 TraesCS3D01G457500 chr5B 79.770 435 71 11 27 456 709036462 709036884 2.740000e-77 300
18 TraesCS3D01G457500 chrUn 79.770 435 71 11 27 456 281107443 281107865 2.740000e-77 300
19 TraesCS3D01G457500 chrUn 79.861 432 70 11 30 456 368650864 368650445 2.740000e-77 300
20 TraesCS3D01G457500 chrUn 79.861 432 70 11 30 456 368660584 368660165 2.740000e-77 300
21 TraesCS3D01G457500 chr7D 78.125 544 68 29 1290 1819 568027331 568027837 9.870000e-77 298


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 TraesCS3D01G457500 chr3D 562705593 562710285 4692 False 8667.00 8667 100.0000 1 4693 1 chr3D.!!$F1 4692
1 TraesCS3D01G457500 chr3A 697781408 697786756 5348 False 1307.75 2667 90.1260 1 4693 4 chr3A.!!$F1 4692
2 TraesCS3D01G457500 chr3B 750353682 750361338 7656 False 1048.40 2036 90.2520 1 4693 5 chr3B.!!$F1 4692
3 TraesCS3D01G457500 chr7B 622670119 622671591 1472 False 418.00 547 81.1075 854 2307 2 chr7B.!!$F1 1453
4 TraesCS3D01G457500 chr7B 622682879 622684351 1472 False 418.00 547 81.1075 854 2307 2 chr7B.!!$F2 1453
5 TraesCS3D01G457500 chr5B 698020026 698020713 687 True 370.00 370 76.8680 30 707 1 chr5B.!!$R1 677
6 TraesCS3D01G457500 chr7D 568027331 568027837 506 False 298.00 298 78.1250 1290 1819 1 chr7D.!!$F1 529

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
846 985 0.324943 CCCACGTTTCAGAGATGGGT 59.675 55.0 0.0 0.00 44.37 4.51 F
1249 1668 1.562672 CGACCCACTTCCCTTCCCAT 61.563 60.0 0.0 0.00 0.00 4.00 F
2077 2748 0.098376 CACCCACGAGTAGCGACTAC 59.902 60.0 0.0 8.42 44.57 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1738 2246 0.882474 ACGAAGGAGACGAGGTTCTG 59.118 55.0 0.00 0.00 34.7 3.02 R
2492 3166 1.395826 GGTATCGAGCAGCTGAGGGT 61.396 60.0 20.43 3.83 0.0 4.34 R
3879 4940 0.033208 CCAACCAGGGCCACACATAT 60.033 55.0 6.18 0.00 0.0 1.78 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
25 27 4.530857 CCACCATCGCTCCCGTCC 62.531 72.222 0.00 0.00 35.54 4.79
123 126 4.355543 TGTGCAAGAAATAAGCCGAATC 57.644 40.909 0.00 0.00 0.00 2.52
307 313 5.688220 AGGAGGTCTAATCCATCCTTCTA 57.312 43.478 0.00 0.00 39.47 2.10
419 428 7.549488 AGACTTTCCTTTATGAACCAATCTACG 59.451 37.037 0.00 0.00 0.00 3.51
420 429 7.166167 ACTTTCCTTTATGAACCAATCTACGT 58.834 34.615 0.00 0.00 0.00 3.57
421 430 7.333672 ACTTTCCTTTATGAACCAATCTACGTC 59.666 37.037 0.00 0.00 0.00 4.34
422 431 6.540438 TCCTTTATGAACCAATCTACGTCT 57.460 37.500 0.00 0.00 0.00 4.18
423 432 6.338146 TCCTTTATGAACCAATCTACGTCTG 58.662 40.000 0.00 0.00 0.00 3.51
434 443 3.878237 TCTACGTCTGGTCTATCCCAT 57.122 47.619 0.00 0.00 33.00 4.00
488 499 1.101331 GAGCTTCTTGAGGCCCAATG 58.899 55.000 0.00 0.00 33.68 2.82
544 555 4.531426 AGGATCGCCTCTCCCGCT 62.531 66.667 0.00 0.00 42.19 5.52
579 598 0.327576 AATCCCTCCGTCCATTCCCT 60.328 55.000 0.00 0.00 0.00 4.20
624 645 6.373005 TTCTGAGGAAGAAACACCATATGA 57.627 37.500 3.65 0.00 42.09 2.15
657 678 2.225496 TGGCCCATTAAAACATGAGGGT 60.225 45.455 0.00 0.00 38.56 4.34
708 731 3.107661 GCGTAACACGACACGGGG 61.108 66.667 2.35 0.00 46.05 5.73
758 781 1.078759 CACGGATTCACGCTGGAGTC 61.079 60.000 0.00 0.00 37.37 3.36
820 959 5.221966 TGGGTAGGTGCAAACTAACTAACAT 60.222 40.000 12.81 0.00 0.00 2.71
844 983 1.026718 GGCCCACGTTTCAGAGATGG 61.027 60.000 0.00 0.00 0.00 3.51
845 984 3.159298 CCCACGTTTCAGAGATGGG 57.841 57.895 0.00 0.00 44.02 4.00
846 985 0.324943 CCCACGTTTCAGAGATGGGT 59.675 55.000 0.00 0.00 44.37 4.51
885 1266 4.463879 CACCTCCAGCTGGCCTCG 62.464 72.222 28.91 16.13 34.44 4.63
890 1271 4.154347 CCAGCTGGCCTCGTCCTC 62.154 72.222 22.33 0.00 0.00 3.71
891 1272 4.154347 CAGCTGGCCTCGTCCTCC 62.154 72.222 5.57 0.00 0.00 4.30
909 1291 4.592351 TCCTCCTCAATCATCCATCTTCTC 59.408 45.833 0.00 0.00 0.00 2.87
992 1392 1.612146 CCAAATCCCCCAACCCACC 60.612 63.158 0.00 0.00 0.00 4.61
993 1393 1.981853 CAAATCCCCCAACCCACCG 60.982 63.158 0.00 0.00 0.00 4.94
994 1394 3.232497 AAATCCCCCAACCCACCGG 62.232 63.158 0.00 0.00 0.00 5.28
1205 1617 5.466058 CAGACCTCTGGTATGTACGTACTAG 59.534 48.000 25.12 25.12 39.74 2.57
1211 1623 9.096160 CCTCTGGTATGTACGTACTAGTATATG 57.904 40.741 27.91 17.45 35.43 1.78
1224 1643 9.872721 CGTACTAGTATATGTCTTCTATCTCCA 57.127 37.037 5.75 0.00 0.00 3.86
1229 1648 7.949696 AGTATATGTCTTCTATCTCCATCCCT 58.050 38.462 0.00 0.00 0.00 4.20
1232 1651 3.138468 TGTCTTCTATCTCCATCCCTCGA 59.862 47.826 0.00 0.00 0.00 4.04
1249 1668 1.562672 CGACCCACTTCCCTTCCCAT 61.563 60.000 0.00 0.00 0.00 4.00
1283 1717 8.243426 TGTATGTAATGCTGATCCAACTTTTTC 58.757 33.333 0.00 0.00 0.00 2.29
1415 1898 2.550830 AGATCCACCACAACTCACAC 57.449 50.000 0.00 0.00 0.00 3.82
1424 1907 2.489329 CCACAACTCACACCCATTCATC 59.511 50.000 0.00 0.00 0.00 2.92
1440 1923 2.757124 ATCCATTCCCCCTCGTGCC 61.757 63.158 0.00 0.00 0.00 5.01
1453 1941 1.662629 CTCGTGCCTGCTTGTGAATAG 59.337 52.381 0.00 0.00 0.00 1.73
1498 1986 9.776158 CTAGTGATTGATGTATCCGTACTAATC 57.224 37.037 0.00 0.00 32.87 1.75
1499 1987 7.306213 AGTGATTGATGTATCCGTACTAATCG 58.694 38.462 0.00 0.00 33.77 3.34
1510 1998 6.822073 TCCGTACTAATCGATCATTTGTTG 57.178 37.500 0.00 0.00 33.21 3.33
1687 2181 7.389053 AGTTCAGTTGATAAAACCAGATCACTC 59.611 37.037 0.00 0.00 31.85 3.51
1759 2267 0.170784 GAACCTCGTCTCCTTCGTCC 59.829 60.000 0.00 0.00 0.00 4.79
1809 2317 2.813908 CTCGCTACCGTTGCCACC 60.814 66.667 0.00 0.00 35.54 4.61
1826 2334 1.746615 CCCAGGTGCGTCAGATTGG 60.747 63.158 0.00 0.00 0.00 3.16
1922 2463 7.454225 ACTAAGGCTCTTTCACAGTAATTTCT 58.546 34.615 0.00 0.00 0.00 2.52
1926 2467 8.273780 AGGCTCTTTCACAGTAATTTCTATTG 57.726 34.615 0.00 0.00 0.00 1.90
1980 2646 1.613925 GCTCTGTTTTCCTTTCCACCC 59.386 52.381 0.00 0.00 0.00 4.61
1981 2647 2.753168 GCTCTGTTTTCCTTTCCACCCT 60.753 50.000 0.00 0.00 0.00 4.34
1984 2650 3.053245 TCTGTTTTCCTTTCCACCCTGAA 60.053 43.478 0.00 0.00 0.00 3.02
2029 2700 1.461127 GTACAGGCACTCTCGCTTTTG 59.539 52.381 0.00 0.00 34.60 2.44
2077 2748 0.098376 CACCCACGAGTAGCGACTAC 59.902 60.000 0.00 8.42 44.57 2.73
2224 2895 3.127721 GGCAGAAGGTGAGAATTGCTTAC 59.872 47.826 0.00 0.00 32.64 2.34
2232 2903 4.273318 GTGAGAATTGCTTACCCTCCAAT 58.727 43.478 0.00 0.00 0.00 3.16
2234 2905 3.026694 AGAATTGCTTACCCTCCAATGC 58.973 45.455 0.00 0.00 30.26 3.56
2235 2906 2.834638 ATTGCTTACCCTCCAATGCT 57.165 45.000 0.00 0.00 0.00 3.79
2268 2939 4.384056 CGCTGATTTCAGATGGGACTATT 58.616 43.478 11.70 0.00 46.59 1.73
2273 2944 7.500559 GCTGATTTCAGATGGGACTATTTAACT 59.499 37.037 11.70 0.00 46.59 2.24
2298 2969 2.864343 GCAAGAGTGCGGTATCGTTAAT 59.136 45.455 0.00 0.00 41.93 1.40
2316 2987 7.395645 TCGTTAATGACAATACGTTTGCTATG 58.604 34.615 0.00 0.00 35.63 2.23
2330 3001 1.271001 TGCTATGTCTGTGCAGCACTT 60.271 47.619 25.83 8.57 39.03 3.16
2362 3033 6.892310 AGCAAACTGAAGAATGTTTTGAAC 57.108 33.333 0.00 0.00 34.60 3.18
2364 3035 5.580297 GCAAACTGAAGAATGTTTTGAACCA 59.420 36.000 0.00 0.00 34.60 3.67
2385 3056 9.369904 GAACCATTAATCAAGCACATATTTTGT 57.630 29.630 0.00 0.00 39.91 2.83
2398 3069 8.487176 AGCACATATTTTGTTTCATCGAAAAAC 58.513 29.630 15.95 15.95 36.00 2.43
2399 3070 8.272176 GCACATATTTTGTTTCATCGAAAAACA 58.728 29.630 19.66 19.66 43.03 2.83
2400 3071 9.566624 CACATATTTTGTTTCATCGAAAAACAC 57.433 29.630 22.01 4.16 44.05 3.32
2401 3072 9.307121 ACATATTTTGTTTCATCGAAAAACACA 57.693 25.926 22.01 16.05 44.05 3.72
2412 3084 8.279695 TCATCGAAAAACACACACATATTTTG 57.720 30.769 0.00 0.00 0.00 2.44
2414 3086 6.269315 TCGAAAAACACACACATATTTTGCT 58.731 32.000 0.00 0.00 0.00 3.91
2415 3087 6.416455 TCGAAAAACACACACATATTTTGCTC 59.584 34.615 0.00 0.00 0.00 4.26
2419 3091 7.467557 AAACACACACATATTTTGCTCTTTG 57.532 32.000 0.00 0.00 0.00 2.77
2434 3107 5.728471 TGCTCTTTGGTTTCATTTGTCAAA 58.272 33.333 0.00 0.00 0.00 2.69
2466 3140 9.747898 TTTGCTGGAAACCTTTATATCTAAAGA 57.252 29.630 11.19 0.00 44.42 2.52
2467 3141 8.732746 TGCTGGAAACCTTTATATCTAAAGAC 57.267 34.615 11.19 2.18 44.42 3.01
2681 3363 5.444663 AGCAATCTGAAGAAAAAGGTGTC 57.555 39.130 0.00 0.00 0.00 3.67
2692 3374 9.179909 TGAAGAAAAAGGTGTCAAAGTTGTATA 57.820 29.630 0.00 0.00 0.00 1.47
2776 3458 8.964772 GGTCAAGTTAGTACTATCCTTTCTACA 58.035 37.037 2.79 0.00 33.17 2.74
2942 3646 1.070577 GTCTTGCTGCAGTTACACACG 60.071 52.381 16.64 2.01 0.00 4.49
2973 3677 7.067615 TGTTTTAGAGTCATAAACCTTGTGCAA 59.932 33.333 14.04 0.00 32.25 4.08
3029 3733 0.251297 CCAAACATGCCCTCAGTGGA 60.251 55.000 0.00 0.00 38.35 4.02
3144 3849 9.657419 AAGAATATTTTGAACCATTAAGCAAGG 57.343 29.630 0.00 0.00 0.00 3.61
3190 3895 2.954316 TCGTCGAGCTTATTTTGCTGA 58.046 42.857 0.00 0.00 41.30 4.26
3269 3974 7.524532 GCTTGATAGCCTCTGTCATAATACTCA 60.525 40.741 0.00 0.00 41.74 3.41
3596 4655 7.542025 ACTGAAAAGATCAATGCCAACTAATC 58.458 34.615 0.00 0.00 37.67 1.75
3598 4657 5.505173 AAAGATCAATGCCAACTAATCCG 57.495 39.130 0.00 0.00 0.00 4.18
3679 4739 0.675633 ACACTGGGTCAAAATGCAGC 59.324 50.000 0.00 0.00 0.00 5.25
3777 4837 7.939039 ACCTGTGCAGCATATTTGTAGTATATT 59.061 33.333 0.00 0.00 0.00 1.28
3780 4840 8.558700 TGTGCAGCATATTTGTAGTATATTGTG 58.441 33.333 0.00 0.00 0.00 3.33
3895 4956 4.852118 AGATTATATATGTGTGGCCCTGGT 59.148 41.667 0.00 0.00 0.00 4.00
4015 5078 9.137459 AGTTATATGTTACTAGCACAGTCTCAT 57.863 33.333 2.11 4.54 38.80 2.90
4019 5082 4.645136 TGTTACTAGCACAGTCTCATAGGG 59.355 45.833 0.00 0.00 38.80 3.53
4020 5083 3.671740 ACTAGCACAGTCTCATAGGGA 57.328 47.619 0.00 0.00 28.33 4.20
4022 5085 4.551671 ACTAGCACAGTCTCATAGGGATT 58.448 43.478 0.00 0.00 28.33 3.01
4023 5086 4.965532 ACTAGCACAGTCTCATAGGGATTT 59.034 41.667 0.00 0.00 28.33 2.17
4026 5089 3.065925 GCACAGTCTCATAGGGATTTTGC 59.934 47.826 0.00 0.00 0.00 3.68
4027 5090 4.521146 CACAGTCTCATAGGGATTTTGCT 58.479 43.478 0.00 0.00 0.00 3.91
4028 5091 4.334759 CACAGTCTCATAGGGATTTTGCTG 59.665 45.833 0.00 0.00 0.00 4.41
4030 5093 4.334759 CAGTCTCATAGGGATTTTGCTGTG 59.665 45.833 0.00 0.00 0.00 3.66
4033 5096 3.355378 TCATAGGGATTTTGCTGTGGTG 58.645 45.455 0.00 0.00 0.00 4.17
4088 7647 4.752879 CCGTGACCATTCGGCGGT 62.753 66.667 7.21 0.00 40.28 5.68
4097 7656 3.768185 ATTCGGCGGTCGGTGATCG 62.768 63.158 7.21 0.00 39.39 3.69
4115 7674 2.588439 GCTCTGCCATCTGCCTCA 59.412 61.111 0.00 0.00 40.16 3.86
4122 7681 1.375098 GCCATCTGCCTCACAGCTTC 61.375 60.000 0.00 0.00 46.76 3.86
4125 7684 2.866085 ATCTGCCTCACAGCTTCGCC 62.866 60.000 0.00 0.00 46.76 5.54
4251 7843 2.509786 CGCACATGCATTTGCCCC 60.510 61.111 27.42 5.69 42.21 5.80
4252 7844 2.125024 GCACATGCATTTGCCCCC 60.125 61.111 24.25 0.00 41.18 5.40
4273 7865 1.503542 CCCGATCTTGTGCTGCAAC 59.496 57.895 2.77 0.00 32.90 4.17
4281 7873 1.000938 CTTGTGCTGCAACCCTTTCTC 60.001 52.381 2.77 0.00 32.90 2.87
4283 7875 0.877743 GTGCTGCAACCCTTTCTCTC 59.122 55.000 2.77 0.00 0.00 3.20
4284 7876 0.250901 TGCTGCAACCCTTTCTCTCC 60.251 55.000 0.00 0.00 0.00 3.71
4285 7877 0.962855 GCTGCAACCCTTTCTCTCCC 60.963 60.000 0.00 0.00 0.00 4.30
4287 7879 0.693049 TGCAACCCTTTCTCTCCCTC 59.307 55.000 0.00 0.00 0.00 4.30
4290 7882 2.545810 CAACCCTTTCTCTCCCTCTCT 58.454 52.381 0.00 0.00 0.00 3.10
4297 7889 5.000591 CCTTTCTCTCCCTCTCTTTGTTTC 58.999 45.833 0.00 0.00 0.00 2.78
4298 7890 4.625607 TTCTCTCCCTCTCTTTGTTTCC 57.374 45.455 0.00 0.00 0.00 3.13
4299 7891 3.863086 TCTCTCCCTCTCTTTGTTTCCT 58.137 45.455 0.00 0.00 0.00 3.36
4306 7906 1.333619 TCTCTTTGTTTCCTTGTGCGC 59.666 47.619 0.00 0.00 0.00 6.09
4310 7910 0.662619 TTGTTTCCTTGTGCGCTCTG 59.337 50.000 9.73 2.44 0.00 3.35
4324 7924 0.176910 GCTCTGGGGCTAGTTCACTC 59.823 60.000 0.00 0.00 0.00 3.51
4336 7936 5.395103 GGCTAGTTCACTCATCAGAGACAAT 60.395 44.000 0.00 0.00 44.98 2.71
4358 7958 3.305897 TGCGCACGTATTCTGAATTACAG 59.694 43.478 5.66 0.00 46.97 2.74
4409 8009 0.108424 TTTTTGGGTGTGTGCACTGC 60.108 50.000 19.41 11.49 44.65 4.40
4410 8010 1.253593 TTTTGGGTGTGTGCACTGCA 61.254 50.000 19.41 14.05 44.65 4.41
4420 8037 1.750206 TGTGCACTGCAGACACAAAAT 59.250 42.857 31.14 4.37 41.11 1.82
4422 8039 3.379688 TGTGCACTGCAGACACAAAATAA 59.620 39.130 31.14 15.96 41.11 1.40
4423 8040 4.142293 TGTGCACTGCAGACACAAAATAAA 60.142 37.500 31.14 15.44 41.11 1.40
4437 8054 5.691754 CACAAAATAAACCTCTTCTTGTGCC 59.308 40.000 0.00 0.00 36.75 5.01
4483 8188 3.170791 TCAAGATGAGTCGATTCAGGC 57.829 47.619 16.14 10.45 0.00 4.85
4492 8197 2.169789 CGATTCAGGCCTCACGCAG 61.170 63.158 0.00 0.00 40.31 5.18
4494 8199 1.078848 ATTCAGGCCTCACGCAGAC 60.079 57.895 0.00 0.00 40.31 3.51
4495 8200 1.548357 ATTCAGGCCTCACGCAGACT 61.548 55.000 0.00 0.00 40.31 3.24
4496 8201 2.433838 CAGGCCTCACGCAGACTG 60.434 66.667 0.00 0.00 40.31 3.51
4497 8202 2.601666 AGGCCTCACGCAGACTGA 60.602 61.111 6.65 0.00 40.31 3.41
4498 8203 2.433318 GGCCTCACGCAGACTGAC 60.433 66.667 6.65 0.00 40.31 3.51
4499 8204 2.653702 GCCTCACGCAGACTGACT 59.346 61.111 6.65 0.00 37.47 3.41
4514 8219 2.425312 ACTGACTGACTATTCGGCAGAG 59.575 50.000 15.34 0.00 36.51 3.35
4532 8237 3.321682 CAGAGGAAATTCAGGCACCAAAA 59.678 43.478 0.00 0.00 0.00 2.44
4533 8238 3.966665 AGAGGAAATTCAGGCACCAAAAA 59.033 39.130 0.00 0.00 0.00 1.94
4540 8245 4.589216 TTCAGGCACCAAAAATCAAGAG 57.411 40.909 0.00 0.00 0.00 2.85
4564 8269 3.665675 GATTCAGGCCCGCACTCGT 62.666 63.158 0.00 0.00 0.00 4.18
4582 8296 1.795872 CGTAGAACAATCAACGGCACA 59.204 47.619 0.00 0.00 0.00 4.57
4610 8324 8.617809 ACATCAATCAACACGGGTATAATTAAC 58.382 33.333 0.00 0.00 0.00 2.01
4611 8325 8.616942 CATCAATCAACACGGGTATAATTAACA 58.383 33.333 0.00 0.00 0.00 2.41
4612 8326 8.563123 TCAATCAACACGGGTATAATTAACAA 57.437 30.769 0.00 0.00 0.00 2.83
4621 8335 7.960738 CACGGGTATAATTAACAACAACAAGAG 59.039 37.037 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.000819 TTGGACGGGAGCGATGGT 61.001 61.111 0.00 0.00 0.00 3.55
25 27 5.880054 ACCATGAAGAATAAAGGACGTTG 57.120 39.130 0.00 0.00 0.00 4.10
123 126 3.507233 TGGCAGAAACTTTGGCTATGAAG 59.493 43.478 0.61 0.00 41.29 3.02
220 223 1.078708 TTAGGGGCACAGCTAACGC 60.079 57.895 0.00 0.00 0.00 4.84
307 313 4.013728 TCCCGCAATGCAACTAGTAAAAT 58.986 39.130 5.91 0.00 0.00 1.82
419 428 5.046950 GGACTTATGATGGGATAGACCAGAC 60.047 48.000 0.00 0.00 45.20 3.51
420 429 5.087323 GGACTTATGATGGGATAGACCAGA 58.913 45.833 0.00 0.00 45.20 3.86
421 430 4.223923 GGGACTTATGATGGGATAGACCAG 59.776 50.000 0.00 0.00 45.20 4.00
422 431 4.168101 GGGACTTATGATGGGATAGACCA 58.832 47.826 0.00 0.00 46.24 4.02
423 432 4.168101 TGGGACTTATGATGGGATAGACC 58.832 47.826 0.00 0.00 38.08 3.85
434 443 4.502604 GCTATTACCGCTTGGGACTTATGA 60.503 45.833 0.00 0.00 39.97 2.15
476 486 3.391296 GGTCTATCTACATTGGGCCTCAA 59.609 47.826 4.53 5.84 40.01 3.02
488 499 1.202615 GCCAAACCGGGGTCTATCTAC 60.203 57.143 6.32 0.00 34.06 2.59
544 555 3.078837 GGGATTAACAAAGCTTGACCGA 58.921 45.455 0.00 0.00 0.00 4.69
579 598 6.780522 AGAAAGCAAAGGGTTTGGAATAAGTA 59.219 34.615 1.80 0.00 44.23 2.24
624 645 7.180051 TGTTTTAATGGGCCAGAAGATACAAAT 59.820 33.333 13.78 0.00 0.00 2.32
657 678 7.054124 AGACATCTAGAAATTTCGCCCATTTA 58.946 34.615 12.42 0.00 0.00 1.40
758 781 0.584396 TTCTGTTACAAGCAACGCCG 59.416 50.000 0.00 0.00 0.00 6.46
844 983 1.627297 AACTAGGGCAGGCAGCTACC 61.627 60.000 0.81 0.00 44.79 3.18
845 984 0.462759 CAACTAGGGCAGGCAGCTAC 60.463 60.000 0.81 0.00 44.79 3.58
846 985 1.626356 CCAACTAGGGCAGGCAGCTA 61.626 60.000 0.81 0.00 44.79 3.32
885 1266 4.347583 AGAAGATGGATGATTGAGGAGGAC 59.652 45.833 0.00 0.00 0.00 3.85
890 1271 3.244840 GGGGAGAAGATGGATGATTGAGG 60.245 52.174 0.00 0.00 0.00 3.86
891 1272 3.244840 GGGGGAGAAGATGGATGATTGAG 60.245 52.174 0.00 0.00 0.00 3.02
1201 1613 9.914834 GGATGGAGATAGAAGACATATACTAGT 57.085 37.037 0.00 0.00 0.00 2.57
1205 1617 7.012894 CGAGGGATGGAGATAGAAGACATATAC 59.987 44.444 0.00 0.00 0.00 1.47
1211 1623 3.504520 GTCGAGGGATGGAGATAGAAGAC 59.495 52.174 0.00 0.00 0.00 3.01
1224 1643 1.689582 GGGAAGTGGGTCGAGGGAT 60.690 63.158 0.00 0.00 0.00 3.85
1229 1648 1.916777 GGGAAGGGAAGTGGGTCGA 60.917 63.158 0.00 0.00 0.00 4.20
1232 1651 0.178831 AGATGGGAAGGGAAGTGGGT 60.179 55.000 0.00 0.00 0.00 4.51
1249 1668 7.233348 TGGATCAGCATTACATACAGATACAGA 59.767 37.037 0.00 0.00 0.00 3.41
1377 1811 0.390340 TTACGAAGCAGAGGCAGCAG 60.390 55.000 0.00 0.00 44.61 4.24
1415 1898 0.862554 AGGGGGAATGGATGAATGGG 59.137 55.000 0.00 0.00 0.00 4.00
1424 1907 3.411517 AGGCACGAGGGGGAATGG 61.412 66.667 0.00 0.00 0.00 3.16
1482 1970 8.304596 ACAAATGATCGATTAGTACGGATACAT 58.695 33.333 0.00 0.00 33.30 2.29
1498 1986 6.488817 TGTTATCATCAGCAACAAATGATCG 58.511 36.000 0.65 0.00 39.95 3.69
1499 1987 7.972277 AGTTGTTATCATCAGCAACAAATGATC 59.028 33.333 8.62 0.00 42.13 2.92
1510 1998 6.057627 CTGGAATCAGTTGTTATCATCAGC 57.942 41.667 0.00 0.00 36.30 4.26
1624 2115 1.684983 GGGGAATGAATGTGCATCCAG 59.315 52.381 2.86 0.00 0.00 3.86
1687 2181 2.871022 CCTGCAAGAAGAGGAATCGATG 59.129 50.000 0.00 0.00 34.07 3.84
1738 2246 0.882474 ACGAAGGAGACGAGGTTCTG 59.118 55.000 0.00 0.00 34.70 3.02
1759 2267 2.001812 CAGAGGTCGAGGTTGTCATG 57.998 55.000 0.00 0.00 0.00 3.07
1809 2317 2.401766 GCCAATCTGACGCACCTGG 61.402 63.158 0.00 0.00 0.00 4.45
1826 2334 4.201685 GCTGATGAAAATGCTTGTTCATGC 60.202 41.667 19.75 14.58 42.98 4.06
1898 2438 7.913674 AGAAATTACTGTGAAAGAGCCTTAG 57.086 36.000 0.00 0.00 0.00 2.18
1960 2626 1.613925 GGGTGGAAAGGAAAACAGAGC 59.386 52.381 0.00 0.00 0.00 4.09
1980 2646 5.794726 ACAGATCAGATCATCCTCTTCAG 57.205 43.478 13.14 0.00 0.00 3.02
1981 2647 6.556974 AAACAGATCAGATCATCCTCTTCA 57.443 37.500 13.14 0.00 0.00 3.02
1984 2650 7.070946 ACATGTAAACAGATCAGATCATCCTCT 59.929 37.037 13.14 0.00 0.00 3.69
2029 2700 1.278238 CTCGTAGAACCATCGCCAAC 58.722 55.000 0.00 0.00 34.09 3.77
2077 2748 3.410850 CACAAAATCTTCATCGCTGTCG 58.589 45.455 0.00 0.00 0.00 4.35
2224 2895 2.134789 AGCAAGTAAGCATTGGAGGG 57.865 50.000 0.00 0.00 36.85 4.30
2288 2959 7.396419 AGCAAACGTATTGTCATTAACGATAC 58.604 34.615 8.56 5.76 45.93 2.24
2298 2969 5.120053 CACAGACATAGCAAACGTATTGTCA 59.880 40.000 10.65 2.37 0.00 3.58
2316 2987 2.351157 GGATGAAAAGTGCTGCACAGAC 60.351 50.000 31.90 19.93 36.74 3.51
2330 3001 6.716628 ACATTCTTCAGTTTGCTAGGATGAAA 59.283 34.615 0.00 0.00 30.50 2.69
2385 3056 8.864069 AAATATGTGTGTGTTTTTCGATGAAA 57.136 26.923 0.00 0.00 0.00 2.69
2398 3069 5.531634 ACCAAAGAGCAAAATATGTGTGTG 58.468 37.500 0.00 0.00 0.00 3.82
2399 3070 5.789643 ACCAAAGAGCAAAATATGTGTGT 57.210 34.783 0.00 0.00 0.00 3.72
2400 3071 6.700960 TGAAACCAAAGAGCAAAATATGTGTG 59.299 34.615 0.00 0.00 0.00 3.82
2401 3072 6.815089 TGAAACCAAAGAGCAAAATATGTGT 58.185 32.000 0.00 0.00 0.00 3.72
2412 3084 6.660887 TTTTGACAAATGAAACCAAAGAGC 57.339 33.333 0.50 0.00 0.00 4.09
2460 3134 7.093354 TCATGAGAGTAACAGCAAGTCTTTAG 58.907 38.462 0.00 0.00 0.00 1.85
2461 3135 6.993079 TCATGAGAGTAACAGCAAGTCTTTA 58.007 36.000 0.00 0.00 0.00 1.85
2462 3136 5.858381 TCATGAGAGTAACAGCAAGTCTTT 58.142 37.500 0.00 0.00 0.00 2.52
2463 3137 5.474578 TCATGAGAGTAACAGCAAGTCTT 57.525 39.130 0.00 0.00 0.00 3.01
2464 3138 5.070770 CTCATGAGAGTAACAGCAAGTCT 57.929 43.478 18.34 0.00 37.11 3.24
2492 3166 1.395826 GGTATCGAGCAGCTGAGGGT 61.396 60.000 20.43 3.83 0.00 4.34
2554 3228 3.820467 CAGGTTGTGTTCTAAATCCTGCA 59.180 43.478 0.00 0.00 35.37 4.41
2692 3374 8.040727 TGTGTAATCACTAATCAGCATACAACT 58.959 33.333 0.00 0.00 44.14 3.16
2942 3646 7.158099 AGGTTTATGACTCTAAAACAATGGC 57.842 36.000 0.00 0.00 35.33 4.40
2973 3677 5.105957 GGTTGCCAAAATTTGTTTTCCAACT 60.106 36.000 4.92 0.00 35.61 3.16
3029 3733 5.941058 TGGGACGTCAATACATTTACAATGT 59.059 36.000 18.91 7.27 36.13 2.71
3144 3849 3.288809 AGCCAAAGAGAAAAATGCGTC 57.711 42.857 0.00 0.00 0.00 5.19
3292 3997 8.503196 CATGCAGTAGAGTACAAAACAATTACA 58.497 33.333 0.00 0.00 0.00 2.41
3406 4464 6.339194 TCATGGTATATGAAACGTTTGTCG 57.661 37.500 20.10 0.00 46.00 4.35
3483 4542 6.906157 AAGGGCATGATTGGTTCATATAAG 57.094 37.500 0.00 0.00 43.40 1.73
3581 4640 6.183360 GGAAAATACGGATTAGTTGGCATTGA 60.183 38.462 0.00 0.00 0.00 2.57
3587 4646 5.527582 CAGGAGGAAAATACGGATTAGTTGG 59.472 44.000 0.00 0.00 0.00 3.77
3596 4655 1.737793 GCACACAGGAGGAAAATACGG 59.262 52.381 0.00 0.00 0.00 4.02
3598 4657 2.092323 GGGCACACAGGAGGAAAATAC 58.908 52.381 0.00 0.00 0.00 1.89
3679 4739 3.114616 CTTCTCACTGCGGTGGCG 61.115 66.667 25.15 16.23 44.10 5.69
3777 4837 5.299028 GTGCATTACACCATGGAATATCACA 59.701 40.000 21.47 6.17 44.02 3.58
3806 4866 4.175516 GTGAATGGGTGCACAAATGTATG 58.824 43.478 20.43 0.00 35.19 2.39
3876 4937 3.073798 CCAACCAGGGCCACACATATATA 59.926 47.826 6.18 0.00 0.00 0.86
3879 4940 0.033208 CCAACCAGGGCCACACATAT 60.033 55.000 6.18 0.00 0.00 1.78
3895 4956 3.117663 ACAAGTCCTTTCCAACTAGCCAA 60.118 43.478 0.00 0.00 0.00 4.52
3992 5055 9.232473 CCTATGAGACTGTGCTAGTAACATATA 57.768 37.037 14.10 0.00 40.53 0.86
3993 5056 7.177568 CCCTATGAGACTGTGCTAGTAACATAT 59.822 40.741 14.10 0.00 40.53 1.78
3994 5057 6.490381 CCCTATGAGACTGTGCTAGTAACATA 59.510 42.308 1.51 13.56 40.53 2.29
4011 5074 3.379372 CACCACAGCAAAATCCCTATGAG 59.621 47.826 0.00 0.00 0.00 2.90
4015 5078 1.544724 GCACCACAGCAAAATCCCTA 58.455 50.000 0.00 0.00 0.00 3.53
4016 5079 1.526575 CGCACCACAGCAAAATCCCT 61.527 55.000 0.00 0.00 0.00 4.20
4017 5080 1.080569 CGCACCACAGCAAAATCCC 60.081 57.895 0.00 0.00 0.00 3.85
4019 5082 1.734117 GGCGCACCACAGCAAAATC 60.734 57.895 10.83 0.00 35.26 2.17
4020 5083 2.339712 GGCGCACCACAGCAAAAT 59.660 55.556 10.83 0.00 35.26 1.82
4055 7605 3.858225 GGAATCCGTCCCCGTCCC 61.858 72.222 0.00 0.00 41.10 4.46
4088 7647 3.838271 GGCAGAGCCGATCACCGA 61.838 66.667 0.00 0.00 39.62 4.69
4101 7660 3.997057 AAGCTGTGAGGCAGATGGCAG 62.997 57.143 9.22 0.00 43.97 4.85
4125 7684 3.499737 GCATTGGGAGTGCGACGG 61.500 66.667 0.00 0.00 32.29 4.79
4132 7691 0.482446 TGGAACCTTGCATTGGGAGT 59.518 50.000 10.46 0.00 0.00 3.85
4133 7692 0.890683 GTGGAACCTTGCATTGGGAG 59.109 55.000 10.46 0.00 0.00 4.30
4203 7795 1.002659 TCTTGCTTAGCTTGGCCGTTA 59.997 47.619 5.60 0.00 0.00 3.18
4251 7843 4.473520 AGCACAAGATCGGGGCGG 62.474 66.667 8.69 0.00 0.00 6.13
4252 7844 3.197790 CAGCACAAGATCGGGGCG 61.198 66.667 8.69 1.75 0.00 6.13
4273 7865 2.909662 ACAAAGAGAGGGAGAGAAAGGG 59.090 50.000 0.00 0.00 0.00 3.95
4281 7873 3.817647 CACAAGGAAACAAAGAGAGGGAG 59.182 47.826 0.00 0.00 0.00 4.30
4283 7875 2.294512 GCACAAGGAAACAAAGAGAGGG 59.705 50.000 0.00 0.00 0.00 4.30
4284 7876 2.031682 CGCACAAGGAAACAAAGAGAGG 60.032 50.000 0.00 0.00 0.00 3.69
4285 7877 2.603173 GCGCACAAGGAAACAAAGAGAG 60.603 50.000 0.30 0.00 0.00 3.20
4287 7879 1.334869 AGCGCACAAGGAAACAAAGAG 59.665 47.619 11.47 0.00 0.00 2.85
4290 7882 1.065401 CAGAGCGCACAAGGAAACAAA 59.935 47.619 11.47 0.00 0.00 2.83
4298 7890 3.315142 TAGCCCCAGAGCGCACAAG 62.315 63.158 11.47 0.00 38.01 3.16
4299 7891 3.315142 CTAGCCCCAGAGCGCACAA 62.315 63.158 11.47 0.00 38.01 3.33
4306 7906 1.561643 TGAGTGAACTAGCCCCAGAG 58.438 55.000 0.00 0.00 0.00 3.35
4310 7910 2.102252 CTCTGATGAGTGAACTAGCCCC 59.898 54.545 0.00 0.00 35.67 5.80
4324 7924 0.025898 CGTGCGCATTGTCTCTGATG 59.974 55.000 15.91 0.00 0.00 3.07
4336 7936 3.254892 TGTAATTCAGAATACGTGCGCA 58.745 40.909 5.66 5.66 0.00 6.09
4397 7997 1.353103 GTGTCTGCAGTGCACACAC 59.647 57.895 31.78 31.78 46.88 3.82
4398 7998 0.676151 TTGTGTCTGCAGTGCACACA 60.676 50.000 31.01 28.20 41.44 3.72
4399 7999 0.451383 TTTGTGTCTGCAGTGCACAC 59.549 50.000 31.01 27.51 41.99 3.82
4400 8000 1.172175 TTTTGTGTCTGCAGTGCACA 58.828 45.000 29.00 29.00 40.79 4.57
4401 8001 2.497107 ATTTTGTGTCTGCAGTGCAC 57.503 45.000 25.83 25.83 33.79 4.57
4405 8005 5.133221 AGAGGTTTATTTTGTGTCTGCAGT 58.867 37.500 14.67 0.00 0.00 4.40
4409 8009 7.645340 CACAAGAAGAGGTTTATTTTGTGTCTG 59.355 37.037 6.35 0.00 39.15 3.51
4410 8010 7.682021 GCACAAGAAGAGGTTTATTTTGTGTCT 60.682 37.037 13.77 0.00 43.36 3.41
4413 8013 5.691754 GGCACAAGAAGAGGTTTATTTTGTG 59.308 40.000 9.40 9.40 43.93 3.33
4420 8037 2.062636 AGGGGCACAAGAAGAGGTTTA 58.937 47.619 0.00 0.00 0.00 2.01
4422 8039 0.853530 AAGGGGCACAAGAAGAGGTT 59.146 50.000 0.00 0.00 0.00 3.50
4423 8040 0.111253 CAAGGGGCACAAGAAGAGGT 59.889 55.000 0.00 0.00 0.00 3.85
4437 8054 3.031736 TCGATTTAGAGAGTCCCAAGGG 58.968 50.000 0.00 0.00 0.00 3.95
4474 8179 2.125552 TGCGTGAGGCCTGAATCG 60.126 61.111 12.00 10.61 42.61 3.34
4483 8188 0.387878 GTCAGTCAGTCTGCGTGAGG 60.388 60.000 4.64 0.00 43.32 3.86
4492 8197 2.423892 TCTGCCGAATAGTCAGTCAGTC 59.576 50.000 0.00 0.00 0.00 3.51
4494 8199 2.223688 CCTCTGCCGAATAGTCAGTCAG 60.224 54.545 0.00 0.00 0.00 3.51
4495 8200 1.751351 CCTCTGCCGAATAGTCAGTCA 59.249 52.381 0.00 0.00 0.00 3.41
4496 8201 2.025155 TCCTCTGCCGAATAGTCAGTC 58.975 52.381 0.00 0.00 0.00 3.51
4497 8202 2.145397 TCCTCTGCCGAATAGTCAGT 57.855 50.000 0.00 0.00 0.00 3.41
4498 8203 3.526931 TTTCCTCTGCCGAATAGTCAG 57.473 47.619 0.00 0.00 0.00 3.51
4499 8204 4.081142 TGAATTTCCTCTGCCGAATAGTCA 60.081 41.667 0.00 0.00 0.00 3.41
4507 8212 0.677731 TGCCTGAATTTCCTCTGCCG 60.678 55.000 0.00 0.00 0.00 5.69
4510 8215 2.205022 TGGTGCCTGAATTTCCTCTG 57.795 50.000 0.00 0.00 0.00 3.35
4514 8219 4.640364 TGATTTTTGGTGCCTGAATTTCC 58.360 39.130 0.00 0.00 0.00 3.13
4532 8237 3.431486 GCCTGAATCGACTCCTCTTGATT 60.431 47.826 0.00 0.00 33.96 2.57
4533 8238 2.102252 GCCTGAATCGACTCCTCTTGAT 59.898 50.000 0.00 0.00 0.00 2.57
4540 8245 2.107141 CGGGCCTGAATCGACTCC 59.893 66.667 5.28 0.00 0.00 3.85
4564 8269 2.546368 GTGTGTGCCGTTGATTGTTCTA 59.454 45.455 0.00 0.00 0.00 2.10
4582 8296 2.270352 ACCCGTGTTGATTGATGTGT 57.730 45.000 0.00 0.00 0.00 3.72
4621 8335 4.754114 AGTCATTCTCTTGTTGCAAGTCTC 59.246 41.667 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.