Multiple sequence alignment - TraesCS3B01G097600

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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 TraesCS3B01G097600 chr3B 100.000 5829 0 0 1 5829 65340175 65334347 0.000000e+00 10765.0
1 TraesCS3B01G097600 chr5B 98.192 2268 35 2 1507 3774 182439003 182436742 0.000000e+00 3956.0
2 TraesCS3B01G097600 chr5B 96.404 2280 76 4 1496 3773 29566507 29568782 0.000000e+00 3751.0
3 TraesCS3B01G097600 chr5B 96.360 2280 74 5 1494 3773 708974684 708972414 0.000000e+00 3742.0
4 TraesCS3B01G097600 chr5B 76.482 523 82 30 5319 5829 615938305 615938798 4.510000e-61 246.0
5 TraesCS3B01G097600 chr5B 87.619 105 12 1 3841 3945 16174602 16174499 2.850000e-23 121.0
6 TraesCS3B01G097600 chr6B 96.797 2279 69 3 1496 3774 712339433 712337159 0.000000e+00 3801.0
7 TraesCS3B01G097600 chr6B 96.544 2286 68 4 1497 3774 711657793 711655511 0.000000e+00 3773.0
8 TraesCS3B01G097600 chr6B 85.290 639 52 23 843 1462 692638979 692638364 6.420000e-174 621.0
9 TraesCS3B01G097600 chr6B 85.473 592 74 6 3993 4581 692719314 692718732 1.800000e-169 606.0
10 TraesCS3B01G097600 chr6B 83.288 365 37 10 994 1353 692721115 692720770 1.220000e-81 315.0
11 TraesCS3B01G097600 chr6B 92.308 195 15 0 4387 4581 692638358 692638164 1.600000e-70 278.0
12 TraesCS3B01G097600 chr6B 95.946 74 3 0 1391 1464 692720660 692720587 2.850000e-23 121.0
13 TraesCS3B01G097600 chr6B 79.699 133 14 4 847 972 692721308 692721182 3.740000e-12 84.2
14 TraesCS3B01G097600 chr3A 96.708 2278 71 3 1496 3773 474446698 474444425 0.000000e+00 3788.0
15 TraesCS3B01G097600 chr3A 96.444 2278 76 3 1496 3773 66349978 66352250 0.000000e+00 3753.0
16 TraesCS3B01G097600 chr3A 88.971 1079 94 16 162 1230 53295201 53294138 0.000000e+00 1310.0
17 TraesCS3B01G097600 chr3A 93.750 656 41 0 3910 4565 53293857 53293202 0.000000e+00 985.0
18 TraesCS3B01G097600 chr3A 81.368 1111 111 45 4788 5829 53291453 53290370 0.000000e+00 817.0
19 TraesCS3B01G097600 chr3A 94.737 171 8 1 4621 4791 53293053 53292884 1.250000e-66 265.0
20 TraesCS3B01G097600 chr3A 95.536 112 4 1 1387 1497 53294058 53293947 1.670000e-40 178.0
21 TraesCS3B01G097600 chr3A 88.660 97 6 2 3773 3869 53293947 53293856 4.770000e-21 113.0
22 TraesCS3B01G097600 chrUn 96.620 2278 70 5 1496 3773 53742701 53744971 0.000000e+00 3773.0
23 TraesCS3B01G097600 chr1B 96.360 2280 73 5 1496 3773 326007262 326004991 0.000000e+00 3742.0
24 TraesCS3B01G097600 chr3D 91.986 2009 126 23 3835 5827 42396085 42398074 0.000000e+00 2785.0
25 TraesCS3B01G097600 chr3D 92.273 673 22 9 840 1497 42395335 42395992 0.000000e+00 928.0
26 TraesCS3B01G097600 chr3D 88.567 691 67 10 167 851 42394618 42395302 0.000000e+00 828.0
27 TraesCS3B01G097600 chr3D 77.230 426 70 18 5395 5810 458295133 458295541 2.110000e-54 224.0
28 TraesCS3B01G097600 chr3D 89.634 164 16 1 4 167 42394379 42394541 2.130000e-49 207.0
29 TraesCS3B01G097600 chr3D 92.500 80 2 1 3773 3852 42395992 42396067 1.720000e-20 111.0
30 TraesCS3B01G097600 chr6D 93.062 663 40 6 3955 4615 18534343 18535001 0.000000e+00 965.0
31 TraesCS3B01G097600 chr6D 84.592 980 109 23 3963 4928 455496866 455495915 0.000000e+00 935.0
32 TraesCS3B01G097600 chr6D 91.045 670 31 10 840 1497 18533170 18533822 0.000000e+00 878.0
33 TraesCS3B01G097600 chr6D 89.091 550 43 7 4641 5188 18534995 18535529 0.000000e+00 667.0
34 TraesCS3B01G097600 chr6D 85.746 449 43 14 1055 1497 455497383 455496950 6.890000e-124 455.0
35 TraesCS3B01G097600 chr6D 86.611 239 7 7 841 1062 455497782 455497552 2.100000e-59 241.0
36 TraesCS3B01G097600 chr6D 77.938 417 56 23 5437 5825 2365983 2365575 1.630000e-55 228.0
37 TraesCS3B01G097600 chr6D 89.630 135 9 2 3773 3907 18533822 18533951 3.610000e-37 167.0
38 TraesCS3B01G097600 chr6D 91.228 114 6 3 739 851 18533024 18533134 1.010000e-32 152.0
39 TraesCS3B01G097600 chr6D 91.781 73 2 1 3773 3845 455496950 455496882 1.340000e-16 99.0
40 TraesCS3B01G097600 chr6D 89.855 69 7 0 1395 1463 455498479 455498547 8.050000e-14 89.8
41 TraesCS3B01G097600 chr6A 85.396 493 34 12 841 1305 602163129 602162647 1.470000e-130 477.0
42 TraesCS3B01G097600 chr6A 76.969 508 84 28 5332 5828 585496201 585495716 5.790000e-65 259.0
43 TraesCS3B01G097600 chr6A 88.350 103 10 2 3843 3945 442400468 442400368 7.930000e-24 122.0
44 TraesCS3B01G097600 chr6A 89.855 69 7 0 1395 1463 602164936 602165004 8.050000e-14 89.8
45 TraesCS3B01G097600 chr5A 86.667 225 24 6 5604 5826 211640449 211640229 1.620000e-60 244.0
46 TraesCS3B01G097600 chr5D 78.167 371 61 18 5326 5689 342964460 342964103 9.830000e-53 219.0
47 TraesCS3B01G097600 chr5D 79.276 304 47 15 5529 5827 387319281 387319573 1.280000e-46 198.0
48 TraesCS3B01G097600 chr5D 88.776 98 10 1 3847 3944 530428331 530428427 1.030000e-22 119.0
49 TraesCS3B01G097600 chr7A 81.781 247 35 9 5319 5559 566005746 566005988 1.280000e-46 198.0
50 TraesCS3B01G097600 chr7A 82.684 231 27 10 5605 5828 33445998 33446222 5.960000e-45 193.0
51 TraesCS3B01G097600 chr7A 91.667 84 6 1 3847 3930 645464650 645464568 1.330000e-21 115.0
52 TraesCS3B01G097600 chr2D 78.000 350 54 20 5329 5662 190030268 190029926 1.280000e-46 198.0
53 TraesCS3B01G097600 chr4A 77.810 347 58 16 5333 5667 624975063 624974724 4.610000e-46 196.0
54 TraesCS3B01G097600 chr7D 82.479 234 29 12 5333 5559 499969960 499970188 1.660000e-45 195.0
55 TraesCS3B01G097600 chr7D 86.408 103 6 7 3846 3945 554684044 554683947 7.990000e-19 106.0
56 TraesCS3B01G097600 chr7B 76.675 403 61 24 5319 5715 527959809 527960184 5.960000e-45 193.0
57 TraesCS3B01G097600 chr7B 85.714 105 13 2 3842 3946 381868360 381868462 6.180000e-20 110.0
58 TraesCS3B01G097600 chr2B 75.778 450 62 33 5415 5826 495816068 495815628 3.590000e-42 183.0
59 TraesCS3B01G097600 chr4D 88.235 102 7 2 3847 3944 398567993 398568093 3.690000e-22 117.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G097600 chr3B 65334347 65340175 5828 True 10765.000000 10765 100.000000 1 5829 1 chr3B.!!$R1 5828
1 TraesCS3B01G097600 chr5B 182436742 182439003 2261 True 3956.000000 3956 98.192000 1507 3774 1 chr5B.!!$R2 2267
2 TraesCS3B01G097600 chr5B 29566507 29568782 2275 False 3751.000000 3751 96.404000 1496 3773 1 chr5B.!!$F1 2277
3 TraesCS3B01G097600 chr5B 708972414 708974684 2270 True 3742.000000 3742 96.360000 1494 3773 1 chr5B.!!$R3 2279
4 TraesCS3B01G097600 chr6B 712337159 712339433 2274 True 3801.000000 3801 96.797000 1496 3774 1 chr6B.!!$R2 2278
5 TraesCS3B01G097600 chr6B 711655511 711657793 2282 True 3773.000000 3773 96.544000 1497 3774 1 chr6B.!!$R1 2277
6 TraesCS3B01G097600 chr6B 692638164 692638979 815 True 449.500000 621 88.799000 843 4581 2 chr6B.!!$R3 3738
7 TraesCS3B01G097600 chr6B 692718732 692721308 2576 True 281.550000 606 86.101500 847 4581 4 chr6B.!!$R4 3734
8 TraesCS3B01G097600 chr3A 474444425 474446698 2273 True 3788.000000 3788 96.708000 1496 3773 1 chr3A.!!$R1 2277
9 TraesCS3B01G097600 chr3A 66349978 66352250 2272 False 3753.000000 3753 96.444000 1496 3773 1 chr3A.!!$F1 2277
10 TraesCS3B01G097600 chr3A 53290370 53295201 4831 True 611.333333 1310 90.503667 162 5829 6 chr3A.!!$R2 5667
11 TraesCS3B01G097600 chrUn 53742701 53744971 2270 False 3773.000000 3773 96.620000 1496 3773 1 chrUn.!!$F1 2277
12 TraesCS3B01G097600 chr1B 326004991 326007262 2271 True 3742.000000 3742 96.360000 1496 3773 1 chr1B.!!$R1 2277
13 TraesCS3B01G097600 chr3D 42394379 42398074 3695 False 971.800000 2785 90.992000 4 5827 5 chr3D.!!$F2 5823
14 TraesCS3B01G097600 chr6D 18533024 18535529 2505 False 565.800000 965 90.811200 739 5188 5 chr6D.!!$F2 4449
15 TraesCS3B01G097600 chr6D 455495915 455497782 1867 True 432.500000 935 87.182500 841 4928 4 chr6D.!!$R2 4087

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
900 1035 1.005450 GGTACAGCTTCCAATCCCCAA 59.995 52.381 0.0 0.0 0.00 4.12 F
1322 1722 0.876342 GCCTTACTCCTCGAATGCGG 60.876 60.000 0.0 0.0 38.28 5.69 F
2127 2632 1.529744 TTTTGTCCTCCTCCCACCTT 58.470 50.000 0.0 0.0 0.00 3.50 F
3640 4159 1.613520 CGGAGGGAGAGAGTGTGTGTA 60.614 57.143 0.0 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 2585 1.064296 CGTACGAGGCTACCAGCTG 59.936 63.158 10.44 6.78 41.99 4.24 R
2142 2647 2.550830 TGCAAGGAAAGAGTGGAGAC 57.449 50.000 0.00 0.00 0.00 3.36 R
3821 4340 1.069049 ACAAAGTTGGGAACTGCATGC 59.931 47.619 11.82 11.82 41.91 4.06 R
4903 8540 0.034337 AGTTATGGTTCACGCCACGT 59.966 50.000 0.00 0.00 41.94 4.49 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
27 28 2.755103 CTCCCAGGTTATCTTTTGCACC 59.245 50.000 0.00 0.00 0.00 5.01
68 69 4.115401 GGAAAATCCCAACTGCTCATTC 57.885 45.455 0.00 0.00 0.00 2.67
78 79 1.302366 CTGCTCATTCTGCGGCAATA 58.698 50.000 3.44 0.00 34.21 1.90
81 82 3.475575 TGCTCATTCTGCGGCAATATTA 58.524 40.909 3.44 0.00 0.00 0.98
83 84 3.250762 GCTCATTCTGCGGCAATATTACA 59.749 43.478 3.44 0.00 0.00 2.41
90 91 3.085533 TGCGGCAATATTACACCTGTTT 58.914 40.909 0.00 0.00 0.00 2.83
91 92 3.508012 TGCGGCAATATTACACCTGTTTT 59.492 39.130 0.00 0.00 0.00 2.43
92 93 4.021894 TGCGGCAATATTACACCTGTTTTT 60.022 37.500 0.00 0.00 0.00 1.94
109 110 1.006086 TTTGCACATCATAGCGACCG 58.994 50.000 0.00 0.00 0.00 4.79
146 147 2.301346 CTGTCCCATTTGGTAGATGCC 58.699 52.381 0.00 0.00 34.77 4.40
178 256 3.574826 ACAGAGTCTACAGGAACCAGTTC 59.425 47.826 1.77 1.77 38.80 3.01
214 292 2.294512 CAGAAAGTTCCTGCCTGGTTTC 59.705 50.000 0.00 0.00 37.07 2.78
265 345 5.499047 CGGTTTTCTTTAGTCTGTTGTGTC 58.501 41.667 0.00 0.00 0.00 3.67
275 355 4.950050 AGTCTGTTGTGTCTCTTTACTGG 58.050 43.478 0.00 0.00 0.00 4.00
295 376 7.247456 ACTGGTTTTCTGGTTTCCTTTTTAA 57.753 32.000 0.00 0.00 0.00 1.52
591 676 8.655651 TGTTCCCAATTTAAAAATGTTCACTC 57.344 30.769 0.00 0.00 0.00 3.51
636 722 6.720012 ATTTTCAAAGAAACTGTTTGCGTT 57.280 29.167 11.03 4.64 35.29 4.84
719 806 7.265647 TCGAAACTTGTTATCAAATTGACCA 57.734 32.000 0.00 0.00 32.87 4.02
761 848 1.074889 ACAGGTACCCCGCAAAAGAAT 59.925 47.619 8.74 0.00 35.12 2.40
762 849 1.472480 CAGGTACCCCGCAAAAGAATG 59.528 52.381 8.74 0.00 35.12 2.67
764 851 2.164338 GGTACCCCGCAAAAGAATGAA 58.836 47.619 0.00 0.00 0.00 2.57
789 877 1.231221 AAACACGTCAAGCGCCAATA 58.769 45.000 2.29 0.00 46.11 1.90
900 1035 1.005450 GGTACAGCTTCCAATCCCCAA 59.995 52.381 0.00 0.00 0.00 4.12
996 1213 4.394920 GTCTCTCTCTACTGGAGTTCACAG 59.605 50.000 0.00 0.00 42.40 3.66
1000 1217 3.827302 TCTCTACTGGAGTTCACAGTTCC 59.173 47.826 3.23 0.00 46.38 3.62
1001 1218 3.572642 TCTACTGGAGTTCACAGTTCCA 58.427 45.455 3.23 0.00 46.38 3.53
1002 1219 2.622064 ACTGGAGTTCACAGTTCCAC 57.378 50.000 0.00 0.00 46.38 4.02
1003 1220 1.837439 ACTGGAGTTCACAGTTCCACA 59.163 47.619 0.00 0.00 46.38 4.17
1004 1221 2.439507 ACTGGAGTTCACAGTTCCACAT 59.560 45.455 0.00 0.00 46.38 3.21
1010 1227 4.464008 AGTTCACAGTTCCACATCACATT 58.536 39.130 0.00 0.00 0.00 2.71
1245 1640 2.939261 GCCGTCGACCAAGAAGGGA 61.939 63.158 10.58 0.00 43.89 4.20
1272 1667 4.831307 CGCCTCTCCGACGAACCG 62.831 72.222 0.00 0.00 0.00 4.44
1322 1722 0.876342 GCCTTACTCCTCGAATGCGG 60.876 60.000 0.00 0.00 38.28 5.69
1358 1763 6.588756 CGATTAGCCTTGTCGCCTTAAATATA 59.411 38.462 0.00 0.00 0.00 0.86
1360 1765 7.900782 TTAGCCTTGTCGCCTTAAATATATC 57.099 36.000 0.00 0.00 0.00 1.63
1378 1876 9.691362 AAATATATCTTTTTGTGTGTGTGTTCC 57.309 29.630 0.00 0.00 0.00 3.62
1379 1877 6.959639 ATATCTTTTTGTGTGTGTGTTCCT 57.040 33.333 0.00 0.00 0.00 3.36
1381 1879 5.554822 TCTTTTTGTGTGTGTGTTCCTAC 57.445 39.130 0.00 0.00 0.00 3.18
1382 1880 4.093703 TCTTTTTGTGTGTGTGTTCCTACG 59.906 41.667 0.00 0.00 0.00 3.51
1383 1881 2.676632 TTGTGTGTGTGTTCCTACGT 57.323 45.000 0.00 0.00 0.00 3.57
1384 1882 3.797451 TTGTGTGTGTGTTCCTACGTA 57.203 42.857 0.00 0.00 0.00 3.57
1385 1883 3.082698 TGTGTGTGTGTTCCTACGTAC 57.917 47.619 0.00 0.00 0.00 3.67
1504 2004 3.055094 ACACACGCCCTTGATCTCTATTT 60.055 43.478 0.00 0.00 0.00 1.40
1523 2023 7.857456 TCTATTTCTAATGGAGCAGTTGGTAA 58.143 34.615 0.00 0.00 0.00 2.85
1823 2325 7.120726 CGTCCATAACTTTCCTTCCTTATTTGT 59.879 37.037 0.00 0.00 0.00 2.83
2127 2632 1.529744 TTTTGTCCTCCTCCCACCTT 58.470 50.000 0.00 0.00 0.00 3.50
2142 2647 3.181476 CCCACCTTCACTGGTTCTTTTTG 60.181 47.826 0.00 0.00 38.45 2.44
2356 2861 4.261614 GGTCGCATTGGTTCTTTTTCTCTT 60.262 41.667 0.00 0.00 0.00 2.85
2667 3172 4.228567 GCCCCGCCTCTGCTACTC 62.229 72.222 0.00 0.00 34.43 2.59
3388 3893 4.191544 GCCAGTAATGTTCTGTGATGCTA 58.808 43.478 0.00 0.00 0.00 3.49
3640 4159 1.613520 CGGAGGGAGAGAGTGTGTGTA 60.614 57.143 0.00 0.00 0.00 2.90
3665 4184 5.476945 AGAATTTGATGGTAAAAAGGTCGCT 59.523 36.000 0.00 0.00 0.00 4.93
3681 4200 6.650427 AGGTCGCTAATGTCACTTGATATA 57.350 37.500 0.00 0.00 0.00 0.86
3821 4340 3.632189 CAAAAGAGGCAAAAGGTTCGAG 58.368 45.455 0.00 0.00 0.00 4.04
3822 4341 1.239347 AAGAGGCAAAAGGTTCGAGC 58.761 50.000 0.00 0.00 0.00 5.03
3823 4342 0.108585 AGAGGCAAAAGGTTCGAGCA 59.891 50.000 0.53 0.00 0.00 4.26
3824 4343 1.168714 GAGGCAAAAGGTTCGAGCAT 58.831 50.000 0.53 0.00 0.00 3.79
3845 4368 4.647424 TGCAGTTCCCAACTTTGTTTAG 57.353 40.909 0.00 0.00 40.46 1.85
3847 4370 5.194432 TGCAGTTCCCAACTTTGTTTAGTA 58.806 37.500 0.00 0.00 40.46 1.82
3859 4382 3.446442 TGTTTAGTACTCCCTCCGTCT 57.554 47.619 0.00 0.00 0.00 4.18
3860 4383 3.771216 TGTTTAGTACTCCCTCCGTCTT 58.229 45.455 0.00 0.00 0.00 3.01
3937 4861 8.895737 AGTTAAGACACTTATTTTGAAACGGAA 58.104 29.630 0.00 0.00 0.00 4.30
3999 6055 9.834628 TTTTAATCAAAGTTTTGCTATAGTCCG 57.165 29.630 0.84 0.00 38.05 4.79
4191 6256 6.002704 AGAGAAACATGCTCTCTCAAAACAT 58.997 36.000 18.04 0.00 45.24 2.71
4238 6303 4.783227 TCAAGCTAGGACCCAGATTTTACT 59.217 41.667 0.00 0.00 0.00 2.24
4282 6347 0.667184 CCTCATTTGGCGTTGTTGGC 60.667 55.000 0.00 0.00 0.00 4.52
4284 6349 0.249238 TCATTTGGCGTTGTTGGCAC 60.249 50.000 0.00 0.00 44.88 5.01
4337 6402 0.896479 TGTCGAGGACGGTGATGGAA 60.896 55.000 0.00 0.00 40.21 3.53
4406 6471 9.102757 GTATATATAATCGTGACGAGGTTCCTA 57.897 37.037 14.71 1.42 39.91 2.94
4492 6557 4.310740 AGTTCCATAATGAGGGAGGTGAT 58.689 43.478 0.00 0.00 36.73 3.06
4702 6901 7.615365 TCTTTTGTTACATAGAATGAGGCCAAT 59.385 33.333 5.01 0.00 0.00 3.16
4729 6928 6.817184 TCTAAGGCTACATGTGGTCTTATTC 58.183 40.000 29.29 4.72 37.56 1.75
4850 8484 4.308899 AGACAGGAATAAGACCGATTCG 57.691 45.455 0.00 0.00 34.67 3.34
4872 8506 5.792468 TCGTTACAAAACAAAACCGTGTTAC 59.208 36.000 0.00 0.00 40.86 2.50
4903 8540 1.753930 TAATACCTCCGTGACAGCGA 58.246 50.000 0.00 0.00 0.00 4.93
4906 8543 4.039357 CCTCCGTGACAGCGACGT 62.039 66.667 0.00 0.00 34.97 4.34
4977 8623 5.433526 AGCTATAAAGGCGTGAACCATAAA 58.566 37.500 0.00 0.00 34.52 1.40
4980 8626 6.636850 GCTATAAAGGCGTGAACCATAAATTG 59.363 38.462 0.00 0.00 0.00 2.32
4995 8642 8.101654 ACCATAAATTGTTTTAGCACTTCGTA 57.898 30.769 0.00 0.00 31.07 3.43
5050 8698 2.812011 GCTACAAAACGGGCCATATAGG 59.188 50.000 4.39 0.00 41.84 2.57
5051 8699 3.495453 GCTACAAAACGGGCCATATAGGA 60.495 47.826 4.39 0.00 41.22 2.94
5055 8703 4.773149 ACAAAACGGGCCATATAGGAAAAA 59.227 37.500 4.39 0.00 41.22 1.94
5106 8760 6.289901 GCATAAAGCGTGTCGACTATATTTC 58.710 40.000 17.92 0.00 0.00 2.17
5112 8766 4.380678 GCGTGTCGACTATATTTCGCATTA 59.619 41.667 17.92 0.00 41.59 1.90
5138 8792 1.202698 AGTTGGCAGAAAGTCTCGCTT 60.203 47.619 0.00 0.00 39.52 4.68
5162 8816 5.687166 AGGTTTCTACGATAATTGGACCA 57.313 39.130 0.00 0.00 0.00 4.02
5193 8847 4.760715 TGCGTGGGCATACTTAAAGTAAAA 59.239 37.500 0.00 0.00 46.21 1.52
5194 8848 5.241064 TGCGTGGGCATACTTAAAGTAAAAA 59.759 36.000 0.00 0.00 46.21 1.94
5236 8892 2.511637 GGGAGAACCAAGATCAATCCCT 59.488 50.000 0.00 0.00 41.46 4.20
5252 8908 4.586618 CTGGTCTCCAGCGAGTTG 57.413 61.111 2.77 0.00 45.13 3.16
5306 8963 8.674607 GTCCAATTTGTGTTAACTAATAGGGAG 58.325 37.037 7.22 0.00 36.61 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.377146 TGCAAAAGATAACCTGGGAGTTTATC 59.623 38.462 0.00 2.83 0.00 1.75
1 2 6.152831 GTGCAAAAGATAACCTGGGAGTTTAT 59.847 38.462 0.00 0.00 0.00 1.40
2 3 5.475564 GTGCAAAAGATAACCTGGGAGTTTA 59.524 40.000 0.00 0.00 0.00 2.01
12 13 3.365969 CGTCCTTGGTGCAAAAGATAACC 60.366 47.826 11.13 0.00 0.00 2.85
16 17 2.270352 TCGTCCTTGGTGCAAAAGAT 57.730 45.000 11.13 0.00 0.00 2.40
23 24 2.604046 ATCACTATCGTCCTTGGTGC 57.396 50.000 0.00 0.00 0.00 5.01
56 57 1.136147 GCCGCAGAATGAGCAGTTG 59.864 57.895 0.00 0.00 39.69 3.16
63 64 3.563808 GGTGTAATATTGCCGCAGAATGA 59.436 43.478 0.00 0.00 39.69 2.57
68 69 2.288666 ACAGGTGTAATATTGCCGCAG 58.711 47.619 0.00 0.00 0.00 5.18
78 79 5.528043 TGATGTGCAAAAACAGGTGTAAT 57.472 34.783 0.00 0.00 32.52 1.89
81 82 4.559300 GCTATGATGTGCAAAAACAGGTGT 60.559 41.667 0.00 0.00 32.52 4.16
83 84 3.366273 CGCTATGATGTGCAAAAACAGGT 60.366 43.478 0.00 0.00 32.52 4.00
90 91 1.006086 CGGTCGCTATGATGTGCAAA 58.994 50.000 0.00 0.00 0.00 3.68
91 92 0.174617 TCGGTCGCTATGATGTGCAA 59.825 50.000 0.00 0.00 0.00 4.08
92 93 0.389025 ATCGGTCGCTATGATGTGCA 59.611 50.000 0.00 0.00 0.00 4.57
109 110 1.470098 ACAGCCGAATGCAGTTTGATC 59.530 47.619 0.00 0.00 44.83 2.92
132 133 7.936847 TGTAGTTTATAGGGCATCTACCAAATG 59.063 37.037 0.00 0.00 0.00 2.32
146 147 8.623030 GTTCCTGTAGACTCTGTAGTTTATAGG 58.377 40.741 10.71 10.71 45.59 2.57
214 292 4.139038 TGAACCTTCTAAAAAGTTCCCCG 58.861 43.478 0.00 0.00 35.73 5.73
236 314 5.374071 ACAGACTAAAGAAAACCGGTTCAT 58.626 37.500 22.53 13.12 0.00 2.57
265 345 5.828328 AGGAAACCAGAAAACCAGTAAAGAG 59.172 40.000 0.00 0.00 0.00 2.85
341 422 7.053316 TGAACATTTTTCTGAATGTGGTGAT 57.947 32.000 4.23 0.00 46.53 3.06
483 564 9.863845 TTTGGAAAAGAGATTTTCTTAAAACGT 57.136 25.926 11.89 0.00 45.41 3.99
614 699 6.532365 AAACGCAAACAGTTTCTTTGAAAA 57.468 29.167 0.00 0.00 37.23 2.29
618 703 5.508124 TGAAAACGCAAACAGTTTCTTTG 57.492 34.783 0.00 0.00 40.49 2.77
636 722 5.890424 AGAACCAAGAACGTTCTTTGAAA 57.110 34.783 35.50 0.00 46.01 2.69
676 762 5.799827 TCGAAAAAGGTGGGAAAATGAAT 57.200 34.783 0.00 0.00 0.00 2.57
685 771 3.793797 ACAAGTTTCGAAAAAGGTGGG 57.206 42.857 13.10 1.23 0.00 4.61
686 772 6.500041 TGATAACAAGTTTCGAAAAAGGTGG 58.500 36.000 13.10 2.27 0.00 4.61
719 806 1.197721 GCGAACAAACTACAGCAGCAT 59.802 47.619 0.00 0.00 0.00 3.79
745 832 3.926821 TTTCATTCTTTTGCGGGGTAC 57.073 42.857 0.00 0.00 0.00 3.34
900 1035 6.850823 CGTGCATGCTACGTAATGAAATTATT 59.149 34.615 24.88 0.00 41.51 1.40
996 1213 5.065988 GGTGGTATGTAATGTGATGTGGAAC 59.934 44.000 0.00 0.00 37.35 3.62
1000 1217 5.008911 CCATGGTGGTATGTAATGTGATGTG 59.991 44.000 2.57 0.00 31.35 3.21
1001 1218 5.104151 TCCATGGTGGTATGTAATGTGATGT 60.104 40.000 12.58 0.00 39.03 3.06
1002 1219 5.239306 GTCCATGGTGGTATGTAATGTGATG 59.761 44.000 12.58 0.00 39.03 3.07
1003 1220 5.376625 GTCCATGGTGGTATGTAATGTGAT 58.623 41.667 12.58 0.00 39.03 3.06
1004 1221 4.682050 CGTCCATGGTGGTATGTAATGTGA 60.682 45.833 12.58 0.00 39.03 3.58
1010 1227 0.103390 CGCGTCCATGGTGGTATGTA 59.897 55.000 12.58 0.00 39.03 2.29
1245 1640 2.125106 GAGAGGCGCCGGAACATT 60.125 61.111 23.20 0.00 0.00 2.71
1305 1700 2.159226 AGAACCGCATTCGAGGAGTAAG 60.159 50.000 0.00 0.00 42.69 2.34
1358 1763 5.220777 CGTAGGAACACACACACAAAAAGAT 60.221 40.000 0.00 0.00 0.00 2.40
1360 1765 4.142773 ACGTAGGAACACACACACAAAAAG 60.143 41.667 0.00 0.00 0.00 2.27
1383 1881 0.794229 GCGCTGCAACGTACGTAGTA 60.794 55.000 23.12 9.62 45.11 1.82
1384 1882 2.736343 TGCGCTGCAACGTACGTAGT 62.736 55.000 23.12 3.61 39.61 2.73
1385 1883 1.410737 ATGCGCTGCAACGTACGTAG 61.411 55.000 23.12 16.50 43.62 3.51
1437 1936 3.645975 CGCTGGCCGAAAACGTGT 61.646 61.111 0.00 0.00 40.02 4.49
1504 2004 5.451937 CGAGATTACCAACTGCTCCATTAGA 60.452 44.000 0.00 0.00 0.00 2.10
1823 2325 2.618241 CTGCTACCAAACAGTTTCTGCA 59.382 45.455 0.00 3.98 34.37 4.41
2082 2584 1.227002 GTACGAGGCTACCAGCTGC 60.227 63.158 8.66 0.00 41.99 5.25
2083 2585 1.064296 CGTACGAGGCTACCAGCTG 59.936 63.158 10.44 6.78 41.99 4.24
2084 2586 2.119655 CCGTACGAGGCTACCAGCT 61.120 63.158 18.76 0.00 41.99 4.24
2127 2632 3.945285 GTGGAGACAAAAAGAACCAGTGA 59.055 43.478 0.00 0.00 46.06 3.41
2142 2647 2.550830 TGCAAGGAAAGAGTGGAGAC 57.449 50.000 0.00 0.00 0.00 3.36
2356 2861 4.464008 AGTGATTTGCAAGGAAAGAGTGA 58.536 39.130 0.00 0.00 0.00 3.41
3197 3702 4.263683 TGAATCCACAGTCAGAGAGAGAGA 60.264 45.833 0.00 0.00 0.00 3.10
3198 3703 4.015764 TGAATCCACAGTCAGAGAGAGAG 58.984 47.826 0.00 0.00 0.00 3.20
3388 3893 4.895668 AACAATTCCCAAAGTGCATCAT 57.104 36.364 0.00 0.00 33.83 2.45
3640 4159 6.015434 AGCGACCTTTTTACCATCAAATTCTT 60.015 34.615 0.00 0.00 0.00 2.52
3821 4340 1.069049 ACAAAGTTGGGAACTGCATGC 59.931 47.619 11.82 11.82 41.91 4.06
3822 4341 3.457610 AACAAAGTTGGGAACTGCATG 57.542 42.857 0.00 0.00 41.91 4.06
3823 4342 4.649218 ACTAAACAAAGTTGGGAACTGCAT 59.351 37.500 0.00 0.00 41.91 3.96
3824 4343 4.020543 ACTAAACAAAGTTGGGAACTGCA 58.979 39.130 0.00 0.00 41.91 4.41
3845 4368 7.277319 CACTTATTTTTAAGACGGAGGGAGTAC 59.723 40.741 0.03 0.00 0.00 2.73
3847 4370 6.171213 CACTTATTTTTAAGACGGAGGGAGT 58.829 40.000 0.03 0.00 0.00 3.85
3912 4836 9.166126 CTTCCGTTTCAAAATAAGTGTCTTAAC 57.834 33.333 0.00 0.00 0.00 2.01
3937 4861 7.690256 AGTAAATTTGTCATGGAAGTACTCCT 58.310 34.615 0.00 0.00 45.64 3.69
4017 6073 5.502544 GCGCAAGAGCCACTAAGTAATTAAG 60.503 44.000 0.30 0.00 43.02 1.85
4096 6161 3.254470 TGTGAGAACCTGTCGAAAACA 57.746 42.857 0.00 0.00 36.18 2.83
4191 6256 2.767394 ACCATGTATGCCACGTAGGTTA 59.233 45.455 0.00 0.00 40.61 2.85
4238 6303 1.885560 TGAAACGGGAAATCGAAGCA 58.114 45.000 0.00 0.00 0.00 3.91
4282 6347 1.153489 CTGCTGGATCGACTGGGTG 60.153 63.158 0.00 0.00 0.00 4.61
4284 6349 1.903877 AACCTGCTGGATCGACTGGG 61.904 60.000 17.64 1.55 37.04 4.45
4406 6471 4.218852 TGGGAAAACAACGTTCTTTTGAGT 59.781 37.500 17.34 0.00 0.00 3.41
4492 6557 0.252421 AGCTGATGGAGACCTCACCA 60.252 55.000 0.00 0.00 40.76 4.17
4702 6901 4.868268 AGACCACATGTAGCCTTAGAGTA 58.132 43.478 0.00 0.00 0.00 2.59
4850 8484 6.924629 TGTAACACGGTTTTGTTTTGTAAC 57.075 33.333 0.00 0.00 40.29 2.50
4872 8506 7.325097 GTCACGGAGGTATTAAATGTGTTTTTG 59.675 37.037 0.00 0.00 0.00 2.44
4903 8540 0.034337 AGTTATGGTTCACGCCACGT 59.966 50.000 0.00 0.00 41.94 4.49
4977 8623 6.380095 TGGTTTACGAAGTGCTAAAACAAT 57.620 33.333 0.00 0.00 45.73 2.71
4980 8626 7.578852 AGTTATGGTTTACGAAGTGCTAAAAC 58.421 34.615 0.00 0.00 45.73 2.43
4995 8642 3.010138 TGGCTCAGGCTTAGTTATGGTTT 59.990 43.478 0.00 0.00 38.73 3.27
5112 8766 1.604278 GACTTTCTGCCAACTCGCTTT 59.396 47.619 0.00 0.00 0.00 3.51
5121 8775 2.612972 CCTAAAGCGAGACTTTCTGCCA 60.613 50.000 0.00 0.00 45.78 4.92
5138 8792 7.185318 TGGTCCAATTATCGTAGAAACCTAA 57.815 36.000 0.00 0.00 43.58 2.69
5139 8793 6.684613 GCTGGTCCAATTATCGTAGAAACCTA 60.685 42.308 0.00 0.00 43.58 3.08
5236 8892 3.059982 CCAACTCGCTGGAGACCA 58.940 61.111 0.00 0.00 43.27 4.02
5447 9134 9.521841 TGTAGGAAAAATGTTGACCATGTATAA 57.478 29.630 0.00 0.00 32.82 0.98
5448 9135 8.952278 GTGTAGGAAAAATGTTGACCATGTATA 58.048 33.333 0.00 0.00 32.82 1.47
5568 9260 9.208022 GGCAACTCTTAATGAAGCTTTTAATTT 57.792 29.630 0.00 0.00 32.21 1.82
5569 9261 8.367156 TGGCAACTCTTAATGAAGCTTTTAATT 58.633 29.630 0.00 4.40 32.21 1.40
5570 9262 7.895759 TGGCAACTCTTAATGAAGCTTTTAAT 58.104 30.769 0.00 0.00 32.21 1.40
5573 9265 5.789643 TGGCAACTCTTAATGAAGCTTTT 57.210 34.783 0.00 0.00 32.21 2.27


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

AutoCloner maintained by Alex Coulton.