Multiple sequence alignment - TraesCS1D01G001500

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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 TraesCS1D01G001500 chr1D 100.000 5257 0 0 1 5257 391359 396615 0.000000e+00 9708.0
1 TraesCS1D01G001500 chr1D 87.072 2305 281 13 1859 4153 620153 617856 0.000000e+00 2590.0
2 TraesCS1D01G001500 chr1D 84.939 1069 139 16 856 1918 647269 648321 0.000000e+00 1062.0
3 TraesCS1D01G001500 chr1D 83.626 1081 155 14 852 1918 458572 459644 0.000000e+00 996.0
4 TraesCS1D01G001500 chr1D 83.548 310 32 8 508 809 646969 647267 6.710000e-69 272.0
5 TraesCS1D01G001500 chr1D 86.730 211 21 5 4441 4649 462895 463100 1.470000e-55 228.0
6 TraesCS1D01G001500 chr1A 86.238 3248 419 21 922 4154 27212181 27215415 0.000000e+00 3496.0
7 TraesCS1D01G001500 chr1A 85.276 3423 449 32 753 4153 3702515 3699126 0.000000e+00 3478.0
8 TraesCS1D01G001500 chr1A 85.918 2315 311 11 1847 4154 3671518 3669212 0.000000e+00 2455.0
9 TraesCS1D01G001500 chr1A 85.283 1094 137 13 852 1924 3657541 3656451 0.000000e+00 1107.0
10 TraesCS1D01G001500 chr1A 87.429 875 105 5 1054 1925 3454752 3453880 0.000000e+00 1002.0
11 TraesCS1D01G001500 chr1A 76.679 819 108 44 4441 5188 27215808 27216614 1.380000e-100 377.0
12 TraesCS1D01G001500 chr1A 88.514 296 30 3 4150 4442 3699048 3698754 6.480000e-94 355.0
13 TraesCS1D01G001500 chr1A 78.596 570 55 36 4463 4976 3578741 3578183 1.100000e-81 315.0
14 TraesCS1D01G001500 chr1A 83.871 155 21 4 5036 5188 3677181 3677029 1.530000e-30 145.0
15 TraesCS1D01G001500 chr1A 91.566 83 7 0 4905 4987 3698652 3698570 1.200000e-21 115.0
16 TraesCS1D01G001500 chr1A 74.747 297 45 18 392 681 27210239 27210512 7.200000e-19 106.0
17 TraesCS1D01G001500 chr3D 87.265 2285 275 14 1879 4156 560057105 560054830 0.000000e+00 2593.0
18 TraesCS1D01G001500 chr3D 85.926 270 26 10 4447 4711 560054412 560054150 1.440000e-70 278.0
19 TraesCS1D01G001500 chr3D 100.000 30 0 0 4739 4768 183153129 183153100 7.350000e-04 56.5
20 TraesCS1D01G001500 chr1B 86.128 2314 310 10 1847 4154 4509861 4507553 0.000000e+00 2484.0
21 TraesCS1D01G001500 chr1B 86.344 2292 284 24 1866 4142 4115529 4117806 0.000000e+00 2471.0
22 TraesCS1D01G001500 chr1B 86.308 2286 290 19 1879 4154 3943389 3945661 0.000000e+00 2466.0
23 TraesCS1D01G001500 chr1B 85.603 2320 314 18 1847 4153 4560666 4558354 0.000000e+00 2416.0
24 TraesCS1D01G001500 chr1B 85.764 2297 305 20 1871 4153 4855242 4852954 0.000000e+00 2410.0
25 TraesCS1D01G001500 chr1B 91.650 1545 110 6 1 1543 4535881 4534354 0.000000e+00 2121.0
26 TraesCS1D01G001500 chr1B 87.512 1025 96 14 529 1543 4825514 4824512 0.000000e+00 1155.0
27 TraesCS1D01G001500 chr1B 84.594 1071 143 14 869 1924 4856539 4855476 0.000000e+00 1044.0
28 TraesCS1D01G001500 chr1B 86.403 934 117 6 974 1902 4150731 4151659 0.000000e+00 1013.0
29 TraesCS1D01G001500 chr1B 83.841 1083 149 18 852 1918 4561739 4560667 0.000000e+00 1007.0
30 TraesCS1D01G001500 chr1B 84.024 1014 145 12 913 1924 4510925 4509927 0.000000e+00 959.0
31 TraesCS1D01G001500 chr1B 94.589 499 25 2 4759 5257 4499334 4498838 0.000000e+00 771.0
32 TraesCS1D01G001500 chr1B 86.201 558 68 7 3 552 4511743 4511187 3.500000e-166 595.0
33 TraesCS1D01G001500 chr1B 95.608 296 10 2 4150 4442 4507476 4507181 6.160000e-129 472.0
34 TraesCS1D01G001500 chr1B 91.988 337 23 3 62 394 4825847 4825511 2.220000e-128 470.0
35 TraesCS1D01G001500 chr1B 83.502 297 44 4 4150 4442 4529283 4528988 6.710000e-69 272.0
36 TraesCS1D01G001500 chr1B 89.048 210 21 2 4441 4649 4099297 4099505 5.220000e-65 259.0
37 TraesCS1D01G001500 chr1B 83.696 276 37 5 4447 4719 3998120 3998390 2.430000e-63 254.0
38 TraesCS1D01G001500 chr1B 83.212 274 35 8 4443 4711 4154555 4154822 1.890000e-59 241.0
39 TraesCS1D01G001500 chr1B 88.500 200 22 1 4447 4645 4528922 4528723 1.890000e-59 241.0
40 TraesCS1D01G001500 chr1B 87.006 177 18 3 4447 4622 4861916 4861744 1.490000e-45 195.0
41 TraesCS1D01G001500 chr1B 84.884 172 23 2 4274 4442 4862153 4861982 2.520000e-38 171.0
42 TraesCS1D01G001500 chr1B 78.041 296 30 14 4150 4442 3997792 3998055 2.540000e-33 154.0
43 TraesCS1D01G001500 chr1B 81.579 152 23 3 4738 4889 3946010 3946156 2.570000e-23 121.0
44 TraesCS1D01G001500 chr1B 77.083 240 24 13 4970 5188 687789413 687789642 5.570000e-20 110.0
45 TraesCS1D01G001500 chr1B 77.941 136 26 4 5036 5170 3998689 3998821 1.210000e-11 82.4
46 TraesCS1D01G001500 chr1B 90.741 54 5 0 724 777 3942149 3942202 7.300000e-09 73.1
47 TraesCS1D01G001500 chr1B 97.436 39 0 1 5182 5219 4498818 4498780 1.220000e-06 65.8
48 TraesCS1D01G001500 chr3B 100.000 30 0 0 4739 4768 737606205 737606176 7.350000e-04 56.5


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 TraesCS1D01G001500 chr1D 391359 396615 5256 False 9708.000000 9708 100.000000 1 5257 1 chr1D.!!$F1 5256
1 TraesCS1D01G001500 chr1D 617856 620153 2297 True 2590.000000 2590 87.072000 1859 4153 1 chr1D.!!$R1 2294
2 TraesCS1D01G001500 chr1D 646969 648321 1352 False 667.000000 1062 84.243500 508 1918 2 chr1D.!!$F3 1410
3 TraesCS1D01G001500 chr1D 458572 463100 4528 False 612.000000 996 85.178000 852 4649 2 chr1D.!!$F2 3797
4 TraesCS1D01G001500 chr1A 3669212 3671518 2306 True 2455.000000 2455 85.918000 1847 4154 1 chr1A.!!$R4 2307
5 TraesCS1D01G001500 chr1A 27210239 27216614 6375 False 1326.333333 3496 79.221333 392 5188 3 chr1A.!!$F1 4796
6 TraesCS1D01G001500 chr1A 3698570 3702515 3945 True 1316.000000 3478 88.452000 753 4987 3 chr1A.!!$R6 4234
7 TraesCS1D01G001500 chr1A 3656451 3657541 1090 True 1107.000000 1107 85.283000 852 1924 1 chr1A.!!$R3 1072
8 TraesCS1D01G001500 chr1A 3453880 3454752 872 True 1002.000000 1002 87.429000 1054 1925 1 chr1A.!!$R1 871
9 TraesCS1D01G001500 chr1A 3578183 3578741 558 True 315.000000 315 78.596000 4463 4976 1 chr1A.!!$R2 513
10 TraesCS1D01G001500 chr3D 560054150 560057105 2955 True 1435.500000 2593 86.595500 1879 4711 2 chr3D.!!$R2 2832
11 TraesCS1D01G001500 chr1B 4115529 4117806 2277 False 2471.000000 2471 86.344000 1866 4142 1 chr1B.!!$F2 2276
12 TraesCS1D01G001500 chr1B 4534354 4535881 1527 True 2121.000000 2121 91.650000 1 1543 1 chr1B.!!$R1 1542
13 TraesCS1D01G001500 chr1B 4852954 4856539 3585 True 1727.000000 2410 85.179000 869 4153 2 chr1B.!!$R7 3284
14 TraesCS1D01G001500 chr1B 4558354 4561739 3385 True 1711.500000 2416 84.722000 852 4153 2 chr1B.!!$R5 3301
15 TraesCS1D01G001500 chr1B 4507181 4511743 4562 True 1127.500000 2484 87.990250 3 4442 4 chr1B.!!$R3 4439
16 TraesCS1D01G001500 chr1B 3942149 3946156 4007 False 886.700000 2466 86.209333 724 4889 3 chr1B.!!$F4 4165
17 TraesCS1D01G001500 chr1B 4824512 4825847 1335 True 812.500000 1155 89.750000 62 1543 2 chr1B.!!$R6 1481
18 TraesCS1D01G001500 chr1B 4150731 4154822 4091 False 627.000000 1013 84.807500 974 4711 2 chr1B.!!$F6 3737
19 TraesCS1D01G001500 chr1B 4498780 4499334 554 True 418.400000 771 96.012500 4759 5257 2 chr1B.!!$R2 498
20 TraesCS1D01G001500 chr1B 4528723 4529283 560 True 256.500000 272 86.001000 4150 4645 2 chr1B.!!$R4 495

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
74 75 0.601558 GCAACCAGTCACGAGTCCTA 59.398 55.0 0.00 0.0 0.00 2.94 F
1036 2632 0.452184 CAAGCCATCTTGCTCAGCAG 59.548 55.0 0.00 0.0 42.66 4.24 F
2150 4683 0.028902 AAGTTGCAAAGCGTCCGAAC 59.971 50.0 0.00 0.0 0.00 3.95 F
2788 5333 0.108774 GGAACTAGGGGCCTGCATAC 59.891 60.0 0.84 0.0 0.00 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 3042 0.110486 TTTCCCCTGTGAGCTGGTTC 59.890 55.000 0.00 0.00 32.49 3.62 R
2853 5399 0.175760 TGATCTGCAGACCCGCTAAC 59.824 55.000 20.97 4.09 0.00 2.34 R
3423 5969 1.066858 CCGTCTTGAAGCTCTGCCTTA 60.067 52.381 0.00 0.00 0.00 2.69 R
4732 7590 0.320946 CCTTGCGGGGAAAACTACGA 60.321 55.000 0.00 0.00 0.00 3.43 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
45 46 5.324409 AGAATTCCAGCACCTAATTTGTCA 58.676 37.500 0.65 0.00 0.00 3.58
49 50 3.763360 TCCAGCACCTAATTTGTCATTGG 59.237 43.478 0.00 0.00 0.00 3.16
74 75 0.601558 GCAACCAGTCACGAGTCCTA 59.398 55.000 0.00 0.00 0.00 2.94
194 200 2.158769 TCAGCTTGTGTGGTGAAGATGT 60.159 45.455 0.00 0.00 40.82 3.06
198 204 0.943673 TGTGTGGTGAAGATGTTGCG 59.056 50.000 0.00 0.00 0.00 4.85
225 231 1.466167 CACAGGCTTTGAGAATCCACG 59.534 52.381 0.00 0.00 0.00 4.94
399 408 3.986006 GCCACCGGTCACGAGTCA 61.986 66.667 2.59 0.00 44.60 3.41
492 505 7.033791 CACAAGCTGCTTCAATTTCTTCATAT 58.966 34.615 12.82 0.00 0.00 1.78
545 558 3.753272 ACAAATCACAGGAGAAACCATCG 59.247 43.478 0.00 0.00 42.04 3.84
812 838 1.177401 GGTAGCAGCTTCCAAAAGGG 58.823 55.000 13.10 0.00 38.37 3.95
883 961 3.588955 CGACACTGAAGAATGGTCATCA 58.411 45.455 0.00 0.00 30.99 3.07
907 1014 0.871057 GCAGCTTCCACTCAACTGTC 59.129 55.000 0.00 0.00 0.00 3.51
910 1017 1.765314 AGCTTCCACTCAACTGTCTGT 59.235 47.619 0.00 0.00 0.00 3.41
911 1018 2.139118 GCTTCCACTCAACTGTCTGTC 58.861 52.381 0.00 0.00 0.00 3.51
923 2499 1.854743 CTGTCTGTCTGTGTGTTCACG 59.145 52.381 0.00 0.00 46.49 4.35
1036 2632 0.452184 CAAGCCATCTTGCTCAGCAG 59.548 55.000 0.00 0.00 42.66 4.24
1072 2668 5.074804 TCTACTGCCTACTGTTAGTGTCAA 58.925 41.667 0.00 0.00 0.00 3.18
1107 2703 1.859427 AAGAAGCACATGCAGCACGG 61.859 55.000 12.59 0.00 45.16 4.94
1191 2787 2.267006 CCACCGCTGCAGATGAGT 59.733 61.111 20.43 5.15 0.00 3.41
1357 2953 2.039216 TCGGCACTTCCATTCCTTACAA 59.961 45.455 0.00 0.00 34.01 2.41
1390 2986 6.367374 TTCATAACAACAGTCTCCATGGTA 57.633 37.500 12.58 0.00 0.00 3.25
1403 2999 3.794481 TGGTACACTGCCCGCTAA 58.206 55.556 0.00 0.00 0.00 3.09
1443 3039 7.604164 TCAGCACTTTCTGATCTTAACCTTAAG 59.396 37.037 0.00 0.00 38.11 1.85
1446 3042 7.625185 GCACTTTCTGATCTTAACCTTAAGCAG 60.625 40.741 0.00 0.00 39.90 4.24
1462 3058 1.002868 CAGAACCAGCTCACAGGGG 60.003 63.158 0.00 0.00 0.00 4.79
1507 3103 0.957362 GCAAAGTCTCAGGCAGCTTT 59.043 50.000 0.00 0.00 32.10 3.51
1524 3120 6.082984 GCAGCTTTCTCTCTCATTTAACAAC 58.917 40.000 0.00 0.00 0.00 3.32
1608 3204 2.025416 CCAAACCATGGTATCAGGTCCA 60.025 50.000 20.12 0.00 44.85 4.02
1614 3210 3.117550 CCATGGTATCAGGTCCAATTCCA 60.118 47.826 2.57 5.45 37.27 3.53
1627 3223 3.200825 TCCAATTCCAGAGGAGATTGGAC 59.799 47.826 23.60 0.00 44.41 4.02
1635 3231 1.480954 GAGGAGATTGGACGGCTTGTA 59.519 52.381 0.00 0.00 0.00 2.41
1680 3276 1.026718 ACAGCACCTTAAGCGGCATC 61.027 55.000 15.99 0.00 37.01 3.91
1771 3367 3.324268 GCCTATACCCCAAGAACTAGGAC 59.676 52.174 0.00 0.00 0.00 3.85
1810 3406 7.442969 TGCAAATTCTTGAGCTTGATTCAAATT 59.557 29.630 0.01 0.00 34.41 1.82
1836 3432 4.934797 TTCAGGTCCAATTCCAATCTCT 57.065 40.909 0.00 0.00 0.00 3.10
1934 4322 3.127721 GGCAACTTGCTAAATCTCCAGTC 59.872 47.826 13.43 0.00 44.28 3.51
1946 4334 9.825109 GCTAAATCTCCAGTCTTTAGTCTTATT 57.175 33.333 0.00 0.00 35.73 1.40
1981 4369 3.696306 GGCTCTATTCCTGACAGCC 57.304 57.895 0.00 0.00 42.87 4.85
2050 4583 2.043953 GTGGTTCCATCCCCCAGC 60.044 66.667 0.00 0.00 0.00 4.85
2089 4622 2.728007 ACCTCAAATCCTTAGCCTTGC 58.272 47.619 0.00 0.00 0.00 4.01
2106 4639 3.392882 CTTGCACCAGAACCAAATTTCC 58.607 45.455 0.00 0.00 0.00 3.13
2147 4680 1.082104 GGAAGTTGCAAAGCGTCCG 60.082 57.895 0.00 0.00 0.00 4.79
2150 4683 0.028902 AAGTTGCAAAGCGTCCGAAC 59.971 50.000 0.00 0.00 0.00 3.95
2160 4693 0.725784 GCGTCCGAACACTGCAAATG 60.726 55.000 0.00 0.00 0.00 2.32
2193 4726 6.881602 ACAAATTATCAGGTTCTCTTCCTCAC 59.118 38.462 0.00 0.00 32.37 3.51
2219 4752 3.566351 TCGGAGATCTCATAAGCCTTGA 58.434 45.455 23.85 4.78 0.00 3.02
2220 4753 3.319405 TCGGAGATCTCATAAGCCTTGAC 59.681 47.826 23.85 1.45 0.00 3.18
2305 4838 4.083590 GCAGACTTCAAATTCTCACTGTCC 60.084 45.833 0.00 0.00 0.00 4.02
2307 4840 5.528690 CAGACTTCAAATTCTCACTGTCCAA 59.471 40.000 0.00 0.00 0.00 3.53
2337 4878 1.139498 TCACTGGCCCCATTCCAAGA 61.139 55.000 0.00 0.00 32.41 3.02
2355 4896 8.974060 TTCCAAGAAGTTTAAAGACATGTACT 57.026 30.769 0.00 0.00 0.00 2.73
2362 4903 8.535690 AAGTTTAAAGACATGTACTAGTCTGC 57.464 34.615 17.54 8.90 43.88 4.26
2407 4948 9.710818 AGAACCAACTAACAGGAGATATAACTA 57.289 33.333 0.00 0.00 0.00 2.24
2466 5007 3.065925 GCTTGGCATCAAATAGACTCACC 59.934 47.826 0.00 0.00 31.77 4.02
2508 5049 1.065418 GGTGCATGTACCCAGCTAACT 60.065 52.381 21.39 0.00 34.56 2.24
2511 5052 1.668419 CATGTACCCAGCTAACTGCC 58.332 55.000 0.00 0.00 43.02 4.85
2521 5066 3.451178 CCAGCTAACTGCCCTAACTCTAA 59.549 47.826 0.00 0.00 43.02 2.10
2523 5068 3.133183 AGCTAACTGCCCTAACTCTAAGC 59.867 47.826 0.00 0.00 44.23 3.09
2571 5116 6.794534 ACCTCCAATCCTTTCTAAATTGTCT 58.205 36.000 0.00 0.00 0.00 3.41
2579 5124 9.907229 AATCCTTTCTAAATTGTCTAACCTAGG 57.093 33.333 7.41 7.41 0.00 3.02
2676 5221 3.932710 TGCTGAACTTATCATCGAACCAC 59.067 43.478 0.00 0.00 37.44 4.16
2689 5234 2.698797 TCGAACCACTTATCTGGATCCC 59.301 50.000 9.90 0.00 35.04 3.85
2709 5254 7.070821 GGATCCCTACCTACACAGATAGAAAAA 59.929 40.741 0.00 0.00 0.00 1.94
2788 5333 0.108774 GGAACTAGGGGCCTGCATAC 59.891 60.000 0.84 0.00 0.00 2.39
2790 5335 0.546598 AACTAGGGGCCTGCATACAC 59.453 55.000 0.84 0.00 0.00 2.90
2818 5363 6.322201 ACAATCCTTGAAGATCAACAACAACT 59.678 34.615 0.00 0.00 32.21 3.16
2819 5364 6.966534 ATCCTTGAAGATCAACAACAACTT 57.033 33.333 0.00 0.00 32.21 2.66
2820 5365 6.773976 TCCTTGAAGATCAACAACAACTTT 57.226 33.333 0.00 0.00 32.21 2.66
2825 5370 7.810766 TGAAGATCAACAACAACTTTTTCAC 57.189 32.000 0.00 0.00 0.00 3.18
2853 5399 2.107950 TGCCTGGTACGATTGGAAAG 57.892 50.000 0.00 0.00 0.00 2.62
2859 5405 3.255725 TGGTACGATTGGAAAGTTAGCG 58.744 45.455 0.00 0.00 0.00 4.26
2905 5451 1.885887 GCAACAATAACCTCAGTGGCA 59.114 47.619 0.00 0.00 40.22 4.92
3038 5584 2.604914 CACTCGATGTGTCCTACAATGC 59.395 50.000 6.79 0.00 43.77 3.56
3066 5612 2.993937 GGACCAATCCCAATAACACGA 58.006 47.619 0.00 0.00 39.39 4.35
3123 5669 3.888930 CCAACAAAGGTCTGTGTGGTAAT 59.111 43.478 0.00 0.00 0.00 1.89
3161 5707 6.464222 CACCTTGTTATTCAACTCCAGTAGA 58.536 40.000 0.00 0.00 35.56 2.59
3184 5730 4.647611 TGGTCACCATAAACGAAAGACAT 58.352 39.130 0.00 0.00 0.00 3.06
3186 5732 6.231951 TGGTCACCATAAACGAAAGACATTA 58.768 36.000 0.00 0.00 0.00 1.90
3188 5734 7.228906 TGGTCACCATAAACGAAAGACATTAAA 59.771 33.333 0.00 0.00 0.00 1.52
3190 5736 9.061610 GTCACCATAAACGAAAGACATTAAATG 57.938 33.333 0.00 0.00 0.00 2.32
3198 5744 8.419076 AACGAAAGACATTAAATGTGCTTTTT 57.581 26.923 1.59 0.00 45.03 1.94
3233 5779 1.136110 GGTGGGTTTCGGCATTATTGG 59.864 52.381 0.00 0.00 0.00 3.16
3261 5807 7.305418 GCAATTGTTGTCGTAATAATGCTTAGC 60.305 37.037 7.40 0.00 0.00 3.09
3264 5810 4.310357 TGTCGTAATAATGCTTAGCCGA 57.690 40.909 0.29 0.00 0.00 5.54
3273 5819 6.699575 ATAATGCTTAGCCGAAACAAGAAT 57.300 33.333 0.29 0.00 0.00 2.40
3279 5825 5.106277 GCTTAGCCGAAACAAGAATAAACCT 60.106 40.000 0.00 0.00 0.00 3.50
3280 5826 4.766404 AGCCGAAACAAGAATAAACCTG 57.234 40.909 0.00 0.00 0.00 4.00
3295 5841 9.274206 AGAATAAACCTGAAGAAAGTGTTACTC 57.726 33.333 0.00 0.00 0.00 2.59
3309 5855 2.708861 TGTTACTCCTGAAGCAAGGGAA 59.291 45.455 0.79 0.00 37.96 3.97
3423 5969 3.322254 CAGGAGGATACGGCAAAGTCTAT 59.678 47.826 0.00 0.00 46.39 1.98
3430 5976 2.906354 ACGGCAAAGTCTATAAGGCAG 58.094 47.619 0.00 0.00 0.00 4.85
3432 5978 3.126831 CGGCAAAGTCTATAAGGCAGAG 58.873 50.000 0.00 0.00 0.00 3.35
3474 6020 3.479489 TGCTGTGAAGAAGCTTCATCAA 58.521 40.909 30.05 20.20 41.42 2.57
3547 6099 2.743636 AACACAGATCCGACAACGAT 57.256 45.000 0.00 0.00 42.66 3.73
3566 6118 4.799949 ACGATGCATTGTCAAAATGTATGC 59.200 37.500 14.16 0.00 41.39 3.14
3627 6179 1.289160 ACATTCAGCAGGGAAGCCTA 58.711 50.000 0.00 0.00 34.23 3.93
3643 6195 2.037772 AGCCTACGCAGGATATTGGAAG 59.962 50.000 5.66 0.00 45.91 3.46
3770 6322 2.485814 TCCATCGAGATATCACGAGCAG 59.514 50.000 25.48 18.30 41.74 4.24
3922 6564 6.487299 ACTAGAAACCTTTCTTCTCACACT 57.513 37.500 5.63 0.00 44.70 3.55
4017 6668 2.869801 GTTGTGACGGAGAAATGTGACA 59.130 45.455 0.00 0.00 30.32 3.58
4158 6890 1.452145 GCCGACAACACCAACCATGT 61.452 55.000 0.00 0.00 0.00 3.21
4285 7025 2.096248 CCGAGTTCTAGTGAGAAGCCT 58.904 52.381 0.00 0.00 42.46 4.58
4329 7069 4.632251 CGTTTTAGGTTTTGGTTTTGCCTT 59.368 37.500 0.00 0.00 38.35 4.35
4378 7139 8.078060 TGTTGAAGTCTGTAATCCTATCATGA 57.922 34.615 0.00 0.00 0.00 3.07
4427 7189 3.777106 ATAATGACCGATCCATGCAGT 57.223 42.857 0.00 0.00 0.00 4.40
4439 7202 1.611410 CCATGCAGTGTGAGCCTGTTA 60.611 52.381 0.00 0.00 32.41 2.41
4506 7332 1.082756 CACGTTCGTGAAGCTTGGC 60.083 57.895 18.64 0.00 38.30 4.52
4523 7349 1.103398 GGCCATGGCGCAAGATTAGT 61.103 55.000 29.90 0.00 43.06 2.24
4532 7358 4.811024 TGGCGCAAGATTAGTATCTTTCTG 59.189 41.667 10.83 0.00 46.53 3.02
4533 7359 4.811557 GGCGCAAGATTAGTATCTTTCTGT 59.188 41.667 10.83 0.00 46.53 3.41
4534 7360 5.294552 GGCGCAAGATTAGTATCTTTCTGTT 59.705 40.000 10.83 0.00 46.53 3.16
4535 7361 6.479001 GGCGCAAGATTAGTATCTTTCTGTTA 59.521 38.462 10.83 0.00 46.53 2.41
4594 7426 6.058183 AGAAGAGAACAAAGCAGAAAAGCTA 58.942 36.000 0.00 0.00 45.89 3.32
4598 7430 6.095440 AGAGAACAAAGCAGAAAAGCTACAAA 59.905 34.615 0.00 0.00 45.89 2.83
4608 7440 6.075572 GCAGAAAAGCTACAAAGTTTTACACG 60.076 38.462 0.00 0.00 35.36 4.49
4609 7441 7.184106 CAGAAAAGCTACAAAGTTTTACACGA 58.816 34.615 0.00 0.00 35.36 4.35
4622 7454 6.101332 AGTTTTACACGACGCAAATATCCTA 58.899 36.000 0.00 0.00 0.00 2.94
4645 7477 5.825593 AGTGTTCACTAATTCTTCTCCCA 57.174 39.130 3.47 0.00 0.00 4.37
4684 7522 6.070767 ACAATATATACCTCGGGATGAGTTGG 60.071 42.308 0.00 0.00 43.64 3.77
4732 7590 3.169099 AGACACTCTCCTATTGTGTGCT 58.831 45.455 2.63 0.00 43.81 4.40
4733 7591 3.194542 AGACACTCTCCTATTGTGTGCTC 59.805 47.826 2.63 0.00 43.81 4.26
4736 7594 3.128764 CACTCTCCTATTGTGTGCTCGTA 59.871 47.826 0.00 0.00 0.00 3.43
4796 7655 4.279420 GCCCCATGTTCTTGATATTTCTCC 59.721 45.833 0.00 0.00 0.00 3.71
4983 7870 1.003580 TGCTCCCATGAACCTGAAGAC 59.996 52.381 0.00 0.00 0.00 3.01
5034 7936 0.107703 GGCGGTCACAATGATCAGGA 60.108 55.000 0.09 0.00 0.00 3.86
5060 7962 0.779997 ACCTTGGACCAAGCAGGAAT 59.220 50.000 26.34 6.19 39.85 3.01
5087 7989 0.179076 ATGATCAAGCGGTCGATGCA 60.179 50.000 14.02 0.00 33.85 3.96
5156 8059 8.194769 ACAAAAAGGAAAATTACCACAGTACTG 58.805 33.333 21.44 21.44 0.00 2.74
5197 8101 3.564790 GGGTTGTAGGGCATAAAAAGGGA 60.565 47.826 0.00 0.00 0.00 4.20
5216 8120 8.631480 AAAGGGAAAATTACCACTGTACTAAG 57.369 34.615 0.00 0.00 31.71 2.18
5245 8149 6.266168 AGTTTTGATCGGTTGATGCATAAA 57.734 33.333 0.00 0.00 34.09 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
194 200 3.898509 GCCTGTGCAACCACGCAA 61.899 61.111 0.00 0.00 45.14 4.85
198 204 0.031178 CTCAAAGCCTGTGCAACCAC 59.969 55.000 0.00 0.00 42.40 4.16
225 231 5.642491 GGAAATGAGGTAGTGGTTGTAACTC 59.358 44.000 0.00 0.00 35.15 3.01
345 354 1.281419 TGAGGGGAAATTCCGTGCTA 58.719 50.000 5.87 0.00 37.43 3.49
492 505 8.232913 AGTATTTCTTTGGTAACTGCTTCAAA 57.767 30.769 0.00 0.00 37.61 2.69
574 592 5.955961 TCATTTGATGGTATCTCCTGTCA 57.044 39.130 0.00 0.00 37.07 3.58
575 593 7.337942 AGTTTTCATTTGATGGTATCTCCTGTC 59.662 37.037 0.00 0.00 37.07 3.51
769 795 1.953686 CCGCCTGTTTTCCTTCTTCAA 59.046 47.619 0.00 0.00 0.00 2.69
793 819 1.177401 CCCTTTTGGAAGCTGCTACC 58.823 55.000 0.90 0.00 44.07 3.18
803 829 3.219281 GAAACTAGCACACCCTTTTGGA 58.781 45.455 0.00 0.00 44.07 3.53
812 838 4.789802 GCTCTTGTTTGGAAACTAGCACAC 60.790 45.833 14.51 0.00 40.15 3.82
907 1014 1.491670 CTCCGTGAACACACAGACAG 58.508 55.000 5.80 0.00 34.59 3.51
910 1017 0.387929 GTCCTCCGTGAACACACAGA 59.612 55.000 5.80 0.00 34.59 3.41
911 1018 0.600255 GGTCCTCCGTGAACACACAG 60.600 60.000 5.80 0.45 34.59 3.66
978 2569 0.184692 TGTGTTTGGCTGGGTGATGA 59.815 50.000 0.00 0.00 0.00 2.92
1033 2629 3.929610 CAGTAGAGGTAGAACAAAGCTGC 59.070 47.826 0.00 0.00 0.00 5.25
1036 2632 3.055747 AGGCAGTAGAGGTAGAACAAAGC 60.056 47.826 0.00 0.00 0.00 3.51
1072 2668 4.219264 CTTCTTCCAAGAGATGAAGGCT 57.781 45.455 9.36 0.00 46.04 4.58
1107 2703 1.301558 CAGCGAGATCCCTCCATGC 60.302 63.158 0.00 0.00 36.04 4.06
1134 2730 3.731728 TGGAGGAGGGCCATGTGC 61.732 66.667 6.18 0.00 36.29 4.57
1357 2953 7.556844 AGACTGTTGTTATGAAGGTCGATATT 58.443 34.615 0.00 0.00 0.00 1.28
1390 2986 1.541233 GCTGATATTAGCGGGCAGTGT 60.541 52.381 3.45 0.00 33.46 3.55
1403 2999 3.298619 AGTGCTGACAGAGAGCTGATAT 58.701 45.455 6.65 0.00 45.17 1.63
1443 3039 1.673665 CCCTGTGAGCTGGTTCTGC 60.674 63.158 0.00 0.00 32.49 4.26
1446 3042 0.110486 TTTCCCCTGTGAGCTGGTTC 59.890 55.000 0.00 0.00 32.49 3.62
1462 3058 5.221322 GGCCACCAATCTCATAAGGAATTTC 60.221 44.000 0.00 0.00 0.00 2.17
1507 3103 6.419484 TGTGAGGTTGTTAAATGAGAGAGA 57.581 37.500 0.00 0.00 0.00 3.10
1608 3204 2.171448 CCGTCCAATCTCCTCTGGAATT 59.829 50.000 0.00 0.00 43.32 2.17
1614 3210 0.539051 CAAGCCGTCCAATCTCCTCT 59.461 55.000 0.00 0.00 0.00 3.69
1635 3231 6.940298 TGCTTAGCTGTAGATTTTGTAGGTTT 59.060 34.615 5.60 0.00 0.00 3.27
1680 3276 6.014669 TCAGATTTCCAAGGGTTTTTGGTATG 60.015 38.462 4.84 0.00 46.23 2.39
1771 3367 1.959042 ATTTGCAGATGGACTAGCCG 58.041 50.000 0.00 0.00 40.66 5.52
1810 3406 7.895429 AGAGATTGGAATTGGACCTGAAAAATA 59.105 33.333 0.00 0.00 0.00 1.40
1908 4296 3.367395 GGAGATTTAGCAAGTTGCCCAAC 60.367 47.826 24.02 11.95 46.52 3.77
1946 4334 3.197766 AGAGCCAGATATTTGGTTGTCGA 59.802 43.478 13.50 0.00 40.49 4.20
2050 4583 6.632909 TGAGGTTTATCAGATTGCCAATTTG 58.367 36.000 1.66 1.66 0.00 2.32
2089 4622 2.723124 CCGGAAATTTGGTTCTGGTG 57.277 50.000 0.00 0.00 45.51 4.17
2147 4680 8.741101 TTTGTTATCATACATTTGCAGTGTTC 57.259 30.769 11.40 0.00 0.00 3.18
2193 4726 3.923461 GGCTTATGAGATCTCCGAATTCG 59.077 47.826 20.92 20.92 39.44 3.34
2219 4752 5.631119 AGTTGTTAGCTAACCCAAGATTGT 58.369 37.500 29.15 5.38 35.37 2.71
2220 4753 5.705441 TGAGTTGTTAGCTAACCCAAGATTG 59.295 40.000 29.15 0.00 35.37 2.67
2305 4838 4.520492 GGGGCCAGTGAACATATTAGATTG 59.480 45.833 4.39 0.00 0.00 2.67
2307 4840 3.721575 TGGGGCCAGTGAACATATTAGAT 59.278 43.478 4.39 0.00 0.00 1.98
2337 4878 8.368668 AGCAGACTAGTACATGTCTTTAAACTT 58.631 33.333 15.22 0.00 41.06 2.66
2374 4915 7.060421 TCTCCTGTTAGTTGGTTCTTTTCAAT 58.940 34.615 0.00 0.00 0.00 2.57
2404 4945 4.263727 TGGATACACACCAAAATGCCTAGT 60.264 41.667 0.00 0.00 46.17 2.57
2407 4948 3.168035 TGGATACACACCAAAATGCCT 57.832 42.857 0.00 0.00 46.17 4.75
2466 5007 1.134280 AGATTTGGTGAGATCTGCCCG 60.134 52.381 0.00 0.00 31.65 6.13
2508 5049 7.116075 TCATATTTTTGCTTAGAGTTAGGGCA 58.884 34.615 0.00 0.00 0.00 5.36
2521 5066 4.097892 GGAACCCGTGATCATATTTTTGCT 59.902 41.667 0.00 0.00 0.00 3.91
2523 5068 5.574891 TGGAACCCGTGATCATATTTTTG 57.425 39.130 0.00 0.00 0.00 2.44
2649 5194 6.292381 GGTTCGATGATAAGTTCAGCATGTAC 60.292 42.308 0.00 0.00 40.90 2.90
2654 5199 3.932710 GTGGTTCGATGATAAGTTCAGCA 59.067 43.478 0.00 0.00 40.90 4.41
2676 5221 5.394738 TGTGTAGGTAGGGATCCAGATAAG 58.605 45.833 15.23 0.00 0.00 1.73
2689 5234 9.303537 GCTTAGTTTTTCTATCTGTGTAGGTAG 57.696 37.037 0.00 0.00 38.71 3.18
2728 5273 7.794683 ACCCAGTCTATTCCCAGAAATATCTAA 59.205 37.037 0.00 0.00 33.50 2.10
2730 5275 6.043706 CACCCAGTCTATTCCCAGAAATATCT 59.956 42.308 0.00 0.00 35.88 1.98
2736 5281 2.196595 CCACCCAGTCTATTCCCAGAA 58.803 52.381 0.00 0.00 0.00 3.02
2745 5290 5.784023 TCAGGTATTAATCCACCCAGTCTA 58.216 41.667 4.10 0.00 35.25 2.59
2818 5363 2.430332 CAGGCAAACTCCCAGTGAAAAA 59.570 45.455 0.00 0.00 0.00 1.94
2819 5364 2.031120 CAGGCAAACTCCCAGTGAAAA 58.969 47.619 0.00 0.00 0.00 2.29
2820 5365 1.691196 CAGGCAAACTCCCAGTGAAA 58.309 50.000 0.00 0.00 0.00 2.69
2825 5370 0.673644 CGTACCAGGCAAACTCCCAG 60.674 60.000 0.00 0.00 0.00 4.45
2853 5399 0.175760 TGATCTGCAGACCCGCTAAC 59.824 55.000 20.97 4.09 0.00 2.34
2859 5405 3.827008 TCTAACATGATCTGCAGACCC 57.173 47.619 20.97 14.55 0.00 4.46
3059 5605 4.890088 AGCATTTTGGAGTAGTCGTGTTA 58.110 39.130 0.00 0.00 0.00 2.41
3105 5651 4.899502 AGAGATTACCACACAGACCTTTG 58.100 43.478 0.00 0.00 0.00 2.77
3161 5707 4.647611 TGTCTTTCGTTTATGGTGACCAT 58.352 39.130 22.24 22.24 46.99 3.55
3184 5730 8.729805 AGAACAATTGGAAAAAGCACATTTAA 57.270 26.923 10.83 0.00 0.00 1.52
3186 5732 7.121020 ACAAGAACAATTGGAAAAAGCACATTT 59.879 29.630 10.83 0.00 34.36 2.32
3188 5734 6.037391 CACAAGAACAATTGGAAAAAGCACAT 59.963 34.615 10.83 0.00 34.36 3.21
3190 5736 5.220643 CCACAAGAACAATTGGAAAAAGCAC 60.221 40.000 10.83 0.00 34.36 4.40
3198 5744 2.315176 CCCACCACAAGAACAATTGGA 58.685 47.619 10.83 0.00 34.36 3.53
3233 5779 5.799936 AGCATTATTACGACAACAATTGCAC 59.200 36.000 5.05 0.00 0.00 4.57
3261 5807 6.554334 TCTTCAGGTTTATTCTTGTTTCGG 57.446 37.500 0.00 0.00 0.00 4.30
3264 5810 8.749354 ACACTTTCTTCAGGTTTATTCTTGTTT 58.251 29.630 0.00 0.00 0.00 2.83
3273 5819 6.990349 CAGGAGTAACACTTTCTTCAGGTTTA 59.010 38.462 0.00 0.00 0.00 2.01
3279 5825 5.057149 GCTTCAGGAGTAACACTTTCTTCA 58.943 41.667 0.00 0.00 0.00 3.02
3280 5826 5.057149 TGCTTCAGGAGTAACACTTTCTTC 58.943 41.667 0.00 0.00 0.00 2.87
3295 5841 4.080638 AGAGAATAGTTCCCTTGCTTCAGG 60.081 45.833 0.00 0.00 0.00 3.86
3309 5855 8.526147 CCATCAAAATTCCAAACAGAGAATAGT 58.474 33.333 0.00 0.00 32.46 2.12
3423 5969 1.066858 CCGTCTTGAAGCTCTGCCTTA 60.067 52.381 0.00 0.00 0.00 2.69
3430 5976 2.394563 GCTGCCCGTCTTGAAGCTC 61.395 63.158 0.00 0.00 0.00 4.09
3432 5978 1.079127 TAGCTGCCCGTCTTGAAGC 60.079 57.895 0.00 0.00 0.00 3.86
3474 6020 6.119240 TCATCATCCAACTCTTCTTCAGTT 57.881 37.500 0.00 0.00 34.24 3.16
3547 6099 6.311690 CAGAATGCATACATTTTGACAATGCA 59.688 34.615 12.78 12.78 46.32 3.96
3566 6118 1.164662 CGCTGGATGGGAGCAGAATG 61.165 60.000 0.00 0.00 36.12 2.67
3627 6179 3.244353 CCTCATCTTCCAATATCCTGCGT 60.244 47.826 0.00 0.00 0.00 5.24
3643 6195 3.550437 TTCCTTTGCTAGCTCCTCATC 57.450 47.619 17.23 0.00 0.00 2.92
3685 6237 2.751259 GAGCCACATCATTTGCAAGAGA 59.249 45.455 0.00 2.02 0.00 3.10
3695 6247 4.726583 AGATATTGCTTGAGCCACATCAT 58.273 39.130 0.00 0.00 41.18 2.45
3770 6322 6.743575 AGGTTGTATCAAGTAAGATGTTGC 57.256 37.500 0.00 0.00 0.00 4.17
3922 6564 9.803507 ATAAATGGATTGAGATGAATGCTTCTA 57.196 29.630 0.00 0.00 0.00 2.10
4017 6668 3.206150 CAACCACGCCAAAGCTATAGAT 58.794 45.455 3.21 0.00 36.60 1.98
4098 6749 7.630082 TCATTTACCAGTATAGCTTGTTCCTT 58.370 34.615 0.00 0.00 0.00 3.36
4158 6890 0.840288 AGTGTGTGGTATGCCTCCCA 60.840 55.000 0.16 0.00 35.27 4.37
4285 7025 2.418197 GGCTTCCGCTACAATAGACACA 60.418 50.000 0.00 0.00 36.09 3.72
4308 7048 5.805728 TCAAGGCAAAACCAAAACCTAAAA 58.194 33.333 0.00 0.00 43.14 1.52
4329 7069 8.377799 ACATATATAGTTGGCATGAATGACTCA 58.622 33.333 0.00 0.00 36.54 3.41
4378 7139 7.553334 TGCTAGAAATAAAACCTACGAGATGT 58.447 34.615 0.00 0.00 0.00 3.06
4493 7319 1.675310 CCATGGCCAAGCTTCACGA 60.675 57.895 10.96 0.00 0.00 4.35
4506 7332 3.668447 AGATACTAATCTTGCGCCATGG 58.332 45.455 7.63 7.63 39.55 3.66
4532 7358 8.809478 GCTCATTAGCTCAACTAACTAACTAAC 58.191 37.037 0.00 0.00 43.60 2.34
4533 7359 8.928270 GCTCATTAGCTCAACTAACTAACTAA 57.072 34.615 0.00 0.00 43.60 2.24
4573 7405 5.126067 TGTAGCTTTTCTGCTTTGTTCTCT 58.874 37.500 0.00 0.00 43.74 3.10
4594 7426 3.743567 TTGCGTCGTGTAAAACTTTGT 57.256 38.095 0.00 0.00 0.00 2.83
4598 7430 4.933400 AGGATATTTGCGTCGTGTAAAACT 59.067 37.500 0.00 0.00 35.73 2.66
4608 7440 5.581085 AGTGAACACTTAGGATATTTGCGTC 59.419 40.000 1.32 0.00 38.83 5.19
4609 7441 5.488341 AGTGAACACTTAGGATATTTGCGT 58.512 37.500 1.32 0.00 38.83 5.24
4622 7454 5.998363 GTGGGAGAAGAATTAGTGAACACTT 59.002 40.000 12.66 0.00 42.54 3.16
4645 7477 7.075009 AGGTATATATTGTTGGAGGAAATGGGT 59.925 37.037 0.00 0.00 0.00 4.51
4684 7522 8.721478 ACAACACATAGAATTACATTGAGTCAC 58.279 33.333 0.00 0.00 0.00 3.67
4714 7553 2.094494 ACGAGCACACAATAGGAGAGTG 60.094 50.000 0.00 0.00 39.12 3.51
4732 7590 0.320946 CCTTGCGGGGAAAACTACGA 60.321 55.000 0.00 0.00 0.00 3.43
4733 7591 2.168054 CCTTGCGGGGAAAACTACG 58.832 57.895 0.00 0.00 0.00 3.51
4768 7626 3.959495 ATCAAGAACATGGGGCACTAT 57.041 42.857 0.00 0.00 0.00 2.12
4774 7632 5.448654 TGGAGAAATATCAAGAACATGGGG 58.551 41.667 0.00 0.00 0.00 4.96
4900 7784 1.529010 CCCTTGCAGACAACAGCCA 60.529 57.895 0.00 0.00 0.00 4.75
5034 7936 4.956075 CCTGCTTGGTCCAAGGTATTTTAT 59.044 41.667 28.96 0.00 41.31 1.40
5077 7979 1.934589 TCCTGTTTATGCATCGACCG 58.065 50.000 0.19 0.00 0.00 4.79
5087 7989 9.855021 GTGCTAACATTATTTGTTCCTGTTTAT 57.145 29.630 0.00 0.00 45.55 1.40
5156 8059 7.443477 ACAACCCTCTCTAAGTTCTTTTACTC 58.557 38.462 0.00 0.00 0.00 2.59
5216 8120 5.739161 GCATCAACCGATCAAAACTTCATAC 59.261 40.000 0.00 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.