Multiple sequence alignment - TraesCS2A01G416000

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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 TraesCS2A01G416000 chr2A 100.000 3425 0 0 1 3425 672425251 672428675 0.000000e+00 6325.0
1 TraesCS2A01G416000 chr2A 92.495 533 13 3 2903 3425 775380706 775380191 0.000000e+00 737.0
2 TraesCS2A01G416000 chr2D 90.396 2322 142 45 6 2295 527642094 527644366 0.000000e+00 2977.0
3 TraesCS2A01G416000 chr2D 93.421 608 24 7 2298 2904 644343538 644342946 0.000000e+00 887.0
4 TraesCS2A01G416000 chr2D 90.566 530 33 12 2903 3425 607025451 607025970 0.000000e+00 686.0
5 TraesCS2A01G416000 chr2B 93.914 1906 87 13 403 2295 624994792 624996681 0.000000e+00 2850.0
6 TraesCS2A01G416000 chr6A 96.636 535 8 4 2901 3425 519225592 519225058 0.000000e+00 880.0
7 TraesCS2A01G416000 chr6A 96.082 536 11 1 2900 3425 604630549 604630014 0.000000e+00 865.0
8 TraesCS2A01G416000 chr6A 90.909 55 5 0 1255 1309 455495273 455495327 1.320000e-09 75.0
9 TraesCS2A01G416000 chrUn 92.763 608 28 8 2298 2904 15331243 15330651 0.000000e+00 865.0
10 TraesCS2A01G416000 chrUn 76.384 271 58 6 21 287 272028134 272027866 1.280000e-29 141.0
11 TraesCS2A01G416000 chr7A 94.184 533 21 4 2903 3425 564248698 564248166 0.000000e+00 804.0
12 TraesCS2A01G416000 chr7A 91.353 532 29 11 2901 3425 436173187 436172666 0.000000e+00 712.0
13 TraesCS2A01G416000 chr7A 90.189 530 34 12 2903 3425 63727416 63726898 0.000000e+00 675.0
14 TraesCS2A01G416000 chr7A 78.548 303 61 4 5 304 116545694 116545393 2.700000e-46 196.0
15 TraesCS2A01G416000 chr1A 93.832 535 23 6 2901 3425 21991353 21990819 0.000000e+00 797.0
16 TraesCS2A01G416000 chr5D 90.943 530 31 11 2903 3425 475187451 475187970 0.000000e+00 697.0
17 TraesCS2A01G416000 chr3D 90.566 530 33 11 2903 3425 8886795 8887314 0.000000e+00 686.0
18 TraesCS2A01G416000 chr3D 90.862 383 28 3 2903 3278 507757448 507757830 1.100000e-139 507.0
19 TraesCS2A01G416000 chr5B 89.513 534 30 10 2903 3425 349356536 349357054 0.000000e+00 652.0
20 TraesCS2A01G416000 chr5B 79.343 213 40 4 5 213 249372376 249372164 2.750000e-31 147.0
21 TraesCS2A01G416000 chr5A 93.487 261 16 1 2901 3161 692045218 692044959 1.490000e-103 387.0
22 TraesCS2A01G416000 chr6B 79.927 274 50 5 1 270 681258340 681258612 2.700000e-46 196.0
23 TraesCS2A01G416000 chr6B 90.000 60 6 0 1255 1314 506383239 506383180 1.020000e-10 78.7
24 TraesCS2A01G416000 chr7D 76.230 366 70 15 5 360 484990961 484991319 9.770000e-41 178.0
25 TraesCS2A01G416000 chr4A 76.384 271 58 6 21 287 668169114 668168846 1.280000e-29 141.0
26 TraesCS2A01G416000 chr4A 76.015 271 59 6 21 287 668176989 668176721 5.960000e-28 135.0
27 TraesCS2A01G416000 chr4A 76.015 271 59 6 21 287 668266604 668266336 5.960000e-28 135.0
28 TraesCS2A01G416000 chr4A 75.277 271 60 7 21 287 668227326 668227059 4.640000e-24 122.0
29 TraesCS2A01G416000 chr6D 90.000 60 6 0 1255 1314 318078765 318078824 1.020000e-10 78.7


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 TraesCS2A01G416000 chr2A 672425251 672428675 3424 False 6325 6325 100.000 1 3425 1 chr2A.!!$F1 3424
1 TraesCS2A01G416000 chr2A 775380191 775380706 515 True 737 737 92.495 2903 3425 1 chr2A.!!$R1 522
2 TraesCS2A01G416000 chr2D 527642094 527644366 2272 False 2977 2977 90.396 6 2295 1 chr2D.!!$F1 2289
3 TraesCS2A01G416000 chr2D 644342946 644343538 592 True 887 887 93.421 2298 2904 1 chr2D.!!$R1 606
4 TraesCS2A01G416000 chr2D 607025451 607025970 519 False 686 686 90.566 2903 3425 1 chr2D.!!$F2 522
5 TraesCS2A01G416000 chr2B 624994792 624996681 1889 False 2850 2850 93.914 403 2295 1 chr2B.!!$F1 1892
6 TraesCS2A01G416000 chr6A 519225058 519225592 534 True 880 880 96.636 2901 3425 1 chr6A.!!$R1 524
7 TraesCS2A01G416000 chr6A 604630014 604630549 535 True 865 865 96.082 2900 3425 1 chr6A.!!$R2 525
8 TraesCS2A01G416000 chrUn 15330651 15331243 592 True 865 865 92.763 2298 2904 1 chrUn.!!$R1 606
9 TraesCS2A01G416000 chr7A 564248166 564248698 532 True 804 804 94.184 2903 3425 1 chr7A.!!$R4 522
10 TraesCS2A01G416000 chr7A 436172666 436173187 521 True 712 712 91.353 2901 3425 1 chr7A.!!$R3 524
11 TraesCS2A01G416000 chr7A 63726898 63727416 518 True 675 675 90.189 2903 3425 1 chr7A.!!$R1 522
12 TraesCS2A01G416000 chr1A 21990819 21991353 534 True 797 797 93.832 2901 3425 1 chr1A.!!$R1 524
13 TraesCS2A01G416000 chr5D 475187451 475187970 519 False 697 697 90.943 2903 3425 1 chr5D.!!$F1 522
14 TraesCS2A01G416000 chr3D 8886795 8887314 519 False 686 686 90.566 2903 3425 1 chr3D.!!$F1 522
15 TraesCS2A01G416000 chr5B 349356536 349357054 518 False 652 652 89.513 2903 3425 1 chr5B.!!$F1 522

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
242 243 0.034337 GTTGGCCACGGTAGTCAGAA 59.966 55.0 3.88 0.0 0.0 3.02 F
846 855 0.035439 TCCCGTCCATTCTCTTTGCC 60.035 55.0 0.00 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1916 1944 0.592148 CTACAGGATCGTAGCCGGTC 59.408 60.0 1.9 0.0 43.60 4.79 R
2746 2778 0.473755 TCGCCAATGCATATCCAGGT 59.526 50.0 0.0 0.0 37.32 4.00 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
24 25 4.159506 TGTGGGTTAAATAGAGGCATTTGC 59.840 41.667 0.00 0.00 41.14 3.68
40 41 2.789917 GCATGCAGCGAGGAAGTG 59.210 61.111 14.21 0.00 0.00 3.16
45 46 0.463654 TGCAGCGAGGAAGTGTGTTT 60.464 50.000 0.00 0.00 0.00 2.83
46 47 1.202592 TGCAGCGAGGAAGTGTGTTTA 60.203 47.619 0.00 0.00 0.00 2.01
95 96 2.403378 GGCGCGCCACTTTAATGGA 61.403 57.895 43.55 0.00 43.02 3.41
103 104 2.432444 CCACTTTAATGGACGAGGCAA 58.568 47.619 0.00 0.00 43.02 4.52
109 110 2.322355 AATGGACGAGGCAATGAGAG 57.678 50.000 0.00 0.00 0.00 3.20
111 112 1.144936 GGACGAGGCAATGAGAGGG 59.855 63.158 0.00 0.00 0.00 4.30
114 115 2.586792 GAGGCAATGAGAGGGCGT 59.413 61.111 0.00 0.00 34.32 5.68
116 117 3.512516 GGCAATGAGAGGGCGTGC 61.513 66.667 0.00 0.00 34.42 5.34
118 119 2.270205 CAATGAGAGGGCGTGCCT 59.730 61.111 11.25 0.00 36.10 4.75
120 121 3.984193 AATGAGAGGGCGTGCCTGC 62.984 63.158 11.25 3.21 36.10 4.85
134 135 2.348998 CTGCCCTGAGCCGTCTTT 59.651 61.111 0.00 0.00 42.71 2.52
138 139 1.017387 GCCCTGAGCCGTCTTTAATG 58.983 55.000 0.00 0.00 34.35 1.90
144 145 1.666189 GAGCCGTCTTTAATGTGGAGC 59.334 52.381 6.59 0.00 0.00 4.70
146 147 1.722011 CCGTCTTTAATGTGGAGCGT 58.278 50.000 0.00 0.00 0.00 5.07
148 149 1.320555 CGTCTTTAATGTGGAGCGTCG 59.679 52.381 0.00 0.00 0.00 5.12
151 152 0.388778 TTTAATGTGGAGCGTCGCGA 60.389 50.000 12.30 3.71 0.00 5.87
156 157 1.283181 GTGGAGCGTCGCGATCTAT 59.717 57.895 14.06 0.00 42.17 1.98
157 158 0.999228 GTGGAGCGTCGCGATCTATG 60.999 60.000 14.06 1.17 42.17 2.23
158 159 1.164041 TGGAGCGTCGCGATCTATGA 61.164 55.000 14.06 0.00 42.17 2.15
159 160 0.169230 GGAGCGTCGCGATCTATGAT 59.831 55.000 14.06 0.00 42.17 2.45
160 161 1.254882 GAGCGTCGCGATCTATGATG 58.745 55.000 14.06 0.00 39.28 3.07
164 165 2.856398 CGTCGCGATCTATGATGACAT 58.144 47.619 14.06 0.00 40.16 3.06
170 171 4.624452 CGCGATCTATGATGACATGAATGT 59.376 41.667 0.00 0.00 45.16 2.71
174 175 5.635278 TCTATGATGACATGAATGTGGGT 57.365 39.130 0.00 0.00 41.95 4.51
225 226 2.229203 GGAAGGAGGGGTTCGGGTT 61.229 63.158 0.00 0.00 0.00 4.11
234 235 4.941309 GTTCGGGTTGGCCACGGT 62.941 66.667 3.88 0.00 36.17 4.83
235 236 3.240011 TTCGGGTTGGCCACGGTA 61.240 61.111 3.88 0.00 36.17 4.02
237 238 4.011517 CGGGTTGGCCACGGTAGT 62.012 66.667 3.88 0.00 36.17 2.73
239 240 2.745037 GGTTGGCCACGGTAGTCA 59.255 61.111 3.88 0.00 34.09 3.41
241 242 1.669440 GTTGGCCACGGTAGTCAGA 59.331 57.895 3.88 0.00 0.00 3.27
242 243 0.034337 GTTGGCCACGGTAGTCAGAA 59.966 55.000 3.88 0.00 0.00 3.02
243 244 0.759959 TTGGCCACGGTAGTCAGAAA 59.240 50.000 3.88 0.00 0.00 2.52
244 245 0.034337 TGGCCACGGTAGTCAGAAAC 59.966 55.000 0.00 0.00 0.00 2.78
245 246 0.034337 GGCCACGGTAGTCAGAAACA 59.966 55.000 0.00 0.00 0.00 2.83
246 247 1.338769 GGCCACGGTAGTCAGAAACAT 60.339 52.381 0.00 0.00 0.00 2.71
247 248 2.093869 GGCCACGGTAGTCAGAAACATA 60.094 50.000 0.00 0.00 0.00 2.29
248 249 2.928116 GCCACGGTAGTCAGAAACATAC 59.072 50.000 0.00 0.00 0.00 2.39
255 256 3.040147 AGTCAGAAACATACGTGGGTG 57.960 47.619 0.00 0.00 0.00 4.61
261 262 0.035739 AACATACGTGGGTGGTGTCC 59.964 55.000 0.00 0.00 0.00 4.02
263 264 2.652095 ATACGTGGGTGGTGTCCGG 61.652 63.158 0.00 0.00 0.00 5.14
265 266 4.675029 CGTGGGTGGTGTCCGGAC 62.675 72.222 28.17 28.17 0.00 4.79
280 281 4.344865 GACGCCCTCAAAGCCCCA 62.345 66.667 0.00 0.00 0.00 4.96
281 282 4.660938 ACGCCCTCAAAGCCCCAC 62.661 66.667 0.00 0.00 0.00 4.61
290 291 0.310854 CAAAGCCCCACGTTTGTCTC 59.689 55.000 0.00 0.00 0.00 3.36
292 293 1.990160 AAGCCCCACGTTTGTCTCCA 61.990 55.000 0.00 0.00 0.00 3.86
298 299 3.408634 CCCACGTTTGTCTCCAGTTTAT 58.591 45.455 0.00 0.00 0.00 1.40
300 301 4.062293 CCACGTTTGTCTCCAGTTTATGA 58.938 43.478 0.00 0.00 0.00 2.15
301 302 4.513692 CCACGTTTGTCTCCAGTTTATGAA 59.486 41.667 0.00 0.00 0.00 2.57
303 304 6.459024 CCACGTTTGTCTCCAGTTTATGAAAA 60.459 38.462 0.00 0.00 0.00 2.29
324 325 2.109425 AAGTATGTCCAAACCGAGCC 57.891 50.000 0.00 0.00 0.00 4.70
336 337 4.578913 CGAGCCGCGGATCAATAT 57.421 55.556 38.97 11.42 36.03 1.28
340 341 0.108138 AGCCGCGGATCAATATAGGC 60.108 55.000 33.48 8.61 43.07 3.93
344 345 0.249398 GCGGATCAATATAGGCCCGT 59.751 55.000 0.00 0.00 39.18 5.28
353 354 1.796017 TATAGGCCCGTGTTGGATGA 58.204 50.000 0.00 0.00 42.00 2.92
355 356 0.907704 TAGGCCCGTGTTGGATGAGT 60.908 55.000 0.00 0.00 42.00 3.41
357 358 1.305930 GGCCCGTGTTGGATGAGTTC 61.306 60.000 0.00 0.00 42.00 3.01
366 367 3.442996 GGATGAGTTCCGTGGTCTG 57.557 57.895 0.00 0.00 33.93 3.51
369 370 1.482593 GATGAGTTCCGTGGTCTGGAT 59.517 52.381 0.00 0.00 34.91 3.41
370 371 2.225382 TGAGTTCCGTGGTCTGGATA 57.775 50.000 0.00 0.00 34.91 2.59
371 372 2.531771 TGAGTTCCGTGGTCTGGATAA 58.468 47.619 0.00 0.00 34.91 1.75
372 373 2.232941 TGAGTTCCGTGGTCTGGATAAC 59.767 50.000 0.00 0.00 34.91 1.89
373 374 1.203994 AGTTCCGTGGTCTGGATAACG 59.796 52.381 0.00 0.00 34.91 3.18
374 375 0.108520 TTCCGTGGTCTGGATAACGC 60.109 55.000 0.00 0.00 34.91 4.84
376 377 1.876714 CGTGGTCTGGATAACGCGG 60.877 63.158 12.47 0.00 33.65 6.46
377 378 2.171725 GTGGTCTGGATAACGCGGC 61.172 63.158 12.47 0.00 0.00 6.53
379 380 3.627218 GTCTGGATAACGCGGCGC 61.627 66.667 24.21 24.21 0.00 6.53
391 392 3.180614 CGGCGCGCGGTTTAAGTA 61.181 61.111 33.06 0.00 0.00 2.24
392 393 2.519175 CGGCGCGCGGTTTAAGTAT 61.519 57.895 33.06 0.00 0.00 2.12
393 394 1.717348 GGCGCGCGGTTTAAGTATT 59.283 52.632 33.06 0.00 0.00 1.89
434 441 2.080286 GCTCTGTTTTCTGGAGCGTA 57.920 50.000 0.00 0.00 42.03 4.42
584 591 1.195448 CACATGACGAGACCTGCAAAC 59.805 52.381 0.00 0.00 0.00 2.93
669 677 2.472934 CGCCAAACGCTACGGTTC 59.527 61.111 0.00 0.00 33.19 3.62
730 738 1.101049 CCCAAAGGATTACCGCGCAT 61.101 55.000 8.75 0.00 41.83 4.73
751 759 0.457853 CGAGTCCTTTTCGATCGCCA 60.458 55.000 11.09 0.00 40.36 5.69
761 770 5.348451 CCTTTTCGATCGCCAAATGATTTTT 59.652 36.000 11.09 0.00 0.00 1.94
766 775 4.442073 CGATCGCCAAATGATTTTTGATCC 59.558 41.667 0.26 3.08 29.71 3.36
845 854 2.044123 ATCCCGTCCATTCTCTTTGC 57.956 50.000 0.00 0.00 0.00 3.68
846 855 0.035439 TCCCGTCCATTCTCTTTGCC 60.035 55.000 0.00 0.00 0.00 4.52
875 887 4.872124 GCCTTTGCTCCCATAAATTCTTTG 59.128 41.667 0.00 0.00 33.53 2.77
877 889 4.470334 TTGCTCCCATAAATTCTTTGCC 57.530 40.909 0.00 0.00 0.00 4.52
881 893 4.280819 CTCCCATAAATTCTTTGCCTCCA 58.719 43.478 0.00 0.00 0.00 3.86
887 899 1.497309 ATTCTTTGCCTCCACCCCGA 61.497 55.000 0.00 0.00 0.00 5.14
889 901 2.852075 TTTGCCTCCACCCCGAGT 60.852 61.111 0.00 0.00 0.00 4.18
890 902 2.411765 CTTTGCCTCCACCCCGAGTT 62.412 60.000 0.00 0.00 0.00 3.01
891 903 2.690653 TTTGCCTCCACCCCGAGTTG 62.691 60.000 0.00 0.00 0.00 3.16
893 905 3.322466 CCTCCACCCCGAGTTGCT 61.322 66.667 0.00 0.00 0.00 3.91
894 906 2.266055 CTCCACCCCGAGTTGCTC 59.734 66.667 0.00 0.00 0.00 4.26
927 939 1.275856 CAAGTCTGCAGCTTCCTCTCT 59.724 52.381 17.10 1.18 0.00 3.10
930 942 1.550072 GTCTGCAGCTTCCTCTCTTCT 59.450 52.381 9.47 0.00 0.00 2.85
1020 1032 1.211709 GATCAAACAAACCCGGCCG 59.788 57.895 21.04 21.04 0.00 6.13
1058 1074 2.794350 CCAAGTCACGCACAAATTTTCC 59.206 45.455 0.00 0.00 0.00 3.13
1172 1188 1.079057 GGAGCTCTTGTTCCCGTCC 60.079 63.158 14.64 0.00 37.58 4.79
1433 1452 3.068691 CCGCTGGTCTTCGAGGGA 61.069 66.667 0.00 0.00 35.14 4.20
1499 1527 1.453762 GCTCGCAGTACTACCCCGAT 61.454 60.000 0.00 0.00 0.00 4.18
1615 1643 1.024271 CCGGGCAATGTAAGTGATGG 58.976 55.000 0.00 0.00 30.28 3.51
1916 1944 1.151668 CAACGAGGAGGAGCACTTTG 58.848 55.000 0.00 0.00 0.00 2.77
1934 1962 0.107066 TGACCGGCTACGATCCTGTA 60.107 55.000 0.00 0.00 44.60 2.74
2081 2112 2.027003 ACTACGACGAAGAGGGAGAG 57.973 55.000 0.00 0.00 0.00 3.20
2082 2113 1.301423 CTACGACGAAGAGGGAGAGG 58.699 60.000 0.00 0.00 0.00 3.69
2083 2114 0.107312 TACGACGAAGAGGGAGAGGG 60.107 60.000 0.00 0.00 0.00 4.30
2084 2115 1.077644 CGACGAAGAGGGAGAGGGA 60.078 63.158 0.00 0.00 0.00 4.20
2085 2116 1.098712 CGACGAAGAGGGAGAGGGAG 61.099 65.000 0.00 0.00 0.00 4.30
2086 2117 0.256464 GACGAAGAGGGAGAGGGAGA 59.744 60.000 0.00 0.00 0.00 3.71
2087 2118 0.257616 ACGAAGAGGGAGAGGGAGAG 59.742 60.000 0.00 0.00 0.00 3.20
2148 2179 3.589654 TTTGAGCTGGCGACGAGGG 62.590 63.158 0.00 0.00 0.00 4.30
2321 2352 3.809832 CCTCACATCAGAACGTTTTCAGT 59.190 43.478 0.46 0.00 33.72 3.41
2335 2366 4.688021 GTTTTCAGTTAATGTGGCAACCA 58.312 39.130 0.00 0.00 0.00 3.67
2350 2381 4.100963 TGGCAACCATACTCGATATTCTGT 59.899 41.667 0.00 0.00 0.00 3.41
2389 2420 1.074248 CCTTAACCCGGGCTGTGTT 59.926 57.895 24.08 9.82 0.00 3.32
2434 2466 7.550906 GCTATGCCCTATCCTCTTATTAACTTG 59.449 40.741 0.00 0.00 0.00 3.16
2503 2535 3.273434 TGTGCTGCAGGAATCTATTGTC 58.727 45.455 17.12 0.00 0.00 3.18
2519 2551 6.398095 TCTATTGTCGAAATCAGCAGAAAGA 58.602 36.000 0.00 0.00 0.00 2.52
2520 2552 4.732285 TTGTCGAAATCAGCAGAAAGAC 57.268 40.909 0.00 0.00 0.00 3.01
2521 2553 2.731451 TGTCGAAATCAGCAGAAAGACG 59.269 45.455 0.00 0.00 0.00 4.18
2522 2554 2.731976 GTCGAAATCAGCAGAAAGACGT 59.268 45.455 0.00 0.00 0.00 4.34
2549 2581 2.346847 GCGAGATCTGCACAAGTAAGTG 59.653 50.000 0.00 0.00 42.37 3.16
2550 2582 3.838120 CGAGATCTGCACAAGTAAGTGA 58.162 45.455 0.00 0.00 42.05 3.41
2551 2583 4.428209 CGAGATCTGCACAAGTAAGTGAT 58.572 43.478 0.00 0.00 42.05 3.06
2566 2598 8.783093 CAAGTAAGTGATCATAAAACTGGTTCA 58.217 33.333 0.00 0.00 0.00 3.18
2567 2599 8.918202 AGTAAGTGATCATAAAACTGGTTCAA 57.082 30.769 0.00 0.00 0.00 2.69
2568 2600 9.003658 AGTAAGTGATCATAAAACTGGTTCAAG 57.996 33.333 0.00 0.00 0.00 3.02
2569 2601 8.999431 GTAAGTGATCATAAAACTGGTTCAAGA 58.001 33.333 0.00 0.00 0.00 3.02
2570 2602 8.641498 AAGTGATCATAAAACTGGTTCAAGAT 57.359 30.769 0.00 0.00 0.00 2.40
2588 2620 6.647229 TCAAGATGAGATCTGCACAAGTAAT 58.353 36.000 0.00 0.00 40.13 1.89
2594 2626 7.776933 TGAGATCTGCACAAGTAATTCATAC 57.223 36.000 0.00 0.00 34.52 2.39
2626 2658 5.248248 TCATGGACTTACTGGTCATCTTTCA 59.752 40.000 0.00 0.00 37.91 2.69
2677 2709 2.715749 TGATTCATGGCCGTCTCATT 57.284 45.000 0.00 0.00 0.00 2.57
2746 2778 7.122799 CGGATTTCCATAGAGTCCATATAGACA 59.877 40.741 4.07 0.00 36.00 3.41
2895 2927 7.770897 ACTCTGTTTATTATTGCCAGACCTAAG 59.229 37.037 0.00 0.00 0.00 2.18
3154 3186 3.787001 GCCGCTACAGCCCTTCCT 61.787 66.667 0.00 0.00 37.91 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.163416 GCAAATGCCTCTATTTAACCCACAT 60.163 40.000 0.00 0.00 34.31 3.21
1 2 4.159506 GCAAATGCCTCTATTTAACCCACA 59.840 41.667 0.00 0.00 34.31 4.17
2 3 4.159506 TGCAAATGCCTCTATTTAACCCAC 59.840 41.667 2.46 0.00 41.18 4.61
3 4 4.348486 TGCAAATGCCTCTATTTAACCCA 58.652 39.130 2.46 0.00 41.18 4.51
4 5 5.291971 CATGCAAATGCCTCTATTTAACCC 58.708 41.667 2.46 0.00 41.18 4.11
9 10 3.740141 GCTGCATGCAAATGCCTCTATTT 60.740 43.478 22.88 0.00 46.43 1.40
13 14 1.515954 GCTGCATGCAAATGCCTCT 59.484 52.632 22.88 0.00 46.43 3.69
24 25 0.952497 ACACACTTCCTCGCTGCATG 60.952 55.000 0.00 0.00 0.00 4.06
29 30 1.608283 GGCTAAACACACTTCCTCGCT 60.608 52.381 0.00 0.00 0.00 4.93
37 38 1.959226 CACGCCGGCTAAACACACT 60.959 57.895 26.68 0.00 0.00 3.55
39 40 3.350612 GCACGCCGGCTAAACACA 61.351 61.111 26.68 0.00 0.00 3.72
40 41 3.308878 CTGCACGCCGGCTAAACAC 62.309 63.158 26.68 8.32 34.04 3.32
76 77 2.277247 CATTAAAGTGGCGCGCCG 60.277 61.111 41.73 23.24 39.42 6.46
79 80 1.060308 CGTCCATTAAAGTGGCGCG 59.940 57.895 0.00 0.00 39.19 6.86
85 86 3.941483 CTCATTGCCTCGTCCATTAAAGT 59.059 43.478 0.00 0.00 0.00 2.66
86 87 4.191544 TCTCATTGCCTCGTCCATTAAAG 58.808 43.478 0.00 0.00 0.00 1.85
95 96 2.586792 GCCCTCTCATTGCCTCGT 59.413 61.111 0.00 0.00 0.00 4.18
103 104 4.479993 GCAGGCACGCCCTCTCAT 62.480 66.667 3.95 0.00 44.09 2.90
116 117 1.899437 TAAAGACGGCTCAGGGCAGG 61.899 60.000 0.00 0.00 44.01 4.85
118 119 0.618458 ATTAAAGACGGCTCAGGGCA 59.382 50.000 0.00 0.00 44.01 5.36
120 121 2.009774 CACATTAAAGACGGCTCAGGG 58.990 52.381 0.00 0.00 0.00 4.45
121 122 2.009774 CCACATTAAAGACGGCTCAGG 58.990 52.381 0.00 0.00 0.00 3.86
124 125 1.666189 GCTCCACATTAAAGACGGCTC 59.334 52.381 0.00 0.00 0.00 4.70
134 135 0.594028 GATCGCGACGCTCCACATTA 60.594 55.000 12.93 0.00 0.00 1.90
138 139 0.999228 CATAGATCGCGACGCTCCAC 60.999 60.000 12.93 6.67 0.00 4.02
144 145 2.316119 TGTCATCATAGATCGCGACG 57.684 50.000 12.93 0.00 0.00 5.12
146 147 4.503741 TTCATGTCATCATAGATCGCGA 57.496 40.909 13.09 13.09 32.47 5.87
148 149 5.163884 CCACATTCATGTCATCATAGATCGC 60.164 44.000 0.00 0.00 39.39 4.58
151 152 6.196918 ACCCACATTCATGTCATCATAGAT 57.803 37.500 0.00 0.00 39.39 1.98
156 157 3.200605 AGCTACCCACATTCATGTCATCA 59.799 43.478 0.00 0.00 39.39 3.07
157 158 3.562973 CAGCTACCCACATTCATGTCATC 59.437 47.826 0.00 0.00 39.39 2.92
158 159 3.548770 CAGCTACCCACATTCATGTCAT 58.451 45.455 0.00 0.00 39.39 3.06
159 160 2.356022 CCAGCTACCCACATTCATGTCA 60.356 50.000 0.00 0.00 39.39 3.58
160 161 2.292267 CCAGCTACCCACATTCATGTC 58.708 52.381 0.00 0.00 39.39 3.06
164 165 1.078497 CGCCAGCTACCCACATTCA 60.078 57.895 0.00 0.00 0.00 2.57
207 208 2.229203 AACCCGAACCCCTCCTTCC 61.229 63.158 0.00 0.00 0.00 3.46
209 210 2.535331 CCAACCCGAACCCCTCCTT 61.535 63.158 0.00 0.00 0.00 3.36
225 226 0.034337 GTTTCTGACTACCGTGGCCA 59.966 55.000 0.00 0.00 0.00 5.36
234 235 3.056393 CCACCCACGTATGTTTCTGACTA 60.056 47.826 0.00 0.00 0.00 2.59
235 236 2.289444 CCACCCACGTATGTTTCTGACT 60.289 50.000 0.00 0.00 0.00 3.41
237 238 1.695242 ACCACCCACGTATGTTTCTGA 59.305 47.619 0.00 0.00 0.00 3.27
239 240 1.418637 ACACCACCCACGTATGTTTCT 59.581 47.619 0.00 0.00 0.00 2.52
241 242 1.543871 GGACACCACCCACGTATGTTT 60.544 52.381 0.00 0.00 0.00 2.83
242 243 0.035739 GGACACCACCCACGTATGTT 59.964 55.000 0.00 0.00 0.00 2.71
243 244 1.675219 GGACACCACCCACGTATGT 59.325 57.895 0.00 0.00 0.00 2.29
244 245 1.447140 CGGACACCACCCACGTATG 60.447 63.158 0.00 0.00 0.00 2.39
245 246 2.652095 CCGGACACCACCCACGTAT 61.652 63.158 0.00 0.00 0.00 3.06
246 247 3.304721 CCGGACACCACCCACGTA 61.305 66.667 0.00 0.00 0.00 3.57
248 249 4.675029 GTCCGGACACCACCCACG 62.675 72.222 29.75 0.00 0.00 4.94
263 264 4.344865 TGGGGCTTTGAGGGCGTC 62.345 66.667 0.00 0.00 0.00 5.19
270 271 0.106918 AGACAAACGTGGGGCTTTGA 60.107 50.000 2.59 0.00 32.63 2.69
279 280 5.666969 TTCATAAACTGGAGACAAACGTG 57.333 39.130 0.00 0.00 42.06 4.49
280 281 6.687081 TTTTCATAAACTGGAGACAAACGT 57.313 33.333 0.00 0.00 42.06 3.99
303 304 2.817844 GGCTCGGTTTGGACATACTTTT 59.182 45.455 0.00 0.00 0.00 2.27
307 308 1.702491 GCGGCTCGGTTTGGACATAC 61.702 60.000 0.00 0.00 0.00 2.39
308 309 1.448893 GCGGCTCGGTTTGGACATA 60.449 57.895 0.00 0.00 0.00 2.29
320 321 1.927895 CCTATATTGATCCGCGGCTC 58.072 55.000 23.51 22.55 0.00 4.70
322 323 1.090052 GGCCTATATTGATCCGCGGC 61.090 60.000 23.51 8.29 35.41 6.53
324 325 0.806102 CGGGCCTATATTGATCCGCG 60.806 60.000 0.84 0.00 0.00 6.46
328 329 3.074412 CCAACACGGGCCTATATTGATC 58.926 50.000 0.84 0.00 0.00 2.92
329 330 2.708861 TCCAACACGGGCCTATATTGAT 59.291 45.455 0.84 0.00 34.36 2.57
330 331 2.120312 TCCAACACGGGCCTATATTGA 58.880 47.619 0.84 0.00 34.36 2.57
331 332 2.631160 TCCAACACGGGCCTATATTG 57.369 50.000 0.84 2.96 34.36 1.90
332 333 2.708861 TCATCCAACACGGGCCTATATT 59.291 45.455 0.84 0.00 34.36 1.28
333 334 2.303022 CTCATCCAACACGGGCCTATAT 59.697 50.000 0.84 0.00 34.36 0.86
334 335 1.691976 CTCATCCAACACGGGCCTATA 59.308 52.381 0.84 0.00 34.36 1.31
335 336 0.469917 CTCATCCAACACGGGCCTAT 59.530 55.000 0.84 0.00 34.36 2.57
336 337 0.907704 ACTCATCCAACACGGGCCTA 60.908 55.000 0.84 0.00 34.36 3.93
353 354 1.203994 CGTTATCCAGACCACGGAACT 59.796 52.381 0.00 0.00 35.77 3.01
355 356 0.108520 GCGTTATCCAGACCACGGAA 60.109 55.000 0.00 0.00 35.77 4.30
357 358 1.876714 CGCGTTATCCAGACCACGG 60.877 63.158 0.00 0.00 33.17 4.94
359 360 2.171725 GCCGCGTTATCCAGACCAC 61.172 63.158 4.92 0.00 0.00 4.16
360 361 2.185867 GCCGCGTTATCCAGACCA 59.814 61.111 4.92 0.00 0.00 4.02
361 362 2.960129 CGCCGCGTTATCCAGACC 60.960 66.667 4.92 0.00 0.00 3.85
374 375 2.027628 AATACTTAAACCGCGCGCCG 62.028 55.000 27.36 22.49 0.00 6.46
376 377 0.587985 CCAATACTTAAACCGCGCGC 60.588 55.000 27.36 23.91 0.00 6.86
377 378 1.000884 TCCAATACTTAAACCGCGCG 58.999 50.000 25.67 25.67 0.00 6.86
379 380 3.303132 GCATCTCCAATACTTAAACCGCG 60.303 47.826 0.00 0.00 0.00 6.46
380 381 3.003378 GGCATCTCCAATACTTAAACCGC 59.997 47.826 0.00 0.00 34.01 5.68
381 382 3.564225 GGGCATCTCCAATACTTAAACCG 59.436 47.826 0.00 0.00 36.21 4.44
382 383 4.793201 AGGGCATCTCCAATACTTAAACC 58.207 43.478 0.00 0.00 36.21 3.27
383 384 6.826741 TGTTAGGGCATCTCCAATACTTAAAC 59.173 38.462 0.00 0.00 36.21 2.01
386 387 6.763715 ATGTTAGGGCATCTCCAATACTTA 57.236 37.500 0.00 0.00 36.21 2.24
390 391 4.597075 TGCTATGTTAGGGCATCTCCAATA 59.403 41.667 0.00 0.00 36.21 1.90
391 392 3.395607 TGCTATGTTAGGGCATCTCCAAT 59.604 43.478 0.00 0.00 36.21 3.16
392 393 2.777114 TGCTATGTTAGGGCATCTCCAA 59.223 45.455 0.00 0.00 36.21 3.53
393 394 2.104792 GTGCTATGTTAGGGCATCTCCA 59.895 50.000 0.00 0.00 38.27 3.86
434 441 1.272769 GTTCAGTCGCTAGGTTCAGGT 59.727 52.381 0.00 0.00 0.00 4.00
472 479 2.442188 CGGCGCTGAAAGGACGTAC 61.442 63.158 11.90 0.00 32.11 3.67
495 502 0.670162 GAAGCTTGGACTTTGCAGCA 59.330 50.000 2.10 0.00 0.00 4.41
499 506 2.747436 CTTTGGAAGCTTGGACTTTGC 58.253 47.619 2.10 0.00 0.00 3.68
584 591 1.182385 GGCTCTCCTACCGGATGAGG 61.182 65.000 9.46 12.20 39.01 3.86
710 718 2.478033 GCGCGGTAATCCTTTGGGG 61.478 63.158 8.83 0.00 0.00 4.96
715 723 0.386476 TCGTATGCGCGGTAATCCTT 59.614 50.000 8.83 0.00 38.14 3.36
730 738 1.202222 GGCGATCGAAAAGGACTCGTA 60.202 52.381 21.57 0.00 37.56 3.43
751 759 5.138125 ACGTGCTGGATCAAAAATCATTT 57.862 34.783 0.00 0.00 0.00 2.32
845 854 2.259511 GGAGCAAAGGCAAAGCGG 59.740 61.111 0.00 0.00 44.61 5.52
846 855 1.880819 ATGGGAGCAAAGGCAAAGCG 61.881 55.000 0.00 0.00 44.61 4.68
877 889 1.831652 AAGAGCAACTCGGGGTGGAG 61.832 60.000 0.60 0.00 39.97 3.86
881 893 2.032681 GCAAGAGCAACTCGGGGT 59.967 61.111 0.00 0.00 41.58 4.95
887 899 0.603975 GTCGGGAAGCAAGAGCAACT 60.604 55.000 0.00 0.00 45.49 3.16
889 901 1.302511 GGTCGGGAAGCAAGAGCAA 60.303 57.895 0.00 0.00 45.49 3.91
890 902 2.050836 TTGGTCGGGAAGCAAGAGCA 62.051 55.000 0.00 0.00 45.49 4.26
891 903 1.302511 TTGGTCGGGAAGCAAGAGC 60.303 57.895 0.00 0.00 40.34 4.09
927 939 2.433145 CGCGCTCTTGCTGGAGAA 60.433 61.111 5.56 0.00 35.52 2.87
930 942 3.315142 AATCCGCGCTCTTGCTGGA 62.315 57.895 5.56 2.56 42.63 3.86
1020 1032 3.525545 GGGTCTCGGGCTACGGAC 61.526 72.222 11.37 11.37 44.45 4.79
1058 1074 1.590932 CCATTGCGGGAGAAGATGAG 58.409 55.000 0.00 0.00 0.00 2.90
1348 1367 0.974383 GACGACCTTGGAAGAAGGGA 59.026 55.000 5.48 0.00 41.71 4.20
1499 1527 1.712018 CGACTACGACGAGGGCATCA 61.712 60.000 0.00 0.00 42.66 3.07
1615 1643 0.806102 TGCTTCTTCATCGGTAGCGC 60.806 55.000 9.99 0.00 34.65 5.92
1854 1882 2.818274 CCTGCTCCGTAAACCCGC 60.818 66.667 0.00 0.00 0.00 6.13
1916 1944 0.592148 CTACAGGATCGTAGCCGGTC 59.408 60.000 1.90 0.00 43.60 4.79
1934 1962 1.994507 CTTGATCGTCGGACGGAGCT 61.995 60.000 28.07 12.17 42.81 4.09
2010 2041 4.457496 CCTGGCCATGTCGTCGCT 62.457 66.667 5.51 0.00 0.00 4.93
2012 2043 3.770040 TCCCTGGCCATGTCGTCG 61.770 66.667 5.51 0.00 0.00 5.12
2085 2116 4.798682 TTCCCGCCCCTCCTCCTC 62.799 72.222 0.00 0.00 0.00 3.71
2086 2117 4.806339 CTTCCCGCCCCTCCTCCT 62.806 72.222 0.00 0.00 0.00 3.69
2295 2326 4.602340 AAACGTTCTGATGTGAGGTAGT 57.398 40.909 0.00 0.00 0.00 2.73
2296 2327 4.988540 TGAAAACGTTCTGATGTGAGGTAG 59.011 41.667 0.00 0.00 34.60 3.18
2321 2352 4.209307 TCGAGTATGGTTGCCACATTAA 57.791 40.909 0.00 0.00 35.80 1.40
2335 2366 5.392487 CGATGGCTGACAGAATATCGAGTAT 60.392 44.000 21.66 0.00 39.60 2.12
2350 2381 1.275010 TGAGCAGTAAACGATGGCTGA 59.725 47.619 0.00 0.00 34.44 4.26
2389 2420 2.221169 GCCAATGCTTGTCATCGGATA 58.779 47.619 0.00 0.00 30.56 2.59
2434 2466 3.692576 ACTGTAGTATTCGACGATGTGC 58.307 45.455 0.00 0.00 0.00 4.57
2503 2535 3.241364 CGTACGTCTTTCTGCTGATTTCG 60.241 47.826 7.22 0.99 0.00 3.46
2519 2551 2.015382 CAGATCTCGCTCCGTACGT 58.985 57.895 15.21 0.00 0.00 3.57
2520 2552 1.369448 GCAGATCTCGCTCCGTACG 60.369 63.158 8.69 8.69 0.00 3.67
2521 2553 0.592754 GTGCAGATCTCGCTCCGTAC 60.593 60.000 15.20 0.99 0.00 3.67
2522 2554 1.029947 TGTGCAGATCTCGCTCCGTA 61.030 55.000 15.20 0.00 0.00 4.02
2549 2581 8.498054 TCTCATCTTGAACCAGTTTTATGATC 57.502 34.615 0.00 0.00 0.00 2.92
2550 2582 9.118300 GATCTCATCTTGAACCAGTTTTATGAT 57.882 33.333 0.00 0.00 0.00 2.45
2551 2583 8.324306 AGATCTCATCTTGAACCAGTTTTATGA 58.676 33.333 0.00 0.00 35.76 2.15
2566 2598 7.108194 TGAATTACTTGTGCAGATCTCATCTT 58.892 34.615 0.00 0.00 37.58 2.40
2567 2599 6.647229 TGAATTACTTGTGCAGATCTCATCT 58.353 36.000 0.00 0.00 41.15 2.90
2568 2600 6.915544 TGAATTACTTGTGCAGATCTCATC 57.084 37.500 0.00 0.00 0.00 2.92
2569 2601 7.989170 TGTATGAATTACTTGTGCAGATCTCAT 59.011 33.333 0.00 0.00 0.00 2.90
2570 2602 7.330262 TGTATGAATTACTTGTGCAGATCTCA 58.670 34.615 0.00 0.00 0.00 3.27
2588 2620 5.241403 AGTCCATGAACCAGTTGTATGAA 57.759 39.130 0.00 0.00 0.00 2.57
2594 2626 3.753272 CCAGTAAGTCCATGAACCAGTTG 59.247 47.826 0.00 0.00 0.00 3.16
2677 2709 1.294138 CGCCGGTCTACCCTGAAAA 59.706 57.895 1.90 0.00 0.00 2.29
2746 2778 0.473755 TCGCCAATGCATATCCAGGT 59.526 50.000 0.00 0.00 37.32 4.00
2883 2915 1.555075 CTTACCTGCTTAGGTCTGGCA 59.445 52.381 1.62 0.00 42.99 4.92
2895 2927 2.698855 TTGGAGATGCTCTTACCTGC 57.301 50.000 0.00 0.00 0.00 4.85
2943 2975 2.221986 GCGCGCTAAATTGACGTTTTTC 60.222 45.455 26.67 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.